Psyllid ID: psy879

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------
Protein Sequence
IEKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDIIGNIFRVAKTLDIPEPLKLSIIQEIGNVHLRISEGVNSLLQLSGLLARLCIVGSKNKKTD
Secondary Structure (PSIPRED)
cccccccccccccccHHHHHHHHHHHHcccccEEEEEccccccHHHHHHHHHHHHccccccccEEEEccccccHHHHHHHHHHHHHHHccccccccEEEEEEEccccccHHHHHHHHHHHHHcccccEEEEEcccccccccccHHccccEEcccccHHHHHHHHHHHHHHccccccHHHHHHHHHHccccHHHHHHHHHHHHHccccccHHHHHHccccccHHHHHHHHHHHHcccHHHHHHHHHHHHHccccHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHcccccc
Secondary Structure Prediction (SSPRO)
ccccccccHHHHcccHHHHHHHHHHHHcccccEEEEEccccccHHHHHHHHHHHHHcHHHHHHHHHHcccccccHHHHHHHHHHHHHccccccccccEEEEEccHHHccHHHHHHHHHHHHHHHcccEEEEEEcccccccccHHccEEEEEEccccHHHHHHHHHHHHHHccccccHHHHHHHHHHHccHHHHHHHHHHHHHHHcccccHHHEEEEcccccHHHHHHHHHHHHcccHHHHHHHHHHHHHccccHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHcccccccc
Coil and Loop (DISEMBL)
iekyrpqtfsdivgneDTVERLKVFsssgnvpniiisgppgvgktTTILCLARILLGPSFKDAVLELNasndrgidTVRNKIKMFAQqkvtlppgrhkivildeadsmtDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKenishtndglEAIVFTAQGDMRQALNNLqsthngfghVTAEYVFkvcdephplAVKEMLLNCVEGNMKDSYKIIHHLYklgyapediIGNIFRVAktldipeplKLSIIQEIGNVHLRISEGVNSLLQLSGLLARLCIvgsknkktd
Flexible Loop (DISEMBL)
iekyrpqtfsdivgnedTVERLKVfsssgnvpniiisgppgvGKTTTILCLARILLGPSFKDAVLELNAsndrgidtVRNKIKMFaqqkvtlppgrhKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDIIGNIFRVAKTLDIPEPLKLSIIQEIGNVHLRISEGVNSLLQLSGLlarlcivgsknkktd
Low Complexity Region (SEG)
IEKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDIIGNIFRVAKTLDIPEPLKLSIIQEIGNVHLRISEGVNSllqlsgllarlCIVGSKNKKTD
Disordered region (IsUnstruct)
*****************TVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEA********QALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDIIGNIFRVAKTLDIPEPLKLSIIQEIGNVHLRISEGVNSLLQLSGLLARLCIVG*******
Disordered Region (DISOPRED)
IEKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDIIGNIFRVAKTLDIPEPLKLSIIQEIGNVHLRISEGVNSLLQLSGLLARLCI**SK*****
Disordered Region (DISEMBL)
IEKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDIIGNIFRVAKTLDIPEPLKLSIIQEIGNVHLRISEGVNSLLQLSGLLARLCIVGSKNKKTD
Disordered Region (DISPRO)
*EKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDIIGNIFRVAKTLDIPEPLKLSIIQEIGNVHLRISEGVNSLLQLSGLLARLCIVGS******
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
IEKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDIIGNIFRVAKTLDIPEPLKLSIIQEIGNVHLRISEGVNSLLQLSGLLARLCIVGSKNKKTD
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	317	2.2.26 [Sep-21-2011]
P53033	359	Replication factor C subu	yes	N/A	0.968	0.855	0.742	1e-141
Q641W4	349	Replication factor C subu	yes	N/A	0.968	0.879	0.745	1e-140
Q9WUK4	349	Replication factor C subu	yes	N/A	0.968	0.879	0.742	1e-139
P35250	354	Replication factor C subu	yes	N/A	0.968	0.867	0.745	1e-139
Q05B83	352	Replication factor C subu	yes	N/A	0.968	0.872	0.742	1e-139
P53034	331	Replication factor C subu	yes	N/A	0.987	0.945	0.725	1e-134
O94449	342	Replication factor C subu	yes	N/A	0.968	0.897	0.620	1e-114
Q54E21	338	Probable replication fact	yes	N/A	0.990	0.928	0.6	1e-112
P40339	323	Replication factor C subu	yes	N/A	0.955	0.938	0.607	1e-108
Q975D3	327	Replication factor C smal	yes	N/A	0.968	0.938	0.452	3e-71

>sp|P53033|RFC2_CHICK Replication factor C subunit 2 OS=Gallus gallus GN=RFC2 PE=2 SV=1

 Score =  500 bits (1287), Expect = e-141,   Method: Compositional matrix adjust.
 Identities = 228/307 (74%), Positives = 273/307 (88%)

Query: 1   IEKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSF 60
           +EKYRP    ++VGNEDTV RL+VF+  GNVPNIII+GPPG GKTT+ILCLAR LLGP+ 
Sbjct: 44  VEKYRPLKLCEVVGNEDTVSRLEVFAKEGNVPNIIIAGPPGTGKTTSILCLARALLGPAL 103

Query: 61  KDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTM 120
           KDAVLELNASNDRGID VRNKIKMFAQQKVTLP GRHKI+ILDEADSMTDGAQQALRRTM
Sbjct: 104 KDAVLELNASNDRGIDVVRNKIKMFAQQKVTLPKGRHKIIILDEADSMTDGAQQALRRTM 163

Query: 121 EIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGL 180
           EIYS TTRFALACN S+KIIEPIQSRCA+LRY KLTD+Q+L+++++I EKE++ +T+DGL
Sbjct: 164 EIYSKTTRFALACNASDKIIEPIQSRCAVLRYTKLTDSQILARLLKIVEKEDVPYTDDGL 223

Query: 181 EAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEMLLNCVEGNMKDS 240
           EAI+FTAQGDMRQALNNLQST++GFG + +E VFKVCDEPHPL VKEM+ +C+  N+ ++
Sbjct: 224 EAIIFTAQGDMRQALNNLQSTYSGFGFINSENVFKVCDEPHPLLVKEMIQHCINANIDEA 283

Query: 241 YKIIHHLYKLGYAPEDIIGNIFRVAKTLDIPEPLKLSIIQEIGNVHLRISEGVNSLLQLS 300
           YKI+ HL++LGY+PED+IGNIFRV KT  +PE LKL  I+EIG  H++I+EGVNSLLQ++
Sbjct: 284 YKILAHLWRLGYSPEDVIGNIFRVCKTFQMPEYLKLEFIKEIGYTHMKIAEGVNSLLQMA 343

Query: 301 GLLARLC 307
           GLLARLC
Sbjct: 344 GLLARLC 350

The elongation of primed DNA templates by DNA polymerase delta and epsilon requires the action of the accessory proteins proliferating cell nuclear antigen (PCNA) and activator 1. This subunit binds ATP.
Gallus gallus (taxid: 9031)

>sp|Q641W4|RFC2_RAT Replication factor C subunit 2 OS=Rattus norvegicus GN=Rfc2 PE=2 SV=1

 Score =  496 bits (1278), Expect = e-140,   Method: Compositional matrix adjust.
 Identities = 229/307 (74%), Positives = 271/307 (88%)

Query: 1   IEKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSF 60
           +EKYRP   ++IVGNEDTV RL+VF+  GNVPNIII+GPPG GKTT+ILCLAR LLGP+ 
Sbjct: 34  VEKYRPVKLNEIVGNEDTVSRLEVFAREGNVPNIIIAGPPGTGKTTSILCLARALLGPAL 93

Query: 61  KDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTM 120
           KDAVLELNASNDRGID VRNKIKMFAQQKVTLP GRHKI+ILDEADSMTDGAQQALRRTM
Sbjct: 94  KDAVLELNASNDRGIDVVRNKIKMFAQQKVTLPKGRHKIIILDEADSMTDGAQQALRRTM 153

Query: 121 EIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGL 180
           EIYS TTRFALACN S+KIIEPIQSRCA+LRY KLTDAQ+LS+++ + EKE + +T+DGL
Sbjct: 154 EIYSKTTRFALACNASDKIIEPIQSRCAVLRYTKLTDAQVLSRLMNVIEKEKVPYTDDGL 213

Query: 181 EAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEMLLNCVEGNMKDS 240
           EAI+FTAQGDMRQALNNLQST +GFG++ +E VFKVCDEPHPL VKEM+ +CV+ N+ ++
Sbjct: 214 EAIIFTAQGDMRQALNNLQSTFSGFGYINSENVFKVCDEPHPLLVKEMIQHCVDANIDEA 273

Query: 241 YKIIHHLYKLGYAPEDIIGNIFRVAKTLDIPEPLKLSIIQEIGNVHLRISEGVNSLLQLS 300
           YKI+ HL+ LGY+PED+IGNIFRV KT  + E LKL  I+EIG  H++++EGVNSLLQ++
Sbjct: 274 YKILAHLWHLGYSPEDVIGNIFRVCKTFPMAEYLKLEFIKEIGYTHMKVAEGVNSLLQMA 333

Query: 301 GLLARLC 307
           GLLARLC
Sbjct: 334 GLLARLC 340

The elongation of primed DNA templates by DNA polymerase delta and epsilon requires the action of the accessory proteins proliferating cell nuclear antigen (PCNA) and activator 1. This subunit binds ATP.

Rattus norvegicus (taxid: 10116)

>sp|Q9WUK4|RFC2_MOUSE Replication factor C subunit 2 OS=Mus musculus GN=Rfc2 PE=2 SV=1

 Score =  495 bits (1274), Expect = e-139,   Method: Compositional matrix adjust.
 Identities = 228/307 (74%), Positives = 271/307 (88%)

Query: 1   IEKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSF 60
           +EKYRP   ++IVGNEDTV RL+VF+  GNVPNIII+GPPG GKTT+ILCLAR LLGP+ 
Sbjct: 34  VEKYRPLKLNEIVGNEDTVSRLEVFAREGNVPNIIIAGPPGTGKTTSILCLARALLGPAL 93

Query: 61  KDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTM 120
           KDAVLELNASNDRGID VRNKIKMFAQQKVTLP GRHKI+ILDEADSMTDGAQQALRRTM
Sbjct: 94  KDAVLELNASNDRGIDVVRNKIKMFAQQKVTLPKGRHKIIILDEADSMTDGAQQALRRTM 153

Query: 121 EIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGL 180
           EIYS TTRFALACN S+KIIEPIQSRCA+LRY KLTDAQ+L++++ + EKE + +T+DGL
Sbjct: 154 EIYSKTTRFALACNASDKIIEPIQSRCAVLRYTKLTDAQVLTRLMNVIEKEKVPYTDDGL 213

Query: 181 EAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEMLLNCVEGNMKDS 240
           EAI+FTAQGDMRQALNNLQST +GFG++ +E VFKVCDEPHPL VKEM+ +CV+ N+ ++
Sbjct: 214 EAIIFTAQGDMRQALNNLQSTFSGFGYINSENVFKVCDEPHPLLVKEMIQHCVDANIDEA 273

Query: 241 YKIIHHLYKLGYAPEDIIGNIFRVAKTLDIPEPLKLSIIQEIGNVHLRISEGVNSLLQLS 300
           YKI+ HL+ LGY+PED+IGNIFRV KT  + E LKL  I+EIG  H++++EGVNSLLQ++
Sbjct: 274 YKILAHLWHLGYSPEDVIGNIFRVCKTFPMAEYLKLEFIKEIGYTHMKVAEGVNSLLQMA 333

Query: 301 GLLARLC 307
           GLLARLC
Sbjct: 334 GLLARLC 340

The elongation of primed DNA templates by DNA polymerase delta and epsilon requires the action of the accessory proteins proliferating cell nuclear antigen (PCNA) and activator 1. This subunit binds ATP.

Mus musculus (taxid: 10090)

>sp|P35250|RFC2_HUMAN Replication factor C subunit 2 OS=Homo sapiens GN=RFC2 PE=1 SV=3

 Score =  493 bits (1270), Expect = e-139,   Method: Compositional matrix adjust.
 Identities = 229/307 (74%), Positives = 269/307 (87%)

Query: 1   IEKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSF 60
           +EKYRP   ++IVGNEDTV RL+VF+  GNVPNIII+GPPG GKTT+ILCLAR LLGP+ 
Sbjct: 39  VEKYRPVKLNEIVGNEDTVSRLEVFAREGNVPNIIIAGPPGTGKTTSILCLARALLGPAL 98

Query: 61  KDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTM 120
           KDA+LELNASNDRGID VRNKIKMFAQQKVTLP GRHKI+ILDEADSMTDGAQQALRRTM
Sbjct: 99  KDAMLELNASNDRGIDVVRNKIKMFAQQKVTLPKGRHKIIILDEADSMTDGAQQALRRTM 158

Query: 121 EIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGL 180
           EIYS TTRFALACN S+KIIEPIQSRCA+LRY KLTDAQ+L++++ + EKE + +T+DGL
Sbjct: 159 EIYSKTTRFALACNASDKIIEPIQSRCAVLRYTKLTDAQILTRLMNVIEKERVPYTDDGL 218

Query: 181 EAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEMLLNCVEGNMKDS 240
           EAI+FTAQGDMRQALNNLQST +GFG + +E VFKVCDEPHPL VKEM+ +CV  N+ ++
Sbjct: 219 EAIIFTAQGDMRQALNNLQSTFSGFGFINSENVFKVCDEPHPLLVKEMIQHCVNANIDEA 278

Query: 241 YKIIHHLYKLGYAPEDIIGNIFRVAKTLDIPEPLKLSIIQEIGNVHLRISEGVNSLLQLS 300
           YKI+ HL+ LGY+PEDIIGNIFRV KT  + E LKL  I+EIG  H++I+EGVNSLLQ++
Sbjct: 279 YKILAHLWHLGYSPEDIIGNIFRVCKTFQMAEYLKLEFIKEIGYTHMKIAEGVNSLLQMA 338

Query: 301 GLLARLC 307
           GLLARLC
Sbjct: 339 GLLARLC 345

The elongation of primed DNA templates by DNA polymerase delta and epsilon requires the action of the accessory proteins proliferating cell nuclear antigen (PCNA) and activator 1. This subunit binds ATP.

Homo sapiens (taxid: 9606)

>sp|Q05B83|RFC2_BOVIN Replication factor C subunit 2 OS=Bos taurus GN=RFC2 PE=2 SV=1

 Score =  493 bits (1269), Expect = e-139,   Method: Compositional matrix adjust.
 Identities = 228/307 (74%), Positives = 269/307 (87%)

Query: 1   IEKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSF 60
           +EKYRP   ++IVGNEDTV RL+VF+  GNVPNIII+GPPG GKTT+ILCLAR LLGP+ 
Sbjct: 37  VEKYRPVKLNEIVGNEDTVSRLEVFAREGNVPNIIIAGPPGTGKTTSILCLARALLGPAL 96

Query: 61  KDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTM 120
           KDAVLELNASNDRGID VRNKIKMFAQQKVTLP GRHKI+ILDEADSMTDGAQQALRRTM
Sbjct: 97  KDAVLELNASNDRGIDVVRNKIKMFAQQKVTLPKGRHKIIILDEADSMTDGAQQALRRTM 156

Query: 121 EIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGL 180
           EIYS TTRFALACN S+KIIEPIQSRCA+LRY KLTD Q+L++++ + EKE + +T+DGL
Sbjct: 157 EIYSKTTRFALACNASDKIIEPIQSRCAVLRYTKLTDMQILARLLSVIEKEKVQYTDDGL 216

Query: 181 EAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEMLLNCVEGNMKDS 240
           EAI+FTAQGDMRQALNNLQST++GFG + +E VFKVCDEPHPL VKEM+ +CV  ++ ++
Sbjct: 217 EAIIFTAQGDMRQALNNLQSTYSGFGFINSENVFKVCDEPHPLLVKEMIQHCVSADIDEA 276

Query: 241 YKIIHHLYKLGYAPEDIIGNIFRVAKTLDIPEPLKLSIIQEIGNVHLRISEGVNSLLQLS 300
           YKI+ HL+ LGY+PEDIIGNIFRV KT  + E LKL  I+EIG  H++I+EGVNSLLQ++
Sbjct: 277 YKILAHLWHLGYSPEDIIGNIFRVCKTFQMAEYLKLEFIKEIGYTHMKIAEGVNSLLQMA 336

Query: 301 GLLARLC 307
           GLLARLC
Sbjct: 337 GLLARLC 343

The elongation of primed DNA templates by DNA polymerase delta and epsilon requires the action of the accessory proteins proliferating cell nuclear antigen (PCNA) and activator 1. This subunit binds ATP.

Bos taurus (taxid: 9913)

>sp|P53034|RFC2_DROME Replication factor C subunit 2 OS=Drosophila melanogaster GN=RfC4 PE=2 SV=1

 Score =  479 bits (1232), Expect = e-134,   Method: Compositional matrix adjust.
 Identities = 227/313 (72%), Positives = 267/313 (85%)

Query: 1   IEKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSF 60
           IEKYRP  F +IVGNEDTV RL VF++ GN PNIII+GPPGVGKTTTI CLARILLG S+
Sbjct: 19  IEKYRPVKFKEIVGNEDTVARLSVFATQGNAPNIIIAGPPGVGKTTTIQCLARILLGDSY 78

Query: 61  KDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTM 120
           K+AVLELNASN+RGID VRNKIKMFAQQKVTLP GRHKIVILDEADSMT+GAQQALRRTM
Sbjct: 79  KEAVLELNASNERGIDVVRNKIKMFAQQKVTLPRGRHKIVILDEADSMTEGAQQALRRTM 138

Query: 121 EIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGL 180
           EIYS+TTRFALACN SEKIIEPIQSRCAMLR+ KL+DAQ+L+K+IE+ + E +++T DGL
Sbjct: 139 EIYSSTTRFALACNTSEKIIEPIQSRCAMLRFTKLSDAQVLAKLIEVAKWEKLNYTEDGL 198

Query: 181 EAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEMLLNCVEGNMKDS 240
           EAIVFTAQGDMRQ LNNLQST  GFG +TAE VFKVCDEPHP  ++EM+ +C   ++  +
Sbjct: 199 EAIVFTAQGDMRQGLNNLQSTAQGFGDITAENVFKVCDEPHPKLLEEMIHHCAANDIHKA 258

Query: 241 YKIIHHLYKLGYAPEDIIGNIFRVAKTLDIPEPLKLSIIQEIGNVHLRISEGVNSLLQLS 300
           YKI+  L+KLGY+PEDII NIFRV K ++I E LKL  I+EIG  H++I +G+NSLLQL+
Sbjct: 259 YKILAKLWKLGYSPEDIIANIFRVCKRINIDEHLKLDFIREIGITHMKIIDGINSLLQLT 318

Query: 301 GLLARLCIVGSKN 313
            LLA+LCI   K+
Sbjct: 319 ALLAKLCIAAEKH 331

The elongation of primed DNA templates by DNA polymerase delta and epsilon requires the action of the accessory proteins proliferating cell nuclear antigen (PCNA) and activator 1. Subunit 2 binds ATP.

Drosophila melanogaster (taxid: 7227)

>sp|O94449|RFC4_SCHPO Replication factor C subunit 4 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rfc4 PE=1 SV=1

 Score =  412 bits (1059), Expect = e-114,   Method: Compositional matrix adjust.
 Identities = 191/308 (62%), Positives = 248/308 (80%), Gaps = 1/308 (0%)

Query: 1   IEKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSF 60
           +EKYRP    DIVGNE+T++RLKV +  GN+P+++ISG PG+GKTT+ILCLA  LLGP++
Sbjct: 24  VEKYRPIVLDDIVGNEETIDRLKVIAKEGNMPHLVISGMPGIGKTTSILCLAHALLGPAY 83

Query: 61  KDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTM 120
           K+ VLELNAS++RGID VRN+IK FAQ+KV LPPGRHKI+ILDEADSMT GAQQALRRTM
Sbjct: 84  KEGVLELNASDERGIDVVRNRIKAFAQKKVILPPGRHKIIILDEADSMTAGAQQALRRTM 143

Query: 121 EIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGL 180
           EIYSNTTRFALACN S KIIEPIQSRCA+LRY++LTD Q+L +++ IC+ E +++T+DGL
Sbjct: 144 EIYSNTTRFALACNQSNKIIEPIQSRCAILRYSRLTDQQVLQRLLNICKAEKVNYTDDGL 203

Query: 181 EAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEMLLNCVEGNMKDS 240
            A++ TA+GDMRQA+NNLQST  GFG V  E VF+V D+P P+A+  ML  C  GN+  +
Sbjct: 204 AALIMTAEGDMRQAVNNLQSTVAGFGLVNGENVFRVADQPSPVAIHAMLTACQSGNIDVA 263

Query: 241 YKIIHHLYKLGYAPEDIIGNIFRVAKTLD-IPEPLKLSIIQEIGNVHLRISEGVNSLLQL 299
            + +  ++ LG++  DI+ N+FRV KT+D IPE  +L +++EIG  H+ I EGV +LLQL
Sbjct: 264 LEKLQGIWDLGFSAVDIVTNMFRVVKTMDSIPEFSRLEMLKEIGQTHMIILEGVQTLLQL 323

Query: 300 SGLLARLC 307
           SGL+ RL 
Sbjct: 324 SGLVCRLA 331

The elongation of primed DNA templates by DNA polymerase delta and epsilon requires the action of the accessory proteins PCNA and activator 1.

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

>sp|Q54E21|RFC2_DICDI Probable replication factor C subunit 2 OS=Dictyostelium discoideum GN=rfc2 PE=3 SV=1

 Score =  403 bits (1036), Expect = e-112,   Method: Compositional matrix adjust.
 Identities = 189/315 (60%), Positives = 248/315 (78%), Gaps = 1/315 (0%)

Query: 1   IEKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSF 60
           +EKYRP    DIVGNE+TV RL+  S  GN+PNIIISGPPG GKT++ILCLAR LLG ++
Sbjct: 23  VEKYRPILIKDIVGNEETVSRLESISKDGNLPNIIISGPPGTGKTSSILCLARALLGANY 82

Query: 61  KDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTM 120
           K+AV ELNAS+DR +D VR+KIK FA +KVTLP GRHKI+ILDE DSMT GAQQALRR M
Sbjct: 83  KEAVYELNASDDRTLDVVRDKIKSFAMKKVTLPAGRHKIIILDEVDSMTSGAQQALRRIM 142

Query: 121 EIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGL 180
           EIYS TTRFA ACN S KIIEPIQSRCA+LR+ +L+D+Q+L+++ E+ + E + +T+DGL
Sbjct: 143 EIYSGTTRFAFACNQSTKIIEPIQSRCAVLRFTRLSDSQILTRLREVVQIEKVPYTDDGL 202

Query: 181 EAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEMLLNCVEGNMKDS 240
            AI+FTA+GDMRQALNNLQ+TH+GFG + AE V KVCD+PHPL +K+++  C + + K++
Sbjct: 203 AAIIFTAEGDMRQALNNLQATHSGFGLINAENVTKVCDQPHPLIIKQIIALCAKSDFKEA 262

Query: 241 YKIIHHLYKLGYAPEDIIGNIFRVAKTL-DIPEPLKLSIIQEIGNVHLRISEGVNSLLQL 299
           Y  +  L+  GY+  DII  +F + K+  +IPE  KL  ++EIG  +LR + GVN+L+QL
Sbjct: 263 YPFLKKLWDDGYSSIDIISALFSITKSSNNIPEYQKLEFLKEIGFCNLRATTGVNTLVQL 322

Query: 300 SGLLARLCIVGSKNK 314
           +GLL++LC+V  K K
Sbjct: 323 TGLLSKLCLVSIKMK 337

The elongation of primed DNA templates by DNA polymerase delta and epsilon requires the action of the accessory proteins PCNA and activator 1.

Dictyostelium discoideum (taxid: 44689)

>sp|P40339|RFC4_YEAST Replication factor C subunit 4 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RFC4 PE=1 SV=1

 Score =  390 bits (1001), Expect = e-108,   Method: Compositional matrix adjust.
 Identities = 187/308 (60%), Positives = 245/308 (79%), Gaps = 5/308 (1%)

Query: 1   IEKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSF 60
           +EKYRPQ  SDIVGN++T++RL+  +  GN+P++IISG PG+GKTT++ CLA  LLG S+
Sbjct: 12  VEKYRPQVLSDIVGNKETIDRLQQIAKDGNMPHMIISGMPGIGKTTSVHCLAHELLGRSY 71

Query: 61  KDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTM 120
            D VLELNAS+DRGID VRN+IK FAQ+K+ LPPG+HKIVILDEADSMT GAQQALRRTM
Sbjct: 72  ADGVLELNASDDRGIDVVRNQIKHFAQKKLHLPPGKHKIVILDEADSMTAGAQQALRRTM 131

Query: 121 EIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGL 180
           E+YSN+TRFA ACN S KIIEP+QSRCA+LRY+KL+D  +L ++++I + E++ +TNDGL
Sbjct: 132 ELYSNSTRFAFACNQSNKIIEPLQSRCAILRYSKLSDEDVLKRLLQIIKLEDVKYTNDGL 191

Query: 181 EAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEMLLNCVEGNMKDS 240
           EAI+FTA+GDMRQA+NNLQST  G G V A+ VFK+ D PHPL VK+MLL     N++DS
Sbjct: 192 EAIIFTAEGDMRQAINNLQSTVAGHGLVNADNVFKIVDSPHPLIVKKMLL---ASNLEDS 248

Query: 241 YKIIH-HLYKLGYAPEDIIGNIFRVAKTL-DIPEPLKLSIIQEIGNVHLRISEGVNSLLQ 298
            +I+   L+K GY+  DI+   FRV K L  + E ++L +I+EIG  H+RI EGV + LQ
Sbjct: 249 IQILRTDLWKKGYSSIDIVTTSFRVTKNLAQVKESVRLEMIKEIGLTHMRILEGVGTYLQ 308

Query: 299 LSGLLARL 306
           L+ +LA++
Sbjct: 309 LASMLAKI 316

Component of ATP-dependent clamp loader (RFC and RFC-like) complexes for DNA clamps, such as the POL30/PCNA homotrimer and the checkpoint clamp DDC1:MEC3:RAD17 complex. During a clamp loading circle, the RFC:clamp complex binds to DNA and the recognition of the double-stranded/single-stranded junction stimulates ATP hydrolysis by RFC. The complex presumably provides bipartite ATP sites in which one subunit supplies a catalytic site for hydrolysis of ATP bound to the neighboring subunit. Dissociation of RFC from the clamp leaves the clamp encircling DNA. Component of the replication factor C (RFC or activator 1) complex which loads POL30/PCNA and acts during elongation of primed DNA templates by DNA polymerase delta and epsilon. RFC has an essential but redundant activity in sister chromatid cohesion establishment. Component of the RFC-like complex CTF18-RFC which is required for efficient establishment of chromosome cohesion during S-phase and may load or unload POL30/PCNA. Component of the RFC-like RAD24-RFC complex which loads the checkpoint clamp DDC1:MEC3:RAD17 complex and is involved in DNA repair pathways. Component of the RFC-like ELG1-RFC complex which appears to have a role in DNA replication, replication fork re-start, recombination and repair.

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (taxid: 559292)

>sp|Q975D3|RFCS_SULTO Replication factor C small subunit OS=Sulfolobus tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7) GN=rfcS PE=3 SV=1

 Score =  268 bits (686), Expect = 3e-71,   Method: Compositional matrix adjust.
 Identities = 143/316 (45%), Positives = 201/316 (63%), Gaps = 9/316 (2%)

Query: 2   EKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFK 61
           EKYRP++  DIV  +D VERLK F    N+P+++ SGPPG GKTT  L L   L G +++
Sbjct: 11  EKYRPRSLDDIVNQKDIVERLKRFVKDKNMPHLLFSGPPGTGKTTAALALVHDLYGDNYR 70

Query: 62  DAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGR--HKIVILDEADSMTDGAQQALRRT 119
              LELNAS++RGID +RNK+K FA+   T+  G    K+V+LDEAD+MT  AQQALRRT
Sbjct: 71  QYFLELNASDERGIDVIRNKVKEFAR---TVAGGNVPFKVVLLDEADNMTADAQQALRRT 127

Query: 120 MEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDG 179
           ME+Y+ TTRF LACN   KIIEPIQSR A+ R+  L    +++++  I + E + +    
Sbjct: 128 MELYTETTRFILACNYLSKIIEPIQSRTALFRFYPLKKEDVVARLAYIAKNEKVEYDQKA 187

Query: 180 LEAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEMLLNCVEGN-MK 238
           LE I    QGDMR+A+N LQ++ + +G VT E V+KV     P  ++EM++  ++GN +K
Sbjct: 188 LETIYDITQGDMRKAINILQAS-SVYGKVTVEAVYKVLGLAQPKEIREMIMLALQGNFLK 246

Query: 239 DSYKIIHHLYKLGYAPEDIIGNIFR--VAKTLDIPEPLKLSIIQEIGNVHLRISEGVNSL 296
              K+   L   G + EDII  I R      ++IP+ LK+ ++  IG V  RI EG +  
Sbjct: 247 AREKLRELLVNYGLSGEDIIKQIHREVTGNEINIPDDLKVLLVDYIGEVEYRIMEGADDE 306

Query: 297 LQLSGLLARLCIVGSK 312
           +QL+ LLA+L + G K
Sbjct: 307 IQLNALLAKLAVYGEK 322

Part of the RFC clamp loader complex which loads the PCNA sliding clamp onto DNA.

Sulfolobus tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7) (taxid: 273063)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	317
193605856	363	PREDICTED: replication factor C subunit	0.984	0.859	0.762	1e-141
327289387	329	PREDICTED: replication factor C subunit	0.968	0.933	0.768	1e-141
350401447	351	PREDICTED: replication factor C subunit	0.968	0.874	0.771	1e-141
340729148	351	PREDICTED: replication factor C subunit	0.968	0.874	0.771	1e-141
340729088	316	PREDICTED: replication factor C subunit	0.968	0.971	0.771	1e-141
66513962	350	PREDICTED: replication factor C subunit	0.968	0.877	0.778	1e-141
380013855	351	PREDICTED: LOW QUALITY PROTEIN: replicat	0.968	0.874	0.778	1e-141
158285610	341	AGAP007477-PA [Anopheles gambiae str. PE	0.968	0.900	0.758	1e-140
449282866	316	Replication factor C subunit 2, partial	0.968	0.971	0.752	1e-140
260820974	362	hypothetical protein BRAFLDRAFT_123856 [	0.971	0.850	0.753	1e-139

>gi|193605856|ref|XP_001945771.1| PREDICTED: replication factor C subunit 2-like isoform 1 [Acyrthosiphon pisum] gi|328696454|ref|XP_003240029.1| PREDICTED: replication factor C subunit 2-like isoform 2 [Acyrthosiphon pisum]

 Score =  508 bits (1308), Expect = e-141,   Method: Compositional matrix adjust.
 Identities = 238/312 (76%), Positives = 277/312 (88%)

Query: 1   IEKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSF 60
           IEKYRP++F+DIVGNE+TV RL+ FSS GNVPNIII+GPPGVGKTTTIL LARILLG +F
Sbjct: 49  IEKYRPKSFTDIVGNEETVLRLEKFSSCGNVPNIIIAGPPGVGKTTTILALARILLGGAF 108

Query: 61  KDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTM 120
           K+AVLELNAS+DRGIDTVRNKIKMFAQQKVTLPPGRHKI+ILDEADSMTDGAQQALRRTM
Sbjct: 109 KEAVLELNASSDRGIDTVRNKIKMFAQQKVTLPPGRHKIIILDEADSMTDGAQQALRRTM 168

Query: 121 EIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGL 180
           E++SNTTRFALACNNS+KIIE IQSRCAMLRY KL+D +++++++++C+ E +S + DGL
Sbjct: 169 ELWSNTTRFALACNNSDKIIEAIQSRCAMLRYGKLSDQEVMTQMLKVCKSEEVSFSADGL 228

Query: 181 EAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEMLLNCVEGNMKDS 240
           EA+VFTAQGDMRQALNNLQST NGF HV +  VFKVCDEPHPL VKEMLL C + N+  +
Sbjct: 229 EAVVFTAQGDMRQALNNLQSTWNGFRHVDSTNVFKVCDEPHPLLVKEMLLECADQNISKA 288

Query: 241 YKIIHHLYKLGYAPEDIIGNIFRVAKTLDIPEPLKLSIIQEIGNVHLRISEGVNSLLQLS 300
           YKI+ HL+KLGYAPEDII NIFRVAK L+I E LKL  +QEIG  H+RI EG+NSLLQLS
Sbjct: 289 YKIMAHLWKLGYAPEDIITNIFRVAKHLEIKESLKLKFVQEIGMAHIRIVEGMNSLLQLS 348

Query: 301 GLLARLCIVGSK 312
           GLLA+LC V +K
Sbjct: 349 GLLAKLCTVSAK 360

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|327289387|ref|XP_003229406.1| PREDICTED: replication factor C subunit 2-like [Anolis carolinensis]

 Score =  507 bits (1306), Expect = e-141,   Method: Compositional matrix adjust.
 Identities = 236/307 (76%), Positives = 273/307 (88%)

Query: 1   IEKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSF 60
           +EKYRP   S+IVGNEDTV RL+VF+  GNVPNIII+GPPG GKTT+ILCLAR LLGP+ 
Sbjct: 14  VEKYRPLKLSEIVGNEDTVSRLEVFAREGNVPNIIIAGPPGTGKTTSILCLARALLGPAL 73

Query: 61  KDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTM 120
           KDAVLELNASNDRGID VRNKIKMFAQQKVTLP GRHKI+ILDEADSMTDGAQQALRRTM
Sbjct: 74  KDAVLELNASNDRGIDVVRNKIKMFAQQKVTLPKGRHKIIILDEADSMTDGAQQALRRTM 133

Query: 121 EIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGL 180
           EIYS TTRFALACN S+KIIEPIQSRCA+LRY+KLTD Q+L+++++I EKEN+ +T+DGL
Sbjct: 134 EIYSKTTRFALACNASDKIIEPIQSRCAVLRYSKLTDGQVLARLMKIVEKENVQYTDDGL 193

Query: 181 EAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEMLLNCVEGNMKDS 240
           EAI+FTAQGDMRQALNNLQSTH+GFG V +E VFKVCDEPHPL VKEML +CV  N+ ++
Sbjct: 194 EAIIFTAQGDMRQALNNLQSTHSGFGFVNSENVFKVCDEPHPLLVKEMLGHCVSANIDEA 253

Query: 241 YKIIHHLYKLGYAPEDIIGNIFRVAKTLDIPEPLKLSIIQEIGNVHLRISEGVNSLLQLS 300
           YKI+ HL+KLGY+PEDIIGNIFRV KT  + E LKL  I+EIG  H++I+EGVNSLLQ++
Sbjct: 254 YKILAHLWKLGYSPEDIIGNIFRVCKTFQMAEYLKLEFIKEIGYTHMKIAEGVNSLLQMA 313

Query: 301 GLLARLC 307
           GLLARLC
Sbjct: 314 GLLARLC 320

Source: Anolis carolinensis

Species: Anolis carolinensis

Genus: Anolis

Family: Iguanidae

Order: Squamata

Phylum: Chordata

Superkingdom: Eukaryota

>gi|350401447|ref|XP_003486155.1| PREDICTED: replication factor C subunit 2-like [Bombus impatiens]

 Score =  507 bits (1305), Expect = e-141,   Method: Compositional matrix adjust.
 Identities = 237/307 (77%), Positives = 270/307 (87%)

Query: 1   IEKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSF 60
           IEKYRPQ FSDIVGNEDTV RL VF+  GN PNIII+GPPGVGKTTTILCLARILLGP+F
Sbjct: 39  IEKYRPQIFSDIVGNEDTVSRLSVFAEHGNCPNIIIAGPPGVGKTTTILCLARILLGPAF 98

Query: 61  KDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTM 120
           K+AVLELNASN+RGID VRNKIKMFAQ++V L  G+HKI+ILDEADSMTDGAQQALRRTM
Sbjct: 99  KEAVLELNASNERGIDVVRNKIKMFAQKRVNLAKGKHKIIILDEADSMTDGAQQALRRTM 158

Query: 121 EIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGL 180
           EIYSNTTRFALACN SEKIIEPIQSRCAMLRY KL+DAQ+L+K+IE+C+KE++SHT+DGL
Sbjct: 159 EIYSNTTRFALACNTSEKIIEPIQSRCAMLRYGKLSDAQILAKIIEVCQKEDVSHTDDGL 218

Query: 181 EAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEMLLNCVEGNMKDS 240
           EAIVFTAQGDMRQALNNLQST+NGFGHV +E VFKVCDEPHPL VKEML  C +G +  +
Sbjct: 219 EAIVFTAQGDMRQALNNLQSTYNGFGHVNSENVFKVCDEPHPLLVKEMLELCAQGKISKA 278

Query: 241 YKIIHHLYKLGYAPEDIIGNIFRVAKTLDIPEPLKLSIIQEIGNVHLRISEGVNSLLQLS 300
           Y I+ HL+K+GY+ ED+I NIFRV   L I EPLKL  I+EIG  HL I +G+NSLLQ++
Sbjct: 279 YGIMEHLWKMGYSAEDLISNIFRVCTNLSIEEPLKLDFIKEIGITHLGIVDGINSLLQMN 338

Query: 301 GLLARLC 307
            LLARLC
Sbjct: 339 SLLARLC 345

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340729148|ref|XP_003402870.1| PREDICTED: replication factor C subunit 2-like [Bombus terrestris]

 Score =  507 bits (1305), Expect = e-141,   Method: Compositional matrix adjust.
 Identities = 237/307 (77%), Positives = 269/307 (87%)

Query: 1   IEKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSF 60
           IEKYRPQ FSDIVGNEDTV RL VF+  GN PNIII+GPPGVGKTTTILCLARILLGP F
Sbjct: 39  IEKYRPQIFSDIVGNEDTVSRLSVFAEHGNCPNIIIAGPPGVGKTTTILCLARILLGPVF 98

Query: 61  KDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTM 120
           K+AVLELNASN+RGID VRNKIKMFAQ+KV L  G+HKI+ILDEADSMTDGAQQALRRTM
Sbjct: 99  KEAVLELNASNERGIDVVRNKIKMFAQKKVNLAKGKHKIIILDEADSMTDGAQQALRRTM 158

Query: 121 EIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGL 180
           EIYSNTTRFALACN SEKIIEPIQSRCAMLRY KL+DAQ+L+K+IE+C+KE++SHT+DGL
Sbjct: 159 EIYSNTTRFALACNTSEKIIEPIQSRCAMLRYGKLSDAQILAKIIEVCQKEDVSHTDDGL 218

Query: 181 EAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEMLLNCVEGNMKDS 240
           EAIVFTAQGDMRQALNNLQST+NGFGHV +E VFKVCDEPHPL VKEML  C +G +  +
Sbjct: 219 EAIVFTAQGDMRQALNNLQSTYNGFGHVNSENVFKVCDEPHPLLVKEMLELCAQGKISKA 278

Query: 241 YKIIHHLYKLGYAPEDIIGNIFRVAKTLDIPEPLKLSIIQEIGNVHLRISEGVNSLLQLS 300
           Y I+ HL+K+GY+ ED++ NIFRV   L I EPLKL  I+EIG  HL I +G+NSLLQ++
Sbjct: 279 YGIMEHLWKMGYSAEDLVSNIFRVCTNLSIEEPLKLDFIKEIGITHLGIVDGINSLLQMN 338

Query: 301 GLLARLC 307
            LLARLC
Sbjct: 339 SLLARLC 345

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340729088|ref|XP_003402840.1| PREDICTED: replication factor C subunit 2-like [Bombus terrestris]

 Score =  507 bits (1305), Expect = e-141,   Method: Compositional matrix adjust.
 Identities = 237/307 (77%), Positives = 269/307 (87%)

Query: 1   IEKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSF 60
           IEKYRPQ FSDIVGNEDTV RL VF+  GN PNIII+GPPGVGKTTTILCLARILLGP F
Sbjct: 4   IEKYRPQIFSDIVGNEDTVSRLSVFAEHGNCPNIIIAGPPGVGKTTTILCLARILLGPVF 63

Query: 61  KDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTM 120
           K+AVLELNASN+RGID VRNKIKMFAQ+KV L  G+HKI+ILDEADSMTDGAQQALRRTM
Sbjct: 64  KEAVLELNASNERGIDVVRNKIKMFAQKKVNLAKGKHKIIILDEADSMTDGAQQALRRTM 123

Query: 121 EIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGL 180
           EIYSNTTRFALACN SEKIIEPIQSRCAMLRY KL+DAQ+L+K+IE+C+KE++SHT+DGL
Sbjct: 124 EIYSNTTRFALACNTSEKIIEPIQSRCAMLRYGKLSDAQILAKIIEVCQKEDVSHTDDGL 183

Query: 181 EAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEMLLNCVEGNMKDS 240
           EAIVFTAQGDMRQALNNLQST+NGFGHV +E VFKVCDEPHPL VKEML  C +G +  +
Sbjct: 184 EAIVFTAQGDMRQALNNLQSTYNGFGHVNSENVFKVCDEPHPLLVKEMLELCAQGKISKA 243

Query: 241 YKIIHHLYKLGYAPEDIIGNIFRVAKTLDIPEPLKLSIIQEIGNVHLRISEGVNSLLQLS 300
           Y I+ HL+K+GY+ ED++ NIFRV   L I EPLKL  I+EIG  HL I +G+NSLLQ++
Sbjct: 244 YGIMEHLWKMGYSAEDLVSNIFRVCTNLSIEEPLKLDFIKEIGITHLGIVDGINSLLQMN 303

Query: 301 GLLARLC 307
            LLARLC
Sbjct: 304 SLLARLC 310

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|66513962|ref|XP_623937.1| PREDICTED: replication factor C subunit 2 [Apis mellifera]

 Score =  506 bits (1304), Expect = e-141,   Method: Compositional matrix adjust.
 Identities = 239/307 (77%), Positives = 271/307 (88%)

Query: 1   IEKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSF 60
           IEKYRPQ FSDIVGNEDTV RL VF+  GN PNIII+GPPGVGKTTTILCLARILLGP F
Sbjct: 39  IEKYRPQVFSDIVGNEDTVSRLSVFAQQGNCPNIIIAGPPGVGKTTTILCLARILLGPIF 98

Query: 61  KDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTM 120
           K+AVLELNASNDRGID VRNKIKMFAQ++V LP G+HKI+ILDEADSMT GAQQALRRTM
Sbjct: 99  KEAVLELNASNDRGIDVVRNKIKMFAQKRVNLPKGKHKIIILDEADSMTAGAQQALRRTM 158

Query: 121 EIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGL 180
           EIYSNTTRFALACN+S+KIIEPIQSRCAMLRY KL+DAQ+L+K+I+IC+KE++SHT+DGL
Sbjct: 159 EIYSNTTRFALACNSSDKIIEPIQSRCAMLRYGKLSDAQILAKIIDICKKEDVSHTDDGL 218

Query: 181 EAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEMLLNCVEGNMKDS 240
           EAIVFTAQGDMRQALNNLQSTHNGF HV +E VFKVCDEPHPL VKEML  C EGN+  +
Sbjct: 219 EAIVFTAQGDMRQALNNLQSTHNGFNHVNSENVFKVCDEPHPLLVKEMLEFCTEGNISKA 278

Query: 241 YKIIHHLYKLGYAPEDIIGNIFRVAKTLDIPEPLKLSIIQEIGNVHLRISEGVNSLLQLS 300
           Y ++ HL+K+GY+ EDII NIF+VAK L I E LKL  ++EIG  HL I +GVNSLLQ++
Sbjct: 279 YGVMEHLWKMGYSAEDIINNIFKVAKNLLIDETLKLDFVKEIGITHLGIVDGVNSLLQMN 338

Query: 301 GLLARLC 307
            LLARLC
Sbjct: 339 SLLARLC 345

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|380013855|ref|XP_003690961.1| PREDICTED: LOW QUALITY PROTEIN: replication factor C subunit 2-like [Apis florea]

 Score =  506 bits (1302), Expect = e-141,   Method: Compositional matrix adjust.
 Identities = 239/307 (77%), Positives = 271/307 (88%)

Query: 1   IEKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSF 60
           IEKYRPQ FSDIVGNEDTV RL VF+  GN PNIII+GPPGVGKTTTILCLARILLGP F
Sbjct: 40  IEKYRPQIFSDIVGNEDTVSRLSVFAQQGNCPNIIIAGPPGVGKTTTILCLARILLGPIF 99

Query: 61  KDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTM 120
           K+AVLELNASNDRGID VRNKIKMFAQ++V LP G+HKI+ILDEADSMT GAQQALRRTM
Sbjct: 100 KEAVLELNASNDRGIDVVRNKIKMFAQKRVNLPKGKHKIIILDEADSMTSGAQQALRRTM 159

Query: 121 EIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGL 180
           EIYSNTTRFALACN+S+KIIEPIQSRCAMLRY KL+DAQ+L+K+I+IC+KE++SHT+DGL
Sbjct: 160 EIYSNTTRFALACNSSDKIIEPIQSRCAMLRYGKLSDAQILAKIIDICKKEDVSHTDDGL 219

Query: 181 EAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEMLLNCVEGNMKDS 240
           EAIVFTAQGDMRQALNNLQSTHNGF HV +E VFKVCDEPHPL VKEML  C EGN+  +
Sbjct: 220 EAIVFTAQGDMRQALNNLQSTHNGFNHVNSENVFKVCDEPHPLLVKEMLEFCKEGNISKA 279

Query: 241 YKIIHHLYKLGYAPEDIIGNIFRVAKTLDIPEPLKLSIIQEIGNVHLRISEGVNSLLQLS 300
           Y ++ HL+K+GY+ EDII NIF+VAK L I E LKL  ++EIG  HL I +GVNSLLQ++
Sbjct: 280 YGVMEHLWKMGYSAEDIINNIFKVAKNLLIDETLKLDFVKEIGITHLGIVDGVNSLLQMN 339

Query: 301 GLLARLC 307
            LLARLC
Sbjct: 340 SLLARLC 346

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|158285610|ref|XP_308395.4| AGAP007477-PA [Anopheles gambiae str. PEST] gi|157020075|gb|EAA04621.4| AGAP007477-PA [Anopheles gambiae str. PEST]

 Score =  503 bits (1296), Expect = e-140,   Method: Compositional matrix adjust.
 Identities = 233/307 (75%), Positives = 275/307 (89%)

Query: 1   IEKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSF 60
           IEKYRPQ F +IVGNE+TV RL +F+S GN PNIII+GPPGVGKTTTILCLARILLGP+F
Sbjct: 28  IEKYRPQRFEEIVGNEETVARLGIFASQGNAPNIIIAGPPGVGKTTTILCLARILLGPNF 87

Query: 61  KDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTM 120
           ++AVLELNASN+RGID VR+KIKMFAQQKVTLP GRHKIVILDEADSMT+GAQQALRRTM
Sbjct: 88  REAVLELNASNERGIDVVRSKIKMFAQQKVTLPRGRHKIVILDEADSMTEGAQQALRRTM 147

Query: 121 EIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGL 180
           EIYSNTTRFALACN SEKIIEPIQSRCAMLR++KL+DAQ+L+KV+EIC+ EN+S+  DGL
Sbjct: 148 EIYSNTTRFALACNTSEKIIEPIQSRCAMLRFSKLSDAQVLAKVVEICQHENLSYDEDGL 207

Query: 181 EAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEMLLNCVEGNMKDS 240
           EAIVFTAQGDMRQALNNLQST NGFGH++   VFKVCDEPHPL V++ML +CV+G++  +
Sbjct: 208 EAIVFTAQGDMRQALNNLQSTANGFGHISGANVFKVCDEPHPLLVQDMLQHCVKGDIHKA 267

Query: 241 YKIIHHLYKLGYAPEDIIGNIFRVAKTLDIPEPLKLSIIQEIGNVHLRISEGVNSLLQLS 300
           YKI+  L+KLGYA EDIIGN+FRV + +D+ E LKL  I+EIG  H++I +G+NSLLQ+S
Sbjct: 268 YKIMSKLWKLGYAAEDIIGNVFRVCRRMDMNEKLKLYFIREIGETHMKIVDGLNSLLQMS 327

Query: 301 GLLARLC 307
           GLLAR+C
Sbjct: 328 GLLARMC 334

Source: Anopheles gambiae str. PEST

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|449282866|gb|EMC89612.1| Replication factor C subunit 2, partial [Columba livia]

 Score =  503 bits (1295), Expect = e-140,   Method: Compositional matrix adjust.
 Identities = 231/307 (75%), Positives = 273/307 (88%)

Query: 1   IEKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSF 60
           +EKYRP    +IVGNEDTV RL+VF+  GNVPNIII+GPPG GKTT+ILCLAR LLGP+ 
Sbjct: 1   VEKYRPMKLCEIVGNEDTVSRLEVFAKEGNVPNIIIAGPPGTGKTTSILCLARALLGPAL 60

Query: 61  KDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTM 120
           KDAVLELNASNDRGID VRNKIKMFAQQKVTLP GRHKI+ILDEADSMTDGAQQALRRTM
Sbjct: 61  KDAVLELNASNDRGIDVVRNKIKMFAQQKVTLPKGRHKIIILDEADSMTDGAQQALRRTM 120

Query: 121 EIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGL 180
           EIYS TTRFALACN S+KIIEPIQSRCA+LRY KLTD+Q+L+++++I EKE++ +T+DGL
Sbjct: 121 EIYSKTTRFALACNASDKIIEPIQSRCAVLRYTKLTDSQILARLLKIVEKEDVPYTDDGL 180

Query: 181 EAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEMLLNCVEGNMKDS 240
           EAI+FTAQGDMRQALNNLQST++GFG + +E VFKVCDEPHPL VKEM+ +CV  N+ ++
Sbjct: 181 EAIIFTAQGDMRQALNNLQSTYSGFGFINSENVFKVCDEPHPLLVKEMIQHCVNANIDEA 240

Query: 241 YKIIHHLYKLGYAPEDIIGNIFRVAKTLDIPEPLKLSIIQEIGNVHLRISEGVNSLLQLS 300
           YKI+ HL++LGYAPED+IGNIFRV KT  +PE LKL  I+EIG  H++I+EGVNSLLQ++
Sbjct: 241 YKILAHLWRLGYAPEDVIGNIFRVCKTFQMPEYLKLEFIKEIGYTHMKIAEGVNSLLQMA 300

Query: 301 GLLARLC 307
           GLLARLC
Sbjct: 301 GLLARLC 307

Source: Columba livia

Species: Columba livia

Genus: Columba

Family: Columbidae

Order: Columbiformes

Class: Aves

Phylum: Chordata

Superkingdom: Eukaryota

>gi|260820974|ref|XP_002605809.1| hypothetical protein BRAFLDRAFT_123856 [Branchiostoma floridae] gi|229291144|gb|EEN61819.1| hypothetical protein BRAFLDRAFT_123856 [Branchiostoma floridae]

 Score =  501 bits (1291), Expect = e-139,   Method: Compositional matrix adjust.
 Identities = 232/308 (75%), Positives = 272/308 (88%)

Query: 1   IEKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSF 60
           +EKYRP    D+VGNEDTV RL+VFS  GN+PNIII+G PG+GKTT+ILCLAR LLGP++
Sbjct: 45  VEKYRPAKLCDVVGNEDTVSRLEVFSQQGNMPNIIIAGSPGIGKTTSILCLARTLLGPAY 104

Query: 61  KDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTM 120
           KDAVLELNASNDRGID VRNKIKMFAQQKVTLP GRHKI+ILDEADSMTDGAQQALRRTM
Sbjct: 105 KDAVLELNASNDRGIDVVRNKIKMFAQQKVTLPKGRHKIIILDEADSMTDGAQQALRRTM 164

Query: 121 EIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGL 180
           EIYS TTRFALACN S+KIIE IQSRCA+LRY+KLTD Q+L +++ +CEKEN+ HT+DGL
Sbjct: 165 EIYSKTTRFALACNASDKIIEAIQSRCAVLRYSKLTDNQILERLLYVCEKENVEHTDDGL 224

Query: 181 EAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEMLLNCVEGNMKDS 240
           EA++FTAQGDMRQALNNLQST +GFG+V +E VFKVCDEPHPL VKEML +CV+ N+ ++
Sbjct: 225 EAVIFTAQGDMRQALNNLQSTWSGFGYVNSENVFKVCDEPHPLLVKEMLGHCVDANIDEA 284

Query: 241 YKIIHHLYKLGYAPEDIIGNIFRVAKTLDIPEPLKLSIIQEIGNVHLRISEGVNSLLQLS 300
           YKI+ HL+K+GY+PEDIIGNIFRV KT  + E LKL  I+EIG  H+RI +GV+SLLQLS
Sbjct: 285 YKILKHLWKMGYSPEDIIGNIFRVCKTYQMHEYLKLEFIKEIGYTHMRIVQGVDSLLQLS 344

Query: 301 GLLARLCI 308
           GLLARLC+
Sbjct: 345 GLLARLCL 352

Source: Branchiostoma floridae

Species: Branchiostoma floridae

Genus: Branchiostoma

Family: Branchiostomidae

Phylum: Chordata

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	317
UNIPROTKB|P53033	359	RFC2 "Replication factor C sub	0.930	0.821	0.738	1.4e-119
RGD|621198	349	Rfc2 "replication factor C (ac	0.930	0.845	0.742	7.7e-119
MGI|MGI:1341868	349	Rfc2 "replication factor C (ac	0.930	0.845	0.738	1.6e-118
UNIPROTKB|P35250	354	RFC2 "Replication factor C sub	0.930	0.833	0.742	4.2e-118
UNIPROTKB|Q05B83	352	RFC2 "Replication factor C sub	0.930	0.838	0.738	6.9e-118
UNIPROTKB|F6ULR2	364	RFC2 "Uncharacterized protein"	0.930	0.810	0.732	3.8e-117
ZFIN|ZDB-GENE-050306-29	384	rfc2 "replication factor C (ac	0.930	0.768	0.738	6.2e-117
FB|FBgn0260985	331	RfC4 "Replication factor C sub	0.987	0.945	0.699	6.4e-115
UNIPROTKB|E2QSU1	316	RFC2 "Uncharacterized protein"	0.883	0.886	0.735	2.6e-111
UNIPROTKB|I3LHX6	295	RFC2 "Uncharacterized protein"	0.864	0.928	0.751	1.4e-110

UNIPROTKB|P53033 RFC2 "Replication factor C subunit 2" [Gallus gallus (taxid:9031)]

 Score = 1177 (419.4 bits), Expect = 1.4e-119, P = 1.4e-119
 Identities = 218/295 (73%), Positives = 261/295 (88%)

Query:     1 IEKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSF 60
             +EKYRP    ++VGNEDTV RL+VF+  GNVPNIII+GPPG GKTT+ILCLAR LLGP+ 
Sbjct:    44 VEKYRPLKLCEVVGNEDTVSRLEVFAKEGNVPNIIIAGPPGTGKTTSILCLARALLGPAL 103

Query:    61 KDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTM 120
             KDAVLELNASNDRGID VRNKIKMFAQQKVTLP GRHKI+ILDEADSMTDGAQQALRRTM
Sbjct:   104 KDAVLELNASNDRGIDVVRNKIKMFAQQKVTLPKGRHKIIILDEADSMTDGAQQALRRTM 163

Query:   121 EIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGL 180
             EIYS TTRFALACN S+KIIEPIQSRCA+LRY KLTD+Q+L+++++I EKE++ +T+DGL
Sbjct:   164 EIYSKTTRFALACNASDKIIEPIQSRCAVLRYTKLTDSQILARLLKIVEKEDVPYTDDGL 223

Query:   181 EAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEMLLNCVEGNMKDS 240
             EAI+FTAQGDMRQALNNLQST++GFG + +E VFKVCDEPHPL VKEM+ +C+  N+ ++
Sbjct:   224 EAIIFTAQGDMRQALNNLQSTYSGFGFINSENVFKVCDEPHPLLVKEMIQHCINANIDEA 283

Query:   241 YKIIHHLYKLGYAPEDIIGNIFRVAKTLDIPEPLKLSIIQEIGNVHLRISEGVNS 295
             YKI+ HL++LGY+PED+IGNIFRV KT  +PE LKL  I+EIG  H++I+EGVNS
Sbjct:   284 YKILAHLWRLGYSPEDVIGNIFRVCKTFQMPEYLKLEFIKEIGYTHMKIAEGVNS 338

GO:0003677 "DNA binding" evidence=IEA

GO:0017111 "nucleoside-triphosphatase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0006260 "DNA replication" evidence=IEA

GO:0005663 "DNA replication factor C complex" evidence=IEA

GO:0000724 "double-strand break repair via homologous recombination" evidence=TAS

GO:0005654 "nucleoplasm" evidence=TAS

GO:0006281 "DNA repair" evidence=TAS

GO:0006302 "double-strand break repair" evidence=TAS

RGD|621198 Rfc2 "replication factor C (activator 1) 2" [Rattus norvegicus (taxid:10116)]

 Score = 1170 (416.9 bits), Expect = 7.7e-119, P = 7.7e-119
 Identities = 219/295 (74%), Positives = 259/295 (87%)

Query:     1 IEKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSF 60
             +EKYRP   ++IVGNEDTV RL+VF+  GNVPNIII+GPPG GKTT+ILCLAR LLGP+ 
Sbjct:    34 VEKYRPVKLNEIVGNEDTVSRLEVFAREGNVPNIIIAGPPGTGKTTSILCLARALLGPAL 93

Query:    61 KDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTM 120
             KDAVLELNASNDRGID VRNKIKMFAQQKVTLP GRHKI+ILDEADSMTDGAQQALRRTM
Sbjct:    94 KDAVLELNASNDRGIDVVRNKIKMFAQQKVTLPKGRHKIIILDEADSMTDGAQQALRRTM 153

Query:   121 EIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGL 180
             EIYS TTRFALACN S+KIIEPIQSRCA+LRY KLTDAQ+LS+++ + EKE + +T+DGL
Sbjct:   154 EIYSKTTRFALACNASDKIIEPIQSRCAVLRYTKLTDAQVLSRLMNVIEKEKVPYTDDGL 213

Query:   181 EAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEMLLNCVEGNMKDS 240
             EAI+FTAQGDMRQALNNLQST +GFG++ +E VFKVCDEPHPL VKEM+ +CV+ N+ ++
Sbjct:   214 EAIIFTAQGDMRQALNNLQSTFSGFGYINSENVFKVCDEPHPLLVKEMIQHCVDANIDEA 273

Query:   241 YKIIHHLYKLGYAPEDIIGNIFRVAKTLDIPEPLKLSIIQEIGNVHLRISEGVNS 295
             YKI+ HL+ LGY+PED+IGNIFRV KT  + E LKL  I+EIG  H++++EGVNS
Sbjct:   274 YKILAHLWHLGYSPEDVIGNIFRVCKTFPMAEYLKLEFIKEIGYTHMKVAEGVNS 328

GO:0003674 "molecular_function" evidence=ND

GO:0003677 "DNA binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

GO:0005634 "nucleus" evidence=IEA

GO:0005663 "DNA replication factor C complex" evidence=IEA;ISO

GO:0006260 "DNA replication" evidence=IEA

GO:0008150 "biological_process" evidence=ND

GO:0017111 "nucleoside-triphosphatase activity" evidence=IEA

MGI|MGI:1341868 Rfc2 "replication factor C (activator 1) 2" [Mus musculus (taxid:10090)]

 Score = 1167 (415.9 bits), Expect = 1.6e-118, P = 1.6e-118
 Identities = 218/295 (73%), Positives = 259/295 (87%)

Query:     1 IEKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSF 60
             +EKYRP   ++IVGNEDTV RL+VF+  GNVPNIII+GPPG GKTT+ILCLAR LLGP+ 
Sbjct:    34 VEKYRPLKLNEIVGNEDTVSRLEVFAREGNVPNIIIAGPPGTGKTTSILCLARALLGPAL 93

Query:    61 KDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTM 120
             KDAVLELNASNDRGID VRNKIKMFAQQKVTLP GRHKI+ILDEADSMTDGAQQALRRTM
Sbjct:    94 KDAVLELNASNDRGIDVVRNKIKMFAQQKVTLPKGRHKIIILDEADSMTDGAQQALRRTM 153

Query:   121 EIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGL 180
             EIYS TTRFALACN S+KIIEPIQSRCA+LRY KLTDAQ+L++++ + EKE + +T+DGL
Sbjct:   154 EIYSKTTRFALACNASDKIIEPIQSRCAVLRYTKLTDAQVLTRLMNVIEKEKVPYTDDGL 213

Query:   181 EAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEMLLNCVEGNMKDS 240
             EAI+FTAQGDMRQALNNLQST +GFG++ +E VFKVCDEPHPL VKEM+ +CV+ N+ ++
Sbjct:   214 EAIIFTAQGDMRQALNNLQSTFSGFGYINSENVFKVCDEPHPLLVKEMIQHCVDANIDEA 273

Query:   241 YKIIHHLYKLGYAPEDIIGNIFRVAKTLDIPEPLKLSIIQEIGNVHLRISEGVNS 295
             YKI+ HL+ LGY+PED+IGNIFRV KT  + E LKL  I+EIG  H++++EGVNS
Sbjct:   274 YKILAHLWHLGYSPEDVIGNIFRVCKTFPMAEYLKLEFIKEIGYTHMKVAEGVNS 328

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005663 "DNA replication factor C complex" evidence=ISO

GO:0006260 "DNA replication" evidence=IEA

GO:0017111 "nucleoside-triphosphatase activity" evidence=IEA

UNIPROTKB|P35250 RFC2 "Replication factor C subunit 2" [Homo sapiens (taxid:9606)]

 Score = 1163 (414.5 bits), Expect = 4.2e-118, P = 4.2e-118
 Identities = 219/295 (74%), Positives = 257/295 (87%)

Query:     1 IEKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSF 60
             +EKYRP   ++IVGNEDTV RL+VF+  GNVPNIII+GPPG GKTT+ILCLAR LLGP+ 
Sbjct:    39 VEKYRPVKLNEIVGNEDTVSRLEVFAREGNVPNIIIAGPPGTGKTTSILCLARALLGPAL 98

Query:    61 KDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTM 120
             KDA+LELNASNDRGID VRNKIKMFAQQKVTLP GRHKI+ILDEADSMTDGAQQALRRTM
Sbjct:    99 KDAMLELNASNDRGIDVVRNKIKMFAQQKVTLPKGRHKIIILDEADSMTDGAQQALRRTM 158

Query:   121 EIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGL 180
             EIYS TTRFALACN S+KIIEPIQSRCA+LRY KLTDAQ+L++++ + EKE + +T+DGL
Sbjct:   159 EIYSKTTRFALACNASDKIIEPIQSRCAVLRYTKLTDAQILTRLMNVIEKERVPYTDDGL 218

Query:   181 EAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEMLLNCVEGNMKDS 240
             EAI+FTAQGDMRQALNNLQST +GFG + +E VFKVCDEPHPL VKEM+ +CV  N+ ++
Sbjct:   219 EAIIFTAQGDMRQALNNLQSTFSGFGFINSENVFKVCDEPHPLLVKEMIQHCVNANIDEA 278

Query:   241 YKIIHHLYKLGYAPEDIIGNIFRVAKTLDIPEPLKLSIIQEIGNVHLRISEGVNS 295
             YKI+ HL+ LGY+PEDIIGNIFRV KT  + E LKL  I+EIG  H++I+EGVNS
Sbjct:   279 YKILAHLWHLGYSPEDIIGNIFRVCKTFQMAEYLKLEFIKEIGYTHMKIAEGVNS 333

GO:0003677 "DNA binding" evidence=IEA

GO:0017111 "nucleoside-triphosphatase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005663 "DNA replication factor C complex" evidence=IDA

GO:0000075 "cell cycle checkpoint" evidence=TAS

GO:0000084 "S phase of mitotic cell cycle" evidence=TAS

GO:0000278 "mitotic cell cycle" evidence=TAS

GO:0000722 "telomere maintenance via recombination" evidence=TAS

GO:0000723 "telomere maintenance" evidence=TAS

GO:0005654 "nucleoplasm" evidence=TAS

GO:0006260 "DNA replication" evidence=TAS

GO:0006271 "DNA strand elongation involved in DNA replication" evidence=TAS

GO:0006281 "DNA repair" evidence=TAS

GO:0006283 "transcription-coupled nucleotide-excision repair" evidence=TAS

GO:0006289 "nucleotide-excision repair" evidence=TAS

GO:0006297 "nucleotide-excision repair, DNA gap filling" evidence=TAS

GO:0032201 "telomere maintenance via semi-conservative replication" evidence=TAS

GO:0005515 "protein binding" evidence=IPI

UNIPROTKB|Q05B83 RFC2 "Replication factor C subunit 2" [Bos taurus (taxid:9913)]

 Score = 1161 (413.8 bits), Expect = 6.9e-118, P = 6.9e-118
 Identities = 218/295 (73%), Positives = 257/295 (87%)

Query:     1 IEKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSF 60
             +EKYRP   ++IVGNEDTV RL+VF+  GNVPNIII+GPPG GKTT+ILCLAR LLGP+ 
Sbjct:    37 VEKYRPVKLNEIVGNEDTVSRLEVFAREGNVPNIIIAGPPGTGKTTSILCLARALLGPAL 96

Query:    61 KDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTM 120
             KDAVLELNASNDRGID VRNKIKMFAQQKVTLP GRHKI+ILDEADSMTDGAQQALRRTM
Sbjct:    97 KDAVLELNASNDRGIDVVRNKIKMFAQQKVTLPKGRHKIIILDEADSMTDGAQQALRRTM 156

Query:   121 EIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGL 180
             EIYS TTRFALACN S+KIIEPIQSRCA+LRY KLTD Q+L++++ + EKE + +T+DGL
Sbjct:   157 EIYSKTTRFALACNASDKIIEPIQSRCAVLRYTKLTDMQILARLLSVIEKEKVQYTDDGL 216

Query:   181 EAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEMLLNCVEGNMKDS 240
             EAI+FTAQGDMRQALNNLQST++GFG + +E VFKVCDEPHPL VKEM+ +CV  ++ ++
Sbjct:   217 EAIIFTAQGDMRQALNNLQSTYSGFGFINSENVFKVCDEPHPLLVKEMIQHCVSADIDEA 276

Query:   241 YKIIHHLYKLGYAPEDIIGNIFRVAKTLDIPEPLKLSIIQEIGNVHLRISEGVNS 295
             YKI+ HL+ LGY+PEDIIGNIFRV KT  + E LKL  I+EIG  H++I+EGVNS
Sbjct:   277 YKILAHLWHLGYSPEDIIGNIFRVCKTFQMAEYLKLEFIKEIGYTHMKIAEGVNS 331

GO:0005524 "ATP binding" evidence=IEA

GO:0017111 "nucleoside-triphosphatase activity" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005663 "DNA replication factor C complex" evidence=IEA

GO:0006260 "DNA replication" evidence=IEA

UNIPROTKB|F6ULR2 RFC2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 1154 (411.3 bits), Expect = 3.8e-117, P = 3.8e-117
 Identities = 216/295 (73%), Positives = 257/295 (87%)

Query:     1 IEKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSF 60
             +EKYRP   ++IVGNEDTV RL+VF+  GNVPNIII+GPPG GKTT+ILCLAR LLGP+ 
Sbjct:    49 VEKYRPVKLNEIVGNEDTVSRLEVFAKEGNVPNIIIAGPPGTGKTTSILCLARALLGPAL 108

Query:    61 KDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTM 120
             KDAVLELNASNDRGID VRNKIKMFAQQKVTLP GRHKI+ILDEADSMTDGAQQALRRTM
Sbjct:   109 KDAVLELNASNDRGIDVVRNKIKMFAQQKVTLPKGRHKIIILDEADSMTDGAQQALRRTM 168

Query:   121 EIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGL 180
             EIYS TTRFALACN S+KIIEPIQSRCA+LRY KL+DAQ+L++++ + E+E + +T+DGL
Sbjct:   169 EIYSKTTRFALACNASDKIIEPIQSRCAVLRYTKLSDAQVLARLLTVLEQEKVPYTDDGL 228

Query:   181 EAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEMLLNCVEGNMKDS 240
             EA++FTAQGDMRQALNN+QST +GFG + +E VFKVCDEPHPL VKEM+ +CV  N+ ++
Sbjct:   229 EAVIFTAQGDMRQALNNVQSTFSGFGFINSENVFKVCDEPHPLLVKEMIQHCVNANIDEA 288

Query:   241 YKIIHHLYKLGYAPEDIIGNIFRVAKTLDIPEPLKLSIIQEIGNVHLRISEGVNS 295
             YKI+ HL+ LGY+PEDIIGNIFRV KT  + E LKL  I+EIG  H++I+EGVNS
Sbjct:   289 YKILAHLWHLGYSPEDIIGNIFRVCKTFQMAEYLKLEFIKEIGYTHMKIAEGVNS 343

GO:0005524 "ATP binding" evidence=IEA

GO:0017111 "nucleoside-triphosphatase activity" evidence=IEA

GO:0006260 "DNA replication" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

ZFIN|ZDB-GENE-050306-29 rfc2 "replication factor C (activator 1) 2" [Danio rerio (taxid:7955)]

 Score = 1152 (410.6 bits), Expect = 6.2e-117, P = 6.2e-117
 Identities = 218/295 (73%), Positives = 255/295 (86%)

Query:     1 IEKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSF 60
             +EKYRP   ++IVGNE+TV RL+VF+  GNVPNIII+GPPG GKTT+ILCLAR LLGP+ 
Sbjct:    69 VEKYRPLKLNEIVGNEETVSRLEVFAREGNVPNIIIAGPPGTGKTTSILCLARALLGPAM 128

Query:    61 KDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTM 120
             KDAVLELNASNDRGID VRNKIKMFAQQKVTLP GRHKI+ILDEADSMTDGAQQALRRTM
Sbjct:   129 KDAVLELNASNDRGIDVVRNKIKMFAQQKVTLPKGRHKIIILDEADSMTDGAQQALRRTM 188

Query:   121 EIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGL 180
             EIYS TTRFALACN S+KIIEPIQSRCA+LRY+KL D Q++ ++ E+ EKEN+  TNDGL
Sbjct:   189 EIYSKTTRFALACNASDKIIEPIQSRCAVLRYSKLRDEQIMMRLTEVVEKENLHVTNDGL 248

Query:   181 EAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEMLLNCVEGNMKDS 240
             EAI+FTAQGDMRQALNNLQST++GFG++ +E VFKVCDEPHPL VK ML +CV  N+ ++
Sbjct:   249 EAIIFTAQGDMRQALNNLQSTNSGFGYINSENVFKVCDEPHPLLVKSMLEHCVNANIDEA 308

Query:   241 YKIIHHLYKLGYAPEDIIGNIFRVAKTLDIPEPLKLSIIQEIGNVHLRISEGVNS 295
             YKII  L+ LGY+PEDIIGNIFRV KT  + E LKL  I+EIG  H++++EGVNS
Sbjct:   309 YKIIEQLWSLGYSPEDIIGNIFRVCKTFQMAEYLKLEYIKEIGYTHMKVAEGVNS 363

GO:0003677 "DNA binding" evidence=IEA

GO:0017111 "nucleoside-triphosphatase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0006260 "DNA replication" evidence=IEA

FB|FBgn0260985 RfC4 "Replication factor C subunit 4" [Drosophila melanogaster (taxid:7227)]

 Score = 1133 (403.9 bits), Expect = 6.4e-115, P = 6.4e-115
 Identities = 219/313 (69%), Positives = 257/313 (82%)

Query:     1 IEKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSF 60
             IEKYRP  F +IVGNEDTV RL VF++ GN PNIII+GPPGVGKTTTI CLARILLG S+
Sbjct:    19 IEKYRPVKFKEIVGNEDTVARLSVFATQGNAPNIIIAGPPGVGKTTTIQCLARILLGDSY 78

Query:    61 KDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTM 120
             K+AVLELNASN+RGID VRNKIKMFAQQKVTLP GRHKIVILDEADSMT+GAQQALRRTM
Sbjct:    79 KEAVLELNASNERGIDVVRNKIKMFAQQKVTLPRGRHKIVILDEADSMTEGAQQALRRTM 138

Query:   121 EIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGL 180
             EIYS+TTRFALACN SEKIIEPIQSRCAMLR+ KL+DAQ+L+K+IE+ + E +++T DGL
Sbjct:   139 EIYSSTTRFALACNTSEKIIEPIQSRCAMLRFTKLSDAQVLAKLIEVAKWEKLNYTEDGL 198

Query:   181 EAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEMLLNCVEGNMKDS 240
             EAIVFTAQGDMRQ LNNLQST  GFG +TAE VFKVCDEPHP  ++EM+ +C   ++  +
Sbjct:   199 EAIVFTAQGDMRQGLNNLQSTAQGFGDITAENVFKVCDEPHPKLLEEMIHHCAANDIHKA 258

Query:   241 YKIIHHLYKLGYAPEDIIGNIFRVAKTLDIPEPLKLSIIQEIGNVHLRISEGVNSXXXXX 300
             YKI+  L+KLGY+PEDII NIFRV K ++I E LKL  I+EIG  H++I +G+NS     
Sbjct:   259 YKILAKLWKLGYSPEDIIANIFRVCKRINIDEHLKLDFIREIGITHMKIIDGINSLLQLT 318

Query:   301 XXXXXXCIVGSKN 313
                   CI   K+
Sbjct:   319 ALLAKLCIAAEKH 331

GO:0007076 "mitotic chromosome condensation" evidence=IMP;NAS

GO:0000819 "sister chromatid segregation" evidence=NAS

GO:0006281 "DNA repair" evidence=TAS

GO:0006271 "DNA strand elongation involved in DNA replication" evidence=NAS;TAS

GO:0006260 "DNA replication" evidence=ISS;NAS;TAS

GO:0005663 "DNA replication factor C complex" evidence=ISS;NAS

GO:0004003 "ATP-dependent DNA helicase activity" evidence=ISS

GO:0003677 "DNA binding" evidence=IEA;NAS

GO:0016321 "female meiosis chromosome segregation" evidence=IMP

GO:0007067 "mitosis" evidence=IMP

GO:0005634 "nucleus" evidence=NAS;IDA

GO:0000077 "DNA damage checkpoint" evidence=IMP

GO:0000076 "DNA replication checkpoint" evidence=IMP

GO:0005524 "ATP binding" evidence=IEA

GO:0005875 "microtubule associated complex" evidence=IDA

GO:0022008 "neurogenesis" evidence=IMP

GO:0046331 "lateral inhibition" evidence=IMP

UNIPROTKB|E2QSU1 RFC2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 1099 (391.9 bits), Expect = 2.6e-111, P = 2.6e-111
 Identities = 206/280 (73%), Positives = 244/280 (87%)

Query:     1 IEKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSF 60
             +EKYRP   ++IVGNEDTV RL+VF+  GNVPNIII+GPPG GKTT+ILCLAR LLGP+ 
Sbjct:    37 VEKYRPVKLNEIVGNEDTVSRLEVFAKEGNVPNIIIAGPPGTGKTTSILCLARALLGPAL 96

Query:    61 KDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTM 120
             KDAVLELNASNDRGID VRNKIKMFAQQKVTLP GRHKI+ILDEADSMTDGAQQALRRTM
Sbjct:    97 KDAVLELNASNDRGIDVVRNKIKMFAQQKVTLPKGRHKIIILDEADSMTDGAQQALRRTM 156

Query:   121 EIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGL 180
             EIYS TTRFALACN S+KIIEPIQSRCA+LRY KL+DAQ+L++++ + E+E + +T+DGL
Sbjct:   157 EIYSKTTRFALACNASDKIIEPIQSRCAVLRYTKLSDAQVLARLLTVLEQEKVPYTDDGL 216

Query:   181 EAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEMLLNCVEGNMKDS 240
             EA++FTAQGDMRQALNN+QST +GFG + +E VFKVCDEPHPL VKEM+ +CV  N+ ++
Sbjct:   217 EAVIFTAQGDMRQALNNVQSTFSGFGFINSENVFKVCDEPHPLLVKEMIQHCVNANIDEA 276

Query:   241 YKIIHHLYKLGYAPEDIIGNIFRVAKTLDIPEPLKLSIIQ 280
             YKI+ HL+ LGY+PEDIIGNIFRV KT  + E LKL  I+
Sbjct:   277 YKILAHLWHLGYSPEDIIGNIFRVCKTFQMAEYLKLEFIK 316

GO:0005663 "DNA replication factor C complex" evidence=IEA

GO:0017111 "nucleoside-triphosphatase activity" evidence=IEA

GO:0006260 "DNA replication" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|I3LHX6 RFC2 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 1092 (389.5 bits), Expect = 1.4e-110, P = 1.4e-110
 Identities = 206/274 (75%), Positives = 240/274 (87%)

Query:    22 LKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNK 81
             L+VF+  GNVPNIII+GPPG GKTT+ILCLAR LLGP+ KDAVLELNASNDRGID VRNK
Sbjct:     1 LQVFAREGNVPNIIIAGPPGTGKTTSILCLARALLGPALKDAVLELNASNDRGIDVVRNK 60

Query:    82 IKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIE 141
             IKMFAQQKVTLP GRHKI+ILDEADSMTDGAQQALRRTMEIYS TTRFALACN S+KIIE
Sbjct:    61 IKMFAQQKVTLPKGRHKIIILDEADSMTDGAQQALRRTMEIYSKTTRFALACNASDKIIE 120

Query:   142 PIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQST 201
             PIQSRCA+LRY KLTDAQ+L++++ + EKE + +T+DGLEAI+FTAQGDMRQALNNLQST
Sbjct:   121 PIQSRCAVLRYTKLTDAQILARLLNVIEKEKVPYTDDGLEAIIFTAQGDMRQALNNLQST 180

Query:   202 HNGFGHVTAEYVFKVCDEPHPLAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDIIGNI 261
              +GFG + +E VFKVCDEPHPL VKEM+ +CV  N+ ++YKI+ HL+ LGY+PEDIIGNI
Sbjct:   181 FSGFGFINSENVFKVCDEPHPLLVKEMIQHCVSANIDEAYKILAHLWHLGYSPEDIIGNI 240

Query:   262 FRVAKTLDIPEPLKLSIIQEIGNVHLRISEGVNS 295
             FRV KT  + E LKL  I+EIG  H+R++EGVNS
Sbjct:   241 FRVCKTFQMAEYLKLEFIKEIGYTHMRVAEGVNS 274

GO:0005663 "DNA replication factor C complex" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0017111 "nucleoside-triphosphatase activity" evidence=IEA

GO:0006260 "DNA replication" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
P35250	RFC2_HUMAN	No assigned EC number	0.7459	0.9684	0.8672	yes	N/A
B0R7H7	RFCS_HALS3	No assigned EC number	0.3948	0.9652	0.9503	yes	N/A
A1RV38	RFCS2_PYRIL	No assigned EC number	0.4110	0.9558	0.9468	yes	N/A
Q5UZE5	RFCS_HALMA	No assigned EC number	0.4025	0.9621	0.9384	yes	N/A
A6US36	RFCS_METVS	No assigned EC number	0.4153	0.9621	0.9682	yes	N/A
Q9WUK4	RFC2_MOUSE	No assigned EC number	0.7426	0.9684	0.8796	yes	N/A
A7I8Y0	RFCS_METB6	No assigned EC number	0.4069	0.9810	0.9658	yes	N/A
O26343	RFCS_METTH	No assigned EC number	0.4147	0.9589	0.9470	yes	N/A
Q2FQT9	RFCS_METHJ	No assigned EC number	0.3805	0.9842	0.9659	yes	N/A
Q8ZWS2	RFCS2_PYRAE	No assigned EC number	0.4174	0.9558	0.9498	yes	N/A
O28219	RFCS_ARCFU	No assigned EC number	0.4095	0.9747	0.9686	yes	N/A
A9A6K6	RFCS_METM6	No assigned EC number	0.4064	0.9716	0.9777	yes	N/A
A4WLY0	RFCS2_PYRAR	No assigned EC number	0.4110	0.9558	0.9409	yes	N/A
Q2NH89	RFCS_METST	No assigned EC number	0.3980	0.9684	0.9563	yes	N/A
Q8PVY4	RFCS_METMA	No assigned EC number	0.3975	0.9621	0.9023	yes	N/A
O94449	RFC4_SCHPO	No assigned EC number	0.6201	0.9684	0.8976	yes	N/A
Q6L1I0	RFCS_PICTO	No assigned EC number	0.375	0.9747	0.9716	yes	N/A
Q9HN27	RFCS_HALSA	No assigned EC number	0.3948	0.9652	0.9503	yes	N/A
Q9UXF5	RFCS_SULSO	No assigned EC number	0.4272	0.9684	0.9303	yes	N/A
A6VJ61	RFCS_METM7	No assigned EC number	0.4294	0.9652	0.9714	yes	N/A
Q4JAB0	RFCS_SULAC	No assigned EC number	0.4208	0.9684	0.9446	yes	N/A
Q8SQM0	RFC4_ENCCU	No assigned EC number	0.4423	0.9558	0.9805	yes	N/A
A2SQT3	RFCS_METLZ	No assigned EC number	0.4076	0.9684	0.9563	yes	N/A
Q3ITJ2	RFCS_NATPD	No assigned EC number	0.4101	0.9211	0.8984	yes	N/A
Q977Z9	RFCS_THEVO	No assigned EC number	0.375	0.9747	0.9716	yes	N/A
Q8TSX5	RFCS_METAC	No assigned EC number	0.3975	0.9621	0.9023	yes	N/A
P53033	RFC2_CHICK	No assigned EC number	0.7426	0.9684	0.8551	yes	N/A
P40339	RFC4_YEAST	No assigned EC number	0.6071	0.9558	0.9380	yes	N/A
Q9HI47	RFCS_THEAC	No assigned EC number	0.375	0.9747	0.9716	yes	N/A
P53034	RFC2_DROME	No assigned EC number	0.7252	0.9873	0.9456	yes	N/A
A4FZ74	RFCS_METM5	No assigned EC number	0.4064	0.9716	0.9777	yes	N/A
Q0W037	RFCS_UNCMA	No assigned EC number	0.4006	0.9810	0.9658	yes	N/A
A5UMF3	RFCS_METS3	No assigned EC number	0.3858	0.9589	0.9650	yes	N/A
P60374	RFCS_NANEQ	No assigned EC number	0.3943	0.9747	0.9596	yes	N/A
A3CUX9	RFCS_METMJ	No assigned EC number	0.3904	0.9873	0.9720	yes	N/A
Q46C63	RFCS_METBF	No assigned EC number	0.3919	0.9558	0.9071	yes	N/A
Q6M044	RFCS_METMP	No assigned EC number	0.4096	0.9716	0.9777	yes	N/A
Q54E21	RFC2_DICDI	No assigned EC number	0.6	0.9905	0.9289	yes	N/A
Q9YBS7	RFCS_AERPE	No assigned EC number	0.4095	0.9779	0.9538	yes	N/A
Q641W4	RFC2_RAT	No assigned EC number	0.7459	0.9684	0.8796	yes	N/A
Q975D3	RFCS_SULTO	No assigned EC number	0.4525	0.9684	0.9388	yes	N/A
Q05B83	RFC2_BOVIN	No assigned EC number	0.7426	0.9684	0.8721	yes	N/A
A1RWU7	RFCS_THEPD	No assigned EC number	0.4179	0.9779	0.9538	yes	N/A
A3DNV9	RFCS_STAMF	No assigned EC number	0.4245	0.9747	0.9392	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	317
PLN03025	319	PLN03025, PLN03025, replication factor C subunit;	0.0
PRK00440	319	PRK00440, rfc, replication factor C small subunit;	1e-128
PRK04132	846	PRK04132, PRK04132, replication factor C small sub	4e-75
PRK12402	337	PRK12402, PRK12402, replication factor C small sub	1e-67
PHA02544	316	PHA02544, 44, clamp loader, small subunit; Provisi	8e-40
COG2812	515	COG2812, DnaX, DNA polymerase III, gamma/tau subun	4e-32
PRK14953	486	PRK14953, PRK14953, DNA polymerase III subunits ga	3e-31
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	4e-30
TIGR02397	355	TIGR02397, dnaX_nterm, DNA polymerase III, subunit	8e-30
PRK14962	472	PRK14962, PRK14962, DNA polymerase III subunits ga	5e-28
PRK14963	504	PRK14963, PRK14963, DNA polymerase III subunits ga	2e-25
PRK14970	367	PRK14970, PRK14970, DNA polymerase III subunits ga	3e-25
pfam08542	89	pfam08542, Rep_fac_C, Replication factor C C-termi	4e-25
PRK13342	413	PRK13342, PRK13342, recombination factor protein R	1e-23
PRK14964	491	PRK14964, PRK14964, DNA polymerase III subunits ga	3e-22
cd00009	151	cd00009, AAA, The AAA+ (ATPases Associated with a	1e-21
PRK14950	585	PRK14950, PRK14950, DNA polymerase III subunits ga	6e-21
COG0470	230	COG0470, HolB, ATPase involved in DNA replication	2e-20
PRK14965	576	PRK14965, PRK14965, DNA polymerase III subunits ga	2e-20
PRK07133	725	PRK07133, PRK07133, DNA polymerase III subunits ga	1e-19
PRK06305	451	PRK06305, PRK06305, DNA polymerase III subunits ga	2e-18
PRK08691	709	PRK08691, PRK08691, DNA polymerase III subunits ga	1e-17
PRK14956	484	PRK14956, PRK14956, DNA polymerase III subunits ga	1e-17
PRK14971	614	PRK14971, PRK14971, DNA polymerase III subunits ga	3e-17
PRK06647	563	PRK06647, PRK06647, DNA polymerase III subunits ga	1e-16
COG2256	436	COG2256, MGS1, ATPase related to the helicase subu	2e-16
PRK14959	624	PRK14959, PRK14959, DNA polymerase III subunits ga	6e-16
PRK08451	535	PRK08451, PRK08451, DNA polymerase III subunits ga	1e-15
PRK05896	605	PRK05896, PRK05896, DNA polymerase III subunits ga	1e-15
PRK05563	559	PRK05563, PRK05563, DNA polymerase III subunits ga	1e-15
PRK14961	363	PRK14961, PRK14961, DNA polymerase III subunits ga	4e-15
PRK12323	700	PRK12323, PRK12323, DNA polymerase III subunits ga	2e-14
PRK14952	584	PRK14952, PRK14952, DNA polymerase III subunits ga	2e-14
PRK14957	546	PRK14957, PRK14957, DNA polymerase III subunits ga	7e-14
PRK14969	527	PRK14969, PRK14969, DNA polymerase III subunits ga	2e-13
PRK14954	620	PRK14954, PRK14954, DNA polymerase III subunits ga	3e-13
PRK14955	397	PRK14955, PRK14955, DNA polymerase III subunits ga	3e-13
PRK06645	507	PRK06645, PRK06645, DNA polymerase III subunits ga	5e-13
PRK09111	598	PRK09111, PRK09111, DNA polymerase III subunits ga	8e-13
PRK07003	830	PRK07003, PRK07003, DNA polymerase III subunits ga	4e-12
PRK13341	725	PRK13341, PRK13341, recombination factor protein R	5e-12
pfam13177	161	pfam13177, DNA_pol3_delta2, DNA polymerase III, de	6e-12
PRK14958	509	PRK14958, PRK14958, DNA polymerase III subunits ga	8e-12
PRK04132	846	PRK04132, PRK04132, replication factor C small sub	3e-11
TIGR00678	188	TIGR00678, holB, DNA polymerase III, delta' subuni	3e-11
PRK14951	618	PRK14951, PRK14951, DNA polymerase III subunits ga	4e-11
PRK14960	702	PRK14960, PRK14960, DNA polymerase III subunits ga	1e-10
smart00382	148	smart00382, AAA, ATPases associated with a variety	4e-10
PRK05564	313	PRK05564, PRK05564, DNA polymerase III subunit del	5e-10
pfam00004	131	pfam00004, AAA, ATPase family associated with vari	9e-10
PRK14948	620	PRK14948, PRK14948, DNA polymerase III subunits ga	4e-09
PRK09112	351	PRK09112, PRK09112, DNA polymerase III subunit del	4e-08
TIGR02902	531	TIGR02902, spore_lonB, ATP-dependent protease LonB	5e-08
PRK07399	314	PRK07399, PRK07399, DNA polymerase III subunit del	1e-07
PRK07471	365	PRK07471, PRK07471, DNA polymerase III subunit del	1e-07
PRK00080	328	PRK00080, ruvB, Holliday junction DNA helicase Ruv	8e-07
PRK06871	325	PRK06871, PRK06871, DNA polymerase III subunit del	2e-06
COG2255	332	COG2255, RuvB, Holliday junction resolvasome, heli	4e-06
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	5e-06
TIGR00602	637	TIGR00602, rad24, checkpoint protein rad24	6e-06
pfam03215	490	pfam03215, Rad17, Rad17 cell cycle checkpoint prot	9e-06
TIGR02903	615	TIGR02903, spore_lon_C, ATP-dependent protease, Lo	9e-06
pfam05496	231	pfam05496, RuvB_N, Holliday junction DNA helicase	1e-05
PRK06090	319	PRK06090, PRK06090, DNA polymerase III subunit del	2e-05
PRK07993	334	PRK07993, PRK07993, DNA polymerase III subunit del	2e-05
pfam13401	124	pfam13401, AAA_22, AAA domain	3e-05
PRK07940	394	PRK07940, PRK07940, DNA polymerase III subunit del	3e-05
pfam13191	154	pfam13191, AAA_16, AAA ATPase domain	2e-04
PRK08769	319	PRK08769, PRK08769, DNA polymerase III subunit del	4e-04
PRK08058	329	PRK08058, PRK08058, DNA polymerase III subunit del	4e-04
pfam13173	127	pfam13173, AAA_14, AAA domain	5e-04
cd00267	157	cd00267, ABC_ATPase, ATP-binding cassette transpor	6e-04
PRK13695	174	PRK13695, PRK13695, putative NTPase; Provisional	0.001
COG1474	366	COG1474, CDC6, Cdc6-related protein, AAA superfami	0.001
TIGR00635	305	TIGR00635, ruvB, Holliday junction DNA helicase, R	0.003
pfam01443	226	pfam01443, Viral_helicase1, Viral (Superfamily 1)	0.004

>gnl|CDD|178596 PLN03025, PLN03025, replication factor C subunit; Provisional

 Score =  541 bits (1395), Expect = 0.0
 Identities = 208/315 (66%), Positives = 255/315 (80%)

Query: 1   IEKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSF 60
           +EKYRP    DIVGNED V RL+V +  GN+PN+I+SGPPG GKTT+IL LA  LLGP++
Sbjct: 4   VEKYRPTKLDDIVGNEDAVSRLQVIARDGNMPNLILSGPPGTGKTTSILALAHELLGPNY 63

Query: 61  KDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTM 120
           K+AVLELNAS+DRGID VRNKIKMFAQ+KVTLPPGRHKIVILDEADSMT GAQQALRRTM
Sbjct: 64  KEAVLELNASDDRGIDVVRNKIKMFAQKKVTLPPGRHKIVILDEADSMTSGAQQALRRTM 123

Query: 121 EIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGL 180
           EIYSNTTRFALACN S KIIEPIQSRCA++R+++L+D ++L +++++ E E + +  +GL
Sbjct: 124 EIYSNTTRFALACNTSSKIIEPIQSRCAIVRFSRLSDQEILGRLMKVVEAEKVPYVPEGL 183

Query: 181 EAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEMLLNCVEGNMKDS 240
           EAI+FTA GDMRQALNNLQ+TH+GFG V  E VFKVCD+PHPL VK ++ NC++G   D+
Sbjct: 184 EAIIFTADGDMRQALNNLQATHSGFGFVNQENVFKVCDQPHPLHVKNIVRNCLKGKFDDA 243

Query: 241 YKIIHHLYKLGYAPEDIIGNIFRVAKTLDIPEPLKLSIIQEIGNVHLRISEGVNSLLQLS 300
              +  LY LGY+P DII  +FRV K  D+PE LKL  ++EIG  H+RI +GV SLLQLS
Sbjct: 244 CDGLKQLYDLGYSPTDIITTLFRVVKNYDMPEFLKLEYLREIGFAHMRICDGVGSLLQLS 303

Query: 301 GLLARLCIVGSKNKK 315
           GLLA+LC+V    K 
Sbjct: 304 GLLAKLCLVRETAKA 318

Length = 319

>gnl|CDD|234763 PRK00440, rfc, replication factor C small subunit; Reviewed

 Score =  369 bits (950), Expect = e-128
 Identities = 148/315 (46%), Positives = 204/315 (64%), Gaps = 6/315 (1%)

Query: 1   IEKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSF 60
           +EKYRP+T  +IVG E+ VERLK +    N+P+++ +GPPG GKTT  L LAR L G  +
Sbjct: 8   VEKYRPRTLDEIVGQEEIVERLKSYVKEKNMPHLLFAGPPGTGKTTAALALARELYGEDW 67

Query: 61  KDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPG--RHKIVILDEADSMTDGAQQALRR 118
           ++  LELNAS++RGID +RNKIK FA+   T P G    KI+ LDEAD++T  AQQALRR
Sbjct: 68  RENFLELNASDERGIDVIRNKIKEFAR---TAPVGGAPFKIIFLDEADNLTSDAQQALRR 124

Query: 119 TMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTND 178
           TME+YS  TRF L+CN S KII+PIQSRCA+ R++ L    +  ++  I E E I  T+D
Sbjct: 125 TMEMYSQNTRFILSCNYSSKIIDPIQSRCAVFRFSPLKKEAVAERLRYIAENEGIEITDD 184

Query: 179 GLEAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEMLLNCVEGNMK 238
            LEAI + ++GDMR+A+N LQ+       VT E V+K+     P  ++EM+   + G+  
Sbjct: 185 ALEAIYYVSEGDMRKAINALQAAAATGKEVTEEAVYKITGTARPEEIREMIELALNGDFT 244

Query: 239 DSYKIIHHL-YKLGYAPEDIIGNIFRVAKTLDIPEPLKLSIIQEIGNVHLRISEGVNSLL 297
           ++ + +  L    G + EDII  I R   +LDIPE LK+ +I  IG    RI+EG N  +
Sbjct: 245 EAREKLRDLMIDYGLSGEDIIKQIHREVWSLDIPEELKVELIDAIGEADFRITEGANERI 304

Query: 298 QLSGLLARLCIVGSK 312
           QL  LLA+L ++G K
Sbjct: 305 QLEALLAKLALLGKK 319

Length = 319

>gnl|CDD|235223 PRK04132, PRK04132, replication factor C small subunit; Provisional

 Score =  246 bits (629), Expect = 4e-75
 Identities = 120/286 (41%), Positives = 175/286 (61%), Gaps = 13/286 (4%)

Query: 28  SGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFAQ 87
            GN+P +       +  TT  L LAR L G +++   LELNAS++RGI+ +R K+K FA+
Sbjct: 570 GGNLPTV-------LHNTTAALALARELFGENWRHNFLELNASDERGINVIREKVKEFAR 622

Query: 88  QKVTLPPG--RHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQS 145
            K   P G    KI+ LDEAD++T  AQQALRRTME++S+  RF L+CN S KIIEPIQS
Sbjct: 623 TK---PIGGASFKIIFLDEADALTQDAQQALRRTMEMFSSNVRFILSCNYSSKIIEPIQS 679

Query: 146 RCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHNGF 205
           RCA+ R+  L D  +  ++  I E E +  T +GL+AI++ A+GDMR+A+N LQ+     
Sbjct: 680 RCAIFRFRPLRDEDIAKRLRYIAENEGLELTEEGLQAILYIAEGDMRRAINILQAAAALD 739

Query: 206 GHVTAEYVFKVCDEPHPLAVKEMLLNCVEGN-MKDSYKIIHHLYKLGYAPEDIIGNIFRV 264
             +T E VF V     P  ++EM+L  ++GN +K   K+   L K G + ED++  + R 
Sbjct: 740 DKITDENVFLVASRARPEDIREMMLLALKGNFLKAREKLREILLKQGLSGEDVLVQMHRE 799

Query: 265 AKTLDIPEPLKLSIIQEIGNVHLRISEGVNSLLQLSGLLARLCIVG 310
              L I EP K+ +  +IG  + R+ EG N ++QL  LLA+  ++G
Sbjct: 800 VFNLPIDEPKKVELADKIGEYNFRLVEGANEMIQLEALLAQFTLMG 845

Length = 846

>gnl|CDD|237090 PRK12402, PRK12402, replication factor C small subunit 2; Reviewed

 Score =  214 bits (547), Expect = 1e-67
 Identities = 104/332 (31%), Positives = 169/332 (50%), Gaps = 27/332 (8%)

Query: 1   IEKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSF 60
            EKYRP    DI+G ++ VERL     S N+P++++ GPPG GKT  +  LAR L G  +
Sbjct: 6   TEKYRPALLEDILGQDEVVERLSRAVDSPNLPHLLVQGPPGSGKTAAVRALARELYGDPW 65

Query: 61  KDAVLELNASN--DRG-------------IDTVRN----KIKMFAQ---QKVTLPP--GR 96
           ++   E N ++  D+G             + T +     KI  F     +  +  P    
Sbjct: 66  ENNFTEFNVADFFDQGKKYLVEDPRFAHFLGTDKRIRSSKIDNFKHVLKEYASYRPLSAD 125

Query: 97  HKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLT 156
           +K ++LD A+++ + AQQALRR ME YS T RF +A     K+I PI+SRC  L +   T
Sbjct: 126 YKTILLDNAEALREDAQQALRRIMEQYSRTCRFIIATRQPSKLIPPIRSRCLPLFFRAPT 185

Query: 157 DAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKV 216
           D +L+  +  I E E + + +DGLE I + A GD+R+A+  LQ+     G +T E  ++ 
Sbjct: 186 DDELVDVLESIAEAEGVDYDDDGLELIAYYAGGDLRKAILTLQTAALAAGEITMEAAYEA 245

Query: 217 C-DEPHPLAVKEMLLNCVEGNMKDSYKIIHHL-YKLGYAPEDIIGNIFRVAKTLDIPEPL 274
             D      ++ +L     G+  D+ K +  L    G +  +++  + RVA++    + L
Sbjct: 246 LGDVGTDEVIESLLDAAEAGDFTDARKTLDDLLIDEGLSGGEVLEELLRVARSRYRGDNL 305

Query: 275 KLSIIQEIGNVHLRISEGVNSLLQLSGLLARL 306
              + +   +   R+++G N  +QL  LLA L
Sbjct: 306 AR-LHRLAADADARLTDGANDRIQLEALLAEL 336

Length = 337

>gnl|CDD|222866 PHA02544, 44, clamp loader, small subunit; Provisional

 Score =  141 bits (358), Expect = 8e-40
 Identities = 70/209 (33%), Positives = 100/209 (47%), Gaps = 19/209 (9%)

Query: 2   EKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIII-SGPPGVGKTTTILCLARILLGPSF 60
           +KYRP T  + +      E  K     G +PN+++ S  PG GKTT    L   +     
Sbjct: 13  QKYRPSTIDECILPAADKETFKSIVKKGRIPNMLLHSPSPGTGKTTVAKALCNEV----- 67

Query: 61  KDA-VLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEAD-SMTDGAQQALRR 118
             A VL +N S+ R ID VRN++  FA   V+L  G  K++I+DE D      AQ+ LR 
Sbjct: 68  -GAEVLFVNGSDCR-IDFVRNRLTRFAST-VSLTGG-GKVIIIDEFDRLGLADAQRHLRS 123

Query: 119 TMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDA-------QLLSKVIEICEKE 171
            ME YS    F +  NN   IIEP++SRC ++ +   T         Q++ +   I E E
Sbjct: 124 FMEAYSKNCSFIITANNKNGIIEPLRSRCRVIDFGVPTKEEQIEMMKQMIVRCKGILEAE 183

Query: 172 NISHTNDGLEAIVFTAQGDMRQALNNLQS 200
            +      L A+V     D R+ +N LQ 
Sbjct: 184 GVEVDMKVLAALVKKNFPDFRRTINELQR 212

Length = 316

>gnl|CDD|225369 COG2812, DnaX, DNA polymerase III, gamma/tau subunits [DNA replication, recombination, and repair]

 Score =  124 bits (314), Expect = 4e-32
 Identities = 88/310 (28%), Positives = 146/310 (47%), Gaps = 37/310 (11%)

Query: 3   KYRPQTFSDIVGNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTT-------TILCLARI 54
           KYRP+TF D+VG E  V+ L     +G + +  + SGP GVGKTT        + C    
Sbjct: 9   KYRPKTFDDVVGQEHVVKTLSNALENGRIAHAYLFSGPRGVGKTTIARILAKALNCENGP 68

Query: 55  LLGP-------------SFKDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPP--GRHKI 99
              P             S  D V+E++A+++ G+D +R  I     +KV   P  GR+K+
Sbjct: 69  TAEPCGKCISCKEINEGSLID-VIEIDAASNTGVDDIREII-----EKVNYAPSEGRYKV 122

Query: 100 VILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQ 159
            I+DE   ++  A  AL +T+E   +  +F LA    +KI   I SRC    + +L   +
Sbjct: 123 YIIDEVHMLSKQAFNALLKTLEEPPSHVKFILATTEPQKIPNTILSRCQRFDFKRLDLEE 182

Query: 160 LLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNL-QSTHNGFGHVTAEYVFKVCD 218
           +   +  I +KE I+   D L  I   A+G +R AL+ L Q+   G G +T E V  +  
Sbjct: 183 IAKHLAAILDKEGINIEEDALSLIARAAEGSLRDALSLLDQAIAFGEGEITLESVRDMLG 242

Query: 219 EPHPLAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDIIGNIFR-------VAKTLDIP 271
                 +  +L   ++G+ K++ ++I+ L + G  PE  + ++           +T+   
Sbjct: 243 LTDIEKLLSLLEAILKGDAKEALRLINELIEEGKDPEAFLEDLLNFLRDLLLFKQTVPNE 302

Query: 272 EPLKLSIIQE 281
             L  + I+E
Sbjct: 303 LQLNTTEIEE 312

Length = 515

>gnl|CDD|237867 PRK14953, PRK14953, DNA polymerase III subunits gamma and tau; Provisional

 Score =  121 bits (305), Expect = 3e-31
 Identities = 95/334 (28%), Positives = 159/334 (47%), Gaps = 43/334 (12%)

Query: 3   KYRPQTFSDIVGNEDTVERLKVFSSSGNVPNI-IISGPPGVGKTTTILCLARIL--LGP- 58
           KYRP+ F +++G E  V  LK       V +  I +GP G GKTT    LA++L  L P 
Sbjct: 9   KYRPKFFKEVIGQEIVVRILKNAVKLQRVSHAYIFAGPRGTGKTTIARILAKVLNCLNPQ 68

Query: 59  -----------------SFKDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPP--GRHKI 99
                            SF D + E++A+++RGID +R       +  V+  P  G++K+
Sbjct: 69  EGEPCGKCENCVEIDKGSFPDLI-EIDAASNRGIDDIRA-----LRDAVSYTPIKGKYKV 122

Query: 100 VILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQ 159
            I+DEA  +T  A  AL +T+E     T F L     +KI   I SRC    ++K T  Q
Sbjct: 123 YIIDEAHMLTKEAFNALLKTLEEPPPRTIFILCTTEYDKIPPTILSRCQRFIFSKPTKEQ 182

Query: 160 LLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNL-QSTHNGFGHVTAEYVFKVCD 218
           +   +  IC +E I +    L+ +   ++G MR A + L Q++  G G VT + V +   
Sbjct: 183 IKEYLKRICNEEKIEYEEKALDLLAQASEGGMRDAASLLDQASTYGEGKVTIKVVEEFLG 242

Query: 219 EPHPLAVKEMLLNCVEGNMKDSYKIIHHLYKLGY-------APEDIIGNIFRVAKTLDIP 271
                +V++ L   +E ++ ++ K +  L + GY         E+ I NI  + K+L  P
Sbjct: 243 IVSQESVRKFLNLLLESDVDEAIKFLRTLEEKGYNLNKFWKQLEEEIRNIL-LNKSLKNP 301

Query: 272 EPLKLSIIQEIGNVHLRISEGVNSLLQLSGLLAR 305
           E     + Q   + + ++ + + +LL L  ++ +
Sbjct: 302 E----EVFQV-EDFYRKLEKPLEALLYLEDVINK 330

Length = 486

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score =  118 bits (298), Expect = 4e-30
 Identities = 69/222 (31%), Positives = 115/222 (51%), Gaps = 17/222 (7%)

Query: 1   IEKYRPQTFSDIVGNEDTVERLKVFSSS---GNVPN-IIISGPPGVGKTTTILCLARILL 56
           +EKYRP+T SD+VGNE   E+L+ +  S   G     +++ GPPGVGKT+    LA    
Sbjct: 5   VEKYRPKTLSDVVGNEKAKEQLREWIESWLKGKPKKALLLYGPPGVGKTSLAHALAN--- 61

Query: 57  GPSFKDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSM---TD-GA 112
              +   V+ELNAS+ R  D +       A    +L   R K+++LDE D +    D G 
Sbjct: 62  --DYGWEVIELNASDQRTADVIERVAGEAATSG-SLFGARRKLILLDEVDGIHGNEDRGG 118

Query: 113 QQALRRTMEIYSNTTRFALACNNS-EKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKE 171
            +A+   ++         L  N+  +  +  +++ C M+ + +L+   ++  +  IC KE
Sbjct: 119 ARAILELIKKAKQP--IILTANDPYDPSLRELRNACLMIEFKRLSTRSIVPVLKRICRKE 176

Query: 172 NISHTNDGLEAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYV 213
            I   ++ L+ I   + GD+R A+N+LQ+   G+G +T E V
Sbjct: 177 GIECDDEALKEIAERSGGDLRSAINDLQAIAEGYGKLTLEDV 218

Length = 482

>gnl|CDD|233847 TIGR02397, dnaX_nterm, DNA polymerase III, subunit gamma and tau

 Score =  115 bits (291), Expect = 8e-30
 Identities = 81/289 (28%), Positives = 137/289 (47%), Gaps = 42/289 (14%)

Query: 3   KYRPQTFSDIVGNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARIL------ 55
           KYRPQTF D++G E  V+ LK    +G + +  + SGP G GKT+     ARI       
Sbjct: 7   KYRPQTFEDVIGQEHIVQTLKNAIKNGRIAHAYLFSGPRGTGKTSI----ARIFAKALNC 62

Query: 56  -LGPSFK-----------------DAVLELNASNDRGIDTVRNKIKMFAQQKVTLPP--G 95
             GP  +                 D V+E++A+++ G+D +R  +       V   P  G
Sbjct: 63  QNGPDGEPCNECESCKEINSGSSLD-VIEIDAASNNGVDDIREILD-----NVKYAPSSG 116

Query: 96  RHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYN-- 153
           ++K+ I+DE   ++  A  AL +T+E       F LA     KI   I SRC   R++  
Sbjct: 117 KYKVYIIDEVHMLSKSAFNALLKTLEEPPEHVVFILATTEPHKIPATILSRC--QRFDFK 174

Query: 154 KLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNL-QSTHNGFGHVTAEY 212
           ++    ++ ++ +I +KE I   ++ LE I   A G +R AL+ L Q    G G++T E 
Sbjct: 175 RIPLEDIVERLKKILDKEGIKIEDEALELIARAADGSLRDALSLLDQLISFGNGNITYED 234

Query: 213 VFKVCDEPHPLAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDIIGNI 261
           V ++        + E+L   +  +  ++ KI+  + + G  PE  + ++
Sbjct: 235 VNELLGLVDDEKLIELLEAILNKDTAEALKILDEILESGVDPEKFLEDL 283

This model represents the well-conserved first ~ 365 amino acids of the translation of the dnaX gene. The full-length product of the dnaX gene in the model bacterium E. coli is the DNA polymerase III tau subunit. A translational frameshift leads to early termination and a truncated protein subunit gamma, about 1/3 shorter than tau and present in roughly equal amounts. This frameshift mechanism is not necessarily universal for species with DNA polymerase III but appears conserved in the exterme thermophile Thermus thermophilis [DNA metabolism, DNA replication, recombination, and repair]. Length = 355

>gnl|CDD|237869 PRK14962, PRK14962, DNA polymerase III subunits gamma and tau; Provisional

 Score =  112 bits (282), Expect = 5e-28
 Identities = 86/285 (30%), Positives = 141/285 (49%), Gaps = 40/285 (14%)

Query: 3   KYRPQTFSDIVGNEDTVERLKVFSSSGNVPN--IIISGPPGVGKTTTILCLARIL----- 55
           KYRP+TFS++VG +D V++L + +   N  +   I +GP G GKTT    LA+ L     
Sbjct: 7   KYRPKTFSEVVG-QDHVKKLIINALKKNSISHAYIFAGPRGTGKTTVARILAKSLNCENR 65

Query: 56  --LGP-------------SFKDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPP--GRHK 98
             + P             +F D V+EL+A+++RGID +R KI+      V   P  G++K
Sbjct: 66  KGVEPCNECRACRSIDEGTFMD-VIELDAASNRGIDEIR-KIR----DAVGYRPMEGKYK 119

Query: 99  IVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDA 158
           + I+DE   +T  A  AL +T+E   +   F LA  N EK+   I SRC ++ +  ++D 
Sbjct: 120 VYIIDEVHMLTKEAFNALLKTLEEPPSHVVFVLATTNLEKVPPTIISRCQVIEFRNISDE 179

Query: 159 QLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHN-GFGHVTAEYVFK-- 215
            ++ ++ E+ E E I    + L  I   A G +R AL  L+       G +T E V +  
Sbjct: 180 LIIKRLQEVAEAEGIEIDREALSFIAKRASGGLRDALTMLEQVWKFSEGKITLETVHEAL 239

Query: 216 --VCDEPHPLAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDII 258
             +  E     V++ +     G++K  + ++  +Y  G   E +I
Sbjct: 240 GLIPIE----VVRDYINAIFNGDVKRVFTVLDDVYYSGKDYEVLI 280

Length = 472

>gnl|CDD|184927 PRK14963, PRK14963, DNA polymerase III subunits gamma and tau; Provisional

 Score =  105 bits (264), Expect = 2e-25
 Identities = 77/282 (27%), Positives = 126/282 (44%), Gaps = 34/282 (12%)

Query: 2   EKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNI-IISGPPGVGKTTTILCLARIL----- 55
           ++ RP TF ++VG E   E L      G + +  + SGP GVGKTTT    AR++     
Sbjct: 6   QRARPITFDEVVGQEHVKEVLLAALRQGRLGHAYLFSGPRGVGKTTT----ARLIAMAVN 61

Query: 56  -LGPSFKDA----------------VLELNASNDRGIDTVRNKIKMFAQQKVTLPP--GR 96
             G   K                  VLE++A+++  ++ VR+      ++KV L P  G 
Sbjct: 62  CSGEDPKPCGECESCLAVRRGAHPDVLEIDAASNNSVEDVRD-----LREKVLLAPLRGG 116

Query: 97  HKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLT 156
            K+ ILDEA  M+  A  AL +T+E       F LA    EK+   I SR    R+ +LT
Sbjct: 117 RKVYILDEAHMMSKSAFNALLKTLEEPPEHVIFILATTEPEKMPPTILSRTQHFRFRRLT 176

Query: 157 DAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKV 216
           + ++  K+  + E E      + L+ +   A G MR A + L+        VT + V + 
Sbjct: 177 EEEIAGKLRRLLEAEGREAEPEALQLVARLADGAMRDAESLLERLLALGTPVTRKQVEEA 236

Query: 217 CDEPHPLAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDII 258
              P    ++ +     +G+  ++      LY+ G+A   ++
Sbjct: 237 LGLPPQERLRGIAAALAQGDAAEALSGAAQLYRDGFAARTLV 278

Length = 504

>gnl|CDD|184934 PRK14970, PRK14970, DNA polymerase III subunits gamma and tau; Provisional

 Score =  103 bits (259), Expect = 3e-25
 Identities = 67/204 (32%), Positives = 100/204 (49%), Gaps = 15/204 (7%)

Query: 3   KYRPQTFSDIVGNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARILLGPSFK 61
           KYRPQTF D+VG       L     + ++   ++  GP GVGKTT    LAR +  P + 
Sbjct: 10  KYRPQTFDDVVGQSHITNTLLNAIENNHLAQALLFCGPRGVGKTTCARILARKINQPGYD 69

Query: 62  DA-------VLELNASNDRGIDTVRNKIKMFAQQKVTLPP--GRHKIVILDEADSMTDGA 112
           D        + EL+A+++  +D +RN I      +V +PP  G++KI I+DE   ++  A
Sbjct: 70  DPNEDFSFNIFELDAASNNSVDDIRNLI-----DQVRIPPQTGKYKIYIIDEVHMLSSAA 124

Query: 113 QQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKEN 172
             A  +T+E       F LA     KII  I SRC +  + ++T   +   +  I  KE 
Sbjct: 125 FNAFLKTLEEPPAHAIFILATTEKHKIIPTILSRCQIFDFKRITIKDIKEHLAGIAVKEG 184

Query: 173 ISHTNDGLEAIVFTAQGDMRQALN 196
           I   +D L  I   A G +R AL+
Sbjct: 185 IKFEDDALHIIAQKADGALRDALS 208

Length = 367

>gnl|CDD|203973 pfam08542, Rep_fac_C, Replication factor C C-terminal domain

 Score = 96.0 bits (240), Expect = 4e-25
 Identities = 29/89 (32%), Positives = 53/89 (59%)

Query: 218 DEPHPLAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDIIGNIFRVAKTLDIPEPLKLS 277
             P P  +KE+L + ++G+  ++ + ++ L   G + EDI+  +  V   LDIP+ LKL 
Sbjct: 1   GWPPPEDIKEILDSILKGDFDEARETLYELLVEGISAEDILKQLHEVLIRLDIPDSLKLE 60

Query: 278 IIQEIGNVHLRISEGVNSLLQLSGLLARL 306
           II+E+  +  R+S+G   ++QL  L+A+ 
Sbjct: 61  IIKELAEIEHRLSDGAKEIIQLEALIAKF 89

This is the C-terminal domain of RFC (replication factor-C) protein of the clamp loader complex which binds to the DNA sliding clamp (proliferating cell nuclear antigen, PCNA). The five modules of RFC assemble into a right-handed spiral, which results in only three of the five RFC subunits (RFC-A, RFC-B and RFC-C) making contact with PCNA, leaving a wedge-shaped gap between RFC-E and the PCNA clamp-loader complex. The C-terminal is vital for the correct orientation of RFC-E with respect to RFC-A. Length = 89

>gnl|CDD|237355 PRK13342, PRK13342, recombination factor protein RarA; Reviewed

 Score = 99.8 bits (250), Expect = 1e-23
 Identities = 61/223 (27%), Positives = 102/223 (45%), Gaps = 25/223 (11%)

Query: 2   EKYRPQTFSDIVGNEDTVERLKVFSS---SGNVPNIIISGPPGVGKTTTILCLARILLGP 58
           E+ RP+T  ++VG E  +   K       +G + ++I+ GPPG GKTT    LARI+ G 
Sbjct: 4   ERMRPKTLDEVVGQEHLLGPGKPLRRMIEAGRLSSMILWGPPGTGKTT----LARIIAG- 58

Query: 59  SFKDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQAL-- 116
           +       L+A    G+  +R   ++  + +     GR  I+ +DE        Q AL  
Sbjct: 59  ATDAPFEALSAVTS-GVKDLR---EVIEEARQRRSAGRRTILFIDEIHRFNKAQQDALLP 114

Query: 117 ---RRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDA---QLLSKVIEICEK 170
                T+ +   TT      N S ++   + SR  +     L++    QLL + +E  E+
Sbjct: 115 HVEDGTITLIGATTE-----NPSFEVNPALLSRAQVFELKPLSEEDIEQLLKRALEDKER 169

Query: 171 ENISHTNDGLEAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYV 213
             +   ++ L+A+   A GD R+ALN L+    G   +T E +
Sbjct: 170 GLVELDDEALDALARLANGDARRALNLLELAALGVDSITLELL 212

Length = 413

>gnl|CDD|237870 PRK14964, PRK14964, DNA polymerase III subunits gamma and tau; Provisional

 Score = 96.4 bits (240), Expect = 3e-22
 Identities = 65/218 (29%), Positives = 105/218 (48%), Gaps = 33/218 (15%)

Query: 3   KYRPQTFSDIVGNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARIL------ 55
           KYRP +F D+VG +  V  L+   +   +P  I++ G  GVGKTT     ARI+      
Sbjct: 6   KYRPSSFKDLVGQDVLVRILRNAFTLNKIPQSILLVGASGVGKTTC----ARIISLCLNC 61

Query: 56  -LGPSFKDA----------------VLELNASNDRGIDTVRNKIKMFAQQKVTLP-PGRH 97
             GP+                    V+E++A+++  +D     IK+  +    LP   + 
Sbjct: 62  SNGPTSDPCGTCHNCISIKNSNHPDVIEIDAASNTSVD----DIKVILENSCYLPISSKF 117

Query: 98  KIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTD 157
           K+ I+DE   +++ A  AL +T+E  +   +F LA    +KI   I SRC      K+  
Sbjct: 118 KVYIIDEVHMLSNSAFNALLKTLEEPAPHVKFILATTEVKKIPVTIISRCQRFDLQKIPT 177

Query: 158 AQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQAL 195
            +L+  +++I +KENI H  + L+ I   + G MR AL
Sbjct: 178 DKLVEHLVDIAKKENIEHDEESLKLIAENSSGSMRNAL 215

Length = 491

>gnl|CDD|99707 cd00009, AAA, The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold

 Score = 89.1 bits (221), Expect = 1e-21
 Identities = 39/145 (26%), Positives = 58/145 (40%), Gaps = 12/145 (8%)

Query: 13  VGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASND 72
           VG E+ +E L+         N+++ GPPG GKTT    +A  L  P      L LNAS+ 
Sbjct: 1   VGQEEAIEALREALELPPPKNLLLYGPPGTGKTTLARAIANELFRPGAP--FLYLNASDL 58

Query: 73  RGIDTVRNKIKMFA--QQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTT--- 127
                V      F            +  ++ +DE DS++ GAQ AL R +E  ++     
Sbjct: 59  LEGLVVAELFGHFLVRLLFELAEKAKPGVLFIDEIDSLSRGAQNALLRVLETLNDLRIDR 118

Query: 128 ---RFALACNNSE--KIIEPIQSRC 147
              R   A N      +   +  R 
Sbjct: 119 ENVRVIGATNRPLLGDLDRALYDRL 143

The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases. Length = 151

>gnl|CDD|237864 PRK14950, PRK14950, DNA polymerase III subunits gamma and tau; Provisional

 Score = 93.0 bits (231), Expect = 6e-21
 Identities = 67/226 (29%), Positives = 103/226 (45%), Gaps = 36/226 (15%)

Query: 3   KYRPQTFSDIVGNEDTVERLKVFSSSGNVPNI-IISGPPGVGKTTTILCLARIL------ 55
           K+R QTF+++VG E  V+ L+   + G V +  + +GP GVGKT+T    ARIL      
Sbjct: 9   KWRSQTFAELVGQEHVVQTLRNAIAEGRVAHAYLFTGPRGVGKTST----ARILAKAVNC 64

Query: 56  LGPSFKDA------------------VLELNASNDRGIDTVRNKIKMFAQQKVTLPPG-- 95
                K                    V+E++A++   +D  R  I     ++V   P   
Sbjct: 65  TTNDPKGRPCGTCEMCRAIAEGSAVDVIEMDAASHTSVDDAREII-----ERVQFRPALA 119

Query: 96  RHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKL 155
           R+K+ I+DE   ++  A  AL +T+E       F LA     K+   I SRC    +++ 
Sbjct: 120 RYKVYIIDEVHMLSTAAFNALLKTLEEPPPHAIFILATTEVHKVPATILSRCQRFDFHRH 179

Query: 156 TDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQST 201
           + A + + + +I   E I+     LEAI   A G MR A N LQ  
Sbjct: 180 SVADMAAHLRKIAAAEGINLEPGALEAIARAATGSMRDAENLLQQL 225

Length = 585

>gnl|CDD|223546 COG0470, HolB, ATPase involved in DNA replication [DNA replication, recombination, and repair]

 Score = 88.2 bits (218), Expect = 2e-20
 Identities = 51/200 (25%), Positives = 83/200 (41%), Gaps = 21/200 (10%)

Query: 121 EIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGL 180
                 TRF L  N+  KI+  I+SRC  +R+   +          I   E     + GL
Sbjct: 39  TAPPKNTRFILITNDPSKILPTIRSRCQRIRFKPPSRL------EAIAWLE-----DQGL 87

Query: 181 EAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHP-----LAVKEMLLNCVEG 235
           E I   A+GD R+A+N LQ+       +  E +++      P     LA  E+L      
Sbjct: 88  EEIAAVAEGDARKAINPLQALA--ALEIGEESIYEALLLALPESLAQLAALELLKLAENK 145

Query: 236 NMKDSYKIIHHLYKLGYAPEDIIGNIFRVAKTLD---IPEPLKLSIIQEIGNVHLRISEG 292
            ++   K+   L   G   ED++  + R    LD   I E     ++  +     R+ +G
Sbjct: 146 FLEALEKLWLLLLLEGLLGEDLLDQLQRELLKLDKALIQEEKAAELLDALAQARRRLLDG 205

Query: 293 VNSLLQLSGLLARLCIVGSK 312
           + +L+QL  LLA L ++   
Sbjct: 206 LLALIQLENLLAELLLLQLL 225

Length = 230

>gnl|CDD|237871 PRK14965, PRK14965, DNA polymerase III subunits gamma and tau; Provisional

 Score = 91.0 bits (226), Expect = 2e-20
 Identities = 61/220 (27%), Positives = 102/220 (46%), Gaps = 31/220 (14%)

Query: 3   KYRPQTFSDIVGNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARIL---LGP 58
           KYRPQTFSD+ G E     L+    +G V +  + +G  GVGKT+T   LA+ L    G 
Sbjct: 9   KYRPQTFSDLTGQEHVSRTLQNAIDTGRVAHAFLFTGARGVGKTSTARILAKALNCEQGL 68

Query: 59  SFKDA----------------VLELNASNDRGIDTVR---NKIKMFAQQKVTLPP-GRHK 98
           + +                  V E++ +++ G+D +R     +K        LP   R+K
Sbjct: 69  TAEPCNVCPPCVEITEGRSVDVFEIDGASNTGVDDIRELRENVKY-------LPSRSRYK 121

Query: 99  IVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDA 158
           I I+DE   ++  A  AL +T+E      +F  A     K+   I SRC    + ++   
Sbjct: 122 IFIIDEVHMLSTNAFNALLKTLEEPPPHVKFIFATTEPHKVPITILSRCQRFDFRRIPLQ 181

Query: 159 QLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNL 198
           +++ ++  I ++E IS ++  L  +     G MR +L+ L
Sbjct: 182 KIVDRLRYIADQEGISISDAALALVARKGDGSMRDSLSTL 221

Length = 576

>gnl|CDD|235943 PRK07133, PRK07133, DNA polymerase III subunits gamma and tau; Validated

 Score = 89.1 bits (221), Expect = 1e-19
 Identities = 81/314 (25%), Positives = 146/314 (46%), Gaps = 44/314 (14%)

Query: 3   KYRPQTFSDIVGNEDTVERLKVFSSSGNVPN-IIISGPPGVGKT-------TTILCLARI 54
           KYRP+TF DIVG +  V+ LK    S  + +  + SGP G GKT         + C  + 
Sbjct: 11  KYRPKTFDDIVGQDHIVQTLKNIIKSNKISHAYLFSGPRGTGKTSVAKIFANALNCSHKT 70

Query: 55  -LLGP------SFKDA--VLELNASNDRGIDTVRN---KIKMFAQQKVTLPPGRHKIVIL 102
            LL P      +  ++  ++E++A+++ G+D +R     +K    Q       ++KI I+
Sbjct: 71  DLLEPCQECIENVNNSLDIIEMDAASNNGVDEIRELIENVKNLPTQ------SKYKIYII 124

Query: 103 DEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLS 162
           DE   ++  A  AL +T+E       F LA     KI   I SR     + ++++ +++S
Sbjct: 125 DEVHMLSKSAFNALLKTLEEPPKHVIFILATTEVHKIPLTILSRVQRFNFRRISEDEIVS 184

Query: 163 KVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHN-GFGHVTAEYVFKVCDEPH 221
           ++  I EKENIS+  + L+ I   + G +R AL+  +     G   +T + V    +E  
Sbjct: 185 RLEFILEKENISYEKNALKLIAKLSSGSLRDALSIAEQVSIFGNNKITLKNV----EELF 240

Query: 222 PLAVKEMLLNCVE----GNMKDSYKIIHHLYKLGYAPE-------DIIGN--IFRVAKTL 268
            L   E L+N +      ++K+   I++ + + G  PE       +++    IF   K  
Sbjct: 241 GLVSNENLINLLNLLYSKDIKEVLNILNQIKEQGIDPELLLISLINLVKEFIIFNKTKDN 300

Query: 269 DIPEPLKLSIIQEI 282
            + E      ++++
Sbjct: 301 SLLEYYSEEDLEKL 314

Length = 725

>gnl|CDD|180523 PRK06305, PRK06305, DNA polymerase III subunits gamma and tau; Validated

 Score = 84.8 bits (210), Expect = 2e-18
 Identities = 68/223 (30%), Positives = 102/223 (45%), Gaps = 44/223 (19%)

Query: 3   KYRPQTFSDIVGNEDTVERLK---VFSSSGNVPNIIISGPPGVGKTTTILCLARIL---- 55
           KYRPQTFS+I+G +  V  LK    F+ + +    + SG  G GKTT    LARI     
Sbjct: 10  KYRPQTFSEILGQDAVVAVLKNALRFNRAAHA--YLFSGIRGTGKTT----LARIFAKAL 63

Query: 56  ----------------------LGPSFKDAVLELNASNDRGIDTVR--NKIKMFAQQKVT 91
                                  G S    VLE++ ++ RGI+ +R  N+  +F   K  
Sbjct: 64  NCQNPTEDQEPCNQCASCKEISSGTSLD--VLEIDGASHRGIEDIRQINETVLFTPSK-- 119

Query: 92  LPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLR 151
               R+KI I+DE   +T  A  +L +T+E      +F LA     KI   I SRC  + 
Sbjct: 120 ---SRYKIYIIDEVHMLTKEAFNSLLKTLEEPPQHVKFFLATTEIHKIPGTILSRCQKMH 176

Query: 152 YNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQA 194
             ++ +  ++ K+  I ++E I  + + L  I   AQG +R A
Sbjct: 177 LKRIPEETIIDKLALIAKQEGIETSREALLPIARAAQGSLRDA 219

Length = 451

>gnl|CDD|236333 PRK08691, PRK08691, DNA polymerase III subunits gamma and tau; Validated

 Score = 83.2 bits (205), Expect = 1e-17
 Identities = 65/232 (28%), Positives = 112/232 (48%), Gaps = 24/232 (10%)

Query: 3   KYRPQTFSDIVGNEDTVERLKVFSSSGNVPNI-IISGPPGVGKTTTILCLARILLGPSFK 61
           K+RP+TF+D+VG E  V+ L+     G + +  +++G  GVGKTT    LA+ L   + +
Sbjct: 9   KWRPKTFADLVGQEHVVKALQNALDEGRLHHAYLLTGTRGVGKTTIARILAKSLNCENAQ 68

Query: 62  DA-------------------VLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVIL 102
                                +LE++A+++ GID +R  ++  AQ   T   G++K+ I+
Sbjct: 69  HGEPCGVCQSCTQIDAGRYVDLLEIDAASNTGIDNIREVLEN-AQYAPTA--GKYKVYII 125

Query: 103 DEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLS 162
           DE   ++  A  A+ +T+E      +F LA  +  K+   + SRC       +T  Q+  
Sbjct: 126 DEVHMLSKSAFNAMLKTLEEPPEHVKFILATTDPHKVPVTVLSRCLQFVLRNMTAQQVAD 185

Query: 163 KVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNL-QSTHNGFGHVTAEYV 213
            +  + + E I++    L+ +   A G MR AL+ L Q+   G G V    V
Sbjct: 186 HLAHVLDSEKIAYEPPALQLLGRAAAGSMRDALSLLDQAIALGSGKVAENDV 237

Length = 709

>gnl|CDD|184920 PRK14956, PRK14956, DNA polymerase III subunits gamma and tau; Provisional

 Score = 82.7 bits (204), Expect = 1e-17
 Identities = 64/216 (29%), Positives = 100/216 (46%), Gaps = 27/216 (12%)

Query: 3   KYRPQTFSDIVGNEDTVERLKVFSSSGNVPNI-IISGPPGVGKTTTILCLARIL------ 55
           KYRPQ F D++  +  +  L+    SG + +  I  GP GVGKTT    LA+ L      
Sbjct: 11  KYRPQFFRDVIHQDLAIGALQNALKSGKIGHAYIFFGPRGVGKTTIARILAKRLNCENPI 70

Query: 56  -------------LGPSFKDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPP--GRHKIV 100
                        +       VLE++A+++RGI+ +R       +  V   P  G++K+ 
Sbjct: 71  GNEPCNECTSCLEITKGISSDVLEIDAASNRGIENIRE-----LRDNVKFAPMGGKYKVY 125

Query: 101 ILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQL 160
           I+DE   +TD +  AL +T+E       F LA     KI E I SRC    + K+  + L
Sbjct: 126 IIDEVHMLTDQSFNALLKTLEEPPAHIVFILATTEFHKIPETILSRCQDFIFKKVPLSVL 185

Query: 161 LSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALN 196
                ++C+ EN+ +  +GL  I     G +R  L+
Sbjct: 186 QDYSEKLCKIENVQYDQEGLFWIAKKGDGSVRDMLS 221

Length = 484

>gnl|CDD|237874 PRK14971, PRK14971, DNA polymerase III subunits gamma and tau; Provisional

 Score = 81.7 bits (202), Expect = 3e-17
 Identities = 66/216 (30%), Positives = 104/216 (48%), Gaps = 28/216 (12%)

Query: 3   KYRPQTFSDIVGNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTT-------TILCLARI 54
           KYRP TF  +VG E     LK   ++  + +  +  GP GVGKTT       TI C    
Sbjct: 10  KYRPSTFESVVGQEALTTTLKNAIATNKLAHAYLFCGPRGVGKTTCARIFAKTINCQNLT 69

Query: 55  LLGP---------SFKDA----VLELNASNDRGIDTVRNKIKMFAQQKVTLPP--GRHKI 99
             G          +F +     + EL+A+++  +D +RN I     ++V +PP  G++KI
Sbjct: 70  ADGEACNECESCVAFNEQRSYNIHELDAASNNSVDDIRNLI-----EQVRIPPQIGKYKI 124

Query: 100 VILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQ 159
            I+DE   ++  A  A  +T+E   +   F LA     KI+  I SRC +  +N++  A 
Sbjct: 125 YIIDEVHMLSQAAFNAFLKTLEEPPSYAIFILATTEKHKILPTILSRCQIFDFNRIQVAD 184

Query: 160 LLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQAL 195
           +++ +  +  KE I+   + L  I   A G MR AL
Sbjct: 185 IVNHLQYVASKEGITAEPEALNVIAQKADGGMRDAL 220

Length = 614

>gnl|CDD|235845 PRK06647, PRK06647, DNA polymerase III subunits gamma and tau; Validated

 Score = 79.8 bits (197), Expect = 1e-16
 Identities = 59/214 (27%), Positives = 105/214 (49%), Gaps = 27/214 (12%)

Query: 3   KYRPQTFSDIVGNEDTVERLKVFSSSGNVPNI-IISGPPGVGKTTTILCLARIL---LGP 58
           K RP+ F+ + G +  VE LK    S  + N  I SGP GVGKT++    AR L    GP
Sbjct: 9   KRRPRDFNSLEGQDFVVETLKHSIESNKIANAYIFSGPRGVGKTSSARAFARCLNCVNGP 68

Query: 59  ---------SFKDA-------VLELNASNDRGIDTVRNKIKMFAQQKVTLPP--GRHKIV 100
                    S K         V+E++ +++  +  VR +IK    +++  PP   R+++ 
Sbjct: 69  TPMPCGECSSCKSIDNDNSLDVIEIDGASNTSVQDVR-QIK----EEIMFPPASSRYRVY 123

Query: 101 ILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQL 160
           I+DE   +++ A  AL +T+E       F  A     K+   I+SRC    +  L+  ++
Sbjct: 124 IIDEVHMLSNSAFNALLKTIEEPPPYIVFIFATTEVHKLPATIKSRCQHFNFRLLSLEKI 183

Query: 161 LSKVIEICEKENISHTNDGLEAIVFTAQGDMRQA 194
            + + ++C ++ I + ++ L+ I + + G +R A
Sbjct: 184 YNMLKKVCLEDQIKYEDEALKWIAYKSTGSVRDA 217

Length = 563

>gnl|CDD|225165 COG2256, MGS1, ATPase related to the helicase subunit of the Holliday junction resolvase [DNA replication, recombination, and repair]

 Score = 79.2 bits (196), Expect = 2e-16
 Identities = 56/207 (27%), Positives = 95/207 (45%), Gaps = 19/207 (9%)

Query: 2   EKYRPQTFSDIVGNEDTVERLKVFS---SSGNVPNIIISGPPGVGKTTTILCLARILLGP 58
           E+ RP++  ++VG E  +   K       +G++ ++I+ GPPG GKTT    LAR++ G 
Sbjct: 16  ERLRPKSLDEVVGQEHLLGEGKPLRRAVEAGHLHSMILWGPPGTGKTT----LARLIAG- 70

Query: 59  SFKDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRR 118
           +   A   L+A    G+  +R  I+   + +     GR  I+ LDE        Q AL  
Sbjct: 71  TTNAAFEALSAVTS-GVKDLREIIE---EARKNRLLGRRTILFLDEIHRFNKAQQDALLP 126

Query: 119 TMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDA---QLLSKVIEICEK----E 171
            +E  +     A   N S ++   + SR  +     L+     +LL + +   E+    +
Sbjct: 127 HVENGTIILIGATTENPSFELNPALLSRARVFELKPLSSEDIKKLLKRALLDEERGLGGQ 186

Query: 172 NISHTNDGLEAIVFTAQGDMRQALNNL 198
            I    + L+ +V  + GD R+ALN L
Sbjct: 187 IIVLDEEALDYLVRLSNGDARRALNLL 213

Length = 436

>gnl|CDD|184923 PRK14959, PRK14959, DNA polymerase III subunits gamma and tau; Provisional

 Score = 77.8 bits (191), Expect = 6e-16
 Identities = 60/219 (27%), Positives = 104/219 (47%), Gaps = 29/219 (13%)

Query: 3   KYRPQTFSDIVGNEDTVERLKVFSSSGN--VPNIIISGPPGVGKTTTILCLARIL---LG 57
           +YRPQTF+++ G E TV+ +   ++  N   P  + SG  GVGKTT     A+ L     
Sbjct: 9   RYRPQTFAEVAGQE-TVKAILSRAAQENRVAPAYLFSGTRGVGKTTIARIFAKALNCETA 67

Query: 58  PSFKDA----------------VLELNASNDRGIDTVRNKIKMFAQQKVTLPP--GRHKI 99
           P+ +                  V+E++ +++RGID  +       ++ +   P  GR+K+
Sbjct: 68  PTGEPCNTCEQCRKVTQGMHVDVVEIDGASNRGIDDAKR-----LKEAIGYAPMEGRYKV 122

Query: 100 VILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQ 159
            I+DEA  +T  A  AL +T+E       F LA     K    I SRC    + +L++A 
Sbjct: 123 FIIDEAHMLTREAFNALLKTLEEPPARVTFVLATTEPHKFPVTIVSRCQHFTFTRLSEAG 182

Query: 160 LLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNL 198
           L + + ++  +E + +    +  I   A G +R +++ L
Sbjct: 183 LEAHLTKVLGREGVDYDPAAVRLIARRAAGSVRDSMSLL 221

Length = 624

>gnl|CDD|236267 PRK08451, PRK08451, DNA polymerase III subunits gamma and tau; Validated

 Score = 77.4 bits (191), Expect = 1e-15
 Identities = 65/232 (28%), Positives = 109/232 (46%), Gaps = 24/232 (10%)

Query: 3   KYRPQTFSDIVGNEDTVERLKVFSSSGNVPNI-IISGPPGVGKTTTILCLARILL---GP 58
           KYRP+ F +++G E   + L +   +  + +  + SG  G GKT++    AR L+   GP
Sbjct: 7   KYRPKHFDELIGQESVSKTLSLALDNNRLAHAYLFSGLRGSGKTSSARIFARALVCEQGP 66

Query: 59  SFKDA----------------VLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVIL 102
           S                    ++E++A+++RGID +R  I+   Q K      R KI I+
Sbjct: 67  SSTPCDTCIQCQSALENRHIDIIEMDAASNRGIDDIRELIE---QTKYKPSMARFKIFII 123

Query: 103 DEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLS 162
           DE   +T  A  AL +T+E   +  +F LA  +  K+   I SR    R+ ++    ++S
Sbjct: 124 DEVHMLTKEAFNALLKTLEEPPSYVKFILATTDPLKLPATILSRTQHFRFKQIPQNSIIS 183

Query: 163 KVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNL-QSTHNGFGHVTAEYV 213
            +  I EKE +S+  + LE +  +  G +R  L  L Q+       +T   V
Sbjct: 184 HLKTILEKEGVSYEPEALEILARSGNGSLRDTLTLLDQAIIYCKNAITESKV 235

Length = 535

>gnl|CDD|235638 PRK05896, PRK05896, DNA polymerase III subunits gamma and tau; Validated

 Score = 77.2 bits (190), Expect = 1e-15
 Identities = 61/218 (27%), Positives = 99/218 (45%), Gaps = 23/218 (10%)

Query: 2   EKYRPQTFSDIVGNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARIL--LGP 58
            KYRP  F  I+G E   + L     +  + +  I SGP G+GKT+     A+ +  L P
Sbjct: 8   RKYRPHNFKQIIGQELIKKILVNAILNNKLTHAYIFSGPRGIGKTSIAKIFAKAINCLNP 67

Query: 59  SFKDA-----------------VLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVI 101
              D                  ++EL+A+++ G+D +RN I        T    ++K+ I
Sbjct: 68  KDGDCCNSCSVCESINTNQSVDIVELDAASNNGVDEIRNIIDNINYLPTTF---KYKVYI 124

Query: 102 LDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLL 161
           +DEA  ++  A  AL +T+E       F  A    +KI   I SRC    + KL +++L 
Sbjct: 125 IDEAHMLSTSAWNALLKTLEEPPKHVVFIFATTEFQKIPLTIISRCQRYNFKKLNNSELQ 184

Query: 162 SKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQ 199
             +  I +KE I   ++ ++ I   A G +R  L+ L 
Sbjct: 185 ELLKSIAKKEKIKIEDNAIDKIADLADGSLRDGLSILD 222

Length = 605

>gnl|CDD|235505 PRK05563, PRK05563, DNA polymerase III subunits gamma and tau; Validated

 Score = 76.8 bits (190), Expect = 1e-15
 Identities = 78/297 (26%), Positives = 126/297 (42%), Gaps = 86/297 (28%)

Query: 3   KYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIII----------SGPPGVGKTTTILCLA 52
           K+RPQTF D+VG E   + LK         N I           SGP G GKT+     A
Sbjct: 9   KWRPQTFEDVVGQEHITKTLK---------NAIKQGKISHAYLFSGPRGTGKTSAAKIFA 59

Query: 53  RILLGPSFKDA-------------------VLELNASNDRGIDTVRNKIKMFAQQKVTLP 93
           + +   +  D                    V+E++A+++ G+D +R+        KV   
Sbjct: 60  KAVNCLNPPDGEPCNECEICKAITNGSLMDVIEIDAASNNGVDEIRDIR-----DKVKYA 114

Query: 94  P--GRHKIVILDEADSMTDGAQQALRRTME------IYSNTTRFALACNNSEKIIEPIQS 145
           P   ++K+ I+DE   ++ GA  AL +T+E      I      F LA     KI   I S
Sbjct: 115 PSEAKYKVYIIDEVHMLSTGAFNALLKTLEEPPAHVI------FILATTEPHKIPATILS 168

Query: 146 RCAMLRYN--KLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNL-Q--S 200
           RC   R++  +++   ++ ++  I +KE I + ++ L  I   A+G MR AL+ L Q  S
Sbjct: 169 RCQ--RFDFKRISVEDIVERLKYILDKEGIEYEDEALRLIARAAEGGMRDALSILDQAIS 226

Query: 201 THNGF----------GHVTAEYVFKVCDEPHPLAVKEMLLNCVEGNMKDSYKIIHHL 247
             +G           G V+ E +              ++   VEG++  + KI+  L
Sbjct: 227 FGDGKVTYEDALEVTGSVSQEALDD------------LVDAIVEGDVAKALKILEEL 271

Length = 559

>gnl|CDD|184925 PRK14961, PRK14961, DNA polymerase III subunits gamma and tau; Provisional

 Score = 74.8 bits (184), Expect = 4e-15
 Identities = 71/273 (26%), Positives = 125/273 (45%), Gaps = 35/273 (12%)

Query: 3   KYRPQTFSDIVGNEDTVERLKVFSSSGNVPNI-IISGPPGVGKTTTILCLAR-------I 54
           K+RPQ F DI+G +  V  +    S G + +  ++SG  GVGKTT    LA+       I
Sbjct: 9   KWRPQYFRDIIGQKHIVTAISNGLSLGRIHHAWLLSGTRGVGKTTIARLLAKSLNCQNGI 68

Query: 55  LLGP-------------SFKDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVI 101
              P                D ++E++A++   ++ +R   ++      +    R K+ +
Sbjct: 69  TSNPCRKCIICKEIEKGLCLD-LIEIDAASRTKVEEMR---EILDNIYYSPSKSRFKVYL 124

Query: 102 LDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLL 161
           +DE   ++  +  AL +T+E      +F LA  + EKI + I SRC   +   +++ ++ 
Sbjct: 125 IDEVHMLSRHSFNALLKTLEEPPQHIKFILATTDVEKIPKTILSRCLQFKLKIISEEKIF 184

Query: 162 SKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNL-QSTHNGFGHVTAEYVFK---VC 217
           + +  I  KE+I      L+ I + A G MR ALN L  + + G G++  + V     + 
Sbjct: 185 NFLKYILIKESIDTDEYALKLIAYHAHGSMRDALNLLEHAINLGKGNINIKNVTDMLGLL 244

Query: 218 DEPHPLAVKEMLLNCVEGNMKDSYKIIHHLYKL 250
           +E     + + LL       KDS K +  L K+
Sbjct: 245 NEKQSFLLTDALLK------KDSKKTMLLLNKI 271

Length = 363

>gnl|CDD|237057 PRK12323, PRK12323, DNA polymerase III subunits gamma and tau; Provisional

 Score = 73.8 bits (181), Expect = 2e-14
 Identities = 61/224 (27%), Positives = 101/224 (45%), Gaps = 40/224 (17%)

Query: 3   KYRPQTFSDIVGNEDTVERLKVFSSSGNVPNI-IISGPPGVGKTTTILCLARIL------ 55
           K+RP+ F+ +VG E  V  L        + +  + +G  GVGKTT    L+RIL      
Sbjct: 9   KWRPRDFTTLVGQEHVVRALTHALEQQRLHHAYLFTGTRGVGKTT----LSRILAKSLNC 64

Query: 56  LGPS-----------------------FKDAVLELNASNDRGIDTVRNKIKMFAQQKVTL 92
            G                         F D  +E++A+++RG+D    ++     + V  
Sbjct: 65  TGADGEGGITAQPCGQCRACTEIDAGRFVD-YIEMDAASNRGVD----EMAQLLDKAVYA 119

Query: 93  P-PGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLR 151
           P  GR K+ ++DE   +T+ A  A+ +T+E      +F LA  + +KI   + SRC    
Sbjct: 120 PTAGRFKVYMIDEVHMLTNHAFNAMLKTLEEPPEHVKFILATTDPQKIPVTVLSRCLQFN 179

Query: 152 YNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQAL 195
             ++    ++S +  I  +E I+H  + L  +   AQG MR AL
Sbjct: 180 LKQMPPGHIVSHLDAILGEEGIAHEVNALRLLAQAAQGSMRDAL 223

Length = 700

>gnl|CDD|237866 PRK14952, PRK14952, DNA polymerase III subunits gamma and tau; Provisional

 Score = 73.0 bits (179), Expect = 2e-14
 Identities = 65/237 (27%), Positives = 104/237 (43%), Gaps = 35/237 (14%)

Query: 3   KYRPQTFSDIVGNEDTVERLKVFSSSGNVPNI-IISGPPGVGKTTTILCLARIL------ 55
           KYRP TF+++VG E   E L     +G + +  + SGP G GKT++   LAR L      
Sbjct: 6   KYRPATFAEVVGQEHVTEPLSSALDAGRINHAYLFSGPRGCGKTSSARILARSLNCAQGP 65

Query: 56  -------------LGPSFKDA--VLELNASNDRGIDTVRNKIKMFAQQKVTLPPG--RHK 98
                        L P+   +  V+EL+A++  G+D  R       + +    P   R++
Sbjct: 66  TATPCGVCESCVALAPNGPGSIDVVELDAASHGGVDDTRE-----LRDRAFYAPAQSRYR 120

Query: 99  IVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDA 158
           I I+DEA  +T     AL + +E       F  A    EK++  I+SR     +  L   
Sbjct: 121 IFIVDEAHMVTTAGFNALLKIVEEPPEHLIFIFATTEPEKVLPTIRSRTHHYPFRLLPPR 180

Query: 159 QLLSKVIEICEKENISHTNDGLEAIVFTAQG----DMRQALNNLQSTHNGFGHVTAE 211
            + + +  ICE+E +   +D +  +V  A G    D    L+ L +      HVT +
Sbjct: 181 TMRALIARICEQEGVV-VDDAVYPLVIRAGGGSPRDTLSVLDQLLAGAAD-THVTYQ 235

Length = 584

>gnl|CDD|184921 PRK14957, PRK14957, DNA polymerase III subunits gamma and tau; Provisional

 Score = 71.7 bits (175), Expect = 7e-14
 Identities = 61/220 (27%), Positives = 104/220 (47%), Gaps = 31/220 (14%)

Query: 3   KYRPQTFSDIVGNEDTVERLKVFSSSGNVPNI-IISGPPGVGKTTTILCLARILL----- 56
           KYRPQ+F+++ G +  +  L     +  V +  + +G  GVGKTT    LA+ L      
Sbjct: 9   KYRPQSFAEVAGQQHALNSLVHALETQKVHHAYLFTGTRGVGKTTLGRLLAKCLNCKTGV 68

Query: 57  ---------------GPSFKDAVLELNASNDRGIDTVR---NKIKMFAQQKVTLPPGRHK 98
                            SF D ++E++A++  G++  +   + I+    Q      GR+K
Sbjct: 69  TAEPCNKCENCVAINNNSFID-LIEIDAASRTGVEETKEILDNIQYMPSQ------GRYK 121

Query: 99  IVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDA 158
           + ++DE   ++  +  AL +T+E      +F LA  +  KI   I SRC  L    ++ A
Sbjct: 122 VYLIDEVHMLSKQSFNALLKTLEEPPEYVKFILATTDYHKIPVTILSRCIQLHLKHISQA 181

Query: 159 QLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNL 198
            +  ++  I  KENI+     LE I + A+G +R AL+ L
Sbjct: 182 DIKDQLKIILAKENINSDEQSLEYIAYHAKGSLRDALSLL 221

Length = 546

>gnl|CDD|237873 PRK14969, PRK14969, DNA polymerase III subunits gamma and tau; Provisional

 Score = 70.2 bits (172), Expect = 2e-13
 Identities = 62/218 (28%), Positives = 100/218 (45%), Gaps = 33/218 (15%)

Query: 3   KYRPQTFSDIVGNEDTVERLKVFSSSGNVPNI-IISGPPGVGKTTTILCLARILL----- 56
           K+RP++FS++VG E  V  L        + +  + +G  GVGKTT    LARIL      
Sbjct: 9   KWRPKSFSELVGQEHVVRALTNALEQQRLHHAYLFTGTRGVGKTT----LARILAKSLNC 64

Query: 57  -------------------GPSFKDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRH 97
                                 F D ++E++A+++  +D +R  +   AQ   T   GR 
Sbjct: 65  ETGVTATPCGVCSACLEIDSGRFVD-LIEVDAASNTQVDAMRELLDN-AQYAPTR--GRF 120

Query: 98  KIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTD 157
           K+ I+DE   ++  A  A+ +T+E      +F LA  + +KI   + SRC      ++  
Sbjct: 121 KVYIIDEVHMLSKSAFNAMLKTLEEPPEHVKFILATTDPQKIPVTVLSRCLQFNLKQMPP 180

Query: 158 AQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQAL 195
             ++S +  I E+ENI      L+ +   A G MR AL
Sbjct: 181 PLIVSHLQHILEQENIPFDATALQLLARAAAGSMRDAL 218

Length = 527

>gnl|CDD|184918 PRK14954, PRK14954, DNA polymerase III subunits gamma and tau; Provisional

 Score = 70.0 bits (171), Expect = 3e-13
 Identities = 63/223 (28%), Positives = 91/223 (40%), Gaps = 37/223 (16%)

Query: 3   KYRPQTFSDIVGNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLA------RIL 55
           KYRP  F+DI   E     ++       V +  I SG  GVGKTT     A      R++
Sbjct: 9   KYRPSKFADITAQEHITHTIQNSLRMDRVGHGYIFSGLRGVGKTTAARVFAKAVNCQRMI 68

Query: 56  LGPSFKDAVLE----------------LN------ASNDR--GIDTVRNKIKMFAQQKVT 91
             P +   V E                LN      ASN+    I  +R  ++ +  QK  
Sbjct: 69  DDPVYLQEVTEPCGECESCRDFDAGTSLNISEFDAASNNSVDDIRQLRENVR-YGPQK-- 125

Query: 92  LPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLR 151
              GR+++ I+DE   ++  A  A  +T+E       F  A     KI   I SRC    
Sbjct: 126 ---GRYRVYIIDEVHMLSTAAFNAFLKTLEEPPPHAIFIFATTELHKIPATIASRCQRFN 182

Query: 152 YNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQA 194
           + ++   ++ S++  IC  E I    D L+ I   AQG MR A
Sbjct: 183 FKRIPLDEIQSQLQMICRAEGIQIDADALQLIARKAQGSMRDA 225

Length = 620

>gnl|CDD|184919 PRK14955, PRK14955, DNA polymerase III subunits gamma and tau; Provisional

 Score = 69.5 bits (170), Expect = 3e-13
 Identities = 60/225 (26%), Positives = 93/225 (41%), Gaps = 41/225 (18%)

Query: 3   KYRPQTFSDIVGNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARIL------ 55
           KYRP+ F+DI   E     ++     G V +  I SG  GVGKTT     A+ +      
Sbjct: 9   KYRPKKFADITAQEHITRTIQNSLRMGRVGHGYIFSGLRGVGKTTAARVFAKAVNCQRMI 68

Query: 56  -----------------------LGPSFKDAVLELNASNDRGID---TVRNKIKMFAQQK 89
                                   G S    + E +A+++  +D    +R  ++ +  QK
Sbjct: 69  DDADYLQEVTEPCGECESCRDFDAGTSLN--ISEFDAASNNSVDDIRLLRENVR-YGPQK 125

Query: 90  VTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAM 149
                GR+++ I+DE   ++  A  A  +T+E       F  A     KI   I SRC  
Sbjct: 126 -----GRYRVYIIDEVHMLSIAAFNAFLKTLEEPPPHAIFIFATTELHKIPATIASRCQR 180

Query: 150 LRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQA 194
             + ++   ++  ++  ICE E IS   D L+ I   AQG MR A
Sbjct: 181 FNFKRIPLEEIQQQLQGICEAEGISVDADALQLIGRKAQGSMRDA 225

Length = 397

>gnl|CDD|180643 PRK06645, PRK06645, DNA polymerase III subunits gamma and tau; Validated

 Score = 69.1 bits (169), Expect = 5e-13
 Identities = 58/221 (26%), Positives = 100/221 (45%), Gaps = 27/221 (12%)

Query: 3   KYRPQTFSDIVGNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTT-------TILCLARI 54
           KYRP  F+++ G E  V+ L     +  +    +++G  GVGKTT        + C A I
Sbjct: 14  KYRPSNFAELQGQEVLVKVLSYTILNDRLAGGYLLTGIRGVGKTTSARIIAKAVNCSALI 73

Query: 55  LLGPSFKDA----------------VLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHK 98
               + K                  ++E++A++   +D +R  I+  A+ K     G+HK
Sbjct: 74  TENTTIKTCEQCTNCISFNNHNHPDIIEIDAASKTSVDDIRRIIES-AEYKPLQ--GKHK 130

Query: 99  IVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDA 158
           I I+DE   ++ GA  AL +T+E       F  A    +KI   I SRC      +L+  
Sbjct: 131 IFIIDEVHMLSKGAFNALLKTLEEPPPHIIFIFATTEVQKIPATIISRCQRYDLRRLSFE 190

Query: 159 QLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQ 199
           ++   +  I ++EN+    + L  I + ++G  R A++ L 
Sbjct: 191 EIFKLLEYITKQENLKTDIEALRIIAYKSEGSARDAVSILD 231

Length = 507

>gnl|CDD|236382 PRK09111, PRK09111, DNA polymerase III subunits gamma and tau; Validated

 Score = 68.4 bits (168), Expect = 8e-13
 Identities = 79/263 (30%), Positives = 121/263 (46%), Gaps = 61/263 (23%)

Query: 3   KYRPQTFSDIVGNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARIL------ 55
           KYRPQTF D++G E  V  L     +G +    +++G  GVGKTTT    ARIL      
Sbjct: 17  KYRPQTFDDLIGQEAMVRTLTNAFETGRIAQAFMLTGVRGVGKTTT----ARILARALNY 72

Query: 56  ------LGPSFK--------DA--------VLELNASNDRGIDTVRNKIKMFAQQKVTLP 93
                  GP+           A        VLE++A++  G+D +R  I     + V   
Sbjct: 73  EGPDGDGGPTIDLCGVGEHCQAIMEGRHVDVLEMDAASHTGVDDIREII-----ESVRYR 127

Query: 94  P--GRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQ--SRCAM 149
           P   R+K+ I+DE   ++  A  AL +T+E      +F  A     K+  P+   SRC  
Sbjct: 128 PVSARYKVYIIDEVHMLSTAAFNALLKTLEEPPPHVKFIFATTEIRKV--PVTVLSRCQ- 184

Query: 150 LRYN-KLTDAQLLSKVIE-ICEKENISHTNDGLEAIVFTAQGDMRQALNNL-QSTHNGFG 206
            R++ +  +A +L+  +  I  KE +   ++ L  I   A+G +R  L+ L Q+  +G G
Sbjct: 185 -RFDLRRIEADVLAAHLSRIAAKEGVEVEDEALALIARAAEGSVRDGLSLLDQAIAHGAG 243

Query: 207 HVTAEYVFKVCDEPHPLAVKEML 229
            VTAE            AV++ML
Sbjct: 244 EVTAE------------AVRDML 254

Length = 598

>gnl|CDD|235906 PRK07003, PRK07003, DNA polymerase III subunits gamma and tau; Validated

 Score = 66.4 bits (162), Expect = 4e-12
 Identities = 61/221 (27%), Positives = 99/221 (44%), Gaps = 39/221 (17%)

Query: 3   KYRPQTFSDIVGNEDTVERLKVFSSSGNVPNI-IISGPPGVGKTTTILCLARILLGP--- 58
           K+RP+ F+ +VG E  V  L      G + +  + +G  GVGKTT    L+RI       
Sbjct: 9   KWRPKDFASLVGQEHVVRALTHALDGGRLHHAYLFTGTRGVGKTT----LSRIFAKALNC 64

Query: 59  ---------------------SFKDAVLELNASNDRGIDTVRNKIKMFA--QQKVTLP-P 94
                                 F D V E++A+++RG+D      +M A  ++ V  P  
Sbjct: 65  ETGVTSQPCGVCRACREIDEGRFVDYV-EMDAASNRGVD------EMAALLERAVYAPVD 117

Query: 95  GRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNK 154
            R K+ ++DE   +T+ A  A+ +T+E      +F LA  + +KI   + SRC      +
Sbjct: 118 ARFKVYMIDEVHMLTNHAFNAMLKTLEEPPPHVKFILATTDPQKIPVTVLSRCLQFNLKQ 177

Query: 155 LTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQAL 195
           +    ++S +  I  +E I+     L  +   AQG MR AL
Sbjct: 178 MPAGHIVSHLERILGEERIAFEPQALRLLARAAQGSMRDAL 218

Length = 830

>gnl|CDD|237354 PRK13341, PRK13341, recombination factor protein RarA/unknown domain fusion protein; Reviewed

 Score = 66.2 bits (162), Expect = 5e-12
 Identities = 57/218 (26%), Positives = 95/218 (43%), Gaps = 38/218 (17%)

Query: 2   EKYRPQTFSDIVGN-----EDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILL 56
           ++ RP+T  + VG      E  + R  +   +  V ++I+ GPPGVGKTT    LARI+ 
Sbjct: 20  DRLRPRTLEEFVGQDHILGEGRLLRRAI--KADRVGSLILYGPPGVGKTT----LARIIA 73

Query: 57  GPSFKDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRH---KIVILDEADSMTDGAQ 113
               +     LNA    G+  +R ++   A++++     RH    I+ +DE        Q
Sbjct: 74  N-HTRAHFSSLNAVL-AGVKDLRAEVDR-AKERL----ERHGKRTILFIDEVHRFNKAQQ 126

Query: 114 QAL-----RRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDA---QLLSKVI 165
            AL       T+ +   TT      N   ++ + + SR  + R   L+D    QLL + +
Sbjct: 127 DALLPWVENGTITLIGATTE-----NPYFEVNKALVSRSRLFRLKSLSDEDLHQLLKRAL 181

Query: 166 EICE----KENISHTNDGLEAIVFTAQGDMRQALNNLQ 199
           +  E       +    +  + +V  A GD R  LN L+
Sbjct: 182 QDKERGYGDRKVDLEPEAEKHLVDVANGDARSLLNALE 219

Length = 725

>gnl|CDD|221959 pfam13177, DNA_pol3_delta2, DNA polymerase III, delta subunit

 Score = 62.6 bits (153), Expect = 6e-12
 Identities = 39/164 (23%), Positives = 69/164 (42%), Gaps = 24/164 (14%)

Query: 14  GNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASND 72
           G    ++ LK       + +  + SGP GVGK    L  A+ L   + +D        + 
Sbjct: 1   GQPKVIKLLKNSIKKNKLSHAYLFSGPDGVGKLELALEFAKALFCENPQDDEPCGECKSC 60

Query: 73  R--------------------GIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGA 112
           +                     ID +R  +     +K     G+ K+ I+++A+ MT+ A
Sbjct: 61  KRIENGNHPDVIIIEPEGKSIKIDQIRE-LIEEFSKKPFE--GKKKVYIIEDAEKMTESA 117

Query: 113 QQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLT 156
             AL +T+E     T F L  +N  K++  I+SRC ++ +  L+
Sbjct: 118 ANALLKTLEEPPENTYFILLTSNPNKLLPTIRSRCQVINFKPLS 161

DNA polymerase III, delta subunit (EC 2.7.7.7) is required for, along with delta' subunit, the assembly of the processivity factor beta(2) onto primed DNA in the DNA polymerase III holoenzyme-catalyzed reaction. The delta subunit is also known as HolA. Length = 161

>gnl|CDD|184922 PRK14958, PRK14958, DNA polymerase III subunits gamma and tau; Provisional

 Score = 65.1 bits (158), Expect = 8e-12
 Identities = 75/310 (24%), Positives = 127/310 (40%), Gaps = 43/310 (13%)

Query: 3   KYRPQTFSDIVGNEDTVERLKVFSSSGNVPNI-IISGPPGVGKTTTILCLARILLGPSFK 61
           K+RP+ F +++G    V  L        + +  + +G  GVGKTT    LA+ L      
Sbjct: 9   KWRPRCFQEVIGQAPVVRALSNALDQQYLHHAYLFTGTRGVGKTTISRILAKCLNCEKGV 68

Query: 62  DAVLELNASNDRGID------------TVRNKIKMFAQQKVTLP----PGRHKIVILDEA 105
            A    +  N R ID              R K++   +    +P     GR K+ ++DE 
Sbjct: 69  SANPCNDCENCREIDEGRFPDLFEVDAASRTKVEDTRELLDNIPYAPTKGRFKVYLIDEV 128

Query: 106 DSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVI 165
             ++  +  AL +T+E   +  +F LA  +  K+   + SRC      +L   Q+ +   
Sbjct: 129 HMLSGHSFNALLKTLEEPPSHVKFILATTDHHKLPVTVLSRCLQFHLAQLPPLQIAAHCQ 188

Query: 166 EICEKENISHTNDGLEAIVFTAQGDMRQALNNL-QSTHNGFGHVTAEYVFKVCDEPHPLA 224
            + ++EN+   N  L+ +   A G +R AL+ L QS   G G V    V  +     PL 
Sbjct: 189 HLLKEENVEFENAALDLLARAANGSVRDALSLLDQSIAYGNGKVLIADVKTMLGTIEPLL 248

Query: 225 VKEM-----------LLNCV----------EGNMKDSYKIIHHLYKLGYAPEDIIGN--- 260
           + ++           LL CV             + D   ++H +  +   PE +I N   
Sbjct: 249 LFDILEALAAKAGDRLLGCVTRLVEQGVDFSNALADLLSLLHQIAIIQTVPEALIENDSE 308

Query: 261 -IFRVAKTLD 269
            + ++AK LD
Sbjct: 309 QLRQLAKLLD 318

Length = 509

>gnl|CDD|235223 PRK04132, PRK04132, replication factor C small subunit; Provisional

 Score = 63.7 bits (155), Expect = 3e-11
 Identities = 25/47 (53%), Positives = 35/47 (74%)

Query: 1  IEKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTT 47
          +EKYRPQ   DIVG E  V+RLK +  +G++P+++ +GPPGVGK  T
Sbjct: 10 VEKYRPQRLDDIVGQEHIVKRLKHYVKTGSMPHLLFAGPPGVGKCLT 56

Length = 846

>gnl|CDD|233087 TIGR00678, holB, DNA polymerase III, delta' subunit

 Score = 61.1 bits (149), Expect = 3e-11
 Identities = 37/147 (25%), Positives = 63/147 (42%), Gaps = 23/147 (15%)

Query: 35  IISGPPGVGKTTTILCLARILLGPSFKDA-------------------VLELNASNDR-G 74
           + +GP GVGK    L LA+ LL                          +  L        
Sbjct: 18  LFAGPEGVGKELLALALAKALLCEQPGGGEPCGECPSCRLIEAGNHPDLHRLEPEGQSIK 77

Query: 75  IDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACN 134
           +D VR  ++  ++          ++VI+++A+ M + A  AL +T+E     T F L   
Sbjct: 78  VDQVRELVEFLSRTPQE---SGRRVVIIEDAERMNEAAANALLKTLEEPPPNTLFILITP 134

Query: 135 NSEKIIEPIQSRCAMLRYNKLTDAQLL 161
           + EK++  I+SRC +L +  L++  LL
Sbjct: 135 SPEKLLPTIRSRCQVLPFPPLSEEALL 161

This model describes the N-terminal half of the delta' subunit of DNA polymerase III. Delta' is homologous to the gamma and tau subunits, which form an outgroup for phylogenetic comparison. The gamma/tau branch of the tree is much more tighly conserved than the delta' branch, and some members of that branch score more highly against this model than some proteins classisified as delta'. The noise cutoff is set to detect weakly scoring delta' subunits rather than to exclude gamma/tau subunits. At position 126-127 of the seed alignment, this family lacks the HM motif of gamma/tau; at 132 it has a near-invariant A vs. an invariant F in gamma/tau [DNA metabolism, DNA replication, recombination, and repair]. Length = 188

>gnl|CDD|237865 PRK14951, PRK14951, DNA polymerase III subunits gamma and tau; Provisional

 Score = 63.2 bits (154), Expect = 4e-11
 Identities = 70/261 (26%), Positives = 119/261 (45%), Gaps = 57/261 (21%)

Query: 3   KYRPQTFSDIVGNEDTVERLKVFSSSGNVPNI-IISGPPGVGKTTTILCLARIL------ 55
           KYRP++FS++VG E  V+ L    +   + +  + +G  GVGKTT    ++RIL      
Sbjct: 9   KYRPRSFSEMVGQEHVVQALTNALTQQRLHHAYLFTGTRGVGKTT----VSRILAKSLNC 64

Query: 56  LGPS-----------------------FKDAVLELNASNDRGIDTVRNKIKMFAQQKVTL 92
            GP                        F D   EL+A+++RG+D    +++   +Q V  
Sbjct: 65  QGPDGQGGITATPCGVCQACRDIDSGRFVDYT-ELDAASNRGVD----EVQQLLEQAVYK 119

Query: 93  P-PGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLR 151
           P  GR K+ ++DE   +T+ A  A+ +T+E      +F LA  + +K+   + SRC  L+
Sbjct: 120 PVQGRFKVFMIDEVHMLTNTAFNAMLKTLEEPPEYLKFVLATTDPQKVPVTVLSRC--LQ 177

Query: 152 YN--KLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALN-NLQSTHNGFGHV 208
           +N   +    +L  + ++   EN+      L  +   A+G MR AL+   Q+   G G +
Sbjct: 178 FNLRPMAPETVLEHLTQVLAAENVPAEPQALRLLARAARGSMRDALSLTDQAIAFGSGQL 237

Query: 209 TAEYVFKVCDEPHPLAVKEML 229
                          AV++ML
Sbjct: 238 QEA------------AVRQML 246

Length = 618

>gnl|CDD|237868 PRK14960, PRK14960, DNA polymerase III subunits gamma and tau; Provisional

 Score = 62.4 bits (151), Expect = 1e-10
 Identities = 85/332 (25%), Positives = 146/332 (43%), Gaps = 49/332 (14%)

Query: 3   KYRPQTFSDIVGNEDTVERLKVFSSSGNVPNI-IISGPPGVGKTTTILCLARIL-----L 56
           KYRP+ F+++VG       L      G + +  + +G  GVGKTT    LA+ L     +
Sbjct: 8   KYRPRNFNELVGQNHVSRALSSALERGRLHHAYLFTGTRGVGKTTIARILAKCLNCETGV 67

Query: 57  GPSFKDAVLELNASND-RGIDTV------RNKIKMFAQQKVTLP----PGRHKIVILDEA 105
             +  +      A N+ R ID +      R K++   +    +P     GR K+ ++DE 
Sbjct: 68  TSTPCEVCATCKAVNEGRFIDLIEIDAASRTKVEDTRELLDNVPYAPTQGRFKVYLIDEV 127

Query: 106 DSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVI 165
             ++  +  AL +T+E      +F  A  + +K+   + SRC       L   ++   + 
Sbjct: 128 HMLSTHSFNALLKTLEEPPEHVKFLFATTDPQKLPITVISRCLQFTLRPLAVDEITKHLG 187

Query: 166 EICEKENISHTNDGLEAIVFTAQGDMRQALN-NLQSTHNGFGHVTAEYVFKVCDEPHPLA 224
            I EKE I+   D +  I  +AQG +R AL+   Q+   G G V            H   
Sbjct: 188 AILEKEQIAADQDAIWQIAESAQGSLRDALSLTDQAIAYGQGAV------------HHQD 235

Query: 225 VKEM-----------LLNCVEGNMKDSYKIIHHLYKLGYAPEDIIGNIFRVAKTLDIPEP 273
           VKEM           L+  V  N ++  K+   L +  Y   D+   + ++  TL     
Sbjct: 236 VKEMLGLIDRTIIYDLILAVHQNQRE--KVSQLLLQFRYQALDVSLVLDQLISTLH---- 289

Query: 274 LKLSIIQEIGNVHLRISEGVNS-LLQLSGLLA 304
            +L+++Q +  + L+ SE +N+ +LQLS L++
Sbjct: 290 -ELALLQYLPELGLKYSEEINAKILQLSKLIS 320

Length = 702

>gnl|CDD|214640 smart00382, AAA, ATPases associated with a variety of cellular activities

 Score = 57.0 bits (137), Expect = 4e-10
 Identities = 29/132 (21%), Positives = 49/132 (37%), Gaps = 23/132 (17%)

Query: 33  NIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFAQQKVTL 92
            I+I GPPG GKTT    LAR L  P     V+ ++  +       +  + +   +K + 
Sbjct: 4   VILIVGPPGSGKTTLARALARELGPPGGG--VIYIDGEDILEEVLDQLLLIIVGGKKASG 61

Query: 93  PPG-------------RHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFA--------L 131
                           +  ++ILDE  S+ D  Q+AL   +E                 L
Sbjct: 62  SGELRLRLALALARKLKPDVLILDEITSLLDAEQEALLLLLEELRLLLLLKSEKNLTVIL 121

Query: 132 ACNNSEKIIEPI 143
             N+ + +   +
Sbjct: 122 TTNDEKDLGPAL 133

AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment. Length = 148

>gnl|CDD|180132 PRK05564, PRK05564, DNA polymerase III subunit delta'; Validated

 Score = 59.3 bits (144), Expect = 5e-10
 Identities = 46/155 (29%), Positives = 78/155 (50%), Gaps = 13/155 (8%)

Query: 9   FSDIVGNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARILLG-PSFKDAV-- 64
           F  I+G+E+   R+K         +  II G  G+GK+     +A  +LG    ++ V  
Sbjct: 3   FHTIIGHENIKNRIKNSIIKNRFSHAHIIVGEDGIGKSLLAKEIALKILGKSQQREYVDI 62

Query: 65  LELNASNDR--GIDTVRNKIKMFAQQKVTLPP--GRHKIVILDEADSMTDGAQQALRRTM 120
           +E    N +  G+D +RN I+     +V   P  G  K++I+  ++ MT+ AQ A  +T+
Sbjct: 63  IEFKPINKKSIGVDDIRNIIE-----EVNKKPYEGDKKVIIIYNSEKMTEQAQNAFLKTI 117

Query: 121 EIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKL 155
           E         L C N E+I++ I+SRC + + N+L
Sbjct: 118 EEPPKGVFIILLCENLEQILDTIKSRCQIYKLNRL 152

Length = 313

>gnl|CDD|215649 pfam00004, AAA, ATPase family associated with various cellular activities (AAA)

 Score = 55.7 bits (135), Expect = 9e-10
 Identities = 23/137 (16%), Positives = 53/137 (38%), Gaps = 27/137 (19%)

Query: 34  IIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRG---IDTVRNKIKMFAQQKV 90
           +++ GPPG GKTT    +A+ L         +E++ S        ++ +   ++F   K 
Sbjct: 1   LLLYGPPGTGKTTLAKAVAKEL-----GAPFIEISGSELVSKYVGESEKRLRELFEAAKK 55

Query: 91  TLPPGRHKIVILDEADSM-----------TDGAQQALRRTMEIYSNTTR---FALACNNS 136
             P     ++ +DE D++           +      L   ++ ++++        A N  
Sbjct: 56  LAPC----VIFIDEIDALAGSRGSGGDSESRRVVNQLLTELDGFTSSLSKVIVIAATNRP 111

Query: 137 EKIIEPI-QSRCAMLRY 152
           +K+   + + R   +  
Sbjct: 112 DKLDPALLRGRFDRIIE 128

AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes. Length = 131

>gnl|CDD|237862 PRK14948, PRK14948, DNA polymerase III subunits gamma and tau; Provisional

 Score = 57.3 bits (139), Expect = 4e-09
 Identities = 59/218 (27%), Positives = 100/218 (45%), Gaps = 33/218 (15%)

Query: 3   KYRPQTFSDIVGNEDTVERLKVFSSSGNV-PNIIISGPPGVGKTTTILCLARILLGPSFK 61
           KYRPQ F ++VG E     LK    S  + P  + +GP G GKT++   LA+ L   +  
Sbjct: 9   KYRPQRFDELVGQEAIATTLKNALISNRIAPAYLFTGPRGTGKTSSARILAKSLNCLNSD 68

Query: 62  DA---------------------VLELNASNDRGIDTVRNKIK--MFAQQKVTLPP--GR 96
                                  V+E++A+++ G+D +R  I+   FA       P   R
Sbjct: 69  KPTPEPCGKCELCRAIAAGNALDVIEIDAASNTGVDNIRELIERAQFA-------PVQAR 121

Query: 97  HKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLT 156
            K+ ++DE   ++  A  AL +T+E       F LA  + ++++  I SRC    + ++ 
Sbjct: 122 WKVYVIDECHMLSTAAFNALLKTLEEPPPRVVFVLATTDPQRVLPTIISRCQRFDFRRIP 181

Query: 157 DAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQA 194
              ++  + EI EKE+I    + L  +   +QG +R A
Sbjct: 182 LEAMVQHLSEIAEKESIEIEPEALTLVAQRSQGGLRDA 219

Length = 620

>gnl|CDD|169667 PRK09112, PRK09112, DNA polymerase III subunit delta'; Validated

 Score = 53.9 bits (130), Expect = 4e-08
 Identities = 51/225 (22%), Positives = 89/225 (39%), Gaps = 40/225 (17%)

Query: 6   PQTFSDIVGNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLA-RILLGPSFKDA 63
           P   + + G+E+    L      G + + ++  GP G+GK T    LA  IL  P   +A
Sbjct: 19  PSENTRLFGHEEAEAFLAQAYREGKLHHALLFEGPEGIGKATLAFHLANHILSHPDPAEA 78

Query: 64  ------------------------VLELNASNDRG---------IDTVRNKIKMFAQQKV 90
                                   +L +    D           +D +R      +Q   
Sbjct: 79  PETLADPDPASPVWRQIAQGAHPNLLHITRPFDEKTGKFKTAITVDEIRRVGHFLSQ--- 135

Query: 91  TLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAML 150
           T   G  +IVI+D AD M   A  A+ +T+E       F L  ++S +++  I+SRC  +
Sbjct: 136 TSGDGNWRIVIIDPADDMNRNAANAILKTLEEPPARALFILISHSSGRLLPTIRSRCQPI 195

Query: 151 RYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQAL 195
               L D +L   +  +   +      +  EA++  ++G +R+AL
Sbjct: 196 SLKPLDDDELKKALSHLGSSQGS--DGEITEALLQRSKGSVRKAL 238

Length = 351

>gnl|CDD|131948 TIGR02902, spore_lonB, ATP-dependent protease LonB

 Score = 54.0 bits (130), Expect = 5e-08
 Identities = 32/87 (36%), Positives = 50/87 (57%), Gaps = 17/87 (19%)

Query: 2   EKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILL----- 56
           EK RP++F +I+G E+ ++ LK      N  ++II GPPGVGKT      AR++L     
Sbjct: 57  EKTRPKSFDEIIGQEEGIKALKAALCGPNPQHVIIYGPPGVGKTAA----ARLVLEEAKK 112

Query: 57  --GPSFKD--AVLELNAS----NDRGI 75
                FK+  A +E++A+    ++RGI
Sbjct: 113 NPASPFKEGAAFVEIDATTARFDERGI 139

Members of this protein are LonB, a paralog of the ATP-dependent protease La (LonA, TIGR00763). LonB proteins are found strictly, and almost universally, in endospore-forming bacteria. This protease was shown, in Bacillus subtilis, to be expressed specifically in the forespore, during sporulation, under control of sigma(F). The lonB gene, despite location immediately upstream of lonA, was shown to be monocistronic. LonB appears able to act on sigma(H) for post-translation control, but lonB mutation did not produce an obvious sporulation defect under the conditions tested. Note that additional paralogs of LonA and LonB occur in the Clostridium lineage and this model selects only one per species as the protein that corresponds to LonB in B. subtilis [Protein fate, Degradation of proteins, peptides, and glycopeptides, Cellular processes, Sporulation and germination]. Length = 531

>gnl|CDD|236011 PRK07399, PRK07399, DNA polymerase III subunit delta'; Validated

 Score = 52.2 bits (126), Expect = 1e-07
 Identities = 52/228 (22%), Positives = 95/228 (41%), Gaps = 44/228 (19%)

Query: 9   FSDIVGNEDTVERLKVFSSSGNV-PNIIISGPPGVGKTTTILCLA--------------- 52
           F++++G    +E L        + P  + +GP GVG+    LC                 
Sbjct: 3   FANLIGQPLAIELLTAAIKQNRIAPAYLFAGPEGVGRKLAALCFIEGLLSQGSPSKNIRR 62

Query: 53  RILLG---------PSF-------KDAVLELNASNDRG-----IDTVRNKIKMFAQQKVT 91
           R+  G         P++         +  E      +      ++ +R  IK F  +   
Sbjct: 63  RLEEGNHPDLLWVEPTYQHQGKLITASEAEEAGLKRKAPPQIRLEQIRE-IKRFLSRP-P 120

Query: 92  LPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLR 151
           L   R K+V++++A++M + A  AL +T+E   N T   L   + E ++  I SRC ++ 
Sbjct: 121 LEAPR-KVVVIEDAETMNEAAANALLKTLEEPGNGT-LILIAPSPESLLPTIVSRCQIIP 178

Query: 152 YNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQ 199
           + +L+D QL   V++    E I   N     ++  AQG    A+ N++
Sbjct: 179 FYRLSDEQLEQ-VLKRLGDEEIL--NINFPELLALAQGSPGAAIANIE 223

Length = 314

>gnl|CDD|236022 PRK07471, PRK07471, DNA polymerase III subunit delta'; Validated

 Score = 52.3 bits (126), Expect = 1e-07
 Identities = 41/165 (24%), Positives = 62/165 (37%), Gaps = 41/165 (24%)

Query: 36  ISGPPGVGKTTTILCLARILL------GPSFKDAV--LELNAS----------------- 70
           I GP G+GK T    +AR LL      G         L ++                   
Sbjct: 46  IGGPQGIGKATLAYRMARFLLATPPPGGDGAVPPPTSLAIDPDHPVARRIAAGAHGGLLT 105

Query: 71  -----NDRG--------IDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALR 117
                N++G        +D VR  I  F    +T   G  ++VI+D AD M   A  AL 
Sbjct: 106 LERSWNEKGKRLRTVITVDEVRELISFFG---LTAAEGGWRVVIVDTADEMNANAANALL 162

Query: 118 RTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLS 162
           + +E     + F L  +   +++  I+SRC  LR   L    ++ 
Sbjct: 163 KVLEEPPARSLFLLVSHAPARLLPTIRSRCRKLRLRPLAPEDVID 207

Length = 365

>gnl|CDD|234619 PRK00080, ruvB, Holliday junction DNA helicase RuvB; Reviewed

 Score = 49.4 bits (119), Expect = 8e-07
 Identities = 20/56 (35%), Positives = 32/56 (57%), Gaps = 9/56 (16%)

Query: 5  RPQTFSDIVGNEDTVERLKVFSSS----GNVPN-IIISGPPGVGKTTTILCLARIL 55
          RP++  + +G E   E LK+F  +    G   + +++ GPPG+GKTT    LA I+
Sbjct: 20 RPKSLDEFIGQEKVKENLKIFIEAAKKRGEALDHVLLYGPPGLGKTT----LANII 71

Length = 328

>gnl|CDD|180738 PRK06871, PRK06871, DNA polymerase III subunit delta'; Validated

 Score = 48.6 bits (116), Expect = 2e-06
 Identities = 27/79 (34%), Positives = 40/79 (50%), Gaps = 9/79 (11%)

Query: 72  DRGIDTVRN---KIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTR 128
           D G+D VR    K+   AQQ      G +K+V +  A+ +T+ A  AL +T+E     T 
Sbjct: 86  DIGVDQVREINEKVSQHAQQ------GGNKVVYIQGAERLTEAAANALLKTLEEPRPNTY 139

Query: 129 FALACNNSEKIIEPIQSRC 147
           F L  + S  ++  I SRC
Sbjct: 140 FLLQADLSAALLPTIYSRC 158

Length = 325

>gnl|CDD|225164 COG2255, RuvB, Holliday junction resolvasome, helicase subunit [DNA replication, recombination, and repair]

 Score = 47.6 bits (114), Expect = 4e-06
 Identities = 23/65 (35%), Positives = 37/65 (56%), Gaps = 12/65 (18%)

Query: 5  RPQTFSDIVGNEDTVERLKVFSSS----GNVPN-IIISGPPGVGKTTTILCLARIL---L 56
          RP+T  + +G E   E+L++F  +    G   + +++ GPPG+GKTT    LA I+   L
Sbjct: 21 RPKTLDEFIGQEKVKEQLQIFIKAAKKRGEALDHVLLFGPPGLGKTT----LAHIIANEL 76

Query: 57 GPSFK 61
          G + K
Sbjct: 77 GVNLK 81

Length = 332

>gnl|CDD|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated

 Score = 47.7 bits (114), Expect = 5e-06
 Identities = 43/136 (31%), Positives = 61/136 (44%), Gaps = 47/136 (34%)

Query: 3   KYRPQTFSDIVGNEDTVERLKVFSSSGNVPN--IIISGPPGVGKTTTILCLARIL----- 55
           +YRP TF++++G E   E L     SG + N   + SGP G GKT++    ARIL     
Sbjct: 8   RYRPATFAEVIGQEHVTEPLSTALDSGRI-NHAYLFSGPRGCGKTSS----ARILARSLN 62

Query: 56  ------------------L---GPSFKDAVLELNASNDRGID---TVRNKIKMFAQQKVT 91
                             L   GP   D V E++A++  G+D    +R +   FA     
Sbjct: 63  CVEGPTSTPCGECDSCVALAPGGPGSLD-VTEIDAASHGGVDDARELRER-AFFA----- 115

Query: 92  LPPG--RHKIVILDEA 105
             P   R+KI I+DEA
Sbjct: 116 --PAESRYKIFIIDEA 129

Length = 824

>gnl|CDD|129690 TIGR00602, rad24, checkpoint protein rad24

 Score = 47.3 bits (112), Expect = 6e-06
 Identities = 45/252 (17%), Positives = 93/252 (36%), Gaps = 54/252 (21%)

Query: 1   IEKYRPQTFSDIVGNEDTVERLKVFSSSGNVPN-----IIISGPPGVGKTTTILCLARIL 55
           +EKY+P+T  ++  ++  +E ++ +  +  + N     ++I+GP G GK+TTI  L++  
Sbjct: 75  VEKYKPETQHELAVHKKKIEEVETWLKAQVLENAPKRILLITGPSGCGKSTTIKILSKE- 133

Query: 56  LGPSFKDAVLELN---ASND-RGIDTVRNKIKMFAQQKVTLPP----------------- 94
           LG   ++           ND +   ++ +    F  Q                       
Sbjct: 134 LGIQVQEWSNPTLPDFQKNDHKVTLSLESCFSNFQSQIEVFSEFLLRATNKLQMLGDDLM 193

Query: 95  GRHKIVILDEADSMTDGAQQALRRTME-IYSNTTRFALAC---------NNSEKIIEP-- 142
              KI+++++  +      +AL   +   Y +  R  L           NN  +++ P  
Sbjct: 194 TDKKIILVEDLPNQFYRDTRALHEILRWKYVSIGRCPLVFIITESLEGDNNQRRLLFPAE 253

Query: 143 ------IQSRCAM--LRYNKLTDAQLLSKVIEICEKE-------NISHTNDGLEAIVFTA 187
                 I     +  + +N +    +   +  I   E               +E +    
Sbjct: 254 TIMNKEILEEPRVSNISFNPIAPTIMKKFLNRIVTIEAKKNGEKIKVPKKTSVELLCQGC 313

Query: 188 QGDMRQALNNLQ 199
            GD+R A+N+LQ
Sbjct: 314 SGDIRSAINSLQ 325

All proteins in this family for which functions are known are involved in DNA damage tolerance (likely cell cycle checkpoints).This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) [DNA metabolism, DNA replication, recombination, and repair]. Length = 637

>gnl|CDD|217429 pfam03215, Rad17, Rad17 cell cycle checkpoint protein

 Score = 46.6 bits (110), Expect = 9e-06
 Identities = 44/246 (17%), Positives = 95/246 (38%), Gaps = 48/246 (19%)

Query: 2   EKYRPQTFSDIVGNEDTVERLK-----VFSSSGNVPNIIISGPPGVGKTTTILCLARILL 56
           EKY+P+   ++  ++  +  +      VF  S     ++++GP G GK+TT+  L++ L 
Sbjct: 11  EKYKPRRRDELAIHKKKIAEVDHWLKAVFLESNKQLILLLTGPSGCGKSTTVKVLSKELG 70

Query: 57  --------GPSFKDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRH----------K 98
                        +   E    + RG   V +  +M   ++  L   R+          K
Sbjct: 71  IEIIEWSNPEYLHNPDNECQKPDFRGDCIVNSLSQMEQFREFLLRGARYGSLQGGGLKKK 130

Query: 99  IVILDE----ADSMTDGAQQALRRTME-------IYSNTTRFALACNNSEKIIEP----- 142
           +++++E      S  +  ++ +R  ++       I+  T   +L  +N++          
Sbjct: 131 LILVEELPNQFYSDAEKFREVIREVLQSIWHLPLIFCLTECNSLEGDNNQDRFGIDAETI 190

Query: 143 ------IQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQ---GDMRQ 193
                 I  R   + +N +    +   ++ I  +E    +      +    Q   GD+R 
Sbjct: 191 MTKDILIMPRIDTITFNPIAPTFMKKALVRISVQEGKLKSPKSDSKLEVICQEAGGDLRS 250

Query: 194 ALNNLQ 199
           A+N+LQ
Sbjct: 251 AINSLQ 256

Length = 490

>gnl|CDD|234053 TIGR02903, spore_lon_C, ATP-dependent protease, Lon family

 Score = 46.7 bits (111), Expect = 9e-06
 Identities = 24/52 (46%), Positives = 32/52 (61%), Gaps = 4/52 (7%)

Query: 5   RPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILL 56
           RP+ FS+IVG E  ++ L    +S    +II+ GPPGVGKTT     AR+ L
Sbjct: 149 RPRAFSEIVGQERAIKALLAKVASPFPQHIILYGPPGVGKTTA----ARLAL 196

Members of this protein family resemble the widely distributed ATP-dependent protease La, also called Lon and LonA. It resembles even more closely LonB, which is a LonA paralog found in genomes if and only if the species is capable of endospore formation (as in Bacillus subtilis, Clostridium tetani, and select other members of the Firmicutes) and expressed specifically in the forespore compartment. Members of this family are restricted to a subset of spore-forming species, and are very likely to participate in the program of endospore formation. We propose the designation LonC [Protein fate, Degradation of proteins, peptides, and glycopeptides, Cellular processes, Sporulation and germination]. Length = 615

>gnl|CDD|203260 pfam05496, RuvB_N, Holliday junction DNA helicase ruvB N-terminus

 Score = 45.5 bits (109), Expect = 1e-05
 Identities = 20/65 (30%), Positives = 34/65 (52%), Gaps = 12/65 (18%)

Query: 5  RPQTFSDIVGNEDTVERLKVF---SSSGNVP--NIIISGPPGVGKTTTILCLARIL---L 56
          RP+   + +G E   E LK+F   +        ++++ GPPG+GKTT    LA I+   +
Sbjct: 19 RPRRLDEYIGQEKVKENLKIFIEAAKKRGEALDHVLLYGPPGLGKTT----LANIIANEM 74

Query: 57 GPSFK 61
          G + +
Sbjct: 75 GVNIR 79

The RuvB protein makes up part of the RuvABC revolvasome which catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. Branch migration is catalyzed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein. This family contains the N-terminal region of the protein. Length = 231

>gnl|CDD|180394 PRK06090, PRK06090, DNA polymerase III subunit delta'; Validated

 Score = 45.2 bits (107), Expect = 2e-05
 Identities = 31/152 (20%), Positives = 67/152 (44%), Gaps = 29/152 (19%)

Query: 20  ERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARILLGPSFKDAVL------ELNASND 72
           +  K    +G +P  +++    G+G  + +   +R LL  +++          EL  S +
Sbjct: 13  QNWKAGLDAGRIPGALLLQSDEGLGVESLVELFSRALLCQNYQSEACGFCHSCELMQSGN 72

Query: 73  R---------------GIDTVR--NKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQA 115
                            ++ +R  N++   AQ+   L    +++ +++ AD+M + A  A
Sbjct: 73  HPDLHVIKPEKEGKSITVEQIRQCNRL---AQESSQL--NGYRLFVIEPADAMNESASNA 127

Query: 116 LRRTMEIYSNTTRFALACNNSEKIIEPIQSRC 147
           L +T+E  +    F L  +N ++++  I SRC
Sbjct: 128 LLKTLEEPAPNCLFLLVTHNQKRLLPTIVSRC 159

Length = 319

>gnl|CDD|181190 PRK07993, PRK07993, DNA polymerase III subunit delta'; Validated

 Score = 45.1 bits (107), Expect = 2e-05
 Identities = 26/77 (33%), Positives = 39/77 (50%), Gaps = 9/77 (11%)

Query: 74  GIDTVRN---KIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFA 130
           G+D VR    K+   A+       G  K+V L +A  +TD A  AL +T+E     T F 
Sbjct: 89  GVDAVREVTEKLYEHARL------GGAKVVWLPDAALLTDAAANALLKTLEEPPENTWFF 142

Query: 131 LACNNSEKIIEPIQSRC 147
           LAC    +++  ++SRC
Sbjct: 143 LACREPARLLATLRSRC 159

Length = 334

>gnl|CDD|222104 pfam13401, AAA_22, AAA domain

 Score = 42.6 bits (101), Expect = 3e-05
 Identities = 21/111 (18%), Positives = 38/111 (34%), Gaps = 14/111 (12%)

Query: 34  IIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDR-----------GIDTVRNKI 82
            +++G  G GKTT +  LAR L         +E  +               G+       
Sbjct: 7   GVLTGESGSGKTTLLRRLARQLPNRRV--VYVEAPSLGTPKDLLRKILRALGLPLSGGTT 64

Query: 83  K-MFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALA 132
             +       L      ++I+DEA  ++  A + LR   ++     +  L 
Sbjct: 65  AELLEAILDALKRRGRPLLIIDEAQHLSLEALEELRDLYDLSEKGIQVILV 115

Length = 124

>gnl|CDD|236134 PRK07940, PRK07940, DNA polymerase III subunit delta'; Validated

 Score = 44.9 bits (107), Expect = 3e-05
 Identities = 44/169 (26%), Positives = 72/169 (42%), Gaps = 34/169 (20%)

Query: 9   FSDIVGNEDTVERLK----------VFSSSGNVPNIIISGPPGVGKTTTILCLARILLGP 58
           + D+VG E  V  L+            + SG     + +GPPG G++      A  L   
Sbjct: 4   WDDLVGQEAVVAELRAAARAARADVAAAGSGMTHAWLFTGPPGSGRSVAARAFAAALQCT 63

Query: 59  SFKD----------AVLELNASNDR---------GIDTVRNKIKMFAQQKVTLPPGRHKI 99
              +           VL     + R         G+D VR  + + A++  T   GR +I
Sbjct: 64  DPDEPGCGECRACRTVLAGTHPDVRVVAPEGLSIGVDEVRELVTIAARRPST---GRWRI 120

Query: 100 VILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNS-EKIIEPIQSRC 147
           V++++AD +T+ A  AL + +E     T + L C  S E ++  I+SRC
Sbjct: 121 VVIEDADRLTERAANALLKAVEEPPPRTVWLL-CAPSPEDVLPTIRSRC 168

Length = 394

>gnl|CDD|221970 pfam13191, AAA_16, AAA ATPase domain

 Score = 41.0 bits (96), Expect = 2e-04
 Identities = 21/60 (35%), Positives = 33/60 (55%), Gaps = 3/60 (5%)

Query: 12 IVGNEDTVERLKVF---SSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELN 68
          +VG E+ +ERL      + SG  P+++++GP G GKT+ +  L   LL  + K    E N
Sbjct: 2  LVGREEELERLLDALRRARSGGPPSVLLTGPSGTGKTSLLRELLEGLLVAAGKCDQAERN 61

This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Length = 154

>gnl|CDD|181551 PRK08769, PRK08769, DNA polymerase III subunit delta'; Validated

 Score = 41.1 bits (96), Expect = 4e-04
 Identities = 40/146 (27%), Positives = 60/146 (41%), Gaps = 32/146 (21%)

Query: 34  IIISGPPGVGKTTTILCLARILLGPSFKDAV---------------LEL-----NASNDR 73
           ++I GP G+GK    L LA  +L      A                L+L     N + D+
Sbjct: 29  LLICGPEGLGKRAVALALAEHVLASGPDPAAAQRTRQLIAAGTHPDLQLVSFIPNRTGDK 88

Query: 74  -----GIDTVRNKIKMFAQQKVTLPP--GRHKIVILDEADSMTDGAQQALRRTMEIYSNT 126
                 I+ VR        QK+ L P  G  ++VI+D AD++   A  AL +T+E  S  
Sbjct: 89  LRTEIVIEQVRE-----ISQKLALTPQYGIAQVVIVDPADAINRAACNALLKTLEEPSPG 143

Query: 127 TRFALACNNSEKIIEPIQSRCAMLRY 152
               L      ++   I+SRC  L +
Sbjct: 144 RYLWLISAQPARLPATIRSRCQRLEF 169

Length = 319

>gnl|CDD|181214 PRK08058, PRK08058, DNA polymerase III subunit delta'; Validated

 Score = 41.1 bits (97), Expect = 4e-04
 Identities = 25/81 (30%), Positives = 40/81 (49%), Gaps = 6/81 (7%)

Query: 98  KIVILDEADSMTDGAQQALRRTMEIYS-NTTRFALACNNSEKIIEPIQSRCAMLRYNKLT 156
           K+ I++ AD MT  A  +L + +E  S  TT   L   N  +I+  I SRC ++ +  L 
Sbjct: 112 KVYIIEHADKMTASAANSLLKFLEEPSGGTTAILLT-ENKHQILPTILSRCQVVEFRPLP 170

Query: 157 DAQLLSKVIEICEKENISHTN 177
              L+ ++ E    E IS + 
Sbjct: 171 PESLIQRLQE----EGISESL 187

Length = 329

>gnl|CDD|221955 pfam13173, AAA_14, AAA domain

 Score = 39.1 bits (92), Expect = 5e-04
 Identities = 24/94 (25%), Positives = 39/94 (41%), Gaps = 8/94 (8%)

Query: 32  PNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFAQQKVT 91
             I+I+GP  VGKTT    L    L     + +L +N  + R    +R  +    ++ + 
Sbjct: 3   KIIVITGPRQVGKTT----LLLQFLKELLSENILYINLDDPR---FLRLALLDLLEEFLK 55

Query: 92  LPPGRHKIVILDEADSMTDGAQQALRRTMEIYSN 125
           L     K + LDE        + AL+R  +   N
Sbjct: 56  LLLPGKKYLFLDEI-QKVPDWEDALKRLYDDGRN 88

This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Length = 127

>gnl|CDD|213179 cd00267, ABC_ATPase, ATP-binding cassette transporter nucleotide-binding domain

 Score = 39.5 bits (93), Expect = 6e-04
 Identities = 28/132 (21%), Positives = 56/132 (42%), Gaps = 19/132 (14%)

Query: 34  IIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFAQ------ 87
           + + GP G GK+T +  +A  LL P+  + +++        ++ +R +I    Q      
Sbjct: 28  VALVGPNGSGKSTLLRAIAG-LLKPTSGEILIDGKDIAKLPLEELRRRIGYVPQLSGGQR 86

Query: 88  QKVTL-------PPGRHKIVILDEADSMTDGA-QQALRRTMEIYSNTTRFALACNNSEKI 139
           Q+V L       P     +++LDE  S  D A ++ L   +   +   R  +   +  ++
Sbjct: 87  QRVALARALLLNPD----LLLLDEPTSGLDPASRERLLELLRELAEEGRTVIIVTHDPEL 142

Query: 140 IEPIQSRCAMLR 151
            E    R  +L+
Sbjct: 143 AELAADRVIVLK 154

ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins. Length = 157

>gnl|CDD|237475 PRK13695, PRK13695, putative NTPase; Provisional

 Score = 39.1 bits (92), Expect = 0.001
 Identities = 15/29 (51%), Positives = 20/29 (68%)

Query: 33 NIIISGPPGVGKTTTILCLARILLGPSFK 61
           I I+GPPGVGKTT +L +A +L    +K
Sbjct: 2  KIGITGPPGVGKTTLVLKIAELLKEEGYK 30

Length = 174

>gnl|CDD|224391 COG1474, CDC6, Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]

 Score = 39.6 bits (93), Expect = 0.001
 Identities = 32/109 (29%), Positives = 43/109 (39%), Gaps = 23/109 (21%)

Query: 28  SGNVP-NIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFA 86
            G  P NIII GP G GKT T+  +   L   S    V+ +N    R    V +KI    
Sbjct: 38  RGERPSNIIIYGPTGTGKTATVKFVMEELEESSANVEVVYINCLELRTPYQVLSKI---L 94

Query: 87  QQKVTLPP-------------------GRHKIVILDEADSMTDGAQQAL 116
            +   +P                    G+  IVILDE D++ D   + L
Sbjct: 95  NKLGKVPLTGDSSLEILKRLYDNLSKKGKTVIVILDEVDALVDKDGEVL 143

Length = 366

>gnl|CDD|129721 TIGR00635, ruvB, Holliday junction DNA helicase, RuvB subunit

 Score = 38.4 bits (90), Expect = 0.003
 Identities = 16/54 (29%), Positives = 32/54 (59%), Gaps = 9/54 (16%)

Query: 7  QTFSDIVGNEDTVERLKVF--SSSGN---VPNIIISGPPGVGKTTTILCLARIL 55
          +  ++ +G E   E+L++F  ++      + ++++ GPPG+GKTT    LA I+
Sbjct: 1  KLLAEFIGQEKVKEQLQLFIEAAKMRQEALDHLLLYGPPGLGKTT----LAHII 50

All proteins in this family for which functions are known are 5'-3' DNA helicases that, as part of a complex with RuvA homologs serve as a 5'-3' Holliday junction helicase. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions [DNA metabolism, DNA replication, recombination, and repair]. Length = 305

>gnl|CDD|216506 pfam01443, Viral_helicase1, Viral (Superfamily 1) RNA helicase

 Score = 37.4 bits (87), Expect = 0.004
 Identities = 18/72 (25%), Positives = 26/72 (36%), Gaps = 4/72 (5%)

Query: 34  IIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFAQQKVTLP 93
           I++ G PG GK+T I  L R                  +   D     ++      + L 
Sbjct: 1   IVVHGVPGCGKSTLIRKLLR----TDLTVIRPTAELRTEGKPDLPNLNVRTVDTFLMALL 56

Query: 94  PGRHKIVILDEA 105
               KI+ILDE 
Sbjct: 57  KPTGKILILDEY 68

Helicase activity for this family has been demonstrated and NTPase activity. This helicase has multiple roles at different stages of viral RNA replication, as dissected by mutational analysis. Length = 226

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	317
KOG0991|consensus	333		100.0
PLN03025	319	replication factor C subunit; Provisional	100.0
KOG0989|consensus	346		100.0
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	100.0
PRK06305	451	DNA polymerase III subunits gamma and tau; Validat	100.0
PRK08451	535	DNA polymerase III subunits gamma and tau; Validat	100.0
PRK14964	491	DNA polymerase III subunits gamma and tau; Provisi	100.0
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	100.0
PRK14965	576	DNA polymerase III subunits gamma and tau; Provisi	100.0
PRK14955	397	DNA polymerase III subunits gamma and tau; Provisi	100.0
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	100.0
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	100.0
PRK14958	509	DNA polymerase III subunits gamma and tau; Provisi	100.0
PRK14954	620	DNA polymerase III subunits gamma and tau; Provisi	100.0
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	100.0
PRK09111	598	DNA polymerase III subunits gamma and tau; Validat	100.0
PRK05563	559	DNA polymerase III subunits gamma and tau; Validat	100.0
PRK00440	319	rfc replication factor C small subunit; Reviewed	100.0
PRK14971	614	DNA polymerase III subunits gamma and tau; Provisi	100.0
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	100.0
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	100.0
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	100.0
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	100.0
PRK07764	824	DNA polymerase III subunits gamma and tau; Validat	100.0
PRK14951	618	DNA polymerase III subunits gamma and tau; Provisi	100.0
PRK07133	725	DNA polymerase III subunits gamma and tau; Validat	100.0
PRK06647	563	DNA polymerase III subunits gamma and tau; Validat	100.0
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	100.0
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	100.0
PRK14959	624	DNA polymerase III subunits gamma and tau; Provisi	100.0
PRK14953	486	DNA polymerase III subunits gamma and tau; Provisi	100.0
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	100.0
COG2812	515	DnaX DNA polymerase III, gamma/tau subunits [DNA r	100.0
PRK14957	546	DNA polymerase III subunits gamma and tau; Provisi	100.0
TIGR02397	355	dnaX_nterm DNA polymerase III, subunit gamma and t	100.0
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	100.0
PRK14970	367	DNA polymerase III subunits gamma and tau; Provisi	100.0
PRK14950	585	DNA polymerase III subunits gamma and tau; Provisi	100.0
PRK12402	337	replication factor C small subunit 2; Reviewed	100.0
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	100.0
PRK14948	620	DNA polymerase III subunits gamma and tau; Provisi	100.0
KOG2035|consensus	351		100.0
PRK04132	846	replication factor C small subunit; Provisional	100.0
COG2256	436	MGS1 ATPase related to the helicase subunit of the	100.0
KOG0990|consensus	360		100.0
PHA02544	316	44 clamp loader, small subunit; Provisional	100.0
PRK05564	313	DNA polymerase III subunit delta'; Validated	100.0
PRK04195	482	replication factor C large subunit; Provisional	100.0
PRK13342	413	recombination factor protein RarA; Reviewed	100.0
PRK13341	725	recombination factor protein RarA/unknown domain f	100.0
PRK07940	394	DNA polymerase III subunit delta'; Validated	100.0
PRK07399	314	DNA polymerase III subunit delta'; Validated	100.0
PRK08058	329	DNA polymerase III subunit delta'; Validated	100.0
PRK07993	334	DNA polymerase III subunit delta'; Validated	100.0
PRK05707	328	DNA polymerase III subunit delta'; Validated	100.0
PRK09112	351	DNA polymerase III subunit delta'; Validated	100.0
KOG2028|consensus	554		100.0
PRK07471	365	DNA polymerase III subunit delta'; Validated	100.0
PRK08769	319	DNA polymerase III subunit delta'; Validated	100.0
PRK06871	325	DNA polymerase III subunit delta'; Validated	99.98
PRK06964	342	DNA polymerase III subunit delta'; Validated	99.97
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	99.97
PRK06090	319	DNA polymerase III subunit delta'; Validated	99.97
PRK05917	290	DNA polymerase III subunit delta'; Validated	99.97
PRK07132	299	DNA polymerase III subunit delta'; Validated	99.97
COG0470	325	HolB ATPase involved in DNA replication [DNA repli	99.97
PRK05907	311	hypothetical protein; Provisional	99.95
TIGR00678	188	holB DNA polymerase III, delta' subunit. At positi	99.95
PRK08699	325	DNA polymerase III subunit delta'; Validated	99.95
PRK07276	290	DNA polymerase III subunit delta'; Validated	99.95
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	99.95
PF13177	162	DNA_pol3_delta2: DNA polymerase III, delta subunit	99.95
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	99.94
COG2255	332	RuvB Holliday junction resolvasome, helicase subun	99.94
PRK07914	320	hypothetical protein; Reviewed	99.93
KOG1969|consensus	877		99.93
PTZ00112	1164	origin recognition complex 1 protein; Provisional	99.93
TIGR02902	531	spore_lonB ATP-dependent protease LonB. Members of	99.93
PRK05629	318	hypothetical protein; Validated	99.93
PRK07452	326	DNA polymerase III subunit delta; Validated	99.92
PRK06585	343	holA DNA polymerase III subunit delta; Reviewed	99.92
PRK05818	261	DNA polymerase III subunit delta'; Validated	99.92
PRK08487	328	DNA polymerase III subunit delta; Validated	99.92
PRK00411	394	cdc6 cell division control protein 6; Reviewed	99.91
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	99.91
PRK05574	340	holA DNA polymerase III subunit delta; Reviewed	99.91
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	99.9
TIGR01128	302	holA DNA polymerase III, delta subunit. subunit ar	99.9
PRK08084	235	DNA replication initiation factor; Provisional	99.89
COG1223	368	Predicted ATPase (AAA+ superfamily) [General funct	99.89
PRK06893	229	DNA replication initiation factor; Validated	99.89
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	99.88
TIGR00602	637	rad24 checkpoint protein rad24. This family is bas	99.88
PRK08727	233	hypothetical protein; Validated	99.87
TIGR02903	615	spore_lon_C ATP-dependent protease, Lon family. Me	99.86
PRK08903	227	DnaA regulatory inactivator Hda; Validated	99.86
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	99.85
PRK06581	263	DNA polymerase III subunit delta'; Validated	99.84
CHL00181	287	cbbX CbbX; Provisional	99.84
COG1222	406	RPT1 ATP-dependent 26S proteasome regulatory subun	99.83
PRK05642	234	DNA replication initiation factor; Validated	99.81
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	99.81
COG1466	334	HolA DNA polymerase III, delta subunit [DNA replic	99.8
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	99.8
PRK00149	450	dnaA chromosomal replication initiation protein; R	99.8
PRK06620	214	hypothetical protein; Validated	99.8
PRK14087	450	dnaA chromosomal replication initiation protein; P	99.79
PRK14088	440	dnaA chromosomal replication initiation protein; P	99.78
TIGR01241	495	FtsH_fam ATP-dependent metalloprotease FtsH. HflB(	99.78
KOG1970|consensus	634		99.78
PF03215	519	Rad17: Rad17 cell cycle checkpoint protein	99.78
KOG0730|consensus	693		99.78
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	99.78
PRK09087	226	hypothetical protein; Validated	99.77
PTZ00361	438	26 proteosome regulatory subunit 4-like protein; P	99.77
PRK12422	445	chromosomal replication initiation protein; Provis	99.77
CHL00195	489	ycf46 Ycf46; Provisional	99.76
PRK14086	617	dnaA chromosomal replication initiation protein; P	99.76
PRK03992	389	proteasome-activating nucleotidase; Provisional	99.75
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	99.75
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	99.75
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	99.75
COG1224	450	TIP49 DNA helicase TIP49, TBP-interacting protein	99.75
CHL00176	638	ftsH cell division protein; Validated	99.75
PF06068	398	TIP49: TIP49 C-terminus; InterPro: IPR010339 This	99.74
TIGR03689	512	pup_AAA proteasome ATPase. In the Actinobacteria,	99.74
TIGR00763	775	lon ATP-dependent protease La. This protein is ind	99.74
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	99.72
PRK14700	300	recombination factor protein RarA; Provisional	99.72
KOG0733|consensus	802		99.7
TIGR01242	364	26Sp45 26S proteasome subunit P45 family. Many pro	99.7
PRK08485	206	DNA polymerase III subunit delta'; Validated	99.69
KOG0734|consensus	752		99.68
KOG2227|consensus	529		99.68
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	99.68
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	99.67
PRK13407	334	bchI magnesium chelatase subunit I; Provisional	99.67
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	99.67
COG0593	408	DnaA ATPase involved in DNA replication initiation	99.66
CHL00095	821	clpC Clp protease ATP binding subunit	99.66
KOG0733|consensus	802		99.65
PRK10865	857	protein disaggregation chaperone; Provisional	99.65
PRK10787	784	DNA-binding ATP-dependent protease La; Provisional	99.65
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	99.64
PLN00020	413	ribulose bisphosphate carboxylase/oxygenase activa	99.64
KOG1942|consensus	456		99.64
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	99.63
KOG0731|consensus	774		99.63
COG0466	782	Lon ATP-dependent Lon protease, bacterial type [Po	99.63
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	99.62
KOG0727|consensus	408		99.62
CHL00095	821	clpC Clp protease ATP binding subunit	99.62
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	99.61
TIGR02030	337	BchI-ChlI magnesium chelatase ATPase subunit I. Th	99.61
PRK10865	857	protein disaggregation chaperone; Provisional	99.61
KOG0742|consensus	630		99.61
KOG0743|consensus	457		99.6
KOG0738|consensus	491		99.6
CHL00081	350	chlI Mg-protoporyphyrin IX chelatase	99.6
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	99.6
PF00004	132	AAA: ATPase family associated with various cellula	99.59
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	99.59
PRK10733	644	hflB ATP-dependent metalloprotease; Reviewed	99.59
PRK05342	412	clpX ATP-dependent protease ATP-binding subunit Cl	99.58
PF05673	249	DUF815: Protein of unknown function (DUF815); Inte	99.58
PRK13531	498	regulatory ATPase RavA; Provisional	99.57
KOG0739|consensus	439		99.57
KOG1514|consensus	767		99.56
TIGR01817	534	nifA Nif-specific regulatory protein. This model r	99.56
KOG2004|consensus	906		99.56
KOG0728|consensus	404		99.56
KOG1968|consensus	871		99.56
COG0464	494	SpoVK ATPases of the AAA+ class [Posttranslational	99.55
CHL00206	2281	ycf2 Ycf2; Provisional	99.54
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	99.54
KOG0652|consensus	424		99.54
TIGR00382	413	clpX endopeptidase Clp ATP-binding regulatory subu	99.53
KOG0737|consensus	386		99.53
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	99.53
KOG0736|consensus	953		99.52
TIGR02442	633	Cob-chelat-sub cobaltochelatase subunit. A number	99.52
KOG0726|consensus	440		99.51
TIGR01650	327	PD_CobS cobaltochelatase, CobS subunit. This model	99.51
KOG0740|consensus	428		99.5
PRK10820	520	DNA-binding transcriptional regulator TyrR; Provis	99.49
TIGR02974	329	phageshock_pspF psp operon transcriptional activat	99.49
COG0465	596	HflB ATP-dependent Zn proteases [Posttranslational	99.48
KOG2680|consensus	454		99.48
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	99.45
PF01637	234	Arch_ATPase: Archaeal ATPase; InterPro: IPR011579	99.45
TIGR02329	526	propionate_PrpR propionate catabolism operon regul	99.44
PRK11608	326	pspF phage shock protein operon transcriptional ac	99.44
TIGR00764	608	lon_rel lon-related putative ATP-dependent proteas	99.44
PF01078	206	Mg_chelatase: Magnesium chelatase, subunit ChlI; I	99.44
KOG0729|consensus	435		99.44
COG2204	464	AtoC Response regulator containing CheY-like recei	99.43
PRK11388	638	DNA-binding transcriptional regulator DhaR; Provis	99.42
COG0714	329	MoxR-like ATPases [General function prediction onl	99.42
TIGR00390	441	hslU ATP-dependent protease HslVU, ATPase subunit.	99.41
PRK15424	538	propionate catabolism operon regulatory protein Pr	99.41
KOG0735|consensus	952		99.41
TIGR00368	499	Mg chelatase-related protein. The N-terminal end m	99.4
PHA02244	383	ATPase-like protein	99.39
PRK13765	637	ATP-dependent protease Lon; Provisional	99.38
PRK05201	443	hslU ATP-dependent protease ATP-binding subunit Hs	99.37
PRK05022	509	anaerobic nitric oxide reductase transcription reg	99.37
smart00350	509	MCM minichromosome maintenance proteins.	99.36
COG2607	287	Predicted ATPase (AAA+ superfamily) [General funct	99.36
COG1221	403	PspF Transcriptional regulators containing an AAA-	99.36
COG3829	560	RocR Transcriptional regulator containing PAS, AAA	99.33
KOG0730|consensus	693		99.32
PF05621	302	TniB: Bacterial TniB protein; InterPro: IPR008868	99.32
PF07728	139	AAA_5: AAA domain (dynein-related subfamily); Inte	99.32
PF07724	171	AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR	99.31
PRK15429	686	formate hydrogenlyase transcriptional activator Fh	99.31
KOG0732|consensus	1080		99.3
KOG0744|consensus	423		99.3
PF06144	172	DNA_pol3_delta: DNA polymerase III, delta subunit;	99.29
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	99.28
TIGR02915	445	PEP_resp_reg putative PEP-CTERM system response re	99.24
KOG0651|consensus	388		99.23
TIGR02031	589	BchD-ChlD magnesium chelatase ATPase subunit D. Th	99.22
PRK10923	469	glnG nitrogen regulation protein NR(I); Provisiona	99.22
PF00158	168	Sigma54_activat: Sigma-54 interaction domain; Inte	99.22
smart00763	361	AAA_PrkA PrkA AAA domain. This is a family of PrkA	99.2
PF07726	131	AAA_3: ATPase family associated with various cellu	99.19
PRK09862	506	putative ATP-dependent protease; Provisional	99.18
COG3604	550	FhlA Transcriptional regulator containing GAF, AAA	99.18
KOG0735|consensus	952		99.15
PRK12377	248	putative replication protein; Provisional	99.15
PRK08181	269	transposase; Validated	99.15
TIGR01818	463	ntrC nitrogen regulation protein NR(I). This model	99.15
PRK15115	444	response regulator GlrR; Provisional	99.14
PRK11361	457	acetoacetate metabolism regulatory protein AtoC; P	99.13
KOG2170|consensus	344		99.12
COG0606	490	Predicted ATPase with chaperone activity [Posttran	99.12
COG3283	511	TyrR Transcriptional regulator of aromatic amino a	99.12
PTZ00111	915	DNA replication licensing factor MCM4; Provisional	99.09
PRK07952	244	DNA replication protein DnaC; Validated	99.09
COG1219	408	ClpX ATP-dependent protease Clp, ATPase subunit [P	99.08
COG1239	423	ChlI Mg-chelatase subunit ChlI [Coenzyme metabolis	99.08
PRK08116	268	hypothetical protein; Validated	99.06
PF08542	89	Rep_fac_C: Replication factor C C-terminal domain;	99.06
PF14532	138	Sigma54_activ_2: Sigma-54 interaction domain; PDB:	99.06
PF00931	287	NB-ARC: NB-ARC domain; InterPro: IPR002182 This is	99.04
KOG0741|consensus	744		99.03
KOG0745|consensus	564		99.03
PRK06526	254	transposase; Provisional	99.02
KOG1051|consensus	898		99.01
smart00382	148	AAA ATPases associated with a variety of cellular	99.01
PRK10365	441	transcriptional regulatory protein ZraR; Provision	98.99
COG3267	269	ExeA Type II secretory pathway, component ExeA (pr	98.96
PF13173	128	AAA_14: AAA domain	98.96
COG1241	682	MCM2 Predicted ATPase involved in replication cont	98.96
KOG0478|consensus	804		98.95
KOG0482|consensus	721		98.95
PRK13406	584	bchD magnesium chelatase subunit D; Provisional	98.93
PHA00729	226	NTP-binding motif containing protein	98.9
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	98.88
PRK06921	266	hypothetical protein; Provisional	98.84
PRK09183	259	transposase/IS protein; Provisional	98.83
PF12775	272	AAA_7: P-loop containing dynein motor region D3; P	98.83
KOG0480|consensus	764		98.82
PF12774	231	AAA_6: Hydrolytic ATP binding site of dynein motor	98.82
PF05729	166	NACHT: NACHT domain	98.81
COG1220	444	HslU ATP-dependent protease HslVU (ClpYQ), ATPase	98.81
PRK06835	329	DNA replication protein DnaC; Validated	98.81
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	98.8
KOG0477|consensus	854		98.79
KOG0736|consensus	953		98.79
PRK04841	903	transcriptional regulator MalT; Provisional	98.74
PF12169	143	DNA_pol3_gamma3: DNA polymerase III subunits gamma	98.71
PRK08939	306	primosomal protein DnaI; Reviewed	98.7
COG1484	254	DnaC DNA replication protein [DNA replication, rec	98.7
COG1125	309	OpuBA ABC-type proline/glycine betaine transport s	98.68
COG1126	240	GlnQ ABC-type polar amino acid transport system, A	98.68
PF14516	331	AAA_35: AAA-like domain	98.68
PLN03210	1153	Resistant to P. syringae 6; Provisional	98.68
COG1618	179	Predicted nucleotide kinase [Nucleotide transport	98.68
PRK04132	846	replication factor C small subunit; Provisional	98.64
PHA02774	613	E1; Provisional	98.63
COG3284	606	AcoR Transcriptional activator of acetoin/glycerol	98.58
PF00493	331	MCM: MCM2/3/5 family This family extends the MCM d	98.58
PF03266	168	NTPase_1: NTPase; InterPro: IPR004948 This entry r	98.58
COG4619	223	ABC-type uncharacterized transport system, ATPase	98.57
PF13191	185	AAA_16: AAA ATPase domain; PDB: 2V1U_A.	98.52
TIGR02688	449	conserved hypothetical protein TIGR02688. Members	98.5
COG2884	223	FtsE Predicted ATPase involved in cell division [C	98.49
KOG0481|consensus	729		98.49
COG5271	4600	MDN1 AAA ATPase containing von Willebrand factor t	98.42
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	98.41
PF00910	107	RNA_helicase: RNA helicase; InterPro: IPR000605 He	98.39
KOG2543|consensus	438		98.35
COG4650	531	RtcR Sigma54-dependent transcription regulator con	98.34
PHA02624	647	large T antigen; Provisional	98.33
PF12780	268	AAA_8: P-loop containing dynein motor region D4; I	98.31
KOG0741|consensus	744		98.29
KOG2228|consensus	408		98.28
PRK10536	262	hypothetical protein; Provisional	98.26
PF07693	325	KAP_NTPase: KAP family P-loop domain; InterPro: IP	98.24
cd03246	173	ABCC_Protease_Secretion This family represents the	98.24
PF10443	431	RNA12: RNA12 protein; InterPro: IPR018850 Mitochon	98.23
cd03228	171	ABCC_MRP_Like The MRP (Mutidrug Resistance Protein	98.23
COG2274	709	SunT ABC-type bacteriocin/lantibiotic exporters, c	98.22
PRK04296	190	thymidine kinase; Provisional	98.22
cd03247	178	ABCC_cytochrome_bd The CYD subfamily implicated in	98.22
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	98.21
cd03214	180	ABC_Iron-Siderophores_B12_Hemin ABC transporters,	98.2
COG1127	263	Ttg2A ABC-type transport system involved in resist	98.2
COG5271	4600	MDN1 AAA ATPase containing von Willebrand factor t	98.18
TIGR02868	529	CydC thiol reductant ABC exporter, CydC subunit. T	98.17
cd03216	163	ABC_Carb_Monos_I This family represents the domain	98.16
) proteins. It has been suggested that torsins play a role in effectively managing protein folding and that possible breakdown in a neuroprotective mechanism that is, in part, mediated by torsins may be responsible for the neuronal dysfunction associated with dystonia [].; GO: 0005524 ATP binding, 0051085 chaperone mediated protein folding requiring cofactor" target="_blank" href="http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=PF06309">PF06309	127	Torsin: Torsin; InterPro: IPR010448 This family co	98.15
TIGR02858	270	spore_III_AA stage III sporulation protein AA. Mem	98.13
COG2909	894	MalT ATP-dependent transcriptional regulator [Tran	98.12
PRK11174	588	cysteine/glutathione ABC transporter membrane/ATP-	98.12
COG1119	257	ModF ABC-type molybdenum transport system, ATPase	98.11
cd03222	177	ABC_RNaseL_inhibitor The ABC ATPase RNase L inhibi	98.11
COG1117	253	PstB ABC-type phosphate transport system, ATPase c	98.1
COG1124	252	DppF ABC-type dipeptide/oligopeptide/nickel transp	98.1
cd00561	159	CobA_CobO_BtuR ATP:corrinoid adenosyltransferase B	98.09
cd03221	144	ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is	98.09
KOG0058|consensus	716		98.07
cd00267	157	ABC_ATPase ABC (ATP-binding cassette) transporter	98.07
PF04665	241	Pox_A32: Poxvirus A32 protein; InterPro: IPR006758	98.07
cd03229	178	ABC_Class3 This class is comprised of all BPD (Bin	98.06
PRK11176	582	lipid transporter ATP-binding/permease protein; Pr	98.05
PRK15455	644	PrkA family serine protein kinase; Provisional	98.04
PRK13695	174	putative NTPase; Provisional	98.04
COG1120	258	FepC ABC-type cobalamin/Fe3+-siderophores transpor	98.04
KOG3347|consensus	176		98.02
COG4608	268	AppF ABC-type oligopeptide transport system, ATPas	98.01
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	98.01
KOG0479|consensus	818		98.01
COG1116	248	TauB ABC-type nitrate/sulfonate/bicarbonate transp	98.01
cd03230	173	ABC_DR_subfamily_A This family of ATP-binding prot	98.01
PRK13657	588	cyclic beta-1,2-glucan ABC transporter; Provisiona	98.0
COG4172	534	ABC-type uncharacterized transport system, duplica	98.0
PF03969	362	AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654	98.0
PTZ00202	550	tuzin; Provisional	97.99
cd03223	166	ABCD_peroxisomal_ALDP Peroxisomal ATP-binding cass	97.99
TIGR01618	220	phage_P_loop phage nucleotide-binding protein. Thi	97.98
cd03213	194	ABCG_EPDR ABCG transporters are involved in eye pi	97.98
TIGR02203	571	MsbA_lipidA lipid A export permease/ATP-binding pr	97.96
TIGR02857	529	CydD thiol reductant ABC exporter, CydD subunit. U	97.96
TIGR03375	694	type_I_sec_LssB type I secretion system ATPase, Ls	97.96
PRK10790	592	putative multidrug transporter membrane\ATP-bindin	97.95
cd03263	220	ABC_subfamily_A The ABCA subfamily mediates the tr	97.94
PRK13539	207	cytochrome c biogenesis protein CcmA; Provisional	97.93
TIGR02204	576	MsbA_rel ABC transporter, permease/ATP-binding pro	97.92
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	97.92
COG1373	398	Predicted ATPase (AAA+ superfamily) [General funct	97.91
PF04851	184	ResIII: Type III restriction enzyme, res subunit;	97.91
cd03215	182	ABC_Carb_Monos_II This family represents domain II	97.9
TIGR01846	694	type_I_sec_HlyB type I secretion system ABC transp	97.89
cd03232	192	ABC_PDR_domain2 The pleiotropic drug resistance-li	97.89
cd03217	200	ABC_FeS_Assembly ABC-type transport system involve	97.89
TIGR01192	585	chvA glucan exporter ATP-binding protein. This mod	97.88
cd03369	207	ABCC_NFT1 Domain 2 of NFT1 (New full-length MRP-ty	97.88
COG1131	293	CcmA ABC-type multidrug transport system, ATPase c	97.88
PRK10875	615	recD exonuclease V subunit alpha; Provisional	97.88
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	97.88
COG4988	559	CydD ABC-type transport system involved in cytochr	97.87
PRK11160	574	cysteine/glutathione ABC transporter membrane/ATP-	97.87
COG4178	604	ABC-type uncharacterized transport system, permeas	97.87
PRK10789	569	putative multidrug transporter membrane\ATP-bindin	97.87
COG4088	261	Predicted nucleotide kinase [Nucleotide transport	97.87
COG1122	235	CbiO ABC-type cobalt transport system, ATPase comp	97.85
cd03264	211	ABC_drug_resistance_like ABC-type multidrug transp	97.85
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	97.85
COG3842	352	PotA ABC-type spermidine/putrescine transport syst	97.84
TIGR03796	710	NHPM_micro_ABC1 NHPM bacteriocin system ABC transp	97.84
TIGR03797	686	NHPM_micro_ABC2 NHPM bacteriocin system ABC transp	97.84
TIGR02237	209	recomb_radB DNA repair and recombination protein R	97.83
TIGR03410	230	urea_trans_UrtE urea ABC transporter, ATP-binding	97.83
TIGR01448	720	recD_rel helicase, putative, RecD/TraA family. Thi	97.83
TIGR02768	744	TraA_Ti Ti-type conjugative transfer relaxase TraA	97.83
KOG0055|consensus	1228		97.83
PRK13540	200	cytochrome c biogenesis protein CcmA; Provisional	97.82
PRK13900	332	type IV secretion system ATPase VirB11; Provisiona	97.82
PF09848	352	DUF2075: Uncharacterized conserved protein (DUF207	97.82
PF00519	432	PPV_E1_C: Papillomavirus helicase; InterPro: IPR00	97.81
PRK14974	336	cell division protein FtsY; Provisional	97.81
cd00046	144	DEXDc DEAD-like helicases superfamily. A diverse f	97.81
TIGR01193	708	bacteriocin_ABC ABC-type bacteriocin transporter.	97.81
PLN03232	1495	ABC transporter C family member; Provisional	97.81
PLN03130	1622	ABC transporter C family member; Provisional	97.81
PRK10247	225	putative ABC transporter ATP-binding protein YbbL;	97.8
cd03268	208	ABC_BcrA_bacitracin_resist The BcrA subfamily repr	97.8
PRK06067	234	flagellar accessory protein FlaH; Validated	97.79
TIGR01447	586	recD exodeoxyribonuclease V, alpha subunit. This f	97.79
COG3839	338	MalK ABC-type sugar transport systems, ATPase comp	97.79
cd03251	234	ABCC_MsbA MsbA is an essential ABC transporter, cl	97.78
PF10236	309	DAP3: Mitochondrial ribosomal death-associated pro	97.78
PRK13648	269	cbiO cobalt transporter ATP-binding subunit; Provi	97.78
cd03225	211	ABC_cobalt_CbiO_domain1 Domain I of the ABC compon	97.77
TIGR01188	302	drrA daunorubicin resistance ABC transporter ATP-b	97.77
TIGR00958	711	3a01208 Conjugate Transporter-2 (CT2) Family prote	97.77
PF05272	198	VirE: Virulence-associated protein E; InterPro: IP	97.77
COG1123	539	ATPase components of various ABC-type transport sy	97.77
cd03244	221	ABCC_MRP_domain2 Domain 2 of the ABC subfamily C.	97.76
PRK13635	279	cbiO cobalt transporter ATP-binding subunit; Provi	97.76
PF05707	193	Zot: Zonular occludens toxin (Zot); InterPro: IPR0	97.76
cd03252	237	ABCC_Hemolysin The ABC-transporter hemolysin B is	97.76
TIGR00960	216	3a0501s02 Type II (General) Secretory Pathway (IIS	97.76
TIGR03522	301	GldA_ABC_ATP gliding motility-associated ABC trans	97.75
PRK13537	306	nodulation ABC transporter NodI; Provisional	97.74
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	97.74
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	97.74
PRK13650	279	cbiO cobalt transporter ATP-binding subunit; Provi	97.74
cd03261	235	ABC_Org_Solvent_Resistant ABC (ATP-binding cassett	97.74
cd03266	218	ABC_NatA_sodium_exporter NatA is the ATPase compon	97.73
TIGR02673	214	FtsE cell division ATP-binding protein FtsE. This	97.73
PRK12727	559	flagellar biosynthesis regulator FlhF; Provisional	97.73
TIGR01842	544	type_I_sec_PrtD type I secretion system ABC transp	97.73
PRK05986	191	cob(I)alamin adenolsyltransferase/cobinamide ATP-d	97.73
cd03269	210	ABC_putative_ATPase This subfamily is involved in	97.73
TIGR01166	190	cbiO cobalt transport protein ATP-binding subunit.	97.72
KOG0055|consensus	1228		97.72
cd03238	176	ABC_UvrA The excision repair protein UvrA; Nucleot	97.72
PF05970	364	PIF1: PIF1-like helicase; InterPro: IPR010285 This	97.72
TIGR03608	206	L_ocin_972_ABC putative bacteriocin export ABC tra	97.72
cd03262	213	ABC_HisP_GlnQ_permeases HisP and GlnQ are the ATP-	97.71
cd03253	236	ABCC_ATM1_transporter ATM1 is an ABC transporter t	97.71
cd03292	214	ABC_FtsE_transporter FtsE is a hydrophilic nucleot	97.71
PRK13889	988	conjugal transfer relaxase TraA; Provisional	97.7
PRK08533	230	flagellar accessory protein FlaH; Reviewed	97.7
cd03254	229	ABCC_Glucan_exporter_like Glucan exporter ATP-bind	97.7
TIGR01189	198	ccmA heme ABC exporter, ATP-binding protein CcmA.	97.7
cd03258	233	ABC_MetN_methionine_transporter MetN (also known a	97.7
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	97.7
cd03224	222	ABC_TM1139_LivF_branched LivF (TM1139) is part of	97.7
COG1132	567	MdlB ABC-type multidrug transport system, ATPase a	97.69
TIGR00708	173	cobA cob(I)alamin adenosyltransferase. Alternate n	97.69
cd03249	238	ABC_MTABC3_MDL1_MDL2 MTABC3 (also known as ABCB6)	97.69
cd03245	220	ABCC_bacteriocin_exporters ABC-type bacteriocin ex	97.69
TIGR01613	304	primase_Cterm phage/plasmid primase, P4 family, C-	97.69
TIGR01359	183	UMP_CMP_kin_fam UMP-CMP kinase family. This subfam	97.68
PRK13538	204	cytochrome c biogenesis protein CcmA; Provisional	97.68
cd03218	232	ABC_YhbG The ABC transporters belonging to the Yhb	97.68
cd03248	226	ABCC_TAP TAP, the Transporter Associated with Anti	97.68
PF13207	121	AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6	97.67
TIGR01277	213	thiQ thiamine ABC transporter, ATP-binding protein	97.67
PRK14532	188	adenylate kinase; Provisional	97.67
cd03259	213	ABC_Carb_Solutes_like ABC Carbohydrate and Solute	97.67
COG0444	316	DppD ABC-type dipeptide/oligopeptide/nickel transp	97.67
COG2842	297	Uncharacterized ATPase, putative transposase [Gene	97.66
cd03233	202	ABC_PDR_domain1 The pleiotropic drug resistance (P	97.66
PRK10908	222	cell division protein FtsE; Provisional	97.66
TIGR02788	308	VirB11 P-type DNA transfer ATPase VirB11. The VirB	97.65
COG4987	573	CydC ABC-type transport system involved in cytochr	97.65
PRK13536	340	nodulation factor exporter subunit NodI; Provision	97.65
TIGR03574	249	selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal. Mem	97.65
PF10923	416	DUF2791: P-loop Domain of unknown function (DUF279	97.64
TIGR01271	1490	CFTR_protein cystic fibrosis transmembrane conduct	97.64
PRK13632	271	cbiO cobalt transporter ATP-binding subunit; Provi	97.64
TIGR03864	236	PQQ_ABC_ATP ABC transporter, ATP-binding subunit,	97.64
smart00487	201	DEXDc DEAD-like helicases superfamily.	97.63
cd03288	257	ABCC_SUR2 The SUR domain 2. The sulfonylurea recep	97.63
cd03231	201	ABC_CcmA_heme_exporter CcmA, the ATP-binding compo	97.63
COG4525	259	TauB ABC-type taurine transport system, ATPase com	97.63
PRK13652	277	cbiO cobalt transporter ATP-binding subunit; Provi	97.63
COG4555	245	NatA ABC-type Na+ transport system, ATPase compone	97.63
PRK14247	250	phosphate ABC transporter ATP-binding protein; Pro	97.62
PRK14269	246	phosphate ABC transporter ATP-binding protein; Pro	97.62
cd03295	242	ABC_OpuCA_Osmoprotection OpuCA is a the ATP bindin	97.62
PRK14250	241	phosphate ABC transporter ATP-binding protein; Pro	97.61
PRK00771	437	signal recognition particle protein Srp54; Provisi	97.61
COG4618	580	ArpD ABC-type protease/lipase transport system, AT	97.6
COG1118	345	CysA ABC-type sulfate/molybdate transport systems,	97.6
cd03289	275	ABCC_CFTR2 The CFTR subfamily domain 2. The cystic	97.6
TIGR02211	221	LolD_lipo_ex lipoprotein releasing system, ATP-bin	97.6
PRK10584	228	putative ABC transporter ATP-binding protein YbbA;	97.6
COG3899	849	Predicted ATPase [General function prediction only	97.59
PRK13647	274	cbiO cobalt transporter ATP-binding subunit; Provi	97.59
PRK13541	195	cytochrome c biogenesis protein CcmA; Provisional	97.59
PTZ00265	1466	multidrug resistance protein (mdr1); Provisional	97.59
PRK13644	274	cbiO cobalt transporter ATP-binding subunit; Provi	97.59
cd03301	213	ABC_MalK_N The N-terminal ATPase domain of the mal	97.58
cd03237	246	ABC_RNaseL_inhibitor_domain2 The ATPase domain 2 o	97.58
cd03256	241	ABC_PhnC_transporter ABC-type phosphate/phosphonat	97.58
cd03265	220	ABC_DrrA DrrA is the ATP-binding protein component	97.58
PRK10895	241	lipopolysaccharide ABC transporter ATP-binding pro	97.57
PRK11153	343	metN DL-methionine transporter ATP-binding subunit	97.57
cd03283	199	ABC_MutS-like MutS-like homolog in eukaryotes. The	97.57
TIGR00957	1522	MRP_assoc_pro multi drug resistance-associated pro	97.57
TIGR03411	242	urea_trans_UrtD urea ABC transporter, ATP-binding	97.57
PRK11124	242	artP arginine transporter ATP-binding subunit; Pro	97.57
cd02021	150	GntK Gluconate kinase (GntK) catalyzes the phospho	97.57
PRK14737	186	gmk guanylate kinase; Provisional	97.56
KOG0054|consensus	1381		97.56
cd01128	249	rho_factor Transcription termination factor rho is	97.56
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	97.56
TIGR01288	303	nodI ATP-binding ABC transporter family nodulation	97.55
COG1136	226	SalX ABC-type antimicrobial peptide transport syst	97.55
PRK10253	265	iron-enterobactin transporter ATP-binding protein;	97.55
PRK09493	240	glnQ glutamine ABC transporter ATP-binding protein	97.55
COG3910	233	Predicted ATPase [General function prediction only	97.55
PRK11650	356	ugpC glycerol-3-phosphate transporter ATP-binding	97.55
PRK13642	277	cbiO cobalt transporter ATP-binding subunit; Provi	97.54

>KOG0991|consensus

Probab=100.00  E-value=9.3e-62  Score=383.25  Aligned_cols=313  Identities=72%  Similarity=1.138  Sum_probs=306.4

Q ss_pred             CcccCCCCCCcccCCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHH
Q psy879            1 IEKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRN   80 (317)
Q Consensus         1 ~~ky~P~~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~   80 (317)
                      +|||||..+.|++|+++.++.++.+.+.|+.||++|.||||+||||.+.++|++|.++.....++++|++++++++.+|+
T Consensus        18 VeKYrP~~l~dIVGNe~tv~rl~via~~gnmP~liisGpPG~GKTTsi~~LAr~LLG~~~ke~vLELNASdeRGIDvVRn   97 (333)
T KOG0991|consen   18 VEKYRPSVLQDIVGNEDTVERLSVIAKEGNMPNLIISGPPGTGKTTSILCLARELLGDSYKEAVLELNASDERGIDVVRN   97 (333)
T ss_pred             HHhhCchHHHHhhCCHHHHHHHHHHHHcCCCCceEeeCCCCCchhhHHHHHHHHHhChhhhhHhhhccCccccccHHHHH
Confidence            58999999999999999999999999999999999999999999999999999999988888899999999999999999


Q ss_pred             HHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcCchhHhhhcceeeecCCCHHHH
Q psy879           81 KIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQL  160 (317)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~~~i~sR~~~i~f~~~~~~~~  160 (317)
                      .++.|++..+.+|.++.+++|+||+|.|+..+|.+|.+.||-++..++|.++||...++.++|+|||..++|..+++.++
T Consensus        98 ~IK~FAQ~kv~lp~grhKIiILDEADSMT~gAQQAlRRtMEiyS~ttRFalaCN~s~KIiEPIQSRCAiLRysklsd~qi  177 (333)
T KOG0991|consen   98 KIKMFAQKKVTLPPGRHKIIILDEADSMTAGAQQALRRTMEIYSNTTRFALACNQSEKIIEPIQSRCAILRYSKLSDQQI  177 (333)
T ss_pred             HHHHHHHhhccCCCCceeEEEeeccchhhhHHHHHHHHHHHHHcccchhhhhhcchhhhhhhHHhhhHhhhhcccCHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhhCCCcccHHHHHhhcCCCCHHHHHHHHHHHhcCCHHHH
Q psy879          161 LSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEMLLNCVEGNMKDS  240 (317)
Q Consensus       161 ~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~~~~~i~~~~v~~~~~~~~~~~i~~l~~~~~~~~~~~~  240 (317)
                      ...|.++++.|++.++++.++.++..+.||+|+++|.||..+.+.+.++.|.|.++++.+++..+.+++.++..++..+|
T Consensus       178 L~Rl~~v~k~Ekv~yt~dgLeaiifta~GDMRQalNnLQst~~g~g~Vn~enVfKv~d~PhP~~v~~ml~~~~~~~~~~A  257 (333)
T KOG0991|consen  178 LKRLLEVAKAEKVNYTDDGLEAIIFTAQGDMRQALNNLQSTVNGFGLVNQENVFKVCDEPHPLLVKKMLQACLKRNIDEA  257 (333)
T ss_pred             HHHHHHHHHHhCCCCCcchHHHhhhhccchHHHHHHHHHHHhccccccchhhhhhccCCCChHHHHHHHHHHHhccHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHHHhHHhcCCCcHHHHHHHHHHHHHhhccC
Q psy879          241 YKIIHHLYKLGYAPEDIIGNIFRVAKTLDIPEPLKLSIIQEIGNVHLRISEGVNSLLQLSGLLARLCIVGSKN  313 (317)
Q Consensus       241 ~~~~~~l~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~g~~~~l~le~~~~~~~~~~~~~  313 (317)
                      +.++..+.+.|++|.+|+..+||.++.+..++..+.+++..++-++.++..|+|..|+|..|++++|.+..+.
T Consensus       258 ~~il~~lw~lgysp~Dii~~~FRv~K~~~~~E~~rlE~ikeig~thmrI~eGv~s~LQl~glla~l~~~~~k~  330 (333)
T KOG0991|consen  258 LKILAELWKLGYSPEDIITTLFRVVKNMDVAESLRLEFIKEIGLTHMRILEGVNSLLQLSGLLAKLCKVGEKA  330 (333)
T ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhhHHhHHHhhHhHHHHHHHHHHHHHHhcccc
Confidence            9999999999999999999999999999999999999999999999999999999999999999999887764

>PLN03025 replication factor C subunit; Provisional

Probab=100.00  E-value=2.2e-54  Score=378.68  Aligned_cols=312  Identities=66%  Similarity=1.096  Sum_probs=290.5

Q ss_pred             CcccCCCCCCcccCCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHH
Q psy879            1 IEKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRN   80 (317)
Q Consensus         1 ~~ky~P~~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~   80 (317)
                      +|||||++|++++||+++++.|+.++.+++.||++|+||||+|||++++++|+++.|..+...++++++++..+.+.+++
T Consensus         4 ~~kyrP~~l~~~~g~~~~~~~L~~~~~~~~~~~lll~Gp~G~GKTtla~~la~~l~~~~~~~~~~eln~sd~~~~~~vr~   83 (319)
T PLN03025          4 VEKYRPTKLDDIVGNEDAVSRLQVIARDGNMPNLILSGPPGTGKTTSILALAHELLGPNYKEAVLELNASDDRGIDVVRN   83 (319)
T ss_pred             hhhcCCCCHHHhcCcHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHhcccCccceeeecccccccHHHHHH
Confidence            58999999999999999999999999999999999999999999999999999998876666788999988888899998


Q ss_pred             HHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcCchhHhhhcceeeecCCCHHHH
Q psy879           81 KIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQL  160 (317)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~~~i~sR~~~i~f~~~~~~~~  160 (317)
                      .+..+.+.......+.++++||||+|.|+..++++|++++|.++.+++||++||...++.++++|||..++|++++.+++
T Consensus        84 ~i~~~~~~~~~~~~~~~kviiiDE~d~lt~~aq~aL~~~lE~~~~~t~~il~~n~~~~i~~~L~SRc~~i~f~~l~~~~l  163 (319)
T PLN03025         84 KIKMFAQKKVTLPPGRHKIVILDEADSMTSGAQQALRRTMEIYSNTTRFALACNTSSKIIEPIQSRCAIVRFSRLSDQEI  163 (319)
T ss_pred             HHHHHHhccccCCCCCeEEEEEechhhcCHHHHHHHHHHHhcccCCceEEEEeCCccccchhHHHhhhcccCCCCCHHHH
Confidence            88877766543334678999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhhCCCcccHHHHHhhcCCCCHHHHHHHHHHHhcCCHHHH
Q psy879          161 LSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEMLLNCVEGNMKDS  240 (317)
Q Consensus       161 ~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~~~~~i~~~~v~~~~~~~~~~~i~~l~~~~~~~~~~~~  240 (317)
                      ..+|..+++++|+.++++++++++..++||+|.+++.||.++.+.+.|+.+++.++++...++.++++++++..++...+
T Consensus       164 ~~~L~~i~~~egi~i~~~~l~~i~~~~~gDlR~aln~Lq~~~~~~~~i~~~~v~~~~~~~~~~~i~~~i~~~~~~~~~~a  243 (319)
T PLN03025        164 LGRLMKVVEAEKVPYVPEGLEAIIFTADGDMRQALNNLQATHSGFGFVNQENVFKVCDQPHPLHVKNIVRNCLKGKFDDA  243 (319)
T ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCHHHHHHHcCCCCHHHHHHHHHHHHcCCHHHH
Confidence            99999999999999999999999999999999999999977666678999999999999999999999999999999999


Q ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHHHhHHhcCCCcHHHHHHHHHHHHHhhcc
Q psy879          241 YKIIHHLYKLGYAPEDIIGNIFRVAKTLDIPEPLKLSIIQEIGNVHLRISEGVNSLLQLSGLLARLCIVGSK  312 (317)
Q Consensus       241 ~~~~~~l~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~g~~~~l~le~~~~~~~~~~~~  312 (317)
                      +.++++|+..|++|..|+..+++.+....+++..+.+++.+++++++++..|.++.++|+.|+++++.+..+
T Consensus       244 ~~~l~~ll~~g~~~~~Il~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~l~a~~~~~~~~~~~  315 (319)
T PLN03025        244 CDGLKQLYDLGYSPTDIITTLFRVVKNYDMPEFLKLEYLREIGFAHMRICDGVGSLLQLSGLLAKLCLVRET  315 (319)
T ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999999988877677888899999999999999999999999999999999987543

>KOG0989|consensus

Probab=100.00  E-value=2.2e-53  Score=349.13  Aligned_cols=310  Identities=36%  Similarity=0.534  Sum_probs=283.0

Q ss_pred             CcccCCCCCCcccCCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCC-CCCceEEecCCCCcChHHHH
Q psy879            1 IEKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPS-FKDAVLELNASNDRGIDTVR   79 (317)
Q Consensus         1 ~~ky~P~~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~-~~~~~~~~~~~~~~~~~~i~   79 (317)
                      +|||||++|+++.||+++++.|.+.+..+..||||||||||||||+++++++++++|+. ....+.+.|+++.+|+..++
T Consensus        27 teKYrPkt~de~~gQe~vV~~L~~a~~~~~lp~~LFyGPpGTGKTStalafar~L~~~~~~~~rvl~lnaSderGisvvr  106 (346)
T KOG0989|consen   27 TEKYRPKTFDELAGQEHVVQVLKNALLRRILPHYLFYGPPGTGKTSTALAFARALNCEQLFPCRVLELNASDERGISVVR  106 (346)
T ss_pred             HHHhCCCcHHhhcchHHHHHHHHHHHhhcCCceEEeeCCCCCcHhHHHHHHHHHhcCccccccchhhhcccccccccchh
Confidence            58999999999999999999999999998889999999999999999999999999844 55667888999999999889


Q ss_pred             HHHHHHHhhcccC------CCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcCchhHhhhcceeeec
Q psy879           80 NKIKMFAQQKVTL------PPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYN  153 (317)
Q Consensus        80 ~~~~~~~~~~~~~------~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~~~i~sR~~~i~f~  153 (317)
                      +.+..|++.....      +...++|+|+||+|.|+.++|++|++.||.++.+++||++||..++++.++.|||+.++|+
T Consensus       107 ~Kik~fakl~~~~~~~~~~~~~~fKiiIlDEcdsmtsdaq~aLrr~mE~~s~~trFiLIcnylsrii~pi~SRC~KfrFk  186 (346)
T KOG0989|consen  107 EKIKNFAKLTVLLKRSDGYPCPPFKIIILDECDSMTSDAQAALRRTMEDFSRTTRFILICNYLSRIIRPLVSRCQKFRFK  186 (346)
T ss_pred             hhhcCHHHHhhccccccCCCCCcceEEEEechhhhhHHHHHHHHHHHhccccceEEEEEcCChhhCChHHHhhHHHhcCC
Confidence            8888877654332      2245699999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhhCCCcccHHH-HHhhcCCCCHHHHHHHHHHH
Q psy879          154 KLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHNGFGHVTAEY-VFKVCDEPHPLAVKEMLLNC  232 (317)
Q Consensus       154 ~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~~~~~i~~~~-v~~~~~~~~~~~i~~l~~~~  232 (317)
                      ++.++.+...|+.+|.+||+++++++++.++..++||+|+|+..||.++..++.|+... ++.+.+...++.+.++++..
T Consensus       187 ~L~d~~iv~rL~~Ia~~E~v~~d~~al~~I~~~S~GdLR~Ait~Lqsls~~gk~It~~~~~e~~~GvVp~~~l~~lle~a  266 (346)
T KOG0989|consen  187 KLKDEDIVDRLEKIASKEGVDIDDDALKLIAKISDGDLRRAITTLQSLSLLGKRITTSLVNEELAGVVPDEKLLDLLELA  266 (346)
T ss_pred             CcchHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCcHHHHHHHHHHhhccCcccchHHHHHHHhccCCHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999888999554 44555588888999999999


Q ss_pred             hcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhc-CCChHHHHHHHHHHHHHHhHHhcCCCcHHHHHHHHHHHHHhh
Q psy879          233 VEGNMKDSYKIIHHLYKLGYAPEDIIGNIFRVAKTL-DIPEPLKLSIIQEIGNVHLRISEGVNSLLQLSGLLARLCIVG  310 (317)
Q Consensus       233 ~~~~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~~~~-~~~~~~~~~~~~~l~~~~~~l~~g~~~~l~le~~~~~~~~~~  310 (317)
                      ...|..+....+++++..|++|..+++++..+.... +..+..+.++...+.+.+.++..|.+.+++|-.|.....+.+
T Consensus       267 ~S~d~~~~v~~~Rei~~sg~~~~~lmsQLa~vi~~~~g~~d~~k~~~~~kl~~~~~~~~dg~~l~~~L~~L~~~~~ql~  345 (346)
T KOG0989|consen  267 LSADTPNTVKRVREIMRSGYSPLQLMSQLAEVIMDIIGLSDEQKAQISLKLFTRDKRLEDGEDLELALKDLLEAEKQLR  345 (346)
T ss_pred             HccChHHHHHHHHHHHHhccCHHHHHHHHHHHHHhccccchHHHHHHHHHHHhccchhhcchhHHHHHHHHHHHHHHHh
Confidence            999999999999999999999999999998877655 888889999999999999999999999999999988776543

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=100.00  E-value=3.2e-48  Score=357.40  Aligned_cols=304  Identities=23%  Similarity=0.311  Sum_probs=266.4

Q ss_pred             cccCCCCCCcccCCHHHHHHHHHHHhcCCCce-EEEECCCCCCHHHHHHHHHHHHcCCC---------------------
Q psy879            2 EKYRPQTFSDIVGNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARILLGPS---------------------   59 (317)
Q Consensus         2 ~ky~P~~~~~~~g~~~~~~~l~~~l~~~~~~~-~ll~G~~G~GKt~la~~la~~l~~~~---------------------   59 (317)
                      +||||++|++++||+++++.|..++.+|+++| |||+||+|+||||+|+.+|+.++|..                     
T Consensus         5 ~kyRP~~f~eivGq~~i~~~L~~~i~~~r~~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~~~pCg~C~~C~~i~~~~~   84 (584)
T PRK14952          5 RKYRPATFAEVVGQEHVTEPLSSALDAGRINHAYLFSGPRGCGKTSSARILARSLNCAQGPTATPCGVCESCVALAPNGP   84 (584)
T ss_pred             HHhCCCcHHHhcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhccccCCCCCcccccHHHHHhhcccC
Confidence            69999999999999999999999999999999 89999999999999999999998742                     


Q ss_pred             CCCceEEecCCCCcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcC
Q psy879           60 FKDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKI  139 (317)
Q Consensus        60 ~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l  139 (317)
                      ....++++++.+..+++++++........+.   .++++|+||||+|.|+.+++|+|+++||+|+++++||++|+.+.++
T Consensus        85 ~~~dvieidaas~~gvd~iRel~~~~~~~P~---~~~~KVvIIDEah~Lt~~A~NALLK~LEEpp~~~~fIL~tte~~kl  161 (584)
T PRK14952         85 GSIDVVELDAASHGGVDDTRELRDRAFYAPA---QSRYRIFIVDEAHMVTTAGFNALLKIVEEPPEHLIFIFATTEPEKV  161 (584)
T ss_pred             CCceEEEeccccccCHHHHHHHHHHHHhhhh---cCCceEEEEECCCcCCHHHHHHHHHHHhcCCCCeEEEEEeCChHhh
Confidence            1234667777667789999887766655443   3789999999999999999999999999999999999999999999


Q ss_pred             chhHhhhcceeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhhC--CCcccHHHHHhhc
Q psy879          140 IEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHNG--FGHVTAEYVFKVC  217 (317)
Q Consensus       140 ~~~i~sR~~~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~~--~~~i~~~~v~~~~  217 (317)
                      +++|+|||+.++|.+++.+++.+||..+++++|+.++++++..++..++||+|.++++|++++..  .+.|+.+++..++
T Consensus       162 l~TI~SRc~~~~F~~l~~~~i~~~L~~i~~~egi~i~~~al~~Ia~~s~GdlR~aln~Ldql~~~~~~~~It~~~v~~ll  241 (584)
T PRK14952        162 LPTIRSRTHHYPFRLLPPRTMRALIARICEQEGVVVDDAVYPLVIRAGGGSPRDTLSVLDQLLAGAADTHVTYQRALGLL  241 (584)
T ss_pred             HHHHHHhceEEEeeCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHhccCCCCcCHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999987653  5689999999999


Q ss_pred             CCCCHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhc---C-------------------------
Q psy879          218 DEPHPLAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDIIGNIFRVAKTL---D-------------------------  269 (317)
Q Consensus       218 ~~~~~~~i~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~~~~---~-------------------------  269 (317)
                      +....+.++++++++..++...++.++.+++..|.++..++..+.++++.+   .                         
T Consensus       242 g~~~~~~i~~lv~al~~~d~~~al~~l~~l~~~g~d~~~~l~~L~~~~RdLll~k~~~~~~~~~l~~~~~~~~~~l~~qa  321 (584)
T PRK14952        242 GATDVALIDDAVDALAADDAAALFGAIESVIDAGHDPRRFATDLLERFRDLIVLQAVPDAAARGVVDAPEDVLERMREQA  321 (584)
T ss_pred             CCCCHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHhhcchhhhcccccCCHHHHHHHHHHH
Confidence            999999999999999999999999999999999999999988875554333   0                         


Q ss_pred             --CChHHHHHHHHHHHHHHhHHhcCCCcHHHHHHHHHHHHH
Q psy879          270 --IPEPLKLSIIQEIGNVHLRISEGVNSLLQLSGLLARLCI  308 (317)
Q Consensus       270 --~~~~~~~~~~~~l~~~~~~l~~g~~~~l~le~~~~~~~~  308 (317)
                        ++.....++++.+.+....++.+.++++.+|.++.++|.
T Consensus       322 ~~~s~~~L~~~i~~l~~~~~~~~~~~~~rl~LE~llikl~~  362 (584)
T PRK14952        322 ARIGLATLTRYAEVVQAGLGEMRGATAPRLLLEVVCARLLL  362 (584)
T ss_pred             HhCCHHHHHHHHHHHHHHHHHhccCCChHHHHHHHHHHHhc
Confidence              111223346775566666666666999999999999995

>PRK06305 DNA polymerase III subunits gamma and tau; Validated

Probab=100.00  E-value=4.4e-48  Score=350.29  Aligned_cols=308  Identities=24%  Similarity=0.298  Sum_probs=273.0

Q ss_pred             cccCCCCCCcccCCHHHHHHHHHHHhcCCCce-EEEECCCCCCHHHHHHHHHHHHcCCCC--------------------
Q psy879            2 EKYRPQTFSDIVGNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARILLGPSF--------------------   60 (317)
Q Consensus         2 ~ky~P~~~~~~~g~~~~~~~l~~~l~~~~~~~-~ll~G~~G~GKt~la~~la~~l~~~~~--------------------   60 (317)
                      +||||++|++++||+++++.|..+++.|+++| +|||||+|+|||++|+.+++.+.|...                    
T Consensus         9 ~kyRP~~~~diiGq~~~v~~L~~~i~~~~i~ha~Lf~Gp~G~GKtt~A~~lAk~l~c~~~~~~~~~c~~c~~C~~i~~~~   88 (451)
T PRK06305          9 RKYRPQTFSEILGQDAVVAVLKNALRFNRAAHAYLFSGIRGTGKTTLARIFAKALNCQNPTEDQEPCNQCASCKEISSGT   88 (451)
T ss_pred             HHhCCCCHHHhcCcHHHHHHHHHHHHcCCCceEEEEEcCCCCCHHHHHHHHHHHhcCCCcccCCCCCcccHHHHHHhcCC
Confidence            79999999999999999999999999999988 999999999999999999999987521                    


Q ss_pred             CCceEEecCCCCcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcCc
Q psy879           61 KDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKII  140 (317)
Q Consensus        61 ~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~  140 (317)
                      ...++++++....+.+++++........+   ..++++|+||||+|.|+.+.+++|++++|+|++++++|++++...++.
T Consensus        89 ~~d~~~i~g~~~~gid~ir~i~~~l~~~~---~~~~~kvvIIdead~lt~~~~n~LLk~lEep~~~~~~Il~t~~~~kl~  165 (451)
T PRK06305         89 SLDVLEIDGASHRGIEDIRQINETVLFTP---SKSRYKIYIIDEVHMLTKEAFNSLLKTLEEPPQHVKFFLATTEIHKIP  165 (451)
T ss_pred             CCceEEeeccccCCHHHHHHHHHHHHhhh---hcCCCEEEEEecHHhhCHHHHHHHHHHhhcCCCCceEEEEeCChHhcc
Confidence            12355566555667788887665554443   236899999999999999999999999999999999999999999999


Q ss_pred             hhHhhhcceeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhh-CCCcccHHHHHhhcCC
Q psy879          141 EPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHN-GFGHVTAEYVFKVCDE  219 (317)
Q Consensus       141 ~~i~sR~~~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~-~~~~i~~~~v~~~~~~  219 (317)
                      ++|+|||..++|++++++++..|+..+++++|+.+++++++.++..++||+|.+++++++... ..+.|+.++|.++++.
T Consensus       166 ~tI~sRc~~v~f~~l~~~el~~~L~~~~~~eg~~i~~~al~~L~~~s~gdlr~a~~~Lekl~~~~~~~It~~~V~~l~~~  245 (451)
T PRK06305        166 GTILSRCQKMHLKRIPEETIIDKLALIAKQEGIETSREALLPIARAAQGSLRDAESLYDYVVGLFPKSLDPDSVAKALGL  245 (451)
T ss_pred             hHHHHhceEEeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhccCCcCHHHHHHHHCC
Confidence            999999999999999999999999999999999999999999999999999999999998654 2356999999999999


Q ss_pred             CCHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhc--------------CCChHHHHHHHHHHHHH
Q psy879          220 PHPLAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDIIGNIFRVAKTL--------------DIPEPLKLSIIQEIGNV  285 (317)
Q Consensus       220 ~~~~~i~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~~~~--------------~~~~~~~~~~~~~l~~~  285 (317)
                      ..++.++++++++..++..+++.++++|+..|++|..++..+.++++.+              .++.....++++.+.++
T Consensus       246 ~~~~~vf~L~~ai~~~d~~~al~~l~~L~~~g~~~~~iL~~L~~~fR~ll~vk~~~~~~~~a~~~s~~~L~~ii~~l~e~  325 (451)
T PRK06305        246 LSQDSLYTLDEAITTQNYAQALEPVTDAMNSGVAPAHFLHDLTLFFRNILLKQYNKQLSSVATKYSSEQLLEIIDFLGES  325 (451)
T ss_pred             CCHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCcCHHHHHHHHHHHHHHHHHHhhhhHHHHHHHhCCHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999988765544432              45666778899999999


Q ss_pred             HhHHhcCCCcHHHHHHHHHHHHHhhcc
Q psy879          286 HLRISEGVNSLLQLSGLLARLCIVGSK  312 (317)
Q Consensus       286 ~~~l~~g~~~~l~le~~~~~~~~~~~~  312 (317)
                      |++|++|.++.+.||.|+.+++.....
T Consensus       326 d~~lk~~~~~k~~lE~lll~l~~~~~~  352 (451)
T PRK06305        326 AKHIQLTIFEKTFLETVIIHLIRIYQR  352 (451)
T ss_pred             HHHHHhCCChHHHHHHHHHHHHHHhcC
Confidence            999999999999999999999976543

>PRK08451 DNA polymerase III subunits gamma and tau; Validated

Probab=100.00  E-value=6.7e-48  Score=350.26  Aligned_cols=306  Identities=23%  Similarity=0.349  Sum_probs=273.7

Q ss_pred             CcccCCCCCCcccCCHHHHHHHHHHHhcCCCce-EEEECCCCCCHHHHHHHHHHHHcCCCC-------------------
Q psy879            1 IEKYRPQTFSDIVGNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARILLGPSF-------------------   60 (317)
Q Consensus         1 ~~ky~P~~~~~~~g~~~~~~~l~~~l~~~~~~~-~ll~G~~G~GKt~la~~la~~l~~~~~-------------------   60 (317)
                      .+||||++|++++||+++.+.|..++++|+++| ||||||+|+|||++|+++++.+.|...                   
T Consensus         5 ~~KyRP~~fdeiiGqe~v~~~L~~~I~~grl~hayLf~Gp~G~GKTt~Ar~LAk~L~c~~~~~~~pC~~C~~C~~~~~~~   84 (535)
T PRK08451          5 ALKYRPKHFDELIGQESVSKTLSLALDNNRLAHAYLFSGLRGSGKTSSARIFARALVCEQGPSSTPCDTCIQCQSALENR   84 (535)
T ss_pred             HHHHCCCCHHHccCcHHHHHHHHHHHHcCCCCeeEEEECCCCCcHHHHHHHHHHHhcCCCCCCCCCCcccHHHHHHhhcC
Confidence            379999999999999999999999999999999 899999999999999999999986432                   


Q ss_pred             CCceEEecCCCCcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcCc
Q psy879           61 KDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKII  140 (317)
Q Consensus        61 ~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~  140 (317)
                      ...++++++.+..+++++++.+......+   ..++++|+||||+|.|+.+++++|+++||+||++++||++|+++.+++
T Consensus        85 h~dv~eldaas~~gId~IRelie~~~~~P---~~~~~KVvIIDEad~Lt~~A~NALLK~LEEpp~~t~FIL~ttd~~kL~  161 (535)
T PRK08451         85 HIDIIEMDAASNRGIDDIRELIEQTKYKP---SMARFKIFIIDEVHMLTKEAFNALLKTLEEPPSYVKFILATTDPLKLP  161 (535)
T ss_pred             CCeEEEeccccccCHHHHHHHHHHHhhCc---ccCCeEEEEEECcccCCHHHHHHHHHHHhhcCCceEEEEEECChhhCc
Confidence            23467777766678899998887654443   237899999999999999999999999999999999999999999999


Q ss_pred             hhHhhhcceeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhh-CCCcccHHHHHhhcCC
Q psy879          141 EPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHN-GFGHVTAEYVFKVCDE  219 (317)
Q Consensus       141 ~~i~sR~~~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~-~~~~i~~~~v~~~~~~  219 (317)
                      ++|+|||+.++|.+++.+++..|+..++.++|+.++++++..++..++||+|.+++.|+.+.. ..+.|+.++|.++++.
T Consensus       162 ~tI~SRc~~~~F~~Ls~~ei~~~L~~Il~~EGi~i~~~Al~~Ia~~s~GdlR~alnlLdqai~~~~~~It~~~V~~~lg~  241 (535)
T PRK08451        162 ATILSRTQHFRFKQIPQNSIISHLKTILEKEGVSYEPEALEILARSGNGSLRDTLTLLDQAIIYCKNAITESKVADMLGL  241 (535)
T ss_pred             hHHHhhceeEEcCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCcHHHHHHHHHHHHHhcCCCCCHHHHHHHhCC
Confidence            999999999999999999999999999999999999999999999999999999999987655 4568999999999999


Q ss_pred             CCHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhc------CCChHHHHHHHHHHHHHHhHHhcCC
Q psy879          220 PHPLAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDIIGNIFRVAKTL------DIPEPLKLSIIQEIGNVHLRISEGV  293 (317)
Q Consensus       220 ~~~~~i~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~~~~------~~~~~~~~~~~~~l~~~~~~l~~g~  293 (317)
                      ...+.++++++++..++...++.++.++  .|+++..++..+...++..      ........+.+..+.+.+..+..|.
T Consensus       242 ~~~~~I~~li~ai~~~d~~~a~~~l~~L--~g~~~~~~l~~l~~~l~~~~~~~~~~~~l~~l~r~~riL~~~k~~l~~g~  319 (535)
T PRK08451        242 LDPSKLEDFFQAILNQDKEKLFELLKEL--EDYEAEMVLDEMMLFLKEKFLSKDSEFSILLYERFFRILSSAKSLLKEGA  319 (535)
T ss_pred             CCHHHHHHHHHHHHhcCHHHHHHHHHHH--HCCCHHHHHHHHHHHHHHHhhcccccccHHHHHHHHHHHHHHHHHHHhCC
Confidence            9999999999999999999999999998  5799999999987766532      2344457788999999999999999


Q ss_pred             CcHHHHHHHHHHHHHhhc
Q psy879          294 NSLLQLSGLLARLCIVGS  311 (317)
Q Consensus       294 ~~~l~le~~~~~~~~~~~  311 (317)
                      +++++++.++.++|....
T Consensus       320 ~~~i~l~~~~~~~~~~~~  337 (535)
T PRK08451        320 DDGFVLLLMLFKMKEALK  337 (535)
T ss_pred             CcHHHHHHHHHHHHHhcC
Confidence            999999999999998543

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional

Probab=100.00  E-value=4.9e-48  Score=348.32  Aligned_cols=306  Identities=22%  Similarity=0.346  Sum_probs=271.1

Q ss_pred             cccCCCCCCcccCCHHHHHHHHHHHhcCCCce-EEEECCCCCCHHHHHHHHHHHHcCCCC-------------------C
Q psy879            2 EKYRPQTFSDIVGNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARILLGPSF-------------------K   61 (317)
Q Consensus         2 ~ky~P~~~~~~~g~~~~~~~l~~~l~~~~~~~-~ll~G~~G~GKt~la~~la~~l~~~~~-------------------~   61 (317)
                      +||||++|++++||+++++.|.+++..|+++| +||+||+|+||||+|+.+|+.++|...                   .
T Consensus         5 ~KyRP~~f~dliGQe~vv~~L~~a~~~~ri~ha~Lf~Gp~G~GKTT~ArilAk~LnC~~~~~~~pCg~C~~C~~i~~~~~   84 (491)
T PRK14964          5 LKYRPSSFKDLVGQDVLVRILRNAFTLNKIPQSILLVGASGVGKTTCARIISLCLNCSNGPTSDPCGTCHNCISIKNSNH   84 (491)
T ss_pred             HHhCCCCHHHhcCcHHHHHHHHHHHHcCCCCceEEEECCCCccHHHHHHHHHHHHcCcCCCCCCCccccHHHHHHhccCC
Confidence            69999999999999999999999999999997 999999999999999999999876432                   2


Q ss_pred             CceEEecCCCCcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcCch
Q psy879           62 DAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIE  141 (317)
Q Consensus        62 ~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~~  141 (317)
                      ..++++++.+..+++++++.+......++   .++++|+||||+|.|+.+++++|++++|+||+++.||++|+...++.+
T Consensus        85 ~Dv~eidaas~~~vddIR~Iie~~~~~P~---~~~~KVvIIDEah~Ls~~A~NaLLK~LEePp~~v~fIlatte~~Kl~~  161 (491)
T PRK14964         85 PDVIEIDAASNTSVDDIKVILENSCYLPI---SSKFKVYIIDEVHMLSNSAFNALLKTLEEPAPHVKFILATTEVKKIPV  161 (491)
T ss_pred             CCEEEEecccCCCHHHHHHHHHHHHhccc---cCCceEEEEeChHhCCHHHHHHHHHHHhCCCCCeEEEEEeCChHHHHH
Confidence            45788888888899999998887766653   378999999999999999999999999999999999999999999999


Q ss_pred             hHhhhcceeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhh-CCCcccHHHHHhhcCCC
Q psy879          142 PIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHN-GFGHVTAEYVFKVCDEP  220 (317)
Q Consensus       142 ~i~sR~~~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~-~~~~i~~~~v~~~~~~~  220 (317)
                      +|+|||+.++|.+++.+++..|+..+++++|+.+++++++.+++.++||+|.++++++++.. ..+.|+.++|.++++..
T Consensus       162 tI~SRc~~~~f~~l~~~el~~~L~~ia~~Egi~i~~eAL~lIa~~s~GslR~alslLdqli~y~~~~It~e~V~~llg~~  241 (491)
T PRK14964        162 TIISRCQRFDLQKIPTDKLVEHLVDIAKKENIEHDEESLKLIAENSSGSMRNALFLLEQAAIYSNNKISEKSVRDLLGCV  241 (491)
T ss_pred             HHHHhheeeecccccHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHccC
Confidence            99999999999999999999999999999999999999999999999999999999988654 45689999999999988


Q ss_pred             CHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhc-----------C--------------CChHHH
Q psy879          221 HPLAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDIIGNIFRVAKTL-----------D--------------IPEPLK  275 (317)
Q Consensus       221 ~~~~i~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~~~~-----------~--------------~~~~~~  275 (317)
                      ..+.++++++++..+|..+++.++++|+..| +|..++..+...+..+           .              ++....
T Consensus       242 ~~~~If~L~~aI~~~d~~~Al~~l~~Ll~~g-~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l  320 (491)
T PRK14964        242 DKHILEDLVEAILLGDAQSALNVFRELCNTS-NPVIILEGMLQIIYEICYFSITKEIDFLLGEDLITRIKSLKIGSTIFL  320 (491)
T ss_pred             CHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-CHHHHHHHHHHHHHHHHHHhcCccccccCCHHHHHHHHHHhCCCHHHH
Confidence            8899999999999999999999999999876 6777776654322111           1              233344


Q ss_pred             HHHHHHHHHHHhHHhcCCCcHHHHHHHHHHHHHhhc
Q psy879          276 LSIIQEIGNVHLRISEGVNSLLQLSGLLARLCIVGS  311 (317)
Q Consensus       276 ~~~~~~l~~~~~~l~~g~~~~l~le~~~~~~~~~~~  311 (317)
                      .++++.+.+....++...++++++|+++.++|....
T Consensus       321 ~~~~~~l~~~~~~~~~~~~~~~~~e~~~~rl~~~~~  356 (491)
T PRK14964        321 SRLWQMLLKGIQEVKSSTCVKQAAEMMIIRLCYLSD  356 (491)
T ss_pred             HHHHHHHHHHHHHhccCCCchHHHHHHHHHHHhcCC
Confidence            568899999999999999999999999999997543

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=100.00  E-value=9.9e-48  Score=341.43  Aligned_cols=305  Identities=23%  Similarity=0.301  Sum_probs=266.1

Q ss_pred             cccCCCCCCcccCCHHHHHHHHHHHhcCCCce-EEEECCCCCCHHHHHHHHHHHHcCCCCC-------------------
Q psy879            2 EKYRPQTFSDIVGNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARILLGPSFK-------------------   61 (317)
Q Consensus         2 ~ky~P~~~~~~~g~~~~~~~l~~~l~~~~~~~-~ll~G~~G~GKt~la~~la~~l~~~~~~-------------------   61 (317)
                      +||||++|++++||+++++.|..++..|+++| ++|+||+|+||||+|+++++.+.|....                   
T Consensus         8 ~kyrP~~~~~iiGq~~~~~~l~~~~~~~~~~h~~L~~Gp~G~GKTtla~~la~~l~c~~~~~~~pc~~c~~c~~~~~~~~   87 (363)
T PRK14961          8 RKWRPQYFRDIIGQKHIVTAISNGLSLGRIHHAWLLSGTRGVGKTTIARLLAKSLNCQNGITSNPCRKCIICKEIEKGLC   87 (363)
T ss_pred             HHhCCCchhhccChHHHHHHHHHHHHcCCCCeEEEEecCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCCHHHHHHhcCCC
Confidence            79999999999999999999999999999999 8999999999999999999999764211                   


Q ss_pred             CceEEecCCCCcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcCch
Q psy879           62 DAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIE  141 (317)
Q Consensus        62 ~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~~  141 (317)
                      ..+.++++....+.+++++.+..+...+   ..++++|+||||+|.++..++++|++++|+|++++.||++|++.+++.+
T Consensus        88 ~d~~~~~~~~~~~v~~ir~i~~~~~~~p---~~~~~kviIIDEa~~l~~~a~naLLk~lEe~~~~~~fIl~t~~~~~l~~  164 (363)
T PRK14961         88 LDLIEIDAASRTKVEEMREILDNIYYSP---SKSRFKVYLIDEVHMLSRHSFNALLKTLEEPPQHIKFILATTDVEKIPK  164 (363)
T ss_pred             CceEEecccccCCHHHHHHHHHHHhcCc---ccCCceEEEEEChhhcCHHHHHHHHHHHhcCCCCeEEEEEcCChHhhhH
Confidence            1344555544467778887776655443   2367899999999999999999999999999999999999999999999


Q ss_pred             hHhhhcceeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhh-CCCcccHHHHHhhcCCC
Q psy879          142 PIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHN-GFGHVTAEYVFKVCDEP  220 (317)
Q Consensus       142 ~i~sR~~~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~-~~~~i~~~~v~~~~~~~  220 (317)
                      +++|||..++|++++.+++.+|+..+++++|+.+++++++.++..++||+|.+++.++.++. +.+.|+.++|.++++..
T Consensus       165 tI~SRc~~~~~~~l~~~el~~~L~~~~~~~g~~i~~~al~~ia~~s~G~~R~al~~l~~~~~~~~~~It~~~v~~~l~~~  244 (363)
T PRK14961        165 TILSRCLQFKLKIISEEKIFNFLKYILIKESIDTDEYALKLIAYHAHGSMRDALNLLEHAINLGKGNINIKNVTDMLGLL  244 (363)
T ss_pred             HHHhhceEEeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHCCC
Confidence            99999999999999999999999999999999999999999999999999999999987644 56789999999999999


Q ss_pred             CHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhc------C---------------------CChH
Q psy879          221 HPLAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDIIGNIFRVAKTL------D---------------------IPEP  273 (317)
Q Consensus       221 ~~~~i~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~~~~------~---------------------~~~~  273 (317)
                      .+..++++++++..++..+++.+++++...|++|..++..+...++.+      +                     .+..
T Consensus       245 ~~~~i~~l~~ai~~~~~~~~~~~~~~l~~~g~~~~~il~~l~~~~~d~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  324 (363)
T PRK14961        245 NEKQSFLLTDALLKKDSKKTMLLLNKISSIGIEWENILIEMLRFLHHISMSQSFPKIWNTIFIKNYKNQIQKIAQNNKKT  324 (363)
T ss_pred             CHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHhcCchhhcccchHHHHHHHHHHHcCCHH
Confidence            999999999999999999999999999999999999998875543322      1                     1112


Q ss_pred             HHHHHHHHHHHHHhHHhcCCCcHHHHHHHHHHHHHh
Q psy879          274 LKLSIIQEIGNVHLRISEGVNSLLQLSGLLARLCIV  309 (317)
Q Consensus       274 ~~~~~~~~l~~~~~~l~~g~~~~l~le~~~~~~~~~  309 (317)
                      ...++++.+.+...+++.++|+++++|.++.+++.-
T Consensus       325 ~l~~~~~~~~~~~~~l~~~~~~~~~~e~~l~~~~~~  360 (363)
T PRK14961        325 NIQLCYQILLNGRKELKFAPDQKIGVEMTLLRAINA  360 (363)
T ss_pred             HHHHHHHHHHHHHHHHccCCCchHHHHHHHHHHHhC
Confidence            233378999999999999999999999999999864

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional

Probab=100.00  E-value=4e-48  Score=360.48  Aligned_cols=305  Identities=22%  Similarity=0.317  Sum_probs=271.3

Q ss_pred             cccCCCCCCcccCCHHHHHHHHHHHhcCCCce-EEEECCCCCCHHHHHHHHHHHHcCCCC-------------------C
Q psy879            2 EKYRPQTFSDIVGNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARILLGPSF-------------------K   61 (317)
Q Consensus         2 ~ky~P~~~~~~~g~~~~~~~l~~~l~~~~~~~-~ll~G~~G~GKt~la~~la~~l~~~~~-------------------~   61 (317)
                      +||||++|++++||+++++.|..++.+|+++| ||||||+|+|||++++.+++.+.|...                   .
T Consensus         8 ~k~RP~~f~~iiGq~~v~~~L~~~i~~~~~~hayLf~Gp~G~GKtt~A~~lak~l~c~~~~~~~~c~~c~~c~~i~~g~~   87 (576)
T PRK14965          8 RKYRPQTFSDLTGQEHVSRTLQNAIDTGRVAHAFLFTGARGVGKTSTARILAKALNCEQGLTAEPCNVCPPCVEITEGRS   87 (576)
T ss_pred             HHhCCCCHHHccCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHhhcCCCCCCCCCCCccHHHHHHhcCCC
Confidence            79999999999999999999999999999999 899999999999999999999987532                   2


Q ss_pred             CceEEecCCCCcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcCch
Q psy879           62 DAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIE  141 (317)
Q Consensus        62 ~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~~  141 (317)
                      ..++++++.+..+++++++.+......+.   .++++|+||||+|.|+..++|+|+++||+|+++++||++|+.++++++
T Consensus        88 ~d~~eid~~s~~~v~~ir~l~~~~~~~p~---~~~~KVvIIdev~~Lt~~a~naLLk~LEepp~~~~fIl~t~~~~kl~~  164 (576)
T PRK14965         88 VDVFEIDGASNTGVDDIRELRENVKYLPS---RSRYKIFIIDEVHMLSTNAFNALLKTLEEPPPHVKFIFATTEPHKVPI  164 (576)
T ss_pred             CCeeeeeccCccCHHHHHHHHHHHHhccc---cCCceEEEEEChhhCCHHHHHHHHHHHHcCCCCeEEEEEeCChhhhhH
Confidence            23566776666788899888777655542   378999999999999999999999999999999999999999999999


Q ss_pred             hHhhhcceeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhh-CCCcccHHHHHhhcCCC
Q psy879          142 PIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHN-GFGHVTAEYVFKVCDEP  220 (317)
Q Consensus       142 ~i~sR~~~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~-~~~~i~~~~v~~~~~~~  220 (317)
                      +|+|||+.++|++++.+++..|+..+++++|+.++++++..++..++||+|.++++|+++.. ..+.|+.++|..+++..
T Consensus       165 tI~SRc~~~~f~~l~~~~i~~~L~~i~~~egi~i~~~al~~la~~a~G~lr~al~~Ldqliay~g~~It~edV~~llG~~  244 (576)
T PRK14965        165 TILSRCQRFDFRRIPLQKIVDRLRYIADQEGISISDAALALVARKGDGSMRDSLSTLDQVLAFCGDAVGDDDVAELLGVV  244 (576)
T ss_pred             HHHHhhhhhhcCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhccCCCCHHHHHHHhCCC
Confidence            99999999999999999999999999999999999999999999999999999999987654 44679999999999999


Q ss_pred             CHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhc----------------------------CCCh
Q psy879          221 HPLAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDIIGNIFRVAKTL----------------------------DIPE  272 (317)
Q Consensus       221 ~~~~i~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~~~~----------------------------~~~~  272 (317)
                      ..+.++++++++..++...++.++.++...|.++..++..+.++++.+                            .++.
T Consensus       245 ~~~~l~~ll~al~~~d~~~al~~l~~l~~~G~~~~~~l~~Ll~~~RdLl~~k~~~~~~~~l~~~~~~~~~~~~~A~~~s~  324 (576)
T PRK14965        245 DRRLLLDISAAVFGRDTRALLEIVERVDEFGYNMRQFCQELIDHLRNLVVLRAVGEPGDLLDLSEAELAELRAQAAAADA  324 (576)
T ss_pred             CHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHhcCchhhhccCCHHHHHHHHHHHHcCCH
Confidence            999999999999999999999999999999999998888765543322                            1122


Q ss_pred             HHHHHHHHHHHHHHhHHhcCCCcHHHHHHHHHHHHHh
Q psy879          273 PLKLSIIQEIGNVHLRISEGVNSLLQLSGLLARLCIV  309 (317)
Q Consensus       273 ~~~~~~~~~l~~~~~~l~~g~~~~l~le~~~~~~~~~  309 (317)
                      ....++++.+.+.++.|+.+.++++.||.++.++|..
T Consensus       325 ~~L~~~l~~l~~~~~~lk~~~~~~l~lE~lllkl~~~  361 (576)
T PRK14965        325 ADLQRHLTLLLRAEGEMAHASFPRLVLEMALLKMATL  361 (576)
T ss_pred             HHHHHHHHHHHHHHHHHhcCCCcHHHHHHHHHHHhhc
Confidence            2344489999999999999999999999999999974

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional

Probab=100.00  E-value=6.5e-48  Score=346.24  Aligned_cols=307  Identities=22%  Similarity=0.323  Sum_probs=269.4

Q ss_pred             CcccCCCCCCcccCCHHHHHHHHHHHhcCCCce-EEEECCCCCCHHHHHHHHHHHHcCCCC-------------------
Q psy879            1 IEKYRPQTFSDIVGNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARILLGPSF-------------------   60 (317)
Q Consensus         1 ~~ky~P~~~~~~~g~~~~~~~l~~~l~~~~~~~-~ll~G~~G~GKt~la~~la~~l~~~~~-------------------   60 (317)
                      .+||||++|++++||+++++.|..++++|+.+| |+|+||||+||||+|+++|+.+.|...                   
T Consensus         7 ~~k~RP~~~~eiiGq~~~~~~L~~~~~~~~~~ha~lf~Gp~G~GKtt~A~~~a~~l~c~~~~~~~~~~~~~~~~c~~c~~   86 (397)
T PRK14955          7 ARKYRPKKFADITAQEHITRTIQNSLRMGRVGHGYIFSGLRGVGKTTAARVFAKAVNCQRMIDDADYLQEVTEPCGECES   86 (397)
T ss_pred             HHhcCCCcHhhccChHHHHHHHHHHHHhCCcceeEEEECCCCCCHHHHHHHHHHHhcCCCCcCcccccccCCCCCCCCHH
Confidence            379999999999999999999999999999999 999999999999999999999988421                   


Q ss_pred             --------CCceEEecCCCCcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEE
Q psy879           61 --------KDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALA  132 (317)
Q Consensus        61 --------~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~  132 (317)
                              ...+.++++....+.+++++....+...++   .++++|+||||+|.|+.+.++.|++++|+|++.++||++
T Consensus        87 c~~~~~~~~~n~~~~~~~~~~~id~Ir~l~~~~~~~p~---~~~~kvvIIdea~~l~~~~~~~LLk~LEep~~~t~~Il~  163 (397)
T PRK14955         87 CRDFDAGTSLNISEFDAASNNSVDDIRLLRENVRYGPQ---KGRYRVYIIDEVHMLSIAAFNAFLKTLEEPPPHAIFIFA  163 (397)
T ss_pred             HHHHhcCCCCCeEeecccccCCHHHHHHHHHHHhhchh---cCCeEEEEEeChhhCCHHHHHHHHHHHhcCCCCeEEEEE
Confidence                    012344555455668888887777765553   378999999999999999999999999999999999999


Q ss_pred             ecCCCcCchhHhhhcceeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhh------CCC
Q psy879          133 CNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHN------GFG  206 (317)
Q Consensus       133 ~~~~~~l~~~i~sR~~~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~------~~~  206 (317)
                      ++...++.++++|||+.++|.+++++++..|+..+++.+|+.+++++++.++..++||+|.++++++++..      +.+
T Consensus       164 t~~~~kl~~tl~sR~~~v~f~~l~~~ei~~~l~~~~~~~g~~i~~~al~~l~~~s~g~lr~a~~~L~kl~~~~~~~~~~~  243 (397)
T PRK14955        164 TTELHKIPATIASRCQRFNFKRIPLEEIQQQLQGICEAEGISVDADALQLIGRKAQGSMRDAQSILDQVIAFSVESEGEG  243 (397)
T ss_pred             eCChHHhHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhccccCCCC
Confidence            98889999999999999999999999999999999999999999999999999999999999999997532      346


Q ss_pred             cccHHHHHhhcCCCCHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhc------------------
Q psy879          207 HVTAEYVFKVCDEPHPLAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDIIGNIFRVAKTL------------------  268 (317)
Q Consensus       207 ~i~~~~v~~~~~~~~~~~i~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~~~~------------------  268 (317)
                      .|+.++|.+++....++.+|++++++..++...++.++++|...|++|..|+..+.++++.+                  
T Consensus       244 ~It~~~v~~~v~~~~~~~vf~l~~ai~~~~~~~al~~~~~l~~~~~~~~~iL~ll~~~~R~ll~~k~~~~~~~~~~~~~~  323 (397)
T PRK14955        244 SIRYDKVAELLNYIDDEHFFAVTDAVADGDAVAMLDVAQFVIRNGYDEQDFLEKLIEHLRNFLVVHNLRSTRLVERPDAV  323 (397)
T ss_pred             ccCHHHHHHHHCCCCHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHhccccccccCCHHH
Confidence            89999999999999999999999999999999999999999999999999988875554332                  


Q ss_pred             ---------CCChHHHHHHHHHHHHHHhHHhcCCCcHHHHHHHHHHHHHhh
Q psy879          269 ---------DIPEPLKLSIIQEIGNVHLRISEGVNSLLQLSGLLARLCIVG  310 (317)
Q Consensus       269 ---------~~~~~~~~~~~~~l~~~~~~l~~g~~~~l~le~~~~~~~~~~  310 (317)
                               .++.....++++.+.++|+++++|.|+++.+|.|+.+++...
T Consensus       324 ~~~~~~~a~~~s~~~L~~~l~~l~e~d~~lK~~~~~~l~lE~lll~l~~~~  374 (397)
T PRK14955        324 RERYERDAAKFSPEVIMQMTDLLLQTQKELKFQFEYQFRFELALLKLIEIG  374 (397)
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHHHHHHHHHhcCCCccHHHHHHHHHHHhhC
Confidence                     122222334899999999999999999999999999999755

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=100.00  E-value=5.3e-48  Score=344.21  Aligned_cols=304  Identities=24%  Similarity=0.325  Sum_probs=258.0

Q ss_pred             cccCCCCCCcccCCHHHHHHHHHHHhcCCCce-EEEECCCCCCHHHHHHHHHHHHcCCCC-------------------C
Q psy879            2 EKYRPQTFSDIVGNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARILLGPSF-------------------K   61 (317)
Q Consensus         2 ~ky~P~~~~~~~g~~~~~~~l~~~l~~~~~~~-~ll~G~~G~GKt~la~~la~~l~~~~~-------------------~   61 (317)
                      +||||++|++++||+++++.|..++.+++++| |+|+||+|+||||+|+.+|+.+.|...                   .
T Consensus        10 ~KyRP~~f~dvVGQe~iv~~L~~~i~~~ri~ha~Lf~GP~GtGKTTlAriLAk~Lnce~~~~~~pCg~C~sC~~i~~g~~   89 (484)
T PRK14956         10 RKYRPQFFRDVIHQDLAIGALQNALKSGKIGHAYIFFGPRGVGKTTIARILAKRLNCENPIGNEPCNECTSCLEITKGIS   89 (484)
T ss_pred             HHhCCCCHHHHhChHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHhcCcccccCccccCCCcHHHHHHccCC
Confidence            79999999999999999999999999999998 999999999999999999999987431                   1


Q ss_pred             CceEEecCCCCcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcCch
Q psy879           62 DAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIE  141 (317)
Q Consensus        62 ~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~~  141 (317)
                      ..++++++....+.+.+++....+...+   ..++++|+||||+|.|+.+++++|++.+|+|+.+++||++|+.+.++.+
T Consensus        90 ~dviEIdaas~~gVd~IReL~e~l~~~p---~~g~~KV~IIDEah~Ls~~A~NALLKtLEEPp~~viFILaTte~~kI~~  166 (484)
T PRK14956         90 SDVLEIDAASNRGIENIRELRDNVKFAP---MGGKYKVYIIDEVHMLTDQSFNALLKTLEEPPAHIVFILATTEFHKIPE  166 (484)
T ss_pred             ccceeechhhcccHHHHHHHHHHHHhhh---hcCCCEEEEEechhhcCHHHHHHHHHHhhcCCCceEEEeecCChhhccH
Confidence            2356777766778888888776665443   2367899999999999999999999999999999999999999999999


Q ss_pred             hHhhhcceeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhh-hCCCcccHHHHHhhcCCC
Q psy879          142 PIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTH-NGFGHVTAEYVFKVCDEP  220 (317)
Q Consensus       142 ~i~sR~~~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~-~~~~~i~~~~v~~~~~~~  220 (317)
                      +|+|||+.++|++++.+++..+|..++.++|+.++++++..+++.++||+|.+++.|+.+. ...+.|+.+.|.++++..
T Consensus       167 TI~SRCq~~~f~~ls~~~i~~~L~~i~~~Egi~~e~eAL~~Ia~~S~Gd~RdAL~lLeq~i~~~~~~it~~~V~~~lg~~  246 (484)
T PRK14956        167 TILSRCQDFIFKKVPLSVLQDYSEKLCKIENVQYDQEGLFWIAKKGDGSVRDMLSFMEQAIVFTDSKLTGVKIRKMIGYH  246 (484)
T ss_pred             HHHhhhheeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCChHHHHHHHHHHHHHhCCCCcCHHHHHHHhCCC
Confidence            9999999999999999999999999999999999999999999999999999999998754 345679999999999999


Q ss_pred             CHHHHHHHHHHHhcCCH-HHHHHHHHHHHHcCCCHHHHHHHHHHHHHhc-------------CCChHHH-----------
Q psy879          221 HPLAVKEMLLNCVEGNM-KDSYKIIHHLYKLGYAPEDIIGNIFRVAKTL-------------DIPEPLK-----------  275 (317)
Q Consensus       221 ~~~~i~~l~~~~~~~~~-~~~~~~~~~l~~~~~~~~~i~~~~~~~~~~~-------------~~~~~~~-----------  275 (317)
                      ..+.++++++++..+|. .+++.++..++..|++|..++..+...++.+             ..++...           
T Consensus       247 ~~~~~~~l~~si~~~d~~~~al~~l~~l~~~G~d~~~~~~~l~~~~r~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  326 (484)
T PRK14956        247 GIEFLTSFIKSLIDPDNHSKSLEILESLYQEGQDIYKFLWDSIEFTHTLNLIRDSLADRESVNFPKEDLQKMKSDFENVD  326 (484)
T ss_pred             CHHHHHHHHHHHHcCCcHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHhhcccchhhccCCHHHHHHHHHHHHhcC
Confidence            99999999999999875 6899999999999999999887764433322             1122111           


Q ss_pred             ----HHHHHHH----HHH-HhHHhcCCCcHHHHHHHHHHHHH
Q psy879          276 ----LSIIQEI----GNV-HLRISEGVNSLLQLSGLLARLCI  308 (317)
Q Consensus       276 ----~~~~~~l----~~~-~~~l~~g~~~~l~le~~~~~~~~  308 (317)
                          .+++..+    ..+ +.+++...++++.+|..++++|.
T Consensus       327 ~~~l~~~~~~~~~~~~~~~~~~~~~s~~~r~~~E~~~~~l~~  368 (484)
T PRK14956        327 SSKLNFLSGKLFEIYEKIKTIRLRNSFEIKVFTEIQIKKLVE  368 (484)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhhhccCCCchHHHHHHHHHHhc
Confidence                1122222    222 45567778999999999999995

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=100.00  E-value=9.9e-48  Score=353.93  Aligned_cols=308  Identities=20%  Similarity=0.257  Sum_probs=269.5

Q ss_pred             cccCCCCCCcccCCHHHHHHHHHHHhcCCCce-EEEECCCCCCHHHHHHHHHHHHcCCCC-------------------C
Q psy879            2 EKYRPQTFSDIVGNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARILLGPSF-------------------K   61 (317)
Q Consensus         2 ~ky~P~~~~~~~g~~~~~~~l~~~l~~~~~~~-~ll~G~~G~GKt~la~~la~~l~~~~~-------------------~   61 (317)
                      +||||++|++++||+++++.|..++.+|+++| |||+||+|+||||+++.+++.++|...                   .
T Consensus         8 rKYRPqtFdEVIGQe~Vv~~L~~aL~~gRL~HAyLFtGPpGvGKTTlAriLAKaLnCe~~~~~~PCG~C~sCr~I~~G~h   87 (830)
T PRK07003          8 RKWRPKDFASLVGQEHVVRALTHALDGGRLHHAYLFTGTRGVGKTTLSRIFAKALNCETGVTSQPCGVCRACREIDEGRF   87 (830)
T ss_pred             HHhCCCcHHHHcCcHHHHHHHHHHHhcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCccCCCCCCCcccHHHHHHhcCCC
Confidence            79999999999999999999999999999999 899999999999999999999987421                   1


Q ss_pred             CceEEecCCCCcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcCch
Q psy879           62 DAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIE  141 (317)
Q Consensus        62 ~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~~  141 (317)
                      ..+++++..+.++++++++.+......+   ..++++|+||||+|.|+...+|+|+++||+++.+++||++|++..++++
T Consensus        88 ~DviEIDAas~rgVDdIReLIe~a~~~P---~~gr~KVIIIDEah~LT~~A~NALLKtLEEPP~~v~FILaTtd~~KIp~  164 (830)
T PRK07003         88 VDYVEMDAASNRGVDEMAALLERAVYAP---VDARFKVYMIDEVHMLTNHAFNAMLKTLEEPPPHVKFILATTDPQKIPV  164 (830)
T ss_pred             ceEEEecccccccHHHHHHHHHHHHhcc---ccCCceEEEEeChhhCCHHHHHHHHHHHHhcCCCeEEEEEECChhhccc
Confidence            2467788777788999999887765444   2368999999999999999999999999999999999999999999999


Q ss_pred             hHhhhcceeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhh-hCCCcccHHHHHhhcCCC
Q psy879          142 PIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTH-NGFGHVTAEYVFKVCDEP  220 (317)
Q Consensus       142 ~i~sR~~~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~-~~~~~i~~~~v~~~~~~~  220 (317)
                      +|+|||+.++|++++.+++.++|..++.++++.++++++..|++.++||+|.++++++.+. .+.+.|+.+.|..+++..
T Consensus       165 TIrSRCq~f~Fk~Ls~eeIv~~L~~Il~~EgI~id~eAL~lIA~~A~GsmRdALsLLdQAia~~~~~It~~~V~~~LG~~  244 (830)
T PRK07003        165 TVLSRCLQFNLKQMPAGHIVSHLERILGEERIAFEPQALRLLARAAQGSMRDALSLTDQAIAYSANEVTETAVSGMLGAL  244 (830)
T ss_pred             hhhhheEEEecCCcCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhccCCcCHHHHHHHhCCC
Confidence            9999999999999999999999999999999999999999999999999999999986544 456789999999999999


Q ss_pred             CHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhc-------------------------CCChHHH
Q psy879          221 HPLAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDIIGNIFRVAKTL-------------------------DIPEPLK  275 (317)
Q Consensus       221 ~~~~i~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~~~~-------------------------~~~~~~~  275 (317)
                      ....++++++.+..++...++.++.+|...|.+...++..+..++..+                         .++....
T Consensus       245 d~~~i~~ll~aL~~~d~~~~l~~~~~l~~~g~~~~~~l~dLl~~l~~~~~~q~~~~~~~~~~~e~~~~~~~a~~~s~~~l  324 (830)
T PRK07003        245 DQTYMVRLLDALAAGDGPEILAVADEMALRSLSFSTALQDLASLLHRIAWAQFAPASVLDEWPEAADLRRFAELLSPEQV  324 (830)
T ss_pred             CHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHhCccccccccchHHHHHHHHHhCCHHHH
Confidence            999999999999999999999999999999998876666543332211                         1222223


Q ss_pred             HHHHHHHHHHHhHHhcCCCcHHHHHHHHHHHHHhhcc
Q psy879          276 LSIIQEIGNVHLRISEGVNSLLQLSGLLARLCIVGSK  312 (317)
Q Consensus       276 ~~~~~~l~~~~~~l~~g~~~~l~le~~~~~~~~~~~~  312 (317)
                      ..+++++......++...++++++|+.+++++.....
T Consensus       325 ~~~~qi~l~g~~el~~ap~~~~~~Em~llr~l~~~p~  361 (830)
T PRK07003        325 QLFYQIATVGRGELGLAPDEYAGFTMTLLRMLAFEPA  361 (830)
T ss_pred             HHHHHHHHhHHHHhhcCCCHHHHHHHHHHHHhcCCCc
Confidence            3488999999999999999999999999999875543

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional

Probab=100.00  E-value=9.8e-48  Score=351.70  Aligned_cols=307  Identities=20%  Similarity=0.262  Sum_probs=268.9

Q ss_pred             cccCCCCCCcccCCHHHHHHHHHHHhcCCCce-EEEECCCCCCHHHHHHHHHHHHcCCCC-------------------C
Q psy879            2 EKYRPQTFSDIVGNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARILLGPSF-------------------K   61 (317)
Q Consensus         2 ~ky~P~~~~~~~g~~~~~~~l~~~l~~~~~~~-~ll~G~~G~GKt~la~~la~~l~~~~~-------------------~   61 (317)
                      +||||++|++++||+++++.|..++.+++++| |||+||+|+|||++|+.+|+.++|...                   .
T Consensus         8 ~kyRP~~f~divGq~~v~~~L~~~~~~~~l~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~~~pCg~C~~C~~i~~g~~   87 (509)
T PRK14958          8 RKWRPRCFQEVIGQAPVVRALSNALDQQYLHHAYLFTGTRGVGKTTISRILAKCLNCEKGVSANPCNDCENCREIDEGRF   87 (509)
T ss_pred             HHHCCCCHHHhcCCHHHHHHHHHHHHhCCCCeeEEEECCCCCCHHHHHHHHHHHhcCCCCCCcccCCCCHHHHHHhcCCC
Confidence            79999999999999999999999999999999 899999999999999999999987531                   1


Q ss_pred             CceEEecCCCCcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcCch
Q psy879           62 DAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIE  141 (317)
Q Consensus        62 ~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~~  141 (317)
                      ..++++++.+..+++++++.+..+...+   ..++++|+||||+|.|+.+++++|+++||+||++++||++|+++.++++
T Consensus        88 ~d~~eidaas~~~v~~iR~l~~~~~~~p---~~~~~kV~iIDE~~~ls~~a~naLLk~LEepp~~~~fIlattd~~kl~~  164 (509)
T PRK14958         88 PDLFEVDAASRTKVEDTRELLDNIPYAP---TKGRFKVYLIDEVHMLSGHSFNALLKTLEEPPSHVKFILATTDHHKLPV  164 (509)
T ss_pred             ceEEEEcccccCCHHHHHHHHHHHhhcc---ccCCcEEEEEEChHhcCHHHHHHHHHHHhccCCCeEEEEEECChHhchH
Confidence            2367788777789999999887766554   3378999999999999999999999999999999999999999999999


Q ss_pred             hHhhhcceeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhh-CCCcccHHHHHhhcCCC
Q psy879          142 PIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHN-GFGHVTAEYVFKVCDEP  220 (317)
Q Consensus       142 ~i~sR~~~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~-~~~~i~~~~v~~~~~~~  220 (317)
                      +|+|||..++|.+++.+++..++..+++++|+.++++++..++..++||+|.++++++.+.. +.+.|+.++|.++++..
T Consensus       165 tI~SRc~~~~f~~l~~~~i~~~l~~il~~egi~~~~~al~~ia~~s~GslR~al~lLdq~ia~~~~~It~~~V~~~lg~~  244 (509)
T PRK14958        165 TVLSRCLQFHLAQLPPLQIAAHCQHLLKEENVEFENAALDLLARAANGSVRDALSLLDQSIAYGNGKVLIADVKTMLGTI  244 (509)
T ss_pred             HHHHHhhhhhcCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCcHHHHHHHHHHHHhcCCCCcCHHHHHHHHCCC
Confidence            99999999999999999999999999999999999999999999999999999999976544 56789999999999999


Q ss_pred             CHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhc-----------------------CCChHHHHH
Q psy879          221 HPLAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDIIGNIFRVAKTL-----------------------DIPEPLKLS  277 (317)
Q Consensus       221 ~~~~i~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~~~~-----------------------~~~~~~~~~  277 (317)
                      .++.++++++++..++...++..+++|...|+++..++..+...+..+                       .++......
T Consensus       245 ~~~~i~~ll~al~~~d~~~~l~~~~~l~~~g~~~~~il~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  324 (509)
T PRK14958        245 EPLLLFDILEALAAKAGDRLLGCVTRLVEQGVDFSNALADLLSLLHQIAIIQTVPEALIENDSEQLRQLAKLLDREDVQL  324 (509)
T ss_pred             CHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHhhCccccccchHHHHHHHHHhCCHHHHHH
Confidence            999999999999999999999999999999999987777754432221                       111122223


Q ss_pred             HHHHHHHHHhHHhcCCCcHHHHHHHHHHHHHhhc
Q psy879          278 IIQEIGNVHLRISEGVNSLLQLSGLLARLCIVGS  311 (317)
Q Consensus       278 ~~~~l~~~~~~l~~g~~~~l~le~~~~~~~~~~~  311 (317)
                      +++........++...++++.+|+.+.+++.-.+
T Consensus       325 ~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~  358 (509)
T PRK14958        325 FYQIGLIGQRDLAYSPTPQTGFEMTLLRMLAFYP  358 (509)
T ss_pred             HHHHHHHHHHHhccCCChhHHHHHHHHHHHhcCC
Confidence            5666666778888888999999999999997554

>PRK14954 DNA polymerase III subunits gamma and tau; Provisional

Probab=100.00  E-value=1.5e-47  Score=355.22  Aligned_cols=306  Identities=21%  Similarity=0.282  Sum_probs=270.2

Q ss_pred             cccCCCCCCcccCCHHHHHHHHHHHhcCCCce-EEEECCCCCCHHHHHHHHHHHHcCCCCC-------------------
Q psy879            2 EKYRPQTFSDIVGNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARILLGPSFK-------------------   61 (317)
Q Consensus         2 ~ky~P~~~~~~~g~~~~~~~l~~~l~~~~~~~-~ll~G~~G~GKt~la~~la~~l~~~~~~-------------------   61 (317)
                      +||||++|++++||+++++.|+.++++|+.+| |||+||+|+||||+|+.+|+.+.|....                   
T Consensus         8 ~kyRP~~f~eivGQe~i~~~L~~~i~~~ri~ha~Lf~Gp~GvGKttlA~~lAk~L~c~~~~~~~~~~~~~~~~Cg~C~sC   87 (620)
T PRK14954          8 RKYRPSKFADITAQEHITHTIQNSLRMDRVGHGYIFSGLRGVGKTTAARVFAKAVNCQRMIDDPVYLQEVTEPCGECESC   87 (620)
T ss_pred             HHHCCCCHHHhcCcHHHHHHHHHHHHcCCCCeeEEEECCCCCCHHHHHHHHHHHhCCCCcCCccccccccCCCCccCHHH
Confidence            69999999999999999999999999999999 9999999999999999999999884310                   


Q ss_pred             --------CceEEecCCCCcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEe
Q psy879           62 --------DAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALAC  133 (317)
Q Consensus        62 --------~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~  133 (317)
                              ..+.++++....+++++++....+...++   .++++|+||||+|.|+..++++|+++||+|+++++||+++
T Consensus        88 ~~~~~g~~~n~~~~d~~s~~~vd~Ir~l~e~~~~~P~---~~~~KVvIIdEad~Lt~~a~naLLK~LEePp~~tv~IL~t  164 (620)
T PRK14954         88 RDFDAGTSLNISEFDAASNNSVDDIRQLRENVRYGPQ---KGRYRVYIIDEVHMLSTAAFNAFLKTLEEPPPHAIFIFAT  164 (620)
T ss_pred             HHHhccCCCCeEEecccccCCHHHHHHHHHHHHhhhh---cCCCEEEEEeChhhcCHHHHHHHHHHHhCCCCCeEEEEEe
Confidence                    12344544455678899988877765553   3789999999999999999999999999999999999999


Q ss_pred             cCCCcCchhHhhhcceeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhh------CCCc
Q psy879          134 NNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHN------GFGH  207 (317)
Q Consensus       134 ~~~~~l~~~i~sR~~~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~------~~~~  207 (317)
                      +...++.++|+|||+.++|.+++.+++..|+..+++++|+.+++++++.++..++||+|.++++++++..      ..+.
T Consensus       165 ~~~~kLl~TI~SRc~~vef~~l~~~ei~~~L~~i~~~egi~I~~eal~~La~~s~Gdlr~al~eLeKL~~y~~~~~~~~~  244 (620)
T PRK14954        165 TELHKIPATIASRCQRFNFKRIPLDEIQSQLQMICRAEGIQIDADALQLIARKAQGSMRDAQSILDQVIAFSVGSEAEKV  244 (620)
T ss_pred             CChhhhhHHHHhhceEEecCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhCCCHHHHHHHHHHHHHhccccccCCc
Confidence            9889999999999999999999999999999999999999999999999999999999999999997544      2568


Q ss_pred             ccHHHHHhhcCCCCHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhc---------C---------
Q psy879          208 VTAEYVFKVCDEPHPLAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDIIGNIFRVAKTL---------D---------  269 (317)
Q Consensus       208 i~~~~v~~~~~~~~~~~i~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~~~~---------~---------  269 (317)
                      |+.++|.+++....++.+|++++++..++..+++.++++|...|++|..|+..+.++++.+         +         
T Consensus       245 It~~~V~~lv~~~~e~~iF~L~dai~~~d~~~al~~l~~Ll~~ge~p~~iL~lL~~~fRdLL~vK~~~~~~l~~~~~~v~  324 (620)
T PRK14954        245 IAYQGVAELLNYIDDEQFFDVTDAIAENDAVKMLEVARFVIDNGYDEQDFLEKLIEHFRNFLVLYNLRSTRLIERPESVK  324 (620)
T ss_pred             cCHHHHHHHHcCCCHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHhccccccccCCHHHH
Confidence            9999999999999999999999999999999999999999999999999999876655433         1         


Q ss_pred             ---------CChHHHHHHHHHHHHHHhHHhcCCCcHHHHHHHHHHHHHhh
Q psy879          270 ---------IPEPLKLSIIQEIGNVHLRISEGVNSLLQLSGLLARLCIVG  310 (317)
Q Consensus       270 ---------~~~~~~~~~~~~l~~~~~~l~~g~~~~l~le~~~~~~~~~~  310 (317)
                               .+.....++++.+.++|.+|+++.|+++.+|.|+.++|...
T Consensus       325 ~~l~~qA~~fs~~~L~~~l~~l~e~d~~LKtn~n~~l~lEllLlkl~~~~  374 (620)
T PRK14954        325 ERYQQSAGGLTPAAVMQMTDFLMKTQGELKFQFEYQFRFELALLRLIELV  374 (620)
T ss_pred             HHHHHHHHhCCHHHHHHHHHHHHHHHHHHhhCCCcHHHHHHHHHHHHhcc
Confidence                     11112333799999999999998899999999999999865

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=100.00  E-value=2e-47  Score=358.16  Aligned_cols=305  Identities=19%  Similarity=0.277  Sum_probs=267.7

Q ss_pred             cccCCCCCCcccCCHHHHHHHHHHHhcCCCce-EEEECCCCCCHHHHHHHHHHHHcCCCC-------------------C
Q psy879            2 EKYRPQTFSDIVGNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARILLGPSF-------------------K   61 (317)
Q Consensus         2 ~ky~P~~~~~~~g~~~~~~~l~~~l~~~~~~~-~ll~G~~G~GKt~la~~la~~l~~~~~-------------------~   61 (317)
                      +||||++|++++||+++++.|++++.+|+++| |||+||+|+|||++|+++++.+.|...                   .
T Consensus         8 eKyRP~tFddIIGQe~Iv~~LknaI~~~rl~HAyLFtGPpGtGKTTLARiLAk~Lnce~~~~~~pCg~C~sC~~i~~g~~   87 (944)
T PRK14949          8 RKWRPATFEQMVGQSHVLHALTNALTQQRLHHAYLFTGTRGVGKTSLARLFAKGLNCEQGVTATPCGVCSSCVEIAQGRF   87 (944)
T ss_pred             HHhCCCCHHHhcCcHHHHHHHHHHHHhCCCCeEEEEECCCCCCHHHHHHHHHHhccCccCCCCCCCCCchHHHHHhcCCC
Confidence            69999999999999999999999999999999 799999999999999999999987521                   1


Q ss_pred             CceEEecCCCCcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcCch
Q psy879           62 DAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIE  141 (317)
Q Consensus        62 ~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~~  141 (317)
                      ..++++++.+..+++.+|+.+..+...+.   .++++|+||||+|.|+.+++++|+++||+|+.+++||++|+++.++++
T Consensus        88 ~DviEidAas~~kVDdIReLie~v~~~P~---~gk~KViIIDEAh~LT~eAqNALLKtLEEPP~~vrFILaTTe~~kLl~  164 (944)
T PRK14949         88 VDLIEVDAASRTKVDDTRELLDNVQYRPS---RGRFKVYLIDEVHMLSRSSFNALLKTLEEPPEHVKFLLATTDPQKLPV  164 (944)
T ss_pred             ceEEEeccccccCHHHHHHHHHHHHhhhh---cCCcEEEEEechHhcCHHHHHHHHHHHhccCCCeEEEEECCCchhchH
Confidence            12455666555788889988877655442   378999999999999999999999999999999999999999999999


Q ss_pred             hHhhhcceeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhh-hCCCcccHHHHHhhcCCC
Q psy879          142 PIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTH-NGFGHVTAEYVFKVCDEP  220 (317)
Q Consensus       142 ~i~sR~~~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~-~~~~~i~~~~v~~~~~~~  220 (317)
                      +|+|||+.++|++++.+++..+|..++..+++.++++++..|+..++|++|.++++++.+. .+.+.++.+.|..+++..
T Consensus       165 TIlSRCq~f~fkpLs~eEI~~~L~~il~~EgI~~edeAL~lIA~~S~Gd~R~ALnLLdQala~~~~~It~~~V~~llG~i  244 (944)
T PRK14949        165 TVLSRCLQFNLKSLTQDEIGTQLNHILTQEQLPFEAEALTLLAKAANGSMRDALSLTDQAIAFGGGQVMLTQVQTMLGSI  244 (944)
T ss_pred             HHHHhheEEeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhcCCcccHHHHHHHhCCC
Confidence            9999999999999999999999999999999999999999999999999999999997543 356789999999999888


Q ss_pred             CHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhc------------------------CCChHHHH
Q psy879          221 HPLAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDIIGNIFRVAKTL------------------------DIPEPLKL  276 (317)
Q Consensus       221 ~~~~i~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~~~~------------------------~~~~~~~~  276 (317)
                      ....+..+++.+..++...++.++..|+..|+++..|+..+...++.+                        .++.....
T Consensus       245 D~~~V~~llksI~~~D~~aaL~~l~~Ll~~G~D~~~ILr~Ll~~lRDill~k~~~~~~~l~i~~e~i~~~a~~~s~~~L~  324 (944)
T PRK14949        245 DEQHVIALLKALTDADIGVLMQTCAQVLAFGADAQEVLRSLLELLHQITLTQFAPAAAQQSLYSEQIRAFAEQLSPEQVQ  324 (944)
T ss_pred             CHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHhccchhhccchHHHHHHHHHhCCHHHHH
Confidence            888899999999999999999999999999999999998865543322                        11222234


Q ss_pred             HHHHHHHHHHhHHhcCCCcHHHHHHHHHHHHHh
Q psy879          277 SIIQEIGNVHLRISEGVNSLLQLSGLLARLCIV  309 (317)
Q Consensus       277 ~~~~~l~~~~~~l~~g~~~~l~le~~~~~~~~~  309 (317)
                      ++++.+.+...+|+.+.|+++.||+++++++..
T Consensus       325 ~~ie~l~~a~~~L~~n~n~rl~lE~~LLrl~~~  357 (944)
T PRK14949        325 LYYQILLTGRKDLPHAPDPKSGLEMALLRAVAF  357 (944)
T ss_pred             HHHHHHHHHHHHHhhCCChHHHHHHHHHHHHHc
Confidence            479999999999999999999999999999864

>PRK09111 DNA polymerase III subunits gamma and tau; Validated

Probab=100.00  E-value=3.4e-47  Score=352.50  Aligned_cols=306  Identities=25%  Similarity=0.371  Sum_probs=272.1

Q ss_pred             cccCCCCCCcccCCHHHHHHHHHHHhcCCCce-EEEECCCCCCHHHHHHHHHHHHcCCCCC-------------------
Q psy879            2 EKYRPQTFSDIVGNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARILLGPSFK-------------------   61 (317)
Q Consensus         2 ~ky~P~~~~~~~g~~~~~~~l~~~l~~~~~~~-~ll~G~~G~GKt~la~~la~~l~~~~~~-------------------   61 (317)
                      +||||++|++++||+++++.|..++..|+.+| +||+||+|+|||++|+.+|+.++|....                   
T Consensus        16 ~KyRP~~f~dliGq~~~v~~L~~~~~~gri~ha~L~~Gp~GvGKTt~Ar~lAk~L~c~~~~~~~~~~~~~cg~c~~C~~i   95 (598)
T PRK09111         16 RKYRPQTFDDLIGQEAMVRTLTNAFETGRIAQAFMLTGVRGVGKTTTARILARALNYEGPDGDGGPTIDLCGVGEHCQAI   95 (598)
T ss_pred             hhhCCCCHHHhcCcHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHhhCcCCccccCCCccccCcccHHHHHH
Confidence            79999999999999999999999999999998 9999999999999999999999875321                   


Q ss_pred             -----CceEEecCCCCcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCC
Q psy879           62 -----DAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNS  136 (317)
Q Consensus        62 -----~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~  136 (317)
                           ..++++++.+..+++++++.+......++   .++++||||||+|.|+..++++|+++||+|+++++|||+|+..
T Consensus        96 ~~g~h~Dv~e~~a~s~~gvd~IReIie~~~~~P~---~a~~KVvIIDEad~Ls~~a~naLLKtLEePp~~~~fIl~tte~  172 (598)
T PRK09111         96 MEGRHVDVLEMDAASHTGVDDIREIIESVRYRPV---SARYKVYIIDEVHMLSTAAFNALLKTLEEPPPHVKFIFATTEI  172 (598)
T ss_pred             hcCCCCceEEecccccCCHHHHHHHHHHHHhchh---cCCcEEEEEEChHhCCHHHHHHHHHHHHhCCCCeEEEEEeCCh
Confidence                 13456666666789999998877665553   3789999999999999999999999999999999999999999


Q ss_pred             CcCchhHhhhcceeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhh-CCCcccHHHHHh
Q psy879          137 EKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHN-GFGHVTAEYVFK  215 (317)
Q Consensus       137 ~~l~~~i~sR~~~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~-~~~~i~~~~v~~  215 (317)
                      .+++++|+|||+.++|.+++++++..|+..+++++|+.+++++++.++..++||+|.++++++++.. +.+.|+.++|.+
T Consensus       173 ~kll~tI~SRcq~~~f~~l~~~el~~~L~~i~~kegi~i~~eAl~lIa~~a~Gdlr~al~~Ldkli~~g~g~It~e~V~~  252 (598)
T PRK09111        173 RKVPVTVLSRCQRFDLRRIEADVLAAHLSRIAAKEGVEVEDEALALIARAAEGSVRDGLSLLDQAIAHGAGEVTAEAVRD  252 (598)
T ss_pred             hhhhHHHHhheeEEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHhhcCCCcCHHHHHH
Confidence            9999999999999999999999999999999999999999999999999999999999999987543 556899999999


Q ss_pred             hcCCCCHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhc-------------CC------------
Q psy879          216 VCDEPHPLAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDIIGNIFRVAKTL-------------DI------------  270 (317)
Q Consensus       216 ~~~~~~~~~i~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~~~~-------------~~------------  270 (317)
                      +++......++++++++..++...++.++.+++..|.+|..++..+.++++.+             ++            
T Consensus       253 llg~~~~~~if~L~~ai~~gd~~~Al~~l~~l~~~G~~p~~il~~L~~~~r~L~~vK~~~~~a~~~~~~p~~~~kl~~~A  332 (598)
T PRK09111        253 MLGLADRARVIDLFEALMRGDVAAALAEFRAQYDAGADPVVVLTDLAEFTHLVTRLKIVPDAAEDPSLSEAERTRGAEFA  332 (598)
T ss_pred             HhCCCCHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHhccchhhcccCCHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999988876544321             12            


Q ss_pred             ---ChHHHHHHHHHHHHHHhHHhcCCCcHHHHHHHHHHHHHhh
Q psy879          271 ---PEPLKLSIIQEIGNVHLRISEGVNSLLQLSGLLARLCIVG  310 (317)
Q Consensus       271 ---~~~~~~~~~~~l~~~~~~l~~g~~~~l~le~~~~~~~~~~  310 (317)
                         +.....++++.+.+.+..++++.|+++++|+++.++|...
T Consensus       333 ~~~s~~~L~r~~q~Ll~~~~~vK~~~n~~lalE~lLlrl~~~~  375 (598)
T PRK09111        333 KKLSMRVLSRLWQMLLKGIEEVQGAPRPLAAAEMVLIRLAYAA  375 (598)
T ss_pred             hcCCHHHHHHHHHHHHHHHHHhccCCCcHHHHHHHHHHHHhhc
Confidence               2223445999999999999999999999999999998643

>PRK05563 DNA polymerase III subunits gamma and tau; Validated

Probab=100.00  E-value=4.1e-47  Score=352.16  Aligned_cols=304  Identities=27%  Similarity=0.419  Sum_probs=272.3

Q ss_pred             cccCCCCCCcccCCHHHHHHHHHHHhcCCCce-EEEECCCCCCHHHHHHHHHHHHcCCCC-------------------C
Q psy879            2 EKYRPQTFSDIVGNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARILLGPSF-------------------K   61 (317)
Q Consensus         2 ~ky~P~~~~~~~g~~~~~~~l~~~l~~~~~~~-~ll~G~~G~GKt~la~~la~~l~~~~~-------------------~   61 (317)
                      +||||++|++++||+++.+.|..++.+++++| |||+||+|+|||++|+.+++.+.|...                   .
T Consensus         8 ~k~rP~~f~~viGq~~v~~~L~~~i~~~~~~hayLf~Gp~GtGKTt~Ak~lAkal~c~~~~~~~pC~~C~~C~~i~~g~~   87 (559)
T PRK05563          8 RKWRPQTFEDVVGQEHITKTLKNAIKQGKISHAYLFSGPRGTGKTSAAKIFAKAVNCLNPPDGEPCNECEICKAITNGSL   87 (559)
T ss_pred             HHhCCCcHHhccCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCccHHHHHHhcCCC
Confidence            68999999999999999999999999999999 999999999999999999999987542                   2


Q ss_pred             CceEEecCCCCcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcCch
Q psy879           62 DAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIE  141 (317)
Q Consensus        62 ~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~~  141 (317)
                      ..++++++.+..+.+++++........+.   .++++|+||||+|.|+..++++|++++|+||.+++||++|+.+.++++
T Consensus        88 ~dv~eidaas~~~vd~ir~i~~~v~~~p~---~~~~kViIIDE~~~Lt~~a~naLLKtLEepp~~~ifIlatt~~~ki~~  164 (559)
T PRK05563         88 MDVIEIDAASNNGVDEIRDIRDKVKYAPS---EAKYKVYIIDEVHMLSTGAFNALLKTLEEPPAHVIFILATTEPHKIPA  164 (559)
T ss_pred             CCeEEeeccccCCHHHHHHHHHHHhhCcc---cCCeEEEEEECcccCCHHHHHHHHHHhcCCCCCeEEEEEeCChhhCcH
Confidence            34667777667888889888777665543   378999999999999999999999999999999999999999999999


Q ss_pred             hHhhhcceeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhh-CCCcccHHHHHhhcCCC
Q psy879          142 PIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHN-GFGHVTAEYVFKVCDEP  220 (317)
Q Consensus       142 ~i~sR~~~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~-~~~~i~~~~v~~~~~~~  220 (317)
                      +|+|||+.+.|++++.+++..|+..+++++|+.++++++..++..++||+|.+++.|+.+.. +.+.|+.++|.++++..
T Consensus       165 tI~SRc~~~~f~~~~~~ei~~~L~~i~~~egi~i~~~al~~ia~~s~G~~R~al~~Ldq~~~~~~~~It~~~V~~vlg~~  244 (559)
T PRK05563        165 TILSRCQRFDFKRISVEDIVERLKYILDKEGIEYEDEALRLIARAAEGGMRDALSILDQAISFGDGKVTYEDALEVTGSV  244 (559)
T ss_pred             HHHhHheEEecCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhccCCCCHHHHHHHhCCC
Confidence            99999999999999999999999999999999999999999999999999999999987644 46679999999999999


Q ss_pred             CHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhc---------------------------CCChH
Q psy879          221 HPLAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDIIGNIFRVAKTL---------------------------DIPEP  273 (317)
Q Consensus       221 ~~~~i~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~~~~---------------------------~~~~~  273 (317)
                      ..+.++++++++..+|...++.++.++...|.++..++..+.++++.+                           .++..
T Consensus       245 ~~~~i~~l~~al~~~d~~~al~~l~~l~~~g~d~~~~l~~L~~~~Rdll~~k~~~~~~~~~~~~~~~~~~~~~a~~~s~~  324 (559)
T PRK05563        245 SQEALDDLVDAIVEGDVAKALKILEELLDEGKDPNRFIEDLIYYLRDLLLVKTSPELEILDESTENDELFKELSEKLDIE  324 (559)
T ss_pred             CHHHHHHHHHHHHccCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHhhcCcccccccCHHHHHHHHHHHHhCCHH
Confidence            999999999999999999999999999999999998887765543322                           12233


Q ss_pred             HHHHHHHHHHHHHhHHhcCCCcHHHHHHHHHHHHH
Q psy879          274 LKLSIIQEIGNVHLRISEGVNSLLQLSGLLARLCI  308 (317)
Q Consensus       274 ~~~~~~~~l~~~~~~l~~g~~~~l~le~~~~~~~~  308 (317)
                      ...++++.+.+++.+++.|.++++.+|.++.++|.
T Consensus       325 ~L~~~i~~L~~~~~~lk~~~~~~l~lE~lllkl~~  359 (559)
T PRK05563        325 RLYRMIDILNDAQQQIKWTNQPRIYLEVALVKLCE  359 (559)
T ss_pred             HHHHHHHHHHHHHHHHhhCCChHHHHHHHHHHHHh
Confidence            35558999999999999999999999999999997

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=100.00  E-value=1.8e-46  Score=330.58  Aligned_cols=310  Identities=46%  Similarity=0.771  Sum_probs=278.0

Q ss_pred             CcccCCCCCCcccCCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHH
Q psy879            1 IEKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRN   80 (317)
Q Consensus         1 ~~ky~P~~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~   80 (317)
                      +|||||++|++++|++++++.+..+++.+..||++|+||||+|||++++++++.+.+..+...++++++++..+.+.+++
T Consensus         8 ~~kyrP~~~~~~~g~~~~~~~l~~~i~~~~~~~~ll~G~~G~GKt~~~~~l~~~l~~~~~~~~~i~~~~~~~~~~~~~~~   87 (319)
T PRK00440          8 VEKYRPRTLDEIVGQEEIVERLKSYVKEKNMPHLLFAGPPGTGKTTAALALARELYGEDWRENFLELNASDERGIDVIRN   87 (319)
T ss_pred             chhhCCCcHHHhcCcHHHHHHHHHHHhCCCCCeEEEECCCCCCHHHHHHHHHHHHcCCccccceEEeccccccchHHHHH
Confidence            48999999999999999999999999999999999999999999999999999998776666677887766555555555


Q ss_pred             HHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcCchhHhhhcceeeecCCCHHHH
Q psy879           81 KIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQL  160 (317)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~~~i~sR~~~i~f~~~~~~~~  160 (317)
                      .+..+..... ...+.+++|+|||+|.+..+.++.|+++++.+++++.+|++++...++.+++++||..++|++++++++
T Consensus        88 ~i~~~~~~~~-~~~~~~~vviiDe~~~l~~~~~~~L~~~le~~~~~~~lIl~~~~~~~l~~~l~sr~~~~~~~~l~~~ei  166 (319)
T PRK00440         88 KIKEFARTAP-VGGAPFKIIFLDEADNLTSDAQQALRRTMEMYSQNTRFILSCNYSSKIIDPIQSRCAVFRFSPLKKEAV  166 (319)
T ss_pred             HHHHHHhcCC-CCCCCceEEEEeCcccCCHHHHHHHHHHHhcCCCCCeEEEEeCCccccchhHHHHhheeeeCCCCHHHH
Confidence            5555443321 112468899999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhhCCCcccHHHHHhhcCCCCHHHHHHHHHHHhcCCHHHH
Q psy879          161 LSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEMLLNCVEGNMKDS  240 (317)
Q Consensus       161 ~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~~~~~i~~~~v~~~~~~~~~~~i~~l~~~~~~~~~~~~  240 (317)
                      ..++..++.++|+.+++++++.++..++||+|.+++.++.++...+.|+.++|.+++....++.++++++++..++..++
T Consensus       167 ~~~l~~~~~~~~~~i~~~al~~l~~~~~gd~r~~~~~l~~~~~~~~~it~~~v~~~~~~~~~~~i~~l~~~~~~~~~~~a  246 (319)
T PRK00440        167 AERLRYIAENEGIEITDDALEAIYYVSEGDMRKAINALQAAAATGKEVTEEAVYKITGTARPEEIREMIELALNGDFTEA  246 (319)
T ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCCHHHHHHHHHHHHcCCHHHH
Confidence            99999999999999999999999999999999999999988777678999999999999999999999999999999999


Q ss_pred             HHHHHHHH-HcCCCHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHHHhHHhcCCCcHHHHHHHHHHHHHhhc
Q psy879          241 YKIIHHLY-KLGYAPEDIIGNIFRVAKTLDIPEPLKLSIIQEIGNVHLRISEGVNSLLQLSGLLARLCIVGS  311 (317)
Q Consensus       241 ~~~~~~l~-~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~g~~~~l~le~~~~~~~~~~~  311 (317)
                      +.++++|+ ..|+++..|+..+...+...+.++....++++++.++|+++++|.|+.++||.|++++|.+..
T Consensus       247 ~~~l~~ll~~~g~~~~~i~~~l~~~~~~~~~~~~~l~~~~~~~~~~d~~~k~g~~~~~~le~~i~~~~~~~~  318 (319)
T PRK00440        247 REKLRDLMIDYGLSGEDIIKQIHREVWSLDIPEELKVELIDAIGEADFRITEGANERIQLEALLAKLALLGK  318 (319)
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHhcc
Confidence            99999997 589999999988876554447889999999999999999999999999999999999997754

>PRK14971 DNA polymerase III subunits gamma and tau; Provisional

Probab=100.00  E-value=7e-47  Score=352.80  Aligned_cols=306  Identities=24%  Similarity=0.360  Sum_probs=270.8

Q ss_pred             cccCCCCCCcccCCHHHHHHHHHHHhcCCCce-EEEECCCCCCHHHHHHHHHHHHcCCCC--------------------
Q psy879            2 EKYRPQTFSDIVGNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARILLGPSF--------------------   60 (317)
Q Consensus         2 ~ky~P~~~~~~~g~~~~~~~l~~~l~~~~~~~-~ll~G~~G~GKt~la~~la~~l~~~~~--------------------   60 (317)
                      +||||++|++++||+++++.|..++++|+++| ||||||+|+|||++|+.+++.+.|...                    
T Consensus         9 ~kyRP~~f~~viGq~~~~~~L~~~i~~~~l~hayLf~Gp~G~GKtt~A~~lAk~l~c~~~~~~~~~Cg~C~sC~~~~~~~   88 (614)
T PRK14971          9 RKYRPSTFESVVGQEALTTTLKNAIATNKLAHAYLFCGPRGVGKTTCARIFAKTINCQNLTADGEACNECESCVAFNEQR   88 (614)
T ss_pred             HHHCCCCHHHhcCcHHHHHHHHHHHHcCCCCeeEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCCCCcchHHHHHhcCC
Confidence            79999999999999999999999999999999 999999999999999999999986421                    


Q ss_pred             CCceEEecCCCCcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcCc
Q psy879           61 KDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKII  140 (317)
Q Consensus        61 ~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~  140 (317)
                      ...+.++++.+..+.+++++.+..+...++   .++++|+||||++.|+.+++++|+++||+||++++||++|+...++.
T Consensus        89 ~~n~~~ld~~~~~~vd~Ir~li~~~~~~P~---~~~~KVvIIdea~~Ls~~a~naLLK~LEepp~~tifIL~tt~~~kIl  165 (614)
T PRK14971         89 SYNIHELDAASNNSVDDIRNLIEQVRIPPQ---IGKYKIYIIDEVHMLSQAAFNAFLKTLEEPPSYAIFILATTEKHKIL  165 (614)
T ss_pred             CCceEEecccccCCHHHHHHHHHHHhhCcc---cCCcEEEEEECcccCCHHHHHHHHHHHhCCCCCeEEEEEeCCchhch
Confidence            234566666656678889888876655553   37899999999999999999999999999999999999999999999


Q ss_pred             hhHhhhcceeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhh-CCCcccHHHHHhhcCC
Q psy879          141 EPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHN-GFGHVTAEYVFKVCDE  219 (317)
Q Consensus       141 ~~i~sR~~~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~-~~~~i~~~~v~~~~~~  219 (317)
                      ++|+|||+.++|.+++++++..|+..++.++|+.+++++++.++..++||+|.+++++++.+. ..+.|+.++|.+.+..
T Consensus       166 ~tI~SRc~iv~f~~ls~~ei~~~L~~ia~~egi~i~~~al~~La~~s~gdlr~al~~Lekl~~y~~~~It~~~V~~~l~~  245 (614)
T PRK14971        166 PTILSRCQIFDFNRIQVADIVNHLQYVASKEGITAEPEALNVIAQKADGGMRDALSIFDQVVSFTGGNITYKSVIENLNI  245 (614)
T ss_pred             HHHHhhhheeecCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhccCCccHHHHHHHhCC
Confidence            999999999999999999999999999999999999999999999999999999999988543 3344999999999999


Q ss_pred             CCHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhc---------------------------CCCh
Q psy879          220 PHPLAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDIIGNIFRVAKTL---------------------------DIPE  272 (317)
Q Consensus       220 ~~~~~i~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~~~~---------------------------~~~~  272 (317)
                      ...+.+|++++++..++...++..+++|+..|+++..|+..+.++++.+                           ..+.
T Consensus       246 ~~~~~iF~L~dai~~~~~~~al~ll~~Ll~~g~~~~~iL~~L~~~fRdlL~~K~~~~~~ll~v~~~~~~~~~~qa~~~s~  325 (614)
T PRK14971        246 LDYDYYFRLTDALLAGKVSDSLLLFDEILNKGFDGSHFITGLASHFRDLLVCKDAATLQLLEVGESIRQRYLEQAQKCPM  325 (614)
T ss_pred             CCHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHhhcccccccccCCHHHHHHHHHHHHhCCH
Confidence            9999999999999999999999999999999999999998876654433                           1112


Q ss_pred             HHHHHHHHHHHHHHhHHhcCCCcHHHHHHHHHHHHHhh
Q psy879          273 PLKLSIIQEIGNVHLRISEGVNSLLQLSGLLARLCIVG  310 (317)
Q Consensus       273 ~~~~~~~~~l~~~~~~l~~g~~~~l~le~~~~~~~~~~  310 (317)
                      ....++++.+.++|+++++|.|+++.+|.|+.++|...
T Consensus       326 ~~L~~~l~~l~e~d~~lK~~~n~~l~lE~lllkL~~~~  363 (614)
T PRK14971        326 SFLYRALKLCNQCDLNYRASKNKRLLVELTLIQLAQLT  363 (614)
T ss_pred             HHHHHHHHHHHHHHHHHHcCCChHHHHHHHHHHHhccC
Confidence            22344899999999999999999999999999999864

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=100.00  E-value=5.8e-47  Score=344.90  Aligned_cols=307  Identities=21%  Similarity=0.278  Sum_probs=269.2

Q ss_pred             cccCCCCCCcccCCHHHHHHHHHHHhcCCCce-EEEECCCCCCHHHHHHHHHHHHcCCCC--------------------
Q psy879            2 EKYRPQTFSDIVGNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARILLGPSF--------------------   60 (317)
Q Consensus         2 ~ky~P~~~~~~~g~~~~~~~l~~~l~~~~~~~-~ll~G~~G~GKt~la~~la~~l~~~~~--------------------   60 (317)
                      +||||++|++++||+++++.|.+++.+|+++| |||+||+|+||||+++.+++.++|...                    
T Consensus         8 rKYRPqtFddVIGQe~vv~~L~~al~~gRLpHA~LFtGP~GvGKTTLAriLAkaLnC~~p~~~~g~~~~PCG~C~sC~~I   87 (700)
T PRK12323          8 RKWRPRDFTTLVGQEHVVRALTHALEQQRLHHAYLFTGTRGVGKTTLSRILAKSLNCTGADGEGGITAQPCGQCRACTEI   87 (700)
T ss_pred             HHhCCCcHHHHcCcHHHHHHHHHHHHhCCCceEEEEECCCCCCHHHHHHHHHHHhcCCCccccccCCCCCCcccHHHHHH
Confidence            69999999999999999999999999999999 899999999999999999999988321                    


Q ss_pred             ----CCceEEecCCCCcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCC
Q psy879           61 ----KDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNS  136 (317)
Q Consensus        61 ----~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~  136 (317)
                          ...+++++..+..+++++++.+......+   ..++++|+||||+|.|+...+|+||++||+|+.++.||++|+++
T Consensus        88 ~aG~hpDviEIdAas~~gVDdIReLie~~~~~P---~~gr~KViIIDEah~Ls~~AaNALLKTLEEPP~~v~FILaTtep  164 (700)
T PRK12323         88 DAGRFVDYIEMDAASNRGVDEMAQLLDKAVYAP---TAGRFKVYMIDEVHMLTNHAFNAMLKTLEEPPEHVKFILATTDP  164 (700)
T ss_pred             HcCCCCcceEecccccCCHHHHHHHHHHHHhch---hcCCceEEEEEChHhcCHHHHHHHHHhhccCCCCceEEEEeCCh
Confidence                01466777777788999999888766554   23789999999999999999999999999999999999999999


Q ss_pred             CcCchhHhhhcceeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHH-hhhCCCcccHHHHHh
Q psy879          137 EKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQS-THNGFGHVTAEYVFK  215 (317)
Q Consensus       137 ~~l~~~i~sR~~~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~-~~~~~~~i~~~~v~~  215 (317)
                      .+++++|+|||+.++|++++.+++.++|..++.++++.+++++++.++..++|++|.++++++. +..+.+.|+.+.|.+
T Consensus       165 ~kLlpTIrSRCq~f~f~~ls~eei~~~L~~Il~~Egi~~d~eAL~~IA~~A~Gs~RdALsLLdQaia~~~~~It~~~V~~  244 (700)
T PRK12323        165 QKIPVTVLSRCLQFNLKQMPPGHIVSHLDAILGEEGIAHEVNALRLLAQAAQGSMRDALSLTDQAIAYSAGNVSEEAVRG  244 (700)
T ss_pred             HhhhhHHHHHHHhcccCCCChHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhccCCcCHHHHHH
Confidence            9999999999999999999999999999999999999999999999999999999999999975 334567899999999


Q ss_pred             hcCCCCHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhc-------------------------CC
Q psy879          216 VCDEPHPLAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDIIGNIFRVAKTL-------------------------DI  270 (317)
Q Consensus       216 ~~~~~~~~~i~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~~~~-------------------------~~  270 (317)
                      +++....+.+.++++.+..++...++.++..+...|.++..++..+...+..+                         .+
T Consensus       245 ~LG~~d~~~i~~Ll~aL~~~d~~~~l~l~~~l~~~G~d~~~~L~dLl~~l~~l~l~q~~~~~~~~~~~~~~~~~~~a~~~  324 (700)
T PRK12323        245 MLGAIDQSYLVRLLDALAAEDGAALLAIADEMAGRSLSFAGALQDLASLLQKIALAQVVPAAVQDDWPEADDIRRLAGRF  324 (700)
T ss_pred             HhCCCCHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHhhCchhcccccchHHHHHHHHHhC
Confidence            99999988999999999999999999999999999999766665543222111                         12


Q ss_pred             ChHHHHHHHHHHHHHHhHHhcCCCcHHHHHHHHHHHHHhhc
Q psy879          271 PEPLKLSIIQEIGNVHLRISEGVNSLLQLSGLLARLCIVGS  311 (317)
Q Consensus       271 ~~~~~~~~~~~l~~~~~~l~~g~~~~l~le~~~~~~~~~~~  311 (317)
                      +......+++.+......++...++++++|+.+++++....
T Consensus       325 s~~~l~~~~q~~~~~~~el~~a~~~~~~~Em~llrll~~~p  365 (700)
T PRK12323        325 DAQEVQLFYQIANLGRSELALAPDEYAGFTMTLLRMLAFRP  365 (700)
T ss_pred             CHHHHHHHHHHHHHHHHHhccCCCHHHHHHHHHHHHhhCCC
Confidence            33334458899999999999999999999999999997654

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=100.00  E-value=1.2e-46  Score=342.15  Aligned_cols=307  Identities=22%  Similarity=0.323  Sum_probs=269.8

Q ss_pred             cccCCCCCCcccCCHHHHHHHHHHHhcCCCce-EEEECCCCCCHHHHHHHHHHHHcCCCC--------------------
Q psy879            2 EKYRPQTFSDIVGNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARILLGPSF--------------------   60 (317)
Q Consensus         2 ~ky~P~~~~~~~g~~~~~~~l~~~l~~~~~~~-~ll~G~~G~GKt~la~~la~~l~~~~~--------------------   60 (317)
                      +||||++|++++||+++++.|..++.+++.+| ++|+||+|+||||+|+.+|+.+.|...                    
T Consensus        13 ~kyRP~~f~dliGq~~vv~~L~~ai~~~ri~~a~Lf~Gp~G~GKTT~ArilAk~Lnc~~~~~~~~~~~~C~~C~~C~~i~   92 (507)
T PRK06645         13 RKYRPSNFAELQGQEVLVKVLSYTILNDRLAGGYLLTGIRGVGKTTSARIIAKAVNCSALITENTTIKTCEQCTNCISFN   92 (507)
T ss_pred             hhhCCCCHHHhcCcHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHHhcCccccccCcCcCCCCCChHHHHHh
Confidence            69999999999999999999999999999887 999999999999999999999987431                    


Q ss_pred             ---CCceEEecCCCCcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCC
Q psy879           61 ---KDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSE  137 (317)
Q Consensus        61 ---~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~  137 (317)
                         ...++++++.+..+++++++.+......++   .++++|+||||++.++..++++|++++|+|+++++||++|+...
T Consensus        93 ~~~h~Dv~eidaas~~~vd~Ir~iie~a~~~P~---~~~~KVvIIDEa~~Ls~~a~naLLk~LEepp~~~vfI~aTte~~  169 (507)
T PRK06645         93 NHNHPDIIEIDAASKTSVDDIRRIIESAEYKPL---QGKHKIFIIDEVHMLSKGAFNALLKTLEEPPPHIIFIFATTEVQ  169 (507)
T ss_pred             cCCCCcEEEeeccCCCCHHHHHHHHHHHHhccc---cCCcEEEEEEChhhcCHHHHHHHHHHHhhcCCCEEEEEEeCChH
Confidence               124566777667889999998877665553   37899999999999999999999999999999999999999999


Q ss_pred             cCchhHhhhcceeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhh-C---CCcccHHHH
Q psy879          138 KIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHN-G---FGHVTAEYV  213 (317)
Q Consensus       138 ~l~~~i~sR~~~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~-~---~~~i~~~~v  213 (317)
                      +++++++|||+.++|++++.+++..|+..+++++|+.+++++++.++..++||+|.++++|++++. .   .+.|+.++|
T Consensus       170 kI~~tI~SRc~~~ef~~ls~~el~~~L~~i~~~egi~ie~eAL~~Ia~~s~GslR~al~~Ldkai~~~~~~~~~It~~~V  249 (507)
T PRK06645        170 KIPATIISRCQRYDLRRLSFEEIFKLLEYITKQENLKTDIEALRIIAYKSEGSARDAVSILDQAASMSAKSDNIISPQVI  249 (507)
T ss_pred             HhhHHHHhcceEEEccCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhhccCCCCcCHHHH
Confidence            999999999999999999999999999999999999999999999999999999999999998744 2   347999999


Q ss_pred             HhhcCCCCHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhc-------C-----------------
Q psy879          214 FKVCDEPHPLAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDIIGNIFRVAKTL-------D-----------------  269 (317)
Q Consensus       214 ~~~~~~~~~~~i~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~~~~-------~-----------------  269 (317)
                      .++++...++.++++++++..++...++.++++|+..|++|..++..+..+++.+       +                 
T Consensus       250 ~~llg~~~~~~if~L~~ai~~~d~~~Al~~l~~L~~~g~~~~~~l~~l~~~~~~l~~~k~~~~~~~~~~~~~~~~~~~~~  329 (507)
T PRK06645        250 NQMLGLVDSSVIIEFVEYIIHRETEKAINLINKLYGSSVNLEIFIESVSDFIAYLNKVKMLPNYSLPIYESFNDRTKSIL  329 (507)
T ss_pred             HHHHCCCCHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHhccccccccchhHHHHHHHHH
Confidence            9999999999999999999999999999999999999999999877654332211       1                 


Q ss_pred             --CChHHHHHHHHHHHHHHhHHhcCCCcHHHHHHHHHHHHHhhc
Q psy879          270 --IPEPLKLSIIQEIGNVHLRISEGVNSLLQLSGLLARLCIVGS  311 (317)
Q Consensus       270 --~~~~~~~~~~~~l~~~~~~l~~g~~~~l~le~~~~~~~~~~~  311 (317)
                        ++.....++++.+.+....++...++++++|+++.++|....
T Consensus       330 ~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~e~~l~r~~~~~~  373 (507)
T PRK06645        330 DKISLPHLSILWQIYNKGVGEIKISYNQLTETEMLVIKSIYSTS  373 (507)
T ss_pred             HhCCHHHHHHHHHHHHHHHHHhccCCCchHHHHHHHHHHHHhcc
Confidence              111223348889999999999999999999999999987543

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=100.00  E-value=9.7e-47  Score=344.27  Aligned_cols=309  Identities=20%  Similarity=0.264  Sum_probs=270.5

Q ss_pred             CcccCCCCCCcccCCHHHHHHHHHHHhcCCCce-EEEECCCCCCHHHHHHHHHHHHcCCCC-------------------
Q psy879            1 IEKYRPQTFSDIVGNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARILLGPSF-------------------   60 (317)
Q Consensus         1 ~~ky~P~~~~~~~g~~~~~~~l~~~l~~~~~~~-~ll~G~~G~GKt~la~~la~~l~~~~~-------------------   60 (317)
                      .+||||++|++++||+++.+.|..++.+|+++| |||+||+|+|||++|+++|+.+.|...                   
T Consensus         6 arKyRPktFddVIGQe~vv~~L~~aI~~grl~HAyLF~GPpGvGKTTlAriLAK~LnC~~~~~~~pCg~C~sC~~I~~g~   85 (702)
T PRK14960          6 ARKYRPRNFNELVGQNHVSRALSSALERGRLHHAYLFTGTRGVGKTTIARILAKCLNCETGVTSTPCEVCATCKAVNEGR   85 (702)
T ss_pred             HHHhCCCCHHHhcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhCCCcCCCCCCCccCHHHHHHhcCC
Confidence            379999999999999999999999999999988 899999999999999999999987421                   


Q ss_pred             CCceEEecCCCCcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcCc
Q psy879           61 KDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKII  140 (317)
Q Consensus        61 ~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~  140 (317)
                      ...++++++.+..+++++|+.+......+.   .++++|+||||+|.|+..++++|++++|++++++.||++|+++.+++
T Consensus        86 hpDviEIDAAs~~~VddIReli~~~~y~P~---~gk~KV~IIDEVh~LS~~A~NALLKtLEEPP~~v~FILaTtd~~kIp  162 (702)
T PRK14960         86 FIDLIEIDAASRTKVEDTRELLDNVPYAPT---QGRFKVYLIDEVHMLSTHSFNALLKTLEEPPEHVKFLFATTDPQKLP  162 (702)
T ss_pred             CCceEEecccccCCHHHHHHHHHHHhhhhh---cCCcEEEEEechHhcCHHHHHHHHHHHhcCCCCcEEEEEECChHhhh
Confidence            124677777767788999988876655542   36889999999999999999999999999999999999999999999


Q ss_pred             hhHhhhcceeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhh-hCCCcccHHHHHhhcCC
Q psy879          141 EPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTH-NGFGHVTAEYVFKVCDE  219 (317)
Q Consensus       141 ~~i~sR~~~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~-~~~~~i~~~~v~~~~~~  219 (317)
                      ++++|||..++|.+++.+++.++|..++.++|+.++++++..++..++||+|.++++++.+. .+.+.|+.++|..+++.
T Consensus       163 ~TIlSRCq~feFkpLs~eEI~k~L~~Il~kEgI~id~eAL~~IA~~S~GdLRdALnLLDQaIayg~g~IT~edV~~lLG~  242 (702)
T PRK14960        163 ITVISRCLQFTLRPLAVDEITKHLGAILEKEQIAADQDAIWQIAESAQGSLRDALSLTDQAIAYGQGAVHHQDVKEMLGL  242 (702)
T ss_pred             HHHHHhhheeeccCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhcCCCcCHHHHHHHhcc
Confidence            99999999999999999999999999999999999999999999999999999999997644 36678999999999999


Q ss_pred             CCHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhc--------------------------CCChH
Q psy879          220 PHPLAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDIIGNIFRVAKTL--------------------------DIPEP  273 (317)
Q Consensus       220 ~~~~~i~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~~~~--------------------------~~~~~  273 (317)
                      ...+.++++++++..++...++.++.++...|.++..++..+...++.+                          .++..
T Consensus       243 ~d~e~IfdLldAI~k~d~~~al~~L~el~~~g~d~~~~l~~Ll~~lrdlll~~~~~~~~~~~~~~~~~~~~~la~~~s~~  322 (702)
T PRK14960        243 IDRTIIYDLILAVHQNQREKVSQLLLQFRYQALDVSLVLDQLISTLHELALLQYLPELGLKYSEEINAKILQLSKLISAQ  322 (702)
T ss_pred             CCHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHhcccccccccHHHHHHHHHHHHcCCHH
Confidence            9999999999999999999999999999999999987777654332211                          12222


Q ss_pred             HHHHHHHHHHHHHhHHhcCCCcHHHHHHHHHHHHHhhcc
Q psy879          274 LKLSIIQEIGNVHLRISEGVNSLLQLSGLLARLCIVGSK  312 (317)
Q Consensus       274 ~~~~~~~~l~~~~~~l~~g~~~~l~le~~~~~~~~~~~~  312 (317)
                      ....+++.+......++...++++++|+++.+++...+.
T Consensus       323 ~l~~~~qi~l~~~~~l~~s~~~r~~lEm~llrl~~~~p~  361 (702)
T PRK14960        323 DLQLYYQIACKGRSDLQLAVTQEQGFEMCVLRLLAFRPL  361 (702)
T ss_pred             HHHHHHHHHHHHHHHhccCCChhHHHHHHHHHHHhCCCC
Confidence            334488888899999999999999999999999976543

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=100.00  E-value=1.4e-46  Score=343.27  Aligned_cols=303  Identities=26%  Similarity=0.352  Sum_probs=272.9

Q ss_pred             cccCCCCCCcccCCHHHHHHHHHHHhcCCCce-EEEECCCCCCHHHHHHHHHHHHcCCCC------------------CC
Q psy879            2 EKYRPQTFSDIVGNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARILLGPSF------------------KD   62 (317)
Q Consensus         2 ~ky~P~~~~~~~g~~~~~~~l~~~l~~~~~~~-~ll~G~~G~GKt~la~~la~~l~~~~~------------------~~   62 (317)
                      +||||++|++++||+++++.|..++.+++++| +|||||||+||||+|+++++.+.|...                  ..
T Consensus         6 ~KyRP~~~~dvvGq~~v~~~L~~~i~~~~l~ha~Lf~GppGtGKTTlA~~lA~~l~c~~~~~~~cg~C~sc~~i~~~~h~   85 (504)
T PRK14963          6 QRARPITFDEVVGQEHVKEVLLAALRQGRLGHAYLFSGPRGVGKTTTARLIAMAVNCSGEDPKPCGECESCLAVRRGAHP   85 (504)
T ss_pred             HhhCCCCHHHhcChHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHHhccCCCCCCCCcChhhHHHhcCCCC
Confidence            79999999999999999999999999999999 699999999999999999999976421                  23


Q ss_pred             ceEEecCCCCcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcCchh
Q psy879           63 AVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEP  142 (317)
Q Consensus        63 ~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~~~  142 (317)
                      .++++++....+.+.+++....+...++   .+.++|+||||+|.++.+.+++|++++++++.++++|++++.+.++.++
T Consensus        86 dv~el~~~~~~~vd~iR~l~~~~~~~p~---~~~~kVVIIDEad~ls~~a~naLLk~LEep~~~t~~Il~t~~~~kl~~~  162 (504)
T PRK14963         86 DVLEIDAASNNSVEDVRDLREKVLLAPL---RGGRKVYILDEAHMMSKSAFNALLKTLEEPPEHVIFILATTEPEKMPPT  162 (504)
T ss_pred             ceEEecccccCCHHHHHHHHHHHhhccc---cCCCeEEEEECccccCHHHHHHHHHHHHhCCCCEEEEEEcCChhhCChH
Confidence            4667777667788888887665554442   3688999999999999999999999999999999999999999999999


Q ss_pred             HhhhcceeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhhCCCcccHHHHHhhcCCCCH
Q psy879          143 IQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHP  222 (317)
Q Consensus       143 i~sR~~~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~~~~~i~~~~v~~~~~~~~~  222 (317)
                      ++|||..++|.+++.+++..|+..++.++|+.++++++..++..++||+|.++++|+++....+.|+.++|.++++...+
T Consensus       163 I~SRc~~~~f~~ls~~el~~~L~~i~~~egi~i~~~Al~~ia~~s~GdlR~aln~Lekl~~~~~~It~~~V~~~l~~~~~  242 (504)
T PRK14963        163 ILSRTQHFRFRRLTEEEIAGKLRRLLEAEGREAEPEALQLVARLADGAMRDAESLLERLLALGTPVTRKQVEEALGLPPQ  242 (504)
T ss_pred             HhcceEEEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCHHHHHHHHCCCcH
Confidence            99999999999999999999999999999999999999999999999999999999997766668999999999999999


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHh-------------cCCChHHHHHHHHHHHHHHhHH
Q psy879          223 LAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDIIGNIFRVAKT-------------LDIPEPLKLSIIQEIGNVHLRI  289 (317)
Q Consensus       223 ~~i~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~~~-------------~~~~~~~~~~~~~~l~~~~~~l  289 (317)
                      +.++++++++..++..+++.++++|+..|++|..|+..+.++++.             +..++....+++..+.+.++++
T Consensus       243 ~~if~Li~al~~~d~~~Al~~l~~Ll~~G~~~~~Il~~L~~~~r~ll~~k~~~~~~~~~~~~~~~~~~~l~~l~~~~~~~  322 (504)
T PRK14963        243 ERLRGIAAALAQGDAAEALSGAAQLYRDGFAARTLVEGLLEAFRAALYAELGLGGGPRLEGAEPRLLAAMTALDEQMERF  322 (504)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHhccCcccccccCcHHHHHHHHHHHHHHHHH
Confidence            999999999999999999999999999999999999998877662             2335556788999999999999


Q ss_pred             hcCCCcHHHHHHHHHHHHH
Q psy879          290 SEGVNSLLQLSGLLARLCI  308 (317)
Q Consensus       290 ~~g~~~~l~le~~~~~~~~  308 (317)
                      .++.+ +..+|..++++|.
T Consensus       323 ~~~~~-~~~l~~~l~~~~~  340 (504)
T PRK14963        323 ARRSD-ALSLELALLHALL  340 (504)
T ss_pred             Hhccc-hhHHHHHHHHHHh
Confidence            88885 7889999999985

>PRK07764 DNA polymerase III subunits gamma and tau; Validated

Probab=100.00  E-value=7.4e-47  Score=360.46  Aligned_cols=304  Identities=22%  Similarity=0.311  Sum_probs=267.5

Q ss_pred             cccCCCCCCcccCCHHHHHHHHHHHhcCCCce-EEEECCCCCCHHHHHHHHHHHHcCCCC--------------------
Q psy879            2 EKYRPQTFSDIVGNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARILLGPSF--------------------   60 (317)
Q Consensus         2 ~ky~P~~~~~~~g~~~~~~~l~~~l~~~~~~~-~ll~G~~G~GKt~la~~la~~l~~~~~--------------------   60 (317)
                      +||||++|++++||+++++.|..++.+++++| |||+||+|+|||++++.|++.|+|...                    
T Consensus         7 ~KyRP~~f~eiiGqe~v~~~L~~~i~~~ri~Ha~Lf~Gp~G~GKTt~A~~lAr~L~C~~~~~~~pCg~C~sC~~~~~g~~   86 (824)
T PRK07764          7 RRYRPATFAEVIGQEHVTEPLSTALDSGRINHAYLFSGPRGCGKTSSARILARSLNCVEGPTSTPCGECDSCVALAPGGP   86 (824)
T ss_pred             HHhCCCCHHHhcCcHHHHHHHHHHHHhCCCCceEEEECCCCCCHHHHHHHHHHHhCcccCCCCCCCcccHHHHHHHcCCC
Confidence            69999999999999999999999999999999 999999999999999999999987431                    


Q ss_pred             -CCceEEecCCCCcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcC
Q psy879           61 -KDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKI  139 (317)
Q Consensus        61 -~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l  139 (317)
                       ...+++++..+..+++++++........+   ..++++|+||||+|.|+...+|+|+++||+++.+++|||+|++.+++
T Consensus        87 ~~~dv~eidaas~~~Vd~iR~l~~~~~~~p---~~~~~KV~IIDEad~lt~~a~NaLLK~LEEpP~~~~fIl~tt~~~kL  163 (824)
T PRK07764         87 GSLDVTEIDAASHGGVDDARELRERAFFAP---AESRYKIFIIDEAHMVTPQGFNALLKIVEEPPEHLKFIFATTEPDKV  163 (824)
T ss_pred             CCCcEEEecccccCCHHHHHHHHHHHHhch---hcCCceEEEEechhhcCHHHHHHHHHHHhCCCCCeEEEEEeCChhhh
Confidence             23456677666678899998766554443   23789999999999999999999999999999999999999999999


Q ss_pred             chhHhhhcceeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhh--CCCcccHHHHHhhc
Q psy879          140 IEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHN--GFGHVTAEYVFKVC  217 (317)
Q Consensus       140 ~~~i~sR~~~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~--~~~~i~~~~v~~~~  217 (317)
                      +++|+|||+.++|.+++.+++.+||.++++++|+.++++++..++..++||+|.++++|++++.  +.+.|+.+++..++
T Consensus       164 l~TIrSRc~~v~F~~l~~~~l~~~L~~il~~EGv~id~eal~lLa~~sgGdlR~Al~eLEKLia~~~~~~IT~e~V~all  243 (824)
T PRK07764        164 IGTIRSRTHHYPFRLVPPEVMRGYLERICAQEGVPVEPGVLPLVIRAGGGSVRDSLSVLDQLLAGAGPEGVTYERAVALL  243 (824)
T ss_pred             hHHHHhheeEEEeeCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHh
Confidence            9999999999999999999999999999999999999999999999999999999999998765  35679999999999


Q ss_pred             CCCCHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhc-----C-----------------------
Q psy879          218 DEPHPLAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDIIGNIFRVAKTL-----D-----------------------  269 (317)
Q Consensus       218 ~~~~~~~i~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~~~~-----~-----------------------  269 (317)
                      +......++++++++..+|...++.++.+|+..|+++..|+..+.+.++.+     .                       
T Consensus       244 g~~~~~~I~~lidAL~~~D~a~al~~l~~Li~~G~dp~~~L~~LL~~fRDLL~vka~~~~~~~~l~~~p~d~~~~L~~qA  323 (824)
T PRK07764        244 GVTDSALIDEAVDALAAGDGAALFGTVDRVIEAGHDPRRFAEDLLERLRDLIVLQAVPDAAERGLVDAPADQLDRMRAQA  323 (824)
T ss_pred             cCCCHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHhcCcchhhhhccCCHHHHHHHHHHH
Confidence            999999999999999999999999999999999999988877765544332     0                       


Q ss_pred             --CChHHHHHHHHHHHHHHhHHhcCCCcHHHHHHHHHHHHH
Q psy879          270 --IPEPLKLSIIQEIGNVHLRISEGVNSLLQLSGLLARLCI  308 (317)
Q Consensus       270 --~~~~~~~~~~~~l~~~~~~l~~g~~~~l~le~~~~~~~~  308 (317)
                        ++.....++++.+.+....++.+.|++|.+|.|+.+++.
T Consensus       324 ~~~s~~~L~r~ie~l~ea~~~lrgn~nprL~LElLllrLll  364 (824)
T PRK07764        324 QRLGPAELTRAADVVNDGLTEMRGATSPRLLLELLCARMLL  364 (824)
T ss_pred             HhCCHHHHHHHHHHHHHHHHHHhhCCCcHHHHHHHHHHHHh
Confidence              111123337889999988888888999999999999985

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional

Probab=100.00  E-value=1.3e-46  Score=347.70  Aligned_cols=307  Identities=22%  Similarity=0.321  Sum_probs=272.6

Q ss_pred             cccCCCCCCcccCCHHHHHHHHHHHhcCCCce-EEEECCCCCCHHHHHHHHHHHHcCCCC--------------------
Q psy879            2 EKYRPQTFSDIVGNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARILLGPSF--------------------   60 (317)
Q Consensus         2 ~ky~P~~~~~~~g~~~~~~~l~~~l~~~~~~~-~ll~G~~G~GKt~la~~la~~l~~~~~--------------------   60 (317)
                      +||||++|++++||+++++.|.+++.+++.+| |||+||+|+||||+++.+++.++|...                    
T Consensus         8 ~KyRP~~f~dviGQe~vv~~L~~~l~~~rl~ha~Lf~Gp~GvGKTtlAr~lAk~LnC~~~~~~~~~~~~pCg~C~~C~~i   87 (618)
T PRK14951          8 RKYRPRSFSEMVGQEHVVQALTNALTQQRLHHAYLFTGTRGVGKTTVSRILAKSLNCQGPDGQGGITATPCGVCQACRDI   87 (618)
T ss_pred             HHHCCCCHHHhcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCCCcccccCCCCCCCCccHHHHHH
Confidence            79999999999999999999999999999999 899999999999999999999987421                    


Q ss_pred             ----CCceEEecCCCCcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCC
Q psy879           61 ----KDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNS  136 (317)
Q Consensus        61 ----~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~  136 (317)
                          ...++++++.+..+++++++.+......+.   .++++|+||||+|.|+...+|+|++++|+|++++.||++|+++
T Consensus        88 ~~g~h~D~~eldaas~~~Vd~iReli~~~~~~p~---~g~~KV~IIDEvh~Ls~~a~NaLLKtLEEPP~~~~fIL~Ttd~  164 (618)
T PRK14951         88 DSGRFVDYTELDAASNRGVDEVQQLLEQAVYKPV---QGRFKVFMIDEVHMLTNTAFNAMLKTLEEPPEYLKFVLATTDP  164 (618)
T ss_pred             HcCCCCceeecCcccccCHHHHHHHHHHHHhCcc---cCCceEEEEEChhhCCHHHHHHHHHhcccCCCCeEEEEEECCc
Confidence                124667777777889999998887665552   3789999999999999999999999999999999999999999


Q ss_pred             CcCchhHhhhcceeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhh-hCCCcccHHHHHh
Q psy879          137 EKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTH-NGFGHVTAEYVFK  215 (317)
Q Consensus       137 ~~l~~~i~sR~~~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~-~~~~~i~~~~v~~  215 (317)
                      .+++++++|||..++|++++.+++..||..++.++|+.++++++..++..++||+|.++++++++. .+.+.|+.++|.+
T Consensus       165 ~kil~TIlSRc~~~~f~~Ls~eei~~~L~~i~~~egi~ie~~AL~~La~~s~GslR~al~lLdq~ia~~~~~It~~~V~~  244 (618)
T PRK14951        165 QKVPVTVLSRCLQFNLRPMAPETVLEHLTQVLAAENVPAEPQALRLLARAARGSMRDALSLTDQAIAFGSGQLQEAAVRQ  244 (618)
T ss_pred             hhhhHHHHHhceeeecCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhcCCCcCHHHHHH
Confidence            999999999999999999999999999999999999999999999999999999999999997644 3667899999999


Q ss_pred             hcCCCCHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhc--------------------------C
Q psy879          216 VCDEPHPLAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDIIGNIFRVAKTL--------------------------D  269 (317)
Q Consensus       216 ~~~~~~~~~i~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~~~~--------------------------~  269 (317)
                      +++....+.++++++++..++...++.++++|...|+++..|+..+...++.+                          .
T Consensus       245 ~Lg~~~~~~i~~LldaL~~~d~~~al~~l~~l~~~G~~~~~il~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~  324 (618)
T PRK14951        245 MLGSVDRSHVFRLIDALAQGDGRTVVETADELRLNGLSAASTLEEMAAVLQRMAVLQAVPQAAAAATDPEAAEVARLAAL  324 (618)
T ss_pred             HHcCCCHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHhCcccccccChHHHHHHHHHHHh
Confidence            99999999999999999999999999999999999999999988875544322                          1


Q ss_pred             CChHHHHHHHHHHHHHHhHHhcCCCcHHHHHHHHHHHHHhhc
Q psy879          270 IPEPLKLSIIQEIGNVHLRISEGVNSLLQLSGLLARLCIVGS  311 (317)
Q Consensus       270 ~~~~~~~~~~~~l~~~~~~l~~g~~~~l~le~~~~~~~~~~~  311 (317)
                      ++......+++.+......+....++++++|+.+.+++....
T Consensus       325 ~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~em~l~r~~~~~~  366 (618)
T PRK14951        325 MPADETQLLYSICLHGRAELGLAPDEYAALTMVLLRLLAFKP  366 (618)
T ss_pred             CCHHHHHHHHHHHHHHHHHhccCCCHHHHHHHHHHHHhhCCC
Confidence            122223348888999999999989999999999999986554

>PRK07133 DNA polymerase III subunits gamma and tau; Validated

Probab=100.00  E-value=1.5e-46  Score=349.39  Aligned_cols=308  Identities=25%  Similarity=0.364  Sum_probs=270.1

Q ss_pred             cccCCCCCCcccCCHHHHHHHHHHHhcCCCce-EEEECCCCCCHHHHHHHHHHHHcCCCC----------------CCce
Q psy879            2 EKYRPQTFSDIVGNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARILLGPSF----------------KDAV   64 (317)
Q Consensus         2 ~ky~P~~~~~~~g~~~~~~~l~~~l~~~~~~~-~ll~G~~G~GKt~la~~la~~l~~~~~----------------~~~~   64 (317)
                      +||||++|++++||+++++.|..++.+|+++| |||+||+|+|||++|+++|+.+.|...                ...+
T Consensus        10 ~KyRP~~f~dIiGQe~~v~~L~~aI~~~rl~HAYLF~GP~GtGKTt~AriLAk~LnC~~~~~~~~pC~~C~~~~~~~~Dv   89 (725)
T PRK07133         10 RKYRPKTFDDIVGQDHIVQTLKNIIKSNKISHAYLFSGPRGTGKTSVAKIFANALNCSHKTDLLEPCQECIENVNNSLDI   89 (725)
T ss_pred             HHhCCCCHHHhcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCcHHHHHHHHHHHhcccccCCCCCchhHHHHhhcCCCcE
Confidence            69999999999999999999999999999999 899999999999999999999987532                1234


Q ss_pred             EEecCCCCcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcCchhHh
Q psy879           65 LELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQ  144 (317)
Q Consensus        65 ~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~~~i~  144 (317)
                      +++++....+.+++++.+..+...+.   .++++|+||||+|.|+.+++++|+++||+||++++||++|+.+++++++|+
T Consensus        90 ieidaasn~~vd~IReLie~~~~~P~---~g~~KV~IIDEa~~LT~~A~NALLKtLEEPP~~tifILaTte~~KLl~TI~  166 (725)
T PRK07133         90 IEMDAASNNGVDEIRELIENVKNLPT---QSKYKIYIIDEVHMLSKSAFNALLKTLEEPPKHVIFILATTEVHKIPLTIL  166 (725)
T ss_pred             EEEeccccCCHHHHHHHHHHHHhchh---cCCCEEEEEEChhhCCHHHHHHHHHHhhcCCCceEEEEEcCChhhhhHHHH
Confidence            45555455678889988877766553   378999999999999999999999999999999999999999999999999


Q ss_pred             hhcceeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhh-CCCcccHHHHHhhcCCCCHH
Q psy879          145 SRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHN-GFGHVTAEYVFKVCDEPHPL  223 (317)
Q Consensus       145 sR~~~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~-~~~~i~~~~v~~~~~~~~~~  223 (317)
                      |||+.++|.+++.+++..||..++.++|+.++++++..++..++|++|.|+++++..+. +.+.|+.++|.++++....+
T Consensus       167 SRcq~ieF~~L~~eeI~~~L~~il~kegI~id~eAl~~LA~lS~GslR~AlslLekl~~y~~~~It~e~V~ellg~~~~e  246 (725)
T PRK07133        167 SRVQRFNFRRISEDEIVSRLEFILEKENISYEKNALKLIAKLSSGSLRDALSIAEQVSIFGNNKITLKNVEELFGLVSNE  246 (725)
T ss_pred             hhceeEEccCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhccCCCCHHHHHHHHcCCCHH
Confidence            99999999999999999999999999999999999999999999999999999997543 45569999999999999999


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhc-----------------------CCChHHHHHHHH
Q psy879          224 AVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDIIGNIFRVAKTL-----------------------DIPEPLKLSIIQ  280 (317)
Q Consensus       224 ~i~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~~~~-----------------------~~~~~~~~~~~~  280 (317)
                      .++.+++++..++...++.++.++...|.+|..++..+...++.+                       .++.....++++
T Consensus       247 ~If~Ll~aI~~kd~~~aL~~l~~L~~~ged~~~iL~~Ll~~~RDlLl~k~~~~~~ll~~~d~~~l~~~~~s~~~l~~~le  326 (725)
T PRK07133        247 NLINLLNLLYSKDIKEVLNILNQIKEQGIDPELLLISLINLVKEFIIFNKTKDNSLLEYYSEEDLEKLKIDDDFAYKFIE  326 (725)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHhcCchhhhccCCHHHHHHhcCCHHHHHHHHH
Confidence            999999999999999999999999999999998888764433221                       112223445789


Q ss_pred             HHHHHHhHHhcCCCcHHHHHHHHHHHHHhhcc
Q psy879          281 EIGNVHLRISEGVNSLLQLSGLLARLCIVGSK  312 (317)
Q Consensus       281 ~l~~~~~~l~~g~~~~l~le~~~~~~~~~~~~  312 (317)
                      .+.+...+++.++|+++++|.++.+++.....
T Consensus       327 ~i~~~~~~L~~n~n~~l~lE~lll~L~~~~~~  358 (725)
T PRK07133        327 ILFDLLKDLKISDNPNDTLEILIIKLLALSEL  358 (725)
T ss_pred             HHHHHHHHHHhCCCHHHHHHHHHHHHhhcCCC
Confidence            99999999999999999999999999976543

>PRK06647 DNA polymerase III subunits gamma and tau; Validated

Probab=100.00  E-value=2.3e-46  Score=345.62  Aligned_cols=306  Identities=20%  Similarity=0.291  Sum_probs=269.5

Q ss_pred             cccCCCCCCcccCCHHHHHHHHHHHhcCCCce-EEEECCCCCCHHHHHHHHHHHHcCCCC-------------------C
Q psy879            2 EKYRPQTFSDIVGNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARILLGPSF-------------------K   61 (317)
Q Consensus         2 ~ky~P~~~~~~~g~~~~~~~l~~~l~~~~~~~-~ll~G~~G~GKt~la~~la~~l~~~~~-------------------~   61 (317)
                      +||||++|++++||+++++.|..++++|+++| ||||||+|+|||++|+++++.+.|...                   .
T Consensus         8 ~kyRP~~f~diiGqe~iv~~L~~~i~~~~i~hayLf~Gp~G~GKTt~Ar~lAk~L~c~~~~~~~pC~~C~~C~~i~~~~~   87 (563)
T PRK06647          8 TKRRPRDFNSLEGQDFVVETLKHSIESNKIANAYIFSGPRGVGKTSSARAFARCLNCVNGPTPMPCGECSSCKSIDNDNS   87 (563)
T ss_pred             HHhCCCCHHHccCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHhhccccCCCCCCCccchHHHHHHcCCC
Confidence            69999999999999999999999999999999 999999999999999999999987421                   1


Q ss_pred             CceEEecCCCCcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcCch
Q psy879           62 DAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIE  141 (317)
Q Consensus        62 ~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~~  141 (317)
                      ..++++++....+.+++++........+.   .++++|+||||++.|+.+++++|++++|+||++++||++++.+.++.+
T Consensus        88 ~dv~~idgas~~~vddIr~l~e~~~~~p~---~~~~KVvIIDEa~~Ls~~a~naLLK~LEepp~~~vfI~~tte~~kL~~  164 (563)
T PRK06647         88 LDVIEIDGASNTSVQDVRQIKEEIMFPPA---SSRYRVYIIDEVHMLSNSAFNALLKTIEEPPPYIVFIFATTEVHKLPA  164 (563)
T ss_pred             CCeEEecCcccCCHHHHHHHHHHHHhchh---cCCCEEEEEEChhhcCHHHHHHHHHhhccCCCCEEEEEecCChHHhHH
Confidence            23455655545677888877665554442   378999999999999999999999999999999999999999899999


Q ss_pred             hHhhhcceeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhh-CCCcccHHHHHhhcCCC
Q psy879          142 PIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHN-GFGHVTAEYVFKVCDEP  220 (317)
Q Consensus       142 ~i~sR~~~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~-~~~~i~~~~v~~~~~~~  220 (317)
                      +|+|||+.++|.+++.+++..|+..++..+|+.++++++..++..++||+|.+++++++++. ..+.++.+++.++++..
T Consensus       165 tI~SRc~~~~f~~l~~~el~~~L~~i~~~egi~id~eAl~lLa~~s~GdlR~alslLdklis~~~~~It~e~V~~llg~~  244 (563)
T PRK06647        165 TIKSRCQHFNFRLLSLEKIYNMLKKVCLEDQIKYEDEALKWIAYKSTGSVRDAYTLFDQVVSFSDSDITLEQIRSKMGLT  244 (563)
T ss_pred             HHHHhceEEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHhhcCCCCCHHHHHHHhCCC
Confidence            99999999999999999999999999999999999999999999999999999999987544 45679999999999999


Q ss_pred             CHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhc-----C--------------------CChHHH
Q psy879          221 HPLAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDIIGNIFRVAKTL-----D--------------------IPEPLK  275 (317)
Q Consensus       221 ~~~~i~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~~~~-----~--------------------~~~~~~  275 (317)
                      ..+.++++++++..++..+++.++.+++..|+++..++..+.++++.+     +                    ++....
T Consensus       245 ~~~~if~LidaI~~~D~~~al~~l~~Ll~~G~d~~~iL~~Ll~~fRdLL~vK~G~~~~~~l~~~~e~l~k~~~~~s~~~L  324 (563)
T PRK06647        245 GDEFLEKLASSILNEDAKELLCVLDSVFLSGVSVEQFLLDCIEFFRELLFLKHGIKNEAFIGIKAERLPEKLREFDLSQI  324 (563)
T ss_pred             CHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHhcCCchhhhccccHHHHHHHHHhCCHHHH
Confidence            999999999999999999999999999999999999988875544333     2                    222234


Q ss_pred             HHHHHHHHHHHhHHhcCCCcHHHHHHHHHHHHHhh
Q psy879          276 LSIIQEIGNVHLRISEGVNSLLQLSGLLARLCIVG  310 (317)
Q Consensus       276 ~~~~~~l~~~~~~l~~g~~~~l~le~~~~~~~~~~  310 (317)
                      .++++.+.+.+.+++.+.|+++.+|.++.++|...
T Consensus       325 ~~~l~~Llea~~~lK~n~~~~l~lE~llikl~~~~  359 (563)
T PRK06647        325 ERAISVLLETYRDLQFSVNPRYELEINFSKILRLK  359 (563)
T ss_pred             HHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHhcc
Confidence            45899999999999999999999999999999754

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=100.00  E-value=2.5e-46  Score=346.34  Aligned_cols=307  Identities=23%  Similarity=0.304  Sum_probs=267.4

Q ss_pred             cccCCCCCCcccCCHHHHHHHHHHHhcCCCce-EEEECCCCCCHHHHHHHHHHHHcCCCC-------------------C
Q psy879            2 EKYRPQTFSDIVGNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARILLGPSF-------------------K   61 (317)
Q Consensus         2 ~ky~P~~~~~~~g~~~~~~~l~~~l~~~~~~~-~ll~G~~G~GKt~la~~la~~l~~~~~-------------------~   61 (317)
                      +||||++|++++||+++++.|...+.+|+++| |||+||+|+||||+|+.+++.+.|...                   .
T Consensus         8 ~KyRP~~f~divGQe~vv~~L~~~l~~~rl~hAyLf~Gp~GvGKTTlAr~lAk~L~c~~~~~~~pCg~C~~C~~i~~g~~   87 (647)
T PRK07994          8 RKWRPQTFAEVVGQEHVLTALANALDLGRLHHAYLFSGTRGVGKTTIARLLAKGLNCETGITATPCGECDNCREIEQGRF   87 (647)
T ss_pred             HHhCCCCHHHhcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHhhhhccCCCCCCCCCCHHHHHHHcCCC
Confidence            69999999999999999999999999999999 899999999999999999999988421                   0


Q ss_pred             CceEEecCCCCcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcCch
Q psy879           62 DAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIE  141 (317)
Q Consensus        62 ~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~~  141 (317)
                      ..++++++.+..+++++++.+..+...+.   .++++|+||||+|.|+..++|+|+++||+|+++++||++|+++.++++
T Consensus        88 ~D~ieidaas~~~VddiR~li~~~~~~p~---~g~~KV~IIDEah~Ls~~a~NALLKtLEEPp~~v~FIL~Tt~~~kLl~  164 (647)
T PRK07994         88 VDLIEIDAASRTKVEDTRELLDNVQYAPA---RGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPV  164 (647)
T ss_pred             CCceeecccccCCHHHHHHHHHHHHhhhh---cCCCEEEEEechHhCCHHHHHHHHHHHHcCCCCeEEEEecCCccccch
Confidence            13466676656788899988877665542   378999999999999999999999999999999999999999999999


Q ss_pred             hHhhhcceeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhh-CCCcccHHHHHhhcCCC
Q psy879          142 PIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHN-GFGHVTAEYVFKVCDEP  220 (317)
Q Consensus       142 ~i~sR~~~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~-~~~~i~~~~v~~~~~~~  220 (317)
                      +|+|||+.++|++++.+++..+|..++..+++.++++++..++..++||+|.++++++.+.. +.+.|+.+++..+++..
T Consensus       165 TI~SRC~~~~f~~Ls~~ei~~~L~~il~~e~i~~e~~aL~~Ia~~s~Gs~R~Al~lldqaia~~~~~it~~~v~~~lg~~  244 (647)
T PRK07994        165 TILSRCLQFHLKALDVEQIRQQLEHILQAEQIPFEPRALQLLARAADGSMRDALSLTDQAIASGNGQVTTDDVSAMLGTL  244 (647)
T ss_pred             HHHhhheEeeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhcCCCcCHHHHHHHHccC
Confidence            99999999999999999999999999999999999999999999999999999999976443 56789999999998887


Q ss_pred             CHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhc--------------------------CCChHH
Q psy879          221 HPLAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDIIGNIFRVAKTL--------------------------DIPEPL  274 (317)
Q Consensus       221 ~~~~i~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~~~~--------------------------~~~~~~  274 (317)
                      ..+.+.++++++..++...++.++..|...|.++..++..+...++.+                          .++...
T Consensus       245 d~~~~~~ll~al~~~d~~~~l~~~~~l~~~g~d~~~~L~~l~~~lrdil~~q~~~~~~~~~~~d~~~~l~~la~~~s~~~  324 (647)
T PRK07994        245 DDDQALSLLEALVEGDGERVMALINQLAERGPDWEGLLVELLELLHRIAMAQLLPAALDNDMADIELRLRELARTLPPED  324 (647)
T ss_pred             CHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHhccchhcccchhHHHHHHHHHHhCCHHH
Confidence            777899999999999999999999999999999987776653322211                          122222


Q ss_pred             HHHHHHHHHHHHhHHhcCCCcHHHHHHHHHHHHHhhc
Q psy879          275 KLSIIQEIGNVHLRISEGVNSLLQLSGLLARLCIVGS  311 (317)
Q Consensus       275 ~~~~~~~l~~~~~~l~~g~~~~l~le~~~~~~~~~~~  311 (317)
                      ...+++.+.+...+|+.+.|+++++|+++.++..-..
T Consensus       325 l~~~~q~~~~~~~~L~~n~n~~l~lE~~llr~~~~~P  361 (647)
T PRK07994        325 VQLYYQTLLIGRKDLPLAPDRRMGVEMTLLRMLAFHP  361 (647)
T ss_pred             HHHHHHHHHHHHHHHhhCCCHHHHHHHHHHHHHhcCC
Confidence            3347899999999999999999999999999987655

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=100.00  E-value=8.1e-46  Score=341.24  Aligned_cols=307  Identities=23%  Similarity=0.316  Sum_probs=270.8

Q ss_pred             cccCCCCCCcccCCHHHHHHHHHHHhcCCCce-EEEECCCCCCHHHHHHHHHHHHcCCCC-------------------C
Q psy879            2 EKYRPQTFSDIVGNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARILLGPSF-------------------K   61 (317)
Q Consensus         2 ~ky~P~~~~~~~g~~~~~~~l~~~l~~~~~~~-~ll~G~~G~GKt~la~~la~~l~~~~~-------------------~   61 (317)
                      +||||++|++++||+++++.|..++.+++++| |||+||+|+|||++|+.+++.+.|...                   .
T Consensus         8 rKYRP~tFddIIGQe~vv~~L~~ai~~~rl~Ha~Lf~GP~GvGKTTlAriLAk~LnC~~~~~~~pCg~C~sCr~i~~g~~   87 (709)
T PRK08691          8 RKWRPKTFADLVGQEHVVKALQNALDEGRLHHAYLLTGTRGVGKTTIARILAKSLNCENAQHGEPCGVCQSCTQIDAGRY   87 (709)
T ss_pred             HHhCCCCHHHHcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCcHHHHHHHHHHHhcccCCCCCCCCcccHHHHHHhccCc
Confidence            79999999999999999999999999999998 899999999999999999999987532                   1


Q ss_pred             CceEEecCCCCcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcCch
Q psy879           62 DAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIE  141 (317)
Q Consensus        62 ~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~~  141 (317)
                      ..+++++.....+++.+++.+......+.   .++++|+||||+|.|+...+++|+++||+++++++||++|+++.++++
T Consensus        88 ~DvlEidaAs~~gVd~IRelle~a~~~P~---~gk~KVIIIDEad~Ls~~A~NALLKtLEEPp~~v~fILaTtd~~kL~~  164 (709)
T PRK08691         88 VDLLEIDAASNTGIDNIREVLENAQYAPT---AGKYKVYIIDEVHMLSKSAFNAMLKTLEEPPEHVKFILATTDPHKVPV  164 (709)
T ss_pred             cceEEEeccccCCHHHHHHHHHHHHhhhh---hCCcEEEEEECccccCHHHHHHHHHHHHhCCCCcEEEEEeCCccccch
Confidence            13456776667888889888876544442   267899999999999999999999999999999999999999999999


Q ss_pred             hHhhhcceeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhh-CCCcccHHHHHhhcCCC
Q psy879          142 PIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHN-GFGHVTAEYVFKVCDEP  220 (317)
Q Consensus       142 ~i~sR~~~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~-~~~~i~~~~v~~~~~~~  220 (317)
                      +++|||..++|++++.+++..||..++.++|+.++++++..|++.++||+|.++++|+.+.. +.+.|+.++|..+++..
T Consensus       165 TIrSRC~~f~f~~Ls~eeI~~~L~~Il~kEgi~id~eAL~~Ia~~A~GslRdAlnLLDqaia~g~g~It~e~V~~lLG~~  244 (709)
T PRK08691        165 TVLSRCLQFVLRNMTAQQVADHLAHVLDSEKIAYEPPALQLLGRAAAGSMRDALSLLDQAIALGSGKVAENDVRQMIGAV  244 (709)
T ss_pred             HHHHHHhhhhcCCCCHHHHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCCHHHHHHHHHHHHHhcCCCcCHHHHHHHHccc
Confidence            99999999999999999999999999999999999999999999999999999999987554 56789999999999999


Q ss_pred             CHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhc-------------------------CCChHHH
Q psy879          221 HPLAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDIIGNIFRVAKTL-------------------------DIPEPLK  275 (317)
Q Consensus       221 ~~~~i~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~~~~-------------------------~~~~~~~  275 (317)
                      ....++++++++..++...++.++++|...|.++..++..+..+++.+                         .++....
T Consensus       245 d~~~If~LldAL~~~d~~~al~~l~~L~~~G~d~~~~l~~L~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~l  324 (709)
T PRK08691        245 DKQYLYELLTGIINQDGAALLAKAQEMAACAVGFDNALGELAILLQQLALIQAVPSALAHDDPDSDILHRLAQTISGEQI  324 (709)
T ss_pred             CHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHhhcCchhccccchHHHHHHHHHHcCCHHHH
Confidence            999999999999999999999999999999999999888865544332                         1222223


Q ss_pred             HHHHHHHHHHHhHHhcCCCcHHHHHHHHHHHHHhhc
Q psy879          276 LSIIQEIGNVHLRISEGVNSLLQLSGLLARLCIVGS  311 (317)
Q Consensus       276 ~~~~~~l~~~~~~l~~g~~~~l~le~~~~~~~~~~~  311 (317)
                      ..+++.+......++...++++++|+.+++++....
T Consensus       325 ~~~~q~~l~~~~~l~~a~~~~~~~Em~llrl~~~~p  360 (709)
T PRK08691        325 QLYYQIAVHGKRDLSLAPDEYAGFMMTLLRMLAFAP  360 (709)
T ss_pred             HHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHhcCC
Confidence            348899999999999999999999999999987544

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional

Probab=100.00  E-value=1.1e-45  Score=339.13  Aligned_cols=306  Identities=22%  Similarity=0.304  Sum_probs=265.4

Q ss_pred             CcccCCCCCCcccCCHHHHHHHHHHHhcCCCce-EEEECCCCCCHHHHHHHHHHHHcCCCC-------------------
Q psy879            1 IEKYRPQTFSDIVGNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARILLGPSF-------------------   60 (317)
Q Consensus         1 ~~ky~P~~~~~~~g~~~~~~~l~~~l~~~~~~~-~ll~G~~G~GKt~la~~la~~l~~~~~-------------------   60 (317)
                      .+||||++|++++||+++++.|..++.+++.+| |||+||+|+|||++|+.+|+.+.|...                   
T Consensus         7 a~KyRP~sf~dIiGQe~v~~~L~~ai~~~ri~ha~Lf~GPpG~GKTtiArilAk~L~C~~~~~~~pCg~C~sC~~i~~g~   86 (624)
T PRK14959          7 TARYRPQTFAEVAGQETVKAILSRAAQENRVAPAYLFSGTRGVGKTTIARIFAKALNCETAPTGEPCNTCEQCRKVTQGM   86 (624)
T ss_pred             HHHhCCCCHHHhcCCHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHhccccCCCCCCCCcccHHHHHHhcCC
Confidence            379999999999999999999999999999776 999999999999999999999987421                   


Q ss_pred             CCceEEecCCCCcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcCc
Q psy879           61 KDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKII  140 (317)
Q Consensus        61 ~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~  140 (317)
                      ...++++++....++++++.....+...+.   .+.++||||||+|.|+.+.+++|+++||+++.+++||++|+.+.++.
T Consensus        87 hpDv~eId~a~~~~Id~iR~L~~~~~~~p~---~g~~kVIIIDEad~Lt~~a~naLLk~LEEP~~~~ifILaTt~~~kll  163 (624)
T PRK14959         87 HVDVVEIDGASNRGIDDAKRLKEAIGYAPM---EGRYKVFIIDEAHMLTREAFNALLKTLEEPPARVTFVLATTEPHKFP  163 (624)
T ss_pred             CCceEEEecccccCHHHHHHHHHHHHhhhh---cCCceEEEEEChHhCCHHHHHHHHHHhhccCCCEEEEEecCChhhhh
Confidence            123566766666788888876665554442   36789999999999999999999999999999999999999999999


Q ss_pred             hhHhhhcceeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhh-CCCcccHHHHHhhcCC
Q psy879          141 EPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHN-GFGHVTAEYVFKVCDE  219 (317)
Q Consensus       141 ~~i~sR~~~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~-~~~~i~~~~v~~~~~~  219 (317)
                      ++|+|||+.++|++++.+++..+|..++.++++.+++++++.++..++||+|.++++|++++. +.+.|+.++|.++++.
T Consensus       164 ~TI~SRcq~i~F~pLs~~eL~~~L~~il~~egi~id~eal~lIA~~s~GdlR~Al~lLeqll~~g~~~It~d~V~~~lg~  243 (624)
T PRK14959        164 VTIVSRCQHFTFTRLSEAGLEAHLTKVLGREGVDYDPAAVRLIARRAAGSVRDSMSLLGQVLALGESRLTIDGARGVLGL  243 (624)
T ss_pred             HHHHhhhhccccCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhcCCCcCHHHHHHHhCC
Confidence            999999999999999999999999999999999999999999999999999999999986543 5568999999999999


Q ss_pred             CCHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhc------C-----------------------C
Q psy879          220 PHPLAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDIIGNIFRVAKTL------D-----------------------I  270 (317)
Q Consensus       220 ~~~~~i~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~~~~------~-----------------------~  270 (317)
                      ...+.++++++++..++...++.++..|++.|+++..++..+...++.+      +                       +
T Consensus       244 ~~~e~vfeLl~AL~~~D~~aal~~l~~Ll~~g~d~~~iL~~Ll~~~RdLLl~k~~~~~~~~~l~i~~~~~~~~~~~A~~~  323 (624)
T PRK14959        244 AGQELFLRLMEALAAQDCLGVANVVRELLDRGVDMGFFLRELVATWRNLFMLRQAGEAALASLDLPEDEARQWLGWAKRF  323 (624)
T ss_pred             CCHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHhhhccccchhhcccCHHHHHHHHHHHHhC
Confidence            9999999999999999999999999999999999988887764433222      1                       1


Q ss_pred             ChHHHHHHHHHHHHHHhHHhcCCCcHHHHHHHHHHHHHh
Q psy879          271 PEPLKLSIIQEIGNVHLRISEGVNSLLQLSGLLARLCIV  309 (317)
Q Consensus       271 ~~~~~~~~~~~l~~~~~~l~~g~~~~l~le~~~~~~~~~  309 (317)
                      +......+++.+.+...+++.++|+++++|.++.+++..
T Consensus       324 s~~~L~~~l~~il~~~~~l~~n~n~rl~lE~lLL~l~~~  362 (624)
T PRK14959        324 EPAHIHACWQMTLEGQRRVLTSLEPAMALELLLLNLAML  362 (624)
T ss_pred             CHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHhc
Confidence            111223368889999999999999999999999999864

>PRK14953 DNA polymerase III subunits gamma and tau; Provisional

Probab=100.00  E-value=2.6e-45  Score=333.95  Aligned_cols=306  Identities=26%  Similarity=0.374  Sum_probs=268.7

Q ss_pred             cccCCCCCCcccCCHHHHHHHHHHHhcCCCce-EEEECCCCCCHHHHHHHHHHHHcCCCCC-------------------
Q psy879            2 EKYRPQTFSDIVGNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARILLGPSFK-------------------   61 (317)
Q Consensus         2 ~ky~P~~~~~~~g~~~~~~~l~~~l~~~~~~~-~ll~G~~G~GKt~la~~la~~l~~~~~~-------------------   61 (317)
                      +||||++|++++||+++.+.|.+++.+++++| ||||||+|+|||++|+.+|+.+.|....                   
T Consensus         8 ~kyRP~~f~diiGq~~i~~~L~~~i~~~~i~hayLf~Gp~G~GKTtlAr~lAk~L~c~~~~~~~pc~~c~nc~~i~~g~~   87 (486)
T PRK14953          8 RKYRPKFFKEVIGQEIVVRILKNAVKLQRVSHAYIFAGPRGTGKTTIARILAKVLNCLNPQEGEPCGKCENCVEIDKGSF   87 (486)
T ss_pred             HhhCCCcHHHccChHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCcCCCCCCCCCccHHHHHHhcCCC
Confidence            69999999999999999999999999999999 8999999999999999999999863211                   


Q ss_pred             CceEEecCCCCcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcCch
Q psy879           62 DAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIE  141 (317)
Q Consensus        62 ~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~~  141 (317)
                      ..++++++....+.++++.........+.   .+.++|+||||+|.|+.+++++|++++++|++++++|++|+..+++++
T Consensus        88 ~d~~eidaas~~gvd~ir~I~~~~~~~P~---~~~~KVvIIDEad~Lt~~a~naLLk~LEepp~~~v~Il~tt~~~kl~~  164 (486)
T PRK14953         88 PDLIEIDAASNRGIDDIRALRDAVSYTPI---KGKYKVYIIDEAHMLTKEAFNALLKTLEEPPPRTIFILCTTEYDKIPP  164 (486)
T ss_pred             CcEEEEeCccCCCHHHHHHHHHHHHhCcc---cCCeeEEEEEChhhcCHHHHHHHHHHHhcCCCCeEEEEEECCHHHHHH
Confidence            13455665556788888877666655543   378999999999999999999999999999999999999999999999


Q ss_pred             hHhhhcceeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhh-CCCcccHHHHHhhcCCC
Q psy879          142 PIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHN-GFGHVTAEYVFKVCDEP  220 (317)
Q Consensus       142 ~i~sR~~~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~-~~~~i~~~~v~~~~~~~  220 (317)
                      +++|||+.++|++++.+++..|+..+++.+|+.+++++++.++..++||+|.++++|+.++. +.+.|+.++|.++++..
T Consensus       165 tI~SRc~~i~f~~ls~~el~~~L~~i~k~egi~id~~al~~La~~s~G~lr~al~~Ldkl~~~~~~~It~~~V~~~lg~~  244 (486)
T PRK14953        165 TILSRCQRFIFSKPTKEQIKEYLKRICNEEKIEYEEKALDLLAQASEGGMRDAASLLDQASTYGEGKVTIKVVEEFLGIV  244 (486)
T ss_pred             HHHHhceEEEcCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhcCCCcCHHHHHHHhCCC
Confidence            99999999999999999999999999999999999999999999999999999999987644 56689999999999999


Q ss_pred             CHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhc------C----------------CChHHHHHH
Q psy879          221 HPLAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDIIGNIFRVAKTL------D----------------IPEPLKLSI  278 (317)
Q Consensus       221 ~~~~i~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~~~~------~----------------~~~~~~~~~  278 (317)
                      ....++++++++..++...++.++.+|...|+++..++..+.+.++.+      +                .+......+
T Consensus       245 ~~~~vf~Li~ai~~~d~~~al~~l~~L~~~g~~~~~iL~~L~~~~rdll~~k~~~~~~~~~~~~~~~~~~~~~~~~l~~~  324 (486)
T PRK14953        245 SQESVRKFLNLLLESDVDEAIKFLRTLEEKGYNLNKFWKQLEEEIRNILLNKSLKNPEEVFQVEDFYRKLEKPLEALLYL  324 (486)
T ss_pred             CHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHhhcCChhhhcchHHHHHHhcCCHHHHHHH
Confidence            999999999999999999999999999999999999998876654432      1                112233447


Q ss_pred             HHHHHHHHhHHhcCCCcHHHHHHHHHHHHHhhc
Q psy879          279 IQEIGNVHLRISEGVNSLLQLSGLLARLCIVGS  311 (317)
Q Consensus       279 ~~~l~~~~~~l~~g~~~~l~le~~~~~~~~~~~  311 (317)
                      ++.+.+...+++. .|+++++|.++.++|....
T Consensus       325 ~~~~~~~~~~l~~-~~~~~~~E~~ll~l~~~~~  356 (486)
T PRK14953        325 EDVINKAFSEART-RDPLRAYELAILKLLYVKD  356 (486)
T ss_pred             HHHHHHHHHHHhc-cChhHHHHHHHHHHHhhCC
Confidence            8899999999999 9999999999999996543

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=100.00  E-value=1.9e-45  Score=333.40  Aligned_cols=305  Identities=26%  Similarity=0.369  Sum_probs=270.3

Q ss_pred             cccCCCCCCcccCCHHHHHHHHHHHhcCCCce-EEEECCCCCCHHHHHHHHHHHHcCCCC-------------------C
Q psy879            2 EKYRPQTFSDIVGNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARILLGPSF-------------------K   61 (317)
Q Consensus         2 ~ky~P~~~~~~~g~~~~~~~l~~~l~~~~~~~-~ll~G~~G~GKt~la~~la~~l~~~~~-------------------~   61 (317)
                      +||||++|++++||+++.+.|..++.+++++| ++|+||||+||||+|+++++.+.|...                   .
T Consensus         6 ~kyRP~~~~divGq~~i~~~L~~~i~~~~l~~~~Lf~GPpGtGKTTlA~~lA~~l~~~~~~~~~pc~~c~~c~~i~~g~~   85 (472)
T PRK14962          6 RKYRPKTFSEVVGQDHVKKLIINALKKNSISHAYIFAGPRGTGKTTVARILAKSLNCENRKGVEPCNECRACRSIDEGTF   85 (472)
T ss_pred             HHHCCCCHHHccCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhccccCCCCCCCcccHHHHHHhcCCC
Confidence            69999999999999999999999999999988 899999999999999999999876431                   1


Q ss_pred             CceEEecCCCCcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcCch
Q psy879           62 DAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIE  141 (317)
Q Consensus        62 ~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~~  141 (317)
                      ..++++++....+.+.+++........+.   .++++|+||||+|.++.+.+++|+++++++++++++|++|+++.++.+
T Consensus        86 ~dv~el~aa~~~gid~iR~i~~~~~~~p~---~~~~kVvIIDE~h~Lt~~a~~~LLk~LE~p~~~vv~Ilattn~~kl~~  162 (472)
T PRK14962         86 MDVIELDAASNRGIDEIRKIRDAVGYRPM---EGKYKVYIIDEVHMLTKEAFNALLKTLEEPPSHVVFVLATTNLEKVPP  162 (472)
T ss_pred             CccEEEeCcccCCHHHHHHHHHHHhhChh---cCCeEEEEEEChHHhHHHHHHHHHHHHHhCCCcEEEEEEeCChHhhhH
Confidence            24677777767788888876655544432   368899999999999999999999999999999999999998889999


Q ss_pred             hHhhhcceeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhh-CCCcccHHHHHhhcCCC
Q psy879          142 PIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHN-GFGHVTAEYVFKVCDEP  220 (317)
Q Consensus       142 ~i~sR~~~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~-~~~~i~~~~v~~~~~~~  220 (317)
                      +++|||+.+.|.+++.+++..++..++..+++.+++++++.++..++||+|.+++.|+.++. ..+.|+.++|.++++..
T Consensus       163 ~L~SR~~vv~f~~l~~~el~~~L~~i~~~egi~i~~eal~~Ia~~s~GdlR~aln~Le~l~~~~~~~It~e~V~~~l~~~  242 (472)
T PRK14962        163 TIISRCQVIEFRNISDELIIKRLQEVAEAEGIEIDREALSFIAKRASGGLRDALTMLEQVWKFSEGKITLETVHEALGLI  242 (472)
T ss_pred             HHhcCcEEEEECCccHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHcCC
Confidence            99999999999999999999999999999999999999999999999999999999998654 33469999999999999


Q ss_pred             CHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHH-HhcCCCh-HHHHHHHHHHHHHHhHHhcCCCcHHH
Q psy879          221 HPLAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDIIGNIFRVA-KTLDIPE-PLKLSIIQEIGNVHLRISEGVNSLLQ  298 (317)
Q Consensus       221 ~~~~i~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~-~~~~~~~-~~~~~~~~~l~~~~~~l~~g~~~~l~  298 (317)
                      ..+.++++++++.++|..+|+.++.+|+..|++|..|++.+...+ +.++..+ .....+...+.+.-.+++..-...+.
T Consensus       243 ~~~~i~~li~si~~~d~~~Al~~l~~ll~~Gedp~~i~r~l~~~~~edi~~a~~~~~~~~~~~~~~~~~~i~~~e~~~~l  322 (472)
T PRK14962        243 PIEVVRDYINAIFNGDVKRVFTVLDDVYYSGKDYEVLIQQAIEDLVEDLERERANDIIQVSRQLLNILREIKFAEEKRLV  322 (472)
T ss_pred             CHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHccCCCchHHHHHHHHHHHHHHHhCCcchHHHH
Confidence            999999999999999999999999999999999999999987765 4446666 56667788888888888887789999


Q ss_pred             HHHHHHHHHHh
Q psy879          299 LSGLLARLCIV  309 (317)
Q Consensus       299 le~~~~~~~~~  309 (317)
                      .+.++.++|.-
T Consensus       323 ~~~~~~~~~~~  333 (472)
T PRK14962        323 CKLGSASIATR  333 (472)
T ss_pred             HHHHHHHHHHh
Confidence            99999999853

>COG2812 DnaX DNA polymerase III, gamma/tau subunits [DNA replication, recombination, and repair]

Probab=100.00  E-value=2.6e-46  Score=335.70  Aligned_cols=306  Identities=28%  Similarity=0.414  Sum_probs=273.2

Q ss_pred             cccCCCCCCcccCCHHHHHHHHHHHhcCCCce-EEEECCCCCCHHHHHHHHHHHHcCCCC-------------------C
Q psy879            2 EKYRPQTFSDIVGNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARILLGPSF-------------------K   61 (317)
Q Consensus         2 ~ky~P~~~~~~~g~~~~~~~l~~~l~~~~~~~-~ll~G~~G~GKt~la~~la~~l~~~~~-------------------~   61 (317)
                      .||||++|++++||+++.+.|..++..++.+| |+|+||.|+||||+||.+|+.++|...                   .
T Consensus         8 rKyRP~~F~evvGQe~v~~~L~nal~~~ri~hAYlfsG~RGvGKTt~Ari~AkalNC~~~~~~ePC~~C~~Ck~I~~g~~   87 (515)
T COG2812           8 RKYRPKTFDDVVGQEHVVKTLSNALENGRIAHAYLFSGPRGVGKTTIARILAKALNCENGPTAEPCGKCISCKEINEGSL   87 (515)
T ss_pred             HHhCcccHHHhcccHHHHHHHHHHHHhCcchhhhhhcCCCCcCchhHHHHHHHHhcCCCCCCCCcchhhhhhHhhhcCCc
Confidence            58999999999999999999999999999999 999999999999999999999998752                   1


Q ss_pred             CceEEecCCCCcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcCch
Q psy879           62 DAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIE  141 (317)
Q Consensus        62 ~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~~  141 (317)
                      ..++++++.+..+++++|+........|   ..+++||+||||++.|+..+.|+||+++|+||+++.|||+|+.+.++++
T Consensus        88 ~DviEiDaASn~gVddiR~i~e~v~y~P---~~~ryKVyiIDEvHMLS~~afNALLKTLEEPP~hV~FIlATTe~~Kip~  164 (515)
T COG2812          88 IDVIEIDAASNTGVDDIREIIEKVNYAP---SEGRYKVYIIDEVHMLSKQAFNALLKTLEEPPSHVKFILATTEPQKIPN  164 (515)
T ss_pred             ccchhhhhhhccChHHHHHHHHHhccCC---ccccceEEEEecHHhhhHHHHHHHhcccccCccCeEEEEecCCcCcCch
Confidence            2356666667789999999888776665   3489999999999999999999999999999999999999999999999


Q ss_pred             hHhhhcceeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhh-CCCcccHHHHHhhcCCC
Q psy879          142 PIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHN-GFGHVTAEYVFKVCDEP  220 (317)
Q Consensus       142 ~i~sR~~~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~-~~~~i~~~~v~~~~~~~  220 (317)
                      +|.|||+.++|+.++.+++...|..++.++++.++++++..+++.++|++|.++++|+.+.. +.+.|+.+.|...++..
T Consensus       165 TIlSRcq~f~fkri~~~~I~~~L~~i~~~E~I~~e~~aL~~ia~~a~Gs~RDalslLDq~i~~~~~~It~~~v~~~lG~~  244 (515)
T COG2812         165 TILSRCQRFDFKRLDLEEIAKHLAAILDKEGINIEEDALSLIARAAEGSLRDALSLLDQAIAFGEGEITLESVRDMLGLT  244 (515)
T ss_pred             hhhhccccccccCCCHHHHHHHHHHHHHhcCCccCHHHHHHHHHHcCCChhhHHHHHHHHHHccCCcccHHHHHHHhCCC
Confidence            99999999999999999999999999999999999999999999999999999999987665 45789999999999999


Q ss_pred             CHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhc-----C----------------------CChH
Q psy879          221 HPLAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDIIGNIFRVAKTL-----D----------------------IPEP  273 (317)
Q Consensus       221 ~~~~i~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~~~~-----~----------------------~~~~  273 (317)
                      ....+..+++++..+|...++..++.+++.|.++..++..+..+++.+     .                      ++..
T Consensus       245 ~~~~~~~~~~~i~~~d~~~~~~~~~~l~~~G~~~~~~l~dl~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~  324 (515)
T COG2812         245 DIEKLLSLLEAILKGDAKEALRLINELIEEGKDPEAFLEDLLNFLRDLLLFKQTVPNELQLNTTEIEERTKELASQISVL  324 (515)
T ss_pred             CHHHHHHHHHHHHccCHHHHHHHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHhcccchhhccchhhhHHHHHHHHhcCHH
Confidence            999999999999999999999999999999999998887764433221     0                      1111


Q ss_pred             HHHHHHHHHHHHHhHHhcCCCcHHHHHHHHHHHHHhh
Q psy879          274 LKLSIIQEIGNVHLRISEGVNSLLQLSGLLARLCIVG  310 (317)
Q Consensus       274 ~~~~~~~~l~~~~~~l~~g~~~~l~le~~~~~~~~~~  310 (317)
                      ...++++.+......++.+.++++.+|+++.+++...
T Consensus       325 ~l~~~~~~~~~~~~e~~~s~~~~~~~E~~lirl~~~~  361 (515)
T COG2812         325 NLQRLYQLLLPGLKELKRSLSPRLGLEMTLIRLLEAA  361 (515)
T ss_pred             HHHHHHHHHHHHHHHhhcCcchhHHHHHHHHHHHhhc
Confidence            2333778888888899999999999999999999764

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional

Probab=100.00  E-value=3.6e-45  Score=334.19  Aligned_cols=307  Identities=22%  Similarity=0.289  Sum_probs=268.3

Q ss_pred             cccCCCCCCcccCCHHHHHHHHHHHhcCCCce-EEEECCCCCCHHHHHHHHHHHHcCCCC-------------------C
Q psy879            2 EKYRPQTFSDIVGNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARILLGPSF-------------------K   61 (317)
Q Consensus         2 ~ky~P~~~~~~~g~~~~~~~l~~~l~~~~~~~-~ll~G~~G~GKt~la~~la~~l~~~~~-------------------~   61 (317)
                      +||||++|++++||+++++.|..++++|+.+| |+|+||+|+|||++|+.+|+.+.|...                   .
T Consensus         8 ~KyRP~~f~diiGq~~~v~~L~~~i~~~rl~ha~Lf~Gp~GvGKTTlAr~lAk~L~c~~~~~~~pCg~C~sC~~i~~~~~   87 (546)
T PRK14957          8 RKYRPQSFAEVAGQQHALNSLVHALETQKVHHAYLFTGTRGVGKTTLGRLLAKCLNCKTGVTAEPCNKCENCVAINNNSF   87 (546)
T ss_pred             HHHCcCcHHHhcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCCcccHHHHHHhcCCC
Confidence            79999999999999999999999999999999 999999999999999999999987321                   1


Q ss_pred             CceEEecCCCCcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcCch
Q psy879           62 DAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIE  141 (317)
Q Consensus        62 ~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~~  141 (317)
                      ..+++++.....+.+++++.+..+...+.   .++++|+||||+|.|+.+++++|+++||+||+++.||++|++..++++
T Consensus        88 ~dlieidaas~~gvd~ir~ii~~~~~~p~---~g~~kViIIDEa~~ls~~a~naLLK~LEepp~~v~fIL~Ttd~~kil~  164 (546)
T PRK14957         88 IDLIEIDAASRTGVEETKEILDNIQYMPS---QGRYKVYLIDEVHMLSKQSFNALLKTLEEPPEYVKFILATTDYHKIPV  164 (546)
T ss_pred             CceEEeecccccCHHHHHHHHHHHHhhhh---cCCcEEEEEechhhccHHHHHHHHHHHhcCCCCceEEEEECChhhhhh
Confidence            23555665556788888888877665543   378999999999999999999999999999999999999999999999


Q ss_pred             hHhhhcceeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhh-CCCcccHHHHHhhcCCC
Q psy879          142 PIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHN-GFGHVTAEYVFKVCDEP  220 (317)
Q Consensus       142 ~i~sR~~~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~-~~~~i~~~~v~~~~~~~  220 (317)
                      +|+|||+.++|.+++.+++..+|..+++++|+.++++++..++..++||+|.+++.++.++. ..+.|+.++|+++++..
T Consensus       165 tI~SRc~~~~f~~Ls~~eI~~~L~~il~~egi~~e~~Al~~Ia~~s~GdlR~alnlLek~i~~~~~~It~~~V~~~l~~~  244 (546)
T PRK14957        165 TILSRCIQLHLKHISQADIKDQLKIILAKENINSDEQSLEYIAYHAKGSLRDALSLLDQAISFCGGELKQAQIKQMLGII  244 (546)
T ss_pred             hHHHheeeEEeCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhccCCCCHHHHHHHHccC
Confidence            99999999999999999999999999999999999999999999999999999999997654 34789999999999998


Q ss_pred             CHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHHH----HHH--Hhc-------------------CCChHHH
Q psy879          221 HPLAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDIIGNIF----RVA--KTL-------------------DIPEPLK  275 (317)
Q Consensus       221 ~~~~i~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~~~~----~~~--~~~-------------------~~~~~~~  275 (317)
                      ..+.++++++++..++...++.++..+...|.+...++..+.    +.+  +..                   .++....
T Consensus       245 ~~~~v~~ll~Al~~~d~~~~l~~~~~l~~~~~~~~~~l~~l~~~~~r~~~~~~~~~~~~~~~~~~~~i~~~a~~~s~~~l  324 (546)
T PRK14957        245 DSEEVYSIINAIIDNDPKAILPAIKNLALTESSADAVLDRIAEIWFACCIYSFTQSLDAVNDIDVDIINNILAKISIEQA  324 (546)
T ss_pred             CHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHhcccccccchhhHHHHHHHHHhCCHHHH
Confidence            888899999999999999999999999999999888876654    211  100                   2233334


Q ss_pred             HHHHHHHHHHHhHHhcCCCcHHHHHHHHHHHHHhhc
Q psy879          276 LSIIQEIGNVHLRISEGVNSLLQLSGLLARLCIVGS  311 (317)
Q Consensus       276 ~~~~~~l~~~~~~l~~g~~~~l~le~~~~~~~~~~~  311 (317)
                      ..+++.+.+...+|+.+.|+++++|+.+.+++.-.+
T Consensus       325 ~~~~~~~~~~~~~l~~~~~~~~~~em~l~r~~~~~p  360 (546)
T PRK14957        325 HFLYQLTITAKKDIALAPNFETGVTMAILRLIAFQK  360 (546)
T ss_pred             HHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHhcCC
Confidence            458999999999999999999999999999997654

>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau

Probab=100.00  E-value=3.9e-45  Score=326.61  Aligned_cols=304  Identities=26%  Similarity=0.413  Sum_probs=264.9

Q ss_pred             CcccCCCCCCcccCCHHHHHHHHHHHhcCCCce-EEEECCCCCCHHHHHHHHHHHHcCCCC-------------------
Q psy879            1 IEKYRPQTFSDIVGNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARILLGPSF-------------------   60 (317)
Q Consensus         1 ~~ky~P~~~~~~~g~~~~~~~l~~~l~~~~~~~-~ll~G~~G~GKt~la~~la~~l~~~~~-------------------   60 (317)
                      .+||||++|++++||+++++.|..++.+|+++| ++||||||+|||++++.+++.+.|...                   
T Consensus         5 ~~~~rp~~~~~iig~~~~~~~l~~~~~~~~~~~~~Ll~G~~G~GKt~~a~~la~~l~~~~~~~~~~c~~c~~c~~~~~~~   84 (355)
T TIGR02397         5 ARKYRPQTFEDVIGQEHIVQTLKNAIKNGRIAHAYLFSGPRGTGKTSIARIFAKALNCQNGPDGEPCNECESCKEINSGS   84 (355)
T ss_pred             HHHhCCCcHhhccCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCCHHHHHHhcCC
Confidence            479999999999999999999999999999998 999999999999999999999976532                   


Q ss_pred             CCceEEecCCCCcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcCc
Q psy879           61 KDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKII  140 (317)
Q Consensus        61 ~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~  140 (317)
                      ...++++++....+.+.+++.+......+.   .++++||||||+|.++...+++|+++++++++++.+|++++++.++.
T Consensus        85 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~p~---~~~~~vviidea~~l~~~~~~~Ll~~le~~~~~~~lIl~~~~~~~l~  161 (355)
T TIGR02397        85 SLDVIEIDAASNNGVDDIREILDNVKYAPS---SGKYKVYIIDEVHMLSKSAFNALLKTLEEPPEHVVFILATTEPHKIP  161 (355)
T ss_pred             CCCEEEeeccccCCHHHHHHHHHHHhcCcc---cCCceEEEEeChhhcCHHHHHHHHHHHhCCccceeEEEEeCCHHHHH
Confidence            123555665545566777777766554442   37889999999999999999999999999999999999999999999


Q ss_pred             hhHhhhcceeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhh-CCCcccHHHHHhhcCC
Q psy879          141 EPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHN-GFGHVTAEYVFKVCDE  219 (317)
Q Consensus       141 ~~i~sR~~~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~-~~~~i~~~~v~~~~~~  219 (317)
                      ++++|||..++|++++++++..|+..+++++|+.++++++..++..++||+|.+++.+++... ..+.|+.++|.+++..
T Consensus       162 ~~l~sr~~~~~~~~~~~~~l~~~l~~~~~~~g~~i~~~a~~~l~~~~~g~~~~a~~~lekl~~~~~~~it~~~v~~~~~~  241 (355)
T TIGR02397       162 ATILSRCQRFDFKRIPLEDIVERLKKILDKEGIKIEDEALELIARAADGSLRDALSLLDQLISFGNGNITYEDVNELLGL  241 (355)
T ss_pred             HHHHhheeEEEcCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCChHHHHHHHHHHHhhcCCCCCHHHHHHHhCC
Confidence            999999999999999999999999999999999999999999999999999999999988655 4456999999999999


Q ss_pred             CCHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhc------C--------------------CChH
Q psy879          220 PHPLAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDIIGNIFRVAKTL------D--------------------IPEP  273 (317)
Q Consensus       220 ~~~~~i~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~~~~------~--------------------~~~~  273 (317)
                      ..+..++++++++..++..+++.++.++...|++|..++..+.++++.+      +                    ++..
T Consensus       242 ~~~~~i~~l~~ai~~~~~~~a~~~~~~l~~~~~~~~~il~~l~~~~r~l~~~k~~~~~~~~i~~~~~~~l~~~a~~~s~~  321 (355)
T TIGR02397       242 VDDEKLIELLEAILNKDTAEALKILDEILESGVDPEKFLEDLIEILRDLLLIKKTPSNLLAVLESEQEFLKELALKLSLE  321 (355)
T ss_pred             CCHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHhhcCccccccCHHHHHHHHHHHHhCCHH
Confidence            9999999999999999999999999999999999999988876544332      1                    1111


Q ss_pred             HHHHHHHHHHHHHhHHhcCCCcHHHHHHHHHHHH
Q psy879          274 LKLSIIQEIGNVHLRISEGVNSLLQLSGLLARLC  307 (317)
Q Consensus       274 ~~~~~~~~l~~~~~~l~~g~~~~l~le~~~~~~~  307 (317)
                      ....+++.+.+++.++++|.|+++.+|.|+.++|
T Consensus       322 ~L~~~l~~l~~~~~~lk~~~~~~l~le~l~~~~~  355 (355)
T TIGR02397       322 FLLRLLDILLEALKDLRFSNDPRIWLEMTLLRLL  355 (355)
T ss_pred             HHHHHHHHHHHHHHHHhcCCCchHHHHHHHHHhC
Confidence            2233799999999999999999999999999987

This model represents the well-conserved first ~ 365 amino acids of the translation of the dnaX gene. The full-length product of the dnaX gene in the model bacterium E. coli is the DNA polymerase III tau subunit. A translational frameshift leads to early termination and a truncated protein subunit gamma, about 1/3 shorter than tau and present in roughly equal amounts. This frameshift mechanism is not necessarily universal for species with DNA polymerase III but appears conserved in the exterme thermophile Thermus thermophilis.

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=100.00  E-value=4.3e-45  Score=336.48  Aligned_cols=307  Identities=21%  Similarity=0.275  Sum_probs=268.7

Q ss_pred             cccCCCCCCcccCCHHHHHHHHHHHhcCCCce-EEEECCCCCCHHHHHHHHHHHHcCCCC-------------------C
Q psy879            2 EKYRPQTFSDIVGNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARILLGPSF-------------------K   61 (317)
Q Consensus         2 ~ky~P~~~~~~~g~~~~~~~l~~~l~~~~~~~-~ll~G~~G~GKt~la~~la~~l~~~~~-------------------~   61 (317)
                      +||||++|++++||+++++.|..++.+++++| |||+||+|+||||+|+.+++.+.|...                   .
T Consensus         8 ~k~rP~~f~divGq~~v~~~L~~~i~~~~~~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~~~pcg~C~~C~~i~~~~~   87 (527)
T PRK14969          8 RKWRPKSFSELVGQEHVVRALTNALEQQRLHHAYLFTGTRGVGKTTLARILAKSLNCETGVTATPCGVCSACLEIDSGRF   87 (527)
T ss_pred             HHhCCCcHHHhcCcHHHHHHHHHHHHcCCCCEEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCCHHHHHHhcCCC
Confidence            79999999999999999999999999999999 899999999999999999999987431                   1


Q ss_pred             CceEEecCCCCcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcCch
Q psy879           62 DAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIE  141 (317)
Q Consensus        62 ~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~~  141 (317)
                      ..++++++....+.+++++.+......+   ..++++|+||||+|.|+.+++|+|++++|+|+++++||++|+++.++++
T Consensus        88 ~d~~ei~~~~~~~vd~ir~l~~~~~~~p---~~~~~kVvIIDEad~ls~~a~naLLK~LEepp~~~~fIL~t~d~~kil~  164 (527)
T PRK14969         88 VDLIEVDAASNTQVDAMRELLDNAQYAP---TRGRFKVYIIDEVHMLSKSAFNAMLKTLEEPPEHVKFILATTDPQKIPV  164 (527)
T ss_pred             CceeEeeccccCCHHHHHHHHHHHhhCc---ccCCceEEEEcCcccCCHHHHHHHHHHHhCCCCCEEEEEEeCChhhCch
Confidence            1345566655678889998887765554   2378999999999999999999999999999999999999999999999


Q ss_pred             hHhhhcceeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhh-CCCcccHHHHHhhcCCC
Q psy879          142 PIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHN-GFGHVTAEYVFKVCDEP  220 (317)
Q Consensus       142 ~i~sR~~~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~-~~~~i~~~~v~~~~~~~  220 (317)
                      +|+|||+.++|++++.+++..++..+++++|+.++++++..++..++||+|.++++++.+.. +.+.|+.++|..+++..
T Consensus       165 tI~SRc~~~~f~~l~~~~i~~~L~~il~~egi~~~~~al~~la~~s~Gslr~al~lldqai~~~~~~I~~~~v~~~~~~~  244 (527)
T PRK14969        165 TVLSRCLQFNLKQMPPPLIVSHLQHILEQENIPFDATALQLLARAAAGSMRDALSLLDQAIAYGGGTVNESEVRAMLGAI  244 (527)
T ss_pred             hHHHHHHHHhcCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhcCCCcCHHHHHHHHCCC
Confidence            99999999999999999999999999999999999999999999999999999999986544 67789999999999988


Q ss_pred             CHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhc-------------------------CCChHHH
Q psy879          221 HPLAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDIIGNIFRVAKTL-------------------------DIPEPLK  275 (317)
Q Consensus       221 ~~~~i~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~~~~-------------------------~~~~~~~  275 (317)
                      ..+.++++++++..++...++.++.+|...|+++..++..+..+++.+                         .++....
T Consensus       245 ~~~~i~~ll~al~~~~~~~~l~~~~~l~~~~~~~~~~l~~l~~~~rd~~~~~~~~~~~~~~~~~~~~~~~~a~~~s~~~l  324 (527)
T PRK14969        245 DQDYLFALLEALLAQDGAALLAIADAMEERSLSFDAALQDLAALLHRLAIAQTVPDSIADDLPERDRLLDLAKRLSPEDI  324 (527)
T ss_pred             CHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHhhcCcccccccchHHHHHHHHHHcCCHHHH
Confidence            888899999999999999999999999999999988887753332221                         1222334


Q ss_pred             HHHHHHHHHHHhHHhcCCCcHHHHHHHHHHHHHhhc
Q psy879          276 LSIIQEIGNVHLRISEGVNSLLQLSGLLARLCIVGS  311 (317)
Q Consensus       276 ~~~~~~l~~~~~~l~~g~~~~l~le~~~~~~~~~~~  311 (317)
                      ..+++.+.+....++...++++++|+++.+++.-.+
T Consensus       325 ~~~~~~~~~~~~~~~~~~~~~~~~e~~~~r~~~~~~  360 (527)
T PRK14969        325 QLYYQIALHGRRDLGLAPDEYAGFTMTLLRMLAFRP  360 (527)
T ss_pred             HHHHHHHHHHHHHhhcCCCHHHHHHHHHHHHhccCC
Confidence            448999999999999999999999999999986554

>PRK14970 DNA polymerase III subunits gamma and tau; Provisional

Probab=100.00  E-value=2e-44  Score=322.43  Aligned_cols=305  Identities=26%  Similarity=0.371  Sum_probs=266.4

Q ss_pred             cccCCCCCCcccCCHHHHHHHHHHHhcCCCce-EEEECCCCCCHHHHHHHHHHHHcCCC-------CCCceEEecCCCCc
Q psy879            2 EKYRPQTFSDIVGNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARILLGPS-------FKDAVLELNASNDR   73 (317)
Q Consensus         2 ~ky~P~~~~~~~g~~~~~~~l~~~l~~~~~~~-~ll~G~~G~GKt~la~~la~~l~~~~-------~~~~~~~~~~~~~~   73 (317)
                      +||||++|++++||+.+++.+...+++|+++| ++||||||+|||++++++++.+.+..       ....+++++.....
T Consensus         9 ~k~rP~~~~~iig~~~~~~~l~~~i~~~~~~~~~L~~G~~G~GKt~~a~~la~~l~~~~~~~~~~~~~~~~~~l~~~~~~   88 (367)
T PRK14970          9 RKYRPQTFDDVVGQSHITNTLLNAIENNHLAQALLFCGPRGVGKTTCARILARKINQPGYDDPNEDFSFNIFELDAASNN   88 (367)
T ss_pred             HHHCCCcHHhcCCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCcceEEeccccCC
Confidence            79999999999999999999999999999886 99999999999999999999987632       23445666665556


Q ss_pred             ChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcCchhHhhhcceeeec
Q psy879           74 GIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYN  153 (317)
Q Consensus        74 ~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~~~i~sR~~~i~f~  153 (317)
                      +.+++++.+..+...+.   .+++++|+|||+|.++...++.|++++++++.++++|++++...++.++++|||..++|+
T Consensus        89 ~~~~i~~l~~~~~~~p~---~~~~kiviIDE~~~l~~~~~~~ll~~le~~~~~~~~Il~~~~~~kl~~~l~sr~~~v~~~  165 (367)
T PRK14970         89 SVDDIRNLIDQVRIPPQ---TGKYKIYIIDEVHMLSSAAFNAFLKTLEEPPAHAIFILATTEKHKIIPTILSRCQIFDFK  165 (367)
T ss_pred             CHHHHHHHHHHHhhccc---cCCcEEEEEeChhhcCHHHHHHHHHHHhCCCCceEEEEEeCCcccCCHHHHhcceeEecC
Confidence            67788877766544442   367899999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhh-CCCcccHHHHHhhcCCCCHHHHHHHHHHH
Q psy879          154 KLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHN-GFGHVTAEYVFKVCDEPHPLAVKEMLLNC  232 (317)
Q Consensus       154 ~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~-~~~~i~~~~v~~~~~~~~~~~i~~l~~~~  232 (317)
                      +++++++..|+..++.++|+.+++++++.++..++||+|.+++++++.+. ..+.|+.+++..++....++.++++++++
T Consensus       166 ~~~~~~l~~~l~~~~~~~g~~i~~~al~~l~~~~~gdlr~~~~~lekl~~y~~~~it~~~v~~~~~~~~~~~if~l~~ai  245 (367)
T PRK14970        166 RITIKDIKEHLAGIAVKEGIKFEDDALHIIAQKADGALRDALSIFDRVVTFCGKNITRQAVTENLNILDYDTYINVTDLI  245 (367)
T ss_pred             CccHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhCCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCCHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999998764 23349999999999999999999999999


Q ss_pred             hcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhc---------------------------CCChHHHHHHHHHHHHH
Q psy879          233 VEGNMKDSYKIIHHLYKLGYAPEDIIGNIFRVAKTL---------------------------DIPEPLKLSIIQEIGNV  285 (317)
Q Consensus       233 ~~~~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~~~~---------------------------~~~~~~~~~~~~~l~~~  285 (317)
                      ..++..+++.+++++...|++|..|+..+.++++.+                           .++.....++++.+.++
T Consensus       246 ~~~~~~~a~~~~~~l~~~~~~~~~il~~l~~~fr~ll~~k~~~~~~~l~~~~~~~~~~~~~a~~~s~~~L~~~l~~l~~~  325 (367)
T PRK14970        246 LENKIPELLLAFNEILRKGFDGHHFIAGLASHFRDLMVSKTPATIALLEVGEQAKKRYEVQSQKVSQSFLLSGIDIANDC  325 (367)
T ss_pred             HcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHhhccCccccccCCHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            999999999999999999999999998875554333                           11222233489999999


Q ss_pred             HhHHhcCCCcHHHHHHHHHHHHHh
Q psy879          286 HLRISEGVNSLLQLSGLLARLCIV  309 (317)
Q Consensus       286 ~~~l~~g~~~~l~le~~~~~~~~~  309 (317)
                      |.+++++.|+++.+|.++.++|..
T Consensus       326 d~~lK~~~~~~l~lE~~l~~l~~~  349 (367)
T PRK14970        326 DLKYKLSKNQRLLVELALMQLASI  349 (367)
T ss_pred             HHHHhcCCChhHHHHHHHHHHhhc
Confidence            999999999999999999999864

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional

Probab=100.00  E-value=1.5e-44  Score=338.18  Aligned_cols=306  Identities=23%  Similarity=0.319  Sum_probs=269.3

Q ss_pred             cccCCCCCCcccCCHHHHHHHHHHHhcCCCce-EEEECCCCCCHHHHHHHHHHHHcCCCCC-------------------
Q psy879            2 EKYRPQTFSDIVGNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARILLGPSFK-------------------   61 (317)
Q Consensus         2 ~ky~P~~~~~~~g~~~~~~~l~~~l~~~~~~~-~ll~G~~G~GKt~la~~la~~l~~~~~~-------------------   61 (317)
                      +||||++|++++||+++++.|..++.+|+.+| |||+||+|+|||++++.+++.+.|....                   
T Consensus         8 ~kyRP~~~~eiiGq~~~~~~L~~~i~~~~i~~a~Lf~Gp~G~GKTtlA~~lA~~l~c~~~~~~~~~c~~c~~c~~i~~~~   87 (585)
T PRK14950          8 RKWRSQTFAELVGQEHVVQTLRNAIAEGRVAHAYLFTGPRGVGKTSTARILAKAVNCTTNDPKGRPCGTCEMCRAIAEGS   87 (585)
T ss_pred             HHhCCCCHHHhcCCHHHHHHHHHHHHhCCCceEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCccCHHHHHHhcCC
Confidence            79999999999999999999999999999988 8999999999999999999999864321                   


Q ss_pred             -CceEEecCCCCcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcCc
Q psy879           62 -DAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKII  140 (317)
Q Consensus        62 -~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~  140 (317)
                       ..+++++.....+.+++++.+......+.   .++++||||||+|.|+.+.++.|++++|+++.+++||++++..+++.
T Consensus        88 ~~d~~~i~~~~~~~vd~ir~ii~~~~~~p~---~~~~kVvIIDEa~~L~~~a~naLLk~LEepp~~tv~Il~t~~~~kll  164 (585)
T PRK14950         88 AVDVIEMDAASHTSVDDAREIIERVQFRPA---LARYKVYIIDEVHMLSTAAFNALLKTLEEPPPHAIFILATTEVHKVP  164 (585)
T ss_pred             CCeEEEEeccccCCHHHHHHHHHHHhhCcc---cCCeEEEEEeChHhCCHHHHHHHHHHHhcCCCCeEEEEEeCChhhhh
Confidence             23455666556778888887766555443   36899999999999999999999999999999999999999999999


Q ss_pred             hhHhhhcceeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhh-CCCcccHHHHHhhcCC
Q psy879          141 EPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHN-GFGHVTAEYVFKVCDE  219 (317)
Q Consensus       141 ~~i~sR~~~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~-~~~~i~~~~v~~~~~~  219 (317)
                      ++++|||+.+.|.+++..++..++..++.++|+.++++++..++..++||+|.+++.|++.+. ..+.|+.++|..++..
T Consensus       165 ~tI~SR~~~i~f~~l~~~el~~~L~~~a~~egl~i~~eal~~La~~s~Gdlr~al~~LekL~~y~~~~It~e~V~~ll~~  244 (585)
T PRK14950        165 ATILSRCQRFDFHRHSVADMAAHLRKIAAAEGINLEPGALEAIARAATGSMRDAENLLQQLATTYGGEISLSQVQSLLGI  244 (585)
T ss_pred             HHHHhccceeeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHhcC
Confidence            999999999999999999999999999999999999999999999999999999999998655 4568999999999999


Q ss_pred             CCHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhc-----C----------------------CCh
Q psy879          220 PHPLAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDIIGNIFRVAKTL-----D----------------------IPE  272 (317)
Q Consensus       220 ~~~~~i~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~~~~-----~----------------------~~~  272 (317)
                      +.+..++++++++..+|..+++.++++|...|.++..++..+.+.++.+     +                      ++.
T Consensus       245 s~~~~vf~Lidal~~~d~~~al~~l~~L~~~g~~~~~il~~L~~~lR~Ll~lk~g~~~~~l~i~p~~~~~~~~qa~~~s~  324 (585)
T PRK14950        245 SGDEEVKALAEALLAKDLKAALRTLNAVAADGADLRQFTRDLVEYLRQVMLLNSGADRSLLDLTADEKAALQKVSQIANL  324 (585)
T ss_pred             CCHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHhhcCccccccCCHHHHHHHHHHHhcCCH
Confidence            9999999999999999999999999999999999999988765543322     1                      222


Q ss_pred             HHHHHHHHHHHHHHhHHhcCCCcHHHHHHHHHHHHHhh
Q psy879          273 PLKLSIIQEIGNVHLRISEGVNSLLQLSGLLARLCIVG  310 (317)
Q Consensus       273 ~~~~~~~~~l~~~~~~l~~g~~~~l~le~~~~~~~~~~  310 (317)
                      ....++++.+.++|+.+|+|.++++.+|.+++++|...
T Consensus       325 ~~L~~~l~~l~~~D~~lK~~~~~~l~lE~~l~~~~~~~  362 (585)
T PRK14950        325 EALTKWVKAFSQLDFQLRTTSYGQLPLELAVIEALLVP  362 (585)
T ss_pred             HHHHHHHHHHHHHHHHHhcCCCchHHHHHHHHHHhcCC
Confidence            33445899999999999999988999999999999643

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=100.00  E-value=4.5e-44  Score=317.70  Aligned_cols=303  Identities=33%  Similarity=0.547  Sum_probs=262.1

Q ss_pred             CcccCCCCCCcccCCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCc-------
Q psy879            1 IEKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDR-------   73 (317)
Q Consensus         1 ~~ky~P~~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~-------   73 (317)
                      ++||||++|++++|++++++.|..++..+..||++|+||||+|||++++++++.+.+..+...+..+++++..       
T Consensus         6 ~~ky~P~~~~~~~g~~~~~~~L~~~~~~~~~~~lll~Gp~GtGKT~la~~~~~~l~~~~~~~~~~~i~~~~~~~~~~~~~   85 (337)
T PRK12402          6 TEKYRPALLEDILGQDEVVERLSRAVDSPNLPHLLVQGPPGSGKTAAVRALARELYGDPWENNFTEFNVADFFDQGKKYL   85 (337)
T ss_pred             HHhhCCCcHHHhcCCHHHHHHHHHHHhCCCCceEEEECCCCCCHHHHHHHHHHHhcCcccccceEEechhhhhhcchhhh
Confidence            4799999999999999999999999999998999999999999999999999998766544445555553210       


Q ss_pred             -------------------ChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEec
Q psy879           74 -------------------GIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACN  134 (317)
Q Consensus        74 -------------------~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~  134 (317)
                                         ..+.+++.+.......  ...+++++|||||++.+..+.++.|+++++++++++.+|++++
T Consensus        86 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~vlilDe~~~l~~~~~~~L~~~le~~~~~~~~Il~~~  163 (337)
T PRK12402         86 VEDPRFAHFLGTDKRIRSSKIDNFKHVLKEYASYR--PLSADYKTILLDNAEALREDAQQALRRIMEQYSRTCRFIIATR  163 (337)
T ss_pred             hcCcchhhhhhhhhhhccchHHHHHHHHHHHHhcC--CCCCCCcEEEEeCcccCCHHHHHHHHHHHHhccCCCeEEEEeC
Confidence                               1122222222222211  1125678999999999999999999999999988899999999


Q ss_pred             CCCcCchhHhhhcceeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhhCCCcccHHHHH
Q psy879          135 NSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVF  214 (317)
Q Consensus       135 ~~~~l~~~i~sR~~~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~~~~~i~~~~v~  214 (317)
                      .+.++.++++|||..+.|.+++.+++..++..++.++|+.+++++++.++..++||+|.+++.++.++...+.|+.+++.
T Consensus       164 ~~~~~~~~L~sr~~~v~~~~~~~~~~~~~l~~~~~~~~~~~~~~al~~l~~~~~gdlr~l~~~l~~~~~~~~~It~~~v~  243 (337)
T PRK12402        164 QPSKLIPPIRSRCLPLFFRAPTDDELVDVLESIAEAEGVDYDDDGLELIAYYAGGDLRKAILTLQTAALAAGEITMEAAY  243 (337)
T ss_pred             ChhhCchhhcCCceEEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHcCCCCCHHHHH
Confidence            88899999999999999999999999999999999999999999999999999999999999999887766789999999


Q ss_pred             hhcCC-CCHHHHHHHHHHHhcCCHHHHHHHHHHHH-HcCCCHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHHHhHHhcC
Q psy879          215 KVCDE-PHPLAVKEMLLNCVEGNMKDSYKIIHHLY-KLGYAPEDIIGNIFRVAKTLDIPEPLKLSIIQEIGNVHLRISEG  292 (317)
Q Consensus       215 ~~~~~-~~~~~i~~l~~~~~~~~~~~~~~~~~~l~-~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~g  292 (317)
                      +++.. ..+..++++++++..++..+++.++++|+ ..|+++..|+..+.+.+.. ..+.....++++++.++|+++|+|
T Consensus       244 ~~~~~~~~~~~i~~l~~ai~~~~~~~a~~~l~~l~~~~g~~~~~i~~~l~~~~~~-~~~~~~l~~~~~~l~~~d~~lk~g  322 (337)
T PRK12402        244 EALGDVGTDEVIESLLDAAEAGDFTDARKTLDDLLIDEGLSGGEVLEELLRVARS-RYRGDNLARLHRLAADADARLTDG  322 (337)
T ss_pred             HHhCCCCCHHHHHHHHHHHHcCCHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHH-HCCHHHHHHHHHHHHHHHHHHHcC
Confidence            99887 66889999999999999999999999996 7999999999998765544 388888999999999999999999


Q ss_pred             CCcHHHHHHHHHHH
Q psy879          293 VNSLLQLSGLLARL  306 (317)
Q Consensus       293 ~~~~l~le~~~~~~  306 (317)
                      .++.++||.|+.++
T Consensus       323 ~~~~~~le~~i~~~  336 (337)
T PRK12402        323 ANDRIQLEALLAEL  336 (337)
T ss_pred             CCHHHHHHHHHHhh
Confidence            99999999999876

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=100.00  E-value=7e-44  Score=325.64  Aligned_cols=308  Identities=23%  Similarity=0.325  Sum_probs=263.7

Q ss_pred             cccCCCCCCcccCCHHHHHHHHHHHhcCCCce-EEEECCCCCCHHHHHHHHHHHHcCCCCC-------------------
Q psy879            2 EKYRPQTFSDIVGNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARILLGPSFK-------------------   61 (317)
Q Consensus         2 ~ky~P~~~~~~~g~~~~~~~l~~~l~~~~~~~-~ll~G~~G~GKt~la~~la~~l~~~~~~-------------------   61 (317)
                      +||||++|++++||+++++.|..++.+|+++| |||+||+|+|||++|+.+|+.+.|..+.                   
T Consensus         8 ~KyRP~~F~dIIGQe~iv~~L~~aI~~~rl~hA~Lf~GP~GvGKTTlA~~lAk~L~C~~~~~~~~Cg~C~sCr~i~~~~h   87 (605)
T PRK05896          8 RKYRPHNFKQIIGQELIKKILVNAILNNKLTHAYIFSGPRGIGKTSIAKIFAKAINCLNPKDGDCCNSCSVCESINTNQS   87 (605)
T ss_pred             HHhCCCCHHHhcCcHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCcccHHHHHHHcCCC
Confidence            79999999999999999999999999999998 9999999999999999999999875432                   


Q ss_pred             CceEEecCCCCcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcCch
Q psy879           62 DAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIE  141 (317)
Q Consensus        62 ~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~~  141 (317)
                      ..++++++.+..+.+++++.+..+...+..   ++++|+||||+|.|+.+++++|+++||+||+++++|++|+.+.++++
T Consensus        88 ~DiieIdaas~igVd~IReIi~~~~~~P~~---~~~KVIIIDEad~Lt~~A~NaLLKtLEEPp~~tvfIL~Tt~~~KLl~  164 (605)
T PRK05896         88 VDIVELDAASNNGVDEIRNIIDNINYLPTT---FKYKVYIIDEAHMLSTSAWNALLKTLEEPPKHVVFIFATTEFQKIPL  164 (605)
T ss_pred             CceEEeccccccCHHHHHHHHHHHHhchhh---CCcEEEEEechHhCCHHHHHHHHHHHHhCCCcEEEEEECCChHhhhH
Confidence            234566665567888899888776655533   67899999999999999999999999999999999999999999999


Q ss_pred             hHhhhcceeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhh-CCCcccHHHHHhhcCCC
Q psy879          142 PIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHN-GFGHVTAEYVFKVCDEP  220 (317)
Q Consensus       142 ~i~sR~~~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~-~~~~i~~~~v~~~~~~~  220 (317)
                      +++|||+.++|++++++++..|+..++.++|+.++++++..++..++||+|.+++.++.+.. ....|+.++|.++++..
T Consensus       165 TI~SRcq~ieF~~Ls~~eL~~~L~~il~kegi~Is~eal~~La~lS~GdlR~AlnlLekL~~y~~~~It~e~V~ellg~~  244 (605)
T PRK05896        165 TIISRCQRYNFKKLNNSELQELLKSIAKKEKIKIEDNAIDKIADLADGSLRDGLSILDQLSTFKNSEIDIEDINKTFGLV  244 (605)
T ss_pred             HHHhhhhhcccCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCcHHHHHHHHHHHHhhcCCCCCHHHHHHHhccC
Confidence            99999999999999999999999999999999999999999999999999999999998655 33459999999998888


Q ss_pred             CHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhc-----C--------CChHHHHH----------
Q psy879          221 HPLAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDIIGNIFRVAKTL-----D--------IPEPLKLS----------  277 (317)
Q Consensus       221 ~~~~i~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~~~~-----~--------~~~~~~~~----------  277 (317)
                      ....++++++++..++...++.++.+|+..|++|..++..+...++.+     +        .+......          
T Consensus       245 ~~~~Vf~Ll~AI~~kd~~~al~~l~~Ll~~ge~~~~il~~L~~~~RDlL~~k~~~~~~~L~~~~~~~~~~~~~~~~~~~~  324 (605)
T PRK05896        245 DNNKKINLIELIQKNDIEELRNLINELESKGINFEAFCRDLINLLIDLLVYQKTKNINLLKKLSKEQLKTLNLEKQKLLS  324 (605)
T ss_pred             CHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHhhhcCChhhhhcCCHHHHHHHHHHHHHHhh
Confidence            888899999999999999999999999999999999998875544332     1        12211110          


Q ss_pred             -------HHHHHHHHHhHHhcCCCcHHHHHHHHHHHHHhhcc
Q psy879          278 -------IIQEIGNVHLRISEGVNSLLQLSGLLARLCIVGSK  312 (317)
Q Consensus       278 -------~~~~l~~~~~~l~~g~~~~l~le~~~~~~~~~~~~  312 (317)
                             ....+.++-..++..+++...+|.-+.++.+..+-
T Consensus       325 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  366 (605)
T PRK05896        325 IEFNTNFLLNNFVSLINRLKASVNQVFEFEIYLYKIINANPD  366 (605)
T ss_pred             hhcccchHHHHHHHHHHHHHHHhhhHHHHHHHHHHHhccCcc
Confidence                   34455577778888889999998888888765543

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional

Probab=100.00  E-value=1.7e-43  Score=329.99  Aligned_cols=305  Identities=24%  Similarity=0.342  Sum_probs=267.1

Q ss_pred             cccCCCCCCcccCCHHHHHHHHHHHhcCCCce-EEEECCCCCCHHHHHHHHHHHHcCCCCC-------------------
Q psy879            2 EKYRPQTFSDIVGNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARILLGPSFK-------------------   61 (317)
Q Consensus         2 ~ky~P~~~~~~~g~~~~~~~l~~~l~~~~~~~-~ll~G~~G~GKt~la~~la~~l~~~~~~-------------------   61 (317)
                      +||||++|++++||+++++.|..++..++.+| |||+||+|+|||++|+++|+.+.|....                   
T Consensus         8 ~kyRP~~f~~liGq~~i~~~L~~~l~~~rl~~a~Lf~Gp~G~GKttlA~~lAk~L~c~~~~~~~~~~Cg~C~~C~~i~~g   87 (620)
T PRK14948          8 HKYRPQRFDELVGQEAIATTLKNALISNRIAPAYLFTGPRGTGKTSSARILAKSLNCLNSDKPTPEPCGKCELCRAIAAG   87 (620)
T ss_pred             HHhCCCcHhhccChHHHHHHHHHHHHcCCCCceEEEECCCCCChHHHHHHHHHHhcCCCcCCCCCCCCcccHHHHHHhcC
Confidence            69999999999999999999999999998765 9999999999999999999999874311                   


Q ss_pred             --CceEEecCCCCcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcC
Q psy879           62 --DAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKI  139 (317)
Q Consensus        62 --~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l  139 (317)
                        ..+++++.....+++.+++.+......+.   .++++|+||||+|.|+.+++++|+++||+|+.+++||++|+++.++
T Consensus        88 ~h~D~~ei~~~~~~~vd~IReii~~a~~~p~---~~~~KViIIDEad~Lt~~a~naLLK~LEePp~~tvfIL~t~~~~~l  164 (620)
T PRK14948         88 NALDVIEIDAASNTGVDNIRELIERAQFAPV---QARWKVYVIDECHMLSTAAFNALLKTLEEPPPRVVFVLATTDPQRV  164 (620)
T ss_pred             CCccEEEEeccccCCHHHHHHHHHHHhhChh---cCCceEEEEECccccCHHHHHHHHHHHhcCCcCeEEEEEeCChhhh
Confidence              13455665556788899998877655543   3688999999999999999999999999999999999999999999


Q ss_pred             chhHhhhcceeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhhCCCcccHHHHHhhcCC
Q psy879          140 IEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDE  219 (317)
Q Consensus       140 ~~~i~sR~~~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~~~~~i~~~~v~~~~~~  219 (317)
                      .++|+|||+.++|++++.+++..++..++.++++.++++++..++..++||+|.++++++......+.|+.++|.++++.
T Consensus       165 lpTIrSRc~~~~f~~l~~~ei~~~L~~ia~kegi~is~~al~~La~~s~G~lr~A~~lLeklsL~~~~It~e~V~~lvg~  244 (620)
T PRK14948        165 LPTIISRCQRFDFRRIPLEAMVQHLSEIAEKESIEIEPEALTLVAQRSQGGLRDAESLLDQLSLLPGPITPEAVWDLLGA  244 (620)
T ss_pred             hHHHHhheeEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHhccCCCCHHHHHHHhcC
Confidence            99999999999999999999999999999999999999999999999999999999999987665668999999999998


Q ss_pred             CCHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhc-----C-----------------------CC
Q psy879          220 PHPLAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDIIGNIFRVAKTL-----D-----------------------IP  271 (317)
Q Consensus       220 ~~~~~i~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~~~~-----~-----------------------~~  271 (317)
                      ..+..++++++++..++...++.++.+|++.|.++..++..+.++++.+     +                       ++
T Consensus       245 ~~e~~i~~Ll~ai~~~d~~~al~~~~~Ll~~g~~p~~iL~~L~~~~RDLL~~K~~~~~~~l~~i~~d~~~~l~~~A~~~s  324 (620)
T PRK14948        245 VPEQDLLNLLKALASNDPESLLDSCRQLLDRGREPLAILQGLAAFYRDLLLAKTAPNRPDLVAVSQQTWDELCKLAKQIN  324 (620)
T ss_pred             CCHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHhcccchhhhhcCHHHHHHHHHHHhhCC
Confidence            8888899999999999999999999999999999998887765543322     1                       11


Q ss_pred             hHHHHHHHHHHHHHHhHHhcCCCcHHHHHHHHHHHHHh
Q psy879          272 EPLKLSIIQEIGNVHLRISEGVNSLLQLSGLLARLCIV  309 (317)
Q Consensus       272 ~~~~~~~~~~l~~~~~~l~~g~~~~l~le~~~~~~~~~  309 (317)
                      .....++++.+.+++..++++.|+++.+|.++.+++..
T Consensus       325 ~~~L~~~i~~L~eae~~LK~n~nprL~LE~lLl~l~~~  362 (620)
T PRK14948        325 LERILQWQQHLKGSEYQLKNSTQPRLWLEVTLLGLLPS  362 (620)
T ss_pred             HHHHHHHHHHHHHHHHHHhcCCCccHHHHHHHHHhhcc
Confidence            11233378889999999999999999999999999864

>KOG2035|consensus

Probab=100.00  E-value=1e-41  Score=276.08  Aligned_cols=310  Identities=27%  Similarity=0.454  Sum_probs=253.3

Q ss_pred             CcccCCCCCCcccCCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCC-------------------
Q psy879            1 IEKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFK-------------------   61 (317)
Q Consensus         1 ~~ky~P~~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~-------------------   61 (317)
                      ++||||++|+.+.++++....+......+.+||+++|||+|+||.|.+.++.++++|.+..                   
T Consensus         4 vdkyrpksl~~l~~~~e~~~~Lksl~~~~d~PHll~yGPSGaGKKTrimclL~elYG~gveklki~~~t~~tpS~kklEi   83 (351)
T KOG2035|consen    4 VDKYRPKSLDELIYHEELANLLKSLSSTGDFPHLLVYGPSGAGKKTRIMCLLRELYGVGVEKLKIETRTFTTPSKKKLEI   83 (351)
T ss_pred             hhhcCcchhhhcccHHHHHHHHHHhcccCCCCeEEEECCCCCCchhhHHHHHHHHhCCCchheeeeeEEEecCCCceEEE
Confidence            5899999999999999999999999888999999999999999999999999999874421                   


Q ss_pred             -----CceEEecCCCCcC--hHHHHHHHHHHHhhcccCC--CCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEE
Q psy879           62 -----DAVLELNASNDRG--IDTVRNKIKMFAQQKVTLP--PGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALA  132 (317)
Q Consensus        62 -----~~~~~~~~~~~~~--~~~i~~~~~~~~~~~~~~~--~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~  132 (317)
                           ...+++++++...  -..+.+.++.++++.....  ....+||+|.|+|.|+.++|.+|.+.||.+..++++|++
T Consensus        84 stvsS~yHlEitPSDaG~~DRvViQellKevAQt~qie~~~qr~fKvvvi~ead~LT~dAQ~aLRRTMEkYs~~~RlIl~  163 (351)
T KOG2035|consen   84 STVSSNYHLEITPSDAGNYDRVVIQELLKEVAQTQQIETQGQRPFKVVVINEADELTRDAQHALRRTMEKYSSNCRLILV  163 (351)
T ss_pred             EEecccceEEeChhhcCcccHHHHHHHHHHHHhhcchhhccccceEEEEEechHhhhHHHHHHHHHHHHHHhcCceEEEE
Confidence                 1245666665332  2456778888887754322  247899999999999999999999999999999999999


Q ss_pred             ecCCCcCchhHhhhcceeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhhCCCcccHHH
Q psy879          133 CNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHNGFGHVTAEY  212 (317)
Q Consensus       133 ~~~~~~l~~~i~sR~~~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~~~~~i~~~~  212 (317)
                      +|...++.++|+|||..++.+.|+++++..++...++++|+.++.+.+..+++.++||+|+|+-.++.+......-+...
T Consensus       164 cns~SriIepIrSRCl~iRvpaps~eeI~~vl~~v~~kE~l~lp~~~l~rIa~kS~~nLRrAllmlE~~~~~n~~~~a~~  243 (351)
T KOG2035|consen  164 CNSTSRIIEPIRSRCLFIRVPAPSDEEITSVLSKVLKKEGLQLPKELLKRIAEKSNRNLRRALLMLEAVRVNNEPFTANS  243 (351)
T ss_pred             ecCcccchhHHhhheeEEeCCCCCHHHHHHHHHHHHHHhcccCcHHHHHHHHHHhcccHHHHHHHHHHHHhccccccccC
Confidence            99999999999999999999999999999999999999999999999999999999999999999998765432222210


Q ss_pred             HHhhcCCCCHHHHHHHHHHH----hcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHHHhH
Q psy879          213 VFKVCDEPHPLAVKEMLLNC----VEGNMKDSYKIIHHLYKLGYAPEDIIGNIFRVAKTLDIPEPLKLSIIQEIGNVHLR  288 (317)
Q Consensus       213 v~~~~~~~~~~~i~~l~~~~----~~~~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  288 (317)
                       .......=+..+.++...+    ......+.+..+++|+..+++|..|+..+.+.+-. +.+...+..++++.+.+++|
T Consensus       244 -~~i~~~dWe~~i~e~a~~i~~eQs~~~L~~vR~~LYeLL~~CIPP~~Ilk~Ll~~Ll~-~~d~~~k~~~~~~Aa~yEhR  321 (351)
T KOG2035|consen  244 -QVIPKPDWEIYIQEIARVILKEQSPAKLLEVRGRLYELLSHCIPPNTILKELLEELLL-KCDTQLKLEVIQHAAKYEHR  321 (351)
T ss_pred             -CCCCCccHHHHHHHHHHHHHhccCHHHHHHHHHHHHHHHhccCChHHHHHHHHHHHHh-cCCchhHHHHHHHHHHHHHH
Confidence             0000111111233333333    33345667788999999999999999987654332 78888999999999999999


Q ss_pred             HhcCCCcHHHHHHHHHHHHHhhcc
Q psy879          289 ISEGVNSLLQLSGLLARLCIVGSK  312 (317)
Q Consensus       289 l~~g~~~~l~le~~~~~~~~~~~~  312 (317)
                      +..|....+|||.|+++++.+-.+
T Consensus       322 l~lG~KaIfHLEaFVA~fM~iy~~  345 (351)
T KOG2035|consen  322 LRLGQKAIFHLEAFVAKFMCIYKK  345 (351)
T ss_pred             HhhcchhhhhHHHHHHHHHHHHHH
Confidence            999999999999999999877554

>PRK04132 replication factor C small subunit; Provisional

Probab=100.00  E-value=1.2e-38  Score=302.05  Aligned_cols=276  Identities=42%  Similarity=0.685  Sum_probs=253.5

Q ss_pred             EEEEC--CCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHH
Q psy879           34 IIISG--PPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDG  111 (317)
Q Consensus        34 ~ll~G--~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~  111 (317)
                      .+..|  |++.||||+|+++|+.+.+..++..++++|+++.++.+.+++.+..+...... ..++++|+||||+|.|+.+
T Consensus       567 ~~~~G~lPh~lGKTT~A~ala~~l~g~~~~~~~lElNASd~rgid~IR~iIk~~a~~~~~-~~~~~KVvIIDEaD~Lt~~  645 (846)
T PRK04132        567 NFIGGNLPTVLHNTTAALALARELFGENWRHNFLELNASDERGINVIREKVKEFARTKPI-GGASFKIIFLDEADALTQD  645 (846)
T ss_pred             hhhcCCCCCcccHHHHHHHHHHhhhcccccCeEEEEeCCCcccHHHHHHHHHHHHhcCCc-CCCCCEEEEEECcccCCHH
Confidence            56678  88889999999999999887777889999999889999999999877654321 1235799999999999999


Q ss_pred             HHHHHHHHhhhccCCceEEEEecCCCcCchhHhhhcceeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCH
Q psy879          112 AQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDM  191 (317)
Q Consensus       112 ~~~~ll~~le~~~~~~~~il~~~~~~~l~~~i~sR~~~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~  191 (317)
                      +|++|+++||+|+.++.||++||++.++.++|+|||+.++|++++.+++..+|..++.++|+.++++++..++..++||+
T Consensus       646 AQnALLk~lEep~~~~~FILi~N~~~kIi~tIrSRC~~i~F~~ls~~~i~~~L~~I~~~Egi~i~~e~L~~Ia~~s~GDl  725 (846)
T PRK04132        646 AQQALRRTMEMFSSNVRFILSCNYSSKIIEPIQSRCAIFRFRPLRDEDIAKRLRYIAENEGLELTEEGLQAILYIAEGDM  725 (846)
T ss_pred             HHHHHHHHhhCCCCCeEEEEEeCChhhCchHHhhhceEEeCCCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHcCCCH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhhhCCCcccHHHHHhhcCCCCHHHHHHHHHHHhcCCHHHHHHHHHHHH-HcCCCHHHHHHHHHHHHHhcCC
Q psy879          192 RQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEMLLNCVEGNMKDSYKIIHHLY-KLGYAPEDIIGNIFRVAKTLDI  270 (317)
Q Consensus       192 r~~i~~l~~~~~~~~~i~~~~v~~~~~~~~~~~i~~l~~~~~~~~~~~~~~~~~~l~-~~~~~~~~i~~~~~~~~~~~~~  270 (317)
                      |.|++.|+.++...+.|+.+++..+.....++.++++++.+...+..+++..+++++ ..|+++.+++..+++.+....+
T Consensus       726 R~AIn~Lq~~~~~~~~It~~~V~~~~~~~~~~~I~~il~~~l~~~~~~ar~~l~ell~~~G~~~~~iL~~l~~~l~~~~i  805 (846)
T PRK04132        726 RRAINILQAAAALDDKITDENVFLVASRARPEDIREMMLLALKGNFLKAREKLREILLKQGLSGEDVLVQMHREVFNLPI  805 (846)
T ss_pred             HHHHHHHHHHHHhcCCCCHHHHHHHhCCCCHHHHHHHHHHHhcCcHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHhcCC
Confidence            999999998877667899999999999988889999999999999999999999986 8999999999999988876678


Q ss_pred             ChHHHHHHHHHHHHHHhHHhcCCCcHHHHHHHHHHHHHhh
Q psy879          271 PEPLKLSIIQEIGNVHLRISEGVNSLLQLSGLLARLCIVG  310 (317)
Q Consensus       271 ~~~~~~~~~~~l~~~~~~l~~g~~~~l~le~~~~~~~~~~  310 (317)
                      ++..+.+++..+++++.++..|.|+.++|+.|++++|.+.
T Consensus       806 ~~~~k~~ll~~lae~e~rl~~G~n~~iqL~a~la~~~~~~  845 (846)
T PRK04132        806 DEPKKVELADKIGEYNFRLVEGANEMIQLEALLAQFTLMG  845 (846)
T ss_pred             CHHHHHHHHHHHHHHhHHHHCCCCHHHHHHHHHHHHHhhc
Confidence            8889999999999999999999999999999999998653

>COG2256 MGS1 ATPase related to the helicase subunit of the Holliday junction resolvase [DNA replication, recombination, and repair]

Probab=100.00  E-value=4e-38  Score=268.47  Aligned_cols=293  Identities=21%  Similarity=0.306  Sum_probs=237.6

Q ss_pred             cccCCCCCCcccCCHHHHH---HHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHH
Q psy879            2 EKYRPQTFSDIVGNEDTVE---RLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTV   78 (317)
Q Consensus         2 ~ky~P~~~~~~~g~~~~~~---~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i   78 (317)
                      ++.||++|++++||++++.   .|..++++|.+++++|||||||||||+|+.+++..     +..+..+++. ..+..++
T Consensus        16 ~rmRP~~lde~vGQ~HLlg~~~~lrr~v~~~~l~SmIl~GPPG~GKTTlA~liA~~~-----~~~f~~~sAv-~~gvkdl   89 (436)
T COG2256          16 ERLRPKSLDEVVGQEHLLGEGKPLRRAVEAGHLHSMILWGPPGTGKTTLARLIAGTT-----NAAFEALSAV-TSGVKDL   89 (436)
T ss_pred             HHhCCCCHHHhcChHhhhCCCchHHHHHhcCCCceeEEECCCCCCHHHHHHHHHHhh-----CCceEEeccc-cccHHHH
Confidence            5789999999999999985   59999999999999999999999999999999985     4457888876 4678889


Q ss_pred             HHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEec--CCCcCchhHhhhcceeeecCCC
Q psy879           79 RNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACN--NSEKIIEPIQSRCAMLRYNKLT  156 (317)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~--~~~~l~~~i~sR~~~i~f~~~~  156 (317)
                      ++.+....+...   .++..|+||||++++++..|++|+..+|+  +.+.+|.+|+  +...+.++|+|||+++.|.|++
T Consensus        90 r~i~e~a~~~~~---~gr~tiLflDEIHRfnK~QQD~lLp~vE~--G~iilIGATTENPsF~ln~ALlSR~~vf~lk~L~  164 (436)
T COG2256          90 REIIEEARKNRL---LGRRTILFLDEIHRFNKAQQDALLPHVEN--GTIILIGATTENPSFELNPALLSRARVFELKPLS  164 (436)
T ss_pred             HHHHHHHHHHHh---cCCceEEEEehhhhcChhhhhhhhhhhcC--CeEEEEeccCCCCCeeecHHHhhhhheeeeecCC
Confidence            988887755542   26789999999999999999999999995  5566676543  3468999999999999999999


Q ss_pred             HHHHHHHHHHHHH--HcCCC-----CCHHHHHHHHHhcCCCHHHHHHHHHHhhhC---CCcccHHHHHhhcC--------
Q psy879          157 DAQLLSKVIEICE--KENIS-----HTNDGLEAIVFTAQGDMRQALNNLQSTHNG---FGHVTAEYVFKVCD--------  218 (317)
Q Consensus       157 ~~~~~~~l~~~~~--~~~~~-----i~~~~~~~l~~~~~gd~r~~i~~l~~~~~~---~~~i~~~~v~~~~~--------  218 (317)
                      .+++...|.+.+.  .+|+.     +++++.+.++..++||.|.++|.|+.++..   ...++.+.+.+++.        
T Consensus       165 ~~di~~~l~ra~~~~~rgl~~~~~~i~~~a~~~l~~~s~GD~R~aLN~LE~~~~~~~~~~~~~~~~l~~~l~~~~~~~Dk  244 (436)
T COG2256         165 SEDIKKLLKRALLDEERGLGGQIIVLDEEALDYLVRLSNGDARRALNLLELAALSAEPDEVLILELLEEILQRRSARFDK  244 (436)
T ss_pred             HHHHHHHHHHHHhhhhcCCCcccccCCHHHHHHHHHhcCchHHHHHHHHHHHHHhcCCCcccCHHHHHHHHhhhhhccCC
Confidence            9999999998443  34554     789999999999999999999999987652   22334666665442        


Q ss_pred             --CCCHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHH-HhcCCChHHHHHHHHHHHHHHhHHhcCC-C
Q psy879          219 --EPHPLAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDIIGNIFRVA-KTLDIPEPLKLSIIQEIGNVHLRISEGV-N  294 (317)
Q Consensus       219 --~~~~~~i~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~-~~~~~~~~~~~~~~~~l~~~~~~l~~g~-~  294 (317)
                        ..+++.++.+.++++..|.+.|+.|+..|++.|++|..|.+.+.+++ +.+|+.+.....+-....+.  --.-|. .
T Consensus       245 ~gD~hYdliSA~hKSvRGSD~dAALyylARmi~~GeDp~yiARRlv~~AsEDIGlAdP~Al~~a~aa~da--~~~lG~PE  322 (436)
T COG2256         245 DGDAHYDLISALHKSVRGSDPDAALYYLARMIEAGEDPLYIARRLVRIASEDIGLADPNALQVAVAALDA--VERLGSPE  322 (436)
T ss_pred             CcchHHHHHHHHHHhhccCCcCHHHHHHHHHHhcCCCHHHHHHHHHHHHHhhccCCChhHHHHHHHHHHH--HHHhCCch
Confidence              45678899999999999999999999999999999999999998876 44577665544433333333  223455 7


Q ss_pred             cHHHHHHHHHHHH
Q psy879          295 SLLQLSGLLARLC  307 (317)
Q Consensus       295 ~~l~le~~~~~~~  307 (317)
                      .++.|-..+.-+|
T Consensus       323 ~~i~LAqavvyLA  335 (436)
T COG2256         323 ARIALAQAVVYLA  335 (436)
T ss_pred             HHHHHHHHHHHHH
Confidence            7788888887777

>KOG0990|consensus

Probab=100.00  E-value=4.9e-39  Score=265.90  Aligned_cols=309  Identities=33%  Similarity=0.456  Sum_probs=272.1

Q ss_pred             CcccCCCCCCcccCCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcC-CCCCCceEEecCCCCcChHHHH
Q psy879            1 IEKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLG-PSFKDAVLELNASNDRGIDTVR   79 (317)
Q Consensus         1 ~~ky~P~~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~-~~~~~~~~~~~~~~~~~~~~i~   79 (317)
                      ++||||..++++++|++++..+.++...++.||+|||||||+|||+...+.++.+++ ...+..+.++|.+++++++.++
T Consensus        32 vekyrP~~l~dv~~~~ei~st~~~~~~~~~lPh~L~YgPPGtGktsti~a~a~~ly~~~~~~~m~lelnaSd~rgid~vr  111 (360)
T KOG0990|consen   32 VEKYRPPFLGIVIKQEPIWSTENRYSGMPGLPHLLFYGPPGTGKTSTILANARDFYSPHPTTSMLLELNASDDRGIDPVR  111 (360)
T ss_pred             ccCCCCchhhhHhcCCchhhHHHHhccCCCCCcccccCCCCCCCCCchhhhhhhhcCCCCchhHHHHhhccCccCCcchH
Confidence            589999999999999999999999999999999999999999999999999999998 4556668899999999999999


Q ss_pred             HHHHHHHhhcc-cCC--CCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcCchhHhhhcceeeecCCC
Q psy879           80 NKIKMFAQQKV-TLP--PGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLT  156 (317)
Q Consensus        80 ~~~~~~~~~~~-~~~--~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~~~i~sR~~~i~f~~~~  156 (317)
                      +.+..+..+.. ...  ....+.+|+||+|.|+.++|++|.+.+|.+..+++|++++|.+.++.++++|||..++|.|++
T Consensus       112 ~qi~~fast~~~~~fst~~~fKlvILDEADaMT~~AQnALRRviek~t~n~rF~ii~n~~~ki~pa~qsRctrfrf~pl~  191 (360)
T KOG0990|consen  112 QQIHLFASTQQPTTYSTHAAFKLVILDEADAMTRDAQNALRRVIEKYTANTRFATISNPPQKIHPAQQSRCTRFRFAPLT  191 (360)
T ss_pred             HHHHHHHhhccceeccccCceeEEEecchhHhhHHHHHHHHHHHHHhccceEEEEeccChhhcCchhhcccccCCCCCCC
Confidence            88877766542 111  247899999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhhCCCc-----ccHHHHHhhcCCCCHHHHHHHHHH
Q psy879          157 DAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHNGFGH-----VTAEYVFKVCDEPHPLAVKEMLLN  231 (317)
Q Consensus       157 ~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~~~~~-----i~~~~v~~~~~~~~~~~i~~l~~~  231 (317)
                      ..+...++.+++..+...++++....++..+.||+|.++|.|+..+.....     +..+.+..+.+......+..+++.
T Consensus       192 ~~~~~~r~shi~e~e~~~~~~~~~~a~~r~s~gDmr~a~n~Lqs~~~~~~~~~e~~~~~~~vy~c~g~p~~~dI~~I~~~  271 (360)
T KOG0990|consen  192 MAQQTERQSHIRESEQKETNPEGYSALGRLSVGDMRVALNYLQSILKKVMERKELNNPNDLVYQCKGAPQPSDIRQIIEK  271 (360)
T ss_pred             hhhhhhHHHHHHhcchhhcCHHHHHHHHHHhHHHHHHHHHHHHHHHHHhCCCCCCCCchhhHHHhcCCCChhHHHHHHHH
Confidence            999999999999999999999999999999999999999999987663333     455568999988888899999999


Q ss_pred             HhcCCHHHHHHHHHHH-HHcCCCHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHHHhHHhcCCCcHHHHHHHHHHHHHh
Q psy879          232 CVEGNMKDSYKIIHHL-YKLGYAPEDIIGNIFRVAKTLDIPEPLKLSIIQEIGNVHLRISEGVNSLLQLSGLLARLCIV  309 (317)
Q Consensus       232 ~~~~~~~~~~~~~~~l-~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~g~~~~l~le~~~~~~~~~  309 (317)
                      +.+.++.+++.-+..+ ...|..-.+++..+...+.........+..++..+++.++++..|++..+++..++..+...
T Consensus       272 il~~~~~~~~~~is~lk~~~gla~~d~i~~l~~~~~~~~~~~~~~~~I~~~l~~Ie~~ls~g~~~~~ql~aii~~~~~~  350 (360)
T KOG0990|consen  272 RMNGEDIELMLDDSELKKPKGLARQDRRAELEQRFAIVISKTPVEGHILYQLADIEERLSKGCMQKEQLKAIIKNFAAE  350 (360)
T ss_pred             HhcCchHHHHhhhhhhhhhhhhHHHHHHHHHHHHHHHHhcchHHHHHHHHhHHHHHHHHhcchhHHHHHHHHHHHHHHH
Confidence            9999887777777777 45677888888887665554455557788899999999999999999999999999988643

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=100.00  E-value=5.7e-37  Score=269.51  Aligned_cols=293  Identities=27%  Similarity=0.393  Sum_probs=241.6

Q ss_pred             CcccCCCCCCcccCCHHHHHHHHHHHhcCCCce-EEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHH
Q psy879            1 IEKYRPQTFSDIVGNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVR   79 (317)
Q Consensus         1 ~~ky~P~~~~~~~g~~~~~~~l~~~l~~~~~~~-~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~   79 (317)
                      ++||||++|++++||+++.+.+..++++|+.|| ++|+||||+|||++++++++.+.     ..+.++++.. ...+.++
T Consensus        12 ~~kyrP~~~~~~~~~~~~~~~l~~~~~~~~~~~~lll~G~~G~GKT~la~~l~~~~~-----~~~~~i~~~~-~~~~~i~   85 (316)
T PHA02544         12 EQKYRPSTIDECILPAADKETFKSIVKKGRIPNMLLHSPSPGTGKTTVAKALCNEVG-----AEVLFVNGSD-CRIDFVR   85 (316)
T ss_pred             eeccCCCcHHHhcCcHHHHHHHHHHHhcCCCCeEEEeeCcCCCCHHHHHHHHHHHhC-----ccceEeccCc-ccHHHHH
Confidence            489999999999999999999999999999988 66699999999999999999862     2356677765 3355566


Q ss_pred             HHHHHHHhhcccCCCCceeEEEEeCCCCC-CHHHHHHHHHHhhhccCCceEEEEecCCCcCchhHhhhcceeeecCCCHH
Q psy879           80 NKIKMFAQQKVTLPPGRHKIVILDEADSM-TDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDA  158 (317)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~vliiDE~d~l-~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~~~i~sR~~~i~f~~~~~~  158 (317)
                      +.+..+.....  ..+.+++|||||+|.+ ..+.++.|..++++++.++.+|+++|...++.++++|||..+.|+.|+.+
T Consensus        86 ~~l~~~~~~~~--~~~~~~vliiDe~d~l~~~~~~~~L~~~le~~~~~~~~Ilt~n~~~~l~~~l~sR~~~i~~~~p~~~  163 (316)
T PHA02544         86 NRLTRFASTVS--LTGGGKVIIIDEFDRLGLADAQRHLRSFMEAYSKNCSFIITANNKNGIIEPLRSRCRVIDFGVPTKE  163 (316)
T ss_pred             HHHHHHHHhhc--ccCCCeEEEEECcccccCHHHHHHHHHHHHhcCCCceEEEEcCChhhchHHHHhhceEEEeCCCCHH
Confidence            65544433321  1146899999999999 67788889999999999999999999999999999999999999999998


Q ss_pred             HHHHHH-------HHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhhCCCcccHHHHHhhcCCCCHHHHHHHHHH
Q psy879          159 QLLSKV-------IEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEMLLN  231 (317)
Q Consensus       159 ~~~~~l-------~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~~~~~i~~~~v~~~~~~~~~~~i~~l~~~  231 (317)
                      +...++       ..++.++|+.++++++..++..+.||+|.+++.++.++. ...++.+++....    ...+++++++
T Consensus       164 ~~~~il~~~~~~~~~~~~~~~~~i~~~al~~l~~~~~~d~r~~l~~l~~~~~-~~~i~~~~l~~~~----~~~~~~l~~~  238 (316)
T PHA02544        164 EQIEMMKQMIVRCKGILEAEGVEVDMKVLAALVKKNFPDFRRTINELQRYAS-TGKIDAGILSEVT----NSDIDDVVEA  238 (316)
T ss_pred             HHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHHHc-cCCCCHHHHHHhh----HHHHHHHHHH
Confidence            877554       345566899999999999999999999999999997764 3578888877655    5578889999


Q ss_pred             HhcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHHHhHHhcCCCcHHHHHHHHHHHHHhh
Q psy879          232 CVEGNMKDSYKIIHHLYKLGYAPEDIIGNIFRVAKTLDIPEPLKLSIIQEIGNVHLRISEGVNSLLQLSGLLARLCIVG  310 (317)
Q Consensus       232 ~~~~~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~g~~~~l~le~~~~~~~~~~  310 (317)
                      +..++..++.. ...  ..+.++..++..+++.+.. .+.+....++++.+.+.+..+..|.|+.+++|.+++++|..+
T Consensus       239 l~~~d~~~~~~-~~~--~~~~~~~~~l~~~~~~~~~-~~~~~~~~~~~~~l~~~~~~~~~~~~~~l~le~~l~~~~~~~  313 (316)
T PHA02544        239 LKAKDFKAVRA-LAP--NYANDYASFVGKLYDELYP-QVTPPSIIRLIEIIGENNQYHGFAADQEIHLLYLLTQLMLEC  313 (316)
T ss_pred             HHcCCHHHHHH-HHH--HhccCHHHHHHHHHHHHHH-hCCHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHhc
Confidence            99888888777 322  3378888998887665443 456777889999999999999999999999999999998644

>PRK05564 DNA polymerase III subunit delta'; Validated

Probab=100.00  E-value=2.1e-36  Score=264.54  Aligned_cols=280  Identities=21%  Similarity=0.306  Sum_probs=227.5

Q ss_pred             CCCCcccCCHHHHHHHHHHHhcCCCce-EEEECCCCCCHHHHHHHHHHHHcCCCCC---CceEEecC--CCCcChHHHHH
Q psy879            7 QTFSDIVGNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARILLGPSFK---DAVLELNA--SNDRGIDTVRN   80 (317)
Q Consensus         7 ~~~~~~~g~~~~~~~l~~~l~~~~~~~-~ll~G~~G~GKt~la~~la~~l~~~~~~---~~~~~~~~--~~~~~~~~i~~   80 (317)
                      ++|++++||+++++.|..++++|+++| |+|+||+|+|||++|+.+++.+.|....   ..+..+..  ....+.+++++
T Consensus         1 m~~~~i~g~~~~~~~l~~~~~~~~~~ha~Lf~G~~G~Gk~~la~~~a~~l~c~~~~~~h~D~~~~~~~~~~~i~v~~ir~   80 (313)
T PRK05564          1 MSFHTIIGHENIKNRIKNSIIKNRFSHAHIIVGEDGIGKSLLAKEIALKILGKSQQREYVDIIEFKPINKKSIGVDDIRN   80 (313)
T ss_pred             CChhhccCcHHHHHHHHHHHHcCCCCceEEeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCeEEeccccCCCCCHHHHHH
Confidence            469999999999999999999999999 8999999999999999999999875422   12333333  34567889999


Q ss_pred             HHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcCchhHhhhcceeeecCCCHHHH
Q psy879           81 KIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQL  160 (317)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~~~i~sR~~~i~f~~~~~~~~  160 (317)
                      ....+...+..   ++++|+|||++|.|+.+++|+|++++|+||+++.||++|+++++++++|+|||+.++|.+++++++
T Consensus        81 ~~~~~~~~p~~---~~~kv~iI~~ad~m~~~a~naLLK~LEepp~~t~~il~~~~~~~ll~TI~SRc~~~~~~~~~~~~~  157 (313)
T PRK05564         81 IIEEVNKKPYE---GDKKVIIIYNSEKMTEQAQNAFLKTIEEPPKGVFIILLCENLEQILDTIKSRCQIYKLNRLSKEEI  157 (313)
T ss_pred             HHHHHhcCccc---CCceEEEEechhhcCHHHHHHHHHHhcCCCCCeEEEEEeCChHhCcHHHHhhceeeeCCCcCHHHH
Confidence            88877666543   789999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhhCCCcccHHHHHhhcCCCCHHHHHHHHHHHhcCCHHHH
Q psy879          161 LSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEMLLNCVEGNMKDS  240 (317)
Q Consensus       161 ~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~~~~~i~~~~v~~~~~~~~~~~i~~l~~~~~~~~~~~~  240 (317)
                      ..|+...+.    .++++.+..++..++|++..+...+....       ...        ..+.++++++.+..++...+
T Consensus       158 ~~~l~~~~~----~~~~~~~~~l~~~~~g~~~~a~~~~~~~~-------~~~--------~~~~~~~~~~~l~~~~~~~~  218 (313)
T PRK05564        158 EKFISYKYN----DIKEEEKKSAIAFSDGIPGKVEKFIEDDS-------LKN--------IRNMSLEILKDIKKSNINIL  218 (313)
T ss_pred             HHHHHHHhc----CCCHHHHHHHHHHcCCCHHHHHHHhcccH-------HHH--------HHHHHHHHHHHHHcCCHHHH
Confidence            999987653    46788888999999999998886653210       100        12357788888888888888


Q ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHHHhc--------------------------CCChHHHHHHHHHHHHHHhHHhcCCC
Q psy879          241 YKIIHHLYKLGYAPEDIIGNIFRVAKTL--------------------------DIPEPLKLSIIQEIGNVHLRISEGVN  294 (317)
Q Consensus       241 ~~~~~~l~~~~~~~~~i~~~~~~~~~~~--------------------------~~~~~~~~~~~~~l~~~~~~l~~g~~  294 (317)
                      +.++..+...+.++..++..+.++++.+                          ..+.....++++.+.+++..+++|+|
T Consensus       219 l~~~~~l~~~~~~~~~~l~~l~~~~rdll~~k~~~~~~~~~~~~~~~~i~~~a~~~s~~~L~~~~~~l~~~~~~l~~n~n  298 (313)
T PRK05564        219 LKYENFLIKYKENWEEILTCILSYIRDSLLYKETGNEELIINIDKIEDIKHISEKFSYKKLNKMIEIINDTRDNLSSNVN  298 (313)
T ss_pred             HHHHHHHHHcCccHHHHHHHHHHHHHHHHHHhccCchhhhcChhHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHcCC
Confidence            8888888888888877777655443222                          12222344578999999999999999


Q ss_pred             cHHHHHHHHHHHHH
Q psy879          295 SLLQLSGLLARLCI  308 (317)
Q Consensus       295 ~~l~le~~~~~~~~  308 (317)
                      +++.+|.++.++..
T Consensus       299 ~~l~le~lll~~~~  312 (313)
T PRK05564        299 PTLVFDSMLIKMQE  312 (313)
T ss_pred             ccHHHHHHHHhhhc
Confidence            99999999999864

>PRK04195 replication factor C large subunit; Provisional

Probab=100.00  E-value=1.5e-34  Score=266.21  Aligned_cols=293  Identities=26%  Similarity=0.406  Sum_probs=232.9

Q ss_pred             CcccCCCCCCcccCCHHHHHHHHHHHh---cCC-CceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChH
Q psy879            1 IEKYRPQTFSDIVGNEDTVERLKVFSS---SGN-VPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGID   76 (317)
Q Consensus         1 ~~ky~P~~~~~~~g~~~~~~~l~~~l~---~~~-~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~   76 (317)
                      +|||||++|++++||+++++.|..++.   .|. .++++|+||||+|||++|+++++.+     +..++++++++....+
T Consensus         5 ~eKyrP~~l~dlvg~~~~~~~l~~~l~~~~~g~~~~~lLL~GppG~GKTtla~ala~el-----~~~~ielnasd~r~~~   79 (482)
T PRK04195          5 VEKYRPKTLSDVVGNEKAKEQLREWIESWLKGKPKKALLLYGPPGVGKTSLAHALANDY-----GWEVIELNASDQRTAD   79 (482)
T ss_pred             hhhcCCCCHHHhcCCHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHc-----CCCEEEEcccccccHH
Confidence            589999999999999999999998886   344 4469999999999999999999986     3457888888777777


Q ss_pred             HHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCH----HHHHHHHHHhhhccCCceEEEEecCCCcCch-hHhhhcceee
Q psy879           77 TVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTD----GAQQALRRTMEIYSNTTRFALACNNSEKIIE-PIQSRCAMLR  151 (317)
Q Consensus        77 ~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~----~~~~~ll~~le~~~~~~~~il~~~~~~~l~~-~i~sR~~~i~  151 (317)
                      .++..+.......... ...+++|||||+|.++.    ...++|+++++.  ....+|+++|.+..+.+ ++++||..+.
T Consensus        80 ~i~~~i~~~~~~~sl~-~~~~kvIiIDEaD~L~~~~d~~~~~aL~~~l~~--~~~~iIli~n~~~~~~~k~Lrsr~~~I~  156 (482)
T PRK04195         80 VIERVAGEAATSGSLF-GARRKLILLDEVDGIHGNEDRGGARAILELIKK--AKQPIILTANDPYDPSLRELRNACLMIE  156 (482)
T ss_pred             HHHHHHHHhhccCccc-CCCCeEEEEecCcccccccchhHHHHHHHHHHc--CCCCEEEeccCccccchhhHhccceEEE
Confidence            7777666555432211 13689999999999976    568899999984  44668889998887776 8999999999


Q ss_pred             ecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhhCCCcccHHHHHhhcCCCCHHHHHHHHHH
Q psy879          152 YNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEMLLN  231 (317)
Q Consensus       152 f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~~~~~i~~~~v~~~~~~~~~~~i~~l~~~  231 (317)
                      |++++..++..+|..++..+|+.+++++++.++..++||+|.+++.|+.++.+.+.++.+++..+........+|+++..
T Consensus       157 f~~~~~~~i~~~L~~i~~~egi~i~~eaL~~Ia~~s~GDlR~ain~Lq~~a~~~~~it~~~v~~~~~~d~~~~if~~l~~  236 (482)
T PRK04195        157 FKRLSTRSIVPVLKRICRKEGIECDDEALKEIAERSGGDLRSAINDLQAIAEGYGKLTLEDVKTLGRRDREESIFDALDA  236 (482)
T ss_pred             ecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHhcCCCCCcHHHHHHhhcCCCCCCHHHHHHH
Confidence            99999999999999999999999999999999999999999999999997777788999999988877777789999998


Q ss_pred             Hhc-CCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHHHh---HHhcCCCcHHHHHHHHHHH
Q psy879          232 CVE-GNMKDSYKIIHHLYKLGYAPEDIIGNIFRVAKTLDIPEPLKLSIIQEIGNVHL---RISEGVNSLLQLSGLLARL  306 (317)
Q Consensus       232 ~~~-~~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~---~l~~g~~~~l~le~~~~~~  306 (317)
                      +.. ++...++..+.+   ..++|..++..+...+-..-.+.....++++++.+.|.   ++..+.+  .+|..+.+.+
T Consensus       237 i~~~k~~~~a~~~~~~---~~~~~~~i~~~l~en~~~~~~~~~~~~~a~~~ls~ad~~~~~~~~~~~--~~l~~~~~~~  310 (482)
T PRK04195        237 VFKARNADQALEASYD---VDEDPDDLIEWIDENIPKEYDDPEDIARAYDALSRADIFLGRVKRTQN--YDLWRYASDL  310 (482)
T ss_pred             HHCCCCHHHHHHHHHc---ccCCHHHHHHHHHhccccccCCHHHHHHHHHHHhHHHHHHHHHHhcCC--cchHHHHHHH
Confidence            876 778777765543   56788888777655433211233556667777766554   4555555  4445544444

>PRK13342 recombination factor protein RarA; Reviewed

Probab=100.00  E-value=4.7e-34  Score=258.31  Aligned_cols=294  Identities=22%  Similarity=0.339  Sum_probs=234.5

Q ss_pred             CcccCCCCCCcccCCHHHHHH---HHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHH
Q psy879            1 IEKYRPQTFSDIVGNEDTVER---LKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDT   77 (317)
Q Consensus         1 ~~ky~P~~~~~~~g~~~~~~~---l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~   77 (317)
                      .+||||++|++++||++++..   +..++.++..++++|+||||||||++|+.+++.+.     ..+..+++.. .+...
T Consensus         3 a~~~RP~~l~d~vGq~~~v~~~~~L~~~i~~~~~~~ilL~GppGtGKTtLA~~ia~~~~-----~~~~~l~a~~-~~~~~   76 (413)
T PRK13342          3 AERMRPKTLDEVVGQEHLLGPGKPLRRMIEAGRLSSMILWGPPGTGKTTLARIIAGATD-----APFEALSAVT-SGVKD   76 (413)
T ss_pred             hhhhCCCCHHHhcCcHHHhCcchHHHHHHHcCCCceEEEECCCCCCHHHHHHHHHHHhC-----CCEEEEeccc-ccHHH
Confidence            479999999999999999776   99999999988999999999999999999999863     3466666653 45666


Q ss_pred             HHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecC--CCcCchhHhhhcceeeecCC
Q psy879           78 VRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNN--SEKIIEPIQSRCAMLRYNKL  155 (317)
Q Consensus        78 i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~--~~~l~~~i~sR~~~i~f~~~  155 (317)
                      +++.+.......   ..+.+.+++|||+|.++...++.|++.+++  ....+|.+++.  ...+.++++|||..+.|+++
T Consensus        77 ir~ii~~~~~~~---~~g~~~vL~IDEi~~l~~~~q~~LL~~le~--~~iilI~att~n~~~~l~~aL~SR~~~~~~~~l  151 (413)
T PRK13342         77 LREVIEEARQRR---SAGRRTILFIDEIHRFNKAQQDALLPHVED--GTITLIGATTENPSFEVNPALLSRAQVFELKPL  151 (413)
T ss_pred             HHHHHHHHHHhh---hcCCceEEEEechhhhCHHHHHHHHHHhhc--CcEEEEEeCCCChhhhccHHHhccceeeEeCCC
Confidence            776666554332   125788999999999999999999999986  44555555432  35789999999999999999


Q ss_pred             CHHHHHHHHHHHHHHc--CC-CCCHHHHHHHHHhcCCCHHHHHHHHHHhhhCCCcccHHHHHhhcCC----------CCH
Q psy879          156 TDAQLLSKVIEICEKE--NI-SHTNDGLEAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDE----------PHP  222 (317)
Q Consensus       156 ~~~~~~~~l~~~~~~~--~~-~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~~~~~i~~~~v~~~~~~----------~~~  222 (317)
                      +.+++..++...+...  ++ .+++++++.++..++||+|.+++.++.++.....|+.+++..++..          ...
T Consensus       152 s~e~i~~lL~~~l~~~~~~~i~i~~~al~~l~~~s~Gd~R~aln~Le~~~~~~~~It~~~v~~~~~~~~~~~d~~~~~~~  231 (413)
T PRK13342        152 SEEDIEQLLKRALEDKERGLVELDDEALDALARLANGDARRALNLLELAALGVDSITLELLEEALQKRAARYDKDGDEHY  231 (413)
T ss_pred             CHHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHhCCCCHHHHHHHHHHHHHccCCCCHHHHHHHHhhhhhccCCCccHHH
Confidence            9999999999987653  44 7899999999999999999999999987665667999999887653          234


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHH-HhcCCChHHHHHHHHHHHHHHhHHhcCC-CcHHHHH
Q psy879          223 LAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDIIGNIFRVA-KTLDIPEPLKLSIIQEIGNVHLRISEGV-NSLLQLS  300 (317)
Q Consensus       223 ~~i~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~-~~~~~~~~~~~~~~~~l~~~~~~l~~g~-~~~l~le  300 (317)
                      +.+..+.+++...|.+.++.|+..|+..|++|..|.+.+...+ +..|+.+.....+.....+.-..  -|. ..++.|-
T Consensus       232 ~~isa~~ks~rgsd~~aal~~l~~~l~~G~d~~~i~rrl~~~a~edig~a~~~~~~~~~~~~~~~~~--~g~pe~~~~l~  309 (413)
T PRK13342        232 DLISALHKSIRGSDPDAALYYLARMLEAGEDPLFIARRLVIIASEDIGLADPNALQVAVAAADAVER--IGMPEGRIALA  309 (413)
T ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhhcccCHHHHHHHHHHHHHHHH--hCCcHHHHHHH
Confidence            5677888888889999999999999999999999999987755 55677776555544444444333  244 6667777


Q ss_pred             HHHHHHH
Q psy879          301 GLLARLC  307 (317)
Q Consensus       301 ~~~~~~~  307 (317)
                      ..+.-+|
T Consensus       310 ~~~~~l~  316 (413)
T PRK13342        310 QAVIYLA  316 (413)
T ss_pred             HHHHHHH
Confidence            7776666

>PRK13341 recombination factor protein RarA/unknown domain fusion protein; Reviewed

Probab=100.00  E-value=1.6e-33  Score=266.31  Aligned_cols=266  Identities=21%  Similarity=0.313  Sum_probs=212.8

Q ss_pred             cccCCCCCCcccCCHHHHH---HHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHH
Q psy879            2 EKYRPQTFSDIVGNEDTVE---RLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTV   78 (317)
Q Consensus         2 ~ky~P~~~~~~~g~~~~~~---~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i   78 (317)
                      +||||++|++++||++++.   .+..++.+++.+|++||||||+||||+|+++++.+.     ..+..+++.. .+...+
T Consensus        20 ek~RP~tldd~vGQe~ii~~~~~L~~~i~~~~~~slLL~GPpGtGKTTLA~aIA~~~~-----~~f~~lna~~-~~i~di   93 (725)
T PRK13341         20 DRLRPRTLEEFVGQDHILGEGRLLRRAIKADRVGSLILYGPPGVGKTTLARIIANHTR-----AHFSSLNAVL-AGVKDL   93 (725)
T ss_pred             HhcCCCcHHHhcCcHHHhhhhHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHhc-----Ccceeehhhh-hhhHHH
Confidence            6899999999999999984   688899999999999999999999999999999863     2345566542 344455


Q ss_pred             HHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecC--CCcCchhHhhhcceeeecCCC
Q psy879           79 RNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNN--SEKIIEPIQSRCAMLRYNKLT  156 (317)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~--~~~l~~~i~sR~~~i~f~~~~  156 (317)
                      ++.+........  ..+.+.++||||+|.++...+++|++.+++  ...++|.+++.  ...+.+++.|||..+.|++++
T Consensus        94 r~~i~~a~~~l~--~~~~~~IL~IDEIh~Ln~~qQdaLL~~lE~--g~IiLI~aTTenp~~~l~~aL~SR~~v~~l~pLs  169 (725)
T PRK13341         94 RAEVDRAKERLE--RHGKRTILFIDEVHRFNKAQQDALLPWVEN--GTITLIGATTENPYFEVNKALVSRSRLFRLKSLS  169 (725)
T ss_pred             HHHHHHHHHHhh--hcCCceEEEEeChhhCCHHHHHHHHHHhcC--ceEEEEEecCCChHhhhhhHhhccccceecCCCC
Confidence            555544322110  114577999999999999999999999985  34445554433  247889999999999999999


Q ss_pred             HHHHHHHHHHHHH-------HcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhhC---C--C--cccHHHHHhhc-----
Q psy879          157 DAQLLSKVIEICE-------KENISHTNDGLEAIVFTAQGDMRQALNNLQSTHNG---F--G--HVTAEYVFKVC-----  217 (317)
Q Consensus       157 ~~~~~~~l~~~~~-------~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~~---~--~--~i~~~~v~~~~-----  217 (317)
                      .+++..++...+.       .+++.+++++++.++..++||+|++++.|+.++..   .  .  .++.+.+.+++     
T Consensus       170 ~edi~~IL~~~l~~~~~~~g~~~v~I~deaL~~La~~s~GD~R~lln~Le~a~~~~~~~~~~~i~It~~~~~e~l~~~~~  249 (725)
T PRK13341        170 DEDLHQLLKRALQDKERGYGDRKVDLEPEAEKHLVDVANGDARSLLNALELAVESTPPDEDGLIDITLAIAEESIQQRAV  249 (725)
T ss_pred             HHHHHHHHHHHHHHHHhhcCCcccCCCHHHHHHHHHhCCCCHHHHHHHHHHHHHhcccCCCCceeccHHHHHHHHHHhhh
Confidence            9999999999887       46788999999999999999999999999986541   1  1  26666665533     


Q ss_pred             -----CCCCHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHH-hcCCChHHHHH
Q psy879          218 -----DEPHPLAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDIIGNIFRVAK-TLDIPEPLKLS  277 (317)
Q Consensus       218 -----~~~~~~~i~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~~-~~~~~~~~~~~  277 (317)
                           +..+.+.++++++++..+|.++|+.|+..|++.|++|..|.+.+.+.+. ..|+.+.....
T Consensus       250 ~ydk~gd~hyd~Isa~~ksirgsD~daAl~~la~ml~~Gedp~~I~Rrl~~~asEdigladp~al~  315 (725)
T PRK13341        250 LYDKEGDAHFDTISAFIKSLRGSDPDAALYWLARMVEAGEDPRFIFRRMLIAASEDVGLADPQALV  315 (725)
T ss_pred             hcccCCCCCHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhccCCCChHHHH
Confidence                 3467889999999999999999999999999999999999999988776 55775544433

>PRK07940 DNA polymerase III subunit delta'; Validated

Probab=100.00  E-value=6.6e-33  Score=246.17  Aligned_cols=292  Identities=19%  Similarity=0.276  Sum_probs=211.2

Q ss_pred             CCCcccCCHHHHHHHHHHHhcCC---------Cce-EEEECCCCCCHHHHHHHHHHHHcCCCCC----------------
Q psy879            8 TFSDIVGNEDTVERLKVFSSSGN---------VPN-IIISGPPGVGKTTTILCLARILLGPSFK----------------   61 (317)
Q Consensus         8 ~~~~~~g~~~~~~~l~~~l~~~~---------~~~-~ll~G~~G~GKt~la~~la~~l~~~~~~----------------   61 (317)
                      .|++++||+++++.|+.++.+++         ++| |||+||+|+|||++|+.+|+.+.|....                
T Consensus         3 ~f~~IiGq~~~~~~L~~~i~~~~~~~~~~~~~l~ha~Lf~Gp~G~GKt~lA~~lA~~l~c~~~~~~~Cg~C~~C~~~~~~   82 (394)
T PRK07940          3 VWDDLVGQEAVVAELRAAARAARADVAAAGSGMTHAWLFTGPPGSGRSVAARAFAAALQCTDPDEPGCGECRACRTVLAG   82 (394)
T ss_pred             hhhhccChHHHHHHHHHHHHhccccccccCCCCCeEEEEECCCCCcHHHHHHHHHHHhCCCCCCCCCCCCCHHHHHHhcC
Confidence            58999999999999999999887         788 9999999999999999999999886410                


Q ss_pred             --CceEEecC-CCCcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCc
Q psy879           62 --DAVLELNA-SNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEK  138 (317)
Q Consensus        62 --~~~~~~~~-~~~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~  138 (317)
                        ..+..+.+ ....+++++++.+..+...+.   .++++|+||||+|.|++..+|+|+++||+|++++.||++|+++..
T Consensus        83 ~hpD~~~i~~~~~~i~i~~iR~l~~~~~~~p~---~~~~kViiIDead~m~~~aanaLLk~LEep~~~~~fIL~a~~~~~  159 (394)
T PRK07940         83 THPDVRVVAPEGLSIGVDEVRELVTIAARRPS---TGRWRIVVIEDADRLTERAANALLKAVEEPPPRTVWLLCAPSPED  159 (394)
T ss_pred             CCCCEEEeccccccCCHHHHHHHHHHHHhCcc---cCCcEEEEEechhhcCHHHHHHHHHHhhcCCCCCeEEEEECChHH
Confidence              11222222 234678889988877766553   378999999999999999999999999999999999999999999


Q ss_pred             CchhHhhhcceeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhh---------h----CC
Q psy879          139 IIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTH---------N----GF  205 (317)
Q Consensus       139 l~~~i~sR~~~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~---------~----~~  205 (317)
                      ++++|+|||+.+.|++|+.+++..||.+..     .++++.+..++..++|+++.++..+..-.         .    -.
T Consensus       160 llpTIrSRc~~i~f~~~~~~~i~~~L~~~~-----~~~~~~a~~la~~s~G~~~~A~~l~~~~~~~~~r~~~~~~l~~l~  234 (394)
T PRK07940        160 VLPTIRSRCRHVALRTPSVEAVAEVLVRRD-----GVDPETARRAARASQGHIGRARRLATDEEARARRAEVLNLALRLA  234 (394)
T ss_pred             ChHHHHhhCeEEECCCCCHHHHHHHHHHhc-----CCCHHHHHHHHHHcCCCHHHHHHHhcChHHHHHHHHHHHHHHhcc
Confidence            999999999999999999999999998522     36788888999999999999877653200         0    00


Q ss_pred             Cc---c---------cHHHHHhhcCCCCHHHHHHHHHHH--------------------------hc--------CCHHH
Q psy879          206 GH---V---------TAEYVFKVCDEPHPLAVKEMLLNC--------------------------VE--------GNMKD  239 (317)
Q Consensus       206 ~~---i---------~~~~v~~~~~~~~~~~i~~l~~~~--------------------------~~--------~~~~~  239 (317)
                      ..   +         ..+++....+.........+.+.+                          ..        .....
T Consensus       235 ~~~~~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  314 (394)
T PRK07940        235 RVSDAVAAAEELVKAAEAEAKALTAERDEAETEELRTALGAGGTGKGPAKALRGAAGALKDLEKRQKRRATRASRDALDR  314 (394)
T ss_pred             chhHHHHHHHHHHHHHHHHHHhhhccccHHHHHHHHHHhccccccccccccchhHHHHHHHHHHHHhhhchhhhhhhHHH
Confidence            00   0         001111122222222222222221                          00        01222


Q ss_pred             ----HHHHHHHHH--HcCCCHH----HHHHHHHHHHHhcCCChHHHHHHHHHHHHHHhHHhcCCCcHHHHHHHHHHHHHh
Q psy879          240 ----SYKIIHHLY--KLGYAPE----DIIGNIFRVAKTLDIPEPLKLSIIQEIGNVHLRISEGVNSLLQLSGLLARLCIV  309 (317)
Q Consensus       240 ----~~~~~~~l~--~~~~~~~----~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~g~~~~l~le~~~~~~~~~  309 (317)
                          ...|++|++  ..|.+..    +....+...+.  ..+.....+.++.+.+....+..|+|+++.+|.|+.++...
T Consensus       315 ~l~~l~~~~rDll~~~~g~~~~~~n~d~~~~l~~~a~--~~~~~~l~~~~~~~~~a~~~l~~n~n~~L~lE~lll~l~~~  392 (394)
T PRK07940        315 ALVDLAGLYRDVLVVQLGAEVGLINPDMADRLAELAA--RSTPEGLLRRIDAVLACRERLAGNVKPLLAVEAMVAALRQA  392 (394)
T ss_pred             HHHHHHHHHHHHHHHhhcCCccccCHHHHHHHHHHHH--hCCHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHh
Confidence                566677763  3332221    11222333444  45666778899999999999999999999999999999764

>PRK07399 DNA polymerase III subunit delta'; Validated

Probab=100.00  E-value=9.7e-33  Score=239.01  Aligned_cols=272  Identities=18%  Similarity=0.325  Sum_probs=203.6

Q ss_pred             CCCcccCCHHHHHHHHHHHhcCCCce-EEEECCCCCCHHHHHHHHHHHHcCCCC------------C-CceEEecCC---
Q psy879            8 TFSDIVGNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARILLGPSF------------K-DAVLELNAS---   70 (317)
Q Consensus         8 ~~~~~~g~~~~~~~l~~~l~~~~~~~-~ll~G~~G~GKt~la~~la~~l~~~~~------------~-~~~~~~~~~---   70 (317)
                      .|++++||+++++.|..++.+|+++| |||+||+|+||+++|.++++.+.|...            + ..+..+.+.   
T Consensus         2 ~f~~iiGq~~~~~~L~~~i~~~rl~ha~Lf~G~~G~Gk~~~A~~~a~~llc~~~c~~c~~~~~~~~~hPDl~~i~p~~~~   81 (314)
T PRK07399          2 LFANLIGQPLAIELLTAAIKQNRIAPAYLFAGPEGVGRKLAALCFIEGLLSQGSPSKNIRRRLEEGNHPDLLWVEPTYQH   81 (314)
T ss_pred             cHHHhCCHHHHHHHHHHHHHhCCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCCcHhcccccCCCCCEEEEeccccc
Confidence            58999999999999999999999988 999999999999999999999987641            1 112222211   


Q ss_pred             --------------------CCcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEE
Q psy879           71 --------------------NDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFA  130 (317)
Q Consensus        71 --------------------~~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~i  130 (317)
                                          ...+++++++....+...+..   ++++|+|||++|.|+..++|+|+++||+|| ++.||
T Consensus        82 ~g~~~~~~~~~~~~~~~~~~~~I~id~ir~i~~~l~~~p~~---~~~kVvII~~ae~m~~~aaNaLLK~LEEPp-~~~fI  157 (314)
T PRK07399         82 QGKLITASEAEEAGLKRKAPPQIRLEQIREIKRFLSRPPLE---APRKVVVIEDAETMNEAAANALLKTLEEPG-NGTLI  157 (314)
T ss_pred             cccccchhhhhhccccccccccCcHHHHHHHHHHHccCccc---CCceEEEEEchhhcCHHHHHHHHHHHhCCC-CCeEE
Confidence                                124567888877777666543   789999999999999999999999999999 88999


Q ss_pred             EEecCCCcCchhHhhhcceeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhhCCCcccH
Q psy879          131 LACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHNGFGHVTA  210 (317)
Q Consensus       131 l~~~~~~~l~~~i~sR~~~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~~~~~i~~  210 (317)
                      ++|+++++++++|+|||+.++|++++++++.++|......++.   +.....++..++|+++.+++.++...    .+..
T Consensus       158 Li~~~~~~Ll~TI~SRcq~i~f~~l~~~~~~~~L~~~~~~~~~---~~~~~~l~~~a~Gs~~~al~~l~~~~----~~~~  230 (314)
T PRK07399        158 LIAPSPESLLPTIVSRCQIIPFYRLSDEQLEQVLKRLGDEEIL---NINFPELLALAQGSPGAAIANIEQLQ----SIPP  230 (314)
T ss_pred             EEECChHhCcHHHHhhceEEecCCCCHHHHHHHHHHhhccccc---hhHHHHHHHHcCCCHHHHHHHHHHHH----HHHH
Confidence            9999999999999999999999999999999999987543322   22246788999999999999886431    1111


Q ss_pred             HHHHhhcCCCCHHHHHHHHHHHhcCCHHHHHHHHHHHH-HcCCCHH-HHHHHHHHHHHhcCCChHHHHHHHHHHHHHHhH
Q psy879          211 EYVFKVCDEPHPLAVKEMLLNCVEGNMKDSYKIIHHLY-KLGYAPE-DIIGNIFRVAKTLDIPEPLKLSIIQEIGNVHLR  288 (317)
Q Consensus       211 ~~v~~~~~~~~~~~i~~l~~~~~~~~~~~~~~~~~~l~-~~~~~~~-~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  288 (317)
                      +             +...+..+. .+...++.+...+. ..+.+-. .++..+..++..   . .....+++.+.+..+.
T Consensus       231 ~-------------~~~~~~~~~-~~~~~~~~~a~~~~~~~~~e~Q~~~l~~~~~~~~~---~-~~~~~~~~~l~~a~~~  292 (314)
T PRK07399        231 E-------------LLQKLEQPP-KSPLEALELAKDISEELDIEQQLWLIDYLQQHYWQ---K-TKNRQLLKQLEKLRKQ  292 (314)
T ss_pred             H-------------HHHHHHhcc-cCHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHH---h-hcchHHHHHHHHHHHH
Confidence            1             122222222 35556665544442 2222221 223333333432   1 1257789999999999


Q ss_pred             HhcCCCcHHHHHHHHHHHHH
Q psy879          289 ISEGVNSLLQLSGLLARLCI  308 (317)
Q Consensus       289 l~~g~~~~l~le~~~~~~~~  308 (317)
                      +..|+|+++.+|.++.+++.
T Consensus       293 l~~nvn~~lv~e~~~l~l~~  312 (314)
T PRK07399        293 LLSYVQPRLAWEVTLLELSQ  312 (314)
T ss_pred             HHHcCCcchhHHHHHHHHhc
Confidence            99999999999999999974

>PRK08058 DNA polymerase III subunit delta'; Validated

Probab=100.00  E-value=1.4e-32  Score=240.86  Aligned_cols=289  Identities=19%  Similarity=0.232  Sum_probs=204.3

Q ss_pred             CCCcccC-CHHHHHHHHHHHhcCCCce-EEEECCCCCCHHHHHHHHHHHHcCCCCC-------------------CceEE
Q psy879            8 TFSDIVG-NEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARILLGPSFK-------------------DAVLE   66 (317)
Q Consensus         8 ~~~~~~g-~~~~~~~l~~~l~~~~~~~-~ll~G~~G~GKt~la~~la~~l~~~~~~-------------------~~~~~   66 (317)
                      .|+.++| |+++.+.|...+.+|++|| |||+||+|+||+++|+.+++.+.|....                   ..+..
T Consensus         3 ~~~~i~~~q~~~~~~L~~~~~~~~l~ha~Lf~G~~G~gk~~~a~~la~~l~c~~~~~~~~cg~C~~c~~~~~~~hpD~~~   82 (329)
T PRK08058          3 TWEQLTALQPVVVKMLQNSIAKNRLSHAYLFEGAKGTGKKATALWLAKSLFCLERNGVEPCGTCTNCKRIDSGNHPDVHL   82 (329)
T ss_pred             cHHHHHhhHHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCcCHHHHHHhcCCCCCEEE
Confidence            5788999 9999999999999999999 8999999999999999999999876411                   11222


Q ss_pred             ecC-CCCcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcCchhHhh
Q psy879           67 LNA-SNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQS  145 (317)
Q Consensus        67 ~~~-~~~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~~~i~s  145 (317)
                      +.. ....+++++++....+...+.   .++++|+||||+|.|+.+++|+|+++||+||+++.||++|+++.+++++|+|
T Consensus        83 i~~~~~~i~id~ir~l~~~~~~~~~---~~~~kvviI~~a~~~~~~a~NaLLK~LEEPp~~~~~Il~t~~~~~ll~TIrS  159 (329)
T PRK08058         83 VAPDGQSIKKDQIRYLKEEFSKSGV---ESNKKVYIIEHADKMTASAANSLLKFLEEPSGGTTAILLTENKHQILPTILS  159 (329)
T ss_pred             eccccccCCHHHHHHHHHHHhhCCc---ccCceEEEeehHhhhCHHHHHHHHHHhcCCCCCceEEEEeCChHhCcHHHHh
Confidence            222 234677899998887776653   3789999999999999999999999999999999999999999999999999


Q ss_pred             hcceeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhhCCCcccHHHHHhhcCCCCHHHH
Q psy879          146 RCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAV  225 (317)
Q Consensus       146 R~~~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~~~~~i~~~~v~~~~~~~~~~~i  225 (317)
                      ||+.++|++++++++..++.+    +|  ++++....++.. .|+++.|+..++.-......-........+........
T Consensus       160 Rc~~i~~~~~~~~~~~~~L~~----~g--i~~~~~~~l~~~-~g~~~~A~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~  232 (329)
T PRK08058        160 RCQVVEFRPLPPESLIQRLQE----EG--ISESLATLLAGL-TNSVEEALALSEDDWFAQARALVIKLYEALHEKDLQSF  232 (329)
T ss_pred             hceeeeCCCCCHHHHHHHHHH----cC--CChHHHHHHHHH-cCCHHHHHHHhcCchHHHHHHHHHHHHHHHHcCCHHHH
Confidence            999999999999999888865    35  556665566555 57899999877532110000000111111111111112


Q ss_pred             HHHHHHHh----cCC-----HHHHHHHHHHHH--HcCCCHH----HHHHHHHHHHHhcCCChHHHHHHHHHHHHHHhHHh
Q psy879          226 KEMLLNCV----EGN-----MKDSYKIIHHLY--KLGYAPE----DIIGNIFRVAKTLDIPEPLKLSIIQEIGNVHLRIS  290 (317)
Q Consensus       226 ~~l~~~~~----~~~-----~~~~~~~~~~l~--~~~~~~~----~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~  290 (317)
                      ..+.+.+.    .++     ..-...+++|++  ..|.+..    +....+..++.  ..+.....++++.+.+...++.
T Consensus       233 ~~~~~~~~~~~~~~~~~~~~l~~l~~~~rD~l~~~~~~~~~~~n~d~~~~l~~~a~--~~s~~~l~~~~~~~~~~~~~l~  310 (329)
T PRK08058        233 VFVQEKWMPLFKEKDQQQLGLDLLLLIYRDLLYLQLGEEDRLVFREQKEMLQQLAL--SYSQQQIVAALELILEAKRRLN  310 (329)
T ss_pred             HHHHHHHHHhccCHHHHHHHHHHHHHHHHHHHHHhcCCcccccCHHHHHHHHHHHH--hCCHHHHHHHHHHHHHHHHHHH
Confidence            22222121    111     112334456653  2232221    11122233334  5677788889999999999999


Q ss_pred             cCCCcHHHHHHHHHHHHH
Q psy879          291 EGVNSLLQLSGLLARLCI  308 (317)
Q Consensus       291 ~g~~~~l~le~~~~~~~~  308 (317)
                      .|+|+++.+|.++.++.+
T Consensus       311 ~n~n~~L~le~lll~~~~  328 (329)
T PRK08058        311 SNVNFQLVMEQLVLRLQE  328 (329)
T ss_pred             HcCCHHHHHHHHHHhccc
Confidence            999999999999998763

>PRK07993 DNA polymerase III subunit delta'; Validated

Probab=100.00  E-value=9.9e-32  Score=234.41  Aligned_cols=286  Identities=21%  Similarity=0.237  Sum_probs=209.6

Q ss_pred             CCHHHHHHHHHHHhcCCCce-EEEECCCCCCHHHHHHHHHHHHcCCCCC-------------------CceEEecCC---
Q psy879           14 GNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARILLGPSFK-------------------DAVLELNAS---   70 (317)
Q Consensus        14 g~~~~~~~l~~~l~~~~~~~-~ll~G~~G~GKt~la~~la~~l~~~~~~-------------------~~~~~~~~~---   70 (317)
                      .+....+.|...+.+|+.+| +||+||+|+||+++|+++|+.+.|....                   ..+..+.+.   
T Consensus         6 Wl~~~~~~l~~~~~~~rl~HA~Lf~G~~G~Gk~~lA~~~A~~LlC~~~~~~~~Cg~C~sC~~~~~g~HPD~~~i~p~~~~   85 (334)
T PRK07993          6 WLRPDYEQLVGSYQAGRGHHALLIQALPGMGDDALIYALSRWLMCQQPQGHKSCGHCRGCQLMQAGTHPDYYTLTPEKGK   85 (334)
T ss_pred             CChHHHHHHHHHHHcCCcceEEeeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHHcCCCCCEEEEeccccc
Confidence            46788899999999999999 9999999999999999999999885321                   123333322   


Q ss_pred             CCcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcCchhHhhhccee
Q psy879           71 NDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAML  150 (317)
Q Consensus        71 ~~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~~~i~sR~~~i  150 (317)
                      ..++++++|+....+..++.   .+++||+|||++|.|+..++|+|+|+|||||+++.||++|+++++++|||+|||+.+
T Consensus        86 ~~I~idqiR~l~~~~~~~~~---~g~~kV~iI~~ae~m~~~AaNaLLKtLEEPp~~t~fiL~t~~~~~lLpTIrSRCq~~  162 (334)
T PRK07993         86 SSLGVDAVREVTEKLYEHAR---LGGAKVVWLPDAALLTDAAANALLKTLEEPPENTWFFLACREPARLLATLRSRCRLH  162 (334)
T ss_pred             ccCCHHHHHHHHHHHhhccc---cCCceEEEEcchHhhCHHHHHHHHHHhcCCCCCeEEEEEECChhhChHHHHhccccc
Confidence            34789999999888887763   388999999999999999999999999999999999999999999999999999999


Q ss_pred             eecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhhCCCcccHHHHHhhcCCCCHHHHHHHHH
Q psy879          151 RYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEMLL  230 (317)
Q Consensus       151 ~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~~~~~i~~~~v~~~~~~~~~~~i~~l~~  230 (317)
                      .|++++++++..||.+.     ..++++.+..++..++|++..|+..++.-......-..+.+.......   ....++.
T Consensus       163 ~~~~~~~~~~~~~L~~~-----~~~~~~~a~~~~~la~G~~~~Al~l~~~~~~~~r~~~~~~l~~~~~~~---~~~~~~~  234 (334)
T PRK07993        163 YLAPPPEQYALTWLSRE-----VTMSQDALLAALRLSAGAPGAALALLQPERWQQREALCQALAYALPSG---DWLSLLP  234 (334)
T ss_pred             cCCCCCHHHHHHHHHHc-----cCCCHHHHHHHHHHcCCCHHHHHHHhcCchHHHHHHHHHHHHHHhcCC---CHHHHHH
Confidence            99999999999999763     246677777889999999999998875311100000011111112211   2233444


Q ss_pred             HHhcCCHHHHHH----HHHHHH--HcCCCHH---HHHHHHHHHHHhcCCChHHHHHHHHHHHHHHhHHhc--CCCcHHHH
Q psy879          231 NCVEGNMKDSYK----IIHHLY--KLGYAPE---DIIGNIFRVAKTLDIPEPLKLSIIQEIGNVHLRISE--GVNSLLQL  299 (317)
Q Consensus       231 ~~~~~~~~~~~~----~~~~l~--~~~~~~~---~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~--g~~~~l~l  299 (317)
                      .+...+....+.    ++.|++  +.|....   +....+..++.  ..+.....+.++.+.+....+..  |+|+++.+
T Consensus       235 ~~~~~~~~~~L~~l~~~~rD~l~~~~~~~~~~n~d~~~~i~~~a~--~~~~~~l~~~~~~l~~~~~~l~~~~N~N~~L~l  312 (334)
T PRK07993        235 ALNHEQAPARLHWLATLLMDALKRQHGAAYVTNQDQPPLVAQLAN--HLSPARLQAILGDVCHCREQLLSVTGVNRELLL  312 (334)
T ss_pred             HHcccCHHHHHHHHHHHHHHHHHHhcCCcceeCHHHHHHHHHHHH--hCCHHHHHHHHHHHHHHHHHHHhcCCCCHHHHH
Confidence            444344444443    455553  2332111   11112223333  46667777889999999999985  88999999


Q ss_pred             HHHHHHHHHhhcc
Q psy879          300 SGLLARLCIVGSK  312 (317)
Q Consensus       300 e~~~~~~~~~~~~  312 (317)
                      |.++.++......
T Consensus       313 e~lll~~~~~~~~  325 (334)
T PRK07993        313 TDLLLRIEHYLQP  325 (334)
T ss_pred             HHHHHHHHHHHcc
Confidence            9999999876443

>PRK05707 DNA polymerase III subunit delta'; Validated

Probab=100.00  E-value=4.4e-31  Score=229.76  Aligned_cols=282  Identities=18%  Similarity=0.230  Sum_probs=204.7

Q ss_pred             HHHHHHHHhcCCCce-EEEECCCCCCHHHHHHHHHHHHcCCCCC-------------------CceEEecCC---CCcCh
Q psy879           19 VERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARILLGPSFK-------------------DAVLELNAS---NDRGI   75 (317)
Q Consensus        19 ~~~l~~~l~~~~~~~-~ll~G~~G~GKt~la~~la~~l~~~~~~-------------------~~~~~~~~~---~~~~~   75 (317)
                      ...++.++.+|+.+| |||+||+|+||+++|+.+|+.+.|....                   ..+..+.+.   ...++
T Consensus         9 ~~~~~~~~~~~r~~ha~Lf~G~~G~GK~~~A~~~A~~llC~~~~~~~~Cg~C~sC~~~~~g~HPD~~~i~~~~~~~~i~i   88 (328)
T PRK05707          9 QSLWQQLAGRGRHPHAYLLHGPAGIGKRALAERLAAALLCEAPQGGGACGSCKGCQLLRAGSHPDNFVLEPEEADKTIKV   88 (328)
T ss_pred             HHHHHHHHHCCCcceeeeeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHhcCCCCCEEEEeccCCCCCCCH
Confidence            344566677799999 9999999999999999999999985321                   123333322   35788


Q ss_pred             HHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcCchhHhhhcceeeecCC
Q psy879           76 DTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKL  155 (317)
Q Consensus        76 ~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~~~i~sR~~~i~f~~~  155 (317)
                      +++|+....+...+.   .++++|+|||++|.|+.+++|+|+++||+||+++.||++|++++.++++|+|||+.+.|+++
T Consensus        89 d~iR~l~~~~~~~~~---~~~~kv~iI~~a~~m~~~aaNaLLK~LEEPp~~~~fiL~t~~~~~ll~TI~SRc~~~~~~~~  165 (328)
T PRK05707         89 DQVRELVSFVVQTAQ---LGGRKVVLIEPAEAMNRNAANALLKSLEEPSGDTVLLLISHQPSRLLPTIKSRCQQQACPLP  165 (328)
T ss_pred             HHHHHHHHHHhhccc---cCCCeEEEECChhhCCHHHHHHHHHHHhCCCCCeEEEEEECChhhCcHHHHhhceeeeCCCc
Confidence            999998888877663   37899999999999999999999999999999999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhhCCCcccHHHHHhhcCCCCHHHHHHHHHHHhcC
Q psy879          156 TDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEMLLNCVEG  235 (317)
Q Consensus       156 ~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~~~~~i~~~~v~~~~~~~~~~~i~~l~~~~~~~  235 (317)
                      +.+++..||.....    ..+++.+..++..++|++..|+..++.-......-..+.+..+.....  ....+.+.+...
T Consensus       166 ~~~~~~~~L~~~~~----~~~~~~~~~~l~la~Gsp~~A~~l~~~~~~~~r~~~~~~l~~~~~~~~--~~~~~~~~~~k~  239 (328)
T PRK05707        166 SNEESLQWLQQALP----ESDERERIELLTLAGGSPLRALQLHEQGVREQRARVLDGVKKLLKQQQ--SASQLAESWLKV  239 (328)
T ss_pred             CHHHHHHHHHHhcc----cCChHHHHHHHHHcCCCHHHHHHHHCcchHHHHHHHHHHHHHHhcCcc--cHHHHHHHHccC
Confidence            99999999987531    245666677889999999999887643111100111112222222111  344555555544


Q ss_pred             CHHHHHH----HHHHHH--HcCCCH-----HHHHHHHHHHHHhcCCChHHHHHHHHHHHHHHhHHh--cCCCcHHHHHHH
Q psy879          236 NMKDSYK----IIHHLY--KLGYAP-----EDIIGNIFRVAKTLDIPEPLKLSIIQEIGNVHLRIS--EGVNSLLQLSGL  302 (317)
Q Consensus       236 ~~~~~~~----~~~~l~--~~~~~~-----~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~--~g~~~~l~le~~  302 (317)
                      +....+.    +++|++  ..|.+.     .+....+..++.  ..+......+++.+.+...++.  .|+|.++.+|.+
T Consensus       240 ~~~~~l~~l~~~~~D~l~~~~~~~~~~~~n~d~~~~l~~~a~--~~~~~~L~~~~~~l~~~~~~l~~~~NvN~~L~le~l  317 (328)
T PRK05707        240 PLLLLFDWFCDWAHDILRYQLTQDEEGLGLADMRKVLQYLAQ--KSPQAKVLALQDWLLEQRQKVLGKANLNRQLLLEAL  317 (328)
T ss_pred             CHHHHHHHHHHHHHHHHHHHcCCCcccccCHHHHHHHHHHHH--hCCHHHHHHHHHHHHHHHHHhhccCCCCHHHHHHHH
Confidence            5444444    455553  333222     222333444455  4566677788999999999885  789999999999


Q ss_pred             HHHHHHhhc
Q psy879          303 LARLCIVGS  311 (317)
Q Consensus       303 ~~~~~~~~~  311 (317)
                      +.++....+
T Consensus       318 ll~~~~~~~  326 (328)
T PRK05707        318 LVQWAGLPG  326 (328)
T ss_pred             HHHHHHHhc
Confidence            999986543

>PRK09112 DNA polymerase III subunit delta'; Validated

Probab=100.00  E-value=2.7e-30  Score=226.63  Aligned_cols=290  Identities=19%  Similarity=0.267  Sum_probs=209.6

Q ss_pred             ccCCCCCCcccCCHHHHHHHHHHHhcCCCce-EEEECCCCCCHHHHHHHHHHHHcCCCC-----C---------------
Q psy879            3 KYRPQTFSDIVGNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARILLGPSF-----K---------------   61 (317)
Q Consensus         3 ky~P~~~~~~~g~~~~~~~l~~~l~~~~~~~-~ll~G~~G~GKt~la~~la~~l~~~~~-----~---------------   61 (317)
                      ...|..+++++||+++.+.|..++.+|+.|| +||+||+|+|||++++.+++.+.|...     .               
T Consensus        16 ~~~P~~~~~l~Gh~~a~~~L~~a~~~grl~ha~L~~G~~G~GKttlA~~lA~~Llc~~~~~~~~~~~~~~~~~c~~c~~i   95 (351)
T PRK09112         16 VPSPSENTRLFGHEEAEAFLAQAYREGKLHHALLFEGPEGIGKATLAFHLANHILSHPDPAEAPETLADPDPASPVWRQI   95 (351)
T ss_pred             CCCCCchhhccCcHHHHHHHHHHHHcCCCCeeEeeECCCCCCHHHHHHHHHHHHcCCCccccCccccCCCCCCCHHHHHH
Confidence            4689999999999999999999999999999 999999999999999999999987310     0               


Q ss_pred             -----CceEEecC---------CCCcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCc
Q psy879           62 -----DAVLELNA---------SNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTT  127 (317)
Q Consensus        62 -----~~~~~~~~---------~~~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~  127 (317)
                           ..+..+..         ....+++++++....+...+   ..+.++|+||||+|.|+..++|+|++.+|+|+.++
T Consensus        96 ~~~~hPdl~~l~~~~~~~~~~~~~~I~vd~iR~l~~~l~~~~---~~g~~rVviIDeAd~l~~~aanaLLk~LEEpp~~~  172 (351)
T PRK09112         96 AQGAHPNLLHITRPFDEKTGKFKTAITVDEIRRVGHFLSQTS---GDGNWRIVIIDPADDMNRNAANAILKTLEEPPARA  172 (351)
T ss_pred             HcCCCCCEEEeecccccccccccccCCHHHHHHHHHHhhhcc---ccCCceEEEEEchhhcCHHHHHHHHHHHhcCCCCc
Confidence                 00122211         12345788888777766654   33789999999999999999999999999999999


Q ss_pred             eEEEEecCCCcCchhHhhhcceeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhhCCCc
Q psy879          128 RFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHNGFGH  207 (317)
Q Consensus       128 ~~il~~~~~~~l~~~i~sR~~~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~~~~~  207 (317)
                      .||++++.+.+++++++|||+.++|++++.+++..||.......+  ++++.+..++..++|++|.+++.++....   .
T Consensus       173 ~fiLit~~~~~llptIrSRc~~i~l~pl~~~~~~~~L~~~~~~~~--~~~~~~~~i~~~s~G~pr~Al~ll~~~~~---~  247 (351)
T PRK09112        173 LFILISHSSGRLLPTIRSRCQPISLKPLDDDELKKALSHLGSSQG--SDGEITEALLQRSKGSVRKALLLLNYGGL---E  247 (351)
T ss_pred             eEEEEECChhhccHHHHhhccEEEecCCCHHHHHHHHHHhhcccC--CCHHHHHHHHHHcCCCHHHHHHHHhcCcH---H
Confidence            999999999999999999999999999999999999998654333  67888999999999999999999865321   1


Q ss_pred             ccHHHHHhhcC--CCCHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhcCCC-hH----HHHHHHH
Q psy879          208 VTAEYVFKVCD--EPHPLAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDIIGNIFRVAKTLDIP-EP----LKLSIIQ  280 (317)
Q Consensus       208 i~~~~v~~~~~--~~~~~~i~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~~~~~~~-~~----~~~~~~~  280 (317)
                      +. ..+...+.  ........++.+.+...+....+.|+.+++.         ..+.+.+...+.. +.    ...++++
T Consensus       248 ~~-~~~~~~l~~~~~~~~~~~~la~~~~~~~~~~~~~~~~~~l~---------d~l~~~~~~~~~~g~~~~~~~~~~~~~  317 (351)
T PRK09112        248 II-ATIDQLLAGSGPDARKAHKLADALSGRESEVQFDFFRDHLL---------DRIMAEARRAAEAGDLALAERLARLWS  317 (351)
T ss_pred             HH-HHHHHHHhhccCCcchHHHHHHHHhCCChHHHHHHHHHHHH---------HHHHHHHHhhcccCchhhHHHHHHHHH
Confidence            11 12222222  2222345677777777777777777766632         2333333331111 11    1223333


Q ss_pred             HHHHHHhHH-hcCCCcHHHHHHHHHHHHHhh
Q psy879          281 EIGNVHLRI-SEGVNSLLQLSGLLARLCIVG  310 (317)
Q Consensus       281 ~l~~~~~~l-~~g~~~~l~le~~~~~~~~~~  310 (317)
                      .+.+.-..- --|.++.-.+-.++.++.+..
T Consensus       318 ~~~~~~~~~~~~nld~~~~~~~~~~~~~~~~  348 (351)
T PRK09112        318 EIIEEIVEAEAYNLDRKQTVISLLEKLHRAF  348 (351)
T ss_pred             HHHHHHhhhhhhCcCHHHHHHHHHHHHHHHH
Confidence            333222111 235688888888888877654

>KOG2028|consensus

Probab=100.00  E-value=1.2e-31  Score=225.50  Aligned_cols=266  Identities=21%  Similarity=0.331  Sum_probs=218.3

Q ss_pred             cccCCCCCCcccCCHHHHHH---HHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHH
Q psy879            2 EKYRPQTFSDIVGNEDTVER---LKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTV   78 (317)
Q Consensus         2 ~ky~P~~~~~~~g~~~~~~~---l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i   78 (317)
                      |+-||++++|++||++++..   |+.++++++.|.++||||||||||++|+.++..  ....++.++++.+.+ .+..++
T Consensus       130 ermRPktL~dyvGQ~hlv~q~gllrs~ieq~~ipSmIlWGppG~GKTtlArlia~t--sk~~SyrfvelSAt~-a~t~dv  206 (554)
T KOG2028|consen  130 ERMRPKTLDDYVGQSHLVGQDGLLRSLIEQNRIPSMILWGPPGTGKTTLARLIAST--SKKHSYRFVELSATN-AKTNDV  206 (554)
T ss_pred             hhcCcchHHHhcchhhhcCcchHHHHHHHcCCCCceEEecCCCCchHHHHHHHHhh--cCCCceEEEEEeccc-cchHHH
Confidence            68899999999999998874   889999999999999999999999999999986  344557788887754 566677


Q ss_pred             HHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEec--CCCcCchhHhhhcceeeecCCC
Q psy879           79 RNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACN--NSEKIIEPIQSRCAMLRYNKLT  156 (317)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~--~~~~l~~~i~sR~~~i~f~~~~  156 (317)
                      |+.++........  ..++.|+||||++.+++..|+.|+..+|.  +.+.+|.+|+  +...+..++.|||.++.+.+++
T Consensus       207 R~ife~aq~~~~l--~krkTilFiDEiHRFNksQQD~fLP~VE~--G~I~lIGATTENPSFqln~aLlSRC~VfvLekL~  282 (554)
T KOG2028|consen  207 RDIFEQAQNEKSL--TKRKTILFIDEIHRFNKSQQDTFLPHVEN--GDITLIGATTENPSFQLNAALLSRCRVFVLEKLP  282 (554)
T ss_pred             HHHHHHHHHHHhh--hcceeEEEeHHhhhhhhhhhhcccceecc--CceEEEecccCCCccchhHHHHhccceeEeccCC
Confidence            8777654433211  25788999999999999999999999995  5566777643  3468999999999999999999


Q ss_pred             HHHHHHHHHHHHHH----c---------CCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhh---------CCCcccHHHHH
Q psy879          157 DAQLLSKVIEICEK----E---------NISHTNDGLEAIVFTAQGDMRQALNNLQSTHN---------GFGHVTAEYVF  214 (317)
Q Consensus       157 ~~~~~~~l~~~~~~----~---------~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~---------~~~~i~~~~v~  214 (317)
                      .+.+..+|......    +         .+.+++.++++++..+.||.|.++|.|+..+.         ....++.++|+
T Consensus       283 ~n~v~~iL~raia~l~dser~~~~l~n~s~~ve~siidyla~lsdGDaR~aLN~Lems~~m~~tr~g~~~~~~lSidDvk  362 (554)
T KOG2028|consen  283 VNAVVTILMRAIASLGDSERPTDPLPNSSMFVEDSIIDYLAYLSDGDARAALNALEMSLSMFCTRSGQSSRVLLSIDDVK  362 (554)
T ss_pred             HHHHHHHHHHHHHhhccccccCCCCCCcchhhhHHHHHHHHHhcCchHHHHHHHHHHHHHHHHhhcCCcccceecHHHHH
Confidence            99999999985431    1         12467889999999999999999999987632         22368889988


Q ss_pred             hhc----------CCCCHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHH-hcCCChHH
Q psy879          215 KVC----------DEPHPLAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDIIGNIFRVAK-TLDIPEPL  274 (317)
Q Consensus       215 ~~~----------~~~~~~~i~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~~-~~~~~~~~  274 (317)
                      +.+          +..+++.|+.+-+.++..|....+.|+..|++.|++|..+.+.+.|++. .+|+.+.+
T Consensus       363 e~lq~s~~~YDr~Ge~HYntISA~HKSmRG~D~nAslY~LaRMLegGEdPLYVARRlvR~ASEDIGlaD~S  433 (554)
T KOG2028|consen  363 EGLQRSHILYDRAGEEHYNTISALHKSMRGSDQNASLYWLARMLEGGEDPLYVARRLVRFASEDIGLADPS  433 (554)
T ss_pred             HHHhhccceecccchhHHHHHHHHHHhhcCCccchHHHHHHHHHccCCCcHHHHHHHHHHhhcccCcCCch
Confidence            754          3456678999999999999999999999999999999999999999875 44666554

>PRK07471 DNA polymerase III subunit delta'; Validated

Probab=100.00  E-value=3e-30  Score=227.55  Aligned_cols=293  Identities=21%  Similarity=0.288  Sum_probs=203.6

Q ss_pred             cCCCCCCcccCCHHHHHHHHHHHhcCCCce-EEEECCCCCCHHHHHHHHHHHHcCCCCCC--------------------
Q psy879            4 YRPQTFSDIVGNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARILLGPSFKD--------------------   62 (317)
Q Consensus         4 y~P~~~~~~~g~~~~~~~l~~~l~~~~~~~-~ll~G~~G~GKt~la~~la~~l~~~~~~~--------------------   62 (317)
                      .+|+++++++||+++++.|..++.+|++|| +||+||+|+||+++|.++|+.+.|.....                    
T Consensus        13 ~~P~~~~~iiGq~~~~~~L~~~~~~~rl~HA~Lf~Gp~G~GK~~lA~~~A~~Llc~~~~~~~~~~~~~~~l~~~~~c~~c   92 (365)
T PRK07471         13 PHPRETTALFGHAAAEAALLDAYRSGRLHHAWLIGGPQGIGKATLAYRMARFLLATPPPGGDGAVPPPTSLAIDPDHPVA   92 (365)
T ss_pred             CCCCchhhccChHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHHHhCCCCCCCCccccccccccCCCCChHH
Confidence            689999999999999999999999999999 99999999999999999999998754210                    


Q ss_pred             ---------ceEEecC---C------CCcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhcc
Q psy879           63 ---------AVLELNA---S------NDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYS  124 (317)
Q Consensus        63 ---------~~~~~~~---~------~~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~  124 (317)
                               .+..+..   .      ..++++++++....+..++   ..+.++|+||||+|.|+..++|+|++.+|+|+
T Consensus        93 ~~i~~~~HPDl~~i~~~~~~~~~~~~~~I~VdqiR~l~~~~~~~~---~~~~~kVviIDead~m~~~aanaLLK~LEepp  169 (365)
T PRK07471         93 RRIAAGAHGGLLTLERSWNEKGKRLRTVITVDEVRELISFFGLTA---AEGGWRVVIVDTADEMNANAANALLKVLEEPP  169 (365)
T ss_pred             HHHHccCCCCeEEEecccccccccccccccHHHHHHHHHHhCcCc---ccCCCEEEEEechHhcCHHHHHHHHHHHhcCC
Confidence                     1122211   1      2356788888877766554   33789999999999999999999999999999


Q ss_pred             CCceEEEEecCCCcCchhHhhhcceeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhhC
Q psy879          125 NTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHNG  204 (317)
Q Consensus       125 ~~~~~il~~~~~~~l~~~i~sR~~~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~~  204 (317)
                      +++.||++|+++..++++++|||+.+.|++++.+++..+|....    ...++..+..++..++|+++.++..++.-.. 
T Consensus       170 ~~~~~IL~t~~~~~llpti~SRc~~i~l~~l~~~~i~~~L~~~~----~~~~~~~~~~l~~~s~Gsp~~Al~ll~~~~~-  244 (365)
T PRK07471        170 ARSLFLLVSHAPARLLPTIRSRCRKLRLRPLAPEDVIDALAAAG----PDLPDDPRAALAALAEGSVGRALRLAGGDGL-  244 (365)
T ss_pred             CCeEEEEEECCchhchHHhhccceEEECCCCCHHHHHHHHHHhc----ccCCHHHHHHHHHHcCCCHHHHHHHhcccch-
Confidence            99999999999999999999999999999999999999998853    3344555678899999999999998853211 


Q ss_pred             CCcccHHHHHhhcCC---CCHHHHHHHHHHHhcCC----HHHHHHH----HHHHHHcCC----CHHHHH---HHHHHHHH
Q psy879          205 FGHVTAEYVFKVCDE---PHPLAVKEMLLNCVEGN----MKDSYKI----IHHLYKLGY----APEDII---GNIFRVAK  266 (317)
Q Consensus       205 ~~~i~~~~v~~~~~~---~~~~~i~~l~~~~~~~~----~~~~~~~----~~~l~~~~~----~~~~i~---~~~~~~~~  266 (317)
                        .. .+.+...+..   .....+..+.+.+...+    ....+.|    +.++...+.    .+..+.   ..+.....
T Consensus       245 --~~-~~~~~~~l~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~l~~~l~d~~~~~~~~~~~~~~~~~~~~~l~~~~~  321 (365)
T PRK07471        245 --AL-YRRLTALLDTLPRLDRRALHALADAAAGRDRAARFALFLDLLDRWLARLARAGARGAPPPEAVPGEAALLARLAP  321 (365)
T ss_pred             --HH-HHHHHHHHhccccCCHHHHHHHHHHHHccChHHHHHHHHHHHHHHHHHHHHhhccCCCCccccchhhHHHHhhcc
Confidence              11 1122222211   12223355666555555    3333333    344433211    111111   11111111


Q ss_pred             hcCCChHHHHHHHHHHHHHHhHHh-cCCCcHHHHHHHHHHHHHh
Q psy879          267 TLDIPEPLKLSIIQEIGNVHLRIS-EGVNSLLQLSGLLARLCIV  309 (317)
Q Consensus       267 ~~~~~~~~~~~~~~~l~~~~~~l~-~g~~~~l~le~~~~~~~~~  309 (317)
                        ........++++.+.+.-..-. .|.|+++.++.++.++...
T Consensus       322 --~~~~~~~~~~~~~l~~~~~~~~~~~Ln~~l~~~~~l~~~~~~  363 (365)
T PRK07471        322 --DARLRRWAEVWEKIGRRARRTEAVNLDRKALVLDVFGLLAEA  363 (365)
T ss_pred             --chhHHHHHHHHHHHHHHHHhhhccCCCHHHHHHHHHHHHHHh
Confidence              1112223334444444433322 5889999999999998753

>PRK08769 DNA polymerase III subunit delta'; Validated

Probab=100.00  E-value=2.5e-30  Score=222.98  Aligned_cols=280  Identities=16%  Similarity=0.172  Sum_probs=200.0

Q ss_pred             CCHHHHHHHHHHHhcCCCce-EEEECCCCCCHHHHHHHHHHHHcCCCCC----------------CceEEe--cCC----
Q psy879           14 GNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARILLGPSFK----------------DAVLEL--NAS----   70 (317)
Q Consensus        14 g~~~~~~~l~~~l~~~~~~~-~ll~G~~G~GKt~la~~la~~l~~~~~~----------------~~~~~~--~~~----   70 (317)
                      -++.+++.|...+.+|++|| +||+||+|+||+++|.++|+.+.|....                ..+..+  .+.    
T Consensus         8 W~~~~~~~l~~~~~~~rl~HA~Lf~Gp~G~GK~~lA~~lA~~LlC~~~~~~~~c~~c~~~~~g~HPD~~~i~~~p~~~~~   87 (319)
T PRK08769          8 WQQRAYDQTVAALDAGRLGHGLLICGPEGLGKRAVALALAEHVLASGPDPAAAQRTRQLIAAGTHPDLQLVSFIPNRTGD   87 (319)
T ss_pred             cHHHHHHHHHHHHHcCCcceeEeeECCCCCCHHHHHHHHHHHHhCCCCCCCCcchHHHHHhcCCCCCEEEEecCCCcccc
Confidence            47788999999999999999 9999999999999999999999886421                112223  221    


Q ss_pred             ---CCcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcCchhHhhhc
Q psy879           71 ---NDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRC  147 (317)
Q Consensus        71 ---~~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~~~i~sR~  147 (317)
                         ...+++++|+....+...+.   .++++|+|||++|.|+..++|+|+|+||+||+++.||++|+++++++|||+|||
T Consensus        88 k~~~~I~idqIR~l~~~~~~~p~---~g~~kV~iI~~ae~m~~~AaNaLLKtLEEPp~~~~fiL~~~~~~~lLpTIrSRC  164 (319)
T PRK08769         88 KLRTEIVIEQVREISQKLALTPQ---YGIAQVVIVDPADAINRAACNALLKTLEEPSPGRYLWLISAQPARLPATIRSRC  164 (319)
T ss_pred             cccccccHHHHHHHHHHHhhCcc---cCCcEEEEeccHhhhCHHHHHHHHHHhhCCCCCCeEEEEECChhhCchHHHhhh
Confidence               13568899988887776663   378999999999999999999999999999999999999999999999999999


Q ss_pred             ceeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhhCCCcccHHHHHhhcCCCCHHHHHH
Q psy879          148 AMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKE  227 (317)
Q Consensus       148 ~~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~~~~~i~~~~v~~~~~~~~~~~i~~  227 (317)
                      +.+.|++++.+++..||.+.    +  +++..+..++..++|++..|+..++.-......-..+.+..+.....  .+.+
T Consensus       165 q~i~~~~~~~~~~~~~L~~~----~--~~~~~a~~~~~l~~G~p~~A~~~~~~~~~~~r~~~~~~l~~~~~~~~--~~~~  236 (319)
T PRK08769        165 QRLEFKLPPAHEALAWLLAQ----G--VSERAAQEALDAARGHPGLAAQWLREDGLALRRAVAQDLEQIASGRA--GAVD  236 (319)
T ss_pred             eEeeCCCcCHHHHHHHHHHc----C--CChHHHHHHHHHcCCCHHHHHHHhcCchHHHHHHHHHHHHHhccCcc--cHHH
Confidence            99999999999999999762    3  55666667789999999999887743211100001122222222211  2455


Q ss_pred             HHHHHhcCC-HHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHHHhHHhcCCCcHHHHHHHHHHH
Q psy879          228 MLLNCVEGN-MKDSYKIIHHLYKLGYAPEDIIGNIFRVAKTLDIPEPLKLSIIQEIGNVHLRISEGVNSLLQLSGLLARL  306 (317)
Q Consensus       228 l~~~~~~~~-~~~~~~~~~~l~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~g~~~~l~le~~~~~~  306 (317)
                      +.+.+...+ ..-.+.|+.|++..... ...+      ..  . ......+....+.+....+.+|.|++|.+|.++.++
T Consensus       237 ~a~~~~~~~~~~~l~~~~~Dll~~~~~-~~~~------~~--~-~~~~L~~~~~~l~~~~~~~~~~lN~~L~le~lll~~  306 (319)
T PRK08769        237 VAQRWTNDGQADQRLRHAADLALAQAS-AGLT------DP--S-RLHKLATWFDAANRTRDLLRTTVRADLAVTELLLAW  306 (319)
T ss_pred             HHHHHccCCcHHHHHHHHHHHHHHhcC-Cccc------Ch--h-hHHHHHHHHHHHHHHHHhccCCCCHHHHHHHHHHHH
Confidence            555554332 34556666666432111 0000      00  0 112233445556677677778999999999999999


Q ss_pred             HHhhccCC
Q psy879          307 CIVGSKNK  314 (317)
Q Consensus       307 ~~~~~~~~  314 (317)
                      ......++
T Consensus       307 ~~~~~~~~  314 (319)
T PRK08769        307 REGERQPR  314 (319)
T ss_pred             HHHhcccc
Confidence            88765543

>PRK06871 DNA polymerase III subunit delta'; Validated

Probab=99.98  E-value=1.1e-29  Score=219.26  Aligned_cols=281  Identities=21%  Similarity=0.189  Sum_probs=204.2

Q ss_pred             CCHHHHHHHHHHHhcCCCce-EEEECCCCCCHHHHHHHHHHHHcCCCCC-------------------CceEEecC--CC
Q psy879           14 GNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARILLGPSFK-------------------DAVLELNA--SN   71 (317)
Q Consensus        14 g~~~~~~~l~~~l~~~~~~~-~ll~G~~G~GKt~la~~la~~l~~~~~~-------------------~~~~~~~~--~~   71 (317)
                      .+....+.|...+.+|+.+| +||+||+|+||+++|+.+|+.+.|....                   ..+..+.+  ..
T Consensus         6 W~~~~~~~l~~~~~~~rl~HA~Lf~G~~G~GK~~lA~~~A~~llC~~~~~~~~Cg~C~sC~~~~~g~HPD~~~i~p~~~~   85 (325)
T PRK06871          6 WLQPTYQQITQAFQQGLGHHALLFKADSGLGTEQLIRALAQWLMCQTPQGDQPCGQCHSCHLFQAGNHPDFHILEPIDNK   85 (325)
T ss_pred             chHHHHHHHHHHHHcCCcceeEEeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHhcCCCCCEEEEccccCC
Confidence            46778889999999999999 9999999999999999999999985421                   11333332  34


Q ss_pred             CcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcCchhHhhhcceee
Q psy879           72 DRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLR  151 (317)
Q Consensus        72 ~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~~~i~sR~~~i~  151 (317)
                      ..+++++|+....+...+.   .+++||+|||++|.|+..++|+|+|+|||||+++.||++|+++++++|||+|||+.+.
T Consensus        86 ~I~id~iR~l~~~~~~~~~---~g~~KV~iI~~a~~m~~~AaNaLLKtLEEPp~~~~fiL~t~~~~~llpTI~SRC~~~~  162 (325)
T PRK06871         86 DIGVDQVREINEKVSQHAQ---QGGNKVVYIQGAERLTEAAANALLKTLEEPRPNTYFLLQADLSAALLPTIYSRCQTWL  162 (325)
T ss_pred             CCCHHHHHHHHHHHhhccc---cCCceEEEEechhhhCHHHHHHHHHHhcCCCCCeEEEEEECChHhCchHHHhhceEEe
Confidence            5789999998887777663   3789999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhhCCCcccHHHHHhhcCCCCHHHHHHHHHH
Q psy879          152 YNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEMLLN  231 (317)
Q Consensus       152 f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~~~~~i~~~~v~~~~~~~~~~~i~~l~~~  231 (317)
                      |++++++++.+||....     ..++..+...+..++|++..|+..++.-......-..+.+.......   ...+++..
T Consensus       163 ~~~~~~~~~~~~L~~~~-----~~~~~~~~~~~~l~~g~p~~A~~~~~~~~~~~r~~~~~~l~~~~~~~---~~~~~~~~  234 (325)
T PRK06871        163 IHPPEEQQALDWLQAQS-----SAEISEILTALRINYGRPLLALTFLEQGLLEQRKTFLRQFWLFYRRR---SPLELLPL  234 (325)
T ss_pred             CCCCCHHHHHHHHHHHh-----ccChHHHHHHHHHcCCCHHHHHHHhhCChHHHHHHHHHHHHHHhccC---CHHHHHHH
Confidence            99999999999999864     23344466677889999998987764321100000001111111111   22334443


Q ss_pred             HhcCCHH----HHHHHHHHHH--HcCCCH----HHHHHHHHHHHHhcCCChHHHHHHHHHHHHHHhHHh--cCCCcHHHH
Q psy879          232 CVEGNMK----DSYKIIHHLY--KLGYAP----EDIIGNIFRVAKTLDIPEPLKLSIIQEIGNVHLRIS--EGVNSLLQL  299 (317)
Q Consensus       232 ~~~~~~~----~~~~~~~~l~--~~~~~~----~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~--~g~~~~l~l  299 (317)
                      +...+..    -.+.++.|++  +.|.+.    .+....+..++.  ..+.....++++.+.+...++.  .|.|..|.+
T Consensus       235 ~~k~~~~~~l~~l~~~~rD~l~~~~~~~~~~~n~D~~~~i~~~a~--~~s~~~L~~~i~~i~~~r~~L~~~~~iN~~L~l  312 (325)
T PRK06871        235 FDKELVLQQLDWLLAFLSDALKAKLDIASGWICQDLQRGILQFSQ--QQSAQGLLKAHQIIQKVRSDLLQINAVNQELIL  312 (325)
T ss_pred             HhhccHHHHHHHHHHHHHHHHHHHcCCCcccccHhHHHHHHHHHH--hCCHHHHHHHHHHHHHHHHHHHcccccCHHHHH
Confidence            3322332    2445566663  333222    122333444445  5677788889999999999994  555999999


Q ss_pred             HHHHHHHH
Q psy879          300 SGLLARLC  307 (317)
Q Consensus       300 e~~~~~~~  307 (317)
                      +..++.+.
T Consensus       313 ~~~l~~~~  320 (325)
T PRK06871        313 LDGLTRLV  320 (325)
T ss_pred             HHHHHHHH
Confidence            99998875

>PRK06964 DNA polymerase III subunit delta'; Validated

Probab=99.97  E-value=6.6e-29  Score=215.86  Aligned_cols=277  Identities=16%  Similarity=0.182  Sum_probs=199.3

Q ss_pred             CCHHHHHHHHHHHhcCCCce-EEEECCCCCCHHHHHHHHHHHHcCCCC---CC-----------------ceEEecCC--
Q psy879           14 GNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARILLGPSF---KD-----------------AVLELNAS--   70 (317)
Q Consensus        14 g~~~~~~~l~~~l~~~~~~~-~ll~G~~G~GKt~la~~la~~l~~~~~---~~-----------------~~~~~~~~--   70 (317)
                      .+...++.|...  .++.|| |||+||+|+||+++|+.+|+.+.|...   ..                 .+..+.+.  
T Consensus         5 W~~~~~~~l~~~--~~rl~ha~Lf~Gp~G~GK~~lA~~~A~~LlC~~~~~~~~~Cg~C~~C~~~~~~~HPD~~~i~p~~~   82 (342)
T PRK06964          5 WQTDDWNRLQAL--RARLPHALLLHGQAGIGKLDFAQHLAQGLLCETPQPDGEPCGTCAACNWFAQGNHPDYRIVRPEAL   82 (342)
T ss_pred             ccHHHHHHHHHh--cCCcceEEEEECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCCHHHHHHHcCCCCCEEEEecccc
Confidence            356677777764  568888 999999999999999999999998542   11                 12222111  


Q ss_pred             ---------------------------CCcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhc
Q psy879           71 ---------------------------NDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIY  123 (317)
Q Consensus        71 ---------------------------~~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~  123 (317)
                                                 ...+++++++....+...+   ..++++|+|||++|.|+..+.|+|||++|+|
T Consensus        83 ~~~~~~~~~~~~~~~~~~~~~k~~~~~~~I~idqiR~l~~~~~~~~---~~~~~kV~iI~~ae~m~~~AaNaLLKtLEEP  159 (342)
T PRK06964         83 AAEAPGAADEAKEADADEGGKKTKAPSKEIKIEQVRALLDFCGVGT---HRGGARVVVLYPAEALNVAAANALLKTLEEP  159 (342)
T ss_pred             cccccccccccccchhhcccccccccccccCHHHHHHHHHHhccCC---ccCCceEEEEechhhcCHHHHHHHHHHhcCC
Confidence                                       2467789998887766555   3478999999999999999999999999999


Q ss_pred             cCCceEEEEecCCCcCchhHhhhcceeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhh
Q psy879          124 SNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHN  203 (317)
Q Consensus       124 ~~~~~~il~~~~~~~l~~~i~sR~~~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~  203 (317)
                      |+++.||++|+++++++|||+|||+.+.|++++.+++..||.+.    +  +++.  +.++..++|++..|+..+..-  
T Consensus       160 p~~t~fiL~t~~~~~LLpTI~SRcq~i~~~~~~~~~~~~~L~~~----~--~~~~--~~~l~~~~Gsp~~Al~~~~~~--  229 (342)
T PRK06964        160 PPGTVFLLVSARIDRLLPTILSRCRQFPMTVPAPEAAAAWLAAQ----G--VADA--DALLAEAGGAPLAALALASDE--  229 (342)
T ss_pred             CcCcEEEEEECChhhCcHHHHhcCEEEEecCCCHHHHHHHHHHc----C--CChH--HHHHHHcCCCHHHHHHHHCCC--
Confidence            99999999999999999999999999999999999999999874    3  3332  335778899999999877321  


Q ss_pred             CCCcccHHHHHhhcCCCCHHHHHHHHHHHhcCCHHHHH----HHHHHHH--HcCCCHH---HHHHHHHHHHHhcCCChHH
Q psy879          204 GFGHVTAEYVFKVCDEPHPLAVKEMLLNCVEGNMKDSY----KIIHHLY--KLGYAPE---DIIGNIFRVAKTLDIPEPL  274 (317)
Q Consensus       204 ~~~~i~~~~v~~~~~~~~~~~i~~l~~~~~~~~~~~~~----~~~~~l~--~~~~~~~---~i~~~~~~~~~~~~~~~~~  274 (317)
                       .... .+.+...+..........+.+.+...+....+    .++.|++  +.|.++.   +....+...+.  .++...
T Consensus       230 -~~~~-~~~~~~~l~~~~~~~~~~~~~~~~k~~~~~~l~~l~~~lrD~l~~~~~~~~~~~~d~~~~l~~~a~--~~~~~~  305 (342)
T PRK06964        230 -NRPL-RDWTLGQLAAGAACDAFACAETLQKLPVPAVLGWLQRWLYDLLAQRLAGAPRYFPAQRAALARCAA--AVDANA  305 (342)
T ss_pred             -hHHH-HHHHHHHHhccCchhHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHHcCCCceecHhHHHHHHHHHH--cCCHHH
Confidence             1111 11121122222223455566655544544444    4456653  2332221   11223444445  556677


Q ss_pred             HHHHHHHHHHHHhHHhcCCCcHHHHHHHHHHHHHh
Q psy879          275 KLSIIQEIGNVHLRISEGVNSLLQLSGLLARLCIV  309 (317)
Q Consensus       275 ~~~~~~~l~~~~~~l~~g~~~~l~le~~~~~~~~~  309 (317)
                      ..++++.+.+....+..|+|++|.+|.++.++...
T Consensus       306 L~~~~~~i~~~~~~~~~nvn~~L~le~lll~~~~~  340 (342)
T PRK06964        306 LARFAKAVTRQRAVENHPLAARLVFEELFLGYREL  340 (342)
T ss_pred             HHHHHHHHHHHHHHhHCCCCHHHHHHHHHHHHHHH
Confidence            78889999999989999999999999999998754

>PF05496 RuvB_N: Holliday junction DNA helicase ruvB N-terminus; InterPro: IPR008824 The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair

Probab=99.97  E-value=1.1e-30  Score=209.44  Aligned_cols=186  Identities=22%  Similarity=0.290  Sum_probs=138.2

Q ss_pred             cccCCCCCCcccCCHHHHHHHHHHHh-----cCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChH
Q psy879            2 EKYRPQTFSDIVGNEDTVERLKVFSS-----SGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGID   76 (317)
Q Consensus         2 ~ky~P~~~~~~~g~~~~~~~l~~~l~-----~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~   76 (317)
                      ++.||++|+|++||++++..+..+++     +..++|++||||||+||||+|+.+|+++.     ..+...++.......
T Consensus        16 ~~lRP~~L~efiGQ~~l~~~l~i~i~aa~~r~~~l~h~lf~GPPG~GKTTLA~IIA~e~~-----~~~~~~sg~~i~k~~   90 (233)
T PF05496_consen   16 ERLRPKSLDEFIGQEHLKGNLKILIRAAKKRGEALDHMLFYGPPGLGKTTLARIIANELG-----VNFKITSGPAIEKAG   90 (233)
T ss_dssp             HHTS-SSCCCS-S-HHHHHHHHHHHHHHHCTTS---EEEEESSTTSSHHHHHHHHHHHCT-------EEEEECCC--SCH
T ss_pred             HhcCCCCHHHccCcHHHHhhhHHHHHHHHhcCCCcceEEEECCCccchhHHHHHHHhccC-----CCeEeccchhhhhHH
Confidence            46899999999999999998776553     34578999999999999999999999963     234555554333444


Q ss_pred             HHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhcc------------------CCceEEEEecCCCc
Q psy879           77 TVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYS------------------NTTRFALACNNSEK  138 (317)
Q Consensus        77 ~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~------------------~~~~~il~~~~~~~  138 (317)
                      ++...+..+         ..+.|+||||++.+++..++.|+.+||+..                  +...+|.+|+....
T Consensus        91 dl~~il~~l---------~~~~ILFIDEIHRlnk~~qe~LlpamEd~~idiiiG~g~~ar~~~~~l~~FTligATTr~g~  161 (233)
T PF05496_consen   91 DLAAILTNL---------KEGDILFIDEIHRLNKAQQEILLPAMEDGKIDIIIGKGPNARSIRINLPPFTLIGATTRAGL  161 (233)
T ss_dssp             HHHHHHHT-----------TT-EEEECTCCC--HHHHHHHHHHHHCSEEEEEBSSSSS-BEEEEE----EEEEEESSGCC
T ss_pred             HHHHHHHhc---------CCCcEEEEechhhccHHHHHHHHHHhccCeEEEEeccccccceeeccCCCceEeeeeccccc
Confidence            454444322         356799999999999999999999999542                  23447888889899


Q ss_pred             CchhHhhhcce-eeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHh
Q psy879          139 IIEPIQSRCAM-LRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQST  201 (317)
Q Consensus       139 l~~~i~sR~~~-i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~  201 (317)
                      +.+++++||.. .++..|+.+++.+++...+...+++++++++..++..|.|.+|-|.++|+.+
T Consensus       162 ls~pLrdRFgi~~~l~~Y~~~el~~Iv~r~a~~l~i~i~~~~~~~Ia~rsrGtPRiAnrll~rv  225 (233)
T PF05496_consen  162 LSSPLRDRFGIVLRLEFYSEEELAKIVKRSARILNIEIDEDAAEEIARRSRGTPRIANRLLRRV  225 (233)
T ss_dssp             TSHCCCTTSSEEEE----THHHHHHHHHHCCHCTT-EE-HHHHHHHHHCTTTSHHHHHHHHHHH
T ss_pred             cchhHHhhcceecchhcCCHHHHHHHHHHHHHHhCCCcCHHHHHHHHHhcCCChHHHHHHHHHH
Confidence            99999999999 5799999999999999999999999999999999999999999999999875

Branch migration is catalysed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein []. This group of sequences contain this signature which is located in the N-terminal region of the proteins.; GO: 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 1IQP_B 3PFI_B 1IXR_C 1HQC_B 1IXS_B.

>PRK06090 DNA polymerase III subunit delta'; Validated

Probab=99.97  E-value=1.9e-28  Score=211.08  Aligned_cols=279  Identities=13%  Similarity=0.152  Sum_probs=195.3

Q ss_pred             CCHHHHHHHHHHHhcCCCce-EEEECCCCCCHHHHHHHHHHHHcCCCCC------------------CceEEecC---CC
Q psy879           14 GNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARILLGPSFK------------------DAVLELNA---SN   71 (317)
Q Consensus        14 g~~~~~~~l~~~l~~~~~~~-~ll~G~~G~GKt~la~~la~~l~~~~~~------------------~~~~~~~~---~~   71 (317)
                      -+....+.|...+.+|++|| +||+||+|+||+++|+.+|+.+.|....                  ..+..+.+   ..
T Consensus         7 Wl~~~~~~l~~~~~~~rl~hA~L~~G~~G~Gk~~lA~~~a~~llC~~~~~~~Cg~C~sC~~~~~g~HPD~~~i~p~~~~~   86 (319)
T PRK06090          7 WLVPVWQNWKAGLDAGRIPGALLLQSDEGLGVESLVELFSRALLCQNYQSEACGFCHSCELMQSGNHPDLHVIKPEKEGK   86 (319)
T ss_pred             cHHHHHHHHHHHHHcCCcceeEeeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHcCCCCCEEEEecCcCCC
Confidence            46788899999999999999 9999999999999999999999875421                  12333433   23


Q ss_pred             CcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcCchhHhhhcceee
Q psy879           72 DRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLR  151 (317)
Q Consensus        72 ~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~~~i~sR~~~i~  151 (317)
                      .++++++|+.......++.   .+++||+|||++|.|+..++|+|+|++||||+++.||++|+++++++|||+|||+.+.
T Consensus        87 ~I~vdqiR~l~~~~~~~~~---~~~~kV~iI~~ae~m~~~AaNaLLKtLEEPp~~t~fiL~t~~~~~lLpTI~SRCq~~~  163 (319)
T PRK06090         87 SITVEQIRQCNRLAQESSQ---LNGYRLFVIEPADAMNESASNALLKTLEEPAPNCLFLLVTHNQKRLLPTIVSRCQQWV  163 (319)
T ss_pred             cCCHHHHHHHHHHHhhCcc---cCCceEEEecchhhhCHHHHHHHHHHhcCCCCCeEEEEEECChhhChHHHHhcceeEe
Confidence            4788999987776666553   3789999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhhCCCcccHHHHHhhcCCCCHHHHHHHHHH
Q psy879          152 YNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEMLLN  231 (317)
Q Consensus       152 f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~~~~~i~~~~v~~~~~~~~~~~i~~l~~~  231 (317)
                      |++++++++.+||.+.    +++    ....++..++|++..|+..++.-......-..+.+...+.... ..++.+...
T Consensus       164 ~~~~~~~~~~~~L~~~----~~~----~~~~~l~l~~G~p~~A~~~~~~~~~~~~~~~~~~l~~~l~~~~-~~~~~~a~~  234 (319)
T PRK06090        164 VTPPSTAQAMQWLKGQ----GIT----VPAYALKLNMGSPLKTLAMMKEGGLEKYHKLERQLVDALSGPV-SDQLKCASL  234 (319)
T ss_pred             CCCCCHHHHHHHHHHc----CCc----hHHHHHHHcCCCHHHHHHHhCCCcHHHHHHHHHHHHHHHhcCc-ccHHHHHHH
Confidence            9999999999999763    433    2345678899999999987742111100011122222222222 234455555


Q ss_pred             HhcCCHHHHH----HHHHHHH--HcCCCHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHHHhHHh--cCCCcHHHHHHHH
Q psy879          232 CVEGNMKDSY----KIIHHLY--KLGYAPEDIIGNIFRVAKTLDIPEPLKLSIIQEIGNVHLRIS--EGVNSLLQLSGLL  303 (317)
Q Consensus       232 ~~~~~~~~~~----~~~~~l~--~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~--~g~~~~l~le~~~  303 (317)
                      +...+ ...+    .++.|++  ..|....+....+..+ .  ..+.......++.+.+...++.  .+.|..+.++.++
T Consensus       235 ~~~~~-~~~l~~L~~ll~Dll~~~~g~~~~~~~~~~~~l-~--~~~~~~l~~~~~~l~~~~~~L~~~~~ln~elll~~ll  310 (319)
T PRK06090        235 IAADP-LTHLSWLWLLLTDAQKVHFGVQNEYYLPGSAAL-G--PFTYSGLYVSTAKLERLKEQLQQFSGLNTELLIMNWL  310 (319)
T ss_pred             HhcCc-HHHHHHHHHHHHHHHHHHhCCcchhhhHHHHHH-H--hhCHHHHHHHHHHHHHHHHHHHhccccCHHHHHHHHH
Confidence            43322 3333    3445553  2332222222222222 1  2233444556777888888886  3449999999999


Q ss_pred             HHHHH
Q psy879          304 ARLCI  308 (317)
Q Consensus       304 ~~~~~  308 (317)
                      .++..
T Consensus       311 l~~~~  315 (319)
T PRK06090        311 IESRE  315 (319)
T ss_pred             HHHHH
Confidence            98854

>PRK05917 DNA polymerase III subunit delta'; Validated

Probab=99.97  E-value=4.1e-28  Score=204.86  Aligned_cols=255  Identities=17%  Similarity=0.148  Sum_probs=186.3

Q ss_pred             HHHHHHHHHHhcCCCce-EEEECCCCCCHHHHHHHHHHHHcCCCC-----------CCceEEecCC---CCcChHHHHHH
Q psy879           17 DTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARILLGPSF-----------KDAVLELNAS---NDRGIDTVRNK   81 (317)
Q Consensus        17 ~~~~~l~~~l~~~~~~~-~ll~G~~G~GKt~la~~la~~l~~~~~-----------~~~~~~~~~~---~~~~~~~i~~~   81 (317)
                      ..++.|...+++|+.+| |+|+||+|+||+++|..+|+.+.|...           ...+..+.+.   ...+++++|+.
T Consensus         4 ~~~~~L~~~i~~~rl~HAyLf~G~~G~Gk~~lA~~~A~~llC~~~~~~c~~~~~~~HPD~~~i~p~~~~~~I~idqiR~l   83 (290)
T PRK05917          4 AAWEALIQRVRDQKVPSAIILHGQDLSNLSARAYELASLILKETSPEAAYKISQKIHPDIHEFSPQGKGRLHSIETPRAI   83 (290)
T ss_pred             HHHHHHHHHHHcCCcCeeEeeECCCCCcHHHHHHHHHHHHhCCCCccHHHHHhcCCCCCEEEEecCCCCCcCcHHHHHHH
Confidence            45778999999999999 999999999999999999999998531           1223333322   23678999998


Q ss_pred             HHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcCchhHhhhcceeeecCCCHHHHH
Q psy879           82 IKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLL  161 (317)
Q Consensus        82 ~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~~~i~sR~~~i~f~~~~~~~~~  161 (317)
                      ...+...+.   .+.++|+|||++|.|+.+++|+|++++|+||+++.||++|++++.++|||+|||+.+.|+++.     
T Consensus        84 ~~~~~~~p~---e~~~kv~ii~~ad~mt~~AaNaLLK~LEEPp~~~~fiL~~~~~~~ll~TI~SRcq~~~~~~~~-----  155 (290)
T PRK05917         84 KKQIWIHPY---ESPYKIYIIHEADRMTLDAISAFLKVLEDPPQHGVIILTSAKPQRLPPTIRSRSLSIHIPMEE-----  155 (290)
T ss_pred             HHHHhhCcc---CCCceEEEEechhhcCHHHHHHHHHHhhcCCCCeEEEEEeCChhhCcHHHHhcceEEEccchh-----
Confidence            888877764   388999999999999999999999999999999999999999999999999999999999861     


Q ss_pred             HHHHHHHHHcCCCCCHHHHHHHHHhcCCCHH--HHHHHHHHhhhCCCcccHHHHHhhcCCCCHHHHHHHHHHHhcCCHHH
Q psy879          162 SKVIEICEKENISHTNDGLEAIVFTAQGDMR--QALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEMLLNCVEGNMKD  239 (317)
Q Consensus       162 ~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r--~~i~~l~~~~~~~~~i~~~~v~~~~~~~~~~~i~~l~~~~~~~~~~~  239 (317)
                                ...++++.+..++..++|+++  ++...+...        .+......    .+.+..+        .+-
T Consensus       156 ----------~~~i~~~~~~~l~~~~~g~~~~~~~~~~l~~~--------~~~~~~~~----re~~~~~--------L~~  205 (290)
T PRK05917        156 ----------KTLVSKEDIAYLIGYAQGKESVTEVGQIVKGS--------ADTDKQVL----RDKTKAM--------LEV  205 (290)
T ss_pred             ----------ccCCCHHHHHHHHHHhCCChhHHHHHHHHhcc--------hHHHHHHH----HHHHHHH--------HHH
Confidence                      124678888889999999885  223222211        01000000    1112222        234


Q ss_pred             HHHHHHHH--HHcCCCHHH-HHHHHHHHHHhcCCChHHHHHHHHHHHHHHhHHhcCCCcHHHHHHHHHHHHHhhc
Q psy879          240 SYKIIHHL--YKLGYAPED-IIGNIFRVAKTLDIPEPLKLSIIQEIGNVHLRISEGVNSLLQLSGLLARLCIVGS  311 (317)
Q Consensus       240 ~~~~~~~l--~~~~~~~~~-i~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~g~~~~l~le~~~~~~~~~~~  311 (317)
                      .+.+++|+  +..|.+... +.......+...  +......+++.+.+...++..|+|+++.+|.|+.++.....
T Consensus       206 ll~~~RD~l~~~~~~~~~~l~~~d~~~~l~~~--~~~~l~~~i~~i~~a~~~l~~N~N~~l~le~l~l~l~~~~~  278 (290)
T PRK05917        206 LLQLFRDRFLLALKVPASALAYPDLLKEILTL--PVLPLEKVLSIIERAVQALDNSSSAPSCLEWVALQLWSLKN  278 (290)
T ss_pred             HHHHHHHHHHHHcCCchhhhccHHHHHHHHhc--ccccHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHH
Confidence            56667776  344444332 222222222222  22336789999999999999999999999999999976543

>PRK07132 DNA polymerase III subunit delta'; Validated

Probab=99.97  E-value=1.3e-27  Score=204.59  Aligned_cols=277  Identities=14%  Similarity=0.193  Sum_probs=192.7

Q ss_pred             HHHHHHHHHHHhcCCCce-EEEECCCCCCHHHHHHHHHHHHcCCC--------CCCceEEecC-CCCcChHHHHHHHHHH
Q psy879           16 EDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARILLGPS--------FKDAVLELNA-SNDRGIDTVRNKIKMF   85 (317)
Q Consensus        16 ~~~~~~l~~~l~~~~~~~-~ll~G~~G~GKt~la~~la~~l~~~~--------~~~~~~~~~~-~~~~~~~~i~~~~~~~   85 (317)
                      ..+++.+...+++|+++| |||+|++|+||+++++.+++.+.|..        ....+..++. ....+.+++++....+
T Consensus         2 ~~~~~~l~~~i~~~~l~haYLf~G~eg~gk~~~a~~~a~~l~c~~~~~~~~~~~p~n~~~~d~~g~~i~vd~Ir~l~~~~   81 (299)
T PRK07132          2 NNWIKFLDNSATQNKISHSFLLKSNYNEDIDEKILYFLNKFNNLQITNLNEQELPANIILFDIFDKDLSKSEFLSAINKL   81 (299)
T ss_pred             chHHHHHHHHHHhCCCCeEEEEeCCCCCCHHHHHHHHHHHHcCcCCCCCCCCCCCcceEEeccCCCcCCHHHHHHHHHHh
Confidence            356788999999999999 99999999999999999999997732        1112333331 2346778888887776


Q ss_pred             HhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcCchhHhhhcceeeecCCCHHHHHHHHH
Q psy879           86 AQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVI  165 (317)
Q Consensus        86 ~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~~~i~sR~~~i~f~~~~~~~~~~~l~  165 (317)
                      ...+..  .++++|+|||+++.|+..++|+|++++|+||+++.+|++|+++.+++++|+|||+.++|.+++++++..||.
T Consensus        82 ~~~~~~--~~~~KvvII~~~e~m~~~a~NaLLK~LEEPp~~t~~il~~~~~~kll~TI~SRc~~~~f~~l~~~~l~~~l~  159 (299)
T PRK07132         82 YFSSFV--QSQKKILIIKNIEKTSNSLLNALLKTIEEPPKDTYFLLTTKNINKVLPTIVSRCQVFNVKEPDQQKILAKLL  159 (299)
T ss_pred             ccCCcc--cCCceEEEEecccccCHHHHHHHHHHhhCCCCCeEEEEEeCChHhChHHHHhCeEEEECCCCCHHHHHHHHH
Confidence            555421  258999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             HHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhhCCCcccHHHHHhhcCCC--CHHHHHHHHHHHhcCC-----HH
Q psy879          166 EICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEP--HPLAVKEMLLNCVEGN-----MK  238 (317)
Q Consensus       166 ~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~~~~~i~~~~v~~~~~~~--~~~~i~~l~~~~~~~~-----~~  238 (317)
                      ..    +  ++++....++..++ ++.+|+..+.....    -....+.+.+...  ....+....+...+++     ..
T Consensus       160 ~~----~--~~~~~a~~~a~~~~-~~~~a~~~~~~~~~----~~~~~~~~~l~~~~~~~~~l~~~~~~~~~ke~~~~ll~  228 (299)
T PRK07132        160 SK----N--KEKEYNWFYAYIFS-NFEQAEKYINKESE----NLLKKFEEALNKSLKEKYELILFLNKKLTKENALFLLK  228 (299)
T ss_pred             Hc----C--CChhHHHHHHHHcC-CHHHHHHHHhcCCH----HHHHHHHHHHHHhhhhHHHHHHHHHhhcChhhHHHHHH
Confidence            63    3  56676677777777 59999988643211    0011111111000  1112222222222211     12


Q ss_pred             HHHHHHHHHH--HcCCCHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHHHhHHhcCCCcHHHHHHHHHHHHHh
Q psy879          239 DSYKIIHHLY--KLGYAPEDIIGNIFRVAKTLDIPEPLKLSIIQEIGNVHLRISEGVNSLLQLSGLLARLCIV  309 (317)
Q Consensus       239 ~~~~~~~~l~--~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~g~~~~l~le~~~~~~~~~  309 (317)
                      -...|+++++  ..+.+...+... ....+....   ...++++.+.++..++.+|+|..+++|.|+.++.+.
T Consensus       229 ~l~~~~rd~l~~~~~~~~~~i~~~-~~~i~~~~~---s~~~li~~i~~~~~~L~~N~N~~l~~e~lll~l~e~  297 (299)
T PRK07132        229 LLKFFFKSIFANKKKKNPKNIKVA-FSKKKKFKI---EFFELITIIDEFLNSLETNENFNLQKQAFLVKIYEI  297 (299)
T ss_pred             HHHHHHHHHHHHhccCChHhHhhH-HHHHHHHhc---CHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHh
Confidence            2334445553  223444333333 233332222   233458999999999999999999999999999764

>COG0470 HolB ATPase involved in DNA replication [DNA replication, recombination, and repair]

Probab=99.97  E-value=2.7e-28  Score=215.49  Aligned_cols=286  Identities=32%  Similarity=0.469  Sum_probs=205.8

Q ss_pred             CcccCCHHHHHHHHHHHh-cCCCce-EEEECCCCCCHHHHHHHHHHHHcCCC-------------------CCCceEEec
Q psy879           10 SDIVGNEDTVERLKVFSS-SGNVPN-IIISGPPGVGKTTTILCLARILLGPS-------------------FKDAVLELN   68 (317)
Q Consensus        10 ~~~~g~~~~~~~l~~~l~-~~~~~~-~ll~G~~G~GKt~la~~la~~l~~~~-------------------~~~~~~~~~   68 (317)
                      +++++++++...+..+.. .++.|| +||+||||+|||++|.++|+.+.|..                   ....+++++
T Consensus         1 ~~~~~~~~~~~~l~~~~~~~~~~~halL~~Gp~G~Gktt~a~~lA~~l~~~~~~~~~~~~~~~~~~~~~~~~~~d~lel~   80 (325)
T COG0470           1 DELVPWQEAVKRLLVQALESGRLPHALLFYGPPGVGKTTAALALAKELLCENPTGLLPCGHCRSCKLIPAGNHPDFLELN   80 (325)
T ss_pred             CCcccchhHHHHHHHHHHhcCCCCceeeeeCCCCCCHHHHHHHHHHHHhCCCcccCCcccchhhhhHHhhcCCCceEEec
Confidence            367888888888877776 778899 99999999999999999999998755                   235788999


Q ss_pred             CCCCcCh----HHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcCchhHh
Q psy879           69 ASNDRGI----DTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQ  144 (317)
Q Consensus        69 ~~~~~~~----~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~~~i~  144 (317)
                      +++..+.    +.+++........+   ..++++|+||||+|.|+.++++++++.+|+|+.+++||++||.+.++.++|+
T Consensus        81 ~s~~~~~~i~~~~vr~~~~~~~~~~---~~~~~kviiidead~mt~~A~nallk~lEep~~~~~~il~~n~~~~il~tI~  157 (325)
T COG0470          81 PSDLRKIDIIVEQVRELAEFLSESP---LEGGYKVVIIDEADKLTEDAANALLKTLEEPPKNTRFILITNDPSKILPTIR  157 (325)
T ss_pred             ccccCCCcchHHHHHHHHHHhccCC---CCCCceEEEeCcHHHHhHHHHHHHHHHhccCCCCeEEEEEcCChhhccchhh
Confidence            9876663    44444444443332   2378999999999999999999999999999999999999999999999999


Q ss_pred             hhcceeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhhCCCcccHHHHHhhcCCCCHH-
Q psy879          145 SRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPL-  223 (317)
Q Consensus       145 sR~~~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~~~~~i~~~~v~~~~~~~~~~-  223 (317)
                      |||+.++|++++......+..           ++.+..++..+.||+|.+++.++..+..  ......+.......... 
T Consensus       158 SRc~~i~f~~~~~~~~i~~~e-----------~~~l~~i~~~~~gd~r~~i~~lq~~~~~--~~~~~~~~~~~~~~~~~~  224 (325)
T COG0470         158 SRCQRIRFKPPSRLEAIAWLE-----------DQGLEEIAAVAEGDARKAINPLQALAAL--EIGEESIYEALLLALPES  224 (325)
T ss_pred             hcceeeecCCchHHHHHHHhh-----------ccchhHHHHHHHHHHHcCCCHHHHHHHh--cccHHHHHHHHHhhChhh
Confidence            999999999955444444333           5567888899999999999999987664  22333333322222221 


Q ss_pred             ----HHHHHHHHHhcCCHHHHHHHHHH-HHHcCCCHHHHHHHHHHHHHhc---CCChHHHHHHHHHHHHHHhHHhcCCCc
Q psy879          224 ----AVKEMLLNCVEGNMKDSYKIIHH-LYKLGYAPEDIIGNIFRVAKTL---DIPEPLKLSIIQEIGNVHLRISEGVNS  295 (317)
Q Consensus       224 ----~i~~l~~~~~~~~~~~~~~~~~~-l~~~~~~~~~i~~~~~~~~~~~---~~~~~~~~~~~~~l~~~~~~l~~g~~~  295 (317)
                          ...+++..... +...+...... +...+.........+.+.....   .............+...+.++..+.+.
T Consensus       225 ~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  303 (325)
T COG0470         225 LAQLAALELLKLAEN-KFLEALEKLWLLLLLEGLLGEDLLDQLQRELLKLDKALIQEEKAAELLDALAQARRRLLDGLLA  303 (325)
T ss_pred             cccccHHHHHHHHHh-cchhHHHHHHHHHHHcCcchhHHHHHHHHHHhhchhhhhhhhHHHHHHHHHHHHHHHHHHHHHH
Confidence                34444443331 23333333333 3445555555444444433322   134445666788889999999999999


Q ss_pred             HHHHHHHHHHHHHhhcc
Q psy879          296 LLQLSGLLARLCIVGSK  312 (317)
Q Consensus       296 ~l~le~~~~~~~~~~~~  312 (317)
                      .++++.++..+......
T Consensus       304 ~~~~~~~~~~~~~~~~~  320 (325)
T COG0470         304 LIQLENLLAELLLLQLL  320 (325)
T ss_pred             HHHHHHHHHHHHHHHHH
Confidence            99999999888765543

>PRK05907 hypothetical protein; Provisional

Probab=99.95  E-value=3.8e-25  Score=190.87  Aligned_cols=272  Identities=12%  Similarity=0.102  Sum_probs=217.1

Q ss_pred             HHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHHHHHHHhhcccCCCCcee
Q psy879           19 VERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHK   98 (317)
Q Consensus        19 ~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~   98 (317)
                      ...+.+.+++|+ |+|++||..-   ......+.+.+.+...  ..++.+   ....+.   .+......|+.   ++++
T Consensus         7 ~~~~~~~~~~~~-~~y~~~g~~~---~~~~~~l~~~~~~~~~--~~fdg~---~~~~~~---ii~~aetlPfF---aerR   71 (311)
T PRK05907          7 FKDFSQYYEEKR-PAVIVIGSSS---EEDKDIFIELLVSGRK--SEFDGQ---GLLQQE---LLSWTEHFGLF---ASQE   71 (311)
T ss_pred             HHHHHHHHhcCC-ceEEEecCCc---HHHHHHHHHHhCCCcc--ceecCC---CCCHHH---HHHHHhcCCcc---cCeE
Confidence            344566788888 8899999986   5566666666544332  222222   223333   34444444433   7899


Q ss_pred             EEEEeCCCCCCHHHHHHHHHHhhhccCCceEE-EEecCCC---cCchhHhhhccee----eecCCCHHHHHHHHHHHHHH
Q psy879           99 IVILDEADSMTDGAQQALRRTMEIYSNTTRFA-LACNNSE---KIIEPIQSRCAML----RYNKLTDAQLLSKVIEICEK  170 (317)
Q Consensus        99 vliiDE~d~l~~~~~~~ll~~le~~~~~~~~i-l~~~~~~---~l~~~i~sR~~~i----~f~~~~~~~~~~~l~~~~~~  170 (317)
                      +|++.+.+++.....+.|.+++++|++.+.+| ++. ..+   ++.+.+.. +..+    .|+++.+.++.+|+.+++++
T Consensus        72 lV~v~~~~~~~~~~~~~L~~Yl~np~~~~~liv~~~-~~d~~kkl~K~i~k-~~~v~~~~e~~~l~e~~L~~Wi~~~~~~  149 (311)
T PRK05907         72 TIGIYQAEKMSSSTQEFLIRYARNPNPHLTLFLFTT-KQECFSSLSKKLSS-ALCLSLFGEWFADRDKRIAQLLIQRAKE  149 (311)
T ss_pred             EEEEecccccccccHHHHHHHHhCCCCCeEEEEEEe-cccHHHHHHHHHhh-cceeccccccCCCCHHHHHHHHHHHHHH
Confidence            99999888888777889999999999976666 544 322   23344443 4445    89999999999999999999


Q ss_pred             cCCCCCHHHHHHHHHhc-CCCHHHHHHHHHHhhh---CCCcccHHHHHhhcCCCCHHHHHHHHHHHhcCCHHHHHHHHHH
Q psy879          171 ENISHTNDGLEAIVFTA-QGDMRQALNNLQSTHN---GFGHVTAEYVFKVCDEPHPLAVKEMLLNCVEGNMKDSYKIIHH  246 (317)
Q Consensus       171 ~~~~i~~~~~~~l~~~~-~gd~r~~i~~l~~~~~---~~~~i~~~~v~~~~~~~~~~~i~~l~~~~~~~~~~~~~~~~~~  246 (317)
                      +|+.+++++++.++..+ ++|+..+.+++++.+.   +.+.|+.++|.+++..+.+.++|++++++..++..+|+.++++
T Consensus       150 ~g~~i~~~a~~~L~~~~~~~nL~~l~~EleKL~ly~g~~~~It~e~V~~lv~~s~e~nIF~L~dai~~~~~~~Al~il~~  229 (311)
T PRK05907        150 LGISCSLGLASLFVSKFPQTGLFEILSEFQKLLCQMGKKESLEASDIQSFVVKKEAASLWKLRDALLRRDRVEGHSLLRS  229 (311)
T ss_pred             cCCCcCHHHHHHHHHHccCCCHHHHHHHHHHHHHhcCCCCeECHHHHHHHhcCcccccHHHHHHHHHccCHHHHHHHHHH
Confidence            99999999999999999 6999999999999655   4668999999999999999999999999999999999999999


Q ss_pred             HHHc-CCCHHHHHHHHHHHHHhc--------C----------CChHHHHHHHHHHHHHHhHHhcCC-CcHHHHHHHHHHH
Q psy879          247 LYKL-GYAPEDIIGNIFRVAKTL--------D----------IPEPLKLSIIQEIGNVHLRISEGV-NSLLQLSGLLARL  306 (317)
Q Consensus       247 l~~~-~~~~~~i~~~~~~~~~~~--------~----------~~~~~~~~~~~~l~~~~~~l~~g~-~~~l~le~~~~~~  306 (317)
                      |... |++|..|+..+.|++ .+        +          .+.....++++.+.++|+++|+|. ++.+.+|.|+.++
T Consensus       230 Ll~~~ge~p~~ILall~rQf-l~~~k~l~~~g~~~~~p~~vafs~~~L~~~~~~l~~~D~~iKtg~~d~~~~lElli~~~  308 (311)
T PRK05907        230 LLSDMGEDPLGIIAFLRSQC-LYGLRSIEEQSKERKHRIFVAYGKERLLQALNLLFYAESLIKNNVQDPILAVETLVIRM  308 (311)
T ss_pred             HHHhcCCChHHHHHHHHHHH-HHHHHHHHHhcCCCCCCeEEEECHHHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHH
Confidence            9999 999999999988876 32        1          234457789999999999999998 9999999999999


Q ss_pred             HH
Q psy879          307 CI  308 (317)
Q Consensus       307 ~~  308 (317)
                      |.
T Consensus       309 ~~  310 (311)
T PRK05907        309 TN  310 (311)
T ss_pred             hc
Confidence            84

>TIGR00678 holB DNA polymerase III, delta' subunit

Probab=99.95  E-value=3.3e-27  Score=191.80  Aligned_cols=166  Identities=27%  Similarity=0.443  Sum_probs=139.7

Q ss_pred             HHHHHHHhcCCCce-EEEECCCCCCHHHHHHHHHHHHcCCCC-------------------CCceEEecC-CCCcChHHH
Q psy879           20 ERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARILLGPSF-------------------KDAVLELNA-SNDRGIDTV   78 (317)
Q Consensus        20 ~~l~~~l~~~~~~~-~ll~G~~G~GKt~la~~la~~l~~~~~-------------------~~~~~~~~~-~~~~~~~~i   78 (317)
                      +.|.+.+.+++++| +||+||+|+|||++++.+++.+.|...                   ...+..+.. ....+.+++
T Consensus         2 ~~l~~~i~~~~~~~~~L~~G~~G~gkt~~a~~~~~~l~~~~~~~~~~c~~~~~c~~~~~~~~~d~~~~~~~~~~~~~~~i   81 (188)
T TIGR00678         2 QQLKRALEKGRLAHAYLFAGPEGVGKELLALALAKALLCEQPGGGEPCGECPSCRLIEAGNHPDLHRLEPEGQSIKVDQV   81 (188)
T ss_pred             hHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHHcCCCCcEEEeccccCcCCHHHH
Confidence            45788889999988 999999999999999999999987410                   011222222 123567888


Q ss_pred             HHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcCchhHhhhcceeeecCCCHH
Q psy879           79 RNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDA  158 (317)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~~~i~sR~~~i~f~~~~~~  158 (317)
                      ++.+..+...+.   .+.++|+||||+|.++.++++.|++++|++++++.+|++++++.++.++++|||..+.|.+++.+
T Consensus        82 ~~i~~~~~~~~~---~~~~kviiide~~~l~~~~~~~Ll~~le~~~~~~~~il~~~~~~~l~~~i~sr~~~~~~~~~~~~  158 (188)
T TIGR00678        82 RELVEFLSRTPQ---ESGRRVVIIEDAERMNEAAANALLKTLEEPPPNTLFILITPSPEKLLPTIRSRCQVLPFPPLSEE  158 (188)
T ss_pred             HHHHHHHccCcc---cCCeEEEEEechhhhCHHHHHHHHHHhcCCCCCeEEEEEECChHhChHHHHhhcEEeeCCCCCHH
Confidence            887777665553   37899999999999999999999999999999999999999889999999999999999999999


Q ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHH
Q psy879          159 QLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQA  194 (317)
Q Consensus       159 ~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~  194 (317)
                      ++.+||.+.    |  +++++++.++..++||+|+|
T Consensus       159 ~~~~~l~~~----g--i~~~~~~~i~~~~~g~~r~~  188 (188)
T TIGR00678       159 ALLQWLIRQ----G--ISEEAAELLLALAGGSPGAA  188 (188)
T ss_pred             HHHHHHHHc----C--CCHHHHHHHHHHcCCCcccC
Confidence            999999886    4  78999999999999999864

At position 126-127 of the seed alignment, this family lacks the HM motif of gamma/tau; at 132 it has a near-invariant A vs. an invariant F in gamma/tau.

>PRK08699 DNA polymerase III subunit delta'; Validated

Probab=99.95  E-value=1.3e-25  Score=195.32  Aligned_cols=277  Identities=17%  Similarity=0.166  Sum_probs=191.9

Q ss_pred             CCHHHHHHHHHHHhcCCCce-EEEECCCCCCHHHHHHHHHHHHcCCCCC--------------------CceEEecCC--
Q psy879           14 GNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARILLGPSFK--------------------DAVLELNAS--   70 (317)
Q Consensus        14 g~~~~~~~l~~~l~~~~~~~-~ll~G~~G~GKt~la~~la~~l~~~~~~--------------------~~~~~~~~~--   70 (317)
                      .+....+.+...  .++.|| |+|+||+|+|||++|+.+|+.+.|....                    ..+..+.+.  
T Consensus         5 W~~~~w~~l~~~--~~r~~hA~Lf~G~~G~GK~~la~~~a~~llC~~~~~~~~~Cg~C~~C~~~~~~~HpD~~~~~p~~~   82 (325)
T PRK08699          5 WHQEQWRQIAEH--WERRPNAWLFAGKKGIGKTAFARFAAQALLCETPAPGHKPCGECMSCHLFGQGSHPDFYEITPLSD   82 (325)
T ss_pred             ccHHHHHHHHHh--cCCcceEEEeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCcCHHHHHHhcCCCCCEEEEecccc
Confidence            456667777665  578888 9999999999999999999999875421                    224445442  


Q ss_pred             --------CCcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcCchh
Q psy879           71 --------NDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEP  142 (317)
Q Consensus        71 --------~~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~~~  142 (317)
                              ...+++++|+........+..   +.++|+++|+++.|+...+++|++++|+|+.++.||++|+++..++++
T Consensus        83 ~~~~g~~~~~I~id~iR~l~~~~~~~p~~---~~~kV~iiEp~~~Ld~~a~naLLk~LEep~~~~~~Ilvth~~~~ll~t  159 (325)
T PRK08699         83 EPENGRKLLQIKIDAVREIIDNVYLTSVR---GGLRVILIHPAESMNLQAANSLLKVLEEPPPQVVFLLVSHAADKVLPT  159 (325)
T ss_pred             cccccccCCCcCHHHHHHHHHHHhhCccc---CCceEEEEechhhCCHHHHHHHHHHHHhCcCCCEEEEEeCChHhChHH
Confidence                    135789999988777666533   789999999999999999999999999999889999999999999999


Q ss_pred             HhhhcceeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhhCCCcccHHHHHhhcCCCCH
Q psy879          143 IQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHP  222 (317)
Q Consensus       143 i~sR~~~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~~~~~i~~~~v~~~~~~~~~  222 (317)
                      ++|||+.+.|++++.+++..||.+.    +.  ++.. ..+ ..++|.+..+.+       .......+.+...+.....
T Consensus       160 i~SRc~~~~~~~~~~~~~~~~L~~~----~~--~~~~-~~l-~~~~g~p~~~~~-------~~~~~~r~~~~~~l~~~~~  224 (325)
T PRK08699        160 IKSRCRKMVLPAPSHEEALAYLRER----GV--AEPE-ERL-AFHSGAPLFDEE-------PELRALRIKLLDILAEPRL  224 (325)
T ss_pred             HHHHhhhhcCCCCCHHHHHHHHHhc----CC--CcHH-HHH-HHhCCChhhhcC-------chHHHHHHHHHHHHHccCh
Confidence            9999999999999999999999763    43  2321 222 456776643211       0000001112111122233


Q ss_pred             HHHHHHHHHHhcCC--HHH----HHHHHHHHH--HcCCCHH---HHHHHHHHHHHhcCCChHHHHHHHHHHHHHHhHHhc
Q psy879          223 LAVKEMLLNCVEGN--MKD----SYKIIHHLY--KLGYAPE---DIIGNIFRVAKTLDIPEPLKLSIIQEIGNVHLRISE  291 (317)
Q Consensus       223 ~~i~~l~~~~~~~~--~~~----~~~~~~~l~--~~~~~~~---~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~  291 (317)
                      ..+..+.+.+...+  ...    ...++.|++  +.+....   +....+..++.  ..+.....++++.+.+....+..
T Consensus       225 ~~~l~~~~~~~~~k~~~~~~l~~l~~~~rDll~~~~~~~~~~~~d~~~~l~~~a~--~~~~~~L~~~~~~l~~~~~~l~~  302 (325)
T PRK08699        225 LKILDYAALFDKEKLPLAVFVGWMQKWLVDLGLCLQHMKPVYYPAYEDRLLQTAS--GFRPRNVFAAEDMLKQLAPYGFH  302 (325)
T ss_pred             hhHHHHHHHHHhccCCHHHHHHHHHHHHHHHHHHHcCCCcccCHhHHHHHHHHHH--hcCHHHHHHHHHHHHHHHHHhhC
Confidence            34555555554422  333    444556663  2232211   11223334444  45666777889999999999999


Q ss_pred             CCCcHHHHHHHHHHHHHhhcc
Q psy879          292 GVNSLLQLSGLLARLCIVGSK  312 (317)
Q Consensus       292 g~~~~l~le~~~~~~~~~~~~  312 (317)
                      |+|+++.+|.++.++.....-
T Consensus       303 n~n~~L~le~lll~~~~~~~~  323 (325)
T PRK08699        303 TLNVKMQIEHLLINYLELKKE  323 (325)
T ss_pred             CCCHHHHHHHHHHHHHHHhcc
Confidence            999999999999999876543

>PRK07276 DNA polymerase III subunit delta'; Validated

Probab=99.95  E-value=8.5e-26  Score=191.61  Aligned_cols=260  Identities=15%  Similarity=0.198  Sum_probs=182.1

Q ss_pred             CCHHHHHHHHHHHhcCCCce-EEEECCCCCCHHHHHHHHHHHHcCCCCC-------------------CceEEecCC-CC
Q psy879           14 GNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARILLGPSFK-------------------DAVLELNAS-ND   72 (317)
Q Consensus        14 g~~~~~~~l~~~l~~~~~~~-~ll~G~~G~GKt~la~~la~~l~~~~~~-------------------~~~~~~~~~-~~   72 (317)
                      .|+.+++.|..++.+|+++| |||+||  .||+++|+.+|+.+.|....                   ..+..+.+. ..
T Consensus         6 ~q~~~~~~L~~~~~~~rl~hAyLf~G~--~G~~~~A~~~A~~llC~~~~~~~~Cg~C~~C~~i~~~~HPD~~~i~p~~~~   83 (290)
T PRK07276          6 KQPKVFQRFQTILEQDRLNHAYLFSGD--FASFEMALFLAQSLFCEQKEGVLPCGHCRSCRLIEQGEFSDVTVIEPQGQV   83 (290)
T ss_pred             HHHHHHHHHHHHHHcCCcceeeeeeCC--ccHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHhcCCCCCeeeecCCCCc
Confidence            57889999999999999999 999996  68999999999999875421                   123333332 24


Q ss_pred             cChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcCchhHhhhcceeee
Q psy879           73 RGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRY  152 (317)
Q Consensus        73 ~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~~~i~sR~~~i~f  152 (317)
                      .+++++|+....+...+.   .+.++|+|||++|.|+..+.|+|+|++|+||+++.||++|++++.++|||+|||+.++|
T Consensus        84 I~idqIR~l~~~~~~~p~---~~~~kV~II~~ad~m~~~AaNaLLKtLEEPp~~t~~iL~t~~~~~lLpTI~SRcq~i~f  160 (290)
T PRK07276         84 IKTDTIRELVKNFSQSGY---EGKQQVFIIKDADKMHVNAANSLLKVIEEPQSEIYIFLLTNDENKVLPTIKSRTQIFHF  160 (290)
T ss_pred             CCHHHHHHHHHHHhhCcc---cCCcEEEEeehhhhcCHHHHHHHHHHhcCCCCCeEEEEEECChhhCchHHHHcceeeeC
Confidence            678999998888887764   37899999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhhCCCcccHHHHHhhcCCCCHHHHHHHHHHH
Q psy879          153 NKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEMLLNC  232 (317)
Q Consensus       153 ~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~~~~~i~~~~v~~~~~~~~~~~i~~l~~~~  232 (317)
                      ++ +.+++.+++..    +|+  +.+....++.. .|++..|+..++.-    ...  + .        ...+..+.+.+
T Consensus       161 ~~-~~~~~~~~L~~----~g~--~~~~a~~la~~-~~s~~~A~~l~~~~----~~~--~-~--------~~~~~~~~~~l  217 (290)
T PRK07276        161 PK-NEAYLIQLLEQ----KGL--LKTQAELLAKL-AQSTSEAEKLAQNK----KFL--E-L--------IDQAERFVTIL  217 (290)
T ss_pred             CC-cHHHHHHHHHH----cCC--ChHHHHHHHHH-CCCHHHHHHHhCCh----hHH--H-H--------HHHHHHHHHHh
Confidence            77 77777777754    354  44444444444 45899998876311    000  0 0        01122233323


Q ss_pred             hcCCHHHHHHHHHHHHHc---CCCHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHHHhHHhcCCCcHHHHHHHH
Q psy879          233 VEGNMKDSYKIIHHLYKL---GYAPEDIIGNIFRVAKTLDIPEPLKLSIIQEIGNVHLRISEGVNSLLQLSGLL  303 (317)
Q Consensus       233 ~~~~~~~~~~~~~~l~~~---~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~g~~~~l~le~~~  303 (317)
                      ...+...++. +..+...   .+.-..++..+..++.. ........+.+..+.+.+....+|+|....+|.|+
T Consensus       218 ~~~~~~~~l~-~~~l~~~~~~~e~q~~~l~~l~~~~~~-~~~~~~~~~~L~~~~~~r~~w~~Nv~~~~~le~l~  289 (290)
T PRK07276        218 LKDKDEAYLQ-VARLVQLADEKEEQDQVLTLLTLLLAQ-ERMQVNVRTQLEAVYQARKMWQSNVSFQNALEYMV  289 (290)
T ss_pred             ccChHHHHHH-HHHHHHhhhcHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHhHHHHHHhccCHHHHHHHHh
Confidence            3222222222 2333222   12222333333332311 22334456678889999999999999999999986

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=99.95  E-value=5.2e-26  Score=200.32  Aligned_cols=202  Identities=20%  Similarity=0.281  Sum_probs=159.4

Q ss_pred             cccCCCCCCcccCCHHHHHHHHHHHh-----cCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChH
Q psy879            2 EKYRPQTFSDIVGNEDTVERLKVFSS-----SGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGID   76 (317)
Q Consensus         2 ~ky~P~~~~~~~g~~~~~~~l~~~l~-----~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~   76 (317)
                      .+|||++|++++||+++++.+..++.     ++.++|++||||||+|||++++++|+.+..     .+...+........
T Consensus        17 ~~~rP~~~~~~vG~~~~~~~l~~~l~~~~~~~~~~~~~ll~GppG~GKT~la~~ia~~l~~-----~~~~~~~~~~~~~~   91 (328)
T PRK00080         17 RSLRPKSLDEFIGQEKVKENLKIFIEAAKKRGEALDHVLLYGPPGLGKTTLANIIANEMGV-----NIRITSGPALEKPG   91 (328)
T ss_pred             hhcCcCCHHHhcCcHHHHHHHHHHHHHHHhcCCCCCcEEEECCCCccHHHHHHHHHHHhCC-----CeEEEecccccChH
Confidence            48999999999999999998877765     233457999999999999999999999732     12222222222222


Q ss_pred             HHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhcc------------------CCceEEEEecCCCc
Q psy879           77 TVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYS------------------NTTRFALACNNSEK  138 (317)
Q Consensus        77 ~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~------------------~~~~~il~~~~~~~  138 (317)
                      .+...+...         +.+.+++|||++.+....++.|+..++...                  +...+|++|+....
T Consensus        92 ~l~~~l~~l---------~~~~vl~IDEi~~l~~~~~e~l~~~~e~~~~~~~l~~~~~~~~~~~~l~~~~li~at~~~~~  162 (328)
T PRK00080         92 DLAAILTNL---------EEGDVLFIDEIHRLSPVVEEILYPAMEDFRLDIMIGKGPAARSIRLDLPPFTLIGATTRAGL  162 (328)
T ss_pred             HHHHHHHhc---------ccCCEEEEecHhhcchHHHHHHHHHHHhcceeeeeccCccccceeecCCCceEEeecCCccc
Confidence            333322211         457799999999999888888888888542                  23568888999899


Q ss_pred             CchhHhhhcce-eeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhh-----CCCcccHHH
Q psy879          139 IIEPIQSRCAM-LRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHN-----GFGHVTAEY  212 (317)
Q Consensus       139 l~~~i~sR~~~-i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~-----~~~~i~~~~  212 (317)
                      +.++++|||.. +.|.+++.+++.+++...+...++.+++++++.++..++|++|.+.+.++.+..     +...|+.+.
T Consensus       163 l~~~L~sRf~~~~~l~~~~~~e~~~il~~~~~~~~~~~~~~~~~~ia~~~~G~pR~a~~~l~~~~~~a~~~~~~~I~~~~  242 (328)
T PRK00080        163 LTSPLRDRFGIVQRLEFYTVEELEKIVKRSARILGVEIDEEGALEIARRSRGTPRIANRLLRRVRDFAQVKGDGVITKEI  242 (328)
T ss_pred             CCHHHHHhcCeeeecCCCCHHHHHHHHHHHHHHcCCCcCHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHcCCCCCCHHH
Confidence            99999999954 999999999999999999999999999999999999999999999999986432     346788887


Q ss_pred             HHhhc
Q psy879          213 VFKVC  217 (317)
Q Consensus       213 v~~~~  217 (317)
                      +..+.
T Consensus       243 v~~~l  247 (328)
T PRK00080        243 ADKAL  247 (328)
T ss_pred             HHHHH
Confidence            76654

>PF13177 DNA_pol3_delta2: DNA polymerase III, delta subunit; PDB: 1NJF_B 3GLG_G 1XXH_I 1NJG_A 3GLF_B 3GLI_G 1IQP_E 2GNO_A 1SXJ_E 1A5T_A

Probab=99.95  E-value=3.9e-27  Score=185.61  Aligned_cols=140  Identities=36%  Similarity=0.605  Sum_probs=113.0

Q ss_pred             CCHHHHHHHHHHHhcCCCce-EEEECCCCCCHHHHHHHHHHHHcCCCCC------------------CceEEecCCC---
Q psy879           14 GNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARILLGPSFK------------------DAVLELNASN---   71 (317)
Q Consensus        14 g~~~~~~~l~~~l~~~~~~~-~ll~G~~G~GKt~la~~la~~l~~~~~~------------------~~~~~~~~~~---   71 (317)
                      ||+++++.|...++++++|| +||+||+|+||+++|+.+++.+.|....                  ..+..+....   
T Consensus         1 gq~~~~~~L~~~~~~~~l~ha~L~~G~~g~gk~~~a~~~a~~ll~~~~~~~~c~~c~~c~~~~~~~~~d~~~~~~~~~~~   80 (162)
T PF13177_consen    1 GQEEIIELLKNLIKSGRLPHALLFHGPSGSGKKTLALAFARALLCSNPNEDPCGECRSCRRIEEGNHPDFIIIKPDKKKK   80 (162)
T ss_dssp             S-HHHHHHHHHHHHCTC--SEEEEECSTTSSHHHHHHHHHHHHC-TT-CTT--SSSHHHHHHHTT-CTTEEEEETTTSSS
T ss_pred             CcHHHHHHHHHHHHcCCcceeEEEECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHhccCcceEEEecccccc
Confidence            89999999999999999999 8999999999999999999999876543                  2344454443   


Q ss_pred             CcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcCchhHhhhcceee
Q psy879           72 DRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLR  151 (317)
Q Consensus        72 ~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~~~i~sR~~~i~  151 (317)
                      ..+.+++++....+...+.   .+.++|+||||+|.|+.+++|+|+++||+||.++.||++|+++++++++|+|||+.++
T Consensus        81 ~i~i~~ir~i~~~~~~~~~---~~~~KviiI~~ad~l~~~a~NaLLK~LEepp~~~~fiL~t~~~~~il~TI~SRc~~i~  157 (162)
T PF13177_consen   81 SIKIDQIREIIEFLSLSPS---EGKYKVIIIDEADKLTEEAQNALLKTLEEPPENTYFILITNNPSKILPTIRSRCQVIR  157 (162)
T ss_dssp             SBSHHHHHHHHHHCTSS-T---TSSSEEEEEETGGGS-HHHHHHHHHHHHSTTTTEEEEEEES-GGGS-HHHHTTSEEEE
T ss_pred             hhhHHHHHHHHHHHHHHHh---cCCceEEEeehHhhhhHHHHHHHHHHhcCCCCCEEEEEEECChHHChHHHHhhceEEe
Confidence            4678999988777766653   3689999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCC
Q psy879          152 YNKLT  156 (317)
Q Consensus       152 f~~~~  156 (317)
                      |++++
T Consensus       158 ~~~ls  162 (162)
T PF13177_consen  158 FRPLS  162 (162)
T ss_dssp             E----
T ss_pred             cCCCC
Confidence            99875

...

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=99.94  E-value=1.2e-24  Score=190.45  Aligned_cols=199  Identities=18%  Similarity=0.264  Sum_probs=156.0

Q ss_pred             CCCCcccCCHHHHHHHHHHHh-----cCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHH
Q psy879            7 QTFSDIVGNEDTVERLKVFSS-----SGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNK   81 (317)
Q Consensus         7 ~~~~~~~g~~~~~~~l~~~l~-----~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~   81 (317)
                      ++|++++||+++++.|..++.     .+.++|++|+||||+|||++++++++.+..     .+.............+.+.
T Consensus         1 ~~~~~~iG~~~~~~~l~~~l~~~~~~~~~~~~~ll~Gp~G~GKT~la~~ia~~~~~-----~~~~~~~~~~~~~~~l~~~   75 (305)
T TIGR00635         1 KLLAEFIGQEKVKEQLQLFIEAAKMRQEALDHLLLYGPPGLGKTTLAHIIANEMGV-----NLKITSGPALEKPGDLAAI   75 (305)
T ss_pred             CCHHHHcCHHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHhCC-----CEEEeccchhcCchhHHHH
Confidence            579999999999999988886     355668999999999999999999998732     1222322222222333333


Q ss_pred             HHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhcc------------------CCceEEEEecCCCcCchhH
Q psy879           82 IKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYS------------------NTTRFALACNNSEKIIEPI  143 (317)
Q Consensus        82 ~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~------------------~~~~~il~~~~~~~l~~~i  143 (317)
                      +...         +...+++|||++.+.++.++.|+..+++..                  +...+|.+|+.+..+.+++
T Consensus        76 l~~~---------~~~~vl~iDEi~~l~~~~~e~l~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~li~~t~~~~~l~~~l  146 (305)
T TIGR00635        76 LTNL---------EEGDVLFIDEIHRLSPAVEELLYPAMEDFRLDIVIGKGPSARSVRLDLPPFTLVGATTRAGMLTSPL  146 (305)
T ss_pred             HHhc---------ccCCEEEEehHhhhCHHHHHHhhHHHhhhheeeeeccCccccceeecCCCeEEEEecCCccccCHHH
Confidence            2221         346799999999999999999988887432                  2366888888888999999


Q ss_pred             hhhcce-eeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhh-----CCCcccHHHHHhhc
Q psy879          144 QSRCAM-LRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHN-----GFGHVTAEYVFKVC  217 (317)
Q Consensus       144 ~sR~~~-i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~-----~~~~i~~~~v~~~~  217 (317)
                      +|||.. +.|.+++.+++.+++...+...++.+++++++.+++.++|++|.+.+.++.+..     +...|+.+.+..+.
T Consensus       147 ~sR~~~~~~l~~l~~~e~~~il~~~~~~~~~~~~~~al~~ia~~~~G~pR~~~~ll~~~~~~a~~~~~~~it~~~v~~~l  226 (305)
T TIGR00635       147 RDRFGIILRLEFYTVEELAEIVSRSAGLLNVEIEPEAALEIARRSRGTPRIANRLLRRVRDFAQVRGQKIINRDIALKAL  226 (305)
T ss_pred             HhhcceEEEeCCCCHHHHHHHHHHHHHHhCCCcCHHHHHHHHHHhCCCcchHHHHHHHHHHHHHHcCCCCcCHHHHHHHH
Confidence            999965 899999999999999999999999999999999999999999999999876532     34568888877655


Q ss_pred             CC
Q psy879          218 DE  219 (317)
Q Consensus       218 ~~  219 (317)
                      +.
T Consensus       227 ~~  228 (305)
T TIGR00635       227 EM  228 (305)
T ss_pred             HH
Confidence            43

RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.

>COG2255 RuvB Holliday junction resolvasome, helicase subunit [DNA replication, recombination, and repair]

Probab=99.94  E-value=4.8e-25  Score=180.35  Aligned_cols=198  Identities=19%  Similarity=0.285  Sum_probs=158.2

Q ss_pred             ccCCCCCCcccCCHHHHHHHHHHHh-----cCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHH
Q psy879            3 KYRPQTFSDIVGNEDTVERLKVFSS-----SGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDT   77 (317)
Q Consensus         3 ky~P~~~~~~~g~~~~~~~l~~~l~-----~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~   77 (317)
                      ..||++|++++||++++++|.-+++     +..+.|+|||||||.||||+|+.+|+++..     .+-...+.-.....+
T Consensus        19 ~lRP~~l~efiGQ~~vk~~L~ifI~AAk~r~e~lDHvLl~GPPGlGKTTLA~IIA~Emgv-----n~k~tsGp~leK~gD   93 (332)
T COG2255          19 SLRPKTLDEFIGQEKVKEQLQIFIKAAKKRGEALDHVLLFGPPGLGKTTLAHIIANELGV-----NLKITSGPALEKPGD   93 (332)
T ss_pred             ccCcccHHHhcChHHHHHHHHHHHHHHHhcCCCcCeEEeeCCCCCcHHHHHHHHHHHhcC-----CeEecccccccChhh
Confidence            4689999999999999999877764     345679999999999999999999999731     122222222233444


Q ss_pred             HHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhcc------------------CCceEEEEecCCCcC
Q psy879           78 VRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYS------------------NTTRFALACNNSEKI  139 (317)
Q Consensus        78 i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~------------------~~~~~il~~~~~~~l  139 (317)
                      +...+...         .++.|+||||++.+.+...+.|...||.+.                  +...+|.+|+....+
T Consensus        94 laaiLt~L---------e~~DVLFIDEIHrl~~~vEE~LYpaMEDf~lDI~IG~gp~Arsv~ldLppFTLIGATTr~G~l  164 (332)
T COG2255          94 LAAILTNL---------EEGDVLFIDEIHRLSPAVEEVLYPAMEDFRLDIIIGKGPAARSIRLDLPPFTLIGATTRAGML  164 (332)
T ss_pred             HHHHHhcC---------CcCCeEEEehhhhcChhHHHHhhhhhhheeEEEEEccCCccceEeccCCCeeEeeeccccccc
Confidence            44443322         467899999999999999999999999542                  233478889999999


Q ss_pred             chhHhhhcce-eeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhh-----CCCcccHHHH
Q psy879          140 IEPIQSRCAM-LRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHN-----GFGHVTAEYV  213 (317)
Q Consensus       140 ~~~i~sR~~~-i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~-----~~~~i~~~~v  213 (317)
                      ..++++||.+ .++..|+.+|+..++..-+..-+++++++++..++.+|.|-+|-|..+|+..-.     +...|+.+-.
T Consensus       165 t~PLrdRFGi~~rlefY~~~eL~~Iv~r~a~~l~i~i~~~~a~eIA~rSRGTPRIAnRLLrRVRDfa~V~~~~~I~~~ia  244 (332)
T COG2255         165 TNPLRDRFGIIQRLEFYTVEELEEIVKRSAKILGIEIDEEAALEIARRSRGTPRIANRLLRRVRDFAQVKGDGDIDRDIA  244 (332)
T ss_pred             cchhHHhcCCeeeeecCCHHHHHHHHHHHHHHhCCCCChHHHHHHHHhccCCcHHHHHHHHHHHHHHHHhcCCcccHHHH
Confidence            9999999988 889999999999999999999999999999999999999999999999976432     4455655444


Q ss_pred             H
Q psy879          214 F  214 (317)
Q Consensus       214 ~  214 (317)
                      .
T Consensus       245 ~  245 (332)
T COG2255         245 D  245 (332)
T ss_pred             H
Confidence            3

>PRK07914 hypothetical protein; Reviewed

Probab=99.93  E-value=2.4e-23  Score=182.62  Aligned_cols=271  Identities=10%  Similarity=0.099  Sum_probs=215.3

Q ss_pred             ceEEEECCCCCCHHHHHHHHHHHHcC-CC-CCCceEEecCCCCcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCC
Q psy879           32 PNIIISGPPGVGKTTTILCLARILLG-PS-FKDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMT  109 (317)
Q Consensus        32 ~~~ll~G~~G~GKt~la~~la~~l~~-~~-~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~  109 (317)
                      |.|+|||+.-.........+.+.+.. .+ ....+..+++.+ .....+    ......++   .+++++|+++++..+.
T Consensus         6 ~iYll~G~E~~l~~~~~~~i~~~~~~~~~~~~~n~~~~d~~~-~~~~~i----~~~~t~pl---F~~rRlV~v~~~~~~~   77 (320)
T PRK07914          6 PLHLVLGDEELLVERAVAAVLRSARQRAGTADVPVSRMRAGD-VSTYEL----AELLSPSL---FAEERVVVLEAAAEAG   77 (320)
T ss_pred             ceEEEEecHHHHHHHHHHHHHHHHhcCcCCCCCceEEecccc-CCHHHH----HHhcCCCC---CCCceEEEEeChHhcc
Confidence            45999999977777777777766543 22 233455555432 222222    22222232   2789999999998887


Q ss_pred             HHHHHHHHHHhhhccCCceEEEEecCCC---cCchhHhhhc-ceeeecCC-CHHHHHHHHHHHHHHcCCCCCHHHHHHHH
Q psy879          110 DGAQQALRRTMEIYSNTTRFALACNNSE---KIIEPIQSRC-AMLRYNKL-TDAQLLSKVIEICEKENISHTNDGLEAIV  184 (317)
Q Consensus       110 ~~~~~~ll~~le~~~~~~~~il~~~~~~---~l~~~i~sR~-~~i~f~~~-~~~~~~~~l~~~~~~~~~~i~~~~~~~l~  184 (317)
                      ++..+.|..+++.+++.+++|++++...   ++.++++... .++.|.++ ++.++..|+.++++..|+.+++++++.++
T Consensus        78 ~~~~~~l~~~l~~~~~~t~lil~~~~~~~~kk~~K~L~k~g~~~v~~~~~~~~~~l~~wi~~~a~~~g~~i~~~A~~~L~  157 (320)
T PRK07914         78 KDAAALILSAAADLPPGTVLVVVHSGGGRAKALANQLRKLGAEVHPCARITKAAERADFVRKEFRSLRVKVDDDTVTALL  157 (320)
T ss_pred             HHHHHHHHHHHhCCCCCeEEEEEecCCcchhHHHHHHHHCCCEEEecCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHH
Confidence            7778899999999999888888765432   3456777765 47899998 99999999999999999999999999999


Q ss_pred             HhcCCCHHHHHHHHHHhhh-CCCcccHHHHHhhcCCCCHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHHHH
Q psy879          185 FTAQGDMRQALNNLQSTHN-GFGHVTAEYVFKVCDEPHPLAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDIIGNIFR  263 (317)
Q Consensus       185 ~~~~gd~r~~i~~l~~~~~-~~~~i~~~~v~~~~~~~~~~~i~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~~~~~  263 (317)
                      ...++|+..+.+++++.+. ..+.||.++|.+++..+.+.++|++++++..++..+|+.++++|...|++|..|+..+.+
T Consensus       158 ~~~g~dl~~l~~EleKL~~~~~~~It~e~V~~~v~~~~~~~vf~L~dAi~~g~~~~A~~~l~~L~~~ge~p~~il~~l~~  237 (320)
T PRK07914        158 DAVGSDLRELASACSQLVADTGGAVDAAAVRRYHSGKAEVKGFDIADKAVAGDVAGAAEALRWAMMRGEPHVVLADALAE  237 (320)
T ss_pred             HHHCccHHHHHHHHHHHhcCCCCCcCHHHHHHHcCCCeechHHHHHHHHHCCCHHHHHHHHHHHHHCCCchHHHHHHHHH
Confidence            9999999999999999765 457899999999999999999999999999999999999999999999999999877655


Q ss_pred             HHHhc-----------------CC---------------ChHHHHHHHHHHHHHHhHHhcCC-CcHHHHHHHHHHHHHhh
Q psy879          264 VAKTL-----------------DI---------------PEPLKLSIIQEIGNVHLRISEGV-NSLLQLSGLLARLCIVG  310 (317)
Q Consensus       264 ~~~~~-----------------~~---------------~~~~~~~~~~~l~~~~~~l~~g~-~~~l~le~~~~~~~~~~  310 (317)
                      +++.+                 +.               +.....+++..+.++|..+|+|. +++++||.++.++|+..
T Consensus       238 ~~r~L~~~k~~~~~~~~i~~~l~i~p~~~~~~~~~~~~~s~~~L~~~l~~l~~~D~~lK~~~~~~~~~lE~~i~~~~~~~  317 (320)
T PRK07914        238 AVHTIARVGPLSGDPYRLAGELGMPPWRVQKAQKQARRWSRDTVATAMRVVAALNADVKGAAADADYALESAVRRVAELV  317 (320)
T ss_pred             HHHHHHHHHHhcCCHHHHHHHcCCCHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHhhcCCCChHHHHHHHHHHHHHHh
Confidence            43322                 11               11122339999999999999886 99999999999999854

>KOG1969|consensus

Probab=99.93  E-value=4.5e-24  Score=193.95  Aligned_cols=202  Identities=26%  Similarity=0.476  Sum_probs=171.5

Q ss_pred             CcccCCCCCCcccCCHHHHHHHHHHHhc--------------------------------CCCce--EEEECCCCCCHHH
Q psy879            1 IEKYRPQTFSDIVGNEDTVERLKVFSSS--------------------------------GNVPN--IIISGPPGVGKTT   46 (317)
Q Consensus         1 ~~ky~P~~~~~~~g~~~~~~~l~~~l~~--------------------------------~~~~~--~ll~G~~G~GKt~   46 (317)
                      ++||+|+.|.|++|.+.+-+.+..|++.                                ++++.  +||+||||.||||
T Consensus       262 Vdky~Pk~FtdLLsDe~tNR~~L~WLK~WD~~VFg~~vsrl~~s~~~~~ke~~~~~~~~s~RP~kKilLL~GppGlGKTT  341 (877)
T KOG1969|consen  262 VDKYRPKKFTDLLSDEKTNRRMLGWLKQWDPCVFGQKVSRLLASKGPTEKEVLDMELDPSKRPPKKILLLCGPPGLGKTT  341 (877)
T ss_pred             ecccChhHHHHHhcchhHHHHHHHHHHhhcHHhhcchHhhhccccccchhhhhhcccCccCCCccceEEeecCCCCChhH
Confidence            5899999999999999888877766541                                23333  8999999999999


Q ss_pred             HHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHHHHHHHhhcccC-CCCceeEEEEeCCCCCCHHHHHHHHHHhhh---
Q psy879           47 TILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFAQQKVTL-PPGRHKIVILDEADSMTDGAQQALRRTMEI---  122 (317)
Q Consensus        47 la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~-~~~~~~vliiDE~d~l~~~~~~~ll~~le~---  122 (317)
                      +|+.+|+..     ++.++++|+++++....+.+.+..+.+....+ ..+.+.++||||+|...+.+.+.++..++.   
T Consensus       342 LAHViAkqa-----GYsVvEINASDeRt~~~v~~kI~~avq~~s~l~adsrP~CLViDEIDGa~~~~Vdvilslv~a~~k  416 (877)
T KOG1969|consen  342 LAHVIAKQA-----GYSVVEINASDERTAPMVKEKIENAVQNHSVLDADSRPVCLVIDEIDGAPRAAVDVILSLVKATNK  416 (877)
T ss_pred             HHHHHHHhc-----CceEEEecccccccHHHHHHHHHHHHhhccccccCCCcceEEEecccCCcHHHHHHHHHHHHhhcc
Confidence            999999983     67799999999999999999888877765544 457899999999999999999999998871   


Q ss_pred             ---ccC---------------CceEEEEecCCC-cCchhHhhhcceeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHH
Q psy879          123 ---YSN---------------TTRFALACNNSE-KIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAI  183 (317)
Q Consensus       123 ---~~~---------------~~~~il~~~~~~-~l~~~i~sR~~~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l  183 (317)
                         .+.               .-.+|++||+.. --+..++--+.++.|.++++..+.++|+.+|..+|+.++..++..+
T Consensus       417 ~~~Gkq~~~~~~rkkkr~~~L~RPIICICNdLYaPaLR~Lr~~A~ii~f~~p~~s~Lv~RL~~IC~rE~mr~d~~aL~~L  496 (877)
T KOG1969|consen  417 QATGKQAKKDKKRKKKRSKLLTRPIICICNDLYAPALRPLRPFAEIIAFVPPSQSRLVERLNEICHRENMRADSKALNAL  496 (877)
T ss_pred             hhhcCcccchhhhhhhccccccCCEEEEecCccchhhhhcccceEEEEecCCChhHHHHHHHHHHhhhcCCCCHHHHHHH
Confidence               111               134899999864 4567778888999999999999999999999999999999999999


Q ss_pred             HHhcCCCHHHHHHHHHHhhhCCCc
Q psy879          184 VFTAQGDMRQALNNLQSTHNGFGH  207 (317)
Q Consensus       184 ~~~~~gd~r~~i~~l~~~~~~~~~  207 (317)
                      ++.+.+|+|.+||.||.++...+.
T Consensus       497 ~el~~~DIRsCINtLQfLa~~~~r  520 (877)
T KOG1969|consen  497 CELTQNDIRSCINTLQFLASNVDR  520 (877)
T ss_pred             HHHhcchHHHHHHHHHHHHHhccc
Confidence            999999999999999998875444

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=99.93  E-value=8.1e-24  Score=197.28  Aligned_cols=293  Identities=15%  Similarity=0.152  Sum_probs=207.9

Q ss_pred             ccCCCCCCcccCCHHHHHHHHHHH----hcCCCce-EEEECCCCCCHHHHHHHHHHHHcCC----C-CCCceEEecCCCC
Q psy879            3 KYRPQTFSDIVGNEDTVERLKVFS----SSGNVPN-IIISGPPGVGKTTTILCLARILLGP----S-FKDAVLELNASND   72 (317)
Q Consensus         3 ky~P~~~~~~~g~~~~~~~l~~~l----~~~~~~~-~ll~G~~G~GKt~la~~la~~l~~~----~-~~~~~~~~~~~~~   72 (317)
                      -|.|   +.+.|+++.++.|..++    .+..+.+ ++|+|+||||||++++.+.+.+...    . ....++++||...
T Consensus       751 DYVP---D~LPhREeEIeeLasfL~paIkgsgpnnvLYIyG~PGTGKTATVK~VLrELqeeaeqk~lp~f~vVYINCm~L  827 (1164)
T PTZ00112        751 DVVP---KYLPCREKEIKEVHGFLESGIKQSGSNQILYISGMPGTGKTATVYSVIQLLQHKTKQKLLPSFNVFEINGMNV  827 (1164)
T ss_pred             ccCC---CcCCChHHHHHHHHHHHHHHHhcCCCCceEEEECCCCCCHHHHHHHHHHHHHHHHhhccCCCceEEEEeCCcc
Confidence            4677   56789988777765554    4334334 5799999999999999999887421    1 1245678888653


Q ss_pred             cChHHHHHHHH-HH------------------HhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhc---cCCceEE
Q psy879           73 RGIDTVRNKIK-MF------------------AQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIY---SNTTRFA  130 (317)
Q Consensus        73 ~~~~~i~~~~~-~~------------------~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~---~~~~~~i  130 (317)
                      .....+...+. .+                  .... ........||||||+|.|....+..|+.+++.+   ...+.+|
T Consensus       828 stp~sIYqvI~qqL~g~~P~~GlsS~evLerLF~~L-~k~~r~v~IIILDEID~L~kK~QDVLYnLFR~~~~s~SKLiLI  906 (1164)
T PTZ00112        828 VHPNAAYQVLYKQLFNKKPPNALNSFKILDRLFNQN-KKDNRNVSILIIDEIDYLITKTQKVLFTLFDWPTKINSKLVLI  906 (1164)
T ss_pred             CCHHHHHHHHHHHHcCCCCCccccHHHHHHHHHhhh-hcccccceEEEeehHhhhCccHHHHHHHHHHHhhccCCeEEEE
Confidence            43332222111 11                  1000 001123458999999999887778888777743   3346677


Q ss_pred             EEecC---CCcCchhHhhhcce--eeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHH---hcCCCHHHHHHHHHHhh
Q psy879          131 LACNN---SEKIIEPIQSRCAM--LRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVF---TAQGDMRQALNNLQSTH  202 (317)
Q Consensus       131 l~~~~---~~~l~~~i~sR~~~--i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~---~~~gd~r~~i~~l~~~~  202 (317)
                      +++|.   +..+++.++||+..  +.|+||+.+|+.++|..++......+++++++++++   ..+||+|+|+++|+.++
T Consensus       907 GISNdlDLperLdPRLRSRLg~eeIvF~PYTaEQL~dILk~RAe~A~gVLdDdAIELIArkVAq~SGDARKALDILRrAg  986 (1164)
T PTZ00112        907 AISNTMDLPERLIPRCRSRLAFGRLVFSPYKGDEIEKIIKERLENCKEIIDHTAIQLCARKVANVSGDIRKALQICRKAF  986 (1164)
T ss_pred             EecCchhcchhhhhhhhhccccccccCCCCCHHHHHHHHHHHHHhCCCCCCHHHHHHHHHhhhhcCCHHHHHHHHHHHHH
Confidence            78876   35778999999976  999999999999999999986544589999999987   67899999999999877


Q ss_pred             h--CCCcccHHHHHhhcCCCCHHHHHHHHHHHhcCCHHHHHHHHHHHHHc---CCCHHHHHHHHHHHHH----hcCCChH
Q psy879          203 N--GFGHVTAEYVFKVCDEPHPLAVKEMLLNCVEGNMKDSYKIIHHLYKL---GYAPEDIIGNIFRVAK----TLDIPEP  273 (317)
Q Consensus       203 ~--~~~~i~~~~v~~~~~~~~~~~i~~l~~~~~~~~~~~~~~~~~~l~~~---~~~~~~i~~~~~~~~~----~~~~~~~  273 (317)
                      .  +...|+.++|.++........+.+.+..+..+...-.++++..+...   ..+..+|+..|..+|+    .++..+.
T Consensus       987 EikegskVT~eHVrkAleeiE~srI~e~IktLPlHqKLVLlALIlLlk~tg~~~i~TGEVYerYk~Lce~~Gk~iGv~pl 1066 (1164)
T PTZ00112        987 ENKRGQKIVPRDITEATNQLFDSPLTNAINYLPWPFKMFLTCLIVELRMLNDFIIPYKKVLNRYKVLVETSGKYIGMCSN 1066 (1164)
T ss_pred             hhcCCCccCHHHHHHHHHHHHhhhHHHHHHcCCHHHHHHHHHHHHHHhhcCCCceeHHHHHHHHHHHHHhhhhhcCCCCc
Confidence            5  34579999999988776666667777766655555555555554332   3677899999999998    5677777


Q ss_pred             HHHHHHHHHHHHHhHHhcCC---CcHHHHHHHH
Q psy879          274 LKLSIIQEIGNVHLRISEGV---NSLLQLSGLL  303 (317)
Q Consensus       274 ~~~~~~~~l~~~~~~l~~g~---~~~l~le~~~  303 (317)
                      .. ++.+.+.+++..   |.   .|.+-||.+.
T Consensus      1067 Tq-RV~d~L~eL~~L---GIIl~ep~~~~~~~~ 1095 (1164)
T PTZ00112       1067 NE-LFKIMLDKLVKM---GILLIRPYIPLESLA 1095 (1164)
T ss_pred             HH-HHHHHHHHHHhc---CeEEecCCCchhhhh
Confidence            77 888888888764   44   6666666543

>TIGR02902 spore_lonB ATP-dependent protease LonB

Probab=99.93  E-value=7.1e-25  Score=203.22  Aligned_cols=220  Identities=26%  Similarity=0.334  Sum_probs=166.4

Q ss_pred             CcccCCCCCCcccCCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCC-----CCCCceEEecCCCCc-C
Q psy879            1 IEKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGP-----SFKDAVLELNASNDR-G   74 (317)
Q Consensus         1 ~~ky~P~~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~-----~~~~~~~~~~~~~~~-~   74 (317)
                      .+||||++|++++||++.++.+...+..+...|++|+||||||||++|+++.+.....     .....++++++.... .
T Consensus        56 ~~~~rp~~f~~iiGqs~~i~~l~~al~~~~~~~vLi~Ge~GtGKt~lAr~i~~~~~~~~~s~~~~~~~fi~id~~~~~~~  135 (531)
T TIGR02902        56 SEKTRPKSFDEIIGQEEGIKALKAALCGPNPQHVIIYGPPGVGKTAAARLVLEEAKKNPASPFKEGAAFVEIDATTARFD  135 (531)
T ss_pred             HHhhCcCCHHHeeCcHHHHHHHHHHHhCCCCceEEEECCCCCCHHHHHHHHHHHhhhccCCCcCCCCCEEEEccccccCC
Confidence            3799999999999999999999988877777789999999999999999998764211     113467777764311 1


Q ss_pred             hHHHH-HHHHH----HHh-------------hcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhc-------------
Q psy879           75 IDTVR-NKIKM----FAQ-------------QKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIY-------------  123 (317)
Q Consensus        75 ~~~i~-~~~~~----~~~-------------~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~-------------  123 (317)
                      ...+. ..++.    ..+             .+........++++|||++.|++..|+.|++.||+.             
T Consensus       136 ~~~~~~~li~~~~~p~~~~~~~~g~~g~~~~~~G~l~~a~gG~L~IdEI~~L~~~~q~~LL~~Le~~~~~~~~~~~~~~~  215 (531)
T TIGR02902       136 ERGIADPLIGSVHDPIYQGAGPLGIAGIPQPKPGAVTRAHGGVLFIDEIGELHPVQMNKLLKVLEDRKVFLDSAYYNSEN  215 (531)
T ss_pred             ccccchhhcCCcccchhccccccccCCcccccCchhhccCCcEEEEechhhCCHHHHHHHHHHHHhCeeeeccccccccC
Confidence            10111 01100    000             000111245689999999999999999999999852             


Q ss_pred             ---------------cCCceEEEEe-cCCCcCchhHhhhcceeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhc
Q psy879          124 ---------------SNTTRFALAC-NNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTA  187 (317)
Q Consensus       124 ---------------~~~~~~il~~-~~~~~l~~~i~sR~~~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~  187 (317)
                                     +.++++|++| +++..++++++|||..+.|++++.+++..+++..+++.++.+++++++.+...+
T Consensus       216 ~~~~~~~~~~~~~~~~~d~rlI~ATt~~p~~L~paLrsR~~~I~f~pL~~eei~~Il~~~a~k~~i~is~~al~~I~~y~  295 (531)
T TIGR02902       216 PNIPSHIHDIFQNGLPADFRLIGATTRNPEEIPPALRSRCVEIFFRPLLDEEIKEIAKNAAEKIGINLEKHALELIVKYA  295 (531)
T ss_pred             cccccchhhhcccCcccceEEEEEecCCcccCChHHhhhhheeeCCCCCHHHHHHHHHHHHHHcCCCcCHHHHHHHHHhh
Confidence                           1234566554 567899999999999999999999999999999999999999999999887766


Q ss_pred             CCCHHHHHHHHHHhhh-----CCCcccHHHHHhhcCCCC
Q psy879          188 QGDMRQALNNLQSTHN-----GFGHVTAEYVFKVCDEPH  221 (317)
Q Consensus       188 ~gd~r~~i~~l~~~~~-----~~~~i~~~~v~~~~~~~~  221 (317)
                      . |.|++.+.++.++.     +...|+.+++..++....
T Consensus       296 ~-n~Rel~nll~~Aa~~A~~~~~~~It~~dI~~vl~~~~  333 (531)
T TIGR02902       296 S-NGREAVNIVQLAAGIALGEGRKRILAEDIEWVAENGN  333 (531)
T ss_pred             h-hHHHHHHHHHHHHHHHhhCCCcEEcHHHHHHHhCCcc
Confidence            5 89999999988653     334799999988877543

Members of this protein are LonB, a paralog of the ATP-dependent protease La (LonA, TIGR00763). LonB proteins are found strictly, and almost universally, in endospore-forming bacteria. This protease was shown, in Bacillus subtilis, to be expressed specifically in the forespore, during sporulation, under control of sigma(F). The lonB gene, despite location immediately upstream of lonA, was shown to be monocistronic. LonB appears able to act on sigma(H) for post-translation control, but lonB mutation did not produce an obvious sporulation defect under the conditions tested. Note that additional paralogs of LonA and LonB occur in the Clostridium lineage and this model selects only one per species as the protein that corresponds to LonB in B. subtilis.

>PRK05629 hypothetical protein; Validated

Probab=99.93  E-value=5.3e-23  Score=180.38  Aligned_cols=270  Identities=11%  Similarity=0.110  Sum_probs=212.2

Q ss_pred             ceEEEECCCCCCHHHHHHHHHHHHcCCCC-CCceEEecCCCCcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCH
Q psy879           32 PNIIISGPPGVGKTTTILCLARILLGPSF-KDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTD  110 (317)
Q Consensus        32 ~~~ll~G~~G~GKt~la~~la~~l~~~~~-~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~  110 (317)
                      |.|+|||+.-.-.......+.+.+..... ...+..+++.+ .....+.+    ....++   .+++++|++++++...+
T Consensus         7 ~vyL~~G~e~~l~~~~~~~i~~~~~~~~~~~~n~~~~d~~e-~~~~~l~~----~~t~sl---F~~~rlV~v~~~~~~~~   78 (318)
T PRK05629          7 PVHLVLGDDEFLAERARLNIVHDIRSSMADSLQVTTLKASE-VSQGELLD----ALSPSL---FGEDRVIVLTNMEQAGK   78 (318)
T ss_pred             ceEEEEeCHHHHHHHHHHHHHHHHhccCCCCCceEEeeccc-CCHHHHHH----hhCcCc---cCCceEEEEeChHhcCh
Confidence            45999999865555555556655543332 33455555432 23333332    222332   27889999999888766


Q ss_pred             HHHHHHHHHhhhccCCceEEEEecCCC---cCchhHhhhcceeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhc
Q psy879          111 GAQQALRRTMEIYSNTTRFALACNNSE---KIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTA  187 (317)
Q Consensus       111 ~~~~~ll~~le~~~~~~~~il~~~~~~---~l~~~i~sR~~~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~  187 (317)
                      ...+.++.++..+++.+++|+++....   ++.+.++..+..++|.++.+.++..|+.+++++.|+.+++++++.++..+
T Consensus        79 ~~~~~l~~~l~~~~~~~~Lil~~~~~~~~kk~~K~l~k~~~~ve~~~~~~~~l~~wi~~~~~~~g~~i~~~A~~~L~~~~  158 (318)
T PRK05629         79 EPTDLALSAAVDPSPGIYLIIMHSGGGRTKSMVPKLEKIAVVHEAAKLKPRERPGWVTQEFKNHGVRPTPDVVHALLEGV  158 (318)
T ss_pred             hHHHHHHHHHhCCCCCeEEEEEcCCcchhhHHHHHHHhcceEeeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Confidence            677889999999999988888876433   35567888899999999999999999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHhhh-CCCcccHHHHHhhcCCCCHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHH
Q psy879          188 QGDMRQALNNLQSTHN-GFGHVTAEYVFKVCDEPHPLAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDIIGNIFRVAK  266 (317)
Q Consensus       188 ~gd~r~~i~~l~~~~~-~~~~i~~~~v~~~~~~~~~~~i~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~~  266 (317)
                      ++|+..+.+++++.+. ..+.||.++|.+++....+..+|++++++..++...|+.++++|+..|++|..|+..+.+.+.
T Consensus       159 g~dl~~l~~EleKL~~~~~~~It~e~V~~~v~~~~~~~iF~l~dAv~~g~~~~Al~~l~~l~~~g~~pi~il~~l~~~~r  238 (318)
T PRK05629        159 GSDLRELASAISQLVEDTQGNVTVEKVRAYYVGVAEVSGFDIADLACAGQVSKAVASTRRALQLGVSPVALAAALSMKVG  238 (318)
T ss_pred             CccHHHHHHHHHHHHhcCCCCcCHHHHHHHhCCCccchHHHHHHHHHcCCHHHHHHHHHHHHHcCCCcHHHHHHHHHHHH
Confidence            9999999999998764 356899999999999999999999999999999999999999999999999999777654321


Q ss_pred             h---c----C------------CC---------------hHHHHHHHHHHHHHHhHHhcCC-CcHHHHHHHHHHHHHh
Q psy879          267 T---L----D------------IP---------------EPLKLSIIQEIGNVHLRISEGV-NSLLQLSGLLARLCIV  309 (317)
Q Consensus       267 ~---~----~------------~~---------------~~~~~~~~~~l~~~~~~l~~g~-~~~l~le~~~~~~~~~  309 (317)
                      .   +    +            +.               .....+++..+.++|..+|+|. ++.+.||.++.++++.
T Consensus       239 ~l~~l~~~~~~~~~~~ia~~l~i~p~~~~~~~~~ar~~s~~~L~~~l~~l~~~D~~~K~~~~d~~~~lE~~i~~~~~~  316 (318)
T PRK05629        239 QIARLYSTRGRIDSFELAKELGMPPFVVEKTAKVARNWSGDAVSEAVILMADLDAAVKGQGGDPEFAIESAVRRVAEL  316 (318)
T ss_pred             HHHHHHhhcCCCCHHHHHHHcCCChHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHhh
Confidence            1   1    1            11               1112228899999999999876 9999999999999864

>PRK07452 DNA polymerase III subunit delta; Validated

Probab=99.92  E-value=1.7e-22  Score=178.24  Aligned_cols=271  Identities=15%  Similarity=0.193  Sum_probs=210.1

Q ss_pred             ceEEEECCCCCCHHHHHHHHHHHHcCCCC-CCceEEecCCCCcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCC--
Q psy879           32 PNIIISGPPGVGKTTTILCLARILLGPSF-KDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSM--  108 (317)
Q Consensus        32 ~~~ll~G~~G~GKt~la~~la~~l~~~~~-~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l--  108 (317)
                      |.|+|||+...-+...+..+.+.+..+.. ...+..+++.+   .+.+.+.+......++   .+++++|++++++.+  
T Consensus         2 ~~yll~G~e~~l~~~~~~~l~~~~~~~~~~~fn~~~~d~~~---~~~~~~~~~~~~t~pf---f~~~rlVvv~~~~~~~~   75 (326)
T PRK07452          2 PIYLYWGEDDFALNQAIEKLIDQVVDPEWKSFNYSRLDGDD---ADQAIQALNEAMTPPF---GSGGRLVWLKNSPLCQG   75 (326)
T ss_pred             CEEEEEcChHHHHHHHHHHHHHHhCCchhhhcchhhcCCcc---chHHHHHHHHhcCCCC---CCCceEEEEeCchhhcc
Confidence            57999999988888888888877644322 22333333322   2223344443333332   278999999998765  


Q ss_pred             -CHHHHHHHHHHhhhccCCceEEEEec-CCC---cCchhHhhhcceeeecCC---CHHHHHHHHHHHHHHcCCCCCHHHH
Q psy879          109 -TDGAQQALRRTMEIYSNTTRFALACN-NSE---KIIEPIQSRCAMLRYNKL---TDAQLLSKVIEICEKENISHTNDGL  180 (317)
Q Consensus       109 -~~~~~~~ll~~le~~~~~~~~il~~~-~~~---~l~~~i~sR~~~i~f~~~---~~~~~~~~l~~~~~~~~~~i~~~~~  180 (317)
                       ..+..+.|.++++.+++++++|+++. ..+   +..+.+.+.+.+..|.++   +.+++.+|+.+++++.|+.++++++
T Consensus        76 ~~~~~~~~L~~~l~~~~~~~~li~~~~~~~d~r~k~~k~l~k~~~~~~~~~~~~~~~~~l~~~i~~~~~~~g~~i~~~a~  155 (326)
T PRK07452         76 CSEELLAELERTLPLIPENTHLLLTNTKKPDGRLKSTKLLQKLAEEKEFSLIPPWDTEGLKQLVERTAQELGVKLTPEAA  155 (326)
T ss_pred             CCHHHHHHHHHHHcCCCCCcEEEEEeCCCcchHHHHHHHHHHceeEEEecCCCcccHHHHHHHHHHHHHHcCCCCCHHHH
Confidence             56678899999999999998888753 332   456778888888888765   4577999999999999999999999


Q ss_pred             HHHHHhcCCCHHHHHHHHHHhhh----CCCcccHHHHHhhcCCCCHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHH
Q psy879          181 EAIVFTAQGDMRQALNNLQSTHN----GFGHVTAEYVFKVCDEPHPLAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPED  256 (317)
Q Consensus       181 ~~l~~~~~gd~r~~i~~l~~~~~----~~~~i~~~~v~~~~~~~~~~~i~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~  256 (317)
                      +.++..+++|++.+.+++++.+.    +.+.|+.++|.+++... +..+|++++++..++...|+.+++.|...|++|..
T Consensus       156 ~~L~~~~g~dl~~l~~EleKL~ly~~~~~~~It~~~V~~~v~~~-~~~if~l~dai~~~~~~~A~~~l~~L~~~g~~p~~  234 (326)
T PRK07452        156 ELLAEAVGNDSRRLYNELEKLALYAENSTKPISAEEVKALVSNT-TQNSLQLADALLQGNTGKALALLDDLLDANEPALR  234 (326)
T ss_pred             HHHHHHhCccHHHHHHHHHHHHHhccCCCCccCHHHHHHHhccC-cCcHHHHHHHHHCCCHHHHHHHHHHHHHCCCcHHH
Confidence            99999999999999999999765    24579999999998876 57899999999999999999999999999999999


Q ss_pred             HHHHHHHHHHh---------------------cCCC-h---------------HHHHHHHHHHHHHHhHHhcCCCcHHHH
Q psy879          257 IIGNIFRVAKT---------------------LDIP-E---------------PLKLSIIQEIGNVHLRISEGVNSLLQL  299 (317)
Q Consensus       257 i~~~~~~~~~~---------------------~~~~-~---------------~~~~~~~~~l~~~~~~l~~g~~~~l~l  299 (317)
                      |+..+.+.++.                     +++. +               ....+++..+.++|.++|+|.++...|
T Consensus       235 il~~l~~~~r~l~~~k~~~~~G~~~~~~ia~~lgi~~p~~~~~~~~~~~~~s~~~L~~~l~~L~~~D~~iK~g~~~~~~l  314 (326)
T PRK07452        235 IVATLTGQFRTWLWVKLLVESGERDVKVIAKAAGIGNPKRIYFLRKEVQGLSSQQLLKLLPLLLDLEASLKQGANPINAL  314 (326)
T ss_pred             HHHHHHHHHHHHHHHHHHHHcCCCcHHHHHHHhCCCCcHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHhcCCChHHHH
Confidence            98876543322                     1221 1               012228999999999999999888899


Q ss_pred             HHHHHHHHHh
Q psy879          300 SGLLARLCIV  309 (317)
Q Consensus       300 e~~~~~~~~~  309 (317)
                      |.++.++|..
T Consensus       315 e~~i~~~~~~  324 (326)
T PRK07452        315 QDKLIELCQL  324 (326)
T ss_pred             HHHHHHHHHh
Confidence            9999999975

>PRK06585 holA DNA polymerase III subunit delta; Reviewed

Probab=99.92  E-value=7.1e-22  Score=175.46  Aligned_cols=283  Identities=13%  Similarity=0.137  Sum_probs=214.0

Q ss_pred             HHHHHhc--CCCceEEEECCCCCCHHHHHHHHHHHHcCCCC-CCceEEecCCCCcChHHHHHHHHHHHhhcccCCCCcee
Q psy879           22 LKVFSSS--GNVPNIIISGPPGVGKTTTILCLARILLGPSF-KDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHK   98 (317)
Q Consensus        22 l~~~l~~--~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~-~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~   98 (317)
                      +...+.+  +..|.|+|||+........+..+.+.+..... ...+..+.... .. .++.+.+......+++   ++++
T Consensus         9 ~~~~l~~~~~~~~~yll~G~e~~li~~~~~~l~~~~~~~~~~~fn~~~~~~~e-~~-~~~~~~~~~~~t~slF---~~~r   83 (343)
T PRK06585          9 VDRFLARPDPKIRAVLLYGPDRGLVRERARRLAKSVVPDLDDPFAVVRLDGDD-LD-ADPARLEDEANAISLF---GGRR   83 (343)
T ss_pred             HHHHHhCCCCCCeEEEEeCCchHHHHHHHHHHHHHhcCCCCCCcceeeccHHH-hh-cCHHHHHHHHhCCCCC---CCce
Confidence            3444443  35667999999998888888888887654321 12233333221 11 0123334444444433   7889


Q ss_pred             EEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCC---cCchhHh--hhcceeeecCCCHHHHHHHHHHHHHHcCC
Q psy879           99 IVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSE---KIIEPIQ--SRCAMLRYNKLTDAQLLSKVIEICEKENI  173 (317)
Q Consensus        99 vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~---~l~~~i~--sR~~~i~f~~~~~~~~~~~l~~~~~~~~~  173 (317)
                      +|++.+++   +...+.|..+++.+++.+++|+.+...+   ++.+.+.  ..+..+.|.++++.++..|+.++++..|+
T Consensus        84 lViv~~~~---~~~~~~L~~~l~~~~~~~~lil~~~~~~~~~kl~k~~~~~~~~~~v~~~~~~~~~l~~~i~~~~~~~g~  160 (343)
T PRK06585         84 LIWVRAGS---KNLAAALKALLESPPGDAFIVIEAGDLKKGSSLRKLFETAAYAAAIPCYADDERDLARLIDDELAEAGL  160 (343)
T ss_pred             EEEEECCc---hhHHHHHHHHHcCCCCCcEEEEEcCCCCcccHHHHHHhcCCCeeEEecCCCCHHHHHHHHHHHHHHCCC
Confidence            99999654   3455678899999888888888765432   2334332  23455899999999999999999999999


Q ss_pred             CCCHHHHHHHHHhcCCCHHHHHHHHHHhhh---CCCcccHHHHHhhcCCCCHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q psy879          174 SHTNDGLEAIVFTAQGDMRQALNNLQSTHN---GFGHVTAEYVFKVCDEPHPLAVKEMLLNCVEGNMKDSYKIIHHLYKL  250 (317)
Q Consensus       174 ~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~---~~~~i~~~~v~~~~~~~~~~~i~~l~~~~~~~~~~~~~~~~~~l~~~  250 (317)
                      .+++++++.++..++||++.+.+++++.+.   +.+.||.++|.+++....+..+|++++++..++...++.+++.|+..
T Consensus       161 ~i~~~a~~~L~~~~g~dl~~l~~EleKL~ly~~~~~~It~edV~~lv~~~~e~~if~l~dai~~~~~~~a~~~l~~ll~~  240 (343)
T PRK06585        161 RITPDARALLVALLGGDRLASRNEIEKLALYAHGKGEITLDDVRAVVGDASALSLDDAADAALAGDLAAFERALDRALAE  240 (343)
T ss_pred             CCCHHHHHHHHHHhCCCHHHHHHHHHHHHHhcCCCCCCCHHHHHHHhCCcccccHHHHHHHHHCCCHHHHHHHHHHHHHc
Confidence            999999999999999999999999998765   34689999999999999999999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHhc---------CCCh----------------------------HHHHHHHHHHHHHHhHHhcCC
Q psy879          251 GYAPEDIIGNIFRVAKTL---------DIPE----------------------------PLKLSIIQEIGNVHLRISEGV  293 (317)
Q Consensus       251 ~~~~~~i~~~~~~~~~~~---------~~~~----------------------------~~~~~~~~~l~~~~~~l~~g~  293 (317)
                      |++|..|+..+.+.++.+         |.+.                            ....+++..+.++|..+|+|.
T Consensus       241 g~~p~~il~~L~~~~r~L~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~a~~~s~~~L~~~l~~l~~~d~~lK~~~  320 (343)
T PRK06585        241 GTAPVLILRAALRHFQRLHIVRLKVENGKSAEQAIASLRPPVFFKRKPDFEKALRRWSLERLLRALERLQAAELDCRRNP  320 (343)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHhhCCCCCcchHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHhcCC
Confidence            999999988875543322         2111                            112228999999999999888


Q ss_pred             -CcHHHHHHHHHHHHHhhcc
Q psy879          294 -NSLLQLSGLLARLCIVGSK  312 (317)
Q Consensus       294 -~~~l~le~~~~~~~~~~~~  312 (317)
                       ++.+.+|.++.++|.....
T Consensus       321 ~~~~~~le~~i~~~~~~~~~  340 (343)
T PRK06585        321 ALADAIARRVLLSIAVRARR  340 (343)
T ss_pred             CcHHHHHHHHHHHHHHHHHh
Confidence             8999999999999975443

>PRK05818 DNA polymerase III subunit delta'; Validated

Probab=99.92  E-value=6.3e-23  Score=169.63  Aligned_cols=161  Identities=13%  Similarity=0.137  Sum_probs=128.9

Q ss_pred             CCce-EEEECCCCCCHHHHHHHHHHHHcCCCCCC-----------------ceEEecC-CCCcChHHHHHHHHHHHhhcc
Q psy879           30 NVPN-IIISGPPGVGKTTTILCLARILLGPSFKD-----------------AVLELNA-SNDRGIDTVRNKIKMFAQQKV   90 (317)
Q Consensus        30 ~~~~-~ll~G~~G~GKt~la~~la~~l~~~~~~~-----------------~~~~~~~-~~~~~~~~i~~~~~~~~~~~~   90 (317)
                      .+|| +||+||+|+||..+|.++|+.+.|.....                 .+..+.+ ....+++++++....+...+.
T Consensus         5 ~~~HA~Lf~G~~G~G~~~lA~~~A~~llC~~~~~~Cg~C~sC~~i~~~~HPDl~~i~p~~~~I~id~ir~l~~~l~~~s~   84 (261)
T PRK05818          5 NKTHPLLLIERKGSFLKPFLYEYLTSIVCTKANGFCKTCESCLKILNGKYNDFYLIFDQKNPIKKEDALSIINKLNRPSV   84 (261)
T ss_pred             CCCcceeeeCCCCCcHHHHHHHHHHHHcCCCCCCCCCCCHHHHHHhcCCCCCEEEecCCcccCCHHHHHHHHHHHccCch
Confidence            3467 99999999999999999999998864221                 1222222 234678899988877765431


Q ss_pred             cCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcCchhHhhhcceeeecCC----------CHHHH
Q psy879           91 TLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKL----------TDAQL  160 (317)
Q Consensus        91 ~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~~~i~sR~~~i~f~~~----------~~~~~  160 (317)
                      .  .++++|+||+++|+|+..+.|+|++++||||+++.||++|++++.+++||+|||+.+.|+++          ++.++
T Consensus        85 e--~~~~KV~II~~ae~m~~~AaNaLLK~LEEPp~~t~fiLit~~~~~lLpTI~SRCq~~~~~~~~~~~~~~~~~~~~~i  162 (261)
T PRK05818         85 E--SNGKKIYIIYGIEKLNKQSANSLLKLIEEPPKNTYGIFTTRNENNILNTILSRCVQYVVLSKEKKVPFKVESNDRYF  162 (261)
T ss_pred             h--cCCCEEEEeccHhhhCHHHHHHHHHhhcCCCCCeEEEEEECChHhCchHhhhheeeeecCChhhhcccccccChHHH
Confidence            1  25799999999999999999999999999999999999999999999999999999999998          56666


Q ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHh
Q psy879          161 LSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQST  201 (317)
Q Consensus       161 ~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~  201 (317)
                      .+.+....     .+++    .++..++|++.+++..++..
T Consensus       163 ~~~L~~~~-----~~d~----~i~~~a~g~~~~a~~l~~~l  194 (261)
T PRK05818        163 QYILLSFY-----SVDE----QLQAYNNGSFSKLKNIIETL  194 (261)
T ss_pred             HHHHHHcc-----CccH----HHHHHcCCCHHHHHHHHHHH
Confidence            66655532     2443    67788999999999998854

>PRK08487 DNA polymerase III subunit delta; Validated

Probab=99.92  E-value=8.2e-22  Score=173.38  Aligned_cols=280  Identities=13%  Similarity=0.148  Sum_probs=214.7

Q ss_pred             HHHHHHHhcCCCce-EEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHHHHHHHhhcccCCCCcee
Q psy879           20 ERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHK   98 (317)
Q Consensus        20 ~~l~~~l~~~~~~~-~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~   98 (317)
                      +.+...+++|.+++ |+|||+.-.-.......+.+.+.+...... +..+   ..+.   .+.+......++.   ++++
T Consensus         4 ~~l~~~lk~~~l~~vyll~GeE~yli~~~~~~i~~~~~~~~~~~~-~~~~---~~~~---~~i~~~~~t~plF---~~~r   73 (328)
T PRK08487          4 KELDTLLKQNKLPNAFLLYGEDEFQIELYAKKISEKFKPENELKT-LYFD---EYDF---EQAKDFLSQSSLF---GGKN   73 (328)
T ss_pred             HHHHHHHhcCCCCceEEEecCchhHHHHHHHHHHHHhcCchHhhh-hchh---hccH---HHHHHHHhccccc---CCce
Confidence            35677788887755 999999988888888888877643322111 2222   1223   3344444444433   7899


Q ss_pred             EEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCC---cCchhHhhh--cceeeecCCCHHHHHHHHHHHHHHcCC
Q psy879           99 IVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSE---KIIEPIQSR--CAMLRYNKLTDAQLLSKVIEICEKENI  173 (317)
Q Consensus        99 vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~---~l~~~i~sR--~~~i~f~~~~~~~~~~~l~~~~~~~~~  173 (317)
                      +|++.++..+.......|..+++.+++.+++|++.....   ++.+.+...  +..+.|.++++.++..|+.+++++.|+
T Consensus        74 lViv~~~~~~~~~~~~~L~~~l~~~~~~~~lv~~~~~~~k~kkl~k~~~~~k~~~~v~~~~~~~~~l~~~i~~~~~~~g~  153 (328)
T PRK08487         74 LLIIKLDKKIPKKELKLLIELCEKNSDNYFIIELYGADSKTKDIEKLFQKKDEAVFVRFFKPNAREALELLQERAKELGL  153 (328)
T ss_pred             EEEEecccccCHHHHHHHHHHHhcCCCCEEEEEecCCcchhHHHHHHhccCCCceEEEeeCCCHHHHHHHHHHHHHHhCC
Confidence            999998877777777899999999888777776544333   122333322  556999999999999999999999999


Q ss_pred             CCCHHHHHHHHHhcCCCHHHHHHHHHHhhhCCCcccHHHHHhhcCCCCHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCC
Q psy879          174 SHTNDGLEAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEMLLNCVEGNMKDSYKIIHHLYKLGYA  253 (317)
Q Consensus       174 ~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~~~~~i~~~~v~~~~~~~~~~~i~~l~~~~~~~~~~~~~~~~~~l~~~~~~  253 (317)
                      .+++++++.++..+++|+..+.+++++...-.+.||.++|.+++..+.+..+|++++++..++  .++.++++|...|++
T Consensus       154 ~i~~~a~~~L~~~~g~dl~~l~~ELeKL~ly~~~It~edV~~~v~~~~e~~vF~l~dai~~g~--~a~~~l~~L~~~g~~  231 (328)
T PRK08487        154 DIDQNALNHLYFIHNEDLALAANELEKLAILNEPITLKDIQELVFGLGSVSFEDFFEKLLNKK--DIKDDLEKLLEEGFN  231 (328)
T ss_pred             CCCHHHHHHHHHHhCcHHHHHHHHHHHHHHhcCCCCHHHHHHHhcccccccHHHHHHHHHCCC--cHHHHHHHHHHCCCC
Confidence            999999999999999999999999999877555899999999999999999999999999888  588899999999999


Q ss_pred             HHHHHHHHHHHHHhc-------------------CCCh-----------------HHHHHHHHHHHHHHhHHhcCC--Cc
Q psy879          254 PEDIIGNIFRVAKTL-------------------DIPE-----------------PLKLSIIQEIGNVHLRISEGV--NS  295 (317)
Q Consensus       254 ~~~i~~~~~~~~~~~-------------------~~~~-----------------~~~~~~~~~l~~~~~~l~~g~--~~  295 (317)
                      |..|+..+.+++..+                   ++.+                 ....+++..|.++|..+|+|.  +.
T Consensus       232 pi~Il~~L~r~~~~L~~i~~~~~~~~~~~~a~~~~~~~~~f~~~~~~~q~~~~s~~~L~~~l~~L~e~D~~lK~g~~~~~  311 (328)
T PRK08487        232 EIALLNSLERFFYQLFLFFAYIKINGKPDAKEILGYKPPKQIAENLAKQAIKIKEAQYKEIFELLLEWELELKTGQKIDK  311 (328)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHcCCcCHHHHhCCCCCHHHHHHHHHHHhccCHHHHHHHHHHHHHHHHHHHcCCCccH
Confidence            999988876543322                   2211                 112228999999999999996  77


Q ss_pred             HHHHHHHHHHHHHhhc
Q psy879          296 LLQLSGLLARLCIVGS  311 (317)
Q Consensus       296 ~l~le~~~~~~~~~~~  311 (317)
                      .+.+|..++++.++.+
T Consensus       312 ~~~~~~~~~~~~~~~~  327 (328)
T PRK08487        312 NLFLLSTLIKIQKILN  327 (328)
T ss_pred             HHHHHHHHHHHHHHhc
Confidence            8899999999987653

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=99.91  E-value=4.5e-22  Score=180.34  Aligned_cols=277  Identities=18%  Similarity=0.180  Sum_probs=190.3

Q ss_pred             CcccCCHHHHHHHHHHH----hcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHH-HHHHHH
Q psy879           10 SDIVGNEDTVERLKVFS----SSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTV-RNKIKM   84 (317)
Q Consensus        10 ~~~~g~~~~~~~l~~~l----~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i-~~~~~~   84 (317)
                      +.++|++..++.|...+    .++.+++++++||||+|||++++.+++.+........++.+++....+...+ ......
T Consensus        30 ~~l~~Re~e~~~l~~~l~~~~~~~~~~~~lI~G~~GtGKT~l~~~v~~~l~~~~~~~~~v~in~~~~~~~~~~~~~i~~~  109 (394)
T PRK00411         30 ENLPHREEQIEELAFALRPALRGSRPLNVLIYGPPGTGKTTTVKKVFEELEEIAVKVVYVYINCQIDRTRYAIFSEIARQ  109 (394)
T ss_pred             CCCCCHHHHHHHHHHHHHHHhCCCCCCeEEEECCCCCCHHHHHHHHHHHHHHhcCCcEEEEEECCcCCCHHHHHHHHHHH
Confidence            56889988877766665    4445567999999999999999999998754433455677776543332111 111111


Q ss_pred             HHhhc-----------------ccCCCCceeEEEEeCCCCCC----HHHHHHHHHHhhhccC-CceEEEEecCCC---cC
Q psy879           85 FAQQK-----------------VTLPPGRHKIVILDEADSMT----DGAQQALRRTMEIYSN-TTRFALACNNSE---KI  139 (317)
Q Consensus        85 ~~~~~-----------------~~~~~~~~~vliiDE~d~l~----~~~~~~ll~~le~~~~-~~~~il~~~~~~---~l  139 (317)
                      +...+                 .....+.+.||+|||+|.+.    .+....|++.++..+. +..+|+++++..   .+
T Consensus       110 l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~viviDE~d~l~~~~~~~~l~~l~~~~~~~~~~~v~vI~i~~~~~~~~~l  189 (394)
T PRK00411        110 LFGHPPPSSGLSFDELFDKIAEYLDERDRVLIVALDDINYLFEKEGNDVLYSLLRAHEEYPGARIGVIGISSDLTFLYIL  189 (394)
T ss_pred             hcCCCCCCCCCCHHHHHHHHHHHHHhcCCEEEEEECCHhHhhccCCchHHHHHHHhhhccCCCeEEEEEEECCcchhhhc
Confidence            11000                 00011345789999999986    3445666666655443 566888888763   56


Q ss_pred             chhHhhhcc--eeeecCCCHHHHHHHHHHHHHHc--CCCCCHHHHHHHHHhc---CCCHHHHHHHHHHhhh-----CCCc
Q psy879          140 IEPIQSRCA--MLRYNKLTDAQLLSKVIEICEKE--NISHTNDGLEAIVFTA---QGDMRQALNNLQSTHN-----GFGH  207 (317)
Q Consensus       140 ~~~i~sR~~--~i~f~~~~~~~~~~~l~~~~~~~--~~~i~~~~~~~l~~~~---~gd~r~~i~~l~~~~~-----~~~~  207 (317)
                      .+.+++|+.  .+.|+|++.+++.+++..++...  ...+++++++.+++.+   .||+|.+++.+..++.     +...
T Consensus       190 ~~~~~s~~~~~~i~f~py~~~e~~~il~~r~~~~~~~~~~~~~~l~~i~~~~~~~~Gd~r~a~~ll~~a~~~a~~~~~~~  269 (394)
T PRK00411        190 DPRVKSVFRPEEIYFPPYTADEIFDILKDRVEEGFYPGVVDDEVLDLIADLTAREHGDARVAIDLLRRAGLIAEREGSRK  269 (394)
T ss_pred             CHHHHhcCCcceeecCCCCHHHHHHHHHHHHHhhcccCCCCHhHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHcCCCC
Confidence            788888874  49999999999999999988653  2357899999988777   8999999999976542     4467


Q ss_pred             ccHHHHHhhcCCCCHHHHHHHHHHHhcCCHHHHHHHHHHHHH---cCCCHHHHHHHHHHHHHhcCCChHHHHHHHHHHHH
Q psy879          208 VTAEYVFKVCDEPHPLAVKEMLLNCVEGNMKDSYKIIHHLYK---LGYAPEDIIGNIFRVAKTLDIPEPLKLSIIQEIGN  284 (317)
Q Consensus       208 i~~~~v~~~~~~~~~~~i~~l~~~~~~~~~~~~~~~~~~l~~---~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~  284 (317)
                      |+.+++..+.+..........+..+...+..-...+ ..+..   ...+..+++..|..+|+.++.++....++.+.+.+
T Consensus       270 I~~~~v~~a~~~~~~~~~~~~~~~L~~~~k~~L~ai-~~~~~~~~~~~~~~~i~~~y~~l~~~~~~~~~~~~~~~~~l~~  348 (394)
T PRK00411        270 VTEEDVRKAYEKSEIVHLSEVLRTLPLHEKLLLRAI-VRLLKKGGDEVTTGEVYEEYKELCEELGYEPRTHTRFYEYINK  348 (394)
T ss_pred             cCHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHH-HHHHhcCCCcccHHHHHHHHHHHHHHcCCCcCcHHHHHHHHHH
Confidence            999999988877655455555555554433333333 33322   34678899999999999888888666777777776


Q ss_pred             HHh
Q psy879          285 VHL  287 (317)
Q Consensus       285 ~~~  287 (317)
                      ++.
T Consensus       349 L~~  351 (394)
T PRK00411        349 LDM  351 (394)
T ss_pred             HHh
Confidence            654

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=99.91  E-value=4e-22  Score=178.87  Aligned_cols=282  Identities=16%  Similarity=0.159  Sum_probs=185.9

Q ss_pred             cccCCCCCCcccCCHHHHHHHHHHHh----cCCCceEEEECCCCCCHHHHHHHHHHHHcCCCC----CCceEEecCCCCc
Q psy879            2 EKYRPQTFSDIVGNEDTVERLKVFSS----SGNVPNIIISGPPGVGKTTTILCLARILLGPSF----KDAVLELNASNDR   73 (317)
Q Consensus         2 ~ky~P~~~~~~~g~~~~~~~l~~~l~----~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~----~~~~~~~~~~~~~   73 (317)
                      ..|.|.   +++|++..++.|..++.    ++..++++++||||+|||++++.+++.+.....    ...++++++....
T Consensus        10 ~~~~p~---~l~gRe~e~~~l~~~l~~~~~~~~~~~i~I~G~~GtGKT~l~~~~~~~l~~~~~~~~~~~~~v~in~~~~~   86 (365)
T TIGR02928        10 PDYVPD---RIVHRDEQIEELAKALRPILRGSRPSNVFIYGKTGTGKTAVTKYVMKELEEAAEDRDVRVVTVYVNCQILD   86 (365)
T ss_pred             CCCCCC---CCCCcHHHHHHHHHHHHHHHcCCCCCcEEEECCCCCCHHHHHHHHHHHHHHHhhccCCceEEEEEECCCCC
Confidence            468884   68899998887776665    345556999999999999999999998743211    1456677765433


Q ss_pred             ChHH-HHHHHHHHHh--hc-----------------ccCCCCceeEEEEeCCCCCCHHH---HHHHHHH--hhhcc-CCc
Q psy879           74 GIDT-VRNKIKMFAQ--QK-----------------VTLPPGRHKIVILDEADSMTDGA---QQALRRT--MEIYS-NTT  127 (317)
Q Consensus        74 ~~~~-i~~~~~~~~~--~~-----------------~~~~~~~~~vliiDE~d~l~~~~---~~~ll~~--le~~~-~~~  127 (317)
                      +... +......+..  ..                 .....+.+.||+|||+|.+....   ...|+++  ..+.+ .++
T Consensus        87 ~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlvIDE~d~L~~~~~~~L~~l~~~~~~~~~~~~~v  166 (365)
T TIGR02928        87 TLYQVLVELANQLRGSGEEVPTTGLSTSEVFRRLYKELNERGDSLIIVLDEIDYLVGDDDDLLYQLSRARSNGDLDNAKV  166 (365)
T ss_pred             CHHHHHHHHHHHHhhcCCCCCCCCCCHHHHHHHHHHHHHhcCCeEEEEECchhhhccCCcHHHHhHhccccccCCCCCeE
Confidence            3222 2222222210  00                 00012346789999999995332   3344444  22222 567


Q ss_pred             eEEEEecCCC---cCchhHhhhcc--eeeecCCCHHHHHHHHHHHHHH--cCCCCCHHHHHHHH---HhcCCCHHHHHHH
Q psy879          128 RFALACNNSE---KIIEPIQSRCA--MLRYNKLTDAQLLSKVIEICEK--ENISHTNDGLEAIV---FTAQGDMRQALNN  197 (317)
Q Consensus       128 ~~il~~~~~~---~l~~~i~sR~~--~i~f~~~~~~~~~~~l~~~~~~--~~~~i~~~~~~~l~---~~~~gd~r~~i~~  197 (317)
                      .+|+++|.+.   .+.+.+.+|+.  .+.|+|++.+++.+++..++..  .+..+++++++.++   ..+.||+|.+++.
T Consensus       167 ~lI~i~n~~~~~~~l~~~~~s~~~~~~i~f~p~~~~e~~~il~~r~~~~~~~~~~~~~~l~~i~~~~~~~~Gd~R~al~~  246 (365)
T TIGR02928       167 GVIGISNDLKFRENLDPRVKSSLCEEEIIFPPYDAEELRDILENRAEKAFYDGVLDDGVIPLCAALAAQEHGDARKAIDL  246 (365)
T ss_pred             EEEEEECCcchHhhcCHHHhccCCcceeeeCCCCHHHHHHHHHHHHHhhccCCCCChhHHHHHHHHHHHhcCCHHHHHHH
Confidence            7888998764   57888999985  5999999999999999999863  22347788776654   4567999999999


Q ss_pred             HHHhhh-----CCCcccHHHHHhhcCCCCHHHHHHHHHHHhcCCHHHHHHHHHHHHHc---CCCHHHHHHHHHHHHHhcC
Q psy879          198 LQSTHN-----GFGHVTAEYVFKVCDEPHPLAVKEMLLNCVEGNMKDSYKIIHHLYKL---GYAPEDIIGNIFRVAKTLD  269 (317)
Q Consensus       198 l~~~~~-----~~~~i~~~~v~~~~~~~~~~~i~~l~~~~~~~~~~~~~~~~~~l~~~---~~~~~~i~~~~~~~~~~~~  269 (317)
                      ++.++.     +...|+.+++..+.+........+.+..+.. .....+..+..+...   .....+++..|...++..+
T Consensus       247 l~~a~~~a~~~~~~~it~~~v~~a~~~~~~~~~~~~i~~l~~-~~~~~l~ai~~~~~~~~~~~~~~~~~~~y~~~~~~~~  325 (365)
T TIGR02928       247 LRVAGEIAEREGAERVTEDHVEKAQEKIEKDRLLELIRGLPT-HSKLVLLAIANLAANDEDPFRTGEVYEVYKEVCEDIG  325 (365)
T ss_pred             HHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHHHHcCCH-HHHHHHHHHHHHHhcCCCCccHHHHHHHHHHHHHhcC
Confidence            987543     3457999999987776543333333333221 122234444444432   3567788888888888888


Q ss_pred             CChHHHHHHHHHHHHHHh
Q psy879          270 IPEPLKLSIIQEIGNVHL  287 (317)
Q Consensus       270 ~~~~~~~~~~~~l~~~~~  287 (317)
                      ..+....++.+.+.+++.
T Consensus       326 ~~~~~~~~~~~~l~~l~~  343 (365)
T TIGR02928       326 VDPLTQRRISDLLNELDM  343 (365)
T ss_pred             CCCCcHHHHHHHHHHHHh
Confidence            888777888887777654

Members of this protein family are found exclusively in the archaea. This set of DNA binding proteins shows homology to the origin recognition complex subunit 1/cell division control protein 6 family in eukaryotes. Several members may be found in genome and interact with each other.

>PRK05574 holA DNA polymerase III subunit delta; Reviewed

Probab=99.91  E-value=4.2e-21  Score=170.65  Aligned_cols=281  Identities=15%  Similarity=0.169  Sum_probs=208.8

Q ss_pred             HHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCC-CCCceEEecCCCCcChHHHHHHHHHHHhhcccCCCCceeE
Q psy879           21 RLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPS-FKDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKI   99 (317)
Q Consensus        21 ~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~-~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~v   99 (317)
                      .+...++++-.+.|+|||+.-.-+...+..+.+...... ....+..+++.. ...+.+   +......++.   +++++
T Consensus         7 ~~~~~~~~~~~~~~li~G~d~~l~~~~~~~i~~~~~~~~~~~~~~~~~d~~~-~~~~~l---~~~~~t~~lF---~~~kl   79 (340)
T PRK05574          7 QLEKQLKKGLAPLYLLYGDEPLLLQEAKDAIRAAARAQGFDERNVFTFDGSE-TDWDDV---LEACQSLPLF---SDRKL   79 (340)
T ss_pred             HHHHHHhCCCCceEEEEcCcHHHHHHHHHHHHHHHHcCCCceeeEEEeecCC-CCHHHH---HHHhhccCcc---ccCeE
Confidence            355566666333499999996556666666666543222 223344444432 233333   3333333333   68999


Q ss_pred             EEEeCCCCCCHHH----HHHHHHHhhhccCC--ceEEEEecCCC---cC---chhHhhhcceeeecCCCHHHHHHHHHHH
Q psy879          100 VILDEADSMTDGA----QQALRRTMEIYSNT--TRFALACNNSE---KI---IEPIQSRCAMLRYNKLTDAQLLSKVIEI  167 (317)
Q Consensus       100 liiDE~d~l~~~~----~~~ll~~le~~~~~--~~~il~~~~~~---~l---~~~i~sR~~~i~f~~~~~~~~~~~l~~~  167 (317)
                      |+|++++.+....    ...+..++ +++++  .++++.++..+   ++   .+++.+++..+.|.+++..++..|+...
T Consensus        80 vii~~~~~l~~~~~~~~l~~l~~~l-~~~~~~~~~li~~~~~~~~~~k~~k~~k~~~~~~~~~~~~~~~~~~~~~~i~~~  158 (340)
T PRK05574         80 VELRLPEFLTGAKGEKALKRLEAYL-NPLPHPDLLLIVRLPKLDKAKKKSAWFKALKKKAVVVEAQPPKEAELPQWIQQR  158 (340)
T ss_pred             EEEECCCCCCchhHHHHHHHHHHhc-cCCCCCcEEEEEECCcCCHHHHhhHHHHHHHhCceEEEcCCCCHHHHHHHHHHH
Confidence            9999999986652    33444555 44443  34444444332   33   6788889999999999999999999999


Q ss_pred             HHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhh--CCCcccHHHHHhhcCCCCHHHHHHHHHHHhcCCHHHHHHHHH
Q psy879          168 CEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHN--GFGHVTAEYVFKVCDEPHPLAVKEMLLNCVEGNMKDSYKIIH  245 (317)
Q Consensus       168 ~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~--~~~~i~~~~v~~~~~~~~~~~i~~l~~~~~~~~~~~~~~~~~  245 (317)
                      ++..|+.+++++++.++..++||++.+.+++++.+.  +.+.||.++|.+++....+..++++++++..++...++..++
T Consensus       159 ~~~~g~~i~~~a~~~L~~~~~~d~~~l~~El~KL~l~~~~~~It~~~I~~~i~~~~~~~~f~l~dai~~~~~~~a~~~l~  238 (340)
T PRK05574        159 LKQQGLQIDAAALQLLAERVEGNLLALAQELEKLALLYPDGKITLEDVEEAVPDSARFDVFDLVDAILAGKIKRALRILD  238 (340)
T ss_pred             HHHcCCCCCHHHHHHHHHHhCchHHHHHHHHHHHHhhcCCCCCCHHHHHHHHhhhhcCCHHHHHHHHHCCCHHHHHHHHH
Confidence            999999999999999999999999999999999765  334499999999999988899999999999999999999999


Q ss_pred             HHHHcCCCHHHHHHHHHHHHHhc---------CC--------------------------ChHHHHHHHHHHHHHHhHHh
Q psy879          246 HLYKLGYAPEDIIGNIFRVAKTL---------DI--------------------------PEPLKLSIIQEIGNVHLRIS  290 (317)
Q Consensus       246 ~l~~~~~~~~~i~~~~~~~~~~~---------~~--------------------------~~~~~~~~~~~l~~~~~~l~  290 (317)
                      .+...|.+|..|+..+.+.+..+         |.                          +.....+++..+.++|.++|
T Consensus       239 ~l~~~~~~~~~il~~l~~~~~~l~~~k~~~~~g~~~~~~~~~~~i~~~~~~~~~~~~~~~s~~~L~~~l~~L~~~d~~iK  318 (340)
T PRK05574        239 GLRLEGEEPIKLLAALQREFRLLLQLKILSQQGYPLQQLAKELRVWPYRVKLALRALQRLSLKQLKQAIQLLAETDYQIK  318 (340)
T ss_pred             HHHHCCCcHHHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHcCCChhHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence            99999999999988865543221         21                          11223338999999999999


Q ss_pred             cCC--CcHHHHHHHHHHHHHh
Q psy879          291 EGV--NSLLQLSGLLARLCIV  309 (317)
Q Consensus       291 ~g~--~~~l~le~~~~~~~~~  309 (317)
                      +|.  ++.+.||.++.++|.+
T Consensus       319 ~~~~~~~~~~le~~ii~l~~~  339 (340)
T PRK05574        319 TGYGGDKWLELELLLLKLAGA  339 (340)
T ss_pred             CCCCCCHHHHHHHHHHHhccC
Confidence            994  9999999999999964

>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]

Probab=99.90  E-value=2.1e-21  Score=171.21  Aligned_cols=277  Identities=21%  Similarity=0.227  Sum_probs=197.4

Q ss_pred             ccCCCCCCcccCCHHHHHH----HHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHH
Q psy879            3 KYRPQTFSDIVGNEDTVER----LKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTV   78 (317)
Q Consensus         3 ky~P~~~~~~~g~~~~~~~----l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i   78 (317)
                      -|-|..   +.+++..++.    |..++.++.+.|+++|||||||||++++.+++++........++++||....+..++
T Consensus        13 ~~iP~~---l~~Re~ei~~l~~~l~~~~~~~~p~n~~iyG~~GTGKT~~~~~v~~~l~~~~~~~~~~yINc~~~~t~~~i   89 (366)
T COG1474          13 DYIPEE---LPHREEEINQLASFLAPALRGERPSNIIIYGPTGTGKTATVKFVMEELEESSANVEVVYINCLELRTPYQV   89 (366)
T ss_pred             CCCccc---ccccHHHHHHHHHHHHHHhcCCCCccEEEECCCCCCHhHHHHHHHHHHHhhhccCceEEEeeeeCCCHHHH
Confidence            355643   6777776665    455666777777999999999999999999999976655555788888765555444


Q ss_pred             HHHH-HHHHhhccc---------------CCCCceeEEEEeCCCCCCHHHHHHHHHHhh---hccCCceEEEEecCC---
Q psy879           79 RNKI-KMFAQQKVT---------------LPPGRHKIVILDEADSMTDGAQQALRRTME---IYSNTTRFALACNNS---  136 (317)
Q Consensus        79 ~~~~-~~~~~~~~~---------------~~~~~~~vliiDE~d~l~~~~~~~ll~~le---~~~~~~~~il~~~~~---  136 (317)
                      ...+ ..+...+..               ...+..-||++||+|.|.....+.|+.++.   +....+.+|+++|..   
T Consensus        90 ~~~i~~~~~~~p~~g~~~~~~~~~l~~~~~~~~~~~IvvLDEid~L~~~~~~~LY~L~r~~~~~~~~v~vi~i~n~~~~~  169 (366)
T COG1474          90 LSKILNKLGKVPLTGDSSLEILKRLYDNLSKKGKTVIVILDEVDALVDKDGEVLYSLLRAPGENKVKVSIIAVSNDDKFL  169 (366)
T ss_pred             HHHHHHHcCCCCCCCCchHHHHHHHHHHHHhcCCeEEEEEcchhhhccccchHHHHHHhhccccceeEEEEEEeccHHHH
Confidence            3322 222111110               011457799999999998775555555554   333345677778775   


Q ss_pred             CcCchhHhhhcce--eeecCCCHHHHHHHHHHHHHH--cCCCCCHHHHHHHH---HhcCCCHHHHHHHHHHhhh-----C
Q psy879          137 EKIIEPIQSRCAM--LRYNKLTDAQLLSKVIEICEK--ENISHTNDGLEAIV---FTAQGDMRQALNNLQSTHN-----G  204 (317)
Q Consensus       137 ~~l~~~i~sR~~~--i~f~~~~~~~~~~~l~~~~~~--~~~~i~~~~~~~l~---~~~~gd~r~~i~~l~~~~~-----~  204 (317)
                      ..+.+.++|++..  +.|+||+.+|+.++|..+++.  ..-.+++++++.++   ...+||.|.|+++|+.++.     +
T Consensus       170 ~~ld~rv~s~l~~~~I~F~pY~a~el~~Il~~R~~~~~~~~~~~~~vl~lia~~~a~~~GDAR~aidilr~A~eiAe~~~  249 (366)
T COG1474         170 DYLDPRVKSSLGPSEIVFPPYTAEELYDILRERVEEGFSAGVIDDDVLKLIAALVAAESGDARKAIDILRRAGEIAEREG  249 (366)
T ss_pred             HHhhhhhhhccCcceeeeCCCCHHHHHHHHHHHHHhhccCCCcCccHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHhhC
Confidence            3688999999887  789999999999999999874  23347787776665   5568899999999998765     5


Q ss_pred             CCcccHHHHHhhcCCCCHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhcCCChHHHHHHHHHHHH
Q psy879          205 FGHVTAEYVFKVCDEPHPLAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDIIGNIFRVAKTLDIPEPLKLSIIQEIGN  284 (317)
Q Consensus       205 ~~~i~~~~v~~~~~~~~~~~i~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~  284 (317)
                      ...++.+++.++..........+.++.+..++....+.+..-.  ...++..++..+...++.++.   ...++.+++.+
T Consensus       250 ~~~v~~~~v~~a~~~~~~~~~~~~~~~L~~~~ki~L~~i~~~~--~~~~~~~~y~~y~~~~~~~~~---~~~~~~~ii~~  324 (366)
T COG1474         250 SRKVSEDHVREAQEEIERDVLEEVLKTLPLHQKIVLLAIVELT--VEISTGELYDVYESLCERLRT---SQRRFSDIISE  324 (366)
T ss_pred             CCCcCHHHHHHHHHHhhHHHHHHHHHcCCHhHHHHHHHHHHhc--CCCChHHHHHHHHHHHhhhCc---hHHHHHHHHHH
Confidence            6789999999996666666666666666555444433333222  678899999999999987666   56677777777


Q ss_pred             HHh
Q psy879          285 VHL  287 (317)
Q Consensus       285 ~~~  287 (317)
                      ++.
T Consensus       325 L~~  327 (366)
T COG1474         325 LEG  327 (366)
T ss_pred             HHh
Confidence            654

>TIGR01128 holA DNA polymerase III, delta subunit

Probab=99.90  E-value=7.4e-21  Score=166.32  Aligned_cols=253  Identities=15%  Similarity=0.191  Sum_probs=197.1

Q ss_pred             HHHHHHHHcCCCC-CCceEEecCCCCcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCH-HHHHHHHHHhhhccC
Q psy879           48 ILCLARILLGPSF-KDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTD-GAQQALRRTMEIYSN  125 (317)
Q Consensus        48 a~~la~~l~~~~~-~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~-~~~~~ll~~le~~~~  125 (317)
                      +..+++.+....+ ...+..+++. +...+.+.   ......++.   +++++++|++++.+.. ...+.|.++++++++
T Consensus         4 ~~~~~~~~~~~~~~~~~~~~~~~~-e~~~~~l~---~~~~~~slf---~~~kliii~~~~~~~~~~~~~~L~~~l~~~~~   76 (302)
T TIGR01128         4 ADAIRAAALAQGFDEFNVFRIDGE-EFDWNQLL---EEAQTLPLF---SERRLVELRNPEGKPGAKGLKALEEYLANPPP   76 (302)
T ss_pred             HHHHHHHHHhCCCchheeeeeccC-CCCHHHHH---HHhhccCcc---cCCeEEEEECCCCCCCHHHHHHHHHHHhcCCC
Confidence            4445555433322 3344555443 34444433   333333322   6789999999999874 567899999999999


Q ss_pred             CceEEEEecCCCc---CchhHh--hhcceeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHH
Q psy879          126 TTRFALACNNSEK---IIEPIQ--SRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQS  200 (317)
Q Consensus       126 ~~~~il~~~~~~~---l~~~i~--sR~~~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~  200 (317)
                      ++.+|++++..+.   +.+.+.  ++|..+.|.+++..++..|+...++++|+.+++++++.++..++||++.+.+++++
T Consensus        77 ~~~~i~~~~~~~~~~~~~k~~~~~~~~~~i~~~~~~~~~~~~~i~~~~~~~g~~i~~~a~~~l~~~~~~d~~~l~~el~K  156 (302)
T TIGR01128        77 DTLLLIEAPKLDKRKKLTKWLKALKNAQIVECKTPKEQELPRWIQARLKKLGLRIDPDAVQLLAELVEGNLLAIAQELEK  156 (302)
T ss_pred             CEEEEEecCCCCHhHHHHHHHHHhcCeeEEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhCcHHHHHHHHHHH
Confidence            9988888875442   223344  49999999999999999999999999999999999999999999999999999998


Q ss_pred             hhh--CCCcccHHHHHhhcCCCCHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhc---------C
Q psy879          201 THN--GFGHVTAEYVFKVCDEPHPLAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDIIGNIFRVAKTL---------D  269 (317)
Q Consensus       201 ~~~--~~~~i~~~~v~~~~~~~~~~~i~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~~~~---------~  269 (317)
                      .+.  +.+.|+.++|..++....+..++++++++..++...++..++.+...|++|..|+..+.+.+..+         +
T Consensus       157 L~~~~~~~~It~e~I~~~~~~~~~~~if~l~dal~~~~~~~a~~~l~~l~~~~~~~~~il~~l~~~~~~L~~~k~~~~~~  236 (302)
T TIGR01128       157 LALYAPDGKITLEDVEEAVSDSARFNVFDLTDALLEGKAARALRILKGLLGEGEEPLILLALLQRQLRLLLQLKRLAQQG  236 (302)
T ss_pred             HHhhCCCCCCCHHHHHHHHhhhhcCCHHHHHHHHHCCCHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHHHHHHHHHHHcC
Confidence            765  34579999999999988888999999999999999999999999999999998888865543222         2


Q ss_pred             CC--------------------------hHHHHHHHHHHHHHHhHHh-cCC-CcHHHHHHHHHHHH
Q psy879          270 IP--------------------------EPLKLSIIQEIGNVHLRIS-EGV-NSLLQLSGLLARLC  307 (317)
Q Consensus       270 ~~--------------------------~~~~~~~~~~l~~~~~~l~-~g~-~~~l~le~~~~~~~  307 (317)
                      .+                          .....+++..+.++|..+| +|. ++.+.||.++.++|
T Consensus       237 ~~~~~i~~~~~~~~~~~~~~~~~~~~~s~~~L~~~l~~l~~~d~~~K~~~~~~~~~~le~~i~~~~  302 (302)
T TIGR01128       237 GPLAQLASKLGIWPYRRKLALKALRRLSLAKLEQALQELAEADLQLKGTGGGDPWLALERLLLKLA  302 (302)
T ss_pred             CCHHHHHHHcCCCHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHhCcCCCCHHHHHHHHHHHhC
Confidence            11                          1122338999999999999 455 99999999999987

subunit around DNA forming a DNA sliding clamp.

>PRK08084 DNA replication initiation factor; Provisional

Probab=99.89  E-value=1.3e-21  Score=163.97  Aligned_cols=197  Identities=14%  Similarity=0.143  Sum_probs=145.2

Q ss_pred             CCCccc--CCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHHHHHH
Q psy879            8 TFSDIV--GNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMF   85 (317)
Q Consensus         8 ~~~~~~--g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~   85 (317)
                      +|++++  ++..+...+..+......++++||||+|+|||++++++++.+........++..+....    ...+.+..+
T Consensus        20 ~fd~f~~~~n~~a~~~l~~~~~~~~~~~l~l~Gp~G~GKThLl~a~~~~~~~~~~~v~y~~~~~~~~----~~~~~~~~~   95 (235)
T PRK08084         20 TFASFYPGDNDSLLAALQNALRQEHSGYIYLWSREGAGRSHLLHAACAELSQRGRAVGYVPLDKRAW----FVPEVLEGM   95 (235)
T ss_pred             CccccccCccHHHHHHHHHHHhCCCCCeEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEEHHHHhh----hhHHHHHHh
Confidence            588888  47778888888877666667999999999999999999998754332223333322110    111112211


Q ss_pred             HhhcccCCCCceeEEEEeCCCCCCH--HHHHHHHHHhhhc--cCCceEEEEecCC-C---cCchhHhhhc---ceeeecC
Q psy879           86 AQQKVTLPPGRHKIVILDEADSMTD--GAQQALRRTMEIY--SNTTRFALACNNS-E---KIIEPIQSRC---AMLRYNK  154 (317)
Q Consensus        86 ~~~~~~~~~~~~~vliiDE~d~l~~--~~~~~ll~~le~~--~~~~~~il~~~~~-~---~l~~~i~sR~---~~i~f~~  154 (317)
                               ....+++|||++.+..  +.+..|..++...  .++..+|++++.+ .   .+.+.++||+   .++.+.+
T Consensus        96 ---------~~~dlliiDdi~~~~~~~~~~~~lf~l~n~~~e~g~~~li~ts~~~p~~l~~~~~~L~SRl~~g~~~~l~~  166 (235)
T PRK08084         96 ---------EQLSLVCIDNIECIAGDELWEMAIFDLYNRILESGRTRLLITGDRPPRQLNLGLPDLASRLDWGQIYKLQP  166 (235)
T ss_pred             ---------hhCCEEEEeChhhhcCCHHHHHHHHHHHHHHHHcCCCeEEEeCCCChHHcCcccHHHHHHHhCCceeeecC
Confidence                     1235899999999864  4455666666543  2344677877755 2   3679999999   6799999


Q ss_pred             CCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhh----hCCCcccHHHHHhhc
Q psy879          155 LTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTH----NGFGHVTAEYVFKVC  217 (317)
Q Consensus       155 ~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~----~~~~~i~~~~v~~~~  217 (317)
                      |+.+++..++.+.+..+|+.++++++++++..++||+|.+++.++...    .....||.+.+++++
T Consensus       167 ~~~~~~~~~l~~~a~~~~~~l~~~v~~~L~~~~~~d~r~l~~~l~~l~~~~l~~~~~it~~~~k~~l  233 (235)
T PRK08084        167 LSDEEKLQALQLRARLRGFELPEDVGRFLLKRLDREMRTLFMTLDQLDRASITAQRKLTIPFVKEIL  233 (235)
T ss_pred             CCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHH
Confidence            999999999999899899999999999999999999999999998753    135678888776654

>COG1223 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=99.89  E-value=4.4e-22  Score=160.94  Aligned_cols=199  Identities=21%  Similarity=0.254  Sum_probs=144.2

Q ss_pred             CCCCcccCCHHHHHH---HHHHHhcC------CCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCc----
Q psy879            7 QTFSDIVGNEDTVER---LKVFSSSG------NVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDR----   73 (317)
Q Consensus         7 ~~~~~~~g~~~~~~~---l~~~l~~~------~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~----   73 (317)
                      -+|+|++||+++++.   +..++++.      .+.++|||||||||||.+|+++|++.     ..+++.+++....    
T Consensus       118 it~ddViGqEeAK~kcrli~~yLenPe~Fg~WAPknVLFyGppGTGKTm~Akalane~-----kvp~l~vkat~liGehV  192 (368)
T COG1223         118 ITLDDVIGQEEAKRKCRLIMEYLENPERFGDWAPKNVLFYGPPGTGKTMMAKALANEA-----KVPLLLVKATELIGEHV  192 (368)
T ss_pred             ccHhhhhchHHHHHHHHHHHHHhhChHHhcccCcceeEEECCCCccHHHHHHHHhccc-----CCceEEechHHHHHHHh
Confidence            369999999999886   45566542      24569999999999999999999984     4456666654322    


Q ss_pred             --ChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCH------------HHHHHHHHHhhhc--cCCceEEEEecCCC
Q psy879           74 --GIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTD------------GAQQALRRTMEIY--SNTTRFALACNNSE  137 (317)
Q Consensus        74 --~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~------------~~~~~ll~~le~~--~~~~~~il~~~~~~  137 (317)
                        +...+++......+       ..+.|++|||.|.+.-            +..|+|+.-|+..  ...++.|.+||+++
T Consensus       193 Gdgar~Ihely~rA~~-------~aPcivFiDE~DAiaLdRryQelRGDVsEiVNALLTelDgi~eneGVvtIaaTN~p~  265 (368)
T COG1223         193 GDGARRIHELYERARK-------AAPCIVFIDELDAIALDRRYQELRGDVSEIVNALLTELDGIKENEGVVTIAATNRPE  265 (368)
T ss_pred             hhHHHHHHHHHHHHHh-------cCCeEEEehhhhhhhhhhhHHHhcccHHHHHHHHHHhccCcccCCceEEEeecCChh
Confidence              23344444444333       3588999999998642            2478888887744  34577899999999


Q ss_pred             cCchhHhhhcce-eeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCC-CHHHHHHHH------HHhhhCCCccc
Q psy879          138 KIIEPIQSRCAM-LRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQG-DMRQALNNL------QSTHNGFGHVT  209 (317)
Q Consensus       138 ~l~~~i~sR~~~-i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~g-d~r~~i~~l------~~~~~~~~~i~  209 (317)
                      -++++++|||.. |+|..|+.++...++...+++--+.++-. +++++..+.| +-|....-.      ++.+.+...|+
T Consensus       266 ~LD~aiRsRFEeEIEF~LP~~eEr~~ile~y~k~~Plpv~~~-~~~~~~~t~g~SgRdikekvlK~aLh~Ai~ed~e~v~  344 (368)
T COG1223         266 LLDPAIRSRFEEEIEFKLPNDEERLEILEYYAKKFPLPVDAD-LRYLAAKTKGMSGRDIKEKVLKTALHRAIAEDREKVE  344 (368)
T ss_pred             hcCHHHHhhhhheeeeeCCChHHHHHHHHHHHHhCCCccccC-HHHHHHHhCCCCchhHHHHHHHHHHHHHHHhchhhhh
Confidence            999999999998 99999999999999999999877777655 6777776654 333332222      23334566777


Q ss_pred             HHHHHhhcC
Q psy879          210 AEYVFKVCD  218 (317)
Q Consensus       210 ~~~v~~~~~  218 (317)
                      .+++..++.
T Consensus       345 ~edie~al~  353 (368)
T COG1223         345 REDIEKALK  353 (368)
T ss_pred             HHHHHHHHH
Confidence            777765544

>PRK06893 DNA replication initiation factor; Validated

Probab=99.89  E-value=2.7e-21  Score=161.48  Aligned_cols=200  Identities=15%  Similarity=0.180  Sum_probs=140.8

Q ss_pred             CCCCCCcccCCHHHH--HHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHHH
Q psy879            5 RPQTFSDIVGNEDTV--ERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKI   82 (317)
Q Consensus         5 ~P~~~~~~~g~~~~~--~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~   82 (317)
                      .|.+|++++++++..  ..+.........|.++||||||+|||++++++++++.....+..++..+......    .+.+
T Consensus        11 ~~~~fd~f~~~~~~~~~~~~~~~~~~~~~~~l~l~G~~G~GKThL~~ai~~~~~~~~~~~~y~~~~~~~~~~----~~~~   86 (229)
T PRK06893         11 DDETLDNFYADNNLLLLDSLRKNFIDLQQPFFYIWGGKSSGKSHLLKAVSNHYLLNQRTAIYIPLSKSQYFS----PAVL   86 (229)
T ss_pred             CcccccccccCChHHHHHHHHHHhhccCCCeEEEECCCCCCHHHHHHHHHHHHHHcCCCeEEeeHHHhhhhh----HHHH
Confidence            456899999766432  2233333333335589999999999999999999975443334444433211111    1111


Q ss_pred             HHHHhhcccCCCCceeEEEEeCCCCCC--HHHHHHHHHHhhhccC--CceEEEEecCC-C---cCchhHhhhcc---eee
Q psy879           83 KMFAQQKVTLPPGRHKIVILDEADSMT--DGAQQALRRTMEIYSN--TTRFALACNNS-E---KIIEPIQSRCA---MLR  151 (317)
Q Consensus        83 ~~~~~~~~~~~~~~~~vliiDE~d~l~--~~~~~~ll~~le~~~~--~~~~il~~~~~-~---~l~~~i~sR~~---~i~  151 (317)
                      ..+         ....+++|||++.+.  ...+..|+.+++....  .+++|++++.. .   ...+.++||+.   .++
T Consensus        87 ~~~---------~~~dlLilDDi~~~~~~~~~~~~l~~l~n~~~~~~~~illits~~~p~~l~~~~~~L~sRl~~g~~~~  157 (229)
T PRK06893         87 ENL---------EQQDLVCLDDLQAVIGNEEWELAIFDLFNRIKEQGKTLLLISADCSPHALSIKLPDLASRLTWGEIYQ  157 (229)
T ss_pred             hhc---------ccCCEEEEeChhhhcCChHHHHHHHHHHHHHHHcCCcEEEEeCCCChHHccccchhHHHHHhcCCeee
Confidence            111         345799999999885  3345577777775433  34455666653 3   34589999997   699


Q ss_pred             ecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhh----CCCcccHHHHHhhc
Q psy879          152 YNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHN----GFGHVTAEYVFKVC  217 (317)
Q Consensus       152 f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~----~~~~i~~~~v~~~~  217 (317)
                      +++|+.++...++++.+..+++.+++++++++++.++||+|.+++.++....    ..+.||.+.+++++
T Consensus       158 l~~pd~e~~~~iL~~~a~~~~l~l~~~v~~~L~~~~~~d~r~l~~~l~~l~~~~~~~~~~it~~~v~~~L  227 (229)
T PRK06893        158 LNDLTDEQKIIVLQRNAYQRGIELSDEVANFLLKRLDRDMHTLFDALDLLDKASLQAQRKLTIPFVKEIL  227 (229)
T ss_pred             CCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhccCCHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHh
Confidence            9999999999999999999999999999999999999999999999986532    34568888776654

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=99.88  E-value=1.5e-21  Score=166.54  Aligned_cols=190  Identities=19%  Similarity=0.256  Sum_probs=136.0

Q ss_pred             CCCcccCCHHHHHHHHHHHh----------c-----CCCceEEEECCCCCCHHHHHHHHHHHHcCCC--CCCceEEecCC
Q psy879            8 TFSDIVGNEDTVERLKVFSS----------S-----GNVPNIIISGPPGVGKTTTILCLARILLGPS--FKDAVLELNAS   70 (317)
Q Consensus         8 ~~~~~~g~~~~~~~l~~~l~----------~-----~~~~~~ll~G~~G~GKt~la~~la~~l~~~~--~~~~~~~~~~~   70 (317)
                      .+++++|.+.+++.+...+.          .     +..+|++|+||||||||++|+.+++.+....  ....++++++.
T Consensus         4 ~l~~~~Gl~~vk~~i~~~~~~~~~~~~~~~~g~~~~~~~~~vll~GppGtGKTtlA~~ia~~l~~~~~~~~~~~v~~~~~   83 (261)
T TIGR02881         4 ELSRMVGLDEVKALIKEIYAWIQINEKRKEEGLKTSKQVLHMIFKGNPGTGKTTVARILGKLFKEMNVLSKGHLIEVERA   83 (261)
T ss_pred             HHHHhcChHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCcceEEEEcCCCCCHHHHHHHHHHHHHhcCcccCCceEEecHH
Confidence            36789999999988764421          1     2345799999999999999999999874322  12234555443


Q ss_pred             CCcCh--HHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCC--------HHHHHHHHHHhhhccCCceEEEEecCCC---
Q psy879           71 NDRGI--DTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMT--------DGAQQALRRTMEIYSNTTRFALACNNSE---  137 (317)
Q Consensus        71 ~~~~~--~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~--------~~~~~~ll~~le~~~~~~~~il~~~~~~---  137 (317)
                      +..+.  .+....+......      ....|+||||+|.+.        .+.++.|++.|++...+.++|+++....   
T Consensus        84 ~l~~~~~g~~~~~~~~~~~~------a~~~VL~IDE~~~L~~~~~~~~~~~~i~~Ll~~~e~~~~~~~vila~~~~~~~~  157 (261)
T TIGR02881        84 DLVGEYIGHTAQKTREVIKK------ALGGVLFIDEAYSLARGGEKDFGKEAIDTLVKGMEDNRNEFVLILAGYSDEMDY  157 (261)
T ss_pred             HhhhhhccchHHHHHHHHHh------ccCCEEEEechhhhccCCccchHHHHHHHHHHHHhccCCCEEEEecCCcchhHH
Confidence            21110  0001111111111      235699999999875        4567889999998877777777765432   


Q ss_pred             --cCchhHhhhcce-eeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHh----------cCCCHHHHHHHHHHhhh
Q psy879          138 --KIIEPIQSRCAM-LRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFT----------AQGDMRQALNNLQSTHN  203 (317)
Q Consensus       138 --~l~~~i~sR~~~-i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~----------~~gd~r~~i~~l~~~~~  203 (317)
                        .+.|+++|||.. ++|++++.+++.+++...+...+..++++++..+.+.          +.||.|.+.|.++.+..
T Consensus       158 ~~~~~p~L~sRf~~~i~f~~~~~~el~~Il~~~~~~~~~~l~~~a~~~l~~~~~~~~~~~~~~~gn~R~~~n~~e~a~~  236 (261)
T TIGR02881       158 FLSLNPGLRSRFPISIDFPDYTVEELMEIAERMVKEREYKLTEEAKWKLREHLYKVDQLSSREFSNARYVRNIIEKAIR  236 (261)
T ss_pred             HHhcChHHHhccceEEEECCCCHHHHHHHHHHHHHHcCCccCHHHHHHHHHHHHHHHhccCCCCchHHHHHHHHHHHHH
Confidence              467899999954 9999999999999999999998889999998887543          36899999999987643

Members of this protein family are the stage V sporulation protein K (SpoVK), a close homolog of the Rubisco expression protein CbbX (TIGR02880) and a members of the ATPase family associated with various cellular activities (pfam00004). Members are strictly limited to bacterial endospore-forming species, but are not universal in this group and are missing from the Clostridium group.

>TIGR00602 rad24 checkpoint protein rad24

Probab=99.88  E-value=1.2e-21  Score=182.48  Aligned_cols=203  Identities=20%  Similarity=0.299  Sum_probs=134.1

Q ss_pred             CcccCCCCCCcccCCHHHHHHHHHHHhcCCCce-----EEEECCCCCCHHHHHHHHHHHHcCCC--CCCceEEecCCC--
Q psy879            1 IEKYRPQTFSDIVGNEDTVERLKVFSSSGNVPN-----IIISGPPGVGKTTTILCLARILLGPS--FKDAVLELNASN--   71 (317)
Q Consensus         1 ~~ky~P~~~~~~~g~~~~~~~l~~~l~~~~~~~-----~ll~G~~G~GKt~la~~la~~l~~~~--~~~~~~~~~~~~--   71 (317)
                      +|||||+++++++||++.++.+..++.....++     ++|+||+|+||||+++.+++.+...-  +..++......+  
T Consensus        75 ~eKyrP~~ldel~~~~~ki~~l~~~l~~~~~~~~~~~illL~GP~GsGKTTl~~~la~~l~~~~~Ew~npv~~~~~~~~~  154 (637)
T TIGR00602        75 VEKYKPETQHELAVHKKKIEEVETWLKAQVLENAPKRILLITGPSGCGKSTTIKILSKELGIQVQEWSNPTLPDFQKNDH  154 (637)
T ss_pred             HHHhCCCCHHHhcCcHHHHHHHHHHHHhcccccCCCcEEEEECCCCCCHHHHHHHHHHHhhhHHHHHhhhhhhccccccc
Confidence            479999999999999999999999988655433     99999999999999999999864210  000000000000  


Q ss_pred             -------------CcChHHHHHHHHHHHhhcccC---CCCceeEEEEeCCCCCCHHHHHHHHHHhh-h--ccCCceEEEE
Q psy879           72 -------------DRGIDTVRNKIKMFAQQKVTL---PPGRHKIVILDEADSMTDGAQQALRRTME-I--YSNTTRFALA  132 (317)
Q Consensus        72 -------------~~~~~~i~~~~~~~~~~~~~~---~~~~~~vliiDE~d~l~~~~~~~ll~~le-~--~~~~~~~il~  132 (317)
                                   ......+...+..........   ..+.++||+|||++++......++..++. .  ....+.+|++
T Consensus       155 ~~~~s~~~~~~~~~s~~~~F~~fl~~a~~~~~~~g~~~~~~~~IILIDEiPn~~~r~~~~lq~lLr~~~~e~~~~pLI~I  234 (637)
T TIGR00602       155 KVTLSLESCFSNFQSQIEVFSEFLLRATNKLQMLGDDLMTDKKIILVEDLPNQFYRDTRALHEILRWKYVSIGRCPLVFI  234 (637)
T ss_pred             ccchhhhhccccccchHHHHHHHHHHHHhhhcccccccCCceeEEEeecchhhchhhHHHHHHHHHHHhhcCCCceEEEE
Confidence                         011223333333222110000   12568899999998876543223333322 1  1234556666


Q ss_pred             ecCC-C--------cC------chhHhh--hcceeeecCCCHHHHHHHHHHHHHHcCCC------C-CHHHHHHHHHhcC
Q psy879          133 CNNS-E--------KI------IEPIQS--RCAMLRYNKLTDAQLLSKVIEICEKENIS------H-TNDGLEAIVFTAQ  188 (317)
Q Consensus       133 ~~~~-~--------~l------~~~i~s--R~~~i~f~~~~~~~~~~~l~~~~~~~~~~------i-~~~~~~~l~~~~~  188 (317)
                      ++.. .        .+      .+++++  |+..|.|+|++..++.+.|..++..++..      + +++++..++..++
T Consensus       235 ~TE~~~~~~~~~~~~f~~~~lL~~eLls~~rv~~I~FnPia~t~l~K~L~rIl~~E~~~~~~~~~~p~~~~l~~I~~~s~  314 (637)
T TIGR00602       235 ITESLEGDNNQRRLLFPAETIMNKEILEEPRVSNISFNPIAPTIMKKFLNRIVTIEAKKNGEKIKVPKKTSVELLCQGCS  314 (637)
T ss_pred             ecCCccccccccccccchhcccCHhHhcccceeEEEeCCCCHHHHHHHHHHHHHhhhhccccccccCCHHHHHHHHHhCC
Confidence            5531 1        12      278888  55669999999999999999999876432      2 4578999999999


Q ss_pred             CCHHHHHHHHHHhhh
Q psy879          189 GDMRQALNNLQSTHN  203 (317)
Q Consensus       189 gd~r~~i~~l~~~~~  203 (317)
                      ||+|.||+.|+.++.
T Consensus       315 GDiRsAIn~LQf~~~  329 (637)
T TIGR00602       315 GDIRSAINSLQFSSS  329 (637)
T ss_pred             ChHHHHHHHHHHHHh
Confidence            999999999998755

This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>PRK08727 hypothetical protein; Validated

Probab=99.87  E-value=1.6e-20  Score=157.21  Aligned_cols=199  Identities=15%  Similarity=0.241  Sum_probs=141.5

Q ss_pred             CCCCcccCCH-HHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHHHHHH
Q psy879            7 QTFSDIVGNE-DTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMF   85 (317)
Q Consensus         7 ~~~~~~~g~~-~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~   85 (317)
                      .+|+++++.+ .....+.....+.....++|+||+|+|||+++++++..+.....  .+.+++....  ...+.+.+..+
T Consensus        16 ~~f~~f~~~~~n~~~~~~~~~~~~~~~~l~l~G~~G~GKThL~~a~~~~~~~~~~--~~~y~~~~~~--~~~~~~~~~~l   91 (233)
T PRK08727         16 QRFDSYIAAPDGLLAQLQALAAGQSSDWLYLSGPAGTGKTHLALALCAAAEQAGR--SSAYLPLQAA--AGRLRDALEAL   91 (233)
T ss_pred             CChhhccCCcHHHHHHHHHHHhccCCCeEEEECCCCCCHHHHHHHHHHHHHHcCC--cEEEEeHHHh--hhhHHHHHHHH
Confidence            3689888644 44555554444333334999999999999999999998754433  2333332110  11122222221


Q ss_pred             HhhcccCCCCceeEEEEeCCCCCC--HHHHHHHHHHhhhcc-CCceEEEEecCC-C---cCchhHhhh---cceeeecCC
Q psy879           86 AQQKVTLPPGRHKIVILDEADSMT--DGAQQALRRTMEIYS-NTTRFALACNNS-E---KIIEPIQSR---CAMLRYNKL  155 (317)
Q Consensus        86 ~~~~~~~~~~~~~vliiDE~d~l~--~~~~~~ll~~le~~~-~~~~~il~~~~~-~---~l~~~i~sR---~~~i~f~~~  155 (317)
                               ....+|+|||++.+.  +..+..++++++... ....+|++++.+ .   .+.+.++||   |..+.|++|
T Consensus        92 ---------~~~dlLiIDDi~~l~~~~~~~~~lf~l~n~~~~~~~~vI~ts~~~p~~l~~~~~dL~SRl~~~~~~~l~~~  162 (233)
T PRK08727         92 ---------EGRSLVALDGLESIAGQREDEVALFDFHNRARAAGITLLYTARQMPDGLALVLPDLRSRLAQCIRIGLPVL  162 (233)
T ss_pred             ---------hcCCEEEEeCcccccCChHHHHHHHHHHHHHHHcCCeEEEECCCChhhhhhhhHHHHHHHhcCceEEecCC
Confidence                     245699999999885  345667778777532 344588888754 3   357999999   778999999


Q ss_pred             CHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhh----hCCCcccHHHHHhhcC
Q psy879          156 TDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTH----NGFGHVTAEYVFKVCD  218 (317)
Q Consensus       156 ~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~----~~~~~i~~~~v~~~~~  218 (317)
                      +.+++..++..++..+++.+++++++++++.++||+|.+++.++.+.    ...+.||.+.+++++.
T Consensus       163 ~~e~~~~iL~~~a~~~~l~l~~e~~~~La~~~~rd~r~~l~~L~~l~~~~~~~~~~it~~~~~~~l~  229 (233)
T PRK08727        163 DDVARAAVLRERAQRRGLALDEAAIDWLLTHGERELAGLVALLDRLDRESLAAKRRVTVPFLRRVLE  229 (233)
T ss_pred             CHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHh
Confidence            99999999999999999999999999999999999999988887653    2345677777665543

>TIGR02903 spore_lon_C ATP-dependent protease, Lon family

Probab=99.86  E-value=2e-20  Score=176.08  Aligned_cols=219  Identities=24%  Similarity=0.280  Sum_probs=157.9

Q ss_pred             cccCCCCCCcccCCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCC-----CCCceEEecCCCCc-Ch
Q psy879            2 EKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPS-----FKDAVLELNASNDR-GI   75 (317)
Q Consensus         2 ~ky~P~~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~-----~~~~~~~~~~~~~~-~~   75 (317)
                      +.|||.+|++++||+..++.+...+..+.+++++|+|||||||||+|+.+.+......     ....++.+++.... ..
T Consensus       146 ~~~rp~~~~~iiGqs~~~~~l~~~ia~~~~~~vlL~Gp~GtGKTTLAr~i~~~~~~~~~~~~~~~~~fv~i~~~~l~~d~  225 (615)
T TIGR02903       146 SLLRPRAFSEIVGQERAIKALLAKVASPFPQHIILYGPPGVGKTTAARLALEEAKKLKHTPFAEDAPFVEVDGTTLRWDP  225 (615)
T ss_pred             hhcCcCcHHhceeCcHHHHHHHHHHhcCCCCeEEEECCCCCCHHHHHHHHHHhhhhccCCcccCCCCeEEEechhccCCH
Confidence            5799999999999999999988888777777899999999999999999988753211     12346666654321 11


Q ss_pred             HHHHHH-HH------------HHHhh------cccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhcc------------
Q psy879           76 DTVRNK-IK------------MFAQQ------KVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYS------------  124 (317)
Q Consensus        76 ~~i~~~-~~------------~~~~~------~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~------------  124 (317)
                      ..+... ++            .+...      ...+......+++|||++.|....|+.|++.+++..            
T Consensus       226 ~~i~~~llg~~~~~~~~~a~~~l~~~gl~~~~~g~v~~asgGvL~LDEi~~Ld~~~Q~~Ll~~Le~~~v~~~~~~~~~~~  305 (615)
T TIGR02903       226 REVTNPLLGSVHDPIYQGARRDLAETGVPEPKTGLVTDAHGGVLFIDEIGELDPLLQNKLLKVLEDKRVEFSSSYYDPDD  305 (615)
T ss_pred             HHHhHHhcCCccHHHHHHHHHHHHHcCCCchhcCchhhcCCCeEEEeccccCCHHHHHHHHHHHhhCeEEeecceeccCC
Confidence            111100 00            00000      000111345799999999999999999999998521            


Q ss_pred             --------------C--CceEEEE-ecCCCcCchhHhhhcceeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhc
Q psy879          125 --------------N--TTRFALA-CNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTA  187 (317)
Q Consensus       125 --------------~--~~~~il~-~~~~~~l~~~i~sR~~~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~  187 (317)
                                    .  ..++|.+ ++++..+.++++|||..+.|++++.+++..++...+.+.++.+++++++.+...+
T Consensus       306 ~~~~~~ik~~~~~~~~~~~VLI~aTt~~~~~l~~aLrSR~~~i~~~pls~edi~~Il~~~a~~~~v~ls~eal~~L~~ys  385 (615)
T TIGR02903       306 PNVPKYIKKLFEEGAPADFVLIGATTRDPEEINPALRSRCAEVFFEPLTPEDIALIVLNAAEKINVHLAAGVEELIARYT  385 (615)
T ss_pred             cccchhhhhhcccCccceEEEEEeccccccccCHHHHhceeEEEeCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHCC
Confidence                          1  1233333 3456788999999999999999999999999999999888889999888888876


Q ss_pred             CCCHHHHHHHHHHhhh-------------CCCcccHHHHHhhcCCCC
Q psy879          188 QGDMRQALNNLQSTHN-------------GFGHVTAEYVFKVCDEPH  221 (317)
Q Consensus       188 ~gd~r~~i~~l~~~~~-------------~~~~i~~~~v~~~~~~~~  221 (317)
                      . +.|++++.|+.+..             ....|+.+++.+++....
T Consensus       386 ~-~gRraln~L~~~~~~~~~~~~~~~~~~~~~~I~~edv~~~l~~~r  431 (615)
T TIGR02903       386 I-EGRKAVNILADVYGYALYRAAEAGKENDKVTITQDDVYEVIQISR  431 (615)
T ss_pred             C-cHHHHHHHHHHHHHHHHHHHHHhccCCCCeeECHHHHHHHhCCCc
Confidence            5 77999999865421             112578888888777654

Members of this protein family resemble the widely distributed ATP-dependent protease La, also called Lon and LonA. It resembles even more closely LonB, which is a LonA paralog found in genomes if and only if the species is capable of endospore formation (as in Bacillus subtilis, Clostridium tetani, and select other members of the Firmicutes) and expressed specifically in the forespore compartment. Members of this family are restricted to a subset of spore-forming species, and are very likely to participate in the program of endospore formation. We propose the designation LonC.

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=99.86  E-value=3.4e-20  Score=155.21  Aligned_cols=199  Identities=15%  Similarity=0.183  Sum_probs=148.3

Q ss_pred             cCCCCCCccc--CCHHHHHHHHHHHhcC-CCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHH
Q psy879            4 YRPQTFSDIV--GNEDTVERLKVFSSSG-NVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRN   80 (317)
Q Consensus         4 y~P~~~~~~~--g~~~~~~~l~~~l~~~-~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~   80 (317)
                      -+|.+|++++  ++..+...+..+.... ...+++|+||+|+|||++++++++......  ..+..+++....      .
T Consensus        12 ~~~~~~d~f~~~~~~~~~~~l~~~~~~~~~~~~~~l~G~~G~GKT~La~ai~~~~~~~~--~~~~~i~~~~~~------~   83 (227)
T PRK08903         12 PPPPTFDNFVAGENAELVARLRELAAGPVADRFFYLWGEAGSGRSHLLQALVADASYGG--RNARYLDAASPL------L   83 (227)
T ss_pred             CChhhhcccccCCcHHHHHHHHHHHhccCCCCeEEEECCCCCCHHHHHHHHHHHHHhCC--CcEEEEehHHhH------H
Confidence            3567899998  3567777888877633 334699999999999999999999874433  234444432211      1


Q ss_pred             HHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCC--ceEEEEecCCC---cCchhHhhhc---ceeee
Q psy879           81 KIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNT--TRFALACNNSE---KIIEPIQSRC---AMLRY  152 (317)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~--~~~il~~~~~~---~l~~~i~sR~---~~i~f  152 (317)
                      .+.   .      .....+++|||++.+....+..|+.+++.....  ..++++++.+.   .+.+.+.||+   ..+++
T Consensus        84 ~~~---~------~~~~~~liiDdi~~l~~~~~~~L~~~~~~~~~~~~~~vl~~~~~~~~~~~l~~~L~sr~~~~~~i~l  154 (227)
T PRK08903         84 AFD---F------DPEAELYAVDDVERLDDAQQIALFNLFNRVRAHGQGALLVAGPAAPLALPLREDLRTRLGWGLVYEL  154 (227)
T ss_pred             HHh---h------cccCCEEEEeChhhcCchHHHHHHHHHHHHHHcCCcEEEEeCCCCHHhCCCCHHHHHHHhcCeEEEe
Confidence            111   0      134679999999999988899999999764433  23555555332   4568889996   56999


Q ss_pred             cCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhh----hCCCcccHHHHHhhcCC
Q psy879          153 NKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTH----NGFGHVTAEYVFKVCDE  219 (317)
Q Consensus       153 ~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~----~~~~~i~~~~v~~~~~~  219 (317)
                      +++++++...++.+.+..+++.+++++++.+++.+.||+|++.+.++...    ...+.|+...+++++..
T Consensus       155 ~pl~~~~~~~~l~~~~~~~~v~l~~~al~~L~~~~~gn~~~l~~~l~~l~~~~~~~~~~i~~~~~~~~l~~  225 (227)
T PRK08903        155 KPLSDADKIAALKAAAAERGLQLADEVPDYLLTHFRRDMPSLMALLDALDRYSLEQKRPVTLPLLREMLAQ  225 (227)
T ss_pred             cCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhccCCHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHhc
Confidence            99999999999999888899999999999999999999999988887643    35578898888776653

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=99.85  E-value=5.1e-20  Score=154.23  Aligned_cols=199  Identities=14%  Similarity=0.225  Sum_probs=145.9

Q ss_pred             CCCCCCcccC--CHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHHH
Q psy879            5 RPQTFSDIVG--NEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKI   82 (317)
Q Consensus         5 ~P~~~~~~~g--~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~   82 (317)
                      .|.+|+++++  +.++++.++.++.....++++|+||+|||||++++++++......  ..++.+++....  ....+.+
T Consensus        10 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~lll~G~~G~GKT~la~~~~~~~~~~~--~~~~~i~~~~~~--~~~~~~~   85 (226)
T TIGR03420        10 DDPTFDNFYAGGNAELLAALRQLAAGKGDRFLYLWGESGSGKSHLLQAACAAAEERG--KSAIYLPLAELA--QADPEVL   85 (226)
T ss_pred             CchhhcCcCcCCcHHHHHHHHHHHhcCCCCeEEEECCCCCCHHHHHHHHHHHHHhcC--CcEEEEeHHHHH--HhHHHHH
Confidence            4567899984  677899999987766666799999999999999999999875332  234445443211  1111111


Q ss_pred             HHHHhhcccCCCCceeEEEEeCCCCCCHHH--HHHHHHHhhhcc-CCceEEEEecCCC-c--C-chhHhhhcc---eeee
Q psy879           83 KMFAQQKVTLPPGRHKIVILDEADSMTDGA--QQALRRTMEIYS-NTTRFALACNNSE-K--I-IEPIQSRCA---MLRY  152 (317)
Q Consensus        83 ~~~~~~~~~~~~~~~~vliiDE~d~l~~~~--~~~ll~~le~~~-~~~~~il~~~~~~-~--l-~~~i~sR~~---~i~f  152 (317)
                      ..+         ....+++|||++.+....  ++.|..+++... ....+|++++... .  . .+.+.+|+.   .+.+
T Consensus        86 ~~~---------~~~~lLvIDdi~~l~~~~~~~~~L~~~l~~~~~~~~~iIits~~~~~~~~~~~~~L~~r~~~~~~i~l  156 (226)
T TIGR03420        86 EGL---------EQADLVCLDDVEAIAGQPEWQEALFHLYNRVREAGGRLLIAGRAAPAQLPLRLPDLRTRLAWGLVFQL  156 (226)
T ss_pred             hhc---------ccCCEEEEeChhhhcCChHHHHHHHHHHHHHHHcCCeEEEECCCChHHCCcccHHHHHHHhcCeeEec
Confidence            111         234699999999997644  788888777532 3346777776532 2  2 378899974   5999


Q ss_pred             cCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhh----hCCCcccHHHHHhh
Q psy879          153 NKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTH----NGFGHVTAEYVFKV  216 (317)
Q Consensus       153 ~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~----~~~~~i~~~~v~~~  216 (317)
                      ++++.++...++...+.+.++.+++++++.++..++||+|.+.+.++.+.    ...+.|+.+.+.++
T Consensus       157 ~~l~~~e~~~~l~~~~~~~~~~~~~~~l~~L~~~~~gn~r~L~~~l~~~~~~~~~~~~~i~~~~~~~~  224 (226)
T TIGR03420       157 PPLSDEEKIAALQSRAARRGLQLPDEVADYLLRHGSRDMGSLMALLDALDRASLAAKRKITIPFVKEV  224 (226)
T ss_pred             CCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhccCCHHHHHHHHHHHHHHHHHhCCCCCHHHHHHH
Confidence            99999999999999888889999999999999999999999999987633    24567888777654

Members of this protein family are Hda (Homologous to DnaA). These proteins are about half the length of DnaA and homologous over length of Hda. In the model species Escherichia coli, the initiation of DNA replication requires DnaA bound to ATP rather than ADP; Hda helps facilitate the conversion of DnaA-ATP to DnaA-ADP.

>PRK06581 DNA polymerase III subunit delta'; Validated

Probab=99.84  E-value=3.5e-19  Score=144.02  Aligned_cols=176  Identities=15%  Similarity=0.125  Sum_probs=138.9

Q ss_pred             HHHHHHHHhcCCCce-EEEECCCC-CCHHHHHHHHHHHHcCCCC----CCceEEecCC-------CCcChHHHHHHHHHH
Q psy879           19 VERLKVFSSSGNVPN-IIISGPPG-VGKTTTILCLARILLGPSF----KDAVLELNAS-------NDRGIDTVRNKIKMF   85 (317)
Q Consensus        19 ~~~l~~~l~~~~~~~-~ll~G~~G-~GKt~la~~la~~l~~~~~----~~~~~~~~~~-------~~~~~~~i~~~~~~~   85 (317)
                      +..+...++++++.| |||.|..+ +||..++..+++.+.|...    ...+..+.+.       ...+++++|+....+
T Consensus         2 ~~~L~~~iq~~kLshAYLfeG~n~~~~~~~~~~f~~~~l~~~~i~~~~HPD~~~I~pe~~~~~~~~~I~IdqIReL~~~l   81 (263)
T PRK06581          2 IERLEFNLKHNKLYNSWLIEAENIEQALKDLEKFIYIKLFKNSIPLENNPDYHFIARETSATSNAKNISIEQIRKLQDFL   81 (263)
T ss_pred             hHHHHHHHHcCcchheeeEeCCChhhHHHHHHHHHHHHHhccCcccCCCCCEEEEeccccccccCCcccHHHHHHHHHHH
Confidence            457888999999999 99999998 9999999999998876421    1223333322       357889999988887


Q ss_pred             HhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcCchhHhhhcceeeecCCCHHHHHHHHH
Q psy879           86 AQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVI  165 (317)
Q Consensus        86 ~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~~~i~sR~~~i~f~~~~~~~~~~~l~  165 (317)
                      ...+.   .++++|++|+++|.|+..+.|+||+++||||+++.||++|+++..++++|+|||+.+.|+.++.....++..
T Consensus        82 ~~~p~---~g~~KViII~~ae~mt~~AANALLKtLEEPP~~t~fILit~~~~~LLpTIrSRCq~i~~~~p~~~~~~e~~~  158 (263)
T PRK06581         82 SKTSA---ISGYKVAIIYSAELMNLNAANSCLKILEDAPKNSYIFLITSRAASIISTIRSRCFKINVRSSILHAYNELYS  158 (263)
T ss_pred             hhCcc---cCCcEEEEEechHHhCHHHHHHHHHhhcCCCCCeEEEEEeCChhhCchhHhhceEEEeCCCCCHHHHHHHHH
Confidence            77763   379999999999999999999999999999999999999999999999999999999999999988888776


Q ss_pred             HHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHH
Q psy879          166 EICEKENISHTNDGLEAIVFTAQGDMRQALNNLQS  200 (317)
Q Consensus       166 ~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~  200 (317)
                      ..+..   ..+...++.+.+...-|....+...+.
T Consensus       159 ~~~~p---~~~~~~l~~i~~~~~~d~~~w~~~~~~  190 (263)
T PRK06581        159 QFIQP---IADNKTLDFINRFTTKDRELWLDFIDN  190 (263)
T ss_pred             Hhccc---ccccHHHHHHHHHhhhhHHHHHHHHHH
Confidence            65432   123445666666655555544444433

>CHL00181 cbbX CbbX; Provisional

Probab=99.84  E-value=2.5e-19  Score=153.82  Aligned_cols=188  Identities=21%  Similarity=0.232  Sum_probs=132.1

Q ss_pred             CcccCCHHHHHHHHHHHh----------c-----CCCceEEEECCCCCCHHHHHHHHHHHHcCCC--CCCceEEecCCCC
Q psy879           10 SDIVGNEDTVERLKVFSS----------S-----GNVPNIIISGPPGVGKTTTILCLARILLGPS--FKDAVLELNASND   72 (317)
Q Consensus        10 ~~~~g~~~~~~~l~~~l~----------~-----~~~~~~ll~G~~G~GKt~la~~la~~l~~~~--~~~~~~~~~~~~~   72 (317)
                      .+++|.+.+++.+..++.          .     +...|++|+||||||||++|+++++.+....  ....+++++..+.
T Consensus        23 ~~l~Gl~~vK~~i~e~~~~~~~~~~~~~~g~~~~~~~~~ill~G~pGtGKT~lAr~la~~~~~~g~~~~~~~~~v~~~~l  102 (287)
T CHL00181         23 EELVGLAPVKTRIREIAALLLIDRLRKNLGLTSSNPGLHMSFTGSPGTGKTTVALKMADILYKLGYIKKGHLLTVTRDDL  102 (287)
T ss_pred             HhcCCcHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCCceEEEECCCCCCHHHHHHHHHHHHHHcCCCCCCceEEecHHHH
Confidence            379999999887765531          1     1233699999999999999999999874322  1223555553221


Q ss_pred             cCh--HHHHHHHHHHHhhcccCCCCceeEEEEeCCCCC---------CHHHHHHHHHHhhhccCCceEEEEecCCC----
Q psy879           73 RGI--DTVRNKIKMFAQQKVTLPPGRHKIVILDEADSM---------TDGAQQALRRTMEIYSNTTRFALACNNSE----  137 (317)
Q Consensus        73 ~~~--~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l---------~~~~~~~ll~~le~~~~~~~~il~~~~~~----  137 (317)
                      .+.  .............      ..+.|+||||++.+         ..+.++.|++.|+....++++|++++...    
T Consensus       103 ~~~~~g~~~~~~~~~l~~------a~ggVLfIDE~~~l~~~~~~~~~~~e~~~~L~~~me~~~~~~~vI~ag~~~~~~~~  176 (287)
T CHL00181        103 VGQYIGHTAPKTKEVLKK------AMGGVLFIDEAYYLYKPDNERDYGSEAIEILLQVMENQRDDLVVIFAGYKDRMDKF  176 (287)
T ss_pred             HHHHhccchHHHHHHHHH------ccCCEEEEEccchhccCCCccchHHHHHHHHHHHHhcCCCCEEEEEeCCcHHHHHH
Confidence            000  0000001111111      24579999999986         45678899999998877888888775421    


Q ss_pred             -cCchhHhhhcce-eeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHh--------cCCCHHHHHHHHHHhhh
Q psy879          138 -KIIEPIQSRCAM-LRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFT--------AQGDMRQALNNLQSTHN  203 (317)
Q Consensus       138 -~l~~~i~sR~~~-i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~--------~~gd~r~~i~~l~~~~~  203 (317)
                       ...|+++|||.. +.|++++.+++..++...+++.+..+++++...+...        ..||.|.+.+.++.+..
T Consensus       177 ~~~np~L~sR~~~~i~F~~~t~~el~~I~~~~l~~~~~~l~~~~~~~L~~~i~~~~~~~~~GNaR~vrn~ve~~~~  252 (287)
T CHL00181        177 YESNPGLSSRIANHVDFPDYTPEELLQIAKIMLEEQQYQLTPEAEKALLDYIKKRMEQPLFANARSVRNALDRARM  252 (287)
T ss_pred             HhcCHHHHHhCCceEEcCCcCHHHHHHHHHHHHHHhcCCCChhHHHHHHHHHHHhCCCCCCccHHHHHHHHHHHHH
Confidence             345999999986 9999999999999999999999988998877665543        34889999999987543

>COG1222 RPT1 ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones]

Probab=99.83  E-value=5e-19  Score=149.67  Aligned_cols=197  Identities=18%  Similarity=0.284  Sum_probs=141.3

Q ss_pred             CCCCcccCCHHHHHHHHHHHhc-----------C-CCce-EEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCC--
Q psy879            7 QTFSDIVGNEDTVERLKVFSSS-----------G-NVPN-IIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASN--   71 (317)
Q Consensus         7 ~~~~~~~g~~~~~~~l~~~l~~-----------~-~~~~-~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~--   71 (317)
                      .+++++=|-++.++.++..++-           | .+|. +|+|||||||||.+|+++|+..     +..|+.+.++.  
T Consensus       148 vtY~dIGGL~~Qi~EirE~VELPL~~PElF~~~GI~PPKGVLLYGPPGTGKTLLAkAVA~~T-----~AtFIrvvgSElV  222 (406)
T COG1222         148 VTYEDIGGLDEQIQEIREVVELPLKNPELFEELGIDPPKGVLLYGPPGTGKTLLAKAVANQT-----DATFIRVVGSELV  222 (406)
T ss_pred             CChhhccCHHHHHHHHHHHhcccccCHHHHHHcCCCCCCceEeeCCCCCcHHHHHHHHHhcc-----CceEEEeccHHHH
Confidence            3688999999999999888752           2 2343 9999999999999999999984     34466666543  


Q ss_pred             ----CcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCC-----------HHHHHHHHHHhhh-----ccCCceEEE
Q psy879           72 ----DRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMT-----------DGAQQALRRTMEI-----YSNTTRFAL  131 (317)
Q Consensus        72 ----~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~-----------~~~~~~ll~~le~-----~~~~~~~il  131 (317)
                          ..+..-+|+.+.....       ..+.||||||+|...           .+.|..++++|.+     +..++.+|+
T Consensus       223 qKYiGEGaRlVRelF~lAre-------kaPsIIFiDEIDAIg~kR~d~~t~gDrEVQRTmleLL~qlDGFD~~~nvKVI~  295 (406)
T COG1222         223 QKYIGEGARLVRELFELARE-------KAPSIIFIDEIDAIGAKRFDSGTSGDREVQRTMLELLNQLDGFDPRGNVKVIM  295 (406)
T ss_pred             HHHhccchHHHHHHHHHHhh-------cCCeEEEEechhhhhcccccCCCCchHHHHHHHHHHHHhccCCCCCCCeEEEE
Confidence                2344556666665543       358899999999873           2457778777763     567899999


Q ss_pred             EecCCCcCchhHhhhcce---eeecCCCHHHHHHHHHHHHHHcCCCCCH-HHHHHHHHhcCC----CHHHHHHHHHHhhh
Q psy879          132 ACNNSEKIIEPIQSRCAM---LRYNKLTDAQLLSKVIEICEKENISHTN-DGLEAIVFTAQG----DMRQALNNLQSTHN  203 (317)
Q Consensus       132 ~~~~~~~l~~~i~sR~~~---i~f~~~~~~~~~~~l~~~~~~~~~~i~~-~~~~~l~~~~~g----d~r~~i~~l~~~~~  203 (317)
                      +||.++-++|++.+-+..   |+|+.|+.+...++++-+.++-.+  ++ -.++.++..+.|    +++.+-.+.-..+.
T Consensus       296 ATNR~D~LDPALLRPGR~DRkIEfplPd~~gR~~Il~IHtrkM~l--~~dvd~e~la~~~~g~sGAdlkaictEAGm~Ai  373 (406)
T COG1222         296 ATNRPDILDPALLRPGRFDRKIEFPLPDEEGRAEILKIHTRKMNL--ADDVDLELLARLTEGFSGADLKAICTEAGMFAI  373 (406)
T ss_pred             ecCCccccChhhcCCCcccceeecCCCCHHHHHHHHHHHhhhccC--ccCcCHHHHHHhcCCCchHHHHHHHHHHhHHHH
Confidence            999999999999876655   999999999999999988876443  33 336777777654    33322222211221


Q ss_pred             --CCCcccHHHHHhhc
Q psy879          204 --GFGHVTAEYVFKVC  217 (317)
Q Consensus       204 --~~~~i~~~~v~~~~  217 (317)
                        ....++.++..+++
T Consensus       374 R~~R~~Vt~~DF~~Av  389 (406)
T COG1222         374 RERRDEVTMEDFLKAV  389 (406)
T ss_pred             HhccCeecHHHHHHHH
Confidence              55678887765543

>PRK05642 DNA replication initiation factor; Validated

Probab=99.81  E-value=2.6e-18  Score=143.77  Aligned_cols=197  Identities=15%  Similarity=0.198  Sum_probs=137.4

Q ss_pred             CCCcccC--CHHHHHHHHHHHhc--C-CCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHHH
Q psy879            8 TFSDIVG--NEDTVERLKVFSSS--G-NVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKI   82 (317)
Q Consensus         8 ~~~~~~g--~~~~~~~l~~~l~~--~-~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~   82 (317)
                      +|++++.  +..+.+.+..+..+  + ..++++|+||+|+|||++++++++++....  ..+++++..+...  .....+
T Consensus        17 tfdnF~~~~~~~a~~~~~~~~~~~~~~~~~~l~l~G~~G~GKTHLl~a~~~~~~~~~--~~v~y~~~~~~~~--~~~~~~   92 (234)
T PRK05642         17 TFANYYPGANAAALGYVERLCEADAGWTESLIYLWGKDGVGRSHLLQAACLRFEQRG--EPAVYLPLAELLD--RGPELL   92 (234)
T ss_pred             cccccCcCChHHHHHHHHHHhhccccCCCCeEEEECCCCCCHHHHHHHHHHHHHhCC--CcEEEeeHHHHHh--hhHHHH
Confidence            6898883  23334445444332  1 224589999999999999999998875332  2334443321110  011111


Q ss_pred             HHHHhhcccCCCCceeEEEEeCCCCCC--HHHHHHHHHHhhhccC-CceEEEEecCC-C---cCchhHhhhc---ceeee
Q psy879           83 KMFAQQKVTLPPGRHKIVILDEADSMT--DGAQQALRRTMEIYSN-TTRFALACNNS-E---KIIEPIQSRC---AMLRY  152 (317)
Q Consensus        83 ~~~~~~~~~~~~~~~~vliiDE~d~l~--~~~~~~ll~~le~~~~-~~~~il~~~~~-~---~l~~~i~sR~---~~i~f  152 (317)
                      ..+         ....+++|||++.+.  +..+..|+.+++.... ...+|++++.+ .   ...+.++||+   ..+.+
T Consensus        93 ~~~---------~~~d~LiiDDi~~~~~~~~~~~~Lf~l~n~~~~~g~~ilits~~~p~~l~~~~~~L~SRl~~gl~~~l  163 (234)
T PRK05642         93 DNL---------EQYELVCLDDLDVIAGKADWEEALFHLFNRLRDSGRRLLLAASKSPRELPIKLPDLKSRLTLALVFQM  163 (234)
T ss_pred             Hhh---------hhCCEEEEechhhhcCChHHHHHHHHHHHHHHhcCCEEEEeCCCCHHHcCccCccHHHHHhcCeeeec
Confidence            111         234589999999885  3456778888875433 45677776643 2   3479999999   66999


Q ss_pred             cCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhh----CCCcccHHHHHhhc
Q psy879          153 NKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHN----GFGHVTAEYVFKVC  217 (317)
Q Consensus       153 ~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~----~~~~i~~~~v~~~~  217 (317)
                      .+++.++...+++.++...++.+++++++++++.++||+|.+.+.++....    ..+.||...+++++
T Consensus       164 ~~~~~e~~~~il~~ka~~~~~~l~~ev~~~L~~~~~~d~r~l~~~l~~l~~~~l~~~~~it~~~~~~~L  232 (234)
T PRK05642        164 RGLSDEDKLRALQLRASRRGLHLTDEVGHFILTRGTRSMSALFDLLERLDQASLQAQRKLTIPFLKETL  232 (234)
T ss_pred             CCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHcCCcCCHHHHHHHh
Confidence            999999999999988888899999999999999999999999999876532    34678887776654

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=99.81  E-value=1.7e-18  Score=148.79  Aligned_cols=187  Identities=20%  Similarity=0.258  Sum_probs=133.7

Q ss_pred             cccCCHHHHHHHHHHHh----------cCC----C-ceEEEECCCCCCHHHHHHHHHHHHcCCCC--CCceEEecCCCCc
Q psy879           11 DIVGNEDTVERLKVFSS----------SGN----V-PNIIISGPPGVGKTTTILCLARILLGPSF--KDAVLELNASNDR   73 (317)
Q Consensus        11 ~~~g~~~~~~~l~~~l~----------~~~----~-~~~ll~G~~G~GKt~la~~la~~l~~~~~--~~~~~~~~~~~~~   73 (317)
                      +++|.+++++.+...+.          .|-    + .|++|+||||||||++|+++++.+...+.  ...++.+++.+..
T Consensus        23 ~l~Gl~~vk~~i~e~~~~~~~~~~r~~~g~~~~~~~~~vll~G~pGTGKT~lA~~ia~~l~~~g~~~~~~~v~v~~~~l~  102 (284)
T TIGR02880        23 ELIGLKPVKTRIREIAALLLVERLRQRLGLASAAPTLHMSFTGNPGTGKTTVALRMAQILHRLGYVRKGHLVSVTRDDLV  102 (284)
T ss_pred             hccCHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCCCceEEEEcCCCCCHHHHHHHHHHHHHHcCCcccceEEEecHHHHh
Confidence            68999999888765421          121    1 26999999999999999999998853322  2245555542211


Q ss_pred             Ch--HHHHHHHHHHHhhcccCCCCceeEEEEeCCCCC---------CHHHHHHHHHHhhhccCCceEEEEecCC--C---
Q psy879           74 GI--DTVRNKIKMFAQQKVTLPPGRHKIVILDEADSM---------TDGAQQALRRTMEIYSNTTRFALACNNS--E---  137 (317)
Q Consensus        74 ~~--~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l---------~~~~~~~ll~~le~~~~~~~~il~~~~~--~---  137 (317)
                      +.  ......+......      ..+.+++|||++.+         ..+.++.|++.|+....++++|++++..  +   
T Consensus       103 ~~~~g~~~~~~~~~~~~------a~~gvL~iDEi~~L~~~~~~~~~~~~~~~~Ll~~le~~~~~~~vI~a~~~~~~~~~~  176 (284)
T TIGR02880       103 GQYIGHTAPKTKEILKR------AMGGVLFIDEAYYLYRPDNERDYGQEAIEILLQVMENQRDDLVVILAGYKDRMDSFF  176 (284)
T ss_pred             HhhcccchHHHHHHHHH------ccCcEEEEechhhhccCCCccchHHHHHHHHHHHHhcCCCCEEEEEeCCcHHHHHHH
Confidence            00  0000011111111      23579999999987         2456889999999887788888877643  2   


Q ss_pred             cCchhHhhhcce-eeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHh--------cCCCHHHHHHHHHHhhh
Q psy879          138 KIIEPIQSRCAM-LRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFT--------AQGDMRQALNNLQSTHN  203 (317)
Q Consensus       138 ~l~~~i~sR~~~-i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~--------~~gd~r~~i~~l~~~~~  203 (317)
                      .+.|+++|||.. ++|++++.+++..++...+++.+..+++++...+...        ..||.|.+.|.++.+..
T Consensus       177 ~~np~L~sR~~~~i~fp~l~~edl~~I~~~~l~~~~~~l~~~a~~~L~~~l~~~~~~~~~GN~R~lrn~ve~~~~  251 (284)
T TIGR02880       177 ESNPGFSSRVAHHVDFPDYSEAELLVIAGLMLKEQQYRFSAEAEEAFADYIALRRTQPHFANARSIRNAIDRARL  251 (284)
T ss_pred             hhCHHHHhhCCcEEEeCCcCHHHHHHHHHHHHHHhccccCHHHHHHHHHHHHHhCCCCCCChHHHHHHHHHHHHH
Confidence            347999999975 9999999999999999999998888999988877654        46999999999987644

Proteins in this family are now designated CbbX. Some previously were CfxQ (carbon fixation Q). Its gene is often found immmediately downstream of the Rubisco large and small chain genes, and it is suggested to be necessary for Rubisco expression. CbbX has been shown to be necessary for photoautotrophic growth. This protein belongs to the larger family of pfam00004, ATPase family Associated with various cellular Activities. Within that larger family, members of this family are most closely related to the stage V sporulation protein K, or SpoVK, in endospore-forming bacteria such as Bacillus subtilis.

>COG1466 HolA DNA polymerase III, delta subunit [DNA replication, recombination, and repair]

Probab=99.80  E-value=1.2e-16  Score=140.97  Aligned_cols=280  Identities=13%  Similarity=0.210  Sum_probs=205.2

Q ss_pred             HHHHHhcC-CCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHHHHHHHhhcccCCCCceeEE
Q psy879           22 LKVFSSSG-NVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIV  100 (317)
Q Consensus        22 l~~~l~~~-~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~vl  100 (317)
                      +...+.++ ..|.|++||+.---....+..+................... ......+   +......+.+   ++.+++
T Consensus         6 ~~~~l~~~~~~~v~ll~G~d~~l~~e~~~~i~~~~~~~~~~~~~~~~~~~-~~~~~~~---~~~~~s~~lF---~~~~~v   78 (334)
T COG1466           6 LAKHLKKKNLMPVYLLYGEDEGLLEEAADAILKRALADGFDENYSFFDDS-ELDWADL---LSELESPSLF---GEKRLV   78 (334)
T ss_pred             HHHHHhcCCCccEEEEecCChhHHHHHHHHHHHHHhccchhhHHhhcccc-cCCHHHH---HHHhhccccc---cCCeeE
Confidence            34445554 45569999999666666666666655322222222221111 2222222   3332233322   567899


Q ss_pred             EEeCCCCCC-HHHHHHHHHHhhhcc-CCceEEEEecCCC---cCchhHhhh--cceeeecCCCHHHHHHHHHHHHHHcCC
Q psy879          101 ILDEADSMT-DGAQQALRRTMEIYS-NTTRFALACNNSE---KIIEPIQSR--CAMLRYNKLTDAQLLSKVIEICEKENI  173 (317)
Q Consensus       101 iiDE~d~l~-~~~~~~ll~~le~~~-~~~~~il~~~~~~---~l~~~i~sR--~~~i~f~~~~~~~~~~~l~~~~~~~~~  173 (317)
                      .|..++... .+....+......+| ..+.+++..+..+   +..+.+.+-  +.++.+.+++..++.+|+..+++..|+
T Consensus        79 ~l~~~~~~~~~~~~~~l~~~~~~~p~~~~~l~~~~~kl~~~~~~~k~~~~~~~~~~~~~~~~~~~~l~~~i~~~~~~~~l  158 (334)
T COG1466          79 VLKNAEKKPNKDKNLALLELAALLPSTDLLLLVESNKLDKAKKLTKWLKKLAKAVVVECKPLDEAELPQWIKKRAKELGL  158 (334)
T ss_pred             EEECCCCCcCchhHHHHHHHHcCCCCCCEEEEEecCCcchHHHHHHHHHHhccCceEecCCCCHHHHHHHHHHHHHHcCC
Confidence            999998875 455556666666666 5554555554443   233333333  558999999999999999999999999


Q ss_pred             CCCHHHHHHHHHhcCCCHHHHHHHHHHhhh--CCCcccHHHHHhhcCCCCHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC
Q psy879          174 SHTNDGLEAIVFTAQGDMRQALNNLQSTHN--GFGHVTAEYVFKVCDEPHPLAVKEMLLNCVEGNMKDSYKIIHHLYKLG  251 (317)
Q Consensus       174 ~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~--~~~~i~~~~v~~~~~~~~~~~i~~l~~~~~~~~~~~~~~~~~~l~~~~  251 (317)
                      .+++++++.++...+||++.+.+++++.+.  ..+.|+.++|..++.......+|++++++..++..+++..+++|...|
T Consensus       159 ~i~~~a~~~L~~~~~~nl~~i~~Ei~KL~l~~~~~~I~~~~V~~~v~~~~~~~~f~l~dail~g~~~~a~~~l~~L~~~g  238 (334)
T COG1466         159 KIDQEAIQLLLEALGGNLLAIAQEIEKLALYAGDKEITLEDVEEVVSDVAEFNIFDLADALLKGDVKKALRLLRDLLLEG  238 (334)
T ss_pred             CCCHHHHHHHHHHhCCcHHHHHHHHHHHHHhCCCCcCCHHHHHHHHhccccCCHHHHHHHHHCCCHHHHHHHHHHHHHcC
Confidence            999999999999999999999999998766  334899999999999998889999999999999999999999999999


Q ss_pred             CCHHHHHHHHHHHHHhc---------C--------------------------CChHHHHHHHHHHHHHHhHHhcCC-Cc
Q psy879          252 YAPEDIIGNIFRVAKTL---------D--------------------------IPEPLKLSIIQEIGNVHLRISEGV-NS  295 (317)
Q Consensus       252 ~~~~~i~~~~~~~~~~~---------~--------------------------~~~~~~~~~~~~l~~~~~~l~~g~-~~  295 (317)
                      ++|..|+..+.+.+..+         |                          ++.....++++.+.++|..+|+|. ++
T Consensus       239 e~p~~il~~l~~~f~~~~~l~~~~~~g~~~~~~~~~l~~~~~~~~~~~~~~~r~s~~~l~~~l~~l~~~d~~~K~~~~d~  318 (334)
T COG1466         239 EEPLKLLAALTRQFRLLLQLKALAEKGKSLQQAAKSLGIPYRRKKLFKKAARRLSLKQLLKALRLLAQLDYQIKTGYGDP  318 (334)
T ss_pred             CcHHHHHHHHHHHHHHHHHHHHHHHcCcCHHHHHHHhcCcHHHHHHHHHHHHHcCHHHHHHHHHHHHHHHHHHhcCCccc
Confidence            99999998876654322         1                          333344458899999999999999 89


Q ss_pred             HHHHHHHHHHHHH
Q psy879          296 LLQLSGLLARLCI  308 (317)
Q Consensus       296 ~l~le~~~~~~~~  308 (317)
                      ...++.++.+++.
T Consensus       319 ~~~l~~~l~~~~~  331 (334)
T COG1466         319 VWALELFLLRLLE  331 (334)
T ss_pred             hHHHHHHHHHHhh
Confidence            9999999999874

>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA

Probab=99.80  E-value=1.4e-18  Score=167.81  Aligned_cols=211  Identities=17%  Similarity=0.220  Sum_probs=153.5

Q ss_pred             cccCCCCCCcccCCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCC-----CCceEEecCCCC----
Q psy879            2 EKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSF-----KDAVLELNASND----   72 (317)
Q Consensus         2 ~ky~P~~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~-----~~~~~~~~~~~~----   72 (317)
                      ++.||..+++++|+++.++.+...+..+..+|.+|+||||+|||++++.+|+.+.....     +..++.++....    
T Consensus       174 ~~~r~~~l~~~igr~~ei~~~~~~L~~~~~~n~lL~G~pG~GKT~l~~~la~~~~~~~~p~~l~~~~~~~~~~~~l~a~~  253 (731)
T TIGR02639       174 EKAKNGKIDPLIGREDELERTIQVLCRRKKNNPLLVGEPGVGKTAIAEGLALRIAEGKVPENLKNAKIYSLDMGSLLAGT  253 (731)
T ss_pred             HHHhcCCCCcccCcHHHHHHHHHHHhcCCCCceEEECCCCCCHHHHHHHHHHHHHhCCCchhhcCCeEEEecHHHHhhhc
Confidence            56799999999999999999988888888788999999999999999999998743221     234555553211    


Q ss_pred             cChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCH---------HHHHHHHHHhhhccCCceEEEEecCC-----Cc
Q psy879           73 RGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTD---------GAQQALRRTMEIYSNTTRFALACNNS-----EK  138 (317)
Q Consensus        73 ~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~---------~~~~~ll~~le~~~~~~~~il~~~~~-----~~  138 (317)
                      ....++.+.+..+.....   ...+.|+||||+|.+..         +.++.|...++.  +...+|.+|+..     ..
T Consensus       254 ~~~g~~e~~l~~i~~~~~---~~~~~ILfiDEih~l~~~g~~~~~~~~~~~~L~~~l~~--g~i~~IgaTt~~e~~~~~~  328 (731)
T TIGR02639       254 KYRGDFEERLKAVVSEIE---KEPNAILFIDEIHTIVGAGATSGGSMDASNLLKPALSS--GKLRCIGSTTYEEYKNHFE  328 (731)
T ss_pred             cccchHHHHHHHHHHHHh---ccCCeEEEEecHHHHhccCCCCCccHHHHHHHHHHHhC--CCeEEEEecCHHHHHHHhh
Confidence            111122233333322210   12467999999998852         346778888874  567788888863     25


Q ss_pred             CchhHhhhcceeeecCCCHHHHHHHHHHHHHH----cCCCCCHHHHHHHHHhcCC---C---HHHHHHHHHHhhhC----
Q psy879          139 IIEPIQSRCAMLRYNKLTDAQLLSKVIEICEK----ENISHTNDGLEAIVFTAQG---D---MRQALNNLQSTHNG----  204 (317)
Q Consensus       139 l~~~i~sR~~~i~f~~~~~~~~~~~l~~~~~~----~~~~i~~~~~~~l~~~~~g---d---~r~~i~~l~~~~~~----  204 (317)
                      .++++.+||+.+.+++|+.++...+|+.....    .++.++++++..++..++.   +   +++|+++++.++..    
T Consensus       329 ~d~al~rRf~~i~v~~p~~~~~~~il~~~~~~~e~~~~v~i~~~al~~~~~ls~ryi~~r~~P~kai~lld~a~a~~~~~  408 (731)
T TIGR02639       329 KDRALSRRFQKIDVGEPSIEETVKILKGLKEKYEEFHHVKYSDEALEAAVELSARYINDRFLPDKAIDVIDEAGASFRLR  408 (731)
T ss_pred             hhHHHHHhCceEEeCCCCHHHHHHHHHHHHHHHHhccCcccCHHHHHHHHHhhhcccccccCCHHHHHHHHHhhhhhhcC
Confidence            78999999999999999999999999976554    4678999999999887743   3   88899999876541    


Q ss_pred             -----CCcccHHHHHhhc
Q psy879          205 -----FGHVTAEYVFKVC  217 (317)
Q Consensus       205 -----~~~i~~~~v~~~~  217 (317)
                           ...++.+++..++
T Consensus       409 ~~~~~~~~v~~~~i~~~i  426 (731)
T TIGR02639       409 PKAKKKANVSVKDIENVV  426 (731)
T ss_pred             cccccccccCHHHHHHHH
Confidence                 2347777776643

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=99.80  E-value=2.1e-17  Score=151.58  Aligned_cols=204  Identities=16%  Similarity=0.208  Sum_probs=142.6

Q ss_pred             CCCccc-C--CHHHHHHHHHHHhcC--CCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHHH
Q psy879            8 TFSDIV-G--NEDTVERLKVFSSSG--NVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKI   82 (317)
Q Consensus         8 ~~~~~~-g--~~~~~~~l~~~l~~~--~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~   82 (317)
                      +|++++ |  +..+......+..+.  ..+.++||||+|+|||++++++++.+.....+..++++++...  ...+...+
T Consensus       120 tfd~fv~g~~n~~a~~~~~~~~~~~~~~~~~l~l~G~~G~GKThL~~ai~~~~~~~~~~~~v~yi~~~~~--~~~~~~~~  197 (450)
T PRK00149        120 TFDNFVVGKSNRLAHAAALAVAENPGKAYNPLFIYGGVGLGKTHLLHAIGNYILEKNPNAKVVYVTSEKF--TNDFVNAL  197 (450)
T ss_pred             cccccccCCCcHHHHHHHHHHHhCcCccCCeEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEEEHHHH--HHHHHHHH
Confidence            588866 3  344566666666542  2345999999999999999999999865433445555554321  11111111


Q ss_pred             -----HHHHhhcccCCCCceeEEEEeCCCCCCH--HHHHHHHHHhhhcc-CCceEEEEecCCC----cCchhHhhhcc--
Q psy879           83 -----KMFAQQKVTLPPGRHKIVILDEADSMTD--GAQQALRRTMEIYS-NTTRFALACNNSE----KIIEPIQSRCA--  148 (317)
Q Consensus        83 -----~~~~~~~~~~~~~~~~vliiDE~d~l~~--~~~~~ll~~le~~~-~~~~~il~~~~~~----~l~~~i~sR~~--  148 (317)
                           ..+...-     ....+++|||++.+..  ..+..|+.+++... ....+|++++.+.    .+.+.++||+.  
T Consensus       198 ~~~~~~~~~~~~-----~~~dlLiiDDi~~l~~~~~~~~~l~~~~n~l~~~~~~iiits~~~p~~l~~l~~~l~SRl~~g  272 (450)
T PRK00149        198 RNNTMEEFKEKY-----RSVDVLLIDDIQFLAGKERTQEEFFHTFNALHEAGKQIVLTSDRPPKELPGLEERLRSRFEWG  272 (450)
T ss_pred             HcCcHHHHHHHH-----hcCCEEEEehhhhhcCCHHHHHHHHHHHHHHHHCCCcEEEECCCCHHHHHHHHHHHHhHhcCC
Confidence                 1111110     2456999999999854  35677777776432 2344677776542    36789999995  


Q ss_pred             -eeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhh----CCCcccHHHHHhhcC
Q psy879          149 -MLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHN----GFGHVTAEYVFKVCD  218 (317)
Q Consensus       149 -~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~----~~~~i~~~~v~~~~~  218 (317)
                       .+.|.+|+.+++..+|...+...++.++++++++++..++||+|.+...|..+..    ....|+.+.+.+++.
T Consensus       273 l~v~i~~pd~~~r~~il~~~~~~~~~~l~~e~l~~ia~~~~~~~R~l~~~l~~l~~~~~~~~~~it~~~~~~~l~  347 (450)
T PRK00149        273 LTVDIEPPDLETRIAILKKKAEEEGIDLPDEVLEFIAKNITSNVRELEGALNRLIAYASLTGKPITLELAKEALK  347 (450)
T ss_pred             eeEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHcCcCCCHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHH
Confidence             5999999999999999999999999999999999999999999998777765432    456688887766554

>PRK06620 hypothetical protein; Validated

Probab=99.80  E-value=1.1e-17  Score=137.81  Aligned_cols=182  Identities=13%  Similarity=0.201  Sum_probs=126.2

Q ss_pred             CCCcccC---CHHHHHHHHHHHhc-C-CC--ceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHH
Q psy879            8 TFSDIVG---NEDTVERLKVFSSS-G-NV--PNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRN   80 (317)
Q Consensus         8 ~~~~~~g---~~~~~~~l~~~l~~-~-~~--~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~   80 (317)
                      +|++++-   +..+...+..+.+. + .+  +.++||||||+|||++++++++...     ..+  ..... . .   .+
T Consensus        14 tfd~Fvvg~~N~~a~~~~~~~~~~~~~~~~~~~l~l~Gp~G~GKThLl~a~~~~~~-----~~~--~~~~~-~-~---~~   81 (214)
T PRK06620         14 HPDEFIVSSSNDQAYNIIKNWQCGFGVNPYKFTLLIKGPSSSGKTYLTKIWQNLSN-----AYI--IKDIF-F-N---EE   81 (214)
T ss_pred             CchhhEecccHHHHHHHHHHHHHccccCCCcceEEEECCCCCCHHHHHHHHHhccC-----CEE--cchhh-h-c---hh
Confidence            5777773   45677777777653 2 22  4599999999999999999887631     111  11110 0 0   00


Q ss_pred             HHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhcc-CCceEEEEecC-CC--cCchhHhhhcc---eeeec
Q psy879           81 KIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYS-NTTRFALACNN-SE--KIIEPIQSRCA---MLRYN  153 (317)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~-~~~~~il~~~~-~~--~l~~~i~sR~~---~i~f~  153 (317)
                          +.        ....+++|||++.+...   .|..+++... ....++++++. +.  .+ +.++||+.   ++.+.
T Consensus        82 ----~~--------~~~d~lliDdi~~~~~~---~lf~l~N~~~e~g~~ilits~~~p~~l~l-~~L~SRl~~gl~~~l~  145 (214)
T PRK06620         82 ----IL--------EKYNAFIIEDIENWQEP---ALLHIFNIINEKQKYLLLTSSDKSRNFTL-PDLSSRIKSVLSILLN  145 (214)
T ss_pred             ----HH--------hcCCEEEEeccccchHH---HHHHHHHHHHhcCCEEEEEcCCCccccch-HHHHHHHhCCceEeeC
Confidence                00        23468999999977543   3433333211 22345555543 22  34 99999998   79999


Q ss_pred             CCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhh----CCCcccHHHHHhhc
Q psy879          154 KLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHN----GFGHVTAEYVFKVC  217 (317)
Q Consensus       154 ~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~----~~~~i~~~~v~~~~  217 (317)
                      +|+.+++..++.+.+...++.++++++++++..++||+|.+++.++....    ..+.||.+.+++++
T Consensus       146 ~pd~~~~~~~l~k~~~~~~l~l~~ev~~~L~~~~~~d~r~l~~~l~~l~~~~~~~~~~it~~~~~~~l  213 (214)
T PRK06620        146 SPDDELIKILIFKHFSISSVTISRQIIDFLLVNLPREYSKIIEILENINYFALISKRKITISLVKEVL  213 (214)
T ss_pred             CCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHccCCHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHh
Confidence            99999999999999998899999999999999999999999999987432    34567877766543

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=99.79  E-value=1.2e-16  Score=145.48  Aligned_cols=208  Identities=16%  Similarity=0.249  Sum_probs=145.3

Q ss_pred             CCCCCccc-CC--HHHHHHHHHHHhc-CC-CceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcC--hHHH
Q psy879            6 PQTFSDIV-GN--EDTVERLKVFSSS-GN-VPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRG--IDTV   78 (317)
Q Consensus         6 P~~~~~~~-g~--~~~~~~l~~~l~~-~~-~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~--~~~i   78 (317)
                      +-+|+.++ |.  ..+......+..+ |. .+.++|||++|+|||++++++++.+.....+..++++++.....  ...+
T Consensus       111 ~~tFdnFv~g~~n~~A~~aa~~~a~~~~~~~npl~i~G~~G~GKTHLl~Ai~~~l~~~~~~~~v~yv~~~~f~~~~~~~l  190 (450)
T PRK14087        111 ENTFENFVIGSSNEQAFIAVQTVSKNPGISYNPLFIYGESGMGKTHLLKAAKNYIESNFSDLKVSYMSGDEFARKAVDIL  190 (450)
T ss_pred             ccchhcccCCCcHHHHHHHHHHHHhCcCcccCceEEECCCCCcHHHHHHHHHHHHHHhCCCCeEEEEEHHHHHHHHHHHH
Confidence            35788887 33  3345555555553 22 34599999999999999999999875433344555555432100  0111


Q ss_pred             HH---HHHHHHhhcccCCCCceeEEEEeCCCCCC--HHHHHHHHHHhhhcc-CCceEEEEecCCC----cCchhHhhhcc
Q psy879           79 RN---KIKMFAQQKVTLPPGRHKIVILDEADSMT--DGAQQALRRTMEIYS-NTTRFALACNNSE----KIIEPIQSRCA  148 (317)
Q Consensus        79 ~~---~~~~~~~~~~~~~~~~~~vliiDE~d~l~--~~~~~~ll~~le~~~-~~~~~il~~~~~~----~l~~~i~sR~~  148 (317)
                      ..   .+..+...     .....+++|||++.+.  ...++.|..+++... ....+|++++.+.    .+.+.+.||+.
T Consensus       191 ~~~~~~~~~~~~~-----~~~~dvLiIDDiq~l~~k~~~~e~lf~l~N~~~~~~k~iIltsd~~P~~l~~l~~rL~SR~~  265 (450)
T PRK14087        191 QKTHKEIEQFKNE-----ICQNDVLIIDDVQFLSYKEKTNEIFFTIFNNFIENDKQLFFSSDKSPELLNGFDNRLITRFN  265 (450)
T ss_pred             HHhhhHHHHHHHH-----hccCCEEEEeccccccCCHHHHHHHHHHHHHHHHcCCcEEEECCCCHHHHhhccHHHHHHHh
Confidence            11   11111111     1346699999999986  556788888887543 3345788877653    46789999987


Q ss_pred             e---eeecCCCHHHHHHHHHHHHHHcCC--CCCHHHHHHHHHhcCCCHHHHHHHHHHhhh----C--CCcccHHHHHhhc
Q psy879          149 M---LRYNKLTDAQLLSKVIEICEKENI--SHTNDGLEAIVFTAQGDMRQALNNLQSTHN----G--FGHVTAEYVFKVC  217 (317)
Q Consensus       149 ~---i~f~~~~~~~~~~~l~~~~~~~~~--~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~----~--~~~i~~~~v~~~~  217 (317)
                      .   +.+.+|+.++...+|...++..|+  .++++++++|+..++||+|.+.+.|..+..    .  ...|+.+.+.+++
T Consensus       266 ~Gl~~~L~~pd~e~r~~iL~~~~~~~gl~~~l~~evl~~Ia~~~~gd~R~L~gaL~~l~~~a~~~~~~~~it~~~v~~~l  345 (450)
T PRK14087        266 MGLSIAIQKLDNKTATAIIKKEIKNQNIKQEVTEEAINFISNYYSDDVRKIKGSVSRLNFWSQQNPEEKIITIEIVSDLF  345 (450)
T ss_pred             CCceeccCCcCHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHccCCCHHHHHHHHHHHHHHHhcccCCCCCCHHHHHHHH
Confidence            4   999999999999999999998885  699999999999999999999999976532    2  2578888887765


Q ss_pred             C
Q psy879          218 D  218 (317)
Q Consensus       218 ~  218 (317)
                      .
T Consensus       346 ~  346 (450)
T PRK14087        346 R  346 (450)
T ss_pred             h
Confidence            4

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=99.78  E-value=2e-16  Score=143.91  Aligned_cols=206  Identities=13%  Similarity=0.197  Sum_probs=140.9

Q ss_pred             CCCccc-CCH--HHHHHHHHHHhc-CCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcC--hHHHH-H
Q psy879            8 TFSDIV-GNE--DTVERLKVFSSS-GNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRG--IDTVR-N   80 (317)
Q Consensus         8 ~~~~~~-g~~--~~~~~l~~~l~~-~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~--~~~i~-~   80 (317)
                      +|++++ |..  .+......+..+ |.+++++||||+|+|||++++++++.+.....+..++++++.+...  ...++ +
T Consensus       103 tFdnFv~g~~n~~a~~~~~~~~~~~~~~n~l~lyG~~G~GKTHLl~ai~~~l~~~~~~~~v~yi~~~~f~~~~~~~~~~~  182 (440)
T PRK14088        103 TFENFVVGPGNSFAYHAALEVAKNPGRYNPLFIYGGVGLGKTHLLQSIGNYVVQNEPDLRVMYITSEKFLNDLVDSMKEG  182 (440)
T ss_pred             cccccccCCchHHHHHHHHHHHhCcCCCCeEEEEcCCCCcHHHHHHHHHHHHHHhCCCCeEEEEEHHHHHHHHHHHHhcc
Confidence            588888 533  334445555543 3344699999999999999999999986544444555555432100  00010 0


Q ss_pred             HHHHHHhhcccCCCCceeEEEEeCCCCCCH--HHHHHHHHHhhhcc-CCceEEEEecCC-C---cCchhHhhhcc---ee
Q psy879           81 KIKMFAQQKVTLPPGRHKIVILDEADSMTD--GAQQALRRTMEIYS-NTTRFALACNNS-E---KIIEPIQSRCA---ML  150 (317)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~vliiDE~d~l~~--~~~~~ll~~le~~~-~~~~~il~~~~~-~---~l~~~i~sR~~---~i  150 (317)
                      ....+....    .....+++|||++.+..  ..+..|+.+++... ....+|++++.. .   .+.+.+.||+.   .+
T Consensus       183 ~~~~f~~~~----~~~~dvLlIDDi~~l~~~~~~q~elf~~~n~l~~~~k~iIitsd~~p~~l~~l~~rL~SR~~~gl~v  258 (440)
T PRK14088        183 KLNEFREKY----RKKVDVLLIDDVQFLIGKTGVQTELFHTFNELHDSGKQIVICSDREPQKLSEFQDRLVSRFQMGLVA  258 (440)
T ss_pred             cHHHHHHHH----HhcCCEEEEechhhhcCcHHHHHHHHHHHHHHHHcCCeEEEECCCCHHHHHHHHHHHhhHHhcCceE
Confidence            011111110    02467999999998853  34667777776433 234566666543 2   46788999997   59


Q ss_pred             eecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhh----CCCcccHHHHHhhc
Q psy879          151 RYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHN----GFGHVTAEYVFKVC  217 (317)
Q Consensus       151 ~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~----~~~~i~~~~v~~~~  217 (317)
                      .+.+|+.+....++++.+..+++.++++++++++..+.||+|.+...+.....    ....++.+.+.+++
T Consensus       259 ~i~~pd~e~r~~IL~~~~~~~~~~l~~ev~~~Ia~~~~~~~R~L~g~l~~l~~~~~~~~~~it~~~a~~~L  329 (440)
T PRK14088        259 KLEPPDEETRKKIARKMLEIEHGELPEEVLNFVAENVDDNLRRLRGAIIKLLVYKETTGEEVDLKEAILLL  329 (440)
T ss_pred             eeCCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHhccccCHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHH
Confidence            99999999999999999999999999999999999999999998888876432    45678887776544

>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH

Probab=99.78  E-value=1.3e-17  Score=154.61  Aligned_cols=200  Identities=18%  Similarity=0.235  Sum_probs=135.2

Q ss_pred             CCCCCcccCCHHHHHHHHHHHh-----------cCCCc-eEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCC-
Q psy879            6 PQTFSDIVGNEDTVERLKVFSS-----------SGNVP-NIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASND-   72 (317)
Q Consensus         6 P~~~~~~~g~~~~~~~l~~~l~-----------~~~~~-~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~-   72 (317)
                      +.+|+++.|++++++.+..++.           ...+| ++|||||||||||++++++|.+.     +.+++.++++.. 
T Consensus        51 ~~~~~di~g~~~~k~~l~~~~~~l~~~~~~~~~g~~~~~giLL~GppGtGKT~la~alA~~~-----~~~~~~i~~~~~~  125 (495)
T TIGR01241        51 KVTFKDVAGIDEAKEELMEIVDFLKNPSKFTKLGAKIPKGVLLVGPPGTGKTLLAKAVAGEA-----GVPFFSISGSDFV  125 (495)
T ss_pred             CCCHHHhCCHHHHHHHHHHHHHHHHCHHHHHhcCCCCCCcEEEECCCCCCHHHHHHHHHHHc-----CCCeeeccHHHHH
Confidence            3479999999999887766543           13333 49999999999999999999985     234555554321 


Q ss_pred             -----cChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHH--------------HHHHHHHHhhhcc--CCceEEE
Q psy879           73 -----RGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDG--------------AQQALRRTMEIYS--NTTRFAL  131 (317)
Q Consensus        73 -----~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~--------------~~~~ll~~le~~~--~~~~~il  131 (317)
                           .+...++..+.....       ..+.||+|||+|.+...              ..+.|+..|+...  ..+.+|.
T Consensus       126 ~~~~g~~~~~l~~~f~~a~~-------~~p~Il~iDEid~l~~~r~~~~~~~~~~~~~~~~~lL~~~d~~~~~~~v~vI~  198 (495)
T TIGR01241       126 EMFVGVGASRVRDLFEQAKK-------NAPCIIFIDEIDAVGRQRGAGLGGGNDEREQTLNQLLVEMDGFGTNTGVIVIA  198 (495)
T ss_pred             HHHhcccHHHHHHHHHHHHh-------cCCCEEEEechhhhhhccccCcCCccHHHHHHHHHHHhhhccccCCCCeEEEE
Confidence                 122334444443322       34679999999987432              2445666665432  3567888


Q ss_pred             EecCCCcCchhHhh--hcce-eeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcC----CCHHHHHHHHHHhh--
Q psy879          132 ACNNSEKIIEPIQS--RCAM-LRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQ----GDMRQALNNLQSTH--  202 (317)
Q Consensus       132 ~~~~~~~l~~~i~s--R~~~-i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~----gd~r~~i~~l~~~~--  202 (317)
                      +||.++.+++++.+  |+.. +.++.|+.++..+++...+...... ++..+..++..+.    +|++.+++.....+  
T Consensus       199 aTn~~~~ld~al~r~gRfd~~i~i~~Pd~~~R~~il~~~l~~~~~~-~~~~l~~la~~t~G~sgadl~~l~~eA~~~a~~  277 (495)
T TIGR01241       199 ATNRPDVLDPALLRPGRFDRQVVVDLPDIKGREEILKVHAKNKKLA-PDVDLKAVARRTPGFSGADLANLLNEAALLAAR  277 (495)
T ss_pred             ecCChhhcCHHHhcCCcceEEEEcCCCCHHHHHHHHHHHHhcCCCC-cchhHHHHHHhCCCCCHHHHHHHHHHHHHHHHH
Confidence            89999999999987  5654 9999999999999999887654432 2344667777654    45555555432211  


Q ss_pred             hCCCcccHHHHHhhcC
Q psy879          203 NGFGHVTAEYVFKVCD  218 (317)
Q Consensus       203 ~~~~~i~~~~v~~~~~  218 (317)
                      .+...|+.+++..++.
T Consensus       278 ~~~~~i~~~~l~~a~~  293 (495)
T TIGR01241       278 KNKTEITMNDIEEAID  293 (495)
T ss_pred             cCCCCCCHHHHHHHHH
Confidence            2456789998877554

HflB(FtsH) is a pleiotropic protein required for correct cell division in bacteria. It has ATP-dependent zinc metalloprotease activity. It was formerly designated cell division protein FtsH.

>KOG1970|consensus

Probab=99.78  E-value=3.2e-17  Score=145.57  Aligned_cols=239  Identities=16%  Similarity=0.266  Sum_probs=149.0

Q ss_pred             CcccCCCCCCcccCCHHHHHHHHHHHh-----cCCCce--EEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEec-C---
Q psy879            1 IEKYRPQTFSDIVGNEDTVERLKVFSS-----SGNVPN--IIISGPPGVGKTTTILCLARILLGPSFKDAVLELN-A---   69 (317)
Q Consensus         1 ~~ky~P~~~~~~~g~~~~~~~l~~~l~-----~~~~~~--~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~-~---   69 (317)
                      +|||+|.+.+++--|+.-+..++.|++     ..++++  +|++||+||||||+++.+++++. ..    +.+.. +   
T Consensus        73 ~eKy~P~t~eeLAVHkkKI~eVk~WL~~~~~~~~~l~~~iLLltGPsGcGKSTtvkvLskelg-~~----~~Ew~Npi~~  147 (634)
T KOG1970|consen   73 VEKYKPRTLEELAVHKKKISEVKQWLKQVAEFTPKLGSRILLLTGPSGCGKSTTVKVLSKELG-YQ----LIEWSNPINL  147 (634)
T ss_pred             HHhcCcccHHHHhhhHHhHHHHHHHHHHHHHhccCCCceEEEEeCCCCCCchhHHHHHHHhhC-ce----eeeecCCccc
Confidence            589999999999999988888888887     666665  89999999999999999999973 21    22211 1   


Q ss_pred             ---------CCCcC---hHHHHHHHHHHHhhc-----c----cCCCCceeEEEEeCCCCCCHH-HHHHHHHHhhh---cc
Q psy879           70 ---------SNDRG---IDTVRNKIKMFAQQK-----V----TLPPGRHKIVILDEADSMTDG-AQQALRRTMEI---YS  124 (317)
Q Consensus        70 ---------~~~~~---~~~i~~~~~~~~~~~-----~----~~~~~~~~vliiDE~d~l~~~-~~~~ll~~le~---~~  124 (317)
                               +...+   ..++. .++.|....     .    .-..+++++++|||....... ....|...|..   .+
T Consensus       148 ~~~~~~h~~t~~~~~~~~s~L~-~fesFler~~kyg~l~~~g~~~~~~~~liLveDLPn~~~~d~~~~f~evL~~y~s~g  226 (634)
T KOG1970|consen  148 KEPENLHNETSFLMFPYQSQLA-VFESFLLRATKYGSLQMSGDDLRTDKKLILVEDLPNQFYRDDSETFREVLRLYVSIG  226 (634)
T ss_pred             cccccccccchhcccchhhHHH-HHHHHHHHHHhhchhhhcccccccCceEEEeeccchhhhhhhHHHHHHHHHHHHhcC
Confidence                     00111   11111 112222111     0    011246779999999887644 33333333332   22


Q ss_pred             CCceEEEEecCCC--------cCchhHhhhcc--eeeecCCCHHHHHHHHHHHHHHcCCCCC------HHHHHHHHHhcC
Q psy879          125 NTTRFALACNNSE--------KIIEPIQSRCA--MLRYNKLTDAQLLSKVIEICEKENISHT------NDGLEAIVFTAQ  188 (317)
Q Consensus       125 ~~~~~il~~~~~~--------~l~~~i~sR~~--~i~f~~~~~~~~~~~l~~~~~~~~~~i~------~~~~~~l~~~~~  188 (317)
                      ....++++|+...        .+...+.-++.  .|.|+|..+.-+++.|..+|..++...+      ...++.++..++
T Consensus       227 ~~PlIf~iTd~~~~g~nnq~rlf~~d~q~~~ri~~IsFNPIa~T~MKK~L~ric~~e~~~~s~~k~~~~~~v~~i~~~s~  306 (634)
T KOG1970|consen  227 RCPLIFIITDSLSNGNNNQDRLFPKDIQEEPRISNISFNPIAPTIMKKFLKRICRIEANKKSGIKVPDTAEVELICQGSG  306 (634)
T ss_pred             CCcEEEEEeccccCCCcchhhhchhhhhhccCcceEeecCCcHHHHHHHHHHHHHHhcccccCCcCchhHHHHHHHHhcC
Confidence            2223444443321        34555555444  4999999999999999999999887776      566889999999


Q ss_pred             CCHHHHHHHHHHhhh-CCCcc--------cHHHHHhhcCCCCHHHHHHHHHHHhcCCHHHHHHHHHHH
Q psy879          189 GDMRQALNNLQSTHN-GFGHV--------TAEYVFKVCDEPHPLAVKEMLLNCVEGNMKDSYKIIHHL  247 (317)
Q Consensus       189 gd~r~~i~~l~~~~~-~~~~i--------~~~~v~~~~~~~~~~~i~~l~~~~~~~~~~~~~~~~~~l  247 (317)
                      ||+|.||+.||..+. +.-.+        ..+++...-....+....+.++.+..+|  +.+...+.+
T Consensus       307 GDIRsAInsLQlssskg~~~~~~~ks~rs~~s~~~kg~~~~~~s~~nq~i~~ig~~d--e~L~~f~al  372 (634)
T KOG1970|consen  307 GDIRSAINSLQLSSSKGENNLRPRKSGRSGKSDIGKGKSKRMESPENQELQSIGGRD--ESLFLFRAL  372 (634)
T ss_pred             ccHHHHHhHhhhhcccCccCCCcccccccccchhhccccccccCchHHHHHHhhcch--HHHHHHHhh
Confidence            999999999998743 21111        1222222222222222334666666655  455555544

>PF03215 Rad17: Rad17 cell cycle checkpoint protein

Probab=99.78  E-value=1.5e-17  Score=152.56  Aligned_cols=198  Identities=22%  Similarity=0.339  Sum_probs=128.2

Q ss_pred             CcccCCCCCCcccCCHHHHHHHHHHHhcC---CC--ceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEe-cCCC---
Q psy879            1 IEKYRPQTFSDIVGNEDTVERLKVFSSSG---NV--PNIIISGPPGVGKTTTILCLARILLGPSFKDAVLEL-NASN---   71 (317)
Q Consensus         1 ~~ky~P~~~~~~~g~~~~~~~l~~~l~~~---~~--~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~-~~~~---   71 (317)
                      +|||+|++.+|++.+++-++.++.|++..   ..  ..++|+||+||||||+++.+|+++.. .    +.+. ++..   
T Consensus        10 ~~ky~P~~~~eLavhkkKv~eV~~wl~~~~~~~~~~~iLlLtGP~G~GKtttv~~La~elg~-~----v~Ew~np~~~~~   84 (519)
T PF03215_consen   10 VEKYAPKTLDELAVHKKKVEEVRSWLEEMFSGSSPKRILLLTGPSGCGKTTTVKVLAKELGF-E----VQEWINPVSFRE   84 (519)
T ss_pred             chhcCCCCHHHhhccHHHHHHHHHHHHHHhccCCCcceEEEECCCCCCHHHHHHHHHHHhCC-e----eEEecCCCCccc
Confidence            58999999999999998888888887642   22  23899999999999999999999732 1    2211 1110   


Q ss_pred             -------Cc----ChHHHH---HHHHHHHhh--cc-cC------CCCceeEEEEeCCCCCCHHHHHHHHHH----hhhcc
Q psy879           72 -------DR----GIDTVR---NKIKMFAQQ--KV-TL------PPGRHKIVILDEADSMTDGAQQALRRT----MEIYS  124 (317)
Q Consensus        72 -------~~----~~~~i~---~~~~~~~~~--~~-~~------~~~~~~vliiDE~d~l~~~~~~~ll~~----le~~~  124 (317)
                             ..    ..+...   +.+..+...  .. .+      .....+||+|||..+........|...    +....
T Consensus        85 ~~~~~~d~~s~~~~~~~f~sq~~~F~~f~l~~s~y~~l~~~g~~~~~~~kvILVEDlPN~~~~~~~~f~~~L~~~l~~~~  164 (519)
T PF03215_consen   85 SDNQEDDFESDFNKFDEFLSQSDKFSEFLLRASKYSSLSMSGSNSSSNKKVILVEDLPNVFHRDTSRFREALRQYLRSSR  164 (519)
T ss_pred             cccccccccccccccccccchhhhhccccccccccccccccCCCcCCCceEEEeeccccccchhHHHHHHHHHHHHHcCC
Confidence                   00    000001   112222111  00 00      124689999999998765443444444    44323


Q ss_pred             C-CceEEEEe-cC------CC--------cCchhHhhhc--ceeeecCCCHHHHHHHHHHHHHHc-----CC-CCC--HH
Q psy879          125 N-TTRFALAC-NN------SE--------KIIEPIQSRC--AMLRYNKLTDAQLLSKVIEICEKE-----NI-SHT--ND  178 (317)
Q Consensus       125 ~-~~~~il~~-~~------~~--------~l~~~i~sR~--~~i~f~~~~~~~~~~~l~~~~~~~-----~~-~i~--~~  178 (317)
                      . .++||++- +.      ..        -+.+.+...+  ..|.|+|.++.-+.+.|..++..+     +. ..+  .+
T Consensus       165 ~~PlV~iiSe~~~~~~~~~~~~~~~t~~~L~~~~il~~~~i~~I~FNpIa~T~mkKaL~rI~~~E~~~~~~~~~~p~~~~  244 (519)
T PF03215_consen  165 CLPLVFIISETESLSGDNSYRSNSFTAERLFPKEILNHPGITRIKFNPIAPTFMKKALKRILKKEARSSSGKNKVPDKQS  244 (519)
T ss_pred             CCCEEEEEecccccCCCCcccccchhhhhccCHHHHhCCCceEEEecCCCHHHHHHHHHHHHHHHhhhhcCCccCCChHH
Confidence            3 33333331 11      00        2456676654  449999999999999999999987     32 232  34


Q ss_pred             HHHHHHHhcCCCHHHHHHHHHHhhh
Q psy879          179 GLEAIVFTAQGDMRQALNNLQSTHN  203 (317)
Q Consensus       179 ~~~~l~~~~~gd~r~~i~~l~~~~~  203 (317)
                      .++.|+..++||+|.||+.||.++.
T Consensus       245 ~l~~I~~~s~GDIRsAIn~LQf~~~  269 (519)
T PF03215_consen  245 VLDSIAESSNGDIRSAINNLQFWCL  269 (519)
T ss_pred             HHHHHHHhcCchHHHHHHHHHHHhc
Confidence            5889999999999999999999877

>KOG0730|consensus

Probab=99.78  E-value=7.7e-18  Score=152.58  Aligned_cols=182  Identities=20%  Similarity=0.251  Sum_probs=131.3

Q ss_pred             CCCCcccCCHHHHHHHHHHHh-----------cC-CCce-EEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCC--
Q psy879            7 QTFSDIVGNEDTVERLKVFSS-----------SG-NVPN-IIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASN--   71 (317)
Q Consensus         7 ~~~~~~~g~~~~~~~l~~~l~-----------~~-~~~~-~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~--   71 (317)
                      -+|+|+=|++++++.|+..+.           =| .+|. +|||||||||||++|+++|++.     ..+++.+.+..  
T Consensus       431 v~W~dIGGlE~lK~elq~~V~~p~~~pe~F~r~Gi~ppkGVLlyGPPGC~KT~lAkalAne~-----~~nFlsvkgpEL~  505 (693)
T KOG0730|consen  431 VSWDDIGGLEELKRELQQAVEWPLKHPEKFARFGISPPKGVLLYGPPGCGKTLLAKALANEA-----GMNFLSVKGPELF  505 (693)
T ss_pred             CChhhccCHHHHHHHHHHHHhhhhhchHHHHHhcCCCCceEEEECCCCcchHHHHHHHhhhh-----cCCeeeccCHHHH
Confidence            469999999999999987653           23 3344 9999999999999999999985     33455554321  


Q ss_pred             ----CcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHH-----------HHHHHHHHhhhc--cCCceEEEEec
Q psy879           72 ----DRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDG-----------AQQALRRTMEIY--SNTTRFALACN  134 (317)
Q Consensus        72 ----~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~-----------~~~~ll~~le~~--~~~~~~il~~~  134 (317)
                          ..+...+++.+....+.       .+.|+++||+|.+..+           ..+.||.-|+..  ..++.+|.+||
T Consensus       506 sk~vGeSEr~ir~iF~kAR~~-------aP~IiFfDEiDsi~~~R~g~~~~v~~RVlsqLLtEmDG~e~~k~V~ViAATN  578 (693)
T KOG0730|consen  506 SKYVGESERAIREVFRKARQV-------APCIIFFDEIDALAGSRGGSSSGVTDRVLSQLLTEMDGLEALKNVLVIAATN  578 (693)
T ss_pred             HHhcCchHHHHHHHHHHHhhc-------CCeEEehhhHHhHhhccCCCccchHHHHHHHHHHHcccccccCcEEEEeccC
Confidence                22344566666555443       4589999999987543           356666666633  35677888899


Q ss_pred             CCCcCchhHhh--hcce-eeecCCCHHHHHHHHHHHHHHcCCCCCHH-HHHHHHHhcCC-CHHHHHHHHHHhh
Q psy879          135 NSEKIIEPIQS--RCAM-LRYNKLTDAQLLSKVIEICEKENISHTND-GLEAIVFTAQG-DMRQALNNLQSTH  202 (317)
Q Consensus       135 ~~~~l~~~i~s--R~~~-i~f~~~~~~~~~~~l~~~~~~~~~~i~~~-~~~~l~~~~~g-d~r~~i~~l~~~~  202 (317)
                      .++.+++++.+  |+.. +++++|+.+...++++..+++  +.++++ .++.+++.+.| +-+...+.++.++
T Consensus       579 Rpd~ID~ALlRPGRlD~iiyVplPD~~aR~~Ilk~~~kk--mp~~~~vdl~~La~~T~g~SGAel~~lCq~A~  649 (693)
T KOG0730|consen  579 RPDMIDPALLRPGRLDRIIYVPLPDLEARLEILKQCAKK--MPFSEDVDLEELAQATEGYSGAEIVAVCQEAA  649 (693)
T ss_pred             ChhhcCHHHcCCcccceeEeecCccHHHHHHHHHHHHhc--CCCCccccHHHHHHHhccCChHHHHHHHHHHH
Confidence            99999999999  7765 999999999999999998874  455555 57788876543 4444555555543

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=99.78  E-value=1.1e-17  Score=162.85  Aligned_cols=194  Identities=15%  Similarity=0.186  Sum_probs=144.8

Q ss_pred             cccCCCCCCcccCCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCC-----CCceEEecCCC----C
Q psy879            2 EKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSF-----KDAVLELNASN----D   72 (317)
Q Consensus         2 ~ky~P~~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~-----~~~~~~~~~~~----~   72 (317)
                      ++.||.++++++|+++.++.+...+..+..++.+|+||||+|||++++.+++.+.....     +..++.++...    .
T Consensus       179 ~~~r~~~ld~~iGr~~ei~~~i~~l~r~~~~n~lLvG~pGvGKTal~~~La~~i~~~~v~~~l~~~~i~~l~l~~l~ag~  258 (852)
T TIGR03345       179 AQAREGKIDPVLGRDDEIRQMIDILLRRRQNNPILTGEAGVGKTAVVEGLALRIAAGDVPPALRNVRLLSLDLGLLQAGA  258 (852)
T ss_pred             HHhcCCCCCcccCCHHHHHHHHHHHhcCCcCceeEECCCCCCHHHHHHHHHHHHhhCCCCccccCCeEEEeehhhhhccc
Confidence            56799999999999999999988888888888999999999999999999998743211     12233332221    0


Q ss_pred             cCh----HHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCH--------HHHHHHHHHhhhccCCceEEEEecCC----
Q psy879           73 RGI----DTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTD--------GAQQALRRTMEIYSNTTRFALACNNS----  136 (317)
Q Consensus        73 ~~~----~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~--------~~~~~ll~~le~~~~~~~~il~~~~~----  136 (317)
                      ...    ..++..+......      +.+.|+||||++.+..        +..+.|...++.  +...+|.+|+..    
T Consensus       259 ~~~ge~e~~lk~ii~e~~~~------~~~~ILfIDEih~l~~~g~~~~~~d~~n~Lkp~l~~--G~l~~IgaTT~~e~~~  330 (852)
T TIGR03345       259 SVKGEFENRLKSVIDEVKAS------PQPIILFIDEAHTLIGAGGQAGQGDAANLLKPALAR--GELRTIAATTWAEYKK  330 (852)
T ss_pred             ccchHHHHHHHHHHHHHHhc------CCCeEEEEeChHHhccCCCccccccHHHHhhHHhhC--CCeEEEEecCHHHHhh
Confidence            112    2334444443221      3567999999999964        234467888874  667788888764    


Q ss_pred             -CcCchhHhhhcceeeecCCCHHHHHHHHHHHHHH----cCCCCCHHHHHHHHHhcCC------CHHHHHHHHHHhhh
Q psy879          137 -EKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEK----ENISHTNDGLEAIVFTAQG------DMRQALNNLQSTHN  203 (317)
Q Consensus       137 -~~l~~~i~sR~~~i~f~~~~~~~~~~~l~~~~~~----~~~~i~~~~~~~l~~~~~g------d~r~~i~~l~~~~~  203 (317)
                       ...++++.+||+.|.+++|+.++...+|......    .++.++++++..++..+.+      =+.+|+++++.++.
T Consensus       331 ~~~~d~AL~rRf~~i~v~eps~~~~~~iL~~~~~~~e~~~~v~i~d~al~~~~~ls~ryi~~r~LPDKAIdlldea~a  408 (852)
T TIGR03345       331 YFEKDPALTRRFQVVKVEEPDEETAIRMLRGLAPVLEKHHGVLILDEAVVAAVELSHRYIPGRQLPDKAVSLLDTACA  408 (852)
T ss_pred             hhhccHHHHHhCeEEEeCCCCHHHHHHHHHHHHHhhhhcCCCeeCHHHHHHHHHHcccccccccCccHHHHHHHHHHH
Confidence             2578999999999999999999999997655433    4688999999999988854      47889999987654

Members of this protein family are homologs of ClpB, an ATPase associated with chaperone-related functions. These ClpB homologs, designated ClpV1, are a key component of the bacterial pathogenicity-associated type VI secretion system.

>PRK09087 hypothetical protein; Validated

Probab=99.77  E-value=2e-17  Score=137.36  Aligned_cols=187  Identities=14%  Similarity=0.159  Sum_probs=133.1

Q ss_pred             CCCcccC---CHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHHHHH
Q psy879            8 TFSDIVG---NEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKM   84 (317)
Q Consensus         8 ~~~~~~g---~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~~~   84 (317)
                      +|++++.   +..+...+..+.. ...|.++|+||+|+|||++++++++..     +.  ..++.. ..+...    +..
T Consensus        19 ~~~~Fi~~~~N~~a~~~l~~~~~-~~~~~l~l~G~~GsGKThLl~~~~~~~-----~~--~~i~~~-~~~~~~----~~~   85 (226)
T PRK09087         19 GRDDLLVTESNRAAVSLVDHWPN-WPSPVVVLAGPVGSGKTHLASIWREKS-----DA--LLIHPN-EIGSDA----ANA   85 (226)
T ss_pred             ChhceeecCchHHHHHHHHhccc-CCCCeEEEECCCCCCHHHHHHHHHHhc-----CC--EEecHH-HcchHH----HHh
Confidence            6899984   4556666655442 222349999999999999999999763     11  122221 111111    111


Q ss_pred             HHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccC-CceEEEEecCCC----cCchhHhhhc---ceeeecCCC
Q psy879           85 FAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSN-TTRFALACNNSE----KIIEPIQSRC---AMLRYNKLT  156 (317)
Q Consensus        85 ~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~-~~~~il~~~~~~----~l~~~i~sR~---~~i~f~~~~  156 (317)
                                ....+++|||++.+. ..+.+|+++++.... ...+|++++.+.    ...+.++||+   ..+++.+|+
T Consensus        86 ----------~~~~~l~iDDi~~~~-~~~~~lf~l~n~~~~~g~~ilits~~~p~~~~~~~~dL~SRl~~gl~~~l~~pd  154 (226)
T PRK09087         86 ----------AAEGPVLIEDIDAGG-FDETGLFHLINSVRQAGTSLLMTSRLWPSSWNVKLPDLKSRLKAATVVEIGEPD  154 (226)
T ss_pred             ----------hhcCeEEEECCCCCC-CCHHHHHHHHHHHHhCCCeEEEECCCChHHhccccccHHHHHhCCceeecCCCC
Confidence                      112489999999874 335667777765433 456777766432    3479999999   679999999


Q ss_pred             HHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHh---hh-CCCcccHHHHHhhcC
Q psy879          157 DAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQST---HN-GFGHVTAEYVFKVCD  218 (317)
Q Consensus       157 ~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~---~~-~~~~i~~~~v~~~~~  218 (317)
                      .+++..++++.+..+++.++++++++++..+.||++.++..+...   +. ..+.+|...+++++.
T Consensus       155 ~e~~~~iL~~~~~~~~~~l~~ev~~~La~~~~r~~~~l~~~l~~L~~~~~~~~~~it~~~~~~~l~  220 (226)
T PRK09087        155 DALLSQVIFKLFADRQLYVDPHVVYYLVSRMERSLFAAQTIVDRLDRLALERKSRITRALAAEVLN  220 (226)
T ss_pred             HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHH
Confidence            999999999999999999999999999999999999999866543   22 456788877766543

>PTZ00361 26 proteosome regulatory subunit 4-like protein; Provisional

Probab=99.77  E-value=2.2e-17  Score=148.50  Aligned_cols=204  Identities=19%  Similarity=0.233  Sum_probs=131.5

Q ss_pred             cccCCCCCCcccCCHHHHHHHHHHHhc-----------C--CCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEec
Q psy879            2 EKYRPQTFSDIVGNEDTVERLKVFSSS-----------G--NVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELN   68 (317)
Q Consensus         2 ~ky~P~~~~~~~g~~~~~~~l~~~l~~-----------~--~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~   68 (317)
                      +++.+.+|+|+.|.+..++.+..++.-           |  .+.+++||||||||||++|+++|+.+..     .++.+.
T Consensus       175 ~~~p~~~~~DIgGl~~qi~~l~e~v~lpl~~p~~~~~~gi~~p~gVLL~GPPGTGKT~LAraIA~el~~-----~fi~V~  249 (438)
T PTZ00361        175 DKAPLESYADIGGLEQQIQEIKEAVELPLTHPELYDDIGIKPPKGVILYGPPGTGKTLLAKAVANETSA-----TFLRVV  249 (438)
T ss_pred             ccCCCCCHHHhcCHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCcEEEEECCCCCCHHHHHHHHHHhhCC-----CEEEEe
Confidence            566668899999999999888877641           1  2234999999999999999999998632     345444


Q ss_pred             CCCC------cChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCH-----------HHHHHHHHHhhh-----ccCC
Q psy879           69 ASND------RGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTD-----------GAQQALRRTMEI-----YSNT  126 (317)
Q Consensus        69 ~~~~------~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~-----------~~~~~ll~~le~-----~~~~  126 (317)
                      .+..      .+...++..+.....       ..+.|++|||+|.+..           +.+..++.++..     ...+
T Consensus       250 ~seL~~k~~Ge~~~~vr~lF~~A~~-------~~P~ILfIDEID~l~~kR~~~~sgg~~e~qr~ll~LL~~Ldg~~~~~~  322 (438)
T PTZ00361        250 GSELIQKYLGDGPKLVRELFRVAEE-------NAPSIVFIDEIDAIGTKRYDATSGGEKEIQRTMLELLNQLDGFDSRGD  322 (438)
T ss_pred             cchhhhhhcchHHHHHHHHHHHHHh-------CCCcEEeHHHHHHHhccCCCCCCcccHHHHHHHHHHHHHHhhhcccCC
Confidence            4321      112223333332221       3567999999997642           224444444432     2456


Q ss_pred             ceEEEEecCCCcCchhHhh--hcce-eeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhc----CCCHHHHHHHHH
Q psy879          127 TRFALACNNSEKIIEPIQS--RCAM-LRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTA----QGDMRQALNNLQ  199 (317)
Q Consensus       127 ~~~il~~~~~~~l~~~i~s--R~~~-i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~----~gd~r~~i~~l~  199 (317)
                      +.+|++||.++.+++++.+  |+.. |+|++|+.++...++...+.+..+.- +..++.++..+    +.|++.+....-
T Consensus       323 V~VI~ATNr~d~LDpaLlRpGRfd~~I~~~~Pd~~~R~~Il~~~~~k~~l~~-dvdl~~la~~t~g~sgAdI~~i~~eA~  401 (438)
T PTZ00361        323 VKVIMATNRIESLDPALIRPGRIDRKIEFPNPDEKTKRRIFEIHTSKMTLAE-DVDLEEFIMAKDELSGADIKAICTEAG  401 (438)
T ss_pred             eEEEEecCChHHhhHHhccCCeeEEEEEeCCCCHHHHHHHHHHHHhcCCCCc-CcCHHHHHHhcCCCCHHHHHHHHHHHH
Confidence            7899999999999999875  6655 99999999999999998876544321 12244555443    334444433332


Q ss_pred             Hhhh--CCCcccHHHHHhhcC
Q psy879          200 STHN--GFGHVTAEYVFKVCD  218 (317)
Q Consensus       200 ~~~~--~~~~i~~~~v~~~~~  218 (317)
                      ..+.  +...|+.+++..+..
T Consensus       402 ~~Alr~~r~~Vt~~D~~~A~~  422 (438)
T PTZ00361        402 LLALRERRMKVTQADFRKAKE  422 (438)
T ss_pred             HHHHHhcCCccCHHHHHHHHH
Confidence            2222  445788887765443

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=99.77  E-value=2.9e-17  Score=148.97  Aligned_cols=201  Identities=16%  Similarity=0.212  Sum_probs=141.4

Q ss_pred             CCCccc-CCH--HHHHHHHHHHhc-----C-CCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHH
Q psy879            8 TFSDIV-GNE--DTVERLKVFSSS-----G-NVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTV   78 (317)
Q Consensus         8 ~~~~~~-g~~--~~~~~l~~~l~~-----~-~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i   78 (317)
                      +|+.++ |..  .+......+.+.     | ..++++||||+|+|||++++++++.+....  ..+++++.... . ..+
T Consensus       109 tFdnFv~g~~N~~a~~~a~~~a~~~~~~~~~~~npl~L~G~~G~GKTHLl~Ai~~~l~~~~--~~v~yi~~~~f-~-~~~  184 (445)
T PRK12422        109 TFANFLVTPENDLPHRILQEFTKVSEQGKGFPFNPIYLFGPEGSGKTHLMQAAVHALRESG--GKILYVRSELF-T-EHL  184 (445)
T ss_pred             cccceeeCCcHHHHHHHHHHHHhccccccCCCCceEEEEcCCCCCHHHHHHHHHHHHHHcC--CCEEEeeHHHH-H-HHH
Confidence            588887 533  333455555432     2 224599999999999999999999986432  33444443210 0 111


Q ss_pred             HHHH-----HHHHhhcccCCCCceeEEEEeCCCCCCH--HHHHHHHHHhhhc-cCCceEEEEecCC----CcCchhHhhh
Q psy879           79 RNKI-----KMFAQQKVTLPPGRHKIVILDEADSMTD--GAQQALRRTMEIY-SNTTRFALACNNS----EKIIEPIQSR  146 (317)
Q Consensus        79 ~~~~-----~~~~~~~~~~~~~~~~vliiDE~d~l~~--~~~~~ll~~le~~-~~~~~~il~~~~~----~~l~~~i~sR  146 (317)
                      ...+     ..+...     .....+++|||++.+..  ..+..|+.+++.. .....+|++++.+    ..+.+.++||
T Consensus       185 ~~~l~~~~~~~f~~~-----~~~~dvLiIDDiq~l~~k~~~qeelf~l~N~l~~~~k~IIlts~~~p~~l~~l~~rL~SR  259 (445)
T PRK12422        185 VSAIRSGEMQRFRQF-----YRNVDALFIEDIEVFSGKGATQEEFFHTFNSLHTEGKLIVISSTCAPQDLKAMEERLISR  259 (445)
T ss_pred             HHHHhcchHHHHHHH-----cccCCEEEEcchhhhcCChhhHHHHHHHHHHHHHCCCcEEEecCCCHHHHhhhHHHHHhh
Confidence            1111     111111     13567999999999864  4577777776633 2345678887764    3567999999


Q ss_pred             cc---eeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhh---h----CCCcccHHHHHhh
Q psy879          147 CA---MLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTH---N----GFGHVTAEYVFKV  216 (317)
Q Consensus       147 ~~---~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~---~----~~~~i~~~~v~~~  216 (317)
                      +.   .+.+.+|+.+++..+|...+...++.++++++++++....+|+|.+.+.+...+   .    ....++.+.+.++
T Consensus       260 ~~~Gl~~~l~~pd~e~r~~iL~~k~~~~~~~l~~evl~~la~~~~~dir~L~g~l~~l~~~~a~~~~~~~~i~~~~~~~~  339 (445)
T PRK12422        260 FEWGIAIPLHPLTKEGLRSFLERKAEALSIRIEETALDFLIEALSSNVKSLLHALTLLAKRVAYKKLSHQLLYVDDIKAL  339 (445)
T ss_pred             hcCCeEEecCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHH
Confidence            94   599999999999999999999999999999999999999999999999998763   1    3456888877665


Q ss_pred             c
Q psy879          217 C  217 (317)
Q Consensus       217 ~  217 (317)
                      +
T Consensus       340 l  340 (445)
T PRK12422        340 L  340 (445)
T ss_pred             H
Confidence            4

>CHL00195 ycf46 Ycf46; Provisional

Probab=99.76  E-value=4e-17  Score=148.91  Aligned_cols=204  Identities=15%  Similarity=0.125  Sum_probs=139.7

Q ss_pred             CCCCcccCCHHHHHHHHHHHh--------cC-CCc-eEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCC----
Q psy879            7 QTFSDIVGNEDTVERLKVFSS--------SG-NVP-NIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASND----   72 (317)
Q Consensus         7 ~~~~~~~g~~~~~~~l~~~l~--------~~-~~~-~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~----   72 (317)
                      .+|+++.|.+.+++.+.....        -| ..| .+|||||||||||++|+++|+++     +.+++.++....    
T Consensus       225 ~~~~dvgGl~~lK~~l~~~~~~~~~~~~~~gl~~pkGILL~GPpGTGKTllAkaiA~e~-----~~~~~~l~~~~l~~~~  299 (489)
T CHL00195        225 EKISDIGGLDNLKDWLKKRSTSFSKQASNYGLPTPRGLLLVGIQGTGKSLTAKAIANDW-----QLPLLRLDVGKLFGGI  299 (489)
T ss_pred             CCHHHhcCHHHHHHHHHHHHHHhhHHHHhcCCCCCceEEEECCCCCcHHHHHHHHHHHh-----CCCEEEEEhHHhcccc
Confidence            458999999988887765321        12 223 39999999999999999999986     344555554321    


Q ss_pred             c--ChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHH------------HHHHHHHHhhhccCCceEEEEecCCCc
Q psy879           73 R--GIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDG------------AQQALRRTMEIYSNTTRFALACNNSEK  138 (317)
Q Consensus        73 ~--~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~------------~~~~ll~~le~~~~~~~~il~~~~~~~  138 (317)
                      .  +...+++.+.....       ..+.||+|||+|.+...            ..+.|+..|.+....+.+|.|||+++.
T Consensus       300 vGese~~l~~~f~~A~~-------~~P~IL~IDEID~~~~~~~~~~d~~~~~rvl~~lL~~l~~~~~~V~vIaTTN~~~~  372 (489)
T CHL00195        300 VGESESRMRQMIRIAEA-------LSPCILWIDEIDKAFSNSESKGDSGTTNRVLATFITWLSEKKSPVFVVATANNIDL  372 (489)
T ss_pred             cChHHHHHHHHHHHHHh-------cCCcEEEehhhhhhhccccCCCCchHHHHHHHHHHHHHhcCCCceEEEEecCChhh
Confidence            1  22334444443222       35789999999976431            245677788776677788899999999


Q ss_pred             CchhHhh--hcce-eeecCCCHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHhcC----CCHHHHHHHHHH-hhhCCCccc
Q psy879          139 IIEPIQS--RCAM-LRYNKLTDAQLLSKVIEICEKENIS-HTNDGLEAIVFTAQ----GDMRQALNNLQS-THNGFGHVT  209 (317)
Q Consensus       139 l~~~i~s--R~~~-i~f~~~~~~~~~~~l~~~~~~~~~~-i~~~~~~~l~~~~~----gd~r~~i~~l~~-~~~~~~~i~  209 (317)
                      +++++.+  ||.. +.++.|+.++..+++...+.+.+.. .++..++.++..+.    +|++++....-. +......++
T Consensus       373 Ld~allR~GRFD~~i~v~lP~~~eR~~Il~~~l~~~~~~~~~~~dl~~La~~T~GfSGAdI~~lv~eA~~~A~~~~~~lt  452 (489)
T CHL00195        373 LPLEILRKGRFDEIFFLDLPSLEEREKIFKIHLQKFRPKSWKKYDIKKLSKLSNKFSGAEIEQSIIEAMYIAFYEKREFT  452 (489)
T ss_pred             CCHHHhCCCcCCeEEEeCCcCHHHHHHHHHHHHhhcCCCcccccCHHHHHhhcCCCCHHHHHHHHHHHHHHHHHcCCCcC
Confidence            9999976  7765 9999999999999999988775432 23445677777654    466655544432 223556788


Q ss_pred             HHHHHhhcCCCCH
Q psy879          210 AEYVFKVCDEPHP  222 (317)
Q Consensus       210 ~~~v~~~~~~~~~  222 (317)
                      .+++..++....+
T Consensus       453 ~~dl~~a~~~~~P  465 (489)
T CHL00195        453 TDDILLALKQFIP  465 (489)
T ss_pred             HHHHHHHHHhcCC
Confidence            8887766554433

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=99.76  E-value=5.2e-16  Score=143.22  Aligned_cols=205  Identities=15%  Similarity=0.162  Sum_probs=141.3

Q ss_pred             CCCcccC-C--HHHHHHHHHHHhc-CC-CceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcC--hHHHHH
Q psy879            8 TFSDIVG-N--EDTVERLKVFSSS-GN-VPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRG--IDTVRN   80 (317)
Q Consensus         8 ~~~~~~g-~--~~~~~~l~~~l~~-~~-~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~--~~~i~~   80 (317)
                      +|++|+. .  ..+.......+.+ +. .+.++|||++|+|||+|++++++.+.....+..+++++......  ...+++
T Consensus       286 TFDnFvvG~sN~~A~aaa~avae~~~~~~NpL~LyG~sGsGKTHLL~AIa~~a~~~~~g~~V~Yitaeef~~el~~al~~  365 (617)
T PRK14086        286 TFDTFVIGASNRFAHAAAVAVAEAPAKAYNPLFIYGESGLGKTHLLHAIGHYARRLYPGTRVRYVSSEEFTNEFINSIRD  365 (617)
T ss_pred             CHhhhcCCCccHHHHHHHHHHHhCccccCCcEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEeeHHHHHHHHHHHHHh
Confidence            5888873 2  2234344444443 22 22399999999999999999999875322234455554422110  011111


Q ss_pred             -HHHHHHhhcccCCCCceeEEEEeCCCCCCH--HHHHHHHHHhhhccC-CceEEEEecCC----CcCchhHhhhcce---
Q psy879           81 -KIKMFAQQKVTLPPGRHKIVILDEADSMTD--GAQQALRRTMEIYSN-TTRFALACNNS----EKIIEPIQSRCAM---  149 (317)
Q Consensus        81 -~~~~~~~~~~~~~~~~~~vliiDE~d~l~~--~~~~~ll~~le~~~~-~~~~il~~~~~----~~l~~~i~sR~~~---  149 (317)
                       ....+...     .....+|+|||++.+..  ..+..|+.+++.... +..+|++++..    ..+.+.++||+..   
T Consensus       366 ~~~~~f~~~-----y~~~DLLlIDDIq~l~gke~tqeeLF~l~N~l~e~gk~IIITSd~~P~eL~~l~~rL~SRf~~GLv  440 (617)
T PRK14086        366 GKGDSFRRR-----YREMDILLVDDIQFLEDKESTQEEFFHTFNTLHNANKQIVLSSDRPPKQLVTLEDRLRNRFEWGLI  440 (617)
T ss_pred             ccHHHHHHH-----hhcCCEEEEehhccccCCHHHHHHHHHHHHHHHhcCCCEEEecCCChHhhhhccHHHHhhhhcCce
Confidence             11111111     13467999999999854  346778888876544 45577788764    2577899999865   


Q ss_pred             eeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhh----CCCcccHHHHHhhc
Q psy879          150 LRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHN----GFGHVTAEYVFKVC  217 (317)
Q Consensus       150 i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~----~~~~i~~~~v~~~~  217 (317)
                      +.+.+|+.+....+|...+..+++.++++++++|+....+|+|.+...|..+..    ....|+.+.++.++
T Consensus       441 v~I~~PD~EtR~aIL~kka~~r~l~l~~eVi~yLa~r~~rnvR~LegaL~rL~a~a~~~~~~itl~la~~vL  512 (617)
T PRK14086        441 TDVQPPELETRIAILRKKAVQEQLNAPPEVLEFIASRISRNIRELEGALIRVTAFASLNRQPVDLGLTEIVL  512 (617)
T ss_pred             EEcCCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHhccCCHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHH
Confidence            899999999999999999999999999999999999999999999888876432    44567777666544

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=99.75  E-value=1.1e-16  Score=143.67  Aligned_cols=197  Identities=20%  Similarity=0.254  Sum_probs=128.3

Q ss_pred             CCCcccCCHHHHHHHHHHHhc-----------C-C-CceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCc-
Q psy879            8 TFSDIVGNEDTVERLKVFSSS-----------G-N-VPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDR-   73 (317)
Q Consensus         8 ~~~~~~g~~~~~~~l~~~l~~-----------~-~-~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~-   73 (317)
                      +|+++.|.+..++.+..++..           | . +.+++||||||||||++|+++|+.+.     ..++.+.++... 
T Consensus       129 ~~~di~Gl~~~~~~l~~~i~~pl~~~~~~~~~g~~~p~gvLL~GppGtGKT~lAkaia~~~~-----~~~i~v~~~~l~~  203 (389)
T PRK03992        129 TYEDIGGLEEQIREVREAVELPLKKPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHETN-----ATFIRVVGSELVQ  203 (389)
T ss_pred             CHHHhCCcHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCceEEECCCCCChHHHHHHHHHHhC-----CCEEEeehHHHhH
Confidence            588999999998888776531           1 2 23499999999999999999999863     235555543211 


Q ss_pred             -----ChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCC-----------HHHHHHHHHHhhhc-----cCCceEEEE
Q psy879           74 -----GIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMT-----------DGAQQALRRTMEIY-----SNTTRFALA  132 (317)
Q Consensus        74 -----~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~-----------~~~~~~ll~~le~~-----~~~~~~il~  132 (317)
                           +...++..+.....       ..+.||+|||+|.+.           .+.+..+..++.+.     ..++.+|++
T Consensus       204 ~~~g~~~~~i~~~f~~a~~-------~~p~IlfiDEiD~l~~~r~~~~~~~~~~~~~~l~~lL~~ld~~~~~~~v~VI~a  276 (389)
T PRK03992        204 KFIGEGARLVRELFELARE-------KAPSIIFIDEIDAIAAKRTDSGTSGDREVQRTLMQLLAEMDGFDPRGNVKIIAA  276 (389)
T ss_pred             hhccchHHHHHHHHHHHHh-------cCCeEEEEechhhhhcccccCCCCccHHHHHHHHHHHHhccccCCCCCEEEEEe
Confidence                 11222332222211       356799999999883           23455566655432     246789999


Q ss_pred             ecCCCcCchhHhh--hcce-eeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCC----CHHHHHHHHHHhhh--
Q psy879          133 CNNSEKIIEPIQS--RCAM-LRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQG----DMRQALNNLQSTHN--  203 (317)
Q Consensus       133 ~~~~~~l~~~i~s--R~~~-i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~g----d~r~~i~~l~~~~~--  203 (317)
                      ||.++.+++++.+  |+.. ++|++|+.++..+++...++...+.- +..+..++..+.|    |++.+....-..+.  
T Consensus       277 Tn~~~~ld~allRpgRfd~~I~v~~P~~~~R~~Il~~~~~~~~~~~-~~~~~~la~~t~g~sgadl~~l~~eA~~~a~~~  355 (389)
T PRK03992        277 TNRIDILDPAILRPGRFDRIIEVPLPDEEGRLEILKIHTRKMNLAD-DVDLEELAELTEGASGADLKAICTEAGMFAIRD  355 (389)
T ss_pred             cCChhhCCHHHcCCccCceEEEECCCCHHHHHHHHHHHhccCCCCC-cCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHc
Confidence            9999999999985  7755 99999999999999998876443321 1335666766543    44444333322221  


Q ss_pred             CCCcccHHHHHhhc
Q psy879          204 GFGHVTAEYVFKVC  217 (317)
Q Consensus       204 ~~~~i~~~~v~~~~  217 (317)
                      +...|+.+++.+++
T Consensus       356 ~~~~i~~~d~~~A~  369 (389)
T PRK03992        356 DRTEVTMEDFLKAI  369 (389)
T ss_pred             CCCCcCHHHHHHHH
Confidence            34567777665543

>PF00308 Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013317 This entry represents the central domain of bacterial DnaA proteins [, , ] that play an important role in initiating and regulating chromosomal replication

Probab=99.75  E-value=3.9e-17  Score=135.15  Aligned_cols=189  Identities=18%  Similarity=0.265  Sum_probs=127.2

Q ss_pred             CCCccc-C--CHHHHHHHHHHHhcCC--CceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcC--hHHHHH
Q psy879            8 TFSDIV-G--NEDTVERLKVFSSSGN--VPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRG--IDTVRN   80 (317)
Q Consensus         8 ~~~~~~-g--~~~~~~~l~~~l~~~~--~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~--~~~i~~   80 (317)
                      +|+.++ |  ++.+............  .+.+++|||+|+|||++.+++++++.....+..++++++.....  .+.+++
T Consensus         6 tFdnfv~g~~N~~a~~~~~~ia~~~~~~~~~l~l~G~~G~GKTHLL~Ai~~~~~~~~~~~~v~y~~~~~f~~~~~~~~~~   85 (219)
T PF00308_consen    6 TFDNFVVGESNELAYAAAKAIAENPGERYNPLFLYGPSGLGKTHLLQAIANEAQKQHPGKRVVYLSAEEFIREFADALRD   85 (219)
T ss_dssp             SCCCS--TTTTHHHHHHHHHHHHSTTTSSSEEEEEESTTSSHHHHHHHHHHHHHHHCTTS-EEEEEHHHHHHHHHHHHHT
T ss_pred             ccccCCcCCcHHHHHHHHHHHHhcCCCCCCceEEECCCCCCHHHHHHHHHHHHHhccccccceeecHHHHHHHHHHHHHc
Confidence            689986 4  5666666666665433  23489999999999999999999876433344455554321000  000000


Q ss_pred             -HHHHHHhhcccCCCCceeEEEEeCCCCCCHHH--HHHHHHHhhhcc-CCceEEEEecCC-C---cCchhHhhhcce---
Q psy879           81 -KIKMFAQQKVTLPPGRHKIVILDEADSMTDGA--QQALRRTMEIYS-NTTRFALACNNS-E---KIIEPIQSRCAM---  149 (317)
Q Consensus        81 -~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~--~~~ll~~le~~~-~~~~~il~~~~~-~---~l~~~i~sR~~~---  149 (317)
                       .+..+...-     ....+++||+++.+....  +..|..+++... ....+|++++.+ .   .+.+.+.||+..   
T Consensus        86 ~~~~~~~~~~-----~~~DlL~iDDi~~l~~~~~~q~~lf~l~n~~~~~~k~li~ts~~~P~~l~~~~~~L~SRl~~Gl~  160 (219)
T PF00308_consen   86 GEIEEFKDRL-----RSADLLIIDDIQFLAGKQRTQEELFHLFNRLIESGKQLILTSDRPPSELSGLLPDLRSRLSWGLV  160 (219)
T ss_dssp             TSHHHHHHHH-----CTSSEEEEETGGGGTTHHHHHHHHHHHHHHHHHTTSEEEEEESS-TTTTTTS-HHHHHHHHCSEE
T ss_pred             ccchhhhhhh-----hcCCEEEEecchhhcCchHHHHHHHHHHHHHHhhCCeEEEEeCCCCccccccChhhhhhHhhcch
Confidence             011111111     357799999999997654  888888888542 344677777543 3   467899999865   


Q ss_pred             eeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHh
Q psy879          150 LRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQST  201 (317)
Q Consensus       150 i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~  201 (317)
                      +.+.+|+.++..+++...+...|+.+++++++++++...+|+|.+...++..
T Consensus       161 ~~l~~pd~~~r~~il~~~a~~~~~~l~~~v~~~l~~~~~~~~r~L~~~l~~l  212 (219)
T PF00308_consen  161 VELQPPDDEDRRRILQKKAKERGIELPEEVIEYLARRFRRDVRELEGALNRL  212 (219)
T ss_dssp             EEE----HHHHHHHHHHHHHHTT--S-HHHHHHHHHHTTSSHHHHHHHHHHH
T ss_pred             hhcCCCCHHHHHHHHHHHHHHhCCCCcHHHHHHHHHhhcCCHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999999999999988765

DnaA is an ATP- and DNA-binding protein. It binds specifically to 9 bp nucleotide repeats known as dnaA boxes which are found in the chromosome origin of replication (oriC). DnaA is a protein of about 50 kDa that contains two conserved regions: the first is located in the N-terminal half and corresponds to the ATP-binding domain, the second is located in the C-terminal half and could be involved in DNA-binding. The protein may also bind the RNA polymerase beta subunit, the dnaB and dnaZ proteins, and the groE gene products (chaperonins) [].; PDB: 2KJQ_A 2Z4S_A 2Z4R_C 2HCB_B 3R8F_C 1L8Q_A 3SC3_B 3BOS_A.

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=99.75  E-value=1.2e-16  Score=145.04  Aligned_cols=203  Identities=16%  Similarity=0.225  Sum_probs=138.5

Q ss_pred             CCCccc-CCHH--HHHHHHHHHhcC-C-CceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHHH
Q psy879            8 TFSDIV-GNED--TVERLKVFSSSG-N-VPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKI   82 (317)
Q Consensus         8 ~~~~~~-g~~~--~~~~l~~~l~~~-~-~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~   82 (317)
                      +|++++ |...  +......+.... . .+.++||||+|+|||++++++++++.....+..++++++....  ..+...+
T Consensus       108 tfd~fi~g~~n~~a~~~~~~~~~~~~~~~n~l~l~G~~G~GKThL~~ai~~~l~~~~~~~~v~yi~~~~~~--~~~~~~~  185 (405)
T TIGR00362       108 TFDNFVVGKSNRLAHAAALAVAENPGKAYNPLFIYGGVGLGKTHLLHAIGNEILENNPNAKVVYVSSEKFT--NDFVNAL  185 (405)
T ss_pred             cccccccCCcHHHHHHHHHHHHhCcCccCCeEEEECCCCCcHHHHHHHHHHHHHHhCCCCcEEEEEHHHHH--HHHHHHH
Confidence            478854 5433  444455555442 2 2348999999999999999999998644334455666543210  0111100


Q ss_pred             -----HHHHhhcccCCCCceeEEEEeCCCCCCH--HHHHHHHHHhhhc-cCCceEEEEecCC----CcCchhHhhhcc--
Q psy879           83 -----KMFAQQKVTLPPGRHKIVILDEADSMTD--GAQQALRRTMEIY-SNTTRFALACNNS----EKIIEPIQSRCA--  148 (317)
Q Consensus        83 -----~~~~~~~~~~~~~~~~vliiDE~d~l~~--~~~~~ll~~le~~-~~~~~~il~~~~~----~~l~~~i~sR~~--  148 (317)
                           ..+...-     ....+++|||++.+..  ..+..|+.+++.. ..+..+|++++.+    ..+.+.++||+.  
T Consensus       186 ~~~~~~~~~~~~-----~~~dlLiiDDi~~l~~~~~~~~~l~~~~n~~~~~~~~iiits~~~p~~l~~l~~~l~SRl~~g  260 (405)
T TIGR00362       186 RNNKMEEFKEKY-----RSVDLLLIDDIQFLAGKERTQEEFFHTFNALHENGKQIVLTSDRPPKELPGLEERLRSRFEWG  260 (405)
T ss_pred             HcCCHHHHHHHH-----HhCCEEEEehhhhhcCCHHHHHHHHHHHHHHHHCCCCEEEecCCCHHHHhhhhhhhhhhccCC
Confidence                 1111110     2356999999999864  3567788777653 2345577777653    246788999995  


Q ss_pred             -eeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhh----CCCcccHHHHHhhc
Q psy879          149 -MLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHN----GFGHVTAEYVFKVC  217 (317)
Q Consensus       149 -~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~----~~~~i~~~~v~~~~  217 (317)
                       .+.|++|+.++...++...+...++.++++++++++....||+|.+...+..+..    ....|+.+.+.+++
T Consensus       261 ~~v~i~~pd~~~r~~il~~~~~~~~~~l~~e~l~~ia~~~~~~~r~l~~~l~~l~~~a~~~~~~it~~~~~~~L  334 (405)
T TIGR00362       261 LVVDIEPPDLETRLAILQKKAEEEGLELPDEVLEFIAKNIRSNVRELEGALNRLLAYASLTGKPITLELAKEAL  334 (405)
T ss_pred             eEEEeCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHH
Confidence             4999999999999999999999999999999999999999999997776655332    44567777665543

DnaA is involved in DNA biosynthesis; initiation of chromosome replication and can also be transcription regulator. The C-terminal of the family hits the pfam bacterial DnaA (bac_dnaA) domain family. For a review, see Kaguni (2006).

>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional

Probab=99.75  E-value=1.9e-16  Score=141.60  Aligned_cols=197  Identities=20%  Similarity=0.240  Sum_probs=128.1

Q ss_pred             CCCCcccCCHHHHHHHHHHHhc-----------C--CCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCC--
Q psy879            7 QTFSDIVGNEDTVERLKVFSSS-----------G--NVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASN--   71 (317)
Q Consensus         7 ~~~~~~~g~~~~~~~l~~~l~~-----------~--~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~--   71 (317)
                      -+|+++.|.+.+++.+...+..           |  .+.+++||||||||||++++++|+.+.     ..++.+.++.  
T Consensus       142 v~~~digGl~~~k~~l~~~v~~pl~~~~~~~~~Gl~~pkgvLL~GppGTGKT~LAkalA~~l~-----~~fi~i~~s~l~  216 (398)
T PTZ00454        142 VTYSDIGGLDIQKQEIREAVELPLTCPELYEQIGIDPPRGVLLYGPPGTGKTMLAKAVAHHTT-----ATFIRVVGSEFV  216 (398)
T ss_pred             CCHHHcCCHHHHHHHHHHHHHHHhcCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHhcC-----CCEEEEehHHHH
Confidence            4699999999998888776531           2  123499999999999999999999853     2344443321  


Q ss_pred             ----CcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCH-----------HHHHHHHHH---hhhc--cCCceEEE
Q psy879           72 ----DRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTD-----------GAQQALRRT---MEIY--SNTTRFAL  131 (317)
Q Consensus        72 ----~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~-----------~~~~~ll~~---le~~--~~~~~~il  131 (317)
                          ..+...+++.+.....       ..+.||+|||+|.+..           ..+..+..+   ++..  ..++.+|+
T Consensus       217 ~k~~ge~~~~lr~lf~~A~~-------~~P~ILfIDEID~i~~~r~~~~~~~d~~~~r~l~~LL~~ld~~~~~~~v~VI~  289 (398)
T PTZ00454        217 QKYLGEGPRMVRDVFRLARE-------NAPSIIFIDEVDSIATKRFDAQTGADREVQRILLELLNQMDGFDQTTNVKVIM  289 (398)
T ss_pred             HHhcchhHHHHHHHHHHHHh-------cCCeEEEEECHhhhccccccccCCccHHHHHHHHHHHHHhhccCCCCCEEEEE
Confidence                1112233333333221       3578999999998732           223344444   4432  34677899


Q ss_pred             EecCCCcCchhHhh--hcce-eeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCC-CHHHHHHHHHHhhh----
Q psy879          132 ACNNSEKIIEPIQS--RCAM-LRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQG-DMRQALNNLQSTHN----  203 (317)
Q Consensus       132 ~~~~~~~l~~~i~s--R~~~-i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~g-d~r~~i~~l~~~~~----  203 (317)
                      +||.++.+++++.+  |+.. ++|++|+.++...+++..+.+.++.- +-.+..++..+.| +.+.+.++++.++.    
T Consensus       290 aTN~~d~LDpAllR~GRfd~~I~~~~P~~~~R~~Il~~~~~~~~l~~-dvd~~~la~~t~g~sgaDI~~l~~eA~~~A~r  368 (398)
T PTZ00454        290 ATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLIFQTITSKMNLSE-EVDLEDFVSRPEKISAADIAAICQEAGMQAVR  368 (398)
T ss_pred             ecCCchhCCHHHcCCCcccEEEEeCCcCHHHHHHHHHHHHhcCCCCc-ccCHHHHHHHcCCCCHHHHHHHHHHHHHHHHH
Confidence            99999999999986  6655 99999999999999998877655432 2235666666533 44444444544332    


Q ss_pred             -CCCcccHHHHHhh
Q psy879          204 -GFGHVTAEYVFKV  216 (317)
Q Consensus       204 -~~~~i~~~~v~~~  216 (317)
                       +...|+.+++.++
T Consensus       369 ~~~~~i~~~df~~A  382 (398)
T PTZ00454        369 KNRYVILPKDFEKG  382 (398)
T ss_pred             cCCCccCHHHHHHH
Confidence             3446777766554

>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]

Probab=99.75  E-value=1.9e-16  Score=133.93  Aligned_cols=120  Identities=18%  Similarity=0.200  Sum_probs=102.2

Q ss_pred             eeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecC------------CCcCchhHhhhcceeeecCCCHHHHHHHH
Q psy879           97 HKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNN------------SEKIIEPIQSRCAMLRYNKLTDAQLLSKV  164 (317)
Q Consensus        97 ~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~------------~~~l~~~i~sR~~~i~f~~~~~~~~~~~l  164 (317)
                      +.|+||||++.|.-++...|.+.||..- ..++|++||.            |+-++..+..|..++.-.|++.++++.++
T Consensus       292 pGVLFIDEvHmLDIE~FsFlnrAlEse~-aPIii~AtNRG~~kiRGTd~~sPhGIP~DlLDRllII~t~py~~~EireIi  370 (450)
T COG1224         292 PGVLFIDEVHMLDIECFSFLNRALESEL-APIIILATNRGMTKIRGTDIESPHGIPLDLLDRLLIISTRPYSREEIREII  370 (450)
T ss_pred             cceEEEechhhhhHHHHHHHHHHhhccc-CcEEEEEcCCceeeecccCCcCCCCCCHhhhhheeEEecCCCCHHHHHHHH
Confidence            6899999999999999999999999643 2457788875            34688999999999999999999999999


Q ss_pred             HHHHHHcCCCCCHHHHHHHHHhc-CCCHHHHHHHHHHh---hh--CCCcccHHHHHhhc
Q psy879          165 IEICEKENISHTNDGLEAIVFTA-QGDMRQALNNLQST---HN--GFGHVTAEYVFKVC  217 (317)
Q Consensus       165 ~~~~~~~~~~i~~~~~~~l~~~~-~gd~r~~i~~l~~~---~~--~~~~i~~~~v~~~~  217 (317)
                      ..+++.+++.++++++++++... ..++|.++++|.-+   +.  +.+.+..++|..+.
T Consensus       371 ~iRa~ee~i~l~~~Ale~L~~ig~etSLRYa~qLL~pa~iiA~~rg~~~V~~~dVe~a~  429 (450)
T COG1224         371 RIRAKEEDIELSDDALEYLTDIGEETSLRYAVQLLTPASIIAKRRGSKRVEVEDVERAK  429 (450)
T ss_pred             HHhhhhhccccCHHHHHHHHhhchhhhHHHHHHhccHHHHHHHHhCCCeeehhHHHHHH
Confidence            99999999999999999999874 57899999999632   22  56688888887643

>CHL00176 ftsH cell division protein; Validated

Probab=99.75  E-value=1.1e-16  Score=150.56  Aligned_cols=199  Identities=20%  Similarity=0.234  Sum_probs=134.0

Q ss_pred             CCCCcccCCHHHHHHHHHHH---hc--------CC-CceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCC--
Q psy879            7 QTFSDIVGNEDTVERLKVFS---SS--------GN-VPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASND--   72 (317)
Q Consensus         7 ~~~~~~~g~~~~~~~l~~~l---~~--------~~-~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~--   72 (317)
                      .+|+|+.|.+++++.+...+   +.        .. +.++||+||||||||++|+++|.+.     +.+++.++++..  
T Consensus       180 ~~f~dv~G~~~~k~~l~eiv~~lk~~~~~~~~g~~~p~gVLL~GPpGTGKT~LAralA~e~-----~~p~i~is~s~f~~  254 (638)
T CHL00176        180 ITFRDIAGIEEAKEEFEEVVSFLKKPERFTAVGAKIPKGVLLVGPPGTGKTLLAKAIAGEA-----EVPFFSISGSEFVE  254 (638)
T ss_pred             CCHHhccChHHHHHHHHHHHHHHhCHHHHhhccCCCCceEEEECCCCCCHHHHHHHHHHHh-----CCCeeeccHHHHHH
Confidence            46999999998888776654   21        12 2359999999999999999999985     334565554321  


Q ss_pred             ----cChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCH-----------HH---HHHHHHHhhhc--cCCceEEEE
Q psy879           73 ----RGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTD-----------GA---QQALRRTMEIY--SNTTRFALA  132 (317)
Q Consensus        73 ----~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~-----------~~---~~~ll~~le~~--~~~~~~il~  132 (317)
                          .+...++..+....       ...+.|++|||+|.+..           ..   .+.|+..++..  ..++++|.+
T Consensus       255 ~~~g~~~~~vr~lF~~A~-------~~~P~ILfIDEID~l~~~r~~~~~~~~~e~~~~L~~LL~~~dg~~~~~~ViVIaa  327 (638)
T CHL00176        255 MFVGVGAARVRDLFKKAK-------ENSPCIVFIDEIDAVGRQRGAGIGGGNDEREQTLNQLLTEMDGFKGNKGVIVIAA  327 (638)
T ss_pred             HhhhhhHHHHHHHHHHHh-------cCCCcEEEEecchhhhhcccCCCCCCcHHHHHHHHHHHhhhccccCCCCeeEEEe
Confidence                11223333333321       13567999999998842           22   34444445433  345678889


Q ss_pred             ecCCCcCchhHhhh--cce-eeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCC----CHHHHHHHHHHhh--h
Q psy879          133 CNNSEKIIEPIQSR--CAM-LRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQG----DMRQALNNLQSTH--N  203 (317)
Q Consensus       133 ~~~~~~l~~~i~sR--~~~-i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~g----d~r~~i~~l~~~~--~  203 (317)
                      ||+++.+++++.++  +.. +.|++|+.++...+++..++.... .++..+..++..+.|    |++.+++.....+  .
T Consensus       328 TN~~~~LD~ALlRpGRFd~~I~v~lPd~~~R~~IL~~~l~~~~~-~~d~~l~~lA~~t~G~sgaDL~~lvneAal~a~r~  406 (638)
T CHL00176        328 TNRVDILDAALLRPGRFDRQITVSLPDREGRLDILKVHARNKKL-SPDVSLELIARRTPGFSGADLANLLNEAAILTARR  406 (638)
T ss_pred             cCchHhhhhhhhccccCceEEEECCCCHHHHHHHHHHHHhhccc-chhHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHh
Confidence            99999999999874  433 999999999999999998876443 335567888888776    4555554432211  2


Q ss_pred             CCCcccHHHHHhhcC
Q psy879          204 GFGHVTAEYVFKVCD  218 (317)
Q Consensus       204 ~~~~i~~~~v~~~~~  218 (317)
                      +...++.+++..+++
T Consensus       407 ~~~~It~~dl~~Ai~  421 (638)
T CHL00176        407 KKATITMKEIDTAID  421 (638)
T ss_pred             CCCCcCHHHHHHHHH
Confidence            456789888877654

>PF06068 TIP49: TIP49 C-terminus; InterPro: IPR010339 This family consists of the C-terminal region of several eukaryotic and archaeal RuvB-like 1 (Pontin or TIP49a) and RuvB-like 2 (Reptin or TIP49b) proteins

Probab=99.74  E-value=9.1e-17  Score=137.84  Aligned_cols=104  Identities=15%  Similarity=0.230  Sum_probs=79.9

Q ss_pred             eeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCC------------CcCchhHhhhcceeeecCCCHHHHHHHH
Q psy879           97 HKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNS------------EKIIEPIQSRCAMLRYNKLTDAQLLSKV  164 (317)
Q Consensus        97 ~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~------------~~l~~~i~sR~~~i~f~~~~~~~~~~~l  164 (317)
                      +.|+||||++.|.-++...|.+.+|..- ..++|++||+.            +-++..+.+||..+.-.||+++|+.+++
T Consensus       279 pGVLFIDEvHmLDiEcFsfLnralEs~~-sPiiIlATNRg~~~irGt~~~sphGiP~DlLDRllII~t~py~~~ei~~Il  357 (398)
T PF06068_consen  279 PGVLFIDEVHMLDIECFSFLNRALESEL-SPIIILATNRGITKIRGTDIISPHGIPLDLLDRLLIIRTKPYSEEEIKQIL  357 (398)
T ss_dssp             E-EEEEESGGGSBHHHHHHHHHHHTSTT---EEEEEES-SEEE-BTTS-EEETT--HHHHTTEEEEEE----HHHHHHHH
T ss_pred             cceEEecchhhccHHHHHHHHHHhcCCC-CcEEEEecCceeeeccCccCcCCCCCCcchHhhcEEEECCCCCHHHHHHHH
Confidence            6899999999999999999999999643 34578888853            3578899999999999999999999999


Q ss_pred             HHHHHHcCCCCCHHHHHHHHHh-cCCCHHHHHHHHHHh
Q psy879          165 IEICEKENISHTNDGLEAIVFT-AQGDMRQALNNLQST  201 (317)
Q Consensus       165 ~~~~~~~~~~i~~~~~~~l~~~-~~gd~r~~i~~l~~~  201 (317)
                      .-+|+.+++.+++++++.+... ...++|.|++++..+
T Consensus       358 ~iR~~~E~v~i~~~al~~L~~ig~~~SLRYAiqLi~~a  395 (398)
T PF06068_consen  358 KIRAKEEDVEISEDALDLLTKIGVETSLRYAIQLITPA  395 (398)
T ss_dssp             HHHHHHCT--B-HHHHHHHHHHHHHS-HHHHHHCHHHH
T ss_pred             HhhhhhhcCcCCHHHHHHHHHHhhhccHHHHHHhhhhh
Confidence            9999999999999999998876 357899999988654

The N-terminal domain contains the AAA ATPase, central region IPR003959 from INTERPRO domain. In zebrafish, the liebeskummer (lik) mutation, causes development of hyperplastic embryonic hearts. lik encodes Reptin, a component of a DNA-stimulated ATPase complex. Beta-catenin and Pontin, a DNA-stimulated ATPase that is often part of complexes with Reptin, are in the same genetic pathways. The Reptin/Pontin ratio serves to regulate heart growth during development, at least in part via the beta-catenin pathway []. TBP-interacting protein 49 (TIP49) was originally identified as a TBP-binding protein, and two related proteins are encoded by individual genes, tip49a and b. Although the function of this gene family has not been elucidated, they are supposed to play a critical role in nuclear events because they interact with various kinds of nuclear factors and have DNA helicase activities. TIP49a has been suggested to act as an autoantigen in some patients with autoimmune diseases [].; GO: 0003678 DNA helicase activity, 0005524 ATP binding; PDB: 2XSZ_E 2CQA_A 2C9O_C.

>TIGR03689 pup_AAA proteasome ATPase

Probab=99.74  E-value=1.1e-16  Score=145.83  Aligned_cols=171  Identities=19%  Similarity=0.235  Sum_probs=116.3

Q ss_pred             cccCCCCCCcccCCHHHHHHHHHHHhc-----------C-CC-ceEEEECCCCCCHHHHHHHHHHHHcCCC-----CCCc
Q psy879            2 EKYRPQTFSDIVGNEDTVERLKVFSSS-----------G-NV-PNIIISGPPGVGKTTTILCLARILLGPS-----FKDA   63 (317)
Q Consensus         2 ~ky~P~~~~~~~g~~~~~~~l~~~l~~-----------~-~~-~~~ll~G~~G~GKt~la~~la~~l~~~~-----~~~~   63 (317)
                      +++.+.+|+++.|.+..++.++..+..           | .+ .++|||||||||||++++++++.+....     ....
T Consensus       174 ~~~p~v~~~dIgGl~~~i~~i~~~v~lp~~~~~l~~~~gl~~p~GILLyGPPGTGKT~LAKAlA~eL~~~i~~~~~~~~~  253 (512)
T TIGR03689       174 EEVPDVTYADIGGLDSQIEQIRDAVELPFLHPELYREYDLKPPKGVLLYGPPGCGKTLIAKAVANSLAQRIGAETGDKSY  253 (512)
T ss_pred             ecCCCCCHHHcCChHHHHHHHHHHHHHHhhCHHHHHhccCCCCcceEEECCCCCcHHHHHHHHHHhhccccccccCCcee
Confidence            455667899999999999888777531           1 12 3499999999999999999999974321     1122


Q ss_pred             eEEecCCCC------cChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHH------------HHHHHHHHhhhcc-
Q psy879           64 VLELNASND------RGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDG------------AQQALRRTMEIYS-  124 (317)
Q Consensus        64 ~~~~~~~~~------~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~------------~~~~ll~~le~~~-  124 (317)
                      ++.+.....      .....++..+.......   ..+.+.|++|||+|.+...            ..+.|+..|+... 
T Consensus       254 fl~v~~~eLl~kyvGete~~ir~iF~~Ar~~a---~~g~p~IIfIDEiD~L~~~R~~~~s~d~e~~il~~LL~~LDgl~~  330 (512)
T TIGR03689       254 FLNIKGPELLNKYVGETERQIRLIFQRAREKA---SDGRPVIVFFDEMDSIFRTRGSGVSSDVETTVVPQLLSELDGVES  330 (512)
T ss_pred             EEeccchhhcccccchHHHHHHHHHHHHHHHh---hcCCCceEEEehhhhhhcccCCCccchHHHHHHHHHHHHhccccc
Confidence            333322211      11122333333322221   1245789999999987432            2356777776443 


Q ss_pred             -CCceEEEEecCCCcCchhHhh--hcce-eeecCCCHHHHHHHHHHHHHHcCCCCC
Q psy879          125 -NTTRFALACNNSEKIIEPIQS--RCAM-LRYNKLTDAQLLSKVIEICEKENISHT  176 (317)
Q Consensus       125 -~~~~~il~~~~~~~l~~~i~s--R~~~-i~f~~~~~~~~~~~l~~~~~~~~~~i~  176 (317)
                       +++.+|.+||+++.+++++.+  |+.. |+|++|+.++..+++..++.. .+.++
T Consensus       331 ~~~ViVI~ATN~~d~LDpALlRpGRfD~~I~~~~Pd~e~r~~Il~~~l~~-~l~l~  385 (512)
T TIGR03689       331 LDNVIVIGASNREDMIDPAILRPGRLDVKIRIERPDAEAAADIFSKYLTD-SLPLD  385 (512)
T ss_pred             CCceEEEeccCChhhCCHhhcCccccceEEEeCCCCHHHHHHHHHHHhhc-cCCch
Confidence             567789999999999999997  7766 999999999999999988754 34443

In the Actinobacteria, as shown for Mycobacterium tuberculosis, some proteins are modified by ligation between an epsilon-amino group of a lysine side chain and the C-terminal carboxylate of the ubiquitin-like protein Pup. This modification leads to protein degradation by the archaeal-like proteasome found in the Actinobacteria. Members of this protein family belong to the AAA family of ATPases and tend to be clustered with the genes for Pup, the Pup ligase PafA, and structural components of the proteasome. This protein forms hexameric rings with ATPase activity.

>TIGR00763 lon ATP-dependent protease La

Probab=99.74  E-value=5.4e-17  Score=157.61  Aligned_cols=164  Identities=20%  Similarity=0.303  Sum_probs=117.1

Q ss_pred             cccCCHHHHHHHHHHHh----c--CCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChH--------
Q psy879           11 DIVGNEDTVERLKVFSS----S--GNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGID--------   76 (317)
Q Consensus        11 ~~~g~~~~~~~l~~~l~----~--~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~--------   76 (317)
                      +++|++++++.+..++.    .  .+.++++|+||||||||++|+++|+.+..     .++.++........        
T Consensus       321 ~~~G~~~~k~~i~~~~~~~~~~~~~~~~~lll~GppG~GKT~lAk~iA~~l~~-----~~~~i~~~~~~~~~~i~g~~~~  395 (775)
T TIGR00763       321 DHYGLKKVKERILEYLAVQKLRGKMKGPILCLVGPPGVGKTSLGKSIAKALNR-----KFVRFSLGGVRDEAEIRGHRRT  395 (775)
T ss_pred             hcCChHHHHHHHHHHHHHHHhhcCCCCceEEEECCCCCCHHHHHHHHHHHhcC-----CeEEEeCCCcccHHHHcCCCCc
Confidence            48899999999887653    1  23357999999999999999999999732     23333322211111        


Q ss_pred             -------HHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHH----HHHHHHHHhhhc---------------cCCceEE
Q psy879           77 -------TVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDG----AQQALRRTMEIY---------------SNTTRFA  130 (317)
Q Consensus        77 -------~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~----~~~~ll~~le~~---------------~~~~~~i  130 (317)
                             .+.+.+..   .     .....|++|||+|++.++    ..++|++.++..               ..++.||
T Consensus       396 ~~g~~~g~i~~~l~~---~-----~~~~~villDEidk~~~~~~~~~~~aLl~~ld~~~~~~f~d~~~~~~~d~s~v~~I  467 (775)
T TIGR00763       396 YVGAMPGRIIQGLKK---A-----KTKNPLFLLDEIDKIGSSFRGDPASALLEVLDPEQNNAFSDHYLDVPFDLSKVIFI  467 (775)
T ss_pred             eeCCCCchHHHHHHH---h-----CcCCCEEEEechhhcCCccCCCHHHHHHHhcCHHhcCccccccCCceeccCCEEEE
Confidence                   11211111   1     123459999999999764    347888888731               1357789


Q ss_pred             EEecCCCcCchhHhhhcceeeecCCCHHHHHHHHHHHH-----HH-----cCCCCCHHHHHHHHHhc
Q psy879          131 LACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEIC-----EK-----ENISHTNDGLEAIVFTA  187 (317)
Q Consensus       131 l~~~~~~~l~~~i~sR~~~i~f~~~~~~~~~~~l~~~~-----~~-----~~~~i~~~~~~~l~~~~  187 (317)
                      +|+|..+.+++++++||.++.|++|+.++...++...+     ..     +++.++++++..+++..
T Consensus       468 ~TtN~~~~i~~~L~~R~~vi~~~~~~~~e~~~I~~~~l~~~~~~~~~l~~~~~~~~~~~l~~i~~~~  534 (775)
T TIGR00763       468 ATANSIDTIPRPLLDRMEVIELSGYTEEEKLEIAKKYLIPKALEDHGLKPDELKITDEALLLLIKYY  534 (775)
T ss_pred             EecCCchhCCHHHhCCeeEEecCCCCHHHHHHHHHHHHHHHHHHHcCCCcceEEECHHHHHHHHHhc
Confidence            99999999999999999999999999999988887654     22     24578999999988743

This protein is induced by heat shock and other stresses in E. coli, B. subtilis, and other species. The yeast member, designated PIM1, is located in the mitochondrial matrix, required for mitochondrial function, and also induced by heat shock.

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=99.72  E-value=4.4e-16  Score=132.72  Aligned_cols=189  Identities=17%  Similarity=0.163  Sum_probs=125.9

Q ss_pred             HHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHH---------HHHHHH
Q psy879           16 EDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRN---------KIKMFA   86 (317)
Q Consensus        16 ~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~---------~~~~~~   86 (317)
                      ..+.+.+..++..|.  +++|+||||||||++|+++++.+     +..++.+++.......++-.         ....+.
T Consensus         8 ~~l~~~~l~~l~~g~--~vLL~G~~GtGKT~lA~~la~~l-----g~~~~~i~~~~~~~~~dllg~~~~~~~~~~~~~~~   80 (262)
T TIGR02640         8 KRVTSRALRYLKSGY--PVHLRGPAGTGKTTLAMHVARKR-----DRPVMLINGDAELTTSDLVGSYAGYTRKKVHDQFI   80 (262)
T ss_pred             HHHHHHHHHHHhcCC--eEEEEcCCCCCHHHHHHHHHHHh-----CCCEEEEeCCccCCHHHHhhhhcccchhhHHHHHH
Confidence            345566777777776  79999999999999999999875     23355555543322221110         000000


Q ss_pred             ---------------hhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhc----------------cCCceEEEEecC
Q psy879           87 ---------------QQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIY----------------SNTTRFALACNN  135 (317)
Q Consensus        87 ---------------~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~----------------~~~~~~il~~~~  135 (317)
                                     ..+.......+.++++||++.+.++.++.|+.+|++.                +++.++|+|+|.
T Consensus        81 ~~~~~~~~~~~~~~~~g~l~~A~~~g~~lllDEi~r~~~~~q~~Ll~~Le~~~~~i~~~~~~~~~i~~~~~frvIaTsN~  160 (262)
T TIGR02640        81 HNVVKLEDIVRQNWVDNRLTLAVREGFTLVYDEFTRSKPETNNVLLSVFEEGVLELPGKRGTSRYVDVHPEFRVIFTSNP  160 (262)
T ss_pred             HHhhhhhcccceeecCchHHHHHHcCCEEEEcchhhCCHHHHHHHHHHhcCCeEEccCCCCCCceEecCCCCEEEEeeCC
Confidence                           0000000123469999999999999999999999742                235678888887


Q ss_pred             CC-----cCchhHhhhcceeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhc----------CCCHHHHHHHHHH
Q psy879          136 SE-----KIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTA----------QGDMRQALNNLQS  200 (317)
Q Consensus       136 ~~-----~l~~~i~sR~~~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~----------~gd~r~~i~~l~~  200 (317)
                      ..     .+.+++.+||..+.+..|+.++..+++...+     .++++.+++++...          .-.+|.++...+.
T Consensus       161 ~~~~g~~~l~~aL~~R~~~i~i~~P~~~~e~~Il~~~~-----~~~~~~~~~iv~~~~~~R~~~~~~~~~~r~~i~~~~~  235 (262)
T TIGR02640       161 VEYAGVHETQDALLDRLITIFMDYPDIDTETAILRAKT-----DVAEDSAATIVRLVREFRASGDEITSGLRASLMIAEV  235 (262)
T ss_pred             ccccceecccHHHHhhcEEEECCCCCHHHHHHHHHHhh-----CCCHHHHHHHHHHHHHHHhhCCccCCcHHHHHHHHHH
Confidence            52     5689999999999999999999999988864     45677776665432          1237777777766


Q ss_pred             hhh--CCCcccHHHHHhh
Q psy879          201 THN--GFGHVTAEYVFKV  216 (317)
Q Consensus       201 ~~~--~~~~i~~~~v~~~  216 (317)
                      +..  ....++.+++.++
T Consensus       236 ~~~~~~~~~~~~~~~~~~  253 (262)
T TIGR02640       236 ATQQDIPVDVDDEDFVDL  253 (262)
T ss_pred             HHHcCCCCCCCcHHHHHH
Confidence            544  2234566665543

Members of this family are the GvpN protein associated with the production of gas vesicles produced in some prokaryotes to give cells buoyancy. This family belongs to a larger family of ATPases (pfam07728).

>PRK14700 recombination factor protein RarA; Provisional

Probab=99.72  E-value=1.4e-15  Score=127.62  Aligned_cols=181  Identities=14%  Similarity=0.106  Sum_probs=141.0

Q ss_pred             CCceEEEEec--CCCcCchhHhhhcceeeecCCCHHHHHHHHHHHHHHc------CCCCCHHHHHHHHHhcCCCHHHHHH
Q psy879          125 NTTRFALACN--NSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKE------NISHTNDGLEAIVFTAQGDMRQALN  196 (317)
Q Consensus       125 ~~~~~il~~~--~~~~l~~~i~sR~~~i~f~~~~~~~~~~~l~~~~~~~------~~~i~~~~~~~l~~~~~gd~r~~i~  196 (317)
                      +.+.+|.+|+  +...+.++++|||+++.|.+++.+++..+|.+.+..+      .+.+++++++.|+..++||.|.++|
T Consensus         7 G~i~LIGATTENP~f~vn~ALlSR~~v~~l~~L~~~di~~il~ral~~~~~~~~~~~~i~~~al~~ia~~a~GDaR~aLN   86 (300)
T PRK14700          7 GKIILIGATTENPTYYLNDALVSRLFILRLKRLSLVATQKLIEKALSQDEVLAKHKFKIDDGLYNAMHNYNEGDCRKILN   86 (300)
T ss_pred             CcEEEEeecCCCccceecHhhhhhhheeeecCCCHHHHHHHHHHHHHhhhccCCcCCCcCHHHHHHHHHhcCCHHHHHHH
Confidence            4556666543  3368999999999999999999999999999988642      3679999999999999999999999


Q ss_pred             HHHHhhh---CCC--cccHHHHHhhcC----------CCCHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHH
Q psy879          197 NLQSTHN---GFG--HVTAEYVFKVCD----------EPHPLAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDIIGNI  261 (317)
Q Consensus       197 ~l~~~~~---~~~--~i~~~~v~~~~~----------~~~~~~i~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~~~  261 (317)
                      .|+.++.   +..  .||.+.+++++.          ..+.+.++.++++++..|.+.|+.|+..|++.|++|..|.+.+
T Consensus        87 ~LE~a~~~~~~~~~~~it~~~~~~~~~~~~~~yDk~gd~HYd~iSAf~KSiRGSDpDAAlYyLArml~~GEDp~~IaRRL  166 (300)
T PRK14700         87 LLERMFLISTRGDEIYLNKELFDQAVGETSRDFHREGKEFYEQLSAFHKSVRGTDPDAAIFWLSVMLDNGVDPLVIARRM  166 (300)
T ss_pred             HHHHHHhhccccCCCccCHHHHHHHHhHHHhcccCCcchhHHHHHHHHHHhhcCCccHHHHHHHHHHHcCCCHHHHHHHH
Confidence            9998553   122  389988887552          4577899999999999999999999999999999999999999


Q ss_pred             HHHH-HhcCCChHHHHHHHHHHHHHHhHHhcCC-CcHHHHHHHHHHHH
Q psy879          262 FRVA-KTLDIPEPLKLSIIQEIGNVHLRISEGV-NSLLQLSGLLARLC  307 (317)
Q Consensus       262 ~~~~-~~~~~~~~~~~~~~~~l~~~~~~l~~g~-~~~l~le~~~~~~~  307 (317)
                      ...+ +.+|+.+.....+.....+.-.  .-|. ..++.|-..+.-+|
T Consensus       167 ii~AsEDIGlAdP~al~~a~aa~~A~~--~iG~PEa~i~La~aviyLA  212 (300)
T PRK14700        167 LCIASEDIGNADPQALRVAMDAWNAYE--KLGMPEGRLVLAQAAIYLA  212 (300)
T ss_pred             HHHHHhhccCCCHHHHHHHHHHHHHHH--HhCChHHHHHHHHHHHHHH
Confidence            8876 4557766544333332222222  2354 66677777776666

>KOG0733|consensus

Probab=99.70  E-value=6.9e-16  Score=138.60  Aligned_cols=173  Identities=21%  Similarity=0.280  Sum_probs=127.6

Q ss_pred             CCCcccCCHHHHHHHHHHHh----------cC-CCce-EEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCC----
Q psy879            8 TFSDIVGNEDTVERLKVFSS----------SG-NVPN-IIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASN----   71 (317)
Q Consensus         8 ~~~~~~g~~~~~~~l~~~l~----------~~-~~~~-~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~----   71 (317)
                      +|.++=|.+..+..|...+-          -| .+|. +||+||||||||.+|+++|+++     +.+++.+++..    
T Consensus       188 ~f~diGG~d~~~~el~~li~~i~~Pe~~~~lGv~PprGvLlHGPPGCGKT~lA~AiAgel-----~vPf~~isApeivSG  262 (802)
T KOG0733|consen  188 SFSDIGGLDKTLAELCELIIHIKHPEVFSSLGVRPPRGVLLHGPPGCGKTSLANAIAGEL-----GVPFLSISAPEIVSG  262 (802)
T ss_pred             chhhccChHHHHHHHHHHHHHhcCchhHhhcCCCCCCceeeeCCCCccHHHHHHHHhhhc-----CCceEeecchhhhcc
Confidence            48899999888887666542          23 2333 9999999999999999999996     45567666532    


Q ss_pred             --CcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHH-----------HHHHHHHHhhhcc------CCceEEEE
Q psy879           72 --DRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDG-----------AQQALRRTMEIYS------NTTRFALA  132 (317)
Q Consensus        72 --~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~-----------~~~~ll~~le~~~------~~~~~il~  132 (317)
                        ..+...+++.+.....       ..+.|+||||+|.+++.           ....|+..|++..      ..+.+|.+
T Consensus       263 vSGESEkkiRelF~~A~~-------~aPcivFiDeIDAI~pkRe~aqreMErRiVaQLlt~mD~l~~~~~~g~~VlVIgA  335 (802)
T KOG0733|consen  263 VSGESEKKIRELFDQAKS-------NAPCIVFIDEIDAITPKREEAQREMERRIVAQLLTSMDELSNEKTKGDPVLVIGA  335 (802)
T ss_pred             cCcccHHHHHHHHHHHhc-------cCCeEEEeecccccccchhhHHHHHHHHHHHHHHHhhhcccccccCCCCeEEEec
Confidence              3344567777665543       35889999999999764           2456888888653      34668889


Q ss_pred             ecCCCcCchhHhhhcce---eeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHH
Q psy879          133 CNNSEKIIEPIQSRCAM---LRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQ  193 (317)
Q Consensus       133 ~~~~~~l~~~i~sR~~~---i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~  193 (317)
                      ||+|+.+++++++-+..   |.+.-|++.+..++|..+|+...+.- +-...+|+..+.|-...
T Consensus       336 TnRPDslDpaLRRaGRFdrEI~l~vP~e~aR~~IL~~~~~~lrl~g-~~d~~qlA~lTPGfVGA  398 (802)
T KOG0733|consen  336 TNRPDSLDPALRRAGRFDREICLGVPSETAREEILRIICRGLRLSG-DFDFKQLAKLTPGFVGA  398 (802)
T ss_pred             CCCCcccCHHHhccccccceeeecCCchHHHHHHHHHHHhhCCCCC-CcCHHHHHhcCCCccch
Confidence            99999999999876554   99999999999999999998544322 22356788887664433

>TIGR01242 26Sp45 26S proteasome subunit P45 family

Probab=99.70  E-value=6.1e-16  Score=138.33  Aligned_cols=198  Identities=18%  Similarity=0.227  Sum_probs=126.7

Q ss_pred             CCCCcccCCHHHHHHHHHHHhcC------------C-CceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCC-
Q psy879            7 QTFSDIVGNEDTVERLKVFSSSG------------N-VPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASND-   72 (317)
Q Consensus         7 ~~~~~~~g~~~~~~~l~~~l~~~------------~-~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~-   72 (317)
                      -+|+++.|.+..++.+..++...            . +.+++||||||||||++++++++.+..     .++.+..... 
T Consensus       119 ~~~~di~Gl~~~~~~l~~~i~~~~~~~~~~~~~g~~~p~gvLL~GppGtGKT~lakaia~~l~~-----~~~~v~~~~l~  193 (364)
T TIGR01242       119 VSYEDIGGLEEQIREIREAVELPLKHPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHETNA-----TFIRVVGSELV  193 (364)
T ss_pred             CCHHHhCChHHHHHHHHHHHHHHhcCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHhCCC-----CEEecchHHHH
Confidence            46889999999999888776421            1 234999999999999999999998632     2343332211 


Q ss_pred             ---cC--hHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCH-----------HHHHHHHHHhhhc-----cCCceEEE
Q psy879           73 ---RG--IDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTD-----------GAQQALRRTMEIY-----SNTTRFAL  131 (317)
Q Consensus        73 ---~~--~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~-----------~~~~~ll~~le~~-----~~~~~~il  131 (317)
                         .+  ...++..+....       ...+.||+|||+|.+..           ..+..+..++.+.     .+++.+|+
T Consensus       194 ~~~~g~~~~~i~~~f~~a~-------~~~p~il~iDEiD~l~~~~~~~~~~~~~~~~~~l~~ll~~ld~~~~~~~v~vI~  266 (364)
T TIGR01242       194 RKYIGEGARLVREIFELAK-------EKAPSIIFIDEIDAIAAKRTDSGTSGDREVQRTLMQLLAELDGFDPRGNVKVIA  266 (364)
T ss_pred             HHhhhHHHHHHHHHHHHHH-------hcCCcEEEhhhhhhhccccccCCCCccHHHHHHHHHHHHHhhCCCCCCCEEEEE
Confidence               00  111222222111       13467999999998842           2345555555432     34678999


Q ss_pred             EecCCCcCchhHhh--hcce-eeecCCCHHHHHHHHHHHHHHcCCCCCH-HHHHHHHHhcCC----CHHHHHHHHHHhh-
Q psy879          132 ACNNSEKIIEPIQS--RCAM-LRYNKLTDAQLLSKVIEICEKENISHTN-DGLEAIVFTAQG----DMRQALNNLQSTH-  202 (317)
Q Consensus       132 ~~~~~~~l~~~i~s--R~~~-i~f~~~~~~~~~~~l~~~~~~~~~~i~~-~~~~~l~~~~~g----d~r~~i~~l~~~~-  202 (317)
                      +||.++.+++++.+  |+.. +.|+.|+.++..+++...+....+  ++ .....++..+.|    |++.+....-..+ 
T Consensus       267 ttn~~~~ld~al~r~grfd~~i~v~~P~~~~r~~Il~~~~~~~~l--~~~~~~~~la~~t~g~sg~dl~~l~~~A~~~a~  344 (364)
T TIGR01242       267 ATNRPDILDPALLRPGRFDRIIEVPLPDFEGRLEILKIHTRKMKL--AEDVDLEAIAKMTEGASGADLKAICTEAGMFAI  344 (364)
T ss_pred             ecCChhhCChhhcCcccCceEEEeCCcCHHHHHHHHHHHHhcCCC--CccCCHHHHHHHcCCCCHHHHHHHHHHHHHHHH
Confidence            99999999999975  6554 999999999999999887754333  22 235666766644    4444433322211 


Q ss_pred             -hCCCcccHHHHHhhcC
Q psy879          203 -NGFGHVTAEYVFKVCD  218 (317)
Q Consensus       203 -~~~~~i~~~~v~~~~~  218 (317)
                       .+...|+.+++.+++.
T Consensus       345 ~~~~~~i~~~d~~~a~~  361 (364)
T TIGR01242       345 REERDYVTMDDFIKAVE  361 (364)
T ss_pred             HhCCCccCHHHHHHHHH
Confidence             2456788887766543

Many proteins may score above the trusted cutoff because an internal

>PRK08485 DNA polymerase III subunit delta'; Validated

Probab=99.69  E-value=4e-16  Score=123.02  Aligned_cols=123  Identities=20%  Similarity=0.177  Sum_probs=108.1

Q ss_pred             CCcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcCchhHhhhcce-
Q psy879           71 NDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAM-  149 (317)
Q Consensus        71 ~~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~~~i~sR~~~-  149 (317)
                      +..+++++|+.+......+     ...+ +||+++|.|+..++|+|++++|+||.++.||++|+.+.+++++|+|||+. 
T Consensus        35 ~~i~Vd~iReii~~~~~~~-----~~~k-~iI~~a~~l~~~A~NaLLK~LEEPp~~~~fiL~t~~~~~llpTI~SRc~~~  108 (206)
T PRK08485         35 EEFKIEDAKEVIAEAYIAE-----SEEK-IIVIAAPSYGIEAQNALLKILEEPPKNICFIIVAKSKNLLLPTIRSRLIIE  108 (206)
T ss_pred             CCCCHHHHHHHHHHHhhCC-----CCcE-EEEEchHhhCHHHHHHHHHHhcCCCCCeEEEEEeCChHhCchHHHhhheec
Confidence            3689999999888766554     3344 46789999999999999999999999999999999999999999999986 


Q ss_pred             ------------eeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHH
Q psy879          150 ------------LRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQS  200 (317)
Q Consensus       150 ------------i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~  200 (317)
                                  +.|++++.+++..+|.+ ..++++...+++.+.++..+.|.+|.++...+.
T Consensus       109 ~~~~~~~~~~l~l~l~~l~~~~i~~~L~~-~~ke~~~~~~ea~~lIa~la~~s~r~~l~l~~q  170 (206)
T PRK08485        109 KRKQKKPVKPLDLDLKKLDLKDIYEFLKE-LEKENKLSKEELKELIESLLKECVKYKIPLNEE  170 (206)
T ss_pred             cccccccccccccccCCCCHHHHHHHHHH-HHHcccccHHHHHHHHHHHHHHHHHHHcCccHH
Confidence                        77899999999999999 677888778888999999999999998876654

>KOG0734|consensus

Probab=99.68  E-value=1e-15  Score=135.62  Aligned_cols=195  Identities=19%  Similarity=0.211  Sum_probs=134.4

Q ss_pred             CCCCcccCCHHHHHHHHHHHh-----------cCCCce-EEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCC---
Q psy879            7 QTFSDIVGNEDTVERLKVFSS-----------SGNVPN-IIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASN---   71 (317)
Q Consensus         7 ~~~~~~~g~~~~~~~l~~~l~-----------~~~~~~-~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~---   71 (317)
                      .+|+|+.|-+++++.|...+.           .|++|. +|++||||||||.+|+++|.+.     +.+++....+.   
T Consensus       301 v~F~dVkG~DEAK~ELeEiVefLkdP~kftrLGGKLPKGVLLvGPPGTGKTlLARAvAGEA-----~VPFF~~sGSEFdE  375 (752)
T KOG0734|consen  301 VTFEDVKGVDEAKQELEEIVEFLKDPTKFTRLGGKLPKGVLLVGPPGTGKTLLARAVAGEA-----GVPFFYASGSEFDE  375 (752)
T ss_pred             cccccccChHHHHHHHHHHHHHhcCcHHhhhccCcCCCceEEeCCCCCchhHHHHHhhccc-----CCCeEeccccchhh
Confidence            359999999999888877653           577776 9999999999999999999874     45566655543   


Q ss_pred             ---CcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCH-----------HHHHHHHHHhhhcc--CCceEEEEecC
Q psy879           72 ---DRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTD-----------GAQQALRRTMEIYS--NTTRFALACNN  135 (317)
Q Consensus        72 ---~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~-----------~~~~~ll~~le~~~--~~~~~il~~~~  135 (317)
                         ..+...+|+.+.....       ..+.||+|||+|....           ...|.|+--|+.+.  ..+++|.+||.
T Consensus       376 m~VGvGArRVRdLF~aAk~-------~APcIIFIDEiDavG~kR~~~~~~y~kqTlNQLLvEmDGF~qNeGiIvigATNf  448 (752)
T KOG0734|consen  376 MFVGVGARRVRDLFAAAKA-------RAPCIIFIDEIDAVGGKRNPSDQHYAKQTLNQLLVEMDGFKQNEGIIVIGATNF  448 (752)
T ss_pred             hhhcccHHHHHHHHHHHHh-------cCCeEEEEechhhhcccCCccHHHHHHHHHHHHHHHhcCcCcCCceEEEeccCC
Confidence               2344566666655432       4588999999998742           23455665566443  35667778999


Q ss_pred             CCcCchhHhh--hcce-eeecCCCHHHHHHHHHHHHHHcCCCCCHHH-HHHHHHh----cCCCHHHHHHHHHH--hhhCC
Q psy879          136 SEKIIEPIQS--RCAM-LRYNKLTDAQLLSKVIEICEKENISHTNDG-LEAIVFT----AQGDMRQALNNLQS--THNGF  205 (317)
Q Consensus       136 ~~~l~~~i~s--R~~~-i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~-~~~l~~~----~~gd~r~~i~~l~~--~~~~~  205 (317)
                      ++.+++++.+  ||.. |..+.|+-.-..++|..+..+  +..++++ ...|++-    ++.|+...+|....  +..+.
T Consensus       449 pe~LD~AL~RPGRFD~~v~Vp~PDv~GR~eIL~~yl~k--i~~~~~VD~~iiARGT~GFsGAdLaNlVNqAAlkAa~dga  526 (752)
T KOG0734|consen  449 PEALDKALTRPGRFDRHVTVPLPDVRGRTEILKLYLSK--IPLDEDVDPKIIARGTPGFSGADLANLVNQAALKAAVDGA  526 (752)
T ss_pred             hhhhhHHhcCCCccceeEecCCCCcccHHHHHHHHHhc--CCcccCCCHhHhccCCCCCchHHHHHHHHHHHHHHHhcCc
Confidence            9999999975  4444 888999988888888887764  3333222 2334433    35577777776532  22355


Q ss_pred             CcccHHHHHh
Q psy879          206 GHVTAEYVFK  215 (317)
Q Consensus       206 ~~i~~~~v~~  215 (317)
                      ..++..+++-
T Consensus       527 ~~VtM~~LE~  536 (752)
T KOG0734|consen  527 EMVTMKHLEF  536 (752)
T ss_pred             ccccHHHHhh
Confidence            6677766643

>KOG2227|consensus

Probab=99.68  E-value=1.2e-14  Score=127.16  Aligned_cols=276  Identities=16%  Similarity=0.152  Sum_probs=179.2

Q ss_pred             CcccCCHHHHHHHHHHHh----cCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHH-HHHH
Q psy879           10 SDIVGNEDTVERLKVFSS----SGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRN-KIKM   84 (317)
Q Consensus        10 ~~~~g~~~~~~~l~~~l~----~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~-~~~~   84 (317)
                      ..+.|.+.....++.++.    ......+++.|.||+|||.+...+...+.+.......+++|+........+.. .+..
T Consensus       150 ~~l~gRe~e~~~v~~F~~~hle~~t~gSlYVsG~PGtgkt~~l~rvl~~~~~~~~~~~~v~inc~sl~~~~aiF~kI~~~  229 (529)
T KOG2227|consen  150 GTLKGRELEMDIVREFFSLHLELNTSGSLYVSGQPGTGKTALLSRVLDSLSKSSKSPVTVYINCTSLTEASAIFKKIFSS  229 (529)
T ss_pred             CCccchHHHHHHHHHHHHhhhhcccCcceEeeCCCCcchHHHHHHHHHhhhhhcccceeEEEeeccccchHHHHHHHHHH
Confidence            456788877777776654    33444599999999999999999888876655555567888875333322222 1222


Q ss_pred             HHhhccc---------------CCCCceeEEEEeCCCCCCHHHHHHHHHHhhhc---cCCceEEEEecCC---CcCchhH
Q psy879           85 FAQQKVT---------------LPPGRHKIVILDEADSMTDGAQQALRRTMEIY---SNTTRFALACNNS---EKIIEPI  143 (317)
Q Consensus        85 ~~~~~~~---------------~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~---~~~~~~il~~~~~---~~l~~~i  143 (317)
                      +.+....               ......-|+++||.|.|....+..|+.+++.+   ....++|.++|..   +++++.+
T Consensus       230 ~~q~~~s~~~~~~~~~~~~~h~~q~k~~~llVlDEmD~L~tr~~~vLy~lFewp~lp~sr~iLiGiANslDlTdR~LprL  309 (529)
T KOG2227|consen  230 LLQDLVSPGTGMQHLEKFEKHTKQSKFMLLLVLDEMDHLITRSQTVLYTLFEWPKLPNSRIILIGIANSLDLTDRFLPRL  309 (529)
T ss_pred             HHHHhcCCchhHHHHHHHHHHHhcccceEEEEechhhHHhhcccceeeeehhcccCCcceeeeeeehhhhhHHHHHhhhh
Confidence            2111000               01124668999999999988888888888754   4556667778875   4889999


Q ss_pred             hhhcce----eeecCCCHHHHHHHHHHHHHHcCCCC-CHHHHHHHHHh---cCCCHHHHHHHHHHhhh-------C----
Q psy879          144 QSRCAM----LRYNKLTDAQLLSKVIEICEKENISH-TNDGLEAIVFT---AQGDMRQALNNLQSTHN-------G----  204 (317)
Q Consensus       144 ~sR~~~----i~f~~~~~~~~~~~l~~~~~~~~~~i-~~~~~~~l~~~---~~gd~r~~i~~l~~~~~-------~----  204 (317)
                      ..|+..    +.|+||+.+++.+++..+...+.... -+.+++.++..   ..||+|+|+..++.+..       .    
T Consensus       310 ~~~~~~~P~~l~F~PYTk~qI~~Il~~rl~~~~t~~~~~~Aie~~ArKvaa~SGDlRkaLdv~R~aiEI~E~e~r~~~~~  389 (529)
T KOG2227|consen  310 NLDLTIKPKLLVFPPYTKDQIVEILQQRLSEESTSIFLNAAIELCARKVAAPSGDLRKALDVCRRAIEIAEIEKRKILDD  389 (529)
T ss_pred             hhccCCCCceeeecCCCHHHHHHHHHHHHhcccccccchHHHHHHHHHhccCchhHHHHHHHHHHHHHHHHHHHhhcccc
Confidence            987654    99999999999999999988765433 33466776654   47999999999985432       1    


Q ss_pred             ----------CCcccHHHHHhhcCCCCHHHHHHHHHHHhcCCHHHHHHHHHHHHHc---CCCHHHHHHHHHHHHHhcCCC
Q psy879          205 ----------FGHVTAEYVFKVCDEPHPLAVKEMLLNCVEGNMKDSYKIIHHLYKL---GYAPEDIIGNIFRVAKTLDIP  271 (317)
Q Consensus       205 ----------~~~i~~~~v~~~~~~~~~~~i~~l~~~~~~~~~~~~~~~~~~l~~~---~~~~~~i~~~~~~~~~~~~~~  271 (317)
                                .+.|-.+++..+++.......-...+.+ .....-.+..+..+...   ..+..+++..|.+.|....+.
T Consensus       390 ~l~~~~~p~~~~~v~~~~va~viSk~~~s~~~~s~~sl-plqqkiilctl~~l~r~~kkd~s~~eL~e~Y~k~C~~~~I~  468 (529)
T KOG2227|consen  390 PLSPGTSPEKKKKVGVEHVAAVISKVDGSPSARSRESL-PLQQKIILCTLVLLIRGNKKDVSIAELYEAYLKACQKREIA  468 (529)
T ss_pred             CCCCCCCcccccccchHHHHHHhhhhccChhhhhhhhc-CcccchhHHHHHHHHhcccccccHHHHHHHHHHHHHhccCC
Confidence                      1234456666555543332222222211 22233344444444443   347888999999988877777


Q ss_pred             hHHHHHHHHHHHHHH
Q psy879          272 EPLKLSIIQEIGNVH  286 (317)
Q Consensus       272 ~~~~~~~~~~l~~~~  286 (317)
                      +....++...+.=++
T Consensus       469 ~ld~tEF~~i~~ile  483 (529)
T KOG2227|consen  469 PLDRTEFLSICDILE  483 (529)
T ss_pred             cccHHHHHHHHHHHH
Confidence            777777655544443

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=99.68  E-value=1.8e-15  Score=148.39  Aligned_cols=194  Identities=18%  Similarity=0.261  Sum_probs=141.7

Q ss_pred             cccCCCCCCcccCCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCC-----CCCceEEecCCC-----
Q psy879            2 EKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPS-----FKDAVLELNASN-----   71 (317)
Q Consensus         2 ~ky~P~~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~-----~~~~~~~~~~~~-----   71 (317)
                      ++.||..++.++|+++.++.+...+..+..++.+|+||||+|||++++.++..+....     .+..++.++...     
T Consensus       165 ~~~~~~~~~~~igr~~ei~~~~~~l~r~~~~n~lL~G~pGvGKT~l~~~la~~i~~~~~p~~l~~~~~~~l~~~~l~a~~  244 (852)
T TIGR03346       165 ERAREGKLDPVIGRDEEIRRTIQVLSRRTKNNPVLIGEPGVGKTAIVEGLAQRIVNGDVPESLKNKRLLALDMGALIAGA  244 (852)
T ss_pred             HHhhCCCCCcCCCcHHHHHHHHHHHhcCCCCceEEEcCCCCCHHHHHHHHHHHHhccCCchhhcCCeEEEeeHHHHhhcc
Confidence            5789999999999999999999888777777899999999999999999999874321     123344433211     


Q ss_pred             -CcC--hHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCH--------HHHHHHHHHhhhccCCceEEEEecCCC---
Q psy879           72 -DRG--IDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTD--------GAQQALRRTMEIYSNTTRFALACNNSE---  137 (317)
Q Consensus        72 -~~~--~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~--------~~~~~ll~~le~~~~~~~~il~~~~~~---  137 (317)
                       ..+  ...+...+..+...      ..+.|+||||++.+..        +..+.|...++  .+...+|.+|+...   
T Consensus       245 ~~~g~~e~~l~~~l~~~~~~------~~~~ILfIDEih~l~~~g~~~~~~d~~~~Lk~~l~--~g~i~~IgaTt~~e~r~  316 (852)
T TIGR03346       245 KYRGEFEERLKAVLNEVTKS------EGQIILFIDELHTLVGAGKAEGAMDAGNMLKPALA--RGELHCIGATTLDEYRK  316 (852)
T ss_pred             hhhhhHHHHHHHHHHHHHhc------CCCeEEEeccHHHhhcCCCCcchhHHHHHhchhhh--cCceEEEEeCcHHHHHH
Confidence             111  11233333332211      3578999999998863        34566666665  35677888887653   


Q ss_pred             --cCchhHhhhcceeeecCCCHHHHHHHHHHHHHH----cCCCCCHHHHHHHHHhcC---CC---HHHHHHHHHHhhh
Q psy879          138 --KIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEK----ENISHTNDGLEAIVFTAQ---GD---MRQALNNLQSTHN  203 (317)
Q Consensus       138 --~l~~~i~sR~~~i~f~~~~~~~~~~~l~~~~~~----~~~~i~~~~~~~l~~~~~---gd---~r~~i~~l~~~~~  203 (317)
                        ..++++.+||+.+.++.|+.++...+|.....+    .++.++++++...+..+.   .|   +.+|+++|+.++.
T Consensus       317 ~~~~d~al~rRf~~i~v~~p~~~~~~~iL~~~~~~~e~~~~v~~~d~~i~~~~~ls~~yi~~r~lPdkAidlld~a~a  394 (852)
T TIGR03346       317 YIEKDAALERRFQPVFVDEPTVEDTISILRGLKERYEVHHGVRITDPAIVAAATLSHRYITDRFLPDKAIDLIDEAAA  394 (852)
T ss_pred             HhhcCHHHHhcCCEEEeCCCCHHHHHHHHHHHHHHhccccCCCCCHHHHHHHHHhccccccccCCchHHHHHHHHHHH
Confidence              478999999999999999999999998876544    467788888888877664   34   8899999987665

Members of this protein family are the bacterial ATP-dependent chaperone ClpB. This protein belongs to the AAA family, ATPases associated with various cellular activities (pfam00004). This molecular chaperone does not act as a protease, but rather serves to disaggregate misfolded and aggregated proteins.

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=99.67  E-value=2.3e-15  Score=146.70  Aligned_cols=184  Identities=21%  Similarity=0.268  Sum_probs=133.0

Q ss_pred             CcccCCHHHHHHHHHHHhc--------CCC-ceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHH-
Q psy879           10 SDIVGNEDTVERLKVFSSS--------GNV-PNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVR-   79 (317)
Q Consensus        10 ~~~~g~~~~~~~l~~~l~~--------~~~-~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~-   79 (317)
                      ..++||+++++.+...+..        +++ +.++|.||+|+|||.+|+++++.+.+...  .++.++.+.......+. 
T Consensus       566 ~~v~GQ~~Av~~v~~~i~~~~~gl~~~~~p~~~~lf~Gp~GvGKT~lA~~La~~l~~~~~--~~~~~dmse~~~~~~~~~  643 (852)
T TIGR03345       566 ERVIGQDHALEAIAERIRTARAGLEDPRKPLGVFLLVGPSGVGKTETALALAELLYGGEQ--NLITINMSEFQEAHTVSR  643 (852)
T ss_pred             CeEcChHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCCCCHHHHHHHHHHHHhCCCc--ceEEEeHHHhhhhhhhcc
Confidence            4678999999998877642        122 23899999999999999999999865432  23333322111000000 


Q ss_pred             --------------HHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhcc-----------CCceEEEEec
Q psy879           80 --------------NKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYS-----------NTTRFALACN  134 (317)
Q Consensus        80 --------------~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~-----------~~~~~il~~~  134 (317)
                                    ..+.....      ..++.||++||++++.++.++.|++++++..           .++++|+|||
T Consensus       644 l~g~~~gyvg~~~~g~L~~~v~------~~p~svvllDEieka~~~v~~~Llq~ld~g~l~d~~Gr~vd~~n~iiI~TSN  717 (852)
T TIGR03345       644 LKGSPPGYVGYGEGGVLTEAVR------RKPYSVVLLDEVEKAHPDVLELFYQVFDKGVMEDGEGREIDFKNTVILLTSN  717 (852)
T ss_pred             ccCCCCCcccccccchHHHHHH------hCCCcEEEEechhhcCHHHHHHHHHHhhcceeecCCCcEEeccccEEEEeCC
Confidence                          01111111      1357899999999999999999999998654           6788999988


Q ss_pred             CCC-----------------------------cCchhHhhhcceeeecCCCHHHHHHHHHHHHHH-------c-C--CCC
Q psy879          135 NSE-----------------------------KIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEK-------E-N--ISH  175 (317)
Q Consensus       135 ~~~-----------------------------~l~~~i~sR~~~i~f~~~~~~~~~~~l~~~~~~-------~-~--~~i  175 (317)
                      -..                             .+.|.+.+|+.++.|.|++.+++.+++...+..       . +  +.+
T Consensus       718 lg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~PEflnRi~iI~F~pLs~e~l~~Iv~~~L~~l~~rl~~~~gi~l~i  797 (852)
T TIGR03345       718 AGSDLIMALCADPETAPDPEALLEALRPELLKVFKPAFLGRMTVIPYLPLDDDVLAAIVRLKLDRIARRLKENHGAELVY  797 (852)
T ss_pred             CchHHHHHhccCcccCcchHHHHHHHHHHHHHhccHHHhcceeEEEeCCCCHHHHHHHHHHHHHHHHHHHHHhcCceEEE
Confidence            411                             256889999999999999999999998765432       1 4  467


Q ss_pred             CHHHHHHHHHhcCC---CHHHHHHHHHHh
Q psy879          176 TNDGLEAIVFTAQG---DMRQALNNLQST  201 (317)
Q Consensus       176 ~~~~~~~l~~~~~g---d~r~~i~~l~~~  201 (317)
                      +++++++++..+.+   +.|.+.+.++..
T Consensus       798 ~d~a~~~La~~g~~~~~GAR~L~r~Ie~~  826 (852)
T TIGR03345       798 SEALVEHIVARCTEVESGARNIDAILNQT  826 (852)
T ss_pred             CHHHHHHHHHHcCCCCCChHHHHHHHHHH
Confidence            99999999998876   788888888763

Members of this protein family are homologs of ClpB, an ATPase associated with chaperone-related functions. These ClpB homologs, designated ClpV1, are a key component of the bacterial pathogenicity-associated type VI secretion system.

>PRK13407 bchI magnesium chelatase subunit I; Provisional

Probab=99.67  E-value=4e-15  Score=129.58  Aligned_cols=212  Identities=17%  Similarity=0.198  Sum_probs=130.2

Q ss_pred             CCCCCCcccCCHHHHHHHHHHHh-cCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCC--C-------------------
Q psy879            5 RPQTFSDIVGNEDTVERLKVFSS-SGNVPNIIISGPPGVGKTTTILCLARILLGPSFK--D-------------------   62 (317)
Q Consensus         5 ~P~~~~~~~g~~~~~~~l~~~l~-~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~--~-------------------   62 (317)
                      -|..|.+++||+++++.+.-.+- .| ..|+||+|+||+|||++++++++.+.+....  .                   
T Consensus         3 ~~~~f~~i~Gq~~~~~~l~~~~~~~~-~~~vLl~G~pG~gKT~lar~la~llP~~~~~e~~~~~~~~~~~~~~~~~~~~~   81 (334)
T PRK13407          3 KPFPFSAIVGQEEMKQAMVLTAIDPG-IGGVLVFGDRGTGKSTAVRALAALLPLIKAVEGCPVNSARPEDCPEWAHVSST   81 (334)
T ss_pred             CCCCHHHhCCHHHHHHHHHHHHhccC-CCcEEEEcCCCCCHHHHHHHHHHHCCCcchhcccccccCcccCCcccccccCC
Confidence            47789999999999998775443 44 3489999999999999999999987321100  0                   


Q ss_pred             -------ceEEecC--CC--CcChHHHHHHH--HHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhcc-----
Q psy879           63 -------AVLELNA--SN--DRGIDTVRNKI--KMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYS-----  124 (317)
Q Consensus        63 -------~~~~~~~--~~--~~~~~~i~~~~--~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~-----  124 (317)
                             ++..+..  +.  ..|.-++...+  +.+...+..+......++++||++.+.++.++.|++.|++..     
T Consensus        82 ~~~~~~~p~~~~p~~~t~~~l~G~~d~~~~l~~g~~~~~~G~l~~A~~GiL~lDEInrl~~~~q~~Lle~mee~~v~v~r  161 (334)
T PRK13407         82 TMIERPTPVVDLPLGVTEDRVVGALDIERALTRGEKAFEPGLLARANRGYLYIDEVNLLEDHIVDLLLDVAQSGENVVER  161 (334)
T ss_pred             cccccCCccccCCCCCCcceeecchhhhhhhhcCCeeecCCceEEcCCCeEEecChHhCCHHHHHHHHHHHHcCCeEEEE
Confidence                   0000000  00  01111111111  111111111122456799999999999999999999998532     


Q ss_pred             --------CCceEEEEecCCC-cCchhHhhhcce-eeecCCCH-HHHHHHHHHHHH------------------------
Q psy879          125 --------NTTRFALACNNSE-KIIEPIQSRCAM-LRYNKLTD-AQLLSKVIEICE------------------------  169 (317)
Q Consensus       125 --------~~~~~il~~~~~~-~l~~~i~sR~~~-i~f~~~~~-~~~~~~l~~~~~------------------------  169 (317)
                              ....++.++|..+ .+.+++..||.. +...+++. ++..+++.....                        
T Consensus       162 ~G~~~~~p~rfiviAt~NP~e~~l~~aLldRF~~~v~v~~~~~~~e~~~il~~~~~~~~~~~~~~~~~~~~~~~~~~~i~  241 (334)
T PRK13407        162 EGLSIRHPARFVLVGSGNPEEGELRPQLLDRFGLSVEVRSPRDVETRVEVIRRRDAYDADHDAFMAKWGAEDMQLRGRIL  241 (334)
T ss_pred             CCeEEecCCCEEEEecCCcccCCCCHHHHhhcceEEEcCCCCcHHHHHHHHHHhhcccccchhhhccccccccCCHHHHH
Confidence                    2233444445433 688999999986 77776665 454444443211                        


Q ss_pred             -----HcCCCCCHHHHHHHHHhc---C-CCHHHHHHHHHHhh-----hCCCcccHHHHHhhc
Q psy879          170 -----KENISHTNDGLEAIVFTA---Q-GDMRQALNNLQSTH-----NGFGHVTAEYVFKVC  217 (317)
Q Consensus       170 -----~~~~~i~~~~~~~l~~~~---~-gd~r~~i~~l~~~~-----~~~~~i~~~~v~~~~  217 (317)
                           -..+.++++.++++++.+   + .++|..+.++..+.     .+...|+.++|..+.
T Consensus       242 ~a~~~~~~V~v~~~~~~yi~~l~~~~~~~s~Ra~i~l~~aA~a~A~l~Gr~~V~~~Di~~~~  303 (334)
T PRK13407        242 GARARLPQLKTPNTVLHDCAALCIALGSDGLRGELTLLRAARALAAFEGAEAVGRSHLRSVA  303 (334)
T ss_pred             HHHHhcCCcccCHHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHHcCCCeeCHHHHHHHH
Confidence                 134667888888776543   2 36777776554322     267789999987654

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=99.67  E-value=1.8e-15  Score=146.69  Aligned_cols=169  Identities=17%  Similarity=0.193  Sum_probs=120.6

Q ss_pred             CCCCcccCCHHHHHHHHHHHh------------cCCCc-eEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCC-
Q psy879            7 QTFSDIVGNEDTVERLKVFSS------------SGNVP-NIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASND-   72 (317)
Q Consensus         7 ~~~~~~~g~~~~~~~l~~~l~------------~~~~~-~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~-   72 (317)
                      .+|+++.|.+.+++.|...+.            +...| .+|||||||||||++|+++|+++.     ..++.+.++.. 
T Consensus       450 ~~~~di~g~~~~k~~l~~~v~~~~~~~~~~~~~g~~~~~giLL~GppGtGKT~lakalA~e~~-----~~fi~v~~~~l~  524 (733)
T TIGR01243       450 VRWSDIGGLEEVKQELREAVEWPLKHPEIFEKMGIRPPKGVLLFGPPGTGKTLLAKAVATESG-----ANFIAVRGPEIL  524 (733)
T ss_pred             cchhhcccHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHhcC-----CCEEEEehHHHh
Confidence            368999999999998887764            11233 399999999999999999999863     34565554321 


Q ss_pred             -----cChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCH------------HHHHHHHHHhhh--ccCCceEEEEe
Q psy879           73 -----RGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTD------------GAQQALRRTMEI--YSNTTRFALAC  133 (317)
Q Consensus        73 -----~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~------------~~~~~ll~~le~--~~~~~~~il~~  133 (317)
                           .....++..+.....       ..+.|++|||+|.+.+            ...+.|+..|+.  ...++.+|++|
T Consensus       525 ~~~vGese~~i~~~f~~A~~-------~~p~iifiDEid~l~~~r~~~~~~~~~~~~~~~lL~~ldg~~~~~~v~vI~aT  597 (733)
T TIGR01243       525 SKWVGESEKAIREIFRKARQ-------AAPAIIFFDEIDAIAPARGARFDTSVTDRIVNQLLTEMDGIQELSNVVVIAAT  597 (733)
T ss_pred             hcccCcHHHHHHHHHHHHHh-------cCCEEEEEEChhhhhccCCCCCCccHHHHHHHHHHHHhhcccCCCCEEEEEeC
Confidence                 112234444433322       3578999999998742            235667777773  34577889999


Q ss_pred             cCCCcCchhHhh--hcce-eeecCCCHHHHHHHHHHHHHHcCCCCCH-HHHHHHHHhcCC
Q psy879          134 NNSEKIIEPIQS--RCAM-LRYNKLTDAQLLSKVIEICEKENISHTN-DGLEAIVFTAQG  189 (317)
Q Consensus       134 ~~~~~l~~~i~s--R~~~-i~f~~~~~~~~~~~l~~~~~~~~~~i~~-~~~~~l~~~~~g  189 (317)
                      |.++.+++++.+  ||.. +.|++|+.++..++++...++  ..+++ ..++.++..+.|
T Consensus       598 n~~~~ld~allRpgRfd~~i~v~~Pd~~~R~~i~~~~~~~--~~~~~~~~l~~la~~t~g  655 (733)
T TIGR01243       598 NRPDILDPALLRPGRFDRLILVPPPDEEARKEIFKIHTRS--MPLAEDVDLEELAEMTEG  655 (733)
T ss_pred             CChhhCCHhhcCCCccceEEEeCCcCHHHHHHHHHHHhcC--CCCCccCCHHHHHHHcCC
Confidence            999999999985  8876 999999999999998876553  33333 346777777655

This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.

>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]

Probab=99.66  E-value=6.3e-15  Score=129.92  Aligned_cols=204  Identities=16%  Similarity=0.237  Sum_probs=145.8

Q ss_pred             CCCcccC---CHHHHHHHHHHHhcC--CCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcC--hHHHHH
Q psy879            8 TFSDIVG---NEDTVERLKVFSSSG--NVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRG--IDTVRN   80 (317)
Q Consensus         8 ~~~~~~g---~~~~~~~l~~~l~~~--~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~--~~~i~~   80 (317)
                      +|+.++.   +..+......+....  ..+.++||||+|.|||++++++++.......+..++++.......  ...+++
T Consensus        85 tFdnFv~g~~N~~A~aa~~~va~~~g~~~nplfi~G~~GlGKTHLl~Aign~~~~~~~~a~v~y~~se~f~~~~v~a~~~  164 (408)
T COG0593          85 TFDNFVVGPSNRLAYAAAKAVAENPGGAYNPLFIYGGVGLGKTHLLQAIGNEALANGPNARVVYLTSEDFTNDFVKALRD  164 (408)
T ss_pred             chhheeeCCchHHHHHHHHHHHhccCCcCCcEEEECCCCCCHHHHHHHHHHHHHhhCCCceEEeccHHHHHHHHHHHHHh
Confidence            4777774   334444444444432  244599999999999999999999987666666666665432110  111111


Q ss_pred             -HHHHHHhhcccCCCCceeEEEEeCCCCCCHH--HHHHHHHHhhhccCCc-eEEEEecCC-C---cCchhHhhhcce---
Q psy879           81 -KIKMFAQQKVTLPPGRHKIVILDEADSMTDG--AQQALRRTMEIYSNTT-RFALACNNS-E---KIIEPIQSRCAM---  149 (317)
Q Consensus        81 -~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~--~~~~ll~~le~~~~~~-~~il~~~~~-~---~l~~~i~sR~~~---  149 (317)
                       .+..|...     . ...+++||+++.+...  .+..|..+++...... .+|+++..+ .   .+.+.++||+..   
T Consensus       165 ~~~~~Fk~~-----y-~~dlllIDDiq~l~gk~~~qeefFh~FN~l~~~~kqIvltsdr~P~~l~~~~~rL~SR~~~Gl~  238 (408)
T COG0593         165 NEMEKFKEK-----Y-SLDLLLIDDIQFLAGKERTQEEFFHTFNALLENGKQIVLTSDRPPKELNGLEDRLRSRLEWGLV  238 (408)
T ss_pred             hhHHHHHHh-----h-ccCeeeechHhHhcCChhHHHHHHHHHHHHHhcCCEEEEEcCCCchhhccccHHHHHHHhceeE
Confidence             11122111     2 4569999999998654  4888888887654443 567776554 2   466999999876   


Q ss_pred             eeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhh----CCCcccHHHHHhhc
Q psy879          150 LRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHN----GFGHVTAEYVFKVC  217 (317)
Q Consensus       150 i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~----~~~~i~~~~v~~~~  217 (317)
                      +...||+.+....+|...+...++.++++++.+++.....|+|.+...+..+..    ....||.+.+.+++
T Consensus       239 ~~I~~Pd~e~r~aiL~kka~~~~~~i~~ev~~~la~~~~~nvReLegaL~~l~~~a~~~~~~iTi~~v~e~L  310 (408)
T COG0593         239 VEIEPPDDETRLAILRKKAEDRGIEIPDEVLEFLAKRLDRNVRELEGALNRLDAFALFTKRAITIDLVKEIL  310 (408)
T ss_pred             EeeCCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccHHHHHHHHHHHHHHHHhcCccCcHHHHHHHH
Confidence            999999999999999999999999999999999999999999998888865432    45578888776644

>CHL00095 clpC Clp protease ATP binding subunit

Probab=99.66  E-value=5.1e-15  Score=144.80  Aligned_cols=169  Identities=17%  Similarity=0.214  Sum_probs=120.6

Q ss_pred             CcccCCHHHHHHHHHHHhc--------CCCc-eEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHH-
Q psy879           10 SDIVGNEDTVERLKVFSSS--------GNVP-NIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVR-   79 (317)
Q Consensus        10 ~~~~g~~~~~~~l~~~l~~--------~~~~-~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~-   79 (317)
                      +.++||+++++.+..++..        +++. +++|+||+|+|||++|+++|+.+.+...  .++.++.+.......+. 
T Consensus       509 ~~v~GQ~~ai~~l~~~i~~~~~gl~~~~~p~~~~lf~Gp~GvGKt~lA~~LA~~l~~~~~--~~~~~d~s~~~~~~~~~~  586 (821)
T CHL00095        509 KRIIGQDEAVVAVSKAIRRARVGLKNPNRPIASFLFSGPTGVGKTELTKALASYFFGSED--AMIRLDMSEYMEKHTVSK  586 (821)
T ss_pred             CcCcChHHHHHHHHHHHHHHhhcccCCCCCceEEEEECCCCCcHHHHHHHHHHHhcCCcc--ceEEEEchhccccccHHH
Confidence            4678999999999888752        2222 3899999999999999999999876532  23333332211111111 


Q ss_pred             ---------------HHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhc-----------cCCceEEEEe
Q psy879           80 ---------------NKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIY-----------SNTTRFALAC  133 (317)
Q Consensus        80 ---------------~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~-----------~~~~~~il~~  133 (317)
                                     .......       ..++.||++||+|+++++.++.|++++++.           -.+++||+||
T Consensus       587 l~g~~~gyvg~~~~~~l~~~~~-------~~p~~VvllDeieka~~~v~~~Llq~le~g~~~d~~g~~v~~~~~i~I~Ts  659 (821)
T CHL00095        587 LIGSPPGYVGYNEGGQLTEAVR-------KKPYTVVLFDEIEKAHPDIFNLLLQILDDGRLTDSKGRTIDFKNTLIIMTS  659 (821)
T ss_pred             hcCCCCcccCcCccchHHHHHH-------hCCCeEEEECChhhCCHHHHHHHHHHhccCceecCCCcEEecCceEEEEeC
Confidence                           1111111       135689999999999999999999999964           3578899998


Q ss_pred             cCCC-------------------------------------cCchhHhhhc-ceeeecCCCHHHHHHHHHHHHHH-----
Q psy879          134 NNSE-------------------------------------KIIEPIQSRC-AMLRYNKLTDAQLLSKVIEICEK-----  170 (317)
Q Consensus       134 ~~~~-------------------------------------~l~~~i~sR~-~~i~f~~~~~~~~~~~l~~~~~~-----  170 (317)
                      |...                                     .+.|.+.+|+ .++.|.|++.+++.+++...+..     
T Consensus       660 n~g~~~i~~~~~~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~f~peflnRid~ii~F~pL~~~~l~~Iv~~~l~~l~~rl  739 (821)
T CHL00095        660 NLGSKVIETNSGGLGFELSENQLSEKQYKRLSNLVNEELKQFFRPEFLNRLDEIIVFRQLTKNDVWEIAEIMLKNLFKRL  739 (821)
T ss_pred             CcchHHHHhhccccCCcccccccccccHHHHHHHHHHHHHHhcCHHHhccCCeEEEeCCCCHHHHHHHHHHHHHHHHHHH
Confidence            7421                                     1346789999 67999999999999998766543     


Q ss_pred             --cC--CCCCHHHHHHHHHhc
Q psy879          171 --EN--ISHTNDGLEAIVFTA  187 (317)
Q Consensus       171 --~~--~~i~~~~~~~l~~~~  187 (317)
                        .+  +.+++++.+++++..
T Consensus       740 ~~~~i~l~~~~~~~~~La~~~  760 (821)
T CHL00095        740 NEQGIQLEVTERIKTLLIEEG  760 (821)
T ss_pred             HHCCcEEEECHHHHHHHHHhc
Confidence              32  467899999988863

>KOG0733|consensus

Probab=99.65  E-value=3.9e-15  Score=133.82  Aligned_cols=183  Identities=16%  Similarity=0.232  Sum_probs=125.1

Q ss_pred             CCCcccCCHHHHHHHHHHHhc-----------C-CCce-EEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCC--
Q psy879            8 TFSDIVGNEDTVERLKVFSSS-----------G-NVPN-IIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASND--   72 (317)
Q Consensus         8 ~~~~~~g~~~~~~~l~~~l~~-----------~-~~~~-~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~--   72 (317)
                      +|+|+=+.+++...|.-++..           | ..|. +|+|||||||||.+|+++|++-     +.+|+.+.+...  
T Consensus       509 tW~dIGaL~~vR~eL~~aI~~PiK~pd~~k~lGi~~PsGvLL~GPPGCGKTLlAKAVANEa-----g~NFisVKGPELlN  583 (802)
T KOG0733|consen  509 TWDDIGALEEVRLELNMAILAPIKRPDLFKALGIDAPSGVLLCGPPGCGKTLLAKAVANEA-----GANFISVKGPELLN  583 (802)
T ss_pred             ChhhcccHHHHHHHHHHHHhhhccCHHHHHHhCCCCCCceEEeCCCCccHHHHHHHHhhhc-----cCceEeecCHHHHH
Confidence            599999999999888777542           1 2244 9999999999999999999984     445665554321  


Q ss_pred             cChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHH-----------HHHHHHHHhhhc--cCCceEEEEecCCCcC
Q psy879           73 RGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDG-----------AQQALRRTMEIY--SNTTRFALACNNSEKI  139 (317)
Q Consensus        73 ~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~-----------~~~~ll~~le~~--~~~~~~il~~~~~~~l  139 (317)
                      ....+-...+...++.+.   .+.+.|||+||+|.|.+.           ..|.||-=|+..  ...+.+|.+||+|+.+
T Consensus       584 kYVGESErAVR~vFqRAR---~saPCVIFFDEiDaL~p~R~~~~s~~s~RvvNqLLtElDGl~~R~gV~viaATNRPDiI  660 (802)
T KOG0733|consen  584 KYVGESERAVRQVFQRAR---ASAPCVIFFDEIDALVPRRSDEGSSVSSRVVNQLLTELDGLEERRGVYVIAATNRPDII  660 (802)
T ss_pred             HHhhhHHHHHHHHHHHhh---cCCCeEEEecchhhcCcccCCCCchhHHHHHHHHHHHhcccccccceEEEeecCCCccc
Confidence            111122222333333332   257899999999999653           466777766643  3456678889999999


Q ss_pred             chhHhhhcce---eeecCCCHHHHHHHHHHHHHHcCCCCCHHH-HHHHHHh------cCCCHHHHHHHH
Q psy879          140 IEPIQSRCAM---LRYNKLTDAQLLSKVIEICEKENISHTNDG-LEAIVFT------AQGDMRQALNNL  198 (317)
Q Consensus       140 ~~~i~sR~~~---i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~-~~~l~~~------~~gd~r~~i~~l  198 (317)
                      +|++.+-+..   +....|+.++...+|+.+.+..+..+++++ ++.|+..      +|.|+..++...
T Consensus       661 DpAiLRPGRlDk~LyV~lPn~~eR~~ILK~~tkn~k~pl~~dVdl~eia~~~~c~gftGADLaaLvreA  729 (802)
T KOG0733|consen  661 DPAILRPGRLDKLLYVGLPNAEERVAILKTITKNTKPPLSSDVDLDEIARNTKCEGFTGADLAALVREA  729 (802)
T ss_pred             chhhcCCCccCceeeecCCCHHHHHHHHHHHhccCCCCCCcccCHHHHhhcccccCCchhhHHHHHHHH
Confidence            9999876554   778889999999999999885555554433 4555543      344555444443

>PRK10865 protein disaggregation chaperone; Provisional

Probab=99.65  E-value=2.4e-15  Score=146.98  Aligned_cols=194  Identities=17%  Similarity=0.246  Sum_probs=140.3

Q ss_pred             cccCCCCCCcccCCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCC-----CCCceEEecCCC-----
Q psy879            2 EKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPS-----FKDAVLELNASN-----   71 (317)
Q Consensus         2 ~ky~P~~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~-----~~~~~~~~~~~~-----   71 (317)
                      ++.||..+++++|+++.++.+...+.....++.+|+||||+|||++++.++..+....     .+..++.++...     
T Consensus       170 ~~~r~~~l~~vigr~~ei~~~i~iL~r~~~~n~lL~G~pGvGKT~l~~~la~~i~~~~vp~~l~~~~~~~l~l~~l~ag~  249 (857)
T PRK10865        170 ERAEQGKLDPVIGRDEEIRRTIQVLQRRTKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLALDMGALVAGA  249 (857)
T ss_pred             HHHhcCCCCcCCCCHHHHHHHHHHHhcCCcCceEEECCCCCCHHHHHHHHHHHhhcCCCchhhCCCEEEEEehhhhhhcc
Confidence            5678999999999999999999888887777899999999999999999999874311     123344443221     


Q ss_pred             -CcC--hHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHH--------HHHHHHHHhhhccCCceEEEEecCCC---
Q psy879           72 -DRG--IDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDG--------AQQALRRTMEIYSNTTRFALACNNSE---  137 (317)
Q Consensus        72 -~~~--~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~--------~~~~ll~~le~~~~~~~~il~~~~~~---  137 (317)
                       ..+  ...+...+......      ..+.|+||||++.+...        .++.|...++.  +...+|.+|+..+   
T Consensus       250 ~~~g~~e~~lk~~~~~~~~~------~~~~ILfIDEih~l~~~~~~~~~~d~~~~lkp~l~~--g~l~~IgaTt~~e~r~  321 (857)
T PRK10865        250 KYRGEFEERLKGVLNDLAKQ------EGNVILFIDELHTMVGAGKADGAMDAGNMLKPALAR--GELHCVGATTLDEYRQ  321 (857)
T ss_pred             chhhhhHHHHHHHHHHHHHc------CCCeEEEEecHHHhccCCCCccchhHHHHhcchhhc--CCCeEEEcCCCHHHHH
Confidence             111  11233333332221      35679999999998642        57778888764  5677888888764   


Q ss_pred             --cCchhHhhhcceeeecCCCHHHHHHHHHHHHHH----cCCCCCHHHHHHHHHhcC------CCHHHHHHHHHHhhh
Q psy879          138 --KIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEK----ENISHTNDGLEAIVFTAQ------GDMRQALNNLQSTHN  203 (317)
Q Consensus       138 --~l~~~i~sR~~~i~f~~~~~~~~~~~l~~~~~~----~~~~i~~~~~~~l~~~~~------gd~r~~i~~l~~~~~  203 (317)
                        ..++++.+||+.|.+..|+.++...+|......    .++.++++++...+..+.      .=+..|+.+++.++.
T Consensus       322 ~~~~d~al~rRf~~i~v~eP~~~~~~~iL~~l~~~~e~~~~v~~~d~a~~~a~~ls~ry~~~~~~pdkAi~LiD~aaa  399 (857)
T PRK10865        322 YIEKDAALERRFQKVFVAEPSVEDTIAILRGLKERYELHHHVQITDPAIVAAATLSHRYIADRQLPDKAIDLIDEAAS  399 (857)
T ss_pred             HhhhcHHHHhhCCEEEeCCCCHHHHHHHHHHHhhhhccCCCCCcCHHHHHHHHHHhhccccCCCCChHHHHHHHHHhc
Confidence              478999999999999999999999988776543    356778888776655543      236677888777655

>PRK10787 DNA-binding ATP-dependent protease La; Provisional

Probab=99.65  E-value=8.7e-15  Score=141.16  Aligned_cols=201  Identities=17%  Similarity=0.231  Sum_probs=133.4

Q ss_pred             cccCCHHHHHHHHHHHhc------CCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHHHH-
Q psy879           11 DIVGNEDTVERLKVFSSS------GNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIK-   83 (317)
Q Consensus        11 ~~~g~~~~~~~l~~~l~~------~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~~-   83 (317)
                      +++|.+.+++.+..++..      ...+.++|+||||+|||++++.+++.+..     .+..++.........++.... 
T Consensus       323 ~~~g~~~vK~~i~~~l~~~~~~~~~~g~~i~l~GppG~GKTtl~~~ia~~l~~-----~~~~i~~~~~~d~~~i~g~~~~  397 (784)
T PRK10787        323 DHYGLERVKDRILEYLAVQSRVNKIKGPILCLVGPPGVGKTSLGQSIAKATGR-----KYVRMALGGVRDEAEIRGHRRT  397 (784)
T ss_pred             hccCHHHHHHHHHHHHHHHHhcccCCCceEEEECCCCCCHHHHHHHHHHHhCC-----CEEEEEcCCCCCHHHhccchhc
Confidence            488999999988766541      23446999999999999999999998632     244444332222222221111 


Q ss_pred             -----------HHHhhcccCCCCceeEEEEeCCCCCCHHH----HHHHHHHhhhc---------------cCCceEEEEe
Q psy879           84 -----------MFAQQKVTLPPGRHKIVILDEADSMTDGA----QQALRRTMEIY---------------SNTTRFALAC  133 (317)
Q Consensus        84 -----------~~~~~~~~~~~~~~~vliiDE~d~l~~~~----~~~ll~~le~~---------------~~~~~~il~~  133 (317)
                                 .+...     .....|+++||+|++.++.    +++|+.+++.-               -+++.||+|+
T Consensus       398 ~~g~~~G~~~~~l~~~-----~~~~~villDEidk~~~~~~g~~~~aLlevld~~~~~~~~d~~~~~~~dls~v~~i~Ta  472 (784)
T PRK10787        398 YIGSMPGKLIQKMAKV-----GVKNPLFLLDEIDKMSSDMRGDPASALLEVLDPEQNVAFSDHYLEVDYDLSDVMFVATS  472 (784)
T ss_pred             cCCCCCcHHHHHHHhc-----CCCCCEEEEEChhhcccccCCCHHHHHHHHhccccEEEEecccccccccCCceEEEEcC
Confidence                       11111     1245699999999998764    58999999731               1556677777


Q ss_pred             cCCCcCchhHhhhcceeeecCCCHHHHHHHHHHHHHH----------cCCCCCHHHHHHHHHhcC-----CCHHHHHHHH
Q psy879          134 NNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEK----------ENISHTNDGLEAIVFTAQ-----GDMRQALNNL  198 (317)
Q Consensus       134 ~~~~~l~~~i~sR~~~i~f~~~~~~~~~~~l~~~~~~----------~~~~i~~~~~~~l~~~~~-----gd~r~~i~~l  198 (317)
                      |.. .+++++++||.++.|.+|+.++...+....+..          ..+.++++++..+++.+.     .++++.+..+
T Consensus       473 N~~-~i~~aLl~R~~ii~~~~~t~eek~~Ia~~~L~~k~~~~~~l~~~~l~i~~~ai~~ii~~yt~e~GaR~LeR~I~~i  551 (784)
T PRK10787        473 NSM-NIPAPLLDRMEVIRLSGYTEDEKLNIAKRHLLPKQIERNALKKGELTVDDSAIIGIIRYYTREAGVRSLEREISKL  551 (784)
T ss_pred             CCC-CCCHHHhcceeeeecCCCCHHHHHHHHHHhhhHHHHHHhCCCCCeEEECHHHHHHHHHhCCcccCCcHHHHHHHHH
Confidence            665 699999999999999999999999998776631          135688999999886532     2333333332


Q ss_pred             -HHhh----hCC----CcccHHHHHhhcCCCCH
Q psy879          199 -QSTH----NGF----GHVTAEYVFKVCDEPHP  222 (317)
Q Consensus       199 -~~~~----~~~----~~i~~~~v~~~~~~~~~  222 (317)
                       +..+    .+.    -.++.+++.+.++....
T Consensus       552 ~r~~l~~~~~~~~~~~v~v~~~~~~~~lg~~~~  584 (784)
T PRK10787        552 CRKAVKQLLLDKSLKHIEINGDNLHDYLGVQRF  584 (784)
T ss_pred             HHHHHHHHHhcCCCceeeecHHHHHHHhCCCcc
Confidence             1111    111    25788888887776543

>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional

Probab=99.64  E-value=5.9e-15  Score=141.30  Aligned_cols=169  Identities=16%  Similarity=0.256  Sum_probs=119.1

Q ss_pred             cccCCHHHHHHHHHHHhc--------CCC-ceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHH
Q psy879           11 DIVGNEDTVERLKVFSSS--------GNV-PNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNK   81 (317)
Q Consensus        11 ~~~g~~~~~~~l~~~l~~--------~~~-~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~   81 (317)
                      .++||+++++.+..++..        +++ .+++|+||||+|||++|+.+|+.+.     ..++.++++.......+...
T Consensus       459 ~ViGQ~~ai~~l~~~i~~~~~gl~~~~kp~~~~Lf~GP~GvGKT~lAk~LA~~l~-----~~~i~id~se~~~~~~~~~L  533 (758)
T PRK11034        459 LVFGQDKAIEALTEAIKMSRAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKALG-----IELLRFDMSEYMERHTVSRL  533 (758)
T ss_pred             eEeCcHHHHHHHHHHHHHHhccccCCCCCcceEEEECCCCCCHHHHHHHHHHHhC-----CCcEEeechhhcccccHHHH
Confidence            478999999998888762        222 3599999999999999999999973     23455554332211111111


Q ss_pred             HH------------HHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhcc-----------CCceEEEEecCC--
Q psy879           82 IK------------MFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYS-----------NTTRFALACNNS--  136 (317)
Q Consensus        82 ~~------------~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~-----------~~~~~il~~~~~--  136 (317)
                      ++            .+...   ....++.|+++||+|++.++.++.|+++|++..           .++++|+|||..  
T Consensus       534 iG~~~gyvg~~~~g~L~~~---v~~~p~sVlllDEieka~~~v~~~LLq~ld~G~ltd~~g~~vd~rn~iiI~TsN~g~~  610 (758)
T PRK11034        534 IGAPPGYVGFDQGGLLTDA---VIKHPHAVLLLDEIEKAHPDVFNLLLQVMDNGTLTDNNGRKADFRNVVLVMTTNAGVR  610 (758)
T ss_pred             cCCCCCcccccccchHHHH---HHhCCCcEEEeccHhhhhHHHHHHHHHHHhcCeeecCCCceecCCCcEEEEeCCcCHH
Confidence            11            00000   001356899999999999999999999998531           467799998832  


Q ss_pred             -----------------------CcCchhHhhhcc-eeeecCCCHHHHHHHHHHHHH-------HcC--CCCCHHHHHHH
Q psy879          137 -----------------------EKIIEPIQSRCA-MLRYNKLTDAQLLSKVIEICE-------KEN--ISHTNDGLEAI  183 (317)
Q Consensus       137 -----------------------~~l~~~i~sR~~-~i~f~~~~~~~~~~~l~~~~~-------~~~--~~i~~~~~~~l  183 (317)
                                             ..+.|.+..|+. ++.|+|++.+++.+++...+.       ..|  +.+++++++.+
T Consensus       611 ~~~~~~~g~~~~~~~~~~~~~~~~~f~pefl~Rid~ii~f~~L~~~~l~~I~~~~l~~~~~~l~~~~i~l~~~~~~~~~l  690 (758)
T PRK11034        611 ETERKSIGLIHQDNSTDAMEEIKKIFTPEFRNRLDNIIWFDHLSTDVIHQVVDKFIVELQAQLDQKGVSLEVSQEARDWL  690 (758)
T ss_pred             HHhhcccCcccchhhHHHHHHHHHhcCHHHHccCCEEEEcCCCCHHHHHHHHHHHHHHHHHHHHHCCCCceECHHHHHHH
Confidence                                   125688999997 599999999999988875543       234  45688999998


Q ss_pred             HHhc
Q psy879          184 VFTA  187 (317)
Q Consensus       184 ~~~~  187 (317)
                      +...
T Consensus       691 ~~~~  694 (758)
T PRK11034        691 AEKG  694 (758)
T ss_pred             HHhC
Confidence            8654

>PLN00020 ribulose bisphosphate carboxylase/oxygenase activase -RuBisCO activase (RCA); Provisional

Probab=99.64  E-value=2.8e-15  Score=129.13  Aligned_cols=151  Identities=15%  Similarity=0.168  Sum_probs=108.8

Q ss_pred             CCce-EEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCC------CcChHHHHHHHHHHHhhcccCCCCceeEEEE
Q psy879           30 NVPN-IIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASN------DRGIDTVRNKIKMFAQQKVTLPPGRHKIVIL  102 (317)
Q Consensus        30 ~~~~-~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~------~~~~~~i~~~~~~~~~~~~~~~~~~~~vlii  102 (317)
                      ++|. ++||||||||||.+++++|+++.     ..++.++...      ......+++.+........  ..+.+.||+|
T Consensus       146 k~PlgllL~GPPGcGKTllAraiA~elg-----~~~i~vsa~eL~sk~vGEsEk~IR~~F~~A~~~a~--~~~aPcVLFI  218 (413)
T PLN00020        146 KVPLILGIWGGKGQGKSFQCELVFKKMG-----IEPIVMSAGELESENAGEPGKLIRQRYREAADIIK--KKGKMSCLFI  218 (413)
T ss_pred             CCCeEEEeeCCCCCCHHHHHHHHHHHcC-----CCeEEEEHHHhhcCcCCcHHHHHHHHHHHHHHHhh--ccCCCeEEEE
Confidence            4444 99999999999999999999963     3355555432      1223456666665543210  1256889999


Q ss_pred             eCCCCCCHH-----------H-HHHHHHHhhhc--------------cCCceEEEEecCCCcCchhHhh--hcceeeecC
Q psy879          103 DEADSMTDG-----------A-QQALRRTMEIY--------------SNTTRFALACNNSEKIIEPIQS--RCAMLRYNK  154 (317)
Q Consensus       103 DE~d~l~~~-----------~-~~~ll~~le~~--------------~~~~~~il~~~~~~~l~~~i~s--R~~~i~f~~  154 (317)
                      ||+|.+.+.           . ...|+..++.+              ...+.+|.|||+++.+++++++  |+..+ |..
T Consensus       219 DEIDA~~g~r~~~~~tv~~qiV~~tLLnl~D~p~~v~l~G~w~~~~~~~~V~VIaTTNrpd~LDpALlRpGRfDk~-i~l  297 (413)
T PLN00020        219 NDLDAGAGRFGTTQYTVNNQMVNGTLMNIADNPTNVSLGGDWREKEEIPRVPIIVTGNDFSTLYAPLIRDGRMEKF-YWA  297 (413)
T ss_pred             ehhhhcCCCCCCCCcchHHHHHHHHHHHHhcCCccccccccccccccCCCceEEEeCCCcccCCHhHcCCCCCCce-eCC
Confidence            999987542           1 24567766542              3457789999999999999999  77664 458


Q ss_pred             CCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCC
Q psy879          155 LTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGD  190 (317)
Q Consensus       155 ~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd  190 (317)
                      |+.++...++..++++.+  ++...+..++....|-
T Consensus       298 Pd~e~R~eIL~~~~r~~~--l~~~dv~~Lv~~f~gq  331 (413)
T PLN00020        298 PTREDRIGVVHGIFRDDG--VSREDVVKLVDTFPGQ  331 (413)
T ss_pred             CCHHHHHHHHHHHhccCC--CCHHHHHHHHHcCCCC
Confidence            999999999999888765  5578888888887763

>KOG1942|consensus

Probab=99.64  E-value=2e-14  Score=118.82  Aligned_cols=119  Identities=15%  Similarity=0.188  Sum_probs=100.1

Q ss_pred             eeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCC-------------CcCchhHhhhcceeeecCCCHHHHHHH
Q psy879           97 HKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNS-------------EKIIEPIQSRCAMLRYNKLTDAQLLSK  163 (317)
Q Consensus        97 ~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~-------------~~l~~~i~sR~~~i~f~~~~~~~~~~~  163 (317)
                      +.|+||||++.|.-+....|.+.+|.+-. .++||++|.-             +.+++.+..|..+++-.++++++++++
T Consensus       297 PGVLFIDEVhMLDiEcFTyL~kalES~ia-PivifAsNrG~~~irGt~d~~sPhGip~dllDRl~Iirt~~y~~~e~r~I  375 (456)
T KOG1942|consen  297 PGVLFIDEVHMLDIECFTYLHKALESPIA-PIVIFASNRGMCTIRGTEDILSPHGIPPDLLDRLLIIRTLPYDEEEIRQI  375 (456)
T ss_pred             CcceEeeehhhhhhHHHHHHHHHhcCCCC-ceEEEecCCcceeecCCcCCCCCCCCCHHHhhheeEEeeccCCHHHHHHH
Confidence            68999999999999999999999997544 4577877752             368899999999999999999999999


Q ss_pred             HHHHHHHcCCCCCHHHHHHHHHh-cCCCHHHHHHHHHHh---hh--CCCcccHHHHHhh
Q psy879          164 VIEICEKENISHTNDGLEAIVFT-AQGDMRQALNNLQST---HN--GFGHVTAEYVFKV  216 (317)
Q Consensus       164 l~~~~~~~~~~i~~~~~~~l~~~-~~gd~r~~i~~l~~~---~~--~~~~i~~~~v~~~  216 (317)
                      +..+++.+++.++++++..++.. +..++|.++.+|--+   +.  +.+.|..++|+++
T Consensus       376 i~~Ra~~E~l~~~e~a~~~l~~~gt~tsLRy~vqLl~p~~~~ak~~g~~~i~v~dvee~  434 (456)
T KOG1942|consen  376 IKIRAQVEGLQVEEEALDLLAEIGTSTSLRYAVQLLTPASILAKTNGRKEISVEDVEEV  434 (456)
T ss_pred             HHHHHhhhcceecHHHHHHHHhhccchhHHHHHHhcCHHHHHHHHcCCceeecccHHHH
Confidence            99999999999999999999976 467899999988532   22  5557777777653

>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional

Probab=99.63  E-value=7.4e-15  Score=140.62  Aligned_cols=202  Identities=15%  Similarity=0.164  Sum_probs=138.8

Q ss_pred             CCCCCcccCCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCC-----CCceEEecCCCC----cChH
Q psy879            6 PQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSF-----KDAVLELNASND----RGID   76 (317)
Q Consensus         6 P~~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~-----~~~~~~~~~~~~----~~~~   76 (317)
                      -..++.++|++..++.+...+.....++++|+||||+|||++++.++..+.....     +..++.++....    ....
T Consensus       182 ~g~~~~liGR~~ei~~~i~iL~r~~~~n~LLvGppGvGKT~lae~la~~i~~~~vP~~l~~~~~~~l~~~~llaG~~~~G  261 (758)
T PRK11034        182 VGGIDPLIGREKELERAIQVLCRRRKNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDIGSLLAGTKYRG  261 (758)
T ss_pred             cCCCCcCcCCCHHHHHHHHHHhccCCCCeEEECCCCCCHHHHHHHHHHHHHhcCCCchhcCCeEEeccHHHHhcccchhh
Confidence            3457889999999999888888776678999999999999999999987643221     122233221110    0011


Q ss_pred             H----HHHHHHHHHhhcccCCCCceeEEEEeCCCCCCH---------HHHHHHHHHhhhccCCceEEEEecCCC-----c
Q psy879           77 T----VRNKIKMFAQQKVTLPPGRHKIVILDEADSMTD---------GAQQALRRTMEIYSNTTRFALACNNSE-----K  138 (317)
Q Consensus        77 ~----i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~---------~~~~~ll~~le~~~~~~~~il~~~~~~-----~  138 (317)
                      +    ++..+..+..       ..+.+++|||+|.+..         +..+.|..+++.  +...+|.+|+.++     .
T Consensus       262 e~e~rl~~l~~~l~~-------~~~~ILfIDEIh~L~g~g~~~~g~~d~~nlLkp~L~~--g~i~vIgATt~~E~~~~~~  332 (758)
T PRK11034        262 DFEKRFKALLKQLEQ-------DTNSILFIDEIHTIIGAGAASGGQVDAANLIKPLLSS--GKIRVIGSTTYQEFSNIFE  332 (758)
T ss_pred             hHHHHHHHHHHHHHh-------cCCCEEEeccHHHHhccCCCCCcHHHHHHHHHHHHhC--CCeEEEecCChHHHHHHhh
Confidence            2    2222222221       3467999999998731         234456666663  5677888887653     4


Q ss_pred             CchhHhhhcceeeecCCCHHHHHHHHHHHHH----HcCCCCCHHHHHHHHHhcCC------CHHHHHHHHHHhhhC----
Q psy879          139 IIEPIQSRCAMLRYNKLTDAQLLSKVIEICE----KENISHTNDGLEAIVFTAQG------DMRQALNNLQSTHNG----  204 (317)
Q Consensus       139 l~~~i~sR~~~i~f~~~~~~~~~~~l~~~~~----~~~~~i~~~~~~~l~~~~~g------d~r~~i~~l~~~~~~----  204 (317)
                      .++++.+||+.|.+++|+.++...+|.....    .+++.++++++...+..+..      -+.+++++++.++..    
T Consensus       333 ~D~AL~rRFq~I~v~ePs~~~~~~IL~~~~~~ye~~h~v~i~~~al~~a~~ls~ryi~~r~lPdKaidlldea~a~~~~~  412 (758)
T PRK11034        333 KDRALARRFQKIDITEPSIEETVQIINGLKPKYEAHHDVRYTAKAVRAAVELAVKYINDRHLPDKAIDVIDEAGARARLM  412 (758)
T ss_pred             ccHHHHhhCcEEEeCCCCHHHHHHHHHHHHHHhhhccCCCcCHHHHHHHHHHhhccccCccChHHHHHHHHHHHHhhccC
Confidence            6899999999999999999999999987543    35788999999887765532      366999999877641    


Q ss_pred             -----CCcccHHHHHhh
Q psy879          205 -----FGHVTAEYVFKV  216 (317)
Q Consensus       205 -----~~~i~~~~v~~~  216 (317)
                           ...++.++|.++
T Consensus       413 ~~~~~~~~v~~~~i~~v  429 (758)
T PRK11034        413 PVSKRKKTVNVADIESV  429 (758)
T ss_pred             cccccccccChhhHHHH
Confidence                 223566666554

>KOG0731|consensus

Probab=99.63  E-value=1.6e-14  Score=134.94  Aligned_cols=200  Identities=18%  Similarity=0.265  Sum_probs=140.9

Q ss_pred             CCCCcccCCHHHHHHHHHHHh---c--------CCCce-EEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCC---
Q psy879            7 QTFSDIVGNEDTVERLKVFSS---S--------GNVPN-IIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASN---   71 (317)
Q Consensus         7 ~~~~~~~g~~~~~~~l~~~l~---~--------~~~~~-~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~---   71 (317)
                      -+|.|+.|.+++++.|..++.   +        -++|. +||+||||||||.+|+++|.+-     +.+++.++++.   
T Consensus       308 V~FkDVAG~deAK~El~E~V~fLKNP~~Y~~lGAKiPkGvLL~GPPGTGKTLLAKAiAGEA-----gVPF~svSGSEFvE  382 (774)
T KOG0731|consen  308 VKFKDVAGVDEAKEELMEFVKFLKNPEQYQELGAKIPKGVLLVGPPGTGKTLLAKAIAGEA-----GVPFFSVSGSEFVE  382 (774)
T ss_pred             CccccccCcHHHHHHHHHHHHHhcCHHHHHHcCCcCcCceEEECCCCCcHHHHHHHHhccc-----CCceeeechHHHHH
Confidence            469999999999998877653   2        24566 9999999999999999999983     66788777764   


Q ss_pred             ---CcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHH---------------HHHHHHHHhhhc--cCCceEEE
Q psy879           72 ---DRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDG---------------AQQALRRTMEIY--SNTTRFAL  131 (317)
Q Consensus        72 ---~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~---------------~~~~ll~~le~~--~~~~~~il  131 (317)
                         ..+...+++.+.....       ..+.+++|||+|.....               ..|.|+--|+..  ...++++.
T Consensus       383 ~~~g~~asrvr~lf~~ar~-------~aP~iifideida~~~~r~G~~~~~~~~e~e~tlnQll~emDgf~~~~~vi~~a  455 (774)
T KOG0731|consen  383 MFVGVGASRVRDLFPLARK-------NAPSIIFIDEIDAVGRKRGGKGTGGGQDEREQTLNQLLVEMDGFETSKGVIVLA  455 (774)
T ss_pred             HhcccchHHHHHHHHHhhc-------cCCeEEEecccccccccccccccCCCChHHHHHHHHHHHHhcCCcCCCcEEEEe
Confidence               2234445555544322       45889999999976421               234444445432  34566777


Q ss_pred             EecCCCcCchhHhhhcce---eeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCC----CHHHHHHHHHHhh--
Q psy879          132 ACNNSEKIIEPIQSRCAM---LRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQG----DMRQALNNLQSTH--  202 (317)
Q Consensus       132 ~~~~~~~l~~~i~sR~~~---i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~g----d~r~~i~~l~~~~--  202 (317)
                      +||+++-+++++++-...   +....|+.....+++.-.+++-....++..+..++..+.|    |+..+.|+....+  
T Consensus       456 ~tnr~d~ld~allrpGRfdr~i~i~~p~~~~r~~i~~~h~~~~~~~~e~~dl~~~a~~t~gf~gadl~n~~neaa~~a~r  535 (774)
T KOG0731|consen  456 ATNRPDILDPALLRPGRFDRQIQIDLPDVKGRASILKVHLRKKKLDDEDVDLSKLASLTPGFSGADLANLCNEAALLAAR  535 (774)
T ss_pred             ccCCccccCHHhcCCCccccceeccCCchhhhHHHHHHHhhccCCCcchhhHHHHHhcCCCCcHHHHHhhhhHHHHHHHH
Confidence            899999999999875544   9999999999999999988766665456666678877655    4444444443222  


Q ss_pred             hCCCcccHHHHHhhcC
Q psy879          203 NGFGHVTAEYVFKVCD  218 (317)
Q Consensus       203 ~~~~~i~~~~v~~~~~  218 (317)
                      .+...|+.+++..+++
T Consensus       536 ~~~~~i~~~~~~~a~~  551 (774)
T KOG0731|consen  536 KGLREIGTKDLEYAIE  551 (774)
T ss_pred             hccCccchhhHHHHHH
Confidence            2566788877766554

>COG0466 Lon ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]

Probab=99.63  E-value=1.1e-14  Score=133.63  Aligned_cols=166  Identities=21%  Similarity=0.328  Sum_probs=120.1

Q ss_pred             cccCCHHHHHHHHHHHh------cCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHHH--
Q psy879           11 DIVGNEDTVERLKVFSS------SGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKI--   82 (317)
Q Consensus        11 ~~~g~~~~~~~l~~~l~------~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~--   82 (317)
                      +.+|-+++++++..++.      +-+.|.++|+||||+|||++++.+|+.+..     .|+.+.-...+...+||..-  
T Consensus       324 dHYGLekVKeRIlEyLAV~~l~~~~kGpILcLVGPPGVGKTSLgkSIA~al~R-----kfvR~sLGGvrDEAEIRGHRRT  398 (782)
T COG0466         324 DHYGLEKVKERILEYLAVQKLTKKLKGPILCLVGPPGVGKTSLGKSIAKALGR-----KFVRISLGGVRDEAEIRGHRRT  398 (782)
T ss_pred             cccCchhHHHHHHHHHHHHHHhccCCCcEEEEECCCCCCchhHHHHHHHHhCC-----CEEEEecCccccHHHhcccccc
Confidence            56788888888777653      222356999999999999999999999843     35555444334444444321  


Q ss_pred             ----------HHHHhhcccCCCCceeEEEEeCCCCCCHH----HHHHHHHHhh-------------hc--cCCceEEEEe
Q psy879           83 ----------KMFAQQKVTLPPGRHKIVILDEADSMTDG----AQQALRRTME-------------IY--SNTTRFALAC  133 (317)
Q Consensus        83 ----------~~~~~~~~~~~~~~~~vliiDE~d~l~~~----~~~~ll~~le-------------~~--~~~~~~il~~  133 (317)
                                ..+...     ...+.|+++||+|+|..+    -..+||..|+             .+  =+++.||+|+
T Consensus       399 YIGamPGrIiQ~mkka-----~~~NPv~LLDEIDKm~ss~rGDPaSALLEVLDPEQN~~F~DhYLev~yDLS~VmFiaTA  473 (782)
T COG0466         399 YIGAMPGKIIQGMKKA-----GVKNPVFLLDEIDKMGSSFRGDPASALLEVLDPEQNNTFSDHYLEVPYDLSKVMFIATA  473 (782)
T ss_pred             ccccCChHHHHHHHHh-----CCcCCeEEeechhhccCCCCCChHHHHHhhcCHhhcCchhhccccCccchhheEEEeec
Confidence                      111111     135789999999999754    4678888876             11  1467799999


Q ss_pred             cCCCcCchhHhhhcceeeecCCCHHHHHHHHHHHH-----HHc-----CCCCCHHHHHHHHHh
Q psy879          134 NNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEIC-----EKE-----NISHTNDGLEAIVFT  186 (317)
Q Consensus       134 ~~~~~l~~~i~sR~~~i~f~~~~~~~~~~~l~~~~-----~~~-----~~~i~~~~~~~l~~~  186 (317)
                      |..+.++.+++.|..+|++..|+++|-.++.+.++     +..     .+.++++++..+++.
T Consensus       474 Nsl~tIP~PLlDRMEiI~lsgYt~~EKl~IAk~~LiPk~~~~~gL~~~el~i~d~ai~~iI~~  536 (782)
T COG0466         474 NSLDTIPAPLLDRMEVIRLSGYTEDEKLEIAKRHLIPKQLKEHGLKKGELTITDEAIKDIIRY  536 (782)
T ss_pred             CccccCChHHhcceeeeeecCCChHHHHHHHHHhcchHHHHHcCCCccceeecHHHHHHHHHH
Confidence            99999999999999999999999999888877653     333     356789998887754

>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily

Probab=99.62  E-value=7.8e-14  Score=119.90  Aligned_cols=198  Identities=17%  Similarity=0.162  Sum_probs=124.9

Q ss_pred             HHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEE-ecCCC------------------CcChH
Q psy879           16 EDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLE-LNASN------------------DRGID   76 (317)
Q Consensus        16 ~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~-~~~~~------------------~~~~~   76 (317)
                      ..+...+...++.+. +.++++||+|+||||+++.+++.+.+..  ..... .+...                  .....
T Consensus        29 ~~~~~~l~~~~~~~~-~~~~l~G~~G~GKTtl~~~l~~~l~~~~--~~~~~~~~~~~~~~~~l~~i~~~lG~~~~~~~~~  105 (269)
T TIGR03015        29 KRAMAYLEYGLSQRE-GFILITGEVGAGKTTLIRNLLKRLDQER--VVAAKLVNTRVDAEDLLRMVAADFGLETEGRDKA  105 (269)
T ss_pred             HHHHHHHHHHHhcCC-CEEEEEcCCCCCHHHHHHHHHHhcCCCC--eEEeeeeCCCCCHHHHHHHHHHHcCCCCCCCCHH
Confidence            445555665565443 3489999999999999999999875321  11111 11100                  00000


Q ss_pred             HHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhc---cCCceEEEEecCCC------cCchhHhhhc
Q psy879           77 TVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIY---SNTTRFALACNNSE------KIIEPIQSRC  147 (317)
Q Consensus        77 ~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~---~~~~~~il~~~~~~------~l~~~i~sR~  147 (317)
                      .....+..+....  ...+...+++|||++.+.....+.|..+.+..   .....+++++....      .-..++.+|+
T Consensus       106 ~~~~~l~~~l~~~--~~~~~~~vliiDe~~~l~~~~~~~l~~l~~~~~~~~~~~~vvl~g~~~~~~~l~~~~~~~l~~r~  183 (269)
T TIGR03015       106 ALLRELEDFLIEQ--FAAGKRALLVVDEAQNLTPELLEELRMLSNFQTDNAKLLQIFLVGQPEFRETLQSPQLQQLRQRI  183 (269)
T ss_pred             HHHHHHHHHHHHH--HhCCCCeEEEEECcccCCHHHHHHHHHHhCcccCCCCeEEEEEcCCHHHHHHHcCchhHHHHhhe
Confidence            1111111111000  01245679999999999988777765544421   12234455554321      1234678885


Q ss_pred             c-eeeecCCCHHHHHHHHHHHHHHcC----CCCCHHHHHHHHHhcCCCHHHHHHHHHHhh-----hCCCcccHHHHHhhc
Q psy879          148 A-MLRYNKLTDAQLLSKVIEICEKEN----ISHTNDGLEAIVFTAQGDMRQALNNLQSTH-----NGFGHVTAEYVFKVC  217 (317)
Q Consensus       148 ~-~i~f~~~~~~~~~~~l~~~~~~~~----~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~-----~~~~~i~~~~v~~~~  217 (317)
                      . .+++++++.+++..++...+...+    ..+++++++.+.+.++|++|.+...+..+.     .+.+.|+.++|..++
T Consensus       184 ~~~~~l~~l~~~e~~~~l~~~l~~~g~~~~~~~~~~~~~~i~~~s~G~p~~i~~l~~~~~~~a~~~~~~~i~~~~v~~~~  263 (269)
T TIGR03015       184 IASCHLGPLDREETREYIEHRLERAGNRDAPVFSEGAFDAIHRFSRGIPRLINILCDRLLLSAFLEEKREIGGEEVREVI  263 (269)
T ss_pred             eeeeeCCCCCHHHHHHHHHHHHHHcCCCCCCCcCHHHHHHHHHHcCCcccHHHHHHHHHHHHHHHcCCCCCCHHHHHHHH
Confidence            4 489999999999999999887654    368899999999999999999777666542     256788888887654


Q ss_pred             C
Q psy879          218 D  218 (317)
Q Consensus       218 ~  218 (317)
                      .
T Consensus       264 ~  264 (269)
T TIGR03015       264 A  264 (269)
T ss_pred             H
Confidence            4

Members of this protein are marked as probable ATPases by the nucleotide binding P-loop motif GXXGXGKTT, a motif DEAQ similar to the DEAD/H box of helicases, and extensive homology to ATPases of MSHA-type pilus systems and to GspA proteins associated with type II protein secretion systems.

>KOG0727|consensus

Probab=99.62  E-value=2.7e-14  Score=115.65  Aligned_cols=154  Identities=19%  Similarity=0.333  Sum_probs=109.3

Q ss_pred             CCCcccCCHHHHHHHHHHHhc-----------C-CCce-EEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCC---
Q psy879            8 TFSDIVGNEDTVERLKVFSSS-----------G-NVPN-IIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASN---   71 (317)
Q Consensus         8 ~~~~~~g~~~~~~~l~~~l~~-----------~-~~~~-~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~---   71 (317)
                      ++.|+-|-+-.++.++.+++-           | .+|. +|+|||||||||.+++++|+.-     ...++.+.++.   
T Consensus       153 sy~diggld~qkqeireavelplt~~~ly~qigidpprgvllygppg~gktml~kava~~t-----~a~firvvgsefvq  227 (408)
T KOG0727|consen  153 SYADIGGLDVQKQEIREAVELPLTHADLYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT-----TAAFIRVVGSEFVQ  227 (408)
T ss_pred             cccccccchhhHHHHHHHHhccchHHHHHHHhCCCCCcceEEeCCCCCcHHHHHHHHhhcc-----chheeeeccHHHHH
Confidence            467777766555556655431           2 2333 9999999999999999999863     33456655542   


Q ss_pred             ---CcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCH-----------HHHHHHHHHhhh-----ccCCceEEEE
Q psy879           72 ---DRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTD-----------GAQQALRRTMEI-----YSNTTRFALA  132 (317)
Q Consensus        72 ---~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~-----------~~~~~ll~~le~-----~~~~~~~il~  132 (317)
                         ..++.-+++.+.....       ..+.+++|||+|.+..           +.|..|+.++..     ...++.+|++
T Consensus       228 kylgegprmvrdvfrlake-------napsiifideidaiatkrfdaqtgadrevqril~ellnqmdgfdq~~nvkvima  300 (408)
T KOG0727|consen  228 KYLGEGPRMVRDVFRLAKE-------NAPSIIFIDEIDAIATKRFDAQTGADREVQRILIELLNQMDGFDQTTNVKVIMA  300 (408)
T ss_pred             HHhccCcHHHHHHHHHHhc-------cCCcEEEeehhhhHhhhhccccccccHHHHHHHHHHHHhccCcCcccceEEEEe
Confidence               2345556666555433       3578999999997632           356666666653     3457889999


Q ss_pred             ecCCCcCchhHhhhcce---eeecCCCHHHHHHHHHHHHHHcCC
Q psy879          133 CNNSEKIIEPIQSRCAM---LRYNKLTDAQLLSKVIEICEKENI  173 (317)
Q Consensus       133 ~~~~~~l~~~i~sR~~~---i~f~~~~~~~~~~~l~~~~~~~~~  173 (317)
                      ||..+.++|++.+-...   ++|+.++..+-+-+...+..+-++
T Consensus       301 tnradtldpallrpgrldrkiefplpdrrqkrlvf~titskm~l  344 (408)
T KOG0727|consen  301 TNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFSTITSKMNL  344 (408)
T ss_pred             cCcccccCHhhcCCccccccccCCCCchhhhhhhHHhhhhcccC
Confidence            99999999999876655   999999888888888777765544

>CHL00095 clpC Clp protease ATP binding subunit

Probab=99.62  E-value=9.1e-15  Score=143.02  Aligned_cols=195  Identities=17%  Similarity=0.234  Sum_probs=140.3

Q ss_pred             cCCCCCCcccCCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCC-----CCceEEecCCCC----cC
Q psy879            4 YRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSF-----KDAVLELNASND----RG   74 (317)
Q Consensus         4 y~P~~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~-----~~~~~~~~~~~~----~~   74 (317)
                      -+...++.++|++..++.+...+.....+|++|+||||+|||++++.+|..+.....     +..++.++....    ..
T Consensus       173 a~~~~~~~~igr~~ei~~~~~~L~r~~~~n~lL~G~pGvGKTal~~~la~~i~~~~vp~~l~~~~i~~l~~~~l~ag~~~  252 (821)
T CHL00095        173 AIDGNLDPVIGREKEIERVIQILGRRTKNNPILIGEPGVGKTAIAEGLAQRIVNRDVPDILEDKLVITLDIGLLLAGTKY  252 (821)
T ss_pred             HHcCCCCCCCCcHHHHHHHHHHHcccccCCeEEECCCCCCHHHHHHHHHHHHHhCCCChhhcCCeEEEeeHHHHhccCCC
Confidence            356678999999999999999998877778999999999999999999998743211     234555553211    11


Q ss_pred             hHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCH--------HHHHHHHHHhhhccCCceEEEEecCCC-----cCch
Q psy879           75 IDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTD--------GAQQALRRTMEIYSNTTRFALACNNSE-----KIIE  141 (317)
Q Consensus        75 ~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~--------~~~~~ll~~le~~~~~~~~il~~~~~~-----~l~~  141 (317)
                      ..++.+.+..+.....   ...+.|+||||+|.+..        +..+.|...+..  +...+|.+|+...     ...+
T Consensus       253 ~ge~e~rl~~i~~~~~---~~~~~ILfiDEih~l~~~g~~~g~~~~a~lLkp~l~r--g~l~~IgaTt~~ey~~~ie~D~  327 (821)
T CHL00095        253 RGEFEERLKRIFDEIQ---ENNNIILVIDEVHTLIGAGAAEGAIDAANILKPALAR--GELQCIGATTLDEYRKHIEKDP  327 (821)
T ss_pred             ccHHHHHHHHHHHHHH---hcCCeEEEEecHHHHhcCCCCCCcccHHHHhHHHHhC--CCcEEEEeCCHHHHHHHHhcCH
Confidence            1222223332222110   12467999999997753        245667777763  5677888887653     4679


Q ss_pred             hHhhhcceeeecCCCHHHHHHHHHHHHH----HcCCCCCHHHHHHHHHhcCC---C---HHHHHHHHHHhhh
Q psy879          142 PIQSRCAMLRYNKLTDAQLLSKVIEICE----KENISHTNDGLEAIVFTAQG---D---MRQALNNLQSTHN  203 (317)
Q Consensus       142 ~i~sR~~~i~f~~~~~~~~~~~l~~~~~----~~~~~i~~~~~~~l~~~~~g---d---~r~~i~~l~~~~~  203 (317)
                      ++.+||+.+.+..++.++...++.....    ..++.++++++..++..+++   |   +++|+++|+.++.
T Consensus       328 aL~rRf~~I~v~ep~~~e~~aILr~l~~~~e~~~~v~i~deal~~i~~ls~~yi~~r~lPdkaidlld~a~a  399 (821)
T CHL00095        328 ALERRFQPVYVGEPSVEETIEILFGLRSRYEKHHNLSISDKALEAAAKLSDQYIADRFLPDKAIDLLDEAGS  399 (821)
T ss_pred             HHHhcceEEecCCCCHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhhccCccccCchHHHHHHHHHHH
Confidence            9999999999999999998888775432    24677899999988887764   3   8899999987665

>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA

Probab=99.61  E-value=2.1e-14  Score=138.93  Aligned_cols=179  Identities=17%  Similarity=0.248  Sum_probs=124.1

Q ss_pred             CcccCCHHHHHHHHHHHhc--------CCCc-eEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCC--------
Q psy879           10 SDIVGNEDTVERLKVFSSS--------GNVP-NIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASND--------   72 (317)
Q Consensus        10 ~~~~g~~~~~~~l~~~l~~--------~~~~-~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~--------   72 (317)
                      ..++||+++++.+..++..        +++. +++|+||+|+|||++|+++|+.+.+     .++.++.+..        
T Consensus       454 ~~v~GQ~~ai~~l~~~i~~~~~g~~~~~~p~~~~lf~Gp~GvGKT~lA~~la~~l~~-----~~~~~d~se~~~~~~~~~  528 (731)
T TIGR02639       454 AKIFGQDEAIDSLVSSIKRSRAGLGNPNKPVGSFLFTGPTGVGKTELAKQLAEALGV-----HLERFDMSEYMEKHTVSR  528 (731)
T ss_pred             cceeCcHHHHHHHHHHHHHHhcCCCCCCCCceeEEEECCCCccHHHHHHHHHHHhcC-----CeEEEeCchhhhcccHHH
Confidence            3578999999998887763        1232 4999999999999999999999732     2333332211        


Q ss_pred             --------cChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhc-----------cCCceEEEEe
Q psy879           73 --------RGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIY-----------SNTTRFALAC  133 (317)
Q Consensus        73 --------~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~-----------~~~~~~il~~  133 (317)
                              .+.+........+..       ..+.||++||+|++.++.++.|++++++.           -.++++|+|+
T Consensus       529 lig~~~gyvg~~~~~~l~~~~~~-------~p~~VvllDEieka~~~~~~~Ll~~ld~g~~~d~~g~~vd~~~~iii~Ts  601 (731)
T TIGR02639       529 LIGAPPGYVGFEQGGLLTEAVRK-------HPHCVLLLDEIEKAHPDIYNILLQVMDYATLTDNNGRKADFRNVILIMTS  601 (731)
T ss_pred             HhcCCCCCcccchhhHHHHHHHh-------CCCeEEEEechhhcCHHHHHHHHHhhccCeeecCCCcccCCCCCEEEECC
Confidence                    111111111111111       35789999999999999999999999864           2467788888


Q ss_pred             cCCC-------------------------cCchhHhhhcc-eeeecCCCHHHHHHHHHHHHHH-------c--CCCCCHH
Q psy879          134 NNSE-------------------------KIIEPIQSRCA-MLRYNKLTDAQLLSKVIEICEK-------E--NISHTND  178 (317)
Q Consensus       134 ~~~~-------------------------~l~~~i~sR~~-~i~f~~~~~~~~~~~l~~~~~~-------~--~~~i~~~  178 (317)
                      |...                         .+.|.+.+|+. ++.|+|++.+++.+++...+..       .  .+.++++
T Consensus       602 n~g~~~~~~~~~~f~~~~~~~~~~~~~~~~f~pef~~Rid~Vi~F~pLs~e~l~~Iv~~~L~~l~~~l~~~~~~l~i~~~  681 (731)
T TIGR02639       602 NAGASEMSKPPIGFGSENVESKSDKAIKKLFSPEFRNRLDAIIHFNPLSEEVLEKIVQKFVDELSKQLNEKNIKLELTDD  681 (731)
T ss_pred             CcchhhhhhccCCcchhhhHHHHHHHHHhhcChHHHhcCCeEEEcCCCCHHHHHHHHHHHHHHHHHHHHhCCCeEEeCHH
Confidence            7531                         25688899996 5999999999999998876542       2  2567899


Q ss_pred             HHHHHHHhc---CCCHHHHHHHHHH
Q psy879          179 GLEAIVFTA---QGDMRQALNNLQS  200 (317)
Q Consensus       179 ~~~~l~~~~---~gd~r~~i~~l~~  200 (317)
                      ++++++...   ....|..-..++.
T Consensus       682 a~~~La~~~~~~~~GaR~l~r~i~~  706 (731)
T TIGR02639       682 AKKYLAEKGYDEEFGARPLARVIQE  706 (731)
T ss_pred             HHHHHHHhCCCcccCchHHHHHHHH
Confidence            999988764   2234444444443

>TIGR02030 BchI-ChlI magnesium chelatase ATPase subunit I

Probab=99.61  E-value=4.9e-14  Score=123.13  Aligned_cols=209  Identities=19%  Similarity=0.210  Sum_probs=129.6

Q ss_pred             CCcccCCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHc-------CCCC---CCc---------------
Q psy879            9 FSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILL-------GPSF---KDA---------------   63 (317)
Q Consensus         9 ~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~-------~~~~---~~~---------------   63 (317)
                      |..++||++++..|.-.+-.....|+++.|++|+||||++++++..+.       ++..   ..+               
T Consensus         3 f~~ivgq~~~~~al~~~~~~~~~g~vli~G~~G~gKttl~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~   82 (337)
T TIGR02030         3 FTAIVGQDEMKLALLLNVIDPKIGGVMVMGDRGTGKSTAVRALAALLPEIKAVAGCPFNSSPSDPEMMCEEVRIRVDSQE   82 (337)
T ss_pred             ccccccHHHHHHHHHHHhcCCCCCeEEEEcCCCCCHHHHHHHHHHhhcccccccCCCCCCCCCCccccChHHhhhhhccc
Confidence            788999999999876666565566899999999999999999998862       1100   000               


Q ss_pred             ----------eEEecC--C--CCcChHHHHHHHH--HHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhcc---
Q psy879           64 ----------VLELNA--S--NDRGIDTVRNKIK--MFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYS---  124 (317)
Q Consensus        64 ----------~~~~~~--~--~~~~~~~i~~~~~--~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~---  124 (317)
                                +.++..  .  ...+..++...+.  .+...+..+..+.+.++++||++.+.+..|+.|++.|++..   
T Consensus        83 ~~~~~~~~~~~~~lP~~~t~d~l~G~~d~~~~l~~g~~~~~~GlL~~A~~GvL~lDEi~~L~~~~Q~~Ll~~l~~g~~~v  162 (337)
T TIGR02030        83 PLSIIKKPVPVVDLPLGATEDRVCGTLDIERALTEGVKAFEPGLLARANRGILYIDEVNLLEDHLVDVLLDVAASGWNVV  162 (337)
T ss_pred             ccccccCCCCcCCCCCCCcccceecchhHhhHhhcCCEEeecCcceeccCCEEEecChHhCCHHHHHHHHHHHHhCCeEE
Confidence                      011000  0  0111112222111  01111112223456899999999999999999999997531   


Q ss_pred             ----------CCceEEEEecCCC-cCchhHhhhcce-eeecCCCH-HHHHHHHHHHHH----------------------
Q psy879          125 ----------NTTRFALACNNSE-KIIEPIQSRCAM-LRYNKLTD-AQLLSKVIEICE----------------------  169 (317)
Q Consensus       125 ----------~~~~~il~~~~~~-~l~~~i~sR~~~-i~f~~~~~-~~~~~~l~~~~~----------------------  169 (317)
                                ....+|.+.|..+ .+.+++..|+.. +.+.+++. ++..+++.....                      
T Consensus       163 ~r~G~~~~~~~r~iviat~np~eg~l~~~LldRf~l~i~l~~p~~~eer~eIL~~~~~~~~~~~~~~~~~~~e~~~~~~~  242 (337)
T TIGR02030       163 EREGISIRHPARFVLVGSGNPEEGELRPQLLDRFGLHAEIRTVRDVELRVEIVERRTEYDADPHAFCEKWQTEQEALQAK  242 (337)
T ss_pred             EECCEEEEcCCCEEEEeccccccCCCCHHHHhhcceEEECCCCCCHHHHHHHHHhhhhcccCchhhhhhhhhhhhcCHHH
Confidence                      2223333344333 688999999987 77777765 554455544210                      


Q ss_pred             -------HcCCCCCHHHHHHHHHh---cCC-CHHHHHHHHHHhh-----hCCCcccHHHHHhhc
Q psy879          170 -------KENISHTNDGLEAIVFT---AQG-DMRQALNNLQSTH-----NGFGHVTAEYVFKVC  217 (317)
Q Consensus       170 -------~~~~~i~~~~~~~l~~~---~~g-d~r~~i~~l~~~~-----~~~~~i~~~~v~~~~  217 (317)
                             -..+.++++.++++++.   .+. +.|..+..++.+-     .+...++.+||..+.
T Consensus       243 I~~a~~~~~~V~v~d~~~~~i~~l~~~~~~~s~Ra~i~l~raArA~Aal~GR~~V~~dDv~~~a  306 (337)
T TIGR02030       243 IVNAQNLLPQVTIPYDVLVKVAELCAELDVDGLRGELTLNRAAKALAAFEGRTEVTVDDIRRVA  306 (337)
T ss_pred             HHHHHHHhccCcCCHHHHHHHHHHHHHHCCCCCcHHHHHHHHHHHHHHHcCCCCCCHHHHHHHH
Confidence                   13566788887777654   233 4788777775422     266789999987643

This model represents one of two ATPase subunits of the trimeric magnesium chelatase responsible for insertion of magnesium ion into protoporphyrin IX. This is an essential step in the biosynthesis of both chlorophyll and bacteriochlorophyll. This subunit is found in green plants, photosynthetic algae, cyanobacteria and other photosynthetic bacteria.

>PRK10865 protein disaggregation chaperone; Provisional

Probab=99.61  E-value=6.8e-14  Score=136.87  Aligned_cols=187  Identities=16%  Similarity=0.237  Sum_probs=127.1

Q ss_pred             CCcccCCHHHHHHHHHHHhcC--------CC-ceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHH
Q psy879            9 FSDIVGNEDTVERLKVFSSSG--------NV-PNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVR   79 (317)
Q Consensus         9 ~~~~~g~~~~~~~l~~~l~~~--------~~-~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~   79 (317)
                      ...++||+.+++.+...+...        ++ .+++|+||+|+|||++|+++++.+.+..  ..++.++++.........
T Consensus       567 ~~~viGQ~~ai~~l~~~i~~~~~gl~~~~~p~~~~Lf~Gp~G~GKT~lA~aLa~~l~~~~--~~~i~id~se~~~~~~~~  644 (857)
T PRK10865        567 HHRVIGQNEAVEAVSNAIRRSRAGLSDPNRPIGSFLFLGPTGVGKTELCKALANFMFDSD--DAMVRIDMSEFMEKHSVS  644 (857)
T ss_pred             CCeEeCCHHHHHHHHHHHHHHHhcccCCCCCCceEEEECCCCCCHHHHHHHHHHHhhcCC--CcEEEEEhHHhhhhhhHH
Confidence            457889999999988877632        22 2499999999999999999999886443  234545443221111111


Q ss_pred             HHHH------------HHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhc-----------cCCceEEEEecCC
Q psy879           80 NKIK------------MFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIY-----------SNTTRFALACNNS  136 (317)
Q Consensus        80 ~~~~------------~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~-----------~~~~~~il~~~~~  136 (317)
                      ..++            .+... .  ...++.||++||++++.++.++.|++++++.           -.++++|+|||..
T Consensus       645 ~LiG~~pgy~g~~~~g~l~~~-v--~~~p~~vLllDEieka~~~v~~~Ll~ile~g~l~d~~gr~vd~rn~iiI~TSN~g  721 (857)
T PRK10865        645 RLVGAPPGYVGYEEGGYLTEA-V--RRRPYSVILLDEVEKAHPDVFNILLQVLDDGRLTDGQGRTVDFRNTVVIMTSNLG  721 (857)
T ss_pred             HHhCCCCcccccchhHHHHHH-H--HhCCCCeEEEeehhhCCHHHHHHHHHHHhhCceecCCceEEeecccEEEEeCCcc
Confidence            1110            00000 0  0134579999999999999999999999864           2456688888862


Q ss_pred             -------------------------CcCchhHhhhc-ceeeecCCCHHHHHHHHHHHHHH-------cC--CCCCHHHHH
Q psy879          137 -------------------------EKIIEPIQSRC-AMLRYNKLTDAQLLSKVIEICEK-------EN--ISHTNDGLE  181 (317)
Q Consensus       137 -------------------------~~l~~~i~sR~-~~i~f~~~~~~~~~~~l~~~~~~-------~~--~~i~~~~~~  181 (317)
                                               ..+.|.+.+|+ .++.|.|++.+++..++...+..       .+  +.+++++++
T Consensus       722 ~~~~~~~~~~~~~~~~~~~~~~~~~~~f~PELlnRld~iivF~PL~~edl~~Iv~~~L~~l~~rl~~~gi~l~is~~al~  801 (857)
T PRK10865        722 SDLIQERFGELDYAHMKELVLGVVSHNFRPEFINRIDEVVVFHPLGEQHIASIAQIQLQRLYKRLEERGYEIHISDEALK  801 (857)
T ss_pred             hHHHHHhccccchHHHHHHHHHHHcccccHHHHHhCCeeEecCCCCHHHHHHHHHHHHHHHHHHHHhCCCcCcCCHHHHH
Confidence                                     13568899999 66999999999999887765543       23  457899999


Q ss_pred             HHHHhcC---CCHHHHHHHHHH
Q psy879          182 AIVFTAQ---GDMRQALNNLQS  200 (317)
Q Consensus       182 ~l~~~~~---gd~r~~i~~l~~  200 (317)
                      .++....   ...|.+-+.++.
T Consensus       802 ~L~~~gy~~~~GARpL~r~I~~  823 (857)
T PRK10865        802 LLSENGYDPVYGARPLKRAIQQ  823 (857)
T ss_pred             HHHHcCCCccCChHHHHHHHHH
Confidence            9987642   135555555544

>KOG0742|consensus

Probab=99.61  E-value=9.8e-15  Score=125.67  Aligned_cols=157  Identities=19%  Similarity=0.236  Sum_probs=114.3

Q ss_pred             CCCC-CCcccCCHHHHHHHHHHHh--------cCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEec---CCCC
Q psy879            5 RPQT-FSDIVGNEDTVERLKVFSS--------SGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELN---ASND   72 (317)
Q Consensus         5 ~P~~-~~~~~g~~~~~~~l~~~l~--------~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~---~~~~   72 (317)
                      +++. |+++|-++.+.+.+.....        ++.+.|++||||||||||.+|+.+|+.- +-  .+.++...   +...
T Consensus       349 ~gk~pl~~ViL~psLe~Rie~lA~aTaNTK~h~apfRNilfyGPPGTGKTm~ArelAr~S-Gl--DYA~mTGGDVAPlG~  425 (630)
T KOG0742|consen  349 RGKDPLEGVILHPSLEKRIEDLAIATANTKKHQAPFRNILFYGPPGTGKTMFARELARHS-GL--DYAIMTGGDVAPLGA  425 (630)
T ss_pred             cCCCCcCCeecCHHHHHHHHHHHHHhcccccccchhhheeeeCCCCCCchHHHHHHHhhc-CC--ceehhcCCCccccch
Confidence            4555 8999999998888877643        3445679999999999999999999872 22  22222222   2222


Q ss_pred             cChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCH---------H---HHHHHHHHhhhccCCceEEEEecCCCcCc
Q psy879           73 RGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTD---------G---AQQALRRTMEIYSNTTRFALACNNSEKII  140 (317)
Q Consensus        73 ~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~---------~---~~~~ll~~le~~~~~~~~il~~~~~~~l~  140 (317)
                      ..+..|.+++.+...+      .+.-++||||+|.+.-         .   +.|+|+---.+.+..++++++||.+..++
T Consensus       426 qaVTkiH~lFDWakkS------~rGLllFIDEADAFLceRnktymSEaqRsaLNAlLfRTGdqSrdivLvlAtNrpgdlD  499 (630)
T KOG0742|consen  426 QAVTKIHKLFDWAKKS------RRGLLLFIDEADAFLCERNKTYMSEAQRSALNALLFRTGDQSRDIVLVLATNRPGDLD  499 (630)
T ss_pred             HHHHHHHHHHHHHhhc------ccceEEEehhhHHHHHHhchhhhcHHHHHHHHHHHHHhcccccceEEEeccCCccchh
Confidence            3445566666554433      4677999999996532         2   34555444456677889999999999999


Q ss_pred             hhHhhhcce-eeecCCCHHHHHHHHHHHHHH
Q psy879          141 EPIQSRCAM-LRYNKLTDAQLLSKVIEICEK  170 (317)
Q Consensus       141 ~~i~sR~~~-i~f~~~~~~~~~~~l~~~~~~  170 (317)
                      -++-.|+.. ++|+.|-++|..++|..++.+
T Consensus       500 sAV~DRide~veFpLPGeEERfkll~lYlnk  530 (630)
T KOG0742|consen  500 SAVNDRIDEVVEFPLPGEEERFKLLNLYLNK  530 (630)
T ss_pred             HHHHhhhhheeecCCCChHHHHHHHHHHHHH
Confidence            999999976 999999999999998887754

>KOG0743|consensus

Probab=99.60  E-value=5.7e-14  Score=123.09  Aligned_cols=150  Identities=19%  Similarity=0.273  Sum_probs=109.6

Q ss_pred             CCCCCCcccCCHHHHH----HHHHHHhc-------CCC--ceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCC
Q psy879            5 RPQTFSDIVGNEDTVE----RLKVFSSS-------GNV--PNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASN   71 (317)
Q Consensus         5 ~P~~~~~~~g~~~~~~----~l~~~l~~-------~~~--~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~   71 (317)
                      +|.+|+.++=.++.++    .|..++++       |++  ..||||||||||||+++-|+|+.|     ++.+.+++-+.
T Consensus       196 HpstF~TlaMd~~~K~~I~~Dl~~F~k~k~~YkrvGkawKRGYLLYGPPGTGKSS~IaAmAn~L-----~ydIydLeLt~  270 (457)
T KOG0743|consen  196 HPSTFETLAMDPDLKERIIDDLDDFIKGKDFYKRVGKAWKRGYLLYGPPGTGKSSFIAAMANYL-----NYDIYDLELTE  270 (457)
T ss_pred             CCCCccccccChhHHHHHHHHHHHHHhcchHHHhcCcchhccceeeCCCCCCHHHHHHHHHhhc-----CCceEEeeecc
Confidence            5778888887665555    45556553       222  249999999999999999999997     34466666554


Q ss_pred             CcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCH---H---------------HHHHHHHHhhhcc----CCceE
Q psy879           72 DRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTD---G---------------AQQALRRTMEIYS----NTTRF  129 (317)
Q Consensus        72 ~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~---~---------------~~~~ll~~le~~~----~~~~~  129 (317)
                      ...-++++..+...         ..+.||+|+++|.-..   +               ....||.+++..-    ...++
T Consensus       271 v~~n~dLr~LL~~t---------~~kSIivIEDIDcs~~l~~~~~~~~~~~~~~~~~VTlSGLLNfiDGlwSscg~ERIi  341 (457)
T KOG0743|consen  271 VKLDSDLRHLLLAT---------PNKSILLIEDIDCSFDLRERRKKKKENFEGDLSRVTLSGLLNFLDGLWSSCGDERII  341 (457)
T ss_pred             ccCcHHHHHHHHhC---------CCCcEEEEeecccccccccccccccccccCCcceeehHHhhhhhccccccCCCceEE
Confidence            44455566665432         4677999999996421   1               1345888888542    24579


Q ss_pred             EEEecCCCcCchhHhhhcce---eeecCCCHHHHHHHHHHHH
Q psy879          130 ALACNNSEKIIEPIQSRCAM---LRYNKLTDAQLLSKVIEIC  168 (317)
Q Consensus       130 il~~~~~~~l~~~i~sR~~~---i~f~~~~~~~~~~~l~~~~  168 (317)
                      |+|||+.++++|++.+++.+   +++..-+...++....+.+
T Consensus       342 vFTTNh~EkLDPALlRpGRmDmhI~mgyCtf~~fK~La~nYL  383 (457)
T KOG0743|consen  342 VFTTNHKEKLDPALLRPGRMDMHIYMGYCTFEAFKTLASNYL  383 (457)
T ss_pred             EEecCChhhcCHhhcCCCcceeEEEcCCCCHHHHHHHHHHhc
Confidence            99999999999999997666   9999999999888888876

>KOG0738|consensus

Probab=99.60  E-value=7.8e-14  Score=119.45  Aligned_cols=169  Identities=19%  Similarity=0.210  Sum_probs=114.0

Q ss_pred             CCCcccCCHHHHHHHHHHHh----------cCCC--ceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCC---
Q psy879            8 TFSDIVGNEDTVERLKVFSS----------SGNV--PNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASND---   72 (317)
Q Consensus         8 ~~~~~~g~~~~~~~l~~~l~----------~~~~--~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~---   72 (317)
                      .|+|+.|..++++.|+.++-          ..+-  ..+|++||||||||.+|+++|.+..     ..|+.+..+..   
T Consensus       210 kW~DIagl~~AK~lL~EAVvlPi~mPe~F~GirrPWkgvLm~GPPGTGKTlLAKAvATEc~-----tTFFNVSsstltSK  284 (491)
T KOG0738|consen  210 KWDDIAGLHEAKKLLKEAVVLPIWMPEFFKGIRRPWKGVLMVGPPGTGKTLLAKAVATECG-----TTFFNVSSSTLTSK  284 (491)
T ss_pred             ChHhhcchHHHHHHHHHHHhhhhhhHHHHhhcccccceeeeeCCCCCcHHHHHHHHHHhhc-----CeEEEechhhhhhh
Confidence            59999999999999988753          2222  2499999999999999999999842     23555554431   


Q ss_pred             -cC-hHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCH------------HHHHHHHHHhhhcc-----CCceEEEE-
Q psy879           73 -RG-IDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTD------------GAQQALRRTMEIYS-----NTTRFALA-  132 (317)
Q Consensus        73 -~~-~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~------------~~~~~ll~~le~~~-----~~~~~il~-  132 (317)
                       ++ .+.+-..+-.++..      -.+.+|||||+|.+..            ...+.||-.|+...     ...++|++ 
T Consensus       285 wRGeSEKlvRlLFemARf------yAPStIFiDEIDslcs~RG~s~EHEaSRRvKsELLvQmDG~~~t~e~~k~VmVLAA  358 (491)
T KOG0738|consen  285 WRGESEKLVRLLFEMARF------YAPSTIFIDEIDSLCSQRGGSSEHEASRRVKSELLVQMDGVQGTLENSKVVMVLAA  358 (491)
T ss_pred             hccchHHHHHHHHHHHHH------hCCceeehhhHHHHHhcCCCccchhHHHHHHHHHHHHhhccccccccceeEEEEec
Confidence             12 12222333333322      2577999999998853            23566777776321     23455554 


Q ss_pred             ecCCCcCchhHhhhcce-eeecCCCHHHHHHHHHHHHHHcCCCC-CHHHHHHHHHhcCC
Q psy879          133 CNNSEKIIEPIQSRCAM-LRYNKLTDAQLLSKVIEICEKENISH-TNDGLEAIVFTAQG  189 (317)
Q Consensus       133 ~~~~~~l~~~i~sR~~~-i~f~~~~~~~~~~~l~~~~~~~~~~i-~~~~~~~l~~~~~g  189 (317)
                      ||-|-.+++++++|+.. |.++-|+.+.....++..+.  .+.. ++-.++.+++.+.|
T Consensus       359 TN~PWdiDEAlrRRlEKRIyIPLP~~~~R~~Li~~~l~--~~~~~~~~~~~~lae~~eG  415 (491)
T KOG0738|consen  359 TNFPWDIDEALRRRLEKRIYIPLPDAEARSALIKILLR--SVELDDPVNLEDLAERSEG  415 (491)
T ss_pred             cCCCcchHHHHHHHHhhheeeeCCCHHHHHHHHHHhhc--cccCCCCccHHHHHHHhcC
Confidence            77789999999999998 88887877777776666554  2233 34446777776654

>CHL00081 chlI Mg-protoporyphyrin IX chelatase

Probab=99.60  E-value=8.7e-14  Score=121.49  Aligned_cols=211  Identities=20%  Similarity=0.212  Sum_probs=133.5

Q ss_pred             CCC-CCCcccCCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCC--CCceE----------------
Q psy879            5 RPQ-TFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSF--KDAVL----------------   65 (317)
Q Consensus         5 ~P~-~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~--~~~~~----------------   65 (317)
                      +|. .|.+++||++++..|...+.+..+.+++|.|++|||||++++.+++.+.+...  ..++.                
T Consensus        11 ~~~~pf~~ivGq~~~k~al~~~~~~p~~~~vli~G~~GtGKs~~ar~~~~~l~~~~~~~~~pf~~~p~~p~~~~~~~~~~   90 (350)
T CHL00081         11 RPVFPFTAIVGQEEMKLALILNVIDPKIGGVMIMGDRGTGKSTTIRALVDLLPEIEVVKDDPFNSHPSDPELMSDEVREA   90 (350)
T ss_pred             CCCCCHHHHhChHHHHHHHHHhccCCCCCeEEEEcCCCCCHHHHHHHHHHHHhhcCccCCCCCCCCCCChhhhchhhhhh
Confidence            444 59999999999999998888888778999999999999999999988743210  00111                


Q ss_pred             -----------------EecCCCCcChHH------HHHHHHHHH--hhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHh
Q psy879           66 -----------------ELNASNDRGIDT------VRNKIKMFA--QQKVTLPPGRHKIVILDEADSMTDGAQQALRRTM  120 (317)
Q Consensus        66 -----------------~~~~~~~~~~~~------i~~~~~~~~--~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~l  120 (317)
                                       .+..  ....+.      +...+....  ..+..+......++++||++.+.+..|+.|++.|
T Consensus        91 ~~~~~~~~~~~~~~~~~~lp~--~~ted~l~G~iD~~~al~~g~~~~~~GlL~~A~~GiL~lDEInrL~~~~Q~~LLeam  168 (350)
T CHL00081         91 IQNGETIETEKIKIPMVDLPL--GATEDRVCGTIDIEKALTEGVKAFEPGLLAKANRGILYVDEVNLLDDHLVDILLDSA  168 (350)
T ss_pred             hcccccccceeccccceecCC--CCchhhccCcccHHHHhhcCcccccCCeeeecCCCEEEecChHhCCHHHHHHHHHHH
Confidence                             0000  001111      111111000  0111122356789999999999999999999999


Q ss_pred             hhc-------------cCCceEEEEecCCC-cCchhHhhhcce-eeecCCCH-HHHHHHHHHHH----------------
Q psy879          121 EIY-------------SNTTRFALACNNSE-KIIEPIQSRCAM-LRYNKLTD-AQLLSKVIEIC----------------  168 (317)
Q Consensus       121 e~~-------------~~~~~~il~~~~~~-~l~~~i~sR~~~-i~f~~~~~-~~~~~~l~~~~----------------  168 (317)
                      ++.             +....+|.+.|..+ .+.+.+..|+.. +.+..++. ++-.+++....                
T Consensus       169 ~e~~~~ier~G~s~~~p~rfiviaT~np~eg~l~~~LldRf~l~i~l~~~~~~~~e~~il~~~~~~~~~~~~~~~~~~~~  248 (350)
T CHL00081        169 ASGWNTVEREGISIRHPARFVLVGSGNPEEGELRPQLLDRFGMHAEIRTVKDPELRVKIVEQRTSFDKNPQEFREKYEES  248 (350)
T ss_pred             HhCCeEEeeCCeeeecCCCEEEEeccCcccCCCCHHHHHHhCceeecCCCCChHHHHHHHHhhhccccChhhhhhhhccc
Confidence            752             12222333333333 689999999987 77777763 44444443321                


Q ss_pred             -------------HHcCCCCCHHHHHHHHHhc---C-CCHHHHHHHHHHh-----hhCCCcccHHHHHhhc
Q psy879          169 -------------EKENISHTNDGLEAIVFTA---Q-GDMRQALNNLQST-----HNGFGHVTAEYVFKVC  217 (317)
Q Consensus       169 -------------~~~~~~i~~~~~~~l~~~~---~-gd~r~~i~~l~~~-----~~~~~~i~~~~v~~~~  217 (317)
                                   .-..+.+++..+.++++.+   + -++|..+..++.+     ..+...++.+||..+.
T Consensus       249 ~~~~~~~I~~ar~~~~~V~v~~~~~~yi~~l~~~~~~~s~Ra~i~l~raArA~Aal~GR~~V~pdDv~~~a  319 (350)
T CHL00081        249 QEELRSKIVAAQNLLPKVEIDYDLRVKISQICSELDVDGLRGDIVTNRAAKALAAFEGRTEVTPKDIFKVI  319 (350)
T ss_pred             cccCHHHHHHHHHhcCCCccCHHHHHHHHHHHHHHCCCCChHHHHHHHHHHHHHHHcCCCCCCHHHHHHHH
Confidence                         1135678888888777553   2 2588777776542     2267789999887643

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=99.60  E-value=6.9e-14  Score=137.27  Aligned_cols=187  Identities=17%  Similarity=0.225  Sum_probs=130.7

Q ss_pred             CcccCCHHHHHHHHHHHhcC--------CCc-eEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHH
Q psy879           10 SDIVGNEDTVERLKVFSSSG--------NVP-NIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRN   80 (317)
Q Consensus        10 ~~~~g~~~~~~~l~~~l~~~--------~~~-~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~   80 (317)
                      ..++||+++++.+...+...        ++. +++|+||+|+|||++|+++++.+.+..  ..++.++.+.......+..
T Consensus       565 ~~v~GQ~~av~~v~~~i~~~~~gl~~~~~p~~~~Lf~Gp~GvGKt~lA~~La~~l~~~~--~~~i~~d~s~~~~~~~~~~  642 (852)
T TIGR03346       565 ERVVGQDEAVEAVSDAIRRSRAGLSDPNRPIGSFLFLGPTGVGKTELAKALAEFLFDDE--DAMVRIDMSEYMEKHSVAR  642 (852)
T ss_pred             cccCCChHHHHHHHHHHHHHhccCCCCCCCCeEEEEEcCCCCCHHHHHHHHHHHhcCCC--CcEEEEechhhcccchHHH
Confidence            46899999999988887642        222 499999999999999999999986543  2344444432211111111


Q ss_pred             HHH------------HHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhcc-----------CCceEEEEecCCC
Q psy879           81 KIK------------MFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYS-----------NTTRFALACNNSE  137 (317)
Q Consensus        81 ~~~------------~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~-----------~~~~~il~~~~~~  137 (317)
                      .++            .+...-   ....+.||++||++++.++.++.|++++++..           .++++|+|||-..
T Consensus       643 l~g~~~g~~g~~~~g~l~~~v---~~~p~~vlllDeieka~~~v~~~Ll~~l~~g~l~d~~g~~vd~rn~iiI~TSn~g~  719 (852)
T TIGR03346       643 LIGAPPGYVGYEEGGQLTEAV---RRKPYSVVLFDEVEKAHPDVFNVLLQVLDDGRLTDGQGRTVDFRNTVIIMTSNLGS  719 (852)
T ss_pred             hcCCCCCccCcccccHHHHHH---HcCCCcEEEEeccccCCHHHHHHHHHHHhcCceecCCCeEEecCCcEEEEeCCcch
Confidence            110            000000   01346799999999999999999999998652           5677999988621


Q ss_pred             -------------------------cCchhHhhhcc-eeeecCCCHHHHHHHHHHHHH-------Hc--CCCCCHHHHHH
Q psy879          138 -------------------------KIIEPIQSRCA-MLRYNKLTDAQLLSKVIEICE-------KE--NISHTNDGLEA  182 (317)
Q Consensus       138 -------------------------~l~~~i~sR~~-~i~f~~~~~~~~~~~l~~~~~-------~~--~~~i~~~~~~~  182 (317)
                                               .+.|.+..|+. ++.|.|++.+++.+++.....       ..  .+.+++++++.
T Consensus       720 ~~~~~~~~~~~~~~~~~~~~~~~~~~F~pel~~Rid~IivF~PL~~e~l~~I~~l~L~~l~~~l~~~~~~l~i~~~a~~~  799 (852)
T TIGR03346       720 QFIQELAGGDDYEEMREAVMEVLRAHFRPEFLNRIDEIVVFHPLGREQIARIVEIQLGRLRKRLAERKITLELSDAALDF  799 (852)
T ss_pred             HhHhhhcccccHHHHHHHHHHHHHhhcCHHHhcCcCeEEecCCcCHHHHHHHHHHHHHHHHHHHHHCCCeecCCHHHHHH
Confidence                                     14467778884 599999999999888776543       22  25689999999


Q ss_pred             HHHhc---CCCHHHHHHHHHHh
Q psy879          183 IVFTA---QGDMRQALNNLQST  201 (317)
Q Consensus       183 l~~~~---~gd~r~~i~~l~~~  201 (317)
                      +++..   .++.|.+-+.++..
T Consensus       800 L~~~~~~~~~gaR~L~~~i~~~  821 (852)
T TIGR03346       800 LAEAGYDPVYGARPLKRAIQRE  821 (852)
T ss_pred             HHHhCCCCCCCchhHHHHHHHH
Confidence            99873   47788888887764

Members of this protein family are the bacterial ATP-dependent chaperone ClpB. This protein belongs to the AAA family, ATPases associated with various cellular activities (pfam00004). This molecular chaperone does not act as a protease, but rather serves to disaggregate misfolded and aggregated proteins.

>PF00004 AAA: ATPase family associated with various cellular activities (AAA); InterPro: IPR003959 AAA ATPases (ATPases Associated with diverse cellular Activities) form a large protein family and play a number of roles in the cell including cell-cycle regulation, protein proteolysis and disaggregation, organelle biogenesis and intracellular transport

Probab=99.59  E-value=1.1e-14  Score=111.08  Aligned_cols=109  Identities=24%  Similarity=0.344  Sum_probs=80.9

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCc------ChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCC
Q psy879           34 IIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDR------GIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADS  107 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~------~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~  107 (317)
                      ++|+||||+|||++++.+++.+     +..++.+++....      ....+...+......      +.+.|++|||+|.
T Consensus         1 ill~G~~G~GKT~l~~~la~~l-----~~~~~~i~~~~~~~~~~~~~~~~i~~~~~~~~~~------~~~~vl~iDe~d~   69 (132)
T PF00004_consen    1 ILLHGPPGTGKTTLARALAQYL-----GFPFIEIDGSELISSYAGDSEQKIRDFFKKAKKS------AKPCVLFIDEIDK   69 (132)
T ss_dssp             EEEESSTTSSHHHHHHHHHHHT-----TSEEEEEETTHHHTSSTTHHHHHHHHHHHHHHHT------STSEEEEEETGGG
T ss_pred             CEEECcCCCCeeHHHHHHHhhc-----cccccccccccccccccccccccccccccccccc------ccceeeeeccchh
Confidence            6899999999999999999996     3456777665422      122333333332211      1368999999999


Q ss_pred             CCHHH-----------HHHHHHHhhhccC---CceEEEEecCCCcCchhHh-hhcce-eeec
Q psy879          108 MTDGA-----------QQALRRTMEIYSN---TTRFALACNNSEKIIEPIQ-SRCAM-LRYN  153 (317)
Q Consensus       108 l~~~~-----------~~~ll~~le~~~~---~~~~il~~~~~~~l~~~i~-sR~~~-i~f~  153 (317)
                      +....           .+.|+..++....   .+.+|++||..+.+.+++. +||.. ++|+
T Consensus        70 l~~~~~~~~~~~~~~~~~~L~~~l~~~~~~~~~~~vI~ttn~~~~i~~~l~~~rf~~~i~~~  131 (132)
T PF00004_consen   70 LFPKSQPSSSSFEQRLLNQLLSLLDNPSSKNSRVIVIATTNSPDKIDPALLRSRFDRRIEFP  131 (132)
T ss_dssp             TSHHCSTSSSHHHHHHHHHHHHHHHTTTTTSSSEEEEEEESSGGGSCHHHHSTTSEEEEEE-
T ss_pred             cccccccccccccccccceeeecccccccccccceeEEeeCChhhCCHhHHhCCCcEEEEcC
Confidence            98775           7888888887665   4789999999999999999 99987 5554

Some of them function as molecular chaperones, subunits of proteolytic complexes or independent proteases (FtsH, Lon). They also act as DNA helicases and transcription factors []. AAA ATPases belong to the AAA+ superfamily of ringshaped P-loop NTPases, which act via the energy-dependent unfolding of macromolecules [, ]. There are six major clades of AAA domains (proteasome subunits, metalloproteases, domains D1 and D2 of ATPases with two AAA domains, the MSP1/katanin/spastin group and BCS1 and it homologues), as well as a number of deeply branching minor clades []. They assemble into oligomeric assemblies (often hexamers) that form a ring-shaped structure with a central pore. These proteins produce a molecular motor that couples ATP binding and hydrolysis to changes in conformational states that act upon a target substrate, either translocating or remodelling it []. They are found in all living organisms and share the common feature of the presence of a highly conserved AAA domain called the AAA module. This domain is responsible for ATP binding and hydrolysis. It contains 200-250 residues, among them there are two classical motifs, Walker A (GX4GKT) and Walker B (HyDE) []. The functional variety seen between AAA ATPases is in part due to their extensive number of accessory domains and factors, and to their variable organisation within oligomeric assemblies, in addition to changes in key functional residues within the ATPase domain itself. More information about these proteins can be found at Protein of the Month: AAA ATPases [].; GO: 0005524 ATP binding; PDB: 3H4M_A 1NSF_A 1D2N_A 1HQY_E 1DO0_E 1DO2_C 1G4B_E 1HT1_F 1G4A_F 1HT2_G ....

>COG0542 clpA ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]

Probab=99.59  E-value=4.4e-14  Score=132.98  Aligned_cols=188  Identities=17%  Similarity=0.223  Sum_probs=130.0

Q ss_pred             CcccCCHHHHHHHHHHHhcC--------CC-ceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHH
Q psy879           10 SDIVGNEDTVERLKVFSSSG--------NV-PNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRN   80 (317)
Q Consensus        10 ~~~~g~~~~~~~l~~~l~~~--------~~-~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~   80 (317)
                      ..++||++++..+..+++..        ++ .+++|.||+|+|||.+|+++|..|.+...  .++.++-+.......+..
T Consensus       491 ~rViGQd~AV~avs~aIrraRaGL~dp~rPigsFlF~GPTGVGKTELAkaLA~~Lfg~e~--aliR~DMSEy~EkHsVSr  568 (786)
T COG0542         491 KRVIGQDEAVEAVSDAIRRARAGLGDPNRPIGSFLFLGPTGVGKTELAKALAEALFGDEQ--ALIRIDMSEYMEKHSVSR  568 (786)
T ss_pred             cceeChHHHHHHHHHHHHHHhcCCCCCCCCceEEEeeCCCcccHHHHHHHHHHHhcCCCc--cceeechHHHHHHHHHHH
Confidence            46789999999999888631        22 24999999999999999999999976543  334444333222223332


Q ss_pred             HHHHHHhhcccC----------CCCceeEEEEeCCCCCCHHHHHHHHHHhhhcc-----------CCceEEEEecCCC--
Q psy879           81 KIKMFAQQKVTL----------PPGRHKIVILDEADSMTDGAQQALRRTMEIYS-----------NTTRFALACNNSE--  137 (317)
Q Consensus        81 ~~~~~~~~~~~~----------~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~-----------~~~~~il~~~~~~--  137 (317)
                      .++. ....+.+          -..++.||++||+++..++..|.|++.|++..           .++++|+|+|--.  
T Consensus       569 LIGa-PPGYVGyeeGG~LTEaVRr~PySViLlDEIEKAHpdV~nilLQVlDdGrLTD~~Gr~VdFrNtiIImTSN~Gs~~  647 (786)
T COG0542         569 LIGA-PPGYVGYEEGGQLTEAVRRKPYSVILLDEIEKAHPDVFNLLLQVLDDGRLTDGQGRTVDFRNTIIIMTSNAGSEE  647 (786)
T ss_pred             HhCC-CCCCceeccccchhHhhhcCCCeEEEechhhhcCHHHHHHHHHHhcCCeeecCCCCEEecceeEEEEecccchHH
Confidence            2221 0000000          01358899999999999999999999999532           5788999988321  


Q ss_pred             --------------------------cCchhHhhhcc-eeeecCCCHHHHHHHHHHHHH-------HcC--CCCCHHHHH
Q psy879          138 --------------------------KIIEPIQSRCA-MLRYNKLTDAQLLSKVIEICE-------KEN--ISHTNDGLE  181 (317)
Q Consensus       138 --------------------------~l~~~i~sR~~-~i~f~~~~~~~~~~~l~~~~~-------~~~--~~i~~~~~~  181 (317)
                                                .+.|.+..|.. +|.|.+++.+++.+++...+.       ..+  +.+++++.+
T Consensus       648 i~~~~~~~~~~~~~~~~~~v~~~l~~~F~PEFLNRid~II~F~~L~~~~l~~Iv~~~L~~l~~~L~~~~i~l~~s~~a~~  727 (786)
T COG0542         648 ILRDADGDDFADKEALKEAVMEELKKHFRPEFLNRIDEIIPFNPLSKEVLERIVDLQLNRLAKRLAERGITLELSDEAKD  727 (786)
T ss_pred             HHhhccccccchhhhHHHHHHHHHHhhCCHHHHhhcccEEeccCCCHHHHHHHHHHHHHHHHHHHHhCCceEEECHHHHH
Confidence                                      24588888988 699999999999888776543       334  356899999


Q ss_pred             HHHHhcC---CCHHHHHHHHHH
Q psy879          182 AIVFTAQ---GDMRQALNNLQS  200 (317)
Q Consensus       182 ~l~~~~~---gd~r~~i~~l~~  200 (317)
                      .++..+.   ...|-+...++.
T Consensus       728 ~l~~~gyd~~~GARpL~R~Iq~  749 (786)
T COG0542         728 FLAEKGYDPEYGARPLRRAIQQ  749 (786)
T ss_pred             HHHHhccCCCcCchHHHHHHHH
Confidence            9987753   335555555544

>PRK10733 hflB ATP-dependent metalloprotease; Reviewed

Probab=99.59  E-value=3.7e-14  Score=134.94  Aligned_cols=198  Identities=17%  Similarity=0.210  Sum_probs=135.2

Q ss_pred             CCCCcccCCHHHHHHHHHHHh-----------cCCCc-eEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCC---
Q psy879            7 QTFSDIVGNEDTVERLKVFSS-----------SGNVP-NIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASN---   71 (317)
Q Consensus         7 ~~~~~~~g~~~~~~~l~~~l~-----------~~~~~-~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~---   71 (317)
                      .+|+++.|.+..++.+...+.           .+..| +++|+||||+|||++++++++.+.     .+++.+++++   
T Consensus       149 ~~~~di~g~~~~~~~l~~i~~~~~~~~~~~~~~~~~~~gill~G~~G~GKt~~~~~~a~~~~-----~~f~~is~~~~~~  223 (644)
T PRK10733        149 TTFADVAGCDEAKEEVAELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGEAK-----VPFFTISGSDFVE  223 (644)
T ss_pred             CcHHHHcCHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCcEEEECCCCCCHHHHHHHHHHHcC-----CCEEEEehHHhHH
Confidence            458888998888877665542           12223 499999999999999999999862     3455555432   


Q ss_pred             ---CcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHH--------------HHHHHHHHhhhcc--CCceEEEE
Q psy879           72 ---DRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDG--------------AQQALRRTMEIYS--NTTRFALA  132 (317)
Q Consensus        72 ---~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~--------------~~~~ll~~le~~~--~~~~~il~  132 (317)
                         ..+...++..+.....       ..+.|++|||+|.+...              ..+.|+..|+...  ..+++|.+
T Consensus       224 ~~~g~~~~~~~~~f~~a~~-------~~P~IifIDEiD~l~~~r~~~~~g~~~~~~~~ln~lL~~mdg~~~~~~vivIaa  296 (644)
T PRK10733        224 MFVGVGASRVRDMFEQAKK-------AAPCIIFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDGFEGNEGIIVIAA  296 (644)
T ss_pred             hhhcccHHHHHHHHHHHHh-------cCCcEEEehhHhhhhhccCCCCCCCchHHHHHHHHHHHhhhcccCCCCeeEEEe
Confidence               1223344444443321       35689999999988421              3455665566433  35678889


Q ss_pred             ecCCCcCchhHhh--hcce-eeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCC----CHHHHHHHHHHhhh--
Q psy879          133 CNNSEKIIEPIQS--RCAM-LRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQG----DMRQALNNLQSTHN--  203 (317)
Q Consensus       133 ~~~~~~l~~~i~s--R~~~-i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~g----d~r~~i~~l~~~~~--  203 (317)
                      ||.++.+++++.+  |+.. +.|+.|+.++..+++...+++..+.- +..+..+++.+.|    |+..+++.....+.  
T Consensus       297 TN~p~~lD~Al~RpgRfdr~i~v~~Pd~~~R~~Il~~~~~~~~l~~-~~d~~~la~~t~G~sgadl~~l~~eAa~~a~r~  375 (644)
T PRK10733        297 TNRPDVLDPALLRPGRFDRQVVVGLPDVRGREQILKVHMRRVPLAP-DIDAAIIARGTPGFSGADLANLVNEAALFAARG  375 (644)
T ss_pred             cCChhhcCHHHhCCcccceEEEcCCCCHHHHHHHHHHHhhcCCCCC-cCCHHHHHhhCCCCCHHHHHHHHHHHHHHHHHc
Confidence            9999999999985  7755 99999999999999998876543321 2234567777776    77777777654333  


Q ss_pred             CCCcccHHHHHhhc
Q psy879          204 GFGHVTAEYVFKVC  217 (317)
Q Consensus       204 ~~~~i~~~~v~~~~  217 (317)
                      +...|+.+++.++.
T Consensus       376 ~~~~i~~~d~~~a~  389 (644)
T PRK10733        376 NKRVVSMVEFEKAK  389 (644)
T ss_pred             CCCcccHHHHHHHH
Confidence            45678888876654

>PRK05342 clpX ATP-dependent protease ATP-binding subunit ClpX; Provisional

Probab=99.58  E-value=5.1e-14  Score=126.31  Aligned_cols=173  Identities=27%  Similarity=0.318  Sum_probs=109.2

Q ss_pred             CC-cccCCHHHHHHHHHHHhc-------C---------CCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCC
Q psy879            9 FS-DIVGNEDTVERLKVFSSS-------G---------NVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASN   71 (317)
Q Consensus         9 ~~-~~~g~~~~~~~l~~~l~~-------~---------~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~   71 (317)
                      ++ .++||+++++.+..++.+       +         ..++++|+||||||||++|+++++.+..     +++.+++..
T Consensus        69 L~~~ViGq~~ak~~l~~av~~~~~r~~~~~~~~~~~~~~~~~iLl~Gp~GtGKT~lAr~lA~~l~~-----pf~~id~~~  143 (412)
T PRK05342         69 LDQYVIGQERAKKVLSVAVYNHYKRLRHGDKKDDDVELQKSNILLIGPTGSGKTLLAQTLARILDV-----PFAIADATT  143 (412)
T ss_pred             HhhHeeChHHHHHHHHHHHHHHHHhhhcccccccccccCCceEEEEcCCCCCHHHHHHHHHHHhCC-----Cceecchhh
Confidence            44 479999999988666521       1         1246999999999999999999998632     344444332


Q ss_pred             C-----cChHHHHHHHHHHHhh-cccCCCCceeEEEEeCCCCCCHH--------------HHHHHHHHhhhcc-------
Q psy879           72 D-----RGIDTVRNKIKMFAQQ-KVTLPPGRHKIVILDEADSMTDG--------------AQQALRRTMEIYS-------  124 (317)
Q Consensus        72 ~-----~~~~~i~~~~~~~~~~-~~~~~~~~~~vliiDE~d~l~~~--------------~~~~ll~~le~~~-------  124 (317)
                      .     .+. .+...+...... ........+.||+|||+|.+...              .|++|+++||...       
T Consensus       144 l~~~gyvG~-d~e~~l~~l~~~~~~~~~~a~~gIi~iDEIdkl~~~~~~~~~~~d~s~~~vQ~~LL~~Leg~~~~v~~~g  222 (412)
T PRK05342        144 LTEAGYVGE-DVENILLKLLQAADYDVEKAQRGIVYIDEIDKIARKSENPSITRDVSGEGVQQALLKILEGTVASVPPQG  222 (412)
T ss_pred             cccCCcccc-hHHHHHHHHHHhccccHHHcCCcEEEEechhhhccccCCCCcCCCcccHHHHHHHHHHHhcCeEEeCCCC
Confidence            1     111 122222221111 11111246789999999999753              7899999998421       


Q ss_pred             ------CCceEEEEecC--------C------------------------------C--------------cCchhHhhh
Q psy879          125 ------NTTRFALACNN--------S------------------------------E--------------KIIEPIQSR  146 (317)
Q Consensus       125 ------~~~~~il~~~~--------~------------------------------~--------------~l~~~i~sR  146 (317)
                            .++++|.|+|-        .                              .              .+.|.+..|
T Consensus       223 g~~~~~~~~~~i~t~nilfi~~Gaf~g~~~~~~~r~~~~~~gf~~~~~~~~~~~~~~~~~~~~~~~dL~~~gf~PEflgR  302 (412)
T PRK05342        223 GRKHPQQEFIQVDTTNILFICGGAFDGLEKIIKQRLGKKGIGFGAEVKSKKEKRTEGELLKQVEPEDLIKFGLIPEFIGR  302 (412)
T ss_pred             CcCcCCCCeEEeccCCceeeecccccCcHHHHHHHHhhcccCCccccccccccchhHHHHHhcCHHHHHHHhhhHHHhCC
Confidence                  01122222221        0                              0              145777888


Q ss_pred             cce-eeecCCCHHHHHHHHHH----H-------HHHcCC--CCCHHHHHHHHHhc
Q psy879          147 CAM-LRYNKLTDAQLLSKVIE----I-------CEKENI--SHTNDGLEAIVFTA  187 (317)
Q Consensus       147 ~~~-i~f~~~~~~~~~~~l~~----~-------~~~~~~--~i~~~~~~~l~~~~  187 (317)
                      +.. +.|.+++++++.+++..    .       +..+++  .+++++++++++.+
T Consensus       303 ld~iv~f~~L~~~~L~~Il~~~~~~l~~q~~~~l~~~~i~L~~t~~al~~Ia~~~  357 (412)
T PRK05342        303 LPVVATLEELDEEALVRILTEPKNALVKQYQKLFEMDGVELEFTDEALEAIAKKA  357 (412)
T ss_pred             CCeeeecCCCCHHHHHHHHHHHHHHHHHHHHHHHHhCCcEEEECHHHHHHHHHhC
Confidence            866 89999999999999872    2       223443  57899999999864

>PF05673 DUF815: Protein of unknown function (DUF815); InterPro: IPR008533 This domain consists of several bacterial proteins of unknown function

Probab=99.58  E-value=4e-13  Score=110.01  Aligned_cols=188  Identities=15%  Similarity=0.213  Sum_probs=131.1

Q ss_pred             ccCCCCCCcccCCHHHHHHH----HHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHH
Q psy879            3 KYRPQTFSDIVGNEDTVERL----KVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTV   78 (317)
Q Consensus         3 ky~P~~~~~~~g~~~~~~~l----~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i   78 (317)
                      ...|-.+++++|-+..++.|    ..++......|+|++|+.|||||++++++..++...+  ..++++..........+
T Consensus        20 ~~~~~~l~~L~Gie~Qk~~l~~Nt~~Fl~G~pannvLL~G~rGtGKSSlVkall~~y~~~G--LRlIev~k~~L~~l~~l   97 (249)
T PF05673_consen   20 HPDPIRLDDLIGIERQKEALIENTEQFLQGLPANNVLLWGARGTGKSSLVKALLNEYADQG--LRLIEVSKEDLGDLPEL   97 (249)
T ss_pred             CCCCCCHHHhcCHHHHHHHHHHHHHHHHcCCCCcceEEecCCCCCHHHHHHHHHHHHhhcC--ceEEEECHHHhccHHHH
Confidence            34567799999977666654    4455555445599999999999999999999975443  56777766544444444


Q ss_pred             HHHHHHHHhhcccCCCCceeEEEEeCCCCCCHH-HHHHHHHHhh----hccCCceEEEEecCCCcCc-------------
Q psy879           79 RNKIKMFAQQKVTLPPGRHKIVILDEADSMTDG-AQQALRRTME----IYSNTTRFALACNNSEKII-------------  140 (317)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~-~~~~ll~~le----~~~~~~~~il~~~~~~~l~-------------  140 (317)
                      .+   .+...      ..+-||++|+...=..+ .-..|..+||    ..|.|+.+..|+|..+-+.             
T Consensus        98 ~~---~l~~~------~~kFIlf~DDLsFe~~d~~yk~LKs~LeGgle~~P~NvliyATSNRRHLv~E~~~d~~~~~~~e  168 (249)
T PF05673_consen   98 LD---LLRDR------PYKFILFCDDLSFEEGDTEYKALKSVLEGGLEARPDNVLIYATSNRRHLVPESFSDREDIQDDE  168 (249)
T ss_pred             HH---HHhcC------CCCEEEEecCCCCCCCcHHHHHHHHHhcCccccCCCcEEEEEecchhhccchhhhhccCCCccc
Confidence            33   33333      34669999987754433 3445555554    6788888888888643221             


Q ss_pred             ----------hhHhhhcce-eeecCCCHHHHHHHHHHHHHHcCCCCCHHHH-----HHHHHhcCCCHHHHHHHHHHh
Q psy879          141 ----------EPIQSRCAM-LRYNKLTDAQLLSKVIEICEKENISHTNDGL-----EAIVFTAQGDMRQALNNLQST  201 (317)
Q Consensus       141 ----------~~i~sR~~~-i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~-----~~l~~~~~gd~r~~i~~l~~~  201 (317)
                                -++..||.. +.|.+++.++-.+++...+.+.|+.++++.+     ..-..+.+.+.|.|-..++.+
T Consensus       169 ih~~d~~eEklSLsDRFGL~l~F~~~~q~~YL~IV~~~~~~~g~~~~~e~l~~~Al~wa~~rg~RSGRtA~QF~~~l  245 (249)
T PF05673_consen  169 IHPSDTIEEKLSLSDRFGLWLSFYPPDQEEYLAIVRHYAERYGLELDEEELRQEALQWALRRGGRSGRTARQFIDDL  245 (249)
T ss_pred             cCcchHHHHHHhHHHhCCcEEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHcCCCCHHHHHHHHHHH
Confidence                      245677776 9999999999999999999999999986443     333344556888887776654

>PRK13531 regulatory ATPase RavA; Provisional

Probab=99.57  E-value=3.9e-13  Score=120.83  Aligned_cols=197  Identities=16%  Similarity=0.150  Sum_probs=123.5

Q ss_pred             cccCCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCC-----CCcChHHHHHHH--H
Q psy879           11 DIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNAS-----NDRGIDTVRNKI--K   83 (317)
Q Consensus        11 ~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~-----~~~~~~~i~~~~--~   83 (317)
                      .++|++++++.+..++..|.  |++|+||||+|||++|++++.......   .+....+.     +..+...+....  +
T Consensus        21 ~i~gre~vI~lll~aalag~--hVLL~GpPGTGKT~LAraLa~~~~~~~---~F~~~~~~fttp~DLfG~l~i~~~~~~g   95 (498)
T PRK13531         21 GLYERSHAIRLCLLAALSGE--SVFLLGPPGIAKSLIARRLKFAFQNAR---AFEYLMTRFSTPEEVFGPLSIQALKDEG   95 (498)
T ss_pred             hccCcHHHHHHHHHHHccCC--CEEEECCCChhHHHHHHHHHHHhcccC---cceeeeeeecCcHHhcCcHHHhhhhhcC
Confidence            57899999999998888887  899999999999999999999863221   12222211     111111111110  1


Q ss_pred             HHH-hhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhcc---------CCceE-EEEecCCC---cCchhHhhhcce
Q psy879           84 MFA-QQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYS---------NTTRF-ALACNNSE---KIIEPIQSRCAM  149 (317)
Q Consensus        84 ~~~-~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~---------~~~~~-il~~~~~~---~l~~~i~sR~~~  149 (317)
                      .+. ..+.  +-....++++||+..+++..+++|+..|++..         -..++ +++||+..   .+.+++..|+..
T Consensus        96 ~f~r~~~G--~L~~A~lLfLDEI~rasp~~QsaLLeam~Er~~t~g~~~~~lp~rfiv~ATN~LPE~g~~leAL~DRFli  173 (498)
T PRK13531         96 RYQRLTSG--YLPEAEIVFLDEIWKAGPAILNTLLTAINERRFRNGAHEEKIPMRLLVTASNELPEADSSLEALYDRMLI  173 (498)
T ss_pred             chhhhcCC--ccccccEEeecccccCCHHHHHHHHHHHHhCeEecCCeEEeCCCcEEEEECCCCcccCCchHHhHhhEEE
Confidence            111 0110  00134499999999999999999999996432         12334 55555322   355699999965


Q ss_pred             -eeecCCCH-HHHHHHHHHHHH-----------------------HcCCCCCHHHHHHHHHhc------C----CCHHHH
Q psy879          150 -LRYNKLTD-AQLLSKVIEICE-----------------------KENISHTNDGLEAIVFTA------Q----GDMRQA  194 (317)
Q Consensus       150 -i~f~~~~~-~~~~~~l~~~~~-----------------------~~~~~i~~~~~~~l~~~~------~----gd~r~~  194 (317)
                       +..+++++ ++..++|.....                       -..+.+++...+++....      .    -+.|..
T Consensus       174 ri~vp~l~~~~~e~~lL~~~~~~~~~~~~~~~vis~eel~~lq~~v~~V~v~d~v~eyI~~L~~~lr~~r~~~~~SpR~~  253 (498)
T PRK13531        174 RLWLDKVQDKANFRSMLTSQQDENDNPVPASLQITDEEYQQWQKEIGKITLPDHVFELIFQLRQQLDALPNAPYVSDRRW  253 (498)
T ss_pred             EEECCCCCchHHHHHHHHcccccccCCCcccCCCCHHHHHHHHHHhcceeCCHHHHHHHHHHHHHHhcCCCCCCcCcHHH
Confidence             88888863 554556543211                       134566777777766442      1    467777


Q ss_pred             HHHHHH---hh--hCCCcccHHHHH
Q psy879          195 LNNLQS---TH--NGFGHVTAEYVF  214 (317)
Q Consensus       195 i~~l~~---~~--~~~~~i~~~~v~  214 (317)
                      +..+..   .+  .+...++.+|+.
T Consensus       254 ~~l~~~akA~A~l~GR~~V~p~Dv~  278 (498)
T PRK13531        254 KKAIRLLQASAFFSGRDAIAPIDLI  278 (498)
T ss_pred             HHHHHHHHHHHHHCCCCCCCHHHHH
Confidence            766543   22  267789999886

>KOG0739|consensus

Probab=99.57  E-value=5.3e-14  Score=116.55  Aligned_cols=223  Identities=18%  Similarity=0.206  Sum_probs=134.2

Q ss_pred             CCC-CCCcccCCHHHHHHHHHHHh----------cCCCc--eEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCC
Q psy879            5 RPQ-TFSDIVGNEDTVERLKVFSS----------SGNVP--NIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASN   71 (317)
Q Consensus         5 ~P~-~~~~~~g~~~~~~~l~~~l~----------~~~~~--~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~   71 (317)
                      +|+ .|+|+.|-+.+++.|+.++-          .++.|  .+|+||||||||+.+|+++|.+..     ..++.+..++
T Consensus       127 KPNVkWsDVAGLE~AKeALKEAVILPIKFPqlFtGkR~PwrgiLLyGPPGTGKSYLAKAVATEAn-----STFFSvSSSD  201 (439)
T KOG0739|consen  127 KPNVKWSDVAGLEGAKEALKEAVILPIKFPQLFTGKRKPWRGILLYGPPGTGKSYLAKAVATEAN-----STFFSVSSSD  201 (439)
T ss_pred             CCCCchhhhccchhHHHHHHhheeecccchhhhcCCCCcceeEEEeCCCCCcHHHHHHHHHhhcC-----CceEEeehHH
Confidence            454 59999999999999988742          23322  499999999999999999999852     3466666654


Q ss_pred             Cc------ChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHH-----------HHHHHHHHhhhc---cCCceEEE
Q psy879           72 DR------GIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDG-----------AQQALRRTMEIY---SNTTRFAL  131 (317)
Q Consensus        72 ~~------~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~-----------~~~~ll~~le~~---~~~~~~il  131 (317)
                      ..      +..-+.+.+....+       ..+.||+|||+|.+...           ....|+-.|...   ...+.++.
T Consensus       202 LvSKWmGESEkLVknLFemARe-------~kPSIIFiDEiDslcg~r~enEseasRRIKTEfLVQMqGVG~d~~gvLVLg  274 (439)
T KOG0739|consen  202 LVSKWMGESEKLVKNLFEMARE-------NKPSIIFIDEIDSLCGSRSENESEASRRIKTEFLVQMQGVGNDNDGVLVLG  274 (439)
T ss_pred             HHHHHhccHHHHHHHHHHHHHh-------cCCcEEEeehhhhhccCCCCCchHHHHHHHHHHHHhhhccccCCCceEEEe
Confidence            21      12233444444333       46889999999988532           123344445422   23455566


Q ss_pred             EecCCCcCchhHhhhcce-eeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHH--HhhhC-CCc
Q psy879          132 ACNNSEKIIEPIQSRCAM-LRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQ--STHNG-FGH  207 (317)
Q Consensus       132 ~~~~~~~l~~~i~sR~~~-i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~--~~~~~-~~~  207 (317)
                      +||-+..++.+|++||.. |.++.|.........+-.+..-...+++.....++..+.|--..-+.++-  .+... .+.
T Consensus       275 ATNiPw~LDsAIRRRFekRIYIPLPe~~AR~~MF~lhlG~tp~~LT~~d~~eL~~kTeGySGsDisivVrDalmePvRkv  354 (439)
T KOG0739|consen  275 ATNIPWVLDSAIRRRFEKRIYIPLPEAHARARMFKLHLGDTPHVLTEQDFKELARKTEGYSGSDISIVVRDALMEPVRKV  354 (439)
T ss_pred             cCCCchhHHHHHHHHhhcceeccCCcHHHhhhhheeccCCCccccchhhHHHHHhhcCCCCcCceEEEehhhhhhhHHHh
Confidence            788899999999999988 66666655444433333333323356777788888877653221111110  01011 112


Q ss_pred             ccHHHHHhhcCCCCHHHHHHHHHHHhcCCHHH
Q psy879          208 VTAEYVFKVCDEPHPLAVKEMLLNCVEGNMKD  239 (317)
Q Consensus       208 i~~~~v~~~~~~~~~~~i~~l~~~~~~~~~~~  239 (317)
                      -+.-+..++.+.+..+.+..++.-+...+...
T Consensus       355 qsAthFk~v~~~s~~~~~~~lltpcspgd~ga  386 (439)
T KOG0739|consen  355 QSATHFKKVSGPSNPSEVDDLLTPCSPGDPGA  386 (439)
T ss_pred             hhhhhhhccCCCCChhhhccccCCCCCCCcch
Confidence            34445556666555544555554444444443

>KOG1514|consensus

Probab=99.56  E-value=3.5e-13  Score=123.39  Aligned_cols=189  Identities=21%  Similarity=0.264  Sum_probs=132.8

Q ss_pred             CCHHHHHHHHHHHh----c-CCCceEEEECCCCCCHHHHHHHHHHHHc-----CCCCCCceEEecCCCCcChHHHHHHHH
Q psy879           14 GNEDTVERLKVFSS----S-GNVPNIIISGPPGVGKTTTILCLARILL-----GPSFKDAVLELNASNDRGIDTVRNKIK   83 (317)
Q Consensus        14 g~~~~~~~l~~~l~----~-~~~~~~ll~G~~G~GKt~la~~la~~l~-----~~~~~~~~~~~~~~~~~~~~~i~~~~~   83 (317)
                      +++.....+..+++    . +....+++.|-||||||.+++.+.+.|.     +.-....++++|+....+..++.+.+-
T Consensus       400 cRe~E~~~I~~f~~~~i~~~~~g~~mYIsGvPGtGKT~tV~~Vm~~Lq~~s~~~e~p~f~yveINgm~l~~~~~~Y~~I~  479 (767)
T KOG1514|consen  400 CRENEFSEIEDFLRSFISDQGLGSCMYISGVPGTGKTATVLEVMKELQTSSAQKELPKFDYVEINGLRLASPREIYEKIW  479 (767)
T ss_pred             chhHHHHHHHHHHHhhcCCCCCceeEEEecCCCCCceehHHHHHHHHHHHHhhcCCCCccEEEEcceeecCHHHHHHHHH
Confidence            55655555555544    3 3323599999999999999999999875     233456788899876656555444331


Q ss_pred             HHHh----------------hcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhcc---CCceEEEEecCCC---c-Cc
Q psy879           84 MFAQ----------------QKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYS---NTTRFALACNNSE---K-II  140 (317)
Q Consensus        84 ~~~~----------------~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~---~~~~~il~~~~~~---~-l~  140 (317)
                      ....                .....+.....||+|||.|.|....|..|..+++.|.   ...++|.++|..+   + +.
T Consensus       480 ~~lsg~~~~~~~al~~L~~~f~~~k~~~~~~VvLiDElD~Lvtr~QdVlYn~fdWpt~~~sKLvvi~IaNTmdlPEr~l~  559 (767)
T KOG1514|consen  480 EALSGERVTWDAALEALNFRFTVPKPKRSTTVVLIDELDILVTRSQDVLYNIFDWPTLKNSKLVVIAIANTMDLPERLLM  559 (767)
T ss_pred             HhcccCcccHHHHHHHHHHhhccCCCCCCCEEEEeccHHHHhcccHHHHHHHhcCCcCCCCceEEEEecccccCHHHHhc
Confidence            1000                0011133567899999999999999999999998753   3444566666543   3 44


Q ss_pred             hhHhhhcce--eeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHH---hcCCCHHHHHHHHHHhhh
Q psy879          141 EPIQSRCAM--LRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVF---TAQGDMRQALNNLQSTHN  203 (317)
Q Consensus       141 ~~i~sR~~~--i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~---~~~gd~r~~i~~l~~~~~  203 (317)
                      ..+-||...  +.|.||+..|+.+++..+++.. -.++..+++.++.   ...||.|+|++.++.++.
T Consensus       560 nrvsSRlg~tRi~F~pYth~qLq~Ii~~RL~~~-~~f~~~aielvarkVAavSGDaRraldic~RA~E  626 (767)
T KOG1514|consen  560 NRVSSRLGLTRICFQPYTHEQLQEIISARLKGL-DAFENKAIELVARKVAAVSGDARRALDICRRAAE  626 (767)
T ss_pred             cchhhhccceeeecCCCCHHHHHHHHHHhhcch-hhcchhHHHHHHHHHHhccccHHHHHHHHHHHHH
Confidence            577888765  9999999999999999987654 2456777766654   457999999999998765

>TIGR01817 nifA Nif-specific regulatory protein

Probab=99.56  E-value=1.9e-13  Score=128.30  Aligned_cols=209  Identities=15%  Similarity=0.190  Sum_probs=143.1

Q ss_pred             ccCCCCCCcccCCHHHHHHHHHHHhc--CCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHH
Q psy879            3 KYRPQTFSDIVGNEDTVERLKVFSSS--GNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRN   80 (317)
Q Consensus         3 ky~P~~~~~~~g~~~~~~~l~~~l~~--~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~   80 (317)
                      +++.-+|+.++|+...++.+...++.  ....+++|+|++||||+++|+++....  .....+++.++|... ....+..
T Consensus       189 ~~~~~~~~~liG~s~~~~~~~~~~~~~a~~~~pvli~Ge~GtGK~~lA~~ih~~s--~r~~~pfv~i~c~~~-~~~~~~~  265 (534)
T TIGR01817       189 RRRSGKEDGIIGKSPAMRQVVDQARVVARSNSTVLLRGESGTGKELIAKAIHYLS--PRAKRPFVKVNCAAL-SETLLES  265 (534)
T ss_pred             ccccCccCceEECCHHHHHHHHHHHHHhCcCCCEEEECCCCccHHHHHHHHHHhC--CCCCCCeEEeecCCC-CHHHHHH
Confidence            45556799999998877776665542  222369999999999999999999863  223456888888643 2222222


Q ss_pred             H-HHHH----H----hhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhcc-----------CCceEEEEecCC----
Q psy879           81 K-IKMF----A----QQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYS-----------NTTRFALACNNS----  136 (317)
Q Consensus        81 ~-~~~~----~----~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~-----------~~~~~il~~~~~----  136 (317)
                      . ++..    .    .....+......+++|||++.|....|..|++++++..           .++++|++|+..    
T Consensus       266 ~lfg~~~~~~~~~~~~~~g~~~~a~~GtL~ldei~~L~~~~Q~~Ll~~l~~~~~~~~~~~~~~~~~~riI~~s~~~l~~~  345 (534)
T TIGR01817       266 ELFGHEKGAFTGAIAQRKGRFELADGGTLFLDEIGEISPAFQAKLLRVLQEGEFERVGGNRTLKVDVRLVAATNRDLEEA  345 (534)
T ss_pred             HHcCCCCCccCCCCcCCCCcccccCCCeEEEechhhCCHHHHHHHHHHHhcCcEEECCCCceEeecEEEEEeCCCCHHHH
Confidence            1 1100    0    00001122457899999999999999999999998532           246788887754    


Q ss_pred             ---CcCchhHhhhcce--eeecCCC--HHHHHHHHHHHHH----HcC--CCCCHHHHHHHHHh-cCCCHHHHHHHHHHhh
Q psy879          137 ---EKIIEPIQSRCAM--LRYNKLT--DAQLLSKVIEICE----KEN--ISHTNDGLEAIVFT-AQGDMRQALNNLQSTH  202 (317)
Q Consensus       137 ---~~l~~~i~sR~~~--i~f~~~~--~~~~~~~l~~~~~----~~~--~~i~~~~~~~l~~~-~~gd~r~~i~~l~~~~  202 (317)
                         ..+.+.+..|+..  +.+||+.  .+++..++...+.    ..+  ..++++++..+... ..||+|+..+.++.++
T Consensus       346 ~~~~~f~~~L~~rl~~~~i~lPpLreR~eDi~~L~~~~l~~~~~~~~~~~~~s~~a~~~L~~~~WPGNvrEL~~v~~~a~  425 (534)
T TIGR01817       346 VAKGEFRADLYYRINVVPIFLPPLRERREDIPLLAEAFLEKFNRENGRPLTITPSAIRVLMSCKWPGNVRELENCLERTA  425 (534)
T ss_pred             HHcCCCCHHHHHHhcCCeeeCCCcccccccHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHhCCCCChHHHHHHHHHHHH
Confidence               2466777788765  7788887  3556555444433    222  56899999998877 5999999999999766


Q ss_pred             h--CCCcccHHHHH
Q psy879          203 N--GFGHVTAEYVF  214 (317)
Q Consensus       203 ~--~~~~i~~~~v~  214 (317)
                      .  ....|+.+++.
T Consensus       426 ~~~~~~~I~~~~l~  439 (534)
T TIGR01817       426 TLSRSGTITRSDFS  439 (534)
T ss_pred             HhCCCCcccHHHCc
Confidence            4  34578877764

This model represents NifA, a DNA-binding regulatory protein for nitrogen fixation. The model produces scores between the trusted and noise cutoffs for a well-described NifA homolog in Aquifex aeolicus (which lacks nitrogenase), for transcriptional activators of alternative nitrogenases (VFe or FeFe instead of MoFe), and truncated forms.

>KOG2004|consensus

Probab=99.56  E-value=1.5e-13  Score=125.79  Aligned_cols=164  Identities=21%  Similarity=0.347  Sum_probs=116.5

Q ss_pred             CcccCCHHHHHHHHHHHhcC----CC--ceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHH---
Q psy879           10 SDIVGNEDTVERLKVFSSSG----NV--PNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRN---   80 (317)
Q Consensus        10 ~~~~g~~~~~~~l~~~l~~~----~~--~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~---   80 (317)
                      +|.+|-+++++++..++.=|    ..  +.+.|+||||+|||++++.+|+.|...     |+.++-..-....+|+.   
T Consensus       411 eDHYgm~dVKeRILEfiAV~kLrgs~qGkIlCf~GPPGVGKTSI~kSIA~ALnRk-----FfRfSvGG~tDvAeIkGHRR  485 (906)
T KOG2004|consen  411 EDHYGMEDVKERILEFIAVGKLRGSVQGKILCFVGPPGVGKTSIAKSIARALNRK-----FFRFSVGGMTDVAEIKGHRR  485 (906)
T ss_pred             ccccchHHHHHHHHHHHHHHhhcccCCCcEEEEeCCCCCCcccHHHHHHHHhCCc-----eEEEeccccccHHhhcccce
Confidence            46788899999988887522    22  359999999999999999999998433     34433322222222221   


Q ss_pred             ------------HHHHHHhhcccCCCCceeEEEEeCCCCCCH----HHHHHHHHHhh-------------hc--cCCceE
Q psy879           81 ------------KIKMFAQQKVTLPPGRHKIVILDEADSMTD----GAQQALRRTME-------------IY--SNTTRF  129 (317)
Q Consensus        81 ------------~~~~~~~~~~~~~~~~~~vliiDE~d~l~~----~~~~~ll~~le-------------~~--~~~~~~  129 (317)
                                  .++..        ...+.+++|||+|++..    +-..+||..|+             -|  -..+.|
T Consensus       486 TYVGAMPGkiIq~LK~v--------~t~NPliLiDEvDKlG~g~qGDPasALLElLDPEQNanFlDHYLdVp~DLSkVLF  557 (906)
T KOG2004|consen  486 TYVGAMPGKIIQCLKKV--------KTENPLILIDEVDKLGSGHQGDPASALLELLDPEQNANFLDHYLDVPVDLSKVLF  557 (906)
T ss_pred             eeeccCChHHHHHHHhh--------CCCCceEEeehhhhhCCCCCCChHHHHHHhcChhhccchhhhccccccchhheEE
Confidence                        12211        13578999999999863    34677877775             11  135668


Q ss_pred             EEEecCCCcCchhHhhhcceeeecCCCHHHHHHHHHHHHH-----H-----cCCCCCHHHHHHHHHh
Q psy879          130 ALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICE-----K-----ENISHTNDGLEAIVFT  186 (317)
Q Consensus       130 il~~~~~~~l~~~i~sR~~~i~f~~~~~~~~~~~l~~~~~-----~-----~~~~i~~~~~~~l~~~  186 (317)
                      |+|+|..+.++++++.|..+|+.+.|..+|-.++...++-     .     +.+++++.++..+++.
T Consensus       558 icTAN~idtIP~pLlDRMEvIelsGYv~eEKv~IA~~yLip~a~~~~gl~~e~v~is~~al~~lI~~  624 (906)
T KOG2004|consen  558 ICTANVIDTIPPPLLDRMEVIELSGYVAEEKVKIAERYLIPQALKDCGLKPEQVKISDDALLALIER  624 (906)
T ss_pred             EEeccccccCChhhhhhhheeeccCccHHHHHHHHHHhhhhHHHHHcCCCHHhcCccHHHHHHHHHH
Confidence            9999999999999999999999999999998888776542     2     4567888887666644

>KOG0728|consensus

Probab=99.56  E-value=1.1e-13  Score=112.03  Aligned_cols=128  Identities=18%  Similarity=0.270  Sum_probs=95.2

Q ss_pred             ceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCC------CcChHHHHHHHHHHHhhcccCCCCceeEEEEeCC
Q psy879           32 PNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASN------DRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEA  105 (317)
Q Consensus        32 ~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~------~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~  105 (317)
                      ..+++|||||+|||.+|+++|..-.|     .++.++.+.      ..+..-+++.+-....       ..+.++++||+
T Consensus       182 KGvlLygppgtGktLlaraVahht~c-----~firvsgselvqk~igegsrmvrelfvmare-------hapsiifmdei  249 (404)
T KOG0728|consen  182 KGVLLYGPPGTGKTLLARAVAHHTDC-----TFIRVSGSELVQKYIGEGSRMVRELFVMARE-------HAPSIIFMDEI  249 (404)
T ss_pred             cceEEecCCCCchhHHHHHHHhhcce-----EEEEechHHHHHHHhhhhHHHHHHHHHHHHh-------cCCceEeeecc
Confidence            35999999999999999999987433     355555432      1223344555444433       35789999999


Q ss_pred             CCCC-----------HHHHHHHHHHhh-----hccCCceEEEEecCCCcCchhHhhhcce---eeecCCCHHHHHHHHHH
Q psy879          106 DSMT-----------DGAQQALRRTME-----IYSNTTRFALACNNSEKIIEPIQSRCAM---LRYNKLTDAQLLSKVIE  166 (317)
Q Consensus       106 d~l~-----------~~~~~~ll~~le-----~~~~~~~~il~~~~~~~l~~~i~sR~~~---i~f~~~~~~~~~~~l~~  166 (317)
                      |.+.           .+.|...+.++.     +...++.+|++||..+-+++++.+-..+   ++|+||+++...++|+-
T Consensus       250 dsigs~r~e~~~ggdsevqrtmlellnqldgfeatknikvimatnridild~allrpgridrkiefp~p~e~ar~~ilki  329 (404)
T KOG0728|consen  250 DSIGSSRVESGSGGDSEVQRTMLELLNQLDGFEATKNIKVIMATNRIDILDPALLRPGRIDRKIEFPPPNEEARLDILKI  329 (404)
T ss_pred             cccccccccCCCCccHHHHHHHHHHHHhccccccccceEEEEeccccccccHhhcCCCcccccccCCCCCHHHHHHHHHH
Confidence            9873           235666666665     3457889999999999999999877765   99999999999999887


Q ss_pred             HHHHc
Q psy879          167 ICEKE  171 (317)
Q Consensus       167 ~~~~~  171 (317)
                      ..++-
T Consensus       330 hsrkm  334 (404)
T KOG0728|consen  330 HSRKM  334 (404)
T ss_pred             hhhhh
Confidence            76653

>KOG1968|consensus

Probab=99.56  E-value=3.1e-14  Score=136.72  Aligned_cols=196  Identities=27%  Similarity=0.412  Sum_probs=151.3

Q ss_pred             CcccCCCCCCcccCCHHHHHHHHHHHhcC-----------CC---ce--EEEECCCCCCHHHHHHHHHHHHcCCCCCCce
Q psy879            1 IEKYRPQTFSDIVGNEDTVERLKVFSSSG-----------NV---PN--IIISGPPGVGKTTTILCLARILLGPSFKDAV   64 (317)
Q Consensus         1 ~~ky~P~~~~~~~g~~~~~~~l~~~l~~~-----------~~---~~--~ll~G~~G~GKt~la~~la~~l~~~~~~~~~   64 (317)
                      ++||+|.+..+++|+......+..++..-           .+   ..  ++++||||.|||+.++..|+.+     +..+
T Consensus       311 ~~k~~p~~~k~~~~~~~~~~~~~~~l~~~k~~~~~sy~~~~~~ss~~~~~l~~G~pGigKT~~~h~~~k~~-----g~~v  385 (871)
T KOG1968|consen  311 TEKYQPTSSKALEGNASSSKKASKWLAKSKDKEKSSYKENEPDSSKKKALLLSGPPGIGKTTAAHKAAKEL-----GFKV  385 (871)
T ss_pred             ccccccccHHhhhcccchhhhhhhHHHhhhccccccccccCcchhhHHHHHhcCCCCCCchhhHhhhhhhc-----ccce
Confidence            47999999999999887777777766533           11   12  4899999999999999999986     4468


Q ss_pred             EEecCCCCcChHHHHHHHHHHHhhccc-----------CCCCceeEEEEeCCCCCCHHH---HHHHHHHhhhccCCceEE
Q psy879           65 LELNASNDRGIDTVRNKIKMFAQQKVT-----------LPPGRHKIVILDEADSMTDGA---QQALRRTMEIYSNTTRFA  130 (317)
Q Consensus        65 ~~~~~~~~~~~~~i~~~~~~~~~~~~~-----------~~~~~~~vliiDE~d~l~~~~---~~~ll~~le~~~~~~~~i  130 (317)
                      ++.|+++.++...+.+.++.+......           ...+...||++||+|.+..++   ...+-.+.+  .....+|
T Consensus       386 ~E~Nas~~RSk~~l~~~~~~~~~s~si~~~~~~~~~~~~~~~~~~vil~devD~~~~~dRg~v~~l~~l~~--ks~~Piv  463 (871)
T KOG1968|consen  386 VEKNASDVRSKKELLNKLGNATSSHSIKGSKKKKGNRQSLNSDHFLILMDEVDGMFGEDRGGVSKLSSLCK--KSSRPLV  463 (871)
T ss_pred             eecCccccccccHHHhhhhccccccchhhhhcccccccccccceeEEEEeccccccchhhhhHHHHHHHHH--hccCCeE
Confidence            999998777666666655543322111           112345599999999998743   445555555  3445688


Q ss_pred             EEecCCCcC-chhHhhhcceeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhh
Q psy879          131 LACNNSEKI-IEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHN  203 (317)
Q Consensus       131 l~~~~~~~l-~~~i~sR~~~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~  203 (317)
                      ++||+...- ..++.+-|..++|+.|+...+..++..++..+++.++++.++.+.+.++||+|++++.++.+..
T Consensus       464 ~~cndr~~p~sr~~~~~~~~l~f~kP~~~~i~~ri~si~~se~~ki~~~~l~~~s~~~~~DiR~~i~~lq~~~~  537 (871)
T KOG1968|consen  464 CTCNDRNLPKSRALSRACSDLRFSKPSSELIRSRIMSICKSEGIKISDDVLEEISKLSGGDIRQIIMQLQFWSL  537 (871)
T ss_pred             EEecCCCCccccchhhhcceeeecCCcHHHHHhhhhhhhcccceecCcHHHHHHHHhcccCHHHHHHHHhhhhc
Confidence            999887543 4566677788999999999999999999999999999999999999999999999999998743

>COG0464 SpoVK ATPases of the AAA+ class [Posttranslational modification, protein turnover, chaperones]

Probab=99.55  E-value=1.6e-13  Score=127.84  Aligned_cols=200  Identities=18%  Similarity=0.187  Sum_probs=132.3

Q ss_pred             CCCCcccCCHHHHHHHHHHHhc-----------C-CCc-eEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCc
Q psy879            7 QTFSDIVGNEDTVERLKVFSSS-----------G-NVP-NIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDR   73 (317)
Q Consensus         7 ~~~~~~~g~~~~~~~l~~~l~~-----------~-~~~-~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~   73 (317)
                      -+|+++.|-+.+++.+...+..           + +++ .+|||||||||||++|+++|.+.     +..++.+..++..
T Consensus       239 v~~~diggl~~~k~~l~e~v~~~~~~~e~~~~~~~~~~~giLl~GpPGtGKT~lAkava~~~-----~~~fi~v~~~~l~  313 (494)
T COG0464         239 VTLDDIGGLEEAKEELKEAIETPLKRPELFRKLGLRPPKGVLLYGPPGTGKTLLAKAVALES-----RSRFISVKGSELL  313 (494)
T ss_pred             cceehhhcHHHHHHHHHHHHHhHhhChHHHHhcCCCCCCeeEEECCCCCCHHHHHHHHHhhC-----CCeEEEeeCHHHh
Confidence            3588888888777776665431           2 223 49999999999999999999974     3345555544211


Q ss_pred             ------ChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCH-----------HHHHHHHHHhh--hccCCceEEEEec
Q psy879           74 ------GIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTD-----------GAQQALRRTME--IYSNTTRFALACN  134 (317)
Q Consensus        74 ------~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~-----------~~~~~ll~~le--~~~~~~~~il~~~  134 (317)
                            ....+++.+.....       ..+.||++||+|.+..           ...+.|+..++  +...++.+|.+||
T Consensus       314 sk~vGesek~ir~~F~~A~~-------~~p~iiFiDEiDs~~~~r~~~~~~~~~r~~~~lL~~~d~~e~~~~v~vi~aTN  386 (494)
T COG0464         314 SKWVGESEKNIRELFEKARK-------LAPSIIFIDEIDSLASGRGPSEDGSGRRVVGQLLTELDGIEKAEGVLVIAATN  386 (494)
T ss_pred             ccccchHHHHHHHHHHHHHc-------CCCcEEEEEchhhhhccCCCCCchHHHHHHHHHHHHhcCCCccCceEEEecCC
Confidence                  12334444444332       4578999999998742           35677777775  4445666788999


Q ss_pred             CCCcCchhHhh--hcce-eeecCCCHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHhcCC-CHHHHHHHHHHhhh-----C
Q psy879          135 NSEKIIEPIQS--RCAM-LRYNKLTDAQLLSKVIEICEKENIS-HTNDGLEAIVFTAQG-DMRQALNNLQSTHN-----G  204 (317)
Q Consensus       135 ~~~~l~~~i~s--R~~~-i~f~~~~~~~~~~~l~~~~~~~~~~-i~~~~~~~l~~~~~g-d~r~~i~~l~~~~~-----~  204 (317)
                      .++.+++++.+  |+.. +.|++|+.++..++++......+.. .++-.+..+++.+.| +-..+...++.++.     .
T Consensus       387 ~p~~ld~a~lR~gRfd~~i~v~~pd~~~r~~i~~~~~~~~~~~~~~~~~~~~l~~~t~~~sgadi~~i~~ea~~~~~~~~  466 (494)
T COG0464         387 RPDDLDPALLRPGRFDRLIYVPLPDLEERLEIFKIHLRDKKPPLAEDVDLEELAEITEGYSGADIAALVREAALEALREA  466 (494)
T ss_pred             CccccCHhhcccCccceEeecCCCCHHHHHHHHHHHhcccCCcchhhhhHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHh
Confidence            99999999999  8887 9999999999999999988755543 234445666665443 22333333333322     1


Q ss_pred             -CCcccHHHHHhhcC
Q psy879          205 -FGHVTAEYVFKVCD  218 (317)
Q Consensus       205 -~~~i~~~~v~~~~~  218 (317)
                       ...++.+++..+..
T Consensus       467 ~~~~~~~~~~~~a~~  481 (494)
T COG0464         467 RRREVTLDDFLDALK  481 (494)
T ss_pred             ccCCccHHHHHHHHH
Confidence             23456655544433

>CHL00206 ycf2 Ycf2; Provisional

Probab=99.54  E-value=2e-13  Score=137.00  Aligned_cols=125  Identities=7%  Similarity=0.029  Sum_probs=86.1

Q ss_pred             CceeEEEEeCCCCCCHHH-----HHHHHHHhhhc-----cCCceEEEEecCCCcCchhHhh--hcce-eeecCCCHHHHH
Q psy879           95 GRHKIVILDEADSMTDGA-----QQALRRTMEIY-----SNTTRFALACNNSEKIIEPIQS--RCAM-LRYNKLTDAQLL  161 (317)
Q Consensus        95 ~~~~vliiDE~d~l~~~~-----~~~ll~~le~~-----~~~~~~il~~~~~~~l~~~i~s--R~~~-i~f~~~~~~~~~  161 (317)
                      ..+.||+|||+|.+....     .+.|+..|...     ..++++|.+||.++.++|++.+  |+.. |.++.|+..+..
T Consensus      1731 ~SPCIIFIDEIDaL~~~ds~~ltL~qLLneLDg~~~~~s~~~VIVIAATNRPD~LDPALLRPGRFDR~I~Ir~Pd~p~R~ 1810 (2281)
T CHL00206       1731 MSPCIIWIPNIHDLNVNESNYLSLGLLVNSLSRDCERCSTRNILVIASTHIPQKVDPALIAPNKLNTCIKIRRLLIPQQR 1810 (2281)
T ss_pred             CCCeEEEEEchhhcCCCccceehHHHHHHHhccccccCCCCCEEEEEeCCCcccCCHhHcCCCCCCeEEEeCCCCchhHH
Confidence            358899999999997542     56677777632     3456788899999999999998  7765 889988887777


Q ss_pred             HHHHHHHHHcCCCCCHH--HHHHHHHhcCC----CHHHHHHHHHHhhh--CCCcccHHHHHhhcCC
Q psy879          162 SKVIEICEKENISHTND--GLEAIVFTAQG----DMRQALNNLQSTHN--GFGHVTAEYVFKVCDE  219 (317)
Q Consensus       162 ~~l~~~~~~~~~~i~~~--~~~~l~~~~~g----d~r~~i~~l~~~~~--~~~~i~~~~v~~~~~~  219 (317)
                      +++.......|+.+++.  .++.++..+.|    |+..+.++.-..+.  +...|+.+++..++..
T Consensus      1811 kiL~ILl~tkg~~L~~~~vdl~~LA~~T~GfSGADLanLvNEAaliAirq~ks~Id~~~I~~Al~R 1876 (2281)
T CHL00206       1811 KHFFTLSYTRGFHLEKKMFHTNGFGSITMGSNARDLVALTNEALSISITQKKSIIDTNTIRSALHR 1876 (2281)
T ss_pred             HHHHHHHhhcCCCCCcccccHHHHHHhCCCCCHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHH
Confidence            77665544456666543  25777877644    45544444433222  4567888888776553

>cd00009 AAA The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold

Probab=99.54  E-value=2.7e-13  Score=105.24  Aligned_cols=139  Identities=27%  Similarity=0.315  Sum_probs=94.1

Q ss_pred             cCCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHHHHH--HHhhcc
Q psy879           13 VGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKM--FAQQKV   90 (317)
Q Consensus        13 ~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~~~--~~~~~~   90 (317)
                      +|++.++..+...+......+++++||||+|||++++.+++.+...  ...++.+++...............  ......
T Consensus         1 ~~~~~~~~~i~~~~~~~~~~~v~i~G~~G~GKT~l~~~i~~~~~~~--~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~   78 (151)
T cd00009           1 VGQEEAIEALREALELPPPKNLLLYGPPGTGKTTLARAIANELFRP--GAPFLYLNASDLLEGLVVAELFGHFLVRLLFE   78 (151)
T ss_pred             CchHHHHHHHHHHHhCCCCCeEEEECCCCCCHHHHHHHHHHHhhcC--CCCeEEEehhhhhhhhHHHHHhhhhhHhHHHH
Confidence            3678888888888877555579999999999999999999987432  233455544332222211111110  000000


Q ss_pred             cCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhc------cCCceEEEEecCCC--cCchhHhhhc-ceeeec
Q psy879           91 TLPPGRHKIVILDEADSMTDGAQQALRRTMEIY------SNTTRFALACNNSE--KIIEPIQSRC-AMLRYN  153 (317)
Q Consensus        91 ~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~------~~~~~~il~~~~~~--~l~~~i~sR~-~~i~f~  153 (317)
                      ........++++||++.+.......++..++..      +..+.+|++++...  .+.+.+.+|+ ..+.++
T Consensus        79 ~~~~~~~~~lilDe~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~ii~~~~~~~~~~~~~~~~~r~~~~i~~~  150 (151)
T cd00009          79 LAEKAKPGVLFIDEIDSLSRGAQNALLRVLETLNDLRIDRENVRVIGATNRPLLGDLDRALYDRLDIRIVIP  150 (151)
T ss_pred             hhccCCCeEEEEeChhhhhHHHHHHHHHHHHhcCceeccCCCeEEEEecCccccCCcChhHHhhhccEeecC
Confidence            011246789999999999887888888888865      35678888888876  7889999999 556655

The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.

>KOG0652|consensus

Probab=99.54  E-value=2.6e-13  Score=110.58  Aligned_cols=170  Identities=19%  Similarity=0.304  Sum_probs=113.7

Q ss_pred             CCC-CCCcccCCHHHHHHHHHHHh-----------cC-CCce-EEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCC
Q psy879            5 RPQ-TFSDIVGNEDTVERLKVFSS-----------SG-NVPN-IIISGPPGVGKTTTILCLARILLGPSFKDAVLELNAS   70 (317)
Q Consensus         5 ~P~-~~~~~~g~~~~~~~l~~~l~-----------~~-~~~~-~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~   70 (317)
                      +|. +++|+-|-+..++.|..++-           -| ++|. +|+|||||||||.+|+++|..-..     .++-+.+.
T Consensus       165 kPtE~YsDiGGldkQIqELvEAiVLpmth~ekF~~lgi~pPKGvLmYGPPGTGKTlmARAcAaqT~a-----TFLKLAgP  239 (424)
T KOG0652|consen  165 KPTEQYSDIGGLDKQIQELVEAIVLPMTHKEKFENLGIRPPKGVLMYGPPGTGKTLMARACAAQTNA-----TFLKLAGP  239 (424)
T ss_pred             CCcccccccccHHHHHHHHHHHhccccccHHHHHhcCCCCCCceEeeCCCCCcHHHHHHHHHHhccc-----hHHHhcch
Confidence            453 47888888877777665541           12 2333 999999999999999999986421     12211111


Q ss_pred             ------CCcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCC-----------HHHHHHHHHHhhh-----ccCCce
Q psy879           71 ------NDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMT-----------DGAQQALRRTMEI-----YSNTTR  128 (317)
Q Consensus        71 ------~~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~-----------~~~~~~ll~~le~-----~~~~~~  128 (317)
                            -..+..-+|+.+.....       ..+.+++|||+|.+.           .+.|...+.++..     +...+.
T Consensus       240 QLVQMfIGdGAkLVRDAFaLAKE-------kaP~IIFIDElDAIGtKRfDSek~GDREVQRTMLELLNQLDGFss~~~vK  312 (424)
T KOG0652|consen  240 QLVQMFIGDGAKLVRDAFALAKE-------KAPTIIFIDELDAIGTKRFDSEKAGDREVQRTMLELLNQLDGFSSDDRVK  312 (424)
T ss_pred             HHHhhhhcchHHHHHHHHHHhhc-------cCCeEEEEechhhhccccccccccccHHHHHHHHHHHHhhcCCCCccceE
Confidence                  01233445554443322       468899999999873           2356666666653     234577


Q ss_pred             EEEEecCCCcCchhHhhhcce---eeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhc
Q psy879          129 FALACNNSEKIIEPIQSRCAM---LRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTA  187 (317)
Q Consensus       129 ~il~~~~~~~l~~~i~sR~~~---i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~  187 (317)
                      +|.+||+.+-++|++.+....   |+|+.|+++...++++-..++-++. ++-..+.+++.+
T Consensus       313 viAATNRvDiLDPALlRSGRLDRKIEfP~Pne~aRarIlQIHsRKMnv~-~DvNfeELaRsT  373 (424)
T KOG0652|consen  313 VIAATNRVDILDPALLRSGRLDRKIEFPHPNEEARARILQIHSRKMNVS-DDVNFEELARST  373 (424)
T ss_pred             EEeecccccccCHHHhhcccccccccCCCCChHHHHHHHHHhhhhcCCC-CCCCHHHHhhcc
Confidence            899999999999999877765   9999999999999988877765542 222356666554

>TIGR00382 clpX endopeptidase Clp ATP-binding regulatory subunit (clpX)

Probab=99.53  E-value=2.2e-13  Score=121.60  Aligned_cols=184  Identities=24%  Similarity=0.281  Sum_probs=114.8

Q ss_pred             cccCCHHHHHHHHHHHh-------c---CC--------CceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCC-
Q psy879           11 DIVGNEDTVERLKVFSS-------S---GN--------VPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASN-   71 (317)
Q Consensus        11 ~~~g~~~~~~~l~~~l~-------~---~~--------~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~-   71 (317)
                      .++||+++++.+..++.       .   ..        ..+++|+||||+|||++|+++++.+.     .++...++.. 
T Consensus        78 ~ViGQe~A~~~l~~av~~h~~~~~~~~~~~~~~~~~~~~~~iLL~GP~GsGKT~lAraLA~~l~-----~pf~~~da~~L  152 (413)
T TIGR00382        78 YVIGQEQAKKVLSVAVYNHYKRLNFEKNKKSDNGVELSKSNILLIGPTGSGKTLLAQTLARILN-----VPFAIADATTL  152 (413)
T ss_pred             eecCHHHHHHHHHHHHHHHHhhhccccccccccccccCCceEEEECCCCcCHHHHHHHHHHhcC-----CCeEEechhhc
Confidence            35899999998876651       1   11        13699999999999999999998863     2233333221 


Q ss_pred             ----CcChHHHHHHHHHHHhh-cccCCCCceeEEEEeCCCCCCH--------------HHHHHHHHHhhhc---------
Q psy879           72 ----DRGIDTVRNKIKMFAQQ-KVTLPPGRHKIVILDEADSMTD--------------GAQQALRRTMEIY---------  123 (317)
Q Consensus        72 ----~~~~~~i~~~~~~~~~~-~~~~~~~~~~vliiDE~d~l~~--------------~~~~~ll~~le~~---------  123 (317)
                          ..+. +..+.+...... +.......+.+|+|||+|++.+              +.|++|+++||..         
T Consensus       153 ~~~gyvG~-d~e~~L~~~~~~~~~~l~~a~~gIV~lDEIdkl~~~~~~~s~~~dvsg~~vq~~LL~iLeG~~~~v~~~~g  231 (413)
T TIGR00382       153 TEAGYVGE-DVENILLKLLQAADYDVEKAQKGIIYIDEIDKISRKSENPSITRDVSGEGVQQALLKIIEGTVANVPPQGG  231 (413)
T ss_pred             cccccccc-cHHHHHHHHHHhCcccHHhcccceEEecccchhchhhccccccccccchhHHHHHHHHhhccceecccCCC
Confidence                1111 122222222111 1111124567999999999986              5799999999721         


Q ss_pred             ----cCCceEEEEecCC---------------------------C-----------------------cCchhHhhhcce
Q psy879          124 ----SNTTRFALACNNS---------------------------E-----------------------KIIEPIQSRCAM  149 (317)
Q Consensus       124 ----~~~~~~il~~~~~---------------------------~-----------------------~l~~~i~sR~~~  149 (317)
                          ..++++|.|+|-.                           .                       .+.|.+..|+..
T Consensus       232 r~~~~~~~i~i~TsNilfi~~Gaf~g~~~i~~~r~~~~~~gf~~~~~~~~~~~~~~~~~~~~~dl~~~g~~PEflgRld~  311 (413)
T TIGR00382       232 RKHPYQEFIQIDTSNILFICGGAFVGLEKIIKKRTGKSSIGFGAEVKKKSKEKADLLRQVEPEDLVKFGLIPEFIGRLPV  311 (413)
T ss_pred             ccccCCCeEEEEcCCceeeecccccChHHHHHHHhhhccccccccccccchhhHHHHHHHHHHHHHHHhhHHHHhCCCCe
Confidence                1234455555430                           0                       145778888865


Q ss_pred             -eeecCCCHHHHHHHHHHH----HH-------HcC--CCCCHHHHHHHHHhcC---CCHHHHHHHHHH
Q psy879          150 -LRYNKLTDAQLLSKVIEI----CE-------KEN--ISHTNDGLEAIVFTAQ---GDMRQALNNLQS  200 (317)
Q Consensus       150 -i~f~~~~~~~~~~~l~~~----~~-------~~~--~~i~~~~~~~l~~~~~---gd~r~~i~~l~~  200 (317)
                       +.|.|++.+++.+++...    ++       .++  +.+++++++.+++.+.   -..|.+-..++.
T Consensus       312 Iv~f~pL~~~~L~~Il~~~~n~l~kq~~~~l~~~gi~L~~t~~a~~~Ia~~~~~~~~GAR~Lr~iie~  379 (413)
T TIGR00382       312 IATLEKLDEEALIAILTKPKNALVKQYQALFKMDNVELDFEEEALKAIAKKALERKTGARGLRSIVEG  379 (413)
T ss_pred             EeecCCCCHHHHHHHHHHHHHHHHHHHHHHhccCCeEEEECHHHHHHHHHhCCCCCCCchHHHHHHHH
Confidence             889999999999998752    22       123  3568999999998742   224444444443

A member of the ATP-dependent proteases, ClpX has ATP-dependent chaperone activity and is required for specific ATP-dependent proteolytic activities expressed by ClpPX. The gene is also found to be involved in stress tolerance in Bacillus subtilis and is essential for the efficient acquisition of genes specifying type IA and IB restriction.

>KOG0737|consensus

Probab=99.53  E-value=8.7e-14  Score=118.75  Aligned_cols=184  Identities=20%  Similarity=0.225  Sum_probs=119.3

Q ss_pred             CCCcccCCHHHHHHHHHHHh----------cCC----CceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCC--
Q psy879            8 TFSDIVGNEDTVERLKVFSS----------SGN----VPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASN--   71 (317)
Q Consensus         8 ~~~~~~g~~~~~~~l~~~l~----------~~~----~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~--   71 (317)
                      +|+|+-|-+.+++.++..+.          .|+    +..+|+|||||||||.+|+++|++..+     .++.+..+.  
T Consensus        90 ~f~DIggLe~v~~~L~e~VilPlr~pelF~~g~Ll~p~kGiLL~GPpG~GKTmlAKA~Akeaga-----~fInv~~s~lt  164 (386)
T KOG0737|consen   90 SFDDIGGLEEVKDALQELVILPLRRPELFAKGKLLRPPKGILLYGPPGTGKTMLAKAIAKEAGA-----NFINVSVSNLT  164 (386)
T ss_pred             ehhhccchHHHHHHHHHHHhhcccchhhhcccccccCCccceecCCCCchHHHHHHHHHHHcCC-----Ccceeeccccc
Confidence            58999999999999887652          222    224999999999999999999998532     233333322  


Q ss_pred             CcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHH-----------HHHHHHH---hh-hccCCceEEEEecCC
Q psy879           72 DRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGA-----------QQALRRT---ME-IYSNTTRFALACNNS  136 (317)
Q Consensus        72 ~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~-----------~~~ll~~---le-~~~~~~~~il~~~~~  136 (317)
                      +....+-.......+..+.   .=.+.+++|||+|.+....           .+.|.-.   +. .....+.+..+||+|
T Consensus       165 ~KWfgE~eKlv~AvFslAs---Kl~P~iIFIDEvds~L~~R~s~dHEa~a~mK~eFM~~WDGl~s~~~~rVlVlgATNRP  241 (386)
T KOG0737|consen  165 SKWFGEAQKLVKAVFSLAS---KLQPSIIFIDEVDSFLGQRRSTDHEATAMMKNEFMALWDGLSSKDSERVLVLGATNRP  241 (386)
T ss_pred             hhhHHHHHHHHHHHHhhhh---hcCcceeehhhHHHHHhhcccchHHHHHHHHHHHHHHhccccCCCCceEEEEeCCCCC
Confidence            1112222222222222221   1357899999999886321           1111111   11 222335556679999


Q ss_pred             CcCchhHhhhcce-eeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCC-HHHHHHHHHH
Q psy879          137 EKIIEPIQSRCAM-LRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGD-MRQALNNLQS  200 (317)
Q Consensus       137 ~~l~~~i~sR~~~-i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd-~r~~i~~l~~  200 (317)
                      ..++.++.+|+.. ++.+-|+..+..++|+-+++.+.++ ++-.+..++..+.|- -+.+.+.+..
T Consensus       242 ~DlDeAiiRR~p~rf~V~lP~~~qR~kILkviLk~e~~e-~~vD~~~iA~~t~GySGSDLkelC~~  306 (386)
T KOG0737|consen  242 FDLDEAIIRRLPRRFHVGLPDAEQRRKILKVILKKEKLE-DDVDLDEIAQMTEGYSGSDLKELCRL  306 (386)
T ss_pred             ccHHHHHHHhCcceeeeCCCchhhHHHHHHHHhcccccC-cccCHHHHHHhcCCCcHHHHHHHHHH
Confidence            9999999999766 9999999999999999999988765 344467788877663 3333344433

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=99.53  E-value=3.7e-13  Score=130.71  Aligned_cols=171  Identities=17%  Similarity=0.224  Sum_probs=118.5

Q ss_pred             CCCCcccCCHHHHHHHHHHHhc-----------C-C-CceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCC-
Q psy879            7 QTFSDIVGNEDTVERLKVFSSS-----------G-N-VPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASND-   72 (317)
Q Consensus         7 ~~~~~~~g~~~~~~~l~~~l~~-----------~-~-~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~-   72 (317)
                      -+|+++.|.+.+++.+..++..           | . +.+++||||||||||++++++++.+.     ..++.+++... 
T Consensus       175 ~~~~di~G~~~~~~~l~~~i~~~~~~~~~~~~~gi~~~~giLL~GppGtGKT~laraia~~~~-----~~~i~i~~~~i~  249 (733)
T TIGR01243       175 VTYEDIGGLKEAKEKIREMVELPMKHPELFEHLGIEPPKGVLLYGPPGTGKTLLAKAVANEAG-----AYFISINGPEIM  249 (733)
T ss_pred             CCHHHhcCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCceEEEECCCCCChHHHHHHHHHHhC-----CeEEEEecHHHh
Confidence            4699999999999988877632           1 1 22499999999999999999999862     23555554321 


Q ss_pred             ---c--ChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCH-----------HHHHHHHHHhhhcc--CCceEEEEec
Q psy879           73 ---R--GIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTD-----------GAQQALRRTMEIYS--NTTRFALACN  134 (317)
Q Consensus        73 ---~--~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~-----------~~~~~ll~~le~~~--~~~~~il~~~  134 (317)
                         .  ....++..+.....       ..+.+++|||+|.+..           ..++.|+..++...  ..+.+|.+||
T Consensus       250 ~~~~g~~~~~l~~lf~~a~~-------~~p~il~iDEid~l~~~r~~~~~~~~~~~~~~Ll~~ld~l~~~~~vivI~atn  322 (733)
T TIGR01243       250 SKYYGESEERLREIFKEAEE-------NAPSIIFIDEIDAIAPKREEVTGEVEKRVVAQLLTLMDGLKGRGRVIVIGATN  322 (733)
T ss_pred             cccccHHHHHHHHHHHHHHh-------cCCcEEEeehhhhhcccccCCcchHHHHHHHHHHHHhhccccCCCEEEEeecC
Confidence               1  11223333333221       3467999999998743           34677888887543  3455666899


Q ss_pred             CCCcCchhHhh--hcce-eeecCCCHHHHHHHHHHHHHHcCCCCC-HHHHHHHHHhcCCCH
Q psy879          135 NSEKIIEPIQS--RCAM-LRYNKLTDAQLLSKVIEICEKENISHT-NDGLEAIVFTAQGDM  191 (317)
Q Consensus       135 ~~~~l~~~i~s--R~~~-i~f~~~~~~~~~~~l~~~~~~~~~~i~-~~~~~~l~~~~~gd~  191 (317)
                      .++.+++++++  |+.. +.|+.|+.++...++.....  ++.+. +..++.+++.+.|-.
T Consensus       323 ~~~~ld~al~r~gRfd~~i~i~~P~~~~R~~Il~~~~~--~~~l~~d~~l~~la~~t~G~~  381 (733)
T TIGR01243       323 RPDALDPALRRPGRFDREIVIRVPDKRARKEILKVHTR--NMPLAEDVDLDKLAEVTHGFV  381 (733)
T ss_pred             ChhhcCHHHhCchhccEEEEeCCcCHHHHHHHHHHHhc--CCCCccccCHHHHHHhCCCCC
Confidence            99999999987  6654 99999999999999986554  33342 334677888777643

This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.

>KOG0736|consensus

Probab=99.52  E-value=2.4e-13  Score=125.42  Aligned_cols=166  Identities=17%  Similarity=0.189  Sum_probs=110.5

Q ss_pred             CCCcccCCHHHHHHHHHHHhc----------CCC--ceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCC----
Q psy879            8 TFSDIVGNEDTVERLKVFSSS----------GNV--PNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASN----   71 (317)
Q Consensus         8 ~~~~~~g~~~~~~~l~~~l~~----------~~~--~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~----   71 (317)
                      +|+|+=|-++++..+...++-          |-.  ..+|||||||||||.+|+++|.++     +..++.+.+..    
T Consensus       670 ~WdDVGGLeevK~eIldTIqlPL~hpeLfssglrkRSGILLYGPPGTGKTLlAKAVATEc-----sL~FlSVKGPELLNM  744 (953)
T KOG0736|consen  670 SWDDVGGLEEVKTEILDTIQLPLKHPELFSSGLRKRSGILLYGPPGTGKTLLAKAVATEC-----SLNFLSVKGPELLNM  744 (953)
T ss_pred             chhcccCHHHHHHHHHHHhcCcccChhhhhccccccceeEEECCCCCchHHHHHHHHhhc-----eeeEEeecCHHHHHH
Confidence            699999999999988776642          221  249999999999999999999985     34455554432    


Q ss_pred             --CcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHH-------------HHHHHHHHhhhcc----CCceEEEE
Q psy879           72 --DRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDG-------------AQQALRRTMEIYS----NTTRFALA  132 (317)
Q Consensus        72 --~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~-------------~~~~ll~~le~~~----~~~~~il~  132 (317)
                        ..+...+|+++.....       +.+.||++||+|.+.+.             ....|+-=|+..+    ..+.+|.+
T Consensus       745 YVGqSE~NVR~VFerAR~-------A~PCVIFFDELDSlAP~RG~sGDSGGVMDRVVSQLLAELDgls~~~s~~VFViGA  817 (953)
T KOG0736|consen  745 YVGQSEENVREVFERARS-------AAPCVIFFDELDSLAPNRGRSGDSGGVMDRVVSQLLAELDGLSDSSSQDVFVIGA  817 (953)
T ss_pred             HhcchHHHHHHHHHHhhc-------cCCeEEEeccccccCccCCCCCCccccHHHHHHHHHHHhhcccCCCCCceEEEec
Confidence              1233456666665432       57899999999999653             3445555555333    34557778


Q ss_pred             ecCCCcCchhHhhh--cce-eeecCCCHHHHHH-HHHHHHHHcCCCCCHHH-HHHHHHhc
Q psy879          133 CNNSEKIIEPIQSR--CAM-LRYNKLTDAQLLS-KVIEICEKENISHTNDG-LEAIVFTA  187 (317)
Q Consensus       133 ~~~~~~l~~~i~sR--~~~-i~f~~~~~~~~~~-~l~~~~~~~~~~i~~~~-~~~l~~~~  187 (317)
                      ||+|+-++|++.+-  |.. ++..+.+.++-+. +|+..-+  .+.+++++ +..+++.+
T Consensus       818 TNRPDLLDpALLRPGRFDKLvyvG~~~d~esk~~vL~AlTr--kFkLdedVdL~eiAk~c  875 (953)
T KOG0736|consen  818 TNRPDLLDPALLRPGRFDKLVYVGPNEDAESKLRVLEALTR--KFKLDEDVDLVEIAKKC  875 (953)
T ss_pred             CCCccccChhhcCCCccceeEEecCCccHHHHHHHHHHHHH--HccCCCCcCHHHHHhhC
Confidence            99999999999764  444 7777776655544 4444333  33444433 45556554

>TIGR02442 Cob-chelat-sub cobaltochelatase subunit

Probab=99.52  E-value=8.6e-13  Score=125.54  Aligned_cols=208  Identities=17%  Similarity=0.151  Sum_probs=132.5

Q ss_pred             CCcccCCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHc-----------CCCC-----------------
Q psy879            9 FSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILL-----------GPSF-----------------   60 (317)
Q Consensus         9 ~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~-----------~~~~-----------------   60 (317)
                      |.+++||++++..+...+-.+...+++|+|++|+|||++++++++.+-           |...                 
T Consensus         3 f~~ivGq~~~~~al~~~av~~~~g~vli~G~~GtgKs~lar~l~~~lp~~~~~~~~~~~c~p~~~~~~~~~~~~~~~~~~   82 (633)
T TIGR02442         3 FTAIVGQEDLKLALLLNAVDPRIGGVLIRGEKGTAKSTAARGLAALLPPIDVVAGCPFSCDPDDPEEWCEECRRKYRPSE   82 (633)
T ss_pred             cchhcChHHHHHHHHHHhhCCCCCeEEEEcCCCCcHHHHHHHHHHhCCCceeccCCcCCCCCCCccccChhhhhcccccc
Confidence            689999999999988887777777899999999999999999999871           1100                 


Q ss_pred             --CCceEEecCCCC----cChHHHHHHHH--HHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhc---------
Q psy879           61 --KDAVLELNASND----RGIDTVRNKIK--MFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIY---------  123 (317)
Q Consensus        61 --~~~~~~~~~~~~----~~~~~i~~~~~--~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~---------  123 (317)
                        ..+++.+.....    .+..++...+.  .....+..+..+...+++|||++.+.+..++.|+..|++.         
T Consensus        83 ~~~~pfv~~p~~~t~~~l~G~~d~~~~l~~g~~~~~~G~L~~A~~GiL~lDEi~~l~~~~q~~Ll~~le~g~~~v~r~g~  162 (633)
T TIGR02442        83 QRPVPFVNLPLGATEDRVVGSLDIERALREGEKAFQPGLLAEAHRGILYIDEVNLLDDHLVDVLLDAAAMGVNRVEREGL  162 (633)
T ss_pred             cCCCCeeeCCCCCcHHHcCCcccHHHHhhcCCeeecCcceeecCCCeEEeChhhhCCHHHHHHHHHHHhcCCEEEEECCc
Confidence              123333322210    11111221111  0011121222346789999999999999999999999853         


Q ss_pred             ----cCCceEEEEecCC-CcCchhHhhhcce-eeecCCCH-HHHHHHHHHHH----------------------------
Q psy879          124 ----SNTTRFALACNNS-EKIIEPIQSRCAM-LRYNKLTD-AQLLSKVIEIC----------------------------  168 (317)
Q Consensus       124 ----~~~~~~il~~~~~-~~l~~~i~sR~~~-i~f~~~~~-~~~~~~l~~~~----------------------------  168 (317)
                          +..+.+|.++|.. ..+.+++.+|+.. +...++.. ++..+++....                            
T Consensus       163 ~~~~~~~~~lIat~np~eg~l~~~L~dR~~l~i~v~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~ar  242 (633)
T TIGR02442       163 SVSHPARFVLIGTMNPEEGDLRPQLLDRFGLCVDVAAPRDPEERVEIIRRRLAFDADPEAFAARWAAEQEELRNRIARAR  242 (633)
T ss_pred             eeeecCCeEEEEecCCCCCCCCHHHHhhcceEEEccCCCchHHHHHHHHHHHhhccCcHHHHHHhhhhHHHHHHHHHHHH
Confidence                2345566666654 3678999999976 66665542 33333332210                            


Q ss_pred             -HHcCCCCCHHHHHHHHHhc---CC-CHHHHHHHHHHh---h--hCCCcccHHHHHhh
Q psy879          169 -EKENISHTNDGLEAIVFTA---QG-DMRQALNNLQST---H--NGFGHVTAEYVFKV  216 (317)
Q Consensus       169 -~~~~~~i~~~~~~~l~~~~---~g-d~r~~i~~l~~~---~--~~~~~i~~~~v~~~  216 (317)
                       ....+.++++.+++++..+   +- ++|..+..++.+   +  .+...++.+|+..+
T Consensus       243 ~~~~~V~is~~~~~~l~~~~~~~~i~s~Ra~i~~~r~Ara~AaL~gr~~V~~~Dv~~A  300 (633)
T TIGR02442       243 SLLPSVRISDSLIRFISELCIEFGVDGHRADIVMARAARALAALDGRRRVTAEDVREA  300 (633)
T ss_pred             HhCCCCCCCHHHHHHHHHHHHHhCCCCccHHHHHHHHHHHHHHHcCCCcCCHHHHHHH
Confidence             0124677888888777654   22 467777666543   2  26778999999664

A number of genomes (actinobacteria, cyanobacteria, betaproteobacteria and pseudomonads) which apparently biosynthesize B12, encode a cobN gene but are demonstrably lacking cobS and cobT. These genomes do, however contain a homolog (modelled here) of the magnesium chelatase subunits BchI/BchD family. Aside from the cyanobacteria (which have a separate magnesium chelatase trimer), these species do not make chlorins, so do not have any use for a magnesium chelatase. Furthermore, in nearly all cases the members of this family are proximal to either CobN itself or other genes involved in cobalt transport or B12 biosynthesis.

>KOG0726|consensus

Probab=99.51  E-value=1.3e-13  Score=113.92  Aligned_cols=153  Identities=21%  Similarity=0.307  Sum_probs=110.3

Q ss_pred             cccCCCCCCcccCCHHHHHHHHHHHhc-----------C-CCc-eEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEec
Q psy879            2 EKYRPQTFSDIVGNEDTVERLKVFSSS-----------G-NVP-NIIISGPPGVGKTTTILCLARILLGPSFKDAVLELN   68 (317)
Q Consensus         2 ~ky~P~~~~~~~g~~~~~~~l~~~l~~-----------~-~~~-~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~   68 (317)
                      ||-.-.++.|+-|-+..++.++..++-           | .+| .+++||+||||||.+|+++|+.-     +..|+.+-
T Consensus       177 eKaP~Ety~diGGle~QiQEiKEsvELPLthPE~YeemGikpPKGVIlyG~PGTGKTLLAKAVANqT-----SATFlRvv  251 (440)
T KOG0726|consen  177 EKAPQETYADIGGLESQIQEIKESVELPLTHPEYYEEMGIKPPKGVILYGEPGTGKTLLAKAVANQT-----SATFLRVV  251 (440)
T ss_pred             ccCchhhhcccccHHHHHHHHHHhhcCCCCCHHHHHHcCCCCCCeeEEeCCCCCchhHHHHHHhccc-----chhhhhhh
Confidence            444446799999999988888888652           2 233 39999999999999999999863     22233333


Q ss_pred             CCC------CcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCH-----------HHHHHHHHHhhhc-----cCC
Q psy879           69 ASN------DRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTD-----------GAQQALRRTMEIY-----SNT  126 (317)
Q Consensus        69 ~~~------~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~-----------~~~~~ll~~le~~-----~~~  126 (317)
                      .+.      ..+..-+|+.+......       .+.++||||+|....           +.|..++.+++..     .+.
T Consensus       252 GseLiQkylGdGpklvRqlF~vA~e~-------apSIvFiDEIdAiGtKRyds~SggerEiQrtmLELLNQldGFdsrgD  324 (440)
T KOG0726|consen  252 GSELIQKYLGDGPKLVRELFRVAEEH-------APSIVFIDEIDAIGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGD  324 (440)
T ss_pred             hHHHHHHHhccchHHHHHHHHHHHhc-------CCceEEeehhhhhccccccCCCccHHHHHHHHHHHHHhccCccccCC
Confidence            221      24555666666554433       578999999998742           3466777776633     457


Q ss_pred             ceEEEEecCCCcCchhHhhhcce---eeecCCCHHHHHHHHHH
Q psy879          127 TRFALACNNSEKIIEPIQSRCAM---LRYNKLTDAQLLSKVIE  166 (317)
Q Consensus       127 ~~~il~~~~~~~l~~~i~sR~~~---i~f~~~~~~~~~~~l~~  166 (317)
                      +.+|++||..+.++|++.+-..+   |.|+.|++..-.++..-
T Consensus       325 vKvimATnrie~LDPaLiRPGrIDrKIef~~pDe~TkkkIf~I  367 (440)
T KOG0726|consen  325 VKVIMATNRIETLDPALIRPGRIDRKIEFPLPDEKTKKKIFQI  367 (440)
T ss_pred             eEEEEecccccccCHhhcCCCccccccccCCCchhhhceeEEE
Confidence            88999999999999999876665   99999998877766543

>TIGR01650 PD_CobS cobaltochelatase, CobS subunit

Probab=99.51  E-value=2.3e-12  Score=110.85  Aligned_cols=176  Identities=16%  Similarity=0.138  Sum_probs=113.4

Q ss_pred             cCCCCCCcccCCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHH--
Q psy879            4 YRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNK--   81 (317)
Q Consensus         4 y~P~~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~--   81 (317)
                      |.|+.=.+++-.+...+.+...+..++  +++|.||||||||++++.+|+.+.     .+++.++........++-..  
T Consensus        39 ~~p~~d~~y~f~~~~~~~vl~~l~~~~--~ilL~G~pGtGKTtla~~lA~~l~-----~~~~rV~~~~~l~~~DliG~~~  111 (327)
T TIGR01650        39 HVPDIDPAYLFDKATTKAICAGFAYDR--RVMVQGYHGTGKSTHIEQIAARLN-----WPCVRVNLDSHVSRIDLVGKDA  111 (327)
T ss_pred             CCCCCCCCccCCHHHHHHHHHHHhcCC--cEEEEeCCCChHHHHHHHHHHHHC-----CCeEEEEecCCCChhhcCCCce
Confidence            445544556667777777777776665  799999999999999999999973     23444443322222111100  


Q ss_pred             --------HHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhh--------------ccCCceEEEEecCCC--
Q psy879           82 --------IKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEI--------------YSNTTRFALACNNSE--  137 (317)
Q Consensus        82 --------~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~--------------~~~~~~~il~~~~~~--  137 (317)
                              ...|...++......+.++++||+|...++.+++|..+||.              +++..++|.|+|...  
T Consensus       112 ~~l~~g~~~~~f~~GpL~~A~~~g~illlDEin~a~p~~~~~L~~lLE~~~~l~i~~~~~~i~~hp~FrviAT~Np~g~G  191 (327)
T TIGR01650       112 IVLKDGKQITEFRDGILPWALQHNVALCFDEYDAGRPDVMFVIQRVLEAGGKLTLLDQNRVIRAHPAFRLFATANTIGLG  191 (327)
T ss_pred             eeccCCcceeEEecCcchhHHhCCeEEEechhhccCHHHHHHHHHHhccCCeEEECCCceEecCCCCeEEEEeeCCCCcC
Confidence                    00111111111113456799999999999999999999882              234566788888642  


Q ss_pred             ----------cCchhHhhhcce-eeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHh
Q psy879          138 ----------KIIEPIQSRCAM-LRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFT  186 (317)
Q Consensus       138 ----------~l~~~i~sR~~~-i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~  186 (317)
                                .+.++..+|+.+ +.+..|+.++-.+++...+....-..++..++++++.
T Consensus       192 d~~G~y~Gt~~l~~A~lDRF~i~~~~~Yp~~e~E~~Il~~~~~~~~~~~~~~i~~~mV~l  251 (327)
T TIGR01650       192 DTTGLYHGTQQINQAQMDRWSIVTTLNYLEHDNEAAIVLAKAKGFDDTEGKDIINAMVRV  251 (327)
T ss_pred             CCCcceeeeecCCHHHHhheeeEeeCCCCCHHHHHHHHHhhccCCCccchHHHHHHHHHH
Confidence                      468999999986 6899999999999887764211100124455555543

This model describes the aerobic cobalamin pathway Pseudomonas denitrificans CobS gene product, which is a cobalt chelatase subunit, with a MW ~37 kDa. The aerobic pathway cobalt chelatase is a heterotrimeric, ATP-dependent enzyme that catalyzes cobalt insertion during cobalamin biosynthesis. The other two subunits are the P. denitrificans CobT (TIGR01651) and CobN (pfam02514 CobN/Magnesium Chelatase) proteins. To avoid potential confusion with the nonhomologous Salmonella typhimurium/E.coli cobS gene product, the P. denitrificans gene symbol is not used in the name of this model.

>KOG0740|consensus

Probab=99.50  E-value=3.8e-13  Score=118.74  Aligned_cols=175  Identities=19%  Similarity=0.189  Sum_probs=125.1

Q ss_pred             ccCCCCCCcccCCHHHHHHHHHHHh---------cC---CCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCC
Q psy879            3 KYRPQTFSDIVGNEDTVERLKVFSS---------SG---NVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNAS   70 (317)
Q Consensus         3 ky~P~~~~~~~g~~~~~~~l~~~l~---------~~---~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~   70 (317)
                      .-++-.|+++-|.+.+++.+..++-         .|   ....+|++||||+|||.+++++|.+.     ...++.+.++
T Consensus       146 ~~~~v~~~di~gl~~~k~~l~e~vi~p~lr~d~F~glr~p~rglLLfGPpgtGKtmL~~aiAsE~-----~atff~iSas  220 (428)
T KOG0740|consen  146 TLRNVGWDDIAGLEDAKQSLKEAVILPLLRPDLFLGLREPVRGLLLFGPPGTGKTMLAKAIATES-----GATFFNISAS  220 (428)
T ss_pred             cCCcccccCCcchhhHHHHhhhhhhhcccchHhhhccccccchhheecCCCCchHHHHHHHHhhh-----cceEeeccHH
Confidence            3456779999999998888776642         11   12249999999999999999999985     3346666654


Q ss_pred             CCc------ChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHH-----------H-HHHHHHHhh---hccCCceE
Q psy879           71 NDR------GIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDG-----------A-QQALRRTME---IYSNTTRF  129 (317)
Q Consensus        71 ~~~------~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~-----------~-~~~ll~~le---~~~~~~~~  129 (317)
                      +..      +..-++.++.....       ..+.|++|||+|.+..+           . ...|++..-   .+.+++.+
T Consensus       221 sLtsK~~Ge~eK~vralf~vAr~-------~qPsvifidEidslls~Rs~~e~e~srr~ktefLiq~~~~~s~~~drvlv  293 (428)
T KOG0740|consen  221 SLTSKYVGESEKLVRALFKVARS-------LQPSVIFIDEIDSLLSKRSDNEHESSRRLKTEFLLQFDGKNSAPDDRVLV  293 (428)
T ss_pred             HhhhhccChHHHHHHHHHHHHHh-------cCCeEEEechhHHHHhhcCCcccccchhhhhHHHhhhccccCCCCCeEEE
Confidence            321      12233333333221       36889999999987532           1 222333322   34457778


Q ss_pred             EEEecCCCcCchhHhhhcce-eeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCC
Q psy879          130 ALACNNSEKIIEPIQSRCAM-LRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQG  189 (317)
Q Consensus       130 il~~~~~~~l~~~i~sR~~~-i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~g  189 (317)
                      |.+||.+..++.+++.|++. +.++.|+.+....++.+.++..+..+.+..++.+++.+.|
T Consensus       294 igaTN~P~e~Dea~~Rrf~kr~yiplPd~etr~~~~~~ll~~~~~~l~~~d~~~l~~~Teg  354 (428)
T KOG0740|consen  294 IGATNRPWELDEAARRRFVKRLYIPLPDYETRSLLWKQLLKEQPNGLSDLDISLLAKVTEG  354 (428)
T ss_pred             EecCCCchHHHHHHHHHhhceeeecCCCHHHHHHHHHHHHHhCCCCccHHHHHHHHHHhcC
Confidence            88999999999999999987 7788889999999999988888777888888899887643

>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional

Probab=99.49  E-value=2e-12  Score=120.51  Aligned_cols=205  Identities=19%  Similarity=0.173  Sum_probs=137.4

Q ss_pred             CCCCCcccCCHHHHHHHHHHHhc--CCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHH-HH
Q psy879            6 PQTFSDIVGNEDTVERLKVFSSS--GNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRN-KI   82 (317)
Q Consensus         6 P~~~~~~~g~~~~~~~l~~~l~~--~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~-~~   82 (317)
                      ..+|++++|.....+.+...++.  ....+++|+|++||||+++|+++...-  .....+++.++|.... .+.+.. .+
T Consensus       200 ~~~f~~~ig~s~~~~~~~~~~~~~A~~~~pvlI~GE~GtGK~~lA~aiH~~s--~r~~~pfv~inca~~~-~~~~e~elF  276 (520)
T PRK10820        200 DSAFSQIVAVSPKMRQVVEQARKLAMLDAPLLITGDTGTGKDLLAYACHLRS--PRGKKPFLALNCASIP-DDVVESELF  276 (520)
T ss_pred             cccccceeECCHHHHHHHHHHHHHhCCCCCEEEECCCCccHHHHHHHHHHhC--CCCCCCeEEeccccCC-HHHHHHHhc
Confidence            34699999987765555444431  122359999999999999999987652  3334568888886532 222221 11


Q ss_pred             HHHH-------h-hcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhc-----------cCCceEEEEecCCC------
Q psy879           83 KMFA-------Q-QKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIY-----------SNTTRFALACNNSE------  137 (317)
Q Consensus        83 ~~~~-------~-~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~-----------~~~~~~il~~~~~~------  137 (317)
                      +...       . ....+..+....++|||++.|....|..|++++++.           +.++++|++|+..-      
T Consensus       277 G~~~~~~~~~~~~~~g~~e~a~~GtL~LdeI~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~vRiI~st~~~l~~l~~~  356 (520)
T PRK10820        277 GHAPGAYPNALEGKKGFFEQANGGSVLLDEIGEMSPRMQAKLLRFLNDGTFRRVGEDHEVHVDVRVICATQKNLVELVQK  356 (520)
T ss_pred             CCCCCCcCCcccCCCChhhhcCCCEEEEeChhhCCHHHHHHHHHHHhcCCcccCCCCcceeeeeEEEEecCCCHHHHHHc
Confidence            1110       0 000011245688999999999999999999999853           13457888776642      


Q ss_pred             -cCchhHhhhcce--eeecCCCH--HHHHHH----HHHHHHHcCC---CCCHHHHHHHHHh-cCCCHHHHHHHHHHhhh-
Q psy879          138 -KIIEPIQSRCAM--LRYNKLTD--AQLLSK----VIEICEKENI---SHTNDGLEAIVFT-AQGDMRQALNNLQSTHN-  203 (317)
Q Consensus       138 -~l~~~i~sR~~~--i~f~~~~~--~~~~~~----l~~~~~~~~~---~i~~~~~~~l~~~-~~gd~r~~i~~l~~~~~-  203 (317)
                       .+.+.+..|+..  +.+||+.+  +++..+    +...+.+.|.   .+++++++.+... ..||+|+..+.++.++. 
T Consensus       357 g~f~~dL~~rL~~~~i~lPpLreR~~Di~~L~~~fl~~~~~~~g~~~~~ls~~a~~~L~~y~WPGNvreL~nvl~~a~~~  436 (520)
T PRK10820        357 GEFREDLYYRLNVLTLNLPPLRDRPQDIMPLTELFVARFADEQGVPRPKLAADLNTVLTRYGWPGNVRQLKNAIYRALTQ  436 (520)
T ss_pred             CCccHHHHhhcCeeEEeCCCcccChhHHHHHHHHHHHHHHHHcCCCCCCcCHHHHHHHhcCCCCCHHHHHHHHHHHHHHh
Confidence             466778888655  77788765  344433    4444444443   6899999998877 89999999999987765 


Q ss_pred             -CCCcccHHHH
Q psy879          204 -GFGHVTAEYV  213 (317)
Q Consensus       204 -~~~~i~~~~v  213 (317)
                       ....|+.+++
T Consensus       437 ~~~~~i~~~~~  447 (520)
T PRK10820        437 LEGYELRPQDI  447 (520)
T ss_pred             CCCCcccHHHc
Confidence             4557877775

>TIGR02974 phageshock_pspF psp operon transcriptional activator PspF

Probab=99.49  E-value=1.9e-12  Score=113.63  Aligned_cols=198  Identities=14%  Similarity=0.169  Sum_probs=129.7

Q ss_pred             ccCCHHHHHHHHHHHhc--CCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHH-HHHH---
Q psy879           12 IVGNEDTVERLKVFSSS--GNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNK-IKMF---   85 (317)
Q Consensus        12 ~~g~~~~~~~l~~~l~~--~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~-~~~~---   85 (317)
                      ++|+....+.+...++.  ....+++|+|++||||+++|+++...-  .....+++.++|... ....+... ++..   
T Consensus         1 liG~S~~m~~~~~~~~~~a~~~~pVLI~GE~GtGK~~lAr~iH~~s--~r~~~pfv~vnc~~~-~~~~l~~~lfG~~~g~   77 (329)
T TIGR02974         1 LIGESNAFLEVLEQVSRLAPLDRPVLIIGERGTGKELIAARLHYLS--KRWQGPLVKLNCAAL-SENLLDSELFGHEAGA   77 (329)
T ss_pred             CCcCCHHHHHHHHHHHHHhCCCCCEEEECCCCChHHHHHHHHHHhc--CccCCCeEEEeCCCC-ChHHHHHHHhcccccc
Confidence            35665554444433321  122269999999999999999998752  334457888888642 22222221 1110   


Q ss_pred             -H----hhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhcc-----------CCceEEEEecCC-------CcCchh
Q psy879           86 -A----QQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYS-----------NTTRFALACNNS-------EKIIEP  142 (317)
Q Consensus        86 -~----~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~-----------~~~~~il~~~~~-------~~l~~~  142 (317)
                       .    .....+......+++|||++.|..+.|..|++++++..           .++++|++|+..       ..+.+.
T Consensus        78 ~~ga~~~~~G~~~~a~gGtL~Ldei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiI~at~~~l~~~~~~g~fr~d  157 (329)
T TIGR02974        78 FTGAQKRHQGRFERADGGTLFLDELATASLLVQEKLLRVIEYGEFERVGGSQTLQVDVRLVCATNADLPALAAEGRFRAD  157 (329)
T ss_pred             ccCcccccCCchhhCCCCEEEeCChHhCCHHHHHHHHHHHHcCcEEecCCCceeccceEEEEechhhHHHHhhcCchHHH
Confidence             0    00011223467899999999999999999999998532           456788888754       256688


Q ss_pred             Hhhhcce--eeecCCCH--HHHHHHHHHH----HHHcC----CCCCHHHHHHHHHhc-CCCHHHHHHHHHHhhhC--CCc
Q psy879          143 IQSRCAM--LRYNKLTD--AQLLSKVIEI----CEKEN----ISHTNDGLEAIVFTA-QGDMRQALNNLQSTHNG--FGH  207 (317)
Q Consensus       143 i~sR~~~--i~f~~~~~--~~~~~~l~~~----~~~~~----~~i~~~~~~~l~~~~-~gd~r~~i~~l~~~~~~--~~~  207 (317)
                      +..|+..  |.+||+.+  +++..++...    +.+.+    ..+++++++.+.... .||+|+..+.++.++..  ...
T Consensus       158 L~~rl~~~~i~lPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~~ls~~a~~~L~~y~WPGNvrEL~n~i~~~~~~~~~~~  237 (329)
T TIGR02974       158 LLDRLAFDVITLPPLRERQEDIMLLAEHFAIRMARELGLPLFPGFTPQAREQLLEYHWPGNVRELKNVVERSVYRHGLEE  237 (329)
T ss_pred             HHHHhcchhcCCCchhhhhhhHHHHHHHHHHHHHHHhCCCCCCCcCHHHHHHHHhCCCCchHHHHHHHHHHHHHhCCCCc
Confidence            8888854  88888873  5665554443    33333    358999999988774 99999999999876652  234


Q ss_pred             ccHHH
Q psy879          208 VTAEY  212 (317)
Q Consensus       208 i~~~~  212 (317)
                      ++.++
T Consensus       238 ~~~~~  242 (329)
T TIGR02974       238 APIDE  242 (329)
T ss_pred             cchhh
Confidence            55444

Members of this protein family are PspF, the sigma-54-dependent transcriptional activator of the phage shock protein (psp) operon, in Escherichia coli and numerous other species. The psp operon is induced by a number of stress conditions, including heat shock, ethanol, and filamentous phage infection. Changed com_name to adhere to TIGR role notes conventions. 09/15/06 - DMH

>COG0465 HflB ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones]

Probab=99.48  E-value=6.1e-13  Score=122.27  Aligned_cols=195  Identities=17%  Similarity=0.235  Sum_probs=132.3

Q ss_pred             CCCcccCCHHHHHHHHHHH---h--------cCCCce-EEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCC----
Q psy879            8 TFSDIVGNEDTVERLKVFS---S--------SGNVPN-IIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASN----   71 (317)
Q Consensus         8 ~~~~~~g~~~~~~~l~~~l---~--------~~~~~~-~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~----   71 (317)
                      +|.|+.|.+++++.+...+   +        .++.|. ++++||||||||.+|+++|.+.     +.+++.++.++    
T Consensus       148 ~F~DVAG~dEakeel~EiVdfLk~p~ky~~lGakiPkGvlLvGpPGTGKTLLAkAvAgEA-----~VPFf~iSGS~FVem  222 (596)
T COG0465         148 TFADVAGVDEAKEELSELVDFLKNPKKYQALGAKIPKGVLLVGPPGTGKTLLAKAVAGEA-----GVPFFSISGSDFVEM  222 (596)
T ss_pred             ChhhhcCcHHHHHHHHHHHHHHhCchhhHhcccccccceeEecCCCCCcHHHHHHHhccc-----CCCceeccchhhhhh
Confidence            5999999999988876654   3        234555 9999999999999999999884     45566666554    


Q ss_pred             --CcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHH--------------HHHHHHHHhhhccC--CceEEEEe
Q psy879           72 --DRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDG--------------AQQALRRTMEIYSN--TTRFALAC  133 (317)
Q Consensus        72 --~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~--------------~~~~ll~~le~~~~--~~~~il~~  133 (317)
                        ..+...+|+.+......       .+.+++|||+|...+.              ..|.|+--|+....  .++++.+|
T Consensus       223 fVGvGAsRVRdLF~qAkk~-------aP~IIFIDEiDAvGr~Rg~g~GggnderEQTLNQlLvEmDGF~~~~gviviaaT  295 (596)
T COG0465         223 FVGVGASRVRDLFEQAKKN-------APCIIFIDEIDAVGRQRGAGLGGGNDEREQTLNQLLVEMDGFGGNEGVIVIAAT  295 (596)
T ss_pred             hcCCCcHHHHHHHHHhhcc-------CCCeEEEehhhhcccccCCCCCCCchHHHHHHHHHHhhhccCCCCCceEEEecC
Confidence              24556677766654433       4689999999987532              35666666665553  44566678


Q ss_pred             cCCCcCchhHhhhcc---eeeecCCCHHHHHHHHHHHHHHcCCCCCHH-HHHHHHHh----cCCCHHHHHHHHHHhhh--
Q psy879          134 NNSEKIIEPIQSRCA---MLRYNKLTDAQLLSKVIEICEKENISHTND-GLEAIVFT----AQGDMRQALNNLQSTHN--  203 (317)
Q Consensus       134 ~~~~~l~~~i~sR~~---~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~-~~~~l~~~----~~gd~r~~i~~l~~~~~--  203 (317)
                      |+++-+++++.+=.+   .+..+.|+-....++++-.++..  .+++. .+..+++.    ++.|+...+|+..-.+.  
T Consensus       296 NRpdVlD~ALlRpgRFDRqI~V~~PDi~gRe~IlkvH~~~~--~l~~~Vdl~~iAr~tpGfsGAdL~nl~NEAal~aar~  373 (596)
T COG0465         296 NRPDVLDPALLRPGRFDRQILVELPDIKGREQILKVHAKNK--PLAEDVDLKKIARGTPGFSGADLANLLNEAALLAARR  373 (596)
T ss_pred             CCcccchHhhcCCCCcceeeecCCcchhhHHHHHHHHhhcC--CCCCcCCHHHHhhhCCCcccchHhhhHHHHHHHHHHh
Confidence            999999999965433   38888898888889988655543  33322 13345555    45577777766544333  


Q ss_pred             CCCcccHHHHHhh
Q psy879          204 GFGHVTAEYVFKV  216 (317)
Q Consensus       204 ~~~~i~~~~v~~~  216 (317)
                      ....|+..++.++
T Consensus       374 n~~~i~~~~i~ea  386 (596)
T COG0465         374 NKKEITMRDIEEA  386 (596)
T ss_pred             cCeeEeccchHHH
Confidence            4556666665543

>KOG2680|consensus

Probab=99.48  E-value=5.6e-12  Score=104.74  Aligned_cols=119  Identities=15%  Similarity=0.192  Sum_probs=97.6

Q ss_pred             eeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecC------------CCcCchhHhhhcceeeecCCCHHHHHHHH
Q psy879           97 HKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNN------------SEKIIEPIQSRCAMLRYNKLTDAQLLSKV  164 (317)
Q Consensus        97 ~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~------------~~~l~~~i~sR~~~i~f~~~~~~~~~~~l  164 (317)
                      +.|+||||++.|.-+....|.+.+|+--. .+++++||.            ++.++-.+..|..++.-.|++++++.++|
T Consensus       289 pGVLFIDEvHMLDIEcFsFlNrAlE~d~~-PiiimaTNrgit~iRGTn~~SphGiP~D~lDR~lII~t~py~~~d~~~IL  367 (454)
T KOG2680|consen  289 PGVLFIDEVHMLDIECFSFLNRALENDMA-PIIIMATNRGITRIRGTNYRSPHGIPIDLLDRMLIISTQPYTEEDIKKIL  367 (454)
T ss_pred             cceEEEeeehhhhhHHHHHHHHHhhhccC-cEEEEEcCCceEEeecCCCCCCCCCcHHHhhhhheeecccCcHHHHHHHH
Confidence            68999999999999999999999996322 345666664            34688999999999999999999999999


Q ss_pred             HHHHHHcCCCCCHHHHHHHHHh-cCCCHHHHHHHHHHhhh-----CCCcccHHHHHhh
Q psy879          165 IEICEKENISHTNDGLEAIVFT-AQGDMRQALNNLQSTHN-----GFGHVTAEYVFKV  216 (317)
Q Consensus       165 ~~~~~~~~~~i~~~~~~~l~~~-~~gd~r~~i~~l~~~~~-----~~~~i~~~~v~~~  216 (317)
                      .-+|..+++.+++++++.+... ...++|.+++++-.+..     ....+..++|..+
T Consensus       368 ~iRc~EEdv~m~~~A~d~Lt~i~~~tsLRYai~Lit~a~~~~~krk~~~v~~~di~r~  425 (454)
T KOG2680|consen  368 RIRCQEEDVEMNPDALDLLTKIGEATSLRYAIHLITAASLVCLKRKGKVVEVDDIERV  425 (454)
T ss_pred             HhhhhhhccccCHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHhcCceeehhHHHHH
Confidence            9999999999999999998866 45689999999865433     3456666766543

>PRK11331 5-methylcytosine-specific restriction enzyme subunit McrB; Provisional

Probab=99.45  E-value=6.1e-12  Score=112.30  Aligned_cols=151  Identities=21%  Similarity=0.279  Sum_probs=101.1

Q ss_pred             CCcccCCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCC--CCceEEecCC------------CCcC
Q psy879            9 FSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSF--KDAVLELNAS------------NDRG   74 (317)
Q Consensus         9 ~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~--~~~~~~~~~~------------~~~~   74 (317)
                      ++++++.++..+.+...+..++  +++|+||||||||++|+.++..+.+...  ....+.+...            ...+
T Consensus       174 l~d~~i~e~~le~l~~~L~~~~--~iil~GppGtGKT~lA~~la~~l~~~~~~~~v~~VtFHpsySYeDFI~G~rP~~vg  251 (459)
T PRK11331        174 LNDLFIPETTIETILKRLTIKK--NIILQGPPGVGKTFVARRLAYLLTGEKAPQRVNMVQFHQSYSYEDFIQGYRPNGVG  251 (459)
T ss_pred             hhcccCCHHHHHHHHHHHhcCC--CEEEECCCCCCHHHHHHHHHHHhcCCcccceeeEEeecccccHHHHhcccCCCCCC
Confidence            6778888999999888888776  8999999999999999999998754321  1112222211            0001


Q ss_pred             hH----HHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHH-HHHHHHHhhh----------------------ccCCc
Q psy879           75 ID----TVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGA-QQALRRTMEI----------------------YSNTT  127 (317)
Q Consensus        75 ~~----~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~-~~~ll~~le~----------------------~~~~~  127 (317)
                      ..    .+.+.+..+...+     ..+.++||||++....+. ...++.+||.                      .|.+.
T Consensus       252 y~~~~G~f~~~~~~A~~~p-----~~~~vliIDEINRani~kiFGel~~lLE~~~rg~~~~v~l~y~e~d~e~f~iP~Nl  326 (459)
T PRK11331        252 FRRKDGIFYNFCQQAKEQP-----EKKYVFIIDEINRANLSKVFGEVMMLMEHDKRGENWSVPLTYSENDEERFYVPENV  326 (459)
T ss_pred             eEecCchHHHHHHHHHhcc-----cCCcEEEEehhhccCHHHhhhhhhhhccccccccccceeeeccccccccccCCCCe
Confidence            00    1111122222221     457899999999998553 5566666651                      24667


Q ss_pred             eEEEEecCCC----cCchhHhhhcceeeecC-CCHHHHHHHHHH
Q psy879          128 RFALACNNSE----KIIEPIQSRCAMLRYNK-LTDAQLLSKVIE  166 (317)
Q Consensus       128 ~~il~~~~~~----~l~~~i~sR~~~i~f~~-~~~~~~~~~l~~  166 (317)
                      .+|.|+|..+    .++.++++|+..+++.| ++...+.+++..
T Consensus       327 ~IIgTMNt~Drs~~~lD~AlrRRF~fi~i~p~~~~~~~~~~l~~  370 (459)
T PRK11331        327 YIIGLMNTADRSLAVVDYALRRRFSFIDIEPGFDTPQFRNFLLN  370 (459)
T ss_pred             EEEEecCccccchhhccHHHHhhhheEEecCCCChHHHHHHHHh
Confidence            7888888776    58899999999999887 455667776654

>PF01637 Arch_ATPase: Archaeal ATPase; InterPro: IPR011579 This domain has been found in a number of bacterial and archaeal proteins, all of which contain a conserved P-loop motif that is involved in binding ATP

Probab=99.45  E-value=1.9e-12  Score=108.63  Aligned_cols=175  Identities=18%  Similarity=0.332  Sum_probs=106.8

Q ss_pred             ccCCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHH-----------
Q psy879           12 IVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRN-----------   80 (317)
Q Consensus        12 ~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~-----------   80 (317)
                      ++|+++.++.|..++.++...+++++||.|+|||++++.+.+.+.....  ..+.+..........+..           
T Consensus         1 F~gR~~el~~l~~~l~~~~~~~~~l~G~rg~GKTsLl~~~~~~~~~~~~--~~~y~~~~~~~~~~~~~~~~~~~~~~~~l   78 (234)
T PF01637_consen    1 FFGREKELEKLKELLESGPSQHILLYGPRGSGKTSLLKEFINELKEKGY--KVVYIDFLEESNESSLRSFIEETSLADEL   78 (234)
T ss_dssp             S-S-HHHHHHHHHCHHH--SSEEEEEESTTSSHHHHHHHHHHHCT--EE--CCCHHCCTTBSHHHHHHHHHHHHHHHCHC
T ss_pred             CCCHHHHHHHHHHHHHhhcCcEEEEEcCCcCCHHHHHHHHHHHhhhcCC--cEEEEecccchhhhHHHHHHHHHHHHHHH
Confidence            5799999999999999886668999999999999999999998733221  122222211111111111           


Q ss_pred             ------------------------------HHHHHHhhcccCCCCceeEEEEeCCCCCC------HHHHHHHHHHhhh--
Q psy879           81 ------------------------------KIKMFAQQKVTLPPGRHKIVILDEADSMT------DGAQQALRRTMEI--  122 (317)
Q Consensus        81 ------------------------------~~~~~~~~~~~~~~~~~~vliiDE~d~l~------~~~~~~ll~~le~--  122 (317)
                                                    .+..+...      +.+.+|+|||++.+.      ......|..+++.  
T Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~------~~~~iiviDe~~~~~~~~~~~~~~~~~l~~~~~~~~  152 (234)
T PF01637_consen   79 SEALGISIPSITLEKISKDLSEDSFSALERLLEKLKKK------GKKVIIVIDEFQYLAIASEEDKDFLKSLRSLLDSLL  152 (234)
T ss_dssp             HHHHHHHCCTSTTEEEECTS-GG-G--HHHHHHHHHHC------HCCEEEEEETGGGGGBCTTTTHHHHHHHHHHHHH--
T ss_pred             HHHHhhhcccccchhhhhcchhhHHHHHHHHHHHHHhc------CCcEEEEEecHHHHhhcccchHHHHHHHHHHHhhcc
Confidence                                          11111100      234899999999998      3456667777765  


Q ss_pred             ccCCceEEEEecCCC------cCchhHhhhcceeeecCCCHHHHHHHHHHHHHHcCCCC--CHHHHHHHHHhcCCCHHHH
Q psy879          123 YSNTTRFALACNNSE------KIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISH--TNDGLEAIVFTAQGDMRQA  194 (317)
Q Consensus       123 ~~~~~~~il~~~~~~------~l~~~i~sR~~~i~f~~~~~~~~~~~l~~~~~~~~~~i--~~~~~~~l~~~~~gd~r~~  194 (317)
                      ...+..+|+++....      .-..++..|+..+.+++++.++..+++...+... ..+  +++.++.+...++|.++..
T Consensus       153 ~~~~~~~v~~~S~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~e~~~~~~~~~~~~-~~~~~~~~~~~~i~~~~gG~P~~l  231 (234)
T PF01637_consen  153 SQQNVSIVITGSSDSLMEEFLDDKSPLFGRFSHIELKPLSKEEAREFLKELFKEL-IKLPFSDEDIEEIYSLTGGNPRYL  231 (234)
T ss_dssp             --TTEEEEEEESSHHHHHHTT-TTSTTTT---EEEE----HHHHHHHHHHHHHCC-------HHHHHHHHHHHTT-HHHH
T ss_pred             ccCCceEEEECCchHHHHHhhcccCccccccceEEEeeCCHHHHHHHHHHHHHHh-hcccCCHHHHHHHHHHhCCCHHHH
Confidence            234555666655421      2345577888889999999999999999987765 544  8999999999999999865


Q ss_pred             H
Q psy879          195 L  195 (317)
Q Consensus       195 i  195 (317)
                      .
T Consensus       232 ~  232 (234)
T PF01637_consen  232 Q  232 (234)
T ss_dssp             H
T ss_pred             h
Confidence            4

; GO: 0005524 ATP binding; PDB: 2FNA_A 2QEN_A.

>TIGR02329 propionate_PrpR propionate catabolism operon regulatory protein PrpR

Probab=99.44  E-value=7.1e-12  Score=116.01  Aligned_cols=206  Identities=14%  Similarity=0.198  Sum_probs=137.4

Q ss_pred             CCCCcccCCHHHHHHHHHHHhc--CCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHH-HH
Q psy879            7 QTFSDIVGNEDTVERLKVFSSS--GNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNK-IK   83 (317)
Q Consensus         7 ~~~~~~~g~~~~~~~l~~~l~~--~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~-~~   83 (317)
                      -+|++++|+....+.+...++.  ....+++|+|++||||+++|+++...  ......+++.+||.... ...+... ++
T Consensus       209 ~~f~~iiG~S~~m~~~~~~i~~~A~~~~pVLI~GE~GTGKe~lA~~IH~~--S~r~~~pfv~inC~~l~-e~lleseLFG  285 (526)
T TIGR02329       209 YRLDDLLGASAPMEQVRALVRLYARSDATVLILGESGTGKELVAQAIHQL--SGRRDFPFVAINCGAIA-ESLLEAELFG  285 (526)
T ss_pred             cchhheeeCCHHHHHHHHHHHHHhCCCCcEEEECCCCcCHHHHHHHHHHh--cCcCCCCEEEeccccCC-hhHHHHHhcC
Confidence            3588999998877776666542  22336999999999999999999875  23345678888886532 2222221 11


Q ss_pred             H----HH-----hhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhcc-----------CCceEEEEecCCC------
Q psy879           84 M----FA-----QQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYS-----------NTTRFALACNNSE------  137 (317)
Q Consensus        84 ~----~~-----~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~-----------~~~~~il~~~~~~------  137 (317)
                      .    |.     .....+.......++|||++.|....|..|++++++..           .++++|++|+..-      
T Consensus       286 ~~~gaftga~~~~~~Gl~e~A~gGTLfLdeI~~Lp~~~Q~~Ll~~L~~~~~~r~g~~~~~~~dvRiIaat~~~l~~~v~~  365 (526)
T TIGR02329       286 YEEGAFTGARRGGRTGLIEAAHRGTLFLDEIGEMPLPLQTRLLRVLEEREVVRVGGTEPVPVDVRVVAATHCALTTAVQQ  365 (526)
T ss_pred             CcccccccccccccccchhhcCCceEEecChHhCCHHHHHHHHHHHhcCcEEecCCCceeeecceEEeccCCCHHHHhhh
Confidence            0    00     00001112457899999999999999999999998532           2447888887652      


Q ss_pred             -cCchhHhhhcce--eeecCCCH--HHHHHHHHH----HHHHcCCCCCHHHHHH-------HHHh-cCCCHHHHHHHHHH
Q psy879          138 -KIIEPIQSRCAM--LRYNKLTD--AQLLSKVIE----ICEKENISHTNDGLEA-------IVFT-AQGDMRQALNNLQS  200 (317)
Q Consensus       138 -~l~~~i~sR~~~--i~f~~~~~--~~~~~~l~~----~~~~~~~~i~~~~~~~-------l~~~-~~gd~r~~i~~l~~  200 (317)
                       .+.+.+-.|+..  +.+||+.+  +++..+...    .+...++.++++++..       +... ..||+|+..+.++.
T Consensus       366 g~fr~dL~~rL~~~~I~lPPLReR~eDI~~L~~~fl~~~~~~~~~~~~~~a~~~~~~~~~~L~~y~WPGNvrEL~nvier  445 (526)
T TIGR02329       366 GRFRRDLFYRLSILRIALPPLRERPGDILPLAAEYLVQAAAALRLPDSEAAAQVLAGVADPLQRYPWPGNVRELRNLVER  445 (526)
T ss_pred             cchhHHHHHhcCCcEEeCCCchhchhHHHHHHHHHHHHHHHHcCCCCCHHHHHHhHHHHHHHHhCCCCchHHHHHHHHHH
Confidence             345566666654  77888865  455544433    3334466788888776       5544 68999999999998


Q ss_pred             hhh-----CCCcccHHHHHh
Q psy879          201 THN-----GFGHVTAEYVFK  215 (317)
Q Consensus       201 ~~~-----~~~~i~~~~v~~  215 (317)
                      ++.     ....|+.+++..
T Consensus       446 ~~i~~~~~~~~~I~~~~l~~  465 (526)
T TIGR02329       446 LALELSAMPAGALTPDVLRA  465 (526)
T ss_pred             HHHhcccCCCCccCHHHhhh
Confidence            664     235678777643

At least five distinct pathways exists for the catabolism of propionate by way of propionyl-CoA. Members of this family represent the transcriptional regulatory protein PrpR, whose gene is found in most cases divergently transcribed from an operon for the methylcitric acid cycle of propionate catabolism. 2-methylcitric acid, a catabolite by this pathway, is a coactivator of PrpR.

>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional

Probab=99.44  E-value=1e-11  Score=109.06  Aligned_cols=193  Identities=16%  Similarity=0.200  Sum_probs=129.9

Q ss_pred             CCCcccCCHHHHHHHHHHHhc--CCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHHH-HH
Q psy879            8 TFSDIVGNEDTVERLKVFSSS--GNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKI-KM   84 (317)
Q Consensus         8 ~~~~~~g~~~~~~~l~~~l~~--~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~-~~   84 (317)
                      .+++++|.....+.+...++.  ....+++|+|++||||+++|+++...  ......+++.++|... ....+...+ +.
T Consensus         4 ~~~~liG~S~~~~~~~~~i~~~a~~~~pVlI~GE~GtGK~~lA~~iH~~--s~r~~~pfv~v~c~~~-~~~~~~~~lfg~   80 (326)
T PRK11608          4 YKDNLLGEANSFLEVLEQVSRLAPLDKPVLIIGERGTGKELIASRLHYL--SSRWQGPFISLNCAAL-NENLLDSELFGH   80 (326)
T ss_pred             ccCccEECCHHHHHHHHHHHHHhCCCCCEEEECCCCCcHHHHHHHHHHh--CCccCCCeEEEeCCCC-CHHHHHHHHccc
Confidence            578899987766665554432  12226999999999999999999864  3333457888888653 222222211 11


Q ss_pred             HH--------hhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhcc-----------CCceEEEEecCC-------Cc
Q psy879           85 FA--------QQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYS-----------NTTRFALACNNS-------EK  138 (317)
Q Consensus        85 ~~--------~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~-----------~~~~~il~~~~~-------~~  138 (317)
                      ..        .....+......+++|||++.|....|..|++++++..           .++++|++++..       ..
T Consensus        81 ~~~~~~g~~~~~~g~l~~a~gGtL~l~~i~~L~~~~Q~~L~~~l~~~~~~~~g~~~~~~~~~RiI~~s~~~l~~l~~~g~  160 (326)
T PRK11608         81 EAGAFTGAQKRHPGRFERADGGTLFLDELATAPMLVQEKLLRVIEYGELERVGGSQPLQVNVRLVCATNADLPAMVAEGK  160 (326)
T ss_pred             cccccCCcccccCCchhccCCCeEEeCChhhCCHHHHHHHHHHHhcCcEEeCCCCceeeccEEEEEeCchhHHHHHHcCC
Confidence            00        00111123567899999999999999999999998532           246788887754       35


Q ss_pred             CchhHhhhcce--eeecCCCH--HHHHHHHHH----HHHHcC----CCCCHHHHHHHHHh-cCCCHHHHHHHHHHhhh
Q psy879          139 IIEPIQSRCAM--LRYNKLTD--AQLLSKVIE----ICEKEN----ISHTNDGLEAIVFT-AQGDMRQALNNLQSTHN  203 (317)
Q Consensus       139 l~~~i~sR~~~--i~f~~~~~--~~~~~~l~~----~~~~~~----~~i~~~~~~~l~~~-~~gd~r~~i~~l~~~~~  203 (317)
                      +.+.+..|+..  |.+||+.+  +++..++..    .+.+.+    ..++++++..+... ..||+|+..+.++.++.
T Consensus       161 f~~dL~~~l~~~~i~lPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~~~s~~al~~L~~y~WPGNvrEL~~vl~~a~~  238 (326)
T PRK11608        161 FRADLLDRLAFDVVQLPPLRERQSDIMLMAEHFAIQMCRELGLPLFPGFTERARETLLNYRWPGNIRELKNVVERSVY  238 (326)
T ss_pred             chHHHHHhcCCCEEECCChhhhhhhHHHHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHhCCCCcHHHHHHHHHHHHHH
Confidence            66888888854  77888865  345444433    344433    25789999888766 68999999999998665

>TIGR00764 lon_rel lon-related putative ATP-dependent protease

Probab=99.44  E-value=7.3e-12  Score=118.13  Aligned_cols=124  Identities=23%  Similarity=0.184  Sum_probs=86.7

Q ss_pred             ceeEEEEeCCCCCCHHHHHHHHHHhhhc---------------------cCCceEEEEecCC--CcCchhHhhhcc---e
Q psy879           96 RHKIVILDEADSMTDGAQQALRRTMEIY---------------------SNTTRFALACNNS--EKIIEPIQSRCA---M  149 (317)
Q Consensus        96 ~~~vliiDE~d~l~~~~~~~ll~~le~~---------------------~~~~~~il~~~~~--~~l~~~i~sR~~---~  149 (317)
                      ...+++|||++.|.+..|..|++.|++.                     |.++++|+++|..  ..+.+++++|+.   +
T Consensus       217 ngGtL~Ldei~~L~~~~q~~Ll~~L~~~~i~~~g~~e~~~~~~~~~~~ip~dvrvIa~~~~~~l~~l~~~l~~rf~~y~v  296 (608)
T TIGR00764       217 HKGVLYIDEIKTMPLEVQQYLLTALQDKKFPITGQSENSSGAMVRTEPVPCDFILVASGNLDDLEGMHPALRSRIRGYGY  296 (608)
T ss_pred             CCCEEEEEChHhCCHHHHHHHHHHHHhCcEEecCccccccccccCCCCCccceEEEEECCHHHHhhcCHHHHHHhcCCeE
Confidence            4689999999999999999999999742                     1245678888764  578999999998   4


Q ss_pred             -eeecC---CCHHH---HHHHHHHHHHHcC--CCCCHHHHHHHHHhc----------CCCHHHHHHHHHHhh-----hCC
Q psy879          150 -LRYNK---LTDAQ---LLSKVIEICEKEN--ISHTNDGLEAIVFTA----------QGDMRQALNNLQSTH-----NGF  205 (317)
Q Consensus       150 -i~f~~---~~~~~---~~~~l~~~~~~~~--~~i~~~~~~~l~~~~----------~gd~r~~i~~l~~~~-----~~~  205 (317)
                       +.|+.   .+.+.   +..++.+.+++.|  -.+++++++.+.+.+          ..+.|+.-++++.+.     .+.
T Consensus       297 ~v~~~~~~~~~~e~~~~~~~~i~~~~~r~G~l~~~s~~Av~~Li~~~~R~ag~r~~lsl~~R~L~~llR~A~~iA~~~~~  376 (608)
T TIGR00764       297 EVYMKDTMPDTPENRDKLVQFVAQEVKKDGRIPHFTRDAVEEIVREAQRRAGRKDHLTLRLRELGGLVRAAGDIAKSSGK  376 (608)
T ss_pred             EEEeeccCCCCHHHHHHHHHHHHHHHHHhCCCCcCCHHHHHHHHHHHHHHHhcccccCCCHHHHHHHHHHHHHHHHhcCC
Confidence             45543   23433   3455666666653  357899988887432          235788877776642     144


Q ss_pred             CcccHHHHHhhcCC
Q psy879          206 GHVTAEYVFKVCDE  219 (317)
Q Consensus       206 ~~i~~~~v~~~~~~  219 (317)
                      ..|+.+||.+++..
T Consensus       377 ~~I~~ehV~~Ai~~  390 (608)
T TIGR00764       377 VYVTAEHVLKAKKL  390 (608)
T ss_pred             ceecHHHHHHHHHH
Confidence            57899998876543

Members of this family from Pyrococcus horikoshii and Pyrococcus abyssi each contain a predicted intein.

>PF01078 Mg_chelatase: Magnesium chelatase, subunit ChlI; InterPro: IPR000523 Magnesium-chelatase is a three-component enzyme that catalyses the insertion of Mg2+ into protoporphyrin IX

Probab=99.44  E-value=2.2e-13  Score=109.30  Aligned_cols=125  Identities=26%  Similarity=0.378  Sum_probs=76.3

Q ss_pred             CCCcccCCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCC---C------------
Q psy879            8 TFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASN---D------------   72 (317)
Q Consensus         8 ~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~---~------------   72 (317)
                      .|.+++||+.+++.+.-+..++.  |++++||||+|||++|+.+...|-. -......+.....   .            
T Consensus         1 Df~dI~GQe~aKrAL~iAAaG~h--~lLl~GppGtGKTmlA~~l~~lLP~-l~~~e~le~~~i~s~~~~~~~~~~~~~~P   77 (206)
T PF01078_consen    1 DFSDIVGQEEAKRALEIAAAGGH--HLLLIGPPGTGKTMLARRLPSLLPP-LTEEEALEVSKIYSVAGLGPDEGLIRQRP   77 (206)
T ss_dssp             -TCCSSSTHHHHHHHHHHHHCC----EEEES-CCCTHHHHHHHHHHCS---CCEECCESS--S-TT---S---EEEE---
T ss_pred             ChhhhcCcHHHHHHHHHHHcCCC--CeEEECCCCCCHHHHHHHHHHhCCC-CchHHHhhhccccccccCCCCCceecCCC
Confidence            48899999999999999888765  7999999999999999999986521 1111111111000   0            


Q ss_pred             -cC---hHHHHHHHHHHH-hhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhh-------------ccCCceEEEEec
Q psy879           73 -RG---IDTVRNKIKMFA-QQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEI-------------YSNTTRFALACN  134 (317)
Q Consensus        73 -~~---~~~i~~~~~~~~-~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~-------------~~~~~~~il~~~  134 (317)
                       +.   .......++... ..+.....+.+.|+++||+..+.+...++|+..||+             +|.+..+|.++|
T Consensus        78 fr~phhs~s~~~liGgg~~~~PGeislAh~GVLflDE~~ef~~~vld~Lr~ple~g~v~i~R~~~~~~~Pa~f~lv~a~N  157 (206)
T PF01078_consen   78 FRAPHHSASEAALIGGGRPPRPGEISLAHRGVLFLDELNEFDRSVLDALRQPLEDGEVTISRAGGSVTYPARFLLVAAMN  157 (206)
T ss_dssp             EEEE-TT--HHHHHEEGGGEEE-CGGGGTTSEEEECETTTS-HHHHHHHHHHHHHSBEEEEETTEEEEEB--EEEEEEE-
T ss_pred             cccCCCCcCHHHHhCCCcCCCcCHHHHhcCCEEEechhhhcCHHHHHHHHHHHHCCeEEEEECCceEEEecccEEEEEec
Confidence             00   001111222111 122223335789999999999999999999999984             355667788777


Q ss_pred             C
Q psy879          135 N  135 (317)
Q Consensus       135 ~  135 (317)
                      .
T Consensus       158 P  158 (206)
T PF01078_consen  158 P  158 (206)
T ss_dssp             S
T ss_pred             c
Confidence            5

This is the first unique step in the synthesis of (bacterio)chlorophyll. As a result, it is thought that Mg-chelatase has an important role in channeling intermediates into the (bacterio)chlorophyll branch in response to conditions suitable for photosynthetic growth. ChlI and BchD have molecular weights between 38-42 kDa.; GO: 0016851 magnesium chelatase activity, 0015979 photosynthesis, 0015995 chlorophyll biosynthetic process; PDB: 2X31_J 1G8P_A 3K1J_B.

>KOG0729|consensus

Probab=99.44  E-value=1.5e-12  Score=106.44  Aligned_cols=167  Identities=19%  Similarity=0.297  Sum_probs=113.0

Q ss_pred             CCCcccCCHHHHHHHHHHHhc-----------C-CCce-EEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCC---
Q psy879            8 TFSDIVGNEDTVERLKVFSSS-----------G-NVPN-IIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASN---   71 (317)
Q Consensus         8 ~~~~~~g~~~~~~~l~~~l~~-----------~-~~~~-~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~---   71 (317)
                      ++.|+-|-.+.++.++..++.           | .+|. +++|||||+|||.+|+++|+.-     ...++.+-.+.   
T Consensus       175 ty~dvggckeqieklrevve~pll~perfv~lgidppkgvllygppgtgktl~aravanrt-----dacfirvigselvq  249 (435)
T KOG0729|consen  175 TYSDVGGCKEQIEKLREVVELPLLHPERFVNLGIDPPKGVLLYGPPGTGKTLCARAVANRT-----DACFIRVIGSELVQ  249 (435)
T ss_pred             ccccccchHHHHHHHHHHHhccccCHHHHhhcCCCCCCceEEeCCCCCchhHHHHHHhccc-----CceEEeehhHHHHH
Confidence            577888878888887776542           2 2333 9999999999999999999863     23344443332   


Q ss_pred             ---CcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCC-----------HHHHHHHHHHhh-----hccCCceEEEE
Q psy879           72 ---DRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMT-----------DGAQQALRRTME-----IYSNTTRFALA  132 (317)
Q Consensus        72 ---~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~-----------~~~~~~ll~~le-----~~~~~~~~il~  132 (317)
                         ..+..-+++.+.....       .+..++++||+|.+.           .+.|...+.++.     .|.+++.+.++
T Consensus       250 kyvgegarmvrelf~mart-------kkaciiffdeidaiggarfddg~ggdnevqrtmleli~qldgfdprgnikvlma  322 (435)
T KOG0729|consen  250 KYVGEGARMVRELFEMART-------KKACIIFFDEIDAIGGARFDDGAGGDNEVQRTMLELINQLDGFDPRGNIKVLMA  322 (435)
T ss_pred             HHhhhhHHHHHHHHHHhcc-------cceEEEEeeccccccCccccCCCCCcHHHHHHHHHHHHhccCCCCCCCeEEEee
Confidence               1222334444443321       356799999999773           235777777766     45678999999


Q ss_pred             ecCCCcCchhHhhhcce---eeecCCCHHHHHHHHHHHHHHcCCCCCHHH-HHHHHHhcC
Q psy879          133 CNNSEKIIEPIQSRCAM---LRYNKLTDAQLLSKVIEICEKENISHTNDG-LEAIVFTAQ  188 (317)
Q Consensus       133 ~~~~~~l~~~i~sR~~~---i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~-~~~l~~~~~  188 (317)
                      ||.++.++|++.+-...   ++|..|+-+-...+++-.++.  +.++.+. .+.++..|.
T Consensus       323 tnrpdtldpallrpgrldrkvef~lpdlegrt~i~kihaks--msverdir~ellarlcp  380 (435)
T KOG0729|consen  323 TNRPDTLDPALLRPGRLDRKVEFGLPDLEGRTHIFKIHAKS--MSVERDIRFELLARLCP  380 (435)
T ss_pred             cCCCCCcCHhhcCCcccccceeccCCcccccceeEEEeccc--cccccchhHHHHHhhCC
Confidence            99999999999876655   999999887777666655543  3344443 455565553

>COG2204 AtoC Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]

Probab=99.43  E-value=3.9e-11  Score=107.70  Aligned_cols=204  Identities=16%  Similarity=0.206  Sum_probs=141.9

Q ss_pred             CCCcccCCHHHHHHHHHHHhc--CCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHHHHHH
Q psy879            8 TFSDIVGNEDTVERLKVFSSS--GNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMF   85 (317)
Q Consensus         8 ~~~~~~g~~~~~~~l~~~l~~--~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~   85 (317)
                      ...+++|+....+.+...+.+  ....+++|+|++||||..+|+++.+.  ....+.+|+.+||.. ...+-+...+..-
T Consensus       139 ~~~~liG~S~am~~l~~~i~kvA~s~a~VLI~GESGtGKElvAr~IH~~--S~R~~~PFVavNcaA-ip~~l~ESELFGh  215 (464)
T COG2204         139 LGGELVGESPAMQQLRRLIAKVAPSDASVLITGESGTGKELVARAIHQA--SPRAKGPFIAVNCAA-IPENLLESELFGH  215 (464)
T ss_pred             ccCCceecCHHHHHHHHHHHHHhCCCCCEEEECCCCCcHHHHHHHHHhh--CcccCCCceeeeccc-CCHHHHHHHhhcc
Confidence            578999998888877776653  22235999999999999999999986  455567899999864 3333333222111


Q ss_pred             Hhhcc---------cCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhc-----------cCCceEEEEecCC-------Cc
Q psy879           86 AQQKV---------TLPPGRHKIVILDEADSMTDGAQQALRRTMEIY-----------SNTTRFALACNNS-------EK  138 (317)
Q Consensus        86 ~~~~~---------~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~-----------~~~~~~il~~~~~-------~~  138 (317)
                      ...++         .+-.+....+++||+..|.-+.|..|++.+++.           +-++++|.+||..       .+
T Consensus       216 ekGAFTGA~~~r~G~fE~A~GGTLfLDEI~~mpl~~Q~kLLRvLqe~~~~rvG~~~~i~vdvRiIaaT~~dL~~~v~~G~  295 (464)
T COG2204         216 EKGAFTGAITRRIGRFEQANGGTLFLDEIGEMPLELQVKLLRVLQEREFERVGGNKPIKVDVRIIAATNRDLEEEVAAGR  295 (464)
T ss_pred             cccCcCCcccccCcceeEcCCceEEeeccccCCHHHHHHHHHHHHcCeeEecCCCcccceeeEEEeecCcCHHHHHHcCC
Confidence            11111         112256889999999999999999999999843           2356789988875       25


Q ss_pred             CchhHhhhcce--eeecCCCH--HHHH----HHHHHHHHHcC---CCCCHHHHHHHHHh-cCCCHHHHHHHHHHhhh--C
Q psy879          139 IIEPIQSRCAM--LRYNKLTD--AQLL----SKVIEICEKEN---ISHTNDGLEAIVFT-AQGDMRQALNNLQSTHN--G  204 (317)
Q Consensus       139 l~~~i~sR~~~--i~f~~~~~--~~~~----~~l~~~~~~~~---~~i~~~~~~~l~~~-~~gd~r~~i~~l~~~~~--~  204 (317)
                      +-+.+--|..+  ++.||+-+  +++-    .++.+.++..|   ..+++++++.+..+ ..||+|+..|.++.++.  .
T Consensus       296 FReDLyyRLnV~~i~iPpLRER~EDIp~L~~hfl~~~~~~~~~~~~~~s~~a~~~L~~y~WPGNVREL~N~ver~~il~~  375 (464)
T COG2204         296 FREDLYYRLNVVPLRLPPLRERKEDIPLLAEHFLKRFAAELGRPPKGFSPEALAALLAYDWPGNVRELENVVERAVILSE  375 (464)
T ss_pred             cHHHHHhhhccceecCCcccccchhHHHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHhCCCChHHHHHHHHHHHHHhcCC
Confidence            77888888888  55555543  3333    23444444443   46789998887765 79999999999998665  4


Q ss_pred             CCcccHHHHH
Q psy879          205 FGHVTAEYVF  214 (317)
Q Consensus       205 ~~~i~~~~v~  214 (317)
                      ...|+.+++.
T Consensus       376 ~~~i~~~~l~  385 (464)
T COG2204         376 GPEIEVEDLP  385 (464)
T ss_pred             ccccchhhcc
Confidence            4567766643

>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional

Probab=99.42  E-value=8.7e-12  Score=119.68  Aligned_cols=205  Identities=11%  Similarity=0.112  Sum_probs=135.5

Q ss_pred             CCCcccCCHHHHHHHHHHHhc--CCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHH-HHHHH
Q psy879            8 TFSDIVGNEDTVERLKVFSSS--GNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVR-NKIKM   84 (317)
Q Consensus         8 ~~~~~~g~~~~~~~l~~~l~~--~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~-~~~~~   84 (317)
                      +|++++|.....+.+...++.  ....+++|+|++||||+++|+++.+..  .....+++.+||.... .+.+. +.++.
T Consensus       323 ~~~~l~g~s~~~~~~~~~~~~~a~~~~pvli~Ge~GtGK~~~A~~ih~~s--~r~~~pfv~vnc~~~~-~~~~~~elfg~  399 (638)
T PRK11388        323 TFDHMPQDSPQMRRLIHFGRQAAKSSFPVLLCGEEGVGKALLAQAIHNES--ERAAGPYIAVNCQLYP-DEALAEEFLGS  399 (638)
T ss_pred             cccceEECCHHHHHHHHHHHHHhCcCCCEEEECCCCcCHHHHHHHHHHhC--CccCCCeEEEECCCCC-hHHHHHHhcCC
Confidence            699999987766655444332  122259999999999999999999863  2234568888886432 22222 22221


Q ss_pred             HHhh-----cccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhcc-----------CCceEEEEecCC-------CcCch
Q psy879           85 FAQQ-----KVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYS-----------NTTRFALACNNS-------EKIIE  141 (317)
Q Consensus        85 ~~~~-----~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~-----------~~~~~il~~~~~-------~~l~~  141 (317)
                      ....     ...+..+...+++|||++.|....|..|++++++..           -++++|++|+..       ..+.+
T Consensus       400 ~~~~~~~~~~g~~~~a~~GtL~ldei~~l~~~~Q~~Ll~~l~~~~~~~~~~~~~~~~~~riI~~t~~~l~~~~~~~~f~~  479 (638)
T PRK11388        400 DRTDSENGRLSKFELAHGGTLFLEKVEYLSPELQSALLQVLKTGVITRLDSRRLIPVDVRVIATTTADLAMLVEQNRFSR  479 (638)
T ss_pred             CCcCccCCCCCceeECCCCEEEEcChhhCCHHHHHHHHHHHhcCcEEeCCCCceEEeeEEEEEeccCCHHHHHhcCCChH
Confidence            1000     001112457899999999999999999999998532           146688887764       24555


Q ss_pred             hHhhhcce--eeecCCCHH--HHHHHHHHHHH----Hc--CCCCCHHHHHHHHHhc-CCCHHHHHHHHHHhhh--CCCcc
Q psy879          142 PIQSRCAM--LRYNKLTDA--QLLSKVIEICE----KE--NISHTNDGLEAIVFTA-QGDMRQALNNLQSTHN--GFGHV  208 (317)
Q Consensus       142 ~i~sR~~~--i~f~~~~~~--~~~~~l~~~~~----~~--~~~i~~~~~~~l~~~~-~gd~r~~i~~l~~~~~--~~~~i  208 (317)
                      .+--|+..  |.+||+.+.  ++...+...+.    ..  .+.+++++++.+.... .||+|++.+.++.++.  ....|
T Consensus       480 dL~~~l~~~~i~lPpLreR~~Di~~L~~~~l~~~~~~~~~~~~~s~~a~~~L~~y~WPGNvreL~~~l~~~~~~~~~~~i  559 (638)
T PRK11388        480 QLYYALHAFEITIPPLRMRREDIPALVNNKLRSLEKRFSTRLKIDDDALARLVSYRWPGNDFELRSVIENLALSSDNGRI  559 (638)
T ss_pred             HHhhhhceeEEeCCChhhhhhHHHHHHHHHHHHHHHHhCCCCCcCHHHHHHHHcCCCCChHHHHHHHHHHHHHhCCCCee
Confidence            66666655  677777653  45444444332    22  2468999999998875 8999999999998654  34467


Q ss_pred             cHHHHHh
Q psy879          209 TAEYVFK  215 (317)
Q Consensus       209 ~~~~v~~  215 (317)
                      +.+++..
T Consensus       560 ~~~~lp~  566 (638)
T PRK11388        560 RLSDLPE  566 (638)
T ss_pred             cHHHCch
Confidence            7776643

>COG0714 MoxR-like ATPases [General function prediction only]

Probab=99.42  E-value=6.7e-12  Score=110.79  Aligned_cols=149  Identities=21%  Similarity=0.236  Sum_probs=100.8

Q ss_pred             cccCCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHHHHHHHh---
Q psy879           11 DIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFAQ---   87 (317)
Q Consensus        11 ~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~---   87 (317)
                      .++|+++++..+..++..|.  |++|.||||+|||++++.+|+.+.     ..++.+.+.......++.........   
T Consensus        25 ~~~g~~~~~~~~l~a~~~~~--~vll~G~PG~gKT~la~~lA~~l~-----~~~~~i~~t~~l~p~d~~G~~~~~~~~~~   97 (329)
T COG0714          25 VVVGDEEVIELALLALLAGG--HVLLEGPPGVGKTLLARALARALG-----LPFVRIQCTPDLLPSDLLGTYAYAALLLE   97 (329)
T ss_pred             eeeccHHHHHHHHHHHHcCC--CEEEECCCCccHHHHHHHHHHHhC-----CCeEEEecCCCCCHHHhcCchhHhhhhcc
Confidence            37889999888888888887  899999999999999999999973     44666666654444433222111111   


Q ss_pred             ---hccc---CCCCceeEEEEeCCCCCCHHHHHHHHHHhhhc------------cCCceEEEEecC-----CCcCchhHh
Q psy879           88 ---QKVT---LPPGRHKIVILDEADSMTDGAQQALRRTMEIY------------SNTTRFALACNN-----SEKIIEPIQ  144 (317)
Q Consensus        88 ---~~~~---~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~------------~~~~~~il~~~~-----~~~l~~~i~  144 (317)
                         ....   ...+...++++||+++..++.+++|+..|++.            +....+|.++|+     ...+++++.
T Consensus        98 ~~~~~~~~gpl~~~~~~ill~DEInra~p~~q~aLl~~l~e~~vtv~~~~~~~~~~~f~viaT~Np~e~~g~~~l~eA~l  177 (329)
T COG0714          98 PGEFRFVPGPLFAAVRVILLLDEINRAPPEVQNALLEALEERQVTVPGLTTIRLPPPFIVIATQNPGEYEGTYPLPEALL  177 (329)
T ss_pred             CCeEEEecCCcccccceEEEEeccccCCHHHHHHHHHHHhCcEEEECCcCCcCCCCCCEEEEccCccccCCCcCCCHHHH
Confidence               0000   00111149999999999999999999999962            122334444462     346899999


Q ss_pred             hhc-ceeeecCCCHHHHHHHHHH
Q psy879          145 SRC-AMLRYNKLTDAQLLSKVIE  166 (317)
Q Consensus       145 sR~-~~i~f~~~~~~~~~~~l~~  166 (317)
                      .|| ..+.+..|..++...++..
T Consensus       178 dRf~~~~~v~yp~~~~e~~~i~~  200 (329)
T COG0714         178 DRFLLRIYVDYPDSEEEERIILA  200 (329)
T ss_pred             hhEEEEEecCCCCchHHHHHHHH
Confidence            999 5588887745444444433

>TIGR00390 hslU ATP-dependent protease HslVU, ATPase subunit

Probab=99.41  E-value=4.4e-12  Score=111.91  Aligned_cols=108  Identities=19%  Similarity=0.275  Sum_probs=78.8

Q ss_pred             ceeEEEEeCCCCCCHH------------HHHHHHHHhhhc----------cCCceEEEEec----CCCcCchhHhhhcce
Q psy879           96 RHKIVILDEADSMTDG------------AQQALRRTMEIY----------SNTTRFALACN----NSEKIIEPIQSRCAM  149 (317)
Q Consensus        96 ~~~vliiDE~d~l~~~------------~~~~ll~~le~~----------~~~~~~il~~~----~~~~l~~~i~sR~~~  149 (317)
                      ...+|+|||+|++...            .|.+||+++|..          ..++.||++..    .+..+.|.+..|+.+
T Consensus       247 ~~GIVfiDEiDKIa~~~~~~~~DvS~eGVQ~~LLkilEGt~v~~k~~~v~T~~ILFI~~GAF~~~kp~DlIPEl~GR~Pi  326 (441)
T TIGR00390       247 QSGIIFIDEIDKIAKKGESSGADVSREGVQRDLLPIVEGSTVNTKYGMVKTDHILFIAAGAFQLAKPSDLIPELQGRFPI  326 (441)
T ss_pred             cCCEEEEEchhhhcccCCCCCCCCCccchhccccccccCceeeecceeEECCceeEEecCCcCCCChhhccHHHhCccce
Confidence            5689999999998632            589999999942          13444555432    355789999999998


Q ss_pred             -eeecCCCHHHHHHHHHH-----------HHHHcCC--CCCHHHHHHHHHhc--------CCCHHHHHHHHHHhhh
Q psy879          150 -LRYNKLTDAQLLSKVIE-----------ICEKENI--SHTNDGLEAIVFTA--------QGDMRQALNNLQSTHN  203 (317)
Q Consensus       150 -i~f~~~~~~~~~~~l~~-----------~~~~~~~--~i~~~~~~~l~~~~--------~gd~r~~i~~l~~~~~  203 (317)
                       +.+.+++.+++.++|.+           .++.+|+  .++++++..+++.+        +-..|.+...++....
T Consensus       327 ~v~L~~L~~edL~rILteP~nsLikQy~~Lf~~egv~L~Ftd~Al~~IA~~A~~~N~~~~~iGAR~LrtilE~~l~  402 (441)
T TIGR00390       327 RVELQALTTDDFERILTEPKNSLIKQYKALMKTEGVNIEFSDEAIKRIAELAYNVNEKTENIGARRLHTVLERLLE  402 (441)
T ss_pred             EEECCCCCHHHHHHHhcCChhHHHHHHHHHHhhcCcEEEEeHHHHHHHHHHHHHhcccccccchhhHHHHHHHHHH
Confidence             99999999999999832           2344564  45889998888664        4457777777766543

This model represents the ATPase subunit of HslVU, while the proteasome-related peptidase subunit is HslV. Residues 54-61 of the model contain a P-loop ATP-binding motif. Cys-287 of E. coli (position 308 in the seed alignment), studied in PubMed:98389714, is Ser in other members of the seed alignment.

>PRK15424 propionate catabolism operon regulatory protein PrpR; Provisional

Probab=99.41  E-value=1.5e-11  Score=113.88  Aligned_cols=205  Identities=15%  Similarity=0.187  Sum_probs=133.1

Q ss_pred             CCCcccCCHHHHHHHHHHHhc--CCCceEEEECCCCCCHHHHHHHHHHHHc------CCCCCCceEEecCCCCcChHHHH
Q psy879            8 TFSDIVGNEDTVERLKVFSSS--GNVPNIIISGPPGVGKTTTILCLARILL------GPSFKDAVLELNASNDRGIDTVR   79 (317)
Q Consensus         8 ~~~~~~g~~~~~~~l~~~l~~--~~~~~~ll~G~~G~GKt~la~~la~~l~------~~~~~~~~~~~~~~~~~~~~~i~   79 (317)
                      +|++++|+....+.+...++.  ....+++|+|++||||+++|+++...+.      ....+.+++.+||.... ...+.
T Consensus       217 ~f~~iiG~S~~m~~~~~~i~~~A~s~~pVLI~GE~GTGKe~~A~~IH~~~~~~~~~~S~r~~~pfv~inCaal~-e~lle  295 (538)
T PRK15424        217 VLGDLLGQSPQMEQVRQTILLYARSSAAVLIQGETGTGKELAAQAIHREYFARHDARQGKKSHPFVAVNCGAIA-ESLLE  295 (538)
T ss_pred             chhheeeCCHHHHHHHHHHHHHhCCCCcEEEECCCCCCHHHHHHHHHHhhcccccccCccCCCCeEEeecccCC-hhhHH
Confidence            588999998877776666542  2233699999999999999999998621      12245678889887532 22222


Q ss_pred             HH-HHH----HHh-----hcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhc-----------cCCceEEEEecCCC-
Q psy879           80 NK-IKM----FAQ-----QKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIY-----------SNTTRFALACNNSE-  137 (317)
Q Consensus        80 ~~-~~~----~~~-----~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~-----------~~~~~~il~~~~~~-  137 (317)
                      .. ++.    |..     .+..+..+....++|||++.|....|..|++++++.           +.++++|++|+..- 
T Consensus       296 seLFG~~~gaftga~~~~~~Gl~e~A~gGTLfLdeI~~Lp~~~Q~kLl~~L~e~~~~r~G~~~~~~~dvRiIaat~~~L~  375 (538)
T PRK15424        296 AELFGYEEGAFTGSRRGGRAGLFEIAHGGTLFLDEIGEMPLPLQTRLLRVLEEKEVTRVGGHQPVPVDVRVISATHCDLE  375 (538)
T ss_pred             HHhcCCccccccCccccccCCchhccCCCEEEEcChHhCCHHHHHHHHhhhhcCeEEecCCCceeccceEEEEecCCCHH
Confidence            21 110    000     001112245789999999999999999999999853           23457888887652 


Q ss_pred             ------cCchhHhhhcce--eeecCCCH--HHHHHHHHHHHH----HcCCCCCHHHHH-------HHHH-hcCCCHHHHH
Q psy879          138 ------KIIEPIQSRCAM--LRYNKLTD--AQLLSKVIEICE----KENISHTNDGLE-------AIVF-TAQGDMRQAL  195 (317)
Q Consensus       138 ------~l~~~i~sR~~~--i~f~~~~~--~~~~~~l~~~~~----~~~~~i~~~~~~-------~l~~-~~~gd~r~~i  195 (317)
                            .+.+.+--|+..  +++||+.+  +++..++...+.    ..+..++++++.       .+.. ...||+|+.-
T Consensus       376 ~~v~~g~Fr~dL~yrL~~~~I~lPPLReR~eDI~~L~~~fl~~~~~~~~~~~~~~a~~~~~~a~~~L~~y~WPGNvREL~  455 (538)
T PRK15424        376 EDVRQGRFRRDLFYRLSILRLQLPPLRERVADILPLAESFLKQSLAALSAPFSAALRQGLQQCETLLLHYDWPGNVRELR  455 (538)
T ss_pred             HHHhcccchHHHHHHhcCCeecCCChhhchhHHHHHHHHHHHHHHHHcCCCCCHHHHHhhHHHHHHHHhCCCCchHHHHH
Confidence                  345566667655  77777765  455555544443    356677777663       3332 2689999999


Q ss_pred             HHHHHhhh--C---CCcccHHHH
Q psy879          196 NNLQSTHN--G---FGHVTAEYV  213 (317)
Q Consensus       196 ~~l~~~~~--~---~~~i~~~~v  213 (317)
                      |.++.++.  .   ...++.+++
T Consensus       456 nvier~~i~~~~~~~~~i~~~~l  478 (538)
T PRK15424        456 NLMERLALFLSVEPTPDLTPQFL  478 (538)
T ss_pred             HHHHHHHHhcCCCCcCccCHHHh
Confidence            99997654  1   134555544

>KOG0735|consensus

Probab=99.41  E-value=8.4e-12  Score=114.49  Aligned_cols=169  Identities=17%  Similarity=0.188  Sum_probs=118.9

Q ss_pred             CCCcccCCHHHHHHHHHHHhcC------------CC-ceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCC---
Q psy879            8 TFSDIVGNEDTVERLKVFSSSG------------NV-PNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASN---   71 (317)
Q Consensus         8 ~~~~~~g~~~~~~~l~~~l~~~------------~~-~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~---   71 (317)
                      .|+|+-|-.++++.+...+.-.            +. ..+|+|||||||||.+|.+++..     ++..++.+.+..   
T Consensus       665 ~w~digg~~~~k~~l~~~i~~P~kyp~if~~~plr~~~giLLyGppGcGKT~la~a~a~~-----~~~~fisvKGPElL~  739 (952)
T KOG0735|consen  665 RWEDIGGLFEAKKVLEEVIEWPSKYPQIFANCPLRLRTGILLYGPPGCGKTLLASAIASN-----SNLRFISVKGPELLS  739 (952)
T ss_pred             CceecccHHHHHHHHHHHHhccccchHHHhhCCcccccceEEECCCCCcHHHHHHHHHhh-----CCeeEEEecCHHHHH
Confidence            4889989888888887776421            11 24999999999999999999987     344556554422   


Q ss_pred             ---CcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCH-----------HHHHHHHHHhhhc--cCCceEEEEecC
Q psy879           72 ---DRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTD-----------GAQQALRRTMEIY--SNTTRFALACNN  135 (317)
Q Consensus        72 ---~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~-----------~~~~~ll~~le~~--~~~~~~il~~~~  135 (317)
                         ..+...+|+.+....       ..++.|+++||+|.+.+           ...|.|+.-|+.-  -..+.++.+|.+
T Consensus       740 KyIGaSEq~vR~lF~rA~-------~a~PCiLFFDEfdSiAPkRGhDsTGVTDRVVNQlLTelDG~Egl~GV~i~aaTsR  812 (952)
T KOG0735|consen  740 KYIGASEQNVRDLFERAQ-------SAKPCILFFDEFDSIAPKRGHDSTGVTDRVVNQLLTELDGAEGLDGVYILAATSR  812 (952)
T ss_pred             HHhcccHHHHHHHHHHhh-------ccCCeEEEeccccccCcccCCCCCCchHHHHHHHHHhhccccccceEEEEEecCC
Confidence               122344555554432       15789999999998754           4678888888733  234556667888


Q ss_pred             CCcCchhHhhhcce---eeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCC
Q psy879          136 SEKIIEPIQSRCAM---LRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQG  189 (317)
Q Consensus       136 ~~~l~~~i~sR~~~---i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~g  189 (317)
                      ++-++|++.+-+..   +.++.|++.+..++++.......+. ++-.++.++..+.|
T Consensus       813 pdliDpALLRpGRlD~~v~C~~P~~~eRl~il~~ls~s~~~~-~~vdl~~~a~~T~g  868 (952)
T KOG0735|consen  813 PDLIDPALLRPGRLDKLVYCPLPDEPERLEILQVLSNSLLKD-TDVDLECLAQKTDG  868 (952)
T ss_pred             ccccCHhhcCCCccceeeeCCCCCcHHHHHHHHHHhhccCCc-cccchHHHhhhcCC
Confidence            99999999876655   9999999999999998877543321 23335667766544

>TIGR00368 Mg chelatase-related protein

Probab=99.40  E-value=1.8e-11  Score=112.57  Aligned_cols=150  Identities=21%  Similarity=0.277  Sum_probs=100.4

Q ss_pred             CCCcccCCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCc-Ch-----------
Q psy879            8 TFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDR-GI-----------   75 (317)
Q Consensus         8 ~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~-~~-----------   75 (317)
                      .|++++||..+++.+...+..|.  |++|.||||+|||++++.+...+.. ......++....... +.           
T Consensus       190 d~~dv~Gq~~~~~al~~aa~~g~--~vlliG~pGsGKTtlar~l~~llp~-~~~~~~le~~~i~s~~g~~~~~~~~~~~P  266 (499)
T TIGR00368       190 DLKDIKGQQHAKRALEIAAAGGH--NLLLFGPPGSGKTMLASRLQGILPP-LTNEEAIETARIWSLVGKLIDRKQIKQRP  266 (499)
T ss_pred             CHHHhcCcHHHHhhhhhhccCCC--EEEEEecCCCCHHHHHHHHhcccCC-CCCcEEEeccccccchhhhccccccccCC
Confidence            68999999999999998887776  8999999999999999999986532 222222222211000 00           


Q ss_pred             -------HHHHHHHHHH-HhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhc-------------cCCceEEEEec
Q psy879           76 -------DTVRNKIKMF-AQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIY-------------SNTTRFALACN  134 (317)
Q Consensus        76 -------~~i~~~~~~~-~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~-------------~~~~~~il~~~  134 (317)
                             ......++.. ...+..+..+.+.+++|||++.+.+..++.|++.||..             +.++.+|.++|
T Consensus       267 f~~p~~s~s~~~~~ggg~~~~pG~i~lA~~GvLfLDEi~e~~~~~~~~L~~~LE~~~v~i~r~g~~~~~pa~frlIaa~N  346 (499)
T TIGR00368       267 FRSPHHSASKPALVGGGPIPLPGEISLAHNGVLFLDELPEFKRSVLDALREPIEDGSISISRASAKIFYPARFQLVAAMN  346 (499)
T ss_pred             ccccccccchhhhhCCccccchhhhhccCCCeEecCChhhCCHHHHHHHHHHHHcCcEEEEecCcceeccCCeEEEEecC
Confidence                   0000001100 00111122346789999999999999999999999853             34677888887


Q ss_pred             CC------C-----------------cCchhHhhhcce-eeecCCCHHHH
Q psy879          135 NS------E-----------------KIIEPIQSRCAM-LRYNKLTDAQL  160 (317)
Q Consensus       135 ~~------~-----------------~l~~~i~sR~~~-i~f~~~~~~~~  160 (317)
                      +-      .                 ++..++.+|+.. +.+++++.+++
T Consensus       347 pcpcg~~~~~~~~c~c~~~~~~~y~~~is~pllDR~dl~~~~~~~~~~~l  396 (499)
T TIGR00368       347 PCPCGHYGGKNTHCRCSPQQISRYWNKLSGPFLDRIDLSVEVPLLPPEKL  396 (499)
T ss_pred             CcccCcCCCCcccccCCHHHHHHHhhhccHhHHhhCCEEEEEcCCCHHHH
Confidence            52      1                 578999999988 77777755443

The N-terminal end matches very strongly a pfam Mg_chelatase domain.

>PHA02244 ATPase-like protein

Probab=99.39  E-value=3e-12  Score=111.30  Aligned_cols=129  Identities=16%  Similarity=0.122  Sum_probs=88.1

Q ss_pred             HHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHH---HHHHHHhhcccCCCCc
Q psy879           20 ERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRN---KIKMFAQQKVTLPPGR   96 (317)
Q Consensus        20 ~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~---~~~~~~~~~~~~~~~~   96 (317)
                      ..+..++..+.  +++|+||+|||||++|++++..+.     .+++.++....  ...+..   .-+.+...++......
T Consensus       110 ~ri~r~l~~~~--PVLL~GppGtGKTtLA~aLA~~lg-----~pfv~In~l~d--~~~L~G~i~~~g~~~dgpLl~A~~~  180 (383)
T PHA02244        110 ADIAKIVNANI--PVFLKGGAGSGKNHIAEQIAEALD-----LDFYFMNAIMD--EFELKGFIDANGKFHETPFYEAFKK  180 (383)
T ss_pred             HHHHHHHhcCC--CEEEECCCCCCHHHHHHHHHHHhC-----CCEEEEecChH--HHhhcccccccccccchHHHHHhhc
Confidence            34666777766  699999999999999999999863     23555543210  000000   0000000010001145


Q ss_pred             eeEEEEeCCCCCCHHHHHHHHHHhhh-----------ccCCceEEEEecCC-----------CcCchhHhhhcceeeecC
Q psy879           97 HKIVILDEADSMTDGAQQALRRTMEI-----------YSNTTRFALACNNS-----------EKIIEPIQSRCAMLRYNK  154 (317)
Q Consensus        97 ~~vliiDE~d~l~~~~~~~ll~~le~-----------~~~~~~~il~~~~~-----------~~l~~~i~sR~~~i~f~~  154 (317)
                      ..+++|||++.+.++.+..|...+++           .+++.++|+++|..           ..+.+++++||..++|..
T Consensus       181 GgvLiLDEId~a~p~vq~~L~~lLd~r~l~l~g~~i~~h~~FRlIATsN~~~~G~~~~y~G~k~L~~AllDRFv~I~~dy  260 (383)
T PHA02244        181 GGLFFIDEIDASIPEALIIINSAIANKFFDFADERVTAHEDFRVISAGNTLGKGADHIYVARNKIDGATLDRFAPIEFDY  260 (383)
T ss_pred             CCEEEEeCcCcCCHHHHHHHHHHhccCeEEecCcEEecCCCEEEEEeeCCCccCcccccCCCcccCHHHHhhcEEeeCCC
Confidence            68999999999999999999999862           24678899999973           467899999999999998


Q ss_pred             CCH
Q psy879          155 LTD  157 (317)
Q Consensus       155 ~~~  157 (317)
                      +++
T Consensus       261 p~~  263 (383)
T PHA02244        261 DEK  263 (383)
T ss_pred             CcH
Confidence            874

>PRK13765 ATP-dependent protease Lon; Provisional

Probab=99.38  E-value=4.3e-11  Score=112.65  Aligned_cols=211  Identities=18%  Similarity=0.251  Sum_probs=134.6

Q ss_pred             CCCCCCcccCCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcC----------
Q psy879            5 RPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRG----------   74 (317)
Q Consensus         5 ~P~~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~----------   74 (317)
                      .|+.|++++||+++++.|..++.++.  +++|+||||+|||++++++++.+.+......++.-|+.....          
T Consensus        26 ~~~~~~~vigq~~a~~~L~~~~~~~~--~~l~~G~~G~GKttla~~l~~~l~~~~~~~~~~~~np~~~~~~~~~~v~~~~  103 (637)
T PRK13765         26 PERLIDQVIGQEHAVEVIKKAAKQRR--HVMMIGSPGTGKSMLAKAMAELLPKEELQDILVYPNPEDPNNPKIRTVPAGK  103 (637)
T ss_pred             CcccHHHcCChHHHHHHHHHHHHhCC--eEEEECCCCCcHHHHHHHHHHHcChHhHHHheEeeCCCcchHHHHHHHHHhc
Confidence            57889999999999999999998886  899999999999999999999875432111111111110000          


Q ss_pred             ---h----------------------------------------------------------------------------
Q psy879           75 ---I----------------------------------------------------------------------------   75 (317)
Q Consensus        75 ---~----------------------------------------------------------------------------   75 (317)
                         +                                                                            
T Consensus       104 G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nllv~ns~~~~aP  183 (637)
T PRK13765        104 GKQIVEAHKEEARKRNQMRNMLMMIIIAGIIGYAFIYAGQILWGIIAAGLIYMALRYFRPKEDAMVPKLLVNNADKKTAP  183 (637)
T ss_pred             CHHHHHHHHHHhhhhccccchhHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHhhCCcCceEEEEEEEeCCCCCCCC
Confidence               0                                                                            


Q ss_pred             ------HHHHHHHHHHHhh----------------cccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhcc---------
Q psy879           76 ------DTVRNKIKMFAQQ----------------KVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYS---------  124 (317)
Q Consensus        76 ------~~i~~~~~~~~~~----------------~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~---------  124 (317)
                            ....+.++.....                +..+..+...+++|||++.|.+..|..|++.|++..         
T Consensus       184 vi~~~~p~~~~LfG~i~~~~~~~Gg~~t~~~~~i~~G~L~kAnGGtL~LDei~~L~~~~q~~Llr~L~~~~i~i~g~~e~  263 (637)
T PRK13765        184 FVDATGAHAGALLGDVRHDPFQSGGLETPAHDRVEAGAIHKAHKGVLFIDEINTLDLESQQSLLTAMQEKKFPITGQSER  263 (637)
T ss_pred             EEEeCCCCHHHcCCccccccccccccccCccccCCCCceeECCCcEEEEeChHhCCHHHHHHHHHHHHhCCEEecccccc
Confidence                  0000111110000                000011346899999999999999999999996321         


Q ss_pred             ------------CCceEEEEecCC--CcCchhHhhhcc---e-eeecCC---CHHHHHHHHHHHHH---Hc--CCCCCHH
Q psy879          125 ------------NTTRFALACNNS--EKIIEPIQSRCA---M-LRYNKL---TDAQLLSKVIEICE---KE--NISHTND  178 (317)
Q Consensus       125 ------------~~~~~il~~~~~--~~l~~~i~sR~~---~-i~f~~~---~~~~~~~~l~~~~~---~~--~~~i~~~  178 (317)
                                  .++++|++++..  ..+.+.+.+|+.   + +.|+.-   +++....++...++   ++  -..++++
T Consensus       264 ~~~~~~~~~~ip~dvrvI~a~~~~ll~~~dpdL~~rfk~~~v~v~f~~~~~d~~e~~~~~~~~iaqe~~~~G~l~~f~~e  343 (637)
T PRK13765        264 SSGAMVRTEPVPCDFIMVAAGNLDALENMHPALRSRIKGYGYEVYMRDTMEDTPENRRKLVRFVAQEVKRDGKIPHFDRD  343 (637)
T ss_pred             cccccCCCcceeeeeEEEEecCcCHHHhhhHHHHHHhccCeEEEEcccccCCCHHHHHHHHHHHHHHhhhccCCCCCCHH
Confidence                        245688888875  467899999986   2 666643   34555555554443   22  2368999


Q ss_pred             HHHHHHHhc---CCC-------HHHHHHHHHHhhh-----CCCcccHHHHHhhc
Q psy879          179 GLEAIVFTA---QGD-------MRQALNNLQSTHN-----GFGHVTAEYVFKVC  217 (317)
Q Consensus       179 ~~~~l~~~~---~gd-------~r~~i~~l~~~~~-----~~~~i~~~~v~~~~  217 (317)
                      ++..+++.+   .|+       .|++.++++.+..     +.+.++.++|.++.
T Consensus       344 AVa~LI~~~~R~ag~r~~lsl~~~~l~~l~r~a~~~a~~~~~~~i~~~~v~~a~  397 (637)
T PRK13765        344 AVEEIIREAKRRAGRKGHLTLKLRDLGGLVRVAGDIARSEGAELTTAEHVLEAK  397 (637)
T ss_pred             HHHHHHHHHHHHhCCccccccCHHHHHHHHHHHHHHHHhhccceecHHHHHHHH
Confidence            988887643   233       5666666655432     34567888887655

>PRK05201 hslU ATP-dependent protease ATP-binding subunit HslU; Provisional

Probab=99.37  E-value=1.1e-11  Score=109.41  Aligned_cols=108  Identities=19%  Similarity=0.300  Sum_probs=78.7

Q ss_pred             ceeEEEEeCCCCCCHH------------HHHHHHHHhhhc----------cCCceEEEEec----CCCcCchhHhhhcce
Q psy879           96 RHKIVILDEADSMTDG------------AQQALRRTMEIY----------SNTTRFALACN----NSEKIIEPIQSRCAM  149 (317)
Q Consensus        96 ~~~vliiDE~d~l~~~------------~~~~ll~~le~~----------~~~~~~il~~~----~~~~l~~~i~sR~~~  149 (317)
                      ...||+|||+|++...            .|.+||+++|..          ..++.||++..    .+..+.|.+..|+.+
T Consensus       249 ~~GIVfiDEiDKIa~~~~~~~~DvS~eGVQ~~LLki~EG~~v~~k~~~i~T~~ILFI~~GAF~~~kp~DlIPEl~GR~Pi  328 (443)
T PRK05201        249 QNGIVFIDEIDKIAARGGSSGPDVSREGVQRDLLPLVEGSTVSTKYGMVKTDHILFIASGAFHVSKPSDLIPELQGRFPI  328 (443)
T ss_pred             cCCEEEEEcchhhcccCCCCCCCCCccchhcccccccccceeeecceeEECCceeEEecCCcCCCChhhccHHHhCccce
Confidence            5689999999998532            589999999942          13444555432    345789999999998


Q ss_pred             -eeecCCCHHHHHHHHHH----H-------HHHcCC--CCCHHHHHHHHHhc--------CCCHHHHHHHHHHhhh
Q psy879          150 -LRYNKLTDAQLLSKVIE----I-------CEKENI--SHTNDGLEAIVFTA--------QGDMRQALNNLQSTHN  203 (317)
Q Consensus       150 -i~f~~~~~~~~~~~l~~----~-------~~~~~~--~i~~~~~~~l~~~~--------~gd~r~~i~~l~~~~~  203 (317)
                       +.+.+++.+++.++|..    .       ++.+|+  .++++++..+++.+        +-..|.+...++.+..
T Consensus       329 ~v~L~~L~~~dL~~ILteP~nsLikQy~~Lf~~egv~L~Ftd~Al~~IA~~A~~~N~~~~~iGAR~LrtI~E~~L~  404 (443)
T PRK05201        329 RVELDALTEEDFVRILTEPKASLIKQYQALLATEGVTLEFTDDAIRRIAEIAYQVNEKTENIGARRLHTVMEKLLE  404 (443)
T ss_pred             EEECCCCCHHHHHHHhcCChhHHHHHHHHHHhhcCcEEEEcHHHHHHHHHHHHHhcccccccchhhHHHHHHHHHH
Confidence             99999999999999843    2       334565  56899998888664        3457777777766543

>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional

Probab=99.37  E-value=4.3e-11  Score=111.57  Aligned_cols=193  Identities=15%  Similarity=0.164  Sum_probs=130.9

Q ss_pred             CCCcccCCHHHHHHHHHHHhc--CCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHH-HHHH
Q psy879            8 TFSDIVGNEDTVERLKVFSSS--GNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRN-KIKM   84 (317)
Q Consensus         8 ~~~~~~g~~~~~~~l~~~l~~--~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~-~~~~   84 (317)
                      .+.+++|+...++.+...++.  ....+++|+|++||||+++|+++...-  .....+++.++|.... ...+.. .++.
T Consensus       185 ~~~~iig~s~~~~~~~~~i~~~a~~~~pVlI~Ge~GtGK~~~A~~ih~~s--~r~~~p~v~v~c~~~~-~~~~e~~lfG~  261 (509)
T PRK05022        185 KEGEMIGQSPAMQQLKKEIEVVAASDLNVLILGETGVGKELVARAIHAAS--PRADKPLVYLNCAALP-ESLAESELFGH  261 (509)
T ss_pred             cCCceeecCHHHHHHHHHHHHHhCCCCcEEEECCCCccHHHHHHHHHHhC--CcCCCCeEEEEcccCC-hHHHHHHhcCc
Confidence            568899998887776665543  222359999999999999999999863  2335578888886432 222221 1111


Q ss_pred             HH--------hhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhcc-----------CCceEEEEecCC-------Cc
Q psy879           85 FA--------QQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYS-----------NTTRFALACNNS-------EK  138 (317)
Q Consensus        85 ~~--------~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~-----------~~~~~il~~~~~-------~~  138 (317)
                      ..        .....+..+....++|||++.|..+.|..|++++++..           .++++|++|+..       ..
T Consensus       262 ~~g~~~ga~~~~~g~~~~a~gGtL~ldeI~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiI~~t~~~l~~~~~~~~  341 (509)
T PRK05022        262 VKGAFTGAISNRSGKFELADGGTLFLDEIGELPLALQAKLLRVLQYGEIQRVGSDRSLRVDVRVIAATNRDLREEVRAGR  341 (509)
T ss_pred             cccccCCCcccCCcchhhcCCCEEEecChhhCCHHHHHHHHHHHhcCCEeeCCCCcceecceEEEEecCCCHHHHHHcCC
Confidence            00        00001122457789999999999999999999998532           256889988764       24


Q ss_pred             CchhHhhhcce--eeecCCCH--HHHHHHHH----HHHHHc---CCCCCHHHHHHHHHh-cCCCHHHHHHHHHHhhh
Q psy879          139 IIEPIQSRCAM--LRYNKLTD--AQLLSKVI----EICEKE---NISHTNDGLEAIVFT-AQGDMRQALNNLQSTHN  203 (317)
Q Consensus       139 l~~~i~sR~~~--i~f~~~~~--~~~~~~l~----~~~~~~---~~~i~~~~~~~l~~~-~~gd~r~~i~~l~~~~~  203 (317)
                      +.+.+..|+..  |.+||+.+  +++..+..    +.+.+.   ...++++++..+... ..||+|+.-+.++.++.
T Consensus       342 f~~dL~~rl~~~~i~lPpLreR~eDI~~L~~~fl~~~~~~~~~~~~~~s~~a~~~L~~y~WPGNvrEL~~~i~ra~~  418 (509)
T PRK05022        342 FRADLYHRLSVFPLSVPPLRERGDDVLLLAGYFLEQNRARLGLRSLRLSPAAQAALLAYDWPGNVRELEHVISRAAL  418 (509)
T ss_pred             ccHHHHhcccccEeeCCCchhchhhHHHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHhCCCCCcHHHHHHHHHHHHH
Confidence            66777777765  77777765  34444333    333332   356899999988766 68999999999988664

>smart00350 MCM minichromosome maintenance proteins

Probab=99.36  E-value=3e-11  Score=112.43  Aligned_cols=152  Identities=20%  Similarity=0.269  Sum_probs=95.2

Q ss_pred             cccCCHHHHHHHHHHHhcCCC------------ceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcCh--H
Q psy879           11 DIVGNEDTVERLKVFSSSGNV------------PNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGI--D   76 (317)
Q Consensus        11 ~~~g~~~~~~~l~~~l~~~~~------------~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~--~   76 (317)
                      .++|++.++..+.-.+-+|..            .|+||+|+||+|||++++++++....    ..+......+..+.  .
T Consensus       204 ~i~G~~~~k~~l~l~l~gg~~~~~~~~~~~r~~~~vLL~G~pGtGKs~lar~l~~~~~r----~~~~~~~~~~~~~l~~~  279 (509)
T smart00350      204 SIYGHEDIKKAILLLLFGGVHKNLPDGMKIRGDINILLLGDPGTAKSQLLKYVEKTAPR----AVYTTGKGSSAVGLTAA  279 (509)
T ss_pred             cccCcHHHHHHHHHHHhCCCccccCCCccccccceEEEeCCCChhHHHHHHHHHHHcCc----ceEcCCCCCCcCCcccc
Confidence            567888888877766665532            27999999999999999999997421    11111111111111  1


Q ss_pred             HHHHHH-HHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhc-------------cCCceEEEEecCCC-----
Q psy879           77 TVRNKI-KMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIY-------------SNTTRFALACNNSE-----  137 (317)
Q Consensus        77 ~i~~~~-~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~-------------~~~~~~il~~~~~~-----  137 (317)
                      .+++.. +.+...+..+..++..+++|||++.+.+..+.+|+..||+.             +..+.+|.++|+..     
T Consensus       280 ~~~~~~~g~~~~~~G~l~~A~~Gil~iDEi~~l~~~~q~~L~e~me~~~i~i~k~G~~~~l~~~~~viAa~NP~~g~y~~  359 (509)
T smart00350      280 VTRDPETREFTLEGGALVLADNGVCCIDEFDKMDDSDRTAIHEAMEQQTISIAKAGITTTLNARCSVLAAANPIGGRYDP  359 (509)
T ss_pred             ceEccCcceEEecCccEEecCCCEEEEechhhCCHHHHHHHHHHHhcCEEEEEeCCEEEEecCCcEEEEEeCCCCcccCC
Confidence            111100 11111111122356789999999999999999999999853             24566788888642     


Q ss_pred             --------cCchhHhhhcce--eeecCCCHHHHHHHHHH
Q psy879          138 --------KIIEPIQSRCAM--LRYNKLTDAQLLSKVIE  166 (317)
Q Consensus       138 --------~l~~~i~sR~~~--i~f~~~~~~~~~~~l~~  166 (317)
                              .+++++.|||..  +-..+++.+.-.+++..
T Consensus       360 ~~~~~~n~~l~~~lLsRFdLi~~~~d~~~~~~d~~i~~~  398 (509)
T smart00350      360 KLTPEENIDLPAPILSRFDLLFVVLDEVDEERDRELAKH  398 (509)
T ss_pred             CcChhhccCCChHHhCceeeEEEecCCCChHHHHHHHHH
Confidence                    588999999955  44445555544444444

>COG2607 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=99.36  E-value=9.3e-11  Score=94.70  Aligned_cols=189  Identities=16%  Similarity=0.220  Sum_probs=131.1

Q ss_pred             ccCCCCCCcccCCHHHHHHHH----HHHhcCCCc-eEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHH
Q psy879            3 KYRPQTFSDIVGNEDTVERLK----VFSSSGNVP-NIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDT   77 (317)
Q Consensus         3 ky~P~~~~~~~g~~~~~~~l~----~~l~~~~~~-~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~   77 (317)
                      .|-|-.+.+++|-+...+.|.    .++ +|.+. |+|++|..|+|||++++++..++....  ...++++..+......
T Consensus        53 ~~~~i~L~~l~Gvd~qk~~L~~NT~~F~-~G~pANnVLLwGaRGtGKSSLVKA~~~e~~~~g--lrLVEV~k~dl~~Lp~  129 (287)
T COG2607          53 DPDPIDLADLVGVDRQKEALVRNTEQFA-EGLPANNVLLWGARGTGKSSLVKALLNEYADEG--LRLVEVDKEDLATLPD  129 (287)
T ss_pred             CCCCcCHHHHhCchHHHHHHHHHHHHHH-cCCcccceEEecCCCCChHHHHHHHHHHHHhcC--CeEEEEcHHHHhhHHH
Confidence            445566888999777766653    334 45554 599999999999999999999986543  3477777655444444


Q ss_pred             HHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHH-HHHHHHHhh----hccCCceEEEEecCCCcCc------------
Q psy879           78 VRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGA-QQALRRTME----IYSNTTRFALACNNSEKII------------  140 (317)
Q Consensus        78 i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~-~~~ll~~le----~~~~~~~~il~~~~~~~l~------------  140 (317)
                      +-+.+.   ..      ..+-||+.|+..+=..+. -.+|...||    ..|.|+.|..|+|..+-+.            
T Consensus       130 l~~~Lr---~~------~~kFIlFcDDLSFe~gd~~yK~LKs~LeG~ve~rP~NVl~YATSNRRHLl~e~~~dn~~~~~e  200 (287)
T COG2607         130 LVELLR---AR------PEKFILFCDDLSFEEGDDAYKALKSALEGGVEGRPANVLFYATSNRRHLLPEDMKDNEGSTGE  200 (287)
T ss_pred             HHHHHh---cC------CceEEEEecCCCCCCCchHHHHHHHHhcCCcccCCCeEEEEEecCCcccccHhhhhCCCcccc
Confidence            433333   22      356789999887765544 344444554    5678888888888754322            


Q ss_pred             ----------hhHhhhcce-eeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHH-----HhcCCCHHHHHHHHHHhhh
Q psy879          141 ----------EPIQSRCAM-LRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIV-----FTAQGDMRQALNNLQSTHN  203 (317)
Q Consensus       141 ----------~~i~sR~~~-i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~-----~~~~gd~r~~i~~l~~~~~  203 (317)
                                -++..||.. +.|.|.++++-..++...++..++.++++.++.=+     .+.+.+-|.|-..++.++.
T Consensus       201 ih~~eaveEKlSlSDRFGLwL~F~~~~Q~~YL~~V~~~a~~~~l~~~~e~l~~eAl~WAt~rg~RSGR~A~QF~~~~~g  279 (287)
T COG2607         201 IHPSEAVEEKLSLSDRFGLWLSFYPCDQDEYLKIVDHYAKHFGLDISDEELHAEALQWATTRGGRSGRVAWQFIRDLAG  279 (287)
T ss_pred             cChhHHHHHhhchhhhcceeecccCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHhcCCCccHhHHHHHHHHHh
Confidence                      134567766 99999999999999999999999999886665433     3345677777777766554

>COG1221 PspF Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms]

Probab=99.36  E-value=1.4e-11  Score=108.63  Aligned_cols=195  Identities=14%  Similarity=0.185  Sum_probs=130.7

Q ss_pred             CCCcccCCHHHHHHHHHHHhcCCC--ceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHHHHHH
Q psy879            8 TFSDIVGNEDTVERLKVFSSSGNV--PNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMF   85 (317)
Q Consensus         8 ~~~~~~g~~~~~~~l~~~l~~~~~--~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~   85 (317)
                      .+++++|.....+.+...++.-.+  .++|++|++||||+.+|+.+... .......+++.+||......-...+.++..
T Consensus        76 ~~~~LIG~~~~~~~~~eqik~~ap~~~~vLi~GetGtGKel~A~~iH~~-s~r~~~~PFI~~NCa~~~en~~~~eLFG~~  154 (403)
T COG1221          76 ALDDLIGESPSLQELREQIKAYAPSGLPVLIIGETGTGKELFARLIHAL-SARRAEAPFIAFNCAAYSENLQEAELFGHE  154 (403)
T ss_pred             hhhhhhccCHHHHHHHHHHHhhCCCCCcEEEecCCCccHHHHHHHHHHh-hhcccCCCEEEEEHHHhCcCHHHHHHhccc
Confidence            378899987666655555543111  26999999999999999999943 222267889999997643333333333211


Q ss_pred             ---Hhh-----cccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhh-----------ccCCceEEEEecCC--CcCch--h
Q psy879           86 ---AQQ-----KVTLPPGRHKIVILDEADSMTDGAQQALRRTMEI-----------YSNTTRFALACNNS--EKIIE--P  142 (317)
Q Consensus        86 ---~~~-----~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~-----------~~~~~~~il~~~~~--~~l~~--~  142 (317)
                         ...     +..+-....+.+++||+..|....|..|++++++           .+.++++|++|+..  ..+..  +
T Consensus       155 kGaftGa~~~k~Glfe~A~GGtLfLDEI~~LP~~~Q~kLl~~le~g~~~rvG~~~~~~~dVRli~AT~~~l~~~~~~g~d  234 (403)
T COG1221         155 KGAFTGAQGGKAGLFEQANGGTLFLDEIHRLPPEGQEKLLRVLEEGEYRRVGGSQPRPVDVRLICATTEDLEEAVLAGAD  234 (403)
T ss_pred             cceeecccCCcCchheecCCCEEehhhhhhCCHhHHHHHHHHHHcCceEecCCCCCcCCCceeeeccccCHHHHHHhhcc
Confidence               111     1111124678999999999999999999999996           45678888888764  35555  7


Q ss_pred             Hhhhcce--eeecCCCHH--HHHH----HHHHHHHHcCCCC---CHHHHHHHHHh-cCCCHHHHHHHHHHhhh
Q psy879          143 IQSRCAM--LRYNKLTDA--QLLS----KVIEICEKENISH---TNDGLEAIVFT-AQGDMRQALNNLQSTHN  203 (317)
Q Consensus       143 i~sR~~~--i~f~~~~~~--~~~~----~l~~~~~~~~~~i---~~~~~~~l~~~-~~gd~r~~i~~l~~~~~  203 (317)
                      +..|+..  |..||+.+.  ++..    ++...+++.+..+   +++++..+... ..||+|+..|.++.++.
T Consensus       235 l~~rl~~~~I~LPpLrER~~Di~~L~e~Fl~~~~~~l~~~~~~~~~~a~~~L~~y~~pGNirELkN~Ve~~~~  307 (403)
T COG1221         235 LTRRLNILTITLPPLRERKEDILLLAEHFLKSEARRLGLPLSVDSPEALRALLAYDWPGNIRELKNLVERAVA  307 (403)
T ss_pred             hhhhhcCceecCCChhhchhhHHHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHhCCCCCcHHHHHHHHHHHHH
Confidence            7776555  888887764  3322    3444556655544   23556655544 68999999999998665

>COG3829 RocR Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]

Probab=99.33  E-value=7.9e-11  Score=105.89  Aligned_cols=205  Identities=17%  Similarity=0.226  Sum_probs=135.0

Q ss_pred             CCCCcccCCHHHHHHHHHHHhcC--CCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHHHHH
Q psy879            7 QTFSDIVGNEDTVERLKVFSSSG--NVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKM   84 (317)
Q Consensus         7 ~~~~~~~g~~~~~~~l~~~l~~~--~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~~~   84 (317)
                      -+|++++|.......+...++..  ....+|+.|++||||..+|+++-+.  .+..+.+|+.+||.. ....-+...+-.
T Consensus       242 y~f~~Iig~S~~m~~~~~~akr~A~tdstVLi~GESGTGKElfA~~IH~~--S~R~~~PFIaiNCaA-iPe~LlESELFG  318 (560)
T COG3829         242 YTFDDIIGESPAMLRVLELAKRIAKTDSTVLILGESGTGKELFARAIHNL--SPRANGPFIAINCAA-IPETLLESELFG  318 (560)
T ss_pred             cchhhhccCCHHHHHHHHHHHhhcCCCCcEEEecCCCccHHHHHHHHHhc--CcccCCCeEEEeccc-CCHHHHHHHHhC
Confidence            46999999876666655555432  2335999999999999999999986  445567899999864 222222222221


Q ss_pred             HHhhccc----------CCCCceeEEEEeCCCCCCHHHHHHHHHHhhhc-----------cCCceEEEEecCCC------
Q psy879           85 FAQQKVT----------LPPGRHKIVILDEADSMTDGAQQALRRTMEIY-----------SNTTRFALACNNSE------  137 (317)
Q Consensus        85 ~~~~~~~----------~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~-----------~~~~~~il~~~~~~------  137 (317)
                      ....+++          +-.+....+|+||+..|....|..||+.+++.           +-++++|.+||..-      
T Consensus       319 ye~GAFTGA~~~GK~GlfE~A~gGTLFLDEIgempl~LQaKLLRVLQEkei~rvG~t~~~~vDVRIIAATN~nL~~~i~~  398 (560)
T COG3829         319 YEKGAFTGASKGGKPGLFELANGGTLFLDEIGEMPLPLQAKLLRVLQEKEIERVGGTKPIPVDVRIIAATNRNLEKMIAE  398 (560)
T ss_pred             cCCccccccccCCCCcceeeccCCeEEehhhccCCHHHHHHHHHHHhhceEEecCCCCceeeEEEEEeccCcCHHHHHhc
Confidence            1222221          11245789999999999999999999999853           35677899998752      


Q ss_pred             -cCchhHhhhcce--eeecCCCH--HHHHHH----HHHHHHHcC--C-CCCHHHHHHHHHh-cCCCHHHHHHHHHHhhh-
Q psy879          138 -KIIEPIQSRCAM--LRYNKLTD--AQLLSK----VIEICEKEN--I-SHTNDGLEAIVFT-AQGDMRQALNNLQSTHN-  203 (317)
Q Consensus       138 -~l~~~i~sR~~~--i~f~~~~~--~~~~~~----l~~~~~~~~--~-~i~~~~~~~l~~~-~~gd~r~~i~~l~~~~~-  203 (317)
                       .+-..+-=|..+  +..||+-+  +++...    |.+...+.+  + .++++++..+.+. +.||.|+.-|.++.+.. 
T Consensus       399 G~FReDLYYRLNV~~i~iPPLReR~eDI~~L~~~Fl~k~s~~~~~~v~~ls~~a~~~L~~y~WPGNVRELeNviER~v~~  478 (560)
T COG3829         399 GTFREDLYYRLNVIPITIPPLRERKEDIPLLAEYFLDKFSRRYGRNVKGLSPDALALLLRYDWPGNVRELENVIERAVNL  478 (560)
T ss_pred             CcchhhheeeeceeeecCCCcccCcchHHHHHHHHHHHHHHHcCCCcccCCHHHHHHHHhCCCCchHHHHHHHHHHHHhc
Confidence             344444445555  55555542  333333    333233333  2 3788998887765 79999999999998763 


Q ss_pred             --CCCcccHHHHH
Q psy879          204 --GFGHVTAEYVF  214 (317)
Q Consensus       204 --~~~~i~~~~v~  214 (317)
                        +...|+.++.-
T Consensus       479 ~~~~~~I~~~~lp  491 (560)
T COG3829         479 VESDGLIDADDLP  491 (560)
T ss_pred             cCCcceeehhhcc
Confidence              34456666543

>KOG0730|consensus

Probab=99.32  E-value=8.5e-11  Score=107.44  Aligned_cols=147  Identities=17%  Similarity=0.239  Sum_probs=111.5

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCC------CcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCC
Q psy879           33 NIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASN------DRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEAD  106 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~------~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d  106 (317)
                      ..|+|||||+|||.++++++++.     +..++.+++..      ..+...+|..+......      ..+.+++|||+|
T Consensus       220 g~Ll~gppg~Gkt~l~~aVa~e~-----~a~~~~i~~peli~k~~gEte~~LR~~f~~a~k~------~~psii~IdEld  288 (693)
T KOG0730|consen  220 GLLLYGPPGTGKTFLVRAVANEY-----GAFLFLINGPELISKFPGETESNLRKAFAEALKF------QVPSIIFIDELD  288 (693)
T ss_pred             CccccCCCCCChHHHHHHHHHHh-----CceeEecccHHHHHhcccchHHHHHHHHHHHhcc------CCCeeEeHHhHh
Confidence            49999999999999999999985     23455555532      12233445555444322      238899999999


Q ss_pred             CCCH----------HHHHHHHHHhhhcc--CCceEEEEecCCCcCchhHhh-hcce-eeecCCCHHHHHHHHHHHHHHcC
Q psy879          107 SMTD----------GAQQALRRTMEIYS--NTTRFALACNNSEKIIEPIQS-RCAM-LRYNKLTDAQLLSKVIEICEKEN  172 (317)
Q Consensus       107 ~l~~----------~~~~~ll~~le~~~--~~~~~il~~~~~~~l~~~i~s-R~~~-i~f~~~~~~~~~~~l~~~~~~~~  172 (317)
                      .+.+          +...+|+.+|+...  .+++++.++|+++.+.+++++ |+.. +.+.-|+..+..++++...++.+
T Consensus       289 ~l~p~r~~~~~~e~Rv~sqlltL~dg~~~~~~vivl~atnrp~sld~alRRgRfd~ev~IgiP~~~~RldIl~~l~k~~~  368 (693)
T KOG0730|consen  289 ALCPKREGADDVESRVVSQLLTLLDGLKPDAKVIVLAATNRPDSLDPALRRGRFDREVEIGIPGSDGRLDILRVLTKKMN  368 (693)
T ss_pred             hhCCcccccchHHHHHHHHHHHHHhhCcCcCcEEEEEecCCccccChhhhcCCCcceeeecCCCchhHHHHHHHHHHhcC
Confidence            9975          24567888888665  677788889999999999997 7776 99999999999999999988777


Q ss_pred             CCCCHHHHHHHHHhcCCCH
Q psy879          173 ISHTNDGLEAIVFTAQGDM  191 (317)
Q Consensus       173 ~~i~~~~~~~l~~~~~gd~  191 (317)
                      .. ++..+..++..+.|-.
T Consensus       369 ~~-~~~~l~~iA~~thGyv  386 (693)
T KOG0730|consen  369 LL-SDVDLEDIAVSTHGYV  386 (693)
T ss_pred             Cc-chhhHHHHHHHccchh
Confidence            65 5677888888877654

>PF05621 TniB: Bacterial TniB protein; InterPro: IPR008868 This family consists of several bacterial TniB NTP-binding proteins

Probab=99.32  E-value=4e-10  Score=95.46  Aligned_cols=202  Identities=15%  Similarity=0.168  Sum_probs=122.2

Q ss_pred             cCCHHH---HHHHHHHHh---cCCCceEEEECCCCCCHHHHHHHHHHHHcCCCC-----CCceEEecCCCCcChHHHHHH
Q psy879           13 VGNEDT---VERLKVFSS---SGNVPNIIISGPPGVGKTTTILCLARILLGPSF-----KDAVLELNASNDRGIDTVRNK   81 (317)
Q Consensus        13 ~g~~~~---~~~l~~~l~---~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~-----~~~~~~~~~~~~~~~~~i~~~   81 (317)
                      +|.+.+   ++.|...+.   ..+.|+++|+|++|.|||++++.+++.- ....     ..+++.+......+...+...
T Consensus        37 IgY~~A~~~L~~L~~Ll~~P~~~Rmp~lLivG~snnGKT~Ii~rF~~~h-p~~~d~~~~~~PVv~vq~P~~p~~~~~Y~~  115 (302)
T PF05621_consen   37 IGYPRAKEALDRLEELLEYPKRHRMPNLLIVGDSNNGKTMIIERFRRLH-PPQSDEDAERIPVVYVQMPPEPDERRFYSA  115 (302)
T ss_pred             ecCHHHHHHHHHHHHHHhCCcccCCCceEEecCCCCcHHHHHHHHHHHC-CCCCCCCCccccEEEEecCCCCChHHHHHH
Confidence            555544   444555454   4567889999999999999999999863 2221     123444433222222222111


Q ss_pred             HHHHHhhccc---------------CCCCceeEEEEeCCCCCC---HHHHHHHHHHhhhccC--CceEEEEecCC----C
Q psy879           82 IKMFAQQKVT---------------LPPGRHKIVILDEADSMT---DGAQQALRRTMEIYSN--TTRFALACNNS----E  137 (317)
Q Consensus        82 ~~~~~~~~~~---------------~~~~~~~vliiDE~d~l~---~~~~~~ll~~le~~~~--~~~~il~~~~~----~  137 (317)
                      +-.....+..               +..-+.+++||||++++.   ...|..++..+...++  .+.+|++....    -
T Consensus       116 IL~~lgaP~~~~~~~~~~~~~~~~llr~~~vrmLIIDE~H~lLaGs~~~qr~~Ln~LK~L~NeL~ipiV~vGt~~A~~al  195 (302)
T PF05621_consen  116 ILEALGAPYRPRDRVAKLEQQVLRLLRRLGVRMLIIDEFHNLLAGSYRKQREFLNALKFLGNELQIPIVGVGTREAYRAL  195 (302)
T ss_pred             HHHHhCcccCCCCCHHHHHHHHHHHHHHcCCcEEEeechHHHhcccHHHHHHHHHHHHHHhhccCCCeEEeccHHHHHHh
Confidence            1111111110               001257899999999973   2345555555543333  34466665443    2


Q ss_pred             cCchhHhhhcceeeecCCCHH-HHHHHHHHHHHH------cCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhh-----CC
Q psy879          138 KIIEPIQSRCAMLRYNKLTDA-QLLSKVIEICEK------ENISHTNDGLEAIVFTAQGDMRQALNNLQSTHN-----GF  205 (317)
Q Consensus       138 ~l~~~i~sR~~~i~f~~~~~~-~~~~~l~~~~~~------~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~-----~~  205 (317)
                      .-++.+.||+..+..+++..+ +....|...-..      .++ -+++...++...++|.+.....++..++.     +.
T Consensus       196 ~~D~QLa~RF~~~~Lp~W~~d~ef~~LL~s~e~~LPLr~~S~l-~~~~la~~i~~~s~G~iG~l~~ll~~aA~~AI~sG~  274 (302)
T PF05621_consen  196 RTDPQLASRFEPFELPRWELDEEFRRLLASFERALPLRKPSNL-ASPELARRIHERSEGLIGELSRLLNAAAIAAIRSGE  274 (302)
T ss_pred             ccCHHHHhccCCccCCCCCCCcHHHHHHHHHHHhCCCCCCCCC-CCHHHHHHHHHHcCCchHHHHHHHHHHHHHHHhcCC
Confidence            567999999999999999865 444444443221      122 24566789999999999999998876554     66


Q ss_pred             CcccHHHHHhh
Q psy879          206 GHVTAEYVFKV  216 (317)
Q Consensus       206 ~~i~~~~v~~~  216 (317)
                      +.|+.+.+.++
T Consensus       275 E~It~~~l~~~  285 (302)
T PF05621_consen  275 ERITREILDKI  285 (302)
T ss_pred             ceecHHHHhhC
Confidence            78888887664

TniB is a probable ATP-binding protein [] which is involved in Tn5053 mercury resistance transposition [].

>PF07728 AAA_5: AAA domain (dynein-related subfamily); InterPro: IPR011704 The ATPases Associated to a variety of cellular Activities (AAA) are a family distinguished by a highly conserved module of 230 amino acids []

Probab=99.32  E-value=3.3e-12  Score=98.46  Aligned_cols=110  Identities=24%  Similarity=0.356  Sum_probs=72.7

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHHHHH------HHhhcccCCCCceeEEEEeCCC
Q psy879           33 NIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKM------FAQQKVTLPPGRHKIVILDEAD  106 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~~~------~~~~~~~~~~~~~~vliiDE~d  106 (317)
                      +++|+||||+|||++++.+++.+     +..+..++........++......      +...+.........+++|||++
T Consensus         1 ~vlL~G~~G~GKt~l~~~la~~~-----~~~~~~i~~~~~~~~~dl~g~~~~~~~~~~~~~~~l~~a~~~~~il~lDEin   75 (139)
T PF07728_consen    1 PVLLVGPPGTGKTTLARELAALL-----GRPVIRINCSSDTTEEDLIGSYDPSNGQFEFKDGPLVRAMRKGGILVLDEIN   75 (139)
T ss_dssp             EEEEEESSSSSHHHHHHHHHHHH-----TCEEEEEE-TTTSTHHHHHCEEET-TTTTCEEE-CCCTTHHEEEEEEESSCG
T ss_pred             CEEEECCCCCCHHHHHHHHHHHh-----hcceEEEEeccccccccceeeeeecccccccccccccccccceeEEEECCcc
Confidence            58999999999999999999997     334555555544444433211110      0000000001258899999999


Q ss_pred             CCCHHHHHHHHHHhhhc-------------cC------CceEEEEecCCC----cCchhHhhhc
Q psy879          107 SMTDGAQQALRRTMEIY-------------SN------TTRFALACNNSE----KIIEPIQSRC  147 (317)
Q Consensus       107 ~l~~~~~~~ll~~le~~-------------~~------~~~~il~~~~~~----~l~~~i~sR~  147 (317)
                      ...++.++.|+..+++.             +.      +.++|+++|+..    .+.+++++||
T Consensus        76 ~a~~~v~~~L~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~~ii~t~N~~~~~~~~l~~al~~Rf  139 (139)
T PF07728_consen   76 RAPPEVLESLLSLLEERRIQLPEGGEEIKEPNNDLASPNFRIIATMNPRDKGRKELSPALLDRF  139 (139)
T ss_dssp             G--HHHHHTTHHHHSSSEEEE-TSSSEEE--TT------EEEEEEESSST--TTTTCHHHHTT-
T ss_pred             cCCHHHHHHHHHHHhhCcccccCCCcEEecCcccccccceEEEEEEcCCCCCcCcCCHHHHhhC
Confidence            99999999999999832             12      378899999877    8999999997

The highly conserved nature of this module across taxa suggests that it has a key cellular role. Members of the family are involved in diverse cellular functions including gene expression, peroxisome assembly and vesicle mediated transport. Although the role of this ATPase AAA domain is not, as yet, clear, the AAA+ superfamily of proteins to which the AAA ATPases belong has a chaperone-like function in the assembly, operation or disassembly of proteins []. This ATPase domain includes some proteins not detected by the IPR003959 from INTERPRO model.; GO: 0005524 ATP binding, 0016887 ATPase activity; PDB: 3NBX_X 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A.

>PF07724 AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR013093 ATPases Associated to a variety of cellular Activities (AAA) are a family distinguished by a highly conserved module of 230 amino acids []

Probab=99.31  E-value=7.1e-12  Score=99.43  Aligned_cols=101  Identities=25%  Similarity=0.379  Sum_probs=67.0

Q ss_pred             ceEEEECCCCCCHHHHHHHHHHHHc-CCCCCCceEEecCCCCcC----hHHHHHHHHHHHhhcccCCCCceeEEEEeCCC
Q psy879           32 PNIIISGPPGVGKTTTILCLARILL-GPSFKDAVLELNASNDRG----IDTVRNKIKMFAQQKVTLPPGRHKIVILDEAD  106 (317)
Q Consensus        32 ~~~ll~G~~G~GKt~la~~la~~l~-~~~~~~~~~~~~~~~~~~----~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d  106 (317)
                      .+++|+||+|+|||.+++++++.+. +..  ..++.++.+....    ...+...+.... ..  .......||++||+|
T Consensus         4 ~~~ll~GpsGvGKT~la~~la~~l~~~~~--~~~~~~d~s~~~~~~~~~~~~~~l~~~~~-~~--v~~~~~gVVllDEid   78 (171)
T PF07724_consen    4 SNFLLAGPSGVGKTELAKALAELLFVGSE--RPLIRIDMSEYSEGDDVESSVSKLLGSPP-GY--VGAEEGGVVLLDEID   78 (171)
T ss_dssp             EEEEEESSTTSSHHHHHHHHHHHHT-SSC--CEEEEEEGGGHCSHHHCSCHCHHHHHHTT-CH--HHHHHHTEEEEETGG
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHhccCCc--cchHHHhhhcccccchHHhhhhhhhhccc-ce--eeccchhhhhhHHHh
Confidence            3699999999999999999999996 333  3455555543333    111111121110 00  000234599999999


Q ss_pred             CCCH-----------HHHHHHHHHhhhc-----------cCCceEEEEecCCC
Q psy879          107 SMTD-----------GAQQALRRTMEIY-----------SNTTRFALACNNSE  137 (317)
Q Consensus       107 ~l~~-----------~~~~~ll~~le~~-----------~~~~~~il~~~~~~  137 (317)
                      +..+           ..++.|++.+|+.           -.++.||+++|-..
T Consensus        79 Ka~~~~~~~~~v~~~~V~~~LL~~le~g~~~d~~g~~vd~~n~ifI~Tsn~~~  131 (171)
T PF07724_consen   79 KAHPSNSGGADVSGEGVQNSLLQLLEGGTLTDSYGRTVDTSNIIFIMTSNFGA  131 (171)
T ss_dssp             GCSHTTTTCSHHHHHHHHHHHHHHHHHSEEEETTCCEEEGTTEEEEEEESSST
T ss_pred             hccccccccchhhHHHHHHHHHHHhcccceecccceEEEeCCceEEEeccccc
Confidence            9999           9999999999842           25677888888654

The highly conserved nature of this module across taxa suggests that it has a key cellular role. Members of the family are involved in diverse cellular functions including gene expression, peroxisome assembly and vesicle mediated transport. Although the role of ATPase AAA-2 domain is not, as yet, clear, the AAA+ superfamily of proteins to which the AAA ATPases belong has a chaperone-like function in the assembly, operation or disassembly of proteins []. Some of these ATPases function as a chaperone subunit of a proteasome-like degradation complex. This ATPase family includes some proteins not detected by IPR003959 from INTERPRO.; GO: 0005524 ATP binding; PDB: 1R6B_X 1KSF_X 3PXI_C 1KYI_T 1G3I_S 1OFH_B 1OFI_A 1G41_A 1IM2_A 1HQY_E ....

>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional

Probab=99.31  E-value=1.3e-10  Score=112.32  Aligned_cols=194  Identities=15%  Similarity=0.181  Sum_probs=127.0

Q ss_pred             CCCCcccCCHHHHHHHHHHHhc--CCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHH-HH
Q psy879            7 QTFSDIVGNEDTVERLKVFSSS--GNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNK-IK   83 (317)
Q Consensus         7 ~~~~~~~g~~~~~~~l~~~l~~--~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~-~~   83 (317)
                      ..|++++|+...++.+...++.  ....+++|+|++|||||++|+++...-  ...+.+++.++|.... ...+... ++
T Consensus       373 ~~~~~liG~S~~~~~~~~~~~~~a~~~~pVLI~GE~GTGK~~lA~~ih~~s--~r~~~~~v~i~c~~~~-~~~~~~~lfg  449 (686)
T PRK15429        373 SEFGEIIGRSEAMYSVLKQVEMVAQSDSTVLILGETGTGKELIARAIHNLS--GRNNRRMVKMNCAAMP-AGLLESDLFG  449 (686)
T ss_pred             ccccceeecCHHHHHHHHHHHHHhCCCCCEEEECCCCcCHHHHHHHHHHhc--CCCCCCeEEEecccCC-hhHhhhhhcC
Confidence            4688999998777776544432  222369999999999999999998863  2234567777776421 1111111 11


Q ss_pred             HHH--------hhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhcc-----------CCceEEEEecCCC-------
Q psy879           84 MFA--------QQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYS-----------NTTRFALACNNSE-------  137 (317)
Q Consensus        84 ~~~--------~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~-----------~~~~~il~~~~~~-------  137 (317)
                      ...        .....+....+.+++|||++.+..+.|..|++++++..           .++++|++|+..-       
T Consensus       450 ~~~~~~~g~~~~~~g~le~a~~GtL~Ldei~~L~~~~Q~~L~~~l~~~~~~~~g~~~~~~~~~RiI~~t~~~l~~~~~~~  529 (686)
T PRK15429        450 HERGAFTGASAQRIGRFELADKSSLFLDEVGDMPLELQPKLLRVLQEQEFERLGSNKIIQTDVRLIAATNRDLKKMVADR  529 (686)
T ss_pred             cccccccccccchhhHHHhcCCCeEEEechhhCCHHHHHHHHHHHHhCCEEeCCCCCcccceEEEEEeCCCCHHHHHHcC
Confidence            000        00000112356899999999999999999999997532           3567888887642       


Q ss_pred             cCchhHhhhcce--eeecCCCH--HHHHHHHH----HHHHHcCC---CCCHHHHHHHHHh-cCCCHHHHHHHHHHhhh
Q psy879          138 KIIEPIQSRCAM--LRYNKLTD--AQLLSKVI----EICEKENI---SHTNDGLEAIVFT-AQGDMRQALNNLQSTHN  203 (317)
Q Consensus       138 ~l~~~i~sR~~~--i~f~~~~~--~~~~~~l~----~~~~~~~~---~i~~~~~~~l~~~-~~gd~r~~i~~l~~~~~  203 (317)
                      .+.+.+-.|+..  |.+||+.+  +++..++.    +.+.+.|.   .++++++..+... ..||+|+..+.++.++.
T Consensus       530 ~f~~~L~~~l~~~~i~lPpLreR~~Di~~L~~~~l~~~~~~~~~~~~~~s~~al~~L~~y~WPGNvrEL~~~i~~a~~  607 (686)
T PRK15429        530 EFRSDLYYRLNVFPIHLPPLRERPEDIPLLVKAFTFKIARRMGRNIDSIPAETLRTLSNMEWPGNVRELENVIERAVL  607 (686)
T ss_pred             cccHHHHhccCeeEEeCCChhhhHhHHHHHHHHHHHHHHHHcCCCCCCcCHHHHHHHHhCCCCCcHHHHHHHHHHHHH
Confidence            345556666555  77777764  44444433    33433343   4789999888765 68999999999998764

>KOG0732|consensus

Probab=99.30  E-value=7.9e-11  Score=113.61  Aligned_cols=189  Identities=16%  Similarity=0.158  Sum_probs=129.9

Q ss_pred             CCCcccCCHHHHHHHHHHHhc------------CCCce-EEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCC--C
Q psy879            8 TFSDIVGNEDTVERLKVFSSS------------GNVPN-IIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASN--D   72 (317)
Q Consensus         8 ~~~~~~g~~~~~~~l~~~l~~------------~~~~~-~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~--~   72 (317)
                      .|+++-|-++++..|+..+-.            -.+|. +||+||||||||..|+++|..+........++--...+  .
T Consensus       263 ~fd~vggl~~~i~~LKEmVl~PLlyPE~f~~~~itpPrgvL~~GppGTGkTl~araLa~~~s~~~~kisffmrkgaD~ls  342 (1080)
T KOG0732|consen  263 GFDSVGGLENYINQLKEMVLLPLLYPEFFDNFNITPPRGVLFHGPPGTGKTLMARALAAACSRGNRKISFFMRKGADCLS  342 (1080)
T ss_pred             CccccccHHHHHHHHHHHHHhHhhhhhHhhhcccCCCcceeecCCCCCchhHHHHhhhhhhcccccccchhhhcCchhhc
Confidence            589999999999998887531            12344 99999999999999999999864322223232222211  1


Q ss_pred             cChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHH-----------HHHHHHHHhhhcc--CCceEEEEecCCCcC
Q psy879           73 RGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDG-----------AQQALRRTMEIYS--NTTRFALACNNSEKI  139 (317)
Q Consensus        73 ~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~-----------~~~~ll~~le~~~--~~~~~il~~~~~~~l  139 (317)
                      ....+..+.+...+..+.   ...+.|+++||+|.+.+-           ....|+..|...+  +.+++|.+||+++.+
T Consensus       343 kwvgEaERqlrllFeeA~---k~qPSIIffdeIdGlapvrSskqEqih~SIvSTLLaLmdGldsRgqVvvigATnRpda~  419 (1080)
T KOG0732|consen  343 KWVGEAERQLRLLFEEAQ---KTQPSIIFFDEIDGLAPVRSSKQEQIHASIVSTLLALMDGLDSRGQVVVIGATNRPDAI  419 (1080)
T ss_pred             cccCcHHHHHHHHHHHHh---ccCceEEeccccccccccccchHHHhhhhHHHHHHHhccCCCCCCceEEEcccCCcccc
Confidence            222222233333333321   146889999999987531           2456777787554  346677789999999


Q ss_pred             chhHhhhcce---eeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHH
Q psy879          140 IEPIQSRCAM---LRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQ  199 (317)
Q Consensus       140 ~~~i~sR~~~---i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~  199 (317)
                      +++++.....   ++|+.++.+...+++.-.-.+..-.+.......+++.+.|-.+.-+..|.
T Consensus       420 dpaLRRPgrfdref~f~lp~~~ar~~Il~Ihtrkw~~~i~~~l~~~la~~t~gy~gaDlkaLC  482 (1080)
T KOG0732|consen  420 DPALRRPGRFDREFYFPLPDVDARAKILDIHTRKWEPPISRELLLWLAEETSGYGGADLKALC  482 (1080)
T ss_pred             chhhcCCcccceeEeeeCCchHHHHHHHHHhccCCCCCCCHHHHHHHHHhccccchHHHHHHH
Confidence            9999887765   99999999988888877655545567788888999888776666555553

>KOG0744|consensus

Probab=99.30  E-value=2.5e-11  Score=101.97  Aligned_cols=129  Identities=21%  Similarity=0.308  Sum_probs=89.1

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHcC----CCCCCceEEecCCCCc---------ChHHHHHHHHHHHhhcccCCCCceeEE
Q psy879           34 IIISGPPGVGKTTTILCLARILLG----PSFKDAVLELNASNDR---------GIDTVRNKIKMFAQQKVTLPPGRHKIV  100 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~l~~----~~~~~~~~~~~~~~~~---------~~~~i~~~~~~~~~~~~~~~~~~~~vl  100 (317)
                      +|++||||||||++.+++|+.+.-    .......+++|+....         -+..+.+.+......+     +.--.|
T Consensus       180 iLlhGPPGTGKTSLCKaLaQkLSIR~~~~y~~~~liEinshsLFSKWFsESgKlV~kmF~kI~ELv~d~-----~~lVfv  254 (423)
T KOG0744|consen  180 ILLHGPPGTGKTSLCKALAQKLSIRTNDRYYKGQLIEINSHSLFSKWFSESGKLVAKMFQKIQELVEDR-----GNLVFV  254 (423)
T ss_pred             EEEeCCCCCChhHHHHHHHHhheeeecCccccceEEEEehhHHHHHHHhhhhhHHHHHHHHHHHHHhCC-----CcEEEE
Confidence            899999999999999999999841    1122345677764311         1223333344333332     445678


Q ss_pred             EEeCCCCCCH---------------HHHHHHHHHhhhcc--CCceEEEEecCCCcCchhHhhhcce-eeecCCCHHHHHH
Q psy879          101 ILDEADSMTD---------------GAQQALRRTMEIYS--NTTRFALACNNSEKIIEPIQSRCAM-LRYNKLTDAQLLS  162 (317)
Q Consensus       101 iiDE~d~l~~---------------~~~~~ll~~le~~~--~~~~~il~~~~~~~l~~~i~sR~~~-i~f~~~~~~~~~~  162 (317)
                      +|||++.+..               ...|+++..++...  +++.+..|+|-.+.++.++..|... ....+|+...+..
T Consensus       255 LIDEVESLa~aR~s~~S~~EpsDaIRvVNalLTQlDrlK~~~NvliL~TSNl~~siD~AfVDRADi~~yVG~Pt~~ai~~  334 (423)
T KOG0744|consen  255 LIDEVESLAAARTSASSRNEPSDAIRVVNALLTQLDRLKRYPNVLILATSNLTDSIDVAFVDRADIVFYVGPPTAEAIYE  334 (423)
T ss_pred             EeHHHHHHHHHHHhhhcCCCCchHHHHHHHHHHHHHHhccCCCEEEEeccchHHHHHHHhhhHhhheeecCCccHHHHHH
Confidence            9999998743               24788998888643  4444444555668999999999988 7778888888888


Q ss_pred             HHHHH
Q psy879          163 KVIEI  167 (317)
Q Consensus       163 ~l~~~  167 (317)
                      +++.-
T Consensus       335 Ilksc  339 (423)
T KOG0744|consen  335 ILKSC  339 (423)
T ss_pred             HHHHH
Confidence            87764

>PF06144 DNA_pol3_delta: DNA polymerase III, delta subunit; InterPro: IPR010372 DNA polymerase III, delta subunit (2

Probab=99.29  E-value=1.2e-11  Score=99.04  Aligned_cols=162  Identities=15%  Similarity=0.226  Sum_probs=109.7

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHcCCCCC-CceEEecCCCCcChHHHHHHHHHHHhhcccCCCCceeEEEEeCC----CCC
Q psy879           34 IIISGPPGVGKTTTILCLARILLGPSFK-DAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEA----DSM  108 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~l~~~~~~-~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~----d~l  108 (317)
                      |+|||+.-.-+...++.+.+.+...... ..+..+.... ...   .+.+..+...++.   +++++|+|.++    +..
T Consensus         1 Yll~G~d~~l~~~~~~~i~~~~~~~~~~~~~~~~~~~~~-~~~---~~l~~~~~s~slF---~~~klvii~~~~~l~~~~   73 (172)
T PF06144_consen    1 YLLYGEDSFLIEEYIKKIRKALIKKDFDDFNVIVFDGSE-DDI---DELLEELQSPSLF---GDKKLVIIKNAPFLKDKL   73 (172)
T ss_dssp             EEEEES-HHHHHHHHHHHHHHHHTTTEEEEEEEE-STTS--HH---H-HTTTSTTTTSS---SSEEEEEEE-----TT-S
T ss_pred             CEEEeCcHHHHHHHHHHHHHHhhcCCCccceEEEEcccc-CcH---HHHHHHHhcCCcc---CCCeEEEEecCccccccc
Confidence            7899999777777777777775443321 2233333221 111   2233333333322   68999999999    556


Q ss_pred             CHHHHHHHHHHhhhccCCceEEEEec-CCC---cCchhHhhhcceeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHH
Q psy879          109 TDGAQQALRRTMEIYSNTTRFALACN-NSE---KIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIV  184 (317)
Q Consensus       109 ~~~~~~~ll~~le~~~~~~~~il~~~-~~~---~l~~~i~sR~~~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~  184 (317)
                      ..+....|.++++.+++++.+|+.++ ..+   ++.+.+.+.+.++.|.+++..++..|+..++++.|+.+++++++.++
T Consensus        74 ~~~~~~~l~~~l~~~~~~~~lii~~~~~~~~~~k~~k~l~~~~~~~~~~~~~~~~~~~~i~~~~~~~g~~i~~~a~~~L~  153 (172)
T PF06144_consen   74 KKKEIKALIEYLSNPPPDCILIIFSEEKLDKRKKLYKALKKQAIVIECKKPKEQELPRWIKERAKKNGLKIDPDAAQYLI  153 (172)
T ss_dssp             -TTHHHHHHHHTTT--SSEEEEEEES-S--HHHHHHHHHTTTEEEEEE----TTTHHHHHHHHHHHTT-EE-HHHHHHHH
T ss_pred             cHHHHHHHHHHHhCCCCCEEEEEEeCCchhhhhhHHHHHhcccceEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHH
Confidence            77789999999999999999888888 333   57788888999999999999999999999999999999999999999


Q ss_pred             HhcCCCHHHHHHHHHHhh
Q psy879          185 FTAQGDMRQALNNLQSTH  202 (317)
Q Consensus       185 ~~~~gd~r~~i~~l~~~~  202 (317)
                      ...++|++.+.+++++.+
T Consensus       154 ~~~~~d~~~l~~EleKL~  171 (172)
T PF06144_consen  154 ERVGNDLSLLQNELEKLS  171 (172)
T ss_dssp             HHHTT-HHHHHHHHHHHH
T ss_pred             HHhChHHHHHHHHHHHhc
Confidence            999999999999998864

7.7.7 from EC) is required for, along with delta' subunit, the assembly of the processivity factor beta(2) onto primed DNA in the DNA polymerase III holoenzyme-catalysed reaction []. The delta subunit is also known as HolA.; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication, 0009360 DNA polymerase III complex; PDB: 3GLG_F 1XXH_A 1JQL_B 3GLF_F 1JQJ_C 3GLI_F.

>COG0542 clpA ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]

Probab=99.28  E-value=8.1e-11  Score=111.26  Aligned_cols=190  Identities=18%  Similarity=0.274  Sum_probs=138.4

Q ss_pred             CCCCCCcccCCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCC-----CceEEecC------CCCc
Q psy879            5 RPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFK-----DAVLELNA------SNDR   73 (317)
Q Consensus         5 ~P~~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~-----~~~~~~~~------~~~~   73 (317)
                      |-..++.++|+++.++++...+....-+|-++.|+||+|||.++..+|..+......     ..++.++-      ...+
T Consensus       165 r~gklDPvIGRd~EI~r~iqIL~RR~KNNPvLiGEpGVGKTAIvEGLA~rIv~g~VP~~L~~~~i~sLD~g~LvAGakyR  244 (786)
T COG0542         165 REGKLDPVIGRDEEIRRTIQILSRRTKNNPVLVGEPGVGKTAIVEGLAQRIVNGDVPESLKDKRIYSLDLGSLVAGAKYR  244 (786)
T ss_pred             hcCCCCCCcChHHHHHHHHHHHhccCCCCCeEecCCCCCHHHHHHHHHHHHhcCCCCHHHcCCEEEEecHHHHhcccccc
Confidence            345689999999999998888877776678999999999999999999998643321     12333321      1222


Q ss_pred             Ch--HHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCC---------HHHHHHHHHHhhhccCCceEEEEecCCC-----
Q psy879           74 GI--DTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMT---------DGAQQALRRTMEIYSNTTRFALACNNSE-----  137 (317)
Q Consensus        74 ~~--~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~---------~~~~~~ll~~le~~~~~~~~il~~~~~~-----  137 (317)
                      +.  +.+...+.....       +++.++||||++.+.         -++.|.|...|..  +...+|.+|+..+     
T Consensus       245 GeFEeRlk~vl~ev~~-------~~~vILFIDEiHtiVGAG~~~G~a~DAaNiLKPaLAR--GeL~~IGATT~~EYRk~i  315 (786)
T COG0542         245 GEFEERLKAVLKEVEK-------SKNVILFIDEIHTIVGAGATEGGAMDAANLLKPALAR--GELRCIGATTLDEYRKYI  315 (786)
T ss_pred             CcHHHHHHHHHHHHhc-------CCCeEEEEechhhhcCCCcccccccchhhhhHHHHhc--CCeEEEEeccHHHHHHHh
Confidence            21  223334444332       237899999999773         2356778888874  5567788776542     


Q ss_pred             cCchhHhhhcceeeecCCCHHHHHHHHHHHHHH----cCCCCCHHHHHHHHHhcCC------CHHHHHHHHHHhhh
Q psy879          138 KIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEK----ENISHTNDGLEAIVFTAQG------DMRQALNNLQSTHN  203 (317)
Q Consensus       138 ~l~~~i~sR~~~i~f~~~~~~~~~~~l~~~~~~----~~~~i~~~~~~~l~~~~~g------d~r~~i~~l~~~~~  203 (317)
                      .-++++.+||+.|....|+.++...+|.....+    +++.++++++.+.+..|..      =+.+|+++++.++.
T Consensus       316 EKD~AL~RRFQ~V~V~EPs~e~ti~ILrGlk~~yE~hH~V~i~D~Al~aAv~LS~RYI~dR~LPDKAIDLiDeA~a  391 (786)
T COG0542         316 EKDAALERRFQKVLVDEPSVEDTIAILRGLKERYEAHHGVRITDEALVAAVTLSDRYIPDRFLPDKAIDLLDEAGA  391 (786)
T ss_pred             hhchHHHhcCceeeCCCCCHHHHHHHHHHHHHHHHHccCceecHHHHHHHHHHHHhhcccCCCCchHHHHHHHHHH
Confidence            468999999999999999999999998876544    6789999999888776642      36789999987765

>TIGR02915 PEP_resp_reg putative PEP-CTERM system response regulator

Probab=99.24  E-value=5e-10  Score=103.30  Aligned_cols=203  Identities=15%  Similarity=0.152  Sum_probs=132.6

Q ss_pred             CCCcccCCHHHHHHHHHHHhc--CCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHHH-HH
Q psy879            8 TFSDIVGNEDTVERLKVFSSS--GNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKI-KM   84 (317)
Q Consensus         8 ~~~~~~g~~~~~~~l~~~l~~--~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~-~~   84 (317)
                      .+..++|.....+.+...+..  +...+++++|++|+||+++|+.+...-  .....+++.++|... ....+...+ +.
T Consensus       137 ~~~~lig~s~~~~~l~~~i~~~a~~~~~vli~Ge~GtGK~~lA~~ih~~s--~~~~~~~v~v~c~~~-~~~~~~~~lfg~  213 (445)
T TIGR02915       137 ALRGLITSSPGMQKICRTIEKIAPSDITVLLLGESGTGKEVLARALHQLS--DRKDKRFVAINCAAI-PENLLESELFGY  213 (445)
T ss_pred             cccceeecCHHHHHHHHHHHHHhCCCCCEEEECCCCcCHHHHHHHHHHhC--CcCCCCeEEEECCCC-ChHHHHHHhcCC
Confidence            456788877666665555542  222358999999999999999998763  223455777877643 222222211 10


Q ss_pred             H--------HhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhcc-----------CCceEEEEecCC-------Cc
Q psy879           85 F--------AQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYS-----------NTTRFALACNNS-------EK  138 (317)
Q Consensus        85 ~--------~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~-----------~~~~~il~~~~~-------~~  138 (317)
                      .        ......+....+.+++|||++.|....|..|++++++..           .++++|++++..       ..
T Consensus       214 ~~~~~~~~~~~~~g~~~~a~~gtl~l~~i~~l~~~~q~~l~~~l~~~~~~~~~~~~~~~~~~rii~~~~~~l~~~~~~~~  293 (445)
T TIGR02915       214 EKGAFTGAVKQTLGKIEYAHGGTLFLDEIGDLPLNLQAKLLRFLQERVIERLGGREEIPVDVRIVCATNQDLKRMIAEGT  293 (445)
T ss_pred             CCCCcCCCccCCCCceeECCCCEEEEechhhCCHHHHHHHHHHHhhCeEEeCCCCceeeeceEEEEecCCCHHHHHHcCC
Confidence            0        000001112467899999999999999999999998531           256788888765       24


Q ss_pred             CchhHhhhcce--eeecCCCH--HHHHH----HHHHHHHHcC---CCCCHHHHHHHHHh-cCCCHHHHHHHHHHhhh--C
Q psy879          139 IIEPIQSRCAM--LRYNKLTD--AQLLS----KVIEICEKEN---ISHTNDGLEAIVFT-AQGDMRQALNNLQSTHN--G  204 (317)
Q Consensus       139 l~~~i~sR~~~--i~f~~~~~--~~~~~----~l~~~~~~~~---~~i~~~~~~~l~~~-~~gd~r~~i~~l~~~~~--~  204 (317)
                      +.+.+..|+..  |.+||+.+  +++..    ++.+.+...+   ..++++++..+... ..||+|++.+.++.++.  .
T Consensus       294 ~~~~L~~~l~~~~i~lPpLr~R~~Di~~l~~~~l~~~~~~~~~~~~~~~~~a~~~L~~~~wpgNvreL~~~i~~a~~~~~  373 (445)
T TIGR02915       294 FREDLFYRIAEISITIPPLRSRDGDAVLLANAFLERFARELKRKTKGFTDDALRALEAHAWPGNVRELENKVKRAVIMAE  373 (445)
T ss_pred             ccHHHHHHhccceecCCCchhchhhHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHhCCCCChHHHHHHHHHHHHHhCC
Confidence            56667777765  67777754  23333    3333333333   45899999998776 48999999999998765  3


Q ss_pred             CCcccHHHH
Q psy879          205 FGHVTAEYV  213 (317)
Q Consensus       205 ~~~i~~~~v  213 (317)
                      ...|+.+++
T Consensus       374 ~~~i~~~~l  382 (445)
T TIGR02915       374 GNQITAEDL  382 (445)
T ss_pred             CCcccHHHc
Confidence            446777665

Members of this protein family share full-length homology with (but do not include) the acetoacetate metabolism regulatory protein AtoC. These proteins have a Fis family DNA binding sequence (pfam02954), a response regulator receiver domain (pfam00072), and sigma-54 interaction domain (pfam00158).

>KOG0651|consensus

Probab=99.23  E-value=1.1e-10  Score=97.57  Aligned_cols=169  Identities=15%  Similarity=0.214  Sum_probs=105.5

Q ss_pred             CCCcccCCHHHHHHHHHHHh------------cCCCce-EEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCC---
Q psy879            8 TFSDIVGNEDTVERLKVFSS------------SGNVPN-IIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASN---   71 (317)
Q Consensus         8 ~~~~~~g~~~~~~~l~~~l~------------~~~~~~-~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~---   71 (317)
                      +|+++-|--.++..|...+.            +=.+|- ++||||||+|||.++++++..+..     .++-+..+.   
T Consensus       130 s~~~~ggl~~qirelre~ielpl~np~lf~rvgIk~Pkg~ll~GppGtGKTlla~~Vaa~mg~-----nfl~v~ss~lv~  204 (388)
T KOG0651|consen  130 SFENVGGLFYQIRELREVIELPLTNPELFLRVGIKPPKGLLLYGPPGTGKTLLARAVAATMGV-----NFLKVVSSALVD  204 (388)
T ss_pred             CHHHhCChHHHHHHHHhheEeeccCchhccccCCCCCceeEEeCCCCCchhHHHHHHHHhcCC-----ceEEeeHhhhhh
Confidence            68888887777777666542            112344 999999999999999999998632     233333221   


Q ss_pred             -C--cChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCH-----------HHHHHHHHHhhhc-----cCCceEEEE
Q psy879           72 -D--RGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTD-----------GAQQALRRTMEIY-----SNTTRFALA  132 (317)
Q Consensus        72 -~--~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~-----------~~~~~ll~~le~~-----~~~~~~il~  132 (317)
                       .  ....-||+.+......       .+.++++||+|....           ..+..|..++++.     -..+.+|++
T Consensus       205 kyiGEsaRlIRemf~yA~~~-------~pciifmdeiDAigGRr~se~Ts~dreiqrTLMeLlnqmdgfd~l~rVk~Ima  277 (388)
T KOG0651|consen  205 KYIGESARLIRDMFRYAREV-------IPCIIFMDEIDAIGGRRFSEGTSSDREIQRTLMELLNQMDGFDTLHRVKTIMA  277 (388)
T ss_pred             hhcccHHHHHHHHHHHHhhh-------CceEEeehhhhhhccEEeccccchhHHHHHHHHHHHHhhccchhcccccEEEe
Confidence             1  1223345544444433       468999999997532           2456666665532     246789999


Q ss_pred             ecCCCcCchhHhhhcce---eeecCCCHHHHHHHHHHH---HHHcCCCCCHHHHHHHHHhcCC
Q psy879          133 CNNSEKIIEPIQSRCAM---LRYNKLTDAQLLSKVIEI---CEKENISHTNDGLEAIVFTAQG  189 (317)
Q Consensus       133 ~~~~~~l~~~i~sR~~~---i~f~~~~~~~~~~~l~~~---~~~~~~~i~~~~~~~l~~~~~g  189 (317)
                      +|+++.++|++.+-...   ++.+.|.+.....+++-.   ....| .++.+++-++++-.+|
T Consensus       278 tNrpdtLdpaLlRpGRldrk~~iPlpne~~r~~I~Kih~~~i~~~G-eid~eaivK~~d~f~g  339 (388)
T KOG0651|consen  278 TNRPDTLDPALLRPGRLDRKVEIPLPNEQARLGILKIHVQPIDFHG-EIDDEAILKLVDGFNG  339 (388)
T ss_pred             cCCccccchhhcCCccccceeccCCcchhhceeeEeeccccccccc-cccHHHHHHHHhccCh
Confidence            99999999999765554   555555554433333322   12223 4566666666666555

>TIGR02031 BchD-ChlD magnesium chelatase ATPase subunit D

Probab=99.22  E-value=5.1e-10  Score=105.57  Aligned_cols=188  Identities=18%  Similarity=0.185  Sum_probs=117.0

Q ss_pred             hcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCC--CC--cChHHHHHHHH--HHHhhcccCCCCceeEE
Q psy879           27 SSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNAS--ND--RGIDTVRNKIK--MFAQQKVTLPPGRHKIV  100 (317)
Q Consensus        27 ~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~--~~--~~~~~i~~~~~--~~~~~~~~~~~~~~~vl  100 (317)
                      -+....|++|.|++|+|||++++++++.+..   ..+++.+...  ..  .+...+...+.  .+...+..+......++
T Consensus        12 v~p~~g~vLl~G~~GtgKs~lar~l~~~~~~---~~pfv~i~~~~t~d~L~G~idl~~~~~~g~~~~~~G~L~~A~~GvL   88 (589)
T TIGR02031        12 VDPSLGGVAIRARAGTGKTALARALAEILPP---IMPFVELPLGVTEDRLIGGIDVEESLAGGQRVTQPGLLDEAPRGVL   88 (589)
T ss_pred             cCCCcceEEEEcCCCcHHHHHHHHHHHhCCc---CCCeEecCcccchhhcccchhhhhhhhcCcccCCCCCeeeCCCCcE
Confidence            3445778999999999999999999997532   1234444421  11  11111111111  01111112223566899


Q ss_pred             EEeCCCCCCHHHHHHHHHHhhhcc-------------CCceEEEEecCCC---cCchhHhhhcce-eeecCC-CHHHHHH
Q psy879          101 ILDEADSMTDGAQQALRRTMEIYS-------------NTTRFALACNNSE---KIIEPIQSRCAM-LRYNKL-TDAQLLS  162 (317)
Q Consensus       101 iiDE~d~l~~~~~~~ll~~le~~~-------------~~~~~il~~~~~~---~l~~~i~sR~~~-i~f~~~-~~~~~~~  162 (317)
                      ++||++.+.+..|+.|+..|++..             ..+.+|.++|...   .+.+++..|+.. +....+ +.++..+
T Consensus        89 ~lDEi~rl~~~~q~~Ll~al~~g~v~i~r~G~~~~~p~~f~lIAt~np~e~~g~L~~~LldRf~l~v~~~~~~~~~er~e  168 (589)
T TIGR02031        89 YVDMANLLDDGLSNRLLQALDEGVVIVEREGISVVHPAKFALIATYDPAEGGGGLPDHLLDRLALHVSLEDVASQDLRVE  168 (589)
T ss_pred             eccchhhCCHHHHHHHHHHHHcCCeEEEECCCceeecCceEEEEecCCccccCCCCHHHHHhccCeeecCCCCCHHHHHH
Confidence            999999999999999999998532             3456777777654   688999999987 444433 3344333


Q ss_pred             HHHHHH-----------------------HHcCCCCCHHHHHHHHHhc---CC-CHHHHHHHHHHh-----hhCCCcccH
Q psy879          163 KVIEIC-----------------------EKENISHTNDGLEAIVFTA---QG-DMRQALNNLQST-----HNGFGHVTA  210 (317)
Q Consensus       163 ~l~~~~-----------------------~~~~~~i~~~~~~~l~~~~---~g-d~r~~i~~l~~~-----~~~~~~i~~  210 (317)
                      ++....                       ....+.++++.+.+++..+   +- ++|..+..++.+     ..+...++.
T Consensus       169 il~~~~~~~~~~~~~~~~~~~~~i~~ar~~~~~V~i~~~~~~~l~~~~~~~gv~s~Ra~i~~~r~ArA~Aal~gr~~V~~  248 (589)
T TIGR02031       169 IVRRERCNEVFRMNDELELLRGQIEAARELLPQVTISAEQVKELVLTAASLGISGHRADLFAVRAAKAHAALHGRTEVTE  248 (589)
T ss_pred             HHHHHHHhhhhhcchhhHHHHHHHHHHHHhcCCccCCHHHHHHHHHHHHHcCCCCccHHHHHHHHHHHHHHHhCCCCCCH
Confidence            333211                       1135678888887777553   32 377777666542     226778999


Q ss_pred             HHHHhhc
Q psy879          211 EYVFKVC  217 (317)
Q Consensus       211 ~~v~~~~  217 (317)
                      +|+..+.
T Consensus       249 ~Dv~~a~  255 (589)
T TIGR02031       249 EDLKLAV  255 (589)
T ss_pred             HHHHHHH
Confidence            9997644

This model represents one of two ATPase subunits of the trimeric magnesium chelatase responsible for insertion of magnesium ion into protoporphyrin IX. This is an essential step in the biosynthesis of both chlorophyll and bacteriochlorophyll. This subunit is found in green plants, photosynthetic algae, cyanobacteria and other photosynthetic bacteria. Unlike subunit I (TIGR02030), this subunit is not found in archaea.

>PRK10923 glnG nitrogen regulation protein NR(I); Provisional

Probab=99.22  E-value=6.7e-10  Score=103.13  Aligned_cols=204  Identities=17%  Similarity=0.163  Sum_probs=133.6

Q ss_pred             CCCcccCCHHHHHHHHHHHhc--CCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHHH-HH
Q psy879            8 TFSDIVGNEDTVERLKVFSSS--GNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKI-KM   84 (317)
Q Consensus         8 ~~~~~~g~~~~~~~l~~~l~~--~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~-~~   84 (317)
                      .+.+++|.....+.+...+..  ....++++.|++||||+++|+++....  .....+++.++|... ..+.+...+ +.
T Consensus       136 ~~~~lig~s~~~~~l~~~~~~~~~~~~~vli~Ge~GtGK~~lA~~ih~~s--~~~~~~~i~i~c~~~-~~~~~~~~lfg~  212 (469)
T PRK10923        136 PTTDIIGEAPAMQDVFRIIGRLSRSSISVLINGESGTGKELVAHALHRHS--PRAKAPFIALNMAAI-PKDLIESELFGH  212 (469)
T ss_pred             ccccceecCHHHHHHHHHHHHHhccCCeEEEEeCCCCcHHHHHHHHHhcC--CCCCCCeEeeeCCCC-CHHHHHHHhcCC
Confidence            366788877665555444432  122259999999999999999998863  233456788887643 222222221 10


Q ss_pred             HHh--------hcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhcc-----------CCceEEEEecCC-------Cc
Q psy879           85 FAQ--------QKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYS-----------NTTRFALACNNS-------EK  138 (317)
Q Consensus        85 ~~~--------~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~-----------~~~~~il~~~~~-------~~  138 (317)
                      ...        ....+....+..++|||++.|....|..|++++++..           .++++|++++..       ..
T Consensus       213 ~~g~~~~~~~~~~g~~~~a~~Gtl~l~~i~~l~~~~q~~L~~~l~~~~~~~~~~~~~~~~~~rii~~~~~~l~~~~~~~~  292 (469)
T PRK10923        213 EKGAFTGANTIRQGRFEQADGGTLFLDEIGDMPLDVQTRLLRVLADGQFYRVGGYAPVKVDVRIIAATHQNLEQRVQEGK  292 (469)
T ss_pred             CCCCCCCCCcCCCCCeeECCCCEEEEeccccCCHHHHHHHHHHHhcCcEEeCCCCCeEEeeEEEEEeCCCCHHHHHHcCC
Confidence            000        0001112356789999999999999999999998532           245788888754       25


Q ss_pred             CchhHhhhcce--eeecCCCH--HHHHHHHHHH----HHHcCC---CCCHHHHHHHHHh-cCCCHHHHHHHHHHhhh--C
Q psy879          139 IIEPIQSRCAM--LRYNKLTD--AQLLSKVIEI----CEKENI---SHTNDGLEAIVFT-AQGDMRQALNNLQSTHN--G  204 (317)
Q Consensus       139 l~~~i~sR~~~--i~f~~~~~--~~~~~~l~~~----~~~~~~---~i~~~~~~~l~~~-~~gd~r~~i~~l~~~~~--~  204 (317)
                      +.+.+..|+..  +..||+.+  +++..++...    +...+.   .++++++..+... ..||+|+.-+.++.++.  .
T Consensus       293 ~~~~L~~~l~~~~i~~PpLreR~~Di~~l~~~~l~~~~~~~~~~~~~~~~~a~~~L~~~~wpgNv~eL~~~i~~~~~~~~  372 (469)
T PRK10923        293 FREDLFHRLNVIRVHLPPLRERREDIPRLARHFLQVAARELGVEAKLLHPETEAALTRLAWPGNVRQLENTCRWLTVMAA  372 (469)
T ss_pred             chHHHHHHhcceeecCCCcccchhhHHHHHHHHHHHHHHHcCCCCCCcCHHHHHHHHhCCCCChHHHHHHHHHHHHHhCC
Confidence            66888888755  77777764  4444444433    333332   4789999888766 68999999999988765  4


Q ss_pred             CCcccHHHHH
Q psy879          205 FGHVTAEYVF  214 (317)
Q Consensus       205 ~~~i~~~~v~  214 (317)
                      ...|+.+++.
T Consensus       373 ~~~i~~~~l~  382 (469)
T PRK10923        373 GQEVLIQDLP  382 (469)
T ss_pred             CCcccHHHCc
Confidence            4567777763

>PF00158 Sigma54_activat: Sigma-54 interaction domain; InterPro: IPR002078 Some bacterial regulatory proteins activate the expression of genes from promoters recognised by core RNA polymerase associated with the alternative sigma-54 factor

Probab=99.22  E-value=5.5e-11  Score=94.08  Aligned_cols=135  Identities=16%  Similarity=0.229  Sum_probs=81.6

Q ss_pred             ccCCHHHHHHHHHHHhc--CCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHH-HHHHHHhh
Q psy879           12 IVGNEDTVERLKVFSSS--GNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRN-KIKMFAQQ   88 (317)
Q Consensus        12 ~~g~~~~~~~l~~~l~~--~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~-~~~~~~~~   88 (317)
                      ++|.....+.+...++.  ....+++|+|++||||+.+|+++.+.  ......+++.++|... ..+.+.. .++.. ..
T Consensus         1 liG~s~~m~~~~~~~~~~a~~~~pVlI~GE~GtGK~~lA~~IH~~--s~r~~~pfi~vnc~~~-~~~~~e~~LFG~~-~~   76 (168)
T PF00158_consen    1 LIGESPAMKRLREQAKRAASSDLPVLITGETGTGKELLARAIHNN--SPRKNGPFISVNCAAL-PEELLESELFGHE-KG   76 (168)
T ss_dssp             SS--SHHHHHHHHHHHHHTTSTS-EEEECSTTSSHHHHHHHHHHC--STTTTS-EEEEETTTS--HHHHHHHHHEBC-SS
T ss_pred             CEeCCHHHHHHHHHHHHHhCCCCCEEEEcCCCCcHHHHHHHHHHh--hhcccCCeEEEehhhh-hcchhhhhhhccc-cc
Confidence            45665555555444432  22246999999999999999999984  3334567899998753 3333322 22210 00


Q ss_pred             cc---------cCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhc-----------cCCceEEEEecCC-------CcCch
Q psy879           89 KV---------TLPPGRHKIVILDEADSMTDGAQQALRRTMEIY-----------SNTTRFALACNNS-------EKIIE  141 (317)
Q Consensus        89 ~~---------~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~-----------~~~~~~il~~~~~-------~~l~~  141 (317)
                      .+         .+..+...+++|||++.|....|..|++++++.           +.++++|++|+.+       ..+.+
T Consensus        77 ~~~~~~~~~~G~l~~A~~GtL~Ld~I~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiI~st~~~l~~~v~~g~fr~  156 (168)
T PF00158_consen   77 AFTGARSDKKGLLEQANGGTLFLDEIEDLPPELQAKLLRVLEEGKFTRLGSDKPVPVDVRIIASTSKDLEELVEQGRFRE  156 (168)
T ss_dssp             SSTTTSSEBEHHHHHTTTSEEEEETGGGS-HHHHHHHHHHHHHSEEECCTSSSEEE--EEEEEEESS-HHHHHHTTSS-H
T ss_pred             cccccccccCCceeeccceEEeecchhhhHHHHHHHHHHHHhhchhccccccccccccceEEeecCcCHHHHHHcCCChH
Confidence            00         011146789999999999999999999999842           3467788888864       24555


Q ss_pred             hHhhhccee
Q psy879          142 PIQSRCAML  150 (317)
Q Consensus       142 ~i~sR~~~i  150 (317)
                      .+--|...+
T Consensus       157 dLy~rL~~~  165 (168)
T PF00158_consen  157 DLYYRLNVF  165 (168)
T ss_dssp             HHHHHHTTE
T ss_pred             HHHHHhceE
Confidence            555555443

These have a conserved domain of about 230 residues involved in the ATP-dependent [, ] interaction with sigma-54. About half of the proteins in which this domain is found (algB, dcdT, flbD, hoxA, hupR1, hydG, ntrC, pgtA and pilR) belong to signal transduction two-component systems [] and possess a domain that can be phosphorylated by a sensor-kinase protein in their N-terminal section. Almost all of these proteins possess a helix-turn-helix DNA-binding domain in their C-terminal section. The domain which interacts with the sigma-54 factor has an ATPase activity. This may be required to promote a conformational change necessary for the interaction []. The domain contains an atypical ATP-binding motif A (P-loop) as well as a form of motif B. The two ATP-binding motifs are located in the N-terminal section of the domain.; GO: 0005524 ATP binding, 0008134 transcription factor binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1NY6_K 3M0E_G 1NY5_A 1OJL_A 3DZD_B 2C9C_A 2C98_A 2C96_A 2BJV_A 2C99_A ....

>smart00763 AAA_PrkA PrkA AAA domain

Probab=99.20  E-value=1e-09  Score=95.74  Aligned_cols=91  Identities=11%  Similarity=-0.016  Sum_probs=63.7

Q ss_pred             CceeEEEEeCCCCCCHHHHHHHHHHhhhcc-----------CCceEEEEecCC-------CcCchhHhhhcceeeecCCC
Q psy879           95 GRHKIVILDEADSMTDGAQQALRRTMEIYS-----------NTTRFALACNNS-------EKIIEPIQSRCAMLRYNKLT  156 (317)
Q Consensus        95 ~~~~vliiDE~d~l~~~~~~~ll~~le~~~-----------~~~~~il~~~~~-------~~l~~~i~sR~~~i~f~~~~  156 (317)
                      +.++++-++|+.+...+.++.|+..+++..           -..+||.++|..       .+..+++++||..+.++.+.
T Consensus       235 aNrGi~~f~Ei~K~~~~~l~~LL~~~qE~~v~~~~~~~~~~~d~liia~sNe~e~~~~~~~k~~eaf~dR~~~i~vpY~l  314 (361)
T smart00763      235 ANRGILEFVEMFKADIKFLHPLLTATQEGNIKGTGGFAMIPIDGLIIAHSNESEWQRFKSNKKNEALLDRIIKVKVPYCL  314 (361)
T ss_pred             ccCceEEEeehhcCCHHHHHHHhhhhhcceEecCCcccccccceEEEEeCCHHHHhhhhccccchhhhhceEEEeCCCcC
Confidence            467899999999999999999999998531           123355666654       26789999999999888665


Q ss_pred             H-HHHHHHHHHHHHHc---CCCCCHHHHHHHHH
Q psy879          157 D-AQLLSKVIEICEKE---NISHTNDGLEAIVF  185 (317)
Q Consensus       157 ~-~~~~~~l~~~~~~~---~~~i~~~~~~~l~~  185 (317)
                      . .+-.++..+.+...   +..+.+.+++.++.
T Consensus       315 ~~~~E~~Iy~k~~~~s~~~~~~~aP~~le~aa~  347 (361)
T smart00763      315 RVSEEAQIYEKLLRNSDLTEAHIAPHTLEMAAL  347 (361)
T ss_pred             CHHHHHHHHHHHhccCcCcccccCchHHHHHHH
Confidence            4 44445555555432   45666766655443

This is a family of PrkA bacterial and archaeal serine kinases approximately 630 residues long. This is the N-terminal AAA domain.

>PF07726 AAA_3: ATPase family associated with various cellular activities (AAA); InterPro: IPR011703 This entry includes some of the AAA proteins not detected by the IPR003959 from INTERPRO model

Probab=99.19  E-value=3e-11  Score=89.06  Aligned_cols=110  Identities=25%  Similarity=0.238  Sum_probs=58.7

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHHHHHHHh--h--cccCCCCceeEEEEeCCCCC
Q psy879           33 NIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFAQ--Q--KVTLPPGRHKIVILDEADSM  108 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~--~--~~~~~~~~~~vliiDE~d~l  108 (317)
                      |+|+.|+||+|||++++++|+.+..     .+..+....+....++... ..+..  .  .+....--..++++||+...
T Consensus         1 HvLleg~PG~GKT~la~~lA~~~~~-----~f~RIq~tpdllPsDi~G~-~v~~~~~~~f~~~~GPif~~ill~DEiNra   74 (131)
T PF07726_consen    1 HVLLEGVPGVGKTTLAKALARSLGL-----SFKRIQFTPDLLPSDILGF-PVYDQETGEFEFRPGPIFTNILLADEINRA   74 (131)
T ss_dssp             -EEEES---HHHHHHHHHHHHHTT-------EEEEE--TT--HHHHHEE-EEEETTTTEEEEEE-TT-SSEEEEETGGGS
T ss_pred             CEeeECCCccHHHHHHHHHHHHcCC-----ceeEEEecCCCCcccceee-eeeccCCCeeEeecChhhhceeeecccccC
Confidence            7899999999999999999999632     2334433333333333211 00000  0  00001112469999999999


Q ss_pred             CHHHHHHHHHHhhhc-----------cCCceEEEEecCCC-----cCchhHhhhcc
Q psy879          109 TDGAQQALRRTMEIY-----------SNTTRFALACNNSE-----KIIEPIQSRCA  148 (317)
Q Consensus       109 ~~~~~~~ll~~le~~-----------~~~~~~il~~~~~~-----~l~~~i~sR~~  148 (317)
                      .+..|++|++.|++.           |....+|.+.|+.+     .++++...|+.
T Consensus        75 ppktQsAlLeam~Er~Vt~~g~~~~lp~pf~ViATqNp~e~~Gty~Lpea~~DRF~  130 (131)
T PF07726_consen   75 PPKTQSALLEAMEERQVTIDGQTYPLPDPFFVIATQNPVEQEGTYPLPEAQLDRFM  130 (131)
T ss_dssp             -HHHHHHHHHHHHHSEEEETTEEEE--SS-EEEEEE-TT--S------HHHHTTSS
T ss_pred             CHHHHHHHHHHHHcCeEEeCCEEEECCCcEEEEEecCccccCceecCCHHHhcccc
Confidence            999999999999854           23333444555443     67888888874

AAA ATPases form a large, functionally diverse protein family belonging to the AAA+ superfamily of ring-shaped P-loop NTPases, which exert their activity through the energy-dependent unfolding of macromolecules. AAA ATPases contain a P-loop NTPase domain, which is the most abundant class of NTP-binding protein fold, and is found throughout all kingdoms of life []. P-loop NTPase domains act to hydrolyse the beta-gamma phosphate bond of bound nucleoside triphosphate. There are two classes of P-loop domains: the KG (kinase-GTPase) division, and the ASCE division, the latter including the AAA+ group as well as several other ATPases. There are at least six major clades of AAA domains (metalloproteases, meiotic proteins, D1 and D2 domains of ATPases with two AAA domains, proteasome subunits, and BSC1), as well as several minor clades, some of which consist of hypothetical proteins []. The domain organisation of AAA ATPases consists of a non-ATPase N-terminal domain that acts in substrate recognition, followed by one or two AAA domains (D1 and D2), one of which may be degenerate.; GO: 0005524 ATP binding, 0016887 ATPase activity; PDB: 2R44_A.

>PRK09862 putative ATP-dependent protease; Provisional

Probab=99.18  E-value=1.5e-09  Score=99.52  Aligned_cols=147  Identities=22%  Similarity=0.299  Sum_probs=98.0

Q ss_pred             CCCCcccCCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCC---------------
Q psy879            7 QTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASN---------------   71 (317)
Q Consensus         7 ~~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~---------------   71 (317)
                      ..|.+++|+..+++.+.-.+..|.  +++|+||||+|||++++.++..+... .....++.....               
T Consensus       188 ~d~~~v~Gq~~~~~al~laa~~G~--~llliG~~GsGKTtLak~L~gllpp~-~g~e~le~~~i~s~~g~~~~~~~~~~r  264 (506)
T PRK09862        188 HDLSDVIGQEQGKRGLEITAAGGH--NLLLIGPPGTGKTMLASRINGLLPDL-SNEEALESAAILSLVNAESVQKQWRQR  264 (506)
T ss_pred             cCeEEEECcHHHHhhhheeccCCc--EEEEECCCCCcHHHHHHHHhccCCCC-CCcEEEecchhhhhhccccccCCcCCC
Confidence            368888999999999887777776  89999999999999999999876322 222222221100               


Q ss_pred             -CcCh---HHHHHHHHHH-HhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhc-------------cCCceEEEEe
Q psy879           72 -DRGI---DTVRNKIKMF-AQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIY-------------SNTTRFALAC  133 (317)
Q Consensus        72 -~~~~---~~i~~~~~~~-~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~-------------~~~~~~il~~  133 (317)
                       .+.+   ......++.- ...+..+......++++||++.+.+..++.|++.||+.             +.++.+|.++
T Consensus       265 Pfr~ph~~~s~~~l~GGg~~~~pG~l~~A~gGvLfLDEi~e~~~~~~~~L~~~LE~g~v~I~r~g~~~~~pa~f~lIAa~  344 (506)
T PRK09862        265 PFRSPHHSASLTAMVGGGAIPGPGEISLAHNGVLFLDELPEFERRTLDALREPIESGQIHLSRTRAKITYPARFQLVAAM  344 (506)
T ss_pred             CccCCCccchHHHHhCCCceehhhHhhhccCCEEecCCchhCCHHHHHHHHHHHHcCcEEEecCCcceeccCCEEEEEee
Confidence             0000   0011111110 01111222356889999999999999999999999742             4456788888


Q ss_pred             cCCC---------------------cCchhHhhhcce-eeecCCC
Q psy879          134 NNSE---------------------KIIEPIQSRCAM-LRYNKLT  156 (317)
Q Consensus       134 ~~~~---------------------~l~~~i~sR~~~-i~f~~~~  156 (317)
                      |+..                     ++..++.+|+.. +..++++
T Consensus       345 NP~pcG~~~~~~c~c~~~~~~~Y~~~ls~plLDRfdL~v~v~~~~  389 (506)
T PRK09862        345 NPSPTGHYQGNHNRCTPEQTLRYLNRLSGPFLDRFDLSLEIPLPP  389 (506)
T ss_pred             cCccceecCCCCCCcCHHHHHHHHhhCCHhHHhhccEEEEeCCCC
Confidence            7642                     477799999988 7777764

>COG3604 FhlA Transcriptional regulator containing GAF, AAA-type ATPase, and DNA binding domains [Transcription / Signal transduction mechanisms]

Probab=99.18  E-value=1.2e-09  Score=97.17  Aligned_cols=194  Identities=16%  Similarity=0.185  Sum_probs=130.2

Q ss_pred             CCCcccCCHHHHHHHHHHHh--cCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcCh---HHHHHHH
Q psy879            8 TFSDIVGNEDTVERLKVFSS--SGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGI---DTVRNKI   82 (317)
Q Consensus         8 ~~~~~~g~~~~~~~l~~~l~--~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~---~~i~~~~   82 (317)
                      .+.++||+..+...+...++  ..+...+|+.|++||||..+|++|-+.  .+....+++.+||......   .++....
T Consensus       221 ~~~~iIG~S~am~~ll~~i~~VA~Sd~tVLi~GETGtGKElvAraIH~~--S~R~~kPfV~~NCAAlPesLlESELFGHe  298 (550)
T COG3604         221 EVGGIIGRSPAMRQLLKEIEVVAKSDSTVLIRGETGTGKELVARAIHQL--SPRRDKPFVKLNCAALPESLLESELFGHE  298 (550)
T ss_pred             ccccceecCHHHHHHHHHHHHHhcCCCeEEEecCCCccHHHHHHHHHhh--CcccCCCceeeeccccchHHHHHHHhccc
Confidence            46789999888777666554  223236999999999999999999986  4445677889998742211   1111111


Q ss_pred             HHHH-----hhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhc-----------cCCceEEEEecCC-------CcC
Q psy879           83 KMFA-----QQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIY-----------SNTTRFALACNNS-------EKI  139 (317)
Q Consensus        83 ~~~~-----~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~-----------~~~~~~il~~~~~-------~~l  139 (317)
                      +..+     +.+..+-.+++..+++||+.-|....|..|++.+.+.           .-.+++|.+||..       .++
T Consensus       299 KGAFTGA~~~r~GrFElAdGGTLFLDEIGelPL~lQaKLLRvLQegEieRvG~~r~ikVDVRiIAATNRDL~~~V~~G~F  378 (550)
T COG3604         299 KGAFTGAINTRRGRFELADGGTLFLDEIGELPLALQAKLLRVLQEGEIERVGGDRTIKVDVRVIAATNRDLEEMVRDGEF  378 (550)
T ss_pred             ccccccchhccCcceeecCCCeEechhhccCCHHHHHHHHHHHhhcceeecCCCceeEEEEEEEeccchhHHHHHHcCcc
Confidence            1111     1111122257889999999999999999999999843           2356689999975       245


Q ss_pred             chhHhhhcce--eeecCCCH--HH---HHH-HHHHHHHHcC---CCCCHHHHHHHHHh-cCCCHHHHHHHHHHhhh
Q psy879          140 IEPIQSRCAM--LRYNKLTD--AQ---LLS-KVIEICEKEN---ISHTNDGLEAIVFT-AQGDMRQALNNLQSTHN  203 (317)
Q Consensus       140 ~~~i~sR~~~--i~f~~~~~--~~---~~~-~l~~~~~~~~---~~i~~~~~~~l~~~-~~gd~r~~i~~l~~~~~  203 (317)
                      -..+--|..+  +..||+-+  ++   +.. ++++.....|   +.+++++++.+.+. ..||.|...|.++.++.
T Consensus       379 RaDLYyRLsV~Pl~lPPLRER~~DIplLA~~Fle~~~~~~gr~~l~ls~~Al~~L~~y~wPGNVRELen~veRavl  454 (550)
T COG3604         379 RADLYYRLSVFPLELPPLRERPEDIPLLAGYFLEKFRRRLGRAILSLSAEALELLSSYEWPGNVRELENVVERAVL  454 (550)
T ss_pred             hhhhhhcccccccCCCCcccCCccHHHHHHHHHHHHHHhcCCcccccCHHHHHHHHcCCCCCcHHHHHHHHHHHHH
Confidence            5666666666  44455432  12   222 3334334334   46899999998876 68999999999987665

>KOG0735|consensus

Probab=99.15  E-value=1.8e-09  Score=99.48  Aligned_cols=188  Identities=16%  Similarity=0.196  Sum_probs=121.7

Q ss_pred             ceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCC--CcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCC
Q psy879           32 PNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASN--DRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMT  109 (317)
Q Consensus        32 ~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~--~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~  109 (317)
                      +|++++||+|+|||.+++++++++. ...-..+..++|+.  ....+.+...+..+......   ..+.||++|+.|.+.
T Consensus       432 ~~Ill~G~~GsGKT~L~kal~~~~~-k~~~~hv~~v~Cs~l~~~~~e~iQk~l~~vfse~~~---~~PSiIvLDdld~l~  507 (952)
T KOG0735|consen  432 GNILLNGPKGSGKTNLVKALFDYYS-KDLIAHVEIVSCSTLDGSSLEKIQKFLNNVFSEALW---YAPSIIVLDDLDCLA  507 (952)
T ss_pred             ccEEEeCCCCCCHhHHHHHHHHHhc-cccceEEEEEechhccchhHHHHHHHHHHHHHHHHh---hCCcEEEEcchhhhh
Confidence            4699999999999999999999975 33333344445543  34455565555554443322   368899999999885


Q ss_pred             HH-------------HHHHHH-HHhhh---ccCCceEEEEecCCCcCchhHhhh--cce-eeecCCCHHHHHHHHHHHHH
Q psy879          110 DG-------------AQQALR-RTMEI---YSNTTRFALACNNSEKIIEPIQSR--CAM-LRYNKLTDAQLLSKVIEICE  169 (317)
Q Consensus       110 ~~-------------~~~~ll-~~le~---~~~~~~~il~~~~~~~l~~~i~sR--~~~-i~f~~~~~~~~~~~l~~~~~  169 (317)
                      ..             ..+.++ +.+..   ....+.+|.+.+....+.+.+.|-  ++. +.+++|...+...+|...+.
T Consensus       508 ~~s~~e~~q~~~~~~rla~flnqvi~~y~~~~~~ia~Iat~qe~qtl~~~L~s~~~Fq~~~~L~ap~~~~R~~IL~~~~s  587 (952)
T KOG0735|consen  508 SASSNENGQDGVVSERLAAFLNQVIKIYLKRNRKIAVIATGQELQTLNPLLVSPLLFQIVIALPAPAVTRRKEILTTIFS  587 (952)
T ss_pred             ccCcccCCcchHHHHHHHHHHHHHHHHHHccCcEEEEEEechhhhhcChhhcCccceEEEEecCCcchhHHHHHHHHHHH
Confidence            41             112222 33332   233345666677777777777654  443 88999999999999999998


Q ss_pred             HcCCCCCHHHHHHHHHhcCCC-HHHHHHHHHH---------hhhCCCcccHHHHHhhcCCCCHH
Q psy879          170 KENISHTNDGLEAIVFTAQGD-MRQALNNLQS---------THNGFGHVTAEYVFKVCDEPHPL  223 (317)
Q Consensus       170 ~~~~~i~~~~~~~l~~~~~gd-~r~~i~~l~~---------~~~~~~~i~~~~v~~~~~~~~~~  223 (317)
                      +.......+.++.++..++|- ++...-..++         .....+.++.+++.+.+....+.
T Consensus       588 ~~~~~~~~~dLd~ls~~TEGy~~~DL~ifVeRai~~a~leris~~~klltke~f~ksL~~F~P~  651 (952)
T KOG0735|consen  588 KNLSDITMDDLDFLSVKTEGYLATDLVIFVERAIHEAFLERISNGPKLLTKELFEKSLKDFVPL  651 (952)
T ss_pred             hhhhhhhhHHHHHHHHhcCCccchhHHHHHHHHHHHHHHHHhccCcccchHHHHHHHHHhcChH
Confidence            877666677788888888773 3333333333         22244567777777766655543

>PRK12377 putative replication protein; Provisional

Probab=99.15  E-value=3.3e-10  Score=94.99  Aligned_cols=140  Identities=17%  Similarity=0.256  Sum_probs=80.6

Q ss_pred             cCCCCCCccc----CCHHHHHHHHHHHhc--CCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHH
Q psy879            4 YRPQTFSDIV----GNEDTVERLKVFSSS--GNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDT   77 (317)
Q Consensus         4 y~P~~~~~~~----g~~~~~~~l~~~l~~--~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~   77 (317)
                      ++-.+|+.+.    |+.+++.....++.+  ....+++|+||||||||+++.++++.+......  +..+...+  -...
T Consensus        68 ~~~~tFdnf~~~~~~~~~a~~~a~~~a~~~~~~~~~l~l~G~~GtGKThLa~AIa~~l~~~g~~--v~~i~~~~--l~~~  143 (248)
T PRK12377         68 HRKCSFANYQVQNDGQRYALSQAKSIADELMTGCTNFVFSGKPGTGKNHLAAAIGNRLLAKGRS--VIVVTVPD--VMSR  143 (248)
T ss_pred             cccCCcCCcccCChhHHHHHHHHHHHHHHHHhcCCeEEEECCCCCCHHHHHHHHHHHHHHcCCC--eEEEEHHH--HHHH
Confidence            4455788886    344455554444432  123469999999999999999999998644322  33332211  0111


Q ss_pred             HHHHHHHH-HhhcccCCCCceeEEEEeCCC--CCCHHHHHHHHHHhhhccC-CceEEEEecCCC-----cCchhHhhhc
Q psy879           78 VRNKIKMF-AQQKVTLPPGRHKIVILDEAD--SMTDGAQQALRRTMEIYSN-TTRFALACNNSE-----KIIEPIQSRC  147 (317)
Q Consensus        78 i~~~~~~~-~~~~~~~~~~~~~vliiDE~d--~l~~~~~~~ll~~le~~~~-~~~~il~~~~~~-----~l~~~i~sR~  147 (317)
                      +......- ......-......+|||||++  ..+...+..|..+++..-. ....|++||...     .+.+.+.||.
T Consensus       144 l~~~~~~~~~~~~~l~~l~~~dLLiIDDlg~~~~s~~~~~~l~~ii~~R~~~~~ptiitSNl~~~~l~~~~~~ri~dRl  222 (248)
T PRK12377        144 LHESYDNGQSGEKFLQELCKVDLLVLDEIGIQRETKNEQVVLNQIIDRRTASMRSVGMLTNLNHEAMSTLLGERVMDRM  222 (248)
T ss_pred             HHHHHhccchHHHHHHHhcCCCEEEEcCCCCCCCCHHHHHHHHHHHHHHHhcCCCEEEEcCCCHHHHHHHhhHHHHHHH
Confidence            11110000 000000001467799999995  5577788899999986544 466788888642     2334455554

>PRK08181 transposase; Validated

Probab=99.15  E-value=1.9e-10  Score=97.64  Aligned_cols=105  Identities=17%  Similarity=0.306  Sum_probs=65.4

Q ss_pred             HHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHHHHHHHhhc----ccCCCCce
Q psy879           22 LKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFAQQK----VTLPPGRH   97 (317)
Q Consensus        22 l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~----~~~~~~~~   97 (317)
                      ...++.++.  +++|+||||+|||+++.+++..+...+.  .+..+...      .+.+.+.......    ........
T Consensus        99 ~~~~~~~~~--nlll~Gp~GtGKTHLa~Aia~~a~~~g~--~v~f~~~~------~L~~~l~~a~~~~~~~~~l~~l~~~  168 (269)
T PRK08181         99 GDSWLAKGA--NLLLFGPPGGGKSHLAAAIGLALIENGW--RVLFTRTT------DLVQKLQVARRELQLESAIAKLDKF  168 (269)
T ss_pred             HHHHHhcCc--eEEEEecCCCcHHHHHHHHHHHHHHcCC--ceeeeeHH------HHHHHHHHHHhCCcHHHHHHHHhcC
Confidence            345777665  7999999999999999999998754332  23333221      1111111100000    00001356


Q ss_pred             eEEEEeCCCCCC--HHHHHHHHHHhhhccCCceEEEEecCC
Q psy879           98 KIVILDEADSMT--DGAQQALRRTMEIYSNTTRFALACNNS  136 (317)
Q Consensus        98 ~vliiDE~d~l~--~~~~~~ll~~le~~~~~~~~il~~~~~  136 (317)
                      .++||||++...  ...+..|+++++.......+|++||.+
T Consensus       169 dLLIIDDlg~~~~~~~~~~~Lf~lin~R~~~~s~IiTSN~~  209 (269)
T PRK08181        169 DLLILDDLAYVTKDQAETSVLFELISARYERRSILITANQP  209 (269)
T ss_pred             CEEEEeccccccCCHHHHHHHHHHHHHHHhCCCEEEEcCCC
Confidence            799999998774  445678899988655556789998875

>TIGR01818 ntrC nitrogen regulation protein NR(I)

Probab=99.15  E-value=3.1e-09  Score=98.62  Aligned_cols=202  Identities=16%  Similarity=0.161  Sum_probs=131.5

Q ss_pred             CcccCCHHHHHHHHHHHhc--CCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHHH-HHH-
Q psy879           10 SDIVGNEDTVERLKVFSSS--GNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKI-KMF-   85 (317)
Q Consensus        10 ~~~~g~~~~~~~l~~~l~~--~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~-~~~-   85 (317)
                      ..++|.......+...+..  +...++++.|++||||+++++++...-  .....+++.++|... ..+.+...+ +.. 
T Consensus       134 ~~lig~s~~~~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~ih~~~--~~~~~~~~~~~c~~~-~~~~~~~~lfg~~~  210 (463)
T TIGR01818       134 AELIGEAPAMQEVFRAIGRLSRSDITVLINGESGTGKELVARALHRHS--PRANGPFIALNMAAI-PKDLIESELFGHEK  210 (463)
T ss_pred             cceeecCHHHHHHHHHHHHHhCcCCeEEEECCCCCCHHHHHHHHHHhC--CCCCCCeEEEeCCCC-CHHHHHHHhcCCCC
Confidence            4567765544444333321  222358999999999999999998863  223456777877643 223332222 100 


Q ss_pred             ---H----hhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhcc-----------CCceEEEEecCC-------CcCc
Q psy879           86 ---A----QQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYS-----------NTTRFALACNNS-------EKII  140 (317)
Q Consensus        86 ---~----~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~-----------~~~~~il~~~~~-------~~l~  140 (317)
                         .    .....+..+....++|||++.|..+.|..|++++++..           .++++|++++..       ..+.
T Consensus       211 ~~~~~~~~~~~g~~~~a~~gtl~l~ei~~l~~~~q~~ll~~l~~~~~~~~~~~~~~~~~~rii~~~~~~l~~~~~~~~f~  290 (463)
T TIGR01818       211 GAFTGANTRRQGRFEQADGGTLFLDEIGDMPLDAQTRLLRVLADGEFYRVGGRTPIKVDVRIVAATHQNLEALVRQGKFR  290 (463)
T ss_pred             CCCCCcccCCCCcEEECCCCeEEEEchhhCCHHHHHHHHHHHhcCcEEECCCCceeeeeeEEEEeCCCCHHHHHHcCCcH
Confidence               0    00000112346789999999999999999999998532           245788888764       2456


Q ss_pred             hhHhhhcce--eeecCCC--HHHHHHHHHHH----HHHcC---CCCCHHHHHHHHHh-cCCCHHHHHHHHHHhhh--CCC
Q psy879          141 EPIQSRCAM--LRYNKLT--DAQLLSKVIEI----CEKEN---ISHTNDGLEAIVFT-AQGDMRQALNNLQSTHN--GFG  206 (317)
Q Consensus       141 ~~i~sR~~~--i~f~~~~--~~~~~~~l~~~----~~~~~---~~i~~~~~~~l~~~-~~gd~r~~i~~l~~~~~--~~~  206 (317)
                      +.+..|+..  ++.||+.  .+++..++...    +...+   ..++++++..+... ..||+|+.-+.++.++.  ...
T Consensus       291 ~~L~~rl~~~~i~lPpLr~R~~Di~~l~~~~l~~~~~~~~~~~~~~~~~a~~~L~~~~wpgNvreL~~~~~~~~~~~~~~  370 (463)
T TIGR01818       291 EDLFHRLNVIRIHLPPLRERREDIPRLARHFLALAARELDVEPKLLDPEALERLKQLRWPGNVRQLENLCRWLTVMASGD  370 (463)
T ss_pred             HHHHHHhCcceecCCCcccchhhHHHHHHHHHHHHHHHhCCCCCCcCHHHHHHHHhCCCCChHHHHHHHHHHHHHhCCCC
Confidence            688888764  7788887  45666655543    33333   46889999988876 58999999999988665  345


Q ss_pred             cccHHHHH
Q psy879          207 HVTAEYVF  214 (317)
Q Consensus       207 ~i~~~~v~  214 (317)
                      .|+.+++.
T Consensus       371 ~i~~~~l~  378 (463)
T TIGR01818       371 EVLVSDLP  378 (463)
T ss_pred             cccHHhch
Confidence            67777654

This model represents NtrC, a DNA-binding response regulator that is phosphorylated by NtrB and interacts with sigma-54. NtrC usually controls the expression of glutamine synthase, GlnA, and may be called GlnL, GlnG, etc.

>PRK15115 response regulator GlrR; Provisional

Probab=99.14  E-value=4e-09  Score=97.29  Aligned_cols=181  Identities=15%  Similarity=0.219  Sum_probs=117.8

Q ss_pred             ceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHHHHHHHhh---------cccCCCCceeEEEE
Q psy879           32 PNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFAQQ---------KVTLPPGRHKIVIL  102 (317)
Q Consensus        32 ~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~---------~~~~~~~~~~vlii  102 (317)
                      ++++++|++|+||+++|+.+.+.-  ...+.+++.++|... ....+...+......         ...+.....++++|
T Consensus       158 ~~vli~Ge~GtGk~~lA~~ih~~s--~r~~~~f~~i~c~~~-~~~~~~~~lfg~~~~~~~~~~~~~~g~~~~a~~gtl~l  234 (444)
T PRK15115        158 VSVLINGQSGTGKEILAQAIHNAS--PRASKPFIAINCGAL-PEQLLESELFGHARGAFTGAVSNREGLFQAAEGGTLFL  234 (444)
T ss_pred             CeEEEEcCCcchHHHHHHHHHHhc--CCCCCCeEEEeCCCC-CHHHHHHHhcCCCcCCCCCCccCCCCcEEECCCCEEEE
Confidence            359999999999999999998863  223456788887643 222222211100000         00111245679999


Q ss_pred             eCCCCCCHHHHHHHHHHhhhcc-----------CCceEEEEecCC-------CcCchhHhhhcce--eeecCCCH--HHH
Q psy879          103 DEADSMTDGAQQALRRTMEIYS-----------NTTRFALACNNS-------EKIIEPIQSRCAM--LRYNKLTD--AQL  160 (317)
Q Consensus       103 DE~d~l~~~~~~~ll~~le~~~-----------~~~~~il~~~~~-------~~l~~~i~sR~~~--i~f~~~~~--~~~  160 (317)
                      ||++.|....|..|++++++..           .++++|++|+..       ..+.+.+..|+..  +..||+.+  +++
T Consensus       235 ~~i~~l~~~~q~~L~~~l~~~~~~~~g~~~~~~~~~rii~~~~~~l~~~~~~~~f~~~l~~~l~~~~i~lPpLr~R~eDi  314 (444)
T PRK15115        235 DEIGDMPAPLQVKLLRVLQERKVRPLGSNRDIDIDVRIISATHRDLPKAMARGEFREDLYYRLNVVSLKIPALAERTEDI  314 (444)
T ss_pred             EccccCCHHHHHHHHHHHhhCCEEeCCCCceeeeeEEEEEeCCCCHHHHHHcCCccHHHHHhhceeeecCCChHhccccH
Confidence            9999999999999999998532           245788887753       1344555556554  56666654  344


Q ss_pred             HHHHH----HHHHHcC---CCCCHHHHHHHHHhc-CCCHHHHHHHHHHhhh--CCCcccHHHHHh
Q psy879          161 LSKVI----EICEKEN---ISHTNDGLEAIVFTA-QGDMRQALNNLQSTHN--GFGHVTAEYVFK  215 (317)
Q Consensus       161 ~~~l~----~~~~~~~---~~i~~~~~~~l~~~~-~gd~r~~i~~l~~~~~--~~~~i~~~~v~~  215 (317)
                      ..++.    ..+...+   ..+++++++.+.... .||+|+..+.++.++.  ....|+.+++..
T Consensus       315 ~~l~~~~l~~~~~~~~~~~~~~~~~a~~~L~~~~WpgNvreL~~~i~~~~~~~~~~~i~~~~l~~  379 (444)
T PRK15115        315 PLLANHLLRQAAERHKPFVRAFSTDAMKRLMTASWPGNVRQLVNVIEQCVALTSSPVISDALVEQ  379 (444)
T ss_pred             HHHHHHHHHHHHHHhCCCCCCcCHHHHHHHHhCCCCChHHHHHHHHHHHHHhCCCCccChhhhhh
Confidence            43333    3333333   247999999998886 9999999999998654  445677776643

>PRK11361 acetoacetate metabolism regulatory protein AtoC; Provisional

Probab=99.13  E-value=2.9e-09  Score=98.65  Aligned_cols=203  Identities=15%  Similarity=0.127  Sum_probs=126.5

Q ss_pred             CCcccCCHHHHHHHHHHHhc--CCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHHH-HHH
Q psy879            9 FSDIVGNEDTVERLKVFSSS--GNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKI-KMF   85 (317)
Q Consensus         9 ~~~~~g~~~~~~~l~~~l~~--~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~-~~~   85 (317)
                      +..++|.......+...+..  ....+++++|++|+||+++|+++....  .....+++.++|... ....+...+ +..
T Consensus       142 ~~~ii~~S~~~~~~~~~~~~~a~~~~~vli~Ge~GtGK~~lA~~ih~~s--~~~~~~~~~i~c~~~-~~~~~~~~lfg~~  218 (457)
T PRK11361        142 WGHILTNSPAMMDICKDTAKIALSQASVLISGESGTGKELIARAIHYNS--RRAKGPFIKVNCAAL-PESLLESELFGHE  218 (457)
T ss_pred             ccceecccHHHhHHHHHHHHHcCCCcEEEEEcCCCccHHHHHHHHHHhC--CCCCCCeEEEECCCC-CHHHHHHHhcCCC
Confidence            34566665444443333321  122369999999999999999998753  223456777777643 222222211 100


Q ss_pred             H----h----hcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhcc-----------CCceEEEEecCC-------CcC
Q psy879           86 A----Q----QKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYS-----------NTTRFALACNNS-------EKI  139 (317)
Q Consensus        86 ~----~----~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~-----------~~~~~il~~~~~-------~~l  139 (317)
                      .    .    ....+......+++|||++.|....|..|++++++..           .++++|++++..       ..+
T Consensus       219 ~~~~~~~~~~~~g~~~~a~~gtl~ld~i~~l~~~~q~~L~~~l~~~~~~~~~~~~~~~~~~rii~~t~~~l~~~~~~g~~  298 (457)
T PRK11361        219 KGAFTGAQTLRQGLFERANEGTLLLDEIGEMPLVLQAKLLRILQEREFERIGGHQTIKVDIRIIAATNRDLQAMVKEGTF  298 (457)
T ss_pred             CCCCCCCCCCCCCceEECCCCEEEEechhhCCHHHHHHHHHHHhcCcEEeCCCCceeeeceEEEEeCCCCHHHHHHcCCc
Confidence            0    0    0001112456899999999999999999999998531           346788888764       245


Q ss_pred             chhHhhhcce--eeecCCCH--HHHHHH----HHHHHHHcC---CCCCHHHHHHHHHh-cCCCHHHHHHHHHHhhh--CC
Q psy879          140 IEPIQSRCAM--LRYNKLTD--AQLLSK----VIEICEKEN---ISHTNDGLEAIVFT-AQGDMRQALNNLQSTHN--GF  205 (317)
Q Consensus       140 ~~~i~sR~~~--i~f~~~~~--~~~~~~----l~~~~~~~~---~~i~~~~~~~l~~~-~~gd~r~~i~~l~~~~~--~~  205 (317)
                      .+.+-.|+..  +..+|+.+  +++..+    +.+.....+   ..+++++++.+... ..||+|+..+.++.++.  ..
T Consensus       299 ~~~l~~~l~~~~i~~ppLreR~~di~~l~~~~l~~~~~~~~~~~~~~~~~a~~~L~~~~wpgNv~eL~~~~~~~~~~~~~  378 (457)
T PRK11361        299 REDLFYRLNVIHLILPPLRDRREDISLLANHFLQKFSSENQRDIIDIDPMAMSLLTAWSWPGNIRELSNVIERAVVMNSG  378 (457)
T ss_pred             hHHHHHHhccceecCCChhhchhhHHHHHHHHHHHHHHHcCCCCCCcCHHHHHHHHcCCCCCcHHHHHHHHHHHHHhCCC
Confidence            5666666655  56666653  344433    333333222   35889999888876 58999999999987664  34


Q ss_pred             CcccHHHHH
Q psy879          206 GHVTAEYVF  214 (317)
Q Consensus       206 ~~i~~~~v~  214 (317)
                      ..|+.+++.
T Consensus       379 ~~i~~~~l~  387 (457)
T PRK11361        379 PIIFSEDLP  387 (457)
T ss_pred             CcccHHHCh
Confidence            467776654

>KOG2170|consensus

Probab=99.12  E-value=2.1e-09  Score=89.81  Aligned_cols=124  Identities=19%  Similarity=0.308  Sum_probs=82.1

Q ss_pred             ccCCHHHHHH----HHHHHhcCCC--ce-EEEECCCCCCHHHHHHHHHHHHcCCCCCCceEE-----ecCCCCcChHHHH
Q psy879           12 IVGNEDTVER----LKVFSSSGNV--PN-IIISGPPGVGKTTTILCLARILLGPSFKDAVLE-----LNASNDRGIDTVR   79 (317)
Q Consensus        12 ~~g~~~~~~~----l~~~l~~~~~--~~-~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~-----~~~~~~~~~~~i~   79 (317)
                      +.||.-+++.    ++.++.++.+  |- +-|+|++||||+.+++.+|+.++......+++.     .+......++..+
T Consensus        84 lfGQHla~~~Vv~alk~~~~n~~p~KPLvLSfHG~tGTGKN~Va~iiA~n~~~~Gl~S~~V~~fvat~hFP~~~~ie~Yk  163 (344)
T KOG2170|consen   84 LFGQHLAKQLVVNALKSHWANPNPRKPLVLSFHGWTGTGKNYVAEIIAENLYRGGLRSPFVHHFVATLHFPHASKIEDYK  163 (344)
T ss_pred             hhchHHHHHHHHHHHHHHhcCCCCCCCeEEEecCCCCCchhHHHHHHHHHHHhccccchhHHHhhhhccCCChHHHHHHH
Confidence            4577655554    5555555553  22 789999999999999999999875543333321     1112223344444


Q ss_pred             HHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhcc-------CCceEEEEecCCC
Q psy879           80 NKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYS-------NTTRFALACNNSE  137 (317)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~-------~~~~~il~~~~~~  137 (317)
                      ..+.........  .....++|+||+|+|.+...++|..+++.++       .+++||+.+|...
T Consensus       164 ~eL~~~v~~~v~--~C~rslFIFDE~DKmp~gLld~lkpfLdyyp~v~gv~frkaIFIfLSN~gg  226 (344)
T KOG2170|consen  164 EELKNRVRGTVQ--ACQRSLFIFDEVDKLPPGLLDVLKPFLDYYPQVSGVDFRKAIFIFLSNAGG  226 (344)
T ss_pred             HHHHHHHHHHHH--hcCCceEEechhhhcCHhHHHHHhhhhccccccccccccceEEEEEcCCcc
Confidence            444433332221  2578899999999999999999999998543       4677999988653

>COG0606 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]

Probab=99.12  E-value=8.5e-11  Score=104.28  Aligned_cols=112  Identities=23%  Similarity=0.375  Sum_probs=71.8

Q ss_pred             CCCcccCCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEec------CCCCc--------
Q psy879            8 TFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELN------ASNDR--------   73 (317)
Q Consensus         8 ~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~------~~~~~--------   73 (317)
                      .|.|++||++.++.+.-+...|+  |++|+||||||||.+++.+...| .+-.....++.+      .....        
T Consensus       177 D~~DV~GQ~~AKrAleiAAAGgH--nLl~~GpPGtGKTmla~Rl~~lL-Ppls~~E~lE~s~I~s~~g~~~~~~~~~~~r  253 (490)
T COG0606         177 DFKDVKGQEQAKRALEIAAAGGH--NLLLVGPPGTGKTMLASRLPGLL-PPLSIPEALEVSAIHSLAGDLHEGCPLKIHR  253 (490)
T ss_pred             chhhhcCcHHHHHHHHHHHhcCC--cEEEecCCCCchHHhhhhhcccC-CCCChHHHHHHHHHhhhcccccccCccceeC
Confidence            68999999999999999998887  89999999999999999998765 221111111111      00000        


Q ss_pred             -----C-hHHHHHHHHHHH-hhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhh
Q psy879           74 -----G-IDTVRNKIKMFA-QQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEI  122 (317)
Q Consensus        74 -----~-~~~i~~~~~~~~-~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~  122 (317)
                           . .......++... -.+.....+.+.|+|+||...+.....++|..=||+
T Consensus       254 PFr~PHHsaS~~aLvGGG~~p~PGeIsLAH~GVLFLDElpef~~~iLe~LR~PLE~  309 (490)
T COG0606         254 PFRAPHHSASLAALVGGGGVPRPGEISLAHNGVLFLDELPEFKRSILEALREPLEN  309 (490)
T ss_pred             CccCCCccchHHHHhCCCCCCCCCceeeecCCEEEeeccchhhHHHHHHHhCcccc
Confidence                 0 000011111110 000011124688999999999999888888888883

>COG3283 TyrR Transcriptional regulator of aromatic amino acids metabolism [Transcription / Amino acid transport and metabolism]

Probab=99.12  E-value=2e-08  Score=85.92  Aligned_cols=204  Identities=18%  Similarity=0.147  Sum_probs=133.9

Q ss_pred             CCcccCCHHHHHHHHHHHhcCC--CceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHHHHHHH
Q psy879            9 FSDIVGNEDTVERLKVFSSSGN--VPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFA   86 (317)
Q Consensus         9 ~~~~~g~~~~~~~l~~~l~~~~--~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~   86 (317)
                      |+.+++.....+.+....++-.  -..+||.|+.||||..+|++.-..  .+....+++-+||........-.+.++...
T Consensus       203 F~~~v~~S~~mk~~v~qA~k~AmlDAPLLI~GeTGTGKdLlAkaCH~~--S~R~~~pFlalNCA~lPe~~aEsElFG~ap  280 (511)
T COG3283         203 FEQIVAVSPKMKHVVEQAQKLAMLDAPLLITGETGTGKDLLAKACHLA--SPRHSKPFLALNCASLPEDAAESELFGHAP  280 (511)
T ss_pred             hHHHhhccHHHHHHHHHHHHhhccCCCeEEecCCCchHHHHHHHHhhc--CcccCCCeeEeecCCCchhHhHHHHhcCCC
Confidence            7888887766666554443322  124999999999999999987754  455677889999875332222222333222


Q ss_pred             h---hcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhh-----------ccCCceEEEEecCC-------CcCchhHhh
Q psy879           87 Q---QKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEI-----------YSNTTRFALACNNS-------EKIIEPIQS  145 (317)
Q Consensus        87 ~---~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~-----------~~~~~~~il~~~~~-------~~l~~~i~s  145 (317)
                      .   ....+-.+....|++||+.-|++..|..|++++..           ..-++++|++|..+       .++-..+--
T Consensus       281 g~~gk~GffE~AngGTVlLDeIgEmSp~lQaKLLRFL~DGtFRRVGee~Ev~vdVRVIcatq~nL~~lv~~g~fReDLfy  360 (511)
T COG3283         281 GDEGKKGFFEQANGGTVLLDEIGEMSPRLQAKLLRFLNDGTFRRVGEDHEVHVDVRVICATQVNLVELVQKGKFREDLFY  360 (511)
T ss_pred             CCCCccchhhhccCCeEEeehhhhcCHHHHHHHHHHhcCCceeecCCcceEEEEEEEEecccccHHHHHhcCchHHHHHH
Confidence            1   01111224678999999999999999999999973           23467788888765       245566667


Q ss_pred             hcce--eeecCCCH--HH----HHHHHHHHHHHcCC---CCCHHHHHHHHHh-cCCCHHHHHHHHHHhhh--CCCcccHH
Q psy879          146 RCAM--LRYNKLTD--AQ----LLSKVIEICEKENI---SHTNDGLEAIVFT-AQGDMRQALNNLQSTHN--GFGHVTAE  211 (317)
Q Consensus       146 R~~~--i~f~~~~~--~~----~~~~l~~~~~~~~~---~i~~~~~~~l~~~-~~gd~r~~i~~l~~~~~--~~~~i~~~  211 (317)
                      |..+  ++.||+-+  ++    ..-++.+.+.+.|+   +++++.+.++.+. ..|++|+.-|.+-.++.  ....++.+
T Consensus       361 RLNVLtl~~PpLRer~~di~pL~e~Fv~q~s~elg~p~pkl~~~~~~~L~~y~WpGNVRqL~N~iyRA~s~~Eg~~l~i~  440 (511)
T COG3283         361 RLNVLTLNLPPLRERPQDIMPLAELFVQQFSDELGVPRPKLAADLLTVLTRYAWPGNVRQLKNAIYRALTLLEGYELRIE  440 (511)
T ss_pred             HhheeeecCCccccCcccchHHHHHHHHHHHHHhCCCCCccCHHHHHHHHHcCCCccHHHHHHHHHHHHHHhccCccchh
Confidence            7766  55555533  12    23345566666565   4567777777654 68999999999976654  45556666


Q ss_pred             HHH
Q psy879          212 YVF  214 (317)
Q Consensus       212 ~v~  214 (317)
                      ++.
T Consensus       441 ~i~  443 (511)
T COG3283         441 DIL  443 (511)
T ss_pred             hcc
Confidence            553

>PTZ00111 DNA replication licensing factor MCM4; Provisional

Probab=99.09  E-value=1e-09  Score=105.42  Aligned_cols=145  Identities=16%  Similarity=0.180  Sum_probs=90.7

Q ss_pred             cccCCHHHHHHHHHHHhcCC---------------------CceEEEECCCCCCHHHHHHHHHHHHcCCC--CCCceEEe
Q psy879           11 DIVGNEDTVERLKVFSSSGN---------------------VPNIIISGPPGVGKTTTILCLARILLGPS--FKDAVLEL   67 (317)
Q Consensus        11 ~~~g~~~~~~~l~~~l~~~~---------------------~~~~ll~G~~G~GKt~la~~la~~l~~~~--~~~~~~~~   67 (317)
                      .+.|++.+++.+.-.+-+|.                     -.|+||.|+||||||++++++++.-....  .+..+..+
T Consensus       451 ~I~G~e~vK~ailL~L~gG~~k~~~~~~~~dg~~~~~~iRgdihVLLvGDPGTGKSqLAr~Ih~lspR~~ytsG~~~s~v  530 (915)
T PTZ00111        451 SIKARNNVKIGLLCQLFSGNKNSSDFNKSPDACYKVDNFRGIINVLLCGDPGTAKSQLLHYTHLLSPRSIYTSGKSSSSV  530 (915)
T ss_pred             eEECCHHHHHHHHHHHhcCCccccccccccccccccccccCCceEEEeCCCCccHHHHHHHHHHhCCccccCCCCCCccc
Confidence            57799999888765554432                     12799999999999999999998531100  00111111


Q ss_pred             cCCCCcChHHHHHH-HHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhc-------------cCCceEEEEe
Q psy879           68 NASNDRGIDTVRNK-IKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIY-------------SNTTRFALAC  133 (317)
Q Consensus        68 ~~~~~~~~~~i~~~-~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~-------------~~~~~~il~~  133 (317)
                      ++...   ....+. -+.+...+..+..+...+++|||++.|....|.+|++.||+.             +..+.+|.++
T Consensus       531 gLTa~---~~~~d~~tG~~~le~GaLvlAdgGtL~IDEidkms~~~Q~aLlEaMEqqtIsI~KaGi~~tL~ar~rVIAAa  607 (915)
T PTZ00111        531 GLTAS---IKFNESDNGRAMIQPGAVVLANGGVCCIDELDKCHNESRLSLYEVMEQQTVTIAKAGIVATLKAETAILASC  607 (915)
T ss_pred             cccch---hhhcccccCcccccCCcEEEcCCCeEEecchhhCCHHHHHHHHHHHhCCEEEEecCCcceecCCCeEEEEEc
Confidence            11110   000000 011111111222356789999999999999999999999853             2467788888


Q ss_pred             cCCC-------------cCchhHhhhcce--eeecCCCHH
Q psy879          134 NNSE-------------KIIEPIQSRCAM--LRYNKLTDA  158 (317)
Q Consensus       134 ~~~~-------------~l~~~i~sR~~~--i~f~~~~~~  158 (317)
                      |+..             .+++++.|||..  +-...++++
T Consensus       608 NP~~gryd~~~s~~eni~Lp~~LLSRFDLIf~l~D~~d~~  647 (915)
T PTZ00111        608 NPINSRYNKNKAVIENINISPSLFTRFDLIYLVLDHIDQD  647 (915)
T ss_pred             CCcccccCcccCcccccCCChHHhhhhcEEEEecCCCChH
Confidence            8742             478999999966  444555544

>PRK07952 DNA replication protein DnaC; Validated

Probab=99.09  E-value=1.1e-09  Score=91.62  Aligned_cols=146  Identities=14%  Similarity=0.237  Sum_probs=86.9

Q ss_pred             cccCCCCCCcccC----CHHHHHHHHHHHhcC--CCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcCh
Q psy879            2 EKYRPQTFSDIVG----NEDTVERLKVFSSSG--NVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGI   75 (317)
Q Consensus         2 ~ky~P~~~~~~~g----~~~~~~~l~~~l~~~--~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~   75 (317)
                      +.|++.+|+.+..    +..++..+..++++-  ...+++|+|++|+|||+++.+++..+....  ..+..+...+.  .
T Consensus        64 ~~~~~~tFdnf~~~~~~q~~al~~a~~~~~~~~~~~~~~~l~G~~GtGKThLa~aia~~l~~~g--~~v~~it~~~l--~  139 (244)
T PRK07952         64 PLHQNCSFENYRVECEGQMNALSKARQYVEEFDGNIASFIFSGKPGTGKNHLAAAICNELLLRG--KSVLIITVADI--M  139 (244)
T ss_pred             ccccCCccccccCCCchHHHHHHHHHHHHHhhccCCceEEEECCCCCCHHHHHHHHHHHHHhcC--CeEEEEEHHHH--H
Confidence            4677888998863    344666666666532  223699999999999999999999985433  22333322110  0


Q ss_pred             HHHHHHH-------HHHHhhcccCCCCceeEEEEeCCCCCCH--HHHHHHHHHhhhc-cCCceEEEEecCCC-----cCc
Q psy879           76 DTVRNKI-------KMFAQQKVTLPPGRHKIVILDEADSMTD--GAQQALRRTMEIY-SNTTRFALACNNSE-----KII  140 (317)
Q Consensus        76 ~~i~~~~-------~~~~~~~~~~~~~~~~vliiDE~d~l~~--~~~~~ll~~le~~-~~~~~~il~~~~~~-----~l~  140 (317)
                      ..++...       ..+...     .....+|||||++....  -....|..+++.. .....+|++||...     .+.
T Consensus       140 ~~l~~~~~~~~~~~~~~l~~-----l~~~dlLvIDDig~~~~s~~~~~~l~~Ii~~Ry~~~~~tiitSNl~~~~l~~~~g  214 (244)
T PRK07952        140 SAMKDTFSNSETSEEQLLND-----LSNVDLLVIDEIGVQTESRYEKVIINQIVDRRSSSKRPTGMLTNSNMEEMTKLLG  214 (244)
T ss_pred             HHHHHHHhhccccHHHHHHH-----hccCCEEEEeCCCCCCCCHHHHHHHHHHHHHHHhCCCCEEEeCCCCHHHHHHHhC
Confidence            1111100       000000     13567999999987643  3455677788753 34567888888653     344


Q ss_pred             hhHhhhcc-----eeeecCCC
Q psy879          141 EPIQSRCA-----MLRYNKLT  156 (317)
Q Consensus       141 ~~i~sR~~-----~i~f~~~~  156 (317)
                      +.+.||+.     .+.|.-.|
T Consensus       215 ~ri~sRl~~~~~~~i~f~~~s  235 (244)
T PRK07952        215 ERVMDRMRLGNSLWVIFNWDS  235 (244)
T ss_pred             hHHHHHHHHCCceEEEeeCCc
Confidence            55666653     36666443

>COG1219 ClpX ATP-dependent protease Clp, ATPase subunit [Posttranslational modification, protein turnover, chaperones]

Probab=99.08  E-value=1.7e-09  Score=90.89  Aligned_cols=105  Identities=29%  Similarity=0.387  Sum_probs=67.1

Q ss_pred             cccCCHHHHHHHHHHH-------hc----C----CCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCC----
Q psy879           11 DIVGNEDTVERLKVFS-------SS----G----NVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASN----   71 (317)
Q Consensus        11 ~~~g~~~~~~~l~~~l-------~~----~----~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~----   71 (317)
                      .++||+.+++.|.-++       ..    .    .-+|+|+.||.|||||.+|+.+|+.|.     .++---++..    
T Consensus        62 YVIGQe~AKKvLsVAVYNHYKRl~~~~~~~dvEL~KSNILLiGPTGsGKTlLAqTLAk~Ln-----VPFaiADATtLTEA  136 (408)
T COG1219          62 YVIGQEQAKKVLSVAVYNHYKRLNNKEDNDDVELSKSNILLIGPTGSGKTLLAQTLAKILN-----VPFAIADATTLTEA  136 (408)
T ss_pred             heecchhhhceeeeeehhHHHHHhccCCCCceeeeeccEEEECCCCCcHHHHHHHHHHHhC-----CCeeeccccchhhc
Confidence            4678888877653322       11    1    114699999999999999999999973     2233222221    


Q ss_pred             -CcChHHHHHHHHHHHhhcc-cCCCCceeEEEEeCCCCCCHH--------------HHHHHHHHhh
Q psy879           72 -DRGIDTVRNKIKMFAQQKV-TLPPGRHKIVILDEADSMTDG--------------AQQALRRTME  121 (317)
Q Consensus        72 -~~~~~~i~~~~~~~~~~~~-~~~~~~~~vliiDE~d~l~~~--------------~~~~ll~~le  121 (317)
                       ..+ +++.+.+-...+..- ....+.+.+++|||+|++.+.              .|.+|++++|
T Consensus       137 GYVG-EDVENillkLlqaadydV~rAerGIIyIDEIDKIarkSeN~SITRDVSGEGVQQALLKiiE  201 (408)
T COG1219         137 GYVG-EDVENILLKLLQAADYDVERAERGIIYIDEIDKIARKSENPSITRDVSGEGVQQALLKIIE  201 (408)
T ss_pred             cccc-hhHHHHHHHHHHHcccCHHHHhCCeEEEechhhhhccCCCCCcccccCchHHHHHHHHHHc
Confidence             112 334454444444321 112257899999999988542              5999999999

>COG1239 ChlI Mg-chelatase subunit ChlI [Coenzyme metabolism]

Probab=99.08  E-value=6e-09  Score=91.41  Aligned_cols=162  Identities=17%  Similarity=0.147  Sum_probs=107.6

Q ss_pred             CCcccCCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCC----------CCc---------------
Q psy879            9 FSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSF----------KDA---------------   63 (317)
Q Consensus         9 ~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~----------~~~---------------   63 (317)
                      |.-++||+.....|....-.......||.|+.|+||||++++++..|-....          ..+               
T Consensus        16 f~aivGqd~lk~aL~l~av~P~iggvLI~G~kGtaKSt~~Rala~LLp~~~~V~gc~f~cdP~~P~~~c~~c~~k~~e~~   95 (423)
T COG1239          16 FTAIVGQDPLKLALGLNAVDPQIGGALIAGEKGTAKSTLARALADLLPEIEVVIGCPFNCDPDDPEEMCDECRAKGDELE   95 (423)
T ss_pred             hhhhcCchHHHHHHhhhhcccccceeEEecCCCccHHHHHHHHHHhCCccceecCCCCCCCCCChhhhhHHHHhhccccc
Confidence            6778999999888665555566667999999999999999999998732110          000               


Q ss_pred             ----------eEEecCCC----CcChHHHHHHHH--HHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhh-----
Q psy879           64 ----------VLELNASN----DRGIDTVRNKIK--MFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEI-----  122 (317)
Q Consensus        64 ----------~~~~~~~~----~~~~~~i~~~~~--~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~-----  122 (317)
                                ++......    ..+.-++...+.  .-..++..+..+.+.|++|||+..|....+++||..+++     
T Consensus        96 ~~~~~~r~v~~v~lPl~ateDrvvGslDi~ka~~~g~~af~PGlLa~AnRGIlYvDEvnlL~d~lvd~LLd~aaeG~n~v  175 (423)
T COG1239          96 WLPREKRKVPFVALPLGATEDRLVGSLDIEKALEEGPKAFQPGLLARANRGILYVDEVNLLDDHLVDALLDVAAEGVNDV  175 (423)
T ss_pred             cccccceecceecCCCccchhhhccccCHHHHHhcCccccCCcchhhccCCEEEEeccccccHHHHHHHHHHHHhCCcee
Confidence                      11100000    011111111111  111233345557899999999999999999999999985     


Q ss_pred             --------ccCCceEEEEecCCC-cCchhHhhhcce-eeecCCC-HHHHHHHHHHHHHH
Q psy879          123 --------YSNTTRFALACNNSE-KIIEPIQSRCAM-LRYNKLT-DAQLLSKVIEICEK  170 (317)
Q Consensus       123 --------~~~~~~~il~~~~~~-~l~~~i~sR~~~-i~f~~~~-~~~~~~~l~~~~~~  170 (317)
                              +|.++.+|.++|+.. .+-+.|+.||.. +...++. .++...++.+....
T Consensus       176 ereGisi~hpa~fvligTmNPEeGeLrpqLlDRfg~~v~~~~~~~~~~rv~Ii~r~~~f  234 (423)
T COG1239         176 EREGISIRHPARFLLIGTMNPEEGELRPQLLDRFGLEVDTHYPLDLEERVEIIRRRLAF  234 (423)
T ss_pred             eeCceeeccCccEEEEeecCccccccchhhHhhhcceeeccCCCCHHHHHHHHHHHHHh
Confidence                    355666777787764 799999999776 7777665 55666666666544

>PRK08116 hypothetical protein; Validated

Probab=99.06  E-value=7.6e-10  Score=94.42  Aligned_cols=145  Identities=17%  Similarity=0.247  Sum_probs=86.7

Q ss_pred             cCCCCCCcccC---CHHHHHHHHHHHhc----CCC-ceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcCh
Q psy879            4 YRPQTFSDIVG---NEDTVERLKVFSSS----GNV-PNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGI   75 (317)
Q Consensus         4 y~P~~~~~~~g---~~~~~~~l~~~l~~----~~~-~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~   75 (317)
                      |+-.+|+.+..   +..+......++++    ... ..++|+|++|+|||+++.++++.+...  +..++.++....  .
T Consensus        79 ~~~~tFdnf~~~~~~~~a~~~a~~y~~~~~~~~~~~~gl~l~G~~GtGKThLa~aia~~l~~~--~~~v~~~~~~~l--l  154 (268)
T PRK08116         79 FRNSTFENFLFDKGSEKAYKIARKYVKKFEEMKKENVGLLLWGSVGTGKTYLAACIANELIEK--GVPVIFVNFPQL--L  154 (268)
T ss_pred             HHhcchhcccCChHHHHHHHHHHHHHHHHHhhccCCceEEEECCCCCCHHHHHHHHHHHHHHc--CCeEEEEEHHHH--H
Confidence            44456776653   23344444444432    111 249999999999999999999998644  233444432110  1


Q ss_pred             HHHHHHHH--------HHHhhcccCCCCceeEEEEeCC--CCCCHHHHHHHHHHhhhc-cCCceEEEEecCCC-----cC
Q psy879           76 DTVRNKIK--------MFAQQKVTLPPGRHKIVILDEA--DSMTDGAQQALRRTMEIY-SNTTRFALACNNSE-----KI  139 (317)
Q Consensus        76 ~~i~~~~~--------~~~~~~~~~~~~~~~vliiDE~--d~l~~~~~~~ll~~le~~-~~~~~~il~~~~~~-----~l  139 (317)
                      ..+...+.        .+...     .....+|||||+  +..+...+..|..+++.. .....+|++||...     .+
T Consensus       155 ~~i~~~~~~~~~~~~~~~~~~-----l~~~dlLviDDlg~e~~t~~~~~~l~~iin~r~~~~~~~IiTsN~~~~eL~~~~  229 (268)
T PRK08116        155 NRIKSTYKSSGKEDENEIIRS-----LVNADLLILDDLGAERDTEWAREKVYNIIDSRYRKGLPTIVTTNLSLEELKNQY  229 (268)
T ss_pred             HHHHHHHhccccccHHHHHHH-----hcCCCEEEEecccCCCCCHHHHHHHHHHHHHHHHCCCCEEEECCCCHHHHHHHH
Confidence            11111100        00000     134569999999  556777888899988853 34566888888753     24


Q ss_pred             chhHhhh----cceeeecCCCH
Q psy879          140 IEPIQSR----CAMLRYNKLTD  157 (317)
Q Consensus       140 ~~~i~sR----~~~i~f~~~~~  157 (317)
                      .+.+.||    |..+.|..++.
T Consensus       230 ~~ri~sRl~e~~~~v~~~g~d~  251 (268)
T PRK08116        230 GKRIYDRILEMCTPVENEGKSY  251 (268)
T ss_pred             hHHHHHHHHHcCEEEEeeCcCh
Confidence            5677788    66688877664

>PF08542 Rep_fac_C: Replication factor C C-terminal domain; InterPro: IPR013748 Replication factor C (RFC) is a multimeric AAA+ protein complex that loads the DNA polymerase processivity clamp PCNA (Proliferating Cell Nuclear Antigen) onto DNA using ATP to drive the reaction []

Probab=99.06  E-value=5.7e-09  Score=73.68  Aligned_cols=87  Identities=31%  Similarity=0.618  Sum_probs=76.7

Q ss_pred             CCHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHHHhHHhcCCCcHHHH
Q psy879          220 PHPLAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDIIGNIFRVAKTLDIPEPLKLSIIQEIGNVHLRISEGVNSLLQL  299 (317)
Q Consensus       220 ~~~~~i~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~g~~~~l~l  299 (317)
                      +.++.+.++++.+.++++.+++..+++++..|+++.+|+..+++.+....+++..+.+++.+++++|+++..|.++.+++
T Consensus         3 p~~~~i~~i~~~~~~~~~~~~~~~~~~l~~~G~s~~~Il~~l~~~l~~~~~~~~~k~~i~~~la~~e~rl~~G~~e~lQl   82 (89)
T PF08542_consen    3 PPPEVIEEILESCLNGDFKEARKKLYELLVEGYSASDILKQLHEVLVESDIPDSQKAEILKILAEIEYRLSDGASEILQL   82 (89)
T ss_dssp             --HHHHHHHHHHHHHTCHHHHHHHHHHHHHTT--HHHHHHHHHHHHHTSTSSHHHHHHHHHHHHHHHHHHHTTC-HHHHH
T ss_pred             CCHHHHHHHHHHHHhCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhhccHHHHHHHHHHHHHHhHHHHCCCCHHHHH
Confidence            45667889999999999999999999999899999999999999887778889999999999999999999999999999


Q ss_pred             HHHHHHH
Q psy879          300 SGLLARL  306 (317)
Q Consensus       300 e~~~~~~  306 (317)
                      +.|++++
T Consensus        83 ~alva~~   89 (89)
T PF08542_consen   83 EALVAAF   89 (89)
T ss_dssp             HHHHHHH
T ss_pred             HHHHhhC
Confidence            9999875

PCNA functions at multiple levels in directing DNA metabolic pathways []. When bound to DNA, PCNA organises various proteins involved in DNA replication, DNA repair, DNA modification, and chromatin modelling. Replication factor C consists of five subunits in a spiral arrangement: Rfc1, Rfc2, Rfc3, Rfc4, and Rfc5 subunits. Rfc1 and Rfc2 load the PCNA sliding clamp onto DNA, while Rfc3 binds ATP and also acts as a checkpoint sensor. The RFC complex contains four ATP sites (sites A, B, C, and D) located at subunit interfaces. In each ATP site, an arginine residue from one subunit is located near the gamma-phosphate of ATP bound in the adjacent subunit. These arginine residues act as "arginine fingers" that can potentially perform two functions: sensing that ATP is bound and catalyzing ATP hydrolysis []. This entry represents the core domain found in Rfc1-5.; GO: 0003689 DNA clamp loader activity, 0005524 ATP binding, 0006260 DNA replication, 0005663 DNA replication factor C complex; PDB: 1SXJ_B 2CHG_B 2CHV_F 2CHQ_C 1IQP_A.

>PF14532 Sigma54_activ_2: Sigma-54 interaction domain; PDB: 3CO5_B 3N70_H

Probab=99.06  E-value=1.7e-09  Score=83.05  Aligned_cols=122  Identities=16%  Similarity=0.266  Sum_probs=75.9

Q ss_pred             CCHHHHHHHHHH----HhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHHHHHHHhhc
Q psy879           14 GNEDTVERLKVF----SSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFAQQK   89 (317)
Q Consensus        14 g~~~~~~~l~~~----l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~   89 (317)
                      |.....+.+...    .....  +++|+|++||||+++|+++...-  ......++..++.. ..    .+.+..     
T Consensus         2 G~S~~~~~l~~~l~~~a~~~~--pvli~GE~GtGK~~~A~~lh~~~--~~~~~~~~~~~~~~-~~----~~~l~~-----   67 (138)
T PF14532_consen    2 GKSPAMRRLRRQLERLAKSSS--PVLITGEPGTGKSLLARALHRYS--GRANGPFIVIDCAS-LP----AELLEQ-----   67 (138)
T ss_dssp             -SCHHHHHHHHHHHHHHCSSS---EEEECCTTSSHHHHHHCCHHTT--TTCCS-CCCCCHHC-TC----HHHHHH-----
T ss_pred             CCCHHHHHHHHHHHHHhCCCC--cEEEEcCCCCCHHHHHHHHHhhc--CccCCCeEEechhh-Cc----HHHHHH-----
Confidence            444444444443    33333  69999999999999999999863  22223333333322 11    112221     


Q ss_pred             ccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhc-cCCceEEEEecCCC-------cCchhHhhhcce--eeecC
Q psy879           90 VTLPPGRHKIVILDEADSMTDGAQQALRRTMEIY-SNTTRFALACNNSE-------KIIEPIQSRCAM--LRYNK  154 (317)
Q Consensus        90 ~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~-~~~~~~il~~~~~~-------~l~~~i~sR~~~--i~f~~  154 (317)
                           .....++|+|+|.+..+.|..|..+++.. ..++++|+++..+-       .+.+.+-.|+..  +.+||
T Consensus        68 -----a~~gtL~l~~i~~L~~~~Q~~L~~~l~~~~~~~~RlI~ss~~~l~~l~~~~~~~~~L~~~l~~~~i~lPp  137 (138)
T PF14532_consen   68 -----AKGGTLYLKNIDRLSPEAQRRLLDLLKRQERSNVRLIASSSQDLEELVEEGRFSPDLYYRLSQLEIHLPP  137 (138)
T ss_dssp             -----CTTSEEEEECGCCS-HHHHHHHHHHHHHCTTTTSEEEEEECC-CCCHHHHSTHHHHHHHHCSTCEEEE--
T ss_pred             -----cCCCEEEECChHHCCHHHHHHHHHHHHhcCCCCeEEEEEeCCCHHHHhhccchhHHHHHHhCCCEEeCCC
Confidence                 25678999999999999999999999864 56788999887642       355667666655  44443

>PF00931 NB-ARC: NB-ARC domain; InterPro: IPR002182 This is the NB-ARC domain, a novel signalling motif found in bacteria and eukaryotes, shared by plant resistance gene products and regulators of cell death in animals []

Probab=99.04  E-value=8e-09  Score=89.61  Aligned_cols=175  Identities=17%  Similarity=0.258  Sum_probs=97.8

Q ss_pred             HHHHHHHHHHHhc--CCCceEEEECCCCCCHHHHHHHHHHHHc-CCCCCCceEEecCCCCcChHH-HHHHHHHHHhhccc
Q psy879           16 EDTVERLKVFSSS--GNVPNIIISGPPGVGKTTTILCLARILL-GPSFKDAVLELNASNDRGIDT-VRNKIKMFAQQKVT   91 (317)
Q Consensus        16 ~~~~~~l~~~l~~--~~~~~~ll~G~~G~GKt~la~~la~~l~-~~~~~~~~~~~~~~~~~~~~~-i~~~~~~~~~~~~~   91 (317)
                      +..++.+...+..  .....+.++|++|+|||++|..+++... ...+. .++.++......... .......+......
T Consensus         2 e~~~~~l~~~L~~~~~~~~~v~I~G~~G~GKT~LA~~~~~~~~~~~~f~-~v~wv~~~~~~~~~~~~~~i~~~l~~~~~~   80 (287)
T PF00931_consen    2 EKEIEKLKDWLLDNSNEVRVVAIVGMGGIGKTTLARQVARDLRIKNRFD-GVIWVSLSKNPSLEQLLEQILRQLGEPDSS   80 (287)
T ss_dssp             HHHHHHHHHHHHTTTTSSEEEEEEESTTSSHHHHHHHHHCHHHHCCCCT-EEEEEEEES-SCCHHHHHHHHHHHTCC-ST
T ss_pred             HHHHHHHHHHhhCCCCCeEEEEEEcCCcCCcceeeeecccccccccccc-cccccccccccccccccccccccccccccc
Confidence            5567777777776  3444599999999999999999997732 22232 223333222222222 22222222211000


Q ss_pred             C----------------CCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcCchhHhhhcceeeecCC
Q psy879           92 L----------------PPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKL  155 (317)
Q Consensus        92 ~----------------~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~~~i~sR~~~i~f~~~  155 (317)
                      .                ....+.++|+|+++...  ....+...+-..+.++.+|+||... .+..........++..++
T Consensus        81 ~~~~~~~~~~~~~l~~~L~~~~~LlVlDdv~~~~--~~~~l~~~~~~~~~~~kilvTTR~~-~v~~~~~~~~~~~~l~~L  157 (287)
T PF00931_consen   81 ISDPKDIEELQDQLRELLKDKRCLLVLDDVWDEE--DLEELREPLPSFSSGSKILVTTRDR-SVAGSLGGTDKVIELEPL  157 (287)
T ss_dssp             SSCCSSHHHHHHHHHHHHCCTSEEEEEEEE-SHH--HH-------HCHHSS-EEEEEESCG-GGGTTHHSCEEEEECSS-
T ss_pred             cccccccccccccchhhhccccceeeeeeecccc--ccccccccccccccccccccccccc-cccccccccccccccccc
Confidence            0                01347899999987654  3333444444444567788887663 333333333667999999


Q ss_pred             CHHHHHHHHHHHHHHcC---CCCCHHHHHHHHHhcCCCHHHH
Q psy879          156 TDAQLLSKVIEICEKEN---ISHTNDGLEAIVFTAQGDMRQA  194 (317)
Q Consensus       156 ~~~~~~~~l~~~~~~~~---~~i~~~~~~~l~~~~~gd~r~~  194 (317)
                      ++++..+.+...+....   -.-.++....+++.++|.+-.+
T Consensus       158 ~~~ea~~L~~~~~~~~~~~~~~~~~~~~~~i~~~c~glPLal  199 (287)
T PF00931_consen  158 SEEEALELFKKRAGRKESESPEDLEDLAKEIVEKCGGLPLAL  199 (287)
T ss_dssp             -HHHHHHHHHHHHTSHS----TTSCTHHHHHHHHTTT-HHHH
T ss_pred             cccccccccccccccccccccccccccccccccccccccccc
Confidence            99999999999875443   1122456788999999866543

This domain has been structurally characterised in the human protein apoptotic protease-activating factor 1 (Apaf-1) []. It contains the three-layered alpha-beta fold and subsequent short alpha-helical region characteristic of the AAA+ ATPase domain superfamily. While this domain is thought to bind and hyrolyse ATP, only ADP binding has been experimentally verified. It is proposed that binding and hydrolysis of ATP by this domain induces conformational changes the the overall protein, leading to formation of the apoptosome.; GO: 0043531 ADP binding; PDB: 3IZA_E 1Z6T_D 3SFZ_A 3SHF_A 1VT4_M 3IZ8_G 3LQR_A 2A5Y_C 3LQQ_A.

>KOG0741|consensus

Probab=99.03  E-value=6.8e-10  Score=99.08  Aligned_cols=133  Identities=20%  Similarity=0.183  Sum_probs=92.4

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHcCCCCCCceE-E-ecCCCCcChHHHHHHHHHHHhhcc-cCCCCceeEEEEeCCCCCCH
Q psy879           34 IIISGPPGVGKTTTILCLARILLGPSFKDAVL-E-LNASNDRGIDTVRNKIKMFAQQKV-TLPPGRHKIVILDEADSMTD  110 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~-~-~~~~~~~~~~~i~~~~~~~~~~~~-~~~~~~~~vliiDE~d~l~~  110 (317)
                      +|+|||||||||.+||.+-+-|+...+...-- + ++..-..+...+|+.+........ ...++.-.++|+||+|...+
T Consensus       259 iLLyGPPGTGKTLiARqIGkMLNArePKIVNGPeIL~KYVGeSE~NvR~LFaDAEeE~r~~g~~SgLHIIIFDEiDAICK  338 (744)
T KOG0741|consen  259 ILLYGPPGTGKTLIARQIGKMLNAREPKIVNGPEILNKYVGESEENVRKLFADAEEEQRRLGANSGLHIIIFDEIDAICK  338 (744)
T ss_pred             EEEECCCCCChhHHHHHHHHHhcCCCCcccCcHHHHHHhhcccHHHHHHHHHhHHHHHHhhCccCCceEEEehhhHHHHH
Confidence            89999999999999999999987655432100 0 111112334567777766554432 22346678999999997643


Q ss_pred             -------------HHHHHHHHHhhh--ccCCceEEEEecCCCcCchhHhhhcc--e-eeecCCCHHHHHHHHHH
Q psy879          111 -------------GAQQALRRTMEI--YSNTTRFALACNNSEKIIEPIQSRCA--M-LRYNKLTDAQLLSKVIE  166 (317)
Q Consensus       111 -------------~~~~~ll~~le~--~~~~~~~il~~~~~~~l~~~i~sR~~--~-i~f~~~~~~~~~~~l~~  166 (317)
                                   ...|.|+.-|+.  --.++.+|..||+.+-+++++.+-..  + +++.-|++.-..+++.-
T Consensus       339 qRGS~~g~TGVhD~VVNQLLsKmDGVeqLNNILVIGMTNR~DlIDEALLRPGRlEVqmEIsLPDE~gRlQIl~I  412 (744)
T KOG0741|consen  339 QRGSMAGSTGVHDTVVNQLLSKMDGVEQLNNILVIGMTNRKDLIDEALLRPGRLEVQMEISLPDEKGRLQILKI  412 (744)
T ss_pred             hcCCCCCCCCccHHHHHHHHHhcccHHhhhcEEEEeccCchhhHHHHhcCCCceEEEEEEeCCCccCceEEEEh
Confidence                         357888888773  33578889999999999999976544  4 78888888766665543

>KOG0745|consensus

Probab=99.03  E-value=1.1e-08  Score=89.51  Aligned_cols=121  Identities=27%  Similarity=0.346  Sum_probs=73.6

Q ss_pred             ceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCc--C--hHHHHHHHHHHHhhccc-CCCCceeEEEEeCCC
Q psy879           32 PNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDR--G--IDTVRNKIKMFAQQKVT-LPPGRHKIVILDEAD  106 (317)
Q Consensus        32 ~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~--~--~~~i~~~~~~~~~~~~~-~~~~~~~vliiDE~d  106 (317)
                      .|+|+.||+|+|||.+++.+|+.+     +.++...+|....  +  -+++...+..+.+.+.. ...+...||+|||+|
T Consensus       227 SNvLllGPtGsGKTllaqTLAr~l-----dVPfaIcDcTtLTQAGYVGeDVEsvi~KLl~~A~~nVekAQqGIVflDEvD  301 (564)
T KOG0745|consen  227 SNVLLLGPTGSGKTLLAQTLARVL-----DVPFAICDCTTLTQAGYVGEDVESVIQKLLQEAEYNVEKAQQGIVFLDEVD  301 (564)
T ss_pred             ccEEEECCCCCchhHHHHHHHHHh-----CCCeEEecccchhhcccccccHHHHHHHHHHHccCCHHHHhcCeEEEehhh
Confidence            369999999999999999999987     3445545543311  1  12233334333332210 112467899999999


Q ss_pred             CCCH--------------HHHHHHHHHhhhc-------------cC------CceEEEEecC-CCcCchhHhhhcce--e
Q psy879          107 SMTD--------------GAQQALRRTMEIY-------------SN------TTRFALACNN-SEKIIEPIQSRCAM--L  150 (317)
Q Consensus       107 ~l~~--------------~~~~~ll~~le~~-------------~~------~~~~il~~~~-~~~l~~~i~sR~~~--i  150 (317)
                      ++..              ..|.+||+++|..             ..      ++-|+|++.. ...+.+.+..|...  +
T Consensus       302 Ki~~~~~~i~~~RDVsGEGVQQaLLKllEGtvVnVpeK~~~~~~rgd~vqiDTtnILFiasGAF~~Ldk~I~rR~~d~sl  381 (564)
T KOG0745|consen  302 KITKKAESIHTSRDVSGEGVQQALLKLLEGTVVNVPEKGSRRKPRGDTVQIDTTNILFIASGAFVGLDKIISRRLDDKSL  381 (564)
T ss_pred             hhcccCccccccccccchhHHHHHHHHhcccEEcccCCCCCCCCCCCeEEEeccceEEEecccccchHHHHHHhhcchhc
Confidence            9873              2599999999821             11      1113333333 23566777777655  6


Q ss_pred             eecCCCH
Q psy879          151 RYNKLTD  157 (317)
Q Consensus       151 ~f~~~~~  157 (317)
                      -|..++.
T Consensus       382 GFg~~s~  388 (564)
T KOG0745|consen  382 GFGAPSS  388 (564)
T ss_pred             ccCCCCC
Confidence            6666655

>PRK06526 transposase; Provisional

Probab=99.02  E-value=5.5e-10  Score=94.33  Aligned_cols=102  Identities=19%  Similarity=0.261  Sum_probs=61.7

Q ss_pred             HHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHHHHHHHhh----cccCCCCceeEE
Q psy879           25 FSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFAQQ----KVTLPPGRHKIV  100 (317)
Q Consensus        25 ~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~----~~~~~~~~~~vl  100 (317)
                      +++.+.  +++|+||||+|||+++.+++..+...+...  .....      ..+.+.+......    ..........++
T Consensus        94 fi~~~~--nlll~Gp~GtGKThLa~al~~~a~~~g~~v--~f~t~------~~l~~~l~~~~~~~~~~~~l~~l~~~dlL  163 (254)
T PRK06526         94 FVTGKE--NVVFLGPPGTGKTHLAIGLGIRACQAGHRV--LFATA------AQWVARLAAAHHAGRLQAELVKLGRYPLL  163 (254)
T ss_pred             hhhcCc--eEEEEeCCCCchHHHHHHHHHHHHHCCCch--hhhhH------HHHHHHHHHHHhcCcHHHHHHHhccCCEE
Confidence            454443  799999999999999999998874333222  21111      1111111100000    000001356799


Q ss_pred             EEeCCCCC--CHHHHHHHHHHhhhccCCceEEEEecCC
Q psy879          101 ILDEADSM--TDGAQQALRRTMEIYSNTTRFALACNNS  136 (317)
Q Consensus       101 iiDE~d~l--~~~~~~~ll~~le~~~~~~~~il~~~~~  136 (317)
                      ||||++..  .+..++.|..+++.......+|++||.+
T Consensus       164 IIDD~g~~~~~~~~~~~L~~li~~r~~~~s~IitSn~~  201 (254)
T PRK06526        164 IVDEVGYIPFEPEAANLFFQLVSSRYERASLIVTSNKP  201 (254)
T ss_pred             EEcccccCCCCHHHHHHHHHHHHHHHhcCCEEEEcCCC
Confidence            99999977  4667778888887644455688888876

>KOG1051|consensus

Probab=99.01  E-value=3.1e-09  Score=102.06  Aligned_cols=121  Identities=17%  Similarity=0.255  Sum_probs=85.8

Q ss_pred             CcccCCHHHHHHHHHHHhcC-----C--Cce-EEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecC---------C--
Q psy879           10 SDIVGNEDTVERLKVFSSSG-----N--VPN-IIISGPPGVGKTTTILCLARILLGPSFKDAVLELNA---------S--   70 (317)
Q Consensus        10 ~~~~g~~~~~~~l~~~l~~~-----~--~~~-~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~---------~--   70 (317)
                      +.++||++++..+..++..-     +  +.. ++|.||.|+|||-+|+++|..+.+.......+++..         +  
T Consensus       562 ~~V~gQ~eAv~aIa~AI~~sr~gl~~~~~~awflflGpdgvGKt~lAkaLA~~~Fgse~~~IriDmse~~evskligsp~  641 (898)
T KOG1051|consen  562 ERVIGQDEAVAAIAAAIRRSRAGLKDPNPDAWFLFLGPDGVGKTELAKALAEYVFGSEENFIRLDMSEFQEVSKLIGSPP  641 (898)
T ss_pred             hhccchHHHHHHHHHHHHhhhcccCCCCCCeEEEEECCCchhHHHHHHHHHHHHcCCccceEEechhhhhhhhhccCCCc
Confidence            35789999999998887632     2  223 999999999999999999999976654444443332         0  


Q ss_pred             CCcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhc-----------cCCceEEEEecCCC
Q psy879           71 NDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIY-----------SNTTRFALACNNSE  137 (317)
Q Consensus        71 ~~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~-----------~~~~~~il~~~~~~  137 (317)
                      ...+....-...+.+.       ..++.||++||+|+..++.++.|++.+++.           -.+++||+|+|...
T Consensus       642 gyvG~e~gg~Lteavr-------rrP~sVVLfdeIEkAh~~v~n~llq~lD~GrltDs~Gr~Vd~kN~I~IMTsn~~~  712 (898)
T KOG1051|consen  642 GYVGKEEGGQLTEAVK-------RRPYSVVLFEEIEKAHPDVLNILLQLLDRGRLTDSHGREVDFKNAIFIMTSNVGS  712 (898)
T ss_pred             ccccchhHHHHHHHHh-------cCCceEEEEechhhcCHHHHHHHHHHHhcCccccCCCcEeeccceEEEEecccch
Confidence            1122222222222221       246899999999999999999999999954           25788999988643

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=99.01  E-value=9.8e-09  Score=78.70  Aligned_cols=95  Identities=31%  Similarity=0.387  Sum_probs=59.3

Q ss_pred             ceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCc--------------------ChHHHHHHHHHHHhhccc
Q psy879           32 PNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDR--------------------GIDTVRNKIKMFAQQKVT   91 (317)
Q Consensus        32 ~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~--------------------~~~~i~~~~~~~~~~~~~   91 (317)
                      .+++|+||||+|||++++.++..+....  ..++.+++....                    .....+..+.... .   
T Consensus         3 ~~~~l~G~~G~GKTtl~~~l~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~---   76 (148)
T smart00382        3 EVILIVGPPGSGKTTLARALARELGPPG--GGVIYIDGEDILEEVLDQLLLIIVGGKKASGSGELRLRLALALAR-K---   76 (148)
T ss_pred             CEEEEECCCCCcHHHHHHHHHhccCCCC--CCEEEECCEEccccCHHHHHhhhhhccCCCCCHHHHHHHHHHHHH-h---
Confidence            3699999999999999999999875432  234444443211                    1111221122111 1   


Q ss_pred             CCCCceeEEEEeCCCCCCHHHHHHHHH--------HhhhccCCceEEEEecC
Q psy879           92 LPPGRHKIVILDEADSMTDGAQQALRR--------TMEIYSNTTRFALACNN  135 (317)
Q Consensus        92 ~~~~~~~vliiDE~d~l~~~~~~~ll~--------~le~~~~~~~~il~~~~  135 (317)
                         ..+.++++||++.+..........        ..........+|+++|.
T Consensus        77 ---~~~~viiiDei~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~  125 (148)
T smart00382       77 ---LKPDVLILDEITSLLDAEQEALLLLLEELRLLLLLKSEKNLTVILTTND  125 (148)
T ss_pred             ---cCCCEEEEECCcccCCHHHHHHHHhhhhhHHHHHHHhcCCCEEEEEeCC
Confidence               125899999999998776555433        23344566778888885

AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment.

>PRK10365 transcriptional regulatory protein ZraR; Provisional

Probab=98.99  E-value=3.2e-08  Score=91.28  Aligned_cols=179  Identities=12%  Similarity=0.156  Sum_probs=118.0

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHHHHHHHhh---------cccCCCCceeEEEEe
Q psy879           33 NIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFAQQ---------KVTLPPGRHKIVILD  103 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~---------~~~~~~~~~~vliiD  103 (317)
                      .++++|++|+||+++++++...-  .....+++.++|... ....+...+......         ...+....+++++||
T Consensus       164 ~vli~ge~g~gk~~~a~~ih~~s--~~~~~~~i~~~c~~~-~~~~~~~~lfg~~~~~~~~~~~~~~g~~~~a~~gtl~ld  240 (441)
T PRK10365        164 TVLIHGDSGTGKELVARAIHASS--ARSEKPLVTLNCAAL-NESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLD  240 (441)
T ss_pred             eEEEEecCCCCHHHHHHHHHHcC--CCCCCCeeeeeCCCC-CHHHHHHHhcCCCCCCcCCCCcCCCCceeECCCCEEEEe
Confidence            58999999999999999998763  334456888888643 223333222110000         001122457899999


Q ss_pred             CCCCCCHHHHHHHHHHhhhcc-----------CCceEEEEecCCC-------cCchhHhhhcce--eeecCCCH--HHHH
Q psy879          104 EADSMTDGAQQALRRTMEIYS-----------NTTRFALACNNSE-------KIIEPIQSRCAM--LRYNKLTD--AQLL  161 (317)
Q Consensus       104 E~d~l~~~~~~~ll~~le~~~-----------~~~~~il~~~~~~-------~l~~~i~sR~~~--i~f~~~~~--~~~~  161 (317)
                      |++.|....|..|++++++..           .++++|++|+...       .+.+.+..|+..  +..||+.+  +++.
T Consensus       241 ei~~l~~~~q~~l~~~l~~~~~~~~~~~~~~~~~~rii~~t~~~~~~~~~~~~~~~~l~~~l~~~~i~~ppLreR~~Di~  320 (441)
T PRK10365        241 EIGDISPMMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAAEVNAGRFRQDLYYRLNVVAIEVPSLRQRREDIP  320 (441)
T ss_pred             ccccCCHHHHHHHHHHHccCcEEeCCCCceeeeceEEEEeCCCCHHHHHHcCCchHHHHHHhccceecCCChhhcchhHH
Confidence            999999999999999998532           2456787776642       455666666655  55566653  2444


Q ss_pred             HHHHHH----HHHcC---CCCCHHHHHHHHHhc-CCCHHHHHHHHHHhhh--CCCcccHHHHH
Q psy879          162 SKVIEI----CEKEN---ISHTNDGLEAIVFTA-QGDMRQALNNLQSTHN--GFGHVTAEYVF  214 (317)
Q Consensus       162 ~~l~~~----~~~~~---~~i~~~~~~~l~~~~-~gd~r~~i~~l~~~~~--~~~~i~~~~v~  214 (317)
                      .+....    +...+   ..++++++..+.... .||+|++.+.++.++.  ....|+.+++.
T Consensus       321 ~l~~~~l~~~~~~~~~~~~~~~~~a~~~L~~~~wpgN~reL~~~~~~~~~~~~~~~i~~~~l~  383 (441)
T PRK10365        321 LLAGHFLQRFAERNRKAVKGFTPQAMDLLIHYDWPGNIRELENAVERAVVLLTGEYISERELP  383 (441)
T ss_pred             HHHHHHHHHHHHHhCCCCCCcCHHHHHHHHhCCCCCHHHHHHHHHHHHHHhCCCCccchHhCc
Confidence            433333    33223   358899999988875 9999999999998654  44567777664

>COG3267 ExeA Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]

Probab=98.96  E-value=7.4e-08  Score=79.08  Aligned_cols=195  Identities=20%  Similarity=0.201  Sum_probs=123.2

Q ss_pred             CHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHH-HHHHHhhcc---
Q psy879           15 NEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNK-IKMFAQQKV---   90 (317)
Q Consensus        15 ~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~-~~~~~~~~~---   90 (317)
                      +.+.+..+...+..|. ..+.++|+.|+|||.+.+++...+.+..  ...+.+.... .+...+.+. +..+...+.   
T Consensus        36 h~e~l~~l~~~i~d~q-g~~~vtGevGsGKTv~~Ral~~s~~~d~--~~~v~i~~~~-~s~~~~~~ai~~~l~~~p~~~~  111 (269)
T COG3267          36 HNEALLMLHAAIADGQ-GILAVTGEVGSGKTVLRRALLASLNEDQ--VAVVVIDKPT-LSDATLLEAIVADLESQPKVNV  111 (269)
T ss_pred             hhHHHHHHHHHHhcCC-ceEEEEecCCCchhHHHHHHHHhcCCCc--eEEEEecCcc-hhHHHHHHHHHHHhccCccchh
Confidence            4566677777777666 1389999999999999997777764332  2222333221 111111111 110000000   


Q ss_pred             -------------cCCCC-ceeEEEEeCCCCCCHHHHHHHHHHhh---hccCCceEEEEecCCC------cCchhHhhhc
Q psy879           91 -------------TLPPG-RHKIVILDEADSMTDGAQQALRRTME---IYSNTTRFALACNNSE------KIIEPIQSRC  147 (317)
Q Consensus        91 -------------~~~~~-~~~vliiDE~d~l~~~~~~~ll~~le---~~~~~~~~il~~~~~~------~l~~~i~sR~  147 (317)
                                   ....+ .+-++++||++.+..+...+|..+.+   +......++++..+.-      .....+..|+
T Consensus       112 ~~~~e~~~~~L~al~~~g~r~v~l~vdEah~L~~~~le~Lrll~nl~~~~~~~l~ivL~Gqp~L~~~lr~~~l~e~~~R~  191 (269)
T COG3267         112 NAVLEQIDRELAALVKKGKRPVVLMVDEAHDLNDSALEALRLLTNLEEDSSKLLSIVLIGQPKLRPRLRLPVLRELEQRI  191 (269)
T ss_pred             HHHHHHHHHHHHHHHHhCCCCeEEeehhHhhhChhHHHHHHHHHhhcccccCceeeeecCCcccchhhchHHHHhhhheE
Confidence                         00012 34789999999999999888877765   3444455777765532      1246677889


Q ss_pred             ce-eeecCCCHHHHHHHHHHHHHHcCCC---CCHHHHHHHHHhcCCCHHHHHHHHHHhh-----hCCCcccHHHH
Q psy879          148 AM-LRYNKLTDAQLLSKVIEICEKENIS---HTNDGLEAIVFTAQGDMRQALNNLQSTH-----NGFGHVTAEYV  213 (317)
Q Consensus       148 ~~-i~f~~~~~~~~~~~l~~~~~~~~~~---i~~~~~~~l~~~~~gd~r~~i~~l~~~~-----~~~~~i~~~~v  213 (317)
                      .. +..+|++.++...+|..+++..+..   ++++++..+...+.|-+|..-+.+..+.     .+...|+...+
T Consensus       192 ~ir~~l~P~~~~~t~~yl~~~Le~a~~~~~l~~~~a~~~i~~~sqg~P~lin~~~~~Al~~a~~a~~~~v~~a~~  266 (269)
T COG3267         192 DIRIELPPLTEAETGLYLRHRLEGAGLPEPLFSDDALLLIHEASQGIPRLINNLATLALDAAYSAGEDGVSEAEI  266 (269)
T ss_pred             EEEEecCCcChHHHHHHHHHHHhccCCCcccCChhHHHHHHHHhccchHHHHHHHHHHHHHHHHcCCCccchhhc
Confidence            88 9999999999999999998875542   4788899999999997775555543321     24455555443

>PF13173 AAA_14: AAA domain

Probab=98.96  E-value=8.1e-09  Score=78.24  Aligned_cols=119  Identities=24%  Similarity=0.331  Sum_probs=77.0

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHH-HHHHHHHHhhcccCCCCceeEEEEeCCCCCCHH
Q psy879           33 NIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTV-RNKIKMFAQQKVTLPPGRHKIVILDEADSMTDG  111 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i-~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~  111 (317)
                      .++++||.|+||||+++.+++.+.   ....++.++..+....... .+....+...    ...+..+++|||++.+. +
T Consensus         4 ~~~l~G~R~vGKTtll~~~~~~~~---~~~~~~yi~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~i~iDEiq~~~-~   75 (128)
T PF13173_consen    4 IIILTGPRGVGKTTLLKQLAKDLL---PPENILYINFDDPRDRRLADPDLLEYFLEL----IKPGKKYIFIDEIQYLP-D   75 (128)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHhc---ccccceeeccCCHHHHHHhhhhhHHHHHHh----hccCCcEEEEehhhhhc-c
Confidence            589999999999999999998875   1223444554332111100 0011222221    11267899999999985 4


Q ss_pred             HHHHHHHHhhhccCCceEEEEecCCC----cCchhHhhhcceeeecCCCHHHH
Q psy879          112 AQQALRRTMEIYSNTTRFALACNNSE----KIIEPIQSRCAMLRYNKLTDAQL  160 (317)
Q Consensus       112 ~~~~ll~~le~~~~~~~~il~~~~~~----~l~~~i~sR~~~i~f~~~~~~~~  160 (317)
                      ....+..+.+.. ++..+|+++....    .....+..|...+++.|++-.|.
T Consensus        76 ~~~~lk~l~d~~-~~~~ii~tgS~~~~l~~~~~~~l~gr~~~~~l~Plsf~E~  127 (128)
T PF13173_consen   76 WEDALKFLVDNG-PNIKIILTGSSSSLLSKDIAESLAGRVIEIELYPLSFREF  127 (128)
T ss_pred             HHHHHHHHHHhc-cCceEEEEccchHHHhhcccccCCCeEEEEEECCCCHHHh
Confidence            555565666654 5677888877643    34567788888899999998764

>COG1241 MCM2 Predicted ATPase involved in replication control, Cdc46/Mcm family [DNA replication, recombination, and repair]

Probab=98.96  E-value=3.2e-09  Score=99.63  Aligned_cols=137  Identities=21%  Similarity=0.312  Sum_probs=92.3

Q ss_pred             CcccCCHHHHHHHHHHHhcCCC------------ceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChH-
Q psy879           10 SDIVGNEDTVERLKVFSSSGNV------------PNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGID-   76 (317)
Q Consensus        10 ~~~~g~~~~~~~l~~~l~~~~~------------~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~-   76 (317)
                      -.+.|++.+++.+.-.+-+|..            -|+|+.|.||+|||.+.+.+++..    +...+.....++..+.. 
T Consensus       286 PsIyG~e~VKkAilLqLfgGv~k~~~~g~~iRGDInILLvGDPgtaKSqlLk~v~~~a----Pr~vytsgkgss~~GLTA  361 (682)
T COG1241         286 PSIYGHEDVKKAILLQLFGGVKKNLPDGTRIRGDIHILLVGDPGTAKSQLLKYVAKLA----PRGVYTSGKGSSAAGLTA  361 (682)
T ss_pred             ccccCcHHHHHHHHHHhcCCCcccCCCCcccccceeEEEcCCCchhHHHHHHHHHhhC----CceEEEccccccccCcee
Confidence            3578999999887666544321            279999999999999999999874    22233333333333321 


Q ss_pred             -HHHHHH-HHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhc-------------cCCceEEEEecCCC----
Q psy879           77 -TVRNKI-KMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIY-------------SNTTRFALACNNSE----  137 (317)
Q Consensus        77 -~i~~~~-~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~-------------~~~~~~il~~~~~~----  137 (317)
                       .+++.. +.|...+..+..++++|++|||+|+|.....++++..||..             +..+.++.++|+..    
T Consensus       362 av~rd~~tge~~LeaGALVlAD~Gv~cIDEfdKm~~~dr~aihEaMEQQtIsIaKAGI~atLnARcsvLAAaNP~~Gryd  441 (682)
T COG1241         362 AVVRDKVTGEWVLEAGALVLADGGVCCIDEFDKMNEEDRVAIHEAMEQQTISIAKAGITATLNARCSVLAAANPKFGRYD  441 (682)
T ss_pred             EEEEccCCCeEEEeCCEEEEecCCEEEEEeccCCChHHHHHHHHHHHhcEeeecccceeeecchhhhhhhhhCCCCCcCC
Confidence             112211 22222332233368899999999999999999999999943             23445677777653    


Q ss_pred             ---------cCchhHhhhccee
Q psy879          138 ---------KIIEPIQSRCAML  150 (317)
Q Consensus       138 ---------~l~~~i~sR~~~i  150 (317)
                               .+++++.|||..+
T Consensus       442 ~~~~~~enI~l~~~lLSRFDLi  463 (682)
T COG1241         442 PKKTVAENINLPAPLLSRFDLI  463 (682)
T ss_pred             CCCCHHHhcCCChhHHhhCCee
Confidence                     4789999999883

>KOG0478|consensus

Probab=98.95  E-value=1.5e-08  Score=93.08  Aligned_cols=144  Identities=22%  Similarity=0.285  Sum_probs=90.4

Q ss_pred             cccCCHHHHHHHHHHHhcCC---------C---ceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHH
Q psy879           11 DIVGNEDTVERLKVFSSSGN---------V---PNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTV   78 (317)
Q Consensus        11 ~~~g~~~~~~~l~~~l~~~~---------~---~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i   78 (317)
                      .++|++++++-+.-.+-+|.         +   -|+|++|.||+|||.+.+.+.+.+ ..+   .+.....+...+....
T Consensus       430 sIye~edvKkglLLqLfGGt~k~~~~~~~~R~~INILL~GDPGtsKSqlLqyv~~l~-pRg---~yTSGkGsSavGLTay  505 (804)
T KOG0478|consen  430 SIYELEDVKKGLLLQLFGGTRKEDEKSGRFRGDINILLVGDPGTSKSQLLQYCHRLL-PRG---VYTSGKGSSAVGLTAY  505 (804)
T ss_pred             hhhcccchhhhHHHHHhcCCcccccccccccccceEEEecCCCcCHHHHHHHHHHhC-Ccc---eeecCCccchhcceee
Confidence            46678888777655554332         2   269999999999999999999975 211   1221111111111000


Q ss_pred             --HH-HHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhh-------------ccCCceEEEEecCCC-----
Q psy879           79 --RN-KIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEI-------------YSNTTRFALACNNSE-----  137 (317)
Q Consensus        79 --~~-~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~-------------~~~~~~~il~~~~~~-----  137 (317)
                        ++ .-+.+......+.-++..+.+|||+|+|....++.|++.||.             .+..+.++.++|+..     
T Consensus       506 Vtrd~dtkqlVLesGALVLSD~GiCCIDEFDKM~dStrSvLhEvMEQQTvSIAKAGII~sLNAR~SVLAaANP~~skynp  585 (804)
T KOG0478|consen  506 VTKDPDTRQLVLESGALVLSDNGICCIDEFDKMSDSTRSVLHEVMEQQTLSIAKAGIIASLNARCSVLAAANPIRSKYNP  585 (804)
T ss_pred             EEecCccceeeeecCcEEEcCCceEEchhhhhhhHHHHHHHHHHHHHhhhhHhhcceeeeccccceeeeeeccccccCCC
Confidence              00 000111111122236889999999999999999999999993             245566788888532     


Q ss_pred             --------cCchhHhhhcce--eeecCCCHH
Q psy879          138 --------KIIEPIQSRCAM--LRYNKLTDA  158 (317)
Q Consensus       138 --------~l~~~i~sR~~~--i~f~~~~~~  158 (317)
                              .+++++.|||..  +-+.++++.
T Consensus       586 ~k~i~eNI~LpptLLSRFDLIylllD~~DE~  616 (804)
T KOG0478|consen  586 NKSIIENINLPPTLLSRFDLIFLLLDKPDER  616 (804)
T ss_pred             CCchhhccCCChhhhhhhcEEEEEecCcchh
Confidence                    478999999998  455666654

>KOG0482|consensus

Probab=98.95  E-value=3.7e-08  Score=87.74  Aligned_cols=265  Identities=18%  Similarity=0.188  Sum_probs=145.6

Q ss_pred             cccCCHHHHHHHHHHHhcCCC------------ceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHH-
Q psy879           11 DIVGNEDTVERLKVFSSSGNV------------PNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDT-   77 (317)
Q Consensus        11 ~~~g~~~~~~~l~~~l~~~~~------------~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~-   77 (317)
                      +++|++++++.|.-.+-+|.-            -|+++.|.||+.||.+.+.+.+.-  +  ...+....+++..+... 
T Consensus       343 EIyGheDVKKaLLLlLVGgvd~~~~dGMKIRGdINicLmGDPGVAKSQLLkyi~rla--p--RgvYTTGrGSSGVGLTAA  418 (721)
T KOG0482|consen  343 EIYGHEDVKKALLLLLVGGVDKSPGDGMKIRGDINICLMGDPGVAKSQLLKYISRLA--P--RGVYTTGRGSSGVGLTAA  418 (721)
T ss_pred             hhccchHHHHHHHHHhhCCCCCCCCCCceeecceeEEecCCCchhHHHHHHHHHhcC--c--ccceecCCCCCccccchh
Confidence            688999999998777654321            159999999999999999999863  2  11222333333333211 


Q ss_pred             -HHHHH-HHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhc-------------cCCceEEEEecCCC-----
Q psy879           78 -VRNKI-KMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIY-------------SNTTRFALACNNSE-----  137 (317)
Q Consensus        78 -i~~~~-~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~-------------~~~~~~il~~~~~~-----  137 (317)
                       .++-+ +.+......+--++..|.+|||+|+|......++...||.-             ...+.++.++|+..     
T Consensus       419 VmkDpvTgEM~LEGGALVLAD~GICCIDEfDKM~e~DRtAIHEVMEQQTISIaKAGI~TtLNAR~sILaAANPayGRYnp  498 (721)
T KOG0482|consen  419 VMKDPVTGEMVLEGGALVLADGGICCIDEFDKMDESDRTAIHEVMEQQTISIAKAGINTTLNARTSILAAANPAYGRYNP  498 (721)
T ss_pred             hhcCCCCCeeEeccceEEEccCceEeehhhhhhhhhhhHHHHHHHHhhhhhhhhhccccchhhhHHhhhhcCccccccCc
Confidence             11100 00000000111257889999999999999999999999942             23344566666532     


Q ss_pred             --------cCchhHhhhcce-------------------------------eeecCCCHHHHHHHHHHHHHHcCCCCCHH
Q psy879          138 --------KIIEPIQSRCAM-------------------------------LRYNKLTDAQLLSKVIEICEKENISHTND  178 (317)
Q Consensus       138 --------~l~~~i~sR~~~-------------------------------i~f~~~~~~~~~~~l~~~~~~~~~~i~~~  178 (317)
                              .++.++.|||..                               ..|.|++.+-++.++.. |+...--++++
T Consensus       499 rrs~e~NI~LPaALLSRFDll~Li~D~pdrd~D~~LA~HiTyVH~H~~qp~~~fepl~~~~mR~yI~~-ak~~~P~vp~~  577 (721)
T KOG0482|consen  499 RRSPEQNINLPAALLSRFDLLWLIQDRPDRDNDLRLAQHITYVHQHEEQPPLDFEPLDPNLMRRYISL-AKRKNPVVPEA  577 (721)
T ss_pred             ccChhHhcCCcHHHHHhhhhhhhhccCCcccchHHHHHHhHhhhccCCCCCccCCCCCHHHHHHHHHH-HhhcCCCCCHH
Confidence                    478999999833                               45667777777777665 33333345666


Q ss_pred             HHHHHHHh-------c-------CCCHHHHHHHHHHhhh-----CCCcccHHHHHhhcC---CCCHHHHHHHHHHHhcCC
Q psy879          179 GLEAIVFT-------A-------QGDMRQALNNLQSTHN-----GFGHVTAEYVFKVCD---EPHPLAVKEMLLNCVEGN  236 (317)
Q Consensus       179 ~~~~l~~~-------~-------~gd~r~~i~~l~~~~~-----~~~~i~~~~v~~~~~---~~~~~~i~~l~~~~~~~~  236 (317)
                      ..+++...       +       .-.+|..+.+++....     -...+..++|.+++.   .+.+....+--..-....
T Consensus       578 l~dyi~~AYv~~Rrea~~~~~~t~ttpRtLL~IlRls~AlarLRls~~V~~~DV~EALRLme~sK~sL~~~~~~~~~~~~  657 (721)
T KOG0482|consen  578 LADYITGAYVELRREARSSKDFTYTTPRTLLGILRLSTALARLRLSDSVEEDDVNEALRLMEMSKDSLYQDDGQKEDTSA  657 (721)
T ss_pred             HHHHHHHHHHHHHHHhhccCCCcccCHHHHHHHHHHHHHHHHhhhccccchhhHHHHHHHHHhhhcccccccccccccch
Confidence            55555421       1       2467888877764322     123455555554321   111000000000000011


Q ss_pred             HHHHHHHHHHHHH-cCCCHHHHHHHHHHHHHhcCCChHHHHHHHHH
Q psy879          237 MKDSYKIIHHLYK-LGYAPEDIIGNIFRVAKTLDIPEPLKLSIIQE  281 (317)
Q Consensus       237 ~~~~~~~~~~l~~-~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~  281 (317)
                      .+.++.++.+|.. .|..+..+-..+.+.... |.++......++.
T Consensus       658 ~~~if~iirel~~e~g~~~v~~s~~~~r~~~k-Gfs~~ql~~~i~e  702 (721)
T KOG0482|consen  658 TDAIFAIIRELAGEGGKRCVKLSNAEQRCVRK-GFSEAQLKKCIDE  702 (721)
T ss_pred             HHHHHHHHHHHHhhcCCceeeHHHHHHHHHHc-CCCHHHHHHHHHH
Confidence            4455666666654 445544454445454333 5666554444443

>PRK13406 bchD magnesium chelatase subunit D; Provisional

Probab=98.93  E-value=6.4e-08  Score=90.81  Aligned_cols=200  Identities=13%  Similarity=0.133  Sum_probs=126.6

Q ss_pred             CHHHHHHHHHHHhcC-CCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecC--CC--CcChHHHHHHHHHHH--h
Q psy879           15 NEDTVERLKVFSSSG-NVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNA--SN--DRGIDTVRNKIKMFA--Q   87 (317)
Q Consensus        15 ~~~~~~~l~~~l~~~-~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~--~~--~~~~~~i~~~~~~~~--~   87 (317)
                      |++++..|.-..-.. .+..++|.|+.|+||+++++.++..+-.   ..++.....  +.  ..+--++...+..-.  .
T Consensus         8 ~~~~~~Al~l~av~p~~~gGv~i~g~~G~~ks~~~r~l~~llp~---~~p~r~~p~~~t~~~L~Gg~Dl~~~l~~g~~~~   84 (584)
T PRK13406          8 WADAALAAALLAVDPAGLGGVVLRARAGPVRDRWLAALRALLPA---GTPLRRLPPGIADDRLLGGLDLAATLRAGRPVA   84 (584)
T ss_pred             HHHHHHHHHHhCcCccccceEEEEcCCCcHHHHHHHHHHHhcCC---CCCcccCCCCCcHHHccCCchHHhHhhcCCcCC
Confidence            555655554443344 5567999999999999999999998632   122332222  11  122222222222111  2


Q ss_pred             hcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhc-------------cCCceEEEEecC---CCcCchhHhhhcce-e
Q psy879           88 QKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIY-------------SNTTRFALACNN---SEKIIEPIQSRCAM-L  150 (317)
Q Consensus        88 ~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~-------------~~~~~~il~~~~---~~~l~~~i~sR~~~-i  150 (317)
                      .+..+....+.|+++||+..+.+..+++|++.|++.             |....+|.+-|.   ...+.+++..||.. +
T Consensus        85 ~pGlla~Ah~GvL~lDe~n~~~~~~~~aLleame~G~vtIeR~G~s~~~Pa~F~LIat~~~~~~~~~L~~~lLDRf~l~v  164 (584)
T PRK13406         85 QRGLLAEADGGVLVLAMAERLEPGTAARLAAALDTGEVRLERDGLALRLPARFGLVALDEGAEEDERAPAALADRLAFHL  164 (584)
T ss_pred             CCCceeeccCCEEEecCcccCCHHHHHHHHHHHhCCcEEEEECCcEEecCCCcEEEecCCChhcccCCCHHhHhheEEEE
Confidence            233344467899999999999999999999999953             233333443222   13588999999988 8


Q ss_pred             eecCCCHHHHH-------HHHHHHHHHcCCCCCHHHHHHHHHhc---CC-CHHHHHHHHHHhh-----hCCCcccHHHHH
Q psy879          151 RYNKLTDAQLL-------SKVIEICEKENISHTNDGLEAIVFTA---QG-DMRQALNNLQSTH-----NGFGHVTAEYVF  214 (317)
Q Consensus       151 ~f~~~~~~~~~-------~~l~~~~~~~~~~i~~~~~~~l~~~~---~g-d~r~~i~~l~~~~-----~~~~~i~~~~v~  214 (317)
                      .+..++..+..       ++...+..-.++.++++.+.+++..+   +- +.|..+.+++.+.     .+...|+.+||.
T Consensus       165 ~v~~~~~~~~~~~~~~~~~I~~AR~rl~~v~v~~~~l~~i~~~~~~~gv~S~Ra~i~llraARa~AaL~Gr~~V~~~dv~  244 (584)
T PRK13406        165 DLDGLALRDAREIPIDADDIAAARARLPAVGPPPEAIAALCAAAAALGIASLRAPLLALRAARAAAALAGRTAVEEEDLA  244 (584)
T ss_pred             EcCCCChHHhcccCCCHHHHHHHHHHHccCCCCHHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHHHHcCCCCCCHHHHH
Confidence            88877765432       23333333357889999988876543   32 6677777775422     267789999997


Q ss_pred             hhc
Q psy879          215 KVC  217 (317)
Q Consensus       215 ~~~  217 (317)
                      .+.
T Consensus       245 ~Aa  247 (584)
T PRK13406        245 LAA  247 (584)
T ss_pred             HHH
Confidence            744

>PHA00729 NTP-binding motif containing protein

Probab=98.90  E-value=1.5e-08  Score=83.02  Aligned_cols=128  Identities=18%  Similarity=0.103  Sum_probs=75.0

Q ss_pred             HHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCC--CceEEecC---CCCcChHHHHHHHHHHHhhcccCCCC
Q psy879           21 RLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFK--DAVLELNA---SNDRGIDTVRNKIKMFAQQKVTLPPG   95 (317)
Q Consensus        21 ~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~--~~~~~~~~---~~~~~~~~i~~~~~~~~~~~~~~~~~   95 (317)
                      .+...+.++.+.+++|+|+||+|||++|.++++.+...-..  ........   .-....+.+.+.+.......     .
T Consensus         7 ~~~~~l~~~~f~nIlItG~pGvGKT~LA~aLa~~l~~~l~~l~~~~~~~d~~~~~~fid~~~Ll~~L~~a~~~~-----~   81 (226)
T PHA00729          7 KIVSAYNNNGFVSAVIFGKQGSGKTTYALKVARDVFWKLNNLSTKDDAWQYVQNSYFFELPDALEKIQDAIDND-----Y   81 (226)
T ss_pred             HHHHHHhcCCeEEEEEECCCCCCHHHHHHHHHHHHHhhcccccchhhHHhcCCcEEEEEHHHHHHHHHHHHhcC-----C
Confidence            34445567777789999999999999999999986310000  00000000   01122333444443322221     2


Q ss_pred             ceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcCchhHhhhcceeeecCCCHHHHHHHHHHH
Q psy879           96 RHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEI  167 (317)
Q Consensus        96 ~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~~~i~sR~~~i~f~~~~~~~~~~~l~~~  167 (317)
                      ...++||||+........  .  ..+    .      ......+.++++||+..+.|.+++++++...|..+
T Consensus        82 ~~dlLIIDd~G~~~~~~~--w--h~~----~------~~~yf~L~~aLrSR~~l~il~~ls~edL~~~Lr~R  139 (226)
T PHA00729         82 RIPLIIFDDAGIWLSKYV--W--YED----Y------MKTFYKIYALIRTRVSAVIFTTPSPEDLAFYLREK  139 (226)
T ss_pred             CCCEEEEeCCchhhcccc--h--hhh----c------cchHHHHHHHHHhhCcEEEEecCCHHHHHHHHHhC
Confidence            345899999754332100  0  000    0      01123577899999999999999999999988874

>PF01695 IstB_IS21: IstB-like ATP binding protein; InterPro: IPR002611 Proteins in this entry contain an ATP/GTP binding P-loop motif

Probab=98.88  E-value=1.5e-09  Score=86.88  Aligned_cols=93  Identities=25%  Similarity=0.368  Sum_probs=56.8

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCC-------CcChHHHHHHHHHHHhhcccCCCCceeEEEEeCC
Q psy879           33 NIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASN-------DRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEA  105 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~-------~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~  105 (317)
                      +++|+||+|+|||++|.++++++...+..  +..++..+       ........+.+..+         ....++||||+
T Consensus        49 ~l~l~G~~G~GKThLa~ai~~~~~~~g~~--v~f~~~~~L~~~l~~~~~~~~~~~~~~~l---------~~~dlLilDDl  117 (178)
T PF01695_consen   49 NLILYGPPGTGKTHLAVAIANEAIRKGYS--VLFITASDLLDELKQSRSDGSYEELLKRL---------KRVDLLILDDL  117 (178)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHHHTT----EEEEEHHHHHHHHHCCHCCTTHCHHHHHH---------HTSSCEEEETC
T ss_pred             EEEEEhhHhHHHHHHHHHHHHHhccCCcc--eeEeecCceeccccccccccchhhhcCcc---------ccccEeccccc
Confidence            79999999999999999999988653332  33322110       00000111122222         24579999999


Q ss_pred             CCC--CHHHHHHHHHHhhhccCCceEEEEecCC
Q psy879          106 DSM--TDGAQQALRRTMEIYSNTTRFALACNNS  136 (317)
Q Consensus       106 d~l--~~~~~~~ll~~le~~~~~~~~il~~~~~  136 (317)
                      ...  +....+.|.++++..-.+...|++||..
T Consensus       118 G~~~~~~~~~~~l~~ii~~R~~~~~tIiTSN~~  150 (178)
T PF01695_consen  118 GYEPLSEWEAELLFEIIDERYERKPTIITSNLS  150 (178)
T ss_dssp             TSS---HHHHHCTHHHHHHHHHT-EEEEEESS-
T ss_pred             ceeeecccccccchhhhhHhhcccCeEeeCCCc
Confidence            875  4456677888887554445688888864

They are found associated with IS21 family insertion sequences []. Functionally they have not been characterised, but they may be involved in transposition [].; GO: 0005524 ATP binding; PDB: 3EC2_A 3ECC_A 2W58_A 2QGZ_A.

>PRK06921 hypothetical protein; Provisional

Probab=98.84  E-value=2.6e-08  Score=84.89  Aligned_cols=101  Identities=15%  Similarity=0.231  Sum_probs=60.0

Q ss_pred             CceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCC---
Q psy879           31 VPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADS---  107 (317)
Q Consensus        31 ~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~---  107 (317)
                      ..+++|+||+|+|||+++.++++++.... +..++.+....  ....+...+..+...-  .......+|||||++.   
T Consensus       117 ~~~l~l~G~~G~GKThLa~aia~~l~~~~-g~~v~y~~~~~--l~~~l~~~~~~~~~~~--~~~~~~dlLiIDDl~~~~~  191 (266)
T PRK06921        117 KNSIALLGQPGSGKTHLLTAAANELMRKK-GVPVLYFPFVE--GFGDLKDDFDLLEAKL--NRMKKVEVLFIDDLFKPVN  191 (266)
T ss_pred             CCeEEEECCCCCcHHHHHHHHHHHHhhhc-CceEEEEEHHH--HHHHHHHHHHHHHHHH--HHhcCCCEEEEeccccccC
Confidence            34699999999999999999999985431 23344443221  1112222111111000  0013567999999943   


Q ss_pred             ----CCHHHHHHHHHHhhhcc-CCceEEEEecCC
Q psy879          108 ----MTDGAQQALRRTMEIYS-NTTRFALACNNS  136 (317)
Q Consensus       108 ----l~~~~~~~ll~~le~~~-~~~~~il~~~~~  136 (317)
                          .+.-.+..|..+++..- ....+|++||.+
T Consensus       192 g~e~~t~~~~~~lf~iin~R~~~~k~tIitsn~~  225 (266)
T PRK06921        192 GKPRATEWQIEQMYSVLNYRYLNHKPILISSELT  225 (266)
T ss_pred             CCccCCHHHHHHHHHHHHHHHHCCCCEEEECCCC
Confidence                44445667888887543 235578888864

>PRK09183 transposase/IS protein; Provisional

Probab=98.83  E-value=8.1e-09  Score=87.75  Aligned_cols=110  Identities=19%  Similarity=0.244  Sum_probs=64.5

Q ss_pred             HHHHHHHH--HHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHH-----HHHHHHhhc
Q psy879           17 DTVERLKV--FSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRN-----KIKMFAQQK   89 (317)
Q Consensus        17 ~~~~~l~~--~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~-----~~~~~~~~~   89 (317)
                      ..+..|..  ++.+|.  +++|+||||+|||+++.+++..+...+  ..+..++.....  ..+..     .+....+..
T Consensus        88 ~~i~~L~~~~~i~~~~--~v~l~Gp~GtGKThLa~al~~~a~~~G--~~v~~~~~~~l~--~~l~~a~~~~~~~~~~~~~  161 (259)
T PRK09183         88 KQLQSLRSLSFIERNE--NIVLLGPSGVGKTHLAIALGYEAVRAG--IKVRFTTAADLL--LQLSTAQRQGRYKTTLQRG  161 (259)
T ss_pred             HHHHHHhcCCchhcCC--eEEEEeCCCCCHHHHHHHHHHHHHHcC--CeEEEEeHHHHH--HHHHHHHHCCcHHHHHHHH
Confidence            34444432  355555  799999999999999999988753322  223333221100  00000     011111111


Q ss_pred             ccCCCCceeEEEEeCCCCC--CHHHHHHHHHHhhhccCCceEEEEecCC
Q psy879           90 VTLPPGRHKIVILDEADSM--TDGAQQALRRTMEIYSNTTRFALACNNS  136 (317)
Q Consensus        90 ~~~~~~~~~vliiDE~d~l--~~~~~~~ll~~le~~~~~~~~il~~~~~  136 (317)
                          .....++||||++..  .....+.|+.+++..-....+|+|+|.+
T Consensus       162 ----~~~~dlLiiDdlg~~~~~~~~~~~lf~li~~r~~~~s~iiTsn~~  206 (259)
T PRK09183        162 ----VMAPRLLIIDEIGYLPFSQEEANLFFQVIAKRYEKGSMILTSNLP  206 (259)
T ss_pred             ----hcCCCEEEEcccccCCCChHHHHHHHHHHHHHHhcCcEEEecCCC
Confidence                134579999999974  5566778888887544445688888875

>PF12775 AAA_7: P-loop containing dynein motor region D3; PDB: 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A

Probab=98.83  E-value=2.4e-08  Score=85.31  Aligned_cols=145  Identities=20%  Similarity=0.284  Sum_probs=86.7

Q ss_pred             HHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHHHHHHHhh----cccCCCCce
Q psy879           22 LKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFAQQ----KVTLPPGRH   97 (317)
Q Consensus        22 l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~----~~~~~~~~~   97 (317)
                      +..++.++.  +++|+||+|||||++++.+.+.+...  ......++.+.......+...+......    ...++.+++
T Consensus        26 l~~l~~~~~--pvLl~G~~GtGKT~li~~~l~~l~~~--~~~~~~~~~s~~Tts~~~q~~ie~~l~k~~~~~~gP~~~k~  101 (272)
T PF12775_consen   26 LDLLLSNGR--PVLLVGPSGTGKTSLIQNFLSSLDSD--KYLVITINFSAQTTSNQLQKIIESKLEKRRGRVYGPPGGKK  101 (272)
T ss_dssp             HHHHHHCTE--EEEEESSTTSSHHHHHHHHHHCSTTC--CEEEEEEES-TTHHHHHHHHCCCTTECECTTEEEEEESSSE
T ss_pred             HHHHHHcCC--cEEEECCCCCchhHHHHhhhccCCcc--ccceeEeeccCCCCHHHHHHHHhhcEEcCCCCCCCCCCCcE
Confidence            566677776  79999999999999999988765322  2223334444333333333322211111    011223566


Q ss_pred             eEEEEeCCCCCCHH------HHHHHHHHhhhcc------------CCceEEEEecCCC---cCchhHhhhcceeeecCCC
Q psy879           98 KIVILDEADSMTDG------AQQALRRTMEIYS------------NTTRFALACNNSE---KIIEPIQSRCAMLRYNKLT  156 (317)
Q Consensus        98 ~vliiDE~d~l~~~------~~~~ll~~le~~~------------~~~~~il~~~~~~---~l~~~i~sR~~~i~f~~~~  156 (317)
                      -|++|||+..-..+      ..+.|.++++...            .++.+|.++++..   .+.+.+.+.+.++.++.|+
T Consensus       102 lv~fiDDlN~p~~d~ygtq~~iElLRQ~i~~~g~yd~~~~~~~~i~~i~~vaa~~p~~Gr~~is~R~~r~f~i~~~~~p~  181 (272)
T PF12775_consen  102 LVLFIDDLNMPQPDKYGTQPPIELLRQLIDYGGFYDRKKLEWKSIEDIQFVAAMNPTGGRNPISPRFLRHFNILNIPYPS  181 (272)
T ss_dssp             EEEEEETTT-S---TTS--HHHHHHHHHHHCSEEECTTTTEEEEECSEEEEEEESSTTT--SHHHHHHTTEEEEE----T
T ss_pred             EEEEecccCCCCCCCCCCcCHHHHHHHHHHhcCcccCCCcEEEEEeeeEEEEecCCCCCCCCCChHHhhheEEEEecCCC
Confidence            79999999876543      3456666676311            3455777776542   4788999999999999999


Q ss_pred             HHHHHHHHHHHHHH
Q psy879          157 DAQLLSKVIEICEK  170 (317)
Q Consensus       157 ~~~~~~~l~~~~~~  170 (317)
                      .+.+..+...++..
T Consensus       182 ~~sl~~If~~il~~  195 (272)
T PF12775_consen  182 DESLNTIFSSILQS  195 (272)
T ss_dssp             CCHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHhh
Confidence            99999888877653

>KOG0480|consensus

Probab=98.82  E-value=2.2e-08  Score=91.35  Aligned_cols=157  Identities=22%  Similarity=0.259  Sum_probs=102.0

Q ss_pred             CCcccCCHHHHHHHHHHHhcCC------------CceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChH
Q psy879            9 FSDIVGNEDTVERLKVFSSSGN------------VPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGID   76 (317)
Q Consensus         9 ~~~~~g~~~~~~~l~~~l~~~~------------~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~   76 (317)
                      |-.+.|++.++.-+.-.+-+|-            -.|+++.|.||+|||.+.++.+..+    +...+...+.++..+..
T Consensus       344 ~PsIyGhe~VK~GilL~LfGGv~K~a~eg~~lRGDinv~iVGDPgt~KSQfLk~v~~fs----PR~vYtsGkaSSaAGLT  419 (764)
T KOG0480|consen  344 FPSIYGHELVKAGILLSLFGGVHKSAGEGTSLRGDINVCIVGDPGTGKSQFLKAVCAFS----PRSVYTSGKASSAAGLT  419 (764)
T ss_pred             CccccchHHHHhhHHHHHhCCccccCCCCccccCCceEEEeCCCCccHHHHHHHHhccC----CcceEecCcccccccce
Confidence            5567899999887766654331            1379999999999999999999864    23344545544433321


Q ss_pred             --HHHHH-HHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhc-------------cCCceEEEEecCCC---
Q psy879           77 --TVRNK-IKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIY-------------SNTTRFALACNNSE---  137 (317)
Q Consensus        77 --~i~~~-~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~-------------~~~~~~il~~~~~~---  137 (317)
                        .+++. -+.|.-.+..+.-++.+|..|||+|+|....+.++++.||.-             +..+.++.++|+..   
T Consensus       420 aaVvkD~esgdf~iEAGALmLADnGICCIDEFDKMd~~dqvAihEAMEQQtISIaKAGv~aTLnARtSIlAAANPv~GhY  499 (764)
T KOG0480|consen  420 AAVVKDEESGDFTIEAGALMLADNGICCIDEFDKMDVKDQVAIHEAMEQQTISIAKAGVVATLNARTSILAAANPVGGHY  499 (764)
T ss_pred             EEEEecCCCCceeeecCcEEEccCceEEechhcccChHhHHHHHHHHHhheehheecceEEeecchhhhhhhcCCcCCcc
Confidence              11110 011112222233368899999999999999999999999942             34566777788653   


Q ss_pred             ----------cCchhHhhhcce--eeecCCCHHHHHHHHHHHHH
Q psy879          138 ----------KIIEPIQSRCAM--LRYNKLTDAQLLSKVIEICE  169 (317)
Q Consensus       138 ----------~l~~~i~sR~~~--i~f~~~~~~~~~~~l~~~~~  169 (317)
                                ++.++|.|||..  +-...+++..=..+-..+..
T Consensus       500 dR~ktl~eNi~msApimSRFDL~FiLlD~~nE~~D~~ia~hIld  543 (764)
T KOG0480|consen  500 DRKKTLRENINMSAPIMSRFDLFFILLDDCNEVVDYAIARHILD  543 (764)
T ss_pred             ccccchhhhcCCCchhhhhhcEEEEEecCCchHHHHHHHHHHHH
Confidence                      477999999988  44455555443333334433

>PF12774 AAA_6: Hydrolytic ATP binding site of dynein motor region D1; PDB: 3VKH_A 3VKG_A 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A

Probab=98.82  E-value=3.3e-07  Score=76.24  Aligned_cols=132  Identities=19%  Similarity=0.201  Sum_probs=88.2

Q ss_pred             HHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHHHHHHHhhcccCCCCceeE
Q psy879           20 ERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKI   99 (317)
Q Consensus        20 ~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~v   99 (317)
                      ..+..++....  .-.++||+|||||.+++.+++.+     +..++.+|++...+...+.+.+....+.        ..-
T Consensus        23 ~~l~~al~~~~--~~~~~GpagtGKtetik~La~~l-----G~~~~vfnc~~~~~~~~l~ril~G~~~~--------GaW   87 (231)
T PF12774_consen   23 LTLTQALSLNL--GGALSGPAGTGKTETIKDLARAL-----GRFVVVFNCSEQMDYQSLSRILKGLAQS--------GAW   87 (231)
T ss_dssp             HHHHHHHCTTT--EEEEESSTTSSHHHHHHHHHHCT-----T--EEEEETTSSS-HHHHHHHHHHHHHH--------T-E
T ss_pred             HHHHHHhccCC--CCCCcCCCCCCchhHHHHHHHHh-----CCeEEEecccccccHHHHHHHHHHHhhc--------Cch
Confidence            34555565443  45789999999999999999986     3457888998888888888888777654        357


Q ss_pred             EEEeCCCCCCHHHHHHHHHHhhh--------------------ccCCceEEEEecCC----CcCchhHhhhcceeeecCC
Q psy879          100 VILDEADSMTDGAQQALRRTMEI--------------------YSNTTRFALACNNS----EKIIEPIQSRCAMLRYNKL  155 (317)
Q Consensus       100 liiDE~d~l~~~~~~~ll~~le~--------------------~~~~~~~il~~~~~----~~l~~~i~sR~~~i~f~~~  155 (317)
                      +++||++.+..+....+...+..                    ..+++.+.++.|+.    ..+++.+++-++.+.+..|
T Consensus        88 ~cfdefnrl~~~vLS~i~~~i~~i~~al~~~~~~~~~~g~~i~l~~~~~iFiT~np~y~gr~~LP~nLk~lFRpvam~~P  167 (231)
T PF12774_consen   88 LCFDEFNRLSEEVLSVISQQIQSIQDALRAKQKSFTLEGQEIKLNPNCGIFITMNPGYAGRSELPENLKALFRPVAMMVP  167 (231)
T ss_dssp             EEEETCCCSSHHHHHHHHHHHHHHHHHHHCTSSEEEETTCEEE--TT-EEEEEE-B-CCCC--S-HHHCTTEEEEE--S-
T ss_pred             hhhhhhhhhhHHHHHHHHHHHHHHHHhhcccccccccCCCEEEEccceeEEEeeccccCCcccCCHhHHHHhheeEEeCC
Confidence            89999999998876655444431                    12344456666643    4799999999999999999


Q ss_pred             CHHHHHHHHHH
Q psy879          156 TDAQLLSKVIE  166 (317)
Q Consensus       156 ~~~~~~~~l~~  166 (317)
                      +...+.+++..
T Consensus       168 D~~~I~ei~L~  178 (231)
T PF12774_consen  168 DLSLIAEILLL  178 (231)
T ss_dssp             -HHHHHHHHHH
T ss_pred             CHHHHHHHHHH
Confidence            88877776544

>PF05729 NACHT: NACHT domain

Probab=98.81  E-value=4.1e-08  Score=77.68  Aligned_cols=136  Identities=14%  Similarity=0.190  Sum_probs=78.8

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHcCCCCCC----ceEEecCCCCcCh---HHHHHHHHHHHhhcc---------cCCCCce
Q psy879           34 IIISGPPGVGKTTTILCLARILLGPSFKD----AVLELNASNDRGI---DTVRNKIKMFAQQKV---------TLPPGRH   97 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~l~~~~~~~----~~~~~~~~~~~~~---~~i~~~~~~~~~~~~---------~~~~~~~   97 (317)
                      ++++|++|+|||++++.++..+.......    ..+..........   ..+.+.+........         .......
T Consensus         3 l~I~G~~G~GKStll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~   82 (166)
T PF05729_consen    3 LWISGEPGSGKSTLLRKLAQQLAEEEPPPSKFPYPFFFSLRDISDSNNSRSLADLLFDQLPESIAPIEELLQELLEKNKR   82 (166)
T ss_pred             EEEECCCCCChHHHHHHHHHHHHhcCcccccceEEEEEeehhhhhccccchHHHHHHHhhccchhhhHHHHHHHHHcCCc
Confidence            78999999999999999998875443211    1222222111110   112222211100000         0012456


Q ss_pred             eEEEEeCCCCCCHHHH--------HHHHHHhhh-ccCCceEEEEecCCCc-CchhHhhhcceeeecCCCHHHHHHHHHHH
Q psy879           98 KIVILDEADSMTDGAQ--------QALRRTMEI-YSNTTRFALACNNSEK-IIEPIQSRCAMLRYNKLTDAQLLSKVIEI  167 (317)
Q Consensus        98 ~vliiDE~d~l~~~~~--------~~ll~~le~-~~~~~~~il~~~~~~~-l~~~i~sR~~~i~f~~~~~~~~~~~l~~~  167 (317)
                      -+++||-+|.+.....        ..|..++.. .++++.+++++..... -..........+...+++++++.+++.++
T Consensus        83 ~llilDglDE~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~liit~r~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~  162 (166)
T PF05729_consen   83 VLLILDGLDELEEQDQSQERQRLLDLLSQLLPQALPPGVKLIITSRPRAFPDLRRRLKQAQILELEPFSEEDIKQYLRKY  162 (166)
T ss_pred             eEEEEechHhcccchhhhHHHHHHHHHHHHhhhccCCCCeEEEEEcCChHHHHHHhcCCCcEEEECCCCHHHHHHHHHHH
Confidence            7899999998876432        244555555 4566778887765432 12222233356899999999999999887


Q ss_pred             HH
Q psy879          168 CE  169 (317)
Q Consensus       168 ~~  169 (317)
                      +.
T Consensus       163 f~  164 (166)
T PF05729_consen  163 FS  164 (166)
T ss_pred             hh
Confidence            64

>COG1220 HslU ATP-dependent protease HslVU (ClpYQ), ATPase subunit [Posttranslational modification, protein turnover, chaperones]

Probab=98.81  E-value=5e-08  Score=82.88  Aligned_cols=107  Identities=21%  Similarity=0.291  Sum_probs=74.6

Q ss_pred             ceeEEEEeCCCCCCHH------------HHHHHHHHhhhc----------cCCceEEEEe----cCCCcCchhHhhhcce
Q psy879           96 RHKIVILDEADSMTDG------------AQQALRRTMEIY----------SNTTRFALAC----NNSEKIIEPIQSRCAM  149 (317)
Q Consensus        96 ~~~vliiDE~d~l~~~------------~~~~ll~~le~~----------~~~~~~il~~----~~~~~l~~~i~sR~~~  149 (317)
                      ...+|||||+|+....            .|..||.++|..          ..++.||.+.    ..|+.+.|.++-|+.+
T Consensus       250 ~~GIvFIDEIDKIa~~~~~g~~dvSREGVQRDlLPlvEGstV~TKyG~VkTdHILFIasGAFh~sKPSDLiPELQGRfPI  329 (444)
T COG1220         250 QNGIVFIDEIDKIAKRGGSGGPDVSREGVQRDLLPLVEGSTVSTKYGPVKTDHILFIASGAFHVAKPSDLIPELQGRFPI  329 (444)
T ss_pred             hcCeEEEehhhHHHhcCCCCCCCcchhhhcccccccccCceeeccccccccceEEEEecCceecCChhhcChhhcCCCce
Confidence            3589999999987432            477789998832          1233344332    2467899999999998


Q ss_pred             -eeecCCCHHHHHHHHHH-----------HHHHcCC--CCCHHHHHHHHHhc--------CCCHHHHHHHHHHhh
Q psy879          150 -LRYNKLTDAQLLSKVIE-----------ICEKENI--SHTNDGLEAIVFTA--------QGDMRQALNNLQSTH  202 (317)
Q Consensus       150 -i~f~~~~~~~~~~~l~~-----------~~~~~~~--~i~~~~~~~l~~~~--------~gd~r~~i~~l~~~~  202 (317)
                       +++.+++.+++.++|.+           ..+.+|+  .+++++++.++..+        +=..|++...+++..
T Consensus       330 RVEL~~Lt~~Df~rILtep~~sLikQY~aLlkTE~v~l~FtddaI~~iAeiA~~vN~~~ENIGARRLhTvlErlL  404 (444)
T COG1220         330 RVELDALTKEDFERILTEPKASLIKQYKALLKTEGVELEFTDDAIKRIAEIAYQVNEKTENIGARRLHTVLERLL  404 (444)
T ss_pred             EEEcccCCHHHHHHHHcCcchHHHHHHHHHHhhcCeeEEecHHHHHHHHHHHHHhcccccchhHHHHHHHHHHHH
Confidence             99999999999998863           2334554  46788888887654        223666666666543

>PRK06835 DNA replication protein DnaC; Validated

Probab=98.81  E-value=3.4e-08  Score=86.45  Aligned_cols=134  Identities=22%  Similarity=0.260  Sum_probs=75.7

Q ss_pred             HHHHHHHHHhc--CCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHH-HHHHHhhc-ccCC
Q psy879           18 TVERLKVFSSS--GNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNK-IKMFAQQK-VTLP   93 (317)
Q Consensus        18 ~~~~l~~~l~~--~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~-~~~~~~~~-~~~~   93 (317)
                      +.+....++.+  ....+++|+||+|+|||+++.++|+++...+  ..++.+.....  ...+... +....... ....
T Consensus       168 ~~~~~~~f~~~f~~~~~~Lll~G~~GtGKThLa~aIa~~l~~~g--~~V~y~t~~~l--~~~l~~~~~~~~~~~~~~~~~  243 (329)
T PRK06835        168 ILEKCKNFIENFDKNNENLLFYGNTGTGKTFLSNCIAKELLDRG--KSVIYRTADEL--IEILREIRFNNDKELEEVYDL  243 (329)
T ss_pred             HHHHHHHHHHHHhccCCcEEEECCCCCcHHHHHHHHHHHHHHCC--CeEEEEEHHHH--HHHHHHHHhccchhHHHHHHH
Confidence            34434445552  1124699999999999999999999986543  23443333211  1111110 00000000 0000


Q ss_pred             CCceeEEEEeCCCCC--CHHHHHHHHHHhhhcc-CCceEEEEecCCC-----cCchhHhhhcc----eeeecCC
Q psy879           94 PGRHKIVILDEADSM--TDGAQQALRRTMEIYS-NTTRFALACNNSE-----KIIEPIQSRCA----MLRYNKL  155 (317)
Q Consensus        94 ~~~~~vliiDE~d~l--~~~~~~~ll~~le~~~-~~~~~il~~~~~~-----~l~~~i~sR~~----~i~f~~~  155 (317)
                      .....++||||+...  +...+..|..+++..- ....+|++||...     .+.+.+.||+.    ++.|...
T Consensus       244 l~~~DLLIIDDlG~e~~t~~~~~~Lf~iin~R~~~~k~tIiTSNl~~~el~~~~~eri~SRL~~~~~~i~~~G~  317 (329)
T PRK06835        244 LINCDLLIIDDLGTEKITEFSKSELFNLINKRLLRQKKMIISTNLSLEELLKTYSERISSRLLGNFTLLKFYGE  317 (329)
T ss_pred             hccCCEEEEeccCCCCCCHHHHHHHHHHHHHHHHCCCCEEEECCCCHHHHHHHHhHHHHHHHHcCCEEEEecCc
Confidence            135679999999654  5667888999988643 3456888888642     23456666653    3555443

>PF13401 AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S_B

Probab=98.80  E-value=2.1e-08  Score=76.27  Aligned_cols=101  Identities=28%  Similarity=0.359  Sum_probs=59.9

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHcCCC---CCCceEEecCCCCcChHHHHHHHHHHHhhcccC---------------CC
Q psy879           33 NIIISGPPGVGKTTTILCLARILLGPS---FKDAVLELNASNDRGIDTVRNKIKMFAQQKVTL---------------PP   94 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~~~~---~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~---------------~~   94 (317)
                      +++++||+|+|||++++.+++.+....   ....++.+++........+...+......+...               ..
T Consensus         6 ~~~i~G~~G~GKT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~l~~~~~~~l~~   85 (131)
T PF13401_consen    6 ILVISGPPGSGKTTLIKRLARQLNAEAEIKNHPDVIYVNCPSSRTPRDFAQEILEALGLPLKSRQTSDELRSLLIDALDR   85 (131)
T ss_dssp             -EEEEE-TTSSHHHHHHHHHHHHHHHHHHCCCEEEEEEEHHHHSSHHHHHHHHHHHHT-SSSSTS-HHHHHHHHHHHHHH
T ss_pred             ccEEEcCCCCCHHHHHHHHHHHhHHhhhccCCCcEEEEEeCCCCCHHHHHHHHHHHhCccccccCCHHHHHHHHHHHHHh
Confidence            599999999999999999999874210   022334443322223333322222211111100               00


Q ss_pred             CceeEEEEeCCCCC-CHHHHHHHHHHhhhccCCceEEEEecC
Q psy879           95 GRHKIVILDEADSM-TDGAQQALRRTMEIYSNTTRFALACNN  135 (317)
Q Consensus        95 ~~~~vliiDE~d~l-~~~~~~~ll~~le~~~~~~~~il~~~~  135 (317)
                      ....+|+|||+|.+ ..+..+.|..+++  ..++.+|+++++
T Consensus        86 ~~~~~lviDe~~~l~~~~~l~~l~~l~~--~~~~~vvl~G~~  125 (131)
T PF13401_consen   86 RRVVLLVIDEADHLFSDEFLEFLRSLLN--ESNIKVVLVGTP  125 (131)
T ss_dssp             CTEEEEEEETTHHHHTHHHHHHHHHHTC--SCBEEEEEEESS
T ss_pred             cCCeEEEEeChHhcCCHHHHHHHHHHHh--CCCCeEEEEECh
Confidence            13469999999999 8777888877777  566778888766

>KOG0477|consensus

Probab=98.79  E-value=1.4e-08  Score=92.37  Aligned_cols=136  Identities=21%  Similarity=0.315  Sum_probs=88.0

Q ss_pred             cccCCHHHHHHHHHHHhcCCC------------ceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHH-
Q psy879           11 DIVGNEDTVERLKVFSSSGNV------------PNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDT-   77 (317)
Q Consensus        11 ~~~g~~~~~~~l~~~l~~~~~------------~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~-   77 (317)
                      .++|+..++..+.-++-+|..            -|+||.|.|||||+.+.+.+++.-    ....+-...+++..+... 
T Consensus       450 sIyGh~~VK~AvAlaLfGGv~kn~~~khkvRGDinvLL~GDPGTaKSQFLKY~eK~s----~RAV~tTGqGASavGLTa~  525 (854)
T KOG0477|consen  450 SIYGHEDVKRAVALALFGGVPKNPGGKHKVRGDINVLLLGDPGTAKSQFLKYAEKTS----PRAVFTTGQGASAVGLTAY  525 (854)
T ss_pred             hhhchHHHHHHHHHHHhcCCccCCCCCceeccceeEEEecCCCccHHHHHHHHHhcC----cceeEeccCCccccceeEE
Confidence            467899999988877765432            269999999999999999998752    111122222222222110 


Q ss_pred             HH-H-HHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhc-------------cCCceEEEEecCCC-----
Q psy879           78 VR-N-KIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIY-------------SNTTRFALACNNSE-----  137 (317)
Q Consensus        78 i~-~-~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~-------------~~~~~~il~~~~~~-----  137 (317)
                      ++ . .-+.|......+--++++|.+|||+|+|+......+...||.-             ...+.+|.++|+..     
T Consensus       526 v~KdPvtrEWTLEaGALVLADkGvClIDEFDKMndqDRtSIHEAMEQQSISISKAGIVtsLqArctvIAAanPigGRY~~  605 (854)
T KOG0477|consen  526 VRKDPVTREWTLEAGALVLADKGVCLIDEFDKMNDQDRTSIHEAMEQQSISISKAGIVTSLQARCTVIAAANPIGGRYNP  605 (854)
T ss_pred             EeeCCccceeeeccCeEEEccCceEEeehhhhhcccccchHHHHHHhcchhhhhhhHHHHHHhhhhhheecCCCCCccCC
Confidence            00 0 0112222222222367899999999999999988899988843             24455788888631     


Q ss_pred             --------cCchhHhhhccee
Q psy879          138 --------KIIEPIQSRCAML  150 (317)
Q Consensus       138 --------~l~~~i~sR~~~i  150 (317)
                              .+..+|.|||.++
T Consensus       606 s~tFaqNV~ltePIlSRFDiL  626 (854)
T KOG0477|consen  606 SLTFAQNVDLTEPILSRFDIL  626 (854)
T ss_pred             ccchhhccccccchhhhccee
Confidence                    5678999999883

>KOG0736|consensus

Probab=98.79  E-value=9.7e-08  Score=89.15  Aligned_cols=145  Identities=18%  Similarity=0.239  Sum_probs=94.7

Q ss_pred             ceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCC----CcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCC
Q psy879           32 PNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASN----DRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADS  107 (317)
Q Consensus        32 ~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~----~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~  107 (317)
                      +.+|++|+||||||++++++|+++     +..+++++|..    .....+  ..+..+......   ..+.|+++-+.|-
T Consensus       432 ~~vLLhG~~g~GK~t~V~~vas~l-----g~h~~evdc~el~~~s~~~~e--tkl~~~f~~a~~---~~pavifl~~~dv  501 (953)
T KOG0736|consen  432 PSVLLHGPPGSGKTTVVRAVASEL-----GLHLLEVDCYELVAESASHTE--TKLQAIFSRARR---CSPAVLFLRNLDV  501 (953)
T ss_pred             eEEEEeCCCCCChHHHHHHHHHHh-----CCceEeccHHHHhhcccchhH--HHHHHHHHHHhh---cCceEEEEeccce
Confidence            349999999999999999999997     33455555432    111111  122222222211   4678899888887


Q ss_pred             CCHH--------HHHHHHHHhh-----hccCCceEEEEecCCCcCchhHhhhcce-eeecCCCHHHHHHHHHHHHHHcCC
Q psy879          108 MTDG--------AQQALRRTME-----IYSNTTRFALACNNSEKIIEPIQSRCAM-LRYNKLTDAQLLSKVIEICEKENI  173 (317)
Q Consensus       108 l~~~--------~~~~ll~~le-----~~~~~~~~il~~~~~~~l~~~i~sR~~~-i~f~~~~~~~~~~~l~~~~~~~~~  173 (317)
                      +..+        .+..+...+.     ...+.+++|.+++..+.+++.+++-+.. +.++.++++|..+||+....... 
T Consensus       502 l~id~dgged~rl~~~i~~~ls~e~~~~~~~~~ivv~t~~s~~~lp~~i~~~f~~ei~~~~lse~qRl~iLq~y~~~~~-  580 (953)
T KOG0736|consen  502 LGIDQDGGEDARLLKVIRHLLSNEDFKFSCPPVIVVATTSSIEDLPADIQSLFLHEIEVPALSEEQRLEILQWYLNHLP-  580 (953)
T ss_pred             eeecCCCchhHHHHHHHHHHHhcccccCCCCceEEEEeccccccCCHHHHHhhhhhccCCCCCHHHHHHHHHHHHhccc-
Confidence            6422        2333333333     1335667888888999999999999887 99999999999999998876543 


Q ss_pred             CCCHHH-HHHHHHhcC
Q psy879          174 SHTNDG-LEAIVFTAQ  188 (317)
Q Consensus       174 ~i~~~~-~~~l~~~~~  188 (317)
                       ++++. .+.++.++.
T Consensus       581 -~n~~v~~k~~a~~t~  595 (953)
T KOG0736|consen  581 -LNQDVNLKQLARKTS  595 (953)
T ss_pred             -cchHHHHHHHHHhcC
Confidence             33332 334454443

>PRK04841 transcriptional regulator MalT; Provisional

Probab=98.74  E-value=5.5e-06  Score=83.37  Aligned_cols=182  Identities=16%  Similarity=0.143  Sum_probs=114.0

Q ss_pred             CCCCCCcccCCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHHHHH
Q psy879            5 RPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKM   84 (317)
Q Consensus         5 ~P~~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~~~   84 (317)
                      .|..-.+++-++.+.+.|...   ...+-.+++||+|+||||++..++... +   ....+.+...+......+...+..
T Consensus         9 ~p~~~~~~~~R~rl~~~l~~~---~~~~~~~v~apaG~GKTtl~~~~~~~~-~---~~~w~~l~~~d~~~~~f~~~l~~~   81 (903)
T PRK04841          9 RPVRLHNTVVRERLLAKLSGA---NNYRLVLVTSPAGYGKTTLISQWAAGK-N---NLGWYSLDESDNQPERFASYLIAA   81 (903)
T ss_pred             CCCCccccCcchHHHHHHhcc---cCCCeEEEECCCCCCHHHHHHHHHHhC-C---CeEEEecCcccCCHHHHHHHHHHH
Confidence            355567888888888777542   233459999999999999999988642 1   122223332221111111111111


Q ss_pred             HHhh-------------cc--------------cC-CCCceeEEEEeCCCCCCHHH-HHHHHHHhhhccCCceEEEEecC
Q psy879           85 FAQQ-------------KV--------------TL-PPGRHKIVILDEADSMTDGA-QQALRRTMEIYSNTTRFALACNN  135 (317)
Q Consensus        85 ~~~~-------------~~--------------~~-~~~~~~vliiDE~d~l~~~~-~~~ll~~le~~~~~~~~il~~~~  135 (317)
                      +...             ..              .+ ....+-+++||+++.+.... ...+..++...+++..+|+++..
T Consensus        82 l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~lvlDD~h~~~~~~~~~~l~~l~~~~~~~~~lv~~sR~  161 (903)
T PRK04841         82 LQQATNGHCSKSEALAQKRQYASLSSLFAQLFIELADWHQPLYLVIDDYHLITNPEIHEAMRFFLRHQPENLTLVVLSRN  161 (903)
T ss_pred             HHHhcCcccchhhhhhccCCcCCHHHHHHHHHHHHhcCCCCEEEEEeCcCcCCChHHHHHHHHHHHhCCCCeEEEEEeCC
Confidence            1000             00              00 01457799999999997555 44666667777888888887765


Q ss_pred             CCcC-chhHhhhcceeeec----CCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHH
Q psy879          136 SEKI-IEPIQSRCAMLRYN----KLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALN  196 (317)
Q Consensus       136 ~~~l-~~~i~sR~~~i~f~----~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~  196 (317)
                      ...+ ...++-+...+.+.    +++.+|...++....   |..++++.+..+.+.++|.+.-+.-
T Consensus       162 ~~~~~~~~l~~~~~~~~l~~~~l~f~~~e~~~ll~~~~---~~~~~~~~~~~l~~~t~Gwp~~l~l  224 (903)
T PRK04841        162 LPPLGIANLRVRDQLLEIGSQQLAFDHQEAQQFFDQRL---SSPIEAAESSRLCDDVEGWATALQL  224 (903)
T ss_pred             CCCCchHhHHhcCcceecCHHhCCCCHHHHHHHHHhcc---CCCCCHHHHHHHHHHhCChHHHHHH
Confidence            3222 23333333344444    889999999987765   6678999999999999999865443

>PF12169 DNA_pol3_gamma3: DNA polymerase III subunits gamma and tau domain III; InterPro: IPR022754 This domain is found in bacteria and eukaryotes, and is approximately 110 amino acids in length

Probab=98.71  E-value=2.6e-07  Score=71.41  Aligned_cols=104  Identities=20%  Similarity=0.293  Sum_probs=83.5

Q ss_pred             ccHHHHHhhcCCCCHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhc------C------------
Q psy879          208 VTAEYVFKVCDEPHPLAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDIIGNIFRVAKTL------D------------  269 (317)
Q Consensus       208 i~~~~v~~~~~~~~~~~i~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~~~~------~------------  269 (317)
                      ||.++|.++++....+.++++++++.++|..+++..++++...|.+|..++..+..+++.+      +            
T Consensus         1 It~e~V~~~lG~v~~~~i~~l~~ai~~~d~~~~l~~~~~l~~~G~d~~~~l~~L~~~~R~ll~~k~~~~~~~~~~~~~~~   80 (143)
T PF12169_consen    1 ITAEDVREILGLVDEEQIFELLDAILEGDAAEALELLNELLEQGKDPKQFLDDLIEYLRDLLLYKITGDKSNLLELSEEE   80 (143)
T ss_dssp             B-HHHHHHHHTHTSTHHHHHHHHHHHTT-HHHHHHHHHHHHHCT--HHHHHHHHHHHHHHHHHHTTSGGGS-SG--CTTT
T ss_pred             CCHHHHHHHHCCCCHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHhCCchhhcccCCHHH
Confidence            6789999999999999999999999999999999999999999999999998875544332      1            


Q ss_pred             ----------CChHHHHHHHHHHHHHHhHHhcCCCcHHHHHHHHHHHHHhhc
Q psy879          270 ----------IPEPLKLSIIQEIGNVHLRISEGVNSLLQLSGLLARLCIVGS  311 (317)
Q Consensus       270 ----------~~~~~~~~~~~~l~~~~~~l~~g~~~~l~le~~~~~~~~~~~  311 (317)
                                .+.....++++.+.+...+++...++++.+|.++.++|....
T Consensus        81 ~~~~~~~a~~~~~~~l~~~~~~l~~~~~~lr~s~~pr~~lE~~llrl~~~~~  132 (143)
T PF12169_consen   81 EEKLKELAKKFSPERLQRILQILLEAENELRYSSNPRILLEMALLRLCQLKS  132 (143)
T ss_dssp             HHHHHHHHHHS-HHHHHHHHHHHHHHHHHTTTSSSHHHHHHHHHHHHHHTC-
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHHHHhccCCChHHHHHHHHHHHHHHhh
Confidence                      111123338889999999999999999999999999997543

It is found in association with PF00004 from PFAM. This domain is also present in the tau subunit before it undergoes cleavage. Domains I-III are shared between the tau and the gamma subunits, while most of the DnaB-binding Domain IV and all of the alpha-interacting Domain V are unique to tau. ; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 1NJF_B 3GLG_G 1XXH_I 1NJG_A 3GLF_B 3GLI_G.

>PRK08939 primosomal protein DnaI; Reviewed

Probab=98.70  E-value=4.3e-08  Score=85.14  Aligned_cols=128  Identities=15%  Similarity=0.144  Sum_probs=69.4

Q ss_pred             CCCCCCcccC----CHHHHHHHHHHHhcC----CCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChH
Q psy879            5 RPQTFSDIVG----NEDTVERLKVFSSSG----NVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGID   76 (317)
Q Consensus         5 ~P~~~~~~~g----~~~~~~~l~~~l~~~----~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~   76 (317)
                      ...+|+++..    +..+.+....++.+.    ...+++|+||+|+|||+++.++++++...+....++....    -..
T Consensus       122 ~~atf~~~~~~~~~~~~~~~~~~~fi~~~~~~~~~~gl~L~G~~G~GKThLa~Aia~~l~~~g~~v~~~~~~~----l~~  197 (306)
T PRK08939        122 LQASLADIDLDDRDRLDALMAALDFLEAYPPGEKVKGLYLYGDFGVGKSYLLAAIANELAKKGVSSTLLHFPE----FIR  197 (306)
T ss_pred             hcCcHHHhcCCChHHHHHHHHHHHHHHHhhccCCCCeEEEECCCCCCHHHHHHHHHHHHHHcCCCEEEEEHHH----HHH
Confidence            3456777764    233444445555531    2346999999999999999999999854333332332211    001


Q ss_pred             HHHHHHHHHHhhcccCCCCceeEEEEeCCCCC--CHHHHHHHHH-Hhhhc-cCCceEEEEecCC
Q psy879           77 TVRNKIKMFAQQKVTLPPGRHKIVILDEADSM--TDGAQQALRR-TMEIY-SNTTRFALACNNS  136 (317)
Q Consensus        77 ~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l--~~~~~~~ll~-~le~~-~~~~~~il~~~~~  136 (317)
                      .+...+..-......-......++||||+..-  ++-....++. +++.. ......|+|||-+
T Consensus       198 ~lk~~~~~~~~~~~l~~l~~~dlLiIDDiG~e~~s~~~~~~ll~~Il~~R~~~~~~ti~TSNl~  261 (306)
T PRK08939        198 ELKNSISDGSVKEKIDAVKEAPVLMLDDIGAEQMSSWVRDEVLGVILQYRMQEELPTFFTSNFD  261 (306)
T ss_pred             HHHHHHhcCcHHHHHHHhcCCCEEEEecCCCccccHHHHHHHHHHHHHHHHHCCCeEEEECCCC
Confidence            11111100000000000146779999999754  4444544544 44533 4667788888763

>COG1484 DnaC DNA replication protein [DNA replication, recombination, and repair]

Probab=98.70  E-value=4.5e-08  Score=82.80  Aligned_cols=102  Identities=20%  Similarity=0.290  Sum_probs=59.7

Q ss_pred             ceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHHHHHHH-hhcccCCCCceeEEEEeCCCCC--
Q psy879           32 PNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFA-QQKVTLPPGRHKIVILDEADSM--  108 (317)
Q Consensus        32 ~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~-~~~~~~~~~~~~vliiDE~d~l--  108 (317)
                      .+++|+||||+|||+++-++++.+...  +..+..+...+  -...+........ .....-.-....|+||||+...  
T Consensus       106 ~nl~l~G~~G~GKThLa~Ai~~~l~~~--g~sv~f~~~~e--l~~~Lk~~~~~~~~~~~l~~~l~~~dlLIiDDlG~~~~  181 (254)
T COG1484         106 ENLVLLGPPGVGKTHLAIAIGNELLKA--GISVLFITAPD--LLSKLKAAFDEGRLEEKLLRELKKVDLLIIDDIGYEPF  181 (254)
T ss_pred             CcEEEECCCCCcHHHHHHHHHHHHHHc--CCeEEEEEHHH--HHHHHHHHHhcCchHHHHHHHhhcCCEEEEecccCccC
Confidence            379999999999999999999998632  33333333221  1111111111100 0000000146789999999985  


Q ss_pred             CHHHHHHHHHHhhhccCCceEEEEecCCC
Q psy879          109 TDGAQQALRRTMEIYSNTTRFALACNNSE  137 (317)
Q Consensus       109 ~~~~~~~ll~~le~~~~~~~~il~~~~~~  137 (317)
                      +....+.+..++...-.....++++|.+.
T Consensus       182 ~~~~~~~~~q~I~~r~~~~~~~~tsN~~~  210 (254)
T COG1484         182 SQEEADLLFQLISRRYESRSLIITSNLSF  210 (254)
T ss_pred             CHHHHHHHHHHHHHHHhhccceeecCCCh
Confidence            55566777776665433333488888653

>COG1125 OpuBA ABC-type proline/glycine betaine transport systems, ATPase components [Amino acid transport and metabolism]

Probab=98.68  E-value=1.8e-07  Score=76.70  Aligned_cols=198  Identities=17%  Similarity=0.269  Sum_probs=133.3

Q ss_pred             cCCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHHHHHHHhhcccC
Q psy879           13 VGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFAQQKVTL   92 (317)
Q Consensus        13 ~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~   92 (317)
                      +++..+++.+.-.+..|.  -+.|.||+||||||+.+.+-+.+ .++.+..++......+.....+|..+++..+....+
T Consensus        11 y~~~~av~~v~l~I~~ge--f~vliGpSGsGKTTtLkMINrLi-ept~G~I~i~g~~i~~~d~~~LRr~IGYviQqigLF   87 (309)
T COG1125          11 YGNKKAVDDVNLTIEEGE--FLVLIGPSGSGKTTTLKMINRLI-EPTSGEILIDGEDISDLDPVELRRKIGYVIQQIGLF   87 (309)
T ss_pred             cCCceeeeeeeEEecCCe--EEEEECCCCCcHHHHHHHHhccc-CCCCceEEECCeecccCCHHHHHHhhhhhhhhcccC
Confidence            344555555555566666  58999999999999999998865 444444444444444556677888888887765333


Q ss_pred             CCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcCchhHhhhcceeeecCCCHHHHHHHHHHHHHHcC
Q psy879           93 PPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKEN  172 (317)
Q Consensus        93 ~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~~~i~sR~~~i~f~~~~~~~~~~~l~~~~~~~~  172 (317)
                      |+             ++-          +   .|+                   +.+-.+..++.+++.+...+.+..-|
T Consensus        88 Ph-------------~Tv----------~---eNI-------------------a~VP~L~~w~k~~i~~r~~ELl~lvg  122 (309)
T COG1125          88 PH-------------LTV----------A---ENI-------------------ATVPKLLGWDKERIKKRADELLDLVG  122 (309)
T ss_pred             CC-------------ccH----------H---HHH-------------------HhhhhhcCCCHHHHHHHHHHHHHHhC
Confidence            21             110          0   011                   11112347888888888888877655


Q ss_pred             CCCCH-HHHHHHHHhcCCCHHHHHHHHHHhhhCCCcccHHHHHhhcCCCCHHHHHHHHHHHh----------cCCHHHHH
Q psy879          173 ISHTN-DGLEAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEMLLNCV----------EGNMKDSY  241 (317)
Q Consensus       173 ~~i~~-~~~~~l~~~~~gd~r~~i~~l~~~~~~~~~i~~~~v~~~~~~~~~~~i~~l~~~~~----------~~~~~~~~  241 (317)
                      +  ++ +..+.+...-+|.-++-+..+++.+.+...+-.++...+++......+.+.+..+.          .+|.++|+
T Consensus       123 L--~p~~~~~RyP~eLSGGQQQRVGv~RALAadP~ilLMDEPFgALDpI~R~~lQ~e~~~lq~~l~kTivfVTHDidEA~  200 (309)
T COG1125         123 L--DPSEYADRYPHELSGGQQQRVGVARALAADPPILLMDEPFGALDPITRKQLQEEIKELQKELGKTIVFVTHDIDEAL  200 (309)
T ss_pred             C--CHHHHhhcCchhcCcchhhHHHHHHHHhcCCCeEeecCCccccChhhHHHHHHHHHHHHHHhCCEEEEEecCHHHHH
Confidence            4  45 46677777777778999999999999999899998888888776666555555443          46899999


Q ss_pred             HHHHHH--HHcCC-----CHHHHHHH
Q psy879          242 KIIHHL--YKLGY-----APEDIIGN  260 (317)
Q Consensus       242 ~~~~~l--~~~~~-----~~~~i~~~  260 (317)
                      ++-...  ++.|.     +|..|+..
T Consensus       201 kLadri~vm~~G~i~Q~~~P~~il~~  226 (309)
T COG1125         201 KLADRIAVMDAGEIVQYDTPDEILAN  226 (309)
T ss_pred             hhhceEEEecCCeEEEeCCHHHHHhC
Confidence            987765  45553     66666654

>COG1126 GlnQ ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]

Probab=98.68  E-value=3e-08  Score=79.33  Aligned_cols=135  Identities=19%  Similarity=0.340  Sum_probs=81.6

Q ss_pred             CCcccCCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCC-CCcChHHHHHHHHHHHh
Q psy879            9 FSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNAS-NDRGIDTVRNKIKMFAQ   87 (317)
Q Consensus         9 ~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~-~~~~~~~i~~~~~~~~~   87 (317)
                      +..-+|..++++.+.-.+..|.  .+.+.||+|+||||+.|++... ...+.+...++.... .......+|..++..+|
T Consensus         8 l~K~fg~~~VLkgi~l~v~~Ge--vv~iiGpSGSGKSTlLRclN~L-E~~~~G~I~i~g~~~~~~~~~~~~R~~vGmVFQ   84 (240)
T COG1126           8 LSKSFGDKEVLKGISLSVEKGE--VVVIIGPSGSGKSTLLRCLNGL-EEPDSGSITVDGEDVGDKKDILKLRRKVGMVFQ   84 (240)
T ss_pred             eeEEeCCeEEecCcceeEcCCC--EEEEECCCCCCHHHHHHHHHCC-cCCCCceEEECCEeccchhhHHHHHHhcCeecc
Confidence            4455677777777777777887  7999999999999999998764 333333222222111 11133344444444433


Q ss_pred             hcccCCC-------------------------------------------------------------CceeEEEEeCCC
Q psy879           88 QKVTLPP-------------------------------------------------------------GRHKIVILDEAD  106 (317)
Q Consensus        88 ~~~~~~~-------------------------------------------------------------~~~~vliiDE~d  106 (317)
                      ....+|+                                                             -+++++++||..
T Consensus        85 ~fnLFPHlTvleNv~lap~~v~~~~k~eA~~~A~~lL~~VGL~~ka~~yP~qLSGGQqQRVAIARALaM~P~vmLFDEPT  164 (240)
T COG1126          85 QFNLFPHLTVLENVTLAPVKVKKLSKAEAREKALELLEKVGLADKADAYPAQLSGGQQQRVAIARALAMDPKVMLFDEPT  164 (240)
T ss_pred             cccccccchHHHHHHhhhHHHcCCCHHHHHHHHHHHHHHcCchhhhhhCccccCcHHHHHHHHHHHHcCCCCEEeecCCc
Confidence            3221111                                                             157999999998


Q ss_pred             C-CCHHHHHHHHHHhhhccCCc-eEEEEecCCCcCchhHhhhc
Q psy879          107 S-MTDGAQQALRRTMEIYSNTT-RFALACNNSEKIIEPIQSRC  147 (317)
Q Consensus       107 ~-l~~~~~~~ll~~le~~~~~~-~~il~~~~~~~l~~~i~sR~  147 (317)
                      . |.++.....+..|.+..... .+|++| +.-.+...+.+|.
T Consensus       165 SALDPElv~EVL~vm~~LA~eGmTMivVT-HEM~FAr~Vadrv  206 (240)
T COG1126         165 SALDPELVGEVLDVMKDLAEEGMTMIIVT-HEMGFAREVADRV  206 (240)
T ss_pred             ccCCHHHHHHHHHHHHHHHHcCCeEEEEe-chhHHHHHhhheE
Confidence            5 57888888888887655443 345555 4445555555554

>PF14516 AAA_35: AAA-like domain

Probab=98.68  E-value=2.8e-05  Score=68.69  Aligned_cols=230  Identities=14%  Similarity=0.146  Sum_probs=126.6

Q ss_pred             ccCCHHHHHHHHHHHhc-CCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCC---cChHHHHHHH-H---
Q psy879           12 IVGNEDTVERLKVFSSS-GNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASND---RGIDTVRNKI-K---   83 (317)
Q Consensus        12 ~~g~~~~~~~l~~~l~~-~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~---~~~~~i~~~~-~---   83 (317)
                      .+.++.+-+.+...+.+ |.  .+.+.||..+|||++...+.+.+...+....++++.....   ...+.+-..+ .   
T Consensus        13 Yi~R~~~e~~~~~~i~~~G~--~~~I~apRq~GKTSll~~l~~~l~~~~~~~v~id~~~~~~~~~~~~~~f~~~~~~~i~   90 (331)
T PF14516_consen   13 YIERPPAEQECYQEIVQPGS--YIRIKAPRQMGKTSLLLRLLERLQQQGYRCVYIDLQQLGSAIFSDLEQFLRWFCEEIS   90 (331)
T ss_pred             ccCchHHHHHHHHHHhcCCC--EEEEECcccCCHHHHHHHHHHHHHHCCCEEEEEEeecCCCcccCCHHHHHHHHHHHHH
Confidence            34566566666666655 66  6899999999999999999988865443333333332211   1111110000 0   


Q ss_pred             ------------------------HHHhhcccCCCCceeEEEEeCCCCCCH--HH----HHHHHHHhhhcc-----CCce
Q psy879           84 ------------------------MFAQQKVTLPPGRHKIVILDEADSMTD--GA----QQALRRTMEIYS-----NTTR  128 (317)
Q Consensus        84 ------------------------~~~~~~~~~~~~~~~vliiDE~d~l~~--~~----~~~ll~~le~~~-----~~~~  128 (317)
                                              .+...........+-|++|||+|.+..  ..    ...|+.+.+...     ....
T Consensus        91 ~~L~l~~~l~~~w~~~~~~~~~~~~~~~~~ll~~~~~~lVL~iDEiD~l~~~~~~~~dF~~~LR~~~~~~~~~~~~~~L~  170 (331)
T PF14516_consen   91 RQLKLDEKLDEYWDEEIGSKISCTEYFEEYLLKQIDKPLVLFIDEIDRLFEYPQIADDFFGLLRSWYEQRKNNPIWQKLR  170 (331)
T ss_pred             HHcCCChhHHHHHHHhcCChhhHHHHHHHHHHhcCCCCEEEEEechhhhccCcchHHHHHHHHHHHHHhcccCcccceEE
Confidence                                    000000000113577999999998865  22    223333333211     2344


Q ss_pred             EEEEecCCCcCchhH-h---hhcceeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhhC
Q psy879          129 FALACNNSEKIIEPI-Q---SRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHNG  204 (317)
Q Consensus       129 ~il~~~~~~~l~~~i-~---sR~~~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~~  204 (317)
                      +|++...+..+.... .   .-+..++.++.+.+|+...+...    +...++..++.+...++|-+--.-..+..++..
T Consensus       171 li~~~~t~~~~~~~~~~SPFNIg~~i~L~~Ft~~ev~~L~~~~----~~~~~~~~~~~l~~~tgGhP~Lv~~~~~~l~~~  246 (331)
T PF14516_consen  171 LILAGSTEDYIILDINQSPFNIGQPIELPDFTPEEVQELAQRY----GLEFSQEQLEQLMDWTGGHPYLVQKACYLLVEE  246 (331)
T ss_pred             EEEecCcccccccCCCCCCcccccceeCCCCCHHHHHHHHHhh----hccCCHHHHHHHHHHHCCCHHHHHHHHHHHHHc
Confidence            555544322221111 1   33445889999999998866554    667888889999999999998776666665543


Q ss_pred             CCcccHHHHHh-hc-C-CCCHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC
Q psy879          205 FGHVTAEYVFK-VC-D-EPHPLAVKEMLLNCVEGNMKDSYKIIHHLYKLG  251 (317)
Q Consensus       205 ~~~i~~~~v~~-~~-~-~~~~~~i~~l~~~~~~~~~~~~~~~~~~l~~~~  251 (317)
                        .++.+++-+ +. . ....+.+..+.+.+.  +..+...++..++..+
T Consensus       247 --~~~~~~l~~~a~~~~~~~~~hL~~l~~~L~--~~~~L~~~~~~il~~~  292 (331)
T PF14516_consen  247 --QITLEQLLEEAITDNGIYNDHLDRLLDRLQ--QNPELLEAYQQILFSG  292 (331)
T ss_pred             --cCcHHHHHHHHHHhcccHHHHHHHHHHHHc--cCHHHHHHHHHHHhCC
Confidence              444444322 11 1 122234445554441  2235555566655544

>PLN03210 Resistant to P

Probab=98.68  E-value=1.7e-06  Score=88.64  Aligned_cols=188  Identities=17%  Similarity=0.174  Sum_probs=102.5

Q ss_pred             CCCCCcccCCHHHHHHHHHHHhc--CCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEe---cCCC---------
Q psy879            6 PQTFSDIVGNEDTVERLKVFSSS--GNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLEL---NASN---------   71 (317)
Q Consensus         6 P~~~~~~~g~~~~~~~l~~~l~~--~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~---~~~~---------   71 (317)
                      |..+++++|.+..++.+...+.-  +....+.++|++|+||||+|+++++.+........++..   ....         
T Consensus       180 ~~~~~~~vG~~~~l~~l~~lL~l~~~~~~vvgI~G~gGiGKTTLA~~l~~~l~~~F~g~vfv~~~~v~~~~~~~~~~~~~  259 (1153)
T PLN03210        180 SNDFEDFVGIEDHIAKMSSLLHLESEEVRMVGIWGSSGIGKTTIARALFSRLSRQFQSSVFIDRAFISKSMEIYSSANPD  259 (1153)
T ss_pred             CcccccccchHHHHHHHHHHHccccCceEEEEEEcCCCCchHHHHHHHHHHHhhcCCeEEEeeccccccchhhccccccc
Confidence            34588999999888888877743  233349999999999999999999887433211111110   0000         


Q ss_pred             CcC-hHHHH-HHHHHHHhhc-cc---------CCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcC
Q psy879           72 DRG-IDTVR-NKIKMFAQQK-VT---------LPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKI  139 (317)
Q Consensus        72 ~~~-~~~i~-~~~~~~~~~~-~~---------~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l  139 (317)
                      ... ...+. ..+....... ..         ....++-++++|+++..  ...+.|....+...+...+|+||.+..-+
T Consensus       260 ~~~~~~~l~~~~l~~il~~~~~~~~~~~~~~~~L~~krvLLVLDdv~~~--~~l~~L~~~~~~~~~GsrIIiTTrd~~vl  337 (1153)
T PLN03210        260 DYNMKLHLQRAFLSEILDKKDIKIYHLGAMEERLKHRKVLIFIDDLDDQ--DVLDALAGQTQWFGSGSRIIVITKDKHFL  337 (1153)
T ss_pred             ccchhHHHHHHHHHHHhCCCCcccCCHHHHHHHHhCCeEEEEEeCCCCH--HHHHHHHhhCccCCCCcEEEEEeCcHHHH
Confidence            000 00011 1111110000 00         00135668899998753  33444444333334556778887763321


Q ss_pred             chhHhhhcceeeecCCCHHHHHHHHHHHHHHcCCCCC--HHHHHHHHHhcCCCHHHHHHHH
Q psy879          140 IEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHT--NDGLEAIVFTAQGDMRQALNNL  198 (317)
Q Consensus       140 ~~~i~sR~~~i~f~~~~~~~~~~~l~~~~~~~~~~i~--~~~~~~l~~~~~gd~r~~i~~l  198 (317)
                      ...  .-...++...+++++..+.+...+.+....-+  .+....++..++|-+- |+..+
T Consensus       338 ~~~--~~~~~~~v~~l~~~ea~~LF~~~Af~~~~~~~~~~~l~~~iv~~c~GLPL-Al~vl  395 (1153)
T PLN03210        338 RAH--GIDHIYEVCLPSNELALEMFCRSAFKKNSPPDGFMELASEVALRAGNLPL-GLNVL  395 (1153)
T ss_pred             Hhc--CCCeEEEecCCCHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHhCCCcH-HHHHH
Confidence            110  01135788889998888888877754332111  1334567788888654 34333

syringae 6; Provisional

>COG1618 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=98.68  E-value=7.4e-07  Score=68.03  Aligned_cols=126  Identities=20%  Similarity=0.323  Sum_probs=73.4

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHcCCCCC-----------------CceEEecCC----------C-------CcChHHHH
Q psy879           34 IIISGPPGVGKTTTILCLARILLGPSFK-----------------DAVLELNAS----------N-------DRGIDTVR   79 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~l~~~~~~-----------------~~~~~~~~~----------~-------~~~~~~i~   79 (317)
                      ++++|+||+||||++..++..|....++                 +.++++...          .       ....+.+.
T Consensus         8 i~ITG~PGvGKtTl~~ki~e~L~~~g~kvgGf~t~EVR~gGkR~GF~Ivdl~tg~~~~la~~~~~~~rvGkY~V~v~~le   87 (179)
T COG1618           8 IFITGRPGVGKTTLVLKIAEKLREKGYKVGGFITPEVREGGKRIGFKIVDLATGEEGILARVGFSRPRVGKYGVNVEGLE   87 (179)
T ss_pred             EEEeCCCCccHHHHHHHHHHHHHhcCceeeeEEeeeeecCCeEeeeEEEEccCCceEEEEEcCCCCcccceEEeeHHHHH
Confidence            8999999999999999999988654321                 112222210          0       00122222


Q ss_pred             HHHHHHHhhcccCCCCceeEEEEeCCCCC---CHHHHHHHHHHhhhccCCceEEEEecC--CCcCchhHhhhcceeeecC
Q psy879           80 NKIKMFAQQKVTLPPGRHKIVILDEADSM---TDGAQQALRRTMEIYSNTTRFALACNN--SEKIIEPIQSRCAMLRYNK  154 (317)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~vliiDE~d~l---~~~~~~~ll~~le~~~~~~~~il~~~~--~~~l~~~i~sR~~~i~f~~  154 (317)
                      +......+.++    ....++||||+..|   ++....++-.+|..   ...+|.+-+.  .+.+...++++...+-|  
T Consensus        88 ~i~~~al~rA~----~~aDvIIIDEIGpMElks~~f~~~ve~vl~~---~kpliatlHrrsr~P~v~~ik~~~~v~v~--  158 (179)
T COG1618          88 EIAIPALRRAL----EEADVIIIDEIGPMELKSKKFREAVEEVLKS---GKPLIATLHRRSRHPLVQRIKKLGGVYVF--  158 (179)
T ss_pred             HHhHHHHHHHh----hcCCEEEEecccchhhccHHHHHHHHHHhcC---CCcEEEEEecccCChHHHHhhhcCCEEEE--
Confidence            22221112211    23579999999988   44455556666653   2235555543  35677888999888776  


Q ss_pred             CCHHHHHHHHHHHH
Q psy879          155 LTDAQLLSKVIEIC  168 (317)
Q Consensus       155 ~~~~~~~~~l~~~~  168 (317)
                      ++++....++.++.
T Consensus       159 lt~~NR~~i~~~Il  172 (179)
T COG1618         159 LTPENRNRILNEIL  172 (179)
T ss_pred             EccchhhHHHHHHH
Confidence            55555545555544

>PRK04132 replication factor C small subunit; Provisional

Probab=98.64  E-value=1.2e-08  Score=98.52  Aligned_cols=47  Identities=53%  Similarity=1.034  Sum_probs=44.1

Q ss_pred             CcccCCCCCCcccCCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHH
Q psy879            1 IEKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTT   47 (317)
Q Consensus         1 ~~ky~P~~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~l   47 (317)
                      .+||||++|+|++||+++++.|+.++++++.||++|+||||+||+..
T Consensus        10 ~~k~RP~~f~dIiGqe~i~~~Lk~~i~~~~i~h~l~~g~~g~~~cl~   56 (846)
T PRK04132         10 VEKYRPQRLDDIVGQEHIVKRLKHYVKTGSMPHLLFAGPPGVGKCLT   56 (846)
T ss_pred             HHhhCCCCHHHhcCcHHHHHHHHHHHHcCCCCeEEEECCCCCCcccc
Confidence            37999999999999999999999999999999999999999999643

>PHA02774 E1; Provisional

Probab=98.63  E-value=3.9e-07  Score=83.79  Aligned_cols=136  Identities=23%  Similarity=0.291  Sum_probs=82.4

Q ss_pred             HHHHHHHHHhcCCC-ceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHHHHHHHhhcccCCCCc
Q psy879           18 TVERLKVFSSSGNV-PNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGR   96 (317)
Q Consensus        18 ~~~~l~~~l~~~~~-~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~   96 (317)
                      ....|+.++++..- ..++|+||||||||+++.++++.+.+.    .+..+|..+...            ..    +-.+
T Consensus       420 fl~~lk~~l~~~PKknciv~~GPP~TGKS~fa~sL~~~L~G~----vi~fvN~~s~Fw------------Lq----pl~d  479 (613)
T PHA02774        420 FLTALKDFLKGIPKKNCLVIYGPPDTGKSMFCMSLIKFLKGK----VISFVNSKSHFW------------LQ----PLAD  479 (613)
T ss_pred             HHHHHHHHHhcCCcccEEEEECCCCCCHHHHHHHHHHHhCCC----EEEEEECccccc------------cc----hhcc
Confidence            34556666654321 249999999999999999999997432    233344321111            11    1146


Q ss_pred             eeEEEEeCCCCCC-HHHHHHHHHHhhhcc-------------CCceEEEEecCC---CcCchhHhhhcceeeecCC----
Q psy879           97 HKIVILDEADSMT-DGAQQALRRTMEIYS-------------NTTRFALACNNS---EKIIEPIQSRCAMLRYNKL----  155 (317)
Q Consensus        97 ~~vliiDE~d~l~-~~~~~~ll~~le~~~-------------~~~~~il~~~~~---~~l~~~i~sR~~~i~f~~~----  155 (317)
                      .+++++||+-.-. .-....|..+++..+             ..+.+|+|||-.   +.-...+.||...++|+.+    
T Consensus       480 ~ki~vlDD~t~~~w~y~d~~Lrn~LdG~~v~lD~Khk~~~q~k~pPlIITSN~d~~~~~~~~yL~sRi~~f~F~n~~P~d  559 (613)
T PHA02774        480 AKIALLDDATHPCWDYIDTYLRNALDGNPVSIDCKHKAPVQIKCPPLLITSNIDVKAEDRYKYLHSRITVFEFPNPFPLD  559 (613)
T ss_pred             CCEEEEecCcchHHHHHHHHHHHHcCCCcceeeecccCcccccCCCEEEecCCCcccchhhHHhhhhEEEEECCCCCCcC
Confidence            7899999993221 112335666666321             125688888854   2446788999999888743    


Q ss_pred             ---------CHHHHHHHHHHHHHHcCC
Q psy879          156 ---------TDAQLLSKVIEICEKENI  173 (317)
Q Consensus       156 ---------~~~~~~~~l~~~~~~~~~  173 (317)
                               ++...+.+..+.-.+.++
T Consensus       560 ~~G~P~f~ltd~~WKsFF~rlw~~LdL  586 (613)
T PHA02774        560 ENGNPVFELTDANWKSFFERLWSQLDL  586 (613)
T ss_pred             CCCCEeeeeCchhHHHHHHHHHHHcCC
Confidence                     345566665555444333

>COG3284 AcoR Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]

Probab=98.58  E-value=6.3e-06  Score=76.10  Aligned_cols=173  Identities=15%  Similarity=0.171  Sum_probs=111.8

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHHHHHHHhhccc----------CCCCceeEEEE
Q psy879           33 NIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFAQQKVT----------LPPGRHKIVIL  102 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~----------~~~~~~~vlii  102 (317)
                      ++++.|++|+||-.+++++-+.-  . ...+++.+||.. ...+-+.+.+-.+....+.          +.....+.+|+
T Consensus       338 pvll~GEtGtGKe~laraiH~~s--~-~~gpfvAvNCaA-ip~~liesELFGy~~GafTga~~kG~~g~~~~A~gGtlFl  413 (606)
T COG3284         338 PVLLQGETGTGKEVLARAIHQNS--E-AAGPFVAVNCAA-IPEALIESELFGYVAGAFTGARRKGYKGKLEQADGGTLFL  413 (606)
T ss_pred             CeEecCCcchhHHHHHHHHHhcc--c-ccCCeEEEEecc-chHHhhhHHHhccCccccccchhccccccceecCCCccHH
Confidence            59999999999999999999863  2 456678888753 2222222222111111111          11246789999


Q ss_pred             eCCCCCCHHHHHHHHHHhhhc----------cCCceEEEEecCCC-------cCchhHhhhcce--eeecCCCHH-----
Q psy879          103 DEADSMTDGAQQALRRTMEIY----------SNTTRFALACNNSE-------KIIEPIQSRCAM--LRYNKLTDA-----  158 (317)
Q Consensus       103 DE~d~l~~~~~~~ll~~le~~----------~~~~~~il~~~~~~-------~l~~~i~sR~~~--i~f~~~~~~-----  158 (317)
                      ||+..|.-..|..|++.+++.          +-.+.+|.+|+.+-       .+-+.+-=|...  |.+||+.+.     
T Consensus       414 deIgd~p~~~Qs~LLrVl~e~~v~p~g~~~~~vdirvi~ath~dl~~lv~~g~fredLyyrL~~~~i~lP~lr~R~d~~~  493 (606)
T COG3284         414 DEIGDMPLALQSRLLRVLQEGVVTPLGGTRIKVDIRVIAATHRDLAQLVEQGRFREDLYYRLNAFVITLPPLRERSDRIP  493 (606)
T ss_pred             HHhhhchHHHHHHHHHHHhhCceeccCCcceeEEEEEEeccCcCHHHHHHcCCchHHHHHHhcCeeeccCchhcccccHH
Confidence            999999999999999999853          12345777777652       444555555544  555665442     


Q ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHHH-hcCCCHHHHHHHHHHhhh--CCCcccH
Q psy879          159 QLLSKVIEICEKENISHTNDGLEAIVF-TAQGDMRQALNNLQSTHN--GFGHVTA  210 (317)
Q Consensus       159 ~~~~~l~~~~~~~~~~i~~~~~~~l~~-~~~gd~r~~i~~l~~~~~--~~~~i~~  210 (317)
                      -+..++.+... ....++++++..+.. ...||+|+..|.++.++.  +.+.+..
T Consensus       494 ~l~~~~~~~~~-~~~~l~~~~~~~l~~~~WPGNirel~~v~~~~~~l~~~g~~~~  547 (606)
T COG3284         494 LLDRILKREND-WRLQLDDDALARLLAYRWPGNIRELDNVIERLAALSDGGRIRV  547 (606)
T ss_pred             HHHHHHHHccC-CCccCCHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCCCCeeEc
Confidence            23333333222 346789999887654 579999999999997665  4444444

>PF00493 MCM: MCM2/3/5 family This family extends the MCM domain of Prosite

Probab=98.58  E-value=4.7e-09  Score=92.44  Aligned_cols=136  Identities=22%  Similarity=0.311  Sum_probs=73.4

Q ss_pred             cccCCHHHHHHHHHHHhcCC------------CceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcCh--H
Q psy879           11 DIVGNEDTVERLKVFSSSGN------------VPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGI--D   76 (317)
Q Consensus        11 ~~~g~~~~~~~l~~~l~~~~------------~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~--~   76 (317)
                      .++|++.++..+.-.+-+|.            --|+||.|.||+|||.+.+.+++..    +...+.....+...+.  .
T Consensus        25 ~i~g~~~iK~aill~L~~~~~~~~~~~~~~r~~ihiLlvGdpg~gKS~ll~~~~~~~----pr~v~~~g~~~s~~gLta~  100 (331)
T PF00493_consen   25 SIYGHEDIKKAILLQLFGGVEKNDPDGTRIRGNIHILLVGDPGTGKSQLLKYVAKLA----PRSVYTSGKGSSAAGLTAS  100 (331)
T ss_dssp             TTTT-HHHHHHHCCCCTT--SCCCCT-TEE--S--EEEECSCHHCHHHHHHCCCCT-----SSEEEEECCGSTCCCCCEE
T ss_pred             cCcCcHHHHHHHHHHHHhccccccccccccccccceeeccchhhhHHHHHHHHHhhC----CceEEECCCCcccCCccce
Confidence            47788888877544433222            1279999999999999999876542    1111222221111111  0


Q ss_pred             HHHH-HHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhh-------------ccCCceEEEEecCCC-----
Q psy879           77 TVRN-KIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEI-------------YSNTTRFALACNNSE-----  137 (317)
Q Consensus        77 ~i~~-~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~-------------~~~~~~~il~~~~~~-----  137 (317)
                      ..++ .-+.+...+..+..++++|++|||+|++..+...+|++.||.             .+..+.++.++|+..     
T Consensus       101 ~~~d~~~~~~~leaGalvlad~GiccIDe~dk~~~~~~~~l~eaMEqq~isi~kagi~~~l~ar~svlaa~NP~~g~~~~  180 (331)
T PF00493_consen  101 VSRDPVTGEWVLEAGALVLADGGICCIDEFDKMKEDDRDALHEAMEQQTISIAKAGIVTTLNARCSVLAAANPKFGRYDP  180 (331)
T ss_dssp             ECCCGGTSSECEEE-HHHHCTTSEEEECTTTT--CHHHHHHHHHHHCSCEEECTSSSEEEEE---EEEEEE--TT--S-T
T ss_pred             eccccccceeEEeCCchhcccCceeeecccccccchHHHHHHHHHHcCeeccchhhhcccccchhhhHHHHhhhhhhcch
Confidence            0000 000011111111125788999999999999999999999994             245566788888653     


Q ss_pred             --------cCchhHhhhccee
Q psy879          138 --------KIIEPIQSRCAML  150 (317)
Q Consensus       138 --------~l~~~i~sR~~~i  150 (317)
                              .+.+++.|||..+
T Consensus       181 ~~~~~~ni~l~~~LLSRFDLi  201 (331)
T PF00493_consen  181 NKSLSENINLPPPLLSRFDLI  201 (331)
T ss_dssp             TS-CGCCT-S-CCCHCC-SEE
T ss_pred             hhhhHHhcccchhhHhhcCEE
Confidence                    4678999999984

; InterPro: IPR001208 MCM proteins are DNA-dependent ATPases required for the initiation of eukaryotic DNA replication [, , ]. In eukaryotes there is a family of six proteins, MCM2 to MCM7. They were first identified in yeast where most of them have a direct role in the initiation of chromosomal DNA replication by interacting directly with autonomously replicating sequences (ARS). They were thus called minichromosome maintenance proteins, MCM proteins []. This family is also present in the archebacteria in 1 to 4 copies. Methanocaldococcus jannaschii (Methanococcus jannaschii) has four members, MJ0363, MJ0961, MJ1489 and MJECL13. The "MCM motif" contains Walker-A and Walker-B type nucleotide binding motifs. The diagnostic sequence defining the MCMs is IDEFDKM. Only Mcm2 (aka Cdc19 or Nda1) has been subjected to mutational analysis in this region, and most mutations abolish its activity []. The presence of a putative ATP-binding domain implies that these proteins may be involved in an ATP-consuming step in the initiation of DNA replication in eukaryotes. The MCM proteins bind together in a large complex []. Within this complex, individual subunits associate with different affinities, and there is a tightly associated core of Mcm4 (Cdc21), Mcm6 (Mis5) and Mcm7 []. This core complex in human MCMs has been associated with helicase activity in vitro [], leading to the suggestion that the MCM proteins are the eukaryotic replicative helicase. Schizosaccharomyces pombe (Fission yeast) MCMs, like those in metazoans, are found in the nucleus throughout the cell cycle. This is in contrast to the Saccharomyces cerevisiae (Baker's yeast) in which MCM proteins move in and out of the nucleus during each cell cycle. The assembly of the MCM complex in S. pombe is required for MCM localisation, ensuring that only intact MCM complexes remain in the nucleus [].; GO: 0003677 DNA binding, 0005524 ATP binding, 0006260 DNA replication; PDB: 3F8T_A 3F9V_A.

>PF03266 NTPase_1: NTPase; InterPro: IPR004948 This entry represents a family of nucleoside-triphosphatases which have activity towards ATP, GTP, CTP, TTP and UTP and may hydrolyse nucleoside diphosphates with lower efficiency []

Probab=98.58  E-value=2.9e-08  Score=78.52  Aligned_cols=64  Identities=14%  Similarity=0.329  Sum_probs=39.0

Q ss_pred             ceeEEEEeCCCCC---CHHHHHHHHHHhhhccCCceEEEEecC--CCcCchhHhhh--cceeeecCCCHHHHHH
Q psy879           96 RHKIVILDEADSM---TDGAQQALRRTMEIYSNTTRFALACNN--SEKIIEPIQSR--CAMLRYNKLTDAQLLS  162 (317)
Q Consensus        96 ~~~vliiDE~d~l---~~~~~~~ll~~le~~~~~~~~il~~~~--~~~l~~~i~sR--~~~i~f~~~~~~~~~~  162 (317)
                      ...+++|||+..|   .+.-++++.++|+   ++..+|.+-..  ...+.+.+++|  +.++...+-+.+.+..
T Consensus        95 ~~~liviDEIG~mEl~~~~F~~~v~~~l~---s~~~vi~vv~~~~~~~~l~~i~~~~~~~i~~vt~~NRd~l~~  165 (168)
T PF03266_consen   95 SSDLIVIDEIGKMELKSPGFREAVEKLLD---SNKPVIGVVHKRSDNPFLEEIKRRPDVKIFEVTEENRDALPE  165 (168)
T ss_dssp             CCHEEEE---STTCCC-CHHHHHHHHHHC---TTSEEEEE--SS--SCCHHHHHTTTTSEEEE--TTTCCCHHH
T ss_pred             CCCEEEEeccchhhhcCHHHHHHHHHHHc---CCCcEEEEEecCCCcHHHHHHHhCCCcEEEEeChhHHhhHhh
Confidence            5679999999987   4567888888888   33345555443  35789999998  6667776666555443

It includes proteins from bacteria to human, and the function was determined first in a hyperthermophilic bacterium to be an NTPase []. The structure of one member-sequence represents a variation of the RecA fold, and implies that the function might be that of a DNA/RNA modifying enzyme []. The sequence carries both a Walker A and Walker B motif which together are characteristic of ATPases or GTPases. The protein exhibits an increased expression profile in human liver cholangiocarcinoma when compared to normal tissue [].; GO: 0005524 ATP binding, 0016740 transferase activity, 0019204 nucleotide phosphatase activity; PDB: 1YE8_A 2I3B_A.

>COG4619 ABC-type uncharacterized transport system, ATPase component [General function prediction only]

Probab=98.57  E-value=2.5e-06  Score=65.77  Aligned_cols=155  Identities=17%  Similarity=0.206  Sum_probs=98.6

Q ss_pred             HHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHHHHHHHhhcccCCCCceeEEEEeC
Q psy879           25 FSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDE  104 (317)
Q Consensus        25 ~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE  104 (317)
                      .+..|.  .++++||+|||||++.+.+|..+ .++.+..+++....+..++..+|..+....+.+..++..         
T Consensus        25 ~v~~Ge--~iaitGPSG~GKStllk~va~Li-sp~~G~l~f~Ge~vs~~~pea~Rq~VsY~~Q~paLfg~t---------   92 (223)
T COG4619          25 SVRAGE--FIAITGPSGCGKSTLLKIVASLI-SPTSGTLLFEGEDVSTLKPEAYRQQVSYCAQTPALFGDT---------   92 (223)
T ss_pred             eecCCc--eEEEeCCCCccHHHHHHHHHhcc-CCCCceEEEcCccccccChHHHHHHHHHHHcCccccccc---------
Confidence            344555  58999999999999999999975 555566677777777788899999999988887433211         


Q ss_pred             CCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcCchhHhhhcceeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHH-
Q psy879          105 ADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAI-  183 (317)
Q Consensus       105 ~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~~~i~sR~~~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l-  183 (317)
                                     ++   +|.          -++-.++.       ..++.....+.|...      ..+...+.+= 
T Consensus        93 ---------------Ve---DNl----------ifP~~~r~-------rr~dr~aa~~llar~------~l~~~~L~k~i  131 (223)
T COG4619          93 ---------------VE---DNL----------IFPWQIRN-------RRPDRAAALDLLARF------ALPDSILTKNI  131 (223)
T ss_pred             ---------------hh---hcc----------ccchHHhc-------cCCChHHHHHHHHHc------CCchhhhcchh
Confidence                           01   111          11111121       244555555555443      4455555543 


Q ss_pred             HHhcCCCHHHHHHHHHHhhhCCCcccHHHHHhhcCCCCHHHHHHHHHHHh
Q psy879          184 VFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEMLLNCV  233 (317)
Q Consensus       184 ~~~~~gd~r~~i~~l~~~~~~~~~i~~~~v~~~~~~~~~~~i~~l~~~~~  233 (317)
                      ...+|| -++.+.+++..-...+....+++..+++.....++.+++..+.
T Consensus       132 t~lSGG-E~QriAliR~Lq~~P~ILLLDE~TsALD~~nkr~ie~mi~~~v  180 (223)
T COG4619         132 TELSGG-EKQRIALIRNLQFMPKILLLDEITSALDESNKRNIEEMIHRYV  180 (223)
T ss_pred             hhccch-HHHHHHHHHHhhcCCceEEecCchhhcChhhHHHHHHHHHHHh
Confidence            344554 5666666666555666667777777888877777777766554

>PF13191 AAA_16: AAA ATPase domain; PDB: 2V1U_A

Probab=98.52  E-value=2e-07  Score=75.18  Aligned_cols=48  Identities=33%  Similarity=0.565  Sum_probs=33.1

Q ss_pred             cccCCHHHHHHHHHHH---hcCCCceEEEECCCCCCHHHHHHHHHHHHcCC
Q psy879           11 DIVGNEDTVERLKVFS---SSGNVPNIIISGPPGVGKTTTILCLARILLGP   58 (317)
Q Consensus        11 ~~~g~~~~~~~l~~~l---~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~   58 (317)
                      .++|+++.++.+...+   ..+..++++++|++|+|||++++.+...+...
T Consensus         1 ~fvgR~~e~~~l~~~l~~~~~~~~~~~ll~G~~G~GKT~ll~~~~~~~~~~   51 (185)
T PF13191_consen    1 QFVGREEEIERLRDLLDAAQSGSPRNLLLTGESGSGKTSLLRALLDRLAER   51 (185)
T ss_dssp             --TT-HHHHHHHHHTTGGTSS-----EEE-B-TTSSHHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHHHcCCCcEEEEECCCCCCHHHHHHHHHHHHHhc
Confidence            3789999999999888   33444569999999999999999999887543

>TIGR02688 conserved hypothetical protein TIGR02688

Probab=98.50  E-value=2.8e-05  Score=69.43  Aligned_cols=115  Identities=23%  Similarity=0.280  Sum_probs=67.6

Q ss_pred             cCCCCCCcccCCHHH--HHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHH
Q psy879            4 YRPQTFSDIVGNEDT--VERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNK   81 (317)
Q Consensus         4 y~P~~~~~~~g~~~~--~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~   81 (317)
                      |.|..|++   +..+  +..+..+++++.  |+++.||+|||||+++.++...-.+...          ...+...+...
T Consensus       185 ~~P~~~~~---r~k~~~L~rl~~fve~~~--Nli~lGp~GTGKThla~~l~~~~a~~sG----------~f~T~a~Lf~~  249 (449)
T TIGR02688       185 YEPEGFEA---RQKLLLLARLLPLVEPNY--NLIELGPKGTGKSYIYNNLSPYVILISG----------GTITVAKLFYN  249 (449)
T ss_pred             CCcccCCh---HHHHHHHHhhHHHHhcCC--cEEEECCCCCCHHHHHHHHhHHHHHHcC----------CcCcHHHHHHH
Confidence            66766652   2222  223445777776  8999999999999999998876211111          11122221111


Q ss_pred             HHHHHhhcccCCCCceeEEEEeCCCCCC----HHHHHHHHHHhhhc---------cCCceEEEEecCCC
Q psy879           82 IKMFAQQKVTLPPGRHKIVILDEADSMT----DGAQQALRRTMEIY---------SNTTRFALACNNSE  137 (317)
Q Consensus        82 ~~~~~~~~~~~~~~~~~vliiDE~d~l~----~~~~~~ll~~le~~---------~~~~~~il~~~~~~  137 (317)
                      +..   .. ...-+.+.+|++||+..+.    ++..+.+..+|+..         ..+..+|++.|-..
T Consensus       250 L~~---~~-lg~v~~~DlLI~DEvgylp~~~~~~~v~imK~yMesg~fsRG~~~~~a~as~vfvGNi~~  314 (449)
T TIGR02688       250 IST---RQ-IGLVGRWDVVAFDEVATLKFAKPKELIGILKNYMESGSFTRGDETKSSDASFVFLGNVPL  314 (449)
T ss_pred             HHH---HH-HhhhccCCEEEEEcCCCCcCCchHHHHHHHHHHHHhCceeccceeeeeeeEEEEEcccCC
Confidence            111   10 0012578899999999863    23567777778732         34566888877654

Members of this family are uncharacterized proteins sporadically distributed in bacteria and archaea, about 470 amino acids in length. Several members of this family appear in public databases with annotation as ATP-dependent protease La, despite the lack of similarity to families TIGR00763 (ATP-dependent protease La) or pfam02190 (ATP-dependent protease La (LON) domain). This protein is repeatedly found downstream of another uncharacterized protein of about 880 amino acids in length, described by model TIGR02687.

>COG2884 FtsE Predicted ATPase involved in cell division [Cell division and chromosome partitioning]

Probab=98.49  E-value=2e-07  Score=73.16  Aligned_cols=57  Identities=12%  Similarity=0.211  Sum_probs=41.9

Q ss_pred             ceeEEEEeCCC-CCCHHHHHHHHHHhhhccCCceEEEEecCCCcCchhHhhhcceeee
Q psy879           96 RHKIVILDEAD-SMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRY  152 (317)
Q Consensus        96 ~~~vliiDE~d-~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~~~i~sR~~~i~f  152 (317)
                      .+.+++-||.. ++.++....+++++++......-|+++++...+..+.+.|+..++-
T Consensus       155 ~P~vLlADEPTGNLDp~~s~~im~lfeeinr~GtTVl~ATHd~~lv~~~~~rvl~l~~  212 (223)
T COG2884         155 QPAVLLADEPTGNLDPDLSWEIMRLFEEINRLGTTVLMATHDLELVNRMRHRVLALED  212 (223)
T ss_pred             CCCeEeecCCCCCCChHHHHHHHHHHHHHhhcCcEEEEEeccHHHHHhccCcEEEEeC
Confidence            68999999985 7899999999999998766544444444556666777777665443

>KOG0481|consensus

Probab=98.49  E-value=4.4e-06  Score=74.91  Aligned_cols=138  Identities=22%  Similarity=0.315  Sum_probs=84.5

Q ss_pred             cccCCHHHHHHHHHHHhcCCC---c---------eEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcCh--H
Q psy879           11 DIVGNEDTVERLKVFSSSGNV---P---------NIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGI--D   76 (317)
Q Consensus        11 ~~~g~~~~~~~l~~~l~~~~~---~---------~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~--~   76 (317)
                      .+.|++++++.+.=.+-+|.-   |         |+|+.|.||+.|+.+.+.+-+.-    +-..+....+++..+.  .
T Consensus       332 SIfG~~DiKkAiaClLFgGsrK~LpDg~~lRGDINVLLLGDPgtAKSQlLKFvEkvs----PIaVYTSGKGSSAAGLTAS  407 (729)
T KOG0481|consen  332 SIFGHEDIKKAIACLLFGGSRKRLPDGVTLRGDINVLLLGDPGTAKSQLLKFVEKVS----PIAVYTSGKGSSAAGLTAS  407 (729)
T ss_pred             hhcCchhHHHHHHHHhhcCccccCCCcceeccceeEEEecCCchhHHHHHHHHHhcC----ceEEEecCCCcccccceee
Confidence            467999999988766655431   1         69999999999999999776541    1111111222221111  1


Q ss_pred             HHHHHHH-HHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhc-------------cCCceEEEEecCCC-----
Q psy879           77 TVRNKIK-MFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIY-------------SNTTRFALACNNSE-----  137 (317)
Q Consensus        77 ~i~~~~~-~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~-------------~~~~~~il~~~~~~-----  137 (317)
                      .+++-.. .|........-++..|++|||+|+|..+..-++.+.||.-             ...+.++.++|+..     
T Consensus       408 V~RD~~tReFylEGGAMVLADgGVvCIDEFDKMre~DRVAIHEAMEQQTISIAKAGITT~LNSRtSVLAAANpvfGRyDd  487 (729)
T KOG0481|consen  408 VIRDPSTREFYLEGGAMVLADGGVVCIDEFDKMREDDRVAIHEAMEQQTISIAKAGITTTLNSRTSVLAAANPVFGRYDD  487 (729)
T ss_pred             EEecCCcceEEEecceEEEecCCEEEeehhhccCchhhhHHHHHHHhhhHHHhhhcceeeecchhhhhhhcCCccccccc
Confidence            1111100 0000000001157889999999999999999999999942             23444666666542     


Q ss_pred             --------cCchhHhhhcceeee
Q psy879          138 --------KIIEPIQSRCAMLRY  152 (317)
Q Consensus       138 --------~l~~~i~sR~~~i~f  152 (317)
                              .+.++|.|||..|.+
T Consensus       488 ~Kt~~dNIDf~~TILSRFDmIFI  510 (729)
T KOG0481|consen  488 TKTGEDNIDFMPTILSRFDMIFI  510 (729)
T ss_pred             cCCcccccchhhhHhhhccEEEE
Confidence                    367999999988443

>COG5271 MDN1 AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]

Probab=98.42  E-value=2.6e-06  Score=85.64  Aligned_cols=142  Identities=20%  Similarity=0.291  Sum_probs=100.9

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHHHHHHHhhccc---CC-------CCceeEEEE
Q psy879           33 NIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFAQQKVT---LP-------PGRHKIVIL  102 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~---~~-------~~~~~vlii  102 (317)
                      .+|+.||..+|||+++..+|+.. |    ..++.+|....   .++++.++.+......   +.       ..++--+++
T Consensus       890 P~LiQGpTSSGKTSMI~yla~~t-g----hkfVRINNHEH---TdlqeYiGTyvTdd~G~lsFkEGvLVeAlR~GyWIVL  961 (4600)
T COG5271         890 PLLIQGPTSSGKTSMILYLARET-G----HKFVRINNHEH---TDLQEYIGTYVTDDDGSLSFKEGVLVEALRRGYWIVL  961 (4600)
T ss_pred             cEEEecCCCCCcchHHHHHHHHh-C----ccEEEecCccc---chHHHHhhceeecCCCceeeehhHHHHHHhcCcEEEe
Confidence            49999999999999999999985 3    33677765432   2233344433322100   00       013446889


Q ss_pred             eCCCCCCHHHHHHHHHHhhh--------------ccCCceEEEEecCCC------cCchhHhhhcceeeecCCCHHHHHH
Q psy879          103 DEADSMTDGAQQALRRTMEI--------------YSNTTRFALACNNSE------KIIEPIQSRCAMLRYNKLTDAQLLS  162 (317)
Q Consensus       103 DE~d~l~~~~~~~ll~~le~--------------~~~~~~~il~~~~~~------~l~~~i~sR~~~i~f~~~~~~~~~~  162 (317)
                      ||..-...+..++|.+.++.              |+++..+..|-|+|.      .+..+++.|+..++|...+++|+..
T Consensus       962 DELNLApTDVLEaLNRLLDDNRelfIPETqevV~PHp~F~lFATQNppg~YgGRK~LSrAFRNRFlE~hFddipedEle~ 1041 (4600)
T COG5271         962 DELNLAPTDVLEALNRLLDDNRELFIPETQEVVVPHPNFRLFATQNPPGGYGGRKGLSRAFRNRFLEMHFDDIPEDELEE 1041 (4600)
T ss_pred             eccccCcHHHHHHHHHhhccccceecCCcceeeccCCCeeEEeecCCCccccchHHHHHHHHhhhHhhhcccCcHHHHHH
Confidence            99999999999999999972              445554444555442      4679999999999999999999999


Q ss_pred             HHHHHHHHcCCCCCHHHHHHHHHhc
Q psy879          163 KVIEICEKENISHTNDGLEAIVFTA  187 (317)
Q Consensus       163 ~l~~~~~~~~~~i~~~~~~~l~~~~  187 (317)
                      +|..+|     ++.+.-+.++++..
T Consensus      1042 ILh~rc-----~iapSyakKiVeVy 1061 (4600)
T COG5271        1042 ILHGRC-----EIAPSYAKKIVEVY 1061 (4600)
T ss_pred             HHhccC-----ccCHHHHHHHHHHH
Confidence            999854     67888888877654

>PF13604 AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL_A 3E1S_A 3GP8_A

Probab=98.41  E-value=2.4e-06  Score=69.64  Aligned_cols=114  Identities=22%  Similarity=0.344  Sum_probs=66.2

Q ss_pred             HHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHHHH-------HHHhhc
Q psy879           17 DTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIK-------MFAQQK   89 (317)
Q Consensus        17 ~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~~-------~~~~~~   89 (317)
                      +..+.+..++.++. ...++.||||||||++++.+...+....  ..++.+.+. ......+++..+       .+....
T Consensus         5 ~Q~~a~~~~l~~~~-~~~~l~G~aGtGKT~~l~~~~~~~~~~g--~~v~~~apT-~~Aa~~L~~~~~~~a~Ti~~~l~~~   80 (196)
T PF13604_consen    5 EQREAVRAILTSGD-RVSVLQGPAGTGKTTLLKALAEALEAAG--KRVIGLAPT-NKAAKELREKTGIEAQTIHSFLYRI   80 (196)
T ss_dssp             HHHHHHHHHHHCTC-SEEEEEESTTSTHHHHHHHHHHHHHHTT----EEEEESS-HHHHHHHHHHHTS-EEEHHHHTTEE
T ss_pred             HHHHHHHHHHhcCC-eEEEEEECCCCCHHHHHHHHHHHHHhCC--CeEEEECCc-HHHHHHHHHhhCcchhhHHHHHhcC
Confidence            34455566666554 2488899999999999999998875432  334444332 222233333211       111100


Q ss_pred             cc--C----CCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCC
Q psy879           90 VT--L----PPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNS  136 (317)
Q Consensus        90 ~~--~----~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~  136 (317)
                      ..  .    ......++||||+..+.......|++....  ....+|++..+.
T Consensus        81 ~~~~~~~~~~~~~~~vliVDEasmv~~~~~~~ll~~~~~--~~~klilvGD~~  131 (196)
T PF13604_consen   81 PNGDDEGRPELPKKDVLIVDEASMVDSRQLARLLRLAKK--SGAKLILVGDPN  131 (196)
T ss_dssp             CCEECCSSCC-TSTSEEEESSGGG-BHHHHHHHHHHS-T---T-EEEEEE-TT
T ss_pred             CcccccccccCCcccEEEEecccccCHHHHHHHHHHHHh--cCCEEEEECCcc
Confidence            00  0    023457999999999999988888888875  466788887653

>PF00910 RNA_helicase: RNA helicase; InterPro: IPR000605 Helicases have been classified in 5 superfamilies (SF1-SF5)

Probab=98.39  E-value=2.1e-06  Score=62.73  Aligned_cols=71  Identities=34%  Similarity=0.487  Sum_probs=45.5

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHcCCC---CCCceEEecCCCCcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCH
Q psy879           34 IIISGPPGVGKTTTILCLARILLGPS---FKDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTD  110 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~l~~~~---~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~  110 (317)
                      +.||||||+|||++++.+++.+....   ....++..++...           .+ .     ......++++||+.....
T Consensus         1 I~i~G~~G~GKS~l~~~l~~~l~~~~~~~~~~~vy~~~~~~~-----------~w-~-----gY~~q~vvi~DD~~~~~~   63 (107)
T PF00910_consen    1 IWIYGPPGIGKSTLAKELAKDLLKHIGEPTKDSVYTRNPGDK-----------FW-D-----GYQGQPVVIIDDFGQDND   63 (107)
T ss_pred             CEEECCCCCCHHHHHHHHHHHHHHHhccCCCCcEEeCCCccc-----------hh-h-----ccCCCcEEEEeecCcccc
Confidence            47999999999999999998885321   1122333222211           11 1     113568999999998875


Q ss_pred             H----HHHHHHHHhh
Q psy879          111 G----AQQALRRTME  121 (317)
Q Consensus       111 ~----~~~~ll~~le  121 (317)
                      .    ....+++++.
T Consensus        64 ~~~~~~~~~l~~l~s   78 (107)
T PF00910_consen   64 GYNYSDESELIRLIS   78 (107)
T ss_pred             ccchHHHHHHHHHHh
Confidence            4    4566677665

All of the proteins bind ATP and, consequently, all of them carry the classical Walker A (phosphate-binding loop or P-loop) and Walker B (Mg2+-binding aspartic acid) motifs. Superfamily 3 consists of helicases encoded mainly by small DNA viruses and some large nucleocytoplasmic DNA viruses [, ]. Small viruses are very dependent on the host-cell machinery to replicate. SF3 helicase in small viruses is associated with an origin-binding domain. By pairing a domain that recognises the ori with a helicase, the virus can bypass the host-cell-based regulation pathway and initiate its own replication. The protein binds to the viral ori leading to origin unwinding. Cellular replication proteins are then recruited to the ori and the viral DNA is replicated. In SF3 helicases the Walker A and Walker B motifs are separated by spacers of rather uniform, and relatively short, length. In addition to the A and B motifs this family is characterised by a third motif (C) which resides between the B motif and the C terminus of the conserved region. This motif consists of an Asn residue preceded by a run of hydrophobic residues []. Several structures of SF3 helicases have been solved []. They all possess the same core alpha/beta fold, consisting of a five-stranded parallel beta sheet flanked on both sides by several alpha helices. In contrast to SF1 and SF2 helicases, which have RecA-like core folds, the strand connectivity within the alpha/beta core domain is that of AAA+ proteins []. The SF3 helicase proteins assemble into a hexameric ring. Some proteins known to contain an SF3 helicase domain are listed below: Polyomavirus large T antigen. It initiates DNA unwinding and replication via interactions with the viral origin of replication. Papillomavirus E1 protein. An ATP-dependent DNA helicase required for initiation of viral DNA replication. Parvovirus Rep/NS1 protein, which is also required for the initiation of viral replication. Poxviridae and other large DNA viruses D5 protein. Bacteriophage DNA primase/helicase protein. Bacterial prophage DNA primase/helicase protein. The entry represents the core alpha/beta fold of the SF3 helicase domain found predominantly in DNA viruses.; GO: 0003723 RNA binding, 0003724 RNA helicase activity

>KOG2543|consensus

Probab=98.35  E-value=8.5e-06  Score=70.77  Aligned_cols=184  Identities=19%  Similarity=0.208  Sum_probs=103.6

Q ss_pred             cccCCHHHHHHHHHHHhcCC--Cce-EEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCC---------------
Q psy879           11 DIVGNEDTVERLKVFSSSGN--VPN-IIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASND---------------   72 (317)
Q Consensus        11 ~~~g~~~~~~~l~~~l~~~~--~~~-~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~---------------   72 (317)
                      .+.+++..+..|...+-...  .|. +.+||.+|||||.+++.+.+...-     +.+++++...               
T Consensus         7 ~v~~Re~qi~~L~~Llg~~~~~~PS~~~iyG~sgTGKT~~~r~~l~~~n~-----~~vw~n~~ecft~~~lle~IL~~~~   81 (438)
T KOG2543|consen    7 NVPCRESQIRRLKSLLGNNSCTIPSIVHIYGHSGTGKTYLVRQLLRKLNL-----ENVWLNCVECFTYAILLEKILNKSQ   81 (438)
T ss_pred             CccchHHHHHHHHHHhCCCCcccceeEEEeccCCCchhHHHHHHHhhcCC-----cceeeehHHhccHHHHHHHHHHHhc
Confidence            45678888888888775543  455 799999999999999999998621     1222222110               


Q ss_pred             ----c----C--hHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHH---HHHHHHHhhhcc-CCceEEEEecCCCc
Q psy879           73 ----R----G--IDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGA---QQALRRTMEIYS-NTTRFALACNNSEK  138 (317)
Q Consensus        73 ----~----~--~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~---~~~ll~~le~~~-~~~~~il~~~~~~~  138 (317)
                          .    .  .+.+.+.+..+.+.+........-++++|.+|.+.+-.   .+.|++.-+-.+ +.+.++++.....+
T Consensus        82 ~~d~dg~~~~~~~en~~d~i~~l~q~~~~t~~d~~~~liLDnad~lrD~~a~ll~~l~~L~el~~~~~i~iils~~~~e~  161 (438)
T KOG2543|consen   82 LADKDGDKVEGDAENFSDFIYLLVQWPAATNRDQKVFLILDNADALRDMDAILLQCLFRLYELLNEPTIVIILSAPSCEK  161 (438)
T ss_pred             cCCCchhhhhhHHHHHHHHHHHHHhhHHhhccCceEEEEEcCHHhhhccchHHHHHHHHHHHHhCCCceEEEEeccccHH
Confidence                0    0  12222333334442211111345678999999987433   334444433222 35556666554443


Q ss_pred             CchhHhhh--cceeeecCCCHHHHHHHHHHHHHHcCCCCCHHHH--------HHHHHhcCCCHHHHHHHHHHhhh
Q psy879          139 IIEPIQSR--CAMLRYNKLTDAQLLSKVIEICEKENISHTNDGL--------EAIVFTAQGDMRQALNNLQSTHN  203 (317)
Q Consensus       139 l~~~i~sR--~~~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~--------~~l~~~~~gd~r~~i~~l~~~~~  203 (317)
                      ....=-+.  ...++|+.|+.+++..++..---  | ....+..        ..+...|. |++.....+..++-
T Consensus       162 ~y~~n~g~~~i~~l~fP~Ys~~e~~~Il~~~~p--~-~r~~~~ya~fl~v~l~vF~~~cr-d~~eL~~~~~~~wp  232 (438)
T KOG2543|consen  162 QYLINTGTLEIVVLHFPQYSVEETQVILSRDNP--G-KRKLDVYAQFLHVLLQVFYMACR-DVNELRSLISLAWP  232 (438)
T ss_pred             HhhcccCCCCceEEecCCCCHHHHHHHHhcCCc--c-ccchHHHHHHHHHHHHHHHHHhC-CHHHHHHHHHHHHH
Confidence            32211112  23399999999999998876311  0 1222111        22223444 88888888876554

>COG4650 RtcR Sigma54-dependent transcription regulator containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms]

Probab=98.34  E-value=9.7e-06  Score=68.09  Aligned_cols=183  Identities=17%  Similarity=0.207  Sum_probs=108.3

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHc-CCCCCCceEEecCCCCcChHHHHHHHHHHHh---h-----cccCCCCceeEEEEe
Q psy879           33 NIIISGPPGVGKTTTILCLARILL-GPSFKDAVLELNASNDRGIDTVRNKIKMFAQ---Q-----KVTLPPGRHKIVILD  103 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~-~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~---~-----~~~~~~~~~~vliiD  103 (317)
                      .+|+.||.|.||+.+++.+...-. ....+..++++||...++.......++....   .     ...+-..+..++++|
T Consensus       210 p~ll~gptgagksflarriyelk~arhq~sg~fvevncatlrgd~amsalfghvkgaftga~~~r~gllrsadggmlfld  289 (531)
T COG4650         210 PILLNGPTGAGKSFLARRIYELKQARHQFSGAFVEVNCATLRGDTAMSALFGHVKGAFTGARESREGLLRSADGGMLFLD  289 (531)
T ss_pred             CeEeecCCCcchhHHHHHHHHHHHHHHhcCCceEEEeeeeecCchHHHHHHhhhccccccchhhhhhhhccCCCceEehH
Confidence            599999999999999999876422 1234567999999887776555544443211   1     111223578899999


Q ss_pred             CCCCCCHHHHHHHHHHhhhcc-----------CCceEEEEecCC-------CcCchhHhhhcceeeecCCCHHH------
Q psy879          104 EADSMTDGAQQALRRTMEIYS-----------NTTRFALACNNS-------EKIIEPIQSRCAMLRYNKLTDAQ------  159 (317)
Q Consensus       104 E~d~l~~~~~~~ll~~le~~~-----------~~~~~il~~~~~-------~~l~~~i~sR~~~i~f~~~~~~~------  159 (317)
                      |+..+..+.|.-|++.+|+..           ....+|.-|...       ..+-+.+-.|...+.|..|.-.+      
T Consensus       290 eigelgadeqamllkaieekrf~pfgsdr~v~sdfqliagtvrdlrq~vaeg~fredl~arinlwtf~lpgl~qr~edie  369 (531)
T COG4650         290 EIGELGADEQAMLLKAIEEKRFYPFGSDRQVSSDFQLIAGTVRDLRQLVAEGKFREDLYARINLWTFTLPGLRQRQEDIE  369 (531)
T ss_pred             hhhhcCccHHHHHHHHHHhhccCCCCCccccccchHHhhhhHHHHHHHHhccchHHHHHHhhheeeeeccccccCccccC
Confidence            999999999999999999631           111122222111       13445566666666665543221      


Q ss_pred             --HHHHHHHHHHHcC--CCCCHHHHHHHH-------HhcCCCHHHHHHHHHHhhh--CCCcccHHHHHh
Q psy879          160 --LLSKVIEICEKEN--ISHTNDGLEAIV-------FTAQGDMRQALNNLQSTHN--GFGHVTAEYVFK  215 (317)
Q Consensus       160 --~~~~l~~~~~~~~--~~i~~~~~~~l~-------~~~~gd~r~~i~~l~~~~~--~~~~i~~~~v~~  215 (317)
                        +.--|...+...|  +.+..++.....       ....|+.|..-.-+-.++.  +.+.|+.+.|+.
T Consensus       370 pnldyelerha~~~g~~vrfntearra~l~fa~spqa~w~gnfrelsasvtrmatlad~grit~~~ve~  438 (531)
T COG4650         370 PNLDYELERHASLTGDSVRFNTEARRAWLAFATSPQATWRGNFRELSASVTRMATLADSGRITLDVVED  438 (531)
T ss_pred             CCccHHHHHHHHhhCceeeeehHHHHHHHHhccCcchhhcccHHHHhHHHHHHHHHhcCCceeHHHHHH
Confidence              1122333343333  334444433322       2236888877665544332  667888876643

>PHA02624 large T antigen; Provisional

Probab=98.33  E-value=4.3e-06  Score=77.42  Aligned_cols=102  Identities=19%  Similarity=0.191  Sum_probs=64.2

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCH---
Q psy879           34 IIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTD---  110 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~---  110 (317)
                      ++|+||+|||||+++.++++.+.|.     ++.+|.......        .+. .    +..+.+++++|++..-.-   
T Consensus       434 il~~GPpnTGKTtf~~sLl~~L~G~-----vlsVNsPt~ks~--------FwL-~----pl~D~~~~l~dD~t~~~~~~~  495 (647)
T PHA02624        434 WLFKGPVNSGKTTLAAALLDLCGGK-----SLNVNCPPDKLN--------FEL-G----CAIDQFMVVFEDVKGQPADNK  495 (647)
T ss_pred             EEEECCCCCCHHHHHHHHHHHcCCe-----EEEeeCCcchhH--------HHh-h----hhhhceEEEeeeccccccccc
Confidence            9999999999999999999997443     344554332211        111 1    124678999999953211   


Q ss_pred             -----H---HHHHHHHHhhhc--------cCC------ceEEEEecCCCcCchhHhhhcce-eeecC
Q psy879          111 -----G---AQQALRRTMEIY--------SNT------TRFALACNNSEKIIEPIQSRCAM-LRYNK  154 (317)
Q Consensus       111 -----~---~~~~ll~~le~~--------~~~------~~~il~~~~~~~l~~~i~sR~~~-i~f~~  154 (317)
                           .   ...-|+.+|+..        +.+      ..+|+ |.+...++.+++-|+.. +.|.+
T Consensus       496 ~Lp~G~~~dNl~~lRn~LDG~V~v~ld~KH~n~~q~~~PPlli-T~Ney~iP~T~~~Rf~~~~~F~~  561 (647)
T PHA02624        496 DLPSGQGMNNLDNLRDYLDGSVPVNLEKKHLNKRSQIFPPGIV-TMNEYLIPQTVKARFAKVLDFKP  561 (647)
T ss_pred             cCCcccccchhhHHHhhcCCCCccccchhccCchhccCCCeEE-eecCcccchhHHHHHHHhccccc
Confidence                 1   124566666532        111      11344 44558899999999877 77765

>PF12780 AAA_8: P-loop containing dynein motor region D4; InterPro: IPR024317 The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases

Probab=98.31  E-value=4.4e-05  Score=65.00  Aligned_cols=152  Identities=14%  Similarity=0.220  Sum_probs=92.8

Q ss_pred             cccCCHHHHHHHHH---HHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHHHHHHHh
Q psy879           11 DIVGNEDTVERLKV---FSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFAQ   87 (317)
Q Consensus        11 ~~~g~~~~~~~l~~---~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~   87 (317)
                      +++--+++++.+..   .+... ..|.++.|.+|+||+++++..+-..     +..++.+......+..++++.++.+..
T Consensus         9 ~lVlf~~ai~hi~ri~RvL~~~-~Gh~LLvG~~GsGr~sl~rLaa~i~-----~~~~~~i~~~~~y~~~~f~~dLk~~~~   82 (268)
T PF12780_consen    9 NLVLFDEAIEHIARISRVLSQP-RGHALLVGVGGSGRQSLARLAAFIC-----GYEVFQIEITKGYSIKDFKEDLKKALQ   82 (268)
T ss_dssp             -----HHHHHHHHHHHHHHCST-TEEEEEECTTTSCHHHHHHHHHHHT-----TEEEE-TTTSTTTHHHHHHHHHHHHHH
T ss_pred             ceeeHHHHHHHHHHHHHHHcCC-CCCeEEecCCCccHHHHHHHHHHHh-----ccceEEEEeeCCcCHHHHHHHHHHHHH
Confidence            35555666665444   34433 3589999999999999999666542     344666666656667777777766555


Q ss_pred             hcccCCCCceeEEEEeCCCCCCHHHH---------------------HH--------------------H-HHHhhhccC
Q psy879           88 QKVTLPPGRHKIVILDEADSMTDGAQ---------------------QA--------------------L-RRTMEIYSN  125 (317)
Q Consensus        88 ~~~~~~~~~~~vliiDE~d~l~~~~~---------------------~~--------------------l-l~~le~~~~  125 (317)
                      ....  .+.+.+++++|.+-......                     +.                    + --+++.-..
T Consensus        83 ~ag~--~~~~~vfll~d~qi~~~~fLe~in~LL~sGeip~LF~~eE~~~i~~~l~~~~~~~~~~~~~~~~~~~F~~rvr~  160 (268)
T PF12780_consen   83 KAGI--KGKPTVFLLTDSQIVDESFLEDINSLLSSGEIPNLFTKEELDNIISSLREEAKAEGISDSRESLYEFFIERVRK  160 (268)
T ss_dssp             HHHC--S-S-EEEEEECCCSSSCHHHHHHHHHHHCSS-TTTS-TCHHHHHHHHHHHHHHHCT--SSHHHHHHHHHHHHCC
T ss_pred             HHhc--cCCCeEEEecCcccchHhHHHHHHHHHhCCCCCCCccHHHHHHHHHHhHHHHHHcCCCCchHHHHHHHHHHHHh
Confidence            4322  25678888888765432211                     11                    1 111223346


Q ss_pred             CceEEEEecCCC-------cCchhHhhhcceeeecCCCHHHHHHHHHHHHHH
Q psy879          126 TTRFALACNNSE-------KIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEK  170 (317)
Q Consensus       126 ~~~~il~~~~~~-------~l~~~i~sR~~~i~f~~~~~~~~~~~l~~~~~~  170 (317)
                      +..+|++-++..       +..|++.++|.+..|.+++.+.+..+-...+..
T Consensus       161 nLHivl~~sp~~~~~r~~~~~fPaL~~~ctIdW~~~W~~eaL~~Va~~~l~~  212 (268)
T PF12780_consen  161 NLHIVLCMSPVGPNFRDRCRSFPALVNCCTIDWFDPWPEEALLSVANKFLSD  212 (268)
T ss_dssp             CEEEEEEESTTTTCCCHHHHHHCCHHHHSEEEEEES--HHHHHHHHHHHCCH
T ss_pred             heeEEEEECCCCchHHHHHHhCcchhcccEEEeCCcCCHHHHHHHHHHHHHh
Confidence            677888776643       346999999999999999999999887766543

The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four (D1 - D4) correspond to the ATP binding sites with P-loop signatures described previously, and two (D5, D6) are modules in which the P loop has been lost in evolution. This particular entry represents the D4 ATP-binding domain of the motor [].; PDB: 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A.

>KOG0741|consensus

Probab=98.29  E-value=7.3e-05  Score=67.70  Aligned_cols=158  Identities=18%  Similarity=0.274  Sum_probs=87.0

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecC-CCCcChHHH--HHHHHHHHhhcccCCCCceeEEEEeCCCCCC
Q psy879           33 NIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNA-SNDRGIDTV--RNKIKMFAQQKVTLPPGRHKIVILDEADSMT  109 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~-~~~~~~~~i--~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~  109 (317)
                      .+||.||||+|||++|-.+|..     ...+++-+.. .+-.+..+.  ...+...+..+   ..+.-.++++|+++.+.
T Consensus       540 SvLl~Gp~~sGKTaLAA~iA~~-----S~FPFvKiiSpe~miG~sEsaKc~~i~k~F~DA---YkS~lsiivvDdiErLi  611 (744)
T KOG0741|consen  540 SVLLEGPPGSGKTALAAKIALS-----SDFPFVKIISPEDMIGLSESAKCAHIKKIFEDA---YKSPLSIIVVDDIERLL  611 (744)
T ss_pred             EEEEecCCCCChHHHHHHHHhh-----cCCCeEEEeChHHccCccHHHHHHHHHHHHHHh---hcCcceEEEEcchhhhh
Confidence            4999999999999999999976     2345554432 222222221  11222222222   12456799999999874


Q ss_pred             ------HHH----HHHHHHHhhhccCC--ceEEEEecCCCcCchh--Hhhhcce-eeecCCCH-HHHHHHHHHHHHHcCC
Q psy879          110 ------DGA----QQALRRTMEIYSNT--TRFALACNNSEKIIEP--IQSRCAM-LRYNKLTD-AQLLSKVIEICEKENI  173 (317)
Q Consensus       110 ------~~~----~~~ll~~le~~~~~--~~~il~~~~~~~l~~~--i~sR~~~-i~f~~~~~-~~~~~~l~~~~~~~~~  173 (317)
                            +..    ..+|+=++...|+.  -.+|++|+..-.++..  +.+.|.. ++.+.++. +++.+++...    ++
T Consensus       612 D~vpIGPRfSN~vlQaL~VllK~~ppkg~kLli~~TTS~~~vL~~m~i~~~F~~~i~Vpnl~~~~~~~~vl~~~----n~  687 (744)
T KOG0741|consen  612 DYVPIGPRFSNLVLQALLVLLKKQPPKGRKLLIFGTTSRREVLQEMGILDCFSSTIHVPNLTTGEQLLEVLEEL----NI  687 (744)
T ss_pred             cccccCchhhHHHHHHHHHHhccCCCCCceEEEEecccHHHHHHHcCHHHhhhheeecCccCchHHHHHHHHHc----cC
Confidence                  333    34444455554443  4567766654333322  1233333 77777775 7777777764    32


Q ss_pred             CCCHHHHHHHHHhcCC-----CHHHHHHHHHHhhh
Q psy879          174 SHTNDGLEAIVFTAQG-----DMRQALNNLQSTHN  203 (317)
Q Consensus       174 ~i~~~~~~~l~~~~~g-----d~r~~i~~l~~~~~  203 (317)
                       ++++....++....+     .+.+.+.+++.+..
T Consensus       688 -fsd~~~~~~~~~~~~~~~~vgIKklL~lie~a~q  721 (744)
T KOG0741|consen  688 -FSDDEVRAIAEQLLSKKVNVGIKKLLMLIEMARQ  721 (744)
T ss_pred             -CCcchhHHHHHHHhccccchhHHHHHHHHHHHhc
Confidence             445444444433222     25556655555433

>KOG2228|consensus

Probab=98.28  E-value=1.4e-05  Score=68.30  Aligned_cols=154  Identities=18%  Similarity=0.148  Sum_probs=86.5

Q ss_pred             CHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHHHHHHHhh------
Q psy879           15 NEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFAQQ------   88 (317)
Q Consensus        15 ~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~------   88 (317)
                      |.++-+.++..+..|....+++.||.|+|||.+.-.........+.+...+.+|+.-......+.+........      
T Consensus        33 ~~~l~~~lkqt~~~gEsnsviiigprgsgkT~li~~~Ls~~q~~~E~~l~v~Lng~~~~dk~al~~I~rql~~e~~~~~k  112 (408)
T KOG2228|consen   33 QKHLSELLKQTILHGESNSVIIIGPRGSGKTILIDTRLSDIQENGENFLLVRLNGELQTDKIALKGITRQLALELNRIVK  112 (408)
T ss_pred             HHHHHHHHHHHHHhcCCCceEEEccCCCCceEeeHHHHhhHHhcCCeEEEEEECccchhhHHHHHHHHHHHHHHHhhhhe
Confidence            34455556666667776679999999999999877666552222223334455543222111111111111100      


Q ss_pred             ---c--------------ccCCCCceeEEEEeCCCCCCHHH-HHHHHHHhhh---ccCCceEEEEecCCC---cCchhHh
Q psy879           89 ---K--------------VTLPPGRHKIVILDEADSMTDGA-QQALRRTMEI---YSNTTRFALACNNSE---KIIEPIQ  144 (317)
Q Consensus        89 ---~--------------~~~~~~~~~vliiDE~d~l~~~~-~~~ll~~le~---~~~~~~~il~~~~~~---~l~~~i~  144 (317)
                         +              ..-..+.+-++|+||+|.+.+.. |.-|..+++-   ....+++|.+|..-+   .+-+.++
T Consensus       113 ~~gsfte~l~~lL~~L~~~~~~t~~~ViFIldEfDlf~~h~rQtllYnlfDisqs~r~Piciig~Ttrld~lE~LEKRVK  192 (408)
T KOG2228|consen  113 SFGSFTENLSKLLEALKKGDETTSGKVIFILDEFDLFAPHSRQTLLYNLFDISQSARAPICIIGVTTRLDILELLEKRVK  192 (408)
T ss_pred             eecccchhHHHHHHHHhcCCCCCCceEEEEeehhhccccchhhHHHHHHHHHHhhcCCCeEEEEeeccccHHHHHHHHHH
Confidence               0              00011334567788999876554 5555566552   223455677776654   6779999


Q ss_pred             hhcce--eee-cCCCHHHHHHHHHHHH
Q psy879          145 SRCAM--LRY-NKLTDAQLLSKVIEIC  168 (317)
Q Consensus       145 sR~~~--i~f-~~~~~~~~~~~l~~~~  168 (317)
                      |||..  |.+ ++.+-++..+++++..
T Consensus       193 SRFshr~I~m~~~~~l~~yv~l~r~ll  219 (408)
T KOG2228|consen  193 SRFSHRVIFMLPSLPLGDYVDLYRKLL  219 (408)
T ss_pred             hhcccceeeccCCCChHHHHHHHHHHh
Confidence            99975  444 4445677777777654

>PRK10536 hypothetical protein; Provisional

Probab=98.26  E-value=1.1e-05  Score=67.53  Aligned_cols=43  Identities=21%  Similarity=0.161  Sum_probs=31.9

Q ss_pred             cccCCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHH
Q psy879           11 DIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        11 ~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .+.+.......+..++.++.  .+++.||+|||||+++.+++...
T Consensus        56 ~i~p~n~~Q~~~l~al~~~~--lV~i~G~aGTGKT~La~a~a~~~   98 (262)
T PRK10536         56 PILARNEAQAHYLKAIESKQ--LIFATGEAGCGKTWISAAKAAEA   98 (262)
T ss_pred             cccCCCHHHHHHHHHHhcCC--eEEEECCCCCCHHHHHHHHHHHH
Confidence            34444555555666676643  69999999999999999999853

>PF07693 KAP_NTPase: KAP family P-loop domain; InterPro: IPR011646 The KAP (after Kidins220/ARMS and PifA) family of predicted NTPases are sporadically distributed across a wide phylogenetic range in bacteria and in animals

Probab=98.24  E-value=0.00027  Score=62.43  Aligned_cols=76  Identities=13%  Similarity=0.138  Sum_probs=51.1

Q ss_pred             CceeEEEEeCCCCCCHHHHHHHHHHhhhc--cCCceEEEEecCCC---------------cCchhHhhh-cce-eeecCC
Q psy879           95 GRHKIVILDEADSMTDGAQQALRRTMEIY--SNTTRFALACNNSE---------------KIIEPIQSR-CAM-LRYNKL  155 (317)
Q Consensus        95 ~~~~vliiDE~d~l~~~~~~~ll~~le~~--~~~~~~il~~~~~~---------------~l~~~i~sR-~~~-i~f~~~  155 (317)
                      ..+-|++|||.|++.++....+++.+...  .+++.+|++.+...               ..-.....+ ++. +..|++
T Consensus       171 ~~~iViiIDdLDR~~~~~i~~~l~~ik~~~~~~~i~~Il~~D~~~l~~ai~~~~~~~~~~~~~~~yLeKiiq~~~~lP~~  250 (325)
T PF07693_consen  171 KKRIVIIIDDLDRCSPEEIVELLEAIKLLLDFPNIIFILAFDPEILEKAIEKNYGEGFDEIDGREYLEKIIQVPFSLPPP  250 (325)
T ss_pred             CceEEEEEcchhcCCcHHHHHHHHHHHHhcCCCCeEEEEEecHHHHHHHHHhhcCcccccccHHHHHHhhcCeEEEeCCC
Confidence            45778999999999998777776666533  25777888776421               011222223 344 888889


Q ss_pred             CHHHHHHHHHHHHHH
Q psy879          156 TDAQLLSKVIEICEK  170 (317)
Q Consensus       156 ~~~~~~~~l~~~~~~  170 (317)
                      +..++.+++...+..
T Consensus       251 ~~~~~~~~~~~~~~~  265 (325)
T PF07693_consen  251 SPSDLERYLNELLES  265 (325)
T ss_pred             CHHHHHHHHHHHHHH
Confidence            999999888877543

Many of the prokaryotic KAP NTPases are encoded in plasmids and tend to undergo disruption to form pseudogenes. A unique feature of all eukaryotic and certain bacterial KAP NTPases is the presence of two or four transmembrane helices inserted into the P-loop NTPase domain. These transmembrane helices anchor KAP NTPases in the membrane such that the P-loop domain is located on the intracellular side [].

>cd03246 ABCC_Protease_Secretion This family represents the ABC component of the protease secretion system PrtD, a 60-kDa integral membrane protein sharing 37% identity with HlyB, the ABC component of the alpha-hemolysin secretion pathway, in the C-terminal domain

Probab=98.24  E-value=4.1e-06  Score=66.90  Aligned_cols=109  Identities=19%  Similarity=0.297  Sum_probs=60.2

Q ss_pred             HhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHHHHHHHhhccc---------C----
Q psy879           26 SSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFAQQKVT---------L----   92 (317)
Q Consensus        26 l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~---------~----   92 (317)
                      +..|.  .+.+.||+|+||||+.+.++..+.... +...+.............+..+....+.+..         +    
T Consensus        25 i~~Ge--~~~i~G~nGsGKStLl~~l~G~~~~~~-G~i~~~g~~~~~~~~~~~~~~i~~~~q~~~~~~~tv~~~lLS~G~  101 (173)
T cd03246          25 IEPGE--SLAIIGPSGSGKSTLARLILGLLRPTS-GRVRLDGADISQWDPNELGDHVGYLPQDDELFSGSIAENILSGGQ  101 (173)
T ss_pred             ECCCC--EEEEECCCCCCHHHHHHHHHhccCCCC-CeEEECCEEcccCCHHHHHhheEEECCCCccccCcHHHHCcCHHH
Confidence            44555  699999999999999999998753222 1111110000000000111111100000000         0    


Q ss_pred             ---------CCCceeEEEEeCCC-CCCHHHHHHHHHHhhhccC-CceEEEEecCCC
Q psy879           93 ---------PPGRHKIVILDEAD-SMTDGAQQALRRTMEIYSN-TTRFALACNNSE  137 (317)
Q Consensus        93 ---------~~~~~~vliiDE~d-~l~~~~~~~ll~~le~~~~-~~~~il~~~~~~  137 (317)
                               ...+++++++||.. .+.......+.+.+.+... ...+|+++++..
T Consensus       102 ~qrv~la~al~~~p~~lllDEPt~~LD~~~~~~l~~~l~~~~~~~~tii~~sh~~~  157 (173)
T cd03246         102 RQRLGLARALYGNPRILVLDEPNSHLDVEGERALNQAIAALKAAGATRIVIAHRPE  157 (173)
T ss_pred             HHHHHHHHHHhcCCCEEEEECCccccCHHHHHHHHHHHHHHHhCCCEEEEEeCCHH
Confidence                     01468899999997 5677778888888776533 456777787754

They export degradative enzymes by using a type I protein secretion system and lack an N-terminal signal peptide, but contain a C-terminal secretion signal. The Type I secretion apparatus is made up of three components, an ABC transporter, a membrane fusion protein (MFP), and an outer membrane protein (OMP). For the HlyA transporter complex, HlyB (ABC transporter) and HlyD (MFP) reside in the inner membrane of E. coli. The OMP component is TolC, which is thought to interact with the MFP to form a continuous channel across the periplasm from the cytoplasm to the exterior. HlyB belongs to the family of ABC transporters, which are ubiquitous, ATP-dependent transmembrane pumps or channels. The spectrum of transport substra

>PF10443 RNA12: RNA12 protein; InterPro: IPR018850 Mitochondrial escape protein 2 (also known as RNA12) plays a role in maintaining the mitochondrial genome and in controlling mtDNA escape [, ]

Probab=98.23  E-value=0.00014  Score=64.80  Aligned_cols=153  Identities=11%  Similarity=0.158  Sum_probs=87.0

Q ss_pred             ceeEEEEeCCCCCCHHHHHHHHHHhhhc------cCCceEEEEecCCC---cCchhHhhh-cceeeecCCCHHHHHHHHH
Q psy879           96 RHKIVILDEADSMTDGAQQALRRTMEIY------SNTTRFALACNNSE---KIIEPIQSR-CAMLRYNKLTDAQLLSKVI  165 (317)
Q Consensus        96 ~~~vliiDE~d~l~~~~~~~ll~~le~~------~~~~~~il~~~~~~---~l~~~i~sR-~~~i~f~~~~~~~~~~~l~  165 (317)
                      .+.||+||.+..-... .+.+.+.+.+-      ..-..+||.|++..   .+.+++-+| +..+.+...+++.-++++.
T Consensus       148 ~~PVVVIdnF~~k~~~-~~~iy~~laeWAa~Lv~~nIAHVIFlT~dv~~~k~LskaLPn~vf~tI~L~Das~~~Ak~yV~  226 (431)
T PF10443_consen  148 RRPVVVIDNFLHKAEE-NDFIYDKLAEWAASLVQNNIAHVIFLTDDVSYSKPLSKALPNRVFKTISLSDASPESAKQYVL  226 (431)
T ss_pred             cCCEEEEcchhccCcc-cchHHHHHHHHHHHHHhcCccEEEEECCCCchhhhHHHhCCCCceeEEeecCCCHHHHHHHHH
Confidence            4689999998764433 33333333321      24456788887753   455666555 3448899999999999999


Q ss_pred             HHHHHcC-C-------------------CCCHHHHHHHHHhcCCCHHHHHHHHHHhhhCCCcccHHHHHhhcCCCCHHHH
Q psy879          166 EICEKEN-I-------------------SHTNDGLEAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAV  225 (317)
Q Consensus       166 ~~~~~~~-~-------------------~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~~~~~i~~~~v~~~~~~~~~~~i  225 (317)
                      ..+.... .                   ..+...++..+...||-+..+--+.++.-.+.  --.+.|.+.+.++..+..
T Consensus       227 ~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~eld~~i~~LGGRltDLe~lvrRiksGe--~p~~Av~~iI~qsa~eI~  304 (431)
T PF10443_consen  227 SQLDEDTEDSSDSKESNEQNKNDKSAENEKDLAELDECIEPLGGRLTDLEFLVRRIKSGE--SPEEAVEEIISQSASEIR  304 (431)
T ss_pred             HHhcccccccccccccccccccccccccccchHHHHHHHHHcCCcHHHHHHHHHHHHcCC--CHHHHHHHHHHHHHHHHH
Confidence            8876531 0                   12345567777888888887777777664432  223334444433322221


Q ss_pred             HHHHH------HHhcCCHHHHHHHHHHHHHcC
Q psy879          226 KEMLL------NCVEGNMKDSYKIIHHLYKLG  251 (317)
Q Consensus       226 ~~l~~------~~~~~~~~~~~~~~~~l~~~~  251 (317)
                      .-.+.      .-..+...++..++..|.+++
T Consensus       305 k~fl~~~~~~~~~~~Wt~~QaW~LIk~Ls~~~  336 (431)
T PF10443_consen  305 KMFLLDDSDDAKSLKWTREQAWYLIKLLSKND  336 (431)
T ss_pred             HHHhcCCCCcccCCCCCHHHHHHHHHHhccCC
Confidence            11111      112234566666666654433

It is also involved in the regulation of mtDNA nucleotide structure and number []. Additionally, this protein have a dispensable role in the early maturation of pre-rRNA [].

>cd03228 ABCC_MRP_Like The MRP (Mutidrug Resistance Protein)-like transporters are involved in drug, peptide, and lipid export

Probab=98.23  E-value=3.1e-06  Score=67.50  Aligned_cols=109  Identities=19%  Similarity=0.317  Sum_probs=61.6

Q ss_pred             HHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCC--CcChH------------------HHHHH-HH
Q psy879           25 FSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASN--DRGID------------------TVRNK-IK   83 (317)
Q Consensus        25 ~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~--~~~~~------------------~i~~~-~~   83 (317)
                      .+..|.  .+.+.||+|+||||+.+.++..+..... ...  ++...  .....                  .+.+. +.
T Consensus        24 ~i~~G~--~~~l~G~nGsGKstLl~~i~G~~~~~~G-~i~--~~g~~~~~~~~~~~~~~i~~~~~~~~~~~~t~~e~lLS   98 (171)
T cd03228          24 TIKPGE--KVAIVGPSGSGKSTLLKLLLRLYDPTSG-EIL--IDGVDLRDLDLESLRKNIAYVPQDPFLFSGTIRENILS   98 (171)
T ss_pred             EEcCCC--EEEEECCCCCCHHHHHHHHHcCCCCCCC-EEE--ECCEEhhhcCHHHHHhhEEEEcCCchhccchHHHHhhC
Confidence            344555  6999999999999999999997532222 111  11100  00000                  01000 00


Q ss_pred             HHHhhccc---CCCCceeEEEEeCCC-CCCHHHHHHHHHHhhhccCCceEEEEecCCCc
Q psy879           84 MFAQQKVT---LPPGRHKIVILDEAD-SMTDGAQQALRRTMEIYSNTTRFALACNNSEK  138 (317)
Q Consensus        84 ~~~~~~~~---~~~~~~~vliiDE~d-~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~  138 (317)
                      .-......   ....++.++++||.. .+.......+.+.+.+......+|+++++...
T Consensus        99 ~G~~~rl~la~al~~~p~llllDEP~~gLD~~~~~~l~~~l~~~~~~~tii~~sh~~~~  157 (171)
T cd03228          99 GGQRQRIAIARALLRDPPILILDEATSALDPETEALILEALRALAKGKTVIVIAHRLST  157 (171)
T ss_pred             HHHHHHHHHHHHHhcCCCEEEEECCCcCCCHHHHHHHHHHHHHhcCCCEEEEEecCHHH
Confidence            00000000   001467899999997 56777788888888766555667777877544

They belong to the subfamily C of the ATP-binding cassette (ABC) superfamily of transport proteins. The ABCC subfamily contains transporters with a diverse functional spectrum that includes ion transport, cell surface receptor, and toxin secretion activities. The MRP-like family, simlar to all ABC proteins, have a common four-domain core structure constituted by two membrane-spanning domains, each composed of six transmembrane (TM) helices, and two nucleotide-binding domains (NBD). ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>COG2274 SunT ABC-type bacteriocin/lantibiotic exporters, contain an N-terminal double-glycine peptidase domain [Defense mechanisms]

Probab=98.22  E-value=1.5e-06  Score=83.44  Aligned_cols=42  Identities=17%  Similarity=0.252  Sum_probs=33.0

Q ss_pred             CceeEEEEeCCCC-CCHHHHHHHHHHhhhccCCceEEEEecCC
Q psy879           95 GRHKIVILDEADS-MTDGAQQALRRTMEIYSNTTRFALACNNS  136 (317)
Q Consensus        95 ~~~~vliiDE~d~-l~~~~~~~ll~~le~~~~~~~~il~~~~~  136 (317)
                      .+++|+++||+-. +..+....+.+.|.+......+|+++++.
T Consensus       626 ~~P~ILlLDEaTSaLD~~sE~~I~~~L~~~~~~~T~I~IaHRl  668 (709)
T COG2274         626 SKPKILLLDEATSALDPETEAIILQNLLQILQGRTVIIIAHRL  668 (709)
T ss_pred             cCCCEEEEeCcccccCHhHHHHHHHHHHHHhcCCeEEEEEccc
Confidence            3789999999975 56677777888888777667788888774

>PRK04296 thymidine kinase; Provisional

Probab=98.22  E-value=1.1e-05  Score=65.41  Aligned_cols=94  Identities=17%  Similarity=0.186  Sum_probs=53.9

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCC-C----------CcCh-------HHHHHHHHHHHhhcccCCC
Q psy879           33 NIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNAS-N----------DRGI-------DTVRNKIKMFAQQKVTLPP   94 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~-~----------~~~~-------~~i~~~~~~~~~~~~~~~~   94 (317)
                      ..+++||+|+||||++..++..+......  ++.+.+. +          ..+.       ....+.+..+..     ..
T Consensus         4 i~litG~~GsGKTT~~l~~~~~~~~~g~~--v~i~k~~~d~~~~~~~i~~~lg~~~~~~~~~~~~~~~~~~~~-----~~   76 (190)
T PRK04296          4 LEFIYGAMNSGKSTELLQRAYNYEERGMK--VLVFKPAIDDRYGEGKVVSRIGLSREAIPVSSDTDIFELIEE-----EG   76 (190)
T ss_pred             EEEEECCCCCHHHHHHHHHHHHHHHcCCe--EEEEeccccccccCCcEecCCCCcccceEeCChHHHHHHHHh-----hC
Confidence            37899999999999999999876433222  2212110 0          0010       011122222211     12


Q ss_pred             CceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecC
Q psy879           95 GRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNN  135 (317)
Q Consensus        95 ~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~  135 (317)
                      +.+.+|+|||++.+..+....+.+.+.  +....+|++...
T Consensus        77 ~~~dvviIDEaq~l~~~~v~~l~~~l~--~~g~~vi~tgl~  115 (190)
T PRK04296         77 EKIDCVLIDEAQFLDKEQVVQLAEVLD--DLGIPVICYGLD  115 (190)
T ss_pred             CCCCEEEEEccccCCHHHHHHHHHHHH--HcCCeEEEEecC
Confidence            467899999999987765555666654  344556666544

>cd03247 ABCC_cytochrome_bd The CYD subfamily implicated in cytochrome bd biogenesis

Probab=98.22  E-value=2.2e-06  Score=68.86  Aligned_cols=109  Identities=17%  Similarity=0.172  Sum_probs=62.0

Q ss_pred             HHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcC-hHHHHHHHHHHHhhc------------cc
Q psy879           25 FSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRG-IDTVRNKIKMFAQQK------------VT   91 (317)
Q Consensus        25 ~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~-~~~i~~~~~~~~~~~------------~~   91 (317)
                      .+..|.  .+.+.||+|+||||+++.++..+.. ..+.  +.++...... ....+..+....+.+            ..
T Consensus        24 ~i~~Ge--~~~i~G~nGsGKStLl~~l~G~~~~-~~G~--i~~~g~~~~~~~~~~~~~i~~~~q~~~~~~~tv~~~i~~~   98 (178)
T cd03247          24 ELKQGE--KIALLGRSGSGKSTLLQLLTGDLKP-QQGE--ITLDGVPVSDLEKALSSLISVLNQRPYLFDTTLRNNLGRR   98 (178)
T ss_pred             EEcCCC--EEEEECCCCCCHHHHHHHHhccCCC-CCCE--EEECCEEHHHHHHHHHhhEEEEccCCeeecccHHHhhccc
Confidence            344555  6999999999999999999987532 2221  1111110000 000010000000000            00


Q ss_pred             CC-------------CCceeEEEEeCCC-CCCHHHHHHHHHHhhhccCCceEEEEecCCCc
Q psy879           92 LP-------------PGRHKIVILDEAD-SMTDGAQQALRRTMEIYSNTTRFALACNNSEK  138 (317)
Q Consensus        92 ~~-------------~~~~~vliiDE~d-~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~  138 (317)
                      ++             ..+++++++||.. .+.......+.+.+.+......+|+++++...
T Consensus        99 LS~G~~qrv~laral~~~p~~lllDEP~~~LD~~~~~~l~~~l~~~~~~~tii~~sh~~~~  159 (178)
T cd03247          99 FSGGERQRLALARILLQDAPIVLLDEPTVGLDPITERQLLSLIFEVLKDKTLIWITHHLTG  159 (178)
T ss_pred             CCHHHHHHHHHHHHHhcCCCEEEEECCcccCCHHHHHHHHHHHHHHcCCCEEEEEecCHHH
Confidence            00             1468999999997 56777788888888765555667888877654

The CydC and CydD proteins are important for the formation of cytochrome bd terminal oxidase of E. coli and it has been proposed that they were necessary for biosynthesis of the cytochrome bd quinol oxidase and for periplasmic c-type cytochromes. CydCD were proposed to determine a heterooligomeric complex important for heme export into the periplasm or to be involved in the maintenance of the proper redox state of the periplasmic space. In Bacillus subtilius, the absence of CydCD does not affect the presence of halo-cytochrome c in the membrane and this observation suggests that CydCD proteins are not involved in the export of heme in this organism.

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=98.21  E-value=1.4e-05  Score=62.81  Aligned_cols=24  Identities=46%  Similarity=0.574  Sum_probs=21.5

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHc
Q psy879           33 NIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      +++++||||+|||+++..++....
T Consensus         1 ~~~i~G~~G~GKT~l~~~i~~~~~   24 (165)
T cd01120           1 LILVFGPTGSGKTTLALQLALNIA   24 (165)
T ss_pred             CeeEeCCCCCCHHHHHHHHHHHHH
Confidence            368999999999999999998874

This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.

>cd03214 ABC_Iron-Siderophores_B12_Hemin ABC transporters, involved in the uptake of siderophores, heme, and vitamin B12, are widely conserved in bacteria and archaea

Probab=98.20  E-value=1.1e-05  Score=64.97  Aligned_cols=109  Identities=20%  Similarity=0.237  Sum_probs=62.7

Q ss_pred             HhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHHHHHHH------------hh-cccC
Q psy879           26 SSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFA------------QQ-KVTL   92 (317)
Q Consensus        26 l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~------------~~-~~~~   92 (317)
                      +..|.  .+.+.||+|+||||+.+.++..+.. ..+...+............++..+....            .. ...+
T Consensus        22 i~~G~--~~~l~G~nGsGKStLl~~i~G~~~~-~~G~v~~~g~~~~~~~~~~~~~~i~~~~q~l~~~gl~~~~~~~~~~L   98 (180)
T cd03214          22 IEAGE--IVGILGPNGAGKSTLLKTLAGLLKP-SSGEILLDGKDLASLSPKELARKIAYVPQALELLGLAHLADRPFNEL   98 (180)
T ss_pred             ECCCC--EEEEECCCCCCHHHHHHHHhCCCCC-CCcEEEECCEECCcCCHHHHHHHHhHHHHHHHHcCCHhHhcCCcccC
Confidence            44555  6999999999999999999986532 2222222111111111112222221111            00 0001


Q ss_pred             CC-------------CceeEEEEeCCC-CCCHHHHHHHHHHhhhccC--CceEEEEecCCC
Q psy879           93 PP-------------GRHKIVILDEAD-SMTDGAQQALRRTMEIYSN--TTRFALACNNSE  137 (317)
Q Consensus        93 ~~-------------~~~~vliiDE~d-~l~~~~~~~ll~~le~~~~--~~~~il~~~~~~  137 (317)
                      +.             .++.++++||.. .+.......+.+.+.+...  ...+|+++++..
T Consensus        99 S~G~~qrl~laral~~~p~llllDEP~~~LD~~~~~~~~~~l~~~~~~~~~tiii~sh~~~  159 (180)
T cd03214          99 SGGERQRVLLARALAQEPPILLLDEPTSHLDIAHQIELLELLRRLARERGKTVVMVLHDLN  159 (180)
T ss_pred             CHHHHHHHHHHHHHhcCCCEEEEeCCccCCCHHHHHHHHHHHHHHHHhcCCEEEEEeCCHH
Confidence            10             368999999998 5677788888888876543  456777776644

Only very few species lack representatives of the siderophore family transporters. The E. coli BtuCD protein is an ABC transporter mediating vitamin B12 uptake. The two ATP-binding cassettes (BtuD) are in close contact with each other, as are the two membrane-spanning subunits (BtuC); this arrangement is distinct from that observed for the E. coli lipid flippase MsbA. The BtuC subunits provide 20 transmembrane helices grouped around a translocation pathway that is closed to the cytoplasm by a gate region, whereas the dimer arrangement of the BtuD subunits resembles the ATP-bound form of the Rad50 DNA repair enzyme. A prominent cytoplasmic loop of BtuC forms the contact region with the ATP-binding cassette and represent a conserved motif among the ABC transporters.

>COG1127 Ttg2A ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]

Probab=98.20  E-value=8.9e-07  Score=72.17  Aligned_cols=185  Identities=14%  Similarity=0.146  Sum_probs=108.5

Q ss_pred             CCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcCh---HHHHHHHHHHHhhcc
Q psy879           14 GNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGI---DTVRNKIKMFAQQKV   90 (317)
Q Consensus        14 g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~---~~i~~~~~~~~~~~~   90 (317)
                      |...+.+.+.--+.+|+  .+.+.||+|+|||++.+.+...+....... .+........+.   ..++..++..+|.. 
T Consensus        19 G~~~Ild~v~l~V~~Ge--i~~iiGgSGsGKStlLr~I~Gll~P~~GeI-~i~G~~i~~ls~~~~~~ir~r~GvlFQ~g-   94 (263)
T COG1127          19 GDRVILDGVDLDVPRGE--ILAILGGSGSGKSTLLRLILGLLRPDKGEI-LIDGEDIPQLSEEELYEIRKRMGVLFQQG-   94 (263)
T ss_pred             CCEEEecCceeeecCCc--EEEEECCCCcCHHHHHHHHhccCCCCCCeE-EEcCcchhccCHHHHHHHHhheeEEeecc-
Confidence            44555555555566676  689999999999999999999874443322 222211111111   22222222222221 


Q ss_pred             cCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcCchhHhhhcceeeecCCCHHHHHHHHHHHHHH
Q psy879           91 TLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEK  170 (317)
Q Consensus        91 ~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~~~i~sR~~~i~f~~~~~~~~~~~l~~~~~~  170 (317)
                                              +|...|.-. +|+-|                  ...+-..+++..+.+.....++.
T Consensus        95 ------------------------ALFssltV~-eNVaf------------------plre~~~lp~~~i~~lv~~KL~~  131 (263)
T COG1127          95 ------------------------ALFSSLTVF-ENVAF------------------PLREHTKLPESLIRELVLMKLEL  131 (263)
T ss_pred             ------------------------ccccccchh-Hhhhe------------------ehHhhccCCHHHHHHHHHHHHHh
Confidence                                    111111100 11100                  01122367888888887777765


Q ss_pred             cCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhhCCCcccHHHHHhhcCCCCHHHHHHHHHHHh----------cCCHHHH
Q psy879          171 ENISHTNDGLEAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEMLLNCV----------EGNMKDS  240 (317)
Q Consensus       171 ~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~~~~~i~~~~v~~~~~~~~~~~i~~l~~~~~----------~~~~~~~  240 (317)
                      -|  +...+.+.+...-.|.+++-..+.++.+.+..-+-.|+...-.+......+.+++..+.          .+|...+
T Consensus       132 VG--L~~~~~~~~PsELSGGM~KRvaLARAialdPell~~DEPtsGLDPI~a~~~~~LI~~L~~~lg~T~i~VTHDl~s~  209 (263)
T COG1127         132 VG--LRGAAADLYPSELSGGMRKRVALARAIALDPELLFLDEPTSGLDPISAGVIDELIRELNDALGLTVIMVTHDLDSL  209 (263)
T ss_pred             cC--CChhhhhhCchhhcchHHHHHHHHHHHhcCCCEEEecCCCCCCCcchHHHHHHHHHHHHHhhCCEEEEEECChHHH
Confidence            55  45777888888777889999999999888776666665555555555555555655543          4577777


Q ss_pred             HHHHHHH
Q psy879          241 YKIIHHL  247 (317)
Q Consensus       241 ~~~~~~l  247 (317)
                      +.+.+..
T Consensus       210 ~~i~Drv  216 (263)
T COG1127         210 LTIADRV  216 (263)
T ss_pred             HhhhceE
Confidence            7765554

>COG5271 MDN1 AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]

Probab=98.18  E-value=4.5e-05  Score=77.29  Aligned_cols=140  Identities=20%  Similarity=0.266  Sum_probs=92.1

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHHHHHH-----------HhhcccCCCCceeEEE
Q psy879           33 NIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMF-----------AQQKVTLPPGRHKIVI  101 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~-----------~~~~~~~~~~~~~vli  101 (317)
                      .+++.|.||+|||+++.++|+.. |    ..++.+|-+....   +.+.++.-           ...++.....++.-|+
T Consensus      1545 pilLEGsPGVGKTSlItaLAr~t-G----~kliRINLSeQTd---L~DLfGsd~Pve~~Gef~w~dapfL~amr~G~WVl 1616 (4600)
T COG5271        1545 PILLEGSPGVGKTSLITALARKT-G----KKLIRINLSEQTD---LCDLFGSDLPVEEGGEFRWMDAPFLHAMRDGGWVL 1616 (4600)
T ss_pred             ceeecCCCCccHHHHHHHHHHHh-c----CceEEeeccccch---HHHHhCCCCCcccCceeEecccHHHHHhhcCCEEE
Confidence            59999999999999999999985 2    2355555543221   11111110           0011111124567899


Q ss_pred             EeCCCCCCHHHHHHHHHHhhhc--------------cCCceEEEEecCCC------cCchhHhhhcceeeecCCCHHHHH
Q psy879          102 LDEADSMTDGAQQALRRTMEIY--------------SNTTRFALACNNSE------KIIEPIQSRCAMLRYNKLTDAQLL  161 (317)
Q Consensus       102 iDE~d~l~~~~~~~ll~~le~~--------------~~~~~~il~~~~~~------~l~~~i~sR~~~i~f~~~~~~~~~  161 (317)
                      +||+.-.+....+.|...++..              ++++++..+-|+.+      -+++.+..|+.++.+..++.+++.
T Consensus      1617 LDEiNLaSQSVlEGLNacLDhR~eayIPEld~~f~~HpnfrVFAaqNPq~qggGRKgLPkSF~nRFsvV~~d~lt~dDi~ 1696 (4600)
T COG5271        1617 LDEINLASQSVLEGLNACLDHRREAYIPELDKTFDVHPNFRVFAAQNPQDQGGGRKGLPKSFLNRFSVVKMDGLTTDDIT 1696 (4600)
T ss_pred             eehhhhhHHHHHHHHHHHHhhccccccccccceeeccCCeeeeeecCchhcCCCcccCCHHHhhhhheEEecccccchHH
Confidence            9999999888777777776621              35555555545432      589999999999999999999999


Q ss_pred             HHHHHHHHHcCCCCCHHHHHHHH
Q psy879          162 SKVIEICEKENISHTNDGLEAIV  184 (317)
Q Consensus       162 ~~l~~~~~~~~~~i~~~~~~~l~  184 (317)
                      .+......    .+.++...+++
T Consensus      1697 ~Ia~~~yp----~v~~d~~~kii 1715 (4600)
T COG5271        1697 HIANKMYP----QVNEDWRLKII 1715 (4600)
T ss_pred             HHHHhhCC----ccChHHHHHHH
Confidence            88776542    35555554444

>TIGR02868 CydC thiol reductant ABC exporter, CydC subunit

Probab=98.17  E-value=4.2e-06  Score=79.03  Aligned_cols=37  Identities=27%  Similarity=0.511  Sum_probs=28.4

Q ss_pred             HHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHc
Q psy879           18 TVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        18 ~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      +++.+.-.++.|.  .+.+.||+|+||||+++.+++...
T Consensus       350 vL~~isl~i~~G~--~vaIvG~SGsGKSTLl~lL~g~~~  386 (529)
T TIGR02868       350 VLDGVSLDLPPGE--RVAILGPSGSGKSTLLMLLTGLLD  386 (529)
T ss_pred             eeecceEEEcCCC--EEEEECCCCCCHHHHHHHHhcCCC
Confidence            4444444455665  699999999999999999998653

The gene pair cydCD encodes an ABC-family transporter in which each gene contains an N-terminal membrane-spanning domain (pfam00664) and a C-terminal ATP-binding domain (pfam00005). In E. coli these genes were discovered as mutants which caused the terminal heme-copper oxidase complex cytochrome bd to fail to assemble. Recent work has shown that the transporter is involved in export of redox-active thiol compounds such as cysteine and glutathione. The linkage to assembly of the cytochrome bd complex is further supported by the conserved operon structure found outside the gammaproteobacteria (cydABCD) containing both the transporter and oxidase genes components. The genes used as the seed members for this model are all either found in the gammproteobacterial context or the CydABCD context. All members of this family scoring above trusted at the time of its creation were from genomes which encode a cytochrome bd complex.

>cd03216 ABC_Carb_Monos_I This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos)

Probab=98.16  E-value=1.2e-05  Score=63.52  Aligned_cols=102  Identities=16%  Similarity=0.259  Sum_probs=60.0

Q ss_pred             HhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCC--CcCh-HHHH--------------HHHHHHHhh
Q psy879           26 SSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASN--DRGI-DTVR--------------NKIKMFAQQ   88 (317)
Q Consensus        26 l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~--~~~~-~~i~--------------~~~~~~~~~   88 (317)
                      +..|.  .+.|.||+|+||||+.+.++..+. +..+.  +.++...  .... ...+              ..+.....-
T Consensus        23 i~~Ge--~~~l~G~nGsGKSTLl~~i~G~~~-~~~G~--v~~~g~~~~~~~~~~~~~~~i~~~~qLS~G~~qrl~laral   97 (163)
T cd03216          23 VRRGE--VHALLGENGAGKSTLMKILSGLYK-PDSGE--ILVDGKEVSFASPRDARRAGIAMVYQLSVGERQMVEIARAL   97 (163)
T ss_pred             EeCCC--EEEEECCCCCCHHHHHHHHhCCCC-CCCeE--EEECCEECCcCCHHHHHhcCeEEEEecCHHHHHHHHHHHHH
Confidence            45555  799999999999999999998753 22222  1122111  1111 1111              111111000


Q ss_pred             cccCCCCceeEEEEeCCC-CCCHHHHHHHHHHhhhcc-CCceEEEEecCCC
Q psy879           89 KVTLPPGRHKIVILDEAD-SMTDGAQQALRRTMEIYS-NTTRFALACNNSE  137 (317)
Q Consensus        89 ~~~~~~~~~~vliiDE~d-~l~~~~~~~ll~~le~~~-~~~~~il~~~~~~  137 (317)
                           ..+++++++||.. .+.......+.+.+.+.. ....+|+++++..
T Consensus        98 -----~~~p~illlDEP~~~LD~~~~~~l~~~l~~~~~~~~tiii~sh~~~  143 (163)
T cd03216          98 -----ARNARLLILDEPTAALTPAEVERLFKVIRRLRAQGVAVIFISHRLD  143 (163)
T ss_pred             -----hcCCCEEEEECCCcCCCHHHHHHHHHHHHHHHHCCCEEEEEeCCHH
Confidence                 1468999999998 467777888888887653 3455677776643

The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses (such as xylose, arabinose, and ribose), that cannot be broken down to simple sugars by hydrolysis. Pentoses include xylose, arabinose, and ribose. Important hexoses include glucose, galactose, and fructose. In members of the Carb_monos family, the single hydrophobic gene product forms a homodimer while the ABC protein represents a fusion of two nucleotide-binding domains. However, it is assumed that two copies of the ABC domains are present in the assembled transporter.

>PF06309 Torsin: Torsin; InterPro: IPR010448 This family consists of several eukaryotic torsin proteins

Probab=98.15  E-value=6.3e-06  Score=60.89  Aligned_cols=55  Identities=24%  Similarity=0.294  Sum_probs=39.2

Q ss_pred             cccCCHHHHHHH----HHHHhcCCC--ce-EEEECCCCCCHHHHHHHHHHHHcCCCCCCceE
Q psy879           11 DIVGNEDTVERL----KVFSSSGNV--PN-IIISGPPGVGKTTTILCLARILLGPSFKDAVL   65 (317)
Q Consensus        11 ~~~g~~~~~~~l----~~~l~~~~~--~~-~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~   65 (317)
                      .+.||+-+.+.+    ...+.+..+  |- +.|.|++|||||.+++.+|+.++.......++
T Consensus        26 ~l~GQhla~~~v~~ai~~~l~~~~p~KpLVlSfHG~tGtGKn~v~~liA~~ly~~G~~S~~V   87 (127)
T PF06309_consen   26 NLFGQHLAVEVVVNAIKGHLANPNPRKPLVLSFHGWTGTGKNFVSRLIAEHLYKSGMKSPFV   87 (127)
T ss_pred             HccCcHHHHHHHHHHHHHHHcCCCCCCCEEEEeecCCCCcHHHHHHHHHHHHHhcccCCCce
Confidence            578988666654    444544433  22 67999999999999999999988665444433

Torsion dystonia is an autosomal dominant movement disorder characterised by involuntary, repetitive muscle contractions and twisted postures. The most severe early-onset form of dystonia has been linked to mutations in the human DYT1 (TOR1A) gene encoding a protein termed torsinA. While causative genetic alterations have been identified, the function of torsin proteins and the molecular mechanism underlying dystonia remain unknown. Phylogenetic analysis of the torsin protein family indicates these proteins share distant sequence similarity with the large and diverse family of AAA ATPase, central region containing proteins () proteins. It has been suggested that torsins play a role in effectively managing protein folding and that possible breakdown in a neuroprotective mechanism that is, in part, mediated by torsins may be responsible for the neuronal dysfunction associated with dystonia [].; GO: 0005524 ATP binding, 0051085 chaperone mediated protein folding requiring cofactor

>TIGR02858 spore_III_AA stage III sporulation protein AA

Probab=98.13  E-value=1.3e-05  Score=68.42  Aligned_cols=35  Identities=43%  Similarity=0.539  Sum_probs=28.8

Q ss_pred             HHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHc
Q psy879           22 LKVFSSSGNVPNIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        22 l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      +....+.+...++++.||+|+||||+.+.++..+.
T Consensus       102 l~~l~~~~~~~~~~i~g~~g~GKttl~~~l~~~~~  136 (270)
T TIGR02858       102 LPYLVRNNRVLNTLIISPPQCGKTTLLRDLARILS  136 (270)
T ss_pred             HHHHHhCCCeeEEEEEcCCCCCHHHHHHHHhCccC
Confidence            34444567667899999999999999999999874

Members of this protein are the stage III sporulation protein AA, encoded by one of several genes in the spoIIIA locus. It seems that this protein is found in a species if and only if that species is capable of endospore formation.

>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]

Probab=98.12  E-value=0.00074  Score=64.75  Aligned_cols=176  Identities=17%  Similarity=0.166  Sum_probs=105.2

Q ss_pred             CCcccCCHHHHHHHHHHHhcC-CCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHHHHHHH-
Q psy879            9 FSDIVGNEDTVERLKVFSSSG-NVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFA-   86 (317)
Q Consensus         9 ~~~~~g~~~~~~~l~~~l~~~-~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~-   86 (317)
                      ....+-++.    |..-+..+ ...-++|.-|.|+||||++-.++. ...+......+.++.+++......+..+.... 
T Consensus        18 ~~~~v~R~r----L~~~L~~~~~~RL~li~APAGfGKttl~aq~~~-~~~~~~~v~Wlslde~dndp~rF~~yLi~al~~   92 (894)
T COG2909          18 PDNYVVRPR----LLDRLRRANDYRLILISAPAGFGKTTLLAQWRE-LAADGAAVAWLSLDESDNDPARFLSYLIAALQQ   92 (894)
T ss_pred             cccccccHH----HHHHHhcCCCceEEEEeCCCCCcHHHHHHHHHH-hcCcccceeEeecCCccCCHHHHHHHHHHHHHH
Confidence            444444444    44444444 333499999999999999999988 33444444444444443222111111111111 


Q ss_pred             -------------hhcc--------------cCCCCceeEEEEeCCCCCCHHH-HHHHHHHhhhccCCceEEEEecCCCc
Q psy879           87 -------------QQKV--------------TLPPGRHKIVILDEADSMTDGA-QQALRRTMEIYSNTTRFALACNNSEK  138 (317)
Q Consensus        87 -------------~~~~--------------~~~~~~~~vliiDE~d~l~~~~-~~~ll~~le~~~~~~~~il~~~~~~~  138 (317)
                                   +...              .....++-.+++|+-+...... ..++..+++..|++..+|++|.....
T Consensus        93 ~~p~~~~~a~~l~q~~~~~~l~~l~~~L~~Ela~~~~pl~LVlDDyHli~~~~l~~~l~fLl~~~P~~l~lvv~SR~rP~  172 (894)
T COG2909          93 ATPTLGDEAQTLLQKHQYVSLESLLSSLLNELASYEGPLYLVLDDYHLISDPALHEALRFLLKHAPENLTLVVTSRSRPQ  172 (894)
T ss_pred             hCccccHHHHHHHHhcccccHHHHHHHHHHHHHhhcCceEEEeccccccCcccHHHHHHHHHHhCCCCeEEEEEeccCCC
Confidence                         0000              0011356789999999997665 55677777888899988888865432


Q ss_pred             -CchhHhhhcceeeec----CCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHH
Q psy879          139 -IIEPIQSRCAMLRYN----KLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMR  192 (317)
Q Consensus       139 -l~~~i~sR~~~i~f~----~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r  192 (317)
                       -...++=|-..+++.    .++.+|..+++....   +..++...++.+...++|-+.
T Consensus       173 l~la~lRlr~~llEi~~~~Lrf~~eE~~~fl~~~~---~l~Ld~~~~~~L~~~teGW~~  228 (894)
T COG2909         173 LGLARLRLRDELLEIGSEELRFDTEEAAAFLNDRG---SLPLDAADLKALYDRTEGWAA  228 (894)
T ss_pred             CcccceeehhhHHhcChHhhcCChHHHHHHHHHcC---CCCCChHHHHHHHhhcccHHH
Confidence             233333333332222    457788888877753   478889999999999998544

>PRK11174 cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed

Probab=98.12  E-value=7.2e-06  Score=78.51  Aligned_cols=41  Identities=12%  Similarity=0.242  Sum_probs=30.4

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhccCCceEEEEecCC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYSNTTRFALACNNS  136 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~~~~~~il~~~~~  136 (317)
                      +++++++||+-. +..+....+.+.+.+..++..+|++|++.
T Consensus       503 ~~~IliLDE~TSaLD~~te~~i~~~l~~~~~~~TvIiItHrl  544 (588)
T PRK11174        503 PCQLLLLDEPTASLDAHSEQLVMQALNAASRRQTTLMVTHQL  544 (588)
T ss_pred             CCCEEEEeCCccCCCHHHHHHHHHHHHHHhCCCEEEEEecCh
Confidence            579999999985 56667777777777665555577777775

>COG1119 ModF ABC-type molybdenum transport system, ATPase component/photorepair protein PhrA [Inorganic ion transport and metabolism]

Probab=98.11  E-value=2.2e-05  Score=64.48  Aligned_cols=53  Identities=19%  Similarity=0.244  Sum_probs=39.8

Q ss_pred             ceeEEEEeCCC-CCCHHHHHHHHHHhhhc---cCCceEEEEecCCCcCchhHhhhcc
Q psy879           96 RHKIVILDEAD-SMTDGAQQALRRTMEIY---SNTTRFALACNNSEKIIEPIQSRCA  148 (317)
Q Consensus        96 ~~~vliiDE~d-~l~~~~~~~ll~~le~~---~~~~~~il~~~~~~~l~~~i~sR~~  148 (317)
                      .+.++|+||.- .|.......|++.+++.   ++.+.++++|+..+.+++-+-.+..
T Consensus       189 ~P~LLiLDEP~~GLDl~~re~ll~~l~~~~~~~~~~~ll~VtHh~eEi~~~~th~ll  245 (257)
T COG1119         189 DPELLILDEPAQGLDLIAREQLLNRLEELAASPGAPALLFVTHHAEEIPPCFTHRLL  245 (257)
T ss_pred             CCCEEEecCccccCChHHHHHHHHHHHHHhcCCCCceEEEEEcchhhcccccceEEE
Confidence            68999999985 45666777888877753   3456799999999888877655543

>cd03222 ABC_RNaseL_inhibitor The ABC ATPase RNase L inhibitor (RLI) is a key enzyme in ribosomal biogenesis, formation of translation preinitiation complexes, and assembly of HIV capsids

Probab=98.11  E-value=2.2e-05  Score=62.76  Aligned_cols=103  Identities=19%  Similarity=0.173  Sum_probs=59.0

Q ss_pred             HhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCce-----EEecCCCCcChHHHHHHHHHHHhhcccCCCCceeEE
Q psy879           26 SSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAV-----LELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIV  100 (317)
Q Consensus        26 l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~-----~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~vl  100 (317)
                      +..|.  .+.+.||+|+||||+.+.++..+........+     .........+..+ +..+.....-.     .++.++
T Consensus        22 i~~Ge--~~~l~G~nGsGKSTLl~~l~Gl~~p~~G~i~~~g~~i~~~~q~~~LSgGq-~qrv~laral~-----~~p~ll   93 (177)
T cd03222          22 VKEGE--VIGIVGPNGTGKTTAVKILAGQLIPNGDNDEWDGITPVYKPQYIDLSGGE-LQRVAIAAALL-----RNATFY   93 (177)
T ss_pred             ECCCC--EEEEECCCCChHHHHHHHHHcCCCCCCcEEEECCEEEEEEcccCCCCHHH-HHHHHHHHHHh-----cCCCEE
Confidence            34454  69999999999999999999875332221111     0011000011111 12222211111     467899


Q ss_pred             EEeCCC-CCCHHHHHHHHHHhhhccC--CceEEEEecCC
Q psy879          101 ILDEAD-SMTDGAQQALRRTMEIYSN--TTRFALACNNS  136 (317)
Q Consensus       101 iiDE~d-~l~~~~~~~ll~~le~~~~--~~~~il~~~~~  136 (317)
                      ++||.. .+.......+.+.+.+...  ...+|+++++.
T Consensus        94 lLDEPts~LD~~~~~~l~~~l~~~~~~~~~tiiivsH~~  132 (177)
T cd03222          94 LFDEPSAYLDIEQRLNAARAIRRLSEEGKKTALVVEHDL  132 (177)
T ss_pred             EEECCcccCCHHHHHHHHHHHHHHHHcCCCEEEEEECCH
Confidence            999998 4567777777777765432  24567777664

RLI's are not transport proteins, and thus cluster with a group of soluble proteins that lack the transmembrane components commonly found in other members of the family. Structurally, RLI's have an N-terminal Fe-S domain and two nucleotide-binding domains, which are arranged to form two composite active sites in their interface cleft. RLI is one of the most conserved enzymes between archaea and eukaryotes with a sequence identity more than 48%. The high degree of evolutionary conservation suggests that RLI performs a central role in archaeal and eukaryotic physiology.

>COG1117 PstB ABC-type phosphate transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=98.10  E-value=2e-05  Score=63.27  Aligned_cols=185  Identities=17%  Similarity=0.230  Sum_probs=111.2

Q ss_pred             CCCcccCCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCce---EEecCC----CCcChHHHHH
Q psy879            8 TFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAV---LELNAS----NDRGIDTVRN   80 (317)
Q Consensus         8 ~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~---~~~~~~----~~~~~~~i~~   80 (317)
                      .++=.+|..++++.+.--+.++.  ..-|.||+||||||+.+.+-+-. ....+..+   +.+...    .......+|.
T Consensus        12 ~l~~yYg~~~aL~~i~l~i~~~~--VTAlIGPSGcGKST~LR~lNRmn-dl~~~~r~~G~v~~~g~ni~~~~~d~~~lRr   88 (253)
T COG1117          12 DLNLYYGDKHALKDINLDIPKNK--VTALIGPSGCGKSTLLRCLNRMN-DLIPGARVEGEVLLDGKNIYDPKVDVVELRR   88 (253)
T ss_pred             ceeEEECchhhhccCceeccCCc--eEEEECCCCcCHHHHHHHHHhhc-ccCcCceEEEEEEECCeeccCCCCCHHHHHH
Confidence            45666788888777766565555  57899999999999999987642 22111110   111111    1345667788


Q ss_pred             HHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcCchhHhhhcceeeecCCCHHHH
Q psy879           81 KIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQL  160 (317)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~~~i~sR~~~i~f~~~~~~~~  160 (317)
                      .++..++.|.-++.+     |-|++               ...                          .+.......++
T Consensus        89 ~vGMVFQkPnPFp~S-----IydNV---------------ayG--------------------------~r~~g~~~~~l  122 (253)
T COG1117          89 RVGMVFQKPNPFPMS-----IYDNV---------------AYG--------------------------LRLHGIKDKEL  122 (253)
T ss_pred             HheeeccCCCCCCch-----HHHHH---------------HHh--------------------------HHhhccchHHH
Confidence            888777776322210     11111               000                          11112222566


Q ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHHh---cCCCHHHHHHHHHHhhhCCCcccHHHHHhhcCCCCHHHHHHHHHHHhc---
Q psy879          161 LSKVIEICEKENISHTNDGLEAIVFT---AQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEMLLNCVE---  234 (317)
Q Consensus       161 ~~~l~~~~~~~~~~i~~~~~~~l~~~---~~gd~r~~i~~l~~~~~~~~~i~~~~v~~~~~~~~~~~i~~l~~~~~~---  234 (317)
                      .+++...+++..+  =++..+.+.+.   .+|..++.+-+.+..+...+.+-.|+.-.+++...-..+.+++..+..   
T Consensus       123 deiVe~sLk~AaL--WdEVKDrL~~sa~~LSGGQQQRLcIARalAv~PeVlLmDEPtSALDPIsT~kIEeLi~eLk~~yT  200 (253)
T COG1117         123 DEIVESSLKKAAL--WDEVKDRLHKSALGLSGGQQQRLCIARALAVKPEVLLMDEPTSALDPISTLKIEELITELKKKYT  200 (253)
T ss_pred             HHHHHHHHHHhHh--HHHhHHHhhCCccCCChhHHHHHHHHHHHhcCCcEEEecCcccccCchhHHHHHHHHHHHHhccE
Confidence            6666665554332  24444444332   345678888888888888888888888888888888888888888763   


Q ss_pred             -----CCHHHHHHH
Q psy879          235 -----GNMKDSYKI  243 (317)
Q Consensus       235 -----~~~~~~~~~  243 (317)
                           ++..+|-++
T Consensus       201 IviVTHnmqQAaRv  214 (253)
T COG1117         201 IVIVTHNMQQAARV  214 (253)
T ss_pred             EEEEeCCHHHHHHH
Confidence                 355555554

>COG1124 DppF ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]

Probab=98.10  E-value=4.5e-06  Score=68.32  Aligned_cols=166  Identities=16%  Similarity=0.152  Sum_probs=97.0

Q ss_pred             HHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcC-hHHHHHHHHHHHhhcccCCCCc
Q psy879           18 TVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRG-IDTVRNKIKMFAQQKVTLPPGR   96 (317)
Q Consensus        18 ~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~-~~~i~~~~~~~~~~~~~~~~~~   96 (317)
                      +++.+.-.+..|.  .+-+.|++||||||++++++... .+..+...+......... ....+               ..
T Consensus        22 ~l~~VS~~i~~Ge--~lgivGeSGsGKSTL~r~l~Gl~-~p~~G~I~~~G~~~~~~~~~~~~~---------------~~   83 (252)
T COG1124          22 ALNNVSLEIERGE--TLGIVGESGSGKSTLARLLAGLE-KPSSGSILLDGKPLAPKKRAKAFY---------------RP   83 (252)
T ss_pred             hhcceeEEecCCC--EEEEEcCCCCCHHHHHHHHhccc-CCCCceEEECCcccCccccchhhc---------------cc
Confidence            4444444456666  79999999999999999999864 333333233222211110 00111               22


Q ss_pred             eeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcCchhHhhhcceeeecCCCHHHHHHHHHHHHHHcCCCCC
Q psy879           97 HKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHT  176 (317)
Q Consensus        97 ~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~~~i~sR~~~i~f~~~~~~~~~~~l~~~~~~~~~~i~  176 (317)
                      -..|+=|--..+++.  ....+++.+|-..                          ...+..+..  +.+.+.  .+.++
T Consensus        84 VQmVFQDp~~SLnP~--~tv~~~l~Epl~~--------------------------~~~~~~~~~--i~~~L~--~VgL~  131 (252)
T COG1124          84 VQMVFQDPYSSLNPR--RTVGRILSEPLRP--------------------------HGLSKSQQR--IAELLD--QVGLP  131 (252)
T ss_pred             eeEEecCCccccCcc--hhHHHHHhhhhcc--------------------------CCccHHHHH--HHHHHH--HcCCC
Confidence            334444444444432  1122223322111                          223332222  333333  24567


Q ss_pred             HHHHHHHHHhcCCCHHHHHHHHHHhhhCCCcccHHHHHhhcCCCCHHHHHHHHHHHh
Q psy879          177 NDGLEAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEMLLNCV  233 (317)
Q Consensus       177 ~~~~~~l~~~~~gd~r~~i~~l~~~~~~~~~i~~~~v~~~~~~~~~~~i~~l~~~~~  233 (317)
                      ++.+........|.-|+-+.+.++.+...+.+-.|+.-.+++.+....+..++..+.
T Consensus       132 ~~~l~R~P~eLSGGQ~QRiaIARAL~~~PklLIlDEptSaLD~siQa~IlnlL~~l~  188 (252)
T COG1124         132 PSFLDRRPHELSGGQRQRIAIARALIPEPKLLILDEPTSALDVSVQAQILNLLLELK  188 (252)
T ss_pred             HHHHhcCchhcChhHHHHHHHHHHhccCCCEEEecCchhhhcHHHHHHHHHHHHHHH
Confidence            888888887777889999999999888888888888877788777777777666654

>cd00561 CobA_CobO_BtuR ATP:corrinoid adenosyltransferase BtuR/CobO/CobP

Probab=98.09  E-value=2.5e-05  Score=60.77  Aligned_cols=103  Identities=21%  Similarity=0.276  Sum_probs=61.3

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCC----------------------------CcChHHHHHHHHHH
Q psy879           34 IIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASN----------------------------DRGIDTVRNKIKMF   85 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~----------------------------~~~~~~i~~~~~~~   85 (317)
                      +.+|+++|.||||+|..++-...+...+..++.+-...                            ..........-..+
T Consensus         5 i~vy~g~G~Gkt~~a~g~~~ra~~~g~~v~~vQFlKg~~~~gE~~~l~~l~~v~~~~~g~~~~~~~~~~~~~~~~a~~~~   84 (159)
T cd00561           5 IQVYTGNGKGKTTAALGLALRALGHGYRVGVVQFLKGGWKYGELKALERLPNIEIHRMGRGFFWTTENDEEDIAAAAEGW   84 (159)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEEEeCCCCccCHHHHHHhCCCcEEEECCCCCccCCCChHHHHHHHHHHH
Confidence            67888889999999999997765544333222111110                            00111111111111


Q ss_pred             HhhcccCCCCceeEEEEeCCCCCCHH---HHHHHHHHhhhccCCceEEEEecCC
Q psy879           86 AQQKVTLPPGRHKIVILDEADSMTDG---AQQALRRTMEIYSNTTRFALACNNS  136 (317)
Q Consensus        86 ~~~~~~~~~~~~~vliiDE~d~l~~~---~~~~ll~~le~~~~~~~~il~~~~~  136 (317)
                      .........+.+.+||+||+....+-   ..+.+++++++.|+.+-+|+|+.+.
T Consensus        85 ~~a~~~~~~~~~dLlVLDEi~~a~~~gli~~~~v~~ll~~rp~~~evIlTGr~~  138 (159)
T cd00561          85 AFAKEAIASGEYDLVILDEINYALGYGLLDVEEVVDLLKAKPEDLELVLTGRNA  138 (159)
T ss_pred             HHHHHHHhcCCCCEEEEechHhHhhCCCCCHHHHHHHHHcCCCCCEEEEECCCC
Confidence            11111112367899999999876332   3567888999999999999999774

This family consists of the BtuR, CobO, CobP proteins all of which are Cob(I)alamin (vitamin B12) adenosyltransferase, which is involved in cobalamin (vitamin B12) biosynthesis. This enzyme is a homodimer, which catalyzes the adenosylation reaction: ATP + cob(I)alamin + H2O <= phosphate + diphosphate + adenosylcobalamin.

>cd03221 ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth

Probab=98.09  E-value=3.6e-05  Score=59.47  Aligned_cols=99  Identities=16%  Similarity=0.208  Sum_probs=59.6

Q ss_pred             HhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCC------CCcChHHHHHHHHHHHhhcccCCCCceeE
Q psy879           26 SSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNAS------NDRGIDTVRNKIKMFAQQKVTLPPGRHKI   99 (317)
Q Consensus        26 l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~------~~~~~~~i~~~~~~~~~~~~~~~~~~~~v   99 (317)
                      +..|.  .+.+.||+|+||||+++.++..+.... +...  ++..      ...+..+.+ .+.....-.     .++.+
T Consensus        23 ~~~Ge--~~~i~G~nGsGKStLl~~l~G~~~~~~-G~i~--~~~~~~i~~~~~lS~G~~~-rv~laral~-----~~p~i   91 (144)
T cd03221          23 INPGD--RIGLVGRNGAGKSTLLKLIAGELEPDE-GIVT--WGSTVKIGYFEQLSGGEKM-RLALAKLLL-----ENPNL   91 (144)
T ss_pred             ECCCC--EEEEECCCCCCHHHHHHHHcCCCCCCc-eEEE--ECCeEEEEEEccCCHHHHH-HHHHHHHHh-----cCCCE
Confidence            34455  699999999999999999998753222 2111  1110      001222222 122111111     46789


Q ss_pred             EEEeCCC-CCCHHHHHHHHHHhhhccCCceEEEEecCCC
Q psy879          100 VILDEAD-SMTDGAQQALRRTMEIYSNTTRFALACNNSE  137 (317)
Q Consensus       100 liiDE~d-~l~~~~~~~ll~~le~~~~~~~~il~~~~~~  137 (317)
                      +++||.. .+.......+.+.+.+..  ..+++++++.+
T Consensus        92 lllDEP~~~LD~~~~~~l~~~l~~~~--~til~~th~~~  128 (144)
T cd03221          92 LLLDEPTNHLDLESIEALEEALKEYP--GTVILVSHDRY  128 (144)
T ss_pred             EEEeCCccCCCHHHHHHHHHHHHHcC--CEEEEEECCHH
Confidence            9999997 567777888888887652  45666776643

EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated release of the deacylated tRNA from the E site. The reaction requires ATP hydrolysis. EF-3 contains two ATP nucleotide binding sequence (NBS) motifs. NBSI is sufficient for the intrinsic ATPase activity. NBSII is essential for the ribosome-stimulated functions.

>KOG0058|consensus

Probab=98.07  E-value=6e-06  Score=77.33  Aligned_cols=40  Identities=28%  Similarity=0.476  Sum_probs=31.0

Q ss_pred             HHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCC
Q psy879           18 TVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSF   60 (317)
Q Consensus        18 ~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~   60 (317)
                      +.+.+.-.++.|+  .+-+.||+|+||||++..+-+. +.+..
T Consensus       483 Vlk~lsfti~pGe--~vALVGPSGsGKSTiasLL~rf-Y~Pts  522 (716)
T KOG0058|consen  483 VLKNLSFTIRPGE--VVALVGPSGSGKSTIASLLLRF-YDPTS  522 (716)
T ss_pred             hhcCceeeeCCCC--EEEEECCCCCCHHHHHHHHHHh-cCCCC
Confidence            5555555566666  7999999999999999999986 44443

>cd00267 ABC_ATPase ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules

Probab=98.07  E-value=3.5e-05  Score=60.45  Aligned_cols=96  Identities=14%  Similarity=0.266  Sum_probs=57.1

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCC--C---------------cChHHHHHHHHHHHhhcccCCCC
Q psy879           33 NIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASN--D---------------RGIDTVRNKIKMFAQQKVTLPPG   95 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~--~---------------~~~~~i~~~~~~~~~~~~~~~~~   95 (317)
                      .+.|.||+|+||||+.+.++..+... .+.  +.++...  .               .+..+.+ .+.......     .
T Consensus        27 ~~~i~G~nGsGKStll~~l~g~~~~~-~G~--i~~~~~~~~~~~~~~~~~~i~~~~qlS~G~~~-r~~l~~~l~-----~   97 (157)
T cd00267          27 IVALVGPNGSGKSTLLRAIAGLLKPT-SGE--ILIDGKDIAKLPLEELRRRIGYVPQLSGGQRQ-RVALARALL-----L   97 (157)
T ss_pred             EEEEECCCCCCHHHHHHHHhCCCCCC-ccE--EEECCEEcccCCHHHHHhceEEEeeCCHHHHH-HHHHHHHHh-----c
Confidence            69999999999999999999875322 111  1222110  0               0011111 111111111     3


Q ss_pred             ceeEEEEeCCC-CCCHHHHHHHHHHhhhccC-CceEEEEecCCC
Q psy879           96 RHKIVILDEAD-SMTDGAQQALRRTMEIYSN-TTRFALACNNSE  137 (317)
Q Consensus        96 ~~~vliiDE~d-~l~~~~~~~ll~~le~~~~-~~~~il~~~~~~  137 (317)
                      .++++++||.. .+.......+.+.+.+... ...+++++++..
T Consensus        98 ~~~i~ilDEp~~~lD~~~~~~l~~~l~~~~~~~~tii~~sh~~~  141 (157)
T cd00267          98 NPDLLLLDEPTSGLDPASRERLLELLRELAEEGRTVIIVTHDPE  141 (157)
T ss_pred             CCCEEEEeCCCcCCCHHHHHHHHHHHHHHHHCCCEEEEEeCCHH
Confidence            57899999998 5667778888888776533 355677776643

The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>PF04665 Pox_A32: Poxvirus A32 protein; InterPro: IPR006758 This entry contains uncharacterised proteins belonging to the B354L family which include the pox virus A32 protein

Probab=98.07  E-value=0.00056  Score=56.98  Aligned_cols=133  Identities=17%  Similarity=0.167  Sum_probs=76.0

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCC--------------CcChHHHH-------HHHHHHHhhccc
Q psy879           33 NIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASN--------------DRGIDTVR-------NKIKMFAQQKVT   91 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~--------------~~~~~~i~-------~~~~~~~~~~~~   91 (317)
                      .+++.|++|||||++++.+...+.. .....++......              ....+.+.       +.+.........
T Consensus        15 r~viIG~sGSGKT~li~~lL~~~~~-~f~~I~l~t~~~n~~~~~~i~p~~i~~~~~~e~le~~l~~~k~~I~k~~~k~~~   93 (241)
T PF04665_consen   15 RMVIIGKSGSGKTTLIKSLLYYLRH-KFDHIFLITPEYNNEYYKYIWPDHIFKVFDKEELEYILIRQKEKIEKYIKKSPQ   93 (241)
T ss_pred             eEEEECCCCCCHHHHHHHHHHhhcc-cCCEEEEEecCCchhhhhhcchhhccccccHHHHHHHHHHHHHHHHHHhhhhcc
Confidence            4899999999999999999887532 2221111111000              00111111       111122221111


Q ss_pred             CCCCceeEEEEeCCCCCCHHHHHHHHHHhhh-ccCCceEEEEecCCCcCchhHhhhcceeeecCCCHHHHHHHHHHH
Q psy879           92 LPPGRHKIVILDEADSMTDGAQQALRRTMEI-YSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEI  167 (317)
Q Consensus        92 ~~~~~~~vliiDE~d~l~~~~~~~ll~~le~-~~~~~~~il~~~~~~~l~~~i~sR~~~i~f~~~~~~~~~~~l~~~  167 (317)
                      .....+.++|+|++..-. -....+..++.. .+-++.+|+++.....+++.+++-+..+-+-+.+..++..++...
T Consensus        94 ~k~~~~~LiIlDD~~~~~-~k~~~l~~~~~~gRH~~is~i~l~Q~~~~lp~~iR~n~~y~i~~~~s~~dl~~i~~~~  169 (241)
T PF04665_consen   94 KKNNPRFLIILDDLGDKK-LKSKILRQFFNNGRHYNISIIFLSQSYFHLPPNIRSNIDYFIIFNNSKRDLENIYRNM  169 (241)
T ss_pred             cCCCCCeEEEEeCCCCch-hhhHHHHHHHhcccccceEEEEEeeecccCCHHHhhcceEEEEecCcHHHHHHHHHhc
Confidence            112346799999986411 112335555542 345677899999999999999988888554457777776665554

This is thought to be an ATPase involved in viral DNA packaging [].

>cd03229 ABC_Class3 This class is comprised of all BPD (Binding Protein Dependent) systems that are largely represented in archaea and eubacteria and are primarily involved in scavenging solutes from the environment

Probab=98.06  E-value=8.5e-06  Score=65.41  Aligned_cols=43  Identities=14%  Similarity=0.249  Sum_probs=31.4

Q ss_pred             CceeEEEEeCCCC-CCHHHHHHHHHHhhhccC--CceEEEEecCCC
Q psy879           95 GRHKIVILDEADS-MTDGAQQALRRTMEIYSN--TTRFALACNNSE  137 (317)
Q Consensus        95 ~~~~vliiDE~d~-l~~~~~~~ll~~le~~~~--~~~~il~~~~~~  137 (317)
                      ..++++++||... +....+..+.+.+.+...  ...+|+++++..
T Consensus       117 ~~p~llilDEP~~~LD~~~~~~l~~~l~~~~~~~~~tiii~sH~~~  162 (178)
T cd03229         117 MDPDVLLLDEPTSALDPITRREVRALLKSLQAQLGITVVLVTHDLD  162 (178)
T ss_pred             CCCCEEEEeCCcccCCHHHHHHHHHHHHHHHHhcCCEEEEEeCCHH
Confidence            4689999999974 567778888888876543  356777777643

ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>PRK11176 lipid transporter ATP-binding/permease protein; Provisional

Probab=98.05  E-value=1.2e-05  Score=76.81  Aligned_cols=41  Identities=20%  Similarity=0.322  Sum_probs=31.3

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhccCCceEEEEecCC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYSNTTRFALACNNS  136 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~~~~~~il~~~~~  136 (317)
                      +++++++||+.. +.++....+.+.+.+...+..+|++|++.
T Consensus       498 ~~~ililDEptsaLD~~t~~~i~~~l~~~~~~~tvI~VtHr~  539 (582)
T PRK11176        498 DSPILILDEATSALDTESERAIQAALDELQKNRTSLVIAHRL  539 (582)
T ss_pred             CCCEEEEECccccCCHHHHHHHHHHHHHHhCCCEEEEEecch
Confidence            578999999975 56667777878777765566678888775

>PRK15455 PrkA family serine protein kinase; Provisional

Probab=98.04  E-value=7.9e-06  Score=75.41  Aligned_cols=52  Identities=21%  Similarity=0.363  Sum_probs=41.8

Q ss_pred             CCCCCCcccCCHHHHHHHHHHH----hcC--CCceEEEECCCCCCHHHHHHHHHHHHc
Q psy879            5 RPQTFSDIVGNEDTVERLKVFS----SSG--NVPNIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus         5 ~P~~~~~~~g~~~~~~~l~~~l----~~~--~~~~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      +..-|++++|.+++++.+..++    .+.  +-+.++|.||||+|||++++.+++.+.
T Consensus        71 ry~fF~d~yGlee~ieriv~~l~~Aa~gl~~~~~IL~LvGPpG~GKSsLa~~la~~le  128 (644)
T PRK15455         71 RYPAFEEFYGMEEAIEQIVSYFRHAAQGLEEKKQILYLLGPVGGGKSSLAERLKSLME  128 (644)
T ss_pred             cccchhcccCcHHHHHHHHHHHHHHHHhcCCCCceEEEecCCCCCchHHHHHHHHHHH
Confidence            3456899999999999877766    332  223599999999999999999999874

>PRK13695 putative NTPase; Provisional

Probab=98.04  E-value=5e-05  Score=60.72  Aligned_cols=71  Identities=13%  Similarity=0.225  Sum_probs=47.1

Q ss_pred             CceeEEEEeCCCCC---CHHHHHHHHHHhhhccCCceEEEEecCCC--cCchhHhhhcc--eeeecCCCHHHHHHHHHHH
Q psy879           95 GRHKIVILDEADSM---TDGAQQALRRTMEIYSNTTRFALACNNSE--KIIEPIQSRCA--MLRYNKLTDAQLLSKVIEI  167 (317)
Q Consensus        95 ~~~~vliiDE~d~l---~~~~~~~ll~~le~~~~~~~~il~~~~~~--~l~~~i~sR~~--~i~f~~~~~~~~~~~l~~~  167 (317)
                      ..+.++++||+..+   .....+.+...++   ....+|++++...  .+.+.+.+|..  ++++.+-+.+++...+.++
T Consensus        95 ~~~~~lllDE~~~~e~~~~~~~~~l~~~~~---~~~~~i~v~h~~~~~~~~~~i~~~~~~~i~~~~~~~r~~~~~~~~~~  171 (174)
T PRK13695         95 EEADVIIIDEIGKMELKSPKFVKAVEEVLD---SEKPVIATLHRRSVHPFVQEIKSRPGGRVYELTPENRDSLPFEILNR  171 (174)
T ss_pred             CCCCEEEEECCCcchhhhHHHHHHHHHHHh---CCCeEEEEECchhhHHHHHHHhccCCcEEEEEcchhhhhHHHHHHHH
Confidence            46789999997654   3344666666664   2356777777642  45667766644  4788787777777766664


Q ss_pred             H
Q psy879          168 C  168 (317)
Q Consensus       168 ~  168 (317)
                      .
T Consensus       172 ~  172 (174)
T PRK13695        172 L  172 (174)
T ss_pred             H
Confidence            4

>COG1120 FepC ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]

Probab=98.04  E-value=6.3e-07  Score=74.97  Aligned_cols=171  Identities=16%  Similarity=0.153  Sum_probs=91.5

Q ss_pred             CHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHHHHHHHhhcccCCC
Q psy879           15 NEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPP   94 (317)
Q Consensus        15 ~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~   94 (317)
                      ...+++.+.-.+.+|.  ...+.||+||||||+.+++++.+. +..+...++..+.......++...+....|.+..   
T Consensus        14 ~~~il~~ls~~i~~G~--i~~iiGpNG~GKSTLLk~l~g~l~-p~~G~V~l~g~~i~~~~~kelAk~ia~vpQ~~~~---   87 (258)
T COG1120          14 GKPILDDLSFSIPKGE--ITGILGPNGSGKSTLLKCLAGLLK-PKSGEVLLDGKDIASLSPKELAKKLAYVPQSPSA---   87 (258)
T ss_pred             CeeEEecceEEecCCc--EEEEECCCCCCHHHHHHHHhccCC-CCCCEEEECCCchhhcCHHHHhhhEEEeccCCCC---
Confidence            3344445555556666  689999999999999999999764 3333333333333333444454444444443211   


Q ss_pred             CceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcCchhHhhhcce-eeecCCCHHHHHHHHHHHHHHcCC
Q psy879           95 GRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAM-LRYNKLTDAQLLSKVIEICEKENI  173 (317)
Q Consensus        95 ~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~~~i~sR~~~-i~f~~~~~~~~~~~l~~~~~~~~~  173 (317)
                       ...+-+.|                         +|.            ..|... =.|..+++++.... ...++.-++
T Consensus        88 -~~~~tV~d-------------------------~V~------------~GR~p~~~~~~~~~~~D~~~v-~~aL~~~~~  128 (258)
T COG1120          88 -PFGLTVYE-------------------------LVL------------LGRYPHLGLFGRPSKEDEEIV-EEALELLGL  128 (258)
T ss_pred             -CCCcEEee-------------------------hHh------------hcCCcccccccCCCHhHHHHH-HHHHHHhCc
Confidence             11111110                         011            112111 12334555554422 222222232


Q ss_pred             CCCHHHHHHHHHhcCCCHHHHHHHHHHhhhCCCcccHHHHHhhcCCCCHHHHHHHHHHHh
Q psy879          174 SHTNDGLEAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEMLLNCV  233 (317)
Q Consensus       174 ~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~~~~~i~~~~v~~~~~~~~~~~i~~l~~~~~  233 (317)
                        ..-+-..+.+.|+ .-|+..-+..+.+.+.+.+-.|+.-..++..+...+.+++..+.
T Consensus       129 --~~la~r~~~~LSG-GerQrv~iArALaQ~~~iLLLDEPTs~LDi~~Q~evl~ll~~l~  185 (258)
T COG1120         129 --EHLADRPVDELSG-GERQRVLIARALAQETPILLLDEPTSHLDIAHQIEVLELLRDLN  185 (258)
T ss_pred             --HHHhcCcccccCh-hHHHHHHHHHHHhcCCCEEEeCCCccccCHHHHHHHHHHHHHHH
Confidence              2222223334444 57777777788888877777777777777777777777777766

>KOG3347|consensus

Probab=98.02  E-value=1e-05  Score=60.97  Aligned_cols=26  Identities=42%  Similarity=0.676  Sum_probs=23.5

Q ss_pred             CCceEEEECCCCCCHHHHHHHHHHHH
Q psy879           30 NVPNIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        30 ~~~~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      ..|++|++|.||+||||++..+|...
T Consensus         6 ~~PNILvtGTPG~GKstl~~~lae~~   31 (176)
T KOG3347|consen    6 ERPNILVTGTPGTGKSTLAERLAEKT   31 (176)
T ss_pred             cCCCEEEeCCCCCCchhHHHHHHHHh
Confidence            45789999999999999999999774

>COG4608 AppF ABC-type oligopeptide transport system, ATPase component [Amino acid transport and metabolism]

Probab=98.01  E-value=2.7e-05  Score=65.09  Aligned_cols=77  Identities=16%  Similarity=0.107  Sum_probs=58.1

Q ss_pred             HHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhhCCCcccHHHHHhhcCCCCHHHHHHHHHHHhcC
Q psy879          157 DAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEMLLNCVEG  235 (317)
Q Consensus       157 ~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~~~~~i~~~~v~~~~~~~~~~~i~~l~~~~~~~  235 (317)
                      .++..+.+.+.+..-|  ++++.+.......+|..|+-+.+.++.+...+.+..|+...+++.+....+..++..+...
T Consensus        82 ~~~~~~~v~elL~~Vg--l~~~~~~ryPhelSGGQrQRi~IARALal~P~liV~DEpvSaLDvSiqaqIlnLL~dlq~~  158 (268)
T COG4608          82 KEERRERVLELLEKVG--LPEEFLYRYPHELSGGQRQRIGIARALALNPKLIVADEPVSALDVSVQAQILNLLKDLQEE  158 (268)
T ss_pred             hhHHHHHHHHHHHHhC--CCHHHhhcCCcccCchhhhhHHHHHHHhhCCcEEEecCchhhcchhHHHHHHHHHHHHHHH
Confidence            3444444555554445  5677777777777888999999999998888888888888888888888888887776544

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=98.01  E-value=7.6e-05  Score=66.85  Aligned_cols=102  Identities=19%  Similarity=0.247  Sum_probs=54.4

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHcC----CCCCCceEEecCCCCcChHHHHHHHHHHHhhccc------------CCCCc
Q psy879           33 NIIISGPPGVGKTTTILCLARILLG----PSFKDAVLELNASNDRGIDTVRNKIKMFAQQKVT------------LPPGR   96 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~~----~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~------------~~~~~   96 (317)
                      .++|+||+|+||||++..+|..+..    ......++..++.......+++...... ..++.            ....+
T Consensus       176 vi~lvGptGvGKTTT~aKLA~~~~~~~~~~g~~V~lit~Dt~R~aa~eQL~~~a~~l-gvpv~~~~~~~~l~~~L~~~~~  254 (388)
T PRK12723        176 VFILVGPTGVGKTTTIAKLAAIYGINSDDKSLNIKIITIDNYRIGAKKQIQTYGDIM-GIPVKAIESFKDLKEEITQSKD  254 (388)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHhhhccCCCeEEEEeccCccHHHHHHHHHHhhcC-CcceEeeCcHHHHHHHHHHhCC
Confidence            4999999999999999999987642    1222333333332111111111100000 00000            00146


Q ss_pred             eeEEEEeCCCCCCHHH--HHHHHHHhhhcc--CCceEEEEecC
Q psy879           97 HKIVILDEADSMTDGA--QQALRRTMEIYS--NTTRFALACNN  135 (317)
Q Consensus        97 ~~vliiDE~d~l~~~~--~~~ll~~le~~~--~~~~~il~~~~  135 (317)
                      +.+|+||.+..+..+.  ...+.++++...  ..+.+|+.++.
T Consensus       255 ~DlVLIDTaGr~~~~~~~l~el~~~l~~~~~~~e~~LVlsat~  297 (388)
T PRK12723        255 FDLVLVDTIGKSPKDFMKLAEMKELLNACGRDAEFHLAVSSTT  297 (388)
T ss_pred             CCEEEEcCCCCCccCHHHHHHHHHHHHhcCCCCeEEEEEcCCC
Confidence            7899999999887543  345666666432  24556665544

>KOG0479|consensus

Probab=98.01  E-value=5.9e-05  Score=68.91  Aligned_cols=130  Identities=19%  Similarity=0.257  Sum_probs=84.1

Q ss_pred             cccCCHHHHHHHHHHHhc--------CCC----ceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcCh---
Q psy879           11 DIVGNEDTVERLKVFSSS--------GNV----PNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGI---   75 (317)
Q Consensus        11 ~~~g~~~~~~~l~~~l~~--------~~~----~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~---   75 (317)
                      .|+|++.+++.+.-.+-+        |.-    -|+|+.|.|.+.|+.+.+.+.+..-  .  ..-...-+++..+.   
T Consensus       302 SI~GH~~vKkAillLLlGGvEk~L~NGshlRGDINiLlvGDPSvAKSQLLRyVLntAp--l--AI~TTGRGSSGVGLTAA  377 (818)
T KOG0479|consen  302 SIYGHDYVKKAILLLLLGGVEKNLENGSHLRGDINILLVGDPSVAKSQLLRYVLNTAP--L--AIATTGRGSSGVGLTAA  377 (818)
T ss_pred             ccccHHHHHHHHHHHHhccceeccCCCceeccceeEEEecCchHHHHHHHHHHHhccc--c--cccccCCCCCCccceeE
Confidence            478999999987665543        321    1599999999999999999987531  0  00000111111110   


Q ss_pred             -----HHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhc-------------cCCceEEEEecCCC
Q psy879           76 -----DTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIY-------------SNTTRFALACNNSE  137 (317)
Q Consensus        76 -----~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~-------------~~~~~~il~~~~~~  137 (317)
                           +.=...++.   .+..  -+++.||+|||+|+|+.-..-++...||..             ...+.++.++|+..
T Consensus       378 VTtD~eTGERRLEA---GAMV--LADRGVVCIDEFDKMsDiDRvAIHEVMEQqtVTIaKAGIHasLNARCSVlAAANPvy  452 (818)
T KOG0479|consen  378 VTTDQETGERRLEA---GAMV--LADRGVVCIDEFDKMSDIDRVAIHEVMEQQTVTIAKAGIHASLNARCSVLAAANPVY  452 (818)
T ss_pred             Eeeccccchhhhhc---CceE--EccCceEEehhcccccchhHHHHHHHHhcceEEeEeccchhhhccceeeeeecCccc
Confidence                 000011111   1111  157899999999999999999999999943             34566788888642


Q ss_pred             -------------cCchhHhhhcce
Q psy879          138 -------------KIIEPIQSRCAM  149 (317)
Q Consensus       138 -------------~l~~~i~sR~~~  149 (317)
                                   .++..+.|||..
T Consensus       453 G~Yd~~k~P~eNIgLpDSLLSRFDL  477 (818)
T KOG0479|consen  453 GQYDQSKTPMENIGLPDSLLSRFDL  477 (818)
T ss_pred             cccCCCCChhhccCCcHHHHhhhcE
Confidence                         478999999987

>COG1116 TauB ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=98.01  E-value=1.1e-05  Score=66.49  Aligned_cols=97  Identities=13%  Similarity=0.113  Sum_probs=63.6

Q ss_pred             CCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhhCCCcccHHHHHhhcCCCCHHHHHHHHHHHh-
Q psy879          155 LTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEMLLNCV-  233 (317)
Q Consensus       155 ~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~~~~~i~~~~v~~~~~~~~~~~i~~l~~~~~-  233 (317)
                      .+.++...+..+.+..-|+   .+..+....+-+|.+|+-..+.++.+...+.+-.|+...+++......+.+.+..+. 
T Consensus       102 ~~~~e~~~~a~~~L~~VgL---~~~~~~~P~qLSGGMrQRVaiARAL~~~P~lLLlDEPFgALDalTR~~lq~~l~~lw~  178 (248)
T COG1116         102 KSKAEARERAKELLELVGL---AGFEDKYPHQLSGGMRQRVAIARALATRPKLLLLDEPFGALDALTREELQDELLRLWE  178 (248)
T ss_pred             cchHhHHHHHHHHHHHcCC---cchhhcCccccChHHHHHHHHHHHHhcCCCEEEEcCCcchhhHHHHHHHHHHHHHHHH
Confidence            4555555666666665555   344556666777789999999999988888777777777666555444444444433 


Q ss_pred             ---------cCCHHHHHHHHHHHHHcCCCH
Q psy879          234 ---------EGNMKDSYKIIHHLYKLGYAP  254 (317)
Q Consensus       234 ---------~~~~~~~~~~~~~l~~~~~~~  254 (317)
                               .+|.++|+.+-+..+.....|
T Consensus       179 ~~~~TvllVTHdi~EAv~LsdRivvl~~~P  208 (248)
T COG1116         179 ETRKTVLLVTHDVDEAVYLADRVVVLSNRP  208 (248)
T ss_pred             hhCCEEEEEeCCHHHHHhhhCEEEEecCCC
Confidence                     457888888776664333333

>cd03230 ABC_DR_subfamily_A This family of ATP-binding proteins belongs to a multisubunit transporter involved in drug resistance (BcrA and DrrA), nodulation, lipid transport, and lantibiotic immunity

Probab=98.01  E-value=9.5e-06  Score=64.82  Aligned_cols=43  Identities=16%  Similarity=0.248  Sum_probs=31.2

Q ss_pred             CceeEEEEeCCCC-CCHHHHHHHHHHhhhccC-CceEEEEecCCC
Q psy879           95 GRHKIVILDEADS-MTDGAQQALRRTMEIYSN-TTRFALACNNSE  137 (317)
Q Consensus        95 ~~~~vliiDE~d~-l~~~~~~~ll~~le~~~~-~~~~il~~~~~~  137 (317)
                      .+++++++||... +.......+.+.+.+... ...+|+++++..
T Consensus       112 ~~p~illlDEPt~~LD~~~~~~l~~~l~~~~~~g~tiii~th~~~  156 (173)
T cd03230         112 HDPELLILDEPTSGLDPESRREFWELLRELKKEGKTILLSSHILE  156 (173)
T ss_pred             cCCCEEEEeCCccCCCHHHHHHHHHHHHHHHHCCCEEEEECCCHH
Confidence            4789999999985 566778888888876543 355777776643

In bacteria and archaea, these transporters usually include an ATP-binding protein and one or two integral membrane proteins. Eukaryote systems of the ABCA subfamily display ABC domains that are quite similar to this family. The ATP-binding domain shows the highest similarity between all members of the ABC transporter family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>PRK13657 cyclic beta-1,2-glucan ABC transporter; Provisional

Probab=98.00  E-value=1.4e-05  Score=76.59  Aligned_cols=41  Identities=17%  Similarity=0.230  Sum_probs=31.1

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhccCCceEEEEecCC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYSNTTRFALACNNS  136 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~~~~~~il~~~~~  136 (317)
                      +++++++||+.. +..+....+.+.+.....+..+|++|+++
T Consensus       489 ~~~iliLDEpts~LD~~t~~~i~~~l~~~~~~~tvIiitHr~  530 (588)
T PRK13657        489 DPPILILDEATSALDVETEAKVKAALDELMKGRTTFIIAHRL  530 (588)
T ss_pred             CCCEEEEeCCccCCCHHHHHHHHHHHHHHhcCCEEEEEEecH
Confidence            689999999985 56667777888777665556677778775

>COG4172 ABC-type uncharacterized transport system, duplicated ATPase component [General function prediction only]

Probab=98.00  E-value=9.3e-06  Score=71.15  Aligned_cols=166  Identities=17%  Similarity=0.143  Sum_probs=113.9

Q ss_pred             HhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHHHHHHHhhcccCCCCceeEEEEeCC
Q psy879           26 SSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEA  105 (317)
Q Consensus        26 l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~  105 (317)
                      ++.|.  .+-+.|++|+||||+.+++.+.+...  +...+........+..+.+-            ...+-.+||=|-.
T Consensus       310 L~~gq--TlGlVGESGSGKsTlG~allrL~~s~--G~I~F~G~~i~~~~~~~mrp------------lR~~mQvVFQDPy  373 (534)
T COG4172         310 LRRGQ--TLGLVGESGSGKSTLGLALLRLIPSQ--GEIRFDGQDIDGLSRKEMRP------------LRRRMQVVFQDPY  373 (534)
T ss_pred             ecCCC--eEEEEecCCCCcchHHHHHHhhcCcC--ceEEECCccccccChhhhhh------------hhhhceEEEeCCC
Confidence            44454  59999999999999999999986432  22222222221122222111            1134568888877


Q ss_pred             CCCCHHHHHHHHHHhhhccCCceEEEEecCCCcCchhHhhhcceeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHH
Q psy879          106 DSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVF  185 (317)
Q Consensus       106 d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~~~i~sR~~~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~  185 (317)
                      ..+++..  .+-+++++                        ...++=+.++..|..+.+...+..-|  +|+.....+..
T Consensus       374 gSLsPRm--tV~qII~E------------------------GL~vh~~~ls~~eR~~rv~~aL~EVG--LDp~~r~RYPh  425 (534)
T COG4172         374 GSLSPRM--TVGQIIEE------------------------GLRVHEPKLSAAERDQRVIEALEEVG--LDPATRNRYPH  425 (534)
T ss_pred             CCCCccc--CHHHHhhh------------------------hhhhcCCCCCHHHHHHHHHHHHHHcC--CChhHhhcCCc
Confidence            7777642  12223332                        12234457888888888887776544  67999988888


Q ss_pred             hcCCCHHHHHHHHHHhhhCCCcccHHHHHhhcCCCCHHHHHHHHHHHhcC
Q psy879          186 TAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEMLLNCVEG  235 (317)
Q Consensus       186 ~~~gd~r~~i~~l~~~~~~~~~i~~~~v~~~~~~~~~~~i~~l~~~~~~~  235 (317)
                      ..+|.-|+-+.+.++.....+.|..|+...+++.+....+.++++.+..+
T Consensus       426 EFSGGQRQRIAIARAliLkP~~i~LDEPTSALD~SVQaQvv~LLr~LQ~k  475 (534)
T COG4172         426 EFSGGQRQRIAIARALILKPELILLDEPTSALDRSVQAQVLDLLRDLQQK  475 (534)
T ss_pred             ccCcchhhHHHHHHHHhcCCcEEEecCCchHhhHHHHHHHHHHHHHHHHH
Confidence            88889999999999999998989888888888888888888888887644

>PF03969 AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654 ATPase family gene 1 (AFG1) ATPase is a 377 amino acid putative protein with an ATPase motif typical of the protein family including SEC18p PAS1, CDC48-VCP and TBP

Probab=98.00  E-value=2.9e-05  Score=69.02  Aligned_cols=115  Identities=17%  Similarity=0.203  Sum_probs=68.9

Q ss_pred             ceEEEECCCCCCHHHHHHHHHHHHcCCC-CCCceEEe--------cCCCCcChHHHHHHHHHHHhhcccCCCCceeEEEE
Q psy879           32 PNIIISGPPGVGKTTTILCLARILLGPS-FKDAVLEL--------NASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVIL  102 (317)
Q Consensus        32 ~~~ll~G~~G~GKt~la~~la~~l~~~~-~~~~~~~~--------~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~vlii  102 (317)
                      ..++|||++|+|||.+.-.+...+-... ....+...        .... ...+-+......+.        .+.+++++
T Consensus        63 ~GlYl~G~vG~GKT~Lmd~f~~~lp~~~k~R~HFh~Fm~~vh~~l~~~~-~~~~~l~~va~~l~--------~~~~lLcf  133 (362)
T PF03969_consen   63 KGLYLWGPVGRGKTMLMDLFYDSLPIKRKRRVHFHEFMLDVHSRLHQLR-GQDDPLPQVADELA--------KESRLLCF  133 (362)
T ss_pred             ceEEEECCCCCchhHHHHHHHHhCCccccccccccHHHHHHHHHHHHHh-CCCccHHHHHHHHH--------hcCCEEEE
Confidence            3499999999999999999999864311 11111000        0000 00111111111211        45679999


Q ss_pred             eCCCCCCHHHHHHHHHHhhhc-cCCceEEEEecCCC--------------cCchhHhhhcceeeecCC
Q psy879          103 DEADSMTDGAQQALRRTMEIY-SNTTRFALACNNSE--------------KIIEPIQSRCAMLRYNKL  155 (317)
Q Consensus       103 DE~d~l~~~~~~~ll~~le~~-~~~~~~il~~~~~~--------------~l~~~i~sR~~~i~f~~~  155 (317)
                      ||++--.....-.|-++++.. ...+++|.|+|.+.              ...+.|.++|.++++...
T Consensus       134 DEF~V~DiaDAmil~rLf~~l~~~gvvlVaTSN~~P~~Ly~~gl~r~~Flp~I~~l~~~~~vv~ld~~  201 (362)
T PF03969_consen  134 DEFQVTDIADAMILKRLFEALFKRGVVLVATSNRPPEDLYKNGLQRERFLPFIDLLKRRCDVVELDGG  201 (362)
T ss_pred             eeeeccchhHHHHHHHHHHHHHHCCCEEEecCCCChHHHcCCcccHHHHHHHHHHHHhceEEEEecCC
Confidence            999887666555555555432 46677888888652              134677999999888776

AFG1 also has substantial homology to these proteins outside the ATPase domain []. This family of proteins contains a P-loop motif.; GO: 0005524 ATP binding

>PTZ00202 tuzin; Provisional

Probab=97.99  E-value=0.00041  Score=62.26  Aligned_cols=51  Identities=18%  Similarity=0.269  Sum_probs=42.6

Q ss_pred             CCCCCCcccCCHHHHHHHHHHHhcCCC--c-eEEEECCCCCCHHHHHHHHHHHH
Q psy879            5 RPQTFSDIVGNEDTVERLKVFSSSGNV--P-NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus         5 ~P~~~~~~~g~~~~~~~l~~~l~~~~~--~-~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      -|....+++|++...+.|...+.+...  | ...|+||+|+|||++++.+...+
T Consensus       257 lPa~~~~FVGReaEla~Lr~VL~~~d~~~privvLtG~~G~GKTTLlR~~~~~l  310 (550)
T PTZ00202        257 APAVIRQFVSREAEESWVRQVLRRLDTAHPRIVVFTGFRGCGKSSLCRSAVRKE  310 (550)
T ss_pred             CCCCccCCCCcHHHHHHHHHHHhccCCCCceEEEEECCCCCCHHHHHHHHHhcC
Confidence            355678999999999999999875433  3 37999999999999999999875

>cd03223 ABCD_peroxisomal_ALDP Peroxisomal ATP-binding cassette transporter (Pat) is involved in the import of very long-chain fatty acids (VLCFA) into the peroxisome

Probab=97.99  E-value=6.8e-05  Score=59.43  Aligned_cols=107  Identities=21%  Similarity=0.253  Sum_probs=61.1

Q ss_pred             HHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCc------eEEecCCCCcChHHHHHHHHHHHhhcccCC-----
Q psy879           25 FSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDA------VLELNASNDRGIDTVRNKIKMFAQQKVTLP-----   93 (317)
Q Consensus        25 ~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~------~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~-----   93 (317)
                      .+..|.  .+.+.||+|+||||+++.++..+........      +..+..........+.+.+...  ....++     
T Consensus        23 ~i~~Ge--~~~i~G~nGsGKSTLl~~l~G~~~~~~G~i~~~~~~~i~~~~q~~~~~~~tv~~nl~~~--~~~~LS~G~~~   98 (166)
T cd03223          23 EIKPGD--RLLITGPSGTGKSSLFRALAGLWPWGSGRIGMPEGEDLLFLPQRPYLPLGTLREQLIYP--WDDVLSGGEQQ   98 (166)
T ss_pred             EECCCC--EEEEECCCCCCHHHHHHHHhcCCCCCCceEEECCCceEEEECCCCccccccHHHHhhcc--CCCCCCHHHHH
Confidence            344555  6999999999999999999987532222110      1111110000001122222110  000001     


Q ss_pred             --------CCceeEEEEeCCCC-CCHHHHHHHHHHhhhccCCceEEEEecCCC
Q psy879           94 --------PGRHKIVILDEADS-MTDGAQQALRRTMEIYSNTTRFALACNNSE  137 (317)
Q Consensus        94 --------~~~~~vliiDE~d~-l~~~~~~~ll~~le~~~~~~~~il~~~~~~  137 (317)
                              ..+++++++||... +.......+.+.+.+.  ...+|++|++..
T Consensus        99 rv~laral~~~p~~lllDEPt~~LD~~~~~~l~~~l~~~--~~tiiivsh~~~  149 (166)
T cd03223          99 RLAFARLLLHKPKFVFLDEATSALDEESEDRLYQLLKEL--GITVISVGHRPS  149 (166)
T ss_pred             HHHHHHHHHcCCCEEEEECCccccCHHHHHHHHHHHHHh--CCEEEEEeCChh
Confidence                    14689999999985 6677888888888875  255777777753

The peroxisomal membrane forms a permeability barrier for a wide variety of metabolites required for and formed during fatty acid beta-oxidation. To communicate with the cytoplasm and mitochondria, peroxisomes need dedicated proteins to transport such hydrophilic molecules across their membranes. X-linked adrenoleukodystrophy (X-ALD) is caused by mutations in the ALD gene, which encodes ALDP (adrenoleukodystrophy protein ), a peroxisomal integral membrane protein that is a member of the ATP-binding cassette (ABC) transporter protein family. The disease is characterized by a striking and unpredictable variation in phenotypic expression. Phenotypes include the rapidly progressive childhood cerebral form (CCALD), the milder adult form, adrenomyeloneuropathy (AMN), and variants without neurologic involvement (i.e. asympt

>TIGR01618 phage_P_loop phage nucleotide-binding protein

Probab=97.98  E-value=2.1e-05  Score=64.71  Aligned_cols=71  Identities=21%  Similarity=0.267  Sum_probs=40.1

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHc--CCCCC---------CceEEecCCCCcChHHHHHHHHHHHhhcccCCCCceeEEE
Q psy879           33 NIIISGPPGVGKTTTILCLARILL--GPSFK---------DAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVI  101 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~--~~~~~---------~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~vli  101 (317)
                      .++|||+||+||||+|+.++....  ....+         ..+.+++.  ....+.+.+.+......     ...+..|+
T Consensus        14 ~~liyG~~G~GKtt~a~~~~~~~~~~~~d~~~~~l~g~~~~~v~~~d~--~~~~~~~~d~l~~~~~~-----~~~ydtVV   86 (220)
T TIGR01618        14 MYLIYGKPGTGKTSTIKYLPGKTLVLSFDMSSKVLIGDENVDIADHDD--MPPIQAMVEFYVMQNIQ-----AVKYDNIV   86 (220)
T ss_pred             EEEEECCCCCCHHHHHHhcCCCCEEEeccccchhccCCCCCceeecCC--CCCHHHHHHHHHHHHhc-----cccCCEEE
Confidence            499999999999999999874210  11110         11111111  11223343444333222     26789999


Q ss_pred             EeCCCCCCH
Q psy879          102 LDEADSMTD  110 (317)
Q Consensus       102 iDE~d~l~~  110 (317)
                      ||.++.+..
T Consensus        87 IDsI~~l~~   95 (220)
T TIGR01618        87 IDNISALQN   95 (220)
T ss_pred             EecHHHHHH
Confidence            999987644

This model represents an uncharacterized family of proteins from a number of phage of Gram-positive bacteria. This protein contains a P-loop motif, G/A-X-X-G-X-G-K-T near its amino end. The function of this protein is unknown.

>cd03213 ABCG_EPDR ABCG transporters are involved in eye pigment (EP) precursor transport, regulation of lipid-trafficking mechanisms, and pleiotropic drug resistance (DR)

Probab=97.98  E-value=1.3e-05  Score=65.24  Aligned_cols=117  Identities=19%  Similarity=0.219  Sum_probs=64.9

Q ss_pred             HHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHH--cCCCCCCc--------------eEEecCCC-CcChHHHHH
Q psy879           18 TVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARIL--LGPSFKDA--------------VLELNASN-DRGIDTVRN   80 (317)
Q Consensus        18 ~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l--~~~~~~~~--------------~~~~~~~~-~~~~~~i~~   80 (317)
                      +++.+.-.+..|.  .+.+.||+|+||||+.+.++..+  ........              +..+.... ......+.+
T Consensus        24 ~l~~~~~~i~~Ge--~~~l~G~nGsGKStLl~~i~Gl~~~~~~~G~i~~~g~~~~~~~~~~~i~~~~q~~~~~~~~t~~~  101 (194)
T cd03213          24 LLKNVSGKAKPGE--LTAIMGPSGAGKSTLLNALAGRRTGLGVSGEVLINGRPLDKRSFRKIIGYVPQDDILHPTLTVRE  101 (194)
T ss_pred             ceecceEEEcCCc--EEEEECCCCCCHHHHHHHHhCCCCCCCCceEEEECCEeCchHhhhheEEEccCcccCCCCCcHHH
Confidence            4444444455665  79999999999999999999875  32211110              00010000 000011222


Q ss_pred             HHHHHHhhcccCC-------------CCceeEEEEeCCCC-CCHHHHHHHHHHhhhccC-CceEEEEecCCC
Q psy879           81 KIKMFAQQKVTLP-------------PGRHKIVILDEADS-MTDGAQQALRRTMEIYSN-TTRFALACNNSE  137 (317)
Q Consensus        81 ~~~~~~~~~~~~~-------------~~~~~vliiDE~d~-l~~~~~~~ll~~le~~~~-~~~~il~~~~~~  137 (317)
                      .+....... .++             ..++.++++||... +.......+.+.+.+... ...+|+++++..
T Consensus       102 ~i~~~~~~~-~LS~G~~qrv~laral~~~p~illlDEP~~~LD~~~~~~l~~~l~~~~~~~~tiii~sh~~~  172 (194)
T cd03213         102 TLMFAAKLR-GLSGGERKRVSIALELVSNPSLLFLDEPTSGLDSSSALQVMSLLRRLADTGRTIICSIHQPS  172 (194)
T ss_pred             HHHHHHHhc-cCCHHHHHHHHHHHHHHcCCCEEEEeCCCcCCCHHHHHHHHHHHHHHHhCCCEEEEEecCch
Confidence            211110000 011             13678999999975 567778888888876543 456777777754

DR is a well-described phenomenon occurring in fungi and shares several similarities with processes in bacteria and higher eukaryotes. Compared to other members of the ABC transporter subfamilies, the ABCG transporter family is composed of proteins that have an ATP-binding cassette domain at the N-terminus and a TM (transmembrane) domain at the C-terminus.

>TIGR02203 MsbA_lipidA lipid A export permease/ATP-binding protein MsbA

Probab=97.96  E-value=2e-05  Score=75.19  Aligned_cols=41  Identities=20%  Similarity=0.285  Sum_probs=31.2

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhccCCceEEEEecCC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYSNTTRFALACNNS  136 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~~~~~~il~~~~~  136 (317)
                      +++++++||+.. +.......+.+.+....++..+|++|+++
T Consensus       487 ~~~illLDEpts~LD~~~~~~i~~~L~~~~~~~tiIiitH~~  528 (571)
T TIGR02203       487 DAPILILDEATSALDNESERLVQAALERLMQGRTTLVIAHRL  528 (571)
T ss_pred             CCCEEEEeCccccCCHHHHHHHHHHHHHHhCCCEEEEEehhh
Confidence            579999999975 56677777888887765556677777775

This family consists of a single polypeptide chain transporter in the ATP-binding cassette (ABC) transporter family, MsbA, which exports lipid A. It may also act in multidrug resistance. Lipid A, a part of lipopolysaccharide, is found in the outer leaflet of the outer membrane of most Gram-negative bacteria. Members of this family are restricted to the Proteobacteria (although lipid A is more broadly distributed) and often are clustered with lipid A biosynthesis genes.

>TIGR02857 CydD thiol reductant ABC exporter, CydD subunit

Probab=97.96  E-value=2.3e-05  Score=74.04  Aligned_cols=41  Identities=10%  Similarity=0.239  Sum_probs=31.1

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhccCCceEEEEecCC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYSNTTRFALACNNS  136 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~~~~~~il~~~~~  136 (317)
                      +++++++||+.. +..+....+.+.+.+...+..+|+++++.
T Consensus       476 ~~~ililDE~ts~lD~~~~~~i~~~l~~~~~~~t~i~itH~~  517 (529)
T TIGR02857       476 DAPLLLLDEPTAHLDAETEALVTEALRALAQGRTVLLVTHRL  517 (529)
T ss_pred             CCCEEEEeCcccccCHHHHHHHHHHHHHhcCCCEEEEEecCH
Confidence            679999999975 56677777878877665556677777774

Unfortunately, the gene symbol nomenclature adopted based on this operon in B. subtilis assigns cydC to the third gene in the operon where this gene is actually homologous to the E. coli cydD gene. We have chosen to name all homologs in this family in accordance with the precedence of publication of the E. coli name, CydD

>TIGR03375 type_I_sec_LssB type I secretion system ATPase, LssB family

Probab=97.96  E-value=1.5e-05  Score=77.83  Aligned_cols=42  Identities=14%  Similarity=0.358  Sum_probs=31.7

Q ss_pred             ceeEEEEeCCC-CCCHHHHHHHHHHhhhccCCceEEEEecCCC
Q psy879           96 RHKIVILDEAD-SMTDGAQQALRRTMEIYSNTTRFALACNNSE  137 (317)
Q Consensus        96 ~~~vliiDE~d-~l~~~~~~~ll~~le~~~~~~~~il~~~~~~  137 (317)
                      +++++++||+. .+..+....+.+.+.+......+|++|++.+
T Consensus       619 ~p~iliLDE~Ts~LD~~te~~i~~~l~~~~~~~T~iiItHrl~  661 (694)
T TIGR03375       619 DPPILLLDEPTSAMDNRSEERFKDRLKRWLAGKTLVLVTHRTS  661 (694)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHHHHhCCCEEEEEecCHH
Confidence            68999999997 4567777778888876655566777887754

Type I protein secretion is a system in some Gram-negative bacteria to export proteins (often proteases) across both inner and outer membranes to the extracellular medium. This is one of three proteins of the type I secretion apparatus. Targeted proteins are not cleaved at the N-terminus, but rather carry signals located toward the extreme C-terminus to direct type I secretion. This model is related to models TIGR01842 and TIGR01846, and to bacteriocin ABC transporters that cleave their substrates during export.

>PRK10790 putative multidrug transporter membrane\ATP-binding components; Provisional

Probab=97.95  E-value=2.2e-05  Score=75.27  Aligned_cols=41  Identities=24%  Similarity=0.455  Sum_probs=30.7

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhccCCceEEEEecCC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYSNTTRFALACNNS  136 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~~~~~~il~~~~~  136 (317)
                      ++.++++||+.. +.++....+.+.+.+......+|++|++.
T Consensus       494 ~~~illlDEpts~LD~~t~~~i~~~l~~~~~~~tvIivtHr~  535 (592)
T PRK10790        494 TPQILILDEATANIDSGTEQAIQQALAAVREHTTLVVIAHRL  535 (592)
T ss_pred             CCCEEEEeCCcccCCHHHHHHHHHHHHHHhCCCEEEEEecch
Confidence            578999999985 56666777777777665556677888775

>cd03263 ABC_subfamily_A The ABCA subfamily mediates the transport of a variety of lipid compounds

Probab=97.94  E-value=2e-05  Score=65.50  Aligned_cols=42  Identities=14%  Similarity=0.255  Sum_probs=32.4

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhccCCceEEEEecCCC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYSNTTRFALACNNSE  137 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~~~~~~il~~~~~~  137 (317)
                      +++++++||... +.......+.+.+.+......+|+++++..
T Consensus       151 ~p~llllDEP~~~LD~~~~~~l~~~l~~~~~~~tii~~sH~~~  193 (220)
T cd03263         151 GPSVLLLDEPTSGLDPASRRAIWDLILEVRKGRSIILTTHSMD  193 (220)
T ss_pred             CCCEEEECCCCCCCCHHHHHHHHHHHHHHhcCCEEEEEcCCHH
Confidence            689999999975 567778888888877655566777777754

Mutations of members of ABCA subfamily are associated with human genetic diseases, such as, familial high-density lipoprotein (HDL) deficiency, neonatal surfactant deficiency, degenerative retinopathies, and congenital keratinization disorders. The ABCA1 protein is involved in disorders of cholesterol transport and high-density lipoprotein (HDL) biosynthesis. The ABCA4 (ABCR) protein transports vitamin A derivatives in the outer segments of photoreceptor cells, and therefore, performs a crucial step in the visual cycle. The ABCA genes are not present in yeast. However, evolutionary studies of ABCA genes indicate that they arose as transporters that subsequently duplicated and that certain sets of ABCA genes were lost in different eukaryotic lineages.

>PRK13539 cytochrome c biogenesis protein CcmA; Provisional

Probab=97.93  E-value=6e-05  Score=62.08  Aligned_cols=46  Identities=15%  Similarity=0.102  Sum_probs=33.9

Q ss_pred             ceeEEEEeCCC-CCCHHHHHHHHHHhhhc-cCCceEEEEecCCCcCch
Q psy879           96 RHKIVILDEAD-SMTDGAQQALRRTMEIY-SNTTRFALACNNSEKIIE  141 (317)
Q Consensus        96 ~~~vliiDE~d-~l~~~~~~~ll~~le~~-~~~~~~il~~~~~~~l~~  141 (317)
                      +++++++||.. .+.......+.+.+.+. .....+|+++++...+..
T Consensus       145 ~p~llllDEPt~~LD~~~~~~l~~~l~~~~~~~~tiii~sH~~~~~~~  192 (207)
T PRK13539        145 NRPIWILDEPTAALDAAAVALFAELIRAHLAQGGIVIAATHIPLGLPG  192 (207)
T ss_pred             CCCEEEEeCCcccCCHHHHHHHHHHHHHHHHCCCEEEEEeCCchhhcc
Confidence            67999999998 56777788888888754 234567888887665554

>TIGR02204 MsbA_rel ABC transporter, permease/ATP-binding protein

Probab=97.92  E-value=3e-05  Score=74.13  Aligned_cols=42  Identities=19%  Similarity=0.298  Sum_probs=30.4

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhccCCceEEEEecCCC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYSNTTRFALACNNSE  137 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~~~~~~il~~~~~~  137 (317)
                      ++.++++||+.. +.+.....+.+.+....+...+|++|++..
T Consensus       494 ~~~ililDEpts~lD~~~~~~i~~~l~~~~~~~t~IiitH~~~  536 (576)
T TIGR02204       494 DAPILLLDEATSALDAESEQLVQQALETLMKGRTTLIIAHRLA  536 (576)
T ss_pred             CCCeEEEeCcccccCHHHHHHHHHHHHHHhCCCEEEEEecchH
Confidence            578999999975 556666667777776545566778887753

This protein is related to a Proteobacterial ATP transporter that exports lipid A and to eukaryotic P-glycoproteins.

>PF00448 SRP54: SRP54-type protein, GTPase domain; InterPro: IPR000897 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]

Probab=97.92  E-value=5.3e-05  Score=61.61  Aligned_cols=101  Identities=22%  Similarity=0.303  Sum_probs=53.5

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHHHHHHHhhcccC------------------CCC
Q psy879           34 IIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFAQQKVTL------------------PPG   95 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~------------------~~~   95 (317)
                      ++|.||+|+||||++-.+|..+.....+..++..+.......++++..-..+ .-++..                  ...
T Consensus         4 i~lvGptGvGKTTt~aKLAa~~~~~~~~v~lis~D~~R~ga~eQL~~~a~~l-~vp~~~~~~~~~~~~~~~~~l~~~~~~   82 (196)
T PF00448_consen    4 IALVGPTGVGKTTTIAKLAARLKLKGKKVALISADTYRIGAVEQLKTYAEIL-GVPFYVARTESDPAEIAREALEKFRKK   82 (196)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHHHHTT--EEEEEESTSSTHHHHHHHHHHHHH-TEEEEESSTTSCHHHHHHHHHHHHHHT
T ss_pred             EEEECCCCCchHhHHHHHHHHHhhccccceeecCCCCCccHHHHHHHHHHHh-ccccchhhcchhhHHHHHHHHHHHhhc
Confidence            8999999999999999999887544333333333322211222222111111 001000                  002


Q ss_pred             ceeEEEEeCCCCCCHH--HHHHHHHHhhhc-cCCceEEEEecC
Q psy879           96 RHKIVILDEADSMTDG--AQQALRRTMEIY-SNTTRFALACNN  135 (317)
Q Consensus        96 ~~~vliiDE~d~l~~~--~~~~ll~~le~~-~~~~~~il~~~~  135 (317)
                      +..+|+||=+.....+  ....+.++++.. +..+.+|+.++.
T Consensus        83 ~~D~vlIDT~Gr~~~d~~~~~el~~~~~~~~~~~~~LVlsa~~  125 (196)
T PF00448_consen   83 GYDLVLIDTAGRSPRDEELLEELKKLLEALNPDEVHLVLSATM  125 (196)
T ss_dssp             TSSEEEEEE-SSSSTHHHHHHHHHHHHHHHSSSEEEEEEEGGG
T ss_pred             CCCEEEEecCCcchhhHHHHHHHHHHhhhcCCccceEEEeccc
Confidence            3569999998877543  355666666543 445556665544

SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. This entry represents the GTPase domain of the 54 kDa SRP54 component, a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 of the signal recognition particle has a three-domain structure: an N-terminal helical bundle domain, a GTPase domain, and the M-domain that binds the 7s RNA and also binds the signal sequence. The extreme C-terminal region is glycine-rich and lower in complexity and poorly conserved between species. The GTPase domain is evolutionary related to P-loop NTPase domains found in a variety of other proteins []. These proteins include Escherichia coli and Bacillus subtilis ffh protein (P48), which seems to be the prokaryotic counterpart of SRP54; signal recognition particle receptor alpha subunit (docking protein), an integral membrane GTP-binding protein which ensures, in conjunction with SRP, the correct targeting of nascent secretory proteins to the endoplasmic reticulum membrane; bacterial FtsY protein, which is believed to play a similar role to that of the docking protein in eukaryotes; the pilA protein from Neisseria gonorrhoeae, the homologue of ftsY; and bacterial flagellar biosynthesis protein flhF.; GO: 0005525 GTP binding, 0006614 SRP-dependent cotranslational protein targeting to membrane; PDB: 2OG2_A 3B9Q_A 3DM9_B 3DMD_B 3E70_C 3DM5_B 2XXA_C 2J28_9 1ZU5_B 1ZU4_A ....

>COG1373 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=97.91  E-value=0.00026  Score=64.08  Aligned_cols=130  Identities=22%  Similarity=0.239  Sum_probs=78.3

Q ss_pred             HHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCC-cChHHHHHHHHHHHhhcccCCCCceeE
Q psy879           21 RLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASND-RGIDTVRNKIKMFAQQKVTLPPGRHKI   99 (317)
Q Consensus        21 ~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~-~~~~~i~~~~~~~~~~~~~~~~~~~~v   99 (317)
                      .+...+..... .++++||.++||||+++.+.+.+...     .+.++..+. .......+....+.....    .+...
T Consensus        28 ~l~~~~~~~~~-i~~i~GpR~~GKTtll~~l~~~~~~~-----~iy~~~~d~~~~~~~l~d~~~~~~~~~~----~~~~y   97 (398)
T COG1373          28 RLIKKLDLRPF-IILILGPRQVGKTTLLKLLIKGLLEE-----IIYINFDDLRLDRIELLDLLRAYIELKE----REKSY   97 (398)
T ss_pred             HHHhhcccCCc-EEEEECCccccHHHHHHHHHhhCCcc-----eEEEEecchhcchhhHHHHHHHHHHhhc----cCCce
Confidence            34444443333 69999999999999998888775332     333333221 122222333333322221    15579


Q ss_pred             EEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCC----CcCchhHhhhcceeeecCCCHHHHHHH
Q psy879          100 VILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNS----EKIIEPIQSRCAMLRYNKLTDAQLLSK  163 (317)
Q Consensus       100 liiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~----~~l~~~i~sR~~~i~f~~~~~~~~~~~  163 (317)
                      +++||++.... -..++..+.+..+.  .+++++...    .+....+..|...+.+.|+|-.|....
T Consensus        98 ifLDEIq~v~~-W~~~lk~l~d~~~~--~v~itgsss~ll~~~~~~~L~GR~~~~~l~PlSF~Efl~~  162 (398)
T COG1373          98 IFLDEIQNVPD-WERALKYLYDRGNL--DVLITGSSSSLLSKEISESLAGRGKDLELYPLSFREFLKL  162 (398)
T ss_pred             EEEecccCchh-HHHHHHHHHccccc--eEEEECCchhhhccchhhhcCCCceeEEECCCCHHHHHhh
Confidence            99999998764 33344444444333  455555443    356678888888899999999988653

>PF04851 ResIII: Type III restriction enzyme, res subunit; InterPro: IPR006935 This entry represents a domain found in the N terminus of several proteins, including helicases, the R subunit (HsdR) of type I restriction endonucleases (3

Probab=97.91  E-value=8.1e-05  Score=59.67  Aligned_cols=44  Identities=20%  Similarity=0.303  Sum_probs=35.9

Q ss_pred             CCHHHHHHHHHHHhcC-CCceEEEECCCCCCHHHHHHHHHHHHcC
Q psy879           14 GNEDTVERLKVFSSSG-NVPNIIISGPPGVGKTTTILCLARILLG   57 (317)
Q Consensus        14 g~~~~~~~l~~~l~~~-~~~~~ll~G~~G~GKt~la~~la~~l~~   57 (317)
                      .|.++++.+...+... ..++++|.+|+|+|||.++..++..+..
T Consensus         7 ~Q~~ai~~i~~~~~~~~~~~~~ll~~~tGsGKT~~~~~~~~~l~~   51 (184)
T PF04851_consen    7 YQQEAIARIINSLENKKEERRVLLNAPTGSGKTIIALALILELAR   51 (184)
T ss_dssp             HHHHHHHHHHHHHHTTSGCSEEEEEESTTSSHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHhcCCCCCEEEEECCCCCcChhhhhhhhcccc
Confidence            4778888888888776 4558999999999999999987776643

1.21.3 from EC), the Res subunit of type III endonucleases (3.1.21.5 from EC), and the B subunit of excinuclease ABC (uvrB) [, , ].; GO: 0003677 DNA binding, 0005524 ATP binding, 0016787 hydrolase activity; PDB: 2Y3T_B 2W74_B 2FWR_A 2FZ4_A 3UWX_B 3H1T_A 3B6E_A 2FDC_A 1D9Z_A 1T5L_B ....

>cd03215 ABC_Carb_Monos_II This family represents domain II of the carbohydrate uptake proteins that transport only monosaccharides (Monos)

Probab=97.90  E-value=1.7e-05  Score=63.84  Aligned_cols=42  Identities=19%  Similarity=0.290  Sum_probs=30.3

Q ss_pred             CceeEEEEeCCCC-CCHHHHHHHHHHhhhcc-CCceEEEEecCC
Q psy879           95 GRHKIVILDEADS-MTDGAQQALRRTMEIYS-NTTRFALACNNS  136 (317)
Q Consensus        95 ~~~~vliiDE~d~-l~~~~~~~ll~~le~~~-~~~~~il~~~~~  136 (317)
                      .+++++++||... +.......+.+.+.+.. ....+|+++++.
T Consensus       121 ~~p~llllDEP~~~LD~~~~~~l~~~l~~~~~~~~tiii~sh~~  164 (182)
T cd03215         121 RDPRVLILDEPTRGVDVGAKAEIYRLIRELADAGKAVLLISSEL  164 (182)
T ss_pred             cCCCEEEECCCCcCCCHHHHHHHHHHHHHHHHCCCEEEEEeCCH
Confidence            4689999999974 56777778888777653 245577777664

The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses (such as xylose, arabinose, and ribose), that cannot be broken down to simple sugars by hydrolysis. In members of Carb_Monos family the single hydrophobic gene product forms a homodimer, while the ABC protein represents a fusion of two nucleotide-binding domains. However, it is assumed that two copies of the ABC domains are present in the assembled transporter.

>TIGR01846 type_I_sec_HlyB type I secretion system ABC transporter, HlyB family

Probab=97.89  E-value=2.9e-05  Score=75.77  Aligned_cols=42  Identities=19%  Similarity=0.280  Sum_probs=32.3

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhccCCceEEEEecCCC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYSNTTRFALACNNSE  137 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~~~~~~il~~~~~~  137 (317)
                      +++++++||+.. +..+....+.+.+.+...+..+|++|++.+
T Consensus       611 ~~~ililDEpts~LD~~~~~~i~~~l~~~~~~~t~i~itH~~~  653 (694)
T TIGR01846       611 NPRILIFDEATSALDYESEALIMRNMREICRGRTVIIIAHRLS  653 (694)
T ss_pred             CCCEEEEECCCcCCCHHHHHHHHHHHHHHhCCCEEEEEeCChH
Confidence            689999999974 667777788888877655566788888764

Type I protein secretion is a system in some Gram-negative bacteria to export proteins (often proteases) across both inner and outer membranes to the extracellular medium. This is one of three proteins of the type I secretion apparatus. Targeted proteins are not cleaved at the N-terminus, but rather carry signals located toward the extreme C-terminus to direct type I secretion.

>cd03232 ABC_PDR_domain2 The pleiotropic drug resistance-like (PDR) family of ATP-binding cassette (ABC) transporters

Probab=97.89  E-value=2.6e-05  Score=63.37  Aligned_cols=43  Identities=16%  Similarity=0.251  Sum_probs=31.3

Q ss_pred             CceeEEEEeCCCC-CCHHHHHHHHHHhhhcc-CCceEEEEecCCC
Q psy879           95 GRHKIVILDEADS-MTDGAQQALRRTMEIYS-NTTRFALACNNSE  137 (317)
Q Consensus        95 ~~~~vliiDE~d~-l~~~~~~~ll~~le~~~-~~~~~il~~~~~~  137 (317)
                      .+++++++||... +.......+.+.+.+.. ....+|+++++.+
T Consensus       125 ~~p~vlllDEP~~~LD~~~~~~l~~~l~~~~~~~~tiiivtH~~~  169 (192)
T cd03232         125 AKPSILFLDEPTSGLDSQAAYNIVRFLKKLADSGQAILCTIHQPS  169 (192)
T ss_pred             cCCcEEEEeCCCcCCCHHHHHHHHHHHHHHHHcCCEEEEEEcCCh
Confidence            3689999999985 56777778878777653 2456777777754

PDR is a well-described phenomenon occurring in fungi and shares several similarities with processes in bacteria and higher eukaryotes. This PDR subfamily represents domain I of its (ABC-IM)2 organization. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>cd03217 ABC_FeS_Assembly ABC-type transport system involved in Fe-S cluster assembly, ATPase component

Probab=97.89  E-value=3e-05  Score=63.52  Aligned_cols=43  Identities=14%  Similarity=0.183  Sum_probs=31.1

Q ss_pred             CceeEEEEeCCC-CCCHHHHHHHHHHhhhccC-CceEEEEecCCC
Q psy879           95 GRHKIVILDEAD-SMTDGAQQALRRTMEIYSN-TTRFALACNNSE  137 (317)
Q Consensus        95 ~~~~vliiDE~d-~l~~~~~~~ll~~le~~~~-~~~~il~~~~~~  137 (317)
                      .+++++++||.. .+.......+.+.+.+... ...+|+++++..
T Consensus       121 ~~p~illlDEPt~~LD~~~~~~l~~~L~~~~~~~~tiii~sh~~~  165 (200)
T cd03217         121 LEPDLAILDEPDSGLDIDALRLVAEVINKLREEGKSVLIITHYQR  165 (200)
T ss_pred             cCCCEEEEeCCCccCCHHHHHHHHHHHHHHHHCCCEEEEEecCHH
Confidence            368999999997 5667777778777776532 455777777654

Biosynthesis of iron-sulfur clusters (Fe-S) depends on multiprotein systems. The SUF system of E. coli and Erwinia chrysanthemi is important for Fe-S biogenesis under stressful conditions. The SUF system is made of six proteins: SufC is an atypical cytoplasmic ABC-ATPase, which forms a complex with SufB and SufD; SufA plays the role of a scaffold protein for assembly of iron-sulfur clusters and delivery to target proteins; SufS is a cysteine desulfurase which mobilizes the sulfur atom from cysteine and provides it to the cluster; SufE has no associated function yet.

>TIGR01192 chvA glucan exporter ATP-binding protein

Probab=97.88  E-value=3.3e-05  Score=73.78  Aligned_cols=42  Identities=14%  Similarity=0.267  Sum_probs=32.1

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhccCCceEEEEecCCC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYSNTTRFALACNNSE  137 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~~~~~~il~~~~~~  137 (317)
                      +++++++||+.. +..+....+.+.+.+...+..+|++|++.+
T Consensus       489 ~p~ililDEpts~LD~~~~~~i~~~l~~~~~~~tvI~isH~~~  531 (585)
T TIGR01192       489 NAPILVLDEATSALDVETEARVKNAIDALRKNRTTFIIAHRLS  531 (585)
T ss_pred             CCCEEEEECCccCCCHHHHHHHHHHHHHHhCCCEEEEEEcChH
Confidence            689999999975 667777788888876655556788888753

This model describes glucan exporter ATP binding protein in bacteria. It belongs to the larger ABC transporter superfamily with the characteristic ATP binding motif. The In general, this protein is in some ways implicated in osmoregulation and suggested to participate in the export of glucan from the cytoplasm to periplasm. The cyclic beta-1,2-glucan in the bactrerial periplasmic space is suggested to confer the property of high osmolority. It has also been demonstrated that mutants in this loci have lost functions of virulence and motility. It is unclear as to how virulence and osmoadaptaion are related.

>cd03369 ABCC_NFT1 Domain 2 of NFT1 (New full-length MRP-type transporter 1)

Probab=97.88  E-value=3.6e-05  Score=63.39  Aligned_cols=44  Identities=16%  Similarity=0.297  Sum_probs=33.1

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhccCCceEEEEecCCCcC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYSNTTRFALACNNSEKI  139 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l  139 (317)
                      +++++++||... +.......+.+.+.+......+|++|++...+
T Consensus       143 ~p~llllDEP~~~LD~~~~~~l~~~l~~~~~~~tiii~th~~~~~  187 (207)
T cd03369         143 RPRVLVLDEATASIDYATDALIQKTIREEFTNSTILTIAHRLRTI  187 (207)
T ss_pred             CCCEEEEeCCcccCCHHHHHHHHHHHHHhcCCCEEEEEeCCHHHH
Confidence            689999999974 56777888888887665556678888776543

NFT1 belongs to the MRP (mulrtidrug resisitance-associated protein) family of ABC transporters. Some of the MRP members have five additional transmembrane segments in their N-terminas, but the function of these additional membrane-spanning domains is not clear. The MRP was found in the multidrug-resisting lung cancer cell in which p-glycoprotein was not overexpressed. MRP exports glutathione by drug stimulation, as well as, certain substrates in conjugated forms with anions such as glutathione, glucuronate, and sulfate.

>COG1131 CcmA ABC-type multidrug transport system, ATPase component [Defense mechanisms]

Probab=97.88  E-value=7.3e-06  Score=71.05  Aligned_cols=40  Identities=28%  Similarity=0.389  Sum_probs=31.0

Q ss_pred             HHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcC
Q psy879           16 EDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLG   57 (317)
Q Consensus        16 ~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~   57 (317)
                      ..+++.+.-.++.|.  .+.|.||+|+||||+.+.++..+..
T Consensus        18 ~~~l~~vs~~i~~Ge--i~gllG~NGAGKTTllk~l~gl~~p   57 (293)
T COG1131          18 KTALDGVSFEVEPGE--IFGLLGPNGAGKTTLLKILAGLLKP   57 (293)
T ss_pred             CEEEeceeEEEcCCe--EEEEECCCCCCHHHHHHHHhCCcCC
Confidence            445555555566665  6999999999999999999998743

>PRK10875 recD exonuclease V subunit alpha; Provisional

Probab=97.88  E-value=0.00019  Score=68.17  Aligned_cols=100  Identities=20%  Similarity=0.251  Sum_probs=58.2

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHcCCC-CCCceEEecCCCCcChHHHHH----------------------------HHH
Q psy879           33 NIIISGPPGVGKTTTILCLARILLGPS-FKDAVLELNASNDRGIDTVRN----------------------------KIK   83 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~~~~-~~~~~~~~~~~~~~~~~~i~~----------------------------~~~   83 (317)
                      ..+++|+|||||||++..+...+.... .....+.+.+.+..-...+.+                            .++
T Consensus       169 ~~vItGgpGTGKTt~v~~ll~~l~~~~~~~~~~i~l~APTgkAA~rL~e~~~~~~~~~~~~~~~~~~~~~~a~TiHrlLg  248 (615)
T PRK10875        169 ISVISGGPGTGKTTTVAKLLAALIQLADGERCRIRLAAPTGKAAARLTESLGKALRQLPLTDEQKKRIPEEASTLHRLLG  248 (615)
T ss_pred             eEEEEeCCCCCHHHHHHHHHHHHHHhcCCCCcEEEEECCcHHHHHHHHHHHHhhhhccccchhhhhcCCCchHHHHHHhC
Confidence            489999999999999999888763311 111122222222111122222                            221


Q ss_pred             HHHhhcc-cC---CCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecC
Q psy879           84 MFAQQKV-TL---PPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNN  135 (317)
Q Consensus        84 ~~~~~~~-~~---~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~  135 (317)
                      ....... ..   ..-...++||||+..+.-.....|++.+   ++++++|++...
T Consensus       249 ~~~~~~~~~~~~~~~l~~dvlIvDEaSMvd~~lm~~ll~al---~~~~rlIlvGD~  301 (615)
T PRK10875        249 AQPGSQRLRYHAGNPLHLDVLVVDEASMVDLPMMARLIDAL---PPHARVIFLGDR  301 (615)
T ss_pred             cCCCccchhhccccCCCCCeEEEChHhcccHHHHHHHHHhc---ccCCEEEEecch
Confidence            1110000 00   0012369999999999988777777765   577899999865

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=97.88  E-value=0.00023  Score=63.24  Aligned_cols=27  Identities=44%  Similarity=0.655  Sum_probs=23.5

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHcCCC
Q psy879           33 NIIISGPPGVGKTTTILCLARILLGPS   59 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~~~~   59 (317)
                      .++|.||+|+||||++..+|..+....
T Consensus       243 vI~LVGptGvGKTTTiaKLA~~L~~~G  269 (436)
T PRK11889        243 TIALIGPTGVGKTTTLAKMAWQFHGKK  269 (436)
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHHcC
Confidence            489999999999999999999875443

>COG4988 CydD ABC-type transport system involved in cytochrome bd biosynthesis, ATPase and permease components [Energy production and conversion / Posttranslational modification, protein turnover, chaperones]

Probab=97.87  E-value=5e-05  Score=69.77  Aligned_cols=42  Identities=12%  Similarity=0.262  Sum_probs=32.9

Q ss_pred             ceeEEEEeCCC-CCCHHHHHHHHHHhhhccCCceEEEEecCCC
Q psy879           96 RHKIVILDEAD-SMTDGAQQALRRTMEIYSNTTRFALACNNSE  137 (317)
Q Consensus        96 ~~~vliiDE~d-~l~~~~~~~ll~~le~~~~~~~~il~~~~~~  137 (317)
                      +..++++||+- ++..+....+.+.+.+......++++|++..
T Consensus       474 ~~~l~llDEpTA~LD~etE~~i~~~l~~l~~~ktvl~itHrl~  516 (559)
T COG4988         474 PASLLLLDEPTAHLDAETEQIILQALQELAKQKTVLVITHRLE  516 (559)
T ss_pred             CCCEEEecCCccCCCHhHHHHHHHHHHHHHhCCeEEEEEcChH
Confidence            46799999997 5677777778888887777777888888754

>PRK11160 cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed

Probab=97.87  E-value=3.9e-05  Score=73.20  Aligned_cols=42  Identities=7%  Similarity=0.187  Sum_probs=31.0

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhccCCceEEEEecCCC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYSNTTRFALACNNSE  137 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~~~~~~il~~~~~~  137 (317)
                      +++++++||+-. +..+....+.+.+........+|+++++..
T Consensus       493 ~~~ililDE~ts~lD~~t~~~i~~~l~~~~~~~tviiitHr~~  535 (574)
T PRK11160        493 DAPLLLLDEPTEGLDAETERQILELLAEHAQNKTVLMITHRLT  535 (574)
T ss_pred             CCCEEEEeCCcccCCHHHHHHHHHHHHHHcCCCEEEEEecChh
Confidence            679999999975 566677778788776655556777777754

>COG4178 ABC-type uncharacterized transport system, permease and ATPase components [General function prediction only]

Probab=97.87  E-value=6.8e-05  Score=69.93  Aligned_cols=42  Identities=17%  Similarity=0.198  Sum_probs=33.7

Q ss_pred             CceeEEEEeCCC-CCCHHHHHHHHHHhhhccCCceEEEEecCC
Q psy879           95 GRHKIVILDEAD-SMTDGAQQALRRTMEIYSNTTRFALACNNS  136 (317)
Q Consensus        95 ~~~~vliiDE~d-~l~~~~~~~ll~~le~~~~~~~~il~~~~~  136 (317)
                      .+++++++||+- .|.++....+++.+.+.-+.+.+|-+++++
T Consensus       532 ~kP~~v~LDEATsALDe~~e~~l~q~l~~~lp~~tvISV~Hr~  574 (604)
T COG4178         532 HKPKWVFLDEATSALDEETEDRLYQLLKEELPDATVISVGHRP  574 (604)
T ss_pred             cCCCEEEEecchhccChHHHHHHHHHHHhhCCCCEEEEeccch
Confidence            378999999997 567778899999999865667788887764

>PRK10789 putative multidrug transporter membrane\ATP-binding components; Provisional

Probab=97.87  E-value=3.3e-05  Score=73.64  Aligned_cols=42  Identities=14%  Similarity=0.293  Sum_probs=31.0

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhccCCceEEEEecCCC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYSNTTRFALACNNSE  137 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~~~~~~il~~~~~~  137 (317)
                      +++++++||+.. +..+....+.+.+........+|++|++..
T Consensus       469 ~~~illlDEpts~LD~~~~~~i~~~l~~~~~~~tii~itH~~~  511 (569)
T PRK10789        469 NAEILILDDALSAVDGRTEHQILHNLRQWGEGRTVIISAHRLS  511 (569)
T ss_pred             CCCEEEEECccccCCHHHHHHHHHHHHHHhCCCEEEEEecchh
Confidence            679999999985 667777778777776544455777777753

>COG4088 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=97.87  E-value=0.00018  Score=57.51  Aligned_cols=29  Identities=45%  Similarity=0.561  Sum_probs=25.1

Q ss_pred             ceEEEECCCCCCHHHHHHHHHHHHcCCCC
Q psy879           32 PNIIISGPPGVGKTTTILCLARILLGPSF   60 (317)
Q Consensus        32 ~~~ll~G~~G~GKt~la~~la~~l~~~~~   60 (317)
                      |-++|+|+||+||||+++.++++|....+
T Consensus         2 pLiIlTGyPgsGKTtfakeLak~L~~~i~   30 (261)
T COG4088           2 PLIILTGYPGSGKTTFAKELAKELRQEIW   30 (261)
T ss_pred             ceEEEecCCCCCchHHHHHHHHHHHHhhh
Confidence            45899999999999999999999965444

>COG1122 CbiO ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=97.85  E-value=2.3e-05  Score=65.31  Aligned_cols=42  Identities=14%  Similarity=0.245  Sum_probs=30.6

Q ss_pred             ceeEEEEeCCCCC-CHHHHHHHHHHhhhccCC--ceEEEEecCCC
Q psy879           96 RHKIVILDEADSM-TDGAQQALRRTMEIYSNT--TRFALACNNSE  137 (317)
Q Consensus        96 ~~~vliiDE~d~l-~~~~~~~ll~~le~~~~~--~~~il~~~~~~  137 (317)
                      ++.++++||.-.. .+.....+.+.+.+....  ..+|++|++.+
T Consensus       156 ~P~iliLDEPta~LD~~~~~~l~~~l~~L~~~~~~tii~~tHd~~  200 (235)
T COG1122         156 GPEILLLDEPTAGLDPKGRRELLELLKKLKEEGGKTIIIVTHDLE  200 (235)
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHHHHHHHhcCCCeEEEEeCcHH
Confidence            5789999999865 667788888888766544  35677776643

>cd03264 ABC_drug_resistance_like ABC-type multidrug transport system, ATPase component

Probab=97.85  E-value=5.4e-05  Score=62.52  Aligned_cols=42  Identities=17%  Similarity=0.239  Sum_probs=32.3

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhccCCceEEEEecCCC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYSNTTRFALACNNSE  137 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~~~~~~il~~~~~~  137 (317)
                      +++++++||... +....+..+.+++.+......+|+++++..
T Consensus       148 ~p~llllDEPt~~LD~~~~~~l~~~l~~~~~~~tii~vsH~~~  190 (211)
T cd03264         148 DPSILIVDEPTAGLDPEERIRFRNLLSELGEDRIVILSTHIVE  190 (211)
T ss_pred             CCCEEEEcCCcccCCHHHHHHHHHHHHHHhCCCEEEEEcCCHH
Confidence            689999999974 667788888888887655566777776644

The biological function of this family is not well characterized, but display ABC domains similar to members of ABCA subfamily. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=97.85  E-value=0.00044  Score=63.04  Aligned_cols=103  Identities=20%  Similarity=0.253  Sum_probs=52.7

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHc--CCCCCCceEEecCCCCcChHHHHHHHHHHHhhccc------------CCCCcee
Q psy879           33 NIIISGPPGVGKTTTILCLARILL--GPSFKDAVLELNASNDRGIDTVRNKIKMFAQQKVT------------LPPGRHK   98 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~--~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~------------~~~~~~~   98 (317)
                      .++|.||+|+||||++..+|..+.  .......++..+........+++..-.. ...++.            .....+.
T Consensus       223 ~i~~vGptGvGKTTt~~kLA~~~~~~~~g~~V~li~~D~~r~~a~eqL~~~a~~-~~vp~~~~~~~~~l~~~l~~~~~~D  301 (424)
T PRK05703        223 VVALVGPTGVGKTTTLAKLAARYALLYGKKKVALITLDTYRIGAVEQLKTYAKI-MGIPVEVVYDPKELAKALEQLRDCD  301 (424)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHhcCCCeEEEEECCccHHHHHHHHHHHHHH-hCCceEccCCHHhHHHHHHHhCCCC
Confidence            489999999999999999998764  2222233333322110011111110000 000000            0013578


Q ss_pred             EEEEeCCCCCCH--HHHHHHHHHhhh--ccCCceEEEEecCC
Q psy879           99 IVILDEADSMTD--GAQQALRRTMEI--YSNTTRFALACNNS  136 (317)
Q Consensus        99 vliiDE~d~l~~--~~~~~ll~~le~--~~~~~~~il~~~~~  136 (317)
                      +||||-+.....  .....|.++++.  .+..+.+|+.++..
T Consensus       302 lVlIDt~G~~~~d~~~~~~L~~ll~~~~~~~~~~LVl~a~~~  343 (424)
T PRK05703        302 VILIDTAGRSQRDKRLIEELKALIEFSGEPIDVYLVLSATTK  343 (424)
T ss_pred             EEEEeCCCCCCCCHHHHHHHHHHHhccCCCCeEEEEEECCCC
Confidence            999999877543  345566677662  22344556555443

>COG3842 PotA ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]

Probab=97.84  E-value=2.1e-05  Score=68.92  Aligned_cols=195  Identities=19%  Similarity=0.206  Sum_probs=104.8

Q ss_pred             cCCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHHHHHHHhhcccC
Q psy879           13 VGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFAQQKVTL   92 (317)
Q Consensus        13 ~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~   92 (317)
                      +|...+++.+.-.+..|.  -+.|.||+||||||+.+.+|... .++.+.  +.++..+..+..--+..++.++|....+
T Consensus        15 yg~~~av~~isl~i~~Ge--f~~lLGPSGcGKTTlLR~IAGfe-~p~~G~--I~l~G~~i~~lpp~kR~ig~VFQ~YALF   89 (352)
T COG3842          15 FGDFTAVDDISLDIKKGE--FVTLLGPSGCGKTTLLRMIAGFE-QPSSGE--ILLDGEDITDVPPEKRPIGMVFQSYALF   89 (352)
T ss_pred             cCCeeEEecceeeecCCc--EEEEECCCCCCHHHHHHHHhCCC-CCCCce--EEECCEECCCCChhhcccceeecCcccC
Confidence            344444555555666776  47799999999999999999864 333332  2233222111111112233333332111


Q ss_pred             CCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcCchhHhhhcceee-ecCCCHHHHHHHHHHHHHHc
Q psy879           93 PPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLR-YNKLTDAQLLSKVIEICEKE  171 (317)
Q Consensus        93 ~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~~~i~sR~~~i~-f~~~~~~~~~~~l~~~~~~~  171 (317)
                      |+             |+-.         +    |+-                   --+. -..+..+++.+.+.+.++.-
T Consensus        90 PH-------------ltV~---------~----NVa-------------------fGLk~~~~~~~~~i~~rv~e~L~lV  124 (352)
T COG3842          90 PH-------------MTVE---------E----NVA-------------------FGLKVRKKLKKAEIKARVEEALELV  124 (352)
T ss_pred             CC-------------CcHH---------H----Hhh-------------------hhhhhcCCCCHHHHHHHHHHHHHHc
Confidence            10             1100         0    000                   0011 12356677777777776644


Q ss_pred             CCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhhCCCcccHHHHHhhcCCCCHHH----HHHHHHHH------hcCCHHHHH
Q psy879          172 NISHTNDGLEAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLA----VKEMLLNC------VEGNMKDSY  241 (317)
Q Consensus       172 ~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~~~~~i~~~~v~~~~~~~~~~~----i~~l~~~~------~~~~~~~~~  241 (317)
                      +  +++-+..+-.+.|+| .++-..+.++.+...+.+-.|+-..+++......    +.++.+.+      ..+|..+|+
T Consensus       125 ~--L~~~~~R~p~qLSGG-QqQRVALARAL~~~P~vLLLDEPlSaLD~kLR~~mr~Elk~lq~~~giT~i~VTHDqeEAl  201 (352)
T COG3842         125 G--LEGFADRKPHQLSGG-QQQRVALARALVPEPKVLLLDEPLSALDAKLREQMRKELKELQRELGITFVYVTHDQEEAL  201 (352)
T ss_pred             C--chhhhhhChhhhChH-HHHHHHHHHHhhcCcchhhhcCcccchhHHHHHHHHHHHHHHHHhcCCeEEEEECCHHHHh
Confidence            4  434444444555555 6777777777777666666666555555433333    33444444      467899999


Q ss_pred             HHHHHH--HHcC-----CCHHHHHHH
Q psy879          242 KIIHHL--YKLG-----YAPEDIIGN  260 (317)
Q Consensus       242 ~~~~~l--~~~~-----~~~~~i~~~  260 (317)
                      .+-+..  +..|     -+|.+++..
T Consensus       202 ~msDrI~Vm~~G~I~Q~gtP~eiY~~  227 (352)
T COG3842         202 AMSDRIAVMNDGRIEQVGTPEEIYER  227 (352)
T ss_pred             hhccceEEccCCceeecCCHHHHhhC
Confidence            988776  3443     377777755

>TIGR03796 NHPM_micro_ABC1 NHPM bacteriocin system ABC transporter, peptidase/ATP-binding protein

Probab=97.84  E-value=3.2e-05  Score=75.74  Aligned_cols=37  Identities=22%  Similarity=0.378  Sum_probs=28.5

Q ss_pred             HHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHc
Q psy879           18 TVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        18 ~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      +++.+.-.++.|.  .+.+.||+|+||||+++.++..+.
T Consensus       494 vL~~isl~i~~Ge--~vaIvG~sGsGKSTLlklL~gl~~  530 (710)
T TIGR03796       494 LIENFSLTLQPGQ--RVALVGGSGSGKSTIAKLVAGLYQ  530 (710)
T ss_pred             cccceeEEEcCCC--EEEEECCCCCCHHHHHHHHhcCCC
Confidence            4444444455565  799999999999999999998753

This protein describes an multidomain ABC transporter subunit that is one of three protein families associated with some regularity with a distinctive family of putative bacteriocins. It includes a bacteriocin-processing peptidase domain at the N-terminus. Model TIGR03793 describes a conserved propeptide region for this bacteriocin family, unusual because it shows obvious homology a region of the enzyme nitrile hydratase up to the classic Gly-Gly cleavage motif. This family is therefore predicted to be a subunit of a bacteriocin processing and export system characteristic to this system that we designate NHPM, Nitrile Hydratase Propeptide Microcin.

>TIGR03797 NHPM_micro_ABC2 NHPM bacteriocin system ABC transporter, ATP-binding protein

Probab=97.84  E-value=4.4e-05  Score=74.47  Aligned_cols=37  Identities=24%  Similarity=0.395  Sum_probs=28.6

Q ss_pred             HHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHc
Q psy879           18 TVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        18 ~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      +++.+.-.++.|.  .+.+.||+|+||||+++.++....
T Consensus       468 vL~~isl~i~~Ge--~vaIvG~sGsGKSTLlklL~gl~~  504 (686)
T TIGR03797       468 ILDDVSLQIEPGE--FVAIVGPSGSGKSTLLRLLLGFET  504 (686)
T ss_pred             ceeeeEEEECCCC--EEEEECCCCCCHHHHHHHHhCCCC
Confidence            4444444455565  799999999999999999999754

Members of this protein family are ABC transporter ATP-binding subunits, part of a three-gene putative bacteriocin transport operon. The other subunits include another ATP-binding subunit (TIGR03796), which has an N-terminal propeptide cleavage domain, and an HlyD homolog (TIGR03794). In a number of genomes, a conserved propeptide sequence with a classic Gly-Gly motif

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=97.83  E-value=0.00011  Score=60.49  Aligned_cols=25  Identities=40%  Similarity=0.505  Sum_probs=21.9

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHcCC
Q psy879           34 IIISGPPGVGKTTTILCLARILLGP   58 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~l~~~   58 (317)
                      +.++||||+|||+++..++......
T Consensus        15 ~~i~G~~GsGKT~l~~~~~~~~~~~   39 (209)
T TIGR02237        15 TQIYGPPGSGKTNICMILAVNAARQ   39 (209)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHhC
Confidence            8999999999999999999876433

This family consists exclusively of archaeal RadB protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and archaeal RadA (TIGR02236).

>TIGR03410 urea_trans_UrtE urea ABC transporter, ATP-binding protein UrtE

Probab=97.83  E-value=4.6e-05  Score=63.85  Aligned_cols=42  Identities=17%  Similarity=0.261  Sum_probs=31.3

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhccC--CceEEEEecCCC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYSN--TTRFALACNNSE  137 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~~--~~~~il~~~~~~  137 (317)
                      +++++++||... |.......+.+.+.+...  ...+|++|++.+
T Consensus       149 ~p~illlDEPt~~LD~~~~~~l~~~l~~~~~~~~~tii~~sH~~~  193 (230)
T TIGR03410       149 RPKLLLLDEPTEGIQPSIIKDIGRVIRRLRAEGGMAILLVEQYLD  193 (230)
T ss_pred             CCCEEEecCCcccCCHHHHHHHHHHHHHHHHcCCcEEEEEeCCHH
Confidence            679999999974 567778888888876543  456777777654

Members of this protein family are ABC transporter ATP-binding subunits associated with urea transport and metabolism. This protein is found in a conserved five-gene transport operon typically found adjacent to urease genes. It was shown in Cyanobacteria that disruption leads to the loss of high-affinity urea transport activity.

>TIGR01448 recD_rel helicase, putative, RecD/TraA family

Probab=97.83  E-value=0.00017  Score=70.25  Aligned_cols=99  Identities=19%  Similarity=0.201  Sum_probs=59.1

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcCh-----------HHHHHHHHHHHhhccc---CCCCcee
Q psy879           33 NIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGI-----------DTVRNKIKMFAQQKVT---LPPGRHK   98 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~-----------~~i~~~~~~~~~~~~~---~~~~~~~   98 (317)
                      ..+++|+|||||||+++++...+........+.-..++ ....           ..+...+.........   .......
T Consensus       340 ~~iitGgpGTGKTt~l~~i~~~~~~~~~~~~v~l~ApT-g~AA~~L~e~~g~~a~Tih~lL~~~~~~~~~~~~~~~~~~~  418 (720)
T TIGR01448       340 VVILTGGPGTGKTTITRAIIELAEELGGLLPVGLAAPT-GRAAKRLGEVTGLTASTIHRLLGYGPDTFRHNHLEDPIDCD  418 (720)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHHHcCCCceEEEEeCc-hHHHHHHHHhcCCccccHHHHhhccCCccchhhhhccccCC
Confidence            59999999999999999999877433211222222222 1111           1222222211110000   0013467


Q ss_pred             EEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecC
Q psy879           99 IVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNN  135 (317)
Q Consensus        99 vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~  135 (317)
                      ++||||+..+.......|++.+   +..+.+|++...
T Consensus       419 llIvDEaSMvd~~~~~~Ll~~~---~~~~rlilvGD~  452 (720)
T TIGR01448       419 LLIVDESSMMDTWLALSLLAAL---PDHARLLLVGDT  452 (720)
T ss_pred             EEEEeccccCCHHHHHHHHHhC---CCCCEEEEECcc
Confidence            9999999999988887777754   466888888754

This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD.

>TIGR02768 TraA_Ti Ti-type conjugative transfer relaxase TraA

Probab=97.83  E-value=0.00011  Score=71.71  Aligned_cols=111  Identities=16%  Similarity=0.202  Sum_probs=65.1

Q ss_pred             HHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCC----------CcChHHHHHHHHHH
Q psy879           16 EDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASN----------DRGIDTVRNKIKMF   85 (317)
Q Consensus        16 ~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~----------~~~~~~i~~~~~~~   85 (317)
                      ++..+.+...+.+++  ..++.|++||||||+++++...+...+  ..+.-+.++.          ......+...+..+
T Consensus       355 ~~Q~~Av~~i~~s~~--~~il~G~aGTGKTtll~~i~~~~~~~g--~~V~~~ApTg~Aa~~L~~~~g~~a~Ti~~~~~~~  430 (744)
T TIGR02768       355 EEQYEAVRHVTGSGD--IAVVVGRAGTGKSTMLKAAREAWEAAG--YRVIGAALSGKAAEGLQAESGIESRTLASLEYAW  430 (744)
T ss_pred             HHHHHHHHHHhcCCC--EEEEEecCCCCHHHHHHHHHHHHHhCC--CeEEEEeCcHHHHHHHHhccCCceeeHHHHHhhh
Confidence            444445555554333  589999999999999999988764322  2233332221          00111111111111


Q ss_pred             HhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEec
Q psy879           86 AQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACN  134 (317)
Q Consensus        86 ~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~  134 (317)
                      ...  ........++||||+..+.......|++....  ..+.+|++..
T Consensus       431 ~~~--~~~~~~~~llIvDEasMv~~~~~~~Ll~~~~~--~~~kliLVGD  475 (744)
T TIGR02768       431 ANG--RDLLSDKDVLVIDEAGMVGSRQMARVLKEAEE--AGAKVVLVGD  475 (744)
T ss_pred             ccC--cccCCCCcEEEEECcccCCHHHHHHHHHHHHh--cCCEEEEECC
Confidence            111  11124678999999999998888888776553  4567888774

This protein contains domains distinctive of a single strand exonuclease (N-terminus, MobA/MobL, pfam03389) as well as a helicase domain (central region, homologous to the corresponding region of the F-type relaxase TraI, TIGR02760). This protein likely fills the same role as TraI(F), nicking (at the oriT site) and unwinding the coiled plasmid prior to conjugative transfer.

>KOG0055|consensus

Probab=97.83  E-value=4.1e-05  Score=76.18  Aligned_cols=35  Identities=31%  Similarity=0.583  Sum_probs=26.9

Q ss_pred             HHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHH
Q psy879           19 VERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        19 ~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .+.+.-.++.|+  .+-|.||+||||||++..+-+..
T Consensus      1006 l~~l~l~i~~Gq--TvALVG~SGsGKSTvI~LLeRfY 1040 (1228)
T KOG0055|consen 1006 LNNLSLSIRAGQ--TVALVGPSGSGKSTVISLLERFY 1040 (1228)
T ss_pred             hcCCcEEecCCC--EEEEECCCCCCHHHHHHHHHHhc
Confidence            333444455565  69999999999999999998874

>PRK13540 cytochrome c biogenesis protein CcmA; Provisional

Probab=97.82  E-value=8.8e-05  Score=60.71  Aligned_cols=42  Identities=12%  Similarity=0.128  Sum_probs=30.9

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhcc-CCceEEEEecCCC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYS-NTTRFALACNNSE  137 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~-~~~~~il~~~~~~  137 (317)
                      +++++++||... +.......+.+.+.+.. ....+|+++++..
T Consensus       145 ~p~~lilDEP~~~LD~~~~~~l~~~l~~~~~~~~tiii~sh~~~  188 (200)
T PRK13540        145 KAKLWLLDEPLVALDELSLLTIITKIQEHRAKGGAVLLTSHQDL  188 (200)
T ss_pred             CCCEEEEeCCCcccCHHHHHHHHHHHHHHHHcCCEEEEEeCCch
Confidence            679999999975 56777888888887642 3456777777654

>PRK13900 type IV secretion system ATPase VirB11; Provisional

Probab=97.82  E-value=0.0014  Score=57.77  Aligned_cols=40  Identities=35%  Similarity=0.283  Sum_probs=32.6

Q ss_pred             CHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHc
Q psy879           15 NEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        15 ~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      ...+.+.|..+++.+.  +++++|++|+||||+++++...+.
T Consensus       146 ~~~~~~~L~~~v~~~~--nili~G~tgSGKTTll~aL~~~ip  185 (332)
T PRK13900        146 EKKIKEFLEHAVISKK--NIIISGGTSTGKTTFTNAALREIP  185 (332)
T ss_pred             hHHHHHHHHHHHHcCC--cEEEECCCCCCHHHHHHHHHhhCC
Confidence            3345566777777766  899999999999999999999873

>PF09848 DUF2075: Uncharacterized conserved protein (DUF2075); InterPro: IPR018647 This domain, found in putative ATP/GTP binding proteins, has no known function

Probab=97.82  E-value=8.2e-05  Score=66.49  Aligned_cols=87  Identities=24%  Similarity=0.293  Sum_probs=51.6

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH--cCCCCCCceEEecCCCCcChHHHHHHHH----------------HHHhhc--ccC
Q psy879           33 NIIISGPPGVGKTTTILCLARIL--LGPSFKDAVLELNASNDRGIDTVRNKIK----------------MFAQQK--VTL   92 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l--~~~~~~~~~~~~~~~~~~~~~~i~~~~~----------------~~~~~~--~~~   92 (317)
                      .+++.|.||||||.++..++..+  ........++..|...   ...++..+.                .+....  ...
T Consensus         3 v~~I~G~aGTGKTvla~~l~~~l~~~~~~~~~~~l~~n~~l---~~~l~~~l~~~~~~~~~~~~~~~~~~~i~~~~~~~~   79 (352)
T PF09848_consen    3 VILITGGAGTGKTVLALNLAKELQNSEEGKKVLYLCGNHPL---RNKLREQLAKKYNPKLKKSDFRKPTSFINNYSESDK   79 (352)
T ss_pred             EEEEEecCCcCHHHHHHHHHHHhhccccCCceEEEEecchH---HHHHHHHHhhhcccchhhhhhhhhHHHHhhcccccc
Confidence            38999999999999999999998  3333333333333321   111111111                111100  001


Q ss_pred             CCCceeEEEEeCCCCCCHH--------HHHHHHHHhhh
Q psy879           93 PPGRHKIVILDEADSMTDG--------AQQALRRTMEI  122 (317)
Q Consensus        93 ~~~~~~vliiDE~d~l~~~--------~~~~ll~~le~  122 (317)
                      ......+||+||++.+...        ..+.|..++..
T Consensus        80 ~~~~~DviivDEAqrl~~~~~~~~~~~~~~~L~~i~~~  117 (352)
T PF09848_consen   80 EKNKYDVIIVDEAQRLRTKGDQYNNFSEPNQLDEIIKR  117 (352)
T ss_pred             cCCcCCEEEEehhHhhhhccccccccccHHHHHHHHhc
Confidence            2256889999999999873        24667777776

It is found in some proteins described as Schlafen family members, which may have a role in hematopoeitic cell differentiation [].

>PF00519 PPV_E1_C: Papillomavirus helicase; InterPro: IPR001177 Papillomaviruses are a large family of DNA tumour viruses which give rise to warts in their host species

Probab=97.81  E-value=7e-05  Score=65.66  Aligned_cols=115  Identities=23%  Similarity=0.301  Sum_probs=64.7

Q ss_pred             HHHHHHHhcCCCce-EEEECCCCCCHHHHHHHHHHHHcCCCCCCceEE-ecCCCCcChHHHHHHHHHHHhhcccCCCCce
Q psy879           20 ERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARILLGPSFKDAVLE-LNASNDRGIDTVRNKIKMFAQQKVTLPPGRH   97 (317)
Q Consensus        20 ~~l~~~l~~~~~~~-~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~-~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~   97 (317)
                      ..++.++++-.-.+ ++|||||+||||..+..+.+.+.|.     ++. .|..+....            .|    -.+.
T Consensus       250 ~~lk~~Lkg~PKKnClvi~GPPdTGKS~F~~SLi~Fl~Gk-----ViSf~Ns~ShFWL------------qP----L~d~  308 (432)
T PF00519_consen  250 IALKQFLKGIPKKNCLVIYGPPDTGKSMFCMSLIKFLKGK-----VISFVNSKSHFWL------------QP----LADA  308 (432)
T ss_dssp             HHHHHHHHTBTTSSEEEEESSCCCSHHHHHHHHHHHHTSE-----EE-GGGTTSCGGG------------GG----GCT-
T ss_pred             HHHHHHHhCCCcccEEEEECCCCCchhHHHHHHHHHhCCE-----EEEecCCCCcccc------------cc----hhcC
Confidence            34555665422234 9999999999999999999998543     333 333222211            11    2578


Q ss_pred             eEEEEeCCCCCCHHHHH-HHHHHhhhcc-------------CCceEEEEecCC---CcCchhHhhhcceeeecCC
Q psy879           98 KIVILDEADSMTDGAQQ-ALRRTMEIYS-------------NTTRFALACNNS---EKIIEPIQSRCAMLRYNKL  155 (317)
Q Consensus        98 ~vliiDE~d~l~~~~~~-~ll~~le~~~-------------~~~~~il~~~~~---~~l~~~i~sR~~~i~f~~~  155 (317)
                      ++.+||++..-.=+-.+ -|...++..+             .-..+++|||..   +.-..-+.||...++|+.+
T Consensus       309 Ki~llDDAT~~cW~Y~D~ylRNaLDGN~vsiD~KHkap~Qik~PPLlITsN~dv~~~~~~~YLhSRi~~f~F~n~  383 (432)
T PF00519_consen  309 KIALLDDATYPCWDYIDTYLRNALDGNPVSIDCKHKAPVQIKCPPLLITSNIDVKKDDRWKYLHSRITCFEFPNP  383 (432)
T ss_dssp             SSEEEEEE-HHHHHHHHHHTHHHHCTSEEEEEESSSEEEEEE---EEEEESS-TTTSCCCHHHCTTEEEEE--S-
T ss_pred             cEEEEcCCcccHHHHHHHHHHhccCCCeeeeeccCCCceEeecCceEEecCCCCCcchhhhhhhheEEEEEcCCc
Confidence            89999998543222222 2344444211             112367777753   3456888999999999854

The helicase E1 protein is an ATP-dependent DNA helicase required for initiation of viral DNA replication []. It forms a complex with the viral E2 protein, which is a site-specific DNA-binding transcriptional activator. The E1-E2 complex binds to the replication origin which contains binding sites for both proteins []. The E1 protein is a 70 kDa polypeptide with a central DNA-binding domain and a C-terminal ATPase/helicase domain. It binds specific 18 bp DNA sequences at the origin of replication, melts the DNA duplex and functions as a 3' to 5' helicase []. In addition to E2 it also interacts with DNA polymerase alpha and replication protein A to effect DNA replication. The DNA-binding domain forms a five-stranded antiparallel beta sheet bordered by four loosely packed alpha helices on one side and two tightly packed helices on the other []. Two structural modules within this domain, an extended loop and a helix, contain conserved residues and are critical for DNA binding. In solution E1 is a monomer, but binds DNA as a dimer. Recruitment of more E1 subunits to the complex leads to melting of the origin and ultimately to the formation of an E1 hexamer with helicase activity []. The entry represents the C-terminal region of E1, containing both the DNA-binding and ATPase/helical domains.; GO: 0003677 DNA binding, 0004003 ATP-dependent DNA helicase activity, 0005524 ATP binding, 0006260 DNA replication; PDB: 1TUE_K 1R9W_A 2V9P_B 2GXA_I 1KSX_J 1KSY_A 1F08_B.

>PRK14974 cell division protein FtsY; Provisional

Probab=97.81  E-value=0.00027  Score=62.16  Aligned_cols=26  Identities=46%  Similarity=0.469  Sum_probs=22.7

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHcCC
Q psy879           33 NIIISGPPGVGKTTTILCLARILLGP   58 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~~~   58 (317)
                      .++|.||+|+||||++..++..+...
T Consensus       142 vi~~~G~~GvGKTTtiakLA~~l~~~  167 (336)
T PRK14974        142 VIVFVGVNGTGKTTTIAKLAYYLKKN  167 (336)
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHHHc
Confidence            48999999999999999999887543

>cd00046 DEXDc DEAD-like helicases superfamily

Probab=97.81  E-value=0.00013  Score=55.39  Aligned_cols=25  Identities=32%  Similarity=0.523  Sum_probs=22.1

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHcC
Q psy879           33 NIIISGPPGVGKTTTILCLARILLG   57 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~~   57 (317)
                      +++++||+|+|||+++..++..+..
T Consensus         2 ~~~i~~~~G~GKT~~~~~~~~~~~~   26 (144)
T cd00046           2 DVLLAAPTGSGKTLAALLPILELLD   26 (144)
T ss_pred             CEEEECCCCCchhHHHHHHHHHHHh
Confidence            6899999999999999999888753

A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.

>TIGR01193 bacteriocin_ABC ABC-type bacteriocin transporter

Probab=97.81  E-value=3.2e-05  Score=75.65  Aligned_cols=37  Identities=19%  Similarity=0.247  Sum_probs=28.2

Q ss_pred             HHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHc
Q psy879           18 TVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        18 ~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      +++.+.-.++.|.  .+.+.||+|+||||+++.++....
T Consensus       489 iL~~isl~i~~G~--~vaIvG~SGsGKSTLlklL~gl~~  525 (708)
T TIGR01193       489 ILSDISLTIKMNS--KTTIVGMSGSGKSTLAKLLVGFFQ  525 (708)
T ss_pred             ceeceeEEECCCC--EEEEECCCCCCHHHHHHHHhccCC
Confidence            3444444455565  799999999999999999998753

This model describes ABC-type bacteriocin transporter. The amino terminal domain (pfam03412) processes the N-terminal leader peptide from the bacteriocin while C-terminal domains resemble ABC transporter membrane protein and ATP-binding cassette domain. In general, bacteriocins are agents which are responsible for killing or inhibiting the closely related species or even different strains of the same species. Bacteriocins are usually encoded by bacterial plasmids. Bacteriocins are named after the species and hence in literature one encounters various names e.g., leucocin from Leuconostic geldium; pedicocin from Pedicoccus acidilactici; sakacin from Lactobacillus sake etc.

>PLN03232 ABC transporter C family member; Provisional

Probab=97.81  E-value=2.2e-05  Score=82.43  Aligned_cols=38  Identities=26%  Similarity=0.444  Sum_probs=30.1

Q ss_pred             HHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHc
Q psy879           17 DTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        17 ~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      .+++.+.-.++.|.  .+.+.|++|+||||+++.+.+.+.
T Consensus      1250 ~vL~~isl~I~~Ge--kvaIVG~SGSGKSTL~~lL~rl~~ 1287 (1495)
T PLN03232       1250 PVLHGLSFFVSPSE--KVGVVGRTGAGKSSMLNALFRIVE 1287 (1495)
T ss_pred             cccccceEEEcCCC--EEEEECCCCCCHHHHHHHHhCCCc
Confidence            35555555566666  799999999999999999999753

>PLN03130 ABC transporter C family member; Provisional

Probab=97.81  E-value=2.5e-05  Score=82.35  Aligned_cols=37  Identities=27%  Similarity=0.365  Sum_probs=29.6

Q ss_pred             HHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHc
Q psy879           18 TVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        18 ~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      +++.+.-.++.|.  .+.|.|++|+||||+++.+.+.+.
T Consensus      1254 VL~~is~~I~~Ge--kVaIVGrSGSGKSTLl~lL~rl~~ 1290 (1622)
T PLN03130       1254 VLHGLSFEISPSE--KVGIVGRTGAGKSSMLNALFRIVE 1290 (1622)
T ss_pred             eecceeEEEcCCC--EEEEECCCCCCHHHHHHHHhCcCC
Confidence            4555555566666  799999999999999999999753

>PRK10247 putative ABC transporter ATP-binding protein YbbL; Provisional

Probab=97.80  E-value=6.9e-05  Score=62.55  Aligned_cols=43  Identities=12%  Similarity=0.336  Sum_probs=31.7

Q ss_pred             ceeEEEEeCCC-CCCHHHHHHHHHHhhhcc--CCceEEEEecCCCc
Q psy879           96 RHKIVILDEAD-SMTDGAQQALRRTMEIYS--NTTRFALACNNSEK  138 (317)
Q Consensus        96 ~~~vliiDE~d-~l~~~~~~~ll~~le~~~--~~~~~il~~~~~~~  138 (317)
                      ++.++++||.. .|.......+.+.+.+..  ....+|+++++.+.
T Consensus       155 ~p~llllDEPt~~LD~~~~~~l~~~l~~~~~~~~~tvii~sh~~~~  200 (225)
T PRK10247        155 MPKVLLLDEITSALDESNKHNVNEIIHRYVREQNIAVLWVTHDKDE  200 (225)
T ss_pred             CCCEEEEeCCcccCCHHHHHHHHHHHHHHHHhcCCEEEEEECChHH
Confidence            67999999997 466777888888887653  24567777777544

>cd03268 ABC_BcrA_bacitracin_resist The BcrA subfamily represents ABC transporters involved in peptide antibiotic resistance

Probab=97.80  E-value=7.6e-05  Score=61.47  Aligned_cols=42  Identities=14%  Similarity=0.221  Sum_probs=30.2

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhcc-CCceEEEEecCCC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYS-NTTRFALACNNSE  137 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~-~~~~~il~~~~~~  137 (317)
                      +++++++||... |.......+.+++.+.. ....+|++|++..
T Consensus       144 ~p~llllDEPt~~LD~~~~~~l~~~l~~~~~~~~tii~~tH~~~  187 (208)
T cd03268         144 NPDLLILDEPTNGLDPDGIKELRELILSLRDQGITVLISSHLLS  187 (208)
T ss_pred             CCCEEEECCCcccCCHHHHHHHHHHHHHHHHCCCEEEEEcCCHH
Confidence            678999999975 56777888888887653 2455777776643

Bacitracin is a dodecapeptide antibiotic produced by B. licheniformis and B. subtilis. The synthesis of bacitracin is non-ribosomally catalyzed by a multienzyme complex BcrABC. Bacitracin has potent antibiotic activity against gram-positive bacteria. The inhibition of peptidoglycan biosynthesis is the best characterized bacterial effect of bacitracin. The bacitracin resistance of B. licheniformis is mediated by the ABC transporter Bcr which is composed of two identical BcrA ATP-binding subunits and one each of the integral membrane proteins, BcrB and BcrC. B. subtilis cells carrying bcr genes on high-copy number plasmids develop collateral detergent sensitivity, a similar phenomenon in human cells with overexpressed multi-drug resistance P-glycoprotein.

>PRK06067 flagellar accessory protein FlaH; Validated

Probab=97.79  E-value=0.00046  Score=57.95  Aligned_cols=34  Identities=24%  Similarity=0.163  Sum_probs=25.7

Q ss_pred             HHHHHhcCCCce--EEEECCCCCCHHHHHHHHHHHH
Q psy879           22 LKVFSSSGNVPN--IIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        22 l~~~l~~~~~~~--~ll~G~~G~GKt~la~~la~~l   55 (317)
                      |-..+.+|-++.  ++++|+||+|||+++..++...
T Consensus        14 LD~~l~gG~~~g~~~~i~G~~GsGKt~l~~~~~~~~   49 (234)
T PRK06067         14 LDRKLGGGIPFPSLILIEGDHGTGKSVLSQQFVYGA   49 (234)
T ss_pred             HHHhhCCCCcCCcEEEEECCCCCChHHHHHHHHHHH
Confidence            445555554333  8999999999999999997654

>TIGR01447 recD exodeoxyribonuclease V, alpha subunit

Probab=97.79  E-value=0.00029  Score=66.79  Aligned_cols=37  Identities=16%  Similarity=0.259  Sum_probs=29.7

Q ss_pred             ceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecC
Q psy879           96 RHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNN  135 (317)
Q Consensus        96 ~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~  135 (317)
                      ...+|||||+..+.......|++.+   ++.+.+|++...
T Consensus       259 ~~dvlIiDEaSMvd~~l~~~ll~al---~~~~rlIlvGD~  295 (586)
T TIGR01447       259 PLDVLVVDEASMVDLPLMAKLLKAL---PPNTKLILLGDK  295 (586)
T ss_pred             cccEEEEcccccCCHHHHHHHHHhc---CCCCEEEEECCh
Confidence            3579999999999988777777665   567889998765

This family describes the exodeoxyribonuclease V alpha subunit, RecD. RecD is part of a RecBCD complex. A related family in the Gram-positive bacteria separates in a phylogenetic tree, has an additional N-terminal extension of about 200 residues, and is not supported as a member of a RecBCD complex by neighboring genes. The related family is consequently described by a different model.

>COG3839 MalK ABC-type sugar transport systems, ATPase components [Carbohydrate transport and metabolism]

Probab=97.79  E-value=0.00015  Score=63.37  Aligned_cols=106  Identities=11%  Similarity=0.105  Sum_probs=62.1

Q ss_pred             ecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhhCCCcccHHHHHhhcCCCCH----HHHHH
Q psy879          152 YNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHP----LAVKE  227 (317)
Q Consensus       152 f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~~~~~i~~~~v~~~~~~~~~----~~i~~  227 (317)
                      ....+.+++.+.+...++.-++   +..++......+|.-|+-+.+.++.+...+..-.|+-..-++....    ..+.+
T Consensus       102 ~~~~~k~ei~~rV~eva~~L~l---~~lL~r~P~~LSGGQrQRVAlaRAlVr~P~v~L~DEPlSnLDa~lR~~mr~ei~~  178 (338)
T COG3839         102 LRGVPKAEIDKRVKEVAKLLGL---EHLLNRKPLQLSGGQRQRVALARALVRKPKVFLLDEPLSNLDAKLRVLMRSEIKK  178 (338)
T ss_pred             hCCCchHHHHHHHHHHHHHcCC---hhHHhcCcccCChhhHHHHHHHHHHhcCCCEEEecCchhHhhHHHHHHHHHHHHH
Confidence            3456788999999998887665   4556666666667788888888877765554433333222222111    12333


Q ss_pred             HHHHH------hcCCHHHHHHHHHHH--HHcC-----CCHHHHHHH
Q psy879          228 MLLNC------VEGNMKDSYKIIHHL--YKLG-----YAPEDIIGN  260 (317)
Q Consensus       228 l~~~~------~~~~~~~~~~~~~~l--~~~~-----~~~~~i~~~  260 (317)
                      +.+.+      ..+|..+|+.+-+..  +..|     -+|.+++..
T Consensus       179 lh~~l~~T~IYVTHDq~EAmtladri~Vm~~G~i~Q~g~p~ely~~  224 (338)
T COG3839         179 LHERLGTTTIYVTHDQVEAMTLADRIVVMNDGRIQQVGTPLELYER  224 (338)
T ss_pred             HHHhcCCcEEEEcCCHHHHHhhCCEEEEEeCCeeeecCChHHHhhC
Confidence            33322      246788888876554  2233     366666655

>cd03251 ABCC_MsbA MsbA is an essential ABC transporter, closely related to eukaryotic MDR proteins

Probab=97.78  E-value=7e-05  Score=62.91  Aligned_cols=44  Identities=20%  Similarity=0.284  Sum_probs=33.4

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhccCCceEEEEecCCCcC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYSNTTRFALACNNSEKI  139 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l  139 (317)
                      +++++++||... +.......+.+.+.+......+|+++++...+
T Consensus       156 ~p~lllLDEP~~~LD~~~~~~l~~~l~~~~~~~tii~~sh~~~~~  200 (234)
T cd03251         156 DPPILILDEATSALDTESERLVQAALERLMKNRTTFVIAHRLSTI  200 (234)
T ss_pred             CCCEEEEeCccccCCHHHHHHHHHHHHHhcCCCEEEEEecCHHHH
Confidence            678999999974 66777888888887765556688888776544

ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>PF10236 DAP3: Mitochondrial ribosomal death-associated protein 3; InterPro: IPR019368 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=97.78  E-value=0.001  Score=58.20  Aligned_cols=47  Identities=13%  Similarity=0.147  Sum_probs=37.1

Q ss_pred             eeeecCCCHHHHHHHHHHHHHHcCC---CCCHHHHHHHHHhcCCCHHHHH
Q psy879          149 MLRYNKLTDAQLLSKVIEICEKENI---SHTNDGLEAIVFTAQGDMRQAL  195 (317)
Q Consensus       149 ~i~f~~~~~~~~~~~l~~~~~~~~~---~i~~~~~~~l~~~~~gd~r~~i  195 (317)
                      .++.++++.+|....+.......-+   ..++...+.+...++|++|+..
T Consensus       258 ~i~v~~~s~~E~~~ll~yy~~~~~l~~~~~~~~~~e~~~~~s~GNp~el~  307 (309)
T PF10236_consen  258 PIEVPRLSKEEARSLLEYYADSGWLRSRVDEELVLEKLFLSSNGNPRELE  307 (309)
T ss_pred             eEEeCCCCHHHHHHHHHHHHHCCccccCCCCHHHHHHHHHhcCCCHHHhc
Confidence            7899999999999999987765333   2345667788888899999764

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents a family of conserved proteins which were originally described as death-associated-protein-3 (DAP-3). The proteins carry a P-loop DNA-binding motif, and induce apoptosis []. DAP3 has been shown to be a pro-apoptotic factor in the mitochondrial matrix [] and to be crucial for mitochondrial biogenesis and so has also been designated as MRP-S29 (mitochondrial ribosomal protein subunit 29).

>PRK13648 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=97.78  E-value=5.5e-05  Score=64.97  Aligned_cols=44  Identities=20%  Similarity=0.254  Sum_probs=32.2

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhccC--CceEEEEecCCCcC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYSN--TTRFALACNNSEKI  139 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~~--~~~~il~~~~~~~l  139 (317)
                      +++++++||... +.......+.+++.+...  ...+|++|++...+
T Consensus       160 ~p~lllLDEPt~~LD~~~~~~l~~~L~~~~~~~~~tiiivtH~~~~~  206 (269)
T PRK13648        160 NPSVIILDEATSMLDPDARQNLLDLVRKVKSEHNITIISITHDLSEA  206 (269)
T ss_pred             CCCEEEEeCCcccCCHHHHHHHHHHHHHHHHhcCCEEEEEecCchHH
Confidence            679999999975 566778888888776532  45677888776544

>cd03225 ABC_cobalt_CbiO_domain1 Domain I of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota

Probab=97.77  E-value=6.9e-05  Score=61.88  Aligned_cols=42  Identities=12%  Similarity=0.283  Sum_probs=31.1

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhccC-CceEEEEecCCC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYSN-TTRFALACNNSE  137 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~~-~~~~il~~~~~~  137 (317)
                      +++++++||... +.......+.+.+.+... ...+|++|++..
T Consensus       152 ~p~llllDEPt~~LD~~~~~~~~~~l~~~~~~~~tvi~~sH~~~  195 (211)
T cd03225         152 DPDILLLDEPTAGLDPAGRRELLELLKKLKAEGKTIIIVTHDLD  195 (211)
T ss_pred             CCCEEEEcCCcccCCHHHHHHHHHHHHHHHHcCCEEEEEeCCHH
Confidence            679999999974 667778888888876543 456777777643

The transition metal cobalt is an essential component of many enzymes and must be transported into cells in appropriate amounts when needed. This ABC transport system of the CbiMNQO family is involved in cobalt transport in association with the cobalamin (vitamin B12) biosynthetic pathways. Most of cobalt (Cbi) transport systems possess a separate CbiN component, the cobalt-binding periplasmic protein, and they are encoded by the conserved gene cluster cbiMNQO. Both the CbiM and CbiQ proteins are integral cytoplasmic membrane proteins, and the CbiO protein has the linker peptide and the Walker A and B motifs commonly found in the ATPase components of the ABC-type transport systems.

>TIGR01188 drrA daunorubicin resistance ABC transporter ATP-binding subunit

Probab=97.77  E-value=6.2e-05  Score=65.79  Aligned_cols=42  Identities=14%  Similarity=0.268  Sum_probs=31.0

Q ss_pred             ceeEEEEeCCC-CCCHHHHHHHHHHhhhccC-CceEEEEecCCC
Q psy879           96 RHKIVILDEAD-SMTDGAQQALRRTMEIYSN-TTRFALACNNSE  137 (317)
Q Consensus        96 ~~~vliiDE~d-~l~~~~~~~ll~~le~~~~-~~~~il~~~~~~  137 (317)
                      +++++++||.. .|.+.....+.+.+.+... ...+|++|++.+
T Consensus       142 ~p~lllLDEPt~gLD~~~~~~l~~~l~~~~~~g~tvi~~sH~~~  185 (302)
T TIGR01188       142 QPDVLFLDEPTTGLDPRTRRAIWDYIRALKEEGVTILLTTHYME  185 (302)
T ss_pred             CCCEEEEeCCCcCCCHHHHHHHHHHHHHHHhCCCEEEEECCCHH
Confidence            68999999997 4677778888888876542 455777777643

This model describes daunorubicin resistance ABC transporter, ATP binding subunit in bacteria and archaea. This model is restricted in its scope to preferentially recognize the ATP binding subunit associated with effux of the drug, daunorubicin. This transport system belong to the larger ATP-Binding Cassette (ABC) transporter superfamily. The characteristic feature of these transporter is the obligatory coupling of ATP hydrolysis to substrate translocation. The minimal configuration of bacterial ABC transport system: an ATPase or ATP binding subunit; An integral membrane protein; a hydrophilic polypetpide, which likely functions as substrate binding protein. In eukaryotes proteins of similar function include p-gyco proteins, multidrug resistance protein etc.

>TIGR00958 3a01208 Conjugate Transporter-2 (CT2) Family protein

Probab=97.77  E-value=5.7e-05  Score=73.83  Aligned_cols=37  Identities=24%  Similarity=0.427  Sum_probs=28.7

Q ss_pred             HHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHc
Q psy879           18 TVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        18 ~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      +++.+.-.++.|.  .+.+.||+|+||||+++.+++.+.
T Consensus       496 vL~~isl~i~~Ge--~vaIvG~SGsGKSTLl~lL~gl~~  532 (711)
T TIGR00958       496 VLKGLTFTLHPGE--VVALVGPSGSGKSTVAALLQNLYQ  532 (711)
T ss_pred             cccCceEEEcCCC--EEEEECCCCCCHHHHHHHHHhccC
Confidence            4444444455665  699999999999999999999764

>PF05272 VirE: Virulence-associated protein E; InterPro: IPR007936 This family contains several bacterial virulence-associated protein E like proteins

Probab=97.77  E-value=0.00013  Score=59.35  Aligned_cols=99  Identities=21%  Similarity=0.251  Sum_probs=66.8

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHH
Q psy879           34 IIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQ  113 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~  113 (317)
                      ++|.|+-|+|||+..+.+........       ...  ....+.....             ...-++.+||++.+.+...
T Consensus        55 lvl~G~QG~GKStf~~~L~~~~~~d~-------~~~--~~~kd~~~~l-------------~~~~iveldEl~~~~k~~~  112 (198)
T PF05272_consen   55 LVLVGKQGIGKSTFFRKLGPEYFSDS-------IND--FDDKDFLEQL-------------QGKWIVELDELDGLSKKDV  112 (198)
T ss_pred             eeEecCCcccHHHHHHHHhHHhccCc-------ccc--CCCcHHHHHH-------------HHhHheeHHHHhhcchhhH
Confidence            89999999999999999966532211       111  1112222211             1345899999999998888


Q ss_pred             HHHHHHhh---------------hccCCceEEEEecCCCcC-chhHhhhcceeeecC
Q psy879          114 QALRRTME---------------IYSNTTRFALACNNSEKI-IEPIQSRCAMLRYNK  154 (317)
Q Consensus       114 ~~ll~~le---------------~~~~~~~~il~~~~~~~l-~~~i~sR~~~i~f~~  154 (317)
                      +.|..++.               +.+..++||.+||..+-+ +++=-+|+.++.+..
T Consensus       113 ~~lK~~iT~~~~~~R~pY~~~~~~~~R~~~figTtN~~~~L~D~TGnRRf~~v~v~~  169 (198)
T PF05272_consen  113 EALKSFITRRTDTYRPPYGRDPEEFPRRAVFIGTTNDDDFLKDPTGNRRFWPVEVSK  169 (198)
T ss_pred             HHHHHHhcccceeeecCCcCcceeeceeEEEEeccCCcceeeCCCCCeEEEEEEEcC
Confidence            88877775               335667788889886643 345567788887776

>COG1123 ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]

Probab=97.77  E-value=0.00034  Score=64.55  Aligned_cols=170  Identities=18%  Similarity=0.153  Sum_probs=102.4

Q ss_pred             HHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHHHHHHHhhcccCCCCcee
Q psy879           19 VERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHK   98 (317)
Q Consensus        19 ~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~   98 (317)
                      ++.+.--+..|.  .+-|.|++||||||+++.++..+. +..+...+..... .......+.    ..        ....
T Consensus       307 v~~VSf~l~~GE--~lglVGeSGsGKSTlar~i~gL~~-P~~G~i~~~g~~~-~~~~~~~~~----~r--------~~~Q  370 (539)
T COG1123         307 VDDVSFDLREGE--TLGLVGESGSGKSTLARILAGLLP-PSSGSIIFDGQDL-DLTGGELRR----LR--------RRIQ  370 (539)
T ss_pred             eeeeeeEecCCC--EEEEECCCCCCHHHHHHHHhCCCC-CCCceEEEeCccc-ccccchhhh----hh--------hheE
Confidence            333444455666  699999999999999999999753 3333323222211 111111111    00        2445


Q ss_pred             EEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcCchhHhhhcceeeec-CCCHHHHHHHHHHHHHHcCCCCCH
Q psy879           99 IVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYN-KLTDAQLLSKVIEICEKENISHTN  177 (317)
Q Consensus        99 vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~~~i~sR~~~i~f~-~~~~~~~~~~l~~~~~~~~~~i~~  177 (317)
                      ++|-|-...|++..  .+..++.+|-                          .+. .....+..+.+...+..-  .+++
T Consensus       371 mvFQdp~~SLnPr~--tV~~~i~epL--------------------------~~~~~~~~~~~~~rv~~ll~~V--gL~~  420 (539)
T COG1123         371 MVFQDPYSSLNPRM--TVGDILAEPL--------------------------RIHGGGSGAERRARVAELLELV--GLPP  420 (539)
T ss_pred             EEEeCcccccCccc--cHHHHHHhHH--------------------------hhhcccchHHHHHHHHHHHHHc--CCCH
Confidence            67777666666531  1222222211                          111 122344444444444433  4557


Q ss_pred             HHHHHHHHhcCCCHHHHHHHHHHhhhCCCcccHHHHHhhcCCCCHHHHHHHHHHHhc
Q psy879          178 DGLEAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEMLLNCVE  234 (317)
Q Consensus       178 ~~~~~l~~~~~gd~r~~i~~l~~~~~~~~~i~~~~v~~~~~~~~~~~i~~l~~~~~~  234 (317)
                      +.+.......+|.-|+-+.+.++.+...+.+..|+...+++.+....+.+++..+..
T Consensus       421 ~~l~ryP~elSGGQrQRvaIARALa~~P~lli~DEp~SaLDvsvqa~VlnLl~~lq~  477 (539)
T COG1123         421 EFLDRYPHELSGGQRQRVAIARALALEPKLLILDEPVSALDVSVQAQVLNLLKDLQE  477 (539)
T ss_pred             HHHhcCchhcCcchhHHHHHHHHHhcCCCEEEecCCccccCHHHHHHHHHHHHHHHH
Confidence            777777777778899999999999999999989888888888888777777776653

>cd03244 ABCC_MRP_domain2 Domain 2 of the ABC subfamily C

Probab=97.76  E-value=7e-05  Score=62.31  Aligned_cols=43  Identities=16%  Similarity=0.272  Sum_probs=32.6

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhccCCceEEEEecCCCc
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYSNTTRFALACNNSEK  138 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~~~~~~il~~~~~~~  138 (317)
                      ++.++++||... +.......+.+.+.+......+|+++++...
T Consensus       157 ~p~llllDEP~~~LD~~~~~~l~~~l~~~~~~~tii~~sh~~~~  200 (221)
T cd03244         157 KSKILVLDEATASVDPETDALIQKTIREAFKDCTVLTIAHRLDT  200 (221)
T ss_pred             CCCEEEEeCccccCCHHHHHHHHHHHHHhcCCCEEEEEeCCHHH
Confidence            678999999974 5677788888888765555667788877543

This family is also known as MRP (mulrtidrug resisitance-associated protein). Some of the MRP members have five additional transmembrane segments in their N-terminus, but the function of these additional membrane-spanning domains is not clear. The MRP was found in the multidrug-resistance lung cancer cell in which p-glycoprotein was not overexpressed. MRP exports glutathione by drug stimulation, as well as, certain substrates in conjugated forms with anions, such as glutathione, glucuronate, and sulfate.

>PRK13635 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=97.76  E-value=6.1e-05  Score=65.02  Aligned_cols=44  Identities=18%  Similarity=0.268  Sum_probs=33.1

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhccC--CceEEEEecCCCcC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYSN--TTRFALACNNSEKI  139 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~~--~~~~il~~~~~~~l  139 (317)
                      +++++++||... +....+..+.+.+.+...  .+.+|++|++...+
T Consensus       158 ~p~lllLDEPt~gLD~~~~~~l~~~l~~l~~~~~~tilivsH~~~~~  204 (279)
T PRK13635        158 QPDIIILDEATSMLDPRGRREVLETVRQLKEQKGITVLSITHDLDEA  204 (279)
T ss_pred             CCCEEEEeCCcccCCHHHHHHHHHHHHHHHHcCCCEEEEEecCHHHH
Confidence            689999999975 667778888888876543  46677788776543

>PF05707 Zot: Zonular occludens toxin (Zot); InterPro: IPR008900 This entry consists of bacterial and viral proteins which are very similar to the Zonular occludens toxin (Zot)

Probab=97.76  E-value=3.3e-05  Score=62.85  Aligned_cols=60  Identities=13%  Similarity=0.173  Sum_probs=37.6

Q ss_pred             ceeEEEEeCCCCCCHHHH------HHHHHHhhh-ccCCceEEEEecCCCcCchhHhhhcce-eeecCC
Q psy879           96 RHKIVILDEADSMTDGAQ------QALRRTMEI-YSNTTRFALACNNSEKIIEPIQSRCAM-LRYNKL  155 (317)
Q Consensus        96 ~~~vliiDE~d~l~~~~~------~~ll~~le~-~~~~~~~il~~~~~~~l~~~i~sR~~~-i~f~~~  155 (317)
                      ...++||||+....+...      ....+.+.. .+...-++++|.++..+.+.++..+.. +++..+
T Consensus        79 ~~~liviDEa~~~~~~r~~~~~~~~~~~~~l~~hRh~g~diiliTQ~~~~id~~ir~lve~~~~~~k~  146 (193)
T PF05707_consen   79 KGSLIVIDEAQNFFPSRSWKGKKVPEIIEFLAQHRHYGWDIILITQSPSQIDKFIRDLVEYHYHCRKL  146 (193)
T ss_dssp             TT-EEEETTGGGTSB---T-T----HHHHGGGGCCCTT-EEEEEES-GGGB-HHHHCCEEEEEEEEE-
T ss_pred             CCcEEEEECChhhcCCCccccccchHHHHHHHHhCcCCcEEEEEeCCHHHHhHHHHHHHheEEEEEee
Confidence            578999999998754321      233355554 345567999999999999999887766 555544

Zot is elaborated by bacteriophage present in toxigenic strains of Vibrio cholerae. Zot is a single polypeptide chain of 44.8 kDa, with the ability to reversibly alter intestinal epithelial tight junctions, allowing the passage of macromolecules through mucosal barriers.; PDB: 2R2A_B.

>cd03252 ABCC_Hemolysin The ABC-transporter hemolysin B is a central component of the secretion machinery that translocates the toxin, hemolysin A, in a Sec-independent fashion across both membranes of E

Probab=97.76  E-value=6.6e-05  Score=63.19  Aligned_cols=44  Identities=20%  Similarity=0.317  Sum_probs=33.4

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhccCCceEEEEecCCCcC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYSNTTRFALACNNSEKI  139 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l  139 (317)
                      +++++++||... +.......+.+.+.+......+|+++++...+
T Consensus       156 ~p~llllDEP~~~LD~~~~~~l~~~l~~~~~~~tiii~sH~~~~~  200 (237)
T cd03252         156 NPRILIFDEATSALDYESEHAIMRNMHDICAGRTVIIIAHRLSTV  200 (237)
T ss_pred             CCCEEEEeCCcccCCHHHHHHHHHHHHHhcCCCEEEEEeCCHHHH
Confidence            679999999975 56777888888887665556688888776543

coli. The hemolysin A (HlyA) transport machinery is composed of the ATP-binding cassette (ABC) transporter HlyB located in the inner membrane, hemolysin D (HlyD), also anchored in the inner membrane, and TolC, which resides in the outer membrane. HlyD apparently forms a continuous channel that bridges the entire periplasm, interacting with TolC and HlyB. This arrangement prevents the appearance of periplasmic intermediates of HlyA during substrate transport. Little is known about the molecular details of HlyA transport, but it is evident that ATP-hydrolysis by the ABC-transporter HlyB is a necessary source of energy.

>TIGR00960 3a0501s02 Type II (General) Secretory Pathway (IISP) Family protein

Probab=97.76  E-value=6.1e-05  Score=62.44  Aligned_cols=42  Identities=14%  Similarity=0.298  Sum_probs=30.6

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhcc-CCceEEEEecCCC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYS-NTTRFALACNNSE  137 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~-~~~~~il~~~~~~  137 (317)
                      +++++++||... +.......+.+.+.+.. ....+|++|++.+
T Consensus       156 ~p~llllDEPt~~LD~~~~~~l~~~l~~~~~~~~tii~vsH~~~  199 (216)
T TIGR00960       156 KPPLLLADEPTGNLDPELSRDIMRLFEEFNRRGTTVLVATHDIN  199 (216)
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHHHHHHHCCCEEEEEeCCHH
Confidence            679999999975 56677778888777653 2455777887743

>TIGR03522 GldA_ABC_ATP gliding motility-associated ABC transporter ATP-binding subunit GldA

Probab=97.75  E-value=6.7e-05  Score=65.51  Aligned_cols=42  Identities=17%  Similarity=0.292  Sum_probs=31.8

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhccCCceEEEEecCCC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYSNTTRFALACNNSE  137 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~~~~~~il~~~~~~  137 (317)
                      +++++++||... |.+.....+.+.+.+......+|++|+..+
T Consensus       151 ~p~lliLDEPt~gLD~~~~~~l~~~l~~~~~~~tiii~sH~l~  193 (301)
T TIGR03522       151 DPKVLILDEPTTGLDPNQLVEIRNVIKNIGKDKTIILSTHIMQ  193 (301)
T ss_pred             CCCEEEEcCCcccCCHHHHHHHHHHHHHhcCCCEEEEEcCCHH
Confidence            689999999974 677788888888887655566677776643

Members of this protein family are exclusive to the Bacteroidetes phylum (previously Cytophaga-Flavobacteria-Bacteroides). GldA is an ABC transporter ATP-binding protein (pfam00005) linked to a type of rapid surface gliding motility found in certain Bacteroidetes, such as Flavobacterium johnsoniae and Cytophaga hutchinsonii. Knockouts of GldA abolish the gliding phenotype. Gliding motility appears closely linked to chitin utilization in the model species Flavobacterium johnsoniae. Bacteroidetes with members of this protein family appear to have all of the genes associated with gliding motility.

>PRK13537 nodulation ABC transporter NodI; Provisional

Probab=97.74  E-value=5.1e-05  Score=66.38  Aligned_cols=42  Identities=14%  Similarity=0.237  Sum_probs=31.3

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhccC-CceEEEEecCCC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYSN-TTRFALACNNSE  137 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~~-~~~~il~~~~~~  137 (317)
                      +++++++||... |.+..+..+++++.+... ...+|++|+..+
T Consensus       156 ~P~lllLDEPt~gLD~~~~~~l~~~l~~l~~~g~till~sH~l~  199 (306)
T PRK13537        156 DPDVLVLDEPTTGLDPQARHLMWERLRSLLARGKTILLTTHFME  199 (306)
T ss_pred             CCCEEEEeCCCcCCCHHHHHHHHHHHHHHHhCCCEEEEECCCHH
Confidence            689999999974 677888888888876543 455777776644

>PF02562 PhoH: PhoH-like protein; InterPro: IPR003714 PhoH is a cytoplasmic protein and predicted ATPase that is induced by phosphate starvation and belongings to the phosphate regulon (pho) in Escherichia coli []

Probab=97.74  E-value=0.00024  Score=57.76  Aligned_cols=37  Identities=14%  Similarity=0.292  Sum_probs=22.7

Q ss_pred             ceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecC
Q psy879           96 RHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNN  135 (317)
Q Consensus        96 ~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~  135 (317)
                      ...+||+||+.++++.....   ++...+.++.+|++.+.
T Consensus       119 ~~~~iIvDEaQN~t~~~~k~---ilTR~g~~skii~~GD~  155 (205)
T PF02562_consen  119 DNAFIIVDEAQNLTPEELKM---ILTRIGEGSKIIITGDP  155 (205)
T ss_dssp             -SEEEEE-SGGG--HHHHHH---HHTTB-TT-EEEEEE--
T ss_pred             cceEEEEecccCCCHHHHHH---HHcccCCCcEEEEecCc
Confidence            36899999999999865544   45566688899998765

; GO: 0005524 ATP binding; PDB: 3B85_A.

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=97.74  E-value=0.00036  Score=62.11  Aligned_cols=23  Identities=48%  Similarity=0.556  Sum_probs=21.4

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .++|.||+|+||||++..++..+
T Consensus       139 ii~lvGptGvGKTTtiakLA~~~  161 (374)
T PRK14722        139 VFALMGPTGVGKTTTTAKLAARC  161 (374)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            59999999999999999999875

>PRK13650 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=97.74  E-value=7.5e-05  Score=64.46  Aligned_cols=52  Identities=23%  Similarity=0.359  Sum_probs=35.8

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhccC--CceEEEEecCCCcCchhHhhhcce
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYSN--TTRFALACNNSEKIIEPIQSRCAM  149 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~~--~~~~il~~~~~~~l~~~i~sR~~~  149 (317)
                      +++++++||... |.......+.+.+.+...  ...+|++|++...+ . .-.|..+
T Consensus       158 ~p~lLlLDEPt~~LD~~~~~~l~~~l~~l~~~~g~tilivtH~~~~~-~-~~dri~~  212 (279)
T PRK13650        158 RPKIIILDEATSMLDPEGRLELIKTIKGIRDDYQMTVISITHDLDEV-A-LSDRVLV  212 (279)
T ss_pred             CCCEEEEECCcccCCHHHHHHHHHHHHHHHHhcCCEEEEEecCHHHH-H-hCCEEEE
Confidence            689999999975 566778888888776532  46678888776544 2 3444433

>cd03261 ABC_Org_Solvent_Resistant ABC (ATP-binding cassette) transport system involved in resistant to organic solvents; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules

Probab=97.74  E-value=6.9e-05  Score=62.99  Aligned_cols=42  Identities=7%  Similarity=0.150  Sum_probs=30.8

Q ss_pred             ceeEEEEeCCC-CCCHHHHHHHHHHhhhccC--CceEEEEecCCC
Q psy879           96 RHKIVILDEAD-SMTDGAQQALRRTMEIYSN--TTRFALACNNSE  137 (317)
Q Consensus        96 ~~~vliiDE~d-~l~~~~~~~ll~~le~~~~--~~~~il~~~~~~  137 (317)
                      +++++++||.. .+.......+.+.+.+...  ...+|+++++.+
T Consensus       154 ~p~llllDEPt~~LD~~~~~~l~~~l~~~~~~~~~tvi~vsH~~~  198 (235)
T cd03261         154 DPELLLYDEPTAGLDPIASGVIDDLIRSLKKELGLTSIMVTHDLD  198 (235)
T ss_pred             CCCEEEecCCcccCCHHHHHHHHHHHHHHHHhcCcEEEEEecCHH
Confidence            67999999997 4567778888888876532  456777777644

The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>cd03266 ABC_NatA_sodium_exporter NatA is the ATPase component of a bacterial ABC-type Na+ transport system called NatAB, which catalyzes ATP-dependent electrogenic Na+ extrusion without mechanically coupled proton or K+ uptake

Probab=97.73  E-value=6.8e-05  Score=62.26  Aligned_cols=42  Identities=17%  Similarity=0.201  Sum_probs=31.0

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhcc-CCceEEEEecCCC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYS-NTTRFALACNNSE  137 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~-~~~~~il~~~~~~  137 (317)
                      ++.++++||... +.......+.+.+.+.. ....+|++|++..
T Consensus       154 ~p~illlDEPt~~LD~~~~~~l~~~l~~~~~~~~tii~~tH~~~  197 (218)
T cd03266         154 DPPVLLLDEPTTGLDVMATRALREFIRQLRALGKCILFSTHIMQ  197 (218)
T ss_pred             CCCEEEEcCCCcCCCHHHHHHHHHHHHHHHHCCCEEEEEeCCHH
Confidence            689999999975 56777788888887653 3456777777653

NatB possess six putative membrane spanning regions at its C-terminus. In B. subtilus, NatAB is inducible by agents such as ethanol and protonophores, which lower the protonmotive force across the membrane. The closest sequence similarity to NatA is exhibited by DrrA of the two-component daunomycin- and doxorubicin-efflux system. Hence, the functional NatAB is presumably assembled with two copies of a single ATP-binding protein and a single intergral membrane protein.

>TIGR02673 FtsE cell division ATP-binding protein FtsE

Probab=97.73  E-value=5.5e-05  Score=62.60  Aligned_cols=42  Identities=10%  Similarity=0.185  Sum_probs=30.7

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhcc-CCceEEEEecCCC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYS-NTTRFALACNNSE  137 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~-~~~~~il~~~~~~  137 (317)
                      +++++++||... +.......+.+.+.+.. ....+|++|++..
T Consensus       155 ~p~lllLDEPt~~LD~~~~~~l~~~l~~~~~~~~tii~~tH~~~  198 (214)
T TIGR02673       155 SPPLLLADEPTGNLDPDLSERILDLLKRLNKRGTTVIVATHDLS  198 (214)
T ss_pred             CCCEEEEeCCcccCCHHHHHHHHHHHHHHHHcCCEEEEEeCCHH
Confidence            689999999975 56777888888887653 2455777776643

This model describes FtsE, a member of the ABC transporter ATP-binding protein family. This protein, and its permease partner FtsX, localize to the division site. In a number of species, the ftsEX gene pair is located next to FtsY, the signal recognition particle-docking protein.

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional

Probab=97.73  E-value=0.00095  Score=61.68  Aligned_cols=24  Identities=50%  Similarity=0.659  Sum_probs=21.4

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHc
Q psy879           33 NIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      .+.|.||+|+||||++..++..+.
T Consensus       352 vIaLVGPtGvGKTTtaakLAa~la  375 (559)
T PRK12727        352 VIALVGPTGAGKTTTIAKLAQRFA  375 (559)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHH
Confidence            589999999999999999998653

>TIGR01842 type_I_sec_PrtD type I secretion system ABC transporter, PrtD family

Probab=97.73  E-value=7.4e-05  Score=70.86  Aligned_cols=42  Identities=19%  Similarity=0.377  Sum_probs=30.4

Q ss_pred             ceeEEEEeCCC-CCCHHHHHHHHHHhhhcc-CCceEEEEecCCC
Q psy879           96 RHKIVILDEAD-SMTDGAQQALRRTMEIYS-NTTRFALACNNSE  137 (317)
Q Consensus        96 ~~~vliiDE~d-~l~~~~~~~ll~~le~~~-~~~~~il~~~~~~  137 (317)
                      +++++++||+- .+..+....+.+.+.+.. ....+|+++++..
T Consensus       472 ~~~ililDEpts~LD~~~~~~i~~~l~~~~~~~~tvi~ith~~~  515 (544)
T TIGR01842       472 DPKLVVLDEPNSNLDEEGEQALANAIKALKARGITVVVITHRPS  515 (544)
T ss_pred             CCCEEEEeCCccccCHHHHHHHHHHHHHHhhCCCEEEEEeCCHH
Confidence            68999999997 566777777878777653 3445677777753

Type I protein secretion is a system in some Gram-negative bacteria to export proteins (often proteases) across both inner and outer membranes to the extracellular medium. This is one of three proteins of the type I secretion apparatus. Targeted proteins are not cleaved at the N-terminus, but rather carry signals located toward the extreme C-terminus to direct type I secretion.

>PRK05986 cob(I)alamin adenolsyltransferase/cobinamide ATP-dependent adenolsyltransferase; Validated

Probab=97.73  E-value=0.00024  Score=56.82  Aligned_cols=101  Identities=16%  Similarity=0.189  Sum_probs=61.6

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCC----------------------C------CcC---hHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNAS----------------------N------DRG---IDTVRNK   81 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~----------------------~------~~~---~~~i~~~   81 (317)
                      .+.+||++|.||||+|..++-...+......++.+-..                      .      ...   ....++.
T Consensus        24 ~v~v~~g~GkGKtt~a~g~a~ra~g~G~~V~ivQFlKg~~~~GE~~~l~~l~~v~~~~~g~~~~~~~~~~~e~~~~~~~~  103 (191)
T PRK05986         24 LLIVHTGNGKGKSTAAFGMALRAVGHGKKVGVVQFIKGAWSTGERNLLEFGGGVEFHVMGTGFTWETQDRERDIAAAREG  103 (191)
T ss_pred             eEEEECCCCCChHHHHHHHHHHHHHCCCeEEEEEEecCCCccCHHHHHhcCCCcEEEECCCCCcccCCCcHHHHHHHHHH
Confidence            59999999999999999999766543332211111000                      0      000   0111112


Q ss_pred             HHHHHhhcccCCCCceeEEEEeCCCCCCHH---HHHHHHHHhhhccCCceEEEEecCC
Q psy879           82 IKMFAQQKVTLPPGRHKIVILDEADSMTDG---AQQALRRTMEIYSNTTRFALACNNS  136 (317)
Q Consensus        82 ~~~~~~~~~~~~~~~~~vliiDE~d~l~~~---~~~~ll~~le~~~~~~~~il~~~~~  136 (317)
                      +.....   ....+.+.+||+||+-....-   ..+.++++++..|+.+-+|+|..+.
T Consensus       104 ~~~a~~---~l~~~~ydlvVLDEi~~Al~~gli~~eevi~~L~~rp~~~evVlTGR~~  158 (191)
T PRK05986        104 WEEAKR---MLADESYDLVVLDELTYALKYGYLDVEEVLEALNARPGMQHVVITGRGA  158 (191)
T ss_pred             HHHHHH---HHhCCCCCEEEEehhhHHHHCCCccHHHHHHHHHcCCCCCEEEEECCCC
Confidence            222111   112367899999999765432   2456788888889999999998764

>cd03269 ABC_putative_ATPase This subfamily is involved in drug resistance, nodulation, lipid transport, and bacteriocin and lantibiotic immunity

Probab=97.73  E-value=8e-05  Score=61.46  Aligned_cols=42  Identities=17%  Similarity=0.229  Sum_probs=31.0

Q ss_pred             ceeEEEEeCCC-CCCHHHHHHHHHHhhhcc-CCceEEEEecCCC
Q psy879           96 RHKIVILDEAD-SMTDGAQQALRRTMEIYS-NTTRFALACNNSE  137 (317)
Q Consensus        96 ~~~vliiDE~d-~l~~~~~~~ll~~le~~~-~~~~~il~~~~~~  137 (317)
                      +++++++||.. .+.......+.+.+.+.. ....+|+++++..
T Consensus       146 ~p~~lllDEP~~~LD~~~~~~~~~~l~~~~~~~~tii~~sH~~~  189 (210)
T cd03269         146 DPELLILDEPFSGLDPVNVELLKDVIRELARAGKTVILSTHQME  189 (210)
T ss_pred             CCCEEEEeCCCcCCCHHHHHHHHHHHHHHHHCCCEEEEECCCHH
Confidence            67999999998 566777888888887653 3455777776643

In eubacteria and archaea, the typical organization consists of one ABC and one or two IMs. Eukaryote systems of the ABCA subfamily display ABC domains strongly similar to this family. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region in addition to the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>TIGR01166 cbiO cobalt transport protein ATP-binding subunit

Probab=97.72  E-value=3.5e-05  Score=62.52  Aligned_cols=42  Identities=10%  Similarity=0.298  Sum_probs=30.3

Q ss_pred             ceeEEEEeCCC-CCCHHHHHHHHHHhhhccC-CceEEEEecCCC
Q psy879           96 RHKIVILDEAD-SMTDGAQQALRRTMEIYSN-TTRFALACNNSE  137 (317)
Q Consensus        96 ~~~vliiDE~d-~l~~~~~~~ll~~le~~~~-~~~~il~~~~~~  137 (317)
                      +++++++||.. .|.......+.+++.+... ...+|+++++.+
T Consensus       145 ~p~llllDEPt~~LD~~~~~~~~~~l~~~~~~~~tili~sH~~~  188 (190)
T TIGR01166       145 RPDVLLLDEPTAGLDPAGREQMLAILRRLRAEGMTVVISTHDVD  188 (190)
T ss_pred             CCCEEEEcCCcccCCHHHHHHHHHHHHHHHHcCCEEEEEeeccc
Confidence            67999999997 4567777888888776532 456777776643

This model describes the ATP binding subunit of the multisubunit cobalt transporter in bacteria and its equivalents in archaea. The model is restricted to ATP subunit that is a part of the cobalt transporter, which belongs to the ABC transporter superfamily (ATP Binding Cassette). The model excludes ATP binding subunit that are associated with other transporters belonging to ABC transporter superfamily. This superfamily includes two groups, one which catalyze the uptake of small molecules, including ions from the external milieu and the other group which is engaged in the efflux of small molecular weight compounds and ions from within the cell. Energy derived from the hydrolysis of ATP drive the both the process of uptake and efflux.

>KOG0055|consensus

Probab=97.72  E-value=0.00012  Score=72.94  Aligned_cols=39  Identities=33%  Similarity=0.594  Sum_probs=28.5

Q ss_pred             HhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEe
Q psy879           26 SSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLEL   67 (317)
Q Consensus        26 l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~   67 (317)
                      +..|.  .+.+.||+||||||++..+.+.. .+..+..+++.
T Consensus       376 i~~G~--~valVG~SGsGKST~i~LL~Rfy-dP~~G~V~idG  414 (1228)
T KOG0055|consen  376 IPSGQ--TVALVGPSGSGKSTLIQLLARFY-DPTSGEVLIDG  414 (1228)
T ss_pred             eCCCC--EEEEECCCCCCHHHHHHHHHHhc-CCCCceEEEcC
Confidence            44454  59999999999999999999974 54444444443

>cd03238 ABC_UvrA The excision repair protein UvrA; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion

Probab=97.72  E-value=0.00025  Score=56.63  Aligned_cols=41  Identities=17%  Similarity=0.179  Sum_probs=30.2

Q ss_pred             eeEEEEeCCCC-CCHHHHHHHHHHhhhcc-CCceEEEEecCCC
Q psy879           97 HKIVILDEADS-MTDGAQQALRRTMEIYS-NTTRFALACNNSE  137 (317)
Q Consensus        97 ~~vliiDE~d~-l~~~~~~~ll~~le~~~-~~~~~il~~~~~~  137 (317)
                      ++++++||... +.......+.+.+.+.. ....+|+++++.+
T Consensus       108 p~llLlDEPt~~LD~~~~~~l~~~l~~~~~~g~tvIivSH~~~  150 (176)
T cd03238         108 GTLFILDEPSTGLHQQDINQLLEVIKGLIDLGNTVILIEHNLD  150 (176)
T ss_pred             CCEEEEeCCcccCCHHHHHHHHHHHHHHHhCCCEEEEEeCCHH
Confidence            89999999975 56777777777777543 3456777887754

Recognition and cleavage of the damaged DNA is a multistep ATP-dependent reaction that requires the UvrA, UvrB, and UvrC proteins. Both UvrA and UvrB are ATPases, with UvrA having two ATP binding sites, which have the characteristic signature of the family of ABC proteins, and UvrB having one ATP binding site that is structurally related to that of helicases.

>PF05970 PIF1: PIF1-like helicase; InterPro: IPR010285 This entry represents PIF1 helicase and related proteins

Probab=97.72  E-value=0.00021  Score=64.06  Aligned_cols=105  Identities=16%  Similarity=0.245  Sum_probs=58.9

Q ss_pred             CHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCC----Cc-ChHHHHHHHHHHHh--
Q psy879           15 NEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASN----DR-GIDTVRNKIKMFAQ--   87 (317)
Q Consensus        15 ~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~----~~-~~~~i~~~~~~~~~--   87 (317)
                      |..+...+...+......++++.||.|||||++.+++...+....  ..+.-.....    .. +-..+...++.-..  
T Consensus         6 Q~~~~~~v~~~~~~~~~~~~fv~G~~GtGKs~l~~~i~~~~~~~~--~~~~~~a~tg~AA~~i~~G~T~hs~f~i~~~~~   83 (364)
T PF05970_consen    6 QRRVFDTVIEAIENEEGLNFFVTGPAGTGKSFLIKAIIDYLRSRG--KKVLVTAPTGIAAFNIPGGRTIHSFFGIPINNN   83 (364)
T ss_pred             HHHHHHHHHHHHHccCCcEEEEEcCCCCChhHHHHHHHHHhcccc--ceEEEecchHHHHHhccCCcchHHhcCcccccc
Confidence            556666666666655555699999999999999999999874321  1222111110    01 11111111110000  


Q ss_pred             --hcc--------cCCCCceeEEEEeCCCCCCHHHHHHHHHHhh
Q psy879           88 --QKV--------TLPPGRHKIVILDEADSMTDGAQQALRRTME  121 (317)
Q Consensus        88 --~~~--------~~~~~~~~vliiDE~d~l~~~~~~~ll~~le  121 (317)
                        ...        .-.-..-+++||||+..+.......+.+.|.
T Consensus        84 ~~~~~~~~~~~~~~~~l~~~~~lIiDEism~~~~~l~~i~~~lr  127 (364)
T PF05970_consen   84 EKSQCKISKNSRLRERLRKADVLIIDEISMVSADMLDAIDRRLR  127 (364)
T ss_pred             ccccccccccchhhhhhhhheeeecccccchhHHHHHHHHHhhh
Confidence              000        0000245799999999999988777655554

The PIF1 helicase inhibits telomerase activity and is cell cycle regulated [, ].

>TIGR03608 L_ocin_972_ABC putative bacteriocin export ABC transporter, lactococcin 972 group

Probab=97.72  E-value=6e-05  Score=61.99  Aligned_cols=42  Identities=7%  Similarity=0.188  Sum_probs=31.0

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhcc-CCceEEEEecCCC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYS-NTTRFALACNNSE  137 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~-~~~~~il~~~~~~  137 (317)
                      +++++++||... |.......+.+++.+.. ....+|+++++..
T Consensus       152 ~p~llllDEPt~~LD~~~~~~l~~~l~~~~~~~~tii~~sh~~~  195 (206)
T TIGR03608       152 DPPLILADEPTGSLDPKNRDEVLDLLLELNDEGKTIIIVTHDPE  195 (206)
T ss_pred             CCCEEEEeCCcCCCCHHHHHHHHHHHHHHHhcCCEEEEEeCCHH
Confidence            689999999975 56777888888887653 2456777777753

A gene pair with a fairly wide distribution consists of a polypeptide related to the lactococcin 972 (see TIGR01653) and multiple-membrane-spanning putative immunity protein (see TIGR01654). This model represents a small clade within the ABC transporters that regularly are found adjacent to these bacteriocin system gene pairs and are likely serve as export proteins.

>cd03262 ABC_HisP_GlnQ_permeases HisP and GlnQ are the ATP-binding components of the bacterial periplasmic histidine and glutamine permeases, repectively

Probab=97.71  E-value=8.9e-05  Score=61.31  Aligned_cols=42  Identities=10%  Similarity=0.187  Sum_probs=31.0

Q ss_pred             ceeEEEEeCCC-CCCHHHHHHHHHHhhhccC-CceEEEEecCCC
Q psy879           96 RHKIVILDEAD-SMTDGAQQALRRTMEIYSN-TTRFALACNNSE  137 (317)
Q Consensus        96 ~~~vliiDE~d-~l~~~~~~~ll~~le~~~~-~~~~il~~~~~~  137 (317)
                      +++++++||.. .|.......+.+.+.+... ...+|+++++..
T Consensus       153 ~p~llllDEP~~~LD~~~~~~l~~~l~~~~~~~~tvi~~sh~~~  196 (213)
T cd03262         153 NPKVMLFDEPTSALDPELVGEVLDVMKDLAEEGMTMVVVTHEMG  196 (213)
T ss_pred             CCCEEEEeCCccCCCHHHHHHHHHHHHHHHHcCCEEEEEeCCHH
Confidence            68999999997 5677778888888876533 455777777643

Histidine permease is a multisubunit complex containing the HisQ and HisM integral membrane subunits and two copies of HisP. HisP has properties intermediate between those of integral and peripheral membrane proteins and is accessible from both sides of the membrane, presumably by its interaction with HisQ and HisM. The two HisP subunits form a homodimer within the complex. The domain structure of the amino acid uptake systems is typical for prokaryote extracellular solute binding protein-dependent uptake systems. All of the amino acid uptake systems also have at least one, and in a few cases, two extracellular solute binding proteins located in the periplasm of Gram-negative bacteria, or attached to the cell membrane of Gram-positive bacteria. The best-studied member of the PAAT (polar amino acid transport) family is the HisJQM

>cd03253 ABCC_ATM1_transporter ATM1 is an ABC transporter that is expressed in the mitochondria

Probab=97.71  E-value=8.1e-05  Score=62.61  Aligned_cols=44  Identities=16%  Similarity=0.263  Sum_probs=33.0

Q ss_pred             ceeEEEEeCCC-CCCHHHHHHHHHHhhhccCCceEEEEecCCCcC
Q psy879           96 RHKIVILDEAD-SMTDGAQQALRRTMEIYSNTTRFALACNNSEKI  139 (317)
Q Consensus        96 ~~~vliiDE~d-~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l  139 (317)
                      +++++++||.. .|.......+.+.+.+......+|+++++...+
T Consensus       155 ~p~llllDEP~~~LD~~~~~~l~~~l~~~~~~~tiii~sh~~~~~  199 (236)
T cd03253         155 NPPILLLDEATSALDTHTEREIQAALRDVSKGRTTIVIAHRLSTI  199 (236)
T ss_pred             CCCEEEEeCCcccCCHHHHHHHHHHHHHhcCCCEEEEEcCCHHHH
Confidence            68999999997 567777888888887655455677777776543

Although the specific function of ATM1 is unknown, its disruption results in the accumulation of excess mitochondrial iron, loss of mitochondrial cytochromes, oxidative damage to mitochondrial DNA, and decreased levels of cytosolic heme proteins. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>cd03292 ABC_FtsE_transporter FtsE is a hydrophilic nucleotide-binding protein that binds FtsX to form a heterodimeric ATP-binding cassette (ABC)-type transporter that associates with the bacterial inner membrane

Probab=97.71  E-value=8.7e-05  Score=61.39  Aligned_cols=41  Identities=15%  Similarity=0.205  Sum_probs=30.7

Q ss_pred             ceeEEEEeCCC-CCCHHHHHHHHHHhhhcc-CCceEEEEecCC
Q psy879           96 RHKIVILDEAD-SMTDGAQQALRRTMEIYS-NTTRFALACNNS  136 (317)
Q Consensus        96 ~~~vliiDE~d-~l~~~~~~~ll~~le~~~-~~~~~il~~~~~  136 (317)
                      +++++++||.. .+.+.....+.+.+.+.. ....+|++|++.
T Consensus       154 ~p~llllDEPt~~LD~~~~~~~~~~l~~~~~~~~tiiivtH~~  196 (214)
T cd03292         154 SPTILIADEPTGNLDPDTTWEIMNLLKKINKAGTTVVVATHAK  196 (214)
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHHHHHHHcCCEEEEEeCCH
Confidence            68999999997 566777888888887653 345577777764

The FtsE/X transporter is thought to be involved in cell division and is important for assembly or stability of the septal ring.

>PRK13889 conjugal transfer relaxase TraA; Provisional

Probab=97.70  E-value=0.00029  Score=70.12  Aligned_cols=112  Identities=12%  Similarity=0.097  Sum_probs=65.2

Q ss_pred             HHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCC----------CcChHHHHHHHHHH
Q psy879           16 EDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASN----------DRGIDTVRNKIKMF   85 (317)
Q Consensus        16 ~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~----------~~~~~~i~~~~~~~   85 (317)
                      ++..+.+..++..+.  ..++.|++||||||+.+.+...+...  +..++-+.++.          ......+...+..+
T Consensus       349 ~eQr~Av~~il~s~~--v~vv~G~AGTGKTT~l~~~~~~~e~~--G~~V~~~ApTGkAA~~L~e~tGi~a~TI~sll~~~  424 (988)
T PRK13889        349 GEQADALAHVTDGRD--LGVVVGYAGTGKSAMLGVAREAWEAA--GYEVRGAALSGIAAENLEGGSGIASRTIASLEHGW  424 (988)
T ss_pred             HHHHHHHHHHhcCCC--eEEEEeCCCCCHHHHHHHHHHHHHHc--CCeEEEecCcHHHHHHHhhccCcchhhHHHHHhhh
Confidence            334444555554333  57899999999999998887765322  22233332221          11112222222111


Q ss_pred             HhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecC
Q psy879           86 AQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNN  135 (317)
Q Consensus        86 ~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~  135 (317)
                      ....  .......++||||+..+.......|++..+.  ..+.+|++...
T Consensus       425 ~~~~--~~l~~~~vlIVDEASMv~~~~m~~LL~~a~~--~garvVLVGD~  470 (988)
T PRK13889        425 GQGR--DLLTSRDVLVIDEAGMVGTRQLERVLSHAAD--AGAKVVLVGDP  470 (988)
T ss_pred             cccc--cccccCcEEEEECcccCCHHHHHHHHHhhhh--CCCEEEEECCH
Confidence            1111  1124567999999999999888888877663  45778888754

>PRK08533 flagellar accessory protein FlaH; Reviewed

Probab=97.70  E-value=0.00026  Score=59.24  Aligned_cols=24  Identities=33%  Similarity=0.331  Sum_probs=19.7

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHc
Q psy879           33 NIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      .++++||||+|||+++..++..+.
T Consensus        26 ~~~i~G~~G~GKTtl~~~~~~~~~   49 (230)
T PRK08533         26 LILIEGDESTGKSILSQRLAYGFL   49 (230)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHH
Confidence            399999999999999866665543

>cd03254 ABCC_Glucan_exporter_like Glucan exporter ATP-binding protein

Probab=97.70  E-value=7.3e-05  Score=62.55  Aligned_cols=43  Identities=19%  Similarity=0.293  Sum_probs=32.8

Q ss_pred             ceeEEEEeCCC-CCCHHHHHHHHHHhhhccCCceEEEEecCCCc
Q psy879           96 RHKIVILDEAD-SMTDGAQQALRRTMEIYSNTTRFALACNNSEK  138 (317)
Q Consensus        96 ~~~vliiDE~d-~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~  138 (317)
                      +++++++||.. .|.......+.+.+........+|++|++...
T Consensus       157 ~p~llllDEP~~~LD~~~~~~l~~~l~~~~~~~tii~~sh~~~~  200 (229)
T cd03254         157 DPKILILDEATSNIDTETEKLIQEALEKLMKGRTSIIIAHRLST  200 (229)
T ss_pred             CCCEEEEeCccccCCHHHHHHHHHHHHHhcCCCEEEEEecCHHH
Confidence            68999999998 56777788888888766555667888877544

In A. tumefaciens cyclic beta-1, 2-glucan must be transported into the periplasmic space to exert its action as a virluence factor. This subfamily belongs to the MRP-like family and is involved in drug, peptide, and lipid export. The MRP-like family, similar to all ABC proteins, have a common four-domain core structure constituted by two membrane-spanning domains each composed of six transmembrane (TM) helices and two nucleotide-binding domains (NBD). ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>TIGR01189 ccmA heme ABC exporter, ATP-binding protein CcmA

Probab=97.70  E-value=0.00012  Score=59.76  Aligned_cols=43  Identities=16%  Similarity=0.177  Sum_probs=31.4

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhc-cCCceEEEEecCCCc
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIY-SNTTRFALACNNSEK  138 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~-~~~~~~il~~~~~~~  138 (317)
                      +++++++||... |.......+.+.+.+. .....+|++++++..
T Consensus       145 ~p~llllDEPt~~LD~~~~~~l~~~l~~~~~~~~tii~~sH~~~~  189 (198)
T TIGR01189       145 RAPLWILDEPTTALDKAGVALLAGLLRAHLARGGIVLLTTHQDLG  189 (198)
T ss_pred             CCCEEEEeCCCcCCCHHHHHHHHHHHHHHHhCCCEEEEEEccccc
Confidence            689999999974 5677778888888754 234567888877643

This model describes the cyt c biogenesis protein encoded by ccmA in bacteria. An exception is, an arabidopsis protein. Quite likely this is encoded by an organelle. Bacterial c-type cytocromes are located on the periplasmic side of the cytoplasmic membrane. Several gene products encoded in a locus designated as 'ccm' are implicated in the transport and assembly of the functional cytochrome C. This cluster includes genes: ccmA;B;C;D;E;F;G and H. The posttranslational pathway includes the transport of heme moiety, the secretion of the apoprotein and the covalent attachment of the heme with the apoprotein. The proteins ccmA and B represent an ABC transporter; ccmC and D participate in heme transfer to ccmE, which function as a periplasmic heme chaperone. The presence of ccmF, G and H is suggested to be obligatory for the final functional assembly of cytochrome c.

>cd03258 ABC_MetN_methionine_transporter MetN (also known as YusC) is an ABC-type transporter encoded by metN of the metNPQ operon in Bacillus subtilis that is involved in methionine transport

Probab=97.70  E-value=8.4e-05  Score=62.40  Aligned_cols=42  Identities=17%  Similarity=0.241  Sum_probs=31.4

Q ss_pred             ceeEEEEeCCC-CCCHHHHHHHHHHhhhccC--CceEEEEecCCC
Q psy879           96 RHKIVILDEAD-SMTDGAQQALRRTMEIYSN--TTRFALACNNSE  137 (317)
Q Consensus        96 ~~~vliiDE~d-~l~~~~~~~ll~~le~~~~--~~~~il~~~~~~  137 (317)
                      +++++++||.. .+.......+.+++.+...  ...+|+++++.+
T Consensus       158 ~p~lllLDEP~~~LD~~~~~~l~~~l~~~~~~~~~tvii~sH~~~  202 (233)
T cd03258         158 NPKVLLCDEATSALDPETTQSILALLRDINRELGLTIVLITHEME  202 (233)
T ss_pred             CCCEEEecCCCCcCCHHHHHHHHHHHHHHHHHcCCEEEEEeCCHH
Confidence            67899999997 5677788888888876532  456777777644

Other members of this system include the MetP permease and the MetQ substrate binding protein. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>cd01124 KaiC KaiC is a circadian clock protein primarily found in cyanobacteria KaiC is a RecA-like ATPase, having both Walker A and Walker B motifs

Probab=97.70  E-value=0.00019  Score=57.89  Aligned_cols=23  Identities=43%  Similarity=0.546  Sum_probs=20.2

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHc
Q psy879           34 IIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      ++++||||+|||+++..++....
T Consensus         2 ~li~G~~G~GKT~l~~~~~~~~~   24 (187)
T cd01124           2 TLLSGGPGTGKTTFALQFLYAGL   24 (187)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHH
Confidence            68999999999999999887653

A related protein is found in archaea.

>cd03224 ABC_TM1139_LivF_branched LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids

Probab=97.70  E-value=6.3e-05  Score=62.61  Aligned_cols=41  Identities=17%  Similarity=0.289  Sum_probs=30.2

Q ss_pred             ceeEEEEeCCC-CCCHHHHHHHHHHhhhcc-CCceEEEEecCC
Q psy879           96 RHKIVILDEAD-SMTDGAQQALRRTMEIYS-NTTRFALACNNS  136 (317)
Q Consensus        96 ~~~vliiDE~d-~l~~~~~~~ll~~le~~~-~~~~~il~~~~~  136 (317)
                      +++++++||.. .+.......+.+.+.+.. ....+|+++++.
T Consensus       150 ~p~llllDEPt~~LD~~~~~~l~~~l~~~~~~~~tiii~sH~~  192 (222)
T cd03224         150 RPKLLLLDEPSEGLAPKIVEEIFEAIRELRDEGVTILLVEQNA  192 (222)
T ss_pred             CCCEEEECCCcccCCHHHHHHHHHHHHHHHHCCCEEEEEeCCH
Confidence            67999999997 466777888888887654 345677777664

The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a heterodimer of six-helix TM domains (LivM and LivH), and one of two alternative soluble periplasmic substrate binding proteins (LivK or LivJ). ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules.

>COG1132 MdlB ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]

Probab=97.69  E-value=4.5e-05  Score=72.69  Aligned_cols=39  Identities=28%  Similarity=0.449  Sum_probs=29.7

Q ss_pred             HHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcC
Q psy879           17 DTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLG   57 (317)
Q Consensus        17 ~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~   57 (317)
                      .+++.+.-.++.|.  .+.+.||+|+||||+++.+.+....
T Consensus       343 ~vl~~is~~i~~Ge--~vaiVG~sGsGKSTl~~LL~r~~~~  381 (567)
T COG1132         343 PVLKDISFSIEPGE--KVAIVGPSGSGKSTLIKLLLRLYDP  381 (567)
T ss_pred             ccccCceEEEcCCC--EEEEECCCCCCHHHHHHHHhccCCC
Confidence            34444544455665  6889999999999999999997643

>TIGR00708 cobA cob(I)alamin adenosyltransferase

Probab=97.69  E-value=0.00022  Score=56.20  Aligned_cols=101  Identities=17%  Similarity=0.168  Sum_probs=60.2

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCC-Cc-------------------------Ch----HHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASN-DR-------------------------GI----DTVRNKI   82 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~-~~-------------------------~~----~~i~~~~   82 (317)
                      -+.+|+++|.||||+|..++-...+...+..++.+-... ..                         ..    ...++.+
T Consensus         7 li~v~~g~GkGKtt~a~g~a~ra~~~g~~v~ivQFlKg~~~~GE~~~l~~~~~~~~~~g~g~~~~~~~~~~~~~~~~~~~   86 (173)
T TIGR00708         7 IIIVHTGNGKGKTTAAFGMALRALGHGKKVGVIQFIKGAWPNGERAAFEPHGVEFQVMGTGFTWETQNREADTAIAKAAW   86 (173)
T ss_pred             EEEEECCCCCChHHHHHHHHHHHHHCCCeEEEEEEecCCcccChHHHHHhcCcEEEECCCCCeecCCCcHHHHHHHHHHH
Confidence            478888899999999999997765544332211110000 00                         00    1111122


Q ss_pred             HHHHhhcccCCCCceeEEEEeCCCCCCHH---HHHHHHHHhhhccCCceEEEEecCC
Q psy879           83 KMFAQQKVTLPPGRHKIVILDEADSMTDG---AQQALRRTMEIYSNTTRFALACNNS  136 (317)
Q Consensus        83 ~~~~~~~~~~~~~~~~vliiDE~d~l~~~---~~~~ll~~le~~~~~~~~il~~~~~  136 (317)
                      .....   ....+.+.+||+||+.....-   ..+.++++++..|+.+-+|+|..+.
T Consensus        87 ~~a~~---~l~~~~~DlvVLDEi~~A~~~gli~~~~v~~lL~~rp~~~evVlTGR~~  140 (173)
T TIGR00708        87 QHAKE---MLADPELDLVLLDELTYALKYGYLDVEEVVEALQERPGHQHVIITGRGC  140 (173)
T ss_pred             HHHHH---HHhcCCCCEEEehhhHHHHHCCCcCHHHHHHHHHhCCCCCEEEEECCCC
Confidence            22111   112367899999999744322   1346778888889999999998764

Alternate name: corrinoid adenosyltransferase.

>cd03249 ABC_MTABC3_MDL1_MDL2 MTABC3 (also known as ABCB6) is a mitochondrial ATP-binding cassette protein involved in iron homeostasis and one of four ABC transporters expressed in the mitochondrial inner membrane, the other three being MDL1(ABC7), MDL2, and ATM1

Probab=97.69  E-value=8.2e-05  Score=62.65  Aligned_cols=44  Identities=18%  Similarity=0.289  Sum_probs=33.2

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhccCCceEEEEecCCCcC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYSNTTRFALACNNSEKI  139 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l  139 (317)
                      +++++++||... |.......+.+.+.+......+|+++++.+.+
T Consensus       157 ~p~llllDEP~~gLD~~~~~~l~~~l~~~~~g~~vi~~sh~~~~~  201 (238)
T cd03249         157 NPKILLLDEATSALDAESEKLVQEALDRAMKGRTTIVIAHRLSTI  201 (238)
T ss_pred             CCCEEEEeCccccCCHHHHHHHHHHHHHhcCCCEEEEEeCCHHHH
Confidence            678999999974 67777888888887665456678888776543

In fact, the yeast MDL1 (multidrug resistance-like protein 1) and MDL2 (multidrug resistance-like protein 2) transporters are also included in this CD. MDL1 is an ATP-dependent permease that acts as a high-copy suppressor of ATM1 and is thought to have a role in resistance to oxidative stress. Interestingly, subfamily B is more closely related to the carboxyl-terminal component of subfamily C than the two halves of ABCC molecules are with one another.

>cd03245 ABCC_bacteriocin_exporters ABC-type bacteriocin exporters

Probab=97.69  E-value=0.00011  Score=61.08  Aligned_cols=42  Identities=14%  Similarity=0.296  Sum_probs=32.8

Q ss_pred             ceeEEEEeCCC-CCCHHHHHHHHHHhhhccCCceEEEEecCCC
Q psy879           96 RHKIVILDEAD-SMTDGAQQALRRTMEIYSNTTRFALACNNSE  137 (317)
Q Consensus        96 ~~~vliiDE~d-~l~~~~~~~ll~~le~~~~~~~~il~~~~~~  137 (317)
                      +++++++||.. .+.......+.+.+.+......+|++|++.+
T Consensus       158 ~p~llllDEPt~~LD~~~~~~l~~~l~~~~~~~tii~~sH~~~  200 (220)
T cd03245         158 DPPILLLDEPTSAMDMNSEERLKERLRQLLGDKTLIIITHRPS  200 (220)
T ss_pred             CCCEEEEeCccccCCHHHHHHHHHHHHHhcCCCEEEEEeCCHH
Confidence            68999999997 4677788888888887655566778887755

Many non-lantibiotic bacteriocins of lactic acid bacteria are produced as precursors which have N-terminal leader peptides that share similarities in amino acid sequence and contain a conserved processing site of two glycine residues in positions -1 and -2. A dedicated ATP-binding cassette (ABC) transporter is responsible for the proteolytic cleavage of the leader peptides and subsequent translocation of the bacteriocins across the cytoplasmic membrane.

>TIGR01613 primase_Cterm phage/plasmid primase, P4 family, C-terminal domain

Probab=97.69  E-value=0.00072  Score=59.14  Aligned_cols=126  Identities=17%  Similarity=0.245  Sum_probs=70.1

Q ss_pred             CHHHHHHHHHHHh---cC--CCce-EEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHH-HHHHHHh
Q psy879           15 NEDTVERLKVFSS---SG--NVPN-IIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRN-KIKMFAQ   87 (317)
Q Consensus        15 ~~~~~~~l~~~l~---~~--~~~~-~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~-~~~~~~~   87 (317)
                      .++..+.+..++.   .+  .... ++++|+.|+|||++...+...+ +.....    ...  ........+ ....   
T Consensus        54 d~~~~~~l~~~lg~~L~~~~~~~~~~~l~G~g~nGKStl~~~l~~l~-G~~~~~----~~~--~~~~~~~~~~~f~~---  123 (304)
T TIGR01613        54 DNELIEYLQRVIGYSLTGNYTEQKLFFLYGNGGNGKSTFQNLLSNLL-GDYATT----AVA--SLKMNEFQEHRFGL---  123 (304)
T ss_pred             CHHHHHHHHHHHhHHhcCCCCceEEEEEECCCCCcHHHHHHHHHHHh-Chhhcc----CCc--chhhhhccCCCchh---
Confidence            3445555555532   22  2222 8999999999999999887765 432100    000  000111000 0000   


Q ss_pred             hcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhh--------------hccCCceEEEEecCCCcC---chhHhhhccee
Q psy879           88 QKVTLPPGRHKIVILDEADSMTDGAQQALRRTME--------------IYSNTTRFALACNNSEKI---IEPIQSRCAML  150 (317)
Q Consensus        88 ~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le--------------~~~~~~~~il~~~~~~~l---~~~i~sR~~~i  150 (317)
                      .    .-.++++++.||++.-.....+.|..+..              +...+..+|++||....+   ..++.+|+.+|
T Consensus       124 a----~l~gk~l~~~~E~~~~~~~~~~~lK~lt~gd~i~~~~k~k~~~~~~~~~~~i~~tN~~P~~~~~~~a~~RR~~vi  199 (304)
T TIGR01613       124 A----RLEGKRAVIGDEVQKGYRDDESTFKSLTGGDTITARFKNKDPFEFTPKFTLVQSTNHLPRIRGFDGGIKRRLRII  199 (304)
T ss_pred             h----hhcCCEEEEecCCCCCccccHHhhhhhhcCCeEEeecccCCcEEEEEeeEEEEEcCCCCccCCCChhheeeEEEE
Confidence            0    01367899999997532222333333332              123456689999986544   47889999999


Q ss_pred             eecC
Q psy879          151 RYNK  154 (317)
Q Consensus       151 ~f~~  154 (317)
                      .|+.
T Consensus       200 ~f~~  203 (304)
T TIGR01613       200 PFTK  203 (304)
T ss_pred             eccC
Confidence            9874

This model represents a clade within a larger family of proteins from viruses of bacteria and animals. Members of this family are found in phage and plasmids of bacteria and archaea only. The model describes a domain of about 300 residues, found generally toward the protein C-terminus.

>TIGR01359 UMP_CMP_kin_fam UMP-CMP kinase family

Probab=97.68  E-value=0.0012  Score=53.08  Aligned_cols=22  Identities=27%  Similarity=0.484  Sum_probs=20.7

Q ss_pred             EEEECCCCCCHHHHHHHHHHHH
Q psy879           34 IIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~l   55 (317)
                      ++++||||+||||+++.+++.+
T Consensus         2 i~i~G~pGsGKst~a~~la~~~   23 (183)
T TIGR01359         2 VFVLGGPGSGKGTQCAKIVENF   23 (183)
T ss_pred             EEEECCCCCCHHHHHHHHHHHc
Confidence            6899999999999999999986

This subfamily of the adenylate kinase superfamily contains examples of UMP-CMP kinase, as well as others proteins with unknown specificity, some currently designated adenylate kinase. All known members are eukaryotic.

>PRK13538 cytochrome c biogenesis protein CcmA; Provisional

Probab=97.68  E-value=0.00012  Score=60.02  Aligned_cols=43  Identities=16%  Similarity=0.145  Sum_probs=31.9

Q ss_pred             ceeEEEEeCCC-CCCHHHHHHHHHHhhhcc-CCceEEEEecCCCc
Q psy879           96 RHKIVILDEAD-SMTDGAQQALRRTMEIYS-NTTRFALACNNSEK  138 (317)
Q Consensus        96 ~~~vliiDE~d-~l~~~~~~~ll~~le~~~-~~~~~il~~~~~~~  138 (317)
                      +++++++||.. .+.......+.+++.+.. ....+|++|++...
T Consensus       147 ~p~llllDEPt~~LD~~~~~~l~~~l~~~~~~~~tiii~sh~~~~  191 (204)
T PRK13538        147 RAPLWILDEPFTAIDKQGVARLEALLAQHAEQGGMVILTTHQDLP  191 (204)
T ss_pred             CCCEEEEeCCCccCCHHHHHHHHHHHHHHHHCCCEEEEEecChhh
Confidence            68999999997 567788888888887653 34567777776543

>cd03218 ABC_YhbG The ABC transporters belonging to the YhbG family are similar to members of the Mj1267_LivG family, which is involved in the transport of branched-chain amino acids

Probab=97.68  E-value=6.3e-05  Score=63.10  Aligned_cols=42  Identities=19%  Similarity=0.272  Sum_probs=30.8

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhccC-CceEEEEecCCC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYSN-TTRFALACNNSE  137 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~~-~~~~il~~~~~~  137 (317)
                      +++++++||... |.......+.+.+.+... ...+|+++++.+
T Consensus       151 ~p~llllDEPt~~LD~~~~~~~~~~l~~~~~~~~tii~~sH~~~  194 (232)
T cd03218         151 NPKFLLLDEPFAGVDPIAVQDIQKIIKILKDRGIGVLITDHNVR  194 (232)
T ss_pred             CCCEEEecCCcccCCHHHHHHHHHHHHHHHHCCCEEEEEeCCHH
Confidence            689999999974 567777888887765532 456777887754

The genes yhbG and yhbN are located in a single operon and may function together in cell envelope during biogenesis. YhbG is the putative ATP-binding cassette component and YhbN is the putative periplasmic-binding protein. Depletion of each gene product leads to growth arrest, irreversible cell damage and loss of viability in E. coli. The YhbG homolog (NtrA) is essential in Rhizobium meliloti, a symbiotic nitrogen-fixing bacterium.

>cd03248 ABCC_TAP TAP, the Transporter Associated with Antigen Processing; TAP is essential for peptide delivery from the cytosol into the lumen of the endoplasmic reticulum (ER), where these peptides are loaded on major histocompatibility complex (MHC) I molecules

Probab=97.68  E-value=8.2e-05  Score=62.14  Aligned_cols=43  Identities=14%  Similarity=0.304  Sum_probs=33.1

Q ss_pred             ceeEEEEeCCC-CCCHHHHHHHHHHhhhccCCceEEEEecCCCc
Q psy879           96 RHKIVILDEAD-SMTDGAQQALRRTMEIYSNTTRFALACNNSEK  138 (317)
Q Consensus        96 ~~~vliiDE~d-~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~  138 (317)
                      ++.++++||.. .+.......+.+++.+......+|++|++...
T Consensus       168 ~p~llllDEPt~~LD~~~~~~l~~~l~~~~~~~tii~~sh~~~~  211 (226)
T cd03248         168 NPQVLILDEATSALDAESEQQVQQALYDWPERRTVLVIAHRLST  211 (226)
T ss_pred             CCCEEEEeCCcccCCHHHHHHHHHHHHHHcCCCEEEEEECCHHH
Confidence            67999999998 56777888888888765555667888877543

Loaded MHC I leave the ER and display their antigenic cargo on the cell surface to cytotoxic T cells. Subsequently, virus-infected or malignantly transformed cells can be eliminated. TAP belongs to the large family of ATP-binding cassette (ABC) transporters, which translocate a vast variety of solutes across membranes.

>PF13207 AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6_G 2QT1_A 2QSZ_A 2QSY_A 2QT0_A 2QG6_A 2P0E_A

Probab=97.67  E-value=3.7e-05  Score=57.34  Aligned_cols=22  Identities=64%  Similarity=0.857  Sum_probs=21.0

Q ss_pred             EEEECCCCCCHHHHHHHHHHHH
Q psy879           34 IIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~l   55 (317)
                      +++.|+||+||||+++.+++.+
T Consensus         2 I~I~G~~gsGKST~a~~La~~~   23 (121)
T PF13207_consen    2 IIISGPPGSGKSTLAKELAERL   23 (121)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHH
Confidence            7899999999999999999987

...

>TIGR01277 thiQ thiamine ABC transporter, ATP-binding protein

Probab=97.67  E-value=9.1e-05  Score=61.28  Aligned_cols=42  Identities=12%  Similarity=0.178  Sum_probs=31.3

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhccC--CceEEEEecCCC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYSN--TTRFALACNNSE  137 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~~--~~~~il~~~~~~  137 (317)
                      +++++++||... +....+..+.+.+.+...  .+.+|+++++..
T Consensus       146 ~p~llllDEPt~~LD~~~~~~~~~~l~~~~~~~~~tii~vsh~~~  190 (213)
T TIGR01277       146 PNPILLLDEPFSALDPLLREEMLALVKQLCSERQRTLLMVTHHLS  190 (213)
T ss_pred             CCCEEEEcCCCccCCHHHHHHHHHHHHHHHHhcCCEEEEEeCCHH
Confidence            678999999975 567778888888876532  456777777643

This model describes the energy-transducing ATPase subunit ThiQ of the ThiBPQ thiamine (and thiamine pyrophosphate) ABC transporter in several Proteobacteria. This protein is found so far only in Proteobacteria, and is found in complete genomes only if the ThiB and ThiP subunits are also found.

>PRK14532 adenylate kinase; Provisional

Probab=97.67  E-value=0.002  Score=52.06  Aligned_cols=23  Identities=39%  Similarity=0.561  Sum_probs=21.3

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      ++++.||||+||||+++.+++.+
T Consensus         2 ~i~~~G~pGsGKsT~a~~la~~~   24 (188)
T PRK14532          2 NLILFGPPAAGKGTQAKRLVEER   24 (188)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHc
Confidence            48899999999999999999985

>cd03259 ABC_Carb_Solutes_like ABC Carbohydrate and Solute Transporters-like subgroup

Probab=97.67  E-value=7.8e-05  Score=61.65  Aligned_cols=42  Identities=17%  Similarity=0.243  Sum_probs=30.7

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhcc--CCceEEEEecCCC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYS--NTTRFALACNNSE  137 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~--~~~~~il~~~~~~  137 (317)
                      +++++++||... +.......+.+++.+..  ....+|+++++..
T Consensus       148 ~p~~lllDEPt~~LD~~~~~~l~~~l~~~~~~~~~tii~~sH~~~  192 (213)
T cd03259         148 EPSLLLLDEPLSALDAKLREELREELKELQRELGITTIYVTHDQE  192 (213)
T ss_pred             CCCEEEEcCCcccCCHHHHHHHHHHHHHHHHHcCCEEEEEecCHH
Confidence            689999999975 56777888888887653  2455777777643

This family is comprised of proteins involved in the transport of apparently unrelated solutes and proteins specific for di- and oligosaccharides and polyols. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>COG0444 DppD ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]

Probab=97.67  E-value=0.00053  Score=58.80  Aligned_cols=79  Identities=15%  Similarity=0.109  Sum_probs=60.0

Q ss_pred             CHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhhCCCcccHHHHHhhcCCCCHHHHHHHHHHHhc
Q psy879          156 TDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEMLLNCVE  234 (317)
Q Consensus       156 ~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~~~~~i~~~~v~~~~~~~~~~~i~~l~~~~~~  234 (317)
                      +.+|..+...+.++.-|+.-++..+..+....+|.+|+-+-+.-..+...+.+-.|+.-.+++......+.++++.+.+
T Consensus       123 ~~~ea~~~a~~~L~~Vgi~~~~~~~~~YPhelSGGMrQRV~IAmala~~P~LlIADEPTTALDvt~QaqIl~Ll~~l~~  201 (316)
T COG0444         123 SKKEAKERAIELLELVGIPDPERRLKSYPHELSGGMRQRVMIAMALALNPKLLIADEPTTALDVTVQAQILDLLKELQR  201 (316)
T ss_pred             hhHHHHHHHHHHHHHcCCCCHHHHHhhCCcccCCcHHHHHHHHHHHhCCCCEEEeCCCcchhhHHHHHHHHHHHHHHHH
Confidence            4566667777777766776555677888878788899988887777778888888887777777777778888777765

>COG2842 Uncharacterized ATPase, putative transposase [General function prediction only]

Probab=97.66  E-value=0.0014  Score=55.60  Aligned_cols=178  Identities=17%  Similarity=0.199  Sum_probs=101.2

Q ss_pred             CCCCcccCCHHH---HHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHH------
Q psy879            7 QTFSDIVGNEDT---VERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDT------   77 (317)
Q Consensus         7 ~~~~~~~g~~~~---~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~------   77 (317)
                      +...++++-...   ...+..+-+.|.  ...+||-+|.|||+.++.+++.-    +....+..+++.. ....      
T Consensus        69 ~~~~~~l~tkt~r~~~~~~~~A~k~g~--l~~vyg~~g~gKt~a~~~y~~s~----p~~~l~~~~p~~~-a~~~i~~i~~  141 (297)
T COG2842          69 KLAPDFLETKTVRRIFFRTRPASKTGS--LVVVYGYAGLGKTQAAKNYAPSN----PNALLIEADPSYT-ALVLILIICA  141 (297)
T ss_pred             cccccccccchhHhHhhhhhhhhhcCc--eEEEeccccchhHHHHHhhcccC----ccceeecCChhhH-HHHHHHHHHH
Confidence            356677776554   445566666666  68999999999999999988762    1222222222210 0001      


Q ss_pred             ---------HHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCC--------CcCc
Q psy879           78 ---------VRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNS--------EKII  140 (317)
Q Consensus        78 ---------i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~--------~~l~  140 (317)
                               +.+.+.......    ....+.+++||++.|..++.+.+.+..++.+  +-++++.++.        +...
T Consensus       142 ~~~~~~~~~~~d~~~~~~~~l----~~~~~~iivDEA~~L~~~ale~lr~i~d~~G--i~~vLvG~prL~~~l~~~~~~~  215 (297)
T COG2842         142 AAFGATDGTINDLTERLMIRL----RDTVRLIIVDEADRLPYRALEELRRIHDKTG--IGVVLVGMPRLFKVLRRPEDEL  215 (297)
T ss_pred             HHhcccchhHHHHHHHHHHHH----ccCcceeeeehhhccChHHHHHHHHHHHhhC--ceEEEecChHHHhccccchHHH
Confidence                     111111111110    2567899999999999999999999888654  3456665543        1122


Q ss_pred             hhHhhhcce---eeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHh
Q psy879          141 EPIQSRCAM---LRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQST  201 (317)
Q Consensus       141 ~~i~sR~~~---i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~  201 (317)
                      ..+.||..+   +.-.-++.+++..+......    ..++..+..+.....|.+|..-..+..+
T Consensus       216 ~rl~srv~v~~~~~~~~~d~d~~~~~~~~~l~----~~~~~~v~~~~~~~~g~~~~L~~~l~~~  275 (297)
T COG2842         216 SRLYSRVRVGKLLGEKFPDADELAEIAALVLP----TEDELVLMQVIKETEGNIRRLDKILAGA  275 (297)
T ss_pred             HHHHHHhhhHhhhhhhhhhhHHHHHHHHhhCc----cchHHHHHHHHHhcchhHhHHHHHHhhh
Confidence            333344333   11122222333333333221    1456667777788889888877776543

>cd03233 ABC_PDR_domain1 The pleiotropic drug resistance (PDR) family of ATP-binding cassette (ABC) transporters

Probab=97.66  E-value=6.2e-05  Score=61.70  Aligned_cols=30  Identities=27%  Similarity=0.430  Sum_probs=24.9

Q ss_pred             HHhcCCCceEEEECCCCCCHHHHHHHHHHHHc
Q psy879           25 FSSSGNVPNIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        25 ~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      .+..|.  .+.+.||+|+||||+++.++..+.
T Consensus        29 ~i~~Ge--~~~i~G~nGsGKSTLl~~l~G~~~   58 (202)
T cd03233          29 VVKPGE--MVLVLGRPGSGCSTLLKALANRTE   58 (202)
T ss_pred             EECCCc--EEEEECCCCCCHHHHHHHhcccCC
Confidence            344555  699999999999999999999753

PDR is a well-described phenomenon occurring in fungi and shares several similarities with processes in bacteria and higher eukaryotes. This PDR subfamily represents domain I of its (ABC-IM)2 organization. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>PRK10908 cell division protein FtsE; Provisional

Probab=97.66  E-value=0.0001  Score=61.43  Aligned_cols=42  Identities=14%  Similarity=0.313  Sum_probs=30.4

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhcc-CCceEEEEecCCC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYS-NTTRFALACNNSE  137 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~-~~~~~il~~~~~~  137 (317)
                      +++++++||... |....+..+.+.+.+.. ....+|++|++.+
T Consensus       155 ~p~llllDEPt~~LD~~~~~~l~~~l~~~~~~~~tiii~sH~~~  198 (222)
T PRK10908        155 KPAVLLADEPTGNLDDALSEGILRLFEEFNRVGVTVLMATHDIG  198 (222)
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHHHHHHHCCCEEEEEeCCHH
Confidence            678999999975 56677788888777653 3456777777643

>TIGR02788 VirB11 P-type DNA transfer ATPase VirB11

Probab=97.65  E-value=0.00093  Score=58.51  Aligned_cols=36  Identities=42%  Similarity=0.479  Sum_probs=29.3

Q ss_pred             HHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHH
Q psy879           18 TVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        18 ~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      +.+.|...++.|.  ++++.||+|+||||++++++..+
T Consensus       133 ~~~~l~~~v~~~~--~ili~G~tGsGKTTll~al~~~~  168 (308)
T TIGR02788       133 IKEFLRLAIASRK--NIIISGGTGSGKTTFLKSLVDEI  168 (308)
T ss_pred             HHHHHHHHhhCCC--EEEEECCCCCCHHHHHHHHHccC
Confidence            3344556666676  89999999999999999999876

The VirB11 protein is found in the vir locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for DNA transfer. VirB11 is believed to be an ATPase. VirB11 is a homolog of the P-like conjugation system TrbB protein and the Flp pilus sytem protein TadA.

>COG4987 CydC ABC-type transport system involved in cytochrome bd biosynthesis, fused ATPase and permease components [Energy production and conversion / Posttranslational modification, protein turnover, chaperones]

Probab=97.65  E-value=0.00018  Score=65.51  Aligned_cols=38  Identities=24%  Similarity=0.372  Sum_probs=33.0

Q ss_pred             HHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHc
Q psy879           17 DTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        17 ~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      .+++.+.-.++.|.  ++-+.|++||||||+++.+++...
T Consensus       352 ~~L~~~~l~l~~GE--kvAIlG~SGsGKSTllqLl~~~~~  389 (573)
T COG4987         352 KALKNFNLTLAQGE--KVAILGRSGSGKSTLLQLLAGAWD  389 (573)
T ss_pred             chhhccceeecCCC--eEEEECCCCCCHHHHHHHHHhccC
Confidence            57777777788888  899999999999999999998753

>PRK13536 nodulation factor exporter subunit NodI; Provisional

Probab=97.65  E-value=7.6e-05  Score=66.15  Aligned_cols=42  Identities=17%  Similarity=0.238  Sum_probs=30.9

Q ss_pred             ceeEEEEeCCC-CCCHHHHHHHHHHhhhccC-CceEEEEecCCC
Q psy879           96 RHKIVILDEAD-SMTDGAQQALRRTMEIYSN-TTRFALACNNSE  137 (317)
Q Consensus        96 ~~~vliiDE~d-~l~~~~~~~ll~~le~~~~-~~~~il~~~~~~  137 (317)
                      +++++|+||.. .|.+..+..+++++.+... ...+|++|++.+
T Consensus       190 ~P~lLiLDEPt~gLD~~~r~~l~~~l~~l~~~g~tilisSH~l~  233 (340)
T PRK13536        190 DPQLLILDEPTTGLDPHARHLIWERLRSLLARGKTILLTTHFME  233 (340)
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHHHHHHhCCCEEEEECCCHH
Confidence            68999999997 4677888888888876533 455667766543

>TIGR03574 selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal

Probab=97.65  E-value=0.00018  Score=60.99  Aligned_cols=23  Identities=52%  Similarity=0.693  Sum_probs=21.3

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHc
Q psy879           34 IIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      ++|+|+||+||||+|+.+++.+.
T Consensus         2 Ivl~G~pGSGKST~a~~La~~l~   24 (249)
T TIGR03574         2 IILTGLPGVGKSTFSKELAKKLS   24 (249)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHH
Confidence            68999999999999999999874

Members of this protein are L-seryl-tRNA(Sec) kinase. This enzyme is part of a two-step pathway in Eukaryota and Archaea for performing selenocysteine biosynthesis by changing serine misacylated on selenocysteine-tRNA to selenocysteine. This enzyme performs the first step, phosphorylation of the OH group of the serine side chain. This family represents archaeal proteins with this activity.

>PF10923 DUF2791: P-loop Domain of unknown function (DUF2791); InterPro: IPR021228 This is a family of proteins found in archaea and bacteria

Probab=97.64  E-value=0.006  Score=55.02  Aligned_cols=92  Identities=20%  Similarity=0.261  Sum_probs=61.0

Q ss_pred             ceeEEEEeCCCCCCH--------HHHHHHHHHhhhcc----CCceEEEEecCCC--------cCchhHhhhcc-------
Q psy879           96 RHKIVILDEADSMTD--------GAQQALRRTMEIYS----NTTRFALACNNSE--------KIIEPIQSRCA-------  148 (317)
Q Consensus        96 ~~~vliiDE~d~l~~--------~~~~~ll~~le~~~----~~~~~il~~~~~~--------~l~~~i~sR~~-------  148 (317)
                      ..-+|++||++.+.+        ..-+.|++++++..    ++..++++.++..        .-.+++.+|..       
T Consensus       239 ~GLlI~lDE~e~l~kl~~~~~R~~~ye~lr~lidd~~~G~~~gL~~~~~gTPef~eD~rrGv~sY~AL~~RL~~~~~~~~  318 (416)
T PF10923_consen  239 KGLLILLDELENLYKLRNDQAREKNYEALRQLIDDIDQGRAPGLYFVFAGTPEFFEDGRRGVYSYEALAQRLAEEFFADD  318 (416)
T ss_pred             CceEEEEechHHHHhcCChHHHHHHHHHHHHHHHHHhcCCCCceEEEEeeCHHHhhCccccccccHHHHHHHhccccccc
Confidence            356899999997731        24577888887532    4566777765531        23678877753       


Q ss_pred             --------eeeecCCCHHHHHHHHHHHHHH------cCCCCCHHHHHHHHHhc
Q psy879          149 --------MLRYNKLTDAQLLSKVIEICEK------ENISHTNDGLEAIVFTA  187 (317)
Q Consensus       149 --------~i~f~~~~~~~~~~~l~~~~~~------~~~~i~~~~~~~l~~~~  187 (317)
                              +++..+++.+++...+.+...-      ....++++.+..+++.+
T Consensus       319 ~~~n~~~pvIrL~~l~~eel~~l~~klr~i~a~~~~~~~~v~d~~l~~~~~~~  371 (416)
T PF10923_consen  319 GFDNLRAPVIRLQPLTPEELLELLEKLRDIYAEAYGYESRVDDEELKAFAQHV  371 (416)
T ss_pred             cccCccCceecCCCCCHHHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHH
Confidence                    3888999999999877765321      12356777777766554

Some of the proteins in this family are annotated as being methyl-accepting chemotaxis proteins and ATP/GTP binding proteins.

>TIGR01271 CFTR_protein cystic fibrosis transmembrane conductor regulator (CFTR)

Probab=97.64  E-value=6.4e-05  Score=78.95  Aligned_cols=37  Identities=27%  Similarity=0.453  Sum_probs=29.1

Q ss_pred             HHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHH
Q psy879           17 DTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        17 ~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .+++.+.-.++.|.  .+.|+|++|+||||+++.+++..
T Consensus      1233 ~vL~~is~~I~~Ge--kvaIvGrSGsGKSTLl~lL~rl~ 1269 (1490)
T TIGR01271      1233 AVLQDLSFSVEGGQ--RVGLLGRTGSGKSTLLSALLRLL 1269 (1490)
T ss_pred             ceeeccEEEEcCCC--EEEEECCCCCCHHHHHHHHhhhc
Confidence            34444544555666  69999999999999999999975

The model describes the cystis fibrosis transmembrane conductor regulator (CFTR) in eukaryotes. The principal role of this protein is chloride ion conductance. The protein is predicted to consist of 12 transmembrane domains. Mutations or lesions in the genetic loci have been linked to the aetiology of asthma, bronchiectasis, chronic obstructive pulmonary disease etc. Disease-causing mutations have been studied by 36Cl efflux assays in vitro cell cultures and electrophysiology, all of which point to the impairment of chloride channel stability and not the biosynthetic processing per se.

>PRK13632 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=97.64  E-value=0.0001  Score=63.38  Aligned_cols=44  Identities=14%  Similarity=0.299  Sum_probs=32.2

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhccC--CceEEEEecCCCcC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYSN--TTRFALACNNSEKI  139 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~~--~~~~il~~~~~~~l  139 (317)
                      ++.++++||... |.......+.+++.+...  ...+|+++++...+
T Consensus       160 ~p~lllLDEP~~gLD~~~~~~l~~~l~~~~~~~~~tiii~sH~~~~~  206 (271)
T PRK13632        160 NPEIIIFDESTSMLDPKGKREIKKIMVDLRKTRKKTLISITHDMDEA  206 (271)
T ss_pred             CCCEEEEeCCcccCCHHHHHHHHHHHHHHHHhcCcEEEEEEechhHH
Confidence            679999999974 566778888888876532  35677788776544

>TIGR03864 PQQ_ABC_ATP ABC transporter, ATP-binding subunit, PQQ-dependent alcohol dehydrogenase system

Probab=97.64  E-value=0.00012  Score=61.59  Aligned_cols=44  Identities=16%  Similarity=0.260  Sum_probs=32.9

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhcc--CCceEEEEecCCCcC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYS--NTTRFALACNNSEKI  139 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~--~~~~~il~~~~~~~l  139 (317)
                      +++++++||... +.......+.+.+.+..  ....+|++|++.+.+
T Consensus       150 ~p~llllDEP~~~LD~~~~~~l~~~l~~~~~~~~~tiii~sH~~~~~  196 (236)
T TIGR03864       150 RPALLLLDEPTVGLDPASRAAIVAHVRALCRDQGLSVLWATHLVDEI  196 (236)
T ss_pred             CCCEEEEcCCccCCCHHHHHHHHHHHHHHHHhCCCEEEEEecChhhH
Confidence            679999999985 66777888888887653  245678888776554

Members of this protein family are the ATP-binding subunit of an ABC transporter system that is associated with PQQ biosynthesis and PQQ-dependent alcohol dehydrogenases. While this family shows homology to several efflux ABC transporter subunits, the presence of a periplasmic substrate-binding protein and association with systems for catabolism of alcohols suggests a role in import rather than detoxification.

>smart00487 DEXDc DEAD-like helicases superfamily

Probab=97.63  E-value=0.00048  Score=55.56  Aligned_cols=34  Identities=29%  Similarity=0.470  Sum_probs=22.3

Q ss_pred             HHHHHHHhcCCCceEEEECCCCCCHHH-HHHHHHHHH
Q psy879           20 ERLKVFSSSGNVPNIIISGPPGVGKTT-TILCLARIL   55 (317)
Q Consensus        20 ~~l~~~l~~~~~~~~ll~G~~G~GKt~-la~~la~~l   55 (317)
                      +.+...+...  .++++.||+|+|||+ ++..+...+
T Consensus        15 ~~~~~~~~~~--~~~~i~~~~GsGKT~~~~~~~~~~~   49 (201)
T smart00487       15 EAIEALLSGL--RDVILAAPTGSGKTLAALLPALEAL   49 (201)
T ss_pred             HHHHHHHcCC--CcEEEECCCCCchhHHHHHHHHHHh
Confidence            3444444332  379999999999999 455555544

>cd03288 ABCC_SUR2 The SUR domain 2

Probab=97.63  E-value=0.00014  Score=62.01  Aligned_cols=45  Identities=16%  Similarity=0.275  Sum_probs=33.7

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhccCCceEEEEecCCCcCc
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYSNTTRFALACNNSEKII  140 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~  140 (317)
                      +++++++||... +.......+.+.+.+......+|+++++...+.
T Consensus       174 ~p~llllDEPt~gLD~~~~~~l~~~l~~~~~~~tiii~sh~~~~~~  219 (257)
T cd03288         174 KSSILIMDEATASIDMATENILQKVVMTAFADRTVVTIAHRVSTIL  219 (257)
T ss_pred             CCCEEEEeCCccCCCHHHHHHHHHHHHHhcCCCEEEEEecChHHHH
Confidence            579999999975 667777888888876555566788887766543

The sulfonylurea receptor SUR is an ATP binding cassette (ABC) protein of the ABCC/MRP family. Unlike other ABC proteins, it has no intrinsic transport function, neither active nor passive, but associates with the potassium channel proteins Kir6.1 or Kir6.2 to form the ATP-sensitive potassium (K(ATP)) channel. Within the channel complex, SUR serves as a regulatory subunit that fine-tunes the gating of Kir6.x in response to alterations in cellular metabolism. It constitutes a major pharmaceutical target as it binds numerous drugs, K(ATP) channel openers and blockers, capable of up- or down-regulating channel activity.

>cd03231 ABC_CcmA_heme_exporter CcmA, the ATP-binding component of the bacterial CcmAB transporter

Probab=97.63  E-value=0.00017  Score=59.14  Aligned_cols=46  Identities=15%  Similarity=0.170  Sum_probs=32.6

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhcc-CCceEEEEecCCCcCch
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYS-NTTRFALACNNSEKIIE  141 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~-~~~~~il~~~~~~~l~~  141 (317)
                      +++++++||... |.......+.+.+.+.. ....+|+++++...+..
T Consensus       143 ~p~llllDEPt~~LD~~~~~~l~~~l~~~~~~g~tiii~sH~~~~~~~  190 (201)
T cd03231         143 GRPLWILDEPTTALDKAGVARFAEAMAGHCARGGMVVLTTHQDLGLSE  190 (201)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHHHHHhCCCEEEEEecCchhhhh
Confidence            679999999974 56777788888876543 24557778877655443

The CCM family is involved in bacterial cytochrome c biogenesis. Cytochrome c maturation in E. coli requires the ccm operon, which encodes eight membrane proteins (CcmABCDEFGH). CcmE is a periplasmic heme chaperone that binds heme covalently and transfers it onto apocytochrome c in the presence of CcmF, CcmG, and CcmH. The CcmAB proteins represent an ABC transporter and the CcmCD proteins participate in heme transfer to CcmE.

>COG4525 TauB ABC-type taurine transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=97.63  E-value=0.00022  Score=56.63  Aligned_cols=177  Identities=19%  Similarity=0.234  Sum_probs=104.7

Q ss_pred             HHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHHHHHHHhhcccCCCCce
Q psy879           18 TVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRH   97 (317)
Q Consensus        18 ~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~   97 (317)
                      +.+.+.-.+.+|.  .+.+.||+||||||+...+|....... +  .+.++...                  ...|.++.
T Consensus        20 ~le~vsL~ia~ge--~vv~lGpSGcGKTTLLnl~AGf~~P~~-G--~i~l~~r~------------------i~gPgaer   76 (259)
T COG4525          20 ALEDVSLTIASGE--LVVVLGPSGCGKTTLLNLIAGFVTPSR-G--SIQLNGRR------------------IEGPGAER   76 (259)
T ss_pred             hhhccceeecCCC--EEEEEcCCCccHHHHHHHHhcCcCccc-c--eEEECCEe------------------ccCCCccc
Confidence            3344444455666  589999999999999999998652211 1  22222211                  11123456


Q ss_pred             eEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcCchhHhhhcceeeecCCCHHHHHHHHHHHHHHcCCCCCH
Q psy879           98 KIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTN  177 (317)
Q Consensus        98 ~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~~~i~sR~~~i~f~~~~~~~~~~~l~~~~~~~~~~i~~  177 (317)
                      .||+=+|+          |+.++.-.. |+                   .--+.....+..+...+..+.+..-|+.  +
T Consensus        77 gvVFQ~~~----------LlPWl~~~d-Nv-------------------afgL~l~Gi~k~~R~~~a~q~l~~VgL~--~  124 (259)
T COG4525          77 GVVFQNEA----------LLPWLNVID-NV-------------------AFGLQLRGIEKAQRREIAHQMLALVGLE--G  124 (259)
T ss_pred             eeEeccCc----------cchhhHHHH-HH-------------------HHHHHhcCCCHHHHHHHHHHHHHHhCcc--c
Confidence            67664432          333333111 11                   0113334677777777777766655553  3


Q ss_pred             HHHHHHHHhcCCCHHHHHHHHHHhhhCCCcccHHHHHhhcCCCCHHHHHHHHHHHh----------cCCHHHHHHHHHHH
Q psy879          178 DGLEAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEMLLNCV----------EGNMKDSYKIIHHL  247 (317)
Q Consensus       178 ~~~~~l~~~~~gd~r~~i~~l~~~~~~~~~i~~~~v~~~~~~~~~~~i~~l~~~~~----------~~~~~~~~~~~~~l  247 (317)
                      -.-.++.+.| |.+|+-..+.++.+.+....-.|+...+++....+.+.+++-.+.          .++..+|+.+-.+|
T Consensus       125 ~~~~~i~qLS-GGmrQRvGiARALa~eP~~LlLDEPfgAlDa~tRe~mQelLldlw~~tgk~~lliTH~ieEAlflatrL  203 (259)
T COG4525         125 AEHKYIWQLS-GGMRQRVGIARALAVEPQLLLLDEPFGALDALTREQMQELLLDLWQETGKQVLLITHDIEEALFLATRL  203 (259)
T ss_pred             ccccceEeec-chHHHHHHHHHHhhcCcceEeecCchhhHHHHHHHHHHHHHHHHHHHhCCeEEEEeccHHHHHhhhhee
Confidence            2234444555 569999999999888777777777777776665555555543332          34788888888777


Q ss_pred             HHc
Q psy879          248 YKL  250 (317)
Q Consensus       248 ~~~  250 (317)
                      +..
T Consensus       204 vvl  206 (259)
T COG4525         204 VVL  206 (259)
T ss_pred             EEe
Confidence            443

>PRK13652 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=97.63  E-value=0.00014  Score=62.78  Aligned_cols=42  Identities=10%  Similarity=0.210  Sum_probs=31.4

Q ss_pred             ceeEEEEeCCC-CCCHHHHHHHHHHhhhccC--CceEEEEecCCC
Q psy879           96 RHKIVILDEAD-SMTDGAQQALRRTMEIYSN--TTRFALACNNSE  137 (317)
Q Consensus        96 ~~~vliiDE~d-~l~~~~~~~ll~~le~~~~--~~~~il~~~~~~  137 (317)
                      +++++|+||.. .|.......+.+.+.+...  ...+|++|++.+
T Consensus       155 ~p~llilDEPt~gLD~~~~~~l~~~l~~l~~~~g~tvli~tH~~~  199 (277)
T PRK13652        155 EPQVLVLDEPTAGLDPQGVKELIDFLNDLPETYGMTVIFSTHQLD  199 (277)
T ss_pred             CCCEEEEeCCcccCCHHHHHHHHHHHHHHHHhcCCEEEEEecCHH
Confidence            68999999998 5667778888888876532  456777777754

>COG4555 NatA ABC-type Na+ transport system, ATPase component [Energy production and conversion / Inorganic ion transport and metabolism]

Probab=97.63  E-value=0.00023  Score=56.86  Aligned_cols=38  Identities=26%  Similarity=0.359  Sum_probs=29.1

Q ss_pred             HHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCC
Q psy879           19 VERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGP   58 (317)
Q Consensus        19 ~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~   58 (317)
                      .+.+.-.++.|.  ..-+.||+|+||||+.+.++..+...
T Consensus        18 vrdVSF~ae~Ge--i~GlLG~NGAGKTT~LRmiatlL~P~   55 (245)
T COG4555          18 VRDVSFEAEEGE--ITGLLGENGAGKTTLLRMIATLLIPD   55 (245)
T ss_pred             hhheeEEeccce--EEEEEcCCCCCchhHHHHHHHhccCC
Confidence            334444455666  68899999999999999999987543

>PRK14247 phosphate ABC transporter ATP-binding protein; Provisional

Probab=97.62  E-value=0.00015  Score=61.51  Aligned_cols=42  Identities=7%  Similarity=0.169  Sum_probs=31.5

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhccCCceEEEEecCCC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYSNTTRFALACNNSE  137 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~~~~~~il~~~~~~  137 (317)
                      +++++++||... +.......+.+.+.+......+|+++++..
T Consensus       164 ~p~lllLDEP~~~LD~~~~~~l~~~l~~~~~~~tiii~sH~~~  206 (250)
T PRK14247        164 QPEVLLADEPTANLDPENTAKIESLFLELKKDMTIVLVTHFPQ  206 (250)
T ss_pred             CCCEEEEcCCCccCCHHHHHHHHHHHHHHhcCCEEEEEeCCHH
Confidence            689999999975 567778888888876544566777777654

>PRK14269 phosphate ABC transporter ATP-binding protein; Provisional

Probab=97.62  E-value=0.00021  Score=60.50  Aligned_cols=42  Identities=17%  Similarity=0.315  Sum_probs=31.2

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhccCCceEEEEecCCC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYSNTTRFALACNNSE  137 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~~~~~~il~~~~~~  137 (317)
                      +++++++||... +.......+.+.+.+......+|++|++..
T Consensus       160 ~p~lllLDEP~~~LD~~~~~~l~~~l~~~~~~~tiii~tH~~~  202 (246)
T PRK14269        160 KPKLLLLDEPTSALDPISSGVIEELLKELSHNLSMIMVTHNMQ  202 (246)
T ss_pred             CCCEEEEcCCcccCCHHHHHHHHHHHHHHhCCCEEEEEecCHH
Confidence            689999999985 566777888888876544556777777644

>cd03295 ABC_OpuCA_Osmoprotection OpuCA is a the ATP binding component of a bacterial solute transporter that serves a protective role to cells growing in a hyperosmolar environment

Probab=97.62  E-value=0.00016  Score=60.99  Aligned_cols=42  Identities=7%  Similarity=0.208  Sum_probs=31.1

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhccC--CceEEEEecCCC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYSN--TTRFALACNNSE  137 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~~--~~~~il~~~~~~  137 (317)
                      +++++++||... +.......+.+.+.+...  ...+|++|++..
T Consensus       153 ~p~llllDEPt~~LD~~~~~~l~~~L~~~~~~~g~tvii~sH~~~  197 (242)
T cd03295         153 DPPLLLMDEPFGALDPITRDQLQEEFKRLQQELGKTIVFVTHDID  197 (242)
T ss_pred             CCCEEEecCCcccCCHHHHHHHHHHHHHHHHHcCCEEEEEecCHH
Confidence            578999999975 567778888888876532  456778887754

ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition, to the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>PRK14250 phosphate ABC transporter ATP-binding protein; Provisional

Probab=97.61  E-value=0.0001  Score=62.24  Aligned_cols=42  Identities=14%  Similarity=0.225  Sum_probs=30.0

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhcc--CCceEEEEecCCC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYS--NTTRFALACNNSE  137 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~--~~~~~il~~~~~~  137 (317)
                      +++++++||... +.......+.+.+.+..  ....+|++|++..
T Consensus       149 ~p~llllDEPt~~LD~~~~~~l~~~l~~~~~~~g~tii~~sH~~~  193 (241)
T PRK14250        149 NPEVLLLDEPTSALDPTSTEIIEELIVKLKNKMNLTVIWITHNME  193 (241)
T ss_pred             CCCEEEEeCCcccCCHHHHHHHHHHHHHHHHhCCCEEEEEeccHH
Confidence            689999999975 56677777777776543  2455777777654

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=97.61  E-value=0.00092  Score=60.98  Aligned_cols=27  Identities=41%  Similarity=0.495  Sum_probs=23.4

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHcCCC
Q psy879           33 NIIISGPPGVGKTTTILCLARILLGPS   59 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~~~~   59 (317)
                      .++|+|++|+||||++..+|..+....
T Consensus        97 vI~lvG~~GsGKTTtaakLA~~L~~~g  123 (437)
T PRK00771         97 TIMLVGLQGSGKTTTAAKLARYFKKKG  123 (437)
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHHcC
Confidence            389999999999999999999885443

>COG4618 ArpD ABC-type protease/lipase transport system, ATPase and permease components [General function prediction only]

Probab=97.60  E-value=6.7e-05  Score=67.70  Aligned_cols=43  Identities=16%  Similarity=0.286  Sum_probs=31.6

Q ss_pred             CceeEEEEeCCC-CCCHHHHHHHHHHhhhc-cCCceEEEEecCCC
Q psy879           95 GRHKIVILDEAD-SMTDGAQQALRRTMEIY-SNTTRFALACNNSE  137 (317)
Q Consensus        95 ~~~~vliiDE~d-~l~~~~~~~ll~~le~~-~~~~~~il~~~~~~  137 (317)
                      +++++|++||.+ +|..+...+|...+... .....+|++++++.
T Consensus       489 G~P~lvVLDEPNsNLD~~GE~AL~~Ai~~~k~rG~~vvviaHRPs  533 (580)
T COG4618         489 GDPFLVVLDEPNSNLDSEGEAALAAAILAAKARGGTVVVIAHRPS  533 (580)
T ss_pred             CCCcEEEecCCCCCcchhHHHHHHHHHHHHHHcCCEEEEEecCHH
Confidence            578999999998 56777777777766543 45566777888764

>COG1118 CysA ABC-type sulfate/molybdate transport systems, ATPase component [Inorganic ion transport and metabolism]

Probab=97.60  E-value=6.9e-05  Score=63.53  Aligned_cols=103  Identities=12%  Similarity=0.139  Sum_probs=58.1

Q ss_pred             CCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhhCCCcccHHHHHhhcCCCCHHHHHHHHHHH-
Q psy879          154 KLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEMLLNC-  232 (317)
Q Consensus       154 ~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~~~~~i~~~~v~~~~~~~~~~~i~~l~~~~-  232 (317)
                      .|++.+++..+.+.+.--  .++ ...+....+-+|.-|+-+.+.++.+......-.|+...+++......+...+..+ 
T Consensus       108 ~p~~~~~r~rv~elL~lv--qL~-~la~ryP~QLSGGQrQRVALARALA~eP~vLLLDEPf~ALDa~vr~~lr~wLr~~~  184 (345)
T COG1118         108 RPSEAEIRARVEELLRLV--QLE-GLADRYPAQLSGGQRQRVALARALAVEPKVLLLDEPFGALDAKVRKELRRWLRKLH  184 (345)
T ss_pred             CCChhhHHHHHHHHHHHh--ccc-chhhcCchhcChHHHHHHHHHHHhhcCCCeEeecCCchhhhHHHHHHHHHHHHHHH
Confidence            466677777666554422  222 2234444455566888888888877777766666555555443333333333332 


Q ss_pred             ---------hcCCHHHHHHHHHHH--HHcC-----CCHHHHHH
Q psy879          233 ---------VEGNMKDSYKIIHHL--YKLG-----YAPEDIIG  259 (317)
Q Consensus       233 ---------~~~~~~~~~~~~~~l--~~~~-----~~~~~i~~  259 (317)
                               ..+|..+++...+..  +++|     -+|.+++.
T Consensus       185 ~~~~~ttvfVTHD~eea~~ladrvvvl~~G~Ieqvg~p~ev~~  227 (345)
T COG1118         185 DRLGVTTVFVTHDQEEALELADRVVVLNQGRIEQVGPPDEVYD  227 (345)
T ss_pred             HhhCceEEEEeCCHHHHHhhcceEEEecCCeeeeeCCHHHHhc
Confidence                     244777777776665  4444     35666644

>cd03289 ABCC_CFTR2 The CFTR subfamily domain 2

Probab=97.60  E-value=0.00017  Score=61.95  Aligned_cols=42  Identities=24%  Similarity=0.324  Sum_probs=31.0

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhccCCceEEEEecCCC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYSNTTRFALACNNSE  137 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~~~~~~il~~~~~~  137 (317)
                      +++++++||+.. +.......+.+.+.+......+|+++++.+
T Consensus       156 ~p~illlDEpts~LD~~~~~~l~~~l~~~~~~~tii~isH~~~  198 (275)
T cd03289         156 KAKILLLDEPSAHLDPITYQVIRKTLKQAFADCTVILSEHRIE  198 (275)
T ss_pred             CCCEEEEECccccCCHHHHHHHHHHHHHhcCCCEEEEEECCHH
Confidence            679999999975 566667777777775545566788888764

The cystic fibrosis transmembrane regulator (CFTR), the product of the gene mutated in patients with cystic fibrosis, has adapted the ABC transporter structural motif to form a tightly regulated anion channel at the apical surface of many epithelia. Use of the term assembly of a functional ion channel implies the coming together of subunits or at least smaller not-yet functional components of the active whole. In fact, on the basis of current knowledge only the CFTR polypeptide itself is required to form an ATP- and protein kinase A-dependent low-conductance chloride channel of the type present in the apical membrane of many epithelial cells. CFTR displays the typical organization (IM-ABC)2 and carries a characteristic hydrophilic R-domain that separates IM1-ABC1 from IM2-ABC2.

>TIGR02211 LolD_lipo_ex lipoprotein releasing system, ATP-binding protein

Probab=97.60  E-value=0.00016  Score=60.17  Aligned_cols=42  Identities=17%  Similarity=0.264  Sum_probs=31.5

Q ss_pred             ceeEEEEeCCC-CCCHHHHHHHHHHhhhcc--CCceEEEEecCCC
Q psy879           96 RHKIVILDEAD-SMTDGAQQALRRTMEIYS--NTTRFALACNNSE  137 (317)
Q Consensus        96 ~~~vliiDE~d-~l~~~~~~~ll~~le~~~--~~~~~il~~~~~~  137 (317)
                      +++++++||.. .|.......+.+.+.+..  ....+|++|++..
T Consensus       159 ~p~illlDEPt~~LD~~~~~~l~~~l~~~~~~~~~tii~~tH~~~  203 (221)
T TIGR02211       159 QPSLVLADEPTGNLDNNNAKIIFDLMLELNRELNTSFLVVTHDLE  203 (221)
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHHHHHHHhcCCEEEEEeCCHH
Confidence            67999999997 567777888888887653  2456788887754

This model represents LolD, a member of the ABC transporter family (pfam00005). LolD is involved in localization of lipoproteins in some bacteria. It works with a transmembrane protein LolC, which in some species is a paralogous pair LolC and LolE. Depending on whether the residue immediately following the new, modified N-terminal Cys residue, the nascent lipoprotein may be carried further by LolA and LolB to the outer membrane, or remain at the inner membrane. The top scoring proteins excluded by this model include homologs from the archaeal genus Methanosarcina.

>PRK10584 putative ABC transporter ATP-binding protein YbbA; Provisional

Probab=97.60  E-value=0.00017  Score=60.35  Aligned_cols=42  Identities=12%  Similarity=0.222  Sum_probs=31.8

Q ss_pred             ceeEEEEeCCC-CCCHHHHHHHHHHhhhccC--CceEEEEecCCC
Q psy879           96 RHKIVILDEAD-SMTDGAQQALRRTMEIYSN--TTRFALACNNSE  137 (317)
Q Consensus        96 ~~~vliiDE~d-~l~~~~~~~ll~~le~~~~--~~~~il~~~~~~  137 (317)
                      +++++++||.. .+.......+.+.+.+...  ...+|+++++..
T Consensus       164 ~p~llllDEPt~~LD~~~~~~l~~~l~~~~~~~~~tii~~sH~~~  208 (228)
T PRK10584        164 RPDVLFADEPTGNLDRQTGDKIADLLFSLNREHGTTLILVTHDLQ  208 (228)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHHHHHHhcCCEEEEEecCHH
Confidence            68999999997 5677788888888876532  456777887754

>COG3899 Predicted ATPase [General function prediction only]

Probab=97.59  E-value=0.02  Score=57.06  Aligned_cols=107  Identities=13%  Similarity=0.053  Sum_probs=72.0

Q ss_pred             ceeEEEEeCCCCCCHHHHHHHHHHhhhcc--C--CceEEEEecCCCcCchhHhhhcc--eeeecCCCHHHHHHHHHHHHH
Q psy879           96 RHKIVILDEADSMTDGAQQALRRTMEIYS--N--TTRFALACNNSEKIIEPIQSRCA--MLRYNKLTDAQLLSKVIEICE  169 (317)
Q Consensus        96 ~~~vliiDE~d~l~~~~~~~ll~~le~~~--~--~~~~il~~~~~~~l~~~i~sR~~--~i~f~~~~~~~~~~~l~~~~~  169 (317)
                      ++-|+|+|+.+-..+...+.|-..|...+  .  ...+..+.+....+.+..++...  .+...|++..+....+...+.
T Consensus       154 ~plVi~leDlhWaD~~SL~lL~~lm~~~~~~~~~~n~v~~~h~~~~~~~~~~~~~~~i~~I~L~PL~~~d~~~lV~~~l~  233 (849)
T COG3899         154 HPLVIVLEDLHWADSASLKLLQLLMDRIAIGAYRDNEVLLLHPLRPTLGEILKSATNITTITLAPLSRADTNQLVAATLG  233 (849)
T ss_pred             CCeEEEEecccccChhHHHHHHHHHHhcchhhhhccccccCCCccchhhHHhhcCCceeEEecCcCchhhHHHHHHHHhC
Confidence            47899999999999888887777777544  0  00111111111233333444433  399999999999999999875


Q ss_pred             HcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhh
Q psy879          170 KENISHTNDGLEAIVFTAQGDMRQALNNLQSTHN  203 (317)
Q Consensus       170 ~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~  203 (317)
                      .. .....+..+.+.+.+.|++-=+...++....
T Consensus       234 ~~-~~~~~p~~~~i~~kt~GnPfFi~e~lk~l~~  266 (849)
T COG3899         234 CT-KLLPAPLLELIFEKTKGNPFFIEEFLKALYE  266 (849)
T ss_pred             Cc-ccccchHHHHHHHHhcCCCccHHHHHHHHHh
Confidence            42 2455677888999999998777777766544

>PRK13647 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=97.59  E-value=0.00014  Score=62.67  Aligned_cols=42  Identities=14%  Similarity=0.306  Sum_probs=30.7

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhcc-CCceEEEEecCCC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYS-NTTRFALACNNSE  137 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~-~~~~~il~~~~~~  137 (317)
                      +++++++||... +.......+++.+.+.. .+..+|++|++.+
T Consensus       156 ~p~llllDEPt~~LD~~~~~~l~~~l~~~~~~g~tili~tH~~~  199 (274)
T PRK13647        156 DPDVIVLDEPMAYLDPRGQETLMEILDRLHNQGKTVIVATHDVD  199 (274)
T ss_pred             CCCEEEEECCCcCCCHHHHHHHHHHHHHHHHCCCEEEEEeCCHH
Confidence            689999999975 56777888888877653 2456777777644

>PRK13541 cytochrome c biogenesis protein CcmA; Provisional

Probab=97.59  E-value=0.00049  Score=56.07  Aligned_cols=43  Identities=12%  Similarity=0.234  Sum_probs=31.1

Q ss_pred             ceeEEEEeCCC-CCCHHHHHHHHHHhhhc-cCCceEEEEecCCCc
Q psy879           96 RHKIVILDEAD-SMTDGAQQALRRTMEIY-SNTTRFALACNNSEK  138 (317)
Q Consensus        96 ~~~vliiDE~d-~l~~~~~~~ll~~le~~-~~~~~~il~~~~~~~  138 (317)
                      +++++++||.. .+.......+.+++.+. .....+|+++++...
T Consensus       141 ~p~~lllDEP~~~LD~~~~~~l~~~l~~~~~~~~tiii~sh~~~~  185 (195)
T PRK13541        141 QSDLWLLDEVETNLSKENRDLLNNLIVMKANSGGIVLLSSHLESS  185 (195)
T ss_pred             CCCEEEEeCCcccCCHHHHHHHHHHHHHHHhCCCEEEEEeCCccc
Confidence            67999999998 56777788888877632 234567777777553

>PTZ00265 multidrug resistance protein (mdr1); Provisional

Probab=97.59  E-value=0.00021  Score=74.84  Aligned_cols=37  Identities=27%  Similarity=0.314  Sum_probs=28.6

Q ss_pred             HHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHc
Q psy879           18 TVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        18 ~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      +++.+.-.++.|.  .+.|.||+|+||||+++.+.+...
T Consensus      1183 vL~~lsl~i~~G~--~vAIVG~SGsGKSTl~~LL~r~yd 1219 (1466)
T PTZ00265       1183 IYKDLTFSCDSKK--TTAIVGETGSGKSTVMSLLMRFYD 1219 (1466)
T ss_pred             cccCeeEEEcCCC--EEEEECCCCCCHHHHHHHHHHhCC
Confidence            4444444455565  699999999999999999999754

>PRK13644 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=97.59  E-value=0.00014  Score=62.62  Aligned_cols=44  Identities=16%  Similarity=0.242  Sum_probs=32.7

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhcc-CCceEEEEecCCCcC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYS-NTTRFALACNNSEKI  139 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~-~~~~~il~~~~~~~l  139 (317)
                      ++.++++||... +....+..+++.+.+.. ....+|++|++.+.+
T Consensus       154 ~p~lllLDEPt~gLD~~~~~~l~~~l~~l~~~g~til~~tH~~~~~  199 (274)
T PRK13644        154 EPECLIFDEVTSMLDPDSGIAVLERIKKLHEKGKTIVYITHNLEEL  199 (274)
T ss_pred             CCCEEEEeCCcccCCHHHHHHHHHHHHHHHhCCCEEEEEecCHHHH
Confidence            689999999974 56777888888887643 356678888776644

>cd03301 ABC_MalK_N The N-terminal ATPase domain of the maltose transporter, MalK

Probab=97.58  E-value=9.8e-05  Score=61.05  Aligned_cols=42  Identities=14%  Similarity=0.215  Sum_probs=30.7

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhccC--CceEEEEecCCC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYSN--TTRFALACNNSE  137 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~~--~~~~il~~~~~~  137 (317)
                      +++++++||... +.......+.+.+.+...  ...+|++|++..
T Consensus       148 ~p~llllDEPt~~LD~~~~~~l~~~l~~~~~~~~~tvi~~sH~~~  192 (213)
T cd03301         148 EPKVFLMDEPLSNLDAKLRVQMRAELKRLQQRLGTTTIYVTHDQV  192 (213)
T ss_pred             CCCEEEEcCCcccCCHHHHHHHHHHHHHHHHHcCCEEEEEeCCHH
Confidence            679999999975 567778888888876532  456777777643

ATP binding cassette (ABC) proteins function from bacteria to human, mediating the translocation of substances into and out of cells or organelles. ABC transporters contain two transmembrane-spanning domains (TMDs) or subunits and two nucleotide binding domains (NBDs) or subunits that couple transport to the hydrolysis of ATP. In the maltose transport system, the periplasmic maltose binding protein (MBP) stimulates the ATPase activity of the membrane-associated transporter, which consists of two transmembrane subunits, MalF and MalG, and two copies of the ATP binding subunit, MalK, and becomes tightly bound to the transporter in the catalytic transition state, ensuring that maltose is passed to the transporter as ATP is hydrolyzed.

>cd03237 ABC_RNaseL_inhibitor_domain2 The ATPase domain 2 of RNase L inhibitor

Probab=97.58  E-value=0.00063  Score=57.56  Aligned_cols=80  Identities=13%  Similarity=0.151  Sum_probs=45.1

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhcc--CCceEEEEecCCCcCchhHhhhcceee------ecCCCHHHHHHHHHH
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYS--NTTRFALACNNSEKIIEPIQSRCAMLR------YNKLTDAQLLSKVIE  166 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~--~~~~~il~~~~~~~l~~~i~sR~~~i~------f~~~~~~~~~~~l~~  166 (317)
                      ++.++++||... |.......+.+.+.+..  ....+|+++++.. ....+..|+.++.      -..-++..+.+.+..
T Consensus       133 ~p~llllDEPt~~LD~~~~~~l~~~l~~~~~~~~~tiiivsHd~~-~~~~~~d~i~~l~~~~~~~~~~~~~~~~~~~~~~  211 (246)
T cd03237         133 DADIYLLDEPSAYLDVEQRLMASKVIRRFAENNEKTAFVVEHDII-MIDYLADRLIVFEGEPSVNGVANPPQSLRSGMNR  211 (246)
T ss_pred             CCCEEEEeCCcccCCHHHHHHHHHHHHHHHHhcCCEEEEEeCCHH-HHHHhCCEEEEEcCCCeeEEEeCCchHHHHHHHH
Confidence            679999999975 56677777777776643  2456777777643 2223333332221      011233344455555


Q ss_pred             HHHHcCCCCC
Q psy879          167 ICEKENISHT  176 (317)
Q Consensus       167 ~~~~~~~~i~  176 (317)
                      .++.+++.+.
T Consensus       212 ~l~~~~~~~~  221 (246)
T cd03237         212 FLKNLDITFR  221 (246)
T ss_pred             HHHHCCCEEe
Confidence            5555555443

The ABC ATPase, RNase L inhibitor (RLI), is a key enzyme in ribosomal biogenesis, formation of translation preinitiation complexes, and assembly of HIV capsids. RLI's are not transport proteins and thus cluster with a group of soluble proteins that lack the transmembrane components commonly found in other members of the family. Structurally, RLI's have an N-terminal Fe-S domain and two nucleotide-binding domains which are arranged to form two composite active sites in their interface cleft. RLI is one of the most conserved enzymes between archaea and eukaryotes with a sequence identity of more than 48%. The high degree of evolutionary conservation suggests that RLI performs a central role in archaeal and eukaryotic physiology.

>cd03256 ABC_PhnC_transporter ABC-type phosphate/phosphonate transport system

Probab=97.58  E-value=0.00018  Score=60.70  Aligned_cols=43  Identities=7%  Similarity=0.193  Sum_probs=31.3

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhcc--CCceEEEEecCCCc
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYS--NTTRFALACNNSEK  138 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~--~~~~~il~~~~~~~  138 (317)
                      +++++++||... +.......+.+.+.+..  ....+|+++++.+.
T Consensus       162 ~p~llllDEPt~~LD~~~~~~l~~~l~~~~~~~~~tii~~tH~~~~  207 (241)
T cd03256         162 QPKLILADEPVASLDPASSRQVMDLLKRINREEGITVIVSLHQVDL  207 (241)
T ss_pred             CCCEEEEeCccccCCHHHHHHHHHHHHHHHHhcCCEEEEEeCCHHH
Confidence            679999999975 56777788888887653  24567778877543

Phosphonates are a class of organophosphorus compounds characterized by a chemically stable carbon-to-phosphorus (C-P) bond. Phosphonates are widespread among naturally occurring compounds in all kingdoms of wildlife, but only procaryotic microorganisms are able to cleave this bond. Certain bacteria such as E. coli can use alkylphosphonates as a phosphorus source. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>cd03265 ABC_DrrA DrrA is the ATP-binding protein component of a bacterial exporter complex that confers resistance to the antibiotics daunorubicin and doxorubicin

Probab=97.58  E-value=0.00013  Score=60.67  Aligned_cols=42  Identities=17%  Similarity=0.251  Sum_probs=30.6

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhccC--CceEEEEecCCC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYSN--TTRFALACNNSE  137 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~~--~~~~il~~~~~~  137 (317)
                      +++++++||... |.......+.+++.+...  ...+|++|++..
T Consensus       149 ~p~llllDEPt~~LD~~~~~~l~~~l~~~~~~~~~tvi~~tH~~~  193 (220)
T cd03265         149 RPEVLFLDEPTIGLDPQTRAHVWEYIEKLKEEFGMTILLTTHYME  193 (220)
T ss_pred             CCCEEEEcCCccCCCHHHHHHHHHHHHHHHHhcCCEEEEEeCCHH
Confidence            689999999974 567778888888776432  356777777644

In addition to DrrA, the complex includes an integral membrane protein called DrrB. DrrA belongs to the ABC family of transporters and shares sequence and functional similarities with a protein found in cancer cells called P-glycoprotein. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region in addition to the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>PRK10895 lipopolysaccharide ABC transporter ATP-binding protein; Provisional

Probab=97.57  E-value=0.00013  Score=61.52  Aligned_cols=42  Identities=17%  Similarity=0.218  Sum_probs=29.9

Q ss_pred             ceeEEEEeCCC-CCCHHHHHHHHHHhhhccC-CceEEEEecCCC
Q psy879           96 RHKIVILDEAD-SMTDGAQQALRRTMEIYSN-TTRFALACNNSE  137 (317)
Q Consensus        96 ~~~vliiDE~d-~l~~~~~~~ll~~le~~~~-~~~~il~~~~~~  137 (317)
                      +++++++||.. .+.......+.+.+..... ...+|+++++..
T Consensus       155 ~p~llllDEPt~~LD~~~~~~l~~~l~~~~~~g~tiii~sH~~~  198 (241)
T PRK10895        155 NPKFILLDEPFAGVDPISVIDIKRIIEHLRDSGLGVLITDHNVR  198 (241)
T ss_pred             CCCEEEEcCCcccCCHHHHHHHHHHHHHHHhcCCEEEEEEcCHH
Confidence            67999999998 5667777777777765432 455777777643

>PRK11153 metN DL-methionine transporter ATP-binding subunit; Provisional

Probab=97.57  E-value=0.00013  Score=64.87  Aligned_cols=42  Identities=12%  Similarity=0.249  Sum_probs=31.4

Q ss_pred             ceeEEEEeCCC-CCCHHHHHHHHHHhhhccC--CceEEEEecCCC
Q psy879           96 RHKIVILDEAD-SMTDGAQQALRRTMEIYSN--TTRFALACNNSE  137 (317)
Q Consensus        96 ~~~vliiDE~d-~l~~~~~~~ll~~le~~~~--~~~~il~~~~~~  137 (317)
                      ++.++++||.. .|.......+.+++.+...  ...+|++|++.+
T Consensus       158 ~p~iLlLDEPts~LD~~~~~~l~~~L~~l~~~~g~tiilvtH~~~  202 (343)
T PRK11153        158 NPKVLLCDEATSALDPATTRSILELLKDINRELGLTIVLITHEMD  202 (343)
T ss_pred             CCCEEEEeCCcccCCHHHHHHHHHHHHHHHHhcCCEEEEEeCCHH
Confidence            68999999997 5667778888888876532  456778887754

>cd03283 ABC_MutS-like MutS-like homolog in eukaryotes

Probab=97.57  E-value=0.00067  Score=55.41  Aligned_cols=23  Identities=26%  Similarity=0.382  Sum_probs=20.8

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .++|+||+|+||||+.+.++...
T Consensus        27 ~~~ltGpNg~GKSTllr~i~~~~   49 (199)
T cd03283          27 GILITGSNMSGKSTFLRTIGVNV   49 (199)
T ss_pred             EEEEECCCCCChHHHHHHHHHHH
Confidence            58999999999999999998654

The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form slid

>TIGR00957 MRP_assoc_pro multi drug resistance-associated protein (MRP)

Probab=97.57  E-value=0.00019  Score=75.66  Aligned_cols=37  Identities=30%  Similarity=0.415  Sum_probs=28.8

Q ss_pred             HHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHc
Q psy879           18 TVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        18 ~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      +++.+.-.++.|.  .+.++|++|+||||+++.+.+.+.
T Consensus      1301 vL~~is~~I~~Ge--kiaIVGrTGsGKSTL~~lL~rl~~ 1337 (1522)
T TIGR00957      1301 VLRHINVTIHGGE--KVGIVGRTGAGKSSLTLGLFRINE 1337 (1522)
T ss_pred             cccceeEEEcCCC--EEEEECCCCCCHHHHHHHHhcCcc
Confidence            4444444455665  699999999999999999998753

This model describes multi drug resistance-associated protein (MRP) in eukaryotes. The multidrug resistance-associated protein is an integral membrane protein that causes multidrug resistance when overexpressed in mammalian cells. It belongs to ABC transporter superfamily. The protein topology and function was experimentally demonstrated by epitope tagging and immunofluorescence. Insertion of tags in the critical regions associated with drug efflux, abrogated its function. The C-terminal domain seem to highly conserved.

>TIGR03411 urea_trans_UrtD urea ABC transporter, ATP-binding protein UrtD

Probab=97.57  E-value=0.00016  Score=61.03  Aligned_cols=42  Identities=19%  Similarity=0.297  Sum_probs=32.3

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhccCCceEEEEecCCC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYSNTTRFALACNNSE  137 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~~~~~~il~~~~~~  137 (317)
                      +++++++||... |....+..+.+++.+......+|+++++.+
T Consensus       161 ~p~~lllDEPt~~LD~~~~~~l~~~l~~~~~~~tii~~sH~~~  203 (242)
T TIGR03411       161 DPKLLLLDEPVAGMTDEETEKTAELLKSLAGKHSVVVVEHDME  203 (242)
T ss_pred             CCCEEEecCCccCCCHHHHHHHHHHHHHHhcCCEEEEEECCHH
Confidence            579999999974 567778888888887655566777777644

Members of this protein family are ABC transporter ATP-binding subunits associated with urea transport and metabolism. This protein is found in a conserved five-gene transport operon typically found adjacent to urease genes. It was shown in Cyanobacteria that disruption leads to the loss of high-affinity urea transport activity.

>PRK11124 artP arginine transporter ATP-binding subunit; Provisional

Probab=97.57  E-value=0.00015  Score=61.21  Aligned_cols=42  Identities=7%  Similarity=0.202  Sum_probs=30.9

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhccC-CceEEEEecCCC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYSN-TTRFALACNNSE  137 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~~-~~~~il~~~~~~  137 (317)
                      +++++++||... |.......+.+++.+... ...+|+++++..
T Consensus       159 ~p~llilDEPt~~LD~~~~~~l~~~l~~~~~~~~tii~~sh~~~  202 (242)
T PRK11124        159 EPQVLLFDEPTAALDPEITAQIVSIIRELAETGITQVIVTHEVE  202 (242)
T ss_pred             CCCEEEEcCCCCcCCHHHHHHHHHHHHHHHHcCCEEEEEeCCHH
Confidence            678999999974 567778888888876543 455777777654

>cd02021 GntK Gluconate kinase (GntK) catalyzes the phosphoryl transfer from ATP to gluconate

Probab=97.57  E-value=0.00034  Score=54.31  Aligned_cols=22  Identities=41%  Similarity=0.542  Sum_probs=20.4

Q ss_pred             EEEECCCCCCHHHHHHHHHHHH
Q psy879           34 IIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~l   55 (317)
                      ++|+|+||+||||+++.+++.+
T Consensus         2 i~l~G~~GsGKST~a~~l~~~~   23 (150)
T cd02021           2 IVVMGVSGSGKSTVGKALAERL   23 (150)
T ss_pred             EEEEcCCCCCHHHHHHHHHhhc
Confidence            6899999999999999999974

The resulting product gluconate-6-phoshate is an important precursor of gluconate metabolism. GntK acts as a dimmer composed of two identical subunits.

>PRK14737 gmk guanylate kinase; Provisional

Probab=97.56  E-value=0.0047  Score=49.82  Aligned_cols=23  Identities=39%  Similarity=0.365  Sum_probs=21.0

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      -++|.||+|+|||++++.+.+..
T Consensus         6 ~ivl~GpsG~GK~tl~~~l~~~~   28 (186)
T PRK14737          6 LFIISSVAGGGKSTIIQALLEEH   28 (186)
T ss_pred             EEEEECCCCCCHHHHHHHHHhcC
Confidence            48999999999999999998864

>KOG0054|consensus

Probab=97.56  E-value=0.00014  Score=73.92  Aligned_cols=40  Identities=25%  Similarity=0.373  Sum_probs=31.9

Q ss_pred             CHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHc
Q psy879           15 NEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        15 ~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      .+.+++.+.-.++.|.  .+-+.|-.|+|||+++.++.+...
T Consensus      1152 lp~VLk~is~~I~p~e--KVGIVGRTGaGKSSL~~aLFRl~e 1191 (1381)
T KOG0054|consen 1152 LPLVLKGISFTIKPGE--KVGIVGRTGAGKSSLILALFRLVE 1191 (1381)
T ss_pred             CcchhcCceEEEcCCc--eEEEeCCCCCCHHHHHHHHHHhcC
Confidence            4556666665566665  699999999999999999999764

>cd01128 rho_factor Transcription termination factor rho is a bacterial ATP-dependent RNA/DNA helicase

Probab=97.56  E-value=0.00025  Score=59.84  Aligned_cols=26  Identities=31%  Similarity=0.454  Sum_probs=23.0

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHcCC
Q psy879           33 NIIISGPPGVGKTTTILCLARILLGP   58 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~~~   58 (317)
                      .++|+||+|+||||+++.+++.+...
T Consensus        18 r~~I~G~~G~GKTTLlr~I~n~l~~~   43 (249)
T cd01128          18 RGLIVAPPKAGKTTLLQSIANAITKN   43 (249)
T ss_pred             EEEEECCCCCCHHHHHHHHHhccccc
Confidence            59999999999999999999987443

It is a homohexamer. Each monomer consists of an N-terminal domain of the OB fold, which is responsible for binding to cysteine rich nucleotides. This alignment is of the C-terminal ATP binding domain.

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=97.56  E-value=0.0007  Score=60.57  Aligned_cols=36  Identities=42%  Similarity=0.653  Sum_probs=27.1

Q ss_pred             HHHHHhcCCCce--EEEECCCCCCHHHHHHHHHHHHcC
Q psy879           22 LKVFSSSGNVPN--IIISGPPGVGKTTTILCLARILLG   57 (317)
Q Consensus        22 l~~~l~~~~~~~--~ll~G~~G~GKt~la~~la~~l~~   57 (317)
                      |...+..|-.+.  ++++|+||+|||+++..++..+..
T Consensus        71 LD~vLgGGi~~GslvLI~G~pG~GKStLllq~a~~~a~  108 (372)
T cd01121          71 LDRVLGGGLVPGSVILIGGDPGIGKSTLLLQVAARLAK  108 (372)
T ss_pred             HHHhhcCCccCCeEEEEEeCCCCCHHHHHHHHHHHHHh
Confidence            444454444443  899999999999999999987643

This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.

>TIGR01288 nodI ATP-binding ABC transporter family nodulation protein NodI

Probab=97.55  E-value=0.00013  Score=63.79  Aligned_cols=42  Identities=17%  Similarity=0.242  Sum_probs=30.9

Q ss_pred             ceeEEEEeCCC-CCCHHHHHHHHHHhhhcc-CCceEEEEecCCC
Q psy879           96 RHKIVILDEAD-SMTDGAQQALRRTMEIYS-NTTRFALACNNSE  137 (317)
Q Consensus        96 ~~~vliiDE~d-~l~~~~~~~ll~~le~~~-~~~~~il~~~~~~  137 (317)
                      +++++++||.. .|.+.....+.+.+.+.. ....+|++|++..
T Consensus       153 ~p~lllLDEPt~gLD~~~~~~l~~~l~~~~~~g~til~~sH~~~  196 (303)
T TIGR01288       153 DPQLLILDEPTTGLDPHARHLIWERLRSLLARGKTILLTTHFME  196 (303)
T ss_pred             CCCEEEEeCCCcCCCHHHHHHHHHHHHHHHhCCCEEEEECCCHH
Confidence            68999999996 567777888888887653 2455777777644

This model does not recognize the highly divergent NodI from Azorhizobium caulinodans.

>COG1136 SalX ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]

Probab=97.55  E-value=0.00051  Score=56.52  Aligned_cols=73  Identities=15%  Similarity=0.016  Sum_probs=47.8

Q ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhhCCCcccHHHHHhhcCCCCHHHHHHHHHHHh
Q psy879          159 QLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEMLLNCV  233 (317)
Q Consensus       159 ~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~~~~~i~~~~v~~~~~~~~~~~i~~l~~~~~  233 (317)
                      +..++....+..-|+  .+..........+|.-++.+.+.++.+.....|-.|+.-..++......+.+++..+.
T Consensus       117 ~~~~~~~~l~~~lgl--~~~~~~~~p~eLSGGqqQRVAIARAL~~~P~iilADEPTgnLD~~t~~~V~~ll~~~~  189 (226)
T COG1136         117 RRKRAAEELLEVLGL--EDRLLKKKPSELSGGQQQRVAIARALINNPKIILADEPTGNLDSKTAKEVLELLRELN  189 (226)
T ss_pred             HHHHHHHHHHHhcCC--hhhhccCCchhcCHHHHHHHHHHHHHhcCCCeEEeeCccccCChHHHHHHHHHHHHHH
Confidence            444455555443343  3444434455555668888889999988888888887777777766666777766653

>PRK10253 iron-enterobactin transporter ATP-binding protein; Provisional

Probab=97.55  E-value=0.00023  Score=60.94  Aligned_cols=42  Identities=17%  Similarity=0.158  Sum_probs=31.6

Q ss_pred             ceeEEEEeCCC-CCCHHHHHHHHHHhhhccC--CceEEEEecCCC
Q psy879           96 RHKIVILDEAD-SMTDGAQQALRRTMEIYSN--TTRFALACNNSE  137 (317)
Q Consensus        96 ~~~vliiDE~d-~l~~~~~~~ll~~le~~~~--~~~~il~~~~~~  137 (317)
                      +++++++||.. .|.......+.+.+.+...  ...+|+++++..
T Consensus       161 ~p~llllDEPt~gLD~~~~~~l~~~L~~l~~~~~~tiii~tH~~~  205 (265)
T PRK10253        161 ETAIMLLDEPTTWLDISHQIDLLELLSELNREKGYTLAAVLHDLN  205 (265)
T ss_pred             CCCEEEEeCccccCCHHHHHHHHHHHHHHHHhcCCEEEEEeCCHH
Confidence            68999999997 5677888888888876532  456777777654

>PRK09493 glnQ glutamine ABC transporter ATP-binding protein; Reviewed

Probab=97.55  E-value=0.00016  Score=61.05  Aligned_cols=42  Identities=12%  Similarity=0.286  Sum_probs=30.8

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhcc-CCceEEEEecCCC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYS-NTTRFALACNNSE  137 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~-~~~~~il~~~~~~  137 (317)
                      +++++++||... +.......+.+++.+.. ....+|++|++..
T Consensus       154 ~p~llllDEP~~~LD~~~~~~l~~~l~~~~~~~~tiii~sH~~~  197 (240)
T PRK09493        154 KPKLMLFDEPTSALDPELRHEVLKVMQDLAEEGMTMVIVTHEIG  197 (240)
T ss_pred             CCCEEEEcCCcccCCHHHHHHHHHHHHHHHHcCCEEEEEeCCHH
Confidence            679999999975 56777888888887653 2456777777654

>COG3910 Predicted ATPase [General function prediction only]

Probab=97.55  E-value=0.0023  Score=50.63  Aligned_cols=49  Identities=20%  Similarity=0.230  Sum_probs=33.9

Q ss_pred             CCCCCcccCCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHH
Q psy879            6 PQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus         6 P~~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      |.+|.+.-..=-+.+.++..+ .-+.|.-+|+|++|+||||+..++|...
T Consensus        13 ve~~~eYp~slPa~r~l~~~L-eF~apIT~i~GENGsGKSTLLEaiA~~~   61 (233)
T COG3910          13 VESFEEYPFSLPAFRHLEERL-EFRAPITFITGENGSGKSTLLEAIAAGM   61 (233)
T ss_pred             ccchhhCcccchHHHhhhhhc-cccCceEEEEcCCCccHHHHHHHHHhhc
Confidence            444554444444555555433 3445678999999999999999999765

>PRK11650 ugpC glycerol-3-phosphate transporter ATP-binding subunit; Provisional

Probab=97.55  E-value=0.00013  Score=65.07  Aligned_cols=42  Identities=10%  Similarity=0.154  Sum_probs=30.4

Q ss_pred             ceeEEEEeCCC-CCCHHHHHHHHHHhhhccC--CceEEEEecCCC
Q psy879           96 RHKIVILDEAD-SMTDGAQQALRRTMEIYSN--TTRFALACNNSE  137 (317)
Q Consensus        96 ~~~vliiDE~d-~l~~~~~~~ll~~le~~~~--~~~~il~~~~~~  137 (317)
                      +++++++||.. .|.......+.+.+.+...  .+.+|++|++..
T Consensus       152 ~P~llLLDEP~s~LD~~~r~~l~~~l~~l~~~~g~tii~vTHd~~  196 (356)
T PRK11650        152 EPAVFLFDEPLSNLDAKLRVQMRLEIQRLHRRLKTTSLYVTHDQV  196 (356)
T ss_pred             CCCEEEEeCCcccCCHHHHHHHHHHHHHHHHhcCCEEEEEeCCHH
Confidence            68999999998 4566677777777765432  466888888754

>PRK13642 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=97.54  E-value=0.00019  Score=61.93  Aligned_cols=44  Identities=20%  Similarity=0.319  Sum_probs=32.7

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhccC--CceEEEEecCCCcC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYSN--TTRFALACNNSEKI  139 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~~--~~~~il~~~~~~~l  139 (317)
                      +++++++||... |.......+++.+.+...  ...+|++|++...+
T Consensus       158 ~p~llllDEPt~~LD~~~~~~l~~~l~~l~~~~g~tiil~sH~~~~~  204 (277)
T PRK13642        158 RPEIIILDESTSMLDPTGRQEIMRVIHEIKEKYQLTVLSITHDLDEA  204 (277)
T ss_pred             CCCEEEEeCCcccCCHHHHHHHHHHHHHHHHhcCCEEEEEeCCHHHH
Confidence            679999999975 567778888888876543  45677788776554

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	317
1sxj_B	323	Crystal Structure Of The Eukaryotic Clamp Loader (R		1e-105
1iqp_A	327	Crystal Structure Of The Clamp Loader Small Subunit		6e-70
2chq_A	319	Replication Factor C Adpnp Complex Length = 319		6e-69
2chg_A	226	Replication Factor C Domains 1 And 2 Length = 226		9e-57
1sxj_C	340	Crystal Structure Of The Eukaryotic Clamp Loader (R		2e-46
1sxj_D	353	Crystal Structure Of The Eukaryotic Clamp Loader (R		7e-45
1sxj_E	354	Crystal Structure Of The Eukaryotic Clamp Loader (R		5e-20
3u5z_B	324	Structure Of T4 Bacteriophage Clamp Loader Bound To		3e-18
1xxi_B	368	Adp Bound E. Coli Clamp Loader Complex Length = 368		1e-15
3glf_B	395	Crystal Structure Of The Ecoli Clamp Loader Bound T		2e-15
1jr3_A	373	Crystal Structure Of The Processivity Clamp Loader		2e-15
3glh_B	376	Crystal Structure Of The E. Coli Clamp Loader Bound		2e-15
3glg_B	395	Crystal Structure Of A Mutant (Gammat157a) E. Coli		3e-15
1njg_A	250	Nucleotide-Free Form Of An Isolated E. Coli Clamp L		2e-14
1sxj_A	516	Crystal Structure Of The Eukaryotic Clamp Loader (R		6e-09
3pvs_A	447	Structure And Biochemical Activities Of Escherichia		2e-06

>pdb|1SXJ|B Chain B, Crystal Structure Of The Eukaryotic Clamp Loader (Replication Factor C, Rfc) Bound To The Dna Sliding Clamp (Proliferating Cell Nuclear Antigen, Pcna) Length = 323

Iteration: 1
 Score =  377 bits (968), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 181/297 (60%), Positives = 236/297 (79%), Gaps = 5/297 (1%)
Query: 1   IEKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSF 60
           +EKYRPQ  SDIVGN++T++RL+  +  GN+P++IISG PG+GKTT++ CLA  LLG S+
Sbjct: 12  VEKYRPQVLSDIVGNKETIDRLQQIAKDGNMPHMIISGMPGIGKTTSVHCLAHELLGRSY 71
Query: 61  KDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTM 120
            D VLELNAS+DRGID VRN+IK FAQ+K+ LPPG+HKIVILDEADSMT GAQQALRRTM
Sbjct: 72  ADGVLELNASDDRGIDVVRNQIKHFAQKKLHLPPGKHKIVILDEADSMTAGAQQALRRTM 131
Query: 121 EIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGL 180
           E+YSN+TRFA ACN S KIIEP+QS+CA+LRY+KL+D  +L ++++I + E++ +TNDGL
Sbjct: 132 ELYSNSTRFAFACNQSNKIIEPLQSQCAILRYSKLSDEDVLKRLLQIIKLEDVKYTNDGL 191
Query: 181 EAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEMLLNCVEGNMKDS 240
           EAI+FTA+GDMRQA+NNLQST  G G V A+ VFK+ D PHPL VK+MLL     N++DS
Sbjct: 192 EAIIFTAEGDMRQAINNLQSTVAGHGLVNADNVFKIVDSPHPLIVKKMLL---ASNLEDS 248
Query: 241 YKIIH-HLYKLGYAPEDIIGNIFRVAKTL-DIPEPLKLSIIQEIGNVHLRISEGVNS 295
            +I+   L+K GY+  DI+   FRV K L  + E ++L +I+EIG  H+RI EGV +
Sbjct: 249 IQILRTDLWKKGYSSIDIVTTSFRVTKNLAQVKESVRLEMIKEIGLTHMRILEGVGT 305

>pdb|1IQP|A Chain A, Crystal Structure Of The Clamp Loader Small Subunit From Pyrococcus Furiosus Length = 327

Iteration: 1
 Score =  260 bits (665), Expect = 6e-70,   Method: Compositional matrix adjust.
 Identities = 136/315 (43%), Positives = 196/315 (62%), Gaps = 6/315 (1%)
Query: 1   IEKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSF 60
           +EKYRPQ   DIVG E  V+RLK +  +G++P+++ +GPPGVGKTT  L LAR L G ++
Sbjct: 16  VEKYRPQRLDDIVGQEHIVKRLKHYVKTGSMPHLLFAGPPGVGKTTAALALARELFGENW 75
Query: 61  KDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPG--RHKIVILDEADSMTDGAQQALRR 118
           +   LELNAS++RGI+ +R K+K FA+ K   P G    KI+ LDEAD++T  AQQALRR
Sbjct: 76  RHNFLELNASDERGINVIREKVKEFARTK---PIGGASFKIIFLDEADALTQDAQQALRR 132
Query: 119 TMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTND 178
           TME++S+  RF L+CN S KIIEPIQSRCA+ R+  L D  +  ++  I E E +  T +
Sbjct: 133 TMEMFSSNVRFILSCNYSSKIIEPIQSRCAIFRFRPLRDEDIAKRLRYIAENEGLELTEE 192
Query: 179 GLEAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEMLLNCVEGN-M 237
           GL+AI++ A+GDMR+A+N LQ+       +T E VF V     P  ++EM+L  ++GN +
Sbjct: 193 GLQAILYIAEGDMRRAINILQAAAALDKKITDENVFMVASRARPEDIREMMLLALKGNFL 252
Query: 238 KDSYKIIHHLYKLGYAPEDIIGNIFRVAKTLDIPEPLKLSIIQEIGNVHLRISEGVNSXX 297
           K   K+   L K G + ED++  + +    L I EP K+ +  +IG  + R+ EG N   
Sbjct: 253 KAREKLREILLKQGLSGEDVLVQMHKEVFNLPIEEPKKVLLADKIGEYNFRLVEGANEII 312
Query: 298 XXXXXXXXXCIVGSK 312
                     ++G K
Sbjct: 313 QLEALLAQFTLIGKK 327

>pdb|2CHQ|A Chain A, Replication Factor C Adpnp Complex Length = 319

Iteration: 1
 Score =  257 bits (656), Expect = 6e-69,   Method: Compositional matrix adjust.
 Identities = 123/297 (41%), Positives = 195/297 (65%), Gaps = 6/297 (2%)
Query: 1   IEKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSF 60
           +EKYRP+T  ++VG ++ ++RLK +    N+P+++ SGPPG GKT T + LAR L G ++
Sbjct: 8   VEKYRPRTLDEVVGQDEVIQRLKGYVERKNIPHLLFSGPPGTGKTATAIALARDLFGENW 67
Query: 61  KDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGR--HKIVILDEADSMTDGAQQALRR 118
           +D  +E+NAS++RGID VR+KIK FA+   T P G    KI+ LDEAD++T  AQ ALRR
Sbjct: 68  RDNFIEMNASDERGIDVVRHKIKEFAR---TAPIGGAPFKIIFLDEADALTADAQAALRR 124
Query: 119 TMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTND 178
           TME+YS + RF L+CN   +IIEPIQSRCA+ R+  +    +  +++EICEKE +  T D
Sbjct: 125 TMEMYSKSCRFILSCNYVSRIIEPIQSRCAVFRFKPVPKEAMKKRLLEICEKEGVKITED 184
Query: 179 GLEAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEMLLNCVEGNMK 238
           GLEA+++ + GD R+A+N LQ        V A+ ++++     P  + E++   ++GN  
Sbjct: 185 GLEALIYISGGDFRKAINALQGAAAIGEVVDADTIYQITATARPEEMTELIQTALKGNFM 244
Query: 239 DSYKIIHHLY-KLGYAPEDIIGNIFRVAKTLDIPEPLKLSIIQEIGNVHLRISEGVN 294
           ++ +++  L  + G + EDI+  +FR   ++ I + LK+ +I ++G V  R++EG N
Sbjct: 245 EARELLDRLMVEYGMSGEDIVAQLFREIISMPIKDSLKVQLIDKLGEVDFRLTEGAN 301

>pdb|2CHG|A Chain A, Replication Factor C Domains 1 And 2 Length = 226

Iteration: 1
 Score =  216 bits (551), Expect = 9e-57,   Method: Compositional matrix adjust.
 Identities = 102/218 (46%), Positives = 151/218 (69%), Gaps = 5/218 (2%)
Query: 1   IEKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSF 60
           +EKYRP+T  ++VG ++ ++RLK +    N+P+++ SGPPG GKT T + LAR L G ++
Sbjct: 8   VEKYRPRTLDEVVGQDEVIQRLKGYVERKNIPHLLFSGPPGTGKTATAIALARDLFGENW 67
Query: 61  KDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGR--HKIVILDEADSMTDGAQQALRR 118
           +D  +E+NAS++RGID VR+KIK FA+   T P G    KI+ LDEAD++T  AQ ALRR
Sbjct: 68  RDNFIEMNASDERGIDVVRHKIKEFAR---TAPIGGAPFKIIFLDEADALTADAQAALRR 124
Query: 119 TMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTND 178
           TME+YS + RF L+CN   +IIEPIQSRCA+ R+  +    +  +++EICEKE +  T D
Sbjct: 125 TMEMYSKSCRFILSCNYVSRIIEPIQSRCAVFRFKPVPKEAMKKRLLEICEKEGVKITED 184
Query: 179 GLEAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKV 216
           GLEA+++ + GD R+A+N LQ        V A+ ++++
Sbjct: 185 GLEALIYISGGDFRKAINALQGAAAIGEVVDADTIYQI 222

>pdb|1SXJ|C Chain C, Crystal Structure Of The Eukaryotic Clamp Loader (Replication Factor C, Rfc) Bound To The Dna Sliding Clamp (Proliferating Cell Nuclear Antigen, Pcna) Length = 340

Iteration: 1
 Score =  182 bits (463), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 96/301 (31%), Positives = 173/301 (57%), Gaps = 8/301 (2%)
Query: 1   IEKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSF 60
           +EKYRP+T  ++ G  + +  ++ F   G +P+++  GPPG GKT+TI+ LAR + G ++
Sbjct: 16  VEKYRPETLDEVYGQNEVITTVRKFVDEGKLPHLLFYGPPGTGKTSTIVALAREIYGKNY 75
Query: 61  KDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTM 120
            + VLELNAS+DRGID VRN+IK FA  +     G  K++ILDEAD+MT+ AQ ALRR +
Sbjct: 76  SNMVLELNASDDRGIDVVRNQIKDFASTRQIFSKG-FKLIILDEADAMTNAAQNALRRVI 134
Query: 121 EIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGL 180
           E Y+  TRF +  N + K+   + S+C   R+  L    +  ++  +   E +  + +  
Sbjct: 135 ERYTKNTRFCVLANYAHKLTPALLSQCTRFRFQPLPQEAIERRIANVLVHEKLKLSPNAE 194
Query: 181 EAIVFTAQGDMRQALNNLQSTHNGFGH-----VTAEYVFKVCDEPHPLAVKEMLLNCVEG 235
           +A++  + GDMR+ LN LQS      +     ++ + +++ C  P P  +K +L + +E 
Sbjct: 195 KALIELSNGDMRRVLNVLQSCKATLDNPDEDEISDDVIYECCGAPRPSDLKAVLKSILED 254
Query: 236 NMKDSYKIIHHLYKL-GYAPEDIIGNIFRVAKTLDIP-EPLKLSIIQEIGNVHLRISEGV 293
           +   ++  ++ +    G A  D+I  I ++ +  ++  E  ++ ++ ++ ++   IS+G 
Sbjct: 255 DWGTAHYTLNKVRSAKGLALIDLIEGIVKILEDYELQNEETRVHLLTKLADIEYSISKGG 314
Query: 294 N 294
           N
Sbjct: 315 N 315

>pdb|1SXJ|D Chain D, Crystal Structure Of The Eukaryotic Clamp Loader (Replication Factor C, Rfc) Bound To The Dna Sliding Clamp (Proliferating Cell Nuclear Antigen, Pcna) Length = 353

Iteration: 1
 Score =  177 bits (449), Expect = 7e-45,   Method: Compositional matrix adjust.
 Identities = 101/278 (36%), Positives = 156/278 (56%), Gaps = 18/278 (6%)
Query: 1   IEKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSF 60
           +EKYRP+   ++   +  V  LK    S N+P+++  GPPG GKT+TIL L + L GP  
Sbjct: 28  VEKYRPKNLDEVTAQDHAVTVLKKTLKSANLPHMLFYGPPGTGKTSTILALTKELYGPDL 87
Query: 61  -KDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGR---------HKIVILDEADSMTD 110
            K  +LELNAS++RGI  VR K+K FA+  V+ P            +KI+ILDEADSMT 
Sbjct: 88  MKSRILELNASDERGISIVREKVKNFARLTVSKPSKHDLENYPCPPYKIIILDEADSMTA 147
Query: 111 GAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEK 170
            AQ ALRRTME YS  TRF L CN   +II+P+ S+C+  R+  L  +  + ++  I E+
Sbjct: 148 DAQSALRRTMETYSGVTRFCLICNYVTRIIDPLASQCSKFRFKALDASNAIDRLRFISEQ 207
Query: 171 ENISHTNDGLEAIVFTAQGDMRQALNNLQSTHNGFGH------VTAEYVFKVCD-EPHPL 223
           EN+   +  LE I+  + GD+R+ +  LQS   G  +      +T+  V ++    PH +
Sbjct: 208 ENVKCDDGVLERILDISAGDLRRGITLLQSASKGAQYLGDGKNITSTQVEELAGVVPHDI 267
Query: 224 AVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDIIGNI 261
            + E++     G+  +  K ++   K G++   ++  +
Sbjct: 268 LI-EIVEKVKSGDFDEIKKYVNTFMKSGWSAASVVNQL 304

>pdb|1SXJ|E Chain E, Crystal Structure Of The Eukaryotic Clamp Loader (Replication Factor C, Rfc) Bound To The Dna Sliding Clamp (Proliferating Cell Nuclear Antigen, Pcna) Length = 354

Iteration: 1
 Score = 94.7 bits (234), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 70/237 (29%), Positives = 120/237 (50%), Gaps = 39/237 (16%)
Query: 1   IEKYRPQTFSDIVGNEDTVERLKVFSSS-GNVPNIIISGPPGVGKTTTILCLARILLGP- 58
           ++KYRP++ + +  NE+    LK  S    ++P++++ GP G GK T  + L   + GP 
Sbjct: 5   VDKYRPKSLNALSHNEELTNFLKSLSDQPRDLPHLLLYGPNGTGKKTRCMALLESIFGPG 64
Query: 59  ------------SFKDAVLELNA---------------SNDRGIDTVRNKIKMFAQ-QKV 90
                       +  +  LELN                +NDR +  ++  +K  AQ ++V
Sbjct: 65  VYRLKIDVRQFVTASNRKLELNVVSSPYHLEITPSDMGNNDRIV--IQELLKEVAQMEQV 122
Query: 91  TLPPG------RHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQ 144
                      R+K VI++EA+S+T  AQ ALRRTME YS   R  + C++   II PI+
Sbjct: 123 DFQDSKDGLAHRYKCVIINEANSLTKDAQAALRRTMEKYSKNIRLIMVCDSMSPIIAPIK 182
Query: 145 SRCAMLRYNKLTDAQLLSKVIEICEKENIS-HTNDGLEAIVFTAQGDMRQALNNLQS 200
           S+C ++R    +D+++ + + ++   E I   T D L+ I   + G++R +L  L+S
Sbjct: 183 SQCLLIRCPAPSDSEISTILSDVVTNERIQLETKDILKRIAQASNGNLRVSLLMLES 239

>pdb|3U5Z|B Chain B, Structure Of T4 Bacteriophage Clamp Loader Bound To The T4 Clamp, Primer-Template Dna, And Atp Analog Length = 324

Iteration: 1
 Score = 89.0 bits (219), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 68/209 (32%), Positives = 106/209 (50%), Gaps = 18/209 (8%)
Query: 2   EKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGP-PGVGKTTTILCLARILLGPSF 60
           +KYRP T  + +      E  K  +S G +P+II+  P PG GKTT    +A+ L     
Sbjct: 18  QKYRPSTIDECILPAFDKETFKSITSKGKIPHIILHSPSPGTGKTT----VAKALCHDVN 73
Query: 61  KDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEAD-SMTDGAQQALRRT 119
            D +  +N S D  ID VR  +  FA        GR K++++DE D S    +Q+ LR  
Sbjct: 74  ADMMF-VNGS-DCKIDFVRGPLTNFASAASF--DGRQKVIVIDEFDRSGLAESQRHLRSF 129
Query: 120 MEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTD-------AQLLSKVIEICEKEN 172
           ME YS+     +  NN + II+P+QSRC ++ + + TD        Q++ ++ EIC+ E 
Sbjct: 130 MEAYSSNCSIIITANNIDGIIKPLQSRCRVITFGQPTDEDKIEMMKQMIRRLTEICKHEG 189
Query: 173 ISHTN-DGLEAIVFTAQGDMRQALNNLQS 200
           I+  +   + A+V     D R+ +  L S
Sbjct: 190 IAIADMKVVAALVKKNFPDFRKTIGELDS 218

>pdb|1XXI|B Chain B, Adp Bound E. Coli Clamp Loader Complex Length = 368

Iteration: 1
 Score = 80.1 bits (196), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 82/320 (25%), Positives = 144/320 (45%), Gaps = 44/320 (13%)
Query: 3   KYRPQTFSDIVGNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLAR-------I 54
           K+RPQTF+D+VG E  +  L    S G + +  + SG  GVGKT+    LA+       I
Sbjct: 9   KWRPQTFADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKGLNCETGI 68
Query: 55  LLGP-------------SFKDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPP--GRHKI 99
              P              F D ++E++A++   ++  R+ +       V   P  GR K+
Sbjct: 69  TATPCGVCDNCREIEQGRFVD-LIEIDAASRTKVEDTRDLLD-----NVQYAPARGRFKV 122
Query: 100 VILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQ 159
            ++DE   ++  +  AL +T+E      +F LA  + +K+   I SRC       L   Q
Sbjct: 123 YLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTILSRCLQFHLKALDVEQ 182
Query: 160 LLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALN-NLQSTHNGFGHVTAEYV---FK 215
           +  ++  I  +E+I+H    L+ +   A+G +R AL+   Q+  +G G V+ + V     
Sbjct: 183 IRHQLEHILNEEHIAHEPRALQLLARAAEGSLRDALSLTDQAIASGDGQVSTQAVSAMLG 242
Query: 216 VCDEPHPLAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPE----DIIGNIFRVAKTLDIP 271
             D+   L++ E +   VE N +    +I+     G   E    +++G + R+A     P
Sbjct: 243 TLDDDQALSLVEAM---VEANGERVMALINEAAARGIEWEALLVEMLGLLHRIAMVQLSP 299
Query: 272 EPLKLSIIQEIGNVHLRISE 291
             L      ++  + LR+ E
Sbjct: 300 AALG----NDMAAIELRMRE 315

>pdb|3GLF|B Chain B, Crystal Structure Of The Ecoli Clamp Loader Bound To Primer-template Dna Length = 395

Iteration: 1
 Score = 79.7 bits (195), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 82/320 (25%), Positives = 144/320 (45%), Gaps = 44/320 (13%)
Query: 3   KYRPQTFSDIVGNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLAR-------I 54
           K+RPQTF+D+VG E  +  L    S G + +  + SG  GVGKT+    LA+       I
Sbjct: 31  KWRPQTFADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKGLNCETGI 90
Query: 55  LLGP-------------SFKDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPP--GRHKI 99
              P              F D ++E++A++   ++  R+ +       V   P  GR K+
Sbjct: 91  TATPCGVCDNCREIEQGRFVD-LIEIDAASRTKVEDTRDLLD-----NVQYAPARGRFKV 144
Query: 100 VILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQ 159
            ++DE   ++  +  AL +T+E      +F LA  + +K+   I SRC       L   Q
Sbjct: 145 YLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTILSRCLQFHLKALDVEQ 204
Query: 160 LLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALN-NLQSTHNGFGHVTAEYV---FK 215
           +  ++  I  +E+I+H    L+ +   A+G +R AL+   Q+  +G G V+ + V     
Sbjct: 205 IRHQLEHILNEEHIAHEPRALQLLARAAEGSLRDALSLTDQAIASGDGQVSTQAVSAMLG 264
Query: 216 VCDEPHPLAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPE----DIIGNIFRVAKTLDIP 271
             D+   L++ E +   VE N +    +I+     G   E    +++G + R+A     P
Sbjct: 265 TLDDDQALSLVEAM---VEANGERVMALINEAAARGIEWEALLVEMLGLLHRIAMVQLSP 321
Query: 272 EPLKLSIIQEIGNVHLRISE 291
             L      ++  + LR+ E
Sbjct: 322 AALG----NDMAAIELRMRE 337

>pdb|1JR3|A Chain A, Crystal Structure Of The Processivity Clamp Loader Gamma Complex Of E. Coli Dna Polymerase Iii Length = 373

Iteration: 1
 Score = 79.7 bits (195), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 82/320 (25%), Positives = 144/320 (45%), Gaps = 44/320 (13%)
Query: 3   KYRPQTFSDIVGNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLAR-------I 54
           K+RPQTF+D+VG E  +  L    S G + +  + SG  GVGKT+    LA+       I
Sbjct: 9   KWRPQTFADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKGLNCETGI 68
Query: 55  LLGP-------------SFKDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPP--GRHKI 99
              P              F D ++E++A++   ++  R+ +       V   P  GR K+
Sbjct: 69  TATPCGVCDNCREIEQGRFVD-LIEIDAASRTKVEDTRDLLD-----NVQYAPARGRFKV 122
Query: 100 VILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQ 159
            ++DE   ++  +  AL +T+E      +F LA  + +K+   I SRC       L   Q
Sbjct: 123 YLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTILSRCLQFHLKALDVEQ 182
Query: 160 LLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALN-NLQSTHNGFGHVTAEYV---FK 215
           +  ++  I  +E+I+H    L+ +   A+G +R AL+   Q+  +G G V+ + V     
Sbjct: 183 IRHQLEHILNEEHIAHEPRALQLLARAAEGSLRDALSLTDQAIASGDGQVSTQAVSAMLG 242
Query: 216 VCDEPHPLAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPE----DIIGNIFRVAKTLDIP 271
             D+   L++ E +   VE N +    +I+     G   E    +++G + R+A     P
Sbjct: 243 TLDDDQALSLVEAM---VEANGERVMALINEAAARGIEWEALLVEMLGLLHRIAMVQLSP 299
Query: 272 EPLKLSIIQEIGNVHLRISE 291
             L      ++  + LR+ E
Sbjct: 300 AALG----NDMAAIELRMRE 315

>pdb|3GLH|B Chain B, Crystal Structure Of The E. Coli Clamp Loader Bound To Psi Peptide Length = 376

Iteration: 1
 Score = 79.7 bits (195), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 82/320 (25%), Positives = 144/320 (45%), Gaps = 44/320 (13%)
Query: 3   KYRPQTFSDIVGNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLAR-------I 54
           K+RPQTF+D+VG E  +  L    S G + +  + SG  GVGKT+    LA+       I
Sbjct: 12  KWRPQTFADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKGLNCETGI 71
Query: 55  LLGP-------------SFKDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPP--GRHKI 99
              P              F D ++E++A++   ++  R+ +       V   P  GR K+
Sbjct: 72  TATPCGVCDNCREIEQGRFVD-LIEIDAASRTKVEDTRDLLD-----NVQYAPARGRFKV 125
Query: 100 VILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQ 159
            ++DE   ++  +  AL +T+E      +F LA  + +K+   I SRC       L   Q
Sbjct: 126 YLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTILSRCLQFHLKALDVEQ 185
Query: 160 LLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALN-NLQSTHNGFGHVTAEYV---FK 215
           +  ++  I  +E+I+H    L+ +   A+G +R AL+   Q+  +G G V+ + V     
Sbjct: 186 IRHQLEHILNEEHIAHEPRALQLLARAAEGSLRDALSLTDQAIASGDGQVSTQAVSAMLG 245
Query: 216 VCDEPHPLAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPE----DIIGNIFRVAKTLDIP 271
             D+   L++ E +   VE N +    +I+     G   E    +++G + R+A     P
Sbjct: 246 TLDDDQALSLVEAM---VEANGERVMALINEAAARGIEWEALLVEMLGLLHRIAMVQLSP 302
Query: 272 EPLKLSIIQEIGNVHLRISE 291
             L      ++  + LR+ E
Sbjct: 303 AALG----NDMAAIELRMRE 318

>pdb|3GLG|B Chain B, Crystal Structure Of A Mutant (Gammat157a) E. Coli Clamp Loader Bound To Primer-Template Dna Length = 395

Iteration: 1
 Score = 79.3 bits (194), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 82/320 (25%), Positives = 144/320 (45%), Gaps = 44/320 (13%)
Query: 3   KYRPQTFSDIVGNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLAR-------I 54
           K+RPQTF+D+VG E  +  L    S G + +  + SG  GVGKT+    LA+       I
Sbjct: 31  KWRPQTFADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKGLNCETGI 90
Query: 55  LLGP-------------SFKDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPP--GRHKI 99
              P              F D ++E++A++   ++  R+ +       V   P  GR K+
Sbjct: 91  TATPCGVCDNCREIEQGRFVD-LIEIDAASRTKVEDTRDLLD-----NVQYAPARGRFKV 144
Query: 100 VILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQ 159
            ++DE   ++  +  AL +T+E      +F LA  + +K+   I SRC       L   Q
Sbjct: 145 YLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATADPQKLPVTILSRCLQFHLKALDVEQ 204
Query: 160 LLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALN-NLQSTHNGFGHVTAEYV---FK 215
           +  ++  I  +E+I+H    L+ +   A+G +R AL+   Q+  +G G V+ + V     
Sbjct: 205 IRHQLEHILNEEHIAHEPRALQLLARAAEGSLRDALSLTDQAIASGDGQVSTQAVSAMLG 264
Query: 216 VCDEPHPLAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPE----DIIGNIFRVAKTLDIP 271
             D+   L++ E +   VE N +    +I+     G   E    +++G + R+A     P
Sbjct: 265 TLDDDQALSLVEAM---VEANGERVMALINEAAARGIEWEALLVEMLGLLHRIAMVQLSP 321
Query: 272 EPLKLSIIQEIGNVHLRISE 291
             L      ++  + LR+ E
Sbjct: 322 AALG----NDMAAIELRMRE 337

>pdb|1NJG|A Chain A, Nucleotide-Free Form Of An Isolated E. Coli Clamp Loader Gamma Subunit Length = 250

Iteration: 1
 Score = 76.6 bits (187), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 65/235 (27%), Positives = 111/235 (47%), Gaps = 30/235 (12%)
Query: 3   KYRPQTFSDIVGNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLAR-------I 54
           K+RPQTF+D+VG E  +  L    S G + +  + SG  GVGKT+    LA+       I
Sbjct: 16  KWRPQTFADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKGLNCETGI 75
Query: 55  LLGP-------------SFKDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPP--GRHKI 99
              P              F D ++E++A++   ++  R+ +       V   P  GR K+
Sbjct: 76  TATPCGVCDNCREIEQGRFVD-LIEIDAASRTKVEDTRDLLD-----NVQYAPARGRFKV 129
Query: 100 VILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQ 159
            ++DE   ++  +  AL +T+E      +F LA  + +K+   I SRC       L   Q
Sbjct: 130 YLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTILSRCLQFHLKALDVEQ 189
Query: 160 LLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALN-NLQSTHNGFGHVTAEYV 213
           +  ++  I  +E+I+H    L+ +   A+G +R AL+   Q+  +G G V+ + V
Sbjct: 190 IRHQLEHILNEEHIAHEPRALQLLARAAEGSLRDALSLTDQAIASGDGQVSTQAV 244

>pdb|1SXJ|A Chain A, Crystal Structure Of The Eukaryotic Clamp Loader (Replication Factor C, Rfc) Bound To The Dna Sliding Clamp (Proliferating Cell Nuclear Antigen, Pcna) Length = 516

Iteration: 1
 Score = 58.2 bits (139), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 53/226 (23%), Positives = 95/226 (42%), Gaps = 35/226 (15%)
Query: 3   KYRPQTFSDIVGNEDTVERLKVF-----------------SSSGNVPNIIISGPPGVGKT 45
           KY P     + GN+ +V +LK +                   SG     ++ GPPG+GKT
Sbjct: 32  KYAPTNLQQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKT 91
Query: 46  TTILCLARILLGPSFKDAVLELNASNDR-------GIDTVRNKIKMFAQQKVTLPP---- 94
           T     A  L+       +LE NAS+ R       G+    + + +    K         
Sbjct: 92  T-----AAHLVAQELGYDILEQNASDVRSKTLLNAGVKNALDNMSVVGYFKHNEEAQNLN 146
Query: 95  GRHKIVILDEADSMTDGAQQALRRTMEIYSNT-TRFALACNNSE-KIIEPIQSRCAMLRY 152
           G+H ++I+DE D M+ G +  + +  +    T T   L CN      + P    C  +++
Sbjct: 147 GKHFVIIMDEVDGMSGGDRGGVGQLAQFCRKTSTPLILICNERNLPKMRPFDRVCLDIQF 206
Query: 153 NKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNL 198
            +     + S+++ I  +E      + ++ ++ T +GD+RQ +N L
Sbjct: 207 RRPDANSIKSRLMTIAIREKFKLDPNVIDRLIQTTRGDIRQVINLL 252

>pdb|3PVS|A Chain A, Structure And Biochemical Activities Of Escherichia Coli Mgsa Length = 447

Iteration: 1
 Score = 49.7 bits (117), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 50/207 (24%), Positives = 92/207 (44%), Gaps = 19/207 (9%)
Query: 3   KYRPQTFSDIVGNEDTVERLKVFS---SSGNVPNIIISGPPGVGKTTTILCLARILLGPS 59
           + RP+  +  +G +  +   K       +G++ ++I+ GPPG GKTT    +AR      
Sbjct: 19  RMRPENLAQYIGQQHLLAAGKPLPRAIEAGHLHSMILWGPPGTGKTTLAEVIAR------ 72
Query: 60  FKDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRT 119
           + +A +E  ++   G+  +R  I+   Q +     GR  I+ +DE        Q A    
Sbjct: 73  YANADVERISAVTSGVKEIREAIERARQNRNA---GRRTILFVDEVHRFNKSQQDAFLPH 129
Query: 120 MEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTD---AQLLSKVIEICEK----EN 172
           +E  + T   A   N S ++   + SR  +     L+     Q+L++ +E   +    ++
Sbjct: 130 IEDGTITFIGATTENPSFELNSALLSRARVYLLKSLSTEDIEQVLTQAMEDKTRGYGGQD 189
Query: 173 ISHTNDGLEAIVFTAQGDMRQALNNLQ 199
           I   ++   AI     GD R+ALN L+
Sbjct: 190 IVLPDETRRAIAELVNGDARRALNTLE 216

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	317
2chq_A	319	Replication factor C small subunit; DNA-binding pr	1e-159
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	1e-159
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	1e-157
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	1e-149
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	1e-141
2chg_A	226	Replication factor C small subunit; DNA-binding pr	1e-124
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	1e-118
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	1e-117
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	1e-106
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	3e-27
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	2e-26
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	7e-21
3pvs_A	447	Replication-associated recombination protein A; ma	4e-14
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-13
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-05
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	3e-12
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	2e-10
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	2e-09
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	1e-08
1jr3_D	343	DNA polymerase III, delta subunit; processivity, p	2e-07
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	8e-06
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	8e-06
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	9e-06
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	4e-05
1y63_A	184	LMAJ004144AAA protein; structural genomics, protei	1e-04
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	2e-04
3k1j_A	604	LON protease, ATP-dependent protease LON; ATP-bind	3e-04
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	3e-04
2qm8_A	337	GTPase/ATPase; G protein, G3E, metallochaperone, c	6e-04
1g8p_A	350	Magnesium-chelatase 38 kDa subunit; parallel beta	6e-04
2p67_A	341	LAO/AO transport system kinase; ARGK, structural G	7e-04

>2chq_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATP ATP-binding, nucleotide-binding; HET: ANP; 3.5A {Archaeoglobus fulgidus} PDB: 2chv_A Length = 319

 Score =  446 bits (1149), Expect = e-159
 Identities = 126/313 (40%), Positives = 201/313 (64%), Gaps = 2/313 (0%)

Query: 1   IEKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSF 60
           +EKYRP+T  ++VG ++ ++RLK +    N+P+++ SGPPG GKT T + LAR L G ++
Sbjct: 8   VEKYRPRTLDEVVGQDEVIQRLKGYVERKNIPHLLFSGPPGTGKTATAIALARDLFGENW 67

Query: 61  KDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTM 120
           +D  +E+NAS++RGID VR+KIK FA+    +     KI+ LDEAD++T  AQ ALRRTM
Sbjct: 68  RDNFIEMNASDERGIDVVRHKIKEFAR-TAPIGGAPFKIIFLDEADALTADAQAALRRTM 126

Query: 121 EIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGL 180
           E+YS + RF L+CN   +IIEPIQSRCA+ R+  +    +  +++EICEKE +  T DGL
Sbjct: 127 EMYSKSCRFILSCNYVSRIIEPIQSRCAVFRFKPVPKEAMKKRLLEICEKEGVKITEDGL 186

Query: 181 EAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEMLLNCVEGNMKDS 240
           EA+++ + GD R+A+N LQ        V A+ ++++     P  + E++   ++GN  ++
Sbjct: 187 EALIYISGGDFRKAINALQGAAAIGEVVDADTIYQITATARPEEMTELIQTALKGNFMEA 246

Query: 241 YKIIHHL-YKLGYAPEDIIGNIFRVAKTLDIPEPLKLSIIQEIGNVHLRISEGVNSLLQL 299
            +++  L  + G + EDI+  +FR   ++ I + LK+ +I ++G V  R++EG N  +QL
Sbjct: 247 RELLDRLMVEYGMSGEDIVAQLFREIISMPIKDSLKVQLIDKLGEVDFRLTEGANERIQL 306

Query: 300 SGLLARLCIVGSK 312
              LA L  +  K
Sbjct: 307 DAYLAYLSTLAKK 319

>1sxj_B Activator 1 37 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20 Length = 323

 Score =  445 bits (1146), Expect = e-159
 Identities = 187/314 (59%), Positives = 248/314 (78%), Gaps = 5/314 (1%)

Query: 1   IEKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSF 60
           +EKYRPQ  SDIVGN++T++RL+  +  GN+P++IISG PG+GKTT++ CLA  LLG S+
Sbjct: 12  VEKYRPQVLSDIVGNKETIDRLQQIAKDGNMPHMIISGMPGIGKTTSVHCLAHELLGRSY 71

Query: 61  KDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTM 120
            D VLELNAS+DRGID VRN+IK FAQ+K+ LPPG+HKIVILDEADSMT GAQQALRRTM
Sbjct: 72  ADGVLELNASDDRGIDVVRNQIKHFAQKKLHLPPGKHKIVILDEADSMTAGAQQALRRTM 131

Query: 121 EIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGL 180
           E+YSN+TRFA ACN S KIIEP+QS+CA+LRY+KL+D  +L ++++I + E++ +TNDGL
Sbjct: 132 ELYSNSTRFAFACNQSNKIIEPLQSQCAILRYSKLSDEDVLKRLLQIIKLEDVKYTNDGL 191

Query: 181 EAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEMLLNCVEGNMKDS 240
           EAI+FTA+GDMRQA+NNLQST  G G V A+ VFK+ D PHPL VK+MLL     N++DS
Sbjct: 192 EAIIFTAEGDMRQAINNLQSTVAGHGLVNADNVFKIVDSPHPLIVKKMLLAS---NLEDS 248

Query: 241 YKIIH-HLYKLGYAPEDIIGNIFRVAKTL-DIPEPLKLSIIQEIGNVHLRISEGVNSLLQ 298
            +I+   L+K GY+  DI+   FRV K L  + E ++L +I+EIG  H+RI EGV + LQ
Sbjct: 249 IQILRTDLWKKGYSSIDIVTTSFRVTKNLAQVKESVRLEMIKEIGLTHMRILEGVGTYLQ 308

Query: 299 LSGLLARLCIVGSK 312
           L+ +LA++  + +K
Sbjct: 309 LASMLAKIHKLNNK 322

>1iqp_A RFCS; clamp loader, extended AAA-ATPase domain, complex with ADP, replication; HET: ADP; 2.80A {Pyrococcus furiosus} SCOP: a.80.1.1 c.37.1.20 Length = 327

 Score =  440 bits (1133), Expect = e-157
 Identities = 137/313 (43%), Positives = 202/313 (64%), Gaps = 2/313 (0%)

Query: 1   IEKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSF 60
           +EKYRPQ   DIVG E  V+RLK +  +G++P+++ +GPPGVGKTT  L LAR L G ++
Sbjct: 16  VEKYRPQRLDDIVGQEHIVKRLKHYVKTGSMPHLLFAGPPGVGKTTAALALARELFGENW 75

Query: 61  KDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTM 120
           +   LELNAS++RGI+ +R K+K FA+ K  +     KI+ LDEAD++T  AQQALRRTM
Sbjct: 76  RHNFLELNASDERGINVIREKVKEFARTK-PIGGASFKIIFLDEADALTQDAQQALRRTM 134

Query: 121 EIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGL 180
           E++S+  RF L+CN S KIIEPIQSRCA+ R+  L D  +  ++  I E E +  T +GL
Sbjct: 135 EMFSSNVRFILSCNYSSKIIEPIQSRCAIFRFRPLRDEDIAKRLRYIAENEGLELTEEGL 194

Query: 181 EAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEMLLNCVEGNMKDS 240
           +AI++ A+GDMR+A+N LQ+       +T E VF V     P  ++EM+L  ++GN   +
Sbjct: 195 QAILYIAEGDMRRAINILQAAAALDKKITDENVFMVASRARPEDIREMMLLALKGNFLKA 254

Query: 241 YKII-HHLYKLGYAPEDIIGNIFRVAKTLDIPEPLKLSIIQEIGNVHLRISEGVNSLLQL 299
            + +   L K G + ED++  + +    L I EP K+ +  +IG  + R+ EG N ++QL
Sbjct: 255 REKLREILLKQGLSGEDVLVQMHKEVFNLPIEEPKKVLLADKIGEYNFRLVEGANEIIQL 314

Query: 300 SGLLARLCIVGSK 312
             LLA+  ++G K
Sbjct: 315 EALLAQFTLIGKK 327

>1sxj_C Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20 Length = 340

 Score =  421 bits (1085), Expect = e-149
 Identities = 98/316 (31%), Positives = 178/316 (56%), Gaps = 8/316 (2%)

Query: 1   IEKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSF 60
           +EKYRP+T  ++ G  + +  ++ F   G +P+++  GPPG GKT+TI+ LAR + G ++
Sbjct: 16  VEKYRPETLDEVYGQNEVITTVRKFVDEGKLPHLLFYGPPGTGKTSTIVALAREIYGKNY 75

Query: 61  KDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTM 120
            + VLELNAS+DRGID VRN+IK FA  +     G  K++ILDEAD+MT+ AQ ALRR +
Sbjct: 76  SNMVLELNASDDRGIDVVRNQIKDFASTRQIFSKG-FKLIILDEADAMTNAAQNALRRVI 134

Query: 121 EIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGL 180
           E Y+  TRF +  N + K+   + S+C   R+  L    +  ++  +   E +  + +  
Sbjct: 135 ERYTKNTRFCVLANYAHKLTPALLSQCTRFRFQPLPQEAIERRIANVLVHEKLKLSPNAE 194

Query: 181 EAIVFTAQGDMRQALNNLQSTHNGFG-----HVTAEYVFKVCDEPHPLAVKEMLLNCVEG 235
           +A++  + GDMR+ LN LQS            ++ + +++ C  P P  +K +L + +E 
Sbjct: 195 KALIELSNGDMRRVLNVLQSCKATLDNPDEDEISDDVIYECCGAPRPSDLKAVLKSILED 254

Query: 236 NMKDSYKIIHHLYKL-GYAPEDIIGNIFRVAKTLDIP-EPLKLSIIQEIGNVHLRISEGV 293
           +   ++  ++ +    G A  D+I  I ++ +  ++  E  ++ ++ ++ ++   IS+G 
Sbjct: 255 DWGTAHYTLNKVRSAKGLALIDLIEGIVKILEDYELQNEETRVHLLTKLADIEYSISKGG 314

Query: 294 NSLLQLSGLLARLCIV 309
           N  +Q S ++  +   
Sbjct: 315 NDQIQGSAVIGAIKAS 330

>1sxj_D Activator 1 41 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20 Length = 353

 Score =  402 bits (1035), Expect = e-141
 Identities = 110/326 (33%), Positives = 171/326 (52%), Gaps = 17/326 (5%)

Query: 1   IEKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPS- 59
           +EKYRP+   ++   +  V  LK    S N+P+++  GPPG GKT+TIL L + L GP  
Sbjct: 28  VEKYRPKNLDEVTAQDHAVTVLKKTLKSANLPHMLFYGPPGTGKTSTILALTKELYGPDL 87

Query: 60  FKDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGR---------HKIVILDEADSMTD 110
            K  +LELNAS++RGI  VR K+K FA+  V+ P            +KI+ILDEADSMT 
Sbjct: 88  MKSRILELNASDERGISIVREKVKNFARLTVSKPSKHDLENYPCPPYKIIILDEADSMTA 147

Query: 111 GAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEK 170
            AQ ALRRTME YS  TRF L CN   +II+P+ S+C+  R+  L  +  + ++  I E+
Sbjct: 148 DAQSALRRTMETYSGVTRFCLICNYVTRIIDPLASQCSKFRFKALDASNAIDRLRFISEQ 207

Query: 171 ENISHTNDGLEAIVFTAQGDMRQALNNLQSTHNGFGH------VTAEYVFKVCDEPHPLA 224
           EN+   +  LE I+  + GD+R+ +  LQS   G  +      +T+  V ++        
Sbjct: 208 ENVKCDDGVLERILDISAGDLRRGITLLQSASKGAQYLGDGKNITSTQVEELAGVVPHDI 267

Query: 225 VKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDIIGNIFRVAKTLD-IPEPLKLSIIQEIG 283
           + E++     G+  +  K ++   K G++   ++  +     T D      K  I   + 
Sbjct: 268 LIEIVEKVKSGDFDEIKKYVNTFMKSGWSAASVVNQLHEYYITNDNFDTNFKNQISWLLF 327

Query: 284 NVHLRISEGVNSLLQLSGLLARLCIV 309
               R++ G N  +QL  LL ++  +
Sbjct: 328 TTDSRLNNGTNEHIQLLNLLVKISQL 353

>2chg_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATPase, ATP-binding, nucleotide-binding; HET: ANP; 2.1A {Archaeoglobus fulgidus} Length = 226

 Score =  354 bits (912), Expect = e-124
 Identities = 99/218 (45%), Positives = 149/218 (68%), Gaps = 1/218 (0%)

Query: 1   IEKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSF 60
           +EKYRP+T  ++VG ++ ++RLK +    N+P+++ SGPPG GKT T + LAR L G ++
Sbjct: 8   VEKYRPRTLDEVVGQDEVIQRLKGYVERKNIPHLLFSGPPGTGKTATAIALARDLFGENW 67

Query: 61  KDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTM 120
           +D  +E+NAS++RGID VR+KIK FA+    +     KI+ LDEAD++T  AQ ALRRTM
Sbjct: 68  RDNFIEMNASDERGIDVVRHKIKEFAR-TAPIGGAPFKIIFLDEADALTADAQAALRRTM 126

Query: 121 EIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGL 180
           E+YS + RF L+CN   +IIEPIQSRCA+ R+  +    +  +++EICEKE +  T DGL
Sbjct: 127 EMYSKSCRFILSCNYVSRIIEPIQSRCAVFRFKPVPKEAMKKRLLEICEKEGVKITEDGL 186

Query: 181 EAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCD 218
           EA+++ + GD R+A+N LQ        V A+ ++++  
Sbjct: 187 EALIYISGGDFRKAINALQGAAAIGEVVDADTIYQITA 224

>3u61_B DNA polymerase accessory protein 44; AAA+, ATP hydrolase, clamp loader, sliding clamp, primer-TEM DNA, DNA binding protein-DNA complex; HET: DNA ADP 08T; 3.20A {Enterobacteria phage T4} PDB: 3u5z_B* 3u60_B* Length = 324

 Score =  342 bits (878), Expect = e-118
 Identities = 79/316 (25%), Positives = 140/316 (44%), Gaps = 25/316 (7%)

Query: 1   IEKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGP-PGVGKTTTILCLARILLGPS 59
            +KYRP T  + +      E  K  +S G +P+II+  P PG GKTT    L   +    
Sbjct: 17  EQKYRPSTIDECILPAFDKETFKSITSKGKIPHIILHSPSPGTGKTTVAKALCHDVNAD- 75

Query: 60  FKDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEAD-SMTDGAQQALRR 118
               ++ +N S D  ID VR  +  FA        GR K++++DE D S    +Q+ LR 
Sbjct: 76  ----MMFVNGS-DCKIDFVRGPLTNFASAAS--FDGRQKVIVIDEFDRSGLAESQRHLRS 128

Query: 119 TMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTD-------AQLLSKVIEICEKE 171
            ME YS+     +  NN + II+P+QSRC ++ + + TD        Q++ ++ EIC+ E
Sbjct: 129 FMEAYSSNCSIIITANNIDGIIKPLQSRCRVITFGQPTDEDKIEMMKQMIRRLTEICKHE 188

Query: 172 NISHTN-DGLEAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEMLL 230
            I+  +   + A+V     D R+ +  L S     G + A  +  V ++     + ++L 
Sbjct: 189 GIAIADMKVVAALVKKNFPDFRKTIGELDSYS-SKGVLDAGILSLVTNDRGA--IDDVLE 245

Query: 231 NCVEGNMKDSYKIIHHLYKLGYAPEDIIGNIFRVAKTLDIPEPLKLSIIQEIGNVHLRIS 290
           +    ++K    +     K        +G +     +  +     + + + +G  +    
Sbjct: 246 SLKNKDVKQLRALAP---KYAADYSWFVGKLAEEIYS-RVTPQSIIRMYEIVGENNQYHG 301

Query: 291 EGVNSLLQLSGLLARL 306
              N+ L L+ L  +L
Sbjct: 302 IAANTELHLAYLFIQL 317

>1sxj_E Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20 Length = 354

 Score =  340 bits (873), Expect = e-117
 Identities = 80/345 (23%), Positives = 152/345 (44%), Gaps = 39/345 (11%)

Query: 1   IEKYRPQTFSDIVGNEDTVERLKVFSS-SGNVPNIIISGPPGVGKTTTILCLARILLGPS 59
           ++KYRP++ + +  NE+    LK  S    ++P++++ GP G GK T  + L   + GP 
Sbjct: 5   VDKYRPKSLNALSHNEELTNFLKSLSDQPRDLPHLLLYGPNGTGKKTRCMALLESIFGPG 64

Query: 60  F------------------------KDAVLELNASNDRGID--TVRNKIKMFAQQKV--- 90
                                        LE+  S+    D   ++  +K  AQ +    
Sbjct: 65  VYRLKIDVRQFVTASNRKLELNVVSSPYHLEITPSDMGNNDRIVIQELLKEVAQMEQVDF 124

Query: 91  ----TLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSR 146
                    R+K VI++EA+S+T  AQ ALRRTME YS   R  + C++   II PI+S+
Sbjct: 125 QDSKDGLAHRYKCVIINEANSLTKDAQAALRRTMEKYSKNIRLIMVCDSMSPIIAPIKSQ 184

Query: 147 CAMLRYNKLTDAQLLSKVIEICEKENIS-HTNDGLEAIVFTAQGDMRQALNNLQSTH--N 203
           C ++R    +D+++ + + ++   E I   T D L+ I   + G++R +L  L+S    N
Sbjct: 185 CLLIRCPAPSDSEISTILSDVVTNERIQLETKDILKRIAQASNGNLRVSLLMLESMALNN 244

Query: 204 GFGHVTAEYVFKVCDEPHPLA-VKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDIIGNIF 262
                ++  + K           ++++      ++ +   +++ L         I+  + 
Sbjct: 245 ELALKSSSPIIKPDWIIVIHKLTRKIVKERSVNSLIECRAVLYDLLAHCIPANIILKELT 304

Query: 263 RVAKTLD-IPEPLKLSIIQEIGNVHLRISEGVNSLLQLSGLLARL 306
                ++ +    K SII+       R+S G  ++  L G +A++
Sbjct: 305 FSLLDVETLNTTNKSSIIEYSSVFDERLSLGNKAIFHLEGFIAKV 349

>1sxj_A Activator 1 95 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20 Length = 516

 Score =  317 bits (814), Expect = e-106
 Identities = 67/358 (18%), Positives = 132/358 (36%), Gaps = 56/358 (15%)

Query: 1   IEKYRPQTFSDIVGNEDTVERLKVF-----------------SSSGNVPNIIISGPPGVG 43
             KY P     + GN+ +V +LK +                   SG     ++ GPPG+G
Sbjct: 30  TVKYAPTNLQQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIG 89

Query: 44  KTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFAQ-----------QKVTL 92
           KTT    +A+          +LE NAS+ R    +   +K               ++   
Sbjct: 90  KTTAAHLVAQ-----ELGYDILEQNASDVRSKTLLNAGVKNALDNMSVVGYFKHNEEAQN 144

Query: 93  PPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTR-FALACNN-SEKIIEPIQSRCAML 150
             G+H ++I+DE D M+ G +  + +  +    T+    L CN  +   + P    C  +
Sbjct: 145 LNGKHFVIIMDEVDGMSGGDRGGVGQLAQFCRKTSTPLILICNERNLPKMRPFDRVCLDI 204

Query: 151 RYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHNGFGHVTA 210
           ++ +     + S+++ I  +E      + ++ ++ T +GD+RQ +N L +       +  
Sbjct: 205 QFRRPDANSIKSRLMTIAIREKFKLDPNVIDRLIQTTRGDIRQVINLLSTISTTTKTINH 264

Query: 211 EYVFKVCDEPHPL-------AVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDIIG---- 259
           E + ++                 +ML   +  ++      ++    L +   D       
Sbjct: 265 ENINEISKAWEKNIALKPFDIAHKMLDGQIYSDIGSRNFTLNDKIALYFDDFDFTPLMIQ 324

Query: 260 -NIFRVAKTLDIPEPLKLSIIQEIG---------NVHLRISEGVNSLLQLSGLLARLC 307
            N      ++  P    L  + E              +R SE + SLL L  +L+ + 
Sbjct: 325 ENYLSTRPSVLKPGQSHLEAVAEAANCISLGDIVEKKIRSSEQLWSLLPLHAVLSSVY 382

>1njg_A DNA polymerase III subunit gamma; rossman-like fold, AAA+ ATPase domains, sensor 1, sensor 2, transferase; HET: DNA; 2.20A {Escherichia coli} SCOP: c.37.1.20 PDB: 1njf_A* Length = 250

 Score =  106 bits (266), Expect = 3e-27
 Identities = 66/244 (27%), Positives = 116/244 (47%), Gaps = 42/244 (17%)

Query: 3   KYRPQTFSDIVGNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARIL------ 55
           K+RPQTF+D+VG E  +  L    S G + +  + SG  GVGKT+     AR+L      
Sbjct: 16  KWRPQTFADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSI----ARLLAKGLNC 71

Query: 56  -LGP-----------------SFKDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPP--G 95
             G                   F D ++E++A++   ++  R+ +       V   P  G
Sbjct: 72  ETGITATPCGVCDNCREIEQGRFVD-LIEIDAASRTKVEDTRDLL-----DNVQYAPARG 125

Query: 96  RHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYN-- 153
           R K+ ++DE   ++  +  AL +T+E      +F LA  + +K+   I SRC  L+++  
Sbjct: 126 RFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTILSRC--LQFHLK 183

Query: 154 KLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNL-QSTHNGFGHVTAEY 212
            L   Q+  ++  I  +E+I+H    L+ +   A+G +R AL+   Q+  +G G V+ + 
Sbjct: 184 ALDVEQIRHQLEHILNEEHIAHEPRALQLLARAAEGSLRDALSLTDQAIASGDGQVSTQA 243

Query: 213 VFKV 216
           V  +
Sbjct: 244 VSAM 247

>1jr3_A DNA polymerase III subunit gamma; processivity, processivity clamp, clamp loader, AAA+ ATPase, transferase; HET: DNA; 2.70A {Escherichia coli} SCOP: a.80.1.1 c.37.1.20 PDB: 1xxh_B* 3glh_B* 3glf_B* 3gli_B* 3glg_B* 1xxi_B* Length = 373

 Score =  106 bits (267), Expect = 2e-26
 Identities = 72/295 (24%), Positives = 129/295 (43%), Gaps = 54/295 (18%)

Query: 3   KYRPQTFSDIVGNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARIL------ 55
           K+RPQTF+D+VG E  +  L    S G + +  + SG  GVGKT+     AR+L      
Sbjct: 9   KWRPQTFADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSI----ARLLAKGLNC 64

Query: 56  -LGP-----------------SFKDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPP--G 95
             G                   F D ++E++A++   ++  R+ +       V   P  G
Sbjct: 65  ETGITATPCGVCDNCREIEQGRFVD-LIEIDAASRTKVEDTRDLL-----DNVQYAPARG 118

Query: 96  RHKIVILDEADSMTDGAQQALRRTME------IYSNTTRFALACNNSEKIIEPIQSRCAM 149
           R K+ ++DE   ++  +  AL +T+E             F LA  + +K+   I SRC  
Sbjct: 119 RFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVK------FLLATTDPQKLPVTILSRC-- 170

Query: 150 LRYN--KLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNL-QSTHNGFG 206
           L+++   L   Q+  ++  I  +E+I+H    L+ +   A+G +R AL+   Q+  +G G
Sbjct: 171 LQFHLKALDVEQIRHQLEHILNEEHIAHEPRALQLLARAAEGSLRDALSLTDQAIASGDG 230

Query: 207 HVTAEYVFKVCDEPHPLAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDIIGNI 261
            V+ + V  +           ++   VE N +    +I+     G   E ++  +
Sbjct: 231 QVSTQAVSAMLGTLDDDQALSLVEAMVEANGERVMALINEAAARGIEWEALLVEM 285

>1a5t_A Delta prime, HOLB; zinc finger, DNA replication; 2.20A {Escherichia coli K12} SCOP: a.80.1.1 c.37.1.20 PDB: 1jr3_E* 1xxh_E* 1xxi_E* 3glf_E* 3glg_E* 3glh_E* 3gli_E* Length = 334

 Score = 90.2 bits (224), Expect = 7e-21
 Identities = 62/325 (19%), Positives = 118/325 (36%), Gaps = 47/325 (14%)

Query: 16  EDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARILL--GPSFKDA--------- 63
               E+L     +G   + ++I   PG+G    I  L+R LL   P    +         
Sbjct: 8   RPDFEKLVASYQAGRGHHALLIQALPGMGDDALIYALSRYLLCQQPQGHKSCGHCRGCQL 67

Query: 64  --------VLELNASNDR---GIDTVR---NKIKMFAQQKVTLPPGRHKIVILDEADSMT 109
                      L     +   G+D VR    K+   A+       G  K+V + +A  +T
Sbjct: 68  MQAGTHPDYYTLAPEKGKNTLGVDAVREVTEKLNEHARL------GGAKVVWVTDAALLT 121

Query: 110 DGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICE 169
           D A  AL +T+E     T F LA    E+++  ++SRC +       +   ++ +     
Sbjct: 122 DAAANALLKTLEEPPAETWFFLATREPERLLATLRSRCRLHYLAPPPEQYAVTWL----- 176

Query: 170 KENISHTNDGLEAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEML 229
              ++ + D L A +  + G    AL   Q  +        + +          ++   L
Sbjct: 177 SREVTMSQDALLAALRLSAGSPGAALALFQGDNWQARETLCQALAYSVPSGDWYSLLAAL 236

Query: 230 LNC-VEGNMKDSYKIIHHLYKLGYAPE-----DIIGNIFRVAKTLDIPEPLKLSIIQEIG 283
            +      +     ++    K  +        D+ G +  +A  L  P  L  +I+ ++ 
Sbjct: 237 NHEQAPARLHWLATLLMDALKRHHGAAQVTNVDVPGLVAELANHLS-PSRL-QAILGDVC 294

Query: 284 NV--HLRISEGVNSLLQLSGLLARL 306
           ++   L    G+N  L ++ LL R+
Sbjct: 295 HIREQLMSVTGINRELLITDLLLRI 319

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli} Length = 447

 Score = 71.4 bits (176), Expect = 4e-14
 Identities = 51/238 (21%), Positives = 94/238 (39%), Gaps = 50/238 (21%)

Query: 5   RPQTFSDIVGNEDTVER---LKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFK 61
           RP+  +  +G +  +     L     +G++ ++I+ GPPG GKTT    LA ++      
Sbjct: 21  RPENLAQYIGQQHLLAAGKPLPRAIEAGHLHSMILWGPPGTGKTT----LAEVIAR-YAN 75

Query: 62  DAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDG------AQQ- 114
             V  ++A    G+  +R   +   + +     GR  I+ +DE             +QQ 
Sbjct: 76  ADVERISAVTS-GVKEIR---EAIERARQNRNAGRRTILFVDE-------VHRFNKSQQD 124

Query: 115 AL-----RRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDA---QLLSKVIE 166
           A        T+     TT      N S ++   + SR  +     L+     Q+L++ +E
Sbjct: 125 AFLPHIEDGTITFIGATTE-----NPSFELNSALLSRARVYLLKSLSTEDIEQVLTQAME 179

Query: 167 ICEK----ENISHTNDGLEAIVFTAQGDMRQALNNL-------QSTHNGFGHVTAEYV 213
              +    ++I   ++   AI     GD R+ALN L       +   +G   +  E +
Sbjct: 180 DKTRGYGGQDIVLPDETRRAIAELVNGDARRALNTLEMMADMAEVDDSGKRVLKPELL 237

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 69.5 bits (169), Expect = 3e-13
 Identities = 66/369 (17%), Positives = 118/369 (31%), Gaps = 127/369 (34%)

Query: 2   EKYRPQTFSDI-VGNEDTVERLKVFSSSGNV-------PNIIISGPPGVGKTTTILCLA- 52
            + R + ++D  V  +  V RL+ +              N++I G  G GKT     +A 
Sbjct: 113 IEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKT----WVAL 168

Query: 53  ------RILLGPSFKDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIV--ILDE 104
                 ++     FK  +  LN  N    +TV   ++M   QK+      ++I       
Sbjct: 169 DVCLSYKVQCKMDFK--IFWLNLKNCNSPETV---LEM--LQKL-----LYQIDPNWTSR 216

Query: 105 ADSM------TDGAQQALRRTM--EIYSNTTRFAL-----ACNNSEKIIEPIQSRCAML- 150
           +D            Q  LRR +  + Y N     L       N   K        C +L 
Sbjct: 217 SDHSSNIKLRIHSIQAELRRLLKSKPYEN----CLLVLLNVQN--AKAWNAFNLSCKILL 270

Query: 151 --RYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHNGFGHV 208
             R+ ++TD    +    I     + H +  L            +  + L          
Sbjct: 271 TTRFKQVTDFLSAATTTHIS----LDHHSMTLTP---------DEVKSLL---------- 307

Query: 209 TAEYV-FKVCDEP------HPLAVK---EML------------LNC--VEGNMKDSYKII 244
             +Y+  +  D P      +P  +    E +            +NC  +   ++ S  ++
Sbjct: 308 -LKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVL 366

Query: 245 H-----HLYK-LGYAPEDIIGNIFRVAKTLDIPEPLKLSII--QEIGNVHLRISEGVNSL 296
                  ++  L   P               IP  L LS+I    I +  + +   VN L
Sbjct: 367 EPAEYRKMFDRLSVFPPSA-----------HIPTIL-LSLIWFDVIKSDVMVV---VNKL 411

Query: 297 LQLSGLLAR 305
            + S L+ +
Sbjct: 412 HKYS-LVEK 419

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 45.6 bits (107), Expect = 2e-05
 Identities = 29/279 (10%), Positives = 70/279 (25%), Gaps = 77/279 (27%)

Query: 5   RPQTFSDIVGNEDT-----VERLKVFSSS------GNVPNIIISGPPGVGKTTTILCLAR 53
           R +  +D +    T            +            +      P    TT    L+ 
Sbjct: 273 RFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLS- 331

Query: 54  ILLGPSFKDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHK-----IVILDEADSM 108
            ++  S +D +   +       D +   I+        L P  ++     + +   +  +
Sbjct: 332 -IIAESIRDGLATWDNWKHVNCDKLTTIIESSLNV---LEPAEYRKMFDRLSVFPPSAHI 387

Query: 109 TDGAQQALRRTMEIY-SNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEI 167
                      + +   +  +     ++   ++  +     + +  K          I I
Sbjct: 388 P-------TILLSLIWFDVIK-----SDVMVVVNKLHKYSLVEKQPK-------ESTISI 428

Query: 168 CEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKE 227
                       +         +++  L N  + H     +   Y      +   L    
Sbjct: 429 -------P---SI-------YLELKVKLENEYALHR---SIVDHYNIPKTFDSDDLIPPY 468

Query: 228 MLLNCVEGNMKDSY---KIIHHLYKLGYAPEDIIGNIFR 263
           +          D Y    I HHL  + +        +FR
Sbjct: 469 L----------DQYFYSHIGHHLKNIEHPERM---TLFR 494

>2gno_A DNA polymerase III, gamma subunit-related protein; structural genomics, joint center for structural genomics, J protein structure initiative; HET: DNA; 2.00A {Thermotoga maritima} SCOP: a.80.1.1 c.37.1.20 Length = 305

 Score = 65.1 bits (159), Expect = 3e-12
 Identities = 44/293 (15%), Positives = 85/293 (29%), Gaps = 45/293 (15%)

Query: 36  ISGPPGVGKTTT--ILCLARILLGPSFKDAVLELN-ASNDRGIDTVRNKIKMFAQQKVTL 92
           I+G            L        P   D VLE++    + GID +R          +  
Sbjct: 23  INGEDLSYPREVSLELPEYVEKFPPKASD-VLEIDPEGENIGIDDIRTIK-----DFLNY 76

Query: 93  PP--GRHKIVILDEADSMTDGAQQALRRTME------IYSNTTRFALACNNSEKIIEPIQ 144
            P     K VI+ + + MT  A  A  + +E      +        L       ++  I+
Sbjct: 77  SPELYTRKYVIVHDCERMTQQAANAFLKALEEPPEYAV------IVLNTRRWHYLLPTIK 130

Query: 145 SRC------AMLRYNKLTDAQLLSKVIEICE-KENISHTNDGLEAIVFTAQGDMRQ---- 193
           SR           +  L   ++     E+   + +     +  +       G M      
Sbjct: 131 SRVFRVVVNVPKEFRDLVKEKIGDLWEELPLLERDFKTALEAYKLGAEKLSGLMESLKVL 190

Query: 194 ---ALNNLQSTHNGFGHVTAEYV---FKVCDEPHPLAVKEMLLNCVEGN-----MKDSYK 242
               L     +    G++    +   F   +     A+ + + N + G      ++   +
Sbjct: 191 ETEKLLKKVLSKGLEGYLACRELLERFSKVESKEFFALFDQVTNTITGKDAFLLIQRLTR 250

Query: 243 IIHHLYKLGYAPEDIIGNIFRVAKTLDIPEPLKLSIIQEIGNVHLRISEGVNS 295
           II H        +    +       + I        +  I  +H     GVN+
Sbjct: 251 IILHENTWESVEDQKSVSFLDSILRVKIANLNNKLTLMNILAIHRERKRGVNA 303

>1fnn_A CDC6P, cell division control protein 6; ORC1, AAA protein, DNA replication initation factor, cell cycle control factor; HET: ADP; 2.00A {Pyrobaculum aerophilum} SCOP: a.4.5.11 c.37.1.20 Length = 389

 Score = 60.2 bits (145), Expect = 2e-10
 Identities = 45/313 (14%), Positives = 89/313 (28%), Gaps = 53/313 (16%)

Query: 4   YRPQTFSDIVGNEDTVERLKVF------SSSGNVPNIIISGPPGVGKTTTILCLARILLG 57
           Y P+    +   E  +++L +       +   + P   + G PG GKT T+  L   L  
Sbjct: 14  YVPKR---LPHREQQLQQLDILLGNWLRNPGHHYPRATLLGRPGTGKTVTLRKLWE-LYK 69

Query: 58  PSFKDAVLELNASNDRGIDTVRNKIKMFAQQKVTLP-----------------PGRHKIV 100
                  + +N    R    +  +I                               +  +
Sbjct: 70  DKTTARFVYINGFIYRNFTAIIGEIARSLNIPFPRRGLSRDEFLALLVEHLRERDLYMFL 129

Query: 101 ILDEADSMTDGAQQALRRTMEIYSNTTRFALAC-------NNSEKIIEPIQSRCAMLRYN 153
           +LD+A ++         R  +       F +A             +    +         
Sbjct: 130 VLDDAFNLAPDILSTFIRLGQEADKLGAFRIALVIVGHNDAVLNNLDPSTRGIMGKYVIR 189

Query: 154 KLT-DAQLLSKVIEICEKENISHTNDGLEAIVFTAQ------------GDMRQALNNLQS 200
                   +  ++    K  ++  +   + +   A             GD R A++ L  
Sbjct: 190 FSPYTKDQIFDILLDRAKAGLAEGSYSEDILQMIADITGAQTPLDTNRGDARLAIDILYR 249

Query: 201 T-----HNGFGHVTAEYVFKVCDEPHPLAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPE 255
           +      NG  H+  E V K   E      +E+L+     + K     I    K+ + P 
Sbjct: 250 SAYAAQQNGRKHIAPEDVRKSSKEVLFGISEEVLIGLPL-HEKLFLLAIVRSLKISHTPY 308

Query: 256 DIIGNIFRVAKTL 268
              G+     K +
Sbjct: 309 ITFGDAEESYKIV 321

>2qby_B CDC6 homolog 3, cell division control protein 6 homolog 3; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus} Length = 384

 Score = 57.1 bits (137), Expect = 2e-09
 Identities = 41/268 (15%), Positives = 82/268 (30%), Gaps = 42/268 (15%)

Query: 8   TFSDIVGNEDTVERLKVF----SSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDA 63
            F +I   ED +    +       +    + +  G  G GKT     +   +     +D 
Sbjct: 18  VFKEIPFREDILRDAAIAIRYFVKNEVKFSNLFLGLTGTGKTFVSKYIFNEIEEVKKEDE 77

Query: 64  ------VLELNASNDRGIDTVR-----------------NKIKMFAQQKVTLPPGRHKIV 100
                    +N     G                        +  +  +          I+
Sbjct: 78  EYKDVKQAYVNCREVGGTPQAVLSSLAGKLTGFSVPKHGINLGEYIDKIKNGTRNIRAII 137

Query: 101 ILDEADSM--TDGAQQALRRTMEIYSNTTRFALACNNS--EKIIEPIQSRC-AMLRYNKL 155
            LDE D++    G    L + +   +N +   ++ + +  + +   + S     + +   
Sbjct: 138 YLDEVDTLVKRRGGDIVLYQLLRSDANISVIMISNDINVRDYMEPRVLSSLGPSVIFKPY 197

Query: 156 TDAQLLSKVIEICEKENISHTNDGLEAIVFTAQ------GDMRQALNNLQS---THNGFG 206
              QL   + +  E   I  T D  E + + A       GD R+A+N L       +G G
Sbjct: 198 DAEQLKFILSKYAEYGLIKGTYDD-EILSYIAAISAKEHGDARKAVNLLFRAAQLASGGG 256

Query: 207 HVTAEYVFKVCDEPHPLAVKEMLLNCVE 234
            +  E+V K   +     + E +     
Sbjct: 257 IIRKEHVDKAIVDYEQERLIEAVKALPF 284

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D* Length = 368

 Score = 54.6 bits (131), Expect = 1e-08
 Identities = 42/289 (14%), Positives = 83/289 (28%), Gaps = 82/289 (28%)

Query: 7   QTFSDIVGNEDTVERLKVFSS---SGNVPN--IIISGPPGVGKTTTILCLAR-------- 53
           Q    +VG         V       G +    ++I+G PG GKT   + +A+        
Sbjct: 41  QASQGMVGQLAARRAAGVVLEMIREGKIAGRAVLIAGQPGTGKTAIAMGMAQALGPDTPF 100

Query: 54  ------------------------------ILLGPSFKDAVLELNASNDRGIDT------ 77
                                         I  G     ++ E++  N R          
Sbjct: 101 TAIAGSEIFSLEMSKTEALTQAFRRSIGVRIKAGAVHTVSLHEIDVINSRTQGFLALFSG 160

Query: 78  --------VRNKIKMF-----AQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTME--- 121
                   VR +I         + K  + PG   ++ +DE   +   +   L R +E   
Sbjct: 161 DTGEIKSEVREQINAKVAEWREEGKAEIIPG---VLFIDEVHMLDIESFSFLNRALESDM 217

Query: 122 ---IYSNTTRFALACNNSE-----KIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENI 173
              +   T R       +       I   +  R  ++     ++      +   CE+E++
Sbjct: 218 APVLIMATNRGITRIRGTSYQSPHGIPIDLLDRLLIVSTTPYSEKDTKQILRIRCEEEDV 277

Query: 174 SHTNDGLEAIVFTA-QGDMRQALN-----NLQSTHNGFGHVTAEYVFKV 216
             + D    +     +  +R A+      +L         V  + + +V
Sbjct: 278 EMSEDAYTVLTRIGLETSLRYAIQLITAASLVCRKRKGTEVQVDDIKRV 326

>1jr3_D DNA polymerase III, delta subunit; processivity, processivity clamp, clamp loader, AAA+ ATPase, transferase; HET: DNA; 2.70A {Escherichia coli} SCOP: a.80.1.1 c.37.1.20 PDB: 1jqj_C* 1xxh_A* 1xxi_A* 3glf_A* 3glg_A* 3glh_A* 3gli_A* Length = 343

 Score = 51.0 bits (122), Expect = 2e-07
 Identities = 25/182 (13%), Positives = 58/182 (31%), Gaps = 11/182 (6%)

Query: 97  HKIVILDEADS-MTDGAQQALRRTMEIYSNTTRFALACNNSE------KIIEPIQSRCAM 149
            + ++L   ++       + L     +  +     +  N              + +R   
Sbjct: 77  RQTLLLLLPENGPNAAINEQLLTLTGLLHDDLLLIVRGNKLSKAQENAAWFTALANRSVQ 136

Query: 150 LRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDM---RQALNNLQSTHNGFG 206
           +       AQL   V    ++ N+   +   + + +  +G++    QAL  L       G
Sbjct: 137 VTCQTPEQAQLPRWVAARAKQLNLELDDAANQVLCYCYEGNLLALAQALERLSLLWPD-G 195

Query: 207 HVTAEYVFKVCDEPHPLAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDIIGNIFRVAK 266
            +T   V +  ++         +   + G  K +  I+  L   G  P  ++  + R   
Sbjct: 196 KLTLPRVEQAVNDAAHFTPFHWVDALLMGKSKRALHILQQLRLEGSEPVILLRTLQRELL 255

Query: 267 TL 268
            L
Sbjct: 256 LL 257

>1in4_A RUVB, holliday junction DNA helicase RUVB; AAA+-class ATPase, winged-helix domain, ATP hydrolysis, walker A, walker B, sensor 1, sensor 2; HET: ADP; 1.60A {Thermotoga maritima} SCOP: a.4.5.11 c.37.1.20 PDB: 1in5_A* 1in6_A* 1in8_A* 1in7_A* 1j7k_A* Length = 334

 Score = 46.0 bits (110), Expect = 8e-06
 Identities = 17/65 (26%), Positives = 34/65 (52%), Gaps = 12/65 (18%)

Query: 5  RPQTFSDIVGNEDTVERLKVFSSSGNVPN-----IIISGPPGVGKTTTILCLARIL---L 56
          RP++  + +G E+  ++L +   +  +       ++++GPPG+GKTT    LA I+   L
Sbjct: 20 RPKSLDEFIGQENVKKKLSLALEAAKMRGEVLDHVLLAGPPGLGKTT----LAHIIASEL 75

Query: 57 GPSFK 61
            +  
Sbjct: 76 QTNIH 80

>1hqc_A RUVB; extended AAA-ATPase domain, complex with nucleotide, hydrolase; HET: ADE; 3.20A {Thermus thermophilus} SCOP: a.4.5.11 c.37.1.20 PDB: 1ixs_B* 1ixr_C* Length = 324

 Score = 45.6 bits (109), Expect = 8e-06
 Identities = 19/65 (29%), Positives = 35/65 (53%), Gaps = 12/65 (18%)

Query: 5  RPQTFSDIVGNEDTVERLKVFSSSGNVPN-----IIISGPPGVGKTTTILCLARIL---L 56
          RP+T  + +G E   ++L+V+  +          +++ GPPG+GKTT    LA ++   L
Sbjct: 7  RPKTLDEYIGQERLKQKLRVYLEAAKARKEPLEHLLLFGPPGLGKTT----LAHVIAHEL 62

Query: 57 GPSFK 61
          G + +
Sbjct: 63 GVNLR 67

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp} Length = 338

 Score = 45.6 bits (109), Expect = 9e-06
 Identities = 22/65 (33%), Positives = 31/65 (47%), Gaps = 12/65 (18%)

Query: 5  RPQTFSDIVGNEDTVERLKVFSSSGNVPN-----IIISGPPGVGKTTTILCLARIL---L 56
          RP  F   +G E   + L VF ++    N     I+ SGP G+GKTT    LA I+   +
Sbjct: 24 RPSNFDGYIGQESIKKNLNVFIAAAKKRNECLDHILFSGPAGLGKTT----LANIISYEM 79

Query: 57 GPSFK 61
            + K
Sbjct: 80 SANIK 84

>2qby_A CDC6 homolog 1, cell division control protein 6 homolog 1; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus} Length = 386

 Score = 43.9 bits (103), Expect = 4e-05
 Identities = 44/272 (16%), Positives = 80/272 (29%), Gaps = 47/272 (17%)

Query: 4   YRPQTFSDIVGNEDTVERLKVF----SSSGNVPNIIISGPPGVGKTTTILCLARILLGPS 59
           Y P     +   ED + ++              NI I G  G GKT  +  +   L    
Sbjct: 17  YIPDE---LPHREDQIRKIASILAPLYREEKPNNIFIYGLTGTGKTAVVKFVLSKLHKKF 73

Query: 60  FKD-AVLELNASNDRGIDTVRNKI-----------------KMFAQQKVTLPPGRHKIVI 101
                 + +N         V   +                       K     G   +++
Sbjct: 74  LGKFKHVYINTRQIDTPYRVLADLLESLDVKVPFTGLSIAELYRRLVKAVRDYGSQVVIV 133

Query: 102 LDEADSMTDGAQQA----LRRTMEIYSNTTRFALACNNSEKIIEP----IQSRCAMLRY- 152
           LDE D+            L R     + +    +   N  K ++     ++S  +     
Sbjct: 134 LDEIDAFVKKYNDDILYKLSRINSEVNKSKISFIGITNDVKFVDLLDPRVKSSLSEEEII 193

Query: 153 ------NKLTDAQLLSKVIEICEKENISHTNDGLEA-IVFTAQGDMRQALNNLQST---- 201
                  +L D  L  +     +   +      L A +     GD R+AL+ L+ +    
Sbjct: 194 FPPYNAEELED-ILTKRAQMAFKPGVLPDNVIKLCAALAAREHGDARRALDLLRVSGEIA 252

Query: 202 -HNGFGHVTAEYVFKVCDEPHPLAVKEMLLNC 232
                  V  EYV+   +E     V++++L  
Sbjct: 253 ERMKDTKVKEEYVYMAKEEIERDRVRDIILTL 284

>1y63_A LMAJ004144AAA protein; structural genomics, protein structure initiative, PSI, SGPP structural genomics of pathogenic protozoa consortium; HET: ADP; 1.70A {Leishmania major} SCOP: c.37.1.1 Length = 184

 Score = 41.6 bits (97), Expect = 1e-04
 Identities = 12/31 (38%), Positives = 17/31 (54%)

Query: 32 PNIIISGPPGVGKTTTILCLARILLGPSFKD 62
           NI+I+G PG GKT+    +A  L G    +
Sbjct: 11 INILITGTPGTGKTSMAEMIAAELDGFQHLE 41

>3k1j_A LON protease, ATP-dependent protease LON; ATP-binding, nucleotide-binding, Pro hydrolase; HET: ADP PE8; 2.00A {Thermococcus onnurineus} Length = 604

 Score = 41.6 bits (98), Expect = 3e-04
 Identities = 14/67 (20%), Positives = 33/67 (49%), Gaps = 2/67 (2%)

Query: 2  EKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFK 61
           +   +    ++G E  VE +K  +++    ++++ G PG GK+     +A +L   + +
Sbjct: 33 IEVPEKLIDQVIGQEHAVEVIK--TAANQKRHVLLIGEPGTGKSMLGQAMAELLPTETLE 90

Query: 62 DAVLELN 68
          D ++  N
Sbjct: 91 DILVFPN 97

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix} Length = 387

 Score = 41.0 bits (95), Expect = 3e-04
 Identities = 55/313 (17%), Positives = 89/313 (28%), Gaps = 55/313 (17%)

Query: 4   YRPQTFSDIVGNEDTVERLKVF----SSSGNVPNIIISGPPGVGKTTTILCLARILLGPS 59
           Y P     +   E  + RL              N ++ G  G GKT     + R L   +
Sbjct: 16  YVPDV---LPHREAELRRLAEVLAPALRGEKPSNALLYGLTGTGKTAVARLVLRRLEARA 72

Query: 60  FKDA----VLELNASNDRGIDTVRNKI-----------------KMFAQQKVTLPPGRHK 98
                    + +NA +      V + I                       K         
Sbjct: 73  SSLGVLVKPIYVNARHRETPYRVASAIAEAVGVRVPFTGLSVGEVYERLVKRLSRLRGIY 132

Query: 99  IVILDEADSMT-----DGAQQALRRTMEIYSNTTRFAL-ACNNSEKIIEP----IQSRCA 148
           I++LDE D +            + R  +   +    +L    NS   +E     ++S   
Sbjct: 133 IIVLDEIDFLPKRPGGQDLLYRITRINQELGDRVWVSLVGITNSLGFVENLEPRVKSSLG 192

Query: 149 MLRY--NKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQ------GDMRQALNNLQS 200
            +       T  QL   +    E+       D  + +   A       GD R+AL+ L+ 
Sbjct: 193 EVELVFPPYTAPQLRDILETRAEEAFNPGVLDP-DVVPLCAALAAREHGDARRALDLLRV 251

Query: 201 T-----HNGFGHVTAEYVFKVCDEPHPLAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPE 255
                       V  E+V+    E     V E++      + K     I  L   G    
Sbjct: 252 AGEIAERRREERVRREHVYSARAEIERDRVSEVVRTLPL-HAKLVLLSIMMLEDGG--RP 308

Query: 256 DIIGNIFRVAKTL 268
              G I+   K L
Sbjct: 309 ASTGEIYERYKEL 321

>2qm8_A GTPase/ATPase; G protein, G3E, metallochaperone, chaperone; HET: MSE; 1.70A {Methylobacterium extorquens} SCOP: c.37.1.10 PDB: 2qm7_A* Length = 337

 Score = 40.1 bits (94), Expect = 6e-04
 Identities = 18/43 (41%), Positives = 23/43 (53%)

Query: 23 KVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVL 65
           V   +G    + I+G PGVGK+TTI  L  +L     K AVL
Sbjct: 47 AVLPQTGRAIRVGITGVPGVGKSTTIDALGSLLTAAGHKVAVL 89

>1g8p_A Magnesium-chelatase 38 kDa subunit; parallel beta sheet, P-loop, rossman fold, AAA+, photosynthesis, metal transport; 2.10A {Rhodobacter capsulatus} SCOP: c.37.1.20 PDB: 2x31_G Length = 350

 Score = 40.1 bits (94), Expect = 6e-04
 Identities = 27/98 (27%), Positives = 37/98 (37%), Gaps = 19/98 (19%)

Query: 9   FSDIVGNEDTVERLK-------VFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFK 61
           FS IVG ED    +K       V    G V   ++ G  G GK+T +  LA  LL     
Sbjct: 23  FSAIVGQED----MKLALLLTAVDPGIGGV---LVFGDRGTGKSTAVRALAA-LLPEIEA 74

Query: 62  DAVLELNASNDRGIDTVRNKIKMFAQQK----VTLPPG 95
                +++ N   I      +     +K    V LP G
Sbjct: 75  VEGCPVSSPNVEMIPDWATVLSTNVIRKPTPVVDLPLG 112

>2p67_A LAO/AO transport system kinase; ARGK, structural GEN PSI-2, protein structure initiative, NEW YORK SGX research for structural genomics; 1.80A {Escherichia coli} SCOP: c.37.1.10 Length = 341

 Score = 39.8 bits (93), Expect = 7e-04
 Identities = 12/43 (27%), Positives = 21/43 (48%)

Query: 23 KVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVL 65
           +    GN   + ++G PG GK+T +     +L+    K AV+
Sbjct: 48 AIMPYCGNTLRLGVTGTPGAGKSTFLEAFGMLLIREGLKVAVI 90

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	317
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	100.0
2chq_A	319	Replication factor C small subunit; DNA-binding pr	100.0
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	100.0
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	100.0
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	100.0
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	100.0
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	100.0
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	100.0
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	100.0
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	100.0
3pvs_A	447	Replication-associated recombination protein A; ma	100.0
1jr3_D	343	DNA polymerase III, delta subunit; processivity, p	100.0
2chg_A	226	Replication factor C small subunit; DNA-binding pr	100.0
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	99.97
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	99.96
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	99.94
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	99.94
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	99.94
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	99.93
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	99.93
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	99.92
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	99.92
3bos_A	242	Putative DNA replication factor; P-loop containing	99.92
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	99.9
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	99.9
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	99.9
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	99.89
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	99.89
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	99.89
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	99.88
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	99.88
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	99.88
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	99.88
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	99.87
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	99.87
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	99.87
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	99.86
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	99.85
2r44_A	331	Uncharacterized protein; putative ATPase, structur	99.85
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	99.85
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	99.85
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	99.85
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	99.85
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	99.85
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	99.84
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	99.84
1g8p_A	350	Magnesium-chelatase 38 kDa subunit; parallel beta	99.83
3pxg_A	468	Negative regulator of genetic competence CLPC/MEC;	99.83
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	99.83
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	99.82
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	99.8
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	99.8
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	99.8
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	99.79
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	99.78
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	99.78
3k1j_A	604	LON protease, ATP-dependent protease LON; ATP-bind	99.78
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	99.78
3m6a_A	543	ATP-dependent protease LA 1; alpha, beta, ATP-bind	99.77
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	99.77
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	99.77
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	99.77
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	99.76
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	99.76
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	99.76
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	99.75
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	99.75
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	99.74
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	99.73
2dhr_A	499	FTSH; AAA+ protein, hexameric Zn metalloprotease,	99.72
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	99.71
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	99.69
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	99.67
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	99.67
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	99.65
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	99.63
1g41_A	444	Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dep	99.63
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	99.62
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	99.62
3f9v_A	595	Minichromosome maintenance protein MCM; replicativ	99.62
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	99.6
3co5_A	143	Putative two-component system transcriptional RES	99.54
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	99.5
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	99.49
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	99.48
2qen_A	350	Walker-type ATPase; unknown function; HET: ADP; 2.	99.46
3dzd_A	368	Transcriptional regulator (NTRC family); sigma43 a	99.38
1ny5_A	387	Transcriptional regulator (NTRC family); AAA+ ATPa	99.37
1u0j_A	267	DNA replication protein; AAA+ protein, P-loop atpa	99.36
2fna_A	357	Conserved hypothetical protein; structural genomic	99.28
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	99.26
3f8t_A	506	Predicted ATPase involved in replication control,	99.25
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	99.24
1tue_A	212	Replication protein E1; helicase, replication, E1E	99.24
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	99.15
2qgz_A	308	Helicase loader, putative primosome component; str	99.09
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	99.03
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	98.88
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	98.78
1ye8_A	178	Protein THEP1, hypothetical UPF0334 kinase-like pr	98.71
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	98.68
2r2a_A	199	Uncharacterized protein; zonular occludens toxin,	98.61
3sfz_A	1249	APAF-1, apoptotic peptidase activating factor 1; a	98.49
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	98.47
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	98.42
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	98.42
2vhj_A	331	Ntpase P4, P4; non- hydrolysable ATP analogue, hyd	98.19
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	98.16
1g5t_A	196	COB(I)alamin adenosyltransferase; P-loop protein,	98.08
2i3b_A	189	HCR-ntpase, human cancer-related ntpase; AAA, ross	98.0
1jql_B	140	DNA polymerase III, delta subunit; processivity cl	97.99
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	97.98
3e1s_A	574	Exodeoxyribonuclease V, subunit RECD; alpha and be	97.94
3nh6_A	306	ATP-binding cassette SUB-family B member 6, mitoc;	97.94
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	97.94
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	97.91
2ff7_A	247	Alpha-hemolysin translocation ATP-binding protein	97.88
2eyu_A	261	Twitching motility protein PILT; pilus retraction	97.84
2r8r_A	228	Sensor protein; KDPD, PFAM02702, MCSG, structural	97.83
2cvh_A	220	DNA repair and recombination protein RADB; filamen	97.83
1w36_D	608	RECD, exodeoxyribonuclease V alpha chain; recombin	97.81
3tif_A	235	Uncharacterized ABC transporter ATP-binding prote;	97.78
2pt7_A	330	CAG-ALFA; ATPase, protein-protein complex, type IV	97.78
4gp7_A	171	Metallophosphoesterase; polynucleotide kinase phos	97.77
3gfo_A	275	Cobalt import ATP-binding protein CBIO 1; structur	97.75
3tui_C	366	Methionine import ATP-binding protein METN; ABC-tr	97.75
3jvv_A	356	Twitching mobility protein; hexameric P-loop ATPas	97.74
2ixe_A	271	Antigen peptide transporter 1; ABC ATPase, hydrola	97.72
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	97.72
2zr9_A	349	Protein RECA, recombinase A; recombination, RECA m	97.7
1vpl_A	256	ABC transporter, ATP-binding protein; TM0544, stru	97.7
2pcj_A	224	ABC transporter, lipoprotein-releasing system ATP-	97.69
3qf4_B	598	Uncharacterized ABC transporter ATP-binding prote	97.69
3b5x_A	582	Lipid A export ATP-binding/permease protein MSBA;	97.69
4g1u_C	266	Hemin import ATP-binding protein HMUV; membrane tr	97.68
2j9r_A	214	Thymidine kinase; TK1, DNK, lasso, transferase, AT	97.67
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	97.66
2qi9_C	249	Vitamin B12 import ATP-binding protein BTUD; inner	97.66
3dl0_A	216	Adenylate kinase; phosphotransferase, zinc coordin	97.64
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	97.63
2ehv_A	251	Hypothetical protein PH0186; KAIC, RECA ATPase, un	97.62
3hr8_A	356	Protein RECA; alpha and beta proteins (A/B, A+B),	97.62
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	97.62
4a82_A	578	Cystic fibrosis transmembrane conductance regulat;	97.62
1svm_A	377	Large T antigen; AAA+ fold, viral protein; HET: AT	97.61
2olj_A	263	Amino acid ABC transporter; ABC domain, ATPase, hy	97.61
1xx6_A	191	Thymidine kinase; NESG, northeast structural genom	97.6
3qf4_A	587	ABC transporter, ATP-binding protein; multidrug tr	97.6
1s96_A	219	Guanylate kinase, GMP kinase; E.coli, dimer, SAD,	97.6
3a4m_A	260	L-seryl-tRNA(SEC) kinase; P-loop motif, walker A m	97.59
3rlf_A	381	Maltose/maltodextrin import ATP-binding protein M;	97.59
1u94_A	356	RECA protein, recombinase A; homologous recombinat	97.59
3b60_A	582	Lipid A export ATP-binding/permease protein MSBA;	97.58
2ghi_A	260	Transport protein; multidrug resistance protein, M	97.58
3tlx_A	243	Adenylate kinase 2; structural genomics, structura	97.57
2iut_A	574	DNA translocase FTSK; nucleotide-binding, chromoso	97.56
1ji0_A	240	ABC transporter; ATP binding protein, structural g	97.55
4a74_A	231	DNA repair and recombination protein RADA; hydrola	97.54
3gd7_A	390	Fusion complex of cystic fibrosis transmembrane co	97.53
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	97.53
2ga8_A	359	Hypothetical 39.9 kDa protein; YFR007W, YFH7, unkn	97.53
3d31_A	348	Sulfate/molybdate ABC transporter, ATP-binding pro	97.53
2orv_A	234	Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'- (2	97.52
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	97.52
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	97.52
1z47_A	355	CYSA, putative ABC-transporter ATP-binding protein	97.51
2yyz_A	359	Sugar ABC transporter, ATP-binding protein; sugar	97.51
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	97.51
1xp8_A	366	RECA protein, recombinase A; recombination, radior	97.5
3h1t_A	590	Type I site-specific restriction-modification syst	97.5
4f4c_A	1321	Multidrug resistance protein PGP-1; ABC transporte	97.49
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	97.49
2ius_A	512	DNA translocase FTSK; nucleotide-binding, chromoso	97.48
2it1_A	362	362AA long hypothetical maltose/maltodextrin trans	97.48
1v43_A	372	Sugar-binding transport ATP-binding protein; ATPas	97.44
2onk_A	240	Molybdate/tungstate ABC transporter, ATP-binding p	97.44
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	97.44
3lw7_A	179	Adenylate kinase related protein (ADKA-like); AMP,	97.42
3fb4_A	216	Adenylate kinase; psychrophIle, phosphotransferase	97.42
3fvq_A	359	Fe(3+) IONS import ATP-binding protein FBPC; nucle	97.41
2nq2_C	253	Hypothetical ABC transporter ATP-binding protein H	97.41
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	97.41
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	97.4
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	97.39
1cr0_A	296	DNA primase/helicase; RECA-type protein fold, tran	97.37
1pzn_A	349	RAD51, DNA repair and recombination protein RAD51,	97.36
1v5w_A	343	DMC1, meiotic recombination protein DMC1/LIM15 hom	97.35
1nrj_B	218	SR-beta, signal recognition particle receptor beta	97.34
1g29_1	372	MALK, maltose transport protein MALK; ATPase, acti	97.34
2yl4_A	595	ATP-binding cassette SUB-family B member 10, mitoc	97.33
4f4c_A	1321	Multidrug resistance protein PGP-1; ABC transporte	97.33
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	97.33
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	97.31
3bor_A	237	Human initiation factor 4A-II; translation initiat	97.3
2pjz_A	263	Hypothetical protein ST1066; ATP binding protein,	97.29
1w4r_A	195	Thymidine kinase; type II, human, cytosolic, phosp	97.29
3vaa_A	199	Shikimate kinase, SK; structural genomics, center	97.29
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	97.27
3io5_A	333	Recombination and repair protein; storage dimer, i	97.25
3zvl_A	416	Bifunctional polynucleotide phosphatase/kinase; hy	97.24
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	97.24
2z0h_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	97.24
3b6e_A	216	Interferon-induced helicase C domain-containing P;	97.24
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	97.23
3trf_A	185	Shikimate kinase, SK; amino acid biosynthesis, tra	97.23
3g5u_A	1284	MCG1178, multidrug resistance protein 1A; P-glycop	97.2
1qhx_A	178	CPT, protein (chloramphenicol phosphotransferase);	97.2
2z43_A	324	DNA repair and recombination protein RADA; archaea	97.18
4eun_A	200	Thermoresistant glucokinase; putative sugar kinase	97.15
1htw_A	158	HI0065; nucleotide-binding fold, structural genomi	97.14
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	97.14
3kb2_A	173	SPBC2 prophage-derived uncharacterized protein YOR	97.14
3iij_A	180	Coilin-interacting nuclear ATPase protein; alpha a	97.11
1kag_A	173	SKI, shikimate kinase I; transferase, structural g	97.11
1ltq_A	301	Polynucleotide kinase; phosphatase, alpha/beta, P-	97.11
1vma_A	306	Cell division protein FTSY; TM0570, structural gen	97.1
1via_A	175	Shikimate kinase; structural genomics, transferase	97.08
3b85_A	208	Phosphate starvation-inducible protein; PHOH2, ATP	97.08
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	97.07
3g5u_A	1284	MCG1178, multidrug resistance protein 1A; P-glycop	97.05
2px0_A	296	Flagellar biosynthesis protein FLHF; SRP GTPase, f	97.05
3uie_A	200	Adenylyl-sulfate kinase 1, chloroplastic; rossmann	97.04
1gvn_B	287	Zeta; postsegregational killing system, plasmid; 1	97.04
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	97.01
1kgd_A	180	CASK, peripheral plasma membrane CASK; maguk, guan	97.01
1kht_A	192	Adenylate kinase; phosphotransferase, signaling pr	97.01
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	97.0
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	96.99
3sop_A	270	Neuronal-specific septin-3; hydrolase; HET: GDP; 2	96.99
1y63_A	184	LMAJ004144AAA protein; structural genomics, protei	96.98
2p5t_B	253	PEZT; postsegregational killing system, phosphoryl	96.98
3lda_A	400	DNA repair protein RAD51; DNA binding protein, ATP	96.97
1ly1_A	181	Polynucleotide kinase; PNK, phosphatase, transfera	96.97
3nwj_A	250	ATSK2; P loop, shikimate, nucleoside monophosphate	96.97
1zuh_A	168	Shikimate kinase; alpha-beta protein, transferase;	96.96
1nks_A	194	Adenylate kinase; thermophilic, transferase; HET:	96.96
3c8u_A	208	Fructokinase; YP_612366.1, putative fructose trans	96.96
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	96.95
2iyv_A	184	Shikimate kinase, SK; transferase, aromatic amino	96.95
2rhm_A	193	Putative kinase; P-loop containing nucleoside trip	96.95
3ctd_A	213	Putative ATPase, AAA family; structural genomics,	96.95
1aky_A	220	Adenylate kinase; ATP:AMP phosphotransferase, myok	96.93
1zp6_A	191	Hypothetical protein ATU3015; alpha-beta protein.,	96.93
3t61_A	202	Gluconokinase; PSI-biology, structural genomics, p	96.92
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	96.92
3cm0_A	186	Adenylate kinase; ATP-binding, cytoplasm, nucleoti	96.91
3exa_A	322	TRNA delta(2)-isopentenylpyrophosphate transferase	96.91
2c95_A	196	Adenylate kinase 1; transferase, AP4A, nucleotide	96.91
2ewv_A	372	Twitching motility protein PILT; pilus retraction	96.89
3vkw_A	446	Replicase large subunit; alpha/beta domain, helica	96.88
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	96.88
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	96.87
1p9r_A	418	General secretion pathway protein E; bacterial typ	96.85
1tf7_A	525	KAIC; homohexamer, hexamer, circadian clock protei	96.85
3umf_A	217	Adenylate kinase; rossmann fold, transferase; 2.05	96.85
1knq_A	175	Gluconate kinase; ALFA/beta structure, transferase	96.85
1e6c_A	173	Shikimate kinase; phosphoryl transfer, ADP, shikim	96.85
3e2i_A	219	Thymidine kinase; Zn-binding, ATP-binding, DNA syn	96.84
4b3f_X	646	DNA-binding protein smubp-2; hydrolase, helicase;	96.84
2ze6_A	253	Isopentenyl transferase; crown GALL tumor, cytokin	96.83
2v9p_A	305	Replication protein E1; AAA+ molecular motor, DNA	96.82
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	96.79
1zak_A	222	Adenylate kinase; ATP:AMP-phosphotransferase, tran	96.79
2plr_A	213	DTMP kinase, probable thymidylate kinase; TMP-bind	96.79
2cdn_A	201	Adenylate kinase; phosphoryl transfer, associative	96.79
1tev_A	196	UMP-CMP kinase; ploop, NMP binding region, LID reg	96.78
2jeo_A	245	Uridine-cytidine kinase 1; UCK, transferase, ATP-b	96.78
3sr0_A	206	Adenylate kinase; phosphoryl transfer analogue, AL	96.78
2yvu_A	186	Probable adenylyl-sulfate kinase; transferase, str	96.78
2qor_A	204	Guanylate kinase; phosphotransferase, purine metab	96.77
3tr0_A	205	Guanylate kinase, GMP kinase; purines, pyrimidines	96.77
2r9g_A	204	AAA ATPase, central region; structural genomics, P	96.76
1lvg_A	198	Guanylate kinase, GMP kinase; transferase; HET: AD	96.76
2pt5_A	168	Shikimate kinase, SK; aromatic amino acid biosynth	96.75
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	96.75
1ak2_A	233	Adenylate kinase isoenzyme-2; nucleoside monophosp	96.74
2j41_A	207	Guanylate kinase; GMP, GMK, transferase, ATP-bindi	96.73
2jaq_A	205	Deoxyguanosine kinase; transferase, deoxyribonucle	96.73
1ukz_A	203	Uridylate kinase; transferase; HET: ADP AMP; 1.90A	96.73
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	96.73
2bwj_A	199	Adenylate kinase 5; phosphoryl transfer reaction,	96.73
3j16_B	608	RLI1P; ribosome recycling, translation, eukarya, r	96.73
2vli_A	183	Antibiotic resistance protein; transferase, tunica	96.73
1odf_A	290	YGR205W, hypothetical 33.3 kDa protein in ADE3-Ser	96.72
1rz3_A	201	Hypothetical protein rbstp0775; MCSG, structural g	96.72
1znw_A	207	Guanylate kinase, GMP kinase; ATP:GMP-phosphotrans	96.71
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	96.71
1rif_A	282	DAR protein, DNA helicase UVSW; bacteriophage, REC	96.71
3be4_A	217	Adenylate kinase; malaria, cryptosporidium parvum	96.71
2bbw_A	246	Adenylate kinase 4, AK4; nucleotide kinase, nucleo	96.7
1z6g_A	218	Guanylate kinase; structural genomics, SGC, struct	96.69
3bge_A	201	Predicted ATPase; structural genomics, predicted A	96.68
2bdt_A	189	BH3686; alpha-beta protein, structural genomics, P	96.68
1qf9_A	194	UMP/CMP kinase, protein (uridylmonophosphate/cytid	96.67
1zd8_A	227	GTP:AMP phosphotransferase mitochondrial; ATP:AMP	96.66
3ozx_A	538	RNAse L inhibitor; ATP binding cassette protein, h	96.65
2pbr_A	195	DTMP kinase, thymidylate kinase; transferase, nucl	96.65
1cke_A	227	CK, MSSA, protein (cytidine monophosphate kinase);	96.64
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	96.64
2v3c_C	432	SRP54, signal recognition 54 kDa protein; nucleoti	96.62
2wwf_A	212	Thymidilate kinase, putative; transferase, malaria	96.62
3a00_A	186	Guanylate kinase, GMP kinase; domain movement, dim	96.62
3tau_A	208	Guanylate kinase, GMP kinase; structural genomics,	96.61
2xb4_A	223	Adenylate kinase; ATP-binding, nucleotide-binding,	96.61
1ewq_A	765	DNA mismatch repair protein MUTS; multiple domains	96.61
1ls1_A	295	Signal recognition particle protein; FFH, SRP54, S	96.59
1e4v_A	214	Adenylate kinase; transferase(phosphotransferase);	96.58
1nn5_A	215	Similar to deoxythymidylate kinase (thymidylate K;	96.58
1ex7_A	186	Guanylate kinase; substrate-induced FIT, domain mo	96.57
2oap_1	511	GSPE-2, type II secretion system protein; hexameri	96.56
2pez_A	179	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	96.54
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	96.54
2j37_W	504	Signal recognition particle 54 kDa protein (SRP54)	96.53
3bk7_A	607	ABC transporter ATP-binding protein; ABC ATPase, i	96.52
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	96.5
2wsm_A	221	Hydrogenase expression/formation protein (HYPB); m	96.49
1m7g_A	211	Adenylylsulfate kinase; APS kinase, transferase, s	96.49
2r6a_A	454	DNAB helicase, replicative helicase; replication,	96.47
1wms_A	177	RAB-9, RAB9, RAS-related protein RAB-9A; GTPase, p	96.46
2v54_A	204	DTMP kinase, thymidylate kinase; nucleotide biosyn	96.44
1sky_E	473	F1-ATPase, F1-ATP synthase; F1FO ATP synthase, alp	96.44
1xjc_A	169	MOBB protein homolog; structural genomics, midwest	96.43
3asz_A	211	Uridine kinase; cytidine phosphorylation, transfer	96.42
1z0j_A	170	RAB-22, RAS-related protein RAB-22A; RAB GTPase, R	96.41
3szr_A	608	Interferon-induced GTP-binding protein MX1; interf	96.39
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	96.39
1rj9_A	304	FTSY, signal recognition protein; SRP-GTPase domai	96.39
4gzl_A	204	RAS-related C3 botulinum toxin substrate 1; rossma	96.38
3ney_A	197	55 kDa erythrocyte membrane protein; structural ge	96.36
1jjv_A	206	Dephospho-COA kinase; P-loop nucleotide-binding fo	96.34
3r20_A	233	Cytidylate kinase; structural genomics, seattle st	96.34
2if2_A	204	Dephospho-COA kinase; alpha-beta protein, structur	96.32
2hf9_A	226	Probable hydrogenase nickel incorporation protein	96.32
1sq5_A	308	Pantothenate kinase; P-loop, transferase; HET: PAU	96.31
3ozx_A	538	RNAse L inhibitor; ATP binding cassette protein, h	96.29
1uj2_A	252	Uridine-cytidine kinase 2; alpha/beta mononucleoti	96.28
1uf9_A	203	TT1252 protein; P-loop, nucleotide binding domain,	96.27
1kao_A	167	RAP2A; GTP-binding protein, small G protein, GDP,	96.27
3ake_A	208	Cytidylate kinase; CMP kinase, CMP complex, open c	96.27
3e70_C	328	DPA, signal recognition particle receptor; FTSY, S	96.27
2gza_A	361	Type IV secretion system protein VIRB11; ATPase, h	96.26
3tqc_A	321	Pantothenate kinase; biosynthesis of cofactors, pr	96.26
3clv_A	208	RAB5 protein, putative; malaria, GTPase, structura	96.25
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	96.23
1tf7_A	525	KAIC; homohexamer, hexamer, circadian clock protei	96.22
3t1o_A	198	Gliding protein MGLA; G domain containing protein,	96.22
3thx_A	934	DNA mismatch repair protein MSH2; ABC family ATPas	96.2
3lnc_A	231	Guanylate kinase, GMP kinase; ALS collaborative cr	96.19
4e22_A	252	Cytidylate kinase; P-loop, CMP/ATP binding, transf	96.19
3dz8_A	191	RAS-related protein RAB-3B; GDP, GTPase, structura	96.18
3thx_B	918	DNA mismatch repair protein MSH3; ABC family ATPas	96.18
3bc1_A	195	RAS-related protein RAB-27A; RAB27, GTPase, RAB, s	96.17
1g8f_A	511	Sulfate adenylyltransferase; alpha-beta protein, b	96.16
3crm_A	323	TRNA delta(2)-isopentenylpyrophosphate transferase	96.16
4eaq_A	229	DTMP kinase, thymidylate kinase; structural genomi	96.12
1z63_A	500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	96.12
1z0f_A	179	RAB14, member RAS oncogene family; RAB GTPase, ves	96.11
3p32_A	355	Probable GTPase RV1496/MT1543; structural genomics	96.11
1u8z_A	168	RAS-related protein RAL-A; GNP, GTP, GMPPNP, GPPNH	96.1
1z2a_A	168	RAS-related protein RAB-23; RAB GTPase, vesicular	96.1
1gtv_A	214	TMK, thymidylate kinase; transferase, transferase	96.08
3lxw_A	247	GTPase IMAP family member 1; immunity, structural	96.07
2hup_A	201	RAS-related protein RAB-43; G-protein, GDP, struct	96.06
2cbz_A	237	Multidrug resistance-associated protein 1; ABC pro	96.04
1sgw_A	214	Putative ABC transporter; structural genomics, P p	96.04
3lv8_A	236	DTMP kinase, thymidylate kinase; structural genomi	96.04
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	96.03
1np6_A	174	Molybdopterin-guanine dinucleotide biosynthesis pr	96.02
2grj_A	192	Dephospho-COA kinase; TM1387, EC 2.7.1.24, dephosp	96.0
1b0u_A	262	Histidine permease; ABC transporter, transport pro	95.99
2q6t_A	444	DNAB replication FORK helicase; hydrolase; 2.90A {	95.99
3llu_A	196	RAS-related GTP-binding protein C; structural geno	95.98
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	95.97
2d2e_A	250	SUFC protein; ABC-ATPase, SUF protein, 310-helix,	95.97
3aez_A	312	Pantothenate kinase; transferase, homodimer, COA b	95.96
3tw8_B	181	RAS-related protein RAB-35; longin domain, RAB GTP	95.96
4tmk_A	213	Protein (thymidylate kinase); ATP:DTMP phosphotran	95.95
2qt1_A	207	Nicotinamide riboside kinase 1; non-protein kinase	95.95
1g6h_A	257	High-affinity branched-chain amino acid transport	95.95
3con_A	190	GTPase NRAS; structural genomics consortium, SGC,	95.94
2xxa_A	433	Signal recognition particle protein; protein trans	95.94
2qm8_A	337	GTPase/ATPase; G protein, G3E, metallochaperone, c	95.93
1r8s_A	164	ADP-ribosylation factor 1; protein transport/excha	95.93
1wb9_A	800	DNA mismatch repair protein MUTS; DNA-binding, ATP	95.92
2pze_A	229	Cystic fibrosis transmembrane conductance regulat;	95.92
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	95.92
2zu0_C	267	Probable ATP-dependent transporter SUFC; iron-sulf	95.92
1nlf_A	279	Regulatory protein REPA; replicative DNA helicase	95.91
2ce2_X	166	GTPase HRAS; signaling protein, guanine nucleotide	95.91
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	95.91
1j8m_F	297	SRP54, signal recognition 54 kDa protein; signalin	95.89
1mv5_A	243	LMRA, multidrug resistance ABC transporter ATP-bin	95.88
3foz_A	316	TRNA delta(2)-isopentenylpyrophosphate transferas;	95.87
1vht_A	218	Dephospho-COA kinase; structural genomics, transfe	95.86
3kta_A	182	Chromosome segregation protein SMC; structural mai	95.85
3ld9_A	223	DTMP kinase, thymidylate kinase; ssgcid, NIH, niai	95.85
2bov_A	206	RAla, RAS-related protein RAL-A; C3BOT, exoenzyme,	95.85
3j16_B	608	RLI1P; ribosome recycling, translation, eukarya, r	95.84
2qag_B	427	Septin-6, protein NEDD5; cell cycle, cell division	95.84
2qmh_A	205	HPR kinase/phosphorylase; V267F mutation, ATP-bind	95.83
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	95.83
3lxx_A	239	GTPase IMAP family member 4; structural genomics c	95.83
4dkx_A	216	RAS-related protein RAB-6A; GTP binding fold, memb	95.82
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	95.8
1r2q_A	170	RAS-related protein RAB-5A; GTPase, GNP, atomic re	95.8
2ihy_A	279	ABC transporter, ATP-binding protein; ATPase, ABC	95.79
4edh_A	213	DTMP kinase, thymidylate kinase; structural genomi	95.79
3b9q_A	302	Chloroplast SRP receptor homolog, alpha subunit CP	95.77
3d3q_A	340	TRNA delta(2)-isopentenylpyrophosphate transferase	95.76
3a8t_A	339	Adenylate isopentenyltransferase; rossmann fold pr	95.75
2yz2_A	266	Putative ABC transporter ATP-binding protein TM_0;	95.74
1ek0_A	170	Protein (GTP-binding protein YPT51); vesicular tra	95.74
1z06_A	189	RAS-related protein RAB-33B; RAB GTPase, RAB33B GT	95.72
2i1q_A	322	DNA repair and recombination protein RADA; ATPase,	95.71
2efe_B	181	Small GTP-binding protein-like; GEF, GTPase, VPS9,	95.71
1zbd_A	203	Rabphilin-3A; G protein, effector, RABCDR, synapti	95.71
2a9k_A	187	RAS-related protein RAL-A; bacterial ADP-ribosyltr	95.7
2www_A	349	Methylmalonic aciduria type A protein, mitochondri	95.68
1zj6_A	187	ADP-ribosylation factor-like protein 5; ARL, GTP-b	95.68
1q3t_A	236	Cytidylate kinase; nucleotide monophosphate kinase	95.67
1m7b_A	184	RND3/RHOE small GTP-binding protein; small GTPase,	95.64
3cr8_A	552	Sulfate adenylyltranferase, adenylylsulfate kinase	95.64
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	95.63
3bgw_A	444	DNAB-like replicative helicase; ATPase, replicatio	95.63
2ged_A	193	SR-beta, signal recognition particle receptor beta	95.63
3q85_A	169	GTP-binding protein REM 2; G-domain, CAV2 beta, si	95.61
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	95.6
4dsu_A	189	GTPase KRAS, isoform 2B; small G-protein, signalin	95.59
2f6r_A	281	COA synthase, bifunctional coenzyme A synthase; 18	95.57
1mh1_A	186	RAC1; GTP-binding, GTPase, small G-protein, RHO fa	95.56
2fh5_B	214	SR-beta, signal recognition particle receptor beta	95.56
3q72_A	166	GTP-binding protein RAD; G-domain, CAV2 beta, sign	95.55
2gk6_A	624	Regulator of nonsense transcripts 1; UPF1, helicas	95.55
3tkl_A	196	RAS-related protein RAB-1A; vesicle trafficking, p	95.55
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	95.54
2bme_A	186	RAB4A, RAS-related protein RAB4A; GTP-binding prot	95.53
1m8p_A	573	Sulfate adenylyltransferase; rossmann fold, phosph	95.49
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	95.47
3tqf_A	181	HPR(Ser) kinase; transferase, hydrolase; 2.80A {Co	95.47
2f1r_A	171	Molybdopterin-guanine dinucleotide biosynthesis pr	95.47
2og2_A	359	Putative signal recognition particle receptor; nuc	95.46
2zts_A	251	Putative uncharacterized protein PH0186; KAIC like	95.46
1a7j_A	290	Phosphoribulokinase; transferase, calvin cycle; 2.	95.45
3reg_A	194	RHO-like small GTPase; cytoskeleton, nucleotide-bi	95.44
3v9p_A	227	DTMP kinase, thymidylate kinase; ssgcid, STRU geno	95.44
1tq4_A	413	IIGP1, interferon-inducible GTPase; interferon gam	95.44
1c1y_A	167	RAS-related protein RAP-1A; GTP-binding proteins,	95.43
2h92_A	219	Cytidylate kinase; rossmann fold, transferase; HET	95.42
2g6b_A	180	RAS-related protein RAB-26; G-protein, GTP analogu	95.42
3gmt_A	230	Adenylate kinase; ssgcid, ATP-BIN cytoplasm, nucle	95.41
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	95.41
3kkq_A	183	RAS-related protein M-RAS; GTP-binding, GTPase, si	95.39
2ffh_A	425	Protein (FFH); SRP54, signal recognition particle,	95.39
2ew1_A	201	RAS-related protein RAB-30; G-protein, GTP analogu	95.39
2p5s_A	199	RAS and EF-hand domain containing; G-protein, RAB,	95.38
1zd9_A	188	ADP-ribosylation factor-like 10B; transport protei	95.38
2bbs_A	290	Cystic fibrosis transmembrane conductance regulato	95.37
2gks_A	546	Bifunctional SAT/APS kinase; transferase, sulfuryl	95.37
2il1_A	192	RAB12; G-protein, GDP, GTPase, predicted, structur	95.36
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	95.34
1gwn_A	205	RHO-related GTP-binding protein RHOE; GTPase, inac	95.34
3q3j_B	214	RHO-related GTP-binding protein RHO6; RAS-binding	95.33
2dyk_A	161	GTP-binding protein; GTPase, ribosome-binding prot	95.32
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	95.32
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	95.32
2fg5_A	192	RAB-22B, RAS-related protein RAB-31; G-protein, GT	95.31
1f2t_A	149	RAD50 ABC-ATPase; DNA double-strand break repair,	95.3
2yhs_A	503	FTSY, cell division protein FTSY; cell cycle, prot	95.3
2wjy_A	800	Regulator of nonsense transcripts 1; nonsense medi	95.29
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	95.26
2j1l_A	214	RHO-related GTP-binding protein RHOD; GTPase, memb	95.26
2gf0_A	199	GTP-binding protein DI-RAS1; GDP/GTP binding, GTP	95.21
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	95.21
2f9l_A	199	RAB11B, member RAS oncogene family; RAB11B GTPase,	95.2
1lw7_A	365	Transcriptional regulator NADR; NMN, NMN adenylyl	95.2
1oix_A	191	RAS-related protein RAB-11A; small G protein, intr	95.2
3eph_A	409	TRNA isopentenyltransferase; transferase, alternat	95.19
2ocp_A	241	DGK, deoxyguanosine kinase; protein-nucleotide com	95.17
1zu4_A	320	FTSY; GTPase, signal recognition particle, SRP, re	95.16
3pqc_A	195	Probable GTP-binding protein ENGB; rossmann fold,	95.14
1oxx_K	353	GLCV, glucose, ABC transporter, ATP binding protei	95.13
3ux8_A	670	Excinuclease ABC, A subunit; UVRA, nucleotide exci	95.09
1x3s_A	195	RAS-related protein RAB-18; GTPase, GNP, structura	95.09
3tmk_A	216	Thymidylate kinase; phosphotransferase; HET: T5A;	95.06
2obl_A	347	ESCN; ATPase, hydrolase; 1.80A {Escherichia coli O	95.05
2yc2_C	208	IFT27, small RAB-related GTPase; transport protein	95.03
4ag6_A	392	VIRB4 ATPase, type IV secretory pathway VIRB4 comp	95.02
2f7s_A	217	C25KG, RAS-related protein RAB-27B; G-protein, str	94.97
2atx_A	194	Small GTP binding protein TC10; GTPase, P-loop, al	94.96
4hlc_A	205	DTMP kinase, thymidylate kinase; TMK, MRSA, pipiri	94.96
2zpa_A	671	Uncharacterized protein YPFI; RNA modification enz	94.91
3cph_A	213	RAS-related protein SEC4; RAB GTPase, prenylation,	94.9
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	94.87
4dhe_A	223	Probable GTP-binding protein ENGB; melioidosis, RA	94.87
1ko7_A	314	HPR kinase/phosphatase; protein kinase, phosphotra	94.85
2dpy_A	438	FLII, flagellum-specific ATP synthase; beta barrel	94.85
2npi_A	460	Protein CLP1; CLP1-PCF11 complex, ATP binding, ter	94.84
3hjn_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	94.84
3hdt_A	223	Putative kinase; structura genomics, PSI-2, protei	94.83
2axn_A	520	6-phosphofructo-2-kinase/fructose-2,6- biphosphata	94.81

>1sxj_C Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=100.00  E-value=5e-48  Score=342.05  Aligned_cols=309  Identities=31%  Similarity=0.587  Sum_probs=283.0

Q ss_pred             cccCCCCCCcccCCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHH
Q psy879            2 EKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNK   81 (317)
Q Consensus         2 ~ky~P~~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~   81 (317)
                      +||||++|++++||+++++.|..++++|++||++|+||||+||||+++++++.+.+..+...+.+++.++..+.+.+++.
T Consensus        17 ~k~rp~~~~~~~g~~~~~~~L~~~i~~g~~~~~ll~Gp~G~GKTtla~~la~~l~~~~~~~~~~~~~~~~~~~~~~ir~~   96 (340)
T 1sxj_C           17 EKYRPETLDEVYGQNEVITTVRKFVDEGKLPHLLFYGPPGTGKTSTIVALAREIYGKNYSNMVLELNASDDRGIDVVRNQ   96 (340)
T ss_dssp             HHTCCSSGGGCCSCHHHHHHHHHHHHTTCCCCEEEECSSSSSHHHHHHHHHHHHHTTSHHHHEEEECTTSCCSHHHHHTH
T ss_pred             HHhCCCcHHHhcCcHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCccceEEEEcCcccccHHHHHHH
Confidence            69999999999999999999999999999999999999999999999999999987665566788888777778888888


Q ss_pred             HHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcCchhHhhhcceeeecCCCHHHHH
Q psy879           82 IKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLL  161 (317)
Q Consensus        82 ~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~~~i~sR~~~i~f~~~~~~~~~  161 (317)
                      +..+.+.... ..++++|+||||+|.++.+.+++|++++|+++.++.+|+++|.+.++.++++|||..++|++++.+++.
T Consensus        97 i~~~~~~~~~-~~~~~~viiiDe~~~l~~~~~~~L~~~le~~~~~~~~il~~n~~~~i~~~i~sR~~~~~~~~l~~~~~~  175 (340)
T 1sxj_C           97 IKDFASTRQI-FSKGFKLIILDEADAMTNAAQNALRRVIERYTKNTRFCVLANYAHKLTPALLSQCTRFRFQPLPQEAIE  175 (340)
T ss_dssp             HHHHHHBCCS-SSCSCEEEEETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHTTSEEEECCCCCHHHHH
T ss_pred             HHHHHhhccc-CCCCceEEEEeCCCCCCHHHHHHHHHHHhcCCCCeEEEEEecCccccchhHHhhceeEeccCCCHHHHH
Confidence            8777653221 124589999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhhCCC-----cccHHHHHhhcCCCCHHHHHHHHHHHhcCC
Q psy879          162 SKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHNGFG-----HVTAEYVFKVCDEPHPLAVKEMLLNCVEGN  236 (317)
Q Consensus       162 ~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~~~~-----~i~~~~v~~~~~~~~~~~i~~l~~~~~~~~  236 (317)
                      +++..++..+++.++++++..++..++||+|++++.++.++....     .|+.+++.++++......++++++.+..++
T Consensus       176 ~~l~~~~~~~~~~i~~~~~~~i~~~s~G~~r~~~~~l~~~~~~~~~~~~~~it~~~v~~~~~~~~~~~i~~l~~~i~~~~  255 (340)
T 1sxj_C          176 RRIANVLVHEKLKLSPNAEKALIELSNGDMRRVLNVLQSCKATLDNPDEDEISDDVIYECCGAPRPSDLKAVLKSILEDD  255 (340)
T ss_dssp             HHHHHHHHTTTCCBCHHHHHHHHHHHTTCHHHHHHHTTTTTTTTCSSSCCCBCHHHHHHHTTCCCHHHHHHHHHHHHTSC
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhcCCcccccccHHHHHHHhCCCCHHHHHHHHHHHHcCC
Confidence            999999998999999999999999999999999999988765333     699999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHH-cCCCHHHHHHHHHHHHHhcCCC-hHHHHHHHHHHHHHHhHHhcCCCcHHHHHHHHHHHHHhhc
Q psy879          237 MKDSYKIIHHLYK-LGYAPEDIIGNIFRVAKTLDIP-EPLKLSIIQEIGNVHLRISEGVNSLLQLSGLLARLCIVGS  311 (317)
Q Consensus       237 ~~~~~~~~~~l~~-~~~~~~~i~~~~~~~~~~~~~~-~~~~~~~~~~l~~~~~~l~~g~~~~l~le~~~~~~~~~~~  311 (317)
                      ..+++.++.+++. .|++|.+++..+.+++..+.++ .....++++.+.++++++++|+|+.++||.|++++|.+..
T Consensus       256 ~~~al~~l~~l~~~~g~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~g~~~~l~le~l~~~l~~~~~  332 (340)
T 1sxj_C          256 WGTAHYTLNKVRSAKGLALIDLIEGIVKILEDYELQNEETRVHLLTKLADIEYSISKGGNDQIQGSAVIGAIKASFE  332 (340)
T ss_dssp             HHHHHHHHHHHHHTTTCCHHHHHHHHHHHHTTSCCSSHHHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHHCC
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhccCCcHHHHHHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHHhh
Confidence            9999999999998 9999999999999999877777 8889999999999999999999999999999999997654

>2chq_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATP ATP-binding, nucleotide-binding; HET: ANP; 3.5A {Archaeoglobus fulgidus} PDB: 2chv_A

Probab=100.00  E-value=5.4e-46  Score=326.17  Aligned_cols=310  Identities=40%  Similarity=0.750  Sum_probs=279.9

Q ss_pred             CcccCCCCCCcccCCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHH
Q psy879            1 IEKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRN   80 (317)
Q Consensus         1 ~~ky~P~~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~   80 (317)
                      ++||+|++|++++|++++++.+..++.++..+|++|+||||+|||++++++++.+.+......++++++.+..+.+.+++
T Consensus         8 ~~k~~p~~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~   87 (319)
T 2chq_A            8 VEKYRPRTLDEVVGQDEVIQRLKGYVERKNIPHLLFSGPPGTGKTATAIALARDLFGENWRDNFIEMNASDERGIDVVRH   87 (319)
T ss_dssp             TTTTSCSSGGGSCSCHHHHHHHHTTTTTTCCCCEEEESSSSSSHHHHHHHHHHHHHTTCHHHHCEEEETTSTTCTTTSSH
T ss_pred             HHhcCCCCHHHHhCCHHHHHHHHHHHhCCCCCeEEEECcCCcCHHHHHHHHHHHhcCCcccCCeEEEeCccccChHHHHH
Confidence            47999999999999999999999999999988999999999999999999999987665555677788776656666666


Q ss_pred             HHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcCchhHhhhcceeeecCCCHHHH
Q psy879           81 KIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQL  160 (317)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~~~i~sR~~~i~f~~~~~~~~  160 (317)
                      .+..+.... ....+++++++|||+|.++.+.+++|++++++++.++++|+++|.+.++.+++.|||..+.|++++.+++
T Consensus        88 ~~~~~~~~~-~~~~~~~~vliiDe~~~l~~~~~~~L~~~le~~~~~~~~i~~~~~~~~l~~~l~sr~~~i~~~~~~~~~~  166 (319)
T 2chq_A           88 KIKEFARTA-PIGGAPFKIIFLDEADALTADAQAALRRTMEMYSKSCRFILSCNYVSRIIEPIQSRCAVFRFKPVPKEAM  166 (319)
T ss_dssp             HHHHHHHSC-CSSSCCCEEEEEETGGGSCHHHHHTTGGGTSSSSSSEEEEEEESCGGGSCHHHHTTCEEEECCCCCHHHH
T ss_pred             HHHHHHhcC-CCCCCCceEEEEeCCCcCCHHHHHHHHHHHHhcCCCCeEEEEeCChhhcchHHHhhCeEEEecCCCHHHH
Confidence            555554221 1122568999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhhCCCcccHHHHHhhcCCCCHHHHHHHHHHHhcCCHHHH
Q psy879          161 LSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEMLLNCVEGNMKDS  240 (317)
Q Consensus       161 ~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~~~~~i~~~~v~~~~~~~~~~~i~~l~~~~~~~~~~~~  240 (317)
                      ..++..++.++|+.+++++++.++..++||+|.+++.++.++...+.|+.+++.+++....+..++++++++..++...+
T Consensus       167 ~~~l~~~~~~~~~~i~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~~~i~~~~v~~~~~~~~~~~~~~l~~~~~~~~~~~a  246 (319)
T 2chq_A          167 KKRLLEICEKEGVKITEDGLEALIYISGGDFRKAINALQGAAAIGEVVDADTIYQITATARPEEMTELIQTALKGNFMEA  246 (319)
T ss_dssp             HHHHHHHHHTTCCCBCHHHHHHHHHTTTTCHHHHHHHHHHHHHSSSCBCHHHHHHHTTCCCHHHHHHHHHHHHHTCHHHH
T ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHCCCCHHHHHHHHHHHHhCCHHHH
Confidence            99999999999999999999999999999999999999988776678999999999999999999999999999999999


Q ss_pred             HHHHHHHHH-cCCCHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHHHhHHhcCCCcHHHHHHHHHHHHHhhc
Q psy879          241 YKIIHHLYK-LGYAPEDIIGNIFRVAKTLDIPEPLKLSIIQEIGNVHLRISEGVNSLLQLSGLLARLCIVGS  311 (317)
Q Consensus       241 ~~~~~~l~~-~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~g~~~~l~le~~~~~~~~~~~  311 (317)
                      +.++.+++. .|++|..++..+.+.+..+.++.....++++.+.+++.+++.|+|+.+++|.|+.++|.++.
T Consensus       247 ~~~l~~l~~~~g~~~~~i~~~l~~~~~~l~~~~~~l~~~~~~l~~~~~~lk~~~~~~~~le~l~~~l~~~~~  318 (319)
T 2chq_A          247 RELLDRLMVEYGMSGEDIVAQLFREIISMPIKDSLKVQLIDKLGEVDFRLTEGANERIQLDAYLAYLSTLAK  318 (319)
T ss_dssp             HHHHHHHHHHSCCCHHHHHHHHHHHHHTSCSCTTHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHhhc
Confidence            999999987 99999999999999998767888889999999999999999999999999999999997643

>1iqp_A RFCS; clamp loader, extended AAA-ATPase domain, complex with ADP, replication; HET: ADP; 2.80A {Pyrococcus furiosus} SCOP: a.80.1.1 c.37.1.20

Probab=100.00  E-value=3.7e-45  Score=321.97  Aligned_cols=309  Identities=44%  Similarity=0.751  Sum_probs=277.8

Q ss_pred             cccCCCCCCcccCCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHH
Q psy879            2 EKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNK   81 (317)
Q Consensus         2 ~ky~P~~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~   81 (317)
                      +||+|++|++++|++++++.+..++.+++.+|++|+||||+|||++++++++.+.+......++++++.+..+.+.+++.
T Consensus        17 ~k~~p~~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKT~la~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~   96 (327)
T 1iqp_A           17 EKYRPQRLDDIVGQEHIVKRLKHYVKTGSMPHLLFAGPPGVGKTTAALALARELFGENWRHNFLELNASDERGINVIREK   96 (327)
T ss_dssp             HHTCCCSTTTCCSCHHHHHHHHHHHHHTCCCEEEEESCTTSSHHHHHHHHHHHHHGGGHHHHEEEEETTCHHHHHTTHHH
T ss_pred             hccCCCCHHHhhCCHHHHHHHHHHHHcCCCCeEEEECcCCCCHHHHHHHHHHHhcCCcccCceEEeeccccCchHHHHHH
Confidence            68999999999999999999999999999999999999999999999999999865544445777777665555556655


Q ss_pred             HHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcCchhHhhhcceeeecCCCHHHHH
Q psy879           82 IKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLL  161 (317)
Q Consensus        82 ~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~~~i~sR~~~i~f~~~~~~~~~  161 (317)
                      +..+.... ....+++++++|||+|.++.+.+++|++++++++.++++|++++.+.++.+++.+||..+.|++++.+++.
T Consensus        97 ~~~~~~~~-~~~~~~~~vliiDe~~~l~~~~~~~L~~~le~~~~~~~~i~~~~~~~~l~~~l~sr~~~~~~~~l~~~~~~  175 (327)
T 1iqp_A           97 VKEFARTK-PIGGASFKIIFLDEADALTQDAQQALRRTMEMFSSNVRFILSCNYSSKIIEPIQSRCAIFRFRPLRDEDIA  175 (327)
T ss_dssp             HHHHHHSC-CGGGCSCEEEEEETGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHHTEEEEECCCCCHHHHH
T ss_pred             HHHHHhhC-CcCCCCCeEEEEeCCCcCCHHHHHHHHHHHHhcCCCCeEEEEeCCccccCHHHHhhCcEEEecCCCHHHHH
Confidence            55544221 11115689999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhhCCCcccHHHHHhhcCCCCHHHHHHHHHHHhcCCHHHHH
Q psy879          162 SKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEMLLNCVEGNMKDSY  241 (317)
Q Consensus       162 ~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~~~~~i~~~~v~~~~~~~~~~~i~~l~~~~~~~~~~~~~  241 (317)
                      .++..++..+++.+++++++.++..++||+|.+++.++.++.....|+.+++..++....+..++++++++..++...++
T Consensus       176 ~~l~~~~~~~~~~~~~~~~~~l~~~~~g~~r~~~~~l~~~~~~~~~i~~~~v~~~~~~~~~~~i~~l~~~~~~~~~~~~~  255 (327)
T 1iqp_A          176 KRLRYIAENEGLELTEEGLQAILYIAEGDMRRAINILQAAAALDKKITDENVFMVASRARPEDIREMMLLALKGNFLKAR  255 (327)
T ss_dssp             HHHHHHHHTTTCEECHHHHHHHHHHHTTCHHHHHHHHHHHHTTCSEECHHHHHHHTTCCCHHHHHHHHHHHHHTCHHHHH
T ss_pred             HHHHHHHHhcCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHhcCCCCCHHHHHHHHCCCCHHHHHHHHHHHHcCCHHHHH
Confidence            99999999999999999999999999999999999999888766789999999999999999999999999999999999


Q ss_pred             HHHHHHH-HcCCCHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHHHhHHhcCCCcHHHHHHHHHHHHHhhc
Q psy879          242 KIIHHLY-KLGYAPEDIIGNIFRVAKTLDIPEPLKLSIIQEIGNVHLRISEGVNSLLQLSGLLARLCIVGS  311 (317)
Q Consensus       242 ~~~~~l~-~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~g~~~~l~le~~~~~~~~~~~  311 (317)
                      .++++++ ..|++|..++..+.+.+..+.++.....++++.+.+++.++++|.|+.+++|.|+.++|.+..
T Consensus       256 ~~~~~ll~~~g~~~~~i~~~l~~~~~~~~~~~~~l~~~~~~l~~~~~~lk~~~~~~~~le~l~~~l~~~~~  326 (327)
T 1iqp_A          256 EKLREILLKQGLSGEDVLVQMHKEVFNLPIEEPKKVLLADKIGEYNFRLVEGANEIIQLEALLAQFTLIGK  326 (327)
T ss_dssp             HHHHHHHHHHCCCHHHHHHHHHHHGGGSSSCHHHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHhhc
Confidence            9999998 899999999999999888777899999999999999999999999999999999999997654

>1sxj_B Activator 1 37 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=100.00  E-value=4.4e-44  Score=314.52  Aligned_cols=307  Identities=61%  Similarity=0.986  Sum_probs=275.6

Q ss_pred             cccCCCCCCcccCCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHH
Q psy879            2 EKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNK   81 (317)
Q Consensus         2 ~ky~P~~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~   81 (317)
                      +||+|.+|++++|++++++.+..++.+++++|++|+||+|+|||++++.+++.+.+......++++++.+..+.+.+++.
T Consensus        13 ~~~~p~~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~l~~~l~~~~~~~~~~~~~~~~~~~~~~i~~~   92 (323)
T 1sxj_B           13 EKYRPQVLSDIVGNKETIDRLQQIAKDGNMPHMIISGMPGIGKTTSVHCLAHELLGRSYADGVLELNASDDRGIDVVRNQ   92 (323)
T ss_dssp             HHTCCSSGGGCCSCTHHHHHHHHHHHSCCCCCEEEECSTTSSHHHHHHHHHHHHHGGGHHHHEEEECTTSCCSHHHHHTH
T ss_pred             HhcCCCCHHHHHCCHHHHHHHHHHHHcCCCCeEEEECcCCCCHHHHHHHHHHHhcCCcccCCEEEecCccccChHHHHHH
Confidence            68999999999999999999999999999889999999999999999999999866554555778888776678888877


Q ss_pred             HHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcCchhHhhhcceeeecCCCHHHHH
Q psy879           82 IKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLL  161 (317)
Q Consensus        82 ~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~~~i~sR~~~i~f~~~~~~~~~  161 (317)
                      +..+.........+++++++|||+|.++.+.+++|++++++++.++++|++|+...++.++++|||..+.|++++.+++.
T Consensus        93 ~~~~~~~~~~~~~~~~~viiiDe~~~l~~~~~~~L~~~le~~~~~~~~il~~~~~~~l~~~l~sr~~~i~~~~~~~~~~~  172 (323)
T 1sxj_B           93 IKHFAQKKLHLPPGKHKIVILDEADSMTAGAQQALRRTMELYSNSTRFAFACNQSNKIIEPLQSQCAILRYSKLSDEDVL  172 (323)
T ss_dssp             HHHHHHBCCCCCTTCCEEEEEESGGGSCHHHHHTTHHHHHHTTTTEEEEEEESCGGGSCHHHHTTSEEEECCCCCHHHHH
T ss_pred             HHHHHhccccCCCCCceEEEEECcccCCHHHHHHHHHHHhccCCCceEEEEeCChhhchhHHHhhceEEeecCCCHHHHH
Confidence            77665332222234589999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhhCCCcccHHHHHhhcCCCCHHHHHHHHHHHhcCCHHHHH
Q psy879          162 SKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEMLLNCVEGNMKDSY  241 (317)
Q Consensus       162 ~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~~~~~i~~~~v~~~~~~~~~~~i~~l~~~~~~~~~~~~~  241 (317)
                      .++..++..+++.+++++++.++..++||+|.+++.++..+...+.++.++|.+++.......++++++.   ++...++
T Consensus       173 ~~l~~~~~~~~~~~~~~~~~~l~~~~~G~~r~a~~~l~~~~~~~~~i~~~~v~~~~~~~~~~~i~~~~~~---~~~~~~l  249 (323)
T 1sxj_B          173 KRLLQIIKLEDVKYTNDGLEAIIFTAEGDMRQAINNLQSTVAGHGLVNADNVFKIVDSPHPLIVKKMLLA---SNLEDSI  249 (323)
T ss_dssp             HHHHHHHHHHTCCBCHHHHHHHHHHHTTCHHHHHHHHHHHHHHHSSBCHHHHHHHHTSCCHHHHHHHHSC---SSHHHHH
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCcCHHHHHHHHCCCCHHHHHHHHhc---CCHHHHH
Confidence            9999999999999999999999999999999999999987765567999999999999888889998887   7888999


Q ss_pred             HHHHH-HHHcCCCHHHHHHHHHHHHHhcC-CChHHHHHHHHHHHHHHhHHhcCCCcHHHHHHHHHHHHHhhc
Q psy879          242 KIIHH-LYKLGYAPEDIIGNIFRVAKTLD-IPEPLKLSIIQEIGNVHLRISEGVNSLLQLSGLLARLCIVGS  311 (317)
Q Consensus       242 ~~~~~-l~~~~~~~~~i~~~~~~~~~~~~-~~~~~~~~~~~~l~~~~~~l~~g~~~~l~le~~~~~~~~~~~  311 (317)
                      .++.. ++..|+++.+++..+.+++..+. ++.....++++.+.+++.++++|+|+.+++|.|+.+++.+..
T Consensus       250 ~~l~~dl~~~g~~~~~i~~~l~~~~~~l~~~~~~~l~~~l~~l~~~~~~l~~~~~~~l~le~l~~~~~~~~~  321 (323)
T 1sxj_B          250 QILRTDLWKKGYSSIDIVTTSFRVTKNLAQVKESVRLEMIKEIGLTHMRILEGVGTYLQLASMLAKIHKLNN  321 (323)
T ss_dssp             HHHHHTTTTTTCCHHHHHHHHHHHHHTCTTSCHHHHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHHHhcccCCHHHHHHHHHHHHHHHHHHHhccChHHHHHHHHHHHHhhcc
Confidence            99998 88899999999999999888654 788889999999999999999999999999999999998755

>1sxj_D Activator 1 41 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=100.00  E-value=1.2e-43  Score=315.55  Aligned_cols=307  Identities=35%  Similarity=0.569  Sum_probs=272.0

Q ss_pred             cccCCCCCCcccCCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCC-CCCCceEEecCCCCcChHHHHH
Q psy879            2 EKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGP-SFKDAVLELNASNDRGIDTVRN   80 (317)
Q Consensus         2 ~ky~P~~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~-~~~~~~~~~~~~~~~~~~~i~~   80 (317)
                      +||+|++|++++|++++++.+..++..+.++|++|+||||+|||++++++++.+.++ .....+.++++++..+...+++
T Consensus        29 ~k~~p~~~~~i~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~  108 (353)
T 1sxj_D           29 EKYRPKNLDEVTAQDHAVTVLKKTLKSANLPHMLFYGPPGTGKTSTILALTKELYGPDLMKSRILELNASDERGISIVRE  108 (353)
T ss_dssp             HHTCCSSTTTCCSCCTTHHHHHHHTTCTTCCCEEEECSTTSSHHHHHHHHHHHHHHHHHHTTSEEEECSSSCCCHHHHTT
T ss_pred             HhcCCCCHHHhhCCHHHHHHHHHHHhcCCCCEEEEECCCCCCHHHHHHHHHHHhCCCcccccceEEEccccccchHHHHH
Confidence            699999999999999999999999999988899999999999999999999997542 2334577788876667777776


Q ss_pred             HHHHHHhhccc---------CCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcCchhHhhhcceee
Q psy879           81 KIKMFAQQKVT---------LPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLR  151 (317)
Q Consensus        81 ~~~~~~~~~~~---------~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~~~i~sR~~~i~  151 (317)
                      .+..+......         .+.+.+++++|||++.+..+.+++|++++++++.++++|+++|.+..+.+++++||..+.
T Consensus       109 ~~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~~~l~~~~~~~Ll~~le~~~~~~~~il~~~~~~~l~~~l~sR~~~i~  188 (353)
T 1sxj_D          109 KVKNFARLTVSKPSKHDLENYPCPPYKIIILDEADSMTADAQSALRRTMETYSGVTRFCLICNYVTRIIDPLASQCSKFR  188 (353)
T ss_dssp             HHHHHHHSCCCCCCTTHHHHSCCCSCEEEEETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHHHSEEEE
T ss_pred             HHHHHhhhcccccchhhcccCCCCCceEEEEECCCccCHHHHHHHHHHHHhcCCCceEEEEeCchhhCcchhhccCceEE
Confidence            66555443210         122467899999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhh--CC----CcccHHHHHhhcCCCCHHHH
Q psy879          152 YNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHN--GF----GHVTAEYVFKVCDEPHPLAV  225 (317)
Q Consensus       152 f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~--~~----~~i~~~~v~~~~~~~~~~~i  225 (317)
                      |++++.+++..++..++..+++.+++++++.++..++||+|.+++.++.++.  +.    ..|+.++|.+++.......+
T Consensus       189 ~~~~~~~~~~~~l~~~~~~~~~~i~~~~l~~l~~~~~G~~r~~~~~l~~~~~~~~~~~~~~~It~~~v~~~~~~~~~~~~  268 (353)
T 1sxj_D          189 FKALDASNAIDRLRFISEQENVKCDDGVLERILDISAGDLRRGITLLQSASKGAQYLGDGKNITSTQVEELAGVVPHDIL  268 (353)
T ss_dssp             CCCCCHHHHHHHHHHHHHTTTCCCCHHHHHHHHHHTSSCHHHHHHHHHHTHHHHHHHCSCCCCCHHHHHHHHTCCCSHHH
T ss_pred             eCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhcCCCccCccccHHHHHHHhCCCCHHHH
Confidence            9999999999999999999999999999999999999999999999987654  21    17999999999998888899


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhc-CCChHHHHHHHHHHHHHHhHHhcCCCcHHHHHHHHH
Q psy879          226 KEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDIIGNIFRVAKTL-DIPEPLKLSIIQEIGNVHLRISEGVNSLLQLSGLLA  304 (317)
Q Consensus       226 ~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~~~~-~~~~~~~~~~~~~l~~~~~~l~~g~~~~l~le~~~~  304 (317)
                      +++++++..++...++.+++++...|++|..|+..+.+.+... +++.....+++..+.++++++++|.|+.+++|.|++
T Consensus       269 ~~l~~~~~~~~~~~a~~~l~~l~~~g~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~g~~~~l~l~~~~~  348 (353)
T 1sxj_D          269 IEIVEKVKSGDFDEIKKYVNTFMKSGWSAASVVNQLHEYYITNDNFDTNFKNQISWLLFTTDSRLNNGTNEHIQLLNLLV  348 (353)
T ss_dssp             HHHHHHHHSCCHHHHHHHHHHHHHTSCCCTTHHHHHHHHHHHCSSSCHHHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHH
T ss_pred             HHHHHHHhcCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHHHHHHHhCCChHHHHHHHHH
Confidence            9999999999999999999999999999999999888776554 678888999999999999999999999999999999


Q ss_pred             HHHH
Q psy879          305 RLCI  308 (317)
Q Consensus       305 ~~~~  308 (317)
                      ++|.
T Consensus       349 ~~~~  352 (353)
T 1sxj_D          349 KISQ  352 (353)
T ss_dssp             HHHH
T ss_pred             HHHh
Confidence            9985

>1sxj_E Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=100.00  E-value=4.1e-43  Score=312.42  Aligned_cols=307  Identities=25%  Similarity=0.398  Sum_probs=249.5

Q ss_pred             CcccCCCCCCcccCCHHHHHHHHHHH-hcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCC-----------------
Q psy879            1 IEKYRPQTFSDIVGNEDTVERLKVFS-SSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKD-----------------   62 (317)
Q Consensus         1 ~~ky~P~~~~~~~g~~~~~~~l~~~l-~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~-----------------   62 (317)
                      ++||||++|++++||+++++.+..++ ..++.+|++|+||+|+||||+++++++.+.++..+.                 
T Consensus         5 ~~kyrP~~~~~~vg~~~~~~~l~~~~~~~~~~~~~ll~Gp~G~GKTtl~~~la~~l~~~~~g~i~~~~~~~~~~~~~~~~   84 (354)
T 1sxj_E            5 VDKYRPKSLNALSHNEELTNFLKSLSDQPRDLPHLLLYGPNGTGKKTRCMALLESIFGPGVYRLKIDVRQFVTASNRKLE   84 (354)
T ss_dssp             TTTTCCCSGGGCCSCHHHHHHHHTTTTCTTCCCCEEEECSTTSSHHHHHHTHHHHHSCTTCCC-----------------
T ss_pred             hhccCCCCHHHhcCCHHHHHHHHHHHhhCCCCCeEEEECCCCCCHHHHHHHHHHHHcCCCCCeEEecceeecccccccce
Confidence            58999999999999999999999999 888888999999999999999999999876544221                 


Q ss_pred             -------ceEEecCCCCcCh--HHHHHHHHHHHhhcccC------C-CCceeEEEEeCCCCCCHHHHHHHHHHhhhccCC
Q psy879           63 -------AVLELNASNDRGI--DTVRNKIKMFAQQKVTL------P-PGRHKIVILDEADSMTDGAQQALRRTMEIYSNT  126 (317)
Q Consensus        63 -------~~~~~~~~~~~~~--~~i~~~~~~~~~~~~~~------~-~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~  126 (317)
                             .+++++.......  ..+++.+..+.......      . .++++++||||++.++...+++|++++++++.+
T Consensus        85 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~ls~l~~~~~vlilDE~~~L~~~~~~~L~~~le~~~~~  164 (354)
T 1sxj_E           85 LNVVSSPYHLEITPSDMGNNDRIVIQELLKEVAQMEQVDFQDSKDGLAHRYKCVIINEANSLTKDAQAALRRTMEKYSKN  164 (354)
T ss_dssp             -CCEECSSEEEECCC----CCHHHHHHHHHHHTTTTC------------CCEEEEEECTTSSCHHHHHHHHHHHHHSTTT
T ss_pred             eeeecccceEEecHhhcCCcchHHHHHHHHHHHHhccccccccccccCCCCeEEEEeCccccCHHHHHHHHHHHHhhcCC
Confidence                   2334444321111  13555555543322110      0 247899999999999999999999999999999


Q ss_pred             ceEEEEecCCCcCchhHhhhcceeeecCCCHHHHHHHHHHHHHHcCCCCC-HHHHHHHHHhcCCCHHHHHHHHHHhhhCC
Q psy879          127 TRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHT-NDGLEAIVFTAQGDMRQALNNLQSTHNGF  205 (317)
Q Consensus       127 ~~~il~~~~~~~l~~~i~sR~~~i~f~~~~~~~~~~~l~~~~~~~~~~i~-~~~~~~l~~~~~gd~r~~i~~l~~~~~~~  205 (317)
                      +.+|++|+.+.++.++++|||..++|++++.+++..++..++.++|+.++ +++++.++..++||+|++++.++.++...
T Consensus       165 ~~~Il~t~~~~~l~~~l~sR~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~i~~~~~G~~r~a~~~l~~~~~~~  244 (354)
T 1sxj_E          165 IRLIMVCDSMSPIIAPIKSQCLLIRCPAPSDSEISTILSDVVTNERIQLETKDILKRIAQASNGNLRVSLLMLESMALNN  244 (354)
T ss_dssp             EEEEEEESCSCSSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHHTCEECCSHHHHHHHHHHTTCHHHHHHHHTHHHHTT
T ss_pred             CEEEEEeCCHHHHHHHHHhhceEEecCCcCHHHHHHHHHHHHHHcCCCCCcHHHHHHHHHHcCCCHHHHHHHHHHHHHhC
Confidence            99999999999999999999999999999999999999999999999999 99999999999999999999999877644


Q ss_pred             C-cccHHHHHhhcCCCCHHHHHHHHHHHhcCC----HHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhc-CCChHHHHHHH
Q psy879          206 G-HVTAEYVFKVCDEPHPLAVKEMLLNCVEGN----MKDSYKIIHHLYKLGYAPEDIIGNIFRVAKTL-DIPEPLKLSII  279 (317)
Q Consensus       206 ~-~i~~~~v~~~~~~~~~~~i~~l~~~~~~~~----~~~~~~~~~~l~~~~~~~~~i~~~~~~~~~~~-~~~~~~~~~~~  279 (317)
                      . .|+.+++  +.....+..++++++++..++    ...+...+.+++..|+++.+|+..+...+... .++.....+++
T Consensus       245 ~~~i~~~~~--~~~~~~~~~~~~l~~~i~~~~~~~~~~~~~~~l~~l~~~g~~~~~i~~~l~~~~~~~~~~~~~~l~~~~  322 (354)
T 1sxj_E          245 ELALKSSSP--IIKPDWIIVIHKLTRKIVKERSVNSLIECRAVLYDLLAHCIPANIILKELTFSLLDVETLNTTNKSSII  322 (354)
T ss_dssp             TTEECSSCC--CCCCHHHHHHHHHHHHHHHCCSHHHHHHHHHHHHHHHTTTCCHHHHHHHHHHTTTTCTTSCHHHHHHHH
T ss_pred             CCCcCcCcC--CCCccHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhccCCCHHHHHHHH
Confidence            3 5766543  222333457899999988754    44556667777788999999998887655433 37888899999


Q ss_pred             HHHHHHHhHHhcCCCcHHHHHHHHHHHHHh
Q psy879          280 QEIGNVHLRISEGVNSLLQLSGLLARLCIV  309 (317)
Q Consensus       280 ~~l~~~~~~l~~g~~~~l~le~~~~~~~~~  309 (317)
                      +++++.|+++++|.+++++||.+++++|.+
T Consensus       323 ~~l~~~d~~l~~g~~~~~~le~~~~~~~~~  352 (354)
T 1sxj_E          323 EYSSVFDERLSLGNKAIFHLEGFIAKVMCC  352 (354)
T ss_dssp             HHHHHHHHHHHTCSCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCCCHHHHHHHHHHHHHHH
Confidence            999999999999999999999999999865

>3u61_B DNA polymerase accessory protein 44; AAA+, ATP hydrolase, clamp loader, sliding clamp, primer-TEM DNA, DNA binding protein-DNA complex; HET: DNA ADP 08T; 3.20A {Enterobacteria phage T4} PDB: 3u5z_B* 3u60_B*

Probab=100.00  E-value=6.8e-43  Score=307.30  Aligned_cols=294  Identities=26%  Similarity=0.391  Sum_probs=247.9

Q ss_pred             CcccCCCCCCcccCCHHHHHHHHHHHhcCCCce-EEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHH
Q psy879            1 IEKYRPQTFSDIVGNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVR   79 (317)
Q Consensus         1 ~~ky~P~~~~~~~g~~~~~~~l~~~l~~~~~~~-~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~   79 (317)
                      ++||||++|++++|++++++.+..++..+..++ ++++||||+|||++++++++.+     +..+++++++. .+.+.++
T Consensus        17 ~~k~rP~~~~~ivg~~~~~~~l~~~l~~~~~~~~~L~~G~~G~GKT~la~~la~~l-----~~~~~~i~~~~-~~~~~i~   90 (324)
T 3u61_B           17 EQKYRPSTIDECILPAFDKETFKSITSKGKIPHIILHSPSPGTGKTTVAKALCHDV-----NADMMFVNGSD-CKIDFVR   90 (324)
T ss_dssp             HHHSCCCSTTTSCCCHHHHHHHHHHHHTTCCCSEEEECSSTTSSHHHHHHHHHHHT-----TEEEEEEETTT-CCHHHHH
T ss_pred             HHhhCCCCHHHHhCcHHHHHHHHHHHHcCCCCeEEEeeCcCCCCHHHHHHHHHHHh-----CCCEEEEcccc-cCHHHHH
Confidence            379999999999999999999999999999888 7888999999999999999986     34578888765 4477777


Q ss_pred             HHHHHHHhhcccCCCCceeEEEEeCCCCCC-HHHHHHHHHHhhhccCCceEEEEecCCCcCchhHhhhcceeeecCCCHH
Q psy879           80 NKIKMFAQQKVTLPPGRHKIVILDEADSMT-DGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDA  158 (317)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~vliiDE~d~l~-~~~~~~ll~~le~~~~~~~~il~~~~~~~l~~~i~sR~~~i~f~~~~~~  158 (317)
                      +.+..+.....  ..+.+++++|||+|.++ .+.++.|++++++++.++.+|+++|.+.++.++++|||..++|++|+.+
T Consensus        91 ~~~~~~~~~~~--~~~~~~vliiDEi~~l~~~~~~~~L~~~le~~~~~~~iI~~~n~~~~l~~~l~sR~~~i~~~~~~~~  168 (324)
T 3u61_B           91 GPLTNFASAAS--FDGRQKVIVIDEFDRSGLAESQRHLRSFMEAYSSNCSIIITANNIDGIIKPLQSRCRVITFGQPTDE  168 (324)
T ss_dssp             THHHHHHHBCC--CSSCEEEEEEESCCCGGGHHHHHHHHHHHHHHGGGCEEEEEESSGGGSCTTHHHHSEEEECCCCCHH
T ss_pred             HHHHHHHhhcc--cCCCCeEEEEECCcccCcHHHHHHHHHHHHhCCCCcEEEEEeCCccccCHHHHhhCcEEEeCCCCHH
Confidence            76666554421  23578999999999999 9999999999999999999999999999999999999999999999988


Q ss_pred             H-------HHHHHHHHHHHcCCCCCH-HHHHHHHHhcCCCHHHHHHHHHHhhhCCCcccHHHHHhhcCCCCHHHHHHHHH
Q psy879          159 Q-------LLSKVIEICEKENISHTN-DGLEAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEMLL  230 (317)
Q Consensus       159 ~-------~~~~l~~~~~~~~~~i~~-~~~~~l~~~~~gd~r~~i~~l~~~~~~~~~i~~~~v~~~~~~~~~~~i~~l~~  230 (317)
                      +       +..++...+..+++.+++ ++++.++..++||+|.+++.|+.++ ..+.|+.+++..++..  .+.++++++
T Consensus       169 e~~~il~~~~~~l~~~~~~~~~~~~~~~~~~~l~~~~~gd~R~a~~~L~~~~-~~~~i~~~~v~~~~~~--~~~i~~~~~  245 (324)
T 3u61_B          169 DKIEMMKQMIRRLTEICKHEGIAIADMKVVAALVKKNFPDFRKTIGELDSYS-SKGVLDAGILSLVTND--RGAIDDVLE  245 (324)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTCCBSCHHHHHHHHHHTCSCTTHHHHHHHHHG-GGTCBCC--------------CHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHcCCCCCcHHHHHHHHHhCCCCHHHHHHHHHHHh-ccCCCCHHHHHHHhCC--HHHHHHHHH
Confidence            7       456677778889999998 9999999999999999999999988 5567999999988766  457889999


Q ss_pred             HHhcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHHHhHHhcCCCcHHHHHHHHHHHHHh
Q psy879          231 NCVEGNMKDSYKIIHHLYKLGYAPEDIIGNIFRVAKTLDIPEPLKLSIIQEIGNVHLRISEGVNSLLQLSGLLARLCIV  309 (317)
Q Consensus       231 ~~~~~~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~g~~~~l~le~~~~~~~~~  309 (317)
                      ++..++..+++.++.+++.   +|..|+..+...+.. .+++....++++++++.|+++++|.++.+++|.|++++|..
T Consensus       246 ~~~~~~~~~a~~~~~~l~~---~~~~i~~~l~~~~~~-~~~~~~l~~i~~~l~~~d~~l~~g~~~~~~le~~~~~~~~~  320 (324)
T 3u61_B          246 SLKNKDVKQLRALAPKYAA---DYSWFVGKLAEEIYS-RVTPQSIIRMYEIVGENNQYHGIAANTELHLAYLFIQLACE  320 (324)
T ss_dssp             HHHTTCHHHHHHHHHHHSS---CHHHHHHHHHHHHHH-HSCHHHHHHHHHHHHHHHHHTTTCSCHHHHHHHHHHHHHHH
T ss_pred             HHHcCCHHHHHHHHHHhcc---CHHHHHHHHHHHHHH-hCCHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHh
Confidence            9999999999999999866   899999887654432 46788899999999999999999999999999999999864

>1jr3_A DNA polymerase III subunit gamma; processivity, processivity clamp, clamp loader, AAA+ ATPase, transferase; HET: DNA; 2.70A {Escherichia coli} SCOP: a.80.1.1 c.37.1.20 PDB: 1xxh_B* 3glh_B* 3glf_B* 3gli_B* 3glg_B* 1xxi_B*

Probab=100.00  E-value=2.4e-40  Score=296.47  Aligned_cols=307  Identities=23%  Similarity=0.297  Sum_probs=261.5

Q ss_pred             cccCCCCCCcccCCHHHHHHHHHHHhcCCCce-EEEECCCCCCHHHHHHHHHHHHcCCCCC-------------------
Q psy879            2 EKYRPQTFSDIVGNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARILLGPSFK-------------------   61 (317)
Q Consensus         2 ~ky~P~~~~~~~g~~~~~~~l~~~l~~~~~~~-~ll~G~~G~GKt~la~~la~~l~~~~~~-------------------   61 (317)
                      +||||++|++++|++++++.+..++..++.+| ++|+||+|+|||++++++++.+.+....                   
T Consensus         8 ~k~rp~~~~~~vg~~~~~~~L~~~l~~~~~~~~~ll~G~~G~GKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~   87 (373)
T 1jr3_A            8 RKWRPQTFADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKGLNCETGITATPCGVCDNCREIEQGRF   87 (373)
T ss_dssp             HHTCCCSTTTSCSCHHHHHHHHHHHHHTCCCSEEEEESCTTSSHHHHHHHHHHHHSCTTCSCSSCCSSSHHHHHHHTSCC
T ss_pred             HhhCCCchhhccCcHHHHHHHHHHHHhCCCCeEEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCCcccHHHHHHhccCC
Confidence            68999999999999999999999999998888 8999999999999999999998764321                   


Q ss_pred             CceEEecCCCCcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcCch
Q psy879           62 DAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIE  141 (317)
Q Consensus        62 ~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~~  141 (317)
                      ..++.++.....+.+.+++.+..+...+   ..++++|++|||+|.++.+.+++|++++++++.++.+|++++...++.+
T Consensus        88 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~---~~~~~~vliiDe~~~l~~~~~~~Ll~~le~~~~~~~~Il~~~~~~~l~~  164 (373)
T 1jr3_A           88 VDLIEIDAASRTKVEDTRDLLDNVQYAP---ARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPV  164 (373)
T ss_dssp             SSCEEEETTCSCCSSCHHHHHHHTTSCC---SSSSSEEEEEECGGGSCHHHHHHHHHHHHSCCSSEEEEEEESCGGGSCH
T ss_pred             CceEEecccccCCHHHHHHHHHHHhhcc---ccCCeEEEEEECcchhcHHHHHHHHHHHhcCCCceEEEEEeCChHhCcH
Confidence            1234444443345556666666554333   2367899999999999999999999999999999999999999999999


Q ss_pred             hHhhhcceeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhh-CCCcccHHHHHhhcCCC
Q psy879          142 PIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHN-GFGHVTAEYVFKVCDEP  220 (317)
Q Consensus       142 ~i~sR~~~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~-~~~~i~~~~v~~~~~~~  220 (317)
                      ++.|||..++|++++.+++..++..++..+|+.+++++++.++..++||+|.+.+.++.+.. ..+.|+.++|.+++...
T Consensus       165 ~l~sr~~~i~~~~l~~~~~~~~l~~~~~~~~~~~~~~a~~~l~~~~~G~~r~~~~~l~~~~~~~~~~i~~~~v~~~~~~~  244 (373)
T 1jr3_A          165 TILSRCLQFHLKALDVEQIRHQLEHILNEEHIAHEPRALQLLARAAEGSLRDALSLTDQAIASGDGQVSTQAVSAMLGTL  244 (373)
T ss_dssp             HHHTTSEEEECCCCCHHHHHHHHHHHHHHHTCCBCHHHHHHHHHHSSSCHHHHHHHHHHHHHHTTTCBCHHHHHHHTTCC
T ss_pred             HHHhheeEeeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHhcCCcccHHHHHHHhCCC
Confidence            99999999999999999999999999999999999999999999999999999999987654 55789999999999999


Q ss_pred             CHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhc--------------------------CCChHH
Q psy879          221 HPLAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDIIGNIFRVAKTL--------------------------DIPEPL  274 (317)
Q Consensus       221 ~~~~i~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~~~~--------------------------~~~~~~  274 (317)
                      ....++++++++..++...++.++..+...|.++..++..+.+.+..+                          .++...
T Consensus       245 ~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~g~~~~~~l~~l~~~~r~l~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~  324 (373)
T 1jr3_A          245 DDDQALSLVEAMVEANGERVMALINEAAARGIEWEALLVEMLGLLHRIAMVQLSPAALGNDMAAIELRMRELARTIPPTD  324 (373)
T ss_dssp             CHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHTTCTTCCCSGGGGTHHHHHHHHHHSCHHH
T ss_pred             CHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCHHHHHHHHHHHHHHHHHHhhcCccccccchhHHHHHHHHHHhCCHHH
Confidence            888999999999999999999999999999999998887765443221                          112222


Q ss_pred             HHHHHHHHHHHHhHHhcCCCcHHHHHHHHHHHHHhhc
Q psy879          275 KLSIIQEIGNVHLRISEGVNSLLQLSGLLARLCIVGS  311 (317)
Q Consensus       275 ~~~~~~~l~~~~~~l~~g~~~~l~le~~~~~~~~~~~  311 (317)
                      ..++++.+.+++.+++.+.|+++.+|.++.+++...+
T Consensus       325 l~~~~~~l~~~~~~lk~~~~~~l~le~~ll~~~~~~~  361 (373)
T 1jr3_A          325 IQLYYQTLLIGRKELPYAPDRRMGVEMTLLRALAFHP  361 (373)
T ss_dssp             HHHHHHHHHHHHHHTTTSSSHHHHHHHHHHHHHHTCS
T ss_pred             HHHHHHHHHHHHHHHHhCCCchHHHHHHHHHHHhcCC
Confidence            3448889999999999988999999999999997644

>2gno_A DNA polymerase III, gamma subunit-related protein; structural genomics, joint center for structural genomics, J protein structure initiative; HET: DNA; 2.00A {Thermotoga maritima} SCOP: a.80.1.1 c.37.1.20

Probab=100.00  E-value=2e-39  Score=280.58  Aligned_cols=280  Identities=19%  Similarity=0.161  Sum_probs=232.9

Q ss_pred             CCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHc-CCCCCCceEEecCCC-CcChHHHHHHHHHHHhhccc
Q psy879           14 GNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILL-GPSFKDAVLELNASN-DRGIDTVRNKIKMFAQQKVT   91 (317)
Q Consensus        14 g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~-~~~~~~~~~~~~~~~-~~~~~~i~~~~~~~~~~~~~   91 (317)
                      ||+++++.|...+++|+.|+|+||||||+|||++++++++.+. +......+.++++.+ ..+++++++.+..+...+. 
T Consensus         1 g~~~~~~~L~~~i~~~~~~~~Lf~Gp~G~GKtt~a~~la~~~~~~~~~~~d~~~l~~~~~~~~id~ir~li~~~~~~p~-   79 (305)
T 2gno_A            1 GAKDQLETLKRIIEKSEGISILINGEDLSYPREVSLELPEYVEKFPPKASDVLEIDPEGENIGIDDIRTIKDFLNYSPE-   79 (305)
T ss_dssp             ---CHHHHHHHHHHTCSSEEEEEECSSSSHHHHHHHHHHHHHHTSCCCTTTEEEECCSSSCBCHHHHHHHHHHHTSCCS-
T ss_pred             ChHHHHHHHHHHHHCCCCcEEEEECCCCCCHHHHHHHHHHhCchhhccCCCEEEEcCCcCCCCHHHHHHHHHHHhhccc-
Confidence            7899999999999999966799999999999999999998642 222244677788764 6888999998887765553 


Q ss_pred             CCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcCchhHhhhcceeeecCCCHHHHHHHHHHHHHHc
Q psy879           92 LPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKE  171 (317)
Q Consensus        92 ~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~~~i~sR~~~i~f~~~~~~~~~~~l~~~~~~~  171 (317)
                        .++++|+||||+|.|+.+++++|+++||+||++++||++|+++.+++++|+||  .++|++++++++.+||..++   
T Consensus        80 --~~~~kvviIdead~lt~~a~naLLk~LEep~~~t~fIl~t~~~~kl~~tI~SR--~~~f~~l~~~~i~~~L~~~~---  152 (305)
T 2gno_A           80 --LYTRKYVIVHDCERMTQQAANAFLKALEEPPEYAVIVLNTRRWHYLLPTIKSR--VFRVVVNVPKEFRDLVKEKI---  152 (305)
T ss_dssp             --SSSSEEEEETTGGGBCHHHHHHTHHHHHSCCTTEEEEEEESCGGGSCHHHHTT--SEEEECCCCHHHHHHHHHHH---
T ss_pred             --cCCceEEEeccHHHhCHHHHHHHHHHHhCCCCCeEEEEEECChHhChHHHHce--eEeCCCCCHHHHHHHHHHHh---
Confidence              36799999999999999999999999999999999999999999999999999  99999999999999999987   


Q ss_pred             CCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhhC--------CCcccHHHHHhhcCCCCHH--HHHHHHHHHhcCCHHHHH
Q psy879          172 NISHTNDGLEAIVFTAQGDMRQALNNLQSTHNG--------FGHVTAEYVFKVCDEPHPL--AVKEMLLNCVEGNMKDSY  241 (317)
Q Consensus       172 ~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~~--------~~~i~~~~v~~~~~~~~~~--~i~~l~~~~~~~~~~~~~  241 (317)
                      +  ++++++    ..+.||+|.+++.++.....        ...-+.++|..+++.+.++  .++++++++..++..+++
T Consensus       153 ~--i~~~~~----~~~~g~~~~al~~l~~~~~~~~~l~~~~~~~~~~~~v~~~~~~~~~~~~~v~~l~~ai~~~~~~~a~  226 (305)
T 2gno_A          153 G--DLWEEL----PLLERDFKTALEAYKLGAEKLSGLMESLKVLETEKLLKKVLSKGLEGYLACRELLERFSKVESKEFF  226 (305)
T ss_dssp             T--THHHHC----GGGGTCHHHHHHHHHHHHHHHHHHHHHHHHSCHHHHTTTTTCSHHHHHHHHHHHHHHHHHSCGGGHH
T ss_pred             C--CCHHHH----HHHCCCHHHHHHHHHHHHHHHHHHHHHHHhcccHHHHHHHHccCCcchHHHHHHHHHHHCCCHHHHH
Confidence            3  556655    55799999999988632110        0011467888888888755  899999999999999999


Q ss_pred             HHHHHHHH--cCCCHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHHHhHHhc---CCCcHHHHHHHHHHHHHh
Q psy879          242 KIIHHLYK--LGYAPEDIIGNIFRVAKTLDIPEPLKLSIIQEIGNVHLRISE---GVNSLLQLSGLLARLCIV  309 (317)
Q Consensus       242 ~~~~~l~~--~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~---g~~~~l~le~~~~~~~~~  309 (317)
                      ..+++|+.  .|++|.+++..+++.+...+  +..+.+.+..++.+++++..   |.|+.++|+.++.++|..
T Consensus       227 ~~~~~l~~~~~g~~~~~~i~~~~r~l~~~~--~~~~~~~l~~~~~~~~~~~~k~~g~~~~lql~~l~~~~~~~  297 (305)
T 2gno_A          227 ALFDQVTNTITGKDAFLLIQRLTRIILHEN--TWESVEDQKSVSFLDSILRVKIANLNNKLTLMNILAIHRER  297 (305)
T ss_dssp             HHHHHHHHHSCTHHHHHHHHHHHHHHHHTS--CCCSHHHHHHHHHHHHHHTCCGGGCCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhhcCCCHHHHHHHHHHHHHhhc--hhhhHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHh
Confidence            99999988  89999988888888776444  33445677799999999987   889999999999999954

>1a5t_A Delta prime, HOLB; zinc finger, DNA replication; 2.20A {Escherichia coli K12} SCOP: a.80.1.1 c.37.1.20 PDB: 1jr3_E* 1xxh_E* 1xxi_E* 3glf_E* 3glg_E* 3glh_E* 3gli_E*

Probab=100.00  E-value=4.7e-36  Score=264.21  Aligned_cols=284  Identities=20%  Similarity=0.238  Sum_probs=223.4

Q ss_pred             cCCHHHHHHHHHHHhcCCCce-EEEECCCCCCHHHHHHHHHHHHcCCCCC-------------------CceEEecCC--
Q psy879           13 VGNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARILLGPSFK-------------------DAVLELNAS--   70 (317)
Q Consensus        13 ~g~~~~~~~l~~~l~~~~~~~-~ll~G~~G~GKt~la~~la~~l~~~~~~-------------------~~~~~~~~~--   70 (317)
                      -.++++.+.+...+++|+++| |+|+||+|+|||++++++++.+.|....                   ..+..+++.  
T Consensus         5 pw~~~~~~~l~~~i~~~~~~~a~L~~G~~G~GKt~~a~~la~~l~~~~~~~~~~c~~c~~c~~~~~~~~~d~~~~~~~~~   84 (334)
T 1a5t_A            5 PWLRPDFEKLVASYQAGRGHHALLIQALPGMGDDALIYALSRYLLCQQPQGHKSCGHCRGCQLMQAGTHPDYYTLAPEKG   84 (334)
T ss_dssp             GGGHHHHHHHHHHHHTTCCCSEEEEECCTTSCHHHHHHHHHHHHTCSSCBTTBCCSCSHHHHHHHHTCCTTEEEECCCTT
T ss_pred             CchHHHHHHHHHHHHcCCcceeEEEECCCCchHHHHHHHHHHHHhCCCCCCCCCCCCCHHHHHHhcCCCCCEEEEecccc
Confidence            357888999999999999998 9999999999999999999999875421                   335566653  


Q ss_pred             -CCcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcCchhHhhhcce
Q psy879           71 -NDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAM  149 (317)
Q Consensus        71 -~~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~~~i~sR~~~  149 (317)
                       ...+.+++++.+..+...+.   .++++|+||||+|.|+.+++++|++++|+|++++++|++|+++++++++|+|||+.
T Consensus        85 ~~~~~i~~ir~l~~~~~~~~~---~~~~kvviIdead~l~~~a~naLLk~lEep~~~~~~Il~t~~~~~l~~ti~SRc~~  161 (334)
T 1a5t_A           85 KNTLGVDAVREVTEKLNEHAR---LGGAKVVWVTDAALLTDAAANALLKTLEEPPAETWFFLATREPERLLATLRSRCRL  161 (334)
T ss_dssp             CSSBCHHHHHHHHHHTTSCCT---TSSCEEEEESCGGGBCHHHHHHHHHHHTSCCTTEEEEEEESCGGGSCHHHHTTSEE
T ss_pred             CCCCCHHHHHHHHHHHhhccc---cCCcEEEEECchhhcCHHHHHHHHHHhcCCCCCeEEEEEeCChHhCcHHHhhccee
Confidence             45778889888777655542   36799999999999999999999999999999999999999999999999999999


Q ss_pred             eeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhhCCCcccHHHHHhhcCCCCHHHHHHHH
Q psy879          150 LRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEML  229 (317)
Q Consensus       150 i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~~~~~i~~~~v~~~~~~~~~~~i~~l~  229 (317)
                      ++|++++++++.+||..++     .++++++..++..++||+|.+++.++........++.+.+..+...   ..+++++
T Consensus       162 ~~~~~~~~~~~~~~L~~~~-----~~~~~~~~~l~~~s~G~~r~a~~~l~~~~~~~~~~~~~~~~~~~~~---~~~~~~~  233 (334)
T 1a5t_A          162 HYLAPPPEQYAVTWLSREV-----TMSQDALLAALRLSAGSPGAALALFQGDNWQARETLCQALAYSVPS---GDWYSLL  233 (334)
T ss_dssp             EECCCCCHHHHHHHHHHHC-----CCCHHHHHHHHHHTTTCHHHHHHTTSSHHHHHHHHHHHHHHHHHHH---CCCGGGH
T ss_pred             eeCCCCCHHHHHHHHHHhc-----CCCHHHHHHHHHHcCCCHHHHHHHhccchHHHHHHHHHHHHHHHhC---hHHHHHH
Confidence            9999999999999999874     6789999999999999999999999765443334455555554431   1233455


Q ss_pred             HHHhcCCHHHHHHHHH----HHHHcCC-----CHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHHHhHHh--cCCCcHHH
Q psy879          230 LNCVEGNMKDSYKIIH----HLYKLGY-----APEDIIGNIFRVAKTLDIPEPLKLSIIQEIGNVHLRIS--EGVNSLLQ  298 (317)
Q Consensus       230 ~~~~~~~~~~~~~~~~----~l~~~~~-----~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~--~g~~~~l~  298 (317)
                      +.+.+.+....+.++.    +++....     ...+....+.+++.  .++.....++++.+.+.+.+++  .|+|++++
T Consensus       234 ~~l~~~~~~~~l~~l~~~~rdll~~~~~~~~~~~~~~~~~~~~~a~--~~~~~~l~~~~~~l~~~~~~l~~~~~~n~~l~  311 (334)
T 1a5t_A          234 AALNHEQAPARLHWLATLLMDALKRHHGAAQVTNVDVPGLVAELAN--HLSPSRLQAILGDVCHIREQLMSVTGINRELL  311 (334)
T ss_dssp             HHHCSTTHHHHHHHHHHHHHHHTCC------CCCTTCHHHHHHHHH--HSCHHHHHHHHHHHHHHHHHHHHHCCSSHHHH
T ss_pred             HHHhcccHHHHHHHHHHHHHHHHHhccCCccccCHHHHHHHHHHHH--hCCHHHHHHHHHHHHHHHHHHHhcCCCCHHHH
Confidence            5665566666655544    4432211     11123344555555  4677788899999999999999  89999999


Q ss_pred             HHHHHHHHHHh
Q psy879          299 LSGLLARLCIV  309 (317)
Q Consensus       299 le~~~~~~~~~  309 (317)
                      +|.++.+++..
T Consensus       312 le~ll~~l~~~  322 (334)
T 1a5t_A          312 ITDLLLRIEHY  322 (334)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHh
Confidence            99999999864

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=100.00  E-value=7.7e-35  Score=264.49  Aligned_cols=293  Identities=19%  Similarity=0.276  Sum_probs=232.0

Q ss_pred             cccCCCCCCcccCCHHHH---HHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHH
Q psy879            2 EKYRPQTFSDIVGNEDTV---ERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTV   78 (317)
Q Consensus         2 ~ky~P~~~~~~~g~~~~~---~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i   78 (317)
                      ++|||++|++++||++++   +.|...+..+.+++++|+||||||||++++++++.+.     ..++.+++. ..+...+
T Consensus        18 ~r~rP~~l~~ivGq~~~~~~~~~L~~~i~~~~~~~vLL~GppGtGKTtlAr~ia~~~~-----~~f~~l~a~-~~~~~~i   91 (447)
T 3pvs_A           18 ARMRPENLAQYIGQQHLLAAGKPLPRAIEAGHLHSMILWGPPGTGKTTLAEVIARYAN-----ADVERISAV-TSGVKEI   91 (447)
T ss_dssp             HHTCCCSTTTCCSCHHHHSTTSHHHHHHHHTCCCEEEEECSTTSSHHHHHHHHHHHTT-----CEEEEEETT-TCCHHHH
T ss_pred             HHhCCCCHHHhCCcHHHHhchHHHHHHHHcCCCcEEEEECCCCCcHHHHHHHHHHHhC-----CCeEEEEec-cCCHHHH
Confidence            689999999999999999   7899999999998899999999999999999999862     346677664 3566677


Q ss_pred             HHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecC--CCcCchhHhhhcceeeecCCC
Q psy879           79 RNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNN--SEKIIEPIQSRCAMLRYNKLT  156 (317)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~--~~~l~~~i~sR~~~i~f~~~~  156 (317)
                      ++.+........   .+.+.++||||+|.++...++.|++.+++  ..+.+|++|+.  ...+.+++.|||.++.|++++
T Consensus        92 r~~~~~a~~~~~---~~~~~iLfIDEI~~l~~~~q~~LL~~le~--~~v~lI~att~n~~~~l~~aL~sR~~v~~l~~l~  166 (447)
T 3pvs_A           92 REAIERARQNRN---AGRRTILFVDEVHRFNKSQQDAFLPHIED--GTITFIGATTENPSFELNSALLSRARVYLLKSLS  166 (447)
T ss_dssp             HHHHHHHHHHHH---TTCCEEEEEETTTCC------CCHHHHHT--TSCEEEEEESSCGGGSSCHHHHTTEEEEECCCCC
T ss_pred             HHHHHHHHHhhh---cCCCcEEEEeChhhhCHHHHHHHHHHHhc--CceEEEecCCCCcccccCHHHhCceeEEeeCCcC
Confidence            777665544332   25789999999999999999999999997  55677777643  357899999999999999999


Q ss_pred             HHHHHHHHHHHHHH-------cCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhhC-------CCcccHHHHHhhcCCC--
Q psy879          157 DAQLLSKVIEICEK-------ENISHTNDGLEAIVFTAQGDMRQALNNLQSTHNG-------FGHVTAEYVFKVCDEP--  220 (317)
Q Consensus       157 ~~~~~~~l~~~~~~-------~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~~-------~~~i~~~~v~~~~~~~--  220 (317)
                      .+++..++...+..       .++.+++++++.++..++||+|.+++.|+.++..       ...|+.+++.+++...  
T Consensus       167 ~edi~~il~~~l~~~~~~~~~~~~~i~~~al~~L~~~~~Gd~R~lln~Le~a~~~a~~~~~~~~~It~e~v~~~l~~~~~  246 (447)
T 3pvs_A          167 TEDIEQVLTQAMEDKTRGYGGQDIVLPDETRRAIAELVNGDARRALNTLEMMADMAEVDDSGKRVLKPELLTEIAGERSA  246 (447)
T ss_dssp             HHHHHHHHHHHHHCTTTSSTTSSEECCHHHHHHHHHHHCSCHHHHHHHHHHHHHHSCBCTTSCEECCHHHHHHHHTCCCC
T ss_pred             HHHHHHHHHHHHHHHhhhhccccCcCCHHHHHHHHHHCCCCHHHHHHHHHHHHHhcccccCCCCccCHHHHHHHHhhhhh
Confidence            99999999999886       5677999999999999999999999999986641       1369999999988765  


Q ss_pred             --------CHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHH-HhcCCChHHHHHHHHHHHHHHhHHhc
Q psy879          221 --------HPLAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDIIGNIFRVA-KTLDIPEPLKLSIIQEIGNVHLRISE  291 (317)
Q Consensus       221 --------~~~~i~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~-~~~~~~~~~~~~~~~~l~~~~~~l~~  291 (317)
                              +.+.++.+++++...+.+.++.|+..|++.|++|..|.+.+.+.+ +.+|+.+.....+.....+.-.  .-
T Consensus       247 ~~dk~gd~~yd~isal~ksirgsd~daAl~~la~ml~~Gedp~~i~rrl~~~a~edig~a~p~a~~~~~~~~~~~~--~~  324 (447)
T 3pvs_A          247 RFDNKGDRFYDLISALHKSVRGSAPDAALYWYARIITAGGDPLYVARRCLAIASEDVGNADPRAMQVAIAAWDCFT--RV  324 (447)
T ss_dssp             C---CCHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHTTGGGCTHHHHHHHHHHHHHH--HS
T ss_pred             ccCCccchHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhcccCCChhHHHHHHHHHHHHH--Hh
Confidence                    346788999999999999999999999999999999999998875 4446655443333333322222  33


Q ss_pred             CC-CcHHHHHHHHHHHH
Q psy879          292 GV-NSLLQLSGLLARLC  307 (317)
Q Consensus       292 g~-~~~l~le~~~~~~~  307 (317)
                      |. ..++.|...+.-+|
T Consensus       325 g~pe~~~~l~~~~~~la  341 (447)
T 3pvs_A          325 GPAEGERAIAQAIVYLA  341 (447)
T ss_dssp             CHHHHHHHHHHHHHHHH
T ss_pred             CCcHHHHHHHHHHHHHH
Confidence            44 66677777777666

>1jr3_D DNA polymerase III, delta subunit; processivity, processivity clamp, clamp loader, AAA+ ATPase, transferase; HET: DNA; 2.70A {Escherichia coli} SCOP: a.80.1.1 c.37.1.20 PDB: 1jqj_C* 1xxh_A* 1xxi_A* 3glf_A* 3glg_A* 3glh_A* 3gli_A*

Probab=100.00  E-value=4.8e-34  Score=252.70  Aligned_cols=278  Identities=12%  Similarity=0.155  Sum_probs=228.0

Q ss_pred             HHHHHhcCCCce-EEEECCCCCCHHHHHHHHHHHHcCCCCCC-ceEEecCCCCcChHHHHHHHHHHHhhcccCCCCceeE
Q psy879           22 LKVFSSSGNVPN-IIISGPPGVGKTTTILCLARILLGPSFKD-AVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKI   99 (317)
Q Consensus        22 l~~~l~~~~~~~-~ll~G~~G~GKt~la~~la~~l~~~~~~~-~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~v   99 (317)
                      +.+.++ ++.+| |+||||+|+||++.+..+++.+.+.++.. .++.++.  .   .++++.+......+..   ++++|
T Consensus         9 l~~~l~-~~~~~~yl~~G~e~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~--~---~~~~~l~~~~~~~plf---~~~kv   79 (343)
T 1jr3_D            9 LRAQLN-EGLRAAYLLLGNDPLLLQESQDAVRQVAAAQGFEEHHTFSIDP--N---TDWNAIFSLCQAMSLF---ASRQT   79 (343)
T ss_dssp             HHHHHH-HCCCSEEEEEESCHHHHHHHHHHHHHHHHHHTCCEEEEEECCT--T---CCHHHHHHHHHHHHHC---CSCEE
T ss_pred             HHHHHh-cCCCcEEEEECCcHHHHHHHHHHHHHHHHhCCCCeeEEEEecC--C---CCHHHHHHHhcCcCCc---cCCeE
Confidence            455566 45544 99999999999999999999886543221 2334432  2   2344444444444433   68999


Q ss_pred             EEEeCCCC-CCHHHHHHHHHHhhhccCCceEEEEecCC------CcCchhHhhhcceeeecCCCHHHHHHHHHHHHHHcC
Q psy879          100 VILDEADS-MTDGAQQALRRTMEIYSNTTRFALACNNS------EKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKEN  172 (317)
Q Consensus       100 liiDE~d~-l~~~~~~~ll~~le~~~~~~~~il~~~~~------~~l~~~i~sR~~~i~f~~~~~~~~~~~l~~~~~~~~  172 (317)
                      |+|||++. ++.+.+++|++++|+|++++++|++++..      .++.+++.|||..++|.+++.+++..|+..+++.+|
T Consensus        80 vii~~~~~kl~~~~~~aLl~~le~p~~~~~~il~~~~~~~~~~~~k~~~~i~sr~~~~~~~~l~~~~l~~~l~~~~~~~g  159 (343)
T 1jr3_D           80 LLLLLPENGPNAAINEQLLTLTGLLHDDLLLIVRGNKLSKAQENAAWFTALANRSVQVTCQTPEQAQLPRWVAARAKQLN  159 (343)
T ss_dssp             EEEECCSSCCCTTHHHHHHHHHTTCBTTEEEEEEESCCCTTTTTSHHHHHHTTTCEEEEECCCCTTHHHHHHHHHHHHTT
T ss_pred             EEEECCCCCCChHHHHHHHHHHhcCCCCeEEEEEcCCCChhhHhhHHHHHHHhCceEEEeeCCCHHHHHHHHHHHHHHcC
Confidence            99999999 99999999999999999999999998763      468999999999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHhcCCCHHHHHHHHHHhhh--CCCcccHHHHHhhcCCCCHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q psy879          173 ISHTNDGLEAIVFTAQGDMRQALNNLQSTHN--GFGHVTAEYVFKVCDEPHPLAVKEMLLNCVEGNMKDSYKIIHHLYKL  250 (317)
Q Consensus       173 ~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~--~~~~i~~~~v~~~~~~~~~~~i~~l~~~~~~~~~~~~~~~~~~l~~~  250 (317)
                      +.+++++++.++..++||+|.+.+++++++.  +.+.|+.++|.+++.......++++++++..++...++.++..+...
T Consensus       160 ~~i~~~a~~~l~~~~~gdl~~~~~elekl~l~~~~~~It~e~V~~~~~~~~~~~if~l~~ai~~~d~~~al~~l~~l~~~  239 (343)
T 1jr3_D          160 LELDDAANQVLCYCYEGNLLALAQALERLSLLWPDGKLTLPRVEQAVNDAAHFTPFHWVDALLMGKSKRALHILQQLRLE  239 (343)
T ss_dssp             CEECHHHHHHHHHSSTTCHHHHHHHHHHHHHHCTTCEECHHHHHHHHHHHCCCCHHHHHHHHTTSCHHHHHHHHTSSTTT
T ss_pred             CCCCHHHHHHHHHHhchHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHhhhhcCCHHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence            9999999999999999999999999998765  45689999999988777777899999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHhc---------C----------C---------------ChHHHHHHHHHHHHHHhHHhcCC--C
Q psy879          251 GYAPEDIIGNIFRVAKTL---------D----------I---------------PEPLKLSIIQEIGNVHLRISEGV--N  294 (317)
Q Consensus       251 ~~~~~~i~~~~~~~~~~~---------~----------~---------------~~~~~~~~~~~l~~~~~~l~~g~--~  294 (317)
                      |++|..++..+.+.++.+         |          .               +.....++++.+.++|.++|+|.  |
T Consensus       240 g~~~~~il~~l~~~~r~l~~~~~~~~~g~~~~i~~~l~i~~~~~~~~~~~~~~~s~~~L~~~l~~l~~~d~~lK~~~~~~  319 (343)
T 1jr3_D          240 GSEPVILLRTLQRELLLLVNLKRQSAHTPLRALFDKHRVWQNRRGMMGEALNRLSQTQLRQAVQLLTRTELTLKQDYGQS  319 (343)
T ss_dssp             TCCHHHHHHHHHHHHHHHHHHHTCSSSSCHHHHHHHHTCCSSHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHSSCSC
T ss_pred             CCcHHHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHcCCCHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhCCCCCC
Confidence            999999988875544322         1          1               11112338889999999999975  7


Q ss_pred             cHHHHHHHHHHHHH
Q psy879          295 SLLQLSGLLARLCI  308 (317)
Q Consensus       295 ~~l~le~~~~~~~~  308 (317)
                      +++.||.++.++|.
T Consensus       320 ~~~~le~l~l~l~~  333 (343)
T 1jr3_D          320 VWAELEGLSLLLCH  333 (343)
T ss_dssp             HHHHHHHHHHHTTS
T ss_pred             HHHHHHHHHHHHcC
Confidence            88999999999985

>2chg_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATPase, ATP-binding, nucleotide-binding; HET: ANP; 2.1A {Archaeoglobus fulgidus}

Probab=100.00  E-value=8.7e-31  Score=217.32  Aligned_cols=216  Identities=46%  Similarity=0.825  Sum_probs=188.8

Q ss_pred             cccCCCCCCcccCCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHH
Q psy879            2 EKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNK   81 (317)
Q Consensus         2 ~ky~P~~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~   81 (317)
                      ++|+|.+|++++|+++.++.+..++..+..++++|+||+|+|||++++.+++.+.+......++.+++....+...+.+.
T Consensus         9 ~~~~p~~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKT~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   88 (226)
T 2chg_A            9 EKYRPRTLDEVVGQDEVIQRLKGYVERKNIPHLLFSGPPGTGKTATAIALARDLFGENWRDNFIEMNASDERGIDVVRHK   88 (226)
T ss_dssp             HHTSCSSGGGCCSCHHHHHHHHHHHHTTCCCCEEEECSTTSSHHHHHHHHHHHHHGGGGGGGEEEEETTCTTCHHHHHHH
T ss_pred             HhcCCCCHHHHcCcHHHHHHHHHHHhCCCCCeEEEECCCCCCHHHHHHHHHHHHhccccccceEEeccccccChHHHHHH
Confidence            68999999999999999999999999988878999999999999999999998865555556777887766666666666


Q ss_pred             HHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcCchhHhhhcceeeecCCCHHHHH
Q psy879           82 IKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLL  161 (317)
Q Consensus        82 ~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~~~i~sR~~~i~f~~~~~~~~~  161 (317)
                      +..+.... ....+.+.+++|||++.+..+.++.|++++++++.++.+|++++.+..+.+++.+|+..+.|++++.+++.
T Consensus        89 ~~~~~~~~-~~~~~~~~vliiDe~~~l~~~~~~~l~~~l~~~~~~~~~i~~~~~~~~~~~~l~~r~~~i~~~~~~~~~~~  167 (226)
T 2chg_A           89 IKEFARTA-PIGGAPFKIIFLDEADALTADAQAALRRTMEMYSKSCRFILSCNYVSRIIEPIQSRCAVFRFKPVPKEAMK  167 (226)
T ss_dssp             HHHHHTSC-CSTTCSCEEEEEETGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHTTSEEEECCCCCHHHHH
T ss_pred             HHHHhccc-CCCccCceEEEEeChhhcCHHHHHHHHHHHHhcCCCCeEEEEeCChhhcCHHHHHhCceeecCCCCHHHHH
Confidence            65554331 11235788999999999999999999999999888999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhhCCCcccHHHHHhhcC
Q psy879          162 SKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCD  218 (317)
Q Consensus       162 ~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~~~~~i~~~~v~~~~~  218 (317)
                      .++...+...+..+++++++.++..++||+|.+++.++.++...+.|+.+++.++++
T Consensus       168 ~~l~~~~~~~~~~~~~~~~~~l~~~~~g~~r~l~~~l~~~~~~~~~I~~~~v~~~~~  224 (226)
T 2chg_A          168 KRLLEICEKEGVKITEDGLEALIYISGGDFRKAINALQGAAAIGEVVDADTIYQITA  224 (226)
T ss_dssp             HHHHHHHHHHTCCBCHHHHHHHHHHHTTCHHHHHHHHHHHHHTCSCBCHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHhcCceecHHHHHHHhc
Confidence            999999999899999999999999999999999999998877667899999887654

>1njg_A DNA polymerase III subunit gamma; rossman-like fold, AAA+ ATPase domains, sensor 1, sensor 2, transferase; HET: DNA; 2.20A {Escherichia coli} SCOP: c.37.1.20 PDB: 1njf_A*

Probab=99.97  E-value=1.3e-28  Score=206.84  Aligned_cols=214  Identities=28%  Similarity=0.408  Sum_probs=175.9

Q ss_pred             cccCCCCCCcccCCHHHHHHHHHHHhcCCCce-EEEECCCCCCHHHHHHHHHHHHcCCCCC-------------------
Q psy879            2 EKYRPQTFSDIVGNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARILLGPSFK-------------------   61 (317)
Q Consensus         2 ~ky~P~~~~~~~g~~~~~~~l~~~l~~~~~~~-~ll~G~~G~GKt~la~~la~~l~~~~~~-------------------   61 (317)
                      ++|+|..|++++|+++.++.+..++..+..++ ++|+||+|+|||++++.+++.+.+....                   
T Consensus        15 ~~~~p~~~~~~~g~~~~~~~l~~~l~~~~~~~~~ll~G~~G~GKT~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   94 (250)
T 1njg_A           15 RKWRPQTFADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKGLNCETGITATPCGVCDNCREIEQGRF   94 (250)
T ss_dssp             HHTCCCSGGGCCSCHHHHHHHHHHHHHTCCCSEEEEECSTTSCHHHHHHHHHHHHHCTTCSCSSCCSCSHHHHHHHTTCC
T ss_pred             hccCCccHHHHhCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCcccHHHHHHhccCC
Confidence            68999999999999999999999999888766 9999999999999999999988543211                   


Q ss_pred             CceEEecCCCCcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcCch
Q psy879           62 DAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIE  141 (317)
Q Consensus        62 ~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~~  141 (317)
                      ..++..+.........++..+..+...+   ..+.+.+++|||++.+..+.++.|++.+++++.++.+|++++....+.+
T Consensus        95 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~vlviDe~~~l~~~~~~~l~~~l~~~~~~~~~i~~t~~~~~~~~  171 (250)
T 1njg_A           95 VDLIEIDAASRTKVEDTRDLLDNVQYAP---ARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPV  171 (250)
T ss_dssp             SSEEEEETTCGGGHHHHHHHHHSCCCSC---SSSSSEEEEEETGGGSCHHHHHHHHHHHHSCCTTEEEEEEESCGGGSCH
T ss_pred             cceEEecCcccccHHHHHHHHHHhhhch---hcCCceEEEEECcccccHHHHHHHHHHHhcCCCceEEEEEeCChHhCCH
Confidence            0123333332233344444433322111   2256789999999999999999999999998889999999999999999


Q ss_pred             hHhhhcceeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhh-CCCcccHHHHHhhcC
Q psy879          142 PIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHN-GFGHVTAEYVFKVCD  218 (317)
Q Consensus       142 ~i~sR~~~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~-~~~~i~~~~v~~~~~  218 (317)
                      ++.+|+..++|++++.+++.+++..++..++..+++++++.+++.++|++|.+.+.++.++. +.+.|+.+++.++++
T Consensus       172 ~l~~r~~~i~l~~l~~~e~~~~l~~~~~~~~~~~~~~~~~~l~~~~~G~~~~~~~~~~~~~~~~~~~i~~~~v~~~~~  249 (250)
T 1njg_A          172 TILSRCLQFHLKALDVEQIRHQLEHILNEEHIAHEPRALQLLARAAEGSLRDALSLTDQAIASGDGQVSTQAVSAMLG  249 (250)
T ss_dssp             HHHTTSEEEECCCCCHHHHHHHHHHHHHHTTCCBCHHHHHHHHHHHTTCHHHHHHHHHHHHTTTTSSBCHHHHHHHSC
T ss_pred             HHHHHhhhccCCCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHhccCceecHHHHHHHhC
Confidence            99999999999999999999999999999999999999999999999999999999987655 446899999887764

>1sxj_A Activator 1 95 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=99.96  E-value=5.8e-28  Score=224.28  Aligned_cols=227  Identities=24%  Similarity=0.412  Sum_probs=178.2

Q ss_pred             CcccCCCCCCcccCCHHHHHHHHHHHhc-----------------CCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCc
Q psy879            1 IEKYRPQTFSDIVGNEDTVERLKVFSSS-----------------GNVPNIIISGPPGVGKTTTILCLARILLGPSFKDA   63 (317)
Q Consensus         1 ~~ky~P~~~~~~~g~~~~~~~l~~~l~~-----------------~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~   63 (317)
                      ++||+|++|++++|++++++.+..++..                 +..++++|+||||+|||++|+++++.+     +..
T Consensus        30 ~ekyrP~~~~dliG~~~~~~~L~~~l~~~~~~~~~~~~~~g~~~~~~~~~lLL~GppGtGKTtla~~la~~l-----~~~  104 (516)
T 1sxj_A           30 TVKYAPTNLQQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQEL-----GYD  104 (516)
T ss_dssp             HHHTCCSSGGGCCSCHHHHHHHHHHHHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHHHHHHHHT-----TCE
T ss_pred             ccccCCCCHHHhcCCHHHHHHHHHHHHHhHhhchhhccccCccCCCCCcEEEEECCCCCCHHHHHHHHHHHc-----CCC
Confidence            4799999999999999999999998875                 123469999999999999999999996     356


Q ss_pred             eEEecCCCCcChHHHHHHHHHHHhhc-c---c-------CCCCceeEEEEeCCCCCCHHHH---HHHHHHhhhccCCceE
Q psy879           64 VLELNASNDRGIDTVRNKIKMFAQQK-V---T-------LPPGRHKIVILDEADSMTDGAQ---QALRRTMEIYSNTTRF  129 (317)
Q Consensus        64 ~~~~~~~~~~~~~~i~~~~~~~~~~~-~---~-------~~~~~~~vliiDE~d~l~~~~~---~~ll~~le~~~~~~~~  129 (317)
                      +++++++.......+...+....... .   .       ...+.+.||||||+|.+....+   +.|+++++..  ...+
T Consensus       105 ~i~in~s~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~vliIDEid~l~~~~~~~l~~L~~~l~~~--~~~i  182 (516)
T 1sxj_A          105 ILEQNASDVRSKTLLNAGVKNALDNMSVVGYFKHNEEAQNLNGKHFVIIMDEVDGMSGGDRGGVGQLAQFCRKT--STPL  182 (516)
T ss_dssp             EEEECTTSCCCHHHHHHTGGGGTTBCCSTTTTTC----CCSSTTSEEEEECSGGGCCTTSTTHHHHHHHHHHHC--SSCE
T ss_pred             EEEEeCCCcchHHHHHHHHHHHhccccHHHHHhhhhhhhhccCCCeEEEEECCCccchhhHHHHHHHHHHHHhc--CCCE
Confidence            78888877665544443332211110 0   0       0124678999999999976544   7888888863  4457


Q ss_pred             EEEecCCC-cCchhHhhhcceeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhhCCCcc
Q psy879          130 ALACNNSE-KIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHNGFGHV  208 (317)
Q Consensus       130 il~~~~~~-~l~~~i~sR~~~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~~~~~i  208 (317)
                      |++++... ...+++.+||..+.|++|+.+++.+++..++..+++.++++++..+++.++||+|.+++.++.++...+.|
T Consensus       183 Ili~~~~~~~~l~~l~~r~~~i~f~~~~~~~~~~~L~~i~~~~~~~i~~~~l~~la~~s~GdiR~~i~~L~~~~~~~~~I  262 (516)
T 1sxj_A          183 ILICNERNLPKMRPFDRVCLDIQFRRPDANSIKSRLMTIAIREKFKLDPNVIDRLIQTTRGDIRQVINLLSTISTTTKTI  262 (516)
T ss_dssp             EEEESCTTSSTTGGGTTTSEEEECCCCCHHHHHHHHHHHHHHHTCCCCTTHHHHHHHHTTTCHHHHHHHHTHHHHHSSCC
T ss_pred             EEEEcCCCCccchhhHhceEEEEeCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCcHHHHHHHHHHHHhcCCCC
Confidence            77777653 55678999999999999999999999999999999999999999999999999999999999888777889


Q ss_pred             cHHHHHhhcC---CCCHHHHHHHHHHHhc
Q psy879          209 TAEYVFKVCD---EPHPLAVKEMLLNCVE  234 (317)
Q Consensus       209 ~~~~v~~~~~---~~~~~~i~~l~~~~~~  234 (317)
                      +.+++.+++.   ......++++++.+..
T Consensus       263 t~~~v~~~~~~~~~~~~~~~f~~~~~il~  291 (516)
T 1sxj_A          263 NHENINEISKAWEKNIALKPFDIAHKMLD  291 (516)
T ss_dssp             CTTHHHHHHHHHHTTTTSHHHHHHHHHTB
T ss_pred             chHHHHHHHHhhccCCCCCHHHHHHHHhc
Confidence            9988877654   3344457777777665

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=99.94  E-value=4.1e-26  Score=203.75  Aligned_cols=214  Identities=16%  Similarity=0.233  Sum_probs=161.8

Q ss_pred             cccCCCC-CCcccCCHHHHHH---HHHHHhcCCCc--eEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCC----
Q psy879            2 EKYRPQT-FSDIVGNEDTVER---LKVFSSSGNVP--NIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASN----   71 (317)
Q Consensus         2 ~ky~P~~-~~~~~g~~~~~~~---l~~~l~~~~~~--~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~----   71 (317)
                      ++|+|.. |++++|++++++.   +...+..+..+  +++|+||||+|||++++++++.+.+.   .+++.+++..    
T Consensus        35 ~~~~p~~~~~~ivG~~~~~~~l~~l~~~~~~~~~~~~~vLl~GppGtGKT~la~~la~~l~~~---~~~~~~~~~~~~~~  111 (368)
T 3uk6_A           35 DALEPRQASQGMVGQLAARRAAGVVLEMIREGKIAGRAVLIAGQPGTGKTAIAMGMAQALGPD---TPFTAIAGSEIFSL  111 (368)
T ss_dssp             TTSCBCSEETTEESCHHHHHHHHHHHHHHHTTCCTTCEEEEEESTTSSHHHHHHHHHHHHCSS---CCEEEEEGGGGSCS
T ss_pred             cccCcCcchhhccChHHHHHHHHHHHHHHHcCCCCCCEEEEECCCCCCHHHHHHHHHHHhccc---CCcccccchhhhhc
Confidence            6799998 9999999998776   56666777765  69999999999999999999998532   1222222111    


Q ss_pred             C----------------------------------------------cC-----hHHHHHHHHHHHhhccc--CCCCcee
Q psy879           72 D----------------------------------------------RG-----IDTVRNKIKMFAQQKVT--LPPGRHK   98 (317)
Q Consensus        72 ~----------------------------------------------~~-----~~~i~~~~~~~~~~~~~--~~~~~~~   98 (317)
                      .                                              .+     ...+++.+..+......  .....+.
T Consensus       112 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ld~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~g~~~~~~~  191 (368)
T 3uk6_A          112 EMSKTEALTQAFRRSIGVRIKAGAVHTVSLHEIDVINSRTQGFLALFSGDTGEIKSEVREQINAKVAEWREEGKAEIIPG  191 (368)
T ss_dssp             SSCHHHHHHHHHHHSBEECC------CEEHHHHHHHTC----CCSCC-------CHHHHHHHHHHHHHHHHHTC---CBC
T ss_pred             ccchhHHHHHHHHHHHHHHhhhhccccccHhhhhhhhcccccchhhccCcccccHHHHHHHHHHHHHHhhhhccccccCc
Confidence            0                                              00     22333333332221100  0001246


Q ss_pred             EEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEec------------CCCcCchhHhhhcceeeecCCCHHHHHHHHHH
Q psy879           99 IVILDEADSMTDGAQQALRRTMEIYSNTTRFALACN------------NSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIE  166 (317)
Q Consensus        99 vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~------------~~~~l~~~i~sR~~~i~f~~~~~~~~~~~l~~  166 (317)
                      |+||||+|.+..+.++.|++.+++++... ++++++            .+..++++++|||..+.|++|+.+++..++..
T Consensus       192 vl~IDEi~~l~~~~~~~L~~~le~~~~~~-~ii~t~~~~~~i~~t~~~~~~~l~~~l~sR~~~i~~~~~~~~e~~~il~~  270 (368)
T 3uk6_A          192 VLFIDEVHMLDIESFSFLNRALESDMAPV-LIMATNRGITRIRGTSYQSPHGIPIDLLDRLLIVSTTPYSEKDTKQILRI  270 (368)
T ss_dssp             EEEEESGGGSBHHHHHHHHHHTTCTTCCE-EEEEESCSEEECBTSSCEEETTCCHHHHTTEEEEEECCCCHHHHHHHHHH
T ss_pred             eEEEhhccccChHHHHHHHHHhhCcCCCe-eeeecccceeeeeccCCCCcccCCHHHHhhccEEEecCCCHHHHHHHHHH
Confidence            99999999999999999999999877664 444554            35678899999999999999999999999999


Q ss_pred             HHHHcCCCCCHHHHHHHHHhcC-CCHHHHHHHHHHhhh-----CCCcccHHHHHhhcCC
Q psy879          167 ICEKENISHTNDGLEAIVFTAQ-GDMRQALNNLQSTHN-----GFGHVTAEYVFKVCDE  219 (317)
Q Consensus       167 ~~~~~~~~i~~~~~~~l~~~~~-gd~r~~i~~l~~~~~-----~~~~i~~~~v~~~~~~  219 (317)
                      ++..++..+++++++.++..+. ||+|.+++.++.++.     +...|+.+++.+++..
T Consensus       271 ~~~~~~~~~~~~~l~~l~~~~~~G~~r~~~~ll~~a~~~A~~~~~~~It~~~v~~a~~~  329 (368)
T 3uk6_A          271 RCEEEDVEMSEDAYTVLTRIGLETSLRYAIQLITAASLVCRKRKGTEVQVDDIKRVYSL  329 (368)
T ss_dssp             HHHHTTCCBCHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHH
T ss_pred             HHHHcCCCCCHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHH
Confidence            9999999999999999999998 999999999987543     5568999988876554

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=99.94  E-value=1.8e-25  Score=197.35  Aligned_cols=202  Identities=19%  Similarity=0.246  Sum_probs=163.9

Q ss_pred             CcccCCCCCCcccCCHHHHHHHHHHHhc-----CCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcCh
Q psy879            1 IEKYRPQTFSDIVGNEDTVERLKVFSSS-----GNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGI   75 (317)
Q Consensus         1 ~~ky~P~~~~~~~g~~~~~~~l~~~l~~-----~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~   75 (317)
                      .+||+|.+|++++|++.+++.+..++..     +..++++|+||||||||++|+++++.+.     ..++.+++......
T Consensus        20 ~~~~~p~~~~~iiG~~~~~~~l~~~l~~~~~~~~~~~~vll~G~~GtGKT~la~~ia~~~~-----~~~~~~~~~~~~~~   94 (338)
T 3pfi_A           20 ETSLRPSNFDGYIGQESIKKNLNVFIAAAKKRNECLDHILFSGPAGLGKTTLANIISYEMS-----ANIKTTAAPMIEKS   94 (338)
T ss_dssp             ---CCCCSGGGCCSCHHHHHHHHHHHHHHHHTTSCCCCEEEECSTTSSHHHHHHHHHHHTT-----CCEEEEEGGGCCSH
T ss_pred             hhccCCCCHHHhCChHHHHHHHHHHHHHHHhcCCCCCeEEEECcCCCCHHHHHHHHHHHhC-----CCeEEecchhccch
Confidence            3689999999999999999998888764     3445699999999999999999999852     34666666544444


Q ss_pred             HHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhcc------------------CCceEEEEecCCC
Q psy879           76 DTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYS------------------NTTRFALACNNSE  137 (317)
Q Consensus        76 ~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~------------------~~~~~il~~~~~~  137 (317)
                      ..+...+..         .+.+.+++|||++.+..+.++.|++.+++..                  +.+.+|++||...
T Consensus        95 ~~~~~~~~~---------~~~~~vl~lDEi~~l~~~~~~~Ll~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~i~atn~~~  165 (338)
T 3pfi_A           95 GDLAAILTN---------LSEGDILFIDEIHRLSPAIEEVLYPAMEDYRLDIIIGSGPAAQTIKIDLPKFTLIGATTRAG  165 (338)
T ss_dssp             HHHHHHHHT---------CCTTCEEEEETGGGCCHHHHHHHHHHHHTSCC---------CCCCCCCCCCCEEEEEESCGG
T ss_pred             hHHHHHHHh---------ccCCCEEEEechhhcCHHHHHHHHHHHHhccchhhcccCccccceecCCCCeEEEEeCCCcc
Confidence            444433321         1467899999999999999999999998643                  1367899999999


Q ss_pred             cCchhHhhhc-ceeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhh-----CCCcccHH
Q psy879          138 KIIEPIQSRC-AMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHN-----GFGHVTAE  211 (317)
Q Consensus       138 ~l~~~i~sR~-~~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~-----~~~~i~~~  211 (317)
                      .+.+++++|| ..+.|++|+.+++..++...+...+..+++++++.++..+.|++|.+.+.++.+..     +...|+.+
T Consensus       166 ~l~~~L~~R~~~~i~l~~~~~~e~~~il~~~~~~~~~~~~~~~~~~l~~~~~G~~r~l~~~l~~~~~~a~~~~~~~i~~~  245 (338)
T 3pfi_A          166 MLSNPLRDRFGMQFRLEFYKDSELALILQKAALKLNKTCEEKAALEIAKRSRSTPRIALRLLKRVRDFADVNDEEIITEK  245 (338)
T ss_dssp             GSCHHHHTTCSEEEECCCCCHHHHHHHHHHHHHHTTCEECHHHHHHHHHTTTTCHHHHHHHHHHHHHHHHHTTCSEECHH
T ss_pred             ccCHHHHhhcCEEeeCCCcCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHhhcCCccCHH
Confidence            9999999999 66999999999999999999999998899999999999999999999999987532     35568888


Q ss_pred             HHHhh
Q psy879          212 YVFKV  216 (317)
Q Consensus       212 ~v~~~  216 (317)
                      ++..+
T Consensus       246 ~~~~~  250 (338)
T 3pfi_A          246 RANEA  250 (338)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            77654

>2c9o_A RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-binding, chromatin regulator, growth regulation, hydrolase, nuclear protein, DNA recombination; HET: ADP; 2.2A {Homo sapiens} PDB: 2xsz_A*

Probab=99.94  E-value=2.1e-25  Score=204.13  Aligned_cols=122  Identities=15%  Similarity=0.165  Sum_probs=109.2

Q ss_pred             eEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEe---------cC----CCcCchhHhhhcceeeecCCCHHHHHHHH
Q psy879           98 KIVILDEADSMTDGAQQALRRTMEIYSNTTRFALAC---------NN----SEKIIEPIQSRCAMLRYNKLTDAQLLSKV  164 (317)
Q Consensus        98 ~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~---------~~----~~~l~~~i~sR~~~i~f~~~~~~~~~~~l  164 (317)
                      +|+||||++.|+.+++++|++.||+|+.+ +||++|         ..    +..++++++|||+.++|++++.+++.++|
T Consensus       297 ~VliIDEa~~l~~~a~~aLlk~lEe~~~~-~~il~tn~~~~~i~~~~~~~~~~~l~~~i~sR~~~~~~~~~~~~e~~~iL  375 (456)
T 2c9o_A          297 GVLFVDEVHMLDIECFTYLHRALESSIAP-IVIFASNRGNCVIRGTEDITSPHGIPLDLLDRVMIIRTMLYTPQEMKQII  375 (456)
T ss_dssp             CEEEEESGGGCBHHHHHHHHHHTTSTTCC-EEEEEECCSEEECBTTSSCEEETTCCHHHHTTEEEEECCCCCHHHHHHHH
T ss_pred             eEEEEechhhcCHHHHHHHHHHhhccCCC-EEEEecCCccccccccccccccccCChhHHhhcceeeCCCCCHHHHHHHH
Confidence            69999999999999999999999999888 677777         33    66899999999999999999999999999


Q ss_pred             HHHHHHcCCCCCHHHHHHHHHhc-CCCHHHHHHHHHHh---hh--CCCcccHHHHHhhcCCC
Q psy879          165 IEICEKENISHTNDGLEAIVFTA-QGDMRQALNNLQST---HN--GFGHVTAEYVFKVCDEP  220 (317)
Q Consensus       165 ~~~~~~~~~~i~~~~~~~l~~~~-~gd~r~~i~~l~~~---~~--~~~~i~~~~v~~~~~~~  220 (317)
                      ..++..+++.++++++..++..+ .|++|.++++++.+   +.  +...|+.++|.++....
T Consensus       376 ~~~~~~~~~~~~~~~~~~i~~~a~~g~~r~a~~ll~~a~~~A~~~~~~~v~~~~v~~~~~~~  437 (456)
T 2c9o_A          376 KIRAQTEGINISEEALNHLGEIGTKTTLRYSVQLLTPANLLAKINGKDSIEKEHVEEISELF  437 (456)
T ss_dssp             HHHHHHHTCCBCHHHHHHHHHHHHHSCHHHHHHTHHHHHHHHHHTTCSSBCHHHHHHHHHHS
T ss_pred             HHHHHHhCCCCCHHHHHHHHHHccCCCHHHHHHHHHHHHHHHhhcCCCccCHHHHHHHHHHh
Confidence            99999999999999999999998 99999999999875   22  56789999998765543

>1hqc_A RUVB; extended AAA-ATPase domain, complex with nucleotide, hydrolase; HET: ADE; 3.20A {Thermus thermophilus} SCOP: a.4.5.11 c.37.1.20 PDB: 1ixs_B* 1ixr_C*

Probab=99.93  E-value=1.5e-24  Score=190.25  Aligned_cols=202  Identities=21%  Similarity=0.282  Sum_probs=163.0

Q ss_pred             cccCCCCCCcccCCHHHHHHHHHHHhc-----CCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChH
Q psy879            2 EKYRPQTFSDIVGNEDTVERLKVFSSS-----GNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGID   76 (317)
Q Consensus         2 ~ky~P~~~~~~~g~~~~~~~l~~~l~~-----~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~   76 (317)
                      +||+|.+|++++|++.+++.+..++..     +...+++|+||||||||++|+++++.+.     ..++.+++.......
T Consensus         4 ~~~~p~~~~~~ig~~~~~~~l~~~l~~~~~~~~~~~~vll~G~~GtGKT~la~~i~~~~~-----~~~~~~~~~~~~~~~   78 (324)
T 1hqc_A            4 LALRPKTLDEYIGQERLKQKLRVYLEAAKARKEPLEHLLLFGPPGLGKTTLAHVIAHELG-----VNLRVTSGPAIEKPG   78 (324)
T ss_dssp             -CCCCCSTTTCCSCHHHHHHHHHHHHHHHHHCSCCCCCEEECCTTCCCHHHHHHHHHHHT-----CCEEEECTTTCCSHH
T ss_pred             cccCcccHHHhhCHHHHHHHHHHHHHHHHccCCCCCcEEEECCCCCCHHHHHHHHHHHhC-----CCEEEEeccccCChH
Confidence            689999999999999999888877652     2334699999999999999999999873     345666665444433


Q ss_pred             HHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhcc------------------CCceEEEEecCCCc
Q psy879           77 TVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYS------------------NTTRFALACNNSEK  138 (317)
Q Consensus        77 ~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~------------------~~~~~il~~~~~~~  138 (317)
                      .+..   .+...     .+.+.+++|||++.+....++.|++.+++..                  +++.+|++||....
T Consensus        79 ~l~~---~l~~~-----~~~~~~l~lDEi~~l~~~~~~~L~~~l~~~~~~~v~~~~~~~~~~~~~~~~~~~i~~t~~~~~  150 (324)
T 1hqc_A           79 DLAA---ILANS-----LEEGDILFIDEIHRLSRQAEEHLYPAMEDFVMDIVIGQGPAARTIRLELPRFTLIGATTRPGL  150 (324)
T ss_dssp             HHHH---HHTTT-----CCTTCEEEETTTTSCCHHHHHHHHHHHHHSEEEECCSSSSSCCCEEEECCCCEEEEEESCCSS
T ss_pred             HHHH---HHHHh-----ccCCCEEEEECCcccccchHHHHHHHHHhhhhHHhccccccccccccCCCCEEEEEeCCCccc
Confidence            3333   22210     1467799999999999999999999998643                  35679999999999


Q ss_pred             CchhHhhhc-ceeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhh-----CCCcccHHH
Q psy879          139 IIEPIQSRC-AMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHN-----GFGHVTAEY  212 (317)
Q Consensus       139 l~~~i~sR~-~~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~-----~~~~i~~~~  212 (317)
                      +.+++.+|| ..+.|++|+.+++..++...+...+..+++++++.++..++|++|.+.+.++.+..     +...|+.++
T Consensus       151 ~~~~l~~R~~~~i~l~~~~~~e~~~~l~~~~~~~~~~~~~~~~~~l~~~~~G~~r~l~~~l~~~~~~a~~~~~~~i~~~~  230 (324)
T 1hqc_A          151 ITAPLLSRFGIVEHLEYYTPEELAQGVMRDARLLGVRITEEAALEIGRRSRGTMRVAKRLFRRVRDFAQVAGEEVITRER  230 (324)
T ss_dssp             CSCSTTTTCSCEEECCCCCHHHHHHHHHHHHHTTTCCCCHHHHHHHHHHSCSCHHHHHHHHHHHTTTSTTTSCSCCCHHH
T ss_pred             CCHHHHhcccEEEecCCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHccCCHHHHHHHHHHHHHHHHHhcCCCCCHHH
Confidence            999999999 57999999999999999999998899999999999999999999999999987643     234677777


Q ss_pred             HHhh
Q psy879          213 VFKV  216 (317)
Q Consensus       213 v~~~  216 (317)
                      +..+
T Consensus       231 ~~~~  234 (324)
T 1hqc_A          231 ALEA  234 (324)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            6543

>1fnn_A CDC6P, cell division control protein 6; ORC1, AAA protein, DNA replication initation factor, cell cycle control factor; HET: ADP; 2.00A {Pyrobaculum aerophilum} SCOP: a.4.5.11 c.37.1.20

Probab=99.93  E-value=1.4e-23  Score=188.54  Aligned_cols=279  Identities=16%  Similarity=0.157  Sum_probs=194.4

Q ss_pred             cccCCCCCCcccCCHHHHHHHHHHHhc----CCC--ceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcCh
Q psy879            2 EKYRPQTFSDIVGNEDTVERLKVFSSS----GNV--PNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGI   75 (317)
Q Consensus         2 ~ky~P~~~~~~~g~~~~~~~l~~~l~~----~~~--~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~   75 (317)
                      .+|+|   ++++|+++.++.+..++..    +..  ++++|+||+|+|||++++.+++.+.+.. +..++.+++......
T Consensus        12 ~~~~p---~~l~gr~~~~~~l~~~l~~~~~~~~~~~~~~li~G~~G~GKTtl~~~l~~~~~~~~-~~~~~~i~~~~~~~~   87 (389)
T 1fnn_A           12 PSYVP---KRLPHREQQLQQLDILLGNWLRNPGHHYPRATLLGRPGTGKTVTLRKLWELYKDKT-TARFVYINGFIYRNF   87 (389)
T ss_dssp             TTCCC---SCCTTCHHHHHHHHHHHHHHHHSTTSSCCEEEEECCTTSSHHHHHHHHHHHHTTSC-CCEEEEEETTTCCSH
T ss_pred             CccCC---CCCCChHHHHHHHHHHHHHHHcCCCCCCCeEEEECCCCCCHHHHHHHHHHHHhhhc-CeeEEEEeCccCCCH
Confidence            46777   7899999998888777764    332  3799999999999999999999985432 345667776543332


Q ss_pred             HHH-HHHHHHHHhhcc----------------cCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhcc----CCceEEEEec
Q psy879           76 DTV-RNKIKMFAQQKV----------------TLPPGRHKIVILDEADSMTDGAQQALRRTMEIYS----NTTRFALACN  134 (317)
Q Consensus        76 ~~i-~~~~~~~~~~~~----------------~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~----~~~~~il~~~  134 (317)
                      ..+ ......+.....                ....+.+.+++|||++.+..+.++.|++++++.+    .++.+|++++
T Consensus        88 ~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlilDE~~~l~~~~~~~L~~~~~~~~~~~~~~~~iI~~~~  167 (389)
T 1fnn_A           88 TAIIGEIARSLNIPFPRRGLSRDEFLALLVEHLRERDLYMFLVLDDAFNLAPDILSTFIRLGQEADKLGAFRIALVIVGH  167 (389)
T ss_dssp             HHHHHHHHHHTTCCCCSSCCCHHHHHHHHHHHHHHTTCCEEEEEETGGGSCHHHHHHHHHHTTCHHHHSSCCEEEEEEES
T ss_pred             HHHHHHHHHHhCccCCCCCCCHHHHHHHHHHHHhhcCCeEEEEEECccccchHHHHHHHHHHHhCCCCCcCCEEEEEEEC
Confidence            221 111111100000                0001357799999999999999999999998755    4788899998


Q ss_pred             CC---CcCchhHhhhcc--eeeecCCCHHHHHHHHHHHHHHc--CCCCCHHHHHHHHHhc---------CCCHHHHHHHH
Q psy879          135 NS---EKIIEPIQSRCA--MLRYNKLTDAQLLSKVIEICEKE--NISHTNDGLEAIVFTA---------QGDMRQALNNL  198 (317)
Q Consensus       135 ~~---~~l~~~i~sR~~--~i~f~~~~~~~~~~~l~~~~~~~--~~~i~~~~~~~l~~~~---------~gd~r~~i~~l  198 (317)
                      .+   ..+.+.+.+|+.  .+.|+|++.+++..++...+...  ...+++++++.++..+         +||+|.+++.+
T Consensus       168 ~~~~~~~l~~~~~~r~~~~~i~~~pl~~~~~~~~l~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~G~~r~~~~~l  247 (389)
T 1fnn_A          168 NDAVLNNLDPSTRGIMGKYVIRFSPYTKDQIFDILLDRAKAGLAEGSYSEDILQMIADITGAQTPLDTNRGDARLAIDIL  247 (389)
T ss_dssp             STHHHHTSCHHHHHHHTTCEEECCCCBHHHHHHHHHHHHHHHBCTTSSCHHHHHHHHHHHSBSSTTCTTSCCHHHHHHHH
T ss_pred             CchHHHHhCHHhhhcCCCceEEeCCCCHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHhhcccCCCCCCcHHHHHHHH
Confidence            87   578899999998  59999999999999999988752  2368899999999999         89999999999


Q ss_pred             HHhhh-----CCCcccHHHHHhhcCCCCHHHHHHHHHHHhcCCHHHHHHHHHHHH--HcC--CCHHHHHHHHHHHHHhcC
Q psy879          199 QSTHN-----GFGHVTAEYVFKVCDEPHPLAVKEMLLNCVEGNMKDSYKIIHHLY--KLG--YAPEDIIGNIFRVAKTLD  269 (317)
Q Consensus       199 ~~~~~-----~~~~i~~~~v~~~~~~~~~~~i~~l~~~~~~~~~~~~~~~~~~l~--~~~--~~~~~i~~~~~~~~~~~~  269 (317)
                      +.++.     +...++.+++..+........+...++.+.. +...++..+..+.  ..|  .+...+...+..+++..+
T Consensus       248 ~~a~~~a~~~~~~~i~~~~v~~~~~~~~~~~~~~~l~~l~~-~~~~~L~~l~~~~~~~~~~~~~~~~i~~~~~~~~~~~~  326 (389)
T 1fnn_A          248 YRSAYAAQQNGRKHIAPEDVRKSSKEVLFGISEEVLIGLPL-HEKLFLLAIVRSLKISHTPYITFGDAEESYKIVCEEYG  326 (389)
T ss_dssp             HHHHHHHHHTTCSSCCHHHHHHHHHHHSCCCCHHHHHHSCH-HHHHHHHHHHHHHHHHCSSCEEHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHhCCCCcCHHHHHHHHHHHhhhhHHHHHHcCCH-HHHHHHHHHHHHHhhccCCCccHHHHHHHHHHHHHHcC
Confidence            87654     4567899988776544333334455555432 2334444454444  344  456777777777777766


Q ss_pred             CChHHHHHHHHHHHHH
Q psy879          270 IPEPLKLSIIQEIGNV  285 (317)
Q Consensus       270 ~~~~~~~~~~~~l~~~  285 (317)
                      ..+.....+...+.++
T Consensus       327 ~~~~~~~~~~~~l~~L  342 (389)
T 1fnn_A          327 ERPRVHSQLWSYLNDL  342 (389)
T ss_dssp             CCCCCHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHH
Confidence            5554444455555443

>1in4_A RUVB, holliday junction DNA helicase RUVB; AAA+-class ATPase, winged-helix domain, ATP hydrolysis, walker A, walker B, sensor 1, sensor 2; HET: ADP; 1.60A {Thermotoga maritima} SCOP: a.4.5.11 c.37.1.20 PDB: 1in5_A* 1in6_A* 1in8_A* 1in7_A* 1j7k_A*

Probab=99.92  E-value=2.7e-23  Score=182.79  Aligned_cols=204  Identities=17%  Similarity=0.293  Sum_probs=158.9

Q ss_pred             CcccCCCCCCcccCCHHHHHHHHHHHhcC-----CCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcCh
Q psy879            1 IEKYRPQTFSDIVGNEDTVERLKVFSSSG-----NVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGI   75 (317)
Q Consensus         1 ~~ky~P~~~~~~~g~~~~~~~l~~~l~~~-----~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~   75 (317)
                      +++++|++|++++|++++++.+...+..+     .+.+++|+||||+||||+++++++.+.+.     +...++......
T Consensus        16 ~~~lr~~~l~~~~g~~~~~~~l~~~i~~~~~~~~~~~~~ll~Gp~G~GKTTLa~~ia~~l~~~-----~~~~sg~~~~~~   90 (334)
T 1in4_A           16 VQFLRPKSLDEFIGQENVKKKLSLALEAAKMRGEVLDHVLLAGPPGLGKTTLAHIIASELQTN-----IHVTSGPVLVKQ   90 (334)
T ss_dssp             -CTTSCSSGGGCCSCHHHHHHHHHHHHHHHHHTCCCCCEEEESSTTSSHHHHHHHHHHHHTCC-----EEEEETTTCCSH
T ss_pred             HHHcCCccHHHccCcHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCcHHHHHHHHHHHhCCC-----EEEEechHhcCH
Confidence            36899999999999999999988887653     33569999999999999999999997432     222332222223


Q ss_pred             HHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhcc------------------CCceEEEEecCCC
Q psy879           76 DTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYS------------------NTTRFALACNNSE  137 (317)
Q Consensus        76 ~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~------------------~~~~~il~~~~~~  137 (317)
                      ..+......    .     ....|++|||++.+.+..++.|+..++...                  +...++.+++.+.
T Consensus        91 ~~l~~~~~~----~-----~~~~v~~iDE~~~l~~~~~e~L~~~~~~~~~~i~~~~~~~~~~i~~~l~~~~li~at~~~~  161 (334)
T 1in4_A           91 GDMAAILTS----L-----ERGDVLFIDEIHRLNKAVEELLYSAIEDFQIDIMIGKGPSAKSIRIDIQPFTLVGATTRSG  161 (334)
T ss_dssp             HHHHHHHHH----C-----CTTCEEEEETGGGCCHHHHHHHHHHHHTSCCCC---------------CCCEEEEEESCGG
T ss_pred             HHHHHHHHH----c-----cCCCEEEEcchhhcCHHHHHHHHHHHHhcccceeeccCcccccccccCCCeEEEEecCCcc
Confidence            333322211    1     346799999999999988888888877542                  1245667788888


Q ss_pred             cCchhHhhhcce-eeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhh-----CCCcccHH
Q psy879          138 KIIEPIQSRCAM-LRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHN-----GFGHVTAE  211 (317)
Q Consensus       138 ~l~~~i~sR~~~-i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~-----~~~~i~~~  211 (317)
                      .+.+++++||.. +.|.+++.+++.+++...+...++.++++++..++..++|++|.+++.++.+..     +.+.|+.+
T Consensus       162 ~Ls~~l~sR~~l~~~Ld~~~~~~l~~iL~~~~~~~~~~~~~~~~~~ia~~~~G~~R~a~~ll~~~~~~a~~~~~~~It~~  241 (334)
T 1in4_A          162 LLSSPLRSRFGIILELDFYTVKELKEIIKRAASLMDVEIEDAAAEMIAKRSRGTPRIAIRLTKRVRDMLTVVKADRINTD  241 (334)
T ss_dssp             GSCHHHHTTCSEEEECCCCCHHHHHHHHHHHHHHTTCCBCHHHHHHHHHTSTTCHHHHHHHHHHHHHHHHHHTCSSBCHH
T ss_pred             cCCHHHHHhcCceeeCCCCCHHHHHHHHHHHHHHcCCCcCHHHHHHHHHhcCCChHHHHHHHHHHHHHHHHcCCCCcCHH
Confidence            999999999975 899999999999999999988899999999999999999999999999976422     45678888


Q ss_pred             HHHhhcC
Q psy879          212 YVFKVCD  218 (317)
Q Consensus       212 ~v~~~~~  218 (317)
                      ++.++++
T Consensus       242 ~v~~al~  248 (334)
T 1in4_A          242 IVLKTME  248 (334)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            8776543

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=99.92  E-value=7.9e-23  Score=183.35  Aligned_cols=277  Identities=18%  Similarity=0.145  Sum_probs=190.5

Q ss_pred             ccCCCCCCcccCCHHHHHHHHHHHhc----CCCceEEEECCCCCCHHHHHHHHHHHHcCC----CCCCceEEecCCCCcC
Q psy879            3 KYRPQTFSDIVGNEDTVERLKVFSSS----GNVPNIIISGPPGVGKTTTILCLARILLGP----SFKDAVLELNASNDRG   74 (317)
Q Consensus         3 ky~P~~~~~~~g~~~~~~~l~~~l~~----~~~~~~ll~G~~G~GKt~la~~la~~l~~~----~~~~~~~~~~~~~~~~   74 (317)
                      +|.|   ++++|++..++.+..++..    +..++++|+||||+|||++++.+++.+...    ..+..++.+++.....
T Consensus        15 ~~~p---~~~~gr~~~~~~l~~~l~~~~~~~~~~~vll~G~~G~GKT~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~   91 (387)
T 2v1u_A           15 DYVP---DVLPHREAELRRLAEVLAPALRGEKPSNALLYGLTGTGKTAVARLVLRRLEARASSLGVLVKPIYVNARHRET   91 (387)
T ss_dssp             TCCC---SCCTTCHHHHHHHHHTTGGGTSSCCCCCEEECBCTTSSHHHHHHHHHHHHHHHHHHHTCCEEEEEEETTTSCS
T ss_pred             ccCC---CCCCCHHHHHHHHHHHHHHHHcCCCCCcEEEECCCCCCHHHHHHHHHHHHHHHHhccCCCeEEEEEECCcCCC
Confidence            4566   7899999999999888743    444569999999999999999999987321    1134566677654332


Q ss_pred             hHHHH-------------------HHHHHHHhhcccCCCCceeEEEEeCCCCCCHH--HHHHHHHHhhhc-----cCCce
Q psy879           75 IDTVR-------------------NKIKMFAQQKVTLPPGRHKIVILDEADSMTDG--AQQALRRTMEIY-----SNTTR  128 (317)
Q Consensus        75 ~~~i~-------------------~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~--~~~~ll~~le~~-----~~~~~  128 (317)
                      ...+.                   +.+..+....  ...+.+.+++|||++.+...  .++.|..+++..     +.++.
T Consensus        92 ~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l--~~~~~~~vlilDEi~~l~~~~~~~~~l~~l~~~~~~~~~~~~~~  169 (387)
T 2v1u_A           92 PYRVASAIAEAVGVRVPFTGLSVGEVYERLVKRL--SRLRGIYIIVLDEIDFLPKRPGGQDLLYRITRINQELGDRVWVS  169 (387)
T ss_dssp             HHHHHHHHHHHHSCCCCSSCCCHHHHHHHHHHHH--TTSCSEEEEEEETTTHHHHSTTHHHHHHHHHHGGGCC-----CE
T ss_pred             HHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHH--hccCCeEEEEEccHhhhcccCCCChHHHhHhhchhhcCCCceEE
Confidence            22111                   1111111110  01245779999999999876  677777777644     55678


Q ss_pred             EEEEecCC---CcCchhHhhhc--ceeeecCCCHHHHHHHHHHHHHH--cCCCCCHHHHHHHHHhcC---CCHHHHHHHH
Q psy879          129 FALACNNS---EKIIEPIQSRC--AMLRYNKLTDAQLLSKVIEICEK--ENISHTNDGLEAIVFTAQ---GDMRQALNNL  198 (317)
Q Consensus       129 ~il~~~~~---~~l~~~i~sR~--~~i~f~~~~~~~~~~~l~~~~~~--~~~~i~~~~~~~l~~~~~---gd~r~~i~~l  198 (317)
                      +|+++|..   ..+.+.+.+|+  ..+.|++++.+++..++...+..  .+..+++++++.++..++   ||+|.+++.+
T Consensus       170 ~I~~t~~~~~~~~l~~~l~~r~~~~~i~l~~l~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~~~~~~G~~r~~~~~l  249 (387)
T 2v1u_A          170 LVGITNSLGFVENLEPRVKSSLGEVELVFPPYTAPQLRDILETRAEEAFNPGVLDPDVVPLCAALAAREHGDARRALDLL  249 (387)
T ss_dssp             EEEECSCSTTSSSSCHHHHTTTTSEECCBCCCCHHHHHHHHHHHHHHHBCTTTBCSSHHHHHHHHHHSSSCCHHHHHHHH
T ss_pred             EEEEECCCchHhhhCHHHHhcCCCeEEeeCCCCHHHHHHHHHHHHHhhccCCCCCHHHHHHHHHHHHHhccCHHHHHHHH
Confidence            89999887   67899999999  56999999999999999999876  456788999999999988   9999999999


Q ss_pred             HHhhh-----CCCcccHHHHHhhcCCCCHHHHHHHHHHHhcCCHHHHHHHHHHH-HHcC---CCHHHHHHHHHHHHHhcC
Q psy879          199 QSTHN-----GFGHVTAEYVFKVCDEPHPLAVKEMLLNCVEGNMKDSYKIIHHL-YKLG---YAPEDIIGNIFRVAKTLD  269 (317)
Q Consensus       199 ~~~~~-----~~~~i~~~~v~~~~~~~~~~~i~~l~~~~~~~~~~~~~~~~~~l-~~~~---~~~~~i~~~~~~~~~~~~  269 (317)
                      +.++.     +...|+.+++..+.......   .+.+.+..-+..+...++.-+ +..|   ....+++..+...++..+
T Consensus       250 ~~a~~~a~~~~~~~i~~~~v~~a~~~~~~~---~~~~~~~~l~~~~~~~l~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~  326 (387)
T 2v1u_A          250 RVAGEIAERRREERVRREHVYSARAEIERD---RVSEVVRTLPLHAKLVLLSIMMLEDGGRPASTGEIYERYKELTSTLG  326 (387)
T ss_dssp             HHHHHHHHHTTCSCBCHHHHHHHHHHHHHH---HHHHHHHSSCHHHHHHHHHHHHHSSSSCCEEHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHcCCCCcCHHHHHHHHHHHhhc---hHHHHHHcCCHHHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHhcC
Confidence            87654     44679999998876554332   233444455555544444333 2123   345677777777777766


Q ss_pred             CChHHHHHHHHHHHHHHh
Q psy879          270 IPEPLKLSIIQEIGNVHL  287 (317)
Q Consensus       270 ~~~~~~~~~~~~l~~~~~  287 (317)
                      ..+.....+...+.++..
T Consensus       327 ~~~~~~~~~~~~l~~L~~  344 (387)
T 2v1u_A          327 LEHVTLRRVSGIISELDM  344 (387)
T ss_dssp             CCCCCHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHh
Confidence            655555555555555443

>3bos_A Putative DNA replication factor; P-loop containing nucleoside triphosphate hydrolases, struct genomics; HET: MSE CDP; 1.75A {Shewanella amazonensis} PDB: 3sc3_A

Probab=99.92  E-value=6.8e-24  Score=177.93  Aligned_cols=204  Identities=13%  Similarity=0.169  Sum_probs=156.2

Q ss_pred             cccCC-CCCCcccC---CHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHH
Q psy879            2 EKYRP-QTFSDIVG---NEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDT   77 (317)
Q Consensus         2 ~ky~P-~~~~~~~g---~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~   77 (317)
                      .+|+| .+|+++++   ++++++.+..++..+..++++|+||||+|||++++++++.+....  ..+..+++.....  .
T Consensus        19 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~ll~G~~G~GKT~la~~l~~~~~~~~--~~~~~~~~~~~~~--~   94 (242)
T 3bos_A           19 VHLPDDETFTSYYPAAGNDELIGALKSAASGDGVQAIYLWGPVKSGRTHLIHAACARANELE--RRSFYIPLGIHAS--I   94 (242)
T ss_dssp             CCCCTTCSTTTSCC--CCHHHHHHHHHHHHTCSCSEEEEECSTTSSHHHHHHHHHHHHHHTT--CCEEEEEGGGGGG--S
T ss_pred             CCCCCCCChhhccCCCCCHHHHHHHHHHHhCCCCCeEEEECCCCCCHHHHHHHHHHHHHHcC--CeEEEEEHHHHHH--H
Confidence            46788 78999997   368888899988876666799999999999999999999875442  3344444332111  0


Q ss_pred             HHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHH--HHHHHHHhhhccCC--ceEEEEecCCC----cCchhHhhhc--
Q psy879           78 VRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGA--QQALRRTMEIYSNT--TRFALACNNSE----KIIEPIQSRC--  147 (317)
Q Consensus        78 i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~--~~~ll~~le~~~~~--~~~il~~~~~~----~l~~~i~sR~--  147 (317)
                      +.+.+.         ....+.+++|||++.+....  ++.|+.+++.....  ..+|++++...    ...+.+.+||  
T Consensus        95 ~~~~~~---------~~~~~~vliiDe~~~~~~~~~~~~~l~~~l~~~~~~~~~~ii~~~~~~~~~~~~~~~~l~~r~~~  165 (242)
T 3bos_A           95 STALLE---------GLEQFDLICIDDVDAVAGHPLWEEAIFDLYNRVAEQKRGSLIVSASASPMEAGFVLPDLVSRMHW  165 (242)
T ss_dssp             CGGGGT---------TGGGSSEEEEETGGGGTTCHHHHHHHHHHHHHHHHHCSCEEEEEESSCTTTTTCCCHHHHHHHHH
T ss_pred             HHHHHH---------hccCCCEEEEeccccccCCHHHHHHHHHHHHHHHHcCCCeEEEEcCCCHHHHHHhhhhhhhHhhc
Confidence            000010         01356899999999997655  88888888765432  24777777543    4569999999  


Q ss_pred             -ceeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhh----CCCcccHHHHHhhcC
Q psy879          148 -AMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHN----GFGHVTAEYVFKVCD  218 (317)
Q Consensus       148 -~~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~----~~~~i~~~~v~~~~~  218 (317)
                       ..+.|++|+.+++.+++...+...++.+++++++.++..++||+|.+.+.++.+..    ..+.|+.+++.+++.
T Consensus       166 ~~~i~l~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~g~~r~l~~~l~~~~~~a~~~~~~It~~~v~~~l~  241 (242)
T 3bos_A          166 GLTYQLQPMMDDEKLAALQRRAAMRGLQLPEDVGRFLLNRMARDLRTLFDVLDRLDKASMVHQRKLTIPFVKEMLR  241 (242)
T ss_dssp             SEEEECCCCCGGGHHHHHHHHHHHTTCCCCHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHTCCCCHHHHHHHHT
T ss_pred             CceEEeCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHccCCHHHHHHHHHHHHHHHHHhCCCCcHHHHHHHhh
Confidence             78999999999999999999999999999999999999999999999999987543    356799988877653

>2qby_B CDC6 homolog 3, cell division control protein 6 homolog 3; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus}

Probab=99.90  E-value=1.7e-22  Score=181.21  Aligned_cols=269  Identities=13%  Similarity=0.050  Sum_probs=177.8

Q ss_pred             ccCCCCCCcccCCHHHHHHHHHHHh----cCCCceEEEECCCCCCHHHHHHHHHHHHcCC-----CC-CCceEEecCCCC
Q psy879            3 KYRPQTFSDIVGNEDTVERLKVFSS----SGNVPNIIISGPPGVGKTTTILCLARILLGP-----SF-KDAVLELNASND   72 (317)
Q Consensus         3 ky~P~~~~~~~g~~~~~~~l~~~l~----~~~~~~~ll~G~~G~GKt~la~~la~~l~~~-----~~-~~~~~~~~~~~~   72 (317)
                      +|+|   ++++|+++.++.+..++.    .+.+++++|+||||+|||++++.+++.+...     .. +..++.+++...
T Consensus        16 ~~~p---~~l~gr~~~~~~l~~~l~~~~~~~~~~~vll~G~~G~GKT~la~~l~~~~~~~~~~~~~~~~~~~~~i~~~~~   92 (384)
T 2qby_B           16 LSVF---KEIPFREDILRDAAIAIRYFVKNEVKFSNLFLGLTGTGKTFVSKYIFNEIEEVKKEDEEYKDVKQAYVNCREV   92 (384)
T ss_dssp             HHHC---SSCTTCHHHHHHHHHHHHHHHTTCCCCEEEEEECTTSSHHHHHHHHHHHHHHHHHHSSSSTTCEEEEEEHHHH
T ss_pred             ccCC---CCCCChHHHHHHHHHHHHHHHcCCCCCcEEEECCCCCCHHHHHHHHHHHHHHHhhhhcCCCCceEEEEECccC
Confidence            5666   789999999888776554    3444569999999999999999999987332     11 445666665432


Q ss_pred             c-ChHH-HHHHHHH-------------------HHhhcccCCCCceeEEEEeCCCCCCHHH-HHH-HHHHhhhccCCceE
Q psy879           73 R-GIDT-VRNKIKM-------------------FAQQKVTLPPGRHKIVILDEADSMTDGA-QQA-LRRTMEIYSNTTRF  129 (317)
Q Consensus        73 ~-~~~~-i~~~~~~-------------------~~~~~~~~~~~~~~vliiDE~d~l~~~~-~~~-ll~~le~~~~~~~~  129 (317)
                      . .... +...+..                   +....   . ....+|+|||+|.+.... ++. +..+++.. .++.+
T Consensus        93 ~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~l~~~l---~-~~~~vlilDEi~~l~~~~~~~~~l~~l~~~~-~~~~i  167 (384)
T 2qby_B           93 GGTPQAVLSSLAGKLTGFSVPKHGINLGEYIDKIKNGT---R-NIRAIIYLDEVDTLVKRRGGDIVLYQLLRSD-ANISV  167 (384)
T ss_dssp             CSCHHHHHHHHHHHHHCSCCCSSSSCTHHHHHHHHHHH---S-SSCEEEEEETTHHHHHSTTSHHHHHHHHTSS-SCEEE
T ss_pred             CCCHHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHHh---c-cCCCEEEEECHHHhccCCCCceeHHHHhcCC-cceEE
Confidence            2 2111 1111111                   11110   0 122399999999987643 555 55555544 67889


Q ss_pred             EEEecCC---CcCchhHhhhc-ceeeecCCCHHHHHHHHHHHHHH--cCCCCCHHHHHHHHHhcC---CCHHHHHHHHHH
Q psy879          130 ALACNNS---EKIIEPIQSRC-AMLRYNKLTDAQLLSKVIEICEK--ENISHTNDGLEAIVFTAQ---GDMRQALNNLQS  200 (317)
Q Consensus       130 il~~~~~---~~l~~~i~sR~-~~i~f~~~~~~~~~~~l~~~~~~--~~~~i~~~~~~~l~~~~~---gd~r~~i~~l~~  200 (317)
                      |++++..   ..+.+++.+|+ ..+.|+|++.+++..++..++..  .+..+++++++.++..++   ||+|.+++.++.
T Consensus       168 I~~t~~~~~~~~l~~~l~sr~~~~i~l~~l~~~~~~~il~~~~~~~~~~~~~~~~~~~~i~~~~~~~~G~~r~a~~~l~~  247 (384)
T 2qby_B          168 IMISNDINVRDYMEPRVLSSLGPSVIFKPYDAEQLKFILSKYAEYGLIKGTYDDEILSYIAAISAKEHGDARKAVNLLFR  247 (384)
T ss_dssp             EEECSSTTTTTTSCHHHHHTCCCEEEECCCCHHHHHHHHHHHHHHTSCTTSCCSHHHHHHHHHHHTTCCCHHHHHHHHHH
T ss_pred             EEEECCCchHhhhCHHHHhcCCCeEEECCCCHHHHHHHHHHHHHhhcccCCcCHHHHHHHHHHHHhccCCHHHHHHHHHH
Confidence            9999886   67899999995 67999999999999999998875  446788999999999888   999999999987


Q ss_pred             hhh---CCCcccHHHHHhhcCCCCHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhcCCChHHHHH
Q psy879          201 THN---GFGHVTAEYVFKVCDEPHPLAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDIIGNIFRVAKTLDIPEPLKLS  277 (317)
Q Consensus       201 ~~~---~~~~i~~~~v~~~~~~~~~~~i~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~  277 (317)
                      ++.   +...|+.+++..++.......   +.+.+..-+..+. .++..+.. +....++...+..+++.++..+.....
T Consensus       248 a~~~a~~~~~i~~~~v~~~~~~~~~~~---~~~~~~~l~~~~~-~~l~al~~-~~~~~~~~~~~~~~~~~~g~~~~~~~~  322 (384)
T 2qby_B          248 AAQLASGGGIIRKEHVDKAIVDYEQER---LIEAVKALPFHYK-LALRSLIE-SEDVMSAHKMYTDLCNKFKQKPLSYRR  322 (384)
T ss_dssp             HHHHTTSSSCCCHHHHHHHHHHHHHHH---HHHHHHSSCHHHH-HHHHHHHT-CCBHHHHHHHHHHHHHHTTCCCCCHHH
T ss_pred             HHHHhcCCCccCHHHHHHHHHHHhcch---HHHHHHcCCHHHH-HHHHHHHH-hcccChHHHHHHHHHHHcCCCCCCHHH
Confidence            654   346799999988766543322   2233333333332 23333333 333245666666777766655544444


Q ss_pred             HHHHHHH
Q psy879          278 IIQEIGN  284 (317)
Q Consensus       278 ~~~~l~~  284 (317)
                      ++..+..
T Consensus       323 ~~~~l~~  329 (384)
T 2qby_B          323 FSDIISE  329 (384)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            4444444

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=99.90  E-value=5.3e-22  Score=178.21  Aligned_cols=187  Identities=17%  Similarity=0.204  Sum_probs=145.3

Q ss_pred             CcccCCCCCCcccCCHHHHHHHHHHHhc------------CCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEec
Q psy879            1 IEKYRPQTFSDIVGNEDTVERLKVFSSS------------GNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELN   68 (317)
Q Consensus         1 ~~ky~P~~~~~~~g~~~~~~~l~~~l~~------------~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~   68 (317)
                      +++|+|.+|++++|++.+++.+..++..            ....++||+||||||||++|+++++.+     +..++.++
T Consensus       106 ~~~~~~~~~~~iiG~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~vLL~GppGtGKT~la~aia~~~-----~~~~~~v~  180 (389)
T 3vfd_A          106 VDNGTAVKFDDIAGQDLAKQALQEIVILPSLRPELFTGLRAPARGLLLFGPPGNGKTMLAKAVAAES-----NATFFNIS  180 (389)
T ss_dssp             BCCSCCCCGGGSCSCHHHHHHHHHHTHHHHHCTTTSCGGGCCCSEEEEESSTTSCHHHHHHHHHHHT-----TCEEEEEC
T ss_pred             hccCCCCChHHhCCHHHHHHHHHHHHHHhccCHHHhcccCCCCceEEEECCCCCCHHHHHHHHHHhh-----cCcEEEee
Confidence            3689999999999999999999887721            123469999999999999999999985     34577777


Q ss_pred             CCCCcC------hHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCC-----------HHHHHHHHHHhhhc----cCCc
Q psy879           69 ASNDRG------IDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMT-----------DGAQQALRRTMEIY----SNTT  127 (317)
Q Consensus        69 ~~~~~~------~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~-----------~~~~~~ll~~le~~----~~~~  127 (317)
                      +....+      ...++..+.....       ..+.||+|||+|.+.           ...++.|+..++..    +..+
T Consensus       181 ~~~l~~~~~g~~~~~~~~~~~~a~~-------~~~~il~iDEid~l~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~v  253 (389)
T 3vfd_A          181 AASLTSKYVGEGEKLVRALFAVARE-------LQPSIIFIDQVDSLLCERREGEHDASRRLKTEFLIEFDGVQSAGDDRV  253 (389)
T ss_dssp             SCCC-------CHHHHHHHHHHHHH-------SSSEEEEEETGGGGC--------CTHHHHHHHHHHHHHHHC-----CE
T ss_pred             HHHhhccccchHHHHHHHHHHHHHh-------cCCeEEEEECchhhcccCCCccchHHHHHHHHHHHHhhcccccCCCCE
Confidence            754322      1223333332221       246799999999883           34566788877743    4567


Q ss_pred             eEEEEecCCCcCchhHhhhcc-eeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHH
Q psy879          128 RFALACNNSEKIIEPIQSRCA-MLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQ  199 (317)
Q Consensus       128 ~~il~~~~~~~l~~~i~sR~~-~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~  199 (317)
                      ++|++||.++.+.+++.+||. .+.|+.|+.++...++..++...+..++++.+..++..+.|..+..+..|.
T Consensus       254 ~vI~atn~~~~l~~~l~~R~~~~i~i~~p~~~~r~~il~~~~~~~~~~l~~~~~~~la~~~~g~~~~~l~~L~  326 (389)
T 3vfd_A          254 LVMGATNRPQELDEAVLRRFIKRVYVSLPNEETRLLLLKNLLCKQGSPLTQKELAQLARMTDGYSGSDLTALA  326 (389)
T ss_dssp             EEEEEESCGGGCCHHHHTTCCEEEECCCCCHHHHHHHHHHHHTTSCCCSCHHHHHHHHHHTTTCCHHHHHHHH
T ss_pred             EEEEecCCchhcCHHHHcCcceEEEcCCcCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHcCCCCHHHHHHHH
Confidence            888899999999999999997 599999999999999999999888899999999999999998887666654

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=99.90  E-value=1.8e-21  Score=168.53  Aligned_cols=207  Identities=15%  Similarity=0.176  Sum_probs=153.4

Q ss_pred             cccCCCCCCcccCCHHHHHHHHHHHhc------------CCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecC
Q psy879            2 EKYRPQTFSDIVGNEDTVERLKVFSSS------------GNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNA   69 (317)
Q Consensus         2 ~ky~P~~~~~~~g~~~~~~~l~~~l~~------------~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~   69 (317)
                      ++|+|.+|++++|++.+++.+..++..            ....+++|+||||||||++++++++.+.     ..++.+++
T Consensus        13 ~~~~~~~~~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vll~Gp~GtGKT~la~~la~~~~-----~~~~~i~~   87 (297)
T 3b9p_A           13 EGGAKVEWTDIAGQDVAKQALQEMVILPSVRPELFTGLRAPAKGLLLFGPPGNGKTLLARAVATECS-----ATFLNISA   87 (297)
T ss_dssp             CCSSCCCGGGSCCCHHHHHHHHHHTHHHHHCGGGSCGGGCCCSEEEEESSSSSCHHHHHHHHHHHTT-----CEEEEEES
T ss_pred             cCCCCCCHHHhCChHHHHHHHHHHHHhhhhCHHHHhcCCCCCCeEEEECcCCCCHHHHHHHHHHHhC-----CCeEEeeH
Confidence            678899999999999999999887642            1233599999999999999999999862     34566665


Q ss_pred             CCCc------ChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCC-----------HHHHHHHHHHhhhcc-----CCc
Q psy879           70 SNDR------GIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMT-----------DGAQQALRRTMEIYS-----NTT  127 (317)
Q Consensus        70 ~~~~------~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~-----------~~~~~~ll~~le~~~-----~~~  127 (317)
                      ....      ....++..+.....       ..+.+++|||+|.+.           ...++.|+..++..+     ..+
T Consensus        88 ~~l~~~~~~~~~~~~~~~~~~~~~-------~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~v  160 (297)
T 3b9p_A           88 ASLTSKYVGDGEKLVRALFAVARH-------MQPSIIFIDEVDSLLSERSSSEHEASRRLKTEFLVEFDGLPGNPDGDRI  160 (297)
T ss_dssp             TTTSSSSCSCHHHHHHHHHHHHHH-------TCSEEEEEETGGGTSBCC-----CCSHHHHHHHHHHHHHCC------CE
T ss_pred             HHHhhcccchHHHHHHHHHHHHHH-------cCCcEEEeccHHHhccccccCcchHHHHHHHHHHHHHhcccccCCCCcE
Confidence            4321      11223333333221       357899999999884           345677888888764     347


Q ss_pred             eEEEEecCCCcCchhHhhhcce-eeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHH-HHHhhh--
Q psy879          128 RFALACNNSEKIIEPIQSRCAM-LRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNN-LQSTHN--  203 (317)
Q Consensus       128 ~~il~~~~~~~l~~~i~sR~~~-i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~-l~~~~~--  203 (317)
                      .+|++||.++.+.+++.+||.. +.|+.|+.++...++...+...+..++++.+..++..+.|..+..+.. ++.++.  
T Consensus       161 ~vi~~tn~~~~l~~~l~~R~~~~i~~~~p~~~~r~~il~~~~~~~~~~~~~~~~~~la~~~~g~~~~~l~~l~~~a~~~a  240 (297)
T 3b9p_A          161 VVLAATNRPQELDEAALRRFTKRVYVSLPDEQTRELLLNRLLQKQGSPLDTEALRRLAKITDGYSGSDLTALAKDAALEP  240 (297)
T ss_dssp             EEEEEESCGGGBCHHHHHHCCEEEECCCCCHHHHHHHHHHHHGGGSCCSCHHHHHHHHHHTTTCCHHHHHHHHHHHTTHH
T ss_pred             EEEeecCChhhCCHHHHhhCCeEEEeCCcCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHcCCCCHHHHHHHHHHHHHHH
Confidence            7888999999999999999965 899999999999999999988888889999999999999977765543 443321  


Q ss_pred             ---------------CCCcccHHHHHhhcCCC
Q psy879          204 ---------------GFGHVTAEYVFKVCDEP  220 (317)
Q Consensus       204 ---------------~~~~i~~~~v~~~~~~~  220 (317)
                                     ....|+.+++..++...
T Consensus       241 ~r~~~~~~~~~~~~~~~~~i~~~d~~~a~~~~  272 (297)
T 3b9p_A          241 IRELNVEQVKCLDISAMRAITEQDFHSSLKRI  272 (297)
T ss_dssp             HHTCC--------CCCCCCCCHHHHHHHTTSC
T ss_pred             HHHHhhhhcccccccccCCcCHHHHHHHHHHc
Confidence                           12356777776665543

>2qby_A CDC6 homolog 1, cell division control protein 6 homolog 1; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus}

Probab=99.89  E-value=6.2e-22  Score=177.39  Aligned_cols=258  Identities=17%  Similarity=0.190  Sum_probs=171.0

Q ss_pred             ccCCCCCCcccCCHHHHHHHHHHHhc----CCCceEEEECCCCCCHHHHHHHHHHHHcCCCC-CCceEEecCCCC-----
Q psy879            3 KYRPQTFSDIVGNEDTVERLKVFSSS----GNVPNIIISGPPGVGKTTTILCLARILLGPSF-KDAVLELNASND-----   72 (317)
Q Consensus         3 ky~P~~~~~~~g~~~~~~~l~~~l~~----~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~-~~~~~~~~~~~~-----   72 (317)
                      +|.|   ++++|+++.++.+..++..    +...+++|+||+|+|||++++.+++.+..... +..++.+++...     
T Consensus        16 ~~~p---~~~~gr~~e~~~l~~~l~~~~~~~~~~~vli~G~~G~GKTtl~~~l~~~~~~~~~~~~~~~~i~~~~~~~~~~   92 (386)
T 2qby_A           16 DYIP---DELPHREDQIRKIASILAPLYREEKPNNIFIYGLTGTGKTAVVKFVLSKLHKKFLGKFKHVYINTRQIDTPYR   92 (386)
T ss_dssp             SCCC---SCCTTCHHHHHHHHHSSGGGGGTCCCCCEEEEECTTSSHHHHHHHHHHHHHHHTCSSCEEEEEEHHHHCSHHH
T ss_pred             ccCC---CCCCChHHHHHHHHHHHHHHHcCCCCCeEEEECCCCCCHHHHHHHHHHHHHHHhcCCceEEEEECCCCCCHHH
Confidence            4555   7899999999999888773    34446999999999999999999998743211 334455543211     


Q ss_pred             -----------------cChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCC----HHHHHHHHHHhhh-ccCCceEE
Q psy879           73 -----------------RGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMT----DGAQQALRRTMEI-YSNTTRFA  130 (317)
Q Consensus        73 -----------------~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~----~~~~~~ll~~le~-~~~~~~~i  130 (317)
                                       .....+.+.+......     .+.+.+++|||++.+.    .+....|++.++. ...++.+|
T Consensus        93 ~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~-----~~~~~vlilDE~~~l~~~~~~~~l~~l~~~~~~~~~~~~~~I  167 (386)
T 2qby_A           93 VLADLLESLDVKVPFTGLSIAELYRRLVKAVRD-----YGSQVVIVLDEIDAFVKKYNDDILYKLSRINSEVNKSKISFI  167 (386)
T ss_dssp             HHHHHTTTTSCCCCSSSCCHHHHHHHHHHHHHT-----CCSCEEEEEETHHHHHHSSCSTHHHHHHHHHHSCCC--EEEE
T ss_pred             HHHHHHHHhCCCCCCCCCCHHHHHHHHHHHHhc-----cCCeEEEEEcChhhhhccCcCHHHHHHhhchhhcCCCeEEEE
Confidence                             1122222222222211     1347899999999986    4456667776754 34567788


Q ss_pred             EEecCC---CcCchhHhhhc--ceeeecCCCHHHHHHHHHHHHHHc--CCCCCHHHHHHHHHhcC---CCHHHHHHHHHH
Q psy879          131 LACNNS---EKIIEPIQSRC--AMLRYNKLTDAQLLSKVIEICEKE--NISHTNDGLEAIVFTAQ---GDMRQALNNLQS  200 (317)
Q Consensus       131 l~~~~~---~~l~~~i~sR~--~~i~f~~~~~~~~~~~l~~~~~~~--~~~i~~~~~~~l~~~~~---gd~r~~i~~l~~  200 (317)
                      ++++..   ..+.+.+.+|+  ..+.|++++.+++.+++...+...  ...+++++++.++..++   |++|.+++.++.
T Consensus       168 ~~~~~~~~~~~~~~~~~~r~~~~~i~l~~l~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~~~~~~G~~r~~~~ll~~  247 (386)
T 2qby_A          168 GITNDVKFVDLLDPRVKSSLSEEEIIFPPYNAEELEDILTKRAQMAFKPGVLPDNVIKLCAALAAREHGDARRALDLLRV  247 (386)
T ss_dssp             EEESCGGGGGGCTTHHHHTTTTEEEEECCCCHHHHHHHHHHHHHHHBCSSCSCHHHHHHHHHHHHHTTCCHHHHHHHHHH
T ss_pred             EEECCCChHhhhCHHHhccCCCeeEEeCCCCHHHHHHHHHHHHHhhccCCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHH
Confidence            888876   46788999999  579999999999999999987653  35788999999998888   999999999887


Q ss_pred             hhh-----CCCcccHHHHHhhcCCCCHHHHHHHHHHHhcCCHHHHHHHHHHHH---HcCCC---HHHHHHHHHHHHHhcC
Q psy879          201 THN-----GFGHVTAEYVFKVCDEPHPLAVKEMLLNCVEGNMKDSYKIIHHLY---KLGYA---PEDIIGNIFRVAKTLD  269 (317)
Q Consensus       201 ~~~-----~~~~i~~~~v~~~~~~~~~~~i~~l~~~~~~~~~~~~~~~~~~l~---~~~~~---~~~i~~~~~~~~~~~~  269 (317)
                      ++.     +...|+.+++..+........   +.+.+..-. .....++..+.   ..|..   ..+++..+..+++.++
T Consensus       248 a~~~a~~~~~~~i~~~~v~~a~~~~~~~~---~~~~~~~l~-~~~~~il~ai~~~~~~g~~~~~~~~l~~~~~~~~~~~g  323 (386)
T 2qby_A          248 SGEIAERMKDTKVKEEYVYMAKEEIERDR---VRDIILTLP-FHSKLVLMAVVSISSEENVVSTTGAVYETYLNICKKLG  323 (386)
T ss_dssp             HHHHHHHTTCSSCCHHHHHHHHHHHHHHH---HHHHHHTSC-HHHHHHHHHHHHHC-----CEEHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHhcCCCccCHHHHHHHHHHHhhch---HHHHHHcCC-HHHHHHHHHHHHHHhcCCCceeHHHHHHHHHHHHHhcC
Confidence            553     445899999988765543322   222222222 22222333332   23433   4777777777777666


Q ss_pred             CCh
Q psy879          270 IPE  272 (317)
Q Consensus       270 ~~~  272 (317)
                      ..+
T Consensus       324 ~~~  326 (386)
T 2qby_A          324 VEA  326 (386)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            555

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=99.89  E-value=2.3e-22  Score=175.09  Aligned_cols=182  Identities=19%  Similarity=0.264  Sum_probs=142.2

Q ss_pred             cccCCHHHHHHHHHHHh---------------cCCCceEEEECCCCCCHHHHHHHHHHHHcCCCC--CCceEEecCCCCc
Q psy879           11 DIVGNEDTVERLKVFSS---------------SGNVPNIIISGPPGVGKTTTILCLARILLGPSF--KDAVLELNASNDR   73 (317)
Q Consensus        11 ~~~g~~~~~~~l~~~l~---------------~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~--~~~~~~~~~~~~~   73 (317)
                      +++|++.+++.+...+.               .....+++|+||||||||++|+++++.+.....  ...++.+++....
T Consensus        32 ~i~G~~~~~~~l~~~~~~~~~~~~~~~~g~~~~~~~~~vll~G~~GtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~l~  111 (309)
T 3syl_A           32 ELIGLKPVKDRIRETAALLLVERARQKLGLAHETPTLHMSFTGNPGTGKTTVALKMAGLLHRLGYVRKGHLVSVTRDDLV  111 (309)
T ss_dssp             HSSSCHHHHHHHHHHHHHHHHHHHHHHHTCCSSCCCCEEEEEECTTSSHHHHHHHHHHHHHHTTSSSSCCEEEECGGGTC
T ss_pred             HccChHHHHHHHHHHHHHHHhHHHHHHcCCCCCCCCceEEEECCCCCCHHHHHHHHHHHHHhcCCcCCCcEEEEcHHHhh
Confidence            69999999998886654               223346999999999999999999999854322  3356666654321


Q ss_pred             ----C--hHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCC---------CHHHHHHHHHHhhhccCCceEEEEecCCC-
Q psy879           74 ----G--IDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSM---------TDGAQQALRRTMEIYSNTTRFALACNNSE-  137 (317)
Q Consensus        74 ----~--~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l---------~~~~~~~ll~~le~~~~~~~~il~~~~~~-  137 (317)
                          +  ...+...+..          ..+.+++|||+|.+         ..+.++.|++.+++.+.++.+|++++... 
T Consensus       112 ~~~~g~~~~~~~~~~~~----------~~~~vl~iDEid~l~~~~~~~~~~~~~~~~Ll~~l~~~~~~~~~i~~~~~~~~  181 (309)
T 3syl_A          112 GQYIGHTAPKTKEVLKR----------AMGGVLFIDEAYYLYRPDNERDYGQEAIEILLQVMENNRDDLVVILAGYADRM  181 (309)
T ss_dssp             CSSTTCHHHHHHHHHHH----------HTTSEEEEETGGGSCCCC---CCTHHHHHHHHHHHHHCTTTCEEEEEECHHHH
T ss_pred             hhcccccHHHHHHHHHh----------cCCCEEEEEChhhhccCCCcccccHHHHHHHHHHHhcCCCCEEEEEeCChHHH
Confidence                1  1122222221          13469999999977         77889999999999888899999987643 


Q ss_pred             ----cCchhHhhhc-ceeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHh--------cCCCHHHHHHHHHHhh
Q psy879          138 ----KIIEPIQSRC-AMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFT--------AQGDMRQALNNLQSTH  202 (317)
Q Consensus       138 ----~l~~~i~sR~-~~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~--------~~gd~r~~i~~l~~~~  202 (317)
                          .+.+++++|| ..+.|++|+.+++..++..++...+..++++++..++..        ..||+|.+.+.++.++
T Consensus       182 ~~~~~~~~~l~~R~~~~i~~~~~~~~~~~~il~~~l~~~~~~~~~~~~~~l~~~~~~~~~~~~~gn~r~l~~~l~~a~  259 (309)
T 3syl_A          182 ENFFQSNPGFRSRIAHHIEFPDYSDEELFEIAGHMLDDQNYQMTPEAETALRAYIGLRRNQPHFANARSIRNALDRAR  259 (309)
T ss_dssp             HHHHHHSTTHHHHEEEEEEECCCCHHHHHHHHHHHHHHTTCEECHHHHHHHHHHHHHHTTSSSCCHHHHHHHHHHHHH
T ss_pred             HHHHhhCHHHHHhCCeEEEcCCcCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHhccCCCCCcHHHHHHHHHHHH
Confidence                3469999999 679999999999999999999999999999999998875        4589999999998765

>2z4s_A Chromosomal replication initiator protein DNAA; AAA+ ATPase, domain III (ATPase domain), ATP-binding, cytoplasm, DNA replication; HET: ADP; 3.00A {Thermotoga maritima} PDB: 2z4r_A*

Probab=99.89  E-value=4.3e-22  Score=181.02  Aligned_cols=211  Identities=14%  Similarity=0.191  Sum_probs=156.3

Q ss_pred             cCCC-CCCccc-C--CHHHHHHHHHHHhcCC-CceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHH
Q psy879            4 YRPQ-TFSDIV-G--NEDTVERLKVFSSSGN-VPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTV   78 (317)
Q Consensus         4 y~P~-~~~~~~-g--~~~~~~~l~~~l~~~~-~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i   78 (317)
                      ..|+ +|++++ |  +......+........ +++++||||||+|||++++++++.+.....+..++.+++...  ...+
T Consensus        98 l~~~~tfd~fv~g~~n~~a~~~~~~~a~~~~~~~~lll~Gp~G~GKTtLa~aia~~l~~~~~~~~v~~v~~~~~--~~~~  175 (440)
T 2z4s_A           98 LNPDYTFENFVVGPGNSFAYHAALEVAKHPGRYNPLFIYGGVGLGKTHLLQSIGNYVVQNEPDLRVMYITSEKF--LNDL  175 (440)
T ss_dssp             CCTTCSGGGCCCCTTTHHHHHHHHHHHHSTTSSCCEEEECSSSSSHHHHHHHHHHHHHHHCCSSCEEEEEHHHH--HHHH
T ss_pred             CCCCCChhhcCCCCchHHHHHHHHHHHhCCCCCCeEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEeeHHHH--HHHH
Confidence            3454 699988 5  4455556666666543 556999999999999999999998854333445566554321  1111


Q ss_pred             HHHHH-----HHHhhcccCCCC-ceeEEEEeCCCCCCH--HHHHHHHHHhhhcc-CCceEEEEecCC-C---cCchhHhh
Q psy879           79 RNKIK-----MFAQQKVTLPPG-RHKIVILDEADSMTD--GAQQALRRTMEIYS-NTTRFALACNNS-E---KIIEPIQS  145 (317)
Q Consensus        79 ~~~~~-----~~~~~~~~~~~~-~~~vliiDE~d~l~~--~~~~~ll~~le~~~-~~~~~il~~~~~-~---~l~~~i~s  145 (317)
                      .+.+.     .+....     . .+.+++|||++.+..  ..++.|+..++... ....+|++|+.+ .   .+.+++.|
T Consensus       176 ~~~~~~~~~~~~~~~~-----~~~~~vL~IDEi~~l~~~~~~q~~l~~~l~~l~~~~~~iIitt~~~~~~l~~l~~~L~s  250 (440)
T 2z4s_A          176 VDSMKEGKLNEFREKY-----RKKVDILLIDDVQFLIGKTGVQTELFHTFNELHDSGKQIVICSDREPQKLSEFQDRLVS  250 (440)
T ss_dssp             HHHHHTTCHHHHHHHH-----TTTCSEEEEECGGGGSSCHHHHHHHHHHHHHHHTTTCEEEEEESSCGGGCSSCCHHHHH
T ss_pred             HHHHHcccHHHHHHHh-----cCCCCEEEEeCcccccCChHHHHHHHHHHHHHHHCCCeEEEEECCCHHHHHHHHHHHHh
Confidence            11111     111111     2 577999999999986  68889999988643 345677777764 3   37899999


Q ss_pred             hc---ceeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhh----CCCcccHHHHHhhcC
Q psy879          146 RC---AMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHN----GFGHVTAEYVFKVCD  218 (317)
Q Consensus       146 R~---~~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~----~~~~i~~~~v~~~~~  218 (317)
                      ||   ..+.|++|+.+++..++...+...++.+++++++.++..++||+|.+.+.++.+..    ....|+.+++.+++.
T Consensus       251 R~~~g~~i~l~~p~~e~r~~iL~~~~~~~~~~i~~e~l~~la~~~~gn~R~l~~~L~~~~~~a~~~~~~It~~~~~~~l~  330 (440)
T 2z4s_A          251 RFQMGLVAKLEPPDEETRKSIARKMLEIEHGELPEEVLNFVAENVDDNLRRLRGAIIKLLVYKETTGKEVDLKEAILLLK  330 (440)
T ss_dssp             HHHSSBCCBCCCCCHHHHHHHHHHHHHHHTCCCCTTHHHHHHHHCCSCHHHHHHHHHHHHHHHHHSSSCCCHHHHHHHTS
T ss_pred             hccCCeEEEeCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHH
Confidence            99   57999999999999999999999999999999999999999999999999987543    345799999998877


Q ss_pred             CCC
Q psy879          219 EPH  221 (317)
Q Consensus       219 ~~~  221 (317)
                      ...
T Consensus       331 ~~~  333 (440)
T 2z4s_A          331 DFI  333 (440)
T ss_dssp             TTT
T ss_pred             HHh
Confidence            543

>3eie_A Vacuolar protein sorting-associated protein 4; AAA ATPase, ATP-binding cassette, ATP-binding, endosome, MEM nucleotide-binding; 2.70A {Saccharomyces cerevisiae} PDB: 3eih_A* 2rko_A 3mhv_C

Probab=99.88  E-value=1.8e-21  Score=170.43  Aligned_cols=187  Identities=17%  Similarity=0.156  Sum_probs=141.6

Q ss_pred             cccCCCCCCcccCCHHHHHHHHHHHh----------c-CCC-ceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecC
Q psy879            2 EKYRPQTFSDIVGNEDTVERLKVFSS----------S-GNV-PNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNA   69 (317)
Q Consensus         2 ~ky~P~~~~~~~g~~~~~~~l~~~l~----------~-~~~-~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~   69 (317)
                      +++.+.+|++++|++.+++.|..++.          . +.+ .++|||||||||||++|+++++.+.     ..++.+++
T Consensus        10 ~~~~~~~~~di~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vLl~GppGtGKT~la~aia~~~~-----~~~~~v~~   84 (322)
T 3eie_A           10 SEKPNVKWEDVAGLEGAKEALKEAVILPVKFPHLFKGNRKPTSGILLYGPPGTGKSYLAKAVATEAN-----STFFSVSS   84 (322)
T ss_dssp             EECCCCCGGGSCSCHHHHHHHHHHTHHHHHCGGGCCTTCCCCCEEEEECSSSSCHHHHHHHHHHHHT-----CEEEEEEH
T ss_pred             ecCCCCCHHHhcChHHHHHHHHHHHHHHHhCHHHHhcCCCCCCeEEEECCCCCcHHHHHHHHHHHHC-----CCEEEEch
Confidence            46788899999999999999988872          2 222 3499999999999999999999863     34566654


Q ss_pred             CCC----cC--hHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCH-----------HHHHHHHHHhhh---ccCCceE
Q psy879           70 SND----RG--IDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTD-----------GAQQALRRTMEI---YSNTTRF  129 (317)
Q Consensus        70 ~~~----~~--~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~-----------~~~~~ll~~le~---~~~~~~~  129 (317)
                      ...    .+  ...++..+.....       ..+.||+|||+|.+..           ..++.|+..++.   ....+++
T Consensus        85 ~~l~~~~~g~~~~~~~~~f~~a~~-------~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~v~v  157 (322)
T 3eie_A           85 SDLVSKWMGESEKLVKQLFAMARE-------NKPSIIFIDQVDALTGTRGEGESEASRRIKTELLVQMNGVGNDSQGVLV  157 (322)
T ss_dssp             HHHHTTTGGGHHHHHHHHHHHHHH-------TSSEEEEEECGGGGSCC------CCTHHHHHHHHHHHGGGGTSCCCEEE
T ss_pred             HHHhhcccchHHHHHHHHHHHHHh-------cCCeEEEechhhhhhccCCCCcchHHHHHHHHHHHHhccccccCCceEE
Confidence            321    11  1223333333221       3568999999998854           346788888874   3456778


Q ss_pred             EEEecCCCcCchhHhhhcce-eeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCC-CHHHHHHHHHH
Q psy879          130 ALACNNSEKIIEPIQSRCAM-LRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQG-DMRQALNNLQS  200 (317)
Q Consensus       130 il~~~~~~~l~~~i~sR~~~-i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~g-d~r~~i~~l~~  200 (317)
                      |++||.+..+++++++||.. +.|+.|+.++...++...+...+..+++..+..++..+.| +.+.+.++++.
T Consensus       158 i~atn~~~~ld~al~~Rf~~~i~~~~p~~~~r~~il~~~~~~~~~~~~~~~l~~la~~t~g~sg~di~~l~~~  230 (322)
T 3eie_A          158 LGATNIPWQLDSAIRRRFERRIYIPLPDLAARTTMFEINVGDTPCVLTKEDYRTLGAMTEGYSGSDIAVVVKD  230 (322)
T ss_dssp             EEEESCGGGSCHHHHHHCCEEEECCCCCHHHHHHHHHHHHTTCCCCCCHHHHHHHHHTTTTCCHHHHHHHHHH
T ss_pred             EEecCChhhCCHHHHcccCeEEEeCCCCHHHHHHHHHHHhccCCCCCCHHHHHHHHHHcCCCCHHHHHHHHHH
Confidence            88999999999999999965 9999999999999999999888878889999999999877 45555555544

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=99.88  E-value=1.4e-21  Score=168.57  Aligned_cols=189  Identities=11%  Similarity=0.102  Sum_probs=133.1

Q ss_pred             ccCCHHHHHH----HHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCC-----CCCceEEecCCCCcChHHHH-H-
Q psy879           12 IVGNEDTVER----LKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPS-----FKDAVLELNASNDRGIDTVR-N-   80 (317)
Q Consensus        12 ~~g~~~~~~~----l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~-----~~~~~~~~~~~~~~~~~~i~-~-   80 (317)
                      +.|+++..+.    |...+..+.+++++|+||||||||++++.+++.+....     ....++++||....+...+. . 
T Consensus        22 L~~Re~E~~~i~~~L~~~i~~~~~~~lli~GpPGTGKT~~v~~v~~~L~~~~~~~~~~~~~~v~INc~~~~t~~~~~~~I  101 (318)
T 3te6_A           22 LKSQVEDFTRIFLPIYDSLMSSQNKLFYITNADDSTKFQLVNDVMDELITSSARKELPIFDYIHIDALELAGMDALYEKI  101 (318)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTTCCCEEEEECCCSHHHHHHHHHHHHHHHHTTTTTSSCCEEEEEEETTCCC--HHHHHHH
T ss_pred             cCCHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHHHHHhhhccCCceEEEEEeccccCCHHHHHHHH
Confidence            4455555554    55666778888899999999999999999999985321     13456788876533322111 1 


Q ss_pred             ----------------HHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhh---ccCCceEEEEecCCC----
Q psy879           81 ----------------KIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEI---YSNTTRFALACNNSE----  137 (317)
Q Consensus        81 ----------------~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~---~~~~~~~il~~~~~~----  137 (317)
                                      .+..+.... ....+...|+++||+|.+.  .++.|+.+++.   ......+|+++|..+    
T Consensus       102 ~~~L~g~~~~~~~~~~~L~~~f~~~-~~~~~~~~ii~lDE~d~l~--~q~~L~~l~~~~~~~~s~~~vI~i~n~~d~~~~  178 (318)
T 3te6_A          102 WFAISKENLCGDISLEALNFYITNV-PKAKKRKTLILIQNPENLL--SEKILQYFEKWISSKNSKLSIICVGGHNVTIRE  178 (318)
T ss_dssp             HHHHSCCC--CCCCHHHHHHHHHHS-CGGGSCEEEEEEECCSSSC--CTHHHHHHHHHHHCSSCCEEEEEECCSSCCCHH
T ss_pred             HHHhcCCCCCchHHHHHHHHHHHHh-hhccCCceEEEEecHHHhh--cchHHHHHHhcccccCCcEEEEEEecCcccchh
Confidence                            111111110 0012457899999999998  56777777663   334567888888764    


Q ss_pred             cCchhHhhhcc--eeeecCCCHHHHHHHHHHHHHHcCC-----------------------------------CCCHHHH
Q psy879          138 KIIEPIQSRCA--MLRYNKLTDAQLLSKVIEICEKENI-----------------------------------SHTNDGL  180 (317)
Q Consensus       138 ~l~~~i~sR~~--~i~f~~~~~~~~~~~l~~~~~~~~~-----------------------------------~i~~~~~  180 (317)
                      .+.++++||+.  .+.|+||+.+|+.+++..++....-                                   .++++++
T Consensus       179 ~L~~~v~SR~~~~~i~F~pYt~~el~~Il~~Rl~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~ai  258 (318)
T 3te6_A          179 QINIMPSLKAHFTEIKLNKVDKNELQQMIITRLKSLLKPFHVKVNDKKEMTIYNNIREGQNQKIPDNVIVINHKINNKIT  258 (318)
T ss_dssp             HHHTCHHHHTTEEEEECCCCCHHHHHHHHHHHHHHHCCCEEEEECTTCCEEECCCC--------CTTEEEECEECCHHHH
T ss_pred             hcchhhhccCCceEEEeCCCCHHHHHHHHHHHHHhhhccccccccccccccccccccccccccccccccccccccCHHHH
Confidence            35677899985  5999999999999999999876321                                   3689999


Q ss_pred             HHHHH---hcCCCHHHHHHHHHHhhh
Q psy879          181 EAIVF---TAQGDMRQALNNLQSTHN  203 (317)
Q Consensus       181 ~~l~~---~~~gd~r~~i~~l~~~~~  203 (317)
                      +.+++   ..+||+|+|++.|+.++.
T Consensus       259 ~~~A~~vA~~~GD~R~Al~ilr~A~~  284 (318)
T 3te6_A          259 QLIAKNVANVSGSTEKAFKICEAAVE  284 (318)
T ss_dssp             HHHHHHHHHHHCSHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhhCChHHHHHHHHHHHHH
Confidence            99988   578999999999988654

>3d8b_A Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, structural genomics consortium, ATP- hydrolase, magnesium, metal-binding, nucleotide-binding; HET: ADP; 2.00A {Homo sapiens}

Probab=99.88  E-value=6.2e-21  Score=169.14  Aligned_cols=187  Identities=20%  Similarity=0.235  Sum_probs=142.1

Q ss_pred             cccCCCCCCcccCCHHHHHHHHHHHhc------------CCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecC
Q psy879            2 EKYRPQTFSDIVGNEDTVERLKVFSSS------------GNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNA   69 (317)
Q Consensus         2 ~ky~P~~~~~~~g~~~~~~~l~~~l~~------------~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~   69 (317)
                      ++|+|.+|++++|++.+++.|...+..            ....+++|+||||||||++|+++++.+     +..++.+++
T Consensus        76 ~~~~~~~~~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vLl~GppGtGKT~la~aia~~~-----~~~~~~i~~  150 (357)
T 3d8b_A           76 DHGPPVNWEDIAGVEFAKATIKEIVVWPMLRPDIFTGLRGPPKGILLFGPPGTGKTLIGKCIASQS-----GATFFSISA  150 (357)
T ss_dssp             CCSCCCCGGGSCSCHHHHHHHHHHTHHHHHCTTTSCGGGSCCSEEEEESSTTSSHHHHHHHHHHHT-----TCEEEEEEG
T ss_pred             cCCCCCCHHHhCChHHHHHHHHHHHHHHhhChHhHhhccCCCceEEEECCCCCCHHHHHHHHHHHc-----CCeEEEEeh
Confidence            678999999999999999999887742            233459999999999999999999986     334666665


Q ss_pred             CCCcC------hHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCH-----------HHHHHHHHHhhh----ccCCce
Q psy879           70 SNDRG------IDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTD-----------GAQQALRRTMEI----YSNTTR  128 (317)
Q Consensus        70 ~~~~~------~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~-----------~~~~~ll~~le~----~~~~~~  128 (317)
                      .....      ...++..+.....       ..+.+|+|||+|.+..           ..++.|+..++.    .+..+.
T Consensus       151 ~~l~~~~~g~~~~~~~~~~~~a~~-------~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~lL~~l~~~~~~~~~~v~  223 (357)
T 3d8b_A          151 SSLTSKWVGEGEKMVRALFAVARC-------QQPAVIFIDEIDSLLSQRGDGEHESSRRIKTEFLVQLDGATTSSEDRIL  223 (357)
T ss_dssp             GGGCCSSTTHHHHHHHHHHHHHHH-------TCSEEEEEETHHHHTBC------CHHHHHHHHHHHHHHC----CCCCEE
T ss_pred             HHhhccccchHHHHHHHHHHHHHh-------cCCeEEEEeCchhhhccCCCCcchHHHHHHHHHHHHHhcccccCCCCEE
Confidence            43211      1222333322211       3578999999998742           346677777774    245677


Q ss_pred             EEEEecCCCcCchhHhhhcce-eeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCC-CHHHHHHHHHH
Q psy879          129 FALACNNSEKIIEPIQSRCAM-LRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQG-DMRQALNNLQS  200 (317)
Q Consensus       129 ~il~~~~~~~l~~~i~sR~~~-i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~g-d~r~~i~~l~~  200 (317)
                      +|++||.+..+.+++++||.. +.++.|+.++...++...+...+..++++.++.++..+.| +.+.+..+++.
T Consensus       224 vI~atn~~~~l~~~l~~Rf~~~i~i~~p~~~~r~~il~~~~~~~~~~l~~~~l~~la~~t~G~s~~dl~~l~~~  297 (357)
T 3d8b_A          224 VVGATNRPQEIDEAARRRLVKRLYIPLPEASARKQIVINLMSKEQCCLSEEEIEQIVQQSDAFSGADMTQLCRE  297 (357)
T ss_dssp             EEEEESCGGGBCHHHHTTCCEEEECCCCCHHHHHHHHHHHHHTSCBCCCHHHHHHHHHHTTTCCHHHHHHHHHH
T ss_pred             EEEecCChhhCCHHHHhhCceEEEeCCcCHHHHHHHHHHHHhhcCCCccHHHHHHHHHHcCCCCHHHHHHHHHH
Confidence            888999999999999999984 8999999999999999999888888999999999999988 44444444444

>2qp9_X Vacuolar protein sorting-associated protein 4; ATPase domain, beta domain, C-terminal helix, ATP-binding, E nucleotide-binding; 2.90A {Saccharomyces cerevisiae} PDB: 2qpa_A*

Probab=99.88  E-value=4.1e-21  Score=170.06  Aligned_cols=187  Identities=17%  Similarity=0.148  Sum_probs=137.0

Q ss_pred             cccCCCCCCcccCCHHHHHHHHHHHh-----------cCCCc-eEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecC
Q psy879            2 EKYRPQTFSDIVGNEDTVERLKVFSS-----------SGNVP-NIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNA   69 (317)
Q Consensus         2 ~ky~P~~~~~~~g~~~~~~~l~~~l~-----------~~~~~-~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~   69 (317)
                      .++.+.+|++++|++.+++.|..++.           .+.++ ++|||||||||||++|+++++.+.     ..++.+++
T Consensus        43 ~~~~~~~~~di~G~~~~~~~l~~~v~~~~~~~~~~~~~~~~~~~iLL~GppGtGKT~la~ala~~~~-----~~~~~v~~  117 (355)
T 2qp9_X           43 SEKPNVKWEDVAGLEGAKEALKEAVILPVKFPHLFKGNRKPTSGILLYGPPGTGKSYLAKAVATEAN-----STFFSVSS  117 (355)
T ss_dssp             ----CCCGGGSCCGGGHHHHHHHHTHHHHHCGGGGCSSCCCCCCEEEECSTTSCHHHHHHHHHHHHT-----CEEEEEEH
T ss_pred             ccCCCCCHHHhCCHHHHHHHHHHHHHHHHhCHHHHhcCCCCCceEEEECCCCCcHHHHHHHHHHHhC-----CCEEEeeH
Confidence            46778899999999999999988763           12233 499999999999999999999973     33555554


Q ss_pred             CCC------cChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHH-----------HHHHHHHHhhh---ccCCceE
Q psy879           70 SND------RGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDG-----------AQQALRRTMEI---YSNTTRF  129 (317)
Q Consensus        70 ~~~------~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~-----------~~~~ll~~le~---~~~~~~~  129 (317)
                      ...      .....++..+.....       ..+.||||||+|.+...           .++.|+..++.   .+..+++
T Consensus       118 ~~l~~~~~g~~~~~~~~~f~~a~~-------~~~~vl~iDEid~l~~~r~~~~~~~~~~~~~~ll~~l~~~~~~~~~v~v  190 (355)
T 2qp9_X          118 SDLVSKWMGESEKLVKQLFAMARE-------NKPSIIFIDQVDALTGTRGEGESEASRRIKTELLVQMNGVGNDSQGVLV  190 (355)
T ss_dssp             HHHHSCC---CHHHHHHHHHHHHH-------TSSEEEEEECGGGGTC------CTHHHHHHHHHHHHHHHCC---CCEEE
T ss_pred             HHHhhhhcchHHHHHHHHHHHHHH-------cCCeEEEEechHhhcccCCCCcchHHHHHHHHHHHHhhcccccCCCeEE
Confidence            321      112223333333221       35789999999998742           46778888874   3456788


Q ss_pred             EEEecCCCcCchhHhhhcce-eeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCC-CHHHHHHHHHH
Q psy879          130 ALACNNSEKIIEPIQSRCAM-LRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQG-DMRQALNNLQS  200 (317)
Q Consensus       130 il~~~~~~~l~~~i~sR~~~-i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~g-d~r~~i~~l~~  200 (317)
                      |++||.++.+++++++||.. +.+++|+.++...++..++...+..+++..++.++..+.| +.+.+.++++.
T Consensus       191 I~atn~~~~ld~al~rRf~~~i~i~~P~~~~r~~il~~~l~~~~~~~~~~~l~~la~~t~G~sg~dl~~l~~~  263 (355)
T 2qp9_X          191 LGATNIPWQLDSAIRRRFERRIYIPLPDLAARTTMFEINVGDTPSVLTKEDYRTLGAMTEGYSGSDIAVVVKD  263 (355)
T ss_dssp             EEEESCGGGSCHHHHHTCCEEEECCCCCHHHHHHHHHHHHTTSCBCCCHHHHHHHHHHTTTCCHHHHHHHHHH
T ss_pred             EeecCCcccCCHHHHcccCEEEEeCCcCHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHcCCCCHHHHHHHHHH
Confidence            88999999999999999955 9999999999999999999887777889999999999988 45555555544

>1ofh_A ATP-dependent HSL protease ATP-binding subunit HSLU; chaperone, hydrolase, ATP-binding; HET: ADP; 2.5A {Haemophilus influenzae} SCOP: c.37.1.20 PDB: 1ofi_A*

Probab=99.87  E-value=3.9e-21  Score=167.26  Aligned_cols=204  Identities=21%  Similarity=0.292  Sum_probs=145.2

Q ss_pred             CcccCCHHHHHHHHHHHhc--------------CCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcC-
Q psy879           10 SDIVGNEDTVERLKVFSSS--------------GNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRG-   74 (317)
Q Consensus        10 ~~~~g~~~~~~~l~~~l~~--------------~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~-   74 (317)
                      ++++|++++++.+..++..              ..+.+++|+||||||||++++++++.+.     ..++.+++..... 
T Consensus        15 ~~i~G~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~l~-----~~~~~i~~~~~~~~   89 (310)
T 1ofh_A           15 QHIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKLAN-----APFIKVEATKFTEV   89 (310)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHTTSSCHHHHHHCCCCCEEEECCTTSSHHHHHHHHHHHHT-----CCEEEEEGGGGSSC
T ss_pred             hhcCChHHHHHHHHHHHHHHHhhhhhcccccccCCCceEEEECCCCCCHHHHHHHHHHHhC-----CCEEEEcchhcccC
Confidence            3589999999998877754              2344699999999999999999999973     2355555432211 


Q ss_pred             -------hHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHH------------HHHHHHHhhhc----------cC
Q psy879           75 -------IDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGA------------QQALRRTMEIY----------SN  125 (317)
Q Consensus        75 -------~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~------------~~~ll~~le~~----------~~  125 (317)
                             ...+.+.+.... .... ....+.|++|||+|.+..+.            ++.|++++++.          +.
T Consensus        90 ~~~~~~~~~~~~~~~~~~~-~~~~-~~~~~~vl~iDEi~~l~~~~~~~~~~~~~~~~~~~Ll~~le~~~~~~~~~~~~~~  167 (310)
T 1ofh_A           90 GYVGKEVDSIIRDLTDSAG-GAID-AVEQNGIVFIDEIDKICKKGEYSGADVSREGVQRDLLPLVEGSTVSTKHGMVKTD  167 (310)
T ss_dssp             CSGGGSTTHHHHHHHHTTT-TCHH-HHHHHCEEEEECGGGGSCCSSCCSSHHHHHHHHHHHHHHHHCCEEEETTEEEECT
T ss_pred             CccCccHHHHHHHHHHHhh-HHHh-hccCCCEEEEEChhhcCccccccccchhHHHHHHHHHHHhcCCeEecccccccCC
Confidence                   112232222110 0000 00236799999999997654            88999999963          34


Q ss_pred             CceEEEEe----cCCCcCchhHhhhcce-eeecCCCHHHHHHHHHH-----------HHHHcC--CCCCHHHHHHHHHhc
Q psy879          126 TTRFALAC----NNSEKIIEPIQSRCAM-LRYNKLTDAQLLSKVIE-----------ICEKEN--ISHTNDGLEAIVFTA  187 (317)
Q Consensus       126 ~~~~il~~----~~~~~l~~~i~sR~~~-i~f~~~~~~~~~~~l~~-----------~~~~~~--~~i~~~~~~~l~~~~  187 (317)
                      ++.+|+++    +.+..+.+++.+||.. +.|++|+.+++..++..           .+...+  +.+++++++.++..+
T Consensus       168 ~~~~i~~~~~~~~~~~~l~~~l~~R~~~~i~~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~l~~~~  247 (310)
T 1ofh_A          168 HILFIASGAFQVARPSDLIPELQGRLPIRVELTALSAADFERILTEPHASLTEQYKALMATEGVNIAFTTDAVKKIAEAA  247 (310)
T ss_dssp             TCEEEEEECCSSSCGGGSCHHHHHTCCEEEECCCCCHHHHHHHHHSSTTCHHHHHHHHHHHTTCEEEECHHHHHHHHHHH
T ss_pred             cEEEEEcCCcccCCcccCCHHHHhhCCceEEcCCcCHHHHHHHHHhhHHHHHHHHHHHHHhcCCeeccCHHHHHHHHHHh
Confidence            66777774    3556889999999975 99999999999999883           233345  368999999999887


Q ss_pred             --------CCCHHHHHHHHHHhhh--------CCC---cccHHHHHhhcCCC
Q psy879          188 --------QGDMRQALNNLQSTHN--------GFG---HVTAEYVFKVCDEP  220 (317)
Q Consensus       188 --------~gd~r~~i~~l~~~~~--------~~~---~i~~~~v~~~~~~~  220 (317)
                              .||+|.+.+.++.+..        ..+   .|+.+++..++...
T Consensus       248 ~~~~~~~~~g~~R~l~~~l~~~~~~~~~~~~~~~~~~~~i~~~~v~~~l~~~  299 (310)
T 1ofh_A          248 FRVNEKTENIGARRLHTVMERLMDKISFSASDMNGQTVNIDAAYVADALGEV  299 (310)
T ss_dssp             HHHHHHSCCCTTHHHHHHHHHHSHHHHHHGGGCTTCEEEECHHHHHHHTCSS
T ss_pred             hhhcccccccCcHHHHHHHHHHHHhhhcCCccccCCEEEEeeHHHHHHHHhh
Confidence                    7999999999987541        111   48888888877653

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=99.87  E-value=1.1e-20  Score=166.77  Aligned_cols=198  Identities=19%  Similarity=0.226  Sum_probs=137.6

Q ss_pred             CCCCcccCCHHHHHHHHHHHhc-----------C-CCc-eEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCc
Q psy879            7 QTFSDIVGNEDTVERLKVFSSS-----------G-NVP-NIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDR   73 (317)
Q Consensus         7 ~~~~~~~g~~~~~~~l~~~l~~-----------~-~~~-~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~   73 (317)
                      -+|+|+.|.+++++.|+..+.-           | .+| .+|||||||||||++|+++|.++     +..++.++++...
T Consensus       145 v~~~dIgGl~~~k~~l~e~v~~Pl~~pe~f~~~gi~~prGvLL~GPPGTGKTllAkAiA~e~-----~~~f~~v~~s~l~  219 (405)
T 4b4t_J          145 STYDMVGGLTKQIKEIKEVIELPVKHPELFESLGIAQPKGVILYGPPGTGKTLLARAVAHHT-----DCKFIRVSGAELV  219 (405)
T ss_dssp             CCGGGSCSCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCCCEEEESCSSSSHHHHHHHHHHHH-----TCEEEEEEGGGGS
T ss_pred             CCHHHhCCHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCceEEeCCCCCCHHHHHHHHHHhh-----CCCceEEEhHHhh
Confidence            4699999999999998877531           3 233 39999999999999999999997     3446666654321


Q ss_pred             ------ChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHH--------------HHHHHHHHhhh--ccCCceEEE
Q psy879           74 ------GIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDG--------------AQQALRRTMEI--YSNTTRFAL  131 (317)
Q Consensus        74 ------~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~--------------~~~~ll~~le~--~~~~~~~il  131 (317)
                            +...++..+.....       ..+.||+|||+|.+...              ..+.|+..|+.  ...++.+|+
T Consensus       220 sk~vGese~~vr~lF~~Ar~-------~aP~IIFiDEiDai~~~R~~~~~~~~~~~~~~l~~lL~~lDg~~~~~~V~vIa  292 (405)
T 4b4t_J          220 QKYIGEGSRMVRELFVMARE-------HAPSIIFMDEIDSIGSTRVEGSGGGDSEVQRTMLELLNQLDGFETSKNIKIIM  292 (405)
T ss_dssp             CSSTTHHHHHHHHHHHHHHH-------TCSEEEEEESSSCCTTSCSCSSSGGGGHHHHHHHHHHHHHHTTTCCCCEEEEE
T ss_pred             ccccchHHHHHHHHHHHHHH-------hCCceEeeecchhhccCCCCCCCCCcHHHHHHHHHHHHhhhccCCCCCeEEEe
Confidence                  22345555544433       35789999999988431              24566677764  345677899


Q ss_pred             EecCCCcCchhHhh--hcce-eeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCC----CHHHHHHHHHHhh--
Q psy879          132 ACNNSEKIIEPIQS--RCAM-LRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQG----DMRQALNNLQSTH--  202 (317)
Q Consensus       132 ~~~~~~~l~~~i~s--R~~~-i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~g----d~r~~i~~l~~~~--  202 (317)
                      +||.++.+++++.+  |+.. |+|+.|+.++..++++..+++..+. ++..++.++..+.|    |+..+.+..-..+  
T Consensus       293 ATNrpd~LDpAllRpGRfD~~I~i~lPd~~~R~~Il~~~~~~~~l~-~dvdl~~lA~~t~G~SGADi~~l~~eA~~~Air  371 (405)
T 4b4t_J          293 ATNRLDILDPALLRPGRIDRKIEFPPPSVAARAEILRIHSRKMNLT-RGINLRKVAEKMNGCSGADVKGVCTEAGMYALR  371 (405)
T ss_dssp             EESCSSSSCHHHHSTTSSCCEEECCCCCHHHHHHHHHHHHTTSBCC-SSCCHHHHHHHCCSCCHHHHHHHHHHHHHHHHH
T ss_pred             ccCChhhCCHhHcCCCcCceEEEcCCcCHHHHHHHHHHHhcCCCCC-ccCCHHHHHHHCCCCCHHHHHHHHHHHHHHHHH
Confidence            99999999999987  7765 9999999999999998887654432 12237788887765    4444433322111  


Q ss_pred             hCCCcccHHHHHhhc
Q psy879          203 NGFGHVTAEYVFKVC  217 (317)
Q Consensus       203 ~~~~~i~~~~v~~~~  217 (317)
                      .+...|+.+|+..++
T Consensus       372 ~~~~~vt~~Df~~Al  386 (405)
T 4b4t_J          372 ERRIHVTQEDFELAV  386 (405)
T ss_dssp             TTCSBCCHHHHHHHH
T ss_pred             cCCCCcCHHHHHHHH
Confidence            244567777765543

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=99.87  E-value=4.4e-20  Score=161.29  Aligned_cols=187  Identities=17%  Similarity=0.136  Sum_probs=139.7

Q ss_pred             ccCCCCCCcccCCHHHHHHHHHHHh----------c-CCC-ceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCC
Q psy879            3 KYRPQTFSDIVGNEDTVERLKVFSS----------S-GNV-PNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNAS   70 (317)
Q Consensus         3 ky~P~~~~~~~g~~~~~~~l~~~l~----------~-~~~-~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~   70 (317)
                      ++.+.+|+++.|++++++.|...+.          . ..+ .++|||||||||||++|+++++.+.    ...++.+++.
T Consensus         5 ~~~~~~~~di~G~~~~k~~l~~~v~~p~~~~~~~~~~~~~~~~iLL~GppGtGKT~la~ala~~~~----~~~~~~i~~~   80 (322)
T 1xwi_A            5 ERPNVKWSDVAGLEGAKEALKEAVILPIKFPHLFTGKRTPWRGILLFGPPGTGKSYLAKAVATEAN----NSTFFSISSS   80 (322)
T ss_dssp             ECCCCCGGGSCSCHHHHHHHHHHHHHHHHCGGGSCTTCCCCSEEEEESSSSSCHHHHHHHHHHHTT----SCEEEEEECC
T ss_pred             cCCCCCHHHhcCHHHHHHHHHHHHHHHHhCHHHHhCCCCCCceEEEECCCCccHHHHHHHHHHHcC----CCcEEEEEhH
Confidence            4566789999999999999987763          1 122 3499999999999999999999862    2345555554


Q ss_pred             CC------cChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCH-----------HHHHHHHHHhhh---ccCCceEE
Q psy879           71 ND------RGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTD-----------GAQQALRRTMEI---YSNTTRFA  130 (317)
Q Consensus        71 ~~------~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~-----------~~~~~ll~~le~---~~~~~~~i  130 (317)
                      ..      .....++..+.....       ..+.||+|||+|.+..           ...+.|+..++.   ....+.+|
T Consensus        81 ~l~~~~~g~~~~~~~~lf~~a~~-------~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~ll~~ld~~~~~~~~v~vI  153 (322)
T 1xwi_A           81 DLVSKWLGESEKLVKNLFQLARE-------NKPSIIFIDEIDSLCGSRSENESEAARRIKTEFLVQMQGVGVDNDGILVL  153 (322)
T ss_dssp             SSCCSSCCSCHHHHHHHHHHHHH-------TSSEEEEEETTTGGGCCSSSCCTTHHHHHHHHHHHHHHCSSSCCTTEEEE
T ss_pred             HHHhhhhhHHHHHHHHHHHHHHh-------cCCcEEEeecHHHhccccccccchHHHHHHHHHHHHHhcccccCCCEEEE
Confidence            31      122334444443322       3578999999998832           346777888775   34667788


Q ss_pred             EEecCCCcCchhHhhhcc-eeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCC-HHHHHHHHHH
Q psy879          131 LACNNSEKIIEPIQSRCA-MLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGD-MRQALNNLQS  200 (317)
Q Consensus       131 l~~~~~~~l~~~i~sR~~-~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd-~r~~i~~l~~  200 (317)
                      ++||.++.+++++++||. .+.++.|+.++...++...+...+..+++..++.++..+.|- .+.+-.+++.
T Consensus       154 ~atn~~~~ld~al~rRf~~~i~i~~P~~~~r~~il~~~l~~~~~~l~~~~l~~la~~t~G~sgadl~~l~~~  225 (322)
T 1xwi_A          154 GATNIPWVLDSAIRRRFEKRIYIPLPEPHARAAMFKLHLGTTQNSLTEADFRELGRKTDGYSGADISIIVRD  225 (322)
T ss_dssp             EEESCTTTSCHHHHHTCCEEEECCCCCHHHHHHHHHHHHTTCCBCCCHHHHHHHHHTCTTCCHHHHHHHHHH
T ss_pred             EecCCcccCCHHHHhhcCeEEEeCCcCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHcCCCCHHHHHHHHHH
Confidence            899999999999999995 499999999999999999988777778899999999998774 4444444444

>2zan_A Vacuolar protein sorting-associating protein 4B; SKD1, VPS4B, AAA ATPase, ATP-binding, coiled coil, membrane, nucleotide-binding, phosphorylation; HET: ATP; 3.00A {Mus musculus} PDB: 2zam_A* 2zao_A* 2jqh_A 2jqk_A 1wr0_A 2jq9_A 2k3w_A 1yxr_A

Probab=99.86  E-value=1.6e-20  Score=171.04  Aligned_cols=189  Identities=16%  Similarity=0.135  Sum_probs=141.1

Q ss_pred             cccCCCCCCcccCCHHHHHHHHHHHh----------c-CCC-ceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecC
Q psy879            2 EKYRPQTFSDIVGNEDTVERLKVFSS----------S-GNV-PNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNA   69 (317)
Q Consensus         2 ~ky~P~~~~~~~g~~~~~~~l~~~l~----------~-~~~-~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~   69 (317)
                      .++.|.+|++++|++.+++.|...+.          . ..+ .++||+||||||||++|+++++.+.    ...++.+++
T Consensus       126 ~~~~~~~~~di~G~~~~k~~l~~~v~~p~~~~~~~~~~~~~~~~vLL~GppGtGKT~lA~aia~~~~----~~~~~~v~~  201 (444)
T 2zan_A          126 IERPNVKWSDVAGLEGAKEALKEAVILPIKFPHLFTGKRTPWRGILLFGPPGTGKSYLAKAVATEAN----NSTFFSISS  201 (444)
T ss_dssp             CCCCCCCGGGSCSCHHHHHHHHHHHTHHHHCTTTTSGGGCCCSEEEEECSTTSSHHHHHHHHHHHCC----SSEEEEECC
T ss_pred             ccCCCCCHHHhcCHHHHHHHHHHHHHHHhhCHHHhhccCCCCceEEEECCCCCCHHHHHHHHHHHcC----CCCEEEEeH
Confidence            35778889999999999999988762          1 122 3599999999999999999999862    234566665


Q ss_pred             CCCcC------hHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCC-----------HHHHHHHHHHhhh---ccCCceE
Q psy879           70 SNDRG------IDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMT-----------DGAQQALRRTMEI---YSNTTRF  129 (317)
Q Consensus        70 ~~~~~------~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~-----------~~~~~~ll~~le~---~~~~~~~  129 (317)
                      ....+      ...++..+.....       ..+.||+|||+|.+.           ...++.|+..++.   .+..+.+
T Consensus       202 ~~l~~~~~g~~~~~~~~~f~~a~~-------~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~lL~~l~~~~~~~~~v~v  274 (444)
T 2zan_A          202 SDLVSKWLGESEKLVKNLFQLARE-------NKPSIIFIDEIDSLCGSRSENESEAARRIKTEFLVQMQGVGVDNDGILV  274 (444)
T ss_dssp             C---------CCCTHHHHHHHHHH-------SCSEEEEESCTTTTCCCSSCCCCGGGHHHHHHHHTTTTCSSCCCSSCEE
T ss_pred             HHHHhhhcchHHHHHHHHHHHHHH-------cCCeEEEEechHhhccCCCCccccHHHHHHHHHHHHHhCcccCCCCEEE
Confidence            43211      1223333333221       357899999999983           2456778887775   3567889


Q ss_pred             EEEecCCCcCchhHhhhcc-eeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCC-CHHHHHHHHHHh
Q psy879          130 ALACNNSEKIIEPIQSRCA-MLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQG-DMRQALNNLQST  201 (317)
Q Consensus       130 il~~~~~~~l~~~i~sR~~-~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~g-d~r~~i~~l~~~  201 (317)
                      |++||.+..+++++++||. .+.++.|+.++...++...+...+..+++..++.++..+.| +.+.+.++++.+
T Consensus       275 I~atn~~~~ld~al~rRf~~~i~i~~P~~~~r~~il~~~l~~~~~~l~~~~l~~la~~t~G~sgadl~~l~~~a  348 (444)
T 2zan_A          275 LGATNIPWVLDSAIRRRFEKRIYIPLPEAHARAAMFRLHLGSTQNSLTEADFQELGRKTDGYSGADISIIVRDA  348 (444)
T ss_dssp             EEEESCGGGSCHHHHTTCCEEEECCCCCHHHHHHHHHHHHTTSCEECCHHHHHHHHHHTTTCCHHHHHHHHHHH
T ss_pred             EecCCCccccCHHHHhhcceEEEeCCcCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHcCCCCHHHHHHHHHHH
Confidence            9999999999999999996 59999999999999999998877777789999999999988 455555555443

>1l8q_A Chromosomal replication initiator protein DNAA; AAA+, helix-turn-helix, nucleotide-binding, DNA binding, REP initiation, DNA binding protein; HET: ADP; 2.70A {Aquifex aeolicus} SCOP: a.4.12.2 c.37.1.20 PDB: 3r8f_A* 2hcb_A*

Probab=99.85  E-value=8.4e-21  Score=166.35  Aligned_cols=187  Identities=14%  Similarity=0.163  Sum_probs=138.0

Q ss_pred             CCCCccc-C--CHHHHHHHHHHHhcC--CCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHH
Q psy879            7 QTFSDIV-G--NEDTVERLKVFSSSG--NVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNK   81 (317)
Q Consensus         7 ~~~~~~~-g--~~~~~~~l~~~l~~~--~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~   81 (317)
                      .+|++++ |  +......+..++..+  ..++++|+||||+|||++++++++.+...  +..++.+++...  ...+...
T Consensus         8 ~~f~~fv~g~~~~~a~~~~~~~~~~~~~~~~~lll~G~~GtGKT~la~~i~~~~~~~--~~~~~~i~~~~~--~~~~~~~   83 (324)
T 1l8q_A            8 YTLENFIVGEGNRLAYEVVKEALENLGSLYNPIFIYGSVGTGKTHLLQAAGNEAKKR--GYRVIYSSADDF--AQAMVEH   83 (324)
T ss_dssp             CCSSSCCCCTTTHHHHHHHHHHHHTTTTSCSSEEEECSSSSSHHHHHHHHHHHHHHT--TCCEEEEEHHHH--HHHHHHH
T ss_pred             CCcccCCCCCcHHHHHHHHHHHHhCcCCCCCeEEEECCCCCcHHHHHHHHHHHHHHC--CCEEEEEEHHHH--HHHHHHH
Confidence            4699998 4  555666677777664  34569999999999999999999987533  344566654321  1111111


Q ss_pred             HH-----HHHhhcccCCCCceeEEEEeCCCCCCH--HHHHHHHHHhhhc-cCCceEEEEecCC-C---cCchhHhhhc--
Q psy879           82 IK-----MFAQQKVTLPPGRHKIVILDEADSMTD--GAQQALRRTMEIY-SNTTRFALACNNS-E---KIIEPIQSRC--  147 (317)
Q Consensus        82 ~~-----~~~~~~~~~~~~~~~vliiDE~d~l~~--~~~~~ll~~le~~-~~~~~~il~~~~~-~---~l~~~i~sR~--  147 (317)
                      +.     .+....     ..+.+++|||++.+..  ..++.++..++.. .....+|++++.+ .   .+.+++.+|+  
T Consensus        84 ~~~~~~~~~~~~~-----~~~~vL~iDEi~~l~~~~~~~~~l~~~l~~~~~~~~~iii~~~~~~~~l~~l~~~L~sR~~~  158 (324)
T 1l8q_A           84 LKKGTINEFRNMY-----KSVDLLLLDDVQFLSGKERTQIEFFHIFNTLYLLEKQIILASDRHPQKLDGVSDRLVSRFEG  158 (324)
T ss_dssp             HHHTCHHHHHHHH-----HTCSEEEEECGGGGTTCHHHHHHHHHHHHHHHHTTCEEEEEESSCGGGCTTSCHHHHHHHHT
T ss_pred             HHcCcHHHHHHHh-----cCCCEEEEcCcccccCChHHHHHHHHHHHHHHHCCCeEEEEecCChHHHHHhhhHhhhcccC
Confidence            11     111110     2367999999999976  6788888888753 3345667766654 2   5889999999  


Q ss_pred             -ceeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhhC
Q psy879          148 -AMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHNG  204 (317)
Q Consensus       148 -~~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~~  204 (317)
                       ..+.|+| +.++...++...+...++.+++++++.++..+ ||+|.+.+.++.++..
T Consensus       159 ~~~i~l~~-~~~e~~~il~~~~~~~~~~l~~~~l~~l~~~~-g~~r~l~~~l~~~~~~  214 (324)
T 1l8q_A          159 GILVEIEL-DNKTRFKIIKEKLKEFNLELRKEVIDYLLENT-KNVREIEGKIKLIKLK  214 (324)
T ss_dssp             SEEEECCC-CHHHHHHHHHHHHHHTTCCCCHHHHHHHHHHC-SSHHHHHHHHHHHHHH
T ss_pred             ceEEEeCC-CHHHHHHHHHHHHHhcCCCCCHHHHHHHHHhC-CCHHHHHHHHHHHHHc
Confidence             6699999 99999999999999999999999999999999 9999999999876543

>2r44_A Uncharacterized protein; putative ATPase, structural genomics, joint center for struc genomics, JCSG; HET: MSE PG4; 2.00A {Cytophaga hutchinsonii atcc 33406}

Probab=99.85  E-value=3.8e-21  Score=169.08  Aligned_cols=204  Identities=18%  Similarity=0.179  Sum_probs=147.2

Q ss_pred             cccCCCCCCcccCCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHH
Q psy879            2 EKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNK   81 (317)
Q Consensus         2 ~ky~P~~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~   81 (317)
                      ++|+|..+++++|++++++.+...+..+.  +++|+||||||||++++++++.+..     .+..+++........+   
T Consensus        19 ~~~~~~~~~~i~g~~~~~~~l~~~l~~~~--~vll~G~pGtGKT~la~~la~~~~~-----~~~~i~~~~~~~~~~l---   88 (331)
T 2r44_A           19 KEVIDEVGKVVVGQKYMINRLLIGICTGG--HILLEGVPGLAKTLSVNTLAKTMDL-----DFHRIQFTPDLLPSDL---   88 (331)
T ss_dssp             HHHHHHHTTTCCSCHHHHHHHHHHHHHTC--CEEEESCCCHHHHHHHHHHHHHTTC-----CEEEEECCTTCCHHHH---
T ss_pred             HHHHHHhccceeCcHHHHHHHHHHHHcCC--eEEEECCCCCcHHHHHHHHHHHhCC-----CeEEEecCCCCChhhc---
Confidence            57899999999999999999988888776  8999999999999999999998632     3444544322222221   


Q ss_pred             HHHHHh----hc--ccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhc-----------cCCceEEEEecCCC-----cC
Q psy879           82 IKMFAQ----QK--VTLPPGRHKIVILDEADSMTDGAQQALRRTMEIY-----------SNTTRFALACNNSE-----KI  139 (317)
Q Consensus        82 ~~~~~~----~~--~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~-----------~~~~~~il~~~~~~-----~l  139 (317)
                      ++....    ..  .....-...+++|||++.+.++.++.|++.+++.           +....+|.++|+..     .+
T Consensus        89 ~g~~~~~~~~~~~~~~~g~l~~~vl~iDEi~~~~~~~~~~Ll~~l~~~~~~~~g~~~~~~~~~~viat~np~~~~~~~~l  168 (331)
T 2r44_A           89 IGTMIYNQHKGNFEVKKGPVFSNFILADEVNRSPAKVQSALLECMQEKQVTIGDTTYPLDNPFLVLATQNPVEQEGTYPL  168 (331)
T ss_dssp             HEEEEEETTTTEEEEEECTTCSSEEEEETGGGSCHHHHHHHHHHHHHSEEEETTEEEECCSSCEEEEEECTTCCSCCCCC
T ss_pred             CCceeecCCCCceEeccCcccccEEEEEccccCCHHHHHHHHHHHhcCceeeCCEEEECCCCEEEEEecCCCcccCcccC
Confidence            110000    00  0000001369999999999999999999999963           44555666666432     38


Q ss_pred             chhHhhhcce-eeecCCCHHHHHHHHHHHHHH----------------------cCCCCCHHHHHHHHHhc---------
Q psy879          140 IEPIQSRCAM-LRYNKLTDAQLLSKVIEICEK----------------------ENISHTNDGLEAIVFTA---------  187 (317)
Q Consensus       140 ~~~i~sR~~~-i~f~~~~~~~~~~~l~~~~~~----------------------~~~~i~~~~~~~l~~~~---------  187 (317)
                      .+++.+||.. +.+++|+.++..+++...+..                      .++.++++++++++..+         
T Consensus       169 ~~~l~~Rf~~~i~i~~p~~~~~~~il~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~v~~~~~~~~~i~~~~~~~r~~~~~  248 (331)
T 2r44_A          169 PEAQVDRFMMKIHLTYLDKESELEVMRRVSNMNFNYQVQKIVSKNDVLEIRNEINKVTISESLEKYIIELVFATRFPAEY  248 (331)
T ss_dssp             CHHHHTTSSEEEECCCCCHHHHHHHHHHHHCTTCCCCCCCCSCHHHHHHHHHHHHTCBCCHHHHHHHHHHHHHHHSGGGG
T ss_pred             CHHHHhheeEEEEcCCCCHHHHHHHHHhccccCcchhccccCCHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHhccccc
Confidence            8999999986 999999999999999887654                      26778899888887643         


Q ss_pred             -----------CCCHHHHHHHHHHhhh-----CCCcccHHHHHh
Q psy879          188 -----------QGDMRQALNNLQSTHN-----GFGHVTAEYVFK  215 (317)
Q Consensus       188 -----------~gd~r~~i~~l~~~~~-----~~~~i~~~~v~~  215 (317)
                                 +.++|.+++.++.+..     +...++.+++.+
T Consensus       249 ~~~~~~~~~~~~~s~R~~~~ll~~a~a~A~l~g~~~v~~~dv~~  292 (331)
T 2r44_A          249 GLEAEASYILYGASTRAAINLNRVAKAMAFFNNRDYVLPEDIKE  292 (331)
T ss_dssp             TCHHHHHHEEECCCHHHHHHHHHHHHHHHHHTTCSBCCHHHHHH
T ss_pred             cccccccccccCcChhHHHHHHHHHHHHHHHcCCCCCCHHHHHH
Confidence                       2279999888875322     445688877754

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20

Probab=99.85  E-value=1.2e-19  Score=153.87  Aligned_cols=202  Identities=16%  Similarity=0.157  Sum_probs=143.8

Q ss_pred             cccCCCCCCcccCCHHHHHHHHHHHhc-----------CC-CceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecC
Q psy879            2 EKYRPQTFSDIVGNEDTVERLKVFSSS-----------GN-VPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNA   69 (317)
Q Consensus         2 ~ky~P~~~~~~~g~~~~~~~l~~~l~~-----------~~-~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~   69 (317)
                      ++++|.+|++++|++++++.+...+..           .. +.+++|+||||||||++++++++.+.     .+++.+++
T Consensus         4 ~~~~~~~~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~~~-----~~~~~i~~   78 (257)
T 1lv7_A            4 EDQIKTTFADVAGCDEAKEEVAELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGEAK-----VPFFTISG   78 (257)
T ss_dssp             ECSSCCCGGGSCSCHHHHHHTHHHHHHHHCGGGC-----CCCCEEEEECCTTSCHHHHHHHHHHHHT-----CCEEEECS
T ss_pred             ccCCCCCHHHhcCcHHHHHHHHHHHHHHhCHHHHHHcCCCCCCeEEEECcCCCCHHHHHHHHHHHcC-----CCEEEEeH
Confidence            578899999999999999887665431           12 23599999999999999999999873     23566665


Q ss_pred             CCCc------ChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCH--------------HHHHHHHHHhhhc--cCCc
Q psy879           70 SNDR------GIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTD--------------GAQQALRRTMEIY--SNTT  127 (317)
Q Consensus        70 ~~~~------~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~--------------~~~~~ll~~le~~--~~~~  127 (317)
                      ....      ....++..+.....       ..+.++++||+|.+..              ...+.++..++..  ....
T Consensus        79 ~~~~~~~~~~~~~~~~~~~~~a~~-------~~~~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~  151 (257)
T 1lv7_A           79 SDFVEMFVGVGASRVRDMFEQAKK-------AAPCIIFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDGFEGNEGI  151 (257)
T ss_dssp             CSSTTSCCCCCHHHHHHHHHHHHT-------TCSEEEEETTHHHHTCCCSTTSCCTTCHHHHHHHHHHHHHHTCCSSSCE
T ss_pred             HHHHHHhhhhhHHHHHHHHHHHHH-------cCCeeehhhhhhhhccCCCCCcCCCchHHHHHHHHHHHHhhCcccCCCE
Confidence            4321      22333333333211       3467999999987642              3456677777643  4457


Q ss_pred             eEEEEecCCCcCchhHhh--hcce-eeecCCCHHHHHHHHHHHHHHcCCCCCHH-HHHHHHHhcCC-CHHHHHHHHHHhh
Q psy879          128 RFALACNNSEKIIEPIQS--RCAM-LRYNKLTDAQLLSKVIEICEKENISHTND-GLEAIVFTAQG-DMRQALNNLQSTH  202 (317)
Q Consensus       128 ~~il~~~~~~~l~~~i~s--R~~~-i~f~~~~~~~~~~~l~~~~~~~~~~i~~~-~~~~l~~~~~g-d~r~~i~~l~~~~  202 (317)
                      .+|++||.++.+.+++.+  |+.. +.|++|+.++..+++...+....  ++++ ....++..+.| +.|++.+.++.++
T Consensus       152 ~vI~~tn~~~~l~~~l~r~~rf~~~i~i~~P~~~~r~~il~~~~~~~~--l~~~~~~~~la~~~~G~~~~dl~~l~~~a~  229 (257)
T 1lv7_A          152 IVIAATNRPDVLDPALLRPGRFDRQVVVGLPDVRGREQILKVHMRRVP--LAPDIDAAIIARGTPGFSGADLANLVNEAA  229 (257)
T ss_dssp             EEEEEESCTTTSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTSC--BCTTCCHHHHHHTCTTCCHHHHHHHHHHHH
T ss_pred             EEEEeeCCchhCCHHHcCCCcCCeEEEeCCCCHHHHHHHHHHHHhcCC--CCccccHHHHHHHcCCCCHHHHHHHHHHHH
Confidence            788899999999999987  7755 89999999999999988776543  3333 36778888999 8998888887644


Q ss_pred             h-----CCCcccHHHHHhhc
Q psy879          203 N-----GFGHVTAEYVFKVC  217 (317)
Q Consensus       203 ~-----~~~~i~~~~v~~~~  217 (317)
                      .     +...|+.+++..++
T Consensus       230 ~~a~~~~~~~i~~~~~~~a~  249 (257)
T 1lv7_A          230 LFAARGNKRVVSMVEFEKAK  249 (257)
T ss_dssp             HHHHHTTCSSBCHHHHHHHH
T ss_pred             HHHHHhCCCcccHHHHHHHH
Confidence            3     34678888776543

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=99.85  E-value=2.7e-20  Score=166.72  Aligned_cols=200  Identities=18%  Similarity=0.253  Sum_probs=137.3

Q ss_pred             CCCCCcccCCHHHHHHHHHHHh-----------cC-CCc-eEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCC
Q psy879            6 PQTFSDIVGNEDTVERLKVFSS-----------SG-NVP-NIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASND   72 (317)
Q Consensus         6 P~~~~~~~g~~~~~~~l~~~l~-----------~~-~~~-~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~   72 (317)
                      +.+|+|+.|.+++++.|...+.           -| .+| .+|||||||||||++|+++|.++     +..++.++++..
T Consensus       177 ~~t~~digGl~~~k~~l~e~v~~pl~~pe~f~~~g~~~prGvLLyGPPGTGKTllAkAiA~e~-----~~~f~~v~~s~l  251 (434)
T 4b4t_M          177 TETYSDVGGLDKQIEELVEAIVLPMKRADKFKDMGIRAPKGALMYGPPGTGKTLLARACAAQT-----NATFLKLAAPQL  251 (434)
T ss_dssp             SCCGGGSCSCHHHHHHHHHHTHHHHHCSHHHHHHCCCCCCEEEEESCTTSSHHHHHHHHHHHH-----TCEEEEEEGGGG
T ss_pred             CCChHhcCcHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCeeEEECcCCCCHHHHHHHHHHHh-----CCCEEEEehhhh
Confidence            3579999999999999877642           12 233 49999999999999999999997     334666665432


Q ss_pred             ----c--ChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCH-----------H---HHHHHHHHhhhcc--CCceEE
Q psy879           73 ----R--GIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTD-----------G---AQQALRRTMEIYS--NTTRFA  130 (317)
Q Consensus        73 ----~--~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~-----------~---~~~~ll~~le~~~--~~~~~i  130 (317)
                          .  +...++..+......       .+.||+|||+|.+..           .   ..+.|+..|+...  .++.+|
T Consensus       252 ~~~~vGese~~ir~lF~~A~~~-------aP~IifiDEiDal~~~R~~~~~~~~~~~~~~~~~lL~~ldg~~~~~~ViVI  324 (434)
T 4b4t_M          252 VQMYIGEGAKLVRDAFALAKEK-------APTIIFIDELDAIGTKRFDSEKSGDREVQRTMLELLNQLDGFSSDDRVKVL  324 (434)
T ss_dssp             CSSCSSHHHHHHHHHHHHHHHH-------CSEEEEEECTHHHHCCCSSGGGGTTHHHHHHHHHHHHHHTTSCSSCSSEEE
T ss_pred             hhcccchHHHHHHHHHHHHHhc-------CCeEEeecchhhhhhccCCCCCCCchHHHHHHHHHHHHhhccCCCCCEEEE
Confidence                1  123344444443332       478999999997621           1   2445677776543  456788


Q ss_pred             EEecCCCcCchhHhh--hcce-eeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCC----CHHHHHHHHHHh--
Q psy879          131 LACNNSEKIIEPIQS--RCAM-LRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQG----DMRQALNNLQST--  201 (317)
Q Consensus       131 l~~~~~~~l~~~i~s--R~~~-i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~g----d~r~~i~~l~~~--  201 (317)
                      ++||.++.+++++.+  |+.. |+|+.|+.++..++++..+++..+. ++-.++.++..+.|    |++.+.+..-..  
T Consensus       325 aaTNrp~~LD~AllRpGRfD~~I~i~lPd~~~R~~Il~~~~~~~~~~-~dvdl~~lA~~t~G~sGADi~~l~~eA~~~a~  403 (434)
T 4b4t_M          325 AATNRVDVLDPALLRSGRLDRKIEFPLPSEDSRAQILQIHSRKMTTD-DDINWQELARSTDEFNGAQLKAVTVEAGMIAL  403 (434)
T ss_dssp             EECSSCCCCCTTTCSTTSEEEEEECCCCCHHHHHHHHHHHHHHSCBC-SCCCHHHHHHHCSSCCHHHHHHHHHHHHHHHH
T ss_pred             EeCCCchhcCHhHhcCCceeEEEEeCCcCHHHHHHHHHHHhcCCCCC-CcCCHHHHHHhCCCCCHHHHHHHHHHHHHHHH
Confidence            899999999999987  7766 9999999999999999888765432 12236778887755    444444332211  


Q ss_pred             hhCCCcccHHHHHhhcC
Q psy879          202 HNGFGHVTAEYVFKVCD  218 (317)
Q Consensus       202 ~~~~~~i~~~~v~~~~~  218 (317)
                      ..+...|+.+|+..++.
T Consensus       404 r~~~~~i~~~Df~~Al~  420 (434)
T 4b4t_M          404 RNGQSSVKHEDFVEGIS  420 (434)
T ss_dssp             HHTCSSBCHHHHHHHHH
T ss_pred             HcCCCCcCHHHHHHHHH
Confidence            12556788887766544

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=99.85  E-value=6.5e-20  Score=157.75  Aligned_cols=201  Identities=18%  Similarity=0.188  Sum_probs=139.2

Q ss_pred             cCCCCCCcccCCHHHHHHHHHHHhc-------------CCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCC
Q psy879            4 YRPQTFSDIVGNEDTVERLKVFSSS-------------GNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNAS   70 (317)
Q Consensus         4 y~P~~~~~~~g~~~~~~~l~~~l~~-------------~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~   70 (317)
                      ..+.+|++++|++.+++.+..++..             ....+++|+||||||||++++++++.+.     ..++.+++.
T Consensus        11 ~~~~~~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ll~G~~GtGKT~la~~la~~~~-----~~~~~v~~~   85 (285)
T 3h4m_A           11 RPNVRYEDIGGLEKQMQEIREVVELPLKHPELFEKVGIEPPKGILLYGPPGTGKTLLAKAVATETN-----ATFIRVVGS   85 (285)
T ss_dssp             SCCCCGGGSCSCHHHHHHHHHHTHHHHHCHHHHHHHCCCCCSEEEEESSSSSSHHHHHHHHHHHTT-----CEEEEEEGG
T ss_pred             CCCCCHHHhcCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCeEEEECCCCCcHHHHHHHHHHHhC-----CCEEEEehH
Confidence            3445799999999999998887643             2334599999999999999999999862     335555543


Q ss_pred             CCc----C--hHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCC-----------CHHHHHHHHHHhhh-----ccCCce
Q psy879           71 NDR----G--IDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSM-----------TDGAQQALRRTMEI-----YSNTTR  128 (317)
Q Consensus        71 ~~~----~--~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l-----------~~~~~~~ll~~le~-----~~~~~~  128 (317)
                      ...    +  ...+...+.....       ..+.|++|||+|.+           ....+..+..+++.     ....+.
T Consensus        86 ~~~~~~~~~~~~~~~~~~~~~~~-------~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~l~~ll~~~~~~~~~~~~~  158 (285)
T 3h4m_A           86 ELVKKFIGEGASLVKDIFKLAKE-------KAPSIIFIDEIDAIAAKRTDALTGGDREVQRTLMQLLAEMDGFDARGDVK  158 (285)
T ss_dssp             GGCCCSTTHHHHHHHHHHHHHHH-------TCSEEEEEETTHHHHBCCSSSCCGGGGHHHHHHHHHHHHHHTTCSSSSEE
T ss_pred             HHHHhccchHHHHHHHHHHHHHH-------cCCeEEEEECHHHhcccCccccCCccHHHHHHHHHHHHHhhCCCCCCCEE
Confidence            211    1  1222333332221       34679999999987           44556666666653     335678


Q ss_pred             EEEEecCCCcCchhHhh--hcc-eeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCC-CHHHHHHHHHHh---
Q psy879          129 FALACNNSEKIIEPIQS--RCA-MLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQG-DMRQALNNLQST---  201 (317)
Q Consensus       129 ~il~~~~~~~l~~~i~s--R~~-~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~g-d~r~~i~~l~~~---  201 (317)
                      +|++||.+..+.+++.+  |+. .+.|++|+.++..+++...+...+.. ++..+..++..+.| +.+.+..+++.+   
T Consensus       159 vI~ttn~~~~l~~~l~~~~Rf~~~i~~~~p~~~~r~~il~~~~~~~~~~-~~~~~~~l~~~~~g~~~~~i~~l~~~a~~~  237 (285)
T 3h4m_A          159 IIGATNRPDILDPAILRPGRFDRIIEVPAPDEKGRLEILKIHTRKMNLA-EDVNLEEIAKMTEGCVGAELKAICTEAGMN  237 (285)
T ss_dssp             EEEECSCGGGBCHHHHSTTSEEEEEECCCCCHHHHHHHHHHHHTTSCBC-TTCCHHHHHHHCTTCCHHHHHHHHHHHHHH
T ss_pred             EEEeCCCchhcCHHHcCCCcCCeEEEECCCCHHHHHHHHHHHHhcCCCC-CcCCHHHHHHHcCCCCHHHHHHHHHHHHHH
Confidence            89999999999999998  886 49999999999999999988765543 23346777777766 444444444432   


Q ss_pred             hh--CCCcccHHHHHhhc
Q psy879          202 HN--GFGHVTAEYVFKVC  217 (317)
Q Consensus       202 ~~--~~~~i~~~~v~~~~  217 (317)
                      +.  +...|+.+++.+++
T Consensus       238 a~~~~~~~I~~~d~~~al  255 (285)
T 3h4m_A          238 AIRELRDYVTMDDFRKAV  255 (285)
T ss_dssp             HHHTTCSSBCHHHHHHHH
T ss_pred             HHHhccCcCCHHHHHHHH
Confidence            22  45568888876543

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=99.85  E-value=1.3e-19  Score=162.48  Aligned_cols=197  Identities=20%  Similarity=0.256  Sum_probs=135.2

Q ss_pred             CCCCcccCCHHHHHHHHHHHhc-----------C-CCc-eEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCc
Q psy879            7 QTFSDIVGNEDTVERLKVFSSS-----------G-NVP-NIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDR   73 (317)
Q Consensus         7 ~~~~~~~g~~~~~~~l~~~l~~-----------~-~~~-~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~   73 (317)
                      -+|+|+.|.+++++.|...+.-           | .+| .+|||||||||||++|+++|.++.     ..++.++++...
T Consensus       178 v~~~digGl~~~k~~l~e~v~~pl~~p~~f~~~g~~~prGvLL~GPPGtGKTllAkAiA~e~~-----~~~~~v~~s~l~  252 (437)
T 4b4t_L          178 ITFDGIGGLTEQIRELREVIELPLKNPEIFQRVGIKPPKGVLLYGPPGTGKTLLAKAVAATIG-----ANFIFSPASGIV  252 (437)
T ss_dssp             SCSGGGCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCCEEEEESCTTSSHHHHHHHHHHHHT-----CEEEEEEGGGTC
T ss_pred             CChhHhCChHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCeEEEECCCCCcHHHHHHHHHHHhC-----CCEEEEehhhhc
Confidence            3599999999999988776531           2 233 399999999999999999999973     346666654321


Q ss_pred             ----C--hHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCH--------------HHHHHHHHHhhhc--cCCceEEE
Q psy879           74 ----G--IDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTD--------------GAQQALRRTMEIY--SNTTRFAL  131 (317)
Q Consensus        74 ----~--~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~--------------~~~~~ll~~le~~--~~~~~~il  131 (317)
                          +  ...++..+.....       ..+.||+|||+|.+..              ...+.|+..|+..  ..++.+|+
T Consensus       253 sk~~Gese~~ir~~F~~A~~-------~~P~IifiDEiDai~~~R~~~~~~~~~~~~~~l~~lL~~lDg~~~~~~vivI~  325 (437)
T 4b4t_L          253 DKYIGESARIIREMFAYAKE-------HEPCIIFMDEVDAIGGRRFSEGTSADREIQRTLMELLTQMDGFDNLGQTKIIM  325 (437)
T ss_dssp             CSSSSHHHHHHHHHHHHHHH-------SCSEEEEEECCCSSSCCCSSSCCSSTTHHHHHHHHHHHHHHSSSCTTSSEEEE
T ss_pred             cccchHHHHHHHHHHHHHHh-------cCCceeeeecccccccccccCCCCcchHHHHHHHHHHHHhhcccCCCCeEEEE
Confidence                1  2234444433322       3578999999998742              1245677777744  34578999


Q ss_pred             EecCCCcCchhHhhhc--ce-eeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCC----CHHHHHHHHHHh--h
Q psy879          132 ACNNSEKIIEPIQSRC--AM-LRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQG----DMRQALNNLQST--H  202 (317)
Q Consensus       132 ~~~~~~~l~~~i~sR~--~~-i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~g----d~r~~i~~l~~~--~  202 (317)
                      +||.++.+++++++++  .. |+|+.|+.++...+++..+++.... ++..++.++..+.|    |++.+.+..-..  .
T Consensus       326 ATNrp~~LDpAllRpGRfD~~I~i~lPd~~~R~~Il~~~~~~~~~~-~d~dl~~lA~~t~G~sGADi~~l~~eA~~~air  404 (437)
T 4b4t_L          326 ATNRPDTLDPALLRPGRLDRKVEIPLPNEAGRLEIFKIHTAKVKKT-GEFDFEAAVKMSDGFNGADIRNCATEAGFFAIR  404 (437)
T ss_dssp             EESSTTSSCTTTTSTTSEEEEECCCCCCHHHHHHHHHHHHHTSCBC-SCCCHHHHHHTCCSCCHHHHHHHHHHHHHHHHH
T ss_pred             ecCCchhhCHHHhCCCccceeeecCCcCHHHHHHHHHHHhcCCCCC-cccCHHHHHHhCCCCCHHHHHHHHHHHHHHHHH
Confidence            9999999999998774  43 9999999999999998887754332 22336788888765    444444332211  1


Q ss_pred             hCCCcccHHHHHhh
Q psy879          203 NGFGHVTAEYVFKV  216 (317)
Q Consensus       203 ~~~~~i~~~~v~~~  216 (317)
                      .+...|+.+++..+
T Consensus       405 ~~~~~i~~~d~~~A  418 (437)
T 4b4t_L          405 DDRDHINPDDLMKA  418 (437)
T ss_dssp             TTCSSBCHHHHHHH
T ss_pred             cCCCCCCHHHHHHH
Confidence            24556777776543

>2qz4_A Paraplegin; AAA+, SPG7, protease, ADP, structural genomics, structural G consortium, SGC, ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.22A {Homo sapiens}

Probab=99.85  E-value=2.7e-19  Score=151.95  Aligned_cols=197  Identities=16%  Similarity=0.118  Sum_probs=129.5

Q ss_pred             CCCCCcccCCHHHHHHHHHHHhc------------CCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCc
Q psy879            6 PQTFSDIVGNEDTVERLKVFSSS------------GNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDR   73 (317)
Q Consensus         6 P~~~~~~~g~~~~~~~l~~~l~~------------~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~   73 (317)
                      +.+|++++|++++++.+...+..            ....+++|+||||||||++++++++.+.     ..++.+++....
T Consensus         2 ~~~~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~g~~~~~~vll~G~~GtGKT~la~~la~~~~-----~~~~~~~~~~~~   76 (262)
T 2qz4_A            2 GVSFKDVAGMHEAKLEVREFVDYLKSPERFLQLGAKVPKGALLLGPPGCGKTLLAKAVATEAQ-----VPFLAMAGAEFV   76 (262)
T ss_dssp             CCCTTSSCSCHHHHHHHHHHHHHHHCCC------CCCCCEEEEESCTTSSHHHHHHHHHHHHT-----CCEEEEETTTTS
T ss_pred             CCCHHHhCCHHHHHHHHHHHHHHHHCHHHHHHcCCCCCceEEEECCCCCCHHHHHHHHHHHhC-----CCEEEechHHHH
Confidence            35799999999999988776531            2233599999999999999999999873     335656554321


Q ss_pred             C------hHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCH------------HHHHH---HHHHhhh--ccCCceEE
Q psy879           74 G------IDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTD------------GAQQA---LRRTMEI--YSNTTRFA  130 (317)
Q Consensus        74 ~------~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~------------~~~~~---ll~~le~--~~~~~~~i  130 (317)
                      .      ...++..+.....       ..+.+|+|||+|.+..            ..+..   |+..++.  .+..+.+|
T Consensus        77 ~~~~~~~~~~~~~~~~~a~~-------~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~l~~ll~~~~~~~~~~~~~vi  149 (262)
T 2qz4_A           77 EVIGGLGAARVRSLFKEARA-------RAPCIVYIDEIDAVGKKRSTTMSGFSNTEEEQTLNQLLVEMDGMGTTDHVIVL  149 (262)
T ss_dssp             SSSTTHHHHHHHHHHHHHHH-------TCSEEEEEECC-------------------CHHHHHHHHHHHTCCTTCCEEEE
T ss_pred             hhccChhHHHHHHHHHHHHh-------cCCeEEEEeCcchhhccccccccCccchhHHHHHHHHHHHhhCcCCCCCEEEE
Confidence            1      1223333332221       2468999999999832            22333   4444443  23467788


Q ss_pred             EEecCCCcCchhHhh--hcc-eeeecCCCHHHHHHHHHHHHHHcCCCCCHHH-HHHHHHhcCCC-HHHHHHHHHHhhh--
Q psy879          131 LACNNSEKIIEPIQS--RCA-MLRYNKLTDAQLLSKVIEICEKENISHTNDG-LEAIVFTAQGD-MRQALNNLQSTHN--  203 (317)
Q Consensus       131 l~~~~~~~l~~~i~s--R~~-~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~-~~~l~~~~~gd-~r~~i~~l~~~~~--  203 (317)
                      +++|.+..+++++.+  |+. .+.|++|+.++...++...+...+...+.+. ...++..+.|. .+.+.+.++.++.  
T Consensus       150 ~~tn~~~~ld~~l~~~~R~~~~i~i~~p~~~~r~~il~~~~~~~~~~~~~~~~~~~l~~~~~g~~~~~l~~l~~~a~~~a  229 (262)
T 2qz4_A          150 ASTNRADILDGALMRPGRLDRHVFIDLPTLQERREIFEQHLKSLKLTQSSTFYSQRLAELTPGFSGADIANICNEAALHA  229 (262)
T ss_dssp             EEESCGGGGGSGGGSTTSCCEEEECCSCCHHHHHHHHHHHHHHTTCCBTHHHHHHHHHHTCTTCCHHHHHHHHHHHHTC-
T ss_pred             ecCCChhhcCHHHhcCCcCCeEEEeCCcCHHHHHHHHHHHHHhCCCCcchhhHHHHHHHHCCCCCHHHHHHHHHHHHHHH
Confidence            899999999999998  985 4999999999999999999988887776654 46788887764 4455555555433  


Q ss_pred             ---CCCcccHHHHH
Q psy879          204 ---GFGHVTAEYVF  214 (317)
Q Consensus       204 ---~~~~i~~~~v~  214 (317)
                         +...|+.+++.
T Consensus       230 ~~~~~~~i~~~d~~  243 (262)
T 2qz4_A          230 AREGHTSVHTLNFE  243 (262)
T ss_dssp             -------CCBCCHH
T ss_pred             HHcCCCCCCHHHHH
Confidence               22345555443

>4b4t_H 26S protease regulatory subunit 7 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=99.84  E-value=2.7e-19  Score=159.87  Aligned_cols=198  Identities=19%  Similarity=0.249  Sum_probs=136.2

Q ss_pred             CC-CCCCcccCCHHHHHHHHHHHh-----------cC-CCc-eEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCC
Q psy879            5 RP-QTFSDIVGNEDTVERLKVFSS-----------SG-NVP-NIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNAS   70 (317)
Q Consensus         5 ~P-~~~~~~~g~~~~~~~l~~~l~-----------~~-~~~-~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~   70 (317)
                      +| -+|+|+.|.+++++.|+..+.           -| .+| .+|||||||||||++|+++|+++.     ..++.++++
T Consensus       203 ~P~vt~~DIgGl~~~k~~L~e~V~~pl~~pe~f~~~Gi~pprGILLyGPPGTGKTlLAkAiA~e~~-----~~fi~vs~s  277 (467)
T 4b4t_H          203 KPDVTYSDVGGCKDQIEKLREVVELPLLSPERFATLGIDPPKGILLYGPPGTGKTLCARAVANRTD-----ATFIRVIGS  277 (467)
T ss_dssp             SCSCCCSSCTTCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCSEEEECSCTTSSHHHHHHHHHHHHT-----CEEEEEEGG
T ss_pred             CCCCCHHHhccHHHHHHHHHHHHHHHhcCHHHHHHCCCCCCCceEeeCCCCCcHHHHHHHHHhccC-----CCeEEEEhH
Confidence            45 469999999999999887653           13 333 499999999999999999999973     346666654


Q ss_pred             CC----c--ChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCH-----------H---HHHHHHHHhhhc--cCCce
Q psy879           71 ND----R--GIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTD-----------G---AQQALRRTMEIY--SNTTR  128 (317)
Q Consensus        71 ~~----~--~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~-----------~---~~~~ll~~le~~--~~~~~  128 (317)
                      ..    .  +...++..+.....       ..+.||+|||+|.+..           .   ..+.|+..|+..  ...+.
T Consensus       278 ~L~sk~vGesek~ir~lF~~Ar~-------~aP~IIfiDEiDai~~~R~~~~~~~~~~~~~~l~~lL~~lDg~~~~~~Vi  350 (467)
T 4b4t_H          278 ELVQKYVGEGARMVRELFEMART-------KKACIIFFDEIDAVGGARFDDGAGGDNEVQRTMLELITQLDGFDPRGNIK  350 (467)
T ss_dssp             GGCCCSSSHHHHHHHHHHHHHHH-------TCSEEEEEECCTTTSBCCSSSSCGGGGHHHHHHHHHHHHHHSSCCTTTEE
T ss_pred             HhhcccCCHHHHHHHHHHHHHHh-------cCCceEeecccccccccccCcCCCccHHHHHHHHHHHHHhhccCCCCcEE
Confidence            32    1  12334454444332       3578999999998742           1   234555556533  34567


Q ss_pred             EEEEecCCCcCchhHhh--hcce-eeecCCCHHHHHHHHHHHHHHcCCCCCH-HHHHHHHHhcCC----CHHHHHHHHHH
Q psy879          129 FALACNNSEKIIEPIQS--RCAM-LRYNKLTDAQLLSKVIEICEKENISHTN-DGLEAIVFTAQG----DMRQALNNLQS  200 (317)
Q Consensus       129 ~il~~~~~~~l~~~i~s--R~~~-i~f~~~~~~~~~~~l~~~~~~~~~~i~~-~~~~~l~~~~~g----d~r~~i~~l~~  200 (317)
                      +|++||.++.+++++.+  |+.. |+|+.|+.++..++++.++++..+  ++ -.++.++..+.|    |++.+.+..-.
T Consensus       351 VIaATNrpd~LDpALlRpGRFD~~I~i~lPd~~~R~~Ilk~~l~~~~l--~~dvdl~~LA~~T~GfSGADI~~l~~eAa~  428 (467)
T 4b4t_H          351 VMFATNRPNTLDPALLRPGRIDRKVEFSLPDLEGRANIFRIHSKSMSV--ERGIRWELISRLCPNSTGAELRSVCTEAGM  428 (467)
T ss_dssp             EEEECSCTTSBCHHHHSTTTCCEEECCCCCCHHHHHHHHHHHHTTSCB--CSSCCHHHHHHHCCSCCHHHHHHHHHHHHH
T ss_pred             EEeCCCCcccCChhhhccccccEEEEeCCcCHHHHHHHHHHHhcCCCC--CCCCCHHHHHHHCCCCCHHHHHHHHHHHHH
Confidence            88999999999999987  8876 999999999999999888765433  22 236778887765    45444433221


Q ss_pred             h--hhCCCcccHHHHHhh
Q psy879          201 T--HNGFGHVTAEYVFKV  216 (317)
Q Consensus       201 ~--~~~~~~i~~~~v~~~  216 (317)
                      .  ..+...++.+++..+
T Consensus       429 ~Air~~~~~it~~Df~~A  446 (467)
T 4b4t_H          429 FAIRARRKVATEKDFLKA  446 (467)
T ss_dssp             HHHHHTCSSBCHHHHHHH
T ss_pred             HHHHcCCCccCHHHHHHH
Confidence            1  125566777776543

>4b4t_I 26S protease regulatory subunit 4 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=99.84  E-value=2e-19  Score=159.18  Aligned_cols=197  Identities=22%  Similarity=0.260  Sum_probs=135.6

Q ss_pred             CCCCcccCCHHHHHHHHHHHh-----------cC-CCc-eEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCC-
Q psy879            7 QTFSDIVGNEDTVERLKVFSS-----------SG-NVP-NIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASND-   72 (317)
Q Consensus         7 ~~~~~~~g~~~~~~~l~~~l~-----------~~-~~~-~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~-   72 (317)
                      .+|+|+.|.+++++.|...+.           -| .+| .+|||||||||||++|+++|.++     +..++.++.+.. 
T Consensus       179 v~~~DIgGld~~k~~L~e~v~~Pl~~pe~f~~~Gi~~prGvLLyGPPGTGKTlLAkAiA~e~-----~~~fi~v~~s~l~  253 (437)
T 4b4t_I          179 ESYSDIGGLESQIQEIKESVELPLTHPELYEEMGIKPPKGVILYGAPGTGKTLLAKAVANQT-----SATFLRIVGSELI  253 (437)
T ss_dssp             CCGGGTCSCHHHHHHHHHHHHHHHHCCHHHHHHTCCCCSEEEEESSTTTTHHHHHHHHHHHH-----TCEEEEEESGGGC
T ss_pred             CcceecCcHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCCCceECCCCchHHHHHHHHHHHh-----CCCEEEEEHHHhh
Confidence            479999999999999887653           12 233 49999999999999999999997     344666665432 


Q ss_pred             ---cC--hHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCH-----------H---HHHHHHHHhhhc--cCCceEEE
Q psy879           73 ---RG--IDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTD-----------G---AQQALRRTMEIY--SNTTRFAL  131 (317)
Q Consensus        73 ---~~--~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~-----------~---~~~~ll~~le~~--~~~~~~il  131 (317)
                         .+  ...++..+.....       ..+.||+|||+|.+..           .   ..+.|+..++..  ..++.+|+
T Consensus       254 sk~vGesek~ir~lF~~Ar~-------~aP~IIfiDEiDai~~~R~~~~~~~~~~~~~~l~~LL~~lDg~~~~~~ViVIa  326 (437)
T 4b4t_I          254 QKYLGDGPRLCRQIFKVAGE-------NAPSIVFIDEIDAIGTKRYDSNSGGEREIQRTMLELLNQLDGFDDRGDVKVIM  326 (437)
T ss_dssp             CSSSSHHHHHHHHHHHHHHH-------TCSEEEEEEEESSSSCCCSCSSCSSCCHHHHHHHHHHHHHHHCCCSSSEEEEE
T ss_pred             hccCchHHHHHHHHHHHHHh-------cCCcEEEEehhhhhcccCCCCCCCccHHHHHHHHHHHHHhhCcCCCCCEEEEE
Confidence               11  2334444444332       3578999999998742           1   244556666533  35678899


Q ss_pred             EecCCCcCchhHhh--hcce-eeecCCCHHHHHHHHHHHHHHcCCCCCHH-HHHHHHHhcCC----CHHHHHHHHHHhh-
Q psy879          132 ACNNSEKIIEPIQS--RCAM-LRYNKLTDAQLLSKVIEICEKENISHTND-GLEAIVFTAQG----DMRQALNNLQSTH-  202 (317)
Q Consensus       132 ~~~~~~~l~~~i~s--R~~~-i~f~~~~~~~~~~~l~~~~~~~~~~i~~~-~~~~l~~~~~g----d~r~~i~~l~~~~-  202 (317)
                      +||.++.+++++.+  |+.. |+|+.|+.++..+++..++++..  ++++ .++.++..+.|    |+..+.+..-..+ 
T Consensus       327 ATNrpd~LDpALlRpGRfD~~I~v~lPd~~~R~~Il~~~l~~~~--l~~dvdl~~LA~~T~GfSGADI~~l~~eA~~~Ai  404 (437)
T 4b4t_I          327 ATNKIETLDPALIRPGRIDRKILFENPDLSTKKKILGIHTSKMN--LSEDVNLETLVTTKDDLSGADIQAMCTEAGLLAL  404 (437)
T ss_dssp             EESCSTTCCTTSSCTTTEEEEECCCCCCHHHHHHHHHHHHTTSC--BCSCCCHHHHHHHCCSCCHHHHHHHHHHHHHHHH
T ss_pred             eCCChhhcCHHHhcCCceeEEEEcCCcCHHHHHHHHHHHhcCCC--CCCcCCHHHHHHhCCCCCHHHHHHHHHHHHHHHH
Confidence            99999999999987  7765 99999999999999988876543  3332 36778877654    4444443322211 


Q ss_pred             -hCCCcccHHHHHhhc
Q psy879          203 -NGFGHVTAEYVFKVC  217 (317)
Q Consensus       203 -~~~~~i~~~~v~~~~  217 (317)
                       .+...|+.+|+..++
T Consensus       405 r~~~~~It~eDf~~Al  420 (437)
T 4b4t_I          405 RERRMQVTAEDFKQAK  420 (437)
T ss_dssp             HTTCSCBCHHHHHHHH
T ss_pred             HcCCCccCHHHHHHHH
Confidence             244567777765543

>1g8p_A Magnesium-chelatase 38 kDa subunit; parallel beta sheet, P-loop, rossman fold, AAA+, photosynthesis, metal transport; 2.10A {Rhodobacter capsulatus} SCOP: c.37.1.20 PDB: 2x31_G

Probab=99.83  E-value=7.3e-20  Score=162.01  Aligned_cols=211  Identities=18%  Similarity=0.189  Sum_probs=140.5

Q ss_pred             CCCCCCcccCCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcC------CCCCC----------------
Q psy879            5 RPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLG------PSFKD----------------   62 (317)
Q Consensus         5 ~P~~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~------~~~~~----------------   62 (317)
                      +|.+|++++|++++++.+......+...+++|+||||||||++|+++++.+..      ...+.                
T Consensus        19 ~~~~f~~i~G~~~~~~~l~~~~~~~~~~~vLl~G~~GtGKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   98 (350)
T 1g8p_A           19 PVFPFSAIVGQEDMKLALLLTAVDPGIGGVLVFGDRGTGKSTAVRALAALLPEIEAVEGCPVSSPNVEMIPDWATVLSTN   98 (350)
T ss_dssp             CCCCGGGSCSCHHHHHHHHHHHHCGGGCCEEEECCGGGCTTHHHHHHHHHSCCEEEETTCTTCCSSGGGSCTTCCCSCCC
T ss_pred             CCCCchhccChHHHHHHHHHHhhCCCCceEEEECCCCccHHHHHHHHHHhCccccccccccccccccccccchhhhhccc
Confidence            56789999999998887766655444457999999999999999999998642      01100                


Q ss_pred             ------ceEEecCCCCcChHHH------HHHHHHHHhh--cccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhc-----
Q psy879           63 ------AVLELNASNDRGIDTV------RNKIKMFAQQ--KVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIY-----  123 (317)
Q Consensus        63 ------~~~~~~~~~~~~~~~i------~~~~~~~~~~--~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~-----  123 (317)
                            .++.....  .....+      ...+......  +.....+.+.+++|||++.+..+.++.|++.+++.     
T Consensus        99 ~~~~~~~~~~~~~~--~~~~~l~g~~~~~~~~~~~~~~~~~g~~~~a~~~vl~iDEi~~l~~~~~~~Ll~~le~~~~~~~  176 (350)
T 1g8p_A           99 VIRKPTPVVDLPLG--VSEDRVVGALDIERAISKGEKAFEPGLLARANRGYLYIDECNLLEDHIVDLLLDVAQSGENVVE  176 (350)
T ss_dssp             EEEECCCEEEECTT--CCHHHHHCEECHHHHHHHCGGGEECCHHHHHTTEEEEETTGGGSCHHHHHHHHHHHHHSEEEEC
T ss_pred             cccCCCcccccCCC--cchhhheeechhhhhhcCCceeecCceeeecCCCEEEEeChhhCCHHHHHHHHHHHhcCceEEE
Confidence                  01111110  111111      1111110000  00000123679999999999999999999999963     


Q ss_pred             --------cCCceEEEEecCCC-cCchhHhhhcce-eeecCCCH-HHHHHHHHHH-------------------------
Q psy879          124 --------SNTTRFALACNNSE-KIIEPIQSRCAM-LRYNKLTD-AQLLSKVIEI-------------------------  167 (317)
Q Consensus       124 --------~~~~~~il~~~~~~-~l~~~i~sR~~~-i~f~~~~~-~~~~~~l~~~-------------------------  167 (317)
                              +..+.+|+++|... .+.+++.+||.. +.+++|+. ++...++...                         
T Consensus       177 ~~g~~~~~~~~~~li~~~n~~~~~l~~~L~~R~~~~~~l~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~~~~~~~~i  256 (350)
T 1g8p_A          177 RDGLSIRHPARFVLVGSGNPEEGDLRPQLLDRFGLSVEVLSPRDVETRVEVIRRRDTYDADPKAFLEEWRPKDMDIRNQI  256 (350)
T ss_dssp             CTTCCEEEECCEEEEEEECSCSCCCCHHHHTTCSEEEECCCCCSHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHH
T ss_pred             ecceEEeeCCceEEEEEeCCCCCCCCHHHHhhcceEEEcCCCCcHHHHHHHHHHHHhcccCchhhccccccchHHHHHHH
Confidence                    23667788888744 899999999987 99999954 4443555431                         


Q ss_pred             ----HHHcCCCCCHHHHHHHHHhcCC----CHHHHHHHHHHhhh-----CCCcccHHHHHhhc
Q psy879          168 ----CEKENISHTNDGLEAIVFTAQG----DMRQALNNLQSTHN-----GFGHVTAEYVFKVC  217 (317)
Q Consensus       168 ----~~~~~~~i~~~~~~~l~~~~~g----d~r~~i~~l~~~~~-----~~~~i~~~~v~~~~  217 (317)
                          ....++.+++++++.++..+.+    ++|.+++.++.+..     +...|+.+++..++
T Consensus       257 ~~~~~~~~~~~ls~~~~~~l~~~~~~~~~~~~R~~~~ll~~a~~~A~~~~~~~v~~~~v~~a~  319 (350)
T 1g8p_A          257 LEARERLPKVEAPNTALYDCAALCIALGSDGLRGELTLLRSARALAALEGATAVGRDHLKRVA  319 (350)
T ss_dssp             HHHHHHGGGCBCCHHHHHHHHHHHHHSSSCSHHHHHHHHHHHHHHHHHTTCSBCCHHHHHHHH
T ss_pred             HHHHHhCCCCCCCHHHHHHHHHHHHHhCCCCccHHHHHHHHHHHHHHHcCCCcCCHHHHHHHH
Confidence                2234568999999999988766    89999999975432     44568888886543

>3pxg_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 3.65A {Bacillus subtilis}

Probab=99.83  E-value=3.3e-20  Score=169.99  Aligned_cols=189  Identities=17%  Similarity=0.260  Sum_probs=138.1

Q ss_pred             cccCCCCCCcccCCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCC-----CCCceEEecCCC-CcC-
Q psy879            2 EKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPS-----FKDAVLELNASN-DRG-   74 (317)
Q Consensus         2 ~ky~P~~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~-----~~~~~~~~~~~~-~~~-   74 (317)
                      ++|+|.+|++++|++..++.+...+..+..+|++|+||||+|||++++++++.+.+..     .+..++.+++.. ..+ 
T Consensus       172 ~~~r~~~ld~iiGr~~~i~~l~~~l~r~~~~~~LL~G~pG~GKT~la~~la~~l~~~~~p~~l~~~~~~~l~~~~~~~g~  251 (468)
T 3pxg_A          172 AIAKEDSLDPVIGRSKEIQRVIEVLSRRTKNNPVLIGEPGVGKTAIAEGLAQQIINNEVPEILRDKRVMTLDMGTKYRGE  251 (468)
T ss_dssp             HHTTSSCSCCCCCCHHHHHHHHHHHHCSSSCEEEEESCTTTTTHHHHHHHHHHHHSSCSCTTTSSCCEECC---------
T ss_pred             HHHhcCCCCCccCcHHHHHHHHHHHhccCCCCeEEECCCCCCHHHHHHHHHHHHHhCCCChhhcCCeEEEeeCCccccch
Confidence            5799999999999999999999999887777899999999999999999999985422     133455555431 111 


Q ss_pred             -hHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCC-----cCchhHhhhcc
Q psy879           75 -IDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSE-----KIIEPIQSRCA  148 (317)
Q Consensus        75 -~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~-----~l~~~i~sR~~  148 (317)
                       ...+...+..+..       ..+.|++||    ...+.++.|++.|+.  +...+|++||...     .+++++.+||.
T Consensus       252 ~e~~~~~~~~~~~~-------~~~~iLfiD----~~~~a~~~L~~~L~~--g~v~vI~at~~~e~~~~~~~~~al~~Rf~  318 (468)
T 3pxg_A          252 FEDRLKKVMDEIRQ-------AGNIILFID----AAIDASNILKPSLAR--GELQCIGATTLDEYRKYIEKDAALERRFQ  318 (468)
T ss_dssp             -CTTHHHHHHHHHT-------CCCCEEEEC----C--------CCCTTS--SSCEEEEECCTTTTHHHHTTCSHHHHSEE
T ss_pred             HHHHHHHHHHHHHh-------cCCeEEEEe----CchhHHHHHHHhhcC--CCEEEEecCCHHHHHHHhhcCHHHHHhCc
Confidence             1223344443322       346799999    455677888888874  5678888888876     58899999999


Q ss_pred             eeeecCCCHHHHHHHHHHHHHH----cCCCCCHHHHHHHHHhcCC------CHHHHHHHHHHhhh
Q psy879          149 MLRYNKLTDAQLLSKVIEICEK----ENISHTNDGLEAIVFTAQG------DMRQALNNLQSTHN  203 (317)
Q Consensus       149 ~i~f~~~~~~~~~~~l~~~~~~----~~~~i~~~~~~~l~~~~~g------d~r~~i~~l~~~~~  203 (317)
                      .+.|++|+.++...++...+..    +++.++++++..++..+.+      -++.+++.++.++.
T Consensus       319 ~i~v~~p~~e~~~~iL~~~~~~~~~~~~~~i~~~al~~l~~~s~~~~~~~~lp~~ai~ll~~a~~  383 (468)
T 3pxg_A          319 PIQVDQPSVDESIQILQGLRDRYEAHHRVSITDDAIEAAVKLSDRYISDRFLPDKAIDLIDEAGS  383 (468)
T ss_dssp             EEECCCCCHHHHHHHHHHTTTTSGGGSSCSCCHHHHHHHHHHHHHSSCCSCTTHHHHHHHHHHHH
T ss_pred             cceeCCCCHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhccCcCCcHHHHHHHHHHH
Confidence            9999999999999999987765    7888999999998876543      25679988876543

>4fcw_A Chaperone protein CLPB; AAA domain; HET: ADP; 2.35A {Thermus thermophilus} PDB: 4fcv_A* 4fd2_A* 4fct_A*

Probab=99.83  E-value=8.6e-20  Score=158.93  Aligned_cols=185  Identities=15%  Similarity=0.178  Sum_probs=136.8

Q ss_pred             CcccCCHHHHHHHHHHHhcC--------CCc-eEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHH
Q psy879           10 SDIVGNEDTVERLKVFSSSG--------NVP-NIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRN   80 (317)
Q Consensus        10 ~~~~g~~~~~~~l~~~l~~~--------~~~-~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~   80 (317)
                      ++++|++.+++.+...+..+        ++. +++|+||||||||++|+++++.+.+..  ..++.+++...........
T Consensus        17 ~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~ll~G~~GtGKt~la~~la~~~~~~~--~~~~~~~~~~~~~~~~~~~   94 (311)
T 4fcw_A           17 KRVVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAATLFDTE--EAMIRIDMTEYMEKHAVSR   94 (311)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHTCSCTTSCSEEEEEESCSSSSHHHHHHHHHHHHHSCG--GGEEEEEGGGCCSTTHHHH
T ss_pred             hhcCCHHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCCcCHHHHHHHHHHHHcCCC--cceEEeecccccccccHHH
Confidence            46889999999988887654        222 599999999999999999999985433  2344444432222111111


Q ss_pred             HH---------------HHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhcc-----------CCceEEEEec
Q psy879           81 KI---------------KMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYS-----------NTTRFALACN  134 (317)
Q Consensus        81 ~~---------------~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~-----------~~~~~il~~~  134 (317)
                      .+               ......      ..+.+++|||+|.+..+.++.|++++++..           .++.+|++||
T Consensus        95 l~g~~~~~~~~~~~~~~~~~~~~------~~~~vl~lDEi~~l~~~~~~~Ll~~le~~~~~~~~~~~~~~~~~iiI~ttn  168 (311)
T 4fcw_A           95 LIGAPPGYVGYEEGGQLTEAVRR------RPYSVILFDAIEKAHPDVFNILLQMLDDGRLTDSHGRTVDFRNTVIIMTSN  168 (311)
T ss_dssp             HHCCCTTSTTTTTCCHHHHHHHH------CSSEEEEEETGGGSCHHHHHHHHHHHHHSEEECTTSCEEECTTEEEEEEES
T ss_pred             hcCCCCccccccccchHHHHHHh------CCCeEEEEeChhhcCHHHHHHHHHHHhcCEEEcCCCCEEECCCcEEEEecc
Confidence            11               111111      345799999999999999999999999754           3666899999


Q ss_pred             C--------------------------CCcCchhHhhhc-ceeeecCCCHHHHHHHHHHHHHHc---------CCCCCHH
Q psy879          135 N--------------------------SEKIIEPIQSRC-AMLRYNKLTDAQLLSKVIEICEKE---------NISHTND  178 (317)
Q Consensus       135 ~--------------------------~~~l~~~i~sR~-~~i~f~~~~~~~~~~~l~~~~~~~---------~~~i~~~  178 (317)
                      .                          ...+.+++.+|| ..+.|.|++.+++..++...+...         ...++++
T Consensus       169 ~~~~~i~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~R~~~~~~~~p~~~~~~~~i~~~~l~~~~~~~~~~~~~~~~~~~  248 (311)
T 4fcw_A          169 LGSPLILEGLQKGWPYERIRDEVFKVLQQHFRPEFLNRLDEIVVFRPLTKEQIRQIVEIQMSYLRARLAEKRISLELTEA  248 (311)
T ss_dssp             TTHHHHHTTTTSCCCSSTHHHHTHHHHHHHSCHHHHTTCSEEEECCCCCHHHHHHHHHHHTHHHHHHHHTTTCEEEECHH
T ss_pred             cCHHHHHhhhcccccHHHHHHHHHHHHHHhCCHHHHhcCCeEEEeCCCCHHHHHHHHHHHHHHHHHHHHhCCcEEEeCHH
Confidence            8                          346789999999 459999999999999988765542         3568899


Q ss_pred             HHHHHHHhc---CCCHHHHHHHHHHhh
Q psy879          179 GLEAIVFTA---QGDMRQALNNLQSTH  202 (317)
Q Consensus       179 ~~~~l~~~~---~gd~r~~i~~l~~~~  202 (317)
                      +++.++..+   .|++|.+.+.++.++
T Consensus       249 ~~~~l~~~~~~~~gn~R~L~~~i~~~~  275 (311)
T 4fcw_A          249 AKDFLAERGYDPVFGARPLRRVIQREL  275 (311)
T ss_dssp             HHHHHHHHSCBTTTBTTTHHHHHHHHT
T ss_pred             HHHHHHHhCCCccCCchhHHHHHHHHH
Confidence            999999865   489999988887654

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=99.82  E-value=1.1e-18  Score=156.27  Aligned_cols=197  Identities=17%  Similarity=0.277  Sum_probs=135.0

Q ss_pred             CCCCcccCCHHHHHHHHHHHhc-----------C-CCc-eEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCC-
Q psy879            7 QTFSDIVGNEDTVERLKVFSSS-----------G-NVP-NIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASND-   72 (317)
Q Consensus         7 ~~~~~~~g~~~~~~~l~~~l~~-----------~-~~~-~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~-   72 (317)
                      -+|+|+.|.+++++.|...+.-           | .+| .+|||||||||||++|+++|+++     +..++.++++.. 
T Consensus       169 v~~~digGl~~~k~~l~e~v~~pl~~p~~~~~~g~~~prGiLL~GPPGtGKT~lakAiA~~~-----~~~~~~v~~~~l~  243 (428)
T 4b4t_K          169 VTYADVGGLDMQKQEIREAVELPLVQADLYEQIGIDPPRGVLLYGPPGTGKTMLVKAVANST-----KAAFIRVNGSEFV  243 (428)
T ss_dssp             CCGGGSCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCCEEEEESCTTTTHHHHHHHHHHHH-----TCEEEEEEGGGTC
T ss_pred             CCHHHhccHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCceEEEECCCCCCHHHHHHHHHHHh-----CCCeEEEecchhh
Confidence            3699999999999988776531           3 233 39999999999999999999997     344666665432 


Q ss_pred             ---c--ChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCH--------------HHHHHHHHHhhhc--cCCceEEE
Q psy879           73 ---R--GIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTD--------------GAQQALRRTMEIY--SNTTRFAL  131 (317)
Q Consensus        73 ---~--~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~--------------~~~~~ll~~le~~--~~~~~~il  131 (317)
                         .  +...++..+.....       ..+.|+++||+|.+..              ...+.|+..|+..  ..++.+|+
T Consensus       244 ~~~~Ge~e~~ir~lF~~A~~-------~aP~IifiDEiD~i~~~R~~~~~~~~~~~~r~l~~lL~~ldg~~~~~~v~vI~  316 (428)
T 4b4t_K          244 HKYLGEGPRMVRDVFRLARE-------NAPSIIFIDEVDSIATKRFDAQTGSDREVQRILIELLTQMDGFDQSTNVKVIM  316 (428)
T ss_dssp             CSSCSHHHHHHHHHHHHHHH-------TCSEEEEEECTHHHHCSCSSSCSCCCCHHHHHHHHHHHHHHHSCSSCSEEEEE
T ss_pred             ccccchhHHHHHHHHHHHHH-------cCCCeeechhhhhhhccccCCCCCCChHHHHHHHHHHHHhhCCCCCCCEEEEE
Confidence               1  22345555554433       3578999999996521              2356777777753  44677899


Q ss_pred             EecCCCcCchhHhh--hcce-eeec-CCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCC----CHHHHHHHHHH--h
Q psy879          132 ACNNSEKIIEPIQS--RCAM-LRYN-KLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQG----DMRQALNNLQS--T  201 (317)
Q Consensus       132 ~~~~~~~l~~~i~s--R~~~-i~f~-~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~g----d~r~~i~~l~~--~  201 (317)
                      +||.++.+++++.+  |+.. |+|+ .|+.++...++..++++..+. ++..++.++..+.|    |++.+.+..-.  +
T Consensus       317 aTN~~~~LD~AllRpGRfd~~I~~p~lPd~~~R~~Il~~~~~~~~l~-~~~dl~~lA~~t~G~sgadi~~l~~eA~~~a~  395 (428)
T 4b4t_K          317 ATNRADTLDPALLRPGRLDRKIEFPSLRDRRERRLIFGTIASKMSLA-PEADLDSLIIRNDSLSGAVIAAIMQEAGLRAV  395 (428)
T ss_dssp             EESCSSSCCHHHHSSSSEEEEEECCSSCCHHHHHHHHHHHHHSSCBC-TTCCHHHHHHHTTTCCHHHHHHHHHHHHHHHH
T ss_pred             ecCChhhcChhhhcCCcceEEEEcCCCCCHHHHHHHHHHHhcCCCCC-cccCHHHHHHHCCCCCHHHHHHHHHHHHHHHH
Confidence            99999999999987  6665 8996 688899999998887754432 12236788877654    44444433211  1


Q ss_pred             hhCCCcccHHHHHhh
Q psy879          202 HNGFGHVTAEYVFKV  216 (317)
Q Consensus       202 ~~~~~~i~~~~v~~~  216 (317)
                      ..+...|+.+++.++
T Consensus       396 r~~~~~i~~~d~~~A  410 (428)
T 4b4t_K          396 RKNRYVILQSDLEEA  410 (428)
T ss_dssp             HTTCSSBCHHHHHHH
T ss_pred             HCCCCCCCHHHHHHH
Confidence            124556777776554

>3cf0_A Transitional endoplasmic reticulum ATPase; AAA, P97/VCP, ERAD, CDC48, ATP-binding, lipid-binding, nucle binding, nucleus, phosphoprotein, transport; HET: ADP; 3.00A {Mus musculus}

Probab=99.80  E-value=1.7e-18  Score=149.98  Aligned_cols=185  Identities=18%  Similarity=0.200  Sum_probs=128.9

Q ss_pred             ccCCCCCCcccCCHHHHHHHHHHHhc-----------C-CC-ceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecC
Q psy879            3 KYRPQTFSDIVGNEDTVERLKVFSSS-----------G-NV-PNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNA   69 (317)
Q Consensus         3 ky~P~~~~~~~g~~~~~~~l~~~l~~-----------~-~~-~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~   69 (317)
                      ++.+.+|++++|++.+++.|..++..           | .. .+++|+||||||||++++++++.+.     ..++.+++
T Consensus         8 ~~~~~~~~di~G~~~~~~~l~~~v~~~~~~~~~~~~~~~~~~~~vLL~Gp~GtGKT~la~ala~~~~-----~~~i~v~~   82 (301)
T 3cf0_A            8 EVPQVTWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQ-----ANFISIKG   82 (301)
T ss_dssp             ECCCCCGGGSCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCSEEEEECSSSSSHHHHHHHHHHHTT-----CEEEEECH
T ss_pred             cCCCCCHHHhCCHHHHHHHHHHHHHHHhhCHHHHHHcCCCCCceEEEECCCCcCHHHHHHHHHHHhC-----CCEEEEEh
Confidence            45667899999999999998887653           1 22 3499999999999999999999862     34566654


Q ss_pred             CCC------cChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHH--------------HHHHHHHHhhhc--cCCc
Q psy879           70 SND------RGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDG--------------AQQALRRTMEIY--SNTT  127 (317)
Q Consensus        70 ~~~------~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~--------------~~~~ll~~le~~--~~~~  127 (317)
                      ...      .....++..+.....       ..+.+++|||+|.+...              .++.|+..++..  ..++
T Consensus        83 ~~l~~~~~g~~~~~~~~~f~~a~~-------~~p~il~iDEid~l~~~~~~~~~~~~~~~~~~~~~lL~~l~~~~~~~~v  155 (301)
T 3cf0_A           83 PELLTMWFGESEANVREIFDKARQ-------AAPCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEMDGMSTKKNV  155 (301)
T ss_dssp             HHHHHHHHTTCTTHHHHHHHHHHH-------TCSEEEEECSTTHHHHHHTTTTCCSSCSCCHHHHHHHHHHHSSCTTSSE
T ss_pred             HHHHhhhcCchHHHHHHHHHHHHh-------cCCeEEEEEChHHHhhccCCCcCCcchHHHHHHHHHHHHhhcccCCCCE
Confidence            321      111223333333221       24689999999987543              367888888743  4567


Q ss_pred             eEEEEecCCCcCchhHhh--hcce-eeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCC-CHHHHHHHHHH
Q psy879          128 RFALACNNSEKIIEPIQS--RCAM-LRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQG-DMRQALNNLQS  200 (317)
Q Consensus       128 ~~il~~~~~~~l~~~i~s--R~~~-i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~g-d~r~~i~~l~~  200 (317)
                      .+|++||.++.+++++.+  |+.. +.|++|+.++..+++...+++.++. ++..++.++..+.| +.+.+.+.++.
T Consensus       156 ~vi~atn~~~~ld~al~r~gRf~~~i~i~~p~~~~r~~il~~~l~~~~~~-~~~~~~~la~~~~g~sg~dl~~l~~~  231 (301)
T 3cf0_A          156 FIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLRKSPVA-KDVDLEFLAKMTNGFSGADLTEICQR  231 (301)
T ss_dssp             EEEEEESCGGGSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTSCBC-SSCCHHHHHHTCSSCCHHHHHHHHHH
T ss_pred             EEEEecCCccccChHHhcCCccceEEecCCcCHHHHHHHHHHHHccCCCC-ccchHHHHHHHcCCCCHHHHHHHHHH
Confidence            889999999999999988  8864 9999999999999999888765543 22234566666544 23334444433

>2ce7_A Cell division protein FTSH; metalloprotease; HET: ADP; 2.44A {Thermotoga maritima} SCOP: a.269.1.1 c.37.1.20 PDB: 2cea_A* 3kds_E*

Probab=99.80  E-value=3.7e-18  Score=155.23  Aligned_cols=198  Identities=21%  Similarity=0.210  Sum_probs=139.5

Q ss_pred             CCCCcccCCHHHHHHHHHHHhc-----------CCCc-eEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCc-
Q psy879            7 QTFSDIVGNEDTVERLKVFSSS-----------GNVP-NIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDR-   73 (317)
Q Consensus         7 ~~~~~~~g~~~~~~~l~~~l~~-----------~~~~-~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~-   73 (317)
                      .+|++++|++++++.+...+..           .++| +++|+||||||||+++++++..+.     .+++.++++... 
T Consensus        13 ~~f~di~G~~~~~~~l~e~v~~l~~~~~~~~~g~~~p~gvLL~GppGtGKT~Laraia~~~~-----~~f~~is~~~~~~   87 (476)
T 2ce7_A           13 VTFKDVGGAEEAIEELKEVVEFLKDPSKFNRIGARMPKGILLVGPPGTGKTLLARAVAGEAN-----VPFFHISGSDFVE   87 (476)
T ss_dssp             CCGGGCCSCHHHHHHHHHHHHHHHCTHHHHTTTCCCCSEEEEECCTTSSHHHHHHHHHHHHT-----CCEEEEEGGGTTT
T ss_pred             CCHHHhCCcHHHHHHHHHHHHHhhChHHHhhcCCCCCCeEEEECCCCCCHHHHHHHHHHHcC-----CCeeeCCHHHHHH
Confidence            3799999999998887766431           2233 499999999999999999999863     346666554321 


Q ss_pred             -----ChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCH--------------HHHHHHHHHhhh--ccCCceEEEE
Q psy879           74 -----GIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTD--------------GAQQALRRTMEI--YSNTTRFALA  132 (317)
Q Consensus        74 -----~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~--------------~~~~~ll~~le~--~~~~~~~il~  132 (317)
                           +...++..+.....       ..+.+|+|||+|.+..              ..++.|+..|+.  ....+++|++
T Consensus        88 ~~~g~~~~~~r~lf~~A~~-------~~p~ILfIDEid~l~~~r~~~~~g~~~~~~~~l~~LL~~ld~~~~~~~viVIaa  160 (476)
T 2ce7_A           88 LFVGVGAARVRDLFAQAKA-------HAPCIVFIDEIDAVGRHRGAGLGGGHDEREQTLNQLLVEMDGFDSKEGIIVMAA  160 (476)
T ss_dssp             CCTTHHHHHHHHHHHHHHH-------TCSEEEEEETGGGTCCC---------CHHHHHHHHHHHHHHHSCGGGTEEEEEE
T ss_pred             HHhcccHHHHHHHHHHHHh-------cCCCEEEEechhhhhhhcccccCcCcHHHHHHHHHHHHHHhccCCCCCEEEEEe
Confidence                 12233444333322       3578999999998843              245677777764  2456788889


Q ss_pred             ecCCCcCchhHhh--hcce-eeecCCCHHHHHHHHHHHHHHcCCCCCHH-HHHHHHHhcCCCH-HHHHHHHHHhhh----
Q psy879          133 CNNSEKIIEPIQS--RCAM-LRYNKLTDAQLLSKVIEICEKENISHTND-GLEAIVFTAQGDM-RQALNNLQSTHN----  203 (317)
Q Consensus       133 ~~~~~~l~~~i~s--R~~~-i~f~~~~~~~~~~~l~~~~~~~~~~i~~~-~~~~l~~~~~gd~-r~~i~~l~~~~~----  203 (317)
                      ||.++.+++++.+  ||.. +.+++|+.++..+++...++...  ++++ .+..++..+.|.. +.+.+.++.++.    
T Consensus       161 Tn~~~~Ld~allR~gRFd~~i~i~~Pd~~~R~~Il~~~~~~~~--l~~~v~l~~la~~t~G~sgadL~~lv~~Aal~A~~  238 (476)
T 2ce7_A          161 TNRPDILDPALLRPGRFDKKIVVDPPDMLGRKKILEIHTRNKP--LAEDVNLEIIAKRTPGFVGADLENLVNEAALLAAR  238 (476)
T ss_dssp             ESCGGGSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTSC--BCTTCCHHHHHHTCTTCCHHHHHHHHHHHHHHHHH
T ss_pred             cCChhhhchhhcccCcceeEeecCCCCHHHHHHHHHHHHHhCC--CcchhhHHHHHHhcCCCcHHHHHHHHHHHHHHHHH
Confidence            9999999999886  7764 99999999999999988776543  3333 3677888888866 566666654332    


Q ss_pred             -CCCcccHHHHHhhcC
Q psy879          204 -GFGHVTAEYVFKVCD  218 (317)
Q Consensus       204 -~~~~i~~~~v~~~~~  218 (317)
                       +...|+.+++..+++
T Consensus       239 ~~~~~I~~~dl~~al~  254 (476)
T 2ce7_A          239 EGRDKITMKDFEEAID  254 (476)
T ss_dssp             TTCSSBCHHHHHHHHH
T ss_pred             cCCCeecHHHHHHHHH
Confidence             346788888876543

>2bjv_A PSP operon transcriptional activator; AAA, transcription activation, gene regulation, sigma54 activator, enhancer binding protein, PSPF; 1.7A {Escherichia coli} PDB: 2bjw_A 2c96_A* 2c98_A* 2c99_A* 2c9c_A* 2vii_A*

Probab=99.80  E-value=1e-18  Score=148.73  Aligned_cols=203  Identities=15%  Similarity=0.214  Sum_probs=133.7

Q ss_pred             CCCcccCCHHHHHHHHHHHhc--CCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHHH-HH
Q psy879            8 TFSDIVGNEDTVERLKVFSSS--GNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKI-KM   84 (317)
Q Consensus         8 ~~~~~~g~~~~~~~l~~~l~~--~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~-~~   84 (317)
                      +|++++|+...++.+...+..  ....+++|+||||||||++|+++++....  ...+++.+++... ..+.+...+ +.
T Consensus         4 ~f~~~ig~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKt~la~~i~~~~~~--~~~~~~~v~~~~~-~~~~~~~~l~g~   80 (265)
T 2bjv_A            4 YKDNLLGEANSFLEVLEQVSHLAPLDKPVLIIGERGTGKELIASRLHYLSSR--WQGPFISLNCAAL-NENLLDSELFGH   80 (265)
T ss_dssp             ------CCCHHHHHHHHHHHHHTTSCSCEEEECCTTSCHHHHHHHHHHTSTT--TTSCEEEEEGGGS-CHHHHHHHHHCC
T ss_pred             ccccceeCCHHHHHHHHHHHHHhCCCCCEEEECCCCCcHHHHHHHHHHhcCc--cCCCeEEEecCCC-ChhHHHHHhcCC
Confidence            689999998887776655432  22246999999999999999999987532  2345777776542 222222111 10


Q ss_pred             ----HHhh----cccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhc-----------cCCceEEEEecCC-------Cc
Q psy879           85 ----FAQQ----KVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIY-----------SNTTRFALACNNS-------EK  138 (317)
Q Consensus        85 ----~~~~----~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~-----------~~~~~~il~~~~~-------~~  138 (317)
                          +...    ...+......+++|||++.+..+.++.|++++++.           +.++.+|+++|..       ..
T Consensus        81 ~~~~~~g~~~~~~~~l~~a~~~~l~lDEi~~l~~~~q~~Ll~~l~~~~~~~~g~~~~~~~~~~iI~atn~~~~~~~~~~~  160 (265)
T 2bjv_A           81 EAGAFTGAQKRHPGRFERADGGTLFLDELATAPMMVQEKLLRVIEYGELERVGGSQPLQVNVRLVCATNADLPAMVNEGT  160 (265)
T ss_dssp             C---------CCCCHHHHTTTSEEEEESGGGSCHHHHHHHHHHHHHCEECCCCC--CEECCCEEEEEESSCHHHHHHHTS
T ss_pred             cccccccccccccchhhhcCCcEEEEechHhcCHHHHHHHHHHHHhCCeecCCCcccccCCeEEEEecCcCHHHHHHcCC
Confidence                0000    00000124579999999999999999999999863           3567899999875       24


Q ss_pred             CchhHhhhcce--eeecCCCH--HHHHHHH----HHHHHHcCC----CCCHHHHHHHHHhc-CCCHHHHHHHHHHhhh--
Q psy879          139 IIEPIQSRCAM--LRYNKLTD--AQLLSKV----IEICEKENI----SHTNDGLEAIVFTA-QGDMRQALNNLQSTHN--  203 (317)
Q Consensus       139 l~~~i~sR~~~--i~f~~~~~--~~~~~~l----~~~~~~~~~----~i~~~~~~~l~~~~-~gd~r~~i~~l~~~~~--  203 (317)
                      +.+.+.+|+..  +.++++.+  +++..++    ...+...+.    .+++++++.+.... .||+|++.+.++.++.  
T Consensus       161 ~~~~L~~Rl~~~~i~lp~L~~R~~di~~l~~~~l~~~~~~~~~~~~~~~~~~a~~~L~~~~~~gn~reL~~~l~~~~~~~  240 (265)
T 2bjv_A          161 FRADLLDALAFDVVQLPPLRERESDIMLMAEYFAIQMCREIKLPLFPGFTERARETLLNYRWPGNIRELKNVVERSVYRH  240 (265)
T ss_dssp             SCHHHHHHHCSEEEECCCGGGCHHHHHHHHHHHHHHHHHHTTCSSCCCBCHHHHHHHHHSCCTTHHHHHHHHHHHHHHHH
T ss_pred             ccHHHHHhhcCcEEeCCChhhhhHHHHHHHHHHHHHHHHHhCCCcccCcCHHHHHHHHhCCCCCCHHHHHHHHHHHHHhC
Confidence            77999999964  77888876  5665543    344444554    67899999988764 8999999999987653  


Q ss_pred             CCCcccHHHH
Q psy879          204 GFGHVTAEYV  213 (317)
Q Consensus       204 ~~~~i~~~~v  213 (317)
                      ....|+.+++
T Consensus       241 ~~~~i~~~~l  250 (265)
T 2bjv_A          241 GTSDYPLDDI  250 (265)
T ss_dssp             CCSSSCBCCC
T ss_pred             CCCcCcHHHc
Confidence            4456766655

>2r62_A Cell division protease FTSH homolog; ATPase domain, ATP-binding, cell CELL division, hydrolase, membrane, metal-binding; 3.30A {Helicobacter pylori} PDB: 2r65_A*

Probab=99.79  E-value=5.1e-20  Score=157.01  Aligned_cols=206  Identities=17%  Similarity=0.228  Sum_probs=136.3

Q ss_pred             cccCCCCCCcccCCHHHHHHHHHHHh-----------cCCCc-eEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecC
Q psy879            2 EKYRPQTFSDIVGNEDTVERLKVFSS-----------SGNVP-NIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNA   69 (317)
Q Consensus         2 ~ky~P~~~~~~~g~~~~~~~l~~~l~-----------~~~~~-~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~   69 (317)
                      .++.+.+|++++|++.+++.+...+.           ....+ +++|+||||||||++|+++++.+..+     ++.+++
T Consensus         3 ~~~~~~~~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~~~~~-----~~~v~~   77 (268)
T 2r62_A            3 AEKPNVRFKDMAGNEEAKEEVVEIVDFLKYPERYANLGAKIPKGVLLVGPPGTGKTLLAKAVAGEAHVP-----FFSMGG   77 (268)
T ss_dssp             CCCCCCCSTTSSSCTTTHHHHHHHHHHHHCHHHHHHHSCCCCSCCCCBCSSCSSHHHHHHHHHHHHTCC-----CCCCCS
T ss_pred             ccCCCCCHHHhCCcHHHHHHHHHHHHHHHChHHHHHCCCCCCceEEEECCCCCcHHHHHHHHHHHhCCC-----EEEech
Confidence            46777889999999998888877664           12223 49999999999999999999987432     333333


Q ss_pred             CCC------cChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHH---------------HHHHHHHHhhhcc---C
Q psy879           70 SND------RGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDG---------------AQQALRRTMEIYS---N  125 (317)
Q Consensus        70 ~~~------~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~---------------~~~~ll~~le~~~---~  125 (317)
                      ...      .+...++..+.....       ..+.+++|||+|.+...               .++.|+..++...   .
T Consensus        78 ~~~~~~~~~~~~~~~~~~~~~a~~-------~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~  150 (268)
T 2r62_A           78 SSFIEMFVGLGASRVRDLFETAKK-------QAPSIIFIDEIDAIGKSRAAGGVVSGNDEREQTLNQLLAEMDGFGSENA  150 (268)
T ss_dssp             CTTTTSCSSSCSSSSSTTHHHHHH-------SCSCEEEESCGGGTTC----------CCCSCSSTTTTTTTTTCSSCSCS
T ss_pred             HHHHHhhcchHHHHHHHHHHHHHh-------cCCeEEEEeChhhhcccccccccCCCchhHHHHHHHHHHHhhCcccCCC
Confidence            211      011112222222221       24579999999998654               2455666666543   2


Q ss_pred             CceEEEEecCCCcCchhHhh--hcce-eeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCC-CHHHHHHHHHHh
Q psy879          126 TTRFALACNNSEKIIEPIQS--RCAM-LRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQG-DMRQALNNLQST  201 (317)
Q Consensus       126 ~~~~il~~~~~~~l~~~i~s--R~~~-i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~g-d~r~~i~~l~~~  201 (317)
                      .+.+|+++|.+..+.+++.+  |+.. +.|++|+.++...++...+....+. ++..++.++..+.| ..|.+.+.++.+
T Consensus       151 ~v~vi~ttn~~~~ld~~l~r~~Rf~~~i~i~~p~~~~r~~il~~~~~~~~~~-~~~~~~~la~~~~g~~g~dl~~l~~~a  229 (268)
T 2r62_A          151 PVIVLAATNRPEILDPALMRPGRFDRQVLVDKPDFNGRVEILKVHIKGVKLA-NDVNLQEVAKLTAGLAGADLANIINEA  229 (268)
T ss_dssp             CCEEEECBSCCTTSCGGGGSSSSSCCCCBCCCCCTTTHHHHHHHHTSSSCCC-SSCCTTTTTSSSCSSCHHHHHHHHHHH
T ss_pred             CEEEEEecCCchhcCHhHcCCCCCCeEEEecCcCHHHHHHHHHHHHhcCCCC-CccCHHHHHHHcCCCCHHHHHHHHHHH
Confidence            36788889989889999988  6643 9999999999999998877643322 22235566666665 334555555443


Q ss_pred             hh-----CCCcccHHHHHhhcCCC
Q psy879          202 HN-----GFGHVTAEYVFKVCDEP  220 (317)
Q Consensus       202 ~~-----~~~~i~~~~v~~~~~~~  220 (317)
                      +.     +...|+.+++..++...
T Consensus       230 ~~~a~~~~~~~i~~~~~~~a~~~~  253 (268)
T 2r62_A          230 ALLAGRNNQKEVRQQHLKEAVERG  253 (268)
T ss_dssp             HHTTSSSCCCSCCHHHHHTSCTTC
T ss_pred             HHHHHHhccCCcCHHHHHHHHHHH
Confidence            32     24579999988876653

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=99.78  E-value=8.1e-19  Score=141.51  Aligned_cols=159  Identities=16%  Similarity=0.233  Sum_probs=113.2

Q ss_pred             cccCCCCCCcccCCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCC-----CCceEEecCCC----C
Q psy879            2 EKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSF-----KDAVLELNASN----D   72 (317)
Q Consensus         2 ~ky~P~~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~-----~~~~~~~~~~~----~   72 (317)
                      ++|+|.+|++++|+++.++.+...+..+...+++|+||+|+|||++++.+++.+.+...     +..++.+++..    .
T Consensus        14 ~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKT~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   93 (195)
T 1jbk_A           14 ERAEQGKLDPVIGRDEEIRRTIQVLQRRTKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLALDMGALVAGA   93 (195)
T ss_dssp             HHHHTTCSCCCCSCHHHHHHHHHHHTSSSSCEEEEECCTTSCHHHHHHHHHHHHHHTCSCGGGTTCEEEEECHHHHHTTT
T ss_pred             HHHhhccccccccchHHHHHHHHHHhcCCCCceEEECCCCCCHHHHHHHHHHHHHhCCCchhhcCCcEEEeeHHHHhccC
Confidence            57899999999999999999999998877778999999999999999999999753211     23344444321    1


Q ss_pred             cChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHH--------HHHHHHHHhhhccCCceEEEEecCCC-----cC
Q psy879           73 RGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDG--------AQQALRRTMEIYSNTTRFALACNNSE-----KI  139 (317)
Q Consensus        73 ~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~--------~~~~ll~~le~~~~~~~~il~~~~~~-----~l  139 (317)
                      .........+..+.....  ....+.+++|||+|.+...        .++.|..+++.  .++.+|++++.+.     .+
T Consensus        94 ~~~~~~~~~~~~~~~~~~--~~~~~~vl~iDe~~~l~~~~~~~~~~~~~~~l~~~~~~--~~~~~i~~~~~~~~~~~~~~  169 (195)
T 1jbk_A           94 KYRGEFEERLKGVLNDLA--KQEGNVILFIDELHTMVGAGKADGAMDAGNMLKPALAR--GELHCVGATTLDEYRQYIEK  169 (195)
T ss_dssp             CSHHHHHHHHHHHHHHHH--HSTTTEEEEEETGGGGTT------CCCCHHHHHHHHHT--TSCCEEEEECHHHHHHHTTT
T ss_pred             CccccHHHHHHHHHHHHh--hcCCCeEEEEeCHHHHhccCcccchHHHHHHHHHhhcc--CCeEEEEeCCHHHHHHHHhc
Confidence            111122222222211100  0145679999999999633        36677777764  4677888888765     67


Q ss_pred             chhHhhhcceeeecCCCHHHHHHHH
Q psy879          140 IEPIQSRCAMLRYNKLTDAQLLSKV  164 (317)
Q Consensus       140 ~~~i~sR~~~i~f~~~~~~~~~~~l  164 (317)
                      .+++.+||..+.|++|+.++..+++
T Consensus       170 ~~~l~~r~~~i~~~~p~~~~~~~il  194 (195)
T 1jbk_A          170 DAALERRFQKVFVAEPSVEDTIAIL  194 (195)
T ss_dssp             CHHHHTTEEEEECCCCCHHHHHTTC
T ss_pred             CHHHHHHhceeecCCCCHHHHHHHh
Confidence            8999999999999999999987764

>1qvr_A CLPB protein; coiled coil, AAA ATPase, chaperone; HET: ANP; 3.00A {Thermus thermophilus} SCOP: a.174.1.1 c.37.1.20 c.37.1.20

Probab=99.78  E-value=9e-19  Score=171.74  Aligned_cols=194  Identities=15%  Similarity=0.194  Sum_probs=137.3

Q ss_pred             cccCCCCCCcccCCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCC-----CCCceEEecCCCCcC--
Q psy879            2 EKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPS-----FKDAVLELNASNDRG--   74 (317)
Q Consensus         2 ~ky~P~~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~-----~~~~~~~~~~~~~~~--   74 (317)
                      ++|+|.+|++++|+++.++.+...+..+..++++|+||||+|||++++.+++.+.+..     .+..++.+++.....  
T Consensus       162 ~~~r~~~ld~viGr~~~i~~l~~~l~~~~~~~vlL~G~pG~GKT~la~~la~~l~~~~~p~~l~~~~~~~l~~~~l~~g~  241 (854)
T 1qvr_A          162 RLAAEGKLDPVIGRDEEIRRVIQILLRRTKNNPVLIGEPGVGKTAIVEGLAQRIVKGDVPEGLKGKRIVSLQMGSLLAGA  241 (854)
T ss_dssp             HHHHTTCSCCCCSCHHHHHHHHHHHHCSSCCCCEEEECTTSCHHHHHHHHHHHHHHTCSCTTSTTCEEEEECC-------
T ss_pred             HHHhcCCCcccCCcHHHHHHHHHHHhcCCCCceEEEcCCCCCHHHHHHHHHHHHhcCCCchhhcCCeEEEeehHHhhccC
Confidence            5789999999999999999999999888877899999999999999999999984321     134456665543211  


Q ss_pred             ------hHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCC--------HHHHHHHHHHhhhccCCceEEEEecCCC---
Q psy879           75 ------IDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMT--------DGAQQALRRTMEIYSNTTRFALACNNSE---  137 (317)
Q Consensus        75 ------~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~--------~~~~~~ll~~le~~~~~~~~il~~~~~~---  137 (317)
                            ...+...+......      ..+.|++|||++.+.        .+..+.|..+++.  ....+|++|+.+.   
T Consensus       242 ~~~g~~~~~l~~~~~~~~~~------~~~~iL~IDEi~~l~~~~~~~g~~~~~~~L~~~l~~--~~i~~I~at~~~~~~~  313 (854)
T 1qvr_A          242 KYRGEFEERLKAVIQEVVQS------QGEVILFIDELHTVVGAGKAEGAVDAGNMLKPALAR--GELRLIGATTLDEYRE  313 (854)
T ss_dssp             ----CHHHHHHHHHHHHHTT------CSSEEEEECCC-------------------HHHHHT--TCCCEEEEECHHHHHH
T ss_pred             ccchHHHHHHHHHHHHHHhc------CCCeEEEEecHHHHhccCCccchHHHHHHHHHHHhC--CCeEEEEecCchHHhh
Confidence                  11122333332211      356799999999997        3456678888874  4567888887653   


Q ss_pred             -cCchhHhhhcceeeecCCCHHHHHHHHHHHHH----HcCCCCCHHHHHHHHHhcCC------CHHHHHHHHHHhhh
Q psy879          138 -KIIEPIQSRCAMLRYNKLTDAQLLSKVIEICE----KENISHTNDGLEAIVFTAQG------DMRQALNNLQSTHN  203 (317)
Q Consensus       138 -~l~~~i~sR~~~i~f~~~~~~~~~~~l~~~~~----~~~~~i~~~~~~~l~~~~~g------d~r~~i~~l~~~~~  203 (317)
                       .+.+++.+||..+.|++|+.++...++...+.    .+++.++++++..++..+.|      -+.++++.++.++.
T Consensus       314 ~~~d~aL~rRf~~i~l~~p~~~e~~~iL~~~~~~~~~~~~~~i~~~al~~~~~ls~r~i~~~~lp~kai~lldea~a  390 (854)
T 1qvr_A          314 IEKDPALERRFQPVYVDEPTVEETISILRGLKEKYEVHHGVRISDSAIIAAATLSHRYITERRLPDKAIDLIDEAAA  390 (854)
T ss_dssp             HTTCTTTCSCCCCEEECCCCHHHHHHHHHHHHHHHHHHTTCEECHHHHHHHHHHHHHHCCSSCTHHHHHHHHHHHHH
T ss_pred             hccCHHHHhCCceEEeCCCCHHHHHHHHHhhhhhhhhhcCCCCCHHHHHHHHHHHhhhcccccChHHHHHHHHHHHH
Confidence             46899999999999999999999999987655    35788899999988887643      37888888876554

>3k1j_A LON protease, ATP-dependent protease LON; ATP-binding, nucleotide-binding, Pro hydrolase; HET: ADP PE8; 2.00A {Thermococcus onnurineus}

Probab=99.78  E-value=8.5e-19  Score=165.64  Aligned_cols=214  Identities=18%  Similarity=0.213  Sum_probs=146.3

Q ss_pred             cccCCCCCCcccCCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCc--------
Q psy879            2 EKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDR--------   73 (317)
Q Consensus         2 ~ky~P~~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~--------   73 (317)
                      .+|+|+.|++++|++++++.+...+..|.  +++|+|||||||||+++++++.+.+.......+..+..+..        
T Consensus        33 ~~~rp~~l~~i~G~~~~l~~l~~~i~~g~--~vll~Gp~GtGKTtlar~ia~~l~~~~~~~~~~~~~~~~~~~p~i~~~p  110 (604)
T 3k1j_A           33 IEVPEKLIDQVIGQEHAVEVIKTAANQKR--HVLLIGEPGTGKSMLGQAMAELLPTETLEDILVFPNPEDENMPRIKTVP  110 (604)
T ss_dssp             SCCCSSHHHHCCSCHHHHHHHHHHHHTTC--CEEEECCTTSSHHHHHHHHHHTSCCSSCEEEEEECCTTCTTSCEEEEEE
T ss_pred             ccccccccceEECchhhHhhccccccCCC--EEEEEeCCCCCHHHHHHHHhccCCcccCCeEEEeCCcccccCCcEEEEe
Confidence            48999999999999999999999999986  89999999999999999999986433211111111111100        


Q ss_pred             --ChHH--------------------------------------------------HHHHHHHHHhh-------------
Q psy879           74 --GIDT--------------------------------------------------VRNKIKMFAQQ-------------   88 (317)
Q Consensus        74 --~~~~--------------------------------------------------i~~~~~~~~~~-------------   88 (317)
                        ....                                                  ..+.++.....             
T Consensus       111 ~g~~~~~~e~~~~~~~~~~~~r~~~~~~~~~~~~~nl~v~~~~~~~~~~v~~~~~~~~~L~G~~~~~~~~~g~~~~g~~~  190 (604)
T 3k1j_A          111 ACQGRRIVEKYREKAKSQESVKSSNMRLKSTVLVPKLLVDNCGRTKAPFIDATGAHAGALLGDVRHDPFQSGGLGTPAHE  190 (604)
T ss_dssp             TTHHHHHHHHHHHHHHHHTCC-----------CCCEEEECCTTCSSCCEEECTTCCHHHHHCEECCCCC----CCCCGGG
T ss_pred             cchHHHHHHHHHHhhccchhhhhhcccccccccccceeeccccCCCCCEEEcCCCCHHhcCceEEechhhcCCccccccc
Confidence              0000                                                  11111100000             


Q ss_pred             ---cccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhc---------------------cCCceEEEEecCC--CcCchh
Q psy879           89 ---KVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIY---------------------SNTTRFALACNNS--EKIIEP  142 (317)
Q Consensus        89 ---~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~---------------------~~~~~~il~~~~~--~~l~~~  142 (317)
                         +..+..+.+++++|||++.+.+..++.|++.|++.                     +.++++|+++|..  ..+.++
T Consensus       191 ~i~~g~~~~a~~gvL~LDEi~~l~~~~q~~Ll~~Le~~~~~~~g~~~~~~~~~l~~~~~p~~~~vI~atn~~~~~~l~~~  270 (604)
T 3k1j_A          191 RVEPGMIHRAHKGVLFIDEIATLSLKMQQSLLTAMQEKKFPITGQSEMSSGAMVRTEPVPCDFVLVAAGNLDTVDKMHPA  270 (604)
T ss_dssp             GEECCHHHHTTTSEEEETTGGGSCHHHHHHHHHHHHHSEECCBCSCTTSGGGGCBCSCEECCCEEEEEECHHHHHHSCHH
T ss_pred             cccCceeeecCCCEEEEechhhCCHHHHHHHHHHHHcCcEEecccccccccccCCCCccceeEEEEEecCHHHHhhcCHH
Confidence               00000124569999999999999999999999832                     2356789999876  579999


Q ss_pred             Hhhhcc----eeeecCC---CHHHHHHHHHHHHHHc-----CCCCCHHHHHHHHHhc---CC-------CHHHHHHHHHH
Q psy879          143 IQSRCA----MLRYNKL---TDAQLLSKVIEICEKE-----NISHTNDGLEAIVFTA---QG-------DMRQALNNLQS  200 (317)
Q Consensus       143 i~sR~~----~i~f~~~---~~~~~~~~l~~~~~~~-----~~~i~~~~~~~l~~~~---~g-------d~r~~i~~l~~  200 (317)
                      +.+||.    .+.|++.   +++.+..++...+...     ...++++++..+++.+   .|       ++|.+.++++.
T Consensus       271 l~~R~~v~~i~i~l~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~ls~eAl~~Li~~~~r~~g~r~~l~~~~R~l~~llr~  350 (604)
T 3k1j_A          271 LRSRIRGYGYEVYMRTTMPDTIENRRKLVQFVAQEVKRDGKIPHFTKEAVEEIVREAQKRAGRKGHLTLRLRDLGGIVRA  350 (604)
T ss_dssp             HHHHHHHHSEEEECCSEEECCHHHHHHHHHHHHHHHHHHCSSCCBBHHHHHHHHHHHHHTTCSTTEEECCHHHHHHHHHH
T ss_pred             HHHHhhccceEeeccccccCCHHHHHHHHHHHHHHHhhccCcccCCHHHHHHHHHHHhhhhccccccccCHHHHHHHHHH
Confidence            999996    3665433   4455666665544332     2578999999888754   55       59999999876


Q ss_pred             hhh-----CCCcccHHHHHhhc
Q psy879          201 THN-----GFGHVTAEYVFKVC  217 (317)
Q Consensus       201 ~~~-----~~~~i~~~~v~~~~  217 (317)
                      +..     +...|+.+++.++.
T Consensus       351 A~~~A~~~~~~~I~~edv~~A~  372 (604)
T 3k1j_A          351 AGDIAVKKGKKYVEREDVIEAV  372 (604)
T ss_dssp             HHHHHHHTTCSSBCHHHHHHHH
T ss_pred             HHHHHHhcCcccccHHHHHHHH
Confidence            432     45679999888766

>1d2n_A N-ethylmaleimide-sensitive fusion protein; hexamerization domain, ATPase, transport; HET: ANP; 1.75A {Cricetulus griseus} SCOP: c.37.1.20 PDB: 1nsf_A*

Probab=99.78  E-value=3.8e-18  Score=145.72  Aligned_cols=178  Identities=13%  Similarity=0.187  Sum_probs=120.9

Q ss_pred             CcccCCHHHHHHHHH-------HHh---cCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCC-cC--h-
Q psy879           10 SDIVGNEDTVERLKV-------FSS---SGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASND-RG--I-   75 (317)
Q Consensus        10 ~~~~g~~~~~~~l~~-------~l~---~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~-~~--~-   75 (317)
                      ..++|+....+.+..       .+.   .....+++|+||||||||++|+++++.+.     ..++.+++.+. .+  . 
T Consensus        33 ~~~i~~~~~~~~i~~~~~~l~~~l~~~~~~~~~~vLl~G~~GtGKT~la~~ia~~~~-----~~~~~i~~~~~~~g~~~~  107 (272)
T 1d2n_A           33 NGIIKWGDPVTRVLDDGELLVQQTKNSDRTPLVSVLLEGPPHSGKTALAAKIAEESN-----FPFIKICSPDKMIGFSET  107 (272)
T ss_dssp             TCCCCCSHHHHHHHHHHHHHHHHHHHCSSCSEEEEEEECSTTSSHHHHHHHHHHHHT-----CSEEEEECGGGCTTCCHH
T ss_pred             cCCCCccHHHHHHHHHHHHHHHHHhccCCCCCeEEEEECCCCCcHHHHHHHHHHHhC-----CCEEEEeCHHHhcCCchH
Confidence            567787655444333       443   22334599999999999999999999863     34566654321 11  1 


Q ss_pred             ---HHHHHHHHHHHhhcccCCCCceeEEEEeCCCCC----------CHHHHHHHHHHhhh---ccCCceEEEEecCCCcC
Q psy879           76 ---DTVRNKIKMFAQQKVTLPPGRHKIVILDEADSM----------TDGAQQALRRTMEI---YSNTTRFALACNNSEKI  139 (317)
Q Consensus        76 ---~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l----------~~~~~~~ll~~le~---~~~~~~~il~~~~~~~l  139 (317)
                         ..++..+....       ...+.+|+|||+|.+          ....++.|...++.   .+..+.+|++||.+..+
T Consensus       108 ~~~~~~~~~~~~~~-------~~~~~vl~iDEid~l~~~~~~~~~~~~~~l~~L~~~~~~~~~~~~~~~ii~ttn~~~~l  180 (272)
T 1d2n_A          108 AKCQAMKKIFDDAY-------KSQLSCVVVDDIERLLDYVPIGPRFSNLVLQALLVLLKKAPPQGRKLLIIGTTSRKDVL  180 (272)
T ss_dssp             HHHHHHHHHHHHHH-------TSSEEEEEECCHHHHTTCBTTTTBCCHHHHHHHHHHTTCCCSTTCEEEEEEEESCHHHH
T ss_pred             HHHHHHHHHHHHHH-------hcCCcEEEEEChhhhhccCCCChhHHHHHHHHHHHHhcCccCCCCCEEEEEecCChhhc
Confidence               22233333221       145889999999987          44556677777764   33455577778877666


Q ss_pred             ch-hHhhhc-ceeeecCCCH-HHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCC-----CHHHHHHHHHHhhhC
Q psy879          140 IE-PIQSRC-AMLRYNKLTD-AQLLSKVIEICEKENISHTNDGLEAIVFTAQG-----DMRQALNNLQSTHNG  204 (317)
Q Consensus       140 ~~-~i~sR~-~~i~f~~~~~-~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~g-----d~r~~i~~l~~~~~~  204 (317)
                      .+ .+.+|+ ..+.|++++. +++..++...    + .++++.+..++..+.|     ++|++++.++.+...
T Consensus       181 ~~~~l~~rf~~~i~~p~l~~r~~i~~i~~~~----~-~~~~~~~~~l~~~~~g~~~~g~ir~l~~~l~~a~~~  248 (272)
T 1d2n_A          181 QEMEMLNAFSTTIHVPNIATGEQLLEALELL----G-NFKDKERTTIAQQVKGKKVWIGIKKLLMLIEMSLQM  248 (272)
T ss_dssp             HHTTCTTTSSEEEECCCEEEHHHHHHHHHHH----T-CSCHHHHHHHHHHHTTSEEEECHHHHHHHHHHHTTS
T ss_pred             chhhhhcccceEEcCCCccHHHHHHHHHHhc----C-CCCHHHHHHHHHHhcCCCccccHHHHHHHHHHHhhh
Confidence            66 678885 4599999988 6666666542    2 4689999999999988     999999999987553

>3m6a_A ATP-dependent protease LA 1; alpha, beta, ATP-binding, hydrolase, nucleotide-binding, Pro serine protease, stress response; HET: ADP; 3.40A {Bacillus subtilis} PDB: 1x37_A

Probab=99.77  E-value=3.2e-18  Score=159.42  Aligned_cols=202  Identities=20%  Similarity=0.262  Sum_probs=134.8

Q ss_pred             CcccCCHHHHHHHHHHHh------cCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHH----
Q psy879           10 SDIVGNEDTVERLKVFSS------SGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVR----   79 (317)
Q Consensus        10 ~~~~g~~~~~~~l~~~l~------~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~----   79 (317)
                      ++++|++++++.+...+.      ....++++|+||||||||+++++++..+..     .+..+++........+.    
T Consensus        81 ~di~G~~~vk~~i~~~~~l~~~~~~~~g~~vll~Gp~GtGKTtlar~ia~~l~~-----~~~~i~~~~~~~~~~~~g~~~  155 (543)
T 3m6a_A           81 EEHHGLEKVKERILEYLAVQKLTKSLKGPILCLAGPPGVGKTSLAKSIAKSLGR-----KFVRISLGGVRDESEIRGHRR  155 (543)
T ss_dssp             HHCSSCHHHHHHHHHHHHHHHHSSSCCSCEEEEESSSSSSHHHHHHHHHHHHTC-----EEEEECCCC------------
T ss_pred             HHhccHHHHHHHHHHHHHHHHhcccCCCCEEEEECCCCCCHHHHHHHHHHhcCC-----CeEEEEecccchhhhhhhHHH
Confidence            458999999888765432      223346999999999999999999999732     24444443211111110    


Q ss_pred             -------HHHHHHHhhcccCCCCceeEEEEeCCCCCCHH----HHHHHHHHhhhcc---------------CCceEEEEe
Q psy879           80 -------NKIKMFAQQKVTLPPGRHKIVILDEADSMTDG----AQQALRRTMEIYS---------------NTTRFALAC  133 (317)
Q Consensus        80 -------~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~----~~~~ll~~le~~~---------------~~~~~il~~  133 (317)
                             ..+......    ......++++||+|.+..+    .++.|++.|+...               .++++|+++
T Consensus       156 ~~ig~~~~~~~~~~~~----a~~~~~vl~lDEid~l~~~~~~~~~~~LL~~ld~~~~~~~~~~~~~~~~~~~~v~iI~tt  231 (543)
T 3m6a_A          156 TYVGAMPGRIIQGMKK----AGKLNPVFLLDEIDKMSSDFRGDPSSAMLEVLDPEQNSSFSDHYIEETFDLSKVLFIATA  231 (543)
T ss_dssp             --------CHHHHHHT----TCSSSEEEEEEESSSCC---------CCGGGTCTTTTTBCCCSSSCCCCBCSSCEEEEEC
T ss_pred             HHhccCchHHHHHHHH----hhccCCEEEEhhhhhhhhhhccCHHHHHHHHHhhhhcceeecccCCeeecccceEEEecc
Confidence                   111111111    1124459999999999887    4588888887432               457899999


Q ss_pred             cCCCcCchhHhhhcceeeecCCCHHHHHHHHHHHHH-----Hc-----CCCCCHHHHHHHHHhcC--CCHHHHHHHHHHh
Q psy879          134 NNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICE-----KE-----NISHTNDGLEAIVFTAQ--GDMRQALNNLQST  201 (317)
Q Consensus       134 ~~~~~l~~~i~sR~~~i~f~~~~~~~~~~~l~~~~~-----~~-----~~~i~~~~~~~l~~~~~--gd~r~~i~~l~~~  201 (317)
                      |....+++++++||.++.|++|+.++...++...+.     ..     ++.++++++..++....  |++|.+-+.++.+
T Consensus       232 N~~~~l~~aL~~R~~vi~~~~~~~~e~~~Il~~~l~~~~~~~~~~~~~~i~i~~~~l~~l~~~~~~~~~vR~L~~~i~~~  311 (543)
T 3m6a_A          232 NNLATIPGPLRDRMEIINIAGYTEIEKLEIVKDHLLPKQIKEHGLKKSNLQLRDQAILDIIRYYTREAGVRSLERQLAAI  311 (543)
T ss_dssp             SSTTTSCHHHHHHEEEEECCCCCHHHHHHHHHHTHHHHHHHHTTCCGGGCEECHHHHHHHHHHHCCCSSSHHHHHHHHHH
T ss_pred             CccccCCHHHHhhcceeeeCCCCHHHHHHHHHHHHHHHHHHHcCCCcccccCCHHHHHHHHHhCChhhchhHHHHHHHHH
Confidence            999999999999999999999999999999887652     22     44678999998877543  6788777666543


Q ss_pred             hh-----------CCCcccHHHHHhhcCCC
Q psy879          202 HN-----------GFGHVTAEYVFKVCDEP  220 (317)
Q Consensus       202 ~~-----------~~~~i~~~~v~~~~~~~  220 (317)
                      +.           ....|+.+++.++++..
T Consensus       312 ~~~aa~~~~~~~~~~~~It~~~l~~~Lg~~  341 (543)
T 3m6a_A          312 CRKAAKAIVAEERKRITVTEKNLQDFIGKR  341 (543)
T ss_dssp             HHHHHHHHHTTCCSCCEECTTTTHHHHCSC
T ss_pred             HHHHHHHHHhcCCcceecCHHHHHHHhCCc
Confidence            22           12357888887766544

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=99.77  E-value=2.3e-18  Score=167.11  Aligned_cols=189  Identities=17%  Similarity=0.262  Sum_probs=137.5

Q ss_pred             cccCCCCCCcccCCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCC-----CCCceEEecCCCC-cC-
Q psy879            2 EKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPS-----FKDAVLELNASND-RG-   74 (317)
Q Consensus         2 ~ky~P~~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~-----~~~~~~~~~~~~~-~~-   74 (317)
                      ++|+|..|++++|+++.++.+...+..+..+|++|+||||||||++|+++++.+.+..     .+..++.++.... .+ 
T Consensus       172 ~~~~~~~ld~iiG~~~~i~~l~~~l~~~~~~~vLL~G~pGtGKT~la~~la~~l~~~~~p~~l~~~~~~~~~~g~~~~G~  251 (758)
T 3pxi_A          172 AIAKEDSLDPVIGRSKEIQRVIEVLSRRTKNNPVLIGEPGVGKTAIAEGLAQQIINNEVPEILRDKRVMTLDMGTKYRGE  251 (758)
T ss_dssp             HHTTSSCSCCCCCCHHHHHHHHHHHHCSSSCEEEEESCTTTTTHHHHHHHHHHHHSSCSCTTTSSCCEECC---------
T ss_pred             HHHhhCCCCCccCchHHHHHHHHHHhCCCCCCeEEECCCCCCHHHHHHHHHHHHhcCCCChhhcCCeEEEecccccccch
Confidence            5789999999999999999999999888878899999999999999999999984322     1333444443110 11 


Q ss_pred             -hHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCC-----cCchhHhhhcc
Q psy879           75 -IDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSE-----KIIEPIQSRCA  148 (317)
Q Consensus        75 -~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~-----~l~~~i~sR~~  148 (317)
                       ...++..+..+..       ..+.+++||    ...+.++.|+..++  ...+.+|++||...     .+.+++.+||.
T Consensus       252 ~e~~l~~~~~~~~~-------~~~~iLfiD----~~~~~~~~L~~~l~--~~~v~~I~at~~~~~~~~~~~d~al~rRf~  318 (758)
T 3pxi_A          252 FEDRLKKVMDEIRQ-------AGNIILFID----AAIDASNILKPSLA--RGELQCIGATTLDEYRKYIEKDAALERRFQ  318 (758)
T ss_dssp             -CTTHHHHHHHHHT-------CCCCEEEEC----C--------CCCTT--SSSCEEEEECCTTTTHHHHTTCSHHHHSEE
T ss_pred             HHHHHHHHHHHHHh-------cCCEEEEEc----CchhHHHHHHHHHh--cCCEEEEeCCChHHHHHHhhccHHHHhhCc
Confidence             1133444444332       356799999    44567788888888  45688899998877     68999999999


Q ss_pred             eeeecCCCHHHHHHHHHHHHHH----cCCCCCHHHHHHHHHhcC------CCHHHHHHHHHHhhh
Q psy879          149 MLRYNKLTDAQLLSKVIEICEK----ENISHTNDGLEAIVFTAQ------GDMRQALNNLQSTHN  203 (317)
Q Consensus       149 ~i~f~~~~~~~~~~~l~~~~~~----~~~~i~~~~~~~l~~~~~------gd~r~~i~~l~~~~~  203 (317)
                      .+.|++|+.++...++...+..    +++.++++++..++..+.      ..++.++..++.++.
T Consensus       319 ~i~v~~p~~~~~~~il~~~~~~~~~~~~~~i~~~al~~~~~~s~~~i~~~~~p~~ai~ll~~a~~  383 (758)
T 3pxi_A          319 PIQVDQPSVDESIQILQGLRDRYEAHHRVSITDDAIEAAVKLSDRYISDRFLPDKAIDLIDEAGS  383 (758)
T ss_dssp             EEECCCCCHHHHHHHHHHTTTTSGGGSSCSCCHHHHHHHHHHHHHSSCCSCTTHHHHHHHHHHHH
T ss_pred             EEEeCCCCHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhcccccCcCCcHHHHHHHHHHH
Confidence            9999999999999999977655    678899999988887653      345788888876543

>1um8_A ATP-dependent CLP protease ATP-binding subunit CL; CLPP binding loop, chaperone; HET: ADP; 2.60A {Helicobacter pylori} SCOP: c.37.1.20

Probab=99.77  E-value=1.1e-18  Score=155.92  Aligned_cols=203  Identities=19%  Similarity=0.223  Sum_probs=133.8

Q ss_pred             cccCCHHHHHHHHHHHh----c--------------------------CCCceEEEECCCCCCHHHHHHHHHHHHcCCCC
Q psy879           11 DIVGNEDTVERLKVFSS----S--------------------------GNVPNIIISGPPGVGKTTTILCLARILLGPSF   60 (317)
Q Consensus        11 ~~~g~~~~~~~l~~~l~----~--------------------------~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~   60 (317)
                      .++||+++++.+..++.    .                          ....+++|+||||||||++|+++++.+.    
T Consensus        22 ~viGq~~ak~~l~~~~~~~~~~~~~g~~~~~~~~~~~~~p~~~~~~~~~~~~~ill~Gp~GtGKT~la~~la~~l~----   97 (376)
T 1um8_A           22 YVIGQEQAKKVFSVAVYNHYKRLSFKEKLKKQDNQDSNVELEHLEEVELSKSNILLIGPTGSGKTLMAQTLAKHLD----   97 (376)
T ss_dssp             TCCSCHHHHHHHHHHHHHHHHHHHHHHHHHHHCSHHHHHHHHHHHHTTCCCCCEEEECCTTSSHHHHHHHHHHHTT----
T ss_pred             HccCcHHHHHHHHHHHHHHHHHHHhhhhhhhccccccccccccccccccCCCCEEEECCCCCCHHHHHHHHHHHhC----
Confidence            47999999999887762    1                          1233599999999999999999999862    


Q ss_pred             CCceEEecCCCCc--Ch--HHHHHHHHHHHhhc-ccCCCCceeEEEEeCCCCCCHH--------------HHHHHHHHhh
Q psy879           61 KDAVLELNASNDR--GI--DTVRNKIKMFAQQK-VTLPPGRHKIVILDEADSMTDG--------------AQQALRRTME  121 (317)
Q Consensus        61 ~~~~~~~~~~~~~--~~--~~i~~~~~~~~~~~-~~~~~~~~~vliiDE~d~l~~~--------------~~~~ll~~le  121 (317)
                       ..++.+++....  +.  ......+..+.... .......+.+++|||++.+...              .++.|++.|+
T Consensus        98 -~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~vl~iDEi~~l~~~~~~~~~~~~~~~~~~~~~Ll~~le  176 (376)
T 1um8_A           98 -IPIAISDATSLTEAGYVGEDVENILTRLLQASDWNVQKAQKGIVFIDEIDKISRLSENRSITRDVSGEGVQQALLKIVE  176 (376)
T ss_dssp             -CCEEEEEGGGCC--------CTHHHHHHHHHTTTCHHHHTTSEEEEETGGGC--------------CHHHHHHHHHHHH
T ss_pred             -CCEEEecchhhhhcCcCCccHHHHHHHHHhhccchhhhcCCeEEEEcCHHHHhhhcCCCceecccchHHHHHHHHHHhh
Confidence             335555543211  00  01111111111110 0000125689999999999887              8999999999


Q ss_pred             hcc---------------------CCceEEEEecC-----------------------------------------CCcC
Q psy879          122 IYS---------------------NTTRFALACNN-----------------------------------------SEKI  139 (317)
Q Consensus       122 ~~~---------------------~~~~~il~~~~-----------------------------------------~~~l  139 (317)
                      +..                     .++.+|+++|.                                         ...+
T Consensus       177 ~~~~~~~~~~~~~~~~~~~~~i~t~n~~~I~~~~~~~l~~~l~~R~~~~~~g~~~~~~~~~~~~~~~~~~~~~~l~~~~~  256 (376)
T 1um8_A          177 GSLVNIPPKGGRKHPEGNFIQIDTSDILFICAGAFDGLAEIIKKRTTQNVLGFTQEKMSKKEQEAILHLVQTHDLVTYGL  256 (376)
T ss_dssp             CCEEC---------------CEECTTCEEEEEECCTTHHHHTTTSCSSCCCSCCCSSCCTTTTTTSGGGCCHHHHHHTTC
T ss_pred             ccceecccccccccCCcceEEEecCCeEEEecCCHHHHHHHHHHHhcccccCCCchhhhccchhHHHhhcCHHHHhhcCC
Confidence            541                     44567777652                                         1136


Q ss_pred             chhHhhhc-ceeeecCCCHHHHHHHHHH----HHH---------HcCCCCCHHHHHHHHHhcC---CCHHHHHHHHHHhh
Q psy879          140 IEPIQSRC-AMLRYNKLTDAQLLSKVIE----ICE---------KENISHTNDGLEAIVFTAQ---GDMRQALNNLQSTH  202 (317)
Q Consensus       140 ~~~i~sR~-~~i~f~~~~~~~~~~~l~~----~~~---------~~~~~i~~~~~~~l~~~~~---gd~r~~i~~l~~~~  202 (317)
                      .+++.+|+ .++.|++++.+++..++..    .+.         ..++.+++++++.++..+.   |++|.+.+.++.++
T Consensus       257 ~p~l~~R~~~~i~~~~l~~~~l~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~R~L~~~le~~~  336 (376)
T 1um8_A          257 IPELIGRLPVLSTLDSISLEAMVDILQKPKNALIKQYQQLFKMDEVDLIFEEEAIKEIAQLALERKTGARGLRAIIEDFC  336 (376)
T ss_dssp             CHHHHTTCCEEEECCCCCHHHHHHHHHSSTTCHHHHHHHHHHTTTCEEEECHHHHHHHHHHHHHTTCTGGGHHHHHHHHH
T ss_pred             ChHHhcCCCceeeccCCCHHHHHHHHhhhHHHHHHHHHHHHhhcCceEEECHHHHHHHHHHhcccccCcHHHHHHHHHHH
Confidence            78999999 5599999999999998862    111         1245689999999998865   89999999988754


Q ss_pred             hC---------C--CcccHHHHHhhcC
Q psy879          203 NG---------F--GHVTAEYVFKVCD  218 (317)
Q Consensus       203 ~~---------~--~~i~~~~v~~~~~  218 (317)
                      ..         .  ..|+.+++.+...
T Consensus       337 ~~~~~~~~~~~~~~~~i~~~~v~~~~~  363 (376)
T 1um8_A          337 LDIMFDLPKLKGSEVRITKDCVLKQAE  363 (376)
T ss_dssp             HHHHHTGGGGTTSEEEECHHHHTTSSC
T ss_pred             HHHHhhccCCCCCEEEEeHHHhcCCCC
Confidence            31         1  1478887776443

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=99.77  E-value=7.8e-18  Score=145.78  Aligned_cols=203  Identities=14%  Similarity=0.161  Sum_probs=138.1

Q ss_pred             CcccCCHHHHHHHHHHHhc--CCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHHHHHHHh
Q psy879           10 SDIVGNEDTVERLKVFSSS--GNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFAQ   87 (317)
Q Consensus        10 ~~~~g~~~~~~~l~~~l~~--~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~   87 (317)
                      ++++|+....+.+...+..  ....+++|+||||||||++|+++++...  ..+.+++.+++... ....+...+.....
T Consensus         2 ~~iig~s~~~~~~~~~~~~~a~~~~~vLi~Ge~GtGKt~lAr~i~~~~~--~~~~~~v~v~~~~~-~~~l~~~~lfg~~~   78 (304)
T 1ojl_A            2 SHMIGSSPAMQHLLNEIAMVAPSDATVLIHGDSGTGKELVARALHACSA--RSDRPLVTLNCAAL-NESLLESELFGHEK   78 (304)
T ss_dssp             -CCCCCSHHHHHHHHHHHHHCSTTSCEEEESCTTSCHHHHHHHHHHHSS--CSSSCCCEEECSSC-CHHHHHHHHTCCCS
T ss_pred             CCcEECCHHHHHHHHHHHHHhCCCCcEEEECCCCchHHHHHHHHHHhCc--ccCCCeEEEeCCCC-ChHHHHHHhcCccc
Confidence            4688988877776666543  3334699999999999999999999742  23445677776542 22222111100000


Q ss_pred             hccc---------CCCCceeEEEEeCCCCCCHHHHHHHHHHhhhc-----------cCCceEEEEecCC-------CcCc
Q psy879           88 QKVT---------LPPGRHKIVILDEADSMTDGAQQALRRTMEIY-----------SNTTRFALACNNS-------EKII  140 (317)
Q Consensus        88 ~~~~---------~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~-----------~~~~~~il~~~~~-------~~l~  140 (317)
                      ..+.         +......++||||++.+..+.+..|++.+++.           +.++++|++||..       ..+.
T Consensus        79 g~~tg~~~~~~g~~~~a~~g~L~LDEi~~l~~~~q~~Ll~~l~~~~~~~~g~~~~~~~~~riI~atn~~l~~~v~~g~fr  158 (304)
T 1ojl_A           79 GAFTGADKRREGRFVEADGGTLFLDEIGDISPLMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAEEVSAGRFR  158 (304)
T ss_dssp             SCCC---CCCCCHHHHHTTSEEEEESCTTCCHHHHHHHHHHHHSSBCCBTTBCCCCBCCCEEEEEESSCHHHHHHHTSSC
T ss_pred             cccCchhhhhcCHHHhcCCCEEEEeccccCCHHHHHHHHHHHhcCEeeecCCcccccCCeEEEEecCccHHHHHHhCCcH
Confidence            0000         00013469999999999999999999999964           2457899999875       2467


Q ss_pred             hhHhhhcce--eeecCCC--HHHHHHHHHHHH----HHcC---CCCCHHHHHHHHHhc-CCCHHHHHHHHHHhhh--CCC
Q psy879          141 EPIQSRCAM--LRYNKLT--DAQLLSKVIEIC----EKEN---ISHTNDGLEAIVFTA-QGDMRQALNNLQSTHN--GFG  206 (317)
Q Consensus       141 ~~i~sR~~~--i~f~~~~--~~~~~~~l~~~~----~~~~---~~i~~~~~~~l~~~~-~gd~r~~i~~l~~~~~--~~~  206 (317)
                      +.+.+|+..  +.++|+.  .+++..++...+    ...+   ..+++++++.+...+ .||+|++.+.++.++.  ...
T Consensus       159 ~~L~~Rl~~~~i~lPpL~eR~edi~~l~~~~l~~~~~~~~~~~~~~s~~a~~~L~~~~wpGnvReL~~~l~~~~~~~~~~  238 (304)
T 1ojl_A          159 QDLYYRLNVVAIEMPSLRQRREDIPLLADHFLRRFAERNRKVVKGFTPQAMDLLIHYDWPGNIRELENAIERAVVLLTGE  238 (304)
T ss_dssp             HHHHHHHSSEEEECCCSGGGGGGHHHHHHHHHHHHHHHTTCCCCCBCHHHHHHHHHCCCSSHHHHHHHHHHHHHHHCCSS
T ss_pred             HHHHhhcCeeEEeccCHHHhHhhHHHHHHHHHHHHHHHhccCccCCCHHHHHHHHcCCCCCCHHHHHHHHHHHHHhCCCC
Confidence            889999865  6688877  456665555433    3333   568999999999886 9999999999987654  445


Q ss_pred             cccHHHHHh
Q psy879          207 HVTAEYVFK  215 (317)
Q Consensus       207 ~i~~~~v~~  215 (317)
                      .|+.+++..
T Consensus       239 ~i~~~~l~~  247 (304)
T 1ojl_A          239 YISERELPL  247 (304)
T ss_dssp             SBCGGGSCG
T ss_pred             cccHHhhhh
Confidence            677777644

>3hu3_A Transitional endoplasmic reticulum ATPase; VCP, transport protein; HET: AGS; 2.20A {Homo sapiens} PDB: 3hu2_A* 3hu1_A* 1e32_A* 1s3s_A*

Probab=99.76  E-value=6.6e-18  Score=154.78  Aligned_cols=184  Identities=16%  Similarity=0.191  Sum_probs=131.4

Q ss_pred             cCCCCCCcccCCHHHHHHHHHHHhc-------------CCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCC
Q psy879            4 YRPQTFSDIVGNEDTVERLKVFSSS-------------GNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNAS   70 (317)
Q Consensus         4 y~P~~~~~~~g~~~~~~~l~~~l~~-------------~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~   70 (317)
                      +++.+|++++|++..++.+..++..             ....++||+||||||||++|+++++.+     +..++.+++.
T Consensus       198 ~~~~~~~~i~G~~~~~~~l~~~i~~~l~~~~~~~~~g~~~~~~vLL~GppGtGKT~lAraia~~~-----~~~fv~vn~~  272 (489)
T 3hu3_A          198 LNEVGYDDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANET-----GAFFFLINGP  272 (489)
T ss_dssp             HTCCCGGGCCSCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCCEEEEECSTTSSHHHHHHHHHHHC-----SSEEEEEEHH
T ss_pred             cCCCCHHHcCCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCcEEEECcCCCCHHHHHHHHHHHh-----CCCEEEEEch
Confidence            4567899999999999998887753             233359999999999999999999985     3456766653


Q ss_pred             CC----cC--hHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCH-----------HHHHHHHHHhhhc--cCCceEEE
Q psy879           71 ND----RG--IDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTD-----------GAQQALRRTMEIY--SNTTRFAL  131 (317)
Q Consensus        71 ~~----~~--~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~-----------~~~~~ll~~le~~--~~~~~~il  131 (317)
                      ..    .+  ...++..+.....       +.+.+|+|||+|.+..           ..++.|++.|+..  +.++++|.
T Consensus       273 ~l~~~~~g~~~~~~~~~f~~A~~-------~~p~iLfLDEId~l~~~~~~~~~~~~~~~~~~LL~~ld~~~~~~~v~vIa  345 (489)
T 3hu3_A          273 EIMSKLAGESESNLRKAFEEAEK-------NAPAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMA  345 (489)
T ss_dssp             HHHTSCTTHHHHHHHHHHHHHHH-------TCSEEEEEESHHHHCBCTTSCCCHHHHHHHHHHHHHHHHSCTTSCEEEEE
T ss_pred             HhhhhhcchhHHHHHHHHHHHHh-------cCCcEEEecchhhhccccccccchHHHHHHHHHHHHhhccccCCceEEEE
Confidence            21    11  1223333333221       3467999999987643           5688899999853  45677888


Q ss_pred             EecCCCcCchhHhh--hcce-eeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCC-HHHHHHHHHH
Q psy879          132 ACNNSEKIIEPIQS--RCAM-LRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGD-MRQALNNLQS  200 (317)
Q Consensus       132 ~~~~~~~l~~~i~s--R~~~-i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd-~r~~i~~l~~  200 (317)
                      +||.+..+.+++++  ||.. +.|+.|+.++...++..++....+. .+..+..++..+.|. .+.+.++++.
T Consensus       346 aTn~~~~Ld~al~r~gRf~~~i~i~~P~~~eR~~IL~~~~~~~~l~-~~~~l~~la~~t~g~s~~dL~~L~~~  417 (489)
T 3hu3_A          346 ATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLA-DDVDLEQVANETHGHVGADLAALCSE  417 (489)
T ss_dssp             EESCGGGBCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHTTTSCBC-TTCCHHHHHHTCTTCCHHHHHHHHHH
T ss_pred             ecCCccccCHHHhCCCcCceEEEeCCCCHHHHHHHHHHHHhcCCCc-chhhHHHHHHHccCCcHHHHHHHHHH
Confidence            99999999999999  6654 9999999999999999887654443 233467778877774 3334344443

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=99.76  E-value=7.2e-18  Score=163.61  Aligned_cols=184  Identities=16%  Similarity=0.235  Sum_probs=133.0

Q ss_pred             CcccCCHHHHHHHHHHHhcCC--------C-ceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHH-H
Q psy879           10 SDIVGNEDTVERLKVFSSSGN--------V-PNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTV-R   79 (317)
Q Consensus        10 ~~~~g~~~~~~~l~~~l~~~~--------~-~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i-~   79 (317)
                      ++++||+++++.+...+....        + ++++|+||||||||++|+++++.+.+.  ...++.++++........ .
T Consensus       491 ~~viGq~~a~~~l~~~i~~~~~~~~~~~~p~~~~Ll~Gp~GtGKT~lA~ala~~l~~~--~~~~i~i~~s~~~~~~~~~~  568 (758)
T 3pxi_A          491 SRVIGQDEAVVAVAKAVRRARAGLKDPKRPIGSFIFLGPTGVGKTELARALAESIFGD--EESMIRIDMSEYMEKHSTSG  568 (758)
T ss_dssp             TTSCSCHHHHHHHHHHHHHHTTTCSCTTSCSEEEEEESCTTSSHHHHHHHHHHHHHSC--TTCEEEEEGGGGCSSCCCC-
T ss_pred             CcCcChHHHHHHHHHHHHHHHcccCCCCCCceEEEEECCCCCCHHHHHHHHHHHhcCC--CcceEEEechhccccccccc
Confidence            468999999988877775321        1 269999999999999999999998543  234666665432211000 1


Q ss_pred             HHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhh-----------ccCCceEEEEecCCCc----------
Q psy879           80 NKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEI-----------YSNTTRFALACNNSEK----------  138 (317)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~-----------~~~~~~~il~~~~~~~----------  138 (317)
                      ..+......      ..+.|++|||++.+.++.++.|++.|++           ...++++|++||....          
T Consensus       569 ~~l~~~~~~------~~~~vl~lDEi~~~~~~~~~~Ll~~le~g~~~~~~g~~~~~~~~~iI~ttn~~~~~~~~~~~~~~  642 (758)
T 3pxi_A          569 GQLTEKVRR------KPYSVVLLDAIEKAHPDVFNILLQVLEDGRLTDSKGRTVDFRNTILIMTSNVGASEKDKVMGELK  642 (758)
T ss_dssp             --CHHHHHH------CSSSEEEEECGGGSCHHHHHHHHHHHHHSBCC-----CCBCTTCEEEEEESSSTTCCHHHHHHHH
T ss_pred             chhhHHHHh------CCCeEEEEeCccccCHHHHHHHHHHhccCeEEcCCCCEeccCCeEEEEeCCCChhhHHHHHHHHH
Confidence            111111111      3467999999999999999999999997           3457889999996443          


Q ss_pred             --CchhHhhhc-ceeeecCCCHHHHHHHHHHHHHH---------cCCCCCHHHHHHHHHh---cCCCHHHHHHHHHHh
Q psy879          139 --IIEPIQSRC-AMLRYNKLTDAQLLSKVIEICEK---------ENISHTNDGLEAIVFT---AQGDMRQALNNLQST  201 (317)
Q Consensus       139 --l~~~i~sR~-~~i~f~~~~~~~~~~~l~~~~~~---------~~~~i~~~~~~~l~~~---~~gd~r~~i~~l~~~  201 (317)
                        +.|.+.+|+ ..+.|+|++.+++..++...+..         ..+.+++++++.++..   ..|+.|.+-+.++..
T Consensus       643 ~~f~p~l~~Rl~~~i~~~~l~~~~~~~i~~~~l~~~~~~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~R~L~~~i~~~  720 (758)
T 3pxi_A          643 RAFRPEFINRIDEIIVFHSLEKKHLTEIVSLMSDQLTKRLKEQDLSIELTDAAKAKVAEEGVDLEYGARPLRRAIQKH  720 (758)
T ss_dssp             HHSCHHHHTTSSEEEECC--CHHHHHHHHHHHHHHHHHHHHTTTCEEEECHHHHHHHHGGGCCTTTTTTTHHHHHHHH
T ss_pred             hhCCHHHHhhCCeEEecCCCCHHHHHHHHHHHHHHHHHHHHhCCCeEEECHHHHHHHHHhCCCCCCCChHHHHHHHHH
Confidence              789999999 66999999999999998876654         2456889999999875   457788777777654

>1r6b_X CLPA protein; AAA+, N-terminal domain, CLPS, crystal, binding mechanism, hydrolase; HET: ADP; 2.25A {Escherichia coli} SCOP: a.174.1.1 c.37.1.20 c.37.1.20 PDB: 1ksf_X*

Probab=99.76  E-value=9.1e-18  Score=163.05  Aligned_cols=207  Identities=15%  Similarity=0.168  Sum_probs=147.3

Q ss_pred             cccCCCCCCcccCCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCC-----CCceEEecCCC-----
Q psy879            2 EKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSF-----KDAVLELNASN-----   71 (317)
Q Consensus         2 ~ky~P~~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~-----~~~~~~~~~~~-----   71 (317)
                      ++|+|.+|++++|+++.++.+...+......+++|+||||||||++++.+++.+.+...     +..++.++...     
T Consensus       178 ~~~~~~~~d~~iGr~~~i~~l~~~l~~~~~~~vlL~G~~GtGKT~la~~la~~l~~~~v~~~~~~~~~~~~~~~~l~~~~  257 (758)
T 1r6b_X          178 QLARVGGIDPLIGREKELERAIQVLCRRRKNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDIGSLLAGT  257 (758)
T ss_dssp             HHHHTTCSCCCCSCHHHHHHHHHHHTSSSSCEEEEECCTTSSHHHHHHHHHHHHHHTCSCGGGTTCEEEECCCC---CCC
T ss_pred             HHHhcCCCCCccCCHHHHHHHHHHHhccCCCCeEEEcCCCCCHHHHHHHHHHHHHhCCCChhhcCCEEEEEcHHHHhccc
Confidence            57899999999999999999999998877778999999999999999999998853221     22233333221     


Q ss_pred             -CcC--hHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCC---------HHHHHHHHHHhhhccCCceEEEEecCC---
Q psy879           72 -DRG--IDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMT---------DGAQQALRRTMEIYSNTTRFALACNNS---  136 (317)
Q Consensus        72 -~~~--~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~---------~~~~~~ll~~le~~~~~~~~il~~~~~---  136 (317)
                       ..+  ...+...+....       ...+.+++|||++.+.         .+..+.|..+++.  ....+|++|+.+   
T Consensus       258 ~~~g~~e~~l~~~~~~~~-------~~~~~iL~IDEi~~l~~~~~~~~~~~~~~~~L~~~l~~--~~~~~I~at~~~~~~  328 (758)
T 1r6b_X          258 KYRGDFEKRFKALLKQLE-------QDTNSILFIDEIHTIIGAGAASGGQVDAANLIKPLLSS--GKIRVIGSTTYQEFS  328 (758)
T ss_dssp             CCSSCHHHHHHHHHHHHS-------SSSCEEEEETTTTTTTTSCCSSSCHHHHHHHHSSCSSS--CCCEEEEEECHHHHH
T ss_pred             cccchHHHHHHHHHHHHH-------hcCCeEEEEechHHHhhcCCCCcchHHHHHHHHHHHhC--CCeEEEEEeCchHHh
Confidence             111  122333333221       1346899999999982         3345556556653  456778888754   


Q ss_pred             --CcCchhHhhhcceeeecCCCHHHHHHHHHHHHHH----cCCCCCHHHHHHHHHhcCC------CHHHHHHHHHHhhh-
Q psy879          137 --EKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEK----ENISHTNDGLEAIVFTAQG------DMRQALNNLQSTHN-  203 (317)
Q Consensus       137 --~~l~~~i~sR~~~i~f~~~~~~~~~~~l~~~~~~----~~~~i~~~~~~~l~~~~~g------d~r~~i~~l~~~~~-  203 (317)
                        ...++++.+||..+.|++|+.++...++...+..    +++.++++++..++..+.|      .+..+++.++.++. 
T Consensus       329 ~~~~~d~aL~~Rf~~i~v~~p~~~e~~~il~~l~~~~~~~~~v~~~~~al~~~~~~s~~~i~~~~lp~~~i~lld~a~~~  408 (758)
T 1r6b_X          329 NIFEKDRALARRFQKIDITEPSIEETVQIINGLKPKYEAHHDVRYTAKAVRAAVELAVKYINDRHLPDKAIDVIDEAGAR  408 (758)
T ss_dssp             CCCCCTTSSGGGEEEEECCCCCHHHHHHHHHHHHHHHHHHHTCCCCHHHHHHHHHHHHHHCTTSCTTHHHHHHHHHHHHH
T ss_pred             hhhhcCHHHHhCceEEEcCCCCHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhhcccccCchHHHHHHHHHHHH
Confidence              2567899999999999999999999999887654    6788999999888876543      35577777765432 


Q ss_pred             --------CCCcccHHHHHhhc
Q psy879          204 --------GFGHVTAEYVFKVC  217 (317)
Q Consensus       204 --------~~~~i~~~~v~~~~  217 (317)
                              ....++.+++..++
T Consensus       409 ~~~~~~~~~~~~v~~~di~~~~  430 (758)
T 1r6b_X          409 ARLMPVSKRKKTVNVADIESVV  430 (758)
T ss_dssp             HHHSSSCCCCCSCCHHHHHHHH
T ss_pred             HhcccccccCCccCHHHHHHHH
Confidence                    23467787776543

>1r6b_X CLPA protein; AAA+, N-terminal domain, CLPS, crystal, binding mechanism, hydrolase; HET: ADP; 2.25A {Escherichia coli} SCOP: a.174.1.1 c.37.1.20 c.37.1.20 PDB: 1ksf_X*

Probab=99.75  E-value=2.4e-17  Score=160.06  Aligned_cols=180  Identities=16%  Similarity=0.232  Sum_probs=131.5

Q ss_pred             CcccCCHHHHHHHHHHHhc---C-----CC-ceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCc-------
Q psy879           10 SDIVGNEDTVERLKVFSSS---G-----NV-PNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDR-------   73 (317)
Q Consensus        10 ~~~~g~~~~~~~l~~~l~~---~-----~~-~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~-------   73 (317)
                      .+++||+++++.+..++..   |     ++ .+++|+||||||||++|+++++.+.     ..++.++++...       
T Consensus       458 ~~v~g~~~~~~~l~~~i~~~~~g~~~~~~p~~~~ll~G~~GtGKT~la~~la~~l~-----~~~~~i~~s~~~~~~~~~~  532 (758)
T 1r6b_X          458 MLVFGQDKAIEALTEAIKMARAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKALG-----IELLRFDMSEYMERHTVSR  532 (758)
T ss_dssp             TTSCSCHHHHHHHHHHHHHHHTTCSCTTSCSEEEEEECSTTSSHHHHHHHHHHHHT-----CEEEEEEGGGCSSSSCCSS
T ss_pred             hhccCHHHHHHHHHHHHHHHhcccCCCCCCceEEEEECCCCCcHHHHHHHHHHHhc-----CCEEEEechhhcchhhHhh
Confidence            4588999999888777652   1     22 2599999999999999999999972     234444433211       


Q ss_pred             ---------ChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhcc-----------CCceEEEEe
Q psy879           74 ---------GIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYS-----------NTTRFALAC  133 (317)
Q Consensus        74 ---------~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~-----------~~~~~il~~  133 (317)
                               +.+.-......+..       ..+.|++|||++++.++.++.|++.|++..           .++++|+++
T Consensus       533 l~g~~~g~~g~~~~~~l~~~~~~-------~~~~vl~lDEi~~~~~~~~~~Ll~~le~~~~~~~~g~~~~~~~~~iI~ts  605 (758)
T 1r6b_X          533 LIGAPPGYVGFDQGGLLTDAVIK-------HPHAVLLLDEIEKAHPDVFNILLQVMDNGTLTDNNGRKADFRNVVLVMTT  605 (758)
T ss_dssp             SCCCCSCSHHHHHTTHHHHHHHH-------CSSEEEEEETGGGSCHHHHHHHHHHHHHSEEEETTTEEEECTTEEEEEEE
T ss_pred             hcCCCCCCcCccccchHHHHHHh-------CCCcEEEEeCccccCHHHHHHHHHHhcCcEEEcCCCCEEecCCeEEEEec
Confidence                     11111111122211       357899999999999999999999999642           467799999


Q ss_pred             cCCC-------------------------cCchhHhhhc-ceeeecCCCHHHHHHHHHHHHHHc---------CCCCCHH
Q psy879          134 NNSE-------------------------KIIEPIQSRC-AMLRYNKLTDAQLLSKVIEICEKE---------NISHTND  178 (317)
Q Consensus       134 ~~~~-------------------------~l~~~i~sR~-~~i~f~~~~~~~~~~~l~~~~~~~---------~~~i~~~  178 (317)
                      |...                         .+.+++.+|+ ..+.|++++.+++..++...+.+.         .+.++++
T Consensus       606 N~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~l~~R~~~~i~~~~l~~~~~~~i~~~~l~~~~~~~~~~~~~~~~~~~  685 (758)
T 1r6b_X          606 NAGVRETERKSIGLIHQDNSTDAMEEIKKIFTPEFRNRLDNIIWFDHLSTDVIHQVVDKFIVELQVQLDQKGVSLEVSQE  685 (758)
T ss_dssp             CSSCC-----------------CHHHHHHHSCHHHHTTCSEEEECCCCCHHHHHHHHHHHHHHHHHHHHHTTEEEEECHH
T ss_pred             CcchhhhhhcccCccccchHHHHHHHHHHhcCHHHHhhCCcceeeCCCCHHHHHHHHHHHHHHHHHHHHHCCcEEEeCHH
Confidence            8743                         5789999999 569999999999999998877532         3468899


Q ss_pred             HHHHHHHhc---CCCHHHHHHHHHHh
Q psy879          179 GLEAIVFTA---QGDMRQALNNLQST  201 (317)
Q Consensus       179 ~~~~l~~~~---~gd~r~~i~~l~~~  201 (317)
                      +++.+++.+   +++.|.+.+.++..
T Consensus       686 a~~~l~~~~~~~~~g~R~l~~~i~~~  711 (758)
T 1r6b_X          686 ARNWLAEKGYDRAMGARPMARVIQDN  711 (758)
T ss_dssp             HHHHHHHHHCBTTTBTTTHHHHHHHH
T ss_pred             HHHHHHHhCCCcCCCchHHHHHHHHH
Confidence            999999876   55577777777654

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=99.75  E-value=2.1e-18  Score=138.46  Aligned_cols=147  Identities=18%  Similarity=0.226  Sum_probs=106.6

Q ss_pred             cccCCCCCCcccCCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCC-----CCCceEEecCCCC----
Q psy879            2 EKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPS-----FKDAVLELNASND----   72 (317)
Q Consensus         2 ~ky~P~~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~-----~~~~~~~~~~~~~----   72 (317)
                      ++|+|.+|++++|++..++.+...+..+..++++|+||+|+|||++++.+++.+.+..     .+..++.++....    
T Consensus        14 ~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~vll~G~~G~GKT~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   93 (187)
T 2p65_A           14 ALARAGKLDPVIGRDTEIRRAIQILSRRTKNNPILLGDPGVGKTAIVEGLAIKIVQGDVPDSLKGRKLVSLDLSSLIAGA   93 (187)
T ss_dssp             HHHHTTCSCCCCSCHHHHHHHHHHHTSSSSCEEEEESCGGGCHHHHHHHHHHHHHTTCSCTTTTTCEEEEECHHHHHHHC
T ss_pred             HHHhccccchhhcchHHHHHHHHHHhCCCCCceEEECCCCCCHHHHHHHHHHHHHhcCCcchhcCCeEEEEeHHHhhcCC
Confidence            5789999999999999999999999887777899999999999999999999975421     1233444432210    


Q ss_pred             cChHH----HHHHHHHHHhhcccCCCCceeEEEEeCCCCCC---------HHHHHHHHHHhhhccCCceEEEEecCCC--
Q psy879           73 RGIDT----VRNKIKMFAQQKVTLPPGRHKIVILDEADSMT---------DGAQQALRRTMEIYSNTTRFALACNNSE--  137 (317)
Q Consensus        73 ~~~~~----i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~---------~~~~~~ll~~le~~~~~~~~il~~~~~~--  137 (317)
                      .....    +...+..+...      ..+.+++|||++.+.         .+..+.|...++.  ..+.+|++++.+.  
T Consensus        94 ~~~~~~~~~~~~~~~~~~~~------~~~~vl~iDe~~~l~~~~~~~~~~~~~~~~l~~~~~~--~~~~ii~~~~~~~~~  165 (187)
T 2p65_A           94 KYRGDFEERLKSILKEVQDA------EGQVVMFIDEIHTVVGAGAVAEGALDAGNILKPMLAR--GELRCIGATTVSEYR  165 (187)
T ss_dssp             CSHHHHHHHHHHHHHHHHHT------TTSEEEEETTGGGGSSSSSSCTTSCCTHHHHHHHHHT--TCSCEEEEECHHHHH
T ss_pred             CchhHHHHHHHHHHHHHHhc------CCceEEEEeCHHHhcccccccccchHHHHHHHHHHhc--CCeeEEEecCHHHHH
Confidence            01111    22222222211      356799999999986         4456677777764  5677888888654  


Q ss_pred             ---cCchhHhhhcceeeecCCC
Q psy879          138 ---KIIEPIQSRCAMLRYNKLT  156 (317)
Q Consensus       138 ---~l~~~i~sR~~~i~f~~~~  156 (317)
                         .+.+++.+||..+.+++|+
T Consensus       166 ~~~~~~~~l~~R~~~i~i~~p~  187 (187)
T 2p65_A          166 QFIEKDKALERRFQQILVEQPS  187 (187)
T ss_dssp             HHTTTCHHHHHHEEEEECCSCC
T ss_pred             HHHhccHHHHHhcCcccCCCCC
Confidence               5889999999999998875

>1w5s_A Origin recognition complex subunit 2 ORC2; replication, CDC6, DNA replication initiation, DNA BIND protein, AAA+ ATPase; HET: ADP; 2.4A {Aeropyrum pernix} SCOP: a.4.5.11 c.37.1.20 PDB: 1w5t_A*

Probab=99.74  E-value=2.4e-16  Score=142.34  Aligned_cols=203  Identities=20%  Similarity=0.168  Sum_probs=137.3

Q ss_pred             CcccCCHHHHHHHHHHH-h----c--CCCceEEE--ECCCCCCHHHHHHHHHHHHcCC----CCCCceEEecCCCCcChH
Q psy879           10 SDIVGNEDTVERLKVFS-S----S--GNVPNIII--SGPPGVGKTTTILCLARILLGP----SFKDAVLELNASNDRGID   76 (317)
Q Consensus        10 ~~~~g~~~~~~~l~~~l-~----~--~~~~~~ll--~G~~G~GKt~la~~la~~l~~~----~~~~~~~~~~~~~~~~~~   76 (317)
                      ++++|++..++.|..++ .    .  +...++++  +||+|+|||++++.+++.+...    .....++.+++.......
T Consensus        22 ~~l~gR~~el~~l~~~l~~~~~~~~~~~~~~~li~i~G~~G~GKT~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  101 (412)
T 1w5s_A           22 PELRVRRGEAEALARIYLNRLLSGAGLSDVNMIYGSIGRVGIGKTTLAKFTVKRVSEAAAKEGLTVKQAYVNAFNAPNLY  101 (412)
T ss_dssp             SSCSSSCHHHHHHHHHHHHHHHTSSCBCCEEEEEECTTCCSSSHHHHHHHHHHHHHHHHHHTTCCEEEEEEEGGGCCSHH
T ss_pred             CCCCChHHHHHHHHHHHhHHHhcCCCCCCCEEEEeCcCcCCCCHHHHHHHHHHHHHHHHhccCCceeEEEEECCCCCCHH
Confidence            67899998888877776 3    2  24446899  9999999999999999887431    112334555542222221


Q ss_pred             HHH-H---------------------HHHHHHhhcccCCCCceeEEEEeCCCCCCH------HHHHHHHHHhhhcc----
Q psy879           77 TVR-N---------------------KIKMFAQQKVTLPPGRHKIVILDEADSMTD------GAQQALRRTMEIYS----  124 (317)
Q Consensus        77 ~i~-~---------------------~~~~~~~~~~~~~~~~~~vliiDE~d~l~~------~~~~~ll~~le~~~----  124 (317)
                      .+. .                     .+......     .+.+.+|+|||++.+..      +....|++.+++.+    
T Consensus       102 ~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~-----~~~~~llvlDe~~~l~~~~~~~~~~l~~l~~~~~~~~~~~~  176 (412)
T 1w5s_A          102 TILSLIVRQTGYPIQVRGAPALDILKALVDNLYV-----ENHYLLVILDEFQSMLSSPRIAAEDLYTLLRVHEEIPSRDG  176 (412)
T ss_dssp             HHHHHHHHHHTCCCCCTTCCHHHHHHHHHHHHHH-----HTCEEEEEEESTHHHHSCTTSCHHHHHHHHTHHHHSCCTTS
T ss_pred             HHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHHHh-----cCCeEEEEEeCHHHHhhccCcchHHHHHHHHHHHhcccCCC
Confidence            111 1                     11111111     13477999999999853      56666777777654    


Q ss_pred             -CCceEEEEecCCC---cCc---hhHhhhcce-eeecCCCHHHHHHHHHHHHHHcC--CCCCHHHHHHHHHhcC------
Q psy879          125 -NTTRFALACNNSE---KII---EPIQSRCAM-LRYNKLTDAQLLSKVIEICEKEN--ISHTNDGLEAIVFTAQ------  188 (317)
Q Consensus       125 -~~~~~il~~~~~~---~l~---~~i~sR~~~-i~f~~~~~~~~~~~l~~~~~~~~--~~i~~~~~~~l~~~~~------  188 (317)
                       .++.+|++++.+.   .+.   +.+.+++.. +.|+|++.+++.+++...+...+  ..++++++..++..++      
T Consensus       177 ~~~v~lI~~~~~~~~~~~l~~~~~~~~~~~~~~i~l~~l~~~e~~~ll~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~  256 (412)
T 1w5s_A          177 VNRIGFLLVASDVRALSYMREKIPQVESQIGFKLHLPAYKSRELYTILEQRAELGLRDTVWEPRHLELISDVYGEDKGGD  256 (412)
T ss_dssp             CCBEEEEEEEEETHHHHHHHHHCHHHHTTCSEEEECCCCCHHHHHHHHHHHHHHHBCTTSCCHHHHHHHHHHHCGGGTSC
T ss_pred             CceEEEEEEeccccHHHHHhhhcchhhhhcCCeeeeCCCCHHHHHHHHHHHHHhcCCCCCCChHHHHHHHHHHHHhccCC
Confidence             4566787887554   333   566676544 99999999999999988776433  2478899999999999      


Q ss_pred             CCHHHHHHHHHHhhh-----CCCcccHHHHHhhc
Q psy879          189 GDMRQALNNLQSTHN-----GFGHVTAEYVFKVC  217 (317)
Q Consensus       189 gd~r~~i~~l~~~~~-----~~~~i~~~~v~~~~  217 (317)
                      |++|.+++.++.+..     +...++.+++..+.
T Consensus       257 G~p~~~~~l~~~a~~~a~~~~~~~i~~~~v~~~~  290 (412)
T 1w5s_A          257 GSARRAIVALKMACEMAEAMGRDSLSEDLVRKAV  290 (412)
T ss_dssp             CCHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHHH
T ss_pred             CcHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHH
Confidence            999999998876432     33467777776544

>1ixz_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 2.20A {Thermus thermophilus} SCOP: c.37.1.20 PDB: 1iy0_A* 1iy1_A*

Probab=99.73  E-value=1.4e-16  Score=134.57  Aligned_cols=205  Identities=17%  Similarity=0.169  Sum_probs=132.4

Q ss_pred             ccCCCCCCcccCCHHHHHHHHHHHhc-----------CCC-ceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCC
Q psy879            3 KYRPQTFSDIVGNEDTVERLKVFSSS-----------GNV-PNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNAS   70 (317)
Q Consensus         3 ky~P~~~~~~~g~~~~~~~l~~~l~~-----------~~~-~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~   70 (317)
                      .+.+.+|++++|+++++..+......           -.. ++++|+||||+||||++++++..+.     ..++.+++.
T Consensus         9 ~~~~~~~~~i~g~~~~~~~l~~l~~~~~~~~~~~~~~~~~~~g~ll~G~~G~GKTtl~~~i~~~~~-----~~~i~~~~~   83 (254)
T 1ixz_A            9 EAPKVTFKDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEAR-----VPFITASGS   83 (254)
T ss_dssp             CCCSCCGGGCCSCHHHHHHHHHHHHHHHCHHHHHHTTCCCCSEEEEECCTTSSHHHHHHHHHHHTT-----CCEEEEEHH
T ss_pred             CCCCCCHHHhCCcHHHHHHHHHHHHHHHCHHHHHHcCCCCCCeEEEECCCCCCHHHHHHHHHHHhC-----CCEEEeeHH
Confidence            45567899999999888876654321           122 3499999999999999999999863     234444432


Q ss_pred             CC--cChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCH--------------HHHHHHHHHhhhcc--CCceEEEE
Q psy879           71 ND--RGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTD--------------GAQQALRRTMEIYS--NTTRFALA  132 (317)
Q Consensus        71 ~~--~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~--------------~~~~~ll~~le~~~--~~~~~il~  132 (317)
                      +.  .........+....+...   ...+.++++||+|.+..              ...+.++..++...  ....++.+
T Consensus        84 ~~~~~~~~~~~~~i~~~~~~~~---~~~~~i~~~Deid~l~~~~~~~~~~~~~~~~~~~~~ll~~l~g~~~~~~~i~~a~  160 (254)
T 1ixz_A           84 DFVEMFVGVGAARVRDLFETAK---RHAPCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEKDTAIVVMAA  160 (254)
T ss_dssp             HHHHSCTTHHHHHHHHHHHHHT---TSSSEEEEEETHHHHHC---------CHHHHHHHHHHHHHHHTCCTTCCEEEEEE
T ss_pred             HHHHHHhhHHHHHHHHHHHHHH---hcCCeEEEehhhhhhhcccCccccccchHHHHHHHHHHHHHhCCCCCCCEEEEEc
Confidence            10  011112223333333321   12467999999986631              12345555555332  23456667


Q ss_pred             ecCCCcCchhHhh--hcce-eeecCCCHHHHHHHHHHHHHHcCCCCCHHH-HHHHHHhcCCCH-HHHHHHHHHhhh----
Q psy879          133 CNNSEKIIEPIQS--RCAM-LRYNKLTDAQLLSKVIEICEKENISHTNDG-LEAIVFTAQGDM-RQALNNLQSTHN----  203 (317)
Q Consensus       133 ~~~~~~l~~~i~s--R~~~-i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~-~~~l~~~~~gd~-r~~i~~l~~~~~----  203 (317)
                      +|.++.+++++.+  |+.. +.|++|+.++..+++...++  +..++++. +..++..+.|.. +.+.+.++.++.    
T Consensus       161 t~~p~~ld~~l~r~~rf~~~i~i~~p~~~~r~~il~~~~~--~~~~~~~~~~~~la~~~~G~~~~dl~~~~~~a~~~a~~  238 (254)
T 1ixz_A          161 TNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHAR--GKPLAEDVDLALLAKRTPGFVGADLENLLNEAALLAAR  238 (254)
T ss_dssp             ESCGGGSCGGGGSTTSSCEEEECCSCCHHHHHHHHHHHHT--TSCBCTTCCHHHHHHTCTTCCHHHHHHHHHHHHHHHHH
T ss_pred             cCCchhCCHHHcCCCcCCeEEeeCCcCHHHHHHHHHHHHc--CCCCCcccCHHHHHHHcCCCCHHHHHHHHHHHHHHHHH
Confidence            8888999999998  4544 99999999999999987764  44454443 778889888754 566666654332    


Q ss_pred             -CCCcccHHHHHhhc
Q psy879          204 -GFGHVTAEYVFKVC  217 (317)
Q Consensus       204 -~~~~i~~~~v~~~~  217 (317)
                       +...|+.+++.+++
T Consensus       239 ~~~~~I~~~dl~~a~  253 (254)
T 1ixz_A          239 EGRRKITMKDLEEAA  253 (254)
T ss_dssp             TTCSSBCHHHHHHHT
T ss_pred             hcCCCcCHHHHHHHh
Confidence             34568888887654

>2dhr_A FTSH; AAA+ protein, hexameric Zn metalloprotease, hydrolase; HET: ADP; 3.90A {Thermus thermophilus}

Probab=99.72  E-value=1.4e-16  Score=145.62  Aligned_cols=203  Identities=17%  Similarity=0.181  Sum_probs=137.0

Q ss_pred             CCCCCCcccCCHHHHHHHHHHHh---c--------CCCc-eEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCC
Q psy879            5 RPQTFSDIVGNEDTVERLKVFSS---S--------GNVP-NIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASND   72 (317)
Q Consensus         5 ~P~~~~~~~g~~~~~~~l~~~l~---~--------~~~~-~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~   72 (317)
                      .+.+|++++|+++++..+...+.   .        ..+| +++|+||||||||+++++++..+.     ..++.+++.+.
T Consensus        26 ~~~~f~dv~G~~~~k~~l~~lv~~l~~~~~~~~lg~~ip~GvLL~GppGtGKTtLaraIa~~~~-----~~~i~i~g~~~  100 (499)
T 2dhr_A           26 PKVTFKDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEAR-----VPFITASGSDF  100 (499)
T ss_dssp             CCCCTTSSCSCHHHHHHHHHHHHHHHCGGGTTTTSCCCCSEEEEECSSSSSHHHHHHHHHHHTT-----CCEEEEEGGGG
T ss_pred             CCCCHHHcCCcHHHHHHHHHHHHHhhchhhhhhccCCCCceEEEECCCCCCHHHHHHHHHHHhC-----CCEEEEehhHH
Confidence            45679999999999888776543   1        1223 499999999999999999999862     34666665432


Q ss_pred             c--ChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCH--------------HHHHHHHHHhhhc--cCCceEEEEec
Q psy879           73 R--GIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTD--------------GAQQALRRTMEIY--SNTTRFALACN  134 (317)
Q Consensus        73 ~--~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~--------------~~~~~ll~~le~~--~~~~~~il~~~  134 (317)
                      .  ........+....+...   ...+.++++||+|.+..              ...+.|+..|+..  ....+++.++|
T Consensus       101 ~~~~~g~~~~~v~~lfq~a~---~~~p~il~IDEId~l~~~r~~~~~~~~~e~~~~l~~LL~~Ldg~~~~~~viviAatn  177 (499)
T 2dhr_A          101 VEMFVGVGAARVRDLFETAK---RHAPCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEKDTAIVVMAATN  177 (499)
T ss_dssp             TSSCTTHHHHHHHHHTTTSS---SSSSCEEEEECGGGTCCCSSSSTTTSSHHHHHHHHHHHHHGGGCCSSCCCEEEECCS
T ss_pred             HHhhhhhHHHHHHHHHHHHH---hcCCCEEEEehHHHHHHhhccCcCCCcHHHHHHHHHHHHHhcccccCccEEEEEecC
Confidence            1  11222233434333321   12457999999997742              2345566666533  23456777788


Q ss_pred             CCCcCchhHhhhcc---eeeecCCCHHHHHHHHHHHHHHcCCCCCHHH-HHHHHHhcCCCH-HHHHHHHHHhhh-----C
Q psy879          135 NSEKIIEPIQSRCA---MLRYNKLTDAQLLSKVIEICEKENISHTNDG-LEAIVFTAQGDM-RQALNNLQSTHN-----G  204 (317)
Q Consensus       135 ~~~~l~~~i~sR~~---~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~-~~~l~~~~~gd~-r~~i~~l~~~~~-----~  204 (317)
                      .++.+++++.+++.   .+.+++|+.++..+++...++  ++.+++++ +..++..+.|.. +.+.+.+..++.     +
T Consensus       178 ~p~~LD~aLlr~gRfdr~i~i~~Pd~~~R~~IL~~~~~--~~~l~~dv~l~~lA~~t~G~~gadL~~lv~~Aa~~A~~~~  255 (499)
T 2dhr_A          178 RPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHAR--GKPLAEDVDLALLAKRTPGFVGADLENLLNEAALLAAREG  255 (499)
T ss_dssp             CGGGSCTTTSSTTSSCCEEECCCCCHHHHHHHHHHTTS--SSCCCCSSTTHHHHTTSCSCCHHHHHHHHHHHHHHHTTTC
T ss_pred             ChhhcCcccccccccceEEecCCCCHHHHHHHHHHHHh--cCCCChHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhC
Confidence            88889999998544   399999999999999877654  44555444 778888888876 666677665432     2


Q ss_pred             CCcccHHHHHhhc
Q psy879          205 FGHVTAEYVFKVC  217 (317)
Q Consensus       205 ~~~i~~~~v~~~~  217 (317)
                      ...|+.+++..++
T Consensus       256 ~~~It~~dl~~al  268 (499)
T 2dhr_A          256 RRKITMKDLEEAA  268 (499)
T ss_dssp             CSSCCSHHHHHHH
T ss_pred             CCccCHHHHHHHH
Confidence            3578888876644

>1qvr_A CLPB protein; coiled coil, AAA ATPase, chaperone; HET: ANP; 3.00A {Thermus thermophilus} SCOP: a.174.1.1 c.37.1.20 c.37.1.20

Probab=99.71  E-value=2.8e-17  Score=161.21  Aligned_cols=184  Identities=15%  Similarity=0.193  Sum_probs=135.6

Q ss_pred             CcccCCHHHHHHHHHHHhcC--------CC-ceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHH--
Q psy879           10 SDIVGNEDTVERLKVFSSSG--------NV-PNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTV--   78 (317)
Q Consensus        10 ~~~~g~~~~~~~l~~~l~~~--------~~-~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i--   78 (317)
                      ++++|++.+++.+...+...        ++ .+++|+||||||||++|+++++.+.+.  ...++.++++........  
T Consensus       558 ~~viG~~~a~~~l~~~i~~~~~g~~~~~~p~~~vLl~Gp~GtGKT~lA~~la~~~~~~--~~~~i~i~~~~~~~~~~~s~  635 (854)
T 1qvr_A          558 KRVVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAATLFDT--EEAMIRIDMTEYMEKHAVSR  635 (854)
T ss_dssp             HHSCSCHHHHHHHHHHHHHHGGGCSCSSSCSEEEEEBSCSSSSHHHHHHHHHHHHHSS--GGGEEEECTTTCCSSGGGGG
T ss_pred             cccCCcHHHHHHHHHHHHHHhcccCCCCCCceEEEEECCCCCCHHHHHHHHHHHhcCC--CCcEEEEechhccchhHHHH
Confidence            46899999999888777542        12 359999999999999999999998543  234666666532211000  


Q ss_pred             --------------HHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhcc-----------CCceEEEEe
Q psy879           79 --------------RNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYS-----------NTTRFALAC  133 (317)
Q Consensus        79 --------------~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~-----------~~~~~il~~  133 (317)
                                    ......+..       ..+.||+|||++.+.++.++.|+++|++..           .++++|++|
T Consensus       636 l~g~~~~~~G~~~~g~l~~~~~~-------~~~~vl~lDEi~~l~~~~~~~Ll~~l~~~~~~~~~g~~vd~~~~iiI~ts  708 (854)
T 1qvr_A          636 LIGAPPGYVGYEEGGQLTEAVRR-------RPYSVILFDEIEKAHPDVFNILLQILDDGRLTDSHGRTVDFRNTVIILTS  708 (854)
T ss_dssp             C--------------CHHHHHHH-------CSSEEEEESSGGGSCHHHHHHHHHHHTTTEECCSSSCCEECTTEEEEEEC
T ss_pred             HcCCCCCCcCccccchHHHHHHh-------CCCeEEEEecccccCHHHHHHHHHHhccCceECCCCCEeccCCeEEEEec
Confidence                          001111111       246899999999999999999999999653           367799999


Q ss_pred             cCC--------------------------CcCchhHhhhc-ceeeecCCCHHHHHHHHHHHHHH-------c--CCCCCH
Q psy879          134 NNS--------------------------EKIIEPIQSRC-AMLRYNKLTDAQLLSKVIEICEK-------E--NISHTN  177 (317)
Q Consensus       134 ~~~--------------------------~~l~~~i~sR~-~~i~f~~~~~~~~~~~l~~~~~~-------~--~~~i~~  177 (317)
                      |..                          ..+.+.+.+|+ ..+.|.|++.+++..++...+..       .  .+.+++
T Consensus       709 n~~~~~~~~~~~~~~~~~~l~~~v~~~~~~~f~~~l~~Rl~~~i~~~pl~~edi~~i~~~~l~~~~~~~~~~~~~~~~~~  788 (854)
T 1qvr_A          709 NLGSPLILEGLQKGWPYERIRDEVFKVLQQHFRPEFLNRLDEIVVFRPLTKEQIRQIVEIQLSYLRARLAEKRISLELTE  788 (854)
T ss_dssp             CTTHHHHHHHHHTTCCHHHHHHHHHHHHHTTSCHHHHHTCSBCCBCCCCCHHHHHHHHHHHHHHHHHHHHTTTCEEEECH
T ss_pred             CcChHHHhhhcccccchHHHHHHHHHHHHhhCCHHHHHhcCeEEeCCCCCHHHHHHHHHHHHHHHHHHHHhCCceEEECH
Confidence            862                          24678899999 55999999999999998876652       1  346899


Q ss_pred             HHHHHHHHhcC---CCHHHHHHHHHHhh
Q psy879          178 DGLEAIVFTAQ---GDMRQALNNLQSTH  202 (317)
Q Consensus       178 ~~~~~l~~~~~---gd~r~~i~~l~~~~  202 (317)
                      ++++.++..+.   |++|.+.+.++.+.
T Consensus       789 ~a~~~L~~~~~~~~gn~R~L~~~i~~~~  816 (854)
T 1qvr_A          789 AAKDFLAERGYDPVFGARPLRRVIQREL  816 (854)
T ss_dssp             HHHHHHHHHHCBTTTBTSTHHHHHHHHT
T ss_pred             HHHHHHHHcCCCCCCChHHHHHHHHHHH
Confidence            99999998754   89999999887753

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20

Probab=99.69  E-value=1.1e-15  Score=130.78  Aligned_cols=203  Identities=18%  Similarity=0.186  Sum_probs=129.7

Q ss_pred             CCCCCCcccCCHHHHHHHHHHHhc-----------CCC-ceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCC
Q psy879            5 RPQTFSDIVGNEDTVERLKVFSSS-----------GNV-PNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASND   72 (317)
Q Consensus         5 ~P~~~~~~~g~~~~~~~l~~~l~~-----------~~~-~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~   72 (317)
                      .+.+|++++|++++++.+......           -.. ++++|+||||+||||++++++..+.     ..++.+++.+.
T Consensus        35 ~~~~~~~i~g~~~~~~~l~~l~~~~~~~~~l~~~~~~~~~gvll~Gp~GtGKTtl~~~i~~~~~-----~~~i~~~~~~~  109 (278)
T 1iy2_A           35 PKVTFKDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEAR-----VPFITASGSDF  109 (278)
T ss_dssp             CCCCGGGSSSCHHHHHHHHHHHHHHHCHHHHHHTTCCCCCEEEEECCTTSSHHHHHHHHHHHTT-----CCEEEEEHHHH
T ss_pred             CCCCHHHhCChHHHHHHHHHHHHHHHCHHHHHHcCCCCCCeEEEECCCcChHHHHHHHHHHHcC-----CCEEEecHHHH
Confidence            345799999999988877655431           122 2499999999999999999999863     23444443210


Q ss_pred             --cChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCC-----------HHHH---HHHHHHhhhc--cCCceEEEEec
Q psy879           73 --RGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMT-----------DGAQ---QALRRTMEIY--SNTTRFALACN  134 (317)
Q Consensus        73 --~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~-----------~~~~---~~ll~~le~~--~~~~~~il~~~  134 (317)
                        .........+....+....   ..+.++++||+|.+.           ....   +.++..+...  ....+++.++|
T Consensus       110 ~~~~~~~~~~~i~~~~~~~~~---~~~~i~~iDeid~l~~~~~~~~~~~~~~~~~~~~~ll~~lsgg~~~~~~i~~a~t~  186 (278)
T 1iy2_A          110 VEMFVGVGAARVRDLFETAKR---HAPCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEKDTAIVVMAATN  186 (278)
T ss_dssp             HHSTTTHHHHHHHHHHHHHHT---SCSEEEEEETHHHHHCC--------CHHHHHHHHHHHHHHTTCCTTCCEEEEEEES
T ss_pred             HHHHhhHHHHHHHHHHHHHHh---cCCcEEehhhhHhhhcccccccCCcchHHHHHHHHHHHHHhCCCCCCCEEEEEecC
Confidence              0111122223333333211   245799999998652           1122   3333334322  22345666788


Q ss_pred             CCCcCchhHhh--hcce-eeecCCCHHHHHHHHHHHHHHcCCCCCHHH-HHHHHHhcCCCH-HHHHHHHHHhhh-----C
Q psy879          135 NSEKIIEPIQS--RCAM-LRYNKLTDAQLLSKVIEICEKENISHTNDG-LEAIVFTAQGDM-RQALNNLQSTHN-----G  204 (317)
Q Consensus       135 ~~~~l~~~i~s--R~~~-i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~-~~~l~~~~~gd~-r~~i~~l~~~~~-----~  204 (317)
                      .++.+++++.+  |+.. +.|++|+.++..+++...++  +..++++. +..++..+.|.. +.+.+.++.++.     +
T Consensus       187 ~p~~ld~~l~r~~rf~~~i~i~~p~~~~r~~il~~~~~--~~~~~~~~~~~~la~~~~G~~~~dl~~l~~~a~~~a~~~~  264 (278)
T 1iy2_A          187 RPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHAR--GKPLAEDVDLALLAKRTPGFVGADLENLLNEAALLAAREG  264 (278)
T ss_dssp             CTTSSCHHHHSTTSSCCEEECCCCCHHHHHHHHHHHHT--TSCBCTTCCHHHHHHTCTTCCHHHHHHHHHHHHHHHHHTT
T ss_pred             CchhCCHhHcCCCcCCeEEEeCCcCHHHHHHHHHHHHc--cCCCCcccCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhC
Confidence            99999999988  4443 99999999999999987764  34454443 778889988866 555566654332     3


Q ss_pred             CCcccHHHHHhhc
Q psy879          205 FGHVTAEYVFKVC  217 (317)
Q Consensus       205 ~~~i~~~~v~~~~  217 (317)
                      ...|+.+++.+++
T Consensus       265 ~~~I~~~dl~~a~  277 (278)
T 1iy2_A          265 RRKITMKDLEEAA  277 (278)
T ss_dssp             CCSBCHHHHHHHT
T ss_pred             CCCcCHHHHHHHh
Confidence            4578888887654

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli}

Probab=99.67  E-value=1.7e-15  Score=138.75  Aligned_cols=198  Identities=17%  Similarity=0.141  Sum_probs=131.8

Q ss_pred             CcccCCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHH--------
Q psy879           10 SDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNK--------   81 (317)
Q Consensus        10 ~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~--------   81 (317)
                      ..++|++++++.+..++..+.  |++|+||||||||++|+++++.+..   ...+...++.. .....+...        
T Consensus        22 ~~ivGq~~~i~~l~~al~~~~--~VLL~GpPGtGKT~LAraLa~~l~~---~~~f~~~~~~~-~t~~dL~G~~~~~~~~~   95 (500)
T 3nbx_X           22 KGLYERSHAIRLCLLAALSGE--SVFLLGPPGIAKSLIARRLKFAFQN---ARAFEYLMTRF-STPEEVFGPLSIQALKD   95 (500)
T ss_dssp             TTCSSCHHHHHHHHHHHHHTC--EEEEECCSSSSHHHHHHHGGGGBSS---CCEEEEECCTT-CCHHHHHCCBC------
T ss_pred             hhhHHHHHHHHHHHHHHhcCC--eeEeecCchHHHHHHHHHHHHHHhh---hhHHHHHHHhc-CCHHHhcCcccHHHHhh
Confidence            357899999999988888877  8999999999999999999997622   11223333321 122221110        


Q ss_pred             HHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhcc----------CCceEEEEecCCC---cCchhHhhhcc
Q psy879           82 IKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYS----------NTTRFALACNNSE---KIIEPIQSRCA  148 (317)
Q Consensus        82 ~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~----------~~~~~il~~~~~~---~l~~~i~sR~~  148 (317)
                      -+.+.. ....+.....|++|||++.+.++.+++|+..|++..          +...+|++||+..   .+.+++.+|+.
T Consensus        96 ~g~~~~-~~~g~l~~~~IL~IDEI~r~~~~~q~~LL~~lee~~v~i~G~~~~~~~~~iI~ATN~lpe~~~~~~aLldRF~  174 (500)
T 3nbx_X           96 EGRYER-LTSGYLPEAEIVFLDEIWKAGPAILNTLLTAINERQFRNGAHVEKIPMRLLVAASNELPEADSSLEALYDRML  174 (500)
T ss_dssp             ----CB-CCTTSGGGCSEEEEESGGGCCHHHHHHHHHHHHSSEEECSSSEEECCCCEEEEEESSCCCTTCTTHHHHTTCC
T ss_pred             chhHHh-hhccCCCcceeeeHHhHhhhcHHHHHHHHHHHHHHhccCCCCcCCcchhhhhhccccCCCccccHHHHHHHHH
Confidence            011100 000000145699999999999999999999998421          1223577887633   35679999986


Q ss_pred             e-eeecCCCH-HHHHHHHHHHH-----------------------HHcCCCCCHHHHHHHHHhc----------CCCHHH
Q psy879          149 M-LRYNKLTD-AQLLSKVIEIC-----------------------EKENISHTNDGLEAIVFTA----------QGDMRQ  193 (317)
Q Consensus       149 ~-i~f~~~~~-~~~~~~l~~~~-----------------------~~~~~~i~~~~~~~l~~~~----------~gd~r~  193 (317)
                      . +.+++|++ ++...++....                       ...++.+++++.++++...          +.+.|.
T Consensus       175 ~~i~v~~p~~~ee~~~IL~~~~~~~~~~~~~~~~~~~e~l~~~~~~~~~v~v~d~v~e~i~~l~~~lr~~r~~~~iS~R~  254 (500)
T 3nbx_X          175 IRLWLDKVQDKANFRSMLTSQQDENDNPVPDALQVTDEEYERWQKEIGEITLPDHVFELIFMLRQQLDKLPDAPYVSDRR  254 (500)
T ss_dssp             EEEECCSCCCHHHHHHHHTCCCCTTSCCSCTTTSBCHHHHHHHHHHHTTCBCCHHHHHHHHHHHHHHHHCSSSCCCCHHH
T ss_pred             HHHHHHHhhhhhhHHHHHhcccccCCCCCCccceecHHHHHHHHhcCCcccCchHHHHHHHHHHHHhhcCCCCCccchhH
Confidence            6 88888887 55666665432                       1236778899988888665          568888


Q ss_pred             HHHHHHHh---h--hCCCcccHHHHH
Q psy879          194 ALNNLQST---H--NGFGHVTAEYVF  214 (317)
Q Consensus       194 ~i~~l~~~---~--~~~~~i~~~~v~  214 (317)
                      .+..+..+   +  .+...++.+++.
T Consensus       255 ~~~llr~A~A~A~l~gr~~Vt~eDv~  280 (500)
T 3nbx_X          255 WKKAIRLLQASAFFSGRSAVAPVDLI  280 (500)
T ss_dssp             HHHHHHHHHHHHHHTTCSBCCGGGGG
T ss_pred             HHHHHHHHHHHHhhcCCccccchHHH
Confidence            77776542   2  256688999887

>3hws_A ATP-dependent CLP protease ATP-binding subunit CL; CLPXP, AAA+ molecular machine, hexamer, asymmetric,, ATP-BIN chaperone, metal-binding; HET: ADP; 3.25A {Escherichia coli} PDB: 3hte_A

Probab=99.67  E-value=6.9e-17  Score=143.60  Aligned_cols=202  Identities=21%  Similarity=0.277  Sum_probs=131.1

Q ss_pred             ccCCHHHHHHHHHHHh-------------cC--CCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChH
Q psy879           12 IVGNEDTVERLKVFSS-------------SG--NVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGID   76 (317)
Q Consensus        12 ~~g~~~~~~~l~~~l~-------------~~--~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~   76 (317)
                      ++||+.+++.+..++.             ..  ...+++|+||||||||++|+++++.+     +.+++.+++.......
T Consensus        17 i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~~~~vll~GppGtGKT~la~~ia~~~-----~~~~~~~~~~~l~~~~   91 (363)
T 3hws_A           17 VIGQEQAKKVLAVAVYNHYKRLRNGDTSNGVELGKSNILLIGPTGSGKTLLAETLARLL-----DVPFTMADATTLTEAG   91 (363)
T ss_dssp             CCSCHHHHHHHHHHHHHHHHHHHTTSCSSSCCCCCCCEEEECCTTSSHHHHHHHHHHHT-----TCCEEEEEHHHHTTCH
T ss_pred             ccCHHHHHHHHHHHHHHHHhhhccccccccccCCCCeEEEECCCCCCHHHHHHHHHHHc-----CCCEEEechHHhcccc
Confidence            6899999999888772             11  22359999999999999999999986     3446666654321110


Q ss_pred             ----HHHHHHHHHHhhc-ccCCCCceeEEEEeCCCCCCHH--------------HHHHHHHHhhhc--------------
Q psy879           77 ----TVRNKIKMFAQQK-VTLPPGRHKIVILDEADSMTDG--------------AQQALRRTMEIY--------------  123 (317)
Q Consensus        77 ----~i~~~~~~~~~~~-~~~~~~~~~vliiDE~d~l~~~--------------~~~~ll~~le~~--------------  123 (317)
                          .....+....... .......+.+++|||+|.+...              .++.|++.|+..              
T Consensus        92 ~~g~~~~~~~~~~~~~~~~~~~~~~~~vl~lDEid~l~~~~~~~~~~~~~~~~~~~~~Ll~~leg~~~~~~~~~~~~~~~  171 (363)
T 3hws_A           92 YVGEDVENIIQKLLQKCDYDVQKAQRGIVYIDQIDKISRKSDNPSITRDVSGEGVQQALLKLIEGTVAAVPPQGGRKHPQ  171 (363)
T ss_dssp             HHHHHHTHHHHHHHHHTTTCHHHHHHCEEEEECHHHHCCCSSCC---CHHHHHHHHHHHHHHHHCC--------------
T ss_pred             cccccHHHHHHHHHHHhhhhHHhcCCcEEEEeChhhhcccccccccccccchHHHHHHHHHHhcCceeeccCccccccCC
Confidence                1111122111111 0000134679999999988765              899999999921              


Q ss_pred             -------cCCceEEEEecCC----------Cc-----------------------------------CchhHhhhcce-e
Q psy879          124 -------SNTTRFALACNNS----------EK-----------------------------------IIEPIQSRCAM-L  150 (317)
Q Consensus       124 -------~~~~~~il~~~~~----------~~-----------------------------------l~~~i~sR~~~-i  150 (317)
                             ..+..||++++..          .+                                   +.+.+.+|+.. +
T Consensus       172 ~~~~~i~tsn~~~i~~g~~~~l~~~i~~~~~~~~~~gf~~~~~~~~~~~~~~~l~~~v~~~~l~~~~~~~~l~~R~~~~~  251 (363)
T 3hws_A          172 QEFLQVDTSKILFICGGAFAGLDKVISHRVETGSGIGFGATVKAKSDKASEGELLAQVEPEDLIKFGLIPEFIGRLPVVA  251 (363)
T ss_dssp             --CCCCCTTSSEEEEEECCTTHHHHHHHHHCCCC------------CCSCHHHHHHTCCHHHHHHHTCCHHHHTTCCEEE
T ss_pred             CceEEEECCCceEEecCCcHHHHHHHHHhhhccccCCccccccccccchhhHHHHHhCCHHHHHHcCCCHHHhcccCeee
Confidence                   1334455655532          11                                   68999999998 6


Q ss_pred             eecCCCHHHHHHHHHH----HH-------HHcC--CCCCHHHHHHHHHh---cCCCHHHHHHHHHHhhh-------CC-C
Q psy879          151 RYNKLTDAQLLSKVIE----IC-------EKEN--ISHTNDGLEAIVFT---AQGDMRQALNNLQSTHN-------GF-G  206 (317)
Q Consensus       151 ~f~~~~~~~~~~~l~~----~~-------~~~~--~~i~~~~~~~l~~~---~~gd~r~~i~~l~~~~~-------~~-~  206 (317)
                      .|.|++.+++.+++..    .+       ...+  +.+++++++.++..   ..++.|.+-+.++.+..       .. .
T Consensus       252 ~~~pl~~~~~~~I~~~~~~~l~~~~~~~~~~~~~~l~~~~~a~~~L~~~~~~~~~gaR~L~~~ie~~~~~~l~~~~~~~~  331 (363)
T 3hws_A          252 TLNELSEEALIQILKEPKNALTKQYQALFNLEGVDLEFRDEALDAIAKKAMARKTGARGLRSIVEAALLDTMYDLPSMED  331 (363)
T ss_dssp             ECCCCCHHHHHHHHHSSTTCHHHHHHHHHHTTTCEEEECHHHHHHHHHHHHHTTCTTTTHHHHHHHHHHHHHHSTTTCCC
T ss_pred             ecCCCCHHHHHHHHHHHHHHHHHHHHHHHHhcCceEEECHHHHHHHHHhhcCCccCchHHHHHHHHHHHHHHHhcccccC
Confidence            6999999998888765    22       2123  35789999999864   46667777777766443       11 1


Q ss_pred             ----cccHHHHHhhcC
Q psy879          207 ----HVTAEYVFKVCD  218 (317)
Q Consensus       207 ----~i~~~~v~~~~~  218 (317)
                          .|+.++|.+...
T Consensus       332 ~~~~~I~~~~v~~~~~  347 (363)
T 3hws_A          332 VEKVVIDESVIDGQSE  347 (363)
T ss_dssp             SEEEECHHHHTTCCSC
T ss_pred             CceeEEcHHHHhCcCC
Confidence                366677665443

>3cf2_A TER ATPase, transitional endoplasmic reticulum ATPase, valosi; AAA, CDC48, ERAD, transport protein; HET: ADP ANP; 3.50A {Mus musculus} PDB: 3cf1_A* 3cf3_A* 1r7r_A*

Probab=99.65  E-value=1.3e-15  Score=145.96  Aligned_cols=170  Identities=18%  Similarity=0.249  Sum_probs=121.2

Q ss_pred             CCCCcccCCHHHHHHHHHHHhc-----------C-CCc-eEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCC-
Q psy879            7 QTFSDIVGNEDTVERLKVFSSS-----------G-NVP-NIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASND-   72 (317)
Q Consensus         7 ~~~~~~~g~~~~~~~l~~~l~~-----------~-~~~-~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~-   72 (317)
                      -+|+|+.|.+++++.|+.++.-           | .+| ++|||||||||||++|+++|+++     +..++.+++.+. 
T Consensus       201 v~~~dIgGl~~~~~~l~e~v~~pl~~p~~f~~~g~~~p~GILL~GPPGTGKT~LAraiA~el-----g~~~~~v~~~~l~  275 (806)
T 3cf2_A          201 VGYDDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANET-----GAFFFLINGPEIM  275 (806)
T ss_dssp             CCGGGCCSCCTTHHHHHHHHHHHHHCCGGGTSCCCCCCCEEEEECCTTSCHHHHHHHHHTTT-----TCEEEEEEHHHHH
T ss_pred             CChhhhcCHHHHHHHHHHHHHHHccCHHHHhhcCCCCCCeEEEECCCCCCHHHHHHHHHHHh-----CCeEEEEEhHHhh
Confidence            4699999999888888776531           2 233 49999999999999999999985     344666665321 


Q ss_pred             ---c--ChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCH-----------HHHHHHHHHhhhcc--CCceEEEEec
Q psy879           73 ---R--GIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTD-----------GAQQALRRTMEIYS--NTTRFALACN  134 (317)
Q Consensus        73 ---~--~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~-----------~~~~~ll~~le~~~--~~~~~il~~~  134 (317)
                         .  +...++..+.....       ..+.||+|||+|.+.+           ...+.|+..|+...  .++.+|.+||
T Consensus       276 sk~~gese~~lr~lF~~A~~-------~~PsIIfIDEiDal~~~r~~~~~~~~~riv~~LL~~mdg~~~~~~V~VIaaTN  348 (806)
T 3cf2_A          276 SKLAGESESNLRKAFEEAEK-------NAPAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATN  348 (806)
T ss_dssp             SSCTTHHHHHHHHHHHHHTT-------SCSEEEEEESGGGTCCTTTTCCCTTHHHHHHHHHTHHHHCCGGGCEEEEEECS
T ss_pred             cccchHHHHHHHHHHHHHHH-------cCCeEEEEehhcccccccCCCCChHHHHHHHHHHHHHhcccccCCEEEEEecC
Confidence               1  12234444333221       4578999999999853           23567777777543  4567888999


Q ss_pred             CCCcCchhHhh--hcce-eeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCC
Q psy879          135 NSEKIIEPIQS--RCAM-LRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQG  189 (317)
Q Consensus       135 ~~~~l~~~i~s--R~~~-i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~g  189 (317)
                      .++.+++++++  ||.. ++++.|+.++...+++..++..... ++..+..++..+.|
T Consensus       349 ~~d~LD~ALrR~GRFd~~I~i~~Pd~~~R~~IL~~~l~~~~~~-~dvdl~~lA~~T~G  405 (806)
T 3cf2_A          349 RPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLA-DDVDLEQVANETHG  405 (806)
T ss_dssp             STTTSCTTTTSTTSSCEEEECCCCCHHHHHHHHHHTCSSSEEC-TTCCHHHHHHHCCS
T ss_pred             ChhhcCHHHhCCcccceEEecCCCCHHHHHHHHHHHhcCCCCC-cccCHHHHHHhcCC
Confidence            99999999998  7776 9999999999999998766543221 22336777877654

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A

Probab=99.63  E-value=1.2e-14  Score=125.14  Aligned_cols=149  Identities=13%  Similarity=0.151  Sum_probs=95.7

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCC----c--ChHHHHHHHHHHHhhcccCCCCceeEEEEeCCC
Q psy879           33 NIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASND----R--GIDTVRNKIKMFAQQKVTLPPGRHKIVILDEAD  106 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~----~--~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d  106 (317)
                      .++||||||||||++|+++|+.+     +..++.++++..    .  ....+++.+.......   ....+.|++|||+|
T Consensus        38 ~lLl~GppGtGKT~la~aiA~~l-----~~~~i~v~~~~l~~~~~g~~~~~i~~~f~~a~~~~---~~~~~~vl~iDEiD  109 (293)
T 3t15_A           38 ILGIWGGKGQGKSFQCELVFRKM-----GINPIMMSAGELESGNAGEPAKLIRQRYREAAEII---RKGNMCCLFINDLD  109 (293)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHH-----TCCCEEEEHHHHHCC---HHHHHHHHHHHHHHHHH---TTSSCCCEEEECCC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh-----CCCEEEEeHHHhhhccCchhHHHHHHHHHHHHHHH---hcCCCeEEEEechh
Confidence            49999999999999999999997     234555554321    1  1122333333332110   02467899999999


Q ss_pred             CCCHH-------------HHHHHHHHhhh-------------ccCCceEEEEecCCCcCchhHhh--hcceeeecCCCHH
Q psy879          107 SMTDG-------------AQQALRRTMEI-------------YSNTTRFALACNNSEKIIEPIQS--RCAMLRYNKLTDA  158 (317)
Q Consensus       107 ~l~~~-------------~~~~ll~~le~-------------~~~~~~~il~~~~~~~l~~~i~s--R~~~i~f~~~~~~  158 (317)
                      .+.+.             .++.|+..++.             ...++.+|+|||.++.+++++++  |+..+.+ .|+.+
T Consensus       110 ~~~~~~~~~~~~~~~~~~v~~~Ll~~ld~~~~~~~~~~~~~~~~~~v~vI~ttN~~~~ld~al~R~~R~d~~i~-~P~~~  188 (293)
T 3t15_A          110 AGAGRMGGTTQYTVNNQMVNATLMNIADNPTNVQLPGMYNKQENARVPIIVTGNDFSTLYAPLIRDGRMEKFYW-APTRE  188 (293)
T ss_dssp             --------------CHHHHHHHHHHHHHCCC-----------CCCCCCEEEECSSCCC--CHHHHHHHEEEEEE-CCCHH
T ss_pred             hhcCCCCCCccccchHHHHHHHHHHHhccccccccccccccccCCCcEEEEecCCcccCCHHHhCCCCCceeEe-CcCHH
Confidence            88652             34788888862             23467899999999999999986  6655334 46999


Q ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHHHh-cCCCHH
Q psy879          159 QLLSKVIEICEKENISHTNDGLEAIVFT-AQGDMR  192 (317)
Q Consensus       159 ~~~~~l~~~~~~~~~~i~~~~~~~l~~~-~~gd~r  192 (317)
                      +..+++...+...++  +.+.+..+... ++.++.
T Consensus       189 ~r~~Il~~~~~~~~~--~~~~l~~~~~~~~~~~l~  221 (293)
T 3t15_A          189 DRIGVCTGIFRTDNV--PAEDVVKIVDNFPGQSID  221 (293)
T ss_dssp             HHHHHHHHHHGGGCC--CHHHHHHHHHHSCSCCHH
T ss_pred             HHHHHHHHhccCCCC--CHHHHHHHhCCCCcccHH
Confidence            999999988876654  45555555544 445553

>1g41_A Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dependent proteolysis, chaperone; HET: ADP; 2.30A {Haemophilus influenzae} SCOP: c.37.1.20 PDB: 1g3i_A* 1im2_A* 1kyi_A* 1g4a_E* 1g4b_E 1yyf_A* 1do0_A* 1do2_A* 1e94_E* 1hqy_E* 1ht1_E* 1ht2_E*

Probab=99.63  E-value=4.7e-15  Score=133.05  Aligned_cols=123  Identities=20%  Similarity=0.270  Sum_probs=87.3

Q ss_pred             eeEEEEeCCCCCCHH------------HHHHHHHHhhhc----------cCCceEEEEe----cCCCcCchhHhhhcce-
Q psy879           97 HKIVILDEADSMTDG------------AQQALRRTMEIY----------SNTTRFALAC----NNSEKIIEPIQSRCAM-  149 (317)
Q Consensus        97 ~~vliiDE~d~l~~~------------~~~~ll~~le~~----------~~~~~~il~~----~~~~~l~~~i~sR~~~-  149 (317)
                      ..++++||+|++...            .|++|++.+|..          ..++.||+++    +++..+.|.+++|+.+ 
T Consensus       251 ~~il~~DEidki~~~~~~~~~D~s~egvq~aLL~~le~~~~~~~~~~~d~~~ilfI~~gaf~~~~~~dlipel~~R~~i~  330 (444)
T 1g41_A          251 NGIVFIDEIDKICKKGEYSGADVSREGVQRDLLPLVEGSTVSTKHGMVKTDHILFIASGAFQVARPSDLIPELQGRLPIR  330 (444)
T ss_dssp             HCEEEEETGGGGSCCSSCSSSHHHHHHHHHHHHHHHHCCEEEETTEEEECTTCEEEEEECCSSCCGGGSCHHHHTTCCEE
T ss_pred             CCeeeHHHHHHHhhccCCCCCCchHHHHHHHHHHHhcccccccccceecCCcEEEEeccccccCChhhcchHHhccccee
Confidence            568999999998532            578999999941          3456677776    2445577999999998 


Q ss_pred             eeecCCCHHHHHHHHHH-----------HHHHcC--CCCCHHHHHHHHHh--------cCCCHHHHHHHHHHhhh-----
Q psy879          150 LRYNKLTDAQLLSKVIE-----------ICEKEN--ISHTNDGLEAIVFT--------AQGDMRQALNNLQSTHN-----  203 (317)
Q Consensus       150 i~f~~~~~~~~~~~l~~-----------~~~~~~--~~i~~~~~~~l~~~--------~~gd~r~~i~~l~~~~~-----  203 (317)
                      +.|++|+.+++.+++..           .+..++  +.++++++..+++.        -++..|.+.+.++++..     
T Consensus       331 i~l~~lt~~e~~~Il~~~~~~l~~q~~~~~~~~~~~l~~~~~al~~i~~~a~~~~~~t~~~GaR~L~~~ie~~~~~~~~~  410 (444)
T 1g41_A          331 VELTALSAADFERILTEPHASLTEQYKALMATEGVNIAFTTDAVKKIAEAAFRVNEKTENIGARRLHTVMERLMDKISFS  410 (444)
T ss_dssp             EECCCCCHHHHHHHHHSSTTCHHHHHHHHHHTTTCEEEECHHHHHHHHHHHHHHHHHSCCCGGGHHHHHHHHHHHHHHHH
T ss_pred             eeCCCCCHHHHHHHHHHHHHhHHHHHHHHhcccCceEEECHHHHHHHHHHHHHhccCCccCCchHHHHHHHHHHHHHHhh
Confidence            99999999999999841           222234  35789999999875        34667777777765432     


Q ss_pred             --C--CC--cccHHHHHhhcCC
Q psy879          204 --G--FG--HVTAEYVFKVCDE  219 (317)
Q Consensus       204 --~--~~--~i~~~~v~~~~~~  219 (317)
                        +  ..  .|+.+.|.+.++.
T Consensus       411 ~~~~~~~~~~i~~~~v~~~l~~  432 (444)
T 1g41_A          411 ASDMNGQTVNIDAAYVADALGE  432 (444)
T ss_dssp             GGGCTTCEEEECHHHHHHHHTT
T ss_pred             ccccCCCeEEEeHHHHHHhcCc
Confidence              1  11  3677777665544

>3cf2_A TER ATPase, transitional endoplasmic reticulum ATPase, valosi; AAA, CDC48, ERAD, transport protein; HET: ADP ANP; 3.50A {Mus musculus} PDB: 3cf1_A* 3cf3_A* 1r7r_A*

Probab=99.62  E-value=1e-15  Score=146.50  Aligned_cols=179  Identities=19%  Similarity=0.238  Sum_probs=113.7

Q ss_pred             CCCCcccCCHHHHHHHHHHHhc-----------C-CCc-eEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCC--
Q psy879            7 QTFSDIVGNEDTVERLKVFSSS-----------G-NVP-NIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASN--   71 (317)
Q Consensus         7 ~~~~~~~g~~~~~~~l~~~l~~-----------~-~~~-~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~--   71 (317)
                      .+|+++.|.+++++.|...+.-           | .++ .+|||||||||||.+|+++|.++     +.+++.+..+.  
T Consensus       474 v~w~diggl~~~k~~l~e~v~~p~~~p~~f~~~g~~~~~gvLl~GPPGtGKT~lAkaiA~e~-----~~~f~~v~~~~l~  548 (806)
T 3cf2_A          474 VTWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANEC-----QANFISIKGPELL  548 (806)
T ss_dssp             CCSTTCCSCHHHHHHHTTTTTTTTTCSGGGSSSCCCCCSCCEEESSTTSSHHHHHHHHHHTT-----TCEEEECCHHHHH
T ss_pred             CCHHHhCCHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCceEEEecCCCCCchHHHHHHHHHh-----CCceEEeccchhh
Confidence            3589999999999998877531           2 222 39999999999999999999985     33455554322  


Q ss_pred             ----CcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHH--------------HHHHHHHHhhhcc--CCceEEE
Q psy879           72 ----DRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDG--------------AQQALRRTMEIYS--NTTRFAL  131 (317)
Q Consensus        72 ----~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~--------------~~~~ll~~le~~~--~~~~~il  131 (317)
                          ..+...+++.+.....       ..+.||+|||+|.+...              ..+.|+..|+...  ..+.+|.
T Consensus       549 s~~vGese~~vr~lF~~Ar~-------~~P~IifiDEiDsl~~~R~~~~~~~~~~~~rv~~~lL~~mdg~~~~~~V~vi~  621 (806)
T 3cf2_A          549 TMWFGESEANVREIFDKARQ-------AAPCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEMDGMSTKKNVFIIG  621 (806)
T ss_dssp             TTTCSSCHHHHHHHHHHHHT-------TCSEEEECSCGGGCC--------------CHHHHHHHHHHHSSCSSSSEEEEC
T ss_pred             ccccchHHHHHHHHHHHHHH-------cCCceeechhhhHHhhccCCCCCCCchHHHHHHHHHHHHHhCCCCCCCEEEEE
Confidence                2234456666655433       35789999999988532              2567888888543  3456777


Q ss_pred             EecCCCcCchhHhh--hcce-eeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHh----cCCCHHHHHHHH
Q psy879          132 ACNNSEKIIEPIQS--RCAM-LRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFT----AQGDMRQALNNL  198 (317)
Q Consensus       132 ~~~~~~~l~~~i~s--R~~~-i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~----~~gd~r~~i~~l  198 (317)
                      +||.++.+++++.+  |+.. ++|+.|+.++..++++..+++..+. ++..++.+++.    ++.|+..+.+..
T Consensus       622 aTN~p~~lD~AllRpgRfd~~i~v~lPd~~~R~~il~~~l~~~~~~-~~~dl~~la~~t~g~SGadi~~l~~~A  694 (806)
T 3cf2_A          622 ATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLRKSPVA-KDVDLEFLAKMTNGFSGADLTEICQRA  694 (806)
T ss_dssp             C-CCSSSSCHHHHSTTTSCCEEEC-----CHHHHTTTTTSSCC--C-CC----------------CHHHHHHHH
T ss_pred             eCCCchhCCHhHcCCCcceEEEEECCcCHHHHHHHHHHHhcCCCCC-CCCCHHHHHHhCCCCCHHHHHHHHHHH
Confidence            89999999999998  8876 9999999999999988776543322 12234555554    556777665544

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=99.62  E-value=2.9e-15  Score=115.34  Aligned_cols=132  Identities=14%  Similarity=0.176  Sum_probs=91.7

Q ss_pred             cccCCHHHHHHHHHHHhc--CCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHHHHHHHhh
Q psy879           11 DIVGNEDTVERLKVFSSS--GNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFAQQ   88 (317)
Q Consensus        11 ~~~g~~~~~~~l~~~l~~--~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~   88 (317)
                      +++|+...++.+...++.  ....+++|+||||||||++|+++++....  .+.+++ +++............+..    
T Consensus         2 ~iiG~s~~~~~~~~~~~~~a~~~~~vll~G~~GtGKt~lA~~i~~~~~~--~~~~~v-~~~~~~~~~~~~~~~~~~----   74 (145)
T 3n70_A            2 ELIGRSEWINQYRRRLQQLSETDIAVWLYGAPGTGRMTGARYLHQFGRN--AQGEFV-YRELTPDNAPQLNDFIAL----   74 (145)
T ss_dssp             --CCSSHHHHHHHHHHHHHTTCCSCEEEESSTTSSHHHHHHHHHHSSTT--TTSCCE-EEECCTTTSSCHHHHHHH----
T ss_pred             CceeCCHHHHHHHHHHHHHhCCCCCEEEECCCCCCHHHHHHHHHHhCCc--cCCCEE-EECCCCCcchhhhcHHHH----
Confidence            578988888777766542  23336999999999999999999986422  233455 655432222222222221    


Q ss_pred             cccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCC-------cCchhHhhhcce--eeecCC
Q psy879           89 KVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSE-------KIIEPIQSRCAM--LRYNKL  155 (317)
Q Consensus        89 ~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~-------~l~~~i~sR~~~--i~f~~~  155 (317)
                            ....+++|||+|.+..+.|..|++.++..+.++.+|++||.+.       .+.+.+..|+..  ++++|+
T Consensus        75 ------a~~g~l~ldei~~l~~~~q~~Ll~~l~~~~~~~~~I~~t~~~~~~~~~~~~~~~~L~~rl~~~~i~lPpL  144 (145)
T 3n70_A           75 ------AQGGTLVLSHPEHLTREQQYHLVQLQSQEHRPFRLIGIGDTSLVELAASNHIIAELYYCFAMTQIACLPL  144 (145)
T ss_dssp             ------HTTSCEEEECGGGSCHHHHHHHHHHHHSSSCSSCEEEEESSCHHHHHHHSCCCHHHHHHHHHHEEECCCC
T ss_pred             ------cCCcEEEEcChHHCCHHHHHHHHHHHhhcCCCEEEEEECCcCHHHHHHcCCCCHHHHHHhcCCEEeCCCC
Confidence                  1346899999999999999999999988788889999999752       566777777655  555554

>3f9v_A Minichromosome maintenance protein MCM; replicative helicase, DNA replication, MCM complex, AAA+ Pro ATP-binding, DNA-binding, helicase; 4.35A {Sulfolobus solfataricus}

Probab=99.62  E-value=8.4e-17  Score=151.10  Aligned_cols=205  Identities=20%  Similarity=0.147  Sum_probs=122.9

Q ss_pred             CcccCCHHHHHHHHHHHhcCCCc-----------eEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHH
Q psy879           10 SDIVGNEDTVERLKVFSSSGNVP-----------NIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTV   78 (317)
Q Consensus        10 ~~~~g~~~~~~~l~~~l~~~~~~-----------~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i   78 (317)
                      ..++|++++++.+..++.+|...           |+||+||||||||++|+++++.+........ ...++....+ ..+
T Consensus       295 ~~I~G~e~vk~al~~~l~~g~~~~~~~~~~r~~~~vLL~GppGtGKT~LAr~la~~~~r~~~~~~-~~~~~~~l~~-~~~  372 (595)
T 3f9v_A          295 PSIYGHWELKEALALALFGGVPKVLEDTRIRGDIHILIIGDPGTAKSQMLQFISRVAPRAVYTTG-KGSTAAGLTA-AVV  372 (595)
T ss_dssp             STTSCCHHHHHHHTTTTTCCCCEETTTTEECCSCCEEEEESSCCTHHHHHHSSSTTCSCEECCCT-TCSTTTTSEE-ECS
T ss_pred             chhcChHHHHHHHHHHHhCCCcccccCCCcCCCcceEEECCCchHHHHHHHHHHHhCCCceecCC-Cccccccccc-eee
Confidence            46789999999888777777422           7999999999999999999987521100000 0001110000 000


Q ss_pred             HHHH-HHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhc-------------cCCceEEEEecCCC-------
Q psy879           79 RNKI-KMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIY-------------SNTTRFALACNNSE-------  137 (317)
Q Consensus        79 ~~~~-~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~-------------~~~~~~il~~~~~~-------  137 (317)
                      .+.. +.+...+..+..+.+.+++|||+|.+.++.+++|++.||+.             +.++.+|.++|+..       
T Consensus       373 ~~~~~g~~~~~~G~l~~A~~gil~IDEid~l~~~~q~~Ll~~le~~~i~i~~~g~~~~~~~~~~vIaatNp~~G~~~~~~  452 (595)
T 3f9v_A          373 REKGTGEYYLEAGALVLADGGIAVIDEIDKMRDEDRVAIHEAMEQQTVSIAKAGIVAKLNARAAVIAAGNPKFGRYISER  452 (595)
T ss_dssp             SGGGTSSCSEEECHHHHHSSSEECCTTTTCCCSHHHHHHHHHHHSSSEEEESSSSEEEECCCCEEEEEECCTTCCSCTTS
T ss_pred             eccccccccccCCeeEecCCCcEEeehhhhCCHhHhhhhHHHHhCCEEEEecCCcEEEecCceEEEEEcCCcCCccCccc
Confidence            0000 00000000000024579999999999999999999999853             24566888888765       


Q ss_pred             ------cCchhHhhhcc-eeeecCCCHHHHHHHHHHHHHHc-------------------------CCCCCHHHHHHHHH
Q psy879          138 ------KIIEPIQSRCA-MLRYNKLTDAQLLSKVIEICEKE-------------------------NISHTNDGLEAIVF  185 (317)
Q Consensus       138 ------~l~~~i~sR~~-~i~f~~~~~~~~~~~l~~~~~~~-------------------------~~~i~~~~~~~l~~  185 (317)
                            .+.+++.+||. .+.+.+++..+...+.......+                         .-.+++++.+.+..
T Consensus       453 ~~~~ni~l~~aLl~RFDl~~~~~~~~~~e~~~i~~~il~~~~~~~~~~~l~~~~l~~~i~~ar~~~~p~ls~ea~~~l~~  532 (595)
T 3f9v_A          453 PVSDNINLPPTILSRFDLIFILKDQPGEQDRELANYILDVHSGKSTKNIIDIDTLRKYIAYARKYVTPKITSEAKNLITD  532 (595)
T ss_dssp             CSCTTTCSCSSSGGGCSCCEEECCTTHHHHHHHHHHHHTTTCCCSSSSTTCCTTTHHHHHHHHHHHCCCCCCCTHHHHHH
T ss_pred             CchhccCCCHHHHhhCeEEEEeCCCCCHHHHHHHHHHHHHhhccccccCCCHHHHHHHHHHHHHhCCCCCCHHHHHHHHH
Confidence                  78999999995 45565655555333333333211                         11455666666665


Q ss_pred             h---------------cCCCHHHHHHHHHHh---hh--CCCcccHHHHHhh
Q psy879          186 T---------------AQGDMRQALNNLQST---HN--GFGHVTAEYVFKV  216 (317)
Q Consensus       186 ~---------------~~gd~r~~i~~l~~~---~~--~~~~i~~~~v~~~  216 (317)
                      .               .++++|.+.++++.+   +.  +...++.+|+..+
T Consensus       533 ~y~~lR~~~~~~~~~~~~~s~R~l~~lirla~a~A~l~~~~~V~~~dv~~A  583 (595)
T 3f9v_A          533 FFVEMRKKSSETPDSPILITPRQLEALIRISEAYAKMALKAEVTREDAERA  583 (595)
T ss_dssp             HHTTSSCSCCBCSSSCBCSSTTTTTHHHHHHHHHHHTTSSCCSSHHHHHHH
T ss_pred             HHHHHHHhhccCCCccccccHHHHHHHHHHHHHHHHHhCcCCCCHHHHHHH
Confidence            4               466777777776542   21  4556788777653

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens}

Probab=99.60  E-value=6.6e-14  Score=119.21  Aligned_cols=157  Identities=19%  Similarity=0.186  Sum_probs=103.2

Q ss_pred             CCCCCcccCCHHHHHHHHHHHh------------cCCC-ceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCC
Q psy879            6 PQTFSDIVGNEDTVERLKVFSS------------SGNV-PNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASND   72 (317)
Q Consensus         6 P~~~~~~~g~~~~~~~l~~~l~------------~~~~-~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~   72 (317)
                      ..+|+++.|.+++++.|...+.            +-.+ ++++|+||||||||+++++++..+..     .++.+++...
T Consensus         6 ~~~~~di~g~~~~~~~l~~~i~~~~~~~~~l~~~~l~~~~GvlL~Gp~GtGKTtLakala~~~~~-----~~i~i~g~~l   80 (274)
T 2x8a_A            6 NVTWADIGALEDIREELTMAILAPVRNPDQFKALGLVTPAGVLLAGPPGCGKTLLAKAVANESGL-----NFISVKGPEL   80 (274)
T ss_dssp             ------CCHHHHHHHHHHHHHTHHHHSHHHHHHTTCCCCSEEEEESSTTSCHHHHHHHHHHHTTC-----EEEEEETTTT
T ss_pred             CCCHHHhCCHHHHHHHHHHHHHHHhhCHHHHHHcCCCCCCeEEEECCCCCcHHHHHHHHHHHcCC-----CEEEEEcHHH
Confidence            3579999999999998876542            1122 24999999999999999999998522     3555555432


Q ss_pred             c--ChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHH-----------HHHHHHHHhhhc--cCCceEEEEecCCC
Q psy879           73 R--GIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDG-----------AQQALRRTMEIY--SNTTRFALACNNSE  137 (317)
Q Consensus        73 ~--~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~-----------~~~~ll~~le~~--~~~~~~il~~~~~~  137 (317)
                      .  ........+....+....   ..+.++++||+|.+...           ..+.++..|...  .....++.++|+++
T Consensus        81 ~~~~~~~~~~~i~~vf~~a~~---~~p~i~~~Deid~~~~~r~~~~~~~~~~~~~~~l~~Lsgg~~~~~~i~ia~tn~p~  157 (274)
T 2x8a_A           81 LNMYVGESERAVRQVFQRAKN---SAPCVIFFDEVDALCPRRSDRETGASVRVVNQLLTEMDGLEARQQVFIMAATNRPD  157 (274)
T ss_dssp             CSSTTHHHHHHHHHHHHHHHH---TCSEEEEEETCTTTCC---------CTTHHHHHHHHHHTCCSTTCEEEEEEESCGG
T ss_pred             HhhhhhHHHHHHHHHHHHHHh---cCCCeEeeehhhhhhcccCCCcchHHHHHHHHHHHhhhcccccCCEEEEeecCChh
Confidence            1  222333344444443211   24679999999986421           234555555532  23455677899999


Q ss_pred             cCchhHhh--hcce-eeecCCCHHHHHHHHHHHHHH
Q psy879          138 KIIEPIQS--RCAM-LRYNKLTDAQLLSKVIEICEK  170 (317)
Q Consensus       138 ~l~~~i~s--R~~~-i~f~~~~~~~~~~~l~~~~~~  170 (317)
                      .+++++.+  |+.. +.++.|+.++..++++..++.
T Consensus       158 ~LD~al~r~gRfd~~i~~~~P~~~~r~~il~~~~~~  193 (274)
T 2x8a_A          158 IIDPAILRPGRLDKTLFVGLPPPADRLAILKTITKN  193 (274)
T ss_dssp             GSCHHHHSTTSSCEEEECCSCCHHHHHHHHHHHTTT
T ss_pred             hCCHhhcCcccCCeEEEeCCcCHHHHHHHHHHHHhc
Confidence            99999987  7766 999999999999999987653

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=99.54  E-value=1.4e-14  Score=111.21  Aligned_cols=128  Identities=11%  Similarity=0.142  Sum_probs=87.5

Q ss_pred             cccCCHHHHHHHHHHHhc--CCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHHHHHHHhh
Q psy879           11 DIVGNEDTVERLKVFSSS--GNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFAQQ   88 (317)
Q Consensus        11 ~~~g~~~~~~~l~~~l~~--~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~   88 (317)
                      +++|+...++.+...+..  ....+++|+||||||||++|+++++...      .++.+++.... .......+.    .
T Consensus         5 ~~iG~s~~~~~l~~~~~~~~~~~~~vll~G~~GtGKt~lA~~i~~~~~------~~~~~~~~~~~-~~~~~~~~~----~   73 (143)
T 3co5_A            5 DKLGNSAAIQEMNREVEAAAKRTSPVFLTGEAGSPFETVARYFHKNGT------PWVSPARVEYL-IDMPMELLQ----K   73 (143)
T ss_dssp             ---CCCHHHHHHHHHHHHHHTCSSCEEEEEETTCCHHHHHGGGCCTTS------CEECCSSTTHH-HHCHHHHHH----H
T ss_pred             CceeCCHHHHHHHHHHHHHhCCCCcEEEECCCCccHHHHHHHHHHhCC------CeEEechhhCC-hHhhhhHHH----h
Confidence            578998888777766542  2334699999999999999999987641      56777765321 111122211    1


Q ss_pred             cccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhc-cCCceEEEEecCC-Cc----CchhHhhhcce--eeecCC
Q psy879           89 KVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIY-SNTTRFALACNNS-EK----IIEPIQSRCAM--LRYNKL  155 (317)
Q Consensus        89 ~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~-~~~~~~il~~~~~-~~----l~~~i~sR~~~--i~f~~~  155 (317)
                            ....+++|||+|.+..+.+..|++++++. +.++++|++||.+ ..    +.+.+..|+..  +..||+
T Consensus        74 ------a~~~~l~lDei~~l~~~~q~~Ll~~l~~~~~~~~~iI~~tn~~~~~~~~~~~~~L~~rl~~~~i~lPpL  142 (143)
T 3co5_A           74 ------AEGGVLYVGDIAQYSRNIQTGITFIIGKAERCRVRVIASCSYAAGSDGISCEEKLAGLFSESVVRIPPL  142 (143)
T ss_dssp             ------TTTSEEEEEECTTCCHHHHHHHHHHHHHHTTTTCEEEEEEEECTTTC--CHHHHHHHHSSSEEEEECCC
T ss_pred             ------CCCCeEEEeChHHCCHHHHHHHHHHHHhCCCCCEEEEEecCCCHHHHHhCccHHHHHHhcCcEEeCCCC
Confidence                  23569999999999999999999999975 3567889988864 22    45667777655  555554

>3ec2_A DNA replication protein DNAC; helicase loader, replication initiation factor, ATP-binding, nucleotide-binding; HET: DNA ADP; 2.70A {Aquifex aeolicus} PDB: 3ecc_A*

Probab=99.48  E-value=7.5e-14  Score=111.44  Aligned_cols=130  Identities=15%  Similarity=0.222  Sum_probs=82.3

Q ss_pred             cccCCCCCCcccC----CHHHHHHHHHHHhcCCC---ceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcC
Q psy879            2 EKYRPQTFSDIVG----NEDTVERLKVFSSSGNV---PNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRG   74 (317)
Q Consensus         2 ~ky~P~~~~~~~g----~~~~~~~l~~~l~~~~~---~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~   74 (317)
                      +||+|.+|+++++    +.++++.+..++.+-..   .+++|+||+|+||||++++++..+.... +..+..++.     
T Consensus         2 ~r~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~l~G~~G~GKTtL~~~i~~~~~~~~-g~~~~~~~~-----   75 (180)
T 3ec2_A            2 KRYWNANLDTYHPKNVSQNRALLTIRVFVHNFNPEEGKGLTFVGSPGVGKTHLAVATLKAIYEKK-GIRGYFFDT-----   75 (180)
T ss_dssp             CSCTTCCSSSCCCCSHHHHHHHHHHHHHHHSCCGGGCCEEEECCSSSSSHHHHHHHHHHHHHHHS-CCCCCEEEH-----
T ss_pred             chhhhCccccccCCCHHHHHHHHHHHHHHHhccccCCCEEEEECCCCCCHHHHHHHHHHHHHHHc-CCeEEEEEH-----
Confidence            6899999999996    45666777777764332   2599999999999999999999874111 111222221     


Q ss_pred             hHHHHHHHH-HHHhhccc---CCCCceeEEEEeCCC--CCCHHHHHHHHHHhhhcc-CCceEEEEecCCCc
Q psy879           75 IDTVRNKIK-MFAQQKVT---LPPGRHKIVILDEAD--SMTDGAQQALRRTMEIYS-NTTRFALACNNSEK  138 (317)
Q Consensus        75 ~~~i~~~~~-~~~~~~~~---~~~~~~~vliiDE~d--~l~~~~~~~ll~~le~~~-~~~~~il~~~~~~~  138 (317)
                       .++.+.+. .+......   .....+.++|+||++  .+.+..+..|..+++... ....+|++||....
T Consensus        76 -~~~~~~~~~~~~~~~~~~~~~~~~~~~llilDE~~~~~~~~~~~~~l~~ll~~~~~~~~~ii~tsn~~~~  145 (180)
T 3ec2_A           76 -KDLIFRLKHLMDEGKDTKFLKTVLNSPVLVLDDLGSERLSDWQRELISYIITYRYNNLKSTIITTNYSLQ  145 (180)
T ss_dssp             -HHHHHHHHHHHHHTCCSHHHHHHHTCSEEEEETCSSSCCCHHHHHHHHHHHHHHHHTTCEEEEECCCCSC
T ss_pred             -HHHHHHHHHHhcCchHHHHHHHhcCCCEEEEeCCCCCcCCHHHHHHHHHHHHHHHHcCCCEEEEcCCChh
Confidence             11111111 11100000   000246799999998  567777888888887543 55678888887643

>2qen_A Walker-type ATPase; unknown function; HET: ADP; 2.25A {Pyrococcus abyssi}

Probab=99.46  E-value=5.5e-12  Score=111.02  Aligned_cols=180  Identities=12%  Similarity=0.072  Sum_probs=119.9

Q ss_pred             CCCCcccCCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCc------ChHHH--
Q psy879            7 QTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDR------GIDTV--   78 (317)
Q Consensus         7 ~~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~------~~~~i--   78 (317)
                      ..-+.++|+++.++.|..++..|  +.++++||+|+|||++++.+++.. +      ++.+++....      ....+  
T Consensus         9 ~~~~~~~gR~~el~~L~~~l~~~--~~v~i~G~~G~GKT~Ll~~~~~~~-~------~~~~~~~~~~~~~~~~~~~~~~~   79 (350)
T 2qen_A            9 TRREDIFDREEESRKLEESLENY--PLTLLLGIRRVGKSSLLRAFLNER-P------GILIDCRELYAERGHITREELIK   79 (350)
T ss_dssp             CSGGGSCSCHHHHHHHHHHHHHC--SEEEEECCTTSSHHHHHHHHHHHS-S------EEEEEHHHHHHTTTCBCHHHHHH
T ss_pred             CChHhcCChHHHHHHHHHHHhcC--CeEEEECCCcCCHHHHHHHHHHHc-C------cEEEEeecccccccCCCHHHHHH
Confidence            34578999999999999999876  479999999999999999999874 1      2223221100      11111  


Q ss_pred             ----------------------------------HHHHHHHHhhcccCCCCceeEEEEeCCCCCCH-------HHHHHHH
Q psy879           79 ----------------------------------RNKIKMFAQQKVTLPPGRHKIVILDEADSMTD-------GAQQALR  117 (317)
Q Consensus        79 ----------------------------------~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~-------~~~~~ll  117 (317)
                                                        .+.+..+....   ...++.+++|||++.+..       +....|.
T Consensus        80 ~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~---~~~~~~vlvlDe~~~~~~~~~~~~~~~~~~L~  156 (350)
T 2qen_A           80 ELQSTISPFQKFQSKFKISLNLKFLTLEPRKLSLREVFRELNDLG---EELGEFIVAFDEAQYLRFYGSRGGKELLALFA  156 (350)
T ss_dssp             HHHHHSCSHHHHHHHHTCCCCCGGGTSCGGGCCHHHHHHHHHHHH---HHHSCEEEEEETGGGGGGBTTTTTHHHHHHHH
T ss_pred             HHHHHHHHHHhHhhhceeEEEecceeeccccchHHHHHHHHHHHH---hccCCEEEEEeCHHHHhccCccchhhHHHHHH
Confidence                                              11111110000   001267999999999864       3445555


Q ss_pred             HHhhhccCCceEEEEecCCC---------cCchhHhhhc-ceeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhc
Q psy879          118 RTMEIYSNTTRFALACNNSE---------KIIEPIQSRC-AMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTA  187 (317)
Q Consensus       118 ~~le~~~~~~~~il~~~~~~---------~l~~~i~sR~-~~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~  187 (317)
                      ..++.. .+..+|+++....         ....++..|. ..+.+.|++.++..+++...+...+..++++.+..+...+
T Consensus       157 ~~~~~~-~~~~~il~g~~~~~l~~~l~~~~~~~~l~~~~~~~i~l~pl~~~e~~~~l~~~~~~~~~~~~~~~~~~i~~~t  235 (350)
T 2qen_A          157 YAYDSL-PNLKIILTGSEVGLLHDFLKITDYESPLYGRIAGEVLVKPFDKDTSVEFLKRGFREVNLDVPENEIEEAVELL  235 (350)
T ss_dssp             HHHHHC-TTEEEEEEESSHHHHHHHHCTTCTTSTTTTCCCEEEECCCCCHHHHHHHHHHHHHTTTCCCCHHHHHHHHHHH
T ss_pred             HHHHhc-CCeEEEEECCcHHHHHHHHhhcCCCCccccCccceeeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHh
Confidence            555543 4677788775431         1122334454 3699999999999999998887778788899999999999


Q ss_pred             CCCHHHHHHHHH
Q psy879          188 QGDMRQALNNLQ  199 (317)
Q Consensus       188 ~gd~r~~i~~l~  199 (317)
                      +|++..+.....
T Consensus       236 gG~P~~l~~~~~  247 (350)
T 2qen_A          236 DGIPGWLVVFGV  247 (350)
T ss_dssp             TTCHHHHHHHHH
T ss_pred             CCCHHHHHHHHH
Confidence            999986554443

>3dzd_A Transcriptional regulator (NTRC family); sigma43 activator, AAA+ ATPase, response regulator, transcriptional activator, ATP-binding; HET: ADP; 2.40A {Aquifex aeolicus} PDB: 1zit_A 2jrl_A

Probab=99.38  E-value=1.3e-11  Score=109.50  Aligned_cols=189  Identities=15%  Similarity=0.197  Sum_probs=127.2

Q ss_pred             CcccCCHHHHHHHHHHHhc--CCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHH-HHHHHHH
Q psy879           10 SDIVGNEDTVERLKVFSSS--GNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVR-NKIKMFA   86 (317)
Q Consensus        10 ~~~~g~~~~~~~l~~~l~~--~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~-~~~~~~~   86 (317)
                      .+++|+......+...+..  ....+++++|++|+||+.+++++...-. .. .. ++.+||..... ..+. +.++. .
T Consensus       129 ~~~ig~s~~~~~~~~~~~~~a~~~~~vli~GesGtGKe~lAr~ih~~s~-r~-~~-fv~vnc~~~~~-~~~~~~lfg~-~  203 (368)
T 3dzd_A          129 IEFVGEHPKILEIKRLIPKIAKSKAPVLITGESGTGKEIVARLIHRYSG-RK-GA-FVDLNCASIPQ-ELAESELFGH-E  203 (368)
T ss_dssp             CCCCCCSHHHHHHHHHHHHHHTSCSCEEEECCTTSSHHHHHHHHHHHHC-CC-SC-EEEEESSSSCT-TTHHHHHHEE-C
T ss_pred             ccccccchHHHHHHhhhhhhhccchhheEEeCCCchHHHHHHHHHHhcc-cc-CC-cEEEEcccCCh-HHHHHHhcCc-c
Confidence            4577876655554443321  1223599999999999999999998742 22 22 78888865322 2222 12211 0


Q ss_pred             hhcccC---------CCCceeEEEEeCCCCCCHHHHHHHHHHhhhc-----------cCCceEEEEecCC-------CcC
Q psy879           87 QQKVTL---------PPGRHKIVILDEADSMTDGAQQALRRTMEIY-----------SNTTRFALACNNS-------EKI  139 (317)
Q Consensus        87 ~~~~~~---------~~~~~~vliiDE~d~l~~~~~~~ll~~le~~-----------~~~~~~il~~~~~-------~~l  139 (317)
                      ...+..         ..+...++++||++.|..+.|..|++++++.           +-++++|.+||..       ..+
T Consensus       204 ~g~~tga~~~~~g~~~~a~~gtlfldei~~l~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~rii~at~~~l~~~v~~g~f  283 (368)
T 3dzd_A          204 KGAFTGALTRKKGKLELADQGTLFLDEVGELDQRVQAKLLRVLETGSFTRLGGNQKIEVDIRVISATNKNLEEEIKKGNF  283 (368)
T ss_dssp             SCSSSSCCCCEECHHHHTTTSEEEEETGGGSCHHHHHHHHHHHHHSEECCBTCCCBEECCCEEEEEESSCHHHHHHTTSS
T ss_pred             ccccCCcccccCChHhhcCCCeEEecChhhCCHHHHHHHHHHHHhCCcccCCCCcceeeeeEEEEecCCCHHHHHHcCCc
Confidence            001000         0024578999999999999999999999853           2356789998865       256


Q ss_pred             chhHhhhcce--eeecCCCH--HHHHHHHHHH----HHHcC---CCCCHHHHHHHHHhc-CCCHHHHHHHHHHhhh
Q psy879          140 IEPIQSRCAM--LRYNKLTD--AQLLSKVIEI----CEKEN---ISHTNDGLEAIVFTA-QGDMRQALNNLQSTHN  203 (317)
Q Consensus       140 ~~~i~sR~~~--i~f~~~~~--~~~~~~l~~~----~~~~~---~~i~~~~~~~l~~~~-~gd~r~~i~~l~~~~~  203 (317)
                      -+.+..|+..  +.+||+.+  +++...+...    +...+   ..+++++++.+.... .||+|++.|.++.++.
T Consensus       284 r~dL~~rl~~~~i~lPpLreR~~Di~~l~~~~l~~~~~~~~~~~~~~~~~a~~~L~~~~wpGNvreL~n~i~~~~~  359 (368)
T 3dzd_A          284 REDLYYRLSVFQIYLPPLRERGKDVILLAEYFLKKFAKEYKKNCFELSEETKEYLMKQEWKGNVRELKNLIERAVI  359 (368)
T ss_dssp             CHHHHHHHTSEEEECCCGGGSTTHHHHHHHHHHHHHHHHTTCCCCCBCHHHHHHHHTCCCTTHHHHHHHHHHHHHH
T ss_pred             cHHHHHHhCCeEEeCCChhhchhhHHHHHHHHHHHHHHHcCCCCCCcCHHHHHHHHhCCCCcHHHHHHHHHHHHHH
Confidence            7789999887  66888877  5666554443    33333   458999999998875 9999999999998654

>1ny5_A Transcriptional regulator (NTRC family); AAA+ ATPase, sigma54 activator, bacterial transcription, DIM transcription; HET: ADP; 2.40A {Aquifex aeolicus} SCOP: c.23.1.1 c.37.1.20 PDB: 1ny6_A* 3m0e_A* 1zy2_A*

Probab=99.37  E-value=7e-11  Score=105.49  Aligned_cols=203  Identities=16%  Similarity=0.147  Sum_probs=133.7

Q ss_pred             CCcccCCHHHHHHHHHHHhc--CCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHHHHHHH
Q psy879            9 FSDIVGNEDTVERLKVFSSS--GNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFA   86 (317)
Q Consensus         9 ~~~~~g~~~~~~~l~~~l~~--~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~   86 (317)
                      +..++|+....+.+...+..  ....+++++|++|+||+++|+++....  .....+++.+++... ....+...+-...
T Consensus       136 ~~~~ig~s~~m~~l~~~i~~~a~~~~~vli~Ge~GtGK~~lAr~ih~~s--~r~~~~fv~v~~~~~-~~~~~~~elfg~~  212 (387)
T 1ny5_A          136 EEEYVFESPKMKEILEKIKKISCAECPVLITGESGVGKEVVARLIHKLS--DRSKEPFVALNVASI-PRDIFEAELFGYE  212 (387)
T ss_dssp             CCCCCCCSHHHHHHHHHHHHHTTCCSCEEEECSTTSSHHHHHHHHHHHS--TTTTSCEEEEETTTS-CHHHHHHHHHCBC
T ss_pred             chhhhhccHHhhHHHHHHHHhcCCCCCeEEecCCCcCHHHHHHHHHHhc--CCCCCCeEEEecCCC-CHHHHHHHhcCCC
Confidence            45678876666655544432  122248999999999999999999863  233456788887642 2222222111100


Q ss_pred             hhcccC---------CCCceeEEEEeCCCCCCHHHHHHHHHHhhhc-----------cCCceEEEEecCC-------CcC
Q psy879           87 QQKVTL---------PPGRHKIVILDEADSMTDGAQQALRRTMEIY-----------SNTTRFALACNNS-------EKI  139 (317)
Q Consensus        87 ~~~~~~---------~~~~~~vliiDE~d~l~~~~~~~ll~~le~~-----------~~~~~~il~~~~~-------~~l  139 (317)
                      ...+..         ..+.+.++++||++.|..+.|..|++++++.           +.++++|++||..       ..+
T Consensus       213 ~g~~tga~~~~~g~~~~a~~gtlfldei~~l~~~~q~~Ll~~l~~~~~~~~g~~~~~~~~~rii~at~~~l~~~~~~g~f  292 (387)
T 1ny5_A          213 KGAFTGAVSSKEGFFELADGGTLFLDEIGELSLEAQAKLLRVIESGKFYRLGGRKEIEVNVRILAATNRNIKELVKEGKF  292 (387)
T ss_dssp             TTSSTTCCSCBCCHHHHTTTSEEEEESGGGCCHHHHHHHHHHHHHSEECCBTCCSBEECCCEEEEEESSCHHHHHHTTSS
T ss_pred             CCCCCCcccccCCceeeCCCcEEEEcChhhCCHHHHHHHHHHHhcCcEEeCCCCceeeccEEEEEeCCCCHHHHHHcCCc
Confidence            111100         0134679999999999999999999999863           2367789999874       356


Q ss_pred             chhHhhhcce--eeecCCCH--HHHHHHHHH----HHHHcCC---CCCHHHHHHHHHh-cCCCHHHHHHHHHHhhh--CC
Q psy879          140 IEPIQSRCAM--LRYNKLTD--AQLLSKVIE----ICEKENI---SHTNDGLEAIVFT-AQGDMRQALNNLQSTHN--GF  205 (317)
Q Consensus       140 ~~~i~sR~~~--i~f~~~~~--~~~~~~l~~----~~~~~~~---~i~~~~~~~l~~~-~~gd~r~~i~~l~~~~~--~~  205 (317)
                      -+.+-.|+..  +.+||+.+  +++...+..    .+.+.+.   .+++++++.+... ..||+|+..+.++.++.  ..
T Consensus       293 r~dl~~rl~~~~i~lPpLreR~~Di~~l~~~~l~~~~~~~~~~~~~~~~~a~~~l~~~~wpGNvreL~~~i~~~~~~~~~  372 (387)
T 1ny5_A          293 REDLYYRLGVIEIEIPPLRERKEDIIPLANHFLKKFSRKYAKEVEGFTKSAQELLLSYPWYGNVRELKNVIERAVLFSEG  372 (387)
T ss_dssp             CHHHHHHHTTEEEECCCGGGCHHHHHHHHHHHHHHHHHHTTCCCCEECHHHHHHHHHSCCTTHHHHHHHHHHHHHHHCCS
T ss_pred             cHHHHHhhcCCeecCCcchhccccHHHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHhCCCCcHHHHHHHHHHHHHHhCCC
Confidence            7778778765  66677764  555544443    3333343   3789999988866 48999999999997654  44


Q ss_pred             CcccHHHHH
Q psy879          206 GHVTAEYVF  214 (317)
Q Consensus       206 ~~i~~~~v~  214 (317)
                      ..|+.+++.
T Consensus       373 ~~i~~~~l~  381 (387)
T 1ny5_A          373 KFIDRGELS  381 (387)
T ss_dssp             SEECHHHHH
T ss_pred             CcCcHHHCc
Confidence            567776653

>1u0j_A DNA replication protein; AAA+ protein, P-loop atpases, helicase; HET: DNA ADP; 2.10A {Adeno-associated virus - 2} SCOP: c.37.1.20 PDB: 1s9h_A

Probab=99.36  E-value=6.5e-12  Score=104.88  Aligned_cols=137  Identities=15%  Similarity=0.142  Sum_probs=89.4

Q ss_pred             HHHHHHHHHhcCCC--ceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHHHHHHHhhcccCCCC
Q psy879           18 TVERLKVFSSSGNV--PNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPG   95 (317)
Q Consensus        18 ~~~~l~~~l~~~~~--~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~   95 (317)
                      ....+..+++...+  .+++||||||||||++++++|+.+.-      +..++..+.           .+....    ..
T Consensus        89 ~~~~l~~~l~~~~~~~n~~~l~GppgtGKt~~a~ala~~~~l------~G~vn~~~~-----------~f~l~~----~~  147 (267)
T 1u0j_A           89 AASVFLGWATKKFGKRNTIWLFGPATTGKTNIAEAIAHTVPF------YGCVNWTNE-----------NFPFND----CV  147 (267)
T ss_dssp             HHHHHHHHHTTCSTTCCEEEEECSTTSSHHHHHHHHHHHSSC------EEECCTTCS-----------SCTTGG----GS
T ss_pred             HHHHHHHHHhCCCCCCcEEEEECCCCCCHHHHHHHHHhhhcc------cceeecccc-----------cccccc----cc
Confidence            34446666665423  25999999999999999999997311      111221110           000010    02


Q ss_pred             ceeEEEEeCCCCCCHHHHHHHHHHhh--------hcc-----CCceEEEEecCC-----------CcCchhHhhhcceee
Q psy879           96 RHKIVILDEADSMTDGAQQALRRTME--------IYS-----NTTRFALACNNS-----------EKIIEPIQSRCAMLR  151 (317)
Q Consensus        96 ~~~vliiDE~d~l~~~~~~~ll~~le--------~~~-----~~~~~il~~~~~-----------~~l~~~i~sR~~~i~  151 (317)
                      .+++++. |...+..+.++.+.++++        ...     ..+.+|++||..           +...++|+|||..++
T Consensus       148 ~k~i~l~-Ee~~~~~d~~~~lr~i~~G~~~~id~K~k~~~~v~~tPvIitsN~~i~~~~~g~~~s~~~~~~L~sR~~~f~  226 (267)
T 1u0j_A          148 DKMVIWW-EEGKMTAKVVESAKAILGGSKVRVDQKCKSSAQIDPTPVIVTSNTNMCAVIDGNSTTFEHQQPLQDRMFKFE  226 (267)
T ss_dssp             SCSEEEE-CSCCEETTTHHHHHHHHTTCCEEC------CCEECCCCEEEEESSCTTCEEETTEEECTTHHHHHTTEEEEE
T ss_pred             ccEEEEe-ccccchhHHHHHHHHHhCCCcEEEecCcCCcccccCCCEEEEecCCcccccccCccchhhhHHHhhhEEEEE
Confidence            3455554 445556667777888887        322     567799999972           256689999999999


Q ss_pred             ec--------CCCHHHHHHHHHHHHHHcCCCCCH
Q psy879          152 YN--------KLTDAQLLSKVIEICEKENISHTN  177 (317)
Q Consensus       152 f~--------~~~~~~~~~~l~~~~~~~~~~i~~  177 (317)
                      |+        +++++++..++. ++..+..++++
T Consensus       227 F~~~~p~~~~~lt~~~~~~f~~-w~~~~~~~~~~  259 (267)
T 1u0j_A          227 LTRRLDHDFGKVTKQEVKDFFR-WAKDHVVEVEH  259 (267)
T ss_dssp             CCSCCCTTSCCCCHHHHHHHHH-HHHHTCCCCCC
T ss_pred             CCCcCCcccCCCCHHHHHHHHH-HHHHcCCCCcc
Confidence            99        899999999998 45777766543

>2fna_A Conserved hypothetical protein; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2; HET: MSE ADP; 2.00A {Sulfolobus solfataricus} SCOP: a.4.5.11 c.37.1.20

Probab=99.28  E-value=1.7e-10  Score=101.67  Aligned_cols=176  Identities=15%  Similarity=0.151  Sum_probs=114.7

Q ss_pred             CCCcccCCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCC-----cChHHH----
Q psy879            8 TFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASND-----RGIDTV----   78 (317)
Q Consensus         8 ~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~-----~~~~~i----   78 (317)
                      ..+.++|+++.++.|.. +..   +.++++||+|+|||++++.+++.+..   .  ++.+++...     ......    
T Consensus        11 ~~~~~~gR~~el~~L~~-l~~---~~v~i~G~~G~GKT~L~~~~~~~~~~---~--~~~~~~~~~~~~~~~~~~~~~~~l   81 (357)
T 2fna_A           11 NRKDFFDREKEIEKLKG-LRA---PITLVLGLRRTGKSSIIKIGINELNL---P--YIYLDLRKFEERNYISYKDFLLEL   81 (357)
T ss_dssp             SGGGSCCCHHHHHHHHH-TCS---SEEEEEESTTSSHHHHHHHHHHHHTC---C--EEEEEGGGGTTCSCCCHHHHHHHH
T ss_pred             CHHHhcChHHHHHHHHH-hcC---CcEEEECCCCCCHHHHHHHHHHhcCC---C--EEEEEchhhccccCCCHHHHHHHH
Confidence            45789999999999998 765   58999999999999999999998632   1  233332210     111111    


Q ss_pred             HH-------------------------------------------HHHHHHhhcccCCCCceeEEEEeCCCCCCH----H
Q psy879           79 RN-------------------------------------------KIKMFAQQKVTLPPGRHKIVILDEADSMTD----G  111 (317)
Q Consensus        79 ~~-------------------------------------------~~~~~~~~~~~~~~~~~~vliiDE~d~l~~----~  111 (317)
                      .+                                           .+..+...    . .++.+++|||++.+..    +
T Consensus        82 ~~~l~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~----~-~~~~vlvlDe~~~~~~~~~~~  156 (357)
T 2fna_A           82 QKEINKLVKRLPSLLKALKNIQGIVIMGNEIKFNWNRKDRLSFANLLESFEQA----S-KDNVIIVLDEAQELVKLRGVN  156 (357)
T ss_dssp             HHHHHHHHHHCTTHHHHTTTSTTEEECSSSEEEC-----CCCHHHHHHHHHHT----C-SSCEEEEEETGGGGGGCTTCC
T ss_pred             HHHHHHHhhhhhHHHHHhcccceEEecceEEEeccCCcchhhHHHHHHHHHhc----C-CCCeEEEEECHHHhhccCchh
Confidence            11                                           11111100    0 0367899999999864    2


Q ss_pred             HHHHHHHHhhhccCCceEEEEecCCCc---------CchhHhhhc-ceeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHH
Q psy879          112 AQQALRRTMEIYSNTTRFALACNNSEK---------IIEPIQSRC-AMLRYNKLTDAQLLSKVIEICEKENISHTNDGLE  181 (317)
Q Consensus       112 ~~~~ll~~le~~~~~~~~il~~~~~~~---------l~~~i~sR~-~~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~  181 (317)
                      ....|....+.. .+..+|+++.....         ...++..|. ..+.+.|++.++..+++...+...+...++.  .
T Consensus       157 ~~~~l~~~~~~~-~~~~~i~~g~~~~~l~~~l~~~~~~~~l~~r~~~~i~l~~l~~~e~~~~l~~~~~~~~~~~~~~--~  233 (357)
T 2fna_A          157 LLPALAYAYDNL-KRIKFIMSGSEMGLLYDYLRVEDPESPLFGRAFSTVELKPFSREEAIEFLRRGFQEADIDFKDY--E  233 (357)
T ss_dssp             CHHHHHHHHHHC-TTEEEEEEESSHHHHHHHTTTTCTTSTTTTCCCEEEEECCCCHHHHHHHHHHHHHHHTCCCCCH--H
T ss_pred             HHHHHHHHHHcC-CCeEEEEEcCchHHHHHHHhccCCCCccccCccceeecCCCCHHHHHHHHHHHHHHcCCCCCcH--H
Confidence            344444444443 35778888765321         112344454 5699999999999999998876667666544  7


Q ss_pred             HHHHhcCCCHHHHHHHHHH
Q psy879          182 AIVFTAQGDMRQALNNLQS  200 (317)
Q Consensus       182 ~l~~~~~gd~r~~i~~l~~  200 (317)
                      .+...++|++.-+......
T Consensus       234 ~i~~~t~G~P~~l~~~~~~  252 (357)
T 2fna_A          234 VVYEKIGGIPGWLTYFGFI  252 (357)
T ss_dssp             HHHHHHCSCHHHHHHHHHH
T ss_pred             HHHHHhCCCHHHHHHHHHH
Confidence            8889999999876555544

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=99.26  E-value=7.1e-12  Score=101.77  Aligned_cols=122  Identities=14%  Similarity=0.185  Sum_probs=73.4

Q ss_pred             cccCCCCCCcccCCH----HHHHHHHHHHhcCC----CceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCc
Q psy879            2 EKYRPQTFSDIVGNE----DTVERLKVFSSSGN----VPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDR   73 (317)
Q Consensus         2 ~ky~P~~~~~~~g~~----~~~~~l~~~l~~~~----~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~   73 (317)
                      .+|++.+|+++++..    .+++.+..++....    ..+++|+||+|+|||++++++++.+....  ..+..+++... 
T Consensus        17 ~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~G~~GtGKT~la~~i~~~~~~~~--~~~~~~~~~~~-   93 (202)
T 2w58_A           17 REILRASLSDVDLNDDGRIKAIRFAERFVAEYEPGKKMKGLYLHGSFGVGKTYLLAAIANELAKRN--VSSLIVYVPEL-   93 (202)
T ss_dssp             GGGGCCCTTSSCCSSHHHHHHHHHHHHHHHHCCSSCCCCEEEEECSTTSSHHHHHHHHHHHHHTTT--CCEEEEEHHHH-
T ss_pred             HHHHcCCHhhccCCChhHHHHHHHHHHHHHHhhhccCCCeEEEECCCCCCHHHHHHHHHHHHHHcC--CeEEEEEhHHH-
Confidence            357889999999743    35566677776542    14799999999999999999999885432  23333332110 


Q ss_pred             ChHHH---------HHHHHHHHhhcccCCCCceeEEEEeCCCCCCHH--HHHHHH-HHhhhc-cCCceEEEEecCC
Q psy879           74 GIDTV---------RNKIKMFAQQKVTLPPGRHKIVILDEADSMTDG--AQQALR-RTMEIY-SNTTRFALACNNS  136 (317)
Q Consensus        74 ~~~~i---------~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~--~~~~ll-~~le~~-~~~~~~il~~~~~  136 (317)
                       ...+         ...+..+         ....+++|||++.....  .+..++ .+++.. .....+|++||..
T Consensus        94 -~~~~~~~~~~~~~~~~~~~~---------~~~~~lilDei~~~~~~~~~~~~ll~~~l~~~~~~~~~~i~tsn~~  159 (202)
T 2w58_A           94 -FRELKHSLQDQTMNEKLDYI---------KKVPVLMLDDLGAEAMSSWVRDDVFGPILQYRMFENLPTFFTSNFD  159 (202)
T ss_dssp             -HHHHHHC---CCCHHHHHHH---------HHSSEEEEEEECCC---CCGGGTTHHHHHHHHHHTTCCEEEEESSC
T ss_pred             -HHHHHHHhccchHHHHHHHh---------cCCCEEEEcCCCCCcCCHHHHHHHHHHHHHHHHhCCCCEEEEcCCC
Confidence             0000         1111111         12359999999775432  344344 455543 4556788888864

>3f8t_A Predicted ATPase involved in replication control, CDC46/MCM family; helicase, MCM homolog, DNA replication, ATP-binding, DNA-binding; 1.90A {Methanopyrus kandleri AV19}

Probab=99.25  E-value=7.3e-11  Score=105.46  Aligned_cols=198  Identities=13%  Similarity=0.060  Sum_probs=120.9

Q ss_pred             cccCCHHHHHHHHHHHhcCC-----CceEEEECCCCCCHHHHHHHH-HHHHcCCCCCCceEEecCCCCcChHH-HHHHHH
Q psy879           11 DIVGNEDTVERLKVFSSSGN-----VPNIIISGPPGVGKTTTILCL-ARILLGPSFKDAVLELNASNDRGIDT-VRNKIK   83 (317)
Q Consensus        11 ~~~g~~~~~~~l~~~l~~~~-----~~~~ll~G~~G~GKt~la~~l-a~~l~~~~~~~~~~~~~~~~~~~~~~-i~~~~~   83 (317)
                      .++||+.+++.+.-++-+|.     -.|+|+.|+||+ ||++++++ ++.+ ..   ..+.....+...+... +++.-+
T Consensus       214 pI~G~e~vK~aLll~L~GG~~k~rgdihVLL~G~PGt-KS~Lar~i~~~i~-pR---~~ft~g~~ss~~gLt~s~r~~tG  288 (506)
T 3f8t_A          214 PLPGAEEVGKMLALQLFSCVGKNSERLHVLLAGYPVV-CSEILHHVLDHLA-PR---GVYVDLRRTELTDLTAVLKEDRG  288 (506)
T ss_dssp             CSTTCHHHHHHHHHHHTTCCSSGGGCCCEEEESCHHH-HHHHHHHHHHHTC-SS---EEEEEGGGCCHHHHSEEEEESSS
T ss_pred             ccCCCHHHHHHHHHHHcCCccccCCceeEEEECCCCh-HHHHHHHHHHHhC-CC---eEEecCCCCCccCceEEEEcCCC
Confidence            38899999988888877763     227999999999 99999999 6643 21   1122111111000000 000000


Q ss_pred             HHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhh---------ccCCceEEEEecCCC-----------cCchhH
Q psy879           84 MFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEI---------YSNTTRFALACNNSE-----------KIIEPI  143 (317)
Q Consensus        84 ~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~---------~~~~~~~il~~~~~~-----------~l~~~i  143 (317)
                       +...+..+..++..++++||++.+.++.+.+|++.||+         .+..+.+|.++|+..           .+.+++
T Consensus       289 -~~~~~G~l~LAdgGvl~lDEIn~~~~~~qsaLlEaMEe~~VtI~G~~lparf~VIAA~NP~~~yd~~~s~~~~~Lp~al  367 (506)
T 3f8t_A          289 -WALRAGAAVLADGGILAVDHLEGAPEPHRWALMEAMDKGTVTVDGIALNARCAVLAAINPGEQWPSDPPIARIDLDQDF  367 (506)
T ss_dssp             -EEEEECHHHHTTTSEEEEECCTTCCHHHHHHHHHHHHHSEEEETTEEEECCCEEEEEECCCC--CCSCGGGGCCSCHHH
T ss_pred             -cccCCCeeEEcCCCeeehHhhhhCCHHHHHHHHHHHhCCcEEECCEEcCCCeEEEEEeCcccccCCCCCccccCCChHH
Confidence             11111111114578999999999999999999999995         356677888888753           788999


Q ss_pred             hhhcceee--ec-------------CCCHHHHHHHHHHHHH--HcCCCCCHHHHHHHHHh------------------cC
Q psy879          144 QSRCAMLR--YN-------------KLTDAQLLSKVIEICE--KENISHTNDGLEAIVFT------------------AQ  188 (317)
Q Consensus       144 ~sR~~~i~--f~-------------~~~~~~~~~~l~~~~~--~~~~~i~~~~~~~l~~~------------------~~  188 (317)
                      .+||..+.  ..             .++.+++.+++.. ++  .-...+++++.++++..                  .+
T Consensus       368 LDRFDLi~i~~d~pd~e~d~e~~~~~ls~e~L~~yi~~-ar~~~~~p~ls~ea~~yI~~~y~~tR~~~~~~~~~~~~~~g  446 (506)
T 3f8t_A          368 LSHFDLIAFLGVDPRPGEPEEQDTEVPSYTLLRRYLLY-AIREHPAPELTEEARKRLEHWYETRREEVEERLGMGLPTLP  446 (506)
T ss_dssp             HTTCSEEEETTC--------------CCHHHHHHHHHH-HHHHCSCCEECHHHHHHHHHHHHHHHHHHHHHHHTTCCCCC
T ss_pred             hhheeeEEEecCCCChhHhhcccCCCCCHHHHHHHHHH-HHhcCCCceeCHHHHHHHHHHHHHHhcCccccccccccccc
Confidence            99995522  12             2344555555543 33  12556788877666532                  13


Q ss_pred             CCHHHHHHHHHHh---h--hCCCcccHHHHHh
Q psy879          189 GDMRQALNNLQST---H--NGFGHVTAEYVFK  215 (317)
Q Consensus       189 gd~r~~i~~l~~~---~--~~~~~i~~~~v~~  215 (317)
                      -++|....+++.+   +  .+...++.+||..
T Consensus       447 iSpR~leaLiRlA~A~A~L~gR~~V~~eDV~~  478 (506)
T 3f8t_A          447 VTRRQLESVERLAKAHARMRLSDDVEPEDVDI  478 (506)
T ss_dssp             CCHHHHHHHHHHHHHHHHHTTCSEECHHHHHH
T ss_pred             ccHHHHHHHHHHHHHHHHHcCcCCCCHHHHHH
Confidence            4567666666432   1  1556777777754

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=99.24  E-value=2.5e-11  Score=93.48  Aligned_cols=120  Identities=18%  Similarity=0.237  Sum_probs=78.5

Q ss_pred             CCCcccC--CHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHHHHHH
Q psy879            8 TFSDIVG--NEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMF   85 (317)
Q Consensus         8 ~~~~~~g--~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~   85 (317)
                      +|++++.  +..+...+...  .|  ..++|+||+|+|||+++++++..+...  +...+.++.......        .+
T Consensus        15 ~~~~f~~g~n~~~~~~l~~~--~g--~~~~l~G~~G~GKTtL~~~i~~~~~~~--g~~~~~~~~~~~~~~--------~~   80 (149)
T 2kjq_A           15 SFDKFLGTENAELVYVLRHK--HG--QFIYVWGEEGAGKSHLLQAWVAQALEA--GKNAAYIDAASMPLT--------DA   80 (149)
T ss_dssp             CCCCCCSCCTHHHHHHCCCC--CC--SEEEEESSSTTTTCHHHHHHHHHHHTT--TCCEEEEETTTSCCC--------GG
T ss_pred             chhhcCcCccHHHHHHHHhc--CC--CEEEEECCCCCCHHHHHHHHHHHHHhc--CCcEEEEcHHHhhHH--------HH
Confidence            4555553  44444444444  33  369999999999999999999987542  333455554332221        00


Q ss_pred             HhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccC--CceEEEEecCC-CcC--chhHhhhcce
Q psy879           86 AQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSN--TTRFALACNNS-EKI--IEPIQSRCAM  149 (317)
Q Consensus        86 ~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~--~~~~il~~~~~-~~l--~~~i~sR~~~  149 (317)
                              ..++.+++|||++.+....+..|+++++....  .+++|++++.+ ..+  .+.+.||+..
T Consensus        81 --------~~~~~lLilDE~~~~~~~~~~~l~~li~~~~~~g~~~iiits~~~p~~l~~~~~L~SRl~~  141 (149)
T 2kjq_A           81 --------AFEAEYLAVDQVEKLGNEEQALLFSIFNRFRNSGKGFLLLGSEYTPQQLVIREDLRTRMAY  141 (149)
T ss_dssp             --------GGGCSEEEEESTTCCCSHHHHHHHHHHHHHHHHTCCEEEEEESSCTTTSSCCHHHHHHGGG
T ss_pred             --------HhCCCEEEEeCccccChHHHHHHHHHHHHHHHcCCcEEEEECCCCHHHccccHHHHHHHhc
Confidence                    03467999999999988778888888875432  23477788753 322  2999999865

>1tue_A Replication protein E1; helicase, replication, E1E2 complex, AAA+ protein; 2.10A {Human papillomavirus type 18} SCOP: c.37.1.20

Probab=99.24  E-value=2e-11  Score=97.41  Aligned_cols=116  Identities=17%  Similarity=0.280  Sum_probs=73.2

Q ss_pred             HHHHHHHHHhcCCCc---eEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHHHHHHHhhcccCCC
Q psy879           18 TVERLKVFSSSGNVP---NIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPP   94 (317)
Q Consensus        18 ~~~~l~~~l~~~~~~---~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~   94 (317)
                      .+..+..++++  .|   +++||||||||||+++.++++.+.+.     +..+..+.. . .        +.+ +    .
T Consensus        44 f~~~l~~~~~~--iPkkn~ili~GPPGtGKTt~a~ala~~l~g~-----i~~fans~s-~-f--------~l~-~----l  101 (212)
T 1tue_A           44 FLGALKSFLKG--TPKKNCLVFCGPANTGKSYFGMSFIHFIQGA-----VISFVNSTS-H-F--------WLE-P----L  101 (212)
T ss_dssp             HHHHHHHHHHT--CTTCSEEEEESCGGGCHHHHHHHHHHHHTCE-----ECCCCCSSS-C-G--------GGG-G----G
T ss_pred             HHHHHHHHHhc--CCcccEEEEECCCCCCHHHHHHHHHHHhCCC-----eeeEEeccc-h-h--------hhc-c----c
Confidence            34556666653  33   59999999999999999999998532     111111110 0 0        001 1    1


Q ss_pred             CceeEEEEeCCCCCCHHH-HHHHHHHhhhcc-------------CCceEEEEecCC---CcCchhHhhhcceeeecCC
Q psy879           95 GRHKIVILDEADSMTDGA-QQALRRTMEIYS-------------NTTRFALACNNS---EKIIEPIQSRCAMLRYNKL  155 (317)
Q Consensus        95 ~~~~vliiDE~d~l~~~~-~~~ll~~le~~~-------------~~~~~il~~~~~---~~l~~~i~sR~~~i~f~~~  155 (317)
                      .+.+++++||++.-..+. ...+..+++..+             ....+|+|||..   +...+.|.||+..+.|+.+
T Consensus       102 ~~~kIiiLDEad~~~~~~~d~~lrn~ldG~~~~iD~Khr~~~~~~~~PlIITtN~~~~~~~~~~~L~SRi~~f~F~~~  179 (212)
T 1tue_A          102 TDTKVAMLDDATTTCWTYFDTYMRNALDGNPISIDRKHKPLIQLKCPPILLTTNIHPAKDNRWPYLESRITVFEFPNA  179 (212)
T ss_dssp             TTCSSEEEEEECHHHHHHHHHHCHHHHHTCCEEEC----CCEEECCCCEEEEESSCTTSSSSCHHHHTSCEEEECCSC
T ss_pred             CCCCEEEEECCCchhHHHHHHHHHHHhCCCcccHHHhhcCccccCCCCEEEecCCCcccccchhhhhhhEEEEEcCCC
Confidence            346799999998532222 234455555421             235789999974   4556899999999999844

>4akg_A Glutathione S-transferase class-MU 26 kDa isozyme heavy chain cytoplasmic; motor protein, AAA+ protein, ASCE protein, P-loop ntpase; HET: ATP ADP; 3.30A {Schistosoma japonicum} PDB: 4ai6_A* 4akh_A* 4aki_A* 3qmz_A

Probab=99.15  E-value=3.5e-10  Score=120.31  Aligned_cols=143  Identities=20%  Similarity=0.183  Sum_probs=102.9

Q ss_pred             HHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHHHHHHHhhc-------ccC-C
Q psy879           22 LKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFAQQK-------VTL-P   93 (317)
Q Consensus        22 l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~-------~~~-~   93 (317)
                      +..++..++  ++||+||||||||++|+.+....    .+..+..++.+...+...+.+.+.......       ... +
T Consensus      1260 l~~~l~~~~--~vLL~GPpGtGKT~la~~~l~~~----~~~~~~~infsa~ts~~~~~~~i~~~~~~~~~~~g~~~~P~~ 1333 (2695)
T 4akg_A         1260 FYDLLNSKR--GIILCGPPGSGKTMIMNNALRNS----SLYDVVGINFSKDTTTEHILSALHRHTNYVTTSKGLTLLPKS 1333 (2695)
T ss_dssp             HHHHHHHTC--EEEEECSTTSSHHHHHHHHHHSC----SSCEEEEEECCTTCCHHHHHHHHHHHBCCEEETTTEEEEEBS
T ss_pred             HHHHHHCCC--eEEEECCCCCCHHHHHHHHHhcC----CCCceEEEEeecCCCHHHHHHHHHHHhhhccccCCccccCCC
Confidence            566677776  89999999999999997766543    234566777766666666666655432211       011 1


Q ss_pred             CCceeEEEEeCCCCCCH------HHHHHHHHHhhhcc------------CCceEEEEecCC-----CcCchhHhhhccee
Q psy879           94 PGRHKIVILDEADSMTD------GAQQALRRTMEIYS------------NTTRFALACNNS-----EKIIEPIQSRCAML  150 (317)
Q Consensus        94 ~~~~~vliiDE~d~l~~------~~~~~ll~~le~~~------------~~~~~il~~~~~-----~~l~~~i~sR~~~i  150 (317)
                      .+.+.|++|||++....      ...+.|.+.+|...            .++.+|.++|++     ..+.+++.+||.++
T Consensus      1334 ~gk~~VlFiDEinmp~~d~yg~q~~lelLRq~le~gg~yd~~~~~~~~~~~i~lIaA~Npp~~gGR~~l~~rllRrf~vi 1413 (2695)
T 4akg_A         1334 DIKNLVLFCDEINLPKLDKYGSQNVVLFLRQLMEKQGFWKTPENKWVTIERIHIVGACNPPTDPGRIPMSERFTRHAAIL 1413 (2695)
T ss_dssp             SSSCEEEEEETTTCSCCCSSSCCHHHHHHHHHHHTSSEECTTTCCEEEEESEEEEEEECCTTSTTCCCCCHHHHTTEEEE
T ss_pred             CCceEEEEecccccccccccCchhHHHHHHHHHhcCCEEEcCCCcEEEecCEEEEEecCCCccCCCccCChhhhheeeEE
Confidence            34567999999876533      35677777777311            246788889987     37999999999999


Q ss_pred             eecCCCHHHHHHHHHHHHHH
Q psy879          151 RYNKLTDAQLLSKVIEICEK  170 (317)
Q Consensus       151 ~f~~~~~~~~~~~l~~~~~~  170 (317)
                      .++.|+.+++..++..++..
T Consensus      1414 ~i~~P~~~~l~~I~~~il~~ 1433 (2695)
T 4akg_A         1414 YLGYPSGKSLSQIYEIYYKA 1433 (2695)
T ss_dssp             ECCCCTTTHHHHHHHHHHHH
T ss_pred             EeCCCCHHHHHHHHHHHHHH
Confidence            99999999999999888754

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=99.09  E-value=6.4e-11  Score=102.42  Aligned_cols=126  Identities=17%  Similarity=0.172  Sum_probs=70.5

Q ss_pred             ccCCCCCCcccCC----HHHHHHHHHHHhcC---CCceEEEECCCCCCHHHHHHHHHHHHc-CCCCCCceEEecCCCCcC
Q psy879            3 KYRPQTFSDIVGN----EDTVERLKVFSSSG---NVPNIIISGPPGVGKTTTILCLARILL-GPSFKDAVLELNASNDRG   74 (317)
Q Consensus         3 ky~P~~~~~~~g~----~~~~~~l~~~l~~~---~~~~~ll~G~~G~GKt~la~~la~~l~-~~~~~~~~~~~~~~~~~~   74 (317)
                      .+++.+|+++++.    ..+.+.+..++.+.   ...+++|+||||+|||+++.++++.+. ...  ..+..++..    
T Consensus       117 ~~~~~tfd~f~~~~~~~~~~~~~~~~~i~~~~~~~~~~lll~G~~GtGKT~La~aia~~~~~~~g--~~v~~~~~~----  190 (308)
T 2qgz_A          117 SYRHIHLSDIDVNNASRMEAFSAILDFVEQYPSAEQKGLYLYGDMGIGKSYLLAAMAHELSEKKG--VSTTLLHFP----  190 (308)
T ss_dssp             GGGSCCGGGSCCCSHHHHHHHHHHHHHHHHCSCSSCCEEEEECSTTSSHHHHHHHHHHHHHHHSC--CCEEEEEHH----
T ss_pred             HHHhCCHhhCcCCChHHHHHHHHHHHHHHhccccCCceEEEECCCCCCHHHHHHHHHHHHHHhcC--CcEEEEEHH----
Confidence            4567899999963    34555666777653   134699999999999999999999875 332  223333221    


Q ss_pred             hHHHHHHHHH-HHhh---cccCCCCceeEEEEeCCCCC--CHHHHHHHHH-Hhhhc-cCCceEEEEecCC
Q psy879           75 IDTVRNKIKM-FAQQ---KVTLPPGRHKIVILDEADSM--TDGAQQALRR-TMEIY-SNTTRFALACNNS  136 (317)
Q Consensus        75 ~~~i~~~~~~-~~~~---~~~~~~~~~~vliiDE~d~l--~~~~~~~ll~-~le~~-~~~~~~il~~~~~  136 (317)
                        .+...+.. +...   ..........+|||||++..  +...++.|+. +++.. .....+|++||.+
T Consensus       191 --~l~~~l~~~~~~~~~~~~~~~~~~~~lLiiDdig~~~~~~~~~~~ll~~ll~~r~~~~~~~IitSN~~  258 (308)
T 2qgz_A          191 --SFAIDVKNAISNGSVKEEIDAVKNVPVLILDDIGAEQATSWVRDEVLQVILQYRMLEELPTFFTSNYS  258 (308)
T ss_dssp             --HHHHHHHCCCC----CCTTHHHHTSSEEEEETCCC------CTTTTHHHHHHHHHHHTCCEEEEESSC
T ss_pred             --HHHHHHHHHhccchHHHHHHHhcCCCEEEEcCCCCCCCCHHHHHHHHHHHHHHHHHCCCcEEEECCCC
Confidence              11111100 0000   00000023469999999654  3333443433 66543 3456789999854

>3upu_A ATP-dependent DNA helicase DDA; RECA-like domain, SH3 domain, PIN-tower interface, coupling hydrolysis to DNA unwinding, ssDNA; 3.30A {Enterobacteria phage T4}

Probab=99.03  E-value=7.8e-10  Score=101.05  Aligned_cols=129  Identities=14%  Similarity=0.176  Sum_probs=81.2

Q ss_pred             CcccCCCCCCccc-CCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHH
Q psy879            1 IEKYRPQTFSDIV-GNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVR   79 (317)
Q Consensus         1 ~~ky~P~~~~~~~-g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~   79 (317)
                      ++||||.+|+++- +|.+++..+...+.++.. ++++.|++|||||+++..++..+..... ..++-+... ......++
T Consensus        15 ~~~~~p~~~~~Ln~~Q~~av~~~~~~i~~~~~-~~li~G~aGTGKT~ll~~~~~~l~~~~~-~~il~~a~T-~~Aa~~l~   91 (459)
T 3upu_A           15 VPRGSHMTFDDLTEGQKNAFNIVMKAIKEKKH-HVTINGPAGTGATTLTKFIIEALISTGE-TGIILAAPT-HAAKKILS   91 (459)
T ss_dssp             ------CCSSCCCHHHHHHHHHHHHHHHSSSC-EEEEECCTTSCHHHHHHHHHHHHHHTTC-CCEEEEESS-HHHHHHHH
T ss_pred             ccccCCCccccCCHHHHHHHHHHHHHHhcCCC-EEEEEeCCCCCHHHHHHHHHHHHHhcCC-ceEEEecCc-HHHHHHHH
Confidence            4799999999998 788888888888887663 7999999999999999999998864432 122222221 11122222


Q ss_pred             HHHH-------HHHh-hc------------ccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecC
Q psy879           80 NKIK-------MFAQ-QK------------VTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNN  135 (317)
Q Consensus        80 ~~~~-------~~~~-~~------------~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~  135 (317)
                      +.++       .+.. .+            .........++||||+..+....+..|++.+.   ....++++...
T Consensus        92 ~~~~~~~~T~h~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iiiDE~~~~~~~~~~~l~~~~~---~~~~~~~vGD~  164 (459)
T 3upu_A           92 KLSGKEASTIHSILKINPVTYEENVLFEQKEVPDLAKCRVLICDEVSMYDRKLFKILLSTIP---PWCTIIGIGDN  164 (459)
T ss_dssp             HHHSSCEEEHHHHHTEEEEECSSCEEEEECSCCCCSSCSEEEESCGGGCCHHHHHHHHHHSC---TTCEEEEEECT
T ss_pred             hhhccchhhHHHHhccCcccccccchhcccccccccCCCEEEEECchhCCHHHHHHHHHhcc---CCCEEEEECCH
Confidence            2210       1111 00            00111357899999999999988888888775   55667777654

>4akg_A Glutathione S-transferase class-MU 26 kDa isozyme heavy chain cytoplasmic; motor protein, AAA+ protein, ASCE protein, P-loop ntpase; HET: ATP ADP; 3.30A {Schistosoma japonicum} PDB: 4ai6_A* 4akh_A* 4aki_A* 3qmz_A

Probab=98.88  E-value=7.1e-08  Score=103.03  Aligned_cols=166  Identities=14%  Similarity=0.175  Sum_probs=115.6

Q ss_pred             HHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHHHHHHHhhcccCCCCce
Q psy879           18 TVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRH   97 (317)
Q Consensus        18 ~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~   97 (317)
                      ....+..++..+.  ..++.||+|||||++++.+|+.+     +..++.++|+.......+...+....+.        +
T Consensus       634 ~~~tl~~Al~~~~--~~~l~GpaGtGKTe~vk~LA~~l-----g~~~v~~nc~e~ld~~~lg~~~~g~~~~--------G  698 (2695)
T 4akg_A          634 GFATLTDSLHQKY--GGCFFGPAGTGKTETVKAFGQNL-----GRVVVVFNCDDSFDYQVLSRLLVGITQI--------G  698 (2695)
T ss_dssp             HHHHHHHHHHTTC--EEEEECCTTSCHHHHHHHHHHTT-----TCCCEEEETTSSCCHHHHHHHHHHHHHH--------T
T ss_pred             HHHHHHHHHHhCC--CCcccCCCCCCcHHHHHHHHHHh-----CCcEEEEECCCCCChhHhhHHHHHHHhc--------C
Confidence            4445666677665  57899999999999999999986     3447788888888877776666555443        3


Q ss_pred             eEEEEeCCCCCCHHHHHHHHH-------Hhhh-------------ccCCceEEEEecCC----CcCchhHhhhcceeeec
Q psy879           98 KIVILDEADSMTDGAQQALRR-------TMEI-------------YSNTTRFALACNNS----EKIIEPIQSRCAMLRYN  153 (317)
Q Consensus        98 ~vliiDE~d~l~~~~~~~ll~-------~le~-------------~~~~~~~il~~~~~----~~l~~~i~sR~~~i~f~  153 (317)
                      ..+++||++.+..+...++..       .+.+             .++++.+++|.|+.    ..+++++++||..+.+.
T Consensus       699 aw~~~DE~nr~~~evLs~l~~~l~~i~~al~~~~~~i~~~g~~i~l~~~~~vfiT~NPgy~g~~eLP~~Lk~~Fr~v~m~  778 (2695)
T 4akg_A          699 AWGCFDEFNRLDEKVLSAVSANIQQIQNGLQVGKSHITLLEEETPLSPHTAVFITLNPGYNGRSELPENLKKSFREFSMK  778 (2695)
T ss_dssp             CEEEEETTTSSCHHHHHHHHHHHHHHHHHHHHTCSEEECSSSEEECCTTCEEEEEECCCSSSSCCCCHHHHTTEEEEECC
T ss_pred             CEeeehhhhhcChHHHHHHHHHHHHHHHHHHcCCcEEeeCCcEEecCCCceEEEEeCCCccCcccccHHHHhheEEEEee
Confidence            689999999999988777633       3321             12445566666642    47899999999999999


Q ss_pred             CCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHH-------hc------CCCHHHHHHHHHHh
Q psy879          154 KLTDAQLLSKVIEICEKENISHTNDGLEAIVF-------TA------QGDMRQALNNLQST  201 (317)
Q Consensus       154 ~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~-------~~------~gd~r~~i~~l~~~  201 (317)
                      .|+.+.+.+++....   |....+.....++.       +.      +-.+|.....|..+
T Consensus       779 ~Pd~~~i~ei~l~s~---Gf~~a~~la~kiv~~~~l~~e~ls~q~hydfglRalksvL~~a  836 (2695)
T 4akg_A          779 SPQSGTIAEMILQIM---GFEDSKSLASKIVHFLELLSSKCSSMNHYHFGLRTLKGVLRNC  836 (2695)
T ss_dssp             CCCHHHHHHHHHHHH---HCSSHHHHHHHHHHHHHHHHHHSCCCTTCCCSHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHhc---CCCchHHHHHHHHHHHHHHHHHhCcCCcccccHHHHHHHHHHH
Confidence            999998888865432   54433444333332       11      23677777666544

>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor, microtubles, motor protein; HET: ADP SPM; 2.81A {Dictyostelium discoideum} PDB: 3vkh_A*

Probab=98.78  E-value=5.4e-08  Score=104.64  Aligned_cols=142  Identities=21%  Similarity=0.278  Sum_probs=101.2

Q ss_pred             HHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHHHHHHHh-------hcccCC-
Q psy879           22 LKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFAQ-------QKVTLP-   93 (317)
Q Consensus        22 l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~-------~~~~~~-   93 (317)
                      +..++..+.  ++||+||+|||||.++..+...+    .+..++.++.+.......+.+.+.....       .+...+ 
T Consensus      1297 l~~ll~~~~--pvLL~GptGtGKT~li~~~L~~l----~~~~~~~infS~~Tta~~l~~~~e~~~e~~~~~~~G~~~~p~ 1370 (3245)
T 3vkg_A         1297 LHAWLSEHR--PLILCGPPGSGKTMTLTSTLRAF----PDFEVVSLNFSSATTPELLLKTFDHHCEYKRTPSGETVLRPT 1370 (3245)
T ss_dssp             HHHHHHTTC--CCEEESSTTSSHHHHHHHHGGGC----TTEEEEEECCCTTCCHHHHHHHHHHHEEEEECTTSCEEEEES
T ss_pred             HHHHHHCCC--cEEEECCCCCCHHHHHHHHHHhC----CCCceEEEEeeCCCCHHHHHHHHhhcceEEeccCCCcccCCC
Confidence            566677776  79999999999998886655543    2334667887777777766666653221       111112 


Q ss_pred             -CCceeEEEEeCCCCCCH------HHHHHHHHHhhhc------------cCCceEEEEecCC-----CcCchhHhhhcce
Q psy879           94 -PGRHKIVILDEADSMTD------GAQQALRRTMEIY------------SNTTRFALACNNS-----EKIIEPIQSRCAM  149 (317)
Q Consensus        94 -~~~~~vliiDE~d~l~~------~~~~~ll~~le~~------------~~~~~~il~~~~~-----~~l~~~i~sR~~~  149 (317)
                       .+++-|++|||++.-..      ...+.|+.+++..            ..++.+|.++|++     ..+.+++.+||.+
T Consensus      1371 ~~Gk~~VlFiDDiNmp~~D~yGtQ~~ielLrqlld~~g~yd~~~~~~~~i~d~~~vaamnPp~~gGr~~l~~Rf~r~F~v 1450 (3245)
T 3vkg_A         1371 QLGKWLVVFCDEINLPSTDKYGTQRVITFIRQMVEKGGFWRTSDHTWIKLDKIQFVGACNPPTDAGRVQLTHRFLRHAPI 1450 (3245)
T ss_dssp             STTCEEEEEETTTTCCCCCTTSCCHHHHHHHHHHHHSEEEETTTTEEEEESSEEEEEEECCTTSTTCCCCCHHHHTTCCE
T ss_pred             cCCceEEEEecccCCCCccccccccHHHHHHHHHHcCCeEECCCCeEEEecCeEEEEEcCCCCCCCCccCCHHHHhhceE
Confidence             25567899999987654      3677777888731            1345678888876     3689999999999


Q ss_pred             eeecCCCHHHHHHHHHHHHH
Q psy879          150 LRYNKLTDAQLLSKVIEICE  169 (317)
Q Consensus       150 i~f~~~~~~~~~~~l~~~~~  169 (317)
                      +.++.|+.+++..+...+..
T Consensus      1451 i~i~~ps~esL~~If~til~ 1470 (3245)
T 3vkg_A         1451 LLVDFPSTSSLTQIYGTFNR 1470 (3245)
T ss_dssp             EECCCCCHHHHHHHHHHHHH
T ss_pred             EEeCCCCHHHHHHHHHHHHH
Confidence            99999999999999776654

>1ye8_A Protein THEP1, hypothetical UPF0334 kinase-like protein AQ_1292; mixed alpha-beta protein, rossman fold, signaling protein, transferase; 1.40A {Aquifex aeolicus} SCOP: c.37.1.11

Probab=98.71  E-value=1.2e-07  Score=74.90  Aligned_cols=70  Identities=13%  Similarity=0.280  Sum_probs=51.5

Q ss_pred             CceeEEEEeCCC---CCCHHHHHHHHHHhhhccCCceEEEEec--CCCcCchhHhhh--cceeeecCCCHHHHHHHHHH
Q psy879           95 GRHKIVILDEAD---SMTDGAQQALRRTMEIYSNTTRFALACN--NSEKIIEPIQSR--CAMLRYNKLTDAQLLSKVIE  166 (317)
Q Consensus        95 ~~~~vliiDE~d---~l~~~~~~~ll~~le~~~~~~~~il~~~--~~~~l~~~i~sR--~~~i~f~~~~~~~~~~~l~~  166 (317)
                      .++.++++||++   .+....+..+.+.+++.  .+.+|++++  +...+...+.+|  +.++++.+.+.+++...+.+
T Consensus        98 ~~p~llilDEigp~~~ld~~~~~~l~~~l~~~--~~~~i~~~H~~h~~~~~~~i~~r~~~~i~~~~~~~r~~~~~~l~~  174 (178)
T 1ye8_A           98 DRRKVIIIDEIGKMELFSKKFRDLVRQIMHDP--NVNVVATIPIRDVHPLVKEIRRLPGAVLIELTPENRDVILEDILS  174 (178)
T ss_dssp             CTTCEEEECCCSTTGGGCHHHHHHHHHHHTCT--TSEEEEECCSSCCSHHHHHHHTCTTCEEEECCTTTTTTHHHHHHH
T ss_pred             cCCCEEEEeCCCCcccCCHHHHHHHHHHHhcC--CCeEEEEEccCCCchHHHHHHhcCCcEEEEecCcCHHHHHHHHHH
Confidence            467899999953   45677888999999872  344666664  455778888888  78899888887777665544

>1z6t_A APAF-1, apoptotic protease activating factor 1; caspase activation, ADP, nucleotide binding, CARD, apoptosis; HET: ADP; 2.21A {Homo sapiens}

Probab=98.68  E-value=3.8e-07  Score=85.96  Aligned_cols=177  Identities=15%  Similarity=0.152  Sum_probs=100.6

Q ss_pred             CCCCCcccCCHHHHHHHHHHHhc--CCCceEEEECCCCCCHHHHHHHHHHHHc--CCCCCCceEEecCCCCcChHHHHHH
Q psy879            6 PQTFSDIVGNEDTVERLKVFSSS--GNVPNIIISGPPGVGKTTTILCLARILL--GPSFKDAVLELNASNDRGIDTVRNK   81 (317)
Q Consensus         6 P~~~~~~~g~~~~~~~l~~~l~~--~~~~~~ll~G~~G~GKt~la~~la~~l~--~~~~~~~~~~~~~~~~~~~~~i~~~   81 (317)
                      |.....++|++..++.|...+..  +....++++|++|+|||++|..+++...  ...+...++.++.... ....+...
T Consensus       120 P~~~~~~vGR~~~l~~L~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~~~~f~~~v~wv~~~~~-~~~~~~~~  198 (591)
T 1z6t_A          120 PQRPVVFVTRKKLVNAIQQKLSKLKGEPGWVTIHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVSVGKQ-DKSGLLMK  198 (591)
T ss_dssp             CCCCSSCCCCHHHHHHHHHHHTTSTTSCEEEEEECCTTSSHHHHHHHHHCCHHHHHHHCTTCEEEEEEESC-CHHHHHHH
T ss_pred             CCCCCeecccHHHHHHHHHHHhcccCCCceEEEEcCCCCCHHHHHHHHHhchhHHHhhCCCceEEEECCCC-chHHHHHH
Confidence            66678899999999999999874  3334599999999999999999874310  0111111222222111 11111111


Q ss_pred             H----HHHHhhcc---cCC----------------CCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCc
Q psy879           82 I----KMFAQQKV---TLP----------------PGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEK  138 (317)
Q Consensus        82 ~----~~~~~~~~---~~~----------------~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~  138 (317)
                      +    ........   ..+                ..++-++|+|+++..  .       .++..++...+|+||....-
T Consensus       199 l~~l~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~LLVLDdv~~~--~-------~l~~l~~~~~ilvTsR~~~~  269 (591)
T 1z6t_A          199 LQNLCTRLDQDESFSQRLPLNIEEAKDRLRILMLRKHPRSLLILDDVWDS--W-------VLKAFDSQCQILLTTRDKSV  269 (591)
T ss_dssp             HHHHHHHHCSSCCSCSSCCCSHHHHHHHHHHHHHHTCTTCEEEEEEECCH--H-------HHHTTCSSCEEEEEESCGGG
T ss_pred             HHHHHHHhccccccccCCCCCHHHHHHHHHHHHccCCCCeEEEEeCCCCH--H-------HHHHhcCCCeEEEECCCcHH
Confidence            1    11100000   000                014579999999752  1       22333567778887765431


Q ss_pred             CchhHhhhcceeee---cCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHH
Q psy879          139 IIEPIQSRCAMLRY---NKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALN  196 (317)
Q Consensus       139 l~~~i~sR~~~i~f---~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~  196 (317)
                       .....  ...+.+   .+++.++..+.+...+.... .-.++....+++.++|.+-.+..
T Consensus       270 -~~~~~--~~~~~v~~l~~L~~~ea~~L~~~~~~~~~-~~~~~~~~~i~~~~~G~PLal~~  326 (591)
T 1z6t_A          270 -TDSVM--GPKYVVPVESSLGKEKGLEILSLFVNMKK-ADLPEQAHSIIKECKGSPLVVSL  326 (591)
T ss_dssp             -GTTCC--SCEEEEECCSSCCHHHHHHHHHHHHTSCG-GGSCTHHHHHHHHHTTCHHHHHH
T ss_pred             -HHhcC--CCceEeecCCCCCHHHHHHHHHHHhCCCc-ccccHHHHHHHHHhCCCcHHHHH
Confidence             11111  223333   48999999999988764311 11245678899999998764443

>2r2a_A Uncharacterized protein; zonular occludens toxin, structural genomics, APC84050.2, PS protein structure initiative; HET: MSE; 1.82A {Neisseria meningitidis MC58}

Probab=98.61  E-value=7.1e-08  Score=77.57  Aligned_cols=61  Identities=10%  Similarity=0.047  Sum_probs=44.0

Q ss_pred             CceeEEEEeCCCCCCHH---H--HHHHHHHhhhc-cCCceEEEEecCCCcCchhHhhhcce-eeecCC
Q psy879           95 GRHKIVILDEADSMTDG---A--QQALRRTMEIY-SNTTRFALACNNSEKIIEPIQSRCAM-LRYNKL  155 (317)
Q Consensus        95 ~~~~vliiDE~d~l~~~---~--~~~ll~~le~~-~~~~~~il~~~~~~~l~~~i~sR~~~-i~f~~~  155 (317)
                      +...|||||||+.+.+.   .  ...++..++.. .....+|++++++..+..++++|+.. +++.++
T Consensus        86 ~~~~vliIDEAq~l~~~~~~~~e~~rll~~l~~~r~~~~~iil~tq~~~~l~~~lr~ri~~~~~l~~~  153 (199)
T 2r2a_A           86 NIGSIVIVDEAQDVWPARSAGSKIPENVQWLNTHRHQGIDIFVLTQGPKLLDQNLRTLVRKHYHIASN  153 (199)
T ss_dssp             GTTCEEEETTGGGTSBCCCTTCCCCHHHHGGGGTTTTTCEEEEEESCGGGBCHHHHTTEEEEEEEEEC
T ss_pred             cCceEEEEEChhhhccCccccchhHHHHHHHHhcCcCCeEEEEECCCHHHHhHHHHHHhheEEEEcCc
Confidence            45789999999998321   1  11344555543 33456899999999999999999987 777764

>3sfz_A APAF-1, apoptotic peptidase activating factor 1; apoptosis, caspase activation, cytochrome C, procaspase-9, A nucleotide, cytosol; HET: ADP; 3.00A {Mus musculus} PDB: 3shf_A* 3iyt_A* 3iza_A*

Probab=98.49  E-value=2.8e-06  Score=86.63  Aligned_cols=177  Identities=15%  Similarity=0.136  Sum_probs=102.9

Q ss_pred             CCCCCcccCCHHHHHHHHHHHhc--CCCceEEEECCCCCCHHHHHHHHHHHH--cCCCCCCceEEecCCCCcChH---HH
Q psy879            6 PQTFSDIVGNEDTVERLKVFSSS--GNVPNIIISGPPGVGKTTTILCLARIL--LGPSFKDAVLELNASNDRGID---TV   78 (317)
Q Consensus         6 P~~~~~~~g~~~~~~~l~~~l~~--~~~~~~ll~G~~G~GKt~la~~la~~l--~~~~~~~~~~~~~~~~~~~~~---~i   78 (317)
                      |.....++|++..++.|...+..  +....+.|+|+.|+|||++|..+++..  ....+...++.++........   .+
T Consensus       120 p~~~~~~vgR~~~~~~l~~~l~~~~~~~~~v~i~G~gG~GKTtLa~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~  199 (1249)
T 3sfz_A          120 PQRPVIFVTRKKLVHAIQQKLWKLNGEPGWVTIYGMAGCGKSVLAAEAVRDHSLLEGCFSGGVHWVSIGKQDKSGLLMKL  199 (1249)
T ss_dssp             CCCCSSCCCCHHHHHHHHHHHHTTTTSCEEEEEECSTTSSHHHHHHHHTCCHHHHTTTSTTCEEEEECCSCCHHHHHHHH
T ss_pred             CCCCceeccHHHHHHHHHHHHhhccCCCCEEEEEeCCCCCHHHHHHHHhcChhHHHhhCCCeEEEEEECCcCchHHHHHH
Confidence            55567899999999999998853  333348999999999999999887642  122222233333332211111   11


Q ss_pred             HHHHHHHHhhcc-------------------cCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcC
Q psy879           79 RNKIKMFAQQKV-------------------TLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKI  139 (317)
Q Consensus        79 ~~~~~~~~~~~~-------------------~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l  139 (317)
                      ......+.....                   .....++-+||+|+++...         .++..++...+|+||....-.
T Consensus       200 ~~~~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~LlvlDd~~~~~---------~~~~~~~~~~ilvTtR~~~~~  270 (1249)
T 3sfz_A          200 QNLCMRLDQEESFSQRLPLNIEEAKDRLRVLMLRKHPRSLLILDDVWDPW---------VLKAFDNQCQILLTTRDKSVT  270 (1249)
T ss_dssp             HHHHHHHTTTCTTCSSCCSSHHHHHHHHHHHTSSSSCSCEEEEESCCCHH---------HHTTTCSSCEEEEEESSTTTT
T ss_pred             HHHHHHhhhhcccccCCCCCHHHHHHHHHHHHhccCCCEEEEEecCCCHH---------HHHhhcCCCEEEEEcCCHHHH
Confidence            111111111000                   0000236699999998531         233345677788888765321


Q ss_pred             chhHhhhcceeeecC-CCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHH
Q psy879          140 IEPIQSRCAMLRYNK-LTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQ  193 (317)
Q Consensus       140 ~~~i~sR~~~i~f~~-~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~  193 (317)
                       .........+...+ +++++..+.+...+....-. .++....+++.++|-+-.
T Consensus       271 -~~~~~~~~~~~~~~~l~~~~a~~l~~~~~~~~~~~-~~~~~~~i~~~~~glPLa  323 (1249)
T 3sfz_A          271 -DSVMGPKHVVPVESGLGREKGLEILSLFVNMKKED-LPAEAHSIIKECKGSPLV  323 (1249)
T ss_dssp             -TTCCSCBCCEECCSSCCHHHHHHHHHHHHTSCSTT-CCTHHHHHHHHTTTCHHH
T ss_pred             -HhhcCCceEEEecCCCCHHHHHHHHHHhhCCChhh-CcHHHHHHHHHhCCCHHH
Confidence             11122234477775 99999998888776432222 235677889999887653

>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor, microtubles, motor protein; HET: ADP SPM; 2.81A {Dictyostelium discoideum} PDB: 3vkh_A*

Probab=98.47  E-value=5.8e-06  Score=89.38  Aligned_cols=167  Identities=14%  Similarity=0.093  Sum_probs=114.3

Q ss_pred             HHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHHHHHHHhhcccCCCCce
Q psy879           18 TVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRH   97 (317)
Q Consensus        18 ~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~   97 (317)
                      ..-.|..++..+.  ...+.||+|||||.+++.+|+.+     +..++-+||+.......+...+....+.        +
T Consensus       593 cy~tl~~Al~~~~--gg~~~GPaGtGKTet~k~La~~l-----gr~~~vfnC~~~~d~~~~g~i~~G~~~~--------G  657 (3245)
T 3vkg_A          593 CYLTLTQALESRM--GGNPFGPAGTGKTETVKALGSQL-----GRFVLVFCCDEGFDLQAMSRIFVGLCQC--------G  657 (3245)
T ss_dssp             HHHHHHHHHHTTC--EEEEECSTTSSHHHHHHHHHHHT-----TCCEEEEECSSCCCHHHHHHHHHHHHHH--------T
T ss_pred             HHHHHHHHHHhcC--CCCCCCCCCCCHHHHHHHHHHHh-----CCeEEEEeCCCCCCHHHHHHHHhhHhhc--------C
Confidence            3445666776655  45789999999999999999997     3446778888777776666655555443        3


Q ss_pred             eEEEEeCCCCCCHHHHHHHHHHhh-------h--------------ccCCceEEEEecC----CCcCchhHhhhcceeee
Q psy879           98 KIVILDEADSMTDGAQQALRRTME-------I--------------YSNTTRFALACNN----SEKIIEPIQSRCAMLRY  152 (317)
Q Consensus        98 ~vliiDE~d~l~~~~~~~ll~~le-------~--------------~~~~~~~il~~~~----~~~l~~~i~sR~~~i~f  152 (317)
                      .-.++||++.+..+...++...+.       .              .++++.+++|.|+    ...+++.+++||..+.+
T Consensus       658 aW~cfDEfNrl~~~vLSvv~~qi~~I~~a~~~~~~~~~~~~G~~i~l~~~~~vfiTmNpgY~gr~eLP~nLk~lFr~v~m  737 (3245)
T 3vkg_A          658 AWGCFDEFNRLEERILSAVSQQIQTIQVALKENSKEVELLGGKNISLHQDMGIFVTMNPGYAGRSNLPDNLKKLFRSMAM  737 (3245)
T ss_dssp             CEEEEETTTSSCHHHHHHHHHHHHHHHHHHHHTCSEECCC---CEECCTTCEEEECBCCCGGGCCCSCHHHHTTEEEEEC
T ss_pred             cEEEehhhhcCCHHHHHHHHHHHHHHHHHHHcCCCeEEecCCCEEeecCCeEEEEEeCCCccCcccChHHHHhhcEEEEE
Confidence            467999999999988776655443       0              1234556666664    24799999999999999


Q ss_pred             cCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHH-----------hc--CCCHHHHHHHHHHhh
Q psy879          153 NKLTDAQLLSKVIEICEKENISHTNDGLEAIVF-----------TA--QGDMRQALNNLQSTH  202 (317)
Q Consensus       153 ~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~-----------~~--~gd~r~~i~~l~~~~  202 (317)
                      ..|+.+.+.+++..   .+|+.-......+++.           +.  +-.+|.+...|..+.
T Consensus       738 ~~Pd~~~i~ei~L~---s~Gf~~a~~La~k~~~~~~l~~e~LS~Q~HYDfGLRalKsVL~~AG  797 (3245)
T 3vkg_A          738 IKPDREMIAQVMLY---SQGFKTAEVLAGKIVPLFKLCQEQLSAQSHYDFGLRALKSVLVSAG  797 (3245)
T ss_dssp             CSCCHHHHHHHHHH---TTTCSCHHHHHHHHHHHHHHHHHSSCCCTTCCCSHHHHHHHHHHHH
T ss_pred             eCCCHHHHHHHHHH---HcccchHHHHHHHHHHHHHHHHHHhCCCCCCCCChHHHHHHHHHHH
Confidence            99999999888654   2355432333333331           11  235887777776554

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*

Probab=98.42  E-value=2.3e-07  Score=73.74  Aligned_cols=108  Identities=16%  Similarity=0.123  Sum_probs=58.6

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCC-CCc-ChHHHHHHH------------HHHHhhcccCCCCcee
Q psy879           33 NIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNAS-NDR-GIDTVRNKI------------KMFAQQKVTLPPGRHK   98 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~-~~~-~~~~i~~~~------------~~~~~~~~~~~~~~~~   98 (317)
                      .++++||+|+||||++..++..+......  ++.+.+. +.+ +...+....            ..+...    ...++.
T Consensus         5 i~vi~G~~gsGKTT~ll~~~~~~~~~g~~--v~~~~~~~d~r~~~~~i~s~~g~~~~~~~~~~~~~~~~~----~~~~~d   78 (184)
T 2orw_A            5 LTVITGPMYSGKTTELLSFVEIYKLGKKK--VAVFKPKIDSRYHSTMIVSHSGNGVEAHVIERPEEMRKY----IEEDTR   78 (184)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHHHTTCE--EEEEEEC-----CCCEECC----CEECEEESSGGGGGGG----CCTTEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCCe--EEEEeeccccccCcccEEecCCCceeeEEECCHHHHHHH----hcCCCC
Confidence            48899999999999997776655322221  1111110 000 000000000            000000    013578


Q ss_pred             EEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCC------CcCchhHhhhcce
Q psy879           99 IVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNS------EKIIEPIQSRCAM  149 (317)
Q Consensus        99 vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~------~~l~~~i~sR~~~  149 (317)
                      +|+|||+..+.++....|..+.+.   +..+|+++...      ....+.+.+++..
T Consensus        79 vviIDE~Q~~~~~~~~~l~~l~~~---~~~Vi~~Gl~~~f~~~~f~~~~~ll~~ad~  132 (184)
T 2orw_A           79 GVFIDEVQFFNPSLFEVVKDLLDR---GIDVFCAGLDLTHKQNPFETTALLLSLADT  132 (184)
T ss_dssp             EEEECCGGGSCTTHHHHHHHHHHT---TCEEEEEEESBCTTSCBCHHHHHHHHHCSE
T ss_pred             EEEEECcccCCHHHHHHHHHHHHC---CCCEEEEeeccccccCCccchHHHHHHhhh
Confidence            999999999987777777667664   45566665432      2445666777654

>2a5y_B CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis elegans} SCOP: a.4.5.80 a.77.1.3 c.37.1.20 PDB: 3lqq_A* 3lqr_A*

Probab=98.42  E-value=2e-06  Score=80.32  Aligned_cols=173  Identities=13%  Similarity=0.148  Sum_probs=97.8

Q ss_pred             cCCHHHHHHHHHHHhcC---CCceEEEECCCCCCHHHHHHHHHHH---HcCCCCCCceEEecCCCCc--ChHHH-HHHHH
Q psy879           13 VGNEDTVERLKVFSSSG---NVPNIIISGPPGVGKTTTILCLARI---LLGPSFKDAVLELNASNDR--GIDTV-RNKIK   83 (317)
Q Consensus        13 ~g~~~~~~~l~~~l~~~---~~~~~ll~G~~G~GKt~la~~la~~---l~~~~~~~~~~~~~~~~~~--~~~~i-~~~~~   83 (317)
                      +|.+..++.|..++..+   ....+.++|+.|+||||+|+.+++.   -....+. ....++.+...  +...+ ...+.
T Consensus       131 ~GR~~~~~~l~~~L~~~~~~~~~vv~I~G~gGvGKTtLA~~v~~~~~~~~~~~F~-~~~wv~vs~~~~~~~~~~~~~il~  209 (549)
T 2a5y_B          131 YIREYHVDRVIKKLDEMCDLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYD-SIVWLKDSGTAPKSTFDLFTDILL  209 (549)
T ss_dssp             CCCHHHHHHHHHHHHHHTTSSSEEEEEECSTTSSHHHHHHHHHHHCSSTBTTTBS-EEEEEECCCCSTTHHHHHHHHHHH
T ss_pred             CCchHHHHHHHHHHhcccCCCceEEEEEcCCCCCHHHHHHHHHHhhhHHHhccCC-cEEEEEECCCCCCCHHHHHHHHHH
Confidence            49999999998888654   3445999999999999999999972   2222232 22333333221  22221 22222


Q ss_pred             HHHhhcc--cC------------------CCCc-eeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcCchh
Q psy879           84 MFAQQKV--TL------------------PPGR-HKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEP  142 (317)
Q Consensus        84 ~~~~~~~--~~------------------~~~~-~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~~~  142 (317)
                      .+.....  ..                  -.++ +-+||+|+++....-   .+.   .  .+...+|+||.... +...
T Consensus       210 ~l~~~~~~~~~~~~~~~~~~~l~~~l~~~L~~~kr~LlVLDdv~~~~~~---~~~---~--~~gs~ilvTTR~~~-v~~~  280 (549)
T 2a5y_B          210 MLKSEDDLLNFPSVEHVTSVVLKRMICNALIDRPNTLFVFDDVVQEETI---RWA---Q--ELRLRCLVTTRDVE-ISNA  280 (549)
T ss_dssp             HHTTTSCCTTCCCCTTCCHHHHHHHHHHHHTTSTTEEEEEEEECCHHHH---HHH---H--HTTCEEEEEESBGG-GGGG
T ss_pred             HHhcCcccccccccccccHHHHHHHHHHHHcCCCcEEEEEECCCCchhh---ccc---c--cCCCEEEEEcCCHH-HHHH
Confidence            2211100  00                  0133 678999999883211   111   1  14566777776532 2211


Q ss_pred             HhhhcceeeecCCCHHHHHHHHHHHHHHcCC-CCCHHHHHHHHHhcCCCHHHHH
Q psy879          143 IQSRCAMLRYNKLTDAQLLSKVIEICEKENI-SHTNDGLEAIVFTAQGDMRQAL  195 (317)
Q Consensus       143 i~sR~~~i~f~~~~~~~~~~~l~~~~~~~~~-~i~~~~~~~l~~~~~gd~r~~i  195 (317)
                      .......+...+++.++..+.+...+..... .-.++....+++.++|.+-.+.
T Consensus       281 ~~~~~~~~~l~~L~~~ea~~Lf~~~a~~~~~~~~~~~~~~~I~~~c~GlPLAl~  334 (549)
T 2a5y_B          281 ASQTCEFIEVTSLEIDECYDFLEAYGMPMPVGEKEEDVLNKTIELSSGNPATLM  334 (549)
T ss_dssp             CCSCEEEEECCCCCHHHHHHHHHHTSCCCC--CHHHHHHHHHHHHHTTCHHHHH
T ss_pred             cCCCCeEEECCCCCHHHHHHHHHHHhcCCCCchhHHHHHHHHHHHhCCChHHHH
Confidence            1111245889999999999888886432111 0012356788899999776443

>2vhj_A Ntpase P4, P4; non- hydrolysable ATP analogue, hydrolase, virus dsRNA, molecular motor, packaging ATPase, hexameric helicase; HET: ADP; 1.80A {Pseudomonas phage PHI12} PDB: 2vhq_A* 1w44_A* 1w46_A* 1w47_A* 1w48_A* 1w49_A* 1w4a_A* 1w4b_A* 1w4c_A 2vht_A* 2vhu_A* 2vhc_A*

Probab=98.19  E-value=9.9e-06  Score=69.32  Aligned_cols=65  Identities=22%  Similarity=0.367  Sum_probs=38.7

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEe------cCCCCcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCC
Q psy879           34 IIISGPPGVGKTTTILCLARILLGPSFKDAVLEL------NASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADS  107 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~------~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~  107 (317)
                      ++|+||||+|||+++..++.. .+  ....++..      +... .+.+.+.+.+......       .. +||||+++.
T Consensus       126 iLI~GpPGsGKTtLAlqlA~~-~G--~~VlyIs~~~eE~v~~~~-~~le~~l~~i~~~l~~-------~~-LLVIDsI~a  193 (331)
T 2vhj_A          126 VIVTGKGNSGKTPLVHALGEA-LG--GKDKYATVRFGEPLSGYN-TDFNVFVDDIARAMLQ-------HR-VIVIDSLKN  193 (331)
T ss_dssp             EEEECSCSSSHHHHHHHHHHH-HH--TTSCCEEEEBSCSSTTCB-CCHHHHHHHHHHHHHH-------CS-EEEEECCTT
T ss_pred             EEEEcCCCCCHHHHHHHHHHh-CC--CCEEEEEecchhhhhhhh-cCHHHHHHHHHHHHhh-------CC-EEEEecccc
Confidence            799999999999999999986 22  22334444      2111 2233322222221111       12 999999998


Q ss_pred             CCH
Q psy879          108 MTD  110 (317)
Q Consensus       108 l~~  110 (317)
                      +..
T Consensus       194 L~~  196 (331)
T 2vhj_A          194 VIG  196 (331)
T ss_dssp             TC-
T ss_pred             ccc
Confidence            853

>2b8t_A Thymidine kinase; deoxyribonucleoside kinase, zinc-binding domain, TK1, UU-TK, transferase; HET: THM; 2.00A {Ureaplasma parvum} SCOP: c.37.1.24 g.39.1.14 PDB: 2uz3_A*

Probab=98.16  E-value=4e-06  Score=68.41  Aligned_cols=97  Identities=16%  Similarity=0.160  Sum_probs=54.4

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecC--------CCCcC-------hHHHHHHHHHHHhhcccCCCCce
Q psy879           33 NIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNA--------SNDRG-------IDTVRNKIKMFAQQKVTLPPGRH   97 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~--------~~~~~-------~~~i~~~~~~~~~~~~~~~~~~~   97 (317)
                      -++++||+|+||||++..++..+........++....        ....+       .....+.+..+...   .....+
T Consensus        14 i~litG~mGsGKTT~ll~~~~r~~~~g~kVli~~~~~d~r~~~~i~srlG~~~~~~~~~~~~~i~~~i~~~---~~~~~~   90 (223)
T 2b8t_A           14 IEFITGPMFAGKTAELIRRLHRLEYADVKYLVFKPKIDTRSIRNIQSRTGTSLPSVEVESAPEILNYIMSN---SFNDET   90 (223)
T ss_dssp             EEEEECSTTSCHHHHHHHHHHHHHHTTCCEEEEEECCCGGGCSSCCCCCCCSSCCEEESSTHHHHHHHHST---TSCTTC
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHhcCCEEEEEEeccCchHHHHHHHhcCCCccccccCCHHHHHHHHHHH---hhCCCC
Confidence            4899999999999999998887743332222221000        00001       00111222222111   112457


Q ss_pred             eEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecC
Q psy879           98 KIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNN  135 (317)
Q Consensus        98 ~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~  135 (317)
                      .+|+|||+..+..+....+..+.+   ....+|++...
T Consensus        91 dvViIDEaQ~l~~~~ve~l~~L~~---~gi~Vil~Gl~  125 (223)
T 2b8t_A           91 KVIGIDEVQFFDDRICEVANILAE---NGFVVIISGLD  125 (223)
T ss_dssp             CEEEECSGGGSCTHHHHHHHHHHH---TTCEEEEECCS
T ss_pred             CEEEEecCccCcHHHHHHHHHHHh---CCCeEEEEecc
Confidence            899999999998775555544333   25777887763

>1g5t_A COB(I)alamin adenosyltransferase; P-loop protein, cobalamin biosynthesis, RECA fold; HET: ATP; 1.80A {Salmonella typhimurium} SCOP: c.37.1.11 PDB: 1g5r_A* 1g64_A*

Probab=98.08  E-value=1.3e-05  Score=63.68  Aligned_cols=106  Identities=17%  Similarity=0.169  Sum_probs=63.7

Q ss_pred             ceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCC-CcChH--------------------------HHHHHHHH
Q psy879           32 PNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASN-DRGID--------------------------TVRNKIKM   84 (317)
Q Consensus        32 ~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~-~~~~~--------------------------~i~~~~~~   84 (317)
                      ..+++|+++|.||||+|-.++-...+.+....++.+.... ..+..                          +.......
T Consensus        29 g~i~v~tG~GkGKTTaA~GlalRA~g~G~rV~~vQF~Kg~~~~gE~~~l~~L~v~~~~~g~gf~~~~~~~~~~~~~a~~~  108 (196)
T 1g5t_A           29 GIIIVFTGNGKGKTTAAFGTAARAVGHGKNVGVVQFIKGTWPNGERNLLEPHGVEFQVMATGFTWETQNREADTAACMAV  108 (196)
T ss_dssp             CCEEEEESSSSCHHHHHHHHHHHHHHTTCCEEEEESSCCSSCCHHHHHHGGGTCEEEECCTTCCCCGGGHHHHHHHHHHH
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEEeeCCCCCccHHHHHHhCCcEEEEcccccccCCCCcHHHHHHHHHH
Confidence            3589999999999999999998776555444343322210 00000                          01111111


Q ss_pred             HHhhcccCCCCceeEEEEeCCCCCCH---HHHHHHHHHhhhccCCceEEEEecCCC
Q psy879           85 FAQQKVTLPPGRHKIVILDEADSMTD---GAQQALRRTMEIYSNTTRFALACNNSE  137 (317)
Q Consensus        85 ~~~~~~~~~~~~~~vliiDE~d~l~~---~~~~~ll~~le~~~~~~~~il~~~~~~  137 (317)
                      +......+..+.+.+||+||+.....   -..+.++.++...|....+|+|++...
T Consensus       109 l~~a~~~l~~~~yDlvILDEi~~al~~g~l~~~ev~~~l~~Rp~~~~vIlTGr~ap  164 (196)
T 1g5t_A          109 WQHGKRMLADPLLDMVVLDELTYMVAYDYLPLEEVISALNARPGHQTVIITGRGCH  164 (196)
T ss_dssp             HHHHHHHTTCTTCSEEEEETHHHHHHTTSSCHHHHHHHHHTSCTTCEEEEECSSCC
T ss_pred             HHHHHHHHhcCCCCEEEEeCCCccccCCCCCHHHHHHHHHhCcCCCEEEEECCCCc
Confidence            11111122346799999999954211   123457888888889999999998853

>2i3b_A HCR-ntpase, human cancer-related ntpase; AAA, rossmann, hydrolase; NMR {Homo sapiens} SCOP: c.37.1.11

Probab=98.00  E-value=3.3e-05  Score=61.45  Aligned_cols=70  Identities=20%  Similarity=0.322  Sum_probs=43.8

Q ss_pred             CceeEEEEeCCCCC---CHHHHHHHHHHhhhccCCceEE--EE-ecCC-CcCchhHhhh--cceeeecCCCHHHHHHHHH
Q psy879           95 GRHKIVILDEADSM---TDGAQQALRRTMEIYSNTTRFA--LA-CNNS-EKIIEPIQSR--CAMLRYNKLTDAQLLSKVI  165 (317)
Q Consensus        95 ~~~~vliiDE~d~l---~~~~~~~ll~~le~~~~~~~~i--l~-~~~~-~~l~~~i~sR--~~~i~f~~~~~~~~~~~l~  165 (317)
                      .++.++|+||++.+   ......++.++++.+  .+.++  ++ +++. ..+.+.+..+  +.++.+.+-+.+.+..-+.
T Consensus       104 ~~~dvlilDE~g~~~~~~~~~~~~l~~~l~~~--~~~ilgti~vsh~~~~~~vd~i~~~~~~~i~~~~~~nr~~~~~~i~  181 (189)
T 2i3b_A          104 PGQRVCVIDEIGKMELFSQLFIQAVRQTLSTP--GTIILGTIPVPKGKPLALVEEIRNRKDVKVFNVTKENRNHLLPDIV  181 (189)
T ss_dssp             SCCCCEEECCCSTTTTTCSHHHHHHHHHHHCS--SCCEEEECCCCCSSCCTTHHHHHTTCCSEEEECCSSSGGGHHHHHH
T ss_pred             cCCCEEEEeCCCccccccHHHHHHHHHHHhCC--CcEEEEEeecCCCCchHHHHHHeecCCcEEEEeChHhHHHHHHHHH
Confidence            56789999998776   345677788888753  23333  22 2332 3566777664  4567777766666665554


Q ss_pred             H
Q psy879          166 E  166 (317)
Q Consensus       166 ~  166 (317)
                      +
T Consensus       182 ~  182 (189)
T 2i3b_A          182 T  182 (189)
T ss_dssp             H
T ss_pred             H
Confidence            4

>1jql_B DNA polymerase III, delta subunit; processivity clamp, clamp loader, DNA replication, AAA+ ATPase, transferase; HET: DNA; 2.50A {Escherichia coli} SCOP: c.37.1.20

Probab=97.99  E-value=4.9e-05  Score=57.32  Aligned_cols=122  Identities=6%  Similarity=0.103  Sum_probs=75.2

Q ss_pred             HHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCC-ceEEecCCCCcChHHHHHHHHHHHhhcccCCCCceeEEE
Q psy879           23 KVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKD-AVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVI  101 (317)
Q Consensus        23 ~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~-~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~vli  101 (317)
                      ...++++-.|.|+|||+.-.-....+..+.+.+...+... .++.++.  ...   +.+.+......+++   +++++|+
T Consensus        10 ~~~l~~~~~pvyll~G~E~~l~~~~~~~i~~~~~~~~~~e~~~~~~~~--~~~---~~~l~~~~~s~slF---~~rrlV~   81 (140)
T 1jql_B           10 RAQLNEGLRAAYLLLGNDPLLLQESQDAVRQVAAAQGFEEHHTFSIDP--NTD---WNAIFSLCQAMSLF---ASRQTLL   81 (140)
T ss_dssp             HHHHHHCCCSEEEEESSCHHHHHHHHHHHHHHHHHTTCCEEECCCCST--TCC---HHHHHHHHHCCCTT---CCCEEEE
T ss_pred             HHHHhccCCceEEEEcCcHHHHHHHHHHHHHHHHHCCCcceeEEEecC--CCC---HHHHHHHHhcCCCC---CCCEEEE
Confidence            3444445455699999996556666666666554322111 1222222  123   33444444444433   7899999


Q ss_pred             EeCCCC-CCHHHHHHHHHHhhhccCCceEEEEecCCC------cCchhHhhhcceeee
Q psy879          102 LDEADS-MTDGAQQALRRTMEIYSNTTRFALACNNSE------KIIEPIQSRCAMLRY  152 (317)
Q Consensus       102 iDE~d~-l~~~~~~~ll~~le~~~~~~~~il~~~~~~------~l~~~i~sR~~~i~f  152 (317)
                      |.+++. +.++....|..+++.|++.+++|++....+      ++.+++.+.+..+.|
T Consensus        82 v~~~~~~~~~~~~~~L~~yl~~p~~~~~lvi~~~kld~~~~~~k~~k~l~k~g~~v~~  139 (140)
T 1jql_B           82 LLLPENGPNAAINEQLLTLTGLLHDDLLLIVRGNKLSKAQENAAWFTALANRSVQVTC  139 (140)
T ss_dssp             EECCTTCSCTTHHHHHHHHHHHCCSSCCEEEECSSCCTTGGGSHHHHHHGGGCEEEEC
T ss_pred             EECCCCCCChHHHHHHHHHHhcCCCCEEEEEEeCCcChhHHhhHHHHHHHhCeEEEEe
Confidence            999765 666778889999999999999999875432      456666666655544

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A*

Probab=97.98  E-value=7e-05  Score=73.59  Aligned_cols=146  Identities=16%  Similarity=0.163  Sum_probs=80.1

Q ss_pred             cCCHHHHHHHHHHHhc-CCCceEEEECCCCCCHHHHHHHHHHHH-cCCCCCCceEEecCCCCcChHHHHHHHHHH-Hh--
Q psy879           13 VGNEDTVERLKVFSSS-GNVPNIIISGPPGVGKTTTILCLARIL-LGPSFKDAVLELNASNDRGIDTVRNKIKMF-AQ--   87 (317)
Q Consensus        13 ~g~~~~~~~l~~~l~~-~~~~~~ll~G~~G~GKt~la~~la~~l-~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~-~~--   87 (317)
                      +|++..++.|..++.. ...+.+.++|+.|+||||+|+.+++.. ....+...++.++.+.......+...+... ..  
T Consensus       131 VGRe~eLeeL~elL~~~d~~RVV~IvGmGGIGKTTLAk~Vy~d~rV~~~Fd~gV~WVsVs~~~d~~~IL~~Ll~lL~~i~  210 (1221)
T 1vt4_I          131 VSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQID  210 (1221)
T ss_dssp             CCCHHHHHHHHHHHHHCCSSCEEEECCSTTSSHHHHHHHHHHHCHHHHHHSSCEEEEECCCSSSHHHHHHHHHHHHHHHC
T ss_pred             CCcHHHHHHHHHHHhccCCCeEEEEEcCCCccHHHHHHHHHHhhHHHHhCCCcEEEEEeCCCCCHHHHHHHHHHHHhhcC
Confidence            8999999999988875 334459999999999999999998531 011112212323322222222211111100 00  


Q ss_pred             -------------------------hcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcCchh
Q psy879           88 -------------------------QKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEP  142 (317)
Q Consensus        88 -------------------------~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~~~  142 (317)
                                               .......+++-+||+|+++.  .+..    +.+   ++...+|+||...... ..
T Consensus       211 ~~~~~~~d~~~~ip~~leeL~e~Lr~lL~~l~~KRvLLVLDDVwd--~eqL----e~f---~pGSRILVTTRd~~Va-~~  280 (1221)
T 1vt4_I          211 PNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQN--AKAW----NAF---NLSCKILLTTRFKQVT-DF  280 (1221)
T ss_dssp             SSSTTTSCCCSSHHHHHHHHHHHHHHHHHHSTTSSCEEEEESCCC--HHHH----HHH---HSSCCEEEECSCSHHH-HH
T ss_pred             cccccccccccCCCCCHHHHHHHHHHHHHhhcCCCEEEEEeCcCh--HHHH----Hhh---CCCeEEEEeccChHHH-Hh
Confidence                                     00000124567999999988  2222    222   3567778877654321 11


Q ss_pred             Hhhh-cceeeec----CCCHHHHHHHHHHHH
Q psy879          143 IQSR-CAMLRYN----KLTDAQLLSKVIEIC  168 (317)
Q Consensus       143 i~sR-~~~i~f~----~~~~~~~~~~l~~~~  168 (317)
                      +... ...+.++    ++++++..+.+...+
T Consensus       281 l~g~~vy~LeL~d~dL~LS~eEA~eLF~~~~  311 (1221)
T 1vt4_I          281 LSAATTTHISLDHHSMTLTPDEVKSLLLKYL  311 (1221)
T ss_dssp             HHHHSSCEEEECSSSSCCCHHHHHHHHHHHH
T ss_pred             cCCCeEEEecCccccCCcCHHHHHHHHHHHc
Confidence            1111 1224433    789999999887764

>3e1s_A Exodeoxyribonuclease V, subunit RECD; alpha and beta protein, ATP-binding, nucleotide-binding, HYD; 2.20A {Deinococcus radiodurans} PDB: 3gp8_A 3gpl_A*

Probab=97.94  E-value=7.8e-06  Score=76.39  Aligned_cols=113  Identities=19%  Similarity=0.249  Sum_probs=66.3

Q ss_pred             CHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHHHH-------HHHh
Q psy879           15 NEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIK-------MFAQ   87 (317)
Q Consensus        15 ~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~~-------~~~~   87 (317)
                      .+...+.+...+.+   +.+++.||||||||+++..++..+....  ..+.-..+ +......+.+.++       .+..
T Consensus       191 ~~~Q~~Av~~~~~~---~~~~I~G~pGTGKTt~i~~l~~~l~~~g--~~Vl~~Ap-T~~Aa~~L~e~~~~~a~Tih~ll~  264 (574)
T 3e1s_A          191 SEEQASVLDQLAGH---RLVVLTGGPGTGKSTTTKAVADLAESLG--LEVGLCAP-TGKAARRLGEVTGRTASTVHRLLG  264 (574)
T ss_dssp             CHHHHHHHHHHTTC---SEEEEECCTTSCHHHHHHHHHHHHHHTT--CCEEEEES-SHHHHHHHHHHHTSCEEEHHHHTT
T ss_pred             CHHHHHHHHHHHhC---CEEEEEcCCCCCHHHHHHHHHHHHHhcC--CeEEEecC-cHHHHHHhHhhhcccHHHHHHHHc
Confidence            34555555555532   3699999999999999999998875432  22332322 2222222222111       1100


Q ss_pred             h-c--c---cCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCC
Q psy879           88 Q-K--V---TLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNS  136 (317)
Q Consensus        88 ~-~--~---~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~  136 (317)
                      . +  +   ........+|||||+..+.......|++.+   +....+|++....
T Consensus       265 ~~~~~~~~~~~~~~~~dvlIIDEasml~~~~~~~Ll~~~---~~~~~lilvGD~~  316 (574)
T 3e1s_A          265 YGPQGFRHNHLEPAPYDLLIVDEVSMMGDALMLSLLAAV---PPGARVLLVGDTD  316 (574)
T ss_dssp             EETTEESCSSSSCCSCSEEEECCGGGCCHHHHHHHHTTS---CTTCEEEEEECTT
T ss_pred             CCcchhhhhhcccccCCEEEEcCccCCCHHHHHHHHHhC---cCCCEEEEEeccc
Confidence            0 0  0   001125679999999999988777776655   3667788887653

>3nh6_A ATP-binding cassette SUB-family B member 6, mitoc; ABC-transporter, ABCB6, nucleotide binding domain, heme BIOS transport protein; 2.00A {Homo sapiens} PDB: 3nh9_A* 3nha_A* 3nhb_A*

Probab=97.94  E-value=2.4e-06  Score=73.25  Aligned_cols=42  Identities=17%  Similarity=0.289  Sum_probs=30.1

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhccCCceEEEEecCCC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYSNTTRFALACNNSE  137 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~~~~~~il~~~~~~  137 (317)
                      +++++|+||+-. |.......+.+.+.+......+|++|++..
T Consensus       208 ~p~iLlLDEPts~LD~~~~~~i~~~l~~l~~~~Tvi~itH~l~  250 (306)
T 3nh6_A          208 APGIILLDEATSALDTSNERAIQASLAKVCANRTTIVVAHRLS  250 (306)
T ss_dssp             CCSEEEEECCSSCCCHHHHHHHHHHHHHHHTTSEEEEECCSHH
T ss_pred             CCCEEEEECCcccCCHHHHHHHHHHHHHHcCCCEEEEEEcChH
Confidence            578999999975 566667777777766544556777787643

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=97.94  E-value=3.2e-05  Score=80.76  Aligned_cols=26  Identities=31%  Similarity=0.291  Sum_probs=22.9

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHcCC
Q psy879           33 NIIISGPPGVGKTTTILCLARILLGP   58 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~~~   58 (317)
                      +++|+||||||||++|.+++.+....
T Consensus      1429 ~vll~GppGtGKT~LA~ala~ea~~~ 1454 (2050)
T 3cmu_A         1429 IVEIYGPESSGKTTLTLQVIAAAQRE 1454 (2050)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHHTT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHc
Confidence            59999999999999999999886443

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=97.91  E-value=4e-05  Score=62.72  Aligned_cols=24  Identities=38%  Similarity=0.462  Sum_probs=21.4

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHc
Q psy879           33 NIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      .++++||+|+||||+++.++..+.
T Consensus        25 ~~~i~G~~GsGKTtl~~~l~~~~~   48 (235)
T 2w0m_A           25 FIALTGEPGTGKTIFSLHFIAKGL   48 (235)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHH
Confidence            489999999999999999997653

>2ff7_A Alpha-hemolysin translocation ATP-binding protein HLYB; ABC-transporter, transport protein; HET: ADP; 1.60A {Escherichia coli} SCOP: c.37.1.12 PDB: 2ffb_A* 2fgk_A* 2ffa_A* 2fgj_A* 2pmk_A* 3b5j_A* 1mt0_A 1xef_A*

Probab=97.88  E-value=8.3e-06  Score=67.87  Aligned_cols=42  Identities=21%  Similarity=0.314  Sum_probs=31.0

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhccCCceEEEEecCCC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYSNTTRFALACNNSE  137 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~~~~~~il~~~~~~  137 (317)
                      +++++++||... |.......+.+.+.+......+|++|++..
T Consensus       163 ~p~lllLDEPts~LD~~~~~~i~~~l~~~~~g~tviivtH~~~  205 (247)
T 2ff7_A          163 NPKILIFDEATSALDYESEHVIMRNMHKICKGRTVIIIAHRLS  205 (247)
T ss_dssp             CCSEEEECCCCSCCCHHHHHHHHHHHHHHHTTSEEEEECSSGG
T ss_pred             CCCEEEEeCCcccCCHHHHHHHHHHHHHHcCCCEEEEEeCCHH
Confidence            678999999975 566777777777766544566777887754

>2eyu_A Twitching motility protein PILT; pilus retraction motor, C-terminal domain PILT, protein transport; 1.87A {Aquifex aeolicus}

Probab=97.84  E-value=9.2e-05  Score=62.04  Aligned_cols=46  Identities=28%  Similarity=0.369  Sum_probs=31.9

Q ss_pred             CCCCCcccCCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHc
Q psy879            6 PQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus         6 P~~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      +-+++++--. .+++.+.  +..|.  .+++.||+|+||||+++.++..+.
T Consensus         5 ~~~l~~l~~~-~vl~~i~--i~~g~--~v~i~Gp~GsGKSTll~~l~g~~~   50 (261)
T 2eyu_A            5 IPEFKKLGLP-DKVLELC--HRKMG--LILVTGPTGSGKSTTIASMIDYIN   50 (261)
T ss_dssp             -CCGGGSSCC-THHHHGG--GCSSE--EEEEECSTTCSHHHHHHHHHHHHH
T ss_pred             CCChHHCCCH-HHHHHHh--hCCCC--EEEEECCCCccHHHHHHHHHHhCC
Confidence            3345554333 4555554  44443  599999999999999999999864

>2r8r_A Sensor protein; KDPD, PFAM02702, MCSG, structural genomics, protein structure initiative, midwest center for structural genomics, kinase; 2.30A {Pseudomonas syringae PV}

Probab=97.83  E-value=6.9e-05  Score=60.79  Aligned_cols=128  Identities=18%  Similarity=0.230  Sum_probs=74.0

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHHHHHHHhhc-------------ccC---CCCc
Q psy879           33 NIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFAQQK-------------VTL---PPGR   96 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~-------------~~~---~~~~   96 (317)
                      ++++.|++|+||||++..++..+...+....+..+++...  ... ...+......+             ...   -...
T Consensus         8 ~I~~~~kgGvGKTt~a~~la~~l~~~G~~V~v~d~D~q~~--~~~-~al~~gl~~~~~~~~~~~~~~~~e~~l~~~L~~~   84 (228)
T 2r8r_A            8 KVFLGAAPGVGKTYAMLQAAHAQLRQGVRVMAGVVETHGR--AET-EALLNGLPQQPLLRTEYRGMTLEEMDLDALLKAA   84 (228)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHHHHHTTCCEEEEECCCTTC--HHH-HHHHTTSCBCCCEEEEETTEEEEECCHHHHHHHC
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHHCCCCEEEEEeCCCCC--hhH-HHHhcCccccCcceeecCCcccccccHHHHHhcC
Confidence            4999999999999999999988754433333344433211  110 00111000000             000   0024


Q ss_pred             eeEEEEeCCCCCCHH------HHHHHHHHhhhccCCceEEEEecCC------------------CcCchhHhhhcceeee
Q psy879           97 HKIVILDEADSMTDG------AQQALRRTMEIYSNTTRFALACNNS------------------EKIIEPIQSRCAMLRY  152 (317)
Q Consensus        97 ~~vliiDE~d~l~~~------~~~~ll~~le~~~~~~~~il~~~~~------------------~~l~~~i~sR~~~i~f  152 (317)
                      +.++||||+......      ....+..   ..+...-++.++|-.                  +.++..+..++..+.+
T Consensus        85 pdlvIVDElG~~~~~~~r~~~~~qDV~~---~l~sgidVitT~Nlqh~esl~d~v~~itg~~v~e~vpd~~~~~a~~v~l  161 (228)
T 2r8r_A           85 PSLVLVDELAHTNAPGSRHTKRWQDIQE---LLAAGIDVYTTVNVQHLESLNDQVRGITGVQVRETLPDWVLQEAFDLVL  161 (228)
T ss_dssp             CSEEEESCTTCBCCTTCSSSBHHHHHHH---HHHTTCEEEEEEEGGGBGGGHHHHHHHHSCCCCSCBCHHHHHTCSEEEE
T ss_pred             CCEEEEeCCCCCCcccchhHHHHHHHHH---HHcCCCCEEEEccccccccHHHHHHHHcCCCcCCcCccHHHhhCCeEEE
Confidence            679999998875221      1222222   334555677777622                  2467788888888888


Q ss_pred             cCCCHHHHHHHHHH
Q psy879          153 NKLTDAQLLSKVIE  166 (317)
Q Consensus       153 ~~~~~~~~~~~l~~  166 (317)
                      -..+++++.+.+..
T Consensus       162 vD~~p~~l~~rl~~  175 (228)
T 2r8r_A          162 IDLPPRELLERLRD  175 (228)
T ss_dssp             BCCCHHHHHHHHHT
T ss_pred             ecCCHHHHHHHHHC
Confidence            88899988887655

>2cvh_A DNA repair and recombination protein RADB; filament formation, homologous recombination, ATPase domain, hyperthermophIle; HET: DNA; 2.20A {Thermococcus kodakarensis} PDB: 2cvf_A*

Probab=97.83  E-value=0.00014  Score=58.86  Aligned_cols=21  Identities=33%  Similarity=0.281  Sum_probs=19.8

Q ss_pred             eEEEECCCCCCHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLAR   53 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~   53 (317)
                      .++++||||+||||+++.++.
T Consensus        22 ~~~i~G~~GsGKTtl~~~l~~   42 (220)
T 2cvh_A           22 LTQVYGPYASGKTTLALQTGL   42 (220)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            389999999999999999998

>1w36_D RECD, exodeoxyribonuclease V alpha chain; recombination, helicase, hydrolase, DNA repair; HET: DNA; 3.1A {Escherichia coli} SCOP: c.37.1.19 c.37.1.19 PDB: 3k70_D*

Probab=97.81  E-value=0.0001  Score=69.47  Aligned_cols=100  Identities=18%  Similarity=0.238  Sum_probs=57.7

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHcCC--CCCCceEEecCCCCcChHHHHHHHHHHHh-----------------h--cc-
Q psy879           33 NIIISGPPGVGKTTTILCLARILLGP--SFKDAVLELNASNDRGIDTVRNKIKMFAQ-----------------Q--KV-   90 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~~~--~~~~~~~~~~~~~~~~~~~i~~~~~~~~~-----------------~--~~-   90 (317)
                      .++++|+||||||+++..+...+...  ..+..+.-..+ +..-...+.+.+.....                 +  .. 
T Consensus       166 ~~vi~G~pGTGKTt~l~~ll~~l~~~~~~~~~~vll~AP-Tg~AA~~L~e~~~~~~~~l~l~~~~~~~~~~~~~Tih~ll  244 (608)
T 1w36_D          166 ISVISGGPGTGKTTTVAKLLAALIQMADGERCRIRLAAP-TGKAAARLTESLGKALRQLPLTDEQKKRIPEDASTLHRLL  244 (608)
T ss_dssp             EEEEECCTTSTHHHHHHHHHHHHHHTCSSCCCCEEEEBS-SHHHHHHHHHHHTHHHHHSSCCSCCCCSCSCCCBTTTSCC
T ss_pred             CEEEEeCCCCCHHHHHHHHHHHHHHhhhcCCCeEEEEeC-ChhHHHHHHHHHHHHHhcCCCCHHHHhccchhhhhhHhhh
Confidence            69999999999999999888776421  11222332222 22222333333222100                 0  00 


Q ss_pred             ------------cCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCC
Q psy879           91 ------------TLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNS  136 (317)
Q Consensus        91 ------------~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~  136 (317)
                                  ........++||||++.+.......|++.+   +....+|++....
T Consensus       245 ~~~~~~~~~~~~~~~~l~~d~lIIDEAsml~~~~~~~Ll~~l---~~~~~liLvGD~~  299 (608)
T 1w36_D          245 GAQPGSQRLRHHAGNPLHLDVLVVDEASMIDLPMMSRLIDAL---PDHARVIFLGDRD  299 (608)
T ss_dssp             -----------CTTSCCSCSEEEECSGGGCBHHHHHHHHHTC---CTTCEEEEEECTT
T ss_pred             ccCCCchHHHhccCCCCCCCEEEEechhhCCHHHHHHHHHhC---CCCCEEEEEcchh
Confidence                        000014569999999988876666665544   5677888887653

>3tif_A Uncharacterized ABC transporter ATP-binding prote; nucleotide-binding domain, ABC transporter ATPase; HET: ADP; 1.80A {Methanocaldococcus jannaschii dsm 2661ORGANISM_TAXID} PDB: 1l2t_A* 1f3o_A*

Probab=97.78  E-value=1.7e-05  Score=65.43  Aligned_cols=42  Identities=5%  Similarity=0.174  Sum_probs=31.7

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhccC--CceEEEEecCCC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYSN--TTRFALACNNSE  137 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~~--~~~~il~~~~~~  137 (317)
                      +++++++||.-. |.+.....+.+.+.+...  ...+|++|++.+
T Consensus       163 ~p~llllDEPts~LD~~~~~~i~~~l~~l~~~~g~tvi~vtHd~~  207 (235)
T 3tif_A          163 NPPIILADQPTWALDSKTGEKIMQLLKKLNEEDGKTVVVVTHDIN  207 (235)
T ss_dssp             CCSEEEEESTTTTSCHHHHHHHHHHHHHHHHHHCCEEEEECSCHH
T ss_pred             CCCEEEEeCCcccCCHHHHHHHHHHHHHHHHHcCCEEEEEcCCHH
Confidence            689999999985 567778888888876532  456788888754

>2pt7_A CAG-ALFA; ATPase, protein-protein complex, type IV secretion, hydrolas binding complex; 2.40A {Helicobacter pylori} SCOP: c.37.1.11 PDB: 1nly_A* 1nlz_A 1opx_A* 1g6o_A

Probab=97.78  E-value=0.00034  Score=60.64  Aligned_cols=37  Identities=30%  Similarity=0.450  Sum_probs=31.7

Q ss_pred             HHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHc
Q psy879           18 TVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        18 ~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      +.+.+.-.+..|.  .+++.||+|+||||++++++..+.
T Consensus       160 ~l~~l~~~i~~g~--~v~i~G~~GsGKTTll~~l~g~~~  196 (330)
T 2pt7_A          160 AISAIKDGIAIGK--NVIVCGGTGSGKTTYIKSIMEFIP  196 (330)
T ss_dssp             HHHHHHHHHHHTC--CEEEEESTTSCHHHHHHHGGGGSC
T ss_pred             HHhhhhhhccCCC--EEEEECCCCCCHHHHHHHHhCCCc
Confidence            5667777787787  799999999999999999998763

>4gp7_A Metallophosphoesterase; polynucleotide kinase phosphatase, RNA repair, transferase; HET: ATP CIT; 2.00A {Clostridium thermocellum} PDB: 4gp6_A*

Probab=97.77  E-value=8.6e-05  Score=57.98  Aligned_cols=17  Identities=29%  Similarity=0.509  Sum_probs=16.2

Q ss_pred             eEEEECCCCCCHHHHHH
Q psy879           33 NIIISGPPGVGKTTTIL   49 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~   49 (317)
                      .+.+.||+|+||||+++
T Consensus        11 i~~l~G~nGsGKSTl~~   27 (171)
T 4gp7_A           11 LVVLIGSSGSGKSTFAK   27 (171)
T ss_dssp             EEEEECCTTSCHHHHHH
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            48999999999999999

>3gfo_A Cobalt import ATP-binding protein CBIO 1; structural genomics, cell membrane, cobalt transport, hydrolase, ION transport; 2.30A {Clostridium perfringens atcc 13124}

Probab=97.75  E-value=9.8e-06  Score=68.44  Aligned_cols=43  Identities=14%  Similarity=0.202  Sum_probs=31.7

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhcc--CCceEEEEecCCCc
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYS--NTTRFALACNNSEK  138 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~--~~~~~il~~~~~~~  138 (317)
                      +++++|+||.-. |.+..+..+.+.+.+..  ....+|++|++.+.
T Consensus       161 ~P~lLlLDEPts~LD~~~~~~i~~~l~~l~~~~g~tvi~vtHdl~~  206 (275)
T 3gfo_A          161 EPKVLILDEPTAGLDPMGVSEIMKLLVEMQKELGITIIIATHDIDI  206 (275)
T ss_dssp             CCSEEEEECTTTTCCHHHHHHHHHHHHHHHHHHCCEEEEEESCCSS
T ss_pred             CCCEEEEECccccCCHHHHHHHHHHHHHHHhhCCCEEEEEecCHHH
Confidence            689999999975 67777788888776543  24567788877554

>3tui_C Methionine import ATP-binding protein METN; ABC-transporter, type I ABC type importer, methionine uptake transporter, membrane protein; HET: ADP; 2.90A {Escherichia coli} PDB: 3tuj_C 3tuz_C* 3dhw_C

Probab=97.75  E-value=1.7e-05  Score=69.43  Aligned_cols=41  Identities=12%  Similarity=0.190  Sum_probs=30.8

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhcc--CCceEEEEecCC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYS--NTTRFALACNNS  136 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~--~~~~~il~~~~~  136 (317)
                      +++++++||.-. |.+..+..+++++.+..  ....+|++|++.
T Consensus       181 ~P~lLLlDEPTs~LD~~~~~~i~~lL~~l~~~~g~Tii~vTHdl  224 (366)
T 3tui_C          181 NPKVLLCDQATSALDPATTRSILELLKDINRRLGLTILLITHEM  224 (366)
T ss_dssp             CCSEEEEESTTTTSCHHHHHHHHHHHHHHHHHSCCEEEEEESCH
T ss_pred             CCCEEEEECCCccCCHHHHHHHHHHHHHHHHhCCCEEEEEecCH
Confidence            689999999975 56777888888877653  245678888764

>3jvv_A Twitching mobility protein; hexameric P-loop ATPase, secretion ATPase, ATP-binding, FIMB nucleotide-binding, transport; HET: ACP CIT; 2.60A {Pseudomonas aeruginosa} PDB: 3jvu_A*

Probab=97.74  E-value=0.0003  Score=61.57  Aligned_cols=114  Identities=14%  Similarity=0.209  Sum_probs=61.5

Q ss_pred             CCCCCcccCCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecC-CC-------------
Q psy879            6 PQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNA-SN-------------   71 (317)
Q Consensus         6 P~~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~-~~-------------   71 (317)
                      +.+++++...+ ++..+  ....+.  .+++.||+|+||||+.++++..+...... .++.+.. ..             
T Consensus       103 ~~~l~~lg~~~-~l~~l--~~~~~g--~i~I~GptGSGKTTlL~~l~g~~~~~~~~-~i~t~ed~~e~~~~~~~~~v~q~  176 (356)
T 3jvv_A          103 VLTMEELGMGE-VFKRV--SDVPRG--LVLVTGPTGSGKSTTLAAMLDYLNNTKYH-HILTIEDPIEFVHESKKCLVNQR  176 (356)
T ss_dssp             CCCTTTTTCCH-HHHHH--HHCSSE--EEEEECSTTSCHHHHHHHHHHHHHHHCCC-EEEEEESSCCSCCCCSSSEEEEE
T ss_pred             CCCHHHcCChH-HHHHH--HhCCCC--EEEEECCCCCCHHHHHHHHHhcccCCCCc-EEEEccCcHHhhhhccccceeee
Confidence            34577765544 33333  222232  69999999999999999999987432111 1111100 00             


Q ss_pred             --CcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCC
Q psy879           72 --DRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSE  137 (317)
Q Consensus        72 --~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~  137 (317)
                        ......+.+.+....       ..++.++++||+-  ..+....+++..+.  +.+ ++++++..+
T Consensus       177 ~~~~~~~~~~~~La~aL-------~~~PdvillDEp~--d~e~~~~~~~~~~~--G~~-vl~t~H~~~  232 (356)
T 3jvv_A          177 EVHRDTLGFSEALRSAL-------REDPDIILVGEMR--DLETIRLALTAAET--GHL-VFGTLHTTS  232 (356)
T ss_dssp             EBTTTBSCHHHHHHHHT-------TSCCSEEEESCCC--SHHHHHHHHHHHHT--TCE-EEEEESCSS
T ss_pred             eeccccCCHHHHHHHHh-------hhCcCEEecCCCC--CHHHHHHHHHHHhc--CCE-EEEEEccCh
Confidence              000111222222221       1468899999997  45555666666543  333 566666544

>2ixe_A Antigen peptide transporter 1; ABC ATPase, hydrolase; HET: ATP; 2.0A {Rattus norvegicus} PDB: 2ixg_A* 2ixf_A* 1jj7_A*

Probab=97.72  E-value=2.2e-05  Score=66.20  Aligned_cols=42  Identities=21%  Similarity=0.336  Sum_probs=31.9

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhccC--CceEEEEecCCC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYSN--TTRFALACNNSE  137 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~~--~~~~il~~~~~~  137 (317)
                      +++++++||... |.......+.+.+.+...  ...+|++|++..
T Consensus       174 ~p~lllLDEPts~LD~~~~~~i~~~l~~~~~~~g~tviivtHd~~  218 (271)
T 2ixe_A          174 KPRLLILDNATSALDAGNQLRVQRLLYESPEWASRTVLLITQQLS  218 (271)
T ss_dssp             CCSEEEEESTTTTCCHHHHHHHHHHHHHCTTTTTSEEEEECSCHH
T ss_pred             CCCEEEEECCccCCCHHHHHHHHHHHHHHHhhcCCEEEEEeCCHH
Confidence            689999999975 567788888888877643  556777887643

>1t6n_A Probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA processing protein; HET: FLC; 1.94A {Homo sapiens} SCOP: c.37.1.19

Probab=97.72  E-value=0.0013  Score=53.28  Aligned_cols=47  Identities=15%  Similarity=0.249  Sum_probs=32.5

Q ss_pred             CCCCcccCCHHHHHHHHHH---------------HhcCCCceEEEECCCCCCHHHHHHHHHHHH
Q psy879            7 QTFSDIVGNEDTVERLKVF---------------SSSGNVPNIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus         7 ~~~~~~~g~~~~~~~l~~~---------------l~~~~~~~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .+|+++--.+.+.+.+...               +.+|+  ++++.+|+|+|||.++...+-..
T Consensus        14 ~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~--~~li~~~TGsGKT~~~~~~~~~~   75 (220)
T 1t6n_A           14 SGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGM--DVLCQAKSGMGKTAVFVLATLQQ   75 (220)
T ss_dssp             CCSTTSCCCHHHHHHHHHTTCCCCCHHHHHHHHHHHTTC--CEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCC--CEEEECCCCCchhhhhhHHHHHh
Confidence            4577776667766665542               22343  69999999999998876666544

>2zr9_A Protein RECA, recombinase A; recombination, RECA mutants, DNA-repair, ATP-binding, DNA DA recombination, DNA repair, DNA-binding; HET: DTP; 2.50A {Mycobacterium smegmatis str} PDB: 2zr0_A* 2zra_A* 2zrb_A 2zrm_A* 1ubc_A* 1ubf_A* 1ubg_A* 1ube_A* 2g88_A* 2odw_A* 2oe2_A 2oep_A* 2oes_A 2ofo_A 2zr7_A 2odn_A* 2zrn_A 2zro_A* 2zrp_A* 2zre_A* ...

Probab=97.70  E-value=0.00011  Score=64.21  Aligned_cols=24  Identities=38%  Similarity=0.331  Sum_probs=21.4

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHc
Q psy879           33 NIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      .++++||||+||||++..++..+.
T Consensus        63 iv~I~G~pGsGKTtLal~la~~~~   86 (349)
T 2zr9_A           63 VIEIYGPESSGKTTVALHAVANAQ   86 (349)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHH
Confidence            389999999999999999997764

>1vpl_A ABC transporter, ATP-binding protein; TM0544, structural GENO joint center for structural genomics, JCSG, protein structu initiative, PSI; 2.10A {Thermotoga maritima} SCOP: c.37.1.12

Probab=97.70  E-value=2e-05  Score=65.82  Aligned_cols=41  Identities=17%  Similarity=0.276  Sum_probs=30.1

Q ss_pred             ceeEEEEeCCC-CCCHHHHHHHHHHhhhcc-CCceEEEEecCC
Q psy879           96 RHKIVILDEAD-SMTDGAQQALRRTMEIYS-NTTRFALACNNS  136 (317)
Q Consensus        96 ~~~vliiDE~d-~l~~~~~~~ll~~le~~~-~~~~~il~~~~~  136 (317)
                      +++++++||.. .|.+.....+.+++.+.. ....+|++|++.
T Consensus       164 ~p~lllLDEPts~LD~~~~~~l~~~l~~l~~~g~tiiivtHd~  206 (256)
T 1vpl_A          164 NPRLAILDEPTSGLDVLNAREVRKILKQASQEGLTILVSSHNM  206 (256)
T ss_dssp             CCSEEEEESTTTTCCHHHHHHHHHHHHHHHHTTCEEEEEECCH
T ss_pred             CCCEEEEeCCccccCHHHHHHHHHHHHHHHhCCCEEEEEcCCH
Confidence            68999999998 467777777877776553 345677777764

>2pcj_A ABC transporter, lipoprotein-releasing system ATP-binding protein; structural genomics; 1.70A {Aquifex aeolicus} PDB: 2pcl_A

Probab=97.69  E-value=3.1e-05  Score=63.39  Aligned_cols=41  Identities=7%  Similarity=0.149  Sum_probs=30.2

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhcc-CCceEEEEecCC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYS-NTTRFALACNNS  136 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~-~~~~~il~~~~~  136 (317)
                      +++++++||... |.+.....+.+++.+.. ....+|++|++.
T Consensus       158 ~p~lllLDEPt~~LD~~~~~~~~~~l~~l~~~g~tvi~vtHd~  200 (224)
T 2pcj_A          158 EPILLFADEPTGNLDSANTKRVMDIFLKINEGGTSIVMVTHER  200 (224)
T ss_dssp             CCSEEEEESTTTTCCHHHHHHHHHHHHHHHHTTCEEEEECSCH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHHHHHHCCCEEEEEcCCH
Confidence            688999999985 67777888877776543 245677777764

>3qf4_B Uncharacterized ABC transporter ATP-binding prote TM_0288; multidrug transporter, transport protein; HET: ANP; 2.90A {Thermotoga maritima}

Probab=97.69  E-value=1.8e-05  Score=74.53  Aligned_cols=43  Identities=21%  Similarity=0.268  Sum_probs=31.5

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhccCCceEEEEecCCCc
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYSNTTRFALACNNSEK  138 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~~~~~~il~~~~~~~  138 (317)
                      +++++++||+-. +.+.....+.+.+.+......+|++|++...
T Consensus       509 ~p~illlDEpts~LD~~~~~~i~~~l~~~~~~~t~i~itH~l~~  552 (598)
T 3qf4_B          509 NPKILILDEATSNVDTKTEKSIQAAMWKLMEGKTSIIIAHRLNT  552 (598)
T ss_dssp             CCSEEEECCCCTTCCHHHHHHHHHHHHHHHTTSEEEEESCCTTH
T ss_pred             CCCEEEEECCccCCCHHHHHHHHHHHHHHcCCCEEEEEecCHHH
Confidence            689999999975 5666677777777665455667888887653

>3b5x_A Lipid A export ATP-binding/permease protein MSBA; ABC transporter, lipid flippase, hydrolase, inner membrane, lipid transport, membrane; 5.50A {Vibrio cholerae}

Probab=97.69  E-value=4.9e-05  Score=71.31  Aligned_cols=42  Identities=17%  Similarity=0.329  Sum_probs=31.1

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhccCCceEEEEecCCC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYSNTTRFALACNNSE  137 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~~~~~~il~~~~~~  137 (317)
                      +++++++||+-. +.+.....+.+.+.+......+|+++++..
T Consensus       498 ~p~illlDEpts~LD~~~~~~i~~~l~~~~~~~tvi~itH~~~  540 (582)
T 3b5x_A          498 DAPVLILDEATSALDTESERAIQAALDELQKNKTVLVIAHRLS  540 (582)
T ss_pred             CCCEEEEECccccCCHHHHHHHHHHHHHHcCCCEEEEEecCHH
Confidence            689999999975 566677777777776554556777887753

>4g1u_C Hemin import ATP-binding protein HMUV; membrane transporter, type II ABC importer, HMUT, plasma MEM transport protein-hydrolase complex; 3.01A {Yersinia pestis}

Probab=97.68  E-value=1.8e-05  Score=66.50  Aligned_cols=41  Identities=17%  Similarity=0.137  Sum_probs=30.2

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhcc--CCceEEEEecCC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYS--NTTRFALACNNS  136 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~--~~~~~il~~~~~  136 (317)
                      +++++++||.-. |.+..+..+.+.+.+..  ....+|++|++.
T Consensus       165 ~p~lLllDEPts~LD~~~~~~i~~~l~~l~~~~~~tvi~vtHdl  208 (266)
T 4g1u_C          165 TPRWLFLDEPTSALDLYHQQHTLRLLRQLTRQEPLAVCCVLHDL  208 (266)
T ss_dssp             CCEEEEECCCCSSCCHHHHHHHHHHHHHHHHHSSEEEEEECSCH
T ss_pred             CCCEEEEeCccccCCHHHHHHHHHHHHHHHHcCCCEEEEEEcCH
Confidence            789999999975 66777888888877653  234577777764

>2j9r_A Thymidine kinase; TK1, DNK, lasso, transferase, ATP-binding, deoxyribonucleoside kinase, DNA synthesis, phosphate accept nucleotide-binding; HET: THM; 2.7A {Bacillus anthracis} PDB: 2ja1_A*

Probab=97.67  E-value=0.00017  Score=58.06  Aligned_cols=97  Identities=10%  Similarity=0.080  Sum_probs=50.7

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCC-C-cChHHHHHHHHHHHh--------hcccCCCCceeEEEEe
Q psy879           34 IIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASN-D-RGIDTVRNKIKMFAQ--------QKVTLPPGRHKIVILD  103 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~-~-~~~~~i~~~~~~~~~--------~~~~~~~~~~~vliiD  103 (317)
                      ++++||.|+||||.+...+.........  ++-+.+.. . .+...+...++.-..        .-.....+.+.+|+||
T Consensus        31 ~vitG~MgsGKTT~lL~~a~r~~~~g~k--Vli~k~~~d~R~ge~~i~s~~g~~~~a~~~~~~~~~~~~~~~~~dvViID  108 (214)
T 2j9r_A           31 EVICGSMFSGKSEELIRRVRRTQFAKQH--AIVFKPCIDNRYSEEDVVSHNGLKVKAVPVSASKDIFKHITEEMDVIAID  108 (214)
T ss_dssp             EEEECSTTSCHHHHHHHHHHHHHHTTCC--EEEEECC-----------------CCEEECSSGGGGGGGCCSSCCEEEEC
T ss_pred             EEEECCCCCcHHHHHHHHHHHHHHCCCE--EEEEEeccCCcchHHHHHhhcCCeeEEeecCCHHHHHHHHhcCCCEEEEE
Confidence            7899999999999998888776443332  22222221 1 111122222211000        0000011247899999


Q ss_pred             CCCCCCHHHHHHHHHHhhhccCCceEEEEecC
Q psy879          104 EADSMTDGAQQALRRTMEIYSNTTRFALACNN  135 (317)
Q Consensus       104 E~d~l~~~~~~~ll~~le~~~~~~~~il~~~~  135 (317)
                      |+..++++..+.+..+.+   .+..+|++.-+
T Consensus       109 EaQF~~~~~V~~l~~l~~---~~~~Vi~~Gl~  137 (214)
T 2j9r_A          109 EVQFFDGDIVEVVQVLAN---RGYRVIVAGLD  137 (214)
T ss_dssp             CGGGSCTTHHHHHHHHHH---TTCEEEEEECS
T ss_pred             CcccCCHHHHHHHHHHhh---CCCEEEEEecc
Confidence            999998776644433332   36677777654

>1qde_A EIF4A, translation initiation factor 4A; DEAD box protein family, gene regulation; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 1qva_A

Probab=97.66  E-value=0.00038  Score=56.61  Aligned_cols=47  Identities=19%  Similarity=0.348  Sum_probs=30.5

Q ss_pred             CCCCcccCCHHHHHHHHHH---------------HhcCCCceEEEECCCCCCHHHH-HHHHHHHH
Q psy879            7 QTFSDIVGNEDTVERLKVF---------------SSSGNVPNIIISGPPGVGKTTT-ILCLARIL   55 (317)
Q Consensus         7 ~~~~~~~g~~~~~~~l~~~---------------l~~~~~~~~ll~G~~G~GKt~l-a~~la~~l   55 (317)
                      .+|+++--.+.+.+.+...               +.+|+  ++++.+|+|+|||.+ +..+...+
T Consensus        14 ~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~--~~lv~~pTGsGKT~~~~~~~l~~l   76 (224)
T 1qde_A           14 YKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGH--DVLAQAQSGTGKTGTFSIAALQRI   76 (224)
T ss_dssp             CCGGGGTCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTC--CEEEECCTTSSHHHHHHHHHHHHC
T ss_pred             CChhhcCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCC--CEEEECCCCCcHHHHHHHHHHHHH
Confidence            3477766566666655432               23343  699999999999987 44444444

>2qi9_C Vitamin B12 import ATP-binding protein BTUD; inner membrane, membrane, transmembrane, transport, ATP- binding, hydrolase, nucleotide-binding, periplasm; HET: 1PE; 2.60A {Escherichia coli} PDB: 1l7v_C* 4dbl_C

Probab=97.66  E-value=2.3e-05  Score=65.23  Aligned_cols=38  Identities=18%  Similarity=0.332  Sum_probs=28.0

Q ss_pred             EEEEeCCCC-CCHHHHHHHHHHhhhcc-CCceEEEEecCC
Q psy879           99 IVILDEADS-MTDGAQQALRRTMEIYS-NTTRFALACNNS  136 (317)
Q Consensus        99 vliiDE~d~-l~~~~~~~ll~~le~~~-~~~~~il~~~~~  136 (317)
                      ++++||... |....+..+.+.+.+.. ....+|++|++.
T Consensus       154 lllLDEPts~LD~~~~~~l~~~l~~l~~~g~tviivtHd~  193 (249)
T 2qi9_C          154 LLLLDEPMNSLDVAQQSALDKILSALSQQGLAIVMSSHDL  193 (249)
T ss_dssp             EEEESSTTTTCCHHHHHHHHHHHHHHHHTTCEEEEECSCH
T ss_pred             EEEEECCcccCCHHHHHHHHHHHHHHHhCCCEEEEEeCCH
Confidence            999999975 67777888888877653 345577777663

>3dl0_A Adenylate kinase; phosphotransferase, zinc coordination, ATP-binding, binding, nucleotide biosynthesis, nucleotide-binding, trans; HET: AP5; 1.58A {Bacillus subtilis} PDB: 1p3j_A* 2ori_A* 2eu8_A* 2oo7_A* 2p3s_A* 2qaj_A* 2osb_A* 3dkv_A* 1zin_A* 1zio_A* 1zip_A* 1s3g_A*

Probab=97.64  E-value=0.0016  Score=52.62  Aligned_cols=23  Identities=30%  Similarity=0.473  Sum_probs=21.0

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .++|.||||+||||+++.+++.+
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~~   24 (216)
T 3dl0_A            2 NLVLMGLPGAGKGTQGERIVEKY   24 (216)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            37899999999999999999875

>1n0w_A DNA repair protein RAD51 homolog 1; DNA repair, homologous recombination, breast cancer susceptibility, RECA-like ATPase, protein complex; HET: DNA MSE; 1.70A {Homo sapiens} SCOP: c.37.1.11

Probab=97.63  E-value=0.00046  Score=56.77  Aligned_cols=23  Identities=26%  Similarity=0.081  Sum_probs=21.0

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .++|+||||+||||+++.++...
T Consensus        26 ~~~i~G~~GsGKTtl~~~l~~~~   48 (243)
T 1n0w_A           26 ITEMFGEFRTGKTQICHTLAVTC   48 (243)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHT
T ss_pred             EEEEECCCCCcHHHHHHHHHHHH
Confidence            48999999999999999999863

>3hr8_A Protein RECA; alpha and beta proteins (A/B, A+B), ATP-binding, cytoplasm, damage, DNA recombination, DNA repair, DNA-binding; 1.95A {Thermotoga maritima}

Probab=97.62  E-value=0.00042  Score=60.49  Aligned_cols=36  Identities=25%  Similarity=0.273  Sum_probs=26.7

Q ss_pred             HHHHHHhcCCCc---eEEEECCCCCCHHHHHHHHHHHHc
Q psy879           21 RLKVFSSSGNVP---NIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        21 ~l~~~l~~~~~~---~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      .|...+..|.++   .++|+||||+||||++..++..+.
T Consensus        48 ~LD~~Lg~GGi~~G~i~~I~GppGsGKSTLal~la~~~~   86 (356)
T 3hr8_A           48 AIDIATGVGGYPRGRIVEIFGQESSGKTTLALHAIAEAQ   86 (356)
T ss_dssp             HHHHHTSSSSEETTEEEEEEESTTSSHHHHHHHHHHHHH
T ss_pred             HHHHHhccCCccCCcEEEEECCCCCCHHHHHHHHHHHHH
Confidence            355555413332   289999999999999999998764

>2fz4_A DNA repair protein RAD25; RECA-like domain, DNA damage recognition domain, DNA binding; HET: DNA; 2.40A {Archaeoglobus fulgidus} SCOP: c.37.1.19

Probab=97.62  E-value=0.00048  Score=56.78  Aligned_cols=38  Identities=21%  Similarity=0.201  Sum_probs=28.2

Q ss_pred             CHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHH
Q psy879           15 NEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        15 ~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .+...+.+..++..+   +.+++||+|+|||.++..++..+
T Consensus        95 ~~~Q~~ai~~~~~~~---~~ll~~~tG~GKT~~a~~~~~~~  132 (237)
T 2fz4_A           95 RDYQEKALERWLVDK---RGCIVLPTGSGKTHVAMAAINEL  132 (237)
T ss_dssp             CHHHHHHHHHHTTTS---EEEEEESSSTTHHHHHHHHHHHS
T ss_pred             CHHHHHHHHHHHhCC---CEEEEeCCCCCHHHHHHHHHHHc
Confidence            444455555555432   59999999999999999888774

>4a82_A Cystic fibrosis transmembrane conductance regulat; CFTR, ION channel, transport protein, casse protein; 2.00A {Homo sapiens} PDB: 2onj_A* 2hyd_A

Probab=97.62  E-value=1.5e-05  Score=74.73  Aligned_cols=43  Identities=19%  Similarity=0.325  Sum_probs=31.4

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhccCCceEEEEecCCCc
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYSNTTRFALACNNSEK  138 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~~~~~~il~~~~~~~  138 (317)
                      +++++++||+-. +.+.....+.+.+.+......+|++|++.+.
T Consensus       495 ~p~illlDEpts~LD~~~~~~i~~~l~~~~~~~t~i~itH~l~~  538 (578)
T 4a82_A          495 NPPILILDEATSALDLESESIIQEALDVLSKDRTTLIVAHRLST  538 (578)
T ss_dssp             CCSEEEEESTTTTCCHHHHHHHHHHHHHHTTTSEEEEECSSGGG
T ss_pred             CCCEEEEECccccCCHHHHHHHHHHHHHHcCCCEEEEEecCHHH
Confidence            578999999975 5666677777777665555567778887654

>1svm_A Large T antigen; AAA+ fold, viral protein; HET: ATP; 1.94A {Simian virus 40} SCOP: c.37.1.20 PDB: 1svl_A* 1svo_A 1n25_A 2h1l_A

Probab=97.61  E-value=0.0001  Score=65.05  Aligned_cols=24  Identities=29%  Similarity=0.328  Sum_probs=22.0

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHc
Q psy879           33 NIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      .++++||||+||||+++.++..+.
T Consensus       171 ~i~l~G~~GsGKSTl~~~l~~~~~  194 (377)
T 1svm_A          171 YWLFKGPIDSGKTTLAAALLELCG  194 (377)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHhhcC
Confidence            599999999999999999999763

>2olj_A Amino acid ABC transporter; ABC domain, ATPase, hydrolase; HET: ADP; 2.05A {Geobacillus stearothermophilus} PDB: 2olk_A* 2ouk_A 2q0h_A* 3c4j_A* 3c41_J*

Probab=97.61  E-value=2.8e-05  Score=65.17  Aligned_cols=41  Identities=15%  Similarity=0.235  Sum_probs=29.9

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhcc-CCceEEEEecCC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYS-NTTRFALACNNS  136 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~-~~~~~il~~~~~  136 (317)
                      +++++++||.-. |.+..+..+.+++.+.. ....+|++|++.
T Consensus       177 ~p~lllLDEPts~LD~~~~~~~~~~l~~l~~~g~tvi~vtHd~  219 (263)
T 2olj_A          177 EPKIMLFDEPTSALDPEMVGEVLSVMKQLANEGMTMVVVTHEM  219 (263)
T ss_dssp             CCSEEEEESTTTTSCHHHHHHHHHHHHHHHHTTCEEEEECSCH
T ss_pred             CCCEEEEeCCcccCCHHHHHHHHHHHHHHHhCCCEEEEEcCCH
Confidence            689999999975 56777777777776543 245677777663

>1xx6_A Thymidine kinase; NESG, northeast structural genomics consortium, protein STRU initiative, PSI, structural genomics, DNA synthesis; HET: ADP; 2.00A {Clostridium acetobutylicum} SCOP: c.37.1.24 g.39.1.14

Probab=97.60  E-value=5.7e-05  Score=60.08  Aligned_cols=92  Identities=21%  Similarity=0.275  Sum_probs=50.8

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEE--ecCC-------CCcC-------hHHHHHHHHHHHhhcccCCCCc
Q psy879           33 NIIISGPPGVGKTTTILCLARILLGPSFKDAVLE--LNAS-------NDRG-------IDTVRNKIKMFAQQKVTLPPGR   96 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~--~~~~-------~~~~-------~~~i~~~~~~~~~~~~~~~~~~   96 (317)
                      -++++||.|+||||.+..++...........++.  .+..       +..+       .....+.+..+        ...
T Consensus        10 i~v~~G~mgsGKTT~ll~~a~r~~~~g~kV~v~k~~~d~r~~~~~i~s~~g~~~~a~~~~~~~~i~~~~--------~~~   81 (191)
T 1xx6_A           10 VEVIVGPMYSGKSEELIRRIRRAKIAKQKIQVFKPEIDNRYSKEDVVSHMGEKEQAVAIKNSREILKYF--------EED   81 (191)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEEEC-------CEEECTTSCEEECEEESSSTHHHHHC--------CTT
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHHCCCEEEEEEeccCccchHHHHHhhcCCceeeEeeCCHHHHHHHH--------hcc
Confidence            4899999999999999988887643322221111  0000       0000       00001111111        124


Q ss_pred             eeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecC
Q psy879           97 HKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNN  135 (317)
Q Consensus        97 ~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~  135 (317)
                      +.+|+|||+..++++....+..+.+   .+..+|+++-+
T Consensus        82 ~dvViIDEaqfl~~~~v~~l~~l~~---~~~~Vi~~Gl~  117 (191)
T 1xx6_A           82 TEVIAIDEVQFFDDEIVEIVNKIAE---SGRRVICAGLD  117 (191)
T ss_dssp             CSEEEECSGGGSCTHHHHHHHHHHH---TTCEEEEEECS
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHh---CCCEEEEEecc
Confidence            6799999999998776555444333   35667777653

>3qf4_A ABC transporter, ATP-binding protein; multidrug transporter, transport protein; HET: ANP; 2.90A {Thermotoga maritima}

Probab=97.60  E-value=2.7e-05  Score=73.11  Aligned_cols=42  Identities=14%  Similarity=0.261  Sum_probs=31.5

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhccCCceEEEEecCCC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYSNTTRFALACNNSE  137 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~~~~~~il~~~~~~  137 (317)
                      +++++++||+-. +.+.....+.+.+.+...+..+|++|++..
T Consensus       497 ~p~illlDEpts~LD~~~~~~i~~~l~~~~~~~tvi~itH~l~  539 (587)
T 3qf4_A          497 KPKVLILDDCTSSVDPITEKRILDGLKRYTKGCTTFIITQKIP  539 (587)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHHHSTTCEEEEEESCHH
T ss_pred             CCCEEEEECCcccCCHHHHHHHHHHHHHhCCCCEEEEEecChH
Confidence            689999999975 566777777777776555666788887754

>1s96_A Guanylate kinase, GMP kinase; E.coli, dimer, SAD, transferase; 2.00A {Escherichia coli} SCOP: c.37.1.1 PDB: 2an9_A* 2anb_A* 2anc_A 2f3r_A* 2f3t_A*

Probab=97.60  E-value=0.00059  Score=55.49  Aligned_cols=23  Identities=35%  Similarity=0.559  Sum_probs=21.4

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .+.|.||+|+||||+.+.++..+
T Consensus        18 ii~l~GpsGsGKSTLlk~L~g~~   40 (219)
T 1s96_A           18 LYIVSAPSGAGKSSLIQALLKTQ   40 (219)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhccC
Confidence            58999999999999999999975

>3a4m_A L-seryl-tRNA(SEC) kinase; P-loop motif, walker A motif, ATP binding motif, ATP- binding, nucleotide-binding, transferase; HET: ADP; 1.79A {Methanocaldococcus jannaschii} PDB: 3a4l_A* 3a4n_A 3am1_A* 3add_A* 3adc_A* 3adb_A*

Probab=97.59  E-value=0.00046  Score=57.71  Aligned_cols=24  Identities=54%  Similarity=0.719  Sum_probs=22.0

Q ss_pred             ceEEEECCCCCCHHHHHHHHHHHH
Q psy879           32 PNIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        32 ~~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      ..++|.|+||+||||+++.+++.+
T Consensus         5 ~lIvl~G~pGSGKSTla~~La~~L   28 (260)
T 3a4m_A            5 MLIILTGLPGVGKSTFSKNLAKIL   28 (260)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEEEcCCCCCHHHHHHHHHHHH
Confidence            358999999999999999999985

>3rlf_A Maltose/maltodextrin import ATP-binding protein M; integral membrane protein, ATPase, ABC transporter, membrane transmembrane; HET: UMQ MAL PGV ANP; 2.20A {Escherichia coli} PDB: 1q1e_A 1q12_A* 2awo_A* 3fh6_A 3puv_A* 3puw_A* 3pux_A* 3puy_A* 3puz_A* 3pv0_A* 2awn_A* 2r6g_A* 1q1b_A

Probab=97.59  E-value=2.5e-05  Score=68.77  Aligned_cols=42  Identities=12%  Similarity=0.195  Sum_probs=30.0

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhccC--CceEEEEecCCC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYSN--TTRFALACNNSE  137 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~~--~~~~il~~~~~~  137 (317)
                      +++++++||.-. |.......+++.+.+...  .+.+|++|++..
T Consensus       151 ~P~lLLLDEPts~LD~~~~~~l~~~l~~l~~~~g~tii~vTHd~~  195 (381)
T 3rlf_A          151 EPSVFLLDEPLSNLDAALRVQMRIEISRLHKRLGRTMIYVTHDQV  195 (381)
T ss_dssp             CCSEEEEESTTTTSCHHHHHHHHHHHHHHHHHHCCEEEEECSCHH
T ss_pred             CCCEEEEECCCcCCCHHHHHHHHHHHHHHHHhCCCEEEEEECCHH
Confidence            589999999974 566667777777765422  466788887754

>1u94_A RECA protein, recombinase A; homologous recombination, ATPase, DNA repair, DNA binding protein; 1.90A {Escherichia coli} SCOP: c.37.1.11 d.48.1.1 PDB: 1u98_A 1u99_A 1xms_A* 1xmv_A* 2rec_A 2reb_A 1n03_A* 1rea_A 1aa3_A

Probab=97.59  E-value=0.0002  Score=62.72  Aligned_cols=24  Identities=33%  Similarity=0.336  Sum_probs=21.5

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHc
Q psy879           33 NIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      .++++|+||+|||+++..++..+.
T Consensus        65 ii~I~G~pGsGKTtLal~la~~~~   88 (356)
T 1u94_A           65 IVEIYGPESSGKTTLTLQVIAAAQ   88 (356)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHH
Confidence            389999999999999999998764

>3b60_A Lipid A export ATP-binding/permease protein MSBA; ABC transporter, lipid flippase, hydrolase, inner membrane, lipid transport, membrane; HET: ANP; 3.70A {Salmonella typhimurium} SCOP: c.37.1.12 f.37.1.1 PDB: 3b5y_A* 3b5z_A* 3b5w_A

Probab=97.58  E-value=3.5e-05  Score=72.32  Aligned_cols=43  Identities=19%  Similarity=0.309  Sum_probs=31.6

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhccCCceEEEEecCCCc
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYSNTTRFALACNNSEK  138 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~~~~~~il~~~~~~~  138 (317)
                      +++++++||+.. +.+.....+.+.+.+......+|+++++.+.
T Consensus       498 ~p~illlDEpts~LD~~~~~~i~~~l~~~~~~~tvi~itH~~~~  541 (582)
T 3b60_A          498 DSPILILDEATSALDTESERAIQAALDELQKNRTSLVIAHRLST  541 (582)
T ss_dssp             CCSEEEEETTTSSCCHHHHHHHHHHHHHHHTTSEEEEECSCGGG
T ss_pred             CCCEEEEECccccCCHHHHHHHHHHHHHHhCCCEEEEEeccHHH
Confidence            578999999985 5667777777777765445567888877543

>2ghi_A Transport protein; multidrug resistance protein, MDR, structural genomics, structural genomics consortium, SGC; 2.20A {Plasmodium yoelii yoelii str}

Probab=97.58  E-value=2e-05  Score=66.03  Aligned_cols=43  Identities=21%  Similarity=0.327  Sum_probs=31.9

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhccCCceEEEEecCCCc
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYSNTTRFALACNNSEK  138 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~~~~~~il~~~~~~~  138 (317)
                      +++++++||... |.+.....+.+.+.+......+|++|++...
T Consensus       173 ~p~lllLDEPts~LD~~~~~~i~~~l~~l~~~~tviivtH~~~~  216 (260)
T 2ghi_A          173 DPKIVIFDEATSSLDSKTEYLFQKAVEDLRKNRTLIIIAHRLST  216 (260)
T ss_dssp             CCSEEEEECCCCTTCHHHHHHHHHHHHHHTTTSEEEEECSSGGG
T ss_pred             CCCEEEEECccccCCHHHHHHHHHHHHHhcCCCEEEEEcCCHHH
Confidence            578999999975 5667777777777765545667788877553

>3tlx_A Adenylate kinase 2; structural genomics, structural genomics consortium, SGC, RO fold, transferase, ATP binding, phosphorylation; HET: ADP ATP AMP; 2.75A {Plasmodium falciparum}

Probab=97.57  E-value=0.002  Score=53.16  Aligned_cols=23  Identities=39%  Similarity=0.534  Sum_probs=21.6

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .++|.||||+||||+++.+++.+
T Consensus        31 ~I~l~G~~GsGKsT~a~~L~~~~   53 (243)
T 3tlx_A           31 RYIFLGAPGSGKGTQSLNLKKSH   53 (243)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            59999999999999999999886

>2iut_A DNA translocase FTSK; nucleotide-binding, chromosome partition, ATP-binding, DNA- cell division, DNA translocation, KOPS, membrane; HET: DNA SAP; 2.25A {Pseudomonas aeruginosa} PDB: 2iuu_A*

Probab=97.56  E-value=0.0043  Score=57.28  Aligned_cols=69  Identities=13%  Similarity=0.157  Sum_probs=51.2

Q ss_pred             eeEEEEeCCCCCCH----HHHHHHHHHhhhc-cCCceEEEEecCCC--cCchhHhhhcce-eeecCCCHHHHHHHHH
Q psy879           97 HKIVILDEADSMTD----GAQQALRRTMEIY-SNTTRFALACNNSE--KIIEPIQSRCAM-LRYNKLTDAQLLSKVI  165 (317)
Q Consensus        97 ~~vliiDE~d~l~~----~~~~~ll~~le~~-~~~~~~il~~~~~~--~l~~~i~sR~~~-i~f~~~~~~~~~~~l~  165 (317)
                      +-+|||||+..+..    +....|.++.... .-.+.+|++|..+.  .+...+++-|.. +.|..-+..+...+|.
T Consensus       344 ~ivvVIDE~~~L~~~~~~~~~~~L~~Iar~GRa~GIhLIlaTQRPs~d~I~~~Iran~~~RI~lrv~s~~Dsr~ILd  420 (574)
T 2iut_A          344 TIVVVVDEFADMMMIVGKKVEELIARIAQKARAAGIHLILATQRPSVDVITGLIKANIPTRIAFQVSSKIDSRTILD  420 (574)
T ss_dssp             EEEEEESCCTTHHHHTCHHHHHHHHHHHHHCTTTTEEEEEEESCCCTTTSCHHHHHTCCEEEEECCSCHHHHHHHHS
T ss_pred             cEEEEEeCHHHHhhhhhHHHHHHHHHHHHHHhhCCeEEEEEecCcccccccHHHHhhhccEEEEEcCCHHHHHHhcC
Confidence            56899999997743    3445555555543 34566888888886  788889999887 8888888888877764

>1ji0_A ABC transporter; ATP binding protein, structural genomics, PSI, protein structure initiative, midwest center for structural genomics, MCSG; HET: ATP; 2.00A {Thermotoga maritima} SCOP: c.37.1.12

Probab=97.55  E-value=3.3e-05  Score=63.96  Aligned_cols=41  Identities=17%  Similarity=0.240  Sum_probs=30.4

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhcc-CCceEEEEecCC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYS-NTTRFALACNNS  136 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~-~~~~~il~~~~~  136 (317)
                      +++++++||... |.+.....+.+.+.+.. ....+|++|++.
T Consensus       157 ~p~lllLDEPts~LD~~~~~~l~~~l~~~~~~g~tvi~vtHd~  199 (240)
T 1ji0_A          157 RPKLLMMDEPSLGLAPILVSEVFEVIQKINQEGTTILLVEQNA  199 (240)
T ss_dssp             CCSEEEEECTTTTCCHHHHHHHHHHHHHHHHTTCCEEEEESCH
T ss_pred             CCCEEEEcCCcccCCHHHHHHHHHHHHHHHHCCCEEEEEecCH
Confidence            689999999984 66777888888777553 345577777764

>4a74_A DNA repair and recombination protein RADA; hydrolase, recombinase; HET: DNA ANP; 1.48A {Pyrococcus furiosus} PDB: 4a6x_A* 4a6p_A* 4a7o_A*

Probab=97.54  E-value=0.00029  Score=57.48  Aligned_cols=24  Identities=29%  Similarity=0.238  Sum_probs=21.5

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHc
Q psy879           33 NIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      .+.|.||+|+||||+++.++..+.
T Consensus        27 ~~~l~G~nGsGKSTll~~l~g~~~   50 (231)
T 4a74_A           27 ITEVFGEFGSGKTQLAHTLAVMVQ   50 (231)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHTT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHh
Confidence            399999999999999999998653

>3gd7_A Fusion complex of cystic fibrosis transmembrane conductance regulator, residues 1193-1427...; CFTR, ABC transporter, nucleotide binding domain, NBD; HET: B44; 2.70A {Homo sapiens}

Probab=97.53  E-value=2.7e-05  Score=69.02  Aligned_cols=42  Identities=26%  Similarity=0.316  Sum_probs=32.0

Q ss_pred             ceeEEEEeCCC-CCCHHHHHHHHHHhhhccCCceEEEEecCCC
Q psy879           96 RHKIVILDEAD-SMTDGAQQALRRTMEIYSNTTRFALACNNSE  137 (317)
Q Consensus        96 ~~~vliiDE~d-~l~~~~~~~ll~~le~~~~~~~~il~~~~~~  137 (317)
                      +++++++||.- .|.......+.+.+.+....+.+|+++++.+
T Consensus       173 ~P~lLLLDEPts~LD~~~~~~l~~~l~~~~~~~tvi~vtHd~e  215 (390)
T 3gd7_A          173 KAKILLLDEPSAHLDPVTYQIIRRTLKQAFADCTVILCEARIE  215 (390)
T ss_dssp             TCCEEEEESHHHHSCHHHHHHHHHHHHTTTTTSCEEEECSSSG
T ss_pred             CCCEEEEeCCccCCCHHHHHHHHHHHHHHhCCCEEEEEEcCHH
Confidence            68999999986 5677777788887776555566788887754

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=97.53  E-value=0.00068  Score=55.85  Aligned_cols=24  Identities=33%  Similarity=0.385  Sum_probs=20.7

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHc
Q psy879           33 NIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      .++++||||+|||+++..++..+.
T Consensus        25 ~~~i~G~~GsGKTtl~~~~~~~~~   48 (247)
T 2dr3_A           25 VVLLSGGPGTGKTIFSQQFLWNGL   48 (247)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHH
Confidence            489999999999999988876653

>2ga8_A Hypothetical 39.9 kDa protein; YFR007W, YFH7, unknown function; HET: CME; 1.77A {Saccharomyces cerevisiae} PDB: 2gaa_A*

Probab=97.53  E-value=9.4e-05  Score=64.20  Aligned_cols=40  Identities=28%  Similarity=0.359  Sum_probs=33.3

Q ss_pred             HHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHc
Q psy879           17 DTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        17 ~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      .+++.+...+..|..++++|.|++|+||||+++.+++.+.
T Consensus        10 ~il~~l~~~i~~g~~~~i~l~G~~G~GKTTl~~~la~~l~   49 (359)
T 2ga8_A           10 DVLQLLDNRIEDNYRVCVILVGSPGSGKSTIAEELCQIIN   49 (359)
T ss_dssp             HHHHHHHHTTTTCSCEEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhccCCeeEEEEECCCCCcHHHHHHHHHHHhC
Confidence            3455566667788888899999999999999999999873

>3d31_A Sulfate/molybdate ABC transporter, ATP-binding protein; ATP-binding, nucleotide-binding, membrane, transmembrane, transport protein; 3.00A {Methanosarcina acetivorans} SCOP: b.40.6.3 c.37.1.12

Probab=97.53  E-value=5e-05  Score=66.25  Aligned_cols=42  Identities=19%  Similarity=0.298  Sum_probs=30.3

Q ss_pred             ceeEEEEeCCC-CCCHHHHHHHHHHhhhcc--CCceEEEEecCCC
Q psy879           96 RHKIVILDEAD-SMTDGAQQALRRTMEIYS--NTTRFALACNNSE  137 (317)
Q Consensus        96 ~~~vliiDE~d-~l~~~~~~~ll~~le~~~--~~~~~il~~~~~~  137 (317)
                      +++++++||.- .|.......+.+.+.+..  ....+|++|++..
T Consensus       145 ~P~lLLLDEP~s~LD~~~~~~l~~~l~~l~~~~g~tii~vTHd~~  189 (348)
T 3d31_A          145 NPKILLLDEPLSALDPRTQENAREMLSVLHKKNKLTVLHITHDQT  189 (348)
T ss_dssp             CCSEEEEESSSTTSCHHHHHHHHHHHHHHHHHTTCEEEEEESCHH
T ss_pred             CCCEEEEECccccCCHHHHHHHHHHHHHHHHhcCCEEEEEeCCHH
Confidence            68999999997 466777777777776543  2456788887643

>2orv_A Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'- (2'deoxythymidil))tetraphosphate, transferase; HET: 4TA; 2.30A {Homo sapiens} SCOP: c.37.1.24 g.39.1.14

Probab=97.52  E-value=0.00038  Score=56.53  Aligned_cols=98  Identities=15%  Similarity=0.135  Sum_probs=52.6

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHHHHHHHhh-cccC------CCCceeEEEEeCC
Q psy879           33 NIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFAQQ-KVTL------PPGRHKIVILDEA  105 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~-~~~~------~~~~~~vliiDE~  105 (317)
                      -+++||+.|+||||.+...+...........++........+ ..+...++.-... ....      ......+|+|||+
T Consensus        21 l~v~~G~MgsGKTT~lL~~~~r~~~~g~kvli~kp~~D~Ryg-~~i~sr~G~~~~a~~i~~~~di~~~~~~~dvViIDEa   99 (234)
T 2orv_A           21 IQVILGPMFSGKSTELMRRVRRFQIAQYKCLVIKYAKDTRYS-SSFCTHDRNTMEALPACLLRDVAQEALGVAVIGIDEG   99 (234)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHHTTTCCEEEEEETTCCCC------------CEEEEESSGGGGHHHHTTCSEEEESSG
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHHCCCeEEEEeecCCccch-HHHHhhcCCeeEEEecCCHHHHHHHhccCCEEEEEch
Confidence            389999999999988777776654443332222211111112 2222222110000 0000      0034679999999


Q ss_pred             CCCCHHHHHHHHHHhhhccCCceEEEEecC
Q psy879          106 DSMTDGAQQALRRTMEIYSNTTRFALACNN  135 (317)
Q Consensus       106 d~l~~~~~~~ll~~le~~~~~~~~il~~~~  135 (317)
                      ..+.+  ...+.+.+.+  ....+|++.-+
T Consensus       100 QF~~~--v~el~~~l~~--~gi~VI~~GL~  125 (234)
T 2orv_A          100 QFFPD--IVEFCEAMAN--AGKTVIVAALD  125 (234)
T ss_dssp             GGCTT--HHHHHHHHHH--TTCEEEEECCS
T ss_pred             hhhhh--HHHHHHHHHh--CCCEEEEEecc
Confidence            99974  6677777776  45677887665

>3cmw_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 2.80A {Escherichia coli} PDB: 3cmt_A* 3cmx_A* 3cmv_A*

Probab=97.52  E-value=0.00032  Score=72.53  Aligned_cols=22  Identities=36%  Similarity=0.433  Sum_probs=20.7

Q ss_pred             EEEECCCCCCHHHHHHHHHHHH
Q psy879           34 IIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~l   55 (317)
                      +++|||||||||++|++++.+-
T Consensus      1085 ~l~~G~~g~GKT~la~~~~~~~ 1106 (1706)
T 3cmw_A         1085 VEIYGPESSGKTTLTLQVIAAA 1106 (1706)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEEcCCCCChHHHHHHHHHHh
Confidence            9999999999999999999764

>2gxq_A Heat resistant RNA dependent ATPase; RNA helicase, atomic resolution, AMP complex, ribosome biogenesis, thermophilic, hydrolase; HET: AMP; 1.20A {Thermus thermophilus HB27} PDB: 2gxs_A* 2gxu_A 3mwj_A 3mwk_A* 3mwl_A* 3nbf_A* 3nej_A

Probab=97.52  E-value=0.00058  Score=54.67  Aligned_cols=41  Identities=20%  Similarity=0.268  Sum_probs=25.1

Q ss_pred             CceeEEEEeCCCCCCHH-HHHHHHHHhhhccCCceEEEEecC
Q psy879           95 GRHKIVILDEADSMTDG-AQQALRRTMEIYSNTTRFALACNN  135 (317)
Q Consensus        95 ~~~~vliiDE~d~l~~~-~~~~ll~~le~~~~~~~~il~~~~  135 (317)
                      ...+++|+||+|.+... ....+..++...+....+++.|..
T Consensus       143 ~~~~~iViDEah~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT  184 (207)
T 2gxq_A          143 SRVEVAVLDEADEMLSMGFEEEVEALLSATPPSRQTLLFSAT  184 (207)
T ss_dssp             TTCSEEEEESHHHHHHTTCHHHHHHHHHTSCTTSEEEEECSS
T ss_pred             hhceEEEEEChhHhhccchHHHHHHHHHhCCccCeEEEEEEe
Confidence            45689999999987543 233444555555555555555444

>1z47_A CYSA, putative ABC-transporter ATP-binding protein; alpha/beta motif, beta sandwich, ligand binding protein; 1.90A {Alicyclobacillus acidocaldarius}

Probab=97.51  E-value=4e-05  Score=66.96  Aligned_cols=42  Identities=14%  Similarity=0.286  Sum_probs=29.7

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhccC--CceEEEEecCCC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYSN--TTRFALACNNSE  137 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~~--~~~~il~~~~~~  137 (317)
                      +++++++||.-. |.......+.+.+.+...  ...+|++|++.+
T Consensus       163 ~P~lLLLDEP~s~LD~~~r~~l~~~l~~l~~~~g~tvi~vTHd~~  207 (355)
T 1z47_A          163 RPQVLLFDEPFAAIDTQIRRELRTFVRQVHDEMGVTSVFVTHDQE  207 (355)
T ss_dssp             CCSEEEEESTTCCSSHHHHHHHHHHHHHHHHHHTCEEEEECSCHH
T ss_pred             CCCEEEEeCCcccCCHHHHHHHHHHHHHHHHhcCCEEEEECCCHH
Confidence            689999999974 667777777777665422  456777887643

>2yyz_A Sugar ABC transporter, ATP-binding protein; sugar transport, alpha and beta proteins (A/B) TM0421, structural genomics, NPPSFA; 2.11A {Thermotoga maritima}

Probab=97.51  E-value=4.3e-05  Score=66.90  Aligned_cols=42  Identities=12%  Similarity=0.234  Sum_probs=29.9

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhccC--CceEEEEecCCC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYSN--TTRFALACNNSE  137 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~~--~~~~il~~~~~~  137 (317)
                      +++++++||.-. |.......+.+.+.+...  ...+|++|++.+
T Consensus       151 ~P~lLLLDEP~s~LD~~~r~~l~~~l~~l~~~~g~tvi~vTHd~~  195 (359)
T 2yyz_A          151 QPKVLLFDEPLSNLDANLRMIMRAEIKHLQQELGITSVYVTHDQA  195 (359)
T ss_dssp             CCSEEEEESTTTTSCHHHHHHHHHHHHHHHHHHCCEEEEEESCHH
T ss_pred             CCCEEEEECCcccCCHHHHHHHHHHHHHHHHhcCCEEEEEcCCHH
Confidence            689999999974 666777777777665432  456788887743

>3llm_A ATP-dependent RNA helicase A; alpha-beta-alpha, structural genomics, structural genomics consortium, SGC, activator, ATP-binding, DNA-binding; HET: ADP; 2.80A {Homo sapiens}

Probab=97.51  E-value=0.00084  Score=55.14  Aligned_cols=20  Identities=40%  Similarity=0.612  Sum_probs=16.9

Q ss_pred             eEEEECCCCCCHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLA   52 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la   52 (317)
                      .+++.||+|+|||++...+.
T Consensus        78 ~~~i~g~TGsGKTt~~~~~~   97 (235)
T 3llm_A           78 VVIIRGATGCGKTTQVPQFI   97 (235)
T ss_dssp             EEEEECCTTSSHHHHHHHHH
T ss_pred             EEEEEeCCCCCcHHhHHHHH
Confidence            69999999999998766554

>1xp8_A RECA protein, recombinase A; recombination, radioresistance, DNA-repair, ATPase, DNA-BIND protein, DNA binding protein; HET: AGS; 2.50A {Deinococcus radiodurans} SCOP: c.37.1.11 d.48.1.1

Probab=97.50  E-value=0.00064  Score=59.69  Aligned_cols=23  Identities=35%  Similarity=0.355  Sum_probs=20.9

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHc
Q psy879           34 IIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      ++|+||||+|||+++..++..+.
T Consensus        77 i~I~G~pGsGKTtlal~la~~~~   99 (366)
T 1xp8_A           77 TEIYGPESGGKTTLALAIVAQAQ   99 (366)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHHH
T ss_pred             EEEEcCCCCChHHHHHHHHHHHH
Confidence            89999999999999999988764

>3h1t_A Type I site-specific restriction-modification system, R (restriction) subunit; hydrolase, restriction enzyme HSDR, ATP-binding; 2.30A {Vibrio vulnificus}

Probab=97.50  E-value=0.00025  Score=66.60  Aligned_cols=41  Identities=20%  Similarity=0.242  Sum_probs=29.6

Q ss_pred             CHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHc
Q psy879           15 NEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        15 ~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      |.+++..+...+.+|. .++++.+|.|+|||.++-.++..+.
T Consensus       183 Q~~ai~~~~~~~~~~~-~~~ll~~~TGsGKT~~~~~~~~~l~  223 (590)
T 3h1t_A          183 QQIAINRAVQSVLQGK-KRSLITMATGTGKTVVAFQISWKLW  223 (590)
T ss_dssp             HHHHHHHHHHHHHTTC-SEEEEEECTTSCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCC-CceEEEecCCCChHHHHHHHHHHHH
Confidence            4445555555555554 3689999999999999888887764

>4f4c_A Multidrug resistance protein PGP-1; ABC transporter, ATPase, multi-drug transporter, exporter, A binding, hydrolase,protein transport; HET: NDG NAG BMA MAN 0SA; 3.40A {Caenorhabditis elegans}

Probab=97.49  E-value=3.8e-05  Score=78.61  Aligned_cols=43  Identities=16%  Similarity=0.304  Sum_probs=31.7

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhccCCceEEEEecCCCc
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYSNTTRFALACNNSEK  138 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~~~~~~il~~~~~~~  138 (317)
                      +++|+|+||+-. +..+....+.+.+++...+..+|+++++...
T Consensus      1235 ~~~ILiLDEaTSaLD~~tE~~Iq~~l~~~~~~~TvI~IAHRLsT 1278 (1321)
T 4f4c_A         1235 NPKILLLDEATSALDTESEKVVQEALDRAREGRTCIVIAHRLNT 1278 (1321)
T ss_dssp             CCSEEEEESCCCSTTSHHHHHHHHHHTTTSSSSEEEEECSSSST
T ss_pred             CCCEEEEeCccccCCHHHHHHHHHHHHHHcCCCEEEEeccCHHH
Confidence            578999999975 4556667777778776666667778877543

>1vec_A ATP-dependent RNA helicase P54; DEAD-box protein, RNA binding protein; HET: TLA; 2.01A {Homo sapiens} SCOP: c.37.1.19

Probab=97.49  E-value=0.0009  Score=53.52  Aligned_cols=41  Identities=17%  Similarity=0.285  Sum_probs=24.8

Q ss_pred             CceeEEEEeCCCCCCH-HHHHHHHHHhhhccCCceEEEEecC
Q psy879           95 GRHKIVILDEADSMTD-GAQQALRRTMEIYSNTTRFALACNN  135 (317)
Q Consensus        95 ~~~~vliiDE~d~l~~-~~~~~ll~~le~~~~~~~~il~~~~  135 (317)
                      ....++|+||+|.+.. .....+..++...+....+++.|..
T Consensus       145 ~~~~~lViDEah~~~~~~~~~~l~~i~~~~~~~~~~l~~SAT  186 (206)
T 1vec_A          145 DHVQMIVLDEADKLLSQDFVQIMEDIILTLPKNRQILLYSAT  186 (206)
T ss_dssp             TTCCEEEEETHHHHTSTTTHHHHHHHHHHSCTTCEEEEEESC
T ss_pred             ccCCEEEEEChHHhHhhCcHHHHHHHHHhCCccceEEEEEee
Confidence            4568999999997654 2334445555555545555554433

>2ius_A DNA translocase FTSK; nucleotide-binding, chromosome partition, ATP-binding, DNA- binding, cell division, transmembrane, inner membrane; HET: DNA; 2.7A {Escherichia coli} PDB: 2j5p_A*

Probab=97.48  E-value=0.0032  Score=57.60  Aligned_cols=69  Identities=12%  Similarity=0.151  Sum_probs=47.7

Q ss_pred             eEEEEeCCCCCCHHH----HHHHHHHhhhcc-CCceEEEEecCCC--cCchhHhhhcce-eeecCCCHHHHHHHHHH
Q psy879           98 KIVILDEADSMTDGA----QQALRRTMEIYS-NTTRFALACNNSE--KIIEPIQSRCAM-LRYNKLTDAQLLSKVIE  166 (317)
Q Consensus        98 ~vliiDE~d~l~~~~----~~~ll~~le~~~-~~~~~il~~~~~~--~l~~~i~sR~~~-i~f~~~~~~~~~~~l~~  166 (317)
                      -+++|||+..+....    .+.+.++..... -.+.+|++|+.+.  .+...+++.+.. +.|.--++.+...++..
T Consensus       299 ivlvIDE~~~ll~~~~~~~~~~l~~Lar~gRa~GI~LIlaTQrp~~dvl~~~i~~n~~~RI~lrv~s~~dsr~ilg~  375 (512)
T 2ius_A          299 IVVLVDEFADLMMTVGKKVEELIARLAQKARAAGIHLVLATQRPSVDVITGLIKANIPTRIAFTVSSKIDSRTILDQ  375 (512)
T ss_dssp             EEEEEETHHHHHHHHHHHHHHHHHHHHHHCGGGTEEEEEEESCCCTTTSCHHHHHHCCEEEEECCSSHHHHHHHHSS
T ss_pred             EEEEEeCHHHHHhhhhHHHHHHHHHHHHHhhhCCcEEEEEecCCccccccHHHHhhcCCeEEEEcCCHHHHHHhcCC
Confidence            489999997765432    333333333322 2567888888876  577888888876 88888888888877654

>2it1_A 362AA long hypothetical maltose/maltodextrin transport ATP-binding protein; structural genomics, NPPSFA; 1.94A {Pyrococcus horikoshii}

Probab=97.48  E-value=4.5e-05  Score=66.83  Aligned_cols=42  Identities=12%  Similarity=0.188  Sum_probs=29.9

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhccC--CceEEEEecCCC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYSN--TTRFALACNNSE  137 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~~--~~~~il~~~~~~  137 (317)
                      +++++++||.-. |.......+.+.+.+...  ...+|++|++..
T Consensus       151 ~P~lLLLDEP~s~LD~~~r~~l~~~l~~l~~~~g~tvi~vTHd~~  195 (362)
T 2it1_A          151 EPEVLLLDEPLSNLDALLRLEVRAELKRLQKELGITTVYVTHDQA  195 (362)
T ss_dssp             CCSEEEEESGGGGSCHHHHHHHHHHHHHHHHHHTCEEEEEESCHH
T ss_pred             CCCEEEEECccccCCHHHHHHHHHHHHHHHHhCCCEEEEECCCHH
Confidence            689999999974 666777777777765422  456788887743

>1v43_A Sugar-binding transport ATP-binding protein; ATPase, active transport, sugar uptake and regulation, transport protein; 2.20A {Pyrococcus horikoshii} SCOP: b.40.6.3 b.40.6.3 c.37.1.12 PDB: 1vci_A*

Probab=97.44  E-value=5.1e-05  Score=66.75  Aligned_cols=42  Identities=12%  Similarity=0.218  Sum_probs=30.0

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhccC--CceEEEEecCCC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYSN--TTRFALACNNSE  137 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~~--~~~~il~~~~~~  137 (317)
                      +++++++||.-. |.......+...+.+...  ...+|++|++..
T Consensus       159 ~P~lLLLDEP~s~LD~~~r~~l~~~l~~l~~~~g~tvi~vTHd~~  203 (372)
T 1v43_A          159 EPDVLLMDEPLSNLDAKLRVAMRAEIKKLQQKLKVTTIYVTHDQV  203 (372)
T ss_dssp             CCSEEEEESTTTTSCHHHHHHHHHHHHHHHHHHTCEEEEEESCHH
T ss_pred             CCCEEEEcCCCccCCHHHHHHHHHHHHHHHHhCCCEEEEEeCCHH
Confidence            689999999974 666777777777765432  456788887743

>2onk_A Molybdate/tungstate ABC transporter, ATP-binding protein; membrane protein; 3.10A {Archaeoglobus fulgidus} SCOP: c.37.1.12

Probab=97.44  E-value=3.1e-05  Score=64.03  Aligned_cols=41  Identities=12%  Similarity=0.190  Sum_probs=30.4

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhccC--CceEEEEecCC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYSN--TTRFALACNNS  136 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~~--~~~~il~~~~~  136 (317)
                      +++++++||.-. |.+..+..+.+.+.+...  ...+|++|++.
T Consensus       144 ~p~lllLDEPts~LD~~~~~~~~~~l~~l~~~~g~tvi~vtHd~  187 (240)
T 2onk_A          144 QPRLLLLDEPLSAVDLKTKGVLMEELRFVQREFDVPILHVTHDL  187 (240)
T ss_dssp             CCSSBEEESTTSSCCHHHHHHHHHHHHHHHHHHTCCEEEEESCH
T ss_pred             CCCEEEEeCCcccCCHHHHHHHHHHHHHHHHhcCCEEEEEeCCH
Confidence            689999999975 677778888888776532  45577777764

>3dm5_A SRP54, signal recognition 54 kDa protein; protein-RNA, signal recognition particle, SRP-GTPase, protein targeting, cytoplasm, GTP-binding; HET: GDP; 2.51A {Pyrococcus furiosus}

Probab=97.44  E-value=0.0026  Score=57.06  Aligned_cols=27  Identities=37%  Similarity=0.486  Sum_probs=23.6

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHcCCC
Q psy879           33 NIIISGPPGVGKTTTILCLARILLGPS   59 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~~~~   59 (317)
                      .+++.|++|+||||++..+|..+....
T Consensus       102 vIlivG~~G~GKTTt~~kLA~~l~~~G  128 (443)
T 3dm5_A          102 ILLMVGIQGSGKTTTVAKLARYFQKRG  128 (443)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHHTTT
T ss_pred             EEEEECcCCCCHHHHHHHHHHHHHHCC
Confidence            389999999999999999999886543

>3lw7_A Adenylate kinase related protein (ADKA-like); AMP, PSI, MCSG, structural genomics, midwest center for structural genomics; HET: AMP; 2.30A {Sulfolobus solfataricus} PDB: 3h0k_A

Probab=97.42  E-value=0.00059  Score=52.92  Aligned_cols=22  Identities=36%  Similarity=0.514  Sum_probs=19.6

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .++|.||||+||||+++.+ +.+
T Consensus         3 ~I~l~G~~GsGKsT~a~~L-~~~   24 (179)
T 3lw7_A            3 VILITGMPGSGKSEFAKLL-KER   24 (179)
T ss_dssp             EEEEECCTTSCHHHHHHHH-HHT
T ss_pred             EEEEECCCCCCHHHHHHHH-HHC
Confidence            5899999999999999999 553

>3fb4_A Adenylate kinase; psychrophIle, phosphotransferase, ATP-binding, nucleotide-binding, transferase; HET: AP5; 2.00A {Marinibacillus marinus}

Probab=97.42  E-value=0.002  Score=52.00  Aligned_cols=23  Identities=35%  Similarity=0.528  Sum_probs=21.1

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .++|.||||+||||+++.+++.+
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~~   24 (216)
T 3fb4_A            2 NIVLMGLPGAGKGTQAEQIIEKY   24 (216)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            37899999999999999999886

>3fvq_A Fe(3+) IONS import ATP-binding protein FBPC; nucleotide binding domain, ABC motor domain, ferric iron TRA ATP-binding, cell inner membrane; HET: ATP; 1.90A {Neisseria gonorrhoeae}

Probab=97.41  E-value=6.1e-05  Score=65.82  Aligned_cols=27  Identities=41%  Similarity=0.676  Sum_probs=23.0

Q ss_pred             hcCCCceEEEECCCCCCHHHHHHHHHHHH
Q psy879           27 SSGNVPNIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        27 ~~~~~~~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      ..|.  .+.|.||+|+||||+.+.++..+
T Consensus        28 ~~Ge--~~~llGpsGsGKSTLLr~iaGl~   54 (359)
T 3fvq_A           28 DPGE--ILFIIGASGCGKTTLLRCLAGFE   54 (359)
T ss_dssp             CTTC--EEEEEESTTSSHHHHHHHHHTSS
T ss_pred             cCCC--EEEEECCCCchHHHHHHHHhcCC
Confidence            3444  58999999999999999999865

>2nq2_C Hypothetical ABC transporter ATP-binding protein HI1470; putative iron chelatin ABC transporter, nucleotide binding domain; 2.40A {Haemophilus influenzae}

Probab=97.41  E-value=0.00058  Score=56.82  Aligned_cols=41  Identities=15%  Similarity=0.230  Sum_probs=30.7

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhccC--CceEEEEecCC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYSN--TTRFALACNNS  136 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~~--~~~~il~~~~~  136 (317)
                      +++++++||... |.+.....+.+.+.+...  ...+|++|++.
T Consensus       146 ~p~lllLDEPts~LD~~~~~~l~~~l~~l~~~~g~tvi~vtHd~  189 (253)
T 2nq2_C          146 ECKLILLDEPTSALDLANQDIVLSLLIDLAQSQNMTVVFTTHQP  189 (253)
T ss_dssp             TCSEEEESSSSTTSCHHHHHHHHHHHHHHHHTSCCEEEEEESCH
T ss_pred             CCCEEEEeCCcccCCHHHHHHHHHHHHHHHHhcCCEEEEEecCH
Confidence            689999999985 677788888888776532  45677777764

>3fmo_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 2.51A {Homo sapiens}

Probab=97.41  E-value=0.0014  Score=56.04  Aligned_cols=49  Identities=14%  Similarity=0.292  Sum_probs=32.0

Q ss_pred             CCCCcccCCHHHHHHHHH---------------HHhcCCCceEEEECCCCCCHHHHHH-HHHHHH
Q psy879            7 QTFSDIVGNEDTVERLKV---------------FSSSGNVPNIIISGPPGVGKTTTIL-CLARIL   55 (317)
Q Consensus         7 ~~~~~~~g~~~~~~~l~~---------------~l~~~~~~~~ll~G~~G~GKt~la~-~la~~l   55 (317)
                      .+|+++--.+.+.+.|..               .+..|...++++.+|+|+|||.+.. .+...+
T Consensus        92 ~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~ai~~il~~~~~~~l~~a~TGsGKT~a~~lp~l~~l  156 (300)
T 3fmo_B           92 KSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQV  156 (300)
T ss_dssp             CCSGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHTSSSCCCEEEECCTTSSHHHHHHHHHHHHC
T ss_pred             CCHhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCCeEEEECCCCCCccHHHHHHHHHhh
Confidence            467877667776665543               2334433379999999999998743 444444

>3kl4_A SRP54, signal recognition 54 kDa protein; signal recognition particle, SRP, SRP54, FFH, signal sequenc peptide; 3.50A {Sulfolobus solfataricus} PDB: 1qzx_A 1qzw_A

Probab=97.40  E-value=0.0011  Score=59.52  Aligned_cols=26  Identities=38%  Similarity=0.382  Sum_probs=22.9

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHcCCC
Q psy879           34 IIISGPPGVGKTTTILCLARILLGPS   59 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~l~~~~   59 (317)
                      +++.||+|+||||++..++..+....
T Consensus       100 I~lvG~~GsGKTTt~~kLA~~l~~~G  125 (433)
T 3kl4_A          100 IMLVGVQGSGKTTTAGKLAYFYKKRG  125 (433)
T ss_dssp             EEECCCTTSCHHHHHHHHHHHHHHTT
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHcC
Confidence            89999999999999999998875433

>2oxc_A Probable ATP-dependent RNA helicase DDX20; DEAD, structural genomics, structural genomics consortium, SGC, hydrolase; HET: ADP; 1.30A {Homo sapiens} PDB: 3b7g_A*

Probab=97.39  E-value=0.001  Score=54.37  Aligned_cols=47  Identities=21%  Similarity=0.357  Sum_probs=29.6

Q ss_pred             CCCCcccCCHHHHHHHHHH---------------HhcCCCceEEEECCCCCCHHHHH-HHHHHHH
Q psy879            7 QTFSDIVGNEDTVERLKVF---------------SSSGNVPNIIISGPPGVGKTTTI-LCLARIL   55 (317)
Q Consensus         7 ~~~~~~~g~~~~~~~l~~~---------------l~~~~~~~~ll~G~~G~GKt~la-~~la~~l   55 (317)
                      .+|+++--.+.+.+.+...               +.+|+  ++++.+|+|+|||... ..+...+
T Consensus        24 ~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~--~~l~~a~TGsGKT~~~~l~~l~~l   86 (230)
T 2oxc_A           24 ADFESLLLSRPVLEGLRAAGFERPSPVQLKAIPLGRCGL--DLIVQAKSGTGKTCVFSTIALDSL   86 (230)
T ss_dssp             CCGGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTC--CEEEECCTTSSHHHHHHHHHHHHC
T ss_pred             CCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCC--CEEEECCCCCcHHHHHHHHHHHHH
Confidence            3477765556555554332               23343  6999999999999874 3444444

>1cr0_A DNA primase/helicase; RECA-type protein fold, transferase; HET: DNA; 2.30A {Enterobacteria phage T7} SCOP: c.37.1.11 PDB: 1cr1_A* 1cr2_A* 1cr4_A* 1e0j_A* 1e0k_A*

Probab=97.37  E-value=0.00082  Score=57.25  Aligned_cols=24  Identities=25%  Similarity=0.252  Sum_probs=22.0

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHc
Q psy879           33 NIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      .++|.||||+||||+++.++..+.
T Consensus        37 ~~~i~G~~G~GKTTl~~~ia~~~~   60 (296)
T 1cr0_A           37 VIMVTSGSGMGKSTFVRQQALQWG   60 (296)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHH
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHHH
Confidence            589999999999999999998874

>1pzn_A RAD51, DNA repair and recombination protein RAD51, RADA; heptameric ring, heptamer, ring, oligomer, RAD51 polymerizat motif; HET: DNA; 2.85A {Pyrococcus furiosus} SCOP: a.60.4.1 c.37.1.11

Probab=97.36  E-value=0.00094  Score=58.36  Aligned_cols=22  Identities=32%  Similarity=0.326  Sum_probs=20.9

Q ss_pred             EEEECCCCCCHHHHHHHHHHHH
Q psy879           34 IIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~l   55 (317)
                      +.|+||||+||||+++.++...
T Consensus       134 ~~I~G~~GsGKTTL~~~l~~~~  155 (349)
T 1pzn_A          134 TEVFGEFGSGKTQLAHTLAVMV  155 (349)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            8999999999999999999875

>1v5w_A DMC1, meiotic recombination protein DMC1/LIM15 homolog; DNA-binding protein, ring protein, octamer, AAA ATPase; 3.20A {Homo sapiens} SCOP: c.37.1.11 PDB: 2zjb_A

Probab=97.35  E-value=0.0017  Score=56.61  Aligned_cols=22  Identities=23%  Similarity=0.031  Sum_probs=20.5

Q ss_pred             EEEECCCCCCHHHHHHHHHHHH
Q psy879           34 IIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~l   55 (317)
                      ++|+||||+|||+++..++...
T Consensus       125 ~~I~G~~GsGKTtla~~la~~~  146 (343)
T 1v5w_A          125 TEAFGEFRTGKTQLSHTLCVTA  146 (343)
T ss_dssp             EEEECCTTCTHHHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHHHHH
Confidence            8999999999999999999874

>1nrj_B SR-beta, signal recognition particle receptor beta subunit; transmembrane, endoplasmic reticulum, GTP-binding; HET: GTP; 1.70A {Saccharomyces cerevisiae} SCOP: c.37.1.8

Probab=97.34  E-value=0.0012  Score=53.16  Aligned_cols=108  Identities=23%  Similarity=0.354  Sum_probs=55.8

Q ss_pred             CCCceEEEECCCCCCHHHHHHHHHHHHcCCCC--CCceEE-------ecCCCCcChHHHHHHHHHHHhhcccCCCCceeE
Q psy879           29 GNVPNIIISGPPGVGKTTTILCLARILLGPSF--KDAVLE-------LNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKI   99 (317)
Q Consensus        29 ~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~--~~~~~~-------~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~v   99 (317)
                      +..+++++.|++|+|||+++..++........  ..+...       +.-.+..+....+.....+......  ....-+
T Consensus        10 ~~~~~i~~~G~~g~GKTsl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~Dt~G~~~~~~~~~~~~~~~~~--~~~~~i   87 (218)
T 1nrj_B           10 SYQPSIIIAGPQNSGKTSLLTLLTTDSVRPTVVSQEPLSAADYDGSGVTLVDFPGHVKLRYKLSDYLKTRAK--FVKGLI   87 (218)
T ss_dssp             CCCCEEEEECSTTSSHHHHHHHHHHSSCCCBCCCSSCEEETTGGGSSCEEEECCCCGGGTHHHHHHHHHHGG--GEEEEE
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHhcCCCCCeeeecCceEEEEeeCceEEEEECCCcHHHHHHHHHHHHhccc--cCCEEE
Confidence            34567999999999999999999986432210  000000       0001112222232333322222100  023457


Q ss_pred             EEEeCC-CC-CCHHHHHHHHHHhhh----ccCCceEEEEecCCCc
Q psy879          100 VILDEA-DS-MTDGAQQALRRTMEI----YSNTTRFALACNNSEK  138 (317)
Q Consensus       100 liiDE~-d~-l~~~~~~~ll~~le~----~~~~~~~il~~~~~~~  138 (317)
                      +++|-. +. -.......+..++..    .+....++++.|..+.
T Consensus        88 ~v~D~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~ilv~nK~Dl  132 (218)
T 1nrj_B           88 FMVDSTVDPKKLTTTAEFLVDILSITESSCENGIDILIACNKSEL  132 (218)
T ss_dssp             EEEETTSCTTCCHHHHHHHHHHHHHHHHHSTTCCCEEEEEECTTS
T ss_pred             EEEECCCChHHHHHHHHHHHHHHhcccccccCCCCEEEEEEchHh
Confidence            777876 22 223344455555553    3456778888887664

>1g29_1 MALK, maltose transport protein MALK; ATPase, active transport, maltose uptake and regulation, sugar binding protein; 1.90A {Thermococcus litoralis} SCOP: b.40.6.3 b.40.6.3 c.37.1.12 PDB: 2d62_A

Probab=97.34  E-value=5.9e-05  Score=66.43  Aligned_cols=42  Identities=7%  Similarity=0.186  Sum_probs=29.7

Q ss_pred             ceeEEEEeCCC-CCCHHHHHHHHHHhhhccC--CceEEEEecCCC
Q psy879           96 RHKIVILDEAD-SMTDGAQQALRRTMEIYSN--TTRFALACNNSE  137 (317)
Q Consensus        96 ~~~vliiDE~d-~l~~~~~~~ll~~le~~~~--~~~~il~~~~~~  137 (317)
                      +++++++||.- .|.......+.+.+.+...  ...+|++|++..
T Consensus       157 ~P~lLLLDEP~s~LD~~~r~~l~~~l~~l~~~~g~tvi~vTHd~~  201 (372)
T 1g29_1          157 KPQVFLMDEPLSNLDAKLRVRMRAELKKLQRQLGVTTIYVTHDQV  201 (372)
T ss_dssp             CCSEEEEECTTTTSCHHHHHHHHHHHHHHHHHHTCEEEEEESCHH
T ss_pred             CCCEEEECCCCccCCHHHHHHHHHHHHHHHHhcCCEEEEECCCHH
Confidence            68999999997 4666777777776665432  456788887743

>4f4c_A Multidrug resistance protein PGP-1; ABC transporter, ATPase, multi-drug transporter, exporter, A binding, hydrolase,protein transport; HET: NDG NAG BMA MAN 0SA; 3.40A {Caenorhabditis elegans}

Probab=97.33  E-value=7.6e-05  Score=76.42  Aligned_cols=24  Identities=33%  Similarity=0.487  Sum_probs=21.7

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHc
Q psy879           33 NIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      .+.+.||+|+||||+++.+.+.+.
T Consensus       446 ~vaivG~sGsGKSTll~ll~~~~~  469 (1321)
T 4f4c_A          446 TVALVGSSGCGKSTIISLLLRYYD  469 (1321)
T ss_dssp             EEEEEECSSSCHHHHHHHHTTSSC
T ss_pred             EEEEEecCCCcHHHHHHHhccccc
Confidence            589999999999999999998753

>3pey_A ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, ATPase, helicase, mRNA-export, nuclear pore, hydrolase-RNA complex; HET: ADP; 1.40A {Saccharomyces cerevisiae} PDB: 3pew_A* 3pex_A* 3pez_A* 3rrm_A* 3rrn_A* 2kbe_A 3gfp_A 2kbf_A 3pev_A* 3peu_A*

Probab=97.33  E-value=0.0026  Score=56.04  Aligned_cols=42  Identities=31%  Similarity=0.400  Sum_probs=26.1

Q ss_pred             CceeEEEEeCCCCCCH--HHHHHHHHHhhhccCCceEEEEecCC
Q psy879           95 GRHKIVILDEADSMTD--GAQQALRRTMEIYSNTTRFALACNNS  136 (317)
Q Consensus        95 ~~~~vliiDE~d~l~~--~~~~~ll~~le~~~~~~~~il~~~~~  136 (317)
                      ....++|+||+|.+..  .....+..++...+....+++.|...
T Consensus       144 ~~~~~iIiDEah~~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~  187 (395)
T 3pey_A          144 QKIKIFVLDEADNMLDQQGLGDQCIRVKRFLPKDTQLVLFSATF  187 (395)
T ss_dssp             TTCCEEEEETHHHHHHSTTHHHHHHHHHHTSCTTCEEEEEESCC
T ss_pred             ccCCEEEEEChhhhcCccccHHHHHHHHHhCCCCcEEEEEEecC
Confidence            4568999999998764  23344445555555556666655443

>3ber_A Probable ATP-dependent RNA helicase DDX47; DEAD, AMP, structural genomics, structural GEN consortium, SGC, ATP-binding, hydrolase; HET: AMP PGE; 1.40A {Homo sapiens}

Probab=97.31  E-value=0.0017  Score=53.85  Aligned_cols=41  Identities=15%  Similarity=0.261  Sum_probs=24.6

Q ss_pred             CceeEEEEeCCCCCCHH-HHHHHHHHhhhccCCceEEEEecC
Q psy879           95 GRHKIVILDEADSMTDG-AQQALRRTMEIYSNTTRFALACNN  135 (317)
Q Consensus        95 ~~~~vliiDE~d~l~~~-~~~~ll~~le~~~~~~~~il~~~~  135 (317)
                      ....++|+||+|.+... ....+.+++...+....+++.|..
T Consensus       185 ~~~~~lViDEah~l~~~~~~~~l~~i~~~~~~~~~~l~~SAT  226 (249)
T 3ber_A          185 RALKYLVMDEADRILNMDFETEVDKILKVIPRDRKTFLFSAT  226 (249)
T ss_dssp             TTCCEEEECSHHHHHHTTCHHHHHHHHHSSCSSSEEEEEESS
T ss_pred             cccCEEEEcChhhhhccChHHHHHHHHHhCCCCCeEEEEecc
Confidence            45679999999977543 233455555555545555554433

>3bor_A Human initiation factor 4A-II; translation initiation, DEAD BOX, structural genomics, helic binding, HOST-virus interaction, hydrolase; 1.85A {Homo sapiens} PDB: 2g9n_A*

Probab=97.30  E-value=0.0014  Score=53.89  Aligned_cols=41  Identities=20%  Similarity=0.287  Sum_probs=24.5

Q ss_pred             CceeEEEEeCCCCCCHH-HHHHHHHHhhhccCCceEEEEecC
Q psy879           95 GRHKIVILDEADSMTDG-AQQALRRTMEIYSNTTRFALACNN  135 (317)
Q Consensus        95 ~~~~vliiDE~d~l~~~-~~~~ll~~le~~~~~~~~il~~~~  135 (317)
                      ....++|+||+|.+... ....+..++...+....+++.|..
T Consensus       172 ~~~~~lViDEah~~~~~~~~~~l~~i~~~~~~~~~~i~~SAT  213 (237)
T 3bor_A          172 KWIKMFVLDEADEMLSRGFKDQIYEIFQKLNTSIQVVLLSAT  213 (237)
T ss_dssp             TTCCEEEEESHHHHHHTTCHHHHHHHHHHSCTTCEEEEECSS
T ss_pred             ccCcEEEECCchHhhccCcHHHHHHHHHhCCCCCeEEEEEEe
Confidence            35689999999977532 233444555544555565555443

>2pjz_A Hypothetical protein ST1066; ATP binding protein, structural genomics, NPPSFA; 1.90A {Sulfolobus tokodaii}

Probab=97.29  E-value=0.00068  Score=56.72  Aligned_cols=40  Identities=20%  Similarity=0.276  Sum_probs=31.5

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhccCCceEEEEecCCC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYSNTTRFALACNNSE  137 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~~~~~~il~~~~~~  137 (317)
                      +++++++||... |.+.....+.+.+.+...  .+|++|++.+
T Consensus       146 ~p~lllLDEPts~LD~~~~~~l~~~L~~~~~--tviivtHd~~  186 (263)
T 2pjz_A          146 QPEIVGLDEPFENVDAARRHVISRYIKEYGK--EGILVTHELD  186 (263)
T ss_dssp             CCSEEEEECTTTTCCHHHHHHHHHHHHHSCS--EEEEEESCGG
T ss_pred             CCCEEEEECCccccCHHHHHHHHHHHHHhcC--cEEEEEcCHH
Confidence            689999999975 677888889998887655  5777777643

>1w4r_A Thymidine kinase; type II, human, cytosolic, phosphorylation, transferase; HET: TTP; 1.83A {Homo sapiens} PDB: 1xbt_A* 2wvj_A* 2j87_A*

Probab=97.29  E-value=0.00063  Score=53.80  Aligned_cols=95  Identities=14%  Similarity=0.097  Sum_probs=50.2

Q ss_pred             eEEEECCCCCCHH-HHHHHHHHHHcCCCCCCceEEecCC-CCcChHHHHHHHHHHHhh-cccC------CCCceeEEEEe
Q psy879           33 NIIISGPPGVGKT-TTILCLARILLGPSFKDAVLELNAS-NDRGIDTVRNKIKMFAQQ-KVTL------PPGRHKIVILD  103 (317)
Q Consensus        33 ~~ll~G~~G~GKt-~la~~la~~l~~~~~~~~~~~~~~~-~~~~~~~i~~~~~~~~~~-~~~~------~~~~~~vliiD  103 (317)
                      -+++|||.|+||| .+.+++.+.....   ..++.+.+. +.+....+...++..... +...      ......+|+||
T Consensus        22 l~fiyG~MgsGKTt~Ll~~i~n~~~~~---~kvl~~kp~~D~R~~~~i~S~~g~~~~A~~~~~~~d~~~~~~~~DvIlID   98 (195)
T 1w4r_A           22 IQVILGPMFSGKSTELMRRVRRFQIAQ---YKCLVIKYAKDTRYSSSFCTHDRNTMEALPACLLRDVAQEALGVAVIGID   98 (195)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHHHHTT---CCEEEEEETTCCCGGGSCCHHHHHHSEEEEESSGGGGHHHHHTCSEEEES
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHHcC---CeEEEEccccCccchhhhhhccCCcccceecCCHHHHHHhccCCCEEEEE
Confidence            3899999999999 8888888775432   223333322 111111122222110000 0000      00235699999


Q ss_pred             CCCCCCHHHHHHHHHHhhhccCCceEEEEec
Q psy879          104 EADSMTDGAQQALRRTMEIYSNTTRFALACN  134 (317)
Q Consensus       104 E~d~l~~~~~~~ll~~le~~~~~~~~il~~~  134 (317)
                      |+..+ ++ +..++..+.+  .+..+|+++-
T Consensus        99 EaQFf-k~-~ve~~~~L~~--~gk~VI~~GL  125 (195)
T 1w4r_A           99 EGQFF-PD-IVEFCEAMAN--AGKTVIVAAL  125 (195)
T ss_dssp             SGGGC-TT-HHHHHHHHHH--TTCEEEEEEE
T ss_pred             chhhh-HH-HHHHHHHHHH--CCCeEEEEec
Confidence            99999 65 5555555553  3445666543

>3vaa_A Shikimate kinase, SK; structural genomics, center for structural genomics of infec diseases, csgid, metal binding, transferase; 1.70A {Bacteroides thetaiotaomicron}

Probab=97.29  E-value=0.0002  Score=57.36  Aligned_cols=32  Identities=38%  Similarity=0.352  Sum_probs=23.4

Q ss_pred             HHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHH
Q psy879           22 LKVFSSSGNVPNIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        22 l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      +.-.+..+.  .++|.||+|+||||+++.+++.+
T Consensus        18 ~~~~~~~~~--~i~l~G~~GsGKsTl~~~La~~l   49 (199)
T 3vaa_A           18 LYFQSNAMV--RIFLTGYMGAGKTTLGKAFARKL   49 (199)
T ss_dssp             ------CCC--EEEEECCTTSCHHHHHHHHHHHH
T ss_pred             eeEecCCCC--EEEEEcCCCCCHHHHHHHHHHHc
Confidence            443444444  79999999999999999999987

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19

Probab=97.27  E-value=0.0013  Score=53.23  Aligned_cols=43  Identities=21%  Similarity=0.249  Sum_probs=25.4

Q ss_pred             ceeEEEEeCCCCCCHHH-HHHHHHHhhhccCCceEEEE-ecCCCc
Q psy879           96 RHKIVILDEADSMTDGA-QQALRRTMEIYSNTTRFALA-CNNSEK  138 (317)
Q Consensus        96 ~~~vliiDE~d~l~~~~-~~~ll~~le~~~~~~~~il~-~~~~~~  138 (317)
                      ...++|+||+|.+.... ...+..++...+....+++. ++.+..
T Consensus       150 ~~~~lViDEah~~~~~~~~~~l~~i~~~~~~~~~~l~~SAT~~~~  194 (219)
T 1q0u_A          150 TAHILVVDEADLMLDMGFITDVDQIAARMPKDLQMLVFSATIPEK  194 (219)
T ss_dssp             GCCEEEECSHHHHHHTTCHHHHHHHHHTSCTTCEEEEEESCCCGG
T ss_pred             cceEEEEcCchHHhhhChHHHHHHHHHhCCcccEEEEEecCCCHH
Confidence            45789999999875432 33455555555555555544 443333

>3io5_A Recombination and repair protein; storage dimer, inactive conformation, RECA like core domain, binding, DNA damage, DNA recombination; 2.40A {Enterobacteria phage T4}

Probab=97.25  E-value=0.0024  Score=54.45  Aligned_cols=35  Identities=20%  Similarity=0.309  Sum_probs=25.9

Q ss_pred             HHHHHh----cCCCce-EEEECCCCCCHHHHHHHHHHHHc
Q psy879           22 LKVFSS----SGNVPN-IIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        22 l~~~l~----~~~~~~-~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      |...+.    .|-++. ++++||||+|||+++..++....
T Consensus        14 LD~~LGg~~~GGl~~GiteI~G~pGsGKTtL~Lq~~~~~~   53 (333)
T 3io5_A           14 MNIALSGEITGGMQSGLLILAGPSKSFKSNFGLTMVSSYM   53 (333)
T ss_dssp             HHHHHHSSTTCCBCSEEEEEEESSSSSHHHHHHHHHHHHH
T ss_pred             HHHHhCCCCCCCCcCCeEEEECCCCCCHHHHHHHHHHHHH
Confidence            444455    444444 89999999999999888887654

>3zvl_A Bifunctional polynucleotide phosphatase/kinase; hydrolase-transferase complex, base excision repair, BER, non-homologous END-joining, NHEJ; 1.65A {Mus musculus} PDB: 3zvm_A* 3zvn_A* 1yj5_A 3u7e_B* 3u7f_B* 3u7h_B* 3u7g_A*

Probab=97.24  E-value=0.00083  Score=60.23  Aligned_cols=23  Identities=30%  Similarity=0.323  Sum_probs=21.0

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .+++.|+||+||||+++.+++.+
T Consensus       260 lIil~G~pGSGKSTla~~L~~~~  282 (416)
T 3zvl_A          260 VVVAVGFPGAGKSTFIQEHLVSA  282 (416)
T ss_dssp             EEEEESCTTSSHHHHHHHHTGGG
T ss_pred             EEEEECCCCCCHHHHHHHHHHhc
Confidence            38999999999999999999875

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=97.24  E-value=0.00093  Score=70.04  Aligned_cols=26  Identities=31%  Similarity=0.291  Sum_probs=22.6

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHcCC
Q psy879           33 NIIISGPPGVGKTTTILCLARILLGP   58 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~~~   58 (317)
                      +++++||||||||+++..++.+....
T Consensus      1083 ~vll~G~~GtGKT~la~~~~~ea~k~ 1108 (2050)
T 3cmu_A         1083 IVEIYGPESSGKTTLTLQVIAAAQRE 1108 (2050)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHHTT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHc
Confidence            59999999999999999999876433

>3b6e_A Interferon-induced helicase C domain-containing P; DECH, DEXD/H RNA-binding helicase, innate immunity, IFIH1, S genomics; 1.60A {Homo sapiens}

Probab=97.24  E-value=0.00047  Score=55.53  Aligned_cols=38  Identities=32%  Similarity=0.365  Sum_probs=26.7

Q ss_pred             CHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHH
Q psy879           15 NEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        15 ~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .+...+.+..++. +.  ++++.+|+|+|||.++...+...
T Consensus        35 ~~~Q~~~i~~~~~-~~--~~li~~~tGsGKT~~~~~~~~~~   72 (216)
T 3b6e_A           35 RPYQMEVAQPALE-GK--NIIICLPTGSGKTRVAVYIAKDH   72 (216)
T ss_dssp             CHHHHHHHHHHHT-TC--CEEEECSCHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHhc-CC--CEEEEcCCCCCHHHHHHHHHHHH
Confidence            3444444554443 33  69999999999999988877654

>1hv8_A Putative ATP-dependent RNA helicase MJ0669; RNA-binding protein, ATPase, RNA binding protein; 3.00A {Methanocaldococcus jannaschii} SCOP: c.37.1.19 c.37.1.19

Probab=97.23  E-value=0.002  Score=56.22  Aligned_cols=42  Identities=24%  Similarity=0.285  Sum_probs=26.0

Q ss_pred             CceeEEEEeCCCCCCHH-HHHHHHHHhhhccCCceEEEEecCC
Q psy879           95 GRHKIVILDEADSMTDG-AQQALRRTMEIYSNTTRFALACNNS  136 (317)
Q Consensus        95 ~~~~vliiDE~d~l~~~-~~~~ll~~le~~~~~~~~il~~~~~  136 (317)
                      ....++|+||+|.+... ....+.+++...+....+++.|..+
T Consensus       146 ~~~~~iIiDEah~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~  188 (367)
T 1hv8_A          146 KNVKYFILDEADEMLNMGFIKDVEKILNACNKDKRILLFSATM  188 (367)
T ss_dssp             TSCCEEEEETHHHHHTTTTHHHHHHHHHTSCSSCEEEEECSSC
T ss_pred             ccCCEEEEeCchHhhhhchHHHHHHHHHhCCCCceEEEEeecc
Confidence            45689999999987433 2344555555555556666554443

>3trf_A Shikimate kinase, SK; amino acid biosynthesis, transferase; 2.60A {Coxiella burnetii}

Probab=97.23  E-value=0.00022  Score=56.18  Aligned_cols=24  Identities=38%  Similarity=0.448  Sum_probs=22.4

Q ss_pred             ceEEEECCCCCCHHHHHHHHHHHH
Q psy879           32 PNIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        32 ~~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      ++++|.|++|+||||+++.+++.+
T Consensus         6 ~~i~l~G~~GsGKst~a~~La~~l   29 (185)
T 3trf_A            6 TNIYLIGLMGAGKTSVGSQLAKLT   29 (185)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHh
Confidence            369999999999999999999987

>3g5u_A MCG1178, multidrug resistance protein 1A; P-glycoprotein, PGP, cyclic peptide, membrane protein; 3.80A {Mus musculus} PDB: 3g61_A* 3g60_A*

Probab=97.20  E-value=0.00019  Score=73.35  Aligned_cols=42  Identities=17%  Similarity=0.275  Sum_probs=29.0

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhccCCceEEEEecCCC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYSNTTRFALACNNSE  137 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~~~~~~il~~~~~~  137 (317)
                      +++++++||+-. +..+....+.+.+........+|+++++..
T Consensus       544 ~p~iliLDEpts~LD~~~~~~i~~~l~~~~~~~t~i~itH~l~  586 (1284)
T 3g5u_A          544 NPKILLLDEATSALDTESEAVVQAALDKAREGRTTIVIAHRLS  586 (1284)
T ss_dssp             CCSEEEEESTTCSSCHHHHHHHHHHHHHHHTTSEEEEECSCHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHHHHHcCCCEEEEEecCHH
Confidence            578999999985 455566666666665445556777787643

>1qhx_A CPT, protein (chloramphenicol phosphotransferase); kinase, antibiotic resistance, phosphorylation, mononucleoti binding fold; HET: ATP; 2.50A {Streptomyces venezuelae} SCOP: c.37.1.3 PDB: 1grr_A* 1grq_A 1qhs_A* 1qhn_A* 1qhy_A*

Probab=97.20  E-value=0.00019  Score=56.13  Aligned_cols=23  Identities=35%  Similarity=0.697  Sum_probs=21.7

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .+++.|+||+||||+++.+++.+
T Consensus         5 ~i~l~G~~GsGKST~a~~La~~l   27 (178)
T 1qhx_A            5 MIILNGGSSAGKSGIVRCLQSVL   27 (178)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHHhc
Confidence            48999999999999999999986

>2z43_A DNA repair and recombination protein RADA; archaea, filament, DNA binding, molecular SWI RECA, DMC1; HET: DNA; 1.93A {Sulfolobus solfataricus} PDB: 2bke_A* 2dfl_A* 2zub_A* 2zuc_A* 2zud_A*

Probab=97.18  E-value=0.0017  Score=56.20  Aligned_cols=22  Identities=27%  Similarity=0.161  Sum_probs=20.7

Q ss_pred             EEEECCCCCCHHHHHHHHHHHH
Q psy879           34 IIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~l   55 (317)
                      ++++||||+|||+++..++...
T Consensus       110 ~~i~G~~GsGKT~la~~la~~~  131 (324)
T 2z43_A          110 TEFFGEFGSGKTQLCHQLSVNV  131 (324)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHT
T ss_pred             EEEECCCCCCHhHHHHHHHHHH
Confidence            8999999999999999999875

>4eun_A Thermoresistant glucokinase; putative sugar kinase, enzyme function initiative, EFI, STRU genomics, transferase; 1.60A {Janibacter SP}

Probab=97.15  E-value=0.00033  Score=56.07  Aligned_cols=24  Identities=29%  Similarity=0.396  Sum_probs=22.1

Q ss_pred             ceEEEECCCCCCHHHHHHHHHHHH
Q psy879           32 PNIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        32 ~~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      ..+.|.||+|+||||+++.++..+
T Consensus        30 ~~i~l~G~~GsGKSTl~~~L~~~~   53 (200)
T 4eun_A           30 RHVVVMGVSGSGKTTIAHGVADET   53 (200)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHhh
Confidence            369999999999999999999986

>1htw_A HI0065; nucleotide-binding fold, structural genomics, structure 2 function project, S2F, unknown function; HET: ADP; 1.70A {Haemophilus influenzae} SCOP: c.37.1.18 PDB: 1fl9_A

Probab=97.14  E-value=0.00033  Score=53.85  Aligned_cols=23  Identities=26%  Similarity=0.354  Sum_probs=21.8

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .+.|.||.|+||||+++.++..+
T Consensus        35 ~v~L~G~nGaGKTTLlr~l~g~l   57 (158)
T 1htw_A           35 MVYLNGDLGAGKTTLTRGMLQGI   57 (158)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHHhC
Confidence            58999999999999999999987

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens}

Probab=97.14  E-value=0.0028  Score=51.83  Aligned_cols=41  Identities=20%  Similarity=0.294  Sum_probs=25.3

Q ss_pred             CceeEEEEeCCCCCCHHH-HHHHHHHhhhccCCceEEEEecC
Q psy879           95 GRHKIVILDEADSMTDGA-QQALRRTMEIYSNTTRFALACNN  135 (317)
Q Consensus        95 ~~~~vliiDE~d~l~~~~-~~~ll~~le~~~~~~~~il~~~~  135 (317)
                      ....++|+||+|.+.... ...+..++...+....+++.|..
T Consensus       170 ~~~~~lViDEah~~~~~~~~~~~~~i~~~~~~~~~~l~~SAT  211 (236)
T 2pl3_A          170 TDLQMLVLDEADRILDMGFADTMNAVIENLPKKRQTLLFSAT  211 (236)
T ss_dssp             TTCCEEEETTHHHHHHTTTHHHHHHHHHTSCTTSEEEEEESS
T ss_pred             ccccEEEEeChHHHhcCCcHHHHHHHHHhCCCCCeEEEEEee
Confidence            456799999999875432 34455556655555555554433

>3kb2_A SPBC2 prophage-derived uncharacterized protein YORR; alpha-beta protein., structural genomics, PSI-2, protein structure initiative; HET: G3D; 2.20A {Bacillus subtilis} SCOP: c.37.1.1 PDB: 2axp_A*

Probab=97.14  E-value=0.00027  Score=54.84  Aligned_cols=23  Identities=35%  Similarity=0.375  Sum_probs=21.6

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .++|.|++|+||||+++.+++.+
T Consensus         3 ~i~l~G~~GsGKsT~~~~L~~~l   25 (173)
T 3kb2_A            3 LIILEGPDCCFKSTVAAKLSKEL   25 (173)
T ss_dssp             EEEEECSSSSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            58899999999999999999986

>3iij_A Coilin-interacting nuclear ATPase protein; alpha and beta proteins (A/B), protein binding, transferase, phosphotransferase; HET: ADP; 1.76A {Homo sapiens} SCOP: c.37.1.1 PDB: 3iik_A 3iil_A* 3iim_A* 1rkb_A

Probab=97.11  E-value=0.00037  Score=54.66  Aligned_cols=24  Identities=54%  Similarity=0.732  Sum_probs=22.2

Q ss_pred             ceEEEECCCCCCHHHHHHHHHHHH
Q psy879           32 PNIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        32 ~~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      +.++|+|+||+||||+++.+++.+
T Consensus        12 ~~i~i~G~~GsGKst~~~~l~~~~   35 (180)
T 3iij_A           12 PNILLTGTPGVGKTTLGKELASKS   35 (180)
T ss_dssp             CCEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CeEEEEeCCCCCHHHHHHHHHHHh
Confidence            369999999999999999999986

>1kag_A SKI, shikimate kinase I; transferase, structural genomics, PSI, protein structure initiative; 2.05A {Escherichia coli} SCOP: c.37.1.2

Probab=97.11  E-value=0.00029  Score=54.81  Aligned_cols=23  Identities=48%  Similarity=0.626  Sum_probs=21.6

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .+.|.||+|+||||+++.++..+
T Consensus         6 ~i~l~G~~GsGKSTl~~~La~~l   28 (173)
T 1kag_A            6 NIFLVGPMGAGKSTIGRQLAQQL   28 (173)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHT
T ss_pred             eEEEECCCCCCHHHHHHHHHHHh
Confidence            58999999999999999999986

>1ltq_A Polynucleotide kinase; phosphatase, alpha/beta, P-loop, transferase; HET: ADP; 2.33A {Enterobacteria phage T4} SCOP: c.108.1.9 c.37.1.1 PDB: 1rc8_A* 1rpz_A* 1rrc_A* 2ia5_A

Probab=97.11  E-value=0.0028  Score=54.02  Aligned_cols=23  Identities=30%  Similarity=0.264  Sum_probs=20.8

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .++|.|+||+||||+++.+++.+
T Consensus         4 ~I~l~G~~GsGKST~a~~L~~~~   26 (301)
T 1ltq_A            4 IILTIGCPGSGKSTWAREFIAKN   26 (301)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHHhC
Confidence            38999999999999999999863

>1vma_A Cell division protein FTSY; TM0570, structural genomics, JCS protein structure initiative, PSI, joint center for structu genomics; HET: CIT; 1.60A {Thermotoga maritima} SCOP: a.24.13.1 c.37.1.10

Probab=97.10  E-value=0.002  Score=55.05  Aligned_cols=24  Identities=38%  Similarity=0.592  Sum_probs=22.1

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHcC
Q psy879           34 IIISGPPGVGKTTTILCLARILLG   57 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~l~~   57 (317)
                      +++.||+|+||||++..+|..+..
T Consensus       107 i~ivG~~GsGKTTl~~~LA~~l~~  130 (306)
T 1vma_A          107 IMVVGVNGTGKTTSCGKLAKMFVD  130 (306)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHHHH
T ss_pred             EEEEcCCCChHHHHHHHHHHHHHh
Confidence            899999999999999999998753

>1via_A Shikimate kinase; structural genomics, transferase; HET: MSE; 1.57A {Campylobacter jejuni} SCOP: c.37.1.2

Probab=97.08  E-value=0.00036  Score=54.48  Aligned_cols=23  Identities=43%  Similarity=0.514  Sum_probs=21.8

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .++|.|+||+||||+++.+++.+
T Consensus         6 ~i~i~G~~GsGKsTla~~La~~l   28 (175)
T 1via_A            6 NIVFIGFMGSGKSTLARALAKDL   28 (175)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHc
Confidence            58999999999999999999987

>3b85_A Phosphate starvation-inducible protein; PHOH2, ATPase, PFAM: PF02562, ST genomics, PSI-2, protein structure initiative; 2.35A {Corynebacterium glutamicum atcc 13032}

Probab=97.08  E-value=0.00029  Score=56.85  Aligned_cols=42  Identities=26%  Similarity=0.367  Sum_probs=31.9

Q ss_pred             ccCCCCCCcccCCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHH
Q psy879            3 KYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus         3 ky~P~~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~   54 (317)
                      ..+|+++.    +..+++.    +..|.  .+.+.||+|+||||+++.++..
T Consensus         4 ~i~pk~~g----~~~~l~~----i~~Ge--~~~liG~nGsGKSTLl~~l~Gl   45 (208)
T 3b85_A            4 VIRPKTLG----QKHYVDA----IDTNT--IVFGLGPAGSGKTYLAMAKAVQ   45 (208)
T ss_dssp             CCCCCSHH----HHHHHHH----HHHCS--EEEEECCTTSSTTHHHHHHHHH
T ss_pred             ccccCCHh----HHHHHHh----ccCCC--EEEEECCCCCCHHHHHHHHhcC
Confidence            45788764    4444444    35666  6899999999999999999986

>1xti_A Probable ATP-dependent RNA helicase P47; alpha-beta fold, gene regulation; 1.95A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 1xtj_A* 1xtk_A

Probab=97.07  E-value=0.0089  Score=52.60  Aligned_cols=40  Identities=18%  Similarity=0.304  Sum_probs=26.0

Q ss_pred             CceeEEEEeCCCCCCH--HHHHHHHHHhhhccCCceEEEEec
Q psy879           95 GRHKIVILDEADSMTD--GAQQALRRTMEIYSNTTRFALACN  134 (317)
Q Consensus        95 ~~~~vliiDE~d~l~~--~~~~~ll~~le~~~~~~~~il~~~  134 (317)
                      ....++|+||+|.+..  .....+..++...+....+++.|.
T Consensus       151 ~~~~~vViDEaH~~~~~~~~~~~~~~~~~~~~~~~~~i~~SA  192 (391)
T 1xti_A          151 KHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSA  192 (391)
T ss_dssp             TTCSEEEECSHHHHTSSHHHHHHHHHHHHTSCSSSEEEEEES
T ss_pred             cccCEEEEeCHHHHhhccchHHHHHHHHhhCCCCceEEEEEe
Confidence            4567899999998864  444555666665555555555443

>3g5u_A MCG1178, multidrug resistance protein 1A; P-glycoprotein, PGP, cyclic peptide, membrane protein; 3.80A {Mus musculus} PDB: 3g61_A* 3g60_A*

Probab=97.05  E-value=0.00025  Score=72.45  Aligned_cols=44  Identities=16%  Similarity=0.314  Sum_probs=32.5

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhccCCceEEEEecCCCcC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYSNTTRFALACNNSEKI  139 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l  139 (317)
                      +++++++||+-. +.......+.+.+.+......+|+++++.+.+
T Consensus      1189 ~p~iLiLDEpTs~lD~~~~~~i~~~l~~~~~~~tvi~isH~l~~i 1233 (1284)
T 3g5u_A         1189 QPHILLLDEATSALDTESEKVVQEALDKAREGRTCIVIAHRLSTI 1233 (1284)
T ss_dssp             CCSSEEEESCSSSCCHHHHHHHHHHHHHHSSSSCEEEECSCTTGG
T ss_pred             CCCEEEEeCCcccCCHHHHHHHHHHHHHhCCCCEEEEEecCHHHH
Confidence            578999999985 56667777777777655556678888876543

>2px0_A Flagellar biosynthesis protein FLHF; SRP GTPase, flagellum, protein transport, biosynthetic protein; HET: GNP; 3.00A {Bacillus subtilis} PDB: 2px3_A* 3syn_A*

Probab=97.05  E-value=0.004  Score=53.03  Aligned_cols=24  Identities=46%  Similarity=0.641  Sum_probs=22.1

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHc
Q psy879           33 NIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      .+.|.||+|+||||++..++..+.
T Consensus       107 vi~lvG~~GsGKTTl~~~LA~~l~  130 (296)
T 2px0_A          107 YIVLFGSTGAGKTTTLAKLAAISM  130 (296)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHH
Confidence            489999999999999999999874

>3uie_A Adenylyl-sulfate kinase 1, chloroplastic; rossmann fold, transferase-transferase complex; HET: ADX ANP; 1.79A {Arabidopsis thaliana} SCOP: c.37.1.0 PDB: 4fxp_A*

Probab=97.04  E-value=0.00061  Score=54.46  Aligned_cols=24  Identities=33%  Similarity=0.519  Sum_probs=22.3

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHc
Q psy879           33 NIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      .+.|.||+|+||||+++.++..+.
T Consensus        27 ~i~l~G~sGsGKSTl~~~La~~l~   50 (200)
T 3uie_A           27 VIWVTGLSGSGKSTLACALNQMLY   50 (200)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHH
Confidence            599999999999999999999874

>1gvn_B Zeta; postsegregational killing system, plasmid; 1.95A {Streptococcus pyogenes} SCOP: c.37.1.21 PDB: 3q8x_B*

Probab=97.04  E-value=0.00046  Score=58.65  Aligned_cols=22  Identities=27%  Similarity=0.486  Sum_probs=20.9

Q ss_pred             EEEECCCCCCHHHHHHHHHHHH
Q psy879           34 IIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~l   55 (317)
                      ++|.||||+||||+++.+++.+
T Consensus        36 ivl~G~sGsGKSTla~~L~~~~   57 (287)
T 1gvn_B           36 FLLGGQPGSGKTSLRSAIFEET   57 (287)
T ss_dssp             EEEECCTTSCTHHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            8999999999999999999875

>1s2m_A Putative ATP-dependent RNA helicase DHH1; ATP-binding, RNA-binding, RNA binding protein; 2.10A {Saccharomyces cerevisiae} SCOP: c.37.1.19 c.37.1.19 PDB: 2wax_A* 2way_A

Probab=97.01  E-value=0.01  Score=52.50  Aligned_cols=46  Identities=20%  Similarity=0.289  Sum_probs=29.9

Q ss_pred             CCCCcccCCHHHHHHHHH---------------HHhcCCCceEEEECCCCCCHHHHHHHHHHH
Q psy879            7 QTFSDIVGNEDTVERLKV---------------FSSSGNVPNIIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus         7 ~~~~~~~g~~~~~~~l~~---------------~l~~~~~~~~ll~G~~G~GKt~la~~la~~   54 (317)
                      .+|+++--.+.+.+.|..               .+.+|+  ++++.+|+|+|||..+...+-.
T Consensus        21 ~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~--~~li~a~TGsGKT~~~~~~~~~   81 (400)
T 1s2m_A           21 NTFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGR--DILARAKNGTGKTAAFVIPTLE   81 (400)
T ss_dssp             CCGGGGCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTC--CEEEECCTTSCHHHHHHHHHHH
T ss_pred             CChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCC--CEEEECCCCcHHHHHHHHHHHH
Confidence            457777656655555443               122343  5999999999999876555443

>1kgd_A CASK, peripheral plasma membrane CASK; maguk, guanylate kinase like domain, protein binding; 1.31A {Homo sapiens} SCOP: c.37.1.1

Probab=97.01  E-value=0.00045  Score=54.26  Aligned_cols=23  Identities=22%  Similarity=0.356  Sum_probs=21.2

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .+.|.||+|+||||+++.++..+
T Consensus         7 ~i~i~GpsGsGKSTL~~~L~~~~   29 (180)
T 1kgd_A            7 TLVLLGAHGVGRRHIKNTLITKH   29 (180)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHhhC
Confidence            48999999999999999999874

>1kht_A Adenylate kinase; phosphotransferase, signaling protein, transferase; HET: AMP; 2.50A {Methanococcus voltae} SCOP: c.37.1.1 PDB: 3h86_B* 1ki9_A

Probab=97.01  E-value=0.00044  Score=54.60  Aligned_cols=24  Identities=33%  Similarity=0.502  Sum_probs=22.3

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHc
Q psy879           33 NIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      .++|.|+||+||||+++.+++.+.
T Consensus         5 ~I~i~G~~GsGKsT~~~~L~~~l~   28 (192)
T 1kht_A            5 VVVVTGVPGVGSTTSSQLAMDNLR   28 (192)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHH
Confidence            589999999999999999999874

>3fe2_A Probable ATP-dependent RNA helicase DDX5; DEAD, ADP, ATP-binding, hydrolase, nucleotide- RNA-binding, methylation, mRNA processing, mRNA S nucleus; HET: ADP; 2.60A {Homo sapiens} PDB: 4a4d_A

Probab=97.00  E-value=0.0047  Score=50.80  Aligned_cols=41  Identities=22%  Similarity=0.331  Sum_probs=26.0

Q ss_pred             CceeEEEEeCCCCCCHHH-HHHHHHHhhhccCCceEEEEecC
Q psy879           95 GRHKIVILDEADSMTDGA-QQALRRTMEIYSNTTRFALACNN  135 (317)
Q Consensus        95 ~~~~vliiDE~d~l~~~~-~~~ll~~le~~~~~~~~il~~~~  135 (317)
                      ...+++|+||+|.+.... ...+..++...++...+++.|..
T Consensus       175 ~~~~~lViDEah~l~~~~~~~~~~~i~~~~~~~~q~~~~SAT  216 (242)
T 3fe2_A          175 RRTTYLVLDEADRMLDMGFEPQIRKIVDQIRPDRQTLMWSAT  216 (242)
T ss_dssp             TTCCEEEETTHHHHHHTTCHHHHHHHHTTSCSSCEEEEEESC
T ss_pred             ccccEEEEeCHHHHhhhCcHHHHHHHHHhCCccceEEEEEee
Confidence            456799999999876532 44455556655555666555433

>3iuy_A Probable ATP-dependent RNA helicase DDX53; REC-A-like, DEAD-BOX, structural genomics, structural genomi consortium, SGC, ATP-binding, hydrolase; HET: AMP; 2.40A {Homo sapiens}

Probab=96.99  E-value=0.0059  Score=49.59  Aligned_cols=41  Identities=17%  Similarity=0.255  Sum_probs=25.4

Q ss_pred             CceeEEEEeCCCCCCHHH-HHHHHHHhhhccCCceEEEEecC
Q psy879           95 GRHKIVILDEADSMTDGA-QQALRRTMEIYSNTTRFALACNN  135 (317)
Q Consensus        95 ~~~~vliiDE~d~l~~~~-~~~ll~~le~~~~~~~~il~~~~  135 (317)
                      ...+++|+||+|.+.... ...+..++...+.+..+++.|..
T Consensus       166 ~~~~~lViDEah~~~~~~~~~~~~~i~~~~~~~~~~l~~SAT  207 (228)
T 3iuy_A          166 RSITYLVIDEADKMLDMEFEPQIRKILLDVRPDRQTVMTSAT  207 (228)
T ss_dssp             TTCCEEEECCHHHHHHTTCHHHHHHHHHHSCSSCEEEEEESC
T ss_pred             ccceEEEEECHHHHhccchHHHHHHHHHhCCcCCeEEEEEee
Confidence            456899999999875432 34455555555555565555433

>3sop_A Neuronal-specific septin-3; hydrolase; HET: GDP; 2.88A {Homo sapiens}

Probab=96.99  E-value=0.012  Score=49.29  Aligned_cols=24  Identities=33%  Similarity=0.591  Sum_probs=21.7

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHc
Q psy879           33 NIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      ++.+.||+|+||||+.+.++....
T Consensus         4 ~v~lvG~nGaGKSTLln~L~g~~~   27 (270)
T 3sop_A            4 NIMVVGQSGLGKSTLVNTLFKSQV   27 (270)
T ss_dssp             EEEEEESSSSSHHHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHhCCCC
Confidence            478999999999999999998764

>1y63_A LMAJ004144AAA protein; structural genomics, protein structure initiative, PSI, SGPP structural genomics of pathogenic protozoa consortium; HET: ADP; 1.70A {Leishmania major} SCOP: c.37.1.1

Probab=96.98  E-value=0.00054  Score=54.01  Aligned_cols=24  Identities=46%  Similarity=0.681  Sum_probs=22.0

Q ss_pred             ceEEEECCCCCCHHHHHHHHHHHH
Q psy879           32 PNIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        32 ~~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      ..++|+|++|+||||+++.+++.+
T Consensus        11 ~~I~l~G~~GsGKSTv~~~La~~l   34 (184)
T 1y63_A           11 INILITGTPGTGKTSMAEMIAAEL   34 (184)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             CEEEEECCCCCCHHHHHHHHHHhc
Confidence            469999999999999999999983

>2p5t_B PEZT; postsegregational killing system, phosphoryltransferase, HEL helix motif, transcription regulator; 3.20A {Streptococcus pneumoniae}

Probab=96.98  E-value=0.00041  Score=57.77  Aligned_cols=23  Identities=30%  Similarity=0.459  Sum_probs=21.5

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .++|.|+||+||||+++.+++.+
T Consensus        34 ~i~l~G~~GsGKSTla~~L~~~l   56 (253)
T 2p5t_B           34 AILLGGQSGAGKTTIHRIKQKEF   56 (253)
T ss_dssp             EEEEESCGGGTTHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHHhc
Confidence            38999999999999999999986

>3lda_A DNA repair protein RAD51; DNA binding protein, ATP-binding, DNA damage, DNA recombinat repair, nucleotide-binding; HET: DNA; 2.50A {Saccharomyces cerevisiae} PDB: 1szp_A*

Probab=96.97  E-value=0.0022  Score=57.03  Aligned_cols=23  Identities=22%  Similarity=0.060  Sum_probs=19.8

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .+.|+||||+||||+++.++-..
T Consensus       180 i~~I~G~sGsGKTTLl~~la~~~  202 (400)
T 3lda_A          180 ITELFGEFRTGKSQLCHTLAVTC  202 (400)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHT
T ss_pred             EEEEEcCCCCChHHHHHHHHHHh
Confidence            38999999999999999877443

>1ly1_A Polynucleotide kinase; PNK, phosphatase, transferase; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.1

Probab=96.97  E-value=0.00044  Score=54.04  Aligned_cols=22  Identities=32%  Similarity=0.321  Sum_probs=20.2

Q ss_pred             eEEEECCCCCCHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~   54 (317)
                      .++|.|+||+||||+++.+++.
T Consensus         4 ~I~i~G~~GsGKST~a~~L~~~   25 (181)
T 1ly1_A            4 IILTIGCPGSGKSTWAREFIAK   25 (181)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEEecCCCCCHHHHHHHHHhh
Confidence            3899999999999999999983

>3nwj_A ATSK2; P loop, shikimate, nucleoside monophosphate kinase, shikimat ATP binding, chloroplast, transferase; 2.35A {Arabidopsis thaliana}

Probab=96.97  E-value=0.0006  Score=56.61  Aligned_cols=40  Identities=25%  Similarity=0.310  Sum_probs=31.1

Q ss_pred             CCHHHHHHHHHHHhc---CCCceEEEECCCCCCHHHHHHHHHHHH
Q psy879           14 GNEDTVERLKVFSSS---GNVPNIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        14 g~~~~~~~l~~~l~~---~~~~~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      +...+++.+.-.+..   |.  .+.|.|++|+||||+++.+++.+
T Consensus        30 ~~~~~l~~~~~~i~~~l~g~--~i~l~G~~GsGKSTl~~~La~~l   72 (250)
T 3nwj_A           30 EEQQILKKKAEEVKPYLNGR--SMYLVGMMGSGKTTVGKIMARSL   72 (250)
T ss_dssp             --CHHHHHHHHTTHHHHTTC--CEEEECSTTSCHHHHHHHHHHHH
T ss_pred             CcchhhhhhhhhhhhhcCCC--EEEEECCCCCCHHHHHHHHHHhc
Confidence            334566666655665   65  79999999999999999999987

>1zuh_A Shikimate kinase; alpha-beta protein, transferase; 1.80A {Helicobacter pylori} PDB: 1zui_A* 3hr7_A 3muf_A* 3mrs_A 3n2e_A*

Probab=96.96  E-value=0.00055  Score=52.98  Aligned_cols=24  Identities=25%  Similarity=0.355  Sum_probs=22.3

Q ss_pred             ceEEEECCCCCCHHHHHHHHHHHH
Q psy879           32 PNIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        32 ~~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .+++|.|++|+||||+++.+++.+
T Consensus         8 ~~i~l~G~~GsGKSTva~~La~~l   31 (168)
T 1zuh_A            8 QHLVLIGFMGSGKSSLAQELGLAL   31 (168)
T ss_dssp             CEEEEESCTTSSHHHHHHHHHHHH
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHh
Confidence            369999999999999999999987

>1nks_A Adenylate kinase; thermophilic, transferase; HET: AMP ADP; 2.57A {Sulfolobus acidocaldarius} SCOP: c.37.1.1

Probab=96.96  E-value=0.00045  Score=54.60  Aligned_cols=25  Identities=40%  Similarity=0.557  Sum_probs=22.6

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHcC
Q psy879           33 NIIISGPPGVGKTTTILCLARILLG   57 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~~   57 (317)
                      .++|.|+||+||||+++.+++.+..
T Consensus         3 ~I~i~G~~GsGKsT~~~~L~~~l~~   27 (194)
T 1nks_A            3 IGIVTGIPGVGKSTVLAKVKEILDN   27 (194)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHh
Confidence            4899999999999999999998753

>3c8u_A Fructokinase; YP_612366.1, putative fructose transport system kinase, STRU genomics, joint center for structural genomics, JCSG; 1.95A {Silicibacter SP}

Probab=96.96  E-value=0.00092  Score=53.79  Aligned_cols=40  Identities=25%  Similarity=0.215  Sum_probs=28.4

Q ss_pred             HHHHHHHHHHhcC--CCceEEEECCCCCCHHHHHHHHHHHHc
Q psy879           17 DTVERLKVFSSSG--NVPNIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        17 ~~~~~l~~~l~~~--~~~~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      ++.+.+...+...  ....+.|.||+|+||||+++.++..+.
T Consensus         6 ~~~~~~~~~~~~~~~~g~~v~I~G~sGsGKSTl~~~l~~~~~   47 (208)
T 3c8u_A            6 ALCQGVLERLDPRQPGRQLVALSGAPGSGKSTLSNPLAAALS   47 (208)
T ss_dssp             HHHHHHHHHSCTTCCSCEEEEEECCTTSCTHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCCCCeEEEEECCCCCCHHHHHHHHHHHHh
Confidence            3444454444332  222489999999999999999999874

>3fht_A ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box helicase, RNA dependent ATPase, mRNA export, nucleocytoplasmic transport, NUP214, CAN; HET: ANP; 2.20A {Homo sapiens} PDB: 3ews_A* 3g0h_A* 3fhc_B

Probab=96.95  E-value=0.0062  Score=54.02  Aligned_cols=49  Identities=14%  Similarity=0.276  Sum_probs=30.5

Q ss_pred             CCCCcccCCHHHHHHHHHH---------------HhcCCCceEEEECCCCCCHHHHHHH-HHHHH
Q psy879            7 QTFSDIVGNEDTVERLKVF---------------SSSGNVPNIIISGPPGVGKTTTILC-LARIL   55 (317)
Q Consensus         7 ~~~~~~~g~~~~~~~l~~~---------------l~~~~~~~~ll~G~~G~GKt~la~~-la~~l   55 (317)
                      ++|+++--.+.+.+.+...               +.++...++++.+|+|+|||..+.. +...+
T Consensus        25 ~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~~~lv~apTGsGKT~~~~~~~~~~~   89 (412)
T 3fht_A           25 KSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQV   89 (412)
T ss_dssp             SCTGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHHSSSCCCEEEECCTTSCHHHHHHHHHHHHC
T ss_pred             CCHhhCCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCCeEEEECCCCchHHHHHHHHHHHHh
Confidence            4567665566655554332               2334333699999999999988643 44443

>2iyv_A Shikimate kinase, SK; transferase, aromatic amino acid biosynthesis, P-loop kinase, metal- binding, shikimate pathway; HET: ADP; 1.35A {Mycobacterium tuberculosis} SCOP: c.37.1.2 PDB: 2iyr_A* 2iyq_A* 2iyt_A 2iyu_A* 2iys_A* 2iyw_A* 2iyx_A* 2iyy_A* 2iyz_A* 2g1k_A* 1l4y_A* 1u8a_A* 1we2_A* 1zyu_A* 2dfn_A* 2dft_A* 2g1j_A 1l4u_A* 3baf_A*

Probab=96.95  E-value=0.00054  Score=53.89  Aligned_cols=23  Identities=39%  Similarity=0.566  Sum_probs=21.7

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .++|.|+||+||||+++.+++.+
T Consensus         4 ~I~l~G~~GsGKsT~a~~La~~l   26 (184)
T 2iyv_A            4 KAVLVGLPGSGKSTIGRRLAKAL   26 (184)
T ss_dssp             SEEEECSTTSSHHHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHHc
Confidence            58999999999999999999986

>2rhm_A Putative kinase; P-loop containing nucleoside triphosphate hydrolases fold, S genomics, joint center for structural genomics, JCSG; HET: MSE; 1.70A {Chloroflexus aurantiacus}

Probab=96.95  E-value=0.00053  Score=54.24  Aligned_cols=23  Identities=48%  Similarity=0.573  Sum_probs=21.6

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .++|.|+||+||||+++.+++.+
T Consensus         7 ~I~l~G~~GsGKST~~~~L~~~l   29 (193)
T 2rhm_A            7 LIIVTGHPATGKTTLSQALATGL   29 (193)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHc
Confidence            48999999999999999999986

>3ctd_A Putative ATPase, AAA family; structural genomics, unknown function, PSI-2, protein structure initiative; 2.50A {Prochlorococcus marinus subsp} SCOP: a.80.1.2

Probab=96.95  E-value=0.011  Score=46.74  Aligned_cols=88  Identities=16%  Similarity=0.255  Sum_probs=67.2

Q ss_pred             CCCHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHH-HhcCCChHHHHHHHHHHHHHHhHHhcCC-CcH
Q psy879          219 EPHPLAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDIIGNIFRVA-KTLDIPEPLKLSIIQEIGNVHLRISEGV-NSL  296 (317)
Q Consensus       219 ~~~~~~i~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~-~~~~~~~~~~~~~~~~l~~~~~~l~~g~-~~~  296 (317)
                      ..+.+.++.++++++..|.+.|+.|+..|++.|++|..|.+.+.+++ +.+|+.+.....+...+.+.-.++  |. ..+
T Consensus        33 d~HYd~ISAf~KSiRGSDpDAALywLaRMl~~GEDp~~IaRRLvi~AsEDIGlAdP~Al~~a~aa~~a~~~i--G~PE~~  110 (213)
T 3ctd_A           33 QNHFDVISAFIKSIRGSDPDATLYWLANMVEAGEDPNFIFRRLLISACEDIGLADPNAIVVVQSCCDAFDRV--GFPEGL  110 (213)
T ss_dssp             -CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHTTGGGSTTHHHHHHHHHHHHHHH--CTTTTH
T ss_pred             hHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhhccCCCHHHHHHHHHHHHHHHHh--CCCHHH
Confidence            45677899999999999999999999999999999999999998876 455666655544444444444433  55 777


Q ss_pred             HHHHHHHHHHHH
Q psy879          297 LQLSGLLARLCI  308 (317)
Q Consensus       297 l~le~~~~~~~~  308 (317)
                      +.|-..+.-+|.
T Consensus       111 i~LaqaviyLA~  122 (213)
T 3ctd_A          111 FFLSQASLYLAI  122 (213)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHc
Confidence            888777777773

>1aky_A Adenylate kinase; ATP:AMP phosphotransferase, myokinase, transferase (phosphotransferase); HET: AP5; 1.63A {Saccharomyces cerevisiae} SCOP: c.37.1.1 g.41.2.1 PDB: 2aky_A* 3aky_A* 1dvr_A*

Probab=96.93  E-value=0.00066  Score=55.13  Aligned_cols=23  Identities=35%  Similarity=0.660  Sum_probs=21.8

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .++|.|+||+||||+++.+++.+
T Consensus         6 ~I~l~G~~GsGKsT~a~~La~~l   28 (220)
T 1aky_A            6 RMVLIGPPGAGKGTQAPNLQERF   28 (220)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHc
Confidence            58999999999999999999987

>1zp6_A Hypothetical protein ATU3015; alpha-beta protein., structural genomics, PSI, protein struc initiative; 3.20A {Agrobacterium tumefaciens str} SCOP: c.37.1.25

Probab=96.93  E-value=0.00036  Score=55.21  Aligned_cols=22  Identities=41%  Similarity=0.699  Sum_probs=20.5

Q ss_pred             eEEEECCCCCCHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~   54 (317)
                      .+.|.||+|+||||+++.++..
T Consensus        11 ~i~l~G~~GsGKSTl~~~La~~   32 (191)
T 1zp6_A           11 ILLLSGHPGSGKSTIAEALANL   32 (191)
T ss_dssp             EEEEEECTTSCHHHHHHHHHTC
T ss_pred             EEEEECCCCCCHHHHHHHHHhc
Confidence            5899999999999999999885

>3t61_A Gluconokinase; PSI-biology, structural genomics, protein structure initiati YORK structural genomics research consortium, nysgrc; 2.20A {Sinorhizobium meliloti}

Probab=96.92  E-value=0.00055  Score=54.75  Aligned_cols=23  Identities=26%  Similarity=0.433  Sum_probs=21.8

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .++|.|++|+||||+++.+++.+
T Consensus        20 ~I~l~G~~GsGKSTla~~L~~~l   42 (202)
T 3t61_A           20 SIVVMGVSGSGKSSVGEAIAEAC   42 (202)
T ss_dssp             CEEEECSTTSCHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            59999999999999999999986

>3fmp_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 3.19A {Homo sapiens}

Probab=96.92  E-value=0.0046  Score=56.37  Aligned_cols=42  Identities=26%  Similarity=0.344  Sum_probs=26.4

Q ss_pred             CceeEEEEeCCCCCCH--HHHHHHHHHhhhccCCceEEEEecCC
Q psy879           95 GRHKIVILDEADSMTD--GAQQALRRTMEIYSNTTRFALACNNS  136 (317)
Q Consensus        95 ~~~~vliiDE~d~l~~--~~~~~ll~~le~~~~~~~~il~~~~~  136 (317)
                      ...++|||||+|.+..  .....+..++...+....+++.+..+
T Consensus       234 ~~~~~iViDEah~~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~  277 (479)
T 3fmp_B          234 KKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATF  277 (479)
T ss_dssp             GGCCEEEECCHHHHHTSTTHHHHHHHHHTTSCTTSEEEEEESCC
T ss_pred             ccCCEEEEECHHHHhhcCCcHHHHHHHHhhCCccceEEEEeCCC
Confidence            4568999999997743  33444445555555566666655443

>3cm0_A Adenylate kinase; ATP-binding, cytoplasm, nucleotide biosynthesis, nucleotide-binding, transferase, structural genomics; 1.80A {Thermus thermophilus}

Probab=96.91  E-value=0.00059  Score=53.68  Aligned_cols=23  Identities=48%  Similarity=0.717  Sum_probs=21.5

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .++|.|+||+||||+++.+++.+
T Consensus         6 ~I~l~G~~GsGKST~~~~La~~l   28 (186)
T 3cm0_A            6 AVIFLGPPGAGKGTQASRLAQEL   28 (186)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            48999999999999999999886

>3exa_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2, protein structure initiative; 2.30A {Bacillus halodurans} PDB: 2qgn_A

Probab=96.91  E-value=0.0031  Score=53.72  Aligned_cols=23  Identities=48%  Similarity=0.655  Sum_probs=21.4

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .+++.||+|+|||+++..+++.+
T Consensus         5 ~i~i~GptgsGKt~la~~La~~~   27 (322)
T 3exa_A            5 LVAIVGPTAVGKTKTSVMLAKRL   27 (322)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHTT
T ss_pred             EEEEECCCcCCHHHHHHHHHHhC
Confidence            48899999999999999999986

>2c95_A Adenylate kinase 1; transferase, AP4A, nucleotide kinase, transferase ATP-bindi; HET: B4P; 1.71A {Homo sapiens} PDB: 1z83_A* 3adk_A

Probab=96.91  E-value=0.00086  Score=53.14  Aligned_cols=23  Identities=30%  Similarity=0.426  Sum_probs=21.8

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .++|.|+||+||||+++.+++.+
T Consensus        11 ~I~l~G~~GsGKsT~~~~La~~l   33 (196)
T 2c95_A           11 IIFVVGGPGSGKGTQCEKIVQKY   33 (196)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            69999999999999999999986

>2ewv_A Twitching motility protein PILT; pilus retraction motor, ATPase, hexameric PILT, protein TRAN; HET: ADP; 2.80A {Aquifex aeolicus} PDB: 2eww_A* 2gsz_A*

Probab=96.89  E-value=0.0016  Score=57.33  Aligned_cols=24  Identities=38%  Similarity=0.671  Sum_probs=22.2

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHc
Q psy879           33 NIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      .+++.||+|+||||++++++..+.
T Consensus       138 ~i~ivG~~GsGKTTll~~l~~~~~  161 (372)
T 2ewv_A          138 LILVTGPTGSGKSTTIASMIDYIN  161 (372)
T ss_dssp             EEEEECSSSSSHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHhhcC
Confidence            599999999999999999999874

>3vkw_A Replicase large subunit; alpha/beta domain, helicase, transferase; 1.90A {Tomato mosaic virus}

Probab=96.88  E-value=0.0039  Score=55.80  Aligned_cols=107  Identities=18%  Similarity=0.230  Sum_probs=59.6

Q ss_pred             HHHHHHHHHHhcCCC-----ceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHHHHH-------
Q psy879           17 DTVERLKVFSSSGNV-----PNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKM-------   84 (317)
Q Consensus        17 ~~~~~l~~~l~~~~~-----~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~~~-------   84 (317)
                      .+++.|...++.+..     +..++.|+||+|||+++..++..      . ...-+.+. ....+++++.+..       
T Consensus       142 ~~l~~l~~~~~~~~~~~~~~~v~~I~G~aGsGKTt~I~~~~~~------~-~~lVlTpT-~~aa~~l~~kl~~~~~~~~~  213 (446)
T 3vkw_A          142 AKLRTLRRLLKDGEPHVSSAKVVLVDGVPGCGKTKEILSRVNF------E-EDLILVPG-RQAAEMIRRRANASGIIVAT  213 (446)
T ss_dssp             HHHHHHHTTCBTTBCCCCCSEEEEEEECTTSCHHHHHHHHCCT------T-TCEEEESC-HHHHHHHHHHHTTTSCCCCC
T ss_pred             HHHHHHHHHHhhhccccccccEEEEEcCCCCCHHHHHHHHhcc------C-CeEEEeCC-HHHHHHHHHHhhhcCccccc
Confidence            455566666433322     23799999999999999877642      1 11222222 1222333333321       


Q ss_pred             ---------HHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecC
Q psy879           85 ---------FAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNN  135 (317)
Q Consensus        85 ---------~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~  135 (317)
                               +.............++||||+..+......+++..+.   . ..+|++...
T Consensus       214 ~~~V~T~dsfL~~~~~~~~~~~d~liiDE~sm~~~~~l~~l~~~~~---~-~~vilvGD~  269 (446)
T 3vkw_A          214 KDNVRTVDSFLMNYGKGARCQFKRLFIDEGLMLHTGCVNFLVEMSL---C-DIAYVYGDT  269 (446)
T ss_dssp             TTTEEEHHHHHHTTTSSCCCCCSEEEEETGGGSCHHHHHHHHHHTT---C-SEEEEEECT
T ss_pred             cceEEEeHHhhcCCCCCCCCcCCEEEEeCcccCCHHHHHHHHHhCC---C-CEEEEecCc
Confidence                     0000000000126899999999998887777766542   2 667777654

>2j0s_A ATP-dependent RNA helicase DDX48; mRNA processing, phosphorylation, rRNA processing, mRNA splicing, mRNA transport; HET: ANP; 2.21A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 2j0q_A* 2hyi_C* 3ex7_C* 2xb2_A* 2hxy_A 2j0u_A 2j0u_B 2zu6_A

Probab=96.88  E-value=0.008  Score=53.38  Aligned_cols=41  Identities=22%  Similarity=0.320  Sum_probs=25.9

Q ss_pred             CceeEEEEeCCCCCCHH-HHHHHHHHhhhccCCceEEEEecC
Q psy879           95 GRHKIVILDEADSMTDG-AQQALRRTMEIYSNTTRFALACNN  135 (317)
Q Consensus        95 ~~~~vliiDE~d~l~~~-~~~~ll~~le~~~~~~~~il~~~~  135 (317)
                      ....++|+||+|.+... ....+..++...+....+++.|..
T Consensus       178 ~~~~~vViDEah~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT  219 (410)
T 2j0s_A          178 RAIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVVLISAT  219 (410)
T ss_dssp             TTCCEEEEETHHHHTSTTTHHHHHHHHTTSCTTCEEEEEESC
T ss_pred             hheeEEEEccHHHHHhhhhHHHHHHHHHhCccCceEEEEEcC
Confidence            45689999999987543 244555666655555555555433

>2xau_A PRE-mRNA-splicing factor ATP-dependent RNA helica; hydrolase, ribosome biogenesis, ATPase, ATP-binding, OB-fold; HET: ADP; 1.90A {Saccharomyces cerevisiae} PDB: 3kx2_B*

Probab=96.87  E-value=0.0062  Score=58.93  Aligned_cols=28  Identities=25%  Similarity=0.381  Sum_probs=21.0

Q ss_pred             HHhcCCCceEEEECCCCCCHHHHHHHHHHH
Q psy879           25 FSSSGNVPNIIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        25 ~l~~~~~~~~ll~G~~G~GKt~la~~la~~   54 (317)
                      .+.++.  ++++.||+|+|||+++..++..
T Consensus       105 ~l~~~~--~vii~gpTGSGKTtllp~ll~~  132 (773)
T 2xau_A          105 LYQNNQ--IMVFVGETGSGKTTQIPQFVLF  132 (773)
T ss_dssp             HHHHCS--EEEEECCTTSSHHHHHHHHHHH
T ss_pred             HHhCCC--eEEEECCCCCCHHHHHHHHHHH
Confidence            344444  6999999999999977666543

>1p9r_A General secretion pathway protein E; bacterial type II secretion system cytoplasmic protein - GSPE, putative ATPase/ ATP binding protein; 2.50A {Vibrio cholerae} SCOP: c.37.1.11 PDB: 1p9w_A*

Probab=96.85  E-value=0.0024  Score=57.04  Aligned_cols=50  Identities=18%  Similarity=0.277  Sum_probs=35.0

Q ss_pred             CCCcccCCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCC
Q psy879            8 TFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGP   58 (317)
Q Consensus         8 ~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~   58 (317)
                      +++++--.......|...+. ..-..+++.||+|+||||+.++++..+...
T Consensus       145 ~l~~Lg~~~~~~~~L~~l~~-~~ggii~I~GpnGSGKTTlL~allg~l~~~  194 (418)
T 1p9r_A          145 DLHSLGMTAHNHDNFRRLIK-RPHGIILVTGPTGSGKSTTLYAGLQELNSS  194 (418)
T ss_dssp             CGGGSCCCHHHHHHHHHHHT-SSSEEEEEECSTTSCHHHHHHHHHHHHCCT
T ss_pred             CHHHcCCCHHHHHHHHHHHH-hcCCeEEEECCCCCCHHHHHHHHHhhcCCC
Confidence            45555445555555666543 222248999999999999999999988543

>1tf7_A KAIC; homohexamer, hexamer, circadian clock protein; HET: ATP; 2.80A {Synechococcus SP} SCOP: c.37.1.11 c.37.1.11 PDB: 3s1a_A* 1u9i_A* 2gbl_A* 3dvl_A* 3k0a_A* 3k09_A* 3jzm_A* 3k0e_A* 4dug_A* 3ua2_A* 3k0c_A* 3k0f_A*

Probab=96.85  E-value=0.003  Score=58.38  Aligned_cols=36  Identities=22%  Similarity=0.349  Sum_probs=25.3

Q ss_pred             HHHHHHH-HHhcCCCceEEEECCCCCCHHHHHHHH--HHHH
Q psy879           18 TVERLKV-FSSSGNVPNIIISGPPGVGKTTTILCL--ARIL   55 (317)
Q Consensus        18 ~~~~l~~-~l~~~~~~~~ll~G~~G~GKt~la~~l--a~~l   55 (317)
                      +++.+.- -+..|.  .+++.||+|+||||+++.+  +..+
T Consensus        27 ~Ld~i~~G~i~~Ge--~~~l~G~nGsGKSTL~~~~ll~Gl~   65 (525)
T 1tf7_A           27 GFDDISHGGLPIGR--STLVSGTSGTGKTLFSIQFLYNGII   65 (525)
T ss_dssp             THHHHTTSSEETTS--EEEEEESTTSSHHHHHHHHHHHHHH
T ss_pred             hHHHhcCCCCCCCe--EEEEEcCCCCCHHHHHHHHHHHHHH
Confidence            3444433 344555  6999999999999999994  4544

>3umf_A Adenylate kinase; rossmann fold, transferase; 2.05A {Schistosoma mansoni}

Probab=96.85  E-value=0.00086  Score=54.33  Aligned_cols=23  Identities=35%  Similarity=0.465  Sum_probs=21.3

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .++|.||||+||+|.++.+++.+
T Consensus        31 iI~llGpPGsGKgTqa~~L~~~~   53 (217)
T 3umf_A           31 VIFVLGGPGSGKGTQCEKLVQKF   53 (217)
T ss_dssp             EEEEECCTTCCHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            48889999999999999999986

>1knq_A Gluconate kinase; ALFA/beta structure, transferase; 2.00A {Escherichia coli} SCOP: c.37.1.17 PDB: 1ko1_A 1ko4_A 1ko5_A* 1ko8_A* 1kof_A*

Probab=96.85  E-value=0.00072  Score=52.66  Aligned_cols=23  Identities=26%  Similarity=0.359  Sum_probs=21.4

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .++|.||+|+||||+++.++..+
T Consensus        10 ~i~l~G~~GsGKSTl~~~l~~~~   32 (175)
T 1knq_A           10 IYVLMGVSGSGKSAVASEVAHQL   32 (175)
T ss_dssp             EEEEECSTTSCHHHHHHHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHHHHhh
Confidence            48999999999999999999876

>1e6c_A Shikimate kinase; phosphoryl transfer, ADP, shikimate pathway, P-loop protein, transferase; 1.8A {Erwinia chrysanthemi} SCOP: c.37.1.2 PDB: 1shk_A 2shk_A*

Probab=96.85  E-value=0.00073  Score=52.41  Aligned_cols=23  Identities=43%  Similarity=0.479  Sum_probs=21.7

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .++|.|++|+||||+++.+++.+
T Consensus         4 ~I~l~G~~GsGKsT~a~~La~~l   26 (173)
T 1e6c_A            4 PIFMVGARGCGMTTVGRELARAL   26 (173)
T ss_dssp             CEEEESCTTSSHHHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHHh
Confidence            58999999999999999999986

>3e2i_A Thymidine kinase; Zn-binding, ATP-binding, DNA synthesis, nucleotide-B transferase; HET: MSE; 2.01A {Staphylococcus aureus}

Probab=96.84  E-value=0.0018  Score=52.02  Aligned_cols=36  Identities=14%  Similarity=0.192  Sum_probs=26.3

Q ss_pred             CceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEe
Q psy879           95 GRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALAC  133 (317)
Q Consensus        95 ~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~  133 (317)
                      .+..+|+|||+.+++++..+.+.++.+   .+..+|+..
T Consensus       100 ~~~dvV~IDEaQFf~~~~v~~l~~la~---~gi~Vi~~G  135 (219)
T 3e2i_A          100 TNVDVIGIDEVQFFDDEIVSIVEKLSA---DGHRVIVAG  135 (219)
T ss_dssp             TTCSEEEECCGGGSCTHHHHHHHHHHH---TTCEEEEEE
T ss_pred             cCCCEEEEechhcCCHHHHHHHHHHHH---CCCEEEEee
Confidence            456799999999999987777776663   345555554

>4b3f_X DNA-binding protein smubp-2; hydrolase, helicase; 2.50A {Homo sapiens} PDB: 4b3g_A

Probab=96.84  E-value=0.0024  Score=60.60  Aligned_cols=41  Identities=32%  Similarity=0.385  Sum_probs=30.7

Q ss_pred             CCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHc
Q psy879           14 GNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        14 g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      -++...+.+..++.+..  -.++.||||||||+++-.+...+.
T Consensus       190 LN~~Q~~AV~~al~~~~--~~lI~GPPGTGKT~ti~~~I~~l~  230 (646)
T 4b3f_X          190 LDTSQKEAVLFALSQKE--LAIIHGPPGTGKTTTVVEIILQAV  230 (646)
T ss_dssp             CCHHHHHHHHHHHHCSS--EEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHhcCCC--ceEEECCCCCCHHHHHHHHHHHHH
Confidence            36677777888776543  589999999999987766665554

>2ze6_A Isopentenyl transferase; crown GALL tumor, cytokinin biosynthesis; HET: DST AMP; 2.10A {Agrobacterium tumefaciens} PDB: 2ze5_A* 2ze7_A* 2ze8_A

Probab=96.83  E-value=0.00071  Score=56.31  Aligned_cols=23  Identities=30%  Similarity=0.364  Sum_probs=21.5

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .+++.||+|+||||+++.+++.+
T Consensus         3 li~I~G~~GSGKSTla~~La~~~   25 (253)
T 2ze6_A            3 LHLIYGPTCSGKTDMAIQIAQET   25 (253)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHhcC
Confidence            47899999999999999999986

>2v9p_A Replication protein E1; AAA+ molecular motor, DNA replication, DNA translocation, nucleotide-binding, DNA-binding; 3.00A {Bovine papillomavirus type 1} PDB: 2gxa_A*

Probab=96.82  E-value=0.0013  Score=56.22  Aligned_cols=36  Identities=22%  Similarity=0.269  Sum_probs=28.0

Q ss_pred             HHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHH
Q psy879           18 TVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        18 ~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      +++.+.-.+..|.  .+.|+||+|+||||+++.++..+
T Consensus       115 vL~~vsl~i~~Ge--~vaIvGpsGsGKSTLl~lL~gl~  150 (305)
T 2v9p_A          115 ALKLWLKGIPKKN--CLAFIGPPNTGKSMLCNSLIHFL  150 (305)
T ss_dssp             HHHHHHHTCTTCS--EEEEECSSSSSHHHHHHHHHHHH
T ss_pred             hhccceEEecCCC--EEEEECCCCCcHHHHHHHHhhhc
Confidence            3444444445555  69999999999999999999986

>3eiq_A Eukaryotic initiation factor 4A-I; PDCD4, anti-oncogene, apoptosis, cell cycle, nucleus, phosph RNA-binding, ATP-binding, helicase, hydrolase; 3.50A {Homo sapiens}

Probab=96.79  E-value=0.0084  Score=53.23  Aligned_cols=41  Identities=22%  Similarity=0.323  Sum_probs=26.5

Q ss_pred             CceeEEEEeCCCCCCHHH-HHHHHHHhhhccCCceEEEEecC
Q psy879           95 GRHKIVILDEADSMTDGA-QQALRRTMEIYSNTTRFALACNN  135 (317)
Q Consensus        95 ~~~~vliiDE~d~l~~~~-~~~ll~~le~~~~~~~~il~~~~  135 (317)
                      ....++|+||+|.+.... ...+..++...+....+|+.|..
T Consensus       182 ~~~~~vViDEah~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT  223 (414)
T 3eiq_A          182 KYIKMFVLDEADEMLSRGFKDQIYDIFQKLNSNTQVVLLSAT  223 (414)
T ss_dssp             TTCCEEEECSHHHHHHTTTHHHHHHHHTTSCTTCEEEEECSC
T ss_pred             ccCcEEEEECHHHhhccCcHHHHHHHHHhCCCCCeEEEEEEe
Confidence            346799999999875432 34555666665566666665544

>1zak_A Adenylate kinase; ATP:AMP-phosphotransferase, transferase; HET: AP5; 3.50A {Zea mays} SCOP: c.37.1.1 g.41.2.1

Probab=96.79  E-value=0.00085  Score=54.55  Aligned_cols=23  Identities=30%  Similarity=0.472  Sum_probs=21.9

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .++|.|+||+||||+++.+++.+
T Consensus         7 ~I~l~G~~GsGKsT~~~~La~~l   29 (222)
T 1zak_A            7 KVMISGAPASGKGTQCELIKTKY   29 (222)
T ss_dssp             CEEEEESTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            59999999999999999999987

>2plr_A DTMP kinase, probable thymidylate kinase; TMP-binding, ATP-binding, structural GEN NPPSFA; HET: 1PE PGE EPE PG4; 1.60A {Sulfolobus tokodaii}

Probab=96.79  E-value=0.00082  Score=53.97  Aligned_cols=24  Identities=25%  Similarity=0.293  Sum_probs=22.2

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHc
Q psy879           33 NIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      .++|.|+||+||||+++.+++.+.
T Consensus         6 ~I~i~G~~GsGKsT~~~~L~~~l~   29 (213)
T 2plr_A            6 LIAFEGIDGSGKSSQATLLKDWIE   29 (213)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHh
Confidence            489999999999999999999874

>2cdn_A Adenylate kinase; phosphoryl transfer, associative mechanism, ATP-binding, nucleotide biosynthesis, nucleotide-binding, transferase; HET: ADP; 1.9A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1p4s_A

Probab=96.79  E-value=0.0011  Score=52.86  Aligned_cols=23  Identities=43%  Similarity=0.775  Sum_probs=21.6

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .++|.|+||+||||+++.+++.+
T Consensus        22 ~I~l~G~~GsGKST~a~~La~~l   44 (201)
T 2cdn_A           22 RVLLLGPPGAGKGTQAVKLAEKL   44 (201)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            48999999999999999999986

>1tev_A UMP-CMP kinase; ploop, NMP binding region, LID region, conformational changes, transferase; 2.10A {Homo sapiens} SCOP: c.37.1.1

Probab=96.78  E-value=0.00085  Score=53.07  Aligned_cols=23  Identities=26%  Similarity=0.437  Sum_probs=21.4

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .++|.|+||+||||+++.+++.+
T Consensus         5 ~I~l~G~~GsGKsT~a~~L~~~~   27 (196)
T 1tev_A            5 VVFVLGGPGAGKGTQCARIVEKY   27 (196)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            48999999999999999999986

>2jeo_A Uridine-cytidine kinase 1; UCK, transferase, ATP-binding, nucleoside kinase, nucleotide-binding; 2.50A {Homo sapiens} PDB: 2uvq_A*

Probab=96.78  E-value=0.00075  Score=55.84  Aligned_cols=38  Identities=26%  Similarity=0.174  Sum_probs=23.3

Q ss_pred             HHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHH
Q psy879           16 EDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        16 ~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      ..+++.+.-.+..|.  .+.|.||+|+||||+++.++..+
T Consensus        12 ~~~l~~isl~i~~g~--iigI~G~~GsGKSTl~k~L~~~l   49 (245)
T 2jeo_A           12 DLGTENLYFQSMRPF--LIGVSGGTASGKSTVCEKIMELL   49 (245)
T ss_dssp             -----------CCSE--EEEEECSTTSSHHHHHHHHHHHH
T ss_pred             ceeecceeccCCCCE--EEEEECCCCCCHHHHHHHHHHHh
Confidence            344455544444443  58999999999999999999976

>3sr0_A Adenylate kinase; phosphoryl transfer analogue, ALF4, transferase (phosphotran phosphoryl transfer, nucleotide-binding; HET: ADP AMP; 1.56A {Aquifex aeolicus} PDB: 2rh5_A 2rgx_A*

Probab=96.78  E-value=0.00084  Score=54.00  Aligned_cols=22  Identities=41%  Similarity=0.662  Sum_probs=20.8

Q ss_pred             EEEECCCCCCHHHHHHHHHHHH
Q psy879           34 IIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~l   55 (317)
                      ++|.||||+||+|.++.+++.+
T Consensus         3 Iil~GpPGsGKgTqa~~La~~~   24 (206)
T 3sr0_A            3 LVFLGPPGAGKGTQAKRLAKEK   24 (206)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHH
Confidence            7889999999999999999986

>2yvu_A Probable adenylyl-sulfate kinase; transferase, structural genomics, NPPSFA, national P protein structural and functional analyses; 2.10A {Aeropyrum pernix}

Probab=96.78  E-value=0.00085  Score=52.86  Aligned_cols=25  Identities=40%  Similarity=0.547  Sum_probs=22.6

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHcC
Q psy879           33 NIIISGPPGVGKTTTILCLARILLG   57 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~~   57 (317)
                      .++|.|++|+||||+++.++..+..
T Consensus        15 ~i~l~G~~GsGKsT~~~~L~~~l~~   39 (186)
T 2yvu_A           15 VVWLTGLPGSGKTTIATRLADLLQK   39 (186)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHHh
Confidence            4899999999999999999998743

>2qor_A Guanylate kinase; phosphotransferase, purine metabolism, structural genomics, structural genomics of pathogenic protozoa consortium; HET: 5GP POP; 1.80A {Plasmodium vivax}

Probab=96.77  E-value=0.00076  Score=54.07  Aligned_cols=23  Identities=35%  Similarity=0.602  Sum_probs=21.5

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .++|.||||+||||+++.+++.+
T Consensus        14 ~i~l~G~sGsGKsTl~~~L~~~~   36 (204)
T 2qor_A           14 PLVVCGPSGVGKGTLIKKVLSEF   36 (204)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHHhC
Confidence            48999999999999999999986

>3tr0_A Guanylate kinase, GMP kinase; purines, pyrimidines, nucleosides, nucleotides, transferase; HET: 5GP; 1.85A {Coxiella burnetii}

Probab=96.77  E-value=0.00099  Score=53.23  Aligned_cols=23  Identities=43%  Similarity=0.686  Sum_probs=21.2

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .+.|.||+|+||||+++.++..+
T Consensus         9 ii~l~Gp~GsGKSTl~~~L~~~~   31 (205)
T 3tr0_A            9 LFIISAPSGAGKTSLVRALVKAL   31 (205)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHS
T ss_pred             EEEEECcCCCCHHHHHHHHHhhC
Confidence            58999999999999999999874

>2r9g_A AAA ATPase, central region; structural genomics, PSI-2, protein structure initia YORK SGX research center for structural genomics, nysgxrc; 2.09A {Enterococcus faecium} SCOP: a.80.1.2 PDB: 2qw6_A

Probab=96.76  E-value=0.026  Score=44.13  Aligned_cols=87  Identities=10%  Similarity=0.218  Sum_probs=66.1

Q ss_pred             CCCCHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHH-HhcCCChHHHHHHHHHHHHHHhHHhcCC-Cc
Q psy879          218 DEPHPLAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDIIGNIFRVA-KTLDIPEPLKLSIIQEIGNVHLRISEGV-NS  295 (317)
Q Consensus       218 ~~~~~~~i~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~-~~~~~~~~~~~~~~~~l~~~~~~l~~g~-~~  295 (317)
                      +....+.++.++++++..|.+.|+.|+..|++.| +|..|.+.+.+.+ +.+|+.+.....+...+.+.-.+  -|. ..
T Consensus        11 Gd~HYd~iSAf~KSiRGSDpDAAly~LaRml~~G-Dp~~IaRRLvi~AsEDIGlAdP~Al~~a~aa~~a~~~--iG~PE~   87 (204)
T 2r9g_A           11 GDAHYDVISAFQKSIRGSDVDAALHYLARLVEAG-DLASICRRLMVIGYEDIGLGNPAAAARTVNAVLAAEK--LGLPEA   87 (204)
T ss_dssp             -CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT-CHHHHHHHHHHHHHHTTGGGCHHHHHHHHHHHHHHHH--HCTTTT
T ss_pred             chhHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC-CHHHHHHHHHHHHHhhccCCCHHHHHHHHHHHHHHHH--hCCCHH
Confidence            3566788999999999999999999999999999 9999999998875 45576665544444444444333  344 77


Q ss_pred             HHHHHHHHHHHH
Q psy879          296 LLQLSGLLARLC  307 (317)
Q Consensus       296 ~l~le~~~~~~~  307 (317)
                      ++.|-..+.-+|
T Consensus        88 ~i~LaqaviyLA   99 (204)
T 2r9g_A           88 RIPLADVVVDLC   99 (204)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHH
Confidence            778777777777

>1lvg_A Guanylate kinase, GMP kinase; transferase; HET: ADP 5GP; 2.10A {Mus musculus} SCOP: c.37.1.1

Probab=96.76  E-value=0.00095  Score=53.30  Aligned_cols=23  Identities=35%  Similarity=0.589  Sum_probs=21.4

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .+.|.||+|+||||+++.++..+
T Consensus         6 ~i~lvGpsGaGKSTLl~~L~~~~   28 (198)
T 1lvg_A            6 PVVLSGPSGAGKSTLLKKLFQEH   28 (198)
T ss_dssp             CEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHhhC
Confidence            58999999999999999999975

>2pt5_A Shikimate kinase, SK; aromatic amino acid biosynthesis, P-loop kinase, SHI kinase, shikimate pathway; 2.10A {Aquifex aeolicus}

Probab=96.75  E-value=0.00098  Score=51.42  Aligned_cols=23  Identities=35%  Similarity=0.287  Sum_probs=21.4

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .++|.|++|+||||+++.+++.+
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~l   24 (168)
T 2pt5_A            2 RIYLIGFMCSGKSTVGSLLSRSL   24 (168)
T ss_dssp             EEEEESCTTSCHHHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHHh
Confidence            47899999999999999999986

>1ak2_A Adenylate kinase isoenzyme-2; nucleoside monophosphate kinase, phosphotransferase; 1.92A {Bos taurus} SCOP: c.37.1.1 g.41.2.1 PDB: 2ak2_A 2c9y_A*

Probab=96.74  E-value=0.0012  Score=54.13  Aligned_cols=24  Identities=38%  Similarity=0.606  Sum_probs=22.2

Q ss_pred             ceEEEECCCCCCHHHHHHHHHHHH
Q psy879           32 PNIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        32 ~~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      ..++|.|+||+||||+++.+++.+
T Consensus        17 ~~I~l~G~~GsGKsT~a~~La~~l   40 (233)
T 1ak2_A           17 VRAVLLGPPGAGKGTQAPKLAKNF   40 (233)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHh
Confidence            359999999999999999999987

>2j41_A Guanylate kinase; GMP, GMK, transferase, ATP-binding, nucleotide- binding; HET: 5GP; 1.9A {Staphylococcus aureus}

Probab=96.73  E-value=0.00099  Score=53.29  Aligned_cols=23  Identities=39%  Similarity=0.479  Sum_probs=21.4

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .+.|.||+|+||||+++.++..+
T Consensus         8 ~i~l~G~~GsGKSTl~~~L~~~~   30 (207)
T 2j41_A            8 LIVLSGPSGVGKGTVRKRIFEDP   30 (207)
T ss_dssp             EEEEECSTTSCHHHHHHHHHHCT
T ss_pred             EEEEECCCCCCHHHHHHHHHHhh
Confidence            58999999999999999999875

>2jaq_A Deoxyguanosine kinase; transferase, deoxyribonucleoside kinase; HET: DCP; 2.3A {Mycoplasma mycoides subsp} PDB: 2jat_A* 2jas_A*

Probab=96.73  E-value=0.00098  Score=53.16  Aligned_cols=24  Identities=33%  Similarity=0.391  Sum_probs=21.9

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHc
Q psy879           33 NIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      .+.|.|++|+||||+++.+++.+.
T Consensus         2 ~I~i~G~~GsGKsT~~~~L~~~l~   25 (205)
T 2jaq_A            2 KIAIFGTVGAGKSTISAEISKKLG   25 (205)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHC
T ss_pred             EEEEECCCccCHHHHHHHHHHhcC
Confidence            478999999999999999999873

>1ukz_A Uridylate kinase; transferase; HET: ADP AMP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1uky_A*

Probab=96.73  E-value=0.001  Score=53.18  Aligned_cols=23  Identities=35%  Similarity=0.445  Sum_probs=21.3

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .++|.|++|+||||+++.+++.+
T Consensus        17 ~I~l~G~~GsGKsT~~~~L~~~~   39 (203)
T 1ukz_A           17 VIFVLGGPGAGKGTQCEKLVKDY   39 (203)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHHHc
Confidence            48999999999999999999875

>3cmw_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 2.80A {Escherichia coli} PDB: 3cmt_A* 3cmx_A* 3cmv_A*

Probab=96.73  E-value=0.0044  Score=64.23  Aligned_cols=70  Identities=19%  Similarity=0.232  Sum_probs=42.8

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCc---------------------ChHHHHHHHHHHHhhccc
Q psy879           33 NIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDR---------------------GIDTVRNKIKMFAQQKVT   91 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~---------------------~~~~i~~~~~~~~~~~~~   91 (317)
                      .++|+||||+|||+++..++......  +..+++++.....                     ....+.+.+..+...   
T Consensus        36 i~lI~G~pGsGKT~LAlqla~~~~~~--G~~vlYI~te~~~~~l~~~~lg~dl~~i~i~~p~t~e~l~~ll~~L~~~---  110 (1706)
T 3cmw_A           36 IVEIYGPESSGKTTLTLQVIAAAQRE--GKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEICDALARS---  110 (1706)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHHT--TCCEEEECTTSCCCHHHHHHTTCCGGGCEEECCSSHHHHHHHHHHHHHH---
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHhhC--CCceEEEEecCccHHHHHHhhccCccceeeeccCcHHHHHHHHHHHHhc---
Confidence            49999999999999999998764322  2233433332211                     122233333333221   


Q ss_pred             CCCCceeEEEEeCCCCCCH
Q psy879           92 LPPGRHKIVILDEADSMTD  110 (317)
Q Consensus        92 ~~~~~~~vliiDE~d~l~~  110 (317)
                         ...++||||++..+..
T Consensus       111 ---~~~~LVVIDSLt~L~~  126 (1706)
T 3cmw_A          111 ---GAVDVIVVDSVAALTP  126 (1706)
T ss_dssp             ---TCCSEEEESCSTTCCC
T ss_pred             ---cCCCEEEEcchhhhcc
Confidence               3578999999998854

>2bwj_A Adenylate kinase 5; phosphoryl transfer reaction, transferase; HET: AMP; 2.3A {Homo sapiens}

Probab=96.73  E-value=0.00087  Score=53.24  Aligned_cols=23  Identities=39%  Similarity=0.429  Sum_probs=21.8

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .++|.|+||+||||+++.+++.+
T Consensus        14 ~I~l~G~~GsGKsT~a~~L~~~l   36 (199)
T 2bwj_A           14 IIFIIGGPGSGKGTQCEKLVEKY   36 (199)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            59999999999999999999986

>3j16_B RLI1P; ribosome recycling, translation, eukarya, ribosome; HET: ATP; 7.20A {Saccharomyces cerevisiae}

Probab=96.73  E-value=0.012  Score=55.20  Aligned_cols=41  Identities=10%  Similarity=0.091  Sum_probs=29.5

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhccC-CceEEEEecCC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYSN-TTRFALACNNS  136 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~~-~~~~il~~~~~  136 (317)
                      +++++++||.-. |.......+.+++.+... ...+|+++++.
T Consensus       239 ~p~llllDEPts~LD~~~~~~l~~~l~~l~~~g~tvi~vtHdl  281 (608)
T 3j16_B          239 EADVYMFDEPSSYLDVKQRLNAAQIIRSLLAPTKYVICVEHDL  281 (608)
T ss_dssp             CCSEEEEECTTTTCCHHHHHHHHHHHHGGGTTTCEEEEECSCH
T ss_pred             CCCEEEEECcccCCCHHHHHHHHHHHHHHHhCCCEEEEEeCCH
Confidence            678999999975 567777778888776533 34567777664

>2vli_A Antibiotic resistance protein; transferase, tunicamycin, phosphotransferase; 1.95A {Deinococcus radiodurans}

Probab=96.73  E-value=0.00063  Score=53.32  Aligned_cols=23  Identities=52%  Similarity=0.598  Sum_probs=17.5

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .++|.|+||+||||+++.+++.+
T Consensus         7 ~I~l~G~~GsGKST~a~~La~~l   29 (183)
T 2vli_A            7 IIWINGPFGVGKTHTAHTLHERL   29 (183)
T ss_dssp             EEEEECCC----CHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHHhc
Confidence            58999999999999999999886

>1odf_A YGR205W, hypothetical 33.3 kDa protein in ADE3-Ser2 intergenic region; yeast protein, ATP binding protein; 2.25A {Saccharomyces cerevisiae} SCOP: c.37.1.6

Probab=96.72  E-value=0.0023  Score=54.30  Aligned_cols=24  Identities=38%  Similarity=0.562  Sum_probs=22.0

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHc
Q psy879           33 NIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      .+.+.||+|+||||+++.++..+.
T Consensus        33 ii~I~G~sGsGKSTla~~L~~~l~   56 (290)
T 1odf_A           33 FIFFSGPQGSGKSFTSIQIYNHLM   56 (290)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhh
Confidence            389999999999999999999874

>1rz3_A Hypothetical protein rbstp0775; MCSG, structural genomics, PSI, protein structure initiative; 1.90A {Geobacillus stearothermophilus} SCOP: c.37.1.6

Probab=96.72  E-value=0.0023  Score=51.11  Aligned_cols=40  Identities=25%  Similarity=0.103  Sum_probs=28.2

Q ss_pred             HHHHHHHHHHhcCC--Cc-eEEEECCCCCCHHHHHHHHHHHHc
Q psy879           17 DTVERLKVFSSSGN--VP-NIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        17 ~~~~~l~~~l~~~~--~~-~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      +.++.+...+.+..  .+ .+.+.|++|+||||+++.++..+.
T Consensus         5 ~~~~~l~~~~~~~~~~~~~~i~i~G~~GsGKstl~~~l~~~~~   47 (201)
T 1rz3_A            5 DRIDFLCKTILAIKTAGRLVLGIDGLSRSGKTTLANQLSQTLR   47 (201)
T ss_dssp             HHHHHHHHHHHTSCCSSSEEEEEEECTTSSHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhccCCCeEEEEECCCCCCHHHHHHHHHHHHh
Confidence            34444544444322  12 389999999999999999999873

>1znw_A Guanylate kinase, GMP kinase; ATP:GMP-phosphotransferase, TR; 2.10A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1znx_A* 1zny_A* 1znz_A* 1s4q_A 1z8f_A

Probab=96.71  E-value=0.0011  Score=53.36  Aligned_cols=29  Identities=34%  Similarity=0.715  Sum_probs=23.2

Q ss_pred             HHhcCCCceEEEECCCCCCHHHHHHHHHHHH
Q psy879           25 FSSSGNVPNIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        25 ~l~~~~~~~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .+..|.  .+.|.||+|+||||+++.++..+
T Consensus        16 ~i~~Ge--i~~l~GpnGsGKSTLl~~l~gl~   44 (207)
T 1znw_A           16 PAAVGR--VVVLSGPSAVGKSTVVRCLRERI   44 (207)
T ss_dssp             ---CCC--EEEEECSTTSSHHHHHHHHHHHS
T ss_pred             CCCCCC--EEEEECCCCCCHHHHHHHHHhhC
Confidence            345555  58999999999999999999975

>1fuu_A Yeast initiation factor 4A; IF4A, helicase, DEAD-box protein, translation; 2.50A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 2vso_A* 2vsx_A*

Probab=96.71  E-value=0.0058  Score=53.86  Aligned_cols=42  Identities=26%  Similarity=0.410  Sum_probs=25.7

Q ss_pred             CceeEEEEeCCCCCCHHH-HHHHHHHhhhccCCceEEEEecCC
Q psy879           95 GRHKIVILDEADSMTDGA-QQALRRTMEIYSNTTRFALACNNS  136 (317)
Q Consensus        95 ~~~~vliiDE~d~l~~~~-~~~ll~~le~~~~~~~~il~~~~~  136 (317)
                      ....++|+||+|.+.... ...+..++...++...+++.|..+
T Consensus       161 ~~~~~vIiDEah~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~  203 (394)
T 1fuu_A          161 DKIKMFILDEADEMLSSGFKEQIYQIFTLLPPTTQVVLLSATM  203 (394)
T ss_dssp             TTCCEEEEETHHHHHHTTCHHHHHHHHHHSCTTCEEEEECSSC
T ss_pred             hhCcEEEEEChHHhhCCCcHHHHHHHHHhCCCCceEEEEEEec
Confidence            457899999999874432 334445555555556566655443

>1rif_A DAR protein, DNA helicase UVSW; bacteriophage, RECG, SF2, DNA binding protein; HET: DNA; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.23

Probab=96.71  E-value=0.013  Score=49.28  Aligned_cols=38  Identities=16%  Similarity=0.062  Sum_probs=27.3

Q ss_pred             CHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHH
Q psy879           15 NEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        15 ~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .+...+.+..++.++   +.++.+|+|+|||.++..++...
T Consensus       115 ~~~Q~~ai~~~l~~~---~~ll~~~tGsGKT~~~~~~~~~~  152 (282)
T 1rif_A          115 HWYQKDAVFEGLVNR---RRILNLPTSAGRSLIQALLARYY  152 (282)
T ss_dssp             CHHHHHHHHHHHHHS---EEEECCCTTSCHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHhcC---CeEEEcCCCCCcHHHHHHHHHHH
Confidence            444555566556542   46889999999999998877654

>3be4_A Adenylate kinase; malaria, cryptosporidium parvum nonprotein inhibitors, nucleotide-binding, transferase; HET: AP5; 1.60A {Cryptosporidium parvum iowa II}

Probab=96.71  E-value=0.00095  Score=54.11  Aligned_cols=23  Identities=35%  Similarity=0.589  Sum_probs=21.7

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .++|.|+||+||||+++.+++.+
T Consensus         7 ~I~l~G~~GsGKsT~a~~La~~l   29 (217)
T 3be4_A            7 NLILIGAPGSGKGTQCEFIKKEY   29 (217)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            58999999999999999999987

>2bbw_A Adenylate kinase 4, AK4; nucleotide kinase, nucleotide binding, human, structura genomics, structural genomics consortium, SGC, transferase; HET: GP5; 2.05A {Homo sapiens} PDB: 2ar7_A* 3ndp_A

Probab=96.70  E-value=0.0013  Score=54.46  Aligned_cols=24  Identities=38%  Similarity=0.581  Sum_probs=22.1

Q ss_pred             ceEEEECCCCCCHHHHHHHHHHHH
Q psy879           32 PNIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        32 ~~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      ..+.|.||+|+||||+++.+++.+
T Consensus        28 ~~i~l~G~~GsGKSTl~k~La~~l   51 (246)
T 2bbw_A           28 LRAVILGPPGSGKGTVCQRIAQNF   51 (246)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHh
Confidence            359999999999999999999886

>1z6g_A Guanylate kinase; structural genomics, SGC, structural genom consortium, transferase; HET: EPE; 2.18A {Plasmodium falciparum}

Probab=96.69  E-value=0.0011  Score=53.93  Aligned_cols=34  Identities=29%  Similarity=0.287  Sum_probs=23.3

Q ss_pred             HHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHH
Q psy879           20 ERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        20 ~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      +.+.-.+..|.  .+.|.||+|+||||+++.++..+
T Consensus        14 ~~isl~i~~G~--~~~lvGpsGsGKSTLl~~L~g~~   47 (218)
T 1z6g_A           14 LVPRGSMNNIY--PLVICGPSGVGKGTLIKKLLNEF   47 (218)
T ss_dssp             --------CCC--CEEEECSTTSSHHHHHHHHHHHS
T ss_pred             cCCceecCCCC--EEEEECCCCCCHHHHHHHHHhhC
Confidence            33444455665  59999999999999999999975

>3bge_A Predicted ATPase; structural genomics, predicted AAA+ATPase C-terminal fragmen protein structure initiative; 1.85A {Haemophilus influenzae} SCOP: a.80.1.2

Probab=96.68  E-value=0.018  Score=45.00  Aligned_cols=85  Identities=8%  Similarity=0.092  Sum_probs=62.1

Q ss_pred             CHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHH-HhcCCChHHHHHHHHHHHHHHhHHhcCC-CcHHH
Q psy879          221 HPLAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDIIGNIFRVA-KTLDIPEPLKLSIIQEIGNVHLRISEGV-NSLLQ  298 (317)
Q Consensus       221 ~~~~i~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~-~~~~~~~~~~~~~~~~l~~~~~~l~~g~-~~~l~  298 (317)
                      ..+.++.++++++..|.+.|+.|+..|++.|++|..|.+.+.+++ +.+|+.+.....+...+.+.-.+  -|. ..++.
T Consensus         7 HYd~ISAf~KSiRGSDpDAAly~LaRMl~~GEDp~~IaRRLvi~AsEDIGlAdP~Al~~a~aa~~a~~~--iG~PE~~i~   84 (201)
T 3bge_A            7 FYDLISALHKSVRGSAPDAALYWYARILTAGGDPLYVARRLLAIASEDVGNADPRAMQVALAAWDCFTR--VGAYEGERA   84 (201)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHTTGGGCTTHHHHHHHHHHHHHH--TCHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhhccCCCHHHHHHHHHHHHHHHH--HCCcHHHHH
Confidence            456899999999999999999999999999999999999998875 44566555444433333333332  244 55667


Q ss_pred             HHHHHHHHH
Q psy879          299 LSGLLARLC  307 (317)
Q Consensus       299 le~~~~~~~  307 (317)
                      |-..+.-+|
T Consensus        85 LaqaviyLA   93 (201)
T 3bge_A           85 IAQAIIYLS   93 (201)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            666666666

>2bdt_A BH3686; alpha-beta protein, structural genomics, PSI, protein struct initiative, northeast structural genomics consortium, NESG, function; 2.40A {Bacillus halodurans} SCOP: c.37.1.25

Probab=96.68  E-value=0.00098  Score=52.63  Aligned_cols=23  Identities=57%  Similarity=0.712  Sum_probs=20.5

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .++|.||+|+||||+++.++...
T Consensus         4 ii~l~G~~GaGKSTl~~~L~~~~   26 (189)
T 2bdt_A            4 LYIITGPAGVGKSTTCKRLAAQL   26 (189)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHS
T ss_pred             EEEEECCCCCcHHHHHHHHhccc
Confidence            47899999999999999999753

>1qf9_A UMP/CMP kinase, protein (uridylmonophosphate/cytidylmonophosphate kinase); nucleoside monophosphate kinase, NMP kinase; HET: ADP C5P; 1.70A {Dictyostelium discoideum} SCOP: c.37.1.1 PDB: 1uke_A* 2ukd_A* 3ukd_A* 4ukd_A* 5ukd_A*

Probab=96.67  E-value=0.00099  Score=52.56  Aligned_cols=23  Identities=30%  Similarity=0.494  Sum_probs=21.5

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .++|.|+||+||||+++.+++.+
T Consensus         8 ~I~l~G~~GsGKsT~~~~L~~~l   30 (194)
T 1qf9_A            8 VVFVLGGPGSGKGTQCANIVRDF   30 (194)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            48999999999999999999986

>1zd8_A GTP:AMP phosphotransferase mitochondrial; ATP:AMP phosphotransferase, myokinase, structural genomics, structural genomics consortium, SGC; 1.48A {Homo sapiens} PDB: 2ak3_A*

Probab=96.66  E-value=0.001  Score=54.26  Aligned_cols=23  Identities=30%  Similarity=0.485  Sum_probs=21.6

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .++|.|+||+||||+++.+++.+
T Consensus         9 ~I~l~G~~GsGKsT~a~~La~~l   31 (227)
T 1zd8_A            9 RAVIMGAPGSGKGTVSSRITTHF   31 (227)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHHHc
Confidence            59999999999999999999985

>3ozx_A RNAse L inhibitor; ATP binding cassette protein, hydrolase, translation; HET: ADP; 2.05A {Sulfolobus solfataricus}

Probab=96.65  E-value=0.0096  Score=55.03  Aligned_cols=42  Identities=5%  Similarity=0.100  Sum_probs=31.9

Q ss_pred             ceeEEEEeCCC-CCCHHHHHHHHHHhhhccCCceEEEEecCCC
Q psy879           96 RHKIVILDEAD-SMTDGAQQALRRTMEIYSNTTRFALACNNSE  137 (317)
Q Consensus        96 ~~~vliiDE~d-~l~~~~~~~ll~~le~~~~~~~~il~~~~~~  137 (317)
                      +++++++||.- .|....+..+.+++.+......+|+++++..
T Consensus       156 ~p~illlDEPts~LD~~~~~~l~~~l~~l~~g~tii~vsHdl~  198 (538)
T 3ozx_A          156 EADVYIFDQPSSYLDVRERMNMAKAIRELLKNKYVIVVDHDLI  198 (538)
T ss_dssp             CCSEEEEESTTTTCCHHHHHHHHHHHHHHCTTSEEEEECSCHH
T ss_pred             CCCEEEEECCcccCCHHHHHHHHHHHHHHhCCCEEEEEEeChH
Confidence            68899999997 5677778888888876655566778887653

>2pbr_A DTMP kinase, thymidylate kinase; transferase, nucleotide biosynthesis, TMP-binding, A binding, structural genomics, NPPSFA; 1.96A {Aquifex aeolicus}

Probab=96.65  E-value=0.0012  Score=52.14  Aligned_cols=24  Identities=38%  Similarity=0.318  Sum_probs=21.7

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHc
Q psy879           33 NIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      .+.|.|++|+||||+++.+++.+.
T Consensus         2 ~I~l~G~~GsGKsT~~~~L~~~l~   25 (195)
T 2pbr_A            2 LIAFEGIDGSGKTTQAKKLYEYLK   25 (195)
T ss_dssp             EEEEECSTTSCHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHH
Confidence            378999999999999999999873

>1cke_A CK, MSSA, protein (cytidine monophosphate kinase); nucleotide monophosphate kinase,, transferase; 1.75A {Escherichia coli} SCOP: c.37.1.1 PDB: 1kdo_A* 1kdp_A* 1kdr_A* 1kdt_A* 2cmk_A* 2fem_A 2feo_A*

Probab=96.64  E-value=0.0012  Score=53.71  Aligned_cols=23  Identities=43%  Similarity=0.624  Sum_probs=21.6

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .+.|.||+|+||||+++.+++.+
T Consensus         7 ~i~i~G~~GsGKSTl~~~L~~~~   29 (227)
T 1cke_A            7 VITIDGPSGAGKGTLCKAMAEAL   29 (227)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            58999999999999999999976

>3dkp_A Probable ATP-dependent RNA helicase DDX52; DEAD, ADP, structural genomics, structural GEN consortium, SGC, rRNA, ATP-binding, hydrolase; HET: ADP; 2.10A {Homo sapiens}

Probab=96.64  E-value=0.02  Score=46.96  Aligned_cols=23  Identities=30%  Similarity=0.452  Sum_probs=17.3

Q ss_pred             eEEEECCCCCCHHHHHH-HHHHHH
Q psy879           33 NIIISGPPGVGKTTTIL-CLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~-~la~~l   55 (317)
                      ++++.+|+|+|||.+.. .+...+
T Consensus        68 ~~l~~a~TGsGKT~~~~l~~l~~l   91 (245)
T 3dkp_A           68 ELLASAPTGSGKTLAFSIPILMQL   91 (245)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             CEEEECCCCCcHHHHHHHHHHHHH
Confidence            69999999999998743 334444

>2v3c_C SRP54, signal recognition 54 kDa protein; nucleotide-binding, signal recognition particle, GTP-binding, RNA-binding; 2.50A {Methanocaldococcus jannaschii} PDB: 3ndb_B

Probab=96.62  E-value=0.003  Score=56.72  Aligned_cols=24  Identities=46%  Similarity=0.555  Sum_probs=22.0

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHc
Q psy879           33 NIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      .++|+|++|+||||++..++..+.
T Consensus       101 vI~ivG~~GvGKTTla~~La~~l~  124 (432)
T 2v3c_C          101 VILLVGIQGSGKTTTAAKLARYIQ  124 (432)
T ss_dssp             CEEEECCSSSSTTHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHH
Confidence            499999999999999999999874

>2wwf_A Thymidilate kinase, putative; transferase, malaria; HET: TMP ADP; 1.89A {Plasmodium falciparum} PDB: 2wwg_A* 2wwh_A* 2wwi_A*

Probab=96.62  E-value=0.0011  Score=53.20  Aligned_cols=24  Identities=29%  Similarity=0.292  Sum_probs=22.2

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHc
Q psy879           33 NIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      .++|.|++|+||||+++.+++.+.
T Consensus        12 ~I~l~G~~GsGKST~~~~L~~~l~   35 (212)
T 2wwf_A           12 FIVFEGLDRSGKSTQSKLLVEYLK   35 (212)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHH
Confidence            489999999999999999999874

>3tau_A Guanylate kinase, GMP kinase; structural genomics, center for structural genomics of infec diseases, csgid, putative guanylate kinase; HET: MSE; 2.05A {Listeria monocytogenes}

Probab=96.61  E-value=0.0016  Score=52.44  Aligned_cols=23  Identities=39%  Similarity=0.527  Sum_probs=21.3

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .+.|.||+|+||||+++.++..+
T Consensus        10 ~i~l~GpsGsGKsTl~~~L~~~~   32 (208)
T 3tau_A           10 LIVLSGPSGVGKGTVREAVFKDP   32 (208)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHST
T ss_pred             EEEEECcCCCCHHHHHHHHHhhC
Confidence            58999999999999999999875

>2xb4_A Adenylate kinase; ATP-binding, nucleotide-binding, transferase; HET: SRT; 1.80A {Desulfovibrio gigas} PDB: 3l0s_A* 3l0p_A*

Probab=96.61  E-value=0.0013  Score=53.51  Aligned_cols=23  Identities=39%  Similarity=0.463  Sum_probs=21.3

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .++|.|+||+||||+++.+++.+
T Consensus         2 ~I~l~G~~GsGKsT~a~~La~~l   24 (223)
T 2xb4_A            2 NILIFGPNGSGKGTQGNLVKDKY   24 (223)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            37899999999999999999986

>1ewq_A DNA mismatch repair protein MUTS; multiple domains of protein, mostly mixed alpha-beta structures, one domain is entirely helical; HET: DNA; 2.20A {Thermus aquaticus} SCOP: a.113.1.1 c.37.1.12 c.55.6.1 d.75.2.1 PDB: 1nne_A* 1fw6_A* 1ewr_A*

Probab=96.61  E-value=0.0028  Score=60.97  Aligned_cols=23  Identities=35%  Similarity=0.433  Sum_probs=21.0

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .+.|.||+|+||||+.+.++...
T Consensus       578 i~~I~GpNGsGKSTlLr~iagl~  600 (765)
T 1ewq_A          578 LVLITGPNMAGKSTFLRQTALIA  600 (765)
T ss_dssp             EEEEESCSSSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCChHHHHHHHHhhh
Confidence            48999999999999999999765

>1ls1_A Signal recognition particle protein; FFH, SRP54, SRP, GTPase, ultrahigh resolution, protein transport; 1.10A {Thermus aquaticus} SCOP: a.24.13.1 c.37.1.10 PDB: 1jpn_B* 1jpj_A* 1ry1_U* 2j45_A* 1o87_A* 2c04_A* 2j46_A* 1rj9_B* 2c03_A* 2j7p_A* 1okk_A* 2cnw_A* 1ng1_A* 2xkv_A 3ng1_A 1ffh_A 2ng1_A*

Probab=96.59  E-value=0.012  Score=50.08  Aligned_cols=25  Identities=40%  Similarity=0.377  Sum_probs=22.0

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHcC
Q psy879           33 NIIISGPPGVGKTTTILCLARILLG   57 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~~   57 (317)
                      .+.+.|++|+||||++..+|..+..
T Consensus       100 ~i~i~g~~G~GKTT~~~~la~~~~~  124 (295)
T 1ls1_A          100 LWFLVGLQGSGKTTTAAKLALYYKG  124 (295)
T ss_dssp             EEEEECCTTTTHHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHH
Confidence            3788899999999999999998753

>1e4v_A Adenylate kinase; transferase(phosphotransferase); HET: AP5; 1.85A {Escherichia coli} SCOP: c.37.1.1 g.41.2.1 PDB: 1e4y_A* 1ake_A* 1ank_A* 2eck_A* 3hpq_A* 4ake_A 3hpr_A*

Probab=96.58  E-value=0.0012  Score=53.27  Aligned_cols=23  Identities=30%  Similarity=0.417  Sum_probs=21.3

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .++|.|+||+||||+++.+++.+
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~~   24 (214)
T 1e4v_A            2 RIILLGAPVAGKGTQAQFIMEKY   24 (214)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            47899999999999999999986

>1nn5_A Similar to deoxythymidylate kinase (thymidylate K; P-loop, D4TMP, transferase; HET: 2DT ANP; 1.50A {Homo sapiens} SCOP: c.37.1.1 PDB: 1e2e_A* 1e2d_A* 1e2g_A* 1e2q_A* 1e99_A* 1e9a_A* 1e9b_A* 1nmx_A* 1nmz_A* 1nn0_A* 1nn1_A* 1e2f_A* 1nn3_A* 2xx3_A* 1e9c_A* 1e9d_A* 1e9e_A* 1e98_A* 1nmy_A* 1e9f_A*

Probab=96.58  E-value=0.0016  Score=52.36  Aligned_cols=24  Identities=29%  Similarity=0.328  Sum_probs=22.3

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHc
Q psy879           33 NIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      .++|.|++|+||||+++.+++.+.
T Consensus        11 ~I~l~G~~GsGKsT~~~~L~~~l~   34 (215)
T 1nn5_A           11 LIVLEGVDRAGKSTQSRKLVEALC   34 (215)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHH
Confidence            599999999999999999999874

>1ex7_A Guanylate kinase; substrate-induced FIT, domain movement, GMP, ATP, substrate specificity, X-RAY diffraction, transferase; HET: 5GP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1ex6_A* 1gky_A* 3sqk_A 4f4j_A

Probab=96.57  E-value=0.0014  Score=51.65  Aligned_cols=23  Identities=43%  Similarity=0.615  Sum_probs=20.8

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .++|.||+|+||||+++.+.+..
T Consensus         3 pIVi~GPSG~GK~Tl~~~L~~~~   25 (186)
T 1ex7_A            3 PIVISGPSGTGKSTLLKKLFAEY   25 (186)
T ss_dssp             CEEEECCTTSSHHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHHhC
Confidence            38999999999999999998874

>2oap_1 GSPE-2, type II secretion system protein; hexameric ATPase, hydrolase; HET: ANP; 2.95A {Archaeoglobus fulgidus} PDB: 2oaq_1

Probab=96.56  E-value=0.0015  Score=59.96  Aligned_cols=39  Identities=21%  Similarity=0.233  Sum_probs=34.0

Q ss_pred             CHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHH
Q psy879           15 NEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        15 ~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      ...+.+.+...+..|.  ++++.||+|+||||++++++..+
T Consensus       246 ~~~~l~~l~~~v~~g~--~i~I~GptGSGKTTlL~aL~~~i  284 (511)
T 2oap_1          246 PSGVLAYLWLAIEHKF--SAIVVGETASGKTTTLNAIMMFI  284 (511)
T ss_dssp             CHHHHHHHHHHHHTTC--CEEEEESTTSSHHHHHHHHGGGS
T ss_pred             CHHHHHHHHHHHhCCC--EEEEECCCCCCHHHHHHHHHhhC
Confidence            5677778888888887  69999999999999999999876

>2pez_A Bifunctional 3'-phosphoadenosine 5'- phosphosulfate synthetase 1 (PAPS synthetase...; NMP-kinase fold, protein in complex with nucleic acid; HET: GGZ DAT; 1.40A {Homo sapiens} PDB: 2pey_A* 2ax4_A*

Probab=96.54  E-value=0.0019  Score=50.48  Aligned_cols=23  Identities=35%  Similarity=0.602  Sum_probs=21.4

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .+.|.|++|+||||+++.++..+
T Consensus         7 ~i~l~G~~GsGKST~~~~L~~~l   29 (179)
T 2pez_A            7 TVWLTGLSGAGKTTVSMALEEYL   29 (179)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            48899999999999999999986

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=96.54  E-value=0.0055  Score=52.66  Aligned_cols=23  Identities=30%  Similarity=0.475  Sum_probs=21.0

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHc
Q psy879           34 IIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      +++.|+||+|||+++..++....
T Consensus        71 ~li~G~pG~GKTtl~l~ia~~~a   93 (315)
T 3bh0_A           71 VLIAARPSMGKTAFALKQAKNMS   93 (315)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHHH
T ss_pred             EEEEeCCCCCHHHHHHHHHHHHH
Confidence            99999999999999999997654

>2j37_W Signal recognition particle 54 kDa protein (SRP54); ribosome, SRP, translation/RNA; 8.00A {Canis SP} PDB: 1wgw_A

Probab=96.53  E-value=0.028  Score=51.39  Aligned_cols=25  Identities=40%  Similarity=0.356  Sum_probs=22.2

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHcC
Q psy879           33 NIIISGPPGVGKTTTILCLARILLG   57 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~~   57 (317)
                      .++|.|++|+||||++..++..+..
T Consensus       103 vI~ivG~~GvGKTTl~~kLA~~l~~  127 (504)
T 2j37_W          103 VIMFVGLQGSGKTTTCSKLAYYYQR  127 (504)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHh
Confidence            4899999999999999999987753

>3bk7_A ABC transporter ATP-binding protein; ABC ATPase, iron-sulfur cluster, adenosine diphosphate, nucleotide-binding; HET: ADP; 2.80A {Pyrococcus abyssi} PDB: 3j15_B*

Probab=96.52  E-value=0.017  Score=54.27  Aligned_cols=41  Identities=17%  Similarity=0.230  Sum_probs=29.6

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhcc--CCceEEEEecCC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYS--NTTRFALACNNS  136 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~--~~~~~il~~~~~  136 (317)
                      ++.++++||.-. |....+..+.+.+.+..  ....+|+++++.
T Consensus       489 ~p~lLlLDEPt~~LD~~~~~~l~~~l~~l~~~~g~tvi~vsHd~  532 (607)
T 3bk7_A          489 DADIYLLDEPSAYLDVEQRLAVSRAIRHLMEKNEKTALVVEHDV  532 (607)
T ss_dssp             CCSEEEEECTTTTCCHHHHHHHHHHHHHHHHHTTCEEEEECSCH
T ss_pred             CCCEEEEeCCccCCCHHHHHHHHHHHHHHHHhCCCEEEEEeCCH
Confidence            678999999975 56777778888777642  345567777663

>3ly5_A ATP-dependent RNA helicase DDX18; alpha-beta, structural genomics, structural genomics consort ATP-binding, hydrolase, nucleotide-binding, RNA-B; 2.80A {Homo sapiens}

Probab=96.50  E-value=0.0051  Score=51.33  Aligned_cols=40  Identities=18%  Similarity=0.326  Sum_probs=24.5

Q ss_pred             CceeEEEEeCCCCCCHH-HHHHHHHHhhhccCCceEEEEec
Q psy879           95 GRHKIVILDEADSMTDG-AQQALRRTMEIYSNTTRFALACN  134 (317)
Q Consensus        95 ~~~~vliiDE~d~l~~~-~~~~ll~~le~~~~~~~~il~~~  134 (317)
                      ...+++|+||+|.+... ....+..++...+....+++.|-
T Consensus       200 ~~l~~lViDEah~l~~~~~~~~l~~i~~~~~~~~q~l~~SA  240 (262)
T 3ly5_A          200 KNLQCLVIDEADRILDVGFEEELKQIIKLLPTRRQTMLFSA  240 (262)
T ss_dssp             TTCCEEEECSHHHHHHTTCHHHHHHHHHHSCSSSEEEEECS
T ss_pred             ccCCEEEEcChHHHhhhhHHHHHHHHHHhCCCCCeEEEEEe
Confidence            45789999999987543 23344455555555555555443

>2wsm_A Hydrogenase expression/formation protein (HYPB); metal binding protein; 2.30A {Archaeoglobus fulgidus}

Probab=96.49  E-value=0.0018  Score=52.37  Aligned_cols=43  Identities=21%  Similarity=0.133  Sum_probs=34.1

Q ss_pred             CCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHc
Q psy879           14 GNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        14 g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      ++.+..+.+...+..++.+.+++.|++|+||||++..++..+.
T Consensus        13 ~~~~~~~~~~~~~~~~~~~~i~i~G~~g~GKTTl~~~l~~~~~   55 (221)
T 2wsm_A           13 ENKRLAEKNREALRESGTVAVNIMGAIGSGKTLLIERTIERIG   55 (221)
T ss_dssp             HHHHHHHHHHHHHHHHTCEEEEEEECTTSCHHHHHHHHHHHHT
T ss_pred             hcHHHHHHHHHhhcccCceEEEEEcCCCCCHHHHHHHHHHHhc
Confidence            3455566666666666767799999999999999999998863

>1m7g_A Adenylylsulfate kinase; APS kinase, transferase, sulfate Met nucleotide 2 kinase; HET: AV2 ADX ADP; 1.43A {Penicillium chrysogenum} SCOP: c.37.1.4 PDB: 1d6j_A* 1m7h_A* 3cr7_A*

Probab=96.49  E-value=0.0028  Score=51.04  Aligned_cols=24  Identities=29%  Similarity=0.421  Sum_probs=22.1

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHc
Q psy879           33 NIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      .++|.|++|+||||+++.+++.+.
T Consensus        27 ~i~~~G~~GsGKsT~~~~l~~~l~   50 (211)
T 1m7g_A           27 TIWLTGLSASGKSTLAVELEHQLV   50 (211)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhc
Confidence            589999999999999999999874

>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A 2r6e_A 2vyf_A 2vye_A

Probab=96.47  E-value=0.028  Score=50.86  Aligned_cols=23  Identities=39%  Similarity=0.577  Sum_probs=21.2

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHc
Q psy879           34 IIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      +++.|+||+|||+++..++..+.
T Consensus       206 iiI~G~pG~GKTtl~l~ia~~~~  228 (454)
T 2r6a_A          206 IIVAARPSVGKTAFALNIAQNVA  228 (454)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHHH
Confidence            89999999999999999998764

>1wms_A RAB-9, RAB9, RAS-related protein RAB-9A; GTPase, protein transport; HET: GDP; 1.25A {Homo sapiens} SCOP: c.37.1.8 PDB: 1s8f_A* 1yzl_A* 2ocb_A*

Probab=96.46  E-value=0.014  Score=44.82  Aligned_cols=22  Identities=27%  Similarity=0.437  Sum_probs=20.0

Q ss_pred             eEEEECCCCCCHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~   54 (317)
                      .+++.|++|+|||+++..+...
T Consensus         9 ~i~v~G~~~~GKSsli~~l~~~   30 (177)
T 1wms_A            9 KVILLGDGGVGKSSLMNRYVTN   30 (177)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            4899999999999999999864

>2v54_A DTMP kinase, thymidylate kinase; nucleotide biosynthesis, ATP-binding, nucleotide-binding, poxvirus, transferase; HET: TYD POP; 2.4A {Vaccinia virus copenhagen} PDB: 2w0s_A*

Probab=96.44  E-value=0.0014  Score=52.33  Aligned_cols=23  Identities=26%  Similarity=0.364  Sum_probs=21.5

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .+.|.|++|+||||+++.+++.+
T Consensus         6 ~I~l~G~~GsGKsT~~~~L~~~l   28 (204)
T 2v54_A            6 LIVFEGLDKSGKTTQCMNIMESI   28 (204)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHTS
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHH
Confidence            58999999999999999999975

>1sky_E F1-ATPase, F1-ATP synthase; F1FO ATP synthase, alpha3BETA3 SUBC F1-ATPase, hydrolase; 3.20A {Bacillus SP} SCOP: a.69.1.1 b.49.1.1 c.37.1.11

Probab=96.44  E-value=0.0036  Score=56.38  Aligned_cols=36  Identities=33%  Similarity=0.415  Sum_probs=27.3

Q ss_pred             HHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHc
Q psy879           18 TVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        18 ~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      +++.|..+.+.+   ..+|+||+|+|||+++..++....
T Consensus       141 ~ID~L~pi~kGq---~~~i~G~sGvGKTtL~~~l~~~~~  176 (473)
T 1sky_E          141 VVDLLAPYIKGG---KIGLFGGAGVGKTVLIQELIHNIA  176 (473)
T ss_dssp             HHHHHSCEETTC---EEEEECCSSSCHHHHHHHHHHHHH
T ss_pred             HHHHHhhhccCC---EEEEECCCCCCccHHHHHHHhhhh
Confidence            455555555433   589999999999999999987653

>1xjc_A MOBB protein homolog; structural genomics, midwest center for structural GEN PSI, protein structure initiative, MCSG; 2.10A {Geobacillus stearothermophilus} SCOP: c.37.1.10

Probab=96.43  E-value=0.0026  Score=49.23  Aligned_cols=28  Identities=18%  Similarity=0.061  Sum_probs=24.0

Q ss_pred             CceEEEECCCCCCHHHHHHHHHHHHcCC
Q psy879           31 VPNIIISGPPGVGKTTTILCLARILLGP   58 (317)
Q Consensus        31 ~~~~ll~G~~G~GKt~la~~la~~l~~~   58 (317)
                      .+.+.|.|++|+||||++..++..+...
T Consensus         4 ~~~i~i~G~sGsGKTTl~~~L~~~l~~~   31 (169)
T 1xjc_A            4 MNVWQVVGYKHSGKTTLMEKWVAAAVRE   31 (169)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHHHHT
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHhhHhc
Confidence            4468999999999999999999987543

>3asz_A Uridine kinase; cytidine phosphorylation, transferase; HET: C5P; 2.25A {Thermus thermophilus} PDB: 3asy_A*

Probab=96.42  E-value=0.002  Score=51.73  Aligned_cols=23  Identities=48%  Similarity=0.481  Sum_probs=21.5

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .+.|.||+|+||||+++.++..+
T Consensus         8 ~i~i~G~~GsGKSTl~~~l~~~~   30 (211)
T 3asz_A            8 VIGIAGGTASGKTTLAQALARTL   30 (211)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            48999999999999999999986

>1z0j_A RAB-22, RAS-related protein RAB-22A; RAB GTPase, RAB22 GTPase, rabenosyn, endosomal trafficking; HET: GTP; 1.32A {Mus musculus} SCOP: c.37.1.8 PDB: 1yvd_A*

Probab=96.41  E-value=0.0097  Score=45.40  Aligned_cols=22  Identities=23%  Similarity=0.456  Sum_probs=20.1

Q ss_pred             eEEEECCCCCCHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~   54 (317)
                      .+++.|++|+|||++++.+...
T Consensus         8 ~i~v~G~~~~GKSsli~~l~~~   29 (170)
T 1z0j_A            8 KVCLLGDTGVGKSSIMWRFVED   29 (170)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECcCCCCHHHHHHHHHcC
Confidence            3899999999999999999875

>3szr_A Interferon-induced GTP-binding protein MX1; interferon-induced antiviral GTPase, membrane associated, PR binding; 3.50A {Homo sapiens} PDB: 3zys_B

Probab=96.39  E-value=0.0062  Score=57.30  Aligned_cols=26  Identities=23%  Similarity=0.484  Sum_probs=22.9

Q ss_pred             CCceEEEECCCCCCHHHHHHHHHHHH
Q psy879           30 NVPNIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        30 ~~~~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .+|.+.+.||+|+||||+.++++..+
T Consensus        44 ~lp~iaIvG~nGsGKSTLL~~I~Gl~   69 (608)
T 3szr_A           44 ALPAIAVIGDQSSGKSSVLEALSGVA   69 (608)
T ss_dssp             CCCCEECCCCTTSCHHHHHHHHHSCC
T ss_pred             cCCeEEEECCCCChHHHHHHHHhCCC
Confidence            34669999999999999999999864

>1wp9_A ATP-dependent RNA helicase, putative; ATPase, DNA replication, DNA repair, DNA recombina hydrolase; 2.90A {Pyrococcus furiosus} SCOP: c.37.1.19 c.37.1.19

Probab=96.39  E-value=0.014  Score=52.62  Aligned_cols=37  Identities=22%  Similarity=0.199  Sum_probs=27.1

Q ss_pred             CHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHH
Q psy879           15 NEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        15 ~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .+...+.+..++.+    +.++.+|+|+|||..+-.++...
T Consensus        11 ~~~Q~~~i~~~~~~----~~ll~~~tG~GKT~~~~~~~~~~   47 (494)
T 1wp9_A           11 RIYQEVIYAKCKET----NCLIVLPTGLGKTLIAMMIAEYR   47 (494)
T ss_dssp             CHHHHHHHHHGGGS----CEEEECCTTSCHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHhhC----CEEEEcCCCCCHHHHHHHHHHHH
Confidence            44444555555543    78999999999999998887665

>1rj9_A FTSY, signal recognition protein; SRP-GTPase domain, heterodimer, nucleotide twinning, protein complex, protein transport; HET: GCP; 1.90A {Thermus aquaticus} SCOP: a.24.13.1 c.37.1.10 PDB: 2q9c_A* 2q9b_A* 2q9a_A* 1okk_D* 2xkv_D 2iyl_D* 2cnw_D* 2j7p_D*

Probab=96.39  E-value=0.0048  Score=52.71  Aligned_cols=26  Identities=42%  Similarity=0.539  Sum_probs=23.1

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHcCC
Q psy879           33 NIIISGPPGVGKTTTILCLARILLGP   58 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~~~   58 (317)
                      .+.|.||+|+||||+++.++..+...
T Consensus       104 vi~lvG~nGsGKTTll~~Lagll~~~  129 (304)
T 1rj9_A          104 VVLVVGVNGVGKTTTIAKLGRYYQNL  129 (304)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHTT
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHhc
Confidence            48999999999999999999987543

>4gzl_A RAS-related C3 botulinum toxin substrate 1; rossmann fold, GTP binding, membrane, hydrolase; HET: GNP; 2.00A {Homo sapiens} PDB: 3th5_A* 4gzm_A*

Probab=96.38  E-value=0.0029  Score=50.54  Aligned_cols=41  Identities=17%  Similarity=0.240  Sum_probs=20.9

Q ss_pred             CCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHH
Q psy879           14 GNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        14 g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~   54 (317)
                      +++...+.+.......+.-.+++.|++|+|||+++..+...
T Consensus        13 ~~~~~~~~m~~~~~~~~~~ki~vvG~~~~GKSsLi~~l~~~   53 (204)
T 4gzl_A           13 GLVPRGSHMENLYFQGQAIKCVVVGDGAVGKTCLLISYTTN   53 (204)
T ss_dssp             -----------------CEEEEEEESTTSSHHHHHHHHHHS
T ss_pred             CcccchhHHHhHhhcCCeEEEEEECcCCCCHHHHHHHHHhC
Confidence            45555556655555544445999999999999999998864

>3ney_A 55 kDa erythrocyte membrane protein; structural genomics consortium, SGC, 55 kDa erythrocyte MEMB protein; 2.26A {Homo sapiens} SCOP: c.37.1.0

Probab=96.36  E-value=0.0023  Score=50.94  Aligned_cols=23  Identities=22%  Similarity=0.403  Sum_probs=21.1

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .+.|.||+|+||||+++.+++..
T Consensus        21 ~ivl~GPSGaGKsTL~~~L~~~~   43 (197)
T 3ney_A           21 TLVLIGASGVGRSHIKNALLSQN   43 (197)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHC
T ss_pred             EEEEECcCCCCHHHHHHHHHhhC
Confidence            48999999999999999999874

>1jjv_A Dephospho-COA kinase; P-loop nucleotide-binding fold, structure 2 function project, S2F, structural genomics, transferase; HET: ATP; 2.00A {Haemophilus influenzae} SCOP: c.37.1.1

Probab=96.34  E-value=0.0018  Score=51.90  Aligned_cols=21  Identities=29%  Similarity=0.308  Sum_probs=19.5

Q ss_pred             eEEEECCCCCCHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLAR   53 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~   53 (317)
                      .+.|.||+|+||||+++.++.
T Consensus         4 ~i~l~G~~GsGKST~~~~La~   24 (206)
T 1jjv_A            4 IVGLTGGIGSGKTTIANLFTD   24 (206)
T ss_dssp             EEEEECSTTSCHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            478999999999999999987

>3r20_A Cytidylate kinase; structural genomics, seattle structural genomics center for infectious disease, ssgcid, ADP, DCMP, D transferase; 2.00A {Mycobacterium smegmatis} SCOP: c.37.1.0 PDB: 3r8c_A 4die_A*

Probab=96.34  E-value=0.0024  Score=52.22  Aligned_cols=23  Identities=39%  Similarity=0.666  Sum_probs=21.8

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .+.|.||+|+||||+++.+++.+
T Consensus        11 ~i~i~G~~GsGKsTla~~la~~l   33 (233)
T 3r20_A           11 VVAVDGPAGTGKSSVSRGLARAL   33 (233)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            59999999999999999999987

>2if2_A Dephospho-COA kinase; alpha-beta protein, structural genomics, PSI-2, protein STRU initiative, northeast structural genomics consortium, NESG; 3.00A {Aquifex aeolicus}

Probab=96.32  E-value=0.002  Score=51.47  Aligned_cols=22  Identities=32%  Similarity=0.457  Sum_probs=20.4

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .+.+.|++|+||||+++.+++ +
T Consensus         3 ~i~i~G~~GsGKSTl~~~L~~-~   24 (204)
T 2if2_A            3 RIGLTGNIGCGKSTVAQMFRE-L   24 (204)
T ss_dssp             EEEEEECTTSSHHHHHHHHHH-T
T ss_pred             EEEEECCCCcCHHHHHHHHHH-C
Confidence            478999999999999999998 5

>2hf9_A Probable hydrogenase nickel incorporation protein HYPB; alpha and beta protein; HET: GSP; 1.90A {Methanocaldococcus jannaschii} PDB: 2hf8_A*

Probab=96.32  E-value=0.0039  Score=50.53  Aligned_cols=41  Identities=22%  Similarity=0.174  Sum_probs=32.1

Q ss_pred             HHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHc
Q psy879           16 EDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        16 ~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      ++..+.++..+.....+.+++.|++|+||||++..++....
T Consensus        23 ~~~a~~~r~~~~~~~~~~i~ivG~~gvGKTtl~~~l~~~~~   63 (226)
T 2hf9_A           23 KRLADKNRKLLNKHGVVAFDFMGAIGSGKTLLIEKLIDNLK   63 (226)
T ss_dssp             HHHHHHHHHHHHHTTCEEEEEEESTTSSHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHhCCCeEEEEEcCCCCCHHHHHHHHHHHhc
Confidence            33445566666666666799999999999999999998864

>1sq5_A Pantothenate kinase; P-loop, transferase; HET: PAU ADP; 2.20A {Escherichia coli} SCOP: c.37.1.6 PDB: 1esm_A* 1esn_A*

Probab=96.31  E-value=0.0067  Score=51.93  Aligned_cols=24  Identities=42%  Similarity=0.484  Sum_probs=22.0

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHc
Q psy879           33 NIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      .+.|.||+|+||||+++.++..+.
T Consensus        82 iigI~G~~GsGKSTl~~~L~~~l~  105 (308)
T 1sq5_A           82 IISIAGSVAVGKSTTARVLQALLS  105 (308)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHh
Confidence            489999999999999999999874

>3ozx_A RNAse L inhibitor; ATP binding cassette protein, hydrolase, translation; HET: ADP; 2.05A {Sulfolobus solfataricus}

Probab=96.29  E-value=0.008  Score=55.56  Aligned_cols=41  Identities=7%  Similarity=0.142  Sum_probs=29.2

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhcc--CCceEEEEecCC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYS--NTTRFALACNNS  136 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~--~~~~~il~~~~~  136 (317)
                      +++++++||.-. |....+..+.+.+.+..  ....+|+++++.
T Consensus       403 ~p~lLlLDEPT~gLD~~~~~~i~~~l~~l~~~~g~tvi~vsHdl  446 (538)
T 3ozx_A          403 EADLYVLDQPSSYLDVEERYIVAKAIKRVTRERKAVTFIIDHDL  446 (538)
T ss_dssp             CCSEEEEESTTTTCCHHHHHHHHHHHHHHHHHTTCEEEEECSCH
T ss_pred             CCCEEEEeCCccCCCHHHHHHHHHHHHHHHHhCCCEEEEEeCCH
Confidence            679999999975 56677777777776542  345567777663

>1uj2_A Uridine-cytidine kinase 2; alpha/beta mononucleotide-binding HOLD, transferase; HET: C5P ADP; 1.80A {Homo sapiens} SCOP: c.37.1.6 PDB: 1uei_A* 1uej_A* 1udw_A 1ufq_A* 1xrj_A*

Probab=96.28  E-value=0.0027  Score=52.66  Aligned_cols=26  Identities=23%  Similarity=0.266  Sum_probs=22.6

Q ss_pred             CCceEEEECCCCCCHHHHHHHHHHHH
Q psy879           30 NVPNIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        30 ~~~~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      ++..+.|.|++|+||||+++.+++.+
T Consensus        21 ~~~iI~I~G~~GSGKST~a~~L~~~l   46 (252)
T 1uj2_A           21 EPFLIGVSGGTASGKSSVCAKIVQLL   46 (252)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHHT
T ss_pred             CcEEEEEECCCCCCHHHHHHHHHHHh
Confidence            33348999999999999999999986

>1uf9_A TT1252 protein; P-loop, nucleotide binding domain, structural genomics, riken structural genomics/proteomics initiative, RSGI; HET: ATP; 2.80A {Thermus thermophilus} SCOP: c.37.1.1

Probab=96.27  E-value=0.0027  Score=50.49  Aligned_cols=23  Identities=35%  Similarity=0.291  Sum_probs=20.9

Q ss_pred             ceEEEECCCCCCHHHHHHHHHHH
Q psy879           32 PNIIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        32 ~~~ll~G~~G~GKt~la~~la~~   54 (317)
                      ..+.|.|++|+||||+++.+++.
T Consensus         9 ~~I~i~G~~GsGKST~~~~La~~   31 (203)
T 1uf9_A            9 IIIGITGNIGSGKSTVAALLRSW   31 (203)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHHT
T ss_pred             eEEEEECCCCCCHHHHHHHHHHC
Confidence            35899999999999999999985

>1kao_A RAP2A; GTP-binding protein, small G protein, GDP, RAS; HET: GDP; 1.70A {Homo sapiens} SCOP: c.37.1.8 PDB: 2rap_A* 3rap_R*

Probab=96.27  E-value=0.05  Score=41.01  Aligned_cols=22  Identities=23%  Similarity=0.459  Sum_probs=19.8

Q ss_pred             eEEEECCCCCCHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~   54 (317)
                      .+++.|++|+|||+++..+...
T Consensus         5 ~i~v~G~~~~GKSsli~~l~~~   26 (167)
T 1kao_A            5 KVVVLGSGGVGKSALTVQFVTG   26 (167)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            4899999999999999998864

>3ake_A Cytidylate kinase; CMP kinase, CMP complex, open conformation, nucleotide metab transferase; HET: C5P; 1.50A {Thermus thermophilus} PDB: 3akc_A* 3akd_A*

Probab=96.27  E-value=0.003  Score=50.41  Aligned_cols=23  Identities=30%  Similarity=0.475  Sum_probs=21.6

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .+.|.|++|+||||+++.+++.+
T Consensus         4 ~i~i~G~~GsGKst~~~~la~~l   26 (208)
T 3ake_A            4 IVTIDGPSASGKSSVARRVAAAL   26 (208)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHhc
Confidence            58999999999999999999986

>3e70_C DPA, signal recognition particle receptor; FTSY, SRP-GTPase, protein-targeting, transport protein; HET: GDP; 1.97A {Pyrococcus furiosus} PDB: 3dmd_B 3dm9_B*

Probab=96.27  E-value=0.008  Score=51.88  Aligned_cols=25  Identities=48%  Similarity=0.500  Sum_probs=22.6

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHcCC
Q psy879           34 IIISGPPGVGKTTTILCLARILLGP   58 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~l~~~   58 (317)
                      +.|.||+|+||||+++.++..+...
T Consensus       132 i~lvG~nGaGKTTll~~Lag~l~~~  156 (328)
T 3e70_C          132 IMFVGFNGSGKTTTIAKLANWLKNH  156 (328)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHhc
Confidence            8999999999999999999987543

>2gza_A Type IV secretion system protein VIRB11; ATPase, hydrolase; 2.60A {Brucella suis}

Probab=96.26  E-value=0.0034  Score=55.10  Aligned_cols=35  Identities=26%  Similarity=0.324  Sum_probs=30.2

Q ss_pred             HHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHc
Q psy879           20 ERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        20 ~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      +.+.-.+..|.  .+++.||+|+||||++++++..+.
T Consensus       166 ~~l~~~i~~G~--~i~ivG~sGsGKSTll~~l~~~~~  200 (361)
T 2gza_A          166 SFLRRAVQLER--VIVVAGETGSGKTTLMKALMQEIP  200 (361)
T ss_dssp             HHHHHHHHTTC--CEEEEESSSSCHHHHHHHHHTTSC
T ss_pred             HHHHHHHhcCC--EEEEECCCCCCHHHHHHHHHhcCC
Confidence            66777778887  799999999999999999998753

>3tqc_A Pantothenate kinase; biosynthesis of cofactors, prosthetic groups, carriers, TRAN; HET: ADP; 2.30A {Coxiella burnetii}

Probab=96.26  E-value=0.0042  Score=53.39  Aligned_cols=23  Identities=43%  Similarity=0.489  Sum_probs=21.5

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHc
Q psy879           34 IIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      +.|.||+|+||||+++.++..+.
T Consensus        95 igI~GpsGSGKSTl~~~L~~ll~  117 (321)
T 3tqc_A           95 IGIAGSVAVGKSTTSRVLKALLS  117 (321)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHHHHhc
Confidence            89999999999999999999874

>3clv_A RAB5 protein, putative; malaria, GTPase, structural genomics, GTP-binding, nucleotide-binding, signaling protein; HET: GDP; 1.89A {Plasmodium falciparum}

Probab=96.25  E-value=0.012  Score=46.34  Aligned_cols=22  Identities=27%  Similarity=0.530  Sum_probs=20.3

Q ss_pred             eEEEECCCCCCHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~   54 (317)
                      .+++.|++|+|||+++.++...
T Consensus         9 ki~v~G~~~~GKSsli~~l~~~   30 (208)
T 3clv_A            9 KTVLLGESSVGKSSIVLRLTKD   30 (208)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            4999999999999999999875

>2eyq_A TRCF, transcription-repair coupling factor; MFD, SF2 ATPase, hydrolase; HET: EPE; 3.20A {Escherichia coli} SCOP: b.34.18.1 c.37.1.19 c.37.1.19 c.37.1.19 c.37.1.19 d.315.1.1

Probab=96.23  E-value=0.042  Score=55.56  Aligned_cols=38  Identities=16%  Similarity=0.191  Sum_probs=27.8

Q ss_pred             CHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHH
Q psy879           15 NEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLA   52 (317)
Q Consensus        15 ~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la   52 (317)
                      |..++..+...+.+|++.+.+++||.|+|||.++...+
T Consensus       608 Q~~ai~~il~~~~~g~p~d~ll~~~TGsGKT~val~aa  645 (1151)
T 2eyq_A          608 QAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAA  645 (1151)
T ss_dssp             HHHHHHHHHHHHHSSSCCEEEEECCCCTTTHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCCcCcEEEECCCCCCHHHHHHHHH
Confidence            44555555555556776679999999999998876544

>1tf7_A KAIC; homohexamer, hexamer, circadian clock protein; HET: ATP; 2.80A {Synechococcus SP} SCOP: c.37.1.11 c.37.1.11 PDB: 3s1a_A* 1u9i_A* 2gbl_A* 3dvl_A* 3k0a_A* 3k09_A* 3jzm_A* 3k0e_A* 4dug_A* 3ua2_A* 3k0c_A* 3k0f_A*

Probab=96.22  E-value=0.0094  Score=55.08  Aligned_cols=25  Identities=24%  Similarity=0.325  Sum_probs=22.3

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHcC
Q psy879           33 NIIISGPPGVGKTTTILCLARILLG   57 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~~   57 (317)
                      .+++.||+|+||||+++.++..+..
T Consensus       283 i~~i~G~~GsGKSTLl~~l~g~~~~  307 (525)
T 1tf7_A          283 IILATGATGTGKTLLVSRFVENACA  307 (525)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHHHT
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHHHh
Confidence            4899999999999999999987643

>3t1o_A Gliding protein MGLA; G domain containing protein, bacterial GTPase, bacterial POL motility, POLE localisation, alpha/beta protein; HET: GDP; 1.90A {Thermus thermophilus} PDB: 3t12_A* 3t1q_A* 3t1t_A* 3t1v_A*

Probab=96.22  E-value=0.013  Score=45.98  Aligned_cols=23  Identities=30%  Similarity=0.401  Sum_probs=19.8

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .+++.|++|+|||++++.+....
T Consensus        16 ki~vvG~~~~GKssL~~~l~~~~   38 (198)
T 3t1o_A           16 KIVYYGPGLSGKTTNLKWIYSKV   38 (198)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHTS
T ss_pred             EEEEECCCCCCHHHHHHHHHhhc
Confidence            38999999999999998777653

>3thx_A DNA mismatch repair protein MSH2; ABC family ATPase, mismatch recognition, mismatched unpaired DNA binding protein-DNA complex; HET: DNA ADP; 2.70A {Homo sapiens} PDB: 2o8c_A* 2o8d_A* 2o8f_A* 3thw_A* 2o8b_A* 3thy_A* 3thz_A* 2o8e_A*

Probab=96.20  E-value=0.0064  Score=59.76  Aligned_cols=21  Identities=38%  Similarity=0.306  Sum_probs=18.9

Q ss_pred             eEEEECCCCCCHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLAR   53 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~   53 (317)
                      .++|+||+|+||||+.+.++.
T Consensus       664 i~~ItGpNGsGKSTlLr~ial  684 (934)
T 3thx_A          664 FHIITGPNMGGKSTYIRQTGV  684 (934)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            489999999999999999853

>3lnc_A Guanylate kinase, GMP kinase; ALS collaborative crystallography, emerald biostructures, ATP-binding, cytoplasm, nucleotide-binding; HET: 5GP; 1.95A {Anaplasma phagocytophilum}

Probab=96.19  E-value=0.0016  Score=53.20  Aligned_cols=23  Identities=35%  Similarity=0.476  Sum_probs=15.1

Q ss_pred             eEEEECCCCCCHHHHHHHHH-HHH
Q psy879           33 NIIISGPPGVGKTTTILCLA-RIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la-~~l   55 (317)
                      .+.|.||+|+||||+++.++ ..+
T Consensus        29 ii~l~Gp~GsGKSTl~~~L~~~~~   52 (231)
T 3lnc_A           29 ILVLSSPSGCGKTTVANKLLEKQK   52 (231)
T ss_dssp             EEEEECSCC----CHHHHHHC---
T ss_pred             EEEEECCCCCCHHHHHHHHHhcCC
Confidence            58999999999999999999 764

>4e22_A Cytidylate kinase; P-loop, CMP/ATP binding, transferase; 2.32A {Yersinia pseudotuberculosis}

Probab=96.19  E-value=0.0029  Score=52.53  Aligned_cols=23  Identities=43%  Similarity=0.614  Sum_probs=21.6

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .+.|.||+|+||||+++.+++.+
T Consensus        29 ~I~I~G~~GsGKSTl~k~La~~L   51 (252)
T 4e22_A           29 VITVDGPSGAGKGTLCKALAESL   51 (252)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHHhc
Confidence            59999999999999999999876

>3dz8_A RAS-related protein RAB-3B; GDP, GTPase, structural genomics consortium, SGC, cell GTP-binding, lipoprotein, membrane, methylation; HET: GDP; 1.90A {Homo sapiens} SCOP: c.37.1.8

Probab=96.18  E-value=0.017  Score=45.31  Aligned_cols=23  Identities=30%  Similarity=0.431  Sum_probs=20.8

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .+++.|++|+|||+++..+...-
T Consensus        25 ki~v~G~~~~GKSsli~~l~~~~   47 (191)
T 3dz8_A           25 KLLIIGNSSVGKTSFLFRYADDT   47 (191)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHT
T ss_pred             EEEEECCCCcCHHHHHHHHhcCC
Confidence            38999999999999999998764

>3thx_B DNA mismatch repair protein MSH3; ABC family ATPase, mismatch recognition, mismatched unpaired DNA binding protein-DNA complex; HET: DNA ADP; 2.70A {Homo sapiens} PDB: 3thw_B* 3thy_B* 3thz_B*

Probab=96.18  E-value=0.046  Score=53.64  Aligned_cols=22  Identities=41%  Similarity=0.496  Sum_probs=19.6

Q ss_pred             eEEEECCCCCCHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~   54 (317)
                      .++|.||+|+||||+.+.++..
T Consensus       675 i~~ItGPNGaGKSTlLr~i~~i  696 (918)
T 3thx_B          675 VMIITGPNMGGKSSYIKQVALI  696 (918)
T ss_dssp             EEEEESCCCHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCchHHHHHHHHHH
Confidence            4899999999999999998753

>3bc1_A RAS-related protein RAB-27A; RAB27, GTPase, RAB, signaling protein, GDPNP, SLP2A, exophil GTP-binding, lipoprotein, membrane, methylation; HET: GNP; 1.80A {Mus musculus} PDB: 2iey_A* 2if0_A* 2zet_A*

Probab=96.17  E-value=0.017  Score=45.10  Aligned_cols=22  Identities=27%  Similarity=0.425  Sum_probs=20.0

Q ss_pred             eEEEECCCCCCHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~   54 (317)
                      .+++.|++|+|||+++..+...
T Consensus        13 ki~v~G~~~~GKSsli~~l~~~   34 (195)
T 3bc1_A           13 KFLALGDSGVGKTSVLYQYTDG   34 (195)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            4899999999999999999864

>1g8f_A Sulfate adenylyltransferase; alpha-beta protein, beta-barrel, rossmann-fold, kinase fold; 1.95A {Saccharomyces cerevisiae} SCOP: b.122.1.3 c.26.1.5 c.37.1.15 PDB: 1g8g_A* 1g8h_A* 1j70_A 1jec_A 1jed_A* 1jee_A*

Probab=96.16  E-value=0.0053  Score=56.15  Aligned_cols=43  Identities=14%  Similarity=0.168  Sum_probs=32.7

Q ss_pred             CHHHHHHHHHHHh--cCCCceEEEECCCCCCHHHHHHHHHHHHcC
Q psy879           15 NEDTVERLKVFSS--SGNVPNIIISGPPGVGKTTTILCLARILLG   57 (317)
Q Consensus        15 ~~~~~~~l~~~l~--~~~~~~~ll~G~~G~GKt~la~~la~~l~~   57 (317)
                      .+++.+.+.....  ......++|.|.+|+||||+++++++.|..
T Consensus       377 rpeV~~vLr~~~~~~~~~~~~I~l~GlsGsGKSTIa~~La~~L~~  421 (511)
T 1g8f_A          377 YPEVVKILRESNPPRPKQGFSIVLGNSLTVSREQLSIALLSTFLQ  421 (511)
T ss_dssp             CHHHHHHHHHHSCCGGGCCEEEEECTTCCSCHHHHHHHHHHHHTT
T ss_pred             ChhhHHHHHHhcccccccceEEEecccCCCCHHHHHHHHHHHHHH
Confidence            5667677776652  222235999999999999999999999853

>3crm_A TRNA delta(2)-isopentenylpyrophosphate transferase; ATP-binding, nucleotide-binding, nucleotidyltransferase, tRNA processing; 1.90A {Pseudomonas aeruginosa} PDB: 3crq_A 3crr_A

Probab=96.16  E-value=0.0029  Score=54.31  Aligned_cols=23  Identities=39%  Similarity=0.635  Sum_probs=21.7

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .+++.||+|+|||++++.+++.+
T Consensus         7 ~i~i~GptGsGKTtla~~La~~l   29 (323)
T 3crm_A            7 AIFLMGPTAAGKTDLAMALADAL   29 (323)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHHHc
Confidence            48999999999999999999986

>4eaq_A DTMP kinase, thymidylate kinase; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, MTBI, transferase; HET: ATM; 1.85A {Staphylococcus aureus subsp} PDB: 4dwj_A* 4f4i_A

Probab=96.12  E-value=0.0037  Score=51.10  Aligned_cols=25  Identities=40%  Similarity=0.482  Sum_probs=22.6

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHcC
Q psy879           33 NIIISGPPGVGKTTTILCLARILLG   57 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~~   57 (317)
                      .+.|.|++|+||||+++.+++.+..
T Consensus        28 ~i~i~G~~GsGKsT~~~~l~~~l~~   52 (229)
T 4eaq_A           28 FITFEGPEGSGKTTVINEVYHRLVK   52 (229)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHTT
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHhc
Confidence            3899999999999999999999853

>1z63_A Helicase of the SNF2/RAD54 hamily; protein-DNA complex, hydrolase/DNA complex complex; 3.00A {Sulfolobus solfataricus} SCOP: c.37.1.19 c.37.1.19 PDB: 1z6a_A

Probab=96.12  E-value=0.022  Score=52.07  Aligned_cols=118  Identities=15%  Similarity=0.213  Sum_probs=66.4

Q ss_pred             CHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHHHHHHHhh-ccc--
Q psy879           15 NEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFAQQ-KVT--   91 (317)
Q Consensus        15 ~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~-~~~--   91 (317)
                      |.+.+..+......+.  +.++.-+.|+|||..+-+++..+........++-+.+..  -..++.+.+..+... ...  
T Consensus        42 Q~~~v~~l~~~~~~~~--~~ilad~~GlGKT~~ai~~i~~~~~~~~~~~~LIv~P~~--l~~qw~~e~~~~~~~~~v~~~  117 (500)
T 1z63_A           42 QIKGFSWMRFMNKLGF--GICLADDMGLGKTLQTIAVFSDAKKENELTPSLVICPLS--VLKNWEEELSKFAPHLRFAVF  117 (500)
T ss_dssp             HHHHHHHHHHHHHTTC--CEEECCCTTSCHHHHHHHHHHHHHHTTCCSSEEEEECST--THHHHHHHHHHHCTTSCEEEC
T ss_pred             HHHHHHHHHHHhhCCC--CEEEEeCCCCcHHHHHHHHHHHHHhcCCCCCEEEEccHH--HHHHHHHHHHHHCCCceEEEE
Confidence            4444444444334444  688999999999999988887765333223344454432  345555555544311 000  


Q ss_pred             ---------------------------CCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCC
Q psy879           92 ---------------------------LPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSE  137 (317)
Q Consensus        92 ---------------------------~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~  137 (317)
                                                 +......+||+||++.+.... ....+.+...+...++.+++++..
T Consensus       118 ~g~~~~~~~~~~~ivi~t~~~l~~~~~l~~~~~~~vIvDEaH~~kn~~-~~~~~~l~~l~~~~~l~LTaTP~~  189 (500)
T 1z63_A          118 HEDRSKIKLEDYDIILTTYAVLLRDTRLKEVEWKYIVIDEAQNIKNPQ-TKIFKAVKELKSKYRIALTGTPIE  189 (500)
T ss_dssp             SSSTTSCCGGGSSEEEEEHHHHTTCHHHHTCCEEEEEEETGGGGSCTT-SHHHHHHHTSCEEEEEEECSSCST
T ss_pred             ecCchhccccCCcEEEeeHHHHhccchhcCCCcCEEEEeCccccCCHh-HHHHHHHHhhccCcEEEEecCCCC
Confidence                                       001246899999999985432 123334444444556777776644

>1z0f_A RAB14, member RAS oncogene family; RAB GTPase, vesicular trafficking, protein transport; HET: GDP; 2.15A {Homo sapiens} SCOP: c.37.1.8 PDB: 2aed_A* 4drz_A*

Probab=96.11  E-value=0.02  Score=44.01  Aligned_cols=22  Identities=32%  Similarity=0.436  Sum_probs=20.2

Q ss_pred             eEEEECCCCCCHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~   54 (317)
                      .+++.|++|+|||+++..+...
T Consensus        17 ~i~v~G~~~~GKSsli~~l~~~   38 (179)
T 1z0f_A           17 KYIIIGDMGVGKSCLLHQFTEK   38 (179)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            4999999999999999999865

>3p32_A Probable GTPase RV1496/MT1543; structural genomics, seattle structural genomics center for infectious disease, ssgcid, MEAB, MMAA; HET: GDP PGE; 1.90A {Mycobacterium tuberculosis} PDB: 3md0_A* 4gt1_A* 3nxs_A* 3tk1_A*

Probab=96.11  E-value=0.011  Score=51.63  Aligned_cols=40  Identities=40%  Similarity=0.600  Sum_probs=28.7

Q ss_pred             CCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEec
Q psy879           29 GNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELN   68 (317)
Q Consensus        29 ~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~   68 (317)
                      ++.+.+.|.|+||+||||++..++..+........++..+
T Consensus        77 ~~~~~I~i~G~~G~GKSTl~~~L~~~l~~~g~kV~vi~~D  116 (355)
T 3p32_A           77 GNAHRVGITGVPGVGKSTAIEALGMHLIERGHRVAVLAVD  116 (355)
T ss_dssp             CCSEEEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEEEEC
T ss_pred             CCceEEEEECCCCCCHHHHHHHHHHHHHhCCCceEEEecC
Confidence            4444599999999999999999998875443333333333

>1u8z_A RAS-related protein RAL-A; GNP, GTP, GMPPNP, GPPNHP, GDP, GTPase, signaling protein; HET: GDP; 1.50A {Saguinus oedipus} SCOP: c.37.1.8 PDB: 1u8y_A* 1u90_A* 1uad_A* 1zc3_A* 1zc4_A* 2kwi_A* 2ke5_A*

Probab=96.10  E-value=0.022  Score=43.10  Aligned_cols=22  Identities=32%  Similarity=0.487  Sum_probs=20.0

Q ss_pred             eEEEECCCCCCHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~   54 (317)
                      .+++.|++|+|||+++..+...
T Consensus         6 ~i~v~G~~~~GKssl~~~l~~~   27 (168)
T 1u8z_A            6 KVIMVGSGGVGKSALTLQFMYD   27 (168)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            4899999999999999999864

>1z2a_A RAS-related protein RAB-23; RAB GTPase, vesicular trafficking, protein transport; HET: GDP; 1.90A {Mus musculus} SCOP: c.37.1.8 PDB: 1z22_A*

Probab=96.10  E-value=0.0081  Score=45.74  Aligned_cols=22  Identities=23%  Similarity=0.419  Sum_probs=20.1

Q ss_pred             eEEEECCCCCCHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~   54 (317)
                      .+++.|++|+|||+++..+...
T Consensus         7 ~i~v~G~~~~GKssl~~~l~~~   28 (168)
T 1z2a_A            7 KMVVVGNGAVGKSSMIQRYCKG   28 (168)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHC
T ss_pred             EEEEECcCCCCHHHHHHHHHcC
Confidence            4899999999999999999875

>1gtv_A TMK, thymidylate kinase; transferase, transferase (ATP:TMP phosphotransferase); HET: TYD TMP; 1.55A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1g3u_A* 1gsi_A* 1mrn_A* 1mrs_A* 1n5i_A* 1n5j_A* 1n5k_A* 1n5l_A* 1w2g_A* 1w2h_A*

Probab=96.08  E-value=0.0014  Score=52.74  Aligned_cols=24  Identities=33%  Similarity=0.371  Sum_probs=21.7

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHc
Q psy879           33 NIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      .+.|.|++|+||||+++.+++.+.
T Consensus         2 ~I~i~G~~GsGKsTl~~~L~~~l~   25 (214)
T 1gtv_A            2 LIAIEGVDGAGKRTLVEKLSGAFR   25 (214)
T ss_dssp             EEEEEEEEEEEHHHHHHHHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHH
Confidence            378999999999999999999874

>2hup_A RAS-related protein RAB-43; G-protein, GDP, structural genomics, structural genomics consortium, SGC, signaling protein; HET: GDP; 2.05A {Homo sapiens}

Probab=96.06  E-value=0.055  Score=42.80  Aligned_cols=22  Identities=23%  Similarity=0.403  Sum_probs=19.8

Q ss_pred             eEEEECCCCCCHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~   54 (317)
                      .+++.|++|+|||+++..+...
T Consensus        31 ki~vvG~~~vGKSsli~~l~~~   52 (201)
T 2hup_A           31 KLVLVGDASVGKTCVVQRFKTG   52 (201)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEEECcCCCCHHHHHHHHhhC
Confidence            3899999999999999999764

>2cbz_A Multidrug resistance-associated protein 1; ABC proteins, MRP1/ABCC1, nucleotide-binding domain, ATP- binding, hydrolysis, transport; HET: ATP; 1.5A {Homo sapiens}

Probab=96.04  E-value=0.0028  Score=52.07  Aligned_cols=43  Identities=9%  Similarity=0.045  Sum_probs=31.2

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhh---hccCCceEEEEecCCCc
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTME---IYSNTTRFALACNNSEK  138 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le---~~~~~~~~il~~~~~~~  138 (317)
                      +++++++||.-. |.+.....+.+.+.   .......+|++|++...
T Consensus       145 ~p~lllLDEPts~LD~~~~~~i~~~l~~~~~~~~~~tviivtH~~~~  191 (237)
T 2cbz_A          145 NADIYLFDDPLSAVDAHVGKHIFENVIGPKGMLKNKTRILVTHSMSY  191 (237)
T ss_dssp             CCSEEEEESTTTTSCHHHHHHHHHHTTSTTSTTTTSEEEEECSCSTT
T ss_pred             CCCEEEEeCcccccCHHHHHHHHHHHHHHHhhcCCCEEEEEecChHH
Confidence            579999999985 56777888888873   33335567888877654

>1sgw_A Putative ABC transporter; structural genomics, P protein structure initiative, southeast collaboratory for S genomics, secsg; 1.70A {Pyrococcus furiosus} SCOP: c.37.1.12

Probab=96.04  E-value=0.0027  Score=51.29  Aligned_cols=28  Identities=36%  Similarity=0.614  Sum_probs=23.3

Q ss_pred             HhcCCCceEEEECCCCCCHHHHHHHHHHHH
Q psy879           26 SSSGNVPNIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        26 l~~~~~~~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      +..|.  .+.+.||+|+||||+.+.++..+
T Consensus        32 i~~Ge--~~~iiG~NGsGKSTLlk~l~Gl~   59 (214)
T 1sgw_A           32 IEKGN--VVNFHGPNGIGKTTLLKTISTYL   59 (214)
T ss_dssp             EETTC--CEEEECCTTSSHHHHHHHHTTSS
T ss_pred             EcCCC--EEEEECCCCCCHHHHHHHHhcCC
Confidence            34454  58999999999999999999864

>3lv8_A DTMP kinase, thymidylate kinase; structural genomics, in diseases, center for structural genomics of infectious DISE ATP-binding; HET: ADP TMP TYD; 1.80A {Vibrio cholerae o1 biovar eltor} PDB: 3n2i_A*

Probab=96.04  E-value=0.008  Score=49.28  Aligned_cols=26  Identities=35%  Similarity=0.484  Sum_probs=23.1

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHcCC
Q psy879           33 NIIISGPPGVGKTTTILCLARILLGP   58 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~~~   58 (317)
                      -+.|.|++|+||||.++.+++.+...
T Consensus        29 ~i~~eG~~GsGKsT~~~~l~~~l~~~   54 (236)
T 3lv8_A           29 FIVIEGLEGAGKSTAIQVVVETLQQN   54 (236)
T ss_dssp             EEEEEESTTSCHHHHHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHhc
Confidence            48999999999999999999988543

>2db3_A ATP-dependent RNA helicase VASA; DEAD-BOX, protein-RNA complex, ATPase, riken structural genomics/proteomics initiative, RSGI; HET: ANP; 2.20A {Drosophila melanogaster}

Probab=96.03  E-value=0.052  Score=48.71  Aligned_cols=40  Identities=23%  Similarity=0.370  Sum_probs=27.4

Q ss_pred             CCCcccCCHHHHHHHHHH---------------HhcCCCceEEEECCCCCCHHHHHH
Q psy879            8 TFSDIVGNEDTVERLKVF---------------SSSGNVPNIIISGPPGVGKTTTIL   49 (317)
Q Consensus         8 ~~~~~~g~~~~~~~l~~~---------------l~~~~~~~~ll~G~~G~GKt~la~   49 (317)
                      +|+++--.+.+.+.|...               +.+|+  ++++.+|+|+|||....
T Consensus        57 ~f~~~~l~~~l~~~l~~~g~~~pt~iQ~~ai~~i~~g~--d~i~~a~TGsGKT~a~~  111 (434)
T 2db3_A           57 HFTSADLRDIIIDNVNKSGYKIPTPIQKCSIPVISSGR--DLMACAQTGSGKTAAFL  111 (434)
T ss_dssp             CGGGSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTC--CEEEECCTTSSHHHHHH
T ss_pred             ChhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCC--CEEEECCCCCCchHHHH
Confidence            577765566666655432               33454  69999999999998543

>1np6_A Molybdopterin-guanine dinucleotide biosynthesis protein B; mixed alpha-beta fold, elongated beta-sheet, walker A motif, P-loop structural motif; 1.90A {Escherichia coli} SCOP: c.37.1.10 PDB: 1p9n_A

Probab=96.02  E-value=0.0056  Score=47.67  Aligned_cols=26  Identities=31%  Similarity=0.382  Sum_probs=22.9

Q ss_pred             CceEEEECCCCCCHHHHHHHHHHHHc
Q psy879           31 VPNIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        31 ~~~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      .+.+.|.|++|+||||++..++..+.
T Consensus         6 ~~~i~i~G~sGsGKTTl~~~l~~~l~   31 (174)
T 1np6_A            6 IPLLAFAAWSGTGKTTLLKKLIPALC   31 (174)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             ceEEEEEeCCCCCHHHHHHHHHHhcc
Confidence            34689999999999999999998864

>2grj_A Dephospho-COA kinase; TM1387, EC 2.7.1.24, dephosphocoenzyme kinase, structural genomics, joint center for structural GE JCSG; HET: ADP COD; 2.60A {Thermotoga maritima}

Probab=96.00  E-value=0.0046  Score=49.04  Aligned_cols=22  Identities=32%  Similarity=0.376  Sum_probs=20.7

Q ss_pred             EEEECCCCCCHHHHHHHHHHHH
Q psy879           34 IIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~l   55 (317)
                      +.++|++||||||+++.+++.+
T Consensus        15 IgltG~~GSGKSTva~~L~~~l   36 (192)
T 2grj_A           15 IGVTGKIGTGKSTVCEILKNKY   36 (192)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHhc
Confidence            7899999999999999999975

>1b0u_A Histidine permease; ABC transporter, transport protein; HET: ATP; 1.50A {Salmonella typhimurium} SCOP: c.37.1.12

Probab=95.99  E-value=0.0031  Score=52.67  Aligned_cols=27  Identities=33%  Similarity=0.592  Sum_probs=22.9

Q ss_pred             hcCCCceEEEECCCCCCHHHHHHHHHHHH
Q psy879           27 SSGNVPNIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        27 ~~~~~~~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      ..|.  .+.|.||+|+||||+.+.++..+
T Consensus        30 ~~Ge--~~~liG~nGsGKSTLlk~l~Gl~   56 (262)
T 1b0u_A           30 RAGD--VISIIGSSGSGKSTFLRCINFLE   56 (262)
T ss_dssp             CTTC--EEEEECCTTSSHHHHHHHHTTSS
T ss_pred             cCCC--EEEEECCCCCCHHHHHHHHhcCC
Confidence            3444  58999999999999999999864

>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus}

Probab=95.99  E-value=0.088  Score=47.42  Aligned_cols=23  Identities=35%  Similarity=0.443  Sum_probs=21.1

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHc
Q psy879           34 IIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      +++.|+||+|||+++..++....
T Consensus       203 ~ii~G~pg~GKT~lal~ia~~~a  225 (444)
T 2q6t_A          203 NIIAARPAMGKTAFALTIAQNAA  225 (444)
T ss_dssp             EEEEECTTSCHHHHHHHHHHHHH
T ss_pred             EEEEeCCCCCHHHHHHHHHHHHH
Confidence            89999999999999999998764

>3llu_A RAS-related GTP-binding protein C; structural genomics consortium, SGC, cytoplasm, nucleotide-binding, nucleus, phosphoprotein; HET: GNP; 1.40A {Homo sapiens} PDB: 2q3f_A*

Probab=95.98  E-value=0.067  Score=42.02  Aligned_cols=22  Identities=18%  Similarity=0.246  Sum_probs=19.2

Q ss_pred             eEEEECCCCCCHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~   54 (317)
                      .+++.|++|+|||++++.+...
T Consensus        22 ki~~vG~~~vGKTsLi~~l~~~   43 (196)
T 3llu_A           22 RILLMGLRRSGKSSIQKVVFHK   43 (196)
T ss_dssp             EEEEEESTTSSHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHHhc
Confidence            4999999999999999977653

>1wrb_A DJVLGB; RNA helicase, DEAD BOX, VASA, structural genomics, NPPSFA, N project on protein structural and functional analyses; 2.40A {Dugesia japonica} SCOP: c.37.1.19

Probab=95.97  E-value=0.027  Score=46.40  Aligned_cols=23  Identities=26%  Similarity=0.387  Sum_probs=17.4

Q ss_pred             HhcCCCceEEEECCCCCCHHHHHHH
Q psy879           26 SSSGNVPNIIISGPPGVGKTTTILC   50 (317)
Q Consensus        26 l~~~~~~~~ll~G~~G~GKt~la~~   50 (317)
                      +.+|+  ++++.+|+|+|||.+...
T Consensus        57 i~~~~--~~l~~a~TGsGKT~~~~~   79 (253)
T 1wrb_A           57 ILEHR--DIMACAQTGSGKTAAFLI   79 (253)
T ss_dssp             HHTTC--CEEEECCTTSSHHHHHHH
T ss_pred             HhCCC--CEEEECCCCChHHHHHHH
Confidence            33454  699999999999986443

>2d2e_A SUFC protein; ABC-ATPase, SUF protein, 310-helix, riken structural genomics/proteomics initiative, RSGI, structural genomics, binding; 1.70A {Thermus thermophilus} PDB: 2d2f_A*

Probab=95.97  E-value=0.0038  Score=51.76  Aligned_cols=26  Identities=35%  Similarity=0.394  Sum_probs=22.5

Q ss_pred             hcCCCceEEEECCCCCCHHHHHHHHHHH
Q psy879           27 SSGNVPNIIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        27 ~~~~~~~~ll~G~~G~GKt~la~~la~~   54 (317)
                      ..|.  .+.|.||+|+||||+.+.++..
T Consensus        27 ~~Ge--~~~l~G~nGsGKSTLlk~l~Gl   52 (250)
T 2d2e_A           27 PKGE--VHALMGPNGAGKSTLGKILAGD   52 (250)
T ss_dssp             ETTC--EEEEECSTTSSHHHHHHHHHTC
T ss_pred             cCCC--EEEEECCCCCCHHHHHHHHhCC
Confidence            3454  6899999999999999999985

>3aez_A Pantothenate kinase; transferase, homodimer, COA biosynthesis, nucleotide binding binding, cytoplasm, nucleotide-binding; HET: GDP PAZ; 2.20A {Mycobacterium tuberculosis} PDB: 2ges_A* 2geu_A* 2gev_A* 2zs7_A* 2zs8_A* 2zs9_A* 2zsa_A* 2zsb_A* 2zsd_A* 2zse_A* 2zsf_A* 2get_A* 3af0_A* 3af1_A* 3af2_A* 3af3_A* 3af4_A* 3avp_A* 3avo_A* 3avq_A*

Probab=95.96  E-value=0.0046  Score=53.03  Aligned_cols=25  Identities=36%  Similarity=0.416  Sum_probs=22.5

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHcC
Q psy879           33 NIIISGPPGVGKTTTILCLARILLG   57 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~~   57 (317)
                      .+.|.||+|+||||+++.++..+..
T Consensus        92 ivgI~G~sGsGKSTL~~~L~gll~~  116 (312)
T 3aez_A           92 IIGVAGSVAVGKSTTARVLQALLAR  116 (312)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHHT
T ss_pred             EEEEECCCCchHHHHHHHHHhhccc
Confidence            3899999999999999999998753

>3tw8_B RAS-related protein RAB-35; longin domain, RAB GTPase, guanine exchange factor; 2.10A {Homo sapiens}

Probab=95.96  E-value=0.0071  Score=46.73  Aligned_cols=21  Identities=38%  Similarity=0.716  Sum_probs=19.1

Q ss_pred             eEEEECCCCCCHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLAR   53 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~   53 (317)
                      .+++.|++|+|||+++..+..
T Consensus        11 ~i~v~G~~~~GKssl~~~l~~   31 (181)
T 3tw8_B           11 KLLIIGDSGVGKSSLLLRFAD   31 (181)
T ss_dssp             EEEEECCTTSCHHHHHHHHCS
T ss_pred             EEEEECCCCCCHHHHHHHHhc
Confidence            489999999999999999864

>4tmk_A Protein (thymidylate kinase); ATP:DTMP phosphotransferase, transferase; HET: T5A; 1.98A {Escherichia coli} SCOP: c.37.1.1 PDB: 5tmp_A*

Probab=95.95  E-value=0.0099  Score=47.92  Aligned_cols=27  Identities=33%  Similarity=0.377  Sum_probs=23.6

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHcCCC
Q psy879           33 NIIISGPPGVGKTTTILCLARILLGPS   59 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~~~~   59 (317)
                      -+.|.|++|+||||.++.+++.+....
T Consensus         5 ~i~~eG~~gsGKsT~~~~l~~~l~~~~   31 (213)
T 4tmk_A            5 YIVIEGLEGAGKTTARNVVVETLEQLG   31 (213)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHHHHTT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHcC
Confidence            489999999999999999999985443

>2qt1_A Nicotinamide riboside kinase 1; non-protein kinase, NAD+, NRK1, nicotinic acid riboside kinase activity, NAD biosynthesis; HET: NNR; 1.32A {Homo sapiens} PDB: 2qsy_A* 2qsz_A* 2qt0_A* 2p0e_A* 2qg6_A* 2ql6_A*

Probab=95.95  E-value=0.0032  Score=50.45  Aligned_cols=23  Identities=43%  Similarity=0.354  Sum_probs=20.8

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .+.+.|++|+||||+++.+++.+
T Consensus        23 ~i~i~G~~GsGKSTl~~~L~~~~   45 (207)
T 2qt1_A           23 IIGISGVTNSGKTTLAKNLQKHL   45 (207)
T ss_dssp             EEEEEESTTSSHHHHHHHHHTTS
T ss_pred             EEEEECCCCCCHHHHHHHHHHhc
Confidence            38899999999999999999864

>1g6h_A High-affinity branched-chain amino acid transport ATP-binding protein; beta-core domain; HET: ADP; 1.60A {Methanocaldococcus jannaschii} SCOP: c.37.1.12 PDB: 1gaj_A 1g9x_A*

Probab=95.95  E-value=0.0032  Score=52.42  Aligned_cols=28  Identities=36%  Similarity=0.605  Sum_probs=23.4

Q ss_pred             HhcCCCceEEEECCCCCCHHHHHHHHHHHH
Q psy879           26 SSSGNVPNIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        26 l~~~~~~~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      +..|.  .+.+.||+|+||||+.+.++..+
T Consensus        30 i~~Ge--~~~liG~nGsGKSTLlk~l~Gl~   57 (257)
T 1g6h_A           30 VNKGD--VTLIIGPNGSGKSTLINVITGFL   57 (257)
T ss_dssp             EETTC--EEEEECSTTSSHHHHHHHHTTSS
T ss_pred             EeCCC--EEEEECCCCCCHHHHHHHHhCCC
Confidence            33454  58999999999999999999865

>3con_A GTPase NRAS; structural genomics consortium, SGC, GDP, oncogene, disease mutation, golgi apparatus, GTP-binding, lipoprotein membrane, methylation; HET: GDP; 1.65A {Homo sapiens} PDB: 2pmx_A* 3gft_A* 4q21_A*

Probab=95.94  E-value=0.021  Score=44.53  Aligned_cols=22  Identities=27%  Similarity=0.552  Sum_probs=20.1

Q ss_pred             eEEEECCCCCCHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~   54 (317)
                      .+++.|++|+|||+++..++..
T Consensus        23 ki~vvG~~~~GKSsli~~l~~~   44 (190)
T 3con_A           23 KLVVVGAGGVGKSALTIQLIQN   44 (190)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECcCCCCHHHHHHHHHcC
Confidence            3899999999999999999865

>2xxa_A Signal recognition particle protein; protein transport, RNA/RNA binding protein, hydrolase, gtpas; HET: GCP; 3.94A {Escherichia coli} PDB: 2j28_9

Probab=95.94  E-value=0.065  Score=48.05  Aligned_cols=36  Identities=28%  Similarity=0.383  Sum_probs=26.4

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHcCC-CCCCceEEec
Q psy879           33 NIIISGPPGVGKTTTILCLARILLGP-SFKDAVLELN   68 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~~~-~~~~~~~~~~   68 (317)
                      .+++.|++|+||||++-.+|..+... +....++..+
T Consensus       102 vI~ivG~~GvGKTT~a~~LA~~l~~~~G~kVllvd~D  138 (433)
T 2xxa_A          102 VVLMAGLQGAGKTTSVGKLGKFLREKHKKKVLVVSAD  138 (433)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHHTSCCCEEEEECC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHhcCCeEEEEecC
Confidence            38889999999999999999888544 3333333333

>2qm8_A GTPase/ATPase; G protein, G3E, metallochaperone, chaperone; HET: MSE; 1.70A {Methylobacterium extorquens} SCOP: c.37.1.10 PDB: 2qm7_A*

Probab=95.93  E-value=0.0038  Score=54.19  Aligned_cols=25  Identities=48%  Similarity=0.719  Sum_probs=22.5

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHcC
Q psy879           33 NIIISGPPGVGKTTTILCLARILLG   57 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~~   57 (317)
                      .+.|.||||+||||+.+.++..+..
T Consensus        57 ~v~i~G~~GaGKSTLl~~l~g~~~~   81 (337)
T 2qm8_A           57 RVGITGVPGVGKSTTIDALGSLLTA   81 (337)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHhhhh
Confidence            5999999999999999999987643

>1r8s_A ADP-ribosylation factor 1; protein transport/exchange factor, protein transport-exchang complex; HET: GDP; 1.46A {Bos taurus} SCOP: c.37.1.8 PDB: 1re0_A* 1s9d_A* 1u81_A* 1r8q_A* 1rrf_A* 1rrg_A* 1hur_A* 1o3y_A* 1j2j_A* 2j59_A* 1mr3_F* 2k5u_A* 3lrp_A* 3tjz_A* 3rd1_A* 2ksq_A* 2a5d_A* 2a5f_A* 2j5x_A* 1e0s_A* ...

Probab=95.93  E-value=0.19  Score=37.69  Aligned_cols=23  Identities=30%  Similarity=0.307  Sum_probs=20.2

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .+++.|++|+|||+++..+...-
T Consensus         2 ki~~~G~~~~GKssl~~~l~~~~   24 (164)
T 1r8s_A            2 RILMVGLDAAGKTTILYKLKLGE   24 (164)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHcCC
Confidence            47899999999999999998653

>1wb9_A DNA mismatch repair protein MUTS; DNA-binding, ATP-binding, DNA binding, DNA repair, mismatch recognition; HET: DNA ADP; 2.10A {Escherichia coli} SCOP: a.113.1.1 c.37.1.12 c.55.6.1 d.75.2.1 PDB: 1wbb_A* 1e3m_A* 1oh5_A* 1oh6_A* 1oh7_A* 1oh8_A* 1w7a_A* 2wtu_A* 1wbd_A* 1ng9_A* 3k0s_A*

Probab=95.92  E-value=0.015  Score=56.31  Aligned_cols=23  Identities=39%  Similarity=0.408  Sum_probs=20.8

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .++|+||+|+||||+.+.++...
T Consensus       609 i~~ItGpNGsGKSTlLr~iagl~  631 (800)
T 1wb9_A          609 MLIITGPNMGGKSTYMRQTALIA  631 (800)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCChHHHHHHHHHHH
Confidence            48999999999999999999764

>2pze_A Cystic fibrosis transmembrane conductance regulat; NBD, ABC transporter, CFTR, hydrolase; HET: ATP; 1.70A {Homo sapiens} PDB: 2pzg_A* 2pzf_A* 1ckx_A 1cky_A 1ckw_A 1ckz_A

Probab=95.92  E-value=0.0035  Score=51.26  Aligned_cols=41  Identities=7%  Similarity=0.042  Sum_probs=29.3

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHH-hhhccCCceEEEEecCC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRT-MEIYSNTTRFALACNNS  136 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~-le~~~~~~~~il~~~~~  136 (317)
                      +++++++||... +.+.....+.+. +........+|++|++.
T Consensus       148 ~p~lllLDEPts~LD~~~~~~i~~~l~~~~~~~~tvi~vtH~~  190 (229)
T 2pze_A          148 DADLYLLDSPFGYLDVLTEKEIFESCVCKLMANKTRILVTSKM  190 (229)
T ss_dssp             CCSEEEEESTTTTSCHHHHHHHHHHCCCCCTTTSEEEEECCCH
T ss_pred             CCCEEEEECcccCCCHHHHHHHHHHHHHHhhCCCEEEEEcCCh
Confidence            578999999975 567777888876 44443455677777764

>2zj8_A DNA helicase, putative SKI2-type helicase; RECA fold, ATP-binding, hydrolase, nucleotide- binding; 2.00A {Pyrococcus furiosus} PDB: 2zj5_A* 2zj2_A 2zja_A*

Probab=95.92  E-value=0.022  Score=54.68  Aligned_cols=28  Identities=29%  Similarity=0.420  Sum_probs=20.3

Q ss_pred             HhcCCCceEEEECCCCCCHHHHH-HHHHHHH
Q psy879           26 SSSGNVPNIIISGPPGVGKTTTI-LCLARIL   55 (317)
Q Consensus        26 l~~~~~~~~ll~G~~G~GKt~la-~~la~~l   55 (317)
                      +.++.  ++++.||+|+|||+.+ ..+.+.+
T Consensus        36 ~~~~~--~~lv~apTGsGKT~~~~l~il~~~   64 (720)
T 2zj8_A           36 ILEGK--NALISIPTASGKTLIAEIAMVHRI   64 (720)
T ss_dssp             GGGTC--EEEEECCGGGCHHHHHHHHHHHHH
T ss_pred             hcCCC--cEEEEcCCccHHHHHHHHHHHHHH
Confidence            34444  7999999999999988 3444433

>2zu0_C Probable ATP-dependent transporter SUFC; iron-sulfur cluster, ABC-ATPase, ATP-binding, cytoplasm, nucleotide-binding; HET: MES; 2.20A {Escherichia coli} PDB: 2d3w_A

Probab=95.92  E-value=0.0042  Score=52.01  Aligned_cols=22  Identities=41%  Similarity=0.430  Sum_probs=20.7

Q ss_pred             eEEEECCCCCCHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~   54 (317)
                      .+.|.||+|+||||+.+.++..
T Consensus        48 ~~~l~G~NGsGKSTLlk~l~Gl   69 (267)
T 2zu0_C           48 VHAIMGPNGSGKSTLSATLAGR   69 (267)
T ss_dssp             EEEEECCTTSSHHHHHHHHHTC
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            5899999999999999999986

>1nlf_A Regulatory protein REPA; replicative DNA helicase structural changes, replication; 1.95A {Escherichia coli} SCOP: c.37.1.11 PDB: 1g8y_A 1olo_A

Probab=95.91  E-value=0.0043  Score=52.29  Aligned_cols=24  Identities=29%  Similarity=0.322  Sum_probs=21.7

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHc
Q psy879           33 NIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      .++|+||+|+||||+++.++..+.
T Consensus        32 i~~i~G~~GsGKTtl~~~l~~~~~   55 (279)
T 1nlf_A           32 VGALVSPGGAGKSMLALQLAAQIA   55 (279)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHh
Confidence            489999999999999999998664

>2ce2_X GTPase HRAS; signaling protein, guanine nucleotide binding protein, fluor membrane, lipoprotein, palmitate, prenylation; HET: GDP XY2; 1.0A {Homo sapiens} PDB: 2cl0_X* 2cl6_X* 2cl7_X* 2clc_X* 2evw_X* 2cld_X* 1aa9_A* 1ioz_A* 1q21_A* 6q21_A* 3k9l_A* 3k9n_A* 1ctq_A* 1bkd_R 1crp_A* 1crq_A* 1crr_A* 121p_A* 1gnp_A* 1gnq_A* ...

Probab=95.91  E-value=0.019  Score=43.42  Aligned_cols=22  Identities=27%  Similarity=0.552  Sum_probs=20.0

Q ss_pred             eEEEECCCCCCHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~   54 (317)
                      .+++.|++|+|||+++..+...
T Consensus         5 ~i~v~G~~~~GKssl~~~l~~~   26 (166)
T 2ce2_X            5 KLVVVGAGGVGKSALTIQLIQN   26 (166)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            4899999999999999999865

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus}

Probab=95.91  E-value=0.02  Score=54.95  Aligned_cols=20  Identities=25%  Similarity=0.411  Sum_probs=17.1

Q ss_pred             eEEEECCCCCCHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLA   52 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la   52 (317)
                      ++++.||+|+|||+.+-..+
T Consensus        48 ~~lv~apTGsGKT~~~~l~i   67 (715)
T 2va8_A           48 RLLLTSPTGSGKTLIAEMGI   67 (715)
T ss_dssp             CEEEECCTTSCHHHHHHHHH
T ss_pred             cEEEEcCCCCcHHHHHHHHH
Confidence            69999999999999984433

>1j8m_F SRP54, signal recognition 54 kDa protein; signaling protein; 2.00A {Acidianus ambivalens} SCOP: a.24.13.1 c.37.1.10 PDB: 1j8y_F

Probab=95.89  E-value=0.096  Score=44.41  Aligned_cols=24  Identities=42%  Similarity=0.434  Sum_probs=21.7

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHcC
Q psy879           34 IIISGPPGVGKTTTILCLARILLG   57 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~l~~   57 (317)
                      +.+.|++|+||||++..++..+..
T Consensus       101 i~i~G~~G~GKTT~~~~la~~~~~  124 (297)
T 1j8m_F          101 IMLVGVQGTGKTTTAGKLAYFYKK  124 (297)
T ss_dssp             EEEECSSCSSTTHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHH
Confidence            888999999999999999988753

>1mv5_A LMRA, multidrug resistance ABC transporter ATP-binding and permease protein; asymmetric dimer, tetramer, P-glycoprotein; HET: ATP ADP; 3.10A {Lactococcus lactis} SCOP: c.37.1.12

Probab=95.88  E-value=0.0021  Score=53.03  Aligned_cols=23  Identities=39%  Similarity=0.590  Sum_probs=21.2

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .+.+.||+|+||||+.+.++..+
T Consensus        30 ~~~i~G~nGsGKSTLl~~l~Gl~   52 (243)
T 1mv5_A           30 IIAFAGPSGGGKSTIFSLLERFY   52 (243)
T ss_dssp             EEEEECCTTSSHHHHHHHHTTSS
T ss_pred             EEEEECCCCCCHHHHHHHHhcCC
Confidence            58999999999999999999865

>3foz_A TRNA delta(2)-isopentenylpyrophosphate transferas; nucleoside modification, isopentenyl-tRNA transferase, transferase-RNA complex; 2.50A {Escherichia coli k-12} PDB: 2zxu_A* 2zm5_A

Probab=95.87  E-value=0.0063  Score=51.76  Aligned_cols=23  Identities=39%  Similarity=0.647  Sum_probs=21.4

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .+++.||+|+|||+++..+++.+
T Consensus        12 ~i~i~GptgsGKt~la~~La~~~   34 (316)
T 3foz_A           12 AIFLMGPTASGKTALAIELRKIL   34 (316)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHS
T ss_pred             EEEEECCCccCHHHHHHHHHHhC
Confidence            38899999999999999999986

>1vht_A Dephospho-COA kinase; structural genomics, transferase; HET: BA3; 1.59A {Escherichia coli} SCOP: c.37.1.1 PDB: 1vhl_A* 1viy_A 1t3h_A 1n3b_A

Probab=95.86  E-value=0.0051  Score=49.65  Aligned_cols=21  Identities=29%  Similarity=0.420  Sum_probs=19.7

Q ss_pred             eEEEECCCCCCHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLAR   53 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~   53 (317)
                      .+.|.|++|+||||+++.++.
T Consensus         6 ~I~i~G~~GSGKST~~~~L~~   26 (218)
T 1vht_A            6 IVALTGGIGSGKSTVANAFAD   26 (218)
T ss_dssp             EEEEECCTTSCHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            489999999999999999987

>3kta_A Chromosome segregation protein SMC; structural maintenance of chromosomes, ABC ATPase, CFTR adenylate kinase, AP5A, transferase; HET: AP5; 1.63A {Pyrococcus furiosus} PDB: 1xex_A* 1xew_X*

Probab=95.85  E-value=0.0062  Score=47.53  Aligned_cols=25  Identities=28%  Similarity=0.282  Sum_probs=22.2

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHcC
Q psy879           33 NIIISGPPGVGKTTTILCLARILLG   57 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~~   57 (317)
                      ..+|+||+|+||||++.+++-.+.+
T Consensus        28 ~~~i~G~NGsGKStll~ai~~~l~~   52 (182)
T 3kta_A           28 FTAIVGANGSGKSNIGDAILFVLGG   52 (182)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHTTC
T ss_pred             cEEEECCCCCCHHHHHHHHHHHHcC
Confidence            4799999999999999999998743

>3ld9_A DTMP kinase, thymidylate kinase; ssgcid, NIH, niaid, SBRI, UW, emerald biostructures, ehrlich chaffeensis; 2.15A {Ehrlichia chaffeensis}

Probab=95.85  E-value=0.0082  Score=48.72  Aligned_cols=36  Identities=31%  Similarity=0.255  Sum_probs=24.2

Q ss_pred             HHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcC
Q psy879           22 LKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLG   57 (317)
Q Consensus        22 l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~   57 (317)
                      +.......+...+.|.|++|+||||.++.+++.+..
T Consensus        12 ~~~~~~~~~~~~i~~~G~~g~GKst~~~~l~~~l~~   47 (223)
T 3ld9_A           12 LEAQTQGPGSMFITFEGIDGSGKTTQSHLLAEYLSE   47 (223)
T ss_dssp             -------CCCEEEEEECSTTSSHHHHHHHHHHHHHH
T ss_pred             ccccccCCCCeEEEEECCCCCCHHHHHHHHHHHHhh
Confidence            333344334334899999999999999999998854

>2bov_A RAla, RAS-related protein RAL-A; C3BOT, exoenzyme, RAla, GTPase, ribosylating toxin, GTP-binding, lipoprotein, prenylation; HET: GDP; 2.66A {Homo sapiens}

Probab=95.85  E-value=0.034  Score=43.92  Aligned_cols=22  Identities=32%  Similarity=0.487  Sum_probs=20.0

Q ss_pred             eEEEECCCCCCHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~   54 (317)
                      .+++.|++|+|||+++..+...
T Consensus        16 ki~v~G~~~~GKSsli~~l~~~   37 (206)
T 2bov_A           16 KVIMVGSGGVGKSALTLQFMYD   37 (206)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            4999999999999999999864

>3j16_B RLI1P; ribosome recycling, translation, eukarya, ribosome; HET: ATP; 7.20A {Saccharomyces cerevisiae}

Probab=95.84  E-value=0.025  Score=52.99  Aligned_cols=41  Identities=10%  Similarity=0.190  Sum_probs=28.7

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhcc--CCceEEEEecCC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYS--NTTRFALACNNS  136 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~--~~~~~il~~~~~  136 (317)
                      +++++++||.-. |....+..+.+++.+..  ....+|++|++.
T Consensus       485 ~p~lLlLDEPT~gLD~~~~~~i~~ll~~l~~~~g~tviivtHdl  528 (608)
T 3j16_B          485 PADIYLIDEPSAYLDSEQRIICSKVIRRFILHNKKTAFIVEHDF  528 (608)
T ss_dssp             CCSEEEECCTTTTCCHHHHHHHHHHHHHHHHHHTCEEEEECSCH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHHHHHHHhCCCEEEEEeCCH
Confidence            689999999975 56667777777776542  245567777664

>2qag_B Septin-6, protein NEDD5; cell cycle, cell division, GTP-binding, nucleotide-binding, phosphorylation, acetylation, alternative splicing, coiled coil; HET: GDP GTP; 4.00A {Homo sapiens}

Probab=95.84  E-value=0.0039  Score=55.64  Aligned_cols=37  Identities=27%  Similarity=0.260  Sum_probs=30.9

Q ss_pred             HHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHH
Q psy879           19 VERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        19 ~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      ++.+.-.+..|..+++.|.||+|+||||+++.++...
T Consensus        30 L~~vsl~i~~Gei~~vaLvG~nGaGKSTLln~L~G~~   66 (427)
T 2qag_B           30 DQLVNKSVSQGFCFNILCVGETGLGKSTLMDTLFNTK   66 (427)
T ss_dssp             HHHHHHSCC-CCEEEEEEECSTTSSSHHHHHHHHTSC
T ss_pred             cCCCceEecCCCeeEEEEECCCCCCHHHHHHHHhCcc
Confidence            6677777888886669999999999999999998753

>2qmh_A HPR kinase/phosphorylase; V267F mutation, ATP-binding, carbohydrate metabolism, magnesium, metal-binding, multifunctional enzyme; 2.60A {Lactobacillus casei} PDB: 1jb1_A 1kkl_A 1kkm_A*

Probab=95.83  E-value=0.0041  Score=49.27  Aligned_cols=23  Identities=39%  Similarity=0.592  Sum_probs=20.9

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .++|.||+|+|||+++..+++..
T Consensus        36 ~ilI~GpsGsGKStLA~~La~~g   58 (205)
T 2qmh_A           36 GVLITGDSGVGKSETALELVQRG   58 (205)
T ss_dssp             EEEEECCCTTTTHHHHHHHHTTT
T ss_pred             EEEEECCCCCCHHHHHHHHHHhC
Confidence            38999999999999999999864

>2z0m_A 337AA long hypothetical ATP-dependent RNA helicase DEAD; ATP-binding, hydrolase, nucleotide-binding, RNA binding protein, structural genomics; 1.90A {Sulfolobus tokodaii}

Probab=95.83  E-value=0.034  Score=47.62  Aligned_cols=22  Identities=23%  Similarity=0.320  Sum_probs=18.2

Q ss_pred             eEEEECCCCCCHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~   54 (317)
                      ++++.+|+|+|||.++...+-.
T Consensus        33 ~~lv~~~TGsGKT~~~~~~~~~   54 (337)
T 2z0m_A           33 NVVVRAKTGSGKTAAYAIPILE   54 (337)
T ss_dssp             CEEEECCTTSSHHHHHHHHHHH
T ss_pred             CEEEEcCCCCcHHHHHHHHHHh
Confidence            6999999999999877665544

>3lxx_A GTPase IMAP family member 4; structural genomics consortium, SGC, coiled coil, GTP- binding, nucleotide-binding, immune system; HET: GDP; 2.15A {Homo sapiens}

Probab=95.83  E-value=0.084  Score=43.02  Aligned_cols=23  Identities=26%  Similarity=0.362  Sum_probs=20.5

Q ss_pred             ceEEEECCCCCCHHHHHHHHHHH
Q psy879           32 PNIIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        32 ~~~ll~G~~G~GKt~la~~la~~   54 (317)
                      ..++|.|++|+||||++..+...
T Consensus        30 ~~i~lvG~~g~GKStlin~l~g~   52 (239)
T 3lxx_A           30 LRIVLVGKTGAGKSATGNSILGR   52 (239)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHTS
T ss_pred             eEEEEECCCCCCHHHHHHHHcCC
Confidence            35999999999999999999864

>4dkx_A RAS-related protein RAB-6A; GTP binding fold, membrane trafficking, GTP, cytosol, protei transport; HET: GDP; 1.90A {Homo sapiens} PDB: 3bbp_A*

Probab=95.82  E-value=0.019  Score=46.33  Aligned_cols=21  Identities=29%  Similarity=0.370  Sum_probs=19.2

Q ss_pred             EEEECCCCCCHHHHHHHHHHH
Q psy879           34 IIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~   54 (317)
                      +++.|.+|+|||+++..+...
T Consensus        16 ivlvGd~~VGKTsLi~r~~~~   36 (216)
T 4dkx_A           16 LVFLGEQSVGKTSLITRFMYD   36 (216)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECcCCcCHHHHHHHHHhC
Confidence            899999999999999998854

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori}

Probab=95.80  E-value=0.073  Score=45.98  Aligned_cols=23  Identities=30%  Similarity=0.557  Sum_probs=21.2

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHc
Q psy879           34 IIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      +++.|+||+|||+++..++..+.
T Consensus        49 iiIaG~pG~GKTt~al~ia~~~a   71 (338)
T 4a1f_A           49 VIIGARPSMGKTSLMMNMVLSAL   71 (338)
T ss_dssp             EEEEECTTSCHHHHHHHHHHHHH
T ss_pred             EEEEeCCCCCHHHHHHHHHHHHH
Confidence            89999999999999999998764

>1r2q_A RAS-related protein RAB-5A; GTPase, GNP, atomic resolution, protein transport; HET: GNP; 1.05A {Homo sapiens} SCOP: c.37.1.8 PDB: 1n6h_A* 1tu4_A* 1tu3_A* 1n6k_A* 1n6i_A* 1n6l_A* 1n6o_A* 1n6p_A* 1n6n_A* 1n6r_A* 3mjh_A* 1z0d_A* 1huq_A* 2hei_A* 1z07_A*

Probab=95.80  E-value=0.027  Score=42.79  Aligned_cols=22  Identities=23%  Similarity=0.523  Sum_probs=19.8

Q ss_pred             eEEEECCCCCCHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~   54 (317)
                      .+++.|++|+|||+++..+...
T Consensus         8 ~i~v~G~~~~GKssli~~l~~~   29 (170)
T 1r2q_A            8 KLVLLGESAVGKSSLVLRFVKG   29 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            3899999999999999999864

>2ihy_A ABC transporter, ATP-binding protein; ATPase, ABC cassette, hydrolase; HET: MSE; 1.90A {Staphylococcus aureus}

Probab=95.79  E-value=0.0041  Score=52.41  Aligned_cols=27  Identities=33%  Similarity=0.443  Sum_probs=23.0

Q ss_pred             hcCCCceEEEECCCCCCHHHHHHHHHHHH
Q psy879           27 SSGNVPNIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        27 ~~~~~~~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      ..|.  .+.|.||+|+||||+.+.++..+
T Consensus        45 ~~Ge--~~~liG~NGsGKSTLlk~l~Gl~   71 (279)
T 2ihy_A           45 AKGD--KWILYGLNGAGKTTLLNILNAYE   71 (279)
T ss_dssp             ETTC--EEEEECCTTSSHHHHHHHHTTSS
T ss_pred             cCCC--EEEEECCCCCcHHHHHHHHhCCC
Confidence            3444  58999999999999999999865

>4edh_A DTMP kinase, thymidylate kinase; structural genomics, PSI-biology; HET: TMP ADP; 1.32A {Pseudomonas aeruginosa PAO1} PDB: 4e5u_A* 4esh_A* 4gmd_A* 3uwk_A* 3uwo_A* 3uxm_A*

Probab=95.79  E-value=0.015  Score=46.79  Aligned_cols=27  Identities=33%  Similarity=0.434  Sum_probs=23.6

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHcCCC
Q psy879           33 NIIISGPPGVGKTTTILCLARILLGPS   59 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~~~~   59 (317)
                      .+.|.|++|+||||.++.+++.+....
T Consensus         8 ~i~~eG~~gsGKsT~~~~l~~~l~~~~   34 (213)
T 4edh_A            8 FVTLEGPEGAGKSTNRDYLAERLRERG   34 (213)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHTTT
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHHHcC
Confidence            389999999999999999999985443

>3b9q_A Chloroplast SRP receptor homolog, alpha subunit CPFTSY; protein translocation, GTP-binding, nucleotide-binding, protein transport; 1.75A {Arabidopsis thaliana}

Probab=95.77  E-value=0.0053  Score=52.37  Aligned_cols=24  Identities=46%  Similarity=0.494  Sum_probs=22.1

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHcC
Q psy879           34 IIISGPPGVGKTTTILCLARILLG   57 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~l~~   57 (317)
                      +.|.||+|+||||+++.++..+..
T Consensus       103 i~lvG~nGsGKTTll~~Lag~l~~  126 (302)
T 3b9q_A          103 IMIVGVNGGGKTTSLGKLAHRLKN  126 (302)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHHHH
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHH
Confidence            899999999999999999998753

>3d3q_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2; 2.70A {Staphylococcus epidermidis atcc 12228}

Probab=95.76  E-value=0.0057  Score=52.87  Aligned_cols=23  Identities=35%  Similarity=0.531  Sum_probs=21.7

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .+++.||+|+||||++..+++.+
T Consensus         9 lI~I~GptgSGKTtla~~La~~l   31 (340)
T 3d3q_A            9 LIVIVGPTASGKTELSIEVAKKF   31 (340)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHT
T ss_pred             eEEEECCCcCcHHHHHHHHHHHc
Confidence            48999999999999999999986

>3a8t_A Adenylate isopentenyltransferase; rossmann fold protein; HET: ATP; 2.37A {Humulus lupulus}

Probab=95.75  E-value=0.0045  Score=53.38  Aligned_cols=24  Identities=25%  Similarity=0.401  Sum_probs=22.1

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHc
Q psy879           33 NIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      .++|.||+|+|||+++..+|+.+.
T Consensus        42 lIvI~GPTgsGKTtLa~~LA~~l~   65 (339)
T 3a8t_A           42 LLVLMGATGTGKSRLSIDLAAHFP   65 (339)
T ss_dssp             EEEEECSTTSSHHHHHHHHHTTSC
T ss_pred             eEEEECCCCCCHHHHHHHHHHHCC
Confidence            589999999999999999999863

>2yz2_A Putative ABC transporter ATP-binding protein TM_0; cobalt transport, TM02 hydrolase, inner membrane, membrane, nucleotide-binding; 2.30A {Thermotoga maritima}

Probab=95.74  E-value=0.0045  Score=51.84  Aligned_cols=43  Identities=23%  Similarity=0.292  Sum_probs=31.2

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhcc-CCceEEEEecCCCc
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYS-NTTRFALACNNSEK  138 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~-~~~~~il~~~~~~~  138 (317)
                      +++++++||... |.......+.+.+.+.. ....+|++|++.+.
T Consensus       156 ~p~lllLDEPts~LD~~~~~~l~~~l~~l~~~g~tii~vtHd~~~  200 (266)
T 2yz2_A          156 EPDILILDEPLVGLDREGKTDLLRIVEKWKTLGKTVILISHDIET  200 (266)
T ss_dssp             CCSEEEEESTTTTCCHHHHHHHHHHHHHHHHTTCEEEEECSCCTT
T ss_pred             CCCEEEEcCccccCCHHHHHHHHHHHHHHHHcCCEEEEEeCCHHH
Confidence            688999999985 56777778888777653 34567777777543

>1ek0_A Protein (GTP-binding protein YPT51); vesicular traffic, GTP hydrolysis, YPT/RAB protein, endocytosis, hydrolase; HET: MHO GNP GDP; 1.48A {Saccharomyces cerevisiae} SCOP: c.37.1.8

Probab=95.74  E-value=0.029  Score=42.57  Aligned_cols=22  Identities=23%  Similarity=0.514  Sum_probs=19.9

Q ss_pred             eEEEECCCCCCHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~   54 (317)
                      .+++.|++|+|||+++..+...
T Consensus         5 ~i~v~G~~~~GKssli~~l~~~   26 (170)
T 1ek0_A            5 KLVLLGEAAVGKSSIVLRFVSN   26 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            3899999999999999999865

>1z06_A RAS-related protein RAB-33B; RAB GTPase, RAB33B GTPase, vesicular trafficking, protein transport; HET: GNP; 1.81A {Mus musculus} SCOP: c.37.1.8 PDB: 2g77_B*

Probab=95.72  E-value=0.043  Score=42.79  Aligned_cols=22  Identities=32%  Similarity=0.385  Sum_probs=20.0

Q ss_pred             eEEEECCCCCCHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~   54 (317)
                      .+++.|++|+|||+++..+...
T Consensus        22 ki~v~G~~~~GKSsli~~l~~~   43 (189)
T 1z06_A           22 KIIVIGDSNVGKTCLTYRFCAG   43 (189)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            4999999999999999998864

>2i1q_A DNA repair and recombination protein RADA; ATPase, recombinase, ATP complex, calcium stimulation, RECA, DMC1; HET: DNA ANP; 1.90A {Methanococcus voltae} SCOP: a.60.4.1 c.37.1.11 PDB: 1xu4_A* 2b21_A* 2fpk_A* 2fpl_A* 2fpm_A* 1t4g_A* 3fyh_A* 2f1j_A* 2f1i_A* 2f1h_A* 3ntu_A* 3ewa_A* 3ew9_A* 3etl_A* 4dc9_A* 2gdj_A*

Probab=95.71  E-value=0.018  Score=49.50  Aligned_cols=22  Identities=27%  Similarity=0.197  Sum_probs=20.3

Q ss_pred             EEEECCCCCCHHHHHHHHHHHH
Q psy879           34 IIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~l   55 (317)
                      ++++||||+|||+++..++...
T Consensus       101 ~~i~G~~gsGKT~la~~la~~~  122 (322)
T 2i1q_A          101 TEFAGVFGSGKTQIMHQSCVNL  122 (322)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHHHHH
Confidence            8999999999999999999763

>2efe_B Small GTP-binding protein-like; GEF, GTPase, VPS9, nucleotide, transport protein; HET: GNH; 2.08A {Arabidopsis thaliana} PDB: 2efd_B 2efc_B* 2efh_B*

Probab=95.71  E-value=0.034  Score=42.80  Aligned_cols=22  Identities=23%  Similarity=0.540  Sum_probs=19.9

Q ss_pred             eEEEECCCCCCHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~   54 (317)
                      .+++.|++|+|||+++..+...
T Consensus        14 ki~v~G~~~~GKSsli~~l~~~   35 (181)
T 2efe_B           14 KLVLLGDVGAGKSSLVLRFVKD   35 (181)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHC
T ss_pred             EEEEECcCCCCHHHHHHHHHcC
Confidence            3899999999999999999864

>1zbd_A Rabphilin-3A; G protein, effector, RABCDR, synaptic exocytosis, RAB protein, RAB3A; HET: GTP; 2.60A {Rattus norvegicus} SCOP: c.37.1.8

Probab=95.71  E-value=0.034  Score=43.91  Aligned_cols=22  Identities=36%  Similarity=0.489  Sum_probs=19.7

Q ss_pred             eEEEECCCCCCHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~   54 (317)
                      .+++.|++|+|||+++..+...
T Consensus        10 ki~v~G~~~~GKSsli~~l~~~   31 (203)
T 1zbd_A           10 KILIIGNSSVGKTSFLFRYADD   31 (203)
T ss_dssp             EEEEECSTTSSHHHHHHHHHTC
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            4899999999999999998764

>2a9k_A RAS-related protein RAL-A; bacterial ADP-ribosyltransferase, RAL, RHO, GD binding; HET: GDP NAD; 1.73A {Homo sapiens} SCOP: c.37.1.8 PDB: 2a78_A*

Probab=95.70  E-value=0.033  Score=43.10  Aligned_cols=22  Identities=32%  Similarity=0.487  Sum_probs=20.0

Q ss_pred             eEEEECCCCCCHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~   54 (317)
                      .+++.|++|+|||+++..+...
T Consensus        20 ki~v~G~~~~GKSsli~~l~~~   41 (187)
T 2a9k_A           20 KVIMVGSGGVGKSALTLQFMYD   41 (187)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhhC
Confidence            3999999999999999999864

>2www_A Methylmalonic aciduria type A protein, mitochondrial; transport protein, nucleotide-binding; HET: GDP 2PE; 2.64A {Homo sapiens}

Probab=95.68  E-value=0.017  Score=50.35  Aligned_cols=26  Identities=38%  Similarity=0.659  Sum_probs=22.7

Q ss_pred             CceEEEECCCCCCHHHHHHHHHHHHc
Q psy879           31 VPNIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        31 ~~~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      .+.+.|.|+||+||||+..+++..+.
T Consensus        74 ~~~v~lvG~pgaGKSTLln~L~~~~~   99 (349)
T 2www_A           74 AFRVGLSGPPGAGKSTFIEYFGKMLT   99 (349)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             ceEEEEEcCCCCCHHHHHHHHHHHhh
Confidence            34599999999999999999998764

>1zj6_A ADP-ribosylation factor-like protein 5; ARL, GTP-binding, transport protein; HET: G3D; 2.00A {Homo sapiens} SCOP: c.37.1.8

Probab=95.68  E-value=0.044  Score=42.62  Aligned_cols=26  Identities=27%  Similarity=0.363  Sum_probs=21.5

Q ss_pred             cCCCceEEEECCCCCCHHHHHHHHHH
Q psy879           28 SGNVPNIIISGPPGVGKTTTILCLAR   53 (317)
Q Consensus        28 ~~~~~~~ll~G~~G~GKt~la~~la~   53 (317)
                      +.+...+++.|++|+|||+++..+..
T Consensus        13 ~~~~~~i~v~G~~~~GKssl~~~l~~   38 (187)
T 1zj6_A           13 NHQEHKVIIVGLDNAGKTTILYQFSM   38 (187)
T ss_dssp             TTSCEEEEEEESTTSSHHHHHHHHHT
T ss_pred             CCCccEEEEECCCCCCHHHHHHHHhc
Confidence            33434599999999999999999884

>1q3t_A Cytidylate kinase; nucleotide monophosphate kinase, CMP kinase, transferase; NMR {Streptococcus pneumoniae} SCOP: c.37.1.1

Probab=95.67  E-value=0.0094  Score=48.78  Aligned_cols=23  Identities=35%  Similarity=0.554  Sum_probs=21.6

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .+.|.|++|+||||+++.+++.+
T Consensus        18 ~i~i~G~~gsGKst~~~~l~~~l   40 (236)
T 1q3t_A           18 QIAIDGPASSGKSTVAKIIAKDF   40 (236)
T ss_dssp             EEEEECSSCSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHc
Confidence            58999999999999999999976

>1m7b_A RND3/RHOE small GTP-binding protein; small GTPase, signaling protein; HET: GTP; 2.00A {Homo sapiens} SCOP: c.37.1.8 PDB: 2v55_B*

Probab=95.64  E-value=0.01  Score=46.31  Aligned_cols=22  Identities=27%  Similarity=0.472  Sum_probs=20.0

Q ss_pred             eEEEECCCCCCHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~   54 (317)
                      .+++.|++|+|||++++.+...
T Consensus         9 ki~v~G~~~vGKSsli~~l~~~   30 (184)
T 1m7b_A            9 KIVVVGDSQCGKTALLHVFAKD   30 (184)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            3899999999999999999875

>3cr8_A Sulfate adenylyltranferase, adenylylsulfate kinase; APS kinase, transferase, sulfate metabolism, nucleotide 2 kinase; 2.95A {Thiobacillus denitrificans}

Probab=95.64  E-value=0.0071  Score=56.02  Aligned_cols=40  Identities=25%  Similarity=0.395  Sum_probs=30.1

Q ss_pred             HHHHHHHHHHH----hcCCCceEEEECCCCCCHHHHHHHHHHHHcC
Q psy879           16 EDTVERLKVFS----SSGNVPNIIISGPPGVGKTTTILCLARILLG   57 (317)
Q Consensus        16 ~~~~~~l~~~l----~~~~~~~~ll~G~~G~GKt~la~~la~~l~~   57 (317)
                      +++.+.++...    .+|.  .+.|.|++|+||||++++++..+..
T Consensus       352 peV~~vLR~~~~~~~~~G~--iI~LiG~sGSGKSTLar~La~~L~~  395 (552)
T 3cr8_A          352 PEVLAELHRQTPPRERQGF--TVFFTGLSGAGKSTLARALAARLME  395 (552)
T ss_dssp             HHHHHHHHHHSCCGGGSCE--EEEEEESSCHHHHHHHHHHHHHHHT
T ss_pred             cchhhhhhhhcccccccce--EEEEECCCCChHHHHHHHHHHhhcc
Confidence            45555555543    3333  5899999999999999999999853

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4}

Probab=95.63  E-value=0.062  Score=49.21  Aligned_cols=38  Identities=16%  Similarity=0.063  Sum_probs=27.2

Q ss_pred             CHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHH
Q psy879           15 NEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        15 ~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .+...+.+..++..   .+.++.||.|+|||.++..++...
T Consensus       115 ~~~Q~~ai~~~~~~---~~~ll~~~tGsGKT~~~~~~~~~~  152 (510)
T 2oca_A          115 HWYQKDAVFEGLVN---RRRILNLPTSAGRSLIQALLARYY  152 (510)
T ss_dssp             CHHHHHHHHHHHHH---SEEEEECCSTTTHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHhc---CCcEEEeCCCCCHHHHHHHHHHHH
Confidence            44444555555543   268999999999999997777654

>3bgw_A DNAB-like replicative helicase; ATPase, replication; 3.91A {Bacillus phage SPP1}

Probab=95.63  E-value=0.082  Score=47.61  Aligned_cols=23  Identities=30%  Similarity=0.475  Sum_probs=21.2

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHc
Q psy879           34 IIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      +++.|+||+|||+++..++....
T Consensus       200 iiIaG~pG~GKTtlal~ia~~~a  222 (444)
T 3bgw_A          200 VLIAARPSMGKTAFALKQAKNMS  222 (444)
T ss_dssp             EEEEECSSSSHHHHHHHHHHHHH
T ss_pred             EEEEeCCCCChHHHHHHHHHHHH
Confidence            89999999999999999998764

>2ged_A SR-beta, signal recognition particle receptor beta subunit; protein transport, G protein, proline isomerization, circular permutation; 2.20A {Saccharomyces cerevisiae}

Probab=95.63  E-value=0.017  Score=45.32  Aligned_cols=23  Identities=43%  Similarity=0.697  Sum_probs=20.7

Q ss_pred             ceEEEECCCCCCHHHHHHHHHHH
Q psy879           32 PNIIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        32 ~~~ll~G~~G~GKt~la~~la~~   54 (317)
                      ..+++.|++|+|||+++..+...
T Consensus        49 ~~i~vvG~~g~GKSsll~~l~~~   71 (193)
T 2ged_A           49 PSIIIAGPQNSGKTSLLTLLTTD   71 (193)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHS
T ss_pred             CEEEEECCCCCCHHHHHHHHhcC
Confidence            35999999999999999999875

>3q85_A GTP-binding protein REM 2; G-domain, CAV2 beta, signaling protein; HET: GNP; 1.76A {Mus musculus} SCOP: c.37.1.8 PDB: 4aii_A*

Probab=95.61  E-value=0.02  Score=43.60  Aligned_cols=21  Identities=29%  Similarity=0.525  Sum_probs=18.9

Q ss_pred             eEEEECCCCCCHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLAR   53 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~   53 (317)
                      .+++.|++|+|||+++..+..
T Consensus         4 ki~ivG~~~~GKSsli~~l~~   24 (169)
T 3q85_A            4 KVMLVGESGVGKSTLAGTFGG   24 (169)
T ss_dssp             EEEEECSTTSSHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHh
Confidence            489999999999999999863

>2z83_A Helicase/nucleoside triphosphatase; hydrolase, membrane, nucleotide-binding, RNA replication, transmembrane, viral protein; 1.80A {Japanese encephalitis virus} PDB: 2v8o_A 2qeq_A

Probab=95.60  E-value=0.034  Score=50.37  Aligned_cols=31  Identities=16%  Similarity=0.191  Sum_probs=22.5

Q ss_pred             HHHHhcCCCceEEEECCCCCCHHHH-HHHHHHHH
Q psy879           23 KVFSSSGNVPNIIISGPPGVGKTTT-ILCLARIL   55 (317)
Q Consensus        23 ~~~l~~~~~~~~ll~G~~G~GKt~l-a~~la~~l   55 (317)
                      ..++.+|+  ++++.+|+|+|||+. ...+...+
T Consensus        15 ~~~l~~~~--~vlv~a~TGsGKT~~~~l~il~~~   46 (459)
T 2z83_A           15 PNMLRKRQ--MTVLDLHPGSGKTRKILPQIIKDA   46 (459)
T ss_dssp             CGGGSTTC--EEEECCCTTSCTTTTHHHHHHHHH
T ss_pred             HHHHhcCC--cEEEECCCCCCHHHHHHHHHHHHH
Confidence            44566665  799999999999997 44444443

>4dsu_A GTPase KRAS, isoform 2B; small G-protein, signaling, hydrolase; HET: GDP; 1.70A {Homo sapiens} PDB: 4dsn_A* 4dst_A* 4dso_A*

Probab=95.59  E-value=0.039  Score=42.77  Aligned_cols=22  Identities=27%  Similarity=0.566  Sum_probs=20.0

Q ss_pred             eEEEECCCCCCHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~   54 (317)
                      .+++.|++|+|||+++..+...
T Consensus         6 ki~v~G~~~~GKSsli~~l~~~   27 (189)
T 4dsu_A            6 KLVVVGADGVGKSALTIQLIQN   27 (189)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            3899999999999999999864

>2f6r_A COA synthase, bifunctional coenzyme A synthase; 18044849, bifunctional coenzyme A synthase (COA synthase), S genomics; HET: ACO UNL; 1.70A {Mus musculus}

Probab=95.57  E-value=0.0077  Score=50.84  Aligned_cols=21  Identities=24%  Similarity=0.358  Sum_probs=19.5

Q ss_pred             eEEEECCCCCCHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLAR   53 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~   53 (317)
                      .+.|.|++|+||||+++.++.
T Consensus        77 iI~I~G~~GSGKSTva~~La~   97 (281)
T 2f6r_A           77 VLGLTGISGSGKSSVAQRLKN   97 (281)
T ss_dssp             EEEEEECTTSCHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            389999999999999999994

>1mh1_A RAC1; GTP-binding, GTPase, small G-protein, RHO family, RAS super family; HET: GNP; 1.38A {Homo sapiens} SCOP: c.37.1.8 PDB: 1hh4_A* 2p2l_A* 2h7v_A* 1g4u_R* 1i4d_D* 1i4l_D* 2vrw_A 1e96_A* 1i4t_D* 2rmk_A* 2yin_C 1ryf_A* 1ryh_A* 3su8_A* 3sua_A* 2fju_A* 1he1_C* 2nz8_A 1foe_B 3bji_C ...

Probab=95.56  E-value=0.018  Score=44.58  Aligned_cols=22  Identities=23%  Similarity=0.409  Sum_probs=19.7

Q ss_pred             eEEEECCCCCCHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~   54 (317)
                      .+++.|++|+|||+++..+...
T Consensus         7 ~i~~~G~~~~GKssl~~~l~~~   28 (186)
T 1mh1_A            7 KCVVVGDGAVGKTCLLISYTTN   28 (186)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            3899999999999999998864

>2fh5_B SR-beta, signal recognition particle receptor beta subunit; endomembrane targeting, GTPase, GAP, longin domain, SEDL, transport protein; HET: GTP; 2.45A {Mus musculus} SCOP: c.37.1.8 PDB: 2go5_2

Probab=95.56  E-value=0.074  Score=42.32  Aligned_cols=24  Identities=21%  Similarity=0.166  Sum_probs=21.0

Q ss_pred             ceEEEECCCCCCHHHHHHHHHHHH
Q psy879           32 PNIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        32 ~~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      ..+++.|++|+|||+++..+...-
T Consensus         8 ~ki~vvG~~~~GKTsli~~l~~~~   31 (214)
T 2fh5_B            8 RAVLFVGLCDSGKTLLFVRLLTGQ   31 (214)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCC
Confidence            359999999999999999998753

>3q72_A GTP-binding protein RAD; G-domain, CAV2 beta, signaling protein; HET: GNP; 1.66A {Homo sapiens} SCOP: c.37.1.8 PDB: 3q7p_A* 3q7q_A* 2gjs_A* 2dpx_A*

Probab=95.55  E-value=0.018  Score=43.80  Aligned_cols=21  Identities=29%  Similarity=0.634  Sum_probs=18.7

Q ss_pred             eEEEECCCCCCHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLAR   53 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~   53 (317)
                      .+++.|++|+|||++++.+..
T Consensus         4 ki~~vG~~~~GKSsli~~l~~   24 (166)
T 3q72_A            4 KVLLLGAPGVGKSALARIFGG   24 (166)
T ss_dssp             EEEEEESTTSSHHHHHHHHCC
T ss_pred             EEEEECCCCCCHHHHHHHHcC
Confidence            489999999999999998863

>2gk6_A Regulator of nonsense transcripts 1; UPF1, helicase, NMD, hydrolase; HET: ADP; 2.40A {Homo sapiens} PDB: 2gjk_A* 2gk7_A 2xzo_A* 2xzp_A

Probab=95.55  E-value=0.014  Score=55.12  Aligned_cols=39  Identities=36%  Similarity=0.505  Sum_probs=29.6

Q ss_pred             CHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHc
Q psy879           15 NEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        15 ~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      ++...+.+...+.+   +..++.||||||||+++..++..+.
T Consensus       182 n~~Q~~av~~~l~~---~~~li~GppGTGKT~~~~~~i~~l~  220 (624)
T 2gk6_A          182 NHSQVYAVKTVLQR---PLSLIQGPPGTGKTVTSATIVYHLA  220 (624)
T ss_dssp             CHHHHHHHHHHHTC---SEEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHhcC---CCeEEECCCCCCHHHHHHHHHHHHH
Confidence            55566666666642   3689999999999999888887764

>3tkl_A RAS-related protein RAB-1A; vesicle trafficking, protein transport-protein binding compl; HET: GTP; 2.18A {Homo sapiens}

Probab=95.55  E-value=0.026  Score=44.21  Aligned_cols=22  Identities=32%  Similarity=0.578  Sum_probs=20.1

Q ss_pred             eEEEECCCCCCHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~   54 (317)
                      .+++.|++|+|||+++..+...
T Consensus        18 ki~v~G~~~~GKSsli~~l~~~   39 (196)
T 3tkl_A           18 KLLLIGDSGVGKSCLLLRFADD   39 (196)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECcCCCCHHHHHHHHHcC
Confidence            4999999999999999999874

>4a4z_A Antiviral helicase SKI2; hydrolase, ATPase, mRNA degradation, exosome; HET: ANP; 2.40A {Saccharomyces cerevisiae} PDB: 4a4k_A

Probab=95.54  E-value=0.043  Score=54.61  Aligned_cols=26  Identities=15%  Similarity=0.282  Sum_probs=19.2

Q ss_pred             HhcCCCceEEEECCCCCCHHHHHHHHHH
Q psy879           26 SSSGNVPNIIISGPPGVGKTTTILCLAR   53 (317)
Q Consensus        26 l~~~~~~~~ll~G~~G~GKt~la~~la~   53 (317)
                      +.+|+  ++++.||+|+|||.++...+.
T Consensus        51 il~g~--~vlv~apTGsGKTlv~~~~i~   76 (997)
T 4a4z_A           51 LEQGD--SVFVAAHTSAGKTVVAEYAIA   76 (997)
T ss_dssp             HHTTC--EEEEECCTTSCSHHHHHHHHH
T ss_pred             HHcCC--CEEEEECCCCcHHHHHHHHHH
Confidence            44555  799999999999986544443

>2bme_A RAB4A, RAS-related protein RAB4A; GTP-binding protein, vesicular transport, endocytosis, prenylation, protein transport, transport; HET: GNP; 1.57A {Homo sapiens} SCOP: c.37.1.8 PDB: 2bmd_A* 1yu9_A* 1z0k_A*

Probab=95.53  E-value=0.028  Score=43.59  Aligned_cols=22  Identities=18%  Similarity=0.395  Sum_probs=20.0

Q ss_pred             eEEEECCCCCCHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~   54 (317)
                      .+++.|++|+|||+++..+...
T Consensus        12 ki~v~G~~~~GKSsli~~l~~~   33 (186)
T 2bme_A           12 KFLVIGNAGTGKSCLLHQFIEK   33 (186)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            4899999999999999999865

>1m8p_A Sulfate adenylyltransferase; rossmann fold, phosphosulfate binding, T-state; HET: PPS; 2.60A {Penicillium chrysogenum} SCOP: b.122.1.3 c.26.1.5 c.37.1.15 PDB: 1i2d_A*

Probab=95.49  E-value=0.013  Score=54.65  Aligned_cols=24  Identities=25%  Similarity=0.277  Sum_probs=22.1

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHc
Q psy879           33 NIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      .++|.|++|+||||+++.+++.+.
T Consensus       398 ~I~l~GlsGSGKSTiA~~La~~L~  421 (573)
T 1m8p_A          398 TIFLTGYMNSGKDAIARALQVTLN  421 (573)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             EEEeecCCCCCHHHHHHHHHHHhc
Confidence            389999999999999999999874

>3l9o_A ATP-dependent RNA helicase DOB1; REC-A fold, winged-helix-turn-helix, antiparallel-coiled-COI domain, ATP-binding, helicase, hydrolase; 3.39A {Saccharomyces cerevisiae}

Probab=95.47  E-value=0.047  Score=54.98  Aligned_cols=27  Identities=19%  Similarity=0.271  Sum_probs=20.5

Q ss_pred             HhcCCCceEEEECCCCCCHHHHHHHHHHH
Q psy879           26 SSSGNVPNIIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        26 l~~~~~~~~ll~G~~G~GKt~la~~la~~   54 (317)
                      +.+|.  ++++.||.|+|||.++...+..
T Consensus       196 i~~g~--dvLV~ApTGSGKTlva~l~i~~  222 (1108)
T 3l9o_A          196 IDRGE--SVLVSAHTSAGKTVVAEYAIAQ  222 (1108)
T ss_dssp             HTTTC--CEEEECCSSSHHHHHHHHHHHH
T ss_pred             HHcCC--CEEEECCCCCChHHHHHHHHHH
Confidence            45555  6999999999999987554443

>3tqf_A HPR(Ser) kinase; transferase, hydrolase; 2.80A {Coxiella burnetii}

Probab=95.47  E-value=0.0082  Score=46.36  Aligned_cols=22  Identities=27%  Similarity=0.528  Sum_probs=20.2

Q ss_pred             eEEEECCCCCCHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~   54 (317)
                      .++|.|++|+||||++..+.+.
T Consensus        18 gvli~G~SGaGKStlal~L~~r   39 (181)
T 3tqf_A           18 GVLITGEANIGKSELSLALIDR   39 (181)
T ss_dssp             EEEEEESSSSSHHHHHHHHHHT
T ss_pred             EEEEEcCCCCCHHHHHHHHHHc
Confidence            4999999999999999999874

>2f1r_A Molybdopterin-guanine dinucleotide biosynthesis protein B (MOBB); structural genomics, PSI, protein structure initiative; 2.10A {Archaeoglobus fulgidus}

Probab=95.47  E-value=0.0045  Score=48.08  Aligned_cols=25  Identities=36%  Similarity=0.369  Sum_probs=22.6

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHcC
Q psy879           33 NIIISGPPGVGKTTTILCLARILLG   57 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~~   57 (317)
                      .+.|.|++|+||||+++.++..+..
T Consensus         4 ~v~IvG~SGsGKSTL~~~L~~~~~~   28 (171)
T 2f1r_A            4 ILSIVGTSDSGKTTLITRMMPILRE   28 (171)
T ss_dssp             EEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhhh
Confidence            5889999999999999999998753

>2og2_A Putative signal recognition particle receptor; nucleotide-binding, protein transport; 2.00A {Arabidopsis thaliana}

Probab=95.46  E-value=0.0081  Score=52.48  Aligned_cols=24  Identities=46%  Similarity=0.494  Sum_probs=22.1

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHcC
Q psy879           34 IIISGPPGVGKTTTILCLARILLG   57 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~l~~   57 (317)
                      +.|.||+|+||||+++.++..+..
T Consensus       160 i~lvG~nGsGKTTll~~Lag~l~~  183 (359)
T 2og2_A          160 IMIVGVNGGGKTTSLGKLAHRLKN  183 (359)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHHHH
T ss_pred             EEEEcCCCChHHHHHHHHHhhccc
Confidence            899999999999999999998753

>2zts_A Putative uncharacterized protein PH0186; KAIC like protein, ATP-binding, nucleotide-binding, ATP- binding protein; HET: ADP; 2.07A {Pyrococcus horikoshii}

Probab=95.46  E-value=0.0045  Score=50.91  Aligned_cols=21  Identities=29%  Similarity=0.436  Sum_probs=18.9

Q ss_pred             EEEECCCCCCHHHHHHHHHHH
Q psy879           34 IIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~   54 (317)
                      ++++|+||+|||+++..++..
T Consensus        33 ~~i~G~pG~GKT~l~l~~~~~   53 (251)
T 2zts_A           33 VLLTGGTGTGKTTFAAQFIYK   53 (251)
T ss_dssp             EEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEEeCCCCCHHHHHHHHHHH
Confidence            899999999999999987754

>1a7j_A Phosphoribulokinase; transferase, calvin cycle; 2.50A {Rhodobacter sphaeroides} SCOP: c.37.1.6

Probab=95.45  E-value=0.0058  Score=51.85  Aligned_cols=24  Identities=25%  Similarity=0.436  Sum_probs=18.8

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHc
Q psy879           33 NIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      .+.+.||+|+||||+++.+++.+.
T Consensus         7 iIgItG~sGSGKSTva~~L~~~lg   30 (290)
T 1a7j_A            7 IISVTGSSGAGTSTVKHTFDQIFR   30 (290)
T ss_dssp             EEEEESCC---CCTHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHh
Confidence            489999999999999999999763

>3reg_A RHO-like small GTPase; cytoskeleton, nucleotide-binding, GTP-binding, signaling Pro lipoprotein, prenylation; HET: GSP; 1.80A {Entamoeba histolytica} PDB: 3ref_B* 4dvg_A*

Probab=95.44  E-value=0.077  Score=41.49  Aligned_cols=22  Identities=32%  Similarity=0.566  Sum_probs=20.2

Q ss_pred             eEEEECCCCCCHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~   54 (317)
                      .+++.|++|+|||++++.+...
T Consensus        25 ki~~vG~~~~GKSsl~~~l~~~   46 (194)
T 3reg_A           25 KIVVVGDGAVGKTCLLLAFSKG   46 (194)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECcCCCCHHHHHHHHhcC
Confidence            3999999999999999999875

>3v9p_A DTMP kinase, thymidylate kinase; ssgcid, STRU genomics, seattle structural genomics center for infectious transferase; 1.90A {Burkholderia thailandensis}

Probab=95.44  E-value=0.0075  Score=49.14  Aligned_cols=24  Identities=33%  Similarity=0.396  Sum_probs=19.2

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHc
Q psy879           33 NIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      -+.|.|++|+||||.++.+++.+.
T Consensus        27 ~I~~eG~~GsGKsT~~~~l~~~l~   50 (227)
T 3v9p_A           27 FITFEGIDGAGKTTHLQWFCDRLQ   50 (227)
T ss_dssp             EEEEECCC---CHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHH
Confidence            489999999999999999999884

>1tq4_A IIGP1, interferon-inducible GTPase; interferon gamma, dimer, immunology, signaling protein; HET: GDP; 1.95A {Mus musculus} SCOP: c.37.1.8 PDB: 1tqd_A* 1tq6_A* 1tpz_A* 1tq2_A*

Probab=95.44  E-value=0.014  Score=51.89  Aligned_cols=41  Identities=27%  Similarity=0.443  Sum_probs=31.5

Q ss_pred             CHHHHHHHHHHHhcCC------------------CceEEEECCCCCCHHHHHHHHHHHH
Q psy879           15 NEDTVERLKVFSSSGN------------------VPNIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        15 ~~~~~~~l~~~l~~~~------------------~~~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      ...+++.+.-.+..|.                  ...+.|.||+|+||||+.++++..+
T Consensus        35 ~~~~l~~is~~i~~Ge~~~~~~~i~~~L~~~~~~~~~valvG~nGaGKSTLln~L~Gl~   93 (413)
T 1tq4_A           35 SQEILNLIELRMRAGNIQLTNSAISDALKEIDSSVLNVAVTGETGSGKSSFINTLRGIG   93 (413)
T ss_dssp             CHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHCCEEEEEEECTTSSHHHHHHHHHTCC
T ss_pred             CHHHhhhccceecCCCCcccchhhhhhhhhcccCCeEEEEECCCCCcHHHHHHHHhCCC
Confidence            3456666666666666                  1258999999999999999999854

>1c1y_A RAS-related protein RAP-1A; GTP-binding proteins, protein-protein complex, effectors, signaling protein; HET: GTP; 1.90A {Homo sapiens} SCOP: c.37.1.8 PDB: 3kuc_A* 1gua_A* 3cf6_R* 3brw_D*

Probab=95.43  E-value=0.03  Score=42.42  Aligned_cols=22  Identities=23%  Similarity=0.480  Sum_probs=19.9

Q ss_pred             eEEEECCCCCCHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~   54 (317)
                      .+++.|++|+|||++++.+...
T Consensus         5 ki~v~G~~~~GKssli~~l~~~   26 (167)
T 1c1y_A            5 KLVVLGSGGVGKSALTVQFVQG   26 (167)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            4899999999999999999874

>2h92_A Cytidylate kinase; rossmann fold, transferase; HET: C5P PG4; 2.30A {Staphylococcus aureus}

Probab=95.42  E-value=0.0095  Score=48.01  Aligned_cols=23  Identities=39%  Similarity=0.563  Sum_probs=21.4

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .+.|.|++|+||||+++.+++.+
T Consensus         5 ~i~i~G~~gsGkst~~~~l~~~~   27 (219)
T 2h92_A            5 NIALDGPAAAGKSTIAKRVASEL   27 (219)
T ss_dssp             CEEEECCTTSSHHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHHhc
Confidence            48999999999999999999985

>2g6b_A RAS-related protein RAB-26; G-protein, GTP analogue, structural genomics, structural genomics consortium, SGC, unknown function; HET: GNP; 2.00A {Homo sapiens} SCOP: c.37.1.8

Probab=95.42  E-value=0.04  Score=42.40  Aligned_cols=22  Identities=27%  Similarity=0.519  Sum_probs=20.0

Q ss_pred             eEEEECCCCCCHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~   54 (317)
                      .+++.|++|+|||+++..+...
T Consensus        12 ~i~v~G~~~~GKssli~~l~~~   33 (180)
T 2g6b_A           12 KVMLVGDSGVGKTCLLVRFKDG   33 (180)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECcCCCCHHHHHHHHHhC
Confidence            3899999999999999999865

>3gmt_A Adenylate kinase; ssgcid, ATP-BIN cytoplasm, nucleotide biosynthesis, nucleotide-BIND transferase, structural genomics; 2.10A {Burkholderia pseudomallei 1710B}

Probab=95.41  E-value=0.011  Score=48.12  Aligned_cols=22  Identities=32%  Similarity=0.576  Sum_probs=21.0

Q ss_pred             EEEECCCCCCHHHHHHHHHHHH
Q psy879           34 IIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~l   55 (317)
                      +-|.|+||+||||.++.+++.+
T Consensus        11 ~~~~G~pGsGKsT~a~~L~~~~   32 (230)
T 3gmt_A           11 LILLGAPGAGKGTQANFIKEKF   32 (230)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHH
T ss_pred             eeeECCCCCCHHHHHHHHHHHh
Confidence            7899999999999999999986

>2xgj_A ATP-dependent RNA helicase DOB1; hydrolase-RNA complex, hydrolase, tramp, exosome, DEAD, nucleotide-binding; HET: ADP; 2.90A {Saccharomyces cerevisiae}

Probab=95.41  E-value=0.095  Score=52.24  Aligned_cols=34  Identities=15%  Similarity=0.184  Sum_probs=22.8

Q ss_pred             HHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHH
Q psy879           16 EDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLA   52 (317)
Q Consensus        16 ~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la   52 (317)
                      +...+.+.. +.+|.  ++++.+|.|+|||.++....
T Consensus        89 ~~Q~eai~~-l~~g~--~vLV~apTGSGKTlva~lai  122 (1010)
T 2xgj_A           89 PFQDTAISC-IDRGE--SVLVSAHTSAGKTVVAEYAI  122 (1010)
T ss_dssp             HHHHHHHHH-HHHTC--EEEEECCTTSCHHHHHHHHH
T ss_pred             HHHHHHHHH-HHcCC--CEEEECCCCCChHHHHHHHH
Confidence            333334444 34455  79999999999999875433

>3kkq_A RAS-related protein M-RAS; GTP-binding, GTPase, signaling protein; HET: GDP; 1.20A {Mus musculus} SCOP: c.37.1.8 PDB: 3kkp_A* 3kko_A* 3pit_A* 3pir_A* 1x1r_A* 1x1s_A*

Probab=95.39  E-value=0.036  Score=42.89  Aligned_cols=21  Identities=24%  Similarity=0.506  Sum_probs=19.6

Q ss_pred             EEEECCCCCCHHHHHHHHHHH
Q psy879           34 IIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~   54 (317)
                      +++.|++|+|||+++..+...
T Consensus        21 i~v~G~~~~GKSsl~~~l~~~   41 (183)
T 3kkq_A           21 LVVVGDGGVGKSALTIQFFQK   41 (183)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            899999999999999999865

>2ffh_A Protein (FFH); SRP54, signal recognition particle, GTPase, M domain, RNA-binding, signal sequence-binding, helix-turn-helix, protein targeting; 3.20A {Thermus aquaticus} SCOP: a.24.13.1 a.36.1.1 c.37.1.10 PDB: 2iy3_A

Probab=95.39  E-value=0.12  Score=46.17  Aligned_cols=26  Identities=38%  Similarity=0.399  Sum_probs=22.9

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHcCCC
Q psy879           34 IIISGPPGVGKTTTILCLARILLGPS   59 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~l~~~~   59 (317)
                      +.+.|++|+||||++..++..+....
T Consensus       101 i~i~G~~GsGKTT~~~~LA~~l~~~g  126 (425)
T 2ffh_A          101 WFLVGLQGSGKTTTAAKLALYYKGKG  126 (425)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHHHTTT
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHcC
Confidence            88899999999999999999886443

>2ew1_A RAS-related protein RAB-30; G-protein, GTP analogue, structural genomics, structural genomics consortium, SGC, signaling protein; HET: GNP; 2.00A {Homo sapiens} SCOP: c.37.1.8

Probab=95.39  E-value=0.029  Score=44.58  Aligned_cols=23  Identities=35%  Similarity=0.547  Sum_probs=20.5

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .+++.|++|+|||++++.+....
T Consensus        28 ki~lvG~~~vGKSsLi~~l~~~~   50 (201)
T 2ew1_A           28 KIVLIGNAGVGKTCLVRRFTQGL   50 (201)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHSS
T ss_pred             EEEEECcCCCCHHHHHHHHHhCC
Confidence            48999999999999999998753

>2p5s_A RAS and EF-hand domain containing; G-protein, RAB, GDP, structural genomics, SGC, structural genomics consortium, signaling protein; HET: GDP; 2.15A {Homo sapiens}

Probab=95.38  E-value=0.032  Score=44.03  Aligned_cols=22  Identities=27%  Similarity=0.611  Sum_probs=20.0

Q ss_pred             eEEEECCCCCCHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~   54 (317)
                      .+++.|++|+|||+++..+...
T Consensus        30 ki~v~G~~~~GKSsli~~l~~~   51 (199)
T 2p5s_A           30 KIVLAGDAAVGKSSFLMRLCKN   51 (199)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHC
T ss_pred             EEEEECcCCCCHHHHHHHHHhC
Confidence            5999999999999999999864

>1zd9_A ADP-ribosylation factor-like 10B; transport protein, GDP-binding, membrane trafficking, structural genomics, structural genomics consortium, SGC; HET: GDP; 1.70A {Homo sapiens} SCOP: c.37.1.8 PDB: 2al7_A* 2h18_A*

Probab=95.38  E-value=0.11  Score=40.43  Aligned_cols=22  Identities=27%  Similarity=0.262  Sum_probs=20.0

Q ss_pred             eEEEECCCCCCHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~   54 (317)
                      .+++.|++|+|||+++..+...
T Consensus        24 ki~v~G~~~~GKSsli~~l~~~   45 (188)
T 1zd9_A           24 ELTLVGLQYSGKTTFVNVIASG   45 (188)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            3899999999999999999864

>2bbs_A Cystic fibrosis transmembrane conductance regulator; ATP binding cassette, transport protein; HET: ATP; 2.05A {Homo sapiens} PDB: 2bbt_A* 1xmi_A* 1xmj_A* 2bbo_A* 3si7_A* 1r0w_A 1q3h_A 1r0x_A* 1r0y_A* 1r0z_A* 1r10_A* 1xf9_A* 1xfa_A*

Probab=95.37  E-value=0.0065  Score=51.49  Aligned_cols=41  Identities=7%  Similarity=0.042  Sum_probs=29.7

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHH-hhhccCCceEEEEecCC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRT-MEIYSNTTRFALACNNS  136 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~-le~~~~~~~~il~~~~~  136 (317)
                      +++++++||... |.+.....+.+. +........+|++|++.
T Consensus       177 ~p~lllLDEPts~LD~~~~~~i~~~ll~~~~~~~tviivtHd~  219 (290)
T 2bbs_A          177 DADLYLLDSPFGYLDVLTEKEIFESCVCKLMANKTRILVTSKM  219 (290)
T ss_dssp             CCSEEEEESTTTTCCHHHHHHHHHHCCCCCTTTSEEEEECCCH
T ss_pred             CCCEEEEECCcccCCHHHHHHHHHHHHHHhhCCCEEEEEecCH
Confidence            578999999985 677778888886 34433455677788764

>2gks_A Bifunctional SAT/APS kinase; transferase, sulfurylase; HET: ADP; 2.31A {Aquifex aeolicus}

Probab=95.37  E-value=0.018  Score=53.29  Aligned_cols=42  Identities=24%  Similarity=0.209  Sum_probs=30.7

Q ss_pred             CHHHHHHHHHHHh--cCCCceEEEECCCCCCHHHHHHHHHHHHc
Q psy879           15 NEDTVERLKVFSS--SGNVPNIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        15 ~~~~~~~l~~~l~--~~~~~~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      .+++.+.+.....  ......++|.|++|+||||+++.+++.+.
T Consensus       354 r~eV~~~lr~~~~~~~~~~~~I~l~G~~GsGKSTia~~La~~L~  397 (546)
T 2gks_A          354 RPEVAEILAETYVPKHKQGFCVWLTGLPCAGKSTIAEILATMLQ  397 (546)
T ss_dssp             CHHHHHHHHHHSCCGGGCCEEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             chhHHHHHHHhhccccccceEEEccCCCCCCHHHHHHHHHHHhh
Confidence            3556666666652  22222489999999999999999999874

>2il1_A RAB12; G-protein, GDP, GTPase, predicted, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 2.10A {Homo sapiens}

Probab=95.36  E-value=0.033  Score=43.69  Aligned_cols=21  Identities=38%  Similarity=0.539  Sum_probs=18.7

Q ss_pred             EEEECCCCCCHHHHHHHHHHH
Q psy879           34 IIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~   54 (317)
                      +++.|++|+|||+++..+...
T Consensus        29 i~vvG~~~~GKSsLi~~l~~~   49 (192)
T 2il1_A           29 VIIIGSRGVGKTSLMERFTDD   49 (192)
T ss_dssp             EEEECSTTSSHHHHHHHHCC-
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            899999999999999998753

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A

Probab=95.34  E-value=0.083  Score=47.38  Aligned_cols=20  Identities=30%  Similarity=0.434  Sum_probs=16.8

Q ss_pred             eEEEECCCCCCHHHHH-HHHH
Q psy879           33 NIIISGPPGVGKTTTI-LCLA   52 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la-~~la   52 (317)
                      ++++.||+|+|||..+ ..+.
T Consensus         4 ~~lv~a~TGsGKT~~~l~~~l   24 (431)
T 2v6i_A            4 LTVLDLHPGAGKTRRVLPQLV   24 (431)
T ss_dssp             EEEEECCTTSCTTTTHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHHHH
Confidence            6999999999999986 4444

>1gwn_A RHO-related GTP-binding protein RHOE; GTPase, inactive GTPase, signal transduction; HET: GTP; 2.1A {Mus musculus} SCOP: c.37.1.8

Probab=95.34  E-value=0.014  Score=46.50  Aligned_cols=22  Identities=27%  Similarity=0.472  Sum_probs=20.3

Q ss_pred             eEEEECCCCCCHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~   54 (317)
                      .+++.|++|+|||++++.+...
T Consensus        30 ki~vvG~~~vGKSsLi~~l~~~   51 (205)
T 1gwn_A           30 KIVVVGDSQCGKTALLHVFAKD   51 (205)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            3999999999999999999875

>3q3j_B RHO-related GTP-binding protein RHO6; RAS-binding domain, plexin, small GTPase, structural genomic consortium, SGC; HET: GNP; 1.97A {Homo sapiens} PDB: 2rex_B* 2cls_A*

Probab=95.33  E-value=0.017  Score=46.32  Aligned_cols=22  Identities=27%  Similarity=0.462  Sum_probs=20.0

Q ss_pred             eEEEECCCCCCHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~   54 (317)
                      .+++.|++|+|||+++..+...
T Consensus        29 ki~vvG~~~vGKSsL~~~l~~~   50 (214)
T 3q3j_B           29 KLVLVGDVQCGKTAMLQVLAKD   50 (214)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECcCCCCHHHHHHHHhcC
Confidence            4999999999999999999864

>2dyk_A GTP-binding protein; GTPase, ribosome-binding protein, structural genomics; HET: GDP; 1.96A {Thermus thermophilus}

Probab=95.32  E-value=0.012  Score=44.48  Aligned_cols=23  Identities=30%  Similarity=0.533  Sum_probs=20.6

Q ss_pred             ceEEEECCCCCCHHHHHHHHHHH
Q psy879           32 PNIIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        32 ~~~ll~G~~G~GKt~la~~la~~   54 (317)
                      +.+++.|++|+|||+++..+...
T Consensus         2 ~ki~v~G~~~~GKSsli~~l~~~   24 (161)
T 2dyk_A            2 HKVVIVGRPNVGKSSLFNRLLKK   24 (161)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHC
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            46899999999999999999864

>4f92_B U5 small nuclear ribonucleoprotein 200 kDa helica; RNP remodeling, PRE-mRNA splicing, spliceosome catalytic ACT DEXD/H-box RNA helicase; HET: SAN; 2.66A {Homo sapiens} PDB: 4f93_B* 4f91_B

Probab=95.32  E-value=0.093  Score=55.18  Aligned_cols=32  Identities=22%  Similarity=0.377  Sum_probs=23.5

Q ss_pred             HHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHH
Q psy879           19 VERLKVFSSSGNVPNIIISGPPGVGKTTTILCLA   52 (317)
Q Consensus        19 ~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la   52 (317)
                      .+.+...+.++.  ++++.+|.|+|||.++....
T Consensus       932 ~q~~~~l~~~~~--nvlv~APTGSGKTliaelai  963 (1724)
T 4f92_B          932 TQVFNTVYNSDD--NVFVGAPTGSGKTICAEFAI  963 (1724)
T ss_dssp             HHHHHHHHSCCS--CEEEECCTTSCCHHHHHHHH
T ss_pred             HHHHHHHhcCCC--cEEEEeCCCCCchHHHHHHH
Confidence            334555556665  79999999999999886443

>2fwr_A DNA repair protein RAD25; DNA unwinding, XPB, DNA binding protein; HET: DNA; 2.60A {Archaeoglobus fulgidus} SCOP: c.37.1.19 c.37.1.19 PDB: 2fzl_A*

Probab=95.32  E-value=0.049  Score=49.34  Aligned_cols=39  Identities=21%  Similarity=0.158  Sum_probs=29.0

Q ss_pred             CCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHH
Q psy879           14 GNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        14 g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      -.+...+.+..++..+   ..++.||.|+|||..+..++..+
T Consensus        94 l~~~Q~~ai~~i~~~~---~~ll~~~TGsGKT~~~l~~i~~~  132 (472)
T 2fwr_A           94 LRDYQEKALERWLVDK---RGCIVLPTGSGKTHVAMAAINEL  132 (472)
T ss_dssp             BCHHHHHHHHHHTTTT---EEEEECCTTSCHHHHHHHHHHHH
T ss_pred             cCHHHHHHHHHHHhcC---CEEEEeCCCCCHHHHHHHHHHHc
Confidence            3455555666555542   59999999999999998888765

>2fg5_A RAB-22B, RAS-related protein RAB-31; G-protein, GTP analogue, structural genomics, structural genomics consortium, SGC, signaling protein; HET: GNP; 2.80A {Homo sapiens} SCOP: c.37.1.8

Probab=95.31  E-value=0.041  Score=43.07  Aligned_cols=22  Identities=23%  Similarity=0.469  Sum_probs=20.0

Q ss_pred             eEEEECCCCCCHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~   54 (317)
                      .+++.|++|+|||+++..+...
T Consensus        25 ki~vvG~~~~GKSsli~~l~~~   46 (192)
T 2fg5_A           25 KVCLLGDTGVGKSSIVCRFVQD   46 (192)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHC
T ss_pred             EEEEECcCCCCHHHHHHHHhcC
Confidence            3899999999999999999864

>1f2t_A RAD50 ABC-ATPase; DNA double-strand break repair, replication; 1.60A {Pyrococcus furiosus} SCOP: c.37.1.12 PDB: 1f2u_A* 1us8_A*

Probab=95.30  E-value=0.012  Score=44.56  Aligned_cols=25  Identities=24%  Similarity=0.220  Sum_probs=22.2

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHcC
Q psy879           33 NIIISGPPGVGKTTTILCLARILLG   57 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~~   57 (317)
                      ..+|+||+|+|||++..++.-.+.+
T Consensus        25 ~~~I~G~NGsGKStil~Ai~~~l~g   49 (149)
T 1f2t_A           25 INLIIGQNGSGKSSLLDAILVGLYW   49 (149)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHHC
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHcC
Confidence            3799999999999999999987754

>2yhs_A FTSY, cell division protein FTSY; cell cycle, protein targeting, simibi class GTPase, GTP-BIND membrane, nucleotide-binding; 1.60A {Escherichia coli} PDB: 2qy9_A 2xxa_B* 1fts_A

Probab=95.30  E-value=0.0093  Score=54.10  Aligned_cols=25  Identities=52%  Similarity=0.554  Sum_probs=22.4

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHcC
Q psy879           33 NIIISGPPGVGKTTTILCLARILLG   57 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~~   57 (317)
                      .+.|.|++|+||||+++.++..+..
T Consensus       295 VI~LVGpNGSGKTTLl~~LAgll~~  319 (503)
T 2yhs_A          295 VILMVGVNGVGKTTTIGKLARQFEQ  319 (503)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHHH
T ss_pred             EEEEECCCcccHHHHHHHHHHHhhh
Confidence            3899999999999999999998753

>2wjy_A Regulator of nonsense transcripts 1; nonsense mediated decay, zinc-finger, ATP-binding, metal-BIN UPF2, UPF1, helicase, hydrolase; 2.50A {Homo sapiens} PDB: 2wjv_A 2iyk_A

Probab=95.29  E-value=0.023  Score=55.17  Aligned_cols=40  Identities=35%  Similarity=0.484  Sum_probs=30.0

Q ss_pred             CHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcC
Q psy879           15 NEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLG   57 (317)
Q Consensus        15 ~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~   57 (317)
                      ++...+.+...+.+   +..++.||||||||+++..++..+..
T Consensus       358 n~~Q~~Av~~~l~~---~~~lI~GppGTGKT~ti~~~i~~l~~  397 (800)
T 2wjy_A          358 NHSQVYAVKTVLQR---PLSLIQGPPGTGKTVTSATIVYHLAR  397 (800)
T ss_dssp             CHHHHHHHHHHHTS---SEEEEECCTTSCHHHHHHHHHHHHHT
T ss_pred             CHHHHHHHHHhccC---CeEEEEcCCCCCHHHHHHHHHHHHHH
Confidence            45556666666542   36899999999999998888877653

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus}

Probab=95.26  E-value=0.19  Score=46.23  Aligned_cols=33  Identities=33%  Similarity=0.386  Sum_probs=22.9

Q ss_pred             HHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHH
Q psy879           20 ERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        20 ~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      +.+..++ +|+  ++++.+|.|+|||..+...+...
T Consensus        11 ~~i~~~~-~~~--~~l~~~~tGsGKT~~~~~~~~~~   43 (555)
T 3tbk_A           11 ELALPAK-KGK--NTIICAPTGCGKTFVSLLICEHH   43 (555)
T ss_dssp             HHHHHHH-TTC--CEEEECCTTSCHHHHHHHHHHHH
T ss_pred             HHHHHHh-CCC--CEEEEeCCCChHHHHHHHHHHHH
Confidence            3344433 444  69999999999998876666443

>2j1l_A RHO-related GTP-binding protein RHOD; GTPase, membrane, prenylation, hydrolase, nucleotide-binding, methylation, lipoprotein, endosome DYNA; HET: GDP; 2.5A {Homo sapiens}

Probab=95.26  E-value=0.026  Score=45.18  Aligned_cols=22  Identities=27%  Similarity=0.567  Sum_probs=19.3

Q ss_pred             eEEEECCCCCCHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~   54 (317)
                      .+++.|++|+|||+++..+...
T Consensus        36 ki~vvG~~~vGKSsli~~l~~~   57 (214)
T 2j1l_A           36 KVVLVGDGGCGKTSLLMVFADG   57 (214)
T ss_dssp             EEEEEECTTSSHHHHHHHHHC-
T ss_pred             EEEEECcCCCCHHHHHHHHHcC
Confidence            3999999999999999999853

>2gf0_A GTP-binding protein DI-RAS1; GDP/GTP binding, GTP hydrolysis, structural genomics, structural genomics consortium, SGC, transport protein; HET: GDP; 1.90A {Homo sapiens} SCOP: c.37.1.8

Probab=95.21  E-value=0.06  Score=42.15  Aligned_cols=22  Identities=27%  Similarity=0.588  Sum_probs=20.1

Q ss_pred             eEEEECCCCCCHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~   54 (317)
                      .+++.|++|+|||+++..+...
T Consensus        10 ki~vvG~~~~GKSsli~~l~~~   31 (199)
T 2gf0_A           10 RVVVFGAGGVGKSSLVLRFVKG   31 (199)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCcHHHHHHHHHcC
Confidence            4999999999999999999874

>4a2p_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.00A {Anas platyrhynchos} PDB: 4a36_A*

Probab=95.21  E-value=0.18  Score=46.33  Aligned_cols=34  Identities=26%  Similarity=0.394  Sum_probs=23.2

Q ss_pred             HHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHH
Q psy879           19 VERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        19 ~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .+.+..++. |.  ++++.+|.|+|||..+...+...
T Consensus        13 ~~~i~~~~~-~~--~~l~~~~tGsGKT~~~~~~~~~~   46 (556)
T 4a2p_A           13 IELAQPAIN-GK--NALICAPTGSGKTFVSILICEHH   46 (556)
T ss_dssp             HHHHHHHHT-TC--CEEEECCTTSCHHHHHHHHHHHH
T ss_pred             HHHHHHHHc-CC--CEEEEcCCCChHHHHHHHHHHHH
Confidence            334444443 44  69999999999998876665443

>2f9l_A RAB11B, member RAS oncogene family; RAB11B GTPase, vesicle transport, hydrolase; HET: GDP; 1.55A {Homo sapiens} SCOP: c.37.1.8 PDB: 2f9m_A* 1yzk_A* 2hv8_A* 2gzd_A* 2gzh_A* 2d7c_A* 3bfk_A*

Probab=95.20  E-value=0.012  Score=46.59  Aligned_cols=23  Identities=26%  Similarity=0.508  Sum_probs=20.6

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .+.+.|++|+||||+++.++...
T Consensus         7 kv~lvG~~g~GKSTLl~~l~~~~   29 (199)
T 2f9l_A            7 KVVLIGDSGVGKSNLLSRFTRNE   29 (199)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECcCCCCHHHHHHHHhcCC
Confidence            48999999999999999999753

>1lw7_A Transcriptional regulator NADR; NMN, NMN adenylyl transferase, ribosylnicotinamide KINA transferase; HET: NAD; 2.90A {Haemophilus influenzae} SCOP: c.26.1.3 c.37.1.1

Probab=95.20  E-value=0.0089  Score=52.48  Aligned_cols=24  Identities=25%  Similarity=0.332  Sum_probs=22.0

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHc
Q psy879           33 NIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      .+.|.||+|+||||+++.++..+.
T Consensus       172 k~~IvG~nGsGKSTLlk~L~gl~~  195 (365)
T 1lw7_A          172 TVAILGGESSGKSVLVNKLAAVFN  195 (365)
T ss_dssp             EEEEECCTTSHHHHHHHHHHHHTT
T ss_pred             eEEEECCCCCCHHHHHHHHHHHhC
Confidence            489999999999999999999863

>1oix_A RAS-related protein RAB-11A; small G protein, intracellular trafficking, GTP-binding, lipoprotein, prenylation, protein transport; HET: GDP; 1.7A {Homo sapiens} SCOP: c.37.1.8 PDB: 1oiw_A* 1oiv_A* 3rwo_B* 3rwm_B*

Probab=95.20  E-value=0.011  Score=46.56  Aligned_cols=22  Identities=27%  Similarity=0.519  Sum_probs=20.4

Q ss_pred             EEEECCCCCCHHHHHHHHHHHH
Q psy879           34 IIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~l   55 (317)
                      +.+.|++|+||||+++.++...
T Consensus        32 v~lvG~~g~GKSTLl~~l~~~~   53 (191)
T 1oix_A           32 VVLIGDSGVGKSNLLSRFTRNE   53 (191)
T ss_dssp             EEEEECTTSSHHHHHHHHHHSC
T ss_pred             EEEECcCCCCHHHHHHHHhcCC
Confidence            8999999999999999999864

>3eph_A TRNA isopentenyltransferase; transferase, alternative initiation, ATP-binding, cytoplasm, mitochondrion, nucleotide-binding, nucleus; 2.95A {Saccharomyces cerevisiae} PDB: 3epj_A 3epk_A* 3epl_A*

Probab=95.19  E-value=0.013  Score=51.74  Aligned_cols=24  Identities=38%  Similarity=0.559  Sum_probs=21.9

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHc
Q psy879           33 NIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      .++|.||+|+|||+++..+++.+.
T Consensus         4 ~i~i~GptgsGKttla~~La~~~~   27 (409)
T 3eph_A            4 VIVIAGTTGVGKSQLSIQLAQKFN   27 (409)
T ss_dssp             EEEEEECSSSSHHHHHHHHHHHHT
T ss_pred             EEEEECcchhhHHHHHHHHHHHCC
Confidence            488999999999999999999873

>2ocp_A DGK, deoxyguanosine kinase; protein-nucleotide complex, transferase; HET: DTP; 2.80A {Homo sapiens} SCOP: c.37.1.1

Probab=95.17  E-value=0.012  Score=48.30  Aligned_cols=24  Identities=29%  Similarity=0.390  Sum_probs=21.9

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHc
Q psy879           33 NIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      .+.|.|++|+||||+++.+++.+.
T Consensus         4 ~i~~~G~~g~GKtt~~~~l~~~l~   27 (241)
T 2ocp_A            4 RLSIEGNIAVGKSTFVKLLTKTYP   27 (241)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHCT
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHcC
Confidence            489999999999999999999873

>1zu4_A FTSY; GTPase, signal recognition particle, SRP, receptor, protein transport; 1.95A {Mycoplasma mycoides} PDB: 1zu5_A

Probab=95.16  E-value=0.015  Score=50.03  Aligned_cols=25  Identities=28%  Similarity=0.420  Sum_probs=22.4

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHcCC
Q psy879           34 IIISGPPGVGKTTTILCLARILLGP   58 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~l~~~   58 (317)
                      +.+.|++|+||||++..+|..+...
T Consensus       108 I~ivG~~G~GKTT~~~~LA~~l~~~  132 (320)
T 1zu4_A          108 FMLVGVNGTGKTTSLAKMANYYAEL  132 (320)
T ss_dssp             EEEESSTTSSHHHHHHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHC
Confidence            8999999999999999999987543

>3pqc_A Probable GTP-binding protein ENGB; rossmann fold, GTPase, cell cycle, hydrolase; HET: GDP; 1.90A {Thermotoga maritima} PDB: 3pr1_A

Probab=95.14  E-value=0.13  Score=39.84  Aligned_cols=23  Identities=22%  Similarity=0.333  Sum_probs=20.5

Q ss_pred             ceEEEECCCCCCHHHHHHHHHHH
Q psy879           32 PNIIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        32 ~~~ll~G~~G~GKt~la~~la~~   54 (317)
                      +.+++.|++|+|||+++..+...
T Consensus        24 ~~i~v~G~~~~GKSsli~~l~~~   46 (195)
T 3pqc_A           24 GEVAFVGRSNVGKSSLLNALFNR   46 (195)
T ss_dssp             CEEEEEEBTTSSHHHHHHHHHTS
T ss_pred             eEEEEECCCCCCHHHHHHHHHcC
Confidence            45999999999999999998764

>1oxx_K GLCV, glucose, ABC transporter, ATP binding protein; ABC-ATPase, ATP-binding cassette, ATPase, transport protein; 1.45A {Sulfolobus solfataricus} SCOP: b.40.6.3 c.37.1.12 PDB: 1oxs_C 1oxt_A 1oxu_A* 1oxv_A*

Probab=95.13  E-value=0.0054  Score=53.52  Aligned_cols=27  Identities=37%  Similarity=0.537  Sum_probs=22.9

Q ss_pred             hcCCCceEEEECCCCCCHHHHHHHHHHHH
Q psy879           27 SSGNVPNIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        27 ~~~~~~~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      ..|.  .+.|.||+|+||||+.+.++..+
T Consensus        29 ~~Ge--~~~llGpnGsGKSTLLr~iaGl~   55 (353)
T 1oxx_K           29 ENGE--RFGILGPSGAGKTTFMRIIAGLD   55 (353)
T ss_dssp             CTTC--EEEEECSCHHHHHHHHHHHHTSS
T ss_pred             CCCC--EEEEECCCCCcHHHHHHHHhCCC
Confidence            3444  58999999999999999999865

>3ux8_A Excinuclease ABC, A subunit; UVRA, nucleotide excision repair, DNA repair, ABC ATPase, DN binding protein; HET: ADP; 2.10A {Geobacillus}

Probab=95.09  E-value=0.093  Score=49.92  Aligned_cols=41  Identities=17%  Similarity=0.193  Sum_probs=28.8

Q ss_pred             eeEEEEeCCCC-CCHHHHHHHHHHhhhcc-CCceEEEEecCCC
Q psy879           97 HKIVILDEADS-MTDGAQQALRRTMEIYS-NTTRFALACNNSE  137 (317)
Q Consensus        97 ~~vliiDE~d~-l~~~~~~~ll~~le~~~-~~~~~il~~~~~~  137 (317)
                      ++++++||.-. |.+.....+.+++.+.. ....+|+++++..
T Consensus       565 p~llllDEPt~~LD~~~~~~i~~~l~~l~~~g~tvi~vtHd~~  607 (670)
T 3ux8_A          565 RTLYILDEPTTGLHVDDIARLLDVLHRLVDNGDTVLVIEHNLD  607 (670)
T ss_dssp             CEEEEEESTTTTCCHHHHHHHHHHHHHHHHTTCEEEEECCCHH
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHHHHHHHHCCCEEEEEeCCHH
Confidence            57999999975 56677777777766543 2455778887754

>1x3s_A RAS-related protein RAB-18; GTPase, GNP, structural genomics, NPPSFA, national project on protein structural and functional analyses; HET: GNP; 1.32A {Homo sapiens} SCOP: c.37.1.8

Probab=95.09  E-value=0.042  Score=42.88  Aligned_cols=22  Identities=36%  Similarity=0.620  Sum_probs=20.1

Q ss_pred             eEEEECCCCCCHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~   54 (317)
                      .+++.|++|+|||+++..+...
T Consensus        17 ~i~v~G~~~~GKssli~~l~~~   38 (195)
T 1x3s_A           17 KILIIGESGVGKSSLLLRFTDD   38 (195)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            3899999999999999999875

>3tmk_A Thymidylate kinase; phosphotransferase; HET: T5A; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 2tmk_A* 1tmk_A*

Probab=95.06  E-value=0.014  Score=47.11  Aligned_cols=25  Identities=36%  Similarity=0.313  Sum_probs=22.8

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHcC
Q psy879           33 NIIISGPPGVGKTTTILCLARILLG   57 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~~   57 (317)
                      .+.|.|++|+||||.++.+++.+..
T Consensus         7 ~i~~eG~~g~GKst~~~~l~~~l~~   31 (216)
T 3tmk_A            7 LILIEGLDRTGKTTQCNILYKKLQP   31 (216)
T ss_dssp             EEEEEECSSSSHHHHHHHHHHHHCS
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhcc
Confidence            5899999999999999999999843

>2obl_A ESCN; ATPase, hydrolase; 1.80A {Escherichia coli O127} PDB: 2obm_A*

Probab=95.05  E-value=0.014  Score=50.85  Aligned_cols=37  Identities=24%  Similarity=0.279  Sum_probs=29.2

Q ss_pred             HHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHc
Q psy879           17 DTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        17 ~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      .+++.+ --+..|.  .+.|.||+|+||||+.+.++..+.
T Consensus        60 ~ald~l-l~i~~Gq--~~gIiG~nGaGKTTLl~~I~g~~~   96 (347)
T 2obl_A           60 RAIDGL-LTCGIGQ--RIGIFAGSGVGKSTLLGMICNGAS   96 (347)
T ss_dssp             HHHHHH-SCEETTC--EEEEEECTTSSHHHHHHHHHHHSC
T ss_pred             EEEEee-eeecCCC--EEEEECCCCCCHHHHHHHHhcCCC
Confidence            455555 4455565  699999999999999999999853

>2yc2_C IFT27, small RAB-related GTPase; transport protein, cilium, IFT complex; 2.59A {Chlamydomonas reinhardtii} PDB: 2yc4_C

Probab=95.03  E-value=0.026  Score=44.60  Aligned_cols=22  Identities=23%  Similarity=0.392  Sum_probs=4.3

Q ss_pred             eEEEECCCCCCHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~   54 (317)
                      .+++.|++|+|||+++..+...
T Consensus        22 ~i~v~G~~~~GKssli~~l~~~   43 (208)
T 2yc2_C           22 KVAVVGEATVGKSALISMFTSK   43 (208)
T ss_dssp             EEEEC-----------------
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            4899999999999999998865

>4ag6_A VIRB4 ATPase, type IV secretory pathway VIRB4 components-like P; hydrolase, type IV secretion, conjugation; 2.35A {Thermoanaerobacter pseudethanolicus} PDB: 4ag5_A

Probab=95.02  E-value=0.02  Score=50.64  Aligned_cols=28  Identities=29%  Similarity=0.183  Sum_probs=24.1

Q ss_pred             CceEEEECCCCCCHHHHHHHHHHHHcCC
Q psy879           31 VPNIIISGPPGVGKTTTILCLARILLGP   58 (317)
Q Consensus        31 ~~~~ll~G~~G~GKt~la~~la~~l~~~   58 (317)
                      .+|.++.||+|+|||++++.++..+...
T Consensus        35 ~~~~~i~G~~G~GKs~~~~~~~~~~~~~   62 (392)
T 4ag6_A           35 NSNWTILAKPGAGKSFTAKMLLLREYMQ   62 (392)
T ss_dssp             CCCEEEECCTTSSHHHHHHHHHHHHHTT
T ss_pred             cCceEEEcCCCCCHHHHHHHHHHHHHHC
Confidence            3579999999999999999999877543

>2f7s_A C25KG, RAS-related protein RAB-27B; G-protein, structural genomics, structural genomics consortium, SGC, signaling protein; HET: GDP; 2.70A {Homo sapiens} SCOP: c.37.1.8 PDB: 2iez_A*

Probab=94.97  E-value=0.04  Score=44.04  Aligned_cols=22  Identities=32%  Similarity=0.463  Sum_probs=19.5

Q ss_pred             eEEEECCCCCCHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~   54 (317)
                      .+++.|++|+|||+++..+...
T Consensus        27 ki~vvG~~~~GKSsLi~~l~~~   48 (217)
T 2f7s_A           27 KLLALGDSGVGKTTFLYRYTDN   48 (217)
T ss_dssp             EEEEESCTTSSHHHHHHHHHCS
T ss_pred             EEEEECcCCCCHHHHHHHHhcC
Confidence            3899999999999999998753

>2atx_A Small GTP binding protein TC10; GTPase, P-loop, alpha-beta, hydrolase; HET: GNP; 2.65A {Homo sapiens} SCOP: c.37.1.8

Probab=94.96  E-value=0.021  Score=44.75  Aligned_cols=22  Identities=27%  Similarity=0.428  Sum_probs=20.2

Q ss_pred             eEEEECCCCCCHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~   54 (317)
                      .+++.|++|+|||+++..+...
T Consensus        20 ki~v~G~~~~GKssli~~l~~~   41 (194)
T 2atx_A           20 KCVVVGDGAVGKTCLLMSYAND   41 (194)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            4899999999999999999875

>4hlc_A DTMP kinase, thymidylate kinase; TMK, MRSA, pipiridine, transfera transferase inhibitor complex; HET: T05; 1.55A {Staphylococcus aureus subsp} PDB: 2cck_A 4gfd_A* 4gsy_A* 4hdc_A* 4hej_A* 2ccj_A* 4hld_A* 2ccg_A*

Probab=94.96  E-value=0.048  Score=43.54  Aligned_cols=23  Identities=43%  Similarity=0.585  Sum_probs=21.4

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHc
Q psy879           34 IIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      +.|.|+.|+||||.++.+++.+.
T Consensus         5 I~~EG~dGsGKsTq~~~L~~~L~   27 (205)
T 4hlc_A            5 ITFEGPEGSGKTTVINEVYHRLV   27 (205)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHHT
T ss_pred             EEEECCCCCcHHHHHHHHHHHHH
Confidence            78899999999999999999984

>2zpa_A Uncharacterized protein YPFI; RNA modification enzyme, RNA helicase, acetyltransferase, GCN5 acetyltransferase; HET: ACO ADP; 2.35A {Escherichia coli K12}

Probab=94.91  E-value=0.036  Score=52.16  Aligned_cols=92  Identities=15%  Similarity=0.125  Sum_probs=51.5

Q ss_pred             HHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHHHHHH----HhhcccCCC
Q psy879           19 VERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMF----AQQKVTLPP   94 (317)
Q Consensus        19 ~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~----~~~~~~~~~   94 (317)
                      .+.+..++.... .+.+++|+.|.|||+++-.++..+...     + .+.+.+......+.+.....    .........
T Consensus       181 ~~al~~~~~~~~-~~~vlta~RGRGKSa~lG~~~a~~~~~-----~-~vtAP~~~a~~~l~~~~~~~i~~~~Pd~~~~~~  253 (671)
T 2zpa_A          181 QQLLKQLMTMPP-GVAAVTAARGRGKSALAGQLISRIAGR-----A-IVTAPAKASTDVLAQFAGEKFRFIAPDALLASD  253 (671)
T ss_dssp             HHHHHHHTTCCS-EEEEEEECTTSSHHHHHHHHHHHSSSC-----E-EEECSSCCSCHHHHHHHGGGCCBCCHHHHHHSC
T ss_pred             HHHHHHHHHhhh-CeEEEecCCCCCHHHHHHHHHHHHHhC-----c-EEECCCHHHHHHHHHHhhCCeEEeCchhhhhCc
Confidence            334444444222 358999999999999999999987421     2 23333334444443322110    000000011


Q ss_pred             CceeEEEEeCCCCCCHHHHHHHH
Q psy879           95 GRHKIVILDEADSMTDGAQQALR  117 (317)
Q Consensus        95 ~~~~vliiDE~d~l~~~~~~~ll  117 (317)
                      ....++||||+-.+.......|+
T Consensus       254 ~~~dlliVDEAAaIp~pll~~ll  276 (671)
T 2zpa_A          254 EQADWLVVDEAAAIPAPLLHQLV  276 (671)
T ss_dssp             CCCSEEEEETGGGSCHHHHHHHH
T ss_pred             ccCCEEEEEchhcCCHHHHHHHH
Confidence            34679999999999875444443

>3cph_A RAS-related protein SEC4; RAB GTPase, prenylation, vesicular transport, cytoplasm, cytoplasmic vesicle, exocytosis, GTP-binding; HET: GDP; 2.90A {Saccharomyces cerevisiae} SCOP: c.37.1.8

Probab=94.90  E-value=0.048  Score=43.28  Aligned_cols=22  Identities=27%  Similarity=0.539  Sum_probs=20.0

Q ss_pred             eEEEECCCCCCHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~   54 (317)
                      .+++.|++|+|||+++..+...
T Consensus        22 ~i~v~G~~~~GKSsli~~l~~~   43 (213)
T 3cph_A           22 KILLIGDSGVGKSCLLVRFVED   43 (213)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            4899999999999999999864

>4a2q_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.40A {Anas platyrhynchos}

Probab=94.87  E-value=0.2  Score=48.69  Aligned_cols=34  Identities=26%  Similarity=0.394  Sum_probs=23.6

Q ss_pred             HHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHH
Q psy879           19 VERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        19 ~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .+.+..++ +|+  ++++.+|.|+|||..+...+...
T Consensus       254 ~~~i~~~l-~~~--~~ll~~~TGsGKTl~~~~~i~~~  287 (797)
T 4a2q_A          254 IELAQPAI-NGK--NALICAPTGSGKTFVSILICEHH  287 (797)
T ss_dssp             HHHHHHHH-TTC--CEEEECCTTSCHHHHHHHHHHHH
T ss_pred             HHHHHHHH-hCC--CEEEEeCCCChHHHHHHHHHHHH
Confidence            33444443 444  69999999999999877666444

>4dhe_A Probable GTP-binding protein ENGB; melioidosis, RAS-like GTPase, cell division, cell cycle, SEP GTP-binding; 2.20A {Burkholderia thailandensis}

Probab=94.87  E-value=0.19  Score=40.15  Aligned_cols=24  Identities=33%  Similarity=0.517  Sum_probs=20.9

Q ss_pred             CceEEEECCCCCCHHHHHHHHHHH
Q psy879           31 VPNIIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        31 ~~~~ll~G~~G~GKt~la~~la~~   54 (317)
                      .+.+++.|++|+|||+++..+...
T Consensus        29 ~~~i~v~G~~~~GKSslin~l~~~   52 (223)
T 4dhe_A           29 QPEIAFAGRSNAGKSTAINVLCNQ   52 (223)
T ss_dssp             SCEEEEEESCHHHHHHHHHHHTTC
T ss_pred             CCEEEEEcCCCCCHHHHHHHHhCC
Confidence            346999999999999999998764

>1ko7_A HPR kinase/phosphatase; protein kinase, phosphotransfer, protein phosphatase, dual activity, product, substrate, transferase, hydrolase; 1.95A {Staphylococcus xylosus} SCOP: c.98.2.1 c.91.1.2

Probab=94.85  E-value=0.025  Score=48.26  Aligned_cols=22  Identities=36%  Similarity=0.685  Sum_probs=20.3

Q ss_pred             eEEEECCCCCCHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~   54 (317)
                      .++|.|++|+||||++..+...
T Consensus       146 ~vl~~G~sG~GKSt~a~~l~~~  167 (314)
T 1ko7_A          146 GVLITGDSGIGKSETALELIKR  167 (314)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHT
T ss_pred             EEEEEeCCCCCHHHHHHHHHhc
Confidence            5999999999999999999874

>2dpy_A FLII, flagellum-specific ATP synthase; beta barrel, alpha-beta structure, hydrolase; HET: ADP; 2.40A {Salmonella typhimurium}

Probab=94.85  E-value=0.019  Score=51.63  Aligned_cols=36  Identities=22%  Similarity=0.342  Sum_probs=28.7

Q ss_pred             HHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHH
Q psy879           17 DTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        17 ~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .+++.+ --+..|.  .+.|.||+|+||||+++.++...
T Consensus       146 ~vld~v-l~i~~Gq--~~~IvG~sGsGKSTLl~~Iag~~  181 (438)
T 2dpy_A          146 RAINAL-LTVGRGQ--RMGLFAGSGVGKSVLLGMMARYT  181 (438)
T ss_dssp             HHHHHH-SCCBTTC--EEEEEECTTSSHHHHHHHHHHHS
T ss_pred             eEEeee-EEecCCC--EEEEECCCCCCHHHHHHHHhccc
Confidence            455555 4455565  69999999999999999999985

>2npi_A Protein CLP1; CLP1-PCF11 complex, ATP binding, ternary complex, transcript; HET: ATP; 2.95A {Saccharomyces cerevisiae}

Probab=94.84  E-value=0.018  Score=52.16  Aligned_cols=28  Identities=25%  Similarity=0.338  Sum_probs=23.6

Q ss_pred             HhcCCCceEEEECCCCCCHHHHHHHHHHHH
Q psy879           26 SSSGNVPNIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        26 l~~~~~~~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      +..|.  .+.+.||+|+||||+++.++..+
T Consensus       135 i~~Ge--~v~IvGpnGsGKSTLlr~L~Gl~  162 (460)
T 2npi_A          135 NFEGP--RVVIVGGSQTGKTSLSRTLCSYA  162 (460)
T ss_dssp             SSSCC--CEEEEESTTSSHHHHHHHHHHTT
T ss_pred             eCCCC--EEEEECCCCCCHHHHHHHHhCcc
Confidence            44444  69999999999999999999865

>3hjn_A DTMP kinase, thymidylate kinase; ATP-binding, nucleotide biosynth nucleotide-binding, transferase, structural genomics; HET: ADP TYD; 2.10A {Thermotoga maritima}

Probab=94.84  E-value=0.022  Score=45.29  Aligned_cols=25  Identities=40%  Similarity=0.462  Sum_probs=22.1

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHcCC
Q psy879           34 IIISGPPGVGKTTTILCLARILLGP   58 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~l~~~   58 (317)
                      +.|.|+.|+||||.++.+++.|...
T Consensus         3 I~~EG~DGsGKsTq~~~L~~~L~~~   27 (197)
T 3hjn_A            3 ITFEGIDGSGKSTQIQLLAQYLEKR   27 (197)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHC
Confidence            5688999999999999999998644

>3hdt_A Putative kinase; structura genomics, PSI-2, protein structure initiative, midwest CENT structural genomics, MCSG; 2.79A {Clostridium symbiosum atcc 14940}

Probab=94.83  E-value=0.018  Score=46.72  Aligned_cols=23  Identities=30%  Similarity=0.135  Sum_probs=21.7

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .+.+.|++|||||++++.+|+.+
T Consensus        16 iI~i~g~~gsGk~~i~~~la~~l   38 (223)
T 3hdt_A           16 IITIEREYGSGGRIVGKKLAEEL   38 (223)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHH
T ss_pred             EEEEeCCCCCCHHHHHHHHHHHc
Confidence            38999999999999999999987

>2axn_A 6-phosphofructo-2-kinase/fructose-2,6- biphosphatase 3 (6PF-2-K/FRU- 2,6-P2ASE brain/placenta-type...; bifunctional enzyme, EDTA complex; HET: F6P EDT ADP; 2.10A {Homo sapiens} PDB: 2dwo_A* 2dwp_A* 2i1v_B* 3qpu_A* 3qpv_A* 3qpw_A*

Probab=94.81  E-value=0.017  Score=53.11  Aligned_cols=24  Identities=38%  Similarity=0.411  Sum_probs=21.9

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHc
Q psy879           33 NIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      .+++.|.||+||||+++.+++.+.
T Consensus        37 lIvlvGlpGSGKSTia~~La~~L~   60 (520)
T 2axn_A           37 VIVMVGLPARGKTYISKKLTRYLN   60 (520)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHh
Confidence            389999999999999999999873

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	317
d1sxjb2	224	c.37.1.20 (B:7-230) Replication factor C4 {Baker's	9e-53
d1iqpa2	231	c.37.1.20 (A:2-232) Replication factor C {Archaeon	4e-52
d1njfa_	239	c.37.1.20 (A:) delta prime subunit of DNA polymera	1e-51
d1sxjd2	237	c.37.1.20 (D:26-262) Replication factor C2 {Baker'	9e-41
d1sxjc2	227	c.37.1.20 (C:12-238) Replication factor C3 {Baker'	6e-40
d1sxja2	253	c.37.1.20 (A:295-547) Replication factor C1 {Baker	4e-31
d1sxje2	252	c.37.1.20 (E:4-255) Replication factor C5 {Baker's	7e-28
d2gnoa2	198	c.37.1.20 (A:11-208) gamma subunit of DNA polymera	2e-27
d1sxjb1	92	a.80.1.1 (B:231-322) Replication factor C4 {Baker'	1e-24
d1ixsb2	239	c.37.1.20 (B:4-242) Holliday junction helicase Ruv	7e-24
d1iqpa1	95	a.80.1.1 (A:233-327) Replication factor C {Archaeo	5e-23
d1in4a2	238	c.37.1.20 (A:17-254) Holliday junction helicase Ru	4e-21
d1sxjd1	91	a.80.1.1 (D:263-353) Replication factor C2 {Baker'	1e-19
d1sxjc1	95	a.80.1.1 (C:239-333) Replication factor C3 {Baker'	2e-19
d1a5ta2	207	c.37.1.20 (A:1-207) delta prime subunit of DNA pol	2e-18
d1svma_	362	c.37.1.20 (A:) Papillomavirus large T antigen heli	3e-15
d1g8pa_	333	c.37.1.20 (A:) ATPase subunit of magnesium chelata	3e-09
d1w5sa2	287	c.37.1.20 (A:7-293) CDC6-like protein APE0152, N-t	2e-08
d1fnna2	276	c.37.1.20 (A:1-276) CDC6, N-domain {Archaeon Pyrob	2e-08
d1lv7a_	256	c.37.1.20 (A:) AAA domain of cell division protein	4e-05
d1ixza_	247	c.37.1.20 (A:) AAA domain of cell division protein	6e-05
d1vmaa2	213	c.37.1.10 (A:82-294) GTPase domain of the signal r	6e-05
d2fnaa2	283	c.37.1.20 (A:1-283) Archaeal ATPase SSO1545 {Sulfo	9e-05
d2qy9a2	211	c.37.1.10 (A:285-495) GTPase domain of the signal	1e-04
d2i3ba1	189	c.37.1.11 (A:1-189) Cancer-related NTPase, C1orf57	2e-04
d1ofha_	309	c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId	2e-04
d2p67a1	327	c.37.1.10 (A:1-327) LAO/AO transport system kinase	3e-04
d1okkd2	207	c.37.1.10 (D:97-303) GTPase domain of the signal r	5e-04
d2qm8a1	323	c.37.1.10 (A:5-327) Metallochaperone MeaB {Methylo	6e-04
d1gvnb_	273	c.37.1.21 (B:) Plasmid maintenance system epsilon/	9e-04
d1ls1a2	207	c.37.1.10 (A:89-295) GTPase domain of the signal s	0.001
d1rkba_	173	c.37.1.1 (A:) Adenylate kinase {Human (Homo sapien	0.002
d1y63a_	174	c.37.1.1 (A:) Probable kinase LmjF30.1890 {Leishma	0.002
d1j8yf2	211	c.37.1.10 (F:87-297) GTPase domain of the signal s	0.002
d1ye8a1	178	c.37.1.11 (A:1-178) Hypothetical kinase-like prote	0.002
d1nksa_	194	c.37.1.1 (A:) Adenylate kinase {Archaeon Sulfolobu	0.002
d1lw7a2	192	c.37.1.1 (A:220-411) Transcriptional regulator Nad	0.003
d1xjca_	165	c.37.1.10 (A:) Molybdopterin-guanine dinucleotide	0.004

>d1sxjb2 c.37.1.20 (B:7-230) Replication factor C4 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 224

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C4
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score =  170 bits (432), Expect = 9e-53
 Identities = 145/218 (66%), Positives = 185/218 (84%)

Query: 1   IEKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSF 60
           +EKYRPQ  SDIVGN++T++RL+  +  GN+P++IISG PG+GKTT++ CLA  LLG S+
Sbjct: 6   VEKYRPQVLSDIVGNKETIDRLQQIAKDGNMPHMIISGMPGIGKTTSVHCLAHELLGRSY 65

Query: 61  KDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTM 120
            D VLELNAS+DRGID VRN+IK FAQ+K+ LPPG+HKIVILDEADSMT GAQQALRRTM
Sbjct: 66  ADGVLELNASDDRGIDVVRNQIKHFAQKKLHLPPGKHKIVILDEADSMTAGAQQALRRTM 125

Query: 121 EIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGL 180
           E+YSN+TRFA ACN S KIIEP+QS+CA+LRY+KL+D  +L ++++I + E++ +TNDGL
Sbjct: 126 ELYSNSTRFAFACNQSNKIIEPLQSQCAILRYSKLSDEDVLKRLLQIIKLEDVKYTNDGL 185

Query: 181 EAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCD 218
           EAI+FTA+GDMRQA+NNLQST  G G V A+ VFK+ D
Sbjct: 186 EAIIFTAEGDMRQAINNLQSTVAGHGLVNADNVFKIVD 223

>d1iqpa2 c.37.1.20 (A:2-232) Replication factor C {Archaeon Pyrococcus furiosus [TaxId: 2261]} Length = 231

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

 Score =  169 bits (428), Expect = 4e-52
 Identities = 108/216 (50%), Positives = 150/216 (69%), Gaps = 1/216 (0%)

Query: 1   IEKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSF 60
           +EKYRPQ   DIVG E  V+RLK +  +G++P+++ +GPPGVGKTT  L LAR L G ++
Sbjct: 15  VEKYRPQRLDDIVGQEHIVKRLKHYVKTGSMPHLLFAGPPGVGKTTAALALARELFGENW 74

Query: 61  KDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTM 120
           +   LELNAS++RGI+ +R K+K FA+ K  +     KI+ LDEAD++T  AQQALRRTM
Sbjct: 75  RHNFLELNASDERGINVIREKVKEFARTK-PIGGASFKIIFLDEADALTQDAQQALRRTM 133

Query: 121 EIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGL 180
           E++S+  RF L+CN S KIIEPIQSRCA+ R+  L D  +  ++  I E E +  T +GL
Sbjct: 134 EMFSSNVRFILSCNYSSKIIEPIQSRCAIFRFRPLRDEDIAKRLRYIAENEGLELTEEGL 193

Query: 181 EAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKV 216
           +AI++ A+GDMR+A+N LQ+       +T E VF V
Sbjct: 194 QAILYIAEGDMRRAINILQAAAALDKKITDENVFMV 229

>d1njfa_ c.37.1.20 (A:) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]} Length = 239

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

 Score =  168 bits (427), Expect = 1e-51
 Identities = 61/236 (25%), Positives = 109/236 (46%), Gaps = 24/236 (10%)

Query: 2   EKYRPQTFSDIVGNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARILLGPSF 60
            K+RPQTF+D+VG E  +  L    S G + +  + SG  GVGKT+    LA+ L   + 
Sbjct: 4   RKWRPQTFADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKGLNCETG 63

Query: 61  KDA-------------------VLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVI 101
             A                   ++E++A++   ++  R+ +            GR K+ +
Sbjct: 64  ITATPCGVCDNCREIEQGRFVDLIEIDAASRTKVEDTRDLLDNVQYAPAR---GRFKVYL 120

Query: 102 LDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLL 161
           +DE   ++  +  AL +T+E      +F LA  + +K+   I SRC       L   Q+ 
Sbjct: 121 IDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTILSRCLQFHLKALDVEQIR 180

Query: 162 SKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNL-QSTHNGFGHVTAEYVFKV 216
            ++  I  +E+I+H    L+ +   A+G +R AL+   Q+  +G G V+ + V  +
Sbjct: 181 HQLEHILNEEHIAHEPRALQLLARAAEGSLRDALSLTDQAIASGDGQVSTQAVSAM 236

>d1sxjd2 c.37.1.20 (D:26-262) Replication factor C2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 237

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score =  140 bits (352), Expect = 9e-41
 Identities = 94/232 (40%), Positives = 135/232 (58%), Gaps = 16/232 (6%)

Query: 1   IEKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPS- 59
           +EKYRP+   ++   +  V  LK    S N+P+++  GPPG GKT+TIL L + L GP  
Sbjct: 3   VEKYRPKNLDEVTAQDHAVTVLKKTLKSANLPHMLFYGPPGTGKTSTILALTKELYGPDL 62

Query: 60  FKDAVLELNASNDRGIDTVRNKIKMFAQQKV---------TLPPGRHKIVILDEADSMTD 110
            K  +LELNAS++RGI  VR K+K FA+  V           P   +KI+ILDEADSMT 
Sbjct: 63  MKSRILELNASDERGISIVREKVKNFARLTVSKPSKHDLENYPCPPYKIIILDEADSMTA 122

Query: 111 GAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEK 170
            AQ ALRRTME YS  TRF L CN   +II+P+ S+C+  R+  L  +  + ++  I E+
Sbjct: 123 DAQSALRRTMETYSGVTRFCLICNYVTRIIDPLASQCSKFRFKALDASNAIDRLRFISEQ 182

Query: 171 ENISHTNDGLEAIVFTAQGDMRQALNNLQSTHNGF------GHVTAEYVFKV 216
           EN+   +  LE I+  + GD+R+ +  LQS   G        ++T+  V ++
Sbjct: 183 ENVKCDDGVLERILDISAGDLRRGITLLQSASKGAQYLGDGKNITSTQVEEL 234

>d1sxjc2 c.37.1.20 (C:12-238) Replication factor C3 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 227

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C3
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score =  137 bits (346), Expect = 6e-40
 Identities = 81/222 (36%), Positives = 132/222 (59%), Gaps = 6/222 (2%)

Query: 1   IEKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSF 60
           +EKYRP+T  ++ G  + +  ++ F   G +P+++  GPPG GKT+TI+ LAR + G ++
Sbjct: 5   VEKYRPETLDEVYGQNEVITTVRKFVDEGKLPHLLFYGPPGTGKTSTIVALAREIYGKNY 64

Query: 61  KDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTM 120
            + VLELNAS+DRGID VRN+IK FA  +     G  K++ILDEAD+MT+ AQ ALRR +
Sbjct: 65  SNMVLELNASDDRGIDVVRNQIKDFASTRQIFSKG-FKLIILDEADAMTNAAQNALRRVI 123

Query: 121 EIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGL 180
           E Y+  TRF +  N + K+   + S+C   R+  L    +  ++  +   E +  + +  
Sbjct: 124 ERYTKNTRFCVLANYAHKLTPALLSQCTRFRFQPLPQEAIERRIANVLVHEKLKLSPNAE 183

Query: 181 EAIVFTAQGDMRQALNNLQSTH-----NGFGHVTAEYVFKVC 217
           +A++  + GDMR+ LN LQS            ++ + +++ C
Sbjct: 184 KALIELSNGDMRRVLNVLQSCKATLDNPDEDEISDDVIYECC 225

>d1sxja2 c.37.1.20 (A:295-547) Replication factor C1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 253

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score =  115 bits (287), Expect = 4e-31
 Identities = 47/241 (19%), Positives = 96/241 (39%), Gaps = 25/241 (10%)

Query: 1   IEKYRPQTFSDIVGNEDTVERLKVF-----------------SSSGNVPNIIISGPPGVG 43
             KY P     + GN+ +V +LK +                   SG     ++ GPPG+G
Sbjct: 5   TVKYAPTNLQQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIG 64

Query: 44  KTTTILCLARILLGPSFKDAVL------ELNASNDRGIDTVRNKIKMFAQQKVTLPPGRH 97
           KTT    +A+ L     +           LNA     +D +         ++     G+H
Sbjct: 65  KTTAAHLVAQELGYDILEQNASDVRSKTLLNAGVKNALDNMSVVGYFKHNEEAQNLNGKH 124

Query: 98  KIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKII--EPIQSRCAMLRYNKL 155
            ++I+DE D M+ G +  + +  +    T+   +   N   +    P    C  +++ + 
Sbjct: 125 FVIIMDEVDGMSGGDRGGVGQLAQFCRKTSTPLILICNERNLPKMRPFDRVCLDIQFRRP 184

Query: 156 TDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFK 215
               + S+++ I  +E      + ++ ++ T +GD+RQ +N L +       +  E + +
Sbjct: 185 DANSIKSRLMTIAIREKFKLDPNVIDRLIQTTRGDIRQVINLLSTISTTTKTINHENINE 244

Query: 216 V 216
           +
Sbjct: 245 I 245

>d1sxje2 c.37.1.20 (E:4-255) Replication factor C5 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 252

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C5
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score =  106 bits (265), Expect = 7e-28
 Identities = 64/237 (27%), Positives = 107/237 (45%), Gaps = 35/237 (14%)

Query: 1   IEKYRPQTFSDIVGNEDTVERLKVFSSSGNV-PNIIISGPPGVGKTTTILCLARILLGPS 59
           ++KYRP++ + +  NE+    LK  S      P++++ GP G GK T  + L   + GP 
Sbjct: 2   VDKYRPKSLNALSHNEELTNFLKSLSDQPRDLPHLLLYGPNGTGKKTRCMALLESIFGPG 61

Query: 60  ----------------------------FKDAVLELNASNDRGIDTVRNKIKMFAQQ--- 88
                                         +       +NDR +     K     +Q   
Sbjct: 62  VYRLKIDVRQFVTASNRKLELNVVSSPYHLEITPSDMGNNDRIVIQELLKEVAQMEQVDF 121

Query: 89  --KVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSR 146
                    R+K VI++EA+S+T  AQ ALRRTME YS   R  + C++   II PI+S+
Sbjct: 122 QDSKDGLAHRYKCVIINEANSLTKDAQAALRRTMEKYSKNIRLIMVCDSMSPIIAPIKSQ 181

Query: 147 CAMLRYNKLTDAQLLSKVIEICEKENISH-TNDGLEAIVFTAQGDMRQALNNLQSTH 202
           C ++R    +D+++ + + ++   E I   T D L+ I   + G++R +L  L+S  
Sbjct: 182 CLLIRCPAPSDSEISTILSDVVTNERIQLETKDILKRIAQASNGNLRVSLLMLESMA 238

>d2gnoa2 c.37.1.20 (A:11-208) gamma subunit of DNA polymerase III, N-domain {Thermotoga maritima [TaxId: 2336]} Length = 198

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: gamma subunit of DNA polymerase III, N-domain
species: Thermotoga maritima [TaxId: 2336]

 Score =  104 bits (260), Expect = 2e-27
 Identities = 40/192 (20%), Positives = 68/192 (35%), Gaps = 11/192 (5%)

Query: 17  DTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDA-VLELNA-SNDRG 74
           D +E LK         +I+I+G          L L   +     K + VLE++    + G
Sbjct: 1   DQLETLKRIIEKSEGISILINGEDLSYPREVSLELPEYVEKFPPKASDVLEIDPEGENIG 60

Query: 75  IDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACN 134
           ID +R     F      L     K VI+ + + MT  A  A  + +E         L   
Sbjct: 61  IDDIRTIKD-FLNYSPEL--YTRKYVIVHDCERMTQQAANAFLKALEEPPEYAVIVLNTR 117

Query: 135 NSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGL----EAIVFTAQ-- 188
               ++  I+SR   +  N   + + L K       E +           EA    A+  
Sbjct: 118 RWHYLLPTIKSRVFRVVVNVPKEFRDLVKEKIGDLWEELPLLERDFKTALEAYKLGAEKL 177

Query: 189 GDMRQALNNLQS 200
             + ++L  L++
Sbjct: 178 SGLMESLKVLET 189

>d1sxjb1 a.80.1.1 (B:231-322) Replication factor C4 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 92

class: All alpha proteins
fold: post-AAA+ oligomerization domain-like
superfamily: post-AAA+ oligomerization domain-like
family: DNA polymerase III clamp loader subunits, C-terminal domain
domain: Replication factor C4
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 93.4 bits (232), Expect = 1e-24
 Identities = 42/95 (44%), Positives = 63/95 (66%), Gaps = 5/95 (5%)

Query: 220 PHPLAVKEMLLNCVEGNMKDSYKIIH-HLYKLGYAPEDIIGNIFRVAKTL-DIPEPLKLS 277
           PHPL VK+MLL     N++DS +I+   L+K GY+  DI+   FRV K L  + E ++L 
Sbjct: 1   PHPLIVKKMLLAS---NLEDSIQILRTDLWKKGYSSIDIVTTSFRVTKNLAQVKESVRLE 57

Query: 278 IIQEIGNVHLRISEGVNSLLQLSGLLARLCIVGSK 312
           +I+EIG  H+RI EGV + LQL+ +LA++  + +K
Sbjct: 58  MIKEIGLTHMRILEGVGTYLQLASMLAKIHKLNNK 92

>d1ixsb2 c.37.1.20 (B:4-242) Holliday junction helicase RuvB {Thermus thermophilus [TaxId: 274]} Length = 239

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Holliday junction helicase RuvB
species: Thermus thermophilus [TaxId: 274]

 Score = 95.8 bits (237), Expect = 7e-24
 Identities = 40/243 (16%), Positives = 81/243 (33%), Gaps = 42/243 (17%)

Query: 5   RPQTFSDIVGNEDTVERLKVFSSSG-----NVPNIIISGPPGVGKTTTILCLARILLGPS 59
           RP+T  + +G E   ++L+V+  +       + ++++ GPPG+GKTT             
Sbjct: 4   RPKTLDEYIGQERLKQKLRVYLEAAKARKEPLEHLLLFGPPGLGKTTLAHV--------I 55

Query: 60  FKDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRT 119
             +  + L  ++   I+   +   + A            I+ +DE   ++  A++ L   
Sbjct: 56  AHELGVNLRVTSGPAIEKPGDLAAILANS-----LEEGDILFIDEIHRLSRQAEEHLYPA 110

Query: 120 MEIY----------------SNTTRFALACNNSEKIIEPIQSR---CAMLRYNKLTDAQL 160
           ME +                    RF L    +   +           +      T  +L
Sbjct: 111 MEDFVMDIVIGQGPAARTIRLELPRFTLIGATTRPGLITAPLLSRFGIVEHLEYYTPEEL 170

Query: 161 LSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQ-----STHNGFGHVTAEYVFK 215
              V+       +  T +    I   ++G MR A    +     +   G   +T E   +
Sbjct: 171 AQGVMRDARLLGVRITEEAALEIGRRSRGTMRVAKRLFRRVRDFAQVAGEEVITRERALE 230

Query: 216 VCD 218
              
Sbjct: 231 ALA 233

>d1iqpa1 a.80.1.1 (A:233-327) Replication factor C {Archaeon Pyrococcus furiosus [TaxId: 2261]} Length = 95

class: All alpha proteins
fold: post-AAA+ oligomerization domain-like
superfamily: post-AAA+ oligomerization domain-like
family: DNA polymerase III clamp loader subunits, C-terminal domain
domain: Replication factor C
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

 Score = 89.1 bits (221), Expect = 5e-23
 Identities = 29/93 (31%), Positives = 52/93 (55%), Gaps = 1/93 (1%)

Query: 221 HPLAVKEMLLNCVEGNMKDSYKIIH-HLYKLGYAPEDIIGNIFRVAKTLDIPEPLKLSII 279
            P  ++EM+L  ++GN   + + +   L K G + ED++  + +    L I EP K+ + 
Sbjct: 3   RPEDIREMMLLALKGNFLKAREKLREILLKQGLSGEDVLVQMHKEVFNLPIEEPKKVLLA 62

Query: 280 QEIGNVHLRISEGVNSLLQLSGLLARLCIVGSK 312
            +IG  + R+ EG N ++QL  LLA+  ++G K
Sbjct: 63  DKIGEYNFRLVEGANEIIQLEALLAQFTLIGKK 95

>d1in4a2 c.37.1.20 (A:17-254) Holliday junction helicase RuvB {Thermotoga maritima [TaxId: 2336]} Length = 238

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Holliday junction helicase RuvB
species: Thermotoga maritima [TaxId: 2336]

 Score = 88.1 bits (217), Expect = 4e-21
 Identities = 37/235 (15%), Positives = 83/235 (35%), Gaps = 25/235 (10%)

Query: 2   EKYRPQTFSDIVGNEDTVERLKVF-----SSSGNVPNIIISGPPGVGKTTTILCLARILL 56
           +  RP++  + +G E+  ++L +           + +++++GPPG+GKTT    +A  L 
Sbjct: 1   QFLRPKSLDEFIGQENVKKKLSLALEAAKMRGEVLDHVLLAGPPGLGKTTLAHIIASELQ 60

Query: 57  GPSF---------KDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADS 107
                        +  +  +  S +RG     ++I    +    L     +   +D    
Sbjct: 61  TNIHVTSGPVLVKQGDMAAILTSLERGDVLFIDEIHRLNKAVEELLYSAIEDFQIDIMIG 120

Query: 108 MTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSK-VIE 166
               A     +++ I         A   S  +  P++SR  ++        + L + +  
Sbjct: 121 KGPSA-----KSIRIDIQPFTLVGATTRSGLLSSPLRSRFGIILELDFYTVKELKEIIKR 175

Query: 167 ICEKENISHTNDGLEAIVFTAQGDMRQALNNLQ-----STHNGFGHVTAEYVFKV 216
                ++   +   E I   ++G  R A+   +      T      +  + V K 
Sbjct: 176 AASLMDVEIEDAAAEMIAKRSRGTPRIAIRLTKRVRDMLTVVKADRINTDIVLKT 230

>d1sxjd1 a.80.1.1 (D:263-353) Replication factor C2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 91

class: All alpha proteins
fold: post-AAA+ oligomerization domain-like
superfamily: post-AAA+ oligomerization domain-like
family: DNA polymerase III clamp loader subunits, C-terminal domain
domain: Replication factor C2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 79.8 bits (197), Expect = 1e-19
 Identities = 14/84 (16%), Positives = 33/84 (39%), Gaps = 1/84 (1%)

Query: 225 VKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDIIGNIFRVA-KTLDIPEPLKLSIIQEIG 283
           + E++     G+  +  K ++   K G++   ++  +        +     K  I   + 
Sbjct: 6   LIEIVEKVKSGDFDEIKKYVNTFMKSGWSAASVVNQLHEYYITNDNFDTNFKNQISWLLF 65

Query: 284 NVHLRISEGVNSLLQLSGLLARLC 307
               R++ G N  +QL  LL ++ 
Sbjct: 66  TTDSRLNNGTNEHIQLLNLLVKIS 89

>d1sxjc1 a.80.1.1 (C:239-333) Replication factor C3 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 95

class: All alpha proteins
fold: post-AAA+ oligomerization domain-like
superfamily: post-AAA+ oligomerization domain-like
family: DNA polymerase III clamp loader subunits, C-terminal domain
domain: Replication factor C3
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 79.4 bits (196), Expect = 2e-19
 Identities = 16/90 (17%), Positives = 45/90 (50%), Gaps = 2/90 (2%)

Query: 220 PHPLAVKEMLLNCVEGNMKDSYKIIHHLYKL-GYAPEDIIGNIFRVAKTLDIPEP-LKLS 277
           P P  +K +L + +E +   ++  ++ +    G A  D+I  I ++ +  ++     ++ 
Sbjct: 1   PRPSDLKAVLKSILEDDWGTAHYTLNKVRSAKGLALIDLIEGIVKILEDYELQNEETRVH 60

Query: 278 IIQEIGNVHLRISEGVNSLLQLSGLLARLC 307
           ++ ++ ++   IS+G N  +Q S ++  + 
Sbjct: 61  LLTKLADIEYSISKGGNDQIQGSAVIGAIK 90

>d1a5ta2 c.37.1.20 (A:1-207) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]} Length = 207

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

 Score = 79.8 bits (195), Expect = 2e-18
 Identities = 39/204 (19%), Positives = 72/204 (35%), Gaps = 25/204 (12%)

Query: 16  EDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLAR-------------------IL 55
               E+L     +G   + ++I   PG+G    I  L+R                    L
Sbjct: 8   RPDFEKLVASYQAGRGHHALLIQALPGMGDDALIYALSRYLLCQQPQGHKSCGHCRGCQL 67

Query: 56  LGPSFKDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQA 115
           +          L     +    V    ++  +       G  K+V + +A  +TD A  A
Sbjct: 68  MQAGTHPDYYTLAPEKGKNTLGVDAVREVTEKLNEHARLGGAKVVWVTDAALLTDAAANA 127

Query: 116 LRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISH 175
           L +T+E     T F LA    E+++  ++SRC +       +   ++ +        ++ 
Sbjct: 128 LLKTLEEPPAETWFFLATREPERLLATLRSRCRLHYLAPPPEQYAVTWL-----SREVTM 182

Query: 176 TNDGLEAIVFTAQGDMRQALNNLQ 199
           + D L A +  + G    AL   Q
Sbjct: 183 SQDALLAALRLSAGSPGAALALFQ 206

>d1svma_ c.37.1.20 (A:) Papillomavirus large T antigen helicase domain {Simian virus 40 [TaxId: 10633]} Length = 362

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Papillomavirus large T antigen helicase domain
species: Simian virus 40 [TaxId: 10633]

 Score = 73.2 bits (179), Expect = 3e-15
 Identities = 25/182 (13%), Positives = 46/182 (25%), Gaps = 19/182 (10%)

Query: 32  PNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMF------ 85
              +  GP   GKTT    L  +  G       L +N   DR    +   I  F      
Sbjct: 155 RYWLFKGPIDSGKTTLAAALLELCGGK-----ALNVNLPLDRLNFELGVAIDQFLVVFED 209

Query: 86  AQQKVTLPPGRHKIVILDEADSMTD------GAQQALRRTMEIYSNTTRFALACNNS-EK 138
            +              ++  D++ D            +   +         +  N     
Sbjct: 210 VKGTGGESRDLPSGQGINNLDNLRDYLDGSVKVNLEKKHLNKRTQIFPPGIVTMNEYSVP 269

Query: 139 IIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGL-EAIVFTAQGDMRQALNN 197
                +    +    K      L +   + EK  I      L   I +    +  Q++ +
Sbjct: 270 KTLQARFVKQIDFRPKDYLKHCLERSEFLLEKRIIQSGIALLLMLIWYRPVAEFAQSIQS 329

Query: 198 LQ 199
             
Sbjct: 330 RI 331

>d1g8pa_ c.37.1.20 (A:) ATPase subunit of magnesium chelatase, BchI {Rhodobacter capsulatus [TaxId: 1061]} Length = 333

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ATPase subunit of magnesium chelatase, BchI
species: Rhodobacter capsulatus [TaxId: 1061]

 Score = 54.9 bits (131), Expect = 3e-09
 Identities = 28/148 (18%), Positives = 53/148 (35%), Gaps = 6/148 (4%)

Query: 5   RPQ-TFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDA 63
           RP   FS IVG ED    L + +    +  +++ G  G GK+T +  LA +L      + 
Sbjct: 1   RPVFPFSAIVGQEDMKLALLLTAVDPGIGGVLVFGDRGTGKSTAVRALAALLPEIEAVEG 60

Query: 64  VLELNASNDRGI----DTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRT 119
              +++ N   I      +   +       V LP G  +  ++   D     ++      
Sbjct: 61  -CPVSSPNVEMIPDWATVLSTNVIRKPTPVVDLPLGVSEDRVVGALDIERAISKGEKAFE 119

Query: 120 MEIYSNTTRFALACNNSEKIIEPIQSRC 147
             + +   R  L  +    + + I    
Sbjct: 120 PGLLARANRGYLYIDECNLLEDHIVDLL 147

>d1w5sa2 c.37.1.20 (A:7-293) CDC6-like protein APE0152, N-terminal domain {Aeropyrum pernix [TaxId: 56636]} Length = 287

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6-like protein APE0152, N-terminal domain
species: Aeropyrum pernix [TaxId: 56636]

 Score = 52.5 bits (124), Expect = 2e-08
 Identities = 35/279 (12%), Positives = 66/279 (23%), Gaps = 64/279 (22%)

Query: 2   EKYRPQTFSDIVGNEDTVERLKVF---------SSSGNVPNIIISGPPGVGKTTTILCLA 52
           E Y P             E L              S         G  G+GKTT      
Sbjct: 11  ENYIPPEL---RVRRGEAEALARIYLNRLLSGAGLSDVNMIYGSIGRVGIGKTTLAKFTV 67

Query: 53  RILLGPSFKDAV---------------------------LELNASNDRGIDTVRNKIKMF 85
           + +   + K+ +                             +       +D ++  +   
Sbjct: 68  KRVSEAAAKEGLTVKQAYVNAFNAPNLYTILSLIVRQTGYPIQVRGAPALDILKALVDNL 127

Query: 86  AQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSN------------TTRFALAC 133
             +   L     +   +  +  +       L R  E   +             +      
Sbjct: 128 YVENHYLLVILDEFQSMLSSPRIAAEDLYTLLRVHEEIPSRDGVNRIGFLLVASDVRALS 187

Query: 134 NNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKE--NISHTNDGLEAIV------F 185
              EKI +        L        +L + + +  E    +       LE I        
Sbjct: 188 YMREKIPQVESQIGFKLHLPAYKSRELYTILEQRAELGLRDTVWEPRHLELISDVYGEDK 247

Query: 186 TAQGDMRQALNNLQ-----STHNGFGHVTAEYVFKVCDE 219
              G  R+A+  L+     +   G   ++ + V K   E
Sbjct: 248 GGDGSARRAIVALKMACEMAEAMGRDSLSEDLVRKAVSE 286

>d1fnna2 c.37.1.20 (A:1-276) CDC6, N-domain {Archaeon Pyrobaculum aerophilum [TaxId: 13773]} Length = 276

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6, N-domain
species: Archaeon Pyrobaculum aerophilum [TaxId: 13773]

 Score = 52.5 bits (124), Expect = 2e-08
 Identities = 37/265 (13%), Positives = 74/265 (27%), Gaps = 50/265 (18%)

Query: 2   EKYRPQTFSDIVGNEDTVERLKVF------SSSGNVPNIIISGPPGVGKTTTILCLARIL 55
             Y P+        E  +++L +       +   + P   + G PG GKT T+  L  + 
Sbjct: 11  PSYVPKRL---PHREQQLQQLDILLGNWLRNPGHHYPRATLLGRPGTGKTVTLRKLWELY 67

Query: 56  LGPSFKDAVLELNASNDRGIDTVRNKIKMFAQQ----------------KVTLPPGRHKI 99
              +    V             +    +                     +       +  
Sbjct: 68  KDKTTARFVYINGFIYRNFTAIIGEIARSLNIPFPRRGLSRDEFLALLVEHLRERDLYMF 127

Query: 100 VILDEADSMTDGAQQALRRTMEIYSNTTRFALACN---NSEKIIEPIQSRCA-------- 148
           ++LD+A ++         R  +       F +A     +++ ++  +             
Sbjct: 128 LVLDDAFNLAPDILSTFIRLGQEADKLGAFRIALVIVGHNDAVLNNLDPSTRGIMGKYVI 187

Query: 149 MLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIV---------FTAQGDMRQALNNLQ 199
                       +            S++ D L+ I           T +GD R A++ L 
Sbjct: 188 RFSPYTKDQIFDILLDRAKAGLAEGSYSEDILQMIADITGAQTPLDTNRGDARLAIDILY 247

Query: 200 -----STHNGFGHVTAEYVFKVCDE 219
                +  NG  H+  E V K   E
Sbjct: 248 RSAYAAQQNGRKHIAPEDVRKSSKE 272

>d1lv7a_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Escherichia coli [TaxId: 562]} Length = 256

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Escherichia coli [TaxId: 562]

 Score = 42.1 bits (99), Expect = 4e-05
 Identities = 36/171 (21%), Positives = 58/171 (33%), Gaps = 38/171 (22%)

Query: 8   TFSDIVGNEDTVERLK----------VFSSSGNVP--NIIISGPPGVGKTTTILCLARIL 55
           TF+D+ G ++  E +            F   G      +++ GPPG GKT     +A   
Sbjct: 10  TFADVAGCDEAKEEVAELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGEA 69

Query: 56  LGPSFKDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSM------- 108
             P F  +  +       G         MF Q K   P     I+ +DE D++       
Sbjct: 70  KVPFFTISGSDF-VEMFVG-VGASRVRDMFEQAKKAAP----CIIFIDEIDAVGRQRGAG 123

Query: 109 TDGAQQALRRTM--------EIYSNTTRFALACNNSEKIIEPIQSRCAMLR 151
             G      +T+            N     +A  N   +++P     A+LR
Sbjct: 124 LGGGHDEREQTLNQMLVEMDGFEGNEGIIVIAATNRPDVLDP-----ALLR 169

>d1ixza_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Thermus thermophilus [TaxId: 274]} Length = 247

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Thermus thermophilus [TaxId: 274]

 Score = 41.4 bits (97), Expect = 6e-05
 Identities = 39/171 (22%), Positives = 58/171 (33%), Gaps = 38/171 (22%)

Query: 8   TFSDIVGNEDTVERLK----------VFSSSGNVP--NIIISGPPGVGKTTTILCLARIL 55
           TF D+ G E+  E LK           F   G      +++ GPPGVGKT     +A   
Sbjct: 7   TFKDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEA 66

Query: 56  LGPSFKDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSM------- 108
             P    +  +       G         +F   K   P     IV +DE D++       
Sbjct: 67  RVPFITASGSDF-VEMFVG-VGAARVRDLFETAKRHAPC----IVFIDEIDAVGRKRGSG 120

Query: 109 TDGAQQALRRTM--------EIYSNTTRFALACNNSEKIIEPIQSRCAMLR 151
             G      +T+            +T    +A  N   I++P     A+LR
Sbjct: 121 VGGGNDEREQTLNQLLVEMDGFEKDTAIVVMAATNRPDILDP-----ALLR 166

>d1vmaa2 c.37.1.10 (A:82-294) GTPase domain of the signal recognition particle receptor FtsY {Thermotoga maritima [TaxId: 2336]} Length = 213

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Thermotoga maritima [TaxId: 2336]

 Score = 40.9 bits (95), Expect = 6e-05
 Identities = 19/168 (11%), Positives = 46/168 (27%), Gaps = 7/168 (4%)

Query: 28  SGNVPNII-ISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFA 86
               P +I + G  G GKTT+   LA++ +       +   +      I+ ++   +   
Sbjct: 7   PPEPPFVIMVVGVNGTGKTTSCGKLAKMFVDEGKSVVLAAADTFRAAAIEQLKIWGERVG 66

Query: 87  QQKVTLPPG--RHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQ 144
              ++   G     +     A ++       +  T                  K+   ++
Sbjct: 67  ATVISHSEGADPAAVAFDAVAHALARNKDVVIIDTAGRLHTKKNL---MEELRKVHRVVK 123

Query: 145 SRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMR 192
            +     +  L      +       +  I      +  I+ T      
Sbjct: 124 KKIPDAPHETLLVIDATTG-QNGLVQAKIFKEAVNVTGIILTKLDGTA 170

>d2fnaa2 c.37.1.20 (A:1-283) Archaeal ATPase SSO1545 {Sulfolobus solfataricus [TaxId: 2287]} Length = 283

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Archaeal ATPase SSO1545
species: Sulfolobus solfataricus [TaxId: 2287]

 Score = 40.9 bits (94), Expect = 9e-05
 Identities = 31/248 (12%), Positives = 59/248 (23%), Gaps = 28/248 (11%)

Query: 11  DIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNAS 70
           D    E  +E+LK        P  ++ G    GK++ I      L  P     + +    
Sbjct: 13  DFFDREKEIEKLK----GLRAPITLVLGLRRTGKSSIIKIGINELNLPYIYLDLRKFEER 68

Query: 71  NDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFA 130
           N         +++    + V   P   K +   +   +     +      +  S      
Sbjct: 69  NYISYKDFLLELQKEINKLVKRLPSLLKALKNIQGIVIMGNEIKFNWNRKDRLSFANLLE 128

Query: 131 LACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGD 190
                S+  +  +      L   KL    LL  +          +       +  +  G 
Sbjct: 129 SFEQASKDNVIIVLDEAQELV--KLRGVNLLPALAYA-----YDNLKRIKFIMSGSEMGL 181

Query: 191 MRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEMLLNCVEGNMKDSYKIIHHLYKL 250
           +   L         FG   +    K           E L                   + 
Sbjct: 182 LYDYLRVEDPESPLFGRAFSTVELKPFSREE---AIEFLR--------------RGFQEA 224

Query: 251 GYAPEDII 258
               +D  
Sbjct: 225 DIDFKDYE 232

>d2qy9a2 c.37.1.10 (A:285-495) GTPase domain of the signal recognition particle receptor FtsY {Escherichia coli [TaxId: 562]} Length = 211

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Escherichia coli [TaxId: 562]

 Score = 40.0 bits (93), Expect = 1e-04
 Identities = 17/79 (21%), Positives = 30/79 (37%), Gaps = 1/79 (1%)

Query: 28  SGNVPNII-ISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFA 86
            G  P +I + G  GVGKTTTI  LAR          +   +      ++ ++   +   
Sbjct: 5   EGKAPFVILMVGVNGVGKTTTIGKLARQFEQQGKSVMLAAGDTFRAAAVEQLQVWGQRNN 64

Query: 87  QQKVTLPPGRHKIVILDEA 105
              +    G     ++ +A
Sbjct: 65  IPVIAQHTGADSASVIFDA 83

>d2i3ba1 c.37.1.11 (A:1-189) Cancer-related NTPase, C1orf57 {Human (Homo sapiens) [TaxId: 9606]} Length = 189

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Cancer-related NTPase, C1orf57
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.2 bits (90), Expect = 2e-04
 Identities = 11/33 (33%), Positives = 17/33 (51%)

Query: 33 NIIISGPPGVGKTTTILCLARILLGPSFKDAVL 65
          ++ ++GPPGVGKTT I   + +L          
Sbjct: 3  HVFLTGPPGVGKTTLIHKASEVLKSSGVPVDGF 35

>d1ofha_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]} Length = 309

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: HslU
species: Haemophilus influenzae [TaxId: 727]

 Score = 39.8 bits (92), Expect = 2e-04
 Identities = 30/166 (18%), Positives = 52/166 (31%), Gaps = 27/166 (16%)

Query: 33  NIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFAQ-QKVT 91
           NI++ GP GVGKT     LA++   P  K    +       G +       +        
Sbjct: 51  NILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTEVGYVGKEVDSIIRDLTDSAGGAI 110

Query: 92  LPPGRHKIVILDE------------ADSMTDGAQQALRRTMEIYSNTTRF---------- 129
               ++ IV +DE            AD   +G Q+ L   +E  + +T+           
Sbjct: 111 DAVEQNGIVFIDEIDKICKKGEYSGADVSREGVQRDLLPLVEGSTVSTKHGMVKTDHILF 170

Query: 130 ----ALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKE 171
               A        +I  +Q R  +        A    +++      
Sbjct: 171 IASGAFQVARPSDLIPELQGRLPIRVELTALSAADFERILTEPHAS 216

>d2p67a1 c.37.1.10 (A:1-327) LAO/AO transport system kinase ArgK {Escherichia coli [TaxId: 562]} Length = 327

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: LAO/AO transport system kinase ArgK
species: Escherichia coli [TaxId: 562]

 Score = 39.8 bits (92), Expect = 3e-04
 Identities = 12/46 (26%), Positives = 23/46 (50%)

Query: 23 KVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELN 68
           +    GN   + ++G PG GK+T +     +L+    K AV+ ++
Sbjct: 46 AIMPYCGNTLRLGVTGTPGAGKSTFLEAFGMLLIREGLKVAVIAVD 91

>d1okkd2 c.37.1.10 (D:97-303) GTPase domain of the signal recognition particle receptor FtsY {Thermus aquaticus [TaxId: 271]} Length = 207

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Thermus aquaticus [TaxId: 271]

 Score = 38.2 bits (88), Expect = 5e-04
 Identities = 30/149 (20%), Positives = 47/149 (31%), Gaps = 14/149 (9%)

Query: 32  PNII-ISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFAQQKV 90
             ++ + G  GVGKTTTI  L R       K      +     G   +    K  +   +
Sbjct: 6   GRVVLVVGVNGVGKTTTIAKLGRYYQNLGKKVMFCAGDTFRAAGGTQLSEWGKRLSIPVI 65

Query: 91  TLPPGRHKIVILDEADSM------------TDGAQQALRRTMEIYSNTTRFALACNNSEK 138
             P G     +  +A               T G        ME      R A+A  + E+
Sbjct: 66  QGPEGTDPAALAYDAVQAMKARGYDLLFVDTAGRLHTKHNLMEELKKVKR-AIAKADPEE 124

Query: 139 IIEPIQSRCAMLRYNKLTDAQLLSKVIEI 167
             E      A+   N L  A+   + + +
Sbjct: 125 PKEVWLVLDAVTGQNGLEQAKKFHEAVGL 153

>d2qm8a1 c.37.1.10 (A:5-327) Metallochaperone MeaB {Methylobacterium extorquens [TaxId: 408]} Length = 323

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Metallochaperone MeaB
species: Methylobacterium extorquens [TaxId: 408]

 Score = 38.7 bits (89), Expect = 6e-04
 Identities = 21/65 (32%), Positives = 32/65 (49%)

Query: 23  KVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKI 82
            V   +G    + I+G PGVGK+TTI  L  +L     K AVL ++ S+ R   ++    
Sbjct: 43  AVLPQTGRAIRVGITGVPGVGKSTTIDALGSLLTAAGHKVAVLAVDPSSTRTGGSILGDK 102

Query: 83  KMFAQ 87
              A+
Sbjct: 103 TRMAR 107

>d1gvnb_ c.37.1.21 (B:) Plasmid maintenance system epsilon/zeta, toxin zeta subunit {Streptococcus pyogenes [TaxId: 1314]} Length = 273

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
domain: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
species: Streptococcus pyogenes [TaxId: 1314]

 Score = 38.0 bits (87), Expect = 9e-04
 Identities = 24/163 (14%), Positives = 46/163 (28%), Gaps = 9/163 (5%)

Query: 8   TFSDIVGNE---DTVERLKVFSSSGNVP-NIIISGPPGVGKTTTILCLARILLGPSFKDA 63
            F+D        D +E L     +   P   ++ G PG GKT+    +     G      
Sbjct: 5   NFTDKQFENRLNDNLEELIQGKKAVESPTAFLLGGQPGSGKTSLRSAIFEETQGNVIVID 64

Query: 64  VLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIY 123
                  +    + V+   K   +          + +I   +D   +   +   RT ++ 
Sbjct: 65  NDTFKQQHPNFDELVKLYEKDVVKHVTPYSNRMTEAIISRLSDQGYNLVIEGTGRTTDVP 124

Query: 124 SNTTRFALACNNSEKIIEP-----IQSRCAMLRYNKLTDAQLL 161
             T     A     K+              + RY  +     +
Sbjct: 125 IQTATMLQAKGYETKMYVMAVPKINSYLGTIERYETMYADDPM 167

>d1ls1a2 c.37.1.10 (A:89-295) GTPase domain of the signal sequence recognition protein Ffh {Thermus aquaticus [TaxId: 271]} Length = 207

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal sequence recognition protein Ffh
species: Thermus aquaticus [TaxId: 271]

 Score = 37.4 bits (86), Expect = 0.001
 Identities = 20/142 (14%), Positives = 40/142 (28%), Gaps = 6/142 (4%)

Query: 32  PNII-ISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTV-----RNKIKMF 85
            N+  + G  G GKTTT   LA    G   +  ++  +       + +     +  + + 
Sbjct: 10  RNLWFLVGLQGSGKTTTAAKLALYYKGKGRRPLLVAADTQRPAAREQLRLLGEKVGVPVL 69

Query: 86  AQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQS 145
                  P    + V         D         ++I                  E +  
Sbjct: 70  EVMDGESPESIRRRVEEKARLEARDLILVDTAGRLQIDEPLMGELARLKEVLGPDEVLLV 129

Query: 146 RCAMLRYNKLTDAQLLSKVIEI 167
             AM     L+ A+   + + +
Sbjct: 130 LDAMTGQEALSVARAFDEKVGV 151

>d1rkba_ c.37.1.1 (A:) Adenylate kinase {Human (Homo sapiens), isoenzyme 6 [TaxId: 9606]} Length = 173

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Human (Homo sapiens), isoenzyme 6 [TaxId: 9606]

 Score = 36.5 bits (83), Expect = 0.002
 Identities = 13/25 (52%), Positives = 17/25 (68%)

Query: 31 VPNIIISGPPGVGKTTTILCLARIL 55
          +PNI+++G PGVGKTT    LA   
Sbjct: 4  LPNILLTGTPGVGKTTLGKELASKS 28

>d1y63a_ c.37.1.1 (A:) Probable kinase LmjF30.1890 {Leishmania major [TaxId: 5664]} Length = 174

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Probable kinase LmjF30.1890
species: Leishmania major [TaxId: 5664]

 Score = 36.5 bits (83), Expect = 0.002
 Identities = 12/30 (40%), Positives = 17/30 (56%)

Query: 33 NIIISGPPGVGKTTTILCLARILLGPSFKD 62
          NI+I+G PG GKT+    +A  L G    +
Sbjct: 7  NILITGTPGTGKTSMAEMIAAELDGFQHLE 36

>d1j8yf2 c.37.1.10 (F:87-297) GTPase domain of the signal sequence recognition protein Ffh {Archaeon Acidianus ambivalens [TaxId: 2283]} Length = 211

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal sequence recognition protein Ffh
species: Archaeon Acidianus ambivalens [TaxId: 2283]

 Score = 36.7 bits (84), Expect = 0.002
 Identities = 12/59 (20%), Positives = 23/59 (38%), Gaps = 1/59 (1%)

Query: 28 SGNVPNII-ISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMF 85
             +P +I + G  G GK TT   LA       FK  ++  +      ++ ++   +  
Sbjct: 8  PDKIPYVIMLVGVQGTGKATTAGKLAYFYKKKGFKVGLVGADVYRPAALEQLQQLGQQI 66

>d1ye8a1 c.37.1.11 (A:1-178) Hypothetical kinase-like protein Aq_1292 {Aquifex aeolicus [TaxId: 63363]} Length = 178

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hypothetical kinase-like protein Aq 1292
species: Aquifex aeolicus [TaxId: 63363]

 Score = 36.1 bits (82), Expect = 0.002
 Identities = 12/22 (54%), Positives = 15/22 (68%)

Query: 34 IIISGPPGVGKTTTILCLARIL 55
          III+G PGVGKTT +  +   L
Sbjct: 3  IIITGEPGVGKTTLVKKIVERL 24

>d1nksa_ c.37.1.1 (A:) Adenylate kinase {Archaeon Sulfolobus acidocaldarius [TaxId: 2285]} Length = 194

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Archaeon Sulfolobus acidocaldarius [TaxId: 2285]

 Score = 36.1 bits (82), Expect = 0.002
 Identities = 22/161 (13%), Positives = 50/161 (31%), Gaps = 4/161 (2%)

Query: 34  IIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFAQQKVTLP 93
            I++G PGVGK+T +  +  IL           +N  +      ++        +   L 
Sbjct: 4   GIVTGIPGVGKSTVLAKVKEILDNQGIN--NKIINYGDFMLATALKLGYAKDRDEMRKLS 61

Query: 94  PGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYN 153
             + K + +D A  + + A+        ++ +T       +     +             
Sbjct: 62  VEKQKKLQIDAAKGIAEEARAGGEGY--LFIDTHAVIRTPSGYLPGLPSYVITEINPSVI 119

Query: 154 KLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQA 194
            L +A     +         +  +   E+++       R A
Sbjct: 120 FLLEADPKIILSRQKRDTTRNRNDYSDESVILETINFARYA 160

>d1lw7a2 c.37.1.1 (A:220-411) Transcriptional regulator NadR, ribosylnicotinamide kinase domain {Haemophilus influenzae [TaxId: 727]} Length = 192

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Transcriptional regulator NadR, ribosylnicotinamide kinase domain
species: Haemophilus influenzae [TaxId: 727]

 Score = 36.2 bits (82), Expect = 0.003
 Identities = 9/55 (16%), Positives = 15/55 (27%)

Query: 33 NIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFAQ 87
           + I G    GK+  +  LA +    S  +   E       G +           
Sbjct: 9  TVAILGGESSGKSVLVNKLAAVFNTTSAWEYGREFVFEKLGGDEQAMQYSDYPQM 63

>d1xjca_ c.37.1.10 (A:) Molybdopterin-guanine dinucleotide biosynthesis protein MobB {Bacillus stearothermophilus [TaxId: 1422]} Length = 165

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Molybdopterin-guanine dinucleotide biosynthesis protein MobB
species: Bacillus stearothermophilus [TaxId: 1422]

 Score = 35.2 bits (80), Expect = 0.004
 Identities = 5/43 (11%), Positives = 13/43 (30%)

Query: 34 IIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGID 76
            + G    GKTT +       +   ++   ++ +        
Sbjct: 4  WQVVGYKHSGKTTLMEKWVAAAVREGWRVGTVKHHGHGGEPAR 46

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	317
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	100.0
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	100.0
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	100.0
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	100.0
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	100.0
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	100.0
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	100.0
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	100.0
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	99.97
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	99.97
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	99.94
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	99.89
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	99.88
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	99.86
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	99.82
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	99.82
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	99.77
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	99.74
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	99.71
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	99.7
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	99.67
d1g8pa_	333	ATPase subunit of magnesium chelatase, BchI {Rhodo	99.64
d1r6bx3	315	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	99.63
d1qvra3	315	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	99.62
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	99.6
d1ny5a2	247	Transcriptional activator sigm54 (NtrC1), C-termin	99.59
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	99.56
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	99.54
d1svma_	362	Papillomavirus large T antigen helicase domain {Si	99.38
d1w44a_	321	NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}	99.28
d1iqpa1	95	Replication factor C {Archaeon Pyrococcus furiosus	99.23
d2fnaa2	283	Archaeal ATPase SSO1545 {Sulfolobus solfataricus [	99.19
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	99.07
d1sxjd1	91	Replication factor C2 {Baker's yeast (Saccharomyce	99.05
d1sxjc1	95	Replication factor C3 {Baker's yeast (Saccharomyce	99.0
d1sxjb1	92	Replication factor C4 {Baker's yeast (Saccharomyce	98.98
d2a5yb3	277	CED-4, NB-ARC domain {Caenorhabditis elegans [TaxI	98.86
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	98.59
d1tuea_	205	Replication protein E1 helicase domain {Human papi	98.56
d2pmka1	241	Haemolysin B ATP-binding protein {Escherichia coli	98.46
d1sxje1	99	Replication factor C5 {Baker's yeast (Saccharomyce	98.37
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	98.35
d3b60a1	253	Multidrug resistance ABC transporter MsbA, C-termi	98.32
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	98.25
d2hyda1	255	Putative multidrug export ATP-binding/permease pro	98.25
d1jj7a_	251	Peptide transporter Tap1, C-terminal ABC domain {H	98.23
d1jqlb_	140	delta subunit of DNA polymerase III, N-domain {Esc	98.23
d1jr3d1	127	delta subunit {Escherichia coli [TaxId: 562]}	98.21
d1jr3a1	126	gamma subunit {Escherichia coli [TaxId: 562]}	98.12
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	98.11
d1mv5a_	242	Multidrug resistance ABC transporter LmrA, C-termi	98.1
d1u0ja_	267	Rep 40 protein helicase domain {Adeno-associated v	98.09
d1l2ta_	230	MJ0796 {Archaeon Methanococcus jannaschii [TaxId:	98.08
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	98.08
d1yksa1	140	YFV helicase domain {Yellow fever virus [TaxId: 11	98.05
d2qy9a2	211	GTPase domain of the signal recognition particle r	98.0
d3d31a2	229	Sulfate/molybdate ABC transporter, ATP-binding pro	97.97
d1v43a3	239	Hypothetical protein PH0022, N-terminal domain {Py	97.96
d3dhwc1	240	Methionine import ATP-binding protein MetN {Escher	97.94
d1okkd2	207	GTPase domain of the signal recognition particle r	97.94
d1yj5a2	172	5' polynucleotide kinase-3' phosphatase, C-termina	97.93
d2awna2	232	Maltose transport protein MalK, N-terminal domain	97.92
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	97.9
d1vmaa2	213	GTPase domain of the signal recognition particle r	97.89
d1j8yf2	211	GTPase domain of the signal sequence recognition p	97.84
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	97.82
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	97.8
d1e6ca_	170	Shikimate kinase (AroK) {Erwinia chrysanthemi [Tax	97.79
d1veca_	206	DEAD box RNA helicase rck/p54 {Human (Homo sapiens	97.78
d1qdea_	212	Initiation factor 4a {Baker's yeast (Saccharomyces	97.74
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	97.73
d2iyva1	165	Shikimate kinase (AroK) {Mycobacterium tuberculosi	97.73
d2onka1	240	Molybdate/tungstate import ATP-binding protein Wtp	97.73
d1g2912	240	Maltose transport protein MalK, N-terminal domain	97.71
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	97.7
d2g9na1	218	Initiation factor 4a {Human (Homo sapiens) [TaxId:	97.69
d1t6na_	207	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	97.67
d1s2ma1	206	Putative ATP-dependent RNA helicase DHH1 {Baker's	97.67
d1x6va3	195	Adenosine-5'phosphosulfate kinase (APS kinase) {Hu	97.67
d1vpla_	238	Putative ABC transporter TM0544 {Thermotoga mariti	97.66
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	97.65
d1np6a_	170	Molybdopterin-guanine dinucleotide biosynthesis pr	97.65
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	97.65
d1ji0a_	240	Branched chain aminoacid ABC transporter {Thermoto	97.65
d1ls1a2	207	GTPase domain of the signal sequence recognition p	97.63
d2cdna1	181	Adenylate kinase {Mycobacterium tuberculosis [TaxI	97.63
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	97.63
d1qf9a_	194	UMP/CMP kinase {Dictyostelium discoideum [TaxId: 4	97.61
d1viaa_	161	Shikimate kinase (AroK) {Campylobacter jejuni [Tax	97.6
d1g6ha_	254	MJ1267 {Archaeon Methanococcus jannaschii [TaxId:	97.59
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	97.58
d1bifa1	213	6-phosphofructo-2-kinase/fructose-2,6-bisphosphata	97.56
d1wp9a1	200	putative ATP-dependent RNA helicase PF2015 {Pyroco	97.54
d1qhxa_	178	Chloramphenicol phosphotransferase {Streptomyces v	97.52
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	97.51
d1zaka1	189	Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}	97.5
d1sgwa_	200	Putative ABC transporter PF0895 {Pyrococcus furios	97.5
d1r0wa_	281	Cystic fibrosis transmembrane conductance regulato	97.48
d1b0ua_	258	ATP-binding subunit of the histidine permease {Sal	97.48
d1l7vc_	231	ABC transporter involved in vitamin B12 uptake, Bt	97.47
d1hv8a1	208	Putative DEAD box RNA helicase {Archaeon Methanoco	97.46
d1oxxk2	242	Glucose transport protein GlcV, N-terminal domain	97.45
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	97.44
d1ukza_	196	Uridylate kinase {Baker's yeast (Saccharomyces cer	97.44
d1teva_	194	UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]	97.43
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	97.4
d2fz4a1	206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	97.37
d1khta_	190	Adenylate kinase {Archaeon Methanococcus voltae [T	97.37
d1u94a1	263	RecA protein, ATPase-domain {Escherichia coli [Tax	97.36
d1zina1	182	Adenylate kinase {Bacillus stearothermophilus [Tax	97.35
d1q0ua_	209	Probable DEAD box RNA helicase YqfR {Bacillus stea	97.33
d1p9ra_	401	Extracellular secretion NTPase EpsE {Vibrio choler	97.32
d1s3ga1	182	Adenylate kinase {Bacillus globisporus [TaxId: 145	97.26
d2p6ra3	202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	97.26
d1ckea_	225	CMP kinase {Escherichia coli [TaxId: 562]}	97.26
d3adka_	194	Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}	97.24
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	97.23
d1ak2a1	190	Adenylate kinase {Cow (Bos taurus), mitochondrial	97.22
d2ak3a1	189	Adenylate kinase {Cow (Bos taurus), mitochondrial	97.21
d1akya1	180	Adenylate kinase {Baker's yeast (Saccharomyces cer	97.2
d1rz3a_	198	Hypothetical protein rbstp0775 {Bacillus stearothe	97.2
d1e4va1	179	Adenylate kinase {Escherichia coli [TaxId: 562]}	97.15
d1nksa_	194	Adenylate kinase {Archaeon Sulfolobus acidocaldari	97.11
d1m7ga_	208	Adenosine-5'phosphosulfate kinase (APS kinase) {Fu	97.08
d1xp8a1	268	RecA protein, ATPase-domain {Deinococcus radiodura	97.04
d1q3ta_	223	CMP kinase {Streptococcus pneumoniae [TaxId: 1313]	96.95
d4tmka_	210	Thymidylate kinase {Escherichia coli [TaxId: 562]}	96.93
d3ctda1	163	Uncharacterized protein YrvN {Prochlorococcus mari	96.88
d2gj8a1	161	Probable tRNA modification GTPase TrmE (MnmE), G d	96.86
d1xjca_	165	Molybdopterin-guanine dinucleotide biosynthesis pr	96.81
d1z2aa1	164	Rab23 {Mouse (Mus musculus) [TaxId: 10090]}	96.81
d1pzna2	254	DNA repair protein Rad51, catalytic domain {Archae	96.81
d2p67a1	327	LAO/AO transport system kinase ArgK {Escherichia c	96.78
d1mo6a1	269	RecA protein, ATPase-domain {Mycobacterium tubercu	96.7
d1n0wa_	242	DNA repair protein Rad51, catalytic domain {Human	96.7
d2qm8a1	323	Metallochaperone MeaB {Methylobacterium extorquens	96.7
d1gkya_	186	Guanylate kinase {Baker's yeast (Saccharomyces cer	96.69
d1lvga_	190	Guanylate kinase {Mouse (Mus musculus) [TaxId: 100	96.68
d1wf3a1	178	GTPase Era, N-terminal domain {Thermus thermophilu	96.67
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	96.67
d1r8sa_	160	ADP-ribosylation factor {Human (Homo sapiens), ARF	96.64
d2qw6a1	88	Uncharacterized protein EfaeDRAFT_0938 {Enterococc	96.58
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	96.57
d1znwa1	182	Guanylate kinase {Mycobacterium tuberculosis [TaxI	96.56
d1ewqa2	224	DNA repair protein MutS, the C-terminal domain {Th	96.54
d3bgea1	184	Uncharacterized protein NTHI1458 {Haemophilus infl	96.5
d1zj6a1	177	ADP-ribosylation factor {Human (Homo sapiens), ARL	96.5
d1v5wa_	258	Meiotic recombination protein DMC1/LIM15 homolog {	96.49
d1uj2a_	213	Uridine-cytidine kinase 2 {Human (Homo sapiens) [T	96.49
d1wb9a2	234	DNA repair protein MutS, the C-terminal domain {Es	96.49
d1r2qa_	170	Rab5a {Human (Homo sapiens) [TaxId: 9606]}	96.41
d1zd9a1	164	ADP-ribosylation factor {Human (Homo sapiens), ARL	96.36
d2ew1a1	171	Rab30 {Human (Homo sapiens) [TaxId: 9606]}	96.35
d1nn5a_	209	Thymidylate kinase {Human (Homo sapiens) [TaxId: 9	96.34
d2fh5b1	207	Signal recognition particle receptor beta-subunit	96.33
d1htwa_	158	Hypothetical protein HI0065 {Haemophilus influenza	96.33
d1s96a_	205	Guanylate kinase {Escherichia coli [TaxId: 562]}	96.31
d1kaoa_	167	Rap2a {Human (Homo sapiens) [TaxId: 9606]}	96.25
d1odfa_	286	Hypothetical protein Ygr205W {Baker's yeast (Sacch	96.19
d1z0fa1	166	Rab14 {Human (Homo sapiens) [TaxId: 9606]}	96.13
d1kgda_	178	Guanylate kinase-like domain of Cask {Human (Homo	96.1
d2r9ga1	186	Uncharacterized protein EfaeDRAFT_0938 {Enterococc	96.07
d1u8za_	168	Ras-related protein RalA {Cotton-top tamarin (Sagu	96.07
d1ctqa_	166	cH-p21 Ras protein {Human (Homo sapiens) [TaxId: 9	96.06
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	96.06
d1sq5a_	308	Pantothenate kinase PanK {Escherichia coli [TaxId:	96.05
d1kmqa_	177	RhoA {Human (Homo sapiens) [TaxId: 9606]}	96.01
d1tf7a1	242	Circadian clock protein KaiC {Synechococcus sp. st	96.01
d3raba_	169	Rab3a {Rat (Rattus norvegicus) [TaxId: 10116]}	95.99
d1gsia_	208	Thymidylate kinase {Mycobacterium tuberculosis [Ta	95.98
d2i1qa2	258	DNA repair protein Rad51, catalytic domain {Archae	95.96
d1mkya1	171	Probable GTPase Der, N-terminal and middle domains	95.89
d2fn4a1	173	r-Ras {Human (Homo sapiens) [TaxId: 9606]}	95.88
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	95.86
d1a7ja_	288	Phosphoribulokinase {Rhodobacter sphaeroides [TaxI	95.85
d2erya1	171	r-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	95.84
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	95.8
d1g5ta_	157	ATP:corrinoid adenosyltransferase CobA {Salmonella	95.79
d1x1ra1	169	Ras-related protein M-Ras (XRas) {Mouse (Mus muscu	95.78
d1yzqa1	164	Rab6 {Human (Homo sapiens) [TaxId: 9606]}	95.71
d1yrba1	244	ATP(GTP)-binding protein PAB0955 {Pyrococcus abyss	95.66
d2atxa1	185	RhoQ {Human (Homo sapiens) [TaxId: 9606]}	95.63
d2vp4a1	197	Deoxyribonucleoside kinase {Fruit fly (Drosophila	95.63
d2gjsa1	168	Rad {Human (Homo sapiens) [TaxId: 9606]}	95.61
d1h65a_	257	Chloroplast protein translocon GTPase Toc34 {Garde	95.61
d1f6ba_	186	SAR1 {Chinese hamster (Cricetulus griseus) [TaxId:	95.58
d1nrjb_	209	Signal recognition particle receptor beta-subunit	95.57
d1c1ya_	167	Rap1A {Human (Homo sapiens) [TaxId: 9606]}	95.51
d1rifa_	282	DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]	95.5
d1u0la2	225	Probable GTPase EngC (YjeQ), C-terminal domain {Th	95.48
d2bcgy1	194	GTPase Ytp1 {Baker's yeast (Saccharomyces cerevisi	95.45
d1svia_	195	Probable GTPase EngB {Bacillus subtilis [TaxId: 14	95.45
d1kkma_	176	HPr kinase HprK C-terminal domain {Lactobacillus c	95.4
d1i2ma_	170	Ran {Human (Homo sapiens) [TaxId: 9606]}	95.39
d2bmea1	174	Rab4a {Human (Homo sapiens) [TaxId: 9606]}	95.38
d2ngra_	191	CDC42 {Human (Homo sapiens) [TaxId: 9606]}	95.38
d1upta_	169	ADP-ribosylation factor {Human (Homo sapiens), ARL	95.34
d1uf9a_	191	Dephospho-CoA kinase {Thermus thermophilus [TaxId:	95.3
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	95.29
d1tmka_	214	Thymidylate kinase {Baker's yeast (Saccharomyces c	95.29
d2g6ba1	170	Rab26 {Human (Homo sapiens) [TaxId: 9606]}	95.25
d2qtvb1	166	SAR1 {Baker's yeast (Saccharomyces cerevisiae) [Ta	95.25
d1e2ka_	329	Thymidine kinase {Herpes simplex virus type 1, dif	95.2
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	95.12
d1puia_	188	Probable GTPase EngB {Escherichia coli [TaxId: 562	95.12
d2fu5c1	173	Rab8a {Mouse (Mus musculus) [TaxId: 10090]}	95.04
d2a5ja1	173	Rab2b {Human (Homo sapiens) [TaxId: 9606]}	95.02
d1knxa2	177	HPr kinase HprK C-terminal domain {Mycoplasma pneu	95.0
d1ksha_	165	ADP-ribosylation factor {Mouse (Mus musculus), ARL	94.92
d2ocpa1	241	Deoxyguanosine kinase {Human (Homo sapiens) [TaxId	94.86
d1ko7a2	169	HPr kinase HprK C-terminal domain {Staphylococcus	94.82
d1oywa2	206	RecQ helicase domain {Escherichia coli [TaxId: 562	94.8
g1f2t.1	292	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	94.6
d2f9la1	175	Rab11b {Human (Homo sapiens) [TaxId: 9606]}	94.57
d2atva1	168	Ras-like estrogen-regulated growth inhibitor, RERG	94.55
d1z08a1	167	Rab21 {Human (Homo sapiens) [TaxId: 9606]}	94.54
d1vhta_	208	Dephospho-CoA kinase {Escherichia coli [TaxId: 562	94.53
d2f7sa1	186	Rab27b {Human (Homo sapiens) [TaxId: 9606]}	94.53
d1nlfa_	274	Hexameric replicative helicase repA {Escherichia c	94.53
d1wmsa_	174	Rab9a {Human (Homo sapiens) [TaxId: 9606]}	94.51
d1mh1a_	183	Rac {Human (Homo sapiens) [TaxId: 9606]}	94.51
d1p5zb_	241	Deoxycytidine kinase {Human (Homo sapiens) [TaxId:	94.48
d1ky3a_	175	Rab-related protein ypt7p {Baker's yeast (Saccharo	94.4
d1g16a_	166	Rab-related protein Sec4 {Baker's yeast (Saccharom	94.32
d1jjva_	205	Dephospho-CoA kinase {Haemophilus influenzae [TaxI	94.27
d1z06a1	165	Rab-33b {Mouse (Mus musculus) [TaxId: 10090]}	94.24
d2erxa1	171	di-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	94.22
d1ihua2	279	Arsenite-translocating ATPase ArsA {Escherichia co	94.22
d1d0xa2	712	Myosin S1, motor domain {Dictyostelium discoideum	94.14
d1vg8a_	184	Rab7 {Rat (Rattus norvegicus) [TaxId: 10116]}	94.11
d2mysa2	794	Myosin S1, motor domain {Chicken (Gallus gallus),	94.09
d1z63a1	230	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	94.07
d1xtqa1	167	GTP-binding protein RheB {Human (Homo sapiens) [Ta	94.06
d1z0ja1	167	Rab-22a {Mouse (Mus musculus) [TaxId: 10090]}	94.03
d1wb1a4	179	Elongation factor SelB, N-terminal domain {Methano	94.03
d1nija1	222	Hypothetical protein YjiA, N-terminal domain {Esch	94.02
d2cxxa1	184	GTP-binding protein engB {Pyrococcus horikoshii [T	94.02
d1qhla_	222	Cell division protein MukB {Escherichia coli [TaxI	93.99
d1lkxa_	684	Myosin S1, motor domain {Dictyostelium discoideum,	93.98
d1fzqa_	176	ADP-ribosylation factor {Mouse (Mus musculus), ARL	93.96
d1x3sa1	177	Rab18 {Human (Homo sapiens) [TaxId: 9606]}	93.86
d1ihua1	296	Arsenite-translocating ATPase ArsA {Escherichia co	93.85
d1g7sa4	227	Initiation factor IF2/eIF5b, N-terminal (G) domain	93.84
d1ek0a_	170	Ypt51 {Baker's yeast (Saccharomyces cerevisiae) [T	93.8
d2bv3a2	276	Elongation factor G (EF-G), N-terminal (G) domain	93.77
d2g3ya1	172	GTP-binding protein GEM {Human (Homo sapiens) [Tax	93.67
d1e9ra_	433	Bacterial conjugative coupling protein TrwB {Esche	93.65
d1udxa2	180	Obg GTP-binding protein middle domain {Thermus the	93.65
d1br2a2	710	Myosin S1, motor domain {Chicken (Gallus gallus),	93.64
d1e0sa_	173	ADP-ribosylation factor {Human (Homo sapiens), ARF	93.59
d1m7ba_	179	RhoE (RND3) {Mouse (Mus musculus) [TaxId: 10090]}	93.54
d1moza_	182	ADP-ribosylation factor {Baker's yeast (Saccharomy	93.48
d1lnza2	185	Obg GTP-binding protein middle domain {Bacillus su	93.48
d1kk8a2	789	Myosin S1, motor domain {Bay scallop (Aequipecten	93.47
g1xew.1	329	Smc head domain {Pyrococcus furiosus [TaxId: 2261]	93.4
d1deka_	241	Deoxynucleoside monophosphate kinase {Bacteriophag	93.33
g1ii8.1	369	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	93.26
d1w7ja2	730	Myosin S1, motor domain {Chicken (Gallus gallus),	93.16
d1egaa1	179	GTPase Era, N-terminal domain {Escherichia coli [T	92.95
d1n0ua2	341	Elongation factor 2 (eEF-2), N-terminal (G) domain	92.57
d1mkya2	186	Probable GTPase Der, N-terminal and middle domains	92.37
d1zcba2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	92.33
d1g8fa3	122	ATP sulfurylase C-terminal domain {Baker's yeast (	92.12
d1cp2a_	269	Nitrogenase iron protein {Clostridium pasteurianum	92.08
d2bmja1	175	Centaurin gamma 1, G domain {Human (Homo sapiens)	91.95
d1p6xa_	333	Thymidine kinase {Equine herpesvirus type 4 [TaxId	91.88
d1xzpa2	160	TrmE GTPase domain {Thermotoga maritima [TaxId: 23	91.85
d2b8ta1	139	Thymidine kinase, TK1, N-terminal domain {Ureaplas	91.78
d1e69a_	308	Smc head domain {Thermotoga maritima [TaxId: 2336]	91.78
d1xbta1	133	Thymidine kinase, TK1, N-terminal domain {Human (H	91.7
d1tq4a_	400	Interferon-inducible GTPase {Mouse (Mus musculus)	91.69
d1azta2	221	Transducin (alpha subunit) {Cow (Bos taurus) [TaxI	91.66
d1byia_	224	Dethiobiotin synthetase {Escherichia coli [TaxId:	91.62
d2dy1a2	267	Elongation factor G (EF-G), N-terminal (G) domain	91.46
d1osna_	331	Thymidine kinase {Varicella-zoster virus [TaxId: 1	91.19
d2bcjq2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	91.19
d1d2ea3	196	Elongation factor Tu (EF-Tu), N-terminal (G) domai	91.1
d2c78a3	204	Elongation factor Tu (EF-Tu), N-terminal (G) domai	91.09
d1xx6a1	141	Thymidine kinase, TK1, N-terminal domain {Clostrid	91.05
d2jdid3	276	Central domain of beta subunit of F1 ATP synthase	90.97
d1t9ha2	231	Probable GTPase EngC (YjeQ), C-terminal domain {Ba	90.86
d2jdia3	285	Central domain of alpha subunit of F1 ATP synthase	90.86
d1xpua3	289	Transcription termination factor Rho, ATPase domai	90.68
d1w1wa_	427	Smc head domain {Baker's yeast (Saccharomyces cere	90.56
d2afhe1	289	Nitrogenase iron protein {Azotobacter vinelandii [	90.32
d1svsa1	195	Transducin (alpha subunit) {Rat (Rattus norvegicus	89.7
d1j3ba1	318	Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxalo	89.28
d2olra1	313	Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxalo	88.86
d1bg2a_	323	Kinesin {Human (Homo sapiens) [TaxId: 9606]}	88.8
d1z3ix2	298	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	87.93
d1ii2a1	323	Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxalo	87.54
d1hyqa_	232	Cell division regulator MinD {Archaeon Archaeoglob	87.33
d1e69a_	308	Smc head domain {Thermotoga maritima [TaxId: 2336]	86.81
g1f2t.1	292	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	86.66
d1goja_	354	Kinesin {Neurospora crassa [TaxId: 5141]}	86.5
d1ry6a_	330	Kinesin {Malaria parasite (Plasmodium falciparum)	85.78
d1x88a1	345	Kinesin {Human (Homo sapiens), mitotic kinesin eg5	85.33
d2zfia1	349	Kinesin {Mouse (Mus musculus), kif1a [TaxId: 10090	84.73
d1f9va_	342	Kinesin motor Ncd (non-claret disjunctional) {Bake	84.6
d1g3qa_	237	Cell division regulator MinD {Archaeon Pyrococcus	84.0
d2ncda_	368	Kinesin motor Ncd (non-claret disjunctional) {Frui	83.68
d1sdma_	364	Kinesin heavy chain-like protein {Potato (Solanum	83.67
d1t5la1	413	Nucleotide excision repair enzyme UvrB {Bacillus c	83.61
d1fx0a3	276	Central domain of alpha subunit of F1 ATP synthase	83.34
d1v8ka_	362	Kinesin {Mouse (Mus musculus), kif2c [TaxId: 10090	82.93
g1qhh.1	623	DEXX box DNA helicase {Bacillus stearothermophilus	81.27

>d1sxjb2 c.37.1.20 (B:7-230) Replication factor C4 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C4
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=8.2e-43  Score=288.76  Aligned_cols=218  Identities=67%  Similarity=1.066  Sum_probs=202.2

Q ss_pred             CcccCCCCCCcccCCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHH
Q psy879            1 IEKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRN   80 (317)
Q Consensus         1 ~~ky~P~~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~   80 (317)
                      +|||||++|+|++||+++++.|..+++++..||++|+||||+|||++|+.+++++.+......++++++++..+...+..
T Consensus         6 ~eKyrP~~~~d~ig~~~~~~~L~~~~~~~~~~~~ll~Gp~G~GKTt~a~~la~~l~~~~~~~~~~~~n~~~~~~~~~i~~   85 (224)
T d1sxjb2           6 VEKYRPQVLSDIVGNKETIDRLQQIAKDGNMPHMIISGMPGIGKTTSVHCLAHELLGRSYADGVLELNASDDRGIDVVRN   85 (224)
T ss_dssp             HHHTCCSSGGGCCSCTHHHHHHHHHHHSCCCCCEEEECSTTSSHHHHHHHHHHHHHGGGHHHHEEEECTTSCCSHHHHHT
T ss_pred             HhHhCCCCHHHhcCCHHHHHHHHHHHHcCCCCeEEEECCCCCCchhhHHHHHHHHhccccccccccccccccCCceehhh
Confidence            48999999999999999999999999999999999999999999999999999997765556688999998888888888


Q ss_pred             HHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcCchhHhhhcceeeecCCCHHHH
Q psy879           81 KIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQL  160 (317)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~~~i~sR~~~i~f~~~~~~~~  160 (317)
                      .+..+...........++++|+||+|.+....+++|+..+++++.++.++++++...++.++++|||..++|++|+.+++
T Consensus        86 ~~~~~~~~~~~~~~~~~kviiiDe~d~~~~~~~~~ll~~~e~~~~~~~~i~~~~~~~~i~~~l~sr~~~i~~~~~~~~~i  165 (224)
T d1sxjb2          86 QIKHFAQKKLHLPPGKHKIVILDEADSMTAGAQQALRRTMELYSNSTRFAFACNQSNKIIEPLQSQCAILRYSKLSDEDV  165 (224)
T ss_dssp             HHHHHHHBCCCCCTTCCEEEEEESGGGSCHHHHHTTHHHHHHTTTTEEEEEEESCGGGSCHHHHTTSEEEECCCCCHHHH
T ss_pred             HHHHHHHhhccCCCcceEEEEEecccccchhHHHHHhhhccccccceeeeeccCchhhhhhHHHHHHHHhhhcccchhhh
Confidence            88877777666666788999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhhCCCcccHHHHHhhcC
Q psy879          161 LSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCD  218 (317)
Q Consensus       161 ~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~~~~~i~~~~v~~~~~  218 (317)
                      ..+|..+++++++.+++++++.++..++||+|.|++.||.++.+.+.|+.+.|.++++
T Consensus       166 ~~~l~~i~~~e~~~i~~~~l~~I~~~s~Gd~R~ai~~Lq~~~~~~~~i~~~~i~~~~d  223 (224)
T d1sxjb2         166 LKRLLQIIKLEDVKYTNDGLEAIIFTAEGDMRQAINNLQSTVAGHGLVNADNVFKIVD  223 (224)
T ss_dssp             HHHHHHHHHHHTCCBCHHHHHHHHHHHTTCHHHHHHHHHHHHHHHSSBCHHHHHHHHT
T ss_pred             HHHHHHHHHhcccCCCHHHHHHHHHHcCCcHHHHHHHHHHHHHcCCCcCHHHHHHHhC
Confidence            9999999999999999999999999999999999999999888778899988877654

>d1njfa_ c.37.1.20 (A:) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=100.00  E-value=7.6e-42  Score=285.35  Aligned_cols=214  Identities=28%  Similarity=0.412  Sum_probs=191.3

Q ss_pred             cccCCCCCCcccCCHHHHHHHHHHHhcCCCce-EEEECCCCCCHHHHHHHHHHHHcCCCCC-------------------
Q psy879            2 EKYRPQTFSDIVGNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARILLGPSFK-------------------   61 (317)
Q Consensus         2 ~ky~P~~~~~~~g~~~~~~~l~~~l~~~~~~~-~ll~G~~G~GKt~la~~la~~l~~~~~~-------------------   61 (317)
                      +||||++|+|++||+++++.|..++.++++|| +|||||||+|||++|+++++.+.+....                   
T Consensus         4 ~KyrP~~~~dlig~~~~~~~L~~~i~~~~~~~~~Ll~Gp~G~GKtt~a~~~~~~l~~~~~~~~~~~~~~~~~~~i~~~~~   83 (239)
T d1njfa_           4 RKWRPQTFADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKGLNCETGITATPCGVCDNCREIEQGRF   83 (239)
T ss_dssp             HHTCCSSGGGSCSCHHHHHHHHHHHHTTCCCSEEEEECSTTSSHHHHHHHHHHHHHCTTCSCSSCCSCSHHHHHHHHTCC
T ss_pred             hhhCCCCHHHccChHHHHHHHHHHHHcCCCCeeEEEECCCCCcHHHHHHHHHHHhcCccccccCccccchHHHHHHcCCC
Confidence            79999999999999999999999999999988 9999999999999999999998754321                   


Q ss_pred             CceEEecCCCCcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcCch
Q psy879           62 DAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIE  141 (317)
Q Consensus        62 ~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~~  141 (317)
                      ..+++++..+..+.+.+++.++.+...+   ..+.++|+||||+|.|+.+++++|+++||+|+.++.||++||+..++.+
T Consensus        84 ~~~~~~~~~~~~~i~~ir~~~~~~~~~~---~~~~~kviiIde~d~l~~~~q~~Llk~lE~~~~~~~~il~tn~~~~i~~  160 (239)
T d1njfa_          84 VDLIEIDAASRTKVEDTRDLLDNVQYAP---ARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPV  160 (239)
T ss_dssp             TTEEEEETTCSSSHHHHHHHHHSCCCSC---SSSSSEEEEEETGGGSCHHHHHHHHHHHHSCCTTEEEEEEESCGGGSCH
T ss_pred             CeEEEecchhcCCHHHHHHHHHHHHhcc---ccCCCEEEEEECcccCCHHHHHHHHHHHhcCCCCeEEEEEcCCccccCh
Confidence            1356777777778888888776654433   3367899999999999999999999999999999999999999999999


Q ss_pred             hHhhhcceeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHh-hhCCCcccHHHHHhhcC
Q psy879          142 PIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQST-HNGFGHVTAEYVFKVCD  218 (317)
Q Consensus       142 ~i~sR~~~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~-~~~~~~i~~~~v~~~~~  218 (317)
                      +++|||..+.|++++.+++..++..++..++..+++++++.++..++||+|++++.++.+ +.+.+.|+.++|.++++
T Consensus       161 ~i~SRc~~i~~~~~~~~~i~~~l~~i~~~e~~~~~~~~l~~i~~~s~Gd~R~ain~l~~~~~~~~~~I~~~~v~~~lg  238 (239)
T d1njfa_         161 TILSRCLQFHLKALDVEQIRHQLEHILNEEHIAHEPRALQLLARAAEGSLRDALSLTDQAIASGDGQVSTQAVSAMLG  238 (239)
T ss_dssp             HHHTTSEEEECCCCCHHHHHHHHHHHHHHHTCCBCHHHHHHHHHHTTTCHHHHHHHHHHHHHHTTTSBCHHHHHHHHT
T ss_pred             hHhhhhcccccccCcHHHhhhHHHHHHhhhccCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhCCCCcCHHHHHHHhC
Confidence            999999999999999999999999999999999999999999999999999999999864 44678899999987764

>d1sxjc2 c.37.1.20 (C:12-238) Replication factor C3 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C3
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=9.3e-41  Score=276.98  Aligned_cols=217  Identities=37%  Similarity=0.698  Sum_probs=193.4

Q ss_pred             CcccCCCCCCcccCCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHH
Q psy879            1 IEKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRN   80 (317)
Q Consensus         1 ~~ky~P~~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~   80 (317)
                      +|||||++|+|++||+++++.|..++.++.+||++||||||+|||++++++++++.+......+.+.+.++..+.+....
T Consensus         5 ~ekyrP~~~~divg~~~~~~~L~~~i~~~~~~~lLl~Gp~G~GKttl~~~la~~l~~~~~~~~~~e~~~~~~~~~~~~~~   84 (227)
T d1sxjc2           5 VEKYRPETLDEVYGQNEVITTVRKFVDEGKLPHLLFYGPPGTGKTSTIVALAREIYGKNYSNMVLELNASDDRGIDVVRN   84 (227)
T ss_dssp             HHHTCCSSGGGCCSCHHHHHHHHHHHHTTCCCCEEEECSSSSSHHHHHHHHHHHHHTTSHHHHEEEECTTSCCSHHHHHT
T ss_pred             hhhhCCCCHHHccCcHHHHHHHHHHHHcCCCCeEEEECCCCCChhHHHHHHHHHhhcCCCcceeEEecccccCCeeeeec
Confidence            48999999999999999999999999999999999999999999999999999998776666678888887777776665


Q ss_pred             HHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcCchhHhhhcceeeecCCCHHHH
Q psy879           81 KIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQL  160 (317)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~~~i~sR~~~i~f~~~~~~~~  160 (317)
                      ......... ......++++||||+|.+....+++|++.+++++.++.++++++...+++++++|||..+.|++++.+++
T Consensus        85 ~~~~~~~~~-~~~~~~~kiiiiDe~d~~~~~~~~~Ll~~le~~~~~~~~~~~~~~~~~i~~~i~sr~~~i~~~~~~~~~i  163 (227)
T d1sxjc2          85 QIKDFASTR-QIFSKGFKLIILDEADAMTNAAQNALRRVIERYTKNTRFCVLANYAHKLTPALLSQCTRFRFQPLPQEAI  163 (227)
T ss_dssp             HHHHHHHBC-CSSSCSCEEEEETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHTTSEEEECCCCCHHHH
T ss_pred             chhhccccc-cccCCCeEEEEEeccccchhhHHHHHHHHhhhcccceeeccccCcHHHhHHHHHHHHhhhcccccccccc
Confidence            555444432 2234567899999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhh-----CCCcccHHHHHhhcC
Q psy879          161 LSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHN-----GFGHVTAEYVFKVCD  218 (317)
Q Consensus       161 ~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~-----~~~~i~~~~v~~~~~  218 (317)
                      .++|.+++..+++.+++++++.+++.++||+|.+++.||.+..     +...|+.++|.++++
T Consensus       164 ~~~l~~I~~~e~i~i~~~~l~~i~~~s~Gd~R~ain~Lq~~~~~~~~~~~~~It~~~v~e~~g  226 (227)
T d1sxjc2         164 ERRIANVLVHEKLKLSPNAEKALIELSNGDMRRVLNVLQSCKATLDNPDEDEISDDVIYECCG  226 (227)
T ss_dssp             HHHHHHHHHTTTCCBCHHHHHHHHHHHTTCHHHHHHHTTTTTTTTCSSSCCCBCHHHHHHHTT
T ss_pred             ccccccccccccccCCHHHHHHHHHHcCCcHHHHHHHHHHHHHhcCCCCCCeeCHHHHHHHhC
Confidence            9999999999999999999999999999999999999998654     346789998888765

>d1iqpa2 c.37.1.20 (A:2-232) Replication factor C {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=100.00  E-value=1.1e-39  Score=271.26  Aligned_cols=216  Identities=50%  Similarity=0.826  Sum_probs=193.2

Q ss_pred             CcccCCCCCCcccCCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHH
Q psy879            1 IEKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRN   80 (317)
Q Consensus         1 ~~ky~P~~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~   80 (317)
                      +|||+|++|+|++||+++++.|..++++++.||++|+||||+|||++|+++|+++.+......++++++++..+...++.
T Consensus        15 ~~ky~P~~~~diig~~~~~~~l~~~i~~~~~~~lll~Gp~G~GKTtla~~iak~l~~~~~~~~~~e~n~s~~~~~~~~~~   94 (231)
T d1iqpa2          15 VEKYRPQRLDDIVGQEHIVKRLKHYVKTGSMPHLLFAGPPGVGKTTAALALARELFGENWRHNFLELNASDERGINVIRE   94 (231)
T ss_dssp             HHHTCCCSTTTCCSCHHHHHHHHHHHHHTCCCEEEEESCTTSSHHHHHHHHHHHHHGGGHHHHEEEEETTCHHHHHTTHH
T ss_pred             HHHhCCCCHHHccCcHHHHHHHHHHHHcCCCCeEEEECCCCCcHHHHHHHHHHHHHhcccCCCeeEEecCcccchhHHHH
Confidence            48999999999999999999999999999999999999999999999999999997766666788898887666666665


Q ss_pred             HHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcCchhHhhhcceeeecCCCHHHH
Q psy879           81 KIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQL  160 (317)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~~~i~sR~~~i~f~~~~~~~~  160 (317)
                      ........... ....+.++++||+|.+..+.+++|++++++++.++.+|+++|...+++++++|||..+.|++++..++
T Consensus        95 ~~~~~~~~~~~-~~~~~~iilide~d~~~~~~~~~ll~~l~~~~~~~~~i~~~n~~~~i~~~l~sR~~~i~~~~~~~~~~  173 (231)
T d1iqpa2          95 KVKEFARTKPI-GGASFKIIFLDEADALTQDAQQALRRTMEMFSSNVRFILSCNYSSKIIEPIQSRCAIFRFRPLRDEDI  173 (231)
T ss_dssp             HHHHHHHSCCG-GGCSCEEEEEETGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHHTEEEEECCCCCHHHH
T ss_pred             HHHHHHhhhhc-cCCCceEEeehhhhhcchhHHHHHhhhcccCCcceEEEeccCChhhchHhHhCccccccccccchhhH
Confidence            55544433221 22568899999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhhCCCcccHHHHHhhc
Q psy879          161 LSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVC  217 (317)
Q Consensus       161 ~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~~~~~i~~~~v~~~~  217 (317)
                      ..++...+.++++.+++++++.+++.++||+|.+++.|+.++...+.++.++|..+.
T Consensus       174 ~~~l~~~~~~e~i~i~~~~l~~I~~~~~gdiR~ai~~Lq~~~~~~~~it~e~v~~v~  230 (231)
T d1iqpa2         174 AKRLRYIAENEGLELTEEGLQAILYIAEGDMRRAINILQAAAALDKKITDENVFMVA  230 (231)
T ss_dssp             HHHHHHHHHTTTCEECHHHHHHHHHHHTTCHHHHHHHHHHHHTTCSEECHHHHHHHT
T ss_pred             HHHHHHHHHHhCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHcCCCcCHHHHHhhh
Confidence            999999999999999999999999999999999999999988888889999887653

>d1sxjd2 c.37.1.20 (D:26-262) Replication factor C2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=1.4e-37  Score=259.41  Aligned_cols=218  Identities=43%  Similarity=0.696  Sum_probs=185.9

Q ss_pred             CcccCCCCCCcccCCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCC-CCCceEEecCCCCcChHHHH
Q psy879            1 IEKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPS-FKDAVLELNASNDRGIDTVR   79 (317)
Q Consensus         1 ~~ky~P~~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~-~~~~~~~~~~~~~~~~~~i~   79 (317)
                      +|||||++|++++||+++++.|+.++.+++.||++|+||||+|||++++++++++.+.. ......+.+.+...+...+.
T Consensus         3 ~~ky~P~~~~diig~~~~~~~l~~~i~~~~~~~lll~Gp~G~GKTtl~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~~   82 (237)
T d1sxjd2           3 VEKYRPKNLDEVTAQDHAVTVLKKTLKSANLPHMLFYGPPGTGKTSTILALTKELYGPDLMKSRILELNASDERGISIVR   82 (237)
T ss_dssp             HHHTCCSSTTTCCSCCTTHHHHHHHTTCTTCCCEEEECSTTSSHHHHHHHHHHHHHHHHHHTTSEEEECSSSCCCHHHHT
T ss_pred             chhhCCCCHHHccCcHHHHHHHHHHHHcCCCCeEEEECCCCCChHHHHHHHHHHHcCCcccccchhheeccccccchHHH
Confidence            48999999999999999999999999999999999999999999999999999985432 23445667776666665555


Q ss_pred             HHHHHHHhhccc---------CCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcCchhHhhhccee
Q psy879           80 NKIKMFAQQKVT---------LPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAML  150 (317)
Q Consensus        80 ~~~~~~~~~~~~---------~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~~~i~sR~~~i  150 (317)
                      ..+..+......         .....++++||||+|.+..+.++.+++.++.++.++.+|++++...+++++++|||..+
T Consensus        83 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~viiiDe~d~l~~~~~~~l~~~~~~~~~~~~~i~~~~~~~~~~~~l~sr~~~i  162 (237)
T d1sxjd2          83 EKVKNFARLTVSKPSKHDLENYPCPPYKIIILDEADSMTADAQSALRRTMETYSGVTRFCLICNYVTRIIDPLASQCSKF  162 (237)
T ss_dssp             THHHHHHHSCCCCCCTTHHHHSCCCSCEEEEETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHHHSEEE
T ss_pred             HHHHHHhhhhhhhhhHHHHhhccccCceEEEEecccccCHHHHHHHhhccccccccccccccccccccccccccchhhhh
Confidence            444443322211         12246789999999999999999999999999999999999999999999999999999


Q ss_pred             eecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhh------CCCcccHHHHHhhcC
Q psy879          151 RYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHN------GFGHVTAEYVFKVCD  218 (317)
Q Consensus       151 ~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~------~~~~i~~~~v~~~~~  218 (317)
                      +|++++.+++..+|..++.++++.+++++++.++..++||+|++++.|+.++.      ..+.|+.++|+++.+
T Consensus       163 ~f~~~~~~~~~~~L~~i~~~e~i~i~~~~l~~ia~~s~gd~R~ai~~L~~~~~~~~~~~~~~~It~~~i~e~~g  236 (237)
T d1sxjd2         163 RFKALDASNAIDRLRFISEQENVKCDDGVLERILDISAGDLRRGITLLQSASKGAQYLGDGKNITSTQVEELAG  236 (237)
T ss_dssp             ECCCCCHHHHHHHHHHHHHTTTCCCCHHHHHHHHHHTSSCHHHHHHHHHHTHHHHHHHCSCCCCCHHHHHHHHT
T ss_pred             ccccccccccchhhhhhhhhhcCcCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhcCCCCccCHHHHHHhhC
Confidence            99999999999999999999999999999999999999999999999987543      346788888877654

>d1sxje2 c.37.1.20 (E:4-255) Replication factor C5 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C5
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=4.4e-34  Score=240.19  Aligned_cols=204  Identities=31%  Similarity=0.522  Sum_probs=161.2

Q ss_pred             CcccCCCCCCcccCCHHHHHHHHHHHhcCC-CceEEEECCCCCCHHHHHHHHHHHHcCCCCCCc----------------
Q psy879            1 IEKYRPQTFSDIVGNEDTVERLKVFSSSGN-VPNIIISGPPGVGKTTTILCLARILLGPSFKDA----------------   63 (317)
Q Consensus         1 ~~ky~P~~~~~~~g~~~~~~~l~~~l~~~~-~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~----------------   63 (317)
                      +|||||++|++++|++++.+.|..++.++. +||++||||||+|||++|+++++.+.+......                
T Consensus         2 ~eky~P~~~~diig~~~~~~~L~~~~~~~~~~~~lll~Gp~G~GKTt~~~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~   81 (252)
T d1sxje2           2 VDKYRPKSLNALSHNEELTNFLKSLSDQPRDLPHLLLYGPNGTGKKTRCMALLESIFGPGVYRLKIDVRQFVTASNRKLE   81 (252)
T ss_dssp             TTTTCCCSGGGCCSCHHHHHHHHTTTTCTTCCCCEEEECSTTSSHHHHHHTHHHHHSCTTCCC-----------------
T ss_pred             CcccCCCCHHHccCcHHHHHHHHHHHHcCCCCCeEEEECCCCCCHHHHHHHHHHhhcCccccccccccccccccccchhh
Confidence            699999999999999999999999998765 566999999999999999999999864332111                


Q ss_pred             --------eEEecCCC--CcChHHHHHHHHHHHhhcc-------cCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCC
Q psy879           64 --------VLELNASN--DRGIDTVRNKIKMFAQQKV-------TLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNT  126 (317)
Q Consensus        64 --------~~~~~~~~--~~~~~~i~~~~~~~~~~~~-------~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~  126 (317)
                              ........  ..........+........       ....+..++++|||+|.++.+.++.|++.+++++.+
T Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iiiide~d~l~~~~~~~l~~~~e~~~~~  161 (252)
T d1sxje2          82 LNVVSSPYHLEITPSDMGNNDRIVIQELLKEVAQMEQVDFQDSKDGLAHRYKCVIINEANSLTKDAQAALRRTMEKYSKN  161 (252)
T ss_dssp             -CCEECSSEEEECCC----CCHHHHHHHHHHHTTTTC------------CCEEEEEECTTSSCHHHHHHHHHHHHHSTTT
T ss_pred             hhhccCCccceeeecccccCCcceeeehhhhhhhhhhhhhhhcccccCCCceEEEeccccccccccchhhhccccccccc
Confidence                    11111111  1111222222222222111       011245789999999999999999999999999999


Q ss_pred             ceEEEEecCCCcCchhHhhhcceeeecCCCHHHHHHHHHHHHHHcCCCCC-HHHHHHHHHhcCCCHHHHHHHHHHhhhC
Q psy879          127 TRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHT-NDGLEAIVFTAQGDMRQALNNLQSTHNG  204 (317)
Q Consensus       127 ~~~il~~~~~~~l~~~i~sR~~~i~f~~~~~~~~~~~l~~~~~~~~~~i~-~~~~~~l~~~~~gd~r~~i~~l~~~~~~  204 (317)
                      +.||++||+.++++++++|||..++|++|+.+++.+++..++..+++.++ +++++.++..++||+|++++.||.++..
T Consensus       162 ~~~Il~tn~~~~i~~~l~sR~~~i~~~~~~~~~~~~~l~~i~~~e~~~~~~~~~l~~i~~~s~Gd~R~ai~~Lq~~~~~  240 (252)
T d1sxje2         162 IRLIMVCDSMSPIIAPIKSQCLLIRCPAPSDSEISTILSDVVTNERIQLETKDILKRIAQASNGNLRVSLLMLESMALN  240 (252)
T ss_dssp             EEEEEEESCSCSSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHHTCEECCSHHHHHHHHHHTTCHHHHHHHHTHHHHT
T ss_pred             ccceeeeccccchhhhhhcchheeeecccchhhHHHHHHHHHHHcCCCCCcHHHHHHHHHHcCCcHHHHHHHHHHHHHc
Confidence            99999999999999999999999999999999999999999999998775 6788999999999999999999977653

>d1sxja2 c.37.1.20 (A:295-547) Replication factor C1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=1.6e-32  Score=230.72  Aligned_cols=210  Identities=24%  Similarity=0.430  Sum_probs=166.1

Q ss_pred             CcccCCCCCCcccCCHHHHHHHHHHHhc-----------------CCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCc
Q psy879            1 IEKYRPQTFSDIVGNEDTVERLKVFSSS-----------------GNVPNIIISGPPGVGKTTTILCLARILLGPSFKDA   63 (317)
Q Consensus         1 ~~ky~P~~~~~~~g~~~~~~~l~~~l~~-----------------~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~   63 (317)
                      +|||||++|++++|+++.++.|..++..                 +..++++||||||||||++|+++|+++.     ..
T Consensus         5 ~eky~P~~~~dlig~~~~~~~L~~~l~~~~~~~~~~~~~~~~~~~~~~~~lll~GPpG~GKTt~a~~la~~~~-----~~   79 (253)
T d1sxja2           5 TVKYAPTNLQQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQELG-----YD   79 (253)
T ss_dssp             HHHTCCSSGGGCCSCHHHHHHHHHHHHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHHHHHHHHTT-----CE
T ss_pred             ccCcCCCCHHHhcCCHHHHHHHHHHHHhhhhcchhhhhhhcccCCCCCceEEEECCCCCCHHHHHHHHHHHHH-----hh
Confidence            4899999999999999999999988753                 3456799999999999999999999963     34


Q ss_pred             eEEecCCCCcChHHHHHHHHHHHhhcc-----------cCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhc-cCCceEEE
Q psy879           64 VLELNASNDRGIDTVRNKIKMFAQQKV-----------TLPPGRHKIVILDEADSMTDGAQQALRRTMEIY-SNTTRFAL  131 (317)
Q Consensus        64 ~~~~~~~~~~~~~~i~~~~~~~~~~~~-----------~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~-~~~~~~il  131 (317)
                      +..++.+...+...++..+..+.....           ....+...++++||++.++...+..+...++.. .....+++
T Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vi~ide~~~~~~~~~~~~~~~~~~~~~~~~~ii~  159 (253)
T d1sxja2          80 ILEQNASDVRSKTLLNAGVKNALDNMSVVGYFKHNEEAQNLNGKHFVIIMDEVDGMSGGDRGGVGQLAQFCRKTSTPLIL  159 (253)
T ss_dssp             EEEECTTSCCCHHHHHHTGGGGTTBCCSTTTTTC----CCSSTTSEEEEECSGGGCCTTSTTHHHHHHHHHHHCSSCEEE
T ss_pred             hhccccccchhhHHHHHHHHHHhhcchhhhhhhhhhhcccccccceEEEeeeccccccchhhhhHHHhhhhccccccccc
Confidence            677877766665555544332222110           112246789999999999888777666666532 23345566


Q ss_pred             EecC-CCcCchhHhhhcceeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhhCCCcccH
Q psy879          132 ACNN-SEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHNGFGHVTA  210 (317)
Q Consensus       132 ~~~~-~~~l~~~i~sR~~~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~~~~~i~~  210 (317)
                      +++. .....+++++||..++|++|+.+++..++..++.++|+.+++++++.++..++||+|.+++.|+.+....+.++.
T Consensus       160 i~~~~~~~~~~~l~~~~~~i~f~~~~~~~i~~~l~~i~~~e~i~i~~~~l~~i~~~s~GDiR~ai~~L~~~~~~~~~i~~  239 (253)
T d1sxja2         160 ICNERNLPKMRPFDRVCLDIQFRRPDANSIKSRLMTIAIREKFKLDPNVIDRLIQTTRGDIRQVINLLSTISTTTKTINH  239 (253)
T ss_dssp             EESCTTSSTTGGGTTTSEEEECCCCCHHHHHHHHHHHHHHHTCCCCTTHHHHHHHHTTTCHHHHHHHHTHHHHHSSCCCT
T ss_pred             ccccccccccccccceeeeeeccccchhHHHHHHHHHHHHhCCCCCHHHHHHHHHhCCCcHHHHHHHHHHHHHcCCCCCH
Confidence            6554 456777899999999999999999999999999999999999999999999999999999999998887777887


Q ss_pred             HHHHh
Q psy879          211 EYVFK  215 (317)
Q Consensus       211 ~~v~~  215 (317)
                      +++.+
T Consensus       240 ~~~~~  244 (253)
T d1sxja2         240 ENINE  244 (253)
T ss_dssp             THHHH
T ss_pred             HHHHH
Confidence            76543

>d1a5ta2 c.37.1.20 (A:1-207) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=100.00  E-value=7.5e-32  Score=218.96  Aligned_cols=178  Identities=25%  Similarity=0.344  Sum_probs=153.3

Q ss_pred             CCHHHHHHHHHHHhcCCCce-EEEECCCCCCHHHHHHHHHHHHcCCCCC-------------------CceEEecC---C
Q psy879           14 GNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARILLGPSFK-------------------DAVLELNA---S   70 (317)
Q Consensus        14 g~~~~~~~l~~~l~~~~~~~-~ll~G~~G~GKt~la~~la~~l~~~~~~-------------------~~~~~~~~---~   70 (317)
                      +++++.+.|...+.++++|| ++|+||+|+|||++|+.+|+.+.+....                   ..+.....   .
T Consensus         6 w~~~~~~~l~~~~~~~~l~h~lLl~Gp~G~GKtt~a~~~a~~l~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~   85 (207)
T d1a5ta2           6 WLRPDFEKLVASYQAGRGHHALLIQALPGMGDDALIYALSRYLLCQQPQGHKSCGHCRGCQLMQAGTHPDYYTLAPEKGK   85 (207)
T ss_dssp             GGHHHHHHHHHHHHTTCCCSEEEEECCTTSCHHHHHHHHHHHHTCSSCBTTBCCSCSHHHHHHHHTCCTTEEEECCCTTC
T ss_pred             ccHHHHHHHHHHHHcCCcCeEEEEECCCCCcHHHHHHHHHHhcccccccccccccccchhhhhhhccccccchhhhhhcc
Confidence            67889999999999999999 9999999999999999999999754321                   12333332   2


Q ss_pred             CCcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcCchhHhhhccee
Q psy879           71 NDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAML  150 (317)
Q Consensus        71 ~~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~~~i~sR~~~i  150 (317)
                      .....+++++.+..+...+   ..+.++|+||||+|.|+.+++++|+++||+|+.++.||++|++..+++++|+|||+.+
T Consensus        86 ~~i~~~~ir~l~~~~~~~~---~~~~~kviIide~d~l~~~a~n~Llk~lEep~~~~~fIl~t~~~~~ll~tI~SRc~~i  162 (207)
T d1a5ta2          86 NTLGVDAVREVTEKLNEHA---RLGGAKVVWVTDAALLTDAAANALLKTLEEPPAETWFFLATREPERLLATLRSRCRLH  162 (207)
T ss_dssp             SSBCHHHHHHHHHHTTSCC---TTSSCEEEEESCGGGBCHHHHHHHHHHHTSCCTTEEEEEEESCGGGSCHHHHTTSEEE
T ss_pred             cccccchhhHHhhhhhhcc---ccCccceEEechhhhhhhhhhHHHHHHHHhhcccceeeeeecChhhhhhhhcceeEEE
Confidence            3456788888777665544   3368999999999999999999999999999999999999999999999999999999


Q ss_pred             eecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHH
Q psy879          151 RYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQ  199 (317)
Q Consensus       151 ~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~  199 (317)
                      +|++++.+++..+|.+     +..++++++..++..++||+|.|++.||
T Consensus       163 ~~~~~~~~~~~~~L~~-----~~~~~~~~~~~i~~~s~Gs~r~al~~le  206 (207)
T d1a5ta2         163 YLAPPPEQYAVTWLSR-----EVTMSQDALLAALRLSAGSPGAALALFQ  206 (207)
T ss_dssp             ECCCCCHHHHHHHHHH-----HCCCCHHHHHHHHHHTTTCHHHHHHTTS
T ss_pred             ecCCCCHHHHHHHHHH-----cCCCCHHHHHHHHHHcCCCHHHHHHHhC
Confidence            9999999999999976     4568899999999999999999998764

>d1in4a2 c.37.1.20 (A:17-254) Holliday junction helicase RuvB {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Holliday junction helicase RuvB
species: Thermotoga maritima [TaxId: 2336]

Probab=99.97  E-value=2.7e-30  Score=215.07  Aligned_cols=200  Identities=18%  Similarity=0.282  Sum_probs=166.7

Q ss_pred             ccCCCCCCcccCCHHHHHHHHHHHh-----cCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHH
Q psy879            3 KYRPQTFSDIVGNEDTVERLKVFSS-----SGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDT   77 (317)
Q Consensus         3 ky~P~~~~~~~g~~~~~~~l~~~l~-----~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~   77 (317)
                      -.||++|++++||+++++.|..+++     +..+||+|||||||||||++|+++++++.+     .+..++.+.......
T Consensus         2 ~~RP~~~~divGqe~~~~~l~~~i~~~~~~~~~~~~~L~~GPpGtGKT~lA~~la~~~~~-----~~~~~~~~~~~~~~~   76 (238)
T d1in4a2           2 FLRPKSLDEFIGQENVKKKLSLALEAAKMRGEVLDHVLLAGPPGLGKTTLAHIIASELQT-----NIHVTSGPVLVKQGD   76 (238)
T ss_dssp             TTSCSSGGGCCSCHHHHHHHHHHHHHHHHHTCCCCCEEEESSTTSSHHHHHHHHHHHHTC-----CEEEEETTTCCSHHH
T ss_pred             CCCCCcHHHcCChHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCcHHHHHHHHHhccCC-----CcccccCcccccHHH
Confidence            4699999999999999999988875     334678999999999999999999999743     366677776666666


Q ss_pred             HHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhc------------------cCCceEEEEecCCCcC
Q psy879           78 VRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIY------------------SNTTRFALACNNSEKI  139 (317)
Q Consensus        78 i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~------------------~~~~~~il~~~~~~~l  139 (317)
                      +...+...         ....++++||++.+.+..++.++..++..                  ..++++|++|++....
T Consensus        77 ~~~~~~~~---------~~~~~~~ide~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~at~~~~~~  147 (238)
T d1in4a2          77 MAAILTSL---------ERGDVLFIDEIHRLNKAVEELLYSAIEDFQIDIMIGKGPSAKSIRIDIQPFTLVGATTRSGLL  147 (238)
T ss_dssp             HHHHHHHC---------CTTCEEEEETGGGCCHHHHHHHHHHHHTSCCCC---------------CCCEEEEEESCGGGS
T ss_pred             HHHHHHhh---------ccCCchHHHHHHHhhhHHHhhcccceeeeeeeeeecCcccccccccCCCCeEEEEecCCCccc
Confidence            55544321         35679999999999999999998888743                  3467899999999999


Q ss_pred             chhHhhhcce-eeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhh-----hCCCcccHHHH
Q psy879          140 IEPIQSRCAM-LRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTH-----NGFGHVTAEYV  213 (317)
Q Consensus       140 ~~~i~sR~~~-i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~-----~~~~~i~~~~v  213 (317)
                      .+++++||.. +.|++++.+++..++..++..++..++++++..++..++||+|.+++.++.+.     .+...|+.+.+
T Consensus       148 ~~~~~~r~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~i~~~s~gd~R~ai~~l~~~~~~~~~~~~~~it~~~~  227 (238)
T d1in4a2         148 SSPLRSRFGIILELDFYTVKELKEIIKRAASLMDVEIEDAAAEMIAKRSRGTPRIAIRLTKRVRDMLTVVKADRINTDIV  227 (238)
T ss_dssp             CHHHHTTCSEEEECCCCCHHHHHHHHHHHHHHTTCCBCHHHHHHHHHTSTTCHHHHHHHHHHHHHHHHHHTCSSBCHHHH
T ss_pred             cccceeeeeEEEEecCCCHHHHHHHHHHhhhhccchhhHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHhcCCccCHHHH
Confidence            9999999987 79999999999999999999999999999999999999999999999998653     24556777766


Q ss_pred             Hhh
Q psy879          214 FKV  216 (317)
Q Consensus       214 ~~~  216 (317)
                      .++
T Consensus       228 ~~a  230 (238)
T d1in4a2         228 LKT  230 (238)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            543

>d1ixsb2 c.37.1.20 (B:4-242) Holliday junction helicase RuvB {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Holliday junction helicase RuvB
species: Thermus thermophilus [TaxId: 274]

Probab=99.97  E-value=4.2e-29  Score=207.86  Aligned_cols=200  Identities=19%  Similarity=0.231  Sum_probs=159.8

Q ss_pred             cCCCCCCcccCCHHHHHHHHHHHhc-----CCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHH
Q psy879            4 YRPQTFSDIVGNEDTVERLKVFSSS-----GNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTV   78 (317)
Q Consensus         4 y~P~~~~~~~g~~~~~~~l~~~l~~-----~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i   78 (317)
                      -||++|++++||+++++.|+.++..     ..++|+|||||||+|||++|+++++++.     ..+...+++........
T Consensus         3 ~RP~~~ddivGq~~~~~~L~~~i~~~~~~~~~~~~~Ll~GPpG~GKTtla~~la~~~~-----~~~~~~~~~~~~~~~~~   77 (239)
T d1ixsb2           3 LRPKTLDEYIGQERLKQKLRVYLEAAKARKEPLEHLLLFGPPGLGKTTLAHVIAHELG-----VNLRVTSGPAIEKPGDL   77 (239)
T ss_dssp             CCCCSGGGSCSCHHHHHHHHHHHHHHTTSSSCCCCEEEECCTTSCHHHHHHHHHHHHT-----CCEEEEETTTCCSHHHH
T ss_pred             cCCCCHHHhCCHHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHhC-----CCeEeccCCccccchhh
Confidence            4999999999999999999888752     3467899999999999999999999973     33566666655444433


Q ss_pred             HHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhc------------------cCCceEEEEecCCCc-C
Q psy879           79 RNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIY------------------SNTTRFALACNNSEK-I  139 (317)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~------------------~~~~~~il~~~~~~~-l  139 (317)
                      ...+..   .     .....++++||+|.+.+..+..++..++..                  +++.++|++|+++.. .
T Consensus        78 ~~~~~~---~-----~~~~~i~~iDe~~~~~~~~~~~l~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~  149 (239)
T d1ixsb2          78 AAILAN---S-----LEEGDILFIDEIHRLSRQAEEHLYPAMEDFVMDIVIGQGPAARTIRLELPRFTLIGATTRPGLIT  149 (239)
T ss_dssp             HHHHHT---T-----CCTTCEEEEETGGGCCHHHHHHHHHHHHHSEEEEECSCTTCCCEEEEECCCCEEEEEESCCSSCS
T ss_pred             HHHHHh---h-----ccCCCeeeeecccccchhHHHhhhhhhhhhhhhhhhccchhhhhcccCCCCEEEEeeccCccccc
Confidence            332221   1     134679999999999999999999998742                  334567777777654 5


Q ss_pred             chhHhhhcceeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhh-----CCCcccHHHHH
Q psy879          140 IEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHN-----GFGHVTAEYVF  214 (317)
Q Consensus       140 ~~~i~sR~~~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~-----~~~~i~~~~v~  214 (317)
                      .+.++++|..+.|.+++.+++..++...+..+++.++++.+..++..++||+|.+++.++.+..     +...|+.+.+.
T Consensus       150 ~~~l~~~~~~~~~~~~~~~~~~~i~~~~~~~~~i~~~~~~l~~ia~~s~gd~R~a~~~l~~~~~~a~~~~~~~It~~~~~  229 (239)
T d1ixsb2         150 APLLSRFGIVEHLEYYTPEELAQGVMRDARLLGVRITEEAALEIGRRSRGTMRVAKRLFRRVRDFAQVAGEEVITRERAL  229 (239)
T ss_dssp             CGGGGGCSEEEECCCCCHHHHHHHHHHHHGGGCCCBCHHHHHHHHHHTTSSHHHHHHHHHHHHHHHTTSCCSCBCHHHHH
T ss_pred             chhhcccceeeEeeccChhhhhHHHHHHHHHhCCccchHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHhCCCCcCHHHHH
Confidence            5777777888999999999999999999999999999999999999999999999999987532     45668877665


Q ss_pred             hh
Q psy879          215 KV  216 (317)
Q Consensus       215 ~~  216 (317)
                      ++
T Consensus       230 ~~  231 (239)
T d1ixsb2         230 EA  231 (239)
T ss_dssp             HH
T ss_pred             HH
Confidence            43

>d2gnoa2 c.37.1.20 (A:11-208) gamma subunit of DNA polymerase III, N-domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: gamma subunit of DNA polymerase III, N-domain
species: Thermotoga maritima [TaxId: 2336]

Probab=99.94  E-value=1.1e-26  Score=186.23  Aligned_cols=137  Identities=20%  Similarity=0.204  Sum_probs=118.8

Q ss_pred             HHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCC-CCceEEecCCC-CcChHHHHHHHHHHHhhcccCCCC
Q psy879           18 TVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSF-KDAVLELNASN-DRGIDTVRNKIKMFAQQKVTLPPG   95 (317)
Q Consensus        18 ~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~-~~~~~~~~~~~-~~~~~~i~~~~~~~~~~~~~~~~~   95 (317)
                      .++.++.+++++.+++++|+||||+|||++|..+++.+..... ...++++.+.. ..+++++|+....+...+.   .+
T Consensus         2 ~~~~l~~~i~~~~~~~~l~~G~~g~gk~~~a~~l~~~i~~~~~~h~D~~~i~~~~~~I~Id~IR~i~~~~~~~~~---~~   78 (198)
T d2gnoa2           2 QLETLKRIIEKSEGISILINGEDLSYPREVSLELPEYVEKFPPKASDVLEIDPEGENIGIDDIRTIKDFLNYSPE---LY   78 (198)
T ss_dssp             HHHHHHHHHHTCSSEEEEEECSSSSHHHHHHHHHHHHHHTSCCCTTTEEEECCSSSCBCHHHHHHHHHHHTSCCS---SS
T ss_pred             HHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHhccccCCCCEEEEeCCcCCCCHHHHHHHHHHHhhCcc---cC
Confidence            4577899999999889999999999999999999998854432 23577776643 5789999998877766653   37


Q ss_pred             ceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcCchhHhhhcceeeecCCCH
Q psy879           96 RHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTD  157 (317)
Q Consensus        96 ~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~~~i~sR~~~i~f~~~~~  157 (317)
                      .++|+||||+|.|+.+++++|+++||+||.++.||++|+++.+++++|+|||+.+.|++|++
T Consensus        79 ~~KviIId~ad~l~~~aqNaLLK~LEEPp~~t~fiLit~~~~~ll~TI~SRC~~i~~~~p~~  140 (198)
T d2gnoa2          79 TRKYVIVHDCERMTQQAANAFLKALEEPPEYAVIVLNTRRWHYLLPTIKSRVFRVVVNVPKE  140 (198)
T ss_dssp             SSEEEEETTGGGBCHHHHHHTHHHHHSCCTTEEEEEEESCGGGSCHHHHTTSEEEECCCCHH
T ss_pred             CCEEEEEeCccccchhhhhHHHHHHhCCCCCceeeeccCChhhCHHHHhcceEEEeCCCchH
Confidence            89999999999999999999999999999999999999999999999999999999987753

>d1ixza_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Thermus thermophilus [TaxId: 274]

Probab=99.89  E-value=9.8e-23  Score=168.66  Aligned_cols=199  Identities=21%  Similarity=0.296  Sum_probs=137.8

Q ss_pred             CC-CCCcccCCHHHHHHHHHHHh----------cC-CCc-eEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCC
Q psy879            6 PQ-TFSDIVGNEDTVERLKVFSS----------SG-NVP-NIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASND   72 (317)
Q Consensus         6 P~-~~~~~~g~~~~~~~l~~~l~----------~~-~~~-~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~   72 (317)
                      |. +|+|++|.+++++.|+..+.          -| ..| ++|||||||||||++|+++++++     +..++.++++..
T Consensus         4 p~~~~~di~G~~~~k~~l~~~i~~l~~~~~~~~~g~~~~~giLl~GppGtGKT~la~aia~~~-----~~~~~~i~~~~l   78 (247)
T d1ixza_           4 PKVTFKDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEA-----RVPFITASGSDF   78 (247)
T ss_dssp             CSCCGGGCCSCHHHHHHHHHHHHHHHCHHHHHHTTCCCCSEEEEECCTTSSHHHHHHHHHHHT-----TCCEEEEEHHHH
T ss_pred             CCCcHHHHccHHHHHHHHHHHHHHHHCHHHHHHcCCCCCceEEEecCCCCChhHHHHHHHHHc-----CCCEEEEEhHHh
Confidence            54 79999999999988776541          12 223 49999999999999999999986     345777765431


Q ss_pred             ----cC--hHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCH--------------HHHHHHHHHhhhcc--CCceEE
Q psy879           73 ----RG--IDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTD--------------GAQQALRRTMEIYS--NTTRFA  130 (317)
Q Consensus        73 ----~~--~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~--------------~~~~~ll~~le~~~--~~~~~i  130 (317)
                          .+  ...++..+....       ...+.||+|||+|.+..              ...+.|+..|+...  ..+.+|
T Consensus        79 ~~~~~g~~~~~l~~~f~~a~-------~~~p~Ii~iDeid~l~~~r~~~~~~~~~~~~~~~~~ll~~~d~~~~~~~vivi  151 (247)
T d1ixza_          79 VEMFVGVGAARVRDLFETAK-------RHAPCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEKDTAIVVM  151 (247)
T ss_dssp             HHSCTTHHHHHHHHHHHHHT-------TSSSEEEEEETHHHHHC---------CHHHHHHHHHHHHHHHTCCTTCCEEEE
T ss_pred             hhccccHHHHHHHHHHHHHH-------HcCCEEEEEEChhhhCccCCCCCCCCcHHHHHHHHHHHHHhhCCCCCCCEEEE
Confidence                11  122333333221       13577999999997632              13566788887543  445677


Q ss_pred             EEecCCCcCchhHh--hhcc-eeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCC----CHHHHHHHHH--Hh
Q psy879          131 LACNNSEKIIEPIQ--SRCA-MLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQG----DMRQALNNLQ--ST  201 (317)
Q Consensus       131 l~~~~~~~l~~~i~--sR~~-~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~g----d~r~~i~~l~--~~  201 (317)
                      ++||.++.++++++  +|+. .++|++|+.++..++++..+...... ++..++.+++.+.|    |++.+++..-  .+
T Consensus       152 ~tTn~~~~ld~al~R~~Rf~~~i~~~~P~~~eR~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~di~~lv~~A~l~a~  230 (247)
T d1ixza_         152 AATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLA-EDVDLALLAKRTPGFVGADLENLLNEAALLAA  230 (247)
T ss_dssp             EEESCGGGSCGGGGSTTSSCEEEECCSCCHHHHHHHHHHHHTTSCBC-TTCCHHHHHHTCTTCCHHHHHHHHHHHHHHHH
T ss_pred             EeCCCccccCHhHcCCCCCcEEEEECCcCHHHHHHHHHHHhcccCCc-cccCHHHHHHHCCCCCHHHHHHHHHHHHHHHH
Confidence            78999999999997  4886 49999999999999999888665433 34447788888766    5555544321  22


Q ss_pred             hhCCCcccHHHHHhhc
Q psy879          202 HNGFGHVTAEYVFKVC  217 (317)
Q Consensus       202 ~~~~~~i~~~~v~~~~  217 (317)
                      ..+...|+.+++.+++
T Consensus       231 ~~~~~~i~~~d~~~A~  246 (247)
T d1ixza_         231 REGRRKITMKDLEEAA  246 (247)
T ss_dssp             HTTCSSBCHHHHHHHT
T ss_pred             HcCCCCcCHHHHHHhh
Confidence            2355688888887764

>d1lv7a_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Escherichia coli [TaxId: 562]

Probab=99.88  E-value=1.9e-21  Score=161.48  Aligned_cols=197  Identities=17%  Similarity=0.211  Sum_probs=137.8

Q ss_pred             CCCCcccCCHHHHHHHHHHHh-----------cCCCc-eEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCc-
Q psy879            7 QTFSDIVGNEDTVERLKVFSS-----------SGNVP-NIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDR-   73 (317)
Q Consensus         7 ~~~~~~~g~~~~~~~l~~~l~-----------~~~~~-~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~-   73 (317)
                      -+|+|++|.+.+++.|...+.           +.+.| ++|||||||||||++|+++|+++     +..++.+++++.. 
T Consensus         9 ~t~~Di~Gl~~~k~~l~e~v~~~~~~~~~~~~g~~~~~~iLL~GppGtGKT~la~~iA~~~-----~~~~~~i~~~~l~~   83 (256)
T d1lv7a_           9 TTFADVAGCDEAKEEVAELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGEA-----KVPFFTISGSDFVE   83 (256)
T ss_dssp             CCGGGSCSCHHHHHHTHHHHHHHHCGGGC-----CCCCEEEEECCTTSCHHHHHHHHHHHH-----TCCEEEECSCSSTT
T ss_pred             CCHHHHhchHHHHHHHHHHHHHHHCHHHHHHcCCCCCCeEEeeCCCCCCccHHHHHHHHHc-----CCCEEEEEhHHhhh
Confidence            479999999999988876542           12233 49999999999999999999997     3457777765432 


Q ss_pred             -----ChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCH--------------HHHHHHHHHhhhc--cCCceEEEE
Q psy879           74 -----GIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTD--------------GAQQALRRTMEIY--SNTTRFALA  132 (317)
Q Consensus        74 -----~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~--------------~~~~~ll~~le~~--~~~~~~il~  132 (317)
                           +...++..+.....       ..+.|++|||+|.+..              ...+.|+..++..  ...+.+|.+
T Consensus        84 ~~~g~~~~~l~~~f~~A~~-------~~P~il~iDeiD~l~~~r~~~~~~~~~~~~~~~~~ll~~~d~~~~~~~v~vIat  156 (256)
T d1lv7a_          84 MFVGVGASRVRDMFEQAKK-------AAPCIIFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDGFEGNEGIIVIAA  156 (256)
T ss_dssp             SCCCCCHHHHHHHHHHHHT-------TCSEEEEETTHHHHTCCCSTTSCCTTCHHHHHHHHHHHHHHTCCSSSCEEEEEE
T ss_pred             cchhHHHHHHHHHHHHHHH-------cCCEEEEEEChhhhCccCCCCCCCCcHHHHHHHHHHHHHhhCCCCCCCEEEEEe
Confidence                 23445555554432       3578999999997632              1346678888744  345678889


Q ss_pred             ecCCCcCchhHhh--hcc-eeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCC-CHHHHHHHHHHh-----hh
Q psy879          133 CNNSEKIIEPIQS--RCA-MLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQG-DMRQALNNLQST-----HN  203 (317)
Q Consensus       133 ~~~~~~l~~~i~s--R~~-~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~g-d~r~~i~~l~~~-----~~  203 (317)
                      ||.++.+++++++  |+. .+.|++|+.++..++++....+..+. ++..+..+++.+.| +.+.+-+.++.+     ..
T Consensus       157 Tn~~~~ld~al~R~gRfd~~i~i~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~G~s~adi~~l~~~A~~~a~~~  235 (256)
T d1lv7a_         157 TNRPDVLDPALLRPGRFDRQVVVGLPDVRGREQILKVHMRRVPLA-PDIDAAIIARGTPGFSGADLANLVNEAALFAARG  235 (256)
T ss_dssp             ESCTTTSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTSCBC-TTCCHHHHHHTCTTCCHHHHHHHHHHHHHHHHHT
T ss_pred             CCCcccCCHhHcCCCCCCEEEECCCcCHHHHHHHHHHhccCCCcC-cccCHHHHHHhCCCCCHHHHHHHHHHHHHHHHHc
Confidence            9999999999985  785 49999999999999999888665543 34456778887654 334343444322     22


Q ss_pred             CCCcccHHHHHhh
Q psy879          204 GFGHVTAEYVFKV  216 (317)
Q Consensus       204 ~~~~i~~~~v~~~  216 (317)
                      +...++.+++.++
T Consensus       236 ~~~~i~~~d~~~A  248 (256)
T d1lv7a_         236 NKRVVSMVEFEKA  248 (256)
T ss_dssp             TCSSBCHHHHHHH
T ss_pred             CCCccCHHHHHHH
Confidence            4456777776554

>d1fnna2 c.37.1.20 (A:1-276) CDC6, N-domain {Archaeon Pyrobaculum aerophilum [TaxId: 13773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6, N-domain
species: Archaeon Pyrobaculum aerophilum [TaxId: 13773]

Probab=99.86  E-value=1.5e-19  Score=152.18  Aligned_cols=207  Identities=18%  Similarity=0.235  Sum_probs=145.9

Q ss_pred             cccCCCCCCcccCCHHHHHHHHHHHhc------CCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcCh
Q psy879            2 EKYRPQTFSDIVGNEDTVERLKVFSSS------GNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGI   75 (317)
Q Consensus         2 ~ky~P~~~~~~~g~~~~~~~l~~~l~~------~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~   75 (317)
                      ..|+|+   .++|++..++.+..++..      +.+++++|+||||||||++++.+++.+.+. ....++..++......
T Consensus        11 ~~y~p~---~l~~Re~ei~~l~~~l~~~l~~~~~~~~~lll~GppGtGKT~l~~~l~~~l~~~-~~~~~~~~~~~~~~~~   86 (276)
T d1fnna2          11 PSYVPK---RLPHREQQLQQLDILLGNWLRNPGHHYPRATLLGRPGTGKTVTLRKLWELYKDK-TTARFVYINGFIYRNF   86 (276)
T ss_dssp             TTCCCS---CCTTCHHHHHHHHHHHHHHHHSTTSSCCEEEEECCTTSSHHHHHHHHHHHHTTS-CCCEEEEEETTTCCSH
T ss_pred             CCCCCC---CCCCHHHHHHHHHHHHHHHHhCCCCCCCceEEECCCCCCHHHHHHHHHHHHhcc-cCCcEEEecchhhhhh
Confidence            468885   468999877777666642      234579999999999999999999998543 3344555544332222


Q ss_pred             HH----------------------HHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhh----ccCCceE
Q psy879           76 DT----------------------VRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEI----YSNTTRF  129 (317)
Q Consensus        76 ~~----------------------i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~----~~~~~~~  129 (317)
                      ..                      +...+......     .....+.++|++|.+.......+...+..    ......+
T Consensus        87 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~  161 (276)
T d1fnna2          87 TAIIGEIARSLNIPFPRRGLSRDEFLALLVEHLRE-----RDLYMFLVLDDAFNLAPDILSTFIRLGQEADKLGAFRIAL  161 (276)
T ss_dssp             HHHHHHHHHHTTCCCCSSCCCHHHHHHHHHHHHHH-----TTCCEEEEEETGGGSCHHHHHHHHHHTTCHHHHSSCCEEE
T ss_pred             hhhhhhhHHhhhhhhhhhccchhHHHHHHHHHHhh-----cccccccchhHHHHhhhhhhhhHHHHHhccccccccceEE
Confidence            11                      11111111111     13567888999999998877777666553    2344567


Q ss_pred             EEEecCC---CcCchhHhhhcce--eeecCCCHHHHHHHHHHHHHH--cCCCCCHHHHHHHHHh---------cCCCHHH
Q psy879          130 ALACNNS---EKIIEPIQSRCAM--LRYNKLTDAQLLSKVIEICEK--ENISHTNDGLEAIVFT---------AQGDMRQ  193 (317)
Q Consensus       130 il~~~~~---~~l~~~i~sR~~~--i~f~~~~~~~~~~~l~~~~~~--~~~~i~~~~~~~l~~~---------~~gd~r~  193 (317)
                      |++++..   +.+.+.+.+|+..  +.|++++.+++.+++..++..  ....+++++++.+++.         +.||+|.
T Consensus       162 i~~~~~~~~~~~~~~~~~~r~~~~~i~~~~~~~~e~~~il~~r~~~~~~~~~~~~~~l~~ia~~~~~~~~~~~~~G~~R~  241 (276)
T d1fnna2         162 VIVGHNDAVLNNLDPSTRGIMGKYVIRFSPYTKDQIFDILLDRAKAGLAEGSYSEDILQMIADITGAQTPLDTNRGDARL  241 (276)
T ss_dssp             EEEESSTHHHHTSCHHHHHHHTTCEEECCCCBHHHHHHHHHHHHHHHBCTTSSCHHHHHHHHHHHSBSSTTCTTSCCHHH
T ss_pred             eecCCchhhhhhcchhhhhhhcchhccccchhHHHHHHHHHHHHHHhcccccccHHHHHHHHHHhhhhhhhhhcCCCHHH
Confidence            7777764   3678899999854  999999999999999998876  3345789999988765         3799999


Q ss_pred             HHHHHHHhhh-----CCCcccHHHHHhhc
Q psy879          194 ALNNLQSTHN-----GFGHVTAEYVFKVC  217 (317)
Q Consensus       194 ~i~~l~~~~~-----~~~~i~~~~v~~~~  217 (317)
                      +++.++.++.     +...|+.+||+++.
T Consensus       242 a~~ll~~a~~~A~~~~~~~I~~edv~~A~  270 (276)
T d1fnna2         242 AIDILYRSAYAAQQNGRKHIAPEDVRKSS  270 (276)
T ss_dssp             HHHHHHHHHHHHHHTTCSSCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCCCcCHHHHHHHH
Confidence            9999987543     55689999887754

>d1e32a2 c.37.1.20 (A:201-458) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.82  E-value=1.2e-19  Score=151.31  Aligned_cols=176  Identities=18%  Similarity=0.251  Sum_probs=124.3

Q ss_pred             CCCcccCCHHHHHHHHHHHhc-----------C-CCc-eEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCC---
Q psy879            8 TFSDIVGNEDTVERLKVFSSS-----------G-NVP-NIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASN---   71 (317)
Q Consensus         8 ~~~~~~g~~~~~~~l~~~l~~-----------~-~~~-~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~---   71 (317)
                      +|+|+.|.+.+++.|+..+..           | .+| .+|||||||||||++++++|+++     +..++.++++.   
T Consensus         2 ~~~dv~G~~~~k~~l~~~i~~~l~~~~~~~~~g~~~~~giLL~GppGtGKT~l~~ala~~~-----~~~~~~i~~~~l~~   76 (258)
T d1e32a2           2 GYDDVGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANET-----GAFFFLINGPEIMS   76 (258)
T ss_dssp             CGGGCCSCSHHHHHHHHHHHHHHHCHHHHHHCCCCCCCEEEEECCTTSSHHHHHHHHHHHT-----TCEEEEECHHHHTT
T ss_pred             ChhhhccHHHHHHHHHHHHHHHhcCHHHHHhCCCCCCceeEEecCCCCCchHHHHHHHHHh-----CCeEEEEEchhhcc
Confidence            689999999999988876421           3 233 49999999999999999999985     33466666532   


Q ss_pred             -Cc--ChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHH-----------HHHHHHHHhh--hccCCceEEEEecC
Q psy879           72 -DR--GIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDG-----------AQQALRRTME--IYSNTTRFALACNN  135 (317)
Q Consensus        72 -~~--~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~-----------~~~~ll~~le--~~~~~~~~il~~~~  135 (317)
                       ..  ....++..+.....       ..+.|+++||+|.+...           ....++..+.  ....++.+|++||+
T Consensus        77 ~~~g~~~~~l~~~f~~A~~-------~~p~il~iDeid~l~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~vlvi~tTn~  149 (258)
T d1e32a2          77 KLAGESESNLRKAFEEAEK-------NAPAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNR  149 (258)
T ss_dssp             SCTTHHHHHHHHHHHHHHH-------TCSEEEEESSGGGTCCHHHHCCCTTHHHHHHHHHHHHHTCCCSSCEEEEEEESC
T ss_pred             cccccHHHHHHHHHHHHHh-------cCCeEEEehhhhhhccCCCCCCCchHHHHHHHhccccccccccCCccEEEeCCC
Confidence             11  12334444443322       35789999999998643           2344444444  23455678889999


Q ss_pred             CCcCchhHhh--hcce-eeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCC----CHHHHHH
Q psy879          136 SEKIIEPIQS--RCAM-LRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQG----DMRQALN  196 (317)
Q Consensus       136 ~~~l~~~i~s--R~~~-i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~g----d~r~~i~  196 (317)
                      ++.+++++++  |+.. ++|++|+.++...+++..+++..+. ++..++.+++.+.|    |+..+++
T Consensus       150 ~~~ld~al~r~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~G~s~adl~~lv~  216 (258)
T d1e32a2         150 PNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLA-DDVDLEQVANETHGHVGADLAALCS  216 (258)
T ss_dssp             GGGSCGGGTSTTSSCEEEECCCCCHHHHHHHHHHTTTTSCBC-TTCCHHHHHHHCTTCCHHHHHHHHH
T ss_pred             ccccchhhhhcccccceeECCCCCHHHHHHHhhhhccCcccc-cccchhhhhhcccCCCHHHHHHHHH
Confidence            9999999998  7866 9999999999999999887654332 22347888888766    5554443

>d1w5sa2 c.37.1.20 (A:7-293) CDC6-like protein APE0152, N-terminal domain {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6-like protein APE0152, N-terminal domain
species: Aeropyrum pernix [TaxId: 56636]

Probab=99.82  E-value=3e-19  Score=151.15  Aligned_cols=209  Identities=21%  Similarity=0.171  Sum_probs=135.9

Q ss_pred             cccCCCCCCcccCCHHHHHHHHH----HHhcCCCc-----eEEEECCCCCCHHHHHHHHHHHHcCC----CCCCceEEec
Q psy879            2 EKYRPQTFSDIVGNEDTVERLKV----FSSSGNVP-----NIIISGPPGVGKTTTILCLARILLGP----SFKDAVLELN   68 (317)
Q Consensus         2 ~ky~P~~~~~~~g~~~~~~~l~~----~l~~~~~~-----~~ll~G~~G~GKt~la~~la~~l~~~----~~~~~~~~~~   68 (317)
                      ++|+|.++   .|++..++.+..    .+..|..+     +++|+||||||||++++++++.+...    .....+.+.+
T Consensus        11 ~~~~P~~~---~~Re~e~~~l~~~l~~~~~~~~~~~~~~~~l~l~GppGtGKT~l~~~l~~~l~~~~~~~~~~~~~~~~~   87 (287)
T d1w5sa2          11 ENYIPPEL---RVRRGEAEALARIYLNRLLSGAGLSDVNMIYGSIGRVGIGKTTLAKFTVKRVSEAAAKEGLTVKQAYVN   87 (287)
T ss_dssp             TTCCCSSC---SSSCHHHHHHHHHHHHHHHTSSCBCCEEEEEECTTCCSSSHHHHHHHHHHHHHHHHHHTTCCEEEEEEE
T ss_pred             CccCCCCC---CCHHHHHHHHHHHHHHHHHcCCCCCCcceEEEeECCCCCCHHHHHHHHHHHHHhhcccccCCceeeeec
Confidence            57999654   566555554443    34444432     36789999999999999999987421    1112233333


Q ss_pred             CCCCcCh----------------------HHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCC------HHHHHHHHHHh
Q psy879           69 ASNDRGI----------------------DTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMT------DGAQQALRRTM  120 (317)
Q Consensus        69 ~~~~~~~----------------------~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~------~~~~~~ll~~l  120 (317)
                      +......                      ..+.+.+.......     ....++++||+|.+.      .+....+...+
T Consensus        88 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-----~~~~~~iide~d~l~~~~~~~~~~~~~l~~l~  162 (287)
T d1w5sa2          88 AFNAPNLYTILSLIVRQTGYPIQVRGAPALDILKALVDNLYVE-----NHYLLVILDEFQSMLSSPRIAAEDLYTLLRVH  162 (287)
T ss_dssp             GGGCCSHHHHHHHHHHHHTCCCCCTTCCHHHHHHHHHHHHHHH-----TCEEEEEEESTHHHHSCTTSCHHHHHHHHTHH
T ss_pred             cccccchhhHHHHHhhhcccccccccchHHHHHHHHHHHHHhc-----cCccccceeEEEEeccccccchhHHHHHHHHH
Confidence            3222221                      11111121111111     457789999999763      34555666666


Q ss_pred             hhcc-----CCceEEEEecCCC------cCchhHhhhc-ceeeecCCCHHHHHHHHHHHHHHc--CCCCCHHHHHHHHHh
Q psy879          121 EIYS-----NTTRFALACNNSE------KIIEPIQSRC-AMLRYNKLTDAQLLSKVIEICEKE--NISHTNDGLEAIVFT  186 (317)
Q Consensus       121 e~~~-----~~~~~il~~~~~~------~l~~~i~sR~-~~i~f~~~~~~~~~~~l~~~~~~~--~~~i~~~~~~~l~~~  186 (317)
                      +...     ....+|++++...      ...+.+.+|. ..++|++|+.+++.+++..+++..  ...+++++++.+++.
T Consensus       163 ~~l~~~~~~~~~~~i~i~~~~~~~~~~~~~~~~~~~r~~~~i~f~~y~~~el~~Il~~r~~~~~~~~~~~~~al~~ia~~  242 (287)
T d1w5sa2         163 EEIPSRDGVNRIGFLLVASDVRALSYMREKIPQVESQIGFKLHLPAYKSRELYTILEQRAELGLRDTVWEPRHLELISDV  242 (287)
T ss_dssp             HHSCCTTSCCBEEEEEEEEETHHHHHHHHHCHHHHTTCSEEEECCCCCHHHHHHHHHHHHHHHBCTTSCCHHHHHHHHHH
T ss_pred             HhcchhhcccceeEEeecccHHHHHHHHhhccchhcccceeeeccCCcHHHHHHHHhhhHHHhhccCCCCHHHHHHHHHH
Confidence            5432     3455677766553      3346777775 559999999999999999998763  335889999999876


Q ss_pred             c------CCCHHHHHHHHHHhhh-----CCCcccHHHHHhhcC
Q psy879          187 A------QGDMRQALNNLQSTHN-----GFGHVTAEYVFKVCD  218 (317)
Q Consensus       187 ~------~gd~r~~i~~l~~~~~-----~~~~i~~~~v~~~~~  218 (317)
                      +      .||+|++++.|+.++.     +...|+.++|.+++.
T Consensus       243 ~~~~~~~~gd~R~ai~~l~~a~~~A~~~~~~~It~~~V~~A~~  285 (287)
T d1w5sa2         243 YGEDKGGDGSARRAIVALKMACEMAEAMGRDSLSEDLVRKAVS  285 (287)
T ss_dssp             HCGGGTSCCCHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHHHH
T ss_pred             HhccccCCCCHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHh
Confidence            5      6999999999987542     567899999987653

>d1r7ra3 c.37.1.20 (A:471-735) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.77  E-value=9.3e-19  Score=146.36  Aligned_cols=171  Identities=20%  Similarity=0.254  Sum_probs=115.5

Q ss_pred             CC-CCCcccCCHHHHHHHHHHHh-----------cCCC--ceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCC
Q psy879            6 PQ-TFSDIVGNEDTVERLKVFSS-----------SGNV--PNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASN   71 (317)
Q Consensus         6 P~-~~~~~~g~~~~~~~l~~~l~-----------~~~~--~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~   71 (317)
                      |+ +|+++.|.+++++.|..++.           .|-.  .++|||||||||||++++++|.++     +..++.+++++
T Consensus         2 p~~~f~di~G~~~~k~~l~~~i~~~l~~~~~~~~~g~~~~~giLL~Gp~GtGKT~l~~ala~~~-----~~~~~~~~~~~   76 (265)
T d1r7ra3           2 PQVTWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANEC-----QANFISIKGPE   76 (265)
T ss_dssp             CCCSCSSCSSSSCCCCHHHHHTHHHHHCHHHHHHCCCCCCCEEEEBCCTTSSHHHHHHHHHHHT-----TCEEEEECHHH
T ss_pred             CCCCHHHhcCHHHHHHHHHHHHHHHhhCHHHHHhCCCCCCCeEEEECCCCCcchhHHHHHHHHh-----CCcEEEEEHHH
Confidence            66 79999998888777666542           1322  249999999999999999999996     34466666432


Q ss_pred             ----C--cChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHH--------------HHHHHHHHhhhc--cCCceE
Q psy879           72 ----D--RGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDG--------------AQQALRRTMEIY--SNTTRF  129 (317)
Q Consensus        72 ----~--~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~--------------~~~~ll~~le~~--~~~~~~  129 (317)
                          .  .....++..+..+..       ..+.+++|||+|.+...              ..+.|+..++..  ..++.+
T Consensus        77 l~~~~~~~~~~~l~~~f~~A~~-------~~p~il~ideid~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~v  149 (265)
T d1r7ra3          77 LLTMWFGESEANVREIFDKARQ-------AAPCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEMDGMSTKKNVFI  149 (265)
T ss_dssp             HHTSCTTTHHHHHHHHHHHHHH-------TCSEEEEESSGGGTCCHHHHCCCTTHHHHHHHHHHHHHTCC------CCEE
T ss_pred             hhhccccchHHHHHHHHHHHHh-------cCCcceeHHhhhhccccCCCcCCCCcHHHHHHHHHHHHHhhCcCCCCCEEE
Confidence                1  122334444443322       35789999999988532              235666666533  334678


Q ss_pred             EEEecCCCcCchhHhh--hcce-eeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCC
Q psy879          130 ALACNNSEKIIEPIQS--RCAM-LRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQG  189 (317)
Q Consensus       130 il~~~~~~~l~~~i~s--R~~~-i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~g  189 (317)
                      |++||.++.+++++++  |+.. ++|++|+.++..++++..+++.... .+..++.++..+.|
T Consensus       150 i~ttn~~~~ld~al~r~gRf~~~i~~~~p~~~~R~~il~~~l~~~~~~-~~~~l~~la~~t~g  211 (265)
T d1r7ra3         150 IGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLRKSPVA-KDVDLEFLAKMTNG  211 (265)
T ss_dssp             EECCBSCTTTSCGGGSSTTSEEEEECCCCCCHHHHHHHHHHTTCC-----CCCCHHHHHHHCS
T ss_pred             EEeCCCchhCCHHHhCCCCccEEEEecchHHHHHHHHHHHHhccCCch-hhhhHHHHHhcCCC
Confidence            8899999999999986  7765 9999999999999998766532221 12234666666543

>d1l8qa2 c.37.1.20 (A:77-289) Chromosomal replication initiation factor DnaA {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Chromosomal replication initiation factor DnaA
species: Aquifex aeolicus [TaxId: 63363]

Probab=99.74  E-value=3.3e-17  Score=132.21  Aligned_cols=186  Identities=15%  Similarity=0.210  Sum_probs=129.5

Q ss_pred             CCC-CCCccc-C--CHHHHHHHHHHHhcCC--CceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHH
Q psy879            5 RPQ-TFSDIV-G--NEDTVERLKVFSSSGN--VPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTV   78 (317)
Q Consensus         5 ~P~-~~~~~~-g--~~~~~~~l~~~l~~~~--~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i   78 (317)
                      .|+ +|++++ |  ++.+.+.+..+++...  .+.++||||+|+|||++++++++++.....  .++.++....  ...+
T Consensus         4 n~~~tFdnF~vg~~N~~a~~~~~~~~~~~~~~~n~l~l~G~~G~GKTHLl~A~~~~~~~~~~--~~~~~~~~~~--~~~~   79 (213)
T d1l8qa2           4 NPKYTLENFIVGEGNRLAYEVVKEALENLGSLYNPIFIYGSVGTGKTHLLQAAGNEAKKRGY--RVIYSSADDF--AQAM   79 (213)
T ss_dssp             CTTCCSSSCCCCTTTHHHHHHHHHHHHTTTTSCSSEEEECSSSSSHHHHHHHHHHHHHHTTC--CEEEEEHHHH--HHHH
T ss_pred             CCCCChhhccCCCcHHHHHHHHHHHHhCcCCCCCcEEEECCCCCcHHHHHHHHHHHhccCcc--ceEEechHHH--HHHH
Confidence            454 699976 4  6677777888776533  233999999999999999999999854332  3333332210  0111


Q ss_pred             HHHH-----HHHHhhcccCCCCceeEEEEeCCCCCC--HHHHHHHHHHhhhc-cCCceEEEEecCCC----cCchhHhhh
Q psy879           79 RNKI-----KMFAQQKVTLPPGRHKIVILDEADSMT--DGAQQALRRTMEIY-SNTTRFALACNNSE----KIIEPIQSR  146 (317)
Q Consensus        79 ~~~~-----~~~~~~~~~~~~~~~~vliiDE~d~l~--~~~~~~ll~~le~~-~~~~~~il~~~~~~----~l~~~i~sR  146 (317)
                      .+.+     ..+...-     ....+++||+++.+.  +..+..|..+++.. .....+|++++.+.    ...+.++||
T Consensus        80 ~~~~~~~~~~~~~~~~-----~~~dll~iDDi~~i~~~~~~~~~lf~lin~~~~~~~~iiits~~~p~~l~~~~~dL~SR  154 (213)
T d1l8qa2          80 VEHLKKGTINEFRNMY-----KSVDLLLLDDVQFLSGKERTQIEFFHIFNTLYLLEKQIILASDRHPQKLDGVSDRLVSR  154 (213)
T ss_dssp             HHHHHHTCHHHHHHHH-----HTCSEEEEECGGGGTTCHHHHHHHHHHHHHHHHTTCEEEEEESSCGGGCTTSCHHHHHH
T ss_pred             HHHHHccchhhHHHHH-----hhccchhhhhhhhhcCchHHHHHHHHHHHHHhhccceEEEecCCcchhccccchHHHHH
Confidence            1110     0111110     245799999999985  55677788888753 35566777777542    457899999


Q ss_pred             cce---eeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHh
Q psy879          147 CAM---LRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQST  201 (317)
Q Consensus       147 ~~~---i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~  201 (317)
                      +..   +..+ |+.++..++|+..+..+|+.+++++++++++.+ .|+|.....+...
T Consensus       155 L~~g~~~~i~-p~d~~~~~iL~~~a~~rgl~l~~~v~~yl~~~~-~~~R~L~~~l~~l  210 (213)
T d1l8qa2         155 FEGGILVEIE-LDNKTRFKIIKEKLKEFNLELRKEVIDYLLENT-KNVREIEGKIKLI  210 (213)
T ss_dssp             HHTSEEEECC-CCHHHHHHHHHHHHHHTTCCCCHHHHHHHHHHC-SSHHHHHHHHHHH
T ss_pred             hhCceEEEEC-CCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHhc-CcHHHHHHHHHHh
Confidence            865   6665 677889999999999999999999999999987 5888877777654

>d1r6bx2 c.37.1.20 (X:169-436) ClpA, an Hsp100 chaperone, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpA, an Hsp100 chaperone, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=99.71  E-value=3.4e-16  Score=129.37  Aligned_cols=193  Identities=15%  Similarity=0.182  Sum_probs=139.6

Q ss_pred             CCCCCcccCCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCC-----CCCceEEecCCCC----cChH
Q psy879            6 PQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPS-----FKDAVLELNASND----RGID   76 (317)
Q Consensus         6 P~~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~-----~~~~~~~~~~~~~----~~~~   76 (317)
                      -..++.++|+++.++.+...+....-+|.++.||||+|||++++.+|+.+....     .+..++.++....    ....
T Consensus        14 ~~~ld~~igRd~Ei~~l~~iL~r~~k~n~lLVG~~GvGKTalv~~la~ri~~~~vp~~l~~~~i~~l~~~~liag~~~~g   93 (268)
T d1r6bx2          14 VGGIDPLIGREKELERAIQVLCRRRKNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDIGSLLAGTKYRG   93 (268)
T ss_dssp             TTCSCCCCSCHHHHHHHHHHHTSSSSCEEEEECCTTSSHHHHHHHHHHHHHHTCSCGGGTTCEEEECCCC---CCCCCSS
T ss_pred             cCCCCcccChHHHHHHHHHHHhcCccCCcEEECCCCCcHHHHHHHHHHHHHhCCcccccccceeEEeeechHhccCccch
Confidence            345788999999999999999877767899999999999999999999875322     1234566554321    1122


Q ss_pred             HHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCH---------HHHHHHHHHhhhccCCceEEEEecCCC-----cCchh
Q psy879           77 TVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTD---------GAQQALRRTMEIYSNTTRFALACNNSE-----KIIEP  142 (317)
Q Consensus        77 ~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~---------~~~~~ll~~le~~~~~~~~il~~~~~~-----~l~~~  142 (317)
                      ++.+.+.......   ...+.-+++|||++.+..         +..+.|..++.  .+...+|.+|++.+     .-.++
T Consensus        94 ~~e~r~~~i~~~~---~~~~~iIlfiDeih~l~~~g~~~g~~~d~a~~Lkp~L~--rg~i~vIgatT~eey~~~~e~d~a  168 (268)
T d1r6bx2          94 DFEKRFKALLKQL---EQDTNSILFIDEIHTIIGAGAASGGQVDAANLIKPLLS--SGKIRVIGSTTYQEFSNIFEKDRA  168 (268)
T ss_dssp             CHHHHHHHHHHHH---SSSSCEEEEETTTTTTTTSCCSSSCHHHHHHHHSSCSS--SCCCEEEEEECHHHHHCCCCCTTS
T ss_pred             hHHHHHHHHHHHh---hccCCceEEecchHHHhcCCCCCCccccHHHHhhHHHh--CCCCeEEEeCCHHHHHHHHhhcHH
Confidence            3333333222221   114567899999998842         34555666676  46778888877642     55799


Q ss_pred             HhhhcceeeecCCCHHHHHHHHHHHH----HHcCCCCCHHHHHHHHHhc------CCCHHHHHHHHHHhhh
Q psy879          143 IQSRCAMLRYNKLTDAQLLSKVIEIC----EKENISHTNDGLEAIVFTA------QGDMRQALNNLQSTHN  203 (317)
Q Consensus       143 i~sR~~~i~f~~~~~~~~~~~l~~~~----~~~~~~i~~~~~~~l~~~~------~gd~r~~i~~l~~~~~  203 (317)
                      +.+||+.|.+.+|+.++...+|....    ..+++.++++++..++..+      ..=+.+|++.|+.++.
T Consensus       169 l~rrF~~I~V~Eps~e~t~~IL~~~~~~~e~~h~v~~~~~al~~~v~ls~ryi~~~~~PdKAIdllDea~a  239 (268)
T d1r6bx2         169 LARRFQKIDITEPSIEETVQIINGLKPKYEAHHDVRYTAKAVRAAVELAVKYINDRHLPDKAIDVIDEAGA  239 (268)
T ss_dssp             SGGGEEEEECCCCCHHHHHHHHHHHHHHHHHHHTCCCCHHHHHHHHHHHHHHCTTSCTTHHHHHHHHHHHH
T ss_pred             HHhhhcccccCCCCHHHHHHHHHHhhHHHhccCCEEeChHHHHHHHHHHHhhccCCCCCcHHHHHHHHHHH
Confidence            99999999999999999999988654    3478999999998887665      3458899999987653

>d1d2na_ c.37.1.20 (A:) Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein {Chinese hamster (Cricetulus griseus) [TaxId: 10029]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein
species: Chinese hamster (Cricetulus griseus) [TaxId: 10029]

Probab=99.70  E-value=5e-16  Score=127.99  Aligned_cols=151  Identities=13%  Similarity=0.200  Sum_probs=98.7

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCc---C----hHHHHHHHHHHHhhcccCCCCceeEEEEeCCC
Q psy879           34 IIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDR---G----IDTVRNKIKMFAQQKVTLPPGRHKIVILDEAD  106 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~---~----~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d  106 (317)
                      +|||||||||||++|+++|+++     +.+++.+++++..   .    ...++..+.....       ..+.|++|||+|
T Consensus        43 vLL~GppGtGKT~la~alA~~~-----~~~~~~i~~~~~~~g~~~~~~~~~i~~if~~A~~-------~~p~il~iDEid  110 (246)
T d1d2na_          43 VLLEGPPHSGKTALAAKIAEES-----NFPFIKICSPDKMIGFSETAKCQAMKKIFDDAYK-------SQLSCVVVDDIE  110 (246)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHH-----TCSEEEEECGGGCTTCCHHHHHHHHHHHHHHHHT-------SSEEEEEECCHH
T ss_pred             EEEECcCCCCHHHHHHHHhhcc-----cccccccccccccccccccchhhhhhhhhhhhhh-------cccceeehhhhh
Confidence            9999999999999999999996     3456777654311   1    1223333333321       357899999998


Q ss_pred             CCC----------HHHHHHHHHHhhhccC---CceEEEEecCCCcCchh-Hhhhcce-eeecCCC-HHHHHHHHHHHHHH
Q psy879          107 SMT----------DGAQQALRRTMEIYSN---TTRFALACNNSEKIIEP-IQSRCAM-LRYNKLT-DAQLLSKVIEICEK  170 (317)
Q Consensus       107 ~l~----------~~~~~~ll~~le~~~~---~~~~il~~~~~~~l~~~-i~sR~~~-i~f~~~~-~~~~~~~l~~~~~~  170 (317)
                      .+.          ....++|+..++....   .+.+|.|||.++.++++ +++||.. ++++.++ .+++.+++...   
T Consensus       111 ~l~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~v~vi~tTn~~~~ld~~~~~~rF~~~i~~P~~~~r~~il~~l~~~---  187 (246)
T d1d2na_         111 RLLDYVPIGPRFSNLVLQALLVLLKKAPPQGRKLLIIGTTSRKDVLQEMEMLNAFSTTIHVPNIATGEQLLEALELL---  187 (246)
T ss_dssp             HHTTCBTTTTBCCHHHHHHHHHHTTCCCSTTCEEEEEEEESCHHHHHHTTCTTTSSEEEECCCEEEHHHHHHHHHHH---
T ss_pred             hHhhhcccccchhHHHHHHHHHHhcCCCccccceeeeeccCChhhccchhhcCccceEEecCCchhHHHHHHHHHhc---
Confidence            753          2345677787775433   35677788988777654 7788876 7886554 34555554432   


Q ss_pred             cCCCCCHHHHHHHHHhcCC-----CHHHHHHHHHHh
Q psy879          171 ENISHTNDGLEAIVFTAQG-----DMRQALNNLQST  201 (317)
Q Consensus       171 ~~~~i~~~~~~~l~~~~~g-----d~r~~i~~l~~~  201 (317)
                       + .+++.....++..+.|     ++++++..++.+
T Consensus       188 -~-~~~~~~~~~i~~~~~g~~~~~~ik~ll~~ie~a  221 (246)
T d1d2na_         188 -G-NFKDKERTTIAQQVKGKKVWIGIKKLLMLIEMS  221 (246)
T ss_dssp             -T-CSCHHHHHHHHHHHTTSEEEECHHHHHHHHHHH
T ss_pred             -c-CCChHHHHHHHHHcCCCccchhHHHHHHHHHHH
Confidence             2 3566667777777665     366666665544

>d1ofha_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: HslU
species: Haemophilus influenzae [TaxId: 727]

Probab=99.67  E-value=1.2e-16  Score=136.50  Aligned_cols=149  Identities=21%  Similarity=0.279  Sum_probs=97.1

Q ss_pred             ccCCHHHHHHHHHHHhc--------------CCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCc----
Q psy879           12 IVGNEDTVERLKVFSSS--------------GNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDR----   73 (317)
Q Consensus        12 ~~g~~~~~~~l~~~l~~--------------~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~----   73 (317)
                      ++||+++++.+..++.+              ..+.++||+||||||||.+|+++|+.+.     ..++.++.+...    
T Consensus        16 ViGQd~A~~~l~~av~~~~~r~~~~~~~~~~~~~~~iLl~GPpG~GKT~lAkalA~~~~-----~~~~~i~~s~~~~~~~   90 (309)
T d1ofha_          16 IIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKLAN-----APFIKVEATKFTEVGY   90 (309)
T ss_dssp             CCSCHHHHHHHHHHHHHHHHTTSSCHHHHHHCCCCCEEEECCTTSSHHHHHHHHHHHHT-----CCEEEEEGGGGSSCCS
T ss_pred             ccChHHHHHHHHHHHHHHHHHhccCCCCccCCCCceEEEECCCCCCHHHHHHHHhhccc-----cchhccccccccccee
Confidence            68999999998876621              1234599999999999999999999973     234444443211    


Q ss_pred             ChHHHHHHHHHHHhhcccCC--CCceeEEEEeCCCCCCHH------------HHHHHHHHhhhc----------cCCceE
Q psy879           74 GIDTVRNKIKMFAQQKVTLP--PGRHKIVILDEADSMTDG------------AQQALRRTMEIY----------SNTTRF  129 (317)
Q Consensus        74 ~~~~i~~~~~~~~~~~~~~~--~~~~~vliiDE~d~l~~~------------~~~~ll~~le~~----------~~~~~~  129 (317)
                      .........+..........  ...+.||++||+|++.+.            .++.|+..++..          ..++.|
T Consensus        91 ~~~~~~~~~~~~f~~a~~~~~~~~~~~IIf~DEIdki~~~~~~~~~~~~~~gv~~~LL~~~dg~~~~~~~~~i~~s~ilf  170 (309)
T d1ofha_          91 VGKEVDSIIRDLTDSAGGAIDAVEQNGIVFIDEIDKICKKGEYSGADVSREGVQRDLLPLVEGSTVSTKHGMVKTDHILF  170 (309)
T ss_dssp             GGGSTTHHHHHHHHTTTTCHHHHHHHCEEEEECGGGGSCCSSCCSSHHHHHHHHHHHHHHHHCCEEEETTEEEECTTCEE
T ss_pred             EeeeccccccccchhhhcccccccCCceEEehhhhhhhhhccCcccchhhhHHHHHhhHHhcCCEEecCCeEEEccceeE
Confidence            01111111222222211000  013679999999998642            467788888731          123344


Q ss_pred             EEE----ecCCCcCchhHhhhcce-eeecCCCHHHHHHHHH
Q psy879          130 ALA----CNNSEKIIEPIQSRCAM-LRYNKLTDAQLLSKVI  165 (317)
Q Consensus       130 il~----~~~~~~l~~~i~sR~~~-i~f~~~~~~~~~~~l~  165 (317)
                      |++    ++.+..+.|.++.|+.. +.|++|+..++.+++.
T Consensus       171 i~~ga~~~~~~~~~~p~l~~R~~~~i~~~~~~~~~~~~Il~  211 (309)
T d1ofha_         171 IASGAFQVARPSDLIPELQGRLPIRVELTALSAADFERILT  211 (309)
T ss_dssp             EEEECCSSSCGGGSCHHHHHTCCEEEECCCCCHHHHHHHHH
T ss_pred             EeccchhhcCcccchhhhhhhhheeeeccCCCHHHHHHHHH
Confidence            544    34566889999999977 9999999999998864

>d1g8pa_ c.37.1.20 (A:) ATPase subunit of magnesium chelatase, BchI {Rhodobacter capsulatus [TaxId: 1061]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ATPase subunit of magnesium chelatase, BchI
species: Rhodobacter capsulatus [TaxId: 1061]

Probab=99.64  E-value=4.7e-16  Score=134.48  Aligned_cols=209  Identities=20%  Similarity=0.211  Sum_probs=121.9

Q ss_pred             CCC-CCCcccCCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcC-------CCCC---------------
Q psy879            5 RPQ-TFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLG-------PSFK---------------   61 (317)
Q Consensus         5 ~P~-~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~-------~~~~---------------   61 (317)
                      ||. -|.+++||+++++.|.-++-.....|+||+||||||||++|+.++..|-.       ....               
T Consensus         1 ~~~~~f~~I~Gq~~~kral~laa~~~~~h~vLl~G~pG~GKT~lar~~~~iLp~~~~~~~~~~~~~~~~~~~~~~~~~~~   80 (333)
T d1g8pa_           1 RPVFPFSAIVGQEDMKLALLLTAVDPGIGGVLVFGDRGTGKSTAVRALAALLPEIEAVEGCPVSSPNVEMIPDWATVLST   80 (333)
T ss_dssp             CCCCCGGGSCSCHHHHHHHHHHHHCGGGCCEEEECCGGGCTTHHHHHHHHHSCCEEEETTCTTCCSSGGGSCTTCCCSCC
T ss_pred             CCCCChhhccCcHHHHHHHHHHHhccCCCeEEEECCCCccHHHHHHHHHHhCCCchhhccCccccCccccccchhhcccc
Confidence            565 49999999999987664443211127999999999999999999986510       0000               


Q ss_pred             ------CceEEecCCCCcChHHH------HHHHHHH--HhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhc----
Q psy879           62 ------DAVLELNASNDRGIDTV------RNKIKMF--AQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIY----  123 (317)
Q Consensus        62 ------~~~~~~~~~~~~~~~~i------~~~~~~~--~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~----  123 (317)
                            .++.....  ......+      .......  ...+..+..+..+|+++||++.+.++.+++|++.||+.    
T Consensus        81 ~~~~~~~~~~~~~~--~~~~~~l~G~~d~~~~~~~g~~~~~~G~l~~A~~gvl~iDEi~~~~~~~~~aLl~~me~~~v~i  158 (333)
T d1g8pa_          81 NVIRKPTPVVDLPL--GVSEDRVVGALDIERAISKGEKAFEPGLLARANRGYLYIDECNLLEDHIVDLLLDVAQSGENVV  158 (333)
T ss_dssp             CEEEECCCEEEECT--TCCHHHHHCEECHHHHHHHCGGGEECCHHHHHTTEEEEETTGGGSCHHHHHHHHHHHHHSEEEE
T ss_pred             CcccccCceeeccC--CCCcccccCcchhhhccccCcceeeccccccccccEeecccHHHHHHHHHHHHhhhhcCCeEEe
Confidence                  00111111  1111111      1111110  00010011134689999999999999999999999953    


Q ss_pred             ---------cCCceEEEEecCC-CcCchhHhhhcce-eeecCCCHH-HHHHHHHH-------------------------
Q psy879          124 ---------SNTTRFALACNNS-EKIIEPIQSRCAM-LRYNKLTDA-QLLSKVIE-------------------------  166 (317)
Q Consensus       124 ---------~~~~~~il~~~~~-~~l~~~i~sR~~~-i~f~~~~~~-~~~~~l~~-------------------------  166 (317)
                               |..+.++.++|+. .++.+++.+||.. +.+..+... +....+..                         
T Consensus       159 ~r~g~~~~~p~~f~liaa~Np~~~~l~~~llDRf~~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  238 (333)
T d1g8pa_         159 ERDGLSIRHPARFVLVGSGNPEEGDLRPQLLDRFGLSVEVLSPRDVETRVEVIRRRDTYDADPKAFLEEWRPKDMDIRNQ  238 (333)
T ss_dssp             CCTTCCEEEECCEEEEEEECSCSCCCCHHHHTTCSEEEECCCCCSHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHH
T ss_pred             cccCceecCCCCEEEEEecCccccccccchhhhhcceeeccCcchhhHHHHHHHhhhhcccChHHHHHHHHHHHHHHHHH
Confidence                     3445566666654 4799999999987 677665432 21111111                         


Q ss_pred             ----HHHHcCCCCCHHHHHHHHHh---cCC-CHHHHHHHHHHh---h--hCCCcccHHHHHh
Q psy879          167 ----ICEKENISHTNDGLEAIVFT---AQG-DMRQALNNLQST---H--NGFGHVTAEYVFK  215 (317)
Q Consensus       167 ----~~~~~~~~i~~~~~~~l~~~---~~g-d~r~~i~~l~~~---~--~~~~~i~~~~v~~  215 (317)
                          ...-..+.++++....+...   .+. ++|....+++.+   +  .+...|+.+|+.+
T Consensus       239 ~~~~~~~l~~v~~~~~~~~~~~~~~~~~~~~S~R~~~~llrvArtiA~L~gr~~V~~~di~~  300 (333)
T d1g8pa_         239 ILEARERLPKVEAPNTALYDCAALCIALGSDGLRGELTLLRSARALAALEGATAVGRDHLKR  300 (333)
T ss_dssp             HHHHHHHGGGCBCCHHHHHHHHHHHHHSSSCSHHHHHHHHHHHHHHHHHTTCSBCCHHHHHH
T ss_pred             HHHHhhcccceecCHHHHHHHHHHHHHcCCCChHHHHHHHHHHHHHHHHcCCCCCCHHHHHH
Confidence                00112344555555544433   222 678777777542   2  2677888888865

>d1r6bx3 c.37.1.20 (X:437-751) ClpA, an Hsp100 chaperone, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpA, an Hsp100 chaperone, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=99.63  E-value=1.4e-14  Score=123.56  Aligned_cols=166  Identities=16%  Similarity=0.228  Sum_probs=116.1

Q ss_pred             CcccCCHHHHHHHHHHHh--------cCCCc-eEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCC--------
Q psy879           10 SDIVGNEDTVERLKVFSS--------SGNVP-NIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASND--------   72 (317)
Q Consensus        10 ~~~~g~~~~~~~l~~~l~--------~~~~~-~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~--------   72 (317)
                      ..++||+++++.+..++.        ..++. +++|.||+|+|||.+|+.+|+.+..     +++.++.+..        
T Consensus        22 ~~viGQ~~a~~~v~~~v~~~~~~l~~~~~p~~~~lf~Gp~GvGKT~lak~la~~l~~-----~~i~~d~s~~~~~~~~~~   96 (315)
T d1r6bx3          22 MLVFGQDKAIEALTEAIKMARAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKALGI-----ELLRFDMSEYMERHTVSR   96 (315)
T ss_dssp             TTSCSCHHHHHHHHHHHHHHHTTCSCTTSCSEEEEEECSTTSSHHHHHHHHHHHHTC-----EEEEEEGGGCSSSSCCSS
T ss_pred             CeecChHHHHHHHHHHHHHHHccCCCCCCCceEEEEECCCcchhHHHHHHHHhhccC-----CeeEeccccccchhhhhh
Confidence            367899999999877763        12233 4999999999999999999998732     2443332211        


Q ss_pred             --------cChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhc-----------cCCceEEEEe
Q psy879           73 --------RGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIY-----------SNTTRFALAC  133 (317)
Q Consensus        73 --------~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~-----------~~~~~~il~~  133 (317)
                              .+... ...+......      ..+.|+++||+|++.++.++.|++.+++.           -.++++|+++
T Consensus        97 l~g~~~gy~g~~~-~~~l~~~~~~------~~~~vvl~DeieKa~~~V~~~lLqild~G~ltd~~Gr~vdf~n~iiI~Ts  169 (315)
T d1r6bx3          97 LIGAPPGYVGFDQ-GGLLTDAVIK------HPHAVLLLDEIEKAHPDVFNILLQVMDNGTLTDNNGRKADFRNVVLVMTT  169 (315)
T ss_dssp             SCCCCSCSHHHHH-TTHHHHHHHH------CSSEEEEEETGGGSCHHHHHHHHHHHHHSEEEETTTEEEECTTEEEEEEE
T ss_pred             hcccCCCcccccc-CChhhHHHHh------CccchhhhcccccccchHhhhhHHhhccceecCCCCCccCccceEEEecc
Confidence                    01110 0111111111      45789999999999999999999999852           3567788888


Q ss_pred             cCCC-------------------------cCchhHhhhcce-eeecCCCHHHHHHHHHHHHH-------HcC--CCCCHH
Q psy879          134 NNSE-------------------------KIIEPIQSRCAM-LRYNKLTDAQLLSKVIEICE-------KEN--ISHTND  178 (317)
Q Consensus       134 ~~~~-------------------------~l~~~i~sR~~~-i~f~~~~~~~~~~~l~~~~~-------~~~--~~i~~~  178 (317)
                      |-..                         .+.|.+..|+.. +.|.|++.+++.+++...+.       ..+  +.++++
T Consensus       170 nig~~~i~~~~~~~~~~~~~~~~~~~l~~~f~pEflnRid~ii~f~~l~~~~~~~I~~~~l~~~~~~l~~~~i~l~~~~~  249 (315)
T d1r6bx3         170 NAGVRETERKSIGLIHQDNSTDAMEEIKKIFTPEFRNRLDNIIWFDHLSTDVIHQVVDKFIVELQVQLDQKGVSLEVSQE  249 (315)
T ss_dssp             CSSCC-----------------CHHHHHHHSCHHHHTTCSEEEECCCCCHHHHHHHHHHHHHHHHHHHHHTTEEEEECHH
T ss_pred             chhhHHHHhhhccchhhhhhHhHHHHHHHhcCHHHHhhhhhhhcccchhhhHHHHHHHHHHHHHHHHHHhcCcchhhHHH
Confidence            8321                         267888999985 99999999999988765443       223  456889


Q ss_pred             HHHHHHHhc
Q psy879          179 GLEAIVFTA  187 (317)
Q Consensus       179 ~~~~l~~~~  187 (317)
                      ++++++...
T Consensus       250 a~~~l~~~~  258 (315)
T d1r6bx3         250 ARNWLAEKG  258 (315)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHhC
Confidence            999888753

>d1qvra3 c.37.1.20 (A:536-850) ClpB, AAA+ modules {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Thermus thermophilus [TaxId: 274]

Probab=99.62  E-value=7.4e-15  Score=125.09  Aligned_cols=169  Identities=15%  Similarity=0.216  Sum_probs=118.2

Q ss_pred             cccCCHHHHHHHHHHHhc--------CCCc-eEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHH--
Q psy879           11 DIVGNEDTVERLKVFSSS--------GNVP-NIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVR--   79 (317)
Q Consensus        11 ~~~g~~~~~~~l~~~l~~--------~~~~-~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~--   79 (317)
                      .++||+++++.+...+..        .++. .++|+||+|+|||.+|+.+|+.+.+..  ..++.++.+.......+.  
T Consensus        24 ~v~GQ~~ai~~v~~~i~~~~~~l~~~~kp~~~~lf~Gp~G~GKt~lak~la~~l~~~~--~~~~~~~~~~~~~~~~~~~L  101 (315)
T d1qvra3          24 RVVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAATLFDTE--EAMIRIDMTEYMEKHAVSRL  101 (315)
T ss_dssp             HSCSCHHHHHHHHHHHHHHGGGCSCSSSCSEEEEEBSCSSSSHHHHHHHHHHHHHSSG--GGEEEECTTTCCSSGGGGGC
T ss_pred             eEeCHHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCcchHHHHHHHHHHHhcCCC--cceEEEeccccccchhhhhh
Confidence            578999999987766541        1222 489999999999999999999986543  334555443322111100  


Q ss_pred             -------------HHHHHHHhhcccCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhc-----------cCCceEEEEecC
Q psy879           80 -------------NKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIY-----------SNTTRFALACNN  135 (317)
Q Consensus        80 -------------~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~-----------~~~~~~il~~~~  135 (317)
                                   ..+......      ..+.|+++||+|++.++.++.|++++++.           ..++.+|++||-
T Consensus       102 ~g~~~gyvG~~~~~~l~~~~~~------~p~~Vvl~DEieK~~~~v~~~ll~~l~~g~~~~~~gr~v~~~~~i~i~tsnl  175 (315)
T d1qvra3         102 IGAPPGYVGYEEGGQLTEAVRR------RPYSVILFDEIEKAHPDVFNILLQILDDGRLTDSHGRTVDFRNTVIILTSNL  175 (315)
T ss_dssp             --------------CHHHHHHH------CSSEEEEESSGGGSCHHHHHHHHHHHTTTEECCSSSCCEECTTEEEEEECCT
T ss_pred             cCCCCCCcCcccCChHHHHHHh------CCCcEEEEehHhhcCHHHHHHHHHHhccCceeCCCCcEecCcceEEEEeccc
Confidence                         111111111      35789999999999999999999999853           245667888874


Q ss_pred             C--------------------------CcCchhHhhhcce-eeecCCCHHHHHHHHHHHHH-------HcC--CCCCHHH
Q psy879          136 S--------------------------EKIIEPIQSRCAM-LRYNKLTDAQLLSKVIEICE-------KEN--ISHTNDG  179 (317)
Q Consensus       136 ~--------------------------~~l~~~i~sR~~~-i~f~~~~~~~~~~~l~~~~~-------~~~--~~i~~~~  179 (317)
                      -                          ..+.|.+.+|+.. +.|.+++.+++.+++...+.       ..+  +.+++++
T Consensus       176 G~~~i~~~~~~~~~~~~~~~~~~~~l~~~f~pEflnRid~Ii~F~~L~~~~~~~I~~~~l~~l~~rl~~~~i~l~i~~~~  255 (315)
T d1qvra3         176 GSPLILEGLQKGWPYERIRDEVFKVLQQHFRPEFLNRLDEIVVFRPLTKEQIRQIVEIQLSYLRARLAEKRISLELTEAA  255 (315)
T ss_dssp             THHHHHHHHHTTCCHHHHHHHHHHHHHTTSCHHHHHTCSBCCBCCCCCHHHHHHHHHHHHHHHHHHHHTTTCEEEECHHH
T ss_pred             ChHHHhhhcccccchhhhhHHHHHHHHhhcCHHHHhcCCeeeeccchhhhhhHHHHHHHHHHHHHHHHhccccccccHHH
Confidence            2                          2478999999987 68999999999998775433       223  3568999


Q ss_pred             HHHHHHhc
Q psy879          180 LEAIVFTA  187 (317)
Q Consensus       180 ~~~l~~~~  187 (317)
                      ++.|++.+
T Consensus       256 ~~~L~~~~  263 (315)
T d1qvra3         256 KDFLAERG  263 (315)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHhC
Confidence            99998774

>d1qvra2 c.37.1.20 (A:149-535) ClpB, AAA+ modules {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Thermus thermophilus [TaxId: 274]

Probab=99.60  E-value=2e-14  Score=125.17  Aligned_cols=193  Identities=16%  Similarity=0.208  Sum_probs=131.2

Q ss_pred             CCCCcccCCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCC-----CCCceEEecCCCCc----ChHH
Q psy879            7 QTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPS-----FKDAVLELNASNDR----GIDT   77 (317)
Q Consensus         7 ~~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~-----~~~~~~~~~~~~~~----~~~~   77 (317)
                      ..++.++|++..++.+...+.....+|.+|.||||+|||+++..+|+.+....     .+..++.++.....    ...+
T Consensus        19 g~ld~~~gr~~ei~~~~~~L~r~~k~n~llvG~~GvGKtaiv~~la~~i~~~~vp~~l~~~~i~~ld~~~l~ag~~~~g~   98 (387)
T d1qvra2          19 GKLDPVIGRDEEIRRVIQILLRRTKNNPVLIGEPGVGKTAIVEGLAQRIVKGDVPEGLKGKRIVSLQMGSLLAGAKYRGE   98 (387)
T ss_dssp             TCSCCCCSCHHHHHHHHHHHHCSSCCCCEEEECTTSCHHHHHHHHHHHHHHTCSCTTSTTCEEEEECC-----------C
T ss_pred             CCCCCCcCcHHHHHHHHHHHhcCCCCCCeEECCCCCCHHHHHHHHHHHHHhCCCCHHHcCceEEEeeHhhhhcccCcchh
Confidence            45788999999999999988766666789999999999999999998875322     12346666654311    1122


Q ss_pred             HHHHHHHHHhhcccCCCCceeEEEEeCCCCCCH--------HHHHHHHHHhhhccCCceEEEEecCCC----cCchhHhh
Q psy879           78 VRNKIKMFAQQKVTLPPGRHKIVILDEADSMTD--------GAQQALRRTMEIYSNTTRFALACNNSE----KIIEPIQS  145 (317)
Q Consensus        78 i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~--------~~~~~ll~~le~~~~~~~~il~~~~~~----~l~~~i~s  145 (317)
                      +.+.+........  ...++-|++|||++.+..        +..+.|..+|..  +...+|.+|+..+    .-++++.+
T Consensus        99 ~e~r~~~i~~~~~--~~~~~~ilfide~h~l~~~g~~~g~~d~a~~Lkp~L~r--g~~~~I~~tT~~ey~~~e~d~al~r  174 (387)
T d1qvra2          99 FEERLKAVIQEVV--QSQGEVILFIDELHTVVGAGKAEGAVDAGNMLKPALAR--GELRLIGATTLDEYREIEKDPALER  174 (387)
T ss_dssp             HHHHHHHHHHHHH--TTCSSEEEEECCC-------------------HHHHHT--TCCCEEEEECHHHHHHHTTCTTTCS
T ss_pred             HHHHHHHHHHHhc--cCCCceEEEeccHHHHhcCCCCCCcccHHHHHHHHHhC--CCcceeeecCHHHHHHhcccHHHHH
Confidence            3232222211110  012456899999999843        346778888885  6677888877542    34799999


Q ss_pred             hcceeeecCCCHHHHHHHHHHHHH----HcCCCCCHHHHHHHHHhc------CCCHHHHHHHHHHhhh
Q psy879          146 RCAMLRYNKLTDAQLLSKVIEICE----KENISHTNDGLEAIVFTA------QGDMRQALNNLQSTHN  203 (317)
Q Consensus       146 R~~~i~f~~~~~~~~~~~l~~~~~----~~~~~i~~~~~~~l~~~~------~gd~r~~i~~l~~~~~  203 (317)
                      ||+.|.+.+|+.++...+|.....    .+++.++++++...+..+      ..=+.+|+++|+.++.
T Consensus       175 rF~~v~v~ep~~~~~~~il~~~~~~~e~~h~v~~~~~ai~~~v~ls~ryi~~r~~PdKAidlld~a~a  242 (387)
T d1qvra2         175 RFQPVYVDEPTVEETISILRGLKEKYEVHHGVRISDSAIIAAATLSHRYITERRLPDKAIDLIDEAAA  242 (387)
T ss_dssp             CCCCEEECCCCHHHHHHHHHHHHHHHHHHTTCEECHHHHHHHHHHHHHHCCSSCTHHHHHHHHHHHHH
T ss_pred             hcccccCCCCcHHHHHHHHHHHHHHHHhccCCcccHHHHHHHHHhcccccccccChhhHHHHHHHHHH
Confidence            999999999999999999887654    368999999998888765      3579999999997665

>d1ny5a2 c.37.1.20 (A:138-384) Transcriptional activator sigm54 (NtrC1), C-terminal domain {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Transcriptional activator sigm54 (NtrC1), C-terminal domain
species: Aquifex aeolicus [TaxId: 63363]

Probab=99.59  E-value=9.8e-14  Score=114.05  Aligned_cols=203  Identities=16%  Similarity=0.152  Sum_probs=134.1

Q ss_pred             cccCCHHHHHHHHHHHhcC--CCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHHHHHHHhh
Q psy879           11 DIVGNEDTVERLKVFSSSG--NVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFAQQ   88 (317)
Q Consensus        11 ~~~g~~~~~~~l~~~l~~~--~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~   88 (317)
                      ++||+....+.+...++.-  ...+++++||+||||+++|+++...  .......++.+++... ........+......
T Consensus         1 ~~v~~S~~~~~~~~~~~~~a~~~~pvlI~Ge~GtGK~~~A~~ih~~--s~~~~~~~~~~~~~~~-~~~~~~~~lfg~~~~   77 (247)
T d1ny5a2           1 EYVFESPKMKEILEKIKKISCAECPVLITGESGVGKEVVARLIHKL--SDRSKEPFVALNVASI-PRDIFEAELFGYEKG   77 (247)
T ss_dssp             CCCCCSHHHHHHHHHHHHHTTCCSCEEEECSTTSSHHHHHHHHHHH--STTTTSCEEEEETTTS-CHHHHHHHHHCBCTT
T ss_pred             CeEecCHHHHHHHHHHHHHhCCCCCEEEECCCCcCHHHHHHHHHHh--cCCcccccccchhhhh-hhcccHHHhcCcccC
Confidence            5788877777665555431  1225999999999999999999875  3334445666666532 222222221111111


Q ss_pred             cccCC---------CCceeEEEEeCCCCCCHHHHHHHHHHhhhcc-----------CCceEEEEecCC-------CcCch
Q psy879           89 KVTLP---------PGRHKIVILDEADSMTDGAQQALRRTMEIYS-----------NTTRFALACNNS-------EKIIE  141 (317)
Q Consensus        89 ~~~~~---------~~~~~vliiDE~d~l~~~~~~~ll~~le~~~-----------~~~~~il~~~~~-------~~l~~  141 (317)
                      .+...         ...+..++|||+|.|....|..|++++++..           .++++|++|+.+       ..+.+
T Consensus        78 ~~~~~~~~~~g~l~~a~gGtL~l~~i~~L~~~~Q~~L~~~l~~~~~~~~~~~~~~~~~~RlI~~s~~~l~~l~~~~~f~~  157 (247)
T d1ny5a2          78 AFTGAVSSKEGFFELADGGTLFLDEIGELSLEAQAKLLRVIESGKFYRLGGRKEIEVNVRILAATNRNIKELVKEGKFRE  157 (247)
T ss_dssp             SSTTCCSCBCCHHHHTTTSEEEEESGGGCCHHHHHHHHHHHHHSEECCBTCCSBEECCCEEEEEESSCHHHHHHTTSSCH
T ss_pred             CcCCcccccCCHHHccCCCEEEEeChHhCCHHHHHHHHHHHHhCCEEECCCCCceecCeEEEEecCCCHHHHHHcCCCcH
Confidence            11000         1345689999999999999999999998421           246788888764       25777


Q ss_pred             hHhhhcce--eeecCCCH--HHHHHHHHH----HHHHcCC---CCCHHHHHHHHHh-cCCCHHHHHHHHHHhhh--CCCc
Q psy879          142 PIQSRCAM--LRYNKLTD--AQLLSKVIE----ICEKENI---SHTNDGLEAIVFT-AQGDMRQALNNLQSTHN--GFGH  207 (317)
Q Consensus       142 ~i~sR~~~--i~f~~~~~--~~~~~~l~~----~~~~~~~---~i~~~~~~~l~~~-~~gd~r~~i~~l~~~~~--~~~~  207 (317)
                      .+..|+..  +.+||+.+  +++..++..    .+...+.   .++++++..+... ..||+++..+.++.++.  ....
T Consensus       158 ~L~~~l~~~~i~lPpLreR~~Di~~l~~~~l~~~~~~~~~~~~~ls~~al~~L~~~~WPGNl~EL~~~l~~a~~~~~~~~  237 (247)
T d1ny5a2         158 DLYYRLGVIEIEIPPLRERKEDIIPLANHFLKKFSRKYAKEVEGFTKSAQELLLSYPWYGNVRELKNVIERAVLFSEGKF  237 (247)
T ss_dssp             HHHHHHTTEEEECCCGGGCHHHHHHHHHHHHHHHHHHTTCCCCEECHHHHHHHHHSCCTTHHHHHHHHHHHHHHHCCSSE
T ss_pred             HHHhhcCeeeecCCChhhchhhHhhhhhhhhhhhhhhcCCCCCCCCHHHHHHHHhCCCCCHHHHHHHHHHHHHHhCCCCe
Confidence            88888765  77777754  566544444    4444443   3689999988776 48999999999987655  5567


Q ss_pred             ccHHHHHhh
Q psy879          208 VTAEYVFKV  216 (317)
Q Consensus       208 i~~~~v~~~  216 (317)
                      |+.+++-.+
T Consensus       238 I~~~dl~~l  246 (247)
T d1ny5a2         238 IDRGELSCL  246 (247)
T ss_dssp             ECHHHHHHH
T ss_pred             ECHHHcccc
Confidence            888887653

>d1um8a_ c.37.1.20 (A:) ClpX {Helicobacter pylori [TaxId: 210]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpX
species: Helicobacter pylori [TaxId: 210]

Probab=99.56  E-value=9.4e-15  Score=126.64  Aligned_cols=182  Identities=17%  Similarity=0.206  Sum_probs=114.7

Q ss_pred             cccCCHHHHHHHHHHHh------------------------------cCCCceEEEECCCCCCHHHHHHHHHHHHcCCCC
Q psy879           11 DIVGNEDTVERLKVFSS------------------------------SGNVPNIIISGPPGVGKTTTILCLARILLGPSF   60 (317)
Q Consensus        11 ~~~g~~~~~~~l~~~l~------------------------------~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~   60 (317)
                      .++||+++++.+..+++                              +..++++||.||+|+|||.+|+++|+.+.    
T Consensus        18 ~ViGQd~Akkava~Avrn~~rR~~~~~~~r~~~~~~~~~~~~~~~~~~~p~~niLfiGPTGvGKTElAk~LA~~~~----   93 (364)
T d1um8a_          18 YVIGQEQAKKVFSVAVYNHYKRLSFKEKLKKQDNQDSNVELEHLEEVELSKSNILLIGPTGSGKTLMAQTLAKHLD----   93 (364)
T ss_dssp             TCCSCHHHHHHHHHHHHHHHHHHHHHHHHHHHCSHHHHHHHHHHHHTTCCCCCEEEECCTTSSHHHHHHHHHHHTT----
T ss_pred             eecChHHHHHHHHHHHHHHHHHHHHHHHhhccccccccccccccccccCCCcceeeeCCCCccHHHHHHHHHhhcc----
Confidence            57899999998877663                              22344599999999999999999999852    


Q ss_pred             CCceEEecCCCCcC--------hHHHHHHHHHHHhhcccCCCCceeEEEEeCCCC--------------CCHHHHHHHHH
Q psy879           61 KDAVLELNASNDRG--------IDTVRNKIKMFAQQKVTLPPGRHKIVILDEADS--------------MTDGAQQALRR  118 (317)
Q Consensus        61 ~~~~~~~~~~~~~~--------~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~--------------l~~~~~~~ll~  118 (317)
                       .+++.++++....        ...+.+.+......   ....++.++++||+++              ..++.++.|++
T Consensus        94 -~~~ir~D~s~~~e~gyvg~dv~~~i~~l~~~~~~~---v~~~~~~iv~lDEieK~~~~s~~~~~~~d~a~~~V~~~lLq  169 (364)
T d1um8a_          94 -IPIAISDATSLTEAGYVGEDVENILTRLLQASDWN---VQKAQKGIVFIDEIDKISRLSENRSITRDVSGEGVQQALLK  169 (364)
T ss_dssp             -CCEEEEEGGGCC--------CTHHHHHHHHHTTTC---HHHHTTSEEEEETGGGC--------------CHHHHHHHHH
T ss_pred             -cceeehhhhhcccchhhHhhhccchhhhhhhchhH---HHHhhcccchhhhhhhhccccccccccccccchHHHHhhhh
Confidence             2344444332111        12233333221100   0013578999999999              45567999999


Q ss_pred             Hhhhcc-------------CCceEEEEecC-------------------------------------------------C
Q psy879          119 TMEIYS-------------NTTRFALACNN-------------------------------------------------S  136 (317)
Q Consensus       119 ~le~~~-------------~~~~~il~~~~-------------------------------------------------~  136 (317)
                      .++...             .++.++.++|-                                                 .
T Consensus       170 ild~~~~~~~~~~gr~~~~~~~i~i~t~~i~~~~~ga~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  249 (364)
T d1um8a_         170 IVEGSLVNIPPKGGRKHPEGNFIQIDTSDILFICAGAFDGLAEIIKKRTTQNVLGFTQEKMSKKEQEAILHLVQTHDLVT  249 (364)
T ss_dssp             HHHCCEEC---------------CEECTTCEEEEEECCTTHHHHTTTSCSSCCCSCCCSSCCTTTTTTSGGGCCHHHHHH
T ss_pred             hhcCceeccCCCCCCcCCcceeEEEeehhhhhhhcccchhhhhhhhhhcccccccccccccchhhhhhhhccccHHHHhh
Confidence            999311             12233333321                                                 0


Q ss_pred             CcCchhHhhhcce-eeecCCCHHHHHHHHHH-----------HHHHcCC--CCCHHHHHHHHHhc---CCCHHHHHHHHH
Q psy879          137 EKIIEPIQSRCAM-LRYNKLTDAQLLSKVIE-----------ICEKENI--SHTNDGLEAIVFTA---QGDMRQALNNLQ  199 (317)
Q Consensus       137 ~~l~~~i~sR~~~-i~f~~~~~~~~~~~l~~-----------~~~~~~~--~i~~~~~~~l~~~~---~gd~r~~i~~l~  199 (317)
                      ..+.|.+..|+.. +.|.+++.+++.+++..           .++.+|+  .+++++++++++.+   .-..|.+...++
T Consensus       250 ~~f~PEf~gRi~~iv~f~~L~~~~l~~Il~~~~~~l~kq~~~~l~~~gi~L~~td~a~~~la~~g~d~~~GAR~L~riie  329 (364)
T d1um8a_         250 YGLIPELIGRLPVLSTLDSISLEAMVDILQKPKNALIKQYQQLFKMDEVDLIFEEEAIKEIAQLALERKTGARGLRAIIE  329 (364)
T ss_dssp             TTCCHHHHTTCCEEEECCCCCHHHHHHHHHSSTTCHHHHHHHHHHTTTCEEEECHHHHHHHHHHHHHTTCTGGGHHHHHH
T ss_pred             hhhHHHHHHHhcchhhHhhhhHHHHHHHHHHHHHHHHHHHHHHHHhCCcEEEECHHHHHHHHHhccCCCCCchHHHHHHH
Confidence            0256888999987 99999999999999862           2333455  46899999999753   233444444444


Q ss_pred             H
Q psy879          200 S  200 (317)
Q Consensus       200 ~  200 (317)
                      .
T Consensus       330 ~  330 (364)
T d1um8a_         330 D  330 (364)
T ss_dssp             H
T ss_pred             H
Confidence            4

>d1jbka_ c.37.1.20 (A:) ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=99.54  E-value=2.2e-14  Score=112.00  Aligned_cols=157  Identities=16%  Similarity=0.216  Sum_probs=112.3

Q ss_pred             cCCCCCCcccCCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCC-----CCCceEEecCCC----CcC
Q psy879            4 YRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPS-----FKDAVLELNASN----DRG   74 (317)
Q Consensus         4 y~P~~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~-----~~~~~~~~~~~~----~~~   74 (317)
                      -+...++.++|+++.++.+...+....-+|.+|.||||+|||+++..+|+.+....     .+..+++++...    ...
T Consensus        16 a~~g~ld~~igRd~Ei~~l~~iL~r~~k~n~lLvG~pGVGKTalv~~LA~ri~~~~vp~~L~~~~i~~ld~~~LiAg~~~   95 (195)
T d1jbka_          16 AEQGKLDPVIGRDEEIRRTIQVLQRRTKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLALDMGALVAGAKY   95 (195)
T ss_dssp             HHTTCSCCCCSCHHHHHHHHHHHTSSSSCEEEEECCTTSCHHHHHHHHHHHHHHTCSCGGGTTCEEEEECHHHHHTTTCS
T ss_pred             HHcCCCCCCcCcHHHHHHHHHHHhccCCCCeEEEecCCcccHHHHHHHHHHHHhCCCCHHHcCceEEEeeHHHHhccCCc
Confidence            34567889999999999999999877767899999999999999999999885322     134466665422    222


Q ss_pred             hHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHH--------HHHHHHHHhhhccCCceEEEEecCCC-----cCch
Q psy879           75 IDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDG--------AQQALRRTMEIYSNTTRFALACNNSE-----KIIE  141 (317)
Q Consensus        75 ~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~--------~~~~ll~~le~~~~~~~~il~~~~~~-----~l~~  141 (317)
                      ..++.+.+........  .....-|++|||++.+...        ..+.|..+|+.  +...+|.+|+..+     .-.+
T Consensus        96 rG~~E~rl~~il~e~~--~~~~~iILfIDeih~l~~~g~~~g~~d~~~~Lkp~L~r--g~l~~IgatT~eey~~~~e~d~  171 (195)
T d1jbka_          96 RGEFEERLKGVLNDLA--KQEGNVILFIDELHTMVGAGKADGAMDAGNMLKPALAR--GELHCVGATTLDEYRQYIEKDA  171 (195)
T ss_dssp             HHHHHHHHHHHHHHHH--HSTTTEEEEEETGGGGTT------CCCCHHHHHHHHHT--TSCCEEEEECHHHHHHHTTTCH
T ss_pred             cHHHHHHHHHHHHHHh--cCCCcEEEEcchHHHHhcCCCCCCcccHHHHHHHHHhC--CCceEEecCCHHHHHHHHHcCH
Confidence            3344443332221110  0124569999999998543        34778888884  6677888877542     5589


Q ss_pred             hHhhhcceeeecCCCHHHHHHHH
Q psy879          142 PIQSRCAMLRYNKLTDAQLLSKV  164 (317)
Q Consensus       142 ~i~sR~~~i~f~~~~~~~~~~~l  164 (317)
                      ++.+||+.|...+|+.++...+|
T Consensus       172 aL~rrF~~I~V~Ep~~e~t~~IL  194 (195)
T d1jbka_         172 ALERRFQKVFVAEPSVEDTIAIL  194 (195)
T ss_dssp             HHHTTEEEEECCCCCHHHHHTTC
T ss_pred             HHHhcCCEeecCCCCHHHHHHHh
Confidence            99999999999999999877654

>d1svma_ c.37.1.20 (A:) Papillomavirus large T antigen helicase domain {Simian virus 40 [TaxId: 10633]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Papillomavirus large T antigen helicase domain
species: Simian virus 40 [TaxId: 10633]

Probab=99.38  E-value=8.4e-15  Score=126.77  Aligned_cols=163  Identities=15%  Similarity=0.018  Sum_probs=88.9

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHHHHHHHh----h--cccCCCCceeEEEEeCCC
Q psy879           33 NIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFAQ----Q--KVTLPPGRHKIVILDEAD  106 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~----~--~~~~~~~~~~vliiDE~d  106 (317)
                      .++||||||||||++++++|+.+.     ..++.+|.++..+...++........    .  ........+.++++||+|
T Consensus       156 ~~~~~g~~~~gk~~~~~~~~~~~~-----~~~i~in~s~~rs~~~l~~~~~~~~~l~d~~~~~~~~~~~~~~~~~~DeiD  230 (362)
T d1svma_         156 YWLFKGPIDSGKTTLAAALLELCG-----GKALNVNLPLDRLNFELGVAIDQFLVVFEDVKGTGGESRDLPSGQGINNLD  230 (362)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHC-----CEEECCSSCTTTHHHHHGGGTTCSCEEETTCCCSTTTTTTCCCCSHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHHcC-----CCEEEEECcchhhHHHHHhHHHHHHHHHHHHHHhhhhccCCCCeEEEehHh
Confidence            499999999999999999999984     34778887765443322211110000    0  000000123455555555


Q ss_pred             CCCHHHHHHHHHHhhhc------cCCceEEEEecCCC-cCchhHhhhcceeeecCCCHHHHHHHHHHHHHHcCCCCCHHH
Q psy879          107 SMTDGAQQALRRTMEIY------SNTTRFALACNNSE-KIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDG  179 (317)
Q Consensus       107 ~l~~~~~~~ll~~le~~------~~~~~~il~~~~~~-~l~~~i~sR~~~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~  179 (317)
                      .|...........++..      .....+|+|||+.. ....+.+.++.++.+.++.......++..+++++.+.++.+.
T Consensus       231 ~l~~~~dg~~~~~~~~~~~~~~~~~~~p~i~ttN~~~~~~~r~~Rf~~~i~~~~~~~~~~~~~~l~~i~~~~~l~~~~~~  310 (362)
T d1svma_         231 NLRDYLDGSVKVNLEKKHLNKRTQIFPPGIVTMNEYSVPKTLQARFVKQIDFRPKDYLKHCLERSEFLLEKRIIQSGIAL  310 (362)
T ss_dssp             TTHHHHHCSSCEEECCSSSCCEEECCCCEEEEECSCCCCHHHHTTEEEEEECCCCHHHHHHHHTCTHHHHTTCTTCHHHH
T ss_pred             hcccccCCcchhhhhhhhhchhhhccCCceeecccccccccccccCceEEeecCCCcHHHHHHHHHHHhcccCCCCCHHH
Confidence            44322110000000100      01224788888643 233333333444445555556666788888888888877766


Q ss_pred             HHH-HHHhcCCCHHHHHHHHHH
Q psy879          180 LEA-IVFTAQGDMRQALNNLQS  200 (317)
Q Consensus       180 ~~~-l~~~~~gd~r~~i~~l~~  200 (317)
                      +.. +...+++|++..++.+..
T Consensus       311 L~~li~~~s~~D~~~~i~~~~~  332 (362)
T d1svma_         311 LLMLIWYRPVAEFAQSIQSRIV  332 (362)
T ss_dssp             HHHHHHHSCGGGSCGGGHHHHH
T ss_pred             HHHHccCCCHHHHHHHHHHHHH
Confidence            654 446677788888776643

>d1w44a_ c.37.1.11 (A:) NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: NTPase P4
species: Bacteriophage phi-12 [TaxId: 161736]

Probab=99.28  E-value=5.9e-12  Score=106.02  Aligned_cols=120  Identities=15%  Similarity=0.127  Sum_probs=74.8

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCC------cChHHHHHHHHHHHhhcccCCCCceeEEEEeCCC
Q psy879           33 NIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASND------RGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEAD  106 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~------~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d  106 (317)
                      ++|||||||||||.+|+++|.++...   .+++.++.+..      .....+++.+....         .+.|+||||+|
T Consensus       125 ~~l~~G~pG~GKT~la~ala~~~~~~---~~~~~~~~~~~~~~~~G~~e~~~~~~f~~a~---------~~~ilf~DEid  192 (321)
T d1w44a_         125 MVIVTGKGNSGKTPLVHALGEALGGK---DKYATVRFGEPLSGYNTDFNVFVDDIARAML---------QHRVIVIDSLK  192 (321)
T ss_dssp             EEEEECSSSSCHHHHHHHHHHHHHTT---SCCEEEEBSCSSTTCBCCHHHHHHHHHHHHH---------HCSEEEEECCT
T ss_pred             eEEEECCCCccHHHHHHHHHHHhcCC---CCeEEEEhhHhhhcccchHHHHHHHHHHHHh---------hccEEEeehhh
Confidence            37779999999999999999997422   23444554432      12344555554432         23599999999


Q ss_pred             CCCHH------------HHHHHHHHhhhc--cCCceEEEEecCCCcCchhHh------hhcce-eeecCCCHHHHHHHHH
Q psy879          107 SMTDG------------AQQALRRTMEIY--SNTTRFALACNNSEKIIEPIQ------SRCAM-LRYNKLTDAQLLSKVI  165 (317)
Q Consensus       107 ~l~~~------------~~~~ll~~le~~--~~~~~~il~~~~~~~l~~~i~------sR~~~-i~f~~~~~~~~~~~l~  165 (317)
                      .+.+.            ..+.|+.-|+..  ..++++|.+|| +..+++++.      .|+.. +.+.+|+.+.-..+|.
T Consensus       193 ~~~~~r~~~~~~~~~~r~v~~lL~e~dg~~~~~~v~viaatN-~~~~~~~i~~~~~r~~Rf~~~v~v~~pd~~~r~~il~  271 (321)
T d1w44a_         193 NVIGAAGGNTTSGGISRGAFDLLSDIGAMAASRGCVVIASLN-PTSNDDKIVELVKEASRSNSTSLVISTDVDGEWQVLT  271 (321)
T ss_dssp             TTC-----------CCHHHHHHHHHHHHHHHHHTCEEEEECC-CCCCCHHHHHHHHHHHHHSCSEEEEECSSTTEEEEEE
T ss_pred             hhccccccCCCCCcchhhhhhhhhhccccccCCCeEEEEeCC-CcccccchhhhhhccCcccceeecCCCChHHHHHHHH
Confidence            98542            245666666532  34566666776 555555553      44444 8888887776555544

>d1iqpa1 a.80.1.1 (A:233-327) Replication factor C {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: All alpha proteins
fold: post-AAA+ oligomerization domain-like
superfamily: post-AAA+ oligomerization domain-like
family: DNA polymerase III clamp loader subunits, C-terminal domain
domain: Replication factor C
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=99.23  E-value=1.1e-10  Score=80.49  Aligned_cols=92  Identities=29%  Similarity=0.573  Sum_probs=85.2

Q ss_pred             CCHHHHHHHHHHHhcCCHHHHHHHHHHHH-HcCCCHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHHHhHHhcCCCcHHH
Q psy879          220 PHPLAVKEMLLNCVEGNMKDSYKIIHHLY-KLGYAPEDIIGNIFRVAKTLDIPEPLKLSIIQEIGNVHLRISEGVNSLLQ  298 (317)
Q Consensus       220 ~~~~~i~~l~~~~~~~~~~~~~~~~~~l~-~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~g~~~~l~  298 (317)
                      ..++.+.++++.+.++++.+++..+++++ ..|+++.+|+..+.+.+..+.+++..+.+++..++++|+++..|.+++++
T Consensus         2 a~P~~I~~il~~~l~~~f~~a~~~l~~l~~~~G~s~~dIl~~l~~~v~~~~~~~~~k~~ll~~la~~d~rL~~G~~e~iQ   81 (95)
T d1iqpa1           2 ARPEDIREMMLLALKGNFLKAREKLREILLKQGLSGEDVLVQMHKEVFNLPIEEPKKVLLADKIGEYNFRLVEGANEIIQ   81 (95)
T ss_dssp             CCHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHGGGSSSCHHHHHHHHHHHHHHHHHHHTTCCHHHH
T ss_pred             CCcHHHHHHHHHHHcCCHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHHHHHHcCCChHHH
Confidence            45677899999999999999999999984 67999999999999988888899999999999999999999999999999


Q ss_pred             HHHHHHHHHHhhc
Q psy879          299 LSGLLARLCIVGS  311 (317)
Q Consensus       299 le~~~~~~~~~~~  311 (317)
                      |+.|++++|.+.+
T Consensus        82 L~alla~~~~i~~   94 (95)
T d1iqpa1          82 LEALLAQFTLIGK   94 (95)
T ss_dssp             HHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHhc
Confidence            9999999998764

>d2fnaa2 c.37.1.20 (A:1-283) Archaeal ATPase SSO1545 {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Archaeal ATPase SSO1545
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=99.19  E-value=1.7e-10  Score=95.93  Aligned_cols=174  Identities=17%  Similarity=0.169  Sum_probs=106.6

Q ss_pred             CCCCcccCCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCC---CCcChHH------
Q psy879            7 QTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNAS---NDRGIDT------   77 (317)
Q Consensus         7 ~~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~---~~~~~~~------   77 (317)
                      .+-++++|+++.++.|...    ..++++++||+|+|||++++.+++.+....   .++.+...   .......      
T Consensus         9 ~~~~~f~GR~~el~~l~~~----~~~~i~i~G~~G~GKTsLl~~~~~~~~~~~---~~i~~~~~~~~~~~~~~~~~~~~~   81 (283)
T d2fnaa2           9 DNRKDFFDREKEIEKLKGL----RAPITLVLGLRRTGKSSIIKIGINELNLPY---IYLDLRKFEERNYISYKDFLLELQ   81 (283)
T ss_dssp             CSGGGSCCCHHHHHHHHHT----CSSEEEEEESTTSSHHHHHHHHHHHHTCCE---EEEEGGGGTTCSCCCHHHHHHHHH
T ss_pred             CChhhCCChHHHHHHHHhc----cCCEEEEEcCCCCcHHHHHHHHHHHCCCCe---EEEEeccccccccccHHHHHHHHH
Confidence            3578999999999988764    234799999999999999999998863221   11111111   0111111      


Q ss_pred             -----------------------------------------HHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHH----
Q psy879           78 -----------------------------------------VRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGA----  112 (317)
Q Consensus        78 -----------------------------------------i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~----  112 (317)
                                                               +.+.+..+...     ...+.++++||++.+....    
T Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~-----~~~~~~i~id~~~~~~~~~~~~~  156 (283)
T d2fnaa2          82 KEINKLVKRLPSLLKALKNIQGIVIMGNEIKFNWNRKDRLSFANLLESFEQA-----SKDNVIIVLDEAQELVKLRGVNL  156 (283)
T ss_dssp             HHHHHHHHHCTTHHHHTTTSTTEEECSSSEEEC-----CCCHHHHHHHHHHT-----CSSCEEEEEETGGGGGGCTTCCC
T ss_pred             HHhhhhhhhhHHHHHHHHhhhcccccccccccccchhhhhHHHHHHHHHHhh-----cccccccccchhhhhcccchHHH
Confidence                                                     11112221111     1456789999998875433    


Q ss_pred             HHHHHHHhhhccCCceEEEEecCCCc---------Cc-hhHhhhcceeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHH
Q psy879          113 QQALRRTMEIYSNTTRFALACNNSEK---------II-EPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEA  182 (317)
Q Consensus       113 ~~~ll~~le~~~~~~~~il~~~~~~~---------l~-~~i~sR~~~i~f~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~  182 (317)
                      ...+...... ......++++.....         .. +....+...+...+++.++..+++...+...++..  +.++.
T Consensus       157 ~~~l~~~~~~-~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~L~~l~~~e~~~~l~~~~~~~~~~~--~~~~~  233 (283)
T d2fnaa2         157 LPALAYAYDN-LKRIKFIMSGSEMGLLYDYLRVEDPESPLFGRAFSTVELKPFSREEAIEFLRRGFQEADIDF--KDYEV  233 (283)
T ss_dssp             HHHHHHHHHH-CTTEEEEEEESSHHHHHHHTTTTCTTSTTTTCCCEEEEECCCCHHHHHHHHHHHHHHHTCCC--CCHHH
T ss_pred             HHHHHHHHHh-hhhhhhhhccccchHHHHHHHhhhhcchhcccceeEEeeCCCCHHHHHHHHHhhhhhcCCCH--HHHHH
Confidence            2333333333 344555555443211         11 11223345589999999999999999888777654  44688


Q ss_pred             HHHhcCCCHHHHH
Q psy879          183 IVFTAQGDMRQAL  195 (317)
Q Consensus       183 l~~~~~gd~r~~i  195 (317)
                      +.+.++|.+.-+-
T Consensus       234 i~~~~~G~P~~L~  246 (283)
T d2fnaa2         234 VYEKIGGIPGWLT  246 (283)
T ss_dssp             HHHHHCSCHHHHH
T ss_pred             HHHHhCCCHHHHH
Confidence            9999999997433

>d1g41a_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: HslU
species: Haemophilus influenzae [TaxId: 727]

Probab=99.07  E-value=5.7e-09  Score=92.01  Aligned_cols=122  Identities=21%  Similarity=0.277  Sum_probs=76.3

Q ss_pred             eEEEEeCCCCCC------------HHHHHHHHHHhhhc----------cCCceEEEEecC----CCcCchhHhhhcce-e
Q psy879           98 KIVILDEADSMT------------DGAQQALRRTMEIY----------SNTTRFALACNN----SEKIIEPIQSRCAM-L  150 (317)
Q Consensus        98 ~vliiDE~d~l~------------~~~~~~ll~~le~~----------~~~~~~il~~~~----~~~l~~~i~sR~~~-i  150 (317)
                      .++++||+++..            ...+..++..++..          ..+..+|..+..    +..+.|.+..|+.+ +
T Consensus       251 ~~~~~dei~k~~~~~~~~g~d~~~eg~~~~ll~~~e~~~v~~~~~~~~~~~~l~i~~~~~~~~~~~gliPEliGRlPi~v  330 (443)
T d1g41a_         251 GIVFIDEIDKICKKGEYSGADVSREGVQRDLLPLVEGSTVSTKHGMVKTDHILFIASGAFQVARPSDLIPELQGRLPIRV  330 (443)
T ss_dssp             CEEEEETGGGGSCCSSCSSSHHHHHHHHHHHHHHHHCCEEEETTEEEECTTCEEEEEECCSSCCGGGSCHHHHTTCCEEE
T ss_pred             CccccchhhhhhhcccCCCCCcccchhhhhhhhhccccccccccccccccchhhccccchhhcccccchhhhccceEEEE
Confidence            478889888653            12466677777631          122333333322    23688999999988 9


Q ss_pred             eecCCCHHHHHHHHHH-----------HHHHcCCCC--CHHHHHHHHHhcC--------CCHHHHHHHHHHhhh------
Q psy879          151 RYNKLTDAQLLSKVIE-----------ICEKENISH--TNDGLEAIVFTAQ--------GDMRQALNNLQSTHN------  203 (317)
Q Consensus       151 ~f~~~~~~~~~~~l~~-----------~~~~~~~~i--~~~~~~~l~~~~~--------gd~r~~i~~l~~~~~------  203 (317)
                      .+.+++++++.++|.+           .+..+|+++  +++++..+++.+-        -..|.+..+++.+..      
T Consensus       331 ~L~~L~~~dL~rILtEPknsLikQy~~lf~~~gv~L~ft~~al~~iA~~A~~~n~~~~~~GAR~Lr~i~E~~l~~~~f~~  410 (443)
T d1g41a_         331 ELTALSAADFERILTEPHASLTEQYKALMATEGVNIAFTTDAVKKIAEAAFRVNEKTENIGARRLHTVMERLMDKISFSA  410 (443)
T ss_dssp             ECCCCCHHHHHHHHHSSTTCHHHHHHHHHHTTTCEEEECHHHHHHHHHHHHHHHHHSCCCGGGHHHHHHHHHHHHHHHHG
T ss_pred             EccCccHHHHHHHHHhhhhhHHHHHHHHHhhcCcEEEEcHHHHHHHHHHHHHhhhhcccCCchHHHHHHHHHHHHHhccC
Confidence            9999999999999863           233466654  7999999886652        235655555554322      


Q ss_pred             ---CCC--cccHHHHHhhcCC
Q psy879          204 ---GFG--HVTAEYVFKVCDE  219 (317)
Q Consensus       204 ---~~~--~i~~~~v~~~~~~  219 (317)
                         ...  .|+.+.|.+.++.
T Consensus       411 p~~~~~~v~Id~~~v~~~l~~  431 (443)
T d1g41a_         411 SDMNGQTVNIDAAYVADALGE  431 (443)
T ss_dssp             GGCTTCEEEECHHHHHHHHTT
T ss_pred             CCCCCCEEEECHHHHHhhhhc
Confidence               111  3566666655443

>d1sxjd1 a.80.1.1 (D:263-353) Replication factor C2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: post-AAA+ oligomerization domain-like
superfamily: post-AAA+ oligomerization domain-like
family: DNA polymerase III clamp loader subunits, C-terminal domain
domain: Replication factor C2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.05  E-value=1.1e-09  Score=74.77  Aligned_cols=87  Identities=16%  Similarity=0.279  Sum_probs=79.9

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHH-HHhcCCChHHHHHHHHHHHHHHhHHhcCCCcHHHHHH
Q psy879          223 LAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDIIGNIFRV-AKTLDIPEPLKLSIIQEIGNVHLRISEGVNSLLQLSG  301 (317)
Q Consensus       223 ~~i~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~~~~~~-~~~~~~~~~~~~~~~~~l~~~~~~l~~g~~~~l~le~  301 (317)
                      +.+.++++.+.++++.++...+.+++..|+++.+|+..+++. .....+++..+.+++..++++|+|+..|.++.++|..
T Consensus         4 ~~i~~il~~~~~~~f~~a~~~i~~l~~~Gys~~dIl~~l~~~vv~~~~i~~~~k~~i~~~la~~d~rL~~G~~e~lQL~~   83 (91)
T d1sxjd1           4 DILIEIVEKVKSGDFDEIKKYVNTFMKSGWSAASVVNQLHEYYITNDNFDTNFKNQISWLLFTTDSRLNNGTNEHIQLLN   83 (91)
T ss_dssp             HHHHHHHHHHHSCCHHHHHHHHHHHHHTSCCCTTHHHHHHHHHHHCSSSCHHHHHHHHHHHHHHHHHHTTCCCHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHcCCChHHHHHH
Confidence            457889999999999999999999999999999999999875 4545789999999999999999999999999999999


Q ss_pred             HHHHHHHh
Q psy879          302 LLARLCIV  309 (317)
Q Consensus       302 ~~~~~~~~  309 (317)
                      +++++|++
T Consensus        84 lla~i~~i   91 (91)
T d1sxjd1          84 LLVKISQL   91 (91)
T ss_dssp             HHHHHHHC
T ss_pred             HHHHHHcC
Confidence            99999864

>d1sxjc1 a.80.1.1 (C:239-333) Replication factor C3 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: post-AAA+ oligomerization domain-like
superfamily: post-AAA+ oligomerization domain-like
family: DNA polymerase III clamp loader subunits, C-terminal domain
domain: Replication factor C3
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.00  E-value=6.2e-09  Score=71.56  Aligned_cols=91  Identities=18%  Similarity=0.312  Sum_probs=81.0

Q ss_pred             CHHHHHHHHHHHhcCCHHHHHHHHHHHH-HcCCCHHHHHHHHHHHHHhcCCC-hHHHHHHHHHHHHHHhHHhcCCCcHHH
Q psy879          221 HPLAVKEMLLNCVEGNMKDSYKIIHHLY-KLGYAPEDIIGNIFRVAKTLDIP-EPLKLSIIQEIGNVHLRISEGVNSLLQ  298 (317)
Q Consensus       221 ~~~~i~~l~~~~~~~~~~~~~~~~~~l~-~~~~~~~~i~~~~~~~~~~~~~~-~~~~~~~~~~l~~~~~~l~~g~~~~l~  298 (317)
                      +++.+.++++.+.++++.+|+..+++++ ..|+++.+|+..+.+.+...... +..+.+++..++++|+++..|.++.++
T Consensus         2 ~P~~I~~il~~~l~~~f~~a~~~l~~l~~~~G~s~~dIl~~l~~~i~~~~~~~~~~k~~ll~~la~~e~rL~~G~~e~lQ   81 (95)
T d1sxjc1           2 RPSDLKAVLKSILEDDWGTAHYTLNKVRSAKGLALIDLIEGIVKILEDYELQNEETRVHLLTKLADIEYSISKGGNDQIQ   81 (95)
T ss_dssp             CHHHHHHHHHHHHTSCHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHTTSCCSSHHHHHHHHHHHHHHHHHHTTCCCHHHH
T ss_pred             CHHHHHHHHHHHHhCCHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHcCCCcHHH
Confidence            4567889999999999999999999996 56999999999999988776654 556789999999999999999999999


Q ss_pred             HHHHHHHHHHhhc
Q psy879          299 LSGLLARLCIVGS  311 (317)
Q Consensus       299 le~~~~~~~~~~~  311 (317)
                      |..|++.+++...
T Consensus        82 L~~lla~~~~~~e   94 (95)
T d1sxjc1          82 GSAVIGAIKASFE   94 (95)
T ss_dssp             HHHHHHHHHHHCC
T ss_pred             HHHHHHHHHHHhc
Confidence            9999999987543

>d1sxjb1 a.80.1.1 (B:231-322) Replication factor C4 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: post-AAA+ oligomerization domain-like
superfamily: post-AAA+ oligomerization domain-like
family: DNA polymerase III clamp loader subunits, C-terminal domain
domain: Replication factor C4
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.98  E-value=3.8e-09  Score=72.11  Aligned_cols=88  Identities=42%  Similarity=0.728  Sum_probs=76.1

Q ss_pred             CHHHHHHHHHHHhcCCHHHHHHHHHHH-HHcCCCHHHHHHHHHHHHHhc-CCChHHHHHHHHHHHHHHhHHhcCCCcHHH
Q psy879          221 HPLAVKEMLLNCVEGNMKDSYKIIHHL-YKLGYAPEDIIGNIFRVAKTL-DIPEPLKLSIIQEIGNVHLRISEGVNSLLQ  298 (317)
Q Consensus       221 ~~~~i~~l~~~~~~~~~~~~~~~~~~l-~~~~~~~~~i~~~~~~~~~~~-~~~~~~~~~~~~~l~~~~~~l~~g~~~~l~  298 (317)
                      ++..+.++   +...++.+++..+.++ .+.|+++.+|+..+++.+..+ .+++..+.++++.++++++|+..|.++.++
T Consensus         2 ~P~~I~~i---l~~~~f~~a~~~l~~~l~~~Gys~~DIi~~l~~~i~~~~~~~e~~k~~il~~la~~~~rl~~G~~e~lQ   78 (92)
T d1sxjb1           2 HPLIVKKM---LLASNLEDSIQILRTDLWKKGYSSIDIVTTSFRVTKNLAQVKESVRLEMIKEIGLTHMRILEGVGTYLQ   78 (92)
T ss_dssp             CHHHHHHH---HSCSSHHHHHHHHHHTTTTTTCCHHHHHHHHHHHHHTCTTSCHHHHHHHHHHHHHHHHHHHTTCCCHHH
T ss_pred             CHHHHHHH---HHhCCHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHcCCCcHHH
Confidence            34455555   3567899999999886 578999999999999988765 578888999999999999999999999999


Q ss_pred             HHHHHHHHHHhhc
Q psy879          299 LSGLLARLCIVGS  311 (317)
Q Consensus       299 le~~~~~~~~~~~  311 (317)
                      |..|++++|++++
T Consensus        79 L~~lla~i~~i~~   91 (92)
T d1sxjb1          79 LASMLAKIHKLNN   91 (92)
T ss_dssp             HHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHhc
Confidence            9999999998875

>d2a5yb3 c.37.1.20 (B:109-385) CED-4, NB-ARC domain {Caenorhabditis elegans [TaxId: 6239]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CED-4, NB-ARC domain
species: Caenorhabditis elegans [TaxId: 6239]

Probab=98.86  E-value=2.2e-08  Score=83.15  Aligned_cols=174  Identities=11%  Similarity=0.066  Sum_probs=100.8

Q ss_pred             cccCCHHHHHHHHHHHhcC---CCceEEEECCCCCCHHHHHHHHHHHHcCC--CCCCceEEecCCCCcChHHHHHHHHHH
Q psy879           11 DIVGNEDTVERLKVFSSSG---NVPNIIISGPPGVGKTTTILCLARILLGP--SFKDAVLELNASNDRGIDTVRNKIKMF   85 (317)
Q Consensus        11 ~~~g~~~~~~~l~~~l~~~---~~~~~ll~G~~G~GKt~la~~la~~l~~~--~~~~~~~~~~~~~~~~~~~i~~~~~~~   85 (317)
                      +++|++..++.+..++.+.   ....+.++|..|+||||+|+.+++.....  .....++.++.+.......+...+...
T Consensus        21 ~~~gR~~~~~~i~~~L~~~~~~~~~~v~I~GmgGiGKTtLA~~v~~~~~~~~~~~f~~~~Wv~vs~~~~~~~l~~~~~~~  100 (277)
T d2a5yb3          21 TCYIREYHVDRVIKKLDEMCDLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKSTFDLFTDIL  100 (277)
T ss_dssp             CSCCCHHHHHHHHHHHHHHTTSSSEEEEEECSTTSSHHHHHHHHHHHCSSTBTTTBSEEEEEECCCCSTTHHHHHHHHHH
T ss_pred             ceeCcHHHHHHHHHHHHhccCCCceEEEEECCCCCCHHHHHHHHHHhhhhhhhhcCceEEEEEecCCCCHHHHHHHHHHH
Confidence            4679999998888877542   22238899999999999999998873211  111123333333322322222222111


Q ss_pred             Hhh----cc-cC-------------------CCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCcCch
Q psy879           86 AQQ----KV-TL-------------------PPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIE  141 (317)
Q Consensus        86 ~~~----~~-~~-------------------~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l~~  141 (317)
                      ...    .. ..                   ....+-++|+|++...  ...    +.+.  ....++|+||.+ ..+..
T Consensus       101 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~kr~LlVLDDv~~~--~~~----~~~~--~~~srilvTTR~-~~v~~  171 (277)
T d2a5yb3         101 LMLKSEDDLLNFPSVEHVTSVVLKRMICNALIDRPNTLFVFDDVVQE--ETI----RWAQ--ELRLRCLVTTRD-VEISN  171 (277)
T ss_dssp             HHHTTTSCCTTCCCCTTCCHHHHHHHHHHHHTTSTTEEEEEEEECCH--HHH----HHHH--HTTCEEEEEESB-GGGGG
T ss_pred             HHHhcchhhcCCccchhhhhHHHHHHHHHHHhccCCeeEecchhhHH--hhh----hhhc--ccCceEEEEeeh-HHHHH
Confidence            110    00 00                   0134568999998742  211    2222  234566666654 35555


Q ss_pred             hHhhhcceeeecCCCHHHHHHHHHHHHHHcCC-CCCHHHHHHHHHhcCCCHHH
Q psy879          142 PIQSRCAMLRYNKLTDAQLLSKVIEICEKENI-SHTNDGLEAIVFTAQGDMRQ  193 (317)
Q Consensus       142 ~i~sR~~~i~f~~~~~~~~~~~l~~~~~~~~~-~i~~~~~~~l~~~~~gd~r~  193 (317)
                      .+.+++..++..+++.++..+.+...+..... .-.++....+++.|+|.+-.
T Consensus       172 ~~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~iv~~c~GlPLA  224 (277)
T d2a5yb3         172 AASQTCEFIEVTSLEIDECYDFLEAYGMPMPVGEKEEDVLNKTIELSSGNPAT  224 (277)
T ss_dssp             GCCSCEEEEECCCCCHHHHHHHHHHTSCCCC--CHHHHHHHHHHHHHTTCHHH
T ss_pred             hcCCCCceEECCCCCHHHHHHHHHHHhCCccCchhhHHHHHHHHHHhCCCHHH
Confidence            55666677999999999999988765432211 11234567889999998753

>d1ye8a1 c.37.1.11 (A:1-178) Hypothetical kinase-like protein Aq_1292 {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hypothetical kinase-like protein Aq 1292
species: Aquifex aeolicus [TaxId: 63363]

Probab=98.59  E-value=7.5e-08  Score=74.05  Aligned_cols=24  Identities=50%  Similarity=0.697  Sum_probs=22.1

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHc
Q psy879           33 NIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      ++++.||||+||||+++.++..+.
T Consensus         2 ki~I~G~~G~GKSTLl~~i~~~l~   25 (178)
T d1ye8a1           2 KIIITGEPGVGKTTLVKKIVERLG   25 (178)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHG
T ss_pred             EEEEECCCCcHHHHHHHHHHhcCC
Confidence            489999999999999999999874

>d1tuea_ c.37.1.20 (A:) Replication protein E1 helicase domain {Human papillomavirus type 18 [TaxId: 333761]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication protein E1 helicase domain
species: Human papillomavirus type 18 [TaxId: 333761]

Probab=98.56  E-value=1.1e-07  Score=73.21  Aligned_cols=114  Identities=19%  Similarity=0.296  Sum_probs=71.7

Q ss_pred             HHHHHHHHhcCCCc-e-EEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHHHHHHHhhcccCCCCc
Q psy879           19 VERLKVFSSSGNVP-N-IIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGR   96 (317)
Q Consensus        19 ~~~l~~~l~~~~~~-~-~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~   96 (317)
                      +..|..+++ |.+. + ++|+|||+||||+++.++++.+.+.     ++..+.+.. .          |...+    -.+
T Consensus        40 l~~l~~~l~-~~PKkn~i~~~GP~~TGKS~f~~sl~~~l~G~-----vis~~N~~s-~----------F~Lq~----l~~   98 (205)
T d1tuea_          40 LGALKSFLK-GTPKKNCLVFCGPANTGKSYFGMSFIHFIQGA-----VISFVNSTS-H----------FWLEP----LTD   98 (205)
T ss_dssp             HHHHHHHHH-TCTTCSEEEEESCGGGCHHHHHHHHHHHHTCE-----ECCCCCSSS-C----------GGGGG----GTT
T ss_pred             HHHHHHHHc-CCCCceEEEEECCCCccHHHHHHHHHHHhCCE-----EEeccCCCC-C----------ccccc----ccC
Confidence            445666664 4443 3 9999999999999999999998432     122221110 0          11111    146


Q ss_pred             eeEEEEeCCCCCCHHHHHHH-HHHhhhc-------------cCCceEEEEecCC---CcCchhHhhhcceeeec
Q psy879           97 HKIVILDEADSMTDGAQQAL-RRTMEIY-------------SNTTRFALACNNS---EKIIEPIQSRCAMLRYN  153 (317)
Q Consensus        97 ~~vliiDE~d~l~~~~~~~l-l~~le~~-------------~~~~~~il~~~~~---~~l~~~i~sR~~~i~f~  153 (317)
                      .+++++||+......-.+.. ..+++.-             -..+.+|+|+|..   +.-.+.+.||..++.|+
T Consensus        99 ~kv~l~dD~t~~~~~~~d~~lK~ll~G~~vsvd~KhK~~vqi~~pPliITsN~~~~~~d~~~~L~sRi~~f~F~  172 (205)
T d1tuea_          99 TKVAMLDDATTTCWTYFDTYMRNALDGNPISIDRKHKPLIQLKCPPILLTTNIHPAKDNRWPYLESRITVFEFP  172 (205)
T ss_dssp             CSSEEEEEECHHHHHHHHHHCHHHHHTCCEEEC----CCEEECCCCEEEEESSCTTSSSSCHHHHTSCEEEECC
T ss_pred             CeEEEEeccccchHHHHHHHHHhccCCCeeeeecccCCcccccCCCEEEEcCCCCCccccchhhhheEEEEECC
Confidence            78999999977665555553 4455411             0123477788764   34568899999999998

>d2pmka1 c.37.1.12 (A:467-707) Haemolysin B ATP-binding protein {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Haemolysin B ATP-binding protein
species: Escherichia coli [TaxId: 562]

Probab=98.46  E-value=4.6e-08  Score=78.88  Aligned_cols=42  Identities=21%  Similarity=0.314  Sum_probs=32.7

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhccCCceEEEEecCCC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYSNTTRFALACNNSE  137 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~~~~~~il~~~~~~  137 (317)
                      +++++|+||+-. |.......+++.+.+......+|++|++..
T Consensus       157 ~p~ililDEpts~LD~~~~~~i~~~l~~l~~~~Tvi~itH~l~  199 (241)
T d2pmka1         157 NPKILIFDEATSALDYESEHVIMRNMHKICKGRTVIIIAHRLS  199 (241)
T ss_dssp             CCSEEEECCCCSCCCHHHHHHHHHHHHHHHTTSEEEEECSSGG
T ss_pred             ccchhhhhCCccccCHHHHHHHHHHHHHHhCCCEEEEEECCHH
Confidence            679999999975 667777778888877656666788888764

>d1sxje1 a.80.1.1 (E:256-354) Replication factor C5 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: post-AAA+ oligomerization domain-like
superfamily: post-AAA+ oligomerization domain-like
family: DNA polymerase III clamp loader subunits, C-terminal domain
domain: Replication factor C5
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.37  E-value=8.4e-07  Score=59.83  Aligned_cols=73  Identities=16%  Similarity=0.205  Sum_probs=61.8

Q ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHHHHHH-HhcCCChHHHHHHHHHHHHHHhHHhcCCCcHHHHHHHHHHHHHh
Q psy879          237 MKDSYKIIHHLYKLGYAPEDIIGNIFRVA-KTLDIPEPLKLSIIQEIGNVHLRISEGVNSLLQLSGLLARLCIV  309 (317)
Q Consensus       237 ~~~~~~~~~~l~~~~~~~~~i~~~~~~~~-~~~~~~~~~~~~~~~~l~~~~~~l~~g~~~~l~le~~~~~~~~~  309 (317)
                      ..+.+..+++|+..+++|..|+..+...+ .....++..+.+++++.+.++.|++.|..+.+|+|.|++++|..
T Consensus        24 L~~iR~~lYeLL~~cIpp~~Ilk~L~~~Ll~~~~~d~~lk~eii~~aa~yE~Rl~~GsK~IfHLEaFvAkfM~~   97 (99)
T d1sxje1          24 LIECRAVLYDLLAHCIPANIILKELTFSLLDVETLNTTNKSSIIEYSSVFDERLSLGNKAIFHLEGFIAKVMCC   97 (99)
T ss_dssp             HHHHHHHHHHHHTTTCCHHHHHHHHHHTTTTCTTSCHHHHHHHHHHHHHHHHHHHTCSCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhccCCchhHHHHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHhh
Confidence            44566778999999999999999875533 22357788899999999999999999999999999999999854

>d1gvnb_ c.37.1.21 (B:) Plasmid maintenance system epsilon/zeta, toxin zeta subunit {Streptococcus pyogenes [TaxId: 1314]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
domain: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
species: Streptococcus pyogenes [TaxId: 1314]

Probab=98.35  E-value=1.2e-07  Score=78.01  Aligned_cols=57  Identities=21%  Similarity=0.359  Sum_probs=38.7

Q ss_pred             CCCcccCCHHHHHHHHHHHh---cCCCce-EEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecC
Q psy879            8 TFSDIVGNEDTVERLKVFSS---SGNVPN-IIISGPPGVGKTTTILCLARILLGPSFKDAVLELNA   69 (317)
Q Consensus         8 ~~~~~~g~~~~~~~l~~~l~---~~~~~~-~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~   69 (317)
                      +|++.-+++.+.+.+.....   .+..|. ++|+||||||||++|+++|+++.+     .++.++.
T Consensus         5 ~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~ilL~GpPGtGKT~la~~la~~~~~-----~~~~i~~   65 (273)
T d1gvnb_           5 NFTDKQFENRLNDNLEELIQGKKAVESPTAFLLGGQPGSGKTSLRSAIFEETQG-----NVIVIDN   65 (273)
T ss_dssp             CCCHHHHHHHHHHHHHHHHTTCCCCSSCEEEEEECCTTSCTHHHHHHHHHHTTT-----CCEEECT
T ss_pred             ccChHHHHHHHHHHHHHHHhcccCCCCCEEEEEECCCCCCHHHHHHHHHHHhhc-----ceEEEec
Confidence            35555555655555555543   233344 999999999999999999999743     2555654

>d3b60a1 c.37.1.12 (A:329-581) Multidrug resistance ABC transporter MsbA, C-terminal domain {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Multidrug resistance ABC transporter MsbA, C-terminal domain
species: Salmonella typhimurium [TaxId: 90371]

Probab=98.32  E-value=1.5e-07  Score=76.45  Aligned_cols=42  Identities=19%  Similarity=0.316  Sum_probs=31.8

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhccCCceEEEEecCCC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYSNTTRFALACNNSE  137 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~~~~~~il~~~~~~  137 (317)
                      +++++++||+-. +.......+++.+.+...+..+|++|++..
T Consensus       170 ~p~ililDEpts~LD~~~~~~i~~~l~~l~~~~Tvi~itH~l~  212 (253)
T d3b60a1         170 DSPILILDEATSALDTESERAIQAALDELQKNRTSLVIAHRLS  212 (253)
T ss_dssp             CCSEEEEETTTSSCCHHHHHHHHHHHHHHHTTSEEEEECSCGG
T ss_pred             CCCEEEeccccccCCHHHHHHHHHHHHHhccCCEEEEEECCHH
Confidence            578999999985 566677777777776655666788887754

>d2i3ba1 c.37.1.11 (A:1-189) Cancer-related NTPase, C1orf57 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Cancer-related NTPase, C1orf57
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.25  E-value=1.1e-06  Score=67.49  Aligned_cols=25  Identities=44%  Similarity=0.798  Sum_probs=23.2

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHcC
Q psy879           33 NIIISGPPGVGKTTTILCLARILLG   57 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~~   57 (317)
                      |++|+||||+||||+++.+++.+..
T Consensus         3 ~v~ItG~~GtGKTtl~~~i~~~l~~   27 (189)
T d2i3ba1           3 HVFLTGPPGVGKTTLIHKASEVLKS   27 (189)
T ss_dssp             CEEEESCCSSCHHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHH
Confidence            7999999999999999999999853

>d2hyda1 c.37.1.12 (A:324-578) Putative multidrug export ATP-binding/permease protein SAV1866 {Staphylococcus aureus [TaxId: 1280]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Putative multidrug export ATP-binding/permease protein SAV1866
species: Staphylococcus aureus [TaxId: 1280]

Probab=98.25  E-value=1.2e-07  Score=76.91  Aligned_cols=42  Identities=19%  Similarity=0.332  Sum_probs=32.1

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhccCCceEEEEecCCC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYSNTTRFALACNNSE  137 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~~~~~~il~~~~~~  137 (317)
                      +++++|+||+.. |.......+.+.+........+|++|++..
T Consensus       172 ~p~ililDEpts~LD~~t~~~i~~~l~~l~~~~TvI~itH~~~  214 (255)
T d2hyda1         172 NPPILILDEATSALDLESESIIQEALDVLSKDRTTLIVAHRLS  214 (255)
T ss_dssp             CCSEEEEESTTTTCCHHHHHHHHHHHHHHTTTSEEEEECSSGG
T ss_pred             CCCEEEEeCccccCCHHHHHHHHHHHHHHhcCCEEEEEeCCHH
Confidence            578999999985 566777788888876655556778887754

>d1jj7a_ c.37.1.12 (A:) Peptide transporter Tap1, C-terminal ABC domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Peptide transporter Tap1, C-terminal ABC domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.23  E-value=3e-07  Score=74.54  Aligned_cols=41  Identities=17%  Similarity=0.248  Sum_probs=30.0

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhccC--CceEEEEecCC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYSN--TTRFALACNNS  136 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~~--~~~~il~~~~~  136 (317)
                      +++|+|+||+-. +.......+.+.+.+...  +..+|++|++.
T Consensus       169 ~p~ililDEpTs~LD~~~~~~i~~~l~~l~~~~~~Tvi~itH~l  212 (251)
T d1jj7a_         169 KPCVLILDDATSALDANSQLQVEQLLYESPERYSRSVLLITQHL  212 (251)
T ss_dssp             CCSEEEEESTTTTCCHHHHHHHHHHHHTCGGGGGCEEEEECSCH
T ss_pred             CCcEEEecCcCcccChhhHHHHHHHHHHHhhhcCCEEEEEeCCH
Confidence            689999999974 566677778888765433  45577788773

>d1jqlb_ c.37.1.20 (B:) delta subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=98.23  E-value=3.4e-06  Score=61.97  Aligned_cols=125  Identities=6%  Similarity=0.070  Sum_probs=84.2

Q ss_pred             HHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHHHHHHHhhcccCCCCceeEE
Q psy879           21 RLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIV  100 (317)
Q Consensus        21 ~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~vl  100 (317)
                      .|...+++|-.|.|+|||++..-+..+...+.+.+...+........ .......+   +.+......++.   +++++|
T Consensus         8 ~L~~~l~k~l~~vyll~G~E~~L~~~~~~~i~~~~~~~~~~~~~~~~-~~~~~~~~---~l~~~~~t~slF---~~krli   80 (140)
T d1jqlb_           8 QLRAQLNEGLRAAYLLLGNDPLLLQESQDAVRQVAAAQGFEEHHTFS-IDPNTDWN---AIFSLCQAMSLF---ASRQTL   80 (140)
T ss_dssp             GHHHHHHHCCCSEEEEESSCHHHHHHHHHHHHHHHHHTTCCEEECCC-CSTTCCHH---HHHHHHHCCCTT---CCCEEE
T ss_pred             HHHHHHhcCCCcEEEEEcChHHHHHHHHHHHHHHHHhCCcceeeeec-ccccCCHH---HHHHHHcCCCcc---cCcEEE
Confidence            36666776755559999999888888888887776544332222111 11223333   344444444433   789999


Q ss_pred             EEeCCCCCC-HHHHHHHHHHhhhccCCceEEEEecCCC------cCchhHhhhcceeee
Q psy879          101 ILDEADSMT-DGAQQALRRTMEIYSNTTRFALACNNSE------KIIEPIQSRCAMLRY  152 (317)
Q Consensus       101 iiDE~d~l~-~~~~~~ll~~le~~~~~~~~il~~~~~~------~l~~~i~sR~~~i~f  152 (317)
                      +|++++... +...+.|.++++.|++.+++|+++...+      ++.+++.+++.+|.+
T Consensus        81 ~i~~~~~~~~k~~~~~L~~~~~~~~~~~~lii~~~~~~k~~~~~k~~K~l~k~g~vI~C  139 (140)
T d1jqlb_          81 LLLLPENGPNAAINEQLLTLTGLLHDDLLLIVRGNKLSKAQENAAWFTALANRSVQVTC  139 (140)
T ss_dssp             EEECCTTCSCTTHHHHHHHHHHHCCSSCCEEEECSSCCTTGGGSHHHHHHGGGCEEEEC
T ss_pred             EEEcCCCCCcHHHHHHHHHHHhCCCCCEEEEEEcCCCCchhhhhHHHHHHHhCCeEEeC
Confidence            999987654 5667889999999999999999887543      456777777777665

>d1jr3d1 a.80.1.1 (D:212-338) delta subunit {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: post-AAA+ oligomerization domain-like
superfamily: post-AAA+ oligomerization domain-like
family: DNA polymerase III clamp loader subunits, C-terminal domain
domain: delta subunit
species: Escherichia coli [TaxId: 562]

Probab=98.21  E-value=1.2e-06  Score=63.34  Aligned_cols=85  Identities=18%  Similarity=0.221  Sum_probs=68.4

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhc--------C--------------------------
Q psy879          224 AVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDIIGNIFRVAKTL--------D--------------------------  269 (317)
Q Consensus       224 ~i~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~~~~--------~--------------------------  269 (317)
                      .+|++++++..+|...++.+++.|...|++|..++..+.+.++.+        +                          
T Consensus         2 ~~F~L~dai~~gd~~~a~~il~~l~~~g~~~~~il~~l~~~~~~l~~i~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~   81 (127)
T d1jr3d1           2 TPFHWVDALLMGKSKRALHILQQLRLEGSEPVILLRTLQRELLLLVNLKRQSAHTPLRALFDKHRVWQNRRGMMGEALNR   81 (127)
T ss_dssp             CHHHHHHHHTTSCHHHHHHHHTSSTTTTCCHHHHHHHHHHHHHHHHHHHTCSSSSCHHHHHHHHTCCSSHHHHHHHHHHH
T ss_pred             CHHHHHHHHHcCCHHHHHHHHHHHHHcCCchHHHHHHHHHHHHHHHHHHHhhccCCHHHHHHHcCCCHHHHHHHHHHHHh
Confidence            379999999999999999999999999999999988875543322        1                          


Q ss_pred             CChHHHHHHHHHHHHHHhHHhcCC--CcHHHHHHHHHHHHH
Q psy879          270 IPEPLKLSIIQEIGNVHLRISEGV--NSLLQLSGLLARLCI  308 (317)
Q Consensus       270 ~~~~~~~~~~~~l~~~~~~l~~g~--~~~l~le~~~~~~~~  308 (317)
                      ++.....+++..+.++|..+|+|.  ++...||.++.++|.
T Consensus        82 ~s~~~l~~~l~~l~~~D~~~K~~~~~~~~~~le~l~l~lc~  122 (127)
T d1jr3d1          82 LSQTQLRQAVQLLTRTELTLKQDYGQSVWAELEGLSLLLCH  122 (127)
T ss_dssp             SCHHHHHHHHHHHHHHHHHHHHSSCSCHHHHHHHHHHHTTS
T ss_pred             CCHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhC
Confidence            111122338999999999999765  778999999999994

>d1jr3a1 a.80.1.1 (A:243-368) gamma subunit {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: post-AAA+ oligomerization domain-like
superfamily: post-AAA+ oligomerization domain-like
family: DNA polymerase III clamp loader subunits, C-terminal domain
domain: gamma subunit
species: Escherichia coli [TaxId: 562]

Probab=98.12  E-value=2.2e-05  Score=56.31  Aligned_cols=87  Identities=13%  Similarity=0.056  Sum_probs=72.7

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhc--------------------------CCChHHH
Q psy879          222 PLAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDIIGNIFRVAKTL--------------------------DIPEPLK  275 (317)
Q Consensus       222 ~~~i~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~~~~--------------------------~~~~~~~  275 (317)
                      .+.++++++++..+|..+++..++++.+.|.++..++..+...++.+                          .++....
T Consensus         4 ~~~~~~L~~~I~~~d~~~~L~~l~~i~~~G~d~~~~l~~L~~~~r~l~~~k~~~~~~~~~~~~~~~~~~~~a~~~~~~~L   83 (126)
T d1jr3a1           4 DDQALSLVEAMVEANGERVMALINEAAARGIEWEALLVEMLGLLHRIAMVQLSPAALGNDMAAIELRMRELARTIPPTDI   83 (126)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHTTCTTCCCSGGGGTHHHHHHHHHHSCHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHhcccccccchHHHHHHHHHHHHcCCHHHH
Confidence            45789999999999999999999999999999999998875544332                          1222234


Q ss_pred             HHHHHHHHHHHhHHhcCCCcHHHHHHHHHHHHH
Q psy879          276 LSIIQEIGNVHLRISEGVNSLLQLSGLLARLCI  308 (317)
Q Consensus       276 ~~~~~~l~~~~~~l~~g~~~~l~le~~~~~~~~  308 (317)
                      .++++.+.+....++...|+++.+|+.+.|+..
T Consensus        84 ~~~~~il~~~~~~ik~s~~~r~~~Em~llrll~  116 (126)
T d1jr3a1          84 QLYYQTLLIGRKELPYAPDRRMGVEMTLLRALA  116 (126)
T ss_dssp             HHHHHHHHHHHHHTTTSSSHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHH
Confidence            459999999999999999999999999999775

>d1w36d1 c.37.1.19 (D:2-360) Exodeoxyribonuclease V alpha chain (RecD) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Exodeoxyribonuclease V alpha chain (RecD)
species: Escherichia coli [TaxId: 562]

Probab=98.11  E-value=1.6e-05  Score=67.73  Aligned_cols=112  Identities=19%  Similarity=0.168  Sum_probs=61.5

Q ss_pred             HHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcC--CCCCCceEEecCCCCcChHHHHHHHHHHHhhcc----
Q psy879           17 DTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLG--PSFKDAVLELNASNDRGIDTVRNKIKMFAQQKV----   90 (317)
Q Consensus        17 ~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~--~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~----   90 (317)
                      +.+..+..++.+ +  ..+++||||||||+++..+...+..  ...+..+.-. +.+..-...+.+.+........    
T Consensus       152 ~Q~~A~~~al~~-~--~~vI~G~pGTGKTt~i~~~l~~l~~~~~~~~~~I~l~-ApTgkAA~~L~e~~~~~~~~~~~~~~  227 (359)
T d1w36d1         152 WQKVAAAVALTR-R--ISVISGGPGTGKTTTVAKLLAALIQMADGERCRIRLA-APTGKAAARLTESLGKALRQLPLTDE  227 (359)
T ss_dssp             HHHHHHHHHHTB-S--EEEEECCTTSTHHHHHHHHHHHHHHTCSSCCCCEEEE-BSSHHHHHHHHHHHTHHHHHSSCCSC
T ss_pred             HHHHHHHHHHcC-C--eEEEEcCCCCCceehHHHHHHHHHHHHhccCCeEEEe-cCcHHHHHHHHHHHHHHHhhcCchhh
Confidence            344455555543 2  5899999999999998776555431  1122222222 2222222333332221111000    


Q ss_pred             ----------------------------cCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecC
Q psy879           91 ----------------------------TLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNN  135 (317)
Q Consensus        91 ----------------------------~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~  135 (317)
                                                  ....-...++||||+..++......++..   .++.+.+|++...
T Consensus       228 ~~~~~~~~~~t~~~ll~~~~~~~~~~~~~~~~l~~d~lIIDEaSmv~~~l~~~ll~~---~~~~~~lILvGD~  297 (359)
T d1w36d1         228 QKKRIPEDASTLHRLLGAQPGSQRLRHHAGNPLHLDVLVVDEASMIDLPMMSRLIDA---LPDHARVIFLGDR  297 (359)
T ss_dssp             CCCSCSCCCBTTTSCC-----------CTTSCCSCSEEEECSGGGCBHHHHHHHHHT---CCTTCEEEEEECT
T ss_pred             hhhhhhhhhhHHHHHHhhhhcchHHHHhhhcccccceeeehhhhccCHHHHHHHHHH---hcCCCEEEEECCh
Confidence                                        00012356999999999987665555544   4677889998855

>d1mv5a_ c.37.1.12 (A:) Multidrug resistance ABC transporter LmrA, C-terminal domain {Lactococcus lactis [TaxId: 1358]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Multidrug resistance ABC transporter LmrA, C-terminal domain
species: Lactococcus lactis [TaxId: 1358]

Probab=98.10  E-value=8.1e-08  Score=77.54  Aligned_cols=24  Identities=38%  Similarity=0.544  Sum_probs=21.6

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHc
Q psy879           33 NIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      .+.+.||+|+||||+++.++..+.
T Consensus        30 ~vaivG~sGsGKSTLl~ll~gl~~   53 (242)
T d1mv5a_          30 IIAFAGPSGGGKSTIFSLLERFYQ   53 (242)
T ss_dssp             EEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             EEEEECCCCCCHHHHHHHHHHhhC
Confidence            589999999999999999998653

>d1u0ja_ c.37.1.20 (A:) Rep 40 protein helicase domain {Adeno-associated virus 2, AAV2 [TaxId: 10804]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Rep 40 protein helicase domain
species: Adeno-associated virus 2, AAV2 [TaxId: 10804]

Probab=98.09  E-value=1.2e-05  Score=65.60  Aligned_cols=113  Identities=15%  Similarity=0.135  Sum_probs=68.3

Q ss_pred             HHHHHHhcCCCc-e-EEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHHHHHHHhhcccCCCCcee
Q psy879           21 RLKVFSSSGNVP-N-IIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHK   98 (317)
Q Consensus        21 ~l~~~l~~~~~~-~-~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~   98 (317)
                      .|..++..+.+. + ++|+||+++|||+++.++++.+ +.     +..++.+...           +...    +-.+.+
T Consensus        92 ~l~~~L~~~~~k~n~~~l~G~~~tGKS~f~~~i~~~l-g~-----~~~~~~~~~~-----------f~l~----~l~~k~  150 (267)
T d1u0ja_          92 VFLGWATKKFGKRNTIWLFGPATTGKTNIAEAIAHTV-PF-----YGCVNWTNEN-----------FPFN----DCVDKM  150 (267)
T ss_dssp             HHHHHHTTCSTTCCEEEEECSTTSSHHHHHHHHHHHS-SC-----EEECCTTCSS-----------CTTG----GGSSCS
T ss_pred             HHHHHHcCCCCccEEEEEEcCCCCCHHHHHHHHHHHh-cc-----hhhccccCCC-----------cccc----ccCCCE
Confidence            445555444222 3 8999999999999999999986 32     1222222110           0001    114688


Q ss_pred             EEEEeCCCCCCHHHHHHHHHHhh--------------hccCCceEEEEecCCCc----------CchhHhhhcceeeecC
Q psy879           99 IVILDEADSMTDGAQQALRRTME--------------IYSNTTRFALACNNSEK----------IIEPIQSRCAMLRYNK  154 (317)
Q Consensus        99 vliiDE~d~l~~~~~~~ll~~le--------------~~~~~~~~il~~~~~~~----------l~~~i~sR~~~i~f~~  154 (317)
                      ++++||+..-. ...+.+..++.              +..+...+|+++|+.-.          -...+.||...++|+.
T Consensus       151 ~~~~~e~~~~~-~~~~~~K~l~gGd~i~v~~K~k~~~~~~~~p~li~s~n~i~~~~~~~~~~~~~~~~l~~R~~~~~F~~  229 (267)
T d1u0ja_         151 VIWWEEGKMTA-KVVESAKAILGGSKVRVDQKCKSSAQIDPTPVIVTSNTNMCAVIDGNSTTFEHQQPLQDRMFKFELTR  229 (267)
T ss_dssp             EEEECSCCEET-TTHHHHHHHHTTCCEEC------CCEECCCCEEEEESSCTTCEEETTEEECTTHHHHHTTEEEEECCS
T ss_pred             EEEEeCCCccc-cHHHHHHHhcCCCceEeecccCCCcEeeCCeEEEEeCCCcccccCCCccccccchHhhhhEEEEECCC
Confidence            99999987543 33445555554              22345556666665432          2478999999988874


Q ss_pred             C
Q psy879          155 L  155 (317)
Q Consensus       155 ~  155 (317)
                      .
T Consensus       230 ~  230 (267)
T d1u0ja_         230 R  230 (267)
T ss_dssp             C
T ss_pred             c
Confidence            3

>d1l2ta_ c.37.1.12 (A:) MJ0796 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: MJ0796
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=98.08  E-value=2.1e-06  Score=68.26  Aligned_cols=41  Identities=5%  Similarity=0.212  Sum_probs=31.1

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhcc--CCceEEEEecCC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYS--NTTRFALACNNS  136 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~--~~~~~il~~~~~  136 (317)
                      +++++++||.-. |.+.....+++++.+..  .++.+|++|++.
T Consensus       163 ~P~lLllDEPTs~LD~~~~~~i~~~l~~l~~~~g~tii~vTHd~  206 (230)
T d1l2ta_         163 NPPIILADQPTGALDSKTGEKIMQLLKKLNEEDGKTVVVVTHDI  206 (230)
T ss_dssp             CCSEEEEESTTTTSCHHHHHHHHHHHHHHHHTTCCEEEEECSCH
T ss_pred             CCCEEEecCCccccCHHHHHHHHHHHHHHHHhhCCEEEEECCCH
Confidence            689999999974 56777777877777652  356788888764

>d1ly1a_ c.37.1.1 (A:) Polynucleotide kinase, kinase domain {Bacteriophage T4 [TaxId: 10665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Polynucleotide kinase, kinase domain
species: Bacteriophage T4 [TaxId: 10665]

Probab=98.08  E-value=1.5e-05  Score=59.00  Aligned_cols=22  Identities=32%  Similarity=0.318  Sum_probs=19.8

Q ss_pred             EEEECCCCCCHHHHHHHHHHHH
Q psy879           34 IIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~l   55 (317)
                      ++++||||+||||+|+.+++..
T Consensus         5 Iii~G~pGsGKTTla~~L~~~~   26 (152)
T d1ly1a_           5 ILTIGCPGSGKSTWAREFIAKN   26 (152)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHHhC
Confidence            7899999999999999988764

>d1yksa1 c.37.1.14 (A:185-324) YFV helicase domain {Yellow fever virus [TaxId: 11089]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: YFV helicase domain
species: Yellow fever virus [TaxId: 11089]

Probab=98.05  E-value=7.7e-06  Score=59.47  Aligned_cols=28  Identities=25%  Similarity=0.336  Sum_probs=20.1

Q ss_pred             HhcCCCceEEEECCCCCCHHHHHH-HHHHHH
Q psy879           26 SSSGNVPNIIISGPPGVGKTTTIL-CLARIL   55 (317)
Q Consensus        26 l~~~~~~~~ll~G~~G~GKt~la~-~la~~l   55 (317)
                      +++|.  +.++++|+|+|||..+- .+....
T Consensus         4 l~~~~--~~il~~~tGsGKT~~~~~~~~~~~   32 (140)
T d1yksa1           4 LKKGM--TTVLDFHPGAGKTRRFLPQILAEC   32 (140)
T ss_dssp             TSTTC--EEEECCCTTSSTTTTHHHHHHHHH
T ss_pred             HHcCC--cEEEEcCCCCChhHHHHHHHHHHh
Confidence            45565  79999999999996664 434433

>d2qy9a2 c.37.1.10 (A:285-495) GTPase domain of the signal recognition particle receptor FtsY {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Escherichia coli [TaxId: 562]

Probab=98.00  E-value=1.3e-05  Score=62.53  Aligned_cols=30  Identities=50%  Similarity=0.617  Sum_probs=24.8

Q ss_pred             CCCce-EEEECCCCCCHHHHHHHHHHHHcCC
Q psy879           29 GNVPN-IIISGPPGVGKTTTILCLARILLGP   58 (317)
Q Consensus        29 ~~~~~-~ll~G~~G~GKt~la~~la~~l~~~   58 (317)
                      +..|+ ++|.||+|+||||++-.+|..+...
T Consensus         6 ~~~p~vi~lvGptGvGKTTTiAKLA~~~~~~   36 (211)
T d2qy9a2           6 GKAPFVILMVGVNGVGKTTTIGKLARQFEQQ   36 (211)
T ss_dssp             SCTTEEEEEECCTTSCHHHHHHHHHHHHHTT
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHHHHHC
Confidence            44456 8899999999999999999887543

>d3d31a2 c.37.1.12 (A:1-229) Sulfate/molybdate ABC transporter, ATP-binding protein {Methanosarcina acetivorans [TaxId: 2214]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Sulfate/molybdate ABC transporter, ATP-binding protein
species: Methanosarcina acetivorans [TaxId: 2214]

Probab=97.97  E-value=2.5e-06  Score=67.61  Aligned_cols=42  Identities=21%  Similarity=0.306  Sum_probs=30.3

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhcc--CCceEEEEecCCC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYS--NTTRFALACNNSE  137 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~--~~~~~il~~~~~~  137 (317)
                      +++++++||.-. +.+.....+.+.+.+..  ....+|++|++..
T Consensus       145 ~P~iLllDEPts~LD~~~~~~i~~~l~~l~~~~g~tii~vtHd~~  189 (229)
T d3d31a2         145 NPKILLLDEPLSALDPRTQENAREMLSVLHKKNKLTVLHITHDQT  189 (229)
T ss_dssp             CCSEEEEESSSTTSCHHHHHHHHHHHHHHHHHTTCEEEEEESCHH
T ss_pred             cCCceeecCCCcCCCHHHHHHHHHHHHHHHhcCCcEEEEEcCCHH
Confidence            689999999975 56777777777766532  3566788887743

>d1v43a3 c.37.1.12 (A:7-245) Hypothetical protein PH0022, N-terminal domain {Pyrococcus horikoshii [TaxId: 53953]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Hypothetical protein PH0022, N-terminal domain
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=97.96  E-value=1.5e-06  Score=69.46  Aligned_cols=41  Identities=12%  Similarity=0.208  Sum_probs=29.9

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhcc--CCceEEEEecCC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYS--NTTRFALACNNS  136 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~--~~~~~il~~~~~  136 (317)
                      +++++++||.-. +.+.....+++.+.+..  .++.+|++|++.
T Consensus       154 ~P~iLllDEPts~LD~~~~~~i~~ll~~l~~~~g~tii~vTHd~  197 (239)
T d1v43a3         154 EPDVLLMDEPLSNLDAKLRVAMRAEIKKLQQKLKVTTIYVTHDQ  197 (239)
T ss_dssp             CCSEEEEESTTTTSCHHHHHHHHHHHHHHHHHHTCEEEEEESCH
T ss_pred             CCCceeecCCcccCCHHHHHHHHHHHHHHHHhcCCeEEEEeCCH
Confidence            689999999975 56677777777766542  256688888774

>d3dhwc1 c.37.1.12 (C:1-240) Methionine import ATP-binding protein MetN {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Methionine import ATP-binding protein MetN
species: Escherichia coli [TaxId: 562]

Probab=97.94  E-value=2.3e-06  Score=68.39  Aligned_cols=41  Identities=15%  Similarity=0.232  Sum_probs=29.4

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhccC--CceEEEEecCC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYSN--TTRFALACNNS  136 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~~--~~~~il~~~~~  136 (317)
                      +++++++||.-. +.+.....+++.+.+...  .+.+|++|++.
T Consensus       158 ~P~lLllDEPt~~LD~~~~~~i~~~l~~l~~~~g~tvi~vTHdl  201 (240)
T d3dhwc1         158 NPKVLLCDEATSALDPATTRSILELLKDINRRLGLTILLITHEM  201 (240)
T ss_dssp             CCSEEEEESGGGSSCHHHHHHHHHHHHHHHHHHCCEEEEEBSCH
T ss_pred             CCCeEEeccccccCCHHHhhHHHHHHHHHHhccCCEEEEEcCCH
Confidence            689999999974 566777777777765422  46677888764

>d1okkd2 c.37.1.10 (D:97-303) GTPase domain of the signal recognition particle receptor FtsY {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Thermus aquaticus [TaxId: 271]

Probab=97.94  E-value=5.5e-05  Score=58.83  Aligned_cols=27  Identities=41%  Similarity=0.508  Sum_probs=23.1

Q ss_pred             ceEEEECCCCCCHHHHHHHHHHHHcCC
Q psy879           32 PNIIISGPPGVGKTTTILCLARILLGP   58 (317)
Q Consensus        32 ~~~ll~G~~G~GKt~la~~la~~l~~~   58 (317)
                      ..++|.||+|+||||++-.+|..+...
T Consensus         7 ~vi~lvGptGvGKTTTiaKLA~~~~~~   33 (207)
T d1okkd2           7 RVVLVVGVNGVGKTTTIAKLGRYYQNL   33 (207)
T ss_dssp             SEEEEECSTTSSHHHHHHHHHHHHHTT
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHC
Confidence            358999999999999999999887544

>d1yj5a2 c.37.1.1 (A:351-522) 5' polynucleotide kinase-3' phosphatase, C-terminal domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: 5' polynucleotide kinase-3' phosphatase, C-terminal domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.93  E-value=8.4e-06  Score=62.01  Aligned_cols=78  Identities=14%  Similarity=0.089  Sum_probs=43.1

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCCCHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGA  112 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~vliiDE~d~l~~~~  112 (317)
                      -+++.|+||+||||+++.++...     +  +..++.............+....        ..+..+|+|.. +.+...
T Consensus        16 liil~G~pGsGKST~a~~l~~~~-----~--~~~i~~D~~~~~~~~~~~~~~~l--------~~g~~vIiD~t-~~~~~~   79 (172)
T d1yj5a2          16 VVVAVGFPGAGKSTFIQEHLVSA-----G--YVHVNRDTLGSWQRCVSSCQAAL--------RQGKRVVIDNT-NPDVPS   79 (172)
T ss_dssp             EEEEECCTTSSHHHHHHHHTGGG-----T--CEEEEHHHHCSHHHHHHHHHHHH--------HTTCCEEEESC-CCSHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHhc-----C--CEEEchHHHHHHHHHHHHHHHHH--------HCCCCceeeCc-CCCHHH
Confidence            38999999999999999887653     1  22232211122222222222221        12345667644 456666


Q ss_pred             HHHHHHHhhhccCC
Q psy879          113 QQALRRTMEIYSNT  126 (317)
Q Consensus       113 ~~~ll~~le~~~~~  126 (317)
                      ...+.+...+..-.
T Consensus        80 R~~~~~~a~~~~~~   93 (172)
T d1yj5a2          80 RARYIQCAKDAGVP   93 (172)
T ss_dssp             HHHHHHHHHHHTCC
T ss_pred             HHHHHHHHHhcCCC
Confidence            66677766654433

>d2awna2 c.37.1.12 (A:4-235) Maltose transport protein MalK, N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Maltose transport protein MalK, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=97.92  E-value=2.9e-06  Score=67.42  Aligned_cols=41  Identities=12%  Similarity=0.184  Sum_probs=28.5

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhc--cCCceEEEEecCC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIY--SNTTRFALACNNS  136 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~--~~~~~~il~~~~~  136 (317)
                      +++++++||.-. +.+.....++..+.+.  ...+.+|++|++.
T Consensus       148 ~P~illlDEPts~LD~~~~~~i~~~l~~l~~~~g~tii~vTHd~  191 (232)
T d2awna2         148 EPSVFLLDEPLSNLDAALRVQMRIEISRLHKRLGRTMIYVTHDQ  191 (232)
T ss_dssp             CCSEEEEESTTTTSCHHHHHHHHHHHHHHHHHSCCEEEEEESCH
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHHHHHHHHhcCCEEEEEeCCH
Confidence            689999999975 5666666666666543  2356678888764

>d1rkba_ c.37.1.1 (A:) Adenylate kinase {Human (Homo sapiens), isoenzyme 6 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Human (Homo sapiens), isoenzyme 6 [TaxId: 9606]

Probab=97.90  E-value=3.3e-06  Score=63.94  Aligned_cols=25  Identities=52%  Similarity=0.727  Sum_probs=23.2

Q ss_pred             CceEEEECCCCCCHHHHHHHHHHHH
Q psy879           31 VPNIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        31 ~~~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .|.++|.|||||||||+++.+++.+
T Consensus         4 ~~~I~i~G~pGsGKTTia~~La~~l   28 (173)
T d1rkba_           4 LPNILLTGTPGVGKTTLGKELASKS   28 (173)
T ss_dssp             CCCEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHH
Confidence            4679999999999999999999987

>d1vmaa2 c.37.1.10 (A:82-294) GTPase domain of the signal recognition particle receptor FtsY {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Thermotoga maritima [TaxId: 2336]

Probab=97.89  E-value=1.6e-05  Score=62.22  Aligned_cols=38  Identities=26%  Similarity=0.348  Sum_probs=27.3

Q ss_pred             CCce-EEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEe
Q psy879           30 NVPN-IIISGPPGVGKTTTILCLARILLGPSFKDAVLEL   67 (317)
Q Consensus        30 ~~~~-~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~   67 (317)
                      ..|+ ++|.||+|+||||++-.+|..+.....+..++..
T Consensus         9 ~~p~vi~lvGptGvGKTTTiAKLAa~~~~~~~kV~lit~   47 (213)
T d1vmaa2           9 EPPFVIMVVGVNGTGKTTSCGKLAKMFVDEGKSVVLAAA   47 (213)
T ss_dssp             SSCEEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEEE
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHHHCCCceEEEee
Confidence            3456 8999999999999999999887544333333333

>d1j8yf2 c.37.1.10 (F:87-297) GTPase domain of the signal sequence recognition protein Ffh {Archaeon Acidianus ambivalens [TaxId: 2283]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal sequence recognition protein Ffh
species: Archaeon Acidianus ambivalens [TaxId: 2283]

Probab=97.84  E-value=2.5e-05  Score=61.05  Aligned_cols=29  Identities=34%  Similarity=0.447  Sum_probs=19.8

Q ss_pred             CCce-EEEECCCCCCHHHHHHHHHHHHcCC
Q psy879           30 NVPN-IIISGPPGVGKTTTILCLARILLGP   58 (317)
Q Consensus        30 ~~~~-~ll~G~~G~GKt~la~~la~~l~~~   58 (317)
                      +.|+ ++|.||+|+||||++-.+|..+...
T Consensus        10 k~p~vi~lvGptGvGKTTTiAKLA~~~~~~   39 (211)
T d1j8yf2          10 KIPYVIMLVGVQGTGKATTAGKLAYFYKKK   39 (211)
T ss_dssp             SSSEEEEEECSCCC----HHHHHHHHHHHT
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHHHC
Confidence            3456 8899999999999999999877543

>d1knqa_ c.37.1.17 (A:) Gluconate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Gluconate kinase
domain: Gluconate kinase
species: Escherichia coli [TaxId: 562]

Probab=97.82  E-value=7e-06  Score=62.05  Aligned_cols=26  Identities=23%  Similarity=0.333  Sum_probs=23.0

Q ss_pred             CCce-EEEECCCCCCHHHHHHHHHHHH
Q psy879           30 NVPN-IIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        30 ~~~~-~ll~G~~G~GKt~la~~la~~l   55 (317)
                      +-++ ++|.|||||||||+++.+++.+
T Consensus         4 ~~~~iivl~G~~GsGKsT~a~~La~~l   30 (171)
T d1knqa_           4 HDHHIYVLMGVSGSGKSAVASEVAHQL   30 (171)
T ss_dssp             TTSEEEEEECSTTSCHHHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHh
Confidence            3345 8899999999999999999997

>d1kaga_ c.37.1.2 (A:) Shikimate kinase (AroK) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Escherichia coli [TaxId: 562]

Probab=97.80  E-value=5.5e-06  Score=62.05  Aligned_cols=23  Identities=48%  Similarity=0.626  Sum_probs=21.8

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      +++|.||||+||||+++.+|+.+
T Consensus         4 ~I~l~G~~GsGKSTvak~La~~L   26 (169)
T d1kaga_           4 NIFLVGPMGAGKSTIGRQLAQQL   26 (169)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHT
T ss_pred             eEEEECCCCCCHHHHHHHHHHHh
Confidence            68899999999999999999997

>d1e6ca_ c.37.1.2 (A:) Shikimate kinase (AroK) {Erwinia chrysanthemi [TaxId: 556]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Erwinia chrysanthemi [TaxId: 556]

Probab=97.79  E-value=5.6e-05  Score=57.06  Aligned_cols=23  Identities=43%  Similarity=0.479  Sum_probs=21.4

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      +++|.|+||+||||+++.+|+.+
T Consensus         4 ~Iil~G~~GsGKSTia~~LA~~L   26 (170)
T d1e6ca_           4 PIFMVGARGCGMTTVGRELARAL   26 (170)
T ss_dssp             CEEEESCTTSSHHHHHHHHHHHH
T ss_pred             CEEEECCCCCCHHHHHHHHHHHh
Confidence            47788999999999999999997

>d1veca_ c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEAD box RNA helicase rck/p54
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.78  E-value=0.0001  Score=57.48  Aligned_cols=43  Identities=21%  Similarity=0.349  Sum_probs=32.0

Q ss_pred             CCCCCCcccCCHHHHHHHHHH---------------HhcCCCceEEEECCCCCCHHHHHH
Q psy879            5 RPQTFSDIVGNEDTVERLKVF---------------SSSGNVPNIIISGPPGVGKTTTIL   49 (317)
Q Consensus         5 ~P~~~~~~~g~~~~~~~l~~~---------------l~~~~~~~~ll~G~~G~GKt~la~   49 (317)
                      ++++|+++--++++++.|...               +.+|+  ++++..|+|+|||...-
T Consensus         1 k~~~F~~l~L~~~l~~~l~~~g~~~pt~iQ~~aip~il~g~--dvl~~a~TGsGKTlayl   58 (206)
T d1veca_           1 KGNEFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGR--DILARAKNGTGKSGAYL   58 (206)
T ss_dssp             CCSSGGGSCCCHHHHHHHHTTTCCSCCHHHHHHHHHHHTTC--CEEEECCSSSTTHHHHH
T ss_pred             CCCChhccCcCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCC--CEEeeccCccccccccc
Confidence            357888887788887776543               33555  79999999999996543

>d1qdea_ c.37.1.19 (A:) Initiation factor 4a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=97.74  E-value=0.00016  Score=56.68  Aligned_cols=41  Identities=27%  Similarity=0.408  Sum_probs=29.1

Q ss_pred             CceeEEEEeCCCCCCHH-HHHHHHHHhhhccCCceEEEEecC
Q psy879           95 GRHKIVILDEADSMTDG-AQQALRRTMEIYSNTTRFALACNN  135 (317)
Q Consensus        95 ~~~~vliiDE~d~l~~~-~~~~ll~~le~~~~~~~~il~~~~  135 (317)
                      ..-+.+++||+|.+... ..+.+.++++..+....+++.+..
T Consensus       150 ~~l~~lVlDEad~lld~~f~~~v~~I~~~~~~~~Q~vl~SAT  191 (212)
T d1qdea_         150 DKIKMFILDEADEMLSSGFKEQIYQIFTLLPPTTQVVLLSAT  191 (212)
T ss_dssp             TTCCEEEEETHHHHHHTTCHHHHHHHHHHSCTTCEEEEEESS
T ss_pred             CcceEEeehhhhhhcccchHHHHHHHHHhCCCCCeEEEEEee
Confidence            45789999999988654 355667777766666666666544

>d1y63a_ c.37.1.1 (A:) Probable kinase LmjF30.1890 {Leishmania major [TaxId: 5664]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Probable kinase LmjF30.1890
species: Leishmania major [TaxId: 5664]

Probab=97.73  E-value=8.7e-06  Score=61.65  Aligned_cols=24  Identities=46%  Similarity=0.681  Sum_probs=22.2

Q ss_pred             ceEEEECCCCCCHHHHHHHHHHHH
Q psy879           32 PNIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        32 ~~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      -+++|+||||+||||+++.+++.+
T Consensus         6 ~~I~i~G~~GsGKTT~~~~La~~l   29 (174)
T d1y63a_           6 INILITGTPGTGKTSMAEMIAAEL   29 (174)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             CEEEEEeCCCCCHHHHHHHHHHHh
Confidence            359999999999999999999986

>d2iyva1 c.37.1.2 (A:2-166) Shikimate kinase (AroK) {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=97.73  E-value=1e-05  Score=61.05  Aligned_cols=24  Identities=42%  Similarity=0.648  Sum_probs=22.2

Q ss_pred             ceEEEECCCCCCHHHHHHHHHHHH
Q psy879           32 PNIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        32 ~~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      |.++|.|+||+||||+++.+|+.+
T Consensus         2 p~IvliG~~G~GKSTig~~La~~l   25 (165)
T d2iyva1           2 PKAVLVGLPGSGKSTIGRRLAKAL   25 (165)
T ss_dssp             CSEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Confidence            567888999999999999999998

>d2onka1 c.37.1.12 (A:1-240) Molybdate/tungstate import ATP-binding protein WtpC (ModC) {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Molybdate/tungstate import ATP-binding protein WtpC (ModC)
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=97.73  E-value=3.4e-06  Score=67.22  Aligned_cols=42  Identities=12%  Similarity=0.137  Sum_probs=30.0

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhcc--CCceEEEEecCCC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYS--NTTRFALACNNSE  137 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~--~~~~~il~~~~~~  137 (317)
                      +++++++||.-. +.+.....+++.+.+..  ..+.+|++|++..
T Consensus       144 ~P~illlDEPts~LD~~~~~~i~~~i~~l~~~~g~tvi~vtHd~~  188 (240)
T d2onka1         144 QPRLLLLDEPLSAVDLKTKGVLMEELRFVQREFDVPILHVTHDLI  188 (240)
T ss_dssp             CCSSBEEESTTSSCCHHHHHHHHHHHHHHHHHHTCCEEEEESCHH
T ss_pred             cCCceEecCccccCCHHHHHHHHHHHHHHHHhcCCeEEEEeCCHH
Confidence            689999999974 67777777777776542  2456777887643

>d1g2912 c.37.1.12 (1:1-240) Maltose transport protein MalK, N-terminal domain {Archaeon Thermococcus litoralis [TaxId: 2265]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Maltose transport protein MalK, N-terminal domain
species: Archaeon Thermococcus litoralis [TaxId: 2265]

Probab=97.71  E-value=3e-05  Score=61.73  Aligned_cols=41  Identities=10%  Similarity=0.190  Sum_probs=30.3

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhcc--CCceEEEEecCC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYS--NTTRFALACNNS  136 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~--~~~~~il~~~~~  136 (317)
                      +++++++||.-. +.+.....+++.+.+..  ..+.+|++|++.
T Consensus       157 ~P~iLllDEPt~~LD~~~~~~i~~~l~~l~~~~g~tvi~vTHd~  200 (240)
T d1g2912         157 KPQVFLMDEPLSNLDAKLRVRMRAELKKLQRQLGVTTIYVTHDQ  200 (240)
T ss_dssp             CCSEEEEECTTTTSCHHHHHHHHHHHHHHHHHHTCEEEEEESCH
T ss_pred             CCCEEEecCCCcccCHHHHHHHHHHHHHHHhccCCEEEEEcCCH
Confidence            689999999975 56677777777776542  256688888774

>d1a1va1 c.37.1.14 (A:190-325) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: HCV helicase domain
species: Human hepatitis C virus (HCV), different isolates [TaxId: 11103]

Probab=97.70  E-value=0.00011  Score=53.13  Aligned_cols=39  Identities=21%  Similarity=0.262  Sum_probs=24.8

Q ss_pred             CceeEEEEeCCCCCCHHHHHHHHHHhhh--ccCCceEEEEe
Q psy879           95 GRHKIVILDEADSMTDGAQQALRRTMEI--YSNTTRFALAC  133 (317)
Q Consensus        95 ~~~~vliiDE~d~l~~~~~~~ll~~le~--~~~~~~~il~~  133 (317)
                      .+..++|+||++.+..+....+...++.  +.+...+++.|
T Consensus        93 ~~~~~vIiDE~H~~~~~~~~~~~~~l~~~~~~~~~~~l~~T  133 (136)
T d1a1va1          93 GAYDIIICDECHSTDATSILGIGTVLDQAETAGARLVVLAT  133 (136)
T ss_dssp             CCCSEEEEETTTCCSHHHHHHHHHHHHHTTTTTCSEEEEEE
T ss_pred             hcCCEEEEecccccCHHHHHHHHHHHHHHHHCCCCcEEEEe
Confidence            3568999999999988765555555543  22344444443

>d2g9na1 c.37.1.19 (A:21-238) Initiation factor 4a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.69  E-value=0.00022  Score=56.08  Aligned_cols=41  Identities=22%  Similarity=0.300  Sum_probs=30.2

Q ss_pred             CceeEEEEeCCCCCCHH-HHHHHHHHhhhccCCceEEEEecC
Q psy879           95 GRHKIVILDEADSMTDG-AQQALRRTMEIYSNTTRFALACNN  135 (317)
Q Consensus        95 ~~~~vliiDE~d~l~~~-~~~~ll~~le~~~~~~~~il~~~~  135 (317)
                      ..-+.+++||||.|... ..+.+.++++..+.+..+++.+..
T Consensus       154 ~~l~~lVlDEaD~ll~~~f~~~~~~Il~~~~~~~Q~il~SAT  195 (218)
T d2g9na1         154 KYIKMFVLDEADEMLSRGFKDQIYDIFQKLNSNTQVVLLSAT  195 (218)
T ss_dssp             TTCCEEEEESHHHHHHTTCHHHHHHHHHHSCTTCEEEEEESC
T ss_pred             ccceEEEeeecchhhcCchHHHHHHHHHhCCCCCeEEEEEec
Confidence            45689999999998764 356666777776777777776654

>d1t6na_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Spliceosome RNA helicase BAT1 (UAP56)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.67  E-value=0.00055  Score=53.18  Aligned_cols=41  Identities=17%  Similarity=0.301  Sum_probs=29.3

Q ss_pred             CceeEEEEeCCCCCCH--HHHHHHHHHhhhccCCceEEEEecC
Q psy879           95 GRHKIVILDEADSMTD--GAQQALRRTMEIYSNTTRFALACNN  135 (317)
Q Consensus        95 ~~~~vliiDE~d~l~~--~~~~~ll~~le~~~~~~~~il~~~~  135 (317)
                      ..-+.+++||+|.|..  ...+.+.++++..+....+++.+..
T Consensus       144 ~~l~~lVlDEaD~ll~~~~~~~~i~~I~~~~~~~~Q~il~SAT  186 (207)
T d1t6na_         144 KHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSAT  186 (207)
T ss_dssp             TTCCEEEEESHHHHHSSHHHHHHHHHHHHTSCSSSEEEEEESC
T ss_pred             cccceeehhhhhhhhhcCCcHHHHHHHHHhCCCCCEEEEEeee
Confidence            4567999999998764  3556667777776777777775544

>d1s2ma1 c.37.1.19 (A:46-251) Putative ATP-dependent RNA helicase DHH1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative ATP-dependent RNA helicase DHH1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=97.67  E-value=0.00031  Score=54.61  Aligned_cols=41  Identities=20%  Similarity=0.280  Sum_probs=29.5

Q ss_pred             CceeEEEEeCCCCCCHH-HHHHHHHHhhhccCCceEEEEecC
Q psy879           95 GRHKIVILDEADSMTDG-AQQALRRTMEIYSNTTRFALACNN  135 (317)
Q Consensus        95 ~~~~vliiDE~d~l~~~-~~~~ll~~le~~~~~~~~il~~~~  135 (317)
                      ..-+.+++||+|.|... ....+..+++..+....+++.+..
T Consensus       142 ~~l~~lV~DEaD~l~~~~f~~~v~~I~~~l~~~~Q~il~SAT  183 (206)
T d1s2ma1         142 SDCSLFIMDEADKMLSRDFKTIIEQILSFLPPTHQSLLFSAT  183 (206)
T ss_dssp             TTCCEEEEESHHHHSSHHHHHHHHHHHTTSCSSCEEEEEESC
T ss_pred             ccceEEEeechhhhhhhhhHHHHHHHHHhCCCCCEEEEEEEe
Confidence            45678999999998765 456677777777777667666543

>d1x6va3 c.37.1.4 (A:34-228) Adenosine-5'phosphosulfate kinase (APS kinase) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Adenosine-5'phosphosulfate kinase (APS kinase)
domain: Adenosine-5'phosphosulfate kinase (APS kinase)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.67  E-value=5.8e-06  Score=63.96  Aligned_cols=24  Identities=33%  Similarity=0.567  Sum_probs=21.9

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHcC
Q psy879           34 IIISGPPGVGKTTTILCLARILLG   57 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~l~~   57 (317)
                      ++|+|+||+||||+|+.+++.+..
T Consensus        22 I~L~G~pGSGKTTiAk~La~~l~~   45 (195)
T d1x6va3          22 VWLTGLSGAGKTTVSMALEEYLVC   45 (195)
T ss_dssp             EEEESSCHHHHHHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHh
Confidence            779999999999999999998853

>d1vpla_ c.37.1.12 (A:) Putative ABC transporter TM0544 {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Putative ABC transporter TM0544
species: Thermotoga maritima [TaxId: 2336]

Probab=97.66  E-value=5.4e-06  Score=66.36  Aligned_cols=42  Identities=19%  Similarity=0.257  Sum_probs=29.5

Q ss_pred             CceeEEEEeCCCC-CCHHHHHHHHHHhhhcc-CCceEEEEecCC
Q psy879           95 GRHKIVILDEADS-MTDGAQQALRRTMEIYS-NTTRFALACNNS  136 (317)
Q Consensus        95 ~~~~vliiDE~d~-l~~~~~~~ll~~le~~~-~~~~~il~~~~~  136 (317)
                      ..++++++||.-. |.+.....+.+++.+.. ....+|++|++.
T Consensus       150 ~~p~illLDEPt~gLD~~~~~~i~~~i~~~~~~g~tii~~tH~l  193 (238)
T d1vpla_         150 VNPRLAILDEPTSGLDVLNAREVRKILKQASQEGLTILVSSHNM  193 (238)
T ss_dssp             TCCSEEEEESTTTTCCHHHHHHHHHHHHHHHHTTCEEEEEECCH
T ss_pred             cCCCEEEecCCCCCCCHHHHHHHHHHHHHHHhcCCEEEEEeCCH
Confidence            3689999999974 66677777777776543 345577777664

>d1lw7a2 c.37.1.1 (A:220-411) Transcriptional regulator NadR, ribosylnicotinamide kinase domain {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Transcriptional regulator NadR, ribosylnicotinamide kinase domain
species: Haemophilus influenzae [TaxId: 727]

Probab=97.65  E-value=9e-06  Score=62.20  Aligned_cols=23  Identities=26%  Similarity=0.390  Sum_probs=21.8

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .++|.|||||||||+|+++++.+
T Consensus         9 ~I~i~G~~GsGKTTla~~La~~~   31 (192)
T d1lw7a2           9 TVAILGGESSGKSVLVNKLAAVF   31 (192)
T ss_dssp             EEEEECCTTSHHHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            49999999999999999999986

>d1np6a_ c.37.1.10 (A:) Molybdopterin-guanine dinucleotide biosynthesis protein MobB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Molybdopterin-guanine dinucleotide biosynthesis protein MobB
species: Escherichia coli [TaxId: 562]

Probab=97.65  E-value=1.8e-05  Score=59.46  Aligned_cols=31  Identities=26%  Similarity=0.360  Sum_probs=26.0

Q ss_pred             CceEEEECCCCCCHHHHHHHHHHHHcCCCCC
Q psy879           31 VPNIIISGPPGVGKTTTILCLARILLGPSFK   61 (317)
Q Consensus        31 ~~~~ll~G~~G~GKt~la~~la~~l~~~~~~   61 (317)
                      .|.+.|+|++||||||+++.+++.+...+..
T Consensus         2 ~Pvi~itG~~GSGKTTL~~~L~~~l~~~g~~   32 (170)
T d1np6a_           2 IPLLAFAAWSGTGKTTLLKKLIPALCARGIR   32 (170)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHHHHHTTCC
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHHHHCCCe
Confidence            3679999999999999999999988654433

>d2bdta1 c.37.1.25 (A:1-176) Hypothetical protein BH3686 {Bacillus halodurans [TaxId: 86665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Atu3015-like
domain: Hypothetical protein BH3686
species: Bacillus halodurans [TaxId: 86665]

Probab=97.65  E-value=1.1e-05  Score=60.83  Aligned_cols=23  Identities=57%  Similarity=0.712  Sum_probs=21.4

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .++|+||||+||||+|+.+++.+
T Consensus         4 lI~i~G~~GsGKTTva~~L~~~~   26 (176)
T d2bdta1           4 LYIITGPAGVGKSTTCKRLAAQL   26 (176)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHHHc
Confidence            38999999999999999999986

>d1ji0a_ c.37.1.12 (A:) Branched chain aminoacid ABC transporter {Thermotoga maritima, TM1139 [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Branched chain aminoacid ABC transporter
species: Thermotoga maritima, TM1139 [TaxId: 2336]

Probab=97.65  E-value=8e-06  Score=65.43  Aligned_cols=53  Identities=13%  Similarity=0.176  Sum_probs=35.2

Q ss_pred             ceeEEEEeCCC-CCCHHHHHHHHHHhhhcc-CCceEEEEecCCCcCchhHhhhcce
Q psy879           96 RHKIVILDEAD-SMTDGAQQALRRTMEIYS-NTTRFALACNNSEKIIEPIQSRCAM  149 (317)
Q Consensus        96 ~~~vliiDE~d-~l~~~~~~~ll~~le~~~-~~~~~il~~~~~~~l~~~i~sR~~~  149 (317)
                      +++++++||.- .+.+.....+++++.+.. ....+|+++++.+... .+.+|..+
T Consensus       157 ~P~lLllDEPt~gLD~~~~~~i~~~i~~l~~~g~til~~tH~l~~~~-~~~drv~v  211 (240)
T d1ji0a_         157 RPKLLMMDEPSLGLAPILVSEVFEVIQKINQEGTTILLVEQNALGAL-KVAHYGYV  211 (240)
T ss_dssp             CCSEEEEECTTTTCCHHHHHHHHHHHHHHHHTTCCEEEEESCHHHHH-HHCSEEEE
T ss_pred             CCCEeeecCCCcCCCHHHHHHHHHHHHHHHhCCCEEEEEeCCHHHHH-HhCCEEEE
Confidence            68999999997 467778888888777543 3455777777643322 34444443

>d1ls1a2 c.37.1.10 (A:89-295) GTPase domain of the signal sequence recognition protein Ffh {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal sequence recognition protein Ffh
species: Thermus aquaticus [TaxId: 271]

Probab=97.63  E-value=0.00035  Score=54.17  Aligned_cols=26  Identities=38%  Similarity=0.399  Sum_probs=22.5

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHcCCC
Q psy879           34 IIISGPPGVGKTTTILCLARILLGPS   59 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~l~~~~   59 (317)
                      ++|.||+|+||||++-.+|..+....
T Consensus        13 i~lvGp~GvGKTTTiaKLA~~~~~~g   38 (207)
T d1ls1a2          13 WFLVGLQGSGKTTTAAKLALYYKGKG   38 (207)
T ss_dssp             EEEECCTTTTHHHHHHHHHHHHHHTT
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCC
Confidence            88999999999999999998875443

>d2cdna1 c.37.1.1 (A:1-181) Adenylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=97.63  E-value=0.00035  Score=53.00  Aligned_cols=23  Identities=43%  Similarity=0.775  Sum_probs=21.4

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      +++|.||||+||||.++.+++.+
T Consensus         2 ~I~i~G~pGsGKsT~a~~La~~~   24 (181)
T d2cdna1           2 RVLLLGPPGAGKGTQAVKLAEKL   24 (181)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            47899999999999999999997

>d1m8pa3 c.37.1.15 (A:391-573) ATP sulfurylase C-terminal domain {Fungus (Penicillium chrysogenum) [TaxId: 5076]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ATP sulfurylase C-terminal domain
domain: ATP sulfurylase C-terminal domain
species: Fungus (Penicillium chrysogenum) [TaxId: 5076]

Probab=97.63  E-value=1.5e-05  Score=60.61  Aligned_cols=25  Identities=24%  Similarity=0.252  Sum_probs=22.5

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHcC
Q psy879           33 NIIISGPPGVGKTTTILCLARILLG   57 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~~   57 (317)
                      .++|+|+||+||||+|+++++.|..
T Consensus         8 ~I~l~G~~GsGKTTia~~La~~L~~   32 (183)
T d1m8pa3           8 TIFLTGYMNSGKDAIARALQVTLNQ   32 (183)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHhh
Confidence            3889999999999999999999853

>d1qf9a_ c.37.1.1 (A:) UMP/CMP kinase {Dictyostelium discoideum [TaxId: 44689]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: UMP/CMP kinase
species: Dictyostelium discoideum [TaxId: 44689]

Probab=97.61  E-value=1.5e-05  Score=61.71  Aligned_cols=27  Identities=26%  Similarity=0.402  Sum_probs=23.5

Q ss_pred             CCCceEEEECCCCCCHHHHHHHHHHHH
Q psy879           29 GNVPNIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        29 ~~~~~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .+++.+++.||||+||||+++.+++.+
T Consensus         4 ~kp~iI~i~G~pGSGKsT~a~~La~~~   30 (194)
T d1qf9a_           4 SKPNVVFVLGGPGSGKGTQCANIVRDF   30 (194)
T ss_dssp             CCCEEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHHH
Confidence            344458999999999999999999986

>d1viaa_ c.37.1.2 (A:) Shikimate kinase (AroK) {Campylobacter jejuni [TaxId: 197]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Campylobacter jejuni [TaxId: 197]

Probab=97.60  E-value=2.1e-05  Score=58.99  Aligned_cols=23  Identities=43%  Similarity=0.514  Sum_probs=21.6

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      +++|.|+||+||||+++.+|+.+
T Consensus         2 ~I~liG~~GsGKsTi~k~La~~l   24 (161)
T d1viaa_           2 NIVFIGFMGSGKSTLARALAKDL   24 (161)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHH
T ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Confidence            57888999999999999999997

>d1g6ha_ c.37.1.12 (A:) MJ1267 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: MJ1267
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=97.59  E-value=2e-05  Score=63.70  Aligned_cols=52  Identities=10%  Similarity=0.179  Sum_probs=34.0

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhc-cCCceEEEEecCCCcCchhHhhhcc
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIY-SNTTRFALACNNSEKIIEPIQSRCA  148 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~-~~~~~~il~~~~~~~l~~~i~sR~~  148 (317)
                      +++++|+||.-. +.+.....+++.+.+. ...+.+++++++.+.+. .+-.|..
T Consensus       168 ~P~llilDEPt~gLD~~~~~~i~~~i~~l~~~g~til~vsHdl~~~~-~~~Drv~  221 (254)
T d1g6ha_         168 NPKMIVMDEPIAGVAPGLAHDIFNHVLELKAKGITFLIIEHRLDIVL-NYIDHLY  221 (254)
T ss_dssp             CCSEEEEESTTTTCCHHHHHHHHHHHHHHHHTTCEEEEECSCCSTTG-GGCSEEE
T ss_pred             CcCchhhcCCcccCCHHHHHHHHHHHHHHHHCCCEEEEEeCcHHHHH-HhCCEEE
Confidence            689999999975 5666777777776554 34466777777755433 3344443

>d1tf7a2 c.37.1.11 (A:256-497) Circadian clock protein KaiC {Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Circadian clock protein KaiC
species: Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]

Probab=97.58  E-value=0.0002  Score=57.07  Aligned_cols=37  Identities=22%  Similarity=0.330  Sum_probs=27.9

Q ss_pred             HHHHHhcCCCce--EEEECCCCCCHHHHHHHHHHHHcCC
Q psy879           22 LKVFSSSGNVPN--IIISGPPGVGKTTTILCLARILLGP   58 (317)
Q Consensus        22 l~~~l~~~~~~~--~ll~G~~G~GKt~la~~la~~l~~~   58 (317)
                      |...+..|-++.  .+++||||+|||+++..++......
T Consensus        15 LD~~l~GGi~~gsl~li~G~pGsGKT~l~~qia~~~~~~   53 (242)
T d1tf7a2          15 LDEMCGGGFFKDSIILATGATGTGKTLLVSRFVENACAN   53 (242)
T ss_dssp             HHHHTTSSEESSCEEEEEECTTSSHHHHHHHHHHHHHTT
T ss_pred             HHHhhcCCCcCCeEEEEEeCCCCCHHHHHHHHHHHHHHh
Confidence            455555444333  8999999999999999999886543

>d1bifa1 c.37.1.7 (A:37-249) 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain
domain: 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=97.56  E-value=5.3e-05  Score=59.08  Aligned_cols=25  Identities=40%  Similarity=0.531  Sum_probs=22.6

Q ss_pred             ce-EEEECCCCCCHHHHHHHHHHHHc
Q psy879           32 PN-IIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        32 ~~-~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      |. ++++|.||+||||+|+++++.+.
T Consensus         2 p~li~l~GlpgsGKSTla~~L~~~l~   27 (213)
T d1bifa1           2 PTLIVMVGLPARGKTYISKKLTRYLN   27 (213)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHH
Confidence            45 89999999999999999999874

>d1wp9a1 c.37.1.19 (A:1-200) putative ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase PF2015
species: Pyrococcus furiosus [TaxId: 2261]

Probab=97.54  E-value=0.00012  Score=56.57  Aligned_cols=23  Identities=35%  Similarity=0.499  Sum_probs=18.3

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      +.++.+|.|+|||.++..++...
T Consensus        25 n~lv~~pTGsGKT~i~~~~~~~~   47 (200)
T d1wp9a1          25 NCLIVLPTGLGKTLIAMMIAEYR   47 (200)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CeEEEeCCCCcHHHHHHHHHHHH
Confidence            57899999999998777666543

>d1qhxa_ c.37.1.3 (A:) Chloramphenicol phosphotransferase {Streptomyces venezuelae [TaxId: 54571]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Chloramphenicol phosphotransferase
domain: Chloramphenicol phosphotransferase
species: Streptomyces venezuelae [TaxId: 54571]

Probab=97.52  E-value=2.2e-05  Score=59.33  Aligned_cols=23  Identities=35%  Similarity=0.697  Sum_probs=21.7

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .++|+|+||+||||+|+++++.+
T Consensus         5 iI~l~G~~GsGKsTva~~L~~~l   27 (178)
T d1qhxa_           5 MIILNGGSSAGKSGIVRCLQSVL   27 (178)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHHHc
Confidence            48999999999999999999996

>d2j0sa1 c.37.1.19 (A:22-243) Probable ATP-dependent RNA helicase DDX48 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable ATP-dependent RNA helicase DDX48
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.51  E-value=0.00052  Score=53.97  Aligned_cols=41  Identities=22%  Similarity=0.320  Sum_probs=29.4

Q ss_pred             CceeEEEEeCCCCCCHH-HHHHHHHHhhhccCCceEEEEecC
Q psy879           95 GRHKIVILDEADSMTDG-AQQALRRTMEIYSNTTRFALACNN  135 (317)
Q Consensus        95 ~~~~vliiDE~d~l~~~-~~~~ll~~le~~~~~~~~il~~~~  135 (317)
                      ..-+.+++||+|.|... ....+.++++..+....+++.+..
T Consensus       158 ~~l~~lVlDEaD~ll~~~f~~~i~~I~~~l~~~~Q~ilfSAT  199 (222)
T d2j0sa1         158 RAIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVVLISAT  199 (222)
T ss_dssp             TTCCEEEEETHHHHTSTTTHHHHHHHHTTSCTTCEEEEEESC
T ss_pred             ccceeeeecchhHhhhcCcHHHHHHHHHhCCCCCEEEEEEEe
Confidence            45679999999988654 456677777776777766665543

>d1zaka1 c.37.1.1 (A:3-127,A:159-222) Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Maize (Zea mays) [TaxId: 4577]

Probab=97.50  E-value=2.8e-05  Score=59.86  Aligned_cols=25  Identities=28%  Similarity=0.380  Sum_probs=22.7

Q ss_pred             CceEEEECCCCCCHHHHHHHHHHHH
Q psy879           31 VPNIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        31 ~~~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      |.+++|.|||||||||+++.+++.+
T Consensus         3 Pm~I~i~GppGsGKsT~a~~La~~~   27 (189)
T d1zaka1           3 PLKVMISGAPASGKGTQCELIKTKY   27 (189)
T ss_dssp             SCCEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHH
Confidence            3458999999999999999999997

>d1sgwa_ c.37.1.12 (A:) Putative ABC transporter PF0895 {Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Putative ABC transporter PF0895
species: Pyrococcus furiosus [TaxId: 2261]

Probab=97.50  E-value=3.8e-05  Score=59.67  Aligned_cols=29  Identities=34%  Similarity=0.568  Sum_probs=24.2

Q ss_pred             HhcCCCceEEEECCCCCCHHHHHHHHHHHHc
Q psy879           26 SSSGNVPNIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        26 l~~~~~~~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      ++.|.  .+.+.||+|+||||+.+.++..+.
T Consensus        24 i~~Ge--i~~l~G~NGsGKSTLl~~i~gl~~   52 (200)
T d1sgwa_          24 IEKGN--VVNFHGPNGIGKTTLLKTISTYLK   52 (200)
T ss_dssp             EETTC--CEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             EcCCC--EEEEECCCCChHHHHHHHHhcccc
Confidence            34555  589999999999999999998753

>d1r0wa_ c.37.1.12 (A:) Cystic fibrosis transmembrane conductance regulator, CFTR, nucleotide-binding domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Cystic fibrosis transmembrane conductance regulator, CFTR, nucleotide-binding domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.48  E-value=0.0002  Score=58.42  Aligned_cols=41  Identities=7%  Similarity=0.028  Sum_probs=28.1

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHH-hhhccCCceEEEEecCC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRT-MEIYSNTTRFALACNNS  136 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~-le~~~~~~~~il~~~~~  136 (317)
                      +++++++||+-. |.......+++. +.....+..+|++|++.
T Consensus       176 ~p~illLDEPts~LD~~~~~~i~~~~~~~~~~~~tvi~itH~~  218 (281)
T d1r0wa_         176 DADLYLLDSPFGYLDVFTEEQVFESCVCKLMANKTRILVTSKM  218 (281)
T ss_dssp             CCSEEEEESCCCSSCHHHHHHHHHHCCCCCTTTSEEEEECSCH
T ss_pred             CccchhhcCccccCCHHHHHHHHHHHHHHhhCCCEEEEEechH
Confidence            678999999985 455666777654 45444455567777764

>d1b0ua_ c.37.1.12 (A:) ATP-binding subunit of the histidine permease {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: ATP-binding subunit of the histidine permease
species: Salmonella typhimurium [TaxId: 90371]

Probab=97.48  E-value=1.3e-05  Score=64.82  Aligned_cols=53  Identities=11%  Similarity=0.201  Sum_probs=32.7

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhcc-CCceEEEEecCCCcCchhHhhhcce
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYS-NTTRFALACNNSEKIIEPIQSRCAM  149 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~-~~~~~il~~~~~~~l~~~i~sR~~~  149 (317)
                      +++++|+||.-. +....+..+++.+.+.. ....+|++|++... ...+..|+.+
T Consensus       167 ~P~llilDEPT~gLD~~~~~~i~~ll~~l~~~g~til~vtHdl~~-~~~~adri~v  221 (258)
T d1b0ua_         167 EPDVLLFDEPTSALDPELVGEVLRIMQQLAEEGKTMVVVTHEMGF-ARHVSSHVIF  221 (258)
T ss_dssp             CCSEEEEESTTTTSCHHHHHHHHHHHHHHHHTTCCEEEECSCHHH-HHHHCSEEEE
T ss_pred             CCCEEEeccccccCCHHHHHHHHHhhhhhcccCCceEEEeCCHHH-HHHhCCEEEE
Confidence            689999999975 56666666666665432 23457777766332 2344455444

>d1l7vc_ c.37.1.12 (C:) ABC transporter involved in vitamin B12 uptake, BtuD {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: ABC transporter involved in vitamin B12 uptake, BtuD
species: Escherichia coli [TaxId: 562]

Probab=97.47  E-value=5.8e-05  Score=59.97  Aligned_cols=41  Identities=15%  Similarity=0.287  Sum_probs=28.2

Q ss_pred             ceeEEEEeCCCC-CCHHHHHHHHHHhhhcc-CCceEEEEecCC
Q psy879           96 RHKIVILDEADS-MTDGAQQALRRTMEIYS-NTTRFALACNNS  136 (317)
Q Consensus        96 ~~~vliiDE~d~-l~~~~~~~ll~~le~~~-~~~~~il~~~~~  136 (317)
                      .++++++||.-. +....+..+.+++.+.. ..+.+|+++++.
T Consensus       150 ~p~llllDEPt~gLD~~~~~~i~~~i~~l~~~g~tii~vtHdl  192 (231)
T d1l7vc_         150 AGQLLLLDEPMNSLDVAQQSALDKILSALCQQGLAIVMSSHDL  192 (231)
T ss_dssp             TCCEEEESSCSTTCCHHHHHHHHHHHHHHHHTTCEEEECCCCH
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHHHHHHHhCCCEEEEEeCCH
Confidence            458999999975 56677777777776542 345567777653

>d1hv8a1 c.37.1.19 (A:3-210) Putative DEAD box RNA helicase {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative DEAD box RNA helicase
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=97.46  E-value=0.00093  Score=51.87  Aligned_cols=41  Identities=27%  Similarity=0.385  Sum_probs=28.9

Q ss_pred             CceeEEEEeCCCCCCH-HHHHHHHHHhhhccCCceEEEEecC
Q psy879           95 GRHKIVILDEADSMTD-GAQQALRRTMEIYSNTTRFALACNN  135 (317)
Q Consensus        95 ~~~~vliiDE~d~l~~-~~~~~ll~~le~~~~~~~~il~~~~  135 (317)
                      ..-+.+++||+|.+.. +....+.++++..+.+..+++.+..
T Consensus       144 ~~l~~lViDEad~l~~~~~~~~i~~I~~~~~~~~Q~i~~SAT  185 (208)
T d1hv8a1         144 KNVKYFILDEADEMLNMGFIKDVEKILNACNKDKRILLFSAT  185 (208)
T ss_dssp             TSCCEEEEETHHHHHTTTTHHHHHHHHHTSCSSCEEEEECSS
T ss_pred             ccCcEEEEEChHHhhcCCChHHHHHHHHhCCCCCeEEEEEcc
Confidence            4567999999997643 3445677777777777777776543

>d1oxxk2 c.37.1.12 (K:1-242) Glucose transport protein GlcV, N-terminal domain {Archaeon Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Glucose transport protein GlcV, N-terminal domain
species: Archaeon Sulfolobus solfataricus [TaxId: 2287]

Probab=97.45  E-value=4.2e-06  Score=66.81  Aligned_cols=91  Identities=12%  Similarity=0.127  Sum_probs=66.3

Q ss_pred             cCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHhhhCCCcccHHHHHhhcCCCCHHHHHHHHHHH
Q psy879          153 NKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEMLLNC  232 (317)
Q Consensus       153 ~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~l~~~~~gd~r~~i~~l~~~~~~~~~i~~~~v~~~~~~~~~~~i~~l~~~~  232 (317)
                      ...+..+..+.+.+.+..-++   .+..+..+...+|..++-+.+.++.+.+.+.+-.|+....++......+.+++..+
T Consensus       110 ~~~~~~~~~~~v~~~l~~~gL---~~~~~~~p~~LSGGqkQRvaiARaL~~~P~llllDEPt~~LD~~~~~~i~~~i~~l  186 (242)
T d1oxxk2         110 MKMSKEEIRKRVEEVAKILDI---HHVLNHFPRELSGAQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSARALVKEV  186 (242)
T ss_dssp             SSCCHHHHHHHHHHHHHHTTC---GGGTTSCGGGSCHHHHHHHHHHHHHTTCCSEEEEESTTTTSCGGGHHHHHHHHHHH
T ss_pred             hcCCHHHHHHHHHHHHhhcCh---HhhhhCChhhCCHHHHhHHHHHhHHhhcccceeecCCccCCCHHHHHHHHHHHHHH
Confidence            357778888888888876665   33445555666777999999999998888888888888888887777777777665


Q ss_pred             h----------cCCHHHHHHHHHH
Q psy879          233 V----------EGNMKDSYKIIHH  246 (317)
Q Consensus       233 ~----------~~~~~~~~~~~~~  246 (317)
                      .          .+|...+..+.+.
T Consensus       187 ~~~~g~tvi~vTHd~~~~~~~~dr  210 (242)
T d1oxxk2         187 QSRLGVTLLVVSHDPADIFAIADR  210 (242)
T ss_dssp             HHHHCCEEEEEESCHHHHHHHCSE
T ss_pred             HhccCCEEEEEECCHHHHHHhCCE
Confidence            3          2366666665444

>d1g6oa_ c.37.1.11 (A:) Hexameric traffic ATPase, HP0525 {Helicobacter pylori [TaxId: 210]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hexameric traffic ATPase, HP0525
species: Helicobacter pylori [TaxId: 210]

Probab=97.44  E-value=0.00041  Score=57.78  Aligned_cols=38  Identities=32%  Similarity=0.497  Sum_probs=33.8

Q ss_pred             HHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHH
Q psy879           16 EDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        16 ~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      ++....|..+++.+.  +++++||+|+||||+.++++..+
T Consensus       153 ~~~~~~l~~~v~~~~--nili~G~tgSGKTT~l~al~~~i  190 (323)
T d1g6oa_         153 EQAISAIKDGIAIGK--NVIVCGGTGSGKTTYIKSIMEFI  190 (323)
T ss_dssp             HHHHHHHHHHHHHTC--CEEEEESTTSSHHHHHHHHGGGS
T ss_pred             HHHHHHHHHHHHhCC--CEEEEeeccccchHHHHHHhhhc
Confidence            566777888888887  89999999999999999999876

>d1ukza_ c.37.1.1 (A:) Uridylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Uridylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=97.44  E-value=3.8e-05  Score=59.45  Aligned_cols=26  Identities=35%  Similarity=0.451  Sum_probs=23.1

Q ss_pred             CCceEEEECCCCCCHHHHHHHHHHHH
Q psy879           30 NVPNIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        30 ~~~~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      ..|.++|.||||+||||.|+.+++.+
T Consensus         7 ~~~iI~i~GppGSGKsT~a~~La~~~   32 (196)
T d1ukza_           7 QVSVIFVLGGPGAGKGTQCEKLVKDY   32 (196)
T ss_dssp             TCEEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHh
Confidence            44568999999999999999999986

>d1teva_ c.37.1.1 (A:) UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: UMP/CMP kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.43  E-value=4.2e-05  Score=59.04  Aligned_cols=24  Identities=25%  Similarity=0.387  Sum_probs=22.2

Q ss_pred             ceEEEECCCCCCHHHHHHHHHHHH
Q psy879           32 PNIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        32 ~~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      +.++|.||||+||||.|+.+|+.+
T Consensus         2 ~iI~i~GppGSGKsT~a~~La~~~   25 (194)
T d1teva_           2 LVVFVLGGPGAGKGTQCARIVEKY   25 (194)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHh
Confidence            458999999999999999999986

>d1zp6a1 c.37.1.25 (A:6-181) Hypothetical protein Atu3015 {Agrobacterium tumefaciens [TaxId: 358]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Atu3015-like
domain: Hypothetical protein Atu3015
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=97.40  E-value=3.7e-05  Score=58.08  Aligned_cols=23  Identities=39%  Similarity=0.635  Sum_probs=20.9

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .++|.|||||||||+++.+++.+
T Consensus         6 iI~l~G~~GsGKSTia~~La~~l   28 (176)
T d1zp6a1           6 ILLLSGHPGSGKSTIAEALANLP   28 (176)
T ss_dssp             EEEEEECTTSCHHHHHHHHHTCS
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            48999999999999999999864

>d2fz4a1 c.37.1.19 (A:24-229) DNA repair protein RAD25 {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DNA repair protein RAD25
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=97.37  E-value=0.00046  Score=53.58  Aligned_cols=41  Identities=22%  Similarity=0.175  Sum_probs=30.9

Q ss_pred             ccCCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHH
Q psy879           12 IVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        12 ~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      +--.+...+.+..+++++   +.++.+|+|+|||.++-.++..+
T Consensus        69 ~~Lr~yQ~eav~~~~~~~---~~ll~~~tG~GKT~~a~~~~~~~  109 (206)
T d2fz4a1          69 ISLRDYQEKALERWLVDK---RGCIVLPTGSGKTHVAMAAINEL  109 (206)
T ss_dssp             CCCCHHHHHHHHHHTTTS---EEEEEESSSTTHHHHHHHHHHHS
T ss_pred             CCcCHHHHHHHHHHHhCC---CcEEEeCCCCCceehHHhHHHHh
Confidence            345566666777666543   46788999999999998888775

>d1khta_ c.37.1.1 (A:) Adenylate kinase {Archaeon Methanococcus voltae [TaxId: 2188]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Archaeon Methanococcus voltae [TaxId: 2188]

Probab=97.37  E-value=7.7e-05  Score=56.76  Aligned_cols=29  Identities=28%  Similarity=0.413  Sum_probs=24.5

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHcCCCCC
Q psy879           33 NIIISGPPGVGKTTTILCLARILLGPSFK   61 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~~~~~~   61 (317)
                      .++|.|+||+||||+++.+++.+.....+
T Consensus         3 iI~i~G~~GsGKsT~~~~L~~~l~~~~~~   31 (190)
T d1khta_           3 VVVVTGVPGVGSTTSSQLAMDNLRKEGVN   31 (190)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHHTTTCC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHcCCC
Confidence            48999999999999999999998654433

>d1u94a1 c.37.1.11 (A:6-268) RecA protein, ATPase-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Escherichia coli [TaxId: 562]

Probab=97.36  E-value=0.00043  Score=55.86  Aligned_cols=37  Identities=30%  Similarity=0.395  Sum_probs=27.2

Q ss_pred             HHHHHhcCCCc---eEEEECCCCCCHHHHHHHHHHHHcCC
Q psy879           22 LKVFSSSGNVP---NIIISGPPGVGKTTTILCLARILLGP   58 (317)
Q Consensus        22 l~~~l~~~~~~---~~ll~G~~G~GKt~la~~la~~l~~~   58 (317)
                      |..++-.|.+|   ...|+||||+|||+++..++.....+
T Consensus        42 lD~~Lg~GGi~~g~itei~G~~gsGKTtl~l~~~~~~q~~   81 (263)
T d1u94a1          42 LDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIAAAQRE   81 (263)
T ss_dssp             HHHHTSSSSEETTSEEEEECSTTSSHHHHHHHHHHHHHHT
T ss_pred             HHHHhcCCCccCceEEEEecCCCcHHHHHHHHHHHHHHcC
Confidence            44455324433   28999999999999999999887543

>d1zina1 c.37.1.1 (A:1-125,A:161-217) Adenylate kinase {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=97.35  E-value=5.9e-05  Score=57.44  Aligned_cols=23  Identities=30%  Similarity=0.523  Sum_probs=21.4

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      +++|.||||+||||.++.+|+.+
T Consensus         2 ~I~i~G~pGSGKsT~a~~La~~~   24 (182)
T d1zina1           2 NLVLMGLPGAGKGTQAEKIVAAY   24 (182)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            37899999999999999999997

>d1q0ua_ c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable DEAD box RNA helicase YqfR
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=97.33  E-value=0.00069  Score=52.59  Aligned_cols=41  Identities=17%  Similarity=0.208  Sum_probs=28.8

Q ss_pred             CceeEEEEeCCCCCCHHH-HHHHHHHhhhccCCceEEEEecC
Q psy879           95 GRHKIVILDEADSMTDGA-QQALRRTMEIYSNTTRFALACNN  135 (317)
Q Consensus        95 ~~~~vliiDE~d~l~~~~-~~~ll~~le~~~~~~~~il~~~~  135 (317)
                      ..-+.+++||+|.+.... ...+..++...+++..+++.+..
T Consensus       146 ~~l~~lViDEad~ll~~~f~~~v~~I~~~~~~~~Q~il~SAT  187 (209)
T d1q0ua_         146 HTAHILVVDEADLMLDMGFITDVDQIAARMPKDLQMLVFSAT  187 (209)
T ss_dssp             GGCCEEEECSHHHHHHTTCHHHHHHHHHTSCTTCEEEEEESC
T ss_pred             ccceEEEEeecccccccccHHHHHHHHHHCCCCCEEEEEEcc
Confidence            456789999999987653 45566666666677777776543

>d1p9ra_ c.37.1.11 (A:) Extracellular secretion NTPase EpsE {Vibrio cholerae [TaxId: 666]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Extracellular secretion NTPase EpsE
species: Vibrio cholerae [TaxId: 666]

Probab=97.32  E-value=0.00055  Score=58.90  Aligned_cols=51  Identities=18%  Similarity=0.283  Sum_probs=41.4

Q ss_pred             CCCCcccCCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCC
Q psy879            7 QTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGP   58 (317)
Q Consensus         7 ~~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~   58 (317)
                      .+++++--.+...+.+..++...+ .-+++.||.|+||||+..++.+.+..+
T Consensus       135 ~~l~~LG~~~~~~~~l~~l~~~~~-GliLvtGpTGSGKSTTl~~~l~~~~~~  185 (401)
T d1p9ra_         135 LDLHSLGMTAHNHDNFRRLIKRPH-GIILVTGPTGSGKSTTLYAGLQELNSS  185 (401)
T ss_dssp             CCGGGSCCCHHHHHHHHHHHTSSS-EEEEEECSTTSCHHHHHHHHHHHHCCT
T ss_pred             hhhhhhcccHHHHHHHHHHHhhhh-ceEEEEcCCCCCccHHHHHHhhhhcCC
Confidence            457777778888888888876544 239999999999999999999998543

>d1s3ga1 c.37.1.1 (A:1-125,A:161-217) Adenylate kinase {Bacillus globisporus [TaxId: 1459]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Bacillus globisporus [TaxId: 1459]

Probab=97.26  E-value=8.4e-05  Score=56.69  Aligned_cols=23  Identities=35%  Similarity=0.527  Sum_probs=21.3

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .++|.||||+||||.++.+|+.+
T Consensus         2 ~I~i~G~pGSGKsT~a~~La~~~   24 (182)
T d1s3ga1           2 NIVLMGLPGAGKGTQADRIVEKY   24 (182)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            37899999999999999999997

>d2p6ra3 c.37.1.19 (A:1-202) Hel308 helicase {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Hel308 helicase
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=97.26  E-value=0.00024  Score=55.06  Aligned_cols=38  Identities=13%  Similarity=0.132  Sum_probs=25.8

Q ss_pred             ceeEEEEeCCCCCCHH----HHHHHHHHhhhccCCceEEEEe
Q psy879           96 RHKIVILDEADSMTDG----AQQALRRTMEIYSNTTRFALAC  133 (317)
Q Consensus        96 ~~~vliiDE~d~l~~~----~~~~ll~~le~~~~~~~~il~~  133 (317)
                      ...++|+||++.+..+    ....++..+...++++.+|+.|
T Consensus       138 ~~~~ii~DE~h~~~~~~r~~~~~~~l~~i~~~~~~~~~l~lS  179 (202)
T d2p6ra3         138 AVSCLVVDEIHLLDSEKRGATLEILVTKMRRMNKALRVIGLS  179 (202)
T ss_dssp             GCCEEEETTGGGGGCTTTHHHHHHHHHHHHHHCTTCEEEEEE
T ss_pred             hhhhccccHHHHhcccccchHHHHHHHHHHhcCCCCcEEEEc
Confidence            4679999999988543    2445666666666667776654

>d1ckea_ c.37.1.1 (A:) CMP kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: CMP kinase
species: Escherichia coli [TaxId: 562]

Probab=97.26  E-value=9e-05  Score=58.25  Aligned_cols=24  Identities=46%  Similarity=0.703  Sum_probs=22.4

Q ss_pred             ceEEEECCCCCCHHHHHHHHHHHH
Q psy879           32 PNIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        32 ~~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      |.+.+.||||+||+|.++.+++.+
T Consensus         4 piI~I~GppGSGKgT~ak~La~~~   27 (225)
T d1ckea_           4 PVITIDGPSGAGKGTLCKAMAEAL   27 (225)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHh
Confidence            568899999999999999999997

>d3adka_ c.37.1.1 (A:) Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Pig (Sus scrofa) [TaxId: 9823]

Probab=97.24  E-value=8.7e-05  Score=57.25  Aligned_cols=23  Identities=30%  Similarity=0.426  Sum_probs=21.6

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .++|.||||+||||.++.+++.+
T Consensus        10 iI~l~G~pGSGKsT~a~~La~~~   32 (194)
T d3adka_          10 IIFVVGGPGSGKGTQCEKIVQKY   32 (194)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            68999999999999999999985

>d2eyqa3 c.37.1.19 (A:546-778) Transcription-repair coupling factor, TRCF {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Transcription-repair coupling factor, TRCF
species: Escherichia coli [TaxId: 562]

Probab=97.23  E-value=0.0027  Score=49.89  Aligned_cols=44  Identities=14%  Similarity=0.169  Sum_probs=36.0

Q ss_pred             CCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcC
Q psy879           14 GNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLG   57 (317)
Q Consensus        14 g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~   57 (317)
                      .|..+.+.+...+.++.+-+.|++|..|+|||.++...+.....
T Consensus        59 ~Q~~~~~~i~~~~~~~~~~~~LL~GdvGsGKT~V~~~a~~~~~~  102 (233)
T d2eyqa3          59 DQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVD  102 (233)
T ss_dssp             HHHHHHHHHHHHHHSSSCCEEEEECCCCTTTHHHHHHHHHHHHT
T ss_pred             hHHHHHHHHHHHHhccCccCeEEEcCCCCCcHHHHHHHHHHHHH
Confidence            46677777888888888778999999999999998887766543

>d1ak2a1 c.37.1.1 (A:14-146,A:177-233) Adenylate kinase {Cow (Bos taurus), mitochondrial izozyme-2 [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Cow (Bos taurus), mitochondrial izozyme-2 [TaxId: 9913]

Probab=97.22  E-value=0.00012  Score=56.10  Aligned_cols=23  Identities=39%  Similarity=0.658  Sum_probs=21.2

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .++|.||||+||||.++.+|+.+
T Consensus         5 riil~G~pGSGKsT~a~~La~~~   27 (190)
T d1ak2a1           5 RAVLLGPPGAGKGTQAPKLAKNF   27 (190)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            47789999999999999999986

>d2ak3a1 c.37.1.1 (A:0-124,A:162-225) Adenylate kinase {Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]

Probab=97.21  E-value=0.00011  Score=56.41  Aligned_cols=26  Identities=27%  Similarity=0.414  Sum_probs=22.5

Q ss_pred             CCceEEEECCCCCCHHHHHHHHHHHH
Q psy879           30 NVPNIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        30 ~~~~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      +.-.++|.||||+||||.++.+|+.+
T Consensus         5 r~mrIiliG~PGSGKtT~a~~La~~~   30 (189)
T d2ak3a1           5 RLLRAAIMGAPGSGKGTVSSRITKHF   30 (189)
T ss_dssp             CCCEEEEECCTTSSHHHHHHHHHHHB
T ss_pred             cceeEEEECCCCCCHHHHHHHHHHHH
Confidence            33458889999999999999999985

>d1akya1 c.37.1.1 (A:3-130,A:169-220) Adenylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=97.20  E-value=0.0001  Score=56.08  Aligned_cols=22  Identities=36%  Similarity=0.685  Sum_probs=20.7

Q ss_pred             EEEECCCCCCHHHHHHHHHHHH
Q psy879           34 IIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~l   55 (317)
                      ++|.||||+||||.++.+++.+
T Consensus         5 Ivl~G~pGSGKtT~a~~La~~~   26 (180)
T d1akya1           5 MVLIGPPGAGKGTQAPNLQERF   26 (180)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            7788999999999999999986

>d1rz3a_ c.37.1.6 (A:) Hypothetical protein rbstp0775 {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Hypothetical protein rbstp0775
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=97.20  E-value=0.00023  Score=54.49  Aligned_cols=24  Identities=33%  Similarity=0.277  Sum_probs=21.6

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHcC
Q psy879           34 IIISGPPGVGKTTTILCLARILLG   57 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~l~~   57 (317)
                      +.+.||+|+||||+|+.++..+..
T Consensus        25 IgI~G~~GSGKSTla~~L~~~l~~   48 (198)
T d1rz3a_          25 LGIDGLSRSGKTTLANQLSQTLRE   48 (198)
T ss_dssp             EEEEECTTSSHHHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHhcc
Confidence            679999999999999999988753

>d1e4va1 c.37.1.1 (A:1-121,A:157-214) Adenylate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Escherichia coli [TaxId: 562]

Probab=97.15  E-value=0.00012  Score=55.68  Aligned_cols=23  Identities=30%  Similarity=0.417  Sum_probs=21.2

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .++|.||||+||||.++.+++.+
T Consensus         2 ~I~i~G~pGSGKsT~~~~La~~~   24 (179)
T d1e4va1           2 RIILLGAPVAGKGTQAQFIMEKY   24 (179)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            37889999999999999999986

>d1nksa_ c.37.1.1 (A:) Adenylate kinase {Archaeon Sulfolobus acidocaldarius [TaxId: 2285]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Archaeon Sulfolobus acidocaldarius [TaxId: 2285]

Probab=97.11  E-value=0.00016  Score=55.17  Aligned_cols=26  Identities=38%  Similarity=0.533  Sum_probs=22.9

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHcCC
Q psy879           33 NIIISGPPGVGKTTTILCLARILLGP   58 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~~~   58 (317)
                      -++|.|+||+||||+++.+++.+...
T Consensus         3 iivi~G~~GsGKTT~~~~La~~L~~~   28 (194)
T d1nksa_           3 IGIVTGIPGVGKSTVLAKVKEILDNQ   28 (194)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHHHTT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHc
Confidence            47899999999999999999998544

>d1m7ga_ c.37.1.4 (A:) Adenosine-5'phosphosulfate kinase (APS kinase) {Fungus (Penicillium chrysogenum) [TaxId: 5076]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Adenosine-5'phosphosulfate kinase (APS kinase)
domain: Adenosine-5'phosphosulfate kinase (APS kinase)
species: Fungus (Penicillium chrysogenum) [TaxId: 5076]

Probab=97.08  E-value=0.0003  Score=54.79  Aligned_cols=35  Identities=20%  Similarity=0.178  Sum_probs=26.8

Q ss_pred             HHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHc
Q psy879           22 LKVFSSSGNVPNIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        22 l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      .+....+.+.-.++|+|.||+||||+++.+++.+.
T Consensus        15 ~r~~~~~~kg~vIwltGlsGsGKTTia~~L~~~l~   49 (208)
T d1m7ga_          15 ERTELRNQRGLTIWLTGLSASGKSTLAVELEHQLV   49 (208)
T ss_dssp             HHHHHHTSSCEEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             HHHHHhCCCCeEEEEECCCCCCHHHHHHHHHHHHH
Confidence            34444444433499999999999999999998763

>d1xp8a1 c.37.1.11 (A:15-282) RecA protein, ATPase-domain {Deinococcus radiodurans [TaxId: 1299]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Deinococcus radiodurans [TaxId: 1299]

Probab=97.04  E-value=0.0018  Score=52.16  Aligned_cols=25  Identities=32%  Similarity=0.316  Sum_probs=22.1

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHcCC
Q psy879           34 IIISGPPGVGKTTTILCLARILLGP   58 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~l~~~   58 (317)
                      ..|+||+|+|||+++..++......
T Consensus        60 tei~G~~~sGKT~l~l~~~~~aqk~   84 (268)
T d1xp8a1          60 TEIYGPESGGKTTLALAIVAQAQKA   84 (268)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHHHHT
T ss_pred             EEEecCCccchHHHHHHHHHHHHhC
Confidence            8999999999999999999876543

>d1q3ta_ c.37.1.1 (A:) CMP kinase {Streptococcus pneumoniae [TaxId: 1313]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: CMP kinase
species: Streptococcus pneumoniae [TaxId: 1313]

Probab=96.95  E-value=0.00023  Score=55.93  Aligned_cols=22  Identities=36%  Similarity=0.569  Sum_probs=20.5

Q ss_pred             EEEECCCCCCHHHHHHHHHHHH
Q psy879           34 IIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~l   55 (317)
                      +.+.||||+||||.|+.+|+.+
T Consensus         6 IaIdGp~GsGKgT~ak~La~~l   27 (223)
T d1q3ta_           6 IAIDGPASSGKSTVAKIIAKDF   27 (223)
T ss_dssp             EEEECSSCSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            5678999999999999999997

>d4tmka_ c.37.1.1 (A:) Thymidylate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Escherichia coli [TaxId: 562]

Probab=96.93  E-value=0.006  Score=47.00  Aligned_cols=27  Identities=33%  Similarity=0.377  Sum_probs=23.5

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHcCCC
Q psy879           33 NIIISGPPGVGKTTTILCLARILLGPS   59 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~~~~   59 (317)
                      -+.|.|++|+||||.++.+++.+...+
T Consensus         4 fIviEG~dGsGKsT~~~~L~~~L~~~g   30 (210)
T d4tmka_           4 YIVIEGLEGAGKTTARNVVVETLEQLG   30 (210)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHHHHTT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHhCC
Confidence            478999999999999999999886444

>d3ctda1 a.80.1.2 (A:258-420) Uncharacterized protein YrvN {Prochlorococcus marinus [TaxId: 1219]}

class: All alpha proteins
fold: post-AAA+ oligomerization domain-like
superfamily: post-AAA+ oligomerization domain-like
family: MgsA/YrvN C-terminal domain-like
domain: Uncharacterized protein YrvN
species: Prochlorococcus marinus [TaxId: 1219]

Probab=96.88  E-value=0.0065  Score=44.37  Aligned_cols=84  Identities=14%  Similarity=0.205  Sum_probs=61.6

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHH-HhcCCChHHHHHHHHHHHHHHhHHhcCC-CcHHHH
Q psy879          222 PLAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDIIGNIFRVA-KTLDIPEPLKLSIIQEIGNVHLRISEGV-NSLLQL  299 (317)
Q Consensus       222 ~~~i~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~-~~~~~~~~~~~~~~~~l~~~~~~l~~g~-~~~l~l  299 (317)
                      .+.++.+.++++..|.+.|+.|+..|++.|++|..|.+.+.+.+ +.+|+.+.....+.....+.-.+  -|. .-++.|
T Consensus         3 Yd~iSA~~KSiRgSD~dAAly~larml~~Gedp~~i~RRli~~AsEDIGlAdp~Al~~a~aa~~a~~~--iG~PE~~i~L   80 (163)
T d3ctda1           3 FDVISAFIKSIRGSDPDATLYWLANMVEAGEDPNFIFRRLLISACEDIGLADPNAIVVVQSCCDAFDR--VGFPEGLFFL   80 (163)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHTTGGGSTTHHHHHHHHHHHHHH--HCTTTTHHHH
T ss_pred             hHHHHHHHHHHhcCCccHHHHHHHHHHHcCCchHHHHHHHHHHHHHhhcccChhHHHHHHHHHHHHHH--hCCchhHHHH
Confidence            56789999999999999999999999999999999999998875 45566554433333333222222  244 667777


Q ss_pred             HHHHHHHH
Q psy879          300 SGLLARLC  307 (317)
Q Consensus       300 e~~~~~~~  307 (317)
                      -..+.-+|
T Consensus        81 AqaviyLA   88 (163)
T d3ctda1          81 SQASLYLA   88 (163)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            77777776

>d2gj8a1 c.37.1.8 (A:216-376) Probable tRNA modification GTPase TrmE (MnmE), G domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable tRNA modification GTPase TrmE (MnmE), G domain
species: Escherichia coli [TaxId: 562]

Probab=96.86  E-value=0.0066  Score=44.38  Aligned_cols=43  Identities=5%  Similarity=0.099  Sum_probs=27.9

Q ss_pred             CceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCC
Q psy879           95 GRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSE  137 (317)
Q Consensus        95 ~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~  137 (317)
                      ...-++++|.-+.........+...+...+....+|++.|..+
T Consensus        81 ~d~~i~~~d~~~~~~~~~~~~~~~~~~~~~~~~~iilv~NK~D  123 (161)
T d2gj8a1          81 ADRVLFMVDGTTTDAVDPAEIWPEFIARLPAKLPITVVRNKAD  123 (161)
T ss_dssp             CSEEEEEEETTTCCCCSHHHHCHHHHHHSCTTCCEEEEEECHH
T ss_pred             ccccceeeccccccchhhhhhhhhhhhhcccccceeeccchhh
Confidence            4556777776666555555555666666666677788887644

>d1xjca_ c.37.1.10 (A:) Molybdopterin-guanine dinucleotide biosynthesis protein MobB {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Molybdopterin-guanine dinucleotide biosynthesis protein MobB
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=96.81  E-value=0.00039  Score=51.87  Aligned_cols=33  Identities=15%  Similarity=0.106  Sum_probs=25.9

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHcCCCCCCceE
Q psy879           33 NIIISGPPGVGKTTTILCLARILLGPSFKDAVL   65 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~   65 (317)
                      .+.+.|++|+||||++..++..|...+....++
T Consensus         3 ii~I~G~~gSGKTTli~~l~~~L~~~g~~v~vi   35 (165)
T d1xjca_           3 VWQVVGYKHSGKTTLMEKWVAAAVREGWRVGTV   35 (165)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHHHhCCCeEEEE
Confidence            467999999999999999999986554433333

>d1z2aa1 c.37.1.8 (A:8-171) Rab23 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab23
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.81  E-value=0.0021  Score=47.52  Aligned_cols=21  Identities=24%  Similarity=0.426  Sum_probs=19.0

Q ss_pred             EEEECCCCCCHHHHHHHHHHH
Q psy879           34 IIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~   54 (317)
                      +++.|++|+|||+++..+...
T Consensus         5 v~liG~~~vGKSsLi~rl~~~   25 (164)
T d1z2aa1           5 MVVVGNGAVGKSSMIQRYCKG   25 (164)
T ss_dssp             EEEECSTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999988863

>d1pzna2 c.37.1.11 (A:96-349) DNA repair protein Rad51, catalytic domain {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=96.81  E-value=0.0012  Score=52.54  Aligned_cols=35  Identities=26%  Similarity=0.249  Sum_probs=25.9

Q ss_pred             HHHHHhcCCCce--EEEECCCCCCHHHHHHHHHHHHc
Q psy879           22 LKVFSSSGNVPN--IIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        22 l~~~l~~~~~~~--~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      |-..+..|-++.  ++++||||+|||+++..++....
T Consensus        25 LD~ll~GGlp~G~~~li~G~pGsGKT~~~lq~~~~~~   61 (254)
T d1pzna2          25 LDKLLGGGIETQAITEVFGEFGSGKTQLAHTLAVMVQ   61 (254)
T ss_dssp             HHHHHTSSEESSEEEEEEESTTSSHHHHHHHHHHHTT
T ss_pred             HHHhhcCCccCCEEEEEEcCCCCCHHHHHHHHHHHhh
Confidence            444444443333  89999999999999999987653

>d2p67a1 c.37.1.10 (A:1-327) LAO/AO transport system kinase ArgK {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: LAO/AO transport system kinase ArgK
species: Escherichia coli [TaxId: 562]

Probab=96.78  E-value=0.001  Score=55.38  Aligned_cols=45  Identities=29%  Similarity=0.530  Sum_probs=33.6

Q ss_pred             cCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCC
Q psy879           28 SGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASND   72 (317)
Q Consensus        28 ~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~   72 (317)
                      .|+...+-++||||+||||++..++..+........++.+++++.
T Consensus        51 ~~~~~~IgitG~pGaGKSTLi~~l~~~~~~~g~~vavlavDpss~   95 (327)
T d2p67a1          51 CGNTLRLGVTGTPGAGKSTFLEAFGMLLIREGLKVAVIAVDPSSP   95 (327)
T ss_dssp             CSCSEEEEEEECTTSCHHHHHHHHHHHHHHTTCCEEEEEECCC--
T ss_pred             cCCceEEEeeCCCCCCHHHHHHHHHHHHHhcCCceeeecCCCcee
Confidence            455445999999999999999999998876555555666666543

>d1mo6a1 c.37.1.11 (A:1-269) RecA protein, ATPase-domain {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=96.70  E-value=0.0037  Score=50.26  Aligned_cols=23  Identities=39%  Similarity=0.377  Sum_probs=20.2

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHc
Q psy879           34 IIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      ..|+||||+|||+++..++....
T Consensus        63 ~e~~G~~~~GKT~l~l~~~~~~q   85 (269)
T d1mo6a1          63 IEIYGPESSGKTTVALHAVANAQ   85 (269)
T ss_dssp             EEEECSSSSSHHHHHHHHHHHHH
T ss_pred             EEEecCCCcHHHHHHHHHHHHHh
Confidence            89999999999999988877654

>d1n0wa_ c.37.1.11 (A:) DNA repair protein Rad51, catalytic domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.70  E-value=0.00045  Score=53.73  Aligned_cols=35  Identities=23%  Similarity=0.119  Sum_probs=25.7

Q ss_pred             HHHHHhcCCCce--EEEECCCCCCHHHHHHHHHHHHc
Q psy879           22 LKVFSSSGNVPN--IIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        22 l~~~l~~~~~~~--~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      |-..+..|-++.  ++|+||||+|||+++..++....
T Consensus        12 LD~ll~GGi~~G~v~~i~G~~GsGKT~l~l~la~~~~   48 (242)
T d1n0wa_          12 LDKLLQGGIETGSITEMFGEFRTGKTQICHTLAVTCQ   48 (242)
T ss_dssp             HHHHTTTSEETTSEEEEECCTTSSHHHHHHHHHHHTT
T ss_pred             HHHhhcCCCcCCEEEEEEeCCCCCHHHHHHHHHHHHH
Confidence            344444443333  99999999999999999987653

>d2qm8a1 c.37.1.10 (A:5-327) Metallochaperone MeaB {Methylobacterium extorquens [TaxId: 408]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Metallochaperone MeaB
species: Methylobacterium extorquens [TaxId: 408]

Probab=96.70  E-value=0.0013  Score=54.70  Aligned_cols=43  Identities=42%  Similarity=0.597  Sum_probs=32.0

Q ss_pred             cCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCC
Q psy879           28 SGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNAS   70 (317)
Q Consensus        28 ~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~   70 (317)
                      +++...+-++||||+||||++..+...+.....+..++.++++
T Consensus        48 ~~~~~~igitG~pGaGKSTli~~l~~~~~~~g~~vaViavDps   90 (323)
T d2qm8a1          48 TGRAIRVGITGVPGVGKSTTIDALGSLLTAAGHKVAVLAVDPS   90 (323)
T ss_dssp             CCCSEEEEEECCTTSCHHHHHHHHHHHHHHTTCCEEEEEECGG
T ss_pred             cCCceEEeeeCCCCCCHHHHHHHHHHHHhhcCCceeeeecccc
Confidence            3444349999999999999999999987655555555555544

>d1gkya_ c.37.1.1 (A:) Guanylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=96.69  E-value=0.00049  Score=52.51  Aligned_cols=23  Identities=43%  Similarity=0.615  Sum_probs=21.1

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .++|+||+|+||||+++.+++..
T Consensus         3 pIvl~GpsG~GK~tl~~~L~~~~   25 (186)
T d1gkya_           3 PIVISGPSGTGKSTLLKKLFAEY   25 (186)
T ss_dssp             CEEEECCTTSSHHHHHHHHHHHC
T ss_pred             eEEEECCCCCCHHHHHHHHHHhC
Confidence            38899999999999999999885

>d1lvga_ c.37.1.1 (A:) Guanylate kinase {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.68  E-value=0.00053  Score=52.52  Aligned_cols=22  Identities=36%  Similarity=0.629  Sum_probs=20.7

Q ss_pred             EEEECCCCCCHHHHHHHHHHHH
Q psy879           34 IIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~l   55 (317)
                      ++|.||+|+||||+++.+++..
T Consensus         3 Ivl~GPsGsGK~tl~~~L~~~~   24 (190)
T d1lvga_           3 VVLSGPSGAGKSTLLKKLFQEH   24 (190)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHhC
Confidence            7899999999999999999885

>d1wf3a1 c.37.1.8 (A:3-180) GTPase Era, N-terminal domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTPase Era, N-terminal domain
species: Thermus thermophilus [TaxId: 274]

Probab=96.67  E-value=0.036  Score=41.07  Aligned_cols=22  Identities=36%  Similarity=0.531  Sum_probs=19.7

Q ss_pred             eEEEECCCCCCHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~   54 (317)
                      .+.|.|.+|+|||++++++.+.
T Consensus         7 ~I~lvG~~~~GKSSLin~l~~~   28 (178)
T d1wf3a1           7 FVAIVGKPNVGKSTLLNNLLGV   28 (178)
T ss_dssp             EEEEECSTTSSHHHHHHHHHTS
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            4899999999999999998854

>d1szpa2 c.37.1.11 (A:145-395) DNA repair protein Rad51, catalytic domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=96.67  E-value=0.00039  Score=55.18  Aligned_cols=33  Identities=21%  Similarity=0.169  Sum_probs=24.1

Q ss_pred             HHHHHhcCCCce--EEEECCCCCCHHHHHHHHHHH
Q psy879           22 LKVFSSSGNVPN--IIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        22 l~~~l~~~~~~~--~ll~G~~G~GKt~la~~la~~   54 (317)
                      |-..+..|-++.  ++|+||||+|||+++..++..
T Consensus        23 LD~ll~GGi~~G~~~li~G~pGsGKT~l~lq~~~~   57 (251)
T d1szpa2          23 LDTLLGGGVETGSITELFGEFRTGKSQLCHTLAVT   57 (251)
T ss_dssp             HHHHHTSSEESSSEEEEEESTTSSHHHHHHHHTTT
T ss_pred             HHhhhCCCCcCCeEEEEEcCCCCCHHHHHHHHHHH
Confidence            444444443333  999999999999999988754

>d1r8sa_ c.37.1.8 (A:) ADP-ribosylation factor {Human (Homo sapiens), ARF1 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARF1 [TaxId: 9606]

Probab=96.64  E-value=0.016  Score=41.91  Aligned_cols=21  Identities=33%  Similarity=0.376  Sum_probs=19.3

Q ss_pred             EEEECCCCCCHHHHHHHHHHH
Q psy879           34 IIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~   54 (317)
                      +++.|+||+|||++++.+...
T Consensus         3 ivlvG~~~vGKSsLi~~l~~~   23 (160)
T d1r8sa_           3 ILMVGLDAAGKTTILYKLKLG   23 (160)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            789999999999999999865

>d2qw6a1 a.80.1.2 (A:241-328) Uncharacterized protein EfaeDRAFT_0938 {Enterococcus faecium [TaxId: 1352]}

class: All alpha proteins
fold: post-AAA+ oligomerization domain-like
superfamily: post-AAA+ oligomerization domain-like
family: MgsA/YrvN C-terminal domain-like
domain: Uncharacterized protein EfaeDRAFT 0938
species: Enterococcus faecium [TaxId: 1352]

Probab=96.58  E-value=0.034  Score=35.60  Aligned_cols=81  Identities=10%  Similarity=0.215  Sum_probs=56.6

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHH-HhcCCChHHHHHHHHHHHHHHhHHhcCC-CcHHHHHH
Q psy879          224 AVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDIIGNIFRVA-KTLDIPEPLKLSIIQEIGNVHLRISEGV-NSLLQLSG  301 (317)
Q Consensus       224 ~i~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~-~~~~~~~~~~~~~~~~l~~~~~~l~~g~-~~~l~le~  301 (317)
                      .++.+.++++..|.+.++.|+..|++.| +|..|.+.+...+ +..|+.+...........+.-.  +-|. ..++.|-.
T Consensus         3 ~iSA~~KSiRgSD~dAAlywlarml~~G-D~~~i~RRLi~~AsEDIGlAdp~al~~~~~a~~a~~--~iG~PE~~i~La~   79 (88)
T d2qw6a1           3 VISAFQKSIRGSDVDAALHYLARLVEAG-DLASICRRLMVIGYEDIGLGNPAAAARTVNAVLAAE--KLGLPEARIPLAD   79 (88)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHTC---CHHHHHHHHHHHHHHH--HHCTTTTHHHHHH
T ss_pred             HHHHHHHHHHcCCccHHHHHHHHHHHcC-ChhHHHHHHHHHHHHHhhccChHHHHHHHHHHHHHH--HhCCcHHHHHHHH
Confidence            5788999999999999999999999999 8889999987765 5557665544443333333322  3455 66777766


Q ss_pred             HHHHHH
Q psy879          302 LLARLC  307 (317)
Q Consensus       302 ~~~~~~  307 (317)
                      .+.-+|
T Consensus        80 aviyLa   85 (88)
T d2qw6a1          80 VVVDLC   85 (88)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            666665

>d1gkub1 c.37.1.16 (B:1-250) Helicase-like "domain" of reverse gyrase {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Helicase-like "domain" of reverse gyrase
domain: Helicase-like "domain" of reverse gyrase
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=96.57  E-value=0.0052  Score=48.39  Aligned_cols=26  Identities=31%  Similarity=0.487  Sum_probs=20.3

Q ss_pred             cCCCceEEEECCCCCCHHHHHHHHHHHH
Q psy879           28 SGNVPNIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        28 ~~~~~~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .|+  ++++.+|+|+|||.++...+..+
T Consensus        57 ~g~--~~~i~apTGsGKT~~~~~~~~~~   82 (237)
T d1gkub1          57 RKE--SFAATAPTGVGKTSFGLAMSLFL   82 (237)
T ss_dssp             TTC--CEECCCCBTSCSHHHHHHHHHHH
T ss_pred             CCC--CEEEEecCCChHHHHHHHHHHHH
Confidence            455  69999999999998776665444

>d1znwa1 c.37.1.1 (A:20-201) Guanylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=96.56  E-value=0.00081  Score=50.95  Aligned_cols=23  Identities=39%  Similarity=0.839  Sum_probs=20.9

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .++|.||+|+||||+++.+.+..
T Consensus         4 iivl~GpsG~GK~tl~~~L~~~~   26 (182)
T d1znwa1           4 VVVLSGPSAVGKSTVVRCLRERI   26 (182)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhhC
Confidence            48899999999999999998874

>d1ewqa2 c.37.1.12 (A:542-765) DNA repair protein MutS, the C-terminal domain {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: DNA repair protein MutS, the C-terminal domain
species: Thermus aquaticus [TaxId: 271]

Probab=96.54  E-value=0.012  Score=45.77  Aligned_cols=94  Identities=21%  Similarity=0.270  Sum_probs=50.7

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHc-----CCCC---------CCceEEecCCCC--cCh----HHHHHHHHHHHhhcccCC
Q psy879           34 IIISGPPGVGKTTTILCLARILL-----GPSF---------KDAVLELNASND--RGI----DTVRNKIKMFAQQKVTLP   93 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~l~-----~~~~---------~~~~~~~~~~~~--~~~----~~i~~~~~~~~~~~~~~~   93 (317)
                      ++++||+.+|||++.+.++-...     +.-+         ...+..+...+.  .+.    .++.+ +.......    
T Consensus        38 ~iiTGpN~~GKSt~lk~i~l~~ilAq~G~~vpA~~~~i~~~d~I~~~~~~~d~~~~~~StF~~el~~-~~~il~~~----  112 (224)
T d1ewqa2          38 VLITGPNMAGKSTFLRQTALIALLAQVGSFVPAEEAHLPLFDGIYTRIGASDDLAGGKSTFMVEMEE-VALILKEA----  112 (224)
T ss_dssp             EEEESCSSSSHHHHHHHHHHHHHHHTTTCCBSSSEEEECCCSEEEEECCC------CCSHHHHHHHH-HHHHHHHC----
T ss_pred             EEEECCCccccchhhhhhHHHHHHHhccceeecCceEEeecceEEEEECCCccccCCccHHHHhHHH-HHHHhccC----
Confidence            89999999999999998886542     1100         011122222221  111    11221 12222221    


Q ss_pred             CCceeEEEEeCCCCCCHH-----HHHHHHHHhhhccCCceEEEEecC
Q psy879           94 PGRHKIVILDEADSMTDG-----AQQALRRTMEIYSNTTRFALACNN  135 (317)
Q Consensus        94 ~~~~~vliiDE~d~l~~~-----~~~~ll~~le~~~~~~~~il~~~~  135 (317)
                       .++.++++||+.+=+..     ...++++.+.+.  +..++++|+.
T Consensus       113 -~~~sLvliDE~~~gT~~~eg~ala~aile~L~~~--~~~~i~tTH~  156 (224)
T d1ewqa2         113 -TENSLVLLDEVGRGTSSLDGVAIATAVAEALHER--RAYTLFATHY  156 (224)
T ss_dssp             -CTTEEEEEESTTTTSCHHHHHHHHHHHHHHHHHH--TCEEEEECCC
T ss_pred             -CCCcEEeecccccCcchhhhcchHHHHHHHHhhc--CcceEEeeec
Confidence             46789999999988653     244555555543  3456666665

>d3bgea1 a.80.1.2 (A:251-434) Uncharacterized protein NTHI1458 {Haemophilus influenzae [TaxId: 727]}

class: All alpha proteins
fold: post-AAA+ oligomerization domain-like
superfamily: post-AAA+ oligomerization domain-like
family: MgsA/YrvN C-terminal domain-like
domain: Uncharacterized protein NTHI1458
species: Haemophilus influenzae [TaxId: 727]

Probab=96.50  E-value=0.007  Score=45.17  Aligned_cols=85  Identities=7%  Similarity=0.072  Sum_probs=58.3

Q ss_pred             CHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHH-HhcCCChHHHHHHHHHHHHHHhHHhcCC-CcHHH
Q psy879          221 HPLAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDIIGNIFRVA-KTLDIPEPLKLSIIQEIGNVHLRISEGV-NSLLQ  298 (317)
Q Consensus       221 ~~~~i~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~-~~~~~~~~~~~~~~~~l~~~~~~l~~g~-~~~l~  298 (317)
                      +.+.++.++++++..|.+.++.|+..|++.|++|..|.+.+...+ +.+|+.+.....+...+.+.-.  .-|. .-++.
T Consensus         4 hYd~iSA~~KSiRgSD~dAaly~larml~~GeDp~~i~RRl~~~AsEDIGlAdp~al~~a~~~~~a~~--~iG~PE~~i~   81 (184)
T d3bgea1           4 FYDLISALHKSVRGSAPDAALYWYARILTAGGDPLYVARRLLAIASEDVGNADPRAMQVALAAWDCFT--RVGAYEGERA   81 (184)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHTTGGGCTTHHHHHHHHHHHHH--HTCHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCCccHHHHHHHHHHHcCCChHHHHHHHHHHHHhhcCCCCchHHHHHHHHHHHHH--HhCCchHHHH
Confidence            456799999999999999999999999999999999999988775 4446654433222222222211  2344 55555


Q ss_pred             HHHHHHHHH
Q psy879          299 LSGLLARLC  307 (317)
Q Consensus       299 le~~~~~~~  307 (317)
                      |-..+.-+|
T Consensus        82 LaqaviyLA   90 (184)
T d3bgea1          82 IAQAIIYLS   90 (184)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            555555555

>d1zj6a1 c.37.1.8 (A:2-178) ADP-ribosylation factor {Human (Homo sapiens), ARL5A [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARL5A [TaxId: 9606]

Probab=96.50  E-value=0.016  Score=42.83  Aligned_cols=31  Identities=23%  Similarity=0.292  Sum_probs=23.2

Q ss_pred             HHHHHhcCCCceEEEECCCCCCHHHHHHHHHH
Q psy879           22 LKVFSSSGNVPNIIISGPPGVGKTTTILCLAR   53 (317)
Q Consensus        22 l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~   53 (317)
                      +-.++.+.. -.+++.|.||+|||+++..+..
T Consensus         7 ~~~~~~~k~-~kI~vvG~~~~GKSsLi~rl~~   37 (177)
T d1zj6a1           7 IWRLFNHQE-HKVIIVGLDNAGKTTILYQFSM   37 (177)
T ss_dssp             HHHHHTTSC-EEEEEEESTTSSHHHHHHHHHT
T ss_pred             HHHHhCCCe-EEEEEECCCCCCHHHHHHHHhc
Confidence            334444443 2499999999999999998875

>d1v5wa_ c.37.1.11 (A:) Meiotic recombination protein DMC1/LIM15 homolog {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Meiotic recombination protein DMC1/LIM15 homolog
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.49  E-value=0.0012  Score=52.54  Aligned_cols=35  Identities=17%  Similarity=0.021  Sum_probs=26.3

Q ss_pred             HHHHHhcCCCce--EEEECCCCCCHHHHHHHHHHHHc
Q psy879           22 LKVFSSSGNVPN--IIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        22 l~~~l~~~~~~~--~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      |-.++..|-++.  ++|+||||+|||+++..++....
T Consensus        26 LD~~lgGGip~G~~~~i~G~~GsGKT~lalq~~~~~~   62 (258)
T d1v5wa_          26 FDKLLGGGIESMAITEAFGEFRTGKTQLSHTLCVTAQ   62 (258)
T ss_dssp             HHHHTTSSBCSSEEEEEECCTTCTHHHHHHHHHHHTT
T ss_pred             HHHhhcCCCcCCEEEEEECCCCCCHHHHHHHHHHHHH
Confidence            444454554433  89999999999999999997643

>d1uj2a_ c.37.1.6 (A:) Uridine-cytidine kinase 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Uridine-cytidine kinase 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.49  E-value=0.00082  Score=52.28  Aligned_cols=23  Identities=26%  Similarity=0.348  Sum_probs=21.1

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHc
Q psy879           34 IIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      +.+.|++|+||||+++.+++.+.
T Consensus         5 IgI~G~~gSGKSTla~~L~~~l~   27 (213)
T d1uj2a_           5 IGVSGGTASGKSSVCAKIVQLLG   27 (213)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHTT
T ss_pred             EEEECCCCCCHHHHHHHHHHHhc
Confidence            67999999999999999999874

>d1wb9a2 c.37.1.12 (A:567-800) DNA repair protein MutS, the C-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: DNA repair protein MutS, the C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=96.49  E-value=0.019  Score=44.96  Aligned_cols=23  Identities=39%  Similarity=0.408  Sum_probs=20.5

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .++++||+.+|||++.|.++-..
T Consensus        43 ~~iiTGpN~~GKSt~lk~i~l~~   65 (234)
T d1wb9a2          43 MLIITGPNMGGKSTYMRQTALIA   65 (234)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEeccCchhhHHHHHHHHHHH
Confidence            37999999999999999998655

>d1r2qa_ c.37.1.8 (A:) Rab5a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab5a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.41  E-value=0.0043  Score=46.04  Aligned_cols=21  Identities=24%  Similarity=0.536  Sum_probs=19.2

Q ss_pred             EEEECCCCCCHHHHHHHHHHH
Q psy879           34 IIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~   54 (317)
                      +++.|++|+|||++++.+...
T Consensus         9 i~vvG~~~vGKTsLi~~l~~~   29 (170)
T d1r2qa_           9 LVLLGESAVGKSSLVLRFVKG   29 (170)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            799999999999999998864

>d1zd9a1 c.37.1.8 (A:18-181) ADP-ribosylation factor {Human (Homo sapiens), ARL8A [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARL8A [TaxId: 9606]

Probab=96.36  E-value=0.01  Score=43.54  Aligned_cols=21  Identities=29%  Similarity=0.260  Sum_probs=19.1

Q ss_pred             EEEECCCCCCHHHHHHHHHHH
Q psy879           34 IIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~   54 (317)
                      ++|.|++|+|||+++..+...
T Consensus         5 i~i~G~~~~GKTsLl~~l~~~   25 (164)
T d1zd9a1           5 LTLVGLQYSGKTTFVNVIASG   25 (164)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHcC
Confidence            789999999999999998764

>d2ew1a1 c.37.1.8 (A:4-174) Rab30 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab30
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.35  E-value=0.0035  Score=46.64  Aligned_cols=21  Identities=33%  Similarity=0.523  Sum_probs=19.3

Q ss_pred             EEEECCCCCCHHHHHHHHHHH
Q psy879           34 IIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~   54 (317)
                      +++.|++|+|||++++.+...
T Consensus         8 i~lvG~~~vGKTsLi~~l~~~   28 (171)
T d2ew1a1           8 IVLIGNAGVGKTCLVRRFTQG   28 (171)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999999864

>d1nn5a_ c.37.1.1 (A:) Thymidylate kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.34  E-value=0.0018  Score=50.27  Aligned_cols=28  Identities=25%  Similarity=0.294  Sum_probs=23.7

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHcCCCC
Q psy879           33 NIIISGPPGVGKTTTILCLARILLGPSF   60 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~~~~~   60 (317)
                      -+.|.|++|+||||.++.+++.|...+.
T Consensus         5 lI~ieG~dGsGKsT~~~~L~~~L~~~g~   32 (209)
T d1nn5a_           5 LIVLEGVDRAGKSTQSRKLVEALCAAGH   32 (209)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHHHTTC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCC
Confidence            3788899999999999999999865443

>d2fh5b1 c.37.1.8 (B:63-269) Signal recognition particle receptor beta-subunit {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Signal recognition particle receptor beta-subunit
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.33  E-value=0.0092  Score=45.72  Aligned_cols=22  Identities=23%  Similarity=0.218  Sum_probs=20.1

Q ss_pred             eEEEECCCCCCHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~   54 (317)
                      +++|.|+||+|||++..++...
T Consensus         2 ~V~ivG~~~~GKTsLl~~l~~~   23 (207)
T d2fh5b1           2 AVLFVGLCDSGKTLLFVRLLTG   23 (207)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            5899999999999999999864

>d1htwa_ c.37.1.18 (A:) Hypothetical protein HI0065 {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: YjeE-like
domain: Hypothetical protein HI0065
species: Haemophilus influenzae [TaxId: 727]

Probab=96.33  E-value=0.0021  Score=47.13  Aligned_cols=24  Identities=25%  Similarity=0.278  Sum_probs=22.1

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHc
Q psy879           33 NIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      .++|.|+=|+||||+++.+++.+.
T Consensus        35 ii~L~G~LGaGKTtfvr~~~~~lg   58 (158)
T d1htwa_          35 MVYLNGDLGAGKTTLTRGMLQGIG   58 (158)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHTT
T ss_pred             EEEEecCCCccHHHHHHHHHhhcc
Confidence            388999999999999999999984

>d1s96a_ c.37.1.1 (A:) Guanylate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Escherichia coli [TaxId: 562]

Probab=96.31  E-value=0.0015  Score=50.56  Aligned_cols=23  Identities=35%  Similarity=0.559  Sum_probs=21.0

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .++|.||+|+||||+.+.+.+..
T Consensus         4 livi~GPSG~GK~tl~~~L~~~~   26 (205)
T d1s96a_           4 LYIVSAPSGAGKSSLIQALLKTQ   26 (205)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhhC
Confidence            58999999999999999999874

>d1kaoa_ c.37.1.8 (A:) Rap2a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rap2a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.25  E-value=0.028  Score=41.15  Aligned_cols=21  Identities=24%  Similarity=0.468  Sum_probs=19.3

Q ss_pred             EEEECCCCCCHHHHHHHHHHH
Q psy879           34 IIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~   54 (317)
                      +++.|++|+|||+++..+...
T Consensus         6 i~lvG~~~vGKTsLi~r~~~~   26 (167)
T d1kaoa_           6 VVVLGSGGVGKSALTVQFVTG   26 (167)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            799999999999999998864

>d1odfa_ c.37.1.6 (A:) Hypothetical protein Ygr205W {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Hypothetical protein Ygr205W
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=96.19  E-value=0.0037  Score=50.61  Aligned_cols=35  Identities=34%  Similarity=0.568  Sum_probs=25.0

Q ss_pred             HHHHHhcCCC-ce-EEEECCCCCCHHHHHHHHHHHHc
Q psy879           22 LKVFSSSGNV-PN-IIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        22 l~~~l~~~~~-~~-~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      +..+...++- |- +.|.|++|+||||++..+...+.
T Consensus        16 ~~~~~~~~~~~P~iIGi~G~qGSGKSTl~~~l~~~L~   52 (286)
T d1odfa_          16 IPEWFETGNKCPLFIFFSGPQGSGKSFTSIQIYNHLM   52 (286)
T ss_dssp             HHHHHTTTCCSCEEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             HHHHHhcCCCCCEEEEeECCCCCCHHHHHHHHHHHHH
Confidence            3334444433 43 66899999999999999987763

>d1z0fa1 c.37.1.8 (A:8-173) Rab14 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab14
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.13  E-value=0.011  Score=43.56  Aligned_cols=21  Identities=33%  Similarity=0.444  Sum_probs=19.1

Q ss_pred             EEEECCCCCCHHHHHHHHHHH
Q psy879           34 IIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~   54 (317)
                      +++.|++|+|||++++.+...
T Consensus         7 ivlvG~~~vGKTsli~~~~~~   27 (166)
T d1z0fa1           7 YIIIGDMGVGKSCLLHQFTEK   27 (166)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999998864

>d1kgda_ c.37.1.1 (A:) Guanylate kinase-like domain of Cask {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase-like domain of Cask
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.10  E-value=0.0018  Score=48.89  Aligned_cols=23  Identities=22%  Similarity=0.356  Sum_probs=20.6

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .++|.||+|+||+|+++.+++..
T Consensus         5 ~ivl~Gpsg~GK~tl~~~L~~~~   27 (178)
T d1kgda_           5 TLVLLGAHGVGRRHIKNTLITKH   27 (178)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHC
T ss_pred             cEEEECCCCCCHHHHHHHHHHhC
Confidence            48899999999999999999763

>d2r9ga1 a.80.1.2 (A:238-423) Uncharacterized protein EfaeDRAFT_0938 {Enterococcus faecium [TaxId: 1352]}

class: All alpha proteins
fold: post-AAA+ oligomerization domain-like
superfamily: post-AAA+ oligomerization domain-like
family: MgsA/YrvN C-terminal domain-like
domain: Uncharacterized protein EfaeDRAFT 0938
species: Enterococcus faecium [TaxId: 1352]

Probab=96.07  E-value=0.056  Score=40.17  Aligned_cols=84  Identities=11%  Similarity=0.214  Sum_probs=63.1

Q ss_pred             CHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHH-HhcCCChHHHHHHHHHHHHHHhHHhcCC-CcHHH
Q psy879          221 HPLAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDIIGNIFRVA-KTLDIPEPLKLSIIQEIGNVHLRISEGV-NSLLQ  298 (317)
Q Consensus       221 ~~~~i~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~-~~~~~~~~~~~~~~~~l~~~~~~l~~g~-~~~l~  298 (317)
                      +.+.++.+.++++..|.+.|+.|+..|++.| +|..|.+.+...+ +.+|+.+.....+...+.+.-..  -|. .-++.
T Consensus         3 hyd~iSA~~KSiRgSD~daAly~larml~~G-d~~~i~RRL~~~AsEDIGlAdp~al~~a~~a~~a~~~--iG~PE~~i~   79 (186)
T d2r9ga1           3 HYDVISAFQKSIRGSDVDAALHYLARLVEAG-DLASICRRLMVIGYEDIGLGNPAAAARTVNAVLAAEK--LGLPEARIP   79 (186)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT-CHHHHHHHHHHHHHHTTGGGCHHHHHHHHHHHHHHHH--HCTTTTHHH
T ss_pred             HHHHHHHHHHHHhcCCHhHHHHHHHHHHHcC-CchHHHHHHHHHHHHHhhccChHHHHHHHHHHHHHHH--cCCchHHHH
Confidence            4568999999999999999999999999999 8999999988765 55576665544444444433333  355 77777


Q ss_pred             HHHHHHHHH
Q psy879          299 LSGLLARLC  307 (317)
Q Consensus       299 le~~~~~~~  307 (317)
                      |-..+.-+|
T Consensus        80 LaqaviyLA   88 (186)
T d2r9ga1          80 LADVVVDLC   88 (186)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            777777777

>d1u8za_ c.37.1.8 (A:) Ras-related protein RalA {Cotton-top tamarin (Saguinus oedipus) [TaxId: 9490]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ras-related protein RalA
species: Cotton-top tamarin (Saguinus oedipus) [TaxId: 9490]

Probab=96.07  E-value=0.012  Score=43.53  Aligned_cols=21  Identities=33%  Similarity=0.498  Sum_probs=19.1

Q ss_pred             EEEECCCCCCHHHHHHHHHHH
Q psy879           34 IIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~   54 (317)
                      +++.|.+|+|||++++.+...
T Consensus         7 ivlvG~~~vGKTsli~~~~~~   27 (168)
T d1u8za_           7 VIMVGSGGVGKSALTLQFMYD   27 (168)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            899999999999999998753

>d1ctqa_ c.37.1.8 (A:) cH-p21 Ras protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: cH-p21 Ras protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.06  E-value=0.0098  Score=43.79  Aligned_cols=21  Identities=29%  Similarity=0.566  Sum_probs=19.2

Q ss_pred             EEEECCCCCCHHHHHHHHHHH
Q psy879           34 IIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~   54 (317)
                      +++.|++|+|||+++..+...
T Consensus         6 i~viG~~~vGKTsli~~l~~~   26 (166)
T d1ctqa_           6 LVVVGAGGVGKSALTIQLIQN   26 (166)
T ss_dssp             EEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            789999999999999998864

>d1gm5a3 c.37.1.19 (A:286-549) RecG helicase domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecG helicase domain
species: Thermotoga maritima [TaxId: 2336]

Probab=96.06  E-value=0.0065  Score=48.57  Aligned_cols=42  Identities=17%  Similarity=0.087  Sum_probs=34.4

Q ss_pred             CCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHH
Q psy879           14 GNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        14 g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .|..+++.+..-+.++.+-+-|+.|..|+|||.++-..+...
T Consensus        87 ~Q~~ai~ei~~d~~~~~~m~rLL~GdvGSGKT~Va~~a~~~~  128 (264)
T d1gm5a3          87 AQKRAHQEIRNDMISEKPMNRLLQGDVGSGKTVVAQLAILDN  128 (264)
T ss_dssp             HHHHHHHHHHHHHHSSSCCCCEEECCSSSSHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHhhccCcceeeeeccccccccHHHHHHHHHH
Confidence            366777778877888887778999999999999988777554

>d1sq5a_ c.37.1.6 (A:) Pantothenate kinase PanK {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Pantothenate kinase PanK
species: Escherichia coli [TaxId: 562]

Probab=96.05  E-value=0.0071  Score=49.51  Aligned_cols=24  Identities=42%  Similarity=0.509  Sum_probs=22.1

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHcC
Q psy879           34 IIISGPPGVGKTTTILCLARILLG   57 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~l~~   57 (317)
                      +.+.|++|+||||+++.+...+..
T Consensus        83 IGIaG~sgSGKSTla~~L~~lL~~  106 (308)
T d1sq5a_          83 ISIAGSVAVGKSTTARVLQALLSR  106 (308)
T ss_dssp             EEEEECTTSSHHHHHHHHHHHHTT
T ss_pred             EEEeCCCCCCCcHHHHHHHHHHhh
Confidence            789999999999999999998853

>d1kmqa_ c.37.1.8 (A:) RhoA {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: RhoA
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.01  E-value=0.0038  Score=46.74  Aligned_cols=21  Identities=24%  Similarity=0.427  Sum_probs=19.1

Q ss_pred             EEEECCCCCCHHHHHHHHHHH
Q psy879           34 IIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~   54 (317)
                      +++.|++|+|||+++..+...
T Consensus         5 ivvvG~~~vGKTsLi~~~~~~   25 (177)
T d1kmqa_           5 LVIVGDGACGKTCLLIVNSKD   25 (177)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999998865

>d1tf7a1 c.37.1.11 (A:14-255) Circadian clock protein KaiC {Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Circadian clock protein KaiC
species: Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]

Probab=96.01  E-value=0.0015  Score=51.31  Aligned_cols=32  Identities=25%  Similarity=0.321  Sum_probs=23.1

Q ss_pred             HHHHHhcCCCc--eEEEECCCCCCHHHHHHHHHH
Q psy879           22 LKVFSSSGNVP--NIIISGPPGVGKTTTILCLAR   53 (317)
Q Consensus        22 l~~~l~~~~~~--~~ll~G~~G~GKt~la~~la~   53 (317)
                      |-..+..|-++  .++|+|+||+|||+++..++.
T Consensus        15 LD~~l~GGi~~G~~~~I~G~~G~GKT~la~~~~~   48 (242)
T d1tf7a1          15 FDDISHGGLPIGRSTLVSGTSGTGKTLFSIQFLY   48 (242)
T ss_dssp             HHHHTTSSEETTSEEEEEESTTSSHHHHHHHHHH
T ss_pred             HHHhhcCCCcCCeEEEEEeCCCCCHHHHHHHHHH
Confidence            44455444333  389999999999999987654

>d3raba_ c.37.1.8 (A:) Rab3a {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab3a
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=95.99  E-value=0.0099  Score=43.95  Aligned_cols=21  Identities=38%  Similarity=0.499  Sum_probs=19.2

Q ss_pred             EEEECCCCCCHHHHHHHHHHH
Q psy879           34 IIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~   54 (317)
                      +++.|++|+|||+++..+...
T Consensus         8 i~vvG~~~vGKTsLi~~l~~~   28 (169)
T d3raba_           8 ILIIGNSSVGKTSFLFRYADD   28 (169)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHcC
Confidence            789999999999999998864

>d1gsia_ c.37.1.1 (A:) Thymidylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=95.98  E-value=0.0037  Score=48.06  Aligned_cols=26  Identities=31%  Similarity=0.396  Sum_probs=22.4

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHcCCC
Q psy879           34 IIISGPPGVGKTTTILCLARILLGPS   59 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~l~~~~   59 (317)
                      +.|.|+.|+||||+++.+++.+...+
T Consensus         3 I~ieG~dGsGKST~~~~L~~~l~~~g   28 (208)
T d1gsia_           3 IAIEGVDGAGKRTLVEKLSGAFRAAG   28 (208)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHHHTT
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCC
Confidence            67899999999999999999885443

>d2i1qa2 c.37.1.11 (A:65-322) DNA repair protein Rad51, catalytic domain {Archaeon Methanococcus voltae [TaxId: 2188]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Archaeon Methanococcus voltae [TaxId: 2188]

Probab=95.96  E-value=0.002  Score=50.90  Aligned_cols=35  Identities=23%  Similarity=0.131  Sum_probs=25.8

Q ss_pred             HHHHHhcCCCc--eEEEECCCCCCHHHHHHHHHHHHc
Q psy879           22 LKVFSSSGNVP--NIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        22 l~~~l~~~~~~--~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      |-..+..|-++  .++++|+||+|||+++..+|..+.
T Consensus        23 LD~ll~GGl~~G~l~~i~G~~G~GKT~~~l~~a~~~~   59 (258)
T d2i1qa2          23 LDSVLGGGLESQSVTEFAGVFGSGKTQIMHQSCVNLQ   59 (258)
T ss_dssp             HHHHTTSSEETTEEEEEEESTTSSHHHHHHHHHHHTT
T ss_pred             HHHhcCCCccCCeEEEEEeCCCCCHHHHHHHHHHHHH
Confidence            44444443322  289999999999999999997763

>d1mkya1 c.37.1.8 (A:2-172) Probable GTPase Der, N-terminal and middle domains {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase Der, N-terminal and middle domains
species: Thermotoga maritima [TaxId: 2336]

Probab=95.89  E-value=0.045  Score=40.14  Aligned_cols=22  Identities=36%  Similarity=0.590  Sum_probs=18.9

Q ss_pred             eEEEECCCCCCHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~   54 (317)
                      -+.+.|++|+||||+++++...
T Consensus         2 ~V~liG~~n~GKSsLi~~L~~~   23 (171)
T d1mkya1           2 TVLIVGRPNVGKSTLFNKLVKK   23 (171)
T ss_dssp             EEEEECCTTSSHHHHHHHHHC-
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            3789999999999999999743

>d2fn4a1 c.37.1.8 (A:24-196) r-Ras {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: r-Ras
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.88  E-value=0.0056  Score=45.58  Aligned_cols=21  Identities=24%  Similarity=0.520  Sum_probs=19.2

Q ss_pred             EEEECCCCCCHHHHHHHHHHH
Q psy879           34 IIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~   54 (317)
                      +++.|.+|+|||++++.+...
T Consensus         9 v~lvG~~~vGKTsLi~r~~~~   29 (173)
T d2fn4a1           9 LVVVGGGGVGKSALTIQFIQS   29 (173)
T ss_dssp             EEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            899999999999999988763

>d1cr2a_ c.37.1.11 (A:) Gene 4 protein (g4p, DNA primase), helicase domain {Bacteriophage T7 [TaxId: 10760]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Gene 4 protein (g4p, DNA primase), helicase domain
species: Bacteriophage T7 [TaxId: 10760]

Probab=95.86  E-value=0.04  Score=44.02  Aligned_cols=22  Identities=27%  Similarity=0.374  Sum_probs=19.7

Q ss_pred             EEEECCCCCCHHHHHHHHHHHH
Q psy879           34 IIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~l   55 (317)
                      ++|.|+||+|||+++..++..+
T Consensus        38 ~vi~G~~G~GKT~~~~~la~~~   59 (277)
T d1cr2a_          38 IMVTSGSGMGKSTFVRQQALQW   59 (277)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEEeCCCCCHHHHHHHHHHhh
Confidence            8999999999999999998643

>d1a7ja_ c.37.1.6 (A:) Phosphoribulokinase {Rhodobacter sphaeroides [TaxId: 1063]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Phosphoribulokinase
species: Rhodobacter sphaeroides [TaxId: 1063]

Probab=95.85  E-value=0.0011  Score=53.83  Aligned_cols=39  Identities=23%  Similarity=0.368  Sum_probs=25.3

Q ss_pred             CCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEec
Q psy879           30 NVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELN   68 (317)
Q Consensus        30 ~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~   68 (317)
                      +.|.+.+.|++|+||||+++++.+.+.....+..+++.+
T Consensus         3 k~pIIgIaG~SGSGKTTva~~l~~i~~~~~v~~~iI~~D   41 (288)
T d1a7ja_           3 KHPIISVTGSSGAGTSTVKHTFDQIFRREGVKAVSIEGD   41 (288)
T ss_dssp             TSCEEEEESCC---CCTHHHHHHHHHHHHTCCEEEEEGG
T ss_pred             CCCEEEEECCCCCcHHHHHHHHHHHHhhcCCCeEEEeCC
Confidence            445699999999999999999999875333333344444

>d2erya1 c.37.1.8 (A:10-180) r-Ras2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: r-Ras2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.84  E-value=0.011  Score=43.74  Aligned_cols=21  Identities=24%  Similarity=0.520  Sum_probs=19.2

Q ss_pred             EEEECCCCCCHHHHHHHHHHH
Q psy879           34 IIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~   54 (317)
                      +++.|.+|+|||++++.+...
T Consensus         8 i~lvG~~~vGKTsLi~r~~~~   28 (171)
T d2erya1           8 LVVVGGGGVGKSALTIQFIQS   28 (171)
T ss_dssp             EEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            899999999999999998763

>d2bmfa2 c.37.1.14 (A:178-482) Dengue virus helicase {Dengue virus type 2 [TaxId: 11060]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: Dengue virus helicase
species: Dengue virus type 2 [TaxId: 11060]

Probab=95.80  E-value=0.017  Score=46.91  Aligned_cols=21  Identities=29%  Similarity=0.346  Sum_probs=16.6

Q ss_pred             HHhcCCCceEEEECCCCCCHHHH
Q psy879           25 FSSSGNVPNIIISGPPGVGKTTT   47 (317)
Q Consensus        25 ~l~~~~~~~~ll~G~~G~GKt~l   47 (317)
                      ++++|+  +.++.+|+|+|||+.
T Consensus         5 ~~~~~~--~~lv~~~TGsGKT~~   25 (305)
T d2bmfa2           5 IFRKKR--LTIMDLHPGAGKTKR   25 (305)
T ss_dssp             SSSTTC--EEEECCCTTSSTTTT
T ss_pred             HhhcCC--cEEEEECCCCCHHHH
Confidence            345565  789999999999963

>d1g5ta_ c.37.1.11 (A:) ATP:corrinoid adenosyltransferase CobA {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: ATP:corrinoid adenosyltransferase CobA
species: Salmonella typhimurium [TaxId: 90371]

Probab=95.79  E-value=0.018  Score=41.91  Aligned_cols=53  Identities=11%  Similarity=0.091  Sum_probs=36.9

Q ss_pred             CCCceeEEEEeCCCCCCHH---HHHHHHHHhhhccCCceEEEEecCCCcCchhHhhhcc
Q psy879           93 PPGRHKIVILDEADSMTDG---AQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCA  148 (317)
Q Consensus        93 ~~~~~~vliiDE~d~l~~~---~~~~ll~~le~~~~~~~~il~~~~~~~l~~~i~sR~~  148 (317)
                      ..+.+.+||+||+.....-   ..+.++++++..|+.+-+|+|.++.   ++.+..+..
T Consensus        91 ~~~~~dllILDEi~~Ai~~gli~~~~v~~ll~~rp~~~evVlTGr~~---p~~L~e~AD  146 (157)
T d1g5ta_          91 ADPLLDMVVLDELTYMVAYDYLPLEEVISALNARPGHQTVIITGRGC---HRDILDLAD  146 (157)
T ss_dssp             TCTTCSEEEEETHHHHHHTTSSCHHHHHHHHHTSCTTCEEEEECSSC---CHHHHHHCS
T ss_pred             hcCccCEEeHHHHHHHHHcCCCCHHHHHHHHHhCCCCCEEEEECCCC---CHHHHHhcc
Confidence            3467999999999754322   1456778888889999999998763   344444443

>d1x1ra1 c.37.1.8 (A:10-178) Ras-related protein M-Ras (XRas) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ras-related protein M-Ras (XRas)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=95.78  E-value=0.024  Score=41.74  Aligned_cols=21  Identities=24%  Similarity=0.506  Sum_probs=19.1

Q ss_pred             EEEECCCCCCHHHHHHHHHHH
Q psy879           34 IIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~   54 (317)
                      +++.|++|+|||+++..+...
T Consensus         7 i~lvG~~~vGKTsll~~~~~~   27 (169)
T d1x1ra1           7 LVVVGDGGVGKSALTIQFFQK   27 (169)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999998864

>d1yzqa1 c.37.1.8 (A:14-177) Rab6 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab6
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.71  E-value=0.011  Score=43.28  Aligned_cols=21  Identities=29%  Similarity=0.370  Sum_probs=18.9

Q ss_pred             EEEECCCCCCHHHHHHHHHHH
Q psy879           34 IIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~   54 (317)
                      +++.|.+|+|||++++.+...
T Consensus         3 v~vvG~~~vGKTsLi~r~~~~   23 (164)
T d1yzqa1           3 LVFLGEQSVGKTSLITRFMYD   23 (164)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            688999999999999998853

>d1yrba1 c.37.1.10 (A:1-244) ATP(GTP)-binding protein PAB0955 {Pyrococcus abyssi [TaxId: 29292]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: ATP(GTP)-binding protein PAB0955
species: Pyrococcus abyssi [TaxId: 29292]

Probab=95.66  E-value=0.0034  Score=49.42  Aligned_cols=23  Identities=35%  Similarity=0.465  Sum_probs=20.9

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHc
Q psy879           34 IIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      +++.|++|+||||+...+.+.+.
T Consensus         3 i~v~G~~GsGKTTLl~~ll~~~~   25 (244)
T d1yrba1           3 VVFVGTAGSGKTTLTGEFGRYLE   25 (244)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHT
T ss_pred             EEEEcCCCCcHHHHHHHHHHHHh
Confidence            68999999999999999998763

>d2atxa1 c.37.1.8 (A:9-193) RhoQ {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: RhoQ
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.63  E-value=0.01  Score=44.57  Aligned_cols=21  Identities=29%  Similarity=0.436  Sum_probs=19.2

Q ss_pred             EEEECCCCCCHHHHHHHHHHH
Q psy879           34 IIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~   54 (317)
                      +++.|.+|+|||++++.+...
T Consensus        12 i~lvG~~~vGKTsLi~r~~~~   32 (185)
T d2atxa1          12 CVVVGDGAVGKTCLLMSYAND   32 (185)
T ss_dssp             EEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHhhC
Confidence            899999999999999998764

>d2vp4a1 c.37.1.1 (A:12-208) Deoxyribonucleoside kinase {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Deoxyribonucleoside kinase
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=95.63  E-value=0.0019  Score=49.26  Aligned_cols=24  Identities=29%  Similarity=0.412  Sum_probs=21.6

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHc
Q psy879           33 NIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      -+.|.|+.|+||||+++.+++.+.
T Consensus        11 ~I~ieG~~GsGKTTl~~~L~~~l~   34 (197)
T d2vp4a1          11 TVLIEGNIGSGKTTYLNHFEKYKN   34 (197)
T ss_dssp             EEEEECSTTSCHHHHHHTTGGGTT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhC
Confidence            389999999999999999998863

>d2gjsa1 c.37.1.8 (A:91-258) Rad {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rad
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.61  E-value=0.014  Score=42.97  Aligned_cols=21  Identities=29%  Similarity=0.670  Sum_probs=18.5

Q ss_pred             EEEECCCCCCHHHHHHHHHHH
Q psy879           34 IIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~   54 (317)
                      +++.|++|+|||++++.+...
T Consensus         4 i~lvG~~~vGKTsLi~~~~~~   24 (168)
T d2gjsa1           4 VLLLGAPGVGKSALARIFGGV   24 (168)
T ss_dssp             EEEECCTTSSHHHHHHHHHTC
T ss_pred             EEEECCCCcCHHHHHHHHhCC
Confidence            688999999999999988653

>d1h65a_ c.37.1.8 (A:) Chloroplast protein translocon GTPase Toc34 {Garden pea (Pisum sativum) [TaxId: 3888]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Chloroplast protein translocon GTPase Toc34
species: Garden pea (Pisum sativum) [TaxId: 3888]

Probab=95.61  E-value=0.073  Score=42.11  Aligned_cols=22  Identities=32%  Similarity=0.564  Sum_probs=19.9

Q ss_pred             eEEEECCCCCCHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~   54 (317)
                      ++++.|.+|+||||++..+...
T Consensus        34 ~I~LvG~tg~GKSSliN~ilg~   55 (257)
T d1h65a_          34 TILVMGKGGVGKSSTVNSIIGE   55 (257)
T ss_dssp             EEEEEESTTSSHHHHHHHHHTS
T ss_pred             EEEEECCCCCcHHHHHHHHhCC
Confidence            4999999999999999999854

>d1f6ba_ c.37.1.8 (A:) SAR1 {Chinese hamster (Cricetulus griseus) [TaxId: 10029]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: SAR1
species: Chinese hamster (Cricetulus griseus) [TaxId: 10029]

Probab=95.58  E-value=0.0046  Score=46.17  Aligned_cols=21  Identities=29%  Similarity=0.349  Sum_probs=18.9

Q ss_pred             EEEECCCCCCHHHHHHHHHHH
Q psy879           34 IIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~   54 (317)
                      ++|.|++|+||||+..++...
T Consensus        16 I~lvG~~~vGKTsLl~~l~~~   36 (186)
T d1f6ba_          16 LVFLGLDNAGKTTLLHMLKDD   36 (186)
T ss_dssp             EEEEEETTSSHHHHHHHHSCC
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            999999999999999988643

>d1nrjb_ c.37.1.8 (B:) Signal recognition particle receptor beta-subunit {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Signal recognition particle receptor beta-subunit
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=95.57  E-value=0.0039  Score=47.85  Aligned_cols=23  Identities=43%  Similarity=0.697  Sum_probs=20.9

Q ss_pred             ceEEEECCCCCCHHHHHHHHHHH
Q psy879           32 PNIIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        32 ~~~ll~G~~G~GKt~la~~la~~   54 (317)
                      |.++|.|+||+||||+..++...
T Consensus         4 p~V~lvG~~n~GKTSLln~l~~~   26 (209)
T d1nrjb_           4 PSIIIAGPQNSGKTSLLTLLTTD   26 (209)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHS
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            56999999999999999999865

>d1c1ya_ c.37.1.8 (A:) Rap1A {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rap1A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.51  E-value=0.013  Score=43.20  Aligned_cols=21  Identities=24%  Similarity=0.490  Sum_probs=19.3

Q ss_pred             EEEECCCCCCHHHHHHHHHHH
Q psy879           34 IIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~   54 (317)
                      +++.|.+|+|||++++.+...
T Consensus         6 ivvvG~~~vGKTsli~r~~~~   26 (167)
T d1c1ya_           6 LVVLGSGGVGKSALTVQFVQG   26 (167)
T ss_dssp             EEEECSTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHHcC
Confidence            799999999999999998864

>d1rifa_ c.37.1.23 (A:) DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: DNA helicase UvsW
domain: DNA helicase UvsW
species: Bacteriophage T4 [TaxId: 10665]

Probab=95.50  E-value=0.018  Score=46.47  Aligned_cols=41  Identities=17%  Similarity=0.062  Sum_probs=31.1

Q ss_pred             cCCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHc
Q psy879           13 VGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        13 ~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      .-++...+.+..++++++   .++.-|.|+|||.++..++..+.
T Consensus       113 ~~rdyQ~~av~~~l~~~~---~il~~pTGsGKT~i~~~i~~~~~  153 (282)
T d1rifa_         113 EPHWYQKDAVFEGLVNRR---RILNLPTSAGRSLIQALLARYYL  153 (282)
T ss_dssp             CCCHHHHHHHHHHHHHSE---EEECCCTTSCHHHHHHHHHHHHH
T ss_pred             ccchHHHHHHHHHHhcCC---ceeEEEcccCccHHHHHHHHHhh
Confidence            346666777777787654   67788999999999988886653

>d1u0la2 c.37.1.8 (A:69-293) Probable GTPase EngC (YjeQ), C-terminal domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase EngC (YjeQ), C-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=95.48  E-value=0.0072  Score=46.98  Aligned_cols=33  Identities=27%  Similarity=0.455  Sum_probs=24.7

Q ss_pred             HHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHH
Q psy879           19 VERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        19 ~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~   54 (317)
                      ++.|..+++ |+  ..+|.|++|+||||++.++...
T Consensus        86 ~~~L~~~l~-~k--t~~~~G~SGVGKSTLiN~L~~~  118 (225)
T d1u0la2          86 IEELKEYLK-GK--ISTMAGLSGVGKSSLLNAINPG  118 (225)
T ss_dssp             HHHHHHHHS-SS--EEEEECSTTSSHHHHHHHHSTT
T ss_pred             HhhHHHHhc-CC--eEEEECCCCCCHHHHHHhhcch
Confidence            445555553 33  5899999999999999987643

>d2bcgy1 c.37.1.8 (Y:3-196) GTPase Ytp1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTPase Ytp1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=95.45  E-value=0.0077  Score=45.74  Aligned_cols=21  Identities=29%  Similarity=0.569  Sum_probs=19.1

Q ss_pred             EEEECCCCCCHHHHHHHHHHH
Q psy879           34 IIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~   54 (317)
                      +++.|++|+|||+++..+...
T Consensus         9 ivvvG~~~vGKTsli~~l~~~   29 (194)
T d2bcgy1           9 LLLIGNSGVGKSCLLLRFSDD   29 (194)
T ss_dssp             EEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHhhC
Confidence            789999999999999998864

>d1svia_ c.37.1.8 (A:) Probable GTPase EngB {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase EngB
species: Bacillus subtilis [TaxId: 1423]

Probab=95.45  E-value=0.0043  Score=47.16  Aligned_cols=26  Identities=35%  Similarity=0.638  Sum_probs=22.4

Q ss_pred             cCCCceEEEECCCCCCHHHHHHHHHH
Q psy879           28 SGNVPNIIISGPPGVGKTTTILCLAR   53 (317)
Q Consensus        28 ~~~~~~~ll~G~~G~GKt~la~~la~   53 (317)
                      .+..|.+.|.|+||+||||+.+++..
T Consensus        20 ~~~~~~I~lvG~~n~GKSTLin~L~g   45 (195)
T d1svia_          20 EGGLPEIALAGRSNVGKSSFINSLIN   45 (195)
T ss_dssp             CSCCCEEEEEEBTTSSHHHHHHHHHT
T ss_pred             CCCCCEEEEECCCCCCHHHHHHHhcC
Confidence            34567799999999999999999974

>d1kkma_ c.91.1.2 (A:) HPr kinase HprK C-terminal domain {Lactobacillus casei [TaxId: 1582]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: HPr kinase HprK C-terminal domain
domain: HPr kinase HprK C-terminal domain
species: Lactobacillus casei [TaxId: 1582]

Probab=95.40  E-value=0.0049  Score=45.99  Aligned_cols=22  Identities=41%  Similarity=0.685  Sum_probs=19.6

Q ss_pred             eEEEECCCCCCHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~   54 (317)
                      .++|.|++|+|||+++..+.+.
T Consensus        16 gvl~~G~sG~GKStlal~l~~~   37 (176)
T d1kkma_          16 GVLITGDSGVGKSETALELVQR   37 (176)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHT
T ss_pred             EEEEEeCCCCCHHHHHHHHHHc
Confidence            4999999999999999887763

>d1i2ma_ c.37.1.8 (A:) Ran {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ran
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.39  E-value=0.0055  Score=45.50  Aligned_cols=21  Identities=29%  Similarity=0.354  Sum_probs=17.5

Q ss_pred             EEEECCCCCCHHHHHHHHHHH
Q psy879           34 IIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~   54 (317)
                      +++.|++|+|||+++..+...
T Consensus         6 i~vvG~~~vGKTsli~~~~~~   26 (170)
T d1i2ma_           6 LVLVGDGGTGKTTFVKRHLTG   26 (170)
T ss_dssp             EEEEECTTSSHHHHHHTTC--
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            788999999999999987654

>d2bmea1 c.37.1.8 (A:6-179) Rab4a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab4a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.38  E-value=0.019  Score=42.52  Aligned_cols=21  Identities=19%  Similarity=0.401  Sum_probs=18.9

Q ss_pred             EEEECCCCCCHHHHHHHHHHH
Q psy879           34 IIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~   54 (317)
                      +++.|.+|+|||++++.+...
T Consensus         8 I~lvG~~~vGKTsll~~~~~~   28 (174)
T d2bmea1           8 FLVIGNAGTGKSCLLHQFIEK   28 (174)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999998753

>d2ngra_ c.37.1.8 (A:) CDC42 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: CDC42
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.38  E-value=0.015  Score=43.81  Aligned_cols=21  Identities=24%  Similarity=0.415  Sum_probs=19.0

Q ss_pred             EEEECCCCCCHHHHHHHHHHH
Q psy879           34 IIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~   54 (317)
                      +++.|++|+|||+++..+...
T Consensus         6 vvllG~~~vGKTSli~r~~~~   26 (191)
T d2ngra_           6 CVVVGDGAVGKTCLLISYTTN   26 (191)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999988764

>d1upta_ c.37.1.8 (A:) ADP-ribosylation factor {Human (Homo sapiens), ARL1 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARL1 [TaxId: 9606]

Probab=95.34  E-value=0.0049  Score=45.21  Aligned_cols=22  Identities=41%  Similarity=0.477  Sum_probs=19.7

Q ss_pred             eEEEECCCCCCHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~   54 (317)
                      .++|.|.||+||||+.+++...
T Consensus         7 kI~ivG~~~vGKSSLi~~~~~~   28 (169)
T d1upta_           7 RILILGLDGAGKTTILYRLQVG   28 (169)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            3899999999999999998764

>d1uf9a_ c.37.1.1 (A:) Dephospho-CoA kinase {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Dephospho-CoA kinase
species: Thermus thermophilus [TaxId: 274]

Probab=95.30  E-value=0.0047  Score=46.84  Aligned_cols=20  Identities=40%  Similarity=0.454  Sum_probs=17.7

Q ss_pred             EEEECCCCCCHHHHHHHHHH
Q psy879           34 IIISGPPGVGKTTTILCLAR   53 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~   53 (317)
                      +.++|++|+||||+|+.+.+
T Consensus         6 IgitG~~gSGKstva~~l~~   25 (191)
T d1uf9a_           6 IGITGNIGSGKSTVAALLRS   25 (191)
T ss_dssp             EEEEECTTSCHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            66899999999999998854

>d1pjra1 c.37.1.19 (A:1-318) DEXX box DNA helicase {Bacillus stearothermophilus, PcrA [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEXX box DNA helicase
species: Bacillus stearothermophilus, PcrA [TaxId: 1422]

Probab=95.29  E-value=0.0097  Score=48.83  Aligned_cols=24  Identities=25%  Similarity=0.427  Sum_probs=18.0

Q ss_pred             eEEEECCCCCCHHHHH-HHHHHHHc
Q psy879           33 NIIISGPPGVGKTTTI-LCLARILL   56 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la-~~la~~l~   56 (317)
                      ++++.|+||||||+++ ..++..+.
T Consensus        26 ~~lV~g~aGSGKTt~l~~ri~~ll~   50 (318)
T d1pjra1          26 PLLIMAGAGSGKTRVLTHRIAYLMA   50 (318)
T ss_dssp             CEEEEECTTSCHHHHHHHHHHHHHH
T ss_pred             CEEEEecCCccHHHHHHHHHHHHHH
Confidence            5899999999999765 44555543

>d1tmka_ c.37.1.1 (A:) Thymidylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=95.29  E-value=0.0062  Score=47.22  Aligned_cols=24  Identities=38%  Similarity=0.349  Sum_probs=22.2

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHc
Q psy879           33 NIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      -+.|.|+.|+||||.++.+++.|.
T Consensus         5 ~I~iEG~DGsGKST~~~~L~~~L~   28 (214)
T d1tmka_           5 LILIEGLDRTGKTTQCNILYKKLQ   28 (214)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHTT
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHH
Confidence            589999999999999999999874

>d2g6ba1 c.37.1.8 (A:58-227) Rab26 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab26
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.25  E-value=0.029  Score=41.21  Aligned_cols=21  Identities=29%  Similarity=0.531  Sum_probs=19.1

Q ss_pred             EEEECCCCCCHHHHHHHHHHH
Q psy879           34 IIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~   54 (317)
                      +++.|++|+|||++++.+...
T Consensus         9 i~vvG~~~vGKTsli~~~~~~   29 (170)
T d2g6ba1           9 VMLVGDSGVGKTCLLVRFKDG   29 (170)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            799999999999999988764

>d2qtvb1 c.37.1.8 (B:24-189) SAR1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: SAR1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=95.25  E-value=0.0055  Score=44.63  Aligned_cols=21  Identities=29%  Similarity=0.354  Sum_probs=19.3

Q ss_pred             EEEECCCCCCHHHHHHHHHHH
Q psy879           34 IIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~   54 (317)
                      +++.|+||+|||+++..+...
T Consensus         3 I~liG~~nvGKSSLln~l~~~   23 (166)
T d2qtvb1           3 LLFLGLDNAGKTTLLHMLKND   23 (166)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            789999999999999998874

>d1e2ka_ c.37.1.1 (A:) Thymidine kinase {Herpes simplex virus type 1, different strains [TaxId: 10298]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidine kinase
species: Herpes simplex virus type 1, different strains [TaxId: 10298]

Probab=95.20  E-value=0.031  Score=45.93  Aligned_cols=23  Identities=43%  Similarity=0.603  Sum_probs=19.1

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHc
Q psy879           34 IIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      +.|-|+-|+||||+++.+++.+.
T Consensus         7 I~IEG~iGsGKTTl~~~La~~l~   29 (329)
T d1e2ka_           7 VYIDGPHGMGKTTTTQLLVALGS   29 (329)
T ss_dssp             EEECSCTTSSHHHHHHHHTC---
T ss_pred             EEEECCcCCCHHHHHHHHHHHhC
Confidence            78899999999999999998763

>d1uaaa1 c.37.1.19 (A:2-307) DEXX box DNA helicase {Escherichia coli, RepD [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEXX box DNA helicase
species: Escherichia coli, RepD [TaxId: 562]

Probab=95.12  E-value=0.0064  Score=49.56  Aligned_cols=24  Identities=25%  Similarity=0.372  Sum_probs=17.7

Q ss_pred             ceEEEECCCCCCHHHHH-HHHHHHH
Q psy879           32 PNIIISGPPGVGKTTTI-LCLARIL   55 (317)
Q Consensus        32 ~~~ll~G~~G~GKt~la-~~la~~l   55 (317)
                      .++++.|+||||||+++ ..++..+
T Consensus        15 ~~~lI~g~aGTGKTt~l~~rv~~ll   39 (306)
T d1uaaa1          15 GPCLVLAGAGSGKTRVITNKIAHLI   39 (306)
T ss_dssp             SEEEECCCTTSCHHHHHHHHHHHHH
T ss_pred             CCEEEEeeCCccHHHHHHHHHHHHH
Confidence            35899999999999764 4444443

>d1puia_ c.37.1.8 (A:) Probable GTPase EngB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase EngB
species: Escherichia coli [TaxId: 562]

Probab=95.12  E-value=0.054  Score=40.02  Aligned_cols=23  Identities=17%  Similarity=0.343  Sum_probs=19.9

Q ss_pred             CceEEEECCCCCCHHHHHHHHHH
Q psy879           31 VPNIIISGPPGVGKTTTILCLAR   53 (317)
Q Consensus        31 ~~~~ll~G~~G~GKt~la~~la~   53 (317)
                      .+.+.|.|+|++||||+.+++..
T Consensus        16 ~~~I~lvG~~NvGKSSL~n~L~~   38 (188)
T d1puia_          16 GIEVAFAGRSNAGKSSALNTLTN   38 (188)
T ss_dssp             SEEEEEEECTTSSHHHHHTTTCC
T ss_pred             CCEEEEECCCCCCHHHHHHHHhC
Confidence            45699999999999999998753

>d2fu5c1 c.37.1.8 (C:3-175) Rab8a {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab8a
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=95.04  E-value=0.025  Score=41.82  Aligned_cols=21  Identities=29%  Similarity=0.588  Sum_probs=8.4

Q ss_pred             EEEECCCCCCHHHHHHHHHHH
Q psy879           34 IIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~   54 (317)
                      +++.|.+|+|||+++..+...
T Consensus         9 i~vvG~~~vGKTsLi~~l~~~   29 (173)
T d2fu5c1           9 LLLIGDSGVGKTCVLFRFSED   29 (173)
T ss_dssp             EEEECCCCC------------
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999988753

>d2a5ja1 c.37.1.8 (A:9-181) Rab2b {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab2b
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.02  E-value=0.007  Score=45.00  Aligned_cols=21  Identities=38%  Similarity=0.566  Sum_probs=18.9

Q ss_pred             EEEECCCCCCHHHHHHHHHHH
Q psy879           34 IIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~   54 (317)
                      +++.|++|+|||+++..+...
T Consensus         6 ivvvG~~~vGKTsli~r~~~~   26 (173)
T d2a5ja1           6 YIIIGDTGVGKSCLLLQFTDK   26 (173)
T ss_dssp             EEEESSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHhcC
Confidence            789999999999999998754

>d1knxa2 c.91.1.2 (A:133-309) HPr kinase HprK C-terminal domain {Mycoplasma pneumoniae [TaxId: 2104]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: HPr kinase HprK C-terminal domain
domain: HPr kinase HprK C-terminal domain
species: Mycoplasma pneumoniae [TaxId: 2104]

Probab=95.00  E-value=0.0052  Score=45.89  Aligned_cols=21  Identities=29%  Similarity=0.645  Sum_probs=19.0

Q ss_pred             eEEEECCCCCCHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLAR   53 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~   53 (317)
                      .++|.|++|+|||+++..+..
T Consensus        17 gvli~G~sG~GKS~lal~l~~   37 (177)
T d1knxa2          17 GVLLTGRSGIGKSECALDLIN   37 (177)
T ss_dssp             EEEEEESSSSSHHHHHHHHHT
T ss_pred             EEEEEcCCCCCHHHHHHHHHH
Confidence            499999999999999988775

>d1ksha_ c.37.1.8 (A:) ADP-ribosylation factor {Mouse (Mus musculus), ARL2 [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Mouse (Mus musculus), ARL2 [TaxId: 10090]

Probab=94.92  E-value=0.0067  Score=44.60  Aligned_cols=99  Identities=15%  Similarity=0.157  Sum_probs=51.2

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHcCCC---CCCceEEecCC-------CCcChHHHHHHHHHHHhhcccCCCCceeEEEE
Q psy879           33 NIIISGPPGVGKTTTILCLARILLGPS---FKDAVLELNAS-------NDRGIDTVRNKIKMFAQQKVTLPPGRHKIVIL  102 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~~~~---~~~~~~~~~~~-------~~~~~~~i~~~~~~~~~~~~~~~~~~~~vlii  102 (317)
                      .++|.|++|+|||++++.+...-....   .+.....++..       +..+....+..      ..........-++++
T Consensus         4 ki~ivG~~~~GKTsLi~~l~~~~~~~~~~t~~~~~~~~~~~~~~~~~~D~~G~~~~~~~------~~~~~~~~~~~i~v~   77 (165)
T d1ksha_           4 RLLMLGLDNAGKTTILKKFNGEDVDTISPTLGFNIKTLEHRGFKLNIWDVGGQKSLRSY------WRNYFESTDGLIWVV   77 (165)
T ss_dssp             EEEEECSTTSSHHHHHHHHTTCCCSSCCCCSSEEEEEEEETTEEEEEEEECCSHHHHTT------GGGGCTTCSEEEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHcCCCCCcccceEeeeeeeccccccceeeeecCcchhhhhH------HHhhhhhhhcceeee
Confidence            489999999999999999865321110   00011111110       11222222211      111122345677888


Q ss_pred             eCCCCCCH-HHHHHHHHHhhh-ccCCceEEEEecCCC
Q psy879          103 DEADSMTD-GAQQALRRTMEI-YSNTTRFALACNNSE  137 (317)
Q Consensus       103 DE~d~l~~-~~~~~ll~~le~-~~~~~~~il~~~~~~  137 (317)
                      |-.|.-.- +....+...+.. ...+..++++.|..+
T Consensus        78 d~~d~~~~~~~~~~~~~~~~~~~~~~~p~iiv~nK~D  114 (165)
T d1ksha_          78 DSADRQRMQDCQRELQSLLVEERLAGATLLIFANKQD  114 (165)
T ss_dssp             ETTCGGGHHHHHHHHHHHHTCGGGTTCEEEEEEECTT
T ss_pred             ecccchhHHHHHHhhhhhhhhcccCCCceEEEEeccc
Confidence            87776544 334455555543 235566777777654

>d2ocpa1 c.37.1.1 (A:37-277) Deoxyguanosine kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Deoxyguanosine kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.86  E-value=0.0075  Score=47.42  Aligned_cols=24  Identities=29%  Similarity=0.375  Sum_probs=22.0

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHcC
Q psy879           34 IIISGPPGVGKTTTILCLARILLG   57 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~l~~   57 (317)
                      +.|.|+.|+||||+++.+++.+..
T Consensus         5 IviEG~~GsGKST~~~~L~~~l~~   28 (241)
T d2ocpa1           5 LSIEGNIAVGKSTFVKLLTKTYPE   28 (241)
T ss_dssp             EEEEECTTSSHHHHHHHHHHHCTT
T ss_pred             EEEECCCCCcHHHHHHHHHHHHhh
Confidence            899999999999999999998743

>d1ko7a2 c.91.1.2 (A:130-298) HPr kinase HprK C-terminal domain {Staphylococcus xylosus [TaxId: 1288]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: HPr kinase HprK C-terminal domain
domain: HPr kinase HprK C-terminal domain
species: Staphylococcus xylosus [TaxId: 1288]

Probab=94.82  E-value=0.0078  Score=44.59  Aligned_cols=22  Identities=36%  Similarity=0.685  Sum_probs=19.6

Q ss_pred             eEEEECCCCCCHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~   54 (317)
                      .++|.|++|+|||+++..+.+.
T Consensus        17 gvli~G~sg~GKS~la~~l~~~   38 (169)
T d1ko7a2          17 GVLITGDSGIGKSETALELIKR   38 (169)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHT
T ss_pred             EEEEEeCCCCCHHHHHHHHHHc
Confidence            4999999999999999887764

>d1oywa2 c.37.1.19 (A:1-206) RecQ helicase domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecQ helicase domain
species: Escherichia coli [TaxId: 562]

Probab=94.80  E-value=0.016  Score=44.30  Aligned_cols=24  Identities=29%  Similarity=0.372  Sum_probs=18.7

Q ss_pred             hcCCCceEEEECCCCCCHHHHHHHHH
Q psy879           27 SSGNVPNIIISGPPGVGKTTTILCLA   52 (317)
Q Consensus        27 ~~~~~~~~ll~G~~G~GKt~la~~la   52 (317)
                      .+|+  ++++.-|+|+|||.+.....
T Consensus        38 l~g~--~vlv~apTGsGKT~~~~~~~   61 (206)
T d1oywa2          38 LSGR--DCLVVMPTGGGKSLCYQIPA   61 (206)
T ss_dssp             HTTC--CEEEECSCHHHHHHHHHHHH
T ss_pred             HcCC--CEEEEcCCCCCCcchhhhhh
Confidence            3455  79999999999998865444

>d2f9la1 c.37.1.8 (A:8-182) Rab11b {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab11b
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.57  E-value=0.011  Score=44.02  Aligned_cols=21  Identities=29%  Similarity=0.588  Sum_probs=19.1

Q ss_pred             EEEECCCCCCHHHHHHHHHHH
Q psy879           34 IIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~   54 (317)
                      +++.|++|+|||++++.+...
T Consensus         7 i~vvG~~~vGKTsLi~~~~~~   27 (175)
T d2f9la1           7 VVLIGDSGVGKSNLLSRFTRN   27 (175)
T ss_dssp             EEEESSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999998763

>d2atva1 c.37.1.8 (A:5-172) Ras-like estrogen-regulated growth inhibitor, RERG {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ras-like estrogen-regulated growth inhibitor, RERG
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.55  E-value=0.011  Score=43.63  Aligned_cols=21  Identities=29%  Similarity=0.493  Sum_probs=19.2

Q ss_pred             EEEECCCCCCHHHHHHHHHHH
Q psy879           34 IIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~   54 (317)
                      +++.|++|+|||++++.+...
T Consensus         5 i~lvG~~~vGKTsli~r~~~~   25 (168)
T d2atva1           5 LAIFGRAGVGKSALVVRFLTK   25 (168)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            789999999999999998864

>d1z08a1 c.37.1.8 (A:17-183) Rab21 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab21
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.54  E-value=0.011  Score=43.45  Aligned_cols=21  Identities=29%  Similarity=0.450  Sum_probs=19.0

Q ss_pred             EEEECCCCCCHHHHHHHHHHH
Q psy879           34 IIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~   54 (317)
                      +++.|.+|+|||++++.+...
T Consensus         6 ivlvG~~~vGKTsLi~r~~~~   26 (167)
T d1z08a1           6 VVLLGEGCVGKTSLVLRYCEN   26 (167)
T ss_dssp             EEEECCTTSCHHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999998763

>d1vhta_ c.37.1.1 (A:) Dephospho-CoA kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Dephospho-CoA kinase
species: Escherichia coli [TaxId: 562]

Probab=94.53  E-value=0.011  Score=45.45  Aligned_cols=20  Identities=30%  Similarity=0.488  Sum_probs=17.8

Q ss_pred             EEEECCCCCCHHHHHHHHHH
Q psy879           34 IIISGPPGVGKTTTILCLAR   53 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~   53 (317)
                      +.++|++|+||||+++.+.+
T Consensus         6 IgitG~igSGKStv~~~l~~   25 (208)
T d1vhta_           6 VALTGGIGSGKSTVANAFAD   25 (208)
T ss_dssp             EEEECCTTSCHHHHHHHHHH
T ss_pred             EEEECCCcCCHHHHHHHHHH
Confidence            66899999999999998864

>d2f7sa1 c.37.1.8 (A:5-190) Rab27b {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab27b
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.53  E-value=0.01  Score=44.54  Aligned_cols=20  Identities=35%  Similarity=0.542  Sum_probs=18.2

Q ss_pred             EEEECCCCCCHHHHHHHHHH
Q psy879           34 IIISGPPGVGKTTTILCLAR   53 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~   53 (317)
                      +++.|++|+|||++++.+..
T Consensus         8 i~ivG~~~vGKTsLi~~l~~   27 (186)
T d2f7sa1           8 LLALGDSGVGKTTFLYRYTD   27 (186)
T ss_dssp             EEEESCTTSSHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHhc
Confidence            78999999999999998874

>d1nlfa_ c.37.1.11 (A:) Hexameric replicative helicase repA {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hexameric replicative helicase repA
species: Escherichia coli [TaxId: 562]

Probab=94.53  E-value=0.01  Score=47.59  Aligned_cols=24  Identities=29%  Similarity=0.322  Sum_probs=21.1

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHc
Q psy879           33 NIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      ..+|+|+||+|||+++..+|..+.
T Consensus        31 ~~~i~G~~G~GKS~l~l~la~~ia   54 (274)
T d1nlfa_          31 VGALVSPGGAGKSMLALQLAAQIA   54 (274)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHH
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHHH
Confidence            378999999999999999988763

>d1wmsa_ c.37.1.8 (A:) Rab9a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab9a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.51  E-value=0.012  Score=43.71  Aligned_cols=21  Identities=29%  Similarity=0.445  Sum_probs=19.1

Q ss_pred             EEEECCCCCCHHHHHHHHHHH
Q psy879           34 IIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~   54 (317)
                      +++.|++|+|||+++..+...
T Consensus         9 I~vvG~~~vGKSSli~~~~~~   29 (174)
T d1wmsa_           9 VILLGDGGVGKSSLMNRYVTN   29 (174)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            899999999999999988763

>d1mh1a_ c.37.1.8 (A:) Rac {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rac
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.51  E-value=0.013  Score=43.81  Aligned_cols=21  Identities=24%  Similarity=0.415  Sum_probs=19.4

Q ss_pred             EEEECCCCCCHHHHHHHHHHH
Q psy879           34 IIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~   54 (317)
                      +++.|.+|+|||++++.+...
T Consensus         8 ivviG~~~vGKTsli~~~~~~   28 (183)
T d1mh1a_           8 CVVVGDGAVGKTCLLISYTTN   28 (183)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            899999999999999998864

>d1p5zb_ c.37.1.1 (B:) Deoxycytidine kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Deoxycytidine kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.48  E-value=0.0036  Score=49.23  Aligned_cols=24  Identities=29%  Similarity=0.350  Sum_probs=21.8

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHc
Q psy879           33 NIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      -+.|.|+.|+||||+++.+++.+.
T Consensus         4 ~I~ieG~dGsGKST~~~~L~~~l~   27 (241)
T d1p5zb_           4 KISIEGNIAAGKSTFVNILKQLCE   27 (241)
T ss_dssp             EEEEECSTTSSHHHHHTTTGGGCT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHh
Confidence            488999999999999999999864

>d1ky3a_ c.37.1.8 (A:) Rab-related protein ypt7p {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-related protein ypt7p
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=94.40  E-value=0.012  Score=43.53  Aligned_cols=22  Identities=36%  Similarity=0.510  Sum_probs=19.4

Q ss_pred             eEEEECCCCCCHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~   54 (317)
                      .+++.|++|+|||++++.+...
T Consensus         4 Ki~~vG~~~vGKSsLi~~~~~~   25 (175)
T d1ky3a_           4 KVIILGDSGVGKTSLMHRYVND   25 (175)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHcC
Confidence            3789999999999999998753

>d1g16a_ c.37.1.8 (A:) Rab-related protein Sec4 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-related protein Sec4
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=94.32  E-value=0.012  Score=43.31  Aligned_cols=21  Identities=29%  Similarity=0.552  Sum_probs=19.2

Q ss_pred             EEEECCCCCCHHHHHHHHHHH
Q psy879           34 IIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~   54 (317)
                      +++.|++|+|||++++.+...
T Consensus         5 i~vvG~~~vGKTSli~~l~~~   25 (166)
T d1g16a_           5 ILLIGDSGVGKSCLLVRFVED   25 (166)
T ss_dssp             EEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999998864

>d1jjva_ c.37.1.1 (A:) Dephospho-CoA kinase {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Dephospho-CoA kinase
species: Haemophilus influenzae [TaxId: 727]

Probab=94.27  E-value=0.011  Score=45.34  Aligned_cols=20  Identities=30%  Similarity=0.370  Sum_probs=17.4

Q ss_pred             EEEECCCCCCHHHHHHHHHH
Q psy879           34 IIISGPPGVGKTTTILCLAR   53 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~   53 (317)
                      +.++|+.||||||+++.+.+
T Consensus         5 IgITG~igSGKStv~~~l~~   24 (205)
T d1jjva_           5 VGLTGGIGSGKTTIANLFTD   24 (205)
T ss_dssp             EEEECSTTSCHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            56899999999999998753

>d1z06a1 c.37.1.8 (A:32-196) Rab-33b {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-33b
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=94.24  E-value=0.014  Score=42.70  Aligned_cols=21  Identities=33%  Similarity=0.390  Sum_probs=19.2

Q ss_pred             EEEECCCCCCHHHHHHHHHHH
Q psy879           34 IIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~   54 (317)
                      +++.|++|+|||++++.+...
T Consensus         5 v~liG~~~vGKTsLl~~~~~~   25 (165)
T d1z06a1           5 IIVIGDSNVGKTCLTYRFCAG   25 (165)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999998863

>d2erxa1 c.37.1.8 (A:6-176) di-Ras2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: di-Ras2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.22  E-value=0.013  Score=43.18  Aligned_cols=20  Identities=30%  Similarity=0.652  Sum_probs=18.3

Q ss_pred             EEEECCCCCCHHHHHHHHHH
Q psy879           34 IIISGPPGVGKTTTILCLAR   53 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~   53 (317)
                      +++.|.+|+|||+++..+..
T Consensus         5 i~viG~~~vGKTsLi~r~~~   24 (171)
T d2erxa1           5 VAVFGAGGVGKSSLVLRFVK   24 (171)
T ss_dssp             EEEECCTTSSHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHHh
Confidence            78999999999999998875

>d1ihua2 c.37.1.10 (A:308-586) Arsenite-translocating ATPase ArsA {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Arsenite-translocating ATPase ArsA
species: Escherichia coli [TaxId: 562]

Probab=94.22  E-value=0.031  Score=44.70  Aligned_cols=47  Identities=23%  Similarity=0.186  Sum_probs=31.5

Q ss_pred             HHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecC
Q psy879           23 KVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNA   69 (317)
Q Consensus        23 ~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~   69 (317)
                      ...+..+....++++|.-|+||||++-.+|..+...+....+++.++
T Consensus        12 ~~~~~~~~~~iii~sGKGGVGKTT~a~nLA~~lA~~G~rVllvD~Dp   58 (279)
T d1ihua2          12 VDDIARNEHGLIMLMGKGGVGKTTMAAAIAVRLADMGFDVHLTTSDP   58 (279)
T ss_dssp             HHHHHTTSCEEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEESCC
T ss_pred             HHHhhcCCCEEEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEeCCC
Confidence            33344444334888999999999999999988865443444445443

>d1d0xa2 c.37.1.9 (A:2-33,A:80-759) Myosin S1, motor domain {Dictyostelium discoideum [TaxId: 44689]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Myosin S1, motor domain
species: Dictyostelium discoideum [TaxId: 44689]

Probab=94.14  E-value=0.023  Score=51.95  Aligned_cols=35  Identities=20%  Similarity=0.349  Sum_probs=28.9

Q ss_pred             HHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHc
Q psy879           22 LKVFSSSGNVPNIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        22 l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      .+.++..++.-.+++.|++|+|||..++.+.+.+.
T Consensus       116 y~~m~~~~~nQsIiisGeSGaGKTe~~k~il~yL~  150 (712)
T d1d0xa2         116 YRSMLDDRQNQSLLITGESGAGKTENTKKVIQYLA  150 (712)
T ss_dssp             HHHHHHHTCCEEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             HHHHHHhCCCceEEEeCCCCCCHHHHHHHHHHHHH
Confidence            55666667654599999999999999999999873

>d1vg8a_ c.37.1.8 (A:) Rab7 {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab7
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=94.11  E-value=0.015  Score=43.47  Aligned_cols=21  Identities=38%  Similarity=0.528  Sum_probs=19.1

Q ss_pred             EEEECCCCCCHHHHHHHHHHH
Q psy879           34 IIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~   54 (317)
                      +++.|.+|+|||+++..+...
T Consensus         5 v~vvG~~~vGKSSLi~~l~~~   25 (184)
T d1vg8a_           5 VIILGDSGVGKTSLMNQYVNK   25 (184)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999998763

>d2mysa2 c.37.1.9 (A:4-33,A:80-843) Myosin S1, motor domain {Chicken (Gallus gallus), pectoral muscle [TaxId: 9031]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Myosin S1, motor domain
species: Chicken (Gallus gallus), pectoral muscle [TaxId: 9031]

Probab=94.09  E-value=0.03  Score=51.98  Aligned_cols=36  Identities=19%  Similarity=0.343  Sum_probs=29.6

Q ss_pred             HHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHc
Q psy879           21 RLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        21 ~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      ....++..++.-.+++.|++|+|||..++.+.+.|.
T Consensus       113 Ay~~m~~~~~~QsIiisGeSGaGKTe~~K~il~yL~  148 (794)
T d2mysa2         113 AYQFMLTDRENQSILITGESGAGKTVNTKRVIQYFA  148 (794)
T ss_dssp             HHHHHHHHTCCEEEEEEECTTSCHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCCcEEEEEcCCCCCHHHHHHHHHHHHH
Confidence            356666677755699999999999999999998874

>d1z63a1 c.37.1.19 (A:432-661) Helicase of the SNF2/Rad54 hamily {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Helicase of the SNF2/Rad54 hamily
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=94.07  E-value=0.13  Score=39.68  Aligned_cols=140  Identities=14%  Similarity=0.189  Sum_probs=68.0

Q ss_pred             cCCCCCCcccCCHHHHHHH---HHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHH
Q psy879            4 YRPQTFSDIVGNEDTVERL---KVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRN   80 (317)
Q Consensus         4 y~P~~~~~~~g~~~~~~~l---~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~   80 (317)
                      -.|..+.. --.+...+.+   ....+.+.  ..+|.-+.|.|||..+-+++..+........++-+.+..  -.....+
T Consensus         4 ~~P~~~~~-~L~~yQ~~~v~~~~~~~~~~~--g~iLaDe~GlGKT~~~i~~~~~~~~~~~~~~~LIv~p~~--l~~~W~~   78 (230)
T d1z63a1           4 LEPYNIKA-NLRPYQIKGFSWMRFMNKLGF--GICLADDMGLGKTLQTIAVFSDAKKENELTPSLVICPLS--VLKNWEE   78 (230)
T ss_dssp             CCCCSCSS-CCCHHHHHHHHHHHHHHHTTC--CEEECCCTTSCHHHHHHHHHHHHHHTTCCSSEEEEECST--THHHHHH
T ss_pred             cCchhhhc-chhHHHHHHHHHHHHhhhcCC--CEEEEeCCCCChHHHHHHhhhhhhhcccccccceecchh--hhhHHHH
Confidence            35655542 1234443433   33333332  478888999999999988887764332222233333321  1122222


Q ss_pred             HHHHHHhhcc------------------------------cCCCCceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEE
Q psy879           81 KIKMFAQQKV------------------------------TLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFA  130 (317)
Q Consensus        81 ~~~~~~~~~~------------------------------~~~~~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~i  130 (317)
                      .+..+.....                              .+.......+|+||++.+...... -.+.+.......+++
T Consensus        79 e~~~~~~~~~~~~~~~~~~~~~~~~~~vvi~~~~~~~~~~~l~~~~~~~vI~DEah~~k~~~s~-~~~~~~~l~a~~r~~  157 (230)
T d1z63a1          79 ELSKFAPHLRFAVFHEDRSKIKLEDYDIILTTYAVLLRDTRLKEVEWKYIVIDEAQNIKNPQTK-IFKAVKELKSKYRIA  157 (230)
T ss_dssp             HHHHHCTTSCEEECSSSTTSCCGGGSSEEEEEHHHHTTCHHHHTCCEEEEEEETGGGGSCTTSH-HHHHHHTSCEEEEEE
T ss_pred             HHHhhcccccceeeccccchhhccCcCEEEeeHHHHHhHHHHhcccceEEEEEhhhcccccchh-hhhhhhhhccceEEE
Confidence            2222211100                              000125678999999988432111 112222233455677


Q ss_pred             EEecCCCcCchhHhhhcce
Q psy879          131 LACNNSEKIIEPIQSRCAM  149 (317)
Q Consensus       131 l~~~~~~~l~~~i~sR~~~  149 (317)
                      +++++...-+..+.+-+..
T Consensus       158 LTgTPi~n~~~dl~~ll~~  176 (230)
T d1z63a1         158 LTGTPIENKVDDLWSIMTF  176 (230)
T ss_dssp             ECSSCSTTCHHHHHHHHHH
T ss_pred             EecchHHhHHHHHHHHHHh
Confidence            7777655444444444433

>d1xtqa1 c.37.1.8 (A:3-169) GTP-binding protein RheB {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTP-binding protein RheB
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.06  E-value=0.014  Score=42.88  Aligned_cols=21  Identities=29%  Similarity=0.332  Sum_probs=19.0

Q ss_pred             EEEECCCCCCHHHHHHHHHHH
Q psy879           34 IIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~   54 (317)
                      +++.|++|+|||++++.+...
T Consensus         7 v~liG~~~vGKTsLl~~~~~~   27 (167)
T d1xtqa1           7 IAILGYRSVGKSSLTIQFVEG   27 (167)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            889999999999999998753

>d1z0ja1 c.37.1.8 (A:2-168) Rab-22a {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-22a
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=94.03  E-value=0.017  Score=42.51  Aligned_cols=21  Identities=24%  Similarity=0.465  Sum_probs=19.1

Q ss_pred             EEEECCCCCCHHHHHHHHHHH
Q psy879           34 IIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~   54 (317)
                      +++.|.+|+|||++++.+...
T Consensus         7 i~lvG~~~vGKTsli~rl~~~   27 (167)
T d1z0ja1           7 VCLLGDTGVGKSSIMWRFVED   27 (167)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999998864

>d1wb1a4 c.37.1.8 (A:1-179) Elongation factor SelB, N-terminal domain {Methanococcus maripaludis [TaxId: 39152]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor SelB, N-terminal domain
species: Methanococcus maripaludis [TaxId: 39152]

Probab=94.03  E-value=0.65  Score=33.86  Aligned_cols=21  Identities=38%  Similarity=0.302  Sum_probs=19.1

Q ss_pred             eEEEECCCCCCHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLAR   53 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~   53 (317)
                      ++-+.|.|++||||+..++.+
T Consensus         7 nIaiiG~~naGKSTL~n~L~~   27 (179)
T d1wb1a4           7 NLGIFGHIDHGKTTLSKVLTE   27 (179)
T ss_dssp             EEEEEECTTSSHHHHHHHHHT
T ss_pred             EEEEEeCCCCcHHHHHHHHHH
Confidence            488999999999999999974

>d1nija1 c.37.1.10 (A:2-223) Hypothetical protein YjiA, N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Hypothetical protein YjiA, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=94.02  E-value=0.011  Score=45.98  Aligned_cols=25  Identities=24%  Similarity=0.348  Sum_probs=21.9

Q ss_pred             CCceEEEECCCCCCHHHHHHHHHHH
Q psy879           30 NVPNIIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        30 ~~~~~ll~G~~G~GKt~la~~la~~   54 (317)
                      +.|.++++|.-|+||||+.+.+.+.
T Consensus         2 ~iPv~iitGFLGaGKTTll~~lL~~   26 (222)
T d1nija1           2 PIAVTLLTGFLGAGKTTLLRHILNE   26 (222)
T ss_dssp             CEEEEEEEESSSSSCHHHHHHHHHS
T ss_pred             CCCEEEEeeCCCCCHHHHHHHHHhc
Confidence            3467999999999999999998875

>d2cxxa1 c.37.1.8 (A:2-185) GTP-binding protein engB {Pyrococcus horikoshii [TaxId: 53953]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTP-binding protein engB
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=94.02  E-value=0.012  Score=43.85  Aligned_cols=22  Identities=41%  Similarity=0.551  Sum_probs=19.4

Q ss_pred             eEEEECCCCCCHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~   54 (317)
                      .++|.|+||+||||+..++.+.
T Consensus         2 ~I~lvG~~nvGKSsLin~l~~~   23 (184)
T d2cxxa1           2 TIIFAGRSNVGKSTLIYRLTGK   23 (184)
T ss_dssp             EEEEEEBTTSSHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            4789999999999999998753

>d1qhla_ c.37.1.12 (A:) Cell division protein MukB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Cell division protein MukB
species: Escherichia coli [TaxId: 562]

Probab=93.99  E-value=0.0056  Score=46.50  Aligned_cols=26  Identities=31%  Similarity=0.465  Sum_probs=22.5

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHcCCC
Q psy879           34 IIISGPPGVGKTTTILCLARILLGPS   59 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~l~~~~   59 (317)
                      .+|+||.|+|||++..++.-.+.+..
T Consensus        27 tvi~G~NGsGKStil~Ai~~~L~g~~   52 (222)
T d1qhla_          27 TTLSGGNGAGKSTTMAAFVTALIPDL   52 (222)
T ss_dssp             HHHHSCCSHHHHHHHHHHHHHHSCCT
T ss_pred             EEEECCCCCCHHHHHHHHHHHhcCCc
Confidence            57899999999999999998886543

>d1lkxa_ c.37.1.9 (A:) Myosin S1, motor domain {Dictyostelium discoideum, class-I myosin MyoE [TaxId: 44689]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Myosin S1, motor domain
species: Dictyostelium discoideum, class-I myosin MyoE [TaxId: 44689]

Probab=93.98  E-value=0.026  Score=51.42  Aligned_cols=35  Identities=29%  Similarity=0.393  Sum_probs=28.8

Q ss_pred             HHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHc
Q psy879           22 LKVFSSSGNVPNIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        22 l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      ...+...++.-.+++.|++|+|||+.++.+.+.|.
T Consensus        77 y~~l~~~~~~QsIiisGeSGsGKTe~~k~il~yL~  111 (684)
T d1lkxa_          77 YRSMRQSQENQCVIISGESGAGKTEASKKIMQFLT  111 (684)
T ss_dssp             HHHHHHHCCCEEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             HHHHHHcCCCeEEEEEcCCCCCHHHHHHHHHHHHH
Confidence            55556666655699999999999999999999873

>d1fzqa_ c.37.1.8 (A:) ADP-ribosylation factor {Mouse (Mus musculus), ARL3 [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Mouse (Mus musculus), ARL3 [TaxId: 10090]

Probab=93.96  E-value=0.013  Score=43.40  Aligned_cols=20  Identities=40%  Similarity=0.494  Sum_probs=18.2

Q ss_pred             EEEECCCCCCHHHHHHHHHH
Q psy879           34 IIISGPPGVGKTTTILCLAR   53 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~   53 (317)
                      +++.|++|+|||++++.+..
T Consensus        19 I~vvG~~~vGKSsLi~~l~~   38 (176)
T d1fzqa_          19 ILLLGLDNAGKTTLLKQLAS   38 (176)
T ss_dssp             EEEEESTTSSHHHHHHHHCC
T ss_pred             EEEECCCCCCHHHHHHHHhc
Confidence            99999999999999988754

>d1x3sa1 c.37.1.8 (A:2-178) Rab18 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab18
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.86  E-value=0.018  Score=42.78  Aligned_cols=21  Identities=38%  Similarity=0.637  Sum_probs=19.3

Q ss_pred             EEEECCCCCCHHHHHHHHHHH
Q psy879           34 IIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~   54 (317)
                      +++.|.+|+|||++++.+...
T Consensus        10 i~vvG~~~vGKTsli~~l~~~   30 (177)
T d1x3sa1          10 ILIIGESGVGKSSLLLRFTDD   30 (177)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            899999999999999998863

>d1ihua1 c.37.1.10 (A:1-296) Arsenite-translocating ATPase ArsA {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Arsenite-translocating ATPase ArsA
species: Escherichia coli [TaxId: 562]

Probab=93.85  E-value=0.027  Score=45.40  Aligned_cols=36  Identities=22%  Similarity=0.263  Sum_probs=27.1

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEec
Q psy879           33 NIIISGPPGVGKTTTILCLARILLGPSFKDAVLELN   68 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~   68 (317)
                      -++++|.-|+||||++-.+|..+...+....+++.+
T Consensus        10 ~i~~sGKGGVGKTTvaa~lA~~lA~~G~rVLlvD~D   45 (296)
T d1ihua1          10 YLFFTGKGGVGKTSISCATAIRLAEQGKRVLLVSTD   45 (296)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEECC
T ss_pred             EEEEECCCcChHHHHHHHHHHHHHHCCCCEEEEeCC
Confidence            488999999999999999999885444333344444

>d1g7sa4 c.37.1.8 (A:1-227) Initiation factor IF2/eIF5b, N-terminal (G) domain {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Initiation factor IF2/eIF5b, N-terminal (G) domain
species: Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]

Probab=93.84  E-value=0.18  Score=38.87  Aligned_cols=24  Identities=25%  Similarity=0.253  Sum_probs=20.9

Q ss_pred             ceEEEECCCCCCHHHHHHHHHHHH
Q psy879           32 PNIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        32 ~~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      |.+.+.|.+++||||++.++...-
T Consensus         6 p~IaIiGh~d~GKSTL~~~L~~~~   29 (227)
T d1g7sa4           6 PIVSVLGHVDHGKTTLLDHIRGSA   29 (227)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CEEEEEeCCCccHHHHHHHHHhhc
Confidence            458999999999999999998753

>d1ek0a_ c.37.1.8 (A:) Ypt51 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ypt51
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=93.80  E-value=0.019  Score=42.28  Aligned_cols=21  Identities=24%  Similarity=0.526  Sum_probs=19.0

Q ss_pred             EEEECCCCCCHHHHHHHHHHH
Q psy879           34 IIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~   54 (317)
                      +++.|++|+|||+++..+...
T Consensus         6 i~vvG~~~vGKTsLi~~~~~~   26 (170)
T d1ek0a_           6 LVLLGEAAVGKSSIVLRFVSN   26 (170)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999998764

>d2bv3a2 c.37.1.8 (A:7-282) Elongation factor G (EF-G), N-terminal (G) domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor G (EF-G), N-terminal (G) domain
species: Thermus thermophilus [TaxId: 274]

Probab=93.77  E-value=1.2  Score=35.12  Aligned_cols=24  Identities=33%  Similarity=0.196  Sum_probs=21.1

Q ss_pred             ceEEEECCCCCCHHHHHHHHHHHH
Q psy879           32 PNIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        32 ~~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .|+.+.|..|+||||++.++....
T Consensus         7 Rni~i~gh~~~GKTtL~e~ll~~~   30 (276)
T d2bv3a2           7 RNIGIAAHIDAGKTTTTERILYYT   30 (276)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHHHH
T ss_pred             eEEEEEeCCCCCHHHHHHHHHHhc
Confidence            479999999999999999998653

>d2g3ya1 c.37.1.8 (A:73-244) GTP-binding protein GEM {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTP-binding protein GEM
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.67  E-value=0.02  Score=42.38  Aligned_cols=20  Identities=35%  Similarity=0.569  Sum_probs=18.4

Q ss_pred             EEEECCCCCCHHHHHHHHHH
Q psy879           34 IIISGPPGVGKTTTILCLAR   53 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~   53 (317)
                      +++.|++|+|||++++.+..
T Consensus         6 v~lvG~~~vGKTsLi~~~~~   25 (172)
T d2g3ya1           6 VVLIGEQGVGKSTLANIFAG   25 (172)
T ss_dssp             EEEECCTTSSHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            79999999999999998874

>d1e9ra_ c.37.1.11 (A:) Bacterial conjugative coupling protein TrwB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Bacterial conjugative coupling protein TrwB
species: Escherichia coli [TaxId: 562]

Probab=93.65  E-value=0.017  Score=49.54  Aligned_cols=28  Identities=25%  Similarity=0.356  Sum_probs=22.6

Q ss_pred             ceEEEECCCCCCHHHHHHHHHHHHcCCC
Q psy879           32 PNIIISGPPGVGKTTTILCLARILLGPS   59 (317)
Q Consensus        32 ~~~ll~G~~G~GKt~la~~la~~l~~~~   59 (317)
                      .|+++.|++|+|||++++.+...+....
T Consensus        51 ~H~~I~G~tGsGKT~~l~~li~~~~~~g   78 (433)
T d1e9ra_          51 RHLLVNGATGTGKSVLLRELAYTGLLRG   78 (433)
T ss_dssp             GCEEEEECTTSSHHHHHHHHHHHHHHTT
T ss_pred             ceEEEEeCCCCcHHHHHHHHHHHHHhCC
Confidence            3799999999999999987776655443

>d1udxa2 c.37.1.8 (A:157-336) Obg GTP-binding protein middle domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Obg GTP-binding protein middle domain
species: Thermus thermophilus [TaxId: 274]

Probab=93.65  E-value=0.014  Score=43.55  Aligned_cols=22  Identities=23%  Similarity=0.549  Sum_probs=19.6

Q ss_pred             ceEEEECCCCCCHHHHHHHHHH
Q psy879           32 PNIIISGPPGVGKTTTILCLAR   53 (317)
Q Consensus        32 ~~~ll~G~~G~GKt~la~~la~   53 (317)
                      +.+.|.|.||+||||++.++.+
T Consensus         2 ~~VaivG~~nvGKSTLin~L~~   23 (180)
T d1udxa2           2 ADVGLVGYPNAGKSSLLAAMTR   23 (180)
T ss_dssp             CSEEEECCGGGCHHHHHHHHCS
T ss_pred             CEEEEECCCCCCHHHHHHHHhC
Confidence            4688999999999999999864

>d1br2a2 c.37.1.9 (A:80-789) Myosin S1, motor domain {Chicken (Gallus gallus), pectoral muscle [TaxId: 9031]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Myosin S1, motor domain
species: Chicken (Gallus gallus), pectoral muscle [TaxId: 9031]

Probab=93.64  E-value=0.037  Score=50.66  Aligned_cols=35  Identities=20%  Similarity=0.304  Sum_probs=29.0

Q ss_pred             HHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHc
Q psy879           22 LKVFSSSGNVPNIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        22 l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      .+.++..++.-.+++.|++|+|||+.++.+.+.|.
T Consensus        82 y~~m~~~~~~Q~IiisGeSGaGKTe~~k~il~yL~  116 (710)
T d1br2a2          82 YRSMLQDREDQSILCTGESGAGKTENTKKVIQYLA  116 (710)
T ss_dssp             HHHHHHHTCCEEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             HHHHHHhCCCcEEEEEeCCCCCHHHHHHHHHHHHH
Confidence            55566666655699999999999999999999874

>d1e0sa_ c.37.1.8 (A:) ADP-ribosylation factor {Human (Homo sapiens), ARF6 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARF6 [TaxId: 9606]

Probab=93.59  E-value=0.01  Score=44.08  Aligned_cols=21  Identities=33%  Similarity=0.434  Sum_probs=18.7

Q ss_pred             eEEEECCCCCCHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLAR   53 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~   53 (317)
                      .+++.|+||+|||++++.+..
T Consensus        14 kIvlvG~~~vGKTSli~rl~~   34 (173)
T d1e0sa_          14 RILMLGLDAAGKTTILYKLKL   34 (173)
T ss_dssp             EEEEEEETTSSHHHHHHHTTC
T ss_pred             EEEEECCCCCCHHHHHHHHhc
Confidence            499999999999999998763

>d1m7ba_ c.37.1.8 (A:) RhoE (RND3) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: RhoE (RND3)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=93.54  E-value=0.02  Score=42.72  Aligned_cols=21  Identities=29%  Similarity=0.482  Sum_probs=19.2

Q ss_pred             EEEECCCCCCHHHHHHHHHHH
Q psy879           34 IIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~   54 (317)
                      ++|.|.+|+|||++++.+...
T Consensus         5 ivliG~~~vGKTsli~r~~~~   25 (179)
T d1m7ba_           5 IVVVGDSQCGKTALLHVFAKD   25 (179)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999988874

>d1moza_ c.37.1.8 (A:) ADP-ribosylation factor {Baker's yeast (Saccharomyces cerevisiae), ARL1 [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Baker's yeast (Saccharomyces cerevisiae), ARL1 [TaxId: 4932]

Probab=93.48  E-value=0.024  Score=42.21  Aligned_cols=20  Identities=45%  Similarity=0.632  Sum_probs=18.1

Q ss_pred             eEEEECCCCCCHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLA   52 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la   52 (317)
                      .+++.|++|+|||++++.+.
T Consensus        19 KI~lvG~~~vGKTsLi~~l~   38 (182)
T d1moza_          19 RILILGLDGAGKTTILYRLQ   38 (182)
T ss_dssp             EEEEEEETTSSHHHHHHHTC
T ss_pred             EEEEECCCCCCHHHHHHHHh
Confidence            39999999999999999864

>d1lnza2 c.37.1.8 (A:158-342) Obg GTP-binding protein middle domain {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Obg GTP-binding protein middle domain
species: Bacillus subtilis [TaxId: 1423]

Probab=93.48  E-value=0.017  Score=43.22  Aligned_cols=22  Identities=27%  Similarity=0.501  Sum_probs=19.2

Q ss_pred             ceEEEECCCCCCHHHHHHHHHH
Q psy879           32 PNIIISGPPGVGKTTTILCLAR   53 (317)
Q Consensus        32 ~~~ll~G~~G~GKt~la~~la~   53 (317)
                      +.+.|.|+|++||||+..++.+
T Consensus         2 ~~VaiiG~~nvGKSSLin~L~~   23 (185)
T d1lnza2           2 ADVGLVGFPSVGKSTLLSVVSS   23 (185)
T ss_dssp             CCEEEESSTTSSHHHHHHHSEE
T ss_pred             CeEEEECCCCCCHHHHHHHHhC
Confidence            4588999999999999998754

>d1kk8a2 c.37.1.9 (A:1-28,A:77-837) Myosin S1, motor domain {Bay scallop (Aequipecten irradians) [TaxId: 31199]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Myosin S1, motor domain
species: Bay scallop (Aequipecten irradians) [TaxId: 31199]

Probab=93.47  E-value=0.03  Score=51.92  Aligned_cols=36  Identities=19%  Similarity=0.267  Sum_probs=29.3

Q ss_pred             HHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHc
Q psy879           21 RLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        21 ~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      ....++..++.-.+++.|++|+|||..++.+.+.|.
T Consensus       111 Ay~~m~~~~~nQ~IiisGESGaGKTe~~K~il~yL~  146 (789)
T d1kk8a2         111 AYQNMVTDRENQSCLITGESGAGKTENTKKVIMYLA  146 (789)
T ss_dssp             HHHHHHHHTSEEEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             HHHHHHHhCCCcEEEEEeCCCCCHHHHHHHHHHHHH
Confidence            456666677644599999999999999999999874

>d1deka_ c.37.1.1 (A:) Deoxynucleoside monophosphate kinase {Bacteriophage T4 [TaxId: 10665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Deoxynucleoside monophosphate kinase
species: Bacteriophage T4 [TaxId: 10665]

Probab=93.33  E-value=0.026  Score=44.17  Aligned_cols=23  Identities=30%  Similarity=0.255  Sum_probs=20.4

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      .+.|+|+.||||||+|..++...
T Consensus         3 iIgiTG~igSGKsTva~~l~e~~   25 (241)
T d1deka_           3 LIFLSGVKRSGKDTTADFIMSNY   25 (241)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHHhC
Confidence            37899999999999999998863

>d1w7ja2 c.37.1.9 (A:63-792) Myosin S1, motor domain {Chicken (Gallus gallus), Va isoform [TaxId: 9031]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Myosin S1, motor domain
species: Chicken (Gallus gallus), Va isoform [TaxId: 9031]

Probab=93.16  E-value=0.043  Score=50.41  Aligned_cols=35  Identities=29%  Similarity=0.412  Sum_probs=29.0

Q ss_pred             HHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHH
Q psy879           21 RLKVFSSSGNVPNIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        21 ~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      ....++..++.-.+++.|++|+|||..++.+.+.+
T Consensus        84 Ay~~l~~~~~~Q~IiisGeSGsGKTe~~k~il~~l  118 (730)
T d1w7ja2          84 AYKQMARDERNQSIIVSGESGAGKTVSAKYAMRYF  118 (730)
T ss_dssp             HHHHHHHHTCCEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             HHHHHHHhCCCeEEEEEeCCCCCHHHHHHHHHHHH
Confidence            35556666765569999999999999999999887

>d1egaa1 c.37.1.8 (A:4-182) GTPase Era, N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTPase Era, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=92.95  E-value=0.025  Score=41.85  Aligned_cols=21  Identities=43%  Similarity=0.501  Sum_probs=19.2

Q ss_pred             eEEEECCCCCCHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLAR   53 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~   53 (317)
                      .+.|.|.||+||||+..++.+
T Consensus         7 ~I~iiG~~nvGKSSLin~L~~   27 (179)
T d1egaa1           7 FIAIVGRPNVGKSTLLNKLLG   27 (179)
T ss_dssp             EEEEECSSSSSHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            478999999999999999985

>d1n0ua2 c.37.1.8 (A:3-343) Elongation factor 2 (eEF-2), N-terminal (G) domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor 2 (eEF-2), N-terminal (G) domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=92.57  E-value=0.92  Score=37.03  Aligned_cols=41  Identities=12%  Similarity=0.266  Sum_probs=30.1

Q ss_pred             CceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCc
Q psy879           95 GRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEK  138 (317)
Q Consensus        95 ~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~  138 (317)
                      .+..++++|=++.........+....++   +...|++-|..++
T Consensus       120 ~D~allVVda~eGv~~qT~~~~~~a~~~---~~p~i~viNKiDr  160 (341)
T d1n0ua2         120 TDGALVVVDTIEGVCVQTETVLRQALGE---RIKPVVVINKVDR  160 (341)
T ss_dssp             CSEEEEEEETTTBSCHHHHHHHHHHHHT---TCEEEEEEECHHH
T ss_pred             cCceEEEEecccCcchhHHHHHHHHHHc---CCCeEEEEECccc
Confidence            4788999999999999888888777663   3455555566443

>d1mkya2 c.37.1.8 (A:173-358) Probable GTPase Der, N-terminal and middle domains {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase Der, N-terminal and middle domains
species: Thermotoga maritima [TaxId: 2336]

Probab=92.37  E-value=0.038  Score=41.11  Aligned_cols=22  Identities=32%  Similarity=0.516  Sum_probs=19.4

Q ss_pred             eEEEECCCCCCHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~   54 (317)
                      .+.|.|.+|+||||++.++.+.
T Consensus        10 kV~iiG~~~~GKSTLin~l~~~   31 (186)
T d1mkya2          10 KVAIVGRPNVGKSTLFNAILNK   31 (186)
T ss_dssp             EEEEECSTTSSHHHHHHHHHTS
T ss_pred             EEEEECCCCCCHHHHHHHHHCC
Confidence            3889999999999999998753

>d1zcba2 c.37.1.8 (A:47-75,A:202-372) Transducin (alpha subunit) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Transducin (alpha subunit)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=92.33  E-value=0.036  Score=41.72  Aligned_cols=19  Identities=26%  Similarity=0.406  Sum_probs=17.8

Q ss_pred             EEEECCCCCCHHHHHHHHH
Q psy879           34 IIISGPPGVGKTTTILCLA   52 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la   52 (317)
                      +++.|.+|+|||++++.+.
T Consensus         5 ivllG~~~vGKTsll~r~~   23 (200)
T d1zcba2           5 ILLLGAGESGKSTFLKQMR   23 (200)
T ss_dssp             EEEECSTTSSHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHh
Confidence            8999999999999999993

>d1g8fa3 c.37.1.15 (A:390-511) ATP sulfurylase C-terminal domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ATP sulfurylase C-terminal domain
domain: ATP sulfurylase C-terminal domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=92.12  E-value=0.13  Score=35.12  Aligned_cols=26  Identities=15%  Similarity=0.238  Sum_probs=23.3

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHcCC
Q psy879           33 NIIISGPPGVGKTTTILCLARILLGP   58 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~~~   58 (317)
                      .++|.|-+|+||+++|+++...+...
T Consensus         8 ~i~~tg~~~~gk~~ia~al~~~l~q~   33 (122)
T d1g8fa3           8 SIVLGNSLTVSREQLSIALLSTFLQF   33 (122)
T ss_dssp             EEEECTTCCSCHHHHHHHHHHHHTTS
T ss_pred             EEEEeCCCCCCHHHHHHHHHHHHHHh
Confidence            48999999999999999999888664

>d1cp2a_ c.37.1.10 (A:) Nitrogenase iron protein {Clostridium pasteurianum [TaxId: 1501]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Nitrogenase iron protein
species: Clostridium pasteurianum [TaxId: 1501]

Probab=92.08  E-value=0.063  Score=42.62  Aligned_cols=37  Identities=27%  Similarity=0.269  Sum_probs=29.7

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecC
Q psy879           33 NIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNA   69 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~   69 (317)
                      .+.|+|.-|+||||++-.+|..+...+.+..+++.+.
T Consensus         3 ~Iai~gKGGvGKTT~a~nLA~~LA~~G~rVllID~D~   39 (269)
T d1cp2a_           3 QVAIYGKGGIGKSTTTQNLTSGLHAMGKTIMVVGCDP   39 (269)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHHHTTTCCEEEEEECT
T ss_pred             EEEEECCCcCCHHHHHHHHHHHHHhCCCcEEEEecCC
Confidence            3667999999999999999999976655555667664

>d2bmja1 c.37.1.8 (A:66-240) Centaurin gamma 1, G domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Centaurin gamma 1, G domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.95  E-value=0.052  Score=40.16  Aligned_cols=21  Identities=19%  Similarity=0.177  Sum_probs=19.3

Q ss_pred             EEEECCCCCCHHHHHHHHHHH
Q psy879           34 IIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~   54 (317)
                      +++.|++|+|||+++..+...
T Consensus         8 i~vlG~~~vGKTsLi~~~~~~   28 (175)
T d2bmja1           8 LGVLGDARSGKSSLIHRFLTG   28 (175)
T ss_dssp             EEEECCTTTTHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            899999999999999988764

>d1p6xa_ c.37.1.1 (A:) Thymidine kinase {Equine herpesvirus type 4 [TaxId: 10331]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidine kinase
species: Equine herpesvirus type 4 [TaxId: 10331]

Probab=91.88  E-value=0.034  Score=45.86  Aligned_cols=23  Identities=35%  Similarity=0.414  Sum_probs=21.5

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHc
Q psy879           34 IIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      +.|-|+-|+||||+++.+++.+.
T Consensus         9 I~iEG~iGsGKSTl~~~L~~~l~   31 (333)
T d1p6xa_           9 IYLDGVYGIGKSTTGRVMASAAS   31 (333)
T ss_dssp             EEEECSTTSSHHHHHHHHHSGGG
T ss_pred             EEEECCccCCHHHHHHHHHHHhc
Confidence            78999999999999999999874

>d1xzpa2 c.37.1.8 (A:212-371) TrmE GTPase domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: TrmE GTPase domain
species: Thermotoga maritima [TaxId: 2336]

Probab=91.85  E-value=0.012  Score=42.75  Aligned_cols=21  Identities=38%  Similarity=0.580  Sum_probs=19.5

Q ss_pred             EEEECCCCCCHHHHHHHHHHH
Q psy879           34 IIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~   54 (317)
                      +.|.|.||+||||++.++...
T Consensus         3 I~liG~~n~GKSSLin~l~g~   23 (160)
T d1xzpa2           3 MVIVGKPNVGKSTLLNRLLNE   23 (160)
T ss_dssp             EEEECCHHHHTCHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            789999999999999999876

>d2b8ta1 c.37.1.24 (A:11-149) Thymidine kinase, TK1, N-terminal domain {Ureaplasma urealyticum [TaxId: 2130]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Type II thymidine kinase
domain: Thymidine kinase, TK1, N-terminal domain
species: Ureaplasma urealyticum [TaxId: 2130]

Probab=91.78  E-value=0.32  Score=34.23  Aligned_cols=36  Identities=11%  Similarity=0.107  Sum_probs=23.6

Q ss_pred             CceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEe
Q psy879           95 GRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALAC  133 (317)
Q Consensus        95 ~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~  133 (317)
                      ....+|+|||+..+.+ ....+...+.+.  +..+++++
T Consensus        78 ~~~dvI~IDE~QFf~d-~i~~~~~~~~~~--g~~Viv~G  113 (139)
T d2b8ta1          78 DETKVIGIDEVQFFDD-RICEVANILAEN--GFVVIISG  113 (139)
T ss_dssp             TTCCEEEECSGGGSCT-HHHHHHHHHHHT--TCEEEEEC
T ss_pred             cCcCEEEechhhhcch-hHHHHHHHHHhc--CceEEEEE
Confidence            4678999999999974 445566666542  33455543

>d1e69a_ c.37.1.12 (A:) Smc head domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Smc head domain
species: Thermotoga maritima [TaxId: 2336]

Probab=91.78  E-value=0.031  Score=45.39  Aligned_cols=22  Identities=32%  Similarity=0.578  Sum_probs=19.4

Q ss_pred             EEEECCCCCCHHHHHHHHHHHH
Q psy879           34 IIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~l   55 (317)
                      -+|+||.|+|||++..|++-.+
T Consensus        27 nvlvG~NgsGKS~iL~Ai~~~l   48 (308)
T d1e69a_          27 TAIVGPNGSGKSNIIDAIKWVF   48 (308)
T ss_dssp             EEEECCTTTCSTHHHHHHHHTS
T ss_pred             EEEECCCCCcHHHHHHHHHHHh
Confidence            6899999999999999997643

>d1xbta1 c.37.1.24 (A:18-150) Thymidine kinase, TK1, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Type II thymidine kinase
domain: Thymidine kinase, TK1, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.70  E-value=0.22  Score=34.80  Aligned_cols=94  Identities=16%  Similarity=0.135  Sum_probs=44.4

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCC-CCcChHHHHHHHH-HHHhhcccC------CCCceeEEEEeCC
Q psy879           34 IIISGPPGVGKTTTILCLARILLGPSFKDAVLELNAS-NDRGIDTVRNKIK-MFAQQKVTL------PPGRHKIVILDEA  105 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~-~~~~~~~i~~~~~-~~~~~~~~~------~~~~~~vliiDE~  105 (317)
                      -+++||=.+|||+-.-..+......  +..++-+++. +.+....+...-. .........      ......+|+|||+
T Consensus         5 ~li~GpMfsGKTt~Li~~~~~~~~~--g~~v~~ikp~~D~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~I~IDEa   82 (133)
T d1xbta1           5 QVILGPMFSGKSTELMRRVRRFQIA--QYKCLVIKYAKDTRYSSSFCTHDRNTMEALPACLLRDVAQEALGVAVIGIDEG   82 (133)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHHHTT--TCCEEEEEETTCCC--------------CEEESSGGGGHHHHHTCSEEEESSG
T ss_pred             EEEEecccCHHHHHHHHHHHHHHHc--CCcEEEEecccccCCcceeeecCCCcceeeeeechhhhhhhhcccceEEeehh
Confidence            5789999999999877766654322  2223333332 2221111110000 000000000      0024679999999


Q ss_pred             CCCCHHHHHHHHHHhhhccCCceEEEEe
Q psy879          106 DSMTDGAQQALRRTMEIYSNTTRFALAC  133 (317)
Q Consensus       106 d~l~~~~~~~ll~~le~~~~~~~~il~~  133 (317)
                      ..+..  ...+.+.+.+.  +..+++.+
T Consensus        83 QFf~d--l~~~~~~~~~~--~~~Viv~G  106 (133)
T d1xbta1          83 QFFPD--IVEFCEAMANA--GKTVIVAA  106 (133)
T ss_dssp             GGCTT--HHHHHHHHHHT--TCEEEEEC
T ss_pred             HHHHH--HHHHHHHHHhc--CCcEEEEE
Confidence            99963  34455555542  34455543

>d1tq4a_ c.37.1.8 (A:) Interferon-inducible GTPase {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Interferon-inducible GTPase
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=91.69  E-value=0.66  Score=38.89  Aligned_cols=21  Identities=33%  Similarity=0.572  Sum_probs=19.5

Q ss_pred             eEEEECCCCCCHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLAR   53 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~   53 (317)
                      ++.+.|.||+||||++.++..
T Consensus        58 ~Iai~G~~n~GKSSLiNaL~G   78 (400)
T d1tq4a_          58 NVAVTGETGSGKSSFINTLRG   78 (400)
T ss_dssp             EEEEEECTTSSHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            599999999999999999975

>d1azta2 c.37.1.8 (A:35-65,A:202-391) Transducin (alpha subunit) {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Transducin (alpha subunit)
species: Cow (Bos taurus) [TaxId: 9913]

Probab=91.66  E-value=0.051  Score=41.95  Aligned_cols=21  Identities=19%  Similarity=0.385  Sum_probs=19.1

Q ss_pred             EEEECCCCCCHHHHHHHHHHH
Q psy879           34 IIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~   54 (317)
                      +++.|++|+|||++++.+...
T Consensus         9 illlG~~~vGKTsll~~~~~~   29 (221)
T d1azta2           9 LLLLGAGESGKSTIVKQMRIL   29 (221)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            899999999999999998654

>d1byia_ c.37.1.10 (A:) Dethiobiotin synthetase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Dethiobiotin synthetase
species: Escherichia coli [TaxId: 562]

Probab=91.62  E-value=0.046  Score=41.75  Aligned_cols=29  Identities=21%  Similarity=0.382  Sum_probs=24.4

Q ss_pred             eEEEECCC-CCCHHHHHHHHHHHHcCCCCC
Q psy879           33 NIIISGPP-GVGKTTTILCLARILLGPSFK   61 (317)
Q Consensus        33 ~~ll~G~~-G~GKt~la~~la~~l~~~~~~   61 (317)
                      .|+++|.. |+||||++-.+|..+...+.+
T Consensus         3 ~~~i~gt~~GVGKTtvs~~La~aLa~~G~r   32 (224)
T d1byia_           3 RYFVTGTDTEVGKTVASCALLQAAKAAGYR   32 (224)
T ss_dssp             EEEEEESSTTSCHHHHHHHHHHHHHHTTCC
T ss_pred             eEEEEECCCCccHHHHHHHHHHHHHHCCCe
Confidence            58999994 999999999999998655443

>d2dy1a2 c.37.1.8 (A:8-274) Elongation factor G (EF-G), N-terminal (G) domain {Thermus thermophilus, EF-G-2 [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor G (EF-G), N-terminal (G) domain
species: Thermus thermophilus, EF-G-2 [TaxId: 274]

Probab=91.46  E-value=1.1  Score=35.05  Aligned_cols=22  Identities=32%  Similarity=0.388  Sum_probs=19.8

Q ss_pred             eEEEECCCCCCHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~   54 (317)
                      |+.+.|+.|+||||++.++...
T Consensus         4 Nv~iiGh~~~GKTtL~e~ll~~   25 (267)
T d2dy1a2           4 TVALVGHAGSGKTTLTEALLYK   25 (267)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHH
T ss_pred             EEEEEcCCCCcHHHHHHHHHHH
Confidence            6889999999999999999654

>d1osna_ c.37.1.1 (A:) Thymidine kinase {Varicella-zoster virus [TaxId: 10335]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidine kinase
species: Varicella-zoster virus [TaxId: 10335]

Probab=91.19  E-value=0.032  Score=46.01  Aligned_cols=23  Identities=30%  Similarity=0.420  Sum_probs=21.4

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHc
Q psy879           34 IIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      +.|-|+-|+||||+++.+++.+.
T Consensus         8 I~IEG~iGsGKSTl~~~L~~~l~   30 (331)
T d1osna_           8 IYLDGAYGIGKTTAAEEFLHHFA   30 (331)
T ss_dssp             EEEEESSSSCTTHHHHHHHHTTT
T ss_pred             EEEECCCCCCHHHHHHHHHHHHh
Confidence            78999999999999999999874

>d2bcjq2 c.37.1.8 (Q:38-66,Q:184-354) Transducin (alpha subunit) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Transducin (alpha subunit)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=91.19  E-value=0.059  Score=40.35  Aligned_cols=21  Identities=29%  Similarity=0.390  Sum_probs=19.5

Q ss_pred             EEEECCCCCCHHHHHHHHHHH
Q psy879           34 IIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~   54 (317)
                      +++.|.+|+|||++++.+...
T Consensus         5 iv~lG~~~vGKTsll~r~~~~   25 (200)
T d2bcjq2           5 LLLLGTGESGKSTFIKQMRII   25 (200)
T ss_dssp             EEEEESTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            799999999999999999765

>d1d2ea3 c.37.1.8 (A:55-250) Elongation factor Tu (EF-Tu), N-terminal (G) domain {Cow (Bos taurus), mitochondrial [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor Tu (EF-Tu), N-terminal (G) domain
species: Cow (Bos taurus), mitochondrial [TaxId: 9913]

Probab=91.10  E-value=0.56  Score=35.06  Aligned_cols=42  Identities=12%  Similarity=0.106  Sum_probs=27.5

Q ss_pred             CceeEEEEeCCCCCCHHHHHHHHHHhhhccCCceEEEEecCCCc
Q psy879           95 GRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEK  138 (317)
Q Consensus        95 ~~~~vliiDE~d~l~~~~~~~ll~~le~~~~~~~~il~~~~~~~  138 (317)
                      .+..++++|-.+...++....+.-..+..  ...+|++.|..+.
T Consensus        90 aD~allVVda~~G~~~QT~~~~~~a~~~~--~~~iIv~iNK~D~  131 (196)
T d1d2ea3          90 LDGCILVVAANDGPMPQTREHLLLARQIG--VEHVVVYVNKADA  131 (196)
T ss_dssp             CSEEEEEEETTTCSCHHHHHHHHHHHHTT--CCCEEEEEECGGG
T ss_pred             cCeEEEEEEcCCCCchhHHHHHHHHHHhc--CCcEEEEEecccc
Confidence            68899999999998887665554443321  2236666666553

>d2c78a3 c.37.1.8 (A:9-212) Elongation factor Tu (EF-Tu), N-terminal (G) domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor Tu (EF-Tu), N-terminal (G) domain
species: Thermus thermophilus [TaxId: 274]

Probab=91.09  E-value=2.2  Score=31.74  Aligned_cols=21  Identities=29%  Similarity=0.257  Sum_probs=18.9

Q ss_pred             EEEECCCCCCHHHHHHHHHHH
Q psy879           34 IIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~   54 (317)
                      +.+.|.+++||||++.++...
T Consensus         6 i~iiGhvd~GKSTL~~~Ll~~   26 (204)
T d2c78a3           6 VGTIGHVDHGKTTLTAALTYV   26 (204)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEeCCCCcHHHHHHHHHHH
Confidence            889999999999999998654

>d1xx6a1 c.37.1.24 (A:2-142) Thymidine kinase, TK1, N-terminal domain {Clostridium acetobutylicum [TaxId: 1488]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Type II thymidine kinase
domain: Thymidine kinase, TK1, N-terminal domain
species: Clostridium acetobutylicum [TaxId: 1488]

Probab=91.05  E-value=0.29  Score=34.58  Aligned_cols=22  Identities=27%  Similarity=0.347  Sum_probs=18.2

Q ss_pred             EEEECCCCCCHHHHHHHHHHHH
Q psy879           34 IIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~l   55 (317)
                      -+++||=.+||||-.-..+...
T Consensus        10 ~lI~GpMfSGKTteLi~~~~~~   31 (141)
T d1xx6a1          10 EVIVGPMYSGKSEELIRRIRRA   31 (141)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEEeccccHHHHHHHHHHHHh
Confidence            5789999999999877777554

>d2jdid3 c.37.1.11 (D:82-357) Central domain of beta subunit of F1 ATP synthase {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Central domain of beta subunit of F1 ATP synthase
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=90.97  E-value=0.1  Score=41.49  Aligned_cols=23  Identities=39%  Similarity=0.478  Sum_probs=20.8

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      ..+++|++|+|||+++..+++..
T Consensus        70 r~~If~~~g~GKt~l~~~i~~~~   92 (276)
T d2jdid3          70 KIGLFGGAGVGKTVLIMELINNV   92 (276)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHH
T ss_pred             EEEeeCCCCCCHHHHHHHHHHHH
Confidence            49999999999999999998765

>d1t9ha2 c.37.1.8 (A:68-298) Probable GTPase EngC (YjeQ), C-terminal domain {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase EngC (YjeQ), C-terminal domain
species: Bacillus subtilis [TaxId: 1423]

Probab=90.86  E-value=0.02  Score=44.57  Aligned_cols=22  Identities=23%  Similarity=0.516  Sum_probs=18.6

Q ss_pred             eEEEECCCCCCHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~   54 (317)
                      ..+|.|++|+||||++.++...
T Consensus        99 ~~vl~G~SGVGKSSLiN~L~~~  120 (231)
T d1t9ha2          99 TTVFAGQSGVGKSSLLNAISPE  120 (231)
T ss_dssp             EEEEEESHHHHHHHHHHHHCC-
T ss_pred             eEEEECCCCccHHHHHHhhccH
Confidence            4789999999999999988754

>d2jdia3 c.37.1.11 (A:95-379) Central domain of alpha subunit of F1 ATP synthase {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Central domain of alpha subunit of F1 ATP synthase
species: Cow (Bos taurus) [TaxId: 9913]

Probab=90.86  E-value=0.44  Score=37.93  Aligned_cols=34  Identities=21%  Similarity=0.187  Sum_probs=23.9

Q ss_pred             HHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHH
Q psy879           18 TVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        18 ~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~   54 (317)
                      +++.+....+.+   .+++.|++|+|||+++..++..
T Consensus        58 aID~l~pig~GQ---r~~If~~~g~GKt~ll~~~~~~   91 (285)
T d2jdia3          58 AVDSLVPIGRGQ---RELIIGDRQTGKTSIAIDTIIN   91 (285)
T ss_dssp             HHHHHSCCBTTC---BCEEEESTTSSHHHHHHHHHHH
T ss_pred             EEecccCccCCC---EEEeecCCCCChHHHHHHHHHh
Confidence            344444444433   4899999999999998877754

>d1xpua3 c.37.1.11 (A:129-417) Transcription termination factor Rho, ATPase domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Transcription termination factor Rho, ATPase domain
species: Escherichia coli [TaxId: 562]

Probab=90.68  E-value=0.049  Score=43.75  Aligned_cols=24  Identities=29%  Similarity=0.454  Sum_probs=21.5

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHc
Q psy879           33 NIIISGPPGVGKTTTILCLARILL   56 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~   56 (317)
                      ..++.|++|+|||+++..+++...
T Consensus        45 r~~I~g~~g~GKT~l~~~i~~~~~   68 (289)
T d1xpua3          45 RGLIVAPPKAGKTMLLQNIAQSIA   68 (289)
T ss_dssp             EEEEEECSSSSHHHHHHHHHHHHH
T ss_pred             eeeEeCCCCCCHHHHHHHHHHHHh
Confidence            599999999999999999998653

>d1w1wa_ c.37.1.12 (A:) Smc head domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Smc head domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=90.56  E-value=0.062  Score=45.46  Aligned_cols=22  Identities=32%  Similarity=0.557  Sum_probs=19.6

Q ss_pred             EEEECCCCCCHHHHHHHHHHHH
Q psy879           34 IIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~l   55 (317)
                      -+|+||.|+|||++..|++-.|
T Consensus        28 ~~i~G~NGsGKS~ileAi~~~l   49 (427)
T d1w1wa_          28 TSIIGPNGSGKSNMMDAISFVL   49 (427)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            5899999999999999998654

>d2afhe1 c.37.1.10 (E:1-289) Nitrogenase iron protein {Azotobacter vinelandii [TaxId: 354]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Nitrogenase iron protein
species: Azotobacter vinelandii [TaxId: 354]

Probab=90.32  E-value=0.092  Score=42.13  Aligned_cols=38  Identities=26%  Similarity=0.278  Sum_probs=28.6

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCC
Q psy879           33 NIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNAS   70 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~   70 (317)
                      -+.++|.-|+||||++-.+|..+...+.+..++++++.
T Consensus         4 ~IaisgKGGVGKTT~a~NLA~~LA~~G~rVLlID~DpQ   41 (289)
T d2afhe1           4 QCAIYGKGGIGKSTTTQNLVAALAEMGKKVMIVGCDPK   41 (289)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHHHHTTCCEEEEEECSS
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEecCCC
Confidence            35679999999999999999888655445555666643

>d1svsa1 c.37.1.8 (A:32-60,A:182-347) Transducin (alpha subunit) {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Transducin (alpha subunit)
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=89.70  E-value=0.11  Score=38.64  Aligned_cols=21  Identities=24%  Similarity=0.408  Sum_probs=19.0

Q ss_pred             EEEECCCCCCHHHHHHHHHHH
Q psy879           34 IIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        34 ~ll~G~~G~GKt~la~~la~~   54 (317)
                      +++.|..|+|||++++.+...
T Consensus         5 ivllG~~~vGKTsl~~r~~~~   25 (195)
T d1svsa1           5 LLLLGAGESGKSTIVKQMKII   25 (195)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhhC
Confidence            799999999999999988754

>d1j3ba1 c.91.1.1 (A:212-529) Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase) {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: PEP carboxykinase C-terminal domain
domain: Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase)
species: Thermus thermophilus [TaxId: 274]

Probab=89.28  E-value=0.066  Score=43.42  Aligned_cols=18  Identities=33%  Similarity=0.313  Sum_probs=15.5

Q ss_pred             eEEEECCCCCCHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILC   50 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~   50 (317)
                      .-+|+|.+||||||+...
T Consensus        16 valffGLSGTGKTTLs~~   33 (318)
T d1j3ba1          16 VAVFFGLSGTGKTTLSTD   33 (318)
T ss_dssp             EEEEEECTTSCHHHHTCB
T ss_pred             EEEEEccCCCCccccccC
Confidence            479999999999997653

>d2olra1 c.91.1.1 (A:228-540) Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: PEP carboxykinase C-terminal domain
domain: Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase)
species: Escherichia coli [TaxId: 562]

Probab=88.86  E-value=0.085  Score=42.60  Aligned_cols=29  Identities=14%  Similarity=0.174  Sum_probs=20.6

Q ss_pred             hhcceeeecCCCHHHHHHHHHHHHHHcCC
Q psy879          145 SRCAMLRYNKLTDAQLLSKVIEICEKENI  173 (317)
Q Consensus       145 sR~~~i~f~~~~~~~~~~~l~~~~~~~~~  173 (317)
                      |-|---.|-++.+.+-.++|.++.++.+.
T Consensus       179 s~cfg~PFl~~~p~~ya~lL~~ki~~~~~  207 (313)
T d2olra1         179 SACFGAAFLSLHPTQYAEVLVKRMQAAGA  207 (313)
T ss_dssp             CGGGCGGGCSSCHHHHHHHHHHHHHHHTC
T ss_pred             eeccccccccccHHHHHHHHHHHHHhcCC
Confidence            44444567788888888888888776554

>d1bg2a_ c.37.1.9 (A:) Kinesin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.80  E-value=0.19  Score=41.09  Aligned_cols=42  Identities=21%  Similarity=0.248  Sum_probs=27.2

Q ss_pred             CCCcccC----CHHHHHH----HHHHHhcCCCceEEEECCCCCCHHHHHH
Q psy879            8 TFSDIVG----NEDTVER----LKVFSSSGNVPNIIISGPPGVGKTTTIL   49 (317)
Q Consensus         8 ~~~~~~g----~~~~~~~----l~~~l~~~~~~~~ll~G~~G~GKt~la~   49 (317)
                      +|+.+.+    |+++.+.    +...+-+|.-..++-||+.|+|||++..
T Consensus        45 ~FD~vf~~~~~q~~vf~~~~~~lv~~~l~G~n~~i~aYGqtgSGKTyT~~   94 (323)
T d1bg2a_          45 AFDRVFQSSTSQEQVYNDCAKKIVKDVLEGYNGTIFAYGQTSSGKTHTME   94 (323)
T ss_dssp             ECSEEECTTCCHHHHHHHHTHHHHHHHHTTCCEEEEEECSTTSSHHHHHT
T ss_pred             ECCEEECCCCCHHHHHHHHHHHHHHHHHcCCCcceeeecccCCCCceecc
Confidence            3666655    4454443    3333345664459999999999999863

>d1z3ix2 c.37.1.19 (X:92-389) Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxId: 7955]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Rad54-like, Rad54L
species: Zebra fish (Danio rerio) [TaxId: 7955]

Probab=87.93  E-value=1.9  Score=34.18  Aligned_cols=23  Identities=30%  Similarity=0.432  Sum_probs=17.9

Q ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARIL   55 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~l   55 (317)
                      ..+|.-+.|.|||..+-++...+
T Consensus        81 g~iLaDemGlGKT~qaia~l~~l  103 (298)
T d1z3ix2          81 GCIMADEMGLGKTLQCITLIWTL  103 (298)
T ss_dssp             EEEECCCTTSCHHHHHHHHHHHH
T ss_pred             ceEEEeCCCCCHHHHHHHHHHHH
Confidence            47888899999998776665544

>d1ii2a1 c.91.1.1 (A:201-523) Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase) {Trypanosoma cruzi [TaxId: 5693]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: PEP carboxykinase C-terminal domain
domain: Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase)
species: Trypanosoma cruzi [TaxId: 5693]

Probab=87.54  E-value=0.12  Score=41.94  Aligned_cols=31  Identities=19%  Similarity=0.062  Sum_probs=21.1

Q ss_pred             HhhhcceeeecCCCHHHHHHHHHHHHHHcCC
Q psy879          143 IQSRCAMLRYNKLTDAQLLSKVIEICEKENI  173 (317)
Q Consensus       143 i~sR~~~i~f~~~~~~~~~~~l~~~~~~~~~  173 (317)
                      ..|-|--=.|-++.+..-.+.|.+++++.+.
T Consensus       178 tfs~cfg~PFl~~~p~~ya~~L~~~i~~~~~  208 (323)
T d1ii2a1         178 IFSSCFGGPFLVRHATFYGEQLAEKMQKHNS  208 (323)
T ss_dssp             EECGGGCGGGCCSCHHHHHHHHHHHHHHHTC
T ss_pred             ceeccccccccccChHHHHHHHHHHHHhcCc
Confidence            3444555567777888888888887776554

>d1hyqa_ c.37.1.10 (A:) Cell division regulator MinD {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Cell division regulator MinD
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=87.33  E-value=0.22  Score=38.13  Aligned_cols=34  Identities=26%  Similarity=0.339  Sum_probs=24.9

Q ss_pred             EEECCCCCCHHHHHHHHHHHHcCCCCCCceEEec
Q psy879           35 IISGPPGVGKTTTILCLARILLGPSFKDAVLELN   68 (317)
Q Consensus        35 ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~   68 (317)
                      +..|..|+||||++..+|..+...+.+..+++.+
T Consensus         6 v~s~KGGvGKTtia~nlA~~la~~g~~VlliD~D   39 (232)
T d1hyqa_           6 VASGKGGTGKTTITANLGVALAQLGHDVTIVDAD   39 (232)
T ss_dssp             EEESSSCSCHHHHHHHHHHHHHHTTCCEEEEECC
T ss_pred             EECCCCCChHHHHHHHHHHHHHhCCCCEEEEeCC
Confidence            4458899999999999999986544444445544

>d1e69a_ c.37.1.12 (A:) Smc head domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Smc head domain
species: Thermotoga maritima [TaxId: 2336]

Probab=86.81  E-value=0.46  Score=37.96  Aligned_cols=45  Identities=24%  Similarity=0.358  Sum_probs=38.1

Q ss_pred             CceeEEEEeCCCC-CCHHHHHHHHHHhhhccCCceEEEEecCCCcC
Q psy879           95 GRHKIVILDEADS-MTDGAQQALRRTMEIYSNTTRFALACNNSEKI  139 (317)
Q Consensus        95 ~~~~vliiDE~d~-l~~~~~~~ll~~le~~~~~~~~il~~~~~~~l  139 (317)
                      ....+++|||+|. |.+..+..|.+.+++....+.+|+||+.+.-+
T Consensus       240 ~~~~~~~iDEpe~~Lhp~~~~~l~~~l~~~~~~~QviitTHsp~~~  285 (308)
T d1e69a_         240 KPSPFYVLDEVDSPLDDYNAERFKRLLKENSKHTQFIVITHNKIVM  285 (308)
T ss_dssp             SCCSEEEEESCCSSCCHHHHHHHHHHHHHHTTTSEEEEECCCTTGG
T ss_pred             ccCchhhhhhccccCCHHHHHHHHHHHHHhccCCEEEEEECCHHHH
Confidence            4567999999995 68999999999999888889999999887543

>d1goja_ c.37.1.9 (A:) Kinesin {Neurospora crassa [TaxId: 5141]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Neurospora crassa [TaxId: 5141]

Probab=86.50  E-value=0.29  Score=40.43  Aligned_cols=40  Identities=20%  Similarity=0.273  Sum_probs=26.1

Q ss_pred             CCcccC----CHHHHHH----HHHHHhcCCCceEEEECCCCCCHHHHH
Q psy879            9 FSDIVG----NEDTVER----LKVFSSSGNVPNIIISGPPGVGKTTTI   48 (317)
Q Consensus         9 ~~~~~g----~~~~~~~----l~~~l~~~~~~~~ll~G~~G~GKt~la   48 (317)
                      |+.+.+    |+++-+.    +...+-+|.-..++-||+.|+|||++.
T Consensus        50 FD~vf~~~~~q~~vy~~~~~plv~~~l~G~n~ti~aYG~tgSGKT~Tm   97 (354)
T d1goja_          50 FDRVFDMSCKQSDIFDFSIKPTVDDILNGYNGTVFAYGQTGAGKSYTM   97 (354)
T ss_dssp             CSEEECTTCCHHHHHHHHTHHHHHHHTTTCCEEEEEECSTTSSHHHHH
T ss_pred             CCeEcCCCCCHHHHHHHHHHHHHHHhhccCceeEEecccCCCCcceee
Confidence            666664    5555443    222334566444899999999999885

>d1ry6a_ c.37.1.9 (A:) Kinesin {Malaria parasite (Plasmodium falciparum) [TaxId: 5833]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Malaria parasite (Plasmodium falciparum) [TaxId: 5833]

Probab=85.78  E-value=0.15  Score=41.88  Aligned_cols=41  Identities=27%  Similarity=0.333  Sum_probs=26.9

Q ss_pred             CCcccC----CHHHHHH-----HHHHHhcCCCceEEEECCCCCCHHHHHH
Q psy879            9 FSDIVG----NEDTVER-----LKVFSSSGNVPNIIISGPPGVGKTTTIL   49 (317)
Q Consensus         9 ~~~~~g----~~~~~~~-----l~~~l~~~~~~~~ll~G~~G~GKt~la~   49 (317)
                      |+.+.+    |+++.+.     +...+.+|.-..++-||+.|+|||++..
T Consensus        54 fD~Vf~~~~~q~~vy~~~~~plv~~~~~~G~n~~i~aYGqTGSGKTyTm~  103 (330)
T d1ry6a_          54 VDKVFDDTVDNFTVYENTIKPLIIDLYENGCVCSCFAYGQTGSGKTYTML  103 (330)
T ss_dssp             CSEEECTTCCHHHHHHHHTHHHHHHHHHHCCEEEEEEECCTTSSHHHHHH
T ss_pred             CCeecCCCCCHHHHHHHHHHHHHHHHHhcCCCeEEEeeeccccccceeee
Confidence            555554    5555543     3344555663348899999999999864

>d1x88a1 c.37.1.9 (A:18-362) Kinesin {Human (Homo sapiens), mitotic kinesin eg5 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Human (Homo sapiens), mitotic kinesin eg5 [TaxId: 9606]

Probab=85.33  E-value=0.35  Score=39.78  Aligned_cols=40  Identities=28%  Similarity=0.307  Sum_probs=26.0

Q ss_pred             CCcccC----CHHHHHH----HHHHHhcCCCceEEEECCCCCCHHHHH
Q psy879            9 FSDIVG----NEDTVER----LKVFSSSGNVPNIIISGPPGVGKTTTI   48 (317)
Q Consensus         9 ~~~~~g----~~~~~~~----l~~~l~~~~~~~~ll~G~~G~GKt~la   48 (317)
                      |+.+.+    |+++.+.    +...+-.|.-..++-||+.|+|||++.
T Consensus        51 FD~vf~~~~~q~~vy~~~~~~lv~~~l~G~n~~i~aYGqtgSGKTyTm   98 (345)
T d1x88a1          51 FDMVFGASTKQIDVYRSVVCPILDEVIMGYNCTIFAYGQTGTGKTFTM   98 (345)
T ss_dssp             CSEEECTTCCHHHHHHHHHHHHHHHHHTTCEEEEEEEECTTSSHHHHH
T ss_pred             cCEEeCCCCCHHHHHHHHHHHhHHHHhccCCceEEeeeeccccceEEe
Confidence            566654    4555443    333344566334899999999999876

>d2zfia1 c.37.1.9 (A:4-352) Kinesin {Mouse (Mus musculus), kif1a [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Mouse (Mus musculus), kif1a [TaxId: 10090]

Probab=84.73  E-value=0.42  Score=39.35  Aligned_cols=26  Identities=27%  Similarity=0.310  Sum_probs=19.4

Q ss_pred             HHHHhcCCCceEEEECCCCCCHHHHH
Q psy879           23 KVFSSSGNVPNIIISGPPGVGKTTTI   48 (317)
Q Consensus        23 ~~~l~~~~~~~~ll~G~~G~GKt~la   48 (317)
                      ...+-+|.-..++-||+.|+|||++.
T Consensus        79 v~~~l~G~n~ti~aYGqTgSGKT~Tm  104 (349)
T d2zfia1          79 LQHAFEGYNVCIFAYGQTGAGKSYTM  104 (349)
T ss_dssp             HHHHHTTCCEEEEEECSTTSSHHHHH
T ss_pred             HHHHHhccCceeeeeccCCCCCceee
Confidence            33444566445999999999999986

>d1f9va_ c.37.1.9 (A:) Kinesin motor Ncd (non-claret disjunctional) {Baker's yeast (Saccharomyces cerevisiae), Kar [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin motor Ncd (non-claret disjunctional)
species: Baker's yeast (Saccharomyces cerevisiae), Kar [TaxId: 4932]

Probab=84.60  E-value=0.45  Score=39.00  Aligned_cols=41  Identities=32%  Similarity=0.424  Sum_probs=27.7

Q ss_pred             CCcccC----CHHHHHHHHHHH---hcCCCceEEEECCCCCCHHHHHH
Q psy879            9 FSDIVG----NEDTVERLKVFS---SSGNVPNIIISGPPGVGKTTTIL   49 (317)
Q Consensus         9 ~~~~~g----~~~~~~~l~~~l---~~~~~~~~ll~G~~G~GKt~la~   49 (317)
                      |+.+.+    |+++-+.+...+   -+|.-..++-||+.|+|||++..
T Consensus        54 FD~vf~~~~~q~~vy~~v~~~v~~~l~G~n~~i~aYGqtgSGKT~T~~  101 (342)
T d1f9va_          54 FDKIFDQQDTNVDVFKEVGQLVQSSLDGYNVCIFAYGQTGSGKTFTML  101 (342)
T ss_dssp             ESEEECTTCCHHHHHHHHHHHHGGGGGTCCEEEEEECCTTSSHHHHHH
T ss_pred             cCeEeCCCCCHHHHHHHhhhhhcchhcccccceeeeeccCCccccccc
Confidence            666665    566666554443   34653348889999999998863

>d1g3qa_ c.37.1.10 (A:) Cell division regulator MinD {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Cell division regulator MinD
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=84.00  E-value=0.38  Score=36.68  Aligned_cols=35  Identities=31%  Similarity=0.261  Sum_probs=24.7

Q ss_pred             EEEE-CCCCCCHHHHHHHHHHHHcCCCCCCceEEec
Q psy879           34 IIIS-GPPGVGKTTTILCLARILLGPSFKDAVLELN   68 (317)
Q Consensus        34 ~ll~-G~~G~GKt~la~~la~~l~~~~~~~~~~~~~   68 (317)
                      +.++ +..|+||||++..+|..+...+.+..+++.+
T Consensus         5 Iav~~~kGGvGKTtia~nLA~~la~~g~~VlliD~D   40 (237)
T d1g3qa_           5 ISIVSGKGGTGKTTVTANLSVALGDRGRKVLAVDGD   40 (237)
T ss_dssp             EEEECSSTTSSHHHHHHHHHHHHHHTTCCEEEEECC
T ss_pred             EEEECCCCCCcHHHHHHHHHHHHHhCCCCEEEEeCC
Confidence            4455 6799999999999999986544343344443

>d2ncda_ c.37.1.9 (A:) Kinesin motor Ncd (non-claret disjunctional) {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin motor Ncd (non-claret disjunctional)
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=83.68  E-value=0.25  Score=41.15  Aligned_cols=40  Identities=28%  Similarity=0.357  Sum_probs=25.5

Q ss_pred             CCcccC----CHHHHHHHH---HHHhcCCCceEEEECCCCCCHHHHH
Q psy879            9 FSDIVG----NEDTVERLK---VFSSSGNVPNIIISGPPGVGKTTTI   48 (317)
Q Consensus         9 ~~~~~g----~~~~~~~l~---~~l~~~~~~~~ll~G~~G~GKt~la   48 (317)
                      |+.+.+    |+++-+.+.   ..+-+|.-..++-||+.|+|||++.
T Consensus        96 FD~vf~~~~~Q~~Vy~~v~plv~~vl~G~n~ti~aYGqtGSGKT~Tm  142 (368)
T d2ncda_          96 FDQVFHPLSSQSDIFEMVSPLIQSALDGYNICIFAYGQTGSGKTYTM  142 (368)
T ss_dssp             CSEEECTTCCHHHHHTTTHHHHHHHHTTCEEEEEEECSTTSSHHHHH
T ss_pred             CCeEECCCCCccchHHHHHHHHHHHhcccceeEEeeccCCCccceEe
Confidence            666664    455544322   2233565334899999999999874

>d1sdma_ c.37.1.9 (A:) Kinesin heavy chain-like protein {Potato (Solanum tuberosum) [TaxId: 4113]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin heavy chain-like protein
species: Potato (Solanum tuberosum) [TaxId: 4113]

Probab=83.67  E-value=0.25  Score=41.08  Aligned_cols=40  Identities=28%  Similarity=0.366  Sum_probs=25.9

Q ss_pred             CCcccC----CHHHHHHH---HHHHhcCCCceEEEECCCCCCHHHHH
Q psy879            9 FSDIVG----NEDTVERL---KVFSSSGNVPNIIISGPPGVGKTTTI   48 (317)
Q Consensus         9 ~~~~~g----~~~~~~~l---~~~l~~~~~~~~ll~G~~G~GKt~la   48 (317)
                      |+.+.+    |+++-+.+   ...+-+|.-..++-||+.|+|||++.
T Consensus        46 FD~vf~~~~~q~~vy~~v~~lv~~~l~G~n~~i~aYGqTGSGKTyTm   92 (364)
T d1sdma_          46 YDRVFDGNATQDDVFEDTKYLVQSAVDGYNVCIFAYGQTGSGKTFTI   92 (364)
T ss_dssp             CSEEECTTCCHHHHHHTTTHHHHHHHTTCEEEEEEECSTTSSHHHHH
T ss_pred             CCeecCCCCCHHHHHHHHHHHHHHHhcCCceeeeccccCCCCccccc
Confidence            666654    44555443   23333565334889999999999985

>d1t5la1 c.37.1.19 (A:2-414) Nucleotide excision repair enzyme UvrB {Bacillus caldotenax [TaxId: 1395]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Nucleotide excision repair enzyme UvrB
species: Bacillus caldotenax [TaxId: 1395]

Probab=83.61  E-value=0.71  Score=38.81  Aligned_cols=65  Identities=18%  Similarity=0.198  Sum_probs=44.9

Q ss_pred             CCHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCceEEecCCCCcChHHHHHHHHHH
Q psy879           14 GNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMF   85 (317)
Q Consensus        14 g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~   85 (317)
                      -|+++++.|...+++|. .+.++.|-+|+|||.++-.+++....     +++-+... .....++.+.+..+
T Consensus        15 DQP~aI~~l~~~l~~g~-~~q~l~GltGS~ka~~iA~l~~~~~r-----p~LVVt~n-~~~A~qL~~dL~~~   79 (413)
T d1t5la1          15 DQPQAIAKLVDGLRRGV-KHQTLLGATGTGKTFTISNVIAQVNK-----PTLVIAHN-KTLAGQLYSELKEF   79 (413)
T ss_dssp             THHHHHHHHHHHHHHTC-SEEEEEECTTSCHHHHHHHHHHHHTC-----CEEEECSS-HHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHhcCC-CcEEEeCCCCcHHHHHHHHHHHHhCC-----CEEEEeCC-HHHHHHHHHHHHHH
Confidence            37888999998888775 36889999999999999999888632     23434332 23344455555444

>d1fx0a3 c.37.1.11 (A:97-372) Central domain of alpha subunit of F1 ATP synthase {Spinach (Spinacia oleracea), chloroplast [TaxId: 3562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Central domain of alpha subunit of F1 ATP synthase
species: Spinach (Spinacia oleracea), chloroplast [TaxId: 3562]

Probab=83.34  E-value=2  Score=33.73  Aligned_cols=22  Identities=23%  Similarity=0.110  Sum_probs=18.4

Q ss_pred             eEEEECCCCCCHHHHHHHHHHH
Q psy879           33 NIIISGPPGVGKTTTILCLARI   54 (317)
Q Consensus        33 ~~ll~G~~G~GKt~la~~la~~   54 (317)
                      .+++.|++|+|||+++..++..
T Consensus        69 r~~Ifg~~g~GKt~l~~~~~~~   90 (276)
T d1fx0a3          69 RELIIGDRQTGKTAVATDTILN   90 (276)
T ss_dssp             BCBEEESSSSSHHHHHHHHHHT
T ss_pred             eEeeccCCCCChHHHHHHHHhh
Confidence            4889999999999999876543

>d1v8ka_ c.37.1.9 (A:) Kinesin {Mouse (Mus musculus), kif2c [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Mouse (Mus musculus), kif2c [TaxId: 10090]

Probab=82.93  E-value=0.44  Score=39.47  Aligned_cols=41  Identities=27%  Similarity=0.207  Sum_probs=26.7

Q ss_pred             CCcccC----CHHHHHH----HHHHHhcCCCceEEEECCCCCCHHHHHH
Q psy879            9 FSDIVG----NEDTVER----LKVFSSSGNVPNIIISGPPGVGKTTTIL   49 (317)
Q Consensus         9 ~~~~~g----~~~~~~~----l~~~l~~~~~~~~ll~G~~G~GKt~la~   49 (317)
                      |+.+.+    |+++-+.    +...+-+|.-..++-||+.|+|||++..
T Consensus        84 FD~vf~~~~~Q~~Vy~~~~~plv~~~l~G~n~tifaYGqTGSGKTyTm~  132 (362)
T d1v8ka_          84 FDFAFDETASNEVVYRFTARPLVQTIFEGGKATCFAYGQTGSGKTHTMG  132 (362)
T ss_dssp             CSEEECTTCCHHHHHHHTTHHHHHHHHTTCEEEEEEEESTTSSHHHHHH
T ss_pred             CCeecCCCCCHHHHHHHHHHHHHHHHHhccCceEEeeccCCCCCceeee
Confidence            666665    5555543    3333345653348889999999999863