Citrus Sinensis ID: 012111

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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-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-
Protein Sequence
MHLSNSIFTPPTTATHLPKFYKEPVFRIQAIKRSPGPIQELGIQKEAEKDLSKILRTEFAIKNIEKKVSSKKYKNLWPKPVLEALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAYNALGMTEAAQNLENKMIAMKENSGKKLIQC
Secondary Structure (PSIPRED)
cccccccccccccccccccccccHHHHHHHHHHcccccccHHHHHHHHHHHHHHccHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHcccHHHHHHHHHHHHHcccccccHHHHHHHHHHHHccccHHHHHHHHHHHHHccccccHHHHHHHHHHHHccccHHHHHHHHHHHHHcccccccHHHHHHHHHHHHccccHHHHHHHHHHHHHccccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHccccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHccccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHccccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHccccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHccccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHcccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccHHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHcccccccEEEEHHHHHHHHHHcccHHHHHHHHHHHHHHccccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHccccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHHccccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHccccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHcccccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHccccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHccccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHccccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHccccccEHHHHHHHHHHHHcccHHHHHHHHHHHHHcccccccHHHHHHHHHHHHcccHHHHHHHHHHHHHccccccEEEEcc
Coil and Loop (DISEMBL)
mhlsnsiftppttathlpkfykepvfriqaikrspgpiqelgIQKEAEKDLSKILRTEFAIKNIEKKVSskkyknlwpkpVLEALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYgqsglldeAFSTindmksvsdckpdvyTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVesggchpdifTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSygragmydKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMkhrgmkpnsityCSLVSAYSKAGLIMKVDSILRQvensdvildtpfFNCIISAygqagdveKMGELFLTMKerhcvpdniTFATMIQAYNALGMTEAAQNLENKMIAMKENSGKKLIQC
Flexible Loop (DISEMBL)
mhlsnsiftppttathlpkfYKEPVFRIQAIKrspgpiqelgiqKEAEKDLSKILRTEFAIkniekkvsskkyknlwpKPVLEALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAFSTINdmksvsdckPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIEtfgkaghiEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAYNALGMTEAAQNLENKMIAMkensgkkliqc
Low Complexity Region (SEG)
MHLSNSIFTPPTTATHLPKFYKEPVFRIQAIKRSPGPIQELGIQKEAEKDLSKILRTEFAIKNIEKKVSSKKYKNLWPKPVLEALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAYNALGMTEAAQNLENKMIAMKENSGKKLIQC
Disordered region (IsUnstruct)
**************THLPKFYKEPVFRIQAIK******************LSKILRTEFAIKNIEKKVSSKKYKNLWPKPVLEALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEE****FSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAYNALGMTE***********************
Disordered Region (DISOPRED)
*****************************************GIQKEAEKDLSKILRTEFAIKNIEKKVSSKKYKNLWPKPVLEALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAYNALGMTEAAQNLENKMIAMKENSGKKLIQC
Disordered Region (DISEMBL)
MHLSNSIFTPPTTATHLPKFYKEPVFRIQAIKRSPGPIQELGIQKEAEKDLSKILRTEFAIKNIEKKVSSKKYKNLWPKPVLEALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAYNALGMTEAAQNLENKMIAMKEN********
Disordered Region (DISPRO)
*****SIFTPPTTATHLPKFYKEPVFRIQAIKRSPGPIQELGIQKEAEKDLSKILRTEFAIKNIEKKVSSKKYKNLWPKPVLEALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAYNALGMTEAAQNLENKMIAMKENSGKKLIQC
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MHLSNSIFTPPTTATHLPKFYKEPVFRIQAIKRSPGPIQELGIQKEAEKDLSKILRTEFAIKNIEKKVSSKKYKNLWPKPVLEALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAYNxxxxxxxxxxxxxxxxxxxxxSGKKLIQC
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	471	2.2.26 [Sep-21-2011]
Q9SCP4	447	Pentatricopeptide repeat-	yes	no	0.891	0.939	0.661	1e-171
Q9FKC3	508	Pentatricopeptide repeat-	no	no	0.857	0.795	0.457	1e-102
Q9SQU6	486	Pentatricopeptide repeat-	no	no	0.923	0.895	0.396	5e-96
Q9SV96	563	Pentatricopeptide repeat-	no	no	0.760	0.635	0.261	1e-39
Q9S7Q2	862	Pentatricopeptide repeat-	no	no	0.770	0.421	0.256	2e-38
Q9LYZ9	819	Pentatricopeptide repeat-	no	no	0.777	0.446	0.288	2e-37
Q5G1S8	1440	Pentatricopeptide repeat-	no	no	0.779	0.254	0.266	7e-36
Q9FLD8	678	Pentatricopeptide repeat-	no	no	0.755	0.525	0.248	9e-35
Q8GYP6	860	Pentatricopeptide repeat-	no	no	0.685	0.375	0.278	4e-34
O82178	591	Pentatricopeptide repeat-	no	no	0.745	0.593	0.235	7e-34

>sp|Q9SCP4|PP279_ARATH Pentatricopeptide repeat-containing protein At3g53170 OS=Arabidopsis thaliana GN=At3g53170 PE=2 SV=1

 Score =  600 bits (1547), Expect = e-171,   Method: Compositional matrix adjust.
 Identities = 278/420 (66%), Positives = 345/420 (82%)

Query: 44  QKEAEKDLSKILRTEFAIKNIEKKVSSKKYKNLWPKPVLEALDEAIKQKKWQLALKIFGL 103
           Q + +K+LS+ILRT+ A+K IE+K +S+KY  LWPK VLEALDEAIK+ +WQ ALKIF L
Sbjct: 24  QVDPKKELSRILRTDAAVKGIERKANSEKYLTLWPKAVLEALDEAIKENRWQSALKIFNL 83

Query: 104 LRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSG 163
           LR+Q WY+ RC+T+TKL  +LG CKQP+QASLLFEVMLS+GLKP++DVYT+L+S YG+S 
Sbjct: 84  LRKQHWYEPRCKTYTKLFKVLGNCKQPDQASLLFEVMLSEGLKPTIDVYTSLISVYGKSE 143

Query: 164 LLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTY 223
           LLD+AFST+  MKSVSDCKPDV+T+++LI  C K  RFDL++ I+ EMSYLG+ CS VTY
Sbjct: 144 LLDKAFSTLEYMKSVSDCKPDVFTFTVLISCCCKLGRFDLVKSIVLEMSYLGVGCSTVTY 203

Query: 224 NTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFN 283
           NTIIDGYGKA  FEEMES  + M+E G   PD+ TLNS+I +YGN  N+ KME WY+ F 
Sbjct: 204 NTIIDGYGKAGMFEEMESVLADMIEDGDSLPDVCTLNSIIGSYGNGRNMRKMESWYSRFQ 263

Query: 284 LMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIE 343
           LMGV+ DI T NIL  S+G+AGMY KM SVMDFM+KRFF  T VTYNIVIETFGKAG IE
Sbjct: 264 LMGVQPDITTFNILILSFGKAGMYKKMCSVMDFMEKRFFSLTTVTYNIVIETFGKAGRIE 323

Query: 344 KMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCII 403
           KM++ F+KMK++G+KPNSITYCSLV+AYSKAGL++K+DS+LRQ+ NSDV+LDTPFFNCII
Sbjct: 324 KMDDVFRKMKYQGVKPNSITYCSLVNAYSKAGLVVKIDSVLRQIVNSDVVLDTPFFNCII 383

Query: 404 SAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAYNALGMTEAAQNLENKMIAMKEN 463
           +AYGQAGD+  M EL++ M+ER C PD ITFATMI+ Y A G+ +A Q LE +MI+  EN
Sbjct: 384 NAYGQAGDLATMKELYIQMEERKCKPDKITFATMIKTYTAHGIFDAVQELEKQMISSGEN 443

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FKC3|PP424_ARATH Pentatricopeptide repeat-containing protein At5g48730, chloroplastic OS=Arabidopsis thaliana GN=At5g48730 PE=2 SV=2

 Score =  371 bits (953), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 186/407 (45%), Positives = 268/407 (65%), Gaps = 3/407 (0%)

Query: 47  AEKDLSKILRTEFAIKNIEKKVSSKKYKNLWPKPVLEALDEAIKQKKWQLALKIFGLLRQ 106
           + K +S ILR E     IEKK  SKK   L P+ VLE+L E I   +W+ A+++F LLR+
Sbjct: 86  SRKAISIILRREATKSIIEKKKGSKK---LLPRTVLESLHERITALRWESAIQVFELLRE 142

Query: 107 QQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLD 166
           Q WY+     + KL+VMLGKCKQPE+A  LF+ M+++G   + +VYTALVSAY +SG  D
Sbjct: 143 QLWYKPNVGIYVKLIVMLGKCKQPEKAHELFQEMINEGCVVNHEVYTALVSAYSRSGRFD 202

Query: 167 EAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTI 226
            AF+ +  MKS  +C+PDV+TYSILIKS  +   FD ++ +L++M   GI  + +TYNT+
Sbjct: 203 AAFTLLERMKSSHNCQPDVHTYSILIKSFLQVFAFDKVQDLLSDMRRQGIRPNTITYNTL 262

Query: 227 IDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMG 286
           ID YGKAK F EMES+   M+    C PD +T+NS + A+G +G IE ME  Y +F   G
Sbjct: 263 IDAYGKAKMFVEMESTLIQMLGEDDCKPDSWTMNSTLRAFGGNGQIEMMENCYEKFQSSG 322

Query: 287 VKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKME 346
           ++ +I+T NIL  SYG++G Y KM +VM++MQK  +  T+VTYN+VI+ FG+AG +++ME
Sbjct: 323 IEPNIRTFNILLDSYGKSGNYKKMSAVMEYMQKYHYSWTIVTYNVVIDAFGRAGDLKQME 382

Query: 347 EYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAY 406
             F+ M+   + P+ +T CSLV AY +A    K+  +LR +ENSD+ LD  FFNC++ AY
Sbjct: 383 YLFRLMQSERIFPSCVTLCSLVRAYGRASKADKIGGVLRFIENSDIRLDLVFFNCLVDAY 442

Query: 407 GQAGDVEKMGELFLTMKERHCVPDNITFATMIQAYNALGMTEAAQNL 453
           G+     +M  +   M+++   PD IT+ TM++AY   GMT   + L
Sbjct: 443 GRMEKFAEMKGVLELMEKKGFKPDKITYRTMVKAYRISGMTTHVKEL 489

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SQU6|PP216_ARATH Pentatricopeptide repeat-containing protein At3g06430, chloroplastic OS=Arabidopsis thaliana GN=EMB2750 PE=2 SV=1

 Score =  352 bits (902), Expect = 5e-96,   Method: Compositional matrix adjust.
 Identities = 176/444 (39%), Positives = 275/444 (61%), Gaps = 9/444 (2%)

Query: 28  IQAIKRSPGPIQELGIQKEAE--KDLSKILRTEFAIKNIEKKVSSKKYKNLWPKPVLEAL 85
           + A K SPG + +  + K+ E       + +    IKN++KK+  +   N W   V E L
Sbjct: 36  LAASKSSPGSVTKKRLWKDGEFPGITEPVNQRRTPIKNVKKKLDRRSKANGWVNTVTETL 95

Query: 86  DEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGL 145
            + I +K+W  AL++F +LR+Q +YQ +  T+ KL+V+LGK  QP +A  LF+ ML +GL
Sbjct: 96  SDLIAKKQWLQALEVFDMLREQTFYQPKEGTYMKLLVLLGKSGQPNRAQKLFDEMLEEGL 155

Query: 146 KPSVDVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIE 205
           +P+V++YTAL++AY +S L+D+AFS ++ MKS   C+PDV+TYS L+K+C    +FDL++
Sbjct: 156 EPTVELYTALLAAYTRSNLIDDAFSILDKMKSFPQCQPDVFTYSTLLKACVDASQFDLVD 215

Query: 206 KILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISA 265
            +  EM    I  + VT N ++ GYG+  +F++ME   S M+ S  C PD++T+N ++S 
Sbjct: 216 SLYKEMDERLITPNTVTQNIVLSGYGRVGRFDQMEKVLSDMLVSTACKPDVWTMNIILSV 275

Query: 266 YGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPT 325
           +GN G I+ ME WY +F   G++ + +T NIL  SYG+  MYDKM SVM++M+K  F  T
Sbjct: 276 FGNMGKIDMMESWYEKFRNFGIEPETRTFNILIGSYGKKRMYDKMSSVMEYMRKLEFPWT 335

Query: 326 VVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILR 385
             TYN +IE F   G  + ME  F +M+  GMK ++ T+C L++ Y+ AGL  KV S ++
Sbjct: 336 TSTYNNIIEAFADVGDAKNMELTFDQMRSEGMKADTKTFCCLINGYANAGLFHKVISSVQ 395

Query: 386 QVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAYNALG 445
                ++  +T F+N +ISA  +A D+ +M  +++ MKER CV D+ TF  M++AY   G
Sbjct: 396 LAAKFEIPENTAFYNAVISACAKADDLIEMERVYIRMKERQCVCDSRTFEIMVEAYEKEG 455

Query: 446 MTE-------AAQNLENKMIAMKE 462
           M +         Q L ++ +A KE
Sbjct: 456 MNDKIYYLEQERQKLMDRTVATKE 479

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SV96|PP358_ARATH Pentatricopeptide repeat-containing protein At4g39620, chloroplastic OS=Arabidopsis thaliana GN=EMB2453 PE=2 SV=1

 Score =  164 bits (415), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 95/363 (26%), Positives = 176/363 (48%), Gaps = 5/363 (1%)

Query: 85  LDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDG 144
            +E  K  KW   L++F  +++Q+WY      ++KL+ ++GK  Q   A  LF  M + G
Sbjct: 104 FEELGKSDKWLQCLEVFRWMQKQRWYIPDNGVYSKLISVMGKKGQTRMAMWLFSEMKNSG 163

Query: 145 LKPSVDVYTALVSAY----GQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHR 200
            +P   VY AL++A+     ++  L++    ++ MK +  C+P+V TY+IL+++  +  +
Sbjct: 164 CRPDASVYNALITAHLHTRDKAKALEKVRGYLDKMKGIERCQPNVVTYNILLRAFAQSGK 223

Query: 201 FDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLN 260
            D +  +  ++    +     T+N ++D YGK    +EME+  + M  S  C PDI T N
Sbjct: 224 VDQVNALFKDLDMSPVSPDVYTFNGVMDAYGKNGMIKEMEAVLTRM-RSNECKPDIITFN 282

Query: 261 SMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKR 320
            +I +YG     EKME+ +        K  + T N +  +YG+A M DK   V   M   
Sbjct: 283 VLIDSYGKKQEFEKMEQTFKSLMRSKEKPTLPTFNSMIINYGKARMIDKAEWVFKKMNDM 342

Query: 321 FFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKV 380
            + P+ +TY  +I  +G  G + +  E F+++        + T  +++  Y + GL ++ 
Sbjct: 343 NYIPSFITYECMIMMYGYCGSVSRAREIFEEVGESDRVLKASTLNAMLEVYCRNGLYIEA 402

Query: 381 DSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQA 440
           D +        V  D   +  +  AY +A   E++  L   M++   VP+   F   ++ 
Sbjct: 403 DKLFHNASAFRVHPDASTYKFLYKAYTKADMKEQVQILMKKMEKDGIVPNKRFFLEALEV 462

Query: 441 YNA 443
           + +
Sbjct: 463 FGS 465

May play a role in embryogenesis.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9S7Q2|PP124_ARATH Pentatricopeptide repeat-containing protein At1g74850, chloroplastic OS=Arabidopsis thaliana GN=PTAC2 PE=2 SV=1

 Score =  160 bits (405), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 103/401 (25%), Positives = 200/401 (49%), Gaps = 38/401 (9%)

Query: 94  WQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYT 153
           WQ +L++F  +++Q W +     +T ++ +LG+    ++   +F+ M S G+  SV  YT
Sbjct: 121 WQRSLRLFKYMQRQIWCKPNEHIYTIMISLLGREGLLDKCLEVFDEMPSQGVSRSVFSYT 180

Query: 154 ALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFH-RFDLIEKILAEMS 212
           AL++AYG++G  + +   ++ MK+     P + TY+ +I +C +    ++ +  + AEM 
Sbjct: 181 ALINAYGRNGRYETSLELLDRMKN-EKISPSILTYNTVINACARGGLDWEGLLGLFAEMR 239

Query: 213 YLGIECSAVTYNTII--------------------DG---------------YGKAKKFE 237
           + GI+   VTYNT++                    DG               +GK ++ E
Sbjct: 240 HEGIQPDIVTYNTLLSACAIRGLGDEAEMVFRTMNDGGIVPDLTTYSHLVETFGKLRRLE 299

Query: 238 EMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNIL 297
           ++      M  SGG  PDI + N ++ AY  SG+I++    +++    G   +  T ++L
Sbjct: 300 KVCDLLGEMA-SGGSLPDITSYNVLLEAYAKSGSIKEAMGVFHQMQAAGCTPNANTYSVL 358

Query: 298 TKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGM 357
              +G++G YD +R +   M+     P   TYNI+IE FG+ G+ +++   F  M    +
Sbjct: 359 LNLFGQSGRYDDVRQLFLEMKSSNTDPDAATYNILIEVFGEGGYFKEVVTLFHDMVEENI 418

Query: 358 KPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGE 417
           +P+  TY  ++ A  K GL      IL+ +  +D++  +  +  +I A+GQA   E+   
Sbjct: 419 EPDMETYEGIIFACGKGGLHEDARKILQYMTANDIVPSSKAYTGVIEAFGQAALYEEALV 478

Query: 418 LFLTMKERHCVPDNITFATMIQAYNALGMTEAAQNLENKMI 458
            F TM E    P   TF +++ ++   G+ + ++ + ++++
Sbjct: 479 AFNTMHEVGSNPSIETFHSLLYSFARGGLVKESEAILSRLV 519

Involved in plastid gene expression.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LYZ9|PP362_ARATH Pentatricopeptide repeat-containing protein At5g02860 OS=Arabidopsis thaliana GN=At5g02860 PE=2 SV=1

 Score =  157 bits (396), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 107/371 (28%), Positives = 179/371 (48%), Gaps = 5/371 (1%)

Query: 91  QKKWQLALKIFGLLRQQQWYQARCQTFTKLMV--MLGKCKQPEQASLLFEVMLSDGLKPS 148
            KK+ LAL+ F    +Q+ YQ+        ++  MLGK  +   A+ +F  +  DG    
Sbjct: 148 HKKFDLALRAFDWFMKQKDYQSMLDNSVVAIIISMLGKEGRVSSAANMFNGLQEDGFSLD 207

Query: 149 VDVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHR-FDLIEKI 207
           V  YT+L+SA+  SG   EA +    M+    CKP + TY++++    K    ++ I  +
Sbjct: 208 VYSYTSLISAFANSGRYREAVNVFKKMEE-DGCKPTLITYNVILNVFGKMGTPWNKITSL 266

Query: 208 LAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYG 267
           + +M   GI   A TYNT+I    +    +E    F  M  +G  + D  T N+++  YG
Sbjct: 267 VEKMKSDGIAPDAYTYNTLITCCKRGSLHQEAAQVFEEMKAAGFSY-DKVTYNALLDVYG 325

Query: 268 NSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVV 327
            S   ++  K  NE  L G    I T N L  +Y R GM D+   + + M ++   P V 
Sbjct: 326 KSHRPKEAMKVLNEMVLNGFSPSIVTYNSLISAYARDGMLDEAMELKNQMAEKGTKPDVF 385

Query: 328 TYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQV 387
           TY  ++  F +AG +E     F++M++ G KPN  T+ + +  Y   G   ++  I  ++
Sbjct: 386 TYTTLLSGFERAGKVESAMSIFEEMRNAGCKPNICTFNAFIKMYGNRGKFTEMMKIFDEI 445

Query: 388 ENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAYNALGMT 447
               +  D   +N +++ +GQ G   ++  +F  MK    VP+  TF T+I AY+  G  
Sbjct: 446 NVCGLSPDIVTWNTLLAVFGQNGMDSEVSGVFKEMKRAGFVPERETFNTLISAYSRCGSF 505

Query: 448 EAAQNLENKMI 458
           E A  +  +M+
Sbjct: 506 EQAMTVYRRML 516

Arabidopsis thaliana (taxid: 3702)

>sp|Q5G1S8|PP241_ARATH Pentatricopeptide repeat-containing protein At3g18110, chloroplastic OS=Arabidopsis thaliana GN=EMB1270 PE=2 SV=2

 Score =  152 bits (383), Expect = 7e-36,   Method: Compositional matrix adjust.
 Identities = 101/379 (26%), Positives = 181/379 (47%), Gaps = 12/379 (3%)

Query: 87  EAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLF---EVMLSD 143
           +++ Q+ WQ AL++F  L  + W+    +    ++ +LG+  Q   A  +F   E  + D
Sbjct: 164 KSVGQESWQRALEVFEWLNLRHWHSPNARMVAAILGVLGRWNQESLAVEIFTRAEPTVGD 223

Query: 144 GLKPSVDVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRF-- 201
                V VY A++  Y +SG   +A   ++ M+    C PD+ +++ LI +  K      
Sbjct: 224 ----RVQVYNAMMGVYSRSGKFSKAQELVDAMRQ-RGCVPDLISFNTLINARLKSGGLTP 278

Query: 202 DLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNS 261
           +L  ++L  +   G+   A+TYNT++    +    +     F  M E+  C PD++T N+
Sbjct: 279 NLAVELLDMVRNSGLRPDAITYNTLLSACSRDSNLDGAVKVFEDM-EAHRCQPDLWTYNA 337

Query: 262 MISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRF 321
           MIS YG  G   + E+ + E  L G   D  T N L  ++ R    +K++ V   MQK  
Sbjct: 338 MISVYGRCGLAAEAERLFMELELKGFFPDAVTYNSLLYAFARERNTEKVKEVYQQMQKMG 397

Query: 322 FFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKH-RGMKPNSITYCSLVSAYSKAGLIMKV 380
           F    +TYN +I  +GK G ++   + +K MK   G  P++ITY  L+ +  KA   ++ 
Sbjct: 398 FGKDEMTYNTIIHMYGKQGQLDLALQLYKDMKGLSGRNPDAITYTVLIDSLGKANRTVEA 457

Query: 381 DSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQA 440
            +++ ++ +  +      ++ +I  Y +AG  E+  + F  M      PDN+ ++ M+  
Sbjct: 458 AALMSEMLDVGIKPTLQTYSALICGYAKAGKREEAEDTFSCMLRSGTKPDNLAYSVMLDV 517

Query: 441 YNALGMTEAAQNLENKMIA 459
                 T  A  L   MI+
Sbjct: 518 LLRGNETRKAWGLYRDMIS 536

May play a role in embryogenesis.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FLD8|PP408_ARATH Pentatricopeptide repeat-containing protein At5g39980, chloroplastic OS=Arabidopsis thaliana GN=At5g39980 PE=2 SV=1

 Score =  148 bits (373), Expect = 9e-35,   Method: Compositional matrix adjust.
 Identities = 98/395 (24%), Positives = 179/395 (45%), Gaps = 39/395 (9%)

Query: 90  KQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSV 149
           ++  WQ +L +   + ++  Y      +  ++  + + KQ + A  LF+ M    L P  
Sbjct: 131 RENDWQRSLALLDWVHEEAKYTPSVFAYNVVLRNVLRAKQFDIAHGLFDEMRQRALAPDR 190

Query: 150 DVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILA 209
             Y+ L++++G+ G+ D A S +  M+       D+  YS LI+   +   +     I +
Sbjct: 191 YTYSTLITSFGKEGMFDSALSWLQKMEQ-DRVSGDLVLYSNLIELSRRLCDYSKAISIFS 249

Query: 210 EMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESG------------------- 250
            +   GI    V YN++I+ YGKAK F E       M E+G                   
Sbjct: 250 RLKRSGITPDLVAYNSMINVYGKAKLFREARLLIKEMNEAGVLPNTVSYSTLLSVYVENH 309

Query: 251 ---------------GCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLN 295
                           C  D+ T N MI  YG    +++ ++ +     M ++ ++ + N
Sbjct: 310 KFLEALSVFAEMKEVNCALDLTTCNIMIDVYGQLDMVKEADRLFWSLRKMDIEPNVVSYN 369

Query: 296 ILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHR 355
            + + YG A ++ +   +   MQ++     VVTYN +I+ +GK    EK     ++M+ R
Sbjct: 370 TILRVYGEAELFGEAIHLFRLMQRKDIEQNVVTYNTMIKIYGKTMEHEKATNLVQEMQSR 429

Query: 356 GMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKM 415
           G++PN+ITY +++S + KAG + +  ++ +++ +S V +D   +  +I AY + G +   
Sbjct: 430 GIEPNAITYSTIISIWGKAGKLDRAATLFQKLRSSGVEIDQVLYQTMIVAYERVGLMGHA 489

Query: 416 GELFLTMKERHCVPDNITFATMIQAYNALGMTEAA 450
             L   +K    +PDNI   T I      G TE A
Sbjct: 490 KRLLHELK----LPDNIPRETAITILAKAGRTEEA 520

Arabidopsis thaliana (taxid: 3702)

>sp|Q8GYP6|PPR49_ARATH Pentatricopeptide repeat-containing protein At1g18900 OS=Arabidopsis thaliana GN=At1g18900 PE=1 SV=1

 Score =  146 bits (368), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 94/338 (27%), Positives = 165/338 (48%), Gaps = 15/338 (4%)

Query: 63  NIEKKVSSKKYKNLWPKPVLEAL------------DEAIKQ-KKWQLALKIFGLLRQQQW 109
           +I + VSS   +  W     EAL            ++ +KQ   +  AL  F  L++Q  
Sbjct: 300 HIVENVSSVLRRFRWGPAAEEALQNLGLRIDAYQANQVLKQMNDYGNALGFFYWLKRQPG 359

Query: 110 YQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAF 169
           ++    T+T ++  LG+ KQ    + L + M+ DG +P+   Y  L+ +YG++  L+EA 
Sbjct: 360 FKHDGHTYTTMVGNLGRAKQFGAINKLLDEMVRDGCQPNTVTYNRLIHSYGRANYLNEAM 419

Query: 170 STINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDG 229
           +  N M+  + CKPD  TY  LI    K    D+   +   M   G+     TY+ II+ 
Sbjct: 420 NVFNQMQE-AGCKPDRVTYCTLIDIHAKAGFLDIAMDMYQRMQAGGLSPDTFTYSVIINC 478

Query: 230 YGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKA 289
            GKA         F  MV+  GC P++ T N M+  +  + N +   K Y +    G + 
Sbjct: 479 LGKAGHLPAAHKLFCEMVDQ-GCTPNLVTYNIMMDLHAKARNYQNALKLYRDMQNAGFEP 537

Query: 290 DIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYF 349
           D  T +I+ +  G  G  ++  +V   MQ++ + P    Y ++++ +GKAG++EK  +++
Sbjct: 538 DKVTYSIVMEVLGHCGYLEEAEAVFTEMQQKNWIPDEPVYGLLVDLWGKAGNVEKAWQWY 597

Query: 350 KKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQV 387
           + M H G++PN  T  SL+S + +   I +   +L+ +
Sbjct: 598 QAMLHAGLRPNVPTCNSLLSTFLRVNKIAEAYELLQNM 635

Arabidopsis thaliana (taxid: 3702)

>sp|O82178|PP186_ARATH Pentatricopeptide repeat-containing protein At2g35130 OS=Arabidopsis thaliana GN=At2g35130 PE=2 SV=1

 Score =  145 bits (366), Expect = 7e-34,   Method: Compositional matrix adjust.
 Identities = 92/390 (23%), Positives = 184/390 (47%), Gaps = 39/390 (10%)

Query: 91  QKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVD 150
            KKW   + +   + ++  +Q     F  L+   G+  Q ++A  L+  +L     P+ D
Sbjct: 132 NKKWDSIILVCEWILRKSSFQPDVICFNLLIDAYGQKFQYKEAESLYVQLLESRYVPTED 191

Query: 151 VYTALVSAYGQSGLLDEAFSTINDMKS--------------------------------- 177
            Y  L+ AY  +GL++ A   + +M++                                 
Sbjct: 192 TYALLIKAYCMAGLIERAEVVLVEMQNHHVSPKTIGVTVYNAYIEGLMKRKGNTEEAIDV 251

Query: 178 -----VSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGK 232
                   CKP   TY+++I    K  +  +  K+  EM     + +  TY  +++ + +
Sbjct: 252 FQRMKRDRCKPTTETYNLMINLYGKASKSYMSWKLYCEMRSHQCKPNICTYTALVNAFAR 311

Query: 233 AKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQ 292
               E+ E  F  + E G   PD++  N+++ +Y  +G      + ++    MG + D  
Sbjct: 312 EGLCEKAEEIFEQLQEDG-LEPDVYVYNALMESYSRAGYPYGAAEIFSLMQHMGCEPDRA 370

Query: 293 TLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKM 352
           + NI+  +YGRAG++    +V + M++    PT+ ++ +++  + KA  + K E   K+M
Sbjct: 371 SYNIMVDAYGRAGLHSDAEAVFEEMKRLGIAPTMKSHMLLLSAYSKARDVTKCEAIVKEM 430

Query: 353 KHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDV 412
              G++P++    S+++ Y + G   K++ IL ++EN     D   +N +I+ YG+AG +
Sbjct: 431 SENGVEPDTFVLNSMLNLYGRLGQFTKMEKILAEMENGPCTADISTYNILINIYGKAGFL 490

Query: 413 EKMGELFLTMKERHCVPDNITFATMIQAYN 442
           E++ ELF+ +KE++  PD +T+ + I AY+
Sbjct: 491 ERIEELFVELKEKNFRPDVVTWTSRIGAYS 520

Arabidopsis thaliana (taxid: 3702)

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	471
297736301	485	unnamed protein product [Vitis vinifera]	0.949	0.921	0.732	0.0
359487410	538	PREDICTED: pentatricopeptide repeat-cont	0.940	0.823	0.731	0.0
255553476	486	pentatricopeptide repeat-containing prot	0.980	0.950	0.680	0.0
224104097	474	predicted protein [Populus trichocarpa]	0.978	0.972	0.677	0.0
356552149	481	PREDICTED: pentatricopeptide repeat-cont	0.980	0.960	0.669	0.0
357458279	511	Pentatricopeptide repeat-containing prot	0.966	0.890	0.672	0.0
449436321	477	PREDICTED: pentatricopeptide repeat-cont	0.893	0.882	0.686	1e-177
75265624	447	RecName: Full=Pentatricopeptide repeat-c	0.891	0.939	0.661	1e-169
334185941	499	tetratricopeptide repeat domain-containi	0.895	0.845	0.658	1e-168
297820044	439	pentatricopeptide repeat-containing prot	0.868	0.931	0.633	1e-156

>gi|297736301|emb|CBI24939.3| unnamed protein product [Vitis vinifera]

 Score =  696 bits (1795), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 328/448 (73%), Positives = 380/448 (84%), Gaps = 1/448 (0%)

Query: 24  PVFRIQAIKRSPGPIQELGIQKEAEKDLSKILRTEFAIKNIEKKVSSKKYKNLWPKPVLE 83
           P   ++A KRS G  Q  G+Q++ +KDLS+ILRTE AI  IE+K +S+KY  LWPK VLE
Sbjct: 39  PFLFVRAGKRSSGSSQN-GLQRQPKKDLSRILRTEAAISGIERKANSRKYSTLWPKAVLE 97

Query: 84  ALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSD 143
           ALDEAI++ +++ ALKIFGLLR+Q WY+ RCQT+TKL++MLGKCKQPEQASLLFEVMLS+
Sbjct: 98  ALDEAIRENRYESALKIFGLLRKQHWYEPRCQTYTKLLMMLGKCKQPEQASLLFEVMLSE 157

Query: 144 GLKPSVDVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDL 203
           GL+P++DVYTALVSAYG SG LD+AF T+ DMKSVSDCKPDVYTYSILIK CT   RFDL
Sbjct: 158 GLRPTLDVYTALVSAYGHSGQLDKAFCTVEDMKSVSDCKPDVYTYSILIKCCTTLGRFDL 217

Query: 204 IEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMI 263
           IE+I  EMSYLGIECS VTYNTIIDGYGKA  FE MESS + M+ESG C PDIFTLNS I
Sbjct: 218 IERIFTEMSYLGIECSTVTYNTIIDGYGKADMFELMESSLTEMIESGTCLPDIFTLNSFI 277

Query: 264 SAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFF 323
            AYGNSG IEKMEKWY+EF LMG++ DI+T NIL +SYG+A MY+KM SVM+FM+KRF+ 
Sbjct: 278 WAYGNSGQIEKMEKWYDEFQLMGIRPDIKTFNILIRSYGKACMYEKMVSVMEFMKKRFYS 337

Query: 324 PTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSI 383
           PT+VT+NIVIE FG+ G+IEKMEE+F KMKH+G+KPNSITYCSLVSAYSKAG + KVDSI
Sbjct: 338 PTIVTFNIVIEMFGRVGNIEKMEEFFLKMKHQGVKPNSITYCSLVSAYSKAGYLKKVDSI 397

Query: 384 LRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAYNA 443
           LRQ+ENSDV LDTPFFNC++SAYGQAGDVE+MGELFL MKER C PDNITFATMIQAYNA
Sbjct: 398 LRQIENSDVTLDTPFFNCVLSAYGQAGDVERMGELFLVMKERKCKPDNITFATMIQAYNA 457

Query: 444 LGMTEAAQNLENKMIAMKENSGKKLIQC 471
            GM EAAQNLE  MI  K  SG +LI C
Sbjct: 458 QGMIEAAQNLEVNMITTKNKSGTRLIGC 485

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359487410|ref|XP_002273156.2| PREDICTED: pentatricopeptide repeat-containing protein At3g53170-like [Vitis vinifera]

 Score =  689 bits (1778), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 325/444 (73%), Positives = 377/444 (84%), Gaps = 1/444 (0%)

Query: 24  PVFRIQAIKRSPGPIQELGIQKEAEKDLSKILRTEFAIKNIEKKVSSKKYKNLWPKPVLE 83
           P   ++A KRS G  Q  G+Q++ +KDLS+ILRTE AI  IE+K +S+KY  LWPK VLE
Sbjct: 39  PFLFVRAGKRSSGSSQN-GLQRQPKKDLSRILRTEAAISGIERKANSRKYSTLWPKAVLE 97

Query: 84  ALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSD 143
           ALDEAI++ +++ ALKIFGLLR+Q WY+ RCQT+TKL++MLGKCKQPEQASLLFEVMLS+
Sbjct: 98  ALDEAIRENRYESALKIFGLLRKQHWYEPRCQTYTKLLMMLGKCKQPEQASLLFEVMLSE 157

Query: 144 GLKPSVDVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDL 203
           GL+P++DVYTALVSAYG SG LD+AF T+ DMKSVSDCKPDVYTYSILIK CT   RFDL
Sbjct: 158 GLRPTLDVYTALVSAYGHSGQLDKAFCTVEDMKSVSDCKPDVYTYSILIKCCTTLGRFDL 217

Query: 204 IEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMI 263
           IE+I  EMSYLGIECS VTYNTIIDGYGKA  FE MESS + M+ESG C PDIFTLNS I
Sbjct: 218 IERIFTEMSYLGIECSTVTYNTIIDGYGKADMFELMESSLTEMIESGTCLPDIFTLNSFI 277

Query: 264 SAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFF 323
            AYGNSG IEKMEKWY+EF LMG++ DI+T NIL +SYG+A MY+KM SVM+FM+KRF+ 
Sbjct: 278 WAYGNSGQIEKMEKWYDEFQLMGIRPDIKTFNILIRSYGKACMYEKMVSVMEFMKKRFYS 337

Query: 324 PTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSI 383
           PT+VT+NIVIE FG+ G+IEKMEE+F KMKH+G+KPNSITYCSLVSAYSKAG + KVDSI
Sbjct: 338 PTIVTFNIVIEMFGRVGNIEKMEEFFLKMKHQGVKPNSITYCSLVSAYSKAGYLKKVDSI 397

Query: 384 LRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAYNA 443
           LRQ+ENSDV LDTPFFNC++SAYGQAGDVE+MGELFL MKER C PDNITFATMIQAYNA
Sbjct: 398 LRQIENSDVTLDTPFFNCVLSAYGQAGDVERMGELFLVMKERKCKPDNITFATMIQAYNA 457

Query: 444 LGMTEAAQNLENKMIAMKENSGKK 467
            GM EAAQNLE  MI  K  SG +
Sbjct: 458 QGMIEAAQNLEVNMITTKNKSGTR 481

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255553476|ref|XP_002517779.1| pentatricopeptide repeat-containing protein, putative [Ricinus communis] gi|223543051|gb|EEF44586.1| pentatricopeptide repeat-containing protein, putative [Ricinus communis]

 Score =  673 bits (1736), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 321/472 (68%), Positives = 387/472 (81%), Gaps = 10/472 (2%)

Query: 1   MHLSNSIFTPPTTATHLPKFYKE-------PVFRIQAIKRSPGPIQELGIQKEAEKDLSK 53
           ++ S SI TPPT   HL K  KE       P+  I +   S   I  +G ++  +K+LS+
Sbjct: 11  LYWSYSISTPPTI--HLIKVLKERNFHSDPPILGIHSSNLSSDLIP-VGPKRHTKKELSR 67

Query: 54  ILRTEFAIKNIEKKVSSKKYKNLWPKPVLEALDEAIKQKKWQLALKIFGLLRQQQWYQAR 113
            LRT+ AIK IE+K  S KY  LWPK VLEALD+AIK+++W+ ALKIF LLR+Q WY+ R
Sbjct: 68  FLRTDAAIKAIEQKADSSKYNRLWPKAVLEALDDAIKERRWKSALKIFELLRKQHWYEPR 127

Query: 114 CQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAFSTIN 173
           CQT+TKL++MLGKC+QPE+A LLFEVM ++GL+P++DVYTALVSAYG+SGLL +AFST++
Sbjct: 128 CQTYTKLLMMLGKCRQPEEARLLFEVMQTEGLRPTIDVYTALVSAYGESGLLAKAFSTVD 187

Query: 174 DMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKA 233
           +MKSVSDCKPDVYTYS+LI  CTK HRFDLI +IL+EMSYLG+ECS VT+NTII+GYGKA
Sbjct: 188 EMKSVSDCKPDVYTYSVLINICTKLHRFDLIGRILSEMSYLGVECSTVTFNTIINGYGKA 247

Query: 234 KKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQT 293
           K F EME+S + M+E G   PD+FT NS+I AYGNSG IEKMEKWYNEF LMG+  DI+T
Sbjct: 248 KMFREMENSLTNMIEIGNSVPDLFTFNSVIGAYGNSGRIEKMEKWYNEFQLMGISPDIKT 307

Query: 294 LNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMK 353
            NIL KSYG+AGMY+K+ SV++FM+KRFF PTVVTYNI+IETFG+AG IE M+EYFK MK
Sbjct: 308 FNILIKSYGKAGMYEKINSVIEFMKKRFFPPTVVTYNIIIETFGRAGDIENMDEYFKTMK 367

Query: 354 HRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVE 413
           H GMKPN+ITYCSLVSAYSKAGL+MKV+SILRQVENSDV+LDT FFNCII+AYGQAGDV+
Sbjct: 368 HLGMKPNAITYCSLVSAYSKAGLLMKVNSILRQVENSDVVLDTTFFNCIINAYGQAGDVD 427

Query: 414 KMGELFLTMKERHCVPDNITFATMIQAYNALGMTEAAQNLENKMIAMKENSG 465
           KM ELFL M+ER C+PDN+TFATMIQAY   GMTEAAQ LE  M+A K NSG
Sbjct: 428 KMAELFLEMRERECMPDNVTFATMIQAYRGQGMTEAAQALEKMMLAAKGNSG 479

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224104097|ref|XP_002313317.1| predicted protein [Populus trichocarpa] gi|222849725|gb|EEE87272.1| predicted protein [Populus trichocarpa]

 Score =  672 bits (1733), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 321/474 (67%), Positives = 386/474 (81%), Gaps = 13/474 (2%)

Query: 1   MHLSNSIFTPPT-------TATHLPKFYKEPVFRIQAIKRSPGPIQELGIQKEAEKDLSK 53
           M  S SI TPP+            P+F       IQ+ K  P P    G+Q++++K+LS+
Sbjct: 1   MSWSLSISTPPSKNLLTGSNGNQDPQF-----LTIQSSKWCPDPTST-GLQRQSKKELSR 54

Query: 54  ILRTEFAIKNIEKKVSSKKYKNLWPKPVLEALDEAIKQKKWQLALKIFGLLRQQQWYQAR 113
           ILRTE AIK IE+K +SKKY NLWPK VLEALD+AIK+ +W+ ALKIF LLR+Q WY+ R
Sbjct: 55  ILRTEAAIKAIEQKANSKKYNNLWPKAVLEALDDAIKENQWESALKIFELLRKQHWYEPR 114

Query: 114 CQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAFSTIN 173
            +T+TKL++MLGKC+QPE+ S LFEVMLSDGLKP++DVYTALVSAYG+SG LD+AFS + 
Sbjct: 115 TKTYTKLLMMLGKCRQPEEGSFLFEVMLSDGLKPTIDVYTALVSAYGKSGQLDKAFSIVV 174

Query: 174 DMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKA 233
           +MK++S+CKPDVYTYSILI  C K HRF+LI  ILAEMSYLGIECS VTYNTIIDGYGKA
Sbjct: 175 EMKAISECKPDVYTYSILINCCIKLHRFELIRGILAEMSYLGIECSTVTYNTIIDGYGKA 234

Query: 234 KKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQT 293
           K FEEME++ + M+ESG   PD+FT NS+I AYG+ G I+KMEKWY EF LMG++ DI+T
Sbjct: 235 KMFEEMENTLTDMIESGSSVPDLFTFNSIIGAYGSKGRIDKMEKWYTEFQLMGLRQDIKT 294

Query: 294 LNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMK 353
            NIL +SYG+AGMY KMRSV++FM+KRFF P++VT+NI IETFGKAG IE MEEYF KMK
Sbjct: 295 FNILIRSYGKAGMYGKMRSVLEFMEKRFFSPSIVTHNIFIETFGKAGDIETMEEYFSKMK 354

Query: 354 HRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVE 413
           H G+KPN++TYCSLVSAYSKAG IMKVDSILRQVENSDVILDTPFFNC+ISAYG+AGD+E
Sbjct: 355 HLGIKPNTVTYCSLVSAYSKAGHIMKVDSILRQVENSDVILDTPFFNCVISAYGRAGDIE 414

Query: 414 KMGELFLTMKERHCVPDNITFATMIQAYNALGMTEAAQNLENKMIAMKENSGKK 467
           KM ELFL M+ R C PD+ITFATMIQAYNA GM EAAQ +EN MIA ++NSG +
Sbjct: 415 KMSELFLGMEGRKCKPDSITFATMIQAYNAQGMIEAAQGMENMMIATRKNSGMR 468

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356552149|ref|XP_003544432.1| PREDICTED: pentatricopeptide repeat-containing protein At3g53170-like [Glycine max]

 Score =  669 bits (1726), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 310/463 (66%), Positives = 379/463 (81%), Gaps = 1/463 (0%)

Query: 9   TPPTTATHLPKFYKEPVFRIQAIKRSPGPIQELGIQKEAEKDLSKILRTEFAIKNIEKKV 68
           TP T++T+         FR++++KRS  P     + K+  KDLS+ILRTE AI+ +  K 
Sbjct: 20  TPFTSSTNRSPPKTRRGFRVESLKRSSKPASA-ELVKDPNKDLSRILRTEAAIRGVHNKA 78

Query: 69  SSKKYKNLWPKPVLEALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCK 128
            S  +K LWPK +LE+LD+AIK+ +   AL+IF LLR+Q WYQ RC+T+ KL++MLGKC+
Sbjct: 79  KSSSHKQLWPKALLESLDDAIKRCRSHSALEIFALLRKQYWYQPRCRTYAKLLMMLGKCR 138

Query: 129 QPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTY 188
           QPE+ASLLFE+MLS+GLKP+VDVYTALVSAYGQSGLLD+AFST+ DMKSV DC+PDVYTY
Sbjct: 139 QPEEASLLFEIMLSEGLKPTVDVYTALVSAYGQSGLLDQAFSTVEDMKSVVDCEPDVYTY 198

Query: 189 SILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVE 248
           SILI+ C KF RFDLIE +LAEMSYLGI+C+ VTYN+IIDGYGKA  FE+M+ + + M+E
Sbjct: 199 SILIRCCAKFRRFDLIEHVLAEMSYLGIKCNCVTYNSIIDGYGKASMFEQMDDALNDMIE 258

Query: 249 SGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYD 308
           +G  HPD+FTLNS + AYGN+G I+KMEKWY+EF LMG+K DI T N + KSYG+AGMY+
Sbjct: 259 NGNSHPDVFTLNSFVGAYGNAGQIDKMEKWYDEFQLMGIKPDITTFNTMIKSYGKAGMYE 318

Query: 309 KMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLV 368
           KM++VMDFM+KRFF PT+VTYN VIE FGKAG IEKM+++F KMKH G+KPNSITYCSLV
Sbjct: 319 KMKTVMDFMEKRFFTPTIVTYNTVIEVFGKAGEIEKMDQHFLKMKHLGVKPNSITYCSLV 378

Query: 369 SAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCV 428
           SAYSK G I KVDSI+R VENSDV+LDTPFFNCIISAYGQAG+++KMGELFL M+ER C 
Sbjct: 379 SAYSKVGCIDKVDSIMRHVENSDVVLDTPFFNCIISAYGQAGNLKKMGELFLAMRERKCE 438

Query: 429 PDNITFATMIQAYNALGMTEAAQNLENKMIAMKENSGKKLIQC 471
           PDNITFA MIQ+YN  GMTEA QNLEN MI+ K + G KLI C
Sbjct: 439 PDNITFACMIQSYNTQGMTEAVQNLENMMISAKSSLGTKLIGC 481

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357458279|ref|XP_003599420.1| Pentatricopeptide repeat-containing protein [Medicago truncatula] gi|355488468|gb|AES69671.1| Pentatricopeptide repeat-containing protein [Medicago truncatula]

 Score =  652 bits (1682), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 308/458 (67%), Positives = 371/458 (81%), Gaps = 3/458 (0%)

Query: 10  PPTTATHLPK--FYKEPVFRIQAIKRSPGPIQELGIQKEAEKDLSKILRTEFAIKNIEKK 67
           P T +T  P    +    FR+ ++KRS  P  E G+QK+ +KDLS+ILRTE AIK +E K
Sbjct: 27  PITCSTKFPNKNHFHSSSFRVYSLKRSSKPSYE-GLQKDPKKDLSRILRTEAAIKGVENK 85

Query: 68  VSSKKYKNLWPKPVLEALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKC 127
             S K+K LWPK VLEALD+AIK  +WQ AL IF LLR Q WY+ RCQT+TKL++ML KC
Sbjct: 86  AKSWKHKQLWPKAVLEALDDAIKGCQWQNALMIFELLRNQYWYEPRCQTYTKLLMMLSKC 145

Query: 128 KQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYT 187
           KQP++AS L+E ML +GLKP+VDV TALVSAYGQSGL   AFSTI DMKSV DCKPDVYT
Sbjct: 146 KQPKEASQLYETMLFEGLKPTVDVLTALVSAYGQSGLFRHAFSTIEDMKSVVDCKPDVYT 205

Query: 188 YSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMV 247
           YS+LI  C KF RFDLIE++LA+MSY GIEC++VTYN+IIDGYGKA  FE+ME+S + M+
Sbjct: 206 YSVLISCCAKFRRFDLIERVLADMSYSGIECNSVTYNSIIDGYGKAGMFEQMENSLTDMI 265

Query: 248 ESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMY 307
           E+  C PD+FTLNS+I +YGN G I+KMEKWY+EF LM +K DI+T N++ KSYG+AGMY
Sbjct: 266 ENENCQPDVFTLNSLIGSYGNGGKIDKMEKWYDEFQLMSIKPDIKTFNMMIKSYGKAGMY 325

Query: 308 DKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSL 367
           DKM+SVMDFM++RFF PT+VTYN VIE +GKAG IEKM+++FK MKH GMKPNS+TYCSL
Sbjct: 326 DKMKSVMDFMERRFFAPTIVTYNTVIEVYGKAGEIEKMDKHFKNMKHIGMKPNSVTYCSL 385

Query: 368 VSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHC 427
           V+AYSKAGLI K+DSILR VENSDVILDTPFFNCIISAYGQ GD++KMGELFL M+ R C
Sbjct: 386 VNAYSKAGLIRKIDSILRHVENSDVILDTPFFNCIISAYGQVGDLKKMGELFLAMRARKC 445

Query: 428 VPDNITFATMIQAYNALGMTEAAQNLENKMIAMKENSG 465
            PD  TF  MIQAYN  G+TEAA+NLE  MI+ K++SG
Sbjct: 446 EPDRTTFTCMIQAYNTQGITEAAKNLETMMISAKDSSG 483

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449436321|ref|XP_004135941.1| PREDICTED: pentatricopeptide repeat-containing protein At3g53170-like [Cucumis sativus] gi|449514880|ref|XP_004164505.1| PREDICTED: pentatricopeptide repeat-containing protein At3g53170-like [Cucumis sativus]

 Score =  627 bits (1617), Expect = e-177,   Method: Compositional matrix adjust.
 Identities = 289/421 (68%), Positives = 353/421 (83%)

Query: 42  GIQKEAEKDLSKILRTEFAIKNIEKKVSSKKYKNLWPKPVLEALDEAIKQKKWQLALKIF 101
            +Q++ +K LS+ILR + AIK IE+K +SKKY NLWPK VLEALDEAI++  W+ ALKIF
Sbjct: 55  ALQRDPKKGLSRILRRDAAIKAIERKANSKKYNNLWPKAVLEALDEAIQENLWETALKIF 114

Query: 102 GLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQ 161
           GLLRQQQWY+ RCQT+TKL+++LGKCKQPEQASLLFE+M S+GLKPS+DVYTALVSAYGQ
Sbjct: 115 GLLRQQQWYEPRCQTYTKLLMLLGKCKQPEQASLLFEIMFSEGLKPSIDVYTALVSAYGQ 174

Query: 162 SGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAV 221
           SGLL +A ST+++MKS+SDCKPDV+TYSILI  CT+  RFDL++KILA+MS LGI C+ V
Sbjct: 175 SGLLHKAISTVDEMKSISDCKPDVHTYSILIDCCTRLRRFDLLKKILADMSCLGITCNTV 234

Query: 222 TYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNE 281
           TYNTII+G+GKAK FE+MES    M+ES  C PD+ T N+ I AYGNS  IEKMEKWY E
Sbjct: 235 TYNTIINGFGKAKMFEQMESLLLEMIESDSCPPDLITFNTFIRAYGNSEQIEKMEKWYKE 294

Query: 282 FNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGH 341
           F LMG++ DI T N +  SYG+AGMYDKM+SV++FM+KRFF PT+VT N +I++FG+AG+
Sbjct: 295 FQLMGIEPDIWTYNSMISSYGKAGMYDKMKSVLNFMEKRFFSPTIVTMNTIIDSFGRAGN 354

Query: 342 IEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNC 401
           IE+MEEYFK MK +GMKPNS+TYCSLV+AY K+G + KVDSILRQ+ENSDV+ DTP FNC
Sbjct: 355 IEEMEEYFKNMKFQGMKPNSVTYCSLVNAYGKSGDLEKVDSILRQIENSDVVPDTPLFNC 414

Query: 402 IISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAYNALGMTEAAQNLENKMIAMK 461
           +I+ YGQAG+V KMGELFL MKE  CVPD ITFATMI+A  A GMTE AQ LENK+IA  
Sbjct: 415 LINVYGQAGNVRKMGELFLEMKENKCVPDGITFATMIRALKAQGMTEDAQRLENKLIATN 474

Query: 462 E 462
           +
Sbjct: 475 D 475

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|75265624|sp|Q9SCP4.1|PP279_ARATH RecName: Full=Pentatricopeptide repeat-containing protein At3g53170 gi|6630737|emb|CAB64220.1| nodulin / glutamate-ammonia ligase-like protein [Arabidopsis thaliana]

 Score =  600 bits (1547), Expect = e-169,   Method: Compositional matrix adjust.
 Identities = 278/420 (66%), Positives = 345/420 (82%)

Query: 44  QKEAEKDLSKILRTEFAIKNIEKKVSSKKYKNLWPKPVLEALDEAIKQKKWQLALKIFGL 103
           Q + +K+LS+ILRT+ A+K IE+K +S+KY  LWPK VLEALDEAIK+ +WQ ALKIF L
Sbjct: 24  QVDPKKELSRILRTDAAVKGIERKANSEKYLTLWPKAVLEALDEAIKENRWQSALKIFNL 83

Query: 104 LRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSG 163
           LR+Q WY+ RC+T+TKL  +LG CKQP+QASLLFEVMLS+GLKP++DVYT+L+S YG+S 
Sbjct: 84  LRKQHWYEPRCKTYTKLFKVLGNCKQPDQASLLFEVMLSEGLKPTIDVYTSLISVYGKSE 143

Query: 164 LLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTY 223
           LLD+AFST+  MKSVSDCKPDV+T+++LI  C K  RFDL++ I+ EMSYLG+ CS VTY
Sbjct: 144 LLDKAFSTLEYMKSVSDCKPDVFTFTVLISCCCKLGRFDLVKSIVLEMSYLGVGCSTVTY 203

Query: 224 NTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFN 283
           NTIIDGYGKA  FEEMES  + M+E G   PD+ TLNS+I +YGN  N+ KME WY+ F 
Sbjct: 204 NTIIDGYGKAGMFEEMESVLADMIEDGDSLPDVCTLNSIIGSYGNGRNMRKMESWYSRFQ 263

Query: 284 LMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIE 343
           LMGV+ DI T NIL  S+G+AGMY KM SVMDFM+KRFF  T VTYNIVIETFGKAG IE
Sbjct: 264 LMGVQPDITTFNILILSFGKAGMYKKMCSVMDFMEKRFFSLTTVTYNIVIETFGKAGRIE 323

Query: 344 KMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCII 403
           KM++ F+KMK++G+KPNSITYCSLV+AYSKAGL++K+DS+LRQ+ NSDV+LDTPFFNCII
Sbjct: 324 KMDDVFRKMKYQGVKPNSITYCSLVNAYSKAGLVVKIDSVLRQIVNSDVVLDTPFFNCII 383

Query: 404 SAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAYNALGMTEAAQNLENKMIAMKEN 463
           +AYGQAGD+  M EL++ M+ER C PD ITFATMI+ Y A G+ +A Q LE +MI+  EN
Sbjct: 384 NAYGQAGDLATMKELYIQMEERKCKPDKITFATMIKTYTAHGIFDAVQELEKQMISSGEN 443

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|334185941|ref|NP_190885.5| tetratricopeptide repeat domain-containing protein [Arabidopsis thaliana] gi|332645523|gb|AEE79044.1| tetratricopeptide repeat domain-containing protein [Arabidopsis thaliana]

 Score =  598 bits (1542), Expect = e-168,   Method: Compositional matrix adjust.
 Identities = 279/424 (65%), Positives = 347/424 (81%), Gaps = 2/424 (0%)

Query: 44  QKEAEKDLSKILRTEFAIKNIEKKVSSKKYKNLWPKPVLEALDEAIKQKKWQLALKIFGL 103
           Q + +K+LS+ILRT+ A+K IE+K +S+KY  LWPK VLEALDEAIK+ +WQ ALKIF L
Sbjct: 74  QVDPKKELSRILRTDAAVKGIERKANSEKYLTLWPKAVLEALDEAIKENRWQSALKIFNL 133

Query: 104 LRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSG 163
           LR+Q WY+ RC+T+TKL  +LG CKQP+QASLLFEVMLS+GLKP++DVYT+L+S YG+S 
Sbjct: 134 LRKQHWYEPRCKTYTKLFKVLGNCKQPDQASLLFEVMLSEGLKPTIDVYTSLISVYGKSE 193

Query: 164 LLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTY 223
           LLD+AFST+  MKSVSDCKPDV+T+++LI  C K  RFDL++ I+ EMSYLG+ CS VTY
Sbjct: 194 LLDKAFSTLEYMKSVSDCKPDVFTFTVLISCCCKLGRFDLVKSIVLEMSYLGVGCSTVTY 253

Query: 224 NTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFN 283
           NTIIDGYGKA  FEEMES  + M+E G   PD+ TLNS+I +YGN  N+ KME WY+ F 
Sbjct: 254 NTIIDGYGKAGMFEEMESVLADMIEDGDSLPDVCTLNSIIGSYGNGRNMRKMESWYSRFQ 313

Query: 284 LMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIE 343
           LMGV+ DI T NIL  S+G+AGMY KM SVMDFM+KRFF  T VTYNIVIETFGKAG IE
Sbjct: 314 LMGVQPDITTFNILILSFGKAGMYKKMCSVMDFMEKRFFSLTTVTYNIVIETFGKAGRIE 373

Query: 344 KMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCII 403
           KM++ F+KMK++G+KPNSITYCSLV+AYSKAGL++K+DS+LRQ+ NSDV+LDTPFFNCII
Sbjct: 374 KMDDVFRKMKYQGVKPNSITYCSLVNAYSKAGLVVKIDSVLRQIVNSDVVLDTPFFNCII 433

Query: 404 SAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAYNALGMTEAAQNLENKMIAMKEN 463
           +AYGQAGD+  M EL++ M+ER C PD ITFATMI+ Y A G+ +A Q LE +MI+   +
Sbjct: 434 NAYGQAGDLATMKELYIQMEERKCKPDKITFATMIKTYTAHGIFDAVQELEKQMIS--SD 491

Query: 464 SGKK 467
            GKK
Sbjct: 492 IGKK 495

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297820044|ref|XP_002877905.1| pentatricopeptide repeat-containing protein [Arabidopsis lyrata subsp. lyrata] gi|297323743|gb|EFH54164.1| pentatricopeptide repeat-containing protein [Arabidopsis lyrata subsp. lyrata]

 Score =  557 bits (1435), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 266/420 (63%), Positives = 335/420 (79%), Gaps = 11/420 (2%)

Query: 44  QKEAEKDLSKILRTEFAIKNIEKKVSSKKYKNLWPKPVLEALDEAIKQKKWQLALKIFGL 103
           Q + +K+LS+ILRT+ A+K IE+K +S+KY  LWPK VLEALDEAIK+ +WQ ALKIF L
Sbjct: 24  QIDPKKELSRILRTDAAVKGIERKANSEKYLTLWPKAVLEALDEAIKENRWQSALKIFHL 83

Query: 104 LRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSG 163
           LR+Q WY+ +C+T+TKL  +LG CKQP+QASLLFEVMLS+GLKP++DVYT+L++ YG+S 
Sbjct: 84  LRKQHWYEPKCKTYTKLFKVLGNCKQPDQASLLFEVMLSEGLKPTIDVYTSLIAVYGKSE 143

Query: 164 LLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTY 223
           LLD+AFST+  MKSVSDCKPDV+T+++LI+ C K  RFDL+++I+ EMSYLG+ CS VTY
Sbjct: 144 LLDKAFSTLEYMKSVSDCKPDVFTFTVLIRCCCKLGRFDLVKRIILEMSYLGVGCSTVTY 203

Query: 224 NTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFN 283
           NTIIDGYGKA  FEEME+  + M+E G   PD+FTLNS+I   G+S  +   E       
Sbjct: 204 NTIIDGYGKAGMFEEMENVLADMIEDGDSLPDVFTLNSII---GSSEMVAHEED------ 254

Query: 284 LMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIE 343
             G   DI T NIL  S+G+AGMY KM SVMDFM+KRFF  T VTYNIVIETFGKAG IE
Sbjct: 255 --GELPDITTFNILILSFGKAGMYKKMSSVMDFMEKRFFSLTTVTYNIVIETFGKAGKIE 312

Query: 344 KMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCII 403
           KM++ F+KMK++G+KPNSI+YCSLV+AYSKAGL+ K+DSILRQ+ NSDV+LDTPFFNCII
Sbjct: 313 KMDDVFRKMKYQGVKPNSISYCSLVNAYSKAGLVGKIDSILRQIVNSDVVLDTPFFNCII 372

Query: 404 SAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAYNALGMTEAAQNLENKMIAMKEN 463
           +AYGQAGD+  M EL++ M+ER C PD ITFATMI+ Y A G+ +A Q LE +MI+  EN
Sbjct: 373 NAYGQAGDLATMKELYIQMEERKCKPDKITFATMIKTYKAHGIFDAVQELEKQMISTGEN 432

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

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	471
TAIR|locus:2081041	486	PPR2 "pentatricopeptide repeat	0.910	0.882	0.401	2.8e-89
TAIR|locus:2122561	563	EMB2453 "EMBRYO DEFECTIVE 2453	0.870	0.728	0.25	9.6e-41
TAIR|locus:2151281	819	AT5G02860 [Arabidopsis thalian	0.878	0.505	0.269	4.9e-39
TAIR|locus:2027166	862	PTAC2 "plastid transcriptional	0.781	0.426	0.256	3.5e-35
TAIR|locus:2150024	729	AT5G01110 [Arabidopsis thalian	0.717	0.463	0.256	1.4e-32
TAIR|locus:1005716169	831	AT5G21222 [Arabidopsis thalian	0.715	0.405	0.276	1.6e-32
TAIR|locus:2093472	642	AT3G16010 [Arabidopsis thalian	0.717	0.526	0.274	2.4e-32
TAIR|locus:2027212	855	AT1G74750 [Arabidopsis thalian	0.636	0.350	0.280	5.8e-32
TAIR|locus:1009023134	644	AT1G12775 [Arabidopsis thalian	0.779	0.569	0.273	6.7e-32
TAIR|locus:2015494	629	RPF3 "RNA processing factor 3"	0.740	0.554	0.283	7.8e-32

TAIR|locus:2081041 PPR2 "pentatricopeptide repeat 2" [Arabidopsis thaliana (taxid:3702)]

 Score = 891 (318.7 bits), Expect = 2.8e-89, P = 2.8e-89
 Identities = 173/431 (40%), Positives = 273/431 (63%)

Query:    28 IQAIKRSPGPIQELGIQKEAE-KDLSK-ILRTEFAIKNIEKKVSSKKYKNLWPKPVLEAL 85
             + A K SPG + +  + K+ E   +++ + +    IKN++KK+  +   N W   V E L
Sbjct:    36 LAASKSSPGSVTKKRLWKDGEFPGITEPVNQRRTPIKNVKKKLDRRSKANGWVNTVTETL 95

Query:    86 DEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGL 145
              + I +K+W  AL++F +LR+Q +YQ +  T+ KL+V+LGK  QP +A  LF+ ML +GL
Sbjct:    96 SDLIAKKQWLQALEVFDMLREQTFYQPKEGTYMKLLVLLGKSGQPNRAQKLFDEMLEEGL 155

Query:   146 KPSVDVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIE 205
             +P+V++YTAL++AY +S L+D+AFS ++ MKS   C+PDV+TYS L+K+C    +FDL++
Sbjct:   156 EPTVELYTALLAAYTRSNLIDDAFSILDKMKSFPQCQPDVFTYSTLLKACVDASQFDLVD 215

Query:   206 KILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISA 265
              +  EM    I  + VT N ++ GYG+  +F++ME   S M+ S  C PD++T+N ++S 
Sbjct:   216 SLYKEMDERLITPNTVTQNIVLSGYGRVGRFDQMEKVLSDMLVSTACKPDVWTMNIILSV 275

Query:   266 YGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPT 325
             +GN G I+ ME WY +F   G++ + +T NIL  SYG+  MYDKM SVM++M+K  F  T
Sbjct:   276 FGNMGKIDMMESWYEKFRNFGIEPETRTFNILIGSYGKKRMYDKMSSVMEYMRKLEFPWT 335

Query:   326 VVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILR 385
               TYN +IE F   G  + ME  F +M+  GMK ++ T+C L++ Y+ AGL  KV S ++
Sbjct:   336 TSTYNNIIEAFADVGDAKNMELTFDQMRSEGMKADTKTFCCLINGYANAGLFHKVISSVQ 395

Query:   386 QVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAYNALG 445
                  ++  +T F+N +ISA  +A D+ +M  +++ MKER CV D+ TF  M++AY   G
Sbjct:   396 LAAKFEIPENTAFYNAVISACAKADDLIEMERVYIRMKERQCVCDSRTFEIMVEAYEKEG 455

Query:   446 MTEAAQNLENK 456
             M +    LE +
Sbjct:   456 MNDKIYYLEQE 466

GO:0005739 "mitochondrion" evidence=ISM

GO:0009793 "embryo development ending in seed dormancy" evidence=NAS

GO:0048868 "pollen tube development" evidence=IMP

GO:0009507 "chloroplast" evidence=IDA

GO:0009553 "embryo sac development" evidence=IMP

GO:0009555 "pollen development" evidence=IMP

GO:0009790 "embryo development" evidence=IMP

GO:0019843 "rRNA binding" evidence=IDA

TAIR|locus:2122561 EMB2453 "EMBRYO DEFECTIVE 2453" [Arabidopsis thaliana (taxid:3702)]

 Score = 433 (157.5 bits), Expect = 9.6e-41, P = 9.6e-41
 Identities = 105/420 (25%), Positives = 201/420 (47%)

Query:    51 LSKILRTEFAIKNIEKKVSSKKYKNLWPKPVLEALDEAIKQKKWQLALKIFGLLRQQQWY 110
             +S+I   E  +K ++K V   +  + +   +L   +E  K  KW   L++F  +++Q+WY
Sbjct:    75 MSRISDREPLVKTLDKYVKVVRCDHCF---LL--FEELGKSDKWLQCLEVFRWMQKQRWY 129

Query:   111 QARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAY----GQSGLLD 166
                   ++KL+ ++GK  Q   A  LF  M + G +P   VY AL++A+     ++  L+
Sbjct:   130 IPDNGVYSKLISVMGKKGQTRMAMWLFSEMKNSGCRPDASVYNALITAHLHTRDKAKALE 189

Query:   167 EAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTI 226
             +    ++ MK +  C+P+V TY+IL+++  +  + D +  +  ++    +     T+N +
Sbjct:   190 KVRGYLDKMKGIERCQPNVVTYNILLRAFAQSGKVDQVNALFKDLDMSPVSPDVYTFNGV 249

Query:   227 IDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMG 286
             +D YGK    +EME+  + M  S  C PDI T N +I +YG     EKME+ +       
Sbjct:   250 MDAYGKNGMIKEMEAVLTRM-RSNECKPDIITFNVLIDSYGKKQEFEKMEQTFKSLMRSK 308

Query:   287 VKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKME 346
              K  + T N +  +YG+A M DK   V   M    + P+ +TY  +I  +G  G + +  
Sbjct:   309 EKPTLPTFNSMIINYGKARMIDKAEWVFKKMNDMNYIPSFITYECMIMMYGYCGSVSRAR 368

Query:   347 EYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAY 406
             E F+++        + T  +++  Y + GL ++ D +        V  D   +  +  AY
Sbjct:   369 EIFEEVGESDRVLKASTLNAMLEVYCRNGLYIEADKLFHNASAFRVHPDASTYKFLYKAY 428

Query:   407 GQAGDVEKMGELFLTMKERHCVPDNITFATMIQAYNALGMTEAAQNLENKMIAMKENSGK 466
              +A   E++  L   M++   VP+   F   ++ + +      ++N ++   +   +S K
Sbjct:   429 TKADMKEQVQILMKKMEKDGIVPNKRFFLEALEVFGSRLPGSGSENRKSTRSSRSRDSPK 488

GO:0009507 "chloroplast" evidence=ISM

GO:0009793 "embryo development ending in seed dormancy" evidence=IMP;NAS

TAIR|locus:2151281 AT5G02860 [Arabidopsis thaliana (taxid:3702)]

 Score = 425 (154.7 bits), Expect = 4.9e-39, P = 4.9e-39
 Identities = 115/426 (26%), Positives = 201/426 (47%)

Query:    42 GIQKEAEKDLSKILRTEFAIKNIEKKVSS--KKYKNLWPKPVLEALDEAIK----QKKWQ 95
             G+  + ++ L  ++   F    ++  +S   + +K+  P+     L   +K     KK+ 
Sbjct:    94 GLSPQGQQVLRSLIEPNFDSGQLDSVLSELFEPFKDK-PESTSSELLAFLKGLGFHKKFD 152

Query:    96 LALKIFGLLRQQQWYQARCQTFTKLMV--MLGKCKQPEQASLLFEVMLSDGLKPSVDVYT 153
             LAL+ F    +Q+ YQ+        ++  MLGK  +   A+ +F  +  DG    V  YT
Sbjct:   153 LALRAFDWFMKQKDYQSMLDNSVVAIIISMLGKEGRVSSAANMFNGLQEDGFSLDVYSYT 212

Query:   154 ALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHR-FDLIEKILAEMS 212
             +L+SA+  SG   EA +    M+    CKP + TY++++    K    ++ I  ++ +M 
Sbjct:   213 SLISAFANSGRYREAVNVFKKMEE-DGCKPTLITYNVILNVFGKMGTPWNKITSLVEKMK 271

Query:   213 YLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNI 272
               GI   A TYNT+I    +    +E    F  M  +G  + D  T N+++  YG S   
Sbjct:   272 SDGIAPDAYTYNTLITCCKRGSLHQEAAQVFEEMKAAGFSY-DKVTYNALLDVYGKSHRP 330

Query:   273 EKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIV 332
             ++  K  NE  L G    I T N L  +Y R GM D+   + + M ++   P V TY  +
Sbjct:   331 KEAMKVLNEMVLNGFSPSIVTYNSLISAYARDGMLDEAMELKNQMAEKGTKPDVFTYTTL 390

Query:   333 IETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDV 392
             +  F +AG +E     F++M++ G KPN  T+ + +  Y   G   ++  I  ++    +
Sbjct:   391 LSGFERAGKVESAMSIFEEMRNAGCKPNICTFNAFIKMYGNRGKFTEMMKIFDEINVCGL 450

Query:   393 ILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAYNALGMTEAAQN 452
               D   +N +++ +GQ G   ++  +F  MK    VP+  TF T+I AY+  G  E A  
Sbjct:   451 SPDIVTWNTLLAVFGQNGMDSEVSGVFKEMKRAGFVPERETFNTLISAYSRCGSFEQAMT 510

Query:   453 LENKMI 458
             +  +M+
Sbjct:   511 VYRRML 516

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2027166 PTAC2 "plastid transcriptionally active 2" [Arabidopsis thaliana (taxid:3702)]

 Score = 390 (142.3 bits), Expect = 3.5e-35, P = 3.5e-35
 Identities = 95/371 (25%), Positives = 181/371 (48%)

Query:    94 WQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYT 153
             WQ +L++F  +++Q W +     +T ++ +LG+    ++   +F+ M S G+  SV  YT
Sbjct:   121 WQRSLRLFKYMQRQIWCKPNEHIYTIMISLLGREGLLDKCLEVFDEMPSQGVSRSVFSYT 180

Query:   154 ALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHR-FDLIEKILAEMS 212
             AL++AYG++G  + +   ++ MK+     P + TY+ +I +C +    ++ +  + AEM 
Sbjct:   181 ALINAYGRNGRYETSLELLDRMKN-EKISPSILTYNTVINACARGGLDWEGLLGLFAEMR 239

Query:   213 YLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNI 272
             + GI+   VTYNT++         +E E  F  M   GG  PD+ T + ++  +G    +
Sbjct:   240 HEGIQPDIVTYNTLLSACAIRGLGDEAEMVFRTM-NDGGIVPDLTTYSHLVETFGKLRRL 298

Query:   273 EKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIV 332
             EK+     E    G   DI + N+L ++Y ++G   +   V   MQ     P   TY+++
Sbjct:   299 EKVCDLLGEMASGGSLPDITSYNVLLEAYAKSGSIKEAMGVFHQMQAAGCTPNANTYSVL 358

Query:   333 IETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDV 392
             +  FG++G  + + + F +MK     P++ TY  L+  + + G   +V ++   +   ++
Sbjct:   359 LNLFGQSGRYDDVRQLFLEMKSSNTDPDAATYNILIEVFGEGGYFKEVVTLFHDMVEENI 418

Query:   393 ILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAYNALGMTEAAQN 452
               D   +  II A G+ G  E   ++   M     VP +  +  +I+A+    + E A  
Sbjct:   419 EPDMETYEGIIFACGKGGLHEDARKILQYMTANDIVPSSKAYTGVIEAFGQAALYEEALV 478

Query:   453 LENKMIAMKEN 463
               N M  +  N
Sbjct:   479 AFNTMHEVGSN 489

GO:0009507 "chloroplast" evidence=IDA

GO:0009295 "nucleoid" evidence=IDA

GO:0009508 "plastid chromosome" evidence=IDA

GO:0042793 "transcription from plastid promoter" evidence=RCA;IMP

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=RCA;IMP

GO:0006364 "rRNA processing" evidence=RCA

GO:0006399 "tRNA metabolic process" evidence=RCA

GO:0009658 "chloroplast organization" evidence=RCA

GO:0009902 "chloroplast relocation" evidence=RCA

GO:0009965 "leaf morphogenesis" evidence=RCA

GO:0010027 "thylakoid membrane organization" evidence=RCA

GO:0010103 "stomatal complex morphogenesis" evidence=RCA

GO:0010207 "photosystem II assembly" evidence=RCA

GO:0030154 "cell differentiation" evidence=RCA

GO:0034660 "ncRNA metabolic process" evidence=RCA

GO:0035304 "regulation of protein dephosphorylation" evidence=RCA

GO:0045036 "protein targeting to chloroplast" evidence=RCA

TAIR|locus:2150024 AT5G01110 [Arabidopsis thaliana (taxid:3702)]

 Score = 364 (133.2 bits), Expect = 1.4e-32, P = 1.4e-32
 Identities = 88/343 (25%), Positives = 166/343 (48%)

Query:   120 LMVMLGK-CK--QPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAFSTINDMK 176
             L +M+   CK  + E+       +   G+ P +  Y  L+SAY   GL++EAF  +N M 
Sbjct:   238 LNIMVNALCKDGKMEKVGTFLSQVQEKGVYPDIVTYNTLISAYSSKGLMEEAFELMNAMP 297

Query:   177 SVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKF 236
                   P VYTY+ +I    K  +++  +++ AEM   G+   + TY +++    K    
Sbjct:   298 G-KGFSPGVYTYNTVINGLCKHGKYERAKEVFAEMLRSGLSPDSTTYRSLLMEACKKGDV 356

Query:   237 EEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNI 296
              E E  FS M  S    PD+   +SM+S +  SGN++K   ++N     G+  D     I
Sbjct:   357 VETEKVFSDM-RSRDVVPDLVCFSSMMSLFTRSGNLDKALMYFNSVKEAGLIPDNVIYTI 415

Query:   297 LTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRG 356
             L + Y R GM     ++ + M ++     VVTYN ++    K   + + ++ F +M  R 
Sbjct:   416 LIQGYCRKGMISVAMNLRNEMLQQGCAMDVVTYNTILHGLCKRKMLGEADKLFNEMTERA 475

Query:   357 MKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMG 416
             + P+S T   L+  + K G +     + ++++   + LD   +N ++  +G+ GD++   
Sbjct:   476 LFPDSYTLTILIDGHCKLGNLQNAMELFQKMKEKRIRLDVVTYNTLLDGFGKVGDIDTAK 535

Query:   417 ELFLTMKERHCVPDNITFATMIQAYNALGMTEAAQNLENKMIA 459
             E++  M  +  +P  I+++ ++ A  + G    A  + ++MI+
Sbjct:   536 EIWADMVSKEILPTPISYSILVNALCSKGHLAEAFRVWDEMIS 578

GO:0005739 "mitochondrion" evidence=ISM

TAIR|locus:1005716169 AT5G21222 [Arabidopsis thaliana (taxid:3702)]

 Score = 365 (133.5 bits), Expect = 1.6e-32, P = 1.6e-32
 Identities = 95/343 (27%), Positives = 164/343 (47%)

Query:   118 TKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAFSTINDMKS 177
             TKLM  L +  +P++A  +F  ++ +G KPS+  YT LV+A  +        S I+ ++ 
Sbjct:   323 TKLMNGLIERGRPQEAHSIFNTLIEEGHKPSLITYTTLVTALTRQKHFHSLLSLISKVEK 382

Query:   178 VSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFE 237
              +  KPD   ++ +I + ++    D   KI  +M   G + +A T+NT+I GYGK  K E
Sbjct:   383 -NGLKPDTILFNAIINASSESGNLDQAMKIFEKMKESGCKPTASTFNTLIKGYGKIGKLE 441

Query:   238 EMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLM--GVKADIQTLN 295
             E       M+      P+  T N ++ A+ N   IE  E W   + +   GVK D+ T N
Sbjct:   442 ESSRLLDMMLRDEMLQPNDRTCNILVQAWCNQRKIE--EAWNIVYKMQSYGVKPDVVTFN 499

Query:   296 ILTKSYGRAGMYDKMRS-VMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKH 354
              L K+Y R G        ++  M      P V T   ++  + + G +E+   +F +MK 
Sbjct:   500 TLAKAYARIGSTCTAEDMIIPRMLHNKVKPNVRTCGTIVNGYCEEGKMEEALRFFYRMKE 559

Query:   355 RGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEK 414
              G+ PN   + SL+  +     +  V  ++  +E   V  D   F+ +++A+   GD+++
Sbjct:   560 LGVHPNLFVFNSLIKGFLNINDMDGVGEVVDLMEEFGVKPDVVTFSTLMNAWSSVGDMKR 619

Query:   415 MGELFLTMKERHCVPDNITFATMIQAYNALGMTEAAQNLENKM 457
               E++  M E    PD   F+ + + Y   G  E A+ + N+M
Sbjct:   620 CEEIYTDMLEGGIDPDIHAFSILAKGYARAGEPEKAEQILNQM 662

GO:0004672 "protein kinase activity" evidence=IEA;ISS

GO:0004674 "protein serine/threonine kinase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005739 "mitochondrion" evidence=ISM

GO:0006468 "protein phosphorylation" evidence=IEA

GO:0016772 "transferase activity, transferring phosphorus-containing groups" evidence=IEA

TAIR|locus:2093472 AT3G16010 [Arabidopsis thaliana (taxid:3702)]

 Score = 360 (131.8 bits), Expect = 2.4e-32, P = 2.4e-32
 Identities = 94/342 (27%), Positives = 157/342 (45%)

Query:   118 TKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAFSTINDMKS 177
             ++L+  LG+ K   +A  +F        KP+   Y +++    Q G  ++      +M +
Sbjct:   166 SELVKALGRAKMVSKALSVFYQAKGRKCKPTSSTYNSVILMLMQEGQHEKVHEVYTEMCN 225

Query:   178 VSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFE 237
               DC PD  TYS LI S  K  R D   ++  EM    ++ +   Y T++  Y K  K E
Sbjct:   226 EGDCFPDTITYSALISSYEKLGRNDSAIRLFDEMKDNCMQPTEKIYTTLLGIYFKVGKVE 285

Query:   238 EMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNIL 297
             +    F  M +  GC P ++T   +I   G +G +++   +Y +    G+  D+  LN L
Sbjct:   286 KALDLFEEM-KRAGCSPTVYTYTELIKGLGKAGRVDEAYGFYKDMLRDGLTPDVVFLNNL 344

Query:   298 TKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIET-FGKAGHIEKMEEYFKKMKHRG 356
                 G+ G  +++ +V   M      PTVV+YN VI+  F    H+ ++  +F KMK   
Sbjct:   345 MNILGKVGRVEELTNVFSEMGMWRCTPTVVSYNTVIKALFESKAHVSEVSSWFDKMKADS 404

Query:   357 MKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNC-IISAYGQAGDVEKM 415
             + P+  TY  L+  Y K   + K   +L +++        P   C +I+A G+A   E  
Sbjct:   405 VSPSEFTYSILIDGYCKTNRVEKALLLLEEMDEKG-FPPCPAAYCSLINALGKAKRYEAA 463

Query:   416 GELFLTMKERHCVPDNITFATMIQAYNALGMTEAAQNLENKM 457
              ELF  +KE      +  +A MI+ +   G    A +L N+M
Sbjct:   464 NELFKELKENFGNVSSRVYAVMIKHFGKCGKLSEAVDLFNEM 505

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2027212 AT1G74750 [Arabidopsis thaliana (taxid:3702)]

 Score = 360 (131.8 bits), Expect = 5.8e-32, P = 5.8e-32
 Identities = 85/303 (28%), Positives = 152/303 (50%)

Query:    86 DEAIKQK-KWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDG 144
             ++ +KQ   +  AL  F  L++Q  ++    T+T ++  LG+ KQ  + + L + M+ DG
Sbjct:   330 NQVLKQMDNYANALGFFYWLKRQPGFKHDGHTYTTMVGNLGRAKQFGEINKLLDEMVRDG 389

Query:   145 LKPSVDVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLI 204
              KP+   Y  L+ +YG++  L EA +  N M+    C+PD  TY  LI    K    D+ 
Sbjct:   390 CKPNTVTYNRLIHSYGRANYLKEAMNVFNQMQEAG-CEPDRVTYCTLIDIHAKAGFLDIA 448

Query:   205 EKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMIS 264
               +   M   G+     TY+ II+  GKA         F  MV  G C P++ T N MI+
Sbjct:   449 MDMYQRMQEAGLSPDTFTYSVIINCLGKAGHLPAAHRLFCEMVGQG-CTPNLVTFNIMIA 507

Query:   265 AYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFP 324
              +  + N E   K Y +    G + D  T +I+ +  G  G  ++   V   MQ++ + P
Sbjct:   508 LHAKARNYETALKLYRDMQNAGFQPDKVTYSIVMEVLGHCGFLEEAEGVFAEMQRKNWVP 567

Query:   325 TVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSIL 384
                 Y ++++ +GKAG+++K  ++++ M   G++PN  T  SL+S + +   + +  ++L
Sbjct:   568 DEPVYGLLVDLWGKAGNVDKAWQWYQAMLQAGLRPNVPTCNSLLSTFLRVHRMSEAYNLL 627

Query:   385 RQV 387
             + +
Sbjct:   628 QSM 630

GO:0009507 "chloroplast" evidence=ISM

TAIR|locus:1009023134 AT1G12775 [Arabidopsis thaliana (taxid:3702)]

 Score = 356 (130.4 bits), Expect = 6.7e-32, P = 6.7e-32
 Identities = 103/376 (27%), Positives = 174/376 (46%)

Query:    92 KKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQP--EQASLLFEVMLSDGLKPSV 149
             K  Q AL +  LLR+ +    +       +++ G CK    + A  LF  M   G K  +
Sbjct:   240 KSGQTALAM-ELLRKMEERNIKLDAVKYSIIIDGLCKDGSLDNAFNLFNEMEIKGFKADI 298

Query:   150 DVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILA 209
               Y  L+  +  +G  D+    + DM       P+V T+S+LI S  K  +    +++L 
Sbjct:   299 ITYNTLIGGFCNAGRWDDGAKLLRDMIK-RKISPNVVTFSVLIDSFVKEGKLREADQLLK 357

Query:   210 EMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNS 269
             EM   GI  + +TYN++IDG+ K  + EE       M+ S GC PDI T N +I+ Y  +
Sbjct:   358 EMMQRGIAPNTITYNSLIDGFCKENRLEEAIQMVDLMI-SKGCDPDIMTFNILINGYCKA 416

Query:   270 GNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTY 329
               I+   + + E +L GV A+  T N L + + ++G  +  + +   M  R   P +V+Y
Sbjct:   417 NRIDDGLELFREMSLRGVIANTVTYNTLVQGFCQSGKLEVAKKLFQEMVSRRVRPDIVSY 476

Query:   330 NIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVEN 389
              I+++     G +EK  E F K++   M+ +   Y  ++     A  +     +   +  
Sbjct:   477 KILLDGLCDNGELEKALEIFGKIEKSKMELDIGIYMIIIHGMCNASKVDDAWDLFCSLPL 536

Query:   390 SDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAYNALGMTEA 449
               V LD   +N +IS   +   + K   LF  M E    PD +T+  +I+A+  LG  +A
Sbjct:   537 KGVKLDARAYNIMISELCRKDSLSKADILFRKMTEEGHAPDELTYNILIRAH--LGDDDA 594

Query:   450 AQNLENKMIAMKENSG 465
                 E  +I   ++SG
Sbjct:   595 TTAAE--LIEEMKSSG 608

GO:0005739 "mitochondrion" evidence=ISM

TAIR|locus:2015494 RPF3 "RNA processing factor 3" [Arabidopsis thaliana (taxid:3702)]

 Score = 355 (130.0 bits), Expect = 7.8e-32, P = 7.8e-32
 Identities = 101/356 (28%), Positives = 172/356 (48%)

Query:    85 LDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDG 144
             +D     K    AL +F  +   +  +    T+  L+  L    +   AS L   M+   
Sbjct:   262 IDALCNYKNVNDALNLFTEM-DNKGIRPNVVTYNSLIRCLCNYGRWSDASRLLSDMIERK 320

Query:   145 LKPSVDVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLI 204
             + P+V  ++AL+ A+ + G L EA    ++M   S   PD++TYS LI       R D  
Sbjct:   321 INPNVVTFSALIDAFVKEGKLVEAEKLYDEMIKRS-IDPDIFTYSSLINGFCMHDRLDEA 379

Query:   205 EKILAEMSYLGIEC--SAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSM 262
             + +   M  +  +C  + VTYNT+I G+ KAK+ EE    F  M + G     + T N++
Sbjct:   380 KHMFELM--ISKDCFPNVVTYNTLIKGFCKAKRVEEGMELFREMSQRGLVGNTV-TYNTL 436

Query:   263 ISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFF 322
             I     +G+ +  +K + +    GV  DI T +IL     + G  +K   V +++QK   
Sbjct:   437 IQGLFQAGDCDMAQKIFKKMVSDGVPPDIITYSILLDGLCKYGKLEKALVVFEYLQKSKM 496

Query:   323 FPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDS 382
              P + TYNI+IE   KAG +E   + F  +  +G+KPN I Y +++S + + GL  + D+
Sbjct:   497 EPDIYTYNIMIEGMCKAGKVEDGWDLFCSLSLKGVKPNVIIYTTMISGFCRKGLKEEADA 556

Query:   383 ILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMI 438
             + R+++    + ++  +N +I A  + GD     EL   M+    V D  T + +I
Sbjct:   557 LFREMKEDGTLPNSGTYNTLIRARLRDGDKAASAELIKEMRSCGFVGDASTISMVI 612

GO:0005739 "mitochondrion" evidence=ISM;IDA

GO:0006397 "mRNA processing" evidence=IMP

---

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)
Q9SCP4	PP279_ARATH	No assigned EC number	0.6619	0.8917	0.9395	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: GSVIVG00028740001 SubName- Full=Chromosome chr13 scaffold_45, whole genome shotgun sequence; (495 aa) (Vitis vinifera)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	471
PLN03218	1060	PLN03218, PLN03218, maturation of RBCL 1; Provisio	3e-20
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	2e-17
PLN03218	1060	PLN03218, PLN03218, maturation of RBCL 1; Provisio	4e-16
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	5e-15
PLN03218	1060	PLN03218, PLN03218, maturation of RBCL 1; Provisio	1e-14
PLN03218	1060	PLN03218, PLN03218, maturation of RBCL 1; Provisio	1e-14
pfam13041	50	pfam13041, PPR_2, PPR repeat family	2e-13
pfam13041	50	pfam13041, PPR_2, PPR repeat family	3e-12
PLN03081	697	PLN03081, PLN03081, pentatricopeptide (PPR) repeat	6e-12
pfam13041	50	pfam13041, PPR_2, PPR repeat family	9e-10
pfam13041	50	pfam13041, PPR_2, PPR repeat family	2e-09
pfam13041	50	pfam13041, PPR_2, PPR repeat family	7e-09
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	1e-07
PLN03081	697	PLN03081, PLN03081, pentatricopeptide (PPR) repeat	2e-07
TIGR00756	35	TIGR00756, PPR, pentatricopeptide repeat domain (P	2e-07
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	4e-06
pfam13041	50	pfam13041, PPR_2, PPR repeat family	7e-06
pfam13041	50	pfam13041, PPR_2, PPR repeat family	1e-05
pfam13812	34	pfam13812, PPR_3, Pentatricopeptide repeat domain	1e-05
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	3e-05
TIGR00756	35	TIGR00756, PPR, pentatricopeptide repeat domain (P	6e-05
pfam01535	31	pfam01535, PPR, PPR repeat	6e-05
TIGR00756	35	TIGR00756, PPR, pentatricopeptide repeat domain (P	9e-05
pfam01535	31	pfam01535, PPR, PPR repeat	1e-04
pfam12854	34	pfam12854, PPR_1, PPR repeat	1e-04
pfam12854	34	pfam12854, PPR_1, PPR repeat	6e-04
pfam13041	50	pfam13041, PPR_2, PPR repeat family	0.001
TIGR00756	35	TIGR00756, PPR, pentatricopeptide repeat domain (P	0.002
pfam13812	34	pfam13812, PPR_3, Pentatricopeptide repeat domain	0.002
pfam12854	34	pfam12854, PPR_1, PPR repeat	0.002
PLN03081	697	PLN03081, PLN03081, pentatricopeptide (PPR) repeat	0.004

>gnl|CDD|215636 PLN03218, PLN03218, maturation of RBCL 1; Provisional

 Score = 93.8 bits (233), Expect = 3e-20
 Identities = 73/340 (21%), Positives = 151/340 (44%), Gaps = 2/340 (0%)

Query: 115 QTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAFSTIND 174
            TF  LM +    +  + A  +  ++   GLK    +YT L+S   +SG +D  F   ++
Sbjct: 438 STFNMLMSVCASSQDIDGALRVLRLVQEAGLKADCKLYTTLISTCAKSGKVDAMFEVFHE 497

Query: 175 MKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAK 234
           M   +  + +V+T+  LI  C +  +          M    ++   V +N +I   G++ 
Sbjct: 498 M-VNAGVEANVHTFGALIDGCARAGQVAKAFGAYGIMRSKNVKPDRVVFNALISACGQSG 556

Query: 235 KFEEMESSFSAM-VESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQT 293
             +      + M  E+    PD  T+ +++ A  N+G +++ ++ Y   +   +K   + 
Sbjct: 557 AVDRAFDVLAEMKAETHPIDPDHITVGALMKACANAGQVDRAKEVYQMIHEYNIKGTPEV 616

Query: 294 LNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMK 353
             I   S  + G +D   S+ D M+K+   P  V ++ +++  G AG ++K  E  +  +
Sbjct: 617 YTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDAR 676

Query: 354 HRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVE 413
            +G+K  +++Y SL+ A S A    K   +   +++  +       N +I+A  +   + 
Sbjct: 677 KQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGNQLP 736

Query: 414 KMGELFLTMKERHCVPDNITFATMIQAYNALGMTEAAQNL 453
           K  E+   MK     P+ IT++ ++ A       +   +L
Sbjct: 737 KALEVLSEMKRLGLCPNTITYSILLVASERKDDADVGLDL 776

Length = 1060

>gnl|CDD|215561 PLN03077, PLN03077, Protein ECB2; Provisional

 Score = 84.5 bits (209), Expect = 2e-17
 Identities = 75/329 (22%), Positives = 135/329 (41%), Gaps = 45/329 (13%)

Query: 144 GLKPSVDVYT--ALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRF 201
           G  P  D+++   LV  Y ++G  DEA    + M      +PDVYT+  ++++C      
Sbjct: 145 GKMPERDLFSWNVLVGGYAKAGYFDEALCLYHRMLWAG-VRPDVYTFPCVLRTCGGIPDL 203

Query: 202 DLIEKILAEMSYLGIECSAVTYNTIIDGYGK------AKK-FEEMES----SFSAMV--- 247
               ++ A +   G E      N +I  Y K      A+  F+ M      S++AM+   
Sbjct: 204 ARGREVHAHVVRFGFELDVDVVNALITMYVKCGDVVSARLVFDRMPRRDCISWNAMISGY 263

Query: 248 -ESGGCH---------------PDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADI 291
            E+G C                PD+ T+ S+ISA    G+     + +      G   D+
Sbjct: 264 FENGECLEGLELFFTMRELSVDPDLMTITSVISACELLGDERLGREMHGYVVKTGFAVDV 323

Query: 292 QTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKK 351
              N L + Y   G + +   V   M+ +      V++  +I  + K G  +K  E +  
Sbjct: 324 SVCNSLIQMYLSLGSWGEAEKVFSRMETK----DAVSWTAMISGYEKNGLPDKALETYAL 379

Query: 352 MKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGD 411
           M+   + P+ IT  S++SA +  G +     +    E   +I      N +I  Y +   
Sbjct: 380 MEQDNVSPDEITIASVLSACACLGDLDVGVKLHELAERKGLISYVVVANALIEMYSKCKC 439

Query: 412 VEKMGELFLTMKERHCVPDN--ITFATMI 438
           ++K  E+F      H +P+   I++ ++I
Sbjct: 440 IDKALEVF------HNIPEKDVISWTSII 462

Length = 857

>gnl|CDD|215636 PLN03218, PLN03218, maturation of RBCL 1; Provisional

 Score = 80.7 bits (199), Expect = 4e-16
 Identities = 71/335 (21%), Positives = 154/335 (45%), Gaps = 15/335 (4%)

Query: 97  ALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEV---MLSDGLKPSVDVYT 153
           AL++  L+ Q+   +A C+ +T L   +  C +  +   +FEV   M++ G++ +V  + 
Sbjct: 456 ALRVLRLV-QEAGLKADCKLYTTL---ISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFG 511

Query: 154 ALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSY 213
           AL+    ++G + +AF     M+S  + KPD   ++ LI +C +    D    +LAEM  
Sbjct: 512 ALIDGCARAGQVAKAFGAYGIMRS-KNVKPDRVVFNALISACGQSGAVDRAFDVLAEMKA 570

Query: 214 LG--IECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESG--GCHPDIFTLNSMISAYGNS 269
               I+   +T   ++     A + +  +  +  + E    G  P+++T+   +++    
Sbjct: 571 ETHPIDPDHITVGALMKACANAGQVDRAKEVYQMIHEYNIKGT-PEVYTI--AVNSCSQK 627

Query: 270 GNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTY 329
           G+ +     Y++    GVK D    + L    G AG  DK   ++   +K+      V+Y
Sbjct: 628 GDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIKLGTVSY 687

Query: 330 NIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVEN 389
           + ++     A + +K  E ++ +K   ++P   T  +L++A  +   + K   +L +++ 
Sbjct: 688 SSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGNQLPKALEVLSEMKR 747

Query: 390 SDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKE 424
             +  +T  ++ ++ A  +  D +   +L    KE
Sbjct: 748 LGLCPNTITYSILLVASERKDDADVGLDLLSQAKE 782

Length = 1060

>gnl|CDD|215561 PLN03077, PLN03077, Protein ECB2; Provisional

 Score = 77.6 bits (191), Expect = 5e-15
 Identities = 84/376 (22%), Positives = 140/376 (37%), Gaps = 49/376 (13%)

Query: 120 LMVMLGKCKQPEQASLLFEVMLSDGLKPSVDV--YTALVSAYGQSGLLDEAFSTINDMKS 177
           L+ M  KC     A L+F+ M      P  D   + A++S Y ++G   E       M+ 
Sbjct: 228 LITMYVKCGDVVSARLVFDRM------PRRDCISWNAMISGYFENGECLEGLELFFTMRE 281

Query: 178 VSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFE 237
           +S   PD+ T + +I +C       L  ++   +   G        N++I  Y     + 
Sbjct: 282 LS-VDPDLMTITSVISACELLGDERLGREMHGYVVKTGFAVDVSVCNSLIQMYLSLGSWG 340

Query: 238 EMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNIL 297
           E E  FS M        D  +  +MIS Y  +G  +K  + Y       V  D  T+  +
Sbjct: 341 EAEKVFSRMETK-----DAVSWTAMISGYEKNGLPDKALETYALMEQDNVSPDEITIASV 395

Query: 298 TKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKM----- 352
             +    G  D    + +  +++     VV  N +IE + K   I+K  E F  +     
Sbjct: 396 LSACACLGDLDVGVKLHELAERKGLISYVVVANALIEMYSKCKCIDKALEVFHNIPEKDV 455

Query: 353 ------------KHRG-------------MKPNSITYCSLVSAYSKAGLIMKVDSILRQV 387
                        +R              +KPNS+T  + +SA ++ G +M    I   V
Sbjct: 456 ISWTSIIAGLRLNNRCFEALIFFRQMLLTLKPNSVTLIAALSACARIGALMCGKEIHAHV 515

Query: 388 ENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAYNALGMT 447
             + +  D    N ++  Y + G +      F    E+  V  NI    ++  Y A G  
Sbjct: 516 LRTGIGFDGFLPNALLDLYVRCGRMNYAWNQF-NSHEKDVVSWNI----LLTGYVAHGKG 570

Query: 448 EAAQNLENKMIAMKEN 463
             A  L N+M+    N
Sbjct: 571 SMAVELFNRMVESGVN 586

Length = 857

>gnl|CDD|215636 PLN03218, PLN03218, maturation of RBCL 1; Provisional

 Score = 76.5 bits (188), Expect = 1e-14
 Identities = 76/355 (21%), Positives = 150/355 (42%), Gaps = 24/355 (6%)

Query: 125 GKCKQPEQASLLFEVMLSDG-LKPSVDVYTALVSAYGQSGLLD-------EAFSTINDMK 176
           GK K PE     +  +L DG +K  +D    L+    + GLLD       + F      +
Sbjct: 366 GKRKSPEYIDA-YNRLLRDGRIKDCID----LLEDMEKRGLLDMDKIYHAKFFKACKKQR 420

Query: 177 SVSD----CK----PDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIID 228
           +V +     K    P + T+++L+  C      D   ++L  +   G++     Y T+I 
Sbjct: 421 AVKEAFRFAKLIRNPTLSTFNMLMSVCASSQDIDGALRVLRLVQEAGLKADCKLYTTLIS 480

Query: 229 GYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVK 288
              K+ K + M   F  MV + G   ++ T  ++I     +G + K    Y       VK
Sbjct: 481 TCAKSGKVDAMFEVFHEMVNA-GVEANVHTFGALIDGCARAGQVAKAFGAYGIMRSKNVK 539

Query: 289 ADIQTLNILTKSYGRAGMYDKMRSVMDFM--QKRFFFPTVVTYNIVIETFGKAGHIEKME 346
            D    N L  + G++G  D+   V+  M  +     P  +T   +++    AG +++ +
Sbjct: 540 PDRVVFNALISACGQSGAVDRAFDVLAEMKAETHPIDPDHITVGALMKACANAGQVDRAK 599

Query: 347 EYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAY 406
           E ++ +    +K     Y   V++ S+ G      SI   ++   V  D  FF+ ++   
Sbjct: 600 EVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVA 659

Query: 407 GQAGDVEKMGELFLTMKERHCVPDNITFATMIQAYNALGMTEAAQNLENKMIAMK 461
           G AGD++K  E+    +++      +++++++ A +     + A  L   + ++K
Sbjct: 660 GHAGDLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIK 714

Length = 1060

>gnl|CDD|215636 PLN03218, PLN03218, maturation of RBCL 1; Provisional

 Score = 76.5 bits (188), Expect = 1e-14
 Identities = 70/332 (21%), Positives = 124/332 (37%), Gaps = 76/332 (22%)

Query: 111 QARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAFS 170
           +A   TF  L+    +  Q  +A   + +M S  +KP   V+ AL+SA GQSG +D AF 
Sbjct: 504 EANVHTFGALIDGCARAGQVAKAFGAYGIMRSKNVKPDRVVFNALISACGQSGAVDRAFD 563

Query: 171 TINDMKSVSD-CKPD----------------------VY-------------TYSILIKS 194
            + +MK+ +    PD                      VY              Y+I + S
Sbjct: 564 VLAEMKAETHPIDPDHITVGALMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNS 623

Query: 195 CTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVE--SGGC 252
           C++   +D    I  +M   G++   V ++ ++D  G A   ++   +F  + +    G 
Sbjct: 624 CSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDK---AFEILQDARKQGI 680

Query: 253 HPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRS 312
                + +S++ A  N+ N +K  + Y +   + ++                        
Sbjct: 681 KLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLR------------------------ 716

Query: 313 VMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYS 372
                      PTV T N +I    +   + K  E   +MK  G+ PN+ITY  L+ A  
Sbjct: 717 -----------PTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNTITYSILLVASE 765

Query: 373 KAGLIMKVDSILRQVENSDVILDTPFFNCIIS 404
           +         +L Q +   +  +     CI  
Sbjct: 766 RKDDADVGLDLLSQAKEDGIKPNLVMCRCITG 797

Length = 1060

>gnl|CDD|205222 pfam13041, PPR_2, PPR repeat family

 Score = 64.3 bits (158), Expect = 2e-13
 Identities = 22/50 (44%), Positives = 31/50 (62%)

Query: 324 PTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSK 373
           P VVTYN +I+ + K G +E+  + F +MK RG+KPN  TY  L+    K
Sbjct: 1   PDVVTYNTLIDGYCKKGKVEEALKLFNEMKKRGIKPNVYTYSILIDGLCK 50

This repeat has no known function. It is about 35 amino acids long and is found in up to 18 copies in some proteins. The family appears to be greatly expanded in plants and fungi. The repeat has been called PPR. Length = 50

>gnl|CDD|205222 pfam13041, PPR_2, PPR repeat family

 Score = 60.5 bits (148), Expect = 3e-12
 Identities = 22/51 (43%), Positives = 28/51 (54%), Gaps = 1/51 (1%)

Query: 147 PSVDVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTK 197
           P V  Y  L+  Y + G ++EA    N+MK     KP+VYTYSILI    K
Sbjct: 1   PDVVTYNTLIDGYCKKGKVEEALKLFNEMKK-RGIKPNVYTYSILIDGLCK 50

This repeat has no known function. It is about 35 amino acids long and is found in up to 18 copies in some proteins. The family appears to be greatly expanded in plants and fungi. The repeat has been called PPR. Length = 50

>gnl|CDD|215563 PLN03081, PLN03081, pentatricopeptide (PPR) repeat-containing protein; Provisional

 Score = 67.6 bits (165), Expect = 6e-12
 Identities = 63/289 (21%), Positives = 113/289 (39%), Gaps = 23/289 (7%)

Query: 129 QPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAFSTINDMKSVSDCK------ 182
              +A  LF  M  DG       +  ++ A    G            + +  C       
Sbjct: 204 NYREAFALFREMWEDGSDAEPRTFVVMLRASAGLGS-------ARAGQQLHCCVLKTGVV 256

Query: 183 PDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESS 242
            D +    LI   +K    +    +   M     E + V +N+++ GY      EE    
Sbjct: 257 GDTFVSCALIDMYSKCGDIEDARCVFDGMP----EKTTVAWNSMLAGYALHGYSEEALCL 312

Query: 243 FSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYG 302
           +  M +SG    D FT + MI  +     +E  ++ +      G   DI     L   Y 
Sbjct: 313 YYEMRDSG-VSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRTGFPLDIVANTALVDLYS 371

Query: 303 RAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSI 362
           + G  +  R+V D M ++     ++++N +I  +G  G   K  E F++M   G+ PN +
Sbjct: 372 KWGRMEDARNVFDRMPRK----NLISWNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHV 427

Query: 363 TYCSLVSAYSKAGLIMKVDSILRQV-ENSDVILDTPFFNCIISAYGQAG 410
           T+ +++SA   +GL  +   I + + EN  +      + C+I   G+ G
Sbjct: 428 TFLAVLSACRYSGLSEQGWEIFQSMSENHRIKPRAMHYACMIELLGREG 476

Length = 697

>gnl|CDD|205222 pfam13041, PPR_2, PPR repeat family

 Score = 53.6 bits (130), Expect = 9e-10
 Identities = 19/48 (39%), Positives = 27/48 (56%), Gaps = 1/48 (2%)

Query: 221 VTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGN 268
           VTYNT+IDGY K  K EE    F+ M +  G  P+++T + +I     
Sbjct: 4   VTYNTLIDGYCKKGKVEEALKLFNEMKKR-GIKPNVYTYSILIDGLCK 50

This repeat has no known function. It is about 35 amino acids long and is found in up to 18 copies in some proteins. The family appears to be greatly expanded in plants and fungi. The repeat has been called PPR. Length = 50

>gnl|CDD|205222 pfam13041, PPR_2, PPR repeat family

 Score = 52.8 bits (128), Expect = 2e-09
 Identities = 19/50 (38%), Positives = 27/50 (54%)

Query: 183 PDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGK 232
           PDV TY+ LI    K  + +   K+  EM   GI+ +  TY+ +IDG  K
Sbjct: 1   PDVVTYNTLIDGYCKKGKVEEALKLFNEMKKRGIKPNVYTYSILIDGLCK 50

This repeat has no known function. It is about 35 amino acids long and is found in up to 18 copies in some proteins. The family appears to be greatly expanded in plants and fungi. The repeat has been called PPR. Length = 50

>gnl|CDD|205222 pfam13041, PPR_2, PPR repeat family

 Score = 51.3 bits (124), Expect = 7e-09
 Identities = 14/43 (32%), Positives = 24/43 (55%)

Query: 399 FNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAY 441
           +N +I  Y + G VE+  +LF  MK+R   P+  T++ +I   
Sbjct: 6   YNTLIDGYCKKGKVEEALKLFNEMKKRGIKPNVYTYSILIDGL 48

This repeat has no known function. It is about 35 amino acids long and is found in up to 18 copies in some proteins. The family appears to be greatly expanded in plants and fungi. The repeat has been called PPR. Length = 50

>gnl|CDD|215561 PLN03077, PLN03077, Protein ECB2; Provisional

 Score = 54.1 bits (130), Expect = 1e-07
 Identities = 66/307 (21%), Positives = 126/307 (41%), Gaps = 48/307 (15%)

Query: 152 YTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKI--LA 209
           +TA++S Y ++GL D+A  T   M+   +  PD  T + ++ +C      D+  K+  LA
Sbjct: 357 WTAMISGYEKNGLPDKALETYALME-QDNVSPDEITIASVLSACACLGDLDVGVKLHELA 415

Query: 210 E----MSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVE----------SGGC--- 252
           E    +SY+      V  N +I+ Y K K  ++    F  + E          +G     
Sbjct: 416 ERKGLISYV------VVANALIEMYSKCKCIDKALEVFHNIPEKDVISWTSIIAGLRLNN 469

Query: 253 ----------------HPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNI 296
                            P+  TL + +SA    G +   ++ +      G+  D    N 
Sbjct: 470 RCFEALIFFRQMLLTLKPNSVTLIAALSACARIGALMCGKEIHAHVLRTGIGFDGFLPNA 529

Query: 297 LTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRG 356
           L   Y R G  +   +  +  +K      VV++NI++  +   G      E F +M   G
Sbjct: 530 LLDLYVRCGRMNYAWNQFNSHEK-----DVVSWNILLTGYVAHGKGSMAVELFNRMVESG 584

Query: 357 MKPNSITYCSLVSAYSKAGLIMK-VDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKM 415
           + P+ +T+ SL+ A S++G++ + ++      E   +  +   + C++   G+AG + + 
Sbjct: 585 VNPDEVTFISLLCACSRSGMVTQGLEYFHSMEEKYSITPNLKHYACVVDLLGRAGKLTEA 644

Query: 416 GELFLTM 422
                 M
Sbjct: 645 YNFINKM 651

Length = 857

>gnl|CDD|215563 PLN03081, PLN03081, pentatricopeptide (PPR) repeat-containing protein; Provisional

 Score = 53.3 bits (128), Expect = 2e-07
 Identities = 79/387 (20%), Positives = 145/387 (37%), Gaps = 51/387 (13%)

Query: 114 CQTFTKLMVMLGKCKQPEQASLLFEVMLSDG-LKPSVDVYTALVSAYGQSGLLDEAFSTI 172
           C    KL+     C +  +A  LFE++ +          Y ALV A      +    +  
Sbjct: 91  CSQIEKLVA----CGRHREALELFEILEAGCPFTLPASTYDALVEACIALKSIRCVKAVY 146

Query: 173 NDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGK 232
             ++S S  +PD Y  + ++    K        ++  EM     E +  ++ TII G   
Sbjct: 147 WHVES-SGFEPDQYMMNRVLLMHVKCGMLIDARRLFDEMP----ERNLASWGTIIGGLVD 201

Query: 233 AKKFEEMESSFSAMVESGG-CHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADI 291
           A  + E  + F  M E G    P  F +  M+ A    G+    ++ +      GV  D 
Sbjct: 202 AGNYREAFALFREMWEDGSDAEPRTFVV--MLRASAGLGSARAGQQLHCCVLKTGVVGDT 259

Query: 292 QTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKK 351
                L   Y + G  +  R V D M ++    T V +N ++  +   G+ E+    + +
Sbjct: 260 FVSCALIDMYSKCGDIEDARCVFDGMPEK----TTVAWNSMLAGYALHGYSEEALCLYYE 315

Query: 352 MKHRGMKPNSITYCSLVSAYSKAGLIMKVD----SILRQVENSDVILDTPF--------- 398
           M+  G+  +  T+  ++  +S+  L+         ++R     D++ +T           
Sbjct: 316 MRDSGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKWGR 375

Query: 399 ------------------FNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQA 440
                             +N +I+ YG  G   K  E+F  M      P+++TF  ++ A
Sbjct: 376 MEDARNVFDRMPRKNLISWNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTFLAVLSA 435

Query: 441 YNALGMTEAAQNLENKMIAMKENSGKK 467
               G++E    +     +M EN   K
Sbjct: 436 CRYSGLSEQGWEI---FQSMSENHRIK 459

Length = 697

>gnl|CDD|213555 TIGR00756, PPR, pentatricopeptide repeat domain (PPR motif)

 Score = 46.7 bits (112), Expect = 2e-07
 Identities = 17/35 (48%), Positives = 25/35 (71%)

Query: 327 VTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNS 361
           VTYN +I+   KAG +E+  E FK+MK RG++P+ 
Sbjct: 1   VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35

This model describes a domain called the PPR motif, or pentatricopeptide repeat. Its consensus sequence is 35 positions long and typically is found in four or more tandem copies. This family is strongly represented in plant proteins, particularly those sorted to chloroplasts or mitochondria. The pfam model pfam01535, domain of unknown function DUF17, consists of 6 copies of this repeat. This family has a similar consensus to the TPR domain (tetratricopeptide), pfam pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR. Length = 35

>gnl|CDD|215561 PLN03077, PLN03077, Protein ECB2; Provisional

 Score = 49.1 bits (117), Expect = 4e-06
 Identities = 48/186 (25%), Positives = 85/186 (45%), Gaps = 8/186 (4%)

Query: 260 NSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQK 319
           N+M+S +   G +  +  WY  F  M  + D+ + N+L   Y +AG +D+   +   M  
Sbjct: 125 NAMLSMFVRFGEL--VHAWY-VFGKMPER-DLFSWNVLVGGYAKAGYFDEALCLYHRMLW 180

Query: 320 RFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMK 379
               P V T+  V+ T G    + +  E    +   G + +     +L++ Y K G ++ 
Sbjct: 181 AGVRPDVYTFPCVLRTCGGIPDLARGREVHAHVVRFGFELDVDVVNALITMYVKCGDVVS 240

Query: 380 VDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQ 439
              +  ++   D I     +N +IS Y + G+  +  ELF TM+E    PD +T  ++I 
Sbjct: 241 ARLVFDRMPRRDCI----SWNAMISGYFENGECLEGLELFFTMRELSVDPDLMTITSVIS 296

Query: 440 AYNALG 445
           A   LG
Sbjct: 297 ACELLG 302

Length = 857

>gnl|CDD|205222 pfam13041, PPR_2, PPR repeat family

 Score = 42.8 bits (102), Expect = 7e-06
 Identities = 16/50 (32%), Positives = 27/50 (54%)

Query: 254 PDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGR 303
           PD+ T N++I  Y   G +E+  K +NE    G+K ++ T +IL     +
Sbjct: 1   PDVVTYNTLIDGYCKKGKVEEALKLFNEMKKRGIKPNVYTYSILIDGLCK 50

This repeat has no known function. It is about 35 amino acids long and is found in up to 18 copies in some proteins. The family appears to be greatly expanded in plants and fungi. The repeat has been called PPR. Length = 50

>gnl|CDD|205222 pfam13041, PPR_2, PPR repeat family

 Score = 42.4 bits (101), Expect = 1e-05
 Identities = 16/49 (32%), Positives = 26/49 (53%)

Query: 290 DIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGK 338
           D+ T N L   Y + G  ++   + + M+KR   P V TY+I+I+   K
Sbjct: 2   DVVTYNTLIDGYCKKGKVEEALKLFNEMKKRGIKPNVYTYSILIDGLCK 50

This repeat has no known function. It is about 35 amino acids long and is found in up to 18 copies in some proteins. The family appears to be greatly expanded in plants and fungi. The repeat has been called PPR. Length = 50

>gnl|CDD|205985 pfam13812, PPR_3, Pentatricopeptide repeat domain

 Score = 41.8 bits (99), Expect = 1e-05
 Identities = 11/34 (32%), Positives = 18/34 (52%)

Query: 326 VVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKP 359
           + TYN ++    KAG  +      ++MK  G+KP
Sbjct: 1   LETYNALLLALAKAGDPDLALAVLEEMKASGLKP 34

This family matches additional variants of the PPR repeat that were not captured by the model for pfam01535. The exact function is not known. Length = 34

>gnl|CDD|215561 PLN03077, PLN03077, Protein ECB2; Provisional

 Score = 46.4 bits (110), Expect = 3e-05
 Identities = 51/254 (20%), Positives = 103/254 (40%), Gaps = 20/254 (7%)

Query: 120 LMVMLGKCKQPEQASLLFEVMLSDGLKPSVDV--YTALVSAYGQSGLLDEAFSTINDMKS 177
           L+ M  KCK  ++A  +F  +      P  DV  +T++++    +    EA      M  
Sbjct: 430 LIEMYSKCKCIDKALEVFHNI------PEKDVISWTSIIAGLRLNNRCFEALIFFRQMLL 483

Query: 178 VSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFE 237
               KP+  T    + +C +       ++I A +   GI       N ++D Y +  +  
Sbjct: 484 --TLKPNSVTLIAALSACARIGALMCGKEIHAHVLRTGIGFDGFLPNALLDLYVRCGRMN 541

Query: 238 EMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNIL 297
              + F++         D+ + N +++ Y   G      + +N     GV  D  T   L
Sbjct: 542 YAWNQFNS------HEKDVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISL 595

Query: 298 TKSYGRAGMYDKMRSVMDFMQKRF-FFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRG 356
             +  R+GM  +       M++++   P +  Y  V++  G+AG + +   +  KM    
Sbjct: 596 LCACSRSGMVTQGLEYFHSMEEKYSITPNLKHYACVVDLLGRAGKLTEAYNFINKMP--- 652

Query: 357 MKPNSITYCSLVSA 370
           + P+   + +L++A
Sbjct: 653 ITPDPAVWGALLNA 666

Length = 857

>gnl|CDD|213555 TIGR00756, PPR, pentatricopeptide repeat domain (PPR motif)

 Score = 39.8 bits (94), Expect = 6e-05
 Identities = 18/36 (50%), Positives = 21/36 (58%), Gaps = 1/36 (2%)

Query: 221 VTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDI 256
           VTYNT+IDG  KA + EE    F  M E  G  PD+
Sbjct: 1   VTYNTLIDGLCKAGRVEEALELFKEMKER-GIEPDV 35

This model describes a domain called the PPR motif, or pentatricopeptide repeat. Its consensus sequence is 35 positions long and typically is found in four or more tandem copies. This family is strongly represented in plant proteins, particularly those sorted to chloroplasts or mitochondria. The pfam model pfam01535, domain of unknown function DUF17, consists of 6 copies of this repeat. This family has a similar consensus to the TPR domain (tetratricopeptide), pfam pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR. Length = 35

>gnl|CDD|144943 pfam01535, PPR, PPR repeat

 Score = 39.4 bits (93), Expect = 6e-05
 Identities = 16/30 (53%), Positives = 18/30 (60%)

Query: 221 VTYNTIIDGYGKAKKFEEMESSFSAMVESG 250
           VTYN++I GY KA K EE    F  M E G
Sbjct: 1   VTYNSLISGYCKAGKLEEALELFKEMKEKG 30

This repeat has no known function. It is about 35 amino acids long and found in up to 18 copies in some proteins. This family appears to be greatly expanded in plants. This repeat occurs in PET309, which may be involved in RNA stabilisation. This domain occurs in crp1 that is involved in RNA processing. This repeat is associated with a predicted plant protein that has a domain organisation similar to the human BRCA1 protein. The repeat has been called PPR. Length = 31

>gnl|CDD|213555 TIGR00756, PPR, pentatricopeptide repeat domain (PPR motif)

 Score = 39.4 bits (93), Expect = 9e-05
 Identities = 15/32 (46%), Positives = 19/32 (59%)

Query: 399 FNCIISAYGQAGDVEKMGELFLTMKERHCVPD 430
           +N +I    +AG VE+  ELF  MKER   PD
Sbjct: 3   YNTLIDGLCKAGRVEEALELFKEMKERGIEPD 34

This model describes a domain called the PPR motif, or pentatricopeptide repeat. Its consensus sequence is 35 positions long and typically is found in four or more tandem copies. This family is strongly represented in plant proteins, particularly those sorted to chloroplasts or mitochondria. The pfam model pfam01535, domain of unknown function DUF17, consists of 6 copies of this repeat. This family has a similar consensus to the TPR domain (tetratricopeptide), pfam pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR. Length = 35

>gnl|CDD|144943 pfam01535, PPR, PPR repeat

 Score = 38.6 bits (91), Expect = 1e-04
 Identities = 15/31 (48%), Positives = 22/31 (70%)

Query: 327 VTYNIVIETFGKAGHIEKMEEYFKKMKHRGM 357
           VTYN +I  + KAG +E+  E FK+MK +G+
Sbjct: 1   VTYNSLISGYCKAGKLEEALELFKEMKEKGV 31

This repeat has no known function. It is about 35 amino acids long and found in up to 18 copies in some proteins. This family appears to be greatly expanded in plants. This repeat occurs in PET309, which may be involved in RNA stabilisation. This domain occurs in crp1 that is involved in RNA processing. This repeat is associated with a predicted plant protein that has a domain organisation similar to the human BRCA1 protein. The repeat has been called PPR. Length = 31

>gnl|CDD|205109 pfam12854, PPR_1, PPR repeat

 Score = 38.5 bits (91), Expect = 1e-04
 Identities = 11/32 (34%), Positives = 19/32 (59%)

Query: 322 FFPTVVTYNIVIETFGKAGHIEKMEEYFKKMK 353
             P VVTYN +I+   +AG +++  E   +M+
Sbjct: 3   LKPDVVTYNTLIDGLCRAGRVDEAVELLDEME 34

This family matches additional variants of the PPR repeat that were not captured by the model for pfam01535. The exact function is not known. Length = 34

>gnl|CDD|205109 pfam12854, PPR_1, PPR repeat

 Score = 36.9 bits (87), Expect = 6e-04
 Identities = 12/34 (35%), Positives = 20/34 (58%)

Query: 143 DGLKPSVDVYTALVSAYGQSGLLDEAFSTINDMK 176
            GLKP V  Y  L+    ++G +DEA   +++M+
Sbjct: 1   KGLKPDVVTYNTLIDGLCRAGRVDEAVELLDEME 34

This family matches additional variants of the PPR repeat that were not captured by the model for pfam01535. The exact function is not known. Length = 34

>gnl|CDD|205222 pfam13041, PPR_2, PPR repeat family

 Score = 36.6 bits (86), Expect = 0.001
 Identities = 14/44 (31%), Positives = 22/44 (50%)

Query: 116 TFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAY 159
           T+  L+    K  + E+A  LF  M   G+KP+V  Y+ L+   
Sbjct: 5   TYNTLIDGYCKKGKVEEALKLFNEMKKRGIKPNVYTYSILIDGL 48

This repeat has no known function. It is about 35 amino acids long and is found in up to 18 copies in some proteins. The family appears to be greatly expanded in plants and fungi. The repeat has been called PPR. Length = 50

>gnl|CDD|213555 TIGR00756, PPR, pentatricopeptide repeat domain (PPR motif)

 Score = 35.5 bits (83), Expect = 0.002
 Identities = 10/35 (28%), Positives = 17/35 (48%), Gaps = 1/35 (2%)

Query: 151 VYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDV 185
            Y  L+    ++G ++EA     +MK     +PDV
Sbjct: 2   TYNTLIDGLCKAGRVEEALELFKEMKE-RGIEPDV 35

This model describes a domain called the PPR motif, or pentatricopeptide repeat. Its consensus sequence is 35 positions long and typically is found in four or more tandem copies. This family is strongly represented in plant proteins, particularly those sorted to chloroplasts or mitochondria. The pfam model pfam01535, domain of unknown function DUF17, consists of 6 copies of this repeat. This family has a similar consensus to the TPR domain (tetratricopeptide), pfam pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR. Length = 35

>gnl|CDD|205985 pfam13812, PPR_3, Pentatricopeptide repeat domain

 Score = 35.2 bits (82), Expect = 0.002
 Identities = 10/33 (30%), Positives = 17/33 (51%)

Query: 185 VYTYSILIKSCTKFHRFDLIEKILAEMSYLGIE 217
           + TY+ L+ +  K    DL   +L EM   G++
Sbjct: 1   LETYNALLLALAKAGDPDLALAVLEEMKASGLK 33

This family matches additional variants of the PPR repeat that were not captured by the model for pfam01535. The exact function is not known. Length = 34

>gnl|CDD|205109 pfam12854, PPR_1, PPR repeat

 Score = 35.4 bits (83), Expect = 0.002
 Identities = 13/33 (39%), Positives = 19/33 (57%), Gaps = 7/33 (21%)

Query: 215 GIECSAVTYNTIIDGYGKAKK-------FEEME 240
           G++   VTYNT+IDG  +A +        +EME
Sbjct: 2   GLKPDVVTYNTLIDGLCRAGRVDEAVELLDEME 34

This family matches additional variants of the PPR repeat that were not captured by the model for pfam01535. The exact function is not known. Length = 34

>gnl|CDD|215563 PLN03081, PLN03081, pentatricopeptide (PPR) repeat-containing protein; Provisional

 Score = 39.5 bits (92), Expect = 0.004
 Identities = 24/84 (28%), Positives = 43/84 (51%), Gaps = 6/84 (7%)

Query: 131 EQASLLFEVMLSD-GLKPSVDVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYS 189
           EQ   +F+ M  +  +KP    Y  ++   G+ GLLDEA++ I      +  KP V  ++
Sbjct: 443 EQGWEIFQSMSENHRIKPRAMHYACMIELLGREGLLDEAYAMIRR----APFKPTVNMWA 498

Query: 190 ILIKSCTKFHRFDLIEKILAEMSY 213
            L+ +C + H+   + ++ AE  Y
Sbjct: 499 ALLTAC-RIHKNLELGRLAAEKLY 521

Length = 697

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	471
PLN03218	1060	maturation of RBCL 1; Provisional	100.0
PLN03218	1060	maturation of RBCL 1; Provisional	100.0
PLN03081	697	pentatricopeptide (PPR) repeat-containing protein;	100.0
PLN03081	697	pentatricopeptide (PPR) repeat-containing protein;	100.0
PLN03077	857	Protein ECB2; Provisional	100.0
PLN03077	857	Protein ECB2; Provisional	100.0
TIGR02917	899	PEP_TPR_lipo putative PEP-CTERM system TPR-repeat	99.97
TIGR02917	899	PEP_TPR_lipo putative PEP-CTERM system TPR-repeat	99.97
PRK11788	389	tetratricopeptide repeat protein; Provisional	99.93
PRK11788	389	tetratricopeptide repeat protein; Provisional	99.93
PRK15174	656	Vi polysaccharide export protein VexE; Provisional	99.92
TIGR00990	615	3a0801s09 mitochondrial precursor proteins import	99.92
KOG4626	966	consensus O-linked N-acetylglucosamine transferase	99.91
KOG4626	966	consensus O-linked N-acetylglucosamine transferase	99.91
PRK15174	656	Vi polysaccharide export protein VexE; Provisional	99.91
PRK10049	765	pgaA outer membrane protein PgaA; Provisional	99.9
PRK11447	1157	cellulose synthase subunit BcsC; Provisional	99.9
PRK11447	1157	cellulose synthase subunit BcsC; Provisional	99.9
TIGR00990	615	3a0801s09 mitochondrial precursor proteins import	99.89
PRK14574	822	hmsH outer membrane protein; Provisional	99.87
PRK10049	765	pgaA outer membrane protein PgaA; Provisional	99.84
PRK14574	822	hmsH outer membrane protein; Provisional	99.83
PRK09782	987	bacteriophage N4 receptor, outer membrane subunit;	99.8
KOG4422	625	consensus Uncharacterized conserved protein [Funct	99.79
PRK09782	987	bacteriophage N4 receptor, outer membrane subunit;	99.79
KOG2076	895	consensus RNA polymerase III transcription factor	99.78
KOG4422	625	consensus Uncharacterized conserved protein [Funct	99.75
KOG2002	1018	consensus TPR-containing nuclear phosphoprotein th	99.74
PRK10747	398	putative protoheme IX biogenesis protein; Provisio	99.72
TIGR00540	409	hemY_coli hemY protein. This is an uncharacterized	99.72
PRK10747	398	putative protoheme IX biogenesis protein; Provisio	99.7
KOG2003	840	consensus TPR repeat-containing protein [General f	99.69
TIGR00540	409	hemY_coli hemY protein. This is an uncharacterized	99.69
KOG2003	840	consensus TPR repeat-containing protein [General f	99.69
KOG2002	1018	consensus TPR-containing nuclear phosphoprotein th	99.68
KOG0495	913	consensus HAT repeat protein [RNA processing and m	99.67
PF13429	280	TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2	99.67
KOG0547	606	consensus Translocase of outer mitochondrial membr	99.67
KOG1915	677	consensus Cell cycle control protein (crooked neck	99.67
KOG1126	638	consensus DNA-binding cell division cycle control	99.66
KOG0495	913	consensus HAT repeat protein [RNA processing and m	99.66
PF13429	280	TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2	99.65
COG2956	389	Predicted N-acetylglucosaminyl transferase [Carboh	99.64
COG2956	389	Predicted N-acetylglucosaminyl transferase [Carboh	99.64
KOG1155	559	consensus Anaphase-promoting complex (APC), Cdc23	99.64
KOG2076	895	consensus RNA polymerase III transcription factor	99.63
COG3071	400	HemY Uncharacterized enzyme of heme biosynthesis [	99.63
KOG1126	638	consensus DNA-binding cell division cycle control	99.62
COG3071	400	HemY Uncharacterized enzyme of heme biosynthesis [	99.62
KOG1155	559	consensus Anaphase-promoting complex (APC), Cdc23	99.57
KOG1915	677	consensus Cell cycle control protein (crooked neck	99.52
TIGR02521	234	type_IV_pilW type IV pilus biogenesis/stability pr	99.51
KOG1174	564	consensus Anaphase-promoting complex (APC), subuni	99.49
PRK12370	553	invasion protein regulator; Provisional	99.48
KOG3785	557	consensus Uncharacterized conserved protein [Funct	99.47
PRK12370	553	invasion protein regulator; Provisional	99.47
KOG1129	478	consensus TPR repeat-containing protein [General f	99.47
KOG0547	606	consensus Translocase of outer mitochondrial membr	99.47
TIGR02521	234	type_IV_pilW type IV pilus biogenesis/stability pr	99.46
KOG1173	611	consensus Anaphase-promoting complex (APC), Cdc16	99.45
KOG1129	478	consensus TPR repeat-containing protein [General f	99.45
KOG4318	1088	consensus Bicoid mRNA stability factor [RNA proces	99.44
PF12569	517	NARP1: NMDA receptor-regulated protein 1 ; InterPr	99.42
PF12569	517	NARP1: NMDA receptor-regulated protein 1 ; InterPr	99.4
KOG2047	835	consensus mRNA splicing factor [RNA processing and	99.4
KOG1840	508	consensus Kinesin light chain [Cytoskeleton]	99.39
KOG1173	611	consensus Anaphase-promoting complex (APC), Cdc16	99.38
KOG1156	700	consensus N-terminal acetyltransferase [Chromatin	99.36
PF13041	50	PPR_2: PPR repeat family	99.35
KOG4318	1088	consensus Bicoid mRNA stability factor [RNA proces	99.35
KOG2376	652	consensus Signal recognition particle, subunit Srp	99.32
COG3063	250	PilF Tfp pilus assembly protein PilF [Cell motilit	99.32
PF13041	50	PPR_2: PPR repeat family	99.31
KOG2047	835	consensus mRNA splicing factor [RNA processing and	99.29
KOG4162	799	consensus Predicted calmodulin-binding protein [Si	99.28
KOG1156	700	consensus N-terminal acetyltransferase [Chromatin	99.27
KOG4340	459	consensus Uncharacterized conserved protein [Funct	99.26
PRK11189	296	lipoprotein NlpI; Provisional	99.25
cd05804	355	StaR_like StaR_like; a well-conserved protein foun	99.24
KOG1840	508	consensus Kinesin light chain [Cytoskeleton]	99.24
PRK11189	296	lipoprotein NlpI; Provisional	99.22
KOG1174	564	consensus Anaphase-promoting complex (APC), subuni	99.21
cd05804	355	StaR_like StaR_like; a well-conserved protein foun	99.21
KOG0548	539	consensus Molecular co-chaperone STI1 [Posttransla	99.2
KOG3785	557	consensus Uncharacterized conserved protein [Funct	99.19
COG3063	250	PilF Tfp pilus assembly protein PilF [Cell motilit	99.19
PRK04841	903	transcriptional regulator MalT; Provisional	99.19
KOG0624	504	consensus dsRNA-activated protein kinase inhibitor	99.08
KOG4340	459	consensus Uncharacterized conserved protein [Funct	99.05
PF04733	290	Coatomer_E: Coatomer epsilon subunit; InterPro: IP	99.03
PF04733	290	Coatomer_E: Coatomer epsilon subunit; InterPro: IP	99.02
KOG0985	1666	consensus Vesicle coat protein clathrin, heavy cha	99.0
KOG1128	777	consensus Uncharacterized conserved protein, conta	98.97
KOG1125	579	consensus TPR repeat-containing protein [General f	98.96
KOG2376	652	consensus Signal recognition particle, subunit Srp	98.95
PRK04841	903	transcriptional regulator MalT; Provisional	98.94
KOG1125	579	consensus TPR repeat-containing protein [General f	98.94
KOG4162	799	consensus Predicted calmodulin-binding protein [Si	98.94
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	98.89
KOG0624	504	consensus dsRNA-activated protein kinase inhibitor	98.88
PLN02789	320	farnesyltranstransferase	98.86
KOG3617	1416	consensus WD40 and TPR repeat-containing protein [	98.84
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	98.82
PLN02789	320	farnesyltranstransferase	98.81
PRK10370	198	formate-dependent nitrite reductase complex subuni	98.8
KOG3616	1636	consensus Selective LIM binding factor [Transcript	98.79
KOG0985	1666	consensus Vesicle coat protein clathrin, heavy cha	98.77
PF12854	34	PPR_1: PPR repeat	98.77
TIGR03302	235	OM_YfiO outer membrane assembly lipoprotein YfiO.	98.76
KOG3616	1636	consensus Selective LIM binding factor [Transcript	98.74
KOG1914	656	consensus mRNA cleavage and polyadenylation factor	98.73
KOG1914	656	consensus mRNA cleavage and polyadenylation factor	98.73
KOG3617	1416	consensus WD40 and TPR repeat-containing protein [	98.71
COG5010	257	TadD Flp pilus assembly protein TadD, contains TPR	98.71
TIGR03302	235	OM_YfiO outer membrane assembly lipoprotein YfiO.	98.71
KOG3081	299	consensus Vesicle coat complex COPI, epsilon subun	98.7
PF12854	34	PPR_1: PPR repeat	98.7
PRK15179	694	Vi polysaccharide biosynthesis protein TviE; Provi	98.7
KOG1127	1238	consensus TPR repeat-containing protein [RNA proce	98.69
KOG1128	777	consensus Uncharacterized conserved protein, conta	98.69
PRK10370	198	formate-dependent nitrite reductase complex subuni	98.69
KOG2053	932	consensus Mitochondrial inheritance and actin cyto	98.68
COG5010	257	TadD Flp pilus assembly protein TadD, contains TPR	98.67
KOG0548	539	consensus Molecular co-chaperone STI1 [Posttransla	98.67
PRK14720	906	transcript cleavage factor/unknown domain fusion p	98.65
KOG3081	299	consensus Vesicle coat complex COPI, epsilon subun	98.63
PRK15179	694	Vi polysaccharide biosynthesis protein TviE; Provi	98.63
PRK15359	144	type III secretion system chaperone protein SscB;	98.61
PRK15359	144	type III secretion system chaperone protein SscB;	98.61
COG4783	484	Putative Zn-dependent protease, contains TPR repea	98.61
PRK14720	906	transcript cleavage factor/unknown domain fusion p	98.54
TIGR02552	135	LcrH_SycD type III secretion low calcium response	98.53
COG4783	484	Putative Zn-dependent protease, contains TPR repea	98.52
KOG3060	289	consensus Uncharacterized conserved protein [Funct	98.5
KOG3060	289	consensus Uncharacterized conserved protein [Funct	98.46
KOG1127	1238	consensus TPR repeat-containing protein [RNA proce	98.42
TIGR02552	135	LcrH_SycD type III secretion low calcium response	98.4
PF09976	145	TPR_21: Tetratricopeptide repeat; InterPro: IPR018	98.33
PF09295	395	ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); Inter	98.3
TIGR00756	35	PPR pentatricopeptide repeat domain (PPR motif). T	98.23
PF09295	395	ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); Inter	98.22
PF13812	34	PPR_3: Pentatricopeptide repeat domain	98.18
TIGR02795	119	tol_pal_ybgF tol-pal system protein YbgF. Members	98.17
cd00189	100	TPR Tetratricopeptide repeat domain; typically con	98.13
KOG2053	932	consensus Mitochondrial inheritance and actin cyto	98.12
PF10037	429	MRP-S27: Mitochondrial 28S ribosomal protein S27;	98.12
TIGR00756	35	PPR pentatricopeptide repeat domain (PPR motif). T	98.11
PF09976	145	TPR_21: Tetratricopeptide repeat; InterPro: IPR018	98.07
PF13812	34	PPR_3: Pentatricopeptide repeat domain	98.06
PRK10866	243	outer membrane biogenesis protein BamD; Provisiona	98.05
PF08579	120	RPM2: Mitochondrial ribonuclease P subunit (RPM2);	98.01
PF10037	429	MRP-S27: Mitochondrial 28S ribosomal protein S27;	98.01
PRK15363	157	pathogenicity island 2 chaperone protein SscA; Pro	97.96
TIGR02795	119	tol_pal_ybgF tol-pal system protein YbgF. Members	97.94
PLN03088	356	SGT1, suppressor of G2 allele of SKP1; Provisional	97.93
PF12895	84	Apc3: Anaphase-promoting complex, cyclosome, subun	97.93
PF08579	120	RPM2: Mitochondrial ribonuclease P subunit (RPM2);	97.93
PLN03088	356	SGT1, suppressor of G2 allele of SKP1; Provisional	97.91
PF14938	282	SNAP: Soluble NSF attachment protein, SNAP; PDB: 1	97.9
cd00189	100	TPR Tetratricopeptide repeat domain; typically con	97.89
PF05843	280	Suf: Suppressor of forked protein (Suf); InterPro:	97.88
PF12895	84	Apc3: Anaphase-promoting complex, cyclosome, subun	97.88
PRK15363	157	pathogenicity island 2 chaperone protein SscA; Pro	97.86
PF01535	31	PPR: PPR repeat; InterPro: IPR002885 This entry re	97.85
KOG2041	1189	consensus WD40 repeat protein [General function pr	97.84
PRK02603	172	photosystem I assembly protein Ycf3; Provisional	97.83
PRK10153	517	DNA-binding transcriptional activator CadC; Provis	97.82
KOG0550	486	consensus Molecular chaperone (DnaJ superfamily) [	97.82
PF05843	280	Suf: Suppressor of forked protein (Suf); InterPro:	97.8
PRK02603	172	photosystem I assembly protein Ycf3; Provisional	97.8
PF06239	228	ECSIT: Evolutionarily conserved signalling interme	97.78
COG4700	251	Uncharacterized protein conserved in bacteria cont	97.78
PF14938	282	SNAP: Soluble NSF attachment protein, SNAP; PDB: 1	97.78
PRK10866	243	outer membrane biogenesis protein BamD; Provisiona	97.78
PF14559	68	TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN	97.77
PF13432	65	TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL	97.77
KOG0553	304	consensus TPR repeat-containing protein [General f	97.74
KOG0553	304	consensus TPR repeat-containing protein [General f	97.73
PF13414	69	TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A	97.73
PF01535	31	PPR: PPR repeat; InterPro: IPR002885 This entry re	97.69
CHL00033	168	ycf3 photosystem I assembly protein Ycf3	97.67
PF13525	203	YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M	97.65
PRK10803	263	tol-pal system protein YbgF; Provisional	97.62
PF06239	228	ECSIT: Evolutionarily conserved signalling interme	97.6
PRK10153	517	DNA-binding transcriptional activator CadC; Provis	97.6
COG4235	287	Cytochrome c biogenesis factor [Posttranslational	97.58
CHL00033	168	ycf3 photosystem I assembly protein Ycf3	97.57
PF14559	68	TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN	97.56
PF12688	120	TPR_5: Tetratrico peptide repeat	97.47
PF13432	65	TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL	97.46
COG4235	287	Cytochrome c biogenesis factor [Posttranslational	97.42
KOG2796	366	consensus Uncharacterized conserved protein [Funct	97.41
PF13525	203	YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M	97.37
KOG1130	639	consensus Predicted G-alpha GTPase interaction pro	97.37
KOG2796	366	consensus Uncharacterized conserved protein [Funct	97.36
PF13414	69	TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A	97.36
KOG1538	1081	consensus Uncharacterized conserved protein WDR10,	97.32
COG5107	660	RNA14 Pre-mRNA 3'-end processing (cleavage and pol	97.31
PF04840	319	Vps16_C: Vps16, C-terminal region; InterPro: IPR00	97.3
KOG0550	486	consensus Molecular chaperone (DnaJ superfamily) [	97.27
PF12688	120	TPR_5: Tetratrico peptide repeat	97.27
PF03704	146	BTAD: Bacterial transcriptional activator domain;	97.22
KOG2041	1189	consensus WD40 repeat protein [General function pr	97.2
PF13371	73	TPR_9: Tetratricopeptide repeat	97.18
PF13281	374	DUF4071: Domain of unknown function (DUF4071)	97.16
KOG1130	639	consensus Predicted G-alpha GTPase interaction pro	97.13
PF12921	126	ATP13: Mitochondrial ATPase expression; InterPro:	97.1
PF04840	319	Vps16_C: Vps16, C-terminal region; InterPro: IPR00	97.09
PRK10803	263	tol-pal system protein YbgF; Provisional	97.07
COG4700	251	Uncharacterized protein conserved in bacteria cont	97.04
PF13371	73	TPR_9: Tetratricopeptide repeat	96.99
PRK15331	165	chaperone protein SicA; Provisional	96.88
COG3898	531	Uncharacterized membrane-bound protein [Function u	96.85
PF13424	78	TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15	96.85
KOG2280	829	consensus Vacuolar assembly/sorting protein VPS16	96.82
PF03704	146	BTAD: Bacterial transcriptional activator domain;	96.81
PF12921	126	ATP13: Mitochondrial ATPase expression; InterPro:	96.79
COG4105	254	ComL DNA uptake lipoprotein [General function pred	96.77
KOG1538	1081	consensus Uncharacterized conserved protein WDR10,	96.73
COG3898	531	Uncharacterized membrane-bound protein [Function u	96.72
PF04184	539	ST7: ST7 protein; InterPro: IPR007311 The ST7 (for	96.67
PRK15331	165	chaperone protein SicA; Provisional	96.64
COG3118	304	Thioredoxin domain-containing protein [Posttransla	96.59
COG3118	304	Thioredoxin domain-containing protein [Posttransla	96.54
PF09205	161	DUF1955: Domain of unknown function (DUF1955); Int	96.5
PF09205	161	DUF1955: Domain of unknown function (DUF1955); Int	96.5
PF13424	78	TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15	96.42
KOG0543	397	consensus FKBP-type peptidyl-prolyl cis-trans isom	96.4
PF10300	468	DUF3808: Protein of unknown function (DUF3808); In	96.36
PF04053	443	Coatomer_WDAD: Coatomer WD associated region ; Int	96.3
KOG3941	406	consensus Intermediate in Toll signal transduction	96.26
COG1729	262	Uncharacterized protein conserved in bacteria [Fun	96.25
PF10300	468	DUF3808: Protein of unknown function (DUF3808); In	96.25
PLN03098	453	LPA1 LOW PSII ACCUMULATION1; Provisional	96.24
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	96.22
COG4105	254	ComL DNA uptake lipoprotein [General function pred	96.17
smart00299	140	CLH Clathrin heavy chain repeat homology.	96.15
PLN03098	453	LPA1 LOW PSII ACCUMULATION1; Provisional	96.05
KOG0543	397	consensus FKBP-type peptidyl-prolyl cis-trans isom	96.04
PF04053	443	Coatomer_WDAD: Coatomer WD associated region ; Int	96.03
KOG1258	577	consensus mRNA processing protein [RNA processing	96.02
KOG4555	175	consensus TPR repeat-containing protein [Function	96.0
PF13512	142	TPR_18: Tetratricopeptide repeat	95.99
KOG2610	491	consensus Uncharacterized conserved protein [Funct	95.9
COG0457	291	NrfG FOG: TPR repeat [General function prediction	95.88
PF08631	278	SPO22: Meiosis protein SPO22/ZIP4 like; InterPro:	95.78
PF13281	374	DUF4071: Domain of unknown function (DUF4071)	95.7
COG1729	262	Uncharacterized protein conserved in bacteria [Fun	95.68
KOG4555	175	consensus TPR repeat-containing protein [Function	95.68
PF08631	278	SPO22: Meiosis protein SPO22/ZIP4 like; InterPro:	95.55
PF07079	549	DUF1347: Protein of unknown function (DUF1347); In	95.53
COG3629	280	DnrI DNA-binding transcriptional activator of the	95.52
PF13428	44	TPR_14: Tetratricopeptide repeat	95.48
PF13176	36	TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_	95.47
COG5107	660	RNA14 Pre-mRNA 3'-end processing (cleavage and pol	95.4
PRK11906	458	transcriptional regulator; Provisional	95.39
KOG1920	1265	consensus IkappaB kinase complex, IKAP component [	95.36
KOG3941	406	consensus Intermediate in Toll signal transduction	95.36
smart00299	140	CLH Clathrin heavy chain repeat homology.	95.35
PF13512	142	TPR_18: Tetratricopeptide repeat	95.31
PF07035	167	Mic1: Colon cancer-associated protein Mic1-like; I	95.26
PF04184	539	ST7: ST7 protein; InterPro: IPR007311 The ST7 (for	95.26
PF09613	160	HrpB1_HrpK: Bacterial type III secretion protein (	95.18
PF07719	34	TPR_2: Tetratricopeptide repeat; InterPro: IPR0131	95.16
PF13428	44	TPR_14: Tetratricopeptide repeat	95.03
COG4649	221	Uncharacterized protein conserved in bacteria [Fun	95.0
PF00515	34	TPR_1: Tetratricopeptide repeat; InterPro: IPR0014	94.89
KOG1941	518	consensus Acetylcholine receptor-associated protei	94.84
KOG1941	518	consensus Acetylcholine receptor-associated protei	94.76
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	94.58
KOG2280	829	consensus Vacuolar assembly/sorting protein VPS16	94.55
KOG1920	1265	consensus IkappaB kinase complex, IKAP component [	94.53
PF09613	160	HrpB1_HrpK: Bacterial type III secretion protein (	94.45
PF02259	352	FAT: FAT domain; InterPro: IPR003151 The FAT domai	94.36
KOG2066	846	consensus Vacuolar assembly/sorting protein VPS41	94.22
PF13170	297	DUF4003: Protein of unknown function (DUF4003)	94.2
PF07079	549	DUF1347: Protein of unknown function (DUF1347); In	93.96
PRK11906	458	transcriptional regulator; Provisional	93.84
COG3629	280	DnrI DNA-binding transcriptional activator of the	93.62
KOG2610	491	consensus Uncharacterized conserved protein [Funct	93.62
KOG1585	308	consensus Protein required for fusion of vesicles	93.61
cd00923	103	Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va.	93.47
KOG1550	552	consensus Extracellular protein SEL-1 and related	93.45
PF13431	34	TPR_17: Tetratricopeptide repeat	93.33
PF13170	297	DUF4003: Protein of unknown function (DUF4003)	93.25
PF13181	34	TPR_8: Tetratricopeptide repeat; PDB: 3GW4_B 3MA5_	93.1
TIGR02561	153	HrpB1_HrpK type III secretion protein HrpB1/HrpK.	93.09
PF13929	292	mRNA_stabil: mRNA stabilisation	92.91
KOG1585	308	consensus Protein required for fusion of vesicles	92.9
PF13176	36	TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_	92.89
COG2976	207	Uncharacterized protein conserved in bacteria [Fun	92.67
PF02284	108	COX5A: Cytochrome c oxidase subunit Va; InterPro:	92.66
PF10602	177	RPN7: 26S proteasome subunit RPN7; InterPro: IPR01	92.47
PF13431	34	TPR_17: Tetratricopeptide repeat	92.27
PF10602	177	RPN7: 26S proteasome subunit RPN7; InterPro: IPR01	92.23
PF04097	613	Nic96: Nup93/Nic96; InterPro: IPR007231 Nup93/Nic9	92.17
PF13174	33	TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_	92.05
KOG4570	418	consensus Uncharacterized conserved protein [Funct	91.82
PF02284	108	COX5A: Cytochrome c oxidase subunit Va; InterPro:	91.76
COG4649	221	Uncharacterized protein conserved in bacteria [Fun	91.6
COG4455	273	ImpE Protein of avirulence locus involved in tempe	91.15
KOG1550	552	consensus Extracellular protein SEL-1 and related	91.12
PF00515	34	TPR_1: Tetratricopeptide repeat; InterPro: IPR0014	90.94
KOG4570	418	consensus Uncharacterized conserved protein [Funct	90.87
PF02259	352	FAT: FAT domain; InterPro: IPR003151 The FAT domai	90.81
COG4785	297	NlpI Lipoprotein NlpI, contains TPR repeats [Gener	90.72
PF07035	167	Mic1: Colon cancer-associated protein Mic1-like; I	90.66
KOG0276	794	consensus Vesicle coat complex COPI, beta' subunit	90.5
KOG0276	794	consensus Vesicle coat complex COPI, beta' subunit	90.46
cd00923	103	Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va.	90.14
COG4455	273	ImpE Protein of avirulence locus involved in tempe	90.1
PF07719	34	TPR_2: Tetratricopeptide repeat; InterPro: IPR0131	89.83
PF13374	42	TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT	89.53
COG3947	361	Response regulator containing CheY-like receiver a	89.53
COG0457	291	NrfG FOG: TPR repeat [General function prediction	88.91
TIGR02561	153	HrpB1_HrpK type III secretion protein HrpB1/HrpK.	88.61
PF07163	309	Pex26: Pex26 protein; InterPro: IPR010797 This fam	88.5
KOG4648	536	consensus Uncharacterized conserved protein, conta	88.5
PF13374	42	TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT	88.37
PF11207	203	DUF2989: Protein of unknown function (DUF2989); In	87.91
KOG4234	271	consensus TPR repeat-containing protein [General f	87.6
PF11207	203	DUF2989: Protein of unknown function (DUF2989); In	87.53
KOG1464	440	consensus COP9 signalosome, subunit CSN2 [Posttran	87.37
KOG4077	149	consensus Cytochrome c oxidase, subunit Va/COX6 [E	87.12
PF13929	292	mRNA_stabil: mRNA stabilisation	86.78
KOG0890	2382	consensus Protein kinase of the PI-3 kinase family	86.75
PF00637	143	Clathrin: Region in Clathrin and VPS; InterPro: IP	86.74
KOG2396	568	consensus HAT (Half-A-TPR) repeat-containing prote	86.52
KOG4648	536	consensus Uncharacterized conserved protein, conta	85.46
PRK09687	280	putative lyase; Provisional	84.63
COG2909	894	MalT ATP-dependent transcriptional regulator [Tran	84.56
KOG0292	1202	consensus Vesicle coat complex COPI, alpha subunit	84.55
TIGR03504	44	FimV_Cterm FimV C-terminal domain. This protein is	84.26
KOG4234	271	consensus TPR repeat-containing protein [General f	83.91
smart00028	34	TPR Tetratricopeptide repeats. Repeats present in	83.75
PF13174	33	TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_	83.65
PF06552	186	TOM20_plant: Plant specific mitochondrial import r	83.6
PF06552	186	TOM20_plant: Plant specific mitochondrial import r	83.55
PF14853	53	Fis1_TPR_C: Fis1 C-terminal tetratricopeptide repe	83.55
PF07721	26	TPR_4: Tetratricopeptide repeat; InterPro: IPR0117	83.0
COG2909	894	MalT ATP-dependent transcriptional regulator [Tran	82.82
PF13181	34	TPR_8: Tetratricopeptide repeat; PDB: 3GW4_B 3MA5_	82.27
KOG1258	577	consensus mRNA processing protein [RNA processing	82.01
PRK15180	831	Vi polysaccharide biosynthesis protein TviD; Provi	81.93
TIGR03504	44	FimV_Cterm FimV C-terminal domain. This protein is	81.51
PF00637	143	Clathrin: Region in Clathrin and VPS; InterPro: IP	81.49
PF04097	613	Nic96: Nup93/Nic96; InterPro: IPR007231 Nup93/Nic9	81.32
KOG0890	2382	consensus Protein kinase of the PI-3 kinase family	81.07
PF13762	145	MNE1: Mitochondrial splicing apparatus component	80.57
PF11846	193	DUF3366: Domain of unknown function (DUF3366); Int	80.39
PF07163	309	Pex26: Pex26 protein; InterPro: IPR010797 This fam	80.13

>PLN03218 maturation of RBCL 1; Provisional

Probab=100.00  E-value=4.8e-61  Score=477.04  Aligned_cols=416  Identities=20%  Similarity=0.295  Sum_probs=384.6

Q ss_pred             hhhHHHHHHHhhHHHHHHHHHhhhhhhccCCCchHHHHHHHHHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHh
Q 012111           46 EAEKDLSKILRTEFAIKNIEKKVSSKKYKNLWPKPVLEALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLG  125 (471)
Q Consensus        46 ~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~  125 (471)
                      .....+.+.++...+.+.++++.... ......-.....+..+.+.|.+++|+++|+.|..     |+..+|+.++.+|+
T Consensus       375 ~~y~~l~r~G~l~eAl~Lfd~M~~~g-vv~~~~v~~~~li~~~~~~g~~~eAl~lf~~M~~-----pd~~Tyn~LL~a~~  448 (1060)
T PLN03218        375 DAYNRLLRDGRIKDCIDLLEDMEKRG-LLDMDKIYHAKFFKACKKQRAVKEAFRFAKLIRN-----PTLSTFNMLMSVCA  448 (1060)
T ss_pred             HHHHHHHHCcCHHHHHHHHHHHHhCC-CCCchHHHHHHHHHHHHHCCCHHHHHHHHHHcCC-----CCHHHHHHHHHHHH
Confidence            34444555567777777777664421 1111112223556777888899999999988863     89999999999999


Q ss_pred             cCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHH
Q 012111          126 KCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIE  205 (471)
Q Consensus       126 ~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~  205 (471)
                      +.|+++.|.++|+.|.+.|+.||..+|+.||.+|++.|++++|.++|++|.+ .|+.||..+|+.+|.+|++.|++++|.
T Consensus       449 k~g~~e~A~~lf~~M~~~Gl~pD~~tynsLI~~y~k~G~vd~A~~vf~eM~~-~Gv~PdvvTynaLI~gy~k~G~~eeAl  527 (1060)
T PLN03218        449 SSQDIDGALRVLRLVQEAGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVN-AGVEANVHTFGALIDGCARAGQVAKAF  527 (1060)
T ss_pred             hCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCcCHHHHHHHHHHHHH-cCCCCCHHHHHHHHHHHHHCcCHHHHH
Confidence            9999999999999999999999999999999999999999999999999998 799999999999999999999999999


Q ss_pred             HHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHc-CCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 012111          206 KILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVES-GGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNL  284 (471)
Q Consensus       206 ~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  284 (471)
                      ++|++|.+.|+.||..+|+.+|.+|++.|++++|.++|++|.+. .++.||..+|+.++.+|++.|++++|.++|++|.+
T Consensus       528 ~lf~~M~~~Gv~PD~vTYnsLI~a~~k~G~~deA~~lf~eM~~~~~gi~PD~vTynaLI~ay~k~G~ldeA~elf~~M~e  607 (1060)
T PLN03218        528 GAYGIMRSKNVKPDRVVFNALISACGQSGAVDRAFDVLAEMKAETHPIDPDHITVGALMKACANAGQVDRAKEVYQMIHE  607 (1060)
T ss_pred             HHHHHHHHcCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999763 46899999999999999999999999999999999


Q ss_pred             CCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHH
Q 012111          285 MGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITY  364 (471)
Q Consensus       285 ~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~  364 (471)
                      .|+.|+..+|+.+|.+|++.|++++|..+|+.|.+.|+.||..+|+.++.+|++.|++++|.+++++|.+.|+.||..+|
T Consensus       608 ~gi~p~~~tynsLI~ay~k~G~~deAl~lf~eM~~~Gv~PD~~TynsLI~a~~k~G~~eeA~~l~~eM~k~G~~pd~~ty  687 (1060)
T PLN03218        608 YNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIKLGTVSY  687 (1060)
T ss_pred             cCCCCChHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhc
Q 012111          365 CSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAYNAL  444 (471)
Q Consensus       365 ~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~  444 (471)
                      +.+|.+|++.|++++|.++|++|.+.|+.||..+|+.||.+|++.|++++|.++|++|.+.|+.||..||+.++.+|.+.
T Consensus       688 nsLI~ay~k~G~~eeA~~lf~eM~~~g~~PdvvtyN~LI~gy~k~G~~eeAlelf~eM~~~Gi~Pd~~Ty~sLL~a~~k~  767 (1060)
T PLN03218        688 SSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNTITYSILLVASERK  767 (1060)
T ss_pred             HHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCHHHHHHHHHHHHHhhhcCCCCc
Q 012111          445 GMTEAAQNLENKMIAMKENSGKKL  468 (471)
Q Consensus       445 g~~~~A~~~~~~m~~~~~~~~~~~  468 (471)
                      |++++|.+++++|++.+..++..+
T Consensus       768 G~le~A~~l~~~M~k~Gi~pd~~t  791 (1060)
T PLN03218        768 DDADVGLDLLSQAKEDGIKPNLVM  791 (1060)
T ss_pred             CCHHHHHHHHHHHHHcCCCCCHHH
Confidence            999999999999999998887544

>PLN03218 maturation of RBCL 1; Provisional

Probab=100.00  E-value=1.5e-59  Score=466.48  Aligned_cols=389  Identities=18%  Similarity=0.248  Sum_probs=372.2

Q ss_pred             CCchHHHHHHHHHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHH
Q 012111           76 LWPKPVLEALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTAL  155 (471)
Q Consensus        76 ~~~~~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~l  155 (471)
                      .+...+..+|..+++.|+++.|.++|+.|.+.+ +.||..+|+.+|.+|++.|++++|.++|++|.+.|+.||..+|+.+
T Consensus       435 pd~~Tyn~LL~a~~k~g~~e~A~~lf~~M~~~G-l~pD~~tynsLI~~y~k~G~vd~A~~vf~eM~~~Gv~PdvvTynaL  513 (1060)
T PLN03218        435 PTLSTFNMLMSVCASSQDIDGALRVLRLVQEAG-LKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGAL  513 (1060)
T ss_pred             CCHHHHHHHHHHHHhCcCHHHHHHHHHHHHHcC-CCCCHHHHHHHHHHHHhCcCHHHHHHHHHHHHHcCCCCCHHHHHHH
Confidence            456678899999999999999999999999887 8999999999999999999999999999999999999999999999


Q ss_pred             HHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHH--CCCCCCHHHHHHHHHHHHcc
Q 012111          156 VSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSY--LGIECSAVTYNTIIDGYGKA  233 (471)
Q Consensus       156 i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~--~g~~~~~~~~~~l~~~~~~~  233 (471)
                      |.+|++.|++++|.++|++|.+ .|+.||..+|+.+|.+|++.|++++|.++|++|..  .|+.||..+|+.++.+|++.
T Consensus       514 I~gy~k~G~~eeAl~lf~~M~~-~Gv~PD~vTYnsLI~a~~k~G~~deA~~lf~eM~~~~~gi~PD~vTynaLI~ay~k~  592 (1060)
T PLN03218        514 IDGCARAGQVAKAFGAYGIMRS-KNVKPDRVVFNALISACGQSGAVDRAFDVLAEMKAETHPIDPDHITVGALMKACANA  592 (1060)
T ss_pred             HHHHHHCcCHHHHHHHHHHHHH-cCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHC
Confidence            9999999999999999999998 79999999999999999999999999999999986  67899999999999999999


Q ss_pred             CCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHH
Q 012111          234 KKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSV  313 (471)
Q Consensus       234 ~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~  313 (471)
                      |++++|.++|+.|.+.+ +.|+..+|+.+|.+|++.|++++|.++|++|...|+.||..+|+.++.+|++.|++++|.++
T Consensus       593 G~ldeA~elf~~M~e~g-i~p~~~tynsLI~ay~k~G~~deAl~lf~eM~~~Gv~PD~~TynsLI~a~~k~G~~eeA~~l  671 (1060)
T PLN03218        593 GQVDRAKEVYQMIHEYN-IKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEI  671 (1060)
T ss_pred             CCHHHHHHHHHHHHHcC-CCCChHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCCHHHHHHH
Confidence            99999999999998775 89999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCC
Q 012111          314 MDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVI  393 (471)
Q Consensus       314 ~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~  393 (471)
                      |+.|.+.|+.|+..+|+.+|.+|++.|++++|.++|++|.+.|+.||..+|+.+|.+|++.|++++|.++|++|.+.|+.
T Consensus       672 ~~eM~k~G~~pd~~tynsLI~ay~k~G~~eeA~~lf~eM~~~g~~PdvvtyN~LI~gy~k~G~~eeAlelf~eM~~~Gi~  751 (1060)
T PLN03218        672 LQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGNQLPKALEVLSEMKRLGLC  751 (1060)
T ss_pred             HHHHHHcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHh----c-------------------CCHHHH
Q 012111          394 LDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAYNA----L-------------------GMTEAA  450 (471)
Q Consensus       394 ~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~----~-------------------g~~~~A  450 (471)
                      ||..+|+.++.+|++.|++++|.++|++|.+.|+.||..+|+.++..|.+    .                   +..++|
T Consensus       752 Pd~~Ty~sLL~a~~k~G~le~A~~l~~~M~k~Gi~pd~~tynsLIglc~~~y~ka~~l~~~v~~f~~g~~~~~n~w~~~A  831 (1060)
T PLN03218        752 PNTITYSILLVASERKDDADVGLDLLSQAKEDGIKPNLVMCRCITGLCLRRFEKACALGEPVVSFDSGRPQIENKWTSWA  831 (1060)
T ss_pred             CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhhhhhhhhhhhccccccccchHHHH
Confidence            99999999999999999999999999999999999999999999866432    1                   224679


Q ss_pred             HHHHHHHHHhhhcCCCC
Q 012111          451 QNLENKMIAMKENSGKK  467 (471)
Q Consensus       451 ~~~~~~m~~~~~~~~~~  467 (471)
                      ..+|++|++.|..|+..
T Consensus       832 l~lf~eM~~~Gi~Pd~~  848 (1060)
T PLN03218        832 LMVYRETISAGTLPTME  848 (1060)
T ss_pred             HHHHHHHHHCCCCCCHH
Confidence            99999999999888753

>PLN03081 pentatricopeptide (PPR) repeat-containing protein; Provisional

Probab=100.00  E-value=1.6e-55  Score=435.20  Aligned_cols=399  Identities=18%  Similarity=0.274  Sum_probs=257.8

Q ss_pred             HHHHHHhhHHHHHHHHHhhhhhhccCCCchHHHHHHHHHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCC
Q 012111           50 DLSKILRTEFAIKNIEKKVSSKKYKNLWPKPVLEALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQ  129 (471)
Q Consensus        50 ~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  129 (471)
                      .+.+.++..++++.++++.... ...++..++..++..+.+.++++.|.+++..+.+.+ +.|+..+|+.++..|++.|+
T Consensus        96 ~l~~~g~~~~Al~~f~~m~~~~-~~~~~~~t~~~ll~a~~~~~~~~~a~~l~~~m~~~g-~~~~~~~~n~Li~~y~k~g~  173 (697)
T PLN03081         96 KLVACGRHREALELFEILEAGC-PFTLPASTYDALVEACIALKSIRCVKAVYWHVESSG-FEPDQYMMNRVLLMHVKCGM  173 (697)
T ss_pred             HHHcCCCHHHHHHHHHHHHhcC-CCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHhC-CCcchHHHHHHHHHHhcCCC
Confidence            3455556777777777654322 223566788899999999999999999999998876 78999999999999999999


Q ss_pred             HHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHH
Q 012111          130 PEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILA  209 (471)
Q Consensus       130 ~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~  209 (471)
                      ++.|.++|++|.    .||..+|+.+|.+|++.|++++|+++|++|.+ .|+.|+..+|+.++.+|++.|..+.+.+++.
T Consensus       174 ~~~A~~lf~~m~----~~~~~t~n~li~~~~~~g~~~~A~~lf~~M~~-~g~~p~~~t~~~ll~a~~~~~~~~~~~~l~~  248 (697)
T PLN03081        174 LIDARRLFDEMP----ERNLASWGTIIGGLVDAGNYREAFALFREMWE-DGSDAEPRTFVVMLRASAGLGSARAGQQLHC  248 (697)
T ss_pred             HHHHHHHHhcCC----CCCeeeHHHHHHHHHHCcCHHHHHHHHHHHHH-hCCCCChhhHHHHHHHHhcCCcHHHHHHHHH
Confidence            999999999997    47889999999999999999999999999987 5667766666555555555444444444444


Q ss_pred             HHHHCCCCCCH-------------------------------HHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHH
Q 012111          210 EMSYLGIECSA-------------------------------VTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFT  258 (471)
Q Consensus       210 ~~~~~g~~~~~-------------------------------~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~  258 (471)
                      .+.+.|+.+|.                               .+|+.++.+|++.|++++|.++|++|.+.+ +.||..|
T Consensus       249 ~~~~~g~~~d~~~~n~Li~~y~k~g~~~~A~~vf~~m~~~~~vt~n~li~~y~~~g~~~eA~~lf~~M~~~g-~~pd~~t  327 (697)
T PLN03081        249 CVLKTGVVGDTFVSCALIDMYSKCGDIEDARCVFDGMPEKTTVAWNSMLAGYALHGYSEEALCLYYEMRDSG-VSIDQFT  327 (697)
T ss_pred             HHHHhCCCccceeHHHHHHHHHHCCCHHHHHHHHHhCCCCChhHHHHHHHHHHhCCCHHHHHHHHHHHHHcC-CCCCHHH
Confidence            44444444444                               445555555555555555555555553332 4555555


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHh
Q 012111          259 LNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGK  338 (471)
Q Consensus       259 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~  338 (471)
                      |+.++.+|++.|++++|.+++..|.+.|+.||..+|+.|+.+|++.|++++|.++|+.|.+    ||..+|+.||.+|++
T Consensus       328 ~~~ll~a~~~~g~~~~a~~i~~~m~~~g~~~d~~~~~~Li~~y~k~G~~~~A~~vf~~m~~----~d~~t~n~lI~~y~~  403 (697)
T PLN03081        328 FSIMIRIFSRLALLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKWGRMEDARNVFDRMPR----KNLISWNALIAGYGN  403 (697)
T ss_pred             HHHHHHHHHhccchHHHHHHHHHHHHhCCCCCeeehHHHHHHHHHCCCHHHHHHHHHhCCC----CCeeeHHHHHHHHHH
Confidence            5555555555555555555555555555555555555555555555555555555555432    355556666666666


Q ss_pred             cCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHh-CCCCcCHHHHHHHHHHHHhcCCHHHHHH
Q 012111          339 AGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVEN-SDVILDTPFFNCIISAYGQAGDVEKMGE  417 (471)
Q Consensus       339 ~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~-~~~~~~~~~~~~l~~~~~~~g~~~~a~~  417 (471)
                      .|+.++|.++|++|.+.|+.||..||+.++.+|.+.|.+++|.++|+.|.+ .|+.|+..+|+.++.+|++.|++++|.+
T Consensus       404 ~G~~~~A~~lf~~M~~~g~~Pd~~T~~~ll~a~~~~g~~~~a~~~f~~m~~~~g~~p~~~~y~~li~~l~r~G~~~eA~~  483 (697)
T PLN03081        404 HGRGTKAVEMFERMIAEGVAPNHVTFLAVLSACRYSGLSEQGWEIFQSMSENHRIKPRAMHYACMIELLGREGLLDEAYA  483 (697)
T ss_pred             cCCHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhcCCcHHHHHHHHHHHHHhcCCCCCccchHhHHHHHHhcCCHHHHHH
Confidence            666666666666666666666666666666666666666666666666653 4566666666666666666666666666


Q ss_pred             HHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhhhc
Q 012111          418 LFLTMKERHCVPDNITFATMIQAYNALGMTEAAQNLENKMIAMKEN  463 (471)
Q Consensus       418 ~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~  463 (471)
                      ++++|   ++.|+..+|++|+.+|...|+++.|..+++++.+.+|+
T Consensus       484 ~~~~~---~~~p~~~~~~~Ll~a~~~~g~~~~a~~~~~~l~~~~p~  526 (697)
T PLN03081        484 MIRRA---PFKPTVNMWAALLTACRIHKNLELGRLAAEKLYGMGPE  526 (697)
T ss_pred             HHHHC---CCCCCHHHHHHHHHHHHHcCCcHHHHHHHHHHhCCCCC
Confidence            65544   34566666666666666666666666666666655554

>PLN03081 pentatricopeptide (PPR) repeat-containing protein; Provisional

Probab=100.00  E-value=3.2e-55  Score=433.09  Aligned_cols=375  Identities=16%  Similarity=0.242  Sum_probs=306.9

Q ss_pred             hHHHHHHHHHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHH
Q 012111           79 KPVLEALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSA  158 (471)
Q Consensus        79 ~~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~  158 (471)
                      ..+...+..+.+.|++++|+++|++|...+++.|+..+|+.++.+|.+.++++.+.+++..|.+.|+.||..+|+.++.+
T Consensus        88 ~~~~~~i~~l~~~g~~~~Al~~f~~m~~~~~~~~~~~t~~~ll~a~~~~~~~~~a~~l~~~m~~~g~~~~~~~~n~Li~~  167 (697)
T PLN03081         88 VSLCSQIEKLVACGRHREALELFEILEAGCPFTLPASTYDALVEACIALKSIRCVKAVYWHVESSGFEPDQYMMNRVLLM  167 (697)
T ss_pred             eeHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHhCCCcchHHHHHHHHH
Confidence            46778899999999999999999999987667899999999999999999999999999999999999999999999999


Q ss_pred             HHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHH
Q 012111          159 YGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEE  238 (471)
Q Consensus       159 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~  238 (471)
                      |++.|+++.|.++|++|.+     ||..+|+.++.+|++.|++++|.++|++|.+.|+.|+..+|+.++.+|++.|..+.
T Consensus       168 y~k~g~~~~A~~lf~~m~~-----~~~~t~n~li~~~~~~g~~~~A~~lf~~M~~~g~~p~~~t~~~ll~a~~~~~~~~~  242 (697)
T PLN03081        168 HVKCGMLIDARRLFDEMPE-----RNLASWGTIIGGLVDAGNYREAFALFREMWEDGSDAEPRTFVVMLRASAGLGSARA  242 (697)
T ss_pred             HhcCCCHHHHHHHHhcCCC-----CCeeeHHHHHHHHHHCcCHHHHHHHHHHHHHhCCCCChhhHHHHHHHHhcCCcHHH
Confidence            9999999999999999974     79999999999999999999999999999999999999999888888777777777


Q ss_pred             HHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Q 012111          239 MESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQ  318 (471)
Q Consensus       239 a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~  318 (471)
                      +.+++..+.+.+ +.+|..+|+.|+.+|++.|++++|.++|++|.    .+|..+|+.++.+|++.|++++|.++|++|.
T Consensus       243 ~~~l~~~~~~~g-~~~d~~~~n~Li~~y~k~g~~~~A~~vf~~m~----~~~~vt~n~li~~y~~~g~~~eA~~lf~~M~  317 (697)
T PLN03081        243 GQQLHCCVLKTG-VVGDTFVSCALIDMYSKCGDIEDARCVFDGMP----EKTTVAWNSMLAGYALHGYSEEALCLYYEMR  317 (697)
T ss_pred             HHHHHHHHHHhC-CCccceeHHHHHHHHHHCCCHHHHHHHHHhCC----CCChhHHHHHHHHHHhCCCHHHHHHHHHHHH
Confidence            777777776554 67777777777777777777777777777764    3567777777777777777777777777777


Q ss_pred             hCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHH
Q 012111          319 KRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPF  398 (471)
Q Consensus       319 ~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~  398 (471)
                      +.|+.||..||+.++.+|++.|++++|.+++..|.+.|+.||..+|+.|+.+|++.|++++|.++|++|.+    ||..+
T Consensus       318 ~~g~~pd~~t~~~ll~a~~~~g~~~~a~~i~~~m~~~g~~~d~~~~~~Li~~y~k~G~~~~A~~vf~~m~~----~d~~t  393 (697)
T PLN03081        318 DSGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKWGRMEDARNVFDRMPR----KNLIS  393 (697)
T ss_pred             HcCCCCCHHHHHHHHHHHHhccchHHHHHHHHHHHHhCCCCCeeehHHHHHHHHHCCCHHHHHHHHHhCCC----CCeee
Confidence            77777777777777777777777777777777777777777777777777777777777777777777653    46667


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHh-hhcCCCC
Q 012111          399 FNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAYNALGMTEAAQNLENKMIAM-KENSGKK  467 (471)
Q Consensus       399 ~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~-~~~~~~~  467 (471)
                      ||.||.+|++.|+.++|.++|++|.+.|+.||..||+.++.+|.+.|..++|.++|+.|.+. +..|+..
T Consensus       394 ~n~lI~~y~~~G~~~~A~~lf~~M~~~g~~Pd~~T~~~ll~a~~~~g~~~~a~~~f~~m~~~~g~~p~~~  463 (697)
T PLN03081        394 WNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTFLAVLSACRYSGLSEQGWEIFQSMSENHRIKPRAM  463 (697)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhcCCcHHHHHHHHHHHHHhcCCCCCcc
Confidence            77777777777777777777777777777777777777777777777777777777777653 4444433

>PLN03077 Protein ECB2; Provisional

Probab=100.00  E-value=7.7e-53  Score=425.94  Aligned_cols=397  Identities=22%  Similarity=0.258  Sum_probs=267.5

Q ss_pred             HHHHhhHHHHHHHHHhhhhhhccCCCchHHHHHHHHHHHhhcHHHHHHHHHHhhhccCccCChhHH--------------
Q 012111           52 SKILRTEFAIKNIEKKVSSKKYKNLWPKPVLEALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTF--------------  117 (471)
Q Consensus        52 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~--------------  117 (471)
                      .+.++...+...++++..      .+...+..++..+.+.|++++|+++|+.|...+ +.||..+|              
T Consensus       132 ~~~g~~~~A~~~f~~m~~------~d~~~~n~li~~~~~~g~~~~A~~~f~~M~~~g-~~Pd~~t~~~ll~~~~~~~~~~  204 (857)
T PLN03077        132 VRFGELVHAWYVFGKMPE------RDLFSWNVLVGGYAKAGYFDEALCLYHRMLWAG-VRPDVYTFPCVLRTCGGIPDLA  204 (857)
T ss_pred             HhCCChHHHHHHHhcCCC------CCeeEHHHHHHHHHhCCCHHHHHHHHHHHHHcC-CCCChhHHHHHHHHhCCccchh
Confidence            344444555555554432      244577788888899999999999999887664 56665554              


Q ss_pred             ---------------------HHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHhh
Q 012111          118 ---------------------TKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAFSTINDMK  176 (471)
Q Consensus       118 ---------------------~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~  176 (471)
                                           +.++.+|++.|++++|.++|++|.    .||..+||.+|.+|++.|++++|+++|++|.
T Consensus       205 ~~~~~~~~~~~~g~~~~~~~~n~Li~~y~k~g~~~~A~~lf~~m~----~~d~~s~n~li~~~~~~g~~~eAl~lf~~M~  280 (857)
T PLN03077        205 RGREVHAHVVRFGFELDVDVVNALITMYVKCGDVVSARLVFDRMP----RRDCISWNAMISGYFENGECLEGLELFFTMR  280 (857)
T ss_pred             hHHHHHHHHHHcCCCcccchHhHHHHHHhcCCCHHHHHHHHhcCC----CCCcchhHHHHHHHHhCCCHHHHHHHHHHHH
Confidence                                 556666666677777777777765    3566777777777777777777777777777


Q ss_pred             cCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCH
Q 012111          177 SVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDI  256 (471)
Q Consensus       177 ~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~  256 (471)
                      . .|+.||..||+.++.+|++.|+.+.+.+++..|.+.|+.||..+|+.|+.+|++.|++++|.++|++|.     .||.
T Consensus       281 ~-~g~~Pd~~ty~~ll~a~~~~g~~~~a~~l~~~~~~~g~~~d~~~~n~Li~~y~k~g~~~~A~~vf~~m~-----~~d~  354 (857)
T PLN03077        281 E-LSVDPDLMTITSVISACELLGDERLGREMHGYVVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRME-----TKDA  354 (857)
T ss_pred             H-cCCCCChhHHHHHHHHHHhcCChHHHHHHHHHHHHhCCccchHHHHHHHHHHHhcCCHHHHHHHHhhCC-----CCCe
Confidence            6 677788888888888888888888888888888888888888888888888888888888888887773     4677


Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHH
Q 012111          257 FTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETF  336 (471)
Q Consensus       257 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~  336 (471)
                      .+|+.+|.+|++.|++++|.++|++|...|+.||..||+.++.+|++.|+++.|.++++.+.+.|+.|+..+|+.|+.+|
T Consensus       355 ~s~n~li~~~~~~g~~~~A~~lf~~M~~~g~~Pd~~t~~~ll~a~~~~g~~~~a~~l~~~~~~~g~~~~~~~~n~Li~~y  434 (857)
T PLN03077        355 VSWTAMISGYEKNGLPDKALETYALMEQDNVSPDEITIASVLSACACLGDLDVGVKLHELAERKGLISYVVVANALIEMY  434 (857)
T ss_pred             eeHHHHHHHHHhCCCHHHHHHHHHHHHHhCCCCCceeHHHHHHHHhccchHHHHHHHHHHHHHhCCCcchHHHHHHHHHH
Confidence            77888888888888888888888888777777777777777777777777777777777777777777766666666666


Q ss_pred             HhcCCHHHHHHHHHHHHHc------------------------------CCCCCHHHHHHHHHHHHhcCCHHHHHHHHHH
Q 012111          337 GKAGHIEKMEEYFKKMKHR------------------------------GMKPNSITYCSLVSAYSKAGLIMKVDSILRQ  386 (471)
Q Consensus       337 ~~~g~~~~a~~~~~~m~~~------------------------------~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~  386 (471)
                      ++.|++++|.++|++|.+.                              ++.||..||+.++.+|++.|+++.+.+++..
T Consensus       435 ~k~g~~~~A~~vf~~m~~~d~vs~~~mi~~~~~~g~~~eA~~lf~~m~~~~~pd~~t~~~lL~a~~~~g~l~~~~~i~~~  514 (857)
T PLN03077        435 SKCKCIDKALEVFHNIPEKDVISWTSIIAGLRLNNRCFEALIFFRQMLLTLKPNSVTLIAALSACARIGALMCGKEIHAH  514 (857)
T ss_pred             HHcCCHHHHHHHHHhCCCCCeeeHHHHHHHHHHCCCHHHHHHHHHHHHhCCCCCHhHHHHHHHHHhhhchHHHhHHHHHH
Confidence            6666666666666555321                              2344444444333333322222222222222


Q ss_pred             HHhCCC------------------------------CcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHH
Q 012111          387 VENSDV------------------------------ILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFAT  436 (471)
Q Consensus       387 ~~~~~~------------------------------~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~  436 (471)
                      +.+.|+                              .+|..+||.+|.+|++.|+.++|.++|++|.+.|+.||..||+.
T Consensus       515 ~~~~g~~~~~~~~naLi~~y~k~G~~~~A~~~f~~~~~d~~s~n~lI~~~~~~G~~~~A~~lf~~M~~~g~~Pd~~T~~~  594 (857)
T PLN03077        515 VLRTGIGFDGFLPNALLDLYVRCGRMNYAWNQFNSHEKDVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFIS  594 (857)
T ss_pred             HHHhCCCccceechHHHHHHHHcCCHHHHHHHHHhcCCChhhHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCcccHHH
Confidence            222221                              23455566666666666666666666666666666666666666


Q ss_pred             HHHHHHhcCCHHHHHHHHHHHH-HhhhcCC
Q 012111          437 MIQAYNALGMTEAAQNLENKMI-AMKENSG  465 (471)
Q Consensus       437 l~~~~~~~g~~~~A~~~~~~m~-~~~~~~~  465 (471)
                      ++.+|.+.|++++|.++|++|. +.+..|+
T Consensus       595 ll~a~~~~g~v~ea~~~f~~M~~~~gi~P~  624 (857)
T PLN03077        595 LLCACSRSGMVTQGLEYFHSMEEKYSITPN  624 (857)
T ss_pred             HHHHHhhcChHHHHHHHHHHHHHHhCCCCc
Confidence            6666666666666666666666 3444444

>PLN03077 Protein ECB2; Provisional

Probab=100.00  E-value=3.2e-52  Score=421.45  Aligned_cols=359  Identities=20%  Similarity=0.241  Sum_probs=282.3

Q ss_pred             HHHHHHHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHh
Q 012111           82 LEALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQ  161 (471)
Q Consensus        82 ~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~  161 (471)
                      ..++..+.+.|+++.|.++|+.|.     .||..+|+.+|.+|++.|++++|.++|++|...|+.||..+|+.++.+|+.
T Consensus       125 n~li~~~~~~g~~~~A~~~f~~m~-----~~d~~~~n~li~~~~~~g~~~~A~~~f~~M~~~g~~Pd~~t~~~ll~~~~~  199 (857)
T PLN03077        125 NAMLSMFVRFGELVHAWYVFGKMP-----ERDLFSWNVLVGGYAKAGYFDEALCLYHRMLWAGVRPDVYTFPCVLRTCGG  199 (857)
T ss_pred             HHHHHHHHhCCChHHHHHHHhcCC-----CCCeeEHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCChhHHHHHHHHhCC
Confidence            344555666777777777777764     356677777777777777777777777777777777777777777777777


Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHH
Q 012111          162 SGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMES  241 (471)
Q Consensus       162 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~a~~  241 (471)
                      .++++.+.+++..|.+ .|+.||..+|+.++.+|++.|+++.|.++|++|.    .+|..+|+.+|.+|++.|++++|.+
T Consensus       200 ~~~~~~~~~~~~~~~~-~g~~~~~~~~n~Li~~y~k~g~~~~A~~lf~~m~----~~d~~s~n~li~~~~~~g~~~eAl~  274 (857)
T PLN03077        200 IPDLARGREVHAHVVR-FGFELDVDVVNALITMYVKCGDVVSARLVFDRMP----RRDCISWNAMISGYFENGECLEGLE  274 (857)
T ss_pred             ccchhhHHHHHHHHHH-cCCCcccchHhHHHHHHhcCCCHHHHHHHHhcCC----CCCcchhHHHHHHHHhCCCHHHHHH
Confidence            7777777777777776 6777777777777777777788888888887775    3577778888888888888888888


Q ss_pred             HHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCC
Q 012111          242 SFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRF  321 (471)
Q Consensus       242 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~  321 (471)
                      +|++|.+.+ +.||..+|+.++.+|++.|+.+.+.+++..|.+.|+.||..+|+.|+.+|++.|++++|.++|+.|..  
T Consensus       275 lf~~M~~~g-~~Pd~~ty~~ll~a~~~~g~~~~a~~l~~~~~~~g~~~d~~~~n~Li~~y~k~g~~~~A~~vf~~m~~--  351 (857)
T PLN03077        275 LFFTMRELS-VDPDLMTITSVISACELLGDERLGREMHGYVVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRMET--  351 (857)
T ss_pred             HHHHHHHcC-CCCChhHHHHHHHHHHhcCChHHHHHHHHHHHHhCCccchHHHHHHHHHHHhcCCHHHHHHHHhhCCC--
Confidence            888886654 77888888888888888888888888888888888888888888888888888888888888887753  


Q ss_pred             CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHH
Q 012111          322 FFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNC  401 (471)
Q Consensus       322 ~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~  401 (471)
                        ||..+|+.+|.+|++.|++++|.++|++|.+.|+.||..||+.++.+|++.|+++.|.++++.+.+.|+.|+..+|+.
T Consensus       352 --~d~~s~n~li~~~~~~g~~~~A~~lf~~M~~~g~~Pd~~t~~~ll~a~~~~g~~~~a~~l~~~~~~~g~~~~~~~~n~  429 (857)
T PLN03077        352 --KDAVSWTAMISGYEKNGLPDKALETYALMEQDNVSPDEITIASVLSACACLGDLDVGVKLHELAERKGLISYVVVANA  429 (857)
T ss_pred             --CCeeeHHHHHHHHHhCCCHHHHHHHHHHHHHhCCCCCceeHHHHHHHHhccchHHHHHHHHHHHHHhCCCcchHHHHH
Confidence              577788888888888888888888888888888888888888888888888888888888888888888888888888


Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 012111          402 IISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAYNALGMTEAAQNLENKMIA  459 (471)
Q Consensus       402 l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~  459 (471)
                      |+.+|++.|++++|.++|++|.+    +|..+|+.+|.+|.+.|+.++|..+|++|..
T Consensus       430 Li~~y~k~g~~~~A~~vf~~m~~----~d~vs~~~mi~~~~~~g~~~eA~~lf~~m~~  483 (857)
T PLN03077        430 LIEMYSKCKCIDKALEVFHNIPE----KDVISWTSIIAGLRLNNRCFEALIFFRQMLL  483 (857)
T ss_pred             HHHHHHHcCCHHHHHHHHHhCCC----CCeeeHHHHHHHHHHCCCHHHHHHHHHHHHh
Confidence            88888888888888888888764    5777888888888888888888888888875

>TIGR02917 PEP_TPR_lipo putative PEP-CTERM system TPR-repeat lipoprotein

Probab=99.97  E-value=3.9e-25  Score=228.99  Aligned_cols=369  Identities=12%  Similarity=0.053  Sum_probs=220.4

Q ss_pred             HHHHHHHHHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHH
Q 012111           80 PVLEALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAY  159 (471)
Q Consensus        80 ~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~  159 (471)
                      .+......+...|++++|.+.|+.+.+..  +.+..++..+...+.+.|++++|...++++...+. .+...+..++..+
T Consensus       501 ~~~~la~~~~~~g~~~~A~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~l~~~~  577 (899)
T TIGR02917       501 AAANLARIDIQEGNPDDAIQRFEKVLTID--PKNLRAILALAGLYLRTGNEEEAVAWLEKAAELNP-QEIEPALALAQYY  577 (899)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHhC--cCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCc-cchhHHHHHHHHH
Confidence            34444444555666666666666665543  44555566666666666666666666666655432 2445555566666


Q ss_pred             HhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHH
Q 012111          160 GQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEM  239 (471)
Q Consensus       160 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~a  239 (471)
                      ...|++++|..+++.+..  ..+.+...|..+...+...|++++|...++.+.+.. +.+...+..+..++.+.|++++|
T Consensus       578 ~~~~~~~~A~~~~~~~~~--~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A  654 (899)
T TIGR02917       578 LGKGQLKKALAILNEAAD--AAPDSPEAWLMLGRAQLAAGDLNKAVSSFKKLLALQ-PDSALALLLLADAYAVMKNYAKA  654 (899)
T ss_pred             HHCCCHHHHHHHHHHHHH--cCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHcCCHHHH
Confidence            666666666666666654  224455566666666666666666666666665543 33455566666666666666666


Q ss_pred             HHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Q 012111          240 ESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQK  319 (471)
Q Consensus       240 ~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~  319 (471)
                      ...|+++.+..  +.+..++..++..+...|++++|..+++.+.... +.+...+..+...+...|++++|...|..+..
T Consensus       655 ~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~  731 (899)
T TIGR02917       655 ITSLKRALELK--PDNTEAQIGLAQLLLAAKRTESAKKIAKSLQKQH-PKAALGFELEGDLYLRQKDYPAAIQAYRKALK  731 (899)
T ss_pred             HHHHHHHHhcC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-cCChHHHHHHHHHHHHCCCHHHHHHHHHHHHh
Confidence            66666665542  3345556666666666666666666666665543 44555566666666666666666666666665


Q ss_pred             CCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHH
Q 012111          320 RFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFF  399 (471)
Q Consensus       320 ~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~  399 (471)
                      .+  |+..++..+..++...|++++|.+.++++.+.. +.+...+..+...|...|+.++|..+|+++.+..+. +..++
T Consensus       732 ~~--~~~~~~~~l~~~~~~~g~~~~A~~~~~~~l~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~p~-~~~~~  807 (899)
T TIGR02917       732 RA--PSSQNAIKLHRALLASGNTAEAVKTLEAWLKTH-PNDAVLRTALAELYLAQKDYDKAIKHYRTVVKKAPD-NAVVL  807 (899)
T ss_pred             hC--CCchHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHhCCC-CHHHH
Confidence            43  233455556666666666666666666666543 335556666666666666666666666666665543 55566


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhhhc
Q 012111          400 NCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAYNALGMTEAAQNLENKMIAMKEN  463 (471)
Q Consensus       400 ~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~  463 (471)
                      +.+...+...|+ .+|+.+++++.+. .+-+..++..+...+...|++++|.+.++++++.+|.
T Consensus       808 ~~l~~~~~~~~~-~~A~~~~~~~~~~-~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~a~~~~~~  869 (899)
T TIGR02917       808 NNLAWLYLELKD-PRALEYAEKALKL-APNIPAILDTLGWLLVEKGEADRALPLLRKAVNIAPE  869 (899)
T ss_pred             HHHHHHHHhcCc-HHHHHHHHHHHhh-CCCCcHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCC
Confidence            666666666666 5566666666553 1223444555566666666666666666666666654

This protein family occurs in strictly within a subset of Gram-negative bacterial species with the proposed PEP-CTERM/exosortase system, analogous to the LPXTG/sortase system common in Gram-positive bacteria. This protein occurs in a species if and only if a transmembrane histidine kinase (TIGR02916) and a DNA-binding response regulator (TIGR02915) also occur. The present of tetratricopeptide repeats (TPR) suggests protein-protein interaction, possibly for the regulation of PEP-CTERM protein expression, since many PEP-CTERM proteins in these genomes are preceded by a proposed DNA binding site for the response regulator.

>TIGR02917 PEP_TPR_lipo putative PEP-CTERM system TPR-repeat lipoprotein

Probab=99.97  E-value=3.5e-25  Score=229.35  Aligned_cols=388  Identities=11%  Similarity=0.023  Sum_probs=334.4

Q ss_pred             HHHhhHHHHHHHHHhhhhhhccCCCchHHHHHHHHHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHH
Q 012111           53 KILRTEFAIKNIEKKVSSKKYKNLWPKPVLEALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQ  132 (471)
Q Consensus        53 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  132 (471)
                      ..++...+...+...+...   +.....+......+.+.|++++|+..|+.+...+  +.+...+..++..+...|++++
T Consensus       511 ~~g~~~~A~~~~~~~~~~~---~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~  585 (899)
T TIGR02917       511 QEGNPDDAIQRFEKVLTID---PKNLRAILALAGLYLRTGNEEEAVAWLEKAAELN--PQEIEPALALAQYYLGKGQLKK  585 (899)
T ss_pred             HCCCHHHHHHHHHHHHHhC---cCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--ccchhHHHHHHHHHHHCCCHHH
Confidence            3344555555555555432   2234556667777788999999999999998875  6677888999999999999999


Q ss_pred             HHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 012111          133 ASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMS  212 (471)
Q Consensus       133 a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~  212 (471)
                      |..+++.+.+.. +.+...|..+..++...|++++|+..|+++.+..  +.+...+..+...+...|++++|..+++.+.
T Consensus       586 A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~  662 (899)
T TIGR02917       586 ALAILNEAADAA-PDSPEAWLMLGRAQLAAGDLNKAVSSFKKLLALQ--PDSALALLLLADAYAVMKNYAKAITSLKRAL  662 (899)
T ss_pred             HHHHHHHHHHcC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCChHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            999999998764 4478899999999999999999999999998732  4567788899999999999999999999998


Q ss_pred             HCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHH
Q 012111          213 YLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQ  292 (471)
Q Consensus       213 ~~g~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~  292 (471)
                      +.. +.+..++..++..+...|++++|..+++.+.+..  +.+...+..+...+...|++++|...|+.+...+  |+..
T Consensus       663 ~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~~--~~~~  737 (899)
T TIGR02917       663 ELK-PDNTEAQIGLAQLLLAAKRTESAKKIAKSLQKQH--PKAALGFELEGDLYLRQKDYPAAIQAYRKALKRA--PSSQ  737 (899)
T ss_pred             hcC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC--cCChHHHHHHHHHHHHCCCHHHHHHHHHHHHhhC--CCch
Confidence            764 5568899999999999999999999999998764  5677788889999999999999999999998764  5557


Q ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Q 012111          293 TLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYS  372 (471)
Q Consensus       293 ~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~  372 (471)
                      ++..+..++.+.|++++|...+..+.+... .+...+..+...|...|++++|..+|+++.+.. +.+..++..+...+.
T Consensus       738 ~~~~l~~~~~~~g~~~~A~~~~~~~l~~~~-~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~-p~~~~~~~~l~~~~~  815 (899)
T TIGR02917       738 NAIKLHRALLASGNTAEAVKTLEAWLKTHP-NDAVLRTALAELYLAQKDYDKAIKHYRTVVKKA-PDNAVVLNNLAWLYL  815 (899)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHH
Confidence            788899999999999999999999988644 477889999999999999999999999999875 557889999999999


Q ss_pred             hcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHH
Q 012111          373 KAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAYNALGMTEAAQN  452 (471)
Q Consensus       373 ~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~  452 (471)
                      ..|+ .+|..+++++.+..+. +..++..+...+...|++++|.++|+++.+.+. .+..++..+..++.+.|++++|.+
T Consensus       816 ~~~~-~~A~~~~~~~~~~~~~-~~~~~~~~~~~~~~~g~~~~A~~~~~~a~~~~~-~~~~~~~~l~~~~~~~g~~~~A~~  892 (899)
T TIGR02917       816 ELKD-PRALEYAEKALKLAPN-IPAILDTLGWLLVEKGEADRALPLLRKAVNIAP-EAAAIRYHLALALLATGRKAEARK  892 (899)
T ss_pred             hcCc-HHHHHHHHHHHhhCCC-CcHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCC-CChHHHHHHHHHHHHcCCHHHHHH
Confidence            9999 8899999999887655 677888899999999999999999999998753 388999999999999999999999


Q ss_pred             HHHHHH
Q 012111          453 LENKMI  458 (471)
Q Consensus       453 ~~~~m~  458 (471)
                      ++++|+
T Consensus       893 ~~~~~~  898 (899)
T TIGR02917       893 ELDKLL  898 (899)
T ss_pred             HHHHHh
Confidence            999986

This protein family occurs in strictly within a subset of Gram-negative bacterial species with the proposed PEP-CTERM/exosortase system, analogous to the LPXTG/sortase system common in Gram-positive bacteria. This protein occurs in a species if and only if a transmembrane histidine kinase (TIGR02916) and a DNA-binding response regulator (TIGR02915) also occur. The present of tetratricopeptide repeats (TPR) suggests protein-protein interaction, possibly for the regulation of PEP-CTERM protein expression, since many PEP-CTERM proteins in these genomes are preceded by a proposed DNA binding site for the response regulator.

>PRK11788 tetratricopeptide repeat protein; Provisional

Probab=99.93  E-value=5.6e-22  Score=184.57  Aligned_cols=299  Identities=14%  Similarity=0.107  Sum_probs=143.8

Q ss_pred             HHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCC---HHHHHHHHHHHHhcC
Q 012111          123 MLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPD---VYTYSILIKSCTKFH  199 (471)
Q Consensus       123 ~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~---~~~~~~ll~~~~~~~  199 (471)
                      .+...|++++|...|+++.+.+. .+..++..+...+...|++++|..+++.+... +..++   ...+..+...+.+.|
T Consensus        44 ~~~~~~~~~~A~~~~~~al~~~p-~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~-~~~~~~~~~~~~~~La~~~~~~g  121 (389)
T PRK11788         44 NFLLNEQPDKAIDLFIEMLKVDP-ETVELHLALGNLFRRRGEVDRAIRIHQNLLSR-PDLTREQRLLALQELGQDYLKAG  121 (389)
T ss_pred             HHHhcCChHHHHHHHHHHHhcCc-ccHHHHHHHHHHHHHcCcHHHHHHHHHHHhcC-CCCCHHHHHHHHHHHHHHHHHCC
Confidence            34455666666666666665532 24455666666666666666666666666542 11111   123445555555555


Q ss_pred             CHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCC---HHHHHHHHHHHHhcCCHHHHH
Q 012111          200 RFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPD---IFTLNSMISAYGNSGNIEKME  276 (471)
Q Consensus       200 ~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~---~~~~~~l~~~~~~~~~~~~a~  276 (471)
                      +++.|..+|+++.+.. +.+..++..++..+.+.|++++|.+.++.+.+.....+.   ...+..+...+...|++++|.
T Consensus       122 ~~~~A~~~~~~~l~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~  200 (389)
T PRK11788        122 LLDRAEELFLQLVDEG-DFAEGALQQLLEIYQQEKDWQKAIDVAERLEKLGGDSLRVEIAHFYCELAQQALARGDLDAAR  200 (389)
T ss_pred             CHHHHHHHHHHHHcCC-cchHHHHHHHHHHHHHhchHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHHHhCCCHHHHH
Confidence            5555555555555432 234445555555555555555555555555443211111   111223333344444444444


Q ss_pred             HHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC
Q 012111          277 KWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRG  356 (471)
Q Consensus       277 ~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~  356 (471)
                      ..|+++.+.. +.+                                   ...+..+...+.+.|++++|.++++++...+
T Consensus       201 ~~~~~al~~~-p~~-----------------------------------~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~  244 (389)
T PRK11788        201 ALLKKALAAD-PQC-----------------------------------VRASILLGDLALAQGDYAAAIEALERVEEQD  244 (389)
T ss_pred             HHHHHHHhHC-cCC-----------------------------------HHHHHHHHHHHHHCCCHHHHHHHHHHHHHHC
Confidence            4444443321 112                                   2233344444444455555555555444432


Q ss_pred             CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHH
Q 012111          357 MKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFAT  436 (471)
Q Consensus       357 ~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~  436 (471)
                      ......++..++.+|...|++++|...++++.+..  |+...+..++..+.+.|++++|..+++++.+.  .|+..++..
T Consensus       245 p~~~~~~~~~l~~~~~~~g~~~~A~~~l~~~~~~~--p~~~~~~~la~~~~~~g~~~~A~~~l~~~l~~--~P~~~~~~~  320 (389)
T PRK11788        245 PEYLSEVLPKLMECYQALGDEAEGLEFLRRALEEY--PGADLLLALAQLLEEQEGPEAAQALLREQLRR--HPSLRGFHR  320 (389)
T ss_pred             hhhHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCchHHHHHHHHHHHhCCHHHHHHHHHHHHHh--CcCHHHHHH
Confidence            11112334445555555555555555555554442  23333445555555555555555555555543  355555555


Q ss_pred             HHHHHHh---cCCHHHHHHHHHHHHHhhhcC
Q 012111          437 MIQAYNA---LGMTEAAQNLENKMIAMKENS  464 (471)
Q Consensus       437 l~~~~~~---~g~~~~A~~~~~~m~~~~~~~  464 (471)
                      ++..+..   .|+.+++..++++|++....+
T Consensus       321 l~~~~~~~~~~g~~~~a~~~~~~~~~~~~~~  351 (389)
T PRK11788        321 LLDYHLAEAEEGRAKESLLLLRDLVGEQLKR  351 (389)
T ss_pred             HHHHhhhccCCccchhHHHHHHHHHHHHHhC
Confidence            5544432   335555555555555544433

>PRK11788 tetratricopeptide repeat protein; Provisional

Probab=99.93  E-value=1.2e-21  Score=182.47  Aligned_cols=265  Identities=14%  Similarity=0.075  Sum_probs=192.5

Q ss_pred             HHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCC--CHHHHHHHHHHHHhcCCH
Q 012111          195 CTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHP--DIFTLNSMISAYGNSGNI  272 (471)
Q Consensus       195 ~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~~~~~l~~~~~~~~~~  272 (471)
                      +...|+++.|...|.++.+.+ +.+..++..+...+...|++++|..+++.+.+.....+  ....+..+...|...|++
T Consensus        45 ~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~~~~~~~~~~~~~~La~~~~~~g~~  123 (389)
T PRK11788         45 FLLNEQPDKAIDLFIEMLKVD-PETVELHLALGNLFRRRGEVDRAIRIHQNLLSRPDLTREQRLLALQELGQDYLKAGLL  123 (389)
T ss_pred             HHhcCChHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHcCcHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHCCCH
Confidence            344555666666666665543 23445566666666666666666666666654321111  123456666667777777


Q ss_pred             HHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCH----HHHHHHHHHHHhcCCHHHHHHH
Q 012111          273 EKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTV----VTYNIVIETFGKAGHIEKMEEY  348 (471)
Q Consensus       273 ~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~----~~~~~li~~~~~~g~~~~a~~~  348 (471)
                      ++|..+|+++.+.. +.+..++..++..+.+.|++++|...++.+.+.+..+..    ..+..+...+...|++++|...
T Consensus       124 ~~A~~~~~~~l~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~  202 (389)
T PRK11788        124 DRAEELFLQLVDEG-DFAEGALQQLLEIYQQEKDWQKAIDVAERLEKLGGDSLRVEIAHFYCELAQQALARGDLDAARAL  202 (389)
T ss_pred             HHHHHHHHHHHcCC-cchHHHHHHHHHHHHHhchHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHHHhCCCHHHHHHH
Confidence            77777777776542 445666777777777777777777777777665433221    2355677788899999999999


Q ss_pred             HHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCC
Q 012111          349 FKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCV  428 (471)
Q Consensus       349 ~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~  428 (471)
                      ++++.+.. +.+...+..+...+.+.|++++|.++++++.+.++.....+++.++.+|...|++++|...++++.+.  .
T Consensus       203 ~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~l~~~~~~--~  279 (389)
T PRK11788        203 LKKALAAD-PQCVRASILLGDLALAQGDYAAAIEALERVEEQDPEYLSEVLPKLMECYQALGDEAEGLEFLRRALEE--Y  279 (389)
T ss_pred             HHHHHhHC-cCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHChhhHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--C
Confidence            99998763 33466788899999999999999999999998755434567889999999999999999999999885  5


Q ss_pred             CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhhhcC
Q 012111          429 PDNITFATMIQAYNALGMTEAAQNLENKMIAMKENS  464 (471)
Q Consensus       429 p~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~~  464 (471)
                      |+...+..++..+.+.|++++|..+++++++..|+.
T Consensus       280 p~~~~~~~la~~~~~~g~~~~A~~~l~~~l~~~P~~  315 (389)
T PRK11788        280 PGADLLLALAQLLEEQEGPEAAQALLREQLRRHPSL  315 (389)
T ss_pred             CCchHHHHHHHHHHHhCCHHHHHHHHHHHHHhCcCH
Confidence            777777888999999999999999999999887653

>PRK15174 Vi polysaccharide export protein VexE; Provisional

Probab=99.92  E-value=1.9e-20  Score=182.65  Aligned_cols=334  Identities=8%  Similarity=-0.005  Sum_probs=273.9

Q ss_pred             HHHHHHHHHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHH
Q 012111           80 PVLEALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAY  159 (471)
Q Consensus        80 ~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~  159 (471)
                      .+...+..+.+.|++++|+.+++.+....  +.+...+..++.+....|++++|...++.+.+.... +...+..+...+
T Consensus        44 ~~~~~~~~~~~~g~~~~A~~l~~~~l~~~--p~~~~~l~~l~~~~l~~g~~~~A~~~l~~~l~~~P~-~~~a~~~la~~l  120 (656)
T PRK15174         44 NIILFAIACLRKDETDVGLTLLSDRVLTA--KNGRDLLRRWVISPLASSQPDAVLQVVNKLLAVNVC-QPEDVLLVASVL  120 (656)
T ss_pred             CHHHHHHHHHhcCCcchhHHHhHHHHHhC--CCchhHHHHHhhhHhhcCCHHHHHHHHHHHHHhCCC-ChHHHHHHHHHH
Confidence            45566777889999999999999999875  666778888888888999999999999999987543 677888899999


Q ss_pred             HhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHH
Q 012111          160 GQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEM  239 (471)
Q Consensus       160 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~a  239 (471)
                      ...|++++|+..|++....  .+.+...+..+...+...|++++|...++.+.... +.+...+..+ ..+...|++++|
T Consensus       121 ~~~g~~~~Ai~~l~~Al~l--~P~~~~a~~~la~~l~~~g~~~eA~~~~~~~~~~~-P~~~~a~~~~-~~l~~~g~~~eA  196 (656)
T PRK15174        121 LKSKQYATVADLAEQAWLA--FSGNSQIFALHLRTLVLMDKELQAISLARTQAQEV-PPRGDMIATC-LSFLNKSRLPED  196 (656)
T ss_pred             HHcCCHHHHHHHHHHHHHh--CCCcHHHHHHHHHHHHHCCChHHHHHHHHHHHHhC-CCCHHHHHHH-HHHHHcCCHHHH
Confidence            9999999999999999873  24456778889999999999999999999887664 2334444443 347889999999


Q ss_pred             HHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHH----HHHHHH
Q 012111          240 ESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDK----MRSVMD  315 (471)
Q Consensus       240 ~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~----a~~~~~  315 (471)
                      ...++.+.+... .++...+..+..++...|++++|...++++.... +.+...+..+...+...|++++    |...++
T Consensus       197 ~~~~~~~l~~~~-~~~~~~~~~l~~~l~~~g~~~eA~~~~~~al~~~-p~~~~~~~~Lg~~l~~~G~~~eA~~~A~~~~~  274 (656)
T PRK15174        197 HDLARALLPFFA-LERQESAGLAVDTLCAVGKYQEAIQTGESALARG-LDGAALRRSLGLAYYQSGRSREAKLQAAEHWR  274 (656)
T ss_pred             HHHHHHHHhcCC-CcchhHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHcCCchhhHHHHHHHHH
Confidence            999999877631 2334455566778899999999999999998765 5667888889999999999986    899999


Q ss_pred             HHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcC
Q 012111          316 FMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILD  395 (471)
Q Consensus       316 ~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~  395 (471)
                      ...+..+. +...+..+...+...|++++|...+++..... +.+...+..+..++...|++++|...++.+...++. +
T Consensus       275 ~Al~l~P~-~~~a~~~lg~~l~~~g~~~eA~~~l~~al~l~-P~~~~a~~~La~~l~~~G~~~eA~~~l~~al~~~P~-~  351 (656)
T PRK15174        275 HALQFNSD-NVRIVTLYADALIRTGQNEKAIPLLQQSLATH-PDLPYVRAMYARALRQVGQYTAASDEFVQLAREKGV-T  351 (656)
T ss_pred             HHHhhCCC-CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCcc-c
Confidence            98886443 67788899999999999999999999999863 335667788889999999999999999999887544 3


Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHhC
Q 012111          396 TPFFNCIISAYGQAGDVEKMGELFLTMKER  425 (471)
Q Consensus       396 ~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~  425 (471)
                      ...+..+..++...|+.++|+..|++..+.
T Consensus       352 ~~~~~~~a~al~~~G~~deA~~~l~~al~~  381 (656)
T PRK15174        352 SKWNRYAAAALLQAGKTSEAESVFEHYIQA  381 (656)
T ss_pred             hHHHHHHHHHHHHCCCHHHHHHHHHHHHHh
Confidence            344555677889999999999999998874

>TIGR00990 3a0801s09 mitochondrial precursor proteins import receptor (72 kDa mitochondrial outermembrane protein) (mitochondrial import receptor for the ADP/ATP carrier) (translocase of outermembrane tom70)

Probab=99.92  E-value=1.1e-19  Score=178.06  Aligned_cols=370  Identities=12%  Similarity=0.011  Sum_probs=287.1

Q ss_pred             HHHHHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcC
Q 012111           84 ALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSG  163 (471)
Q Consensus        84 ~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~  163 (471)
                      .-..+.+.|++++|++.|+.+...   .|+...|..+..+|.+.|++++|+..++..++.... +...|..+..+|...|
T Consensus       133 ~G~~~~~~~~~~~Ai~~y~~al~~---~p~~~~~~n~a~~~~~l~~~~~Ai~~~~~al~l~p~-~~~a~~~~a~a~~~lg  208 (615)
T TIGR00990       133 KGNKAYRNKDFNKAIKLYSKAIEC---KPDPVYYSNRAACHNALGDWEKVVEDTTAALELDPD-YSKALNRRANAYDGLG  208 (615)
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHhc---CCchHHHHHHHHHHHHhCCHHHHHHHHHHHHHcCCC-CHHHHHHHHHHHHHcC
Confidence            344566789999999999999875   467788999999999999999999999999887433 6778888999999999


Q ss_pred             CHHHHHHHHHHhhcCCCCC-------------------------------CCHHHHHHH---------------------
Q 012111          164 LLDEAFSTINDMKSVSDCK-------------------------------PDVYTYSIL---------------------  191 (471)
Q Consensus       164 ~~~~a~~~~~~~~~~~~~~-------------------------------~~~~~~~~l---------------------  191 (471)
                      ++++|+.-|.......+..                               |........                     
T Consensus       209 ~~~eA~~~~~~~~~~~~~~~~~~~~~~~~~l~~~a~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  288 (615)
T TIGR00990       209 KYADALLDLTASCIIDGFRNEQSAQAVERLLKKFAESKAKEILETKPENLPSVTFVGNYLQSFRPKPRPAGLEDSNELDE  288 (615)
T ss_pred             CHHHHHHHHHHHHHhCCCccHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHccCCcchhhhhccccccc
Confidence            9999987665443211110                               000000000                     


Q ss_pred             ------HHHH------HhcCCHHHHHHHHHHHHHCC-C-CCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHH
Q 012111          192 ------IKSC------TKFHRFDLIEKILAEMSYLG-I-ECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIF  257 (471)
Q Consensus       192 ------l~~~------~~~~~~~~a~~~~~~~~~~g-~-~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~  257 (471)
                            +...      ...+++++|.+.|+...+.+ . +.....+..+...+...|++++|+..|++..+..  +....
T Consensus       289 ~~~~~~~~l~~~~~e~~~~~~y~~A~~~~~~al~~~~~~~~~a~a~~~lg~~~~~~g~~~eA~~~~~kal~l~--P~~~~  366 (615)
T TIGR00990       289 ETGNGQLQLGLKSPESKADESYEEAARAFEKALDLGKLGEKEAIALNLRGTFKCLKGKHLEALADLSKSIELD--PRVTQ  366 (615)
T ss_pred             ccccchHHHHHHHHHhhhhhhHHHHHHHHHHHHhcCCCChhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC--CCcHH
Confidence                  0000      11257889999999998765 2 3345678888889999999999999999998763  33466


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHH
Q 012111          258 TLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFG  337 (471)
Q Consensus       258 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~  337 (471)
                      .|..+...+...|++++|...|+++.+.. +.+..++..+...+...|++++|...|+...+.... +...+..+...+.
T Consensus       367 ~~~~la~~~~~~g~~~eA~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~kal~l~P~-~~~~~~~la~~~~  444 (615)
T TIGR00990       367 SYIKRASMNLELGDPDKAEEDFDKALKLN-SEDPDIYYHRAQLHFIKGEFAQAGKDYQKSIDLDPD-FIFSHIQLGVTQY  444 (615)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCcc-CHHHHHHHHHHHH
Confidence            88889999999999999999999998764 566788999999999999999999999999887433 5667888889999


Q ss_pred             hcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHH------HHHHHHHHHHhcCC
Q 012111          338 KAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTP------FFNCIISAYGQAGD  411 (471)
Q Consensus       338 ~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~------~~~~l~~~~~~~g~  411 (471)
                      +.|++++|+..|++..... +-+...++.+...+...|++++|...|++.....+..+..      .++..+..+...|+
T Consensus       445 ~~g~~~eA~~~~~~al~~~-P~~~~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~p~~~~~~~~~~~l~~~a~~~~~~~~~  523 (615)
T TIGR00990       445 KEGSIASSMATFRRCKKNF-PEAPDVYNYYGELLLDQNKFDEAIEKFDTAIELEKETKPMYMNVLPLINKALALFQWKQD  523 (615)
T ss_pred             HCCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHccCHHHHHHHHHHHHhcCCccccccccHHHHHHHHHHHHHHhhh
Confidence            9999999999999998753 3457889999999999999999999999988765432221      12222233445699


Q ss_pred             HHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhhhc
Q 012111          412 VEKMGELFLTMKERHCVPDNITFATMIQAYNALGMTEAAQNLENKMIAMKEN  463 (471)
Q Consensus       412 ~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~  463 (471)
                      +++|.+++++..+.. +.+...+..+...+.+.|++++|.++++++.+....
T Consensus       524 ~~eA~~~~~kAl~l~-p~~~~a~~~la~~~~~~g~~~eAi~~~e~A~~l~~~  574 (615)
T TIGR00990       524 FIEAENLCEKALIID-PECDIAVATMAQLLLQQGDVDEALKLFERAAELART  574 (615)
T ss_pred             HHHHHHHHHHHHhcC-CCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHHhcc
Confidence            999999999988753 224456888999999999999999999999887654

>KOG4626 consensus O-linked N-acetylglucosamine transferase OGT [Carbohydrate transport and metabolism; Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]

Probab=99.91  E-value=5.2e-21  Score=170.85  Aligned_cols=372  Identities=14%  Similarity=0.160  Sum_probs=297.6

Q ss_pred             hHHHHHHHhhHHHHH----HHHHhhhhhhccCCCchHHHHHHHHHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHH
Q 012111           48 EKDLSKILRTEFAIK----NIEKKVSSKKYKNLWPKPVLEALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVM  123 (471)
Q Consensus        48 ~~~l~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~  123 (471)
                      ...+..+.+..+.++    ..+.+++   ..+-..+.++.....+...|+.+.|.+.|..+.+.+  |...-....+...
T Consensus       119 ysn~aN~~kerg~~~~al~~y~~aie---l~p~fida~inla~al~~~~~~~~a~~~~~~alqln--P~l~ca~s~lgnL  193 (966)
T KOG4626|consen  119 YSNLANILKERGQLQDALALYRAAIE---LKPKFIDAYINLAAALVTQGDLELAVQCFFEALQLN--PDLYCARSDLGNL  193 (966)
T ss_pred             HHHHHHHHHHhchHHHHHHHHHHHHh---cCchhhHHHhhHHHHHHhcCCCcccHHHHHHHHhcC--cchhhhhcchhHH
Confidence            334445555555443    3333333   334456778888888899999999999999998864  3333444555566


Q ss_pred             HhcCCCHHHHHHHHHHHHhCCCCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCC-HHHHHHHHHHHHhcCCH
Q 012111          124 LGKCKQPEQASLLFEVMLSDGLKPS-VDVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPD-VYTYSILIKSCTKFHRF  201 (471)
Q Consensus       124 ~~~~~~~~~a~~~~~~m~~~~~~~~-~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~-~~~~~~ll~~~~~~~~~  201 (471)
                      +-..|+.++|...|.+.++.  .|. ...|+.|...+-.+|+...|++.|++..+.   .|+ ...|-.|...|...+.+
T Consensus       194 lka~Grl~ea~~cYlkAi~~--qp~fAiawsnLg~~f~~~Gei~~aiq~y~eAvkl---dP~f~dAYiNLGnV~ke~~~~  268 (966)
T KOG4626|consen  194 LKAEGRLEEAKACYLKAIET--QPCFAIAWSNLGCVFNAQGEIWLAIQHYEEAVKL---DPNFLDAYINLGNVYKEARIF  268 (966)
T ss_pred             HHhhcccchhHHHHHHHHhh--CCceeeeehhcchHHhhcchHHHHHHHHHHhhcC---CCcchHHHhhHHHHHHHHhcc
Confidence            66789999999999888876  333 467899999999999999999999998873   444 45688899999999999


Q ss_pred             HHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHH
Q 012111          202 DLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNE  281 (471)
Q Consensus       202 ~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~  281 (471)
                      ++|...+.+..... +.....+..+...|..+|..+-|+..|++..+....  -...|+.|..++-..|++.+|.+.|.+
T Consensus       269 d~Avs~Y~rAl~lr-pn~A~a~gNla~iYyeqG~ldlAI~~Ykral~~~P~--F~~Ay~NlanALkd~G~V~ea~~cYnk  345 (966)
T KOG4626|consen  269 DRAVSCYLRALNLR-PNHAVAHGNLACIYYEQGLLDLAIDTYKRALELQPN--FPDAYNNLANALKDKGSVTEAVDCYNK  345 (966)
T ss_pred             hHHHHHHHHHHhcC-CcchhhccceEEEEeccccHHHHHHHHHHHHhcCCC--chHHHhHHHHHHHhccchHHHHHHHHH
Confidence            99999998887653 345778888999999999999999999999886422  245799999999999999999999999


Q ss_pred             HHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCC
Q 012111          282 FNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPT-VVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPN  360 (471)
Q Consensus       282 ~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~  360 (471)
                      ..... +......+.|..+|...|.+++|..+|....+-  .|. ...++.|...|-+.|++++|+..|++.++  +.|+
T Consensus       346 aL~l~-p~hadam~NLgni~~E~~~~e~A~~ly~~al~v--~p~~aaa~nNLa~i~kqqgnl~~Ai~~Ykealr--I~P~  420 (966)
T KOG4626|consen  346 ALRLC-PNHADAMNNLGNIYREQGKIEEATRLYLKALEV--FPEFAAAHNNLASIYKQQGNLDDAIMCYKEALR--IKPT  420 (966)
T ss_pred             HHHhC-CccHHHHHHHHHHHHHhccchHHHHHHHHHHhh--ChhhhhhhhhHHHHHHhcccHHHHHHHHHHHHh--cCch
Confidence            98764 556778899999999999999999999988875  333 45788899999999999999999999887  5776


Q ss_pred             -HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCH-HHHHHHH
Q 012111          361 -SITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDN-ITFATMI  438 (471)
Q Consensus       361 -~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~-~~~~~l~  438 (471)
                       ...|+.+...|-..|+++.|.+.+.+.+..++. -...++.|...|...|++.+|+.-|++..+  ++||. ..|-.++
T Consensus       421 fAda~~NmGnt~ke~g~v~~A~q~y~rAI~~nPt-~AeAhsNLasi~kDsGni~~AI~sY~~aLk--lkPDfpdA~cNll  497 (966)
T KOG4626|consen  421 FADALSNMGNTYKEMGDVSAAIQCYTRAIQINPT-FAEAHSNLASIYKDSGNIPEAIQSYRTALK--LKPDFPDAYCNLL  497 (966)
T ss_pred             HHHHHHhcchHHHHhhhHHHHHHHHHHHHhcCcH-HHHHHhhHHHHhhccCCcHHHHHHHHHHHc--cCCCCchhhhHHH
Confidence             668999999999999999999999999988765 567889999999999999999999999987  56764 3444444


Q ss_pred             HH
Q 012111          439 QA  440 (471)
Q Consensus       439 ~~  440 (471)
                      .+
T Consensus       498 h~  499 (966)
T KOG4626|consen  498 HC  499 (966)
T ss_pred             HH
Confidence            43

>KOG4626 consensus O-linked N-acetylglucosamine transferase OGT [Carbohydrate transport and metabolism; Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]

Probab=99.91  E-value=4.9e-21  Score=171.01  Aligned_cols=372  Identities=14%  Similarity=0.090  Sum_probs=309.4

Q ss_pred             hHHHHHHHHHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHH-HHHHHHH
Q 012111           79 KPVLEALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVD-VYTALVS  157 (471)
Q Consensus        79 ~~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~-~~~~li~  157 (471)
                      +.+......+-..|++++|+..|+.+.+..  +.....|..+..++...|+.+.|.+.|.+.++.  .|+.. ..+.+..
T Consensus       117 e~ysn~aN~~kerg~~~~al~~y~~aiel~--p~fida~inla~al~~~~~~~~a~~~~~~alql--nP~l~ca~s~lgn  192 (966)
T KOG4626|consen  117 EAYSNLANILKERGQLQDALALYRAAIELK--PKFIDAYINLAAALVTQGDLELAVQCFFEALQL--NPDLYCARSDLGN  192 (966)
T ss_pred             HHHHHHHHHHHHhchHHHHHHHHHHHHhcC--chhhHHHhhHHHHHHhcCCCcccHHHHHHHHhc--CcchhhhhcchhH
Confidence            455556666777899999999999998875  567788999999999999999999999888876  44443 3344556


Q ss_pred             HHHhcCCHHHHHHHHHHhhcCCCCCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCH
Q 012111          158 AYGQSGLLDEAFSTINDMKSVSDCKPD-VYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKF  236 (471)
Q Consensus       158 ~~~~~~~~~~a~~~~~~~~~~~~~~~~-~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~  236 (471)
                      .+...|++++|...|.+..+.   .|. ...|+.|.-.+-..|+...|++.|++..+.. +--...|..|...|...+.+
T Consensus       193 Llka~Grl~ea~~cYlkAi~~---qp~fAiawsnLg~~f~~~Gei~~aiq~y~eAvkld-P~f~dAYiNLGnV~ke~~~~  268 (966)
T KOG4626|consen  193 LLKAEGRLEEAKACYLKAIET---QPCFAIAWSNLGCVFNAQGEIWLAIQHYEEAVKLD-PNFLDAYINLGNVYKEARIF  268 (966)
T ss_pred             HHHhhcccchhHHHHHHHHhh---CCceeeeehhcchHHhhcchHHHHHHHHHHhhcCC-CcchHHHhhHHHHHHHHhcc
Confidence            666788999999988887762   343 4568888888888999999999999998763 22377899999999999999


Q ss_pred             HHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHH
Q 012111          237 EEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDF  316 (471)
Q Consensus       237 ~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~  316 (471)
                      +.|...|.+.....  +-....+..+...|...|+.|.|+..|++..+.. +.-...|+.|..++-..|++.+|.+.+..
T Consensus       269 d~Avs~Y~rAl~lr--pn~A~a~gNla~iYyeqG~ldlAI~~Ykral~~~-P~F~~Ay~NlanALkd~G~V~ea~~cYnk  345 (966)
T KOG4626|consen  269 DRAVSCYLRALNLR--PNHAVAHGNLACIYYEQGLLDLAIDTYKRALELQ-PNFPDAYNNLANALKDKGSVTEAVDCYNK  345 (966)
T ss_pred             hHHHHHHHHHHhcC--CcchhhccceEEEEeccccHHHHHHHHHHHHhcC-CCchHHHhHHHHHHHhccchHHHHHHHHH
Confidence            99999999887652  3446778888888999999999999999998764 44577899999999999999999999999


Q ss_pred             HHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcC
Q 012111          317 MQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPN-SITYCSLVSAYSKAGLIMKVDSILRQVENSDVILD  395 (471)
Q Consensus       317 ~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~-~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~  395 (471)
                      ....... .....+.|...|...|.+++|..+|....+-  .|. ...++.|...|-.+|++++|...+++..+..+. -
T Consensus       346 aL~l~p~-hadam~NLgni~~E~~~~e~A~~ly~~al~v--~p~~aaa~nNLa~i~kqqgnl~~Ai~~YkealrI~P~-f  421 (966)
T KOG4626|consen  346 ALRLCPN-HADAMNNLGNIYREQGKIEEATRLYLKALEV--FPEFAAAHNNLASIYKQQGNLDDAIMCYKEALRIKPT-F  421 (966)
T ss_pred             HHHhCCc-cHHHHHHHHHHHHHhccchHHHHHHHHHHhh--ChhhhhhhhhHHHHHHhcccHHHHHHHHHHHHhcCch-H
Confidence            8876332 5667888999999999999999999988874  443 567899999999999999999999999987654 5


Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHHhhhcCCCC
Q 012111          396 TPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPD-NITFATMIQAYNALGMTEAAQNLENKMIAMKENSGKK  467 (471)
Q Consensus       396 ~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~-~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~~~~~  467 (471)
                      ...|+.+...|-..|+.+.|+..+.+.+.  +.|. ...++.|...|-.+|+..+|..-+++.++++|+..+.
T Consensus       422 Ada~~NmGnt~ke~g~v~~A~q~y~rAI~--~nPt~AeAhsNLasi~kDsGni~~AI~sY~~aLklkPDfpdA  492 (966)
T KOG4626|consen  422 ADALSNMGNTYKEMGDVSAAIQCYTRAIQ--INPTFAEAHSNLASIYKDSGNIPEAIQSYRTALKLKPDFPDA  492 (966)
T ss_pred             HHHHHhcchHHHHhhhHHHHHHHHHHHHh--cCcHHHHHHhhHHHHhhccCCcHHHHHHHHHHHccCCCCchh
Confidence            67899999999999999999999999987  4565 4678889999999999999999999999999987654

>PRK15174 Vi polysaccharide export protein VexE; Provisional

Probab=99.91  E-value=2.2e-19  Score=175.29  Aligned_cols=365  Identities=10%  Similarity=0.022  Sum_probs=292.6

Q ss_pred             HHhhcHHHHHHHHHHhhhccC-ccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHH
Q 012111           89 IKQKKWQLALKIFGLLRQQQW-YQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDE  167 (471)
Q Consensus        89 ~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~  167 (471)
                      .++.+|+.---+|....+..- --.+..-...++..+.+.|++++|..+++........ +...+..++.+....|+++.
T Consensus        16 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~l~~~~l~~~p~-~~~~l~~l~~~~l~~g~~~~   94 (656)
T PRK15174         16 LKQEDWEGLCLYFSQHPEKVRDSAGNEQNIILFAIACLRKDETDVGLTLLSDRVLTAKN-GRDLLRRWVISPLASSQPDA   94 (656)
T ss_pred             hhhhchhhHhHHhhcccHhhhhhcccccCHHHHHHHHHhcCCcchhHHHhHHHHHhCCC-chhHHHHHhhhHhhcCCHHH
Confidence            467777766666665543310 0123344566777888999999999999999887544 45666677777888999999


Q ss_pred             HHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHH
Q 012111          168 AFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMV  247 (471)
Q Consensus       168 a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  247 (471)
                      |++.|+++....  +.+...+..+...+...|+++.|...++++.+.. +.+...+..+...+...|++++|...++.+.
T Consensus        95 A~~~l~~~l~~~--P~~~~a~~~la~~l~~~g~~~~Ai~~l~~Al~l~-P~~~~a~~~la~~l~~~g~~~eA~~~~~~~~  171 (656)
T PRK15174         95 VLQVVNKLLAVN--VCQPEDVLLVASVLLKSKQYATVADLAEQAWLAF-SGNSQIFALHLRTLVLMDKELQAISLARTQA  171 (656)
T ss_pred             HHHHHHHHHHhC--CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHCCChHHHHHHHHHHH
Confidence            999999998732  4456778888899999999999999999998863 4467888899999999999999999999887


Q ss_pred             HcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHH
Q 012111          248 ESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVV  327 (471)
Q Consensus       248 ~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~  327 (471)
                      ...  +.+...+..+ ..+...|++++|...++.+......++...+..+...+...|++++|...++.+.+.... +..
T Consensus       172 ~~~--P~~~~a~~~~-~~l~~~g~~~eA~~~~~~~l~~~~~~~~~~~~~l~~~l~~~g~~~eA~~~~~~al~~~p~-~~~  247 (656)
T PRK15174        172 QEV--PPRGDMIATC-LSFLNKSRLPEDHDLARALLPFFALERQESAGLAVDTLCAVGKYQEAIQTGESALARGLD-GAA  247 (656)
T ss_pred             HhC--CCCHHHHHHH-HHHHHcCCHHHHHHHHHHHHhcCCCcchhHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCC-CHH
Confidence            653  2333344333 347889999999999999877643344555566678889999999999999999887543 577


Q ss_pred             HHHHHHHHHHhcCCHHH----HHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHH
Q 012111          328 TYNIVIETFGKAGHIEK----MEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCII  403 (471)
Q Consensus       328 ~~~~li~~~~~~g~~~~----a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~  403 (471)
                      .+..+...+...|++++    |...+++..... +.+...+..+...+...|++++|...++++.+..+. +...+..+.
T Consensus       248 ~~~~Lg~~l~~~G~~~eA~~~A~~~~~~Al~l~-P~~~~a~~~lg~~l~~~g~~~eA~~~l~~al~l~P~-~~~a~~~La  325 (656)
T PRK15174        248 LRRSLGLAYYQSGRSREAKLQAAEHWRHALQFN-SDNVRIVTLYADALIRTGQNEKAIPLLQQSLATHPD-LPYVRAMYA  325 (656)
T ss_pred             HHHHHHHHHHHcCCchhhHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCC-CHHHHHHHH
Confidence            78889999999999986    899999998863 336778999999999999999999999999988765 677788899


Q ss_pred             HHHHhcCCHHHHHHHHHHHHhCCCCCCHHH-HHHHHHHHHhcCCHHHHHHHHHHHHHhhhcCC
Q 012111          404 SAYGQAGDVEKMGELFLTMKERHCVPDNIT-FATMIQAYNALGMTEAAQNLENKMIAMKENSG  465 (471)
Q Consensus       404 ~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~-~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~~~  465 (471)
                      .++...|++++|+..|+++.+.  .|+... +..+..++...|+.++|...++++++..|+..
T Consensus       326 ~~l~~~G~~~eA~~~l~~al~~--~P~~~~~~~~~a~al~~~G~~deA~~~l~~al~~~P~~~  386 (656)
T PRK15174        326 RALRQVGQYTAASDEFVQLARE--KGVTSKWNRYAAAALLQAGKTSEAESVFEHYIQARASHL  386 (656)
T ss_pred             HHHHHCCCHHHHHHHHHHHHHh--CccchHHHHHHHHHHHHCCCHHHHHHHHHHHHHhChhhc
Confidence            9999999999999999999875  465544 33456788999999999999999999988754

>PRK10049 pgaA outer membrane protein PgaA; Provisional

Probab=99.90  E-value=1.1e-18  Score=173.96  Aligned_cols=403  Identities=8%  Similarity=-0.030  Sum_probs=286.2

Q ss_pred             hhHHHHHHHhhHHHHHHHHHhhhhhhccCCCchHHHHHHHHHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhc
Q 012111           47 AEKDLSKILRTEFAIKNIEKKVSSKKYKNLWPKPVLEALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGK  126 (471)
Q Consensus        47 ~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  126 (471)
                      ....+...++..++++.+.....   ..+.....+..+...+...|++++|+++|+.+.+..  |.+...+..++.++..
T Consensus        21 ~~~ia~~~g~~~~A~~~~~~~~~---~~~~~a~~~~~lA~~~~~~g~~~~A~~~~~~al~~~--P~~~~a~~~la~~l~~   95 (765)
T PRK10049         21 WLQIALWAGQDAEVITVYNRYRV---HMQLPARGYAAVAVAYRNLKQWQNSLTLWQKALSLE--PQNDDYQRGLILTLAD   95 (765)
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHh---hCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHH
Confidence            33344444455555444433322   233444456677777778888888888888888764  5666777788888888


Q ss_pred             CCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHH
Q 012111          127 CKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEK  206 (471)
Q Consensus       127 ~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~  206 (471)
                      .|++++|...++++.+... .+.. +..+..++...|+.++|+..++++.+.  .+.+...+..+..++...+..+.|++
T Consensus        96 ~g~~~eA~~~l~~~l~~~P-~~~~-~~~la~~l~~~g~~~~Al~~l~~al~~--~P~~~~~~~~la~~l~~~~~~e~Al~  171 (765)
T PRK10049         96 AGQYDEALVKAKQLVSGAP-DKAN-LLALAYVYKRAGRHWDELRAMTQALPR--APQTQQYPTEYVQALRNNRLSAPALG  171 (765)
T ss_pred             CCCHHHHHHHHHHHHHhCC-CCHH-HHHHHHHHHHCCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHCCChHHHHH
Confidence            8888888888888887632 2555 777888888888888888888888873  23455556667777777788888888


Q ss_pred             HHHHHHHCCCCCCH------HHHHHHHHHHHc-----cCCH---HHHHHHHHHHHHcCCCCCCHH-HH----HHHHHHHH
Q 012111          207 ILAEMSYLGIECSA------VTYNTIIDGYGK-----AKKF---EEMESSFSAMVESGGCHPDIF-TL----NSMISAYG  267 (471)
Q Consensus       207 ~~~~~~~~g~~~~~------~~~~~l~~~~~~-----~~~~---~~a~~~~~~~~~~~~~~~~~~-~~----~~l~~~~~  267 (471)
                      .++....   .|+.      .....+++....     .+++   ++|++.++.+.+.....|+.. .+    ...+.++.
T Consensus       172 ~l~~~~~---~p~~~~~l~~~~~~~~~r~~~~~~~~~~~r~~~ad~Al~~~~~ll~~~~~~p~~~~~~~~a~~d~l~~Ll  248 (765)
T PRK10049        172 AIDDANL---TPAEKRDLEADAAAELVRLSFMPTRSEKERYAIADRALAQYDALEALWHDNPDATADYQRARIDRLGALL  248 (765)
T ss_pred             HHHhCCC---CHHHHHHHHHHHHHHHHHhhcccccChhHHHHHHHHHHHHHHHHHhhcccCCccchHHHHHHHHHHHHHH
Confidence            8876553   2221      112222222221     2234   678888888875422233321 11    11134456


Q ss_pred             hcCCHHHHHHHHHHHHhCCCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCC---CHHHHHHHHHHHHhcCCHH
Q 012111          268 NSGNIEKMEKWYNEFNLMGVK-ADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFP---TVVTYNIVIETFGKAGHIE  343 (471)
Q Consensus       268 ~~~~~~~a~~~~~~~~~~~~~-~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~---~~~~~~~li~~~~~~g~~~  343 (471)
                      ..|++++|+..|+.+.+.+.+ |+. ....+...|...|++++|..+|+.+.+.....   ....+..+..++...|+++
T Consensus       249 ~~g~~~eA~~~~~~ll~~~~~~P~~-a~~~la~~yl~~g~~e~A~~~l~~~l~~~p~~~~~~~~~~~~L~~a~~~~g~~~  327 (765)
T PRK10049        249 ARDRYKDVISEYQRLKAEGQIIPPW-AQRWVASAYLKLHQPEKAQSILTELFYHPETIADLSDEELADLFYSLLESENYP  327 (765)
T ss_pred             HhhhHHHHHHHHHHhhccCCCCCHH-HHHHHHHHHHhcCCcHHHHHHHHHHhhcCCCCCCCChHHHHHHHHHHHhcccHH
Confidence            779999999999999877532 322 22335778999999999999999987653221   1345666777889999999


Q ss_pred             HHHHHHHHHHHcCC-----------CCC---HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhc
Q 012111          344 KMEEYFKKMKHRGM-----------KPN---SITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQA  409 (471)
Q Consensus       344 ~a~~~~~~m~~~~~-----------~p~---~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  409 (471)
                      +|..+++.+.....           .|+   ...+..+...+...|+.++|+++++++....+. +...+..+...+...
T Consensus       328 eA~~~l~~~~~~~P~~~~~~~~~~~~p~~~~~~a~~~~a~~l~~~g~~~eA~~~l~~al~~~P~-n~~l~~~lA~l~~~~  406 (765)
T PRK10049        328 GALTVTAHTINNSPPFLRLYGSPTSIPNDDWLQGQSLLSQVAKYSNDLPQAEMRARELAYNAPG-NQGLRIDYASVLQAR  406 (765)
T ss_pred             HHHHHHHHHhhcCCceEeecCCCCCCCCchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHhc
Confidence            99999999987521           123   234567778899999999999999999988766 788999999999999


Q ss_pred             CCHHHHHHHHHHHHhCCCCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHHhhhcCC
Q 012111          410 GDVEKMGELFLTMKERHCVPD-NITFATMIQAYNALGMTEAAQNLENKMIAMKENSG  465 (471)
Q Consensus       410 g~~~~a~~~~~~~~~~~~~p~-~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~~~  465 (471)
                      |++++|++.+++..+.  .|+ ...+..+...+...|++++|..+++++++..|+..
T Consensus       407 g~~~~A~~~l~~al~l--~Pd~~~l~~~~a~~al~~~~~~~A~~~~~~ll~~~Pd~~  461 (765)
T PRK10049        407 GWPRAAENELKKAEVL--EPRNINLEVEQAWTALDLQEWRQMDVLTDDVVAREPQDP  461 (765)
T ss_pred             CCHHHHHHHHHHHHhh--CCCChHHHHHHHHHHHHhCCHHHHHHHHHHHHHhCCCCH
Confidence            9999999999999985  465 56666777889999999999999999999988754

>PRK11447 cellulose synthase subunit BcsC; Provisional

Probab=99.90  E-value=6.3e-19  Score=183.75  Aligned_cols=360  Identities=11%  Similarity=0.065  Sum_probs=212.7

Q ss_pred             HHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCC-CHHHHH------------
Q 012111           87 EAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKP-SVDVYT------------  153 (471)
Q Consensus        87 ~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~-~~~~~~------------  153 (471)
                      .+...|++++|+..|+.+.+..  |.+..++..+..++.+.|++++|...|++..+..... ....|.            
T Consensus       278 ~~~~~g~~~~A~~~l~~aL~~~--P~~~~a~~~Lg~~~~~~g~~~eA~~~l~~Al~~~p~~~~~~~~~~ll~~~~~~~~~  355 (1157)
T PRK11447        278 AAVDSGQGGKAIPELQQAVRAN--PKDSEALGALGQAYSQQGDRARAVAQFEKALALDPHSSNRDKWESLLKVNRYWLLI  355 (1157)
T ss_pred             HHHHCCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCccchhHHHHHHHhhhHHHHH
Confidence            3456799999999999998875  6678889999999999999999999999988764322 111121            


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHH----
Q 012111          154 ALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDG----  229 (471)
Q Consensus       154 ~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~----  229 (471)
                      .....+.+.|++++|+..|+++....  +.+...+..+...+...|++++|++.|++..+.. +.+...+..+...    
T Consensus       356 ~~g~~~~~~g~~~eA~~~~~~Al~~~--P~~~~a~~~Lg~~~~~~g~~~eA~~~y~~aL~~~-p~~~~a~~~L~~l~~~~  432 (1157)
T PRK11447        356 QQGDAALKANNLAQAERLYQQARQVD--NTDSYAVLGLGDVAMARKDYAAAERYYQQALRMD-PGNTNAVRGLANLYRQQ  432 (1157)
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHhc
Confidence            22446678899999999999998742  4456677788888999999999999999988764 3334444433333    


Q ss_pred             --------------------------------------HHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCC
Q 012111          230 --------------------------------------YGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGN  271 (471)
Q Consensus       230 --------------------------------------~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  271 (471)
                                                            +...|++++|++.|++..+..  +.+...+..+...|.+.|+
T Consensus       433 ~~~~A~~~l~~l~~~~~~~~~~~~~~l~~~~~~~~a~~~~~~g~~~eA~~~~~~Al~~~--P~~~~~~~~LA~~~~~~G~  510 (1157)
T PRK11447        433 SPEKALAFIASLSASQRRSIDDIERSLQNDRLAQQAEALENQGKWAQAAELQRQRLALD--PGSVWLTYRLAQDLRQAGQ  510 (1157)
T ss_pred             CHHHHHHHHHhCCHHHHHHHHHHHHHhhhhHHHHHHHHHHHCCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHcCC
Confidence                                                  334566666666666666542  3344455566666667777


Q ss_pred             HHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHH---------HHHHHHHHHHhcCCH
Q 012111          272 IEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVV---------TYNIVIETFGKAGHI  342 (471)
Q Consensus       272 ~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~---------~~~~li~~~~~~g~~  342 (471)
                      +++|...++++.... +.+...+..+...+...++.++|...++.+......++..         .+..+...+...|+.
T Consensus       511 ~~~A~~~l~~al~~~-P~~~~~~~a~al~l~~~~~~~~Al~~l~~l~~~~~~~~~~~l~~~l~~~~~l~~a~~l~~~G~~  589 (1157)
T PRK11447        511 RSQADALMRRLAQQK-PNDPEQVYAYGLYLSGSDRDRAALAHLNTLPRAQWNSNIQELAQRLQSDQVLETANRLRDSGKE  589 (1157)
T ss_pred             HHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHhCCCHHHHHHHHHhCCchhcChhHHHHHHHHhhhHHHHHHHHHHHCCCH
Confidence            777777776665432 2233333333333444455555555544432211111100         011122333444444


Q ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 012111          343 EKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTM  422 (471)
Q Consensus       343 ~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~  422 (471)
                      ++|..+++.     .+.+...+..+...+.+.|++++|...|+.+.+..+. +...+..++..+...|++++|++.++..
T Consensus       590 ~eA~~~l~~-----~p~~~~~~~~La~~~~~~g~~~~A~~~y~~al~~~P~-~~~a~~~la~~~~~~g~~~eA~~~l~~l  663 (1157)
T PRK11447        590 AEAEALLRQ-----QPPSTRIDLTLADWAQQRGDYAAARAAYQRVLTREPG-NADARLGLIEVDIAQGDLAAARAQLAKL  663 (1157)
T ss_pred             HHHHHHHHh-----CCCCchHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHCCCHHHHHHHHHHH
Confidence            444444431     1223344455555555556666666666555555443 4555555555555556666666655555


Q ss_pred             HhCCCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhhh
Q 012111          423 KERHCVP-DNITFATMIQAYNALGMTEAAQNLENKMIAMKE  462 (471)
Q Consensus       423 ~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~  462 (471)
                      .+.  .| +..++..+..++...|++++|.+++++++...+
T Consensus       664 l~~--~p~~~~~~~~la~~~~~~g~~~eA~~~~~~al~~~~  702 (1157)
T PRK11447        664 PAT--ANDSLNTQRRVALAWAALGDTAAAQRTFNRLIPQAK  702 (1157)
T ss_pred             hcc--CCCChHHHHHHHHHHHhCCCHHHHHHHHHHHhhhCc
Confidence            442  22 233344444555555666666666655555443

>PRK11447 cellulose synthase subunit BcsC; Provisional

Probab=99.90  E-value=1.6e-18  Score=180.72  Aligned_cols=394  Identities=9%  Similarity=-0.013  Sum_probs=298.6

Q ss_pred             HHHHHHhhHHHHHHHHHhhhhhhccCCCchHHHHHHHHHHHhhcHHHHHHHHHHhhhccCccCChhHH------------
Q 012111           50 DLSKILRTEFAIKNIEKKVSSKKYKNLWPKPVLEALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTF------------  117 (471)
Q Consensus        50 ~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~------------  117 (471)
                      .+....+...+...+...+...|   ..+..+..+-..+.+.|++++|++.|+.+.+..+-.+....+            
T Consensus       278 ~~~~~g~~~~A~~~l~~aL~~~P---~~~~a~~~Lg~~~~~~g~~~eA~~~l~~Al~~~p~~~~~~~~~~ll~~~~~~~~  354 (1157)
T PRK11447        278 AAVDSGQGGKAIPELQQAVRANP---KDSEALGALGQAYSQQGDRARAVAQFEKALALDPHSSNRDKWESLLKVNRYWLL  354 (1157)
T ss_pred             HHHHCCCHHHHHHHHHHHHHhCC---CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCccchhHHHHHHHhhhHHHH
Confidence            34445666777777776666433   345666677777889999999999999998764211121111            


Q ss_pred             HHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHH-------
Q 012111          118 TKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSI-------  190 (471)
Q Consensus       118 ~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~-------  190 (471)
                      ......+.+.|++++|...|+++.+... .+...+..+..++...|++++|++.|+++.+..  +.+...+..       
T Consensus       355 ~~~g~~~~~~g~~~eA~~~~~~Al~~~P-~~~~a~~~Lg~~~~~~g~~~eA~~~y~~aL~~~--p~~~~a~~~L~~l~~~  431 (1157)
T PRK11447        355 IQQGDAALKANNLAQAERLYQQARQVDN-TDSYAVLGLGDVAMARKDYAAAERYYQQALRMD--PGNTNAVRGLANLYRQ  431 (1157)
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHh
Confidence            2234567789999999999999998743 367778889999999999999999999988732  222323222       


Q ss_pred             -----------------------------------HHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCC
Q 012111          191 -----------------------------------LIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKK  235 (471)
Q Consensus       191 -----------------------------------ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~  235 (471)
                                                         +...+...|++++|.+.+++..+.. +-+...+..+...|.+.|+
T Consensus       432 ~~~~~A~~~l~~l~~~~~~~~~~~~~~l~~~~~~~~a~~~~~~g~~~eA~~~~~~Al~~~-P~~~~~~~~LA~~~~~~G~  510 (1157)
T PRK11447        432 QSPEKALAFIASLSASQRRSIDDIERSLQNDRLAQQAEALENQGKWAQAAELQRQRLALD-PGSVWLTYRLAQDLRQAGQ  510 (1157)
T ss_pred             cCHHHHHHHHHhCCHHHHHHHHHHHHHhhhhHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCC
Confidence                                               2233456789999999999998774 4467788889999999999


Q ss_pred             HHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHH---------HHHHHHHHHHHcCC
Q 012111          236 FEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQ---------TLNILTKSYGRAGM  306 (471)
Q Consensus       236 ~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~---------~~~~ll~~~~~~~~  306 (471)
                      +++|...++++.+..  +.+...+..+...+...++.++|...++.+......++..         .+..+...+...|+
T Consensus       511 ~~~A~~~l~~al~~~--P~~~~~~~a~al~l~~~~~~~~Al~~l~~l~~~~~~~~~~~l~~~l~~~~~l~~a~~l~~~G~  588 (1157)
T PRK11447        511 RSQADALMRRLAQQK--PNDPEQVYAYGLYLSGSDRDRAALAHLNTLPRAQWNSNIQELAQRLQSDQVLETANRLRDSGK  588 (1157)
T ss_pred             HHHHHHHHHHHHHcC--CCCHHHHHHHHHHHHhCCCHHHHHHHHHhCCchhcChhHHHHHHHHhhhHHHHHHHHHHHCCC
Confidence            999999999998754  3345555555566778999999999998864432222221         23345677889999


Q ss_pred             HHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHH
Q 012111          307 YDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQ  386 (471)
Q Consensus       307 ~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~  386 (471)
                      .++|..+++.     .+.+...+..+...+.+.|++++|+..|++..+.. +.+...+..++..+...|+.++|.+.++.
T Consensus       589 ~~eA~~~l~~-----~p~~~~~~~~La~~~~~~g~~~~A~~~y~~al~~~-P~~~~a~~~la~~~~~~g~~~eA~~~l~~  662 (1157)
T PRK11447        589 EAEAEALLRQ-----QPPSTRIDLTLADWAQQRGDYAAARAAYQRVLTRE-PGNADARLGLIEVDIAQGDLAAARAQLAK  662 (1157)
T ss_pred             HHHHHHHHHh-----CCCCchHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHH
Confidence            9999999872     23456677788899999999999999999999864 34688899999999999999999999999


Q ss_pred             HHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCC--CC---CHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 012111          387 VENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHC--VP---DNITFATMIQAYNALGMTEAAQNLENKMIA  459 (471)
Q Consensus       387 ~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~--~p---~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~  459 (471)
                      +.+..+. +..++..+..++...|++++|.++++++....-  .|   +...+..+...+...|++++|...+++++.
T Consensus       663 ll~~~p~-~~~~~~~la~~~~~~g~~~eA~~~~~~al~~~~~~~~~~~~a~~~~~~a~~~~~~G~~~~A~~~y~~Al~  739 (1157)
T PRK11447        663 LPATAND-SLNTQRRVALAWAALGDTAAAQRTFNRLIPQAKSQPPSMESALVLRDAARFEAQTGQPQQALETYKDAMV  739 (1157)
T ss_pred             HhccCCC-ChHHHHHHHHHHHhCCCHHHHHHHHHHHhhhCccCCcchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            8876544 566777888899999999999999999987421  12   234566677889999999999999999975

>TIGR00990 3a0801s09 mitochondrial precursor proteins import receptor (72 kDa mitochondrial outermembrane protein) (mitochondrial import receptor for the ADP/ATP carrier) (translocase of outermembrane tom70)

Probab=99.89  E-value=7.2e-18  Score=165.20  Aligned_cols=368  Identities=11%  Similarity=-0.015  Sum_probs=283.5

Q ss_pred             hhhHHHHHHHhhHHHHHHHHHhhhhhhccCCCchHHHHHHHHHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHh
Q 012111           46 EAEKDLSKILRTEFAIKNIEKKVSSKKYKNLWPKPVLEALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLG  125 (471)
Q Consensus        46 ~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~  125 (471)
                      .....+.+.+++..++..+...+...+    .+..+......+.+.|++++|++.++.+.+.+  +.+..++..+..++.
T Consensus       132 ~~G~~~~~~~~~~~Ai~~y~~al~~~p----~~~~~~n~a~~~~~l~~~~~Ai~~~~~al~l~--p~~~~a~~~~a~a~~  205 (615)
T TIGR00990       132 EKGNKAYRNKDFNKAIKLYSKAIECKP----DPVYYSNRAACHNALGDWEKVVEDTTAALELD--PDYSKALNRRANAYD  205 (615)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHhcCC----chHHHHHHHHHHHHhCCHHHHHHHHHHHHHcC--CCCHHHHHHHHHHHH
Confidence            345566777888888888888776544    24466677777889999999999999999875  667789999999999


Q ss_pred             cCCCHHHHHHHHHHHHhCCCC--------------------------------CCHHHHHHH------------------
Q 012111          126 KCKQPEQASLLFEVMLSDGLK--------------------------------PSVDVYTAL------------------  155 (471)
Q Consensus       126 ~~~~~~~a~~~~~~m~~~~~~--------------------------------~~~~~~~~l------------------  155 (471)
                      ..|++++|..-|......+..                                |........                  
T Consensus       206 ~lg~~~eA~~~~~~~~~~~~~~~~~~~~~~~~~l~~~a~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  285 (615)
T TIGR00990       206 GLGKYADALLDLTASCIIDGFRNEQSAQAVERLLKKFAESKAKEILETKPENLPSVTFVGNYLQSFRPKPRPAGLEDSNE  285 (615)
T ss_pred             HcCCHHHHHHHHHHHHHhCCCccHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHccCCcchhhhhcccc
Confidence            999999998766544322100                                000000000                  


Q ss_pred             ---------HHHH------HhcCCHHHHHHHHHHhhcCCCCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCC
Q 012111          156 ---------VSAY------GQSGLLDEAFSTINDMKSVSDCKP-DVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECS  219 (471)
Q Consensus       156 ---------i~~~------~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~  219 (471)
                               +...      ...+++++|++.|++........| ....+..+...+...|++++|...++...+.. +-.
T Consensus       286 ~~~~~~~~~~~l~~~~~e~~~~~~y~~A~~~~~~al~~~~~~~~~a~a~~~lg~~~~~~g~~~eA~~~~~kal~l~-P~~  364 (615)
T TIGR00990       286 LDEETGNGQLQLGLKSPESKADESYEEAARAFEKALDLGKLGEKEAIALNLRGTFKCLKGKHLEALADLSKSIELD-PRV  364 (615)
T ss_pred             cccccccchHHHHHHHHHhhhhhhHHHHHHHHHHHHhcCCCChhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCc
Confidence                     0000      112578899999999887322233 44568888888899999999999999998763 334


Q ss_pred             HHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHH
Q 012111          220 AVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTK  299 (471)
Q Consensus       220 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~  299 (471)
                      ...|..+...+...|++++|...|+++.+..  +.+...|..+...+...|++++|...|++..... +.+...+..+..
T Consensus       365 ~~~~~~la~~~~~~g~~~eA~~~~~~al~~~--p~~~~~~~~lg~~~~~~g~~~~A~~~~~kal~l~-P~~~~~~~~la~  441 (615)
T TIGR00990       365 TQSYIKRASMNLELGDPDKAEEDFDKALKLN--SEDPDIYYHRAQLHFIKGEFAQAGKDYQKSIDLD-PDFIFSHIQLGV  441 (615)
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-ccCHHHHHHHHH
Confidence            6788889999999999999999999998864  4567789999999999999999999999998764 556778888999


Q ss_pred             HHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHH------HHHHHHHHHHh
Q 012111          300 SYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSI------TYCSLVSAYSK  373 (471)
Q Consensus       300 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~------~~~~li~~~~~  373 (471)
                      ++.+.|++++|...|+...+... .+...++.+...+...|++++|...|++........+..      .++..+..+..
T Consensus       442 ~~~~~g~~~eA~~~~~~al~~~P-~~~~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~p~~~~~~~~~~~l~~~a~~~~~~  520 (615)
T TIGR00990       442 TQYKEGSIASSMATFRRCKKNFP-EAPDVYNYYGELLLDQNKFDEAIEKFDTAIELEKETKPMYMNVLPLINKALALFQW  520 (615)
T ss_pred             HHHHCCCHHHHHHHHHHHHHhCC-CChHHHHHHHHHHHHccCHHHHHHHHHHHHhcCCccccccccHHHHHHHHHHHHHH
Confidence            99999999999999999887632 357788999999999999999999999988753211111      12222333445


Q ss_pred             cCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhC
Q 012111          374 AGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKER  425 (471)
Q Consensus       374 ~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~  425 (471)
                      .|++++|.+++++..+.++. +...+..+...+.+.|++++|++.|++..+.
T Consensus       521 ~~~~~eA~~~~~kAl~l~p~-~~~a~~~la~~~~~~g~~~eAi~~~e~A~~l  571 (615)
T TIGR00990       521 KQDFIEAENLCEKALIIDPE-CDIAVATMAQLLLQQGDVDEALKLFERAAEL  571 (615)
T ss_pred             hhhHHHHHHHHHHHHhcCCC-cHHHHHHHHHHHHHccCHHHHHHHHHHHHHH
Confidence            69999999999999887654 5667899999999999999999999998864

>PRK14574 hmsH outer membrane protein; Provisional

Probab=99.87  E-value=9.8e-17  Score=157.24  Aligned_cols=410  Identities=11%  Similarity=0.047  Sum_probs=307.5

Q ss_pred             hhhhhhHHHHHHHhhHHHHHHHHHhhhhhhccCCCchHHHHHHHHHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHH
Q 012111           43 IQKEAEKDLSKILRTEFAIKNIEKKVSSKKYKNLWPKPVLEALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMV  122 (471)
Q Consensus        43 ~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~  122 (471)
                      ......-...+.+.+..+++.+.+.+...|..   +..+...+..+...|+.++|+..++.+....  +........+..
T Consensus        36 ~~y~~aii~~r~Gd~~~Al~~L~qaL~~~P~~---~~av~dll~l~~~~G~~~~A~~~~eka~~p~--n~~~~~llalA~  110 (822)
T PRK14574         36 TQYDSLIIRARAGDTAPVLDYLQEESKAGPLQ---SGQVDDWLQIAGWAGRDQEVIDVYERYQSSM--NISSRGLASAAR  110 (822)
T ss_pred             HHHHHHHHHHhCCCHHHHHHHHHHHHhhCccc---hhhHHHHHHHHHHcCCcHHHHHHHHHhccCC--CCCHHHHHHHHH
Confidence            44555666677777888888888887755433   2223366666778899999999999998322  333444444567


Q ss_pred             HHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHH
Q 012111          123 MLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFD  202 (471)
Q Consensus       123 ~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~  202 (471)
                      .+...|++++|.++|+++.+.... +...+..++..+...++.++|++.++++...   .|+...+..++..+...++..
T Consensus       111 ly~~~gdyd~Aiely~kaL~~dP~-n~~~l~gLa~~y~~~~q~~eAl~~l~~l~~~---dp~~~~~l~layL~~~~~~~~  186 (822)
T PRK14574        111 AYRNEKRWDQALALWQSSLKKDPT-NPDLISGMIMTQADAGRGGVVLKQATELAER---DPTVQNYMTLSYLNRATDRNY  186 (822)
T ss_pred             HHHHcCCHHHHHHHHHHHHhhCCC-CHHHHHHHHHHHhhcCCHHHHHHHHHHhccc---CcchHHHHHHHHHHHhcchHH
Confidence            889999999999999999988654 5777888889999999999999999999873   566666655555555566666


Q ss_pred             HHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHH----------------------------------------
Q 012111          203 LIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESS----------------------------------------  242 (471)
Q Consensus       203 ~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~a~~~----------------------------------------  242 (471)
                      +|++.++++.+.. +-+...+..++.++.+.|-...|.++                                        
T Consensus       187 ~AL~~~ekll~~~-P~n~e~~~~~~~~l~~~~~~~~a~~l~~~~p~~f~~~~~~~l~~~~~a~~vr~a~~~~~~~~~r~~  265 (822)
T PRK14574        187 DALQASSEAVRLA-PTSEEVLKNHLEILQRNRIVEPALRLAKENPNLVSAEHYRQLERDAAAEQVRMAVLPTRSETERFD  265 (822)
T ss_pred             HHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCcHHHHHHHHhCccccCHHHHHHHHHHHHHHHHhhcccccccchhhHH
Confidence            6999999999875 44677777777776666644444333                                        


Q ss_pred             --------HHHHHHcCCCCCCH-----HHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHH
Q 012111          243 --------FSAMVESGGCHPDI-----FTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDK  309 (471)
Q Consensus       243 --------~~~~~~~~~~~~~~-----~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~  309 (471)
                              ++.+....+..|..     ....-.+-++...|++.++++.|+.+...+.+....+-..+.++|...+++++
T Consensus       266 ~~d~ala~~~~l~~~~~~~p~~~~~~~~~~~Drl~aL~~r~r~~~vi~~y~~l~~~~~~~P~y~~~a~adayl~~~~P~k  345 (822)
T PRK14574        266 IADKALADYQNLLTRWGKDPEAQADYQRARIDRLGALLVRHQTADLIKEYEAMEAEGYKMPDYARRWAASAYIDRRLPEK  345 (822)
T ss_pred             HHHHHHHHHHHHHhhccCCCccchHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhhcCCCCCHHHHHHHHHHHHhcCCcHH
Confidence                    23333221222321     12223456778899999999999999988876667788899999999999999


Q ss_pred             HHHHHHHHHhCCC-----CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCC-------------CCCH-HHHHHHHHH
Q 012111          310 MRSVMDFMQKRFF-----FPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGM-------------KPNS-ITYCSLVSA  370 (471)
Q Consensus       310 a~~~~~~~~~~~~-----~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~-------------~p~~-~~~~~li~~  370 (471)
                      |..++..+.....     .++......|..++...+++++|..+++.+.+...             .||- ..+..++..
T Consensus       346 A~~l~~~~~~~~~~~~~~~~~~~~~~~L~yA~ld~e~~~~A~~~l~~~~~~~p~~~~~~~~~~~~pn~d~~~~~~l~a~~  425 (822)
T PRK14574        346 AAPILSSLYYSDGKTFRNSDDLLDADDLYYSLNESEQLDKAYQFAVNYSEQTPYQVGVYGLPGKEPNDDWIEGQTLLVQS  425 (822)
T ss_pred             HHHHHHHHhhccccccCCCcchHHHHHHHHHHHhcccHHHHHHHHHHHHhcCCcEEeccCCCCCCCCccHHHHHHHHHHH
Confidence            9999999866431     22344457788999999999999999999987311             1222 234456777


Q ss_pred             HHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCC-HHHHHHHHHHHHhcCCHHH
Q 012111          371 YSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPD-NITFATMIQAYNALGMTEA  449 (471)
Q Consensus       371 ~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~-~~~~~~l~~~~~~~g~~~~  449 (471)
                      +...|+..+|++.++.+....+. |......+...+...|.+.+|.+.++.....  .|+ ..+......++...|++++
T Consensus       426 ~~~~gdl~~Ae~~le~l~~~aP~-n~~l~~~~A~v~~~Rg~p~~A~~~~k~a~~l--~P~~~~~~~~~~~~al~l~e~~~  502 (822)
T PRK14574        426 LVALNDLPTAQKKLEDLSSTAPA-NQNLRIALASIYLARDLPRKAEQELKAVESL--APRSLILERAQAETAMALQEWHQ  502 (822)
T ss_pred             HHHcCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhh--CCccHHHHHHHHHHHHhhhhHHH
Confidence            88999999999999999888776 9999999999999999999999999776653  554 5566677888999999999


Q ss_pred             HHHHHHHHHHhhhcCC
Q 012111          450 AQNLENKMIAMKENSG  465 (471)
Q Consensus       450 A~~~~~~m~~~~~~~~  465 (471)
                      |.++.++.++..|+..
T Consensus       503 A~~~~~~l~~~~Pe~~  518 (822)
T PRK14574        503 MELLTDDVISRSPEDI  518 (822)
T ss_pred             HHHHHHHHHhhCCCch
Confidence            9999999998888754

>PRK10049 pgaA outer membrane protein PgaA; Provisional

Probab=99.84  E-value=1.2e-15  Score=152.38  Aligned_cols=381  Identities=12%  Similarity=0.052  Sum_probs=282.4

Q ss_pred             hhhhHHHHHHHhhHHHHHHHHHhhhhhhccCCCchHHHHHHHHHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHH
Q 012111           45 KEAEKDLSKILRTEFAIKNIEKKVSSKKYKNLWPKPVLEALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVML  124 (471)
Q Consensus        45 ~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~  124 (471)
                      ......+....+...+.+.+...+...|   ..+.........+...|++++|+..++.+.+..  |.+.. +..+..++
T Consensus        53 ~~lA~~~~~~g~~~~A~~~~~~al~~~P---~~~~a~~~la~~l~~~g~~~eA~~~l~~~l~~~--P~~~~-~~~la~~l  126 (765)
T PRK10049         53 AAVAVAYRNLKQWQNSLTLWQKALSLEP---QNDDYQRGLILTLADAGQYDEALVKAKQLVSGA--PDKAN-LLALAYVY  126 (765)
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHhCC---CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC--CCCHH-HHHHHHHH
Confidence            4455667777888888888887776543   335556677777889999999999999999875  66667 88899999


Q ss_pred             hcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCH------HHHHHHHHHHH--
Q 012111          125 GKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDV------YTYSILIKSCT--  196 (471)
Q Consensus       125 ~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~------~~~~~ll~~~~--  196 (471)
                      ...|+.++|+..++++.+.... +...+..+..++...+..+.|+..++....    .|+.      .....++....  
T Consensus       127 ~~~g~~~~Al~~l~~al~~~P~-~~~~~~~la~~l~~~~~~e~Al~~l~~~~~----~p~~~~~l~~~~~~~~~r~~~~~  201 (765)
T PRK10049        127 KRAGRHWDELRAMTQALPRAPQ-TQQYPTEYVQALRNNRLSAPALGAIDDANL----TPAEKRDLEADAAAELVRLSFMP  201 (765)
T ss_pred             HHCCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHCCChHHHHHHHHhCCC----CHHHHHHHHHHHHHHHHHhhccc
Confidence            9999999999999999987544 667777788888899999999999987764    2332      11222222222  


Q ss_pred             ---hcCCH---HHHHHHHHHHHHC-CCCCCHH-HH----HHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Q 012111          197 ---KFHRF---DLIEKILAEMSYL-GIECSAV-TY----NTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMIS  264 (471)
Q Consensus       197 ---~~~~~---~~a~~~~~~~~~~-g~~~~~~-~~----~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~  264 (471)
                         ..+++   +.|++.++.+.+. ...|+.. .+    ...+..+...|++++|+..|+.+.+.+...|+. ....+..
T Consensus       202 ~~~~~~r~~~ad~Al~~~~~ll~~~~~~p~~~~~~~~a~~d~l~~Ll~~g~~~eA~~~~~~ll~~~~~~P~~-a~~~la~  280 (765)
T PRK10049        202 TRSEKERYAIADRALAQYDALEALWHDNPDATADYQRARIDRLGALLARDRYKDVISEYQRLKAEGQIIPPW-AQRWVAS  280 (765)
T ss_pred             ccChhHHHHHHHHHHHHHHHHHhhcccCCccchHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhccCCCCCHH-HHHHHHH
Confidence               12234   6788888888754 1222221 11    111345567799999999999998764222432 2233577


Q ss_pred             HHHhcCCHHHHHHHHHHHHhCCCCC---CHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCC-----------CCC---HH
Q 012111          265 AYGNSGNIEKMEKWYNEFNLMGVKA---DIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFF-----------FPT---VV  327 (471)
Q Consensus       265 ~~~~~~~~~~a~~~~~~~~~~~~~~---~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~-----------~~~---~~  327 (471)
                      +|...|++++|+.+|+++.......   .......+..++...|++++|..+++.+.+...           .|+   ..
T Consensus       281 ~yl~~g~~e~A~~~l~~~l~~~p~~~~~~~~~~~~L~~a~~~~g~~~eA~~~l~~~~~~~P~~~~~~~~~~~~p~~~~~~  360 (765)
T PRK10049        281 AYLKLHQPEKAQSILTELFYHPETIADLSDEELADLFYSLLESENYPGALTVTAHTINNSPPFLRLYGSPTSIPNDDWLQ  360 (765)
T ss_pred             HHHhcCCcHHHHHHHHHHhhcCCCCCCCChHHHHHHHHHHHhcccHHHHHHHHHHHhhcCCceEeecCCCCCCCCchHHH
Confidence            8999999999999999987643111   134566677788999999999999999887632           123   23


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHH
Q 012111          328 TYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYG  407 (471)
Q Consensus       328 ~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  407 (471)
                      .+..+...+...|+.++|+++++++.... +-+...+..+...+...|++++|++.++++....+. +...+..++..+.
T Consensus       361 a~~~~a~~l~~~g~~~eA~~~l~~al~~~-P~n~~l~~~lA~l~~~~g~~~~A~~~l~~al~l~Pd-~~~l~~~~a~~al  438 (765)
T PRK10049        361 GQSLLSQVAKYSNDLPQAEMRARELAYNA-PGNQGLRIDYASVLQARGWPRAAENELKKAEVLEPR-NINLEVEQAWTAL  438 (765)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhhCCC-ChHHHHHHHHHHH
Confidence            45567788899999999999999998863 446788899999999999999999999999988755 6777778888999


Q ss_pred             hcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHH
Q 012111          408 QAGDVEKMGELFLTMKERHCVPDNITFATMIQAY  441 (471)
Q Consensus       408 ~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~  441 (471)
                      ..|++++|..+++++.+.  .|+......+-+.+
T Consensus       439 ~~~~~~~A~~~~~~ll~~--~Pd~~~~~~~~~~~  470 (765)
T PRK10049        439 DLQEWRQMDVLTDDVVAR--EPQDPGVQRLARAR  470 (765)
T ss_pred             HhCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHH
Confidence            999999999999999984  57666554444443

>PRK14574 hmsH outer membrane protein; Provisional

Probab=99.83  E-value=1.5e-15  Score=148.98  Aligned_cols=378  Identities=9%  Similarity=-0.006  Sum_probs=265.0

Q ss_pred             CchHHHHHHHHHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHH
Q 012111           77 WPKPVLEALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALV  156 (471)
Q Consensus        77 ~~~~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li  156 (471)
                      .+......+-...+.|+++.|++.|+.+.+..  |.+......++..+...|+.++|...+++.... ..........+.
T Consensus        33 ~~~~~y~~aii~~r~Gd~~~Al~~L~qaL~~~--P~~~~av~dll~l~~~~G~~~~A~~~~eka~~p-~n~~~~~llalA  109 (822)
T PRK14574         33 MADTQYDSLIIRARAGDTAPVLDYLQEESKAG--PLQSGQVDDWLQIAGWAGRDQEVIDVYERYQSS-MNISSRGLASAA  109 (822)
T ss_pred             chhHHHHHHHHHHhCCCHHHHHHHHHHHHhhC--ccchhhHHHHHHHHHHcCCcHHHHHHHHHhccC-CCCCHHHHHHHH
Confidence            44444455555679999999999999999864  333222338888888999999999999999832 122344444456


Q ss_pred             HHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCH
Q 012111          157 SAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKF  236 (471)
Q Consensus       157 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~  236 (471)
                      ..+...|++++|+++|+++.+..  +-+...+..++..+...++.++|++.++.+...  .|+...+..++..+...++.
T Consensus       110 ~ly~~~gdyd~Aiely~kaL~~d--P~n~~~l~gLa~~y~~~~q~~eAl~~l~~l~~~--dp~~~~~l~layL~~~~~~~  185 (822)
T PRK14574        110 RAYRNEKRWDQALALWQSSLKKD--PTNPDLISGMIMTQADAGRGGVVLKQATELAER--DPTVQNYMTLSYLNRATDRN  185 (822)
T ss_pred             HHHHHcCCHHHHHHHHHHHHhhC--CCCHHHHHHHHHHHhhcCCHHHHHHHHHHhccc--CcchHHHHHHHHHHHhcchH
Confidence            78889999999999999999843  445666778888899999999999999999876  55655565555555556777


Q ss_pred             HHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHH-----------------------------------
Q 012111          237 EEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNE-----------------------------------  281 (471)
Q Consensus       237 ~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~-----------------------------------  281 (471)
                      .+|++.++++.+..  +.+...+..+..++.+.|-...|.++..+                                   
T Consensus       186 ~~AL~~~ekll~~~--P~n~e~~~~~~~~l~~~~~~~~a~~l~~~~p~~f~~~~~~~l~~~~~a~~vr~a~~~~~~~~~r  263 (822)
T PRK14574        186 YDALQASSEAVRLA--PTSEEVLKNHLEILQRNRIVEPALRLAKENPNLVSAEHYRQLERDAAAEQVRMAVLPTRSETER  263 (822)
T ss_pred             HHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHcCCcHHHHHHHHhCccccCHHHHHHHHHHHHHHHHhhcccccccchhh
Confidence            67999999998874  44555666666666666655444443332                                   


Q ss_pred             -------------HHhC-CCCCCH-H----HHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCH
Q 012111          282 -------------FNLM-GVKADI-Q----TLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHI  342 (471)
Q Consensus       282 -------------~~~~-~~~~~~-~----~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~  342 (471)
                                   +... +..|.. .    ...-.+-++...|++.++++.++.+...+.+....+-..+..+|...+++
T Consensus       264 ~~~~d~ala~~~~l~~~~~~~p~~~~~~~~~~~Drl~aL~~r~r~~~vi~~y~~l~~~~~~~P~y~~~a~adayl~~~~P  343 (822)
T PRK14574        264 FDIADKALADYQNLLTRWGKDPEAQADYQRARIDRLGALLVRHQTADLIKEYEAMEAEGYKMPDYARRWAASAYIDRRLP  343 (822)
T ss_pred             HHHHHHHHHHHHHHHhhccCCCccchHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhhcCCCCCHHHHHHHHHHHHhcCCc
Confidence                         2210 111211 1    11223445667788888888888888777554555677788888888888


Q ss_pred             HHHHHHHHHHHHcC-----CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCC-----------CcCH---HHHHHHH
Q 012111          343 EKMEEYFKKMKHRG-----MKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDV-----------ILDT---PFFNCII  403 (471)
Q Consensus       343 ~~a~~~~~~m~~~~-----~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~-----------~~~~---~~~~~l~  403 (471)
                      ++|..+|+.+....     ..++......|..++...+++++|..+++.+.+..+           .|+.   ..+..++
T Consensus       344 ~kA~~l~~~~~~~~~~~~~~~~~~~~~~~L~yA~ld~e~~~~A~~~l~~~~~~~p~~~~~~~~~~~~pn~d~~~~~~l~a  423 (822)
T PRK14574        344 EKAAPILSSLYYSDGKTFRNSDDLLDADDLYYSLNESEQLDKAYQFAVNYSEQTPYQVGVYGLPGKEPNDDWIEGQTLLV  423 (822)
T ss_pred             HHHHHHHHHHhhccccccCCCcchHHHHHHHHHHHhcccHHHHHHHHHHHHhcCCcEEeccCCCCCCCCccHHHHHHHHH
Confidence            88888888886542     122344456788888888888888888888876322           1221   2334456


Q ss_pred             HHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhhhcC
Q 012111          404 SAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAYNALGMTEAAQNLENKMIAMKENS  464 (471)
Q Consensus       404 ~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~~  464 (471)
                      ..+...|+..+|++.++++... -+-|......+...+...|..+.|++.++.+....|..
T Consensus       424 ~~~~~~gdl~~Ae~~le~l~~~-aP~n~~l~~~~A~v~~~Rg~p~~A~~~~k~a~~l~P~~  483 (822)
T PRK14574        424 QSLVALNDLPTAQKKLEDLSST-APANQNLRIALASIYLARDLPRKAEQELKAVESLAPRS  483 (822)
T ss_pred             HHHHHcCCHHHHHHHHHHHHHh-CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhhCCcc
Confidence            6777888888888888888764 23467777778888888888888888887777776553

>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional

Probab=99.80  E-value=4.3e-14  Score=141.81  Aligned_cols=346  Identities=14%  Similarity=0.080  Sum_probs=153.3

Q ss_pred             HhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhC-C-CCCCHHHHHHHHHHHHhcCCH--
Q 012111           90 KQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSD-G-LKPSVDVYTALVSAYGQSGLL--  165 (471)
Q Consensus        90 ~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~-~-~~~~~~~~~~li~~~~~~~~~--  165 (471)
                      ..+...+|.+.+..+.+..  +-+....-.+.-...+.|+.++|.++|+..... + ..++....+-++..|.+.+..  
T Consensus       354 ~~~~~~~~~~~~~~~y~~~--~~~~~~l~q~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~  431 (987)
T PRK09782        354 ATRNKAEALRLARLLYQQE--PANLTRLDQLTWQLMQNGQSREAADLLLQRYPFQGDARLSQTLMARLASLLESHPYLAT  431 (987)
T ss_pred             ccCchhHHHHHHHHHHhcC--CCCHHHHHHHHHHHHHcccHHHHHHHHHHhcCCCcccccCHHHHHHHHHHHHhCCcccc
Confidence            3455555666555555542  345555555555566666677777766666552 1 122344444566666655542  


Q ss_pred             -HHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHH---HHHHHHHHCCCCC--CHHHHHHHHHHHHccCCHHHH
Q 012111          166 -DEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIE---KILAEMSYLGIEC--SAVTYNTIIDGYGKAKKFEEM  239 (471)
Q Consensus       166 -~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~---~~~~~~~~~g~~~--~~~~~~~l~~~~~~~~~~~~a  239 (471)
                       .++..+-..+..     +..         +.-.|+...+.   ..+....... ++  +...|..+..++.. ++.++|
T Consensus       432 ~~~~~~l~~~~~~-----~~~---------~~~~~~~~~~~~~~~~~~~al~~~-p~~~~~~a~~~LG~~l~~-~~~~eA  495 (987)
T PRK09782        432 PAKVAILSKPLPL-----AEQ---------RQWQSQLPGIADNCPAIVRLLGDM-SPSYDAAAWNRLAKCYRD-TLPGVA  495 (987)
T ss_pred             hHHHHHhcccccc-----chh---------HHHHhhhhhhhhhHHHHHHhcccC-CCCCCHHHHHHHHHHHHh-CCcHHH
Confidence             222222110000     000         00011111111   1111111110 22  34444444444443 444455


Q ss_pred             HHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Q 012111          240 ESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQK  319 (471)
Q Consensus       240 ~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~  319 (471)
                      ...+.+....   .|+......+...+...|++++|...|+++...  +|+...+..+...+.+.|++++|...++...+
T Consensus       496 i~a~~~Al~~---~Pd~~~~L~lA~al~~~Gr~eeAi~~~rka~~~--~p~~~a~~~la~all~~Gd~~eA~~~l~qAL~  570 (987)
T PRK09782        496 LYAWLQAEQR---QPDAWQHRAVAYQAYQVEDYATALAAWQKISLH--DMSNEDLLAAANTAQAAGNGAARDRWLQQAEQ  570 (987)
T ss_pred             HHHHHHHHHh---CCchHHHHHHHHHHHHCCCHHHHHHHHHHHhcc--CCCcHHHHHHHHHHHHCCCHHHHHHHHHHHHh
Confidence            5544444332   233222222233334455555555555554322  22233333444444555555555555555544


Q ss_pred             CCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHH
Q 012111          320 RFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFF  399 (471)
Q Consensus       320 ~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~  399 (471)
                      .... ....+..+...+...|++++|...+++..+.  .|+...+..+..++.+.|+.++|...+++.....+. +...+
T Consensus       571 l~P~-~~~l~~~La~~l~~~Gr~~eAl~~~~~AL~l--~P~~~a~~~LA~~l~~lG~~deA~~~l~~AL~l~Pd-~~~a~  646 (987)
T PRK09782        571 RGLG-DNALYWWLHAQRYIPGQPELALNDLTRSLNI--APSANAYVARATIYRQRHNVPAAVSDLRAALELEPN-NSNYQ  646 (987)
T ss_pred             cCCc-cHHHHHHHHHHHHhCCCHHHHHHHHHHHHHh--CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCC-CHHHH
Confidence            3211 1122222222223335555555555555543  334444555555555555555555555555554433 44445


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHhCCCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhhhcC
Q 012111          400 NCIISAYGQAGDVEKMGELFLTMKERHCVP-DNITFATMIQAYNALGMTEAAQNLENKMIAMKENS  464 (471)
Q Consensus       400 ~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~~  464 (471)
                      +.+..++...|++++|+..+++..+.  .| +...+..+..++...|++++|...++++++..|+.
T Consensus       647 ~nLG~aL~~~G~~eeAi~~l~~AL~l--~P~~~~a~~nLA~al~~lGd~~eA~~~l~~Al~l~P~~  710 (987)
T PRK09782        647 AALGYALWDSGDIAQSREMLERAHKG--LPDDPALIRQLAYVNQRLDDMAATQHYARLVIDDIDNQ  710 (987)
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCC
Confidence            55555555555555555555555442  22 33444455555555555555555555555555443

>KOG4422 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.79  E-value=7.7e-15  Score=126.24  Aligned_cols=345  Identities=17%  Similarity=0.171  Sum_probs=263.6

Q ss_pred             cCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHH
Q 012111          111 QARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSI  190 (471)
Q Consensus       111 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~  190 (471)
                      |.+.++|..+|.++++.-..+.|.+++++-.+...+.+..+||.+|.+-.-..+    .+++.+|.. ..+.||..|+|+
T Consensus       204 PKT~et~s~mI~Gl~K~~~~ERA~~L~kE~~~~k~kv~~~aFN~lI~~~S~~~~----K~Lv~EMis-qkm~Pnl~TfNa  278 (625)
T KOG4422|consen  204 PKTDETVSIMIAGLCKFSSLERARELYKEHRAAKGKVYREAFNGLIGASSYSVG----KKLVAEMIS-QKMTPNLFTFNA  278 (625)
T ss_pred             CCCchhHHHHHHHHHHHHhHHHHHHHHHHHHHhhheeeHHhhhhhhhHHHhhcc----HHHHHHHHH-hhcCCchHhHHH
Confidence            567789999999999999999999999999988888899999999986543322    678888988 678999999999


Q ss_pred             HHHHHHhcCCHHH----HHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHH-HHHHHHHHHHc-CC-----C-CCCHHH
Q 012111          191 LIKSCTKFHRFDL----IEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEE-MESSFSAMVES-GG-----C-HPDIFT  258 (471)
Q Consensus       191 ll~~~~~~~~~~~----a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~-a~~~~~~~~~~-~~-----~-~~~~~~  258 (471)
                      ++++..+.|+++.    |.+++.+|++.|+.|...+|..+|..+++.++..+ |..++..+... .|     . +.|...
T Consensus       279 lL~c~akfg~F~~ar~aalqil~EmKeiGVePsLsSyh~iik~f~re~dp~k~as~~i~dI~N~ltGK~fkp~~p~d~~F  358 (625)
T KOG4422|consen  279 LLSCAAKFGKFEDARKAALQILGEMKEIGVEPSLSSYHLIIKNFKRESDPQKVASSWINDIQNSLTGKTFKPITPTDNKF  358 (625)
T ss_pred             HHHHHHHhcchHHHHHHHHHHHHHHHHhCCCcchhhHHHHHHHhcccCCchhhhHHHHHHHHHhhccCcccCCCCchhHH
Confidence            9999999998765    67788999999999999999999999999887644 44555554322 11     1 235566


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHhCC----CCCC---HHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHH
Q 012111          259 LNSMISAYGNSGNIEKMEKWYNEFNLMG----VKAD---IQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNI  331 (471)
Q Consensus       259 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~----~~~~---~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  331 (471)
                      |...+..|.+..+.+-|.++-.-+....    +.|+   ..-|..+....|.....+.....|+.|.-.-.-|+..+...
T Consensus       359 F~~AM~Ic~~l~d~~LA~~v~~ll~tg~N~~~ig~~~~~~fYyr~~~~licq~es~~~~~~~Y~~lVP~~y~p~~~~m~~  438 (625)
T KOG4422|consen  359 FQSAMSICSSLRDLELAYQVHGLLKTGDNWKFIGPDQHRNFYYRKFFDLICQMESIDVTLKWYEDLVPSAYFPHSQTMIH  438 (625)
T ss_pred             HHHHHHHHHHhhhHHHHHHHHHHHHcCCchhhcChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccceecCCchhHHH
Confidence            7888899999999999998877665432    2333   23567788888889999999999999998888899999999


Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcC-CH--------HH-----HHHHH-------HHHHhC
Q 012111          332 VIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAG-LI--------MK-----VDSIL-------RQVENS  390 (471)
Q Consensus       332 li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g-~~--------~~-----a~~~~-------~~~~~~  390 (471)
                      ++++....|.++-.-++|.+++..|..-+.....-++..+++.. ..        ..     |..++       .++.+ 
T Consensus       439 ~lrA~~v~~~~e~ipRiw~D~~~~ght~r~~l~eeil~~L~~~k~hp~tp~r~Ql~~~~ak~aad~~e~~e~~~~R~r~-  517 (625)
T KOG4422|consen  439 LLRALDVANRLEVIPRIWKDSKEYGHTFRSDLREEILMLLARDKLHPLTPEREQLQVAFAKCAADIKEAYESQPIRQRA-  517 (625)
T ss_pred             HHHHHhhcCcchhHHHHHHHHHHhhhhhhHHHHHHHHHHHhcCCCCCCChHHHHHHHHHHHHHHHHHHHHHhhHHHHHh-
Confidence            99999999999999999999998886655555555555555544 11        11     11111       12222 


Q ss_pred             CCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCC-CCCHHHHH---HHHHHHHhcCCHHHHHHHHHHHHHhhh
Q 012111          391 DVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHC-VPDNITFA---TMIQAYNALGMTEAAQNLENKMIAMKE  462 (471)
Q Consensus       391 ~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~-~p~~~~~~---~l~~~~~~~g~~~~A~~~~~~m~~~~~  462 (471)
                       ........+...-.+.+.|..++|.++|..+...+- .|-....+   -++..-.+..+...|...++-|...+.
T Consensus       518 -~~~~~t~l~~ia~Ll~R~G~~qkA~e~l~l~~~~~~~ip~~p~lnAm~El~d~a~~~~spsqA~~~lQ~a~~~n~  592 (625)
T KOG4422|consen  518 -QDWPATSLNCIAILLLRAGRTQKAWEMLGLFLRKHNKIPRSPLLNAMAELMDSAKVSNSPSQAIEVLQLASAFNL  592 (625)
T ss_pred             -ccCChhHHHHHHHHHHHcchHHHHHHHHHHHHhcCCcCCCCcchhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCc
Confidence             334566778888889999999999999999865432 24444444   455666778889999999888865543

>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional

Probab=99.79  E-value=4.7e-14  Score=141.51  Aligned_cols=358  Identities=12%  Similarity=0.026  Sum_probs=236.7

Q ss_pred             HHHHHHHHHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHH
Q 012111           80 PVLEALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAY  159 (471)
Q Consensus        80 ~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~  159 (471)
                      .+...+..+.+.++++.|.++..       +.|.......-.......+...++...+..|.+... -+....-.+.-..
T Consensus       315 ~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~y~~~~-~~~~~l~q~~~~~  386 (987)
T PRK09782        315 VVGATLPVLLKEGQYDAAQKLLA-------TLPANEMLEERYAVSVATRNKAEALRLARLLYQQEP-ANLTRLDQLTWQL  386 (987)
T ss_pred             HHHHHHHHHHhccHHHHHHHHhc-------CCCcchHHHHHHhhccccCchhHHHHHHHHHHhcCC-CCHHHHHHHHHHH
Confidence            34445666666777775554421       123322222222222344666666666666665422 2555555555556


Q ss_pred             HhcCCHHHHHHHHHHhhcC-CCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHH
Q 012111          160 GQSGLLDEAFSTINDMKSV-SDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEE  238 (471)
Q Consensus       160 ~~~~~~~~a~~~~~~~~~~-~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~  238 (471)
                      ...|+.++|.++|+..... .+-..+....+-++..|.+.+......++..-..    +++...-      +.-.|+..+
T Consensus       387 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~l~~----~~~~~~~------~~~~~~~~~  456 (987)
T PRK09782        387 MQNGQSREAADLLLQRYPFQGDARLSQTLMARLASLLESHPYLATPAKVAILSK----PLPLAEQ------RQWQSQLPG  456 (987)
T ss_pred             HHcccHHHHHHHHHHhcCCCcccccCHHHHHHHHHHHHhCCcccchHHHHHhcc----ccccchh------HHHHhhhhh
Confidence            6777788888888777651 1122334445566777777665333322222111    1111111      111344444


Q ss_pred             HHHHHHHHHHcCCC-CC--CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHH
Q 012111          239 MESSFSAMVESGGC-HP--DIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMD  315 (471)
Q Consensus       239 a~~~~~~~~~~~~~-~~--~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~  315 (471)
                      +...+......-+. ++  +...|..+..++.. ++.++|...+.+....  .|+......+...+...|++++|...++
T Consensus       457 ~~~~~~~~~~al~~~p~~~~~~a~~~LG~~l~~-~~~~eAi~a~~~Al~~--~Pd~~~~L~lA~al~~~Gr~eeAi~~~r  533 (987)
T PRK09782        457 IADNCPAIVRLLGDMSPSYDAAAWNRLAKCYRD-TLPGVALYAWLQAEQR--QPDAWQHRAVAYQAYQVEDYATALAAWQ  533 (987)
T ss_pred             hhhhHHHHHHhcccCCCCCCHHHHHHHHHHHHh-CCcHHHHHHHHHHHHh--CCchHHHHHHHHHHHHCCCHHHHHHHHH
Confidence            44444444333222 34  56778888888776 8898999988887654  4665554455666678999999999999


Q ss_pred             HHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcC
Q 012111          316 FMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILD  395 (471)
Q Consensus       316 ~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~  395 (471)
                      .+...  .|+...+..+...+.+.|++++|...+++..+.. +.+...+..+...+...|++++|...+++..+..+  +
T Consensus       534 ka~~~--~p~~~a~~~la~all~~Gd~~eA~~~l~qAL~l~-P~~~~l~~~La~~l~~~Gr~~eAl~~~~~AL~l~P--~  608 (987)
T PRK09782        534 KISLH--DMSNEDLLAAANTAQAAGNGAARDRWLQQAEQRG-LGDNALYWWLHAQRYIPGQPELALNDLTRSLNIAP--S  608 (987)
T ss_pred             HHhcc--CCCcHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-CccHHHHHHHHHHHHhCCCHHHHHHHHHHHHHhCC--C
Confidence            88665  3444556677788899999999999999998864 23334444444555667999999999999998764  5


Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhhhcCC
Q 012111          396 TPFFNCIISAYGQAGDVEKMGELFLTMKERHCVP-DNITFATMIQAYNALGMTEAAQNLENKMIAMKENSG  465 (471)
Q Consensus       396 ~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~~~  465 (471)
                      ...+..+..++.+.|++++|+..+++....  .| +...+..+..++...|+.++|...++++++..|...
T Consensus       609 ~~a~~~LA~~l~~lG~~deA~~~l~~AL~l--~Pd~~~a~~nLG~aL~~~G~~eeAi~~l~~AL~l~P~~~  677 (987)
T PRK09782        609 ANAYVARATIYRQRHNVPAAVSDLRAALEL--EPNNSNYQAALGYALWDSGDIAQSREMLERAHKGLPDDP  677 (987)
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCH
Confidence            788999999999999999999999999985  45 566777888899999999999999999999988754

>KOG2076 consensus RNA polymerase III transcription factor TFIIIC [Transcription]

Probab=99.78  E-value=4.6e-14  Score=132.44  Aligned_cols=369  Identities=11%  Similarity=0.043  Sum_probs=287.9

Q ss_pred             HHHHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCC
Q 012111           85 LDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGL  164 (471)
Q Consensus        85 l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~  164 (471)
                      ...+...|++++|.+++.++.++.  +-+...|.+|..+|-+.|+.+++...+-.....+.. |...|..+.....+.|.
T Consensus       146 AN~lfarg~~eeA~~i~~EvIkqd--p~~~~ay~tL~~IyEqrGd~eK~l~~~llAAHL~p~-d~e~W~~ladls~~~~~  222 (895)
T KOG2076|consen  146 ANNLFARGDLEEAEEILMEVIKQD--PRNPIAYYTLGEIYEQRGDIEKALNFWLLAAHLNPK-DYELWKRLADLSEQLGN  222 (895)
T ss_pred             HHHHHHhCCHHHHHHHHHHHHHhC--ccchhhHHHHHHHHHHcccHHHHHHHHHHHHhcCCC-ChHHHHHHHHHHHhccc
Confidence            344456699999999999999986  778899999999999999999999988776665544 77999999999999999


Q ss_pred             HHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHH----HHHHHHHHccCCHHHHH
Q 012111          165 LDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTY----NTIIDGYGKAKKFEEME  240 (471)
Q Consensus       165 ~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~----~~l~~~~~~~~~~~~a~  240 (471)
                      ++.|.-.|.+..+.  .+++...+---...|-+.|+...|..-|.++.....+.+..-+    ..+++.+...++.+.|.
T Consensus       223 i~qA~~cy~rAI~~--~p~n~~~~~ers~L~~~~G~~~~Am~~f~~l~~~~p~~d~er~~d~i~~~~~~~~~~~~~e~a~  300 (895)
T KOG2076|consen  223 INQARYCYSRAIQA--NPSNWELIYERSSLYQKTGDLKRAMETFLQLLQLDPPVDIERIEDLIRRVAHYFITHNERERAA  300 (895)
T ss_pred             HHHHHHHHHHHHhc--CCcchHHHHHHHHHHHHhChHHHHHHHHHHHHhhCCchhHHHHHHHHHHHHHHHHHhhHHHHHH
Confidence            99999999999973  2556666666778899999999999999999987533333322    34566777888889999


Q ss_pred             HHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHH--------------------------
Q 012111          241 SSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTL--------------------------  294 (471)
Q Consensus       241 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~--------------------------  294 (471)
                      +.++......+-..+...++.++..+.+...++.+......+......+|..-+                          
T Consensus       301 ~~le~~~s~~~~~~~~ed~ni~ael~l~~~q~d~~~~~i~~~~~r~~e~d~~e~~~~~~~~~~~~~~~~~~~~~s~~l~v  380 (895)
T KOG2076|consen  301 KALEGALSKEKDEASLEDLNILAELFLKNKQSDKALMKIVDDRNRESEKDDSEWDTDERRREEPNALCEVGKELSYDLRV  380 (895)
T ss_pred             HHHHHHHhhccccccccHHHHHHHHHHHhHHHHHhhHHHHHHhccccCCChhhhhhhhhccccccccccCCCCCCccchh
Confidence            999888775444556667889999999999999999988887662222222111                          


Q ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Q 012111          295 NILTKSYGRAGMYDKMRSVMDFMQKRF--FFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYS  372 (471)
Q Consensus       295 ~~ll~~~~~~~~~~~a~~~~~~~~~~~--~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~  372 (471)
                      -.++-++...+..+....+.....+..  +.-+...|.-+..+|...|++.+|+.+|..+.....--+...|-.+..+|.
T Consensus       381 ~rl~icL~~L~~~e~~e~ll~~l~~~n~~~~d~~dL~~d~a~al~~~~~~~~Al~~l~~i~~~~~~~~~~vw~~~a~c~~  460 (895)
T KOG2076|consen  381 IRLMICLVHLKERELLEALLHFLVEDNVWVSDDVDLYLDLADALTNIGKYKEALRLLSPITNREGYQNAFVWYKLARCYM  460 (895)
T ss_pred             HhHhhhhhcccccchHHHHHHHHHHhcCChhhhHHHHHHHHHHHHhcccHHHHHHHHHHHhcCccccchhhhHHHHHHHH
Confidence            123334444555555555555555555  333566888999999999999999999999998754556789999999999


Q ss_pred             hcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHH--------hCCCCCCHHHHHHHHHHHHhc
Q 012111          373 KAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMK--------ERHCVPDNITFATMIQAYNAL  444 (471)
Q Consensus       373 ~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~--------~~~~~p~~~~~~~l~~~~~~~  444 (471)
                      ..|..++|.+.|+.+....+. +..+--.|...+.+.|+.++|.+.+..+.        ..+..|+..........+...
T Consensus       461 ~l~e~e~A~e~y~kvl~~~p~-~~D~Ri~Lasl~~~~g~~EkalEtL~~~~~~D~~~~e~~a~~~e~ri~~~r~d~l~~~  539 (895)
T KOG2076|consen  461 ELGEYEEAIEFYEKVLILAPD-NLDARITLASLYQQLGNHEKALETLEQIINPDGRNAEACAWEPERRILAHRCDILFQV  539 (895)
T ss_pred             HHhhHHHHHHHHHHHHhcCCC-chhhhhhHHHHHHhcCCHHHHHHHHhcccCCCccchhhccccHHHHHHHHHHHHHHHh
Confidence            999999999999999987665 66677788888999999999999999854        234566677777777888999


Q ss_pred             CCHHHHHHHHHHHHH
Q 012111          445 GMTEAAQNLENKMIA  459 (471)
Q Consensus       445 g~~~~A~~~~~~m~~  459 (471)
                      |+.++-......|+.
T Consensus       540 gk~E~fi~t~~~Lv~  554 (895)
T KOG2076|consen  540 GKREEFINTASTLVD  554 (895)
T ss_pred             hhHHHHHHHHHHHHH
Confidence            998876666555554

>KOG4422 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.75  E-value=9.8e-14  Score=119.57  Aligned_cols=361  Identities=12%  Similarity=0.133  Sum_probs=265.9

Q ss_pred             CCCchHHHHHHHHHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHH
Q 012111           75 NLWPKPVLEALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTA  154 (471)
Q Consensus        75 ~~~~~~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~  154 (471)
                      +-++.++...|..+++-...+.|.++|++..... .+.+..+||.+|.+-.-..    ..++..+|....+.||..|+|+
T Consensus       204 PKT~et~s~mI~Gl~K~~~~ERA~~L~kE~~~~k-~kv~~~aFN~lI~~~S~~~----~K~Lv~EMisqkm~Pnl~TfNa  278 (625)
T KOG4422|consen  204 PKTDETVSIMIAGLCKFSSLERARELYKEHRAAK-GKVYREAFNGLIGASSYSV----GKKLVAEMISQKMTPNLFTFNA  278 (625)
T ss_pred             CCCchhHHHHHHHHHHHHhHHHHHHHHHHHHHhh-heeeHHhhhhhhhHHHhhc----cHHHHHHHHHhhcCCchHhHHH
Confidence            4567788899999999999999999999998776 4788899999988654332    3789999999999999999999


Q ss_pred             HHHHHHhcCCHHH----HHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHH-HHHHHHHHHHC--C--C----CCCHH
Q 012111          155 LVSAYGQSGLLDE----AFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDL-IEKILAEMSYL--G--I----ECSAV  221 (471)
Q Consensus       155 li~~~~~~~~~~~----a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~-a~~~~~~~~~~--g--~----~~~~~  221 (471)
                      ++.+..+.|+++.    |.+++.+|++ .|+.|...+|..+|..+++.++..+ +..++.++...  |  +    +-+..
T Consensus       279 lL~c~akfg~F~~ar~aalqil~EmKe-iGVePsLsSyh~iik~f~re~dp~k~as~~i~dI~N~ltGK~fkp~~p~d~~  357 (625)
T KOG4422|consen  279 LLSCAAKFGKFEDARKAALQILGEMKE-IGVEPSLSSYHLIIKNFKRESDPQKVASSWINDIQNSLTGKTFKPITPTDNK  357 (625)
T ss_pred             HHHHHHHhcchHHHHHHHHHHHHHHHH-hCCCcchhhHHHHHHHhcccCCchhhhHHHHHHHHHhhccCcccCCCCchhH
Confidence            9999999998764    5678899999 7999999999999999999888754 44444444322  2  2    22455


Q ss_pred             HHHHHHHHHHccCCHHHHHHHHHHHHHcCC---CCCC---HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHH
Q 012111          222 TYNTIIDGYGKAKKFEEMESSFSAMVESGG---CHPD---IFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLN  295 (471)
Q Consensus       222 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~---~~~~---~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~  295 (471)
                      .|...+..|....+.+-|.++...+....+   +.|+   ..-|..+....|.....+....+|+.|+-.-.-|+..+..
T Consensus       358 FF~~AM~Ic~~l~d~~LA~~v~~ll~tg~N~~~ig~~~~~~fYyr~~~~licq~es~~~~~~~Y~~lVP~~y~p~~~~m~  437 (625)
T KOG4422|consen  358 FFQSAMSICSSLRDLELAYQVHGLLKTGDNWKFIGPDQHRNFYYRKFFDLICQMESIDVTLKWYEDLVPSAYFPHSQTMI  437 (625)
T ss_pred             HHHHHHHHHHHhhhHHHHHHHHHHHHcCCchhhcChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccceecCCchhHH
Confidence            667788888899999999888766632211   1222   3456777888899999999999999999888889999999


Q ss_pred             HHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcC-C--------------------HHHHHHHHHHHHH
Q 012111          296 ILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAG-H--------------------IEKMEEYFKKMKH  354 (471)
Q Consensus       296 ~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g-~--------------------~~~a~~~~~~m~~  354 (471)
                      .++++..-.|.++-.-+++..+...|.......-..++..+++.. +                    .+.....-.+|.+
T Consensus       438 ~~lrA~~v~~~~e~ipRiw~D~~~~ght~r~~l~eeil~~L~~~k~hp~tp~r~Ql~~~~ak~aad~~e~~e~~~~R~r~  517 (625)
T KOG4422|consen  438 HLLRALDVANRLEVIPRIWKDSKEYGHTFRSDLREEILMLLARDKLHPLTPEREQLQVAFAKCAADIKEAYESQPIRQRA  517 (625)
T ss_pred             HHHHHHhhcCcchhHHHHHHHHHHhhhhhhHHHHHHHHHHHhcCCCCCCChHHHHHHHHHHHHHHHHHHHHHhhHHHHHh
Confidence            999999999999999999998888775444444444444444433 1                    0111111223343


Q ss_pred             cCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhC-CCCcCHHHHH---HHHHHHHhcCCHHHHHHHHHHHHhCCCCCC
Q 012111          355 RGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENS-DVILDTPFFN---CIISAYGQAGDVEKMGELFLTMKERHCVPD  430 (471)
Q Consensus       355 ~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~-~~~~~~~~~~---~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~  430 (471)
                      .  .-.....+.++-.+.+.|..++|.+++..+.+. +-.|-....|   .++..-.+.++...|..+++-|...+...-
T Consensus       518 ~--~~~~t~l~~ia~Ll~R~G~~qkA~e~l~l~~~~~~~ip~~p~lnAm~El~d~a~~~~spsqA~~~lQ~a~~~n~~~~  595 (625)
T KOG4422|consen  518 Q--DWPATSLNCIAILLLRAGRTQKAWEMLGLFLRKHNKIPRSPLLNAMAELMDSAKVSNSPSQAIEVLQLASAFNLPIC  595 (625)
T ss_pred             c--cCChhHHHHHHHHHHHcchHHHHHHHHHHHHhcCCcCCCCcchhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCchhh
Confidence            3  345567788888899999999999999998543 3334444455   556666778899999999999987654333


Q ss_pred             HHHHHHHHHHHHh
Q 012111          431 NITFATMIQAYNA  443 (471)
Q Consensus       431 ~~~~~~l~~~~~~  443 (471)
                      ...-+.+...|.-
T Consensus       596 E~La~RI~e~f~i  608 (625)
T KOG4422|consen  596 EGLAQRIMEDFAI  608 (625)
T ss_pred             hHHHHHHHHhcCc
Confidence            3233444444433

>KOG2002 consensus TPR-containing nuclear phosphoprotein that regulates K(+) uptake [Inorganic ion transport and metabolism]

Probab=99.74  E-value=1.3e-13  Score=130.38  Aligned_cols=377  Identities=11%  Similarity=0.055  Sum_probs=216.1

Q ss_pred             HHHHHHHHHHhhcHHHHHHHHHHhhhccCccCC-hhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHH
Q 012111           81 VLEALDEAIKQKKWQLALKIFGLLRQQQWYQAR-CQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAY  159 (471)
Q Consensus        81 ~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~  159 (471)
                      +...-+.+...|+++.|...|....+..  +.+ +..+..+...+.+.|+++.+...|+........ +..+...|...|
T Consensus       310 ~Y~~gRs~Ha~Gd~ekA~~yY~~s~k~~--~d~~~l~~~GlgQm~i~~~dle~s~~~fEkv~k~~p~-~~etm~iLG~Ly  386 (1018)
T KOG2002|consen  310 FYQLGRSYHAQGDFEKAFKYYMESLKAD--NDNFVLPLVGLGQMYIKRGDLEESKFCFEKVLKQLPN-NYETMKILGCLY  386 (1018)
T ss_pred             HHHHHHHHHhhccHHHHHHHHHHHHccC--CCCccccccchhHHHHHhchHHHHHHHHHHHHHhCcc-hHHHHHHHHhHH
Confidence            3344444455556666666555555432  122 233444555555556666666655555554211 344444444444


Q ss_pred             HhcC----CHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHH----HHHHCCCCCCHHHHHHHHHHHH
Q 012111          160 GQSG----LLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILA----EMSYLGIECSAVTYNTIIDGYG  231 (471)
Q Consensus       160 ~~~~----~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~----~~~~~g~~~~~~~~~~l~~~~~  231 (471)
                      +..+    ..+.|..++.+..+.  .+.|...|-.+...+... +...++.+|.    .+...+.++.+...|.+...+.
T Consensus       387 a~~~~~~~~~d~a~~~l~K~~~~--~~~d~~a~l~laql~e~~-d~~~sL~~~~~A~d~L~~~~~~ip~E~LNNvaslhf  463 (1018)
T KOG2002|consen  387 AHSAKKQEKRDKASNVLGKVLEQ--TPVDSEAWLELAQLLEQT-DPWASLDAYGNALDILESKGKQIPPEVLNNVASLHF  463 (1018)
T ss_pred             HhhhhhhHHHHHHHHHHHHHHhc--ccccHHHHHHHHHHHHhc-ChHHHHHHHHHHHHHHHHcCCCCCHHHHHhHHHHHH
Confidence            4443    344555555554441  234444554444444332 2222244443    2334444566666777777777


Q ss_pred             ccCCHHHHHHHHHHHHHcCC--CCCC------HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCC-----------------
Q 012111          232 KAKKFEEMESSFSAMVESGG--CHPD------IFTLNSMISAYGNSGNIEKMEKWYNEFNLMG-----------------  286 (471)
Q Consensus       232 ~~~~~~~a~~~~~~~~~~~~--~~~~------~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-----------------  286 (471)
                      ..|++++|...|......-.  ..++      ..+--.+...+-..++++.|.+.|..+....                 
T Consensus       464 ~~g~~~~A~~~f~~A~~~~~~~~n~de~~~~~lt~~YNlarl~E~l~~~~~A~e~Yk~Ilkehp~YId~ylRl~~ma~~k  543 (1018)
T KOG2002|consen  464 RLGNIEKALEHFKSALGKLLEVANKDEGKSTNLTLKYNLARLLEELHDTEVAEEMYKSILKEHPGYIDAYLRLGCMARDK  543 (1018)
T ss_pred             HhcChHHHHHHHHHHhhhhhhhcCccccccchhHHHHHHHHHHHhhhhhhHHHHHHHHHHHHCchhHHHHHHhhHHHHhc
Confidence            77777777777766654300  0111      1122223333444445555555555554321                 


Q ss_pred             ----------------CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCC-CCCCHHHHHHHHHHHHh-----------
Q 012111          287 ----------------VKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRF-FFPTVVTYNIVIETFGK-----------  338 (471)
Q Consensus       287 ----------------~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~li~~~~~-----------  338 (471)
                                      ...++..+..+...+.+...+..|..-|..+.+.- ..+|..+.-.|...|.+           
T Consensus       544 ~~~~ea~~~lk~~l~~d~~np~arsl~G~~~l~k~~~~~a~k~f~~i~~~~~~~~D~YsliaLGN~~~~~l~~~~rn~ek  623 (1018)
T KOG2002|consen  544 NNLYEASLLLKDALNIDSSNPNARSLLGNLHLKKSEWKPAKKKFETILKKTSTKTDAYSLIALGNVYIQALHNPSRNPEK  623 (1018)
T ss_pred             cCcHHHHHHHHHHHhcccCCcHHHHHHHHHHHhhhhhcccccHHHHHHhhhccCCchhHHHHhhHHHHHHhcccccChHH
Confidence                            01122222222333333344444444333333221 11233333334443332           


Q ss_pred             -cCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHH
Q 012111          339 -AGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGE  417 (471)
Q Consensus       339 -~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~  417 (471)
                       .+..++|+++|.+.++.. +-|...-+-+.-.++..|++..|..+|.++.+.... ...+|-.+..+|...|++..|++
T Consensus       624 ~kk~~~KAlq~y~kvL~~d-pkN~yAANGIgiVLA~kg~~~~A~dIFsqVrEa~~~-~~dv~lNlah~~~e~~qy~~AIq  701 (1018)
T KOG2002|consen  624 EKKHQEKALQLYGKVLRND-PKNMYAANGIGIVLAEKGRFSEARDIFSQVREATSD-FEDVWLNLAHCYVEQGQYRLAIQ  701 (1018)
T ss_pred             HHHHHHHHHHHHHHHHhcC-cchhhhccchhhhhhhccCchHHHHHHHHHHHHHhh-CCceeeeHHHHHHHHHHHHHHHH
Confidence             234678889988888764 447777788888899999999999999999887543 56678889999999999999999


Q ss_pred             HHHHHHhC-CCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhhhcCC
Q 012111          418 LFLTMKER-HCVPDNITFATMIQAYNALGMTEAAQNLENKMIAMKENSG  465 (471)
Q Consensus       418 ~~~~~~~~-~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~~~  465 (471)
                      +|+..... +-.-+..+...|.+++.+.|.+.+|.+.+..++...|...
T Consensus       702 mYe~~lkkf~~~~~~~vl~~Lara~y~~~~~~eak~~ll~a~~~~p~~~  750 (1018)
T KOG2002|consen  702 MYENCLKKFYKKNRSEVLHYLARAWYEAGKLQEAKEALLKARHLAPSNT  750 (1018)
T ss_pred             HHHHHHHHhcccCCHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhCCccc
Confidence            99887654 3345778888999999999999999999999888877643

>PRK10747 putative protoheme IX biogenesis protein; Provisional

Probab=99.72  E-value=2.1e-13  Score=125.83  Aligned_cols=285  Identities=11%  Similarity=0.029  Sum_probs=198.1

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHH-HHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHH--HHHHHHHccCCHHH
Q 012111          162 SGLLDEAFSTINDMKSVSDCKPDVYT-YSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYN--TIIDGYGKAKKFEE  238 (471)
Q Consensus       162 ~~~~~~a~~~~~~~~~~~~~~~~~~~-~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~--~l~~~~~~~~~~~~  238 (471)
                      .|+++.|.+.+....+.   .+++.. |.....+..+.|+++.+.+.+.++.+.  .|+.....  .....+...|+++.
T Consensus        97 eGd~~~A~k~l~~~~~~---~~~p~l~~llaA~aA~~~g~~~~A~~~l~~A~~~--~~~~~~~~~l~~a~l~l~~g~~~~  171 (398)
T PRK10747         97 EGDYQQVEKLMTRNADH---AEQPVVNYLLAAEAAQQRGDEARANQHLERAAEL--ADNDQLPVEITRVRIQLARNENHA  171 (398)
T ss_pred             CCCHHHHHHHHHHHHhc---ccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CCcchHHHHHHHHHHHHHCCCHHH
Confidence            57777777666665441   112222 222233446777777777777777654  34433222  33556777778888


Q ss_pred             HHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCH-------HHHHHHHHHHHHcCCHHHHH
Q 012111          239 MESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADI-------QTLNILTKSYGRAGMYDKMR  311 (471)
Q Consensus       239 a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~-------~~~~~ll~~~~~~~~~~~a~  311 (471)
                      |...++.+.+..  +.+......+...|.+.|++++|.+++..+.+.+..++.       .+|..++.......+.+...
T Consensus       172 Al~~l~~~~~~~--P~~~~al~ll~~~~~~~gdw~~a~~~l~~l~k~~~~~~~~~~~l~~~a~~~l~~~~~~~~~~~~l~  249 (398)
T PRK10747        172 ARHGVDKLLEVA--PRHPEVLRLAEQAYIRTGAWSSLLDILPSMAKAHVGDEEHRAMLEQQAWIGLMDQAMADQGSEGLK  249 (398)
T ss_pred             HHHHHHHHHhcC--CCCHHHHHHHHHHHHHHHhHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHhcCHHHHH
Confidence            888777776653  445566777777777778888888777777766543222       12233333333444556666


Q ss_pred             HHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCC
Q 012111          312 SVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSD  391 (471)
Q Consensus       312 ~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~  391 (471)
                      ++++.+.+. .+.++.....+...+...|+.++|.+++++..+.  .++....  ++.+....++.+++.+..+...+..
T Consensus       250 ~~w~~lp~~-~~~~~~~~~~~A~~l~~~g~~~~A~~~L~~~l~~--~~~~~l~--~l~~~l~~~~~~~al~~~e~~lk~~  324 (398)
T PRK10747        250 RWWKNQSRK-TRHQVALQVAMAEHLIECDDHDTAQQIILDGLKR--QYDERLV--LLIPRLKTNNPEQLEKVLRQQIKQH  324 (398)
T ss_pred             HHHHhCCHH-HhCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CCCHHHH--HHHhhccCCChHHHHHHHHHHHhhC
Confidence            666665433 2346777888889999999999999999988874  4555322  2334445689999999999988877


Q ss_pred             CCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhh
Q 012111          392 VILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAYNALGMTEAAQNLENKMIAMK  461 (471)
Q Consensus       392 ~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~  461 (471)
                      +. |...+..+.+.+.+.|++++|.+.|+.+.+.  .|+..++..+...+.+.|+.++|.+++++....-
T Consensus       325 P~-~~~l~l~lgrl~~~~~~~~~A~~~le~al~~--~P~~~~~~~La~~~~~~g~~~~A~~~~~~~l~~~  391 (398)
T PRK10747        325 GD-TPLLWSTLGQLLMKHGEWQEASLAFRAALKQ--RPDAYDYAWLADALDRLHKPEEAAAMRRDGLMLT  391 (398)
T ss_pred             CC-CHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhh
Confidence            66 7788889999999999999999999999874  7999998899999999999999999999887654

>TIGR00540 hemY_coli hemY protein

Probab=99.72  E-value=1.5e-13  Score=127.60  Aligned_cols=292  Identities=10%  Similarity=0.004  Sum_probs=194.5

Q ss_pred             hcCCHHHHHHHHHHhhcCCCCCCCH-HHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHH
Q 012111          161 QSGLLDEAFSTINDMKSVSDCKPDV-YTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEM  239 (471)
Q Consensus       161 ~~~~~~~a~~~~~~~~~~~~~~~~~-~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~a  239 (471)
                      ..|+++.|.+.+.+..+.   .|+. ..+-....+....|+.+.|.+++.+..+....+...........+...|+++.|
T Consensus        96 ~~g~~~~A~~~l~~~~~~---~~~~~~~~llaA~aa~~~g~~~~A~~~l~~a~~~~p~~~l~~~~~~a~l~l~~~~~~~A  172 (409)
T TIGR00540        96 AEGDYAKAEKLIAKNADH---AAEPVLNLIKAAEAAQQRGDEARANQHLEEAAELAGNDNILVEIARTRILLAQNELHAA  172 (409)
T ss_pred             hCCCHHHHHHHHHHHhhc---CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCcCchHHHHHHHHHHHHCCCHHHH
Confidence            467788887777776552   3433 233444556667788888888887776542122222333346777778888888


Q ss_pred             HHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHH-HHHHHH---HHcCCHHHHHHHHH
Q 012111          240 ESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLN-ILTKSY---GRAGMYDKMRSVMD  315 (471)
Q Consensus       240 ~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~-~ll~~~---~~~~~~~~a~~~~~  315 (471)
                      ...++.+.+..  +.+......+...+...|++++|.+.+..+.+.+.. +...+. .-..++   ...+..+++...+.
T Consensus       173 l~~l~~l~~~~--P~~~~~l~ll~~~~~~~~d~~~a~~~l~~l~k~~~~-~~~~~~~l~~~a~~~~l~~~~~~~~~~~L~  249 (409)
T TIGR00540       173 RHGVDKLLEMA--PRHKEVLKLAEEAYIRSGAWQALDDIIDNMAKAGLF-DDEEFADLEQKAEIGLLDEAMADEGIDGLL  249 (409)
T ss_pred             HHHHHHHHHhC--CCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHHcCCC-CHHHHHHHHHHHHHHHHHHHHHhcCHHHHH
Confidence            88888887764  445566777777888888888888888888776533 332221 111111   22222233333444


Q ss_pred             HHHhCCC---CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHH---HHHHHHHHHhcCCHHHHHHHHHHHHh
Q 012111          316 FMQKRFF---FPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSIT---YCSLVSAYSKAGLIMKVDSILRQVEN  389 (471)
Q Consensus       316 ~~~~~~~---~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~---~~~li~~~~~~g~~~~a~~~~~~~~~  389 (471)
                      .+.+...   ..+...+..+...+...|+.++|.+++++..+..  ||...   ...........++.+.+.+.++...+
T Consensus       250 ~~~~~~p~~~~~~~~l~~~~a~~l~~~g~~~~A~~~l~~~l~~~--pd~~~~~~~~l~~~~~l~~~~~~~~~~~~e~~lk  327 (409)
T TIGR00540       250 NWWKNQPRHRRHNIALKIALAEHLIDCDDHDSAQEIIFDGLKKL--GDDRAISLPLCLPIPRLKPEDNEKLEKLIEKQAK  327 (409)
T ss_pred             HHHHHCCHHHhCCHHHHHHHHHHHHHCCChHHHHHHHHHHHhhC--CCcccchhHHHHHhhhcCCCChHHHHHHHHHHHH
Confidence            4443321   1267788888889999999999999999998863  33331   11111222345778888888888887


Q ss_pred             CCCCcCH--HHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhh
Q 012111          390 SDVILDT--PFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAYNALGMTEAAQNLENKMIAMK  461 (471)
Q Consensus       390 ~~~~~~~--~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~  461 (471)
                      ..+. |.  ....++...+.+.|++++|.+.|+........|+...+..+...+.+.|+.++|.+++++....-
T Consensus       328 ~~p~-~~~~~ll~sLg~l~~~~~~~~~A~~~le~a~a~~~~p~~~~~~~La~ll~~~g~~~~A~~~~~~~l~~~  400 (409)
T TIGR00540       328 NVDD-KPKCCINRALGQLLMKHGEFIEAADAFKNVAACKEQLDANDLAMAADAFDQAGDKAEAAAMRQDSLGLM  400 (409)
T ss_pred             hCCC-ChhHHHHHHHHHHHHHcccHHHHHHHHHHhHHhhcCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHH
Confidence            6554 55  67788999999999999999999954433357999999999999999999999999999875543

This is an uncharacterized protein encoded next to a heme-biosynthetic enzyme in two gamma division proteobacteria (E. coli and H. influenzae). It is known in no other species. The gene symbol hemY is unfortunate in that an unrelated protein, protoporphyrinogen oxidase, is designated as HemG in E. coli but as HemY in Bacillus subtilis.

>PRK10747 putative protoheme IX biogenesis protein; Provisional

Probab=99.70  E-value=5.8e-13  Score=122.96  Aligned_cols=288  Identities=9%  Similarity=0.022  Sum_probs=129.4

Q ss_pred             hhcHHHHHHHHHHhhhccCccCChhHHHHH-HHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHH--HHHHHHHhcCCHHH
Q 012111           91 QKKWQLALKIFGLLRQQQWYQARCQTFTKL-MVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYT--ALVSAYGQSGLLDE  167 (471)
Q Consensus        91 ~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l-~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~--~li~~~~~~~~~~~  167 (471)
                      .|+|+.|.+.+....+..   ++...+..+ .....+.|+++.|...+.++.+.  .|+...+.  .....+...|+++.
T Consensus        97 eGd~~~A~k~l~~~~~~~---~~p~l~~llaA~aA~~~g~~~~A~~~l~~A~~~--~~~~~~~~~l~~a~l~l~~g~~~~  171 (398)
T PRK10747         97 EGDYQQVEKLMTRNADHA---EQPVVNYLLAAEAAQQRGDEARANQHLERAAEL--ADNDQLPVEITRVRIQLARNENHA  171 (398)
T ss_pred             CCCHHHHHHHHHHHHhcc---cchHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CCcchHHHHHHHHHHHHHCCCHHH
Confidence            466666665555544321   122222222 22335556666666666666543  23322221  22445555666666


Q ss_pred             HHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHH
Q 012111          168 AFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMV  247 (471)
Q Consensus       168 a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  247 (471)
                      |...++++.+..  +-+...+..+...|.+.|+++.|.+++..+.+.+..++ .....+-                    
T Consensus       172 Al~~l~~~~~~~--P~~~~al~ll~~~~~~~gdw~~a~~~l~~l~k~~~~~~-~~~~~l~--------------------  228 (398)
T PRK10747        172 ARHGVDKLLEVA--PRHPEVLRLAEQAYIRTGAWSSLLDILPSMAKAHVGDE-EHRAMLE--------------------  228 (398)
T ss_pred             HHHHHHHHHhcC--CCCHHHHHHHHHHHHHHHhHHHHHHHHHHHHHcCCCCH-HHHHHHH--------------------
Confidence            666666655421  33444555555556666666666666666655543211 1111000                    


Q ss_pred             HcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHH
Q 012111          248 ESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVV  327 (471)
Q Consensus       248 ~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~  327 (471)
                              ..+|..++.......+.+...++++.+... .+.+......+...+...|+.++|..+++...+.  .++..
T Consensus       229 --------~~a~~~l~~~~~~~~~~~~l~~~w~~lp~~-~~~~~~~~~~~A~~l~~~g~~~~A~~~L~~~l~~--~~~~~  297 (398)
T PRK10747        229 --------QQAWIGLMDQAMADQGSEGLKRWWKNQSRK-TRHQVALQVAMAEHLIECDDHDTAQQIILDGLKR--QYDER  297 (398)
T ss_pred             --------HHHHHHHHHHHHHhcCHHHHHHHHHhCCHH-HhCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CCCHH
Confidence                    011222222222223333333333333211 1334444444555555555555555555444442  22221


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHH
Q 012111          328 TYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYG  407 (471)
Q Consensus       328 ~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  407 (471)
                      .  .++.+....++.+++.+..+...+.. +-|+..+..+...|.+.+++++|.+.|+.+.+.  .|+...+..+..++.
T Consensus       298 l--~~l~~~l~~~~~~~al~~~e~~lk~~-P~~~~l~l~lgrl~~~~~~~~~A~~~le~al~~--~P~~~~~~~La~~~~  372 (398)
T PRK10747        298 L--VLLIPRLKTNNPEQLEKVLRQQIKQH-GDTPLLWSTLGQLLMKHGEWQEASLAFRAALKQ--RPDAYDYAWLADALD  372 (398)
T ss_pred             H--HHHHhhccCCChHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CCCHHHHHHHHHHHH
Confidence            1  11222223355555555555554431 223344445555555555555555555555543  244444455555555


Q ss_pred             hcCCHHHHHHHHHHH
Q 012111          408 QAGDVEKMGELFLTM  422 (471)
Q Consensus       408 ~~g~~~~a~~~~~~~  422 (471)
                      +.|+.++|.+++++.
T Consensus       373 ~~g~~~~A~~~~~~~  387 (398)
T PRK10747        373 RLHKPEEAAAMRRDG  387 (398)
T ss_pred             HcCCHHHHHHHHHHH
Confidence            555555555555544

>KOG2003 consensus TPR repeat-containing protein [General function prediction only]

Probab=99.69  E-value=4e-13  Score=116.74  Aligned_cols=350  Identities=10%  Similarity=0.086  Sum_probs=226.5

Q ss_pred             HHHHhhcHHHHHHHHHHhhhccC-ccC--ChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcC
Q 012111           87 EAIKQKKWQLALKIFGLLRQQQW-YQA--RCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSG  163 (471)
Q Consensus        87 ~~~~~~~~~~A~~~~~~~~~~~~-~~~--~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~  163 (471)
                      ...+...+..|+++|+.+..+-+ +..  .....+.+...+.+.|+++.|+..|+...+.  .|+..+--.|+-++..-|
T Consensus       246 i~~kkr~fskaikfyrmaldqvpsink~~rikil~nigvtfiq~gqy~dainsfdh~m~~--~pn~~a~~nl~i~~f~i~  323 (840)
T KOG2003|consen  246 IHFKKREFSKAIKFYRMALDQVPSINKDMRIKILNNIGVTFIQAGQYDDAINSFDHCMEE--APNFIAALNLIICAFAIG  323 (840)
T ss_pred             eeeehhhHHHHHHHHHHHHhhccccchhhHHHHHhhcCeeEEecccchhhHhhHHHHHHh--CccHHhhhhhhhhheecC
Confidence            35567777777777777665520 000  1123344444556667777777777766654  455544334444444456


Q ss_pred             CHHHHHHHHHHhhcCC-----------CCCCCHHHHHHH-----------------------------------------
Q 012111          164 LLDEAFSTINDMKSVS-----------DCKPDVYTYSIL-----------------------------------------  191 (471)
Q Consensus       164 ~~~~a~~~~~~~~~~~-----------~~~~~~~~~~~l-----------------------------------------  191 (471)
                      +.++..+.|.+|....           ...|+....+..                                         
T Consensus       324 d~ekmkeaf~kli~ip~~~dddkyi~~~ddp~~~ll~eai~nd~lk~~ek~~ka~aek~i~ta~kiiapvi~~~fa~g~d  403 (840)
T KOG2003|consen  324 DAEKMKEAFQKLIDIPGEIDDDKYIKEKDDPDDNLLNEAIKNDHLKNMEKENKADAEKAIITAAKIIAPVIAPDFAAGCD  403 (840)
T ss_pred             cHHHHHHHHHHHhcCCCCCCcccccCCcCCcchHHHHHHHhhHHHHHHHHhhhhhHHHHHHHHHHHhccccccchhcccH
Confidence            6666666665554410           011111111111                                         


Q ss_pred             ----------------------HHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHH--H-------------------
Q 012111          192 ----------------------IKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTII--D-------------------  228 (471)
Q Consensus       192 ----------------------l~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~--~-------------------  228 (471)
                                            ..-+.+.|+++.|.++++-+.+..-..-...-+.|-  +                   
T Consensus       404 wcle~lk~s~~~~la~dlei~ka~~~lk~~d~~~aieilkv~~~kdnk~~saaa~nl~~l~flqggk~~~~aqqyad~al  483 (840)
T KOG2003|consen  404 WCLESLKASQHAELAIDLEINKAGELLKNGDIEGAIEILKVFEKKDNKTASAAANNLCALRFLQGGKDFADAQQYADIAL  483 (840)
T ss_pred             HHHHHHHHhhhhhhhhhhhhhHHHHHHhccCHHHHHHHHHHHHhccchhhHHHhhhhHHHHHHhcccchhHHHHHHHHHh
Confidence                                  012456899999999998776553221111111111  1                   


Q ss_pred             ---------------HHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHH
Q 012111          229 ---------------GYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQT  293 (471)
Q Consensus       229 ---------------~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~  293 (471)
                                     .....|++++|.+.|++.....  .......-.+.-.+...|+.++|+..|-++... +..+..+
T Consensus       484 n~dryn~~a~~nkgn~~f~ngd~dka~~~ykeal~nd--asc~ealfniglt~e~~~~ldeald~f~klh~i-l~nn~ev  560 (840)
T KOG2003|consen  484 NIDRYNAAALTNKGNIAFANGDLDKAAEFYKEALNND--ASCTEALFNIGLTAEALGNLDEALDCFLKLHAI-LLNNAEV  560 (840)
T ss_pred             cccccCHHHhhcCCceeeecCcHHHHHHHHHHHHcCc--hHHHHHHHHhcccHHHhcCHHHHHHHHHHHHHH-HHhhHHH
Confidence                           1123477888888888876542  112222223334567788889998888877542 2456777


Q ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHh
Q 012111          294 LNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSK  373 (471)
Q Consensus       294 ~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~  373 (471)
                      ...+.+.|....+..+|++++.+.... ++.|+...+.|...|-+.|+-.+|.+.+-+--+. ++-+..+...|...|..
T Consensus       561 l~qianiye~led~aqaie~~~q~~sl-ip~dp~ilskl~dlydqegdksqafq~~ydsyry-fp~nie~iewl~ayyid  638 (840)
T KOG2003|consen  561 LVQIANIYELLEDPAQAIELLMQANSL-IPNDPAILSKLADLYDQEGDKSQAFQCHYDSYRY-FPCNIETIEWLAAYYID  638 (840)
T ss_pred             HHHHHHHHHHhhCHHHHHHHHHHhccc-CCCCHHHHHHHHHHhhcccchhhhhhhhhhcccc-cCcchHHHHHHHHHHHh
Confidence            777888888888888888888766554 4457888888999999999999998887665443 35578888889999999


Q ss_pred             cCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHH-HhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCC
Q 012111          374 AGLIMKVDSILRQVENSDVILDTPFFNCIISAY-GQAGDVEKMGELFLTMKERHCVPDNITFATMIQAYNALGM  446 (471)
Q Consensus       374 ~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~-~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~  446 (471)
                      ..-+++++.+|++..-  +.|+..-|..++..| .+.|++..|.++|+...+. ++-|...+.-|++.+...|.
T Consensus       639 tqf~ekai~y~ekaal--iqp~~~kwqlmiasc~rrsgnyqka~d~yk~~hrk-fpedldclkflvri~~dlgl  709 (840)
T KOG2003|consen  639 TQFSEKAINYFEKAAL--IQPNQSKWQLMIASCFRRSGNYQKAFDLYKDIHRK-FPEDLDCLKFLVRIAGDLGL  709 (840)
T ss_pred             hHHHHHHHHHHHHHHh--cCccHHHHHHHHHHHHHhcccHHHHHHHHHHHHHh-CccchHHHHHHHHHhccccc
Confidence            9999999999987654  467888888877655 4679999999999988765 66788888888888887775

>TIGR00540 hemY_coli hemY protein

Probab=99.69  E-value=7.9e-13  Score=122.75  Aligned_cols=292  Identities=11%  Similarity=0.035  Sum_probs=144.8

Q ss_pred             HHhhcHHHHHHHHHHhhhccCccCCh-hHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHH
Q 012111           89 IKQKKWQLALKIFGLLRQQQWYQARC-QTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDE  167 (471)
Q Consensus        89 ~~~~~~~~A~~~~~~~~~~~~~~~~~-~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~  167 (471)
                      ...|+++.|.+.+....+..   |+. ..+-....+..+.|+++.|.+.+....+....+.....-.....+...|+++.
T Consensus        95 ~~~g~~~~A~~~l~~~~~~~---~~~~~~~llaA~aa~~~g~~~~A~~~l~~a~~~~p~~~l~~~~~~a~l~l~~~~~~~  171 (409)
T TIGR00540        95 LAEGDYAKAEKLIAKNADHA---AEPVLNLIKAAEAAQQRGDEARANQHLEEAAELAGNDNILVEIARTRILLAQNELHA  171 (409)
T ss_pred             HhCCCHHHHHHHHHHHhhcC---CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCcCchHHHHHHHHHHHHCCCHHH
Confidence            35677777777777766542   332 33344455666677777777777776654322222333334666677777777


Q ss_pred             HHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHH-HHHHHH---HccCCHHHHHHHH
Q 012111          168 AFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYN-TIIDGY---GKAKKFEEMESSF  243 (471)
Q Consensus       168 a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~-~l~~~~---~~~~~~~~a~~~~  243 (471)
                      |...++.+.+..  +-+...+..+...+...|+++.|.+++..+.+.++. +...+. .-..++   ...+..+.+.+.+
T Consensus       172 Al~~l~~l~~~~--P~~~~~l~ll~~~~~~~~d~~~a~~~l~~l~k~~~~-~~~~~~~l~~~a~~~~l~~~~~~~~~~~L  248 (409)
T TIGR00540       172 ARHGVDKLLEMA--PRHKEVLKLAEEAYIRSGAWQALDDIIDNMAKAGLF-DDEEFADLEQKAEIGLLDEAMADEGIDGL  248 (409)
T ss_pred             HHHHHHHHHHhC--CCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHHcCCC-CHHHHHHHHHHHHHHHHHHHHHhcCHHHH
Confidence            777777777632  335556667777777777777777777777776543 222221 111111   1112222222233


Q ss_pred             HHHHHcCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHH-HHHHHHHHHcCCHHHHHHHHHHHHhC
Q 012111          244 SAMVESGG--CHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTL-NILTKSYGRAGMYDKMRSVMDFMQKR  320 (471)
Q Consensus       244 ~~~~~~~~--~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~-~~ll~~~~~~~~~~~a~~~~~~~~~~  320 (471)
                      ..+.+...  .+.+...+..+...+...|+.++|.+++++..+..  ||.... ..++..                    
T Consensus       249 ~~~~~~~p~~~~~~~~l~~~~a~~l~~~g~~~~A~~~l~~~l~~~--pd~~~~~~~~l~~--------------------  306 (409)
T TIGR00540       249 LNWWKNQPRHRRHNIALKIALAEHLIDCDDHDSAQEIIFDGLKKL--GDDRAISLPLCLP--------------------  306 (409)
T ss_pred             HHHHHHCCHHHhCCHHHHHHHHHHHHHCCChHHHHHHHHHHHhhC--CCcccchhHHHHH--------------------
Confidence            33222210  01244455555555555555555555555554432  221100 001111                    


Q ss_pred             CCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCH--HHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHH
Q 012111          321 FFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNS--ITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPF  398 (471)
Q Consensus       321 ~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~--~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~  398 (471)
                                   ......++.+.+.+.++...+.. +-|+  ....++...+.+.|++++|.+.|+........|+...
T Consensus       307 -------------~~~l~~~~~~~~~~~~e~~lk~~-p~~~~~~ll~sLg~l~~~~~~~~~A~~~le~a~a~~~~p~~~~  372 (409)
T TIGR00540       307 -------------IPRLKPEDNEKLEKLIEKQAKNV-DDKPKCCINRALGQLLMKHGEFIEAADAFKNVAACKEQLDAND  372 (409)
T ss_pred             -------------hhhcCCCChHHHHHHHHHHHHhC-CCChhHHHHHHHHHHHHHcccHHHHHHHHHHhHHhhcCCCHHH
Confidence                         11122244444555555444431 1122  3344555555555555555555553333223344555


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHH
Q 012111          399 FNCIISAYGQAGDVEKMGELFLTM  422 (471)
Q Consensus       399 ~~~l~~~~~~~g~~~~a~~~~~~~  422 (471)
                      +..+...+.+.|+.++|.++|++.
T Consensus       373 ~~~La~ll~~~g~~~~A~~~~~~~  396 (409)
T TIGR00540       373 LAMAADAFDQAGDKAEAAAMRQDS  396 (409)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHH
Confidence            555555555555555555555554

This is an uncharacterized protein encoded next to a heme-biosynthetic enzyme in two gamma division proteobacteria (E. coli and H. influenzae). It is known in no other species. The gene symbol hemY is unfortunate in that an unrelated protein, protoporphyrinogen oxidase, is designated as HemG in E. coli but as HemY in Bacillus subtilis.

>KOG2003 consensus TPR repeat-containing protein [General function prediction only]

Probab=99.69  E-value=3.7e-13  Score=116.95  Aligned_cols=372  Identities=10%  Similarity=0.079  Sum_probs=261.9

Q ss_pred             HHHHHHHHHHhhcHHHHHHHHHHhhhccCccCChh-HHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCC----HHHHHHH
Q 012111           81 VLEALDEAIKQKKWQLALKIFGLLRQQQWYQARCQ-TFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPS----VDVYTAL  155 (471)
Q Consensus        81 ~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~-~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~----~~~~~~l  155 (471)
                      +..+...+-...-..+|+..|+-+.+.. .-|+.. .-..+...+.+...+.+|++.|.-....-...+    ....+.+
T Consensus       204 l~nlaqqy~~ndm~~ealntyeiivknk-mf~nag~lkmnigni~~kkr~fskaikfyrmaldqvpsink~~rikil~ni  282 (840)
T KOG2003|consen  204 LFNLAQQYEANDMTAEALNTYEIIVKNK-MFPNAGILKMNIGNIHFKKREFSKAIKFYRMALDQVPSINKDMRIKILNNI  282 (840)
T ss_pred             HHHHHHHhhhhHHHHHHhhhhhhhhccc-ccCCCceeeeeecceeeehhhHHHHHHHHHHHHhhccccchhhHHHHHhhc
Confidence            3344444445566789999999998876 345544 445677789999999999999988776522222    3456666


Q ss_pred             HHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCC------------CCCHHHH
Q 012111          156 VSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGI------------ECSAVTY  223 (471)
Q Consensus       156 i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~------------~~~~~~~  223 (471)
                      .-.+.+.|+++.|+..|+...+.   .|+..+-..|+-++..-|+-+...+.|..|+..-.            .|+....
T Consensus       283 gvtfiq~gqy~dainsfdh~m~~---~pn~~a~~nl~i~~f~i~d~ekmkeaf~kli~ip~~~dddkyi~~~ddp~~~ll  359 (840)
T KOG2003|consen  283 GVTFIQAGQYDDAINSFDHCMEE---APNFIAALNLIICAFAIGDAEKMKEAFQKLIDIPGEIDDDKYIKEKDDPDDNLL  359 (840)
T ss_pred             CeeEEecccchhhHhhHHHHHHh---CccHHhhhhhhhhheecCcHHHHHHHHHHHhcCCCCCCcccccCCcCCcchHHH
Confidence            67789999999999999998763   68877654555555556777777777777765311            1121111


Q ss_pred             HHH---------------------------------------------------------------HHHHHccCCHHHHH
Q 012111          224 NTI---------------------------------------------------------------IDGYGKAKKFEEME  240 (471)
Q Consensus       224 ~~l---------------------------------------------------------------~~~~~~~~~~~~a~  240 (471)
                      +.-                                                               ..-+.+.|+++.|.
T Consensus       360 ~eai~nd~lk~~ek~~ka~aek~i~ta~kiiapvi~~~fa~g~dwcle~lk~s~~~~la~dlei~ka~~~lk~~d~~~ai  439 (840)
T KOG2003|consen  360 NEAIKNDHLKNMEKENKADAEKAIITAAKIIAPVIAPDFAAGCDWCLESLKASQHAELAIDLEINKAGELLKNGDIEGAI  439 (840)
T ss_pred             HHHHhhHHHHHHHHhhhhhHHHHHHHHHHHhccccccchhcccHHHHHHHHHhhhhhhhhhhhhhHHHHHHhccCHHHHH
Confidence            100                                                               11368899999999


Q ss_pred             HHHHHHHHcCCCCCCHHHHHHH--H----------------------------------HHHHhcCCHHHHHHHHHHHHh
Q 012111          241 SSFSAMVESGGCHPDIFTLNSM--I----------------------------------SAYGNSGNIEKMEKWYNEFNL  284 (471)
Q Consensus       241 ~~~~~~~~~~~~~~~~~~~~~l--~----------------------------------~~~~~~~~~~~a~~~~~~~~~  284 (471)
                      +++.-..+......+. .-+.|  +                                  +.....|+++.|.+.|++...
T Consensus       440 eilkv~~~kdnk~~sa-aa~nl~~l~flqggk~~~~aqqyad~aln~dryn~~a~~nkgn~~f~ngd~dka~~~ykeal~  518 (840)
T KOG2003|consen  440 EILKVFEKKDNKTASA-AANNLCALRFLQGGKDFADAQQYADIALNIDRYNAAALTNKGNIAFANGDLDKAAEFYKEALN  518 (840)
T ss_pred             HHHHHHHhccchhhHH-HhhhhHHHHHHhcccchhHHHHHHHHHhcccccCHHHhhcCCceeeecCcHHHHHHHHHHHHc
Confidence            9998775543111111 11111  0                                  001236788899999988875


Q ss_pred             CCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHH
Q 012111          285 MGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITY  364 (471)
Q Consensus       285 ~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~  364 (471)
                      .+-.-....|| +.-.+-..|++++|++.|-.+...- .-+......+...|....+..+|++++.+.... ++-|+.++
T Consensus       519 ndasc~ealfn-iglt~e~~~~ldeald~f~klh~il-~nn~evl~qianiye~led~aqaie~~~q~~sl-ip~dp~il  595 (840)
T KOG2003|consen  519 NDASCTEALFN-IGLTAEALGNLDEALDCFLKLHAIL-LNNAEVLVQIANIYELLEDPAQAIELLMQANSL-IPNDPAIL  595 (840)
T ss_pred             CchHHHHHHHH-hcccHHHhcCHHHHHHHHHHHHHHH-HhhHHHHHHHHHHHHHhhCHHHHHHHHHHhccc-CCCCHHHH
Confidence            43222222333 2334667889999999887765432 226667777888888899999999999776654 45578899


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHH-HHHh
Q 012111          365 CSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQ-AYNA  443 (471)
Q Consensus       365 ~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~-~~~~  443 (471)
                      ..|...|-+.|+-.+|.+.+-.--+. ++-+..+..-|..-|....-+++++.+|++..-  ++|+..-|..++. ++.+
T Consensus       596 skl~dlydqegdksqafq~~ydsyry-fp~nie~iewl~ayyidtqf~ekai~y~ekaal--iqp~~~kwqlmiasc~rr  672 (840)
T KOG2003|consen  596 SKLADLYDQEGDKSQAFQCHYDSYRY-FPCNIETIEWLAAYYIDTQFSEKAINYFEKAAL--IQPNQSKWQLMIASCFRR  672 (840)
T ss_pred             HHHHHHhhcccchhhhhhhhhhcccc-cCcchHHHHHHHHHHHhhHHHHHHHHHHHHHHh--cCccHHHHHHHHHHHHHh
Confidence            99999999999999999887655554 334788888888899999999999999998865  6899999999885 5567


Q ss_pred             cCCHHHHHHHHHHHHHhhhc
Q 012111          444 LGMTEAAQNLENKMIAMKEN  463 (471)
Q Consensus       444 ~g~~~~A~~~~~~m~~~~~~  463 (471)
                      .|++..|..+++..-++-|.
T Consensus       673 sgnyqka~d~yk~~hrkfpe  692 (840)
T KOG2003|consen  673 SGNYQKAFDLYKDIHRKFPE  692 (840)
T ss_pred             cccHHHHHHHHHHHHHhCcc
Confidence            89999999999998776654

>KOG2002 consensus TPR-containing nuclear phosphoprotein that regulates K(+) uptake [Inorganic ion transport and metabolism]

Probab=99.68  E-value=1.8e-12  Score=122.85  Aligned_cols=357  Identities=12%  Similarity=0.065  Sum_probs=193.5

Q ss_pred             cHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCC--CCHHHHHHHHHHHHhcCCHHHHHH
Q 012111           93 KWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLK--PSVDVYTALVSAYGQSGLLDEAFS  170 (471)
Q Consensus        93 ~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~--~~~~~~~~li~~~~~~~~~~~a~~  170 (471)
                      .+..++.++..+-..+  +.++.+.+.|...|.-.|++..+..+...+......  .-...|-.+.++|-..|+++.|..
T Consensus       251 s~~~~~~ll~~ay~~n--~~nP~~l~~LAn~fyfK~dy~~v~~la~~ai~~t~~~~~~aes~Y~~gRs~Ha~Gd~ekA~~  328 (1018)
T KOG2002|consen  251 SYKKGVQLLQRAYKEN--NENPVALNHLANHFYFKKDYERVWHLAEHAIKNTENKSIKAESFYQLGRSYHAQGDFEKAFK  328 (1018)
T ss_pred             HHHHHHHHHHHHHhhc--CCCcHHHHHHHHHHhhcccHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHhhccHHHHHH
Confidence            3455555555555544  445555666666666666666666666665544211  112335555666666666666666


Q ss_pred             HHHHhhcCCCCCCCH--HHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccC----CHHHHHHHHH
Q 012111          171 TINDMKSVSDCKPDV--YTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAK----KFEEMESSFS  244 (471)
Q Consensus       171 ~~~~~~~~~~~~~~~--~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~----~~~~a~~~~~  244 (471)
                      .|.+..+.   .++.  ..+..+...+.+.|+++.+...|+...+.. +-+..+...|...|...+    ..+.|..++.
T Consensus       329 yY~~s~k~---~~d~~~l~~~GlgQm~i~~~dle~s~~~fEkv~k~~-p~~~etm~iLG~Lya~~~~~~~~~d~a~~~l~  404 (1018)
T KOG2002|consen  329 YYMESLKA---DNDNFVLPLVGLGQMYIKRGDLEESKFCFEKVLKQL-PNNYETMKILGCLYAHSAKKQEKRDKASNVLG  404 (1018)
T ss_pred             HHHHHHcc---CCCCccccccchhHHHHHhchHHHHHHHHHHHHHhC-cchHHHHHHHHhHHHhhhhhhHHHHHHHHHHH
Confidence            66555441   2222  233445555666666666666666655442 223444444444444432    3344444444


Q ss_pred             HHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHH----HhCCCCCCHHHHHHHHHHHHHcCCHHHHH---------
Q 012111          245 AMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEF----NLMGVKADIQTLNILTKSYGRAGMYDKMR---------  311 (471)
Q Consensus       245 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~----~~~~~~~~~~~~~~ll~~~~~~~~~~~a~---------  311 (471)
                      +..+..  +.|...|..+...+....-+ .++..|..+    ...+..+.....|.+...+...|++++|.         
T Consensus       405 K~~~~~--~~d~~a~l~laql~e~~d~~-~sL~~~~~A~d~L~~~~~~ip~E~LNNvaslhf~~g~~~~A~~~f~~A~~~  481 (1018)
T KOG2002|consen  405 KVLEQT--PVDSEAWLELAQLLEQTDPW-ASLDAYGNALDILESKGKQIPPEVLNNVASLHFRLGNIEKALEHFKSALGK  481 (1018)
T ss_pred             HHHhcc--cccHHHHHHHHHHHHhcChH-HHHHHHHHHHHHHHHcCCCCCHHHHHhHHHHHHHhcChHHHHHHHHHHhhh
Confidence            444332  33444444444433322222 113333222    12222344444444444444444444444         


Q ss_pred             -----------------------------------HHHHHHHhCCCCCCHH-HHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 012111          312 -----------------------------------SVMDFMQKRFFFPTVV-TYNIVIETFGKAGHIEKMEEYFKKMKHR  355 (471)
Q Consensus       312 -----------------------------------~~~~~~~~~~~~~~~~-~~~~li~~~~~~g~~~~a~~~~~~m~~~  355 (471)
                                                         ..|..+.+.  .|+.+ .|-.+....-..+...+|...++.....
T Consensus       482 ~~~~~n~de~~~~~lt~~YNlarl~E~l~~~~~A~e~Yk~Ilke--hp~YId~ylRl~~ma~~k~~~~ea~~~lk~~l~~  559 (1018)
T KOG2002|consen  482 LLEVANKDEGKSTNLTLKYNLARLLEELHDTEVAEEMYKSILKE--HPGYIDAYLRLGCMARDKNNLYEASLLLKDALNI  559 (1018)
T ss_pred             hhhhcCccccccchhHHHHHHHHHHHhhhhhhHHHHHHHHHHHH--CchhHHHHHHhhHHHHhccCcHHHHHHHHHHHhc
Confidence                                               444444443  11111 1111111111123444555554444322


Q ss_pred             C-C----------------------------------CCCHHHHHHHHHHHHh------------cCCHHHHHHHHHHHH
Q 012111          356 G-M----------------------------------KPNSITYCSLVSAYSK------------AGLIMKVDSILRQVE  388 (471)
Q Consensus       356 ~-~----------------------------------~p~~~~~~~li~~~~~------------~g~~~~a~~~~~~~~  388 (471)
                      . -                                  .+|..+...|.+.|..            .+..++|.++|.++.
T Consensus       560 d~~np~arsl~G~~~l~k~~~~~a~k~f~~i~~~~~~~~D~YsliaLGN~~~~~l~~~~rn~ek~kk~~~KAlq~y~kvL  639 (1018)
T KOG2002|consen  560 DSSNPNARSLLGNLHLKKSEWKPAKKKFETILKKTSTKTDAYSLIALGNVYIQALHNPSRNPEKEKKHQEKALQLYGKVL  639 (1018)
T ss_pred             ccCCcHHHHHHHHHHHhhhhhcccccHHHHHHhhhccCCchhHHHHhhHHHHHHhcccccChHHHHHHHHHHHHHHHHHH
Confidence            1 1                                  1333333444443332            235678999999999


Q ss_pred             hCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhhh
Q 012111          389 NSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAYNALGMTEAAQNLENKMIAMKE  462 (471)
Q Consensus       389 ~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~  462 (471)
                      +.++. |...-|.+.-.++..|++.+|..+|....+... -+..+|..+..+|...|++..|.++|+...+.-.
T Consensus       640 ~~dpk-N~yAANGIgiVLA~kg~~~~A~dIFsqVrEa~~-~~~dv~lNlah~~~e~~qy~~AIqmYe~~lkkf~  711 (1018)
T KOG2002|consen  640 RNDPK-NMYAANGIGIVLAEKGRFSEARDIFSQVREATS-DFEDVWLNLAHCYVEQGQYRLAIQMYENCLKKFY  711 (1018)
T ss_pred             hcCcc-hhhhccchhhhhhhccCchHHHHHHHHHHHHHh-hCCceeeeHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            88877 888889999999999999999999999988632 3567888899999999999999999998877654

>KOG0495 consensus HAT repeat protein [RNA processing and modification]

Probab=99.67  E-value=6e-11  Score=108.02  Aligned_cols=306  Identities=10%  Similarity=0.044  Sum_probs=177.1

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHH
Q 012111          151 VYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGY  230 (471)
Q Consensus       151 ~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~  230 (471)
                      +|..-.+.|.+.+.++-|..+|....+.  .+-+...|......=-..|..+....+|++.... ++-....|......+
T Consensus       518 tw~~da~~~~k~~~~~carAVya~alqv--fp~k~slWlra~~~ek~hgt~Esl~Allqkav~~-~pkae~lwlM~ake~  594 (913)
T KOG0495|consen  518 TWLDDAQSCEKRPAIECARAVYAHALQV--FPCKKSLWLRAAMFEKSHGTRESLEALLQKAVEQ-CPKAEILWLMYAKEK  594 (913)
T ss_pred             HHhhhHHHHHhcchHHHHHHHHHHHHhh--ccchhHHHHHHHHHHHhcCcHHHHHHHHHHHHHh-CCcchhHHHHHHHHH
Confidence            3444444455555555555566555542  2333444444444444455666666666666544 233344455555555


Q ss_pred             HccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHH
Q 012111          231 GKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKM  310 (471)
Q Consensus       231 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a  310 (471)
                      -..|+...|..++....+..  +.+...|...+..-.....++.|..+|.+...  ..++...|..-+...--.+..++|
T Consensus       595 w~agdv~~ar~il~~af~~~--pnseeiwlaavKle~en~e~eraR~llakar~--~sgTeRv~mKs~~~er~ld~~eeA  670 (913)
T KOG0495|consen  595 WKAGDVPAARVILDQAFEAN--PNSEEIWLAAVKLEFENDELERARDLLAKARS--ISGTERVWMKSANLERYLDNVEEA  670 (913)
T ss_pred             HhcCCcHHHHHHHHHHHHhC--CCcHHHHHHHHHHhhccccHHHHHHHHHHHhc--cCCcchhhHHHhHHHHHhhhHHHH
Confidence            66667777777666666553  33455666666666666667777777666554  345556665555555556666677


Q ss_pred             HHHHHHHHhCCCCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 012111          311 RSVMDFMQKRFFFPT-VVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVEN  389 (471)
Q Consensus       311 ~~~~~~~~~~~~~~~-~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~  389 (471)
                      .++++...+.  .|+ ...|-.+.+.+-+.++++.|.+.|..-.+. ++-....|..+...=-+.|.+-.|..++++..-
T Consensus       671 ~rllEe~lk~--fp~f~Kl~lmlGQi~e~~~~ie~aR~aY~~G~k~-cP~~ipLWllLakleEk~~~~~rAR~ildrarl  747 (913)
T KOG0495|consen  671 LRLLEEALKS--FPDFHKLWLMLGQIEEQMENIEMAREAYLQGTKK-CPNSIPLWLLLAKLEEKDGQLVRARSILDRARL  747 (913)
T ss_pred             HHHHHHHHHh--CCchHHHHHHHhHHHHHHHHHHHHHHHHHhcccc-CCCCchHHHHHHHHHHHhcchhhHHHHHHHHHh
Confidence            7666666554  222 334555555566666666666665543332 222334455555555566666667777766666


Q ss_pred             CCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhC-----------------------------CCCCCHHHHHHHHHH
Q 012111          390 SDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKER-----------------------------HCVPDNITFATMIQA  440 (471)
Q Consensus       390 ~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~-----------------------------~~~p~~~~~~~l~~~  440 (471)
                      .++. +...|-..|+.-.+.|+.+.|..+..+..+.                             .+.-|+.+...+...
T Consensus       748 kNPk-~~~lwle~Ir~ElR~gn~~~a~~lmakALQecp~sg~LWaEaI~le~~~~rkTks~DALkkce~dphVllaia~l  826 (913)
T KOG0495|consen  748 KNPK-NALLWLESIRMELRAGNKEQAELLMAKALQECPSSGLLWAEAIWLEPRPQRKTKSIDALKKCEHDPHVLLAIAKL  826 (913)
T ss_pred             cCCC-cchhHHHHHHHHHHcCCHHHHHHHHHHHHHhCCccchhHHHHHHhccCcccchHHHHHHHhccCCchhHHHHHHH
Confidence            6655 6666666666666777666666555443321                             233455566666677


Q ss_pred             HHhcCCHHHHHHHHHHHHHhhhcCCCC
Q 012111          441 YNALGMTEAAQNLENKMIAMKENSGKK  467 (471)
Q Consensus       441 ~~~~g~~~~A~~~~~~m~~~~~~~~~~  467 (471)
                      |+...+++.|++.|++.++.+|+.++.
T Consensus       827 fw~e~k~~kar~Wf~Ravk~d~d~GD~  853 (913)
T KOG0495|consen  827 FWSEKKIEKAREWFERAVKKDPDNGDA  853 (913)
T ss_pred             HHHHHHHHHHHHHHHHHHccCCccchH
Confidence            777777788888888887777776653

>PF13429 TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2_B

Probab=99.67  E-value=5.9e-16  Score=136.56  Aligned_cols=160  Identities=16%  Similarity=0.155  Sum_probs=51.1

Q ss_pred             HHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHH
Q 012111          223 YNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYG  302 (471)
Q Consensus       223 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~  302 (471)
                      +..++..+...++++++.++++.+.+......+...|..+...+.+.|+.++|++.+++..+.. +.|......++..+.
T Consensus       113 l~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~a~~~~~~G~~~~A~~~~~~al~~~-P~~~~~~~~l~~~li  191 (280)
T PF13429_consen  113 LLSALQLYYRLGDYDEAEELLEKLEELPAAPDSARFWLALAEIYEQLGDPDKALRDYRKALELD-PDDPDARNALAWLLI  191 (280)
T ss_dssp             -----H-HHHTT-HHHHHHHHHHHHH-T---T-HHHHHHHHHHHHHCCHHHHHHHHHHHHHHH--TT-HHHHHHHHHHHC
T ss_pred             hhHHHHHHHHHhHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHH
Confidence            3333444444444444444444433322222333334444444444444444444444443321 222333333444444


Q ss_pred             HcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHH
Q 012111          303 RAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDS  382 (471)
Q Consensus       303 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~  382 (471)
                      ..|+.+++..++....+.. +.++..+..+..++...|+.++|+.+|++..+.. +.|+.....+..++...|+.++|.+
T Consensus       192 ~~~~~~~~~~~l~~~~~~~-~~~~~~~~~la~~~~~lg~~~~Al~~~~~~~~~~-p~d~~~~~~~a~~l~~~g~~~~A~~  269 (280)
T PF13429_consen  192 DMGDYDEAREALKRLLKAA-PDDPDLWDALAAAYLQLGRYEEALEYLEKALKLN-PDDPLWLLAYADALEQAGRKDEALR  269 (280)
T ss_dssp             TTCHHHHHHHHHHHHHHH--HTSCCHCHHHHHHHHHHT-HHHHHHHHHHHHHHS-TT-HHHHHHHHHHHT----------
T ss_pred             HCCChHHHHHHHHHHHHHC-cCHHHHHHHHHHHhcccccccccccccccccccc-ccccccccccccccccccccccccc
Confidence            4444444333333333321 1122233334444444444444444444444321 2233334444444444444444444


Q ss_pred             HHH
Q 012111          383 ILR  385 (471)
Q Consensus       383 ~~~  385 (471)
                      +.+
T Consensus       270 ~~~  272 (280)
T PF13429_consen  270 LRR  272 (280)
T ss_dssp             ---
T ss_pred             ccc
Confidence            433

>KOG0547 consensus Translocase of outer mitochondrial membrane complex, subunit TOM70/TOM72 [Intracellular trafficking, secretion, and vesicular transport]

Probab=99.67  E-value=2.9e-12  Score=112.51  Aligned_cols=363  Identities=13%  Similarity=0.023  Sum_probs=252.2

Q ss_pred             HHHHHhhcHHHHHHHHHHhhhccCccCC-hhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCC-HHHHHHHHHHHHhcC
Q 012111           86 DEAIKQKKWQLALKIFGLLRQQQWYQAR-CQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPS-VDVYTALVSAYGQSG  163 (471)
Q Consensus        86 ~~~~~~~~~~~A~~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~-~~~~~~li~~~~~~~  163 (471)
                      ..+.+.|++++|++.|.++...   .|+ +..|.....+|...|+|+++.+--....+.  .|+ +..+..-..++-..|
T Consensus       123 N~~f~~kkY~eAIkyY~~AI~l---~p~epiFYsNraAcY~~lgd~~~Vied~TkALEl--~P~Y~KAl~RRA~A~E~lg  197 (606)
T KOG0547|consen  123 NKFFRNKKYDEAIKYYTQAIEL---CPDEPIFYSNRAACYESLGDWEKVIEDCTKALEL--NPDYVKALLRRASAHEQLG  197 (606)
T ss_pred             hhhhhcccHHHHHHHHHHHHhc---CCCCchhhhhHHHHHHHHhhHHHHHHHHHHHhhc--CcHHHHHHHHHHHHHHhhc
Confidence            3456899999999999999985   466 778899999999999999998887777765  333 334444455555666


Q ss_pred             CHHHHHH----------------------HHH---------Hhh-cCCCCCCCHHHHHHHHHHHHhc-------------
Q 012111          164 LLDEAFS----------------------TIN---------DMK-SVSDCKPDVYTYSILIKSCTKF-------------  198 (471)
Q Consensus       164 ~~~~a~~----------------------~~~---------~~~-~~~~~~~~~~~~~~ll~~~~~~-------------  198 (471)
                      ++++|+.                      ++.         .+. ....+-|+.....+....+...             
T Consensus       198 ~~~eal~D~tv~ci~~~F~n~s~~~~~eR~Lkk~a~~ka~e~~k~nr~p~lPS~~fi~syf~sF~~~~~~~~~~~~~ksD  277 (606)
T KOG0547|consen  198 KFDEALFDVTVLCILEGFQNASIEPMAERVLKKQAMKKAKEKLKENRPPVLPSATFIASYFGSFHADPKPLFDNKSDKSD  277 (606)
T ss_pred             cHHHHHHhhhHHHHhhhcccchhHHHHHHHHHHHHHHHHHHhhcccCCCCCCcHHHHHHHHhhccccccccccCCCccch
Confidence            6555432                      111         111 0123345555444444433210             


Q ss_pred             ------------C---CHHHHHHHHHHHHH---CCCCCC---------HHHHHHHHHHHHccCCHHHHHHHHHHHHHcCC
Q 012111          199 ------------H---RFDLIEKILAEMSY---LGIECS---------AVTYNTIIDGYGKAKKFEEMESSFSAMVESGG  251 (471)
Q Consensus       199 ------------~---~~~~a~~~~~~~~~---~g~~~~---------~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~  251 (471)
                                  +   .+..|.+.+.+-..   .....+         ..+.......+.-.|+.-.|.+-|+..++.. 
T Consensus       278 a~l~~~l~~l~~~~~e~Y~~a~~~~te~~~~~~~~~~~n~~d~~le~~A~al~~~gtF~fL~g~~~~a~~d~~~~I~l~-  356 (606)
T KOG0547|consen  278 AALAEALEALEKGLEEGYLKAYDKATEECLGSESSLSVNEIDAELEYMAEALLLRGTFHFLKGDSLGAQEDFDAAIKLD-  356 (606)
T ss_pred             hhHHHHHHHHHhhCchhHHHHHHHHHHHhhhhhhhccccccchhHHHHHHHHHHhhhhhhhcCCchhhhhhHHHHHhcC-
Confidence                        0   12222222211110   001111         2222222233455788999999999998764 


Q ss_pred             CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHH
Q 012111          252 CHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNI  331 (471)
Q Consensus       252 ~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  331 (471)
                       +.+...|..+..+|....+.++..+.|++..+.+ +.+..+|..-.+.+.-.+++++|..=|+......+. +...|..
T Consensus       357 -~~~~~lyI~~a~~y~d~~~~~~~~~~F~~A~~ld-p~n~dvYyHRgQm~flL~q~e~A~aDF~Kai~L~pe-~~~~~iQ  433 (606)
T KOG0547|consen  357 -PAFNSLYIKRAAAYADENQSEKMWKDFNKAEDLD-PENPDVYYHRGQMRFLLQQYEEAIADFQKAISLDPE-NAYAYIQ  433 (606)
T ss_pred             -cccchHHHHHHHHHhhhhccHHHHHHHHHHHhcC-CCCCchhHhHHHHHHHHHHHHHHHHHHHHHhhcChh-hhHHHHH
Confidence             2233348888889999999999999999998876 667778888888888889999999999988876332 4556666


Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCC-------cCHHHHHHHHH
Q 012111          332 VIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVI-------LDTPFFNCIIS  404 (471)
Q Consensus       332 li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~-------~~~~~~~~l~~  404 (471)
                      +..+..+.+++++++..|++.+.. ++--+..|+.....+...++++.|.+.|+..++....       +.+.+...++.
T Consensus       434 l~~a~Yr~~k~~~~m~~Fee~kkk-FP~~~Evy~~fAeiLtDqqqFd~A~k~YD~ai~LE~~~~~~~v~~~plV~Ka~l~  512 (606)
T KOG0547|consen  434 LCCALYRQHKIAESMKTFEEAKKK-FPNCPEVYNLFAEILTDQQQFDKAVKQYDKAIELEPREHLIIVNAAPLVHKALLV  512 (606)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHh-CCCCchHHHHHHHHHhhHHhHHHHHHHHHHHHhhccccccccccchhhhhhhHhh
Confidence            667777889999999999999887 4556789999999999999999999999998875433       11222223332


Q ss_pred             HHHhcCCHHHHHHHHHHHHhCCCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhh
Q 012111          405 AYGQAGDVEKMGELFLTMKERHCVP-DNITFATMIQAYNALGMTEAAQNLENKMIAMK  461 (471)
Q Consensus       405 ~~~~~g~~~~a~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~  461 (471)
                      .- -.+++..|..++.+..+.  .| ....|..|...-.+.|+.++|.++|++...+-
T Consensus       513 ~q-wk~d~~~a~~Ll~KA~e~--Dpkce~A~~tlaq~~lQ~~~i~eAielFEksa~lA  567 (606)
T KOG0547|consen  513 LQ-WKEDINQAENLLRKAIEL--DPKCEQAYETLAQFELQRGKIDEAIELFEKSAQLA  567 (606)
T ss_pred             hc-hhhhHHHHHHHHHHHHcc--CchHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHH
Confidence            22 238999999999999985  34 55788899999999999999999999876543

>KOG1915 consensus Cell cycle control protein (crooked neck) [Cell cycle control, cell division, chromosome partitioning]

Probab=99.67  E-value=1.4e-10  Score=101.77  Aligned_cols=203  Identities=8%  Similarity=0.036  Sum_probs=132.2

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHH-------HHHHHHHH---HHHcCCHHHHHHHHHHHHhCCCCC
Q 012111          255 DIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQ-------TLNILTKS---YGRAGMYDKMRSVMDFMQKRFFFP  324 (471)
Q Consensus       255 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~-------~~~~ll~~---~~~~~~~~~a~~~~~~~~~~~~~~  324 (471)
                      |-.+|-..+..-...|+.+...++|+..+.. ++|-..       .|..+=-+   -....+.+.+.+++....+. ++.
T Consensus       321 nYDsWfdylrL~e~~g~~~~Ire~yErAIan-vpp~~ekr~W~RYIYLWinYalyeEle~ed~ertr~vyq~~l~l-IPH  398 (677)
T KOG1915|consen  321 NYDSWFDYLRLEESVGDKDRIRETYERAIAN-VPPASEKRYWRRYIYLWINYALYEELEAEDVERTRQVYQACLDL-IPH  398 (677)
T ss_pred             CchHHHHHHHHHHhcCCHHHHHHHHHHHHcc-CCchhHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhh-cCc
Confidence            3334444455555556666666666666542 333211       11111111   12345666666666666552 222


Q ss_pred             CHHHHHHHH----HHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHH
Q 012111          325 TVVTYNIVI----ETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFN  400 (471)
Q Consensus       325 ~~~~~~~li----~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~  400 (471)
                      ...||.-+-    ..-.++.++..|.+++...+  |..|-..+|...|..=.+.++++.+..+++...+.++. +..+|.
T Consensus       399 kkFtFaKiWlmyA~feIRq~~l~~ARkiLG~AI--G~cPK~KlFk~YIelElqL~efDRcRkLYEkfle~~Pe-~c~~W~  475 (677)
T KOG1915|consen  399 KKFTFAKIWLMYAQFEIRQLNLTGARKILGNAI--GKCPKDKLFKGYIELELQLREFDRCRKLYEKFLEFSPE-NCYAWS  475 (677)
T ss_pred             ccchHHHHHHHHHHHHHHHcccHHHHHHHHHHh--ccCCchhHHHHHHHHHHHHhhHHHHHHHHHHHHhcChH-hhHHHH
Confidence            334444332    22345667777777777655  45788888888888888889999999999999988876 788888


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHhCCC-CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhhh
Q 012111          401 CIISAYGQAGDVEKMGELFLTMKERHC-VPDNITFATMIQAYNALGMTEAAQNLENKMIAMKE  462 (471)
Q Consensus       401 ~l~~~~~~~g~~~~a~~~~~~~~~~~~-~p~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~  462 (471)
                      .....-...|+.+.|..+|.-.++... .-....|.+.|..-...|.++.|+.++++.++...
T Consensus       476 kyaElE~~LgdtdRaRaifelAi~qp~ldmpellwkaYIdFEi~~~E~ekaR~LYerlL~rt~  538 (677)
T KOG1915|consen  476 KYAELETSLGDTDRARAIFELAISQPALDMPELLWKAYIDFEIEEGEFEKARALYERLLDRTQ  538 (677)
T ss_pred             HHHHHHHHhhhHHHHHHHHHHHhcCcccccHHHHHHHhhhhhhhcchHHHHHHHHHHHHHhcc
Confidence            888877888999999999998887521 11234566677777788999999999999887654

>KOG1126 consensus DNA-binding cell division cycle control protein [Cell cycle control, cell division, chromosome partitioning]

Probab=99.66  E-value=6.3e-14  Score=127.53  Aligned_cols=286  Identities=14%  Similarity=0.077  Sum_probs=227.2

Q ss_pred             CHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCC--CCCCHHHHHHHHHHHHccCCHHHHHH
Q 012111          164 LLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLG--IECSAVTYNTIIDGYGKAKKFEEMES  241 (471)
Q Consensus       164 ~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g--~~~~~~~~~~l~~~~~~~~~~~~a~~  241 (471)
                      +..+|+..|.++..  .+.-+......+..+|...+++++|.++|+.+.+..  ..-+..+|...+-.+-+.    -++.
T Consensus       334 ~~~~A~~~~~klp~--h~~nt~wvl~q~GrayFEl~~Y~~a~~~F~~~r~~~p~rv~~meiyST~LWHLq~~----v~Ls  407 (638)
T KOG1126|consen  334 NCREALNLFEKLPS--HHYNTGWVLSQLGRAYFELIEYDQAERIFSLVRRIEPYRVKGMEIYSTTLWHLQDE----VALS  407 (638)
T ss_pred             HHHHHHHHHHhhHH--hcCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccchhHHHHHHHHHHhh----HHHH
Confidence            56789999999665  233444667778889999999999999999998753  112567777777655332    1222


Q ss_pred             -HHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhC
Q 012111          242 -SFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKR  320 (471)
Q Consensus       242 -~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~  320 (471)
                       +-+.+.+..  +-...+|.++.++|...++++.|++.|++.++.+ +-...+|+.+..-+....++|.|...|......
T Consensus       408 ~Laq~Li~~~--~~sPesWca~GNcfSLQkdh~~Aik~f~RAiQld-p~faYayTLlGhE~~~~ee~d~a~~~fr~Al~~  484 (638)
T KOG1126|consen  408 YLAQDLIDTD--PNSPESWCALGNCFSLQKDHDTAIKCFKRAIQLD-PRFAYAYTLLGHESIATEEFDKAMKSFRKALGV  484 (638)
T ss_pred             HHHHHHHhhC--CCCcHHHHHhcchhhhhhHHHHHHHHHHHhhccC-CccchhhhhcCChhhhhHHHHhHHHHHHhhhcC
Confidence             223333442  4456789999999999999999999999998754 447888999999999999999999999988765


Q ss_pred             CCCCCHHHHH---HHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHH
Q 012111          321 FFFPTVVTYN---IVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTP  397 (471)
Q Consensus       321 ~~~~~~~~~~---~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~  397 (471)
                          ++..|+   -+...|.+.++++.|+-.|++..+-+ +-+.+....+...+-+.|+.++|+++++++...+++ |+.
T Consensus       485 ----~~rhYnAwYGlG~vy~Kqek~e~Ae~~fqkA~~IN-P~nsvi~~~~g~~~~~~k~~d~AL~~~~~A~~ld~k-n~l  558 (638)
T KOG1126|consen  485 ----DPRHYNAWYGLGTVYLKQEKLEFAEFHFQKAVEIN-PSNSVILCHIGRIQHQLKRKDKALQLYEKAIHLDPK-NPL  558 (638)
T ss_pred             ----CchhhHHHHhhhhheeccchhhHHHHHHHhhhcCC-ccchhHHhhhhHHHHHhhhhhHHHHHHHHHHhcCCC-Cch
Confidence                555555   45677899999999999999998854 336778888889999999999999999999988877 554


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHHhhhcCCC
Q 012111          398 FFNCIISAYGQAGDVEKMGELFLTMKERHCVPD-NITFATMIQAYNALGMTEAAQNLENKMIAMKENSGK  466 (471)
Q Consensus       398 ~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~-~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~~~~  466 (471)
                      .--..+..+...+++++|+..++++++.  .|+ ...|..+.+.|.+.|+.+.|+.-|--|.+++|++.+
T Consensus       559 ~~~~~~~il~~~~~~~eal~~LEeLk~~--vP~es~v~~llgki~k~~~~~~~Al~~f~~A~~ldpkg~~  626 (638)
T KOG1126|consen  559 CKYHRASILFSLGRYVEALQELEELKEL--VPQESSVFALLGKIYKRLGNTDLALLHFSWALDLDPKGAQ  626 (638)
T ss_pred             hHHHHHHHHHhhcchHHHHHHHHHHHHh--CcchHHHHHHHHHHHHHHccchHHHHhhHHHhcCCCccch
Confidence            4445567778889999999999999984  565 566777779999999999999999999999998776

>KOG0495 consensus HAT repeat protein [RNA processing and modification]

Probab=99.66  E-value=2e-11  Score=111.09  Aligned_cols=379  Identities=10%  Similarity=0.015  Sum_probs=189.5

Q ss_pred             CchHHHHHHHHHHHhhcHHHHHHHHHHhhhccCcc--CChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHH
Q 012111           77 WPKPVLEALDEAIKQKKWQLALKIFGLLRQQQWYQ--ARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTA  154 (471)
Q Consensus        77 ~~~~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~--~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~  154 (471)
                      ..+.++.-...|-..|..-....+.......+ +.  .-..+|..-...|.+.+.++-|..+|...++.- +-+...|..
T Consensus       478 ~rdqWl~eAe~~e~agsv~TcQAIi~avigig-vEeed~~~tw~~da~~~~k~~~~~carAVya~alqvf-p~k~slWlr  555 (913)
T KOG0495|consen  478 NRDQWLKEAEACEDAGSVITCQAIIRAVIGIG-VEEEDRKSTWLDDAQSCEKRPAIECARAVYAHALQVF-PCKKSLWLR  555 (913)
T ss_pred             cHHHHHHHHHHHhhcCChhhHHHHHHHHHhhc-cccchhHhHHhhhHHHHHhcchHHHHHHHHHHHHhhc-cchhHHHHH
Confidence            33444444444444444444444444443332 11  112344444445555555555555555444431 123344444


Q ss_pred             HHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccC
Q 012111          155 LVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAK  234 (471)
Q Consensus       155 li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~  234 (471)
                      ....--..|..+....+|++...  .++-....|......+-..|+...|..++....+.. +.+...|..-+.....+.
T Consensus       556 a~~~ek~hgt~Esl~Allqkav~--~~pkae~lwlM~ake~w~agdv~~ar~il~~af~~~-pnseeiwlaavKle~en~  632 (913)
T KOG0495|consen  556 AAMFEKSHGTRESLEALLQKAVE--QCPKAEILWLMYAKEKWKAGDVPAARVILDQAFEAN-PNSEEIWLAAVKLEFEND  632 (913)
T ss_pred             HHHHHHhcCcHHHHHHHHHHHHH--hCCcchhHHHHHHHHHHhcCCcHHHHHHHHHHHHhC-CCcHHHHHHHHHHhhccc
Confidence            44444444444444455544443  223333334444444444455555555554444432 224444444444444455


Q ss_pred             CHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHH
Q 012111          235 KFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVM  314 (471)
Q Consensus       235 ~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~  314 (471)
                      +++.|..+|.+....   .|+...|..-+..---.++.++|.+++++..+. ++.-...|..+.+.+-+.++++.|...|
T Consensus       633 e~eraR~llakar~~---sgTeRv~mKs~~~er~ld~~eeA~rllEe~lk~-fp~f~Kl~lmlGQi~e~~~~ie~aR~aY  708 (913)
T KOG0495|consen  633 ELERARDLLAKARSI---SGTERVWMKSANLERYLDNVEEALRLLEEALKS-FPDFHKLWLMLGQIEEQMENIEMAREAY  708 (913)
T ss_pred             cHHHHHHHHHHHhcc---CCcchhhHHHhHHHHHhhhHHHHHHHHHHHHHh-CCchHHHHHHHhHHHHHHHHHHHHHHHH
Confidence            555555555444332   333334443333333444445555555444432 1222334444444444444444444444


Q ss_pred             HHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhC----
Q 012111          315 DFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENS----  390 (471)
Q Consensus       315 ~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~----  390 (471)
                      ..-.+. ++-.+..|-.+...=-+.|.+-+|..++++.+-.+ +-+...|...|+.=.+.|+.+.|..++.+..+.    
T Consensus       709 ~~G~k~-cP~~ipLWllLakleEk~~~~~rAR~ildrarlkN-Pk~~~lwle~Ir~ElR~gn~~~a~~lmakALQecp~s  786 (913)
T KOG0495|consen  709 LQGTKK-CPNSIPLWLLLAKLEEKDGQLVRARSILDRARLKN-PKNALLWLESIRMELRAGNKEQAELLMAKALQECPSS  786 (913)
T ss_pred             Hhcccc-CCCCchHHHHHHHHHHHhcchhhHHHHHHHHHhcC-CCcchhHHHHHHHHHHcCCHHHHHHHHHHHHHhCCcc
Confidence            433322 11122333333333334444444444444444332 223444444444444444444444444333221    


Q ss_pred             -------------------------CCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcC
Q 012111          391 -------------------------DVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAYNALG  445 (471)
Q Consensus       391 -------------------------~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g  445 (471)
                                               ....|+.+.-.+...|....+++.|.+.|.+.+..+ +-+..+|.-+...+.++|
T Consensus       787 g~LWaEaI~le~~~~rkTks~DALkkce~dphVllaia~lfw~e~k~~kar~Wf~Ravk~d-~d~GD~wa~fykfel~hG  865 (913)
T KOG0495|consen  787 GLLWAEAIWLEPRPQRKTKSIDALKKCEHDPHVLLAIAKLFWSEKKIEKAREWFERAVKKD-PDNGDAWAWFYKFELRHG  865 (913)
T ss_pred             chhHHHHHHhccCcccchHHHHHHHhccCCchhHHHHHHHHHHHHHHHHHHHHHHHHHccC-CccchHHHHHHHHHHHhC
Confidence                                     012366677778888888899999999999999852 334578888889999999


Q ss_pred             CHHHHHHHHHHHHHhhhcCCCC
Q 012111          446 MTEAAQNLENKMIAMKENSGKK  467 (471)
Q Consensus       446 ~~~~A~~~~~~m~~~~~~~~~~  467 (471)
                      .-+.-.+++.+.....|..++.
T Consensus       866 ~eed~kev~~~c~~~EP~hG~~  887 (913)
T KOG0495|consen  866 TEEDQKEVLKKCETAEPTHGEL  887 (913)
T ss_pred             CHHHHHHHHHHHhccCCCCCcH
Confidence            9999999999999988877653

>PF13429 TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2_B

Probab=99.65  E-value=1.6e-15  Score=133.86  Aligned_cols=260  Identities=14%  Similarity=0.129  Sum_probs=92.5

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHHCC-CCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhc
Q 012111          191 LIKSCTKFHRFDLIEKILAEMSYLG-IECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNS  269 (471)
Q Consensus       191 ll~~~~~~~~~~~a~~~~~~~~~~g-~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  269 (471)
                      +...+.+.|+++.|+++++...... .+.+...|..+.......++++.|.+.++++.+.+  +-+...+..++.. ...
T Consensus        14 ~A~~~~~~~~~~~Al~~L~~~~~~~~~~~~~~~~~~~a~La~~~~~~~~A~~ay~~l~~~~--~~~~~~~~~l~~l-~~~   90 (280)
T PF13429_consen   14 LARLLYQRGDYEKALEVLKKAAQKIAPPDDPEYWRLLADLAWSLGDYDEAIEAYEKLLASD--KANPQDYERLIQL-LQD   90 (280)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc--ccccccccccccc-ccc
Confidence            3555556666666666664433322 12234444445555556667777777777766543  2233445555555 566


Q ss_pred             CCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCC-CCCCHHHHHHHHHHHHhcCCHHHHHHH
Q 012111          270 GNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRF-FFPTVVTYNIVIETFGKAGHIEKMEEY  348 (471)
Q Consensus       270 ~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~li~~~~~~g~~~~a~~~  348 (471)
                      +++++|.+++....+.  .++...+..++..+...++++++..+++.+.... ...+...|..+...+.+.|+.++|.+.
T Consensus        91 ~~~~~A~~~~~~~~~~--~~~~~~l~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~a~~~~~~G~~~~A~~~  168 (280)
T PF13429_consen   91 GDPEEALKLAEKAYER--DGDPRYLLSALQLYYRLGDYDEAEELLEKLEELPAAPDSARFWLALAEIYEQLGDPDKALRD  168 (280)
T ss_dssp             -----------------------------H-HHHTT-HHHHHHHHHHHHH-T---T-HHHHHHHHHHHHHCCHHHHHHHH
T ss_pred             cccccccccccccccc--ccccchhhHHHHHHHHHhHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHcCCHHHHHHH
Confidence            7777777776655433  2445556666677777777777777777765432 234566677777777778888888888


Q ss_pred             HHHHHHcCCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCC
Q 012111          349 FKKMKHRGMKP-NSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHC  427 (471)
Q Consensus       349 ~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~  427 (471)
                      +++..+.  .| |......++..+...|+.+++.++++...+.. ..|...+..+..+|...|+.++|+.+|++.... .
T Consensus       169 ~~~al~~--~P~~~~~~~~l~~~li~~~~~~~~~~~l~~~~~~~-~~~~~~~~~la~~~~~lg~~~~Al~~~~~~~~~-~  244 (280)
T PF13429_consen  169 YRKALEL--DPDDPDARNALAWLLIDMGDYDEAREALKRLLKAA-PDDPDLWDALAAAYLQLGRYEEALEYLEKALKL-N  244 (280)
T ss_dssp             HHHHHHH---TT-HHHHHHHHHHHCTTCHHHHHHHHHHHHHHH--HTSCCHCHHHHHHHHHHT-HHHHHHHHHHHHHH-S
T ss_pred             HHHHHHc--CCCCHHHHHHHHHHHHHCCChHHHHHHHHHHHHHC-cCHHHHHHHHHHHhccccccccccccccccccc-c
Confidence            8877775  34 46667777777777788877777777766554 235556677777888888888888888877764 1


Q ss_pred             CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 012111          428 VPDNITFATMIQAYNALGMTEAAQNLENKMIA  459 (471)
Q Consensus       428 ~p~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~  459 (471)
                      +.|+.+...+..++...|+.++|.++.+++..
T Consensus       245 p~d~~~~~~~a~~l~~~g~~~~A~~~~~~~~~  276 (280)
T PF13429_consen  245 PDDPLWLLAYADALEQAGRKDEALRLRRQALR  276 (280)
T ss_dssp             TT-HHHHHHHHHHHT-----------------
T ss_pred             cccccccccccccccccccccccccccccccc
Confidence            23666666777888888888888777766543

>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]

Probab=99.64  E-value=4.9e-12  Score=105.37  Aligned_cols=281  Identities=12%  Similarity=0.101  Sum_probs=152.9

Q ss_pred             CchHHHHHHHHHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCH------H
Q 012111           77 WPKPVLEALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSV------D  150 (471)
Q Consensus        77 ~~~~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~------~  150 (471)
                      .++.+..-++.+ -.++.++|++.|-.+.+.+  +.+.++.-+|...|-+.|..+.|+++.+.+.++   ||.      .
T Consensus        35 lsr~Yv~GlNfL-Ls~Q~dKAvdlF~e~l~~d--~~t~e~~ltLGnLfRsRGEvDRAIRiHQ~L~~s---pdlT~~qr~l  108 (389)
T COG2956          35 LSRDYVKGLNFL-LSNQPDKAVDLFLEMLQED--PETFEAHLTLGNLFRSRGEVDRAIRIHQTLLES---PDLTFEQRLL  108 (389)
T ss_pred             ccHHHHhHHHHH-hhcCcchHHHHHHHHHhcC--chhhHHHHHHHHHHHhcchHHHHHHHHHHHhcC---CCCchHHHHH
Confidence            344555555543 3556677777777777654  555666677777777777777777777777764   232      2


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCC----HHHHHHH
Q 012111          151 VYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECS----AVTYNTI  226 (471)
Q Consensus       151 ~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~----~~~~~~l  226 (471)
                      ....|.+-|...|-+|+|.++|..+... + ..-......|+..|-...+|++|+++-+++.+.|-.+.    ...|.-+
T Consensus       109 Al~qL~~Dym~aGl~DRAE~~f~~L~de-~-efa~~AlqqLl~IYQ~treW~KAId~A~~L~k~~~q~~~~eIAqfyCEL  186 (389)
T COG2956         109 ALQQLGRDYMAAGLLDRAEDIFNQLVDE-G-EFAEGALQQLLNIYQATREWEKAIDVAERLVKLGGQTYRVEIAQFYCEL  186 (389)
T ss_pred             HHHHHHHHHHHhhhhhHHHHHHHHHhcc-h-hhhHHHHHHHHHHHHHhhHHHHHHHHHHHHHHcCCccchhHHHHHHHHH
Confidence            3344555666677777777777766651 1 23344556666666666777777776666665543322    1233334


Q ss_pred             HHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCC
Q 012111          227 IDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGM  306 (471)
Q Consensus       227 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~  306 (471)
                      ...+....+++.|..++.+..+.+  +..+..-..+.......|+++.|.+.++...+.+...-..+...|..+|...|+
T Consensus       187 Aq~~~~~~~~d~A~~~l~kAlqa~--~~cvRAsi~lG~v~~~~g~y~~AV~~~e~v~eQn~~yl~evl~~L~~~Y~~lg~  264 (389)
T COG2956         187 AQQALASSDVDRARELLKKALQAD--KKCVRASIILGRVELAKGDYQKAVEALERVLEQNPEYLSEVLEMLYECYAQLGK  264 (389)
T ss_pred             HHHHhhhhhHHHHHHHHHHHHhhC--ccceehhhhhhHHHHhccchHHHHHHHHHHHHhChHHHHHHHHHHHHHHHHhCC
Confidence            444444556666666666665542  333333344445555666666666666665555444444455555556666666


Q ss_pred             HHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Q 012111          307 YDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAY  371 (471)
Q Consensus       307 ~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~  371 (471)
                      .++....+..+.+....++.  -..+..........+.|...+.+-...  +|+...+..+|..-
T Consensus       265 ~~~~~~fL~~~~~~~~g~~~--~l~l~~lie~~~G~~~Aq~~l~~Ql~r--~Pt~~gf~rl~~~~  325 (389)
T COG2956         265 PAEGLNFLRRAMETNTGADA--ELMLADLIELQEGIDAAQAYLTRQLRR--KPTMRGFHRLMDYH  325 (389)
T ss_pred             HHHHHHHHHHHHHccCCccH--HHHHHHHHHHhhChHHHHHHHHHHHhh--CCcHHHHHHHHHhh
Confidence            66655555555544322222  222222222233333444333333332  45555555555543

>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]

Probab=99.64  E-value=3.7e-12  Score=106.08  Aligned_cols=226  Identities=14%  Similarity=0.166  Sum_probs=120.5

Q ss_pred             CCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCH--HHHHHHHHHHHhcCCHHHH
Q 012111          127 CKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDV--YTYSILIKSCTKFHRFDLI  204 (471)
Q Consensus       127 ~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~--~~~~~ll~~~~~~~~~~~a  204 (471)
                      ..+.++|.++|-+|.+.... +..+.-+|.+.|-+.|..|+|+.+-+.+.+..+..-+.  .....|..-|...|-++.|
T Consensus        48 s~Q~dKAvdlF~e~l~~d~~-t~e~~ltLGnLfRsRGEvDRAIRiHQ~L~~spdlT~~qr~lAl~qL~~Dym~aGl~DRA  126 (389)
T COG2956          48 SNQPDKAVDLFLEMLQEDPE-TFEAHLTLGNLFRSRGEVDRAIRIHQTLLESPDLTFEQRLLALQQLGRDYMAAGLLDRA  126 (389)
T ss_pred             hcCcchHHHHHHHHHhcCch-hhHHHHHHHHHHHhcchHHHHHHHHHHHhcCCCCchHHHHHHHHHHHHHHHHhhhhhHH
Confidence            45667777777777764222 44555566777777777777777777776632222111  1233444556666666777


Q ss_pred             HHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCC---HHHHHHHHHHHHhcCCHHHHHHHHHH
Q 012111          205 EKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPD---IFTLNSMISAYGNSGNIEKMEKWYNE  281 (471)
Q Consensus       205 ~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~---~~~~~~l~~~~~~~~~~~~a~~~~~~  281 (471)
                      +.+|..+.+.| ..-......|+..|-...+|++|+++-+++.+.++-.-.   ...|.-+...+....+.+.|..++.+
T Consensus       127 E~~f~~L~de~-efa~~AlqqLl~IYQ~treW~KAId~A~~L~k~~~q~~~~eIAqfyCELAq~~~~~~~~d~A~~~l~k  205 (389)
T COG2956         127 EDIFNQLVDEG-EFAEGALQQLLNIYQATREWEKAIDVAERLVKLGGQTYRVEIAQFYCELAQQALASSDVDRARELLKK  205 (389)
T ss_pred             HHHHHHHhcch-hhhHHHHHHHHHHHHHhhHHHHHHHHHHHHHHcCCccchhHHHHHHHHHHHHHhhhhhHHHHHHHHHH
Confidence            77776666544 224455566666666666666666666666554321111   12244444444445555555555555


Q ss_pred             HHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 012111          282 FNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHR  355 (471)
Q Consensus       282 ~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  355 (471)
                      ..+.+ +..+..--.+.+.+...|++++|.+.++.+.+.+..--..+...|..+|...|+.++....+.++.+.
T Consensus       206 Alqa~-~~cvRAsi~lG~v~~~~g~y~~AV~~~e~v~eQn~~yl~evl~~L~~~Y~~lg~~~~~~~fL~~~~~~  278 (389)
T COG2956         206 ALQAD-KKCVRASIILGRVELAKGDYQKAVEALERVLEQNPEYLSEVLEMLYECYAQLGKPAEGLNFLRRAMET  278 (389)
T ss_pred             HHhhC-ccceehhhhhhHHHHhccchHHHHHHHHHHHHhChHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHc
Confidence            54433 22333333344445555555555555555555433333334444455555555555555555555443

>KOG1155 consensus Anaphase-promoting complex (APC), Cdc23 subunit [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]

Probab=99.64  E-value=7.6e-11  Score=103.10  Aligned_cols=333  Identities=11%  Similarity=0.046  Sum_probs=242.1

Q ss_pred             cCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHH--H
Q 012111          111 QARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYT--Y  188 (471)
Q Consensus       111 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~--~  188 (471)
                      ..|...+......+-+.|....|...|......    -+..|.+.+....-.-+.+.+..+..      +.+.|...  =
T Consensus       161 ~~D~fllYL~Gvv~k~~~~~s~A~~sfv~~v~~----~P~~W~AWleL~~lit~~e~~~~l~~------~l~~~~h~M~~  230 (559)
T KOG1155|consen  161 EKDEFLLYLYGVVLKELGLLSLAIDSFVEVVNR----YPWFWSAWLELSELITDIEILSILVV------GLPSDMHWMKK  230 (559)
T ss_pred             cchhHHHHHHHHHHHhhchHHHHHHHHHHHHhc----CCcchHHHHHHHHhhchHHHHHHHHh------cCcccchHHHH
Confidence            445555555666677888888899888887754    22334443333322333333322222      12222111  1


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCC-CCHHHHHHHHHHHH
Q 012111          189 SILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCH-PDIFTLNSMISAYG  267 (471)
Q Consensus       189 ~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~-~~~~~~~~l~~~~~  267 (471)
                      -.+..++......+++.+-.+.....|++-+...-+....+.....++++|+.+|+++.+..... .|..+|+.++-+-.
T Consensus       231 ~F~~~a~~el~q~~e~~~k~e~l~~~gf~~~~~i~~~~A~~~y~~rDfD~a~s~Feei~knDPYRl~dmdlySN~LYv~~  310 (559)
T KOG1155|consen  231 FFLKKAYQELHQHEEALQKKERLSSVGFPNSMYIKTQIAAASYNQRDFDQAESVFEEIRKNDPYRLDDMDLYSNVLYVKN  310 (559)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhccCCccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhcCCCcchhHHHHhHHHHHHh
Confidence            22345566677888888888899989988777666667777778899999999999998875333 25667777764432


Q ss_pred             hcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHH
Q 012111          268 NSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEE  347 (471)
Q Consensus       268 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~  347 (471)
                      ....    +.++.+-...--+--+.|...+.+.|.-.++.++|...|++..+.+.. ....|+.+..-|....+...|.+
T Consensus       311 ~~sk----Ls~LA~~v~~idKyR~ETCCiIaNYYSlr~eHEKAv~YFkRALkLNp~-~~~aWTLmGHEyvEmKNt~AAi~  385 (559)
T KOG1155|consen  311 DKSK----LSYLAQNVSNIDKYRPETCCIIANYYSLRSEHEKAVMYFKRALKLNPK-YLSAWTLMGHEYVEMKNTHAAIE  385 (559)
T ss_pred             hhHH----HHHHHHHHHHhccCCccceeeehhHHHHHHhHHHHHHHHHHHHhcCcc-hhHHHHHhhHHHHHhcccHHHHH
Confidence            2221    112211111111445567888889999999999999999999887543 45678888899999999999999


Q ss_pred             HHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCC
Q 012111          348 YFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHC  427 (471)
Q Consensus       348 ~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~  427 (471)
                      -|++.++-. +-|-..|-.|.++|.-.+...-|+-.|++.....+. |...|.+|..+|.+.++.++|++.|.+....|-
T Consensus       386 sYRrAvdi~-p~DyRAWYGLGQaYeim~Mh~YaLyYfqkA~~~kPn-DsRlw~aLG~CY~kl~~~~eAiKCykrai~~~d  463 (559)
T KOG1155|consen  386 SYRRAVDIN-PRDYRAWYGLGQAYEIMKMHFYALYYFQKALELKPN-DSRLWVALGECYEKLNRLEEAIKCYKRAILLGD  463 (559)
T ss_pred             HHHHHHhcC-chhHHHHhhhhHHHHHhcchHHHHHHHHHHHhcCCC-chHHHHHHHHHHHHhccHHHHHHHHHHHHhccc
Confidence            999999863 447889999999999999999999999999988766 899999999999999999999999999988653


Q ss_pred             CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhh
Q 012111          428 VPDNITFATMIQAYNALGMTEAAQNLENKMIAMK  461 (471)
Q Consensus       428 ~p~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~  461 (471)
                      . +...+..|.+.+-+.++..+|...+++-++..
T Consensus       464 t-e~~~l~~LakLye~l~d~~eAa~~yek~v~~~  496 (559)
T KOG1155|consen  464 T-EGSALVRLAKLYEELKDLNEAAQYYEKYVEVS  496 (559)
T ss_pred             c-chHHHHHHHHHHHHHHhHHHHHHHHHHHHHHH
Confidence            3 66888899999999999999999988877643

>KOG2076 consensus RNA polymerase III transcription factor TFIIIC [Transcription]

Probab=99.63  E-value=1.1e-11  Score=116.77  Aligned_cols=334  Identities=14%  Similarity=0.080  Sum_probs=258.3

Q ss_pred             HHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHH
Q 012111          117 FTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCT  196 (471)
Q Consensus       117 ~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~  196 (471)
                      .-.....+...|++++|.+++.+.++.... ....|..|...|-..|+.+++...+-..-.  -.+-|...|..+.....
T Consensus       142 ll~eAN~lfarg~~eeA~~i~~EvIkqdp~-~~~ay~tL~~IyEqrGd~eK~l~~~llAAH--L~p~d~e~W~~ladls~  218 (895)
T KOG2076|consen  142 LLGEANNLFARGDLEEAEEILMEVIKQDPR-NPIAYYTLGEIYEQRGDIEKALNFWLLAAH--LNPKDYELWKRLADLSE  218 (895)
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHHHhCcc-chhhHHHHHHHHHHcccHHHHHHHHHHHHh--cCCCChHHHHHHHHHHH
Confidence            333444455569999999999999987544 788999999999999999999988766654  23567788999999999


Q ss_pred             hcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHH----HHHHHHHHhcCCH
Q 012111          197 KFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTL----NSMISAYGNSGNI  272 (471)
Q Consensus       197 ~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~----~~l~~~~~~~~~~  272 (471)
                      +.|+++.|.-.|.+.++.. +++...+-.-+..|-+.|+...|.+.|.++.+..+ +.|..-+    ...++.+...++.
T Consensus       219 ~~~~i~qA~~cy~rAI~~~-p~n~~~~~ers~L~~~~G~~~~Am~~f~~l~~~~p-~~d~er~~d~i~~~~~~~~~~~~~  296 (895)
T KOG2076|consen  219 QLGNINQARYCYSRAIQAN-PSNWELIYERSSLYQKTGDLKRAMETFLQLLQLDP-PVDIERIEDLIRRVAHYFITHNER  296 (895)
T ss_pred             hcccHHHHHHHHHHHHhcC-CcchHHHHHHHHHHHHhChHHHHHHHHHHHHhhCC-chhHHHHHHHHHHHHHHHHHhhHH
Confidence            9999999999999999886 66777777778889999999999999999988642 2222222    2345667778888


Q ss_pred             HHHHHHHHHHHhC-CCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCC---------------------------C
Q 012111          273 EKMEKWYNEFNLM-GVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFF---------------------------P  324 (471)
Q Consensus       273 ~~a~~~~~~~~~~-~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~---------------------------~  324 (471)
                      +.|.+.++..... +-..+...++.++..|.+...++.+......+......                           +
T Consensus       297 e~a~~~le~~~s~~~~~~~~ed~ni~ael~l~~~q~d~~~~~i~~~~~r~~e~d~~e~~~~~~~~~~~~~~~~~~~~~s~  376 (895)
T KOG2076|consen  297 ERAAKALEGALSKEKDEASLEDLNILAELFLKNKQSDKALMKIVDDRNRESEKDDSEWDTDERRREEPNALCEVGKELSY  376 (895)
T ss_pred             HHHHHHHHHHHhhccccccccHHHHHHHHHHHhHHHHHhhHHHHHHhccccCCChhhhhhhhhccccccccccCCCCCCc
Confidence            9999998887662 22456667889999999999999998888777652211                           2


Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCC--CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHH
Q 012111          325 TVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKP--NSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCI  402 (471)
Q Consensus       325 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p--~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l  402 (471)
                      +... ..++-++......+....+..........|  +...|.-+..+|...|.+.+|..+|..+......-+...|-.+
T Consensus       377 ~l~v-~rl~icL~~L~~~e~~e~ll~~l~~~n~~~~d~~dL~~d~a~al~~~~~~~~Al~~l~~i~~~~~~~~~~vw~~~  455 (895)
T KOG2076|consen  377 DLRV-IRLMICLVHLKERELLEALLHFLVEDNVWVSDDVDLYLDLADALTNIGKYKEALRLLSPITNREGYQNAFVWYKL  455 (895)
T ss_pred             cchh-HhHhhhhhcccccchHHHHHHHHHHhcCChhhhHHHHHHHHHHHHhcccHHHHHHHHHHHhcCccccchhhhHHH
Confidence            2222 122333444445555555555556555333  5678899999999999999999999999987766688899999


Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhCCCCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 012111          403 ISAYGQAGDVEKMGELFLTMKERHCVPD-NITFATMIQAYNALGMTEAAQNLENKMI  458 (471)
Q Consensus       403 ~~~~~~~g~~~~a~~~~~~~~~~~~~p~-~~~~~~l~~~~~~~g~~~~A~~~~~~m~  458 (471)
                      .++|...|.+++|.+.|+..+..  .|+ ...-.+|-..+-+.|+.++|.+.++.+.
T Consensus       456 a~c~~~l~e~e~A~e~y~kvl~~--~p~~~D~Ri~Lasl~~~~g~~EkalEtL~~~~  510 (895)
T KOG2076|consen  456 ARCYMELGEYEEAIEFYEKVLIL--APDNLDARITLASLYQQLGNHEKALETLEQII  510 (895)
T ss_pred             HHHHHHHhhHHHHHHHHHHHHhc--CCCchhhhhhHHHHHHhcCCHHHHHHHHhccc
Confidence            99999999999999999999874  454 4455567788899999999999999887

>COG3071 HemY Uncharacterized enzyme of heme biosynthesis [Coenzyme metabolism]

Probab=99.63  E-value=2.2e-11  Score=104.66  Aligned_cols=292  Identities=12%  Similarity=0.097  Sum_probs=195.1

Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHH
Q 012111          162 SGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMES  241 (471)
Q Consensus       162 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~a~~  241 (471)
                      .|++..|..+..+-.+ .+ +-....|..-..+.-..|+.+.+-+++.+.-+.--.++...+-...+.....|+++.|..
T Consensus        97 eG~~~qAEkl~~rnae-~~-e~p~l~~l~aA~AA~qrgd~~~an~yL~eaae~~~~~~l~v~ltrarlll~~~d~~aA~~  174 (400)
T COG3071          97 EGDFQQAEKLLRRNAE-HG-EQPVLAYLLAAEAAQQRGDEDRANRYLAEAAELAGDDTLAVELTRARLLLNRRDYPAARE  174 (400)
T ss_pred             cCcHHHHHHHHHHhhh-cC-cchHHHHHHHHHHHHhcccHHHHHHHHHHHhccCCCchHHHHHHHHHHHHhCCCchhHHH
Confidence            5667777766666554 22 222334445555566666777777777666655224445555556666666777777777


Q ss_pred             HHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCH-------HHHHHHHHHHHHcCCHHHHHHHH
Q 012111          242 SFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADI-------QTLNILTKSYGRAGMYDKMRSVM  314 (471)
Q Consensus       242 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~-------~~~~~ll~~~~~~~~~~~a~~~~  314 (471)
                      -+.++.+..  +...........+|.+.|++.....++..+.+.+.-.+.       .+|..+++-....+..+.-...+
T Consensus       175 ~v~~ll~~~--pr~~~vlrLa~r~y~~~g~~~~ll~~l~~L~ka~~l~~~e~~~le~~a~~glL~q~~~~~~~~gL~~~W  252 (400)
T COG3071         175 NVDQLLEMT--PRHPEVLRLALRAYIRLGAWQALLAILPKLRKAGLLSDEEAARLEQQAWEGLLQQARDDNGSEGLKTWW  252 (400)
T ss_pred             HHHHHHHhC--cCChHHHHHHHHHHHHhccHHHHHHHHHHHHHccCCChHHHHHHHHHHHHHHHHHHhccccchHHHHHH
Confidence            776666653  444556666667777777777777777777666654443       24555555555555555544555


Q ss_pred             HHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCc
Q 012111          315 DFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVIL  394 (471)
Q Consensus       315 ~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~  394 (471)
                      +..... ..-++..-..++.-+.+.|+.++|.++..+..+.+..|+   .. ..-.+.+.++.+.-.+..+...+..+. 
T Consensus       253 ~~~pr~-lr~~p~l~~~~a~~li~l~~~~~A~~~i~~~Lk~~~D~~---L~-~~~~~l~~~d~~~l~k~~e~~l~~h~~-  326 (400)
T COG3071         253 KNQPRK-LRNDPELVVAYAERLIRLGDHDEAQEIIEDALKRQWDPR---LC-RLIPRLRPGDPEPLIKAAEKWLKQHPE-  326 (400)
T ss_pred             HhccHH-hhcChhHHHHHHHHHHHcCChHHHHHHHHHHHHhccChh---HH-HHHhhcCCCCchHHHHHHHHHHHhCCC-
Confidence            544332 233566666778888888999999998888888876665   22 222345667777777777666655443 


Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhhhcCC
Q 012111          395 DTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAYNALGMTEAAQNLENKMIAMKENSG  465 (471)
Q Consensus       395 ~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~~~  465 (471)
                      ++..+.+|...|.+.+.|.+|.+.|+...+  ..|+..+|+.+..++.+.|+..+|.+..++....-..++
T Consensus       327 ~p~L~~tLG~L~~k~~~w~kA~~~leaAl~--~~~s~~~~~~la~~~~~~g~~~~A~~~r~e~L~~~~~~~  395 (400)
T COG3071         327 DPLLLSTLGRLALKNKLWGKASEALEAALK--LRPSASDYAELADALDQLGEPEEAEQVRREALLLTRQPN  395 (400)
T ss_pred             ChhHHHHHHHHHHHhhHHHHHHHHHHHHHh--cCCChhhHHHHHHHHHHcCChHHHHHHHHHHHHHhcCCC
Confidence            557888899999999999999999997776  478999999999999999999999999888876554443

>KOG1126 consensus DNA-binding cell division cycle control protein [Cell cycle control, cell division, chromosome partitioning]

Probab=99.62  E-value=8.4e-13  Score=120.32  Aligned_cols=200  Identities=10%  Similarity=0.016  Sum_probs=87.2

Q ss_pred             CHHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHH
Q 012111          219 SAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILT  298 (471)
Q Consensus       219 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll  298 (471)
                      .+.+|.++..+|.-+++.+.|++.|++..+.+  +....+|+.+..-+.....+|.|...|+..+... +-+-..|--+.
T Consensus       420 sPesWca~GNcfSLQkdh~~Aik~f~RAiQld--p~faYayTLlGhE~~~~ee~d~a~~~fr~Al~~~-~rhYnAwYGlG  496 (638)
T KOG1126|consen  420 SPESWCALGNCFSLQKDHDTAIKCFKRAIQLD--PRFAYAYTLLGHESIATEEFDKAMKSFRKALGVD-PRHYNAWYGLG  496 (638)
T ss_pred             CcHHHHHhcchhhhhhHHHHHHHHHHHhhccC--CccchhhhhcCChhhhhHHHHhHHHHHHhhhcCC-chhhHHHHhhh
Confidence            34445555555555555555555555444321  1134444444444444445555555554443211 11111222233


Q ss_pred             HHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHH
Q 012111          299 KSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIM  378 (471)
Q Consensus       299 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~  378 (471)
                      -.|.+.++++.|+-.|+...+.++. +.+....+...+-+.|+.++|++++++...... -|+..--.-+..+...++.+
T Consensus       497 ~vy~Kqek~e~Ae~~fqkA~~INP~-nsvi~~~~g~~~~~~k~~d~AL~~~~~A~~ld~-kn~l~~~~~~~il~~~~~~~  574 (638)
T KOG1126|consen  497 TVYLKQEKLEFAEFHFQKAVEINPS-NSVILCHIGRIQHQLKRKDKALQLYEKAIHLDP-KNPLCKYHRASILFSLGRYV  574 (638)
T ss_pred             hheeccchhhHHHHHHHhhhcCCcc-chhHHhhhhHHHHHhhhhhHHHHHHHHHHhcCC-CCchhHHHHHHHHHhhcchH
Confidence            3444555555555555544443222 333333444444445555555555555444321 12222223333344445555


Q ss_pred             HHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 012111          379 KVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKE  424 (471)
Q Consensus       379 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~  424 (471)
                      +|...++++++.-+. +..+|..+...|.+.|+.+.|+.-|--+.+
T Consensus       575 eal~~LEeLk~~vP~-es~v~~llgki~k~~~~~~~Al~~f~~A~~  619 (638)
T KOG1126|consen  575 EALQELEELKELVPQ-ESSVFALLGKIYKRLGNTDLALLHFSWALD  619 (638)
T ss_pred             HHHHHHHHHHHhCcc-hHHHHHHHHHHHHHHccchHHHHhhHHHhc
Confidence            555555555444322 344444444555555555555555544444

>COG3071 HemY Uncharacterized enzyme of heme biosynthesis [Coenzyme metabolism]

Probab=99.62  E-value=3.6e-11  Score=103.41  Aligned_cols=292  Identities=10%  Similarity=0.089  Sum_probs=147.0

Q ss_pred             hhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHH
Q 012111           91 QKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAFS  170 (471)
Q Consensus        91 ~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~  170 (471)
                      .|+|.+|.+......+.+  .-....|..-..+.-+.|+.+.+-..+.+..+....++...+-+..+.....|++..|..
T Consensus        97 eG~~~qAEkl~~rnae~~--e~p~l~~l~aA~AA~qrgd~~~an~yL~eaae~~~~~~l~v~ltrarlll~~~d~~aA~~  174 (400)
T COG3071          97 EGDFQQAEKLLRRNAEHG--EQPVLAYLLAAEAAQQRGDEDRANRYLAEAAELAGDDTLAVELTRARLLLNRRDYPAARE  174 (400)
T ss_pred             cCcHHHHHHHHHHhhhcC--cchHHHHHHHHHHHHhcccHHHHHHHHHHHhccCCCchHHHHHHHHHHHHhCCCchhHHH
Confidence            455555555555544432  122223333344444455555555555555544223344444444445555555555555


Q ss_pred             HHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHcC
Q 012111          171 TINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESG  250 (471)
Q Consensus       171 ~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  250 (471)
                      -++++.+..  +.++........+|.+.|++.....++..|.+.|+--+...-                     .     
T Consensus       175 ~v~~ll~~~--pr~~~vlrLa~r~y~~~g~~~~ll~~l~~L~ka~~l~~~e~~---------------------~-----  226 (400)
T COG3071         175 NVDQLLEMT--PRHPEVLRLALRAYIRLGAWQALLAILPKLRKAGLLSDEEAA---------------------R-----  226 (400)
T ss_pred             HHHHHHHhC--cCChHHHHHHHHHHHHhccHHHHHHHHHHHHHccCCChHHHH---------------------H-----
Confidence            555544421  233444455555555555555555555555555433222100                     0     


Q ss_pred             CCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHH
Q 012111          251 GCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYN  330 (471)
Q Consensus       251 ~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~  330 (471)
                         -...+|..++.-....+..+.-...|+..-.. .+.++..-..++.-+.++|+.++|.++..+..+++..|...   
T Consensus       227 ---le~~a~~glL~q~~~~~~~~gL~~~W~~~pr~-lr~~p~l~~~~a~~li~l~~~~~A~~~i~~~Lk~~~D~~L~---  299 (400)
T COG3071         227 ---LEQQAWEGLLQQARDDNGSEGLKTWWKNQPRK-LRNDPELVVAYAERLIRLGDHDEAQEIIEDALKRQWDPRLC---  299 (400)
T ss_pred             ---HHHHHHHHHHHHHhccccchHHHHHHHhccHH-hhcChhHHHHHHHHHHHcCChHHHHHHHHHHHHhccChhHH---
Confidence               01124555555555555555544555554322 24445555555666666666666666666666655544411   


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcC
Q 012111          331 IVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAG  410 (471)
Q Consensus       331 ~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g  410 (471)
                       ..-.+.+-++.+.-.+..+.-.+. .+-++..+..|...|.+.+.+.+|.+.|+...+.  .|+...|+.+..++.+.|
T Consensus       300 -~~~~~l~~~d~~~l~k~~e~~l~~-h~~~p~L~~tLG~L~~k~~~w~kA~~~leaAl~~--~~s~~~~~~la~~~~~~g  375 (400)
T COG3071         300 -RLIPRLRPGDPEPLIKAAEKWLKQ-HPEDPLLLSTLGRLALKNKLWGKASEALEAALKL--RPSASDYAELADALDQLG  375 (400)
T ss_pred             -HHHhhcCCCCchHHHHHHHHHHHh-CCCChhHHHHHHHHHHHhhHHHHHHHHHHHHHhc--CCChhhHHHHHHHHHHcC
Confidence             112234445555555555544433 1223455666666666666666666666655543  356666666666666666


Q ss_pred             CHHHHHHHHHHHH
Q 012111          411 DVEKMGELFLTMK  423 (471)
Q Consensus       411 ~~~~a~~~~~~~~  423 (471)
                      +..+|.++.++..
T Consensus       376 ~~~~A~~~r~e~L  388 (400)
T COG3071         376 EPEEAEQVRREAL  388 (400)
T ss_pred             ChHHHHHHHHHHH
Confidence            6666666666554

>KOG1155 consensus Anaphase-promoting complex (APC), Cdc23 subunit [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]

Probab=99.57  E-value=4.8e-11  Score=104.32  Aligned_cols=314  Identities=12%  Similarity=0.071  Sum_probs=146.8

Q ss_pred             HhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHH--HHHHHHHhcCCHHH
Q 012111           90 KQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYT--ALVSAYGQSGLLDE  167 (471)
Q Consensus        90 ~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~--~li~~~~~~~~~~~  167 (471)
                      +.|..+.|+..|......-  |-.-.+|..|...+.   +.+.+..+..     |.+.+.....  .+..++-...+.++
T Consensus       176 ~~~~~s~A~~sfv~~v~~~--P~~W~AWleL~~lit---~~e~~~~l~~-----~l~~~~h~M~~~F~~~a~~el~q~~e  245 (559)
T KOG1155|consen  176 ELGLLSLAIDSFVEVVNRY--PWFWSAWLELSELIT---DIEILSILVV-----GLPSDMHWMKKFFLKKAYQELHQHEE  245 (559)
T ss_pred             hhchHHHHHHHHHHHHhcC--CcchHHHHHHHHhhc---hHHHHHHHHh-----cCcccchHHHHHHHHHHHHHHHHHHH
Confidence            4567778888887776542  434344444433322   1222111111     1111111111  12234444445555


Q ss_pred             HHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCC--CCCHHHHHHHHHHHHccCCHHHHHHHHHH
Q 012111          168 AFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGI--ECSAVTYNTIIDGYGKAKKFEEMESSFSA  245 (471)
Q Consensus       168 a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~--~~~~~~~~~l~~~~~~~~~~~~a~~~~~~  245 (471)
                      +++-.+.... .|.+-+...-+....+.....|+++|+.+|+++.+...  --|..+|..++-.-....++.-   +-+.
T Consensus       246 ~~~k~e~l~~-~gf~~~~~i~~~~A~~~y~~rDfD~a~s~Feei~knDPYRl~dmdlySN~LYv~~~~skLs~---LA~~  321 (559)
T KOG1155|consen  246 ALQKKERLSS-VGFPNSMYIKTQIAAASYNQRDFDQAESVFEEIRKNDPYRLDDMDLYSNVLYVKNDKSKLSY---LAQN  321 (559)
T ss_pred             HHHHHHHHHh-ccCCccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhcCCCcchhHHHHhHHHHHHhhhHHHHH---HHHH
Confidence            5555555544 34333333333333334445556666666666655420  0134444444433221111110   1111


Q ss_pred             HHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCC
Q 012111          246 MVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPT  325 (471)
Q Consensus       246 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~  325 (471)
                      ..+.+...|  .|+..+.+-|.-.++.+.|...|+...+.+ +.....|+.+.+-|....+...|..-++...+..+. |
T Consensus       322 v~~idKyR~--ETCCiIaNYYSlr~eHEKAv~YFkRALkLN-p~~~~aWTLmGHEyvEmKNt~AAi~sYRrAvdi~p~-D  397 (559)
T KOG1155|consen  322 VSNIDKYRP--ETCCIIANYYSLRSEHEKAVMYFKRALKLN-PKYLSAWTLMGHEYVEMKNTHAAIESYRRAVDINPR-D  397 (559)
T ss_pred             HHHhccCCc--cceeeehhHHHHHHhHHHHHHHHHHHHhcC-cchhHHHHHhhHHHHHhcccHHHHHHHHHHHhcCch-h
Confidence            111111222  345555555555555555555555555443 334445555555555555555555555555554222 4


Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHH
Q 012111          326 VVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISA  405 (471)
Q Consensus       326 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  405 (471)
                      -..|-.|.++|...+-..-|+-.|++..... +-|...|..|..+|.+.++.++|++.|.+....+-. +...+..|...
T Consensus       398 yRAWYGLGQaYeim~Mh~YaLyYfqkA~~~k-PnDsRlw~aLG~CY~kl~~~~eAiKCykrai~~~dt-e~~~l~~LakL  475 (559)
T KOG1155|consen  398 YRAWYGLGQAYEIMKMHFYALYYFQKALELK-PNDSRLWVALGECYEKLNRLEEAIKCYKRAILLGDT-EGSALVRLAKL  475 (559)
T ss_pred             HHHHhhhhHHHHHhcchHHHHHHHHHHHhcC-CCchHHHHHHHHHHHHhccHHHHHHHHHHHHhcccc-chHHHHHHHHH
Confidence            4555555555555555555555555555431 224555555555555555555555555555554422 44555555555


Q ss_pred             HHhcCCHHHHHHHHHHHH
Q 012111          406 YGQAGDVEKMGELFLTMK  423 (471)
Q Consensus       406 ~~~~g~~~~a~~~~~~~~  423 (471)
                      |-+.++..+|...|.+.+
T Consensus       476 ye~l~d~~eAa~~yek~v  493 (559)
T KOG1155|consen  476 YEELKDLNEAAQYYEKYV  493 (559)
T ss_pred             HHHHHhHHHHHHHHHHHH
Confidence            555555555555555444

>KOG1915 consensus Cell cycle control protein (crooked neck) [Cell cycle control, cell division, chromosome partitioning]

Probab=99.52  E-value=1.1e-08  Score=90.19  Aligned_cols=241  Identities=10%  Similarity=0.068  Sum_probs=175.0

Q ss_pred             CCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCH--HHHHHHHH-----H---HHhcCCHHHHHHHHHHHHhCC
Q 012111          217 ECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDI--FTLNSMIS-----A---YGNSGNIEKMEKWYNEFNLMG  286 (471)
Q Consensus       217 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~--~~~~~l~~-----~---~~~~~~~~~a~~~~~~~~~~~  286 (471)
                      +.|-.+|--.++.-...|+.+...++|++.+..  ++|-.  ..|...|-     +   -....|.+.+.++|+...+. 
T Consensus       319 p~nYDsWfdylrL~e~~g~~~~Ire~yErAIan--vpp~~ekr~W~RYIYLWinYalyeEle~ed~ertr~vyq~~l~l-  395 (677)
T KOG1915|consen  319 PYNYDSWFDYLRLEESVGDKDRIRETYERAIAN--VPPASEKRYWRRYIYLWINYALYEELEAEDVERTRQVYQACLDL-  395 (677)
T ss_pred             CCCchHHHHHHHHHHhcCCHHHHHHHHHHHHcc--CCchhHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhh-
Confidence            334555566666666778888888888888765  45522  12222221     1   13468899999999998873 


Q ss_pred             CCCCHHHHHHHHHH----HHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHH
Q 012111          287 VKADIQTLNILTKS----YGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSI  362 (471)
Q Consensus       287 ~~~~~~~~~~ll~~----~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~  362 (471)
                      ++....||..+=-.    -.++.++..|.+++.....  ..|...+|...|..=.+.++++.+..+|++.+.-+ +-|..
T Consensus       396 IPHkkFtFaKiWlmyA~feIRq~~l~~ARkiLG~AIG--~cPK~KlFk~YIelElqL~efDRcRkLYEkfle~~-Pe~c~  472 (677)
T KOG1915|consen  396 IPHKKFTFAKIWLMYAQFEIRQLNLTGARKILGNAIG--KCPKDKLFKGYIELELQLREFDRCRKLYEKFLEFS-PENCY  472 (677)
T ss_pred             cCcccchHHHHHHHHHHHHHHHcccHHHHHHHHHHhc--cCCchhHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-hHhhH
Confidence            46666666554433    3467889999999987654  57888899999999999999999999999999875 34778


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhCC-CCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHH
Q 012111          363 TYCSLVSAYSKAGLIMKVDSILRQVENSD-VILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAY  441 (471)
Q Consensus       363 ~~~~li~~~~~~g~~~~a~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~  441 (471)
                      +|......=...|+.+.|..+|..+++.. .......|.+.|..-...|.++.|..+++++.+.  .+...+|..+...-
T Consensus       473 ~W~kyaElE~~LgdtdRaRaifelAi~qp~ldmpellwkaYIdFEi~~~E~ekaR~LYerlL~r--t~h~kvWisFA~fe  550 (677)
T KOG1915|consen  473 AWSKYAELETSLGDTDRARAIFELAISQPALDMPELLWKAYIDFEIEEGEFEKARALYERLLDR--TQHVKVWISFAKFE  550 (677)
T ss_pred             HHHHHHHHHHHhhhHHHHHHHHHHHhcCcccccHHHHHHHhhhhhhhcchHHHHHHHHHHHHHh--cccchHHHhHHHHh
Confidence            88888888889999999999999988653 2233456777777778899999999999999985  44555666655433


Q ss_pred             H-----hcC-----------CHHHHHHHHHHHHHhhhcCC
Q 012111          442 N-----ALG-----------MTEAAQNLENKMIAMKENSG  465 (471)
Q Consensus       442 ~-----~~g-----------~~~~A~~~~~~m~~~~~~~~  465 (471)
                      .     +.|           ....|+.+|+++...-.+.+
T Consensus       551 ~s~~~~~~~~~~~~~e~~~~~~~~AR~iferAn~~~k~~~  590 (677)
T KOG1915|consen  551 ASASEGQEDEDLAELEITDENIKRARKIFERANTYLKEST  590 (677)
T ss_pred             ccccccccccchhhhhcchhHHHHHHHHHHHHHHHHHhcC
Confidence            2     334           56788888888876554443

>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW

Probab=99.51  E-value=4.9e-11  Score=102.62  Aligned_cols=201  Identities=13%  Similarity=0.039  Sum_probs=131.7

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHH
Q 012111          256 IFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIET  335 (471)
Q Consensus       256 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~  335 (471)
                      ...+..+...+...|++++|...+++..... +.+...+..+...+...|++++|...++...+.... +...+..+...
T Consensus        31 ~~~~~~la~~~~~~~~~~~A~~~~~~~l~~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~~~-~~~~~~~~~~~  108 (234)
T TIGR02521        31 AKIRVQLALGYLEQGDLEVAKENLDKALEHD-PDDYLAYLALALYYQQLGELEKAEDSFRRALTLNPN-NGDVLNNYGTF  108 (234)
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCC-CHHHHHHHHHH
Confidence            3445555556666666666666666655432 334455555666666666666666666666554322 34455566666


Q ss_pred             HHhcCCHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHH
Q 012111          336 FGKAGHIEKMEEYFKKMKHRGMK-PNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEK  414 (471)
Q Consensus       336 ~~~~g~~~~a~~~~~~m~~~~~~-p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~  414 (471)
                      +...|++++|...+++....... .....+..+...+...|++++|...+++..+..+. +...+..+...+...|++++
T Consensus       109 ~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~-~~~~~~~la~~~~~~~~~~~  187 (234)
T TIGR02521       109 LCQQGKYEQAMQQFEQAIEDPLYPQPARSLENAGLCALKAGDFDKAEKYLTRALQIDPQ-RPESLLELAELYYLRGQYKD  187 (234)
T ss_pred             HHHcccHHHHHHHHHHHHhccccccchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcC-ChHHHHHHHHHHHHcCCHHH
Confidence            67777777777777776654211 23445666677777888888888888877766543 55667777788888888888


Q ss_pred             HHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHh
Q 012111          415 MGELFLTMKERHCVPDNITFATMIQAYNALGMTEAAQNLENKMIAM  460 (471)
Q Consensus       415 a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~  460 (471)
                      |...++++.+. .+.+...+..+...+...|+.++|..+.+.+...
T Consensus       188 A~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~  232 (234)
T TIGR02521       188 ARAYLERYQQT-YNQTAESLWLGIRIARALGDVAAAQRYGAQLQKL  232 (234)
T ss_pred             HHHHHHHHHHh-CCCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHhh
Confidence            88888887765 3445666667777777888888888887777654

Members of this family are designated PilF in ref (PubMed:8973346) and PilW in ref (PubMed:15612916). This outer membrane protein is required both for pilus stability and for pilus function such as adherence to human cells. Members of this family contain copies of the TPR (tetratricopeptide repeat) domain.

>KOG1174 consensus Anaphase-promoting complex (APC), subunit 7 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]

Probab=99.49  E-value=4e-09  Score=91.26  Aligned_cols=312  Identities=9%  Similarity=-0.035  Sum_probs=222.5

Q ss_pred             CCCHHHHHHHHHHHH--hcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHH
Q 012111          146 KPSVDVYTALVSAYG--QSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTY  223 (471)
Q Consensus       146 ~~~~~~~~~li~~~~--~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~  223 (471)
                      +|...+....+.+++  ..++...|...+-.+.....++-|+.....+.+.+...|+.++|...|+.....+ +-+....
T Consensus       191 ~~~~dwls~wika~Aq~~~~~hs~a~~t~l~le~~~~lr~NvhLl~~lak~~~~~Gdn~~a~~~Fe~~~~~d-py~i~~M  269 (564)
T KOG1174|consen  191 PDHFDWLSKWIKALAQMFNFKHSDASQTFLMLHDNTTLRCNEHLMMALGKCLYYNGDYFQAEDIFSSTLCAN-PDNVEAM  269 (564)
T ss_pred             CCCccHHHHHHHHHHHHHhcccchhhhHHHHHHhhccCCccHHHHHHHhhhhhhhcCchHHHHHHHHHhhCC-hhhhhhH
Confidence            344444444454443  3455555655555554444567788888899999999999999999999887553 1122222


Q ss_pred             HHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHH
Q 012111          224 NTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGR  303 (471)
Q Consensus       224 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~  303 (471)
                      ....-.+.+.|+++....+...+....  ..+...|-.-.......+++..|+.+-++.++.+ +.+...|-.-...+..
T Consensus       270 D~Ya~LL~~eg~~e~~~~L~~~Lf~~~--~~ta~~wfV~~~~l~~~K~~~rAL~~~eK~I~~~-~r~~~alilKG~lL~~  346 (564)
T KOG1174|consen  270 DLYAVLLGQEGGCEQDSALMDYLFAKV--KYTASHWFVHAQLLYDEKKFERALNFVEKCIDSE-PRNHEALILKGRLLIA  346 (564)
T ss_pred             HHHHHHHHhccCHhhHHHHHHHHHhhh--hcchhhhhhhhhhhhhhhhHHHHHHHHHHHhccC-cccchHHHhccHHHHh
Confidence            333344566788888777777765442  3344455555566667788899999888887754 4455566555667778


Q ss_pred             cCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHH-HHHH-hcCCHHHHH
Q 012111          304 AGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLV-SAYS-KAGLIMKVD  381 (471)
Q Consensus       304 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li-~~~~-~~g~~~~a~  381 (471)
                      .|+.++|.-.|...+...+ -+..+|.-|+.+|...|++.+|..+-+...+. +.-+..+...+. ..|. ...--++|.
T Consensus       347 ~~R~~~A~IaFR~Aq~Lap-~rL~~Y~GL~hsYLA~~~~kEA~~~An~~~~~-~~~sA~~LtL~g~~V~~~dp~~rEKAK  424 (564)
T KOG1174|consen  347 LERHTQAVIAFRTAQMLAP-YRLEIYRGLFHSYLAQKRFKEANALANWTIRL-FQNSARSLTLFGTLVLFPDPRMREKAK  424 (564)
T ss_pred             ccchHHHHHHHHHHHhcch-hhHHHHHHHHHHHHhhchHHHHHHHHHHHHHH-hhcchhhhhhhcceeeccCchhHHHHH
Confidence            8999999998988776522 36789999999999999999988877766554 344566666553 3332 223457788


Q ss_pred             HHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhh
Q 012111          382 SILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAYNALGMTEAAQNLENKMIAMK  461 (471)
Q Consensus       382 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~  461 (471)
                      ++++...+..+. -....+.+...+...|....++.++++...  ..||....+.|.+.+...+.+.+|...|..+++.+
T Consensus       425 kf~ek~L~~~P~-Y~~AV~~~AEL~~~Eg~~~D~i~LLe~~L~--~~~D~~LH~~Lgd~~~A~Ne~Q~am~~y~~ALr~d  501 (564)
T KOG1174|consen  425 KFAEKSLKINPI-YTPAVNLIAELCQVEGPTKDIIKLLEKHLI--IFPDVNLHNHLGDIMRAQNEPQKAMEYYYKALRQD  501 (564)
T ss_pred             HHHHhhhccCCc-cHHHHHHHHHHHHhhCccchHHHHHHHHHh--hccccHHHHHHHHHHHHhhhHHHHHHHHHHHHhcC
Confidence            888888776544 345667788889999999999999998887  47899999999999999999999999999999999


Q ss_pred             hcCCC
Q 012111          462 ENSGK  466 (471)
Q Consensus       462 ~~~~~  466 (471)
                      |++..
T Consensus       502 P~~~~  506 (564)
T KOG1174|consen  502 PKSKR  506 (564)
T ss_pred             ccchH
Confidence            87654

>PRK12370 invasion protein regulator; Provisional

Probab=99.48  E-value=1.8e-10  Score=111.20  Aligned_cols=267  Identities=12%  Similarity=0.031  Sum_probs=176.0

Q ss_pred             CCHHHHHHHHHHHHh-----cCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHH---------ccCCHHHHHHHHHHHHH
Q 012111          183 PDVYTYSILIKSCTK-----FHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYG---------KAKKFEEMESSFSAMVE  248 (471)
Q Consensus       183 ~~~~~~~~ll~~~~~-----~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~---------~~~~~~~a~~~~~~~~~  248 (471)
                      .+...|...+.+...     .+++++|.++|++..+.. +-+...|..+..++.         ..+++++|...+++..+
T Consensus       254 ~~~da~~~~lrg~~~~~~~~~~~~~~A~~~~~~Al~ld-P~~a~a~~~La~~~~~~~~~g~~~~~~~~~~A~~~~~~Al~  332 (553)
T PRK12370        254 NSIDSTMVYLRGKHELNQYTPYSLQQALKLLTQCVNMS-PNSIAPYCALAECYLSMAQMGIFDKQNAMIKAKEHAIKATE  332 (553)
T ss_pred             CChHHHHHHHHhHHHHHccCHHHHHHHHHHHHHHHhcC-CccHHHHHHHHHHHHHHHHcCCcccchHHHHHHHHHHHHHh
Confidence            344555555555321     234578888888887663 224555555554443         23457888888888877


Q ss_pred             cCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHH
Q 012111          249 SGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVT  328 (471)
Q Consensus       249 ~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~  328 (471)
                      ..  +.+...+..+...+...|++++|...|++..+.+ +.+...+..+...+...|++++|...+++..+..+. +...
T Consensus       333 ld--P~~~~a~~~lg~~~~~~g~~~~A~~~~~~Al~l~-P~~~~a~~~lg~~l~~~G~~~eAi~~~~~Al~l~P~-~~~~  408 (553)
T PRK12370        333 LD--HNNPQALGLLGLINTIHSEYIVGSLLFKQANLLS-PISADIKYYYGWNLFMAGQLEEALQTINECLKLDPT-RAAA  408 (553)
T ss_pred             cC--CCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCC-Chhh
Confidence            64  4466777778888888899999999998888765 556677788888888899999999999888876443 2223


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHH
Q 012111          329 YNIVIETFGKAGHIEKMEEYFKKMKHRGMKP-NSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYG  407 (471)
Q Consensus       329 ~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  407 (471)
                      +..++..+...|++++|...++++.... .| +...+..+..++...|+.++|...+.++....+. +....+.+...|.
T Consensus       409 ~~~~~~~~~~~g~~eeA~~~~~~~l~~~-~p~~~~~~~~la~~l~~~G~~~eA~~~~~~~~~~~~~-~~~~~~~l~~~~~  486 (553)
T PRK12370        409 GITKLWITYYHTGIDDAIRLGDELRSQH-LQDNPILLSMQVMFLSLKGKHELARKLTKEISTQEIT-GLIAVNLLYAEYC  486 (553)
T ss_pred             HHHHHHHHHhccCHHHHHHHHHHHHHhc-cccCHHHHHHHHHHHHhCCCHHHHHHHHHHhhhccch-hHHHHHHHHHHHh
Confidence            3334445666788899999888877653 23 4555677778888889999999998887655332 4445566666677


Q ss_pred             hcCCHHHHHHHHHHHHhC-CCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhh
Q 012111          408 QAGDVEKMGELFLTMKER-HCVPDNITFATMIQAYNALGMTEAAQNLENKMIAMK  461 (471)
Q Consensus       408 ~~g~~~~a~~~~~~~~~~-~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~  461 (471)
                      ..|  +.|...++.+.+. .-.|....+  +-..+.-.|+.+.+..+ +++.+.+
T Consensus       487 ~~g--~~a~~~l~~ll~~~~~~~~~~~~--~~~~~~~~g~~~~~~~~-~~~~~~~  536 (553)
T PRK12370        487 QNS--ERALPTIREFLESEQRIDNNPGL--LPLVLVAHGEAIAEKMW-NKFKNED  536 (553)
T ss_pred             ccH--HHHHHHHHHHHHHhhHhhcCchH--HHHHHHHHhhhHHHHHH-HHhhccc
Confidence            766  4777777766543 112222222  33344556666666555 6666554

>KOG3785 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.47  E-value=8.7e-10  Score=93.39  Aligned_cols=394  Identities=9%  Similarity=-0.001  Sum_probs=224.2

Q ss_pred             hHHHHHHHhhHHHHHHHHHhhhhhhccCCCchHHHHHHHHHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcC
Q 012111           48 EKDLSKILRTEFAIKNIEKKVSSKKYKNLWPKPVLEALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKC  127 (471)
Q Consensus        48 ~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  127 (471)
                      ...+.....+.+++..++-......+...+...++.  .-..+.|++++|+..|..+.+..  .++.+....|.-++.-.
T Consensus        29 Ledfls~rDytGAislLefk~~~~~EEE~~~~lWia--~C~fhLgdY~~Al~~Y~~~~~~~--~~~~el~vnLAcc~FyL  104 (557)
T KOG3785|consen   29 LEDFLSNRDYTGAISLLEFKLNLDREEEDSLQLWIA--HCYFHLGDYEEALNVYTFLMNKD--DAPAELGVNLACCKFYL  104 (557)
T ss_pred             HHHHHhcccchhHHHHHHHhhccchhhhHHHHHHHH--HHHHhhccHHHHHHHHHHHhccC--CCCcccchhHHHHHHHH
Confidence            333344445666666655444332222211122221  22346788888888888887754  56666777777777777


Q ss_pred             CCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHH
Q 012111          128 KQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKI  207 (471)
Q Consensus       128 ~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~  207 (471)
                      |.+.+|..+.....+     ++-.-..|+...-+.|+-++-..+-+.+..      ...--.+|.+.......+++|+++
T Consensus       105 g~Y~eA~~~~~ka~k-----~pL~~RLlfhlahklndEk~~~~fh~~LqD------~~EdqLSLAsvhYmR~HYQeAIdv  173 (557)
T KOG3785|consen  105 GQYIEAKSIAEKAPK-----TPLCIRLLFHLAHKLNDEKRILTFHSSLQD------TLEDQLSLASVHYMRMHYQEAIDV  173 (557)
T ss_pred             HHHHHHHHHHhhCCC-----ChHHHHHHHHHHHHhCcHHHHHHHHHHHhh------hHHHHHhHHHHHHHHHHHHHHHHH
Confidence            888888877665432     344445555666667776666666555543      112233444444444568899999


Q ss_pred             HHHHHHCCCCCCHHHHHH-HHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHh--
Q 012111          208 LAEMSYLGIECSAVTYNT-IIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNL--  284 (471)
Q Consensus       208 ~~~~~~~g~~~~~~~~~~-l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~--  284 (471)
                      +......  .|+-...|. +.-+|.+..-++-+.+++.-..+.  ++.+....|.......+.=+-..|..-.+++.+  
T Consensus       174 YkrvL~d--n~ey~alNVy~ALCyyKlDYydvsqevl~vYL~q--~pdStiA~NLkacn~fRl~ngr~ae~E~k~ladN~  249 (557)
T KOG3785|consen  174 YKRVLQD--NPEYIALNVYMALCYYKLDYYDVSQEVLKVYLRQ--FPDSTIAKNLKACNLFRLINGRTAEDEKKELADNI  249 (557)
T ss_pred             HHHHHhc--ChhhhhhHHHHHHHHHhcchhhhHHHHHHHHHHh--CCCcHHHHHHHHHHHhhhhccchhHHHHHHHHhcc
Confidence            9988866  345555554 345667778888888888887776  233444444333222221111111111111111  


Q ss_pred             ------------CC------------CCC-----CHHHHHHHHHHHHHcCCHHHHHHHHHHHHhC---------------
Q 012111          285 ------------MG------------VKA-----DIQTLNILTKSYGRAGMYDKMRSVMDFMQKR---------------  320 (471)
Q Consensus       285 ------------~~------------~~~-----~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~---------------  320 (471)
                                  .+            +-|     -+..-..|+-.|.+.+++.+|..+.+.+...               
T Consensus       250 ~~~~~f~~~l~rHNLVvFrngEgALqVLP~L~~~IPEARlNL~iYyL~q~dVqeA~~L~Kdl~PttP~EyilKgvv~aal  329 (557)
T KOG3785|consen  250 DQEYPFIEYLCRHNLVVFRNGEGALQVLPSLMKHIPEARLNLIIYYLNQNDVQEAISLCKDLDPTTPYEYILKGVVFAAL  329 (557)
T ss_pred             cccchhHHHHHHcCeEEEeCCccHHHhchHHHhhChHhhhhheeeecccccHHHHHHHHhhcCCCChHHHHHHHHHHHHh
Confidence                        00            000     0111233444566667777776665543221               


Q ss_pred             -----------------------CCCCCH-HHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCC
Q 012111          321 -----------------------FFFPTV-VTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGL  376 (471)
Q Consensus       321 -----------------------~~~~~~-~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~  376 (471)
                                             +..-|. ..-.++...+.-..++++++..+..+...-..-|. ..-.+.++.+..|+
T Consensus       330 GQe~gSreHlKiAqqffqlVG~Sa~ecDTIpGRQsmAs~fFL~~qFddVl~YlnSi~sYF~NdD~-Fn~N~AQAk~atgn  408 (557)
T KOG3785|consen  330 GQETGSREHLKIAQQFFQLVGESALECDTIPGRQSMASYFFLSFQFDDVLTYLNSIESYFTNDDD-FNLNLAQAKLATGN  408 (557)
T ss_pred             hhhcCcHHHHHHHHHHHHHhcccccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcch-hhhHHHHHHHHhcC
Confidence                                   110010 01112222223333455555555555544222222 23346778888999


Q ss_pred             HHHHHHHHHHHHhCCCCcCHHHH-HHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHH-HHHHhcCCHHHHHHHH
Q 012111          377 IMKVDSILRQVENSDVILDTPFF-NCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMI-QAYNALGMTEAAQNLE  454 (471)
Q Consensus       377 ~~~a~~~~~~~~~~~~~~~~~~~-~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~-~~~~~~g~~~~A~~~~  454 (471)
                      +.+|+++|-++....++ |..+| ..|.++|.+.++.+.|++++-++..   +.+..+...+| .-|.+.+++=-|-+.|
T Consensus       409 y~eaEelf~~is~~~ik-n~~~Y~s~LArCyi~nkkP~lAW~~~lk~~t---~~e~fsLLqlIAn~CYk~~eFyyaaKAF  484 (557)
T KOG3785|consen  409 YVEAEELFIRISGPEIK-NKILYKSMLARCYIRNKKPQLAWDMMLKTNT---PSERFSLLQLIANDCYKANEFYYAAKAF  484 (557)
T ss_pred             hHHHHHHHhhhcChhhh-hhHHHHHHHHHHHHhcCCchHHHHHHHhcCC---chhHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            99999999888877777 55555 5567889999999999887765543   23444444444 7889999999999999


Q ss_pred             HHHHHhhhcCC
Q 012111          455 NKMIAMKENSG  465 (471)
Q Consensus       455 ~~m~~~~~~~~  465 (471)
                      +++..++|.|.
T Consensus       485 d~lE~lDP~pE  495 (557)
T KOG3785|consen  485 DELEILDPTPE  495 (557)
T ss_pred             hHHHccCCCcc
Confidence            99999888765

>PRK12370 invasion protein regulator; Provisional

Probab=99.47  E-value=1.1e-10  Score=112.70  Aligned_cols=147  Identities=8%  Similarity=-0.171  Sum_probs=60.9

Q ss_pred             HHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHH
Q 012111          130 PEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILA  209 (471)
Q Consensus       130 ~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~  209 (471)
                      +++|...+++..+.+.. +...+..+..++...|++++|...|++..+..  +.+...+..+...+...|++++|...++
T Consensus       320 ~~~A~~~~~~Al~ldP~-~~~a~~~lg~~~~~~g~~~~A~~~~~~Al~l~--P~~~~a~~~lg~~l~~~G~~~eAi~~~~  396 (553)
T PRK12370        320 MIKAKEHAIKATELDHN-NPQALGLLGLINTIHSEYIVGSLLFKQANLLS--PISADIKYYYGWNLFMAGQLEEALQTIN  396 (553)
T ss_pred             HHHHHHHHHHHHhcCCC-CHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHCCCHHHHHHHHH
Confidence            44455555544444322 34444444444444455555555555444311  2223334444444444455555555554


Q ss_pred             HHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 012111          210 EMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHP-DIFTLNSMISAYGNSGNIEKMEKWYNEF  282 (471)
Q Consensus       210 ~~~~~g~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~  282 (471)
                      +..+... .+...+..++..+...|++++|...+++..+..  .| +...+..+..++...|+.++|...+.++
T Consensus       397 ~Al~l~P-~~~~~~~~~~~~~~~~g~~eeA~~~~~~~l~~~--~p~~~~~~~~la~~l~~~G~~~eA~~~~~~~  467 (553)
T PRK12370        397 ECLKLDP-TRAAAGITKLWITYYHTGIDDAIRLGDELRSQH--LQDNPILLSMQVMFLSLKGKHELARKLTKEI  467 (553)
T ss_pred             HHHhcCC-CChhhHHHHHHHHHhccCHHHHHHHHHHHHHhc--cccCHHHHHHHHHHHHhCCCHHHHHHHHHHh
Confidence            4444321 111122222222333444444444444443321  12 2222333444444444444444444443

>KOG1129 consensus TPR repeat-containing protein [General function prediction only]

Probab=99.47  E-value=1.2e-11  Score=103.16  Aligned_cols=226  Identities=12%  Similarity=0.009  Sum_probs=93.7

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcC
Q 012111          191 LIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSG  270 (471)
Q Consensus       191 ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  270 (471)
                      +.++|.+.|.+.+|.+.|+.-.+.  .|-+.||..|-+.|.+..+.+.|+.++.+-.+.  .+-++.....+...+...+
T Consensus       229 ~gkCylrLgm~r~AekqlqssL~q--~~~~dTfllLskvY~ridQP~~AL~~~~~gld~--fP~~VT~l~g~ARi~eam~  304 (478)
T KOG1129|consen  229 MGKCYLRLGMPRRAEKQLQSSLTQ--FPHPDTFLLLSKVYQRIDQPERALLVIGEGLDS--FPFDVTYLLGQARIHEAME  304 (478)
T ss_pred             HHHHHHHhcChhhhHHHHHHHhhc--CCchhHHHHHHHHHHHhccHHHHHHHHhhhhhc--CCchhhhhhhhHHHHHHHH
Confidence            444444444444444444444333  333444444444444444444444444444433  1222222223333444444


Q ss_pred             CHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHH
Q 012111          271 NIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFK  350 (471)
Q Consensus       271 ~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~  350 (471)
                      +.++|.++|+...+.. +.++.....+...|.-.++++.|.+.+.++.+.|.. ++..|+.+.-+|...++++-++.-|.
T Consensus       305 ~~~~a~~lYk~vlk~~-~~nvEaiAcia~~yfY~~~PE~AlryYRRiLqmG~~-speLf~NigLCC~yaqQ~D~~L~sf~  382 (478)
T KOG1129|consen  305 QQEDALQLYKLVLKLH-PINVEAIACIAVGYFYDNNPEMALRYYRRILQMGAQ-SPELFCNIGLCCLYAQQIDLVLPSFQ  382 (478)
T ss_pred             hHHHHHHHHHHHHhcC-CccceeeeeeeeccccCCChHHHHHHHHHHHHhcCC-ChHHHhhHHHHHHhhcchhhhHHHHH
Confidence            4444444444443332 233333333333344444444444444444444443 34444444444444444444444444


Q ss_pred             HHHHcCCCCC--HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 012111          351 KMKHRGMKPN--SITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMK  423 (471)
Q Consensus       351 ~m~~~~~~p~--~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~  423 (471)
                      +....--.|+  ..+|..+.......|++..|.+.|+.....+.. +...+|.|.-.-.+.|++++|..+++...
T Consensus       383 RAlstat~~~~aaDvWYNlg~vaV~iGD~nlA~rcfrlaL~~d~~-h~ealnNLavL~~r~G~i~~Arsll~~A~  456 (478)
T KOG1129|consen  383 RALSTATQPGQAADVWYNLGFVAVTIGDFNLAKRCFRLALTSDAQ-HGEALNNLAVLAARSGDILGARSLLNAAK  456 (478)
T ss_pred             HHHhhccCcchhhhhhhccceeEEeccchHHHHHHHHHHhccCcc-hHHHHHhHHHHHhhcCchHHHHHHHHHhh
Confidence            4433221121  223333333344444444444444444443333 33444444444444444444444444443

>KOG0547 consensus Translocase of outer mitochondrial membrane complex, subunit TOM70/TOM72 [Intracellular trafficking, secretion, and vesicular transport]

Probab=99.47  E-value=1.5e-09  Score=95.90  Aligned_cols=361  Identities=11%  Similarity=0.018  Sum_probs=248.1

Q ss_pred             HHHHhhHHHHHHHHHhhhhhhccCCCchHHHHHHHHHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHH
Q 012111           52 SKILRTEFAIKNIEKKVSSKKYKNLWPKPVLEALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPE  131 (471)
Q Consensus        52 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  131 (471)
                      .+.+.+.++++-..+.+...|..   |--+.+....+...|+|++.++.-..+.+.+  |.-+.++..-..++-+.|+++
T Consensus       126 f~~kkY~eAIkyY~~AI~l~p~e---piFYsNraAcY~~lgd~~~Vied~TkALEl~--P~Y~KAl~RRA~A~E~lg~~~  200 (606)
T KOG0547|consen  126 FRNKKYDEAIKYYTQAIELCPDE---PIFYSNRAACYESLGDWEKVIEDCTKALELN--PDYVKALLRRASAHEQLGKFD  200 (606)
T ss_pred             hhcccHHHHHHHHHHHHhcCCCC---chhhhhHHHHHHHHhhHHHHHHHHHHHhhcC--cHHHHHHHHHHHHHHhhccHH
Confidence            45667778888888888766543   3344566666678899999999888888754  444567777777777778777


Q ss_pred             HHHH----------------------HHHH---------HHhCC--CCCCHHHHHHHHHHHHhc--------C-------
Q 012111          132 QASL----------------------LFEV---------MLSDG--LKPSVDVYTALVSAYGQS--------G-------  163 (471)
Q Consensus       132 ~a~~----------------------~~~~---------m~~~~--~~~~~~~~~~li~~~~~~--------~-------  163 (471)
                      +|+.                      ++..         |.+.+  +.|+.....+....+...        +       
T Consensus       201 eal~D~tv~ci~~~F~n~s~~~~~eR~Lkk~a~~ka~e~~k~nr~p~lPS~~fi~syf~sF~~~~~~~~~~~~~ksDa~l  280 (606)
T KOG0547|consen  201 EALFDVTVLCILEGFQNASIEPMAERVLKKQAMKKAKEKLKENRPPVLPSATFIASYFGSFHADPKPLFDNKSDKSDAAL  280 (606)
T ss_pred             HHHHhhhHHHHhhhcccchhHHHHHHHHHHHHHHHHHHhhcccCCCCCCcHHHHHHHHhhccccccccccCCCccchhhH
Confidence            6642                      1111         11111  234444444443333210        0       


Q ss_pred             -------------CHHHHHHHHHHhhcCCCCCC-----CH------HHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCC
Q 012111          164 -------------LLDEAFSTINDMKSVSDCKP-----DV------YTYSILIKSCTKFHRFDLIEKILAEMSYLGIECS  219 (471)
Q Consensus       164 -------------~~~~a~~~~~~~~~~~~~~~-----~~------~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~  219 (471)
                                   .+..|.+.+.+-....-..+     |.      .+.......+.-.|+.-.+..-|+..++.... +
T Consensus       281 ~~~l~~l~~~~~e~Y~~a~~~~te~~~~~~~~~~~n~~d~~le~~A~al~~~gtF~fL~g~~~~a~~d~~~~I~l~~~-~  359 (606)
T KOG0547|consen  281 AEALEALEKGLEEGYLKAYDKATEECLGSESSLSVNEIDAELEYMAEALLLRGTFHFLKGDSLGAQEDFDAAIKLDPA-F  359 (606)
T ss_pred             HHHHHHHHhhCchhHHHHHHHHHHHhhhhhhhccccccchhHHHHHHHHHHhhhhhhhcCCchhhhhhHHHHHhcCcc-c
Confidence                         12222222222111000111     11      11111112233468888999999999887533 3


Q ss_pred             HHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHH
Q 012111          220 AVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTK  299 (471)
Q Consensus       220 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~  299 (471)
                      ...|-.+..+|....+.++....|....+.+  +.+..+|..-.+.+.-.+++++|..-|++.+... +.+...|-.+.-
T Consensus       360 ~~lyI~~a~~y~d~~~~~~~~~~F~~A~~ld--p~n~dvYyHRgQm~flL~q~e~A~aDF~Kai~L~-pe~~~~~iQl~~  436 (606)
T KOG0547|consen  360 NSLYIKRAAAYADENQSEKMWKDFNKAEDLD--PENPDVYYHRGQMRFLLQQYEEAIADFQKAISLD-PENAYAYIQLCC  436 (606)
T ss_pred             chHHHHHHHHHhhhhccHHHHHHHHHHHhcC--CCCCchhHhHHHHHHHHHHHHHHHHHHHHHhhcC-hhhhHHHHHHHH
Confidence            3337778888999999999999999998775  3445568888888888899999999999998765 556667777777


Q ss_pred             HHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC-----CCCCHH--HHHHHHHHHH
Q 012111          300 SYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRG-----MKPNSI--TYCSLVSAYS  372 (471)
Q Consensus       300 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~-----~~p~~~--~~~~li~~~~  372 (471)
                      +..+.+.+++++..|+...++ ++-.+..|+.....+...++++.|.+.|+..+...     +..+..  +.-.++..-.
T Consensus       437 a~Yr~~k~~~~m~~Fee~kkk-FP~~~Evy~~fAeiLtDqqqFd~A~k~YD~ai~LE~~~~~~~v~~~plV~Ka~l~~qw  515 (606)
T KOG0547|consen  437 ALYRQHKIAESMKTFEEAKKK-FPNCPEVYNLFAEILTDQQQFDKAVKQYDKAIELEPREHLIIVNAAPLVHKALLVLQW  515 (606)
T ss_pred             HHHHHHHHHHHHHHHHHHHHh-CCCCchHHHHHHHHHhhHHhHHHHHHHHHHHHhhccccccccccchhhhhhhHhhhch
Confidence            777899999999999999887 44467899999999999999999999999988652     111222  2223333323


Q ss_pred             hcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 012111          373 KAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKE  424 (471)
Q Consensus       373 ~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~  424 (471)
                      + +++..|.+++....+.+++ ....|..|...-.+.|+.++|+++|++...
T Consensus       516 k-~d~~~a~~Ll~KA~e~Dpk-ce~A~~tlaq~~lQ~~~i~eAielFEksa~  565 (606)
T KOG0547|consen  516 K-EDINQAENLLRKAIELDPK-CEQAYETLAQFELQRGKIDEAIELFEKSAQ  565 (606)
T ss_pred             h-hhHHHHHHHHHHHHccCch-HHHHHHHHHHHHHHHhhHHHHHHHHHHHHH
Confidence            3 8999999999999998877 677899999999999999999999998764

>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW

Probab=99.46  E-value=1.6e-10  Score=99.46  Aligned_cols=57  Identities=12%  Similarity=0.060  Sum_probs=21.6

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHH
Q 012111          189 SILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAM  246 (471)
Q Consensus       189 ~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  246 (471)
                      ..+...+...|+++.|.+.+++..+.. +.+...+..+...+...|++++|.+.+++.
T Consensus        69 ~~la~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~  125 (234)
T TIGR02521        69 LALALYYQQLGELEKAEDSFRRALTLN-PNNGDVLNNYGTFLCQQGKYEQAMQQFEQA  125 (234)
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHcccHHHHHHHHHHH
Confidence            333333333444444444443333322 112233333333334444444444444443

Members of this family are designated PilF in ref (PubMed:8973346) and PilW in ref (PubMed:15612916). This outer membrane protein is required both for pilus stability and for pilus function such as adherence to human cells. Members of this family contain copies of the TPR (tetratricopeptide repeat) domain.

>KOG1173 consensus Anaphase-promoting complex (APC), Cdc16 subunit [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]

Probab=99.45  E-value=4.6e-09  Score=94.55  Aligned_cols=382  Identities=12%  Similarity=-0.000  Sum_probs=231.1

Q ss_pred             ccCCCchHHHHHHHHHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHH----HHHhC-----
Q 012111           73 YKNLWPKPVLEALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFE----VMLSD-----  143 (471)
Q Consensus        73 ~~~~~~~~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~----~m~~~-----  143 (471)
                      .....|.+..-+.+.+.-.|++..|..+...-.-.   .-+..+......++.+.+++++|..++.    .+...     
T Consensus        44 ~l~~dp~d~~~~aq~l~~~~~y~ra~~lit~~~le---~~d~~cryL~~~~l~~lk~~~~al~vl~~~~~~~~~f~yy~~  120 (611)
T KOG1173|consen   44 GLTNDPADIYWLAQVLYLGRQYERAAHLITTYKLE---KRDIACRYLAAKCLVKLKEWDQALLVLGRGHVETNPFSYYEK  120 (611)
T ss_pred             hccCChHHHHHHHHHHHhhhHHHHHHHHHHHhhhh---hhhHHHHHHHHHHHHHHHHHHHHHHHhcccchhhcchhhcch
Confidence            33466777777788888888899888877655322   4567777888889999999999999998    22110     


Q ss_pred             ----CCCCCHHH-----------HHHHHHHHHhcCCHHHHHHHHHHhhcC------------------------------
Q 012111          144 ----GLKPSVDV-----------YTALVSAYGQSGLLDEAFSTINDMKSV------------------------------  178 (471)
Q Consensus       144 ----~~~~~~~~-----------~~~li~~~~~~~~~~~a~~~~~~~~~~------------------------------  178 (471)
                          -+.+|..-           +-.-...|....+.++|...|.+....                              
T Consensus       121 ~~~~~l~~n~~~~~~~~~~essic~lRgk~y~al~n~~~ar~~Y~~Al~~D~~c~Ea~~~lvs~~mlt~~Ee~~ll~~l~  200 (611)
T KOG1173|consen  121 DAANTLELNSAGEDLMINLESSICYLRGKVYVALDNREEARDKYKEALLADAKCFEAFEKLVSAHMLTAQEEFELLESLD  200 (611)
T ss_pred             hhhceeccCcccccccccchhceeeeeeehhhhhccHHHHHHHHHHHHhcchhhHHHHHHHHHHHhcchhHHHHHHhccc
Confidence                00011100           000011223333444444444433320                              


Q ss_pred             -------------------------------------CCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHH
Q 012111          179 -------------------------------------SDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAV  221 (471)
Q Consensus       179 -------------------------------------~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~  221 (471)
                                                           .+..-+.........-|...+++.+..++.+.+.+.. ++...
T Consensus       201 ~a~~~~ed~e~l~~lyel~~~k~~n~~~~~r~~~~sl~~l~~~~dll~~~ad~~y~~c~f~~c~kit~~lle~d-pfh~~  279 (611)
T KOG1173|consen  201 LAMLTKEDVERLEILYELKLCKNRNEESLTRNEDESLIGLAENLDLLAEKADRLYYGCRFKECLKITEELLEKD-PFHLP  279 (611)
T ss_pred             HHhhhhhHHHHHHHHHHhhhhhhccccccccCchhhhhhhhhcHHHHHHHHHHHHHcChHHHHHHHhHHHHhhC-CCCcc
Confidence                                                 0001111112222222333445555555555554432 33444


Q ss_pred             HHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHH
Q 012111          222 TYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSY  301 (471)
Q Consensus       222 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~  301 (471)
                      .+..-|.++...|+..+-..+=.++.+..  +....+|-++.--|...|+..+|.+.|.+....+ +.-...|-.+...|
T Consensus       280 ~~~~~ia~l~el~~~n~Lf~lsh~LV~~y--P~~a~sW~aVg~YYl~i~k~seARry~SKat~lD-~~fgpaWl~fghsf  356 (611)
T KOG1173|consen  280 CLPLHIACLYELGKSNKLFLLSHKLVDLY--PSKALSWFAVGCYYLMIGKYSEARRYFSKATTLD-PTFGPAWLAFGHSF  356 (611)
T ss_pred             hHHHHHHHHHHhcccchHHHHHHHHHHhC--CCCCcchhhHHHHHHHhcCcHHHHHHHHHHhhcC-ccccHHHHHHhHHh
Confidence            44444445555555555555555555442  3345566666666666677777777777665433 22234556666666


Q ss_pred             HHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHH
Q 012111          302 GRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVD  381 (471)
Q Consensus       302 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~  381 (471)
                      .-.|.-|+|..-+...-+.-.. ....+-.+.--|.+.++.+.|.+.|....... +-|+..++-+.-.....+.+.+|.
T Consensus       357 a~e~EhdQAmaaY~tAarl~~G-~hlP~LYlgmey~~t~n~kLAe~Ff~~A~ai~-P~Dplv~~Elgvvay~~~~y~~A~  434 (611)
T KOG1173|consen  357 AGEGEHDQAMAAYFTAARLMPG-CHLPSLYLGMEYMRTNNLKLAEKFFKQALAIA-PSDPLVLHELGVVAYTYEEYPEAL  434 (611)
T ss_pred             hhcchHHHHHHHHHHHHHhccC-CcchHHHHHHHHHHhccHHHHHHHHHHHHhcC-CCcchhhhhhhheeehHhhhHHHH
Confidence            6667777766666555442111 11111223334667788888888887776641 336777777777777788999999


Q ss_pred             HHHHHHHh----CCCC--cCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHH
Q 012111          382 SILRQVEN----SDVI--LDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAYNALGMTEAAQNLEN  455 (471)
Q Consensus       382 ~~~~~~~~----~~~~--~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~  455 (471)
                      .+|+....    .+..  --..+++.|..+|.+.+++++|+..+++.... .+-+..++.++.-.|...|+++.|...|.
T Consensus       435 ~~f~~~l~~ik~~~~e~~~w~p~~~NLGH~~Rkl~~~~eAI~~~q~aL~l-~~k~~~~~asig~iy~llgnld~Aid~fh  513 (611)
T KOG1173|consen  435 KYFQKALEVIKSVLNEKIFWEPTLNNLGHAYRKLNKYEEAIDYYQKALLL-SPKDASTHASIGYIYHLLGNLDKAIDHFH  513 (611)
T ss_pred             HHHHHHHHHhhhccccccchhHHHHhHHHHHHHHhhHHHHHHHHHHHHHc-CCCchhHHHHHHHHHHHhcChHHHHHHHH
Confidence            99887652    1111  13456888999999999999999999998875 34588889899889999999999999999


Q ss_pred             HHHHhhhcC
Q 012111          456 KMIAMKENS  464 (471)
Q Consensus       456 ~m~~~~~~~  464 (471)
                      +.+.+.|..
T Consensus       514 KaL~l~p~n  522 (611)
T KOG1173|consen  514 KALALKPDN  522 (611)
T ss_pred             HHHhcCCcc
Confidence            999888765

>KOG1129 consensus TPR repeat-containing protein [General function prediction only]

Probab=99.45  E-value=3.1e-11  Score=100.86  Aligned_cols=241  Identities=10%  Similarity=0.009  Sum_probs=202.3

Q ss_pred             CHHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHH
Q 012111          219 SAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILT  298 (471)
Q Consensus       219 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll  298 (471)
                      |..--+.+.++|.+.|.+.+|++.|+...++   .|-+.||..|-.+|.+..++..|+.++.+-.+. ++.++....-+.
T Consensus       222 dwwWk~Q~gkCylrLgm~r~AekqlqssL~q---~~~~dTfllLskvY~ridQP~~AL~~~~~gld~-fP~~VT~l~g~A  297 (478)
T KOG1129|consen  222 DWWWKQQMGKCYLRLGMPRRAEKQLQSSLTQ---FPHPDTFLLLSKVYQRIDQPERALLVIGEGLDS-FPFDVTYLLGQA  297 (478)
T ss_pred             hHHHHHHHHHHHHHhcChhhhHHHHHHHhhc---CCchhHHHHHHHHHHHhccHHHHHHHHhhhhhc-CCchhhhhhhhH
Confidence            3344467889999999999999999998876   567778999999999999999999999998764 355555567788


Q ss_pred             HHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHH
Q 012111          299 KSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIM  378 (471)
Q Consensus       299 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~  378 (471)
                      ..+...++.++|.++++...+... .++.....+...|...++++-|+.+|+++.+.|+. ++..|+.+.-+|...++++
T Consensus       298 Ri~eam~~~~~a~~lYk~vlk~~~-~nvEaiAcia~~yfY~~~PE~AlryYRRiLqmG~~-speLf~NigLCC~yaqQ~D  375 (478)
T KOG1129|consen  298 RIHEAMEQQEDALQLYKLVLKLHP-INVEAIACIAVGYFYDNNPEMALRYYRRILQMGAQ-SPELFCNIGLCCLYAQQID  375 (478)
T ss_pred             HHHHHHHhHHHHHHHHHHHHhcCC-ccceeeeeeeeccccCCChHHHHHHHHHHHHhcCC-ChHHHhhHHHHHHhhcchh
Confidence            889999999999999999988633 36667777788899999999999999999999954 7889999999999999999


Q ss_pred             HHHHHHHHHHhCCCCc--CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHH
Q 012111          379 KVDSILRQVENSDVIL--DTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAYNALGMTEAAQNLENK  456 (471)
Q Consensus       379 ~a~~~~~~~~~~~~~~--~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~  456 (471)
                      -++.-|++....-..|  -..+|-.+.......||+..|.+.|+-....+ .-+...++.|.-.-.+.|++++|+.+++.
T Consensus       376 ~~L~sf~RAlstat~~~~aaDvWYNlg~vaV~iGD~nlA~rcfrlaL~~d-~~h~ealnNLavL~~r~G~i~~Arsll~~  454 (478)
T KOG1129|consen  376 LVLPSFQRALSTATQPGQAADVWYNLGFVAVTIGDFNLAKRCFRLALTSD-AQHGEALNNLAVLAARSGDILGARSLLNA  454 (478)
T ss_pred             hhHHHHHHHHhhccCcchhhhhhhccceeEEeccchHHHHHHHHHHhccC-cchHHHHHhHHHHHhhcCchHHHHHHHHH
Confidence            9999998887543333  34578888888889999999999999888753 33667888888888899999999999999


Q ss_pred             HHHhhhcCCC
Q 012111          457 MIAMKENSGK  466 (471)
Q Consensus       457 m~~~~~~~~~  466 (471)
                      +.+..|.--+
T Consensus       455 A~s~~P~m~E  464 (478)
T KOG1129|consen  455 AKSVMPDMAE  464 (478)
T ss_pred             hhhhCccccc
Confidence            9988876443

>KOG4318 consensus Bicoid mRNA stability factor [RNA processing and modification]

Probab=99.44  E-value=2e-11  Score=114.72  Aligned_cols=266  Identities=14%  Similarity=0.117  Sum_probs=151.0

Q ss_pred             ccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHH
Q 012111          110 YQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYS  189 (471)
Q Consensus       110 ~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  189 (471)
                      +.|+..+|..+|.-|+..|+.+.|- +|.-|.-...+.+...++.++.+....|+.+.+.            .|...+|.
T Consensus        21 i~PnRvtyqsLiarYc~~gdieaat-if~fm~~ksLpv~e~vf~~lv~sh~~And~Enpk------------ep~aDtyt   87 (1088)
T KOG4318|consen   21 ILPNRVTYQSLIARYCTKGDIEAAT-IFPFMEIKSLPVREGVFRGLVASHKEANDAENPK------------EPLADTYT   87 (1088)
T ss_pred             CCCchhhHHHHHHHHcccCCCcccc-chhhhhcccccccchhHHHHHhcccccccccCCC------------CCchhHHH
Confidence            5666666666666666666666666 6666655555555566666666666555544332            45556666


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhc
Q 012111          190 ILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNS  269 (471)
Q Consensus       190 ~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  269 (471)
                      .|+.+|...||... ++..++           ....+...+...|.......++..+.-..+..||..+   .+......
T Consensus        88 ~Ll~ayr~hGDli~-fe~veq-----------dLe~i~~sfs~~Gvgs~e~~fl~k~~c~p~~lpda~n---~illlv~e  152 (1088)
T KOG4318|consen   88 NLLKAYRIHGDLIL-FEVVEQ-----------DLESINQSFSDHGVGSPERWFLMKIHCCPHSLPDAEN---AILLLVLE  152 (1088)
T ss_pred             HHHHHHHhccchHH-HHHHHH-----------HHHHHHhhhhhhccCcHHHHHHhhcccCcccchhHHH---HHHHHHHH
Confidence            66666666666544 111111           1122333444455554444554444333334444432   23333445


Q ss_pred             CCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHH
Q 012111          270 GNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYF  349 (471)
Q Consensus       270 ~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~  349 (471)
                      |-++.+++++..+-...-. ....+  +++-+..  +..-..++........-.|+..+|..++.+-...|+.+.|..++
T Consensus       153 glwaqllkll~~~Pvsa~~-~p~~v--fLrqnv~--~ntpvekLl~~cksl~e~~~s~~l~a~l~~alaag~~d~Ak~ll  227 (1088)
T KOG4318|consen  153 GLWAQLLKLLAKVPVSAWN-APFQV--FLRQNVV--DNTPVEKLLNMCKSLVEAPTSETLHAVLKRALAAGDVDGAKNLL  227 (1088)
T ss_pred             HHHHHHHHHHhhCCccccc-chHHH--HHHHhcc--CCchHHHHHHHHHHhhcCCChHHHHHHHHHHHhcCchhhHHHHH
Confidence            6666666666554322111 11111  1222221  22233333333322212477888888888888888888888888


Q ss_pred             HHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCC
Q 012111          350 KKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGD  411 (471)
Q Consensus       350 ~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~  411 (471)
                      .+|++.|++.+..-|..|+-+   .++...+..+++.|...|+.|+..|+...+..+...|.
T Consensus       228 ~emke~gfpir~HyFwpLl~g---~~~~q~~e~vlrgmqe~gv~p~seT~adyvip~l~N~~  286 (1088)
T KOG4318|consen  228 YEMKEKGFPIRAHYFWPLLLG---INAAQVFEFVLRGMQEKGVQPGSETQADYVIPQLSNGQ  286 (1088)
T ss_pred             HHHHHcCCCcccccchhhhhc---CccchHHHHHHHHHHHhcCCCCcchhHHHHHhhhcchh
Confidence            888888877777766666655   67777777888888888888888888777777766444

>PF12569 NARP1: NMDA receptor-regulated protein 1 ; InterPro: IPR021183 This group represents N-terminal acetyltransferase A (NatA) auxiliary subunit and represents a non-catalytic component of the NatA N-terminal acetyltransferase, which catalyzes acetylation of proteins beginning with Met-Ser, Met-Gly and Met-Ala

Probab=99.42  E-value=2.3e-09  Score=100.19  Aligned_cols=294  Identities=16%  Similarity=0.132  Sum_probs=210.4

Q ss_pred             HHHHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhc--
Q 012111           85 LDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQS--  162 (471)
Q Consensus        85 l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~--  162 (471)
                      ...+...|++++|++.++.....  +......+......+.+.|+.++|..+|..+++.++. +..-|..+..+..-.  
T Consensus        11 ~~il~e~g~~~~AL~~L~~~~~~--I~Dk~~~~E~rA~ll~kLg~~~eA~~~y~~Li~rNPd-n~~Yy~~L~~~~g~~~~   87 (517)
T PF12569_consen   11 NSILEEAGDYEEALEHLEKNEKQ--ILDKLAVLEKRAELLLKLGRKEEAEKIYRELIDRNPD-NYDYYRGLEEALGLQLQ   87 (517)
T ss_pred             HHHHHHCCCHHHHHHHHHhhhhh--CCCHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCC-cHHHHHHHHHHHhhhcc
Confidence            34556889999999999887665  4556677888899999999999999999999998643 555555565655222  


Q ss_pred             ---CCHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCH-HHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHH
Q 012111          163 ---GLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRF-DLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEE  238 (471)
Q Consensus       163 ---~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~-~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~  238 (471)
                         .+.+...++|+++...   -|.......+.-.+.....+ ..+..++..+...|+|+   +|+.|-..|....+..-
T Consensus        88 ~~~~~~~~~~~~y~~l~~~---yp~s~~~~rl~L~~~~g~~F~~~~~~yl~~~l~KgvPs---lF~~lk~Ly~d~~K~~~  161 (517)
T PF12569_consen   88 LSDEDVEKLLELYDELAEK---YPRSDAPRRLPLDFLEGDEFKERLDEYLRPQLRKGVPS---LFSNLKPLYKDPEKAAI  161 (517)
T ss_pred             cccccHHHHHHHHHHHHHh---CccccchhHhhcccCCHHHHHHHHHHHHHHHHhcCCch---HHHHHHHHHcChhHHHH
Confidence               3577888999998763   24444433333223332233 34566777788888653   45566666665555555


Q ss_pred             HHHHHHHHHHcC-------------CCCCCH--HHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHH
Q 012111          239 MESSFSAMVESG-------------GCHPDI--FTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGR  303 (471)
Q Consensus       239 a~~~~~~~~~~~-------------~~~~~~--~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~  303 (471)
                      ..+++.......             .-.|+.  .++..+...|...|++++|++++++.+... +..+..|..-.+.+-+
T Consensus       162 i~~l~~~~~~~l~~~~~~~~~~~~~~~~p~~~lw~~~~lAqhyd~~g~~~~Al~~Id~aI~ht-Pt~~ely~~KarilKh  240 (517)
T PF12569_consen  162 IESLVEEYVNSLESNGSFSNGDDEEKEPPSTLLWTLYFLAQHYDYLGDYEKALEYIDKAIEHT-PTLVELYMTKARILKH  240 (517)
T ss_pred             HHHHHHHHHHhhcccCCCCCccccccCCchHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhcC-CCcHHHHHHHHHHHHH
Confidence            666666554321             013444  344566778889999999999999998864 4447788888999999


Q ss_pred             cCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHH--------HHHHHHHHHhcC
Q 012111          304 AGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSIT--------YCSLVSAYSKAG  375 (471)
Q Consensus       304 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~--------~~~li~~~~~~g  375 (471)
                      .|++++|...++..+..... |...-+-.+..+.+.|++++|.+++....+.+..|....        ......+|.+.|
T Consensus       241 ~G~~~~Aa~~~~~Ar~LD~~-DRyiNsK~aKy~LRa~~~e~A~~~~~~Ftr~~~~~~~~L~~mQc~Wf~~e~a~a~~r~~  319 (517)
T PF12569_consen  241 AGDLKEAAEAMDEARELDLA-DRYINSKCAKYLLRAGRIEEAEKTASLFTREDVDPLSNLNDMQCMWFETECAEAYLRQG  319 (517)
T ss_pred             CCCHHHHHHHHHHHHhCChh-hHHHHHHHHHHHHHCCCHHHHHHHHHhhcCCCCCcccCHHHHHHHHHHHHHHHHHHHHh
Confidence            99999999999999887554 667777788889999999999999998887765442222        144567788999


Q ss_pred             CHHHHHHHHHHHHh
Q 012111          376 LIMKVDSILRQVEN  389 (471)
Q Consensus       376 ~~~~a~~~~~~~~~  389 (471)
                      ++..|++.|..+.+
T Consensus       320 ~~~~ALk~~~~v~k  333 (517)
T PF12569_consen  320 DYGLALKRFHAVLK  333 (517)
T ss_pred             hHHHHHHHHHHHHH
Confidence            99988887766543

N-terminal acetylation plays a role in normal eukaryotic translation and processing, protect against proteolytic degradation and protein turnover. NAT1 anchors ARD1 and NAT5 to the ribosome and may present the N- terminal of nascent polypeptides for acetylation [], [].

>PF12569 NARP1: NMDA receptor-regulated protein 1 ; InterPro: IPR021183 This group represents N-terminal acetyltransferase A (NatA) auxiliary subunit and represents a non-catalytic component of the NatA N-terminal acetyltransferase, which catalyzes acetylation of proteins beginning with Met-Ser, Met-Gly and Met-Ala

Probab=99.40  E-value=4.5e-09  Score=98.29  Aligned_cols=128  Identities=16%  Similarity=0.159  Sum_probs=78.2

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHH
Q 012111          329 YNIVIETFGKAGHIEKMEEYFKKMKHRGMKPN-SITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYG  407 (471)
Q Consensus       329 ~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~-~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  407 (471)
                      +..+...|...|++++|++++++.+..  .|+ +..|..-.+.+-+.|++.+|.+.++.....+.. |..+-+-.+..+.
T Consensus       197 ~~~lAqhyd~~g~~~~Al~~Id~aI~h--tPt~~ely~~KarilKh~G~~~~Aa~~~~~Ar~LD~~-DRyiNsK~aKy~L  273 (517)
T PF12569_consen  197 LYFLAQHYDYLGDYEKALEYIDKAIEH--TPTLVELYMTKARILKHAGDLKEAAEAMDEARELDLA-DRYINSKCAKYLL  273 (517)
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHHhc--CCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHhCChh-hHHHHHHHHHHHH
Confidence            344456666667777777777766665  343 556666666667777777777777777666655 6666666666666


Q ss_pred             hcCCHHHHHHHHHHHHhCCCCCCHH------HHH--HHHHHHHhcCCHHHHHHHHHHHHH
Q 012111          408 QAGDVEKMGELFLTMKERHCVPDNI------TFA--TMIQAYNALGMTEAAQNLENKMIA  459 (471)
Q Consensus       408 ~~g~~~~a~~~~~~~~~~~~~p~~~------~~~--~l~~~~~~~g~~~~A~~~~~~m~~  459 (471)
                      ++|++++|.+++..+...+..|...      .|.  -...+|.+.|++..|++.|..+.+
T Consensus       274 Ra~~~e~A~~~~~~Ftr~~~~~~~~L~~mQc~Wf~~e~a~a~~r~~~~~~ALk~~~~v~k  333 (517)
T PF12569_consen  274 RAGRIEEAEKTASLFTREDVDPLSNLNDMQCMWFETECAEAYLRQGDYGLALKRFHAVLK  333 (517)
T ss_pred             HCCCHHHHHHHHHhhcCCCCCcccCHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHH
Confidence            7777777777776666554433221      221  223566667777777666655544

N-terminal acetylation plays a role in normal eukaryotic translation and processing, protect against proteolytic degradation and protein turnover. NAT1 anchors ARD1 and NAT5 to the ribosome and may present the N- terminal of nascent polypeptides for acetylation [], [].

>KOG2047 consensus mRNA splicing factor [RNA processing and modification]

Probab=99.40  E-value=8.1e-08  Score=88.00  Aligned_cols=133  Identities=14%  Similarity=0.126  Sum_probs=91.4

Q ss_pred             chHHHHHHHHHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHH
Q 012111           78 PKPVLEALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVS  157 (471)
Q Consensus        78 ~~~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~  157 (471)
                      |..+...+.-+.++|+.......|+.+...-++.-....|...+......+-++-+.+++++.++.    ++..-+.-|.
T Consensus       102 pRIwl~Ylq~l~~Q~~iT~tR~tfdrALraLpvtqH~rIW~lyl~Fv~~~~lPets~rvyrRYLk~----~P~~~eeyie  177 (835)
T KOG2047|consen  102 PRIWLDYLQFLIKQGLITRTRRTFDRALRALPVTQHDRIWDLYLKFVESHGLPETSIRVYRRYLKV----APEAREEYIE  177 (835)
T ss_pred             CHHHHHHHHHHHhcchHHHHHHHHHHHHHhCchHhhccchHHHHHHHHhCCChHHHHHHHHHHHhc----CHHHHHHHHH
Confidence            455666677777888888888888887765433344556777777777788888888888887754    4445666677


Q ss_pred             HHHhcCCHHHHHHHHHHhhcCC---------------------------------------C--CCCCH--HHHHHHHHH
Q 012111          158 AYGQSGLLDEAFSTINDMKSVS---------------------------------------D--CKPDV--YTYSILIKS  194 (471)
Q Consensus       158 ~~~~~~~~~~a~~~~~~~~~~~---------------------------------------~--~~~~~--~~~~~ll~~  194 (471)
                      .++..+++++|-+.+..+....                                       |  .-+|.  ..|.+|.+-
T Consensus       178 ~L~~~d~~~eaa~~la~vln~d~f~sk~gkSn~qlw~elcdlis~~p~~~~slnvdaiiR~gi~rftDq~g~Lw~SLAdY  257 (835)
T KOG2047|consen  178 YLAKSDRLDEAAQRLATVLNQDEFVSKKGKSNHQLWLELCDLISQNPDKVQSLNVDAIIRGGIRRFTDQLGFLWCSLADY  257 (835)
T ss_pred             HHHhccchHHHHHHHHHhcCchhhhhhcccchhhHHHHHHHHHHhCcchhcccCHHHHHHhhcccCcHHHHHHHHHHHHH
Confidence            7777787777777666554310                                       0  01221  357777778


Q ss_pred             HHhcCCHHHHHHHHHHHHHC
Q 012111          195 CTKFHRFDLIEKILAEMSYL  214 (471)
Q Consensus       195 ~~~~~~~~~a~~~~~~~~~~  214 (471)
                      |.+.|.++.|..++++....
T Consensus       258 YIr~g~~ekarDvyeeai~~  277 (835)
T KOG2047|consen  258 YIRSGLFEKARDVYEEAIQT  277 (835)
T ss_pred             HHHhhhhHHHHHHHHHHHHh
Confidence            88888888888888777654

>KOG1840 consensus Kinesin light chain [Cytoskeleton]

Probab=99.39  E-value=6.7e-10  Score=102.49  Aligned_cols=247  Identities=19%  Similarity=0.229  Sum_probs=177.0

Q ss_pred             CCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHc----CC-CCCCHHHH-HHHHHHHHhcCCHHHHHHHHHHHHhC-----
Q 012111          217 ECSAVTYNTIIDGYGKAKKFEEMESSFSAMVES----GG-CHPDIFTL-NSMISAYGNSGNIEKMEKWYNEFNLM-----  285 (471)
Q Consensus       217 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~-~~~~~~~~-~~l~~~~~~~~~~~~a~~~~~~~~~~-----  285 (471)
                      +.-..+...+...|...|+++.|+.+++...+.    .| ..|...+. +.+...|...+++++|..+|+++...     
T Consensus       196 P~~~~~~~~La~~y~~~g~~e~A~~l~k~Al~~l~k~~G~~hl~va~~l~~~a~~y~~~~k~~eAv~ly~~AL~i~e~~~  275 (508)
T KOG1840|consen  196 PERLRTLRNLAEMYAVQGRLEKAEPLCKQALRILEKTSGLKHLVVASMLNILALVYRSLGKYDEAVNLYEEALTIREEVF  275 (508)
T ss_pred             chHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHccCccCHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHhc
Confidence            334566677888899999999999988877654    11 13443333 34677888899999999999888542     


Q ss_pred             C--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhC-----CC-CCCH-HHHHHHHHHHHhcCCHHHHHHHHHHHHHc-
Q 012111          286 G--VKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKR-----FF-FPTV-VTYNIVIETFGKAGHIEKMEEYFKKMKHR-  355 (471)
Q Consensus       286 ~--~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~-----~~-~~~~-~~~~~li~~~~~~g~~~~a~~~~~~m~~~-  355 (471)
                      |  .+.-..+++.|...|.+.|++++|...++...+-     +. .|.+ ..++.+...++..+++++|..+++...+. 
T Consensus       276 G~~h~~va~~l~nLa~ly~~~GKf~EA~~~~e~Al~I~~~~~~~~~~~v~~~l~~~~~~~~~~~~~Eea~~l~q~al~i~  355 (508)
T KOG1840|consen  276 GEDHPAVAATLNNLAVLYYKQGKFAEAEEYCERALEIYEKLLGASHPEVAAQLSELAAILQSMNEYEEAKKLLQKALKIY  355 (508)
T ss_pred             CCCCHHHHHHHHHHHHHHhccCChHHHHHHHHHHHHHHHHhhccChHHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHH
Confidence            2  1122346777888899999999888887765431     11 1222 24666777888999999999999876543 


Q ss_pred             --CCCC----CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhC----CC---CcCHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 012111          356 --GMKP----NSITYCSLVSAYSKAGLIMKVDSILRQVENS----DV---ILDTPFFNCIISAYGQAGDVEKMGELFLTM  422 (471)
Q Consensus       356 --~~~p----~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~----~~---~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~  422 (471)
                        -+.+    -..+++.|...|...|++++|.++++.++..    +-   .-....++.|...|.+.+++.+|.++|.+.
T Consensus       356 ~~~~g~~~~~~a~~~~nl~~l~~~~gk~~ea~~~~k~ai~~~~~~~~~~~~~~~~~l~~la~~~~~~k~~~~a~~l~~~~  435 (508)
T KOG1840|consen  356 LDAPGEDNVNLAKIYANLAELYLKMGKYKEAEELYKKAIQILRELLGKKDYGVGKPLNQLAEAYEELKKYEEAEQLFEEA  435 (508)
T ss_pred             HhhccccchHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHhcccCcChhhhHHHHHHHHHHHHhcccchHHHHHHHH
Confidence              1122    2467899999999999999999999887632    11   112456788899999999999999999876


Q ss_pred             Hh----CCC-CCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHHhhhc
Q 012111          423 KE----RHC-VPD-NITFATMIQAYNALGMTEAAQNLENKMIAMKEN  463 (471)
Q Consensus       423 ~~----~~~-~p~-~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~  463 (471)
                      ..    .|. .|+ ..+|..|...|...|+++.|.++.+.+......
T Consensus       436 ~~i~~~~g~~~~~~~~~~~nL~~~Y~~~g~~e~a~~~~~~~~~~~~~  482 (508)
T KOG1840|consen  436 KDIMKLCGPDHPDVTYTYLNLAALYRAQGNYEAAEELEEKVLNAREQ  482 (508)
T ss_pred             HHHHHHhCCCCCchHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHH
Confidence            53    222 233 467888999999999999999999998865543

>KOG1173 consensus Anaphase-promoting complex (APC), Cdc16 subunit [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]

Probab=99.38  E-value=4.7e-09  Score=94.49  Aligned_cols=286  Identities=12%  Similarity=0.010  Sum_probs=224.7

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHH
Q 012111          148 SVDVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTII  227 (471)
Q Consensus       148 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~  227 (471)
                      +......-.+-+...+++.+..++++.+.+..  +++...+..-|..+...|+..+-..+=..|.+.- |-.+.+|-++.
T Consensus       243 ~~dll~~~ad~~y~~c~f~~c~kit~~lle~d--pfh~~~~~~~ia~l~el~~~n~Lf~lsh~LV~~y-P~~a~sW~aVg  319 (611)
T KOG1173|consen  243 NLDLLAEKADRLYYGCRFKECLKITEELLEKD--PFHLPCLPLHIACLYELGKSNKLFLLSHKLVDLY-PSKALSWFAVG  319 (611)
T ss_pred             cHHHHHHHHHHHHHcChHHHHHHHhHHHHhhC--CCCcchHHHHHHHHHHhcccchHHHHHHHHHHhC-CCCCcchhhHH
Confidence            44555555666778899999999999998744  5666666677778888998888777777787663 55688999999


Q ss_pred             HHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCH
Q 012111          228 DGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMY  307 (471)
Q Consensus       228 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~  307 (471)
                      ..|...|+.++|.+.|.+....+  +.=...|..+...|.-.|..|+|+..|...-+.= +-..--+.-+.--|.+.+..
T Consensus       320 ~YYl~i~k~seARry~SKat~lD--~~fgpaWl~fghsfa~e~EhdQAmaaY~tAarl~-~G~hlP~LYlgmey~~t~n~  396 (611)
T KOG1173|consen  320 CYYLMIGKYSEARRYFSKATTLD--PTFGPAWLAFGHSFAGEGEHDQAMAAYFTAARLM-PGCHLPSLYLGMEYMRTNNL  396 (611)
T ss_pred             HHHHHhcCcHHHHHHHHHHhhcC--ccccHHHHHHhHHhhhcchHHHHHHHHHHHHHhc-cCCcchHHHHHHHHHHhccH
Confidence            99999999999999999886543  2224579999999999999999999998775431 11111223344557788999


Q ss_pred             HHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc----C--CCCCHHHHHHHHHHHHhcCCHHHHH
Q 012111          308 DKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHR----G--MKPNSITYCSLVSAYSKAGLIMKVD  381 (471)
Q Consensus       308 ~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~----~--~~p~~~~~~~li~~~~~~g~~~~a~  381 (471)
                      +.|.+.|.+.....+ -|+..++-+.-.....+.+.+|..+|+..+..    +  ..-...+++.|..+|.+.+.+++|+
T Consensus       397 kLAe~Ff~~A~ai~P-~Dplv~~Elgvvay~~~~y~~A~~~f~~~l~~ik~~~~e~~~w~p~~~NLGH~~Rkl~~~~eAI  475 (611)
T KOG1173|consen  397 KLAEKFFKQALAIAP-SDPLVLHELGVVAYTYEEYPEALKYFQKALEVIKSVLNEKIFWEPTLNNLGHAYRKLNKYEEAI  475 (611)
T ss_pred             HHHHHHHHHHHhcCC-CcchhhhhhhheeehHhhhHHHHHHHHHHHHHhhhccccccchhHHHHhHHHHHHHHhhHHHHH
Confidence            999999998877633 37777888777777789999999999987732    1  1124457889999999999999999


Q ss_pred             HHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHh
Q 012111          382 SILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAYNA  443 (471)
Q Consensus       382 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~  443 (471)
                      ..++......+. +..++.++.-.|...|+++.|++.|.+..-  +.|+..+...++..+..
T Consensus       476 ~~~q~aL~l~~k-~~~~~asig~iy~llgnld~Aid~fhKaL~--l~p~n~~~~~lL~~aie  534 (611)
T KOG1173|consen  476 DYYQKALLLSPK-DASTHASIGYIYHLLGNLDKAIDHFHKALA--LKPDNIFISELLKLAIE  534 (611)
T ss_pred             HHHHHHHHcCCC-chhHHHHHHHHHHHhcChHHHHHHHHHHHh--cCCccHHHHHHHHHHHH
Confidence            999999988776 899999999999999999999999999886  68988877777765543

>KOG1156 consensus N-terminal acetyltransferase [Chromatin structure and dynamics]

Probab=99.36  E-value=9.4e-08  Score=87.70  Aligned_cols=389  Identities=11%  Similarity=0.041  Sum_probs=241.3

Q ss_pred             HHHhhHHHHHHHHHhhhhhhccCCCchHHHHHHHHHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHH
Q 012111           53 KILRTEFAIKNIEKKVSSKKYKNLWPKPVLEALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQ  132 (471)
Q Consensus        53 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  132 (471)
                      ....+...+..++..+..   .+-+++++...=-.+...|+-++|.+........+  ..+...|+.+.-.+-..+++++
T Consensus        19 E~kQYkkgLK~~~~iL~k---~~eHgeslAmkGL~L~~lg~~~ea~~~vr~glr~d--~~S~vCwHv~gl~~R~dK~Y~e   93 (700)
T KOG1156|consen   19 ETKQYKKGLKLIKQILKK---FPEHGESLAMKGLTLNCLGKKEEAYELVRLGLRND--LKSHVCWHVLGLLQRSDKKYDE   93 (700)
T ss_pred             HHHHHHhHHHHHHHHHHh---CCccchhHHhccchhhcccchHHHHHHHHHHhccC--cccchhHHHHHHHHhhhhhHHH
Confidence            344555666666666552   22334444433333456788888888888777654  5566778888877888888888


Q ss_pred             HHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 012111          133 ASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMS  212 (471)
Q Consensus       133 a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~  212 (471)
                      |++.|......+.. |...|.-+.-.-++.++++.....-..+.+.  .+-....|..+..+..-.|+...|..++++..
T Consensus        94 aiKcy~nAl~~~~d-N~qilrDlslLQ~QmRd~~~~~~tr~~LLql--~~~~ra~w~~~Avs~~L~g~y~~A~~il~ef~  170 (700)
T KOG1156|consen   94 AIKCYRNALKIEKD-NLQILRDLSLLQIQMRDYEGYLETRNQLLQL--RPSQRASWIGFAVAQHLLGEYKMALEILEEFE  170 (700)
T ss_pred             HHHHHHHHHhcCCC-cHHHHHHHHHHHHHHHhhhhHHHHHHHHHHh--hhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            88888888876543 6777777766667777777777776666652  13334457777777778888888888888887


Q ss_pred             HCC-CCCCHHHHHHHH------HHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhC
Q 012111          213 YLG-IECSAVTYNTII------DGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLM  285 (471)
Q Consensus       213 ~~g-~~~~~~~~~~l~------~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  285 (471)
                      +.. -.|+...+....      ....+.|..+.|.+.+......  +......-..-...+.+.++.++|..++..+...
T Consensus       171 ~t~~~~~s~~~~e~se~~Ly~n~i~~E~g~~q~ale~L~~~e~~--i~Dkla~~e~ka~l~~kl~~lEeA~~~y~~Ll~r  248 (700)
T KOG1156|consen  171 KTQNTSPSKEDYEHSELLLYQNQILIEAGSLQKALEHLLDNEKQ--IVDKLAFEETKADLLMKLGQLEEAVKVYRRLLER  248 (700)
T ss_pred             HhhccCCCHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHhhhhH--HHHHHHHhhhHHHHHHHHhhHHhHHHHHHHHHhh
Confidence            654 245655554332      2345567777777766555332  1222222334456677888888888888888765


Q ss_pred             CCCCCHHHHH-HHHHHHHHcCCHHHHH-HHHHHHHhC----------------------------------CCCCCHHHH
Q 012111          286 GVKADIQTLN-ILTKSYGRAGMYDKMR-SVMDFMQKR----------------------------------FFFPTVVTY  329 (471)
Q Consensus       286 ~~~~~~~~~~-~ll~~~~~~~~~~~a~-~~~~~~~~~----------------------------------~~~~~~~~~  329 (471)
                        .||...|. .+..++.+..+.-++. .+|....+.                                  |+++   ++
T Consensus       249 --nPdn~~Yy~~l~~~lgk~~d~~~~lk~ly~~ls~~y~r~e~p~Rlplsvl~~eel~~~vdkyL~~~l~Kg~p~---vf  323 (700)
T KOG1156|consen  249 --NPDNLDYYEGLEKALGKIKDMLEALKALYAILSEKYPRHECPRRLPLSVLNGEELKEIVDKYLRPLLSKGVPS---VF  323 (700)
T ss_pred             --CchhHHHHHHHHHHHHHHhhhHHHHHHHHHHHhhcCcccccchhccHHHhCcchhHHHHHHHHHHHhhcCCCc---hh
Confidence              35544443 3444443333333333 444444332                                  2111   11


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHH--------cC----------CCCCHH--HHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 012111          330 NIVIETFGKAGHIEKMEEYFKKMKH--------RG----------MKPNSI--TYCSLVSAYSKAGLIMKVDSILRQVEN  389 (471)
Q Consensus       330 ~~li~~~~~~g~~~~a~~~~~~m~~--------~~----------~~p~~~--~~~~li~~~~~~g~~~~a~~~~~~~~~  389 (471)
                      ..+...|-.   ..++ .+++++..        .|          -+|...  ++-.++..+-+.|+++.|..+++..++
T Consensus       324 ~dl~SLyk~---p~k~-~~le~Lvt~y~~~L~~~~~f~~~D~~~~E~PttllWt~y~laqh~D~~g~~~~A~~yId~AId  399 (700)
T KOG1156|consen  324 KDLRSLYKD---PEKV-AFLEKLVTSYQHSLSGTGMFNFLDDGKQEPPTTLLWTLYFLAQHYDKLGDYEVALEYIDLAID  399 (700)
T ss_pred             hhhHHHHhc---hhHh-HHHHHHHHHHHhhcccccCCCcccccccCCchHHHHHHHHHHHHHHHcccHHHHHHHHHHHhc
Confidence            122221111   1111 13333221        11          134443  344577788899999999999999888


Q ss_pred             CCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhhh
Q 012111          390 SDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAYNALGMTEAAQNLENKMIAMKE  462 (471)
Q Consensus       390 ~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~  462 (471)
                      +-+. -+..|..-.+.+...|++++|..++++..+.+ .||...-..-.....++.+.++|.++.....+.+.
T Consensus       400 HTPT-liEly~~KaRI~kH~G~l~eAa~~l~ea~elD-~aDR~INsKcAKYmLrAn~i~eA~~~~skFTr~~~  470 (700)
T KOG1156|consen  400 HTPT-LIELYLVKARIFKHAGLLDEAAAWLDEAQELD-TADRAINSKCAKYMLRANEIEEAEEVLSKFTREGF  470 (700)
T ss_pred             cCch-HHHHHHHHHHHHHhcCChHHHHHHHHHHHhcc-chhHHHHHHHHHHHHHccccHHHHHHHHHhhhccc
Confidence            6433 34456666688889999999999999988753 35555544566667788899999888888877664

>PF13041 PPR_2: PPR repeat family

Probab=99.35  E-value=2.9e-12  Score=79.39  Aligned_cols=50  Identities=34%  Similarity=0.515  Sum_probs=42.1

Q ss_pred             cCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHh
Q 012111          394 LDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAYNA  443 (471)
Q Consensus       394 ~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~  443 (471)
                      ||..+||.+|.+|++.|++++|.++|++|.+.|+.||..||+.++++|++
T Consensus         1 P~~~~yn~li~~~~~~~~~~~a~~l~~~M~~~g~~P~~~Ty~~li~~~~k   50 (50)
T PF13041_consen    1 PDVVTYNTLISGYCKAGKFEEALKLFKEMKKRGIKPDSYTYNILINGLCK   50 (50)
T ss_pred             CchHHHHHHHHHHHHCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHcC
Confidence            67888888888888888888888888888888888888888888888764

>KOG4318 consensus Bicoid mRNA stability factor [RNA processing and modification]

Probab=99.35  E-value=3.2e-10  Score=106.81  Aligned_cols=276  Identities=14%  Similarity=0.158  Sum_probs=178.5

Q ss_pred             HHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHC
Q 012111          135 LLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYL  214 (471)
Q Consensus       135 ~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~  214 (471)
                      .++-.+...|+.|+..||..+|.-|+..|+.+.|- +|.-|.- ...+.+...|+.++.+....++.+.+.         
T Consensus        11 nfla~~e~~gi~PnRvtyqsLiarYc~~gdieaat-if~fm~~-ksLpv~e~vf~~lv~sh~~And~Enpk---------   79 (1088)
T KOG4318|consen   11 NFLALHEISGILPNRVTYQSLIARYCTKGDIEAAT-IFPFMEI-KSLPVREGVFRGLVASHKEANDAENPK---------   79 (1088)
T ss_pred             hHHHHHHHhcCCCchhhHHHHHHHHcccCCCcccc-chhhhhc-ccccccchhHHHHHhcccccccccCCC---------
Confidence            35566777888888888888888888888888887 7777766 455677778888888877777776655         


Q ss_pred             CCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHh-CCCCCCHHH
Q 012111          215 GIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNL-MGVKADIQT  293 (471)
Q Consensus       215 g~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~-~~~~~~~~~  293 (471)
                        .|.+.+|..|..+|...|+...    |+...+         ....+...+...|.-..-..++..+.- .+.-||..+
T Consensus        80 --ep~aDtyt~Ll~ayr~hGDli~----fe~veq---------dLe~i~~sfs~~Gvgs~e~~fl~k~~c~p~~lpda~n  144 (1088)
T KOG4318|consen   80 --EPLADTYTNLLKAYRIHGDLIL----FEVVEQ---------DLESINQSFSDHGVGSPERWFLMKIHCCPHSLPDAEN  144 (1088)
T ss_pred             --CCchhHHHHHHHHHHhccchHH----HHHHHH---------HHHHHHhhhhhhccCcHHHHHHhhcccCcccchhHHH
Confidence              6778888888888888888765    332221         122233444555555554555544321 123334332


Q ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcC-CHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Q 012111          294 LNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAG-HIEKMEEYFKKMKHRGMKPNSITYCSLVSAYS  372 (471)
Q Consensus       294 ~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g-~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~  372 (471)
                         .+....-.|.++.+.+++..+...... .+...  ++.-+.... .+++-..+-+....   .|++.+|..++.+..
T Consensus       145 ---~illlv~eglwaqllkll~~~Pvsa~~-~p~~v--fLrqnv~~ntpvekLl~~cksl~e---~~~s~~l~a~l~~al  215 (1088)
T KOG4318|consen  145 ---AILLLVLEGLWAQLLKLLAKVPVSAWN-APFQV--FLRQNVVDNTPVEKLLNMCKSLVE---APTSETLHAVLKRAL  215 (1088)
T ss_pred             ---HHHHHHHHHHHHHHHHHHhhCCccccc-chHHH--HHHHhccCCchHHHHHHHHHHhhc---CCChHHHHHHHHHHH
Confidence               333444556677777776554332111 11111  233332222 23333333332222   578888888888888


Q ss_pred             hcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHH
Q 012111          373 KAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAYNALGMTE  448 (471)
Q Consensus       373 ~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~  448 (471)
                      ..|+++.|..++.+|.+.|+..+..-|..|+-+   .++...++.+++-|.+.|+.|+..|+.-.+-.+...|...
T Consensus       216 aag~~d~Ak~ll~emke~gfpir~HyFwpLl~g---~~~~q~~e~vlrgmqe~gv~p~seT~adyvip~l~N~~t~  288 (1088)
T KOG4318|consen  216 AAGDVDGAKNLLYEMKEKGFPIRAHYFWPLLLG---INAAQVFEFVLRGMQEKGVQPGSETQADYVIPQLSNGQTK  288 (1088)
T ss_pred             hcCchhhHHHHHHHHHHcCCCcccccchhhhhc---CccchHHHHHHHHHHHhcCCCCcchhHHHHHhhhcchhhh
Confidence            888888888888888888888777777777655   7788888888888888888888888887776666655433

>KOG2376 consensus Signal recognition particle, subunit Srp72 [Intracellular trafficking, secretion, and vesicular transport]

Probab=99.32  E-value=2e-07  Score=84.70  Aligned_cols=61  Identities=5%  Similarity=-0.027  Sum_probs=37.1

Q ss_pred             HHHHHHccCCHHHHHHHHHHHHHc--------CC----CCCCHHH-HHHHHHHHHhcCCHHHHHHHHHHHHhCC
Q 012111          226 IIDGYGKAKKFEEMESSFSAMVES--------GG----CHPDIFT-LNSMISAYGNSGNIEKMEKWYNEFNLMG  286 (471)
Q Consensus       226 l~~~~~~~~~~~~a~~~~~~~~~~--------~~----~~~~~~~-~~~l~~~~~~~~~~~~a~~~~~~~~~~~  286 (471)
                      ....+...|++..|+++++...+.        ..    +.....+ -.-|.-++-..|+..+|..+|...+...
T Consensus       181 ~Ac~~i~~gky~qA~elL~kA~~~~~e~l~~~d~~eEeie~el~~IrvQlayVlQ~~Gqt~ea~~iy~~~i~~~  254 (652)
T KOG2376|consen  181 TACILIENGKYNQAIELLEKALRICREKLEDEDTNEEEIEEELNPIRVQLAYVLQLQGQTAEASSIYVDIIKRN  254 (652)
T ss_pred             HHHHHHhcccHHHHHHHHHHHHHHHHHhhcccccchhhHHHHHHHHHHHHHHHHHHhcchHHHHHHHHHHHHhc
Confidence            344566788899999888877211        10    0001111 1223445667889999999888887765

>COG3063 PilF Tfp pilus assembly protein PilF [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=99.32  E-value=5.8e-09  Score=83.38  Aligned_cols=201  Identities=14%  Similarity=0.023  Sum_probs=128.5

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHh
Q 012111          259 LNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGK  338 (471)
Q Consensus       259 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~  338 (471)
                      ...|.-.|...|+...|..-+++..+.+ +.+..++..+...|.+.|+.+.|.+.|++....... +..+.|.....+|.
T Consensus        38 rlqLal~YL~~gd~~~A~~nlekAL~~D-Ps~~~a~~~~A~~Yq~~Ge~~~A~e~YrkAlsl~p~-~GdVLNNYG~FLC~  115 (250)
T COG3063          38 RLQLALGYLQQGDYAQAKKNLEKALEHD-PSYYLAHLVRAHYYQKLGENDLADESYRKALSLAPN-NGDVLNNYGAFLCA  115 (250)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHcCChhhHHHHHHHHHhcCCC-ccchhhhhhHHHHh
Confidence            3445555666666666666666666554 445556666666666666666666666666654332 44556666666677


Q ss_pred             cCCHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHH
Q 012111          339 AGHIEKMEEYFKKMKHRGMK-PNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGE  417 (471)
Q Consensus       339 ~g~~~~a~~~~~~m~~~~~~-p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~  417 (471)
                      .|++++|...|++....-.- --..+|..+.-+..+.|+.+.|...|++..+.++. .....-.+.......|++..|..
T Consensus       116 qg~~~eA~q~F~~Al~~P~Y~~~s~t~eN~G~Cal~~gq~~~A~~~l~raL~~dp~-~~~~~l~~a~~~~~~~~y~~Ar~  194 (250)
T COG3063         116 QGRPEEAMQQFERALADPAYGEPSDTLENLGLCALKAGQFDQAEEYLKRALELDPQ-FPPALLELARLHYKAGDYAPARL  194 (250)
T ss_pred             CCChHHHHHHHHHHHhCCCCCCcchhhhhhHHHHhhcCCchhHHHHHHHHHHhCcC-CChHHHHHHHHHHhcccchHHHH
Confidence            77777777777776654211 12456666666777777777777777777766554 44555666666777777777777


Q ss_pred             HHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhhhc
Q 012111          418 LFLTMKERHCVPDNITFATMIQAYNALGMTEAAQNLENKMIAMKEN  463 (471)
Q Consensus       418 ~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~  463 (471)
                      +++.....+. ++..++...|+.--..|+.+.+.++-..+.+.-|.
T Consensus       195 ~~~~~~~~~~-~~A~sL~L~iriak~~gd~~~a~~Y~~qL~r~fP~  239 (250)
T COG3063         195 YLERYQQRGG-AQAESLLLGIRIAKRLGDRAAAQRYQAQLQRLFPY  239 (250)
T ss_pred             HHHHHHhccc-ccHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCC
Confidence            7777766544 67777777777777777777776666665555544

>PF13041 PPR_2: PPR repeat family

Probab=99.31  E-value=7.7e-12  Score=77.47  Aligned_cols=49  Identities=47%  Similarity=0.784  Sum_probs=28.6

Q ss_pred             CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Q 012111          324 PTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYS  372 (471)
Q Consensus       324 ~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~  372 (471)
                      ||..+|+.+|.+|++.|++++|.++|++|.+.|+.||..||+.+|++|+
T Consensus         1 P~~~~yn~li~~~~~~~~~~~a~~l~~~M~~~g~~P~~~Ty~~li~~~~   49 (50)
T PF13041_consen    1 PDVVTYNTLISGYCKAGKFEEALKLFKEMKKRGIKPDSYTYNILINGLC   49 (50)
T ss_pred             CchHHHHHHHHHHHHCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHc
Confidence            4555555555555555555555555555555555555555555555554

>KOG2047 consensus mRNA splicing factor [RNA processing and modification]

Probab=99.29  E-value=3.3e-07  Score=84.17  Aligned_cols=375  Identities=10%  Similarity=0.126  Sum_probs=206.1

Q ss_pred             ccCCCchHHHHHHHHHHHhhcHHHHHHHHHHhhhccC-----ccCChhHHHHHHHHHhcCCCHHH---HHHHHHHHHhCC
Q 012111           73 YKNLWPKPVLEALDEAIKQKKWQLALKIFGLLRQQQW-----YQARCQTFTKLMVMLGKCKQPEQ---ASLLFEVMLSDG  144 (471)
Q Consensus        73 ~~~~~~~~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~-----~~~~~~~~~~l~~~~~~~~~~~~---a~~~~~~m~~~~  144 (471)
                      +-...|....+.+..+++.+++++|.+.+..+..+..     .+.+-..|..+-....+.-+.-.   ...++..+..+ 
T Consensus       164 YLk~~P~~~eeyie~L~~~d~~~eaa~~la~vln~d~f~sk~gkSn~qlw~elcdlis~~p~~~~slnvdaiiR~gi~r-  242 (835)
T KOG2047|consen  164 YLKVAPEAREEYIEYLAKSDRLDEAAQRLATVLNQDEFVSKKGKSNHQLWLELCDLISQNPDKVQSLNVDAIIRGGIRR-  242 (835)
T ss_pred             HHhcCHHHHHHHHHHHHhccchHHHHHHHHHhcCchhhhhhcccchhhHHHHHHHHHHhCcchhcccCHHHHHHhhccc-
Confidence            3345566667778888888899998888887764421     13455566666666665543332   33344444432 


Q ss_pred             CCCC--HHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcC----------------------C
Q 012111          145 LKPS--VDVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFH----------------------R  200 (471)
Q Consensus       145 ~~~~--~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~----------------------~  200 (471)
                       -+|  ...|++|.+-|++.|.+++|.++|++....   ..++.-|..+.++|+...                      +
T Consensus       243 -ftDq~g~Lw~SLAdYYIr~g~~ekarDvyeeai~~---v~tvrDFt~ifd~Ya~FEE~~~~~~me~a~~~~~n~ed~~d  318 (835)
T KOG2047|consen  243 -FTDQLGFLWCSLADYYIRSGLFEKARDVYEEAIQT---VMTVRDFTQIFDAYAQFEESCVAAKMELADEESGNEEDDVD  318 (835)
T ss_pred             -CcHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHh---heehhhHHHHHHHHHHHHHHHHHHHHhhhhhcccChhhhhh
Confidence             233  346888899999999999999998887652   234444555555554321                      1


Q ss_pred             HHHHHHHHHHHHHCC-----------CCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCC------HHHHHHHH
Q 012111          201 FDLIEKILAEMSYLG-----------IECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPD------IFTLNSMI  263 (471)
Q Consensus       201 ~~~a~~~~~~~~~~g-----------~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~------~~~~~~l~  263 (471)
                      ++....-|+.+...+           -+.+...|..-+.  +..|+..+-...|.+..+.  +.|.      ...|..+.
T Consensus       319 l~~~~a~~e~lm~rr~~~lNsVlLRQn~~nV~eW~kRV~--l~e~~~~~~i~tyteAv~~--vdP~ka~Gs~~~Lw~~fa  394 (835)
T KOG2047|consen  319 LELHMARFESLMNRRPLLLNSVLLRQNPHNVEEWHKRVK--LYEGNAAEQINTYTEAVKT--VDPKKAVGSPGTLWVEFA  394 (835)
T ss_pred             HHHHHHHHHHHHhccchHHHHHHHhcCCccHHHHHhhhh--hhcCChHHHHHHHHHHHHc--cCcccCCCChhhHHHHHH
Confidence            222333333333321           0112222222222  2235566666666666554  2221      23567777


Q ss_pred             HHHHhcCCHHHHHHHHHHHHhCCCCCC---HHHHHHHHHHHHHcCCHHHHHHHHHHHHhCC----------CCC------
Q 012111          264 SAYGNSGNIEKMEKWYNEFNLMGVKAD---IQTLNILTKSYGRAGMYDKMRSVMDFMQKRF----------FFP------  324 (471)
Q Consensus       264 ~~~~~~~~~~~a~~~~~~~~~~~~~~~---~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~----------~~~------  324 (471)
                      ..|-..|+.+.|..+|++......+.-   ..+|......-.+..+++.|.+++......-          ..|      
T Consensus       395 klYe~~~~l~~aRvifeka~~V~y~~v~dLa~vw~~waemElrh~~~~~Al~lm~~A~~vP~~~~~~~yd~~~pvQ~rlh  474 (835)
T KOG2047|consen  395 KLYENNGDLDDARVIFEKATKVPYKTVEDLAEVWCAWAEMELRHENFEAALKLMRRATHVPTNPELEYYDNSEPVQARLH  474 (835)
T ss_pred             HHHHhcCcHHHHHHHHHHhhcCCccchHHHHHHHHHHHHHHHhhhhHHHHHHHHHhhhcCCCchhhhhhcCCCcHHHHHH
Confidence            777777777777777777765443222   3455566666667777777777666543210          001      


Q ss_pred             -CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCH-HHHHHH
Q 012111          325 -TVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDT-PFFNCI  402 (471)
Q Consensus       325 -~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~-~~~~~l  402 (471)
                       +...|...++.--..|-++....+|+++.+..+. ++.+.......+-...-++++.+++++-+..-..|+. ..|+..
T Consensus       475 rSlkiWs~y~DleEs~gtfestk~vYdriidLria-TPqii~NyAmfLEeh~yfeesFk~YErgI~LFk~p~v~diW~tY  553 (835)
T KOG2047|consen  475 RSLKIWSMYADLEESLGTFESTKAVYDRIIDLRIA-TPQIIINYAMFLEEHKYFEESFKAYERGISLFKWPNVYDIWNTY  553 (835)
T ss_pred             HhHHHHHHHHHHHHHhccHHHHHHHHHHHHHHhcC-CHHHHHHHHHHHHhhHHHHHHHHHHHcCCccCCCccHHHHHHHH
Confidence             2334555555555667777777777777765432 3333333344444555666666666665544333333 345555


Q ss_pred             HHHHHhc---CCHHHHHHHHHHHHhCCCCCCHHHHHHHH--HHHHhcCCHHHHHHHHHHHH
Q 012111          403 ISAYGQA---GDVEKMGELFLTMKERHCVPDNITFATMI--QAYNALGMTEAAQNLENKMI  458 (471)
Q Consensus       403 ~~~~~~~---g~~~~a~~~~~~~~~~~~~p~~~~~~~l~--~~~~~~g~~~~A~~~~~~m~  458 (471)
                      +.-+.+.   -..+.|..+|+++.+ |++|...-+..|+  ..--+.|....|..+++++.
T Consensus       554 Ltkfi~rygg~klEraRdLFEqaL~-~Cpp~~aKtiyLlYA~lEEe~GLar~amsiyerat  613 (835)
T KOG2047|consen  554 LTKFIKRYGGTKLERARDLFEQALD-GCPPEHAKTIYLLYAKLEEEHGLARHAMSIYERAT  613 (835)
T ss_pred             HHHHHHHhcCCCHHHHHHHHHHHHh-cCCHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHH
Confidence            5544431   346666677766666 4555332221111  22233466666666666654

>KOG4162 consensus Predicted calmodulin-binding protein [Signal transduction mechanisms]

Probab=99.28  E-value=4.9e-07  Score=84.81  Aligned_cols=381  Identities=8%  Similarity=0.013  Sum_probs=224.5

Q ss_pred             chHHHHHHHHHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCC-HHHHHHHH
Q 012111           78 PKPVLEALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPS-VDVYTALV  156 (471)
Q Consensus        78 ~~~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~-~~~~~~li  156 (471)
                      +..+-.+--.+...|++..+.+.|++...--  -...+.|+.+...+...|.-..|..+++........|+ ...+-..-
T Consensus       323 ~ai~d~Lt~al~~~g~f~~lae~fE~~~~~~--~~~~e~w~~~als~saag~~s~Av~ll~~~~~~~~~ps~~s~~Lmas  400 (799)
T KOG4162|consen  323 AAIFDHLTFALSRCGQFEVLAEQFEQALPFS--FGEHERWYQLALSYSAAGSDSKAVNLLRESLKKSEQPSDISVLLMAS  400 (799)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhHhh--hhhHHHHHHHHHHHHHhccchHHHHHHHhhcccccCCCcchHHHHHH
Confidence            3344455556667788888888888776532  34456677777777777777777777776554432232 23333333


Q ss_pred             HHHHh-cCCHHHHHHHHHHhhcCCCC---CCCHHHHHHHHHHHHhc-----------CCHHHHHHHHHHHHHCCCCCCHH
Q 012111          157 SAYGQ-SGLLDEAFSTINDMKSVSDC---KPDVYTYSILIKSCTKF-----------HRFDLIEKILAEMSYLGIECSAV  221 (471)
Q Consensus       157 ~~~~~-~~~~~~a~~~~~~~~~~~~~---~~~~~~~~~ll~~~~~~-----------~~~~~a~~~~~~~~~~g~~~~~~  221 (471)
                      ..|.+ .+.++++++.-.+.....+-   ......|..+.-+|...           ....++.+.+++..+.+ +-|+.
T Consensus       401 klc~e~l~~~eegldYA~kai~~~~~~~~~l~~~~~l~lGi~y~~~A~~a~~~seR~~~h~kslqale~av~~d-~~dp~  479 (799)
T KOG4162|consen  401 KLCIERLKLVEEGLDYAQKAISLLGGQRSHLKPRGYLFLGIAYGFQARQANLKSERDALHKKSLQALEEAVQFD-PTDPL  479 (799)
T ss_pred             HHHHhchhhhhhHHHHHHHHHHHhhhhhhhhhhhHHHHHHHHHHhHhhcCCChHHHHHHHHHHHHHHHHHHhcC-CCCch
Confidence            33332 34455544444443331010   12223333333333211           12345666666665554 22333


Q ss_pred             HHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhC-CC-------------
Q 012111          222 TYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLM-GV-------------  287 (471)
Q Consensus       222 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-~~-------------  287 (471)
                      +...+.--|+..++.+.|.+..++..+.+ ...+...|..|.-.+...+++.+|+.+.+..... |.             
T Consensus       480 ~if~lalq~A~~R~l~sAl~~~~eaL~l~-~~~~~~~whLLALvlSa~kr~~~Al~vvd~al~E~~~N~~l~~~~~~i~~  558 (799)
T KOG4162|consen  480 VIFYLALQYAEQRQLTSALDYAREALALN-RGDSAKAWHLLALVLSAQKRLKEALDVVDAALEEFGDNHVLMDGKIHIEL  558 (799)
T ss_pred             HHHHHHHHHHHHHhHHHHHHHHHHHHHhc-CCccHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHhhhhhhhchhhhhhhh
Confidence            33334444555666667766666666553 2445556666666666666666666666554332 10             


Q ss_pred             -----CCCHHHHHHHHHHHHHc-----------------------CCHHHHHHHHHH----H----HhCC---------C
Q 012111          288 -----KADIQTLNILTKSYGRA-----------------------GMYDKMRSVMDF----M----QKRF---------F  322 (471)
Q Consensus       288 -----~~~~~~~~~ll~~~~~~-----------------------~~~~~a~~~~~~----~----~~~~---------~  322 (471)
                           .....|...++..+-..                       ++..++......    +    ...+         .
T Consensus       559 ~~~~~e~~l~t~~~~L~~we~~~~~q~~~~~g~~~~lk~~l~la~~q~~~a~s~sr~ls~l~a~~~~~~~se~~Lp~s~~  638 (799)
T KOG4162|consen  559 TFNDREEALDTCIHKLALWEAEYGVQQTLDEGKLLRLKAGLHLALSQPTDAISTSRYLSSLVASQLKSAGSELKLPSSTV  638 (799)
T ss_pred             hcccHHHHHHHHHHHHHHHHhhhhHhhhhhhhhhhhhhcccccCcccccccchhhHHHHHHHHhhhhhcccccccCcccc
Confidence                 00011222222222100                       001111111000    0    0000         0


Q ss_pred             --CCC------HHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCc
Q 012111          323 --FPT------VVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVIL  394 (471)
Q Consensus       323 --~~~------~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~  394 (471)
                        .|+      ...|......+.+.+..++|.-.+.+..... ......|......+...|..++|.+.|......++. 
T Consensus       639 ~~~~~~~~~~~~~lwllaa~~~~~~~~~~~a~~CL~Ea~~~~-~l~~~~~~~~G~~~~~~~~~~EA~~af~~Al~ldP~-  716 (799)
T KOG4162|consen  639 LPGPDSLWYLLQKLWLLAADLFLLSGNDDEARSCLLEASKID-PLSASVYYLRGLLLEVKGQLEEAKEAFLVALALDPD-  716 (799)
T ss_pred             cCCCCchHHHHHHHHHHHHHHHHhcCCchHHHHHHHHHHhcc-hhhHHHHHHhhHHHHHHHhhHHHHHHHHHHHhcCCC-
Confidence              111      1234455566778888888888887776642 345667777778888999999999999999988776 


Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHH--HHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhhhcCC
Q 012111          395 DTPFFNCIISAYGQAGDVEKMGE--LFLTMKERHCVPDNITFATMIQAYNALGMTEAAQNLENKMIAMKENSG  465 (471)
Q Consensus       395 ~~~~~~~l~~~~~~~g~~~~a~~--~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~~~  465 (471)
                      ++.+..++..++.+.|+...|..  ++..+.+.+ +-+...|..+...+.+.|+.+.|.+.|.-...+.+..+
T Consensus       717 hv~s~~Ala~~lle~G~~~la~~~~~L~dalr~d-p~n~eaW~~LG~v~k~~Gd~~~Aaecf~aa~qLe~S~P  788 (799)
T KOG4162|consen  717 HVPSMTALAELLLELGSPRLAEKRSLLSDALRLD-PLNHEAWYYLGEVFKKLGDSKQAAECFQAALQLEESNP  788 (799)
T ss_pred             CcHHHHHHHHHHHHhCCcchHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHccchHHHHHHHHHHHhhccCCC
Confidence            77889999999999999888887  999998863 34788999999999999999999999999998887644

>KOG1156 consensus N-terminal acetyltransferase [Chromatin structure and dynamics]

Probab=99.27  E-value=2.2e-07  Score=85.43  Aligned_cols=370  Identities=11%  Similarity=0.137  Sum_probs=251.9

Q ss_pred             HHHHHHHHHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHH
Q 012111           80 PVLEALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAY  159 (471)
Q Consensus        80 ~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~  159 (471)
                      .+...+-.+...+++...+++.+.+.+.  ++...++.....-.+...|+-++|......-....+. +.+.|+++.-.+
T Consensus         9 ~lF~~~lk~yE~kQYkkgLK~~~~iL~k--~~eHgeslAmkGL~L~~lg~~~ea~~~vr~glr~d~~-S~vCwHv~gl~~   85 (700)
T KOG1156|consen    9 ALFRRALKCYETKQYKKGLKLIKQILKK--FPEHGESLAMKGLTLNCLGKKEEAYELVRLGLRNDLK-SHVCWHVLGLLQ   85 (700)
T ss_pred             HHHHHHHHHHHHHHHHhHHHHHHHHHHh--CCccchhHHhccchhhcccchHHHHHHHHHHhccCcc-cchhHHHHHHHH
Confidence            3444555667889999999999999985  4667778888888888999999999999888876554 888999999999


Q ss_pred             HhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHH
Q 012111          160 GQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEM  239 (471)
Q Consensus       160 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~a  239 (471)
                      -...++++|+..|.......  +-|...+.-+.-.-++.++++.....-..+.+.. +-....|..+..++.-.|++..|
T Consensus        86 R~dK~Y~eaiKcy~nAl~~~--~dN~qilrDlslLQ~QmRd~~~~~~tr~~LLql~-~~~ra~w~~~Avs~~L~g~y~~A  162 (700)
T KOG1156|consen   86 RSDKKYDEAIKCYRNALKIE--KDNLQILRDLSLLQIQMRDYEGYLETRNQLLQLR-PSQRASWIGFAVAQHLLGEYKMA  162 (700)
T ss_pred             hhhhhHHHHHHHHHHHHhcC--CCcHHHHHHHHHHHHHHHhhhhHHHHHHHHHHhh-hhhHHHHHHHHHHHHHHHHHHHH
Confidence            88999999999999998732  4566677777666678888888888887777653 33456677888888889999999


Q ss_pred             HHHHHHHHHcCCCCCCHHHHHHHH------HHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHH
Q 012111          240 ESSFSAMVESGGCHPDIFTLNSMI------SAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSV  313 (471)
Q Consensus       240 ~~~~~~~~~~~~~~~~~~~~~~l~------~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~  313 (471)
                      ..+++...+.....|+...|....      ......|..+.|.+.+..-... +.-....-..-...+.+.+++++|..+
T Consensus       163 ~~il~ef~~t~~~~~s~~~~e~se~~Ly~n~i~~E~g~~q~ale~L~~~e~~-i~Dkla~~e~ka~l~~kl~~lEeA~~~  241 (700)
T KOG1156|consen  163 LEILEEFEKTQNTSPSKEDYEHSELLLYQNQILIEAGSLQKALEHLLDNEKQ-IVDKLAFEETKADLLMKLGQLEEAVKV  241 (700)
T ss_pred             HHHHHHHHHhhccCCCHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHhhhhH-HHHHHHHhhhHHHHHHHHhhHHhHHHH
Confidence            999999977653356666655443      3456678888888887765432 111222234445678899999999999


Q ss_pred             HHHHHhCCCCCCHHHHHHHH-HHHHhcCCHHHHH-HHHHH----------------------------------HHHcCC
Q 012111          314 MDFMQKRFFFPTVVTYNIVI-ETFGKAGHIEKME-EYFKK----------------------------------MKHRGM  357 (471)
Q Consensus       314 ~~~~~~~~~~~~~~~~~~li-~~~~~~g~~~~a~-~~~~~----------------------------------m~~~~~  357 (471)
                      +..+...  .||...|...+ .++.+--+.-++. .+|..                                  +.+.|+
T Consensus       242 y~~Ll~r--nPdn~~Yy~~l~~~lgk~~d~~~~lk~ly~~ls~~y~r~e~p~Rlplsvl~~eel~~~vdkyL~~~l~Kg~  319 (700)
T KOG1156|consen  242 YRRLLER--NPDNLDYYEGLEKALGKIKDMLEALKALYAILSEKYPRHECPRRLPLSVLNGEELKEIVDKYLRPLLSKGV  319 (700)
T ss_pred             HHHHHhh--CchhHHHHHHHHHHHHHHhhhHHHHHHHHHHHhhcCcccccchhccHHHhCcchhHHHHHHHHHHHhhcCC
Confidence            9999887  45666555544 3332222222222 33333                                  333333


Q ss_pred             CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHH----hCC----------CCcCHHHH--HHHHHHHHhcCCHHHHHHHHHH
Q 012111          358 KPNSITYCSLVSAYSKAGLIMKVDSILRQVE----NSD----------VILDTPFF--NCIISAYGQAGDVEKMGELFLT  421 (471)
Q Consensus       358 ~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~----~~~----------~~~~~~~~--~~l~~~~~~~g~~~~a~~~~~~  421 (471)
                      ++   ++..+...|-.-...+-..++.-.+.    ..|          -.|....|  -.++..+-+.|+++.|..+++.
T Consensus       320 p~---vf~dl~SLyk~p~k~~~le~Lvt~y~~~L~~~~~f~~~D~~~~E~PttllWt~y~laqh~D~~g~~~~A~~yId~  396 (700)
T KOG1156|consen  320 PS---VFKDLRSLYKDPEKVAFLEKLVTSYQHSLSGTGMFNFLDDGKQEPPTTLLWTLYFLAQHYDKLGDYEVALEYIDL  396 (700)
T ss_pred             Cc---hhhhhHHHHhchhHhHHHHHHHHHHHhhcccccCCCcccccccCCchHHHHHHHHHHHHHHHcccHHHHHHHHHH
Confidence            32   12222222222111111111111111    111          13444444  4567788899999999999999


Q ss_pred             HHhCCCCCCHH-HHHHHHHHHHhcCCHHHHHHHHHHHHHhhhc
Q 012111          422 MKERHCVPDNI-TFATMIQAYNALGMTEAAQNLENKMIAMKEN  463 (471)
Q Consensus       422 ~~~~~~~p~~~-~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~  463 (471)
                      ..+.  .|+.. .|..-.+.+...|+.++|..+++++.+++-.
T Consensus       397 AIdH--TPTliEly~~KaRI~kH~G~l~eAa~~l~ea~elD~a  437 (700)
T KOG1156|consen  397 AIDH--TPTLIELYLVKARIFKHAGLLDEAAAWLDEAQELDTA  437 (700)
T ss_pred             Hhcc--CchHHHHHHHHHHHHHhcCChHHHHHHHHHHHhccch
Confidence            9975  66654 4555568899999999999999999887754

>KOG4340 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.26  E-value=5.3e-08  Score=80.85  Aligned_cols=294  Identities=12%  Similarity=0.087  Sum_probs=209.7

Q ss_pred             chHHHHHHHHHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHH-HH
Q 012111           78 PKPVLEALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTA-LV  156 (471)
Q Consensus        78 ~~~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~-li  156 (471)
                      ......++..+++..++.+|++++..-.++.  +.+......+..+|....++..|...++++-..  .|...-|.. -.
T Consensus        10 EGeftaviy~lI~d~ry~DaI~~l~s~~Er~--p~~rAgLSlLgyCYY~~Q~f~~AA~CYeQL~ql--~P~~~qYrlY~A   85 (459)
T KOG4340|consen   10 EGEFTAVVYRLIRDARYADAIQLLGSELERS--PRSRAGLSLLGYCYYRLQEFALAAECYEQLGQL--HPELEQYRLYQA   85 (459)
T ss_pred             CCchHHHHHHHHHHhhHHHHHHHHHHHHhcC--ccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhh--ChHHHHHHHHHH
Confidence            3456677888889999999999999988875  558888999999999999999999999999875  556555543 34


Q ss_pred             HHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHHHH--HHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccC
Q 012111          157 SAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKS--CTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAK  234 (471)
Q Consensus       157 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~--~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~  234 (471)
                      ..+.+.+.+.+|+.+...|..    .++...-..-+.+  ....+++..+..++++....|   +..+.+.......+.|
T Consensus        86 QSLY~A~i~ADALrV~~~~~D----~~~L~~~~lqLqaAIkYse~Dl~g~rsLveQlp~en---~Ad~~in~gCllykeg  158 (459)
T KOG4340|consen   86 QSLYKACIYADALRVAFLLLD----NPALHSRVLQLQAAIKYSEGDLPGSRSLVEQLPSEN---EADGQINLGCLLYKEG  158 (459)
T ss_pred             HHHHHhcccHHHHHHHHHhcC----CHHHHHHHHHHHHHHhcccccCcchHHHHHhccCCC---ccchhccchheeeccc
Confidence            567788999999999998875    2333322222222  345678888888888877544   5666666777778999


Q ss_pred             CHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC-------------CHH---------
Q 012111          235 KFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKA-------------DIQ---------  292 (471)
Q Consensus       235 ~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~-------------~~~---------  292 (471)
                      +++.|.+-|+...+-+|..|-. .|+..+. ..+.|+++.|++...+++++|++.             |+.         
T Consensus       159 qyEaAvqkFqaAlqvsGyqpll-AYniALa-Hy~~~qyasALk~iSEIieRG~r~HPElgIGm~tegiDvrsvgNt~~lh  236 (459)
T KOG4340|consen  159 QYEAAVQKFQAALQVSGYQPLL-AYNLALA-HYSSRQYASALKHISEIIERGIRQHPELGIGMTTEGIDVRSVGNTLVLH  236 (459)
T ss_pred             cHHHHHHHHHHHHhhcCCCchh-HHHHHHH-HHhhhhHHHHHHHHHHHHHhhhhcCCccCccceeccCchhcccchHHHH
Confidence            9999999999999998887754 6766554 457889999999999998876532             211         


Q ss_pred             ------HHHHHHHHHHHcCCHHHHHHHHHHHHhCC-CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHH
Q 012111          293 ------TLNILTKSYGRAGMYDKMRSVMDFMQKRF-FFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYC  365 (471)
Q Consensus       293 ------~~~~ll~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~  365 (471)
                            .+|.-...+.+.|+++.|.+-+-.|..+. ...|++|...+.-.- ..+++.+..+-+.-+...+. -...||.
T Consensus       237 ~Sal~eAfNLKaAIeyq~~n~eAA~eaLtDmPPRaE~elDPvTLHN~Al~n-~~~~p~~g~~KLqFLL~~nP-fP~ETFA  314 (459)
T KOG4340|consen  237 QSALVEAFNLKAAIEYQLRNYEAAQEALTDMPPRAEEELDPVTLHNQALMN-MDARPTEGFEKLQFLLQQNP-FPPETFA  314 (459)
T ss_pred             HHHHHHHhhhhhhhhhhcccHHHHHHHhhcCCCcccccCCchhhhHHHHhc-ccCCccccHHHHHHHHhcCC-CChHHHH
Confidence                  12323334567889999988888775432 334666655543221 23445555555555555432 3467888


Q ss_pred             HHHHHHHhcCCHHHHHHHHHH
Q 012111          366 SLVSAYSKAGLIMKVDSILRQ  386 (471)
Q Consensus       366 ~li~~~~~~g~~~~a~~~~~~  386 (471)
                      .++-.||++.-++.|-+++.+
T Consensus       315 NlLllyCKNeyf~lAADvLAE  335 (459)
T KOG4340|consen  315 NLLLLYCKNEYFDLAADVLAE  335 (459)
T ss_pred             HHHHHHhhhHHHhHHHHHHhh
Confidence            888888888888888777654

>PRK11189 lipoprotein NlpI; Provisional

Probab=99.25  E-value=1.4e-08  Score=89.83  Aligned_cols=229  Identities=9%  Similarity=-0.028  Sum_probs=155.3

Q ss_pred             hcCCHHHHHHHHHHHHHCC-CCC--CHHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHH
Q 012111          197 KFHRFDLIEKILAEMSYLG-IEC--SAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIE  273 (471)
Q Consensus       197 ~~~~~~~a~~~~~~~~~~g-~~~--~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  273 (471)
                      ..+..+.++.-+.+++... ..|  ....|..+...|...|++++|...|++..+..  +.+...|+.+...+...|+++
T Consensus        38 ~~~~~e~~i~~~~~~l~~~~~~~~~~a~~~~~~g~~~~~~g~~~~A~~~~~~Al~l~--P~~~~a~~~lg~~~~~~g~~~  115 (296)
T PRK11189         38 PTLQQEVILARLNQILASRDLTDEERAQLHYERGVLYDSLGLRALARNDFSQALALR--PDMADAYNYLGIYLTQAGNFD  115 (296)
T ss_pred             CchHHHHHHHHHHHHHccccCCcHhhHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcC--CCCHHHHHHHHHHHHHCCCHH
Confidence            3456677888888887542 122  24567777888889999999999999988764  456788899999999999999


Q ss_pred             HHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 012111          274 KMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMK  353 (471)
Q Consensus       274 ~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~  353 (471)
                      +|...|+...+.. +-+..++..+..++...|++++|...|+...+...  +..........+...++.++|...+.+..
T Consensus       116 ~A~~~~~~Al~l~-P~~~~a~~~lg~~l~~~g~~~eA~~~~~~al~~~P--~~~~~~~~~~l~~~~~~~~~A~~~l~~~~  192 (296)
T PRK11189        116 AAYEAFDSVLELD-PTYNYAYLNRGIALYYGGRYELAQDDLLAFYQDDP--NDPYRALWLYLAESKLDPKQAKENLKQRY  192 (296)
T ss_pred             HHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCC--CCHHHHHHHHHHHccCCHHHHHHHHHHHH
Confidence            9999999988754 44567778888888889999999999998887643  32211222223445678999999997655


Q ss_pred             HcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhC---CCC---cCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCC
Q 012111          354 HRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENS---DVI---LDTPFFNCIISAYGQAGDVEKMGELFLTMKERHC  427 (471)
Q Consensus       354 ~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~---~~~---~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~  427 (471)
                      ... .|+...+ .  ......|+...+ +.+..+.+.   .+.   .....|..+...+...|++++|+..|++..+.+ 
T Consensus       193 ~~~-~~~~~~~-~--~~~~~lg~~~~~-~~~~~~~~~~~~~~~l~~~~~ea~~~Lg~~~~~~g~~~~A~~~~~~Al~~~-  266 (296)
T PRK11189        193 EKL-DKEQWGW-N--IVEFYLGKISEE-TLMERLKAGATDNTELAERLCETYFYLAKYYLSLGDLDEAAALFKLALANN-  266 (296)
T ss_pred             hhC-CccccHH-H--HHHHHccCCCHH-HHHHHHHhcCCCcHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-
Confidence            432 3332221 2  223335555444 344444421   111   123578888889999999999999999988753 


Q ss_pred             CCCHHHHHH
Q 012111          428 VPDNITFAT  436 (471)
Q Consensus       428 ~p~~~~~~~  436 (471)
                      .||..-+..
T Consensus       267 ~~~~~e~~~  275 (296)
T PRK11189        267 VYNFVEHRY  275 (296)
T ss_pred             CchHHHHHH
Confidence            345555544

>cd05804 StaR_like StaR_like; a well-conserved protein found in bacteria, plants, and animals

Probab=99.24  E-value=2.7e-07  Score=84.85  Aligned_cols=62  Identities=19%  Similarity=0.050  Sum_probs=36.5

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHhCCCC-------C-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhhh
Q 012111          401 CIISAYGQAGDVEKMGELFLTMKERHCV-------P-DNITFATMIQAYNALGMTEAAQNLENKMIAMKE  462 (471)
Q Consensus       401 ~l~~~~~~~g~~~~a~~~~~~~~~~~~~-------p-~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~  462 (471)
                      ....++...|+.+.|..+++.+......       . ..........++...|++++|.+.+...+....
T Consensus       269 ~~a~~~~~~~~~~~a~~~L~~l~~~~~~~~~~~~~~~~~~~~~l~A~~~~~~g~~~~A~~~L~~al~~a~  338 (355)
T cd05804         269 HAALALAGAGDKDALDKLLAALKGRASSADDNKQPARDVGLPLAEALYAFAEGNYATALELLGPVRDDLA  338 (355)
T ss_pred             HHHHHHhcCCCHHHHHHHHHHHHHHHhccCchhhhHHhhhHHHHHHHHHHHcCCHHHHHHHHHHHHHHHH
Confidence            4555666777777777777776542111       0 111111222345677888888888887776654

A family member from Streptomyces toyocaensis, StaR is part of a gene cluster involved in the biosynthesis of glycopeptide antibiotics (GPAs), specifically A47934. It has been speculated that StaR could be a flavoprotein hydroxylating a tyrosine sidechain. Some family members have been annotated as proteins containing tetratricopeptide (TPR) repeats, which may at least indicate mostly alpha-helical secondary structure.

>KOG1840 consensus Kinesin light chain [Cytoskeleton]

Probab=99.24  E-value=2.1e-08  Score=92.81  Aligned_cols=130  Identities=17%  Similarity=0.152  Sum_probs=78.3

Q ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHhC---CCCC----CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc-----C-CCC-
Q 012111          294 LNILTKSYGRAGMYDKMRSVMDFMQKR---FFFP----TVVTYNIVIETFGKAGHIEKMEEYFKKMKHR-----G-MKP-  359 (471)
Q Consensus       294 ~~~ll~~~~~~~~~~~a~~~~~~~~~~---~~~~----~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~-----~-~~p-  359 (471)
                      ++.+...++..+++++|..++....+.   -+.+    -..+++.|...|...|++++|.+++++.+..     | ..+ 
T Consensus       328 l~~~~~~~~~~~~~Eea~~l~q~al~i~~~~~g~~~~~~a~~~~nl~~l~~~~gk~~ea~~~~k~ai~~~~~~~~~~~~~  407 (508)
T KOG1840|consen  328 LSELAAILQSMNEYEEAKKLLQKALKIYLDAPGEDNVNLAKIYANLAELYLKMGKYKEAEELYKKAIQILRELLGKKDYG  407 (508)
T ss_pred             HHHHHHHHHHhcchhHHHHHHHHHHHHHHhhccccchHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHhcccCcChh
Confidence            344445555556666665555433221   1111    2346777777777777777777777776543     1 111 


Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHh----CCCC--cCHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 012111          360 NSITYCSLVSAYSKAGLIMKVDSILRQVEN----SDVI--LDTPFFNCIISAYGQAGDVEKMGELFLTMK  423 (471)
Q Consensus       360 ~~~~~~~li~~~~~~g~~~~a~~~~~~~~~----~~~~--~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~  423 (471)
                      ....++.+...|.+.+.+++|.++|.+...    .|+.  -...+|..|...|...|+++.|+++.+...
T Consensus       408 ~~~~l~~la~~~~~~k~~~~a~~l~~~~~~i~~~~g~~~~~~~~~~~nL~~~Y~~~g~~e~a~~~~~~~~  477 (508)
T KOG1840|consen  408 VGKPLNQLAEAYEELKKYEEAEQLFEEAKDIMKLCGPDHPDVTYTYLNLAALYRAQGNYEAAEELEEKVL  477 (508)
T ss_pred             hhHHHHHHHHHHHHhcccchHHHHHHHHHHHHHHhCCCCCchHHHHHHHHHHHHHcccHHHHHHHHHHHH
Confidence            244567777777777777777777765432    2222  134567778888888888888888777655

>PRK11189 lipoprotein NlpI; Provisional

Probab=99.22  E-value=4.4e-08  Score=86.76  Aligned_cols=195  Identities=11%  Similarity=-0.004  Sum_probs=87.4

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHH
Q 012111          188 YSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYG  267 (471)
Q Consensus       188 ~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~  267 (471)
                      |..+...+...|+.+.|...|++..+.. +.+...|+.+...+...|++++|...|++..+..  +.+..++..+..++.
T Consensus        67 ~~~~g~~~~~~g~~~~A~~~~~~Al~l~-P~~~~a~~~lg~~~~~~g~~~~A~~~~~~Al~l~--P~~~~a~~~lg~~l~  143 (296)
T PRK11189         67 HYERGVLYDSLGLRALARNDFSQALALR-PDMADAYNYLGIYLTQAGNFDAAYEAFDSVLELD--PTYNYAYLNRGIALY  143 (296)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHH
Confidence            4444444555555555555555555443 2344555555555555555555555555555432  223344455555555


Q ss_pred             hcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHH
Q 012111          268 NSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEE  347 (471)
Q Consensus       268 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~  347 (471)
                      ..|++++|.+.|+...+..  |+..........+...++.++|...|....... .++...+ .+.  ....|+...+ +
T Consensus       144 ~~g~~~eA~~~~~~al~~~--P~~~~~~~~~~l~~~~~~~~~A~~~l~~~~~~~-~~~~~~~-~~~--~~~lg~~~~~-~  216 (296)
T PRK11189        144 YGGRYELAQDDLLAFYQDD--PNDPYRALWLYLAESKLDPKQAKENLKQRYEKL-DKEQWGW-NIV--EFYLGKISEE-T  216 (296)
T ss_pred             HCCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHccCCHHHHHHHHHHHHhhC-CccccHH-HHH--HHHccCCCHH-H
Confidence            5555555555555554432  221111111122233445555555554433221 1111111 111  1223333222 2


Q ss_pred             HHHHHHHc---CC--CC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCC
Q 012111          348 YFKKMKHR---GM--KP-NSITYCSLVSAYSKAGLIMKVDSILRQVENSDV  392 (471)
Q Consensus       348 ~~~~m~~~---~~--~p-~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~  392 (471)
                      .+..+.+.   .+  .| ....|..+...+...|++++|...|++..+.++
T Consensus       217 ~~~~~~~~~~~~~~l~~~~~ea~~~Lg~~~~~~g~~~~A~~~~~~Al~~~~  267 (296)
T PRK11189        217 LMERLKAGATDNTELAERLCETYFYLAKYYLSLGDLDEAAALFKLALANNV  267 (296)
T ss_pred             HHHHHHhcCCCcHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCC
Confidence            22222211   00  01 224566666666666666666666666666543

>KOG1174 consensus Anaphase-promoting complex (APC), subunit 7 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]

Probab=99.21  E-value=1.4e-07  Score=81.88  Aligned_cols=303  Identities=11%  Similarity=0.039  Sum_probs=195.0

Q ss_pred             cCChhHHHHHHHHHhcC--CCHHHHHHHHHHHHhC-CCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHH-
Q 012111          111 QARCQTFTKLMVMLGKC--KQPEQASLLFEVMLSD-GLKPSVDVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVY-  186 (471)
Q Consensus       111 ~~~~~~~~~l~~~~~~~--~~~~~a~~~~~~m~~~-~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~-  186 (471)
                      +|...+...-+.+++..  ++-..|...+-.+... -++-++.....+..++...|+.++|+..|++....   .|+.. 
T Consensus       191 ~~~~dwls~wika~Aq~~~~~hs~a~~t~l~le~~~~lr~NvhLl~~lak~~~~~Gdn~~a~~~Fe~~~~~---dpy~i~  267 (564)
T KOG1174|consen  191 PDHFDWLSKWIKALAQMFNFKHSDASQTFLMLHDNTTLRCNEHLMMALGKCLYYNGDYFQAEDIFSSTLCA---NPDNVE  267 (564)
T ss_pred             CCCccHHHHHHHHHHHHHhcccchhhhHHHHHHhhccCCccHHHHHHHhhhhhhhcCchHHHHHHHHHhhC---Chhhhh
Confidence            44444444444444332  3333344433333322 24556777888888888888888888888887652   33332 


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHH
Q 012111          187 TYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAY  266 (471)
Q Consensus       187 ~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~  266 (471)
                      ......-.+.+.|+.+....+...+.... .-+...|..-........+++.|+.+-++.++.+  +.+...|..-...+
T Consensus       268 ~MD~Ya~LL~~eg~~e~~~~L~~~Lf~~~-~~ta~~wfV~~~~l~~~K~~~rAL~~~eK~I~~~--~r~~~alilKG~lL  344 (564)
T KOG1174|consen  268 AMDLYAVLLGQEGGCEQDSALMDYLFAKV-KYTASHWFVHAQLLYDEKKFERALNFVEKCIDSE--PRNHEALILKGRLL  344 (564)
T ss_pred             hHHHHHHHHHhccCHhhHHHHHHHHHhhh-hcchhhhhhhhhhhhhhhhHHHHHHHHHHHhccC--cccchHHHhccHHH
Confidence            22333334557788888777777776542 1233334444445556678888888888877653  44455555556677


Q ss_pred             HhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHH-HHHHh-cCCHHH
Q 012111          267 GNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVI-ETFGK-AGHIEK  344 (471)
Q Consensus       267 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li-~~~~~-~g~~~~  344 (471)
                      ...|++++|.-.|+..+... +.+...|..|+..|...|.+.+|.-+-+...+. +..+..+...+. ..+.- ..--++
T Consensus       345 ~~~~R~~~A~IaFR~Aq~La-p~rL~~Y~GL~hsYLA~~~~kEA~~~An~~~~~-~~~sA~~LtL~g~~V~~~dp~~rEK  422 (564)
T KOG1174|consen  345 IALERHTQAVIAFRTAQMLA-PYRLEIYRGLFHSYLAQKRFKEANALANWTIRL-FQNSARSLTLFGTLVLFPDPRMREK  422 (564)
T ss_pred             HhccchHHHHHHHHHHHhcc-hhhHHHHHHHHHHHHhhchHHHHHHHHHHHHHH-hhcchhhhhhhcceeeccCchhHHH
Confidence            78888888888888877643 567788888888888888888887766655443 222444444442 22222 223467


Q ss_pred             HHHHHHHHHHcCCCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 012111          345 MEEYFKKMKHRGMKPN-SITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMK  423 (471)
Q Consensus       345 a~~~~~~m~~~~~~p~-~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~  423 (471)
                      |.++++.-...  .|+ ....+.+...|...|..+.+..+++.....  .||....+.|...+...+.+++|.+.|....
T Consensus       423 AKkf~ek~L~~--~P~Y~~AV~~~AEL~~~Eg~~~D~i~LLe~~L~~--~~D~~LH~~Lgd~~~A~Ne~Q~am~~y~~AL  498 (564)
T KOG1174|consen  423 AKKFAEKSLKI--NPIYTPAVNLIAELCQVEGPTKDIIKLLEKHLII--FPDVNLHNHLGDIMRAQNEPQKAMEYYYKAL  498 (564)
T ss_pred             HHHHHHhhhcc--CCccHHHHHHHHHHHHhhCccchHHHHHHHHHhh--ccccHHHHHHHHHHHHhhhHHHHHHHHHHHH
Confidence            78888776654  554 446677777888888888888888876653  4677788888888888888888888888777


Q ss_pred             hC
Q 012111          424 ER  425 (471)
Q Consensus       424 ~~  425 (471)
                      ..
T Consensus       499 r~  500 (564)
T KOG1174|consen  499 RQ  500 (564)
T ss_pred             hc
Confidence            63

>cd05804 StaR_like StaR_like; a well-conserved protein found in bacteria, plants, and animals

Probab=99.21  E-value=3e-07  Score=84.59  Aligned_cols=306  Identities=10%  Similarity=0.038  Sum_probs=150.3

Q ss_pred             hhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCC-CCCH-HHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHH-
Q 012111          114 CQTFTKLMVMLGKCKQPEQASLLFEVMLSDGL-KPSV-DVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSI-  190 (471)
Q Consensus       114 ~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~-~~~~-~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~-  190 (471)
                      ...|..+...+...|+.+.+...+....+... .++. .........+...|++++|.+++++..+.  .+.+...+.. 
T Consensus         6 ~~a~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~a~~~~~~g~~~~A~~~~~~~l~~--~P~~~~a~~~~   83 (355)
T cd05804           6 ALGHAAAALLLLLGGERPAAAAKAAAAAQALAARATERERAHVEALSAWIAGDLPKALALLEQLLDD--YPRDLLALKLH   83 (355)
T ss_pred             HHHHHHHHHHHHhcCCcchHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH--CCCcHHHHHHh
Confidence            34455555555555666665555555443321 1121 11222233445566777777777766652  1223333331 


Q ss_pred             --HHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHh
Q 012111          191 --LIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGN  268 (471)
Q Consensus       191 --ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  268 (471)
                        ........+..+.+.+.++... ...+........+...+...|++++|...+++..+..  +.+...+..+..++..
T Consensus        84 ~~~~~~~~~~~~~~~~~~~l~~~~-~~~~~~~~~~~~~a~~~~~~G~~~~A~~~~~~al~~~--p~~~~~~~~la~i~~~  160 (355)
T cd05804          84 LGAFGLGDFSGMRDHVARVLPLWA-PENPDYWYLLGMLAFGLEEAGQYDRAEEAARRALELN--PDDAWAVHAVAHVLEM  160 (355)
T ss_pred             HHHHHhcccccCchhHHHHHhccC-cCCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC--CCCcHHHHHHHHHHHH
Confidence              1111112333444444444311 1112223344455566667777777777777776653  3445556666777777


Q ss_pred             cCCHHHHHHHHHHHHhCCC-CCCH--HHHHHHHHHHHHcCCHHHHHHHHHHHHhCCC-CCCHHHH-H--HHHHHHHhcCC
Q 012111          269 SGNIEKMEKWYNEFNLMGV-KADI--QTLNILTKSYGRAGMYDKMRSVMDFMQKRFF-FPTVVTY-N--IVIETFGKAGH  341 (471)
Q Consensus       269 ~~~~~~a~~~~~~~~~~~~-~~~~--~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~~-~--~li~~~~~~g~  341 (471)
                      .|++++|..++++...... .++.  ..|..+...+...|++++|..+++....... .+..... +  .++.-+...|.
T Consensus       161 ~g~~~eA~~~l~~~l~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~  240 (355)
T cd05804         161 QGRFKEGIAFMESWRDTWDCSSMLRGHNWWHLALFYLERGDYEAALAIYDTHIAPSAESDPALDLLDAASLLWRLELAGH  240 (355)
T ss_pred             cCCHHHHHHHHHhhhhccCCCcchhHHHHHHHHHHHHHCCCHHHHHHHHHHHhccccCCChHHHHhhHHHHHHHHHhcCC
Confidence            7777777777777655321 1222  2344566677777777777777777643322 1111111 1  22222233333


Q ss_pred             HHHHHHH--HHHHHHcCC--CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCC------c--CHHHHHHHHHHHHhc
Q 012111          342 IEKMEEY--FKKMKHRGM--KPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVI------L--DTPFFNCIISAYGQA  409 (471)
Q Consensus       342 ~~~a~~~--~~~m~~~~~--~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~------~--~~~~~~~l~~~~~~~  409 (471)
                      ...+.++  +........  ............++...|+.+.|..+++.+......      .  .....-....++...
T Consensus       241 ~~~~~~w~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~a~~~L~~l~~~~~~~~~~~~~~~~~~~~~l~A~~~~~~  320 (355)
T cd05804         241 VDVGDRWEDLADYAAWHFPDHGLAFNDLHAALALAGAGDKDALDKLLAALKGRASSADDNKQPARDVGLPLAEALYAFAE  320 (355)
T ss_pred             CChHHHHHHHHHHHHhhcCcccchHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhccCchhhhHHhhhHHHHHHHHHHHc
Confidence            2222222  111111100  111122234566677778888888888777642211      0  111122222345577


Q ss_pred             CCHHHHHHHHHHHHh
Q 012111          410 GDVEKMGELFLTMKE  424 (471)
Q Consensus       410 g~~~~a~~~~~~~~~  424 (471)
                      |+.++|.+++.....
T Consensus       321 g~~~~A~~~L~~al~  335 (355)
T cd05804         321 GNYATALELLGPVRD  335 (355)
T ss_pred             CCHHHHHHHHHHHHH
Confidence            888888888887765

A family member from Streptomyces toyocaensis, StaR is part of a gene cluster involved in the biosynthesis of glycopeptide antibiotics (GPAs), specifically A47934. It has been speculated that StaR could be a flavoprotein hydroxylating a tyrosine sidechain. Some family members have been annotated as proteins containing tetratricopeptide (TPR) repeats, which may at least indicate mostly alpha-helical secondary structure.

>KOG0548 consensus Molecular co-chaperone STI1 [Posttranslational modification, protein turnover, chaperones]

Probab=99.20  E-value=1.7e-07  Score=84.37  Aligned_cols=365  Identities=13%  Similarity=0.096  Sum_probs=239.7

Q ss_pred             HHHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCH
Q 012111           86 DEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLL  165 (471)
Q Consensus        86 ~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~  165 (471)
                      ..++..|+++.|+..|..+....  |+|...|..-..+|++.|++++|.+=-.+-++.+.. -...|.-...++.-.|++
T Consensus        10 naa~s~~d~~~ai~~~t~ai~l~--p~nhvlySnrsaa~a~~~~~~~al~da~k~~~l~p~-w~kgy~r~Gaa~~~lg~~   86 (539)
T KOG0548|consen   10 NAAFSSGDFETAIRLFTEAIMLS--PTNHVLYSNRSAAYASLGSYEKALKDATKTRRLNPD-WAKGYSRKGAALFGLGDY   86 (539)
T ss_pred             HhhcccccHHHHHHHHHHHHccC--CCccchhcchHHHHHHHhhHHHHHHHHHHHHhcCCc-hhhHHHHhHHHHHhcccH
Confidence            34568999999999999999876  778889999999999999999998877777766432 467899999999999999


Q ss_pred             HHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHH------HHHHHC---CCCCCHHHHHHHHHHHHcc---
Q 012111          166 DEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKIL------AEMSYL---GIECSAVTYNTIIDGYGKA---  233 (471)
Q Consensus       166 ~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~------~~~~~~---g~~~~~~~~~~l~~~~~~~---  233 (471)
                      ++|+.-|.+-.+.  .+.|...++.+..++...  .. +.+.|      ..+...   ........|..++..+-+.   
T Consensus        87 ~eA~~ay~~GL~~--d~~n~~L~~gl~~a~~~~--~~-~~~~~~~p~~~~~l~~~p~t~~~~~~~~~~~~l~~~~~~p~~  161 (539)
T KOG0548|consen   87 EEAILAYSEGLEK--DPSNKQLKTGLAQAYLED--YA-ADQLFTKPYFHEKLANLPLTNYSLSDPAYVKILEIIQKNPTS  161 (539)
T ss_pred             HHHHHHHHHHhhc--CCchHHHHHhHHHhhhHH--HH-hhhhccCcHHHHHhhcChhhhhhhccHHHHHHHHHhhcCcHh
Confidence            9999999988763  245566677777766211  00 01111      111000   0000111222222222111   


Q ss_pred             -------CCHHHHHHHHHHH-----HHcC------CCCC----------------------CHHHHHHHHHHHHhcCCHH
Q 012111          234 -------KKFEEMESSFSAM-----VESG------GCHP----------------------DIFTLNSMISAYGNSGNIE  273 (471)
Q Consensus       234 -------~~~~~a~~~~~~~-----~~~~------~~~~----------------------~~~~~~~l~~~~~~~~~~~  273 (471)
                             ..+..+...+...     ...+      +..|                      -..-...+.++..+..+++
T Consensus       162 l~~~l~d~r~m~a~~~l~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~d~~ee~~~k~~a~~ek~lgnaaykkk~f~  241 (539)
T KOG0548|consen  162 LKLYLNDPRLMKADGQLKGVDELLFYASGIEILASMAEPCKQEHNGFPIIEDNTEERRVKEKAHKEKELGNAAYKKKDFE  241 (539)
T ss_pred             hhcccccHHHHHHHHHHhcCccccccccccccCCCCCCcccccCCCCCccchhHHHHHHHHhhhHHHHHHHHHHHhhhHH
Confidence                   0111111111100     0000      0011                      1123455777788888999


Q ss_pred             HHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHH-------HHHHhcCCHHHHH
Q 012111          274 KMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVI-------ETFGKAGHIEKME  346 (471)
Q Consensus       274 ~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li-------~~~~~~g~~~~a~  346 (471)
                      .|.+.+.......  -+..-++....+|...|.+..+...-+...+.|.. ...-|+.+.       .+|.+.++++.+.
T Consensus       242 ~a~q~y~~a~el~--~~it~~~n~aA~~~e~~~~~~c~~~c~~a~E~gre-~rad~klIak~~~r~g~a~~k~~~~~~ai  318 (539)
T KOG0548|consen  242 TAIQHYAKALELA--TDITYLNNIAAVYLERGKYAECIELCEKAVEVGRE-LRADYKLIAKALARLGNAYTKREDYEGAI  318 (539)
T ss_pred             HHHHHHHHHHhHh--hhhHHHHHHHHHHHhccHHHHhhcchHHHHHHhHH-HHHHHHHHHHHHHHhhhhhhhHHhHHHHH
Confidence            9999999887764  56666777788888888888887777766665543 222333333       3555567788888


Q ss_pred             HHHHHHHHcCCCCCHHHH-------------------------HHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHH
Q 012111          347 EYFKKMKHRGMKPNSITY-------------------------CSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNC  401 (471)
Q Consensus       347 ~~~~~m~~~~~~p~~~~~-------------------------~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~  401 (471)
                      ..|.+.......|+...=                         ..=...+.+.|++..|...|.++++.++. |...|..
T Consensus       319 ~~~~kaLte~Rt~~~ls~lk~~Ek~~k~~e~~a~~~pe~A~e~r~kGne~Fk~gdy~~Av~~YteAIkr~P~-Da~lYsN  397 (539)
T KOG0548|consen  319 KYYQKALTEHRTPDLLSKLKEAEKALKEAERKAYINPEKAEEEREKGNEAFKKGDYPEAVKHYTEAIKRDPE-DARLYSN  397 (539)
T ss_pred             HHHHHHhhhhcCHHHHHHHHHHHHHHHHHHHHHhhChhHHHHHHHHHHHHHhccCHHHHHHHHHHHHhcCCc-hhHHHHH
Confidence            888877655434333221                         11133466789999999999999988866 8889999


Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHhCCCCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHHhhhcC
Q 012111          402 IISAYGQAGDVEKMGELFLTMKERHCVPD-NITFATMIQAYNALGMTEAAQNLENKMIAMKENS  464 (471)
Q Consensus       402 l~~~~~~~g~~~~a~~~~~~~~~~~~~p~-~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~~  464 (471)
                      -.-+|.+.|.+..|++-.+...+.  .|+ ...|..=..++....+++.|.+.|++.++.+|..
T Consensus       398 RAac~~kL~~~~~aL~Da~~~ieL--~p~~~kgy~RKg~al~~mk~ydkAleay~eale~dp~~  459 (539)
T KOG0548|consen  398 RAACYLKLGEYPEALKDAKKCIEL--DPNFIKAYLRKGAALRAMKEYDKALEAYQEALELDPSN  459 (539)
T ss_pred             HHHHHHHHhhHHHHHHHHHHHHhc--CchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCchh
Confidence            999999999999999988888775  343 3445445566667778999999999999888764

>KOG3785 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.19  E-value=2.2e-07  Score=79.17  Aligned_cols=359  Identities=11%  Similarity=0.049  Sum_probs=211.0

Q ss_pred             HHHHHHHhhHHHHHHHHHhhhhhhccCCCchHHHHHHHHHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCC
Q 012111           49 KDLSKILRTEFAIKNIEKKVSSKKYKNLWPKPVLEALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCK  128 (471)
Q Consensus        49 ~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  128 (471)
                      -.-.+++.+++++......+.   ......+....+.-...-.|.+.+|..+-..+.      .++-.-..++...-+.+
T Consensus        65 ~C~fhLgdY~~Al~~Y~~~~~---~~~~~~el~vnLAcc~FyLg~Y~eA~~~~~ka~------k~pL~~RLlfhlahkln  135 (557)
T KOG3785|consen   65 HCYFHLGDYEEALNVYTFLMN---KDDAPAELGVNLACCKFYLGQYIEAKSIAEKAP------KTPLCIRLLFHLAHKLN  135 (557)
T ss_pred             HHHHhhccHHHHHHHHHHHhc---cCCCCcccchhHHHHHHHHHHHHHHHHHHhhCC------CChHHHHHHHHHHHHhC
Confidence            334667777777766665544   222333344444444456788999888766553      33344455666667778


Q ss_pred             CHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHHHH-HHhcCCHHHHHHH
Q 012111          129 QPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKS-CTKFHRFDLIEKI  207 (471)
Q Consensus       129 ~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~-~~~~~~~~~a~~~  207 (471)
                      +-++-..+.+.+.+.     .+---+|.......-.+.+|+++|.++...   .|+-...|..+.. |.+..-++.+.++
T Consensus       136 dEk~~~~fh~~LqD~-----~EdqLSLAsvhYmR~HYQeAIdvYkrvL~d---n~ey~alNVy~ALCyyKlDYydvsqev  207 (557)
T KOG3785|consen  136 DEKRILTFHSSLQDT-----LEDQLSLASVHYMRMHYQEAIDVYKRVLQD---NPEYIALNVYMALCYYKLDYYDVSQEV  207 (557)
T ss_pred             cHHHHHHHHHHHhhh-----HHHHHhHHHHHHHHHHHHHHHHHHHHHHhc---ChhhhhhHHHHHHHHHhcchhhhHHHH
Confidence            888777777766542     233344555544455789999999999862   5666666665554 5677888888899


Q ss_pred             HHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHcCC-------------------------CCCC-----HH
Q 012111          208 LAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGG-------------------------CHPD-----IF  257 (471)
Q Consensus       208 ~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-------------------------~~~~-----~~  257 (471)
                      ++-..+. ++.+....|.......+.-+-..|+.-...+.+...                         +-|.     ..
T Consensus       208 l~vYL~q-~pdStiA~NLkacn~fRl~ngr~ae~E~k~ladN~~~~~~f~~~l~rHNLVvFrngEgALqVLP~L~~~IPE  286 (557)
T KOG3785|consen  208 LKVYLRQ-FPDSTIAKNLKACNLFRLINGRTAEDEKKELADNIDQEYPFIEYLCRHNLVVFRNGEGALQVLPSLMKHIPE  286 (557)
T ss_pred             HHHHHHh-CCCcHHHHHHHHHHHhhhhccchhHHHHHHHHhcccccchhHHHHHHcCeEEEeCCccHHHhchHHHhhChH
Confidence            8887765 233445555444433332111111111111111100                         0010     11


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHH-----------------------------------------HH
Q 012111          258 TLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTL-----------------------------------------NI  296 (471)
Q Consensus       258 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~-----------------------------------------~~  296 (471)
                      .-..|+--|.+.+++.+|..+.+++.-  ..|-....                                         ..
T Consensus       287 ARlNL~iYyL~q~dVqeA~~L~Kdl~P--ttP~EyilKgvv~aalGQe~gSreHlKiAqqffqlVG~Sa~ecDTIpGRQs  364 (557)
T KOG3785|consen  287 ARLNLIIYYLNQNDVQEAISLCKDLDP--TTPYEYILKGVVFAALGQETGSREHLKIAQQFFQLVGESALECDTIPGRQS  364 (557)
T ss_pred             hhhhheeeecccccHHHHHHHHhhcCC--CChHHHHHHHHHHHHhhhhcCcHHHHHHHHHHHHHhcccccccccccchHH
Confidence            122334446677777777776665431  11111111                                         22


Q ss_pred             HHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHH-HHHHHHHhcC
Q 012111          297 LTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYC-SLVSAYSKAG  375 (471)
Q Consensus       297 ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~-~li~~~~~~g  375 (471)
                      +..++.-..++|+++..+..+..--...|...|| +.++++..|++.+|.++|-++....++ |..+|. .|.++|.+.+
T Consensus       365 mAs~fFL~~qFddVl~YlnSi~sYF~NdD~Fn~N-~AQAk~atgny~eaEelf~~is~~~ik-n~~~Y~s~LArCyi~nk  442 (557)
T KOG3785|consen  365 MASYFFLSFQFDDVLTYLNSIESYFTNDDDFNLN-LAQAKLATGNYVEAEELFIRISGPEIK-NKILYKSMLARCYIRNK  442 (557)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhcCcchhhhH-HHHHHHHhcChHHHHHHHhhhcChhhh-hhHHHHHHHHHHHHhcC
Confidence            3333444455666666666666654444555444 678889999999999999776654444 455565 5668889999


Q ss_pred             CHHHHHHHHHHHHhCCCCcCHHHH-HHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHH
Q 012111          376 LIMKVDSILRQVENSDVILDTPFF-NCIISAYGQAGDVEKMGELFLTMKERHCVPDNITF  434 (471)
Q Consensus       376 ~~~~a~~~~~~~~~~~~~~~~~~~-~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~  434 (471)
                      .++.|++++-.+...   .+..+. ..+..-|.+++.+--|.+.|+.+...  .|++..|
T Consensus       443 kP~lAW~~~lk~~t~---~e~fsLLqlIAn~CYk~~eFyyaaKAFd~lE~l--DP~pEnW  497 (557)
T KOG3785|consen  443 KPQLAWDMMLKTNTP---SERFSLLQLIANDCYKANEFYYAAKAFDELEIL--DPTPENW  497 (557)
T ss_pred             CchHHHHHHHhcCCc---hhHHHHHHHHHHHHHHHHHHHHHHHhhhHHHcc--CCCcccc
Confidence            999998877655432   233333 34455688889988888888888764  4665544

>COG3063 PilF Tfp pilus assembly protein PilF [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=99.19  E-value=4.7e-08  Score=78.34  Aligned_cols=192  Identities=14%  Similarity=0.026  Sum_probs=115.9

Q ss_pred             HHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHH
Q 012111           87 EAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLD  166 (471)
Q Consensus        87 ~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~  166 (471)
                      .+...|++..|.+-++++.+.+  |.+..++..+...|-+.|..+.|.+.|+........ +-.+.|.....+|..|+++
T Consensus        44 ~YL~~gd~~~A~~nlekAL~~D--Ps~~~a~~~~A~~Yq~~Ge~~~A~e~YrkAlsl~p~-~GdVLNNYG~FLC~qg~~~  120 (250)
T COG3063          44 GYLQQGDYAQAKKNLEKALEHD--PSYYLAHLVRAHYYQKLGENDLADESYRKALSLAPN-NGDVLNNYGAFLCAQGRPE  120 (250)
T ss_pred             HHHHCCCHHHHHHHHHHHHHhC--cccHHHHHHHHHHHHHcCChhhHHHHHHHHHhcCCC-ccchhhhhhHHHHhCCChH
Confidence            3456667777777777776664  455566666666666777777777777666665332 4556666666666666777


Q ss_pred             HHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHH
Q 012111          167 EAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAM  246 (471)
Q Consensus       167 ~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  246 (471)
                      +|...|++......+.--..+|..+.-+..+.|+++.|...|++..+.. +-...+...+.....+.|++..|...++..
T Consensus       121 eA~q~F~~Al~~P~Y~~~s~t~eN~G~Cal~~gq~~~A~~~l~raL~~d-p~~~~~~l~~a~~~~~~~~y~~Ar~~~~~~  199 (250)
T COG3063         121 EAMQQFERALADPAYGEPSDTLENLGLCALKAGQFDQAEEYLKRALELD-PQFPPALLELARLHYKAGDYAPARLYLERY  199 (250)
T ss_pred             HHHHHHHHHHhCCCCCCcchhhhhhHHHHhhcCCchhHHHHHHHHHHhC-cCCChHHHHHHHHHHhcccchHHHHHHHHH
Confidence            7777766666533233334456666666666666666666666666553 223445555666666666666666666666


Q ss_pred             HHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 012111          247 VESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNL  284 (471)
Q Consensus       247 ~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  284 (471)
                      ...+  .++..+.-..|..-...|+.+.+.++=.++..
T Consensus       200 ~~~~--~~~A~sL~L~iriak~~gd~~~a~~Y~~qL~r  235 (250)
T COG3063         200 QQRG--GAQAESLLLGIRIAKRLGDRAAAQRYQAQLQR  235 (250)
T ss_pred             Hhcc--cccHHHHHHHHHHHHHhccHHHHHHHHHHHHH
Confidence            5543  25555555556666666666665555544443

>PRK04841 transcriptional regulator MalT; Provisional

Probab=99.19  E-value=6.5e-07  Score=93.17  Aligned_cols=344  Identities=9%  Similarity=-0.005  Sum_probs=216.0

Q ss_pred             HHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCC-----CCCH--HHHHHHHHH
Q 012111          122 VMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAFSTINDMKSVSDC-----KPDV--YTYSILIKS  194 (471)
Q Consensus       122 ~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~-----~~~~--~~~~~ll~~  194 (471)
                      ..+...|+++.+..+++.+.......+..........+...|+++++..++.........     .+..  .....+...
T Consensus       382 ~~l~~~g~~~~l~~~l~~lp~~~~~~~~~l~~~~a~~~~~~g~~~~a~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~a~~  461 (903)
T PRK04841        382 WSLFNQGELSLLEECLNALPWEVLLENPRLVLLQAWLAQSQHRYSEVNTLLARAEQELKDRNIELDGTLQAEFNALRAQV  461 (903)
T ss_pred             HHHHhcCChHHHHHHHHhCCHHHHhcCcchHHHHHHHHHHCCCHHHHHHHHHHHHHhccccCcccchhHHHHHHHHHHHH
Confidence            344556777777777766532111112223334455566789999999988876542111     1111  122223344


Q ss_pred             HHhcCCHHHHHHHHHHHHHCCCCCCH----HHHHHHHHHHHccCCHHHHHHHHHHHHHcCC----CCCCHHHHHHHHHHH
Q 012111          195 CTKFHRFDLIEKILAEMSYLGIECSA----VTYNTIIDGYGKAKKFEEMESSFSAMVESGG----CHPDIFTLNSMISAY  266 (471)
Q Consensus       195 ~~~~~~~~~a~~~~~~~~~~g~~~~~----~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~----~~~~~~~~~~l~~~~  266 (471)
                      +...|+++.|...+++....-...+.    ...+.+...+...|++++|...+++......    .......+..+...+
T Consensus       462 ~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~a~~~lg~~~~~~G~~~~A~~~~~~al~~~~~~g~~~~~~~~~~~la~~~  541 (903)
T PRK04841        462 AINDGDPEEAERLAELALAELPLTWYYSRIVATSVLGEVHHCKGELARALAMMQQTEQMARQHDVYHYALWSLLQQSEIL  541 (903)
T ss_pred             HHhCCCHHHHHHHHHHHHhcCCCccHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhhhcchHHHHHHHHHHHHHH
Confidence            56789999999999988763111121    2445566677889999999999988764321    111123455667778


Q ss_pred             HhcCCHHHHHHHHHHHHhC----CCC--C-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCC--CCC--CHHHHHHHHHH
Q 012111          267 GNSGNIEKMEKWYNEFNLM----GVK--A-DIQTLNILTKSYGRAGMYDKMRSVMDFMQKRF--FFP--TVVTYNIVIET  335 (471)
Q Consensus       267 ~~~~~~~~a~~~~~~~~~~----~~~--~-~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~--~~~--~~~~~~~li~~  335 (471)
                      ...|++++|...+++....    +..  + ....+..+...+...|++++|...+.......  ..+  ....+..+...
T Consensus       542 ~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~la~~  621 (903)
T PRK04841        542 FAQGFLQAAYETQEKAFQLIEEQHLEQLPMHEFLLRIRAQLLWEWARLDEAEQCARKGLEVLSNYQPQQQLQCLAMLAKI  621 (903)
T ss_pred             HHCCCHHHHHHHHHHHHHHHHHhccccccHHHHHHHHHHHHHHHhcCHHHHHHHHHHhHHhhhccCchHHHHHHHHHHHH
Confidence            8999999999998876542    211  1 22334555667778899999999988765421  112  23344455667


Q ss_pred             HHhcCCHHHHHHHHHHHHHcC--CCCCHH--H-H-HHHHHHHHhcCCHHHHHHHHHHHHhCCCCcC---HHHHHHHHHHH
Q 012111          336 FGKAGHIEKMEEYFKKMKHRG--MKPNSI--T-Y-CSLVSAYSKAGLIMKVDSILRQVENSDVILD---TPFFNCIISAY  406 (471)
Q Consensus       336 ~~~~g~~~~a~~~~~~m~~~~--~~p~~~--~-~-~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~---~~~~~~l~~~~  406 (471)
                      +...|++++|.+.+.......  ......  . . ...+..+...|+.+.|...+...........   ...+..+..++
T Consensus       622 ~~~~G~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~l~~~~~~~~~~~~~~~~~~~~~a~~~  701 (903)
T PRK04841        622 SLARGDLDNARRYLNRLENLLGNGRYHSDWIANADKVRLIYWQMTGDKEAAANWLRQAPKPEFANNHFLQGQWRNIARAQ  701 (903)
T ss_pred             HHHcCCHHHHHHHHHHHHHHHhcccccHhHhhHHHHHHHHHHHHCCCHHHHHHHHHhcCCCCCccchhHHHHHHHHHHHH
Confidence            788999999999998875431  111111  1 0 1122444567899999999877654322111   11234667788


Q ss_pred             HhcCCHHHHHHHHHHHHhC----CCCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHHhhhcCC
Q 012111          407 GQAGDVEKMGELFLTMKER----HCVPD-NITFATMIQAYNALGMTEAAQNLENKMIAMKENSG  465 (471)
Q Consensus       407 ~~~g~~~~a~~~~~~~~~~----~~~p~-~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~~~  465 (471)
                      ...|++++|...+++....    |..++ ..+...+..++.+.|+.++|...+.++++.....+
T Consensus       702 ~~~g~~~~A~~~l~~al~~~~~~g~~~~~a~~~~~la~a~~~~G~~~~A~~~L~~Al~la~~~g  765 (903)
T PRK04841        702 ILLGQFDEAEIILEELNENARSLRLMSDLNRNLILLNQLYWQQGRKSEAQRVLLEALKLANRTG  765 (903)
T ss_pred             HHcCCHHHHHHHHHHHHHHHHHhCchHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhCccc
Confidence            8999999999999987653    33322 24555666888999999999999999998775544

>KOG0624 consensus dsRNA-activated protein kinase inhibitor P58, contains TPR and DnaJ domains [Defense mechanisms]

Probab=99.08  E-value=1.5e-06  Score=73.94  Aligned_cols=308  Identities=12%  Similarity=-0.001  Sum_probs=177.0

Q ss_pred             HHHHHHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHH-HHHHHHHHh
Q 012111           83 EALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVY-TALVSAYGQ  161 (471)
Q Consensus        83 ~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~-~~li~~~~~  161 (471)
                      ++=..+...|++.+|+.-|..+.+.+  |.+-.++..-...|...|+...|+.=+...++.  +||...- ..-...+.+
T Consensus        43 ElGk~lla~~Q~sDALt~yHaAve~d--p~~Y~aifrRaT~yLAmGksk~al~Dl~rVlel--KpDF~~ARiQRg~vllK  118 (504)
T KOG0624|consen   43 ELGKELLARGQLSDALTHYHAAVEGD--PNNYQAIFRRATVYLAMGKSKAALQDLSRVLEL--KPDFMAARIQRGVVLLK  118 (504)
T ss_pred             HHHHHHHHhhhHHHHHHHHHHHHcCC--chhHHHHHHHHHHHhhhcCCccchhhHHHHHhc--CccHHHHHHHhchhhhh
Confidence            44556778899999999999998764  455566667777888899999999888888876  6664332 223346778


Q ss_pred             cCCHHHHHHHHHHhhcCCCCCCCHHH----H------------HHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHH
Q 012111          162 SGLLDEAFSTINDMKSVSDCKPDVYT----Y------------SILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNT  225 (471)
Q Consensus       162 ~~~~~~a~~~~~~~~~~~~~~~~~~~----~------------~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~  225 (471)
                      .|.++.|..=|+.+...   .|+..+    +            ...+..+...|+...|+..+..+++.. +.+...|..
T Consensus       119 ~Gele~A~~DF~~vl~~---~~s~~~~~eaqskl~~~~e~~~l~~ql~s~~~~GD~~~ai~~i~~llEi~-~Wda~l~~~  194 (504)
T KOG0624|consen  119 QGELEQAEADFDQVLQH---EPSNGLVLEAQSKLALIQEHWVLVQQLKSASGSGDCQNAIEMITHLLEIQ-PWDASLRQA  194 (504)
T ss_pred             cccHHHHHHHHHHHHhc---CCCcchhHHHHHHHHhHHHHHHHHHHHHHHhcCCchhhHHHHHHHHHhcC-cchhHHHHH
Confidence            99999999999998873   232211    1            111222333344444444444444432 334444444


Q ss_pred             HHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcC
Q 012111          226 IIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAG  305 (471)
Q Consensus       226 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~  305 (471)
                      -..+|...|++..|+.=++...+..  ..+..++-.+-..+...|+.+.++...++..+.  .||...+-.      --.
T Consensus       195 Rakc~i~~~e~k~AI~Dlk~askLs--~DnTe~~ykis~L~Y~vgd~~~sL~~iRECLKl--dpdHK~Cf~------~YK  264 (504)
T KOG0624|consen  195 RAKCYIAEGEPKKAIHDLKQASKLS--QDNTEGHYKISQLLYTVGDAENSLKEIRECLKL--DPDHKLCFP------FYK  264 (504)
T ss_pred             HHHHHHhcCcHHHHHHHHHHHHhcc--ccchHHHHHHHHHHHhhhhHHHHHHHHHHHHcc--CcchhhHHH------HHH
Confidence            4444445555444444444333221  223333333444444444444444444444332  233221110      001


Q ss_pred             CHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHH---HHHHHHHHHHhcCCHHHHHH
Q 012111          306 MYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSI---TYCSLVSAYSKAGLIMKVDS  382 (471)
Q Consensus       306 ~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~---~~~~li~~~~~~g~~~~a~~  382 (471)
                      .+.+..+.++.|                ......+++.++++..+...+........   .+..+-.++...|++.+|++
T Consensus       265 klkKv~K~les~----------------e~~ie~~~~t~cle~ge~vlk~ep~~~~ir~~~~r~~c~C~~~d~~~~eAiq  328 (504)
T KOG0624|consen  265 KLKKVVKSLESA----------------EQAIEEKHWTECLEAGEKVLKNEPEETMIRYNGFRVLCTCYREDEQFGEAIQ  328 (504)
T ss_pred             HHHHHHHHHHHH----------------HHHHhhhhHHHHHHHHHHHHhcCCcccceeeeeeheeeecccccCCHHHHHH
Confidence            111111111111                22344567777777777776653221122   33445566777788888888


Q ss_pred             HHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhC
Q 012111          383 ILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKER  425 (471)
Q Consensus       383 ~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~  425 (471)
                      ...++.+..+. |..++..-..+|.-...+++|+.-|+...+.
T Consensus       329 qC~evL~~d~~-dv~~l~dRAeA~l~dE~YD~AI~dye~A~e~  370 (504)
T KOG0624|consen  329 QCKEVLDIDPD-DVQVLCDRAEAYLGDEMYDDAIHDYEKALEL  370 (504)
T ss_pred             HHHHHHhcCch-HHHHHHHHHHHHhhhHHHHHHHHHHHHHHhc
Confidence            88888876544 5777777778888888888888888888774

>KOG4340 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.05  E-value=4.7e-07  Score=75.39  Aligned_cols=293  Identities=10%  Similarity=0.004  Sum_probs=208.2

Q ss_pred             HHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHH-HHHH
Q 012111          116 TFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSI-LIKS  194 (471)
Q Consensus       116 ~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~-ll~~  194 (471)
                      -++..+..+.+..+++.|++++..-.++..+ +......|..+|....++..|-+.|+++..   ..|...-|.. -...
T Consensus        12 eftaviy~lI~d~ry~DaI~~l~s~~Er~p~-~rAgLSlLgyCYY~~Q~f~~AA~CYeQL~q---l~P~~~qYrlY~AQS   87 (459)
T KOG4340|consen   12 EFTAVVYRLIRDARYADAIQLLGSELERSPR-SRAGLSLLGYCYYRLQEFALAAECYEQLGQ---LHPELEQYRLYQAQS   87 (459)
T ss_pred             chHHHHHHHHHHhhHHHHHHHHHHHHhcCcc-chHHHHHHHHHHHHHHHHHHHHHHHHHHHh---hChHHHHHHHHHHHH
Confidence            4667777788899999999999988887433 778889999999999999999999999976   2566555543 2345


Q ss_pred             HHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHH--HHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCH
Q 012111          195 CTKFHRFDLIEKILAEMSYLGIECSAVTYNTII--DGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNI  272 (471)
Q Consensus       195 ~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~--~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  272 (471)
                      +.+.+.+..|+++...|...   ++...-..-+  ......+++..+..++++....    -+..+.+...-...+.|++
T Consensus        88 LY~A~i~ADALrV~~~~~D~---~~L~~~~lqLqaAIkYse~Dl~g~rsLveQlp~e----n~Ad~~in~gCllykegqy  160 (459)
T KOG4340|consen   88 LYKACIYADALRVAFLLLDN---PALHSRVLQLQAAIKYSEGDLPGSRSLVEQLPSE----NEADGQINLGCLLYKEGQY  160 (459)
T ss_pred             HHHhcccHHHHHHHHHhcCC---HHHHHHHHHHHHHHhcccccCcchHHHHHhccCC----CccchhccchheeeccccH
Confidence            67889999999999988753   2222222222  2334578888888888877432    2445555566667789999


Q ss_pred             HHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCC-------------CH--------HHHHH
Q 012111          273 EKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFP-------------TV--------VTYNI  331 (471)
Q Consensus       273 ~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~-------------~~--------~~~~~  331 (471)
                      ++|.+-|+...+-+--.....|+..+. ..+.|+.+.|.+...++.++|+..             |+        ..-+.
T Consensus       161 EaAvqkFqaAlqvsGyqpllAYniALa-Hy~~~qyasALk~iSEIieRG~r~HPElgIGm~tegiDvrsvgNt~~lh~Sa  239 (459)
T KOG4340|consen  161 EAAVQKFQAALQVSGYQPLLAYNLALA-HYSSRQYASALKHISEIIERGIRQHPELGIGMTTEGIDVRSVGNTLVLHQSA  239 (459)
T ss_pred             HHHHHHHHHHHhhcCCCchhHHHHHHH-HHhhhhHHHHHHHHHHHHHhhhhcCCccCccceeccCchhcccchHHHHHHH
Confidence            999999999877654555667776554 456789999999999999887431             21        12233


Q ss_pred             HHHH-------HHhcCCHHHHHHHHHHHHHc-CCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHH
Q 012111          332 VIET-------FGKAGHIEKMEEYFKKMKHR-GMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCII  403 (471)
Q Consensus       332 li~~-------~~~~g~~~~a~~~~~~m~~~-~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~  403 (471)
                      ++.+       +.+.|+++.|.+.+-+|... ....|+.|...+.-.- -.+++....+-++-+...++- ...+|..++
T Consensus       240 l~eAfNLKaAIeyq~~n~eAA~eaLtDmPPRaE~elDPvTLHN~Al~n-~~~~p~~g~~KLqFLL~~nPf-P~ETFANlL  317 (459)
T KOG4340|consen  240 LVEAFNLKAAIEYQLRNYEAAQEALTDMPPRAEEELDPVTLHNQALMN-MDARPTEGFEKLQFLLQQNPF-PPETFANLL  317 (459)
T ss_pred             HHHHhhhhhhhhhhcccHHHHHHHhhcCCCcccccCCchhhhHHHHhc-ccCCccccHHHHHHHHhcCCC-ChHHHHHHH
Confidence            3333       35678899999888888643 2345777776654332 234555566666666666664 567888888


Q ss_pred             HHHHhcCCHHHHHHHHHHH
Q 012111          404 SAYGQAGDVEKMGELFLTM  422 (471)
Q Consensus       404 ~~~~~~g~~~~a~~~~~~~  422 (471)
                      -.||+..-++.|.+++.+-
T Consensus       318 llyCKNeyf~lAADvLAEn  336 (459)
T KOG4340|consen  318 LLYCKNEYFDLAADVLAEN  336 (459)
T ss_pred             HHHhhhHHHhHHHHHHhhC
Confidence            9999999999998887653

>PF04733 Coatomer_E: Coatomer epsilon subunit; InterPro: IPR006822 Proteins synthesised on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment

Probab=99.03  E-value=3.9e-08  Score=85.78  Aligned_cols=82  Identities=12%  Similarity=0.150  Sum_probs=36.3

Q ss_pred             CHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCH-HHHHHHH
Q 012111          341 HIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDV-EKMGELF  419 (471)
Q Consensus       341 ~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~-~~a~~~~  419 (471)
                      .+.+|..+|+++.+. ..+++.+.+.+..++...|++++|.+++.+..+.+.. +..+...++.+....|+. +.+.+++
T Consensus       182 ~~~~A~y~f~El~~~-~~~t~~~lng~A~~~l~~~~~~eAe~~L~~al~~~~~-~~d~LaNliv~~~~~gk~~~~~~~~l  259 (290)
T PF04733_consen  182 KYQDAFYIFEELSDK-FGSTPKLLNGLAVCHLQLGHYEEAEELLEEALEKDPN-DPDTLANLIVCSLHLGKPTEAAERYL  259 (290)
T ss_dssp             CCCHHHHHHHHHHCC-S--SHHHHHHHHHHHHHCT-HHHHHHHHHHHCCC-CC-HHHHHHHHHHHHHHTT-TCHHHHHHH
T ss_pred             hHHHHHHHHHHHHhc-cCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhccC-CHHHHHHHHHHHHHhCCChhHHHHHH
Confidence            345555555554332 3344445555555555555555555555554444333 344444444444444444 3344444


Q ss_pred             HHHHh
Q 012111          420 LTMKE  424 (471)
Q Consensus       420 ~~~~~  424 (471)
                      .++..
T Consensus       260 ~qL~~  264 (290)
T PF04733_consen  260 SQLKQ  264 (290)
T ss_dssp             HHCHH
T ss_pred             HHHHH
Confidence            44443

This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. While clathrin mediates endocytic protein transport, and transport from ER to Golgi, coatomers primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. For example, the coatomer COP1 (coat protein complex 1) is responsible for reverse transport of recycled proteins from Golgi and pre-Golgi compartments back to the ER, while COPII buds vesicles from the ER to the Golgi []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Activated small guanine triphosphatases (GTPases) attract coat proteins to specific membrane export sites, thereby linking coatomers to export cargos. As coat proteins polymerise, vesicles are formed and budded from membrane-bound organelles. Coatomer complexes also influence Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors. In mammals, coatomer complexes can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the epsilon subunit of the coatomer complex, which is involved in the regulation of intracellular protein trafficking between the endoplasmic reticulum and the Golgi complex []. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0005198 structural molecule activity, 0006890 retrograde vesicle-mediated transport, Golgi to ER, 0030126 COPI vesicle coat; PDB: 3MV2_B 3MV3_F 3MKR_A.

>PF04733 Coatomer_E: Coatomer epsilon subunit; InterPro: IPR006822 Proteins synthesised on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment

Probab=99.02  E-value=2.7e-08  Score=86.81  Aligned_cols=251  Identities=13%  Similarity=0.106  Sum_probs=159.4

Q ss_pred             hcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHH
Q 012111          197 KFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKME  276 (471)
Q Consensus       197 ~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~  276 (471)
                      -.|++..++.-.+ .....-.........+.+++...|+++.++   .++.+.  ..|.......+...+...++-+.+.
T Consensus        13 y~G~Y~~~i~e~~-~~~~~~~~~~e~~~~~~Rs~iAlg~~~~vl---~ei~~~--~~~~l~av~~la~y~~~~~~~e~~l   86 (290)
T PF04733_consen   13 YLGNYQQCINEAS-LKSFSPENKLERDFYQYRSYIALGQYDSVL---SEIKKS--SSPELQAVRLLAEYLSSPSDKESAL   86 (290)
T ss_dssp             CTT-HHHHCHHHH-CHTSTCHHHHHHHHHHHHHHHHTT-HHHHH---HHS-TT--SSCCCHHHHHHHHHHCTSTTHHCHH
T ss_pred             HhhhHHHHHHHhh-ccCCCchhHHHHHHHHHHHHHHcCChhHHH---HHhccC--CChhHHHHHHHHHHHhCccchHHHH
Confidence            3466666664444 222211122344455667777777766543   333222  2555555555555444434555555


Q ss_pred             HHHHHHHhCCCCCC-HHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 012111          277 KWYNEFNLMGVKAD-IQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHR  355 (471)
Q Consensus       277 ~~~~~~~~~~~~~~-~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  355 (471)
                      .-+++........+ ..........+...|++++|++++...      .+.......+..|.+.++++.|.+.++.|.+.
T Consensus        87 ~~l~~~~~~~~~~~~~~~~~~~A~i~~~~~~~~~AL~~l~~~------~~lE~~al~Vqi~L~~~R~dlA~k~l~~~~~~  160 (290)
T PF04733_consen   87 EELKELLADQAGESNEIVQLLAATILFHEGDYEEALKLLHKG------GSLELLALAVQILLKMNRPDLAEKELKNMQQI  160 (290)
T ss_dssp             HHHHHCCCTS---CHHHHHHHHHHHHCCCCHHHHHHCCCTTT------TCHHHHHHHHHHHHHTT-HHHHHHHHHHHHCC
T ss_pred             HHHHHHHHhccccccHHHHHHHHHHHHHcCCHHHHHHHHHcc------CcccHHHHHHHHHHHcCCHHHHHHHHHHHHhc
Confidence            55555443332322 223333334556678888888877642      35677778889999999999999999999864


Q ss_pred             CCCCCHHHHHHHHHHHHh----cCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCH
Q 012111          356 GMKPNSITYCSLVSAYSK----AGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDN  431 (471)
Q Consensus       356 ~~~p~~~~~~~li~~~~~----~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~  431 (471)
                        ..| .+...+..++..    .+.+.+|..+|+++.+. ..++..+.+.+..++...|++++|.+++.+..+.+ +-++
T Consensus       161 --~eD-~~l~qLa~awv~l~~g~e~~~~A~y~f~El~~~-~~~t~~~lng~A~~~l~~~~~~eAe~~L~~al~~~-~~~~  235 (290)
T PF04733_consen  161 --DED-SILTQLAEAWVNLATGGEKYQDAFYIFEELSDK-FGSTPKLLNGLAVCHLQLGHYEEAEELLEEALEKD-PNDP  235 (290)
T ss_dssp             --SCC-HHHHHHHHHHHHHHHTTTCCCHHHHHHHHHHCC-S--SHHHHHHHHHHHHHCT-HHHHHHHHHHHCCC--CCHH
T ss_pred             --CCc-HHHHHHHHHHHHHHhCchhHHHHHHHHHHHHhc-cCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhc-cCCH
Confidence              344 344445554433    34699999999998765 45688999999999999999999999999987653 3367


Q ss_pred             HHHHHHHHHHHhcCCH-HHHHHHHHHHHHhhhcC
Q 012111          432 ITFATMIQAYNALGMT-EAAQNLENKMIAMKENS  464 (471)
Q Consensus       432 ~~~~~l~~~~~~~g~~-~~A~~~~~~m~~~~~~~  464 (471)
                      .++..++.+....|+. +.+.+++..+....|..
T Consensus       236 d~LaNliv~~~~~gk~~~~~~~~l~qL~~~~p~h  269 (290)
T PF04733_consen  236 DTLANLIVCSLHLGKPTEAAERYLSQLKQSNPNH  269 (290)
T ss_dssp             HHHHHHHHHHHHTT-TCHHHHHHHHHCHHHTTTS
T ss_pred             HHHHHHHHHHHHhCCChhHHHHHHHHHHHhCCCC
Confidence            7888888888888987 67888998888777653

This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. While clathrin mediates endocytic protein transport, and transport from ER to Golgi, coatomers primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. For example, the coatomer COP1 (coat protein complex 1) is responsible for reverse transport of recycled proteins from Golgi and pre-Golgi compartments back to the ER, while COPII buds vesicles from the ER to the Golgi []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Activated small guanine triphosphatases (GTPases) attract coat proteins to specific membrane export sites, thereby linking coatomers to export cargos. As coat proteins polymerise, vesicles are formed and budded from membrane-bound organelles. Coatomer complexes also influence Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors. In mammals, coatomer complexes can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the epsilon subunit of the coatomer complex, which is involved in the regulation of intracellular protein trafficking between the endoplasmic reticulum and the Golgi complex []. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0005198 structural molecule activity, 0006890 retrograde vesicle-mediated transport, Golgi to ER, 0030126 COPI vesicle coat; PDB: 3MV2_B 3MV3_F 3MKR_A.

>KOG0985 consensus Vesicle coat protein clathrin, heavy chain [Intracellular trafficking, secretion, and vesicular transport]

Probab=99.00  E-value=6.1e-06  Score=79.93  Aligned_cols=307  Identities=11%  Similarity=0.119  Sum_probs=150.5

Q ss_pred             hhhhhhccCCCchHHHHHHHHHHHhhcHHHHHHHHHHhhhccC-ccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCC
Q 012111           67 KVSSKKYKNLWPKPVLEALDEAIKQKKWQLALKIFGLLRQQQW-YQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGL  145 (471)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~  145 (471)
                      +.+..-....+|+.+...+.++...+-+.+-+++++.+.-... +..+...-+.|+-...+ -+...+.+..+++.....
T Consensus       973 Vv~tal~E~~dPe~vS~tVkAfMtadLp~eLIELLEKIvL~~S~Fse~~nLQnLLiLtAik-ad~trVm~YI~rLdnyDa 1051 (1666)
T KOG0985|consen  973 VVQTALPETQDPEEVSVTVKAFMTADLPNELIELLEKIVLDNSVFSENRNLQNLLILTAIK-ADRTRVMEYINRLDNYDA 1051 (1666)
T ss_pred             HHHhcCCccCChHHHHHHHHHHHhcCCcHHHHHHHHHHhcCCcccccchhhhhhHHHHHhh-cChHHHHHHHHHhccCCc
Confidence            3333334455678888888888888889999999998875431 22222333333333333 344555566665544321


Q ss_pred             CCCHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHH
Q 012111          146 KPSVDVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNT  225 (471)
Q Consensus       146 ~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~  225 (471)
                       |+      +...+...+-+++|..+|++..      .+....+.|+.-   -+..+.|.+.-++..      .+.+|..
T Consensus      1052 -~~------ia~iai~~~LyEEAF~ifkkf~------~n~~A~~VLie~---i~~ldRA~efAe~~n------~p~vWsq 1109 (1666)
T KOG0985|consen 1052 -PD------IAEIAIENQLYEEAFAIFKKFD------MNVSAIQVLIEN---IGSLDRAYEFAERCN------EPAVWSQ 1109 (1666)
T ss_pred             -hh------HHHHHhhhhHHHHHHHHHHHhc------ccHHHHHHHHHH---hhhHHHHHHHHHhhC------ChHHHHH
Confidence             12      2233444555666666666543      233333333331   233333333332221      2334555


Q ss_pred             HHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCC-----------------
Q 012111          226 IIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVK-----------------  288 (471)
Q Consensus       226 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-----------------  288 (471)
                      +..+-.+.|...+|.+-|-+.       .|...|..++....+.|.+++..+++....+....                 
T Consensus      1110 lakAQL~~~~v~dAieSyika-------dDps~y~eVi~~a~~~~~~edLv~yL~MaRkk~~E~~id~eLi~AyAkt~rl 1182 (1666)
T KOG0985|consen 1110 LAKAQLQGGLVKDAIESYIKA-------DDPSNYLEVIDVASRTGKYEDLVKYLLMARKKVREPYIDSELIFAYAKTNRL 1182 (1666)
T ss_pred             HHHHHHhcCchHHHHHHHHhc-------CCcHHHHHHHHHHHhcCcHHHHHHHHHHHHHhhcCccchHHHHHHHHHhchH
Confidence            555555555555554443222       12334555555555555555555554444433323                 


Q ss_pred             ---------CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCC
Q 012111          289 ---------ADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKP  359 (471)
Q Consensus       289 ---------~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p  359 (471)
                               |+......+.+-|...+.++.|.-+|.         ++..|..|...+...|++..|.+.-++.      -
T Consensus      1183 ~elE~fi~gpN~A~i~~vGdrcf~~~~y~aAkl~y~---------~vSN~a~La~TLV~LgeyQ~AVD~aRKA------n 1247 (1666)
T KOG0985|consen 1183 TELEEFIAGPNVANIQQVGDRCFEEKMYEAAKLLYS---------NVSNFAKLASTLVYLGEYQGAVDAARKA------N 1247 (1666)
T ss_pred             HHHHHHhcCCCchhHHHHhHHHhhhhhhHHHHHHHH---------HhhhHHHHHHHHHHHHHHHHHHHHhhhc------c
Confidence                     333333333444444444444443333         2333444555555555555554443322      1


Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 012111          360 NSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMK  423 (471)
Q Consensus       360 ~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~  423 (471)
                      +..||..+-.+|...+.+.-|     +|-..++.....-...|+.-|-..|-+++.+.+++...
T Consensus      1248 s~ktWK~VcfaCvd~~EFrlA-----QiCGL~iivhadeLeeli~~Yq~rGyFeElIsl~Ea~L 1306 (1666)
T KOG0985|consen 1248 STKTWKEVCFACVDKEEFRLA-----QICGLNIIVHADELEELIEYYQDRGYFEELISLLEAGL 1306 (1666)
T ss_pred             chhHHHHHHHHHhchhhhhHH-----HhcCceEEEehHhHHHHHHHHHhcCcHHHHHHHHHhhh
Confidence            344555555555544443322     23333334444556667777777777777777666554

>KOG1128 consensus Uncharacterized conserved protein, contains TPR repeats [General function prediction only]

Probab=98.97  E-value=4.2e-07  Score=84.80  Aligned_cols=227  Identities=9%  Similarity=0.023  Sum_probs=183.7

Q ss_pred             CCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHH
Q 012111          216 IECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLN  295 (471)
Q Consensus       216 ~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~  295 (471)
                      ++|-...-..+...+.+.|-...|..+|++..          .|...+.+|+..|+..+|..+..+..+  -+||...|.
T Consensus       394 lpp~Wq~q~~laell~slGitksAl~I~Erle----------mw~~vi~CY~~lg~~~kaeei~~q~le--k~~d~~lyc  461 (777)
T KOG1128|consen  394 LPPIWQLQRLLAELLLSLGITKSALVIFERLE----------MWDPVILCYLLLGQHGKAEEINRQELE--KDPDPRLYC  461 (777)
T ss_pred             CCCcchHHHHHHHHHHHcchHHHHHHHHHhHH----------HHHHHHHHHHHhcccchHHHHHHHHhc--CCCcchhHH
Confidence            45555566677888999999999999998873          577788999999999999999988776  489999999


Q ss_pred             HHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcC
Q 012111          296 ILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAG  375 (471)
Q Consensus       296 ~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g  375 (471)
                      .+.+......-+++|.++.+....+       .-..+.....+.++++++.+.|+.-.+.+ +.-..+|-.+..+..+.+
T Consensus       462 ~LGDv~~d~s~yEkawElsn~~sar-------A~r~~~~~~~~~~~fs~~~~hle~sl~~n-plq~~~wf~~G~~ALqle  533 (777)
T KOG1128|consen  462 LLGDVLHDPSLYEKAWELSNYISAR-------AQRSLALLILSNKDFSEADKHLERSLEIN-PLQLGTWFGLGCAALQLE  533 (777)
T ss_pred             HhhhhccChHHHHHHHHHhhhhhHH-------HHHhhccccccchhHHHHHHHHHHHhhcC-ccchhHHHhccHHHHHHh
Confidence            9999888888889999998876543       11222222344789999999998877653 345678888888889999


Q ss_pred             CHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHH
Q 012111          376 LIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAYNALGMTEAAQNLEN  455 (471)
Q Consensus       376 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~  455 (471)
                      +++.|.+.|.......+. +...||.+-.+|.+.|+-.+|...+++..+.+ .-+...|...+....+.|.+++|.+.+.
T Consensus       534 k~q~av~aF~rcvtL~Pd-~~eaWnNls~ayi~~~~k~ra~~~l~EAlKcn-~~~w~iWENymlvsvdvge~eda~~A~~  611 (777)
T KOG1128|consen  534 KEQAAVKAFHRCVTLEPD-NAEAWNNLSTAYIRLKKKKRAFRKLKEALKCN-YQHWQIWENYMLVSVDVGEFEDAIKAYH  611 (777)
T ss_pred             hhHHHHHHHHHHhhcCCC-chhhhhhhhHHHHHHhhhHHHHHHHHHHhhcC-CCCCeeeechhhhhhhcccHHHHHHHHH
Confidence            999999999998887766 78899999999999999999999999998876 4466677777777889999999999999


Q ss_pred             HHHHhhhcC
Q 012111          456 KMIAMKENS  464 (471)
Q Consensus       456 ~m~~~~~~~  464 (471)
                      ++.......
T Consensus       612 rll~~~~~~  620 (777)
T KOG1128|consen  612 RLLDLRKKY  620 (777)
T ss_pred             HHHHhhhhc
Confidence            988776543

>KOG1125 consensus TPR repeat-containing protein [General function prediction only]

Probab=98.96  E-value=1.2e-07  Score=85.99  Aligned_cols=226  Identities=13%  Similarity=0.112  Sum_probs=167.4

Q ss_pred             HHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCH
Q 012111          228 DGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMY  307 (471)
Q Consensus       228 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~  307 (471)
                      .-+.+.|++.+|.-.|+..+++.  +-+...|..|.......++-..|+..+.+..+.+ +-+......|.-.|...|.-
T Consensus       293 ~~lm~nG~L~~A~LafEAAVkqd--P~haeAW~~LG~~qaENE~E~~ai~AL~rcl~Ld-P~NleaLmaLAVSytNeg~q  369 (579)
T KOG1125|consen  293 CNLMKNGDLSEAALAFEAAVKQD--PQHAEAWQKLGITQAENENEQNAISALRRCLELD-PTNLEALMALAVSYTNEGLQ  369 (579)
T ss_pred             HHHHhcCCchHHHHHHHHHHhhC--hHHHHHHHHhhhHhhhccchHHHHHHHHHHHhcC-CccHHHHHHHHHHHhhhhhH
Confidence            34567788888888888887764  5567788888888888888888888888887765 56677788888888888888


Q ss_pred             HHHHHHHHHHHhCCCCCCHHHHHHHH-----------HHHHhcCCHHHHHHHHHHHH-HcCCCCCHHHHHHHHHHHHhcC
Q 012111          308 DKMRSVMDFMQKRFFFPTVVTYNIVI-----------ETFGKAGHIEKMEEYFKKMK-HRGMKPNSITYCSLVSAYSKAG  375 (471)
Q Consensus       308 ~~a~~~~~~~~~~~~~~~~~~~~~li-----------~~~~~~g~~~~a~~~~~~m~-~~~~~p~~~~~~~li~~~~~~g  375 (471)
                      ..|...++......++     |..+.           ..+.....+....++|-++. ..+..+|+.+...|.-.|--.|
T Consensus       370 ~~Al~~L~~Wi~~~p~-----y~~l~~a~~~~~~~~~~s~~~~~~l~~i~~~fLeaa~~~~~~~DpdvQ~~LGVLy~ls~  444 (579)
T KOG1125|consen  370 NQALKMLDKWIRNKPK-----YVHLVSAGENEDFENTKSFLDSSHLAHIQELFLEAARQLPTKIDPDVQSGLGVLYNLSG  444 (579)
T ss_pred             HHHHHHHHHHHHhCcc-----chhccccCccccccCCcCCCCHHHHHHHHHHHHHHHHhCCCCCChhHHhhhHHHHhcch
Confidence            8888888777654211     00000           01111122334444444443 4444577788888888888889


Q ss_pred             CHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCH-HHHHHHHHHHHhcCCHHHHHHHH
Q 012111          376 LIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDN-ITFATMIQAYNALGMTEAAQNLE  454 (471)
Q Consensus       376 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~-~~~~~l~~~~~~~g~~~~A~~~~  454 (471)
                      ++++|.+.|+.+....+. |..+||.|...++...+..+|+..|+++++  ++|+. .+...|.-+|+..|.+++|.+.|
T Consensus       445 efdraiDcf~~AL~v~Pn-d~~lWNRLGAtLAN~~~s~EAIsAY~rALq--LqP~yVR~RyNlgIS~mNlG~ykEA~~hl  521 (579)
T KOG1125|consen  445 EFDRAVDCFEAALQVKPN-DYLLWNRLGATLANGNRSEEAISAYNRALQ--LQPGYVRVRYNLGISCMNLGAYKEAVKHL  521 (579)
T ss_pred             HHHHHHHHHHHHHhcCCc-hHHHHHHhhHHhcCCcccHHHHHHHHHHHh--cCCCeeeeehhhhhhhhhhhhHHHHHHHH
Confidence            999999999999888776 888999999999999999999999999988  57764 45556777889999999999988


Q ss_pred             HHHHHhhhcC
Q 012111          455 NKMIAMKENS  464 (471)
Q Consensus       455 ~~m~~~~~~~  464 (471)
                      =+++.+..+.
T Consensus       522 L~AL~mq~ks  531 (579)
T KOG1125|consen  522 LEALSMQRKS  531 (579)
T ss_pred             HHHHHhhhcc
Confidence            8888877763

>KOG2376 consensus Signal recognition particle, subunit Srp72 [Intracellular trafficking, secretion, and vesicular transport]

Probab=98.95  E-value=3e-05  Score=71.04  Aligned_cols=359  Identities=13%  Similarity=0.075  Sum_probs=213.6

Q ss_pred             hHHHHHHHHHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHH--H
Q 012111           79 KPVLEALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTAL--V  156 (471)
Q Consensus        79 ~~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~l--i  156 (471)
                      ..+..-+......|++++|++....+....  +.+..++..-+.++.+.+++++|+.+.+.-..      ..+++..  =
T Consensus        13 ~~l~t~ln~~~~~~e~e~a~k~~~Kil~~~--pdd~~a~~cKvValIq~~ky~~ALk~ikk~~~------~~~~~~~~fE   84 (652)
T KOG2376|consen   13 EALLTDLNRHGKNGEYEEAVKTANKILSIV--PDDEDAIRCKVVALIQLDKYEDALKLIKKNGA------LLVINSFFFE   84 (652)
T ss_pred             HHHHHHHHHhccchHHHHHHHHHHHHHhcC--CCcHhhHhhhHhhhhhhhHHHHHHHHHHhcch------hhhcchhhHH
Confidence            355666888888999999999999999875  77788899999999999999999966654321      1122222  2


Q ss_pred             HH--HHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCC-HHHHHHHHHHHHcc
Q 012111          157 SA--YGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECS-AVTYNTIIDGYGKA  233 (471)
Q Consensus       157 ~~--~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~-~~~~~~l~~~~~~~  233 (471)
                      .+  +.+.+..++|+..++-..     +.+..+...-...+.+.+++++|.++|+.+.+.+.+-- ...-..++.+-   
T Consensus        85 KAYc~Yrlnk~Dealk~~~~~~-----~~~~~ll~L~AQvlYrl~~ydealdiY~~L~kn~~dd~d~~~r~nl~a~~---  156 (652)
T KOG2376|consen   85 KAYCEYRLNKLDEALKTLKGLD-----RLDDKLLELRAQVLYRLERYDEALDIYQHLAKNNSDDQDEERRANLLAVA---  156 (652)
T ss_pred             HHHHHHHcccHHHHHHHHhccc-----ccchHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCchHHHHHHHHHHHHH---
Confidence            33  447899999999998333     23444666667788999999999999999988753311 11111122111   


Q ss_pred             CCHHHHHHHHHHHHHcCCCCCCHHHHHHH---HHHHHhcCCHHHHHHHHHHHHhCC-------CCCCH------H-HHHH
Q 012111          234 KKFEEMESSFSAMVESGGCHPDIFTLNSM---ISAYGNSGNIEKMEKWYNEFNLMG-------VKADI------Q-TLNI  296 (471)
Q Consensus       234 ~~~~~a~~~~~~~~~~~~~~~~~~~~~~l---~~~~~~~~~~~~a~~~~~~~~~~~-------~~~~~------~-~~~~  296 (471)
                       -...+. +.+..    ...| ..+|..+   .-.+...|++.+|+++++...+.+       -..+.      . .-..
T Consensus       157 -a~l~~~-~~q~v----~~v~-e~syel~yN~Ac~~i~~gky~qA~elL~kA~~~~~e~l~~~d~~eEeie~el~~IrvQ  229 (652)
T KOG2376|consen  157 -AALQVQ-LLQSV----PEVP-EDSYELLYNTACILIENGKYNQAIELLEKALRICREKLEDEDTNEEEIEEELNPIRVQ  229 (652)
T ss_pred             -HhhhHH-HHHhc----cCCC-cchHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHHHhhcccccchhhHHHHHHHHHHH
Confidence             111111 12222    1223 2244443   345667999999999999883221       01111      1 1233


Q ss_pred             HHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHH----HHHH----------------------------------------
Q 012111          297 LTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVT----YNIV----------------------------------------  332 (471)
Q Consensus       297 ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~----~~~l----------------------------------------  332 (471)
                      +.-++...|+.++|..++..+.+.... |...    -|.|                                        
T Consensus       230 layVlQ~~Gqt~ea~~iy~~~i~~~~~-D~~~~Av~~NNLva~~~d~~~~d~~~l~~k~~~~~~l~~~~l~~Ls~~qk~~  308 (652)
T KOG2376|consen  230 LAYVLQLQGQTAEASSIYVDIIKRNPA-DEPSLAVAVNNLVALSKDQNYFDGDLLKSKKSQVFKLAEFLLSKLSKKQKQA  308 (652)
T ss_pred             HHHHHHHhcchHHHHHHHHHHHHhcCC-CchHHHHHhcchhhhccccccCchHHHHHHHHHHHHhHHHHHHHHHHHHHHH
Confidence            455667889999999999888776432 1100    0000                                        


Q ss_pred             -------HHHHHhc--------------------------------CCHHHHHHHHHHHHHcCCCCC--HHHHHHHHHHH
Q 012111          333 -------IETFGKA--------------------------------GHIEKMEEYFKKMKHRGMKPN--SITYCSLVSAY  371 (471)
Q Consensus       333 -------i~~~~~~--------------------------------g~~~~a~~~~~~m~~~~~~p~--~~~~~~li~~~  371 (471)
                             +..|...                                .....+.+++...-+.  .|.  ..+.-..+...
T Consensus       309 i~~N~~lL~l~tnk~~q~r~~~a~lp~~~p~~~~~~ll~~~t~~~~~~~~ka~e~L~~~~~~--~p~~s~~v~L~~aQl~  386 (652)
T KOG2376|consen  309 IYRNNALLALFTNKMDQVRELSASLPGMSPESLFPILLQEATKVREKKHKKAIELLLQFADG--HPEKSKVVLLLRAQLK  386 (652)
T ss_pred             HHHHHHHHHHHhhhHHHHHHHHHhCCccCchHHHHHHHHHHHHHHHHHHhhhHHHHHHHhcc--CCchhHHHHHHHHHHH
Confidence                   0111000                                0112222222222222  222  33445556667


Q ss_pred             HhcCCHHHHHHHHH--------HHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhC--CCCCCHHHHHHH----
Q 012111          372 SKAGLIMKVDSILR--------QVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKER--HCVPDNITFATM----  437 (471)
Q Consensus       372 ~~~g~~~~a~~~~~--------~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~--~~~p~~~~~~~l----  437 (471)
                      ...|+++.|.+++.        .+.+.+..|  .+...+...+.+.++-+.|..++++....  .-.+.......+    
T Consensus       387 is~gn~~~A~~il~~~~~~~~ss~~~~~~~P--~~V~aiv~l~~~~~~~~~a~~vl~~Ai~~~~~~~t~s~~l~~~~~~a  464 (652)
T KOG2376|consen  387 ISQGNPEVALEILSLFLESWKSSILEAKHLP--GTVGAIVALYYKIKDNDSASAVLDSAIKWWRKQQTGSIALLSLMREA  464 (652)
T ss_pred             HhcCCHHHHHHHHHHHhhhhhhhhhhhccCh--hHHHHHHHHHHhccCCccHHHHHHHHHHHHHHhcccchHHHhHHHHH
Confidence            78888888888888        555554443  34455666677777766677777666531  011222333333    


Q ss_pred             HHHHHhcCCHHHHHHHHHHHHHhhhcCC
Q 012111          438 IQAYNALGMTEAAQNLENKMIAMKENSG  465 (471)
Q Consensus       438 ~~~~~~~g~~~~A~~~~~~m~~~~~~~~  465 (471)
                      ...-.+.|+.++|..+++++.+..|+..
T Consensus       465 a~f~lr~G~~~ea~s~leel~k~n~~d~  492 (652)
T KOG2376|consen  465 AEFKLRHGNEEEASSLLEELVKFNPNDT  492 (652)
T ss_pred             hHHHHhcCchHHHHHHHHHHHHhCCchH
Confidence            3333567999999999999998777643

>PRK04841 transcriptional regulator MalT; Provisional

Probab=98.94  E-value=1.8e-05  Score=82.49  Aligned_cols=337  Identities=9%  Similarity=0.006  Sum_probs=211.4

Q ss_pred             HHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCC------CCC--HHHHHHHHHH
Q 012111           87 EAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGL------KPS--VDVYTALVSA  158 (471)
Q Consensus        87 ~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~------~~~--~~~~~~li~~  158 (471)
                      .+...|++..+...++.+.... ...+..........+...|+++++..+++.....-.      .+.  ......+...
T Consensus       383 ~l~~~g~~~~l~~~l~~lp~~~-~~~~~~l~~~~a~~~~~~g~~~~a~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~a~~  461 (903)
T PRK04841        383 SLFNQGELSLLEECLNALPWEV-LLENPRLVLLQAWLAQSQHRYSEVNTLLARAEQELKDRNIELDGTLQAEFNALRAQV  461 (903)
T ss_pred             HHHhcCChHHHHHHHHhCCHHH-HhcCcchHHHHHHHHHHCCCHHHHHHHHHHHHHhccccCcccchhHHHHHHHHHHHH
Confidence            3445567776666666553211 112222334445556678999999999987754311      111  1222233345


Q ss_pred             HHhcCCHHHHHHHHHHhhcCCCCCCC----HHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCC---CC--CHHHHHHHHHH
Q 012111          159 YGQSGLLDEAFSTINDMKSVSDCKPD----VYTYSILIKSCTKFHRFDLIEKILAEMSYLGI---EC--SAVTYNTIIDG  229 (471)
Q Consensus       159 ~~~~~~~~~a~~~~~~~~~~~~~~~~----~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~---~~--~~~~~~~l~~~  229 (471)
                      +...|++++|...++....... ..+    ....+.+...+...|+++.|...+++.....-   .+  ...++..+...
T Consensus       462 ~~~~g~~~~A~~~~~~al~~~~-~~~~~~~~~a~~~lg~~~~~~G~~~~A~~~~~~al~~~~~~g~~~~~~~~~~~la~~  540 (903)
T PRK04841        462 AINDGDPEEAERLAELALAELP-LTWYYSRIVATSVLGEVHHCKGELARALAMMQQTEQMARQHDVYHYALWSLLQQSEI  540 (903)
T ss_pred             HHhCCCHHHHHHHHHHHHhcCC-CccHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhhhcchHHHHHHHHHHHHH
Confidence            6678999999999998765211 112    12345566667789999999999988764311   11  12345566777


Q ss_pred             HHccCCHHHHHHHHHHHHHc---CCCC--C-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCC--CCC--CHHHHHHHHH
Q 012111          230 YGKAKKFEEMESSFSAMVES---GGCH--P-DIFTLNSMISAYGNSGNIEKMEKWYNEFNLMG--VKA--DIQTLNILTK  299 (471)
Q Consensus       230 ~~~~~~~~~a~~~~~~~~~~---~~~~--~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~--~~~--~~~~~~~ll~  299 (471)
                      +...|+++.|...+++..+.   .+..  + ....+..+...+...|++++|...+.+.....  ..+  ....+..+..
T Consensus       541 ~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~la~  620 (903)
T PRK04841        541 LFAQGFLQAAYETQEKAFQLIEEQHLEQLPMHEFLLRIRAQLLWEWARLDEAEQCARKGLEVLSNYQPQQQLQCLAMLAK  620 (903)
T ss_pred             HHHCCCHHHHHHHHHHHHHHHHHhccccccHHHHHHHHHHHHHHHhcCHHHHHHHHHHhHHhhhccCchHHHHHHHHHHH
Confidence            88899999999998876542   1111  1 22334556667778899999999998875431  112  2334555667


Q ss_pred             HHHHcCCHHHHHHHHHHHHhCCCCC-CHHHH-----HHHHHHHHhcCCHHHHHHHHHHHHHcCCCCC---HHHHHHHHHH
Q 012111          300 SYGRAGMYDKMRSVMDFMQKRFFFP-TVVTY-----NIVIETFGKAGHIEKMEEYFKKMKHRGMKPN---SITYCSLVSA  370 (471)
Q Consensus       300 ~~~~~~~~~~a~~~~~~~~~~~~~~-~~~~~-----~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~---~~~~~~li~~  370 (471)
                      .+...|+++.|...+.......... ....+     ...+..+...|+.+.|..++...........   ...+..+..+
T Consensus       621 ~~~~~G~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~l~~~~~~~~~~~~~~~~~~~~~a~~  700 (903)
T PRK04841        621 ISLARGDLDNARRYLNRLENLLGNGRYHSDWIANADKVRLIYWQMTGDKEAAANWLRQAPKPEFANNHFLQGQWRNIARA  700 (903)
T ss_pred             HHHHcCCHHHHHHHHHHHHHHHhcccccHhHhhHHHHHHHHHHHHCCCHHHHHHHHHhcCCCCCccchhHHHHHHHHHHH
Confidence            7888999999999988775421110 11111     1122445568899999999877554221111   1123456777


Q ss_pred             HHhcCCHHHHHHHHHHHHhC----CCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhC
Q 012111          371 YSKAGLIMKVDSILRQVENS----DVIL-DTPFFNCIISAYGQAGDVEKMGELFLTMKER  425 (471)
Q Consensus       371 ~~~~g~~~~a~~~~~~~~~~----~~~~-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~  425 (471)
                      +...|+.++|...+++....    +... ...++..+..++.+.|+.++|...+.+..+.
T Consensus       701 ~~~~g~~~~A~~~l~~al~~~~~~g~~~~~a~~~~~la~a~~~~G~~~~A~~~L~~Al~l  760 (903)
T PRK04841        701 QILLGQFDEAEIILEELNENARSLRLMSDLNRNLILLNQLYWQQGRKSEAQRVLLEALKL  760 (903)
T ss_pred             HHHcCCHHHHHHHHHHHHHHHHHhCchHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            88999999999999887642    3222 2245666778889999999999999998865

>KOG1125 consensus TPR repeat-containing protein [General function prediction only]

Probab=98.94  E-value=2.5e-07  Score=84.02  Aligned_cols=217  Identities=16%  Similarity=0.153  Sum_probs=98.9

Q ss_pred             HHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHH
Q 012111           89 IKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEA  168 (471)
Q Consensus        89 ~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a  168 (471)
                      .+.|++.+|.-.|+.+.+++  |.+..+|..|...-...++-..|+..+++..+.... +..+.-.|.-.|...|.-..|
T Consensus       296 m~nG~L~~A~LafEAAVkqd--P~haeAW~~LG~~qaENE~E~~ai~AL~rcl~LdP~-NleaLmaLAVSytNeg~q~~A  372 (579)
T KOG1125|consen  296 MKNGDLSEAALAFEAAVKQD--PQHAEAWQKLGITQAENENEQNAISALRRCLELDPT-NLEALMALAVSYTNEGLQNQA  372 (579)
T ss_pred             HhcCCchHHHHHHHHHHhhC--hHHHHHHHHhhhHhhhccchHHHHHHHHHHHhcCCc-cHHHHHHHHHHHhhhhhHHHH
Confidence            45555666666666655554  455556666666555555555666666655554322 445555555555555555556


Q ss_pred             HHHHHHhhcCCCCCCCHHHHHHHH-------HHHHhcCCHHHHHHHHHHHH-HCCCCCCHHHHHHHHHHHHccCCHHHHH
Q 012111          169 FSTINDMKSVSDCKPDVYTYSILI-------KSCTKFHRFDLIEKILAEMS-YLGIECSAVTYNTIIDGYGKAKKFEEME  240 (471)
Q Consensus       169 ~~~~~~~~~~~~~~~~~~~~~~ll-------~~~~~~~~~~~a~~~~~~~~-~~g~~~~~~~~~~l~~~~~~~~~~~~a~  240 (471)
                      +..+++.....  ++-...-..-.       ..+.....+....++|-++. ..+..+|+.++..|.-.|.-.|+++.|.
T Consensus       373 l~~L~~Wi~~~--p~y~~l~~a~~~~~~~~~~s~~~~~~l~~i~~~fLeaa~~~~~~~DpdvQ~~LGVLy~ls~efdrai  450 (579)
T KOG1125|consen  373 LKMLDKWIRNK--PKYVHLVSAGENEDFENTKSFLDSSHLAHIQELFLEAARQLPTKIDPDVQSGLGVLYNLSGEFDRAV  450 (579)
T ss_pred             HHHHHHHHHhC--ccchhccccCccccccCCcCCCCHHHHHHHHHHHHHHHHhCCCCCChhHHhhhHHHHhcchHHHHHH
Confidence            55555554311  00000000000       00111111222333333322 2222344444445555555555555555


Q ss_pred             HHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCC-HHHHHHHHHHHHHcCCHHHHHHHH
Q 012111          241 SSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKAD-IQTLNILTKSYGRAGMYDKMRSVM  314 (471)
Q Consensus       241 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~ll~~~~~~~~~~~a~~~~  314 (471)
                      ..|+..+...  +-|...||.|...++...+.++|+..|.+..+.  .|+ +.+...|.-.|...|.+++|...|
T Consensus       451 Dcf~~AL~v~--Pnd~~lWNRLGAtLAN~~~s~EAIsAY~rALqL--qP~yVR~RyNlgIS~mNlG~ykEA~~hl  521 (579)
T KOG1125|consen  451 DCFEAALQVK--PNDYLLWNRLGATLANGNRSEEAISAYNRALQL--QPGYVRVRYNLGISCMNLGAYKEAVKHL  521 (579)
T ss_pred             HHHHHHHhcC--CchHHHHHHhhHHhcCCcccHHHHHHHHHHHhc--CCCeeeeehhhhhhhhhhhhHHHHHHHH
Confidence            5555554432  334445555555555555555555555555443  222 222233334444455555554444

>KOG4162 consensus Predicted calmodulin-binding protein [Signal transduction mechanisms]

Probab=98.94  E-value=3e-05  Score=73.28  Aligned_cols=352  Identities=14%  Similarity=0.151  Sum_probs=237.1

Q ss_pred             ccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHH
Q 012111          110 YQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYS  189 (471)
Q Consensus       110 ~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  189 (471)
                      +.-+...|..+.-++...|+++.+.+.|++....-+. ..+.|+.+...|...|.-..|+.+++.-.....-++++..+-
T Consensus       319 ~qnd~ai~d~Lt~al~~~g~f~~lae~fE~~~~~~~~-~~e~w~~~als~saag~~s~Av~ll~~~~~~~~~ps~~s~~L  397 (799)
T KOG4162|consen  319 FQNDAAIFDHLTFALSRCGQFEVLAEQFEQALPFSFG-EHERWYQLALSYSAAGSDSKAVNLLRESLKKSEQPSDISVLL  397 (799)
T ss_pred             hcchHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhhhh-hHHHHHHHHHHHHHhccchHHHHHHHhhcccccCCCcchHHH
Confidence            4557788888888999999999999999998754333 677899999999999999999999988765333233444444


Q ss_pred             HHHHHHH-hcCCHHHHHHHHHHHHHC--CC--CCCHHHHHHHHHHHHcc-----------CCHHHHHHHHHHHHHcCCCC
Q 012111          190 ILIKSCT-KFHRFDLIEKILAEMSYL--GI--ECSAVTYNTIIDGYGKA-----------KKFEEMESSFSAMVESGGCH  253 (471)
Q Consensus       190 ~ll~~~~-~~~~~~~a~~~~~~~~~~--g~--~~~~~~~~~l~~~~~~~-----------~~~~~a~~~~~~~~~~~~~~  253 (471)
                      ..-..|. +.+..++++.+-.+....  |.  ......|..+.-+|...           ....++++.+++..+.++..
T Consensus       398 masklc~e~l~~~eegldYA~kai~~~~~~~~~l~~~~~l~lGi~y~~~A~~a~~~seR~~~h~kslqale~av~~d~~d  477 (799)
T KOG4162|consen  398 MASKLCIERLKLVEEGLDYAQKAISLLGGQRSHLKPRGYLFLGIAYGFQARQANLKSERDALHKKSLQALEEAVQFDPTD  477 (799)
T ss_pred             HHHHHHHhchhhhhhHHHHHHHHHHHhhhhhhhhhhhHHHHHHHHHHhHhhcCCChHHHHHHHHHHHHHHHHHHhcCCCC
Confidence            4444454 346667776666666551  11  12234444444444321           23567888899998887667


Q ss_pred             CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCC----------
Q 012111          254 PDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFF----------  323 (471)
Q Consensus       254 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~----------  323 (471)
                      |++..|..+  -|+-.++.+.|.+..++..+.+-.-+...|..|.-.+...+++.+|+.+.+...+.-..          
T Consensus       478 p~~if~lal--q~A~~R~l~sAl~~~~eaL~l~~~~~~~~whLLALvlSa~kr~~~Al~vvd~al~E~~~N~~l~~~~~~  555 (799)
T KOG4162|consen  478 PLVIFYLAL--QYAEQRQLTSALDYAREALALNRGDSAKAWHLLALVLSAQKRLKEALDVVDAALEEFGDNHVLMDGKIH  555 (799)
T ss_pred             chHHHHHHH--HHHHHHhHHHHHHHHHHHHHhcCCccHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHhhhhhhhchhhhh
Confidence            766555444  45677899999999999998866888999999999999999999999999876543111          


Q ss_pred             ---------CCHHHHHHHHHHHHh---------cC--------------CHHHHHHHHHHH--------HHcC-------
Q 012111          324 ---------PTVVTYNIVIETFGK---------AG--------------HIEKMEEYFKKM--------KHRG-------  356 (471)
Q Consensus       324 ---------~~~~~~~~li~~~~~---------~g--------------~~~~a~~~~~~m--------~~~~-------  356 (471)
                               --..|...++..+-.         .|              +..++......+        ...|       
T Consensus       556 i~~~~~~~e~~l~t~~~~L~~we~~~~~q~~~~~g~~~~lk~~l~la~~q~~~a~s~sr~ls~l~a~~~~~~~se~~Lp~  635 (799)
T KOG4162|consen  556 IELTFNDREEALDTCIHKLALWEAEYGVQQTLDEGKLLRLKAGLHLALSQPTDAISTSRYLSSLVASQLKSAGSELKLPS  635 (799)
T ss_pred             hhhhcccHHHHHHHHHHHHHHHHhhhhHhhhhhhhhhhhhhcccccCcccccccchhhHHHHHHHHhhhhhcccccccCc
Confidence                     001122222222210         00              111111111111        0001       


Q ss_pred             --CC--CC------HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCC
Q 012111          357 --MK--PN------SITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERH  426 (471)
Q Consensus       357 --~~--p~------~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~  426 (471)
                        ..  |+      ...|......+.+.+..++|...+.+.....+. ....|......+...|.+.+|.+.|.....  
T Consensus       636 s~~~~~~~~~~~~~~~lwllaa~~~~~~~~~~~a~~CL~Ea~~~~~l-~~~~~~~~G~~~~~~~~~~EA~~af~~Al~--  712 (799)
T KOG4162|consen  636 STVLPGPDSLWYLLQKLWLLAADLFLLSGNDDEARSCLLEASKIDPL-SASVYYLRGLLLEVKGQLEEAKEAFLVALA--  712 (799)
T ss_pred             ccccCCCCchHHHHHHHHHHHHHHHHhcCCchHHHHHHHHHHhcchh-hHHHHHHhhHHHHHHHhhHHHHHHHHHHHh--
Confidence              01  11      122345556677888888998888888776544 677777777888899999999999998887  


Q ss_pred             CCC-CHHHHHHHHHHHHhcCCHHHHHH--HHHHHHHhhhcCCCC
Q 012111          427 CVP-DNITFATMIQAYNALGMTEAAQN--LENKMIAMKENSGKK  467 (471)
Q Consensus       427 ~~p-~~~~~~~l~~~~~~~g~~~~A~~--~~~~m~~~~~~~~~~  467 (471)
                      +.| ++....++...+.+.|+...|..  ++.++.+.+|.+.+.
T Consensus       713 ldP~hv~s~~Ala~~lle~G~~~la~~~~~L~dalr~dp~n~ea  756 (799)
T KOG4162|consen  713 LDPDHVPSMTALAELLLELGSPRLAEKRSLLSDALRLDPLNHEA  756 (799)
T ss_pred             cCCCCcHHHHHHHHHHHHhCCcchHHHHHHHHHHHhhCCCCHHH
Confidence            456 45677888899999999888877  999999999876543

>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]

Probab=98.89  E-value=3.9e-06  Score=83.89  Aligned_cols=237  Identities=11%  Similarity=0.099  Sum_probs=187.9

Q ss_pred             CCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCC---CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHH
Q 012111          217 ECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHP---DIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQT  293 (471)
Q Consensus       217 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~---~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~  293 (471)
                      +-+...|-..|......++.++|.+++++.+..-++.-   -...|.++++.-.-.|.-+...++|+++.+..  -....
T Consensus      1455 PNSSi~WI~YMaf~LelsEiekAR~iaerAL~tIN~REeeEKLNiWiA~lNlEn~yG~eesl~kVFeRAcqyc--d~~~V 1532 (1710)
T KOG1070|consen 1455 PNSSILWIRYMAFHLELSEIEKARKIAERALKTINFREEEEKLNIWIAYLNLENAYGTEESLKKVFERACQYC--DAYTV 1532 (1710)
T ss_pred             CCcchHHHHHHHHHhhhhhhHHHHHHHHHHhhhCCcchhHHHHHHHHHHHhHHHhhCcHHHHHHHHHHHHHhc--chHHH
Confidence            44577888889999999999999999999876532221   13467777777777788899999999988742  33457


Q ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCC---HHHHHHHHHH
Q 012111          294 LNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPN---SITYCSLVSA  370 (471)
Q Consensus       294 ~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~---~~~~~~li~~  370 (471)
                      |..|...|.+.+.+++|.++++.|.+.-- -....|...+..+.+.++-+.|..++.+..+.  -|.   .......+..
T Consensus      1533 ~~~L~~iy~k~ek~~~A~ell~~m~KKF~-q~~~vW~~y~~fLl~~ne~~aa~~lL~rAL~~--lPk~eHv~~IskfAqL 1609 (1710)
T KOG1070|consen 1533 HLKLLGIYEKSEKNDEADELLRLMLKKFG-QTRKVWIMYADFLLRQNEAEAARELLKRALKS--LPKQEHVEFISKFAQL 1609 (1710)
T ss_pred             HHHHHHHHHHhhcchhHHHHHHHHHHHhc-chhhHHHHHHHHHhcccHHHHHHHHHHHHHhh--cchhhhHHHHHHHHHH
Confidence            88999999999999999999999998743 47788999999999999999999999998875  343   3345556666


Q ss_pred             HHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCH--HHHHHHHHHHHhcCCHH
Q 012111          371 YSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDN--ITFATMIQAYNALGMTE  448 (471)
Q Consensus       371 ~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~--~~~~~l~~~~~~~g~~~  448 (471)
                      -.+.|+.+++..+|+......++ -...|+.+++.-.+.|+.+.+.++|++....++.|-.  ..|...+..--..|+-+
T Consensus      1610 EFk~GDaeRGRtlfEgll~ayPK-RtDlW~VYid~eik~~~~~~vR~lfeRvi~l~l~~kkmKfffKkwLeyEk~~Gde~ 1688 (1710)
T KOG1070|consen 1610 EFKYGDAERGRTLFEGLLSAYPK-RTDLWSVYIDMEIKHGDIKYVRDLFERVIELKLSIKKMKFFFKKWLEYEKSHGDEK 1688 (1710)
T ss_pred             HhhcCCchhhHHHHHHHHhhCcc-chhHHHHHHHHHHccCCHHHHHHHHHHHHhcCCChhHhHHHHHHHHHHHHhcCchh
Confidence            77889999999999999887766 7889999999999999999999999999998887753  45666666666667765


Q ss_pred             HHHHHHHHHHH
Q 012111          449 AAQNLENKMIA  459 (471)
Q Consensus       449 ~A~~~~~~m~~  459 (471)
                      .+..+=.++.+
T Consensus      1689 ~vE~VKarA~E 1699 (1710)
T KOG1070|consen 1689 NVEYVKARAKE 1699 (1710)
T ss_pred             hHHHHHHHHHH
Confidence            55544444443

>KOG0624 consensus dsRNA-activated protein kinase inhibitor P58, contains TPR and DnaJ domains [Defense mechanisms]

Probab=98.88  E-value=3.3e-05  Score=66.05  Aligned_cols=281  Identities=12%  Similarity=0.033  Sum_probs=203.6

Q ss_pred             HHHHHHHHHHHhhcHHHHHHHHHHhhhccCccCChh-HHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCC--HHH-----
Q 012111           80 PVLEALDEAIKQKKWQLALKIFGLLRQQQWYQARCQ-TFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPS--VDV-----  151 (471)
Q Consensus        80 ~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~-~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~--~~~-----  151 (471)
                      .+....-.+...|+-+.|+.-|+.+.+.   +||.. +-..-...+.+.|.+++|..=|+..+.....-.  ...     
T Consensus        74 aifrRaT~yLAmGksk~al~Dl~rVlel---KpDF~~ARiQRg~vllK~Gele~A~~DF~~vl~~~~s~~~~~eaqskl~  150 (504)
T KOG0624|consen   74 AIFRRATVYLAMGKSKAALQDLSRVLEL---KPDFMAARIQRGVVLLKQGELEQAEADFDQVLQHEPSNGLVLEAQSKLA  150 (504)
T ss_pred             HHHHHHHHHhhhcCCccchhhHHHHHhc---CccHHHHHHHhchhhhhcccHHHHHHHHHHHHhcCCCcchhHHHHHHHH
Confidence            3344445567789999999999999885   56653 344556678899999999999999998743211  111     


Q ss_pred             -------HHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHH
Q 012111          152 -------YTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYN  224 (471)
Q Consensus       152 -------~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~  224 (471)
                             ....+..+...|+...|++....+.+.  .+.|...|..-..+|...|++..|+.-++...+.. ..+..++.
T Consensus       151 ~~~e~~~l~~ql~s~~~~GD~~~ai~~i~~llEi--~~Wda~l~~~Rakc~i~~~e~k~AI~Dlk~askLs-~DnTe~~y  227 (504)
T KOG0624|consen  151 LIQEHWVLVQQLKSASGSGDCQNAIEMITHLLEI--QPWDASLRQARAKCYIAEGEPKKAIHDLKQASKLS-QDNTEGHY  227 (504)
T ss_pred             hHHHHHHHHHHHHHHhcCCchhhHHHHHHHHHhc--CcchhHHHHHHHHHHHhcCcHHHHHHHHHHHHhcc-ccchHHHH
Confidence                   122344566789999999999999873  36788899999999999999999998888887664 44677777


Q ss_pred             HHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHc
Q 012111          225 TIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRA  304 (471)
Q Consensus       225 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~  304 (471)
                      .+-..+...|+.+.++...++..+   +.||...+-..-      .......+.++.|.                .....
T Consensus       228 kis~L~Y~vgd~~~sL~~iRECLK---ldpdHK~Cf~~Y------KklkKv~K~les~e----------------~~ie~  282 (504)
T KOG0624|consen  228 KISQLLYTVGDAENSLKEIRECLK---LDPDHKLCFPFY------KKLKKVVKSLESAE----------------QAIEE  282 (504)
T ss_pred             HHHHHHHhhhhHHHHHHHHHHHHc---cCcchhhHHHHH------HHHHHHHHHHHHHH----------------HHHhh
Confidence            888889999999999999999877   466654332211      11222333333332                23455


Q ss_pred             CCHHHHHHHHHHHHhCCCCCCHH---HHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCC-HHHHHHHHHHHHhcCCHHHH
Q 012111          305 GMYDKMRSVMDFMQKRFFFPTVV---TYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPN-SITYCSLVSAYSKAGLIMKV  380 (471)
Q Consensus       305 ~~~~~a~~~~~~~~~~~~~~~~~---~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~-~~~~~~li~~~~~~g~~~~a  380 (471)
                      ++|.++..-.+...+........   .+..+-.++...|++.+|++.-.+....  .|+ ..++.--..+|.-...++.|
T Consensus       283 ~~~t~cle~ge~vlk~ep~~~~ir~~~~r~~c~C~~~d~~~~eAiqqC~evL~~--d~~dv~~l~dRAeA~l~dE~YD~A  360 (504)
T KOG0624|consen  283 KHWTECLEAGEKVLKNEPEETMIRYNGFRVLCTCYREDEQFGEAIQQCKEVLDI--DPDDVQVLCDRAEAYLGDEMYDDA  360 (504)
T ss_pred             hhHHHHHHHHHHHHhcCCcccceeeeeeheeeecccccCCHHHHHHHHHHHHhc--CchHHHHHHHHHHHHhhhHHHHHH
Confidence            67777777777777764432222   3444556677789999999999888874  554 88888889999999999999


Q ss_pred             HHHHHHHHhCCCC
Q 012111          381 DSILRQVENSDVI  393 (471)
Q Consensus       381 ~~~~~~~~~~~~~  393 (471)
                      +.-|+...+.+..
T Consensus       361 I~dye~A~e~n~s  373 (504)
T KOG0624|consen  361 IHDYEKALELNES  373 (504)
T ss_pred             HHHHHHHHhcCcc
Confidence            9999999987654

>PLN02789 farnesyltranstransferase

Probab=98.86  E-value=1.1e-05  Score=71.44  Aligned_cols=137  Identities=7%  Similarity=-0.074  Sum_probs=68.8

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccC-CHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcC
Q 012111          192 IKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAK-KFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSG  270 (471)
Q Consensus       192 l~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~-~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  270 (471)
                      -..+...+..++|+.+.+++++.. +-+..+|+..-.++...| ++++++..++++.+..  +.+..+|+.....+.+.|
T Consensus        44 ra~l~~~e~serAL~lt~~aI~ln-P~~ytaW~~R~~iL~~L~~~l~eeL~~~~~~i~~n--pknyqaW~~R~~~l~~l~  120 (320)
T PLN02789         44 RAVYASDERSPRALDLTADVIRLN-PGNYTVWHFRRLCLEALDADLEEELDFAEDVAEDN--PKNYQIWHHRRWLAEKLG  120 (320)
T ss_pred             HHHHHcCCCCHHHHHHHHHHHHHC-chhHHHHHHHHHHHHHcchhHHHHHHHHHHHHHHC--CcchHHhHHHHHHHHHcC
Confidence            333444556666666666666543 223444544444444445 4566666666665543  334444554444444444


Q ss_pred             CH--HHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHH
Q 012111          271 NI--EKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVI  333 (471)
Q Consensus       271 ~~--~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li  333 (471)
                      +.  ++++.+++++.+.+ +-+..+|+...-++...|++++++..++++.+.++. +...|+...
T Consensus       121 ~~~~~~el~~~~kal~~d-pkNy~AW~~R~w~l~~l~~~~eeL~~~~~~I~~d~~-N~sAW~~R~  183 (320)
T PLN02789        121 PDAANKELEFTRKILSLD-AKNYHAWSHRQWVLRTLGGWEDELEYCHQLLEEDVR-NNSAWNQRY  183 (320)
T ss_pred             chhhHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHCCC-chhHHHHHH
Confidence            32  44555555555443 344555555555555555555555555555554333 334444433

>KOG3617 consensus WD40 and TPR repeat-containing protein [General function prediction only]

Probab=98.84  E-value=5.1e-06  Score=78.74  Aligned_cols=317  Identities=12%  Similarity=0.116  Sum_probs=188.4

Q ss_pred             HHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhC-C--------CCCCHHHHHHHHHHH
Q 012111           89 IKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSD-G--------LKPSVDVYTALVSAY  159 (471)
Q Consensus        89 ~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~-~--------~~~~~~~~~~li~~~  159 (471)
                      +..|+.+.|.+-.+.+..       ...|..+..+|.+..+.+-|.-.+..|... |        ..++ ..-....-..
T Consensus       739 vtiG~MD~AfksI~~IkS-------~~vW~nmA~McVkT~RLDVAkVClGhm~~aRgaRAlR~a~q~~~-e~eakvAvLA  810 (1416)
T KOG3617|consen  739 VTIGSMDAAFKSIQFIKS-------DSVWDNMASMCVKTRRLDVAKVCLGHMKNARGARALRRAQQNGE-EDEAKVAVLA  810 (1416)
T ss_pred             EEeccHHHHHHHHHHHhh-------hHHHHHHHHHhhhhccccHHHHhhhhhhhhhhHHHHHHHHhCCc-chhhHHHHHH
Confidence            456888888887776653       358999999999999998888777776532 1        1121 2222233334


Q ss_pred             HhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHH
Q 012111          160 GQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEM  239 (471)
Q Consensus       160 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~a  239 (471)
                      ...|.+++|..+|.+-++          |..|=+.|...|.+++|.++-+.--+..   -..||......+-..++.+.|
T Consensus       811 ieLgMlEeA~~lYr~ckR----------~DLlNKlyQs~g~w~eA~eiAE~~DRiH---Lr~Tyy~yA~~Lear~Di~~A  877 (1416)
T KOG3617|consen  811 IELGMLEEALILYRQCKR----------YDLLNKLYQSQGMWSEAFEIAETKDRIH---LRNTYYNYAKYLEARRDIEAA  877 (1416)
T ss_pred             HHHhhHHHHHHHHHHHHH----------HHHHHHHHHhcccHHHHHHHHhhcccee---hhhhHHHHHHHHHhhccHHHH
Confidence            578899999999998876          4456667778899999998876533322   235666677777778889999


Q ss_pred             HHHHHHHH----------HcC--------CCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHH
Q 012111          240 ESSFSAMV----------ESG--------GCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSY  301 (471)
Q Consensus       240 ~~~~~~~~----------~~~--------~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~  301 (471)
                      ++.|++..          ...        ....|...|......+...|+.+.|+.+|....+         |-.+++..
T Consensus       878 leyyEK~~~hafev~rmL~e~p~~~e~Yv~~~~d~~L~~WWgqYlES~GemdaAl~~Y~~A~D---------~fs~VrI~  948 (1416)
T KOG3617|consen  878 LEYYEKAGVHAFEVFRMLKEYPKQIEQYVRRKRDESLYSWWGQYLESVGEMDAALSFYSSAKD---------YFSMVRIK  948 (1416)
T ss_pred             HHHHHhcCChHHHHHHHHHhChHHHHHHHHhccchHHHHHHHHHHhcccchHHHHHHHHHhhh---------hhhheeeE
Confidence            88887541          110        0012333444444445556666666666655432         34455555


Q ss_pred             HHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCC-----
Q 012111          302 GRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGL-----  376 (471)
Q Consensus       302 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~-----  376 (471)
                      |-.|+.++|-++-++-      -|....-.+...|-..|++.+|..+|.+...         +...|+.|-.++-     
T Consensus       949 C~qGk~~kAa~iA~es------gd~AAcYhlaR~YEn~g~v~~Av~FfTrAqa---------fsnAIRlcKEnd~~d~L~ 1013 (1416)
T KOG3617|consen  949 CIQGKTDKAARIAEES------GDKAACYHLARMYENDGDVVKAVKFFTRAQA---------FSNAIRLCKENDMKDRLA 1013 (1416)
T ss_pred             eeccCchHHHHHHHhc------ccHHHHHHHHHHhhhhHHHHHHHHHHHHHHH---------HHHHHHHHHhcCHHHHHH
Confidence            6666666666665432      2444555677778888888888887776543         2223332222221     


Q ss_pred             ----------HHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHH--------HHhCCCC--CCHHHHHH
Q 012111          377 ----------IMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLT--------MKERHCV--PDNITFAT  436 (471)
Q Consensus       377 ----------~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~--------~~~~~~~--p~~~~~~~  436 (471)
                                .-.|-.+|++.   |.     -+...+..|-++|.+.+|+++--+        ++..++.  .|+...+.
T Consensus      1014 nlal~s~~~d~v~aArYyEe~---g~-----~~~~AVmLYHkAGm~~kALelAF~tqQf~aL~lIa~DLd~~sDp~ll~R 1085 (1416)
T KOG3617|consen 1014 NLALMSGGSDLVSAARYYEEL---GG-----YAHKAVMLYHKAGMIGKALELAFRTQQFSALDLIAKDLDAGSDPKLLRR 1085 (1416)
T ss_pred             HHHhhcCchhHHHHHHHHHHc---ch-----hhhHHHHHHHhhcchHHHHHHHHhhcccHHHHHHHHhcCCCCCHHHHHH
Confidence                      11222222221   11     122334567777777777765321        2222233  35666666


Q ss_pred             HHHHHHhcCCHHHHHHHHHHHH
Q 012111          437 MIQAYNALGMTEAAQNLENKMI  458 (471)
Q Consensus       437 l~~~~~~~g~~~~A~~~~~~m~  458 (471)
                      -...+....++++|..++-...
T Consensus      1086 cadFF~~~~qyekAV~lL~~ar 1107 (1416)
T KOG3617|consen 1086 CADFFENNQQYEKAVNLLCLAR 1107 (1416)
T ss_pred             HHHHHHhHHHHHHHHHHHHHHH
Confidence            6667777777887776665443

>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]

Probab=98.82  E-value=8.2e-06  Score=81.74  Aligned_cols=227  Identities=8%  Similarity=0.052  Sum_probs=149.3

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCC---HHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHH
Q 012111          148 SVDVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPD---VYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYN  224 (471)
Q Consensus       148 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~---~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~  224 (471)
                      +...|-..|..+...++.++|.+++++.....++.-.   ...|.++++.-...|.-+...++|+++.+.-  -...+|.
T Consensus      1457 SSi~WI~YMaf~LelsEiekAR~iaerAL~tIN~REeeEKLNiWiA~lNlEn~yG~eesl~kVFeRAcqyc--d~~~V~~ 1534 (1710)
T KOG1070|consen 1457 SSILWIRYMAFHLELSEIEKARKIAERALKTINFREEEEKLNIWIAYLNLENAYGTEESLKKVFERACQYC--DAYTVHL 1534 (1710)
T ss_pred             cchHHHHHHHHHhhhhhhHHHHHHHHHHhhhCCcchhHHHHHHHHHHHhHHHhhCcHHHHHHHHHHHHHhc--chHHHHH
Confidence            4556777777777778888888888777653222111   2346666666666677777778888777652  2345677


Q ss_pred             HHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCC-CCCHHHHHHHHHHHHH
Q 012111          225 TIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGV-KADIQTLNILTKSYGR  303 (471)
Q Consensus       225 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~~~~ll~~~~~  303 (471)
                      .|...|.+.+++++|.++++.|.+..+  .....|...+..+.+.++-+.|..++.+..+.-- ..........++.-.+
T Consensus      1535 ~L~~iy~k~ek~~~A~ell~~m~KKF~--q~~~vW~~y~~fLl~~ne~~aa~~lL~rAL~~lPk~eHv~~IskfAqLEFk 1612 (1710)
T KOG1070|consen 1535 KLLGIYEKSEKNDEADELLRLMLKKFG--QTRKVWIMYADFLLRQNEAEAARELLKRALKSLPKQEHVEFISKFAQLEFK 1612 (1710)
T ss_pred             HHHHHHHHhhcchhHHHHHHHHHHHhc--chhhHHHHHHHHHhcccHHHHHHHHHHHHHhhcchhhhHHHHHHHHHHHhh
Confidence            777888888888888888888877743  4556677778888888887888888877765311 1134445556666677


Q ss_pred             cCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCC--HHHHHHHHHHHHhcCCHHH
Q 012111          304 AGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPN--SITYCSLVSAYSKAGLIMK  379 (471)
Q Consensus       304 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~--~~~~~~li~~~~~~g~~~~  379 (471)
                      .|+.+.+..+|+......++ -...|+..++.-.++|+.+.+..+|++....++.|-  -..|...+..=-..|+-..
T Consensus      1613 ~GDaeRGRtlfEgll~ayPK-RtDlW~VYid~eik~~~~~~vR~lfeRvi~l~l~~kkmKfffKkwLeyEk~~Gde~~ 1689 (1710)
T KOG1070|consen 1613 YGDAERGRTLFEGLLSAYPK-RTDLWSVYIDMEIKHGDIKYVRDLFERVIELKLSIKKMKFFFKKWLEYEKSHGDEKN 1689 (1710)
T ss_pred             cCCchhhHHHHHHHHhhCcc-chhHHHHHHHHHHccCCHHHHHHHHHHHHhcCCChhHhHHHHHHHHHHHHhcCchhh
Confidence            78888888888777665332 456777778777788888888888888877766553  2334444444334444433

>PLN02789 farnesyltranstransferase

Probab=98.81  E-value=1.6e-05  Score=70.47  Aligned_cols=148  Identities=5%  Similarity=-0.069  Sum_probs=105.7

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcC-CHHHHHHHHHHHHHCCCCCCHHHHHHHHH
Q 012111          150 DVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFH-RFDLIEKILAEMSYLGIECSAVTYNTIID  228 (471)
Q Consensus       150 ~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~-~~~~a~~~~~~~~~~g~~~~~~~~~~l~~  228 (471)
                      .++..+-..+...++.++|+.++.++....  +-+..+|+..-..+...| ++++++..++.+.+.. +-+..+|+....
T Consensus        38 ~a~~~~ra~l~~~e~serAL~lt~~aI~ln--P~~ytaW~~R~~iL~~L~~~l~eeL~~~~~~i~~n-pknyqaW~~R~~  114 (320)
T PLN02789         38 EAMDYFRAVYASDERSPRALDLTADVIRLN--PGNYTVWHFRRLCLEALDADLEEELDFAEDVAEDN-PKNYQIWHHRRW  114 (320)
T ss_pred             HHHHHHHHHHHcCCCCHHHHHHHHHHHHHC--chhHHHHHHHHHHHHHcchhHHHHHHHHHHHHHHC-CcchHHhHHHHH
Confidence            345555566667788899999999988732  334445666666666666 5788999998888765 446667776665


Q ss_pred             HHHccCCH--HHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHH
Q 012111          229 GYGKAKKF--EEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGR  303 (471)
Q Consensus       229 ~~~~~~~~--~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~  303 (471)
                      .+.+.|..  +++..+++.+.+..  +.+..+|+....++...|+++++++.++++++.+ +-+...|+.....+.+
T Consensus       115 ~l~~l~~~~~~~el~~~~kal~~d--pkNy~AW~~R~w~l~~l~~~~eeL~~~~~~I~~d-~~N~sAW~~R~~vl~~  188 (320)
T PLN02789        115 LAEKLGPDAANKELEFTRKILSLD--AKNYHAWSHRQWVLRTLGGWEDELEYCHQLLEED-VRNNSAWNQRYFVITR  188 (320)
T ss_pred             HHHHcCchhhHHHHHHHHHHHHhC--cccHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHC-CCchhHHHHHHHHHHh
Confidence            66666653  67788888887764  6678888888888888899999999999998876 4455666655544443

>PRK10370 formate-dependent nitrite reductase complex subunit NrfG; Provisional

Probab=98.80  E-value=2.5e-06  Score=70.32  Aligned_cols=154  Identities=10%  Similarity=0.047  Sum_probs=98.5

Q ss_pred             HHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHH
Q 012111          264 SAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIE  343 (471)
Q Consensus       264 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~  343 (471)
                      ..|...|+++.+....+.+..    |.        ..+...++.+++...+....+... .+...|..+...|...|+++
T Consensus        24 ~~Y~~~g~~~~v~~~~~~~~~----~~--------~~~~~~~~~~~~i~~l~~~L~~~P-~~~~~w~~Lg~~~~~~g~~~   90 (198)
T PRK10370         24 GSYLLSPKWQAVRAEYQRLAD----PL--------HQFASQQTPEAQLQALQDKIRANP-QNSEQWALLGEYYLWRNDYD   90 (198)
T ss_pred             HHHHHcchHHHHHHHHHHHhC----cc--------ccccCchhHHHHHHHHHHHHHHCC-CCHHHHHHHHHHHHHCCCHH
Confidence            457777777776544432221    10        011124556666666666655533 36667777777777888888


Q ss_pred             HHHHHHHHHHHcCCCCCHHHHHHHHHHH-HhcCC--HHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHH
Q 012111          344 KMEEYFKKMKHRGMKPNSITYCSLVSAY-SKAGL--IMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFL  420 (471)
Q Consensus       344 ~a~~~~~~m~~~~~~p~~~~~~~li~~~-~~~g~--~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~  420 (471)
                      +|...|++..+.. +-+...+..+..++ ...|+  .++|.+++++..+.++. +..++..+...+...|++++|+..|+
T Consensus        91 ~A~~a~~~Al~l~-P~~~~~~~~lA~aL~~~~g~~~~~~A~~~l~~al~~dP~-~~~al~~LA~~~~~~g~~~~Ai~~~~  168 (198)
T PRK10370         91 NALLAYRQALQLR-GENAELYAALATVLYYQAGQHMTPQTREMIDKALALDAN-EVTALMLLASDAFMQADYAQAIELWQ  168 (198)
T ss_pred             HHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHhCCC-ChhHHHHHHHHHHHcCCHHHHHHHHH
Confidence            8888887777753 23566666666653 55565  47788888887777666 67777777777777788888888888


Q ss_pred             HHHhCCCCCCHHH
Q 012111          421 TMKERHCVPDNIT  433 (471)
Q Consensus       421 ~~~~~~~~p~~~~  433 (471)
                      ++.+. .+|+..-
T Consensus       169 ~aL~l-~~~~~~r  180 (198)
T PRK10370        169 KVLDL-NSPRVNR  180 (198)
T ss_pred             HHHhh-CCCCccH
Confidence            77765 3444433

>KOG3616 consensus Selective LIM binding factor [Transcription]

Probab=98.79  E-value=1.1e-05  Score=75.58  Aligned_cols=109  Identities=13%  Similarity=0.178  Sum_probs=57.1

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCH
Q 012111          263 ISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHI  342 (471)
Q Consensus       263 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~  342 (471)
                      +.+......+.+|+.+++.+.+..  .-...|..+.+.|...|+++.|.++|-+.         ..++-.|.+|.+.|++
T Consensus       739 ieaai~akew~kai~ildniqdqk--~~s~yy~~iadhyan~~dfe~ae~lf~e~---------~~~~dai~my~k~~kw  807 (1636)
T KOG3616|consen  739 IEAAIGAKEWKKAISILDNIQDQK--TASGYYGEIADHYANKGDFEIAEELFTEA---------DLFKDAIDMYGKAGKW  807 (1636)
T ss_pred             HHHHhhhhhhhhhHhHHHHhhhhc--cccccchHHHHHhccchhHHHHHHHHHhc---------chhHHHHHHHhccccH
Confidence            344445556666666666555432  22334555666666666666666666432         1234455666666666


Q ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHH
Q 012111          343 EKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSIL  384 (471)
Q Consensus       343 ~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~  384 (471)
                      +.|.++-.+..  |.......|..-..-+-+.|++.+|.++|
T Consensus       808 ~da~kla~e~~--~~e~t~~~yiakaedldehgkf~eaeqly  847 (1636)
T KOG3616|consen  808 EDAFKLAEECH--GPEATISLYIAKAEDLDEHGKFAEAEQLY  847 (1636)
T ss_pred             HHHHHHHHHhc--CchhHHHHHHHhHHhHHhhcchhhhhhee
Confidence            66666554433  22223344444444445555555555544

>KOG0985 consensus Vesicle coat protein clathrin, heavy chain [Intracellular trafficking, secretion, and vesicular transport]

Probab=98.77  E-value=0.00014  Score=71.00  Aligned_cols=178  Identities=13%  Similarity=0.157  Sum_probs=113.7

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHH
Q 012111          257 FTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETF  336 (471)
Q Consensus       257 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~  336 (471)
                      ..|+.+..+-.+.|...+|.+-|-+      .-|+..|..+++...+.|.+++-.+.+...++..-.|...  +.||-+|
T Consensus      1105 ~vWsqlakAQL~~~~v~dAieSyik------adDps~y~eVi~~a~~~~~~edLv~yL~MaRkk~~E~~id--~eLi~Ay 1176 (1666)
T KOG0985|consen 1105 AVWSQLAKAQLQGGLVKDAIESYIK------ADDPSNYLEVIDVASRTGKYEDLVKYLLMARKKVREPYID--SELIFAY 1176 (1666)
T ss_pred             HHHHHHHHHHHhcCchHHHHHHHHh------cCCcHHHHHHHHHHHhcCcHHHHHHHHHHHHHhhcCccch--HHHHHHH
Confidence            4577777777777777777766644      3466778888888888888888888888777766655544  4677788


Q ss_pred             HhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHH
Q 012111          337 GKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMG  416 (471)
Q Consensus       337 ~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~  416 (471)
                      ++.++..+..+++       .-||......+..-|...|.++.|.-+|..+         .-|..|...+...|++..|.
T Consensus      1177 Akt~rl~elE~fi-------~gpN~A~i~~vGdrcf~~~~y~aAkl~y~~v---------SN~a~La~TLV~LgeyQ~AV 1240 (1666)
T KOG0985|consen 1177 AKTNRLTELEEFI-------AGPNVANIQQVGDRCFEEKMYEAAKLLYSNV---------SNFAKLASTLVYLGEYQGAV 1240 (1666)
T ss_pred             HHhchHHHHHHHh-------cCCCchhHHHHhHHHhhhhhhHHHHHHHHHh---------hhHHHHHHHHHHHHHHHHHH
Confidence            8888877755544       2466666666666677777776666665533         23444555555555555554


Q ss_pred             HHHHH------------------------HHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 012111          417 ELFLT------------------------MKERHCVPDNITFATMIQAYNALGMTEAAQNLENKMI  458 (471)
Q Consensus       417 ~~~~~------------------------~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~m~  458 (471)
                      +.-++                        |...++.....-..-|+..|-..|-+++-..+++..+
T Consensus      1241 D~aRKAns~ktWK~VcfaCvd~~EFrlAQiCGL~iivhadeLeeli~~Yq~rGyFeElIsl~Ea~L 1306 (1666)
T KOG0985|consen 1241 DAARKANSTKTWKEVCFACVDKEEFRLAQICGLNIIVHADELEELIEYYQDRGYFEELISLLEAGL 1306 (1666)
T ss_pred             HHhhhccchhHHHHHHHHHhchhhhhHHHhcCceEEEehHhHHHHHHHHHhcCcHHHHHHHHHhhh
Confidence            33222                        1112223344556666777777777777777766554

>PF12854 PPR_1: PPR repeat

Probab=98.77  E-value=1.4e-08  Score=56.25  Aligned_cols=32  Identities=34%  Similarity=0.624  Sum_probs=24.9

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 012111          426 HCVPDNITFATMIQAYNALGMTEAAQNLENKM  457 (471)
Q Consensus       426 ~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~m  457 (471)
                      |+.||..||++||.+|++.|+.++|.++|++|
T Consensus         2 G~~Pd~~ty~~lI~~~Ck~G~~~~A~~l~~~M   33 (34)
T PF12854_consen    2 GCEPDVVTYNTLIDGYCKAGRVDEAFELFDEM   33 (34)
T ss_pred             CCCCcHhHHHHHHHHHHHCCCHHHHHHHHHhC
Confidence            67777777777777777777777777777776

>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO

Probab=98.76  E-value=4.3e-06  Score=71.84  Aligned_cols=189  Identities=16%  Similarity=0.084  Sum_probs=124.4

Q ss_pred             CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCH---HHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHH--
Q 012111          253 HPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADI---QTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVV--  327 (471)
Q Consensus       253 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~---~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~--  327 (471)
                      ......+..+...+...|++++|...|+++.... +.+.   ..+..+..++...|++++|...++.+.+........  
T Consensus        30 ~~~~~~~~~~g~~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~a~~~la~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~  108 (235)
T TIGR03302        30 EWPAEELYEEAKEALDSGDYTEAIKYFEALESRY-PFSPYAEQAQLDLAYAYYKSGDYAEAIAAADRFIRLHPNHPDADY  108 (235)
T ss_pred             cCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCchhHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCCchHH
Confidence            3455677777888888999999999998887643 2222   456777888888899999999998888764432221  


Q ss_pred             HHHHHHHHHHhc--------CCHHHHHHHHHHHHHcCCCCCH-HHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHH
Q 012111          328 TYNIVIETFGKA--------GHIEKMEEYFKKMKHRGMKPNS-ITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPF  398 (471)
Q Consensus       328 ~~~~li~~~~~~--------g~~~~a~~~~~~m~~~~~~p~~-~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~  398 (471)
                      .+..+..++...        |+.++|.+.++.+...  .|+. ..+..+.....    ...      ..        ...
T Consensus       109 a~~~~g~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~--~p~~~~~~~a~~~~~~----~~~------~~--------~~~  168 (235)
T TIGR03302       109 AYYLRGLSNYNQIDRVDRDQTAAREAFEAFQELIRR--YPNSEYAPDAKKRMDY----LRN------RL--------AGK  168 (235)
T ss_pred             HHHHHHHHHHHhcccccCCHHHHHHHHHHHHHHHHH--CCCChhHHHHHHHHHH----HHH------HH--------HHH
Confidence            344444445443        6678888888888765  3432 22222211100    000      00        001


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHhCCC-CC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhhh
Q 012111          399 FNCIISAYGQAGDVEKMGELFLTMKERHC-VP-DNITFATMIQAYNALGMTEAAQNLENKMIAMKE  462 (471)
Q Consensus       399 ~~~l~~~~~~~g~~~~a~~~~~~~~~~~~-~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~  462 (471)
                      ...+...+.+.|++.+|+..+++..+..- .| ....+..+..++...|++++|..+++.+....|
T Consensus       169 ~~~~a~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~a~~~l~~~~~~lg~~~~A~~~~~~l~~~~~  234 (235)
T TIGR03302       169 ELYVARFYLKRGAYVAAINRFETVVENYPDTPATEEALARLVEAYLKLGLKDLAQDAAAVLGANYP  234 (235)
T ss_pred             HHHHHHHHHHcCChHHHHHHHHHHHHHCCCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCC
Confidence            12456678899999999999999987521 12 356788899999999999999999888876554

Members of this protein family include YfiO, a near-essential protein of the outer membrane, part of a complex involved in protein insertion into the bacterial outer membrane. Many proteins in this family are annotated as ComL, based on the involvement of this protein in natural transformation with exogenous DNA in Neisseria gonorrhoeae. This protein family shows sequence similarity to, but is distinct from, the tol-pal system protein YbgF (TIGR02795).

>KOG3616 consensus Selective LIM binding factor [Transcription]

Probab=98.74  E-value=6.4e-05  Score=70.75  Aligned_cols=199  Identities=15%  Similarity=0.245  Sum_probs=133.5

Q ss_pred             HHHHHHHHHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHH
Q 012111           80 PVLEALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAY  159 (471)
Q Consensus        80 ~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~  159 (471)
                      .+..++.+......|..|+.+++.+..+.   .-..-|..+...|...|+++.|.++|.+.-         .++..|..|
T Consensus       734 ~~~kaieaai~akew~kai~ildniqdqk---~~s~yy~~iadhyan~~dfe~ae~lf~e~~---------~~~dai~my  801 (1636)
T KOG3616|consen  734 CLIKAIEAAIGAKEWKKAISILDNIQDQK---TASGYYGEIADHYANKGDFEIAEELFTEAD---------LFKDAIDMY  801 (1636)
T ss_pred             hHHHHHHHHhhhhhhhhhHhHHHHhhhhc---cccccchHHHHHhccchhHHHHHHHHHhcc---------hhHHHHHHH
Confidence            45566777777888888888888887653   334557777888888888888888886532         356677888


Q ss_pred             HhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHH
Q 012111          160 GQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEM  239 (471)
Q Consensus       160 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~a  239 (471)
                      .+.|+|+.|.++-++...   -......|.+-..-+-+.|.+.+|.+++-.+.    .|+     ..|.+|-+.|..+..
T Consensus       802 ~k~~kw~da~kla~e~~~---~e~t~~~yiakaedldehgkf~eaeqlyiti~----~p~-----~aiqmydk~~~~ddm  869 (1636)
T KOG3616|consen  802 GKAGKWEDAFKLAEECHG---PEATISLYIAKAEDLDEHGKFAEAEQLYITIG----EPD-----KAIQMYDKHGLDDDM  869 (1636)
T ss_pred             hccccHHHHHHHHHHhcC---chhHHHHHHHhHHhHHhhcchhhhhheeEEcc----Cch-----HHHHHHHhhCcchHH
Confidence            888888888888776643   23445556555556677788888777765432    333     246677777887777


Q ss_pred             HHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHH
Q 012111          240 ESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMD  315 (471)
Q Consensus       240 ~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~  315 (471)
                      +++.++-..    ..-..|...+..-+...|+...|...|-+..         -|..-++.|-..+.|++|.++-.
T Consensus       870 irlv~k~h~----d~l~dt~~~f~~e~e~~g~lkaae~~flea~---------d~kaavnmyk~s~lw~dayriak  932 (1636)
T KOG3616|consen  870 IRLVEKHHG----DHLHDTHKHFAKELEAEGDLKAAEEHFLEAG---------DFKAAVNMYKASELWEDAYRIAK  932 (1636)
T ss_pred             HHHHHHhCh----hhhhHHHHHHHHHHHhccChhHHHHHHHhhh---------hHHHHHHHhhhhhhHHHHHHHHh
Confidence            776655421    1122355566667777888888877765543         25556677777777777776644

>KOG1914 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA14 [RNA processing and modification]

Probab=98.73  E-value=0.00018  Score=65.44  Aligned_cols=340  Identities=9%  Similarity=0.107  Sum_probs=184.0

Q ss_pred             cCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHH
Q 012111          111 QARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSI  190 (471)
Q Consensus       111 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~  190 (471)
                      |-|...|..|++-+... .++++.+.++++... ++-....|..-|..-...++++....+|.+....   ..+...|..
T Consensus        17 P~di~sw~~lire~qt~-~~~~~R~~YEq~~~~-FP~s~r~W~~yi~~El~skdfe~VEkLF~RCLvk---vLnlDLW~l   91 (656)
T KOG1914|consen   17 PYDIDSWSQLIREAQTQ-PIDKVRETYEQLVNV-FPSSPRAWKLYIERELASKDFESVEKLFSRCLVK---VLNLDLWKL   91 (656)
T ss_pred             CccHHHHHHHHHHHccC-CHHHHHHHHHHHhcc-CCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHH---HhhHhHHHH
Confidence            77889999999977666 999999999999865 3346788999999999999999999999997762   456777777


Q ss_pred             HHHHHHhc-CCH----HHHHHHHHHH-HHCCCCCC-HHHHHHHHHHH---------HccCCHHHHHHHHHHHHHcCCCCC
Q 012111          191 LIKSCTKF-HRF----DLIEKILAEM-SYLGIECS-AVTYNTIIDGY---------GKAKKFEEMESSFSAMVESGGCHP  254 (471)
Q Consensus       191 ll~~~~~~-~~~----~~a~~~~~~~-~~~g~~~~-~~~~~~l~~~~---------~~~~~~~~a~~~~~~~~~~~~~~~  254 (471)
                      .++-.-+. ++.    +...+.|+-. .+.|+.+- ...|+..+..+         ..+.+.+...++|+++....  -.
T Consensus        92 Yl~YVR~~~~~~~~~r~~m~qAy~f~l~kig~di~s~siW~eYi~FL~~vea~gk~ee~QRI~~vRriYqral~tP--m~  169 (656)
T KOG1914|consen   92 YLSYVRETKGKLFGYREKMVQAYDFALEKIGMDIKSYSIWDEYINFLEGVEAVGKYEENQRITAVRRIYQRALVTP--MH  169 (656)
T ss_pred             HHHHHHHHccCcchHHHHHHHHHHHHHHHhccCcccchhHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHhcCc--cc
Confidence            77654432 222    2233444433 34564433 33444444432         33345667777888886432  11


Q ss_pred             CH-HHHHH------HHHH-------HHhcCCHHHHHHHHHHHHh--CCCCCCHH---------------HHHHHHH----
Q 012111          255 DI-FTLNS------MISA-------YGNSGNIEKMEKWYNEFNL--MGVKADIQ---------------TLNILTK----  299 (471)
Q Consensus       255 ~~-~~~~~------l~~~-------~~~~~~~~~a~~~~~~~~~--~~~~~~~~---------------~~~~ll~----  299 (471)
                      +. ..|+-      =|+.       --+...+..|.++++++..  .|......               .|..+|.    
T Consensus       170 nlEkLW~DY~~fE~~IN~~tarK~i~e~s~~Ym~AR~~~qel~~lt~GL~r~~~~vp~~~T~~e~~qv~~W~n~I~wEks  249 (656)
T KOG1914|consen  170 NLEKLWKDYEAFEQEINIITARKFIGERSPEYMNARRVYQELQNLTRGLNRNAPAVPPKGTKDEIQQVELWKNWIKWEKS  249 (656)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHHHHHHhhhcccCCCCCCCCChHHHHHHHHHHHHHHHHhc
Confidence            21 12221      1111       1123345556666665532  12111100               0111111    


Q ss_pred             ---------------------------------------------HHHHcCC-------HHHHHHHHHHHHhCCCCCCHH
Q 012111          300 ---------------------------------------------SYGRAGM-------YDKMRSVMDFMQKRFFFPTVV  327 (471)
Q Consensus       300 ---------------------------------------------~~~~~~~-------~~~a~~~~~~~~~~~~~~~~~  327 (471)
                                                                   .+...|+       .+++..+++.....-..-+..
T Consensus       250 NpL~t~~~~~~~~Rv~yayeQ~ll~l~~~peiWy~~s~yl~~~s~l~~~~~d~~~a~~~t~e~~~~yEr~I~~l~~~~~~  329 (656)
T KOG1914|consen  250 NPLRTLDGTMLTRRVMYAYEQCLLYLGYHPEIWYDYSMYLIEISDLLTEKGDVPDAKSLTDEAASIYERAIEGLLKENKL  329 (656)
T ss_pred             CCcccccccHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhhHHHHHhcccccchhhHHHHHHHHHHHHHHHHHHHHH
Confidence                                                         1111222       223333333332221111222


Q ss_pred             HHHHHHHHHHhc---CCHHHHHHHHHHHHHcC-CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCc-CHHHHHHH
Q 012111          328 TYNIVIETFGKA---GHIEKMEEYFKKMKHRG-MKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVIL-DTPFFNCI  402 (471)
Q Consensus       328 ~~~~li~~~~~~---g~~~~a~~~~~~m~~~~-~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~-~~~~~~~l  402 (471)
                      +|..+...--..   ...+....+++++...- +.| ..+|..+++...+..-+..|..+|.++.+.+..+ ++.+++++
T Consensus       330 Ly~~~a~~eE~~~~~n~~~~~~~~~~~ll~~~~~~~-tLv~~~~mn~irR~eGlkaaR~iF~kaR~~~r~~hhVfVa~A~  408 (656)
T KOG1914|consen  330 LYFALADYEESRYDDNKEKKVHEIYNKLLKIEDIDL-TLVYCQYMNFIRRAEGLKAARKIFKKAREDKRTRHHVFVAAAL  408 (656)
T ss_pred             HHHHHHhhHHHhcccchhhhhHHHHHHHHhhhccCC-ceehhHHHHHHHHhhhHHHHHHHHHHHhhccCCcchhhHHHHH
Confidence            222222111111   12344455555554432 223 2356667777777777777777777777666555 56666777


Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHh
Q 012111          403 ISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAYNALGMTEAAQNLENKMIAM  460 (471)
Q Consensus       403 ~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~  460 (471)
                      +.-+|. ++..-|.++|+--... +.-++..-...+.-+...++-..|+.+|++.+..
T Consensus       409 mEy~cs-kD~~~AfrIFeLGLkk-f~d~p~yv~~YldfL~~lNdd~N~R~LFEr~l~s  464 (656)
T KOG1914|consen  409 MEYYCS-KDKETAFRIFELGLKK-FGDSPEYVLKYLDFLSHLNDDNNARALFERVLTS  464 (656)
T ss_pred             HHHHhc-CChhHHHHHHHHHHHh-cCCChHHHHHHHHHHHHhCcchhHHHHHHHHHhc
Confidence            766654 6667777777765543 2222333345566666666666666666666655

>KOG1914 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA14 [RNA processing and modification]

Probab=98.73  E-value=0.00019  Score=65.32  Aligned_cols=188  Identities=11%  Similarity=0.043  Sum_probs=127.9

Q ss_pred             HHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcC---CHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHH
Q 012111          273 EKMEKWYNEFNLMGVKADIQTLNILTKSYGRAG---MYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYF  349 (471)
Q Consensus       273 ~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~---~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~  349 (471)
                      +++..+++..+..-..-+..+|..+...--..-   ..+....+++.+......--.-+|...+...-+...+..|..+|
T Consensus       310 ~e~~~~yEr~I~~l~~~~~~Ly~~~a~~eE~~~~~n~~~~~~~~~~~ll~~~~~~~tLv~~~~mn~irR~eGlkaaR~iF  389 (656)
T KOG1914|consen  310 DEAASIYERAIEGLLKENKLLYFALADYEESRYDDNKEKKVHEIYNKLLKIEDIDLTLVYCQYMNFIRRAEGLKAARKIF  389 (656)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHhcccchhhhhHHHHHHHHhhhccCCceehhHHHHHHHHhhhHHHHHHHH
Confidence            445555555443322333333433333221111   24455555665554422222346777888888888899999999


Q ss_pred             HHHHHcCCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCC
Q 012111          350 KKMKHRGMKP-NSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCV  428 (471)
Q Consensus       350 ~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~  428 (471)
                      .++.+.+..+ ...++++++..+| .++..-|.++|+.=.+.-.. ++..-...+.-+...|+-..|..+|++....++.
T Consensus       390 ~kaR~~~r~~hhVfVa~A~mEy~c-skD~~~AfrIFeLGLkkf~d-~p~yv~~YldfL~~lNdd~N~R~LFEr~l~s~l~  467 (656)
T KOG1914|consen  390 KKAREDKRTRHHVFVAAALMEYYC-SKDKETAFRIFELGLKKFGD-SPEYVLKYLDFLSHLNDDNNARALFERVLTSVLS  467 (656)
T ss_pred             HHHhhccCCcchhhHHHHHHHHHh-cCChhHHHHHHHHHHHhcCC-ChHHHHHHHHHHHHhCcchhHHHHHHHHHhccCC
Confidence            9999988777 6777788887665 57888899999875543222 3444466777888889999999999999988666


Q ss_pred             CC--HHHHHHHHHHHHhcCCHHHHHHHHHHHHHhhh
Q 012111          429 PD--NITFATMIQAYNALGMTEAAQNLENKMIAMKE  462 (471)
Q Consensus       429 p~--~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~  462 (471)
                      |+  ...|..++..-..-|+...+.++-+++...-+
T Consensus       468 ~~ks~~Iw~r~l~yES~vGdL~si~~lekR~~~af~  503 (656)
T KOG1914|consen  468 ADKSKEIWDRMLEYESNVGDLNSILKLEKRRFTAFP  503 (656)
T ss_pred             hhhhHHHHHHHHHHHHhcccHHHHHHHHHHHHHhcc
Confidence            65  47899999988889999999999888877665

>KOG3617 consensus WD40 and TPR repeat-containing protein [General function prediction only]

Probab=98.71  E-value=0.00013  Score=69.58  Aligned_cols=210  Identities=15%  Similarity=0.105  Sum_probs=137.3

Q ss_pred             hHHHHHHHHHHHhhcHHHHHHHHHHhhhccCc--------cCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHH
Q 012111           79 KPVLEALDEAIKQKKWQLALKIFGLLRQQQWY--------QARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVD  150 (471)
Q Consensus        79 ~~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~--------~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~  150 (471)
                      ..+.+..+.+++.++++-|.-.+..|....+.        .++ .+=..........|..++|..+|.+.++        
T Consensus       758 ~vW~nmA~McVkT~RLDVAkVClGhm~~aRgaRAlR~a~q~~~-e~eakvAvLAieLgMlEeA~~lYr~ckR--------  828 (1416)
T KOG3617|consen  758 SVWDNMASMCVKTRRLDVAKVCLGHMKNARGARALRRAQQNGE-EDEAKVAVLAIELGMLEEALILYRQCKR--------  828 (1416)
T ss_pred             HHHHHHHHHhhhhccccHHHHhhhhhhhhhhHHHHHHHHhCCc-chhhHHHHHHHHHhhHHHHHHHHHHHHH--------
Confidence            45667778888888888877666555432211        121 3333444455678999999999999875        


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHH----------HHCC-----
Q 012111          151 VYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEM----------SYLG-----  215 (471)
Q Consensus       151 ~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~----------~~~g-----  215 (471)
                       |..|=..|-..|.+++|.++-+.-.+   +. =..||.....-+-..+|.+.|++.|++.          ....     
T Consensus       829 -~DLlNKlyQs~g~w~eA~eiAE~~DR---iH-Lr~Tyy~yA~~Lear~Di~~AleyyEK~~~hafev~rmL~e~p~~~e  903 (1416)
T KOG3617|consen  829 -YDLLNKLYQSQGMWSEAFEIAETKDR---IH-LRNTYYNYAKYLEARRDIEAALEYYEKAGVHAFEVFRMLKEYPKQIE  903 (1416)
T ss_pred             -HHHHHHHHHhcccHHHHHHHHhhccc---ee-hhhhHHHHHHHHHhhccHHHHHHHHHhcCChHHHHHHHHHhChHHHH
Confidence             33445567778999999998775432   11 2345555555566667777777776542          1111     


Q ss_pred             ----CCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCH
Q 012111          216 ----IECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADI  291 (471)
Q Consensus       216 ----~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  291 (471)
                          -..|...|......+-..|+.+.|+.+|....+          |-.++...|-.|+.++|-++-++      .-|.
T Consensus       904 ~Yv~~~~d~~L~~WWgqYlES~GemdaAl~~Y~~A~D----------~fs~VrI~C~qGk~~kAa~iA~e------sgd~  967 (1416)
T KOG3617|consen  904 QYVRRKRDESLYSWWGQYLESVGEMDAALSFYSSAKD----------YFSMVRIKCIQGKTDKAARIAEE------SGDK  967 (1416)
T ss_pred             HHHHhccchHHHHHHHHHHhcccchHHHHHHHHHhhh----------hhhheeeEeeccCchHHHHHHHh------cccH
Confidence                012344455555555667888888888877632          55667777778888888887766      3356


Q ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHH
Q 012111          292 QTLNILTKSYGRAGMYDKMRSVMDFMQ  318 (471)
Q Consensus       292 ~~~~~ll~~~~~~~~~~~a~~~~~~~~  318 (471)
                      ...-.|.+.|-..|++.+|...|.+.+
T Consensus       968 AAcYhlaR~YEn~g~v~~Av~FfTrAq  994 (1416)
T KOG3617|consen  968 AACYHLARMYENDGDVVKAVKFFTRAQ  994 (1416)
T ss_pred             HHHHHHHHHhhhhHHHHHHHHHHHHHH
Confidence            666778888888888888888887654

>COG5010 TadD Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking and secretion]

Probab=98.71  E-value=9.4e-06  Score=66.86  Aligned_cols=163  Identities=13%  Similarity=0.062  Sum_probs=106.6

Q ss_pred             ChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHH
Q 012111          113 RCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILI  192 (471)
Q Consensus       113 ~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll  192 (471)
                      +... ..+-..+...|+-+....+........ +-|....+..+....+.|++..|+..+.+...  .-++|..+|+.+.
T Consensus        66 d~~i-~~~a~a~~~~G~a~~~l~~~~~~~~~~-~~d~~ll~~~gk~~~~~g~~~~A~~~~rkA~~--l~p~d~~~~~~lg  141 (257)
T COG5010          66 DLSI-AKLATALYLRGDADSSLAVLQKSAIAY-PKDRELLAAQGKNQIRNGNFGEAVSVLRKAAR--LAPTDWEAWNLLG  141 (257)
T ss_pred             hHHH-HHHHHHHHhcccccchHHHHhhhhccC-cccHHHHHHHHHHHHHhcchHHHHHHHHHHhc--cCCCChhhhhHHH
Confidence            3334 555556666676666666666644332 22555666677777777777777777777765  3366777777777


Q ss_pred             HHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCH
Q 012111          193 KSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNI  272 (471)
Q Consensus       193 ~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  272 (471)
                      -+|.+.|+++.|..-|.+..+.- +-+...++.+.-.+.-.|+.+.|..++.......  .-|...-..+..+....|++
T Consensus       142 aaldq~Gr~~~Ar~ay~qAl~L~-~~~p~~~nNlgms~~L~gd~~~A~~lll~a~l~~--~ad~~v~~NLAl~~~~~g~~  218 (257)
T COG5010         142 AALDQLGRFDEARRAYRQALELA-PNEPSIANNLGMSLLLRGDLEDAETLLLPAYLSP--AADSRVRQNLALVVGLQGDF  218 (257)
T ss_pred             HHHHHccChhHHHHHHHHHHHhc-cCCchhhhhHHHHHHHcCCHHHHHHHHHHHHhCC--CCchHHHHHHHHHHhhcCCh
Confidence            77777777777777777776653 2345566667777777777777777777765542  33555666666677777777


Q ss_pred             HHHHHHHHHH
Q 012111          273 EKMEKWYNEF  282 (471)
Q Consensus       273 ~~a~~~~~~~  282 (471)
                      ++|..+...-
T Consensus       219 ~~A~~i~~~e  228 (257)
T COG5010         219 REAEDIAVQE  228 (257)
T ss_pred             HHHHhhcccc
Confidence            7777666543

>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO

Probab=98.71  E-value=4.5e-06  Score=71.73  Aligned_cols=189  Identities=14%  Similarity=0.065  Sum_probs=129.4

Q ss_pred             cCCCchHHHHHHHHHHHhhcHHHHHHHHHHhhhccCccCCh---hHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCH-
Q 012111           74 KNLWPKPVLEALDEAIKQKKWQLALKIFGLLRQQQWYQARC---QTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSV-  149 (471)
Q Consensus        74 ~~~~~~~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~---~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~-  149 (471)
                      ....+.........+...|++++|+..|+.+....  +.+.   .++..+..++.+.|++++|...++.+.+....... 
T Consensus        29 ~~~~~~~~~~~g~~~~~~~~~~~A~~~~~~~~~~~--p~~~~~~~a~~~la~~~~~~~~~~~A~~~~~~~l~~~p~~~~~  106 (235)
T TIGR03302        29 EEWPAEELYEEAKEALDSGDYTEAIKYFEALESRY--PFSPYAEQAQLDLAYAYYKSGDYAEAIAAADRFIRLHPNHPDA  106 (235)
T ss_pred             ccCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCchhHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCCch
Confidence            34455667777778889999999999999998764  3332   46788888999999999999999999876432111 


Q ss_pred             -HHHHHHHHHHHhc--------CCHHHHHHHHHHhhcCCCCCCCH-HHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCC
Q 012111          150 -DVYTALVSAYGQS--------GLLDEAFSTINDMKSVSDCKPDV-YTYSILIKSCTKFHRFDLIEKILAEMSYLGIECS  219 (471)
Q Consensus       150 -~~~~~li~~~~~~--------~~~~~a~~~~~~~~~~~~~~~~~-~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~  219 (471)
                       .++..+..++...        |+.+.|.+.|+.+...   .|+. ..+..+.....    ..      ....       
T Consensus       107 ~~a~~~~g~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~---~p~~~~~~~a~~~~~~----~~------~~~~-------  166 (235)
T TIGR03302       107 DYAYYLRGLSNYNQIDRVDRDQTAAREAFEAFQELIRR---YPNSEYAPDAKKRMDY----LR------NRLA-------  166 (235)
T ss_pred             HHHHHHHHHHHHHhcccccCCHHHHHHHHHHHHHHHHH---CCCChhHHHHHHHHHH----HH------HHHH-------
Confidence             2455555555544        6788899999888763   2332 22222211100    00      0000       


Q ss_pred             HHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhC
Q 012111          220 AVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHP-DIFTLNSMISAYGNSGNIEKMEKWYNEFNLM  285 (471)
Q Consensus       220 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  285 (471)
                       .....+...+.+.|++.+|...++...+..+-.| ....+..+..++...|++++|..+++.+...
T Consensus       167 -~~~~~~a~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~a~~~l~~~~~~lg~~~~A~~~~~~l~~~  232 (235)
T TIGR03302       167 -GKELYVARFYLKRGAYVAAINRFETVVENYPDTPATEEALARLVEAYLKLGLKDLAQDAAAVLGAN  232 (235)
T ss_pred             -HHHHHHHHHHHHcCChHHHHHHHHHHHHHCCCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence             1112456678899999999999999887642222 3567889999999999999999999888654

Members of this protein family include YfiO, a near-essential protein of the outer membrane, part of a complex involved in protein insertion into the bacterial outer membrane. Many proteins in this family are annotated as ComL, based on the involvement of this protein in natural transformation with exogenous DNA in Neisseria gonorrhoeae. This protein family shows sequence similarity to, but is distinct from, the tol-pal system protein YbgF (TIGR02795).

>KOG3081 consensus Vesicle coat complex COPI, epsilon subunit [Intracellular trafficking, secretion, and vesicular transport]

Probab=98.70  E-value=3e-05  Score=63.97  Aligned_cols=149  Identities=13%  Similarity=0.139  Sum_probs=74.4

Q ss_pred             HHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHh----c
Q 012111          264 SAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGK----A  339 (471)
Q Consensus       264 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~----~  339 (471)
                      ..|+..|++++|++.....      -+......=+..+.+..+++-|.+.++.|.+.   .+..+.+.|..++.+    .
T Consensus       116 ~i~~~~~~~deAl~~~~~~------~~lE~~Al~VqI~lk~~r~d~A~~~lk~mq~i---ded~tLtQLA~awv~la~gg  186 (299)
T KOG3081|consen  116 IIYMHDGDFDEALKALHLG------ENLEAAALNVQILLKMHRFDLAEKELKKMQQI---DEDATLTQLAQAWVKLATGG  186 (299)
T ss_pred             HHhhcCCChHHHHHHHhcc------chHHHHHHHHHHHHHHHHHHHHHHHHHHHHcc---chHHHHHHHHHHHHHHhccc
Confidence            3455555566555555441      11222222233444555555566666555553   233444444444433    2


Q ss_pred             CCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHH-HHHHH
Q 012111          340 GHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVE-KMGEL  418 (471)
Q Consensus       340 g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~-~a~~~  418 (471)
                      +.+.+|.-+|++|-.+ ..|+..+.+....++...|++++|..+++........ ++.+...++.+-...|... -..+.
T Consensus       187 ek~qdAfyifeE~s~k-~~~T~~llnG~Av~~l~~~~~eeAe~lL~eaL~kd~~-dpetL~Nliv~a~~~Gkd~~~~~r~  264 (299)
T KOG3081|consen  187 EKIQDAFYIFEELSEK-TPPTPLLLNGQAVCHLQLGRYEEAESLLEEALDKDAK-DPETLANLIVLALHLGKDAEVTERN  264 (299)
T ss_pred             hhhhhHHHHHHHHhcc-cCCChHHHccHHHHHHHhcCHHHHHHHHHHHHhccCC-CHHHHHHHHHHHHHhCCChHHHHHH
Confidence            3455666666666543 3556666666666666666666666666666655444 4444444444444444432 23334


Q ss_pred             HHHHH
Q 012111          419 FLTMK  423 (471)
Q Consensus       419 ~~~~~  423 (471)
                      +..++
T Consensus       265 l~QLk  269 (299)
T KOG3081|consen  265 LSQLK  269 (299)
T ss_pred             HHHHH
Confidence            44443

>PF12854 PPR_1: PPR repeat

Probab=98.70  E-value=3.3e-08  Score=54.76  Aligned_cols=32  Identities=38%  Similarity=0.763  Sum_probs=17.5

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHh
Q 012111          144 GLKPSVDVYTALVSAYGQSGLLDEAFSTINDM  175 (471)
Q Consensus       144 ~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~  175 (471)
                      |+.||..+|+.||.+|++.|++++|.++|++|
T Consensus         2 G~~Pd~~ty~~lI~~~Ck~G~~~~A~~l~~~M   33 (34)
T PF12854_consen    2 GCEPDVVTYNTLIDGYCKAGRVDEAFELFDEM   33 (34)
T ss_pred             CCCCcHhHHHHHHHHHHHCCCHHHHHHHHHhC
Confidence            44555555555555555555555555555554

>PRK15179 Vi polysaccharide biosynthesis protein TviE; Provisional

Probab=98.70  E-value=1.1e-05  Score=78.93  Aligned_cols=147  Identities=7%  Similarity=-0.011  Sum_probs=98.4

Q ss_pred             ccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHH
Q 012111          110 YQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYS  189 (471)
Q Consensus       110 ~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  189 (471)
                      ++.++.++..|..+..+.|++++|..+++...+.... +......+..++.+.+++++|+..+++....  -+-+.....
T Consensus        82 ~~~~~~~~~~La~i~~~~g~~~ea~~~l~~~~~~~Pd-~~~a~~~~a~~L~~~~~~eeA~~~~~~~l~~--~p~~~~~~~  158 (694)
T PRK15179         82 YPHTELFQVLVARALEAAHRSDEGLAVWRGIHQRFPD-SSEAFILMLRGVKRQQGIEAGRAEIELYFSG--GSSSAREIL  158 (694)
T ss_pred             ccccHHHHHHHHHHHHHcCCcHHHHHHHHHHHhhCCC-cHHHHHHHHHHHHHhccHHHHHHHHHHHhhc--CCCCHHHHH
Confidence            4566777777777777777777777777777765322 4455666777777777777777777777652  234455566


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHH
Q 012111          190 ILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSM  262 (471)
Q Consensus       190 ~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l  262 (471)
                      .+..++.+.|++++|..+|+++...+ +-+..++..+...+.+.|+.++|...|++..+..  .+....|+.+
T Consensus       159 ~~a~~l~~~g~~~~A~~~y~~~~~~~-p~~~~~~~~~a~~l~~~G~~~~A~~~~~~a~~~~--~~~~~~~~~~  228 (694)
T PRK15179        159 LEAKSWDEIGQSEQADACFERLSRQH-PEFENGYVGWAQSLTRRGALWRARDVLQAGLDAI--GDGARKLTRR  228 (694)
T ss_pred             HHHHHHHHhcchHHHHHHHHHHHhcC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhh--CcchHHHHHH
Confidence            66666777777777777777777632 3456677777777777777777777777776653  3444444443

>KOG1127 consensus TPR repeat-containing protein [RNA processing and modification]

Probab=98.69  E-value=2.6e-05  Score=75.78  Aligned_cols=184  Identities=9%  Similarity=0.013  Sum_probs=133.8

Q ss_pred             cHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHH
Q 012111           93 KWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAFSTI  172 (471)
Q Consensus        93 ~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~  172 (471)
                      +...|+..|-...+.+  +.-...|..|...|....+...|.+.|+...+.... +...+......|++..+++.|..+.
T Consensus       473 ~~~~al~ali~alrld--~~~apaf~~LG~iYrd~~Dm~RA~kCf~KAFeLDat-daeaaaa~adtyae~~~we~a~~I~  549 (1238)
T KOG1127|consen  473 NSALALHALIRALRLD--VSLAPAFAFLGQIYRDSDDMKRAKKCFDKAFELDAT-DAEAAAASADTYAEESTWEEAFEIC  549 (1238)
T ss_pred             hHHHHHHHHHHHHhcc--cchhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCch-hhhhHHHHHHHhhccccHHHHHHHH
Confidence            4566777776666543  334568999999999888999999999999877543 6778888999999999999999985


Q ss_pred             HHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCC
Q 012111          173 NDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGC  252 (471)
Q Consensus       173 ~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~  252 (471)
                      -..-+......-...|....-.|.+.++...+..-|+...+.. +-|...|..+..+|.++|.+..|.++|.+....   
T Consensus       550 l~~~qka~a~~~k~nW~~rG~yyLea~n~h~aV~~fQsALR~d-PkD~n~W~gLGeAY~~sGry~~AlKvF~kAs~L---  625 (1238)
T KOG1127|consen  550 LRAAQKAPAFACKENWVQRGPYYLEAHNLHGAVCEFQSALRTD-PKDYNLWLGLGEAYPESGRYSHALKVFTKASLL---  625 (1238)
T ss_pred             HHHhhhchHHHHHhhhhhccccccCccchhhHHHHHHHHhcCC-chhHHHHHHHHHHHHhcCceehHHHhhhhhHhc---
Confidence            4433311111112223334445677889999999998888765 457888999999999999999999999888653   


Q ss_pred             CCCHHHHHHH--HHHHHhcCCHHHHHHHHHHHHh
Q 012111          253 HPDIFTLNSM--ISAYGNSGNIEKMEKWYNEFNL  284 (471)
Q Consensus       253 ~~~~~~~~~l--~~~~~~~~~~~~a~~~~~~~~~  284 (471)
                      .|+. .|...  ...-+..|.+.+|+..+.....
T Consensus       626 rP~s-~y~~fk~A~~ecd~GkYkeald~l~~ii~  658 (1238)
T KOG1127|consen  626 RPLS-KYGRFKEAVMECDNGKYKEALDALGLIIY  658 (1238)
T ss_pred             CcHh-HHHHHHHHHHHHHhhhHHHHHHHHHHHHH
Confidence            4543 33332  2335678899999888887654

>KOG1128 consensus Uncharacterized conserved protein, contains TPR repeats [General function prediction only]

Probab=98.69  E-value=1.3e-05  Score=75.17  Aligned_cols=211  Identities=8%  Similarity=-0.040  Sum_probs=104.7

Q ss_pred             HHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccC
Q 012111          155 LVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAK  234 (471)
Q Consensus       155 li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~  234 (471)
                      +...+...|-...|+.+|+++..          |..++.+|+..|+...|..+..+..+.  +|++..|..+.+.....-
T Consensus       404 laell~slGitksAl~I~Erlem----------w~~vi~CY~~lg~~~kaeei~~q~lek--~~d~~lyc~LGDv~~d~s  471 (777)
T KOG1128|consen  404 LAELLLSLGITKSALVIFERLEM----------WDPVILCYLLLGQHGKAEEINRQELEK--DPDPRLYCLLGDVLHDPS  471 (777)
T ss_pred             HHHHHHHcchHHHHHHHHHhHHH----------HHHHHHHHHHhcccchHHHHHHHHhcC--CCcchhHHHhhhhccChH
Confidence            44455555555566666555432          344555555556555565555555542  455555555555544444


Q ss_pred             CHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHH
Q 012111          235 KFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVM  314 (471)
Q Consensus       235 ~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~  314 (471)
                      -+++|.++.+.....        .-..+.....+.+++.++.+.|+.-.+.. +....+|-.+.-+..+.+++..|.+.|
T Consensus       472 ~yEkawElsn~~sar--------A~r~~~~~~~~~~~fs~~~~hle~sl~~n-plq~~~wf~~G~~ALqlek~q~av~aF  542 (777)
T KOG1128|consen  472 LYEKAWELSNYISAR--------AQRSLALLILSNKDFSEADKHLERSLEIN-PLQLGTWFGLGCAALQLEKEQAAVKAF  542 (777)
T ss_pred             HHHHHHHHhhhhhHH--------HHHhhccccccchhHHHHHHHHHHHhhcC-ccchhHHHhccHHHHHHhhhHHHHHHH
Confidence            455555555443221        11111111223455555555555544332 333444444444555555555555555


Q ss_pred             HHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 012111          315 DFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVE  388 (471)
Q Consensus       315 ~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~  388 (471)
                      .......+. +...||.+-.+|.+.++..+|...+.+..+.+ .-+...|...+....+.|.+++|.+.+.++.
T Consensus       543 ~rcvtL~Pd-~~eaWnNls~ayi~~~~k~ra~~~l~EAlKcn-~~~w~iWENymlvsvdvge~eda~~A~~rll  614 (777)
T KOG1128|consen  543 HRCVTLEPD-NAEAWNNLSTAYIRLKKKKRAFRKLKEALKCN-YQHWQIWENYMLVSVDVGEFEDAIKAYHRLL  614 (777)
T ss_pred             HHHhhcCCC-chhhhhhhhHHHHHHhhhHHHHHHHHHHhhcC-CCCCeeeechhhhhhhcccHHHHHHHHHHHH
Confidence            544443111 33455555555555555555555555555544 2233444445555555555555555555543

>PRK10370 formate-dependent nitrite reductase complex subunit NrfG; Provisional

Probab=98.69  E-value=9.9e-06  Score=66.79  Aligned_cols=121  Identities=12%  Similarity=0.020  Sum_probs=52.6

Q ss_pred             CCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHH-HhcCC--HHHHH
Q 012111          340 GHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAY-GQAGD--VEKMG  416 (471)
Q Consensus       340 g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~-~~~g~--~~~a~  416 (471)
                      ++.+++...++...+.+ +.|...|..+...|...|++++|...|++..+.++. +...+..+..++ ...|+  .++|.
T Consensus        53 ~~~~~~i~~l~~~L~~~-P~~~~~w~~Lg~~~~~~g~~~~A~~a~~~Al~l~P~-~~~~~~~lA~aL~~~~g~~~~~~A~  130 (198)
T PRK10370         53 QTPEAQLQALQDKIRAN-PQNSEQWALLGEYYLWRNDYDNALLAYRQALQLRGE-NAELYAALATVLYYQAGQHMTPQTR  130 (198)
T ss_pred             hhHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHhcCCCCcHHHH
Confidence            33344444444443332 224444444444444444444444444444444433 444444444432 33333  24444


Q ss_pred             HHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhhhc
Q 012111          417 ELFLTMKERHCVPDNITFATMIQAYNALGMTEAAQNLENKMIAMKEN  463 (471)
Q Consensus       417 ~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~  463 (471)
                      +++++..+.+ +-+...+..+...+.+.|++++|...|+++++..|.
T Consensus       131 ~~l~~al~~d-P~~~~al~~LA~~~~~~g~~~~Ai~~~~~aL~l~~~  176 (198)
T PRK10370        131 EMIDKALALD-ANEVTALMLLASDAFMQADYAQAIELWQKVLDLNSP  176 (198)
T ss_pred             HHHHHHHHhC-CCChhHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCC
Confidence            4444444431 113334444444444444444444444444444443

>KOG2053 consensus Mitochondrial inheritance and actin cytoskeleton organization protein [Cytoskeleton]

Probab=98.68  E-value=0.00042  Score=66.98  Aligned_cols=222  Identities=14%  Similarity=0.089  Sum_probs=118.7

Q ss_pred             HhhHHHHHHHHHhhhhhhccCCCchHHHHHHHHHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHH
Q 012111           55 LRTEFAIKNIEKKVSSKKYKNLWPKPVLEALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQAS  134 (471)
Q Consensus        55 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~  134 (471)
                      ..++.+++.+...++..|..  ..-.+..++ .+.+.|+.++|..+++.....+  ..|..+...+-.+|...++.++|.
T Consensus        23 ~qfkkal~~~~kllkk~Pn~--~~a~vLkaL-sl~r~gk~~ea~~~Le~~~~~~--~~D~~tLq~l~~~y~d~~~~d~~~   97 (932)
T KOG2053|consen   23 SQFKKALAKLGKLLKKHPNA--LYAKVLKAL-SLFRLGKGDEALKLLEALYGLK--GTDDLTLQFLQNVYRDLGKLDEAV   97 (932)
T ss_pred             HHHHHHHHHHHHHHHHCCCc--HHHHHHHHH-HHHHhcCchhHHHHHhhhccCC--CCchHHHHHHHHHHHHHhhhhHHH
Confidence            34455666666665543322  111111222 2346777777777777666554  346667777777777777777777


Q ss_pred             HHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcC-C---------HHHH
Q 012111          135 LLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFH-R---------FDLI  204 (471)
Q Consensus       135 ~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~-~---------~~~a  204 (471)
                      .+|+.....  -|+......+..+|++.+.+.+-.+.--++-+  ..+-+...+=++++...... .         ..-|
T Consensus        98 ~~Ye~~~~~--~P~eell~~lFmayvR~~~yk~qQkaa~~LyK--~~pk~~yyfWsV~Slilqs~~~~~~~~~~i~l~LA  173 (932)
T KOG2053|consen   98 HLYERANQK--YPSEELLYHLFMAYVREKSYKKQQKAALQLYK--NFPKRAYYFWSVISLILQSIFSENELLDPILLALA  173 (932)
T ss_pred             HHHHHHHhh--CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--hCCcccchHHHHHHHHHHhccCCcccccchhHHHH
Confidence            777777665  45566666677777776665543333322222  11223333333444333211 1         2235


Q ss_pred             HHHHHHHHHCC-CCCCHHHHHHHHHHHHccCCHHHHHHHHH-HHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 012111          205 EKILAEMSYLG-IECSAVTYNTIIDGYGKAKKFEEMESSFS-AMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEF  282 (471)
Q Consensus       205 ~~~~~~~~~~g-~~~~~~~~~~l~~~~~~~~~~~~a~~~~~-~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  282 (471)
                      .+.++.+.+.+ -.-+..-.......+...|++++|.+++. ...+.. ..-+...-+.-+..+...+++.+..++-.++
T Consensus       174 ~~m~~~~l~~~gk~~s~aE~~Lyl~iL~~~~k~~eal~~l~~~la~~l-~~~~~~l~~~~~dllk~l~~w~~l~~l~~~L  252 (932)
T KOG2053|consen  174 EKMVQKLLEKKGKIESEAEIILYLLILELQGKYQEALEFLAITLAEKL-TSANLYLENKKLDLLKLLNRWQELFELSSRL  252 (932)
T ss_pred             HHHHHHHhccCCccchHHHHHHHHHHHHhcccHHHHHHHHHHHHHHhc-cccchHHHHHHHHHHHHhcChHHHHHHHHHH
Confidence            55555555443 11122222223344455677888887773 332221 2233333445566677778888877777777


Q ss_pred             HhCC
Q 012111          283 NLMG  286 (471)
Q Consensus       283 ~~~~  286 (471)
                      ...|
T Consensus       253 l~k~  256 (932)
T KOG2053|consen  253 LEKG  256 (932)
T ss_pred             HHhC
Confidence            7665

>COG5010 TadD Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking and secretion]

Probab=98.67  E-value=1.6e-05  Score=65.49  Aligned_cols=157  Identities=11%  Similarity=0.017  Sum_probs=82.4

Q ss_pred             HHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHH
Q 012111          224 NTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGR  303 (471)
Q Consensus       224 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~  303 (471)
                      ..+-..+...|+-+....+.......  ...|.......+....+.|++..|...+.+..... ++|...|+.+.-+|.+
T Consensus        70 ~~~a~a~~~~G~a~~~l~~~~~~~~~--~~~d~~ll~~~gk~~~~~g~~~~A~~~~rkA~~l~-p~d~~~~~~lgaaldq  146 (257)
T COG5010          70 AKLATALYLRGDADSSLAVLQKSAIA--YPKDRELLAAQGKNQIRNGNFGEAVSVLRKAARLA-PTDWEAWNLLGAALDQ  146 (257)
T ss_pred             HHHHHHHHhcccccchHHHHhhhhcc--CcccHHHHHHHHHHHHHhcchHHHHHHHHHHhccC-CCChhhhhHHHHHHHH
Confidence            33444445555555555554443322  13333344445555556666666666666655433 5555566666666666


Q ss_pred             cCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHH
Q 012111          304 AGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSI  383 (471)
Q Consensus       304 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~  383 (471)
                      .|+++.|..-|.+..+.... ++..++.+.-.+.-.|+.+.|..++......+ .-|..+-..+.......|++++|.++
T Consensus       147 ~Gr~~~Ar~ay~qAl~L~~~-~p~~~nNlgms~~L~gd~~~A~~lll~a~l~~-~ad~~v~~NLAl~~~~~g~~~~A~~i  224 (257)
T COG5010         147 LGRFDEARRAYRQALELAPN-EPSIANNLGMSLLLRGDLEDAETLLLPAYLSP-AADSRVRQNLALVVGLQGDFREAEDI  224 (257)
T ss_pred             ccChhHHHHHHHHHHHhccC-CchhhhhHHHHHHHcCCHHHHHHHHHHHHhCC-CCchHHHHHHHHHHhhcCChHHHHhh
Confidence            66666666555555554222 34445555555555566666666665555542 22444455555555555666555555


Q ss_pred             HH
Q 012111          384 LR  385 (471)
Q Consensus       384 ~~  385 (471)
                      ..
T Consensus       225 ~~  226 (257)
T COG5010         225 AV  226 (257)
T ss_pred             cc
Confidence            43

>KOG0548 consensus Molecular co-chaperone STI1 [Posttranslational modification, protein turnover, chaperones]

Probab=98.67  E-value=0.00029  Score=64.14  Aligned_cols=237  Identities=14%  Similarity=0.016  Sum_probs=138.8

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHH-------
Q 012111          189 SILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNS-------  261 (471)
Q Consensus       189 ~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~-------  261 (471)
                      ..+.++..+..++..+.+-++......  -+..-++....+|...|.+...........+.++  -...-|+.       
T Consensus       228 k~lgnaaykkk~f~~a~q~y~~a~el~--~~it~~~n~aA~~~e~~~~~~c~~~c~~a~E~gr--e~rad~klIak~~~r  303 (539)
T KOG0548|consen  228 KELGNAAYKKKDFETAIQHYAKALELA--TDITYLNNIAAVYLERGKYAECIELCEKAVEVGR--ELRADYKLIAKALAR  303 (539)
T ss_pred             HHHHHHHHHhhhHHHHHHHHHHHHhHh--hhhHHHHHHHHHHHhccHHHHhhcchHHHHHHhH--HHHHHHHHHHHHHHH
Confidence            345555555666666776666666553  2444455555666666666666665555544431  11112222       


Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCC
Q 012111          262 MISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGH  341 (471)
Q Consensus       262 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~  341 (471)
                      +..+|.+.++++.+...|.+.......|+.         ..+....+++....+...-.+... ..-...-...+.+.|+
T Consensus       304 ~g~a~~k~~~~~~ai~~~~kaLte~Rt~~~---------ls~lk~~Ek~~k~~e~~a~~~pe~-A~e~r~kGne~Fk~gd  373 (539)
T KOG0548|consen  304 LGNAYTKREDYEGAIKYYQKALTEHRTPDL---------LSKLKEAEKALKEAERKAYINPEK-AEEEREKGNEAFKKGD  373 (539)
T ss_pred             hhhhhhhHHhHHHHHHHHHHHhhhhcCHHH---------HHHHHHHHHHHHHHHHHHhhChhH-HHHHHHHHHHHHhccC
Confidence            233455566667777777665544333222         112223333333333322221111 1111122455677889


Q ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHH
Q 012111          342 IEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLT  421 (471)
Q Consensus       342 ~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~  421 (471)
                      +..|+..|.+++... +-|...|..-.-+|.+.|.+..|+.-.+..++.++. ....|..-..++....+++.|.+.|++
T Consensus       374 y~~Av~~YteAIkr~-P~Da~lYsNRAac~~kL~~~~~aL~Da~~~ieL~p~-~~kgy~RKg~al~~mk~ydkAleay~e  451 (539)
T KOG0548|consen  374 YPEAVKHYTEAIKRD-PEDARLYSNRAACYLKLGEYPEALKDAKKCIELDPN-FIKAYLRKGAALRAMKEYDKALEAYQE  451 (539)
T ss_pred             HHHHHHHHHHHHhcC-CchhHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCch-HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999988875 447788888899999999999998888888877544 455555556666677788888888888


Q ss_pred             HHhCCCCCCHHHHHHHHHHHHh
Q 012111          422 MKERHCVPDNITFATMIQAYNA  443 (471)
Q Consensus       422 ~~~~~~~p~~~~~~~l~~~~~~  443 (471)
                      ..+.  .|+..-+.--+.-|..
T Consensus       452 ale~--dp~~~e~~~~~~rc~~  471 (539)
T KOG0548|consen  452 ALEL--DPSNAEAIDGYRRCVE  471 (539)
T ss_pred             HHhc--CchhHHHHHHHHHHHH
Confidence            8874  4655544444433433

>PRK14720 transcript cleavage factor/unknown domain fusion protein; Provisional

Probab=98.65  E-value=5e-05  Score=75.36  Aligned_cols=59  Identities=12%  Similarity=0.286  Sum_probs=30.2

Q ss_pred             HHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 012111          222 TYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFN  283 (471)
Q Consensus       222 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  283 (471)
                      .+..+..+|-+.|+.++|..+|+++.+..  +.+....|.+...|... +.++|.+++.+.+
T Consensus       118 Al~~LA~~Ydk~g~~~ka~~~yer~L~~D--~~n~~aLNn~AY~~ae~-dL~KA~~m~~KAV  176 (906)
T PRK14720        118 ALRTLAEAYAKLNENKKLKGVWERLVKAD--RDNPEIVKKLATSYEEE-DKEKAITYLKKAI  176 (906)
T ss_pred             HHHHHHHHHHHcCChHHHHHHHHHHHhcC--cccHHHHHHHHHHHHHh-hHHHHHHHHHHHH
Confidence            44455555555555555555555555443  33444555555555555 5555555555443

>KOG3081 consensus Vesicle coat complex COPI, epsilon subunit [Intracellular trafficking, secretion, and vesicular transport]

Probab=98.63  E-value=9.5e-05  Score=61.12  Aligned_cols=119  Identities=14%  Similarity=0.120  Sum_probs=53.4

Q ss_pred             HhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHH----cCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCH
Q 012111          267 GNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGR----AGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHI  342 (471)
Q Consensus       267 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~  342 (471)
                      .+..+.+-|.+.+++|.+.   -+..|.+.|..+|.+    .+.+..|.-+|++|.++ ..|+..+.+-...++...|++
T Consensus       148 lk~~r~d~A~~~lk~mq~i---ded~tLtQLA~awv~la~ggek~qdAfyifeE~s~k-~~~T~~llnG~Av~~l~~~~~  223 (299)
T KOG3081|consen  148 LKMHRFDLAEKELKKMQQI---DEDATLTQLAQAWVKLATGGEKIQDAFYIFEELSEK-TPPTPLLLNGQAVCHLQLGRY  223 (299)
T ss_pred             HHHHHHHHHHHHHHHHHcc---chHHHHHHHHHHHHHHhccchhhhhHHHHHHHHhcc-cCCChHHHccHHHHHHHhcCH
Confidence            3444444455555554432   133333333333322    23345555555555443 334555555555555555555


Q ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHH-HHHHHHHHHHhC
Q 012111          343 EKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIM-KVDSILRQVENS  390 (471)
Q Consensus       343 ~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~-~a~~~~~~~~~~  390 (471)
                      ++|..+++....+. .-++.+...++.+....|... ...+.+.++...
T Consensus       224 eeAe~lL~eaL~kd-~~dpetL~Nliv~a~~~Gkd~~~~~r~l~QLk~~  271 (299)
T KOG3081|consen  224 EEAESLLEEALDKD-AKDPETLANLIVLALHLGKDAEVTERNLSQLKLS  271 (299)
T ss_pred             HHHHHHHHHHHhcc-CCCHHHHHHHHHHHHHhCCChHHHHHHHHHHHhc
Confidence            55555555555543 223444444444433444332 233444444443

>PRK15179 Vi polysaccharide biosynthesis protein TviE; Provisional

Probab=98.63  E-value=1.9e-05  Score=77.31  Aligned_cols=147  Identities=7%  Similarity=0.019  Sum_probs=107.5

Q ss_pred             CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHH
Q 012111          287 VKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCS  366 (471)
Q Consensus       287 ~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~  366 (471)
                      .+.+...+..|.......|..++|..+++...+..+. +......+...+.+.+++++|+..+++..... +-+......
T Consensus        82 ~~~~~~~~~~La~i~~~~g~~~ea~~~l~~~~~~~Pd-~~~a~~~~a~~L~~~~~~eeA~~~~~~~l~~~-p~~~~~~~~  159 (694)
T PRK15179         82 YPHTELFQVLVARALEAAHRSDEGLAVWRGIHQRFPD-SSEAFILMLRGVKRQQGIEAGRAEIELYFSGG-SSSAREILL  159 (694)
T ss_pred             ccccHHHHHHHHHHHHHcCCcHHHHHHHHHHHhhCCC-cHHHHHHHHHHHHHhccHHHHHHHHHHHhhcC-CCCHHHHHH
Confidence            3556777888888888888888888888888775322 34456667777888888888888888888763 224566677


Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHH
Q 012111          367 LVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATM  437 (471)
Q Consensus       367 li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l  437 (471)
                      +..++...|++++|..+|+++...++. +..++..+..++...|+.++|...|++..+. ..|....|+.+
T Consensus       160 ~a~~l~~~g~~~~A~~~y~~~~~~~p~-~~~~~~~~a~~l~~~G~~~~A~~~~~~a~~~-~~~~~~~~~~~  228 (694)
T PRK15179        160 EAKSWDEIGQSEQADACFERLSRQHPE-FENGYVGWAQSLTRRGALWRARDVLQAGLDA-IGDGARKLTRR  228 (694)
T ss_pred             HHHHHHHhcchHHHHHHHHHHHhcCCC-cHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh-hCcchHHHHHH
Confidence            777888888888888888888875443 5777788888888888888888888888765 34455554443

>PRK15359 type III secretion system chaperone protein SscB; Provisional

Probab=98.61  E-value=6.7e-06  Score=64.06  Aligned_cols=95  Identities=8%  Similarity=-0.126  Sum_probs=67.9

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHh
Q 012111          329 YNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQ  408 (471)
Q Consensus       329 ~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  408 (471)
                      +..+...+...|++++|...|+...... +.+...+..+..++...|++++|...|+.....++. +...+..+..++..
T Consensus        27 ~~~~g~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~lg~~~~~~g~~~~A~~~y~~Al~l~p~-~~~a~~~lg~~l~~  104 (144)
T PRK15359         27 VYASGYASWQEGDYSRAVIDFSWLVMAQ-PWSWRAHIALAGTWMMLKEYTTAINFYGHALMLDAS-HPEPVYQTGVCLKM  104 (144)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCC-CcHHHHHHHHHHHH
Confidence            4445666677777777777777777653 335667777777777777777777777777776654 66777777777777


Q ss_pred             cCCHHHHHHHHHHHHhC
Q 012111          409 AGDVEKMGELFLTMKER  425 (471)
Q Consensus       409 ~g~~~~a~~~~~~~~~~  425 (471)
                      .|++++|+..|+...+.
T Consensus       105 ~g~~~eAi~~~~~Al~~  121 (144)
T PRK15359        105 MGEPGLAREAFQTAIKM  121 (144)
T ss_pred             cCCHHHHHHHHHHHHHh
Confidence            77777777777777763

>PRK15359 type III secretion system chaperone protein SscB; Provisional

Probab=98.61  E-value=1.9e-06  Score=67.11  Aligned_cols=113  Identities=8%  Similarity=-0.052  Sum_probs=96.5

Q ss_pred             HHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCC
Q 012111          347 EYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERH  426 (471)
Q Consensus       347 ~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~  426 (471)
                      .++++..+.  .|+  .+..+...+...|++++|...|+.+...++. +...|..+..++...|++++|+..|++.... 
T Consensus        14 ~~~~~al~~--~p~--~~~~~g~~~~~~g~~~~A~~~~~~al~~~P~-~~~a~~~lg~~~~~~g~~~~A~~~y~~Al~l-   87 (144)
T PRK15359         14 DILKQLLSV--DPE--TVYASGYASWQEGDYSRAVIDFSWLVMAQPW-SWRAHIALAGTWMMLKEYTTAINFYGHALML-   87 (144)
T ss_pred             HHHHHHHHc--CHH--HHHHHHHHHHHcCCHHHHHHHHHHHHHcCCC-cHHHHHHHHHHHHHHhhHHHHHHHHHHHHhc-
Confidence            456665553  344  3556788889999999999999999998776 8899999999999999999999999999985 


Q ss_pred             CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhhhcCC
Q 012111          427 CVPDNITFATMIQAYNALGMTEAAQNLENKMIAMKENSG  465 (471)
Q Consensus       427 ~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~~~  465 (471)
                      -+.+...+..+..++...|+.++|...+++.++..|...
T Consensus        88 ~p~~~~a~~~lg~~l~~~g~~~eAi~~~~~Al~~~p~~~  126 (144)
T PRK15359         88 DASHPEPVYQTGVCLKMMGEPGLAREAFQTAIKMSYADA  126 (144)
T ss_pred             CCCCcHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCh
Confidence            234778888999999999999999999999999988754

>COG4783 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]

Probab=98.61  E-value=2.4e-05  Score=70.23  Aligned_cols=140  Identities=16%  Similarity=0.081  Sum_probs=105.8

Q ss_pred             HHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCC-HHHHHHHHHHHHhcCCH
Q 012111           87 EAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPS-VDVYTALVSAYGQSGLL  165 (471)
Q Consensus        87 ~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~-~~~~~~li~~~~~~~~~  165 (471)
                      .....|+++.|+..++.+....  |.|..........+.+.++..+|.+.++.+...  .|+ ....-.+..++.+.|+.
T Consensus       315 ~~~~~~~~d~A~~~l~~L~~~~--P~N~~~~~~~~~i~~~~nk~~~A~e~~~kal~l--~P~~~~l~~~~a~all~~g~~  390 (484)
T COG4783         315 QTYLAGQYDEALKLLQPLIAAQ--PDNPYYLELAGDILLEANKAKEAIERLKKALAL--DPNSPLLQLNLAQALLKGGKP  390 (484)
T ss_pred             HHHHhcccchHHHHHHHHHHhC--CCCHHHHHHHHHHHHHcCChHHHHHHHHHHHhc--CCCccHHHHHHHHHHHhcCCh
Confidence            3446788888888888887763  566666677777888888888888888888876  444 55666777888888888


Q ss_pred             HHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHH
Q 012111          166 DEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSA  245 (471)
Q Consensus       166 ~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~  245 (471)
                      .+|+.+++....  ..+-|+..|..|..+|...|+..++.....+.                  |...|+++.|...+..
T Consensus       391 ~eai~~L~~~~~--~~p~dp~~w~~LAqay~~~g~~~~a~~A~AE~------------------~~~~G~~~~A~~~l~~  450 (484)
T COG4783         391 QEAIRILNRYLF--NDPEDPNGWDLLAQAYAELGNRAEALLARAEG------------------YALAGRLEQAIIFLMR  450 (484)
T ss_pred             HHHHHHHHHHhh--cCCCCchHHHHHHHHHHHhCchHHHHHHHHHH------------------HHhCCCHHHHHHHHHH
Confidence            888888888775  34677788888888888888877766555443                  4456888888888877


Q ss_pred             HHHcC
Q 012111          246 MVESG  250 (471)
Q Consensus       246 ~~~~~  250 (471)
                      ..+..
T Consensus       451 A~~~~  455 (484)
T COG4783         451 ASQQV  455 (484)
T ss_pred             HHHhc
Confidence            76653

>PRK14720 transcript cleavage factor/unknown domain fusion protein; Provisional

Probab=98.54  E-value=0.00011  Score=72.97  Aligned_cols=219  Identities=16%  Similarity=0.156  Sum_probs=142.4

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHH-HHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHH
Q 012111          148 SVDVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVY-TYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTI  226 (471)
Q Consensus       148 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~-~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l  226 (471)
                      +...+..|+..+...+++++|.++.+...+.   .|+.. .|-.+...+.+.++.+.+..+                 .+
T Consensus        30 n~~a~~~Li~~~~~~~~~deai~i~~~~l~~---~P~~i~~yy~~G~l~~q~~~~~~~~lv-----------------~~   89 (906)
T PRK14720         30 KFKELDDLIDAYKSENLTDEAKDICEEHLKE---HKKSISALYISGILSLSRRPLNDSNLL-----------------NL   89 (906)
T ss_pred             hHHHHHHHHHHHHhcCCHHHHHHHHHHHHHh---CCcceehHHHHHHHHHhhcchhhhhhh-----------------hh
Confidence            4667888888888888888888888877663   33332 233333355555554443333                 34


Q ss_pred             HHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCC
Q 012111          227 IDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGM  306 (471)
Q Consensus       227 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~  306 (471)
                      +.......++..+..+...+.+.   .-+...+..+..+|-+.|+.++|..+|+++.+.. +-+..+.|.+...|... +
T Consensus        90 l~~~~~~~~~~~ve~~~~~i~~~---~~~k~Al~~LA~~Ydk~g~~~ka~~~yer~L~~D-~~n~~aLNn~AY~~ae~-d  164 (906)
T PRK14720         90 IDSFSQNLKWAIVEHICDKILLY---GENKLALRTLAEAYAKLNENKKLKGVWERLVKAD-RDNPEIVKKLATSYEEE-D  164 (906)
T ss_pred             hhhcccccchhHHHHHHHHHHhh---hhhhHHHHHHHHHHHHcCChHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHh-h
Confidence            44445555665555555555543   3345578889999999999999999999999887 77889999999999999 9


Q ss_pred             HHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc-------------------CCCCCHHHHHHH
Q 012111          307 YDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHR-------------------GMKPNSITYCSL  367 (471)
Q Consensus       307 ~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~-------------------~~~p~~~~~~~l  367 (471)
                      +++|..++.+....               +...+++..+.++|.++...                   |..--..++..+
T Consensus       165 L~KA~~m~~KAV~~---------------~i~~kq~~~~~e~W~k~~~~~~~d~d~f~~i~~ki~~~~~~~~~~~~~~~l  229 (906)
T PRK14720        165 KEKAITYLKKAIYR---------------FIKKKQYVGIEEIWSKLVHYNSDDFDFFLRIERKVLGHREFTRLVGLLEDL  229 (906)
T ss_pred             HHHHHHHHHHHHHH---------------HHhhhcchHHHHHHHHHHhcCcccchHHHHHHHHHHhhhccchhHHHHHHH
Confidence            99999998877654               34444555555555555543                   212223334444


Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHH
Q 012111          368 VSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYG  407 (471)
Q Consensus       368 i~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  407 (471)
                      -..|...++++++..+++.+.+.... |......++.+|.
T Consensus       230 ~~~y~~~~~~~~~i~iLK~iL~~~~~-n~~a~~~l~~~y~  268 (906)
T PRK14720        230 YEPYKALEDWDEVIYILKKILEHDNK-NNKAREELIRFYK  268 (906)
T ss_pred             HHHHhhhhhhhHHHHHHHHHHhcCCc-chhhHHHHHHHHH
Confidence            45555666666666666666665554 5555555555554

>TIGR02552 LcrH_SycD type III secretion low calcium response chaperone LcrH/SycD

Probab=98.53  E-value=5.1e-06  Score=64.37  Aligned_cols=92  Identities=11%  Similarity=-0.003  Sum_probs=42.7

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcC
Q 012111          331 IVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAG  410 (471)
Q Consensus       331 ~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g  410 (471)
                      .+...+...|++++|...++.+...+ +.+...+..+...+...|++++|..+++...+.++. +...+..+...+...|
T Consensus        22 ~~a~~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~p~-~~~~~~~la~~~~~~g   99 (135)
T TIGR02552        22 ALAYNLYQQGRYDEALKLFQLLAAYD-PYNSRYWLGLAACCQMLKEYEEAIDAYALAAALDPD-DPRPYFHAAECLLALG   99 (135)
T ss_pred             HHHHHHHHcccHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC-ChHHHHHHHHHHHHcC
Confidence            33344444455555555555444432 223444444444444555555555555544444322 3344444444444555


Q ss_pred             CHHHHHHHHHHHHh
Q 012111          411 DVEKMGELFLTMKE  424 (471)
Q Consensus       411 ~~~~a~~~~~~~~~  424 (471)
                      ++++|...|+...+
T Consensus       100 ~~~~A~~~~~~al~  113 (135)
T TIGR02552       100 EPESALKALDLAIE  113 (135)
T ss_pred             CHHHHHHHHHHHHH
Confidence            55555555544444

ScyD/LcrH contains three central tetratricopeptide-like repeats that are predicted to fold into an all-alpha-helical array.

>COG4783 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]

Probab=98.52  E-value=0.00033  Score=63.20  Aligned_cols=116  Identities=18%  Similarity=0.117  Sum_probs=76.3

Q ss_pred             HHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCC-HHHHHHHHHHHHhcCCHHH
Q 012111          301 YGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPN-SITYCSLVSAYSKAGLIMK  379 (471)
Q Consensus       301 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~-~~~~~~li~~~~~~g~~~~  379 (471)
                      +...|++++|+..+..+....+ -|+..+....+.+...++.++|.+.++++...  .|+ ......+..++.+.|++.+
T Consensus       316 ~~~~~~~d~A~~~l~~L~~~~P-~N~~~~~~~~~i~~~~nk~~~A~e~~~kal~l--~P~~~~l~~~~a~all~~g~~~e  392 (484)
T COG4783         316 TYLAGQYDEALKLLQPLIAAQP-DNPYYLELAGDILLEANKAKEAIERLKKALAL--DPNSPLLQLNLAQALLKGGKPQE  392 (484)
T ss_pred             HHHhcccchHHHHHHHHHHhCC-CCHHHHHHHHHHHHHcCChHHHHHHHHHHHhc--CCCccHHHHHHHHHHHhcCChHH
Confidence            4456677777777777666522 24555555566777777777777777777765  444 4455566677777777777


Q ss_pred             HHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHH
Q 012111          380 VDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFL  420 (471)
Q Consensus       380 a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~  420 (471)
                      |..+++......+. |+..|..|.++|...|+..++..-..
T Consensus       393 ai~~L~~~~~~~p~-dp~~w~~LAqay~~~g~~~~a~~A~A  432 (484)
T COG4783         393 AIRILNRYLFNDPE-DPNGWDLLAQAYAELGNRAEALLARA  432 (484)
T ss_pred             HHHHHHHHhhcCCC-CchHHHHHHHHHHHhCchHHHHHHHH
Confidence            77777777666555 67777777777777777666655443

>KOG3060 consensus Uncharacterized conserved protein [Function unknown]

Probab=98.50  E-value=0.00026  Score=58.14  Aligned_cols=187  Identities=14%  Similarity=0.061  Sum_probs=120.6

Q ss_pred             CCHHHHHHHHHHHHhC---C-CCCCHH-HHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHH
Q 012111          128 KQPEQASLLFEVMLSD---G-LKPSVD-VYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFD  202 (471)
Q Consensus       128 ~~~~~a~~~~~~m~~~---~-~~~~~~-~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~  202 (471)
                      .+.++.++++..+...   | ..++.. .|..++-+....|+.+.|...++.+....  +-+...-..-...+-..|+++
T Consensus        26 rnseevv~l~~~~~~~~k~~~~g~e~w~l~EqV~IAAld~~~~~lAq~C~~~L~~~f--p~S~RV~~lkam~lEa~~~~~  103 (289)
T KOG3060|consen   26 RNSEEVVQLGSEVLNYSKSGALGDEIWTLYEQVFIAALDTGRDDLAQKCINQLRDRF--PGSKRVGKLKAMLLEATGNYK  103 (289)
T ss_pred             cCHHHHHHHHHHHHHHhhhcccCchHHHHHHHHHHHHHHhcchHHHHHHHHHHHHhC--CCChhHHHHHHHHHHHhhchh
Confidence            4556666666665532   2 334443 34555666667788888888888877633  222222222222244567788


Q ss_pred             HHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 012111          203 LIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEF  282 (471)
Q Consensus       203 ~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  282 (471)
                      +|.++++.+.+.. +.|..++-.-+...-..|+.-+|++.+....+.  +..|...|.-+...|...|+++.|.-.++++
T Consensus       104 ~A~e~y~~lL~dd-pt~~v~~KRKlAilka~GK~l~aIk~ln~YL~~--F~~D~EAW~eLaeiY~~~~~f~kA~fClEE~  180 (289)
T KOG3060|consen  104 EAIEYYESLLEDD-PTDTVIRKRKLAILKAQGKNLEAIKELNEYLDK--FMNDQEAWHELAEIYLSEGDFEKAAFCLEEL  180 (289)
T ss_pred             hHHHHHHHHhccC-cchhHHHHHHHHHHHHcCCcHHHHHHHHHHHHH--hcCcHHHHHHHHHHHHhHhHHHHHHHHHHHH
Confidence            8888888887765 556666666666666677777888888777776  4778888888888888888888888888888


Q ss_pred             HhCCCCCCHHHHHHHHHHHHHcC---CHHHHHHHHHHHHhC
Q 012111          283 NLMGVKADIQTLNILTKSYGRAG---MYDKMRSVMDFMQKR  320 (471)
Q Consensus       283 ~~~~~~~~~~~~~~ll~~~~~~~---~~~~a~~~~~~~~~~  320 (471)
                      .-.. |.+...+..+...+.-.|   +.+.+.++|.+..+.
T Consensus       181 ll~~-P~n~l~f~rlae~~Yt~gg~eN~~~arkyy~~alkl  220 (289)
T KOG3060|consen  181 LLIQ-PFNPLYFQRLAEVLYTQGGAENLELARKYYERALKL  220 (289)
T ss_pred             HHcC-CCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHh
Confidence            7543 445555555555544333   455667777766665

>KOG3060 consensus Uncharacterized conserved protein [Function unknown]

Probab=98.46  E-value=0.00043  Score=56.92  Aligned_cols=189  Identities=8%  Similarity=0.038  Sum_probs=128.2

Q ss_pred             CCHHHHHHHHHHHHH---CC-CCCCH-HHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHH
Q 012111          199 HRFDLIEKILAEMSY---LG-IECSA-VTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIE  273 (471)
Q Consensus       199 ~~~~~a~~~~~~~~~---~g-~~~~~-~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  273 (471)
                      .+.++..+++.+++.   .| ..++. ..|..++-+....|+.+.|...++.+..+.  +-+...-..-...+-..|+++
T Consensus        26 rnseevv~l~~~~~~~~k~~~~g~e~w~l~EqV~IAAld~~~~~lAq~C~~~L~~~f--p~S~RV~~lkam~lEa~~~~~  103 (289)
T KOG3060|consen   26 RNSEEVVQLGSEVLNYSKSGALGDEIWTLYEQVFIAALDTGRDDLAQKCINQLRDRF--PGSKRVGKLKAMLLEATGNYK  103 (289)
T ss_pred             cCHHHHHHHHHHHHHHhhhcccCchHHHHHHHHHHHHHHhcchHHHHHHHHHHHHhC--CCChhHHHHHHHHHHHhhchh
Confidence            355666666665543   23 33343 345566666777888888888888887663  223222222223345678888


Q ss_pred             HHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 012111          274 KMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMK  353 (471)
Q Consensus       274 ~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~  353 (471)
                      +|.++|+.+.+.+ +.|..++..=+-..-..|.--+|++-+....+. +..|...|.-+...|...|++++|.-.++++.
T Consensus       104 ~A~e~y~~lL~dd-pt~~v~~KRKlAilka~GK~l~aIk~ln~YL~~-F~~D~EAW~eLaeiY~~~~~f~kA~fClEE~l  181 (289)
T KOG3060|consen  104 EAIEYYESLLEDD-PTDTVIRKRKLAILKAQGKNLEAIKELNEYLDK-FMNDQEAWHELAEIYLSEGDFEKAAFCLEELL  181 (289)
T ss_pred             hHHHHHHHHhccC-cchhHHHHHHHHHHHHcCCcHHHHHHHHHHHHH-hcCcHHHHHHHHHHHHhHhHHHHHHHHHHHHH
Confidence            8888888888766 666677766666666677777787777777766 44588899999999999999999999999888


Q ss_pred             HcCCCCCHHHHHHHHHHHHhcC---CHHHHHHHHHHHHhCCC
Q 012111          354 HRGMKPNSITYCSLVSAYSKAG---LIMKVDSILRQVENSDV  392 (471)
Q Consensus       354 ~~~~~p~~~~~~~li~~~~~~g---~~~~a~~~~~~~~~~~~  392 (471)
                      -.. +.++..+..+...+.-.|   +.+.+.++|.+..+...
T Consensus       182 l~~-P~n~l~f~rlae~~Yt~gg~eN~~~arkyy~~alkl~~  222 (289)
T KOG3060|consen  182 LIQ-PFNPLYFQRLAEVLYTQGGAENLELARKYYERALKLNP  222 (289)
T ss_pred             HcC-CCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHhCh
Confidence            753 335555566666655444   56678888888887654

>KOG1127 consensus TPR repeat-containing protein [RNA processing and modification]

Probab=98.42  E-value=0.0011  Score=64.89  Aligned_cols=155  Identities=10%  Similarity=-0.021  Sum_probs=112.7

Q ss_pred             HHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCC-CCHHHHHHHHHHHHhcCCHHH
Q 012111           89 IKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLK-PSVDVYTALVSAYGQSGLLDE  167 (471)
Q Consensus        89 ~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~-~~~~~~~~li~~~~~~~~~~~  167 (471)
                      +...+...|.+.|+.+.+.+  ..+..........|++..+++.|..+.-...+.... .-...|....-.|.+.++...
T Consensus       503 rd~~Dm~RA~kCf~KAFeLD--atdaeaaaa~adtyae~~~we~a~~I~l~~~qka~a~~~k~nW~~rG~yyLea~n~h~  580 (1238)
T KOG1127|consen  503 RDSDDMKRAKKCFDKAFELD--ATDAEAAAASADTYAEESTWEEAFEICLRAAQKAPAFACKENWVQRGPYYLEAHNLHG  580 (1238)
T ss_pred             HHHHHHHHHHHHHHHHhcCC--chhhhhHHHHHHHhhccccHHHHHHHHHHHhhhchHHHHHhhhhhccccccCccchhh
Confidence            34447778999999998876  667788899999999999999999884333332110 011223344456777889999


Q ss_pred             HHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCC-HHHHHHHHHHHHccCCHHHHHHHHHHH
Q 012111          168 AFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECS-AVTYNTIIDGYGKAKKFEEMESSFSAM  246 (471)
Q Consensus       168 a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~  246 (471)
                      |+.-|+...+.  -+.|...|..+..+|...|++..|.++|.+.....  |+ ...-......-+..|++.+|+..+..+
T Consensus       581 aV~~fQsALR~--dPkD~n~W~gLGeAY~~sGry~~AlKvF~kAs~Lr--P~s~y~~fk~A~~ecd~GkYkeald~l~~i  656 (1238)
T KOG1127|consen  581 AVCEFQSALRT--DPKDYNLWLGLGEAYPESGRYSHALKVFTKASLLR--PLSKYGRFKEAVMECDNGKYKEALDALGLI  656 (1238)
T ss_pred             HHHHHHHHhcC--CchhHHHHHHHHHHHHhcCceehHHHhhhhhHhcC--cHhHHHHHHHHHHHHHhhhHHHHHHHHHHH
Confidence            99999988763  35678899999999999999999999999887653  33 222223334456689999999988877


Q ss_pred             HHc
Q 012111          247 VES  249 (471)
Q Consensus       247 ~~~  249 (471)
                      ...
T Consensus       657 i~~  659 (1238)
T KOG1127|consen  657 IYA  659 (1238)
T ss_pred             HHH
Confidence            643

>TIGR02552 LcrH_SycD type III secretion low calcium response chaperone LcrH/SycD

Probab=98.40  E-value=2.8e-05  Score=60.17  Aligned_cols=103  Identities=11%  Similarity=0.079  Sum_probs=70.9

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHH
Q 012111          361 SITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQA  440 (471)
Q Consensus       361 ~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~  440 (471)
                      ......+...+...|++++|...++.+...++. +...+..+...+...|++++|..+++...+.+ +.+...+..+...
T Consensus        17 ~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~p~-~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~~la~~   94 (135)
T TIGR02552        17 LEQIYALAYNLYQQGRYDEALKLFQLLAAYDPY-NSRYWLGLAACCQMLKEYEEAIDAYALAAALD-PDDPRPYFHAAEC   94 (135)
T ss_pred             HHHHHHHHHHHHHcccHHHHHHHHHHHHHhCCC-cHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC-CCChHHHHHHHHH
Confidence            344556666677777777777777777766544 66677777777777777777777777776642 3355666666677


Q ss_pred             HHhcCCHHHHHHHHHHHHHhhhcCC
Q 012111          441 YNALGMTEAAQNLENKMIAMKENSG  465 (471)
Q Consensus       441 ~~~~g~~~~A~~~~~~m~~~~~~~~  465 (471)
                      +...|++++|...+++.++..|+..
T Consensus        95 ~~~~g~~~~A~~~~~~al~~~p~~~  119 (135)
T TIGR02552        95 LLALGEPESALKALDLAIEICGENP  119 (135)
T ss_pred             HHHcCCHHHHHHHHHHHHHhccccc
Confidence            7777777777777777777776544

ScyD/LcrH contains three central tetratricopeptide-like repeats that are predicted to fold into an all-alpha-helical array.

>PF09976 TPR_21: Tetratricopeptide repeat; InterPro: IPR018704 This domain, found in various hypothetical prokaryotic proteins, has no known function

Probab=98.33  E-value=6.8e-05  Score=58.68  Aligned_cols=126  Identities=13%  Similarity=0.082  Sum_probs=85.9

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCC---HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCH--HHHHHH
Q 012111          328 TYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPN---SITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDT--PFFNCI  402 (471)
Q Consensus       328 ~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~---~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~--~~~~~l  402 (471)
                      .|..++..+ ..++...+...++.+.... +.+   ....-.+...+...|++++|...|+.+......++.  .....|
T Consensus        14 ~y~~~~~~~-~~~~~~~~~~~~~~l~~~~-~~s~ya~~A~l~lA~~~~~~g~~~~A~~~l~~~~~~~~d~~l~~~a~l~L   91 (145)
T PF09976_consen   14 LYEQALQAL-QAGDPAKAEAAAEQLAKDY-PSSPYAALAALQLAKAAYEQGDYDEAKAALEKALANAPDPELKPLARLRL   91 (145)
T ss_pred             HHHHHHHHH-HCCCHHHHHHHHHHHHHHC-CCChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCCCHHHHHHHHHHH
Confidence            344455444 4778888888888887763 222   223344556777888888888888888876533322  244456


Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 012111          403 ISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAYNALGMTEAAQNLENKM  457 (471)
Q Consensus       403 ~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~m  457 (471)
                      ...+...|++++|+..++.....  ......+......+.+.|++++|...|+++
T Consensus        92 A~~~~~~~~~d~Al~~L~~~~~~--~~~~~~~~~~Gdi~~~~g~~~~A~~~y~~A  144 (145)
T PF09976_consen   92 ARILLQQGQYDEALATLQQIPDE--AFKALAAELLGDIYLAQGDYDEARAAYQKA  144 (145)
T ss_pred             HHHHHHcCCHHHHHHHHHhccCc--chHHHHHHHHHHHHHHCCCHHHHHHHHHHh
Confidence            77788889999998888764432  234455666778888999999998888765

>PF09295 ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); InterPro: IPR015374 ChAPs (Chs5p-Arf1p-binding proteins) are required for the export of specialised cargo from the Golgi

Probab=98.30  E-value=7.5e-05  Score=67.71  Aligned_cols=122  Identities=16%  Similarity=0.145  Sum_probs=85.9

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhc
Q 012111          330 NIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQA  409 (471)
Q Consensus       330 ~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  409 (471)
                      ..|+..+...++++.|..+++++.+..  |+  ....+++.+...++-.+|.+++.+..+..+. +...+......|.+.
T Consensus       173 ~~Ll~~l~~t~~~~~ai~lle~L~~~~--pe--v~~~LA~v~l~~~~E~~AI~ll~~aL~~~p~-d~~LL~~Qa~fLl~k  247 (395)
T PF09295_consen  173 DTLLKYLSLTQRYDEAIELLEKLRERD--PE--VAVLLARVYLLMNEEVEAIRLLNEALKENPQ-DSELLNLQAEFLLSK  247 (395)
T ss_pred             HHHHHHHhhcccHHHHHHHHHHHHhcC--Cc--HHHHHHHHHHhcCcHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHhc
Confidence            344555556677888888888877753  44  3344666677777777788888777765544 666666667777788


Q ss_pred             CCHHHHHHHHHHHHhCCCCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 012111          410 GDVEKMGELFLTMKERHCVPD-NITFATMIQAYNALGMTEAAQNLENKMI  458 (471)
Q Consensus       410 g~~~~a~~~~~~~~~~~~~p~-~~~~~~l~~~~~~~g~~~~A~~~~~~m~  458 (471)
                      ++++.|+.+.+++.+.  .|+ ..+|..|..+|...|+++.|+..++.+-
T Consensus       248 ~~~~lAL~iAk~av~l--sP~~f~~W~~La~~Yi~~~d~e~ALlaLNs~P  295 (395)
T PF09295_consen  248 KKYELALEIAKKAVEL--SPSEFETWYQLAECYIQLGDFENALLALNSCP  295 (395)
T ss_pred             CCHHHHHHHHHHHHHh--CchhHHHHHHHHHHHHhcCCHHHHHHHHhcCc
Confidence            8888888888888774  554 4577788888888888888877776553

They physically interact with Chs3, Chs5 and the small GTPase Arf1, and they also form interactions with each other [].

>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif)

Probab=98.23  E-value=2.8e-06  Score=47.88  Aligned_cols=33  Identities=42%  Similarity=0.567  Sum_probs=27.4

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCC
Q 012111          398 FFNCIISAYGQAGDVEKMGELFLTMKERHCVPD  430 (471)
Q Consensus       398 ~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~  430 (471)
                      +||.+|.+|++.|++++|.++|++|.+.|+.||
T Consensus         2 ~~n~li~~~~~~~~~~~a~~~~~~M~~~g~~p~   34 (35)
T TIGR00756         2 TYNTLIDGLCKAGRVEEALELFKEMLERGIEPD   34 (35)
T ss_pred             cHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCC
Confidence            578888888888888888888888888888876

This family has a similar consensus to the TPR domain (tetratricopeptide), pfam pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR.

>PF09295 ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); InterPro: IPR015374 ChAPs (Chs5p-Arf1p-binding proteins) are required for the export of specialised cargo from the Golgi

Probab=98.22  E-value=9.7e-05  Score=67.01  Aligned_cols=125  Identities=12%  Similarity=0.054  Sum_probs=78.7

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHH
Q 012111          258 TLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFG  337 (471)
Q Consensus       258 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~  337 (471)
                      ....|+..+...++++.|..+++++.+..  |+  ....+++.+...++..+|.+++.+..+... -+......-...+.
T Consensus       171 Lv~~Ll~~l~~t~~~~~ai~lle~L~~~~--pe--v~~~LA~v~l~~~~E~~AI~ll~~aL~~~p-~d~~LL~~Qa~fLl  245 (395)
T PF09295_consen  171 LVDTLLKYLSLTQRYDEAIELLEKLRERD--PE--VAVLLARVYLLMNEEVEAIRLLNEALKENP-QDSELLNLQAEFLL  245 (395)
T ss_pred             HHHHHHHHHhhcccHHHHHHHHHHHHhcC--Cc--HHHHHHHHHHhcCcHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHH
Confidence            34455556666677777777777776543  43  333466666666666777777766665422 24455555556666


Q ss_pred             hcCCHHHHHHHHHHHHHcCCCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 012111          338 KAGHIEKMEEYFKKMKHRGMKPN-SITYCSLVSAYSKAGLIMKVDSILRQVEN  389 (471)
Q Consensus       338 ~~g~~~~a~~~~~~m~~~~~~p~-~~~~~~li~~~~~~g~~~~a~~~~~~~~~  389 (471)
                      +.++++.|+.+.+++...  .|+ -.+|..|..+|...|+++.|+..++.+--
T Consensus       246 ~k~~~~lAL~iAk~av~l--sP~~f~~W~~La~~Yi~~~d~e~ALlaLNs~Pm  296 (395)
T PF09295_consen  246 SKKKYELALEIAKKAVEL--SPSEFETWYQLAECYIQLGDFENALLALNSCPM  296 (395)
T ss_pred             hcCCHHHHHHHHHHHHHh--CchhHHHHHHHHHHHHhcCCHHHHHHHHhcCcC
Confidence            777777777777777764  443 34677777777777777777776665543

They physically interact with Chs3, Chs5 and the small GTPase Arf1, and they also form interactions with each other [].

>PF13812 PPR_3: Pentatricopeptide repeat domain

Probab=98.18  E-value=3.4e-06  Score=47.10  Aligned_cols=33  Identities=33%  Similarity=0.508  Sum_probs=22.9

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC
Q 012111          397 PFFNCIISAYGQAGDVEKMGELFLTMKERHCVP  429 (471)
Q Consensus       397 ~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p  429 (471)
                      .+|+.++.+|.+.|+++.|.++|++|.+.|+.|
T Consensus         2 ~ty~~ll~a~~~~g~~~~a~~~~~~M~~~gv~P   34 (34)
T PF13812_consen    2 HTYNALLRACAKAGDPDAALQLFDEMKEQGVKP   34 (34)
T ss_pred             cHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCC
Confidence            356777777777777777777777777766665

>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF

Probab=98.17  E-value=7.7e-05  Score=56.19  Aligned_cols=102  Identities=15%  Similarity=0.076  Sum_probs=53.2

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhCCCC--cCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCC--CCCHHHHHHHH
Q 012111          363 TYCSLVSAYSKAGLIMKVDSILRQVENSDVI--LDTPFFNCIISAYGQAGDVEKMGELFLTMKERHC--VPDNITFATMI  438 (471)
Q Consensus       363 ~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~--~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~--~p~~~~~~~l~  438 (471)
                      ++..++..+.+.|++++|.+.+..+.+..+.  .....+..+..++...|++++|...|+.+....-  ......+..+.
T Consensus         4 ~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~~~~~~   83 (119)
T TIGR02795         4 AYYDAALLVLKAGDYADAIQAFQAFLKKYPKSTYAPNAHYWLGEAYYAQGKYADAAKAFLAVVKKYPKSPKAPDALLKLG   83 (119)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCccccHHHHHHHHHHHHhhccHHHHHHHHHHHHHHCCCCCcccHHHHHHH
Confidence            3444455555556666666666555543221  0123444455566666666666666666554310  01133445555


Q ss_pred             HHHHhcCCHHHHHHHHHHHHHhhhcC
Q 012111          439 QAYNALGMTEAAQNLENKMIAMKENS  464 (471)
Q Consensus       439 ~~~~~~g~~~~A~~~~~~m~~~~~~~  464 (471)
                      .++.+.|+.++|.+.++++++..|++
T Consensus        84 ~~~~~~~~~~~A~~~~~~~~~~~p~~  109 (119)
T TIGR02795        84 MSLQELGDKEKAKATLQQVIKRYPGS  109 (119)
T ss_pred             HHHHHhCChHHHHHHHHHHHHHCcCC
Confidence            55666666666666666666665543

Members of this protein family are the product of one of seven genes regularly clustered in operons to encode the proteins of the tol-pal system, which is critical for maintaining the integrity of the bacterial outer membrane. The gene for this periplasmic protein has been designated orf2 and ybgF. All members of the seed alignment were from unique tol-pal gene regions from completed bacterial genomes. The architecture of this protein is a signal sequence, a low-complexity region usually rich in Asn and Gln, a well-conserved region with tandem repeats that resemble the tetratricopeptide (TPR) repeat, involved in protein-protein interaction.

>cd00189 TPR Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and C

Probab=98.13  E-value=6.5e-05  Score=53.74  Aligned_cols=97  Identities=19%  Similarity=0.148  Sum_probs=57.1

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHh
Q 012111          364 YCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAYNA  443 (471)
Q Consensus       364 ~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~  443 (471)
                      +..+...+...|++++|...++.+.+.... +...+..+...+...|++++|.+.++...+.. +.+..++..+...+..
T Consensus         3 ~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~~~~~~~   80 (100)
T cd00189           3 LLNLGNLYYKLGDYDEALEYYEKALELDPD-NADAYYNLAAAYYKLGKYEEALEDYEKALELD-PDNAKAYYNLGLAYYK   80 (100)
T ss_pred             HHHHHHHHHHHhcHHHHHHHHHHHHhcCCc-cHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC-CcchhHHHHHHHHHHH
Confidence            334455555566666666666666554332 33455556666666666777777666666542 2233455566666666


Q ss_pred             cCCHHHHHHHHHHHHHhhh
Q 012111          444 LGMTEAAQNLENKMIAMKE  462 (471)
Q Consensus       444 ~g~~~~A~~~~~~m~~~~~  462 (471)
                      .|+++.|...+++.++..|
T Consensus        81 ~~~~~~a~~~~~~~~~~~~   99 (100)
T cd00189          81 LGKYEEALEAYEKALELDP   99 (100)
T ss_pred             HHhHHHHHHHHHHHHccCC
Confidence            6777777777666665443

>KOG2053 consensus Mitochondrial inheritance and actin cytoskeleton organization protein [Cytoskeleton]

Probab=98.12  E-value=0.011  Score=57.65  Aligned_cols=193  Identities=12%  Similarity=0.037  Sum_probs=123.4

Q ss_pred             HHHHHHhhHHHHHHHHHhhhhhhccCCCchHHHHHHHHH-HHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCC
Q 012111           50 DLSKILRTEFAIKNIEKKVSSKKYKNLWPKPVLEALDEA-IKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCK  128 (471)
Q Consensus        50 ~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~-~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  128 (471)
                      .+.+.++..++...++..-.    ...+.+..++.+..+ ...++.++|..+|+.+.+..   |+.+....+..+|.+.+
T Consensus        52 sl~r~gk~~ea~~~Le~~~~----~~~~D~~tLq~l~~~y~d~~~~d~~~~~Ye~~~~~~---P~eell~~lFmayvR~~  124 (932)
T KOG2053|consen   52 SLFRLGKGDEALKLLEALYG----LKGTDDLTLQFLQNVYRDLGKLDEAVHLYERANQKY---PSEELLYHLFMAYVREK  124 (932)
T ss_pred             HHHHhcCchhHHHHHhhhcc----CCCCchHHHHHHHHHHHHHhhhhHHHHHHHHHHhhC---CcHHHHHHHHHHHHHHH
Confidence            34667777777744443322    222234444445444 46799999999999999874   66888888889999998


Q ss_pred             CHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcC-C---------HHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhc
Q 012111          129 QPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSG-L---------LDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKF  198 (471)
Q Consensus       129 ~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~-~---------~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~  198 (471)
                      ++.+-.++--+|-+. ++-+...+=+++..+...- .         ..-|...++.+.+..|---+..-...-...+...
T Consensus       125 ~yk~qQkaa~~LyK~-~pk~~yyfWsV~Slilqs~~~~~~~~~~i~l~LA~~m~~~~l~~~gk~~s~aE~~Lyl~iL~~~  203 (932)
T KOG2053|consen  125 SYKKQQKAALQLYKN-FPKRAYYFWSVISLILQSIFSENELLDPILLALAEKMVQKLLEKKGKIESEAEIILYLLILELQ  203 (932)
T ss_pred             HHHHHHHHHHHHHHh-CCcccchHHHHHHHHHHhccCCcccccchhHHHHHHHHHHHhccCCccchHHHHHHHHHHHHhc
Confidence            887665555555443 2223333334444443321 1         2346667777776444222222233344455677


Q ss_pred             CCHHHHHHHH-HHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHcC
Q 012111          199 HRFDLIEKIL-AEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESG  250 (471)
Q Consensus       199 ~~~~~a~~~~-~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  250 (471)
                      |.+++|..++ ....+.-...+...-+.-+..+...+++.+..++-.++...+
T Consensus       204 ~k~~eal~~l~~~la~~l~~~~~~l~~~~~dllk~l~~w~~l~~l~~~Ll~k~  256 (932)
T KOG2053|consen  204 GKYQEALEFLAITLAEKLTSANLYLENKKLDLLKLLNRWQELFELSSRLLEKG  256 (932)
T ss_pred             ccHHHHHHHHHHHHHHhccccchHHHHHHHHHHHHhcChHHHHHHHHHHHHhC
Confidence            8899999999 444444444566666778889999999999999999998875

>PF10037 MRP-S27: Mitochondrial 28S ribosomal protein S27; InterPro: IPR019266 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=98.12  E-value=5.9e-05  Score=68.67  Aligned_cols=121  Identities=11%  Similarity=0.141  Sum_probs=65.8

Q ss_pred             CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhC--CCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHH
Q 012111          288 KADIQTLNILTKSYGRAGMYDKMRSVMDFMQKR--FFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYC  365 (471)
Q Consensus       288 ~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~--~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~  365 (471)
                      +.+......+++.+....+.+.+..++.+.+..  ....-..|..++++.|...|..+.++.++..=...|+-||..+++
T Consensus        63 ~vS~~dld~fvn~~~~~~~~d~~~~~L~k~R~s~~~~~~~~~t~ha~vR~~l~~~~~~~~l~~L~n~~~yGiF~D~~s~n  142 (429)
T PF10037_consen   63 PVSSLDLDIFVNNVESKDDLDEVEDVLYKFRHSPNCSYLLPSTHHALVRQCLELGAEDELLELLKNRLQYGIFPDNFSFN  142 (429)
T ss_pred             CCcHHHHHHHHhhcCCHhHHHHHHHHHHHHHcCcccccccCccHHHHHHHHHhcCCHHHHHHHHhChhhcccCCChhhHH
Confidence            445555555555555555566666655555443  111122333456666666666666666666655666666666666


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHh
Q 012111          366 SLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQ  408 (471)
Q Consensus       366 ~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  408 (471)
                      .|+..+.+.|++..|.++...|...+...+..++..-+.+|.+
T Consensus       143 ~Lmd~fl~~~~~~~A~~V~~~~~lQe~~~~~~t~~L~l~~~~~  185 (429)
T PF10037_consen  143 LLMDHFLKKGNYKSAAKVATEMMLQEEFDNPSTQALALYSCYK  185 (429)
T ss_pred             HHHHHHhhcccHHHHHHHHHHHHHhhccCCchHHHHHHHHHHH
Confidence            6666666666666666666555544444444444444444443

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 small ribosomal proteins possessing one of three conserved sequence blocks found in proteins that stimulate the dissociation of guanine nucleotides from G-proteins. This leaves open the possibility that they may be functional partners of GTP-binding ribosomal proteins [].

>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif)

Probab=98.11  E-value=6.7e-06  Score=46.25  Aligned_cols=33  Identities=45%  Similarity=0.813  Sum_probs=21.8

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCC
Q 012111          328 TYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPN  360 (471)
Q Consensus       328 ~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~  360 (471)
                      +|+.+|.+|++.|++++|.++|++|.+.|+.||
T Consensus         2 ~~n~li~~~~~~~~~~~a~~~~~~M~~~g~~p~   34 (35)
T TIGR00756         2 TYNTLIDGLCKAGRVEEALELFKEMLERGIEPD   34 (35)
T ss_pred             cHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCC
Confidence            466666666666666666666666666666665

This family has a similar consensus to the TPR domain (tetratricopeptide), pfam pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR.

>PF09976 TPR_21: Tetratricopeptide repeat; InterPro: IPR018704 This domain, found in various hypothetical prokaryotic proteins, has no known function

Probab=98.07  E-value=0.00037  Score=54.52  Aligned_cols=116  Identities=14%  Similarity=0.056  Sum_probs=62.3

Q ss_pred             HhhcHHHHHHHHHHhhhccCccCC---hhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCH--HHHHHHHHHHHhcCC
Q 012111           90 KQKKWQLALKIFGLLRQQQWYQAR---CQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSV--DVYTALVSAYGQSGL  164 (471)
Q Consensus        90 ~~~~~~~A~~~~~~~~~~~~~~~~---~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~--~~~~~li~~~~~~~~  164 (471)
                      ..+++..+.+.++.+....  +.+   ....-.+...+...|++++|...|+........++.  ...-.|...+...|+
T Consensus        23 ~~~~~~~~~~~~~~l~~~~--~~s~ya~~A~l~lA~~~~~~g~~~~A~~~l~~~~~~~~d~~l~~~a~l~LA~~~~~~~~  100 (145)
T PF09976_consen   23 QAGDPAKAEAAAEQLAKDY--PSSPYAALAALQLAKAAYEQGDYDEAKAALEKALANAPDPELKPLARLRLARILLQQGQ  100 (145)
T ss_pred             HCCCHHHHHHHHHHHHHHC--CCChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCCCHHHHHHHHHHHHHHHHHcCC
Confidence            4566666666666666543  222   222333445566666666666666666665422221  123334556666666


Q ss_pred             HHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHH
Q 012111          165 LDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAE  210 (471)
Q Consensus       165 ~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~  210 (471)
                      +++|+..++....   -......+......+.+.|+.++|...|+.
T Consensus       101 ~d~Al~~L~~~~~---~~~~~~~~~~~Gdi~~~~g~~~~A~~~y~~  143 (145)
T PF09976_consen  101 YDEALATLQQIPD---EAFKALAAELLGDIYLAQGDYDEARAAYQK  143 (145)
T ss_pred             HHHHHHHHHhccC---cchHHHHHHHHHHHHHHCCCHHHHHHHHHH
Confidence            6666666655332   123334455555566666666666666554

>PF13812 PPR_3: Pentatricopeptide repeat domain

Probab=98.06  E-value=8.8e-06  Score=45.40  Aligned_cols=32  Identities=38%  Similarity=0.690  Sum_probs=16.2

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCC
Q 012111          328 TYNIVIETFGKAGHIEKMEEYFKKMKHRGMKP  359 (471)
Q Consensus       328 ~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p  359 (471)
                      +|+.++.+|++.|+++.|.++|+.|.+.|++|
T Consensus         3 ty~~ll~a~~~~g~~~~a~~~~~~M~~~gv~P   34 (34)
T PF13812_consen    3 TYNALLRACAKAGDPDAALQLFDEMKEQGVKP   34 (34)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCC
Confidence            44555555555555555555555555554444

>PRK10866 outer membrane biogenesis protein BamD; Provisional

Probab=98.05  E-value=0.0039  Score=53.28  Aligned_cols=185  Identities=11%  Similarity=0.035  Sum_probs=104.9

Q ss_pred             CchHHHHHHHHHHHhhcHHHHHHHHHHhhhccCccCChhH---HHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHH
Q 012111           77 WPKPVLEALDEAIKQKKWQLALKIFGLLRQQQWYQARCQT---FTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYT  153 (471)
Q Consensus        77 ~~~~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~---~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~  153 (471)
                      ++.........+...|++++|++.|+.+....  |-+...   .-.++.++.+.+++++|...+++..+.-+.-...-|.
T Consensus        31 ~~~~~Y~~A~~~~~~g~y~~Ai~~f~~l~~~y--P~s~~a~~a~l~la~ayy~~~~y~~A~~~~e~fi~~~P~~~~~~~a  108 (243)
T PRK10866         31 PPSEIYATAQQKLQDGNWKQAITQLEALDNRY--PFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPNIDYV  108 (243)
T ss_pred             CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC--CCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCcCCCchHHH
Confidence            44455555666678899999999999988764  333322   2466677888899999999998888764332222333


Q ss_pred             HHHHHHHh--cC---------------C---HHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 012111          154 ALVSAYGQ--SG---------------L---LDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSY  213 (471)
Q Consensus       154 ~li~~~~~--~~---------------~---~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~  213 (471)
                      ..+.+.+.  .+               +   ...|+..|+.+.+                -|-...-..+|...+..+..
T Consensus       109 ~Y~~g~~~~~~~~~~~~~~~~~~~~~rD~~~~~~A~~~~~~li~----------------~yP~S~ya~~A~~rl~~l~~  172 (243)
T PRK10866        109 LYMRGLTNMALDDSALQGFFGVDRSDRDPQHARAAFRDFSKLVR----------------GYPNSQYTTDATKRLVFLKD  172 (243)
T ss_pred             HHHHHHhhhhcchhhhhhccCCCccccCHHHHHHHHHHHHHHHH----------------HCcCChhHHHHHHHHHHHHH
Confidence            33333321  11               1   1233334444333                22222233344443333322


Q ss_pred             CCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCC-CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 012111          214 LGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGC-HPDIFTLNSMISAYGNSGNIEKMEKWYNEFN  283 (471)
Q Consensus       214 ~g~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  283 (471)
                      .    =...-..+.+.|.+.|.+..|..-++.+.+...- +........++.+|...|..++|..+...+.
T Consensus       173 ~----la~~e~~ia~~Y~~~~~y~AA~~r~~~v~~~Yp~t~~~~eal~~l~~ay~~lg~~~~a~~~~~~l~  239 (243)
T PRK10866        173 R----LAKYELSVAEYYTKRGAYVAVVNRVEQMLRDYPDTQATRDALPLMENAYRQLQLNAQADKVAKIIA  239 (243)
T ss_pred             H----HHHHHHHHHHHHHHcCchHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHcCChHHHHHHHHHHh
Confidence            1    0111124566677888888888888888765422 2223455566677777788777777666543

>PF08579 RPM2: Mitochondrial ribonuclease P subunit (RPM2); InterPro: IPR013888 Ribonuclease P (RNase P) generates mature tRNA molecules by cleaving their 5' ends

Probab=98.01  E-value=0.00014  Score=51.75  Aligned_cols=69  Identities=4%  Similarity=0.227  Sum_probs=35.6

Q ss_pred             CCHHHHHHHHHHHHhCCC-CcCHHHHHHHHHHHHhc--------CCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHh
Q 012111          375 GLIMKVDSILRQVENSDV-ILDTPFFNCIISAYGQA--------GDVEKMGELFLTMKERHCVPDNITFATMIQAYNA  443 (471)
Q Consensus       375 g~~~~a~~~~~~~~~~~~-~~~~~~~~~l~~~~~~~--------g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~  443 (471)
                      +++.....+|+.+++.|+ .|+..+|+.++.+.++.        ++.-..+.+|+.|...+++|+..+|+.++..+.+
T Consensus        39 ~d~N~I~~lYqslkRN~i~lPsv~~Yn~VL~Si~~R~lD~~~ie~kl~~LLtvYqDiL~~~lKP~~etYnivl~~Llk  116 (120)
T PF08579_consen   39 EDYNIINPLYQSLKRNGITLPSVELYNKVLKSIAKRELDSEDIENKLTNLLTVYQDILSNKLKPNDETYNIVLGSLLK  116 (120)
T ss_pred             cchHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHccccchhHHHHHHHHHHHHHHHHHhccCCcHHHHHHHHHHHHH
Confidence            444444444444444444 34444444444433322        1233455666677766677777777777666544

Rpm2 is a protein subunit of the yeast mitochondrial RNase P. It has the ability to act as a transcriptional activator in the nucleus, where it plays a role in defining the steady-state levels of mRNAs for some nucleus-encoded mitochondrial components. Rpm2p is also involved in maturation of Rpm1 and in translation of mitochondrial mRNAs [, , ].

>PF10037 MRP-S27: Mitochondrial 28S ribosomal protein S27; InterPro: IPR019266 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=98.01  E-value=0.00013  Score=66.53  Aligned_cols=123  Identities=14%  Similarity=0.147  Sum_probs=106.2

Q ss_pred             CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhC--CCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHH
Q 012111          252 CHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLM--GVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTY  329 (471)
Q Consensus       252 ~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~--~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~  329 (471)
                      .+.+......+++.+....+.+.+..++.++...  ....-..|..++++.|.+.|..+.+..++..=...|+-||..++
T Consensus        62 ~~vS~~dld~fvn~~~~~~~~d~~~~~L~k~R~s~~~~~~~~~t~ha~vR~~l~~~~~~~~l~~L~n~~~yGiF~D~~s~  141 (429)
T PF10037_consen   62 KPVSSLDLDIFVNNVESKDDLDEVEDVLYKFRHSPNCSYLLPSTHHALVRQCLELGAEDELLELLKNRLQYGIFPDNFSF  141 (429)
T ss_pred             CCCcHHHHHHHHhhcCCHhHHHHHHHHHHHHHcCcccccccCccHHHHHHHHHhcCCHHHHHHHHhChhhcccCCChhhH
Confidence            4567778888999999999999999999998765  22233456679999999999999999999999999999999999


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhc
Q 012111          330 NIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKA  374 (471)
Q Consensus       330 ~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~  374 (471)
                      +.||..+.+.|++..|.++...|...+...+..|+..-+.+|.+.
T Consensus       142 n~Lmd~fl~~~~~~~A~~V~~~~~lQe~~~~~~t~~L~l~~~~~~  186 (429)
T PF10037_consen  142 NLLMDHFLKKGNYKSAAKVATEMMLQEEFDNPSTQALALYSCYKY  186 (429)
T ss_pred             HHHHHHHhhcccHHHHHHHHHHHHHhhccCCchHHHHHHHHHHHh
Confidence            999999999999999999999999887777778887777777665

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 small ribosomal proteins possessing one of three conserved sequence blocks found in proteins that stimulate the dissociation of guanine nucleotides from G-proteins. This leaves open the possibility that they may be functional partners of GTP-binding ribosomal proteins [].

>PRK15363 pathogenicity island 2 chaperone protein SscA; Provisional

Probab=97.96  E-value=0.00034  Score=53.83  Aligned_cols=91  Identities=4%  Similarity=-0.122  Sum_probs=51.6

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCC
Q 012111          332 VIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGD  411 (471)
Q Consensus       332 li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~  411 (471)
                      +...+...|++++|..+|+.+.... +-+..-|..|..++-..|++++|+..|......++. |+..+-.+..++...|+
T Consensus        41 ~A~~ly~~G~l~~A~~~f~~L~~~D-p~~~~y~~gLG~~~Q~~g~~~~AI~aY~~A~~L~~d-dp~~~~~ag~c~L~lG~  118 (157)
T PRK15363         41 YAMQLMEVKEFAGAARLFQLLTIYD-AWSFDYWFRLGECCQAQKHWGEAIYAYGRAAQIKID-APQAPWAAAECYLACDN  118 (157)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCC-CchHHHHHHHHHHHcCC
Confidence            3444455666666666666555532 113444455555555666666666666666655543 55555556666666666


Q ss_pred             HHHHHHHHHHHHh
Q 012111          412 VEKMGELFLTMKE  424 (471)
Q Consensus       412 ~~~a~~~~~~~~~  424 (471)
                      .+.|.+.|+..+.
T Consensus       119 ~~~A~~aF~~Ai~  131 (157)
T PRK15363        119 VCYAIKALKAVVR  131 (157)
T ss_pred             HHHHHHHHHHHHH
Confidence            6666666665544

>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF

Probab=97.94  E-value=0.00041  Score=52.17  Aligned_cols=98  Identities=13%  Similarity=0.012  Sum_probs=59.7

Q ss_pred             HHHHHHHHHHHhhcHHHHHHHHHHhhhccCc-cCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCC--CCHHHHHHHH
Q 012111           80 PVLEALDEAIKQKKWQLALKIFGLLRQQQWY-QARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLK--PSVDVYTALV  156 (471)
Q Consensus        80 ~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~--~~~~~~~~li  156 (471)
                      .+......+.+.|++++|.+.|+.+.+..+- +.....+..+..++.+.|+++.|...|+.+......  ....++..+.
T Consensus         4 ~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~~~~~~   83 (119)
T TIGR02795         4 AYYDAALLVLKAGDYADAIQAFQAFLKKYPKSTYAPNAHYWLGEAYYAQGKYADAAKAFLAVVKKYPKSPKAPDALLKLG   83 (119)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCccccHHHHHHHHHHHHhhccHHHHHHHHHHHHHHCCCCCcccHHHHHHH
Confidence            4445555566777777777777777654310 111345556667777777777777777776654221  1234566666


Q ss_pred             HHHHhcCCHHHHHHHHHHhhc
Q 012111          157 SAYGQSGLLDEAFSTINDMKS  177 (471)
Q Consensus       157 ~~~~~~~~~~~a~~~~~~~~~  177 (471)
                      .++...|+.++|...++++..
T Consensus        84 ~~~~~~~~~~~A~~~~~~~~~  104 (119)
T TIGR02795        84 MSLQELGDKEKAKATLQQVIK  104 (119)
T ss_pred             HHHHHhCChHHHHHHHHHHHH
Confidence            666677777777777777665

Members of this protein family are the product of one of seven genes regularly clustered in operons to encode the proteins of the tol-pal system, which is critical for maintaining the integrity of the bacterial outer membrane. The gene for this periplasmic protein has been designated orf2 and ybgF. All members of the seed alignment were from unique tol-pal gene regions from completed bacterial genomes. The architecture of this protein is a signal sequence, a low-complexity region usually rich in Asn and Gln, a well-conserved region with tandem repeats that resemble the tetratricopeptide (TPR) repeat, involved in protein-protein interaction.

>PLN03088 SGT1, suppressor of G2 allele of SKP1; Provisional

Probab=97.93  E-value=0.00031  Score=63.93  Aligned_cols=94  Identities=11%  Similarity=0.014  Sum_probs=80.4

Q ss_pred             HHHHHHHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHh
Q 012111           82 LEALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQ  161 (471)
Q Consensus        82 ~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~  161 (471)
                      ......+...|++++|++.|+.+.+..  +.+...|..+..++...|++++|+..++..+..... +...|..+..+|..
T Consensus         6 ~~~a~~a~~~~~~~~Ai~~~~~Al~~~--P~~~~a~~~~a~~~~~~g~~~eAl~~~~~Al~l~P~-~~~a~~~lg~~~~~   82 (356)
T PLN03088          6 EDKAKEAFVDDDFALAVDLYTQAIDLD--PNNAELYADRAQANIKLGNFTEAVADANKAIELDPS-LAKAYLRKGTACMK   82 (356)
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcC-CHHHHHHHHHHHHH
Confidence            334556678999999999999999876  667788999999999999999999999999887533 67788889999999


Q ss_pred             cCCHHHHHHHHHHhhcC
Q 012111          162 SGLLDEAFSTINDMKSV  178 (471)
Q Consensus       162 ~~~~~~a~~~~~~~~~~  178 (471)
                      .|++++|+..|++....
T Consensus        83 lg~~~eA~~~~~~al~l   99 (356)
T PLN03088         83 LEEYQTAKAALEKGASL   99 (356)
T ss_pred             hCCHHHHHHHHHHHHHh
Confidence            99999999999998873

>PF12895 Apc3: Anaphase-promoting complex, cyclosome, subunit 3; PDB: 3KAE_D 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2XPI_A 3ULQ_A

Probab=97.93  E-value=2.8e-05  Score=54.26  Aligned_cols=80  Identities=18%  Similarity=0.140  Sum_probs=48.4

Q ss_pred             cCCHHHHHHHHHHHHhCCCC-cCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCC-HHHHHHHHHHHHhcCCHHHHH
Q 012111          374 AGLIMKVDSILRQVENSDVI-LDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPD-NITFATMIQAYNALGMTEAAQ  451 (471)
Q Consensus       374 ~g~~~~a~~~~~~~~~~~~~-~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~-~~~~~~l~~~~~~~g~~~~A~  451 (471)
                      .|+++.|+.+++++.+..+. ++...+-.+..+|.+.|++++|..+++. .+  ..|+ ......+..+|.+.|++++|.
T Consensus         2 ~~~y~~Ai~~~~k~~~~~~~~~~~~~~~~la~~~~~~~~y~~A~~~~~~-~~--~~~~~~~~~~l~a~~~~~l~~y~eAi   78 (84)
T PF12895_consen    2 QGNYENAIKYYEKLLELDPTNPNSAYLYNLAQCYFQQGKYEEAIELLQK-LK--LDPSNPDIHYLLARCLLKLGKYEEAI   78 (84)
T ss_dssp             TT-HHHHHHHHHHHHHHHCGTHHHHHHHHHHHHHHHTTHHHHHHHHHHC-HT--HHHCHHHHHHHHHHHHHHTT-HHHHH
T ss_pred             CccHHHHHHHHHHHHHHCCCChhHHHHHHHHHHHHHCCCHHHHHHHHHH-hC--CCCCCHHHHHHHHHHHHHhCCHHHHH
Confidence            46677777777777765442 2344445567777777777777777766 22  1222 233344457777777777777


Q ss_pred             HHHHH
Q 012111          452 NLENK  456 (471)
Q Consensus       452 ~~~~~  456 (471)
                      +.+++
T Consensus        79 ~~l~~   83 (84)
T PF12895_consen   79 KALEK   83 (84)
T ss_dssp             HHHHH
T ss_pred             HHHhc
Confidence            77765

>PF08579 RPM2: Mitochondrial ribonuclease P subunit (RPM2); InterPro: IPR013888 Ribonuclease P (RNase P) generates mature tRNA molecules by cleaving their 5' ends

Probab=97.93  E-value=0.00025  Score=50.51  Aligned_cols=75  Identities=9%  Similarity=0.247  Sum_probs=38.0

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHHcCC-CCCHHHHHHHHHHHHhcC--------CHHHHHHHHHHHHhCCCCcCHHHHHHHH
Q 012111          333 IETFGKAGHIEKMEEYFKKMKHRGM-KPNSITYCSLVSAYSKAG--------LIMKVDSILRQVENSDVILDTPFFNCII  403 (471)
Q Consensus       333 i~~~~~~g~~~~a~~~~~~m~~~~~-~p~~~~~~~li~~~~~~g--------~~~~a~~~~~~~~~~~~~~~~~~~~~l~  403 (471)
                      |..+...+++.....+|+.+++.|+ .|+..+|+.++.+.++..        ++-..+.+|+.|...+++|+..+|+.++
T Consensus        32 I~~~~~~~d~N~I~~lYqslkRN~i~lPsv~~Yn~VL~Si~~R~lD~~~ie~kl~~LLtvYqDiL~~~lKP~~etYnivl  111 (120)
T PF08579_consen   32 INSCFENEDYNIINPLYQSLKRNGITLPSVELYNKVLKSIAKRELDSEDIENKLTNLLTVYQDILSNKLKPNDETYNIVL  111 (120)
T ss_pred             HHHHHhhcchHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHccccchhHHHHHHHHHHHHHHHHHhccCCcHHHHHHHH
Confidence            3333344555555555555555555 555555555555544332        1223445555555555555555555555


Q ss_pred             HHHH
Q 012111          404 SAYG  407 (471)
Q Consensus       404 ~~~~  407 (471)
                      ..+.
T Consensus       112 ~~Ll  115 (120)
T PF08579_consen  112 GSLL  115 (120)
T ss_pred             HHHH
Confidence            5544

Rpm2 is a protein subunit of the yeast mitochondrial RNase P. It has the ability to act as a transcriptional activator in the nucleus, where it plays a role in defining the steady-state levels of mRNAs for some nucleus-encoded mitochondrial components. Rpm2p is also involved in maturation of Rpm1 and in translation of mitochondrial mRNAs [, , ].

>PLN03088 SGT1, suppressor of G2 allele of SKP1; Provisional

Probab=97.91  E-value=0.00032  Score=63.88  Aligned_cols=103  Identities=10%  Similarity=-0.002  Sum_probs=86.0

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCC
Q 012111          332 VIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGD  411 (471)
Q Consensus       332 li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~  411 (471)
                      -...+...|++++|+..|.+++... +-+...|..+..+|...|++++|...++++.+.++. +...|..+..+|...|+
T Consensus         8 ~a~~a~~~~~~~~Ai~~~~~Al~~~-P~~~~a~~~~a~~~~~~g~~~eAl~~~~~Al~l~P~-~~~a~~~lg~~~~~lg~   85 (356)
T PLN03088          8 KAKEAFVDDDFALAVDLYTQAIDLD-PNNAELYADRAQANIKLGNFTEAVADANKAIELDPS-LAKAYLRKGTACMKLEE   85 (356)
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcC-CHHHHHHHHHHHHHhCC
Confidence            3456678899999999999999864 346778888999999999999999999999988765 77888899999999999


Q ss_pred             HHHHHHHHHHHHhCCCCCCHHHHHHHH
Q 012111          412 VEKMGELFLTMKERHCVPDNITFATMI  438 (471)
Q Consensus       412 ~~~a~~~~~~~~~~~~~p~~~~~~~l~  438 (471)
                      +++|+..|++..+.  .|+.......+
T Consensus        86 ~~eA~~~~~~al~l--~P~~~~~~~~l  110 (356)
T PLN03088         86 YQTAKAALEKGASL--APGDSRFTKLI  110 (356)
T ss_pred             HHHHHHHHHHHHHh--CCCCHHHHHHH
Confidence            99999999999974  56655554444

>PF14938 SNAP: Soluble NSF attachment protein, SNAP; PDB: 1QQE_A 2IFU_A

Probab=97.90  E-value=0.0018  Score=57.15  Aligned_cols=124  Identities=15%  Similarity=0.172  Sum_probs=54.5

Q ss_pred             HHHhc-CCHHHHHHHHHHHHHc----CCCC--CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCc-----CHH-HHHH
Q 012111          335 TFGKA-GHIEKMEEYFKKMKHR----GMKP--NSITYCSLVSAYSKAGLIMKVDSILRQVENSDVIL-----DTP-FFNC  401 (471)
Q Consensus       335 ~~~~~-g~~~~a~~~~~~m~~~----~~~p--~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~-----~~~-~~~~  401 (471)
                      .|... |++++|++.|++....    + .+  -..++..+...+.+.|++++|.++|+++.......     +.. .|-.
T Consensus       123 ~ye~~~~d~e~Ai~~Y~~A~~~y~~e~-~~~~a~~~~~~~A~l~~~l~~y~~A~~~~e~~~~~~l~~~l~~~~~~~~~l~  201 (282)
T PF14938_consen  123 IYEEQLGDYEKAIEYYQKAAELYEQEG-SPHSAAECLLKAADLYARLGRYEEAIEIYEEVAKKCLENNLLKYSAKEYFLK  201 (282)
T ss_dssp             HHCCTT--HHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTCCCHCTTGHHHHHHHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHHHHHHCC-ChhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHhhcccccchhHHHHHHH
Confidence            34444 5556666655554432    1 11  12234455556666666666666666655432211     111 1222


Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHhC--CCCCC--HHHHHHHHHHHHhc--CCHHHHHHHHHHHHH
Q 012111          402 IISAYGQAGDVEKMGELFLTMKER--HCVPD--NITFATMIQAYNAL--GMTEAAQNLENKMIA  459 (471)
Q Consensus       402 l~~~~~~~g~~~~a~~~~~~~~~~--~~~p~--~~~~~~l~~~~~~~--g~~~~A~~~~~~m~~  459 (471)
                      .+-++...||...|.+.+++....  ++..+  ......|+.++-..  ..++.|..-|+.+.+
T Consensus       202 a~l~~L~~~D~v~A~~~~~~~~~~~~~F~~s~E~~~~~~l~~A~~~~D~e~f~~av~~~d~~~~  265 (282)
T PF14938_consen  202 AILCHLAMGDYVAARKALERYCSQDPSFASSREYKFLEDLLEAYEEGDVEAFTEAVAEYDSISR  265 (282)
T ss_dssp             HHHHHHHTT-HHHHHHHHHHHGTTSTTSTTSHHHHHHHHHHHHHHTT-CCCHHHHCHHHTTSS-
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHhhCCCCCCcHHHHHHHHHHHHHHhCCHHHHHHHHHHHcccCc
Confidence            233445556666666666666543  12212  23344455555322  235555544444433

>cd00189 TPR Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and C

Probab=97.89  E-value=0.00044  Score=49.30  Aligned_cols=94  Identities=20%  Similarity=0.179  Sum_probs=60.6

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHh
Q 012111          329 YNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQ  408 (471)
Q Consensus       329 ~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  408 (471)
                      +..+...+...|++++|...++...+.. +.+...+..+...+...|++++|.+.++...+.... +..++..+...+..
T Consensus         3 ~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~~~~~~~~   80 (100)
T cd00189           3 LLNLGNLYYKLGDYDEALEYYEKALELD-PDNADAYYNLAAAYYKLGKYEEALEDYEKALELDPD-NAKAYYNLGLAYYK   80 (100)
T ss_pred             HHHHHHHHHHHhcHHHHHHHHHHHHhcC-CccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCc-chhHHHHHHHHHHH
Confidence            3345555666677777777777666542 223355666666677777777777777776665443 44566666677777


Q ss_pred             cCCHHHHHHHHHHHHh
Q 012111          409 AGDVEKMGELFLTMKE  424 (471)
Q Consensus       409 ~g~~~~a~~~~~~~~~  424 (471)
                      .|+++.|...+....+
T Consensus        81 ~~~~~~a~~~~~~~~~   96 (100)
T cd00189          81 LGKYEEALEAYEKALE   96 (100)
T ss_pred             HHhHHHHHHHHHHHHc
Confidence            7777777777776654

>PF05843 Suf: Suppressor of forked protein (Suf); InterPro: IPR008847 This domain consists of several eukaryotic suppressor of forked (Suf) like proteins

Probab=97.88  E-value=0.00049  Score=60.35  Aligned_cols=131  Identities=11%  Similarity=0.070  Sum_probs=81.2

Q ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHH-HHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Q 012111          292 QTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIET-FGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSA  370 (471)
Q Consensus       292 ~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~-~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~  370 (471)
                      .+|..+++..-+.+..+.|..+|.+..+.+. .+...|...... +...++.+.|..+|+...+. +..+...|...+..
T Consensus         2 ~v~i~~m~~~~r~~g~~~aR~vF~~a~~~~~-~~~~vy~~~A~~E~~~~~d~~~A~~Ife~glk~-f~~~~~~~~~Y~~~   79 (280)
T PF05843_consen    2 LVWIQYMRFMRRTEGIEAARKVFKRARKDKR-CTYHVYVAYALMEYYCNKDPKRARKIFERGLKK-FPSDPDFWLEYLDF   79 (280)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC-S-THHHHHHHHHHHHTCS-HHHHHHHHHHHHHH-HTT-HHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCChHHHHHHHHHHHcCCC-CCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHH-CCCCHHHHHHHHHH
Confidence            3566777777777777778888877775422 233344443333 22245666677777777765 34466667777777


Q ss_pred             HHhcCCHHHHHHHHHHHHhCCCCcC---HHHHHHHHHHHHhcCCHHHHHHHHHHHHhC
Q 012111          371 YSKAGLIMKVDSILRQVENSDVILD---TPFFNCIISAYGQAGDVEKMGELFLTMKER  425 (471)
Q Consensus       371 ~~~~g~~~~a~~~~~~~~~~~~~~~---~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~  425 (471)
                      +...|+.+.|..+|++.... +.++   ...|...+..=.+.|+.+.+.++.+++.+.
T Consensus        80 l~~~~d~~~aR~lfer~i~~-l~~~~~~~~iw~~~i~fE~~~Gdl~~v~~v~~R~~~~  136 (280)
T PF05843_consen   80 LIKLNDINNARALFERAISS-LPKEKQSKKIWKKFIEFESKYGDLESVRKVEKRAEEL  136 (280)
T ss_dssp             HHHTT-HHHHHHHHHHHCCT-SSCHHHCHHHHHHHHHHHHHHS-HHHHHHHHHHHHHH
T ss_pred             HHHhCcHHHHHHHHHHHHHh-cCchhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            77777777777777777654 2211   236777777777777777777777777763

The Drosophila melanogaster suppressor of forked [Su(f)] protein shares homology with the Saccharomyces cerevisiae RNA14 protein and the 77 kDa subunit of Homo sapiens cleavage stimulation factor, which are proteins involved in mRNA 3' end formation. This suggests a role for Su(f) in mRNA 3' end formation in Drosophila. The su(f) gene produces three transcripts; two of them are polyadenylated at the end of the transcription unit, and one is a truncated transcript, polyadenylated in intron 4. It is thought that su(f) plays a role in the regulation of poly(A) site utilisation and the GU-rich sequence is important for this regulation to occur [].; GO: 0006397 mRNA processing, 0005634 nucleus; PDB: 2L9B_B 2OND_B 2OOE_A 4E85_B 4EBA_C 4E6H_A 2UY1_B.

>PF12895 Apc3: Anaphase-promoting complex, cyclosome, subunit 3; PDB: 3KAE_D 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2XPI_A 3ULQ_A

Probab=97.88  E-value=3.2e-05  Score=53.94  Aligned_cols=82  Identities=17%  Similarity=0.127  Sum_probs=53.1

Q ss_pred             hhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHH
Q 012111           91 QKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAFS  170 (471)
Q Consensus        91 ~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~  170 (471)
                      .|+++.|+.+|+.+.+.....++...+..+..++.+.|++++|..+++. ...+. .+....-.+..++.+.|++++|++
T Consensus         2 ~~~y~~Ai~~~~k~~~~~~~~~~~~~~~~la~~~~~~~~y~~A~~~~~~-~~~~~-~~~~~~~l~a~~~~~l~~y~eAi~   79 (84)
T PF12895_consen    2 QGNYENAIKYYEKLLELDPTNPNSAYLYNLAQCYFQQGKYEEAIELLQK-LKLDP-SNPDIHYLLARCLLKLGKYEEAIK   79 (84)
T ss_dssp             TT-HHHHHHHHHHHHHHHCGTHHHHHHHHHHHHHHHTTHHHHHHHHHHC-HTHHH-CHHHHHHHHHHHHHHTT-HHHHHH
T ss_pred             CccHHHHHHHHHHHHHHCCCChhHHHHHHHHHHHHHCCCHHHHHHHHHH-hCCCC-CCHHHHHHHHHHHHHhCCHHHHHH
Confidence            5778888888888887642112344555577888888888888888877 32221 133444455777888888888888


Q ss_pred             HHHH
Q 012111          171 TIND  174 (471)
Q Consensus       171 ~~~~  174 (471)
                      +|++
T Consensus        80 ~l~~   83 (84)
T PF12895_consen   80 ALEK   83 (84)
T ss_dssp             HHHH
T ss_pred             HHhc
Confidence            7765

>PRK15363 pathogenicity island 2 chaperone protein SscA; Provisional

Probab=97.86  E-value=0.00087  Score=51.63  Aligned_cols=97  Identities=11%  Similarity=0.042  Sum_probs=79.0

Q ss_pred             HHHHHHHHHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHH
Q 012111           80 PVLEALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAY  159 (471)
Q Consensus        80 ~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~  159 (471)
                      .+-..-..+...|++++|.++|+.+...+  +.+..-|..|..++-..|++++|+..|.......+. ++..+-.+..++
T Consensus        37 ~lY~~A~~ly~~G~l~~A~~~f~~L~~~D--p~~~~y~~gLG~~~Q~~g~~~~AI~aY~~A~~L~~d-dp~~~~~ag~c~  113 (157)
T PRK15363         37 TLYRYAMQLMEVKEFAGAARLFQLLTIYD--AWSFDYWFRLGECCQAQKHWGEAIYAYGRAAQIKID-APQAPWAAAECY  113 (157)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHhC--cccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCC-CchHHHHHHHHH
Confidence            34445556678899999999999988865  566677888888888889999999999998888753 788888889999


Q ss_pred             HhcCCHHHHHHHHHHhhcCC
Q 012111          160 GQSGLLDEAFSTINDMKSVS  179 (471)
Q Consensus       160 ~~~~~~~~a~~~~~~~~~~~  179 (471)
                      ...|+.+.|.+.|+......
T Consensus       114 L~lG~~~~A~~aF~~Ai~~~  133 (157)
T PRK15363        114 LACDNVCYAIKALKAVVRIC  133 (157)
T ss_pred             HHcCCHHHHHHHHHHHHHHh
Confidence            99999999999998877643

>PF01535 PPR: PPR repeat; InterPro: IPR002885 This entry represents the PPR repeat

Probab=97.85  E-value=2.2e-05  Score=42.65  Aligned_cols=29  Identities=38%  Similarity=0.603  Sum_probs=16.6

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhCC
Q 012111          398 FFNCIISAYGQAGDVEKMGELFLTMKERH  426 (471)
Q Consensus       398 ~~~~l~~~~~~~g~~~~a~~~~~~~~~~~  426 (471)
                      +|+.++++|++.|++++|.++|++|.+.|
T Consensus         2 ~y~~li~~~~~~~~~~~a~~~~~~M~~~g   30 (31)
T PF01535_consen    2 TYNSLISGYCKMGQFEEALEVFDEMRERG   30 (31)
T ss_pred             cHHHHHHHHHccchHHHHHHHHHHHhHCc
Confidence            45555555555555555555555555544

Pentatricopeptide repeat (PPR) proteins are characterised by tandem repeats of a degenerate 35 amino acid motif []. Most of PPR proteins have roles in mitochondria or plastid []. PPR repeats were discovered while screening Arabidopsis proteins for those predicted to be targeted to mitochondria or chloroplast [, ]. Some of these proteins have been shown to play a role in post-transcriptional processes within organelles and they are thought to be sequence-specific RNA-binding proteins [, , ]. Plant genomes have between one hundred to five hundred PPR genes per genome whereas non-plant genomes encode two to six PPR proteins. Although no PPR structures are yet known, the motif is predicted to fold into a helix-turn-helix structure similar to those found in the tetratricopeptide repeat (TPR) family (see PDOC50005 from PROSITEDOC) []. The plant PPR protein family has been divided in two subfamilies on the basis of their motif content and organisation [, ]. Examples of PPR repeat-containing proteins include PET309 P32522 from SWISSPROT, which may be involved in RNA stabilisation [], and crp1, which is involved in RNA processing []. The repeat is associated with a predicted plant protein O49549 from SWISSPROT that has a domain organisation similar to the human BRCA1 protein.

>KOG2041 consensus WD40 repeat protein [General function prediction only]

Probab=97.84  E-value=0.03  Score=53.24  Aligned_cols=124  Identities=11%  Similarity=-0.007  Sum_probs=67.7

Q ss_pred             CCCchHHHHHHHHHHHhhcHHHHHHHHHHhhhccCccC--------ChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCC
Q 012111           75 NLWPKPVLEALDEAIKQKKWQLALKIFGLLRQQQWYQA--------RCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLK  146 (471)
Q Consensus        75 ~~~~~~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~--------~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~  146 (471)
                      ++.|+.+..+.......-.++.|...|-....-.|++.        +...-.  ...-+--|++++|.++|-+|.++.+ 
T Consensus       689 nPHprLWrllAe~Al~Kl~l~tAE~AFVrc~dY~Gik~vkrl~~i~s~~~q~--aei~~~~g~feeaek~yld~drrDL-  765 (1189)
T KOG2041|consen  689 NPHPRLWRLLAEYALFKLALDTAEHAFVRCGDYAGIKLVKRLRTIHSKEQQR--AEISAFYGEFEEAEKLYLDADRRDL-  765 (1189)
T ss_pred             CCchHHHHHHHHHHHHHHhhhhHhhhhhhhccccchhHHHHhhhhhhHHHHh--HhHhhhhcchhHhhhhhhccchhhh-
Confidence            45566666666666667777788877766654332211        001111  1112234889999999988876522 


Q ss_pred             CCHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHH
Q 012111          147 PSVDVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILA  209 (471)
Q Consensus       147 ~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~  209 (471)
                              .|..+.+.|++-...++++.--......--...|+.+...+.....++.|.+.+.
T Consensus       766 --------Aielr~klgDwfrV~qL~r~g~~d~dD~~~e~A~r~ig~~fa~~~~We~A~~yY~  820 (1189)
T KOG2041|consen  766 --------AIELRKKLGDWFRVYQLIRNGGSDDDDEGKEDAFRNIGETFAEMMEWEEAAKYYS  820 (1189)
T ss_pred             --------hHHHHHhhhhHHHHHHHHHccCCCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence                    3555666777776666665422110011112345666665555555555555554

>PRK02603 photosystem I assembly protein Ycf3; Provisional

Probab=97.83  E-value=0.001  Score=53.76  Aligned_cols=88  Identities=16%  Similarity=0.122  Sum_probs=52.0

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCC--HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHH
Q 012111          328 TYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPN--SITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISA  405 (471)
Q Consensus       328 ~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~--~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  405 (471)
                      .+..+...+...|++++|...|++..+....+.  ...+..+...+.+.|++++|...+++..+..+. +...+..+..+
T Consensus        37 ~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~lg~~  115 (172)
T PRK02603         37 VYYRDGMSAQADGEYAEALENYEEALKLEEDPNDRSYILYNMGIIYASNGEHDKALEYYHQALELNPK-QPSALNNIAVI  115 (172)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcc-cHHHHHHHHHH
Confidence            455555566666777777777776665432221  345666666666777777777777666665433 45555555666


Q ss_pred             HHhcCCHHHHH
Q 012111          406 YGQAGDVEKMG  416 (471)
Q Consensus       406 ~~~~g~~~~a~  416 (471)
                      +...|+...+.
T Consensus       116 ~~~~g~~~~a~  126 (172)
T PRK02603        116 YHKRGEKAEEA  126 (172)
T ss_pred             HHHcCChHhHh
Confidence            66655544443

>PRK10153 DNA-binding transcriptional activator CadC; Provisional

Probab=97.82  E-value=0.0019  Score=61.61  Aligned_cols=140  Identities=6%  Similarity=0.090  Sum_probs=79.4

Q ss_pred             CCCCHHHHHHHHHHHHhc--C---CHHHHHHHHHHHHHcCCCCC-HHHHHHHHHHHHhc--------CCHHHHHHHHHHH
Q 012111          322 FFPTVVTYNIVIETFGKA--G---HIEKMEEYFKKMKHRGMKPN-SITYCSLVSAYSKA--------GLIMKVDSILRQV  387 (471)
Q Consensus       322 ~~~~~~~~~~li~~~~~~--g---~~~~a~~~~~~m~~~~~~p~-~~~~~~li~~~~~~--------g~~~~a~~~~~~~  387 (471)
                      ...+...|...+.+....  +   +.+.|..+|++..+.  .|+ ...|..+..++...        ++...+.+..++.
T Consensus       333 ~~~~~~Ay~~~lrg~~~~~~~~~~~~~~A~~lle~Ai~l--dP~~a~a~A~la~~~~~~~~~~~~~~~~l~~a~~~~~~a  410 (517)
T PRK10153        333 LPHQGAALTLFYQAHHYLNSGDAKSLNKASDLLEEILKS--EPDFTYAQAEKALADIVRHSQQPLDEKQLAALSTELDNI  410 (517)
T ss_pred             CCCCHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHh--CCCcHHHHHHHHHHHHHHHhcCCccHHHHHHHHHHHHHh
Confidence            344556666666554332  1   255677777776664  443 33343333322221        1122333333333


Q ss_pred             HhC-CCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhhhcCC
Q 012111          388 ENS-DVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAYNALGMTEAAQNLENKMIAMKENSG  465 (471)
Q Consensus       388 ~~~-~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~~~  465 (471)
                      ... ....+...|..+.-.....|++++|...++++.+.  .|+...|..+...+...|+.++|.+.++++..++|..+
T Consensus       411 ~al~~~~~~~~~~~ala~~~~~~g~~~~A~~~l~rAl~L--~ps~~a~~~lG~~~~~~G~~~eA~~~~~~A~~L~P~~p  487 (517)
T PRK10153        411 VALPELNVLPRIYEILAVQALVKGKTDEAYQAINKAIDL--EMSWLNYVLLGKVYELKGDNRLAADAYSTAFNLRPGEN  487 (517)
T ss_pred             hhcccCcCChHHHHHHHHHHHhcCCHHHHHHHHHHHHHc--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCCc
Confidence            222 12224456666655556667777777777777774  46777777777777777777777777777777777654

>KOG0550 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=97.82  E-value=0.0084  Score=53.21  Aligned_cols=341  Identities=9%  Similarity=-0.079  Sum_probs=164.8

Q ss_pred             HHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHH
Q 012111           88 AIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDE  167 (471)
Q Consensus        88 ~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~  167 (471)
                      +.+..++..|+..+..+....  +.++.-|..-+..+...+++++|.--.+.-.+.... ....+.-.-+++...++..+
T Consensus        59 ~yk~k~Y~nal~~yt~Ai~~~--pd~a~yy~nRAa~~m~~~~~~~a~~dar~~~r~kd~-~~k~~~r~~~c~~a~~~~i~  135 (486)
T KOG0550|consen   59 FYKQKTYGNALKNYTFAIDMC--PDNASYYSNRAATLMMLGRFEEALGDARQSVRLKDG-FSKGQLREGQCHLALSDLIE  135 (486)
T ss_pred             HHHHhhHHHHHHHHHHHHHhC--ccchhhhchhHHHHHHHHhHhhcccchhhheecCCC-ccccccchhhhhhhhHHHHH
Confidence            446677788888888887764  566666777777777777777776666554443111 11222333333333444444


Q ss_pred             HHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCC-CCCHHHHHHH-HHHHHccCCHHHHHHHHHH
Q 012111          168 AFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGI-ECSAVTYNTI-IDGYGKAKKFEEMESSFSA  245 (471)
Q Consensus       168 a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~-~~~~~~~~~l-~~~~~~~~~~~~a~~~~~~  245 (471)
                      |.+.++.-.          .|           ....++..++....... +|.-.++..+ ..++.-.|++++|..+--.
T Consensus       136 A~~~~~~~~----------~~-----------~~anal~~~~~~~~s~s~~pac~~a~~lka~cl~~~~~~~~a~~ea~~  194 (486)
T KOG0550|consen  136 AEEKLKSKQ----------AY-----------KAANALPTLEKLAPSHSREPACFKAKLLKAECLAFLGDYDEAQSEAID  194 (486)
T ss_pred             HHHHhhhhh----------hh-----------HHhhhhhhhhcccccccCCchhhHHHHhhhhhhhhcccchhHHHHHHH
Confidence            443333100          00           00111111111111111 1222222222 2334445566666555555


Q ss_pred             HHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHH-------------HHHHHHHcCCHHHHHH
Q 012111          246 MVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNI-------------LTKSYGRAGMYDKMRS  312 (471)
Q Consensus       246 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~-------------ll~~~~~~~~~~~a~~  312 (471)
                      +.+..  ..+....-.-..++.-.++.+.+...|++.+..  .|+...-..             =.+-..+.|.+..|.+
T Consensus       195 ilkld--~~n~~al~vrg~~~yy~~~~~ka~~hf~qal~l--dpdh~~sk~~~~~~k~le~~k~~gN~~fk~G~y~~A~E  270 (486)
T KOG0550|consen  195 ILKLD--ATNAEALYVRGLCLYYNDNADKAINHFQQALRL--DPDHQKSKSASMMPKKLEVKKERGNDAFKNGNYRKAYE  270 (486)
T ss_pred             HHhcc--cchhHHHHhcccccccccchHHHHHHHhhhhcc--ChhhhhHHhHhhhHHHHHHHHhhhhhHhhccchhHHHH
Confidence            54432  111111111122333455556666666655443  233221111             1123457788888888


Q ss_pred             HHHHHHhCC---CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 012111          313 VMDFMQKRF---FFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPN-SITYCSLVSAYSKAGLIMKVDSILRQVE  388 (471)
Q Consensus       313 ~~~~~~~~~---~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~-~~~~~~li~~~~~~g~~~~a~~~~~~~~  388 (471)
                      .+.+.+...   ..++...|.....+..+.|+.++|+.--+...+.  .+. ...|..-..++...+++++|.+-++...
T Consensus       271 ~Yteal~idP~n~~~naklY~nra~v~~rLgrl~eaisdc~~Al~i--D~syikall~ra~c~l~le~~e~AV~d~~~a~  348 (486)
T KOG0550|consen  271 CYTEALNIDPSNKKTNAKLYGNRALVNIRLGRLREAISDCNEALKI--DSSYIKALLRRANCHLALEKWEEAVEDYEKAM  348 (486)
T ss_pred             HHHHhhcCCccccchhHHHHHHhHhhhcccCCchhhhhhhhhhhhc--CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            888776542   4455566777777777888888888777766653  221 2233334445666688888888888777


Q ss_pred             hCCCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHH---HhcCCHHHHHHHHHHHHH
Q 012111          389 NSDVIL-DTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAY---NALGMTEAAQNLENKMIA  459 (471)
Q Consensus       389 ~~~~~~-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~---~~~g~~~~A~~~~~~m~~  459 (471)
                      +..-.+ ...++.....++-+..+. .=..++--.......|....|..+.-.+   ...|.-.+|...|.+.-+
T Consensus       349 q~~~s~e~r~~l~~A~~aLkkSkRk-d~ykilGi~~~as~~eikkayrk~AL~~Hpd~~agsq~eaE~kFkevge  422 (486)
T KOG0550|consen  349 QLEKDCEIRRTLREAQLALKKSKRK-DWYKILGISRNASDDEIKKAYRKLALVHHPDKNAGSQKEAEAKFKEVGE  422 (486)
T ss_pred             hhccccchHHHHHHHHHHHHHhhhh-hHHHHhhhhhhcccchhhhHHHHHHHHhCCCcCcchhHHHHHHHHHHHH
Confidence            653321 122222222233222211 1111111112222335555665443333   234555777777766543

>PF05843 Suf: Suppressor of forked protein (Suf); InterPro: IPR008847 This domain consists of several eukaryotic suppressor of forked (Suf) like proteins

Probab=97.80  E-value=0.0011  Score=58.25  Aligned_cols=130  Identities=14%  Similarity=0.170  Sum_probs=92.2

Q ss_pred             HHHHHHHHHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHH-HhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHH
Q 012111           80 PVLEALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVM-LGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSA  158 (471)
Q Consensus        80 ~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~-~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~  158 (471)
                      .++..++...+.+..+.|..+|..+.+..  ..+..+|...... +...++.+.|..+|+...+. +..+...|..-++.
T Consensus         3 v~i~~m~~~~r~~g~~~aR~vF~~a~~~~--~~~~~vy~~~A~~E~~~~~d~~~A~~Ife~glk~-f~~~~~~~~~Y~~~   79 (280)
T PF05843_consen    3 VWIQYMRFMRRTEGIEAARKVFKRARKDK--RCTYHVYVAYALMEYYCNKDPKRARKIFERGLKK-FPSDPDFWLEYLDF   79 (280)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHCCC--CS-THHHHHHHHHHHHTCS-HHHHHHHHHHHHHH-HTT-HHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCChHHHHHHHHHHHcCC--CCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHH-CCCCHHHHHHHHHH
Confidence            45667777778888999999999998654  3344555555554 33356777799999988775 44577888888888


Q ss_pred             HHhcCCHHHHHHHHHHhhcCCCCCCCH---HHHHHHHHHHHhcCCHHHHHHHHHHHHHC
Q 012111          159 YGQSGLLDEAFSTINDMKSVSDCKPDV---YTYSILIKSCTKFHRFDLIEKILAEMSYL  214 (471)
Q Consensus       159 ~~~~~~~~~a~~~~~~~~~~~~~~~~~---~~~~~ll~~~~~~~~~~~a~~~~~~~~~~  214 (471)
                      +...|+.+.|..+|++....  +.++.   ..|...+..=.+.|+.+.+.++.+++.+.
T Consensus        80 l~~~~d~~~aR~lfer~i~~--l~~~~~~~~iw~~~i~fE~~~Gdl~~v~~v~~R~~~~  136 (280)
T PF05843_consen   80 LIKLNDINNARALFERAISS--LPKEKQSKKIWKKFIEFESKYGDLESVRKVEKRAEEL  136 (280)
T ss_dssp             HHHTT-HHHHHHHHHHHCCT--SSCHHHCHHHHHHHHHHHHHHS-HHHHHHHHHHHHHH
T ss_pred             HHHhCcHHHHHHHHHHHHHh--cCchhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            88999999999999998863  33322   47888888778888888888888877764

The Drosophila melanogaster suppressor of forked [Su(f)] protein shares homology with the Saccharomyces cerevisiae RNA14 protein and the 77 kDa subunit of Homo sapiens cleavage stimulation factor, which are proteins involved in mRNA 3' end formation. This suggests a role for Su(f) in mRNA 3' end formation in Drosophila. The su(f) gene produces three transcripts; two of them are polyadenylated at the end of the transcription unit, and one is a truncated transcript, polyadenylated in intron 4. It is thought that su(f) plays a role in the regulation of poly(A) site utilisation and the GU-rich sequence is important for this regulation to occur [].; GO: 0006397 mRNA processing, 0005634 nucleus; PDB: 2L9B_B 2OND_B 2OOE_A 4E85_B 4EBA_C 4E6H_A 2UY1_B.

>PRK02603 photosystem I assembly protein Ycf3; Provisional

Probab=97.80  E-value=0.0028  Score=51.27  Aligned_cols=93  Identities=13%  Similarity=0.016  Sum_probs=69.3

Q ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCC--HHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHH
Q 012111          291 IQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPT--VVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLV  368 (471)
Q Consensus       291 ~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li  368 (471)
                      ...+..+...+...|++++|...|++..+....+.  ...+..+...+...|++++|...+.+..... +-+...+..+.
T Consensus        35 a~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg  113 (172)
T PRK02603         35 AFVYYRDGMSAQADGEYAEALENYEEALKLEEDPNDRSYILYNMGIIYASNGEHDKALEYYHQALELN-PKQPSALNNIA  113 (172)
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cccHHHHHHHH
Confidence            44567777888889999999999998887543332  3577788888899999999999999888753 22466677777


Q ss_pred             HHHHhcCCHHHHHHHH
Q 012111          369 SAYSKAGLIMKVDSIL  384 (471)
Q Consensus       369 ~~~~~~g~~~~a~~~~  384 (471)
                      ..+...|+...+..-+
T Consensus       114 ~~~~~~g~~~~a~~~~  129 (172)
T PRK02603        114 VIYHKRGEKAEEAGDQ  129 (172)
T ss_pred             HHHHHcCChHhHhhCH
Confidence            7888877766555433

>PF06239 ECSIT: Evolutionarily conserved signalling intermediate in Toll pathway; InterPro: IPR010418 Activation of NF-kappaB as a consequence of signalling through the Toll and IL-1 receptors is a major element of innate immune responses

Probab=97.78  E-value=0.00098  Score=53.91  Aligned_cols=116  Identities=15%  Similarity=0.178  Sum_probs=77.4

Q ss_pred             HHHHHHHhhhccCccCChhHHHHHHHHHhcC-----CCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHH
Q 012111           97 ALKIFGLLRQQQWYQARCQTFTKLMVMLGKC-----KQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAFST  171 (471)
Q Consensus        97 A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-----~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~  171 (471)
                      -...|+.+...   ..+-.+|..+++.+.+.     |.++-....+..|.+.|+.-|..+|+.|++.+=+ |.+- -..+
T Consensus        33 ~~~~f~~~~~~---~k~K~~F~~~V~~f~~~~~~RRGHVeFI~aAL~~M~efgv~kDL~~Y~~LLDvFPK-g~fv-p~n~  107 (228)
T PF06239_consen   33 HEELFERAPGQ---AKDKATFLEAVDIFKQRDVRRRGHVEFIYAALKKMDEFGVEKDLEVYKALLDVFPK-GKFV-PRNF  107 (228)
T ss_pred             hHHHHHHHhhc---cccHHHHHHHHHHHHhcCCCCcChHHHHHHHHHHHHHcCCcccHHHHHHHHHhCCC-CCcc-cccH
Confidence            35556555432   45677788888877643     6677777788888888888888888888877653 2211 1111


Q ss_pred             HHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCC
Q 012111          172 INDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKK  235 (471)
Q Consensus       172 ~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~  235 (471)
                      |+.+                ..-|  -.+-+-|++++++|...|+.||..++..++..+.+.+.
T Consensus       108 fQ~~----------------F~hy--p~Qq~c~i~lL~qME~~gV~Pd~Et~~~ll~iFG~~s~  153 (228)
T PF06239_consen  108 FQAE----------------FMHY--PRQQECAIDLLEQMENNGVMPDKETEQMLLNIFGRKSH  153 (228)
T ss_pred             HHHH----------------hccC--cHHHHHHHHHHHHHHHcCCCCcHHHHHHHHHHhccccH
Confidence            1111                1111  12456788999999999999999999999999977665

ECSIT plays an important role in signalling to NF-kappaB, functioning as the intermediate in the signalling pathways between TRAF-6 and MEKK-1 [].

>COG4700 Uncharacterized protein conserved in bacteria containing a divergent form of TPR repeats [Function unknown]

Probab=97.78  E-value=0.01  Score=46.67  Aligned_cols=131  Identities=11%  Similarity=0.029  Sum_probs=69.2

Q ss_pred             CChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHH
Q 012111          112 ARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSIL  191 (471)
Q Consensus       112 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l  191 (471)
                      |++.....|...+...|+..+|...|++...--+.-|....-.+.++....+++..|...++++.+...-..++.+...+
T Consensus        87 pTvqnr~rLa~al~elGr~~EA~~hy~qalsG~fA~d~a~lLglA~Aqfa~~~~A~a~~tLe~l~e~~pa~r~pd~~Ll~  166 (251)
T COG4700          87 PTVQNRYRLANALAELGRYHEAVPHYQQALSGIFAHDAAMLLGLAQAQFAIQEFAAAQQTLEDLMEYNPAFRSPDGHLLF  166 (251)
T ss_pred             hhHHHHHHHHHHHHHhhhhhhhHHHHHHHhccccCCCHHHHHHHHHHHHhhccHHHHHHHHHHHhhcCCccCCCCchHHH
Confidence            45555555666666666666666666665543344455555566666666666666666666655422111122233344


Q ss_pred             HHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHH
Q 012111          192 IKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFS  244 (471)
Q Consensus       192 l~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~a~~~~~  244 (471)
                      .+.+...|....|...|+.....  -|+...-......+.+.|+.+++..-+.
T Consensus       167 aR~laa~g~~a~Aesafe~a~~~--ypg~~ar~~Y~e~La~qgr~~ea~aq~~  217 (251)
T COG4700         167 ARTLAAQGKYADAESAFEVAISY--YPGPQARIYYAEMLAKQGRLREANAQYV  217 (251)
T ss_pred             HHHHHhcCCchhHHHHHHHHHHh--CCCHHHHHHHHHHHHHhcchhHHHHHHH
Confidence            55555566666666666666554  3343333333444455555554444333

>PF14938 SNAP: Soluble NSF attachment protein, SNAP; PDB: 1QQE_A 2IFU_A

Probab=97.78  E-value=0.0052  Score=54.18  Aligned_cols=113  Identities=15%  Similarity=0.121  Sum_probs=54.3

Q ss_pred             HHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHcc-CCHHHHHHHHHHHHHcCCCCCC----HHHHHHHHHHHH
Q 012111          193 KSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKA-KKFEEMESSFSAMVESGGCHPD----IFTLNSMISAYG  267 (471)
Q Consensus       193 ~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~-~~~~~a~~~~~~~~~~~~~~~~----~~~~~~l~~~~~  267 (471)
                      ..|...|++..|-+++..+               ...|... |+++.|.+.|++..+.......    ...+..+...+.
T Consensus       102 ~~y~~~G~~~~aA~~~~~l---------------A~~ye~~~~d~e~Ai~~Y~~A~~~y~~e~~~~~a~~~~~~~A~l~~  166 (282)
T PF14938_consen  102 EIYREAGRFSQAAKCLKEL---------------AEIYEEQLGDYEKAIEYYQKAAELYEQEGSPHSAAECLLKAADLYA  166 (282)
T ss_dssp             HHHHHCT-HHHHHHHHHHH---------------HHHHCCTT--HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH
T ss_pred             HHHHhcCcHHHHHHHHHHH---------------HHHHHHHcCCHHHHHHHHHHHHHHHHHCCChhhHHHHHHHHHHHHH
Confidence            3455556555555544443               3345555 6777777777665432100001    223445556666


Q ss_pred             hcCCHHHHHHHHHHHHhCCCCC-----CHH-HHHHHHHHHHHcCCHHHHHHHHHHHHhC
Q 012111          268 NSGNIEKMEKWYNEFNLMGVKA-----DIQ-TLNILTKSYGRAGMYDKMRSVMDFMQKR  320 (471)
Q Consensus       268 ~~~~~~~a~~~~~~~~~~~~~~-----~~~-~~~~ll~~~~~~~~~~~a~~~~~~~~~~  320 (471)
                      +.|++++|.++|+++.......     +.. .|...+-++...|+...|...++.....
T Consensus       167 ~l~~y~~A~~~~e~~~~~~l~~~l~~~~~~~~~l~a~l~~L~~~D~v~A~~~~~~~~~~  225 (282)
T PF14938_consen  167 RLGRYEEAIEIYEEVAKKCLENNLLKYSAKEYFLKAILCHLAMGDYVAARKALERYCSQ  225 (282)
T ss_dssp             HTT-HHHHHHHHHHHHHTCCCHCTTGHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHGTT
T ss_pred             HhCCHHHHHHHHHHHHHHhhcccccchhHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            7777777777777665432211     111 2222333445556666666666665543

>PRK10866 outer membrane biogenesis protein BamD; Provisional

Probab=97.78  E-value=0.015  Score=49.70  Aligned_cols=58  Identities=14%  Similarity=0.170  Sum_probs=44.0

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHhC--CCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 012111          401 CIISAYGQAGDVEKMGELFLTMKER--HCVPDNITFATMIQAYNALGMTEAAQNLENKMI  458 (471)
Q Consensus       401 ~l~~~~~~~g~~~~a~~~~~~~~~~--~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~m~  458 (471)
                      .+.+-|.+.|.+..|+.-++.+.+.  +-+........++.+|...|..++|........
T Consensus       180 ~ia~~Y~~~~~y~AA~~r~~~v~~~Yp~t~~~~eal~~l~~ay~~lg~~~~a~~~~~~l~  239 (243)
T PRK10866        180 SVAEYYTKRGAYVAVVNRVEQMLRDYPDTQATRDALPLMENAYRQLQLNAQADKVAKIIA  239 (243)
T ss_pred             HHHHHHHHcCchHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHcCChHHHHHHHHHHh
Confidence            4566788899999999999998875  222344566678899999999999988776543

>PF14559 TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN_B 3QOU_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 3FP3_A 3LCA_A

Probab=97.77  E-value=9.9e-05  Score=49.03  Aligned_cols=63  Identities=22%  Similarity=0.231  Sum_probs=44.7

Q ss_pred             HHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHH
Q 012111           89 IKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTAL  155 (471)
Q Consensus        89 ~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~l  155 (471)
                      .+.|++++|++.|+.+.+..  |.+...+..+..+|.+.|++++|..+++.+...  .|+...|..+
T Consensus         2 l~~~~~~~A~~~~~~~l~~~--p~~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~--~~~~~~~~~l   64 (68)
T PF14559_consen    2 LKQGDYDEAIELLEKALQRN--PDNPEARLLLAQCYLKQGQYDEAEELLERLLKQ--DPDNPEYQQL   64 (68)
T ss_dssp             HHTTHHHHHHHHHHHHHHHT--TTSHHHHHHHHHHHHHTT-HHHHHHHHHCCHGG--GTTHHHHHHH
T ss_pred             hhccCHHHHHHHHHHHHHHC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH--CcCHHHHHHH
Confidence            46788888888888887764  567777778888888888888888888887766  4454444333

...

>PF13432 TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL_A 3CVQ_A 3CV0_A 2GW1_B 3CVN_A 3QKY_A 2PL2_B

Probab=97.77  E-value=0.00018  Score=47.26  Aligned_cols=62  Identities=11%  Similarity=0.124  Sum_probs=46.2

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhhhcC
Q 012111          402 IISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAYNALGMTEAAQNLENKMIAMKENS  464 (471)
Q Consensus       402 l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~~  464 (471)
                      +...+...|++++|.+.|+++.+.. +-+...+..+..++...|++++|..+++++++..|++
T Consensus         3 ~a~~~~~~g~~~~A~~~~~~~l~~~-P~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~~~P~~   64 (65)
T PF13432_consen    3 LARALYQQGDYDEAIAAFEQALKQD-PDNPEAWYLLGRILYQQGRYDEALAYYERALELDPDN   64 (65)
T ss_dssp             HHHHHHHCTHHHHHHHHHHHHHCCS-TTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcCC
Confidence            4556778888888888888888763 2255667777788888888888888888888887764

>KOG0553 consensus TPR repeat-containing protein [General function prediction only]

Probab=97.74  E-value=0.00064  Score=57.53  Aligned_cols=91  Identities=15%  Similarity=0.059  Sum_probs=60.1

Q ss_pred             HHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHhcCCH
Q 012111          299 KSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKP-NSITYCSLVSAYSKAGLI  377 (471)
Q Consensus       299 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~  377 (471)
                      .-+.+.+++.+|+..|...++.... |.+-|..-..+|.+.|.++.|++-.+..+..  .| ...+|..|..+|...|++
T Consensus        89 N~~m~~~~Y~eAv~kY~~AI~l~P~-nAVyycNRAAAy~~Lg~~~~AVkDce~Al~i--Dp~yskay~RLG~A~~~~gk~  165 (304)
T KOG0553|consen   89 NKLMKNKDYQEAVDKYTEAIELDPT-NAVYYCNRAAAYSKLGEYEDAVKDCESALSI--DPHYSKAYGRLGLAYLALGKY  165 (304)
T ss_pred             HHHHHhhhHHHHHHHHHHHHhcCCC-cchHHHHHHHHHHHhcchHHHHHHHHHHHhc--ChHHHHHHHHHHHHHHccCcH
Confidence            3455667777777777777765332 5666666677777777777777766666653  33 345677777777777777


Q ss_pred             HHHHHHHHHHHhCCC
Q 012111          378 MKVDSILRQVENSDV  392 (471)
Q Consensus       378 ~~a~~~~~~~~~~~~  392 (471)
                      ++|.+.|+...+.++
T Consensus       166 ~~A~~aykKaLeldP  180 (304)
T KOG0553|consen  166 EEAIEAYKKALELDP  180 (304)
T ss_pred             HHHHHHHHhhhccCC
Confidence            777777777666543

>KOG0553 consensus TPR repeat-containing protein [General function prediction only]

Probab=97.73  E-value=0.00066  Score=57.46  Aligned_cols=102  Identities=21%  Similarity=0.167  Sum_probs=82.8

Q ss_pred             HHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHH
Q 012111           87 EAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLD  166 (471)
Q Consensus        87 ~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~  166 (471)
                      .+.+.++|.+|+..|..+.+..  |.|..-|..-..+|.+.|.++.|++-.+..+..+.. ...+|..|..+|...|+++
T Consensus        90 ~~m~~~~Y~eAv~kY~~AI~l~--P~nAVyycNRAAAy~~Lg~~~~AVkDce~Al~iDp~-yskay~RLG~A~~~~gk~~  166 (304)
T KOG0553|consen   90 KLMKNKDYQEAVDKYTEAIELD--PTNAVYYCNRAAAYSKLGEYEDAVKDCESALSIDPH-YSKAYGRLGLAYLALGKYE  166 (304)
T ss_pred             HHHHhhhHHHHHHHHHHHHhcC--CCcchHHHHHHHHHHHhcchHHHHHHHHHHHhcChH-HHHHHHHHHHHHHccCcHH
Confidence            3467889999999999999875  677788888999999999999999988888876432 4678999999999999999


Q ss_pred             HHHHHHHHhhcCCCCCCCHHHHHHHHHH
Q 012111          167 EAFSTINDMKSVSDCKPDVYTYSILIKS  194 (471)
Q Consensus       167 ~a~~~~~~~~~~~~~~~~~~~~~~ll~~  194 (471)
                      +|++.|++..+   +.|+-.+|-.=+..
T Consensus       167 ~A~~aykKaLe---ldP~Ne~~K~nL~~  191 (304)
T KOG0553|consen  167 EAIEAYKKALE---LDPDNESYKSNLKI  191 (304)
T ss_pred             HHHHHHHhhhc---cCCCcHHHHHHHHH
Confidence            99999998876   46777666544443

>PF13414 TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2PL2_B 3IEG_B 2FBN_A

Probab=97.73  E-value=0.00022  Score=47.52  Aligned_cols=67  Identities=22%  Similarity=0.182  Sum_probs=51.4

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcC-CHHHHHHHHHHHHHhhh
Q 012111          395 DTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAYNALG-MTEAAQNLENKMIAMKE  462 (471)
Q Consensus       395 ~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g-~~~~A~~~~~~m~~~~~  462 (471)
                      +..+|..+...+...|++++|+..|++.++.. +-+...|..+..++...| ++++|.+.+++.++.+|
T Consensus         2 ~a~~~~~~g~~~~~~~~~~~A~~~~~~ai~~~-p~~~~~~~~~g~~~~~~~~~~~~A~~~~~~al~l~P   69 (69)
T PF13414_consen    2 NAEAWYNLGQIYFQQGDYEEAIEYFEKAIELD-PNNAEAYYNLGLAYMKLGKDYEEAIEDFEKALKLDP   69 (69)
T ss_dssp             SHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHS-TTHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHST
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHhCccHHHHHHHHHHHHHcCc
Confidence            45677778888888888888888888888752 225567777778888888 68888888888887765

...

>PF01535 PPR: PPR repeat; InterPro: IPR002885 This entry represents the PPR repeat

Probab=97.69  E-value=6.6e-05  Score=40.70  Aligned_cols=29  Identities=41%  Similarity=0.722  Sum_probs=15.1

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHcC
Q 012111          328 TYNIVIETFGKAGHIEKMEEYFKKMKHRG  356 (471)
Q Consensus       328 ~~~~li~~~~~~g~~~~a~~~~~~m~~~~  356 (471)
                      +|+.++++|++.|++++|.++|++|.+.|
T Consensus         2 ~y~~li~~~~~~~~~~~a~~~~~~M~~~g   30 (31)
T PF01535_consen    2 TYNSLISGYCKMGQFEEALEVFDEMRERG   30 (31)
T ss_pred             cHHHHHHHHHccchHHHHHHHHHHHhHCc
Confidence            35555555555555555555555555443

Pentatricopeptide repeat (PPR) proteins are characterised by tandem repeats of a degenerate 35 amino acid motif []. Most of PPR proteins have roles in mitochondria or plastid []. PPR repeats were discovered while screening Arabidopsis proteins for those predicted to be targeted to mitochondria or chloroplast [, ]. Some of these proteins have been shown to play a role in post-transcriptional processes within organelles and they are thought to be sequence-specific RNA-binding proteins [, , ]. Plant genomes have between one hundred to five hundred PPR genes per genome whereas non-plant genomes encode two to six PPR proteins. Although no PPR structures are yet known, the motif is predicted to fold into a helix-turn-helix structure similar to those found in the tetratricopeptide repeat (TPR) family (see PDOC50005 from PROSITEDOC) []. The plant PPR protein family has been divided in two subfamilies on the basis of their motif content and organisation [, ]. Examples of PPR repeat-containing proteins include PET309 P32522 from SWISSPROT, which may be involved in RNA stabilisation [], and crp1, which is involved in RNA processing []. The repeat is associated with a predicted plant protein O49549 from SWISSPROT that has a domain organisation similar to the human BRCA1 protein.

>CHL00033 ycf3 photosystem I assembly protein Ycf3

Probab=97.67  E-value=0.0014  Score=52.80  Aligned_cols=92  Identities=14%  Similarity=0.059  Sum_probs=48.4

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCC--CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHH
Q 012111          328 TYNIVIETFGKAGHIEKMEEYFKKMKHRGMKP--NSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISA  405 (471)
Q Consensus       328 ~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p--~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  405 (471)
                      .|..+...+...|++++|...|++.......+  ...++..+...+...|++++|...++........ ....+..+...
T Consensus        37 ~~~~~g~~~~~~g~~~~A~~~~~~al~l~~~~~~~~~~~~~lg~~~~~~g~~~eA~~~~~~Al~~~~~-~~~~~~~la~i  115 (168)
T CHL00033         37 TYYRDGMSAQSEGEYAEALQNYYEAMRLEIDPYDRSYILYNIGLIHTSNGEHTKALEYYFQALERNPF-LPQALNNMAVI  115 (168)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHhccccchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcC-cHHHHHHHHHH
Confidence            34445555555666666666666665432111  1235555666666666666666666666554322 33344444444


Q ss_pred             HH-------hcCCHHHHHHHHH
Q 012111          406 YG-------QAGDVEKMGELFL  420 (471)
Q Consensus       406 ~~-------~~g~~~~a~~~~~  420 (471)
                      +.       ..|++++|...++
T Consensus       116 ~~~~~~~~~~~g~~~~A~~~~~  137 (168)
T CHL00033        116 CHYRGEQAIEQGDSEIAEAWFD  137 (168)
T ss_pred             HHHhhHHHHHcccHHHHHHHHH
Confidence            44       5566554444444

>PF13525 YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M_A 2YHC_A

Probab=97.65  E-value=0.012  Score=48.99  Aligned_cols=179  Identities=19%  Similarity=0.111  Sum_probs=101.6

Q ss_pred             chHHHHHHHHHHHhhcHHHHHHHHHHhhhccCccC-ChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHH
Q 012111           78 PKPVLEALDEAIKQKKWQLALKIFGLLRQQQWYQA-RCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALV  156 (471)
Q Consensus        78 ~~~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li  156 (471)
                      ++.+..........|++.+|++.|+.+....+..+ ...+.-.++.++.+.|+++.|...++...+.-+.-....+...+
T Consensus         5 ~~~lY~~a~~~~~~g~y~~Ai~~f~~l~~~~P~s~~a~~A~l~la~a~y~~~~y~~A~~~~~~fi~~yP~~~~~~~A~Y~   84 (203)
T PF13525_consen    5 AEALYQKALEALQQGDYEEAIKLFEKLIDRYPNSPYAPQAQLMLAYAYYKQGDYEEAIAAYERFIKLYPNSPKADYALYM   84 (203)
T ss_dssp             HHHHHHHHHHHHHCT-HHHHHHHHHHHHHH-TTSTTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-TTHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCcchhhHHHH
Confidence            44555666677889999999999999988742222 23556778888999999999999999988763221122233222


Q ss_pred             HHHHhcCC-------------HHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHH
Q 012111          157 SAYGQSGL-------------LDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTY  223 (471)
Q Consensus       157 ~~~~~~~~-------------~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~  223 (471)
                      .+.+....             ..+|+.                .+..++.-|-...-...|...+..+.+.    =...-
T Consensus        85 ~g~~~~~~~~~~~~~~~D~~~~~~A~~----------------~~~~li~~yP~S~y~~~A~~~l~~l~~~----la~~e  144 (203)
T PF13525_consen   85 LGLSYYKQIPGILRSDRDQTSTRKAIE----------------EFEELIKRYPNSEYAEEAKKRLAELRNR----LAEHE  144 (203)
T ss_dssp             HHHHHHHHHHHHH-TT---HHHHHHHH----------------HHHHHHHH-TTSTTHHHHHHHHHHHHHH----HHHHH
T ss_pred             HHHHHHHhCccchhcccChHHHHHHHH----------------HHHHHHHHCcCchHHHHHHHHHHHHHHH----HHHHH
Confidence            22221111             112222                2344444444555555665555554322    11112


Q ss_pred             HHHHHHHHccCCHHHHHHHHHHHHHcCCCCC-CHHHHHHHHHHHHhcCCHHHHH
Q 012111          224 NTIIDGYGKAKKFEEMESSFSAMVESGGCHP-DIFTLNSMISAYGNSGNIEKME  276 (471)
Q Consensus       224 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~a~  276 (471)
                      -.+.+.|.+.|.+..|..-++.+.+...-.+ .......++.++.+.|..+.+.
T Consensus       145 ~~ia~~Y~~~~~y~aA~~r~~~v~~~yp~t~~~~~al~~l~~~y~~l~~~~~a~  198 (203)
T PF13525_consen  145 LYIARFYYKRGKYKAAIIRFQYVIENYPDTPAAEEALARLAEAYYKLGLKQAAD  198 (203)
T ss_dssp             HHHHHHHHCTT-HHHHHHHHHHHHHHSTTSHHHHHHHHHHHHHHHHTT-HHHHH
T ss_pred             HHHHHHHHHcccHHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHhCChHHHH
Confidence            3366778888899888888888887631111 1234456677777777776443

>PRK10803 tol-pal system protein YbgF; Provisional

Probab=97.62  E-value=0.002  Score=55.59  Aligned_cols=99  Identities=8%  Similarity=-0.009  Sum_probs=49.1

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcC--HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCC----HHHHHHH
Q 012111          364 YCSLVSAYSKAGLIMKVDSILRQVENSDVILD--TPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPD----NITFATM  437 (471)
Q Consensus       364 ~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~--~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~----~~~~~~l  437 (471)
                      |...+..+.+.|++++|...|+.+.+..+...  ...+-.+..+|...|++++|...|+.+.+.  .|+    ...+..+
T Consensus       146 Y~~A~~l~~~~~~y~~Ai~af~~fl~~yP~s~~a~~A~y~LG~~y~~~g~~~~A~~~f~~vv~~--yP~s~~~~dAl~kl  223 (263)
T PRK10803        146 YNAAIALVQDKSRQDDAIVAFQNFVKKYPDSTYQPNANYWLGQLNYNKGKKDDAAYYFASVVKN--YPKSPKAADAMFKV  223 (263)
T ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH--CCCCcchhHHHHHH
Confidence            33333333444555555555555554433211  234444555555566666666666655542  121    2333334


Q ss_pred             HHHHHhcCCHHHHHHHHHHHHHhhhcC
Q 012111          438 IQAYNALGMTEAAQNLENKMIAMKENS  464 (471)
Q Consensus       438 ~~~~~~~g~~~~A~~~~~~m~~~~~~~  464 (471)
                      ...+...|+.++|.+.++++++..|+.
T Consensus       224 g~~~~~~g~~~~A~~~~~~vi~~yP~s  250 (263)
T PRK10803        224 GVIMQDKGDTAKAKAVYQQVIKKYPGT  250 (263)
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHCcCC
Confidence            445555666666666666666555543

>PF06239 ECSIT: Evolutionarily conserved signalling intermediate in Toll pathway; InterPro: IPR010418 Activation of NF-kappaB as a consequence of signalling through the Toll and IL-1 receptors is a major element of innate immune responses

Probab=97.60  E-value=0.0021  Score=52.00  Aligned_cols=71  Identities=24%  Similarity=0.376  Sum_probs=39.6

Q ss_pred             CCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhc----------------CCHHHHHHHHHHHHhCCCCcCHHHHHHHH
Q 012111          340 GHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKA----------------GLIMKVDSILRQVENSDVILDTPFFNCII  403 (471)
Q Consensus       340 g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~----------------g~~~~a~~~~~~~~~~~~~~~~~~~~~l~  403 (471)
                      |..+=....+..|.+-|+.-|..+|+.|++.+-+.                .+-+-|++++++|.+.|+.||..++..++
T Consensus        66 GHVeFI~aAL~~M~efgv~kDL~~Y~~LLDvFPKg~fvp~n~fQ~~F~hyp~Qq~c~i~lL~qME~~gV~Pd~Et~~~ll  145 (228)
T PF06239_consen   66 GHVEFIYAALKKMDEFGVEKDLEVYKALLDVFPKGKFVPRNFFQAEFMHYPRQQECAIDLLEQMENNGVMPDKETEQMLL  145 (228)
T ss_pred             ChHHHHHHHHHHHHHcCCcccHHHHHHHHHhCCCCCcccccHHHHHhccCcHHHHHHHHHHHHHHHcCCCCcHHHHHHHH
Confidence            33444444444444444444444444444443321                23455677777777777777777777777


Q ss_pred             HHHHhcC
Q 012111          404 SAYGQAG  410 (471)
Q Consensus       404 ~~~~~~g  410 (471)
                      ..+.+.+
T Consensus       146 ~iFG~~s  152 (228)
T PF06239_consen  146 NIFGRKS  152 (228)
T ss_pred             HHhcccc
Confidence            7775544

ECSIT plays an important role in signalling to NF-kappaB, functioning as the intermediate in the signalling pathways between TRAF-6 and MEKK-1 [].

>PRK10153 DNA-binding transcriptional activator CadC; Provisional

Probab=97.60  E-value=0.011  Score=56.46  Aligned_cols=63  Identities=10%  Similarity=0.002  Sum_probs=33.9

Q ss_pred             CHHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 012111          219 SAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNL  284 (471)
Q Consensus       219 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  284 (471)
                      +...|..+.-.....|++++|...+++..+.   .|+...|..+...+...|+.++|...+++...
T Consensus       419 ~~~~~~ala~~~~~~g~~~~A~~~l~rAl~L---~ps~~a~~~lG~~~~~~G~~~eA~~~~~~A~~  481 (517)
T PRK10153        419 LPRIYEILAVQALVKGKTDEAYQAINKAIDL---EMSWLNYVLLGKVYELKGDNRLAADAYSTAFN  481 (517)
T ss_pred             ChHHHHHHHHHHHhcCCHHHHHHHHHHHHHc---CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            3344444444444455566666666555543   34555555555555556666666655555544

>COG4235 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]

Probab=97.58  E-value=0.0065  Score=51.89  Aligned_cols=99  Identities=12%  Similarity=0.111  Sum_probs=63.1

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhc---CCHHHHHHHHHHHHhCCCCcCHHHHHH
Q 012111          325 TVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKA---GLIMKVDSILRQVENSDVILDTPFFNC  401 (471)
Q Consensus       325 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~---g~~~~a~~~~~~~~~~~~~~~~~~~~~  401 (471)
                      |...|-.|...|...|+++.|...|.+..+.. .+++..+..+..++..+   ....++..+|+++...++. |......
T Consensus       155 d~egW~~Lg~~ym~~~~~~~A~~AY~~A~rL~-g~n~~~~~g~aeaL~~~a~~~~ta~a~~ll~~al~~D~~-~iral~l  232 (287)
T COG4235         155 DAEGWDLLGRAYMALGRASDALLAYRNALRLA-GDNPEILLGLAEALYYQAGQQMTAKARALLRQALALDPA-NIRALSL  232 (287)
T ss_pred             CchhHHHHHHHHHHhcchhHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhcCCc-cHHHHHH
Confidence            56667777777777777777777777666642 33455555555554433   2344566777777766655 6666666


Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHhC
Q 012111          402 IISAYGQAGDVEKMGELFLTMKER  425 (471)
Q Consensus       402 l~~~~~~~g~~~~a~~~~~~~~~~  425 (471)
                      |...+...|++.+|...|+.|.+.
T Consensus       233 LA~~afe~g~~~~A~~~Wq~lL~~  256 (287)
T COG4235         233 LAFAAFEQGDYAEAAAAWQMLLDL  256 (287)
T ss_pred             HHHHHHHcccHHHHHHHHHHHHhc
Confidence            666677777777777777777664

>CHL00033 ycf3 photosystem I assembly protein Ycf3

Probab=97.57  E-value=0.003  Score=50.85  Aligned_cols=61  Identities=11%  Similarity=-0.099  Sum_probs=26.3

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHCCCCC--CHHHHHHHHHHHHccCCHHHHHHHHHHHHH
Q 012111          188 YSILIKSCTKFHRFDLIEKILAEMSYLGIEC--SAVTYNTIIDGYGKAKKFEEMESSFSAMVE  248 (471)
Q Consensus       188 ~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~--~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  248 (471)
                      |..+...+...|++++|...|+........+  ...++..+...+...|++++|+..+++..+
T Consensus        38 ~~~~g~~~~~~g~~~~A~~~~~~al~l~~~~~~~~~~~~~lg~~~~~~g~~~eA~~~~~~Al~  100 (168)
T CHL00033         38 YYRDGMSAQSEGEYAEALQNYYEAMRLEIDPYDRSYILYNIGLIHTSNGEHTKALEYYFQALE  100 (168)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHhccccchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            3333334444444444444444443331111  122444444455555555555555555443

>PF14559 TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN_B 3QOU_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 3FP3_A 3LCA_A

Probab=97.56  E-value=0.00039  Score=46.13  Aligned_cols=60  Identities=17%  Similarity=0.202  Sum_probs=35.1

Q ss_pred             hcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHH
Q 012111          373 KAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFA  435 (471)
Q Consensus       373 ~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~  435 (471)
                      ..|++++|.++|+.+....+. +..++..+..+|.+.|++++|.++++++...  .|+...|.
T Consensus         3 ~~~~~~~A~~~~~~~l~~~p~-~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~--~~~~~~~~   62 (68)
T PF14559_consen    3 KQGDYDEAIELLEKALQRNPD-NPEARLLLAQCYLKQGQYDEAEELLERLLKQ--DPDNPEYQ   62 (68)
T ss_dssp             HTTHHHHHHHHHHHHHHHTTT-SHHHHHHHHHHHHHTT-HHHHHHHHHCCHGG--GTTHHHHH
T ss_pred             hccCHHHHHHHHHHHHHHCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH--CcCHHHHH
Confidence            456666666666666655544 5555556666666666666666666666653  35544433

...

>PF12688 TPR_5: Tetratrico peptide repeat

Probab=97.47  E-value=0.016  Score=43.01  Aligned_cols=105  Identities=13%  Similarity=0.098  Sum_probs=60.0

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHHcCCCCC--HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCC--cCHHHHHHHHHHHHh
Q 012111          333 IETFGKAGHIEKMEEYFKKMKHRGMKPN--SITYCSLVSAYSKAGLIMKVDSILRQVENSDVI--LDTPFFNCIISAYGQ  408 (471)
Q Consensus       333 i~~~~~~g~~~~a~~~~~~m~~~~~~p~--~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~--~~~~~~~~l~~~~~~  408 (471)
                      ..++-..|+.++|+.+|++....|....  ...+..+...+...|++++|..+++......+.  .+......+..++..
T Consensus         8 A~a~d~~G~~~~Ai~~Y~~Al~~gL~~~~~~~a~i~lastlr~LG~~deA~~~L~~~~~~~p~~~~~~~l~~f~Al~L~~   87 (120)
T PF12688_consen    8 AWAHDSLGREEEAIPLYRRALAAGLSGADRRRALIQLASTLRNLGRYDEALALLEEALEEFPDDELNAALRVFLALALYN   87 (120)
T ss_pred             HHHHHhcCCHHHHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCccccHHHHHHHHHHHHH
Confidence            4455566777777777777777665443  234555666677777777777777776654322  011222223345566


Q ss_pred             cCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHH
Q 012111          409 AGDVEKMGELFLTMKERHCVPDNITFATMIQAY  441 (471)
Q Consensus       409 ~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~  441 (471)
                      .|+.++|++.+-....    ++...|..-|..|
T Consensus        88 ~gr~~eAl~~~l~~la----~~~~~y~ra~~~y  116 (120)
T PF12688_consen   88 LGRPKEALEWLLEALA----ETLPRYRRAIRFY  116 (120)
T ss_pred             CCCHHHHHHHHHHHHH----HHHHHHHHHHHHH
Confidence            7777777777655443    2333444444444

>PF13432 TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL_A 3CVQ_A 3CV0_A 2GW1_B 3CVN_A 3QKY_A 2PL2_B

Probab=97.46  E-value=0.00076  Score=44.20  Aligned_cols=57  Identities=14%  Similarity=0.048  Sum_probs=39.8

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 012111          367 LVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKE  424 (471)
Q Consensus       367 li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~  424 (471)
                      +...+...|++++|...|+++.+..+. +...+..+..++...|++++|..+|+++.+
T Consensus         3 ~a~~~~~~g~~~~A~~~~~~~l~~~P~-~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~   59 (65)
T PF13432_consen    3 LARALYQQGDYDEAIAAFEQALKQDPD-NPEAWYLLGRILYQQGRYDEALAYYERALE   59 (65)
T ss_dssp             HHHHHHHCTHHHHHHHHHHHHHCCSTT-HHHHHHHHHHHHHHTT-HHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            345566777777777777777776644 666777777777777777777777777765

>COG4235 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]

Probab=97.42  E-value=0.015  Score=49.83  Aligned_cols=107  Identities=10%  Similarity=-0.043  Sum_probs=78.4

Q ss_pred             CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcC---CHHHHHHHHHHHHhCCCCCCHHHH
Q 012111          358 KPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAG---DVEKMGELFLTMKERHCVPDNITF  434 (471)
Q Consensus       358 ~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g---~~~~a~~~~~~~~~~~~~p~~~~~  434 (471)
                      +-|...|..|...|...|+.+.|..-|....+...+ +...+..+..++....   +..++..+|+++.... +-|....
T Consensus       153 P~d~egW~~Lg~~ym~~~~~~~A~~AY~~A~rL~g~-n~~~~~g~aeaL~~~a~~~~ta~a~~ll~~al~~D-~~~iral  230 (287)
T COG4235         153 PGDAEGWDLLGRAYMALGRASDALLAYRNALRLAGD-NPEILLGLAEALYYQAGQQMTAKARALLRQALALD-PANIRAL  230 (287)
T ss_pred             CCCchhHHHHHHHHHHhcchhHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhcC-CccHHHH
Confidence            447778888888888888888888888888877554 7777777777665443   3557788888887742 2355555


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHHhhhcCCC
Q 012111          435 ATMIQAYNALGMTEAAQNLENKMIAMKENSGK  466 (471)
Q Consensus       435 ~~l~~~~~~~g~~~~A~~~~~~m~~~~~~~~~  466 (471)
                      ..|...++..|++.+|...|+.|.+..|..++
T Consensus       231 ~lLA~~afe~g~~~~A~~~Wq~lL~~lp~~~~  262 (287)
T COG4235         231 SLLAFAAFEQGDYAEAAAAWQMLLDLLPADDP  262 (287)
T ss_pred             HHHHHHHHHcccHHHHHHHHHHHHhcCCCCCc
Confidence            66667888888888888888888888776654

>KOG2796 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.41  E-value=0.055  Score=45.22  Aligned_cols=132  Identities=15%  Similarity=0.068  Sum_probs=87.9

Q ss_pred             HHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHH---
Q 012111          116 TFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILI---  192 (471)
Q Consensus       116 ~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll---  192 (471)
                      +.+.++.++...|.+.-...++.+.++...+.++.....|++.-.+.|+.+.|...|++..+.. -..|..+.+.++   
T Consensus       179 Vmy~~~~~llG~kEy~iS~d~~~~vi~~~~e~~p~L~s~Lgr~~MQ~GD~k~a~~yf~~vek~~-~kL~~~q~~~~V~~n  257 (366)
T KOG2796|consen  179 VMYSMANCLLGMKEYVLSVDAYHSVIKYYPEQEPQLLSGLGRISMQIGDIKTAEKYFQDVEKVT-QKLDGLQGKIMVLMN  257 (366)
T ss_pred             HHHHHHHHHhcchhhhhhHHHHHHHHHhCCcccHHHHHHHHHHHHhcccHHHHHHHHHHHHHHH-hhhhccchhHHHHhh
Confidence            4566777777788888888888888887766677788888888888888888888888766522 233333333332   


Q ss_pred             --HHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHc
Q 012111          193 --KSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVES  249 (471)
Q Consensus       193 --~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  249 (471)
                        ..+.-.+++..|...+++..... +.|+...|.-.-+..-.|+..+|++.++.+.+.
T Consensus       258 ~a~i~lg~nn~a~a~r~~~~i~~~D-~~~~~a~NnKALcllYlg~l~DAiK~~e~~~~~  315 (366)
T KOG2796|consen  258 SAFLHLGQNNFAEAHRFFTEILRMD-PRNAVANNNKALCLLYLGKLKDALKQLEAMVQQ  315 (366)
T ss_pred             hhhheecccchHHHHHHHhhccccC-CCchhhhchHHHHHHHHHHHHHHHHHHHHHhcc
Confidence              23445567777777777766554 334555554444444557777777777777664

>PF13525 YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M_A 2YHC_A

Probab=97.37  E-value=0.04  Score=45.83  Aligned_cols=81  Identities=22%  Similarity=0.269  Sum_probs=46.9

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCH----HHHHHHHHH
Q 012111          365 CSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDN----ITFATMIQA  440 (471)
Q Consensus       365 ~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~----~~~~~l~~~  440 (471)
                      ..++.-|-...-..+|...+..+.+.    =...--.+...|.+.|.+..|..-++.+++.  -|+.    .....++.+
T Consensus       114 ~~li~~yP~S~y~~~A~~~l~~l~~~----la~~e~~ia~~Y~~~~~y~aA~~r~~~v~~~--yp~t~~~~~al~~l~~~  187 (203)
T PF13525_consen  114 EELIKRYPNSEYAEEAKKRLAELRNR----LAEHELYIARFYYKRGKYKAAIIRFQYVIEN--YPDTPAAEEALARLAEA  187 (203)
T ss_dssp             HHHHHH-TTSTTHHHHHHHHHHHHHH----HHHHHHHHHHHHHCTT-HHHHHHHHHHHHHH--STTSHHHHHHHHHHHHH
T ss_pred             HHHHHHCcCchHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHcccHHHHHHHHHHHHHH--CCCCchHHHHHHHHHHH
Confidence            33444444445555665555544431    0011123566788889999999999888875  3443    345667788


Q ss_pred             HHhcCCHHHHH
Q 012111          441 YNALGMTEAAQ  451 (471)
Q Consensus       441 ~~~~g~~~~A~  451 (471)
                      +.+.|..+.|.
T Consensus       188 y~~l~~~~~a~  198 (203)
T PF13525_consen  188 YYKLGLKQAAD  198 (203)
T ss_dssp             HHHTT-HHHHH
T ss_pred             HHHhCChHHHH
Confidence            88888887553

>KOG1130 consensus Predicted G-alpha GTPase interaction protein, contains GoLoco domain [Signal transduction mechanisms]

Probab=97.37  E-value=0.0047  Score=54.72  Aligned_cols=136  Identities=12%  Similarity=0.034  Sum_probs=80.0

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHH----HcCCC-CCHHHHHHHHHHHHhcCCHHHHHHHHHHHH----hCCCC-cCHH
Q 012111          328 TYNIVIETFGKAGHIEKMEEYFKKMK----HRGMK-PNSITYCSLVSAYSKAGLIMKVDSILRQVE----NSDVI-LDTP  397 (471)
Q Consensus       328 ~~~~li~~~~~~g~~~~a~~~~~~m~----~~~~~-p~~~~~~~li~~~~~~g~~~~a~~~~~~~~----~~~~~-~~~~  397 (471)
                      .|..|...|.-.|+++.|+...+.-.    +-|-+ .....+..+..++.-.|+++.|.+.|+...    +.|-. ....
T Consensus       197 a~GnLGNTyYlLGdf~~ai~~H~~RL~ia~efGDrAaeRRA~sNlgN~hiflg~fe~A~ehYK~tl~LAielg~r~vEAQ  276 (639)
T KOG1130|consen  197 AYGNLGNTYYLLGDFDQAIHFHKLRLEIAQEFGDRAAERRAHSNLGNCHIFLGNFELAIEHYKLTLNLAIELGNRTVEAQ  276 (639)
T ss_pred             hhcccCceeeeeccHHHHHHHHHHHHHHHHHhhhHHHHHHhhcccchhhhhhcccHhHHHHHHHHHHHHHHhcchhHHHH
Confidence            45555555556677777776554322    11211 123456667777777788888877776533    22211 1233


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHh----C-CCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhhhc
Q 012111          398 FFNCIISAYGQAGDVEKMGELFLTMKE----R-HCVPDNITFATMIQAYNALGMTEAAQNLENKMIAMKEN  463 (471)
Q Consensus       398 ~~~~l~~~~~~~g~~~~a~~~~~~~~~----~-~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~  463 (471)
                      +...|...|.-..+++.|+.++.+-..    . ...-....+.+|..+|...|.-+.|+.+.+.-.+....
T Consensus       277 scYSLgNtytll~e~~kAI~Yh~rHLaIAqeL~DriGe~RacwSLgna~~alg~h~kAl~fae~hl~~s~e  347 (639)
T KOG1130|consen  277 SCYSLGNTYTLLKEVQKAITYHQRHLAIAQELEDRIGELRACWSLGNAFNALGEHRKALYFAELHLRSSLE  347 (639)
T ss_pred             HHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHH
Confidence            445566666666777777777654321    1 12234567778888888888888887777666555443

>KOG2796 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.36  E-value=0.013  Score=48.87  Aligned_cols=140  Identities=9%  Similarity=0.004  Sum_probs=85.3

Q ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHH-----
Q 012111          293 TLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSL-----  367 (471)
Q Consensus       293 ~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l-----  367 (471)
                      +.+.++..+...|.+.-....+..+++...+-++...+.+.+.-.+.|+.+.|...|++..+..-..|..+.+.+     
T Consensus       179 Vmy~~~~~llG~kEy~iS~d~~~~vi~~~~e~~p~L~s~Lgr~~MQ~GD~k~a~~yf~~vek~~~kL~~~q~~~~V~~n~  258 (366)
T KOG2796|consen  179 VMYSMANCLLGMKEYVLSVDAYHSVIKYYPEQEPQLLSGLGRISMQIGDIKTAEKYFQDVEKVTQKLDGLQGKIMVLMNS  258 (366)
T ss_pred             HHHHHHHHHhcchhhhhhHHHHHHHHHhCCcccHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHhhhhccchhHHHHhhh
Confidence            344555555566666666666666666655556666667777777777777777777765544223333333322     


Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHH
Q 012111          368 VSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFA  435 (471)
Q Consensus       368 i~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~  435 (471)
                      ...+.-++++..|...+.++...+.. |+...|.-.-+....|+..+|++.++.|.+.  .|...+-+
T Consensus       259 a~i~lg~nn~a~a~r~~~~i~~~D~~-~~~a~NnKALcllYlg~l~DAiK~~e~~~~~--~P~~~l~e  323 (366)
T KOG2796|consen  259 AFLHLGQNNFAEAHRFFTEILRMDPR-NAVANNNKALCLLYLGKLKDALKQLEAMVQQ--DPRHYLHE  323 (366)
T ss_pred             hhheecccchHHHHHHHhhccccCCC-chhhhchHHHHHHHHHHHHHHHHHHHHHhcc--CCccchhh
Confidence            23344556677777777777666544 5555555555555668888888888888774  45444433

>PF13414 TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2PL2_B 3IEG_B 2FBN_A

Probab=97.36  E-value=0.0011  Score=44.15  Aligned_cols=63  Identities=17%  Similarity=0.130  Sum_probs=39.9

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcC-CHHHHHHHHHHHHh
Q 012111          361 SITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAG-DVEKMGELFLTMKE  424 (471)
Q Consensus       361 ~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g-~~~~a~~~~~~~~~  424 (471)
                      +.+|..+...+...|++++|+..|++..+.++. +...|..+..++...| ++++|++.+++..+
T Consensus         3 a~~~~~~g~~~~~~~~~~~A~~~~~~ai~~~p~-~~~~~~~~g~~~~~~~~~~~~A~~~~~~al~   66 (69)
T PF13414_consen    3 AEAWYNLGQIYFQQGDYEEAIEYFEKAIELDPN-NAEAYYNLGLAYMKLGKDYEEAIEDFEKALK   66 (69)
T ss_dssp             HHHHHHHHHHHHHTTHHHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHTTTHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCC-CHHHHHHHHHHHHHhCccHHHHHHHHHHHHH
Confidence            455666666666666666666666666665544 5556666666666666 56666666666554

...

>KOG1538 consensus Uncharacterized conserved protein WDR10, contains WD40 repeats [General function prediction only]

Probab=97.32  E-value=0.066  Score=50.60  Aligned_cols=89  Identities=10%  Similarity=0.026  Sum_probs=51.1

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHH--------
Q 012111          361 SITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNI--------  432 (471)
Q Consensus       361 ~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~--------  432 (471)
                      ..+...+...+.+...+..|-++|..|-+.         ..+++.....++|++|..+-++.-+  +.||..        
T Consensus       747 re~l~~~a~ylk~l~~~gLAaeIF~k~gD~---------ksiVqlHve~~~W~eAFalAe~hPe--~~~dVy~pyaqwLA  815 (1081)
T KOG1538|consen  747 REPLLLCATYLKKLDSPGLAAEIFLKMGDL---------KSLVQLHVETQRWDEAFALAEKHPE--FKDDVYMPYAQWLA  815 (1081)
T ss_pred             hhHHHHHHHHHhhccccchHHHHHHHhccH---------HHHhhheeecccchHhHhhhhhCcc--ccccccchHHHHhh
Confidence            344445555555556666666666665432         2455566667777777776665544  233322        


Q ss_pred             ---HHHHHHHHHHhcCCHHHHHHHHHHHHHh
Q 012111          433 ---TFATMIQAYNALGMTEAAQNLENKMIAM  460 (471)
Q Consensus       433 ---~~~~l~~~~~~~g~~~~A~~~~~~m~~~  460 (471)
                         -|.-.-++|.++|+..+|.++++.+...
T Consensus       816 E~DrFeEAqkAfhkAGr~~EA~~vLeQLtnn  846 (1081)
T KOG1538|consen  816 ENDRFEEAQKAFHKAGRQREAVQVLEQLTNN  846 (1081)
T ss_pred             hhhhHHHHHHHHHHhcchHHHHHHHHHhhhh
Confidence               1233345677777777777777766543

>COG5107 RNA14 Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification]

Probab=97.31  E-value=0.12  Score=46.74  Aligned_cols=144  Identities=8%  Similarity=0.071  Sum_probs=92.4

Q ss_pred             HHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHhhc
Q 012111           98 LKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAFSTINDMKS  177 (471)
Q Consensus        98 ~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~  177 (471)
                      +++=+.+...   |.|...|..|+..+...+..++..+++++|..- ++--..+|..-+.+-...+++.....+|.+...
T Consensus        29 lrLRerIkdN---PtnI~S~fqLiq~~~tq~s~~~~re~yeq~~~p-fp~~~~aw~ly~s~ELA~~df~svE~lf~rCL~  104 (660)
T COG5107          29 LRLRERIKDN---PTNILSYFQLIQYLETQESMDAEREMYEQLSSP-FPIMEHAWRLYMSGELARKDFRSVESLFGRCLK  104 (660)
T ss_pred             HHHHHHhhcC---chhHHHHHHHHHHHhhhhhHHHHHHHHHHhcCC-CccccHHHHHHhcchhhhhhHHHHHHHHHHHHh
Confidence            4555555543   678889999999999999999999999999753 233456788888877778899999999998876


Q ss_pred             CCCCCCCHHHHHHHHHHHHhcCC------HHHHHHHHHHHHH-CCCCCC-HHHHHH---HHHHHHccCCHH------HHH
Q 012111          178 VSDCKPDVYTYSILIKSCTKFHR------FDLIEKILAEMSY-LGIECS-AVTYNT---IIDGYGKAKKFE------EME  240 (471)
Q Consensus       178 ~~~~~~~~~~~~~ll~~~~~~~~------~~~a~~~~~~~~~-~g~~~~-~~~~~~---l~~~~~~~~~~~------~a~  240 (471)
                       .  ..+...|...+.-..+...      -....+.|+-... .++.|- ...|+.   .+...-..|.++      ...
T Consensus       105 -k--~l~ldLW~lYl~YIRr~n~~~tGq~r~~i~~ayefv~~~~~~e~~s~~~W~ey~~fle~~~~~~kwEeQqrid~iR  181 (660)
T COG5107         105 -K--SLNLDLWMLYLEYIRRVNNLITGQKRFKIYEAYEFVLGCAIFEPQSENYWDEYGLFLEYIEELGKWEEQQRIDKIR  181 (660)
T ss_pred             -h--hccHhHHHHHHHHHHhhCcccccchhhhhHHHHHHHHhcccccccccchHHHHHHHHHhccccccHHHHHHHHHHH
Confidence             2  3556677777765544331      1122334443332 345443 233443   344444455554      445


Q ss_pred             HHHHHHHH
Q 012111          241 SSFSAMVE  248 (471)
Q Consensus       241 ~~~~~~~~  248 (471)
                      +.+.++..
T Consensus       182 ~~Y~ral~  189 (660)
T COG5107         182 NGYMRALQ  189 (660)
T ss_pred             HHHHHHHc
Confidence            55666654

>PF04840 Vps16_C: Vps16, C-terminal region; InterPro: IPR006925 This protein forms part of the Class C vacuolar protein sorting (Vps) complex

Probab=97.30  E-value=0.11  Score=46.23  Aligned_cols=110  Identities=15%  Similarity=0.192  Sum_probs=65.4

Q ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Q 012111          293 TLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYS  372 (471)
Q Consensus       293 ~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~  372 (471)
                      +.+.-+.-+...|+...|.++-...    -.|+..-|-..+.+++..++|++...+...   .   -++.-|..++.+|.
T Consensus       179 Sl~~Ti~~li~~~~~k~A~kl~k~F----kv~dkrfw~lki~aLa~~~~w~eL~~fa~s---k---KsPIGyepFv~~~~  248 (319)
T PF04840_consen  179 SLNDTIRKLIEMGQEKQAEKLKKEF----KVPDKRFWWLKIKALAENKDWDELEKFAKS---K---KSPIGYEPFVEACL  248 (319)
T ss_pred             CHHHHHHHHHHCCCHHHHHHHHHHc----CCcHHHHHHHHHHHHHhcCCHHHHHHHHhC---C---CCCCChHHHHHHHH
Confidence            3344455556666666666654433    235666677777777777777766554321   1   12355777777777


Q ss_pred             hcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 012111          373 KAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTM  422 (471)
Q Consensus       373 ~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~  422 (471)
                      +.|+..+|..+...+.          +..-+..|.+.|++.+|.+.--+.
T Consensus       249 ~~~~~~eA~~yI~k~~----------~~~rv~~y~~~~~~~~A~~~A~~~  288 (319)
T PF04840_consen  249 KYGNKKEASKYIPKIP----------DEERVEMYLKCGDYKEAAQEAFKE  288 (319)
T ss_pred             HCCCHHHHHHHHHhCC----------hHHHHHHHHHCCCHHHHHHHHHHc
Confidence            7777777776666511          134556667777777776654433

Vps16 is essential for vacuolar protein sorting, which is essential for viability in plants, but not yeast []. The Class C Vps complex is required for SNARE-mediated membrane fusion at the lysosome-like yeast vacuole. It is thought to play essential roles in membrane docking and fusion at the Golgi-to-endosome and endosome-to-vacuole stages of transport []. The role of VPS16 in this complex is not known.; GO: 0006886 intracellular protein transport, 0005737 cytoplasm

>KOG0550 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=97.27  E-value=0.13  Score=46.11  Aligned_cols=281  Identities=11%  Similarity=-0.018  Sum_probs=149.5

Q ss_pred             hhhhHHHHHHHhhHHHHHHHHHhhhhhhccCCCchHHHHHHHHHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHH
Q 012111           45 KEAEKDLSKILRTEFAIKNIEKKVSSKKYKNLWPKPVLEALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVML  124 (471)
Q Consensus        45 ~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~  124 (471)
                      +....+--+..++.+++......++..+..   ...+...+..+...|++++|+--.+.-.+..  +.....+...-.++
T Consensus        53 k~~gn~~yk~k~Y~nal~~yt~Ai~~~pd~---a~yy~nRAa~~m~~~~~~~a~~dar~~~r~k--d~~~k~~~r~~~c~  127 (486)
T KOG0550|consen   53 KEEGNAFYKQKTYGNALKNYTFAIDMCPDN---ASYYSNRAATLMMLGRFEEALGDARQSVRLK--DGFSKGQLREGQCH  127 (486)
T ss_pred             HhhcchHHHHhhHHHHHHHHHHHHHhCccc---hhhhchhHHHHHHHHhHhhcccchhhheecC--CCccccccchhhhh
Confidence            344555567778888888887777755433   4455566666777888988887776665532  22233445555555


Q ss_pred             hcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHHH-HHHhcCCHHH
Q 012111          125 GKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIK-SCTKFHRFDL  203 (471)
Q Consensus       125 ~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~-~~~~~~~~~~  203 (471)
                      ...++..+|.+.++.-         ..|           ....++..++.+....--+|...++..+-. ++.-.++.++
T Consensus       128 ~a~~~~i~A~~~~~~~---------~~~-----------~~anal~~~~~~~~s~s~~pac~~a~~lka~cl~~~~~~~~  187 (486)
T KOG0550|consen  128 LALSDLIEAEEKLKSK---------QAY-----------KAANALPTLEKLAPSHSREPACFKAKLLKAECLAFLGDYDE  187 (486)
T ss_pred             hhhHHHHHHHHHhhhh---------hhh-----------HHhhhhhhhhcccccccCCchhhHHHHhhhhhhhhcccchh
Confidence            5556666666555511         111           112233333333321111233334333322 2344566666


Q ss_pred             HHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHH----------HHHHHHHhcCCHH
Q 012111          204 IEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLN----------SMISAYGNSGNIE  273 (471)
Q Consensus       204 a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~----------~l~~~~~~~~~~~  273 (471)
                      |.++--..++.. ..+......--.++.-.++.+.|...|++.+..+.-..+..+..          .-.+-..+.|++.
T Consensus       188 a~~ea~~ilkld-~~n~~al~vrg~~~yy~~~~~ka~~hf~qal~ldpdh~~sk~~~~~~k~le~~k~~gN~~fk~G~y~  266 (486)
T KOG0550|consen  188 AQSEAIDILKLD-ATNAEALYVRGLCLYYNDNADKAINHFQQALRLDPDHQKSKSASMMPKKLEVKKERGNDAFKNGNYR  266 (486)
T ss_pred             HHHHHHHHHhcc-cchhHHHHhcccccccccchHHHHHHHhhhhccChhhhhHHhHhhhHHHHHHHHhhhhhHhhccchh
Confidence            666655555442 11222221112223345566666666666654321111111111          1123345678888


Q ss_pred             HHHHHHHHHHhCC---CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHH---HHHHHHHHHHhcCCHHHHHH
Q 012111          274 KMEKWYNEFNLMG---VKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVV---TYNIVIETFGKAGHIEKMEE  347 (471)
Q Consensus       274 ~a~~~~~~~~~~~---~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~---~~~~li~~~~~~g~~~~a~~  347 (471)
                      .|.+.|.+.+...   +.++...|........+.|+.++|+.--+...+.    |..   .|-.-..++.-.++|++|++
T Consensus       267 ~A~E~Yteal~idP~n~~~naklY~nra~v~~rLgrl~eaisdc~~Al~i----D~syikall~ra~c~l~le~~e~AV~  342 (486)
T KOG0550|consen  267 KAYECYTEALNIDPSNKKTNAKLYGNRALVNIRLGRLREAISDCNEALKI----DSSYIKALLRRANCHLALEKWEEAVE  342 (486)
T ss_pred             HHHHHHHHhhcCCccccchhHHHHHHhHhhhcccCCchhhhhhhhhhhhc----CHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            8888888876542   3455556666666777788888887777666653    332   22222334455677888888


Q ss_pred             HHHHHHHc
Q 012111          348 YFKKMKHR  355 (471)
Q Consensus       348 ~~~~m~~~  355 (471)
                      -++...+.
T Consensus       343 d~~~a~q~  350 (486)
T KOG0550|consen  343 DYEKAMQL  350 (486)
T ss_pred             HHHHHHhh
Confidence            88777655

>PF12688 TPR_5: Tetratrico peptide repeat

Probab=97.27  E-value=0.032  Score=41.48  Aligned_cols=55  Identities=22%  Similarity=0.266  Sum_probs=24.2

Q ss_pred             HHhcCCCHHHHHHHHHHHHhCCCCCC--HHHHHHHHHHHHhcCCHHHHHHHHHHhhc
Q 012111          123 MLGKCKQPEQASLLFEVMLSDGLKPS--VDVYTALVSAYGQSGLLDEAFSTINDMKS  177 (471)
Q Consensus       123 ~~~~~~~~~~a~~~~~~m~~~~~~~~--~~~~~~li~~~~~~~~~~~a~~~~~~~~~  177 (471)
                      ++-..|+.++|+.+|++....|....  ...+-.+...+...|++++|+.++++...
T Consensus        10 a~d~~G~~~~Ai~~Y~~Al~~gL~~~~~~~a~i~lastlr~LG~~deA~~~L~~~~~   66 (120)
T PF12688_consen   10 AHDSLGREEEAIPLYRRALAAGLSGADRRRALIQLASTLRNLGRYDEALALLEEALE   66 (120)
T ss_pred             HHHhcCCHHHHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            33444444555555554444443322  12233344444444555555555544443

>PF03704 BTAD: Bacterial transcriptional activator domain; InterPro: IPR005158 Found in the DNRI/REDD/AFSR family of regulators, this region of AFSR (P25941 from SWISSPROT) along with the C-terminal region is capable of independently directing actinorhodin production

Probab=97.22  E-value=0.0049  Score=48.26  Aligned_cols=72  Identities=18%  Similarity=0.156  Sum_probs=48.1

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHH-----hCCCCCCHHHHH
Q 012111          363 TYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMK-----ERHCVPDNITFA  435 (471)
Q Consensus       363 ~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~-----~~~~~p~~~~~~  435 (471)
                      +...++..+...|++++|..+++.+...++. +...|..+|.+|...|+..+|.++|+++.     +.|+.|+..+-.
T Consensus        64 ~~~~l~~~~~~~~~~~~a~~~~~~~l~~dP~-~E~~~~~lm~~~~~~g~~~~A~~~Y~~~~~~l~~elg~~Ps~~~~~  140 (146)
T PF03704_consen   64 ALERLAEALLEAGDYEEALRLLQRALALDPY-DEEAYRLLMRALAAQGRRAEALRVYERYRRRLREELGIEPSPETRA  140 (146)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT--HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHS----HHHHH
T ss_pred             HHHHHHHHHHhccCHHHHHHHHHHHHhcCCC-CHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhCcCcCHHHHH
Confidence            4555666677778888888888888877665 77788888888888888888888887765     347777776643

It is important for the formation of secondary metabolites.; PDB: 2FF4_B 2FEZ_A.

>KOG2041 consensus WD40 repeat protein [General function prediction only]

Probab=97.20  E-value=0.23  Score=47.67  Aligned_cols=192  Identities=11%  Similarity=0.052  Sum_probs=108.9

Q ss_pred             HHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhC-CCCCCHHHHHHHHHHHHhcCCHHH
Q 012111           89 IKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSD-GLKPSVDVYTALVSAYGQSGLLDE  167 (471)
Q Consensus        89 ~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~-~~~~~~~~~~~li~~~~~~~~~~~  167 (471)
                      .--|++++|.++|-.+.+++          ..+..+.+.|++-.+.+++..--.. .-..-...|+.+...++....++.
T Consensus       745 ~~~g~feeaek~yld~drrD----------LAielr~klgDwfrV~qL~r~g~~d~dD~~~e~A~r~ig~~fa~~~~We~  814 (1189)
T KOG2041|consen  745 AFYGEFEEAEKLYLDADRRD----------LAIELRKKLGDWFRVYQLIRNGGSDDDDEGKEDAFRNIGETFAEMMEWEE  814 (1189)
T ss_pred             hhhcchhHhhhhhhccchhh----------hhHHHHHhhhhHHHHHHHHHccCCCcchHHHHHHHHHHHHHHHHHHHHHH
Confidence            34688888888887776543          3455666777777777666542111 001123467778888888888888


Q ss_pred             HHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHH
Q 012111          168 AFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMV  247 (471)
Q Consensus       168 a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  247 (471)
                      |.+.|..-..          ....+.++.+..++++-+.+-..+     +-+....-.+..++.+.|.-++|.+.|-+..
T Consensus       815 A~~yY~~~~~----------~e~~~ecly~le~f~~LE~la~~L-----pe~s~llp~~a~mf~svGMC~qAV~a~Lr~s  879 (1189)
T KOG2041|consen  815 AAKYYSYCGD----------TENQIECLYRLELFGELEVLARTL-----PEDSELLPVMADMFTSVGMCDQAVEAYLRRS  879 (1189)
T ss_pred             HHHHHHhccc----------hHhHHHHHHHHHhhhhHHHHHHhc-----CcccchHHHHHHHHHhhchHHHHHHHHHhcc
Confidence            8888775432          122455555555555544444433     3344555566677777777777777665441


Q ss_pred             HcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHH--------------HHHHHHHHHcCCHHHHHHH
Q 012111          248 ESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTL--------------NILTKSYGRAGMYDKMRSV  313 (471)
Q Consensus       248 ~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~--------------~~ll~~~~~~~~~~~a~~~  313 (471)
                           .|.     ..+..|...+++.+|.++-+...    -|.+.+.              .--|..+.+.|..-.|.++
T Consensus       880 -----~pk-----aAv~tCv~LnQW~~avelaq~~~----l~qv~tliak~aaqll~~~~~~eaIe~~Rka~~~~daarl  945 (1189)
T KOG2041|consen  880 -----LPK-----AAVHTCVELNQWGEAVELAQRFQ----LPQVQTLIAKQAAQLLADANHMEAIEKDRKAGRHLDAARL  945 (1189)
T ss_pred             -----CcH-----HHHHHHHHHHHHHHHHHHHHhcc----chhHHHHHHHHHHHHHhhcchHHHHHHhhhcccchhHHHH
Confidence                 222     23445566666666666554432    1222221              1124456666666666666


Q ss_pred             HHHHHh
Q 012111          314 MDFMQK  319 (471)
Q Consensus       314 ~~~~~~  319 (471)
                      +.+|.+
T Consensus       946 l~qmae  951 (1189)
T KOG2041|consen  946 LSQMAE  951 (1189)
T ss_pred             HHHHhH
Confidence            666643

>PF13371 TPR_9: Tetratricopeptide repeat

Probab=97.18  E-value=0.0022  Score=43.19  Aligned_cols=54  Identities=17%  Similarity=0.019  Sum_probs=25.9

Q ss_pred             HHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 012111          370 AYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKE  424 (471)
Q Consensus       370 ~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~  424 (471)
                      .|.+.+++++|.++++.+...++. +...+.....++...|++++|.+.|++..+
T Consensus         4 ~~~~~~~~~~A~~~~~~~l~~~p~-~~~~~~~~a~~~~~~g~~~~A~~~l~~~l~   57 (73)
T PF13371_consen    4 IYLQQEDYEEALEVLERALELDPD-DPELWLQRARCLFQLGRYEEALEDLERALE   57 (73)
T ss_pred             HHHhCCCHHHHHHHHHHHHHhCcc-cchhhHHHHHHHHHhccHHHHHHHHHHHHH
Confidence            344445555555555555444433 444444444444455555555555554444

>PF13281 DUF4071: Domain of unknown function (DUF4071)

Probab=97.16  E-value=0.14  Score=46.24  Aligned_cols=166  Identities=14%  Similarity=0.093  Sum_probs=96.1

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhCC---CCCCHHHHHHHHHHHHH---cCCHHHHHHHHHHHHhCCCCCCHHHHHH
Q 012111          258 TLNSMISAYGNSGNIEKMEKWYNEFNLMG---VKADIQTLNILTKSYGR---AGMYDKMRSVMDFMQKRFFFPTVVTYNI  331 (471)
Q Consensus       258 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~---~~~~~~~~~~ll~~~~~---~~~~~~a~~~~~~~~~~~~~~~~~~~~~  331 (471)
                      +...++-+|....+++...++.+.+....   +.-....--...-++.+   .|+.++|.+++..+......+++.+|..
T Consensus       143 iv~~lllSyRdiqdydamI~Lve~l~~~p~~~~~~~~~i~~~yafALnRrn~~gdre~Al~il~~~l~~~~~~~~d~~gL  222 (374)
T PF13281_consen  143 IVINLLLSYRDIQDYDAMIKLVETLEALPTCDVANQHNIKFQYAFALNRRNKPGDREKALQILLPVLESDENPDPDTLGL  222 (374)
T ss_pred             HHHHHHHHhhhhhhHHHHHHHHHHhhccCccchhcchHHHHHHHHHHhhcccCCCHHHHHHHHHHHHhccCCCChHHHHH
Confidence            34455566888888898888888887642   11122222334445556   7888888888888666666677788887


Q ss_pred             HHHHHHh----c-----CCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHH----HHHHHH---HH-HHhCC---
Q 012111          332 VIETFGK----A-----GHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIM----KVDSIL---RQ-VENSD---  391 (471)
Q Consensus       332 li~~~~~----~-----g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~----~a~~~~---~~-~~~~~---  391 (471)
                      +...|-.    .     ...++|...|.+.-..  .|+..+-..++..+...|...    +..++-   .. +.+.|   
T Consensus       223 ~GRIyKD~~~~s~~~d~~~ldkAi~~Y~kgFe~--~~~~Y~GIN~AtLL~~~g~~~~~~~el~~i~~~l~~llg~kg~~~  300 (374)
T PF13281_consen  223 LGRIYKDLFLESNFTDRESLDKAIEWYRKGFEI--EPDYYSGINAATLLMLAGHDFETSEELRKIGVKLSSLLGRKGSLE  300 (374)
T ss_pred             HHHHHHHHHHHcCccchHHHHHHHHHHHHHHcC--CccccchHHHHHHHHHcCCcccchHHHHHHHHHHHHHHHhhcccc
Confidence            7766532    1     2356677777665553  355443333333333344322    222332   11 11222   


Q ss_pred             CCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhC
Q 012111          392 VILDTPFFNCIISAYGQAGDVEKMGELFLTMKER  425 (471)
Q Consensus       392 ~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~  425 (471)
                      ...+.-.+.+++.++.-.|+.++|.+..++|...
T Consensus       301 ~~~dYWd~ATl~Ea~vL~~d~~ka~~a~e~~~~l  334 (374)
T PF13281_consen  301 KMQDYWDVATLLEASVLAGDYEKAIQAAEKAFKL  334 (374)
T ss_pred             ccccHHHHHHHHHHHHHcCCHHHHHHHHHHHhhc
Confidence            2234445566777777777777777777777764

>KOG1130 consensus Predicted G-alpha GTPase interaction protein, contains GoLoco domain [Signal transduction mechanisms]

Probab=97.13  E-value=0.014  Score=51.82  Aligned_cols=268  Identities=14%  Similarity=0.041  Sum_probs=154.4

Q ss_pred             HHHHHhhcHHHHHHHHHHhhhccCccCCh----hHHHHHHHHHhcCCCHHHHHHHHHHH--HhC--CCC-CCHHHHHHHH
Q 012111           86 DEAIKQKKWQLALKIFGLLRQQQWYQARC----QTFTKLMVMLGKCKQPEQASLLFEVM--LSD--GLK-PSVDVYTALV  156 (471)
Q Consensus        86 ~~~~~~~~~~~A~~~~~~~~~~~~~~~~~----~~~~~l~~~~~~~~~~~~a~~~~~~m--~~~--~~~-~~~~~~~~li  156 (471)
                      ..+++.|+....+.+|+.+.+.+  ..|.    ..|..|..+|.-.+++++|++....=  ..+  |-+ -...+...|.
T Consensus        25 ERLck~gdcraGv~ff~aA~qvG--TeDl~tLSAIYsQLGNAyfyL~DY~kAl~yH~hDltlar~lgdklGEAKssgNLG  102 (639)
T KOG1130|consen   25 ERLCKMGDCRAGVDFFKAALQVG--TEDLSTLSAIYSQLGNAYFYLKDYEKALKYHTHDLTLARLLGDKLGEAKSSGNLG  102 (639)
T ss_pred             HHHHhccchhhhHHHHHHHHHhc--chHHHHHHHHHHHhcchhhhHhhHHHHHhhhhhhHHHHHHhcchhcccccccccc
Confidence            45789999999999999999876  4443    34667777777778899998764321  111  111 1222333444


Q ss_pred             HHHHhcCCHHHHHHHHHHh----hcCCCCCCCHHHHHHHHHHHHhcCC--------------------HHHHHHHHHHHH
Q 012111          157 SAYGQSGLLDEAFSTINDM----KSVSDCKPDVYTYSILIKSCTKFHR--------------------FDLIEKILAEMS  212 (471)
Q Consensus       157 ~~~~~~~~~~~a~~~~~~~----~~~~~~~~~~~~~~~ll~~~~~~~~--------------------~~~a~~~~~~~~  212 (471)
                      ..+--.|.+++|+-.-.+-    .+...-......+-.+...|...|.                    ++.|.+.|.+-.
T Consensus       103 NtlKv~G~fdeA~~cc~rhLd~areLgDrv~e~RAlYNlgnvYhakGk~~g~~~pee~g~f~~ev~~al~~Av~fy~eNL  182 (639)
T KOG1130|consen  103 NTLKVKGAFDEALTCCFRHLDFARELGDRVLESRALYNLGNVYHAKGKCTGLEAPEEKGAFNAEVTSALENAVKFYMENL  182 (639)
T ss_pred             chhhhhcccchHHHHHHHHhHHHHHHhHHHhhhHHHhhhhhhhhhcccccCCCChhhcccccHHHHHHHHHHHHHHHHHH
Confidence            4455556666665432211    1100001122333444555443322                    233444443221


Q ss_pred             ----HCCCC-CCHHHHHHHHHHHHccCCHHHHHHHHHHHH----HcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 012111          213 ----YLGIE-CSAVTYNTIIDGYGKAKKFEEMESSFSAMV----ESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFN  283 (471)
Q Consensus       213 ----~~g~~-~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~----~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  283 (471)
                          +.|-. .--..|..|...|.-.|+++.|+...+.-.    +-+.-......+..+.+++.-.|+++.|.+.|+.-.
T Consensus       183 ~l~~~lgDr~aqGRa~GnLGNTyYlLGdf~~ai~~H~~RL~ia~efGDrAaeRRA~sNlgN~hiflg~fe~A~ehYK~tl  262 (639)
T KOG1130|consen  183 ELSEKLGDRLAQGRAYGNLGNTYYLLGDFDQAIHFHKLRLEIAQEFGDRAAERRAHSNLGNCHIFLGNFELAIEHYKLTL  262 (639)
T ss_pred             HHHHHhhhHHhhcchhcccCceeeeeccHHHHHHHHHHHHHHHHHhhhHHHHHHhhcccchhhhhhcccHhHHHHHHHHH
Confidence                12200 012345556666667788998887654332    112112234568888889999999999998887653


Q ss_pred             h----CC-CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHh----CC-CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 012111          284 L----MG-VKADIQTLNILTKSYGRAGMYDKMRSVMDFMQK----RF-FFPTVVTYNIVIETFGKAGHIEKMEEYFKKMK  353 (471)
Q Consensus       284 ~----~~-~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~----~~-~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~  353 (471)
                      .    .| -.......-.|.+.|.-..++++|+.++.+-..    .+ ..-....+-+|..+|...|..++|+.+.+..+
T Consensus       263 ~LAielg~r~vEAQscYSLgNtytll~e~~kAI~Yh~rHLaIAqeL~DriGe~RacwSLgna~~alg~h~kAl~fae~hl  342 (639)
T KOG1130|consen  263 NLAIELGNRTVEAQSCYSLGNTYTLLKEVQKAITYHQRHLAIAQELEDRIGELRACWSLGNAFNALGEHRKALYFAELHL  342 (639)
T ss_pred             HHHHHhcchhHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHhhhhHHHHHHHHHHHH
Confidence            2    22 123445566778888888888888887764322    11 11234566778888888888888888777655


Q ss_pred             Hc
Q 012111          354 HR  355 (471)
Q Consensus       354 ~~  355 (471)
                      +.
T Consensus       343 ~~  344 (639)
T KOG1130|consen  343 RS  344 (639)
T ss_pred             HH
Confidence            43

>PF12921 ATP13: Mitochondrial ATPase expression; InterPro: IPR024319 ATPase expression protein 2 (also known as ATP13 in some species) is necessary for the expression of subunit 9 of mitochondrial ATPase

Probab=97.10  E-value=0.01  Score=44.60  Aligned_cols=80  Identities=14%  Similarity=0.188  Sum_probs=41.7

Q ss_pred             hhHHHHHHHHHhcCCCHHHHHHHHHHHHhC---------------CCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHhhcC
Q 012111          114 CQTFTKLMVMLGKCKQPEQASLLFEVMLSD---------------GLKPSVDVYTALVSAYGQSGLLDEAFSTINDMKSV  178 (471)
Q Consensus       114 ~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~---------------~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~  178 (471)
                      ..++..++.++++.|+.+....+++..-..               ...|+..+..+++.+|+..|++..|+++++...+.
T Consensus         2 e~~~~~ii~al~r~g~~~~i~~~i~~~WgI~~~~~~~~~~~~~~spl~Pt~~lL~AIv~sf~~n~~i~~al~~vd~fs~~   81 (126)
T PF12921_consen    2 EELLCNIIYALGRSGQLDSIKSYIKSVWGIDVNGKKKEGDYPPSSPLYPTSRLLIAIVHSFGYNGDIFSALKLVDFFSRK   81 (126)
T ss_pred             hHHHHHHHHHHhhcCCHHHHHHHHHHhcCCCCCCccccCccCCCCCCCCCHHHHHHHHHHHHhcccHHHHHHHHHHHHHH
Confidence            456677777777777777777766554321               12344444444444444444444444444444444


Q ss_pred             CCCCCCHHHHHHHHH
Q 012111          179 SDCKPDVYTYSILIK  193 (471)
Q Consensus       179 ~~~~~~~~~~~~ll~  193 (471)
                      .+++.+..+|..|+.
T Consensus        82 Y~I~i~~~~W~~Ll~   96 (126)
T PF12921_consen   82 YPIPIPKEFWRRLLE   96 (126)
T ss_pred             cCCCCCHHHHHHHHH
Confidence            444444444444444

The protein has a basic amino terminal signal sequence that is cleaved upon import into mitochondria [].

>PF04840 Vps16_C: Vps16, C-terminal region; InterPro: IPR006925 This protein forms part of the Class C vacuolar protein sorting (Vps) complex

Probab=97.09  E-value=0.19  Score=44.79  Aligned_cols=106  Identities=13%  Similarity=0.155  Sum_probs=67.9

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHH
Q 012111          328 TYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYG  407 (471)
Q Consensus       328 ~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  407 (471)
                      +.+..|.-+...|+...|.++-.+..    .|+..-|...+.+++..+++++-.++-..  +    -++.-|..++.+|.
T Consensus       179 Sl~~Ti~~li~~~~~k~A~kl~k~Fk----v~dkrfw~lki~aLa~~~~w~eL~~fa~s--k----KsPIGyepFv~~~~  248 (319)
T PF04840_consen  179 SLNDTIRKLIEMGQEKQAEKLKKEFK----VPDKRFWWLKIKALAENKDWDELEKFAKS--K----KSPIGYEPFVEACL  248 (319)
T ss_pred             CHHHHHHHHHHCCCHHHHHHHHHHcC----CcHHHHHHHHHHHHHhcCCHHHHHHHHhC--C----CCCCChHHHHHHHH
Confidence            34444556666777777776655543    46777777788888888888776665432  1    13456777777888


Q ss_pred             hcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHH
Q 012111          408 QAGDVEKMGELFLTMKERHCVPDNITFATMIQAYNALGMTEAAQNL  453 (471)
Q Consensus       408 ~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~  453 (471)
                      +.|+..+|..+..++     + +    ..-+..|.+.|++.+|.+.
T Consensus       249 ~~~~~~eA~~yI~k~-----~-~----~~rv~~y~~~~~~~~A~~~  284 (319)
T PF04840_consen  249 KYGNKKEASKYIPKI-----P-D----EERVEMYLKCGDYKEAAQE  284 (319)
T ss_pred             HCCCHHHHHHHHHhC-----C-h----HHHHHHHHHCCCHHHHHHH
Confidence            888887877777652     1 1    2334566777777777433

Vps16 is essential for vacuolar protein sorting, which is essential for viability in plants, but not yeast []. The Class C Vps complex is required for SNARE-mediated membrane fusion at the lysosome-like yeast vacuole. It is thought to play essential roles in membrane docking and fusion at the Golgi-to-endosome and endosome-to-vacuole stages of transport []. The role of VPS16 in this complex is not known.; GO: 0006886 intracellular protein transport, 0005737 cytoplasm

>PRK10803 tol-pal system protein YbgF; Provisional

Probab=97.07  E-value=0.014  Score=50.37  Aligned_cols=86  Identities=9%  Similarity=0.008  Sum_probs=37.7

Q ss_pred             HhhcHHHHHHHHHHhhhccCccCC---hhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCC--CCCHHHHHHHHHHHHhcCC
Q 012111           90 KQKKWQLALKIFGLLRQQQWYQAR---CQTFTKLMVMLGKCKQPEQASLLFEVMLSDGL--KPSVDVYTALVSAYGQSGL  164 (471)
Q Consensus        90 ~~~~~~~A~~~~~~~~~~~~~~~~---~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~--~~~~~~~~~li~~~~~~~~  164 (471)
                      +.|++++|+..|+.+.+..  |.+   ..++..+...|...|++++|...|+.+...-.  +.....+-.+...+...|+
T Consensus       155 ~~~~y~~Ai~af~~fl~~y--P~s~~a~~A~y~LG~~y~~~g~~~~A~~~f~~vv~~yP~s~~~~dAl~klg~~~~~~g~  232 (263)
T PRK10803        155 DKSRQDDAIVAFQNFVKKY--PDSTYQPNANYWLGQLNYNKGKKDDAAYYFASVVKNYPKSPKAADAMFKVGVIMQDKGD  232 (263)
T ss_pred             hcCCHHHHHHHHHHHHHHC--cCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCcchhHHHHHHHHHHHHcCC
Confidence            3455555555555555432  211   13444445555555555555555555543211  0112233333344444455


Q ss_pred             HHHHHHHHHHhhc
Q 012111          165 LDEAFSTINDMKS  177 (471)
Q Consensus       165 ~~~a~~~~~~~~~  177 (471)
                      .+.|..+|+.+.+
T Consensus       233 ~~~A~~~~~~vi~  245 (263)
T PRK10803        233 TAKAKAVYQQVIK  245 (263)
T ss_pred             HHHHHHHHHHHHH
Confidence            5555555554443

>COG4700 Uncharacterized protein conserved in bacteria containing a divergent form of TPR repeats [Function unknown]

Probab=97.04  E-value=0.11  Score=41.11  Aligned_cols=65  Identities=9%  Similarity=0.041  Sum_probs=27.0

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHH
Q 012111          184 DVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVE  248 (471)
Q Consensus       184 ~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  248 (471)
                      ++..-..|..++...|+..+|...|++...--+.-|....-.+.++....+++..|...++.+.+
T Consensus        88 Tvqnr~rLa~al~elGr~~EA~~hy~qalsG~fA~d~a~lLglA~Aqfa~~~~A~a~~tLe~l~e  152 (251)
T COG4700          88 TVQNRYRLANALAELGRYHEAVPHYQQALSGIFAHDAAMLLGLAQAQFAIQEFAAAQQTLEDLME  152 (251)
T ss_pred             hHHHHHHHHHHHHHhhhhhhhHHHHHHHhccccCCCHHHHHHHHHHHHhhccHHHHHHHHHHHhh
Confidence            33333334444444444444444444443322223333444444444444444444444444433

>PF13371 TPR_9: Tetratricopeptide repeat

Probab=96.99  E-value=0.0066  Score=40.77  Aligned_cols=60  Identities=18%  Similarity=0.132  Sum_probs=37.5

Q ss_pred             HHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhhhcC
Q 012111          404 SAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAYNALGMTEAAQNLENKMIAMKENS  464 (471)
Q Consensus       404 ~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~~  464 (471)
                      ..|.+.+++++|.++++++...+ +.+...+.....++.+.|++++|.+.+++.++..|+.
T Consensus         3 ~~~~~~~~~~~A~~~~~~~l~~~-p~~~~~~~~~a~~~~~~g~~~~A~~~l~~~l~~~p~~   62 (73)
T PF13371_consen    3 QIYLQQEDYEEALEVLERALELD-PDDPELWLQRARCLFQLGRYEEALEDLERALELSPDD   62 (73)
T ss_pred             HHHHhCCCHHHHHHHHHHHHHhC-cccchhhHHHHHHHHHhccHHHHHHHHHHHHHHCCCc
Confidence            35566677777777777766641 2244455556666667777777777777777666643

>PRK15331 chaperone protein SicA; Provisional

Probab=96.88  E-value=0.018  Score=44.74  Aligned_cols=90  Identities=12%  Similarity=-0.024  Sum_probs=65.7

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCH
Q 012111          333 IETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDV  412 (471)
Q Consensus       333 i~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~  412 (471)
                      ..-+...|++++|..+|.-+.-.+ .-+..-+..|..++-..+++++|...|......+.. |+..+-....++...|+.
T Consensus        44 Ay~~y~~Gk~~eA~~~F~~L~~~d-~~n~~Y~~GLaa~~Q~~k~y~~Ai~~Y~~A~~l~~~-dp~p~f~agqC~l~l~~~  121 (165)
T PRK15331         44 AYEFYNQGRLDEAETFFRFLCIYD-FYNPDYTMGLAAVCQLKKQFQKACDLYAVAFTLLKN-DYRPVFFTGQCQLLMRKA  121 (165)
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHhC-cCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccC-CCCccchHHHHHHHhCCH
Confidence            334557788888888888877654 224555667777777788888888888776655443 444555667888888888


Q ss_pred             HHHHHHHHHHHh
Q 012111          413 EKMGELFLTMKE  424 (471)
Q Consensus       413 ~~a~~~~~~~~~  424 (471)
                      +.|...|+...+
T Consensus       122 ~~A~~~f~~a~~  133 (165)
T PRK15331        122 AKARQCFELVNE  133 (165)
T ss_pred             HHHHHHHHHHHh
Confidence            888888888876

>COG3898 Uncharacterized membrane-bound protein [Function unknown]

Probab=96.85  E-value=0.31  Score=43.42  Aligned_cols=284  Identities=12%  Similarity=0.075  Sum_probs=170.8

Q ss_pred             cCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHH--HHhcCCHHHHHHHHHHhhcCCCCCCCHHH--HHHHHHHHHhcCCH
Q 012111          126 KCKQPEQASLLFEVMLSDGLKPSVDVYTALVSA--YGQSGLLDEAFSTINDMKSVSDCKPDVYT--YSILIKSCTKFHRF  201 (471)
Q Consensus       126 ~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~--~~~~~~~~~a~~~~~~~~~~~~~~~~~~~--~~~ll~~~~~~~~~  201 (471)
                      ..|+-..|.++-.+-... +.-|....-.++.+  -.-.|+++.|.+-|+.|..    .|....  ...|.-...+.|+.
T Consensus        96 gAGda~lARkmt~~~~~l-lssDqepLIhlLeAQaal~eG~~~~Ar~kfeAMl~----dPEtRllGLRgLyleAqr~Gar  170 (531)
T COG3898          96 GAGDASLARKMTARASKL-LSSDQEPLIHLLEAQAALLEGDYEDARKKFEAMLD----DPETRLLGLRGLYLEAQRLGAR  170 (531)
T ss_pred             ccCchHHHHHHHHHHHhh-hhccchHHHHHHHHHHHHhcCchHHHHHHHHHHhc----ChHHHHHhHHHHHHHHHhcccH
Confidence            457777777776654422 22244444445543  3346899999999999986    233322  22233334567888


Q ss_pred             HHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHH--HHHHHHHH--H-hcCCHHHHH
Q 012111          202 DLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFT--LNSMISAY--G-NSGNIEKME  276 (471)
Q Consensus       202 ~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~--~~~l~~~~--~-~~~~~~~a~  276 (471)
                      +.|.++-+.....- +--...+...+...+..|+|+.|+++++.-.+..-+.++..-  -..|+.+-  . -.-+...|.
T Consensus       171 eaAr~yAe~Aa~~A-p~l~WA~~AtLe~r~~~gdWd~AlkLvd~~~~~~vie~~~aeR~rAvLLtAkA~s~ldadp~~Ar  249 (531)
T COG3898         171 EAARHYAERAAEKA-PQLPWAARATLEARCAAGDWDGALKLVDAQRAAKVIEKDVAERSRAVLLTAKAMSLLDADPASAR  249 (531)
T ss_pred             HHHHHHHHHHHhhc-cCCchHHHHHHHHHHhcCChHHHHHHHHHHHHHHhhchhhHHHHHHHHHHHHHHHHhcCChHHHH
Confidence            88888887776542 223566778888899999999999999877665445555432  12222211  1 123455555


Q ss_pred             HHHHHHHhCCCCCCHH-HHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 012111          277 KWYNEFNLMGVKADIQ-TLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHR  355 (471)
Q Consensus       277 ~~~~~~~~~~~~~~~~-~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  355 (471)
                      ..-.+..+  +.||.. .-..-..++.+.|+..++-.+++.+-+....|+..    .+..+.+.|+  .+..-+++..+.
T Consensus       250 ~~A~~a~K--L~pdlvPaav~AAralf~d~~~rKg~~ilE~aWK~ePHP~ia----~lY~~ar~gd--ta~dRlkRa~~L  321 (531)
T COG3898         250 DDALEANK--LAPDLVPAAVVAARALFRDGNLRKGSKILETAWKAEPHPDIA----LLYVRARSGD--TALDRLKRAKKL  321 (531)
T ss_pred             HHHHHHhh--cCCccchHHHHHHHHHHhccchhhhhhHHHHHHhcCCChHHH----HHHHHhcCCC--cHHHHHHHHHHH
Confidence            55444433  344432 22334567888888888888888887775544432    1222344444  333333333322


Q ss_pred             -CCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHh-cCCHHHHHHHHHHHHhC
Q 012111          356 -GMKP-NSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQ-AGDVEKMGELFLTMKER  425 (471)
Q Consensus       356 -~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~-~g~~~~a~~~~~~~~~~  425 (471)
                       .++| +......+..+....|++..|..--+...+.  .|....|..|.+.-.. .||-.++...+.+.+..
T Consensus       322 ~slk~nnaes~~~va~aAlda~e~~~ARa~Aeaa~r~--~pres~~lLlAdIeeAetGDqg~vR~wlAqav~A  392 (531)
T COG3898         322 ESLKPNNAESSLAVAEAALDAGEFSAARAKAEAAARE--APRESAYLLLADIEEAETGDQGKVRQWLAQAVKA  392 (531)
T ss_pred             HhcCccchHHHHHHHHHHHhccchHHHHHHHHHHhhh--CchhhHHHHHHHHHhhccCchHHHHHHHHHHhcC
Confidence             2344 4556667777778888888887766666654  4566677766665543 48888888888777753

>PF13424 TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 4A1S_B 3CEQ_B 3EDT_H

Probab=96.85  E-value=0.0039  Score=42.57  Aligned_cols=65  Identities=18%  Similarity=0.255  Sum_probs=40.9

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhC--CCC---CC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHHhh
Q 012111          397 PFFNCIISAYGQAGDVEKMGELFLTMKER--HCV---PD-NITFATMIQAYNALGMTEAAQNLENKMIAMK  461 (471)
Q Consensus       397 ~~~~~l~~~~~~~g~~~~a~~~~~~~~~~--~~~---p~-~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~  461 (471)
                      .+|+.+...|...|++++|+..|++..+.  ...   |+ ..++..+..++...|++++|.+++++.++..
T Consensus         6 ~~~~~la~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~al~i~   76 (78)
T PF13424_consen    6 NAYNNLARVYRELGRYDEALDYYEKALDIEEQLGDDHPDTANTLNNLGECYYRLGDYEEALEYYQKALDIF   76 (78)
T ss_dssp             HHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhh
Confidence            45666777777777777777777766532  011   22 3456666677777777777777777776543

...

>KOG2280 consensus Vacuolar assembly/sorting protein VPS16 [Intracellular trafficking, secretion, and vesicular transport]

Probab=96.82  E-value=0.54  Score=45.63  Aligned_cols=338  Identities=12%  Similarity=0.086  Sum_probs=171.1

Q ss_pred             ccCCCchHHH-----HHHHHHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCC--HHHHHHHHHHHHhCCC
Q 012111           73 YKNLWPKPVL-----EALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQ--PEQASLLFEVMLSDGL  145 (471)
Q Consensus        73 ~~~~~~~~~~-----~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~--~~~a~~~~~~m~~~~~  145 (471)
                      +.+++.+.+.     .+++.+...+.+..|+++-.++....  .-....|......+.+..+  -+++.+.+++=.....
T Consensus       427 gIplT~~qy~~l~~~~vi~Rl~~r~~Y~vaIQva~~l~~p~--~~~~~Vl~~Wa~~kI~~~d~~d~~vld~I~~kls~~~  504 (829)
T KOG2280|consen  427 GIPLTHEQYRHLSEEVVIDRLVDRHLYSVAIQVAKLLNLPE--SQGDRVLLEWARRKIKQSDKMDEEVLDKIDEKLSAKL  504 (829)
T ss_pred             CccccHHHHhhhchhhhhHHHHhcchhHHHHHHHHHhCCcc--ccccHHHHHHHHHHHhccCccchHHHHHHHHHhcccC
Confidence            4455554443     45777888899999999998886532  1124566666666666532  2333333333332222


Q ss_pred             CCCHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCC----CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHH
Q 012111          146 KPSVDVYTALVSAYGQSGLLDEAFSTINDMKSVSDCK----PDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAV  221 (471)
Q Consensus       146 ~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~----~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~  221 (471)
                       -....|..+.+.....|+.+.|..+++.=.. .+..    .+..-+...+.-+...|+.+....++-.+.+.-   +..
T Consensus       505 -~~~iSy~~iA~~Ay~~GR~~LA~kLle~E~~-~~~qV~lLL~m~~~~~AL~kaies~d~~Li~~Vllhlk~~~---~~s  579 (829)
T KOG2280|consen  505 -TPGISYAAIARRAYQEGRFELARKLLELEPR-SGEQVPLLLKMKDSSLALKKAIESGDTDLIIQVLLHLKNKL---NRS  579 (829)
T ss_pred             -CCceeHHHHHHHHHhcCcHHHHHHHHhcCCC-ccchhHHHhccchHHHHHHHHHhcCCchhHHHHHHHHHHHH---HHH
Confidence             2445677777777788999999888764332 1110    122234455566677777777777776665431   111


Q ss_pred             HHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHH--HH----HhCCCCCCHHHHH
Q 012111          222 TYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYN--EF----NLMGVKADIQTLN  295 (471)
Q Consensus       222 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~--~~----~~~~~~~~~~~~~  295 (471)
                      .|...      ..+...|..+|.+..+..+    ..   .+-..| +.++-.++...|.  ..    ...+..|+.   .
T Consensus       580 ~l~~~------l~~~p~a~~lY~~~~r~~~----~~---~l~d~y-~q~dn~~~~a~~~~q~~~~~~~~~~r~~~l---k  642 (829)
T KOG2280|consen  580 SLFMT------LRNQPLALSLYRQFMRHQD----RA---TLYDFY-NQDDNHQALASFHLQASYAAETIEGRIPAL---K  642 (829)
T ss_pred             HHHHH------HHhchhhhHHHHHHHHhhc----hh---hhhhhh-hcccchhhhhhhhhhhhhhhhhhcccchhH---H
Confidence            11111      1233345555555443221    10   011111 1111111111111  00    001112222   2


Q ss_pred             HHHHHHHHcCCHH----------HHHHHHHHHHh-CCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHH
Q 012111          296 ILTKSYGRAGMYD----------KMRSVMDFMQK-RFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITY  364 (471)
Q Consensus       296 ~ll~~~~~~~~~~----------~a~~~~~~~~~-~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~  364 (471)
                      ...+.+.+.....          +-+.+...+.. .+..-...+.+--+.-+...|+..+|.++-.+.+    -||...|
T Consensus       643 ~~a~~~a~sk~~s~e~ka~ed~~kLl~lQ~~Le~q~~~~f~dlSl~dTv~~li~~g~~k~a~ql~~~Fk----ipdKr~~  718 (829)
T KOG2280|consen  643 TAANAFAKSKEKSFEAKALEDQMKLLKLQRTLEDQFGGSFVDLSLHDTVTTLILIGQNKRAEQLKSDFK----IPDKRLW  718 (829)
T ss_pred             HHHHHHhhhhhhhhHHHHHHHHHHHHHHHHHHHHHhccccccCcHHHHHHHHHHccchHHHHHHHHhcC----CcchhhH
Confidence            2223333322211          11112222211 1111222234444555666677777777666554    5677777


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhc
Q 012111          365 CSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAYNAL  444 (471)
Q Consensus       365 ~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~  444 (471)
                      -.=+.+++..+++++-+++-+...      .+.-|...+.+|.+.|+.++|.+++-+....     .    -...+|.+.
T Consensus       719 wLk~~aLa~~~kweeLekfAkskk------sPIGy~PFVe~c~~~~n~~EA~KYiprv~~l-----~----ekv~ay~~~  783 (829)
T KOG2280|consen  719 WLKLTALADIKKWEELEKFAKSKK------SPIGYLPFVEACLKQGNKDEAKKYIPRVGGL-----Q----EKVKAYLRV  783 (829)
T ss_pred             HHHHHHHHhhhhHHHHHHHHhccC------CCCCchhHHHHHHhcccHHHHhhhhhccCCh-----H----HHHHHHHHh
Confidence            777777777777777666554433      2334556677777777777777776654321     1    344567777


Q ss_pred             CCHHHHHHH
Q 012111          445 GMTEAAQNL  453 (471)
Q Consensus       445 g~~~~A~~~  453 (471)
                      |++.+|.++
T Consensus       784 ~~~~eAad~  792 (829)
T KOG2280|consen  784 GDVKEAADL  792 (829)
T ss_pred             ccHHHHHHH
Confidence            777766544

>PF03704 BTAD: Bacterial transcriptional activator domain; InterPro: IPR005158 Found in the DNRI/REDD/AFSR family of regulators, this region of AFSR (P25941 from SWISSPROT) along with the C-terminal region is capable of independently directing actinorhodin production

Probab=96.81  E-value=0.0075  Score=47.23  Aligned_cols=72  Identities=19%  Similarity=0.176  Sum_probs=39.7

Q ss_pred             HHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHhhc----CCCCCCCHHHH
Q 012111          116 TFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAFSTINDMKS----VSDCKPDVYTY  188 (471)
Q Consensus       116 ~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~----~~~~~~~~~~~  188 (471)
                      +...++..+...|++++|..+.+.+....+- +...|..+|.+|...|+...|++.|+.+..    ..|+.|+..+-
T Consensus        64 ~~~~l~~~~~~~~~~~~a~~~~~~~l~~dP~-~E~~~~~lm~~~~~~g~~~~A~~~Y~~~~~~l~~elg~~Ps~~~~  139 (146)
T PF03704_consen   64 ALERLAEALLEAGDYEEALRLLQRALALDPY-DEEAYRLLMRALAAQGRRAEALRVYERYRRRLREELGIEPSPETR  139 (146)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT--HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHS----HHHH
T ss_pred             HHHHHHHHHHhccCHHHHHHHHHHHHhcCCC-CHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhCcCcCHHHH
Confidence            4455555666667777777777766665322 566667777777777777777766665533    14566665553

It is important for the formation of secondary metabolites.; PDB: 2FF4_B 2FEZ_A.

>PF12921 ATP13: Mitochondrial ATPase expression; InterPro: IPR024319 ATPase expression protein 2 (also known as ATP13 in some species) is necessary for the expression of subunit 9 of mitochondrial ATPase

Probab=96.79  E-value=0.032  Score=41.91  Aligned_cols=98  Identities=10%  Similarity=-0.028  Sum_probs=55.9

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHH
Q 012111          148 SVDVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTII  227 (471)
Q Consensus       148 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~  227 (471)
                      |..++..+|.++++.|+.+....+++..-   |+.++...-         .+.         .-......|+..+..+++
T Consensus         1 de~~~~~ii~al~r~g~~~~i~~~i~~~W---gI~~~~~~~---------~~~---------~~~~spl~Pt~~lL~AIv   59 (126)
T PF12921_consen    1 DEELLCNIIYALGRSGQLDSIKSYIKSVW---GIDVNGKKK---------EGD---------YPPSSPLYPTSRLLIAIV   59 (126)
T ss_pred             ChHHHHHHHHHHhhcCCHHHHHHHHHHhc---CCCCCCccc---------cCc---------cCCCCCCCCCHHHHHHHH
Confidence            34556666666666666666666665442   333221100         000         111223456677777777


Q ss_pred             HHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHH
Q 012111          228 DGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAY  266 (471)
Q Consensus       228 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~  266 (471)
                      .+|+..|++..|.++.+...+..+++.+...|..|+.-.
T Consensus        60 ~sf~~n~~i~~al~~vd~fs~~Y~I~i~~~~W~~Ll~W~   98 (126)
T PF12921_consen   60 HSFGYNGDIFSALKLVDFFSRKYPIPIPKEFWRRLLEWA   98 (126)
T ss_pred             HHHHhcccHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Confidence            777777777777777777766666666666666666543

The protein has a basic amino terminal signal sequence that is cleaved upon import into mitochondria [].

>COG4105 ComL DNA uptake lipoprotein [General function prediction only]

Probab=96.77  E-value=0.27  Score=41.40  Aligned_cols=189  Identities=12%  Similarity=0.032  Sum_probs=104.8

Q ss_pred             CchHHHHHHHHHHHhhcHHHHHHHHHHhhhccCccC-ChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHH
Q 012111           77 WPKPVLEALDEAIKQKKWQLALKIFGLLRQQQWYQA-RCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTAL  155 (471)
Q Consensus        77 ~~~~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~l  155 (471)
                      .++.+-.......+.|+|++|.+.|+.+..+.+..| ...+.-.++.++.+.+++++|+..+++....-..-....|-.-
T Consensus        33 p~~~LY~~g~~~L~~gn~~~A~~~fe~l~~~~p~s~~~~qa~l~l~yA~Yk~~~y~~A~~~~drFi~lyP~~~n~dY~~Y  112 (254)
T COG4105          33 PASELYNEGLTELQKGNYEEAIKYFEALDSRHPFSPYSEQAQLDLAYAYYKNGEYDLALAYIDRFIRLYPTHPNADYAYY  112 (254)
T ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCcccHHHHHHHHHHHHhcccHHHHHHHHHHHHHhCCCCCChhHHHH
Confidence            345555666666789999999999999988753332 3456667777888889999999988888776332223344444


Q ss_pred             HHHHHhc-------CCHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHH
Q 012111          156 VSAYGQS-------GLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIID  228 (471)
Q Consensus       156 i~~~~~~-------~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~  228 (471)
                      |.+++.-       .+...+.+.+..+..             ++.-|=...-...|...+..+...    =...=..+.+
T Consensus       113 lkgLs~~~~i~~~~rDq~~~~~A~~~f~~-------------~i~ryPnS~Ya~dA~~~i~~~~d~----LA~~Em~Iar  175 (254)
T COG4105         113 LKGLSYFFQIDDVTRDQSAARAAFAAFKE-------------LVQRYPNSRYAPDAKARIVKLNDA----LAGHEMAIAR  175 (254)
T ss_pred             HHHHHHhccCCccccCHHHHHHHHHHHHH-------------HHHHCCCCcchhhHHHHHHHHHHH----HHHHHHHHHH
Confidence            5544421       122222222222221             111111111112222222211110    0000123567


Q ss_pred             HHHccCCHHHHHHHHHHHHHcCCCCCC---HHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 012111          229 GYGKAKKFEEMESSFSAMVESGGCHPD---IFTLNSMISAYGNSGNIEKMEKWYNEFNL  284 (471)
Q Consensus       229 ~~~~~~~~~~a~~~~~~~~~~~~~~~~---~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  284 (471)
                      .|.+.|.+..|..-++.|.+..  +.+   ...+-.+..+|...|-.++|.+.-.-+..
T Consensus       176 yY~kr~~~~AA~nR~~~v~e~y--~~t~~~~eaL~~l~eaY~~lgl~~~a~~~~~vl~~  232 (254)
T COG4105         176 YYLKRGAYVAAINRFEEVLENY--PDTSAVREALARLEEAYYALGLTDEAKKTAKVLGA  232 (254)
T ss_pred             HHHHhcChHHHHHHHHHHHhcc--ccccchHHHHHHHHHHHHHhCChHHHHHHHHHHHh
Confidence            7888888888888888887763  222   23344556777777777777766655543

>KOG1538 consensus Uncharacterized conserved protein WDR10, contains WD40 repeats [General function prediction only]

Probab=96.73  E-value=0.2  Score=47.52  Aligned_cols=55  Identities=5%  Similarity=-0.041  Sum_probs=33.3

Q ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 012111          291 IQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKH  354 (471)
Q Consensus       291 ~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  354 (471)
                      ..+...+...+-+...+.-|.++|..|-..         ..+++.....+++++|..+-++..+
T Consensus       747 re~l~~~a~ylk~l~~~gLAaeIF~k~gD~---------ksiVqlHve~~~W~eAFalAe~hPe  801 (1081)
T KOG1538|consen  747 REPLLLCATYLKKLDSPGLAAEIFLKMGDL---------KSLVQLHVETQRWDEAFALAEKHPE  801 (1081)
T ss_pred             hhHHHHHHHHHhhccccchHHHHHHHhccH---------HHHhhheeecccchHhHhhhhhCcc
Confidence            344444444555556666777777665432         2456666777778887777766544

>COG3898 Uncharacterized membrane-bound protein [Function unknown]

Probab=96.72  E-value=0.4  Score=42.77  Aligned_cols=294  Identities=10%  Similarity=0.024  Sum_probs=186.4

Q ss_pred             HHHHHHHHHHh--cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHHHH--HHhcCCHHHHHHHHHHHHHCCCCCCHH--HHH
Q 012111          151 VYTALVSAYGQ--SGLLDEAFSTINDMKSVSDCKPDVYTYSILIKS--CTKFHRFDLIEKILAEMSYLGIECSAV--TYN  224 (471)
Q Consensus       151 ~~~~li~~~~~--~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~--~~~~~~~~~a~~~~~~~~~~g~~~~~~--~~~  224 (471)
                      .|..|-.+++.  .|+-..|.++-.+..+  -+..|......++.+  -.-.|+++.|.+-|+.|...   |...  -..
T Consensus        84 gyqALStGliAagAGda~lARkmt~~~~~--llssDqepLIhlLeAQaal~eG~~~~Ar~kfeAMl~d---PEtRllGLR  158 (531)
T COG3898          84 GYQALSTGLIAAGAGDASLARKMTARASK--LLSSDQEPLIHLLEAQAALLEGDYEDARKKFEAMLDD---PETRLLGLR  158 (531)
T ss_pred             HHHHHhhhhhhhccCchHHHHHHHHHHHh--hhhccchHHHHHHHHHHHHhcCchHHHHHHHHHHhcC---hHHHHHhHH
Confidence            34555554443  5677788777766543  233455555555544  34579999999999999852   2221  122


Q ss_pred             HHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCC-CCCCHHH--HHHHHHHH
Q 012111          225 TIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMG-VKADIQT--LNILTKSY  301 (471)
Q Consensus       225 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~--~~~ll~~~  301 (471)
                      .|.-.--+.|..+.|...-+......  +.-...+...+...|..|+++.|+++.+.-.... +.++..-  -..|+.+-
T Consensus       159 gLyleAqr~GareaAr~yAe~Aa~~A--p~l~WA~~AtLe~r~~~gdWd~AlkLvd~~~~~~vie~~~aeR~rAvLLtAk  236 (531)
T COG3898         159 GLYLEAQRLGAREAARHYAERAAEKA--PQLPWAARATLEARCAAGDWDGALKLVDAQRAAKVIEKDVAERSRAVLLTAK  236 (531)
T ss_pred             HHHHHHHhcccHHHHHHHHHHHHhhc--cCCchHHHHHHHHHHhcCChHHHHHHHHHHHHHHhhchhhHHHHHHHHHHHH
Confidence            33333456899999999888876653  3345678889999999999999999998875543 2344322  12222221


Q ss_pred             H---HcCCHHHHHHHHHHHHhCCCCCCHHHH-HHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCH
Q 012111          302 G---RAGMYDKMRSVMDFMQKRFFFPTVVTY-NIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLI  377 (471)
Q Consensus       302 ~---~~~~~~~a~~~~~~~~~~~~~~~~~~~-~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~  377 (471)
                      .   -..+...|...-.+..+  +.|+...- -.-..++.+.|+..++-.+++.+-+....|+  +...  ....+.|+ 
T Consensus       237 A~s~ldadp~~Ar~~A~~a~K--L~pdlvPaav~AAralf~d~~~rKg~~ilE~aWK~ePHP~--ia~l--Y~~ar~gd-  309 (531)
T COG3898         237 AMSLLDADPASARDDALEANK--LAPDLVPAAVVAARALFRDGNLRKGSKILETAWKAEPHPD--IALL--YVRARSGD-  309 (531)
T ss_pred             HHHHhcCChHHHHHHHHHHhh--cCCccchHHHHHHHHHHhccchhhhhhHHHHHHhcCCChH--HHHH--HHHhcCCC-
Confidence            1   12234445444443333  45554432 2334788999999999999999998755554  3322  22344554 


Q ss_pred             HHHHHHHHHHH---hCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHH-hcCCHHHHHHH
Q 012111          378 MKVDSILRQVE---NSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAYN-ALGMTEAAQNL  453 (471)
Q Consensus       378 ~~a~~~~~~~~---~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~-~~g~~~~A~~~  453 (471)
                       .+..-+++..   ..... +....-.+..+-...|++..|..--+...+  ..|....|..|.+.-. ..|+-.+++.+
T Consensus       310 -ta~dRlkRa~~L~slk~n-naes~~~va~aAlda~e~~~ARa~Aeaa~r--~~pres~~lLlAdIeeAetGDqg~vR~w  385 (531)
T COG3898         310 -TALDRLKRAKKLESLKPN-NAESSLAVAEAALDAGEFSAARAKAEAAAR--EAPRESAYLLLADIEEAETGDQGKVRQW  385 (531)
T ss_pred             -cHHHHHHHHHHHHhcCcc-chHHHHHHHHHHHhccchHHHHHHHHHHhh--hCchhhHHHHHHHHHhhccCchHHHHHH
Confidence             3333333332   22222 566677788888899999988887776665  4788888888887654 44999999999


Q ss_pred             HHHHHHhhh
Q 012111          454 ENKMIAMKE  462 (471)
Q Consensus       454 ~~~m~~~~~  462 (471)
                      +-+.++.--
T Consensus       386 lAqav~APr  394 (531)
T COG3898         386 LAQAVKAPR  394 (531)
T ss_pred             HHHHhcCCC
Confidence            888776543

>PF04184 ST7: ST7 protein; InterPro: IPR007311 The ST7 (for suppression of tumorigenicity 7) protein is thought to be a tumour suppressor gene

Probab=96.67  E-value=0.24  Score=45.81  Aligned_cols=109  Identities=12%  Similarity=0.084  Sum_probs=68.4

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCC-cCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCC-HHHHHHHH
Q 012111          361 SITYCSLVSAYSKAGLIMKVDSILRQVENSDVI-LDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPD-NITFATMI  438 (471)
Q Consensus       361 ~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~-~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~-~~~~~~l~  438 (471)
                      ..+-..+..++.+.|+.++|.+.++++.+..+. -+..+...|+.++...+.+.++..++.+..+...+.+ ...|+..+
T Consensus       259 ~y~KrRLAmCarklGr~~EAIk~~rdLlke~p~~~~l~IrenLie~LLelq~Yad~q~lL~kYdDi~lpkSAti~YTaAL  338 (539)
T PF04184_consen  259 VYAKRRLAMCARKLGRLREAIKMFRDLLKEFPNLDNLNIRENLIEALLELQAYADVQALLAKYDDISLPKSATICYTAAL  338 (539)
T ss_pred             hhhHHHHHHHHHHhCChHHHHHHHHHHHhhCCccchhhHHHHHHHHHHhcCCHHHHHHHHHHhccccCCchHHHHHHHHH
Confidence            333455777777888888888888887754332 2444667788888888888888888888765333222 23444433


Q ss_pred             HHHHhcCC---------------HHHHHHHHHHHHHhhhcCCCCcc
Q 012111          439 QAYNALGM---------------TEAAQNLENKMIAMKENSGKKLI  469 (471)
Q Consensus       439 ~~~~~~g~---------------~~~A~~~~~~m~~~~~~~~~~~~  469 (471)
                      -.+...|+               -..|.+.+.++.+.+|...+-++
T Consensus       339 LkaRav~d~fs~e~a~rRGls~ae~~aveAi~RAvefNPHVp~YLL  384 (539)
T PF04184_consen  339 LKARAVGDKFSPEAASRRGLSPAEMNAVEAIHRAVEFNPHVPKYLL  384 (539)
T ss_pred             HHHHhhccccCchhhhhcCCChhHHHHHHHHHHHHHhCCCCchhhh
Confidence            33332232               13456788888888887665443

The molecular function of this protein is uncertain.

>PRK15331 chaperone protein SicA; Provisional

Probab=96.64  E-value=0.063  Score=41.84  Aligned_cols=92  Identities=13%  Similarity=-0.087  Sum_probs=66.7

Q ss_pred             HHHHHHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhc
Q 012111           83 EALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQS  162 (471)
Q Consensus        83 ~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~  162 (471)
                      ...-.+...|++++|..+|..+--.+  +-+..-+..|..++-..+++++|...|......+.. |+..+-....++...
T Consensus        42 ~~Ay~~y~~Gk~~eA~~~F~~L~~~d--~~n~~Y~~GLaa~~Q~~k~y~~Ai~~Y~~A~~l~~~-dp~p~f~agqC~l~l  118 (165)
T PRK15331         42 AHAYEFYNQGRLDEAETFFRFLCIYD--FYNPDYTMGLAAVCQLKKQFQKACDLYAVAFTLLKN-DYRPVFFTGQCQLLM  118 (165)
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHhC--cCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccC-CCCccchHHHHHHHh
Confidence            44455567888888888888887755  445555667777777778888888888876655432 555566677788888


Q ss_pred             CCHHHHHHHHHHhhc
Q 012111          163 GLLDEAFSTINDMKS  177 (471)
Q Consensus       163 ~~~~~a~~~~~~~~~  177 (471)
                      |+.+.|...|+....
T Consensus       119 ~~~~~A~~~f~~a~~  133 (165)
T PRK15331        119 RKAAKARQCFELVNE  133 (165)
T ss_pred             CCHHHHHHHHHHHHh
Confidence            888888888888776

>COG3118 Thioredoxin domain-containing protein [Posttranslational modification, protein turnover, chaperones]

Probab=96.59  E-value=0.32  Score=41.77  Aligned_cols=144  Identities=10%  Similarity=0.032  Sum_probs=66.8

Q ss_pred             HhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHH
Q 012111          124 LGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDL  203 (471)
Q Consensus       124 ~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~  203 (471)
                      ....|++.+|..+|......... +...--.+..+|...|+.+.|..++..+.... -.........-|..+.+.....+
T Consensus       144 ~~~~e~~~~a~~~~~~al~~~~~-~~~~~~~la~~~l~~g~~e~A~~iL~~lP~~~-~~~~~~~l~a~i~ll~qaa~~~~  221 (304)
T COG3118         144 LIEAEDFGEAAPLLKQALQAAPE-NSEAKLLLAECLLAAGDVEAAQAILAALPLQA-QDKAAHGLQAQIELLEQAAATPE  221 (304)
T ss_pred             hhhccchhhHHHHHHHHHHhCcc-cchHHHHHHHHHHHcCChHHHHHHHHhCcccc-hhhHHHHHHHHHHHHHHHhcCCC
Confidence            34445555555555555444222 23344445555555555555555555544311 01111111122333333333333


Q ss_pred             HHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCC
Q 012111          204 IEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGN  271 (471)
Q Consensus       204 a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  271 (471)
                      ...+-.+.-..  +-|...-..+...+...|+.+.|.+.+-.+.+++.-.-|...-..++..+.-.|.
T Consensus       222 ~~~l~~~~aad--Pdd~~aa~~lA~~~~~~g~~e~Ale~Ll~~l~~d~~~~d~~~Rk~lle~f~~~g~  287 (304)
T COG3118         222 IQDLQRRLAAD--PDDVEAALALADQLHLVGRNEAALEHLLALLRRDRGFEDGEARKTLLELFEAFGP  287 (304)
T ss_pred             HHHHHHHHHhC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhcccccCcHHHHHHHHHHHhcCC
Confidence            33333333332  2355555556666666666666666555554443233344455556666555553

>COG3118 Thioredoxin domain-containing protein [Posttranslational modification, protein turnover, chaperones]

Probab=96.54  E-value=0.3  Score=41.94  Aligned_cols=152  Identities=11%  Similarity=0.026  Sum_probs=99.1

Q ss_pred             HHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHH
Q 012111          158 AYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFE  237 (471)
Q Consensus       158 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~  237 (471)
                      .....|++.+|..+|.......  +-+...-..+..+|...|+.+.|..++..+...--.........-|..+.+.....
T Consensus       143 ~~~~~e~~~~a~~~~~~al~~~--~~~~~~~~~la~~~l~~g~~e~A~~iL~~lP~~~~~~~~~~l~a~i~ll~qaa~~~  220 (304)
T COG3118         143 ELIEAEDFGEAAPLLKQALQAA--PENSEAKLLLAECLLAAGDVEAAQAILAALPLQAQDKAAHGLQAQIELLEQAAATP  220 (304)
T ss_pred             hhhhccchhhHHHHHHHHHHhC--cccchHHHHHHHHHHHcCChHHHHHHHHhCcccchhhHHHHHHHHHHHHHHHhcCC
Confidence            4556888888888888887632  33455666788888899999999999988765422222222233455555555555


Q ss_pred             HHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCC-CCCCHHHHHHHHHHHHHcCCHHHHHHHH
Q 012111          238 EMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMG-VKADIQTLNILTKSYGRAGMYDKMRSVM  314 (471)
Q Consensus       238 ~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~ll~~~~~~~~~~~a~~~~  314 (471)
                      +...+-.+.-..   +-|...-..+...+...|+.+.|.+.+-.+.+.+ -..|...-..++..+.-.|..+.+...+
T Consensus       221 ~~~~l~~~~aad---Pdd~~aa~~lA~~~~~~g~~e~Ale~Ll~~l~~d~~~~d~~~Rk~lle~f~~~g~~Dp~~~~~  295 (304)
T COG3118         221 EIQDLQRRLAAD---PDDVEAALALADQLHLVGRNEAALEHLLALLRRDRGFEDGEARKTLLELFEAFGPADPLVLAY  295 (304)
T ss_pred             CHHHHHHHHHhC---CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhcccccCcHHHHHHHHHHHhcCCCCHHHHHH
Confidence            555554444321   3366677778888888899998888777665543 2456667777888888777555443333

>PF09205 DUF1955: Domain of unknown function (DUF1955); InterPro: IPR015288 Members of this family are found in hypothetical proteins synthesised by the Archaeal organism Sulfolobus

Probab=96.50  E-value=0.22  Score=36.99  Aligned_cols=62  Identities=15%  Similarity=0.380  Sum_probs=30.9

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCC
Q 012111          330 NIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDV  392 (471)
Q Consensus       330 ~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~  392 (471)
                      ...+..+...|+-+...+++..+.+.+ .+++...-.+..+|.+.|+..++.+++.++-+.|+
T Consensus        90 D~ALd~lv~~~kkDqLdki~~~l~kn~-~~~p~~L~kia~Ay~klg~~r~~~ell~~ACekG~  151 (161)
T PF09205_consen   90 DLALDILVKQGKKDQLDKIYNELKKNE-EINPEFLVKIANAYKKLGNTREANELLKEACEKGL  151 (161)
T ss_dssp             HHHHHHHHHTT-HHHHHHHHHHH------S-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHTT-
T ss_pred             HHHHHHHHHhccHHHHHHHHHHHhhcc-CCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHhch
Confidence            344455555566666666665555432 45555555666666666666666666666555554

Their exact function has not, as yet, been determined. ; PDB: 1WY6_A.

>PF09205 DUF1955: Domain of unknown function (DUF1955); InterPro: IPR015288 Members of this family are found in hypothetical proteins synthesised by the Archaeal organism Sulfolobus

Probab=96.50  E-value=0.22  Score=36.99  Aligned_cols=61  Identities=15%  Similarity=0.246  Sum_probs=26.2

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhh
Q 012111          400 NCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAYNALGMTEAAQNLENKMIAMK  461 (471)
Q Consensus       400 ~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~  461 (471)
                      ...+..+...|+-+.-.+++..+... -.+++.....+..+|.+.|+..++.+++.++.+.|
T Consensus        90 D~ALd~lv~~~kkDqLdki~~~l~kn-~~~~p~~L~kia~Ay~klg~~r~~~ell~~ACekG  150 (161)
T PF09205_consen   90 DLALDILVKQGKKDQLDKIYNELKKN-EEINPEFLVKIANAYKKLGNTREANELLKEACEKG  150 (161)
T ss_dssp             HHHHHHHHHTT-HHHHHHHHHHH------S-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHhccHHHHHHHHHHHhhc-cCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHhc
Confidence            33344444445555545555444421 23444444455555555555555555555555444

Their exact function has not, as yet, been determined. ; PDB: 1WY6_A.

>PF13424 TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 4A1S_B 3CEQ_B 3EDT_H

Probab=96.42  E-value=0.018  Score=39.26  Aligned_cols=61  Identities=18%  Similarity=0.172  Sum_probs=33.9

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhC----CCC-cC-HHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 012111          363 TYCSLVSAYSKAGLIMKVDSILRQVENS----DVI-LD-TPFFNCIISAYGQAGDVEKMGELFLTMK  423 (471)
Q Consensus       363 ~~~~li~~~~~~g~~~~a~~~~~~~~~~----~~~-~~-~~~~~~l~~~~~~~g~~~~a~~~~~~~~  423 (471)
                      +++.+...|...|++++|+..|++..+.    |.. |+ ..+++.+..++...|++++|++++++..
T Consensus         7 ~~~~la~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~al   73 (78)
T PF13424_consen    7 AYNNLARVYRELGRYDEALDYYEKALDIEEQLGDDHPDTANTLNNLGECYYRLGDYEEALEYYQKAL   73 (78)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            4555555666666666666665554421    111 11 3456666666777777777777766654

...

>KOG0543 consensus FKBP-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=96.40  E-value=0.1  Score=46.68  Aligned_cols=100  Identities=13%  Similarity=0.033  Sum_probs=70.0

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHH
Q 012111          362 ITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAY  441 (471)
Q Consensus       362 ~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~  441 (471)
                      .++..+..++.+.+++..|++........+.. |....-.=..+|...|+++.|+..|+++.+  +.|+......=+..|
T Consensus       258 ~~~lNlA~c~lKl~~~~~Ai~~c~kvLe~~~~-N~KALyRrG~A~l~~~e~~~A~~df~ka~k--~~P~Nka~~~el~~l  334 (397)
T KOG0543|consen  258 ACHLNLAACYLKLKEYKEAIESCNKVLELDPN-NVKALYRRGQALLALGEYDLARDDFQKALK--LEPSNKAARAELIKL  334 (397)
T ss_pred             HHhhHHHHHHHhhhhHHHHHHHHHHHHhcCCC-chhHHHHHHHHHHhhccHHHHHHHHHHHHH--hCCCcHHHHHHHHHH
Confidence            45677777888888888888888888877655 666666667788888888888888888887  467665555444333


Q ss_pred             -HhcCCH-HHHHHHHHHHHHhhhcC
Q 012111          442 -NALGMT-EAAQNLENKMIAMKENS  464 (471)
Q Consensus       442 -~~~g~~-~~A~~~~~~m~~~~~~~  464 (471)
                       -+..+. +...++|..|...-...
T Consensus       335 ~~k~~~~~~kekk~y~~mF~k~~~~  359 (397)
T KOG0543|consen  335 KQKIREYEEKEKKMYANMFAKLAEE  359 (397)
T ss_pred             HHHHHHHHHHHHHHHHHHhhccccc
Confidence             333333 33477888887665543

>PF10300 DUF3808: Protein of unknown function (DUF3808); InterPro: IPR019412 This entry represents a family of proteins conserved from fungi to humans

Probab=96.36  E-value=0.33  Score=46.22  Aligned_cols=121  Identities=19%  Similarity=0.163  Sum_probs=76.8

Q ss_pred             cCCHHHHHHHHHHHHHcCCCCCHHHHHHH-HHHHHhcCCHHHHHHHHHHHHhCC---CCcCHHHHHHHHHHHHhcCCHHH
Q 012111          339 AGHIEKMEEYFKKMKHRGMKPNSITYCSL-VSAYSKAGLIMKVDSILRQVENSD---VILDTPFFNCIISAYGQAGDVEK  414 (471)
Q Consensus       339 ~g~~~~a~~~~~~m~~~~~~p~~~~~~~l-i~~~~~~g~~~~a~~~~~~~~~~~---~~~~~~~~~~l~~~~~~~g~~~~  414 (471)
                      ....+.|.+++..+.+.  -|+...|... .+.+...|++++|.+.|+......   .......+--+...+.-.++|++
T Consensus       246 ~~~~~~a~~lL~~~~~~--yP~s~lfl~~~gR~~~~~g~~~~Ai~~~~~a~~~q~~~~Ql~~l~~~El~w~~~~~~~w~~  323 (468)
T PF10300_consen  246 DVPLEEAEELLEEMLKR--YPNSALFLFFEGRLERLKGNLEEAIESFERAIESQSEWKQLHHLCYFELAWCHMFQHDWEE  323 (468)
T ss_pred             CCCHHHHHHHHHHHHHh--CCCcHHHHHHHHHHHHHhcCHHHHHHHHHHhccchhhHHhHHHHHHHHHHHHHHHHchHHH
Confidence            34667788888887775  5665555433 345566788888888887654311   11223345556667778889999


Q ss_pred             HHHHHHHHHhCCCCCCHHHHHHHH-HHHHhcCCH-------HHHHHHHHHHHHhhh
Q 012111          415 MGELFLTMKERHCVPDNITFATMI-QAYNALGMT-------EAAQNLENKMIAMKE  462 (471)
Q Consensus       415 a~~~~~~~~~~~~~p~~~~~~~l~-~~~~~~g~~-------~~A~~~~~~m~~~~~  462 (471)
                      |.+.|..+.+.. ..+..+|..+. -++...|+.       ++|.+++.++.....
T Consensus       324 A~~~f~~L~~~s-~WSka~Y~Y~~a~c~~~l~~~~~~~~~~~~a~~l~~~vp~l~~  378 (468)
T PF10300_consen  324 AAEYFLRLLKES-KWSKAFYAYLAAACLLMLGREEEAKEHKKEAEELFRKVPKLKQ  378 (468)
T ss_pred             HHHHHHHHHhcc-ccHHHHHHHHHHHHHHhhccchhhhhhHHHHHHHHHHHHHHHh
Confidence            999998888753 23444444444 334566777       788888877766554

In humans this protein is expressed in primary breast carcinomas but not in normal breast tissue, and has a putative eukaryotic RNP-1 RNA binding region and a candidate anchoring transmembrane domain. The human protein is coordinately regulated with oestrogen receptor, but is not necessarily oestradiol-responsive []. Members of this family carry a tetratricopeptide repeat (IPR013105 from INTERPRO) at their C terminus.

>PF04053 Coatomer_WDAD: Coatomer WD associated region ; InterPro: IPR006692 Proteins synthesised on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment

Probab=96.30  E-value=0.17  Score=47.34  Aligned_cols=160  Identities=16%  Similarity=0.117  Sum_probs=83.1

Q ss_pred             HHHHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCC
Q 012111           85 LDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGL  164 (471)
Q Consensus        85 l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~  164 (471)
                      .+.++-.++++++.++.+.-.-..  .......+.++..+-+.|-.+.|+++-.+-..            -.....+.|+
T Consensus       268 fk~av~~~d~~~v~~~i~~~~ll~--~i~~~~~~~i~~fL~~~G~~e~AL~~~~D~~~------------rFeLAl~lg~  333 (443)
T PF04053_consen  268 FKTAVLRGDFEEVLRMIAASNLLP--NIPKDQGQSIARFLEKKGYPELALQFVTDPDH------------RFELALQLGN  333 (443)
T ss_dssp             HHHHHHTT-HHH-----HHHHTGG--G--HHHHHHHHHHHHHTT-HHHHHHHSS-HHH------------HHHHHHHCT-
T ss_pred             HHHHHHcCChhhhhhhhhhhhhcc--cCChhHHHHHHHHHHHCCCHHHHHhhcCChHH------------HhHHHHhcCC
Confidence            344455677777666654111111  11134466777777777777777766543221            2334456677


Q ss_pred             HHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHH
Q 012111          165 LDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFS  244 (471)
Q Consensus       165 ~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~a~~~~~  244 (471)
                      ++.|.++.++.       .+...|..|.....+.|+++.|++.|.+...         +..|+-.|.-.|+.+...++.+
T Consensus       334 L~~A~~~a~~~-------~~~~~W~~Lg~~AL~~g~~~lAe~c~~k~~d---------~~~L~lLy~~~g~~~~L~kl~~  397 (443)
T PF04053_consen  334 LDIALEIAKEL-------DDPEKWKQLGDEALRQGNIELAEECYQKAKD---------FSGLLLLYSSTGDREKLSKLAK  397 (443)
T ss_dssp             HHHHHHHCCCC-------STHHHHHHHHHHHHHTTBHHHHHHHHHHCT----------HHHHHHHHHHCT-HHHHHHHHH
T ss_pred             HHHHHHHHHhc-------CcHHHHHHHHHHHHHcCCHHHHHHHHHhhcC---------ccccHHHHHHhCCHHHHHHHHH
Confidence            77776655432       3555677777777777777777777766442         3455556666677666666665


Q ss_pred             HHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHH
Q 012111          245 AMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNE  281 (471)
Q Consensus       245 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~  281 (471)
                      .....+       -++....++...|+.++..+++.+
T Consensus       398 ~a~~~~-------~~n~af~~~~~lgd~~~cv~lL~~  427 (443)
T PF04053_consen  398 IAEERG-------DINIAFQAALLLGDVEECVDLLIE  427 (443)
T ss_dssp             HHHHTT--------HHHHHHHHHHHT-HHHHHHHHHH
T ss_pred             HHHHcc-------CHHHHHHHHHHcCCHHHHHHHHHH
Confidence            554443       144444555555666666655544

This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. While clathrin mediates endocytic protein transport, and transport from ER to Golgi, coatomers primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. For example, the coatomer COP1 (coat protein complex 1) is responsible for reverse transport of recycled proteins from Golgi and pre-Golgi compartments back to the ER, while COPII buds vesicles from the ER to the Golgi []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Activated small guanine triphosphatases (GTPases) attract coat proteins to specific membrane export sites, thereby linking coatomers to export cargos. As coat proteins polymerise, vesicles are formed and budded from membrane-bound organelles. Coatomer complexes also influence Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors. In mammals, coatomer complexes can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the WD-associated region found in coatomer subunits alpha, beta and beta' subunits. The alpha-subunit (RET1P) of the coatomer complex in Saccharomyces cerevisiae (Baker's yeast), participates in membrane transport between the endoplasmic reticulum and Golgi apparatus. The protein contains six WD-40 repeat motifs in its N-terminal region []. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0005198 structural molecule activity, 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030117 membrane coat; PDB: 3MKQ_B.

>KOG3941 consensus Intermediate in Toll signal transduction pathway (ECSIT) [Signal transduction mechanisms]

Probab=96.26  E-value=0.12  Score=43.79  Aligned_cols=104  Identities=13%  Similarity=0.255  Sum_probs=66.1

Q ss_pred             CChhHHHHHHHHHhc-----CCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHH
Q 012111          112 ARCQTFTKLMVMLGK-----CKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVY  186 (471)
Q Consensus       112 ~~~~~~~~l~~~~~~-----~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~  186 (471)
                      -|-..|...+..+..     .+.++-.-..+..|.+.|+..|..+|+.|+..+-+..                 ..|...
T Consensus        65 RdK~sfl~~V~~F~E~sVr~R~HveFIy~ALk~m~eyGVerDl~vYk~LlnvfPKgk-----------------fiP~nv  127 (406)
T KOG3941|consen   65 RDKDSFLAAVATFKEKSVRGRTHVEFIYTALKYMKEYGVERDLDVYKGLLNVFPKGK-----------------FIPQNV  127 (406)
T ss_pred             ccHHHHHHHHHHHHHhhhcccchHHHHHHHHHHHHHhcchhhHHHHHHHHHhCcccc-----------------cccHHH
Confidence            344556666665543     2456666667777777777777777777776653321                 122211


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCC
Q 012111          187 TYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKK  235 (471)
Q Consensus       187 ~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~  235 (471)
                       +....-.|-  .+-+-+++++++|...|+.||..+-..|+.++.+.+-
T Consensus       128 -fQ~~F~HYP--~QQ~C~I~vLeqME~hGVmPdkE~e~~lvn~FGr~~~  173 (406)
T KOG3941|consen  128 -FQKVFLHYP--QQQNCAIKVLEQMEWHGVMPDKEIEDILVNAFGRWNF  173 (406)
T ss_pred             -HHHHHhhCc--hhhhHHHHHHHHHHHcCCCCchHHHHHHHHHhccccc
Confidence             111111111  1235588999999999999999999999999988775

>COG1729 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=96.25  E-value=0.11  Score=44.08  Aligned_cols=102  Identities=13%  Similarity=0.105  Sum_probs=58.5

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCc--CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhC-CCCC-CHHHHHHHH
Q 012111          363 TYCSLVSAYSKAGLIMKVDSILRQVENSDVIL--DTPFFNCIISAYGQAGDVEKMGELFLTMKER-HCVP-DNITFATMI  438 (471)
Q Consensus       363 ~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~--~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~-~~~p-~~~~~~~l~  438 (471)
                      .|+.-+.. .+.|++..|...|...++..+.-  ....+--|..++...|++++|..+|..+.+. +-.| -+..+-.|.
T Consensus       144 ~Y~~A~~~-~ksgdy~~A~~~F~~fi~~YP~s~~~~nA~yWLGe~~y~qg~y~~Aa~~f~~~~k~~P~s~KApdallKlg  222 (262)
T COG1729         144 LYNAALDL-YKSGDYAEAEQAFQAFIKKYPNSTYTPNAYYWLGESLYAQGDYEDAAYIFARVVKDYPKSPKAPDALLKLG  222 (262)
T ss_pred             HHHHHHHH-HHcCCHHHHHHHHHHHHHcCCCCcccchhHHHHHHHHHhcccchHHHHHHHHHHHhCCCCCCChHHHHHHH
Confidence            34444333 34555666666666666543221  1223444666677777777777777666653 1112 235556666


Q ss_pred             HHHHhcCCHHHHHHHHHHHHHhhhcCC
Q 012111          439 QAYNALGMTEAAQNLENKMIAMKENSG  465 (471)
Q Consensus       439 ~~~~~~g~~~~A~~~~~~m~~~~~~~~  465 (471)
                      .+..+.|+.++|...|+++++..|+.+
T Consensus       223 ~~~~~l~~~d~A~atl~qv~k~YP~t~  249 (262)
T COG1729         223 VSLGRLGNTDEACATLQQVIKRYPGTD  249 (262)
T ss_pred             HHHHHhcCHHHHHHHHHHHHHHCCCCH
Confidence            666777777777777777777666543

>PF10300 DUF3808: Protein of unknown function (DUF3808); InterPro: IPR019412 This entry represents a family of proteins conserved from fungi to humans

Probab=96.25  E-value=0.35  Score=46.01  Aligned_cols=180  Identities=12%  Similarity=0.060  Sum_probs=120.9

Q ss_pred             HHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCH------HHHHHHHHHHHh----cCC
Q 012111           95 QLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSV------DVYTALVSAYGQ----SGL  164 (471)
Q Consensus        95 ~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~------~~~~~li~~~~~----~~~  164 (471)
                      .--.-+|..+..-  +||.   +..++...+=.|+-+.+++.+....+.+--..+      -.|+.++..++.    ...
T Consensus       174 ~~G~G~f~L~lSl--LPp~---~~kll~~vGF~gdR~~GL~~L~~~~~~~~i~~~la~L~LL~y~~~~~~~~~~~~~~~~  248 (468)
T PF10300_consen  174 YFGFGLFNLVLSL--LPPK---VLKLLSFVGFSGDRELGLRLLWEASKSENIRSPLAALVLLWYHLVVPSFLGIDGEDVP  248 (468)
T ss_pred             HHHHHHHHHHHHh--CCHH---HHHHHhhcCcCCcHHHHHHHHHHHhccCCcchHHHHHHHHHHHHHHHHHcCCcccCCC
Confidence            3445566666654  3554   577888888889999999999887664321122      235555554444    347


Q ss_pred             HHHHHHHHHHhhcCCCCCCCHHHHHHHH-HHHHhcCCHHHHHHHHHHHHHCC---CCCCHHHHHHHHHHHHccCCHHHHH
Q 012111          165 LDEAFSTINDMKSVSDCKPDVYTYSILI-KSCTKFHRFDLIEKILAEMSYLG---IECSAVTYNTIIDGYGKAKKFEEME  240 (471)
Q Consensus       165 ~~~a~~~~~~~~~~~~~~~~~~~~~~ll-~~~~~~~~~~~a~~~~~~~~~~g---~~~~~~~~~~l~~~~~~~~~~~~a~  240 (471)
                      .+.|.++++.+...   -|+...|...- +.+...|+++.|.+.|+......   .+.....+--+.-.+.-.++|++|.
T Consensus       249 ~~~a~~lL~~~~~~---yP~s~lfl~~~gR~~~~~g~~~~Ai~~~~~a~~~q~~~~Ql~~l~~~El~w~~~~~~~w~~A~  325 (468)
T PF10300_consen  249 LEEAEELLEEMLKR---YPNSALFLFFEGRLERLKGNLEEAIESFERAIESQSEWKQLHHLCYFELAWCHMFQHDWEEAA  325 (468)
T ss_pred             HHHHHHHHHHHHHh---CCCcHHHHHHHHHHHHHhcCHHHHHHHHHHhccchhhHHhHHHHHHHHHHHHHHHHchHHHHH
Confidence            88999999999874   46766654433 45677899999999999765321   1223344555667788889999999


Q ss_pred             HHHHHHHHcCCCCCCHHHHHHHHHH-HHhcCCH-------HHHHHHHHHHHh
Q 012111          241 SSFSAMVESGGCHPDIFTLNSMISA-YGNSGNI-------EKMEKWYNEFNL  284 (471)
Q Consensus       241 ~~~~~~~~~~~~~~~~~~~~~l~~~-~~~~~~~-------~~a~~~~~~~~~  284 (471)
                      +.|..+.+..  .-+...|.-+..+ +...|+.       ++|.++|.+...
T Consensus       326 ~~f~~L~~~s--~WSka~Y~Y~~a~c~~~l~~~~~~~~~~~~a~~l~~~vp~  375 (468)
T PF10300_consen  326 EYFLRLLKES--KWSKAFYAYLAAACLLMLGREEEAKEHKKEAEELFRKVPK  375 (468)
T ss_pred             HHHHHHHhcc--ccHHHHHHHHHHHHHHhhccchhhhhhHHHHHHHHHHHHH
Confidence            9999998864  3344455554433 4456666       889999988743

In humans this protein is expressed in primary breast carcinomas but not in normal breast tissue, and has a putative eukaryotic RNP-1 RNA binding region and a candidate anchoring transmembrane domain. The human protein is coordinately regulated with oestrogen receptor, but is not necessarily oestradiol-responsive []. Members of this family carry a tetratricopeptide repeat (IPR013105 from INTERPRO) at their C terminus.

>PLN03098 LPA1 LOW PSII ACCUMULATION1; Provisional

Probab=96.24  E-value=0.1  Score=47.81  Aligned_cols=64  Identities=14%  Similarity=0.063  Sum_probs=49.6

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCH----HHHHHHHHHHHhcCCHHHHHHHHHHHHhC
Q 012111          325 TVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNS----ITYCSLVSAYSKAGLIMKVDSILRQVENS  390 (471)
Q Consensus       325 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~----~~~~~li~~~~~~g~~~~a~~~~~~~~~~  390 (471)
                      +...++.+..+|...|++++|+..|++.++.  .|+.    .+|..+..+|...|+.++|...+++..+.
T Consensus        74 ~a~a~~NLG~AL~~lGryeEAIa~f~rALeL--~Pd~aeA~~A~yNLAcaya~LGr~dEAla~LrrALel  141 (453)
T PLN03098         74 TAEDAVNLGLSLFSKGRVKDALAQFETALEL--NPNPDEAQAAYYNKACCHAYREEGKKAADCLRTALRD  141 (453)
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh--CCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            5567788888888888888888888887775  4543    35788888888888888888888888775

>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]

Probab=96.22  E-value=1.4  Score=43.50  Aligned_cols=184  Identities=12%  Similarity=0.161  Sum_probs=114.2

Q ss_pred             CCCchHHHHHHHHHHHhhcHHHHHHHHHHhhhccCccCC--hhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHH
Q 012111           75 NLWPKPVLEALDEAIKQKKWQLALKIFGLLRQQQWYQAR--CQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVY  152 (471)
Q Consensus        75 ~~~~~~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~--~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~  152 (471)
                      .+.+.++...|+.+.+..-++.|+.+-+.-..    .++  ..........+.+.|++++|...|-+-+.. +.|     
T Consensus       331 ~L~ek~le~kL~iL~kK~ly~~Ai~LAk~~~~----d~d~~~~i~~kYgd~Ly~Kgdf~~A~~qYI~tI~~-le~-----  400 (933)
T KOG2114|consen  331 ELIEKDLETKLDILFKKNLYKVAINLAKSQHL----DEDTLAEIHRKYGDYLYGKGDFDEATDQYIETIGF-LEP-----  400 (933)
T ss_pred             eeeeccHHHHHHHHHHhhhHHHHHHHHHhcCC----CHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHccc-CCh-----
Confidence            34566778888888999999999887654432    222  233445555667889999998888765532 122     


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHc
Q 012111          153 TALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGK  232 (471)
Q Consensus       153 ~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~  232 (471)
                      ..+|.-|....+...-...++.+.+ .|+ .+...-..|+.+|.+.++.+...+..+.-. .|..  ..-....+..+.+
T Consensus       401 s~Vi~kfLdaq~IknLt~YLe~L~~-~gl-a~~dhttlLLncYiKlkd~~kL~efI~~~~-~g~~--~fd~e~al~Ilr~  475 (933)
T KOG2114|consen  401 SEVIKKFLDAQRIKNLTSYLEALHK-KGL-ANSDHTTLLLNCYIKLKDVEKLTEFISKCD-KGEW--FFDVETALEILRK  475 (933)
T ss_pred             HHHHHHhcCHHHHHHHHHHHHHHHH-ccc-ccchhHHHHHHHHHHhcchHHHHHHHhcCC-Ccce--eeeHHHHHHHHHH
Confidence            2345555566666666777777776 343 445555678889999998887766665544 2211  1113445666666


Q ss_pred             cCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 012111          233 AKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEF  282 (471)
Q Consensus       233 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  282 (471)
                      .+-.++|.-+-.....      .......+   +-..+++++|+++++.+
T Consensus       476 snyl~~a~~LA~k~~~------he~vl~il---le~~~ny~eAl~yi~sl  516 (933)
T KOG2114|consen  476 SNYLDEAELLATKFKK------HEWVLDIL---LEDLHNYEEALRYISSL  516 (933)
T ss_pred             hChHHHHHHHHHHhcc------CHHHHHHH---HHHhcCHHHHHHHHhcC
Confidence            6777777665544421      22233333   34667888888888765

>COG4105 ComL DNA uptake lipoprotein [General function prediction only]

Probab=96.17  E-value=0.66  Score=39.13  Aligned_cols=62  Identities=23%  Similarity=0.226  Sum_probs=42.4

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHhCCCCCCH---HHHHHHHHHHHhcCCHHHHHHHHHHHHHhhhc
Q 012111          401 CIISAYGQAGDVEKMGELFLTMKERHCVPDN---ITFATMIQAYNALGMTEAAQNLENKMIAMKEN  463 (471)
Q Consensus       401 ~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~---~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~  463 (471)
                      .+.+-|.+.|.+-.|..-+++|++. .+-+.   ..+-.+..+|...|-.++|.+.-+-+....|+
T Consensus       172 ~IaryY~kr~~~~AA~nR~~~v~e~-y~~t~~~~eaL~~l~eaY~~lgl~~~a~~~~~vl~~N~p~  236 (254)
T COG4105         172 AIARYYLKRGAYVAAINRFEEVLEN-YPDTSAVREALARLEEAYYALGLTDEAKKTAKVLGANYPD  236 (254)
T ss_pred             HHHHHHHHhcChHHHHHHHHHHHhc-cccccchHHHHHHHHHHHHHhCChHHHHHHHHHHHhcCCC
Confidence            3456778888888888888888876 33222   34445667888888888887776655555444

>smart00299 CLH Clathrin heavy chain repeat homology

Probab=96.15  E-value=0.44  Score=36.86  Aligned_cols=85  Identities=12%  Similarity=0.055  Sum_probs=47.3

Q ss_pred             HHHHHHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhc
Q 012111           83 EALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQS  162 (471)
Q Consensus        83 ~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~  162 (471)
                      .++..+.+.+.+.....+++.+...+  +.+...++.++..|++.+ .......+..  .    .+......+++.|.+.
T Consensus        12 ~vv~~~~~~~~~~~l~~yLe~~~~~~--~~~~~~~~~li~ly~~~~-~~~ll~~l~~--~----~~~yd~~~~~~~c~~~   82 (140)
T smart00299       12 EVVELFEKRNLLEELIPYLESALKLN--SENPALQTKLIELYAKYD-PQKEIERLDN--K----SNHYDIEKVGKLCEKA   82 (140)
T ss_pred             HHHHHHHhCCcHHHHHHHHHHHHccC--ccchhHHHHHHHHHHHHC-HHHHHHHHHh--c----cccCCHHHHHHHHHHc
Confidence            44444445667777777777777665  355666777777776553 2333333331  1    1222233455666666


Q ss_pred             CCHHHHHHHHHHhh
Q 012111          163 GLLDEAFSTINDMK  176 (471)
Q Consensus       163 ~~~~~a~~~~~~~~  176 (471)
                      +.++++.-++.++.
T Consensus        83 ~l~~~~~~l~~k~~   96 (140)
T smart00299       83 KLYEEAVELYKKDG   96 (140)
T ss_pred             CcHHHHHHHHHhhc
Confidence            66666666665543

>PLN03098 LPA1 LOW PSII ACCUMULATION1; Provisional

Probab=96.05  E-value=0.13  Score=47.18  Aligned_cols=64  Identities=8%  Similarity=-0.034  Sum_probs=30.0

Q ss_pred             CchHHHHHHHHHHHhhcHHHHHHHHHHhhhccCccCCh---hHHHHHHHHHhcCCCHHHHHHHHHHHHh
Q 012111           77 WPKPVLEALDEAIKQKKWQLALKIFGLLRQQQWYQARC---QTFTKLMVMLGKCKQPEQASLLFEVMLS  142 (471)
Q Consensus        77 ~~~~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~---~~~~~l~~~~~~~~~~~~a~~~~~~m~~  142 (471)
                      ++..+.+.-..+.+.|++++|+..|+.+.+.+  |.+.   .+|..+..+|...|++++|+..+++..+
T Consensus        74 ~a~a~~NLG~AL~~lGryeEAIa~f~rALeL~--Pd~aeA~~A~yNLAcaya~LGr~dEAla~LrrALe  140 (453)
T PLN03098         74 TAEDAVNLGLSLFSKGRVKDALAQFETALELN--PNPDEAQAAYYNKACCHAYREEGKKAADCLRTALR  140 (453)
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC--CCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            33444444444455555555555555554432  1111   1245555555555555555555555444

>KOG0543 consensus FKBP-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=96.04  E-value=0.22  Score=44.72  Aligned_cols=139  Identities=10%  Similarity=0.007  Sum_probs=95.8

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCH
Q 012111          263 ISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHI  342 (471)
Q Consensus       263 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~  342 (471)
                      .+.+.+.|++..|..-|+..+..            +. |...-+.++......        .-..++..+.-++.+.+++
T Consensus       215 Gn~~fK~gk~~~A~~~Yerav~~------------l~-~~~~~~~ee~~~~~~--------~k~~~~lNlA~c~lKl~~~  273 (397)
T KOG0543|consen  215 GNVLFKEGKFKLAKKRYERAVSF------------LE-YRRSFDEEEQKKAEA--------LKLACHLNLAACYLKLKEY  273 (397)
T ss_pred             hhHHHhhchHHHHHHHHHHHHHH------------hh-ccccCCHHHHHHHHH--------HHHHHhhHHHHHHHhhhhH
Confidence            46777888888888877776431            00 011111121111111        1334677788888999999


Q ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHH-HHHHHHH
Q 012111          343 EKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEK-MGELFLT  421 (471)
Q Consensus       343 ~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~-a~~~~~~  421 (471)
                      ..|++.-.+.+..+ ++|...+-.=..++...|+++.|+..|+.+.+..+. |..+-+.|+.+-.+..+..+ ..++|..
T Consensus       274 ~~Ai~~c~kvLe~~-~~N~KALyRrG~A~l~~~e~~~A~~df~ka~k~~P~-Nka~~~el~~l~~k~~~~~~kekk~y~~  351 (397)
T KOG0543|consen  274 KEAIESCNKVLELD-PNNVKALYRRGQALLALGEYDLARDDFQKALKLEPS-NKAARAELIKLKQKIREYEEKEKKMYAN  351 (397)
T ss_pred             HHHHHHHHHHHhcC-CCchhHHHHHHHHHHhhccHHHHHHHHHHHHHhCCC-cHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999998888875 567888888889999999999999999999988766 66676777766665555444 4778888


Q ss_pred             HHh
Q 012111          422 MKE  424 (471)
Q Consensus       422 ~~~  424 (471)
                      |..
T Consensus       352 mF~  354 (397)
T KOG0543|consen  352 MFA  354 (397)
T ss_pred             Hhh
Confidence            875

>PF04053 Coatomer_WDAD: Coatomer WD associated region ; InterPro: IPR006692 Proteins synthesised on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment

Probab=96.03  E-value=0.5  Score=44.40  Aligned_cols=155  Identities=18%  Similarity=0.161  Sum_probs=72.4

Q ss_pred             HHccCCHHHHHHHHH--HHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCH
Q 012111          230 YGKAKKFEEMESSFS--AMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMY  307 (471)
Q Consensus       230 ~~~~~~~~~a~~~~~--~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~  307 (471)
                      ..-.++++++.+...  .+...  +  +....+.++..+.+.|..+.|+++..+-.            .-.....+.|++
T Consensus       271 av~~~d~~~v~~~i~~~~ll~~--i--~~~~~~~i~~fL~~~G~~e~AL~~~~D~~------------~rFeLAl~lg~L  334 (443)
T PF04053_consen  271 AVLRGDFEEVLRMIAASNLLPN--I--PKDQGQSIARFLEKKGYPELALQFVTDPD------------HRFELALQLGNL  334 (443)
T ss_dssp             HHHTT-HHH-----HHHHTGGG------HHHHHHHHHHHHHTT-HHHHHHHSS-HH------------HHHHHHHHCT-H
T ss_pred             HHHcCChhhhhhhhhhhhhccc--C--ChhHHHHHHHHHHHCCCHHHHHhhcCChH------------HHhHHHHhcCCH
Confidence            344556666555553  11111  1  13345556666666666666665443321            112334455666


Q ss_pred             HHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 012111          308 DKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQV  387 (471)
Q Consensus       308 ~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~  387 (471)
                      +.|.++.+..      .+...|..|.......|+++-|.+.|.+...         +..|+-.|.-.|+.+.-.++.+..
T Consensus       335 ~~A~~~a~~~------~~~~~W~~Lg~~AL~~g~~~lAe~c~~k~~d---------~~~L~lLy~~~g~~~~L~kl~~~a  399 (443)
T PF04053_consen  335 DIALEIAKEL------DDPEKWKQLGDEALRQGNIELAEECYQKAKD---------FSGLLLLYSSTGDREKLSKLAKIA  399 (443)
T ss_dssp             HHHHHHCCCC------STHHHHHHHHHHHHHTTBHHHHHHHHHHCT----------HHHHHHHHHHCT-HHHHHHHHHHH
T ss_pred             HHHHHHHHhc------CcHHHHHHHHHHHHHcCCHHHHHHHHHhhcC---------ccccHHHHHHhCCHHHHHHHHHHH
Confidence            6665543321      2455666666666666666666666655432         445555555666666655555555


Q ss_pred             HhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHH
Q 012111          388 ENSDVILDTPFFNCIISAYGQAGDVEKMGELFLT  421 (471)
Q Consensus       388 ~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~  421 (471)
                      ...|-      ++....++.-.|+.++..+++.+
T Consensus       400 ~~~~~------~n~af~~~~~lgd~~~cv~lL~~  427 (443)
T PF04053_consen  400 EERGD------INIAFQAALLLGDVEECVDLLIE  427 (443)
T ss_dssp             HHTT-------HHHHHHHHHHHT-HHHHHHHHHH
T ss_pred             HHccC------HHHHHHHHHHcCCHHHHHHHHHH
Confidence            54431      34444445555666666555543

This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. While clathrin mediates endocytic protein transport, and transport from ER to Golgi, coatomers primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. For example, the coatomer COP1 (coat protein complex 1) is responsible for reverse transport of recycled proteins from Golgi and pre-Golgi compartments back to the ER, while COPII buds vesicles from the ER to the Golgi []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Activated small guanine triphosphatases (GTPases) attract coat proteins to specific membrane export sites, thereby linking coatomers to export cargos. As coat proteins polymerise, vesicles are formed and budded from membrane-bound organelles. Coatomer complexes also influence Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors. In mammals, coatomer complexes can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the WD-associated region found in coatomer subunits alpha, beta and beta' subunits. The alpha-subunit (RET1P) of the coatomer complex in Saccharomyces cerevisiae (Baker's yeast), participates in membrane transport between the endoplasmic reticulum and Golgi apparatus. The protein contains six WD-40 repeat motifs in its N-terminal region []. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0005198 structural molecule activity, 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030117 membrane coat; PDB: 3MKQ_B.

>KOG1258 consensus mRNA processing protein [RNA processing and modification]

Probab=96.02  E-value=1.5  Score=41.75  Aligned_cols=338  Identities=12%  Similarity=0.107  Sum_probs=174.4

Q ss_pred             hcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHH-hcCCHHHHHH
Q 012111           92 KKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYG-QSGLLDEAFS  170 (471)
Q Consensus        92 ~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~-~~~~~~~a~~  170 (471)
                      ...+.+..++..+...  +|--..-|......=.+.|..+.+.++|++... |++.+...|.....-+. ..|+.+....
T Consensus        59 ~~~~~~r~~y~~fL~k--yPl~~gyW~kfA~~E~klg~~~~s~~Vfergv~-aip~SvdlW~~Y~~f~~n~~~d~~~lr~  135 (577)
T KOG1258|consen   59 EDVDALREVYDIFLSK--YPLCYGYWKKFADYEYKLGNAENSVKVFERGVQ-AIPLSVDLWLSYLAFLKNNNGDPETLRD  135 (577)
T ss_pred             hHHHHHHHHHHHHHhh--CccHHHHHHHHHHHHHHhhhHHHHHHHHHHHHH-hhhhHHHHHHHHHHHHhccCCCHHHHHH
Confidence            3445666677777654  243344566667777788999999999998875 46667777777665544 4567778888


Q ss_pred             HHHHhhcCCCCC-CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHH---cc------CCHHHHH
Q 012111          171 TINDMKSVSDCK-PDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYG---KA------KKFEEME  240 (471)
Q Consensus       171 ~~~~~~~~~~~~-~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~---~~------~~~~~a~  240 (471)
                      .|+.....-|.. .....|...|..-...+++.....++++.++.    ....|+....-|.   ..      ...+++.
T Consensus       136 ~fe~A~~~vG~dF~S~~lWdkyie~en~qks~k~v~~iyeRilei----P~~~~~~~f~~f~~~l~~~~~~~l~~~d~~~  211 (577)
T KOG1258|consen  136 LFERAKSYVGLDFLSDPLWDKYIEFENGQKSWKRVANIYERILEI----PLHQLNRHFDRFKQLLNQNEEKILLSIDELI  211 (577)
T ss_pred             HHHHHHHhcccchhccHHHHHHHHHHhccccHHHHHHHHHHHHhh----hhhHhHHHHHHHHHHHhcCChhhhcCHHHHH
Confidence            888887754433 23445777777777788888999999888864    2222332222221   11      1222222


Q ss_pred             HHHHHHHHc---CCCCCCHHHHHHHHHHHH-hcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHH
Q 012111          241 SSFSAMVES---GGCHPDIFTLNSMISAYG-NSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDF  316 (471)
Q Consensus       241 ~~~~~~~~~---~~~~~~~~~~~~l~~~~~-~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~  316 (471)
                      ++-......   ....+.......-+.--. ..+..+++.....+.           ...--.++............|+.
T Consensus       212 ~l~~~~~~~~~~~~~~~~~e~~~~~v~~~~~~s~~l~~~~~~l~~~-----------~~~~~~~~~~s~~~~~kr~~fE~  280 (577)
T KOG1258|consen  212 QLRSDVAERSKITHSQEPLEELEIGVKDSTDPSKSLTEEKTILKRI-----------VSIHEKVYQKSEEEEEKRWGFEE  280 (577)
T ss_pred             HHhhhHHhhhhcccccChhHHHHHHHhhccCccchhhHHHHHHHHH-----------HHHHHHHHHhhHhHHHHHHhhhh
Confidence            222211110   000000001110000000 000011111100000           00001112222222233333333


Q ss_pred             HHhCC-------CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 012111          317 MQKRF-------FFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVEN  389 (471)
Q Consensus       317 ~~~~~-------~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~  389 (471)
                      -.+.-       ..++..+|..-+..-...|+.+.+.-+|++..-. +..-...|-..+......|+.+.|..++....+
T Consensus       281 ~IkrpYfhvkpl~~aql~nw~~yLdf~i~~g~~~~~~~l~ercli~-cA~Y~efWiky~~~m~~~~~~~~~~~~~~~~~~  359 (577)
T KOG1258|consen  281 GIKRPYFHVKPLDQAQLKNWRYYLDFEITLGDFSRVFILFERCLIP-CALYDEFWIKYARWMESSGDVSLANNVLARACK  359 (577)
T ss_pred             hccccccccCcccHHHHHHHHHHhhhhhhcccHHHHHHHHHHHHhH-HhhhHHHHHHHHHHHHHcCchhHHHHHHHhhhh
Confidence            22221       1224456777777777788888888888776532 222334555556666666888888877777665


Q ss_pred             CCCCcCHHHHHHHHHH-HHhcCCHHHHHHHHHHHHhCCCCCCHHHH-HHHHHHHHhcCCHHHHH
Q 012111          390 SDVILDTPFFNCIISA-YGQAGDVEKMGELFLTMKERHCVPDNITF-ATMIQAYNALGMTEAAQ  451 (471)
Q Consensus       390 ~~~~~~~~~~~~l~~~-~~~~g~~~~a~~~~~~~~~~~~~p~~~~~-~~l~~~~~~~g~~~~A~  451 (471)
                      ...+ +......+-.. .-..|+++.|..+++...+. + |+.... ..-+....+.|+.+.+.
T Consensus       360 i~~k-~~~~i~L~~a~f~e~~~n~~~A~~~lq~i~~e-~-pg~v~~~l~~~~~e~r~~~~~~~~  420 (577)
T KOG1258|consen  360 IHVK-KTPIIHLLEARFEESNGNFDDAKVILQRIESE-Y-PGLVEVVLRKINWERRKGNLEDAN  420 (577)
T ss_pred             hcCC-CCcHHHHHHHHHHHhhccHHHHHHHHHHHHhh-C-CchhhhHHHHHhHHHHhcchhhhh
Confidence            5433 22222222222 23457888888888888765 3 544322 22334455666666665

>KOG4555 consensus TPR repeat-containing protein [Function unknown]

Probab=96.00  E-value=0.23  Score=36.79  Aligned_cols=90  Identities=13%  Similarity=0.035  Sum_probs=57.4

Q ss_pred             HHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhC-CCCcCHHH---HHHHHHHHHhcC
Q 012111          335 TFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENS-DVILDTPF---FNCIISAYGQAG  410 (471)
Q Consensus       335 ~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~-~~~~~~~~---~~~l~~~~~~~g  410 (471)
                      ++...|+.+.|++.|.+.+.. .+-....||.-..++.-.|+.++|++-+++..+. |.. ....   |..-...|...|
T Consensus        52 alaE~g~Ld~AlE~F~qal~l-~P~raSayNNRAQa~RLq~~~e~ALdDLn~AleLag~~-trtacqa~vQRg~lyRl~g  129 (175)
T KOG4555|consen   52 ALAEAGDLDGALELFGQALCL-APERASAYNNRAQALRLQGDDEEALDDLNKALELAGDQ-TRTACQAFVQRGLLYRLLG  129 (175)
T ss_pred             HHHhccchHHHHHHHHHHHHh-cccchHhhccHHHHHHHcCChHHHHHHHHHHHHhcCcc-chHHHHHHHHHHHHHHHhC
Confidence            456677788888887777664 2335677777777777778888877777776653 222 2222   222233455667


Q ss_pred             CHHHHHHHHHHHHhCC
Q 012111          411 DVEKMGELFLTMKERH  426 (471)
Q Consensus       411 ~~~~a~~~~~~~~~~~  426 (471)
                      +-+.|..=|+..-+.|
T Consensus       130 ~dd~AR~DFe~AA~LG  145 (175)
T KOG4555|consen  130 NDDAARADFEAAAQLG  145 (175)
T ss_pred             chHHHHHhHHHHHHhC
Confidence            7777777777776654

>PF13512 TPR_18: Tetratricopeptide repeat

Probab=95.99  E-value=0.25  Score=37.61  Aligned_cols=89  Identities=13%  Similarity=0.095  Sum_probs=66.0

Q ss_pred             CCCchHHHHHHHHHHHhhcHHHHHHHHHHhhhccCccC-ChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHH
Q 012111           75 NLWPKPVLEALDEAIKQKKWQLALKIFGLLRQQQWYQA-RCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYT  153 (471)
Q Consensus        75 ~~~~~~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~  153 (471)
                      ..++..+........+.|++++|++.|+.+..+.+..+ ...+--.++.++.+.+++++|...+++.++..+.-.-.-|.
T Consensus         7 ~~~~~~ly~~a~~~l~~~~Y~~A~~~le~L~~ryP~g~ya~qAqL~l~yayy~~~~y~~A~a~~~rFirLhP~hp~vdYa   86 (142)
T PF13512_consen    7 DKSPQELYQEAQEALQKGNYEEAIKQLEALDTRYPFGEYAEQAQLDLAYAYYKQGDYEEAIAAYDRFIRLHPTHPNVDYA   86 (142)
T ss_pred             CCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHhcCCCCcccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCCCCccHH
Confidence            34556677777788899999999999999998853333 34667788999999999999999999999875443334455


Q ss_pred             HHHHHHHhcC
Q 012111          154 ALVSAYGQSG  163 (471)
Q Consensus       154 ~li~~~~~~~  163 (471)
                      ..+.+++...
T Consensus        87 ~Y~~gL~~~~   96 (142)
T PF13512_consen   87 YYMRGLSYYE   96 (142)
T ss_pred             HHHHHHHHHH
Confidence            5555555443

>KOG2610 consensus Uncharacterized conserved protein [Function unknown]

Probab=95.90  E-value=0.46  Score=41.52  Aligned_cols=153  Identities=7%  Similarity=0.016  Sum_probs=104.4

Q ss_pred             HhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHH----HHHHHHhcCCH
Q 012111          267 GNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNI----VIETFGKAGHI  342 (471)
Q Consensus       267 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~----li~~~~~~g~~  342 (471)
                      -..|++.+|-..++++.+. .+.|...+...=.+|.-.|+.+.-...++++... ..++...|..    ..-++...|-+
T Consensus       114 ~~~g~~h~a~~~wdklL~d-~PtDlla~kfsh~a~fy~G~~~~~k~ai~kIip~-wn~dlp~~sYv~GmyaFgL~E~g~y  191 (491)
T KOG2610|consen  114 WGRGKHHEAAIEWDKLLDD-YPTDLLAVKFSHDAHFYNGNQIGKKNAIEKIIPK-WNADLPCYSYVHGMYAFGLEECGIY  191 (491)
T ss_pred             hccccccHHHHHHHHHHHh-CchhhhhhhhhhhHHHhccchhhhhhHHHHhccc-cCCCCcHHHHHHHHHHhhHHHhccc
Confidence            3567777887788887764 4777778888888888889888888888877654 2334433333    33445578889


Q ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhC----CCCcCHHHHHHHHHHHHhcCCHHHHHHH
Q 012111          343 EKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENS----DVILDTPFFNCIISAYGQAGDVEKMGEL  418 (471)
Q Consensus       343 ~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~----~~~~~~~~~~~l~~~~~~~g~~~~a~~~  418 (471)
                      ++|.+.-++..+.+ +.|......+...+.-.|+..++.+++..-.+.    .+. -..-|-...-.+...+.++.|+++
T Consensus       192 ~dAEk~A~ralqiN-~~D~Wa~Ha~aHVlem~~r~Keg~eFM~~ted~Wr~s~ml-asHNyWH~Al~~iE~aeye~aleI  269 (491)
T KOG2610|consen  192 DDAEKQADRALQIN-RFDCWASHAKAHVLEMNGRHKEGKEFMYKTEDDWRQSWML-ASHNYWHTALFHIEGAEYEKALEI  269 (491)
T ss_pred             hhHHHHHHhhccCC-CcchHHHHHHHHHHHhcchhhhHHHHHHhcccchhhhhHH-HhhhhHHHHHhhhcccchhHHHHH
Confidence            99999888887764 456777777888888889999998887765432    111 111222333345566889999999


Q ss_pred             HHHHH
Q 012111          419 FLTMK  423 (471)
Q Consensus       419 ~~~~~  423 (471)
                      |++=+
T Consensus       270 yD~ei  274 (491)
T KOG2610|consen  270 YDREI  274 (491)
T ss_pred             HHHHH
Confidence            87543

>COG0457 NrfG FOG: TPR repeat [General function prediction only]

Probab=95.88  E-value=0.92  Score=38.34  Aligned_cols=223  Identities=12%  Similarity=-0.040  Sum_probs=110.3

Q ss_pred             CCHHHHHHHHHHHHHCCCC-CCHHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHH
Q 012111          199 HRFDLIEKILAEMSYLGIE-CSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEK  277 (471)
Q Consensus       199 ~~~~~a~~~~~~~~~~g~~-~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~  277 (471)
                      +....+...+......... .....+......+...+.+..+...+...............+......+...+++..+..
T Consensus        37 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  116 (291)
T COG0457          37 GELAEALELLEEALELLPNSDLAGLLLLLALALLKLGRLEEALELLEKALELELLPNLAEALLNLGLLLEALGKYEEALE  116 (291)
T ss_pred             hhHHHHHHHHHHHHhcCccccchHHHHHHHHHHHHcccHHHHHHHHHHHHhhhhccchHHHHHHHHHHHHHHhhHHHHHH
Confidence            4445555555555544221 124555666666666677776666666664310023344455555556666666666666


Q ss_pred             HHHHHHhCCCCCCHHHHHHHHH-HHHHcCCHHHHHHHHHHHHhCCC--CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 012111          278 WYNEFNLMGVKADIQTLNILTK-SYGRAGMYDKMRSVMDFMQKRFF--FPTVVTYNIVIETFGKAGHIEKMEEYFKKMKH  354 (471)
Q Consensus       278 ~~~~~~~~~~~~~~~~~~~ll~-~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  354 (471)
                      .+.........+ ......... .+...|+++.+...+........  ......+......+...++.+.+...+.....
T Consensus       117 ~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~  195 (291)
T COG0457         117 LLEKALALDPDP-DLAEALLALGALYELGDYEEALELYEKALELDPELNELAEALLALGALLEALGRYEEALELLEKALK  195 (291)
T ss_pred             HHHHHHcCCCCc-chHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCccchHHHHHHhhhHHHHhcCHHHHHHHHHHHHh
Confidence            666665533222 111222222 55666666666666666543211  01222233333334455566666666666555


Q ss_pred             cCCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 012111          355 RGMKP-NSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKE  424 (471)
Q Consensus       355 ~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~  424 (471)
                      .. .. ....+..+...+...++.+.+...+......... ....+..+...+...|..+.+...+.....
T Consensus       196 ~~-~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  264 (291)
T COG0457         196 LN-PDDDAEALLNLGLLYLKLGKYEEALEYYEKALELDPD-NAEALYNLALLLLELGRYEEALEALEKALE  264 (291)
T ss_pred             hC-cccchHHHHHhhHHHHHcccHHHHHHHHHHHHhhCcc-cHHHHhhHHHHHHHcCCHHHHHHHHHHHHH
Confidence            42 11 2444555555555555666666666555544322 122333333333344455555555555554

>PF08631 SPO22: Meiosis protein SPO22/ZIP4 like; InterPro: IPR013940 SPO22 is a meiosis-specific protein with similarity to phospholipase A2, involved in completion of nuclear divisions during meiosis; induced early in meiosis []

Probab=95.78  E-value=1.2  Score=39.11  Aligned_cols=163  Identities=12%  Similarity=0.113  Sum_probs=81.2

Q ss_pred             HHHHHHHHHHHcCCHH---HHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHH
Q 012111          293 TLNILTKSYGRAGMYD---KMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVS  369 (471)
Q Consensus       293 ~~~~ll~~~~~~~~~~---~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~  369 (471)
                      ++..++.+|...+..+   +|..+++.+...... .+..+-.-+..+.+.++.+.+.+.+.+|+..- .-....+..++.
T Consensus        86 iL~~La~~~l~~~~~~~~~ka~~~l~~l~~e~~~-~~~~~~L~l~il~~~~~~~~~~~~L~~mi~~~-~~~e~~~~~~l~  163 (278)
T PF08631_consen   86 ILRLLANAYLEWDTYESVEKALNALRLLESEYGN-KPEVFLLKLEILLKSFDEEEYEEILMRMIRSV-DHSESNFDSILH  163 (278)
T ss_pred             HHHHHHHHHHcCCChHHHHHHHHHHHHHHHhCCC-CcHHHHHHHHHHhccCChhHHHHHHHHHHHhc-ccccchHHHHHH
Confidence            4556666666665543   455566666444322 24444455566666777888888888887752 212233444444


Q ss_pred             HH---HhcCCHHHHHHHHHHHHhCCCCcCHH-HHHH-HHH---HHHhcCC------HHHHHHHHHHHHh-CCCCCCHHHH
Q 012111          370 AY---SKAGLIMKVDSILRQVENSDVILDTP-FFNC-IIS---AYGQAGD------VEKMGELFLTMKE-RHCVPDNITF  434 (471)
Q Consensus       370 ~~---~~~g~~~~a~~~~~~~~~~~~~~~~~-~~~~-l~~---~~~~~g~------~~~a~~~~~~~~~-~~~~p~~~~~  434 (471)
                      .+   ... ....+...++.+....+.|... .... ++.   ...+.++      ++...++++.... .+.+.+..+-
T Consensus       164 ~i~~l~~~-~~~~a~~~ld~~l~~r~~~~~~~~~e~~vl~~~~~~~~~~~~~~~~~i~~l~~~~~~v~~~~~~~ls~~~~  242 (278)
T PF08631_consen  164 HIKQLAEK-SPELAAFCLDYLLLNRFKSSEDQWLEKLVLTRVLLTTQSKDLSSSEKIESLEELLSIVEHSLGKQLSAEAA  242 (278)
T ss_pred             HHHHHHhh-CcHHHHHHHHHHHHHHhCCChhHHHHHHHHHHHHHHcCCccccchhHHHHHHHHHHHHHHHhcCCCCHHHH
Confidence            33   332 3345555555555443443432 1111 111   1111111      4444444543322 1223344332


Q ss_pred             H---HHH----HHHHhcCCHHHHHHHHHHHH
Q 012111          435 A---TMI----QAYNALGMTEAAQNLENKMI  458 (471)
Q Consensus       435 ~---~l~----~~~~~~g~~~~A~~~~~~m~  458 (471)
                      .   +++    ..+.+.+++++|.++++-..
T Consensus       243 ~a~~~LLW~~~~~~~~~k~y~~A~~w~~~al  273 (278)
T PF08631_consen  243 SAIHTLLWNKGKKHYKAKNYDEAIEWYELAL  273 (278)
T ss_pred             HHHHHHHHHHHHHHHhhcCHHHHHHHHHHHH
Confidence            2   333    34567899999999988544

It is also involved in sporulation [].

>PF13281 DUF4071: Domain of unknown function (DUF4071)

Probab=95.70  E-value=1.6  Score=39.68  Aligned_cols=102  Identities=17%  Similarity=0.112  Sum_probs=62.2

Q ss_pred             CCCchHHHHHHHHHHHhhcHHHHHHHHHHhhhccCc--cCChhHHHHHHHHHhc---CCCHHHHHHHHHHHHhCCCCCCH
Q 012111           75 NLWPKPVLEALDEAIKQKKWQLALKIFGLLRQQQWY--QARCQTFTKLMVMLGK---CKQPEQASLLFEVMLSDGLKPSV  149 (471)
Q Consensus        75 ~~~~~~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~--~~~~~~~~~l~~~~~~---~~~~~~a~~~~~~m~~~~~~~~~  149 (471)
                      -++++.+...+-.+....+|+..+++.+.+......  ..+...-....-++.+   .|+.++|++++..+......+++
T Consensus       138 ~ls~div~~lllSyRdiqdydamI~Lve~l~~~p~~~~~~~~~i~~~yafALnRrn~~gdre~Al~il~~~l~~~~~~~~  217 (374)
T PF13281_consen  138 LLSPDIVINLLLSYRDIQDYDAMIKLVETLEALPTCDVANQHNIKFQYAFALNRRNKPGDREKALQILLPVLESDENPDP  217 (374)
T ss_pred             hcChhHHHHHHHHhhhhhhHHHHHHHHHHhhccCccchhcchHHHHHHHHHHhhcccCCCHHHHHHHHHHHHhccCCCCh
Confidence            456677777777777778888888888887764211  1112222233334455   67888888888776555556677


Q ss_pred             HHHHHHHHHHHhc---------CCHHHHHHHHHHhh
Q 012111          150 DVYTALVSAYGQS---------GLLDEAFSTINDMK  176 (471)
Q Consensus       150 ~~~~~li~~~~~~---------~~~~~a~~~~~~~~  176 (471)
                      .+|..+.+.|-..         ...++|+..|.+.-
T Consensus       218 d~~gL~GRIyKD~~~~s~~~d~~~ldkAi~~Y~kgF  253 (374)
T PF13281_consen  218 DTLGLLGRIYKDLFLESNFTDRESLDKAIEWYRKGF  253 (374)
T ss_pred             HHHHHHHHHHHHHHHHcCccchHHHHHHHHHHHHHH
Confidence            7777777665321         12455666665543

>COG1729 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=95.68  E-value=0.21  Score=42.36  Aligned_cols=86  Identities=12%  Similarity=0.062  Sum_probs=38.6

Q ss_pred             CCHHHHHHHHHHHHHCCC--CCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCC-HHHHHHHHHHHHhcCCHHHH
Q 012111          199 HRFDLIEKILAEMSYLGI--ECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPD-IFTLNSMISAYGNSGNIEKM  275 (471)
Q Consensus       199 ~~~~~a~~~~~~~~~~g~--~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~~~~~~a  275 (471)
                      |++..|.+.|...++...  .-....+..|..++...|++++|..+|..+.+..+-.|. ...+-.|.....+.|+.++|
T Consensus       155 gdy~~A~~~F~~fi~~YP~s~~~~nA~yWLGe~~y~qg~y~~Aa~~f~~~~k~~P~s~KApdallKlg~~~~~l~~~d~A  234 (262)
T COG1729         155 GDYAEAEQAFQAFIKKYPNSTYTPNAYYWLGESLYAQGDYEDAAYIFARVVKDYPKSPKAPDALLKLGVSLGRLGNTDEA  234 (262)
T ss_pred             CCHHHHHHHHHHHHHcCCCCcccchhHHHHHHHHHhcccchHHHHHHHHHHHhCCCCCCChHHHHHHHHHHHHhcCHHHH
Confidence            334444444444444320  111233344555555555555555555555444322221 23444444445555555555


Q ss_pred             HHHHHHHHh
Q 012111          276 EKWYNEFNL  284 (471)
Q Consensus       276 ~~~~~~~~~  284 (471)
                      ..+|+++.+
T Consensus       235 ~atl~qv~k  243 (262)
T COG1729         235 CATLQQVIK  243 (262)
T ss_pred             HHHHHHHHH
Confidence            555555543

>KOG4555 consensus TPR repeat-containing protein [Function unknown]

Probab=95.68  E-value=0.6  Score=34.69  Aligned_cols=91  Identities=12%  Similarity=-0.011  Sum_probs=51.7

Q ss_pred             HHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHH---HHHHHHHHHHHcC
Q 012111          229 GYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQ---TLNILTKSYGRAG  305 (471)
Q Consensus       229 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~---~~~~ll~~~~~~~  305 (471)
                      ++...|+.+.|++.|.+....  .+.....||.-..++.-.|+.++|+.-+++..+..-..+..   .|..-...|...|
T Consensus        52 alaE~g~Ld~AlE~F~qal~l--~P~raSayNNRAQa~RLq~~~e~ALdDLn~AleLag~~trtacqa~vQRg~lyRl~g  129 (175)
T KOG4555|consen   52 ALAEAGDLDGALELFGQALCL--APERASAYNNRAQALRLQGDDEEALDDLNKALELAGDQTRTACQAFVQRGLLYRLLG  129 (175)
T ss_pred             HHHhccchHHHHHHHHHHHHh--cccchHhhccHHHHHHHcCChHHHHHHHHHHHHhcCccchHHHHHHHHHHHHHHHhC
Confidence            345566777777777666654  24455567777777777777777776666665432222222   2222233455566


Q ss_pred             CHHHHHHHHHHHHhCC
Q 012111          306 MYDKMRSVMDFMQKRF  321 (471)
Q Consensus       306 ~~~~a~~~~~~~~~~~  321 (471)
                      +-+.|..=|+...+.|
T Consensus       130 ~dd~AR~DFe~AA~LG  145 (175)
T KOG4555|consen  130 NDDAARADFEAAAQLG  145 (175)
T ss_pred             chHHHHHhHHHHHHhC
Confidence            6666666666555543

>PF08631 SPO22: Meiosis protein SPO22/ZIP4 like; InterPro: IPR013940 SPO22 is a meiosis-specific protein with similarity to phospholipase A2, involved in completion of nuclear divisions during meiosis; induced early in meiosis []

Probab=95.55  E-value=1.5  Score=38.54  Aligned_cols=125  Identities=17%  Similarity=0.125  Sum_probs=65.1

Q ss_pred             HHHhhcHHHHHHHHHHhhhcc-CccCCh-----hHHHHHHHHHhcCC-CHHHHHHHHHHHHhC--------CCCCC----
Q 012111           88 AIKQKKWQLALKIFGLLRQQQ-WYQARC-----QTFTKLMVMLGKCK-QPEQASLLFEVMLSD--------GLKPS----  148 (471)
Q Consensus        88 ~~~~~~~~~A~~~~~~~~~~~-~~~~~~-----~~~~~l~~~~~~~~-~~~~a~~~~~~m~~~--------~~~~~----  148 (471)
                      ..++|+.+.|..++.++.... ...|+.     ..+..+.....+.+ +++.|...+++..+.        ...++    
T Consensus         3 A~~~~~~~~A~~~~~K~~~~~~~~~~~~~~~La~~~yn~G~~l~~~~~~~~~a~~wL~~a~~~l~~~~~~~~~~~~~~el   82 (278)
T PF08631_consen    3 AWKQGDLDLAEHMYSKAKDLLNSLDPDMAEELARVCYNIGKSLLSKKDKYEEAVKWLQRAYDILEKPGKMDKLSPDGSEL   82 (278)
T ss_pred             chhhCCHHHHHHHHHHhhhHHhcCCcHHHHHHHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHhhhhccccCCcHHHH
Confidence            357889999999998887643 223332     12223333334445 777777766654432        11122    


Q ss_pred             -HHHHHHHHHHHHhcCCH---HHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHC
Q 012111          149 -VDVYTALVSAYGQSGLL---DEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYL  214 (471)
Q Consensus       149 -~~~~~~li~~~~~~~~~---~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~  214 (471)
                       ..++..++.+|...+..   ++|..+++.+....+-  .+.++..-+..+.+.++.+.+.+++.+|...
T Consensus        83 r~~iL~~La~~~l~~~~~~~~~ka~~~l~~l~~e~~~--~~~~~~L~l~il~~~~~~~~~~~~L~~mi~~  150 (278)
T PF08631_consen   83 RLSILRLLANAYLEWDTYESVEKALNALRLLESEYGN--KPEVFLLKLEILLKSFDEEEYEEILMRMIRS  150 (278)
T ss_pred             HHHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHhCCC--CcHHHHHHHHHHhccCChhHHHHHHHHHHHh
Confidence             22444555556555543   3445555555442222  2333434445555556666666666666554

It is also involved in sporulation [].

>PF07079 DUF1347: Protein of unknown function (DUF1347); InterPro: IPR010764 This family consists of several hypothetical bacterial proteins of around 610 residues in length

Probab=95.53  E-value=1.9  Score=39.54  Aligned_cols=116  Identities=12%  Similarity=0.036  Sum_probs=69.8

Q ss_pred             hcCC-HHHHHHHHHHHHHcCCCC-CHHHHHHHH----HHHHh---cCCHHHHHHHHHHHHhCCCCcC----HHHHHHHHH
Q 012111          338 KAGH-IEKMEEYFKKMKHRGMKP-NSITYCSLV----SAYSK---AGLIMKVDSILRQVENSDVILD----TPFFNCIIS  404 (471)
Q Consensus       338 ~~g~-~~~a~~~~~~m~~~~~~p-~~~~~~~li----~~~~~---~g~~~~a~~~~~~~~~~~~~~~----~~~~~~l~~  404 (471)
                      +.|. -++|+.+++....-  .+ |...-+.+.    .+|..   ...+.+-..+-+-+.+.|+.|-    ...-|.|..
T Consensus       391 ~~g~~dekalnLLk~il~f--t~yD~ec~n~v~~fvKq~Y~qaLs~~~~~rLlkLe~fi~e~gl~~i~i~e~eian~LaD  468 (549)
T PF07079_consen  391 EIGQCDEKALNLLKLILQF--TNYDIECENIVFLFVKQAYKQALSMHAIPRLLKLEDFITEVGLTPITISEEEIANFLAD  468 (549)
T ss_pred             hcCCccHHHHHHHHHHHHh--ccccHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHhcCCCcccccHHHHHHHHHH
Confidence            3443 66777777777653  22 322222211    22221   2334444444455556666643    234444444


Q ss_pred             H--HHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 012111          405 A--YGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAYNALGMTEAAQNLENKM  457 (471)
Q Consensus       405 ~--~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~m  457 (471)
                      +  +...|++.++.-.-.-+.+  +.|++.+|..+.-++....++++|..++.+.
T Consensus       469 AEyLysqgey~kc~~ys~WL~~--iaPS~~~~RLlGl~l~e~k~Y~eA~~~l~~L  521 (549)
T PF07079_consen  469 AEYLYSQGEYHKCYLYSSWLTK--IAPSPQAYRLLGLCLMENKRYQEAWEYLQKL  521 (549)
T ss_pred             HHHHHhcccHHHHHHHHHHHHH--hCCcHHHHHHHHHHHHHHhhHHHHHHHHHhC
Confidence            3  4456888887766555555  7899999999998889999999999888764

Members of this family are highly conserved and seem to be specific to Chlamydia species. The function of this family is unknown.

>COG3629 DnrI DNA-binding transcriptional activator of the SARP family [Signal transduction mechanisms]

Probab=95.52  E-value=0.21  Score=43.05  Aligned_cols=77  Identities=18%  Similarity=0.122  Sum_probs=49.1

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHh-----CCCCCCHHHHHHH
Q 012111          363 TYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKE-----RHCVPDNITFATM  437 (471)
Q Consensus       363 ~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~-----~~~~p~~~~~~~l  437 (471)
                      ++..++..+...|+.+.+...++++....+. +...|..++.+|.+.|+...|++.|+.+.+     .|+.|...+...+
T Consensus       155 ~l~~lae~~~~~~~~~~~~~~l~~Li~~dp~-~E~~~~~lm~~y~~~g~~~~ai~~y~~l~~~~~edlgi~P~~~~~~~y  233 (280)
T COG3629         155 ALTKLAEALIACGRADAVIEHLERLIELDPY-DEPAYLRLMEAYLVNGRQSAAIRAYRQLKKTLAEELGIDPAPELRALY  233 (280)
T ss_pred             HHHHHHHHHHhcccHHHHHHHHHHHHhcCcc-chHHHHHHHHHHHHcCCchHHHHHHHHHHHHhhhhcCCCccHHHHHHH
Confidence            4555666666666666666666666666555 666666677777777776666666665543     4666666666555


Q ss_pred             HHH
Q 012111          438 IQA  440 (471)
Q Consensus       438 ~~~  440 (471)
                      ...
T Consensus       234 ~~~  236 (280)
T COG3629         234 EEI  236 (280)
T ss_pred             HHH
Confidence            554

>PF13428 TPR_14: Tetratricopeptide repeat

Probab=95.48  E-value=0.035  Score=32.75  Aligned_cols=26  Identities=15%  Similarity=0.280  Sum_probs=14.0

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHh
Q 012111          399 FNCIISAYGQAGDVEKMGELFLTMKE  424 (471)
Q Consensus       399 ~~~l~~~~~~~g~~~~a~~~~~~~~~  424 (471)
                      +..+...|...|++++|+++|+++.+
T Consensus         4 ~~~la~~~~~~G~~~~A~~~~~~~l~   29 (44)
T PF13428_consen    4 WLALARAYRRLGQPDEAERLLRRALA   29 (44)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            44455555555555555555555554

>PF13176 TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_A 3RO2_A

Probab=95.47  E-value=0.05  Score=30.36  Aligned_cols=33  Identities=15%  Similarity=0.236  Sum_probs=21.1

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHhhhcCC
Q 012111          433 TFATMIQAYNALGMTEAAQNLENKMIAMKENSG  465 (471)
Q Consensus       433 ~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~~~  465 (471)
                      +|..|...|.+.|++++|.+++++++.....+.
T Consensus         1 al~~Lg~~~~~~g~~~~Ai~~y~~aL~l~~~~~   33 (36)
T PF13176_consen    1 ALNNLGRIYRQQGDYEKAIEYYEQALALARDPE   33 (36)
T ss_dssp             HHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHCT
T ss_pred             CHHHHHHHHHHcCCHHHHHHHHHHHHHhccccc
Confidence            355667777777777777777777665554443

>COG5107 RNA14 Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification]

Probab=95.40  E-value=2.1  Score=39.21  Aligned_cols=135  Identities=16%  Similarity=0.205  Sum_probs=90.9

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC-CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHH
Q 012111          326 VVTYNIVIETFGKAGHIEKMEEYFKKMKHRG-MKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIIS  404 (471)
Q Consensus       326 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~-~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  404 (471)
                      ...|...+....+...++.|..+|-++.+.| +.++..++++++..++ .|+...|..+|+.-...-.. +...-+..+.
T Consensus       397 t~v~C~~~N~v~r~~Gl~aaR~~F~k~rk~~~~~h~vyi~~A~~E~~~-~~d~~ta~~ifelGl~~f~d-~~~y~~kyl~  474 (660)
T COG5107         397 TFVFCVHLNYVLRKRGLEAARKLFIKLRKEGIVGHHVYIYCAFIEYYA-TGDRATAYNIFELGLLKFPD-STLYKEKYLL  474 (660)
T ss_pred             hhHHHHHHHHHHHHhhHHHHHHHHHHHhccCCCCcceeeeHHHHHHHh-cCCcchHHHHHHHHHHhCCC-chHHHHHHHH
Confidence            3456677777777777888888888888777 5567777777777654 56777788887764443222 2222344556


Q ss_pred             HHHhcCCHHHHHHHHHHHHhCCCCCC--HHHHHHHHHHHHhcCCHHHHHHHHHHHHHhhhc
Q 012111          405 AYGQAGDVEKMGELFLTMKERHCVPD--NITFATMIQAYNALGMTEAAQNLENKMIAMKEN  463 (471)
Q Consensus       405 ~~~~~g~~~~a~~~~~~~~~~~~~p~--~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~  463 (471)
                      -+...++-..|..+|+..+++ +.-+  ...|..+|..-..-|+...+..+-++|...-|.
T Consensus       475 fLi~inde~naraLFetsv~r-~~~~q~k~iy~kmi~YEs~~G~lN~v~sLe~rf~e~~pQ  534 (660)
T COG5107         475 FLIRINDEENARALFETSVER-LEKTQLKRIYDKMIEYESMVGSLNNVYSLEERFRELVPQ  534 (660)
T ss_pred             HHHHhCcHHHHHHHHHHhHHH-HHHhhhhHHHHHHHHHHHhhcchHHHHhHHHHHHHHcCc
Confidence            667778888888888866543 3333  467777887777778887777777777665554

>PRK11906 transcriptional regulator; Provisional

Probab=95.39  E-value=0.94  Score=41.88  Aligned_cols=147  Identities=9%  Similarity=-0.019  Sum_probs=98.0

Q ss_pred             CHHHHHHHHHHHHh-CCCCCC-HHHHHHHHHHHHhc---------CCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhc
Q 012111          306 MYDKMRSVMDFMQK-RFFFPT-VVTYNIVIETFGKA---------GHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKA  374 (471)
Q Consensus       306 ~~~~a~~~~~~~~~-~~~~~~-~~~~~~li~~~~~~---------g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~  374 (471)
                      ..+.|..+|.+... ....|+ ...|..+..++...         ....+|.++.++..+.+ +-|+.....+..+....
T Consensus       273 ~~~~Al~lf~ra~~~~~ldp~~a~a~~~lA~~h~~~~~~g~~~~~~~~~~a~~~A~rAveld-~~Da~a~~~~g~~~~~~  351 (458)
T PRK11906        273 SIYRAMTIFDRLQNKSDIQTLKTECYCLLAECHMSLALHGKSELELAAQKALELLDYVSDIT-TVDGKILAIMGLITGLS  351 (458)
T ss_pred             HHHHHHHHHHHHhhcccCCcccHHHHHHHHHHHHHHHHhcCCCchHHHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHhh
Confidence            35678888888772 223444 34555555444322         23456777777777765 45788888888888888


Q ss_pred             CCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHH---HHHHHHHHHHhcCCHHHHH
Q 012111          375 GLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNI---TFATMIQAYNALGMTEAAQ  451 (471)
Q Consensus       375 g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~---~~~~l~~~~~~~g~~~~A~  451 (471)
                      ++++.|...|++....++. ...+|......+.-.|+.++|.+.+++..+.  .|...   .....+..|+..+ .++|.
T Consensus       352 ~~~~~a~~~f~rA~~L~Pn-~A~~~~~~~~~~~~~G~~~~a~~~i~~alrL--sP~~~~~~~~~~~~~~~~~~~-~~~~~  427 (458)
T PRK11906        352 GQAKVSHILFEQAKIHSTD-IASLYYYRALVHFHNEKIEEARICIDKSLQL--EPRRRKAVVIKECVDMYVPNP-LKNNI  427 (458)
T ss_pred             cchhhHHHHHHHHhhcCCc-cHHHHHHHHHHHHHcCCHHHHHHHHHHHhcc--CchhhHHHHHHHHHHHHcCCc-hhhhH
Confidence            8899999999999887765 5666666666777789999999999987763  45433   2223334555544 67777


Q ss_pred             HHHHHH
Q 012111          452 NLENKM  457 (471)
Q Consensus       452 ~~~~~m  457 (471)
                      +++-+-
T Consensus       428 ~~~~~~  433 (458)
T PRK11906        428 KLYYKE  433 (458)
T ss_pred             HHHhhc
Confidence            776543

>KOG1920 consensus IkappaB kinase complex, IKAP component [Transcription]

Probab=95.36  E-value=4.1  Score=42.25  Aligned_cols=131  Identities=11%  Similarity=0.180  Sum_probs=66.2

Q ss_pred             chHHHHHHHHHHHhhcHHHHHHHHHHhhhccC--ccCChhHHHHHHHHHhcC-CCHHHHHHHHHHHHhCCCCCCHHHHHH
Q 012111           78 PKPVLEALDEAIKQKKWQLALKIFGLLRQQQW--YQARCQTFTKLMVMLGKC-KQPEQASLLFEVMLSDGLKPSVDVYTA  154 (471)
Q Consensus        78 ~~~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~--~~~~~~~~~~l~~~~~~~-~~~~~a~~~~~~m~~~~~~~~~~~~~~  154 (471)
                      ...++..++.++...++.+|+++-++-+-.-.  +..+...|..-+.++.+. ++.+-...++..+....+  +...|..
T Consensus       677 R~lVLa~vr~~l~~~~y~~AF~~~RkhRidlnii~d~~~~~Fl~nv~afl~~in~~~~l~lfl~~lk~eDv--tk~~y~~  754 (1265)
T KOG1920|consen  677 RILVLAKVRTLLDRLRYKEAFEVMRKHRIDLNIIFDYDPKRFLKNVPAFLKQINRVNHLELFLTELKEEDV--TKTMYSS  754 (1265)
T ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHHHhccCccchhhcCHHHHHhhHHHHhccCCcHHHHHHHHhhcccchh--hhhhccc
Confidence            34566888888899999988776655432210  122344444444455443 455555555555553321  1111211


Q ss_pred             HH----HHHHhc----CCHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcC--CHHHHHHHHHHHHH
Q 012111          155 LV----SAYGQS----GLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFH--RFDLIEKILAEMSY  213 (471)
Q Consensus       155 li----~~~~~~----~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~--~~~~a~~~~~~~~~  213 (471)
                      ..    ..|...    +..+...+.+.....  ...|+ .....+|.++.+.+  ..+.+++...+...
T Consensus       755 ~~~s~k~~~~~r~~~d~kv~~vc~~vr~~l~--~~~~~-~~~~~ilTs~vk~~~~~ie~aL~kI~~l~~  820 (1265)
T KOG1920|consen  755 TSGSGKQVYMSRDPYDNKVNSVCDAVRNALE--RRAPD-KFNLFILTSYVKSNPPEIEEALQKIKELQL  820 (1265)
T ss_pred             cccccceeEEeccchhhHHHHHHHHHHHHHh--hcCcc-hhhHHHHHHHHhcCcHHHHHHHHHHHHHHh
Confidence            11    111111    223333444444333  12455 44566777777776  66677776666654

>KOG3941 consensus Intermediate in Toll signal transduction pathway (ECSIT) [Signal transduction mechanisms]

Probab=95.36  E-value=0.2  Score=42.57  Aligned_cols=33  Identities=18%  Similarity=0.268  Sum_probs=19.9

Q ss_pred             HHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCC
Q 012111          309 KMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGH  341 (471)
Q Consensus       309 ~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~  341 (471)
                      -++.++++|...|+.||..+-..++.++.+.+-
T Consensus       141 C~I~vLeqME~hGVmPdkE~e~~lvn~FGr~~~  173 (406)
T KOG3941|consen  141 CAIKVLEQMEWHGVMPDKEIEDILVNAFGRWNF  173 (406)
T ss_pred             HHHHHHHHHHHcCCCCchHHHHHHHHHhccccc
Confidence            355566666666666666666666666655543

>smart00299 CLH Clathrin heavy chain repeat homology

Probab=95.35  E-value=0.96  Score=34.92  Aligned_cols=40  Identities=10%  Similarity=0.155  Sum_probs=17.5

Q ss_pred             HHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHh
Q 012111          298 TKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGK  338 (471)
Q Consensus       298 l~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~  338 (471)
                      +..+...+.......+++.+...+. .+...++.++..|++
T Consensus        14 v~~~~~~~~~~~l~~yLe~~~~~~~-~~~~~~~~li~ly~~   53 (140)
T smart00299       14 VELFEKRNLLEELIPYLESALKLNS-ENPALQTKLIELYAK   53 (140)
T ss_pred             HHHHHhCCcHHHHHHHHHHHHccCc-cchhHHHHHHHHHHH
Confidence            3333344444444444444444432 234444444444444

>PF13512 TPR_18: Tetratricopeptide repeat

Probab=95.31  E-value=0.94  Score=34.60  Aligned_cols=75  Identities=11%  Similarity=0.024  Sum_probs=44.7

Q ss_pred             HHHHhcCCHHHHHHHHHHHHHcCC--CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHh
Q 012111          334 ETFGKAGHIEKMEEYFKKMKHRGM--KPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQ  408 (471)
Q Consensus       334 ~~~~~~g~~~~a~~~~~~m~~~~~--~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  408 (471)
                      ....+.|++++|.+.|+.+...-.  +-....--.++.++.+.+++++|...++++++.++.....-|...+.+++.
T Consensus        18 ~~~l~~~~Y~~A~~~le~L~~ryP~g~ya~qAqL~l~yayy~~~~y~~A~a~~~rFirLhP~hp~vdYa~Y~~gL~~   94 (142)
T PF13512_consen   18 QEALQKGNYEEAIKQLEALDTRYPFGEYAEQAQLDLAYAYYKQGDYEEAIAAYDRFIRLHPTHPNVDYAYYMRGLSY   94 (142)
T ss_pred             HHHHHhCCHHHHHHHHHHHHhcCCCCcccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCCCCccHHHHHHHHHH
Confidence            344556777777777777665510  112344556667777777777777777777766655444445555555443

>PF07035 Mic1: Colon cancer-associated protein Mic1-like; InterPro: IPR009755 This entry represents the C terminus (approximately 160 residues) of a number of proteins that resemble colon cancer-associated protein Mic1

Probab=95.26  E-value=1.2  Score=35.34  Aligned_cols=134  Identities=12%  Similarity=0.117  Sum_probs=71.6

Q ss_pred             HHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 012111          134 SLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSY  213 (471)
Q Consensus       134 ~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~  213 (471)
                      .+.+..+.+.|++|+...+..+++.+.+.|++.....++.     .++-+|.......+-.+..  ....+.++=-+|.+
T Consensus        14 lEYirSl~~~~i~~~~~L~~lli~lLi~~~~~~~L~qllq-----~~Vi~DSk~lA~~LLs~~~--~~~~~~Ql~lDMLk   86 (167)
T PF07035_consen   14 LEYIRSLNQHNIPVQHELYELLIDLLIRNGQFSQLHQLLQ-----YHVIPDSKPLACQLLSLGN--QYPPAYQLGLDMLK   86 (167)
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHHHHHHHcCCHHHHHHHHh-----hcccCCcHHHHHHHHHhHc--cChHHHHHHHHHHH
Confidence            3455556667778888888888888888887666555544     3444554444333322222  22223333323322


Q ss_pred             C-CCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 012111          214 L-GIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNL  284 (471)
Q Consensus       214 ~-g~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  284 (471)
                      . |     ..+..+++.+...|++-+|.++.+......  .   .....++.+..+.+|...-..+++-+..
T Consensus        87 RL~-----~~~~~iievLL~~g~vl~ALr~ar~~~~~~--~---~~~~~fLeAA~~~~D~~lf~~V~~ff~~  148 (167)
T PF07035_consen   87 RLG-----TAYEEIIEVLLSKGQVLEALRYARQYHKVD--S---VPARKFLEAAANSNDDQLFYAVFRFFEE  148 (167)
T ss_pred             Hhh-----hhHHHHHHHHHhCCCHHHHHHHHHHcCCcc--c---CCHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            1 1     124556677777788877777776642221  1   1224455555566665555555544433

>PF04184 ST7: ST7 protein; InterPro: IPR007311 The ST7 (for suppression of tumorigenicity 7) protein is thought to be a tumour suppressor gene

Probab=95.26  E-value=1.3  Score=41.23  Aligned_cols=169  Identities=12%  Similarity=0.105  Sum_probs=98.0

Q ss_pred             HHHHHHHHHHHhhcHHHHHHHHHHhhhccCccCCh-hHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHH
Q 012111           80 PVLEALDEAIKQKKWQLALKIFGLLRQQQWYQARC-QTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSA  158 (471)
Q Consensus        80 ~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~-~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~  158 (471)
                      ....++...-+..+.+.-++.-.++.+..   |+. ..|..|..  -......++.+++++..+.|-.    .+.     
T Consensus       170 ~Aq~IMq~AWRERnp~aRIkaA~eALei~---pdCAdAYILLAE--EeA~Ti~Eae~l~rqAvkAgE~----~lg-----  235 (539)
T PF04184_consen  170 PAQEIMQKAWRERNPQARIKAAKEALEIN---PDCADAYILLAE--EEASTIVEAEELLRQAVKAGEA----SLG-----  235 (539)
T ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHhh---hhhhHHHhhccc--ccccCHHHHHHHHHHHHHHHHH----hhc-----
Confidence            44566777778888888888888887753   443 33333322  2345678888888887764311    111     


Q ss_pred             HHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCC-CCHHHHHHHHHHHHccCCHH
Q 012111          159 YGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIE-CSAVTYNTIIDGYGKAKKFE  237 (471)
Q Consensus       159 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~-~~~~~~~~l~~~~~~~~~~~  237 (471)
                        +....+..-..++.+.. ....+-..+-..+..++-+.|+.++|.+.+.+|.+.... -+..+...|+.++...+.+.
T Consensus       236 --~s~~~~~~g~~~e~~~~-Rdt~~~~y~KrRLAmCarklGr~~EAIk~~rdLlke~p~~~~l~IrenLie~LLelq~Ya  312 (539)
T PF04184_consen  236 --KSQFLQHHGHFWEAWHR-RDTNVLVYAKRRLAMCARKLGRLREAIKMFRDLLKEFPNLDNLNIRENLIEALLELQAYA  312 (539)
T ss_pred             --hhhhhhcccchhhhhhc-cccchhhhhHHHHHHHHHHhCChHHHHHHHHHHHhhCCccchhhHHHHHHHHHHhcCCHH
Confidence              00000000011111221 222333344445666677889999999999988765312 23456778899999999999


Q ss_pred             HHHHHHHHHHHcCCCCCCHHHHHHHHHH
Q 012111          238 EMESSFSAMVESGGCHPDIFTLNSMISA  265 (471)
Q Consensus       238 ~a~~~~~~~~~~~~~~~~~~~~~~l~~~  265 (471)
                      ++..++.+..+....+.-...|+..+-.
T Consensus       313 d~q~lL~kYdDi~lpkSAti~YTaALLk  340 (539)
T PF04184_consen  313 DVQALLAKYDDISLPKSATICYTAALLK  340 (539)
T ss_pred             HHHHHHHHhccccCCchHHHHHHHHHHH
Confidence            9999988874332112234456655433

The molecular function of this protein is uncertain.

>PF09613 HrpB1_HrpK: Bacterial type III secretion protein (HrpB1_HrpK); InterPro: IPR013394 This family of proteins is encoded by genes found within type III secretion operons in a limited range of species including Xanthomonas, Ralstonia and Burkholderia

Probab=95.18  E-value=0.83  Score=35.63  Aligned_cols=117  Identities=15%  Similarity=0.029  Sum_probs=65.4

Q ss_pred             HHHHHHHHH---HHhcCCHHHHHHHHHHHHHcCCCCCHHHH-HHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHH
Q 012111          327 VTYNIVIET---FGKAGHIEKMEEYFKKMKHRGMKPNSITY-CSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCI  402 (471)
Q Consensus       327 ~~~~~li~~---~~~~g~~~~a~~~~~~m~~~~~~p~~~~~-~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l  402 (471)
                      .+.+.||..   -...++.+++..++..+.-.  .|..... ..-...+...|++.+|..+|+.+.+..  |....-..|
T Consensus         8 ~iv~gLie~~~~al~~~~~~D~e~lL~ALrvL--RP~~~e~~~~~~~l~i~r~~w~dA~rlLr~l~~~~--~~~p~~kAL   83 (160)
T PF09613_consen    8 EIVGGLIEVLSVALRLGDPDDAEALLDALRVL--RPEFPELDLFDGWLHIVRGDWDDALRLLRELEERA--PGFPYAKAL   83 (160)
T ss_pred             HHHHHHHHHHHHHHccCChHHHHHHHHHHHHh--CCCchHHHHHHHHHHHHhCCHHHHHHHHHHHhccC--CCChHHHHH
Confidence            344444443   35678889999999888874  5543332 223345678899999999999987654  233344455


Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHH
Q 012111          403 ISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAYNALGMTEAA  450 (471)
Q Consensus       403 ~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A  450 (471)
                      +..|....+-..=...-+++.+.+-  |+.+- .+++.+....+...|
T Consensus        84 lA~CL~~~~D~~Wr~~A~evle~~~--d~~a~-~Lv~~Ll~~~~~~~a  128 (160)
T PF09613_consen   84 LALCLYALGDPSWRRYADEVLESGA--DPDAR-ALVRALLARADLEPA  128 (160)
T ss_pred             HHHHHHHcCChHHHHHHHHHHhcCC--ChHHH-HHHHHHHHhccccch
Confidence            5555444332233333445555532  33332 344555444444444

>PF07719 TPR_2: Tetratricopeptide repeat; InterPro: IPR013105 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]

Probab=95.16  E-value=0.081  Score=28.85  Aligned_cols=32  Identities=28%  Similarity=0.287  Sum_probs=23.9

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHHhhhc
Q 012111          432 ITFATMIQAYNALGMTEAAQNLENKMIAMKEN  463 (471)
Q Consensus       432 ~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~  463 (471)
                      ..|..+...+...|++++|.+.++++++..|+
T Consensus         2 ~~~~~lg~~~~~~~~~~~A~~~~~~al~l~p~   33 (34)
T PF07719_consen    2 EAWYYLGQAYYQLGNYEEAIEYFEKALELDPN   33 (34)
T ss_dssp             HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT
T ss_pred             HHHHHHHHHHHHhCCHHHHHHHHHHHHHHCcC
Confidence            35666777888888888888888888887775

It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. This repeat includes outlying Tetratricopeptide-like repeats (TPR) that are not matched by IPR001440 from INTERPRO.; PDB: 1XNF_B 3Q15_A 4ABN_A 1OUV_A 3U4T_A 3MA5_C 2KCV_A 2KCL_A 2XEV_A 3NF1_A ....

>PF13428 TPR_14: Tetratricopeptide repeat

Probab=95.03  E-value=0.081  Score=31.15  Aligned_cols=38  Identities=21%  Similarity=0.320  Sum_probs=20.6

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHH
Q 012111          363 TYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNC  401 (471)
Q Consensus       363 ~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~  401 (471)
                      ++..+...|...|++++|.++|+++.+..+. |...+..
T Consensus         3 ~~~~la~~~~~~G~~~~A~~~~~~~l~~~P~-~~~a~~~   40 (44)
T PF13428_consen    3 AWLALARAYRRLGQPDEAERLLRRALALDPD-DPEAWRA   40 (44)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHCcC-CHHHHHH
Confidence            3445555566666666666666666555444 4444433

>COG4649 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=95.00  E-value=1.4  Score=34.76  Aligned_cols=52  Identities=13%  Similarity=0.073  Sum_probs=23.8

Q ss_pred             hcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHH
Q 012111          197 KFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVE  248 (471)
Q Consensus       197 ~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  248 (471)
                      ..|.++......+.+...|-+.....-..|.-+-.+.|++.+|...|..+..
T Consensus       144 D~gsy~dV~srvepLa~d~n~mR~sArEALglAa~kagd~a~A~~~F~qia~  195 (221)
T COG4649         144 DNGSYDDVSSRVEPLAGDGNPMRHSAREALGLAAYKAGDFAKAKSWFVQIAN  195 (221)
T ss_pred             ccccHHHHHHHhhhccCCCChhHHHHHHHHhHHHHhccchHHHHHHHHHHHc
Confidence            3444444444444444333333333334444444455555555555555543

>PF00515 TPR_1: Tetratricopeptide repeat; InterPro: IPR001440 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]

Probab=94.89  E-value=0.1  Score=28.54  Aligned_cols=32  Identities=19%  Similarity=0.272  Sum_probs=22.9

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHHhhhc
Q 012111          432 ITFATMIQAYNALGMTEAAQNLENKMIAMKEN  463 (471)
Q Consensus       432 ~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~  463 (471)
                      .+|..+...+...|++++|...++++++.+|+
T Consensus         2 ~~~~~~g~~~~~~~~~~~A~~~~~~al~~~p~   33 (34)
T PF00515_consen    2 EAYYNLGNAYFQLGDYEEALEYYQRALELDPD   33 (34)
T ss_dssp             HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT
T ss_pred             HHHHHHHHHHHHhCCchHHHHHHHHHHHHCcC
Confidence            45666777777778888888888887777764

It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. The X-ray structure of a domain containing three TPRs from protein phosphatase 5 revealed that TPR adopts a helix-turn-helix arrangement, with adjacent TPR motifs packing in a parallel fashion, resulting in a spiral of repeating anti-parallel alpha-helices []. The two helices are denoted helix A and helix B. The packing angle between helix A and helix B is ~24 degrees; within a single TPR and generates a right-handed superhelical shape. Helix A interacts with helix B and with helix A' of the next TPR. Two protein surfaces are generated: the inner concave surface is contributed to mainly by residue on helices A, and the other surface presents residues from both helices A and B. ; GO: 0005515 protein binding; PDB: 3SF4_C 2LNI_A 1ELW_A 2C0M_A 1FCH_B 3R9A_B 2J9Q_A 2C0L_A 1KT1_A 3FWV_A ....

>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]

Probab=94.84  E-value=1.9  Score=38.26  Aligned_cols=227  Identities=10%  Similarity=0.049  Sum_probs=97.0

Q ss_pred             HhcCCHHHHHHHHHHHHHC--CCCCCHHHHHHHHHHHHccCCHHHHHHHHHHH----HHcCCCCCCHHHHHHHHHHHHhc
Q 012111          196 TKFHRFDLIEKILAEMSYL--GIECSAVTYNTIIDGYGKAKKFEEMESSFSAM----VESGGCHPDIFTLNSMISAYGNS  269 (471)
Q Consensus       196 ~~~~~~~~a~~~~~~~~~~--g~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~----~~~~~~~~~~~~~~~l~~~~~~~  269 (471)
                      ....+.++++..+..-...  ...-...++..+..+.++.|.+++++..--..    .+.....--...|..+..++.+.
T Consensus        17 y~s~~~~~al~~w~~~L~~l~~~~~Rf~~lG~l~~a~s~~g~y~~mL~~a~sqi~~a~~~~ds~~~~ea~lnlar~~e~l   96 (518)
T KOG1941|consen   17 YQSNQTEKALQVWTKVLEKLSDLMGRFRVLGCLVTAHSEMGRYKEMLKFAVSQIDTARELEDSDFLLEAYLNLARSNEKL   96 (518)
T ss_pred             hcCchHHHHHHHHHHHHHHHHHHHHHHHHhccchhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3445566666666554432  11112345555666666666666655432221    11100000112333344444444


Q ss_pred             CCHHHHHHHHHHHHhC-CCCC---CHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCC-----CCCHHHHHHHHHHHHhcC
Q 012111          270 GNIEKMEKWYNEFNLM-GVKA---DIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFF-----FPTVVTYNIVIETFGKAG  340 (471)
Q Consensus       270 ~~~~~a~~~~~~~~~~-~~~~---~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~-----~~~~~~~~~li~~~~~~g  340 (471)
                      -++.+++.+-..-... |..+   .......+..++...+.++++++.|+...+...     ......|..|-..|.+..
T Consensus        97 ~~f~kt~~y~k~~l~lpgt~~~~~~gq~~l~~~~Ahlgls~fq~~Lesfe~A~~~A~~~~D~~LElqvcv~Lgslf~~l~  176 (518)
T KOG1941|consen   97 CEFHKTISYCKTCLGLPGTRAGQLGGQVSLSMGNAHLGLSVFQKALESFEKALRYAHNNDDAMLELQVCVSLGSLFAQLK  176 (518)
T ss_pred             HHhhhHHHHHHHHhcCCCCCcccccchhhhhHHHHhhhHHHHHHHHHHHHHHHHHhhccCCceeeeehhhhHHHHHHHHH
Confidence            4444444433332211 1111   112233345555555666666666655443211     111234555666666666


Q ss_pred             CHHHHHHHHHHHHHc----CCCCCHHHH-----HHHHHHHHhcCCHHHHHHHHHHHHh----CCCCc-CHHHHHHHHHHH
Q 012111          341 HIEKMEEYFKKMKHR----GMKPNSITY-----CSLVSAYSKAGLIMKVDSILRQVEN----SDVIL-DTPFFNCIISAY  406 (471)
Q Consensus       341 ~~~~a~~~~~~m~~~----~~~p~~~~~-----~~li~~~~~~g~~~~a~~~~~~~~~----~~~~~-~~~~~~~l~~~~  406 (471)
                      ++++|.-+..+..+.    ++.--..-|     ..+.-++...|....|.+..++..+    .|-.+ .......+.+.|
T Consensus       177 D~~Kal~f~~kA~~lv~s~~l~d~~~kyr~~~lyhmaValR~~G~LgdA~e~C~Ea~klal~~Gdra~~arc~~~~aDIy  256 (518)
T KOG1941|consen  177 DYEKALFFPCKAAELVNSYGLKDWSLKYRAMSLYHMAVALRLLGRLGDAMECCEEAMKLALQHGDRALQARCLLCFADIY  256 (518)
T ss_pred             hhhHHhhhhHhHHHHHHhcCcCchhHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHhCChHHHHHHHHHHHHHH
Confidence            666665555443321    211111112     2233344555555555555554332    22111 112233444555


Q ss_pred             HhcCCHHHHHHHHHHH
Q 012111          407 GQAGDVEKMGELFLTM  422 (471)
Q Consensus       407 ~~~g~~~~a~~~~~~~  422 (471)
                      ...|+.+.|+.-|+..
T Consensus       257 R~~gd~e~af~rYe~A  272 (518)
T KOG1941|consen  257 RSRGDLERAFRRYEQA  272 (518)
T ss_pred             HhcccHhHHHHHHHHH
Confidence            5566666665555544

>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]

Probab=94.76  E-value=1.7  Score=38.66  Aligned_cols=229  Identities=9%  Similarity=0.013  Sum_probs=122.5

Q ss_pred             HHhhcHHHHHHHHHHhhhcc-CccCChhHHHHHHHHHhcCCCHHHHHHHH----HHHHhCC-CCCCHHHHHHHHHHHHhc
Q 012111           89 IKQKKWQLALKIFGLLRQQQ-WYQARCQTFTKLMVMLGKCKQPEQASLLF----EVMLSDG-LKPSVDVYTALVSAYGQS  162 (471)
Q Consensus        89 ~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~l~~~~~~~~~~~~a~~~~----~~m~~~~-~~~~~~~~~~li~~~~~~  162 (471)
                      ....+..+|+..+.....+- ..-.-..+|..+..+.+..|.+++++..-    +...+.. -..--..|-.+.+++-+.
T Consensus        17 y~s~~~~~al~~w~~~L~~l~~~~~Rf~~lG~l~~a~s~~g~y~~mL~~a~sqi~~a~~~~ds~~~~ea~lnlar~~e~l   96 (518)
T KOG1941|consen   17 YQSNQTEKALQVWTKVLEKLSDLMGRFRVLGCLVTAHSEMGRYKEMLKFAVSQIDTARELEDSDFLLEAYLNLARSNEKL   96 (518)
T ss_pred             hcCchHHHHHHHHHHHHHHHHHHHHHHHHhccchhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            35566666666665554431 00112345566666777777776665422    2111110 011123455555555555


Q ss_pred             CCHHHHHHHHHHhhcCCCCCCCH---HHHHHHHHHHHhcCCHHHHHHHHHHHHHCCC-----CCCHHHHHHHHHHHHccC
Q 012111          163 GLLDEAFSTINDMKSVSDCKPDV---YTYSILIKSCTKFHRFDLIEKILAEMSYLGI-----ECSAVTYNTIIDGYGKAK  234 (471)
Q Consensus       163 ~~~~~a~~~~~~~~~~~~~~~~~---~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~-----~~~~~~~~~l~~~~~~~~  234 (471)
                      -++.+++.+-..-....|..|..   ....++..++...+.++++++.|+...+.-.     .....++..|-..|.+..
T Consensus        97 ~~f~kt~~y~k~~l~lpgt~~~~~~gq~~l~~~~Ahlgls~fq~~Lesfe~A~~~A~~~~D~~LElqvcv~Lgslf~~l~  176 (518)
T KOG1941|consen   97 CEFHKTISYCKTCLGLPGTRAGQLGGQVSLSMGNAHLGLSVFQKALESFEKALRYAHNNDDAMLELQVCVSLGSLFAQLK  176 (518)
T ss_pred             HHhhhHHHHHHHHhcCCCCCcccccchhhhhHHHHhhhHHHHHHHHHHHHHHHHHhhccCCceeeeehhhhHHHHHHHHH
Confidence            56666666555444433433321   2233355566666778888888877654311     122456777888888888


Q ss_pred             CHHHHHHHHHHHHH---cCCCCCCHHHHH-----HHHHHHHhcCCHHHHHHHHHHHHh----CCC-CCCHHHHHHHHHHH
Q 012111          235 KFEEMESSFSAMVE---SGGCHPDIFTLN-----SMISAYGNSGNIEKMEKWYNEFNL----MGV-KADIQTLNILTKSY  301 (471)
Q Consensus       235 ~~~~a~~~~~~~~~---~~~~~~~~~~~~-----~l~~~~~~~~~~~~a~~~~~~~~~----~~~-~~~~~~~~~ll~~~  301 (471)
                      ++++|.-+..+..+   ..++..-..-|.     .|..++...|....|.+.-++..+    .|- .........+.+.|
T Consensus       177 D~~Kal~f~~kA~~lv~s~~l~d~~~kyr~~~lyhmaValR~~G~LgdA~e~C~Ea~klal~~Gdra~~arc~~~~aDIy  256 (518)
T KOG1941|consen  177 DYEKALFFPCKAAELVNSYGLKDWSLKYRAMSLYHMAVALRLLGRLGDAMECCEEAMKLALQHGDRALQARCLLCFADIY  256 (518)
T ss_pred             hhhHHhhhhHhHHHHHHhcCcCchhHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHhCChHHHHHHHHHHHHHH
Confidence            88887766554432   211111111222     233456667777667666665533    232 12234456677788


Q ss_pred             HHcCCHHHHHHHHHHH
Q 012111          302 GRAGMYDKMRSVMDFM  317 (471)
Q Consensus       302 ~~~~~~~~a~~~~~~~  317 (471)
                      ...|+.+.|+.-|+..
T Consensus       257 R~~gd~e~af~rYe~A  272 (518)
T KOG1941|consen  257 RSRGDLERAFRRYEQA  272 (518)
T ss_pred             HhcccHhHHHHHHHHH
Confidence            8888888887777654

>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]

Probab=94.58  E-value=1.3  Score=43.76  Aligned_cols=141  Identities=11%  Similarity=0.175  Sum_probs=69.7

Q ss_pred             HHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCH
Q 012111          228 DGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMY  307 (471)
Q Consensus       228 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~  307 (471)
                      ..+.+.|++++|...|-+....  +.|.     .+|.-|...........+++.+.+.|+. +...-..|+.+|.+.++.
T Consensus       376 d~Ly~Kgdf~~A~~qYI~tI~~--le~s-----~Vi~kfLdaq~IknLt~YLe~L~~~gla-~~dhttlLLncYiKlkd~  447 (933)
T KOG2114|consen  376 DYLYGKGDFDEATDQYIETIGF--LEPS-----EVIKKFLDAQRIKNLTSYLEALHKKGLA-NSDHTTLLLNCYIKLKDV  447 (933)
T ss_pred             HHHHhcCCHHHHHHHHHHHccc--CChH-----HHHHHhcCHHHHHHHHHHHHHHHHcccc-cchhHHHHHHHHHHhcch
Confidence            3445567777776666555432  2332     2344444555555566666666666633 333445566777777776


Q ss_pred             HHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 012111          308 DKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQV  387 (471)
Q Consensus       308 ~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~  387 (471)
                      ++-.+..+... .|..  ..-....+..+.+.+-.++|..+-.+...     .......+   +-..+++++|.++++.+
T Consensus       448 ~kL~efI~~~~-~g~~--~fd~e~al~Ilr~snyl~~a~~LA~k~~~-----he~vl~il---le~~~ny~eAl~yi~sl  516 (933)
T KOG2114|consen  448 EKLTEFISKCD-KGEW--FFDVETALEILRKSNYLDEAELLATKFKK-----HEWVLDIL---LEDLHNYEEALRYISSL  516 (933)
T ss_pred             HHHHHHHhcCC-Ccce--eeeHHHHHHHHHHhChHHHHHHHHHHhcc-----CHHHHHHH---HHHhcCHHHHHHHHhcC
Confidence            66665555433 1111  01123344455555555555544433221     22222222   23456666666666543

>KOG2280 consensus Vacuolar assembly/sorting protein VPS16 [Intracellular trafficking, secretion, and vesicular transport]

Probab=94.55  E-value=5.2  Score=39.32  Aligned_cols=301  Identities=10%  Similarity=0.080  Sum_probs=167.0

Q ss_pred             hCCCCCCHHHHHH-----HHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCC--HHHHHHHHHHHHHC
Q 012111          142 SDGLKPSVDVYTA-----LVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHR--FDLIEKILAEMSYL  214 (471)
Q Consensus       142 ~~~~~~~~~~~~~-----li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~--~~~a~~~~~~~~~~  214 (471)
                      ..|++.+..-|..     +|+-+...+.+..|+++-..+....  .-+...|.....-+.+..+  -+.+.+.+++=.+.
T Consensus       425 ~~gIplT~~qy~~l~~~~vi~Rl~~r~~Y~vaIQva~~l~~p~--~~~~~Vl~~Wa~~kI~~~d~~d~~vld~I~~kls~  502 (829)
T KOG2280|consen  425 RIGIPLTHEQYRHLSEEVVIDRLVDRHLYSVAIQVAKLLNLPE--SQGDRVLLEWARRKIKQSDKMDEEVLDKIDEKLSA  502 (829)
T ss_pred             ccCccccHHHHhhhchhhhhHHHHhcchhHHHHHHHHHhCCcc--ccccHHHHHHHHHHHhccCccchHHHHHHHHHhcc
Confidence            4477777766654     5666777888999999888776411  1125566666666665532  22333333332222


Q ss_pred             CCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCC---CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhC------
Q 012111          215 GIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCH---PDIFTLNSMISAYGNSGNIEKMEKWYNEFNLM------  285 (471)
Q Consensus       215 g~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~---~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~------  285 (471)
                      .. .....|..+.+-....|+.+-|..+++.=...+...   .+..-+...+.-+...|+.+-...++-.+...      
T Consensus       503 ~~-~~~iSy~~iA~~Ay~~GR~~LA~kLle~E~~~~~qV~lLL~m~~~~~AL~kaies~d~~Li~~Vllhlk~~~~~s~l  581 (829)
T KOG2280|consen  503 KL-TPGISYAAIARRAYQEGRFELARKLLELEPRSGEQVPLLLKMKDSSLALKKAIESGDTDLIIQVLLHLKNKLNRSSL  581 (829)
T ss_pred             cC-CCceeHHHHHHHHHhcCcHHHHHHHHhcCCCccchhHHHhccchHHHHHHHHHhcCCchhHHHHHHHHHHHHHHHHH
Confidence            22 344567777777777889888888775432211000   11223444555666677777666665554332      


Q ss_pred             -----CCCCCHHHHHHHHHH--------HHHcCCHHHHHHHHH--HH----HhCCCCCCHHHHHHHHHHHHhcCCH----
Q 012111          286 -----GVKADIQTLNILTKS--------YGRAGMYDKMRSVMD--FM----QKRFFFPTVVTYNIVIETFGKAGHI----  342 (471)
Q Consensus       286 -----~~~~~~~~~~~ll~~--------~~~~~~~~~a~~~~~--~~----~~~~~~~~~~~~~~li~~~~~~g~~----  342 (471)
                           ..+.....|.-+++-        +...++-.++...|.  ..    ...+..|+.   ......+.+....    
T Consensus       582 ~~~l~~~p~a~~lY~~~~r~~~~~~l~d~y~q~dn~~~~a~~~~q~~~~~~~~~~r~~~l---k~~a~~~a~sk~~s~e~  658 (829)
T KOG2280|consen  582 FMTLRNQPLALSLYRQFMRHQDRATLYDFYNQDDNHQALASFHLQASYAAETIEGRIPAL---KTAANAFAKSKEKSFEA  658 (829)
T ss_pred             HHHHHhchhhhHHHHHHHHhhchhhhhhhhhcccchhhhhhhhhhhhhhhhhhcccchhH---HHHHHHHhhhhhhhhHH
Confidence                 112222222222221        111111112211111  10    001222222   2233344433321    


Q ss_pred             ------HHHHHHHHHHHHc-CCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHH
Q 012111          343 ------EKMEEYFKKMKHR-GMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKM  415 (471)
Q Consensus       343 ------~~a~~~~~~m~~~-~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a  415 (471)
                            .+-+.+.+.+... |......+.+--+.-+...|+..+|.++-.+++    .||...|-.-+.+++..++|++-
T Consensus       659 ka~ed~~kLl~lQ~~Le~q~~~~f~dlSl~dTv~~li~~g~~k~a~ql~~~Fk----ipdKr~~wLk~~aLa~~~kweeL  734 (829)
T KOG2280|consen  659 KALEDQMKLLKLQRTLEDQFGGSFVDLSLHDTVTTLILIGQNKRAEQLKSDFK----IPDKRLWWLKLTALADIKKWEEL  734 (829)
T ss_pred             HHHHHHHHHHHHHHHHHHHhccccccCcHHHHHHHHHHccchHHHHHHHHhcC----CcchhhHHHHHHHHHhhhhHHHH
Confidence                  1112222222221 333444556666777888899999998877665    36888999999999999999988


Q ss_pred             HHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 012111          416 GELFLTMKERHCVPDNITFATMIQAYNALGMTEAAQNLENKMI  458 (471)
Q Consensus       416 ~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~m~  458 (471)
                      +++-+.+.      .+.-|.-.+.+|.+.|+.++|.+++-+.-
T Consensus       735 ekfAkskk------sPIGy~PFVe~c~~~~n~~EA~KYiprv~  771 (829)
T KOG2280|consen  735 EKFAKSKK------SPIGYLPFVEACLKQGNKDEAKKYIPRVG  771 (829)
T ss_pred             HHHHhccC------CCCCchhHHHHHHhcccHHHHhhhhhccC
Confidence            87766554      25566778899999999999999886653

>KOG1920 consensus IkappaB kinase complex, IKAP component [Transcription]

Probab=94.53  E-value=7  Score=40.70  Aligned_cols=133  Identities=12%  Similarity=0.088  Sum_probs=79.6

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHH----HHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHh
Q 012111          263 ISAYGNSGNIEKMEKWYNEFNLMGVKADIQTL----NILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGK  338 (471)
Q Consensus       263 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~----~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~  338 (471)
                      ++.-.+.|.+.+|+.++        .|+...+    .+..+.+.....+++|.-.|+..-+         ..-.+.+|..
T Consensus       915 ~n~I~kh~Ly~~aL~ly--------~~~~e~~k~i~~~ya~hL~~~~~~~~Aal~Ye~~Gk---------lekAl~a~~~  977 (1265)
T KOG1920|consen  915 KNYIKKHGLYDEALALY--------KPDSEKQKVIYEAYADHLREELMSDEAALMYERCGK---------LEKALKAYKE  977 (1265)
T ss_pred             HHHHHhcccchhhhhee--------ccCHHHHHHHHHHHHHHHHHhccccHHHHHHHHhcc---------HHHHHHHHHH
Confidence            33334555555555544        4455444    4444445566777777777665432         1234677788


Q ss_pred             cCCHHHHHHHHHHHHHcCCCCCHH--HHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHH
Q 012111          339 AGHIEKMEEYFKKMKHRGMKPNSI--TYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMG  416 (471)
Q Consensus       339 ~g~~~~a~~~~~~m~~~~~~p~~~--~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~  416 (471)
                      +|+|.+|+.+..++...   -+..  +-..|+.-+...++.-+|-++..+....        ....+..|++...|++|+
T Consensus       978 ~~dWr~~l~~a~ql~~~---~de~~~~a~~L~s~L~e~~kh~eAa~il~e~~sd--------~~~av~ll~ka~~~~eAl 1046 (1265)
T KOG1920|consen  978 CGDWREALSLAAQLSEG---KDELVILAEELVSRLVEQRKHYEAAKILLEYLSD--------PEEAVALLCKAKEWEEAL 1046 (1265)
T ss_pred             hccHHHHHHHHHhhcCC---HHHHHHHHHHHHHHHHHcccchhHHHHHHHHhcC--------HHHHHHHHhhHhHHHHHH
Confidence            88888888887766532   1222  2256777778888888888877766542        123344566667777777


Q ss_pred             HHHHHHH
Q 012111          417 ELFLTMK  423 (471)
Q Consensus       417 ~~~~~~~  423 (471)
                      ++.....
T Consensus      1047 rva~~~~ 1053 (1265)
T KOG1920|consen 1047 RVASKAK 1053 (1265)
T ss_pred             HHHHhcc
Confidence            7765443

>PF09613 HrpB1_HrpK: Bacterial type III secretion protein (HrpB1_HrpK); InterPro: IPR013394 This family of proteins is encoded by genes found within type III secretion operons in a limited range of species including Xanthomonas, Ralstonia and Burkholderia

Probab=94.45  E-value=1.9  Score=33.75  Aligned_cols=19  Identities=16%  Similarity=0.244  Sum_probs=9.3

Q ss_pred             HHhcCCHHHHHHHHHHhhc
Q 012111          159 YGQSGLLDEAFSTINDMKS  177 (471)
Q Consensus       159 ~~~~~~~~~a~~~~~~~~~  177 (471)
                      ++..|++.+|+.+|+.+..
T Consensus        54 ~i~r~~w~dA~rlLr~l~~   72 (160)
T PF09613_consen   54 HIVRGDWDDALRLLRELEE   72 (160)
T ss_pred             HHHhCCHHHHHHHHHHHhc
Confidence            3444555555555555443

>PF02259 FAT: FAT domain; InterPro: IPR003151 The FAT domain is a domain present in the PIK-related kinases

Probab=94.36  E-value=4.1  Score=37.32  Aligned_cols=53  Identities=11%  Similarity=0.213  Sum_probs=29.6

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHH
Q 012111          192 IKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVE  248 (471)
Q Consensus       192 l~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  248 (471)
                      ..+.-+.|+++...+........  .++...+..+...  ..++++++...++.+..
T Consensus         5 ~eaaWrl~~Wd~l~~~~~~~~~~--~~~~~~~~al~~l--~~~~~~~~~~~i~~~r~   57 (352)
T PF02259_consen    5 AEAAWRLGDWDLLEEYLSQSNED--SPEYSFYRALLAL--RQGDYDEAKKYIEKARQ   57 (352)
T ss_pred             HHHHHhcCChhhHHHHHhhccCC--ChhHHHHHHHHHH--hCccHHHHHHHHHHHHH
Confidence            45566777777755555444422  2234444444333  66777777777766644

Members of the family of PIK-related kinases may act as intracellular sensors that govern radial and horizontal pathways [].; GO: 0005515 protein binding

>KOG2066 consensus Vacuolar assembly/sorting protein VPS41 [Intracellular trafficking, secretion, and vesicular transport]

Probab=94.22  E-value=6.3  Score=38.98  Aligned_cols=105  Identities=12%  Similarity=0.096  Sum_probs=74.5

Q ss_pred             HHHHHHHHHhhcHHHHHHHHHHhhhccCccC---ChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHH
Q 012111           82 LEALDEAIKQKKWQLALKIFGLLRQQQWYQA---RCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSA  158 (471)
Q Consensus        82 ~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~---~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~  158 (471)
                      ..-++-+.+.+.+++|+.+-+.....   .+   -.......+..+...|++++|-...-.|...    +..-|...+..
T Consensus       360 ~Dhi~Wll~~k~yeeAl~~~k~~~~~---~~~~~i~kv~~~yI~HLl~~~~y~~Aas~~p~m~gn----~~~eWe~~V~~  432 (846)
T KOG2066|consen  360 EDHIDWLLEKKKYEEALDAAKASIGN---EERFVIKKVGKTYIDHLLFEGKYDEAASLCPKMLGN----NAAEWELWVFK  432 (846)
T ss_pred             chhHHHHHHhhHHHHHHHHHHhccCC---ccccchHHHHHHHHHHHHhcchHHHHHhhhHHHhcc----hHHHHHHHHHH
Confidence            45678888999999999988776553   33   3456788888899999999999999888854    66777777777


Q ss_pred             HHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHh
Q 012111          159 YGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTK  197 (471)
Q Consensus       159 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~  197 (471)
                      +...++......+   +.. ..-..+...|..++..+..
T Consensus       433 f~e~~~l~~Ia~~---lPt-~~~rL~p~vYemvLve~L~  467 (846)
T KOG2066|consen  433 FAELDQLTDIAPY---LPT-GPPRLKPLVYEMVLVEFLA  467 (846)
T ss_pred             hccccccchhhcc---CCC-CCcccCchHHHHHHHHHHH
Confidence            7777665543332   332 2223456677777777766

>PF13170 DUF4003: Protein of unknown function (DUF4003)

Probab=94.20  E-value=3.8  Score=36.32  Aligned_cols=132  Identities=11%  Similarity=0.178  Sum_probs=75.1

Q ss_pred             HHHHHHHHHHHhCCCCCCHHHHHHHHHHHHH--cC----CHHHHHHHHHHHHhCCC---CCCHHHHHHHHHHHHhcCC--
Q 012111          273 EKMEKWYNEFNLMGVKADIQTLNILTKSYGR--AG----MYDKMRSVMDFMQKRFF---FPTVVTYNIVIETFGKAGH--  341 (471)
Q Consensus       273 ~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~--~~----~~~~a~~~~~~~~~~~~---~~~~~~~~~li~~~~~~g~--  341 (471)
                      ++...+++.|.+.|+.-+..+|.+..-....  ..    ....|..+++.|.+.-+   .++...+..++..  ..++  
T Consensus        79 ~~~~~~y~~L~~~gFk~~~y~~laA~~i~~~~~~~~~~~~~~ra~~iy~~mKk~H~fLTs~~D~~~a~lLA~--~~~~~e  156 (297)
T PF13170_consen   79 KEVLDIYEKLKEAGFKRSEYLYLAALIILEEEEKEDYDEIIQRAKEIYKEMKKKHPFLTSPEDYPFAALLAM--TSEDVE  156 (297)
T ss_pred             HHHHHHHHHHHHhccCccChHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHhCccccCccchhHHHHHhc--ccccHH
Confidence            3455667777777777776666543333322  12    24567778888877542   2233445554433  2232  


Q ss_pred             --HHHHHHHHHHHHHcCCCCCH--HHHHHHHHHHHhcCC--HHHHHHHHHHHHhCCCCcCHHHHHHHHHHH
Q 012111          342 --IEKMEEYFKKMKHRGMKPNS--ITYCSLVSAYSKAGL--IMKVDSILRQVENSDVILDTPFFNCIISAY  406 (471)
Q Consensus       342 --~~~a~~~~~~m~~~~~~p~~--~~~~~li~~~~~~g~--~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  406 (471)
                        .+.+..+|+.+.+.|+..+.  .....++..+.....  +.++.++++.+.+.|+++....|..+.-..
T Consensus       157 ~l~~~~E~~Y~~L~~~~f~kgn~LQ~LS~iLaL~~~~~~~~v~r~~~l~~~l~~~~~kik~~~yp~lGlLa  227 (297)
T PF13170_consen  157 ELAERMEQCYQKLADAGFKKGNDLQFLSHILALSEGDDQEKVARVIELYNALKKNGVKIKYMHYPTLGLLA  227 (297)
T ss_pred             HHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHhccccchHHHHHHHHHHHHHHHcCCccccccccHHHHHH
Confidence              35667777777777765532  233333333322222  446777888888888887777776655443

>PF07079 DUF1347: Protein of unknown function (DUF1347); InterPro: IPR010764 This family consists of several hypothetical bacterial proteins of around 610 residues in length

Probab=93.96  E-value=5.1  Score=36.97  Aligned_cols=138  Identities=16%  Similarity=0.109  Sum_probs=74.7

Q ss_pred             HHhhcHHHHHHHHHHhhhccCccCCh-----hH-HHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHH--HH
Q 012111           89 IKQKKWQLALKIFGLLRQQQWYQARC-----QT-FTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSA--YG  160 (471)
Q Consensus        89 ~~~~~~~~A~~~~~~~~~~~~~~~~~-----~~-~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~--~~  160 (471)
                      -+++++.+|.++|.++.+..  ..+.     +. -+.++.+|. ..+.+.....+..+.+.  .| ...|-.+..+  +.
T Consensus        17 qkq~~~~esEkifskI~~e~--~~~~f~lkeEvl~grilnAff-l~nld~Me~~l~~l~~~--~~-~s~~l~LF~~L~~Y   90 (549)
T PF07079_consen   17 QKQKKFQESEKIFSKIYDEK--ESSPFLLKEEVLGGRILNAFF-LNNLDLMEKQLMELRQQ--FG-KSAYLPLFKALVAY   90 (549)
T ss_pred             HHHhhhhHHHHHHHHHHHHh--hcchHHHHHHHHhhHHHHHHH-HhhHHHHHHHHHHHHHh--cC-CchHHHHHHHHHHH
Confidence            46777888888888776653  2221     22 234444444 34555555555555443  11 2223333332  34


Q ss_pred             hcCCHHHHHHHHHHhhcCC-CCC------------CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCC----CCCCHHHH
Q 012111          161 QSGLLDEAFSTINDMKSVS-DCK------------PDVYTYSILIKSCTKFHRFDLIEKILAEMSYLG----IECSAVTY  223 (471)
Q Consensus       161 ~~~~~~~a~~~~~~~~~~~-~~~------------~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g----~~~~~~~~  223 (471)
                      +.+.+.+|++.+....... +..            +|...=+..+..+...|++.++..+++++...=    ...+..+|
T Consensus        91 ~~k~~~kal~~ls~w~~~~~~~~~~~Ld~ni~~l~~df~l~~i~a~sLIe~g~f~EgR~iLn~i~~~llkrE~~w~~d~y  170 (549)
T PF07079_consen   91 KQKEYRKALQALSVWKEQIKGTESPWLDTNIQQLFSDFFLDEIEAHSLIETGRFSEGRAILNRIIERLLKRECEWNSDMY  170 (549)
T ss_pred             HhhhHHHHHHHHHHHHhhhcccccchhhhhHHHHhhHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHhhhhhcccHHHH
Confidence            5677777777776655420 111            122223445566777888888887777775543    33677777


Q ss_pred             HHHHHHHHc
Q 012111          224 NTIIDGYGK  232 (471)
Q Consensus       224 ~~l~~~~~~  232 (471)
                      +.++-.+.+
T Consensus       171 d~~vlmlsr  179 (549)
T PF07079_consen  171 DRAVLMLSR  179 (549)
T ss_pred             HHHHHHHhH
Confidence            765554443

Members of this family are highly conserved and seem to be specific to Chlamydia species. The function of this family is unknown.

>PRK11906 transcriptional regulator; Provisional

Probab=93.84  E-value=1.8  Score=40.10  Aligned_cols=79  Identities=10%  Similarity=0.005  Sum_probs=34.1

Q ss_pred             HHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCC-HHHHHHHHHHHHhcCCHHHHHHHH
Q 012111          130 PEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPD-VYTYSILIKSCTKFHRFDLIEKIL  208 (471)
Q Consensus       130 ~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~-~~~~~~ll~~~~~~~~~~~a~~~~  208 (471)
                      ..+|.++-+...+.+.. |......+..+..-.++++.|..+|++....   .|| ..+|......+.-.|+.++|.+.+
T Consensus       320 ~~~a~~~A~rAveld~~-Da~a~~~~g~~~~~~~~~~~a~~~f~rA~~L---~Pn~A~~~~~~~~~~~~~G~~~~a~~~i  395 (458)
T PRK11906        320 AQKALELLDYVSDITTV-DGKILAIMGLITGLSGQAKVSHILFEQAKIH---STDIASLYYYRALVHFHNEKIEEARICI  395 (458)
T ss_pred             HHHHHHHHHHHHhcCCC-CHHHHHHHHHHHHhhcchhhHHHHHHHHhhc---CCccHHHHHHHHHHHHHcCCHHHHHHHH
Confidence            33444444444444322 4444444444444444455555555554442   222 122222222333345555555555


Q ss_pred             HHHH
Q 012111          209 AEMS  212 (471)
Q Consensus       209 ~~~~  212 (471)
                      ++..
T Consensus       396 ~~al  399 (458)
T PRK11906        396 DKSL  399 (458)
T ss_pred             HHHh
Confidence            5543

>COG3629 DnrI DNA-binding transcriptional activator of the SARP family [Signal transduction mechanisms]

Probab=93.62  E-value=0.94  Score=39.23  Aligned_cols=84  Identities=17%  Similarity=0.156  Sum_probs=70.5

Q ss_pred             ChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHhhc----CCCCCCCHHHH
Q 012111          113 RCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAFSTINDMKS----VSDCKPDVYTY  188 (471)
Q Consensus       113 ~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~----~~~~~~~~~~~  188 (471)
                      -..++..++..+...|+++.+...++.+...... +...|..+|.+|.+.|+...|+..|+++.+    ..|+.|...+.
T Consensus       152 ~~~~l~~lae~~~~~~~~~~~~~~l~~Li~~dp~-~E~~~~~lm~~y~~~g~~~~ai~~y~~l~~~~~edlgi~P~~~~~  230 (280)
T COG3629         152 FIKALTKLAEALIACGRADAVIEHLERLIELDPY-DEPAYLRLMEAYLVNGRQSAAIRAYRQLKKTLAEELGIDPAPELR  230 (280)
T ss_pred             HHHHHHHHHHHHHhcccHHHHHHHHHHHHhcCcc-chHHHHHHHHHHHHcCCchHHHHHHHHHHHHhhhhcCCCccHHHH
Confidence            3567889999999999999999999999987544 788999999999999999999999988765    36788988888


Q ss_pred             HHHHHHHHh
Q 012111          189 SILIKSCTK  197 (471)
Q Consensus       189 ~~ll~~~~~  197 (471)
                      .........
T Consensus       231 ~~y~~~~~~  239 (280)
T COG3629         231 ALYEEILRQ  239 (280)
T ss_pred             HHHHHHhcc
Confidence            777777433

>KOG2610 consensus Uncharacterized conserved protein [Function unknown]

Probab=93.62  E-value=4.8  Score=35.52  Aligned_cols=116  Identities=12%  Similarity=0.104  Sum_probs=52.0

Q ss_pred             cCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhC---CCCCCHHHHHHHHHHHHHcCCHHH
Q 012111          233 AKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLM---GVKADIQTLNILTKSYGRAGMYDK  309 (471)
Q Consensus       233 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~---~~~~~~~~~~~ll~~~~~~~~~~~  309 (471)
                      .|++.+|-..++++.+.  .+.|...+...-.+|...|+.+.-...++++...   +++..+..-..+.-++...|-+++
T Consensus       116 ~g~~h~a~~~wdklL~d--~PtDlla~kfsh~a~fy~G~~~~~k~ai~kIip~wn~dlp~~sYv~GmyaFgL~E~g~y~d  193 (491)
T KOG2610|consen  116 RGKHHEAAIEWDKLLDD--YPTDLLAVKFSHDAHFYNGNQIGKKNAIEKIIPKWNADLPCYSYVHGMYAFGLEECGIYDD  193 (491)
T ss_pred             cccccHHHHHHHHHHHh--CchhhhhhhhhhhHHHhccchhhhhhHHHHhccccCCCCcHHHHHHHHHHhhHHHhccchh
Confidence            34555555555555544  2444444554555555555555555555554322   111111122222233344555555


Q ss_pred             HHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHH
Q 012111          310 MRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKK  351 (471)
Q Consensus       310 a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~  351 (471)
                      |++.-++..+.+.. |.-.-.+....+...|++.++.+++.+
T Consensus       194 AEk~A~ralqiN~~-D~Wa~Ha~aHVlem~~r~Keg~eFM~~  234 (491)
T KOG2610|consen  194 AEKQADRALQINRF-DCWASHAKAHVLEMNGRHKEGKEFMYK  234 (491)
T ss_pred             HHHHHHhhccCCCc-chHHHHHHHHHHHhcchhhhHHHHHHh
Confidence            55555544443221 333333444444455555555555443

>KOG1585 consensus Protein required for fusion of vesicles in vesicular transport, gamma-SNAP [Intracellular trafficking, secretion, and vesicular transport]

Probab=93.61  E-value=3.8  Score=34.38  Aligned_cols=55  Identities=18%  Similarity=0.332  Sum_probs=29.1

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHhC---CCCcCHHHHHHHHHHHHhcCCHHHHHHHH
Q 012111          364 YCSLVSAYSKAGLIMKVDSILRQVENS---DVILDTPFFNCIISAYGQAGDVEKMGELF  419 (471)
Q Consensus       364 ~~~li~~~~~~g~~~~a~~~~~~~~~~---~~~~~~~~~~~l~~~~~~~g~~~~a~~~~  419 (471)
                      |...|-.+....++..|...++.-.+.   .-.-+..+...|+.+|- .||.+++.+++
T Consensus       193 ~va~ilv~L~~~Dyv~aekc~r~~~qip~f~~sed~r~lenLL~ayd-~gD~E~~~kvl  250 (308)
T KOG1585|consen  193 YVAAILVYLYAHDYVQAEKCYRDCSQIPAFLKSEDSRSLENLLTAYD-EGDIEEIKKVL  250 (308)
T ss_pred             HHHHHHHHhhHHHHHHHHHHhcchhcCccccChHHHHHHHHHHHHhc-cCCHHHHHHHH
Confidence            344444455556666676666653321   11224556666666653 46666655543

>cd00923 Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va

Probab=93.47  E-value=0.87  Score=31.77  Aligned_cols=61  Identities=10%  Similarity=0.213  Sum_probs=36.1

Q ss_pred             HHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHH
Q 012111          377 IMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMI  438 (471)
Q Consensus       377 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~  438 (471)
                      .-++.+-++.+...++.|++.+..+.+++|.+.+|+..|.++|+..+.+ +..+...|..++
T Consensus        23 ~we~rr~mN~l~~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~vK~K-~~~~~~~y~~~l   83 (103)
T cd00923          23 GWELRRGLNNLFGYDLVPEPKVIEAALRACRRVNDFALAVRILEAIKDK-CGAHKEIYPYIL   83 (103)
T ss_pred             HHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHH-ccCchhhHHHHH
Confidence            3345555566666666677777777777777777777777777665532 222334454444

Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit Va is one of three mammalian subunits that lacks a transmembrane region. Subunit Va is located on the matrix side of the membrane and binds thyroid hormone T2, releasing allosteric inhibition caused by the binding of ATP to subunit IV and allowing high turnover at elevated intramitochondrial ATP/ADP ratios.

>KOG1550 consensus Extracellular protein SEL-1 and related proteins [Cell wall/membrane/envelope biogenesis; Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]

Probab=93.45  E-value=8.4  Score=37.84  Aligned_cols=275  Identities=11%  Similarity=0.065  Sum_probs=156.8

Q ss_pred             HHHHHHHHHHhhcCCCCCCCHHHHHHHH----HH-HHhcCCHHHHHHHHHHHHH-------CCCCCCHHHHHHHHHHHHc
Q 012111          165 LDEAFSTINDMKSVSDCKPDVYTYSILI----KS-CTKFHRFDLIEKILAEMSY-------LGIECSAVTYNTIIDGYGK  232 (471)
Q Consensus       165 ~~~a~~~~~~~~~~~~~~~~~~~~~~ll----~~-~~~~~~~~~a~~~~~~~~~-------~g~~~~~~~~~~l~~~~~~  232 (471)
                      ...|...++...+. |   +...-..+.    .+ +....|.+.|+.+|+.+.+       .|   .......+..+|.+
T Consensus       228 ~~~a~~~~~~~a~~-g---~~~a~~~~g~~y~~G~~g~~~d~e~a~~~l~~aa~~~~~~a~~~---~~~a~~~lg~~Y~~  300 (552)
T KOG1550|consen  228 LSEAFKYYREAAKL-G---HSEAQYALGICYLAGTYGVTQDLESAIEYLKLAAESFKKAATKG---LPPAQYGLGRLYLQ  300 (552)
T ss_pred             hhHHHHHHHHHHhh-c---chHHHHHHHHHHhhccccccccHHHHHHHHHHHHHHHHHHHhhc---CCccccHHHHHHhc
Confidence            46788888887763 2   222222222    22 4456789999999998877       55   33345667777766


Q ss_pred             cC-----CHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHh-cCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHH----
Q 012111          233 AK-----KFEEMESSFSAMVESGGCHPDIFTLNSMISAYGN-SGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYG----  302 (471)
Q Consensus       233 ~~-----~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~-~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~----  302 (471)
                      ..     +.+.|..++....+.+  .|+.......+..... ..+...|.++|......|.   ...+-.+..+|.    
T Consensus       301 g~~~~~~d~~~A~~~~~~aA~~g--~~~a~~~lg~~~~~g~~~~d~~~A~~yy~~Aa~~G~---~~A~~~la~~y~~G~g  375 (552)
T KOG1550|consen  301 GLGVEKIDYEKALKLYTKAAELG--NPDAQYLLGVLYETGTKERDYRRAFEYYSLAAKAGH---ILAIYRLALCYELGLG  375 (552)
T ss_pred             CCCCccccHHHHHHHHHHHHhcC--CchHHHHHHHHHHcCCccccHHHHHHHHHHHHHcCC---hHHHHHHHHHHHhCCC
Confidence            43     6778999999887765  5665444333332222 2467899999999988772   222323333332    


Q ss_pred             HcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHH-HHH---Hh----c
Q 012111          303 RAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLV-SAY---SK----A  374 (471)
Q Consensus       303 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li-~~~---~~----~  374 (471)
                      -..+...|..++.+..+.|........ ..+..+.. ++++.+.-.+..+...|.+. ..+-...+ ...   ..    .
T Consensus       376 v~r~~~~A~~~~k~aA~~g~~~A~~~~-~~~~~~g~-~~~~~~~~~~~~~a~~g~~~-~q~~a~~l~~~~~~~~~~~~~~  452 (552)
T KOG1550|consen  376 VERNLELAFAYYKKAAEKGNPSAAYLL-GAFYEYGV-GRYDTALALYLYLAELGYEV-AQSNAAYLLDQSEEDLFSRGVI  452 (552)
T ss_pred             cCCCHHHHHHHHHHHHHccChhhHHHH-HHHHHHcc-ccccHHHHHHHHHHHhhhhH-HhhHHHHHHHhccccccccccc
Confidence            234678899999998888732222222 22233333 77777777777777766432 22211111 111   11    1


Q ss_pred             CCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhc----CCHHHHHHHHHHHHhCCCCCCHHHHHHHHH----HHHhcCC
Q 012111          375 GLIMKVDSILRQVENSDVILDTPFFNCIISAYGQA----GDVEKMGELFLTMKERHCVPDNITFATMIQ----AYNALGM  446 (471)
Q Consensus       375 g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~----g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~----~~~~~g~  446 (471)
                      .+.+.+...+.+....|   +......|...|...    .+++.|...+......+   ....|+ +..    +..... 
T Consensus       453 ~~~~~~~~~~~~a~~~g---~~~a~~~lgd~y~~g~g~~~d~~~a~~~y~~a~~~~---~~~~~n-lg~~~e~g~g~~~-  524 (552)
T KOG1550|consen  453 STLERAFSLYSRAAAQG---NADAILKLGDYYYYGLGTGRDPEKAAAQYARASEQG---AQALFN-LGYMHEHGEGIKV-  524 (552)
T ss_pred             cchhHHHHHHHHHHhcc---CHHHHhhhcceeeecCCCCCChHHHHHHHHHHHHhh---hHHHhh-hhhHHhcCcCcch-
Confidence            24556666676666554   455555555555443    34777888787777654   222222 221    112223 


Q ss_pred             HHHHHHHHHHHHHhhh
Q 012111          447 TEAAQNLENKMIAMKE  462 (471)
Q Consensus       447 ~~~A~~~~~~m~~~~~  462 (471)
                      +..|.++++.....+.
T Consensus       525 ~~~a~~~~~~~~~~~~  540 (552)
T KOG1550|consen  525 LHLAKRYYDQASEEDS  540 (552)
T ss_pred             hHHHHHHHHHHHhcCc
Confidence            6778888877766543

>PF13431 TPR_17: Tetratricopeptide repeat

Probab=93.33  E-value=0.12  Score=28.37  Aligned_cols=21  Identities=24%  Similarity=0.430  Sum_probs=10.1

Q ss_pred             CHHHHHHHHHHHHhcCCHHHH
Q 012111          395 DTPFFNCIISAYGQAGDVEKM  415 (471)
Q Consensus       395 ~~~~~~~l~~~~~~~g~~~~a  415 (471)
                      +...|+.+...|...|++++|
T Consensus        12 n~~a~~nla~~~~~~g~~~~A   32 (34)
T PF13431_consen   12 NAEAYNNLANLYLNQGDYEEA   32 (34)
T ss_pred             CHHHHHHHHHHHHHCcCHHhh
Confidence            444444444444444444444

>PF13170 DUF4003: Protein of unknown function (DUF4003)

Probab=93.25  E-value=5.6  Score=35.24  Aligned_cols=130  Identities=14%  Similarity=0.212  Sum_probs=61.6

Q ss_pred             HHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHc--cC----CHHHHHHHHHHHHHcCCC--CCCHHHHHHHHHHHHhcCCH
Q 012111          201 FDLIEKILAEMSYLGIECSAVTYNTIIDGYGK--AK----KFEEMESSFSAMVESGGC--HPDIFTLNSMISAYGNSGNI  272 (471)
Q Consensus       201 ~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~--~~----~~~~a~~~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~  272 (471)
                      ++....+++.|.+.|+.-+..+|-+..-....  ..    ....|..+|+.|.+....  .++..++..++..  ..++.
T Consensus        78 ~~~~~~~y~~L~~~gFk~~~y~~laA~~i~~~~~~~~~~~~~~ra~~iy~~mKk~H~fLTs~~D~~~a~lLA~--~~~~~  155 (297)
T PF13170_consen   78 FKEVLDIYEKLKEAGFKRSEYLYLAALIILEEEEKEDYDEIIQRAKEIYKEMKKKHPFLTSPEDYPFAALLAM--TSEDV  155 (297)
T ss_pred             HHHHHHHHHHHHHhccCccChHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHhCccccCccchhHHHHHhc--ccccH
Confidence            34556667777777777666555443322222  11    245677777777765433  2333444444433  23332


Q ss_pred             ----HHHHHHHHHHHhCCCCCCH--HHHHHHHHHHHHcCC--HHHHHHHHHHHHhCCCCCCHHHHHHH
Q 012111          273 ----EKMEKWYNEFNLMGVKADI--QTLNILTKSYGRAGM--YDKMRSVMDFMQKRFFFPTVVTYNIV  332 (471)
Q Consensus       273 ----~~a~~~~~~~~~~~~~~~~--~~~~~ll~~~~~~~~--~~~a~~~~~~~~~~~~~~~~~~~~~l  332 (471)
                          +.++.+|+.+.+.|+..+.  .....++.......+  ...+..+++.+.+.|+++....|..+
T Consensus       156 e~l~~~~E~~Y~~L~~~~f~kgn~LQ~LS~iLaL~~~~~~~~v~r~~~l~~~l~~~~~kik~~~yp~l  223 (297)
T PF13170_consen  156 EELAERMEQCYQKLADAGFKKGNDLQFLSHILALSEGDDQEKVARVIELYNALKKNGVKIKYMHYPTL  223 (297)
T ss_pred             HHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHhccccchHHHHHHHHHHHHHHHcCCccccccccHH
Confidence                3445555555555543322  222222222211111  22445555555555555554444433

>PF13181 TPR_8: Tetratricopeptide repeat; PDB: 3GW4_B 3MA5_C 2KCV_A 2KCL_A 3FP3_A 3LCA_A 3FP4_A 3FP2_A 1W3B_B 1ELW_A

Probab=93.10  E-value=0.38  Score=26.14  Aligned_cols=31  Identities=19%  Similarity=0.273  Sum_probs=24.0

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHHhhh
Q 012111          432 ITFATMIQAYNALGMTEAAQNLENKMIAMKE  462 (471)
Q Consensus       432 ~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~  462 (471)
                      .+|..+...|...|++++|.+.|++.++..|
T Consensus         2 ~~~~~lg~~y~~~~~~~~A~~~~~~a~~~~~   32 (34)
T PF13181_consen    2 EAYYNLGKIYEQLGDYEEALEYFEKALELNP   32 (34)
T ss_dssp             HHHHHHHHHHHHTTSHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHhhCC
Confidence            3566677778888888888888888888776

...

>TIGR02561 HrpB1_HrpK type III secretion protein HrpB1/HrpK

Probab=93.09  E-value=3.2  Score=31.93  Aligned_cols=53  Identities=13%  Similarity=0.053  Sum_probs=34.3

Q ss_pred             HhcCCHHHHHHHHHHHHHcCCCCCHHHH-HHHHHHHHhcCCHHHHHHHHHHHHhCC
Q 012111          337 GKAGHIEKMEEYFKKMKHRGMKPNSITY-CSLVSAYSKAGLIMKVDSILRQVENSD  391 (471)
Q Consensus       337 ~~~g~~~~a~~~~~~m~~~~~~p~~~~~-~~li~~~~~~g~~~~a~~~~~~~~~~~  391 (471)
                      ...++++++..++..|.-.  .|+..-. ..-...+...|++++|..+|+++.+.+
T Consensus        21 L~~~d~~D~e~lLdALrvL--rP~~~e~d~~dg~l~i~rg~w~eA~rvlr~l~~~~   74 (153)
T TIGR02561        21 LRSADPYDAQAMLDALRVL--RPNLKELDMFDGWLLIARGNYDEAARILRELLSSA   74 (153)
T ss_pred             HhcCCHHHHHHHHHHHHHh--CCCccccchhHHHHHHHcCCHHHHHHHHHhhhccC
Confidence            3467888888888877764  4432221 222334567788888888888887765

This gene is found within type III secretion operons in a limited range of species including Xanthomonas, Ralstonia and Burkholderia.

>PF13929 mRNA_stabil: mRNA stabilisation

Probab=92.91  E-value=5.8  Score=34.42  Aligned_cols=63  Identities=14%  Similarity=0.125  Sum_probs=31.5

Q ss_pred             CCCHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHH
Q 012111          146 KPSVDVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKIL  208 (471)
Q Consensus       146 ~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~  208 (471)
                      .++..+...++..+++.+++.+-.++++......+..-|...|..+|+.....|+..-..++.
T Consensus       199 ~l~~~vi~~Il~~L~~~~dW~kl~~fW~~~~~~~~~~~D~rpW~~FI~li~~sgD~~~~~kiI  261 (292)
T PF13929_consen  199 SLTRNVIISILEILAESRDWNKLFQFWEQCIPNSVPGNDPRPWAEFIKLIVESGDQEVMRKII  261 (292)
T ss_pred             CCChhHHHHHHHHHHhcccHHHHHHHHHHhcccCCCCCCCchHHHHHHHHHHcCCHHHHHHHh
Confidence            344455555555555555555555555554442233344455555555555555544444443

>KOG1585 consensus Protein required for fusion of vesicles in vesicular transport, gamma-SNAP [Intracellular trafficking, secretion, and vesicular transport]

Probab=92.90  E-value=5  Score=33.73  Aligned_cols=206  Identities=11%  Similarity=0.104  Sum_probs=111.3

Q ss_pred             HHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHH
Q 012111          221 VTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKS  300 (471)
Q Consensus       221 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~  300 (471)
                      ..|..-..+|....++++|...+.+..+-.  ..+...|.       -...++.|.-+.+++...  ..-+..|+.-...
T Consensus        32 s~yekAAvafRnAk~feKakdcLlkA~~~y--Ennrslfh-------AAKayEqaamLake~~kl--sEvvdl~eKAs~l  100 (308)
T KOG1585|consen   32 SLYEKAAVAFRNAKKFEKAKDCLLKASKGY--ENNRSLFH-------AAKAYEQAAMLAKELSKL--SEVVDLYEKASEL  100 (308)
T ss_pred             HHHHHHHHHHHhhccHHHHHHHHHHHHHHH--HhcccHHH-------HHHHHHHHHHHHHHHHHh--HHHHHHHHHHHHH
Confidence            345555566666677777776666654321  22221111       122234455555554431  2223445566667


Q ss_pred             HHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc---C--CCCCHHHHHHHHHHHHhcC
Q 012111          301 YGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHR---G--MKPNSITYCSLVSAYSKAG  375 (471)
Q Consensus       301 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~---~--~~p~~~~~~~li~~~~~~g  375 (471)
                      |..+|..+.|-..+++.-+.                ...-++++|+++|++...-   +  ..--...+...-..+.+..
T Consensus       101 Y~E~GspdtAAmaleKAak~----------------lenv~Pd~AlqlYqralavve~~dr~~ma~el~gk~sr~lVrl~  164 (308)
T KOG1585|consen  101 YVECGSPDTAAMALEKAAKA----------------LENVKPDDALQLYQRALAVVEEDDRDQMAFELYGKCSRVLVRLE  164 (308)
T ss_pred             HHHhCCcchHHHHHHHHHHH----------------hhcCCHHHHHHHHHHHHHHHhccchHHHHHHHHHHhhhHhhhhH
Confidence            77777777666666544331                2234455555555554321   0  0011223444555666777


Q ss_pred             CHHHHHHHHHHHH----hCCCCcCH-HHHHHHHHHHHhcCCHHHHHHHHHHHHhCCC---CCCHHHHHHHHHHHHhcCCH
Q 012111          376 LIMKVDSILRQVE----NSDVILDT-PFFNCIISAYGQAGDVEKMGELFLTMKERHC---VPDNITFATMIQAYNALGMT  447 (471)
Q Consensus       376 ~~~~a~~~~~~~~----~~~~~~~~-~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~---~p~~~~~~~l~~~~~~~g~~  447 (471)
                      .+++|-..+.+-.    +..-.++. ..|...|-.+....|+..|.+.++...+.+-   .-+..+...|+.+| ..|+.
T Consensus       165 kf~Eaa~a~lKe~~~~~~~~~y~~~~k~~va~ilv~L~~~Dyv~aekc~r~~~qip~f~~sed~r~lenLL~ay-d~gD~  243 (308)
T KOG1585|consen  165 KFTEAATAFLKEGVAADKCDAYNSQCKAYVAAILVYLYAHDYVQAEKCYRDCSQIPAFLKSEDSRSLENLLTAY-DEGDI  243 (308)
T ss_pred             HhhHHHHHHHHhhhHHHHHhhcccHHHHHHHHHHHHhhHHHHHHHHHHhcchhcCccccChHHHHHHHHHHHHh-ccCCH
Confidence            7777665554322    11111222 3456666777888899999999988654321   23567788888877 67888


Q ss_pred             HHHHHHH
Q 012111          448 EAAQNLE  454 (471)
Q Consensus       448 ~~A~~~~  454 (471)
                      +++..++
T Consensus       244 E~~~kvl  250 (308)
T KOG1585|consen  244 EEIKKVL  250 (308)
T ss_pred             HHHHHHH
Confidence            8876554

>PF13176 TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_A 3RO2_A

Probab=92.89  E-value=0.29  Score=27.20  Aligned_cols=26  Identities=31%  Similarity=0.299  Sum_probs=19.9

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHH
Q 012111          398 FFNCIISAYGQAGDVEKMGELFLTMK  423 (471)
Q Consensus       398 ~~~~l~~~~~~~g~~~~a~~~~~~~~  423 (471)
                      +|+.|...|.+.|++++|+++|++..
T Consensus         1 al~~Lg~~~~~~g~~~~Ai~~y~~aL   26 (36)
T PF13176_consen    1 ALNNLGRIYRQQGDYEKAIEYYEQAL   26 (36)
T ss_dssp             HHHHHHHHHHHCT-HHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            36778888888888888888888754

>COG2976 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=92.67  E-value=4.6  Score=32.67  Aligned_cols=94  Identities=16%  Similarity=0.014  Sum_probs=58.9

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHhCCCCcC--HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhc
Q 012111          367 LVSAYSKAGLIMKVDSILRQVENSDVILD--TPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAYNAL  444 (471)
Q Consensus       367 li~~~~~~g~~~~a~~~~~~~~~~~~~~~--~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~  444 (471)
                      +...+...|++++|..-++........-+  ..+--.|.+.....|.+++|+.+++...+.+.  .......-.+.+...
T Consensus        95 lAk~~ve~~~~d~A~aqL~~~l~~t~De~lk~l~~lRLArvq~q~~k~D~AL~~L~t~~~~~w--~~~~~elrGDill~k  172 (207)
T COG2976          95 LAKAEVEANNLDKAEAQLKQALAQTKDENLKALAALRLARVQLQQKKADAALKTLDTIKEESW--AAIVAELRGDILLAK  172 (207)
T ss_pred             HHHHHHhhccHHHHHHHHHHHHccchhHHHHHHHHHHHHHHHHHhhhHHHHHHHHhccccccH--HHHHHHHhhhHHHHc
Confidence            34556777888888877776654311111  11223455667777888888888876665432  233333445778888


Q ss_pred             CCHHHHHHHHHHHHHhhh
Q 012111          445 GMTEAAQNLENKMIAMKE  462 (471)
Q Consensus       445 g~~~~A~~~~~~m~~~~~  462 (471)
                      |+.++|+.-|++.+..++
T Consensus       173 g~k~~Ar~ay~kAl~~~~  190 (207)
T COG2976         173 GDKQEARAAYEKALESDA  190 (207)
T ss_pred             CchHHHHHHHHHHHHccC
Confidence            888888888888877753

>PF02284 COX5A: Cytochrome c oxidase subunit Va; InterPro: IPR003204 Cytochrome c oxidase (1

Probab=92.66  E-value=0.8  Score=32.31  Aligned_cols=46  Identities=11%  Similarity=0.186  Sum_probs=26.6

Q ss_pred             HHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 012111          379 KVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKE  424 (471)
Q Consensus       379 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~  424 (471)
                      +..+-++.+...++.|++.+..+.+++|.+.+++..|.++|+..+.
T Consensus        28 e~rrglN~l~~~DlVP~P~ii~aALrAcRRvND~a~AVR~lE~iK~   73 (108)
T PF02284_consen   28 ELRRGLNNLFGYDLVPEPKIIEAALRACRRVNDFALAVRILEGIKD   73 (108)
T ss_dssp             HHHHHHHHHTTSSB---HHHHHHHHHHHHHTT-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhccccCCChHHHHHHHHHHHHhhhHHHHHHHHHHHHH
Confidence            3445555555666666666666666666666666666666666654

9.3.1 from EC) is an oligomeric enzymatic complex which is a component of the respiratory chain complex and is involved in the transfer of electrons from cytochrome c to oxygen []. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. In eukaryotes, in addition to the three large subunits, I, II and III, that form the catalytic centre of the enzyme complex, there are a variable number of small polypeptidic subunits. One of these subunits is known as Va.; GO: 0004129 cytochrome-c oxidase activity; PDB: 2DYR_R 3AG1_E 3ABL_E 1V54_R 2EIJ_R 1OCR_E 2DYS_E 2EIM_E 2OCC_E 3ASN_R ....

>PF10602 RPN7: 26S proteasome subunit RPN7; InterPro: IPR019585 This entry represents the regulatory subunit RPN7 (known as the non-ATPase regulatory subunit 6 in higher eukaryotes) of the 26S proteasome

Probab=92.47  E-value=3.1  Score=33.63  Aligned_cols=61  Identities=11%  Similarity=0.180  Sum_probs=33.5

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCC--HHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 012111          328 TYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPN--SITYCSLVSAYSKAGLIMKVDSILRQVE  388 (471)
Q Consensus       328 ~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~--~~~~~~li~~~~~~g~~~~a~~~~~~~~  388 (471)
                      .+..+...|++.|+.+.|.+.|.++......+.  ...+-.+|......+++..+...+.++.
T Consensus        38 ~~~~l~~~~~~~Gd~~~A~k~y~~~~~~~~~~~~~id~~l~~irv~i~~~d~~~v~~~i~ka~  100 (177)
T PF10602_consen   38 ALEDLADHYCKIGDLEEALKAYSRARDYCTSPGHKIDMCLNVIRVAIFFGDWSHVEKYIEKAE  100 (177)
T ss_pred             HHHHHHHHHHHhhhHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence            455556666666666666666666655533332  2234455555555566666555555443

This entry also matches the evolutionarily related subunit 1 of the COP9 signalosome complex (CSN) from Arabidopsis []. The 26S proteasome plays a major role in ATP-dependent degradation of ubiquitinated proteins. Substrate specificity is conferred by the regulatory particle (RP), which can dissociate into stable lid and base subcomplexes. The regulatory subunit RPN7 is one of the lid subunits of the 26S proteasome and has been shown in Saccharomyces cerevisiae (Baker's yeast) to be required for structural integrity []. The COP9 signalosome is a conserved protein complex composed of eight subunits, where Individual subunits of the complex have been linked to various signal transduction pathways leading to gene expression and cell cycle control []. The overall organisation and the amino acid sequences of the COP9 signalosome subunits resemble the lid subcomplex of the 19 S regulatory particle for the 26 S proteasome []. COP9 subunit 1 (CSN1 or GPS1) of the COP9 complex is an essential subunit of the complex with regard to both structural integrity and functionality. The N-terminal region of subunit 1 (CSN1-N) can inhibit c-fos expression from either a transfected template or a chromosomal transgene (fos-lacZ), and may contain the activity domain that confers most of the repression functions of CSN1. The C-terminal region of subunit 1 (CSN1-C) allows integration of the protein into the COP9 signalosome.

>PF13431 TPR_17: Tetratricopeptide repeat

Probab=92.27  E-value=0.15  Score=28.00  Aligned_cols=24  Identities=13%  Similarity=0.134  Sum_probs=15.2

Q ss_pred             cCChhHHHHHHHHHhcCCCHHHHH
Q 012111          111 QARCQTFTKLMVMLGKCKQPEQAS  134 (471)
Q Consensus       111 ~~~~~~~~~l~~~~~~~~~~~~a~  134 (471)
                      |.+..+|+.+...|...|++++|+
T Consensus        10 P~n~~a~~nla~~~~~~g~~~~A~   33 (34)
T PF13431_consen   10 PNNAEAYNNLANLYLNQGDYEEAI   33 (34)
T ss_pred             CCCHHHHHHHHHHHHHCcCHHhhc
Confidence            555666666666666666666654

>PF10602 RPN7: 26S proteasome subunit RPN7; InterPro: IPR019585 This entry represents the regulatory subunit RPN7 (known as the non-ATPase regulatory subunit 6 in higher eukaryotes) of the 26S proteasome

Probab=92.23  E-value=5  Score=32.46  Aligned_cols=60  Identities=13%  Similarity=0.141  Sum_probs=28.6

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCC--HHHHHHHHHHHHHcCCHHHHHHHHHHH
Q 012111          258 TLNSMISAYGNSGNIEKMEKWYNEFNLMGVKAD--IQTLNILTKSYGRAGMYDKMRSVMDFM  317 (471)
Q Consensus       258 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~~~~ll~~~~~~~~~~~a~~~~~~~  317 (471)
                      .+..+...|++.|+.+.|.+.|.++.+....+.  ...+-.+|......+++..+...+.+.
T Consensus        38 ~~~~l~~~~~~~Gd~~~A~k~y~~~~~~~~~~~~~id~~l~~irv~i~~~d~~~v~~~i~ka   99 (177)
T PF10602_consen   38 ALEDLADHYCKIGDLEEALKAYSRARDYCTSPGHKIDMCLNVIRVAIFFGDWSHVEKYIEKA   99 (177)
T ss_pred             HHHHHHHHHHHhhhHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH
Confidence            344455555555555555555555544332222  123344444555555555555544443

This entry also matches the evolutionarily related subunit 1 of the COP9 signalosome complex (CSN) from Arabidopsis []. The 26S proteasome plays a major role in ATP-dependent degradation of ubiquitinated proteins. Substrate specificity is conferred by the regulatory particle (RP), which can dissociate into stable lid and base subcomplexes. The regulatory subunit RPN7 is one of the lid subunits of the 26S proteasome and has been shown in Saccharomyces cerevisiae (Baker's yeast) to be required for structural integrity []. The COP9 signalosome is a conserved protein complex composed of eight subunits, where Individual subunits of the complex have been linked to various signal transduction pathways leading to gene expression and cell cycle control []. The overall organisation and the amino acid sequences of the COP9 signalosome subunits resemble the lid subcomplex of the 19 S regulatory particle for the 26 S proteasome []. COP9 subunit 1 (CSN1 or GPS1) of the COP9 complex is an essential subunit of the complex with regard to both structural integrity and functionality. The N-terminal region of subunit 1 (CSN1-N) can inhibit c-fos expression from either a transfected template or a chromosomal transgene (fos-lacZ), and may contain the activity domain that confers most of the repression functions of CSN1. The C-terminal region of subunit 1 (CSN1-C) allows integration of the protein into the COP9 signalosome.

>PF04097 Nic96: Nup93/Nic96; InterPro: IPR007231 Nup93/Nic96 is a component of the nuclear pore complex

Probab=92.17  E-value=14  Score=36.94  Aligned_cols=355  Identities=11%  Similarity=0.074  Sum_probs=146.9

Q ss_pred             CchHHHHHHHHHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCC-------HHHHHHHHHHHHhCCCCCCH
Q 012111           77 WPKPVLEALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQ-------PEQASLLFEVMLSDGLKPSV  149 (471)
Q Consensus        77 ~~~~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~-------~~~a~~~~~~m~~~~~~~~~  149 (471)
                      ....+...+-.|.+.|++++|+++.......  +......+...+..|....+       -+....-|++........|+
T Consensus       110 ~~~p~Wa~Iyy~LR~G~~~~A~~~~~~~~~~--~~~~~~~f~~~l~~~~~s~~~~l~~~~~~~l~~ey~~~~r~~~~~Dp  187 (613)
T PF04097_consen  110 NGDPIWALIYYCLRCGDYDEALEVANENRNQ--FQKIERSFPTYLKAYASSPDRRLPPELRDKLKLEYNQRIRNSTDGDP  187 (613)
T ss_dssp             TTEEHHHHHHHHHTTT-HHHHHHHHHHTGGG--S-TTTTHHHHHHHHCTTTTSS---TCCCHHHHHHHHHHTTT-TTS-H
T ss_pred             CCCccHHHHHHHHhcCCHHHHHHHHHHhhhh--hcchhHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHHhcCCCCCCh
Confidence            4556778888888999999999988665544  35555677777887776532       23555566665554332233


Q ss_pred             H---HHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcC-----------CHHHHHHHHHHHHHCC
Q 012111          150 D---VYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFH-----------RFDLIEKILAEMSYLG  215 (471)
Q Consensus       150 ~---~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~-----------~~~~a~~~~~~~~~~g  215 (471)
                      .   +|..+..  +...+-  -.         ..+..+..-|--+=-.+.+..           .++...+.+...-+..
T Consensus       188 yK~AvY~ilg~--cD~~~~--~~---------~~V~~tiED~LW~~L~~vr~~~~~~~~~~e~~~L~~LQ~~i~~~Ge~~  254 (613)
T PF04097_consen  188 YKRAVYKILGR--CDLSRR--HL---------PEVARTIEDWLWLQLSLVREDERSSSSAYERYTLEDLQKLILKYGESH  254 (613)
T ss_dssp             HHHHHHHHHHT----CCC---S----------TTC--SHHHHHHHHHHH---TTSSSSSSS----HHHHHHHHHHH-GGG
T ss_pred             HHHHHHHHHhc--CCcccc--ch---------HHHhCcHHHHHHHHHHhhccCCCccccccccccHHHHHHHHHHhchhh
Confidence            2   2332211  111000  00         011111111110000111111           1122222222333332


Q ss_pred             CCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCC-CCCCHHHH
Q 012111          216 IECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMG-VKADIQTL  294 (471)
Q Consensus       216 ~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~  294 (471)
                      +.+ ..........+.-.|+++.|.+.+-.. +  ....+.+.+...+.-|.-.+-.+...   ..+.... -.+....+
T Consensus       255 F~~-~~~p~~Yf~~LlLtgqFE~AI~~L~~~-~--~~~~dAVH~AIaL~~~gLL~~~~~~~---~~lls~~~~~~~~ln~  327 (613)
T PF04097_consen  255 FNA-GSNPLLYFQVLLLTGQFEAAIEFLYRN-E--FNRVDAVHFAIALAYYGLLRVSDSSS---APLLSVDPGDPPPLNF  327 (613)
T ss_dssp             CTT-------HHHHHHHTT-HHHHHHHHHT-----T-HHHHHHHHHHHHHTT---------------------------H
T ss_pred             ccc-chhHHHHHHHHHHHhhHHHHHHHHHhh-c--cCcccHHHHHHHHHHcCCCCCCCccc---cceeeecCCCCCCcCH
Confidence            333 111122344555678999998887762 1  13445555555444332222111111   2221111 01112456


Q ss_pred             HHHHHHHHH---cCCHHHHHHHHHHHHhCCCCCCHHHHHHHH-HHHHhcCCHHHHH-----------HHHHH---HHHcC
Q 012111          295 NILTKSYGR---AGMYDKMRSVMDFMQKRFFFPTVVTYNIVI-ETFGKAGHIEKME-----------EYFKK---MKHRG  356 (471)
Q Consensus       295 ~~ll~~~~~---~~~~~~a~~~~~~~~~~~~~~~~~~~~~li-~~~~~~g~~~~a~-----------~~~~~---m~~~~  356 (471)
                      ..||..|.+   ..+..+|.+++-.+....-+.....+...+ ......++++.-+           .++++   +.  +
T Consensus       328 arLI~~Y~~~F~~td~~~Al~Y~~li~~~~~~~~~~l~~~~l~eLvletref~~LLG~i~~dG~r~~G~i~~~~~Li--~  405 (613)
T PF04097_consen  328 ARLIGQYTRSFEITDPREALQYLYLICLFKDPEQRNLFHECLRELVLETREFDLLLGDINPDGSRTPGLIERRLSLI--K  405 (613)
T ss_dssp             HHHHHHHHHTTTTT-HHHHHHHHHGGGGS-SCCHHHHHHHHHHHHHHHH--HHHHHEEE-TTS-EEE-HHHHTGGGG--T
T ss_pred             HHHHHHHHHHHhccCHHHHHHHHHHHHHcCCchHHHHHHHHHHHHHHccCCHHHHCCCCCCCCccccceeecccccc--C
Confidence            777777775   356778888877666543221222222222 2223333322211           11111   11  1


Q ss_pred             CC-CCHH---HHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHH-hcCC-----------HHHHHHHHH
Q 012111          357 MK-PNSI---TYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYG-QAGD-----------VEKMGELFL  420 (471)
Q Consensus       357 ~~-p~~~---~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~-~~g~-----------~~~a~~~~~  420 (471)
                      .. ++..   .......-+...|+++.|..+|..+.+.+.  -....|.++.-.. ....           ...|..+.+
T Consensus       406 ~~~~~~~~~~i~~~~A~~~e~~g~~~dAi~Ly~La~~~d~--vl~lln~~Ls~~l~~~~~~~~~~s~~~~l~~la~~i~~  483 (613)
T PF04097_consen  406 FDDDEDFLREIIEQAAREAEERGRFEDAILLYHLAEEYDK--VLSLLNRLLSQVLSQPSSSSLSDSERERLIELAKEILE  483 (613)
T ss_dssp             -SSSSHHHHHHHHHHHHHHHHCT-HHHHHHHHHHTT-HHH--HHHHHHHHHHHHHHCSSTSSSSSTTTTSHHHHHHHHHH
T ss_pred             CCCcHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHhhHHH--HHHHHHHHHHHHHcCccccccccchhhhHHHHHHHHHH
Confidence            11 1222   223334446677888888888877654321  1223333333222 2222           344555555


Q ss_pred             HHHhCC-----CCC-CHHHHHHHHH-----HHHhcCCHHHHHHHHHHH
Q 012111          421 TMKERH-----CVP-DNITFATMIQ-----AYNALGMTEAAQNLENKM  457 (471)
Q Consensus       421 ~~~~~~-----~~p-~~~~~~~l~~-----~~~~~g~~~~A~~~~~~m  457 (471)
                      .....+     +.+ +..|+..|++     .+...|+++.|++.++++
T Consensus       484 ~y~~~~~~~~~~~~~~~~t~~~Ll~L~~ff~~~~~g~~~~AL~~i~~L  531 (613)
T PF04097_consen  484 RYKSNPHISSKVSRKNRETFQLLLDLAEFFDLYHAGQYEQALDIIEKL  531 (613)
T ss_dssp             HHTTSHHHHTTS-HHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHT
T ss_pred             HHHhCcchHhhccHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHhC
Confidence            444321     111 2455665553     346889999998877764

It is required for the correct assembly of the nuclear pore complex []. In Saccharomyces cerevisiae, Nic96 has been shown to be involved in the distribution and cellular concentration of the GTPase Gsp1 []. The structure of Nic96 has revealed a mostly alpha helical structure [].; GO: 0006810 transport, 0005643 nuclear pore; PDB: 2QX5_B 2RFO_A.

>PF13174 TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_A 3URZ_B 2Q7F_A

Probab=92.05  E-value=0.38  Score=25.81  Aligned_cols=28  Identities=18%  Similarity=0.280  Sum_probs=18.4

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHHhhhc
Q 012111          436 TMIQAYNALGMTEAAQNLENKMIAMKEN  463 (471)
Q Consensus       436 ~l~~~~~~~g~~~~A~~~~~~m~~~~~~  463 (471)
                      .+..++.+.|++++|.+.|+++++..|+
T Consensus         5 ~~a~~~~~~g~~~~A~~~~~~~~~~~P~   32 (33)
T PF13174_consen    5 RLARCYYKLGDYDEAIEYFQRLIKRYPD   32 (33)
T ss_dssp             HHHHHHHHHCHHHHHHHHHHHHHHHSTT
T ss_pred             HHHHHHHHccCHHHHHHHHHHHHHHCcC
Confidence            4455666667777777777777766654

>KOG4570 consensus Uncharacterized conserved protein [Function unknown]

Probab=91.82  E-value=3  Score=36.32  Aligned_cols=105  Identities=16%  Similarity=0.145  Sum_probs=63.8

Q ss_pred             CCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCC--CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCH
Q 012111          214 LGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGC--HPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADI  291 (471)
Q Consensus       214 ~g~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  291 (471)
                      .|.+....+...++..-....+++.++..+-++......  .++. +-...++ ++..-++++++.++..=+..|+-||.
T Consensus        58 ~g~~~s~~~Vd~~V~v~~~~~~idd~~~~LyKlRhs~~a~~~~~~-~~~~~ir-lllky~pq~~i~~l~npIqYGiF~dq  135 (418)
T KOG4570|consen   58 RGLPVSSLTVDRLVDVISSREEIDDAEYYLYKLRHSPNAWYLRNW-TIHTWIR-LLLKYDPQKAIYTLVNPIQYGIFPDQ  135 (418)
T ss_pred             cCCCcceeehhhhhhccccccchhHHHHHHHHHhcCcchhhhccc-cHHHHHH-HHHccChHHHHHHHhCcchhccccch
Confidence            344555555555665555566777777777666433210  1111 1111222 22334566777777777777888888


Q ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHhC
Q 012111          292 QTLNILTKSYGRAGMYDKMRSVMDFMQKR  320 (471)
Q Consensus       292 ~~~~~ll~~~~~~~~~~~a~~~~~~~~~~  320 (471)
                      ++++.+|+.+.+.+++.+|.++.-.|...
T Consensus       136 f~~c~l~D~flk~~n~~~aa~vvt~~~~q  164 (418)
T KOG4570|consen  136 FTFCLLMDSFLKKENYKDAASVVTEVMMQ  164 (418)
T ss_pred             hhHHHHHHHHHhcccHHHHHHHHHHHHHH
Confidence            88888888888888888777776665543

>PF02284 COX5A: Cytochrome c oxidase subunit Va; InterPro: IPR003204 Cytochrome c oxidase (1

Probab=91.76  E-value=1.4  Score=31.15  Aligned_cols=61  Identities=11%  Similarity=0.126  Sum_probs=39.7

Q ss_pred             HHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHHH
Q 012111          131 EQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIK  193 (471)
Q Consensus       131 ~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~  193 (471)
                      -+..+-++.+......|++.+..+.+++|-+.+++..|+++|+.++..-+  .....|..++.
T Consensus        27 we~rrglN~l~~~DlVP~P~ii~aALrAcRRvND~a~AVR~lE~iK~K~~--~~~~~Y~~~lq   87 (108)
T PF02284_consen   27 WELRRGLNNLFGYDLVPEPKIIEAALRACRRVNDFALAVRILEGIKDKCG--NKKEIYPYILQ   87 (108)
T ss_dssp             HHHHHHHHHHTTSSB---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHTT--T-TTHHHHHHH
T ss_pred             HHHHHHHHHHhccccCCChHHHHHHHHHHHHhhhHHHHHHHHHHHHHHcc--ChHHHHHHHHH
Confidence            35667777777777788888888888888888888888888888776433  22225555543

9.3.1 from EC) is an oligomeric enzymatic complex which is a component of the respiratory chain complex and is involved in the transfer of electrons from cytochrome c to oxygen []. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. In eukaryotes, in addition to the three large subunits, I, II and III, that form the catalytic centre of the enzyme complex, there are a variable number of small polypeptidic subunits. One of these subunits is known as Va.; GO: 0004129 cytochrome-c oxidase activity; PDB: 2DYR_R 3AG1_E 3ABL_E 1V54_R 2EIJ_R 1OCR_E 2DYS_E 2EIM_E 2OCC_E 3ASN_R ....

>COG4649 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=91.60  E-value=5.7  Score=31.45  Aligned_cols=132  Identities=16%  Similarity=0.148  Sum_probs=62.1

Q ss_pred             hHHHHHHHHHHHhhcHHHHHHHHHHhhhccCccC-ChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHH-HHHHHH
Q 012111           79 KPVLEALDEAIKQKKWQLALKIFGLLRQQQWYQA-RCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVD-VYTALV  156 (471)
Q Consensus        79 ~~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~-~~~~li  156 (471)
                      +.+...|+ +.+.+..++|+.-|..+.+.+ +.. .+-..........+.|+...|...|+++-.....|... -...|=
T Consensus        60 d~flaAL~-lA~~~k~d~Alaaf~~lektg-~g~YpvLA~mr~at~~a~kgdta~AV~aFdeia~dt~~P~~~rd~ARlr  137 (221)
T COG4649          60 DAFLAALK-LAQENKTDDALAAFTDLEKTG-YGSYPVLARMRAATLLAQKGDTAAAVAAFDEIAADTSIPQIGRDLARLR  137 (221)
T ss_pred             HHHHHHHH-HHHcCCchHHHHHHHHHHhcC-CCcchHHHHHHHHHHHhhcccHHHHHHHHHHHhccCCCcchhhHHHHHH
Confidence            33444443 345555666666666665543 111 11122233334455566666666666665543333222 111111


Q ss_pred             --HHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 012111          157 --SAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSY  213 (471)
Q Consensus       157 --~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~  213 (471)
                        -.+...|.++......+.+.. .+.+.....-..|.-+-.+.|++..|.+.|..+..
T Consensus       138 aa~lLvD~gsy~dV~srvepLa~-d~n~mR~sArEALglAa~kagd~a~A~~~F~qia~  195 (221)
T COG4649         138 AAYLLVDNGSYDDVSSRVEPLAG-DGNPMRHSAREALGLAAYKAGDFAKAKSWFVQIAN  195 (221)
T ss_pred             HHHHHhccccHHHHHHHhhhccC-CCChhHHHHHHHHhHHHHhccchHHHHHHHHHHHc
Confidence              123445556665555555543 23233333444455555566666666666665554

>COG4455 ImpE Protein of avirulence locus involved in temperature-dependent protein secretion [General function prediction only]

Probab=91.15  E-value=2.1  Score=35.21  Aligned_cols=76  Identities=12%  Similarity=0.067  Sum_probs=58.0

Q ss_pred             HHHHHHHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCC--CCCCHHHHHHHHHHH
Q 012111           82 LEALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDG--LKPSVDVYTALVSAY  159 (471)
Q Consensus        82 ~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~--~~~~~~~~~~li~~~  159 (471)
                      ...+..+.+.++..+|+...+.-.+..  |.+...-..++..|+-.|++++|..-++..-+..  ..+....|..+|++-
T Consensus         5 ~~t~seLL~~~sL~dai~~a~~qVkak--Ptda~~RhflfqLlcvaGdw~kAl~Ql~l~a~l~p~~t~~a~lyr~lir~e   82 (273)
T COG4455           5 RDTISELLDDNSLQDAIGLARDQVKAK--PTDAGGRHFLFQLLCVAGDWEKALAQLNLAATLSPQDTVGASLYRHLIRCE   82 (273)
T ss_pred             HHHHHHHHHhccHHHHHHHHHHHHhcC--CccccchhHHHHHHhhcchHHHHHHHHHHHhhcCcccchHHHHHHHHHHHH
Confidence            345667778999999999988777765  6677788899999999999999998888776542  233456677777653

>KOG1550 consensus Extracellular protein SEL-1 and related proteins [Cell wall/membrane/envelope biogenesis; Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]

Probab=91.12  E-value=17  Score=35.85  Aligned_cols=180  Identities=14%  Similarity=0.113  Sum_probs=94.3

Q ss_pred             HHHHHHHHHHhhhccCccCChhHHHHHHHH---HhcCCCHHHHHHHHHHHHh-------CCCCCCHHHHHHHHHHHHhcC
Q 012111           94 WQLALKIFGLLRQQQWYQARCQTFTKLMVM---LGKCKQPEQASLLFEVMLS-------DGLKPSVDVYTALVSAYGQSG  163 (471)
Q Consensus        94 ~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~---~~~~~~~~~a~~~~~~m~~-------~~~~~~~~~~~~li~~~~~~~  163 (471)
                      ...|.++++.+...+  ..........+..   +....+.+.|...|....+       .|   .......+..+|.+..
T Consensus       228 ~~~a~~~~~~~a~~g--~~~a~~~~g~~y~~G~~g~~~d~e~a~~~l~~aa~~~~~~a~~~---~~~a~~~lg~~Y~~g~  302 (552)
T KOG1550|consen  228 LSEAFKYYREAAKLG--HSEAQYALGICYLAGTYGVTQDLESAIEYLKLAAESFKKAATKG---LPPAQYGLGRLYLQGL  302 (552)
T ss_pred             hhHHHHHHHHHHhhc--chHHHHHHHHHHhhccccccccHHHHHHHHHHHHHHHHHHHhhc---CCccccHHHHHHhcCC
Confidence            467888888888765  2222222222222   3355788899998888876       44   2334555666665532


Q ss_pred             -----CHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHh-cCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHH----cc
Q 012111          164 -----LLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTK-FHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYG----KA  233 (471)
Q Consensus       164 -----~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~-~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~----~~  233 (471)
                           +.+.|+.+|.+.-. .| .|+...+...+..... ..+...|.++|....+.|..   ..+-.+..+|.    ..
T Consensus       303 ~~~~~d~~~A~~~~~~aA~-~g-~~~a~~~lg~~~~~g~~~~d~~~A~~yy~~Aa~~G~~---~A~~~la~~y~~G~gv~  377 (552)
T KOG1550|consen  303 GVEKIDYEKALKLYTKAAE-LG-NPDAQYLLGVLYETGTKERDYRRAFEYYSLAAKAGHI---LAIYRLALCYELGLGVE  377 (552)
T ss_pred             CCccccHHHHHHHHHHHHh-cC-CchHHHHHHHHHHcCCccccHHHHHHHHHHHHHcCCh---HHHHHHHHHHHhCCCcC
Confidence                 55667777777665 23 3444443333222222 24566777777777777632   22222222222    23


Q ss_pred             CCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCC
Q 012111          234 KKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMG  286 (471)
Q Consensus       234 ~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  286 (471)
                      .+...|..++.+..+.+  .|...--...+..+.. ++++.+.-.+..+...|
T Consensus       378 r~~~~A~~~~k~aA~~g--~~~A~~~~~~~~~~g~-~~~~~~~~~~~~~a~~g  427 (552)
T KOG1550|consen  378 RNLELAFAYYKKAAEKG--NPSAAYLLGAFYEYGV-GRYDTALALYLYLAELG  427 (552)
T ss_pred             CCHHHHHHHHHHHHHcc--ChhhHHHHHHHHHHcc-ccccHHHHHHHHHHHhh
Confidence            45667777777766554  2222111222222333 55555555555554443

>PF00515 TPR_1: Tetratricopeptide repeat; InterPro: IPR001440 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]

Probab=90.94  E-value=0.69  Score=25.08  Aligned_cols=27  Identities=30%  Similarity=0.284  Sum_probs=16.6

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 012111          398 FFNCIISAYGQAGDVEKMGELFLTMKE  424 (471)
Q Consensus       398 ~~~~l~~~~~~~g~~~~a~~~~~~~~~  424 (471)
                      +|..+..+|...|++++|+..|++.++
T Consensus         3 ~~~~~g~~~~~~~~~~~A~~~~~~al~   29 (34)
T PF00515_consen    3 AYYNLGNAYFQLGDYEEALEYYQRALE   29 (34)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCchHHHHHHHHHHH
Confidence            455566666666666666666666655

It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. The X-ray structure of a domain containing three TPRs from protein phosphatase 5 revealed that TPR adopts a helix-turn-helix arrangement, with adjacent TPR motifs packing in a parallel fashion, resulting in a spiral of repeating anti-parallel alpha-helices []. The two helices are denoted helix A and helix B. The packing angle between helix A and helix B is ~24 degrees; within a single TPR and generates a right-handed superhelical shape. Helix A interacts with helix B and with helix A' of the next TPR. Two protein surfaces are generated: the inner concave surface is contributed to mainly by residue on helices A, and the other surface presents residues from both helices A and B. ; GO: 0005515 protein binding; PDB: 3SF4_C 2LNI_A 1ELW_A 2C0M_A 1FCH_B 3R9A_B 2J9Q_A 2C0L_A 1KT1_A 3FWV_A ....

>KOG4570 consensus Uncharacterized conserved protein [Function unknown]

Probab=90.87  E-value=1.5  Score=38.15  Aligned_cols=47  Identities=19%  Similarity=0.288  Sum_probs=23.3

Q ss_pred             HHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 012111          165 LDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMS  212 (471)
Q Consensus       165 ~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~  212 (471)
                      .++++.++..=.. +|+-||..+++.+|+.+.+.+++..|.++...|.
T Consensus       116 pq~~i~~l~npIq-YGiF~dqf~~c~l~D~flk~~n~~~aa~vvt~~~  162 (418)
T KOG4570|consen  116 PQKAIYTLVNPIQ-YGIFPDQFTFCLLMDSFLKKENYKDAASVVTEVM  162 (418)
T ss_pred             hHHHHHHHhCcch-hccccchhhHHHHHHHHHhcccHHHHHHHHHHHH
Confidence            3344444444443 4555555555555555555555555555444443

>PF02259 FAT: FAT domain; InterPro: IPR003151 The FAT domain is a domain present in the PIK-related kinases

Probab=90.81  E-value=13  Score=34.03  Aligned_cols=65  Identities=11%  Similarity=-0.049  Sum_probs=41.0

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC---CHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Q 012111          255 DIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKA---DIQTLNILTKSYGRAGMYDKMRSVMDFMQK  319 (471)
Q Consensus       255 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~---~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~  319 (471)
                      ...+|..+...+.+.|.++.|...+..+...+...   .......-++..-..|+..+|...++...+
T Consensus       145 ~~~~~l~~a~~aRk~g~~~~A~~~l~~~~~~~~~~~~~~~~v~~e~akllw~~g~~~~Ai~~L~~~~~  212 (352)
T PF02259_consen  145 LAETWLKFAKLARKAGNFQLALSALNRLFQLNPSSESLLPRVFLEYAKLLWAQGEQEEAIQKLRELLK  212 (352)
T ss_pred             HHHHHHHHHHHHHHCCCcHHHHHHHHHHhccCCcccCCCcchHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            34567777777777777777777777776533111   333444445566666777777777766665

Members of the family of PIK-related kinases may act as intracellular sensors that govern radial and horizontal pathways [].; GO: 0005515 protein binding

>COG4785 NlpI Lipoprotein NlpI, contains TPR repeats [General function prediction only]

Probab=90.72  E-value=8.5  Score=31.81  Aligned_cols=180  Identities=12%  Similarity=-0.003  Sum_probs=95.8

Q ss_pred             hhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHH
Q 012111           91 QKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAFS  170 (471)
Q Consensus        91 ~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~  170 (471)
                      .|-+..|.--|.+.....  |.-+.+||.+...+...|+++.|.+.|+...+....-+-...|.-|. +.-.|++..|.+
T Consensus        78 lGL~~LAR~DftQaLai~--P~m~~vfNyLG~Yl~~a~~fdaa~eaFds~~ELDp~y~Ya~lNRgi~-~YY~gR~~LAq~  154 (297)
T COG4785          78 LGLRALARNDFSQALAIR--PDMPEVFNYLGIYLTQAGNFDAAYEAFDSVLELDPTYNYAHLNRGIA-LYYGGRYKLAQD  154 (297)
T ss_pred             hhHHHHHhhhhhhhhhcC--CCcHHHHHHHHHHHHhcccchHHHHHhhhHhccCCcchHHHhcccee-eeecCchHhhHH
Confidence            344555555555555543  44567889998899999999999999999988744333333333333 334688888888


Q ss_pred             HHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHH-HHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHc
Q 012111          171 TINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKIL-AEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVES  249 (471)
Q Consensus       171 ~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~-~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  249 (471)
                      -+...-....-.|-...|.-+.   -..-++.+|..-+ ++....    +..-|...|-.|.- |+..+ ..+++++...
T Consensus       155 d~~~fYQ~D~~DPfR~LWLYl~---E~k~dP~~A~tnL~qR~~~~----d~e~WG~~iV~~yL-gkiS~-e~l~~~~~a~  225 (297)
T COG4785         155 DLLAFYQDDPNDPFRSLWLYLN---EQKLDPKQAKTNLKQRAEKS----DKEQWGWNIVEFYL-GKISE-ETLMERLKAD  225 (297)
T ss_pred             HHHHHHhcCCCChHHHHHHHHH---HhhCCHHHHHHHHHHHHHhc----cHhhhhHHHHHHHH-hhccH-HHHHHHHHhh
Confidence            7776665332233333333222   2334566665443 333322    44444433332221 22211 2233333221


Q ss_pred             CCCCCC-------HHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 012111          250 GGCHPD-------IFTLNSMISAYGNSGNIEKMEKWYNEFNL  284 (471)
Q Consensus       250 ~~~~~~-------~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  284 (471)
                      .  ..+       ..||--+..-+...|+.++|..+|+-.+.
T Consensus       226 a--~~n~~~Ae~LTEtyFYL~K~~l~~G~~~~A~~LfKLaia  265 (297)
T COG4785         226 A--TDNTSLAEHLTETYFYLGKYYLSLGDLDEATALFKLAVA  265 (297)
T ss_pred             c--cchHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHHHHH
Confidence            1  111       23455566666666666666666665543

>PF07035 Mic1: Colon cancer-associated protein Mic1-like; InterPro: IPR009755 This entry represents the C terminus (approximately 160 residues) of a number of proteins that resemble colon cancer-associated protein Mic1

Probab=90.66  E-value=7.3  Score=30.95  Aligned_cols=130  Identities=9%  Similarity=0.086  Sum_probs=62.4

Q ss_pred             HHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcC--CHHHHHHHHHHHHhCC
Q 012111          314 MDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAG--LIMKVDSILRQVENSD  391 (471)
Q Consensus       314 ~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g--~~~~a~~~~~~~~~~~  391 (471)
                      +..+.+.++.|+...|..++..+.+.|++...    ..+...++-+|.......+-.+....  -.+-|.+++.++..  
T Consensus        17 irSl~~~~i~~~~~L~~lli~lLi~~~~~~~L----~qllq~~Vi~DSk~lA~~LLs~~~~~~~~~Ql~lDMLkRL~~--   90 (167)
T PF07035_consen   17 IRSLNQHNIPVQHELYELLIDLLIRNGQFSQL----HQLLQYHVIPDSKPLACQLLSLGNQYPPAYQLGLDMLKRLGT--   90 (167)
T ss_pred             HHHHHHcCCCCCHHHHHHHHHHHHHcCCHHHH----HHHHhhcccCCcHHHHHHHHHhHccChHHHHHHHHHHHHhhh--
Confidence            34444556666666667777777766665443    33344444555444443332222111  12223333333321  


Q ss_pred             CCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 012111          392 VILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAYNALGMTEAAQNLENKMIA  459 (471)
Q Consensus       392 ~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~  459 (471)
                            .+..+++.+...|++-+|+++.+.....    +......++.+..+.++...-..+++-...
T Consensus        91 ------~~~~iievLL~~g~vl~ALr~ar~~~~~----~~~~~~~fLeAA~~~~D~~lf~~V~~ff~~  148 (167)
T PF07035_consen   91 ------AYEEIIEVLLSKGQVLEALRYARQYHKV----DSVPARKFLEAAANSNDDQLFYAVFRFFEE  148 (167)
T ss_pred             ------hHHHHHHHHHhCCCHHHHHHHHHHcCCc----ccCCHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence                  2345566667777777777776654221    111123345555555554444444443333

>KOG0276 consensus Vesicle coat complex COPI, beta' subunit [Intracellular trafficking, secretion, and vesicular transport]

Probab=90.50  E-value=14  Score=35.67  Aligned_cols=46  Identities=20%  Similarity=-0.091  Sum_probs=22.1

Q ss_pred             hcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHhh
Q 012111          125 GKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAFSTINDMK  176 (471)
Q Consensus       125 ~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~  176 (471)
                      .+.|+++.|.++..+..      +..-|..|.++....+++..|.+.|....
T Consensus       648 l~lgrl~iA~~la~e~~------s~~Kw~~Lg~~al~~~~l~lA~EC~~~a~  693 (794)
T KOG0276|consen  648 LKLGRLDIAFDLAVEAN------SEVKWRQLGDAALSAGELPLASECFLRAR  693 (794)
T ss_pred             hhcCcHHHHHHHHHhhc------chHHHHHHHHHHhhcccchhHHHHHHhhc
Confidence            34455555544443322      33445555555555555555555554443

>KOG0276 consensus Vesicle coat complex COPI, beta' subunit [Intracellular trafficking, secretion, and vesicular transport]

Probab=90.46  E-value=3.7  Score=39.21  Aligned_cols=131  Identities=17%  Similarity=0.140  Sum_probs=74.2

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHh
Q 012111          259 LNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGK  338 (471)
Q Consensus       259 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~  338 (471)
                      -+.++..+.+.|-.++|+++-.       .|+. -    .....+.|+++.|.++..+..      +..-|..|..+..+
T Consensus       617 rt~va~Fle~~g~~e~AL~~s~-------D~d~-r----Felal~lgrl~iA~~la~e~~------s~~Kw~~Lg~~al~  678 (794)
T KOG0276|consen  617 RTKVAHFLESQGMKEQALELST-------DPDQ-R----FELALKLGRLDIAFDLAVEAN------SEVKWRQLGDAALS  678 (794)
T ss_pred             hhhHHhHhhhccchHhhhhcCC-------Chhh-h----hhhhhhcCcHHHHHHHHHhhc------chHHHHHHHHHHhh
Confidence            3445555666666666654321       1111 1    122345577777766654332      45567777777777


Q ss_pred             cCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHH
Q 012111          339 AGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGEL  418 (471)
Q Consensus       339 ~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~  418 (471)
                      .|++..|.+.|.+...         |..|+-.+...|+-+....+-....+.|..      |...-+|...|+++++.++
T Consensus       679 ~~~l~lA~EC~~~a~d---------~~~LlLl~t~~g~~~~l~~la~~~~~~g~~------N~AF~~~~l~g~~~~C~~l  743 (794)
T KOG0276|consen  679 AGELPLASECFLRARD---------LGSLLLLYTSSGNAEGLAVLASLAKKQGKN------NLAFLAYFLSGDYEECLEL  743 (794)
T ss_pred             cccchhHHHHHHhhcc---------hhhhhhhhhhcCChhHHHHHHHHHHhhccc------chHHHHHHHcCCHHHHHHH
Confidence            7777777777765543         445555566666666555555555554432      3334455666777777776


Q ss_pred             HHHH
Q 012111          419 FLTM  422 (471)
Q Consensus       419 ~~~~  422 (471)
                      +..-
T Consensus       744 Li~t  747 (794)
T KOG0276|consen  744 LIST  747 (794)
T ss_pred             HHhc
Confidence            6543

>cd00923 Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va

Probab=90.14  E-value=5  Score=28.19  Aligned_cols=63  Identities=13%  Similarity=0.117  Sum_probs=46.3

Q ss_pred             CHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHHH
Q 012111          129 QPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIK  193 (471)
Q Consensus       129 ~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~  193 (471)
                      +.-++.+-++.+......|++.+..+.+++|-+.+++..|+++|+.++..-  ..+...|..++.
T Consensus        22 D~we~rr~mN~l~~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~vK~K~--~~~~~~y~~~lq   84 (103)
T cd00923          22 DGWELRRGLNNLFGYDLVPEPKVIEAALRACRRVNDFALAVRILEAIKDKC--GAHKEIYPYILQ   84 (103)
T ss_pred             cHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHc--cCchhhHHHHHH
Confidence            455677778888888888888888888888888888888888888877422  224445555543

Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit Va is one of three mammalian subunits that lacks a transmembrane region. Subunit Va is located on the matrix side of the membrane and binds thyroid hormone T2, releasing allosteric inhibition caused by the binding of ATP to subunit IV and allowing high turnover at elevated intramitochondrial ATP/ADP ratios.

>COG4455 ImpE Protein of avirulence locus involved in temperature-dependent protein secretion [General function prediction only]

Probab=90.10  E-value=3  Score=34.34  Aligned_cols=131  Identities=11%  Similarity=0.051  Sum_probs=79.5

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCC--CcCHHHHHHHHHH
Q 012111          328 TYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDV--ILDTPFFNCIISA  405 (471)
Q Consensus       328 ~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~--~~~~~~~~~l~~~  405 (471)
                      |.+..++.+.+.+.+.+++...++-++.+ +-|..+-..+++.++-.|++++|..-++...+..+  .+-...|..+|.+
T Consensus         3 Tl~~t~seLL~~~sL~dai~~a~~qVkak-Ptda~~RhflfqLlcvaGdw~kAl~Ql~l~a~l~p~~t~~a~lyr~lir~   81 (273)
T COG4455           3 TLRDTISELLDDNSLQDAIGLARDQVKAK-PTDAGGRHFLFQLLCVAGDWEKALAQLNLAATLSPQDTVGASLYRHLIRC   81 (273)
T ss_pred             chHHHHHHHHHhccHHHHHHHHHHHHhcC-CccccchhHHHHHHhhcchHHHHHHHHHHHhhcCcccchHHHHHHHHHHH
Confidence            34566778889999999999999888763 34667778899999999999999988877765433  2344566666654


Q ss_pred             HHhcCCHHHHHHHHHHHHhCCCCC-CHHHHHHHH-HHHH-hc-CCHHHHHHHHHHHHHhhhcCC
Q 012111          406 YGQAGDVEKMGELFLTMKERHCVP-DNITFATMI-QAYN-AL-GMTEAAQNLENKMIAMKENSG  465 (471)
Q Consensus       406 ~~~~g~~~~a~~~~~~~~~~~~~p-~~~~~~~l~-~~~~-~~-g~~~~A~~~~~~m~~~~~~~~  465 (471)
                      -.-.      .++|.--..-|+.- ....|...+ .+.. +. |.-+.+..+-+...+..|.+.
T Consensus        82 ea~R------~evfag~~~Pgflg~p~p~wva~L~aala~h~dg~gea~~alreqal~aa~~~i  139 (273)
T COG4455          82 EAAR------NEVFAGGAVPGFLGGPSPEWVAALLAALALHSDGAGEARTALREQALKAAPVPI  139 (273)
T ss_pred             HHHH------HHHhccCCCCCCcCCCCHHHHHHHHHHHhcccCCcchHHHHHHHHHHhhCCCCC
Confidence            3211      11222111112221 234454433 3332 23 344445566666666666543

>PF07719 TPR_2: Tetratricopeptide repeat; InterPro: IPR013105 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]

Probab=89.83  E-value=0.97  Score=24.37  Aligned_cols=27  Identities=30%  Similarity=0.268  Sum_probs=16.8

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 012111          398 FFNCIISAYGQAGDVEKMGELFLTMKE  424 (471)
Q Consensus       398 ~~~~l~~~~~~~g~~~~a~~~~~~~~~  424 (471)
                      .+..+...+...|++++|++.|++..+
T Consensus         3 ~~~~lg~~~~~~~~~~~A~~~~~~al~   29 (34)
T PF07719_consen    3 AWYYLGQAYYQLGNYEEAIEYFEKALE   29 (34)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence            455566666666777777777766655

It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. This repeat includes outlying Tetratricopeptide-like repeats (TPR) that are not matched by IPR001440 from INTERPRO.; PDB: 1XNF_B 3Q15_A 4ABN_A 1OUV_A 3U4T_A 3MA5_C 2KCV_A 2KCL_A 2XEV_A 3NF1_A ....

>PF13374 TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT_H 3NF1_A

Probab=89.53  E-value=1.3  Score=25.28  Aligned_cols=29  Identities=24%  Similarity=0.360  Sum_probs=16.5

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHHh
Q 012111          432 ITFATMIQAYNALGMTEAAQNLENKMIAM  460 (471)
Q Consensus       432 ~~~~~l~~~~~~~g~~~~A~~~~~~m~~~  460 (471)
                      .+++.|...|...|++++|..+++++++.
T Consensus         3 ~~~~~la~~~~~~g~~~~A~~~~~~al~~   31 (42)
T PF13374_consen    3 SALNNLANAYRAQGRYEEALELLEEALEI   31 (42)
T ss_dssp             HHHHHHHHHHHHCT-HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhhhcchhhHHHHHHHHH
Confidence            34555556666666666666666665544

>COG3947 Response regulator containing CheY-like receiver and SARP domains [Signal transduction mechanisms]

Probab=89.53  E-value=13  Score=32.24  Aligned_cols=40  Identities=15%  Similarity=-0.026  Sum_probs=21.8

Q ss_pred             HHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHH
Q 012111          131 EQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAFSTI  172 (471)
Q Consensus       131 ~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~  172 (471)
                      .+|.++|.-+.++.-  ...+-..++..+....+..+|...+
T Consensus       150 ~KA~ELFayLv~hkg--k~v~~~~~ie~lwpe~D~kka~s~l  189 (361)
T COG3947         150 RKALELFAYLVEHKG--KEVTSWEAIEALWPEKDEKKASSLL  189 (361)
T ss_pred             hHHHHHHHHHHHhcC--CcccHhHHHHHHccccchhhHHHHH
Confidence            467777777766521  2233344555565555555554443

>COG0457 NrfG FOG: TPR repeat [General function prediction only]

Probab=88.91  E-value=12  Score=31.11  Aligned_cols=202  Identities=14%  Similarity=0.048  Sum_probs=106.4

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHHC-CCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Q 012111          186 YTYSILIKSCTKFHRFDLIEKILAEMSYL-GIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMIS  264 (471)
Q Consensus       186 ~~~~~ll~~~~~~~~~~~a~~~~~~~~~~-g~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~  264 (471)
                      ..+......+...+.+..+...+...... ........+......+...+++..+.+.+.......  ..+.........
T Consensus        60 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~  137 (291)
T COG0457          60 GLLLLLALALLKLGRLEEALELLEKALELELLPNLAEALLNLGLLLEALGKYEEALELLEKALALD--PDPDLAEALLAL  137 (291)
T ss_pred             HHHHHHHHHHHHcccHHHHHHHHHHHHhhhhccchHHHHHHHHHHHHHHhhHHHHHHHHHHHHcCC--CCcchHHHHHHH
Confidence            44444445555555555555555554431 113334444455555555555666666666554432  111111222222


Q ss_pred             -HHHhcCCHHHHHHHHHHHHhCCC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCC
Q 012111          265 -AYGNSGNIEKMEKWYNEFNLMGV--KADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGH  341 (471)
Q Consensus       265 -~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~  341 (471)
                       .+...|+++.+...+.+......  ......+......+...++.+.+...+..............+..+...+...++
T Consensus       138 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  217 (291)
T COG0457         138 GALYELGDYEEALELYEKALELDPELNELAEALLALGALLEALGRYEEALELLEKALKLNPDDDAEALLNLGLLYLKLGK  217 (291)
T ss_pred             HHHHHcCCHHHHHHHHHHHHhcCCCccchHHHHHHhhhHHHHhcCHHHHHHHHHHHHhhCcccchHHHHHhhHHHHHccc
Confidence             55666666666666666643111  012233333333455666777777777666654222134556666666777777


Q ss_pred             HHHHHHHHHHHHHcCCCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCC
Q 012111          342 IEKMEEYFKKMKHRGMKPN-SITYCSLVSAYSKAGLIMKVDSILRQVENSD  391 (471)
Q Consensus       342 ~~~a~~~~~~m~~~~~~p~-~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~  391 (471)
                      ++.+...+......  .|+ ...+..+...+...+..+.+...+.......
T Consensus       218 ~~~a~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  266 (291)
T COG0457         218 YEEALEYYEKALEL--DPDNAEALYNLALLLLELGRYEEALEALEKALELD  266 (291)
T ss_pred             HHHHHHHHHHHHhh--CcccHHHHhhHHHHHHHcCCHHHHHHHHHHHHHhC
Confidence            77777777777664  232 3344444444446666777777777776653

>TIGR02561 HrpB1_HrpK type III secretion protein HrpB1/HrpK

Probab=88.61  E-value=9.6  Score=29.42  Aligned_cols=59  Identities=19%  Similarity=0.075  Sum_probs=29.5

Q ss_pred             HHHHHHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhC
Q 012111           83 EALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSD  143 (471)
Q Consensus        83 ~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~  143 (471)
                      +++......++.+++..+++-+.--.+-.+...++  -...+...|++++|.++|+++.+.
T Consensus        15 ~~~~~aL~~~d~~D~e~lLdALrvLrP~~~e~d~~--dg~l~i~rg~w~eA~rvlr~l~~~   73 (153)
T TIGR02561        15 EVLMYALRSADPYDAQAMLDALRVLRPNLKELDMF--DGWLLIARGNYDEAARILRELLSS   73 (153)
T ss_pred             HHHHHHHhcCCHHHHHHHHHHHHHhCCCccccchh--HHHHHHHcCCHHHHHHHHHhhhcc
Confidence            33444445566666666666665432111222222  223345566666666666666654

This gene is found within type III secretion operons in a limited range of species including Xanthomonas, Ralstonia and Burkholderia.

>PF07163 Pex26: Pex26 protein; InterPro: IPR010797 This family consists of Pex26 and related mammalian proteins

Probab=88.50  E-value=15  Score=31.67  Aligned_cols=130  Identities=15%  Similarity=0.139  Sum_probs=60.0

Q ss_pred             hhhhhhhhHHHHHHHhhHHHHHHHHHhhhhhh------ccCCCc-----hHHHHHHHHHHHhhcHHHHHHHHHHhhhc-c
Q 012111           41 LGIQKEAEKDLSKILRTEFAIKNIEKKVSSKK------YKNLWP-----KPVLEALDEAIKQKKWQLALKIFGLLRQQ-Q  108 (471)
Q Consensus        41 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~------~~~~~~-----~~~~~~l~~~~~~~~~~~A~~~~~~~~~~-~  108 (471)
                      ....-.+.+.|.-..++..+++..+.-++.-.      ....+.     ..-+--|+++...++|.+++...-+--+. .
T Consensus        35 ~~lLe~Aad~LvV~rdF~aal~tCerglqsL~~~a~~ee~~~~~~evK~sLcvvGIQALAEmnrWreVLsWvlqyYq~pE  114 (309)
T PF07163_consen   35 VSLLEEAADLLVVHRDFQAALETCERGLQSLASDADAEEPAGSSLEVKCSLCVVGIQALAEMNRWREVLSWVLQYYQVPE  114 (309)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccccccccchhhhhhhhhhhhHHHHHHHhhHHHHHHHHHHHhcCcc
Confidence            34444555555555566666655554443210      000000     11123366666677776665533222221 1


Q ss_pred             CccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHh-----cCCHHHHHHHH
Q 012111          109 WYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQ-----SGLLDEAFSTI  172 (471)
Q Consensus       109 ~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~-----~~~~~~a~~~~  172 (471)
                      .+||  .....-|-.|.+.+.+..+.++-..-....-..+...|..++..|..     .|.+++|.++.
T Consensus       115 klPp--kIleLCILLysKv~Ep~amlev~~~WL~~p~Nq~lp~y~~vaELyLl~VLlPLG~~~eAeelv  181 (309)
T PF07163_consen  115 KLPP--KILELCILLYSKVQEPAAMLEVASAWLQDPSNQSLPEYGTVAELYLLHVLLPLGHFSEAEELV  181 (309)
T ss_pred             cCCH--HHHHHHHHHHHHhcCHHHHHHHHHHHHhCcccCCchhhHHHHHHHHHHHHhccccHHHHHHHH
Confidence            1222  33444445566666666666655554443222233335554444433     46666666555

Pex26 is a type II peroxisomal membrane protein that recruits Pex6-Pex1 complexes to peroxisomes []. Mutations in Pex26 can lead to human disorders [].; GO: 0032403 protein complex binding, 0045046 protein import into peroxisome membrane, 0005779 integral to peroxisomal membrane

>KOG4648 consensus Uncharacterized conserved protein, contains LRR repeats [Function unknown]

Probab=88.50  E-value=1.9  Score=37.98  Aligned_cols=95  Identities=17%  Similarity=0.120  Sum_probs=60.4

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCC
Q 012111          333 IETFGKAGHIEKMEEYFKKMKHRGMKP-NSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGD  411 (471)
Q Consensus       333 i~~~~~~g~~~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~  411 (471)
                      ..-|.+.|.+++|+++|......  .| |++++..-..+|.+...+..|+.-.......+-. -...|..-+.+-...|+
T Consensus       104 GN~yFKQgKy~EAIDCYs~~ia~--~P~NpV~~~NRA~AYlk~K~FA~AE~DC~~AiaLd~~-Y~KAYSRR~~AR~~Lg~  180 (536)
T KOG4648|consen  104 GNTYFKQGKYEEAIDCYSTAIAV--YPHNPVYHINRALAYLKQKSFAQAEEDCEAAIALDKL-YVKAYSRRMQARESLGN  180 (536)
T ss_pred             hhhhhhccchhHHHHHhhhhhcc--CCCCccchhhHHHHHHHHHHHHHHHHhHHHHHHhhHH-HHHHHHHHHHHHHHHhh
Confidence            45678889999999999877764  45 7888888888888888888888777766654311 12223333333333455


Q ss_pred             HHHHHHHHHHHHhCCCCCCHH
Q 012111          412 VEKMGELFLTMKERHCVPDNI  432 (471)
Q Consensus       412 ~~~a~~~~~~~~~~~~~p~~~  432 (471)
                      ..+|.+-++...+  +.|+..
T Consensus       181 ~~EAKkD~E~vL~--LEP~~~  199 (536)
T KOG4648|consen  181 NMEAKKDCETVLA--LEPKNI  199 (536)
T ss_pred             HHHHHHhHHHHHh--hCcccH
Confidence            5555555555554  456643

>PF13374 TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT_H 3NF1_A

Probab=88.37  E-value=1.4  Score=25.08  Aligned_cols=28  Identities=29%  Similarity=0.313  Sum_probs=21.7

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 012111          397 PFFNCIISAYGQAGDVEKMGELFLTMKE  424 (471)
Q Consensus       397 ~~~~~l~~~~~~~g~~~~a~~~~~~~~~  424 (471)
                      .+++.|...|...|++++|..++++..+
T Consensus         3 ~~~~~la~~~~~~g~~~~A~~~~~~al~   30 (42)
T PF13374_consen    3 SALNNLANAYRAQGRYEEALELLEEALE   30 (42)
T ss_dssp             HHHHHHHHHHHHCT-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhhhcchhhHHHHHHHH
Confidence            4677888888888888888888887764

>PF11207 DUF2989: Protein of unknown function (DUF2989); InterPro: IPR021372 Some members in this bacterial family of proteins are annotated as lipoproteins however this cannot be confirmed

Probab=87.91  E-value=14  Score=30.35  Aligned_cols=82  Identities=11%  Similarity=0.048  Sum_probs=61.0

Q ss_pred             HHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCC--CCCCCHHHHHHHHHHHHhcC
Q 012111          122 VMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAFSTINDMKSVS--DCKPDVYTYSILIKSCTKFH  199 (471)
Q Consensus       122 ~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~--~~~~~~~~~~~ll~~~~~~~  199 (471)
                      -.+.+.|+ +.|.+.|-.+...+.--++.....|...|. ..+.++++.++....+..  +-.+|+..+.+|...+.+.+
T Consensus       115 y~Wsr~~d-~~A~~~fL~~E~~~~l~t~elq~aLAtyY~-krD~~Kt~~ll~~~L~l~~~~~~~n~eil~sLas~~~~~~  192 (203)
T PF11207_consen  115 YHWSRFGD-QEALRRFLQLEGTPELETAELQYALATYYT-KRDPEKTIQLLLRALELSNPDDNFNPEILKSLASIYQKLK  192 (203)
T ss_pred             HHhhccCc-HHHHHHHHHHcCCCCCCCHHHHHHHHHHHH-ccCHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHhc
Confidence            33455555 668888888887776656666666666665 678899999888876642  23678999999999999999


Q ss_pred             CHHHHH
Q 012111          200 RFDLIE  205 (471)
Q Consensus       200 ~~~~a~  205 (471)
                      +++.|.
T Consensus       193 ~~e~AY  198 (203)
T PF11207_consen  193 NYEQAY  198 (203)
T ss_pred             chhhhh
Confidence            998874

>KOG4234 consensus TPR repeat-containing protein [General function prediction only]

Probab=87.60  E-value=12  Score=30.58  Aligned_cols=95  Identities=15%  Similarity=0.078  Sum_probs=69.3

Q ss_pred             HHHHhcCCHHHHHHHHHHHHHcCCCCC-----HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHh
Q 012111          334 ETFGKAGHIEKMEEYFKKMKHRGMKPN-----SITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQ  408 (471)
Q Consensus       334 ~~~~~~g~~~~a~~~~~~m~~~~~~p~-----~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  408 (471)
                      .-+...|++++|..-|...+.. +++.     ...|..-..++.+.+.++.|+.-....++.++. .......-..+|.+
T Consensus       103 N~~F~ngdyeeA~skY~~Ale~-cp~~~~e~rsIly~Nraaa~iKl~k~e~aI~dcsKaiel~pt-y~kAl~RRAeayek  180 (271)
T KOG4234|consen  103 NELFKNGDYEEANSKYQEALES-CPSTSTEERSILYSNRAAALIKLRKWESAIEDCSKAIELNPT-YEKALERRAEAYEK  180 (271)
T ss_pred             HHhhhcccHHHHHHHHHHHHHh-CccccHHHHHHHHhhhHHHHHHhhhHHHHHHHHHhhHhcCch-hHHHHHHHHHHHHh
Confidence            3467889999999999998876 2332     234555556788889999999988888887755 33344444567888


Q ss_pred             cCCHHHHHHHHHHHHhCCCCCCHH
Q 012111          409 AGDVEKMGELFLTMKERHCVPDNI  432 (471)
Q Consensus       409 ~g~~~~a~~~~~~~~~~~~~p~~~  432 (471)
                      ...+++|++=|+.+.+.  .|...
T Consensus       181 ~ek~eealeDyKki~E~--dPs~~  202 (271)
T KOG4234|consen  181 MEKYEEALEDYKKILES--DPSRR  202 (271)
T ss_pred             hhhHHHHHHHHHHHHHh--CcchH
Confidence            88999999999999884  45544

>PF11207 DUF2989: Protein of unknown function (DUF2989); InterPro: IPR021372 Some members in this bacterial family of proteins are annotated as lipoproteins however this cannot be confirmed

Probab=87.53  E-value=12  Score=30.57  Aligned_cols=74  Identities=18%  Similarity=0.100  Sum_probs=53.2

Q ss_pred             HHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhC---CCCCCHHHHHHHHHHHHhcCCHHHHH
Q 012111          377 IMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKER---HCVPDNITFATMIQAYNALGMTEAAQ  451 (471)
Q Consensus       377 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~---~~~p~~~~~~~l~~~~~~~g~~~~A~  451 (471)
                      -+.|.+.|-.+...+..-++.....|...|. ..|.++++.++.+..+.   +-.+|+..+..|...+.+.|+++.|.
T Consensus       122 d~~A~~~fL~~E~~~~l~t~elq~aLAtyY~-krD~~Kt~~ll~~~L~l~~~~~~~n~eil~sLas~~~~~~~~e~AY  198 (203)
T PF11207_consen  122 DQEALRRFLQLEGTPELETAELQYALATYYT-KRDPEKTIQLLLRALELSNPDDNFNPEILKSLASIYQKLKNYEQAY  198 (203)
T ss_pred             cHHHHHHHHHHcCCCCCCCHHHHHHHHHHHH-ccCHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHhcchhhhh
Confidence            3566777766766655546666666665555 57788888888877653   33678888889999999999888874

>KOG1464 consensus COP9 signalosome, subunit CSN2 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]

Probab=87.37  E-value=18  Score=31.06  Aligned_cols=174  Identities=16%  Similarity=0.128  Sum_probs=89.6

Q ss_pred             CCCCCHHHHHHHHHHH-HccCCHHHHHHHHHHHHHcCCCCCC--HHHHHHHHHHHHhcCCHHHHHHHHHHHHhC---CC-
Q 012111          215 GIECSAVTYNTIIDGY-GKAKKFEEMESSFSAMVESGGCHPD--IFTLNSMISAYGNSGNIEKMEKWYNEFNLM---GV-  287 (471)
Q Consensus       215 g~~~~~~~~~~l~~~~-~~~~~~~~a~~~~~~~~~~~~~~~~--~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~---~~-  287 (471)
                      +-.||+..-|..-.+- .+..+.++|+.-|+++.+..|-+-+  -.....++....+.+++++....|.++...   .+ 
T Consensus        21 ~sEpdVDlENQYYnsK~l~e~~p~~Al~sF~kVlelEgEKgeWGFKALKQmiKI~f~l~~~~eMm~~Y~qlLTYIkSAVT  100 (440)
T KOG1464|consen   21 NSEPDVDLENQYYNSKGLKEDEPKEALSSFQKVLELEGEKGEWGFKALKQMIKINFRLGNYKEMMERYKQLLTYIKSAVT  100 (440)
T ss_pred             CCCCCcchHhhhhccccccccCHHHHHHHHHHHHhcccccchhHHHHHHHHHHHHhccccHHHHHHHHHHHHHHHHHHHh
Confidence            3355554433322211 2345788888888888776533222  234455677788888888888888877431   11 


Q ss_pred             -CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHh----C-CCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCC----
Q 012111          288 -KADIQTLNILTKSYGRAGMYDKMRSVMDFMQK----R-FFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGM----  357 (471)
Q Consensus       288 -~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~----~-~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~----  357 (471)
                       ..+..+.|.++.......+.+-....++.-.+    . +-..-..|-.-|...|...|.+.+..++++++...--    
T Consensus       101 rNySEKsIN~IlDyiStS~~m~LLQ~FYeTTL~ALkdAKNeRLWFKTNtKLgkl~fd~~e~~kl~KIlkqLh~SCq~edG  180 (440)
T KOG1464|consen  101 RNYSEKSINSILDYISTSKNMDLLQEFYETTLDALKDAKNERLWFKTNTKLGKLYFDRGEYTKLQKILKQLHQSCQTEDG  180 (440)
T ss_pred             ccccHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHhhhcceeeeeccchHhhhheeHHHHHHHHHHHHHHHHHhccccC
Confidence             23344556666665555555555444443221    1 0000111223444555555666666666666554310    


Q ss_pred             CCC-------HHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 012111          358 KPN-------SITYCSLVSAYSKAGLIMKVDSILRQVE  388 (471)
Q Consensus       358 ~p~-------~~~~~~li~~~~~~g~~~~a~~~~~~~~  388 (471)
                      .-|       ...|..=|+.|..+.+-.....++++..
T Consensus       181 edD~kKGtQLLEiYAlEIQmYT~qKnNKkLK~lYeqal  218 (440)
T KOG1464|consen  181 EDDQKKGTQLLEIYALEIQMYTEQKNNKKLKALYEQAL  218 (440)
T ss_pred             chhhhccchhhhhHhhHhhhhhhhcccHHHHHHHHHHH
Confidence            111       1234555555555555555555555543

>KOG4077 consensus Cytochrome c oxidase, subunit Va/COX6 [Energy production and conversion]

Probab=87.12  E-value=6.1  Score=29.28  Aligned_cols=46  Identities=13%  Similarity=0.229  Sum_probs=28.1

Q ss_pred             HHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhC
Q 012111          380 VDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKER  425 (471)
Q Consensus       380 a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~  425 (471)
                      ..+-+..+...++.|++.+...-+++|.+.+|+..|.++|+-.+.+
T Consensus        68 vrkglN~l~~yDlVP~pkvIEaaLRA~RRvNDfa~aVRilE~iK~K  113 (149)
T KOG4077|consen   68 VRKGLNNLFDYDLVPSPKVIEAALRACRRVNDFATAVRILEAIKDK  113 (149)
T ss_pred             HHHHHHhhhccccCCChHHHHHHHHHHHHhccHHHHHHHHHHHHHh
Confidence            3344445555566666666666666666666666666666666543

>PF13929 mRNA_stabil: mRNA stabilisation

Probab=86.78  E-value=21  Score=31.20  Aligned_cols=116  Identities=13%  Similarity=0.133  Sum_probs=54.6

Q ss_pred             HHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHh-cC-CHHHHHHHHHHHHH-CCCCCCHHHHHHHHHHHHccCCHHHHHH
Q 012111          165 LDEAFSTINDMKSVSDCKPDVYTYSILIKSCTK-FH-RFDLIEKILAEMSY-LGIECSAVTYNTIIDGYGKAKKFEEMES  241 (471)
Q Consensus       165 ~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~-~~-~~~~a~~~~~~~~~-~g~~~~~~~~~~l~~~~~~~~~~~~a~~  241 (471)
                      +.+|+.+|+.......+--|..+...+++.... .+ ....-.++.+-+.. .|-.++..+...++..+++.+++.+-.+
T Consensus       144 Vv~aL~L~~~~~~~~~Ii~d~evislLL~sMv~~~~~~l~alYEvV~~l~~t~~~~l~~~vi~~Il~~L~~~~dW~kl~~  223 (292)
T PF13929_consen  144 VVEALKLYDGLNPDESIIFDEEVISLLLKSMVIDENTKLNALYEVVDFLVSTFSKSLTRNVIISILEILAESRDWNKLFQ  223 (292)
T ss_pred             HHHHHHHhhccCcccceeeChHHHHHHHHHHHhccccchhhHHHHHHHHHhccccCCChhHHHHHHHHHHhcccHHHHHH
Confidence            344555554322111233445555555555443 11 12222233333322 1234555555566666666666666666


Q ss_pred             HHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHH
Q 012111          242 SFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYN  280 (471)
Q Consensus       242 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~  280 (471)
                      +++......+...|...|..+|......|+..-..++.+
T Consensus       224 fW~~~~~~~~~~~D~rpW~~FI~li~~sgD~~~~~kiI~  262 (292)
T PF13929_consen  224 FWEQCIPNSVPGNDPRPWAEFIKLIVESGDQEVMRKIID  262 (292)
T ss_pred             HHHHhcccCCCCCCCchHHHHHHHHHHcCCHHHHHHHhh
Confidence            665554442334455556666666666666554444443

>KOG0890 consensus Protein kinase of the PI-3 kinase family involved in mitotic growth, DNA repair and meiotic recombination [Signal transduction mechanisms; Chromatin structure and dynamics; Replication, recombination and repair; Cell cycle control, cell division, chromosome partitioning]

Probab=86.75  E-value=66  Score=36.99  Aligned_cols=360  Identities=11%  Similarity=0.045  Sum_probs=180.8

Q ss_pred             HHhhcHHHHHHHHHHhhhccC-ccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHH
Q 012111           89 IKQKKWQLALKIFGLLRQQQW-YQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDE  167 (471)
Q Consensus        89 ~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~  167 (471)
                      .+.+.+.+|+-.++.-..... ..-....|..+...|+..++++...-+...-..     +...+. -|-.....|+++.
T Consensus      1394 frc~~y~RalmylEs~~~~ek~~~~~e~l~fllq~lY~~i~dpDgV~Gv~~~r~a-----~~sl~~-qil~~e~~g~~~d 1467 (2382)
T KOG0890|consen 1394 FRCKAYARALMYLESHRSTEKEKETEEALYFLLQNLYGSIHDPDGVEGVSARRFA-----DPSLYQ-QILEHEASGNWAD 1467 (2382)
T ss_pred             HhhHHHHHHHHHHHHhccccchhHHHHHHHHHHHHHHHhcCCcchhhhHHHHhhc-----CccHHH-HHHHHHhhccHHH
Confidence            467888999999988421110 012233455555589999999988877764221     222333 3444567899999


Q ss_pred             HHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHH-HHHHHHHccCCHHHHHHHHHHH
Q 012111          168 AFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYN-TIIDGYGKAKKFEEMESSFSAM  246 (471)
Q Consensus       168 a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~-~l~~~~~~~~~~~~a~~~~~~~  246 (471)
                      |...|+.+.+..  ++....++-++......|.+..+.-..+-....- .+....++ .-+.+-.+.++++.......  
T Consensus      1468 a~~Cye~~~q~~--p~~~~~~~g~l~sml~~~~l~t~i~~~dg~~~~~-se~~~~~~s~~~eaaW~l~qwD~~e~~l~-- 1542 (2382)
T KOG0890|consen 1468 AAACYERLIQKD--PDKEKHHSGVLKSMLAIQHLSTEILHLDGLIINR-SEEVDELNSLGVEAAWRLSQWDLLESYLS-- 1542 (2382)
T ss_pred             HHHHHHHhhcCC--CccccchhhHHHhhhcccchhHHHhhhcchhhcc-CHHHHHHHHHHHHHHhhhcchhhhhhhhh--
Confidence            999999998732  3346677877777777777777776655554332 22233333 23444467777777666554  


Q ss_pred             HHcCCCCCCHHHHHHH--HHHHHhcC--CHHHHHHHHHHHHhC--------CCCC-CHHHHHHHHHHHHHcCCHHHHHHH
Q 012111          247 VESGGCHPDIFTLNSM--ISAYGNSG--NIEKMEKWYNEFNLM--------GVKA-DIQTLNILTKSYGRAGMYDKMRSV  313 (471)
Q Consensus       247 ~~~~~~~~~~~~~~~l--~~~~~~~~--~~~~a~~~~~~~~~~--------~~~~-~~~~~~~ll~~~~~~~~~~~a~~~  313 (471)
                       ..     +..+|...  .....+..  |.-.-.+..+.+.+.        +..- -...|..+++...-..--.....+
T Consensus      1543 -~~-----n~e~w~~~~~g~~ll~~~~kD~~~~~~~i~~~r~~~i~~lsa~s~~~Sy~~~Y~~~~kLH~l~el~~~~~~l 1616 (2382)
T KOG0890|consen 1543 -DR-----NIEYWSVESIGKLLLRNKKKDEIATLDLIENSRELVIENLSACSIEGSYVRSYEILMKLHLLLELENSIEEL 1616 (2382)
T ss_pred             -cc-----cccchhHHHHHHHHHhhcccchhhHHHHHHHHHHHhhhhHHHhhccchHHHHHHHHHHHHHHHHHHHHHHHh
Confidence             11     11222222  22222222  111111222222211        1110 113344444433222111111111


Q ss_pred             HHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHH-HHHcCCCC-----CHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 012111          314 MDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKK-MKHRGMKP-----NSITYCSLVSAYSKAGLIMKVDSILRQV  387 (471)
Q Consensus       314 ~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~-m~~~~~~p-----~~~~~~~li~~~~~~g~~~~a~~~~~~~  387 (471)
                      ...=......-+..-|..-+..-....+..+-+--+++ +......|     -..+|-...+...+.|.++.|...+-..
T Consensus      1617 ~~~s~~~~s~~~sd~W~~Rl~~tq~s~~~~epILa~RRs~l~~~~~~~~~~~~ge~wLqsAriaR~aG~~q~A~nall~A 1696 (2382)
T KOG0890|consen 1617 KKVSYDEDSANNSDNWKNRLERTQPSFRIKEPILAFRRSMLDLRMRSNLKSRLGECWLQSARIARLAGHLQRAQNALLNA 1696 (2382)
T ss_pred             hccCccccccccchhHHHHHHHhchhHHHHhHHHHHHHHHHHHhccccccchhHHHHHHHHHHHHhcccHHHHHHHHHhh
Confidence            10000000000111122222111111111111111111 11111121     2456777888888899999998877666


Q ss_pred             HhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCC--------HHHHHHHHH---------HHHhcCC--HH
Q 012111          388 ENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPD--------NITFATMIQ---------AYNALGM--TE  448 (471)
Q Consensus       388 ~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~--------~~~~~~l~~---------~~~~~g~--~~  448 (471)
                      .+.+   -...+-.....+...|+...|+.++++-.+.. .|+        +..-+.++.         -....|+  .+
T Consensus      1697 ~e~r---~~~i~~E~AK~lW~~gd~~~Al~~Lq~~l~~~-~~~~~~~~~~~p~~~n~~i~~~~~L~~~~~~~es~n~~s~ 1772 (2382)
T KOG0890|consen 1697 KESR---LPEIVLERAKLLWQTGDELNALSVLQEILSKN-FPDLHTPYTDTPQSVNLLIFKKAKLKITKYLEESGNFESK 1772 (2382)
T ss_pred             hhcc---cchHHHHHHHHHHhhccHHHHHHHHHHHHHhh-cccccCCccccchhhhhhhhhhHHHHHHHHHHHhcchhHH
Confidence            6655   23445566677888899999999998887542 222        222222221         1223344  33


Q ss_pred             HHHHHHHHHHHhhhcCCCCcc
Q 012111          449 AAQNLENKMIAMKENSGKKLI  469 (471)
Q Consensus       449 ~A~~~~~~m~~~~~~~~~~~~  469 (471)
                      ...+.++++.+..+..+++.+
T Consensus      1773 ~ilk~Y~~~~ail~ewe~~hy 1793 (2382)
T KOG0890|consen 1773 DILKYYHDAKAILPEWEDKHY 1793 (2382)
T ss_pred             HHHHHHHHHHHHcccccCcee
Confidence            447888888888876666554

>PF00637 Clathrin: Region in Clathrin and VPS; InterPro: IPR000547 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment

Probab=86.74  E-value=0.15  Score=39.66  Aligned_cols=86  Identities=19%  Similarity=0.187  Sum_probs=56.8

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcC
Q 012111          331 IVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAG  410 (471)
Q Consensus       331 ~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g  410 (471)
                      .++..+.+.+.++....+++.+...+..-+....+.++..|++.+..+...++++....       .-...++..|.+.|
T Consensus        12 ~vi~~~~~~~~~~~l~~yLe~~~~~~~~~~~~~~~~L~~ly~~~~~~~~l~~~L~~~~~-------yd~~~~~~~c~~~~   84 (143)
T PF00637_consen   12 EVISAFEERNQPEELIEYLEALVKENKENNPDLHTLLLELYIKYDPYEKLLEFLKTSNN-------YDLDKALRLCEKHG   84 (143)
T ss_dssp             CCHHHCTTTT-GGGCTCCHHHHHHTSTC-SHHHHHHHHHHHHCTTTCCHHHHTTTSSSS-------S-CTHHHHHHHTTT
T ss_pred             HHHHHHHhCCCHHHHHHHHHHHHhcccccCHHHHHHHHHHHHhcCCchHHHHHcccccc-------cCHHHHHHHHHhcc
Confidence            35666666777777777888777665555677778888888888777777777662211       22245667777777


Q ss_pred             CHHHHHHHHHHHH
Q 012111          411 DVEKMGELFLTMK  423 (471)
Q Consensus       411 ~~~~a~~~~~~~~  423 (471)
                      .+++|.-++.++-
T Consensus        85 l~~~a~~Ly~~~~   97 (143)
T PF00637_consen   85 LYEEAVYLYSKLG   97 (143)
T ss_dssp             SHHHHHHHHHCCT
T ss_pred             hHHHHHHHHHHcc
Confidence            7877777777654

These vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transport []. Clathrin coats contain both clathrin (acts as a scaffold) and adaptor complexes that link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. The two major types of clathrin adaptor complexes are the heterotetrameric adaptor protein (AP) complexes, and the monomeric GGA (Golgi-localising, Gamma-adaptin ear domain homology, ARF-binding proteins) adaptors [, ]. Clathrin is a trimer composed of three heavy chains and three light chains, each monomer projecting outwards like a leg; this three-legged structure is known as a triskelion [, ]. The heavy chains form the legs, their N-terminal beta-propeller regions extending outwards, while their C-terminal alpha-alpha-superhelical regions form the central hub of the triskelion. Peptide motifs can bind between the beta-propeller blades. The light chains appear to have a regulatory role, and may help orient the assembly and disassembly of clathrin coats as they interact with hsc70 uncoating ATPase []. Clathrin triskelia self-polymerise into a curved lattice by twisting individual legs together. The clathrin lattice forms around a vesicle as it buds from the TGN, plasma membrane or endosomes, acting to stabilise the vesicle and facilitate the budding process []. The multiple blades created when the triskelia polymerise are involved in multiple protein interactions, enabling the recruitment of different cargo adaptors and membrane attachment proteins []. This entry represents the 7-fold alpha-alpha-superhelical ARM-type repeat found at the C-terminal of clathrin heavy chains and in VPS (vacuolar protein sorting-associated) proteins. In clathrin heavy chains, the C-terminal 7-fold ARM-type repeats interact to form the central hub of the triskelion. VPS proteins are required for vacuolar assembly and vacuolar traffick, and contain one clathrin-type repeat []. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0006886 intracellular protein transport, 0016192 vesicle-mediated transport; PDB: 3LVH_A 3LVG_C 1B89_A 3QIL_L.

>KOG2396 consensus HAT (Half-A-TPR) repeat-containing protein [General function prediction only]

Probab=86.52  E-value=29  Score=32.75  Aligned_cols=99  Identities=11%  Similarity=0.152  Sum_probs=72.4

Q ss_pred             CCCHHHH-HHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHh--cCCHHHHHHHHHHHHhC-CCCCCHHH
Q 012111          358 KPNSITY-CSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQ--AGDVEKMGELFLTMKER-HCVPDNIT  433 (471)
Q Consensus       358 ~p~~~~~-~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~--~g~~~~a~~~~~~~~~~-~~~p~~~~  433 (471)
                      .|+..++ +.++..+.+.|-..+|..++..+... ++|+...|..+|..-..  .-+...+..+|+.|... |  -|+..
T Consensus       456 ~~~~~tl~s~~l~~~~e~~~~~~ark~y~~l~~l-pp~sl~l~r~miq~e~~~~sc~l~~~r~~yd~a~~~fg--~d~~l  532 (568)
T KOG2396|consen  456 GADSVTLKSKYLDWAYESGGYKKARKVYKSLQEL-PPFSLDLFRKMIQFEKEQESCNLANIREYYDRALREFG--ADSDL  532 (568)
T ss_pred             CCceeehhHHHHHHHHHhcchHHHHHHHHHHHhC-CCccHHHHHHHHHHHhhHhhcCchHHHHHHHHHHHHhC--CChHH
Confidence            4454444 45777788889999999999998887 45588888888764321  22378888999988754 5  68888


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHH
Q 012111          434 FATMIQAYNALGMTEAAQNLENKMIA  459 (471)
Q Consensus       434 ~~~l~~~~~~~g~~~~A~~~~~~m~~  459 (471)
                      |--.+.--...|..+.+-.++.++.+
T Consensus       533 w~~y~~~e~~~g~~en~~~~~~ra~k  558 (568)
T KOG2396|consen  533 WMDYMKEELPLGRPENCGQIYWRAMK  558 (568)
T ss_pred             HHHHHHhhccCCCcccccHHHHHHHH
Confidence            88777766789999888776666554

>KOG4648 consensus Uncharacterized conserved protein, contains LRR repeats [Function unknown]

Probab=85.46  E-value=5.7  Score=35.17  Aligned_cols=92  Identities=15%  Similarity=0.078  Sum_probs=66.6

Q ss_pred             HHHHHcCCHHHHHHHHHHHHhCCCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCH
Q 012111          299 KSYGRAGMYDKMRSVMDFMQKRFFFP-TVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLI  377 (471)
Q Consensus       299 ~~~~~~~~~~~a~~~~~~~~~~~~~~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~  377 (471)
                      +-|.+.|.+++|++.|......  .| +++++..-..+|.+..++..|..--...+..+ ..-...|..-+.+-...|..
T Consensus       105 N~yFKQgKy~EAIDCYs~~ia~--~P~NpV~~~NRA~AYlk~K~FA~AE~DC~~AiaLd-~~Y~KAYSRR~~AR~~Lg~~  181 (536)
T KOG4648|consen  105 NTYFKQGKYEEAIDCYSTAIAV--YPHNPVYHINRALAYLKQKSFAQAEEDCEAAIALD-KLYVKAYSRRMQARESLGNN  181 (536)
T ss_pred             hhhhhccchhHHHHHhhhhhcc--CCCCccchhhHHHHHHHHHHHHHHHHhHHHHHHhh-HHHHHHHHHHHHHHHHHhhH
Confidence            5799999999999999877765  34 78888888899999999988877666665542 22234455555555566777


Q ss_pred             HHHHHHHHHHHhCCCC
Q 012111          378 MKVDSILRQVENSDVI  393 (471)
Q Consensus       378 ~~a~~~~~~~~~~~~~  393 (471)
                      .+|.+-++...+..+.
T Consensus       182 ~EAKkD~E~vL~LEP~  197 (536)
T KOG4648|consen  182 MEAKKDCETVLALEPK  197 (536)
T ss_pred             HHHHHhHHHHHhhCcc
Confidence            7777777777765443

>PRK09687 putative lyase; Provisional

Probab=84.63  E-value=28  Score=30.73  Aligned_cols=234  Identities=12%  Similarity=0.025  Sum_probs=109.7

Q ss_pred             CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCH----HHHHHHHHHHHHcCCCCCCHHH
Q 012111          183 PDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKF----EEMESSFSAMVESGGCHPDIFT  258 (471)
Q Consensus       183 ~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~----~~a~~~~~~~~~~~~~~~~~~~  258 (471)
                      +|.......+.++...|. +.+...+..+...   +|...-...+.++...|+.    .++...+..+...   .++...
T Consensus        35 ~d~~vR~~A~~aL~~~~~-~~~~~~l~~ll~~---~d~~vR~~A~~aLg~lg~~~~~~~~a~~~L~~l~~~---D~d~~V  107 (280)
T PRK09687         35 HNSLKRISSIRVLQLRGG-QDVFRLAIELCSS---KNPIERDIGADILSQLGMAKRCQDNVFNILNNLALE---DKSACV  107 (280)
T ss_pred             CCHHHHHHHHHHHHhcCc-chHHHHHHHHHhC---CCHHHHHHHHHHHHhcCCCccchHHHHHHHHHHHhc---CCCHHH
Confidence            344444444444444443 2222223333322   2444444445555555542    3445555444222   334444


Q ss_pred             HHHHHHHHHhcCCH-----HHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHH
Q 012111          259 LNSMISAYGNSGNI-----EKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVI  333 (471)
Q Consensus       259 ~~~l~~~~~~~~~~-----~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li  333 (471)
                      -...+.++...+..     ..+...+.....   .++..+-...+.++.+.++. .+...+-.+.+.   ++...-...+
T Consensus       108 R~~A~~aLG~~~~~~~~~~~~a~~~l~~~~~---D~~~~VR~~a~~aLg~~~~~-~ai~~L~~~L~d---~~~~VR~~A~  180 (280)
T PRK09687        108 RASAINATGHRCKKNPLYSPKIVEQSQITAF---DKSTNVRFAVAFALSVINDE-AAIPLLINLLKD---PNGDVRNWAA  180 (280)
T ss_pred             HHHHHHHHhcccccccccchHHHHHHHHHhh---CCCHHHHHHHHHHHhccCCH-HHHHHHHHHhcC---CCHHHHHHHH
Confidence            44444444433211     122222222221   23445555556666666653 344444444432   3444444444


Q ss_pred             HHHHhcC-CHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCH
Q 012111          334 ETFGKAG-HIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDV  412 (471)
Q Consensus       334 ~~~~~~g-~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~  412 (471)
                      .++.+.+ +...+...+..+..   .++..+-...+.++.+.|+. .+...+-...+.+   +  .....+.++...|+.
T Consensus       181 ~aLg~~~~~~~~~~~~L~~~L~---D~~~~VR~~A~~aLg~~~~~-~av~~Li~~L~~~---~--~~~~a~~ALg~ig~~  251 (280)
T PRK09687        181 FALNSNKYDNPDIREAFVAMLQ---DKNEEIRIEAIIGLALRKDK-RVLSVLIKELKKG---T--VGDLIIEAAGELGDK  251 (280)
T ss_pred             HHHhcCCCCCHHHHHHHHHHhc---CCChHHHHHHHHHHHccCCh-hHHHHHHHHHcCC---c--hHHHHHHHHHhcCCH
Confidence            5555442 23345555555553   34666666677777777764 3444443333332   1  233566667777774


Q ss_pred             HHHHHHHHHHHhCCCCCCHHHHHHHHHHHH
Q 012111          413 EKMGELFLTMKERHCVPDNITFATMIQAYN  442 (471)
Q Consensus       413 ~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~  442 (471)
                       +|...+..+.+.  .||..+-...+.+|.
T Consensus       252 -~a~p~L~~l~~~--~~d~~v~~~a~~a~~  278 (280)
T PRK09687        252 -TLLPVLDTLLYK--FDDNEIITKAIDKLK  278 (280)
T ss_pred             -hHHHHHHHHHhh--CCChhHHHHHHHHHh
Confidence             577777766653  356666555555543

>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]

Probab=84.56  E-value=51  Score=33.71  Aligned_cols=270  Identities=13%  Similarity=0.041  Sum_probs=129.4

Q ss_pred             HHHHHHHHHhhcHHHHHHHHHHhhhcc--------------CccCCh-----hHHHHHHHHHhcCCCHHHHHHHHHHHHh
Q 012111           82 LEALDEAIKQKKWQLALKIFGLLRQQQ--------------WYQARC-----QTFTKLMVMLGKCKQPEQASLLFEVMLS  142 (471)
Q Consensus        82 ~~~l~~~~~~~~~~~A~~~~~~~~~~~--------------~~~~~~-----~~~~~l~~~~~~~~~~~~a~~~~~~m~~  142 (471)
                      .++++.+++.|+++.|..+++....+-              .+|++.     ...-.-+-......++++|..++.++..
T Consensus       364 ~eAI~hAlaA~d~~~aa~lle~~~~~L~~~~~lsll~~~~~~lP~~~l~~~P~Lvll~aW~~~s~~r~~ea~~li~~l~~  443 (894)
T COG2909         364 SEAIDHALAAGDPEMAADLLEQLEWQLFNGSELSLLLAWLKALPAELLASTPRLVLLQAWLLASQHRLAEAETLIARLEH  443 (894)
T ss_pred             HHHHHHHHhCCCHHHHHHHHHhhhhhhhcccchHHHHHHHHhCCHHHHhhCchHHHHHHHHHHHccChHHHHHHHHHHHH
Confidence            355666667777777777766652110              011111     0111111223456778888888777665


Q ss_pred             CCCCCCH-------HHHHHHHH-HHHhcCCHHHHHHHHHHhhcC---CCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 012111          143 DGLKPSV-------DVYTALVS-AYGQSGLLDEAFSTINDMKSV---SDCKPDVYTYSILIKSCTKFHRFDLIEKILAEM  211 (471)
Q Consensus       143 ~~~~~~~-------~~~~~li~-~~~~~~~~~~a~~~~~~~~~~---~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~  211 (471)
                      .-..|+.       ..++.+-. .....|+++.|.++-+.....   ....+....+..+..+..-.|++++|..+..+.
T Consensus       444 ~l~~~~~~~~~~l~ae~~aL~a~val~~~~~e~a~~lar~al~~L~~~~~~~r~~~~sv~~~a~~~~G~~~~Al~~~~~a  523 (894)
T COG2909         444 FLKAPMHSRQGDLLAEFQALRAQVALNRGDPEEAEDLARLALVQLPEAAYRSRIVALSVLGEAAHIRGELTQALALMQQA  523 (894)
T ss_pred             HhCcCcccchhhHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhcccccchhhhhhhhhhhHHHHHhchHHHHHHHHHHH
Confidence            4222221       12333322 233467778887777666542   112334555666667777778888888877666


Q ss_pred             HHCCCCCCHHHHHH---H--HHHHHccCC--HHHHHHHHHHHHHcCCCC-----CCHHHHHHHHHHHHhc-CCHHHHHHH
Q 012111          212 SYLGIECSAVTYNT---I--IDGYGKAKK--FEEMESSFSAMVESGGCH-----PDIFTLNSMISAYGNS-GNIEKMEKW  278 (471)
Q Consensus       212 ~~~g~~~~~~~~~~---l--~~~~~~~~~--~~~a~~~~~~~~~~~~~~-----~~~~~~~~l~~~~~~~-~~~~~a~~~  278 (471)
                      .+..-.-+...+..   +  ...+...|+  +.+.+..|..........     +-..++..++.++.+. +...++..-
T Consensus       524 ~~~a~~~~~~~l~~~~~~~~s~il~~qGq~~~a~~~~~~~~~~~q~l~q~~~~~f~~~~r~~ll~~~~r~~~~~~ear~~  603 (894)
T COG2909         524 EQMARQHDVYHLALWSLLQQSEILEAQGQVARAEQEKAFNLIREQHLEQKPRHEFLVRIRAQLLRAWLRLDLAEAEARLG  603 (894)
T ss_pred             HHHHHHcccHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhhhcccchhHHHHHHHHHHHHHHHhhhhHHhhhc
Confidence            54422223332222   2  233455663  333333444433221111     1123344444444441 111222222


Q ss_pred             HHHHHhCCCCCCHHHH--HHHHHHHHHcCCHHHHHHHHHHHHhCCCCC----CHHHHHHHHHH--HHhcCCHHHHHHHHH
Q 012111          279 YNEFNLMGVKADIQTL--NILTKSYGRAGMYDKMRSVMDFMQKRFFFP----TVVTYNIVIET--FGKAGHIEKMEEYFK  350 (471)
Q Consensus       279 ~~~~~~~~~~~~~~~~--~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~----~~~~~~~li~~--~~~~g~~~~a~~~~~  350 (471)
                      ++.-......+-...+  ..|+......|+.++|...++++......+    +..+....+..  ....|+.+.+.....
T Consensus       604 ~~~~~~~~~~~~~~~~~~~~LA~l~~~~Gdl~~A~~~l~~~~~l~~~~~~~~~~~a~~~~v~~~lwl~qg~~~~a~~~l~  683 (894)
T COG2909         604 IEVGSVYTPQPLLSRLALSMLAELEFLRGDLDKALAQLDELERLLLNGQYHVDYLAAAYKVKLILWLAQGDKELAAEWLL  683 (894)
T ss_pred             chhhhhcccchhHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHhcCCCCCchHHHHHHHhhHHHhcccCCHHHHHHHHH
Confidence            2222221112222222  366777788888888888887776543322    22222222222  334677776666555


Q ss_pred             H
Q 012111          351 K  351 (471)
Q Consensus       351 ~  351 (471)
                      +
T Consensus       684 ~  684 (894)
T COG2909         684 K  684 (894)
T ss_pred             h
Confidence            4

>KOG0292 consensus Vesicle coat complex COPI, alpha subunit [Intracellular trafficking, secretion, and vesicular transport]

Probab=84.55  E-value=51  Score=33.70  Aligned_cols=94  Identities=13%  Similarity=0.137  Sum_probs=61.3

Q ss_pred             HhcCCHHHHHHHHHHHHhC------CCCcCHHHHHHHHHHHH---------------hcCCHHHHHHHHHHHHhCCCCCC
Q 012111          372 SKAGLIMKVDSILRQVENS------DVILDTPFFNCIISAYG---------------QAGDVEKMGELFLTMKERHCVPD  430 (471)
Q Consensus       372 ~~~g~~~~a~~~~~~~~~~------~~~~~~~~~~~l~~~~~---------------~~g~~~~a~~~~~~~~~~~~~p~  430 (471)
                      ...|.+.+|.+.|+.++-.      +-.-+..-...++..+.               ..+..+.+.++-..+....++|-
T Consensus      1002 tt~gKf~eAie~Frsii~~i~l~vvd~~~e~aea~~li~i~~eYi~gL~~E~~Rr~l~~~~~~~~~ElAaYFt~~~Lqp~ 1081 (1202)
T KOG0292|consen 1002 TTEGKFGEAIEKFRSIIYSIPLLVVDSKEEEAEADELIKICREYIVGLSVELERRKLKKPNLEQQLELAAYFTHCKLQPM 1081 (1202)
T ss_pred             hccCcHHHHHHHHHHHHhheeEEEecchhhHHHHHHHHHHHHHHHhhheeeeeecccCCchHHHHHHHHHHhhcCCCCcH
Confidence            3568999999998886532      11112333334444331               12445556555555556667775


Q ss_pred             HH--HHHHHHHHHHhcCCHHHHHHHHHHHHHhhhcCC
Q 012111          431 NI--TFATMIQAYNALGMTEAAQNLENKMIAMKENSG  465 (471)
Q Consensus       431 ~~--~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~~~  465 (471)
                      ..  +..+.+..+.+.+++..|..+..++++..|.++
T Consensus      1082 H~ilalrtA~n~ffK~kN~ktAs~fa~rLlel~~~~~ 1118 (1202)
T KOG0292|consen 1082 HRILALRTAMNVFFKLKNLKTAAEFARRLLELAPSPP 1118 (1202)
T ss_pred             HHHHHHHHHHHHHHHhccHHHHHHHHHHHHhhCCCCh
Confidence            44  455677889999999999999999999988765

>TIGR03504 FimV_Cterm FimV C-terminal domain

Probab=84.26  E-value=1.6  Score=25.63  Aligned_cols=22  Identities=32%  Similarity=0.513  Sum_probs=11.3

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHH
Q 012111          437 MIQAYNALGMTEAAQNLENKMI  458 (471)
Q Consensus       437 l~~~~~~~g~~~~A~~~~~~m~  458 (471)
                      |.++|...|+.+.|++++++.+
T Consensus         5 LA~ayie~Gd~e~Ar~lL~evl   26 (44)
T TIGR03504         5 LARAYIEMGDLEGARELLEEVI   26 (44)
T ss_pred             HHHHHHHcCChHHHHHHHHHHH
Confidence            3345555555555555555555

This protein is found at the extreme C-terminus of FimV from Pseudomonas aeruginosa, and of TspA of Neisseria meningitidis. Disruption of the former blocks twitching motility from type IV pili; Semmler, et al. suggest a role in peptidoglycan layer remodelling required by type IV fimbrial systems.

>KOG4234 consensus TPR repeat-containing protein [General function prediction only]

Probab=83.91  E-value=22  Score=29.10  Aligned_cols=91  Identities=14%  Similarity=0.027  Sum_probs=42.1

Q ss_pred             HHHcCCHHHHHHHHHHHHhCCCCCC----HHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCC
Q 012111          301 YGRAGMYDKMRSVMDFMQKRFFFPT----VVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGL  376 (471)
Q Consensus       301 ~~~~~~~~~a~~~~~~~~~~~~~~~----~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~  376 (471)
                      +.+.|++++|..-|....+.-....    ...|..-..++.+.+.++.|+.--.+.+..+ +-....+..-..+|.+...
T Consensus       105 ~F~ngdyeeA~skY~~Ale~cp~~~~e~rsIly~Nraaa~iKl~k~e~aI~dcsKaiel~-pty~kAl~RRAeayek~ek  183 (271)
T KOG4234|consen  105 LFKNGDYEEANSKYQEALESCPSTSTEERSILYSNRAAALIKLRKWESAIEDCSKAIELN-PTYEKALERRAEAYEKMEK  183 (271)
T ss_pred             hhhcccHHHHHHHHHHHHHhCccccHHHHHHHHhhhHHHHHHhhhHHHHHHHHHhhHhcC-chhHHHHHHHHHHHHhhhh
Confidence            3444555555554444444311111    1223333444555556666555555555432 1122223333445556666


Q ss_pred             HHHHHHHHHHHHhCCC
Q 012111          377 IMKVDSILRQVENSDV  392 (471)
Q Consensus       377 ~~~a~~~~~~~~~~~~  392 (471)
                      ++.|+.-|+.+.+..+
T Consensus       184 ~eealeDyKki~E~dP  199 (271)
T KOG4234|consen  184 YEEALEDYKKILESDP  199 (271)
T ss_pred             HHHHHHHHHHHHHhCc
Confidence            6666666666665543

>smart00028 TPR Tetratricopeptide repeats

Probab=83.75  E-value=1.9  Score=22.17  Aligned_cols=28  Identities=21%  Similarity=0.275  Sum_probs=14.9

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHhh
Q 012111          434 FATMIQAYNALGMTEAAQNLENKMIAMK  461 (471)
Q Consensus       434 ~~~l~~~~~~~g~~~~A~~~~~~m~~~~  461 (471)
                      |..+...+...|+++.|...++..++..
T Consensus         4 ~~~~a~~~~~~~~~~~a~~~~~~~~~~~   31 (34)
T smart00028        4 LYNLGNAYLKLGDYDEALEYYEKALELD   31 (34)
T ss_pred             HHHHHHHHHHHhhHHHHHHHHHHHHccC
Confidence            3444455555555555555555555443

Repeats present in 4 or more copies in proteins. Contain a minimum of 34 amino acids each and self-associate via a "knobs and holes" mechanism.

>PF13174 TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_A 3URZ_B 2Q7F_A

Probab=83.65  E-value=2.2  Score=22.64  Aligned_cols=25  Identities=24%  Similarity=0.381  Sum_probs=16.5

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHhC
Q 012111          401 CIISAYGQAGDVEKMGELFLTMKER  425 (471)
Q Consensus       401 ~l~~~~~~~g~~~~a~~~~~~~~~~  425 (471)
                      .+..++.+.|++++|.+.|+++++.
T Consensus         5 ~~a~~~~~~g~~~~A~~~~~~~~~~   29 (33)
T PF13174_consen    5 RLARCYYKLGDYDEAIEYFQRLIKR   29 (33)
T ss_dssp             HHHHHHHHHCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHccCHHHHHHHHHHHHHH
Confidence            3455666667777777777776653

>PF06552 TOM20_plant: Plant specific mitochondrial import receptor subunit TOM20; InterPro: IPR010547 This family consists of several plant specific mitochondrial import receptor subunit TOM20 (translocase of outer membrane 20 kDa subunit) proteins

Probab=83.60  E-value=14  Score=29.57  Aligned_cols=32  Identities=9%  Similarity=-0.074  Sum_probs=14.0

Q ss_pred             HHHHHHHHHHhhhccCccCChhHHHHHHHHHhcC
Q 012111           94 WQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKC  127 (471)
Q Consensus        94 ~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  127 (471)
                      +++|+.-|+.+...+  |....++..+..+|...
T Consensus        51 iedAisK~eeAL~I~--P~~hdAlw~lGnA~ts~   82 (186)
T PF06552_consen   51 IEDAISKFEEALKIN--PNKHDALWCLGNAYTSL   82 (186)
T ss_dssp             HHHHHHHHHHHHHH---TT-HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcC--CchHHHHHHHHHHHHHH
Confidence            344444445555432  22335555555555433

Most mitochondrial proteins are encoded by the nuclear genome, and are synthesised in the cytosol. TOM20 is a general import receptor that binds to mitochondrial pre-sequences in the early step of protein import into the mitochondria [].; GO: 0045040 protein import into mitochondrial outer membrane, 0005742 mitochondrial outer membrane translocase complex; PDB: 1ZU2_A.

>PF06552 TOM20_plant: Plant specific mitochondrial import receptor subunit TOM20; InterPro: IPR010547 This family consists of several plant specific mitochondrial import receptor subunit TOM20 (translocase of outer membrane 20 kDa subunit) proteins

Probab=83.55  E-value=17  Score=29.16  Aligned_cols=26  Identities=19%  Similarity=0.249  Sum_probs=10.7

Q ss_pred             HHHHHHHHHHhCCCCCCHHHHHHHHHHH
Q 012111          414 KMGELFLTMKERHCVPDNITFATMIQAY  441 (471)
Q Consensus       414 ~a~~~~~~~~~~~~~p~~~~~~~l~~~~  441 (471)
                      +|.+.|++..+  ..|+..+|+.-+...
T Consensus        98 kA~~~FqkAv~--~~P~ne~Y~ksLe~~  123 (186)
T PF06552_consen   98 KATEYFQKAVD--EDPNNELYRKSLEMA  123 (186)
T ss_dssp             HHHHHHHHHHH--H-TT-HHHHHHHHHH
T ss_pred             HHHHHHHHHHh--cCCCcHHHHHHHHHH
Confidence            33344444433  245555555544443

Most mitochondrial proteins are encoded by the nuclear genome, and are synthesised in the cytosol. TOM20 is a general import receptor that binds to mitochondrial pre-sequences in the early step of protein import into the mitochondria [].; GO: 0045040 protein import into mitochondrial outer membrane, 0005742 mitochondrial outer membrane translocase complex; PDB: 1ZU2_A.

>PF14853 Fis1_TPR_C: Fis1 C-terminal tetratricopeptide repeat; PDB: 1IYG_A 1PC2_A 1NZN_A 3UUX_C 1Y8M_A 2PQR_A 2PQN_A 3O48_A

Probab=83.55  E-value=4.1  Score=25.08  Aligned_cols=33  Identities=21%  Similarity=0.187  Sum_probs=15.9

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHH
Q 012111          403 ISAYGQAGDVEKMGELFLTMKERHCVPDNITFATM  437 (471)
Q Consensus       403 ~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l  437 (471)
                      .-++.+.|++++|.+..+.+.+  +.|+..-...|
T Consensus         8 Aig~ykl~~Y~~A~~~~~~lL~--~eP~N~Qa~~L   40 (53)
T PF14853_consen    8 AIGHYKLGEYEKARRYCDALLE--IEPDNRQAQSL   40 (53)
T ss_dssp             HHHHHHTT-HHHHHHHHHHHHH--HTTS-HHHHHH
T ss_pred             HHHHHHhhhHHHHHHHHHHHHh--hCCCcHHHHHH
Confidence            3345555555555555555555  34555444333

>PF07721 TPR_4: Tetratricopeptide repeat; InterPro: IPR011717 This entry includes tetratricopeptide-like repeats not detected by the IPR001440 from INTERPRO, IPR013105 from INTERPRO and IPR011716 from INTERPRO models

Probab=83.00  E-value=2.1  Score=21.60  Aligned_cols=18  Identities=28%  Similarity=0.292  Sum_probs=9.0

Q ss_pred             HHHHHHhcCCHHHHHHHH
Q 012111          437 MIQAYNALGMTEAAQNLE  454 (471)
Q Consensus       437 l~~~~~~~g~~~~A~~~~  454 (471)
                      +..++...|+.++|..++
T Consensus         7 la~~~~~~G~~~eA~~~l   24 (26)
T PF07721_consen    7 LARALLAQGDPDEAERLL   24 (26)
T ss_pred             HHHHHHHcCCHHHHHHHH
Confidence            344455555555555444

The tetratricopeptide repeat (TPR) motif is a protein-protein interaction module found in multiple copies in a number of functionally different proteins that facilitates specific interactions with a partner protein(s) [].; GO: 0042802 identical protein binding

>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]

Probab=82.82  E-value=60  Score=33.23  Aligned_cols=226  Identities=12%  Similarity=0.043  Sum_probs=120.9

Q ss_pred             HhcCCHHHHHHHHHHHHHCCCCCCHH-------HHHHHH-HHHHccCCHHHHHHHHHHHHHcC---CCCCCHHHHHHHHH
Q 012111          196 TKFHRFDLIEKILAEMSYLGIECSAV-------TYNTII-DGYGKAKKFEEMESSFSAMVESG---GCHPDIFTLNSMIS  264 (471)
Q Consensus       196 ~~~~~~~~a~~~~~~~~~~g~~~~~~-------~~~~l~-~~~~~~~~~~~a~~~~~~~~~~~---~~~~~~~~~~~l~~  264 (471)
                      ....++.+|..++.++...-..|+..       .++.+- ......|++++|.++.+.....-   -..+....+..+..
T Consensus       426 ~s~~r~~ea~~li~~l~~~l~~~~~~~~~~l~ae~~aL~a~val~~~~~e~a~~lar~al~~L~~~~~~~r~~~~sv~~~  505 (894)
T COG2909         426 ASQHRLAEAETLIARLEHFLKAPMHSRQGDLLAEFQALRAQVALNRGDPEEAEDLARLALVQLPEAAYRSRIVALSVLGE  505 (894)
T ss_pred             HHccChHHHHHHHHHHHHHhCcCcccchhhHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhcccccchhhhhhhhhhhH
Confidence            45678899999988876542222211       223222 22345688999999888776542   12345566777888


Q ss_pred             HHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHH-----HHHHHcCCHH--HHHHHHHHHHhCC----C--CCCHHHHHH
Q 012111          265 AYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILT-----KSYGRAGMYD--KMRSVMDFMQKRF----F--FPTVVTYNI  331 (471)
Q Consensus       265 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll-----~~~~~~~~~~--~a~~~~~~~~~~~----~--~~~~~~~~~  331 (471)
                      +..-.|++++|..+..+..+..-..++..+..+.     ..+...|+..  +.+..|.......    .  .+-..++..
T Consensus       506 a~~~~G~~~~Al~~~~~a~~~a~~~~~~~l~~~~~~~~s~il~~qGq~~~a~~~~~~~~~~~q~l~q~~~~~f~~~~r~~  585 (894)
T COG2909         506 AAHIRGELTQALALMQQAEQMARQHDVYHLALWSLLQQSEILEAQGQVARAEQEKAFNLIREQHLEQKPRHEFLVRIRAQ  585 (894)
T ss_pred             HHHHhchHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhhhcccchhHHHHHHH
Confidence            8888999999999888776543333444333222     2345566332  2333333332211    0  011233444


Q ss_pred             HHHHHHhc-CCHHHHHHHHHHHHHcCCCCCHH--HHHHHHHHHHhcCCHHHHHHHHHHHHhCCCC----cCHHHHHHHHH
Q 012111          332 VIETFGKA-GHIEKMEEYFKKMKHRGMKPNSI--TYCSLVSAYSKAGLIMKVDSILRQVENSDVI----LDTPFFNCIIS  404 (471)
Q Consensus       332 li~~~~~~-g~~~~a~~~~~~m~~~~~~p~~~--~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~----~~~~~~~~l~~  404 (471)
                      +..++.+. +...++..-+.--......|-..  .+..|+......|+.++|...++++......    ++...-...+.
T Consensus       586 ll~~~~r~~~~~~ear~~~~~~~~~~~~~~~~~~~~~~LA~l~~~~Gdl~~A~~~l~~~~~l~~~~~~~~~~~a~~~~v~  665 (894)
T COG2909         586 LLRAWLRLDLAEAEARLGIEVGSVYTPQPLLSRLALSMLAELEFLRGDLDKALAQLDELERLLLNGQYHVDYLAAAYKVK  665 (894)
T ss_pred             HHHHHHHHhhhhHHhhhcchhhhhcccchhHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHhcCCCCCchHHHHHHHhh
Confidence            44444442 12222222222222222222222  2236778888899999999988887753322    22222222222


Q ss_pred             --HHHhcCCHHHHHHHHHH
Q 012111          405 --AYGQAGDVEKMGELFLT  421 (471)
Q Consensus       405 --~~~~~g~~~~a~~~~~~  421 (471)
                        .....|+...+.....+
T Consensus       666 ~~lwl~qg~~~~a~~~l~~  684 (894)
T COG2909         666 LILWLAQGDKELAAEWLLK  684 (894)
T ss_pred             HHHhcccCCHHHHHHHHHh
Confidence              23456888777776655

>PF13181 TPR_8: Tetratricopeptide repeat; PDB: 3GW4_B 3MA5_C 2KCV_A 2KCL_A 3FP3_A 3LCA_A 3FP4_A 3FP2_A 1W3B_B 1ELW_A

Probab=82.27  E-value=4.7  Score=21.60  Aligned_cols=27  Identities=30%  Similarity=0.302  Sum_probs=21.1

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 012111          398 FFNCIISAYGQAGDVEKMGELFLTMKE  424 (471)
Q Consensus       398 ~~~~l~~~~~~~g~~~~a~~~~~~~~~  424 (471)
                      +|..+...|...|++++|...|++..+
T Consensus         3 ~~~~lg~~y~~~~~~~~A~~~~~~a~~   29 (34)
T PF13181_consen    3 AYYNLGKIYEQLGDYEEALEYFEKALE   29 (34)
T ss_dssp             HHHHHHHHHHHTTSHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            566777788888888888888887765

...

>KOG1258 consensus mRNA processing protein [RNA processing and modification]

Probab=82.01  E-value=52  Score=31.92  Aligned_cols=356  Identities=10%  Similarity=0.068  Sum_probs=206.5

Q ss_pred             CCchHHHHHHHHHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHh-cCCCHHHHHHHHHHHHhC-CCC-CCHHHH
Q 012111           76 LWPKPVLEALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLG-KCKQPEQASLLFEVMLSD-GLK-PSVDVY  152 (471)
Q Consensus        76 ~~~~~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~-~~~~~~~a~~~~~~m~~~-~~~-~~~~~~  152 (471)
                      ....-+..-...-.+.|..+.+.++|++..+.  ++-+...|...+..+. ..|+.+.....|+..... |.. .+...|
T Consensus        77 l~~gyW~kfA~~E~klg~~~~s~~Vfergv~a--ip~SvdlW~~Y~~f~~n~~~d~~~lr~~fe~A~~~vG~dF~S~~lW  154 (577)
T KOG1258|consen   77 LCYGYWKKFADYEYKLGNAENSVKVFERGVQA--IPLSVDLWLSYLAFLKNNNGDPETLRDLFERAKSYVGLDFLSDPLW  154 (577)
T ss_pred             cHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHh--hhhHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHhcccchhccHHH
Confidence            33444445555556889999999999999875  5778888877766554 458888888999988765 321 256678


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHH---h------cCCHHHHHHHHHHHHH----------
Q 012111          153 TALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCT---K------FHRFDLIEKILAEMSY----------  213 (471)
Q Consensus       153 ~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~---~------~~~~~~a~~~~~~~~~----------  213 (471)
                      ...|.--...+++.....+|+++.+.    |. .-|+.....|.   +      ....+.+.++-.....          
T Consensus       155 dkyie~en~qks~k~v~~iyeRilei----P~-~~~~~~f~~f~~~l~~~~~~~l~~~d~~~~l~~~~~~~~~~~~~~~~  229 (577)
T KOG1258|consen  155 DKYIEFENGQKSWKRVANIYERILEI----PL-HQLNRHFDRFKQLLNQNEEKILLSIDELIQLRSDVAERSKITHSQEP  229 (577)
T ss_pred             HHHHHHHhccccHHHHHHHHHHHHhh----hh-hHhHHHHHHHHHHHhcCChhhhcCHHHHHHHhhhHHhhhhcccccCh
Confidence            88888888888999999999999872    22 12222222221   1      1233333333322221          


Q ss_pred             ----------CCCCCCHH--HHHHHHH-------HHHccCCHHHHHHHHHHHHHcC--CC----CCCHHHHHHHHHHHHh
Q 012111          214 ----------LGIECSAV--TYNTIID-------GYGKAKKFEEMESSFSAMVESG--GC----HPDIFTLNSMISAYGN  268 (471)
Q Consensus       214 ----------~g~~~~~~--~~~~l~~-------~~~~~~~~~~a~~~~~~~~~~~--~~----~~~~~~~~~l~~~~~~  268 (471)
                                .+-+.+..  ..+.+-.       ++-......+..-.|+.-.+..  .+    .++..+|..-+..-..
T Consensus       230 ~e~~~~~v~~~~~~s~~l~~~~~~l~~~~~~~~~~~~~s~~~~~kr~~fE~~IkrpYfhvkpl~~aql~nw~~yLdf~i~  309 (577)
T KOG1258|consen  230 LEELEIGVKDSTDPSKSLTEEKTILKRIVSIHEKVYQKSEEEEEKRWGFEEGIKRPYFHVKPLDQAQLKNWRYYLDFEIT  309 (577)
T ss_pred             hHHHHHHHhhccCccchhhHHHHHHHHHHHHHHHHHHhhHhHHHHHHhhhhhccccccccCcccHHHHHHHHHHhhhhhh
Confidence                      11011110  0111111       1111112222222222222211  11    2345678888888889


Q ss_pred             cCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHH-HHhcCCHHHHHH
Q 012111          269 SGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIET-FGKAGHIEKMEE  347 (471)
Q Consensus       269 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~-~~~~g~~~~a~~  347 (471)
                      .|+.+.+.-+|+...-.- ..=...|-..+.-....|+.+-|..++....+-..+-.+. ...+-.. .-..|++..|..
T Consensus       310 ~g~~~~~~~l~ercli~c-A~Y~efWiky~~~m~~~~~~~~~~~~~~~~~~i~~k~~~~-i~L~~a~f~e~~~n~~~A~~  387 (577)
T KOG1258|consen  310 LGDFSRVFILFERCLIPC-ALYDEFWIKYARWMESSGDVSLANNVLARACKIHVKKTPI-IHLLEARFEESNGNFDDAKV  387 (577)
T ss_pred             cccHHHHHHHHHHHHhHH-hhhHHHHHHHHHHHHHcCchhHHHHHHHhhhhhcCCCCcH-HHHHHHHHHHhhccHHHHHH
Confidence            999999999988875321 1222333334444445588888888877665543332222 2222222 334689999999


Q ss_pred             HHHHHHHcCCCCCHH-HHHHHHHHHHhcCCHHHHH---HHHHHHHhCCCCcCHHHHHHHHH-----HHHhcCCHHHHHHH
Q 012111          348 YFKKMKHRGMKPNSI-TYCSLVSAYSKAGLIMKVD---SILRQVENSDVILDTPFFNCIIS-----AYGQAGDVEKMGEL  418 (471)
Q Consensus       348 ~~~~m~~~~~~p~~~-~~~~li~~~~~~g~~~~a~---~~~~~~~~~~~~~~~~~~~~l~~-----~~~~~g~~~~a~~~  418 (471)
                      +++.+.+.-  |+.. .-..-+....+.|+.+.+.   .++........  +......+.-     .+.-.++.+.|..+
T Consensus       388 ~lq~i~~e~--pg~v~~~l~~~~~e~r~~~~~~~~~~~~l~s~~~~~~~--~~~i~~~l~~~~~r~~~~i~~d~~~a~~~  463 (577)
T KOG1258|consen  388 ILQRIESEY--PGLVEVVLRKINWERRKGNLEDANYKNELYSSIYEGKE--NNGILEKLYVKFARLRYKIREDADLARII  463 (577)
T ss_pred             HHHHHHhhC--CchhhhHHHHHhHHHHhcchhhhhHHHHHHHHhccccc--CcchhHHHHHHHHHHHHHHhcCHHHHHHH
Confidence            999998873  5432 3334455566778888877   33333332211  2222222222     23346889999999


Q ss_pred             HHHHHhCCCCCCHHHHHHHHHHHHhcC
Q 012111          419 FLTMKERHCVPDNITFATMIQAYNALG  445 (471)
Q Consensus       419 ~~~~~~~~~~p~~~~~~~l~~~~~~~g  445 (471)
                      +.++.+. ++++...|..+++.+...+
T Consensus       464 l~~~~~~-~~~~k~~~~~~~~~~~~~~  489 (577)
T KOG1258|consen  464 LLEANDI-LPDCKVLYLELIRFELIQP  489 (577)
T ss_pred             HHHhhhc-CCccHHHHHHHHHHHHhCC
Confidence            9999986 6778888888888776665

>PRK15180 Vi polysaccharide biosynthesis protein TviD; Provisional

Probab=81.93  E-value=46  Score=31.31  Aligned_cols=131  Identities=14%  Similarity=0.033  Sum_probs=74.1

Q ss_pred             hHHHHHHHHHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHH
Q 012111           79 KPVLEALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSA  158 (471)
Q Consensus        79 ~~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~  158 (471)
                      ++....+......|+...|-+-+..+.++.  +-++.............|+++.+.+.+...... +.....+...+++.
T Consensus       290 ~~~~~si~k~~~~gd~~aas~~~~~~lr~~--~~~p~~i~l~~~i~~~lg~ye~~~~~~s~~~~~-~~s~~~~~~~~~r~  366 (831)
T PRK15180        290 REITLSITKQLADGDIIAASQQLFAALRNQ--QQDPVLIQLRSVIFSHLGYYEQAYQDISDVEKI-IGTTDSTLRCRLRS  366 (831)
T ss_pred             hHHHHHHHHHhhccCHHHHHHHHHHHHHhC--CCCchhhHHHHHHHHHhhhHHHHHHHhhchhhh-hcCCchHHHHHHHh
Confidence            445555666667777776655444443332  223333333344456677888877777655432 22345566777777


Q ss_pred             HHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHC
Q 012111          159 YGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYL  214 (471)
Q Consensus       159 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~  214 (471)
                      ....|+++.|..+-+.|.. ..+ .+...........-..|-++++.-.++++...
T Consensus       367 ~~~l~r~~~a~s~a~~~l~-~ei-e~~ei~~iaa~sa~~l~~~d~~~~~wk~~~~~  420 (831)
T PRK15180        367 LHGLARWREALSTAEMMLS-NEI-EDEEVLTVAAGSADALQLFDKSYHYWKRVLLL  420 (831)
T ss_pred             hhchhhHHHHHHHHHHHhc-ccc-CChhheeeecccHHHHhHHHHHHHHHHHHhcc
Confidence            7778888888887777765 222 23333333333333455667777777666544

>TIGR03504 FimV_Cterm FimV C-terminal domain

Probab=81.51  E-value=4  Score=23.92  Aligned_cols=23  Identities=35%  Similarity=0.468  Sum_probs=12.8

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHh
Q 012111          402 IISAYGQAGDVEKMGELFLTMKE  424 (471)
Q Consensus       402 l~~~~~~~g~~~~a~~~~~~~~~  424 (471)
                      |..+|...|+.+.|.+++++...
T Consensus         5 LA~ayie~Gd~e~Ar~lL~evl~   27 (44)
T TIGR03504         5 LARAYIEMGDLEGARELLEEVIE   27 (44)
T ss_pred             HHHHHHHcCChHHHHHHHHHHHH
Confidence            44555555555555555555554

This protein is found at the extreme C-terminus of FimV from Pseudomonas aeruginosa, and of TspA of Neisseria meningitidis. Disruption of the former blocks twitching motility from type IV pili; Semmler, et al. suggest a role in peptidoglycan layer remodelling required by type IV fimbrial systems.

>PF00637 Clathrin: Region in Clathrin and VPS; InterPro: IPR000547 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment

Probab=81.49  E-value=0.48  Score=36.80  Aligned_cols=128  Identities=14%  Similarity=0.129  Sum_probs=81.7

Q ss_pred             HHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCC
Q 012111          297 LTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGL  376 (471)
Q Consensus       297 ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~  376 (471)
                      ++..+.+.+.++....+++.+...+...+....+.++..|++.++.++..++++.   .    +..-...++..|.+.|.
T Consensus        13 vi~~~~~~~~~~~l~~yLe~~~~~~~~~~~~~~~~L~~ly~~~~~~~~l~~~L~~---~----~~yd~~~~~~~c~~~~l   85 (143)
T PF00637_consen   13 VISAFEERNQPEELIEYLEALVKENKENNPDLHTLLLELYIKYDPYEKLLEFLKT---S----NNYDLDKALRLCEKHGL   85 (143)
T ss_dssp             CHHHCTTTT-GGGCTCCHHHHHHTSTC-SHHHHHHHHHHHHCTTTCCHHHHTTTS---S----SSS-CTHHHHHHHTTTS
T ss_pred             HHHHHHhCCCHHHHHHHHHHHHhcccccCHHHHHHHHHHHHhcCCchHHHHHccc---c----cccCHHHHHHHHHhcch
Confidence            5677777888999999999999877666788999999999999888888888771   1    11333556677777777


Q ss_pred             HHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCC
Q 012111          377 IMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAYNALGM  446 (471)
Q Consensus       377 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~  446 (471)
                      ++++.-++.++....-.         +..+...++++.|.+++.   +   .++...|..++..|...++
T Consensus        86 ~~~a~~Ly~~~~~~~~a---------l~i~~~~~~~~~a~e~~~---~---~~~~~l~~~l~~~~l~~~~  140 (143)
T PF00637_consen   86 YEEAVYLYSKLGNHDEA---------LEILHKLKDYEEAIEYAK---K---VDDPELWEQLLKYCLDSKP  140 (143)
T ss_dssp             HHHHHHHHHCCTTHTTC---------SSTSSSTHCSCCCTTTGG---G---CSSSHHHHHHHHHHCTSTC
T ss_pred             HHHHHHHHHHcccHHHH---------HHHHHHHccHHHHHHHHH---h---cCcHHHHHHHHHHHHhcCc
Confidence            77766666553322111         111223344444442221   1   2467888888888776654

These vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transport []. Clathrin coats contain both clathrin (acts as a scaffold) and adaptor complexes that link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. The two major types of clathrin adaptor complexes are the heterotetrameric adaptor protein (AP) complexes, and the monomeric GGA (Golgi-localising, Gamma-adaptin ear domain homology, ARF-binding proteins) adaptors [, ]. Clathrin is a trimer composed of three heavy chains and three light chains, each monomer projecting outwards like a leg; this three-legged structure is known as a triskelion [, ]. The heavy chains form the legs, their N-terminal beta-propeller regions extending outwards, while their C-terminal alpha-alpha-superhelical regions form the central hub of the triskelion. Peptide motifs can bind between the beta-propeller blades. The light chains appear to have a regulatory role, and may help orient the assembly and disassembly of clathrin coats as they interact with hsc70 uncoating ATPase []. Clathrin triskelia self-polymerise into a curved lattice by twisting individual legs together. The clathrin lattice forms around a vesicle as it buds from the TGN, plasma membrane or endosomes, acting to stabilise the vesicle and facilitate the budding process []. The multiple blades created when the triskelia polymerise are involved in multiple protein interactions, enabling the recruitment of different cargo adaptors and membrane attachment proteins []. This entry represents the 7-fold alpha-alpha-superhelical ARM-type repeat found at the C-terminal of clathrin heavy chains and in VPS (vacuolar protein sorting-associated) proteins. In clathrin heavy chains, the C-terminal 7-fold ARM-type repeats interact to form the central hub of the triskelion. VPS proteins are required for vacuolar assembly and vacuolar traffick, and contain one clathrin-type repeat []. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0006886 intracellular protein transport, 0016192 vesicle-mediated transport; PDB: 3LVH_A 3LVG_C 1B89_A 3QIL_L.

>PF04097 Nic96: Nup93/Nic96; InterPro: IPR007231 Nup93/Nic96 is a component of the nuclear pore complex

Probab=81.32  E-value=62  Score=32.42  Aligned_cols=42  Identities=17%  Similarity=0.214  Sum_probs=25.4

Q ss_pred             HHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhc
Q 012111          155 LVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKF  198 (471)
Q Consensus       155 li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~  198 (471)
                      +|-.|.+.|++++|.++......  ........+...+..|...
T Consensus       117 ~Iyy~LR~G~~~~A~~~~~~~~~--~~~~~~~~f~~~l~~~~~s  158 (613)
T PF04097_consen  117 LIYYCLRCGDYDEALEVANENRN--QFQKIERSFPTYLKAYASS  158 (613)
T ss_dssp             HHHHHHTTT-HHHHHHHHHHTGG--GS-TTTTHHHHHHHHCTTT
T ss_pred             HHHHHHhcCCHHHHHHHHHHhhh--hhcchhHHHHHHHHHHHhC
Confidence            44556788888888888865554  2344445566667766654

It is required for the correct assembly of the nuclear pore complex []. In Saccharomyces cerevisiae, Nic96 has been shown to be involved in the distribution and cellular concentration of the GTPase Gsp1 []. The structure of Nic96 has revealed a mostly alpha helical structure [].; GO: 0006810 transport, 0005643 nuclear pore; PDB: 2QX5_B 2RFO_A.

>KOG0890 consensus Protein kinase of the PI-3 kinase family involved in mitotic growth, DNA repair and meiotic recombination [Signal transduction mechanisms; Chromatin structure and dynamics; Replication, recombination and repair; Cell cycle control, cell division, chromosome partitioning]

Probab=81.07  E-value=1.1e+02  Score=35.28  Aligned_cols=319  Identities=12%  Similarity=0.066  Sum_probs=163.4

Q ss_pred             HHHHHHhcCCCHHHHHHHHHHHHhCCC--CCCHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHH
Q 012111          119 KLMVMLGKCKQPEQASLLFEVMLSDGL--KPSVDVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCT  196 (471)
Q Consensus       119 ~l~~~~~~~~~~~~a~~~~~~m~~~~~--~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~  196 (471)
                      .+..+-.+++.+..|...++.-.....  ......|-.+...|+..+++|....+......    .|+  .+. -|....
T Consensus      1388 tLa~aSfrc~~y~RalmylEs~~~~ek~~~~~e~l~fllq~lY~~i~dpDgV~Gv~~~r~a----~~s--l~~-qil~~e 1460 (2382)
T KOG0890|consen 1388 TLARASFRCKAYARALMYLESHRSTEKEKETEEALYFLLQNLYGSIHDPDGVEGVSARRFA----DPS--LYQ-QILEHE 1460 (2382)
T ss_pred             HHHHHHHhhHHHHHHHHHHHHhccccchhHHHHHHHHHHHHHHHhcCCcchhhhHHHHhhc----Ccc--HHH-HHHHHH
Confidence            445566678888888888888421111  11223344455588888888887777664222    222  222 333456


Q ss_pred             hcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHH-HHHHHhcCCHHHH
Q 012111          197 KFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSM-ISAYGNSGNIEKM  275 (471)
Q Consensus       197 ~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l-~~~~~~~~~~~~a  275 (471)
                      ..|++..|...|+.+.+.+ ++...+++.++......|.++.+.-..+-....  ..+....++.+ +.+--+.+++|..
T Consensus      1461 ~~g~~~da~~Cye~~~q~~-p~~~~~~~g~l~sml~~~~l~t~i~~~dg~~~~--~se~~~~~~s~~~eaaW~l~qwD~~ 1537 (2382)
T KOG0890|consen 1461 ASGNWADAAACYERLIQKD-PDKEKHHSGVLKSMLAIQHLSTEILHLDGLIIN--RSEEVDELNSLGVEAAWRLSQWDLL 1537 (2382)
T ss_pred             hhccHHHHHHHHHHhhcCC-CccccchhhHHHhhhcccchhHHHhhhcchhhc--cCHHHHHHHHHHHHHHhhhcchhhh
Confidence            6789999999999998775 444777888887777788888877765555433  13333333333 3444567777766


Q ss_pred             HHHHHHHHhCCCCCCHHHHHH--HHHHHHHcCCHH--HHHHHHHHHHhCCCCC---------CHHHHHHHHHHHHhcCCH
Q 012111          276 EKWYNEFNLMGVKADIQTLNI--LTKSYGRAGMYD--KMRSVMDFMQKRFFFP---------TVVTYNIVIETFGKAGHI  342 (471)
Q Consensus       276 ~~~~~~~~~~~~~~~~~~~~~--ll~~~~~~~~~~--~a~~~~~~~~~~~~~~---------~~~~~~~li~~~~~~g~~  342 (471)
                      .....   ..    +..+|..  +.....+...-|  .-.+..+.+++.-+.|         =...|..++....-..  
T Consensus      1538 e~~l~---~~----n~e~w~~~~~g~~ll~~~~kD~~~~~~~i~~~r~~~i~~lsa~s~~~Sy~~~Y~~~~kLH~l~e-- 1608 (2382)
T KOG0890|consen 1538 ESYLS---DR----NIEYWSVESIGKLLLRNKKKDEIATLDLIENSRELVIENLSACSIEGSYVRSYEILMKLHLLLE-- 1608 (2382)
T ss_pred             hhhhh---cc----cccchhHHHHHHHHHhhcccchhhHHHHHHHHHHHhhhhHHHhhccchHHHHHHHHHHHHHHHH--
Confidence            66554   11    1111111  222222222211  1112233222221110         0123333333222111  


Q ss_pred             HHHHHHHHHHHHcCCCCCHH------HHHHHHHHHHhcCCHHHHHHHHHH-HHhCCCCc-----CHHHHHHHHHHHHhcC
Q 012111          343 EKMEEYFKKMKHRGMKPNSI------TYCSLVSAYSKAGLIMKVDSILRQ-VENSDVIL-----DTPFFNCIISAYGQAG  410 (471)
Q Consensus       343 ~~a~~~~~~m~~~~~~p~~~------~~~~li~~~~~~g~~~~a~~~~~~-~~~~~~~~-----~~~~~~~l~~~~~~~g  410 (471)
                        -....+...  +..++..      -|..-+..-....+..+-.--+++ +......|     -..+|-...+....+|
T Consensus      1609 --l~~~~~~l~--~~s~~~~s~~~sd~W~~Rl~~tq~s~~~~epILa~RRs~l~~~~~~~~~~~~ge~wLqsAriaR~aG 1684 (2382)
T KOG0890|consen 1609 --LENSIEELK--KVSYDEDSANNSDNWKNRLERTQPSFRIKEPILAFRRSMLDLRMRSNLKSRLGECWLQSARIARLAG 1684 (2382)
T ss_pred             --HHHHHHHhh--ccCccccccccchhHHHHHHHhchhHHHHhHHHHHHHHHHHHhccccccchhHHHHHHHHHHHHhcc
Confidence              111111111  1222211      111111111111111111111111 11111111     2457888888888899


Q ss_pred             CHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhhhc
Q 012111          411 DVEKMGELFLTMKERHCVPDNITFATMIQAYNALGMTEAAQNLENKMIAMKEN  463 (471)
Q Consensus       411 ~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~  463 (471)
                      .++.|...+-...+.+ .  +..+--..+-++..|+...|..++++.++..-.
T Consensus      1685 ~~q~A~nall~A~e~r-~--~~i~~E~AK~lW~~gd~~~Al~~Lq~~l~~~~~ 1734 (2382)
T KOG0890|consen 1685 HLQRAQNALLNAKESR-L--PEIVLERAKLLWQTGDELNALSVLQEILSKNFP 1734 (2382)
T ss_pred             cHHHHHHHHHhhhhcc-c--chHHHHHHHHHHhhccHHHHHHHHHHHHHhhcc
Confidence            9999998887777654 2  334444567789999999999999999865543

>PF13762 MNE1: Mitochondrial splicing apparatus component

Probab=80.57  E-value=24  Score=27.24  Aligned_cols=47  Identities=15%  Similarity=0.147  Sum_probs=22.7

Q ss_pred             HHHHHHHHHHHhcCC-HHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHc
Q 012111          186 YTYSILIKSCTKFHR-FDLIEKILAEMSYLGIECSAVTYNTIIDGYGK  232 (471)
Q Consensus       186 ~~~~~ll~~~~~~~~-~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~  232 (471)
                      ..|..++.+..+... ---+..+|..|.+.+.+.+..-|..++.++.+
T Consensus        80 ssf~~if~SlsnSsSaK~~~~~Lf~~Lk~~~~~~t~~dy~~li~~~l~  127 (145)
T PF13762_consen   80 SSFHIIFKSLSNSSSAKLTSLTLFNFLKKNDIEFTPSDYSCLIKAALR  127 (145)
T ss_pred             chHHHHHHHHccChHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHc
Confidence            345555555544433 23344455555554455555555555555443

>PF11846 DUF3366: Domain of unknown function (DUF3366); InterPro: IPR021797 This domain is functionally uncharacterised

Probab=80.39  E-value=11  Score=30.91  Aligned_cols=35  Identities=20%  Similarity=0.201  Sum_probs=23.0

Q ss_pred             CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhhh
Q 012111          428 VPDNITFATMIQAYNALGMTEAAQNLENKMIAMKE  462 (471)
Q Consensus       428 ~p~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~  462 (471)
                      .|++.+|..++.++...|+.++|.+..+++...-|
T Consensus       141 ~P~~~~~~~~a~~l~~~G~~~eA~~~~~~~~~lyP  175 (193)
T PF11846_consen  141 RPDPNVYQRYALALALLGDPEEARQWLARARRLYP  175 (193)
T ss_pred             CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC
Confidence            56666666666666666666666666666665555

This domain is found in bacteria. This presumed domain is about 200 amino acids in length.

>PF07163 Pex26: Pex26 protein; InterPro: IPR010797 This family consists of Pex26 and related mammalian proteins

Probab=80.13  E-value=39  Score=29.35  Aligned_cols=87  Identities=17%  Similarity=0.186  Sum_probs=55.3

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHh----
Q 012111          263 ISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGK----  338 (471)
Q Consensus       263 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~----  338 (471)
                      |++++..|++.+++.+.-+.-+..-+.........|-.|.+.+++..+.++-......--.-+...|..+++.|..    
T Consensus        90 IQALAEmnrWreVLsWvlqyYq~pEklPpkIleLCILLysKv~Ep~amlev~~~WL~~p~Nq~lp~y~~vaELyLl~VLl  169 (309)
T PF07163_consen   90 IQALAEMNRWREVLSWVLQYYQVPEKLPPKILELCILLYSKVQEPAAMLEVASAWLQDPSNQSLPEYGTVAELYLLHVLL  169 (309)
T ss_pred             HHHHHHHhhHHHHHHHHHHHhcCcccCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHhCcccCCchhhHHHHHHHHHHHHh
Confidence            6777777888777766555433222334445556666777888888777777766654333344457777666654    


Q ss_pred             -cCCHHHHHHHH
Q 012111          339 -AGHIEKMEEYF  349 (471)
Q Consensus       339 -~g~~~~a~~~~  349 (471)
                       .|.+++|.++.
T Consensus       170 PLG~~~eAeelv  181 (309)
T PF07163_consen  170 PLGHFSEAEELV  181 (309)
T ss_pred             ccccHHHHHHHH
Confidence             57888887766

Pex26 is a type II peroxisomal membrane protein that recruits Pex6-Pex1 complexes to peroxisomes []. Mutations in Pex26 can lead to human disorders [].; GO: 0032403 protein complex binding, 0045046 protein import into peroxisome membrane, 0005779 integral to peroxisomal membrane

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	471
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	1e-16
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	3e-15
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	3e-15
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	1e-14
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-11
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-09

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens} Length = 1134

 Score = 81.8 bits (200), Expect = 1e-16
 Identities = 25/223 (11%), Positives = 72/223 (32%), Gaps = 4/223 (1%)

Query: 239 MESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILT 298
           M              P    L  ++       +++  +    + +   +    Q L    
Sbjct: 75  MAGCLEDCTRQAPESPWEEQLARLLQEAPGKLSLDVEQAPSGQHSQAQLSGQQQRLLAFF 134

Query: 299 KSYGRAGMYDKMRSVMDFMQKRF---FFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHR 355
           K             ++     +       T+  YN V+  + + G  +++      +K  
Sbjct: 135 KCCLLTDQLPLAHHLLVVHHGQRQKRKLLTLDMYNAVMLGWARQGAFKELVYVLFMVKDA 194

Query: 356 GMKPNSITYCSLVSAYSKAGLIMK-VDSILRQVENSDVILDTPFFNCIISAYGQAGDVEK 414
           G+ P+ ++Y + +    +       ++  L Q+    + L   F   ++S   +A  ++ 
Sbjct: 195 GLTPDLLSYAAALQCMGRQDQDAGTIERCLEQMSQEGLKLQALFTAVLLSEEDRATVLKA 254

Query: 415 MGELFLTMKERHCVPDNITFATMIQAYNALGMTEAAQNLENKM 457
           + ++  T      +P  +  + +++   A     +   L   +
Sbjct: 255 VHKVKPTFSLPPQLPPPVNTSKLLRDVYAKDGRVSYPKLHLPL 297

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens} Length = 1134

 Score = 77.9 bits (190), Expect = 3e-15
 Identities = 29/239 (12%), Positives = 72/239 (30%), Gaps = 11/239 (4%)

Query: 229 GYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVK 288
                K   ++E + S              L +       +  +          +    K
Sbjct: 100 QEAPGKLSLDVEQAPSGQHSQAQLSGQQQRLLAFFKCCLLTDQLPLAHHLLVVHHGQRQK 159

Query: 289 ---ADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKM 345
                +   N +   + R G + ++  V+  ++     P +++Y   ++  G+       
Sbjct: 160 RKLLTLDMYNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAAALQCMGRQDQDAGT 219

Query: 346 -EEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIIS 404
            E   ++M   G+K  ++    L+S   +A ++  V  +         +      + ++ 
Sbjct: 220 IERCLEQMSQEGLKLQALFTAVLLSEEDRATVLKAVHKVKPTFSLPPQLPPPVNTSKLLR 279

Query: 405 AYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAYNALGMTEAAQNLENKMIAMKEN 463
                       +L L +K   C+          Q +  L       ++E   +  KE 
Sbjct: 280 DVYAKDGRVSYPKLHLPLKTLQCLF-------EKQLHMELASRVCVVSVEKPTLPSKEV 331

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens} Length = 1134

 Score = 77.5 bits (189), Expect = 3e-15
 Identities = 31/278 (11%), Positives = 79/278 (28%), Gaps = 6/278 (2%)

Query: 52  SKILRTEFAIKNIEKKVSSKKYKNLWPKPVLEALDEAIKQKKWQLALKIFGLL---RQQQ 108
           +KIL  +   + +  +    K +  +     +AL   ++ +   L+ ++ G L    +Q 
Sbjct: 27  AKILEKDKRTQQMRMQRLKAKLQMPFQSGEFKALTRRLQVEPRLLSKQMAGCLEDCTRQA 86

Query: 109 WYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEA 168
                 +   +L+         +             L        A       +  L  A
Sbjct: 87  PESPWEEQLARLLQEAPGKLSLDVEQAPSGQHSQAQLSGQQQRLLAFFKCCLLTDQLPLA 146

Query: 169 FSTINDMKS--VSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTI 226
              +              +  Y+ ++    +   F  +  +L  +   G+    ++Y   
Sbjct: 147 HHLLVVHHGQRQKRKLLTLDMYNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAAA 206

Query: 227 IDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMG 286
           +   G+  +           +   G          ++S    +  ++ + K    F+L  
Sbjct: 207 LQCMGRQDQDAGTIERCLEQMSQEGLKLQALFTAVLLSEEDRATVLKAVHKVKPTFSLPP 266

Query: 287 VKADIQ-TLNILTKSYGRAGMYDKMRSVMDFMQKRFFF 323
                  T  +L   Y + G     +  +     +  F
Sbjct: 267 QLPPPVNTSKLLRDVYAKDGRVSYPKLHLPLKTLQCLF 304

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens} Length = 1134

 Score = 76.0 bits (185), Expect = 1e-14
 Identities = 56/455 (12%), Positives = 136/455 (29%), Gaps = 18/455 (3%)

Query: 27  RIQAIKRSPGPIQELGIQKEAEKDLSKILRT-EFAIKNIEKKVSSKKYKNLWPKPVLEAL 85
           R+Q +K       + G  K   + L    R     +    +  + +  ++ W + +   L
Sbjct: 40  RMQRLKAKLQMPFQSGEFKALTRRLQVEPRLLSKQMAGCLEDCTRQAPESPWEEQLARLL 99

Query: 86  DEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEV---MLS 142
            EA  +    +     G   Q Q    + Q             Q   A  L  V      
Sbjct: 100 QEAPGKLSLDVEQAPSGQHSQAQ-LSGQQQRLLAFFKCCLLTDQLPLAHHLLVVHHGQRQ 158

Query: 143 DGLKPSVDVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFD 202
                ++D+Y A++  + + G   E    +  +K  +   PD+ +Y+  ++   +  +  
Sbjct: 159 KRKLLTLDMYNAVMLGWARQGAFKELVYVLFMVKD-AGLTPDLLSYAAALQCMGRQDQDA 217

Query: 203 -LIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNS 261
             IE+ L +MS  G++  A+    ++    +A   + +              P + T   
Sbjct: 218 GTIERCLEQMSQEGLKLQALFTAVLLSEEDRATVLKAVHKVKPTFSLPPQLPPPVNTSKL 277

Query: 262 MISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRF 321
           +   Y   G +   +               + L++   S       +K       ++   
Sbjct: 278 LRDVYAKDGRVSYPKLHLPLKT--LQCLFEKQLHMELASRVCVVSVEKPTLPSKEVKHAR 335

Query: 322 FFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMK-V 380
                +               +   E         + P    +  L+       ++++ +
Sbjct: 336 KTLKTLRDQWEKALCRALRETKNRLEREVYEGRFSLYP----FLCLLDEREVVRMLLQVL 391

Query: 381 DSILRQVENS----DVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFAT 436
            ++  Q E+       +    F   ++     +G V+ +   +            +    
Sbjct: 392 QALPAQGESFTTLARELSARTFSRHVVQRQRVSGQVQALQNHYRKYLCLLASDAEVPEPC 451

Query: 437 MIQAYNALGMTEAAQNLENKMIAMKENSGKKLIQC 471
           + + Y        A   +   + ++   GK L + 
Sbjct: 452 LPRQYWEALGAPEALREQPWPLPVQMELGKLLAEM 486

>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 = 65.3 bits (158), Expect = 2e-11
 Identities = 93/587 (15%), Positives = 175/587 (29%), Gaps = 208/587 (35%)

Query: 40  ELGIQKEAEKDLSKILRTEFAIKNIE-KKVSSKKYKNLWPKPVL--EALDEAIKQK-KWQ 95
           E G  +   KD+  +    F + N + K V         PK +L  E +D  I  K    
Sbjct: 10  ETGEHQYQYKDILSVFEDAF-VDNFDCKDVQD------MPKSILSKEEIDHIIMSKDAVS 62

Query: 96  LALKIFGLLRQQQ-----------------WYQARCQTFTKLMVMLGKCKQPEQASLLF- 137
             L++F  L  +Q                 +  +  +T         + +QP   + ++ 
Sbjct: 63  GTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKT---------EQRQPSMMTRMYI 113

Query: 138 ---EVMLSDG----------LKPSVDVYTAL--------VSAYGQSG----------LLD 166
              + + +D           L+P + +  AL        V   G  G           L 
Sbjct: 114 EQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLS 173

Query: 167 EAFSTINDMK----SVSDCKPDVYTYSILIKSCTKF---------------HRFDLIE-- 205
                  D K    ++ +C        +L K   +                 R   I+  
Sbjct: 174 YKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAE 233

Query: 206 --KILAEMSY------------------LGIECSA-VT--YNTIIDGYGKAKKF------ 236
             ++L    Y                    + C   +T  +  + D    A         
Sbjct: 234 LRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDH 293

Query: 237 -------EEMESSFSAMV---------ESGGCHPDIFTLNSMISAYGNSGNIEKMEKW-- 278
                  +E++S     +         E    +P    L S+I+        + +  W  
Sbjct: 294 HSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNP--RRL-SIIAES----IRDGLATWDN 346

Query: 279 YNEFNLMGVKADIQ-TLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNI---VIE 334
           +   N   +   I+ +LN+L  +  R  M+D++            FP     +I   ++ 
Sbjct: 347 WKHVNCDKLTTIIESSLNVLEPAEYRK-MFDRL----------SVFPPSA--HIPTILLS 393

Query: 335 TFGKAGHIEKMEEYFKKMKHRGM---KPNSITYCSLVSAYSKAGLIMKVD---------- 381
                     +     K+    +   +P   T  S+ S Y +  L +K++          
Sbjct: 394 LIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTI-SIPSIYLE--LKVKLENEYALHRSIV 450

Query: 382 ---SILRQVENSDVI---LDTPFFNCIISAY--GQAGDVEKMGEL--------FLTMKER 425
              +I +  ++ D+I   LD  F++ I   +        E+M           FL  K R
Sbjct: 451 DHYNIPKTFDSDDLIPPYLDQYFYSHI--GHHLKNIEHPERMTLFRMVFLDFRFLEQKIR 508

Query: 426 HCVPDNITFATMIQAYNALG-MTEAAQNLEN--KMIAMKENSGKKLI 469
           H             A+NA G +    Q L+     I   +   ++L+
Sbjct: 509 HDST----------AWNASGSILNTLQQLKFYKPYICDNDPKYERLV 545

>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 = 57.9 bits (139), Expect = 4e-09
 Identities = 55/366 (15%), Positives = 104/366 (28%), Gaps = 115/366 (31%)

Query: 44  QKEAEKDLSKILRTEFAIKNIEKKVSSKKYK-------NLWPKPVLEALDEAIKQK---- 92
              ++   +  LR       + + + SK Y+       N+       A +  +  K    
Sbjct: 214 TSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFN--LSCKILLT 271

Query: 93  --KWQLALKIFGLLRQQQWYQARCQTFTK--LMVMLGKC------KQPEQA--------S 134
               Q+   +               T T   +  +L K         P +         S
Sbjct: 272 TRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLS 331

Query: 135 LLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVY-------- 186
           ++ E  + DGL        A    +       +  +TI +  S++  +P  Y        
Sbjct: 332 IIAE-SIRDGL--------ATWDNWKHVNC--DKLTTIIES-SLNVLEPAEYRKMFDRLS 379

Query: 187 -----------TYSIL----IKSC-----TKFHRFDLIEKILAEMSY--------LGIEC 218
                        S++    IKS       K H++ L+EK   E +         L ++ 
Sbjct: 380 VFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKL 439

Query: 219 SAVTY--NTIIDGYGKAKKFEEMESSFSAMVESG------GCHPDIFTLNSMISAYGNSG 270
                   +I+D Y   K F+                   G H         +    +  
Sbjct: 440 ENEYALHRSIVDHYNIPKTFD--SDDLIPPYLDQYFYSHIGHH---------LKNIEHPE 488

Query: 271 NIEKMEKWYNEFNLMGVK---------ADIQTLNILT--KSYGR-----AGMYDKM-RSV 313
            +      + +F  +  K         A    LN L   K Y          Y+++  ++
Sbjct: 489 RMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAI 548

Query: 314 MDFMQK 319
           +DF+ K
Sbjct: 549 LDFLPK 554

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	471
2xpi_A	597	Anaphase-promoting complex subunit CUT9; cell cycl	100.0
2xpi_A	597	Anaphase-promoting complex subunit CUT9; cell cycl	100.0
1w3b_A	388	UDP-N-acetylglucosamine--peptide N-acetylglucosami	100.0
4g26_A	501	Pentatricopeptide repeat-containing protein AT2G3	100.0
4g26_A	501	Pentatricopeptide repeat-containing protein AT2G3	100.0
1w3b_A	388	UDP-N-acetylglucosamine--peptide N-acetylglucosami	99.98
2gw1_A	514	Mitochondrial precursor proteins import receptor;	99.95
2y4t_A	450	DNAJ homolog subfamily C member 3; chaperone, endo	99.95
2y4t_A	450	DNAJ homolog subfamily C member 3; chaperone, endo	99.95
3fp2_A	537	TPR repeat-containing protein YHR117W; TOM71, mito	99.93
2gw1_A	514	Mitochondrial precursor proteins import receptor;	99.93
3ieg_A	359	DNAJ homolog subfamily C member 3; TPR motif, chap	99.91
3ieg_A	359	DNAJ homolog subfamily C member 3; TPR motif, chap	99.91
3fp2_A	537	TPR repeat-containing protein YHR117W; TOM71, mito	99.9
2xm6_A	490	Protein corresponding to locus C5321 from CFT073 s	99.88
3hym_B	330	Cell division cycle protein 16 homolog; APC, anaph	99.88
3hym_B	330	Cell division cycle protein 16 homolog; APC, anaph	99.87
1fch_A	368	Peroxisomal targeting signal 1 receptor; protein-p	99.87
2ooe_A	530	Cleavage stimulation factor 77 kDa subunit; HAT do	99.85
4eqf_A	365	PEX5-related protein; accessory protein, tetratric	99.85
1fch_A	368	Peroxisomal targeting signal 1 receptor; protein-p	99.84
2xm6_A	490	Protein corresponding to locus C5321 from CFT073 s	99.82
3cv0_A	327	Peroxisome targeting signal 1 receptor PEX5; TPR m	99.82
4eqf_A	365	PEX5-related protein; accessory protein, tetratric	99.82
3cv0_A	327	Peroxisome targeting signal 1 receptor PEX5; TPR m	99.81
4g1t_A	472	Interferon-induced protein with tetratricopeptide	99.8
3mkr_A	291	Coatomer subunit epsilon; tetratricopeptide repeat	99.8
2ooe_A	530	Cleavage stimulation factor 77 kDa subunit; HAT do	99.8
3mkr_A	291	Coatomer subunit epsilon; tetratricopeptide repeat	99.8
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	99.77
1xi4_A	1630	Clathrin heavy chain; alpha-ZIG-ZAG, beta-propelle	99.77
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	99.77
1b89_A	449	Protein (clathrin heavy chain); triskelion, coated	99.76
1b89_A	449	Protein (clathrin heavy chain); triskelion, coated	99.76
3uq3_A	258	Heat shock protein STI1; HSP90, peptide binding, c	99.73
4g1t_A	472	Interferon-induced protein with tetratricopeptide	99.73
2pl2_A	217	Hypothetical conserved protein TTC0263; TPR, prote	99.71
3uq3_A	258	Heat shock protein STI1; HSP90, peptide binding, c	99.71
1ouv_A	273	Conserved hypothetical secreted protein; TPR repea	99.7
2ho1_A	252	Type 4 fimbrial biogenesis protein PILF; type IV p	99.69
1xi4_A	1630	Clathrin heavy chain; alpha-ZIG-ZAG, beta-propelle	99.69
2pl2_A	217	Hypothetical conserved protein TTC0263; TPR, prote	99.68
3u4t_A	272	TPR repeat-containing protein; structural genomics	99.68
3e4b_A	452	ALGK; tetratricopeptide repeat, superhelix, algina	99.67
2ho1_A	252	Type 4 fimbrial biogenesis protein PILF; type IV p	99.67
2vq2_A	225	PILW, putative fimbrial biogenesis and twitching m	99.66
2h6f_A	382	Protein farnesyltransferase/geranylgeranyltransfer	99.66
2q7f_A	243	YRRB protein; TPR, protein binding; 2.49A {Bacillu	99.65
3u4t_A	272	TPR repeat-containing protein; structural genomics	99.65
1xnf_A	275	Lipoprotein NLPI; TPR, tetratricopeptide, structur	99.65
2vq2_A	225	PILW, putative fimbrial biogenesis and twitching m	99.65
1ouv_A	273	Conserved hypothetical secreted protein; TPR repea	99.65
1xnf_A	275	Lipoprotein NLPI; TPR, tetratricopeptide, structur	99.64
2h6f_A	382	Protein farnesyltransferase/geranylgeranyltransfer	99.64
2q7f_A	243	YRRB protein; TPR, protein binding; 2.49A {Bacillu	99.63
3e4b_A	452	ALGK; tetratricopeptide repeat, superhelix, algina	99.62
2ond_A	308	Cleavage stimulation factor 77 kDa subunit; HAT do	99.61
4e6h_A	679	MRNA 3'-END-processing protein RNA14; HAT domain,	99.61
4a1s_A	411	PINS, partner of inscuteable; cell cycle, LGN, mit	99.59
3sf4_A	406	G-protein-signaling modulator 2; tetratricopeptide	99.59
3sf4_A	406	G-protein-signaling modulator 2; tetratricopeptide	99.59
3ro2_A	338	PINS homolog, G-protein-signaling modulator 2; TPR	99.58
3vtx_A	184	MAMA; tetratricopeptide repeats (TPR) containing p	99.57
3ro2_A	338	PINS homolog, G-protein-signaling modulator 2; TPR	99.56
3ulq_A	383	Response regulator aspartate phosphatase F; tetrat	99.55
4a1s_A	411	PINS, partner of inscuteable; cell cycle, LGN, mit	99.55
4abn_A	474	Tetratricopeptide repeat protein 5; P53 cofactor,	99.53
2ond_A	308	Cleavage stimulation factor 77 kDa subunit; HAT do	99.53
3vtx_A	184	MAMA; tetratricopeptide repeats (TPR) containing p	99.53
3ulq_A	383	Response regulator aspartate phosphatase F; tetrat	99.51
4abn_A	474	Tetratricopeptide repeat protein 5; P53 cofactor,	99.51
1hz4_A	373	MALT regulatory protein; two-helix bundles, helix	99.49
3nf1_A	311	KLC 1, kinesin light chain 1; TPR, structural geno	99.49
3q15_A	378	PSP28, response regulator aspartate phosphatase H;	99.48
3nf1_A	311	KLC 1, kinesin light chain 1; TPR, structural geno	99.48
3as5_A	186	MAMA; tetratricopeptide repeats (TPR) containing p	99.47
4e6h_A	679	MRNA 3'-END-processing protein RNA14; HAT domain,	99.47
3q15_A	378	PSP28, response regulator aspartate phosphatase H;	99.41
1hz4_A	373	MALT regulatory protein; two-helix bundles, helix	99.41
4i17_A	228	Hypothetical protein; TPR repeats protein, structu	99.39
3as5_A	186	MAMA; tetratricopeptide repeats (TPR) containing p	99.38
4gyw_A	723	UDP-N-acetylglucosamine--peptide N- acetylglucosam	99.38
4gyw_A	723	UDP-N-acetylglucosamine--peptide N- acetylglucosam	99.35
3edt_B	283	KLC 2, kinesin light chain 2; superhelical, struct	99.3
4i17_A	228	Hypothetical protein; TPR repeats protein, structu	99.29
3edt_B	283	KLC 2, kinesin light chain 2; superhelical, struct	99.27
2fo7_A	136	Synthetic consensus TPR protein; tetratricopeptide	99.26
1qqe_A	292	Vesicular transport protein SEC17; helix-turn-heli	99.21
3mv2_B	310	Coatomer subunit epsilon; vesicular membrane coat	99.21
3mv2_B	310	Coatomer subunit epsilon; vesicular membrane coat	99.21
3qky_A	261	Outer membrane assembly lipoprotein YFIO; membrane	99.17
2uy1_A	493	Cleavage stimulation factor 77; RNA-binding protei	99.15
3urz_A	208	Uncharacterized protein; tetratricopeptide repeats	99.13
1qqe_A	292	Vesicular transport protein SEC17; helix-turn-heli	99.13
3dra_A	306	Protein farnesyltransferase/geranylgeranyltransfer	99.11
2fo7_A	136	Synthetic consensus TPR protein; tetratricopeptide	99.1
3urz_A	208	Uncharacterized protein; tetratricopeptide repeats	99.1
2yhc_A	225	BAMD, UPF0169 lipoprotein YFIO; essential BAM comp	99.09
2pzi_A	681	Probable serine/threonine-protein kinase PKNG; ATP	99.08
3qky_A	261	Outer membrane assembly lipoprotein YFIO; membrane	99.07
3dra_A	306	Protein farnesyltransferase/geranylgeranyltransfer	99.07
2pzi_A	681	Probable serine/threonine-protein kinase PKNG; ATP	99.05
2vsy_A	568	XCC0866; transferase, glycosyl transferase, GT-B,	99.05
3rjv_A	212	Putative SEL1 repeat protein; alpha-alpha superhel	99.03
2r5s_A	176	Uncharacterized protein VP0806; APC090868.1, vibri	99.02
3qou_A	287	Protein YBBN; thioredoxin-like fold, tetratricopep	99.01
2uy1_A	493	Cleavage stimulation factor 77; RNA-binding protei	99.01
2r5s_A	176	Uncharacterized protein VP0806; APC090868.1, vibri	99.0
3qou_A	287	Protein YBBN; thioredoxin-like fold, tetratricopep	98.99
4ga2_A	150	E3 SUMO-protein ligase ranbp2; TPR motif, nuclear	98.98
2ifu_A	307	Gamma-SNAP; membrane fusion, snare complex disasse	98.98
2ifu_A	307	Gamma-SNAP; membrane fusion, snare complex disasse	98.98
3rjv_A	212	Putative SEL1 repeat protein; alpha-alpha superhel	98.97
4ga2_A	150	E3 SUMO-protein ligase ranbp2; TPR motif, nuclear	98.97
2vsy_A	568	XCC0866; transferase, glycosyl transferase, GT-B,	98.96
3u3w_A	293	Transcriptional activator PLCR protein; ternary co	98.93
1hh8_A	213	P67PHOX, NCF-2, neutrophil cytosol factor 2; cell	98.92
2yhc_A	225	BAMD, UPF0169 lipoprotein YFIO; essential BAM comp	98.92
3u3w_A	293	Transcriptional activator PLCR protein; ternary co	98.86
3gyz_A	151	Chaperone protein IPGC; asymmetric homodimer, tetr	98.86
1a17_A	166	Serine/threonine protein phosphatase 5; hydrolase,	98.86
3q7a_A	349	Farnesyltransferase alpha subunit; protein prenylt	98.85
4gco_A	126	Protein STI-1; structural genomics, PSI-biology, m	98.84
2qfc_A	293	PLCR protein; TPR, HTH, transcription regulation;	98.83
3q7a_A	349	Farnesyltransferase alpha subunit; protein prenylt	98.79
3gw4_A	203	Uncharacterized protein; structural genomics, PSI-	98.79
2vgx_A	148	Chaperone SYCD; alternative dimer assembly, tetrat	98.78
1hh8_A	213	P67PHOX, NCF-2, neutrophil cytosol factor 2; cell	98.77
2qfc_A	293	PLCR protein; TPR, HTH, transcription regulation;	98.76
3gyz_A	151	Chaperone protein IPGC; asymmetric homodimer, tetr	98.74
2e2e_A	177	Formate-dependent nitrite reductase complex NRFG;	98.73
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	98.73
4gco_A	126	Protein STI-1; structural genomics, PSI-biology, m	98.72
1a17_A	166	Serine/threonine protein phosphatase 5; hydrolase,	98.72
4f3v_A	282	ESX-1 secretion system protein ECCA1; tetratricope	98.72
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	98.71
3dss_A	331	Geranylgeranyl transferase type-2 subunit alpha; p	98.7
1na0_A	125	Designed protein CTPR3; de novo protein; HET: IPT;	98.7
1p5q_A	336	FKBP52, FK506-binding protein 4; isomerase; 2.80A	98.68
2xcb_A	142	PCRH, regulatory protein PCRH; protein transport,	98.66
2vyi_A	131	SGTA protein; chaperone, TPR repeat, phosphoprotei	98.66
1na0_A	125	Designed protein CTPR3; de novo protein; HET: IPT;	98.65
3sz7_A	164	HSC70 cochaperone (SGT); TPR domain, GET4, GET5, G	98.64
3q49_B	137	STIP1 homology and U box-containing protein 1; E3	98.63
3gw4_A	203	Uncharacterized protein; structural genomics, PSI-	98.63
2e2e_A	177	Formate-dependent nitrite reductase complex NRFG;	98.62
4f3v_A	282	ESX-1 secretion system protein ECCA1; tetratricope	98.62
2vyi_A	131	SGTA protein; chaperone, TPR repeat, phosphoprotei	98.61
2lni_A	133	Stress-induced-phosphoprotein 1; structural genomi	98.6
3upv_A	126	Heat shock protein STI1; TPR-fold, adaptor protein	98.6
2lni_A	133	Stress-induced-phosphoprotein 1; structural genomi	98.6
1p5q_A	336	FKBP52, FK506-binding protein 4; isomerase; 2.80A	98.6
4gcn_A	127	Protein STI-1; structural genomics, PSI-biology, m	98.59
2vgx_A	148	Chaperone SYCD; alternative dimer assembly, tetrat	98.56
4b4t_Q	434	26S proteasome regulatory subunit RPN6; hydrolase,	98.56
3dss_A	331	Geranylgeranyl transferase type-2 subunit alpha; p	98.55
3upv_A	126	Heat shock protein STI1; TPR-fold, adaptor protein	98.55
2kck_A	112	TPR repeat; tetratricopeptide repeat, structural g	98.55
1hxi_A	121	PEX5, peroxisome targeting signal 1 receptor PEX5;	98.55
1elw_A	118	TPR1-domain of HOP; HOP, TPR-domain, peptide-compl	98.53
4gcn_A	127	Protein STI-1; structural genomics, PSI-biology, m	98.51
1elw_A	118	TPR1-domain of HOP; HOP, TPR-domain, peptide-compl	98.49
2fbn_A	198	70 kDa peptidylprolyl isomerase, putative; sulfur	98.46
3sz7_A	164	HSC70 cochaperone (SGT); TPR domain, GET4, GET5, G	98.44
4b4t_Q	434	26S proteasome regulatory subunit RPN6; hydrolase,	98.43
2xcb_A	142	PCRH, regulatory protein PCRH; protein transport,	98.43
1elr_A	131	TPR2A-domain of HOP; HOP, TPR-domain, peptide-comp	98.43
2fbn_A	198	70 kDa peptidylprolyl isomerase, putative; sulfur	98.42
3q49_B	137	STIP1 homology and U box-containing protein 1; E3	98.41
2dba_A	148	Smooth muscle cell associated protein-1, isoform 2	98.4
3ro3_A	164	PINS homolog, G-protein-signaling modulator 2; asy	98.38
2xev_A	129	YBGF; tetratricopeptide, alpha-helical, metal bind	98.38
1elr_A	131	TPR2A-domain of HOP; HOP, TPR-domain, peptide-comp	98.36
2dba_A	148	Smooth muscle cell associated protein-1, isoform 2	98.35
1hxi_A	121	PEX5, peroxisome targeting signal 1 receptor PEX5;	98.35
2hr2_A	159	Hypothetical protein; alpha-alpha superhelix fold,	98.34
2kck_A	112	TPR repeat; tetratricopeptide repeat, structural g	98.32
3rkv_A	162	Putative peptidylprolyl isomerase; structural geno	98.3
3k9i_A	117	BH0479 protein; putative protein binding protein,	98.27
1kt0_A	457	FKBP51, 51 kDa FK506-binding protein; FKBP-like pp	98.27
2if4_A	338	ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha,	98.26
3k9i_A	117	BH0479 protein; putative protein binding protein,	98.23
2xev_A	129	YBGF; tetratricopeptide, alpha-helical, metal bind	98.23
1wao_1	477	Serine/threonine protein phosphatase 5; hydrolase,	98.22
1kt0_A	457	FKBP51, 51 kDa FK506-binding protein; FKBP-like pp	98.2
3ro3_A	164	PINS homolog, G-protein-signaling modulator 2; asy	98.18
3rkv_A	162	Putative peptidylprolyl isomerase; structural geno	98.17
1ihg_A	370	Cyclophilin 40; ppiase immunophilin tetratricopept	98.16
1wao_1	477	Serine/threonine protein phosphatase 5; hydrolase,	98.14
2kat_A	115	Uncharacterized protein; NESG, structure, structur	98.06
1ihg_A	370	Cyclophilin 40; ppiase immunophilin tetratricopept	98.03
1klx_A	138	Cysteine rich protein B; structural genomics, heli	98.02
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	97.97
2hr2_A	159	Hypothetical protein; alpha-alpha superhelix fold,	97.97
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	97.92
3n71_A	490	Histone lysine methyltransferase SMYD1; heart deve	97.89
1klx_A	138	Cysteine rich protein B; structural genomics, heli	97.87
2if4_A	338	ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha,	97.83
2kat_A	115	Uncharacterized protein; NESG, structure, structur	97.82
2l6j_A	111	TPR repeat-containing protein associated with HSP;	97.82
1zu2_A	158	Mitochondrial import receptor subunit TOM20-3; TPR	97.79
1zu2_A	158	Mitochondrial import receptor subunit TOM20-3; TPR	97.78
3n71_A	490	Histone lysine methyltransferase SMYD1; heart deve	97.77
2l6j_A	111	TPR repeat-containing protein associated with HSP;	97.73
3ma5_A	100	Tetratricopeptide repeat domain protein; NESG, str	97.7
1na3_A	91	Designed protein CTPR2; de novo protein; HET: IPT;	97.69
1na3_A	91	Designed protein CTPR2; de novo protein; HET: IPT;	97.66
3ma5_A	100	Tetratricopeptide repeat domain protein; NESG, str	97.55
2kc7_A	99	BFR218_protein; tetratricopeptide repeat, all-alph	97.41
3ly7_A	372	Transcriptional activator CADC; alpha/beta domain,	97.2
3ly7_A	372	Transcriptional activator CADC; alpha/beta domain,	97.19
1pc2_A	152	Mitochondria fission protein; unknown function; NM	97.11
3mkq_A	814	Coatomer beta'-subunit; beta-propeller, alpha-sole	96.96
2kc7_A	99	BFR218_protein; tetratricopeptide repeat, all-alph	96.94
3qww_A	433	SET and MYND domain-containing protein 2; methyltr	96.89
3mkq_A	814	Coatomer beta'-subunit; beta-propeller, alpha-sole	96.88
3qwp_A	429	SET and MYND domain-containing protein 3; SMYD3,SE	96.87
3qwp_A	429	SET and MYND domain-containing protein 3; SMYD3,SE	96.86
2v5f_A	104	Prolyl 4-hydroxylase subunit alpha-1; endoplasmic	96.84
3qww_A	433	SET and MYND domain-containing protein 2; methyltr	96.8
3bee_A	93	Putative YFRE protein; putaive YFRE protein, struc	96.7
4h7y_A	161	Dual specificity protein kinase TTK; mitotic check	96.61
3mkq_B	177	Coatomer subunit alpha; beta-propeller, alpha-sole	96.58
3bee_A	93	Putative YFRE protein; putaive YFRE protein, struc	96.53
1pc2_A	152	Mitochondria fission protein; unknown function; NM	96.51
4ady_A	963	RPN2, 26S proteasome regulatory subunit RPN2; prot	96.31
3mkq_B	177	Coatomer subunit alpha; beta-propeller, alpha-sole	96.29
1wy6_A	172	Hypothetical protein ST1625; helical repeat protei	96.04
2v5f_A	104	Prolyl 4-hydroxylase subunit alpha-1; endoplasmic	95.97
4h7y_A	161	Dual specificity protein kinase TTK; mitotic check	95.88
1nzn_A	126	CGI-135 protein, fission protein FIS1P; TPR, unkno	95.87
1wy6_A	172	Hypothetical protein ST1625; helical repeat protei	95.72
3u64_A	301	Protein TP_0956; tetratrico peptide repeat, protei	95.47
3u64_A	301	Protein TP_0956; tetratrico peptide repeat, protei	95.44
1nzn_A	126	CGI-135 protein, fission protein FIS1P; TPR, unkno	95.36
4ady_A	963	RPN2, 26S proteasome regulatory subunit RPN2; prot	94.8
1v54_E	109	Cytochrome C oxidase polypeptide VA; oxidoreductas	94.22
2ff4_A	388	Probable regulatory protein EMBR; winged-helix, te	94.06
3o48_A	134	Mitochondria fission 1 protein; tetratricopeptide	93.98
4b4t_P	445	26S proteasome regulatory subunit RPN5; hydrolase,	93.87
4fhn_B	1139	Nucleoporin NUP120; protein complex,structural pro	93.85
1y8m_A	144	FIS1; mitochondria, unknown function; NMR {Sacchar	93.58
4gns_B	754	Protein CSD3, chitin biosynthesis protein CHS6; FN	93.57
2ff4_A	388	Probable regulatory protein EMBR; winged-helix, te	93.08
3ffl_A	167	Anaphase-promoting complex subunit 7; tetratricope	92.97
1qsa_A	618	Protein (soluble lytic transglycosylase SLT70); al	92.89
2y69_E	152	Cytochrome C oxidase subunit 5A; electron transpor	92.59
1v54_E	109	Cytochrome C oxidase polypeptide VA; oxidoreductas	92.37
4fhn_B	1139	Nucleoporin NUP120; protein complex,structural pro	92.34
4gns_B	754	Protein CSD3, chitin biosynthesis protein CHS6; FN	92.11
4b4t_P	445	26S proteasome regulatory subunit RPN5; hydrolase,	90.88
3o48_A	134	Mitochondria fission 1 protein; tetratricopeptide	90.84
2y69_E	152	Cytochrome C oxidase subunit 5A; electron transpor	89.69
3lvg_A	624	Clathrin heavy chain 1; SELF assembly, coated PIT,	89.64
1zbp_A	273	Hypothetical protein VPA1032; alpha-beta protein,	88.88
3lvg_A	624	Clathrin heavy chain 1; SELF assembly, coated PIT,	86.61
3ffl_A	167	Anaphase-promoting complex subunit 7; tetratricope	86.03
1y8m_A	144	FIS1; mitochondria, unknown function; NMR {Sacchar	85.9
3lpz_A	336	GET4 (YOR164C homolog); protein targeting, tail-an	84.78
1zbp_A	273	Hypothetical protein VPA1032; alpha-beta protein,	84.09

>2xpi_A Anaphase-promoting complex subunit CUT9; cell cycle, TPR, ubiquitin ligase; 2.60A {Schizosaccharomyces pombe}

Probab=100.00  E-value=8.7e-35  Score=285.75  Aligned_cols=400  Identities=11%  Similarity=-0.029  Sum_probs=309.1

Q ss_pred             HHHHhhHHHHHHHHHhhhhhhccCCCchHHHHHHHHHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHH
Q 012111           52 SKILRTEFAIKNIEKKVSSKKYKNLWPKPVLEALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPE  131 (471)
Q Consensus        52 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  131 (471)
                      .+.++...+...+..++...+    .+..+..+...+.+.|++++|+++|+.+...   +++..+++.++.+|.+.|+++
T Consensus        95 ~~~g~~~~A~~~~~~~~~~~p----~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~---~~~~~~~~~l~~~~~~~g~~~  167 (597)
T 2xpi_A           95 LMQQQYKCAAFVGEKVLDITG----NPNDAFWLAQVYCCTGDYARAKCLLTKEDLY---NRSSACRYLAAFCLVKLYDWQ  167 (597)
T ss_dssp             HHTTCHHHHHHHHHHHHHHHC----CHHHHHHHHHHHHHTTCHHHHHHHHHHTCGG---GTCHHHHHHHHHHHHHTTCHH
T ss_pred             HHccCchHHHHHHHHHHhhCC----CchHHHHHHHHHHHcCcHHHHHHHHHHHhcc---ccchhHHHHHHHHHHHHhhHH
Confidence            344456667777776664333    3356677888888999999999999988653   678888999999999999999


Q ss_pred             HHHHHHHHHHhC---------------CCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCC---------------
Q 012111          132 QASLLFEVMLSD---------------GLKPSVDVYTALVSAYGQSGLLDEAFSTINDMKSVSDC---------------  181 (471)
Q Consensus       132 ~a~~~~~~m~~~---------------~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~---------------  181 (471)
                      +|.++|+++...               |.+.+..+|+.++.+|.+.|++++|+++|+++.+....               
T Consensus       168 ~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~  247 (597)
T 2xpi_A          168 GALNLLGETNPFRKDEKNANKLLMQDGGIKLEASMCYLRGQVYTNLSNFDRAKECYKEALMVDAKCYEAFDQLVSNHLLT  247 (597)
T ss_dssp             HHHHHHCSSCTTC----------CCCSSCCHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHTTCSC
T ss_pred             HHHHHHhccCCccccccccccccccccccchhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCchhhHHHHHHHHhhccc
Confidence            999999853221               22335788999999999999999999988888652210               


Q ss_pred             ------------------------------------------------------CCCHHHHHHHHHHHHhcCCHHHHHHH
Q 012111          182 ------------------------------------------------------KPDVYTYSILIKSCTKFHRFDLIEKI  207 (471)
Q Consensus       182 ------------------------------------------------------~~~~~~~~~ll~~~~~~~~~~~a~~~  207 (471)
                                                                            +++..+++.++..+.+.|++++|.++
T Consensus       248 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~  327 (597)
T 2xpi_A          248 ADEEWDLVLKLNYSTYSKEDAAFLRSLYMLKLNKTSHEDELRRAEDYLSSINGLEKSSDLLLCKADTLFVRSRFIDVLAI  327 (597)
T ss_dssp             HHHHHHHHHHSCTHHHHGGGHHHHHHHHHTTSCTTTTHHHHHHHHHHHHTSTTGGGCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             chhHHHHHHhcCCcccccchHHHHHHHHHHHHHHHcCcchHHHHHHHHHHhhcCCchHHHHHHHHHHHHHhcCHHHHHHH
Confidence                                                                  14556666666677777777777777


Q ss_pred             HHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCC
Q 012111          208 LAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGV  287 (471)
Q Consensus       208 ~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~  287 (471)
                      |+++.+.+ +.+..++..++.++.+.|++++|.++++.+.+..  +.+..++..++..|.+.|++++|.++|+++.+.. 
T Consensus       328 ~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~--~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-  403 (597)
T 2xpi_A          328 TTKILEID-PYNLDVYPLHLASLHESGEKNKLYLISNDLVDRH--PEKAVTWLAVGIYYLCVNKISEARRYFSKSSTMD-  403 (597)
T ss_dssp             HHHHHHHC-TTCCTTHHHHHHHHHHHTCHHHHHHHHHHHHHHC--TTSHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-
T ss_pred             HHHHHHcC-cccHHHHHHHHHHHHHhCCHHHHHHHHHHHHhhC--cccHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC-
Confidence            77776554 3355666677777777777777777777776542  5567788888888889999999999998887653 


Q ss_pred             CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHH
Q 012111          288 KADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSL  367 (471)
Q Consensus       288 ~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l  367 (471)
                      +.+..+|+.++.+|.+.|++++|..+|+.+.+.+. .+..+|..++.+|.+.|++++|.++|+++.+.. +.+..+|..+
T Consensus       404 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~-~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l  481 (597)
T 2xpi_A          404 PQFGPAWIGFAHSFAIEGEHDQAISAYTTAARLFQ-GTHLPYLFLGMQHMQLGNILLANEYLQSSYALF-QYDPLLLNEL  481 (597)
T ss_dssp             TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTT-TCSHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-CCCHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCc-cchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCChHHHHHH
Confidence            55677888889999999999999999988887643 367788888888999999999999999888764 4478888899


Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhC----CCCcC--HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHH
Q 012111          368 VSAYSKAGLIMKVDSILRQVENS----DVILD--TPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAY  441 (471)
Q Consensus       368 i~~~~~~g~~~~a~~~~~~~~~~----~~~~~--~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~  441 (471)
                      +..|.+.|++++|.++|+++.+.    +..|+  ..+|..++.+|.+.|++++|.++|+++.+.+ +.+..+|..+..+|
T Consensus       482 ~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-p~~~~~~~~l~~~~  560 (597)
T 2xpi_A          482 GVVAFNKSDMQTAINHFQNALLLVKKTQSNEKPWAATWANLGHAYRKLKMYDAAIDALNQGLLLS-TNDANVHTAIALVY  560 (597)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHHHHSCCCSGGGHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-SCCHHHHHHHHHHH
T ss_pred             HHHHHHhCCHHHHHHHHHHHHHhhhccccchhhHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCChHHHHHHHHHH
Confidence            99999999999999999888765    55666  6788899999999999999999999888753 34788888888999


Q ss_pred             HhcCCHHHHHHHHHHHHHhhhcCC
Q 012111          442 NALGMTEAAQNLENKMIAMKENSG  465 (471)
Q Consensus       442 ~~~g~~~~A~~~~~~m~~~~~~~~  465 (471)
                      .+.|++++|.+.++++++..|+..
T Consensus       561 ~~~g~~~~A~~~~~~~l~~~p~~~  584 (597)
T 2xpi_A          561 LHKKIPGLAITHLHESLAISPNEI  584 (597)
T ss_dssp             HHTTCHHHHHHHHHHHHHHCTTCH
T ss_pred             HHhCCHHHHHHHHHHHHhcCCCCh
Confidence            999999999999999988887653

>2xpi_A Anaphase-promoting complex subunit CUT9; cell cycle, TPR, ubiquitin ligase; 2.60A {Schizosaccharomyces pombe}

Probab=100.00  E-value=1.7e-34  Score=283.67  Aligned_cols=376  Identities=12%  Similarity=0.006  Sum_probs=310.3

Q ss_pred             chHHHHHHHHHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHH
Q 012111           78 PKPVLEALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVS  157 (471)
Q Consensus        78 ~~~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~  157 (471)
                      ...+...+..+.+.|++++|+++|+.+...   .|+..++..++.+|.+.|++++|..+|+.+...  +++..+++.++.
T Consensus        84 ~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~---~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~--~~~~~~~~~l~~  158 (597)
T 2xpi_A           84 EDYLRLWRHDALMQQQYKCAAFVGEKVLDI---TGNPNDAFWLAQVYCCTGDYARAKCLLTKEDLY--NRSSACRYLAAF  158 (597)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHH---HCCHHHHHHHHHHHHHTTCHHHHHHHHHHTCGG--GTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHccCchHHHHHHHHHHhh---CCCchHHHHHHHHHHHcCcHHHHHHHHHHHhcc--ccchhHHHHHHH
Confidence            345678888999999999999999999864   568889999999999999999999999998654  678999999999


Q ss_pred             HHHhcCCHHHHHHHHHHhhcCC--------------CCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCC-------
Q 012111          158 AYGQSGLLDEAFSTINDMKSVS--------------DCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGI-------  216 (471)
Q Consensus       158 ~~~~~~~~~~a~~~~~~~~~~~--------------~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~-------  216 (471)
                      +|.+.|++++|.++|+++....              +.+.+..+|+.++.+|.+.|++++|.++|++|.+.+.       
T Consensus       159 ~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~  238 (597)
T 2xpi_A          159 CLVKLYDWQGALNLLGETNPFRKDEKNANKLLMQDGGIKLEASMCYLRGQVYTNLSNFDRAKECYKEALMVDAKCYEAFD  238 (597)
T ss_dssp             HHHHTTCHHHHHHHHCSSCTTC----------CCCSSCCHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHH
T ss_pred             HHHHHhhHHHHHHHHhccCCccccccccccccccccccchhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCchhhHHHH
Confidence            9999999999999999644322              2345688999999999999999999999999876541       


Q ss_pred             ---------------------------------------------------------------CCCHHHHHHHHHHHHcc
Q 012111          217 ---------------------------------------------------------------ECSAVTYNTIIDGYGKA  233 (471)
Q Consensus       217 ---------------------------------------------------------------~~~~~~~~~l~~~~~~~  233 (471)
                                                                                     +++..+++.++.+|.+.
T Consensus       239 ~l~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~l~~~~~~~  318 (597)
T 2xpi_A          239 QLVSNHLLTADEEWDLVLKLNYSTYSKEDAAFLRSLYMLKLNKTSHEDELRRAEDYLSSINGLEKSSDLLLCKADTLFVR  318 (597)
T ss_dssp             HHHHTTCSCHHHHHHHHHHSCTHHHHGGGHHHHHHHHHTTSCTTTTHHHHHHHHHHHHTSTTGGGCHHHHHHHHHHHHHT
T ss_pred             HHHHhhcccchhHHHHHHhcCCcccccchHHHHHHHHHHHHHHHcCcchHHHHHHHHHHhhcCCchHHHHHHHHHHHHHh
Confidence                                                                           14566666777777777


Q ss_pred             CCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHH
Q 012111          234 KKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSV  313 (471)
Q Consensus       234 ~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~  313 (471)
                      |++++|.++|+++.+.+  +.+..++..++.++.+.|++++|..+++++.... +.+..++..++..|.+.|++++|..+
T Consensus       319 g~~~~A~~~~~~~~~~~--~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~  395 (597)
T 2xpi_A          319 SRFIDVLAITTKILEID--PYNLDVYPLHLASLHESGEKNKLYLISNDLVDRH-PEKAVTWLAVGIYYLCVNKISEARRY  395 (597)
T ss_dssp             TCHHHHHHHHHHHHHHC--TTCCTTHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTSHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             cCHHHHHHHHHHHHHcC--cccHHHHHHHHHHHHHhCCHHHHHHHHHHHHhhC-cccHHHHHHHHHHHHHhccHHHHHHH
Confidence            77777777777776653  3355567777777777777777777777776543 56788888888999999999999999


Q ss_pred             HHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCC
Q 012111          314 MDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVI  393 (471)
Q Consensus       314 ~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~  393 (471)
                      |+.+.+... .+..+|+.++.+|.+.|++++|.++|+++.+.+ +.+..+|..++.+|.+.|++++|.++|+++.+..+.
T Consensus       396 ~~~~~~~~~-~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~  473 (597)
T 2xpi_A          396 FSKSSTMDP-QFGPAWIGFAHSFAIEGEHDQAISAYTTAARLF-QGTHLPYLFLGMQHMQLGNILLANEYLQSSYALFQY  473 (597)
T ss_dssp             HHHHHHHCT-TCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTT-TTCSHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCCC
T ss_pred             HHHHHHhCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-ccchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC
Confidence            998877533 367788999999999999999999999988764 447788899999999999999999999998877655


Q ss_pred             cCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhC----CCCCC--HHHHHHHHHHHHhcCCHHHHHHHHHHHHHhhhcC
Q 012111          394 LDTPFFNCIISAYGQAGDVEKMGELFLTMKER----HCVPD--NITFATMIQAYNALGMTEAAQNLENKMIAMKENS  464 (471)
Q Consensus       394 ~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~----~~~p~--~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~~  464 (471)
                       +..+|+.++.+|.+.|++++|.++|+++.+.    +..|+  ..+|..++.+|.+.|++++|.++++++++.+|..
T Consensus       474 -~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~  549 (597)
T 2xpi_A          474 -DPLLLNELGVVAFNKSDMQTAINHFQNALLLVKKTQSNEKPWAATWANLGHAYRKLKMYDAAIDALNQGLLLSTND  549 (597)
T ss_dssp             -CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCSGGGHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSSCC
T ss_pred             -ChHHHHHHHHHHHHhCCHHHHHHHHHHHHHhhhccccchhhHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCCC
Confidence             7888999999999999999999999988765    66777  7889999999999999999999999999887653

>1w3b_A UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110; OGT, glcnac, nucleoporin, O-linked glycosylation, TPR repeat, protein binding; 2.85A {Homo sapiens} SCOP: a.118.8.1

Probab=100.00  E-value=3.3e-29  Score=232.43  Aligned_cols=367  Identities=10%  Similarity=0.089  Sum_probs=317.9

Q ss_pred             HHHHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCC
Q 012111           85 LDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGL  164 (471)
Q Consensus        85 l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~  164 (471)
                      ...+.+.|++++|++.|+.+.+..  |.+...+..+...+...|++++|...++...+.. +.+..+|..+..++...|+
T Consensus         6 a~~~~~~g~~~~A~~~~~~~~~~~--p~~~~~~~~l~~~~~~~~~~~~a~~~~~~a~~~~-p~~~~~~~~lg~~~~~~g~   82 (388)
T 1w3b_A            6 AHREYQAGDFEAAERHCMQLWRQE--PDNTGVLLLLSSIHFQCRRLDRSAHFSTLAIKQN-PLLAEAYSNLGNVYKERGQ   82 (388)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCchHHHHHHHHHHHHCCC
Confidence            445678999999999999998875  6667788888889999999999999999888764 4478899999999999999


Q ss_pred             HHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHH
Q 012111          165 LDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFS  244 (471)
Q Consensus       165 ~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~a~~~~~  244 (471)
                      +++|+..|+++.+..  +.+..+|..+..++...|++++|.+.++++.+.. +.+...+..+...+...|++++|.+.|+
T Consensus        83 ~~~A~~~~~~al~~~--p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~  159 (388)
T 1w3b_A           83 LQEAIEHYRHALRLK--PDFIDGYINLAAALVAAGDMEGAVQAYVSALQYN-PDLYCVRSDLGNLLKALGRLEEAKACYL  159 (388)
T ss_dssp             HHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHSCSSHHHHHHHHHHHHC-TTCTHHHHHHHHHHHTTSCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcC--cchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHccCHHHHHHHHH
Confidence            999999999998732  4456679999999999999999999999998774 4456777888899999999999999999


Q ss_pred             HHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCC
Q 012111          245 AMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFP  324 (471)
Q Consensus       245 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~  324 (471)
                      ++.+..  +.+..+|..+...+...|++++|...|+++...+ +.+...+..+...+...|++++|...+.+..+.... 
T Consensus       160 ~al~~~--p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~-  235 (388)
T 1w3b_A          160 KAIETQ--PNFAVAWSNLGCVFNAQGEIWLAIHHFEKAVTLD-PNFLDAYINLGNVLKEARIFDRAVAAYLRALSLSPN-  235 (388)
T ss_dssp             HHHHHC--TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCTTHHHHHHHHHHHHCTT-
T ss_pred             HHHHhC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCcC-
Confidence            998863  5567889999999999999999999999998765 566788999999999999999999999988876432 


Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHH
Q 012111          325 TVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIIS  404 (471)
Q Consensus       325 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  404 (471)
                      +..++..+...+...|++++|...|+++.+.+ +.+..++..+...+.+.|++++|...++++.+..+. +..++..+..
T Consensus       236 ~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~l~~  313 (388)
T 1w3b_A          236 HAVVHGNLACVYYEQGLIDLAIDTYRRAIELQ-PHFPDAYCNLANALKEKGSVAEAEDCYNTALRLCPT-HADSLNNLAN  313 (388)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTC-SSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHCTT-CHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCcc-cHHHHHHHHH
Confidence            57788899999999999999999999999864 335788999999999999999999999999987654 7889999999


Q ss_pred             HHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhhhcC
Q 012111          405 AYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAYNALGMTEAAQNLENKMIAMKENS  464 (471)
Q Consensus       405 ~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~~  464 (471)
                      .+...|++++|.+.++++.+. .+.+..++..+...+.+.|++++|.+.++++++..|..
T Consensus       314 ~~~~~g~~~~A~~~~~~al~~-~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~p~~  372 (388)
T 1w3b_A          314 IKREQGNIEEAVRLYRKALEV-FPEFAAAHSNLASVLQQQGKLQEALMHYKEAIRISPTF  372 (388)
T ss_dssp             HHHTTTCHHHHHHHHHHHTTS-CTTCHHHHHHHHHHHHTTTCCHHHHHHHHHHHTTCTTC
T ss_pred             HHHHcCCHHHHHHHHHHHHhc-CCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCC
Confidence            999999999999999999875 34467889999999999999999999999999887754

>4g26_A Pentatricopeptide repeat-containing protein AT2G3 mitochondrial; metallonuclease, prorp, ribonuclease, PIN, tRNA processing, NYN domain; 1.75A {Arabidopsis thaliana} PDB: 4g23_A* 4g25_A 4g24_A

Probab=100.00  E-value=3.8e-32  Score=256.22  Aligned_cols=188  Identities=14%  Similarity=0.171  Sum_probs=147.1

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCC---------HHHHHHHHHHHHhCCCCCCHH
Q 012111          257 FTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGM---------YDKMRSVMDFMQKRFFFPTVV  327 (471)
Q Consensus       257 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~---------~~~a~~~~~~~~~~~~~~~~~  327 (471)
                      ..++.+|.+|++.|++++|.++|++|.+.|+.||..+|+.||.+|++.+.         ++.|.++|++|.+.|+.||..
T Consensus        27 ~~l~~~id~c~k~G~~~~A~~lf~~M~~~Gv~pd~~tyn~Li~~c~~~~~~~~~~~~~~l~~A~~lf~~M~~~G~~Pd~~  106 (501)
T 4g26_A           27 ALLKQKLDMCSKKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDIFKQMIVDKVVPNEA  106 (501)
T ss_dssp             HHHHHHHHHTTTSCCHHHHHHHHHHHHHHTCCCCHHHHHHHHHHHTTCCCCSSSSCCHHHHHHHHHHHHHHHTTCCCCHH
T ss_pred             HHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHhHHHHHHHHHHhCCchhhhhhcchHHHHHHHHHHHHHhCCCCCHH
Confidence            34666667777777777777777777777777777777777777665543         567788888888888888888


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHH
Q 012111          328 TYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYG  407 (471)
Q Consensus       328 ~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  407 (471)
                      +|+.+|.+|++.|++++|.++|++|.+.|+.||..+|+.+|.+|++.|++++|.++|++|.+.|+.||..+|+.||.+|+
T Consensus       107 tyn~lI~~~~~~g~~~~A~~l~~~M~~~g~~Pd~~tyn~lI~~~~~~g~~~~A~~l~~~M~~~G~~Pd~~ty~~Li~~~~  186 (501)
T 4g26_A          107 TFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDADKAYEVDAHMVESEVVPEEPELAALLKVSM  186 (501)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCccceehHHHHHHHHCCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHh
Confidence            88888888888888888888888888888888888888888888888888888888888888888888888888888888


Q ss_pred             hcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhc
Q 012111          408 QAGDVEKMGELFLTMKERHCVPDNITFATMIQAYNAL  444 (471)
Q Consensus       408 ~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~  444 (471)
                      +.|++++|.++|++|.+.|+.|+..||+.++..|...
T Consensus       187 ~~g~~d~A~~ll~~Mr~~g~~ps~~T~~~l~~~F~s~  223 (501)
T 4g26_A          187 DTKNADKVYKTLQRLRDLVRQVSKSTFDMIEEWFKSE  223 (501)
T ss_dssp             HTTCHHHHHHHHHHHHHHTSSBCHHHHHHHHHHHHSH
T ss_pred             hCCCHHHHHHHHHHHHHhCCCcCHHHHHHHHHHHhcC
Confidence            8888888888888888888888888888887777653

>4g26_A Pentatricopeptide repeat-containing protein AT2G3 mitochondrial; metallonuclease, prorp, ribonuclease, PIN, tRNA processing, NYN domain; 1.75A {Arabidopsis thaliana} PDB: 4g23_A* 4g25_A 4g24_A

Probab=100.00  E-value=6.9e-31  Score=247.65  Aligned_cols=203  Identities=12%  Similarity=0.103  Sum_probs=115.9

Q ss_pred             HHHHHHhhcCCCCCCCH-HHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCC---------HHH
Q 012111          169 FSTINDMKSVSDCKPDV-YTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKK---------FEE  238 (471)
Q Consensus       169 ~~~~~~~~~~~~~~~~~-~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~---------~~~  238 (471)
                      ..+.+++.+ .+....+ ..++.+|++|++.|++++|.++|++|.+.|+.||..+|+.||.+|++.+.         ++.
T Consensus        10 e~L~~~~~~-k~~~~spe~~l~~~id~c~k~G~~~~A~~lf~~M~~~Gv~pd~~tyn~Li~~c~~~~~~~~~~~~~~l~~   88 (501)
T 4g26_A           10 ENLSRKAKK-KAIQQSPEALLKQKLDMCSKKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSR   88 (501)
T ss_dssp             ---------------CHHHHHHHHHHHTTTSCCHHHHHHHHHHHHHHTCCCCHHHHHHHHHHHTTCCCCSSSSCCHHHHH
T ss_pred             HHHHHHHHH-hcccCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHhHHHHHHHHHHhCCchhhhhhcchHHH
Confidence            334444444 3333332 34666677777777777777777777777777777777777777765543         455


Q ss_pred             HHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Q 012111          239 MESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQ  318 (471)
Q Consensus       239 a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~  318 (471)
                      |.++|++|.+.+ +.||..+|+.||.+|++.|++++|.++|++|.+.|+.||..+|+.+|.+|++.|++++|.++|+.|.
T Consensus        89 A~~lf~~M~~~G-~~Pd~~tyn~lI~~~~~~g~~~~A~~l~~~M~~~g~~Pd~~tyn~lI~~~~~~g~~~~A~~l~~~M~  167 (501)
T 4g26_A           89 GFDIFKQMIVDK-VVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDADKAYEVDAHMV  167 (501)
T ss_dssp             HHHHHHHHHHTT-CCCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhC-CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCccceehHHHHHHHHCCCHHHHHHHHHHHH
Confidence            555666654443 5566666666666666666666666666666555556666666666666666666666666666666


Q ss_pred             hCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHh
Q 012111          319 KRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSK  373 (471)
Q Consensus       319 ~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~  373 (471)
                      +.|+.||..+|+.||.+|++.|++++|.+++++|.+.|..|+..||+.++..|+.
T Consensus       168 ~~G~~Pd~~ty~~Li~~~~~~g~~d~A~~ll~~Mr~~g~~ps~~T~~~l~~~F~s  222 (501)
T 4g26_A          168 ESEVVPEEPELAALLKVSMDTKNADKVYKTLQRLRDLVRQVSKSTFDMIEEWFKS  222 (501)
T ss_dssp             HTTCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTSSBCHHHHHHHHHHHHS
T ss_pred             hcCCCCCHHHHHHHHHHHhhCCCHHHHHHHHHHHHHhCCCcCHHHHHHHHHHHhc
Confidence            5566666666666666666666666666666666655555666666555555544

>1w3b_A UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110; OGT, glcnac, nucleoporin, O-linked glycosylation, TPR repeat, protein binding; 2.85A {Homo sapiens} SCOP: a.118.8.1

Probab=99.98  E-value=2.5e-27  Score=219.78  Aligned_cols=381  Identities=10%  Similarity=-0.004  Sum_probs=325.6

Q ss_pred             HHHHHHHhhHHHHHHHHHhhhhhhccCCCchHHHHHHHHHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCC
Q 012111           49 KDLSKILRTEFAIKNIEKKVSSKKYKNLWPKPVLEALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCK  128 (471)
Q Consensus        49 ~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  128 (471)
                      ..+.+.++..++.+.+...+...|   ..+..+......+...|++++|...++.+.+..  |.+..+|..+...+.+.|
T Consensus         7 ~~~~~~g~~~~A~~~~~~~~~~~p---~~~~~~~~l~~~~~~~~~~~~a~~~~~~a~~~~--p~~~~~~~~lg~~~~~~g   81 (388)
T 1w3b_A            7 HREYQAGDFEAAERHCMQLWRQEP---DNTGVLLLLSSIHFQCRRLDRSAHFSTLAIKQN--PLLAEAYSNLGNVYKERG   81 (388)
T ss_dssp             HHHHHHTCHHHHHHHHHHHHHHCT---TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHT
T ss_pred             HHHHHCCCHHHHHHHHHHHHHhCC---CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC--CCchHHHHHHHHHHHHCC
Confidence            445667777788777777666443   334455555666778999999999999999875  778899999999999999


Q ss_pred             CHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHH
Q 012111          129 QPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKIL  208 (471)
Q Consensus       129 ~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~  208 (471)
                      ++++|...|+++.+... .+..+|..+..++...|++++|.+.|+++.+..  +.+...+..+...+...|++++|.+.|
T Consensus        82 ~~~~A~~~~~~al~~~p-~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~~l~~~~~~~g~~~~A~~~~  158 (388)
T 1w3b_A           82 QLQEAIEHYRHALRLKP-DFIDGYINLAAALVAAGDMEGAVQAYVSALQYN--PDLYCVRSDLGNLLKALGRLEEAKACY  158 (388)
T ss_dssp             CHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHHSCSSHHHHHHHHHHHHC--TTCTHHHHHHHHHHHTTSCHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCc-chHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCcHHHHHHHHHHHHHccCHHHHHHHH
Confidence            99999999999988643 367789999999999999999999999998732  334556778888899999999999999


Q ss_pred             HHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCC
Q 012111          209 AEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVK  288 (471)
Q Consensus       209 ~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~  288 (471)
                      +++.+.. +.+..+|..+...+...|++++|...|+++.+..  +.+...+..+...+...|++++|...+++..... +
T Consensus       159 ~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~-p  234 (388)
T 1w3b_A          159 LKAIETQ-PNFAVAWSNLGCVFNAQGEIWLAIHHFEKAVTLD--PNFLDAYINLGNVLKEARIFDRAVAAYLRALSLS-P  234 (388)
T ss_dssp             HHHHHHC-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHTTTCTTHHHHHHHHHHHHC-T
T ss_pred             HHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC--CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-c
Confidence            9998874 4468899999999999999999999999998874  5567889999999999999999999999998764 5


Q ss_pred             CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHH
Q 012111          289 ADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLV  368 (471)
Q Consensus       289 ~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li  368 (471)
                      .+..++..+...+...|++++|...|+.+.+.... +..+|..+...+.+.|++++|...++++.+.. +.+..++..+.
T Consensus       235 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~  312 (388)
T 1w3b_A          235 NHAVVHGNLACVYYEQGLIDLAIDTYRRAIELQPH-FPDAYCNLANALKEKGSVAEAEDCYNTALRLC-PTHADSLNNLA  312 (388)
T ss_dssp             TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTCSS-CHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHC-TTCHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-cccHHHHHHHH
Confidence            56889999999999999999999999999987433 57789999999999999999999999999874 56788999999


Q ss_pred             HHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC-CHHHHHHHHHHHHhcCC
Q 012111          369 SAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVP-DNITFATMIQAYNALGM  446 (471)
Q Consensus       369 ~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~  446 (471)
                      ..+...|++++|...++++.+..+. +..++..+..++.+.|++++|.+.|+++.+.  .| +...|..+...+...|+
T Consensus       313 ~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~--~p~~~~a~~~lg~~~~~~~~  388 (388)
T 1w3b_A          313 NIKREQGNIEEAVRLYRKALEVFPE-FAAAHSNLASVLQQQGKLQEALMHYKEAIRI--SPTFADAYSNMGNTLKEMQD  388 (388)
T ss_dssp             HHHHTTTCHHHHHHHHHHHTTSCTT-CHHHHHHHHHHHHTTTCCHHHHHHHHHHHTT--CTTCHHHHHHHHHHHHHTCC
T ss_pred             HHHHHcCCHHHHHHHHHHHHhcCCC-cHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh--CCCCHHHHHhHHHHHHHccC
Confidence            9999999999999999999987654 7889999999999999999999999999974  45 56777777777766653

>2gw1_A Mitochondrial precursor proteins import receptor; TPR, protein transport; 3.00A {Saccharomyces cerevisiae}

Probab=99.95  E-value=1.7e-24  Score=208.43  Aligned_cols=374  Identities=9%  Similarity=-0.028  Sum_probs=301.3

Q ss_pred             HHHHHHHHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHH
Q 012111           81 VLEALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYG  160 (471)
Q Consensus        81 ~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~  160 (471)
                      +...-..+.+.|++++|++.|+.+.+..   |+..++..+..++.+.|++++|...++.+.+.+. .+..+|..+..++.
T Consensus         9 ~~~~g~~~~~~g~~~~A~~~~~~al~~~---p~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p-~~~~~~~~l~~~~~   84 (514)
T 2gw1_A            9 LKDKGNQFFRNKKYDDAIKYYNWALELK---EDPVFYSNLSACYVSVGDLKKVVEMSTKALELKP-DYSKVLLRRASANE   84 (514)
T ss_dssp             HHHHHHHHHHTSCHHHHHHHHHHHHHHC---CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCS-CCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhccHHHHHHHHHHHHhcC---ccHHHHHhHHHHHHHHhhHHHHHHHHHHHhccCh-HHHHHHHHHHHHHH
Confidence            4444566677888888888888888753   5778888888888888888888888888877653 36678888888888


Q ss_pred             hcCCHHHHHHHHHHhhcCCCC-----------------------------------------------------------
Q 012111          161 QSGLLDEAFSTINDMKSVSDC-----------------------------------------------------------  181 (471)
Q Consensus       161 ~~~~~~~a~~~~~~~~~~~~~-----------------------------------------------------------  181 (471)
                      ..|++++|+..|+++....+.                                                           
T Consensus        85 ~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  164 (514)
T 2gw1_A           85 GLGKFADAMFDLSVLSLNGDFNDASIEPMLERNLNKQAMSKLKEKFGDIDTATATPTELSTQPAKERKDKQENLPSVTSM  164 (514)
T ss_dssp             HTTCHHHHHHHHHHHHHSSSCCGGGTHHHHHHHHHHHHHHHHTTC---------------------------CCCCHHHH
T ss_pred             HHhhHHHHHHHHHHHHhcCCCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccCChhhHHHhhccCCchhHHH
Confidence            888888888888877653210                                                           


Q ss_pred             ------------------CCCHHHHHHHHHHHHh---cCCHHHHHHHHHHHHH-----CCC--------CCCHHHHHHHH
Q 012111          182 ------------------KPDVYTYSILIKSCTK---FHRFDLIEKILAEMSY-----LGI--------ECSAVTYNTII  227 (471)
Q Consensus       182 ------------------~~~~~~~~~ll~~~~~---~~~~~~a~~~~~~~~~-----~g~--------~~~~~~~~~l~  227 (471)
                                        +.+...+......+..   .|+++.|..+++++.+     ...        +.+..++..+.
T Consensus       165 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  244 (514)
T 2gw1_A          165 ASFFGIFKPELTFANYDESNEADKELMNGLSNLYKRSPESYDKADESFTKAARLFEEQLDKNNEDEKLKEKLAISLEHTG  244 (514)
T ss_dssp             HHHHTTSCCCCCCSSCCSSCHHHHHHHHHHHHHSSCCTTHHHHHHHHHHHHHHHHHHHTTTSTTCHHHHHHHHHHHHHHH
T ss_pred             HHHHhhcCHHHHHHHhcCCcHHHHHHHHHHHHHHhhhhccHHHHHHHHHHHHHHhhhhhccCccccccChHHHHHHHHHH
Confidence                              0012333333333343   7999999999999987     311        22356788889


Q ss_pred             HHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCH
Q 012111          228 DGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMY  307 (471)
Q Consensus       228 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~  307 (471)
                      ..+...|++++|...|+++.+..   |+...+..+..++...|++++|...++++.... +.+...+..+...+...|++
T Consensus       245 ~~~~~~~~~~~A~~~~~~~l~~~---~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~  320 (514)
T 2gw1_A          245 IFKFLKNDPLGAHEDIKKAIELF---PRVNSYIYMALIMADRNDSTEYYNYFDKALKLD-SNNSSVYYHRGQMNFILQNY  320 (514)
T ss_dssp             HHHHHSSCHHHHHHHHHHHHHHC---CCHHHHHHHHHHHHTSSCCTTGGGHHHHHHTTC-TTCTHHHHHHHHHHHHTTCT
T ss_pred             HHHHHCCCHHHHHHHHHHHHhhC---ccHHHHHHHHHHHHHCCCHHHHHHHHHHHhhcC-cCCHHHHHHHHHHHHHhCCH
Confidence            99999999999999999998864   338889999999999999999999999998764 55778899999999999999


Q ss_pred             HHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 012111          308 DKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQV  387 (471)
Q Consensus       308 ~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~  387 (471)
                      ++|...++.+.+.... +...+..+...+...|++++|..+++++.+.. +.+..++..+...+...|++++|...++.+
T Consensus       321 ~~A~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~a  398 (514)
T 2gw1_A          321 DQAGKDFDKAKELDPE-NIFPYIQLACLAYRENKFDDCETLFSEAKRKF-PEAPEVPNFFAEILTDKNDFDKALKQYDLA  398 (514)
T ss_dssp             THHHHHHHHHHHTCSS-CSHHHHHHHHHTTTTTCHHHHHHHHHHHHHHS-TTCSHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhChh-hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHc-ccCHHHHHHHHHHHHHCCCHHHHHHHHHHH
Confidence            9999999999887543 56788889999999999999999999998863 336778999999999999999999999998


Q ss_pred             HhCCCCc-C----HHHHHHHHHHHHh---cCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 012111          388 ENSDVIL-D----TPFFNCIISAYGQ---AGDVEKMGELFLTMKERHCVPDNITFATMIQAYNALGMTEAAQNLENKMIA  459 (471)
Q Consensus       388 ~~~~~~~-~----~~~~~~l~~~~~~---~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~  459 (471)
                      .+..+.. +    ...+..+..++..   .|++++|...++++.+.. +.+..++..+...+.+.|++++|...++++++
T Consensus       399 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~  477 (514)
T 2gw1_A          399 IELENKLDGIYVGIAPLVGKATLLTRNPTVENFIEATNLLEKASKLD-PRSEQAKIGLAQMKLQQEDIDEAITLFEESAD  477 (514)
T ss_dssp             HHHHHTSSSCSSCSHHHHHHHHHHHTSCCTTHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHhhhccchHHHHHHHHHHHHHHHhhhhhcCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHhcCHHHHHHHHHHHHH
Confidence            7653321 1    3488899999999   999999999999998752 34678888999999999999999999999999


Q ss_pred             hhhcCC
Q 012111          460 MKENSG  465 (471)
Q Consensus       460 ~~~~~~  465 (471)
                      ..|..+
T Consensus       478 ~~~~~~  483 (514)
T 2gw1_A          478 LARTME  483 (514)
T ss_dssp             HCSSHH
T ss_pred             hccccH
Confidence            887643

>2y4t_A DNAJ homolog subfamily C member 3; chaperone, endoplasmic reticulum, protein folding, tetratricopeptiderepeat, J domain, unfolded protein respons; 3.00A {Homo sapiens} PDB: 2y4u_A

Probab=99.95  E-value=6.6e-24  Score=200.79  Aligned_cols=303  Identities=12%  Similarity=0.017  Sum_probs=170.2

Q ss_pred             chHHHHHHHHHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHH
Q 012111           78 PKPVLEALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVS  157 (471)
Q Consensus        78 ~~~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~  157 (471)
                      ...+......+.+.|++++|+++|+.+.+..  +.+..++..+..++...|++++|...|+.+.+.+.. +..++..+..
T Consensus        26 ~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~~--p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~l~~  102 (450)
T 2y4t_A           26 VEKHLELGKKLLAAGQLADALSQFHAAVDGD--PDNYIAYYRRATVFLAMGKSKAALPDLTKVIQLKMD-FTAARLQRGH  102 (450)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC--CccHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCC-cHHHHHHHHH
Confidence            3445555666667777777777777776653  455666777777777777777777777777665432 5666777777


Q ss_pred             HHHhcCCHHHHHHHHHHhhcCCCCCCCH---HHHHHHHHH------------HHhcCCHHHHHHHHHHHHHCCCCCCHHH
Q 012111          158 AYGQSGLLDEAFSTINDMKSVSDCKPDV---YTYSILIKS------------CTKFHRFDLIEKILAEMSYLGIECSAVT  222 (471)
Q Consensus       158 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~---~~~~~ll~~------------~~~~~~~~~a~~~~~~~~~~g~~~~~~~  222 (471)
                      +|...|++++|.+.|+++....  +.+.   ..+..+...            +...|++++|...++.+.+.. +.+..+
T Consensus       103 ~~~~~g~~~~A~~~~~~~~~~~--~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~  179 (450)
T 2y4t_A          103 LLLKQGKLDEAEDDFKKVLKSN--PSENEEKEAQSQLIKSDEMQRLRSQALNAFGSGDYTAAIAFLDKILEVC-VWDAEL  179 (450)
T ss_dssp             HHHHTTCHHHHHHHHHHHHTSC--CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHhcC--CCChhhHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCChHH
Confidence            7777777777777777776521  2223   445544333            555566666666666665543 335555


Q ss_pred             HHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHH-----
Q 012111          223 YNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNIL-----  297 (471)
Q Consensus       223 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l-----  297 (471)
                      +..+..+|.+.|++++|.+.|+++.+..  +.+..++..+..++...|++++|...|+++.... +.+...+..+     
T Consensus       180 ~~~l~~~~~~~g~~~~A~~~~~~~~~~~--~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-p~~~~~~~~~~~~~~  256 (450)
T 2y4t_A          180 RELRAECFIKEGEPRKAISDLKAASKLK--NDNTEAFYKISTLYYQLGDHELSLSEVRECLKLD-QDHKRCFAHYKQVKK  256 (450)
T ss_dssp             HHHHHHHHHHTTCGGGGHHHHHHHHHHH--CSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CChHHHHHHHHHHHH
Confidence            6666666666666666666666655542  3345556666666666666666666666655432 2233333333     


Q ss_pred             -------HHHHHHcCCHHHHHHHHHHHHhCCCCCC----HHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHH
Q 012111          298 -------TKSYGRAGMYDKMRSVMDFMQKRFFFPT----VVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCS  366 (471)
Q Consensus       298 -------l~~~~~~~~~~~a~~~~~~~~~~~~~~~----~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~  366 (471)
                             ...+...|++++|...|+.+.+.... +    ...|..+...+.+.|++++|...++++.... +.+..++..
T Consensus       257 ~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~~p~-~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~-p~~~~~~~~  334 (450)
T 2y4t_A          257 LNKLIESAEELIRDGRYTDATSKYESVMKTEPS-IAEYTVRSKERICHCFSKDEKPVEAIRVCSEVLQME-PDNVNALKD  334 (450)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCCS-SHHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHC-TTCHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCc-chHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-cccHHHHHH
Confidence                   44455555555555555555443211 1    2244444555555555555555555554431 223455555


Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHhCC
Q 012111          367 LVSAYSKAGLIMKVDSILRQVENSD  391 (471)
Q Consensus       367 li~~~~~~g~~~~a~~~~~~~~~~~  391 (471)
                      +..+|...|++++|...++++.+..
T Consensus       335 l~~~~~~~~~~~~A~~~~~~al~~~  359 (450)
T 2y4t_A          335 RAEAYLIEEMYDEAIQDYETAQEHN  359 (450)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHTTS
T ss_pred             HHHHHHHhcCHHHHHHHHHHHHHhC
Confidence            5555555555555555555555443

>2y4t_A DNAJ homolog subfamily C member 3; chaperone, endoplasmic reticulum, protein folding, tetratricopeptiderepeat, J domain, unfolded protein respons; 3.00A {Homo sapiens} PDB: 2y4u_A

Probab=99.95  E-value=1.1e-23  Score=199.35  Aligned_cols=354  Identities=10%  Similarity=-0.008  Sum_probs=281.2

Q ss_pred             HHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHh
Q 012111           96 LALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAFSTINDM  175 (471)
Q Consensus        96 ~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~  175 (471)
                      .+...+..+....  +.+...+..++..+.+.|++++|..+|+.+.+.. +.+..+|..+..++...|++++|+..|+++
T Consensus        10 ~~~~~~~~~~~~~--p~~~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~a   86 (450)
T 2y4t_A           10 GVDLGTENLYFQS--MADVEKHLELGKKLLAAGQLADALSQFHAAVDGD-PDNYIAYYRRATVFLAMGKSKAALPDLTKV   86 (450)
T ss_dssp             ---------------CHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             ccccccccccccc--HHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHCCCHHHHHHHHHHH
Confidence            3444555555543  6678889999999999999999999999998764 347889999999999999999999999999


Q ss_pred             hcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCH---HHHHHH------------HHHHHccCCHHHHH
Q 012111          176 KSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSA---VTYNTI------------IDGYGKAKKFEEME  240 (471)
Q Consensus       176 ~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~---~~~~~l------------~~~~~~~~~~~~a~  240 (471)
                      .+..  +.+...+..+...+.+.|++++|.+.|+++.+.. +.+.   ..+..+            ...+...|++++|.
T Consensus        87 l~~~--p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~A~  163 (450)
T 2y4t_A           87 IQLK--MDFTAARLQRGHLLLKQGKLDEAEDDFKKVLKSN-PSENEEKEAQSQLIKSDEMQRLRSQALNAFGSGDYTAAI  163 (450)
T ss_dssp             HHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSC-CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHH
T ss_pred             HhcC--CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCChhhHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHH
Confidence            8732  4567889999999999999999999999999764 2234   555555            44488899999999


Q ss_pred             HHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhC
Q 012111          241 SSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKR  320 (471)
Q Consensus       241 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~  320 (471)
                      ..|+++.+..  +.+...+..+..+|...|++++|..+|+++.... +.+..++..+..+|...|++++|...|+.+.+.
T Consensus       164 ~~~~~~~~~~--~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  240 (450)
T 2y4t_A          164 AFLDKILEVC--VWDAELRELRAECFIKEGEPRKAISDLKAASKLK-NDNTEAFYKISTLYYQLGDHELSLSEVRECLKL  240 (450)
T ss_dssp             HHHHHHHHHC--TTCHHHHHHHHHHHHHTTCGGGGHHHHHHHHHHH-CSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhC--CCChHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            9999998864  5678889999999999999999999999997754 567889999999999999999999999999876


Q ss_pred             CCCCCHHHHHHH------------HHHHHhcCCHHHHHHHHHHHHHcCCCCC-----HHHHHHHHHHHHhcCCHHHHHHH
Q 012111          321 FFFPTVVTYNIV------------IETFGKAGHIEKMEEYFKKMKHRGMKPN-----SITYCSLVSAYSKAGLIMKVDSI  383 (471)
Q Consensus       321 ~~~~~~~~~~~l------------i~~~~~~g~~~~a~~~~~~m~~~~~~p~-----~~~~~~li~~~~~~g~~~~a~~~  383 (471)
                      ... +...+..+            ...+...|++++|..+|+++...  .|+     ...+..+...+.+.|++++|...
T Consensus       241 ~p~-~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~--~p~~~~~~~~~~~~l~~~~~~~g~~~~A~~~  317 (450)
T 2y4t_A          241 DQD-HKRCFAHYKQVKKLNKLIESAEELIRDGRYTDATSKYESVMKT--EPSIAEYTVRSKERICHCFSKDEKPVEAIRV  317 (450)
T ss_dssp             CTT-CHHHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--CCSSHHHHHHHHHHHHHHHHTTTCHHHHHHH
T ss_pred             CCC-hHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc--CCcchHHHHHHHHHHHHHHHHCCCHHHHHHH
Confidence            332 44445444            78899999999999999999885  444     44788899999999999999999


Q ss_pred             HHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC-CHHHHHHHHH------------HHHhcC-----
Q 012111          384 LRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVP-DNITFATMIQ------------AYNALG-----  445 (471)
Q Consensus       384 ~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p-~~~~~~~l~~------------~~~~~g-----  445 (471)
                      ++.+.+..+. +..+|..+..+|...|++++|...|+++.+.  .| +...+..+..            .|...|     
T Consensus       318 ~~~a~~~~p~-~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~l~~~~~~~~~~~~~~~y~~lg~~~~~  394 (450)
T 2y4t_A          318 CSEVLQMEPD-NVNALKDRAEAYLIEEMYDEAIQDYETAQEH--NENDQQIREGLEKAQRLLKQSQKRDYYKILGVKRNA  394 (450)
T ss_dssp             HHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT--SSSCHHHHHHHHHHHHHHHHHHSCCSGGGSCSSTTC
T ss_pred             HHHHHHhCcc-cHHHHHHHHHHHHHhcCHHHHHHHHHHHHHh--CcchHHHHHHHHHHHHHhhcccchhHHHHhCCCccC
Confidence            9999877544 7889999999999999999999999999884  45 4555555552            344445     


Q ss_pred             CHHHHHHHHHH-HHHhhhcC
Q 012111          446 MTEAAQNLENK-MIAMKENS  464 (471)
Q Consensus       446 ~~~~A~~~~~~-m~~~~~~~  464 (471)
                      +.+++.+.+++ .++..|+.
T Consensus       395 ~~~~~~~~y~~~~l~~~pd~  414 (450)
T 2y4t_A          395 KKQEIIKAYRKLALQWHPDN  414 (450)
T ss_dssp             CTTHHHHHHHHHHHHSCGGG
T ss_pred             CHHHHHHHHHHHHHHhCCCC
Confidence            56777888876 56666553

>3fp2_A TPR repeat-containing protein YHR117W; TOM71, mitochondria translocation, allosteric REG phosphoprotein, TPR repeat, ATP-binding; 1.98A {Saccharomyces cerevisiae} PDB: 3fp3_A 3fp4_A 3lca_A

Probab=99.93  E-value=1.4e-22  Score=196.21  Aligned_cols=375  Identities=9%  Similarity=-0.018  Sum_probs=278.2

Q ss_pred             HHHHHHHHHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHH
Q 012111           80 PVLEALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAY  159 (471)
Q Consensus        80 ~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~  159 (471)
                      .+...-..+.+.|++++|++.|+.+.+..  |.+..++..+..++.+.|++++|.+.|+.+.+.+.. +..++..+..++
T Consensus        27 ~~~~~g~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~la~~~  103 (537)
T 3fp2_A           27 QLKNRGNHFFTAKNFNEAIKYYQYAIELD--PNEPVFYSNISACYISTGDLEKVIEFTTKALEIKPD-HSKALLRRASAN  103 (537)
T ss_dssp             HHHHHHHHHHHTTCCC-CHHHHHHHHHHC--TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhccHHHHHHHHHHHHhhC--CCCcHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCc-hHHHHHHHHHHH
Confidence            33444555566777777777777776654  556666777777777777777777777777665432 566677777777


Q ss_pred             HhcCCHHHHHHHHHHhhcCC-----------------------------------CCCCCHH------------------
Q 012111          160 GQSGLLDEAFSTINDMKSVS-----------------------------------DCKPDVY------------------  186 (471)
Q Consensus       160 ~~~~~~~~a~~~~~~~~~~~-----------------------------------~~~~~~~------------------  186 (471)
                      ...|++++|+..|+.+....                                   ...|+..                  
T Consensus       104 ~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  183 (537)
T 3fp2_A          104 ESLGNFTDAMFDLSVLSLNGDFDGASIEPMLERNLNKQAMKVLNENLSKDEGRGSQVLPSNTSLASFFGIFDSHLEVSSV  183 (537)
T ss_dssp             HHHTCHHHHHHHHHHHC-----------CHHHHHHHHHHHHHHHHHCC-------CCCCCHHHHHHHHHTSCHHHHHHTS
T ss_pred             HHcCCHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHHHHHHHHHHHHhCccccccccchHhHHHHHHHhcChHHHHHHH
Confidence            77777777777665332100                                   0011111                  


Q ss_pred             ------------HHHHHHHHHHh--------cCCHHHHHHHHHHHHHCCCCCCH-------HHHHHHHHHHHccCCHHHH
Q 012111          187 ------------TYSILIKSCTK--------FHRFDLIEKILAEMSYLGIECSA-------VTYNTIIDGYGKAKKFEEM  239 (471)
Q Consensus       187 ------------~~~~ll~~~~~--------~~~~~~a~~~~~~~~~~g~~~~~-------~~~~~l~~~~~~~~~~~~a  239 (471)
                                  ....+...+..        .++++.|..+++.+.+.. +.+.       .++..+...+...|++++|
T Consensus       184 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~a~~~~~~A~~~~~~~l~~~-p~~~~~~~~~~~~~~~~g~~~~~~~~~~~A  262 (537)
T 3fp2_A          184 NTSSNYDTAYALLSDALQRLYSATDEGYLVANDLLTKSTDMYHSLLSAN-TVDDPLRENAALALCYTGIFHFLKNNLLDA  262 (537)
T ss_dssp             CCCCSSCSSHHHHHHHHHHHHTCSHHHHHHHHHHHHHHHHHHHHHHC---CCCHHHHHHHHHHHHHHHHHHHHTTCHHHH
T ss_pred             hhccccccHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHC-CCcchhhHHHHHHHHHHHHHHHhcccHHHH
Confidence                        11111111111        247889999999998764 2232       3566777888899999999


Q ss_pred             HHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Q 012111          240 ESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQK  319 (471)
Q Consensus       240 ~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~  319 (471)
                      ...|+.+.+.   .|+...+..+...+...|++++|...++++.... +.+..++..+...+...|++++|...++.+.+
T Consensus       263 ~~~~~~~~~~---~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~  338 (537)
T 3fp2_A          263 QVLLQESINL---HPTPNSYIFLALTLADKENSQEFFKFFQKAVDLN-PEYPPTYYHRGQMYFILQDYKNAKEDFQKAQS  338 (537)
T ss_dssp             HHHHHHHHHH---CCCHHHHHHHHHHTCCSSCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhc---CCCchHHHHHHHHHHHhcCHHHHHHHHHHHhccC-CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Confidence            9999999886   4558889999999999999999999999998765 56788999999999999999999999999988


Q ss_pred             CCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCC-----c
Q 012111          320 RFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVI-----L  394 (471)
Q Consensus       320 ~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~-----~  394 (471)
                      .... +...+..+...+...|++++|..+++++.+.. +.+...+..+...+...|++++|...++++.+..+.     .
T Consensus       339 ~~~~-~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~  416 (537)
T 3fp2_A          339 LNPE-NVYPYIQLACLLYKQGKFTESEAFFNETKLKF-PTLPEVPTFFAEILTDRGDFDTAIKQYDIAKRLEEVQEKIHV  416 (537)
T ss_dssp             HCTT-CSHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHCSSCSS
T ss_pred             hCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHhCCHHHHHHHHHHHHHcCCcchhhHH
Confidence            6443 56788899999999999999999999999874 446778999999999999999999999998754321     1


Q ss_pred             CHHHHHHHHHHHHhc----------CCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhhhcC
Q 012111          395 DTPFFNCIISAYGQA----------GDVEKMGELFLTMKERHCVPDNITFATMIQAYNALGMTEAAQNLENKMIAMKENS  464 (471)
Q Consensus       395 ~~~~~~~l~~~~~~~----------g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~~  464 (471)
                      ....+..+..++...          |++++|...|+++.+. .+.+...+..+...+...|++++|.+.++++++..|..
T Consensus       417 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~-~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~  495 (537)
T 3fp2_A          417 GIGPLIGKATILARQSSQDPTQLDEEKFNAAIKLLTKACEL-DPRSEQAKIGLAQLKLQMEKIDEAIELFEDSAILARTM  495 (537)
T ss_dssp             TTHHHHHHHHHHHHHHTC----CCHHHHHHHHHHHHHHHHH-CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--C
T ss_pred             HHHHHHHHHHHHHHHhhccchhhhHhHHHHHHHHHHHHHHh-CCCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCCc
Confidence            222344556677777          9999999999999875 23467888899999999999999999999999988765


Q ss_pred             C
Q 012111          465 G  465 (471)
Q Consensus       465 ~  465 (471)
                      +
T Consensus       496 ~  496 (537)
T 3fp2_A          496 D  496 (537)
T ss_dssp             H
T ss_pred             H
Confidence            3

>2gw1_A Mitochondrial precursor proteins import receptor; TPR, protein transport; 3.00A {Saccharomyces cerevisiae}

Probab=99.93  E-value=5.8e-22  Score=190.73  Aligned_cols=372  Identities=9%  Similarity=-0.057  Sum_probs=307.4

Q ss_pred             hhHHHHHHHhhHHHHHHHHHhhhhhhccCCCchHHHHHHHHHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhc
Q 012111           47 AEKDLSKILRTEFAIKNIEKKVSSKKYKNLWPKPVLEALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGK  126 (471)
Q Consensus        47 ~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  126 (471)
                      ....+...+++..+...+.+.+...|    .+..+......+.+.|++++|++.|+.+.+..  |.+..++..+..++..
T Consensus        12 ~g~~~~~~g~~~~A~~~~~~al~~~p----~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~~l~~~~~~   85 (514)
T 2gw1_A           12 KGNQFFRNKKYDDAIKYYNWALELKE----DPVFYSNLSACYVSVGDLKKVVEMSTKALELK--PDYSKVLLRRASANEG   85 (514)
T ss_dssp             HHHHHHHTSCHHHHHHHHHHHHHHCC----CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC--SCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHhccHHHHHHHHHHHHhcCc----cHHHHHhHHHHHHHHhhHHHHHHHHHHHhccC--hHHHHHHHHHHHHHHH
Confidence            44556677788888888888877553    46677788888999999999999999999875  6777899999999999


Q ss_pred             CCCHHHHHHHHHHHHhCCCCC-----------------------------------------------------------
Q 012111          127 CKQPEQASLLFEVMLSDGLKP-----------------------------------------------------------  147 (471)
Q Consensus       127 ~~~~~~a~~~~~~m~~~~~~~-----------------------------------------------------------  147 (471)
                      .|++++|...|+.+...+...                                                           
T Consensus        86 ~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  165 (514)
T 2gw1_A           86 LGKFADAMFDLSVLSLNGDFNDASIEPMLERNLNKQAMSKLKEKFGDIDTATATPTELSTQPAKERKDKQENLPSVTSMA  165 (514)
T ss_dssp             TTCHHHHHHHHHHHHHSSSCCGGGTHHHHHHHHHHHHHHHHTTC---------------------------CCCCHHHHH
T ss_pred             HhhHHHHHHHHHHHHhcCCCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccCChhhHHHhhccCCchhHHHH
Confidence            999999999999987764310                                                           


Q ss_pred             -------------------CHHHHHHHHHHHHh---cCCHHHHHHHHHHhhc-----CCCC-------CCCHHHHHHHHH
Q 012111          148 -------------------SVDVYTALVSAYGQ---SGLLDEAFSTINDMKS-----VSDC-------KPDVYTYSILIK  193 (471)
Q Consensus       148 -------------------~~~~~~~li~~~~~---~~~~~~a~~~~~~~~~-----~~~~-------~~~~~~~~~ll~  193 (471)
                                         +...+......+..   .|++++|+..|+++..     ....       +.+..++..+..
T Consensus       166 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  245 (514)
T 2gw1_A          166 SFFGIFKPELTFANYDESNEADKELMNGLSNLYKRSPESYDKADESFTKAARLFEEQLDKNNEDEKLKEKLAISLEHTGI  245 (514)
T ss_dssp             HHHTTSCCCCCCSSCCSSCHHHHHHHHHHHHHSSCCTTHHHHHHHHHHHHHHHHHHHTTTSTTCHHHHHHHHHHHHHHHH
T ss_pred             HHHhhcCHHHHHHHhcCCcHHHHHHHHHHHHHHhhhhccHHHHHHHHHHHHHHhhhhhccCccccccChHHHHHHHHHHH
Confidence                               13333444444444   8999999999999876     2111       223567888889


Q ss_pred             HHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHH
Q 012111          194 SCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIE  273 (471)
Q Consensus       194 ~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  273 (471)
                      .+...|+++.|..+++.+.+..  |+...+..+..++...|++++|...++.+.+..  +.+...+..+...+...|+++
T Consensus       246 ~~~~~~~~~~A~~~~~~~l~~~--~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~  321 (514)
T 2gw1_A          246 FKFLKNDPLGAHEDIKKAIELF--PRVNSYIYMALIMADRNDSTEYYNYFDKALKLD--SNNSSVYYHRGQMNFILQNYD  321 (514)
T ss_dssp             HHHHSSCHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHTSSCCTTGGGHHHHHHTTC--TTCTHHHHHHHHHHHHTTCTT
T ss_pred             HHHHCCCHHHHHHHHHHHHhhC--ccHHHHHHHHHHHHHCCCHHHHHHHHHHHhhcC--cCCHHHHHHHHHHHHHhCCHH
Confidence            9999999999999999998875  338889999999999999999999999998764  456678999999999999999


Q ss_pred             HHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 012111          274 KMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMK  353 (471)
Q Consensus       274 ~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~  353 (471)
                      +|...++++.... +.+...+..+...+...|++++|...++.+.+.... +...+..+...+...|++++|...++++.
T Consensus       322 ~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~la~~~~~~~~~~~A~~~~~~a~  399 (514)
T 2gw1_A          322 QAGKDFDKAKELD-PENIFPYIQLACLAYRENKFDDCETLFSEAKRKFPE-APEVPNFFAEILTDKNDFDKALKQYDLAI  399 (514)
T ss_dssp             HHHHHHHHHHHTC-SSCSHHHHHHHHHTTTTTCHHHHHHHHHHHHHHSTT-CSHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhC-hhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHccc-CHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            9999999998765 556778899999999999999999999999876433 56788899999999999999999999988


Q ss_pred             HcCCC-CC----HHHHHHHHHHHHh---cCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhC
Q 012111          354 HRGMK-PN----SITYCSLVSAYSK---AGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKER  425 (471)
Q Consensus       354 ~~~~~-p~----~~~~~~li~~~~~---~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~  425 (471)
                      ..... ++    ...+..+...+..   .|++++|...++.+.+..+. +..++..+..+|...|++++|...|+++.+.
T Consensus       400 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~A~~~~~~a~~~~~~-~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~  478 (514)
T 2gw1_A          400 ELENKLDGIYVGIAPLVGKATLLTRNPTVENFIEATNLLEKASKLDPR-SEQAKIGLAQMKLQQEDIDEAITLFEESADL  478 (514)
T ss_dssp             HHHHTSSSCSSCSHHHHHHHHHHHTSCCTTHHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HhhhccchHHHHHHHHHHHHHHHhhhhhcCCHHHHHHHHHHHHHhCcc-cHHHHHHHHHHHHHhcCHHHHHHHHHHHHHh
Confidence            65211 11    3488999999999   99999999999999987654 7888999999999999999999999999985


Q ss_pred             CCCCCHHH
Q 012111          426 HCVPDNIT  433 (471)
Q Consensus       426 ~~~p~~~~  433 (471)
                        .|+...
T Consensus       479 --~~~~~~  484 (514)
T 2gw1_A          479 --ARTMEE  484 (514)
T ss_dssp             --CSSHHH
T ss_pred             --ccccHH
Confidence              565443

>3ieg_A DNAJ homolog subfamily C member 3; TPR motif, chaperone, endoplasmic reticulum, TPR repeat, UNF protein response; 2.51A {Mus musculus}

Probab=99.91  E-value=7.5e-20  Score=167.25  Aligned_cols=327  Identities=10%  Similarity=-0.005  Sum_probs=212.1

Q ss_pred             hHHHHHHHHHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHH
Q 012111           79 KPVLEALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSA  158 (471)
Q Consensus        79 ~~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~  158 (471)
                      +.+......+...|++++|++.|+.+.+..  +.+..++..+..++...|++++|...++.+.+.... +...+..+..+
T Consensus         4 ~~~~~~~~~~~~~g~~~~A~~~~~~~l~~~--p~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~l~~~   80 (359)
T 3ieg_A            4 EKHLELGKKLLAAGQLADALSQFHAAVDGD--PDNYIAYYRRATVFLAMGKSKAALPDLTKVIALKMD-FTAARLQRGHL   80 (359)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHhhC--cccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCC-cchHHHHHHHH
Confidence            344555566667777777777777777654  556667777777777777777777777777765322 56677777777


Q ss_pred             HHhcCCHHHHHHHHHHhhcCCCCCC----CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccC
Q 012111          159 YGQSGLLDEAFSTINDMKSVSDCKP----DVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAK  234 (471)
Q Consensus       159 ~~~~~~~~~a~~~~~~~~~~~~~~~----~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~  234 (471)
                      +...|++++|...|+++.+.   .|    +...+..+.....                       ...+..+...+...|
T Consensus        81 ~~~~~~~~~A~~~~~~~~~~---~~~~~~~~~~~~~l~~~~~-----------------------~~~~~~~a~~~~~~~  134 (359)
T 3ieg_A           81 LLKQGKLDEAEDDFKKVLKS---NPSEQEEKEAESQLVKADE-----------------------MQRLRSQALDAFDGA  134 (359)
T ss_dssp             HHHHTCHHHHHHHHHHHHTS---CCCHHHHHHHHHHHHHHHH-----------------------HHHHHHHHHHHHHTT
T ss_pred             HHHcCChHHHHHHHHHHHhc---CCcccChHHHHHHHHHHHH-----------------------HHHHHHHHHHHHHcc
Confidence            77777777777777777652   33    2223332211100                       011222345566667


Q ss_pred             CHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHH
Q 012111          235 KFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVM  314 (471)
Q Consensus       235 ~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~  314 (471)
                      ++++|.+.++++.+..  +.+...+..+...+...|++++|...++++.... +.+..++..+...+...|++++|...+
T Consensus       135 ~~~~A~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~  211 (359)
T 3ieg_A          135 DYTAAITFLDKILEVC--VWDAELRELRAECFIKEGEPRKAISDLKAASKLK-SDNTEAFYKISTLYYQLGDHELSLSEV  211 (359)
T ss_dssp             CHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC-SCCHHHHHHHHHHHHHHTCHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHhC--CCchHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHH
Confidence            7777777777766653  4455666666777777777777777777766543 455666667777777777777777777


Q ss_pred             HHHHhCCCCCCHHHHH------------HHHHHHHhcCCHHHHHHHHHHHHHcCCCCCH----HHHHHHHHHHHhcCCHH
Q 012111          315 DFMQKRFFFPTVVTYN------------IVIETFGKAGHIEKMEEYFKKMKHRGMKPNS----ITYCSLVSAYSKAGLIM  378 (471)
Q Consensus       315 ~~~~~~~~~~~~~~~~------------~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~----~~~~~li~~~~~~g~~~  378 (471)
                      +...+.... +...+.            .+...+...|++++|...++++...... +.    ..+..+...+...|+++
T Consensus       212 ~~a~~~~~~-~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~~~~~la~~~~~~~~~~  289 (359)
T 3ieg_A          212 RECLKLDQD-HKRCFAHYKQVKKLNKLIESAEELIRDGRYTDATSKYESVMKTEPS-VAEYTVRSKERICHCFSKDEKPV  289 (359)
T ss_dssp             HHHHHHCTT-CHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCS-SHHHHHHHHHHHHHHHHHTTCHH
T ss_pred             HHHHhhCcc-chHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCC-chHHHHHHHHHHHHHHHHccCHH
Confidence            766654322 222222            2255677888888888888888775322 22    23445677788888888


Q ss_pred             HHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCC-HHHHHHHHHHHH
Q 012111          379 KVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPD-NITFATMIQAYN  442 (471)
Q Consensus       379 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~-~~~~~~l~~~~~  442 (471)
                      +|...++.+.+..+. +..++..+..++...|++++|.+.|+++.+.  .|+ ...+..+..+..
T Consensus       290 ~A~~~~~~~~~~~~~-~~~~~~~~~~~~~~~g~~~~A~~~~~~a~~~--~p~~~~~~~~l~~~~~  351 (359)
T 3ieg_A          290 EAIRICSEVLQMEPD-NVNALKDRAEAYLIEEMYDEAIQDYEAAQEH--NENDQQIREGLEKAQR  351 (359)
T ss_dssp             HHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT--CTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCcc-cHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc--CCCChHHHHHHHHHHH
Confidence            888888888776544 6778888888888888888888888888874  454 445555544443

>3ieg_A DNAJ homolog subfamily C member 3; TPR motif, chaperone, endoplasmic reticulum, TPR repeat, UNF protein response; 2.51A {Mus musculus}

Probab=99.91  E-value=6.9e-20  Score=167.48  Aligned_cols=326  Identities=12%  Similarity=-0.016  Sum_probs=210.2

Q ss_pred             hhhHHHHHHHhhHHHHHHHHHhhhhhhccCCCchHHHHHHHHHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHh
Q 012111           46 EAEKDLSKILRTEFAIKNIEKKVSSKKYKNLWPKPVLEALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLG  125 (471)
Q Consensus        46 ~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~  125 (471)
                      .....+...+++..+...+...+...|   ..+..+......+...|++++|++.|+.+.+..  +.+...+..+..++.
T Consensus         8 ~~~~~~~~~g~~~~A~~~~~~~l~~~p---~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~l~~~~~   82 (359)
T 3ieg_A            8 ELGKKLLAAGQLADALSQFHAAVDGDP---DNYIAYYRRATVFLAMGKSKAALPDLTKVIALK--MDFTAARLQRGHLLL   82 (359)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHCT---TCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHhhCc---ccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC--CCcchHHHHHHHHHH
Confidence            345566777888888888888877543   456777788888899999999999999999875  567789999999999


Q ss_pred             cCCCHHHHHHHHHHHHhCCCC--CCHHHHHHH------------HHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHH
Q 012111          126 KCKQPEQASLLFEVMLSDGLK--PSVDVYTAL------------VSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSIL  191 (471)
Q Consensus       126 ~~~~~~~a~~~~~~m~~~~~~--~~~~~~~~l------------i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l  191 (471)
                      ..|++++|...|+.+.+....  .+...+..+            ...+...|++++|++.++++.+.  .+.+...+..+
T Consensus        83 ~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~--~~~~~~~~~~~  160 (359)
T 3ieg_A           83 KQGKLDEAEDDFKKVLKSNPSEQEEKEAESQLVKADEMQRLRSQALDAFDGADYTAAITFLDKILEV--CVWDAELRELR  160 (359)
T ss_dssp             HHTCHHHHHHHHHHHHTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHH
T ss_pred             HcCChHHHHHHHHHHHhcCCcccChHHHHHHHHHHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHh--CCCchHHHHHH
Confidence            999999999999999986320  144445444            34555555555555555555542  13344455555


Q ss_pred             HHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCC
Q 012111          192 IKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGN  271 (471)
Q Consensus       192 l~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  271 (471)
                      ...+...|++++|...++.+.+.. +.+..++..+...+...|++++|...|+...+..  +.+...+..+...      
T Consensus       161 ~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~--~~~~~~~~~~~~~------  231 (359)
T 3ieg_A          161 AECFIKEGEPRKAISDLKAASKLK-SDNTEAFYKISTLYYQLGDHELSLSEVRECLKLD--QDHKRCFAHYKQV------  231 (359)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHTTC-SCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHH------
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC--ccchHHHHHHHHH------
Confidence            555555555555555555555442 3344555555555555555555555555554432  1122211111000      


Q ss_pred             HHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCH----HHHHHHHHHHHhcCCHHHHHH
Q 012111          272 IEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTV----VTYNIVIETFGKAGHIEKMEE  347 (471)
Q Consensus       272 ~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~----~~~~~li~~~~~~g~~~~a~~  347 (471)
                                 .      .......+...+.+.|++++|...++.+.+.... +.    ..+..+...+...|++++|..
T Consensus       232 -----------~------~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~~~~~la~~~~~~~~~~~A~~  293 (359)
T 3ieg_A          232 -----------K------KLNKLIESAEELIRDGRYTDATSKYESVMKTEPS-VAEYTVRSKERICHCFSKDEKPVEAIR  293 (359)
T ss_dssp             -----------H------HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCS-SHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             -----------H------HHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCC-chHHHHHHHHHHHHHHHHccCHHHHHH
Confidence                       0      0011122355677778888888888777765332 22    224456677888888888888


Q ss_pred             HHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHH
Q 012111          348 YFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYG  407 (471)
Q Consensus       348 ~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  407 (471)
                      .+++..+.. +.+..++..+...+...|++++|...|+++.+..+. +...+..+..+..
T Consensus       294 ~~~~~~~~~-~~~~~~~~~~~~~~~~~g~~~~A~~~~~~a~~~~p~-~~~~~~~l~~~~~  351 (359)
T 3ieg_A          294 ICSEVLQME-PDNVNALKDRAEAYLIEEMYDEAIQDYEAAQEHNEN-DQQIREGLEKAQR  351 (359)
T ss_dssp             HHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTT-CHHHHHHHHHHHH
T ss_pred             HHHHHHHhC-cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCC-ChHHHHHHHHHHH
Confidence            888887763 336778888888888888888888888888877654 5556665555543

>3fp2_A TPR repeat-containing protein YHR117W; TOM71, mitochondria translocation, allosteric REG phosphoprotein, TPR repeat, ATP-binding; 1.98A {Saccharomyces cerevisiae} PDB: 3fp3_A 3fp4_A 3lca_A

Probab=99.90  E-value=3.2e-20  Score=179.58  Aligned_cols=367  Identities=10%  Similarity=0.002  Sum_probs=288.9

Q ss_pred             hhHHHHHHHhhHHHHHHHHHhhhhhhccCCCchHHHHHHHHHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhc
Q 012111           47 AEKDLSKILRTEFAIKNIEKKVSSKKYKNLWPKPVLEALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGK  126 (471)
Q Consensus        47 ~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  126 (471)
                      ....+.+.+++..+...+...+...|   ..+..+......+.+.|++++|++.|+.+.+.+  |.+..++..+..++..
T Consensus        31 ~g~~~~~~g~~~~A~~~~~~al~~~p---~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~~la~~~~~  105 (537)
T 3fp2_A           31 RGNHFFTAKNFNEAIKYYQYAIELDP---NEPVFYSNISACYISTGDLEKVIEFTTKALEIK--PDHSKALLRRASANES  105 (537)
T ss_dssp             HHHHHHHTTCCC-CHHHHHHHHHHCT---TCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHhccHHHHHHHHHHHHhhCC---CCcHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC--CchHHHHHHHHHHHHH
Confidence            44555666777778888887777543   446777788888899999999999999999875  6778899999999999


Q ss_pred             CCCHHHHHHHHHHHHhCCCC------------------------------------CCHH--------------------
Q 012111          127 CKQPEQASLLFEVMLSDGLK------------------------------------PSVD--------------------  150 (471)
Q Consensus       127 ~~~~~~a~~~~~~m~~~~~~------------------------------------~~~~--------------------  150 (471)
                      .|++++|...|+.+......                                    |+..                    
T Consensus       106 ~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  185 (537)
T 3fp2_A          106 LGNFTDAMFDLSVLSLNGDFDGASIEPMLERNLNKQAMKVLNENLSKDEGRGSQVLPSNTSLASFFGIFDSHLEVSSVNT  185 (537)
T ss_dssp             HTCHHHHHHHHHHHC-----------CHHHHHHHHHHHHHHHHHCC-------CCCCCHHHHHHHHHTSCHHHHHHTSCC
T ss_pred             cCCHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHHHHHHHHHHHHhCccccccccchHhHHHHHHHhcChHHHHHHHhh
Confidence            99999999999644211100                                    1111                    


Q ss_pred             ----------HHHHHHHHHH--------hcCCHHHHHHHHHHhhcCCCCCCC-----HHHHHHHHHHHHhcCCHHHHHHH
Q 012111          151 ----------VYTALVSAYG--------QSGLLDEAFSTINDMKSVSDCKPD-----VYTYSILIKSCTKFHRFDLIEKI  207 (471)
Q Consensus       151 ----------~~~~li~~~~--------~~~~~~~a~~~~~~~~~~~~~~~~-----~~~~~~ll~~~~~~~~~~~a~~~  207 (471)
                                ....+...+.        ..|++++|+.+|+++.+.....++     ..++..+...+...|+++.|...
T Consensus       186 ~~~~~~~~~~~~~~l~~~~~~~~~~~~~a~~~~~~A~~~~~~~l~~~p~~~~~~~~~~~~~~~~g~~~~~~~~~~~A~~~  265 (537)
T 3fp2_A          186 SSNYDTAYALLSDALQRLYSATDEGYLVANDLLTKSTDMYHSLLSANTVDDPLRENAALALCYTGIFHFLKNNLLDAQVL  265 (537)
T ss_dssp             CCSSCSSHHHHHHHHHHHHTCSHHHHHHHHHHHHHHHHHHHHHHC--CCCHHHHHHHHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             ccccccHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHCCCcchhhHHHHHHHHHHHHHHHhcccHHHHHHH
Confidence                      1111111111        124788999999999873221111     23566777788899999999999


Q ss_pred             HHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCC
Q 012111          208 LAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGV  287 (471)
Q Consensus       208 ~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~  287 (471)
                      ++.+.+.  .|+...+..+...+...|++++|.+.|+++.+..  +.+..++..+...+...|++++|...++++.... 
T Consensus       266 ~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-  340 (537)
T 3fp2_A          266 LQESINL--HPTPNSYIFLALTLADKENSQEFFKFFQKAVDLN--PEYPPTYYHRGQMYFILQDYKNAKEDFQKAQSLN-  340 (537)
T ss_dssp             HHHHHHH--CCCHHHHHHHHHHTCCSSCCHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-
T ss_pred             HHHHHhc--CCCchHHHHHHHHHHHhcCHHHHHHHHHHHhccC--CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhC-
Confidence            9999987  4568889999999999999999999999998874  5568889999999999999999999999998765 


Q ss_pred             CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC-----CCCCHH
Q 012111          288 KADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRG-----MKPNSI  362 (471)
Q Consensus       288 ~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~-----~~p~~~  362 (471)
                      +.+...+..+...+...|++++|...++.+.+... .+...+..+...+...|++++|...++++.+..     ......
T Consensus       341 ~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~-~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~  419 (537)
T 3fp2_A          341 PENVYPYIQLACLLYKQGKFTESEAFFNETKLKFP-TLPEVPTFFAEILTDRGDFDTAIKQYDIAKRLEEVQEKIHVGIG  419 (537)
T ss_dssp             TTCSHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHCSSCSSTTH
T ss_pred             CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC-CChHHHHHHHHHHHHhCCHHHHHHHHHHHHHcCCcchhhHHHHH
Confidence            45678899999999999999999999999988743 356788899999999999999999999987642     111223


Q ss_pred             HHHHHHHHHHhc----------CCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhC
Q 012111          363 TYCSLVSAYSKA----------GLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKER  425 (471)
Q Consensus       363 ~~~~li~~~~~~----------g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~  425 (471)
                      .+......+...          |++++|...++.+.+..+. +..++..+..+|...|++++|.+.|+++.+.
T Consensus       420 ~~~~~a~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~p~-~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~  491 (537)
T 3fp2_A          420 PLIGKATILARQSSQDPTQLDEEKFNAAIKLLTKACELDPR-SEQAKIGLAQLKLQMEKIDEAIELFEDSAIL  491 (537)
T ss_dssp             HHHHHHHHHHHHHTC----CCHHHHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhccchhhhHhHHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHhccHHHHHHHHHHHHHh
Confidence            345556777777          9999999999999987665 7889999999999999999999999999885

>2xm6_A Protein corresponding to locus C5321 from CFT073 strain; unknown function, SEL1-like repeats; 1.68A {Escherichia coli}

Probab=99.88  E-value=5.8e-17  Score=154.62  Aligned_cols=339  Identities=11%  Similarity=0.000  Sum_probs=290.9

Q ss_pred             hhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhc----CCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHh----c
Q 012111           91 QKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGK----CKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQ----S  162 (471)
Q Consensus        91 ~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~----~  162 (471)
                      .+++++|++.|+.+.+.+    +...+..+...|..    .+++++|...|++..+.|   +...+..|...|..    .
T Consensus        56 ~~~~~~A~~~~~~a~~~~----~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~~---~~~a~~~Lg~~y~~g~g~~  128 (490)
T 2xm6_A           56 TKDLTQAMDWFRRAAEQG----YTPAEYVLGLRYMNGEGVPQDYAQAVIWYKKAALKG---LPQAQQNLGVMYHEGNGVK  128 (490)
T ss_dssp             CCCHHHHHHHHHHHHHTT----CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSC
T ss_pred             CcCHHHHHHHHHHHHHCC----CHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCC
Confidence            789999999999998754    56788888888888    899999999999998864   67788888888888    7


Q ss_pred             CCHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHh----cCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHc----cC
Q 012111          163 GLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTK----FHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGK----AK  234 (471)
Q Consensus       163 ~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~----~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~----~~  234 (471)
                      +++++|+..|++... .   -+...+..+...|..    .+++++|.+.|++..+.|   +...+..+...|..    .+
T Consensus       129 ~~~~~A~~~~~~a~~-~---~~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~a~~~~---~~~a~~~Lg~~y~~g~g~~~  201 (490)
T 2xm6_A          129 VDKAESVKWFRLAAE-Q---GRDSGQQSMGDAYFEGDGVTRDYVMAREWYSKAAEQG---NVWSCNQLGYMYSRGLGVER  201 (490)
T ss_dssp             CCHHHHHHHHHHHHH-T---TCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCC
T ss_pred             CCHHHHHHHHHHHHH-C---CCHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHhcCCCCCc
Confidence            899999999999987 2   356777888888877    789999999999999876   77888888888887    89


Q ss_pred             CHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHh----cCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHH----cCC
Q 012111          235 KFEEMESSFSAMVESGGCHPDIFTLNSMISAYGN----SGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGR----AGM  306 (471)
Q Consensus       235 ~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~----~~~  306 (471)
                      +.++|.+.|++..+.+    +...+..+...|..    .+++++|..+|++..+.+   +...+..+...|..    .++
T Consensus       202 ~~~~A~~~~~~a~~~~----~~~a~~~lg~~y~~g~g~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~y~~g~~~~~d  274 (490)
T 2xm6_A          202 NDAISAQWYRKSATSG----DELGQLHLADMYYFGIGVTQDYTQSRVLFSQSAEQG---NSIAQFRLGYILEQGLAGAKE  274 (490)
T ss_dssp             CHHHHHHHHHHHHHTT----CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHTTT---CHHHHHHHHHHHHHTTTSSCC
T ss_pred             CHHHHHHHHHHHHHCC----CHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHCCCCCCCC
Confidence            9999999999998754    56678888888876    889999999999998754   56677777888887    899


Q ss_pred             HHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhc-----CCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcC---CHH
Q 012111          307 YDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKA-----GHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAG---LIM  378 (471)
Q Consensus       307 ~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~-----g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g---~~~  378 (471)
                      .++|...|+...+.+   +...+..+...|...     +++++|...|++..+.|   +...+..+...|...|   +.+
T Consensus       275 ~~~A~~~~~~a~~~~---~~~a~~~Lg~~y~~~~~g~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~y~~~g~~~~~~  348 (490)
T 2xm6_A          275 PLKALEWYRKSAEQG---NSDGQYYLAHLYDKGAEGVAKNREQAISWYTKSAEQG---DATAQANLGAIYFRLGSEEEHK  348 (490)
T ss_dssp             HHHHHHHHHHHHTTT---CHHHHHHHHHHHHHCBTTBCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHSCCHHHHH
T ss_pred             HHHHHHHHHHHHHcC---CHHHHHHHHHHHHcCCCCCcCCHHHHHHHHHHHHhcC---CHHHHHHHHHHHHhCCCcccHH
Confidence            999999999988763   556777788888877     89999999999999875   5567788888888766   789


Q ss_pred             HHHHHHHHHHhCCCCcCHHHHHHHHHHHHh----cCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHh----cCCHHHH
Q 012111          379 KVDSILRQVENSDVILDTPFFNCIISAYGQ----AGDVEKMGELFLTMKERHCVPDNITFATMIQAYNA----LGMTEAA  450 (471)
Q Consensus       379 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~----~g~~~~A  450 (471)
                      +|.+.|++..+.+   +...+..|...|..    .+++++|...|++..+.|   +...+..|...|..    .++.++|
T Consensus       349 ~A~~~~~~a~~~~---~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~A~~~~---~~~a~~~Lg~~y~~g~g~~~d~~~A  422 (490)
T 2xm6_A          349 KAVEWFRKAAAKG---EKAAQFNLGNALLQGKGVKKDEQQAAIWMRKAAEQG---LSAAQVQLGEIYYYGLGVERDYVQA  422 (490)
T ss_dssp             HHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHH
T ss_pred             HHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHhCC---CHHHHHHHHHHHHcCCCCCCCHHHH
Confidence            9999999999874   67888899999998    899999999999999865   67788888888888    8999999


Q ss_pred             HHHHHHHHHhhh
Q 012111          451 QNLENKMIAMKE  462 (471)
Q Consensus       451 ~~~~~~m~~~~~  462 (471)
                      ...++++.+.++
T Consensus       423 ~~~~~~A~~~~~  434 (490)
T 2xm6_A          423 WAWFDTASTNDM  434 (490)
T ss_dssp             HHHHHHHHHHHC
T ss_pred             HHHHHHHHHCCC
Confidence            999999999984

>3hym_B Cell division cycle protein 16 homolog; APC, anaphase promoting complex, cell cycle, mitosis, cyclosome, TPR, ubiquitin, ubiquitin ligase, twinning; 2.80A {Homo sapiens}

Probab=99.88  E-value=1.7e-19  Score=162.99  Aligned_cols=287  Identities=10%  Similarity=-0.026  Sum_probs=156.7

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHH
Q 012111          151 VYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGY  230 (471)
Q Consensus       151 ~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~  230 (471)
                      .+..+...+...|++++|+++|+++.+..  +.+...+..++..+...|++++|..+++++.+.. +.+...+..+...+
T Consensus        24 ~~~~~a~~~~~~g~~~~A~~~~~~~l~~~--p~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~  100 (330)
T 3hym_B           24 VVVSLAERHYYNCDFKMCYKLTSVVMEKD--PFHASCLPVHIGTLVELNKANELFYLSHKLVDLY-PSNPVSWFAVGCYY  100 (330)
T ss_dssp             THHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCTTTHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTSTHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHcC--CCChhhHHHHHHHHHHhhhHHHHHHHHHHHHHhC-cCCHHHHHHHHHHH
Confidence            34444444444455555555555444321  2223333344444445555555555555554432 22344455555555


Q ss_pred             HccC-CHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHH
Q 012111          231 GKAK-KFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDK  309 (471)
Q Consensus       231 ~~~~-~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~  309 (471)
                      ...| ++++|.+.|+++.+..  +.+...+..+...+...|++++|...++++.... +.+...+..+...+...|++++
T Consensus       101 ~~~~~~~~~A~~~~~~a~~~~--~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~  177 (330)
T 3hym_B          101 LMVGHKNEHARRYLSKATTLE--KTYGPAWIAYGHSFAVESEHDQAMAAYFTAAQLM-KGCHLPMLYIGLEYGLTNNSKL  177 (330)
T ss_dssp             HHSCSCHHHHHHHHHHHHTTC--TTCTHHHHHHHHHHHHHTCHHHHHHHHHHHHHHT-TTCSHHHHHHHHHHHHTTCHHH
T ss_pred             HHhhhhHHHHHHHHHHHHHhC--CccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhc-cccHHHHHHHHHHHHHHhhHHH
Confidence            5555 5555555555554432  2233445555555555555555555555554432 2233444445555555666666


Q ss_pred             HHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC--------CCCCHHHHHHHHHHHHhcCCHHHHH
Q 012111          310 MRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRG--------MKPNSITYCSLVSAYSKAGLIMKVD  381 (471)
Q Consensus       310 a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~--------~~p~~~~~~~li~~~~~~g~~~~a~  381 (471)
                      |...++.+.+... .+...+..+...+...|++++|...++++.+..        .+.+..++..+...+...|++++|.
T Consensus       178 A~~~~~~al~~~~-~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~  256 (330)
T 3hym_B          178 AERFFSQALSIAP-EDPFVMHEVGVVAFQNGEWKTAEKWFLDALEKIKAIGNEVTVDKWEPLLNNLGHVCRKLKKYAEAL  256 (330)
T ss_dssp             HHHHHHHHHTTCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTTSCSCTTTTCCHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHHHHHhCC-CChHHHHHHHHHHHHcccHHHHHHHHHHHHHHhhhccccccccHHHHHHHHHHHHHHHhcCHHHHH
Confidence            6666655555432 244556666666666666666666666665431        1223456677777777777777777


Q ss_pred             HHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC-CHHHHHHHHHHH-HhcCCH
Q 012111          382 SILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVP-DNITFATMIQAY-NALGMT  447 (471)
Q Consensus       382 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p-~~~~~~~l~~~~-~~~g~~  447 (471)
                      ..++++.+..+. +...+..+..++...|++++|.+.|+++.+.  .| +...+..+..++ ...|+.
T Consensus       257 ~~~~~a~~~~~~-~~~~~~~la~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~l~~~~~~~~g~~  321 (330)
T 3hym_B          257 DYHRQALVLIPQ-NASTYSAIGYIHSLMGNFENAVDYFHTALGL--RRDDTFSVTMLGHCIEMYIGDS  321 (330)
T ss_dssp             HHHHHHHHHSTT-CSHHHHHHHHHHHHHTCHHHHHHHHHTTTTT--CSCCHHHHHHHHHHHHTTTTC-
T ss_pred             HHHHHHHhhCcc-chHHHHHHHHHHHHhccHHHHHHHHHHHHcc--CCCchHHHHHHHHHHHHHhCch
Confidence            777777665544 5667777777777777777777777777664  34 555666666666 344543

>3hym_B Cell division cycle protein 16 homolog; APC, anaphase promoting complex, cell cycle, mitosis, cyclosome, TPR, ubiquitin, ubiquitin ligase, twinning; 2.80A {Homo sapiens}

Probab=99.87  E-value=3.8e-19  Score=160.60  Aligned_cols=289  Identities=11%  Similarity=-0.008  Sum_probs=153.2

Q ss_pred             chHHHHHHHHHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHH
Q 012111           78 PKPVLEALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVS  157 (471)
Q Consensus        78 ~~~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~  157 (471)
                      +..+......+...|++++|+++|+.+.+..  +.+...+..++..+...|++++|..+++.+.+.... +...|..+..
T Consensus        22 ~~~~~~~a~~~~~~g~~~~A~~~~~~~l~~~--p~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~l~~   98 (330)
T 3hym_B           22 LDVVVSLAERHYYNCDFKMCYKLTSVVMEKD--PFHASCLPVHIGTLVELNKANELFYLSHKLVDLYPS-NPVSWFAVGC   98 (330)
T ss_dssp             CTTHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCTTTHHHHHHHHHHHTCHHHHHHHHHHHHHHCTT-STHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC--CCChhhHHHHHHHHHHhhhHHHHHHHHHHHHHhCcC-CHHHHHHHHH
Confidence            4445555555555666666666666665543  444445555555555666666666666665554322 4455555555


Q ss_pred             HHHhcC-CHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCH
Q 012111          158 AYGQSG-LLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKF  236 (471)
Q Consensus       158 ~~~~~~-~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~  236 (471)
                      .+...| ++++|...|++.....  +.+...|..+...+...|++++|...++++.+.. +.+...+..+...+...|++
T Consensus        99 ~~~~~~~~~~~A~~~~~~a~~~~--~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~  175 (330)
T 3hym_B           99 YYLMVGHKNEHARRYLSKATTLE--KTYGPAWIAYGHSFAVESEHDQAMAAYFTAAQLM-KGCHLPMLYIGLEYGLTNNS  175 (330)
T ss_dssp             HHHHSCSCHHHHHHHHHHHHTTC--TTCTHHHHHHHHHHHHHTCHHHHHHHHHHHHHHT-TTCSHHHHHHHHHHHHTTCH
T ss_pred             HHHHhhhhHHHHHHHHHHHHHhC--CccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhc-cccHHHHHHHHHHHHHHhhH
Confidence            555555 5566666665555421  2233445555555555555555555555554432 22233344444445555555


Q ss_pred             HHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHH
Q 012111          237 EEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDF  316 (471)
Q Consensus       237 ~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~  316 (471)
                      ++|.+.++++.+.                                    . +.+...+..+...+...|++++|...++.
T Consensus       176 ~~A~~~~~~al~~------------------------------------~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~  218 (330)
T 3hym_B          176 KLAERFFSQALSI------------------------------------A-PEDPFVMHEVGVVAFQNGEWKTAEKWFLD  218 (330)
T ss_dssp             HHHHHHHHHHHTT------------------------------------C-TTCHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHh------------------------------------C-CCChHHHHHHHHHHHHcccHHHHHHHHHH
Confidence            5555555554443                                    2 33344444444445555555555555444


Q ss_pred             HHhCC--------CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 012111          317 MQKRF--------FFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVE  388 (471)
Q Consensus       317 ~~~~~--------~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~  388 (471)
                      +.+..        .......+..+...+...|++++|...+++..+.. +.+...+..+...+...|++++|...++++.
T Consensus       219 a~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~al  297 (330)
T 3hym_B          219 ALEKIKAIGNEVTVDKWEPLLNNLGHVCRKLKKYAEALDYHRQALVLI-PQNASTYSAIGYIHSLMGNFENAVDYFHTAL  297 (330)
T ss_dssp             HHHHHTTTSCSCTTTTCCHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCSHHHHHHHHHHHHHTCHHHHHHHHHTTT
T ss_pred             HHHHhhhccccccccHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHhhC-ccchHHHHHHHHHHHHhccHHHHHHHHHHHH
Confidence            43321        12234456666666666666666666666666543 2245566666666666677777777666666


Q ss_pred             hCCCCcCHHHHHHHHHHH-HhcCC
Q 012111          389 NSDVILDTPFFNCIISAY-GQAGD  411 (471)
Q Consensus       389 ~~~~~~~~~~~~~l~~~~-~~~g~  411 (471)
                      +..+. +...+..+..++ ...|+
T Consensus       298 ~~~p~-~~~~~~~l~~~~~~~~g~  320 (330)
T 3hym_B          298 GLRRD-DTFSVTMLGHCIEMYIGD  320 (330)
T ss_dssp             TTCSC-CHHHHHHHHHHHHTTTTC
T ss_pred             ccCCC-chHHHHHHHHHHHHHhCc
Confidence            65443 555556565555 33444

>1fch_A Peroxisomal targeting signal 1 receptor; protein-peptide complex, tetratricopeptide repeat, TPR, helical repeat, signaling protein; 2.20A {Homo sapiens} SCOP: a.118.8.1 PDB: 2j9q_A 3imz_B* 3r9a_B* 2c0m_A 2c0l_A

Probab=99.87  E-value=7e-20  Score=168.25  Aligned_cols=293  Identities=9%  Similarity=-0.037  Sum_probs=204.5

Q ss_pred             cCCHHHHHH-HHHHhhcCCCCCC--CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHH
Q 012111          162 SGLLDEAFS-TINDMKSVSDCKP--DVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEE  238 (471)
Q Consensus       162 ~~~~~~a~~-~~~~~~~~~~~~~--~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~  238 (471)
                      .|++++|++ .|++........|  +...+..+...+...|++++|...++++.+.. +.+..++..+..++...|++++
T Consensus        38 ~~~~~~a~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~  116 (368)
T 1fch_A           38 LSDYDDLTSATYDKGYQFEEENPLRDHPQPFEEGLRRLQEGDLPNAVLLFEAAVQQD-PKHMEAWQYLGTTQAENEQELL  116 (368)
T ss_dssp             --------CHHHHCCCCCCSSCTTTTCSSHHHHHHHHHHTTCHHHHHHHHHHHHHSC-TTCHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHhhhhhHHHhcCCCCcccchHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCcCHHH
Confidence            456666666 6665443221112  23445566666667777777777777776654 3456666667777777777777


Q ss_pred             HHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHH---------------HHHHHHH
Q 012111          239 MESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNI---------------LTKSYGR  303 (471)
Q Consensus       239 a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~---------------ll~~~~~  303 (471)
                      |...|+++.+..  +.+..++..+...+...|++++|...++++.... +.+...+..               .+..+..
T Consensus       117 A~~~~~~al~~~--~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  193 (368)
T 1fch_A          117 AISALRRCLELK--PDNQTALMALAVSFTNESLQRQACEILRDWLRYT-PAYAHLVTPAEEGAGGAGLGPSKRILGSLLS  193 (368)
T ss_dssp             HHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTS-TTTGGGCC---------------CTTHHHHH
T ss_pred             HHHHHHHHHhcC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cCcHHHHHHHHHHhhhhcccHHHHHHHHHhh
Confidence            777777766653  4456666677777777777777777777766543 112111111               2333348


Q ss_pred             cCCHHHHHHHHHHHHhCCCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHH
Q 012111          304 AGMYDKMRSVMDFMQKRFFFP-TVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDS  382 (471)
Q Consensus       304 ~~~~~~a~~~~~~~~~~~~~~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~  382 (471)
                      .|++++|...++.+.+..... +...+..+...+...|++++|...++++.... +.+..++..+...+...|++++|..
T Consensus       194 ~~~~~~A~~~~~~a~~~~p~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~g~~~~A~~  272 (368)
T 1fch_A          194 DSLFLEVKELFLAAVRLDPTSIDPDVQCGLGVLFNLSGEYDKAVDCFTAALSVR-PNDYLLWNKLGATLANGNQSEEAVA  272 (368)
T ss_dssp             HHHHHHHHHHHHHHHHHSTTSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             cccHHHHHHHHHHHHHhCcCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHcCCHHHHHH
Confidence            899999999999888764332 47788889999999999999999999988863 4467889999999999999999999


Q ss_pred             HHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCC----------CCHHHHHHHHHHHHhcCCHHHHHH
Q 012111          383 ILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCV----------PDNITFATMIQAYNALGMTEAAQN  452 (471)
Q Consensus       383 ~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~----------p~~~~~~~l~~~~~~~g~~~~A~~  452 (471)
                      .++++.+..+. +..++..+..+|...|++++|...|+++.+..-.          ....+|..+..++...|+.++|..
T Consensus       273 ~~~~al~~~~~-~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~  351 (368)
T 1fch_A          273 AYRRALELQPG-YIRSRYNLGISCINLGAHREAVEHFLEALNMQRKSRGPRGEGGAMSENIWSTLRLALSMLGQSDAYGA  351 (368)
T ss_dssp             HHHHHHHHCTT-CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHTC------CCCCCHHHHHHHHHHHHHHTCGGGHHH
T ss_pred             HHHHHHHhCCC-cHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCCCccccccchhhHHHHHHHHHHHHhCChHhHHH
Confidence            99998887654 7788999999999999999999999988763111          126889999999999999999998


Q ss_pred             HHHHHHHh
Q 012111          453 LENKMIAM  460 (471)
Q Consensus       453 ~~~~m~~~  460 (471)
                      ++++.++.
T Consensus       352 ~~~~~l~~  359 (368)
T 1fch_A          352 ADARDLST  359 (368)
T ss_dssp             HHTTCHHH
T ss_pred             hHHHHHHH
Confidence            88765543

>2ooe_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 3.00A {Mus musculus} SCOP: a.118.8.7

Probab=99.85  E-value=1.1e-16  Score=154.33  Aligned_cols=397  Identities=9%  Similarity=0.021  Sum_probs=264.8

Q ss_pred             HhhHHHHHHHHHhhhhhhccCCCchHHHHHHHHHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHH-hcCCCHHHH
Q 012111           55 LRTEFAIKNIEKKVSSKKYKNLWPKPVLEALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVML-GKCKQPEQA  133 (471)
Q Consensus        55 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~-~~~~~~~~a  133 (471)
                      .+...+...++..+..   .+..+..+...+....+.|++++|.++|+.+....   |+...|...+... ...|+.+.|
T Consensus        26 ~~~~~a~~~~e~al~~---~P~~~~~w~~~~~~~~~~~~~~~a~~~~~ral~~~---p~~~lw~~~~~~~~~~~~~~~~a   99 (530)
T 2ooe_A           26 QPIDKARKTYERLVAQ---FPSSGRFWKLYIEAEIKAKNYDKVEKLFQRCLMKV---LHIDLWKCYLSYVRETKGKLPSY   99 (530)
T ss_dssp             SCHHHHHHHHHHHHTT---CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTTC---CCHHHHHHHHHHHHHHTTTSTTH
T ss_pred             CCHHHHHHHHHHHHHH---CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcC---CChHHHHHHHHHHHHHccchhhH
Confidence            3444444445544442   23445566677777777778888888888777653   4666666665432 344565555


Q ss_pred             HH----HHHHHHhC-CCC-CCHHHHHHHHHHHHh---------cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHH---
Q 012111          134 SL----LFEVMLSD-GLK-PSVDVYTALVSAYGQ---------SGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSC---  195 (471)
Q Consensus       134 ~~----~~~~m~~~-~~~-~~~~~~~~li~~~~~---------~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~---  195 (471)
                      .+    +|+..... |.. .+...|...+.....         .|+++.|..+|++..+ .+.......|.......   
T Consensus       100 ~~~~~~~~~~al~~~g~~~~~~~~w~~~~~~~~~~~~~~~~~~~~~~~~a~~~y~~al~-~P~~~~~~~~~~~~~~e~~~  178 (530)
T 2ooe_A          100 KEKMAQAYDFALDKIGMEIMSYQIWVDYINFLKGVEAVGSYAENQRITAVRRVYQRGCV-NPMINIEQLWRDYNKYEEGI  178 (530)
T ss_dssp             HHHHHHHHHHHHHHTTTSTTCHHHHHHHHHHHHHSCCCSSTTHHHHHHHHHHHHHHHTT-SCCTTHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHCCCCcccHHHHHHHHHHHhcCCCcccHHHHhHHHHHHHHHHHHHh-chhhhHHHHHHHHHHHHHhh
Confidence            44    66655442 433 245667766665544         5677888888888776 22111123333222211   


Q ss_pred             ----------HhcCCHHHHHHHHHHHH------HCC---CCCC--------HHHHHHHHHHHHcc----CCH----HHHH
Q 012111          196 ----------TKFHRFDLIEKILAEMS------YLG---IECS--------AVTYNTIIDGYGKA----KKF----EEME  240 (471)
Q Consensus       196 ----------~~~~~~~~a~~~~~~~~------~~g---~~~~--------~~~~~~l~~~~~~~----~~~----~~a~  240 (471)
                                .+.+++..|..++..+.      +..   ++|+        ...|...+......    ++.    ..+.
T Consensus       179 ~~~~~~~~l~~~~~~~~~A~~~~~~~~~~~~~l~~~~~~~~p~~~~~~~~~~~~w~~~~~~e~~~~~~~~~~~~~~~~a~  258 (530)
T 2ooe_A          179 NIHLAKKMIEDRSRDYMNARRVAKEYETVMKGLDRNAPSVPPQNTPQEAQQVDMWKKYIQWEKSNPLRTEDQTLITKRVM  258 (530)
T ss_dssp             CHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHCCSSSCCCCCC--CCHHHHHHHHHHHHHHHHHCSSCCSCSHHHHHHHH
T ss_pred             chhHHHHHHHHhhHHHHHHHHHHHHHHHHHHHhccccccCCCCCChhHHHHHHHHHHHHHHHHcCCccCCcchhHHHHHH
Confidence                      12344556666655422      111   2333        23444444333221    222    3677


Q ss_pred             HHHHHHHHcCCCCCCHHHHHHHHHHHHh-------cCCHH-------HHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCC
Q 012111          241 SSFSAMVESGGCHPDIFTLNSMISAYGN-------SGNIE-------KMEKWYNEFNLMGVKADIQTLNILTKSYGRAGM  306 (471)
Q Consensus       241 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~-------~~~~~-------~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~  306 (471)
                      .+|++.....  +.+...|..++..+.+       .|+++       +|..+|++....-.+.+...+..++..+.+.|+
T Consensus       259 ~~y~~al~~~--p~~~~~w~~~~~~~~~~~~~~~~~g~~~~a~~~~~~A~~~~~~Al~~~~p~~~~l~~~~~~~~~~~g~  336 (530)
T 2ooe_A          259 FAYEQCLLVL--GHHPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANIYERAISTLLKKNMLLYFAYADYEESRMK  336 (530)
T ss_dssp             HHHHHHHHHH--TTCHHHHHHHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHHHHHHTTTTCSSCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHhC--CCCHHHHHHHHHHHHHhchhhhhccchhhhhhhhHHHHHHHHHHHHHhCcccHHHHHHHHHHHHhcCC
Confidence            7888887763  4567778888887775       68877       899999998863235568889999999999999


Q ss_pred             HHHHHHHHHHHHhCCCCCCH-HHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHH-HHhcCCHHHHHHHH
Q 012111          307 YDKMRSVMDFMQKRFFFPTV-VTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSA-YSKAGLIMKVDSIL  384 (471)
Q Consensus       307 ~~~a~~~~~~~~~~~~~~~~-~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~-~~~~g~~~~a~~~~  384 (471)
                      +++|..+|+.+.+.... +. ..|..++..+.+.|++++|..+|++..+.. +.+...|...+.. +...|+.++|..+|
T Consensus       337 ~~~A~~~~~~al~~~p~-~~~~~~~~~~~~~~~~~~~~~A~~~~~~Al~~~-~~~~~~~~~~a~~~~~~~~~~~~A~~~~  414 (530)
T 2ooe_A          337 YEKVHSIYNRLLAIEDI-DPTLVYIQYMKFARRAEGIKSGRMIFKKAREDA-RTRHHVYVTAALMEYYCSKDKSVAFKIF  414 (530)
T ss_dssp             HHHHHHHHHHHHHSSSS-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCT-TCCTHHHHHHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHHHHHhCcccc-CchHHHHHHHHHHHHhcCHHHHHHHHHHHHhcc-CCchHHHHHHHHHHHHHcCChhHHHHHH
Confidence            99999999999886322 32 478888888889999999999999998753 2233333332222 34689999999999


Q ss_pred             HHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCC-CCCC--HHHHHHHHHHHHhcCCHHHHHHHHHHHHHhh
Q 012111          385 RQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERH-CVPD--NITFATMIQAYNALGMTEAAQNLENKMIAMK  461 (471)
Q Consensus       385 ~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~-~~p~--~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~  461 (471)
                      +...+..+. +...|..++..+.+.|+.++|..+|++....+ ..|+  ...|...+......|+.+.+..+.+++.+.-
T Consensus       415 e~al~~~p~-~~~~~~~~~~~~~~~g~~~~Ar~~~~~al~~~~~~~~~~~~lw~~~~~~e~~~G~~~~~~~~~~r~~~~~  493 (530)
T 2ooe_A          415 ELGLKKYGD-IPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSGEIWARFLAFESNIGDLASILKVEKRRFTAF  493 (530)
T ss_dssp             HHHHHHHTT-CHHHHHHHHHHHTTTTCHHHHHHHHHHHHHSCCSCGGGCHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHT
T ss_pred             HHHHHHCCC-CHHHHHHHHHHHHhCCCHhhHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC
Confidence            998876544 68889999999999999999999999998863 2232  4578888888888999999999999999888


Q ss_pred             hc
Q 012111          462 EN  463 (471)
Q Consensus       462 ~~  463 (471)
                      |.
T Consensus       494 p~  495 (530)
T 2ooe_A          494 RE  495 (530)
T ss_dssp             HH
T ss_pred             ch
Confidence            74

>4eqf_A PEX5-related protein; accessory protein, tetratricopeptide repeat, TPR; 3.00A {Mus musculus}

Probab=99.85  E-value=1.4e-19  Score=166.12  Aligned_cols=266  Identities=8%  Similarity=-0.082  Sum_probs=208.1

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHH
Q 012111          184 DVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMI  263 (471)
Q Consensus       184 ~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~  263 (471)
                      +...+..+...+.+.|++++|..+|+++.+.. +.+..++..+..++...|++++|...|+++.+..  +.+...+..+.
T Consensus        64 ~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~~l~  140 (365)
T 4eqf_A           64 DWPGAFEEGLKRLKEGDLPVTILFMEAAILQD-PGDAEAWQFLGITQAENENEQAAIVALQRCLELQ--PNNLKALMALA  140 (365)
T ss_dssp             TCTTHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHH
T ss_pred             chhHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC--CCCHHHHHHHH
Confidence            34457777788888888888888888887764 4567888888888888888888888888887763  45677888888


Q ss_pred             HHHHhcCCHHHHHHHHHHHHhCCCCCC-----------HHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCC-CCHHHHHH
Q 012111          264 SAYGNSGNIEKMEKWYNEFNLMGVKAD-----------IQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFF-PTVVTYNI  331 (471)
Q Consensus       264 ~~~~~~~~~~~a~~~~~~~~~~~~~~~-----------~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~~  331 (471)
                      .+|...|++++|...++++....  |+           ...+..+...+...|++++|...++.+.+.... .+...+..
T Consensus       141 ~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~  218 (365)
T 4eqf_A          141 VSYTNTSHQQDACEALKNWIKQN--PKYKYLVKNKKGSPGLTRRMSKSPVDSSVLEGVKELYLEAAHQNGDMIDPDLQTG  218 (365)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHC--HHHHCC-------------------CCHHHHHHHHHHHHHHHHSCSSCCHHHHHH
T ss_pred             HHHHccccHHHHHHHHHHHHHhC--ccchHHHhhhccchHHHHHHHHHHhhhhhHHHHHHHHHHHHHhCcCccCHHHHHH
Confidence            88888888888888888886642  21           223345577888999999999999999886433 15788899


Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCC
Q 012111          332 VIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGD  411 (471)
Q Consensus       332 li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~  411 (471)
                      +...+...|++++|...++++.+.. +.+..++..+..++...|++++|...++++.+..+. +..++..+..+|...|+
T Consensus       219 l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~l~~~~~~~g~  296 (365)
T 4eqf_A          219 LGVLFHLSGEFNRAIDAFNAALTVR-PEDYSLWNRLGATLANGDRSEEAVEAYTRALEIQPG-FIRSRYNLGISCINLGA  296 (365)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCC-chHHHHHHHHHHHHCCC
Confidence            9999999999999999999998864 446889999999999999999999999999887655 68889999999999999


Q ss_pred             HHHHHHHHHHHHhCC---CC--------CCHHHHHHHHHHHHhcCCHHHHHHHHHH
Q 012111          412 VEKMGELFLTMKERH---CV--------PDNITFATMIQAYNALGMTEAAQNLENK  456 (471)
Q Consensus       412 ~~~a~~~~~~~~~~~---~~--------p~~~~~~~l~~~~~~~g~~~~A~~~~~~  456 (471)
                      +++|...|+++.+..   ..        .+...|..+..++...|+.+.+.++.++
T Consensus       297 ~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~  352 (365)
T 4eqf_A          297 YREAVSNFLTALSLQRKSRNQQQVPHPAISGNIWAALRIALSLMDQPELFQAANLG  352 (365)
T ss_dssp             CHHHHHHHHHHHHHHHCC------------CHHHHHHHHHHHHHTCHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHhCcccCCCcccchhhhHHHHHHHHHHHHHHcCcHHHHHHHHHh
Confidence            999999999987631   00        1357888999999999999998877665

>1fch_A Peroxisomal targeting signal 1 receptor; protein-peptide complex, tetratricopeptide repeat, TPR, helical repeat, signaling protein; 2.20A {Homo sapiens} SCOP: a.118.8.1 PDB: 2j9q_A 3imz_B* 3r9a_B* 2c0m_A 2c0l_A

Probab=99.84  E-value=8.1e-19  Score=161.13  Aligned_cols=305  Identities=10%  Similarity=-0.028  Sum_probs=171.5

Q ss_pred             HhhcHHHHHH-HHHHhhhccCccC--ChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHH
Q 012111           90 KQKKWQLALK-IFGLLRQQQWYQA--RCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLD  166 (471)
Q Consensus        90 ~~~~~~~A~~-~~~~~~~~~~~~~--~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~  166 (471)
                      -.|++++|++ .|+.+.....-.|  +...+..+...+.+.|++++|...|+.+.+... .+..++..+..++...|+++
T Consensus        37 ~~~~~~~a~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~p-~~~~~~~~l~~~~~~~g~~~  115 (368)
T 1fch_A           37 WLSDYDDLTSATYDKGYQFEEENPLRDHPQPFEEGLRRLQEGDLPNAVLLFEAAVQQDP-KHMEAWQYLGTTQAENEQEL  115 (368)
T ss_dssp             ---------CHHHHCCCCCCSSCTTTTCSSHHHHHHHHHHTTCHHHHHHHHHHHHHSCT-TCHHHHHHHHHHHHHTTCHH
T ss_pred             HHHHHHHHHhhhhhHHHhcCCCCcccchHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHCcCHH
Confidence            3466777776 6666554321112  244566777777777777777777777776643 25667777777777777777


Q ss_pred             HHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHH
Q 012111          167 EAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAM  246 (471)
Q Consensus       167 ~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  246 (471)
                      +|+..|+++.+..  +.+..++..+...+...|++++|...++++.+.. +.+...+..+..       ..         
T Consensus       116 ~A~~~~~~al~~~--~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~~~~-------~~---------  176 (368)
T 1fch_A          116 LAISALRRCLELK--PDNQTALMALAVSFTNESLQRQACEILRDWLRYT-PAYAHLVTPAEE-------GA---------  176 (368)
T ss_dssp             HHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTS-TTTGGGCC----------------------
T ss_pred             HHHHHHHHHHhcC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cCcHHHHHHHHH-------Hh---------
Confidence            7777777766522  3456666677777777777777777777776653 111111111000       00         


Q ss_pred             HHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC--CHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCC
Q 012111          247 VESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKA--DIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFP  324 (471)
Q Consensus       247 ~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~--~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~  324 (471)
                       ..  ..+. ..+..+ ..+...|++++|...++++.... +.  +..++..+...+...|++++|...++.+.+... .
T Consensus       177 -~~--~~~~-~~~~~~-~~~~~~~~~~~A~~~~~~a~~~~-p~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~-~  249 (368)
T 1fch_A          177 -GG--AGLG-PSKRIL-GSLLSDSLFLEVKELFLAAVRLD-PTSIDPDVQCGLGVLFNLSGEYDKAVDCFTAALSVRP-N  249 (368)
T ss_dssp             -------------CTT-HHHHHHHHHHHHHHHHHHHHHHS-TTSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-T
T ss_pred             -hh--hccc-HHHHHH-HHHhhcccHHHHHHHHHHHHHhC-cCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCc-C
Confidence             00  0000 001112 22225566666666666665543 12  455666666666666666666666666655422 2


Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCc----------
Q 012111          325 TVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVIL----------  394 (471)
Q Consensus       325 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~----------  394 (471)
                      +...+..+...+...|++++|...++++.... +.+..++..+...+.+.|++++|...++++.+..+..          
T Consensus       250 ~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~  328 (368)
T 1fch_A          250 DYLLWNKLGATLANGNQSEEAVAAYRRALELQ-PGYIRSRYNLGISCINLGAHREAVEHFLEALNMQRKSRGPRGEGGAM  328 (368)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHTC------CCCC
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCCCccccccch
Confidence            45566666666667777777777777666542 3345666667777777777777777776665432221          


Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 012111          395 DTPFFNCIISAYGQAGDVEKMGELFLTM  422 (471)
Q Consensus       395 ~~~~~~~l~~~~~~~g~~~~a~~~~~~~  422 (471)
                      ...+|..+..+|...|++++|..++++.
T Consensus       329 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~  356 (368)
T 1fch_A          329 SENIWSTLRLALSMLGQSDAYGAADARD  356 (368)
T ss_dssp             CHHHHHHHHHHHHHHTCGGGHHHHHTTC
T ss_pred             hhHHHHHHHHHHHHhCChHhHHHhHHHH
Confidence            1566777777777777777777766543

>2xm6_A Protein corresponding to locus C5321 from CFT073 strain; unknown function, SEL1-like repeats; 1.68A {Escherichia coli}

Probab=99.82  E-value=4.9e-15  Score=141.28  Aligned_cols=332  Identities=15%  Similarity=0.054  Sum_probs=281.0

Q ss_pred             HHHHHHHhhhccCccCChhHHHHHHHHHhc----CCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHh----cCCHHHH
Q 012111           97 ALKIFGLLRQQQWYQARCQTFTKLMVMLGK----CKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQ----SGLLDEA  168 (471)
Q Consensus        97 A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~----~~~~~~a  168 (471)
                      +++.++...+.    .+...+..+...|..    .+++++|...|+...+.|   +...+..|...|..    .+++++|
T Consensus        26 ~~~~~~~~a~~----g~~~a~~~lg~~y~~g~~~~~~~~~A~~~~~~a~~~~---~~~a~~~Lg~~y~~g~g~~~~~~~A   98 (490)
T 2xm6_A           26 NLEQLKQKAES----GEAKAQLELGYRYFQGNETTKDLTQAMDWFRRAAEQG---YTPAEYVLGLRYMNGEGVPQDYAQA   98 (490)
T ss_dssp             CHHHHHHHHHT----TCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHH
T ss_pred             HHHHHHHHHHC----CCHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCCCHHHH
Confidence            45555555543    366778888888877    899999999999998864   67888889999998    8999999


Q ss_pred             HHHHHHhhcCCCCCCCHHHHHHHHHHHHh----cCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHc----cCCHHHHH
Q 012111          169 FSTINDMKSVSDCKPDVYTYSILIKSCTK----FHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGK----AKKFEEME  240 (471)
Q Consensus       169 ~~~~~~~~~~~~~~~~~~~~~~ll~~~~~----~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~----~~~~~~a~  240 (471)
                      ++.|++..+ .   -+...+..|...|..    .+++++|.+.|+...+.|   +...+..+...|..    .+++++|.
T Consensus        99 ~~~~~~a~~-~---~~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~~---~~~a~~~Lg~~y~~g~g~~~d~~~A~  171 (490)
T 2xm6_A           99 VIWYKKAAL-K---GLPQAQQNLGVMYHEGNGVKVDKAESVKWFRLAAEQG---RDSGQQSMGDAYFEGDGVTRDYVMAR  171 (490)
T ss_dssp             HHHHHHHHH-T---TCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHH
T ss_pred             HHHHHHHHH-C---CCHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCCCHHHHH
Confidence            999999987 2   366777788888887    789999999999999876   67788888888887    78999999


Q ss_pred             HHHHHHHHcCCCCCCHHHHHHHHHHHHh----cCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHH----cCCHHHHHH
Q 012111          241 SSFSAMVESGGCHPDIFTLNSMISAYGN----SGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGR----AGMYDKMRS  312 (471)
Q Consensus       241 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~----~~~~~~a~~  312 (471)
                      +.|++..+.+    +...+..+...|..    .++.++|.++|++..+.+   +...+..+...|..    .+++++|..
T Consensus       172 ~~~~~a~~~~----~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~y~~g~g~~~~~~~A~~  244 (490)
T 2xm6_A          172 EWYSKAAEQG----NVWSCNQLGYMYSRGLGVERNDAISAQWYRKSATSG---DELGQLHLADMYYFGIGVTQDYTQSRV  244 (490)
T ss_dssp             HHHHHHHHTT----CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHH
T ss_pred             HHHHHHHHCC----CHHHHHHHHHHHhcCCCCCcCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCCCHHHHHH
Confidence            9999998764    67788888888888    899999999999998865   56778888888886    789999999


Q ss_pred             HHHHHHhCCCCCCHHHHHHHHHHHHh----cCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhc-----CCHHHHHHH
Q 012111          313 VMDFMQKRFFFPTVVTYNIVIETFGK----AGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKA-----GLIMKVDSI  383 (471)
Q Consensus       313 ~~~~~~~~~~~~~~~~~~~li~~~~~----~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~-----g~~~~a~~~  383 (471)
                      .|+...+.+   +...+..+...|..    .++.++|..+|++..+.|   +...+..+...|...     ++.++|...
T Consensus       245 ~~~~a~~~~---~~~a~~~lg~~y~~g~~~~~d~~~A~~~~~~a~~~~---~~~a~~~Lg~~y~~~~~g~~~~~~~A~~~  318 (490)
T 2xm6_A          245 LFSQSAEQG---NSIAQFRLGYILEQGLAGAKEPLKALEWYRKSAEQG---NSDGQYYLAHLYDKGAEGVAKNREQAISW  318 (490)
T ss_dssp             HHHHHHTTT---CHHHHHHHHHHHHHTTTSSCCHHHHHHHHHHHHTTT---CHHHHHHHHHHHHHCBTTBCCCHHHHHHH
T ss_pred             HHHHHHHCC---CHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHcC---CHHHHHHHHHHHHcCCCCCcCCHHHHHHH
Confidence            999988763   45667777777877    899999999999998765   566778888888887     899999999


Q ss_pred             HHHHHhCCCCcCHHHHHHHHHHHHhcC---CHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHh----cCCHHHHHHHHHH
Q 012111          384 LRQVENSDVILDTPFFNCIISAYGQAG---DVEKMGELFLTMKERHCVPDNITFATMIQAYNA----LGMTEAAQNLENK  456 (471)
Q Consensus       384 ~~~~~~~~~~~~~~~~~~l~~~~~~~g---~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~----~g~~~~A~~~~~~  456 (471)
                      +++..+.+   +...+..+...|...|   ++++|+++|++..+.   .++..+..|...|..    .++.++|.+++++
T Consensus       319 ~~~a~~~~---~~~a~~~lg~~y~~~g~~~~~~~A~~~~~~a~~~---~~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~  392 (490)
T 2xm6_A          319 YTKSAEQG---DATAQANLGAIYFRLGSEEEHKKAVEWFRKAAAK---GEKAAQFNLGNALLQGKGVKKDEQQAAIWMRK  392 (490)
T ss_dssp             HHHHHHTT---CHHHHHHHHHHHHHSCCHHHHHHHHHHHHHHHHT---TCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHH
T ss_pred             HHHHHhcC---CHHHHHHHHHHHHhCCCcccHHHHHHHHHHHHHC---CCHHHHHHHHHHHHcCCCCCCCHHHHHHHHHH
Confidence            99999876   5677888888888766   899999999999986   368888889999988    8999999999999


Q ss_pred             HHHhh
Q 012111          457 MIAMK  461 (471)
Q Consensus       457 m~~~~  461 (471)
                      +.+.+
T Consensus       393 A~~~~  397 (490)
T 2xm6_A          393 AAEQG  397 (490)
T ss_dssp             HHHTT
T ss_pred             HHhCC
Confidence            98765

>3cv0_A Peroxisome targeting signal 1 receptor PEX5; TPR motifs, TPR protein, peroxin 5, PEX5, PTS1 binding domain, protein-peptide complex, receptor; 2.00A {Trypanosoma brucei} PDB: 3cvl_A 3cvn_A 3cvp_A 3cvq_A

Probab=99.82  E-value=6e-18  Score=152.50  Aligned_cols=266  Identities=5%  Similarity=-0.058  Sum_probs=174.4

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHh
Q 012111          189 SILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGN  268 (471)
Q Consensus       189 ~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  268 (471)
                      ..+...+...|++++|..+++++.+.. +.+...+..+..++...|++++|...++++.+..  +.+...+..+...+..
T Consensus        25 ~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~--~~~~~~~~~la~~~~~  101 (327)
T 3cv0_A           25 MEEGLSMLKLANLAEAALAFEAVCQAA-PEREEAWRSLGLTQAENEKDGLAIIALNHARMLD--PKDIAVHAALAVSHTN  101 (327)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC--cCCHHHHHHHHHHHHH
Confidence            333444444445555555554444432 2244444444555555555555555555544432  2334444455555555


Q ss_pred             cCCHHHHHHHHHHHHhCCCCCCHHHHHHH--------------HH-HHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHH
Q 012111          269 SGNIEKMEKWYNEFNLMGVKADIQTLNIL--------------TK-SYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVI  333 (471)
Q Consensus       269 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~l--------------l~-~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li  333 (471)
                      .|++++|...++++.... +.+...+..+              .. .+...|++++|...++.+.+.... +...+..+.
T Consensus       102 ~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~la  179 (327)
T 3cv0_A          102 EHNANAALASLRAWLLSQ-PQYEQLGSVNLQADVDIDDLNVQSEDFFFAAPNEYRECRTLLHAALEMNPN-DAQLHASLG  179 (327)
T ss_dssp             TTCHHHHHHHHHHHHHTS-TTTTTC--------------------CCTTSHHHHHHHHHHHHHHHHHSTT-CHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHHhC-CccHHHHHHHhHHHHHHHHHHHHHHhHHHHHcccHHHHHHHHHHHHhhCCC-CHHHHHHHH
Confidence            555555555555544332 1111111111              22 366677888888888888776433 677788888


Q ss_pred             HHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHH
Q 012111          334 ETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVE  413 (471)
Q Consensus       334 ~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~  413 (471)
                      ..+...|++++|...++++.... +.+..++..+...+...|++++|...++++.+..+. +..++..+..++...|+++
T Consensus       180 ~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~-~~~~~~~l~~~~~~~g~~~  257 (327)
T 3cv0_A          180 VLYNLSNNYDSAAANLRRAVELR-PDDAQLWNKLGATLANGNRPQEALDAYNRALDINPG-YVRVMYNMAVSYSNMSQYD  257 (327)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHH
T ss_pred             HHHHHhccHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCC-CHHHHHHHHHHHHHhccHH
Confidence            88888999999999998888763 346778888889999999999999999988876554 6778888999999999999


Q ss_pred             HHHHHHHHHHhCCCCCC-------------HHHHHHHHHHHHhcCCHHHHHHHHHHHHHhhhc
Q 012111          414 KMGELFLTMKERHCVPD-------------NITFATMIQAYNALGMTEAAQNLENKMIAMKEN  463 (471)
Q Consensus       414 ~a~~~~~~~~~~~~~p~-------------~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~  463 (471)
                      +|.+.++++.+.  .|+             ...+..+..++...|++++|..++++.++.-++
T Consensus       258 ~A~~~~~~a~~~--~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~l~~~~~  318 (327)
T 3cv0_A          258 LAAKQLVRAIYM--QVGGTTPTGEASREATRSMWDFFRMLLNVMNRPDLVELTYAQNVEPFAK  318 (327)
T ss_dssp             HHHHHHHHHHHH--HTTSCC-----CCTHHHHHHHHHHHHHHHTTCHHHHHHHTTCCSHHHHH
T ss_pred             HHHHHHHHHHHh--CCccccccccchhhcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhcch
Confidence            999999988764  233             678888889999999999999998877666554

>4eqf_A PEX5-related protein; accessory protein, tetratricopeptide repeat, TPR; 3.00A {Mus musculus}

Probab=99.82  E-value=6.2e-18  Score=155.08  Aligned_cols=265  Identities=9%  Similarity=-0.059  Sum_probs=134.0

Q ss_pred             HHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHH
Q 012111          117 FTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCT  196 (471)
Q Consensus       117 ~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~  196 (471)
                      +..+...+.+.|++++|...|+.+.+... .+..+|..+..++...|++++|+..|+++.+..  +.+..++..+...+.
T Consensus        68 ~~~~~~~~~~~g~~~~A~~~~~~al~~~p-~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~~l~~~~~  144 (365)
T 4eqf_A           68 AFEEGLKRLKEGDLPVTILFMEAAILQDP-GDAEAWQFLGITQAENENEQAAIVALQRCLELQ--PNNLKALMALAVSYT  144 (365)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHhCc-CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC--CCCHHHHHHHHHHHH
Confidence            44444444444444444444444444321 134444444444444444444444444444311  223444444444444


Q ss_pred             hcCCHHHHHHHHHHHHHCCCC---------CCHHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHH
Q 012111          197 KFHRFDLIEKILAEMSYLGIE---------CSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYG  267 (471)
Q Consensus       197 ~~~~~~~a~~~~~~~~~~g~~---------~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~  267 (471)
                      ..|++++|...++++.+....         .....+..+...+...|++++|...|+++.+..+...+...+..+...+.
T Consensus       145 ~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~l~~~~~  224 (365)
T 4eqf_A          145 NTSHQQDACEALKNWIKQNPKYKYLVKNKKGSPGLTRRMSKSPVDSSVLEGVKELYLEAAHQNGDMIDPDLQTGLGVLFH  224 (365)
T ss_dssp             HTTCHHHHHHHHHHHHHHCHHHHCC-------------------CCHHHHHHHHHHHHHHHHSCSSCCHHHHHHHHHHHH
T ss_pred             ccccHHHHHHHHHHHHHhCccchHHHhhhccchHHHHHHHHHHhhhhhHHHHHHHHHHHHHhCcCccCHHHHHHHHHHHH
Confidence            444444444444444432100         01122333455566666666666666666655322224556666666666


Q ss_pred             hcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHH
Q 012111          268 NSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEE  347 (471)
Q Consensus       268 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~  347 (471)
                      ..|++++|...|+++.... +.+..++..+..+|...|++++|...|+.+.+.... +...+..+..+|...|++++|..
T Consensus       225 ~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~l~~~~~~~g~~~~A~~  302 (365)
T 4eqf_A          225 LSGEFNRAIDAFNAALTVR-PEDYSLWNRLGATLANGDRSEEAVEAYTRALEIQPG-FIRSRYNLGISCINLGAYREAVS  302 (365)
T ss_dssp             HHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHTCCHHHHH
T ss_pred             HCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCC-chHHHHHHHHHHHHCCCHHHHHH
Confidence            6666666666666665543 445566666666666666666666666666554222 35566666666666666666666


Q ss_pred             HHHHHHHcCCC-----------CCHHHHHHHHHHHHhcCCHHHHHHHHHH
Q 012111          348 YFKKMKHRGMK-----------PNSITYCSLVSAYSKAGLIMKVDSILRQ  386 (471)
Q Consensus       348 ~~~~m~~~~~~-----------p~~~~~~~li~~~~~~g~~~~a~~~~~~  386 (471)
                      .|+++.+....           .+..+|..+..++...|+.+.+..+..+
T Consensus       303 ~~~~al~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~  352 (365)
T 4eqf_A          303 NFLTALSLQRKSRNQQQVPHPAISGNIWAALRIALSLMDQPELFQAANLG  352 (365)
T ss_dssp             HHHHHHHHHHCC------------CHHHHHHHHHHHHHTCHHHHHHHHTT
T ss_pred             HHHHHHHhCcccCCCcccchhhhHHHHHHHHHHHHHHcCcHHHHHHHHHh
Confidence            66666543100           0245667777777777777776666544

>3cv0_A Peroxisome targeting signal 1 receptor PEX5; TPR motifs, TPR protein, peroxin 5, PEX5, PTS1 binding domain, protein-peptide complex, receptor; 2.00A {Trypanosoma brucei} PDB: 3cvl_A 3cvn_A 3cvp_A 3cvq_A

Probab=99.81  E-value=1.9e-17  Score=149.24  Aligned_cols=277  Identities=10%  Similarity=-0.004  Sum_probs=164.9

Q ss_pred             hHHHHHHHHHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHH
Q 012111           79 KPVLEALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSA  158 (471)
Q Consensus        79 ~~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~  158 (471)
                      ..+......+...|++++|+++|+.+.+..  +.+...+..+..++...|++++|...++.+.+... .+..++..+...
T Consensus        22 ~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~-~~~~~~~~la~~   98 (327)
T 3cv0_A           22 ENPMEEGLSMLKLANLAEAALAFEAVCQAA--PEREEAWRSLGLTQAENEKDGLAIIALNHARMLDP-KDIAVHAALAVS   98 (327)
T ss_dssp             SCHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhccHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCc-CCHHHHHHHHHH
Confidence            445566667778889999999998888764  56777888888888888999999998888887643 367788888888


Q ss_pred             HHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHH--HHHccCCH
Q 012111          159 YGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIID--GYGKAKKF  236 (471)
Q Consensus       159 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~--~~~~~~~~  236 (471)
                      +...|++++|.+.++++....  +.+...+..+...+                      ++......+..  .+...|++
T Consensus        99 ~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~~~~~~----------------------~~~~~~~~~~~~~~~~~~~~~  154 (327)
T 3cv0_A           99 HTNEHNANAALASLRAWLLSQ--PQYEQLGSVNLQAD----------------------VDIDDLNVQSEDFFFAAPNEY  154 (327)
T ss_dssp             HHHTTCHHHHHHHHHHHHHTS--TTTTTC------------------------------------------CCTTSHHHH
T ss_pred             HHHcCCHHHHHHHHHHHHHhC--CccHHHHHHHhHHH----------------------HHHHHHHHHHHhHHHHHcccH
Confidence            888888888888888887632  12222222220000                      00001111111  24445555


Q ss_pred             HHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHH
Q 012111          237 EEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDF  316 (471)
Q Consensus       237 ~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~  316 (471)
                      ++|...++++.+..  +.+...+..+...+...|++++|...++++.... +.+..++..+...+...|++++|...++.
T Consensus       155 ~~A~~~~~~~~~~~--~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~  231 (327)
T 3cv0_A          155 RECRTLLHAALEMN--PNDAQLHASLGVLYNLSNNYDSAAANLRRAVELR-PDDAQLWNKLGATLANGNRPQEALDAYNR  231 (327)
T ss_dssp             HHHHHHHHHHHHHS--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhC--CCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            55555555555442  3344555555555555555555555555555432 33455555556666666666666666665


Q ss_pred             HHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCC-----------CHHHHHHHHHHHHhcCCHHHHHHHHH
Q 012111          317 MQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKP-----------NSITYCSLVSAYSKAGLIMKVDSILR  385 (471)
Q Consensus       317 ~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p-----------~~~~~~~li~~~~~~g~~~~a~~~~~  385 (471)
                      +.+... .+...+..+...+...|++++|...++++.......           +..++..+..++...|+.++|..+++
T Consensus       232 a~~~~~-~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~  310 (327)
T 3cv0_A          232 ALDINP-GYVRVMYNMAVSYSNMSQYDLAAKQLVRAIYMQVGGTTPTGEASREATRSMWDFFRMLLNVMNRPDLVELTYA  310 (327)
T ss_dssp             HHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTSCC-----CCTHHHHHHHHHHHHHHHTTCHHHHHHHTT
T ss_pred             HHHcCC-CCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCccccccccchhhcCHHHHHHHHHHHHhcCCHHHHHHHHH
Confidence            555422 244555566666666666666666666665542111           24556666666666666666666665


Q ss_pred             H
Q 012111          386 Q  386 (471)
Q Consensus       386 ~  386 (471)
                      .
T Consensus       311 ~  311 (327)
T 3cv0_A          311 Q  311 (327)
T ss_dssp             C
T ss_pred             H
Confidence            4

>4g1t_A Interferon-induced protein with tetratricopeptide 2; ISG, all alpha helix, antivirus, antiviral protein; 2.80A {Homo sapiens}

Probab=99.80  E-value=2.7e-16  Score=149.47  Aligned_cols=364  Identities=8%  Similarity=-0.089  Sum_probs=210.5

Q ss_pred             HHHHHHHhhcHHHHHHHHHHhhhc----cC---ccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhC-----C--CCCCH
Q 012111           84 ALDEAIKQKKWQLALKIFGLLRQQ----QW---YQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSD-----G--LKPSV  149 (471)
Q Consensus        84 ~l~~~~~~~~~~~A~~~~~~~~~~----~~---~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~-----~--~~~~~  149 (471)
                      +-......|++++|++.|+++.+.    .+   -+....+|+.+..+|...|++++|...+++..+.     +  .....
T Consensus        57 Lg~~~~~~G~~~eAl~~~~kAl~~~~~~~~~~~~~~~~~~~~nla~~y~~~g~~~~A~~~~~ka~~i~~~~~~~~~~~~~  136 (472)
T 4g1t_A           57 LAYLKHLKGQNEAALECLRKAEELIQQEHADQAEIRSLVTWGNYAWVYYHMGRLSDVQIYVDKVKHVCEKFSSPYRIESP  136 (472)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHHHHHSGGGCTTTTHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCSSCCCCH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHHHHhcCccccchHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHhHhcccccchhhH
Confidence            334445678888888888876542    00   1223456777888888888888888888776542     1  11235


Q ss_pred             HHHHHHHHHHHhc--CCHHHHHHHHHHhhcCCCCCCCHHHHHHHHHH---HHhcCCHHHHHHHHHHHHHCCCCCCHHHHH
Q 012111          150 DVYTALVSAYGQS--GLLDEAFSTINDMKSVSDCKPDVYTYSILIKS---CTKFHRFDLIEKILAEMSYLGIECSAVTYN  224 (471)
Q Consensus       150 ~~~~~li~~~~~~--~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~---~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~  224 (471)
                      .++..+..++...  +++++|++.|++..+..  +-+...+..+..+   +...++.++|++.+++..+.. +.+..++.
T Consensus       137 ~~~~~~g~~~~~~~~~~y~~A~~~~~kal~~~--p~~~~~~~~~~~~~~~l~~~~~~~~al~~~~~al~l~-p~~~~~~~  213 (472)
T 4g1t_A          137 ELDCEEGWTRLKCGGNQNERAKVCFEKALEKK--PKNPEFTSGLAIASYRLDNWPPSQNAIDPLRQAIRLN-PDNQYLKV  213 (472)
T ss_dssp             HHHHHHHHHHHHHCTTHHHHHHHHHHHHHHHS--TTCHHHHHHHHHHHHHHHHSCCCCCTHHHHHHHHHHC-SSCHHHHH
T ss_pred             HHHHHHHHHHHHHccccHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHhcCchHHHHHHHHHHHHhhcC-CcchHHHH
Confidence            5666665555543  46788888888877632  2334444444443   334566677777777777654 34556665


Q ss_pred             HHHHHHHc----cCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHH
Q 012111          225 TIIDGYGK----AKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKS  300 (471)
Q Consensus       225 ~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~  300 (471)
                      .+...+..    .|++++|.+.+++..+..  +.+...+..+...|...|++++|...+++..+.. +.+..++..+..+
T Consensus       214 ~l~~~~~~~~~~~~~~~~a~~~~~~al~~~--~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~  290 (472)
T 4g1t_A          214 LLALKLHKMREEGEEEGEGEKLVEEALEKA--PGVTDVLRSAAKFYRRKDEPDKAIELLKKALEYI-PNNAYLHCQIGCC  290 (472)
T ss_dssp             HHHHHHHHCC------CHHHHHHHHHHHHC--SSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhhhHHHHHHHHHHHHHHhC--ccHHHHHHHHHHHHHHcCchHHHHHHHHHHHHhC-CChHHHHHHHHHH
Confidence            55544443    456777888888777653  5566677778888888888888888888877653 4456666666666


Q ss_pred             HHHc-------------------CCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCH
Q 012111          301 YGRA-------------------GMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNS  361 (471)
Q Consensus       301 ~~~~-------------------~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~  361 (471)
                      |...                   +..+.|...++...+.... +...+..+...+...|++++|...|++..+....+..
T Consensus       291 y~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~-~~~~~~~lg~~~~~~~~~~~A~~~~~kaL~~~~~~~~  369 (472)
T 4g1t_A          291 YRAKVFQVMNLRENGMYGKRKLLELIGHAVAHLKKADEANDN-LFRVCSILASLHALADQYEEAEYYFQKEFSKELTPVA  369 (472)
T ss_dssp             HHHHHHHHHHC------CHHHHHHHHHHHHHHHHHHHHHCTT-TCCCHHHHHHHHHHTTCHHHHHHHHHHHHHSCCCHHH
T ss_pred             HHHHHHHhhhHHHHHHHHHHHHHhhHHHHHHHHHHHhhcCCc-hhhhhhhHHHHHHHhccHHHHHHHHHHHHhcCCCChH
Confidence            6432                   1245566666666554322 3445667777777888888888888877765332221


Q ss_pred             H--HHHHHHH-HHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHH
Q 012111          362 I--TYCSLVS-AYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMI  438 (471)
Q Consensus       362 ~--~~~~li~-~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~  438 (471)
                      .  .+..+.. .....|+.++|+..|++..+..+.  .....         +....+.++++...+. -+.+..+|..+.
T Consensus       370 ~~~~~~~~~~~~~~~~~~~~~Ai~~y~kal~i~~~--~~~~~---------~~~~~l~~~~~~~l~~-~p~~~~~~~~LG  437 (472)
T 4g1t_A          370 KQLLHLRYGNFQLYQMKCEDKAIHHFIEGVKINQK--SREKE---------KMKDKLQKIAKMRLSK-NGADSEALHVLA  437 (472)
T ss_dssp             HHHHHHHHHHHHHHTSSCHHHHHHHHHHHHHSCCC--CHHHH---------HHHHHHHHHHHHHHHH-CC-CTTHHHHHH
T ss_pred             HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCcc--cHHHH---------HHHHHHHHHHHHHHHh-CCCCHHHHHHHH
Confidence            1  1222222 234567778888888777765433  21111         1123344455555443 234678899999


Q ss_pred             HHHHhcCCHHHHHHHHHHHHHhhhcCCC
Q 012111          439 QAYNALGMTEAAQNLENKMIAMKENSGK  466 (471)
Q Consensus       439 ~~~~~~g~~~~A~~~~~~m~~~~~~~~~  466 (471)
                      .+|...|++++|.+.++++++.++..+.
T Consensus       438 ~~~~~~g~~~~A~~~y~kALe~~~~~p~  465 (472)
T 4g1t_A          438 FLQELNEKMQQADEDSERGLESGSLIPS  465 (472)
T ss_dssp             HHHHHHHHCC------------------
T ss_pred             HHHHHcCCHHHHHHHHHHHHhcCCCCCc
Confidence            9999999999999999999999887654

>3mkr_A Coatomer subunit epsilon; tetratricopeptide repeats (TPR), beta-hairpin, alpha-solenoi transport protein; 2.60A {Bos taurus}

Probab=99.80  E-value=9.3e-17  Score=141.51  Aligned_cols=248  Identities=8%  Similarity=0.068  Sum_probs=131.8

Q ss_pred             HhcCCHHHHHHHHHHhhcCCCCCCCH--HHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHH
Q 012111          160 GQSGLLDEAFSTINDMKSVSDCKPDV--YTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFE  237 (471)
Q Consensus       160 ~~~~~~~~a~~~~~~~~~~~~~~~~~--~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~  237 (471)
                      ...|++..|+..++++..   ..|+.  .....+.++|...|+++.|...++.   . -+|+..++..+...+...++.+
T Consensus        10 ~~~g~y~~ai~~~~~~~~---~~p~~~~e~~~~l~r~yi~~g~~~~al~~~~~---~-~~~~~~a~~~la~~~~~~~~~~   82 (291)
T 3mkr_A           10 FYIGSYQQCINEAQRVKP---SSPERDVERDVFLYRAYLAQRKYGVVLDEIKP---S-SAPELQAVRMFAEYLASHSRRD   82 (291)
T ss_dssp             HHTTCHHHHHHHHHHSCC---CSHHHHHHHHHHHHHHHHHTTCHHHHHHHSCT---T-SCHHHHHHHHHHHHHHCSTTHH
T ss_pred             HHHHHHHHHHHHHHhccc---CCchhhHHHHHHHHHHHHHCCCHHHHHHHhcc---c-CChhHHHHHHHHHHHcCCCcHH
Confidence            345555555555554432   12222  2333344555555555555544432   1 1334455555555555555555


Q ss_pred             HHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHH
Q 012111          238 EMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFM  317 (471)
Q Consensus       238 ~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~  317 (471)
                      +|++.++++....-.+.+...+..+..++...|++++|++.+++      +.+...+..++..+.+.|++++|...++.+
T Consensus        83 ~A~~~l~~ll~~~~~P~~~~~~~~la~~~~~~g~~~~Al~~l~~------~~~~~~~~~l~~~~~~~g~~~~A~~~l~~~  156 (291)
T 3mkr_A           83 AIVAELDREMSRSVDVTNTTFLLMAASIYFYDQNPDAALRTLHQ------GDSLECMAMTVQILLKLDRLDLARKELKKM  156 (291)
T ss_dssp             HHHHHHHHHHHSCCCCSCHHHHHHHHHHHHHTTCHHHHHHHHTT------CCSHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcccCCCCHHHHHHHHHHHHHCCCHHHHHHHHhC------CCCHHHHHHHHHHHHHCCCHHHHHHHHHHH
Confidence            55555555544320122333444444555555666666555554      344555555556666666666666666665


Q ss_pred             HhCCCCCCHHHH---HHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCc
Q 012111          318 QKRFFFPTVVTY---NIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVIL  394 (471)
Q Consensus       318 ~~~~~~~~~~~~---~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~  394 (471)
                      .+..  |+....   ...+..+...|++++|..+|+++.+.. +.+...++.+..++.+.|++++|...++++.+..+. 
T Consensus       157 ~~~~--p~~~~~~l~~a~~~l~~~~~~~~eA~~~~~~~l~~~-p~~~~~~~~la~~~~~~g~~~eA~~~l~~al~~~p~-  232 (291)
T 3mkr_A          157 QDQD--EDATLTQLATAWVSLAAGGEKLQDAYYIFQEMADKC-SPTLLLLNGQAACHMAQGRWEAAEGVLQEALDKDSG-  232 (291)
T ss_dssp             HHHC--TTCHHHHHHHHHHHHHHCTTHHHHHHHHHHHHHHHS-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-
T ss_pred             HhhC--cCcHHHHHHHHHHHHHhCchHHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-
Confidence            5542  222111   112222333466666777766666652 445666666666666677777777777666665544 


Q ss_pred             CHHHHHHHHHHHHhcCCHHH-HHHHHHHHHh
Q 012111          395 DTPFFNCIISAYGQAGDVEK-MGELFLTMKE  424 (471)
Q Consensus       395 ~~~~~~~l~~~~~~~g~~~~-a~~~~~~~~~  424 (471)
                      +..++..++..+...|+.++ +.++++++.+
T Consensus       233 ~~~~l~~l~~~~~~~g~~~eaa~~~~~~~~~  263 (291)
T 3mkr_A          233 HPETLINLVVLSQHLGKPPEVTNRYLSQLKD  263 (291)
T ss_dssp             CHHHHHHHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCCHHHHHHHHHHHHH
Confidence            56666666666666666654 4566666665

>2ooe_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 3.00A {Mus musculus} SCOP: a.118.8.7

Probab=99.80  E-value=1.8e-15  Score=145.79  Aligned_cols=379  Identities=9%  Similarity=0.023  Sum_probs=278.4

Q ss_pred             CCCchHHHHHHHHHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHH
Q 012111           75 NLWPKPVLEALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTA  154 (471)
Q Consensus        75 ~~~~~~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~  154 (471)
                      +.+...+...+. +.+.|++++|..+|+.+.+..  |.+...|...+..+.+.|++++|..+|+++...  .|+...|..
T Consensus        10 P~~~~~w~~l~~-~~~~~~~~~a~~~~e~al~~~--P~~~~~w~~~~~~~~~~~~~~~a~~~~~ral~~--~p~~~lw~~   84 (530)
T 2ooe_A           10 PYDLDAWSILIR-EAQNQPIDKARKTYERLVAQF--PSSGRFWKLYIEAEIKAKNYDKVEKLFQRCLMK--VLHIDLWKC   84 (530)
T ss_dssp             TTCHHHHHHHHH-HHHSSCHHHHHHHHHHHHTTC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTT--CCCHHHHHH
T ss_pred             CCCHHHHHHHHH-HHHhCCHHHHHHHHHHHHHHC--CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhc--CCChHHHHH
Confidence            445667777777 478899999999999999874  778889999999999999999999999999987  468888888


Q ss_pred             HHHHH-HhcCCHHHHHH----HHHHhhcCCCCCC-CHHHHHHHHHHHHh---------cCCHHHHHHHHHHHHHCCCCCC
Q 012111          155 LVSAY-GQSGLLDEAFS----TINDMKSVSDCKP-DVYTYSILIKSCTK---------FHRFDLIEKILAEMSYLGIECS  219 (471)
Q Consensus       155 li~~~-~~~~~~~~a~~----~~~~~~~~~~~~~-~~~~~~~ll~~~~~---------~~~~~~a~~~~~~~~~~g~~~~  219 (471)
                      .+... ...|+.+.|.+    +|+......|..| +...|...+.....         .|+++.|..+|++..+......
T Consensus        85 ~~~~~~~~~~~~~~a~~~~~~~~~~al~~~g~~~~~~~~w~~~~~~~~~~~~~~~~~~~~~~~~a~~~y~~al~~P~~~~  164 (530)
T 2ooe_A           85 YLSYVRETKGKLPSYKEKMAQAYDFALDKIGMEIMSYQIWVDYINFLKGVEAVGSYAENQRITAVRRVYQRGCVNPMINI  164 (530)
T ss_dssp             HHHHHHHHTTTSTTHHHHHHHHHHHHHHHTTTSTTCHHHHHHHHHHHHHSCCCSSTTHHHHHHHHHHHHHHHTTSCCTTH
T ss_pred             HHHHHHHHccchhhHHHHHHHHHHHHHHHCCCCcccHHHHHHHHHHHhcCCCcccHHHHhHHHHHHHHHHHHHhchhhhH
Confidence            77533 35677766654    7777765445443 56678887776654         6889999999999987311111


Q ss_pred             HHHHHHHHHHH-------------HccCCHHHHHHHHHHHH------HcC--CCCCC--------HHHHHHHHHHHHhc-
Q 012111          220 AVTYNTIIDGY-------------GKAKKFEEMESSFSAMV------ESG--GCHPD--------IFTLNSMISAYGNS-  269 (471)
Q Consensus       220 ~~~~~~l~~~~-------------~~~~~~~~a~~~~~~~~------~~~--~~~~~--------~~~~~~l~~~~~~~-  269 (471)
                      ...|.......             .+.+++..|..++....      +..  .+.|+        ...|...+...... 
T Consensus       165 ~~~~~~~~~~e~~~~~~~~~~~l~~~~~~~~~A~~~~~~~~~~~~~l~~~~~~~~p~~~~~~~~~~~~w~~~~~~e~~~~  244 (530)
T 2ooe_A          165 EQLWRDYNKYEEGINIHLAKKMIEDRSRDYMNARRVAKEYETVMKGLDRNAPSVPPQNTPQEAQQVDMWKKYIQWEKSNP  244 (530)
T ss_dssp             HHHHHHHHHHHHHHCHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHCCSSSCCCCCC--CCHHHHHHHHHHHHHHHHHCS
T ss_pred             HHHHHHHHHHHHhhchhHHHHHHHHhhHHHHHHHHHHHHHHHHHHHhccccccCCCCCChhHHHHHHHHHHHHHHHHcCC
Confidence            23443322211             13456777777776532      110  02333        24555555433322 


Q ss_pred             ---CCH----HHHHHHHHHHHhCCCCCCHHHHHHHHHHHHH-------cCCHH-------HHHHHHHHHHhCCCCCCHHH
Q 012111          270 ---GNI----EKMEKWYNEFNLMGVKADIQTLNILTKSYGR-------AGMYD-------KMRSVMDFMQKRFFFPTVVT  328 (471)
Q Consensus       270 ---~~~----~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~-------~~~~~-------~a~~~~~~~~~~~~~~~~~~  328 (471)
                         ++.    ..+..+|++..... +.+...|..++..+.+       .|+++       +|..++++..+.-.+.+...
T Consensus       245 ~~~~~~~~~~~~a~~~y~~al~~~-p~~~~~w~~~~~~~~~~~~~~~~~g~~~~a~~~~~~A~~~~~~Al~~~~p~~~~l  323 (530)
T 2ooe_A          245 LRTEDQTLITKRVMFAYEQCLLVL-GHHPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANIYERAISTLLKKNMLL  323 (530)
T ss_dssp             SCCSCSHHHHHHHHHHHHHHHHHH-TTCHHHHHHHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHHHHHHTTTTCSSCHHH
T ss_pred             ccCCcchhHHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhchhhhhccchhhhhhhhHHHHHHHHHHHHHhCcccHHH
Confidence               232    47778898887753 6678888888888876       68887       89999999886323336788


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCC-H-HHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHH-
Q 012111          329 YNIVIETFGKAGHIEKMEEYFKKMKHRGMKPN-S-ITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISA-  405 (471)
Q Consensus       329 ~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~-~-~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~-  405 (471)
                      |..++..+.+.|++++|..+|+++.+.  .|+ . ..|..++..+.+.|++++|..+|++..+.... +...|...+.. 
T Consensus       324 ~~~~~~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~~~~~~~~~~~~~~~A~~~~~~Al~~~~~-~~~~~~~~a~~~  400 (530)
T 2ooe_A          324 YFAYADYEESRMKYEKVHSIYNRLLAI--EDIDPTLVYIQYMKFARRAEGIKSGRMIFKKAREDART-RHHVYVTAALME  400 (530)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHS--SSSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCTTC-CTHHHHHHHHHH
T ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHhCc--cccCchHHHHHHHHHHHHhcCHHHHHHHHHHHHhccCC-chHHHHHHHHHH
Confidence            999999999999999999999999985  454 3 58899999999999999999999999986433 33334333222 


Q ss_pred             HHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhhhc
Q 012111          406 YGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAYNALGMTEAAQNLENKMIAMKEN  463 (471)
Q Consensus       406 ~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~  463 (471)
                      +...|+.++|..+|++..+. .+-+...|..++..+.+.|+.++|+.+|++++...+.
T Consensus       401 ~~~~~~~~~A~~~~e~al~~-~p~~~~~~~~~~~~~~~~g~~~~Ar~~~~~al~~~~~  457 (530)
T 2ooe_A          401 YYCSKDKSVAFKIFELGLKK-YGDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSL  457 (530)
T ss_dssp             HHHTCCHHHHHHHHHHHHHH-HTTCHHHHHHHHHHHTTTTCHHHHHHHHHHHHHSCCS
T ss_pred             HHHcCChhHHHHHHHHHHHH-CCCCHHHHHHHHHHHHhCCCHhhHHHHHHHHHhccCC
Confidence            34689999999999999875 2336888999999999999999999999999988654

>3mkr_A Coatomer subunit epsilon; tetratricopeptide repeats (TPR), beta-hairpin, alpha-solenoi transport protein; 2.60A {Bos taurus}

Probab=99.80  E-value=4.6e-17  Score=143.47  Aligned_cols=256  Identities=8%  Similarity=0.042  Sum_probs=209.7

Q ss_pred             HHHHhcCCHHHHHHHHHHHHHCCCCCC--HHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcC
Q 012111          193 KSCTKFHRFDLIEKILAEMSYLGIECS--AVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSG  270 (471)
Q Consensus       193 ~~~~~~~~~~~a~~~~~~~~~~g~~~~--~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  270 (471)
                      +.....|+++.|+..++.....  .|+  ......+.++|...|+++.|...++..     ..|+..++..+...+...+
T Consensus         7 ~~~~~~g~y~~ai~~~~~~~~~--~p~~~~e~~~~l~r~yi~~g~~~~al~~~~~~-----~~~~~~a~~~la~~~~~~~   79 (291)
T 3mkr_A            7 KNAFYIGSYQQCINEAQRVKPS--SPERDVERDVFLYRAYLAQRKYGVVLDEIKPS-----SAPELQAVRMFAEYLASHS   79 (291)
T ss_dssp             HHHHHTTCHHHHHHHHHHSCCC--SHHHHHHHHHHHHHHHHHTTCHHHHHHHSCTT-----SCHHHHHHHHHHHHHHCST
T ss_pred             HHHHHHHHHHHHHHHHHhcccC--CchhhHHHHHHHHHHHHHCCCHHHHHHHhccc-----CChhHHHHHHHHHHHcCCC
Confidence            3455679999999998876543  333  245566789999999999999876542     3667788889999999999


Q ss_pred             CHHHHHHHHHHHHhCCC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHH
Q 012111          271 NIEKMEKWYNEFNLMGV-KADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYF  349 (471)
Q Consensus       271 ~~~~a~~~~~~~~~~~~-~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~  349 (471)
                      +.++|++.++++...+. +-+...+..+...+...|++++|...++.      ..+...+..++..+.+.|++++|.+.+
T Consensus        80 ~~~~A~~~l~~ll~~~~~P~~~~~~~~la~~~~~~g~~~~Al~~l~~------~~~~~~~~~l~~~~~~~g~~~~A~~~l  153 (291)
T 3mkr_A           80 RRDAIVAELDREMSRSVDVTNTTFLLMAASIYFYDQNPDAALRTLHQ------GDSLECMAMTVQILLKLDRLDLARKEL  153 (291)
T ss_dssp             THHHHHHHHHHHHHSCCCCSCHHHHHHHHHHHHHTTCHHHHHHHHTT------CCSHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             cHHHHHHHHHHHHhcccCCCCHHHHHHHHHHHHHCCCHHHHHHHHhC------CCCHHHHHHHHHHHHHCCCHHHHHHHH
Confidence            99999999999988764 44566777788999999999999999987      357888999999999999999999999


Q ss_pred             HHHHHcCCCCCHHHH---HHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCC
Q 012111          350 KKMKHRGMKPNSITY---CSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERH  426 (471)
Q Consensus       350 ~~m~~~~~~p~~~~~---~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~  426 (471)
                      +++.+..  |+....   ...+..+...|++++|..+|+++.+..+. +...++.+..++.+.|++++|...|++..+..
T Consensus       154 ~~~~~~~--p~~~~~~l~~a~~~l~~~~~~~~eA~~~~~~~l~~~p~-~~~~~~~la~~~~~~g~~~eA~~~l~~al~~~  230 (291)
T 3mkr_A          154 KKMQDQD--EDATLTQLATAWVSLAAGGEKLQDAYYIFQEMADKCSP-TLLLLNGQAACHMAQGRWEAAEGVLQEALDKD  230 (291)
T ss_dssp             HHHHHHC--TTCHHHHHHHHHHHHHHCTTHHHHHHHHHHHHHHHSCC-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHhhC--cCcHHHHHHHHHHHHHhCchHHHHHHHHHHHHHHhCCC-cHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC
Confidence            9999874  553211   22334445569999999999999987654 88999999999999999999999999998752


Q ss_pred             CCCCHHHHHHHHHHHHhcCCHHH-HHHHHHHHHHhhhcCC
Q 012111          427 CVPDNITFATMIQAYNALGMTEA-AQNLENKMIAMKENSG  465 (471)
Q Consensus       427 ~~p~~~~~~~l~~~~~~~g~~~~-A~~~~~~m~~~~~~~~  465 (471)
                       +-++.++..++..+...|+.++ +.++++++++..|+..
T Consensus       231 -p~~~~~l~~l~~~~~~~g~~~eaa~~~~~~~~~~~P~~~  269 (291)
T 3mkr_A          231 -SGHPETLINLVVLSQHLGKPPEVTNRYLSQLKDAHRSHP  269 (291)
T ss_dssp             -TTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCTTCH
T ss_pred             -CCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhCCCCh
Confidence             3378899999999999999876 6799999999998753

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens}

Probab=99.77  E-value=1.4e-18  Score=168.81  Aligned_cols=113  Identities=12%  Similarity=0.232  Sum_probs=54.6

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHh---CCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHH
Q 012111          257 FTLNSMISAYGNSGNIEKMEKWYNEFNL---MGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVI  333 (471)
Q Consensus       257 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~---~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li  333 (471)
                      .+|++||.+||+.|++++|.++|.+|.+   .|+.||..|||.||.+|++.|++++|.++|++|.+.|+.||..||+++|
T Consensus       128 ~TynaLIdglcK~G~leeA~~Lf~eM~~m~~kG~~PdvvTYNtLI~Glck~G~~~eA~~Lf~eM~~~G~~PDvvTYntLI  207 (1134)
T 3spa_A          128 QRLLAFFKCCLLTDQLPLAHHLLVVHHGQRQKRKLLTLDMYNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAAAL  207 (1134)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHHSHHHHTTCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCCCCHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCHHHHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCcHHHHHHHH
Confidence            3455555555555555555555544432   2344455555555555555555555555555554444444555555555


Q ss_pred             HHHHhcCC-HHHHHHHHHHHHHcCCCCCHHHHHHHHH
Q 012111          334 ETFGKAGH-IEKMEEYFKKMKHRGMKPNSITYCSLVS  369 (471)
Q Consensus       334 ~~~~~~g~-~~~a~~~~~~m~~~~~~p~~~~~~~li~  369 (471)
                      .++++.|+ .++|.++|++|.+.|+.||..+|+.++.
T Consensus       208 ~glcK~G~~~e~A~~Ll~EM~~kG~~PD~vtY~~ll~  244 (1134)
T 3spa_A          208 QCMGRQDQDAGTIERCLEQMSQEGLKLQALFTAVLLS  244 (1134)
T ss_dssp             HHHHHHTCCHHHHHHHHHHHHHHTCCSHHHHHHSCCC
T ss_pred             HHHHhCCCcHHHHHHHHHHHHHcCCCCChhhcccccC
Confidence            44444444 2344444455544444444444444443

>1xi4_A Clathrin heavy chain; alpha-ZIG-ZAG, beta-propeller, endocytosis-exocyto complex; 7.90A {Bos taurus} SCOP: i.23.1.1 PDB: 1xi5_A 3iyv_A

Probab=99.77  E-value=1.1e-14  Score=146.35  Aligned_cols=330  Identities=11%  Similarity=0.090  Sum_probs=216.5

Q ss_pred             ccCCCchHHHHHHHHHHHhhcHHHHHHHHHHhhhccC-ccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHH
Q 012111           73 YKNLWPKPVLEALDEAIKQKKWQLALKIFGLLRQQQW-YQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDV  151 (471)
Q Consensus        73 ~~~~~~~~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~  151 (471)
                      .....|+.+....+.+...|.+.+|+++++.+.-.+. +..+...-+.++....+. +..+..+..+.+...    +   
T Consensus       980 ~e~~~PeeVs~~vKaf~~aglp~EaieLLEKivl~~s~fs~n~~LqnlLi~tAIka-D~~Rv~eyI~kLd~~----d--- 1051 (1630)
T 1xi4_A          980 SETQDPEEVSVTVKAFMTADLPNELIELLEKIVLDNSVFSEHRNLQNLLILTAIKA-DRTRVMEYINRLDNY----D--- 1051 (1630)
T ss_pred             ccccCHHHhHHHHHHHHhCCCHHHHHHHHHHHHcCCCcccccHHHHHHHHHHHHHh-ChhhHHHHHHHhhhc----c---
Confidence            3467788999999999999999999999999985431 223445556666665555 445555555554421    1   


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHH
Q 012111          152 YTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYG  231 (471)
Q Consensus       152 ~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~  231 (471)
                      ...+...+...|.+++|..+|++...      .....+.++.   ..+++++|.++.++.      -+..+|..+..++.
T Consensus      1052 ~~eIA~Iai~lglyEEAf~IYkKa~~------~~~A~~VLie---~i~nldrAiE~Aerv------n~p~vWsqLAKAql 1116 (1630)
T 1xi4_A         1052 APDIANIAISNELFEEAFAIFRKFDV------NTSAVQVLIE---HIGNLDRAYEFAERC------NEPAVWSQLAKAQL 1116 (1630)
T ss_pred             HHHHHHHHHhCCCHHHHHHHHHHcCC------HHHHHHHHHH---HHhhHHHHHHHHHhc------CCHHHHHHHHHHHH
Confidence            23366667778888888888877532      1222222322   556777777777754      24667777778888


Q ss_pred             ccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHH
Q 012111          232 KAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMR  311 (471)
Q Consensus       232 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~  311 (471)
                      ..|++++|.+.|.+.       .|...|..++.++.+.|++++|.++|....+..  ++....+.++.+|++.+++++..
T Consensus      1117 ~~G~~kEAIdsYiKA-------dD~say~eVa~~~~~lGkyEEAIeyL~mArk~~--~e~~Idt~LafaYAKl~rleele 1187 (1630)
T 1xi4_A         1117 QKGMVKEAIDSYIKA-------DDPSSYMEVVQAANTSGNWEELVKYLQMARKKA--RESYVETELIFALAKTNRLAELE 1187 (1630)
T ss_pred             hCCCHHHHHHHHHhc-------CChHHHHHHHHHHHHcCCHHHHHHHHHHHHhhc--ccccccHHHHHHHHhhcCHHHHH
Confidence            888888888777543       255567777777888888888888877665543  33333334777777777777544


Q ss_pred             HHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCC
Q 012111          312 SVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSD  391 (471)
Q Consensus       312 ~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~  391 (471)
                      ...    +   .++...|..+...|...|++++|..+|...         ..|..+..++.+.|++++|.+.+++..   
T Consensus      1188 ~fI----~---~~n~ad~~~iGd~le~eg~YeeA~~~Y~kA---------~ny~rLA~tLvkLge~q~AIEaarKA~--- 1248 (1630)
T 1xi4_A         1188 EFI----N---GPNNAHIQQVGDRCYDEKMYDAAKLLYNNV---------SNFGRLASTLVHLGEYQAAVDGARKAN--- 1248 (1630)
T ss_pred             HHH----h---CCCHHHHHHHHHHHHhcCCHHHHHHHHHhh---------hHHHHHHHHHHHhCCHHHHHHHHHHhC---
Confidence            332    1   235556666777777777777777777763         367777777777777777777777652   


Q ss_pred             CCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhh
Q 012111          392 VILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAYNALGMTEAAQNLENKMIAMK  461 (471)
Q Consensus       392 ~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~  461 (471)
                         +..+|..+..+|...|++..|......     +..++..+..++..|.+.|.+++|..+++..+..+
T Consensus      1249 ---n~~aWkev~~acve~~Ef~LA~~cgl~-----Iiv~~deLeeli~yYe~~G~feEAI~LlE~aL~Le 1310 (1630)
T 1xi4_A         1249 ---STRTWKEVCFACVDGKEFRLAQMCGLH-----IVVHADELEELINYYQDRGYFEELITMLEAALGLE 1310 (1630)
T ss_pred             ---CHHHHHHHHHHHhhhhHHHHHHHHHHh-----hhcCHHHHHHHHHHHHHcCCHHHHHHHHHHHhccC
Confidence               456666666777777776666665443     22355556666677777777777777776665544

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens}

Probab=99.77  E-value=1.1e-18  Score=169.57  Aligned_cols=119  Identities=14%  Similarity=0.224  Sum_probs=86.7

Q ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHH---hCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHH
Q 012111          290 DIQTLNILTKSYGRAGMYDKMRSVMDFMQ---KRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCS  366 (471)
Q Consensus       290 ~~~~~~~ll~~~~~~~~~~~a~~~~~~~~---~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~  366 (471)
                      -..||++||++|++.|++++|..+|..|.   ..|+.||..+||+||.+|++.|++++|.++|++|.+.|+.||..||++
T Consensus       126 ~~~TynaLIdglcK~G~leeA~~Lf~eM~~m~~kG~~PdvvTYNtLI~Glck~G~~~eA~~Lf~eM~~~G~~PDvvTYnt  205 (1134)
T 3spa_A          126 QQQRLLAFFKCCLLTDQLPLAHHLLVVHHGQRQKRKLLTLDMYNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAA  205 (1134)
T ss_dssp             HHHHHHHHHHHHHHHTCHHHHHHHHHHHHHSHHHHTTCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCCCCHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCcHHHHHH
Confidence            44577777777777777777777776654   346777777777777777777777777777777777777777777777


Q ss_pred             HHHHHHhcCC-HHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHh
Q 012111          367 LVSAYSKAGL-IMKVDSILRQVENSDVILDTPFFNCIISAYGQ  408 (471)
Q Consensus       367 li~~~~~~g~-~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  408 (471)
                      +|.++++.|+ .++|.++|++|.+.|+.||..+|+.++.++.+
T Consensus       206 LI~glcK~G~~~e~A~~Ll~EM~~kG~~PD~vtY~~ll~~~eR  248 (1134)
T 3spa_A          206 ALQCMGRQDQDAGTIERCLEQMSQEGLKLQALFTAVLLSEEDR  248 (1134)
T ss_dssp             HHHHHHHHTCCHHHHHHHHHHHHHHTCCSHHHHHHSCCCHHHH
T ss_pred             HHHHHHhCCCcHHHHHHHHHHHHHcCCCCChhhcccccChhhH
Confidence            7777777776 35677777777777777777777777765554

>1b89_A Protein (clathrin heavy chain); triskelion, coated vesicles, endocytosis, SELF- assembly, alpha-alpha superhelix; 2.60A {Bos taurus} SCOP: a.118.1.3

Probab=99.76  E-value=7.3e-18  Score=151.81  Aligned_cols=318  Identities=11%  Similarity=0.058  Sum_probs=141.6

Q ss_pred             HhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHH
Q 012111           90 KQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAF  169 (471)
Q Consensus        90 ~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~  169 (471)
                      +.|++++|.++++.+       ++..+|..++.++.+.|++++|++.|.+.      +|..+|..++.++...|++++|+
T Consensus        15 ~~~~ld~A~~fae~~-------~~~~vWs~La~A~l~~g~~~eAIdsfika------~D~~~y~~V~~~ae~~g~~EeAi   81 (449)
T 1b89_A           15 HIGNLDRAYEFAERC-------NEPAVWSQLAKAQLQKGMVKEAIDSYIKA------DDPSSYMEVVQAANTSGNWEELV   81 (449)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HccCHHHHHHHHHhC-------CChHHHHHHHHHHHHcCCHHHHHHHHHcC------CCHHHHHHHHHHHHhCCCHHHHH
Confidence            567788899888877       23358899999999999999999999653      47778888899998899999999


Q ss_pred             HHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHc
Q 012111          170 STINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVES  249 (471)
Q Consensus       170 ~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  249 (471)
                      ..++...+ .  .+++.+.+.++.+|.+.|+++++.++++       .|+..+|..+...|...|.+++|...|..+   
T Consensus        82 ~yl~~ark-~--~~~~~i~~~Li~~Y~Klg~l~e~e~f~~-------~pn~~a~~~IGd~~~~~g~yeeA~~~Y~~a---  148 (449)
T 1b89_A           82 KYLQMARK-K--ARESYVETELIFALAKTNRLAELEEFIN-------GPNNAHIQQVGDRCYDEKMYDAAKLLYNNV---  148 (449)
T ss_dssp             ------------------------------CHHHHTTTTT-------CC----------------CTTTHHHHHHHT---
T ss_pred             HHHHHHHH-h--CccchhHHHHHHHHHHhCCHHHHHHHHc-------CCcHHHHHHHHHHHHHcCCHHHHHHHHHHh---
Confidence            97776665 2  4557778888999999999988887774       366678999999999999999999999877   


Q ss_pred             CCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHH
Q 012111          250 GGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTY  329 (471)
Q Consensus       250 ~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~  329 (471)
                             ..|..++.++.+.|++++|.+.+.++      .++.+|..++.+|...|+++.|......+.     ..+...
T Consensus       149 -------~n~~~LA~~L~~Lg~yq~AVea~~KA------~~~~~Wk~v~~aCv~~~ef~lA~~~~l~L~-----~~ad~l  210 (449)
T 1b89_A          149 -------SNFGRLASTLVHLGEYQAAVDGARKA------NSTRTWKEVCFACVDGKEFRLAQMCGLHIV-----VHADEL  210 (449)
T ss_dssp             -------TCHHHHHHHHHTTTCHHHHHHHHHHH------TCHHHHHHHHHHHHHTTCHHHHHHTTTTTT-----TCHHHH
T ss_pred             -------hhHHHHHHHHHHhccHHHHHHHHHHc------CCchhHHHHHHHHHHcCcHHHHHHHHHHHH-----hCHhhH
Confidence                   25888999999999999999999887      378889999999999999999955544322     244445


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHH-hCCCCc------CHHHHHHH
Q 012111          330 NIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVE-NSDVIL------DTPFFNCI  402 (471)
Q Consensus       330 ~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~-~~~~~~------~~~~~~~l  402 (471)
                      ..++..|.+.|++++|..+++...... +-....|+-+..+|++- ++++..+.++... +.+++|      +...|..+
T Consensus       211 ~~lv~~Yek~G~~eEai~lLe~aL~le-~ah~~~ftel~il~~ky-~p~k~~ehl~~~~~~ini~k~~~~~~~~~~w~e~  288 (449)
T 1b89_A          211 EELINYYQDRGYFEELITMLEAALGLE-RAHMGMFTELAILYSKF-KPQKMREHLELFWSRVNIPKVLRAAEQAHLWAEL  288 (449)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHTTST-TCCHHHHHHHHHHHHTT-CHHHHHHHHHHHSTTSCHHHHHHHHHTTTCHHHH
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHhCCc-HHHHHHHHHHHHHHHhc-CHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHH
Confidence            568888899999999999998887654 44566777777777655 3344333333322 222322      34567888


Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 012111          403 ISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAYNALGMTEAAQNLENKMI  458 (471)
Q Consensus       403 ~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~m~  458 (471)
                      ...|...++++.|..   .|.+.  +|+.-.-..+.....+.++.+--.+...=-+
T Consensus       289 ~~ly~~~~e~d~A~~---tm~~h--~~~a~~~~~f~~~~~kv~n~elyYkai~fyl  339 (449)
T 1b89_A          289 VFLYDKYEEYDNAII---TMMNH--PTDAWKEGQFKDIITKVANVELYYRAIQFYL  339 (449)
T ss_dssp             HHHHHHTTCHHHHHH---HHHHS--TTTTCCHHHHHHHHHHCSSTHHHHHHHHHHH
T ss_pred             HHHHHhhchHHHHHH---HHHhC--ChhhhhhHHHHHHHhchhHHHHHHHHHHHHH
Confidence            888888888887766   56664  3343333334455556666555444443333

>1b89_A Protein (clathrin heavy chain); triskelion, coated vesicles, endocytosis, SELF- assembly, alpha-alpha superhelix; 2.60A {Bos taurus} SCOP: a.118.1.3

Probab=99.76  E-value=3.3e-17  Score=147.58  Aligned_cols=330  Identities=12%  Similarity=0.076  Sum_probs=151.1

Q ss_pred             CchHHHHHHHHHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHH
Q 012111           77 WPKPVLEALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALV  156 (471)
Q Consensus        77 ~~~~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li  156 (471)
                      .+..+..+..++.+.|++++|++.|.+.       +|..+|..++..+...|++++|...++..++.  .+++.+.+.++
T Consensus        31 ~~~vWs~La~A~l~~g~~~eAIdsfika-------~D~~~y~~V~~~ae~~g~~EeAi~yl~~ark~--~~~~~i~~~Li  101 (449)
T 1b89_A           31 EPAVWSQLAKAQLQKGMVKEAIDSYIKA-------DDPSSYMEVVQAANTSGNWEELVKYLQMARKK--ARESYVETELI  101 (449)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             ChHHHHHHHHHHHHcCCHHHHHHHHHcC-------CCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHh--CccchhHHHHH
Confidence            3457778888888889999999888543       45568888888888889999998877766653  44577788888


Q ss_pred             HHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCH
Q 012111          157 SAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKF  236 (471)
Q Consensus       157 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~  236 (471)
                      .+|.+.|+++++.++++        .|+..+|+.+...|...|.+++|..+|..+         ..|..++.++.+.|++
T Consensus       102 ~~Y~Klg~l~e~e~f~~--------~pn~~a~~~IGd~~~~~g~yeeA~~~Y~~a---------~n~~~LA~~L~~Lg~y  164 (449)
T 1b89_A          102 FALAKTNRLAELEEFIN--------GPNNAHIQQVGDRCYDEKMYDAAKLLYNNV---------SNFGRLASTLVHLGEY  164 (449)
T ss_dssp             -------CHHHHTTTTT--------CC----------------CTTTHHHHHHHT---------TCHHHHHHHHHTTTCH
T ss_pred             HHHHHhCCHHHHHHHHc--------CCcHHHHHHHHHHHHHcCCHHHHHHHHHHh---------hhHHHHHHHHHHhccH
Confidence            89999898888877663        366678888888999999999999988876         3578888899999999


Q ss_pred             HHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHH
Q 012111          237 EEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDF  316 (471)
Q Consensus       237 ~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~  316 (471)
                      ++|.+.+.++       .++.+|..++.+|...|+++.|......     +...+.-...++..|.+.|.+++|..+++.
T Consensus       165 q~AVea~~KA-------~~~~~Wk~v~~aCv~~~ef~lA~~~~l~-----L~~~ad~l~~lv~~Yek~G~~eEai~lLe~  232 (449)
T 1b89_A          165 QAAVDGARKA-------NSTRTWKEVCFACVDGKEFRLAQMCGLH-----IVVHADELEELINYYQDRGYFEELITMLEA  232 (449)
T ss_dssp             HHHHHHHHHH-------TCHHHHHHHHHHHHHTTCHHHHHHTTTT-----TTTCHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHc-------CCchhHHHHHHHHHHcCcHHHHHHHHHH-----HHhCHhhHHHHHHHHHHCCCHHHHHHHHHH
Confidence            9999888877       1678888889999999999888554443     233444455688888889999999888888


Q ss_pred             HHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc-CCCC------CHHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 012111          317 MQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHR-GMKP------NSITYCSLVSAYSKAGLIMKVDSILRQVEN  389 (471)
Q Consensus       317 ~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~-~~~p------~~~~~~~li~~~~~~g~~~~a~~~~~~~~~  389 (471)
                      ..... .-....|+-+.-.|++- ++++..+.++...+. +++|      +...|.-++..|...++++.|..   .|.+
T Consensus       233 aL~le-~ah~~~ftel~il~~ky-~p~k~~ehl~~~~~~ini~k~~~~~~~~~~w~e~~~ly~~~~e~d~A~~---tm~~  307 (449)
T 1b89_A          233 ALGLE-RAHMGMFTELAILYSKF-KPQKMREHLELFWSRVNIPKVLRAAEQAHLWAELVFLYDKYEEYDNAII---TMMN  307 (449)
T ss_dssp             HTTST-TCCHHHHHHHHHHHHTT-CHHHHHHHHHHHSTTSCHHHHHHHHHTTTCHHHHHHHHHHTTCHHHHHH---HHHH
T ss_pred             HhCCc-HHHHHHHHHHHHHHHhc-CHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHHHHhhchHHHHHH---HHHh
Confidence            77654 33566777776666654 334433333322221 2222      23456677777777778777665   3343


Q ss_pred             C-CCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHH
Q 012111          390 S-DVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAYNALGMTEAAQNLENK  456 (471)
Q Consensus       390 ~-~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~  456 (471)
                      . ....+...|   .....+..+.+---+...-..+.  .|  ..++-|+.++...=+...+..++++
T Consensus       308 h~~~a~~~~~f---~~~~~kv~n~elyYkai~fyl~~--~p--~~l~~ll~~l~~~ld~~r~v~~~~~  368 (449)
T 1b89_A          308 HPTDAWKEGQF---KDIITKVANVELYYRAIQFYLEF--KP--LLLNDLLMVLSPRLDHTRAVNYFSK  368 (449)
T ss_dssp             STTTTCCHHHH---HHHHHHCSSTHHHHHHHHHHHHH--CG--GGHHHHHHHHGGGCCHHHHHHHHHH
T ss_pred             CChhhhhhHHH---HHHHhchhHHHHHHHHHHHHHhc--CH--HHHHHHHHHHHhccCcHHHHHHHHH
Confidence            3 122233333   34445555544333333333332  23  3366677777666677777666654

>3uq3_A Heat shock protein STI1; HSP90, peptide binding, chaperone; 2.60A {Saccharomyces cerevisiae}

Probab=99.73  E-value=3.2e-15  Score=129.59  Aligned_cols=224  Identities=13%  Similarity=0.008  Sum_probs=114.2

Q ss_pred             HHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCC--CCC----HHHHHH
Q 012111          223 YNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGV--KAD----IQTLNI  296 (471)
Q Consensus       223 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~----~~~~~~  296 (471)
                      +..+...+...|++++|...|+++.+..   .+...+..+..++...|++++|...++++.....  .++    ..++..
T Consensus         8 ~~~~g~~~~~~~~~~~A~~~~~~a~~~~---~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~   84 (258)
T 3uq3_A            8 EKAEGNKFYKARQFDEAIEHYNKAWELH---KDITYLNNRAAAEYEKGEYETAISTLNDAVEQGREMRADYKVISKSFAR   84 (258)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHS---CCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHhccHHHHHHHHHHHHHhh---ccHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccccchHHHHHHHHH
Confidence            3334444444444444444444444332   3333444444444444444444444444433210  011    244444


Q ss_pred             HHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCC
Q 012111          297 LTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGL  376 (471)
Q Consensus       297 ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~  376 (471)
                      +...+...|++++|...++.+.+..  |+.       ..+...|++++|...++++.... +.+...+..+...+...|+
T Consensus        85 l~~~~~~~~~~~~A~~~~~~a~~~~--~~~-------~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~  154 (258)
T 3uq3_A           85 IGNAYHKLGDLKKTIEYYQKSLTEH--RTA-------DILTKLRNAEKELKKAEAEAYVN-PEKAEEARLEGKEYFTKSD  154 (258)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHC--CCH-------HHHHHHHHHHHHHHHHHHHHHCC-HHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHcccHHHHHHHHHHHHhcC--chh-------HHHHHHhHHHHHHHHHHHHHHcC-cchHHHHHHHHHHHHHhcC
Confidence            4555555555555555555544431  221       22344455556666666555531 1234455555666666666


Q ss_pred             HHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHH
Q 012111          377 IMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAYNALGMTEAAQNLENK  456 (471)
Q Consensus       377 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~  456 (471)
                      +++|...++++.+..+. +..++..+..++...|++++|+..++++.+.. +.+...+..+..++...|++++|...+++
T Consensus       155 ~~~A~~~~~~a~~~~~~-~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~  232 (258)
T 3uq3_A          155 WPNAVKAYTEMIKRAPE-DARGYSNRAAALAKLMSFPEAIADCNKAIEKD-PNFVRAYIRKATAQIAVKEYASALETLDA  232 (258)
T ss_dssp             HHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCcc-cHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhC-HHHHHHHHHHHHHHHHHhhHHHHHHHHHH
Confidence            66666666666555433 45566666666666666666666666665531 22455566666666666666666666666


Q ss_pred             HHHhh
Q 012111          457 MIAMK  461 (471)
Q Consensus       457 m~~~~  461 (471)
                      +++..
T Consensus       233 a~~~~  237 (258)
T 3uq3_A          233 ARTKD  237 (258)
T ss_dssp             HHHHH
T ss_pred             HHHhC
Confidence            66665

>4g1t_A Interferon-induced protein with tetratricopeptide 2; ISG, all alpha helix, antivirus, antiviral protein; 2.80A {Homo sapiens}

Probab=99.73  E-value=1.2e-14  Score=137.95  Aligned_cols=369  Identities=11%  Similarity=-0.037  Sum_probs=245.2

Q ss_pred             hhHHHHHHHhhHHHHHHHHHhhhhhhc---cCCCc---hHHHHHHHHHHHhhcHHHHHHHHHHhhhccC-----c-cCCh
Q 012111           47 AEKDLSKILRTEFAIKNIEKKVSSKKY---KNLWP---KPVLEALDEAIKQKKWQLALKIFGLLRQQQW-----Y-QARC  114 (471)
Q Consensus        47 ~~~~l~~~~~~~~~~~~~~~~~~~~~~---~~~~~---~~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~-----~-~~~~  114 (471)
                      ........+++++|++.+...+...+.   ....+   ..+...-..+...|++++|+..|+.+.+...     . ....
T Consensus        57 Lg~~~~~~G~~~eAl~~~~kAl~~~~~~~~~~~~~~~~~~~~nla~~y~~~g~~~~A~~~~~ka~~i~~~~~~~~~~~~~  136 (472)
T 4g1t_A           57 LAYLKHLKGQNEAALECLRKAEELIQQEHADQAEIRSLVTWGNYAWVYYHMGRLSDVQIYVDKVKHVCEKFSSPYRIESP  136 (472)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHHHHHSGGGCTTTTHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCSSCCCCH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHHHHhcCccccchHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHhHhcccccchhhH
Confidence            345556677888898888877664221   11222   2344566677889999999999998875320     1 1234


Q ss_pred             hHHHHHHHHHhc--CCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHH---HHhcCCHHHHHHHHHHhhcCCCCCCCHHHHH
Q 012111          115 QTFTKLMVMLGK--CKQPEQASLLFEVMLSDGLKPSVDVYTALVSA---YGQSGLLDEAFSTINDMKSVSDCKPDVYTYS  189 (471)
Q Consensus       115 ~~~~~l~~~~~~--~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~---~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  189 (471)
                      .++..+..++..  .+++++|...|++..+..+. ++..+..+..+   +...++.++|++.+++..+..  +.+..++.
T Consensus       137 ~~~~~~g~~~~~~~~~~y~~A~~~~~kal~~~p~-~~~~~~~~~~~~~~l~~~~~~~~al~~~~~al~l~--p~~~~~~~  213 (472)
T 4g1t_A          137 ELDCEEGWTRLKCGGNQNERAKVCFEKALEKKPK-NPEFTSGLAIASYRLDNWPPSQNAIDPLRQAIRLN--PDNQYLKV  213 (472)
T ss_dssp             HHHHHHHHHHHHHCTTHHHHHHHHHHHHHHHSTT-CHHHHHHHHHHHHHHHHSCCCCCTHHHHHHHHHHC--SSCHHHHH
T ss_pred             HHHHHHHHHHHHHccccHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHhcCchHHHHHHHHHHHHhhcC--CcchHHHH
Confidence            566666555544  46799999999999887433 56666666555   445678889999999887732  44566666


Q ss_pred             HHHHHHHh----cCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHH
Q 012111          190 ILIKSCTK----FHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISA  265 (471)
Q Consensus       190 ~ll~~~~~----~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~  265 (471)
                      .+...+..    .+++++|.+++++..... +.+..++..+...|...|++++|...+++..+..  +.+..++..+..+
T Consensus       214 ~l~~~~~~~~~~~~~~~~a~~~~~~al~~~-~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~--p~~~~~~~~lg~~  290 (472)
T 4g1t_A          214 LLALKLHKMREEGEEEGEGEKLVEEALEKA-PGVTDVLRSAAKFYRRKDEPDKAIELLKKALEYI--PNNAYLHCQIGCC  290 (472)
T ss_dssp             HHHHHHHHCC------CHHHHHHHHHHHHC-SSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS--TTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhhhHHHHHHHHHHHHHHhC-ccHHHHHHHHHHHHHHcCchHHHHHHHHHHHHhC--CChHHHHHHHHHH
Confidence            66555544    467889999999988765 5578889999999999999999999999998874  5567778888777


Q ss_pred             HHhc-------------------CCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCH
Q 012111          266 YGNS-------------------GNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTV  326 (471)
Q Consensus       266 ~~~~-------------------~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~  326 (471)
                      |...                   +..+.|...+++..... +.+..++..+...|...|++++|...|++..+....+..
T Consensus       291 y~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~lg~~~~~~~~~~~A~~~~~kaL~~~~~~~~  369 (472)
T 4g1t_A          291 YRAKVFQVMNLRENGMYGKRKLLELIGHAVAHLKKADEAN-DNLFRVCSILASLHALADQYEEAEYYFQKEFSKELTPVA  369 (472)
T ss_dssp             HHHHHHHHHHC------CHHHHHHHHHHHHHHHHHHHHHC-TTTCCCHHHHHHHHHHTTCHHHHHHHHHHHHHSCCCHHH
T ss_pred             HHHHHHHhhhHHHHHHHHHHHHHhhHHHHHHHHHHHhhcC-CchhhhhhhHHHHHHHhccHHHHHHHHHHHHhcCCCChH
Confidence            7542                   23567788888876654 555667888999999999999999999999887544332


Q ss_pred             H--HHHHHHH-HHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHH
Q 012111          327 V--TYNIVIE-TFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCII  403 (471)
Q Consensus       327 ~--~~~~li~-~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~  403 (471)
                      .  .+..+.. .....|+.++|+..|.+..+.  .|+......         ....+.++++.....++. +..+|..+.
T Consensus       370 ~~~~~~~~~~~~~~~~~~~~~Ai~~y~kal~i--~~~~~~~~~---------~~~~l~~~~~~~l~~~p~-~~~~~~~LG  437 (472)
T 4g1t_A          370 KQLLHLRYGNFQLYQMKCEDKAIHHFIEGVKI--NQKSREKEK---------MKDKLQKIAKMRLSKNGA-DSEALHVLA  437 (472)
T ss_dssp             HHHHHHHHHHHHHHTSSCHHHHHHHHHHHHHS--CCCCHHHHH---------HHHHHHHHHHHHHHHCC--CTTHHHHHH
T ss_pred             HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CcccHHHHH---------HHHHHHHHHHHHHHhCCC-CHHHHHHHH
Confidence            2  2222322 235679999999999999885  555432222         234455666666666654 788999999


Q ss_pred             HHHHhcCCHHHHHHHHHHHHhCC-CCCCHHHH
Q 012111          404 SAYGQAGDVEKMGELFLTMKERH-CVPDNITF  434 (471)
Q Consensus       404 ~~~~~~g~~~~a~~~~~~~~~~~-~~p~~~~~  434 (471)
                      .+|...|++++|++.|++..+.| ..|++.+|
T Consensus       438 ~~~~~~g~~~~A~~~y~kALe~~~~~p~a~~~  469 (472)
T 4g1t_A          438 FLQELNEKMQQADEDSERGLESGSLIPSASSW  469 (472)
T ss_dssp             HHHHHHHHCC----------------------
T ss_pred             HHHHHcCCHHHHHHHHHHHHhcCCCCCcHhhc
Confidence            99999999999999999998754 23554443

>2pl2_A Hypothetical conserved protein TTC0263; TPR, protein binding; 2.50A {Thermus thermophilus}

Probab=99.71  E-value=3.4e-15  Score=125.69  Aligned_cols=114  Identities=14%  Similarity=0.049  Sum_probs=52.1

Q ss_pred             CCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHH
Q 012111          340 GHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELF  419 (471)
Q Consensus       340 g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~  419 (471)
                      |++++|...+++..+.. +-+...+..+...+...|++++|...|+++.+.+  .+...+..+..+|...|++++|+..|
T Consensus        98 g~~~~A~~~~~~al~~~-P~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~--~~~~~~~~la~~~~~~g~~~~A~~~~  174 (217)
T 2pl2_A           98 GYLEQALSVLKDAERVN-PRYAPLHLQRGLVYALLGERDKAEASLKQALALE--DTPEIRSALAELYLSMGRLDEALAQY  174 (217)
T ss_dssp             HHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHHHTCHHHHHHHH
T ss_pred             cCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHcCChHHHHHHHHHHHhcc--cchHHHHHHHHHHHHcCCHHHHHHHH
Confidence            55555555555555432 1234455555555555555555555555555544  35555555555555555555555555


Q ss_pred             HHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 012111          420 LTMKERHCVPDNITFATMIQAYNALGMTEAAQNLENKM  457 (471)
Q Consensus       420 ~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~m  457 (471)
                      ++..+. -+.+...+..+...+...|++++|.+.+++.
T Consensus       175 ~~al~~-~P~~~~~~~~la~~~~~~g~~~~A~~~~~~~  211 (217)
T 2pl2_A          175 AKALEQ-APKDLDLRVRYASALLLKGKAEEAARAAALE  211 (217)
T ss_dssp             HHHHHH-STTCHHHHHHHHHHHTC--------------
T ss_pred             HHHHHh-CCCChHHHHHHHHHHHHccCHHHHHHHHHHH
Confidence            555543 1123444555555555555555555555443

>3uq3_A Heat shock protein STI1; HSP90, peptide binding, chaperone; 2.60A {Saccharomyces cerevisiae}

Probab=99.71  E-value=1.1e-14  Score=126.27  Aligned_cols=225  Identities=11%  Similarity=0.007  Sum_probs=143.9

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHcCC-CCCC----HHHHHH
Q 012111          187 TYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGG-CHPD----IFTLNS  261 (471)
Q Consensus       187 ~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-~~~~----~~~~~~  261 (471)
                      .+..+...+...|++++|..++++..+..  .+...+..+..++...|++++|.+.+++..+... ..++    ...+..
T Consensus         7 ~~~~~g~~~~~~~~~~~A~~~~~~a~~~~--~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~   84 (258)
T 3uq3_A            7 KEKAEGNKFYKARQFDEAIEHYNKAWELH--KDITYLNNRAAAEYEKGEYETAISTLNDAVEQGREMRADYKVISKSFAR   84 (258)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHS--CCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhccHHHHHHHHHHHHHhh--ccHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccccchHHHHHHHHH
Confidence            34445555555555555555555555544  4455555555666666666666666655544310 0111    355566


Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCC
Q 012111          262 MISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGH  341 (471)
Q Consensus       262 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~  341 (471)
                      +...+...|++++|...|+++...  .|+.       ..+...|++++|...++.+..... .+...+..+...+...|+
T Consensus        85 l~~~~~~~~~~~~A~~~~~~a~~~--~~~~-------~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~  154 (258)
T 3uq3_A           85 IGNAYHKLGDLKKTIEYYQKSLTE--HRTA-------DILTKLRNAEKELKKAEAEAYVNP-EKAEEARLEGKEYFTKSD  154 (258)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHH--CCCH-------HHHHHHHHHHHHHHHHHHHHHCCH-HHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHcccHHHHHHHHHHHHhc--Cchh-------HHHHHHhHHHHHHHHHHHHHHcCc-chHHHHHHHHHHHHHhcC
Confidence            666666666666666666666553  2332       334555667777777777666422 134566677777778888


Q ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHH
Q 012111          342 IEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLT  421 (471)
Q Consensus       342 ~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~  421 (471)
                      +++|...++++.... +.+..++..+...+...|++++|...++.+.+..+. +...+..+..++...|++++|.+.|++
T Consensus       155 ~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~-~~~~~~~l~~~~~~~g~~~~A~~~~~~  232 (258)
T 3uq3_A          155 WPNAVKAYTEMIKRA-PEDARGYSNRAAALAKLMSFPEAIADCNKAIEKDPN-FVRAYIRKATAQIAVKEYASALETLDA  232 (258)
T ss_dssp             HHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhCHH-HHHHHHHHHHHHHHHhhHHHHHHHHHH
Confidence            888888888877753 335677778888888888888888888887776544 577778888888888888888888887


Q ss_pred             HHhC
Q 012111          422 MKER  425 (471)
Q Consensus       422 ~~~~  425 (471)
                      ..+.
T Consensus       233 a~~~  236 (258)
T 3uq3_A          233 ARTK  236 (258)
T ss_dssp             HHHH
T ss_pred             HHHh
Confidence            7653

>1ouv_A Conserved hypothetical secreted protein; TPR repeat, HCP repeat, cysteine rich protein, loop-helix-TU repeat protein, hydrolase; 2.00A {Helicobacter pylori} SCOP: a.118.18.1

Probab=99.70  E-value=1.6e-13  Score=120.13  Aligned_cols=225  Identities=12%  Similarity=0.004  Sum_probs=127.9

Q ss_pred             HHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHh----cCCHHHHHHHHHHHHhCCCCCCHHHHH
Q 012111          220 AVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGN----SGNIEKMEKWYNEFNLMGVKADIQTLN  295 (471)
Q Consensus       220 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~  295 (471)
                      ..++..+...+...|++++|...|++..+.    .+...+..+...+..    .+++++|...|++..+.+   +...+.
T Consensus         6 ~~a~~~lg~~~~~~~~~~~A~~~~~~a~~~----~~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~---~~~a~~   78 (273)
T 1ouv_A            6 PKELVGLGAKSYKEKDFTQAKKYFEKACDL----KENSGCFNLGVLYYQGQGVEKNLKKAASFYAKACDLN---YSNGCH   78 (273)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHT----TCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHH
T ss_pred             hHHHHHHHHHHHhCCCHHHHHHHHHHHHHC----CCHHHHHHHHHHHHcCCCcCCCHHHHHHHHHHHHHCC---CHHHHH
Confidence            444445555555555555555555555442    133444555555555    555555555555555443   445555


Q ss_pred             HHHHHHHH----cCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHh----cCCHHHHHHHHHHHHHcCCCCCHHHHHHH
Q 012111          296 ILTKSYGR----AGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGK----AGHIEKMEEYFKKMKHRGMKPNSITYCSL  367 (471)
Q Consensus       296 ~ll~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~----~g~~~~a~~~~~~m~~~~~~p~~~~~~~l  367 (471)
                      .+...|..    .+++++|...|+...+.+   +...+..+...|..    .+++++|...|++..+.+   +...+..+
T Consensus        79 ~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~~~~~~~~~~~~~~A~~~~~~a~~~~---~~~a~~~l  152 (273)
T 1ouv_A           79 LLGNLYYSGQGVSQNTNKALQYYSKACDLK---YAEGCASLGGIYHDGKVVTRDFKKAVEYFTKACDLN---DGDGCTIL  152 (273)
T ss_dssp             HHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHCSSSCCCHHHHHHHHHHHHHTT---CHHHHHHH
T ss_pred             HHHHHHhCCCCcccCHHHHHHHHHHHHHcC---CccHHHHHHHHHHcCCCcccCHHHHHHHHHHHHhcC---cHHHHHHH
Confidence            55555555    556666666665555542   44555555555555    566666666666666543   44455555


Q ss_pred             HHHHHh----cCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHh----cCCHHHHHHHHHHHHhCCCCCCHHHHHHHHH
Q 012111          368 VSAYSK----AGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQ----AGDVEKMGELFLTMKERHCVPDNITFATMIQ  439 (471)
Q Consensus       368 i~~~~~----~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~  439 (471)
                      ...+..    .+++++|...+++..+.+   +...+..+...|..    .+++++|+..|++..+.+   +...+..+..
T Consensus       153 g~~~~~~~~~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~---~~~a~~~l~~  226 (273)
T 1ouv_A          153 GSLYDAGRGTPKDLKKALASYDKACDLK---DSPGCFNAGNMYHHGEGATKNFKEALARYSKACELE---NGGGCFNLGA  226 (273)
T ss_dssp             HHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTCSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHH
T ss_pred             HHHHHcCCCCCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCccHHHHHHHHHHHHhCC---CHHHHHHHHH
Confidence            555555    666666666666666543   34555566666666    666666666666666542   2455555556


Q ss_pred             HHHh----cCCHHHHHHHHHHHHHhhhc
Q 012111          440 AYNA----LGMTEAAQNLENKMIAMKEN  463 (471)
Q Consensus       440 ~~~~----~g~~~~A~~~~~~m~~~~~~  463 (471)
                      .|..    .+++++|.+.++++++.+|.
T Consensus       227 ~~~~g~~~~~~~~~A~~~~~~a~~~~~~  254 (273)
T 1ouv_A          227 MQYNGEGVTRNEKQAIENFKKGCKLGAK  254 (273)
T ss_dssp             HHHTTSSSSCCSTTHHHHHHHHHHHTCH
T ss_pred             HHHcCCCcccCHHHHHHHHHHHHHcCCH
Confidence            6666    66666666666666666554

>2ho1_A Type 4 fimbrial biogenesis protein PILF; type IV pilus biogenesis, TPR, superhelix, protein binding; HET: MSE; 2.00A {Pseudomonas aeruginosa} PDB: 2fi7_A

Probab=99.69  E-value=3.5e-14  Score=122.66  Aligned_cols=200  Identities=10%  Similarity=0.025  Sum_probs=91.4

Q ss_pred             HHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHH
Q 012111          220 AVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTK  299 (471)
Q Consensus       220 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~  299 (471)
                      ...+..+...+...|++++|.+.|+++.+..  +.+...+..+...+...|++++|.+.++++.... +.+...+..+..
T Consensus        37 ~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~--~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~  113 (252)
T 2ho1_A           37 RDAYIQLGLGYLQRGNTEQAKVPLRKALEID--PSSADAHAALAVVFQTEMEPKLADEEYRKALASD-SRNARVLNNYGG  113 (252)
T ss_dssp             HHHHHHHHHHHHHTTCTGGGHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCChHHHHHHHHHHHhcC--CChHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC-cCcHHHHHHHHH
Confidence            3444555555555555555555555555442  3344455555555555555555555555554432 233444444444


Q ss_pred             HHHHcCCHHHHHHHHHHHHhCCCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHH
Q 012111          300 SYGRAGMYDKMRSVMDFMQKRFFFP-TVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIM  378 (471)
Q Consensus       300 ~~~~~~~~~~a~~~~~~~~~~~~~~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~  378 (471)
                      .+...|++++|...++.+.+.+..| +...+..+...+...|++++|...++++.+.. +.+...+..+...+...|+++
T Consensus       114 ~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~g~~~  192 (252)
T 2ho1_A          114 FLYEQKRYEEAYQRLLEASQDTLYPERSRVFENLGLVSLQMKKPAQAKEYFEKSLRLN-RNQPSVALEMADLLYKEREYV  192 (252)
T ss_dssp             HHHHTTCHHHHHHHHHHHTTCTTCTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHH
T ss_pred             HHHHHhHHHHHHHHHHHHHhCccCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHcCCHH
Confidence            5555555555555554444411122 22334444444444444444444444444432 112334444444444444444


Q ss_pred             HHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 012111          379 KVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKE  424 (471)
Q Consensus       379 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~  424 (471)
                      +|...++.+.+..+. +...+..+...+...|++++|.++++++.+
T Consensus       193 ~A~~~~~~~~~~~~~-~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~  237 (252)
T 2ho1_A          193 PARQYYDLFAQGGGQ-NARSLLLGIRLAKVFEDRDTAASYGLQLKR  237 (252)
T ss_dssp             HHHHHHHHHHTTSCC-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCcC-cHHHHHHHHHHHHHccCHHHHHHHHHHHHH
Confidence            444444444433222 333344444444444444444444444443

>1xi4_A Clathrin heavy chain; alpha-ZIG-ZAG, beta-propeller, endocytosis-exocyto complex; 7.90A {Bos taurus} SCOP: i.23.1.1 PDB: 1xi5_A 3iyv_A

Probab=99.69  E-value=3e-13  Score=136.22  Aligned_cols=314  Identities=14%  Similarity=0.137  Sum_probs=232.8

Q ss_pred             HHHHHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcC
Q 012111           84 ALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSG  163 (471)
Q Consensus        84 ~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~  163 (471)
                      ....+...|.+++|..+|++...      .....+.++   -..+++++|.++.++..      +..+|..+..++...|
T Consensus      1055 IA~Iai~lglyEEAf~IYkKa~~------~~~A~~VLi---e~i~nldrAiE~Aervn------~p~vWsqLAKAql~~G 1119 (1630)
T 1xi4_A         1055 IANIAISNELFEEAFAIFRKFDV------NTSAVQVLI---EHIGNLDRAYEFAERCN------EPAVWSQLAKAQLQKG 1119 (1630)
T ss_pred             HHHHHHhCCCHHHHHHHHHHcCC------HHHHHHHHH---HHHhhHHHHHHHHHhcC------CHHHHHHHHHHHHhCC
Confidence            34455678888888888888632      112223332   26678888888887652      5778888999999999


Q ss_pred             CHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHH
Q 012111          164 LLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSF  243 (471)
Q Consensus       164 ~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~a~~~~  243 (471)
                      ++++|++.|.+.       -|...|..++..+.+.|++++|.+.|....+..  ++....+.++.+|++.+++++...+.
T Consensus      1120 ~~kEAIdsYiKA-------dD~say~eVa~~~~~lGkyEEAIeyL~mArk~~--~e~~Idt~LafaYAKl~rleele~fI 1190 (1630)
T 1xi4_A         1120 MVKEAIDSYIKA-------DDPSSYMEVVQAANTSGNWEELVKYLQMARKKA--RESYVETELIFALAKTNRLAELEEFI 1190 (1630)
T ss_pred             CHHHHHHHHHhc-------CChHHHHHHHHHHHHcCCHHHHHHHHHHHHhhc--ccccccHHHHHHHHhhcCHHHHHHHH
Confidence            999999988653       366777888888999999999999998877654  33333445888888888887544332


Q ss_pred             HHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCC
Q 012111          244 SAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFF  323 (471)
Q Consensus       244 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~  323 (471)
                          +    .++...|..+...|...|++++|..+|...         ..|..+..++.+.|++++|.+.+.+.      
T Consensus      1191 ----~----~~n~ad~~~iGd~le~eg~YeeA~~~Y~kA---------~ny~rLA~tLvkLge~q~AIEaarKA------ 1247 (1630)
T 1xi4_A         1191 ----N----GPNNAHIQQVGDRCYDEKMYDAAKLLYNNV---------SNFGRLASTLVHLGEYQAAVDGARKA------ 1247 (1630)
T ss_pred             ----h----CCCHHHHHHHHHHHHhcCCHHHHHHHHHhh---------hHHHHHHHHHHHhCCHHHHHHHHHHh------
Confidence                2    345566777888889999999999999884         37888899999999999999888865      


Q ss_pred             CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHH
Q 012111          324 PTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCII  403 (471)
Q Consensus       324 ~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~  403 (471)
                      .+..+|..+..+|...|++..|......     +..++..+..++..|.+.|.+++|+.+++.....+ .-....|+-|.
T Consensus      1248 ~n~~aWkev~~acve~~Ef~LA~~cgl~-----Iiv~~deLeeli~yYe~~G~feEAI~LlE~aL~Le-raH~gmftELa 1321 (1630)
T 1xi4_A         1248 NSTRTWKEVCFACVDGKEFRLAQMCGLH-----IVVHADELEELINYYQDRGYFEELITMLEAALGLE-RAHMGMFTELA 1321 (1630)
T ss_pred             CCHHHHHHHHHHHhhhhHHHHHHHHHHh-----hhcCHHHHHHHHHHHHHcCCHHHHHHHHHHHhccC-hhHhHHHHHHH
Confidence            2568888888888888888888876653     33466778899999999999999999998888766 33666777777


Q ss_pred             HHHHhc--CCHHHHHHHHHHHHhCCCCC------CHHHHHHHHHHHHhcCCHHHHHH
Q 012111          404 SAYGQA--GDVEKMGELFLTMKERHCVP------DNITFATMIQAYNALGMTEAAQN  452 (471)
Q Consensus       404 ~~~~~~--g~~~~a~~~~~~~~~~~~~p------~~~~~~~l~~~~~~~g~~~~A~~  452 (471)
                      .+|.+.  ++..++.++|..-..  ++|      +...|.-++-.|.+.|+++.|..
T Consensus      1322 iLyaKy~peklmEhlk~f~~rin--i~k~~r~~e~~~lW~elv~LY~~~~e~dnA~~ 1376 (1630)
T 1xi4_A         1322 ILYSKFKPQKMREHLELFWSRVN--IPKVLRAAEQAHLWAELVFLYDKYEEYDNAII 1376 (1630)
T ss_pred             HHHHhCCHHHHHHHHHHHHHhcc--cchHhHHHHHHHHHHHHHHHHHhcccHHHHHH
Confidence            777764  445555555553322  222      56778888899999999999873

>2pl2_A Hypothetical conserved protein TTC0263; TPR, protein binding; 2.50A {Thermus thermophilus}

Probab=99.68  E-value=1.1e-14  Score=122.52  Aligned_cols=200  Identities=11%  Similarity=-0.019  Sum_probs=166.3

Q ss_pred             CCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHH
Q 012111          217 ECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNI  296 (471)
Q Consensus       217 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  296 (471)
                      +++...+..+...+.+.|++++|...|++..+..  +.+...+..+..++.+.|++++|...+++..+.. +.+...+..
T Consensus         2 p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~--p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~   78 (217)
T 2pl2_A            2 QTAEQNPLRLGVQLYALGRYDAALTLFERALKEN--PQDPEALYWLARTQLKLGLVNPALENGKTLVART-PRYLGGYMV   78 (217)
T ss_dssp             --CCHHHHHHHHHHHHTTCHHHHHHHHHHHHTTS--SSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHH
T ss_pred             CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCcHHHHHH
Confidence            5677889999999999999999999999998764  5678889999999999999999999999998865 667888999


Q ss_pred             HHHHHHHc-----------CCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHH
Q 012111          297 LTKSYGRA-----------GMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYC  365 (471)
Q Consensus       297 ll~~~~~~-----------~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~  365 (471)
                      +..++...           |++++|...++...+..+. +...+..+...+...|++++|...|++..+..  .+...+.
T Consensus        79 lg~~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~P~-~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~--~~~~~~~  155 (217)
T 2pl2_A           79 LSEAYVALYRQAEDRERGKGYLEQALSVLKDAERVNPR-YAPLHLQRGLVYALLGERDKAEASLKQALALE--DTPEIRS  155 (217)
T ss_dssp             HHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--CCHHHHH
T ss_pred             HHHHHHHhhhhhhhhcccccCHHHHHHHHHHHHHhCcc-cHHHHHHHHHHHHHcCChHHHHHHHHHHHhcc--cchHHHH
Confidence            99999999           9999999999999887443 67788899999999999999999999999987  6889999


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 012111          366 SLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMK  423 (471)
Q Consensus       366 ~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~  423 (471)
                      .+..++...|++++|...|+++.+..+. +...+..+..++...|++++|+..|++..
T Consensus       156 ~la~~~~~~g~~~~A~~~~~~al~~~P~-~~~~~~~la~~~~~~g~~~~A~~~~~~~~  212 (217)
T 2pl2_A          156 ALAELYLSMGRLDEALAQYAKALEQAPK-DLDLRVRYASALLLKGKAEEAARAAALEH  212 (217)
T ss_dssp             HHHHHHHHHTCHHHHHHHHHHHHHHSTT-CHHHHHHHHHHHTC---------------
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHhCCC-ChHHHHHHHHHHHHccCHHHHHHHHHHHh
Confidence            9999999999999999999999988765 78889999999999999999999988754

>3u4t_A TPR repeat-containing protein; structural genomics, PSI- protein structure initiative, northeast structural genomics consortium, NESG; 2.28A {Cytophaga hutchinsonii}

Probab=99.68  E-value=1.5e-14  Score=126.44  Aligned_cols=233  Identities=12%  Similarity=-0.002  Sum_probs=100.8

Q ss_pred             HHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC--CHHHHHHHHHHHHH
Q 012111          226 IIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKA--DIQTLNILTKSYGR  303 (471)
Q Consensus       226 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~--~~~~~~~ll~~~~~  303 (471)
                      ....+...|++++|...|+++.+..  +.+...+..+..++...|++++|...++++...+..+  ....|..+...+..
T Consensus         9 ~a~~~~~~~~~~~A~~~~~~~l~~~--p~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~lg~~~~~   86 (272)
T 3u4t_A            9 YADFLFKNNNYAEAIEVFNKLEAKK--YNSPYIYNRRAVCYYELAKYDLAQKDIETYFSKVNATKAKSADFEYYGKILMK   86 (272)
T ss_dssp             HHHHHHTTTCHHHHHHHHHHHHHTT--CCCSTTHHHHHHHHHHTTCHHHHHHHHHHHHTTSCTTTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHhcCHHHHHHHHHHHHHhC--CCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhccCchhHHHHHHHHHHHHHHH
Confidence            3344444444444444444444432  1122234444444444444444444444444321111  12224444444444


Q ss_pred             cCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHH
Q 012111          304 AGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSI  383 (471)
Q Consensus       304 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~  383 (471)
                      .|++++|...++...+.... +...+..+...+...|++++|...+++..+.. +.+...+..+...+...+++++|...
T Consensus        87 ~~~~~~A~~~~~~a~~~~~~-~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~  164 (272)
T 3u4t_A           87 KGQDSLAIQQYQAAVDRDTT-RLDMYGQIGSYFYNKGNFPLAIQYMEKQIRPT-TTDPKVFYELGQAYYYNKEYVKADSS  164 (272)
T ss_dssp             TTCHHHHHHHHHHHHHHSTT-CTHHHHHHHHHHHHTTCHHHHHHHHGGGCCSS-CCCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             cccHHHHHHHHHHHHhcCcc-cHHHHHHHHHHHHHccCHHHHHHHHHHHhhcC-CCcHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44444444444444443221 33444444455555555555555555444431 22333444444222233355555555


Q ss_pred             HHHHHhCCCCcCHHHHHHHHHHHHhcCC---HHHHHHHHHHHHhCC-CCCC------HHHHHHHHHHHHhcCCHHHHHHH
Q 012111          384 LRQVENSDVILDTPFFNCIISAYGQAGD---VEKMGELFLTMKERH-CVPD------NITFATMIQAYNALGMTEAAQNL  453 (471)
Q Consensus       384 ~~~~~~~~~~~~~~~~~~l~~~~~~~g~---~~~a~~~~~~~~~~~-~~p~------~~~~~~l~~~~~~~g~~~~A~~~  453 (471)
                      ++++.+..+. +...+..+..++...|+   +++|...++++.+.. -.|+      ...|..+...|...|++++|.+.
T Consensus       165 ~~~a~~~~p~-~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~  243 (272)
T 3u4t_A          165 FVKVLELKPN-IYIGYLWRARANAAQDPDTKQGLAKPYYEKLIEVCAPGGAKYKDELIEANEYIAYYYTINRDKVKADAA  243 (272)
T ss_dssp             HHHHHHHSTT-CHHHHHHHHHHHHHHSTTCSSCTTHHHHHHHHHHHGGGGGGGHHHHHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHhCcc-chHHHHHHHHHHHHcCcchhhHHHHHHHHHHHHHHhcccccchHHHHHHHHHHHHHHHHcCCHHHHHHH
Confidence            5555444332 34444444444444444   444555554444320 0121      13444444555555555555555


Q ss_pred             HHHHHHhhhc
Q 012111          454 ENKMIAMKEN  463 (471)
Q Consensus       454 ~~~m~~~~~~  463 (471)
                      ++++++..|+
T Consensus       244 ~~~al~~~p~  253 (272)
T 3u4t_A          244 WKNILALDPT  253 (272)
T ss_dssp             HHHHHHHCTT
T ss_pred             HHHHHhcCcc
Confidence            5555555544

>3e4b_A ALGK; tetratricopeptide repeat, superhelix, alginate biosynt pseudomonas, protein binding; 2.50A {Pseudomonas fluorescens}

Probab=99.67  E-value=1.4e-14  Score=136.17  Aligned_cols=224  Identities=15%  Similarity=0.106  Sum_probs=122.0

Q ss_pred             HHHHHHHHHHccC---CHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhc----CCHHHHHHHHHHHHhCCCCCCHHHH
Q 012111          222 TYNTIIDGYGKAK---KFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNS----GNIEKMEKWYNEFNLMGVKADIQTL  294 (471)
Q Consensus       222 ~~~~l~~~~~~~~---~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~----~~~~~a~~~~~~~~~~~~~~~~~~~  294 (471)
                      .+..|...|...|   +.++|++.|++..+.+  .++...+..+...|...    +++++|..+|++.. .   -+...+
T Consensus       178 a~~~Lg~~~~~~g~~~~~~~A~~~~~~aa~~g--~~~a~~~~~Lg~~y~~g~~~~~d~~~A~~~~~~aa-~---g~~~a~  251 (452)
T 3e4b_A          178 CYVELATVYQKKQQPEQQAELLKQMEAGVSRG--TVTAQRVDSVARVLGDATLGTPDEKTAQALLEKIA-P---GYPASW  251 (452)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTT--CSCHHHHHHHHHHHTCGGGSSCCHHHHHHHHHHHG-G---GSTHHH
T ss_pred             HHHHHHHHHHHcCCcccHHHHHHHHHHHHHCC--CHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHc-C---CCHHHH
Confidence            5556666666666   6666666666666554  44444445555555443    56666666666665 2   233444


Q ss_pred             HHHHHH-H--HHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcC-----CHHHHHHHHHHHHHcCCCCCHHHHHH
Q 012111          295 NILTKS-Y--GRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAG-----HIEKMEEYFKKMKHRGMKPNSITYCS  366 (471)
Q Consensus       295 ~~ll~~-~--~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g-----~~~~a~~~~~~m~~~~~~p~~~~~~~  366 (471)
                      ..+... +  ...+++++|...|++..+.|   +...+..+...|. .|     ++++|...|++.. .|   +...+..
T Consensus       252 ~~Lg~~~~~~~~~~d~~~A~~~~~~Aa~~g---~~~A~~~Lg~~y~-~G~g~~~d~~~A~~~~~~Aa-~g---~~~A~~~  323 (452)
T 3e4b_A          252 VSLAQLLYDFPELGDVEQMMKYLDNGRAAD---QPRAELLLGKLYY-EGKWVPADAKAAEAHFEKAV-GR---EVAADYY  323 (452)
T ss_dssp             HHHHHHHHHSGGGCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHH-HCSSSCCCHHHHHHHHHTTT-TT---CHHHHHH
T ss_pred             HHHHHHHHhCCCCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHH-cCCCCCCCHHHHHHHHHHHh-CC---CHHHHHH
Confidence            444444 2  34566666666666666553   4445555555554 34     6666666666655 22   4455555


Q ss_pred             HHHHHHh----cCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHh----cCCHHHHHHHHHHHHhCCCCCCHHHHHHHH
Q 012111          367 LVSAYSK----AGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQ----AGDVEKMGELFLTMKERHCVPDNITFATMI  438 (471)
Q Consensus       367 li~~~~~----~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~  438 (471)
                      |...|..    ..+.++|...|+...+.|   +......|...|..    ..+..+|..+|+...+.|. ++.......+
T Consensus       324 Lg~~y~~G~g~~~d~~~A~~~~~~Aa~~g---~~~A~~~Lg~~y~~G~g~~~d~~~A~~~~~~A~~~g~-~~a~~~l~~l  399 (452)
T 3e4b_A          324 LGQIYRRGYLGKVYPQKALDHLLTAARNG---QNSADFAIAQLFSQGKGTKPDPLNAYVFSQLAKAQDT-PEANDLATQL  399 (452)
T ss_dssp             HHHHHHTTTTSSCCHHHHHHHHHHHHTTT---CTTHHHHHHHHHHSCTTBCCCHHHHHHHHHHHHTTCC-HHHHHHHHHH
T ss_pred             HHHHHHCCCCCCcCHHHHHHHHHHHHhhC---hHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHCCC-HHHHHHHHHH
Confidence            5555554    236666666666666654   23344455555543    3466666666666666542 2222222222


Q ss_pred             HHHHhcCCHHHHHHHHHHHHHhhhc
Q 012111          439 QAYNALGMTEAAQNLENKMIAMKEN  463 (471)
Q Consensus       439 ~~~~~~g~~~~A~~~~~~m~~~~~~  463 (471)
                      ......++.++|.++.++..+..+.
T Consensus       400 ~~~~~~~~~~~a~~~~~~~~~~~~~  424 (452)
T 3e4b_A          400 EAPLTPAQRAEGQRLVQQELAARGT  424 (452)
T ss_dssp             HTTCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHhCCHHHHHHHHHHHHHHHHhccc
Confidence            2222334556666666666555444

>2ho1_A Type 4 fimbrial biogenesis protein PILF; type IV pilus biogenesis, TPR, superhelix, protein binding; HET: MSE; 2.00A {Pseudomonas aeruginosa} PDB: 2fi7_A

Probab=99.67  E-value=1.1e-13  Score=119.54  Aligned_cols=203  Identities=6%  Similarity=-0.079  Sum_probs=113.0

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHH
Q 012111          257 FTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETF  336 (471)
Q Consensus       257 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~  336 (471)
                      ..+..+...+...|++++|...|+++.... +.+...+..+...+...|++++|...++.+.+.... +...+..+...+
T Consensus        38 ~~~~~~a~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~-~~~~~~~la~~~  115 (252)
T 2ho1_A           38 DAYIQLGLGYLQRGNTEQAKVPLRKALEID-PSSADAHAALAVVFQTEMEPKLADEEYRKALASDSR-NARVLNNYGGFL  115 (252)
T ss_dssp             HHHHHHHHHHHHTTCTGGGHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCChHHHHHHHHHHHhcC-CChHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcC-cHHHHHHHHHHH
Confidence            345555555566666666666666655443 334555555566666666666666666655554222 445555555566


Q ss_pred             HhcCCHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHH
Q 012111          337 GKAGHIEKMEEYFKKMKHRGMKP-NSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKM  415 (471)
Q Consensus       337 ~~~g~~~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a  415 (471)
                      ...|++++|.++++++...+..| +...+..+...+...|++++|...++++.+..+. +...+..+...+...|++++|
T Consensus       116 ~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~-~~~~~~~la~~~~~~g~~~~A  194 (252)
T 2ho1_A          116 YEQKRYEEAYQRLLEASQDTLYPERSRVFENLGLVSLQMKKPAQAKEYFEKSLRLNRN-QPSVALEMADLLYKEREYVPA  194 (252)
T ss_dssp             HHTTCHHHHHHHHHHHTTCTTCTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSC-CHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHhHHHHHHHHHHHHHhCccCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCcc-cHHHHHHHHHHHHHcCCHHHH
Confidence            66666666666666655522233 3445555555566666666666666665554433 455555566666666666666


Q ss_pred             HHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhhhc
Q 012111          416 GELFLTMKERHCVPDNITFATMIQAYNALGMTEAAQNLENKMIAMKEN  463 (471)
Q Consensus       416 ~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~  463 (471)
                      ..+++++.+. .+.+...+..+...+...|+.++|.++++++++..|.
T Consensus       195 ~~~~~~~~~~-~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~~p~  241 (252)
T 2ho1_A          195 RQYYDLFAQG-GGQNARSLLLGIRLAKVFEDRDTAASYGLQLKRLYPG  241 (252)
T ss_dssp             HHHHHHHHTT-SCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT
T ss_pred             HHHHHHHHHh-CcCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHHCCC
Confidence            6666665543 2234445555555566666666666666666655544

>2vq2_A PILW, putative fimbrial biogenesis and twitching motility protein; secretin, TPR repeat, type IV pilus, bacterail virulence; 1.54A {Neisseria meningitidis}

Probab=99.66  E-value=1.4e-13  Score=116.41  Aligned_cols=202  Identities=10%  Similarity=0.027  Sum_probs=109.6

Q ss_pred             CHHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHH
Q 012111          219 SAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILT  298 (471)
Q Consensus       219 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll  298 (471)
                      +...+..+...+...|++++|.+.|+.+.+..  +.+...+..+...+...|++++|...++++.... +.+..++..+.
T Consensus         7 ~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~   83 (225)
T 2vq2_A            7 VSNIKTQLAMEYMRGQDYRQATASIEDALKSD--PKNELAWLVRAEIYQYLKVNDKAQESFRQALSIK-PDSAEINNNYG   83 (225)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhC--ccchHHHHHHHHHHHHcCChHHHHHHHHHHHHhC-CCChHHHHHHH
Confidence            34555666666666666666666666665542  3345556666666666666666666666665443 33455555555


Q ss_pred             HHHHHc-CCHHHHHHHHHHHHhCCCCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCC
Q 012111          299 KSYGRA-GMYDKMRSVMDFMQKRFFFPT-VVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGL  376 (471)
Q Consensus       299 ~~~~~~-~~~~~a~~~~~~~~~~~~~~~-~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~  376 (471)
                      ..+... |++++|...++.+.+.+..|+ ...+..+...+...|++++|...++++.+.. +.+...+..+...+...|+
T Consensus        84 ~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~  162 (225)
T 2vq2_A           84 WFLCGRLNRPAESMAYFDKALADPTYPTPYIANLNKGICSAKQGQFGLAEAYLKRSLAAQ-PQFPPAFKELARTKMLAGQ  162 (225)
T ss_dssp             HHHHTTTCCHHHHHHHHHHHHTSTTCSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHTC
T ss_pred             HHHHHhcCcHHHHHHHHHHHHcCcCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCchHHHHHHHHHHHcCC
Confidence            556666 666666666655555211222 3445555555555555555555555555442 2234455555555555555


Q ss_pred             HHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 012111          377 IMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKE  424 (471)
Q Consensus       377 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~  424 (471)
                      +++|...++.+.+..+..+...+..+...+...|+.+.|..+++.+.+
T Consensus       163 ~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~  210 (225)
T 2vq2_A          163 LGDADYYFKKYQSRVEVLQADDLLLGWKIAKALGNAQAAYEYEAQLQA  210 (225)
T ss_dssp             HHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHHHHH
Confidence            555555555555443312444444444555555555555555555543

>2h6f_A Protein farnesyltransferase/geranylgeranyltransferase type I alpha subunit; ftase, farnesyltransferase, farnesyl transferase, prenyltransferase, CAAX, RAS, lipid modification, prenylation; HET: SUC FAR; 1.50A {Homo sapiens} SCOP: a.118.6.1 PDB: 1jcq_A* 1ld7_A* 1mzc_A* 1s63_A* 1sa4_A* 1tn6_A* 1ld8_A* 2h6g_A* 2h6h_A* 2h6i_A* 2iej_A* 3e37_A* 2f0y_A* 3ksl_A* 2zir_A* 2zis_A* 1o5m_A* 3ksq_A* 1o1t_A* 1o1s_A* ...

Probab=99.66  E-value=5.2e-14  Score=128.18  Aligned_cols=217  Identities=9%  Similarity=0.018  Sum_probs=135.4

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCC-HHHHHHHHHHHHHcCCCCCCHHHHHHHH
Q 012111          185 VYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKK-FEEMESSFSAMVESGGCHPDIFTLNSMI  263 (471)
Q Consensus       185 ~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~-~~~a~~~~~~~~~~~~~~~~~~~~~~l~  263 (471)
                      ...|..+...+...|++++|++.+++.++.. +-+..+|+.+..++...|+ +++|+..|+++.+..  +.+...|..+.
T Consensus        97 ~~a~~~lg~~~~~~g~~~~Al~~~~~al~l~-P~~~~a~~~~g~~l~~~g~d~~eAl~~~~~al~l~--P~~~~a~~~~g  173 (382)
T 2h6f_A           97 RDVYDYFRAVLQRDERSERAFKLTRDAIELN-AANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQ--PKNYQVWHHRR  173 (382)
T ss_dssp             HHHHHHHHHHHHHTCCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHC--TTCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCChHHHHHHHHHHHHhC-ccCHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHC--CCCHHHHHHHH
Confidence            4456667777777777888888887777664 4457777777777777775 777777777777653  44566777777


Q ss_pred             HHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHh-cCCH
Q 012111          264 SAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGK-AGHI  342 (471)
Q Consensus       264 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~-~g~~  342 (471)
                      .++...|++++|+..|+++.... +-+...|..+..++...|++++|+..++++.+.... +...|+.+..++.. .|..
T Consensus       174 ~~~~~~g~~~eAl~~~~kal~ld-P~~~~a~~~lg~~~~~~g~~~eAl~~~~~al~l~P~-~~~a~~~lg~~l~~l~~~~  251 (382)
T 2h6f_A          174 VLVEWLRDPSQELEFIADILNQD-AKNYHAWQHRQWVIQEFKLWDNELQYVDQLLKEDVR-NNSVWNQRYFVISNTTGYN  251 (382)
T ss_dssp             HHHHHHTCCTTHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCSC
T ss_pred             HHHHHccCHHHHHHHHHHHHHhC-ccCHHHHHHHHHHHHHcCChHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHhcCcc
Confidence            77777777777777777776654 455666666666666677777777777666665333 45566666666666 4443


Q ss_pred             HHH-----HHHHHHHHHcCCCCCHHHHHHHHHHHHhcC--CHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhc
Q 012111          343 EKM-----EEYFKKMKHRGMKPNSITYCSLVSAYSKAG--LIMKVDSILRQVENSDVILDTPFFNCIISAYGQA  409 (471)
Q Consensus       343 ~~a-----~~~~~~m~~~~~~p~~~~~~~li~~~~~~g--~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  409 (471)
                      ++|     +..+++.+... +-+...|..+...+...|  ++++|.+.+..+ +.++. +...+..+..+|.+.
T Consensus       252 ~eA~~~~el~~~~~Al~l~-P~~~~a~~~l~~ll~~~g~~~~~~a~~~~~~~-~~~p~-~~~al~~La~~~~~~  322 (382)
T 2h6f_A          252 DRAVLEREVQYTLEMIKLV-PHNESAWNYLKGILQDRGLSKYPNLLNQLLDL-QPSHS-SPYLIAFLVDIYEDM  322 (382)
T ss_dssp             SHHHHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHTTTCGGGCHHHHHHHHHH-TTTCC-CHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHccCccchHHHHHHHHHh-ccCCC-CHHHHHHHHHHHHHH
Confidence            555     35555555532 223445555555555555  355555555555 32222 444555555555544

>2q7f_A YRRB protein; TPR, protein binding; 2.49A {Bacillus subtilis} SCOP: k.38.1.1

Probab=99.65  E-value=2.1e-14  Score=123.24  Aligned_cols=199  Identities=11%  Similarity=0.115  Sum_probs=100.5

Q ss_pred             HHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHH
Q 012111          220 AVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTK  299 (471)
Q Consensus       220 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~  299 (471)
                      ...+..+...+...|++++|...|+++.+..  +.+...+..+...+...|++++|...++++.... +.+...+..+..
T Consensus        23 ~~~~~~~a~~~~~~~~~~~A~~~~~~~l~~~--~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~   99 (243)
T 2q7f_A           23 SMTGGQQMGRGSEFGDYEKAAEAFTKAIEEN--KEDAIPYINFANLLSSVNELERALAFYDKALELD-SSAATAYYGAGN   99 (243)
T ss_dssp             -------------------CCTTHHHHHTTC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhhCHHHHHHHHHHHHHhC--cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CcchHHHHHHHH
Confidence            4445555566666666666666666665542  3345556666666666666666666666665443 334555555566


Q ss_pred             HHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHH
Q 012111          300 SYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMK  379 (471)
Q Consensus       300 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~  379 (471)
                      .+...|++++|...++.+.+... .+...+..+...+...|++++|...++++.+.. +.+...+..+...+...|++++
T Consensus       100 ~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~  177 (243)
T 2q7f_A          100 VYVVKEMYKEAKDMFEKALRAGM-ENGDLFYMLGTVLVKLEQPKLALPYLQRAVELN-ENDTEARFQFGMCLANEGMLDE  177 (243)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHTC-CSHHHHHHHHHHHHHTSCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCCHH
T ss_pred             HHHHhccHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHcCCHHH
Confidence            66666666666666665555432 244455555555556666666666666555542 2244555555555555555555


Q ss_pred             HHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 012111          380 VDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKE  424 (471)
Q Consensus       380 a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~  424 (471)
                      |...++++.+..+. +..++..+..+|...|++++|.+.++++.+
T Consensus       178 A~~~~~~~~~~~~~-~~~~~~~la~~~~~~~~~~~A~~~~~~~~~  221 (243)
T 2q7f_A          178 ALSQFAAVTEQDPG-HADAFYNAGVTYAYKENREKALEMLDKAID  221 (243)
T ss_dssp             HHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCTTHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCcc-cHHHHHHHHHHHHHccCHHHHHHHHHHHHc
Confidence            55555555544332 444555555555555555555555555554

>3u4t_A TPR repeat-containing protein; structural genomics, PSI- protein structure initiative, northeast structural genomics consortium, NESG; 2.28A {Cytophaga hutchinsonii}

Probab=99.65  E-value=6.5e-14  Score=122.42  Aligned_cols=197  Identities=11%  Similarity=0.052  Sum_probs=118.8

Q ss_pred             HHHHHHHHHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCC--CHHHHHHHHH
Q 012111           80 PVLEALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKP--SVDVYTALVS  157 (471)
Q Consensus        80 ~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~--~~~~~~~li~  157 (471)
                      .+......+...|++++|++.|+.+.+..  +.+...+..+..++...|++++|...++...+.+..+  ...+|..+..
T Consensus         5 ~~~~~a~~~~~~~~~~~A~~~~~~~l~~~--p~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~lg~   82 (272)
T 3u4t_A            5 VEFRYADFLFKNNNYAEAIEVFNKLEAKK--YNSPYIYNRRAVCYYELAKYDLAQKDIETYFSKVNATKAKSADFEYYGK   82 (272)
T ss_dssp             CHHHHHHHHHTTTCHHHHHHHHHHHHHTT--CCCSTTHHHHHHHHHHTTCHHHHHHHHHHHHTTSCTTTCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHHHHhC--CCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhccCchhHHHHHHHHHHH
Confidence            44455556667777777777777777654  4455567777777777777777777777777632111  2334666777


Q ss_pred             HHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHH
Q 012111          158 AYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFE  237 (471)
Q Consensus       158 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~  237 (471)
                      .+...|++++|+..|++..+..  +.+..++..+...+...|++++|...+++..+.. +.+...+..+...+...++++
T Consensus        83 ~~~~~~~~~~A~~~~~~a~~~~--~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~~~~~  159 (272)
T 3u4t_A           83 ILMKKGQDSLAIQQYQAAVDRD--TTRLDMYGQIGSYFYNKGNFPLAIQYMEKQIRPT-TTDPKVFYELGQAYYYNKEYV  159 (272)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHS--TTCTHHHHHHHHHHHHTTCHHHHHHHHGGGCCSS-CCCHHHHHHHHHHHHHTTCHH
T ss_pred             HHHHcccHHHHHHHHHHHHhcC--cccHHHHHHHHHHHHHccCHHHHHHHHHHHhhcC-CCcHHHHHHHHHHHHHHHHHH
Confidence            7777777777777777766522  2344556666666666666666666666665542 334555555552233334666


Q ss_pred             HHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCC---HHHHHHHHHHHH
Q 012111          238 EMESSFSAMVESGGCHPDIFTLNSMISAYGNSGN---IEKMEKWYNEFN  283 (471)
Q Consensus       238 ~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~---~~~a~~~~~~~~  283 (471)
                      +|.+.|+++.+..  +.+...+..+..++...|+   +++|...+++..
T Consensus       160 ~A~~~~~~a~~~~--p~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~  206 (272)
T 3u4t_A          160 KADSSFVKVLELK--PNIYIGYLWRARANAAQDPDTKQGLAKPYYEKLI  206 (272)
T ss_dssp             HHHHHHHHHHHHS--TTCHHHHHHHHHHHHHHSTTCSSCTTHHHHHHHH
T ss_pred             HHHHHHHHHHHhC--ccchHHHHHHHHHHHHcCcchhhHHHHHHHHHHH
Confidence            6666666665542  3334555555555555555   555555555543

>1xnf_A Lipoprotein NLPI; TPR, tetratricopeptide, structural genomi unknown function; 1.98A {Escherichia coli} SCOP: a.118.8.1

Probab=99.65  E-value=1.2e-14  Score=127.42  Aligned_cols=245  Identities=11%  Similarity=-0.031  Sum_probs=132.3

Q ss_pred             CCHHHHHHHHHHHHHCCC---CCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHH
Q 012111          199 HRFDLIEKILAEMSYLGI---ECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKM  275 (471)
Q Consensus       199 ~~~~~a~~~~~~~~~~g~---~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  275 (471)
                      |++++|...++++.+...   +.+..++..+...+...|++++|...|+++.+..  +.+...+..+...+...|++++|
T Consensus        19 ~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~--~~~~~~~~~la~~~~~~~~~~~A   96 (275)
T 1xnf_A           19 LQQEVILARMEQILASRALTDDERAQLLYERGVLYDSLGLRALARNDFSQALAIR--PDMPEVFNYLGIYLTQAGNFDAA   96 (275)
T ss_dssp             HHHHHHHHHHHHHHTSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--CCCHHHHHHHHHHHHHTTCHHHH
T ss_pred             chHHHHHHHHHHHHhcccccCchhHHHHHHHHHHHHHcccHHHHHHHHHHHHHcC--CCcHHHHHHHHHHHHHccCHHHH
Confidence            445555555555554321   1123445555555555566666666555555542  33455555555556666666666


Q ss_pred             HHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 012111          276 EKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHR  355 (471)
Q Consensus       276 ~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  355 (471)
                      ...|+++.... +.+..++..+..++...|++++|...++.+.+..  |+.......+..+...|++++|...+.+....
T Consensus        97 ~~~~~~al~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~--~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~  173 (275)
T 1xnf_A           97 YEAFDSVLELD-PTYNYAHLNRGIALYYGGRDKLAQDDLLAFYQDD--PNDPFRSLWLYLAEQKLDEKQAKEVLKQHFEK  173 (275)
T ss_dssp             HHHHHHHHHHC-TTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhcC-ccccHHHHHHHHHHHHhccHHHHHHHHHHHHHhC--CCChHHHHHHHHHHHhcCHHHHHHHHHHHHhc
Confidence            66666555432 3344555556666666666666666666655542  22222333333444556666777666655554


Q ss_pred             CCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCc---CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHH
Q 012111          356 GMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVIL---DTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNI  432 (471)
Q Consensus       356 ~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~---~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~  432 (471)
                      . +++...+ .++..+...++.++|...++.+.+.....   +...+..+...|...|++++|...|+++.+.  .|+. 
T Consensus       174 ~-~~~~~~~-~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~--~p~~-  248 (275)
T 1xnf_A          174 S-DKEQWGW-NIVEFYLGNISEQTLMERLKADATDNTSLAEHLSETNFYLGKYYLSLGDLDSATALFKLAVAN--NVHN-  248 (275)
T ss_dssp             S-CCCSTHH-HHHHHHTTSSCHHHHHHHHHHHCCSHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT--CCTT-
T ss_pred             C-CcchHHH-HHHHHHHHhcCHHHHHHHHHHHhcccccccccccHHHHHHHHHHHHcCCHHHHHHHHHHHHhC--Cchh-
Confidence            2 2232222 35555556666666666666665432211   1456677777777788888888888877764  3422 


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHH
Q 012111          433 TFATMIQAYNALGMTEAAQNLE  454 (471)
Q Consensus       433 ~~~~l~~~~~~~g~~~~A~~~~  454 (471)
                       +.....++...|++++|.+.+
T Consensus       249 -~~~~~~~~~~l~~~~~a~~~~  269 (275)
T 1xnf_A          249 -FVEHRYALLELSLLGQDQDDL  269 (275)
T ss_dssp             -CHHHHHHHHHHHHHHHC----
T ss_pred             -HHHHHHHHHHHHHHHhhHHHH
Confidence             222344566677777776655

>2vq2_A PILW, putative fimbrial biogenesis and twitching motility protein; secretin, TPR repeat, type IV pilus, bacterail virulence; 1.54A {Neisseria meningitidis}

Probab=99.65  E-value=2.1e-13  Score=115.31  Aligned_cols=203  Identities=13%  Similarity=0.022  Sum_probs=100.5

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHH
Q 012111          257 FTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETF  336 (471)
Q Consensus       257 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~  336 (471)
                      ..+..+...+...|++++|...++++.... +.+...+..+...+...|++++|...++.+.+... .+...+..+...+
T Consensus         9 ~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~-~~~~~~~~l~~~~   86 (225)
T 2vq2_A            9 NIKTQLAMEYMRGQDYRQATASIEDALKSD-PKNELAWLVRAEIYQYLKVNDKAQESFRQALSIKP-DSAEINNNYGWFL   86 (225)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhhHHHHHHHHHHHHHhC-ccchHHHHHHHHHHHHcCChHHHHHHHHHHHHhCC-CChHHHHHHHHHH
Confidence            344445555555555555555555554432 33344555555555555555555555555544322 1344455555555


Q ss_pred             Hhc-CCHHHHHHHHHHHHHcCCCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHH
Q 012111          337 GKA-GHIEKMEEYFKKMKHRGMKPN-SITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEK  414 (471)
Q Consensus       337 ~~~-g~~~~a~~~~~~m~~~~~~p~-~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~  414 (471)
                      ... |++++|...++++.+.+..|+ ...+..+...+...|++++|...++++.+..+. +...+..+..++...|++++
T Consensus        87 ~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~la~~~~~~~~~~~  165 (225)
T 2vq2_A           87 CGRLNRPAESMAYFDKALADPTYPTPYIANLNKGICSAKQGQFGLAEAYLKRSLAAQPQ-FPPAFKELARTKMLAGQLGD  165 (225)
T ss_dssp             HTTTCCHHHHHHHHHHHHTSTTCSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTT-CHHHHHHHHHHHHHHTCHHH
T ss_pred             HHhcCcHHHHHHHHHHHHcCcCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-CchHHHHHHHHHHHcCCHHH
Confidence            555 555555555555554211222 344455555555555555555555555544332 34455555555555555555


Q ss_pred             HHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhhh
Q 012111          415 MGELFLTMKERHCVPDNITFATMIQAYNALGMTEAAQNLENKMIAMKE  462 (471)
Q Consensus       415 a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~  462 (471)
                      |.++++++.+..-..+...+..+...+...|+.+.|..+++.+.+..|
T Consensus       166 A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~p  213 (225)
T 2vq2_A          166 ADYYFKKYQSRVEVLQADDLLLGWKIAKALGNAQAAYEYEAQLQANFP  213 (225)
T ss_dssp             HHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT
T ss_pred             HHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHHHHHhCC
Confidence            555555554431102344444444455555555555555555554444

>1ouv_A Conserved hypothetical secreted protein; TPR repeat, HCP repeat, cysteine rich protein, loop-helix-TU repeat protein, hydrolase; 2.00A {Helicobacter pylori} SCOP: a.118.18.1

Probab=99.65  E-value=1.4e-12  Score=114.00  Aligned_cols=219  Identities=11%  Similarity=-0.028  Sum_probs=105.4

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHc----cCCHHHHHHHHHHHHHcCCCCCCHHHHHHHH
Q 012111          188 YSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGK----AKKFEEMESSFSAMVESGGCHPDIFTLNSMI  263 (471)
Q Consensus       188 ~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~  263 (471)
                      +..+...+...|++++|.+.|++..+.+   +...+..+...|..    .+++++|...|++..+.+    +...+..+.
T Consensus         9 ~~~lg~~~~~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~----~~~a~~~lg   81 (273)
T 1ouv_A            9 LVGLGAKSYKEKDFTQAKKYFEKACDLK---ENSGCFNLGVLYYQGQGVEKNLKKAASFYAKACDLN----YSNGCHLLG   81 (273)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT----CHHHHHHHH
T ss_pred             HHHHHHHHHhCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCcCCCHHHHHHHHHHHHHCC----CHHHHHHHH
Confidence            3333344444444444444444444321   23334444444444    444444444444444332    333444444


Q ss_pred             HHHHh----cCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHH----cCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHH
Q 012111          264 SAYGN----SGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGR----AGMYDKMRSVMDFMQKRFFFPTVVTYNIVIET  335 (471)
Q Consensus       264 ~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~  335 (471)
                      ..|..    .+++++|...|++..+.+   +...+..+...|..    .+++++|...|++..+.+   +...+..+...
T Consensus        82 ~~~~~g~~~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~~~~~~~~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~  155 (273)
T 1ouv_A           82 NLYYSGQGVSQNTNKALQYYSKACDLK---YAEGCASLGGIYHDGKVVTRDFKKAVEYFTKACDLN---DGDGCTILGSL  155 (273)
T ss_dssp             HHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHCSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHH
T ss_pred             HHHhCCCCcccCHHHHHHHHHHHHHcC---CccHHHHHHHHHHcCCCcccCHHHHHHHHHHHHhcC---cHHHHHHHHHH
Confidence            44444    444444444444444432   34444444444444    455555555555544432   33344444444


Q ss_pred             HHh----cCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHh----cCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHH
Q 012111          336 FGK----AGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSK----AGLIMKVDSILRQVENSDVILDTPFFNCIISAYG  407 (471)
Q Consensus       336 ~~~----~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~----~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  407 (471)
                      |..    .+++++|...|++..+.+   +...+..+...|..    .+++++|...+++..+.+   +...+..+...|.
T Consensus       156 ~~~~~~~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~---~~~a~~~l~~~~~  229 (273)
T 1ouv_A          156 YDAGRGTPKDLKKALASYDKACDLK---DSPGCFNAGNMYHHGEGATKNFKEALARYSKACELE---NGGGCFNLGAMQY  229 (273)
T ss_dssp             HHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTCSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHH
T ss_pred             HHcCCCCCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCccHHHHHHHHHHHHhCC---CHHHHHHHHHHHH
Confidence            444    555555555555555542   34445555555555    556666666665555543   2444555555555


Q ss_pred             h----cCCHHHHHHHHHHHHhC
Q 012111          408 Q----AGDVEKMGELFLTMKER  425 (471)
Q Consensus       408 ~----~g~~~~a~~~~~~~~~~  425 (471)
                      .    .+++++|.+.|++..+.
T Consensus       230 ~g~~~~~~~~~A~~~~~~a~~~  251 (273)
T 1ouv_A          230 NGEGVTRNEKQAIENFKKGCKL  251 (273)
T ss_dssp             TTSSSSCCSTTHHHHHHHHHHH
T ss_pred             cCCCcccCHHHHHHHHHHHHHc
Confidence            5    56666666666665554

>1xnf_A Lipoprotein NLPI; TPR, tetratricopeptide, structural genomi unknown function; 1.98A {Escherichia coli} SCOP: a.118.8.1

Probab=99.64  E-value=9.5e-15  Score=127.95  Aligned_cols=223  Identities=11%  Similarity=-0.000  Sum_probs=147.1

Q ss_pred             HhhcHHHHHHHHHHhhhccCc--cCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHH
Q 012111           90 KQKKWQLALKIFGLLRQQQWY--QARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDE  167 (471)
Q Consensus        90 ~~~~~~~A~~~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~  167 (471)
                      ..|++++|++.|+.+.+....  +.+..++..+...+...|++++|...|+.+.+.... +..+|..+..++...|++++
T Consensus        17 ~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~-~~~~~~~la~~~~~~~~~~~   95 (275)
T 1xnf_A           17 PTLQQEVILARMEQILASRALTDDERAQLLYERGVLYDSLGLRALARNDFSQALAIRPD-MPEVFNYLGIYLTQAGNFDA   95 (275)
T ss_dssp             CCHHHHHHHHHHHHHHTSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCC-CHHHHHHHHHHHHHTTCHHH
T ss_pred             ccchHHHHHHHHHHHHhcccccCchhHHHHHHHHHHHHHcccHHHHHHHHHHHHHcCCC-cHHHHHHHHHHHHHccCHHH
Confidence            457888888888888875311  224567788888888888888888888888776433 67788888888888888888


Q ss_pred             HHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHH
Q 012111          168 AFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMV  247 (471)
Q Consensus       168 a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  247 (471)
                      |+..|++..+..  +.+...+..+...+...|++++|...++++.+..  |+.......+..+...|++++|...+....
T Consensus        96 A~~~~~~al~~~--~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~--~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~  171 (275)
T 1xnf_A           96 AYEAFDSVLELD--PTYNYAHLNRGIALYYGGRDKLAQDDLLAFYQDD--PNDPFRSLWLYLAEQKLDEKQAKEVLKQHF  171 (275)
T ss_dssp             HHHHHHHHHHHC--TTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcC--ccccHHHHHHHHHHHHhccHHHHHHHHHHHHHhC--CCChHHHHHHHHHHHhcCHHHHHHHHHHHH
Confidence            888888887632  3356677777778888888888888888877653  333333334444456677888888777666


Q ss_pred             HcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCC---CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhC
Q 012111          248 ESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVK---ADIQTLNILTKSYGRAGMYDKMRSVMDFMQKR  320 (471)
Q Consensus       248 ~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~---~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~  320 (471)
                      ...  +++...+ .++..+...++.++|...+.+.......   .+...+..+...|...|++++|...|+...+.
T Consensus       172 ~~~--~~~~~~~-~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~  244 (275)
T 1xnf_A          172 EKS--DKEQWGW-NIVEFYLGNISEQTLMERLKADATDNTSLAEHLSETNFYLGKYYLSLGDLDSATALFKLAVAN  244 (275)
T ss_dssp             HHS--CCCSTHH-HHHHHHTTSSCHHHHHHHHHHHCCSHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT
T ss_pred             hcC--CcchHHH-HHHHHHHHhcCHHHHHHHHHHHhcccccccccccHHHHHHHHHHHHcCCHHHHHHHHHHHHhC
Confidence            653  3333333 3555566667777777777766543210   01344555555555666666666666555554

>2h6f_A Protein farnesyltransferase/geranylgeranyltransferase type I alpha subunit; ftase, farnesyltransferase, farnesyl transferase, prenyltransferase, CAAX, RAS, lipid modification, prenylation; HET: SUC FAR; 1.50A {Homo sapiens} SCOP: a.118.6.1 PDB: 1jcq_A* 1ld7_A* 1mzc_A* 1s63_A* 1sa4_A* 1tn6_A* 1ld8_A* 2h6g_A* 2h6h_A* 2h6i_A* 2iej_A* 3e37_A* 2f0y_A* 3ksl_A* 2zir_A* 2zis_A* 1o5m_A* 3ksq_A* 1o1t_A* 1o1s_A* ...

Probab=99.64  E-value=1.7e-13  Score=124.82  Aligned_cols=197  Identities=9%  Similarity=0.010  Sum_probs=117.9

Q ss_pred             hhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCC-HHHHHHHHHHhhcCCCCCCCHHHHHHHH
Q 012111          114 CQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGL-LDEAFSTINDMKSVSDCKPDVYTYSILI  192 (471)
Q Consensus       114 ~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~-~~~a~~~~~~~~~~~~~~~~~~~~~~ll  192 (471)
                      ..+|..+..++.+.|++++|+..++..++.... +..+|+.+..++...|+ +++|+..|++.....  +-+...|..+.
T Consensus        97 ~~a~~~lg~~~~~~g~~~~Al~~~~~al~l~P~-~~~a~~~~g~~l~~~g~d~~eAl~~~~~al~l~--P~~~~a~~~~g  173 (382)
T 2h6f_A           97 RDVYDYFRAVLQRDERSERAFKLTRDAIELNAA-NYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQ--PKNYQVWHHRR  173 (382)
T ss_dssp             HHHHHHHHHHHHHTCCCHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHC--TTCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCChHHHHHHHHHHHHhCcc-CHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHC--CCCHHHHHHHH
Confidence            456666777777777777777777777765433 56677777777777775 777777777776521  33556666666


Q ss_pred             HHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHh-cCC
Q 012111          193 KSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGN-SGN  271 (471)
Q Consensus       193 ~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~-~~~  271 (471)
                      .++...|++++|+..|+++++.. +-+...|..+..++...|++++|+..|+++++..  +.+...|+.+..++.. .|.
T Consensus       174 ~~~~~~g~~~eAl~~~~kal~ld-P~~~~a~~~lg~~~~~~g~~~eAl~~~~~al~l~--P~~~~a~~~lg~~l~~l~~~  250 (382)
T 2h6f_A          174 VLVEWLRDPSQELEFIADILNQD-AKNYHAWQHRQWVIQEFKLWDNELQYVDQLLKED--VRNNSVWNQRYFVISNTTGY  250 (382)
T ss_dssp             HHHHHHTCCTTHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCS
T ss_pred             HHHHHccCHHHHHHHHHHHHHhC-ccCHHHHHHHHHHHHHcCChHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHhcCc
Confidence            66667777777777777666654 3356666666666666666666666666666653  3455566666666666 444


Q ss_pred             HHHH-----HHHHHHHHhCCCCCCHHHHHHHHHHHHHcC--CHHHHHHHHHHH
Q 012111          272 IEKM-----EKWYNEFNLMGVKADIQTLNILTKSYGRAG--MYDKMRSVMDFM  317 (471)
Q Consensus       272 ~~~a-----~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~--~~~~a~~~~~~~  317 (471)
                      .++|     +..|++.+... +-+...|..+..++...|  ++++|...+..+
T Consensus       251 ~~eA~~~~el~~~~~Al~l~-P~~~~a~~~l~~ll~~~g~~~~~~a~~~~~~~  302 (382)
T 2h6f_A          251 NDRAVLEREVQYTLEMIKLV-PHNESAWNYLKGILQDRGLSKYPNLLNQLLDL  302 (382)
T ss_dssp             CSHHHHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHTTTCGGGCHHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHccCccchHHHHHHHHHh
Confidence            3444     24444444432 233444444444444444  244444444433

>2q7f_A YRRB protein; TPR, protein binding; 2.49A {Bacillus subtilis} SCOP: k.38.1.1

Probab=99.63  E-value=5.9e-14  Score=120.38  Aligned_cols=199  Identities=7%  Similarity=0.008  Sum_probs=91.4

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHH
Q 012111          188 YSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYG  267 (471)
Q Consensus       188 ~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~  267 (471)
                      |..+...+...|+++.|..+++++.+.. +.+...+..+...+...|++++|...++++.+..  +.+...+..+...+.
T Consensus        26 ~~~~a~~~~~~~~~~~A~~~~~~~l~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~la~~~~  102 (243)
T 2q7f_A           26 GGQQMGRGSEFGDYEKAAEAFTKAIEEN-KEDAIPYINFANLLSSVNELERALAFYDKALELD--SSAATAYYGAGNVYV  102 (243)
T ss_dssp             ----------------CCTTHHHHHTTC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC--CcchHHHHHHHHHHH
Confidence            3333344444444444444444444332 2234444444444444455555555554444432  223444444445555


Q ss_pred             hcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHH
Q 012111          268 NSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEE  347 (471)
Q Consensus       268 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~  347 (471)
                      ..|++++|...++++.+.. +.+...+..+...+...|++++|...++.+.+... .+...+..+...+...|++++|..
T Consensus       103 ~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~A~~  180 (243)
T 2q7f_A          103 VKEMYKEAKDMFEKALRAG-MENGDLFYMLGTVLVKLEQPKLALPYLQRAVELNE-NDTEARFQFGMCLANEGMLDEALS  180 (243)
T ss_dssp             HTTCHHHHHHHHHHHHHHT-CCSHHHHHHHHHHHHHTSCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHHTCCHHHHH
T ss_pred             HhccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCC-ccHHHHHHHHHHHHHcCCHHHHHH
Confidence            5555555555555544432 33344445555555555555555555555544322 134455555555556666666666


Q ss_pred             HHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCC
Q 012111          348 YFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDV  392 (471)
Q Consensus       348 ~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~  392 (471)
                      .++++.... +.+..++..+...+...|++++|...++++.+..+
T Consensus       181 ~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~p  224 (243)
T 2q7f_A          181 QFAAVTEQD-PGHADAFYNAGVTYAYKENREKALEMLDKAIDIQP  224 (243)
T ss_dssp             HHHHHHHHC-TTCHHHHHHHHHHHHHTTCTTHHHHHHHHHHHHCT
T ss_pred             HHHHHHHhC-cccHHHHHHHHHHHHHccCHHHHHHHHHHHHccCc
Confidence            666555542 22455556666666666666666666666655443

>3e4b_A ALGK; tetratricopeptide repeat, superhelix, alginate biosynt pseudomonas, protein binding; 2.50A {Pseudomonas fluorescens}

Probab=99.62  E-value=4e-13  Score=126.17  Aligned_cols=344  Identities=12%  Similarity=0.060  Sum_probs=234.8

Q ss_pred             HHHHHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCH---HHHHHHHHHHHhCCCCCCHHHHHHHHHHHH
Q 012111           84 ALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQP---EQASLLFEVMLSDGLKPSVDVYTALVSAYG  160 (471)
Q Consensus        84 ~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~---~~a~~~~~~m~~~~~~~~~~~~~~li~~~~  160 (471)
                      +...+.+.|++++|++.|+.+.+.+    +...+..+...|...|+.   ++|...|+...+.    ++..+..|...+.
T Consensus         9 la~~~~~~g~~~~A~~~~~~aa~~g----~~~A~~~Lg~~y~~~g~~~d~~~A~~~~~~A~~~----~~~A~~~Lg~~~~   80 (452)
T 3e4b_A            9 LANEALKRGDTVTAQQNYQQLAELG----YSEAQVGLADIQVGTRDPAQIKQAEATYRAAADT----SPRAQARLGRLLA   80 (452)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHT----CCTGGGTCC--------------------------------CHHHHHHHHH
T ss_pred             HHHHHHhCCCHHHHHHHHHHHHHCC----CHHHHHHHHHHHHccCCCCCHHHHHHHHHHHHhC----CHHHHHHHHHHHH
Confidence            3455678999999999999998764    445566677777778888   8999999998864    5666777777565


Q ss_pred             hcC-----CHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCH---HHHHHHHHHHHHCCCCCCHHHHHHHHHHHHc
Q 012111          161 QSG-----LLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRF---DLIEKILAEMSYLGIECSAVTYNTIIDGYGK  232 (471)
Q Consensus       161 ~~~-----~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~---~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~  232 (471)
                      ..+     +.++|+..|++... .| .++  .+..|...|...+..   ..+.+.+......|   +......+...|..
T Consensus        81 ~~~~~~~~~~~~A~~~~~~Aa~-~g-~~~--A~~~Lg~~y~~~~~~~~~~~a~~~~~~a~~~g---~~~a~~~Lg~~y~~  153 (452)
T 3e4b_A           81 AKPGATEAEHHEAESLLKKAFA-NG-EGN--TLIPLAMLYLQYPHSFPNVNAQQQISQWQAAG---YPEAGLAQVLLYRT  153 (452)
T ss_dssp             TC--CCHHHHHHHHHHHHHHHH-TT-CSS--CHHHHHHHHHHCGGGCTTCCHHHHHHHHHHHT---CTTHHHHHHHHHHH
T ss_pred             hCCCCCCcCHHHHHHHHHHHHH-CC-CHH--HHHHHHHHHHhCCCCCCCHHHHHHHHHHHHCC---CHHHHHHHHHHHHc
Confidence            555     78899999999987 33 233  566677777665543   34566666666555   34556677777877


Q ss_pred             cCCHHHHH----HHHHHHHHcCCCCCCHHHHHHHHHHHHhcC---CHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHc-
Q 012111          233 AKKFEEME----SSFSAMVESGGCHPDIFTLNSMISAYGNSG---NIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRA-  304 (471)
Q Consensus       233 ~~~~~~a~----~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~---~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~-  304 (471)
                      .+.++.+.    .+++... .  ..|+  .+..|...|...|   +.++|+.+|++..+.| .++...+..+...|... 
T Consensus       154 ~~~~~~~~~~a~~~~~~a~-~--~~~~--a~~~Lg~~~~~~g~~~~~~~A~~~~~~aa~~g-~~~a~~~~~Lg~~y~~g~  227 (452)
T 3e4b_A          154 QGTYDQHLDDVERICKAAL-N--TTDI--CYVELATVYQKKQQPEQQAELLKQMEAGVSRG-TVTAQRVDSVARVLGDAT  227 (452)
T ss_dssp             HTCGGGGHHHHHHHHHHHT-T--TCTT--HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTT-CSCHHHHHHHHHHHTCGG
T ss_pred             CCCcccCHHHHHHHHHHHH-c--CCHH--HHHHHHHHHHHcCCcccHHHHHHHHHHHHHCC-CHHHHHHHHHHHHHhCCC
Confidence            77554444    4444432 2  1333  7888888999999   9999999999999887 66777666777777655 


Q ss_pred             ---CCHHHHHHHHHHHHhCCCCCCHHHHHHHHHH-H--HhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcC---
Q 012111          305 ---GMYDKMRSVMDFMQKRFFFPTVVTYNIVIET-F--GKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAG---  375 (471)
Q Consensus       305 ---~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~-~--~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g---  375 (471)
                         +++++|...|+... .   -+...+..+... +  ...+++++|...|++..+.|   +...+..+...|. .|   
T Consensus       228 ~~~~d~~~A~~~~~~aa-~---g~~~a~~~Lg~~~~~~~~~~d~~~A~~~~~~Aa~~g---~~~A~~~Lg~~y~-~G~g~  299 (452)
T 3e4b_A          228 LGTPDEKTAQALLEKIA-P---GYPASWVSLAQLLYDFPELGDVEQMMKYLDNGRAAD---QPRAELLLGKLYY-EGKWV  299 (452)
T ss_dssp             GSSCCHHHHHHHHHHHG-G---GSTHHHHHHHHHHHHSGGGCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHH-HCSSS
T ss_pred             CCCCCHHHHHHHHHHHc-C---CCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHH-cCCCC
Confidence               79999999999887 3   355666666666 3  46899999999999999876   6777888888877 55   


Q ss_pred             --CHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHh----cCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHh----cC
Q 012111          376 --LIMKVDSILRQVENSDVILDTPFFNCIISAYGQ----AGDVEKMGELFLTMKERHCVPDNITFATMIQAYNA----LG  445 (471)
Q Consensus       376 --~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~----~g  445 (471)
                        ++++|...|++.. .|   +...+..|...|..    ..++++|..+|++..+.|.   ......|...|..    ..
T Consensus       300 ~~d~~~A~~~~~~Aa-~g---~~~A~~~Lg~~y~~G~g~~~d~~~A~~~~~~Aa~~g~---~~A~~~Lg~~y~~G~g~~~  372 (452)
T 3e4b_A          300 PADAKAAEAHFEKAV-GR---EVAADYYLGQIYRRGYLGKVYPQKALDHLLTAARNGQ---NSADFAIAQLFSQGKGTKP  372 (452)
T ss_dssp             CCCHHHHHHHHHTTT-TT---CHHHHHHHHHHHHTTTTSSCCHHHHHHHHHHHHTTTC---TTHHHHHHHHHHSCTTBCC
T ss_pred             CCCHHHHHHHHHHHh-CC---CHHHHHHHHHHHHCCCCCCcCHHHHHHHHHHHHhhCh---HHHHHHHHHHHHhCCCCCC
Confidence              9999999999988 43   67788888888776    3499999999999998764   3344455555553    45


Q ss_pred             CHHHHHHHHHHHHHhhhc
Q 012111          446 MTEAAQNLENKMIAMKEN  463 (471)
Q Consensus       446 ~~~~A~~~~~~m~~~~~~  463 (471)
                      +.++|..++++..+.+..
T Consensus       373 d~~~A~~~~~~A~~~g~~  390 (452)
T 3e4b_A          373 DPLNAYVFSQLAKAQDTP  390 (452)
T ss_dssp             CHHHHHHHHHHHHTTCCH
T ss_pred             CHHHHHHHHHHHHHCCCH
Confidence            899999999998876643

>2ond_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 2.80A {Mus musculus} SCOP: a.118.8.7

Probab=99.61  E-value=3.2e-12  Score=113.81  Aligned_cols=223  Identities=9%  Similarity=0.019  Sum_probs=125.2

Q ss_pred             HHHHHHHHHHHHcCCCCCCHHHHHHHHHHHH-------hcCCH-------HHHHHHHHHHHhCCCCCCHHHHHHHHHHHH
Q 012111          237 EEMESSFSAMVESGGCHPDIFTLNSMISAYG-------NSGNI-------EKMEKWYNEFNLMGVKADIQTLNILTKSYG  302 (471)
Q Consensus       237 ~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~-------~~~~~-------~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~  302 (471)
                      ++|..+|++..+..  +.+...|..++..+.       ..|++       ++|..+|++....-.+-+...|..++..+.
T Consensus        33 ~~a~~~~~~al~~~--p~~~~~w~~~~~~~~~~~~~l~~~g~~~~~~~~~~~A~~~~~rAl~~~~p~~~~~~~~~~~~~~  110 (308)
T 2ond_A           33 KRVMFAYEQCLLVL--GHHPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANIYERAISTLLKKNMLLYFAYADYEE  110 (308)
T ss_dssp             HHHHHHHHHHHHHH--TTCHHHHHHHHHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHHHHTTTTTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHc--CCCHHHHHHHHHHHHHhchhhhhccchhhcccchHHHHHHHHHHHHHhCcccHHHHHHHHHHHH
Confidence            34555555555442  334444555544443       23553       566666666654211334445666666666


Q ss_pred             HcCCHHHHHHHHHHHHhCCCCCCHH-HHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH-hcCCHHHH
Q 012111          303 RAGMYDKMRSVMDFMQKRFFFPTVV-TYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYS-KAGLIMKV  380 (471)
Q Consensus       303 ~~~~~~~a~~~~~~~~~~~~~~~~~-~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~-~~g~~~~a  380 (471)
                      +.|++++|..+|+++.+.... +.. .|..++..+.+.|++++|..+|++..+.. +.+...|........ ..|+.++|
T Consensus       111 ~~~~~~~A~~~~~~al~~~p~-~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~-p~~~~~~~~~a~~~~~~~~~~~~A  188 (308)
T 2ond_A          111 SRMKYEKVHSIYNRLLAIEDI-DPTLVYIQYMKFARRAEGIKSGRMIFKKAREDA-RTRHHVYVTAALMEYYCSKDKSVA  188 (308)
T ss_dssp             HTTCHHHHHHHHHHHHTSSSS-CTHHHHHHHHHHHHHHHCHHHHHHHHHHHHTST-TCCTHHHHHHHHHHHHTSCCHHHH
T ss_pred             hcCCHHHHHHHHHHHHhcccc-CccHHHHHHHHHHHHhcCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHHcCCHHHH
Confidence            666666666666666653211 222 56666666666666666666666666543 223333333222211 25667777


Q ss_pred             HHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCC-CCC--CHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 012111          381 DSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERH-CVP--DNITFATMIQAYNALGMTEAAQNLENKM  457 (471)
Q Consensus       381 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~-~~p--~~~~~~~l~~~~~~~g~~~~A~~~~~~m  457 (471)
                      ..+|+...+..+. +...|..++..+.+.|++++|..+|++..+.. +.|  ....|..++..+.+.|+.+.|..+++++
T Consensus       189 ~~~~~~al~~~p~-~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~~l~p~~~~~l~~~~~~~~~~~g~~~~a~~~~~~a  267 (308)
T 2ond_A          189 FKIFELGLKKYGD-IPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSGEIWARFLAFESNIGDLASILKVEKRR  267 (308)
T ss_dssp             HHHHHHHHHHHTT-CHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSSSSCGGGCHHHHHHHHHHHHHHSCHHHHHHHHHHH
T ss_pred             HHHHHHHHHhCCC-cHHHHHHHHHHHHHCCCHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            7777666655443 56666666666666677777777777766642 333  3456666666666667777777777777


Q ss_pred             HHhhhcC
Q 012111          458 IAMKENS  464 (471)
Q Consensus       458 ~~~~~~~  464 (471)
                      ++..|+.
T Consensus       268 ~~~~p~~  274 (308)
T 2ond_A          268 FTAFREE  274 (308)
T ss_dssp             HHHTTTT
T ss_pred             HHHcccc
Confidence            7666653

>4e6h_A MRNA 3'-END-processing protein RNA14; HAT domain, heat repeat, CLP1, PCF11, structural protein; 2.30A {Kluyveromyces lactis} PDB: 4e85_A 4eba_A

Probab=99.61  E-value=3.2e-11  Score=117.20  Aligned_cols=385  Identities=10%  Similarity=0.081  Sum_probs=236.7

Q ss_pred             CCCchHHHHHHHHHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCC---HHHHHHHHHHHHhCC-CCCCHH
Q 012111           75 NLWPKPVLEALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQ---PEQASLLFEVMLSDG-LKPSVD  150 (471)
Q Consensus        75 ~~~~~~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~---~~~a~~~~~~m~~~~-~~~~~~  150 (471)
                      +.+...+...++.+.+.+.++.|..+|+.+...  +|.+...|...+..-.+.++   ++.+..+|++..... ..|++.
T Consensus        63 p~d~~~W~~yi~~~~~~~~~~~aR~vyEraL~~--fP~~~~lW~~Yi~~E~~~~~~~~~~~v~~lfeRal~~~~~~~sv~  140 (679)
T 4e6h_A           63 PTDIFLYVKLLKHHVSLKQWKQVYETFDKLHDR--FPLMANIWCMRLSLEFDKMEELDAAVIEPVLARCLSKELGNNDLS  140 (679)
T ss_dssp             TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHTC--CCCHHHHHHHHHHHTCSSSCCCCHH
T ss_pred             cCCHHHHHHHHHHHHhcCcHHHHHHHHHHHHHH--CCCCHHHHHHHHHHHHhhCCcchHHHHHHHHHHHHHhcCCCCCHH
Confidence            345566666676666667777777777777765  35666667777776667676   777777777776653 135666


Q ss_pred             HHHHHHHHHHhcCCH--------HHHHHHHHHhhcCCCC-CCC-HHHHHHHHHHHHh---------cCCHHHHHHHHHHH
Q 012111          151 VYTALVSAYGQSGLL--------DEAFSTINDMKSVSDC-KPD-VYTYSILIKSCTK---------FHRFDLIEKILAEM  211 (471)
Q Consensus       151 ~~~~li~~~~~~~~~--------~~a~~~~~~~~~~~~~-~~~-~~~~~~ll~~~~~---------~~~~~~a~~~~~~~  211 (471)
                      .|...+....+.++.        +.+.++|+.....-|. .++ ...|...+.....         .++++.+.++|+..
T Consensus       141 LW~~Yl~f~~~~~~~~~~~~~~r~~vr~~FErAl~~vG~~d~~s~~iW~~Yi~f~~~~~~~~~~eeq~~~~~~R~iy~ra  220 (679)
T 4e6h_A          141 LWLSYITYVRKKNDIITGGEEARNIVIQAFQVVVDKCAIFEPKSIQFWNEYLHFLEHWKPVNKFEEQQRVQYIRKLYKTL  220 (679)
T ss_dssp             HHHHHHHHHHHHSCSTTTHHHHHHHHHHHHHHHHHHTTTTCSSCHHHHHHHHHHHHTCCCCSHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcccccccchhHHHHHHHHHHHHHHhCcccccchHHHHHHHHHHHhccccCcHHHHhHHHHHHHHHHHH
Confidence            766666554444332        2334566665543444 333 3456555544321         22345555555555


Q ss_pred             HHCCCCCCHHH---------------------------------------------------------------------
Q 012111          212 SYLGIECSAVT---------------------------------------------------------------------  222 (471)
Q Consensus       212 ~~~g~~~~~~~---------------------------------------------------------------------  222 (471)
                      +......-..+                                                                     
T Consensus       221 L~iP~~~~~~~w~~Y~~fe~~~~~~~a~~~~~e~~~~y~~Ar~~~~e~~~~~~~l~r~~p~~~~~~~~~~~p~~~~~~~~  300 (679)
T 4e6h_A          221 LCQPMDCLESMWQRYTQWEQDVNQLTARRHIGELSAQYMNARSLYQDWLNITKGLKRNLPITLNQATESNLPKPNEYDVQ  300 (679)
T ss_dssp             TTSCCSSHHHHHHHHHHHHHHHCTTTHHHHHHHHHHHHHHHHHHHHHHHHHTTTCCCCCCSSSTTCCTTTSCCTTCCCHH
T ss_pred             HhCccHHHHHHHHHHHHHHHhcCcchHHHHHHHhhHHHHHHHHHHHHHHHHHHhHhhccccccccchhccCCCCchhHHH
Confidence            53211100111                                                                     


Q ss_pred             ----HHHHHHHHHccC-------CHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHH-HHHHHHHhCCCCCC
Q 012111          223 ----YNTIIDGYGKAK-------KFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKME-KWYNEFNLMGVKAD  290 (471)
Q Consensus       223 ----~~~l~~~~~~~~-------~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~-~~~~~~~~~~~~~~  290 (471)
                          |...+..--..+       ..+.+..+|++++..  ++-....|...+..+...|+.++|. .+|+..... ++.+
T Consensus       301 ql~lW~~yi~fEk~~~~~l~~~~~~~Rv~~~Ye~aL~~--~p~~~~lW~~ya~~~~~~~~~~~a~r~il~rAi~~-~P~s  377 (679)
T 4e6h_A          301 QLLIWLEWIRWESDNKLELSDDLHKARMTYVYMQAAQH--VCFAPEIWFNMANYQGEKNTDSTVITKYLKLGQQC-IPNS  377 (679)
T ss_dssp             HHHHHHHHHHHHHTCTTCCCHHHHHHHHHHHHHHHHHH--TTTCHHHHHHHHHHHHHHSCCTTHHHHHHHHHHHH-CTTC
T ss_pred             HHHHHHHHHHHHHhCCccccchhhHHHHHHHHHHHHHH--cCCCHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHh-CCCC
Confidence                111111111111       012233445555444  2334555666666666778888886 888888753 3556


Q ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCC---------CCC------------HHHHHHHHHHHHhcCCHHHHHHHH
Q 012111          291 IQTLNILTKSYGRAGMYDKMRSVMDFMQKRFF---------FPT------------VVTYNIVIETFGKAGHIEKMEEYF  349 (471)
Q Consensus       291 ~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~---------~~~------------~~~~~~li~~~~~~g~~~~a~~~~  349 (471)
                      ...+...+....+.|+++.|..+|+.+.+...         .|+            ...|...+....+.|+.+.|..+|
T Consensus       378 ~~Lwl~~a~~ee~~~~~e~aR~iyek~l~~l~~~~~~~~~~~p~~~~~~~~~~~~~~~vWi~y~~~erR~~~l~~AR~vf  457 (679)
T 4e6h_A          378 AVLAFSLSEQYELNTKIPEIETTILSCIDRIHLDLAALMEDDPTNESAINQLKSKLTYVYCVYMNTMKRIQGLAASRKIF  457 (679)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHhhhhhhccCcchhhhhhhccchHHHHHHHHHHHHHcCCHHHHHHHH
Confidence            66677788888888999999999888775310         121            235777777777788889999999


Q ss_pred             HHHHHcCCCCCHHHHHHHHHHHHhc-CCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCC
Q 012111          350 KKMKHRGMKPNSITYCSLVSAYSKA-GLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCV  428 (471)
Q Consensus       350 ~~m~~~~~~p~~~~~~~li~~~~~~-g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~  428 (471)
                      .+.++.........|...+..-.+. ++.+.|.++|+...+.-+ -+...+...+......|+.+.|..+|++.......
T Consensus       458 ~~A~~~~~~~~~~lyi~~A~lE~~~~~d~e~Ar~ife~~Lk~~p-~~~~~w~~y~~fe~~~~~~~~AR~lferal~~~~~  536 (679)
T 4e6h_A          458 GKCRRLKKLVTPDIYLENAYIEYHISKDTKTACKVLELGLKYFA-TDGEYINKYLDFLIYVNEESQVKSLFESSIDKISD  536 (679)
T ss_dssp             HHHHHTGGGSCTHHHHHHHHHHHTTTSCCHHHHHHHHHHHHHHT-TCHHHHHHHHHHHHHHTCHHHHHHHHHHHTTTSSS
T ss_pred             HHHHHhcCCCChHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHCC-CchHHHHHHHHHHHhCCCHHHHHHHHHHHHHhcCC
Confidence            9888751112334444333333344 458899999988877633 36667778888888889999999999988875321


Q ss_pred             C--CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhhhcCC
Q 012111          429 P--DNITFATMIQAYNALGMTEAAQNLENKMIAMKENSG  465 (471)
Q Consensus       429 p--~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~~~  465 (471)
                      +  ....|...+..-.+.|+.+.+.++.+++.+..|+.+
T Consensus       537 ~~~~~~lw~~~~~fE~~~G~~~~~~~v~~R~~~~~P~~~  575 (679)
T 4e6h_A          537 SHLLKMIFQKVIFFESKVGSLNSVRTLEKRFFEKFPEVN  575 (679)
T ss_dssp             TTHHHHHHHHHHHHHHHTCCSHHHHHHHHHHHHHSTTCC
T ss_pred             HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCc
Confidence            1  345777777877888999999999999998888754

>4a1s_A PINS, partner of inscuteable; cell cycle, LGN, mitotic spindle orientation, asymmetric CEL divisions; 2.10A {Drosophila melanogaster}

Probab=99.59  E-value=8.9e-14  Score=129.50  Aligned_cols=279  Identities=10%  Similarity=-0.029  Sum_probs=155.6

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCH----HHHHHHHHHHHhcCCHHHHHHHHHHHHHC----CC-CCCHHH
Q 012111          152 YTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDV----YTYSILIKSCTKFHRFDLIEKILAEMSYL----GI-ECSAVT  222 (471)
Q Consensus       152 ~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~----~~~~~ll~~~~~~~~~~~a~~~~~~~~~~----g~-~~~~~~  222 (471)
                      +..+...+...|++++|+..|+++.+..  +.+.    ..+..+...+...|++++|...+++..+.    +. +....+
T Consensus        51 l~~~g~~~~~~g~~~~A~~~~~~al~~~--~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~  128 (411)
T 4a1s_A           51 LALEGERLCNAGDCRAGVAFFQAAIQAG--TEDLRTLSAIYSQLGNAYFYLGDYNKAMQYHKHDLTLAKSMNDRLGEAKS  128 (411)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHC--CSCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHHHhCcHHHHHHHHHHHHHhc--ccChhHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHccCchHHHHH
Confidence            3444555666666666666666665521  1122    34555555566666666666666555432    10 112334


Q ss_pred             HHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHH
Q 012111          223 YNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYG  302 (471)
Q Consensus       223 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~  302 (471)
                      +..+...|...|++++|...+++..+......+                               .+....++..+...|.
T Consensus       129 ~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~-------------------------------~~~~~~~~~~l~~~~~  177 (411)
T 4a1s_A          129 SGNLGNTLKVMGRFDEAAICCERHLTLARQLGD-------------------------------RLSEGRALYNLGNVYH  177 (411)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTC-------------------------------HHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhhc-------------------------------hHHHHHHHHHHHHHHH
Confidence            445555555555555555555554332100000                               0111223444444444


Q ss_pred             HcCC-----------------HHHHHHHHHHHHhC----CCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCC-CC
Q 012111          303 RAGM-----------------YDKMRSVMDFMQKR----FFFP-TVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGM-KP  359 (471)
Q Consensus       303 ~~~~-----------------~~~a~~~~~~~~~~----~~~~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~-~p  359 (471)
                      ..|+                 +++|...+.+..+.    +..+ ....+..+...+...|++++|...+++..+... ..
T Consensus       178 ~~g~~~~~~~~~~~~~~a~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~  257 (411)
T 4a1s_A          178 AKGKHLGQRNPGKFGDDVKEALTRAVEFYQENLKLMRDLGDRGAQGRACGNLGNTYYLLGDFQAAIEHHQERLRIAREFG  257 (411)
T ss_dssp             HHHHHHHHHSTTCCCHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHT
T ss_pred             HcCcccccccchhhhhhhhHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHhcC
Confidence            4444                 45555444443221    1111 223566666777777777777777777654310 01


Q ss_pred             C----HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCC-----cCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhC----C
Q 012111          360 N----SITYCSLVSAYSKAGLIMKVDSILRQVENSDVI-----LDTPFFNCIISAYGQAGDVEKMGELFLTMKER----H  426 (471)
Q Consensus       360 ~----~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~-----~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~----~  426 (471)
                      +    ..++..+...+...|++++|...+++..+....     ....++..+...|...|++++|...+++..+.    +
T Consensus       258 ~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~  337 (411)
T 4a1s_A          258 DRAAERRANSNLGNSHIFLGQFEDAAEHYKRTLALAVELGEREVEAQSCYSLGNTYTLLHEFNTAIEYHNRHLAIAQELG  337 (411)
T ss_dssp             CHHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHT
T ss_pred             CcHHHHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCC
Confidence            1    236677777788888888888888776543211     12456777888888888888888888877642    1


Q ss_pred             CCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhhhc
Q 012111          427 CVP-DNITFATMIQAYNALGMTEAAQNLENKMIAMKEN  463 (471)
Q Consensus       427 ~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~  463 (471)
                      ..+ ...++..+...|...|++++|.+.++++++....
T Consensus       338 ~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~  375 (411)
T 4a1s_A          338 DRIGEARACWSLGNAHSAIGGHERALKYAEQHLQLAXX  375 (411)
T ss_dssp             CHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCH
T ss_pred             ChHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHhh
Confidence            111 1346667778888888888888888888776543

>3sf4_A G-protein-signaling modulator 2; tetratricopeptide repeat, TPR, cell polarity, asymmetric CEL division, mitotic spindle orientation; 2.60A {Homo sapiens}

Probab=99.59  E-value=4.9e-14  Score=130.88  Aligned_cols=303  Identities=14%  Similarity=0.050  Sum_probs=157.4

Q ss_pred             CChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCC----HHHHHHHHHHHHhcCCHHHHHHHHHHhhcC---CCCCC-
Q 012111          112 ARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPS----VDVYTALVSAYGQSGLLDEAFSTINDMKSV---SDCKP-  183 (471)
Q Consensus       112 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~----~~~~~~li~~~~~~~~~~~a~~~~~~~~~~---~~~~~-  183 (471)
                      .....+......+...|++++|...|+...+.+.. +    ..++..+...+...|++++|...+++....   .+..| 
T Consensus         7 ~~~~~l~~~g~~~~~~g~~~~A~~~~~~al~~~~~-~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~   85 (406)
T 3sf4_A            7 ASCLELALEGERLCKSGDCRAGVSFFEAAVQVGTE-DLKTLSAIYSQLGNAYFYLHDYAKALEYHHHDLTLARTIGDQLG   85 (406)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCS-CHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHHHHHHHHhccHHHHHHHHHHHHhcCcc-cHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhccccHH
Confidence            34445556666666677777777777766665322 2    245566666666667777776666665431   11011 


Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCC-CCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHH
Q 012111          184 DVYTYSILIKSCTKFHRFDLIEKILAEMSYLGI-ECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSM  262 (471)
Q Consensus       184 ~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~-~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l  262 (471)
                      ...++..+...+...|++++|...+++..+... ..+.                                .....++..+
T Consensus        86 ~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~--------------------------------~~~~~~~~~l  133 (406)
T 3sf4_A           86 EAKASGNLGNTLKVLGNFDEAIVCCQRHLDISRELNDK--------------------------------VGEARALYNL  133 (406)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCH--------------------------------HHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcccc--------------------------------cchHHHHHHH
Confidence            123344455555555555555555554433210 0010                                0002234444


Q ss_pred             HHHHHhcCC--------------------HHHHHHHHHHHHhC----CC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHH
Q 012111          263 ISAYGNSGN--------------------IEKMEKWYNEFNLM----GV-KADIQTLNILTKSYGRAGMYDKMRSVMDFM  317 (471)
Q Consensus       263 ~~~~~~~~~--------------------~~~a~~~~~~~~~~----~~-~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~  317 (471)
                      ...+...|+                    +++|...+.+....    +. .....++..+...+...|++++|...++..
T Consensus       134 ~~~~~~~g~~~~~~~~~~~~~~~~~a~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a  213 (406)
T 3sf4_A          134 GNVYHAKGKSFGCPGPQDVGEFPEEVRDALQAAVDFYEENLSLVTALGDRAAQGRAFGNLGNTHYLLGNFRDAVIAHEQR  213 (406)
T ss_dssp             HHHHHHHHHTCC-------CCCCHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTBHHHHHHHHHHH
T ss_pred             HHHHHHcCCcccccccchhhhhhhhHHHHHHHHHHHHHHHHHHHHhccCcHHHHHHHHHHHHHHHHccCHHHHHHHHHHH
Confidence            444444444                    44444444443221    10 111234555555666666666666666554


Q ss_pred             HhCCC-CCC----HHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCC-CCC----HHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 012111          318 QKRFF-FPT----VVTYNIVIETFGKAGHIEKMEEYFKKMKHRGM-KPN----SITYCSLVSAYSKAGLIMKVDSILRQV  387 (471)
Q Consensus       318 ~~~~~-~~~----~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~-~p~----~~~~~~li~~~~~~g~~~~a~~~~~~~  387 (471)
                      .+... .++    ...+..+...+...|++++|...+++...... ..+    ..++..+...+...|++++|...+++.
T Consensus       214 l~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a  293 (406)
T 3sf4_A          214 LLIAKEFGDKAAERRAYSNLGNAYIFLGEFETASEYYKKTLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKH  293 (406)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHhcCCcHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHhCcCchHHHHHHHHHHHHHHHhCcHHHHHHHHHHH
Confidence            43210 011    22556666667777777777777776654210 011    445666777777777777777777766


Q ss_pred             HhCCCC-----cCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhC----CCCC-CHHHHHHHHHHHHhcCCH
Q 012111          388 ENSDVI-----LDTPFFNCIISAYGQAGDVEKMGELFLTMKER----HCVP-DNITFATMIQAYNALGMT  447 (471)
Q Consensus       388 ~~~~~~-----~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~----~~~p-~~~~~~~l~~~~~~~g~~  447 (471)
                      .+....     ....++..+...|...|++++|.+.+++..+.    +..+ ...++..+...+...|+.
T Consensus       294 ~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~  363 (406)
T 3sf4_A          294 LAIAQELNDRIGEGRACWSLGNAYTALGNHDQAMHFAEKHLEISREVGDKSGELTARLNLSDLQMVLGLS  363 (406)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHhcCCcHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCcchhHHHHHHHHHHHHhhHh
Confidence            532111     11445667777777778888888777766532    1111 234455566666666654

>3sf4_A G-protein-signaling modulator 2; tetratricopeptide repeat, TPR, cell polarity, asymmetric CEL division, mitotic spindle orientation; 2.60A {Homo sapiens}

Probab=99.59  E-value=2.3e-13  Score=126.34  Aligned_cols=281  Identities=11%  Similarity=0.033  Sum_probs=191.3

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCC----HHHHHHHHHHHHccCCHHHHHHHHHHHHHcC---CCC-CC
Q 012111          184 DVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECS----AVTYNTIIDGYGKAKKFEEMESSFSAMVESG---GCH-PD  255 (471)
Q Consensus       184 ~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~---~~~-~~  255 (471)
                      ....+......+...|++++|...|++..+.+ +.+    ..++..+...+...|++++|...+++..+..   +.. ..
T Consensus         8 ~~~~l~~~g~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~   86 (406)
T 3sf4_A            8 SCLELALEGERLCKSGDCRAGVSFFEAAVQVG-TEDLKTLSAIYSQLGNAYFYLHDYAKALEYHHHDLTLARTIGDQLGE   86 (406)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-CSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHHHHHHHHHHHhccHHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhccccHHH
Confidence            34444455555566666666666666665542 222    2345566666666677777766666553321   011 11


Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCC-CCC----HHHHHHHHHHHHHcCC--------------------HHHH
Q 012111          256 IFTLNSMISAYGNSGNIEKMEKWYNEFNLMGV-KAD----IQTLNILTKSYGRAGM--------------------YDKM  310 (471)
Q Consensus       256 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-~~~----~~~~~~ll~~~~~~~~--------------------~~~a  310 (471)
                      ...+..+...+...|++++|...+++...... ..+    ..++..+...|...|+                    +++|
T Consensus        87 ~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~~~~a~~~~~~A  166 (406)
T 3sf4_A           87 AKASGNLGNTLKVLGNFDEAIVCCQRHLDISRELNDKVGEARALYNLGNVYHAKGKSFGCPGPQDVGEFPEEVRDALQAA  166 (406)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHTCC-------CCCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcccccchHHHHHHHHHHHHHcCCcccccccchhhhhhhhHHHHHHHH
Confidence            34566667777777888887777776644210 011    4477888888999999                    9999


Q ss_pred             HHHHHHHHhC----CCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCC-CCC----HHHHHHHHHHHHhcCCHHHH
Q 012111          311 RSVMDFMQKR----FFFP-TVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGM-KPN----SITYCSLVSAYSKAGLIMKV  380 (471)
Q Consensus       311 ~~~~~~~~~~----~~~~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~-~p~----~~~~~~li~~~~~~g~~~~a  380 (471)
                      ...+....+.    +..+ ....+..+...+...|++++|...+++...... .++    ..++..+...+...|++++|
T Consensus       167 ~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A  246 (406)
T 3sf4_A          167 VDFYEENLSLVTALGDRAAQGRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERRAYSNLGNAYIFLGEFETA  246 (406)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTBHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHHHHHHHHHhccCcHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCChHHH
Confidence            9988876542    1111 234678888899999999999999998875410 112    34788889999999999999


Q ss_pred             HHHHHHHHhCCCC----c-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhC----CCCC-CHHHHHHHHHHHHhcCCHHHH
Q 012111          381 DSILRQVENSDVI----L-DTPFFNCIISAYGQAGDVEKMGELFLTMKER----HCVP-DNITFATMIQAYNALGMTEAA  450 (471)
Q Consensus       381 ~~~~~~~~~~~~~----~-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~----~~~p-~~~~~~~l~~~~~~~g~~~~A  450 (471)
                      ...+++..+....    + ...++..+...|...|++++|...+++..+.    +..+ ...++..+...|...|++++|
T Consensus       247 ~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A  326 (406)
T 3sf4_A          247 SEYYKKTLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELNDRIGEGRACWSLGNAYTALGNHDQA  326 (406)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHH
T ss_pred             HHHHHHHHHHHHhCcCchHHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCCHHHH
Confidence            9999987643211    1 1557888999999999999999999988753    1111 155777888999999999999


Q ss_pred             HHHHHHHHHhhhcCC
Q 012111          451 QNLENKMIAMKENSG  465 (471)
Q Consensus       451 ~~~~~~m~~~~~~~~  465 (471)
                      .+.++++++..+..+
T Consensus       327 ~~~~~~al~~~~~~~  341 (406)
T 3sf4_A          327 MHFAEKHLEISREVG  341 (406)
T ss_dssp             HHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHhc
Confidence            999999988866543

>3ro2_A PINS homolog, G-protein-signaling modulator 2; TPR repeat, protein-protein interaction, protein-binding, PR binding; 2.30A {Mus musculus}

Probab=99.58  E-value=1.2e-13  Score=124.48  Aligned_cols=139  Identities=16%  Similarity=0.120  Sum_probs=95.3

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHHc----CCC-CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCC-----cCH
Q 012111          327 VTYNIVIETFGKAGHIEKMEEYFKKMKHR----GMK-PNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVI-----LDT  396 (471)
Q Consensus       327 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~----~~~-p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~-----~~~  396 (471)
                      ..+..+...+...|++++|...+++..+.    +.. ....++..+...+...|++++|...+++..+....     ...
T Consensus       184 ~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~  263 (338)
T 3ro2_A          184 RAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERRAYSNLGNAYIFLGEFETASEYYKKTLLLARQLKDRAVEA  263 (338)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhhcchhHHH
Confidence            35666677777788888888887776543    100 01236777788888888888888888876642111     114


Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhC----CCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhhhcCC
Q 012111          397 PFFNCIISAYGQAGDVEKMGELFLTMKER----HCVP-DNITFATMIQAYNALGMTEAAQNLENKMIAMKENSG  465 (471)
Q Consensus       397 ~~~~~l~~~~~~~g~~~~a~~~~~~~~~~----~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~~~  465 (471)
                      .++..+...+...|++++|...++++.+.    +-.+ ...++..+...+...|++++|...++++++..+..+
T Consensus       264 ~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~~~  337 (338)
T 3ro2_A          264 QSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELKDRIGEGRACWSLGNAYTALGNHDQAMHFAEKHLEISREVG  337 (338)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHC-----
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHhhc
Confidence            56778888899999999999999887643    1111 134677788899999999999999999988776543

>3vtx_A MAMA; tetratricopeptide repeats (TPR) containing protein, peptide protein, protein binding; 1.75A {Candidatus magnetobacterium bavaricum} PDB: 3vty_A

Probab=99.57  E-value=1.5e-12  Score=106.41  Aligned_cols=171  Identities=15%  Similarity=0.053  Sum_probs=114.6

Q ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHH
Q 012111          290 DIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVS  369 (471)
Q Consensus       290 ~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~  369 (471)
                      +..+|..+...|...|++++|...|++..+..+. +...+..+...+...|++++|...+....... +-+...+..+..
T Consensus         4 ~~~iy~~lG~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~~~   81 (184)
T 3vtx_A            4 TTTIYMDIGDKKRTKGDFDGAIRAYKKVLKADPN-NVETLLKLGKTYMDIGLPNDAIESLKKFVVLD-TTSAEAYYILGS   81 (184)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-CCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-chhHHHHHHHHH
Confidence            4556666666666666777776666666665332 45566666667777777777777777666653 234556666666


Q ss_pred             HHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHH
Q 012111          370 AYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAYNALGMTEA  449 (471)
Q Consensus       370 ~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~  449 (471)
                      .+...++++.+...+....+..+. +...+..+..++...|++++|++.|++..+.. +-+...|..+..+|.+.|++++
T Consensus        82 ~~~~~~~~~~a~~~~~~a~~~~~~-~~~~~~~lg~~~~~~g~~~~A~~~~~~~l~~~-p~~~~~~~~lg~~~~~~g~~~~  159 (184)
T 3vtx_A           82 ANFMIDEKQAAIDALQRAIALNTV-YADAYYKLGLVYDSMGEHDKAIEAYEKTISIK-PGFIRAYQSIGLAYEGKGLRDE  159 (184)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHhCcc-chHHHHHHHHHHHHhCCchhHHHHHHHHHHhc-chhhhHHHHHHHHHHHCCCHHH
Confidence            677777777777777776665544 56667777777777777777777777776642 2356667777777777777777


Q ss_pred             HHHHHHHHHHhhhcC
Q 012111          450 AQNLENKMIAMKENS  464 (471)
Q Consensus       450 A~~~~~~m~~~~~~~  464 (471)
                      |.+.++++++.+|+.
T Consensus       160 A~~~~~~al~~~p~~  174 (184)
T 3vtx_A          160 AVKYFKKALEKEEKK  174 (184)
T ss_dssp             HHHHHHHHHHTTHHH
T ss_pred             HHHHHHHHHhCCccC
Confidence            777777777776653

>3ro2_A PINS homolog, G-protein-signaling modulator 2; TPR repeat, protein-protein interaction, protein-binding, PR binding; 2.30A {Mus musculus}

Probab=99.56  E-value=2.2e-13  Score=122.85  Aligned_cols=275  Identities=12%  Similarity=0.002  Sum_probs=151.7

Q ss_pred             HHHHHHHHhhcHHHHHHHHHHhhhccCccCC----hhHHHHHHHHHhcCCCHHHHHHHHHHHHhC----CCC-CCHHHHH
Q 012111           83 EALDEAIKQKKWQLALKIFGLLRQQQWYQAR----CQTFTKLMVMLGKCKQPEQASLLFEVMLSD----GLK-PSVDVYT  153 (471)
Q Consensus        83 ~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~----~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~----~~~-~~~~~~~  153 (471)
                      ..-..+...|++++|+..|+.+.+..  +.+    ...+..+...+...|++++|...++...+.    +.. ....++.
T Consensus        10 ~~g~~~~~~g~~~~A~~~~~~al~~~--~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~   87 (338)
T 3ro2_A           10 LEGERLCKSGDCRAGVSFFEAAVQVG--TEDLKTLSAIYSQLGNAYFYLHDYAKALEYHHHDLTLARTIGDQLGEAKASG   87 (338)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHC--CSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHH
T ss_pred             HHHHHHHHhccHHHHHHHHHHHHhhC--cccHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhcccccHHHHHHHH
Confidence            33455667888999999998888764  333    356778888888888888888888876542    111 1245677


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHhhcCCCCCCC----HHHHHHHHHHHHhcCC--------------------HHHHHHHHH
Q 012111          154 ALVSAYGQSGLLDEAFSTINDMKSVSDCKPD----VYTYSILIKSCTKFHR--------------------FDLIEKILA  209 (471)
Q Consensus       154 ~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~----~~~~~~ll~~~~~~~~--------------------~~~a~~~~~  209 (471)
                      .+...+...|++++|...+++......-.++    ..++..+...+...|+                    ++.|.+.++
T Consensus        88 ~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~A~~~~~  167 (338)
T 3ro2_A           88 NLGNTLKVLGNFDEAIVCCQRHLDISRELNDKVGEARALYNLGNVYHAKGKSFGCPGPQDTGEFPEDVRNALQAAVDLYE  167 (338)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHTSSSSSCC----CCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHccCHHHHHHHHHHHHHHHHHhcCchHHHHHHHHHHHHHHHcCcccccchhhhhhhhhhhHHHHHHHHHHHHH
Confidence            7777888888888888887776542111112    2356666666666666                    666666665


Q ss_pred             HHHHC----CC-CCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 012111          210 EMSYL----GI-ECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNL  284 (471)
Q Consensus       210 ~~~~~----g~-~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  284 (471)
                      +....    +. .....++..+...+...|++++|...+++..+.....++.                            
T Consensus       168 ~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~----------------------------  219 (338)
T 3ro2_A          168 ENLSLVTALGDRAAQGRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDK----------------------------  219 (338)
T ss_dssp             HHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCH----------------------------
T ss_pred             HHHHHHHhcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcCCh----------------------------
Confidence            54321    10 0112344445555555555555555555543221000110                            


Q ss_pred             CCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCC----CCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc----
Q 012111          285 MGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRF----FFP-TVVTYNIVIETFGKAGHIEKMEEYFKKMKHR----  355 (471)
Q Consensus       285 ~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~----~~~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~----  355 (471)
                         .....++..+...+...|++++|...++...+..    ..+ ...++..+...+...|++++|...+++....    
T Consensus       220 ---~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~~  296 (338)
T 3ro2_A          220 ---AAERRAYSNLGNAYIFLGEFETASEYYKKTLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQEL  296 (338)
T ss_dssp             ---HHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHH
T ss_pred             ---HHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhhcchhHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhc
Confidence               0011234444444455555555555444433210    000 1334555556666666666666666655432    


Q ss_pred             CCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhC
Q 012111          356 GMKP-NSITYCSLVSAYSKAGLIMKVDSILRQVENS  390 (471)
Q Consensus       356 ~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~  390 (471)
                      +..+ ...++..+...+...|++++|...+++..+.
T Consensus       297 ~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~  332 (338)
T 3ro2_A          297 KDRIGEGRACWSLGNAYTALGNHDQAMHFAEKHLEI  332 (338)
T ss_dssp             TCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHC
T ss_pred             CCcHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHH
Confidence            1000 1335566666677777777777777666653

>3ulq_A Response regulator aspartate phosphatase F; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis}

Probab=99.55  E-value=9.5e-13  Score=121.26  Aligned_cols=237  Identities=11%  Similarity=-0.044  Sum_probs=171.7

Q ss_pred             HHHHHHccCCHHHHHHHHHHHHHcCCCCCC----HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCC--C----CCCHHHHH
Q 012111          226 IIDGYGKAKKFEEMESSFSAMVESGGCHPD----IFTLNSMISAYGNSGNIEKMEKWYNEFNLMG--V----KADIQTLN  295 (471)
Q Consensus       226 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~--~----~~~~~~~~  295 (471)
                      ....+...|++++|...|++..+.....++    ..++..+...+...|+++.|...+.+..+..  .    .....+++
T Consensus       109 ~g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~  188 (383)
T 3ulq_A          109 RGMYELDQREYLSAIKFFKKAESKLIFVKDRIEKAEFFFKMSESYYYMKQTYFSMDYARQAYEIYKEHEAYNIRLLQCHS  188 (383)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHTTGGGCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTCSTTHHHHHHHHH
T ss_pred             HHHHHHHhcCHHHHHHHHHHHHHHHhhCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCccchHHHHHHHH
Confidence            455667788888888888888653111222    3567778888888889888888888875431  1    11235677


Q ss_pred             HHHHHHHHcCCHHHHHHHHHHHHhCCCC-CC----HHHHHHHHHHHHhcCCHHHHHHHHHHHHHc----CC-CCCHHHHH
Q 012111          296 ILTKSYGRAGMYDKMRSVMDFMQKRFFF-PT----VVTYNIVIETFGKAGHIEKMEEYFKKMKHR----GM-KPNSITYC  365 (471)
Q Consensus       296 ~ll~~~~~~~~~~~a~~~~~~~~~~~~~-~~----~~~~~~li~~~~~~g~~~~a~~~~~~m~~~----~~-~p~~~~~~  365 (471)
                      .+...|...|++++|...+....+.... ++    ..++..+...|...|++++|...+++..+.    +. +....++.
T Consensus       189 ~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~  268 (383)
T 3ulq_A          189 LFATNFLDLKQYEDAISHFQKAYSMAEAEKQPQLMGRTLYNIGLCKNSQSQYEDAIPYFKRAIAVFEESNILPSLPQAYF  268 (383)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCGGGHHHHHH
T ss_pred             HHHHHHHHhcCHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhccchhHHHHHH
Confidence            8888888999999999988877643111 11    236778888999999999999999988762    22 33466788


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHhC----CCCcCHHHHHHHHHHHHhcCC---HHHHHHHHHHHHhCCCCCC-HHHHHHH
Q 012111          366 SLVSAYSKAGLIMKVDSILRQVENS----DVILDTPFFNCIISAYGQAGD---VEKMGELFLTMKERHCVPD-NITFATM  437 (471)
Q Consensus       366 ~li~~~~~~g~~~~a~~~~~~~~~~----~~~~~~~~~~~l~~~~~~~g~---~~~a~~~~~~~~~~~~~p~-~~~~~~l  437 (471)
                      .+...+...|++++|...+++..+.    +-......+..+...+...|+   +++|+.++++.   +..|+ ...+..+
T Consensus       269 ~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~al~~~~~~---~~~~~~~~~~~~l  345 (383)
T 3ulq_A          269 LITQIHYKLGKIDKAHEYHSKGMAYSQKAGDVIYLSEFEFLKSLYLSGPDEEAIQGFFDFLESK---MLYADLEDFAIDV  345 (383)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTSSCCHHHHHHHHHHHHHT---TCHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHC---cCHHHHHHHHHHH
Confidence            8999999999999999999887643    111122335677888888898   77777777766   23333 3466678


Q ss_pred             HHHHHhcCCHHHHHHHHHHHHHhhhcCC
Q 012111          438 IQAYNALGMTEAAQNLENKMIAMKENSG  465 (471)
Q Consensus       438 ~~~~~~~g~~~~A~~~~~~m~~~~~~~~  465 (471)
                      ...|...|++++|.+.++++++......
T Consensus       346 a~~y~~~g~~~~A~~~~~~al~~~~~i~  373 (383)
T 3ulq_A          346 AKYYHERKNFQKASAYFLKVEQVRQLIQ  373 (383)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHHTSCS
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHHHHHhh
Confidence            8999999999999999999998876543

>4a1s_A PINS, partner of inscuteable; cell cycle, LGN, mitotic spindle orientation, asymmetric CEL divisions; 2.10A {Drosophila melanogaster}

Probab=99.55  E-value=4.1e-13  Score=124.98  Aligned_cols=282  Identities=12%  Similarity=0.031  Sum_probs=180.9

Q ss_pred             CChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCH----HHHHHHHHHHHhcCCHHHHHHHHHHhhcC---CC-CCC
Q 012111          112 ARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSV----DVYTALVSAYGQSGLLDEAFSTINDMKSV---SD-CKP  183 (471)
Q Consensus       112 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~----~~~~~li~~~~~~~~~~~a~~~~~~~~~~---~~-~~~  183 (471)
                      .....+..+...+...|++++|...|+++.+.+.. +.    .+|..+...|...|++++|+..+++....   .+ ...
T Consensus        46 ~~~~~l~~~g~~~~~~g~~~~A~~~~~~al~~~~~-~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~  124 (411)
T 4a1s_A           46 SMCLELALEGERLCNAGDCRAGVAFFQAAIQAGTE-DLRTLSAIYSQLGNAYFYLGDYNKAMQYHKHDLTLAKSMNDRLG  124 (411)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCS-CHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHhccc-ChhHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHccCchH
Confidence            34456667888899999999999999999987433 33    57888999999999999999999988652   11 123


Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHC----C-CCCCHHHHHHHHHHHHccCC-----------------HHHHHH
Q 012111          184 DVYTYSILIKSCTKFHRFDLIEKILAEMSYL----G-IECSAVTYNTIIDGYGKAKK-----------------FEEMES  241 (471)
Q Consensus       184 ~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~----g-~~~~~~~~~~l~~~~~~~~~-----------------~~~a~~  241 (471)
                      ...++..+...+...|++++|...+++..+.    + .+....++..+...|...|+                 +++|.+
T Consensus       125 ~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~a~~~~~~A~~  204 (411)
T 4a1s_A          125 EAKSSGNLGNTLKVMGRFDEAAICCERHLTLARQLGDRLSEGRALYNLGNVYHAKGKHLGQRNPGKFGDDVKEALTRAVE  204 (411)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHHHHHHSTTCCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhhchHHHHHHHHHHHHHHHHcCcccccccchhhhhhhhHHHHHHHH
Confidence            3456888888999999999999999987654    1 11224466677777777777                 666666


Q ss_pred             HHHHHHHcC---CC-CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHH
Q 012111          242 SFSAMVESG---GC-HPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFM  317 (471)
Q Consensus       242 ~~~~~~~~~---~~-~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~  317 (471)
                      .+++..+..   +. ......+..+...+...|++++|...+++......               ..++           
T Consensus       205 ~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~---------------~~~~-----------  258 (411)
T 4a1s_A          205 FYQENLKLMRDLGDRGAQGRACGNLGNTYYLLGDFQAAIEHHQERLRIAR---------------EFGD-----------  258 (411)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHH---------------HHTC-----------
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHH---------------hcCC-----------
Confidence            666543310   00 00112344444444445555555544444432100               0000           


Q ss_pred             HhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCC--C---CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCC
Q 012111          318 QKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGM--K---PNSITYCSLVSAYSKAGLIMKVDSILRQVENSDV  392 (471)
Q Consensus       318 ~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~--~---p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~  392 (471)
                          .......+..+...|...|++++|...+++......  .   ....++..+...+...|++++|...+++..+...
T Consensus       259 ----~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~  334 (411)
T 4a1s_A          259 ----RAAERRANSNLGNSHIFLGQFEDAAEHYKRTLALAVELGEREVEAQSCYSLGNTYTLLHEFNTAIEYHNRHLAIAQ  334 (411)
T ss_dssp             ----HHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHH
T ss_pred             ----cHHHHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHH
Confidence                000122556666677777777777777776654310  0   1145667777778888888888888777654211


Q ss_pred             -----CcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 012111          393 -----ILDTPFFNCIISAYGQAGDVEKMGELFLTMKE  424 (471)
Q Consensus       393 -----~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~  424 (471)
                           .....++..+..+|...|++++|...+++..+
T Consensus       335 ~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  371 (411)
T 4a1s_A          335 ELGDRIGEARACWSLGNAHSAIGGHERALKYAEQHLQ  371 (411)
T ss_dssp             HHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HCCChHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHH
Confidence                 11234677778888888888888888888775

>4abn_A Tetratricopeptide repeat protein 5; P53 cofactor, stress-response, DNA repair, gene regulation; 2.05A {Mus musculus}

Probab=99.53  E-value=8e-13  Score=124.93  Aligned_cols=215  Identities=8%  Similarity=-0.020  Sum_probs=163.3

Q ss_pred             hhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCH-HHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHH
Q 012111           91 QKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQP-EQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAF  169 (471)
Q Consensus        91 ~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~-~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~  169 (471)
                      ..++++|++.++......  +.+...+..+...+...|++ ++|...|++..+.... +...|..+..+|...|++++|+
T Consensus        81 ~~~~~~al~~l~~~~~~~--~~~a~~~~~lg~~~~~~g~~~~~A~~~~~~al~~~p~-~~~a~~~lg~~~~~~g~~~~A~  157 (474)
T 4abn_A           81 QEEMEKTLQQMEEVLGSA--QVEAQALMLKGKALNVTPDYSPEAEVLLSKAVKLEPE-LVEAWNQLGEVYWKKGDVTSAH  157 (474)
T ss_dssp             HHHHHHHHHHHHHHHTTC--CCCHHHHHHHHHHHTSSSSCCHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHTCHHHHH
T ss_pred             HHHHHHHHHHHHHHhccC--chhHHHHHHHHHHHHhccccHHHHHHHHHHHHhhCCC-CHHHHHHHHHHHHHcCCHHHHH
Confidence            445777888888776654  55778888888889999999 9999999988876433 6788888888898999999999


Q ss_pred             HHHHHhhcCCCCCCCHHHHHHHHHHHHhc---------CCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHcc-------
Q 012111          170 STINDMKSVSDCKPDVYTYSILIKSCTKF---------HRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKA-------  233 (471)
Q Consensus       170 ~~~~~~~~~~~~~~~~~~~~~ll~~~~~~---------~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~-------  233 (471)
                      +.|++..+.   .|+...+..+...+...         |++++|.+.+++..+.. +-+...|..+..+|...       
T Consensus       158 ~~~~~al~~---~p~~~~~~~lg~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~~~  233 (474)
T 4abn_A          158 TCFSGALTH---CKNKVSLQNLSMVLRQLQTDSGDEHSRHVMDSVRQAKLAVQMD-VLDGRSWYILGNAYLSLYFNTGQN  233 (474)
T ss_dssp             HHHHHHHTT---CCCHHHHHHHHHHHTTCCCSCHHHHHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHTTCC
T ss_pred             HHHHHHHhh---CCCHHHHHHHHHHHHHhccCChhhhhhhHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHHHhhccc
Confidence            999888863   46677788888888888         88888888888887764 44677777788888777       


Q ss_pred             -CCHHHHHHHHHHHHHcCCCC---CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHH
Q 012111          234 -KKFEEMESSFSAMVESGGCH---PDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDK  309 (471)
Q Consensus       234 -~~~~~a~~~~~~~~~~~~~~---~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~  309 (471)
                       |++++|++.|++..+..  +   .+...|..+..+|...|++++|...|++..+.. +.+...+..+..++...|++++
T Consensus       234 ~g~~~~A~~~~~~al~~~--p~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~-p~~~~a~~~l~~~~~~lg~~~e  310 (474)
T 4abn_A          234 PKISQQALSAYAQAEKVD--RKASSNPDLHLNRATLHKYEESYGEALEGFSQAAALD-PAWPEPQQREQQLLEFLSRLTS  310 (474)
T ss_dssp             HHHHHHHHHHHHHHHHHC--GGGGGCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHHH
T ss_pred             cchHHHHHHHHHHHHHhC--CCcccCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHHHHHH
Confidence             77888888888877653  2   366777777788888888888888887776654 4455666777777777777777


Q ss_pred             HHHHHH
Q 012111          310 MRSVMD  315 (471)
Q Consensus       310 a~~~~~  315 (471)
                      |...+.
T Consensus       311 Ai~~~~  316 (474)
T 4abn_A          311 LLESKG  316 (474)
T ss_dssp             HHHHTT
T ss_pred             HHHHhc
Confidence            766543

>2ond_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 2.80A {Mus musculus} SCOP: a.118.8.7

Probab=99.53  E-value=1.3e-11  Score=109.86  Aligned_cols=218  Identities=10%  Similarity=-0.040  Sum_probs=154.2

Q ss_pred             HHHHHHHHHhhhccCccCChhHHHHHHHHHh-------cCCCH-------HHHHHHHHHHHhCCCCCCHHHHHHHHHHHH
Q 012111           95 QLALKIFGLLRQQQWYQARCQTFTKLMVMLG-------KCKQP-------EQASLLFEVMLSDGLKPSVDVYTALVSAYG  160 (471)
Q Consensus        95 ~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~-------~~~~~-------~~a~~~~~~m~~~~~~~~~~~~~~li~~~~  160 (471)
                      ++|+.+|+.+....  |.+...|..++..+.       +.|++       ++|..+|++..+.-.+-+...|..++..+.
T Consensus        33 ~~a~~~~~~al~~~--p~~~~~w~~~~~~~~~~~~~l~~~g~~~~~~~~~~~A~~~~~rAl~~~~p~~~~~~~~~~~~~~  110 (308)
T 2ond_A           33 KRVMFAYEQCLLVL--GHHPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANIYERAISTLLKKNMLLYFAYADYEE  110 (308)
T ss_dssp             HHHHHHHHHHHHHH--TTCHHHHHHHHHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHHHHTTTTTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHc--CCCHHHHHHHHHHHHHhchhhhhccchhhcccchHHHHHHHHHHHHHhCcccHHHHHHHHHHHH
Confidence            68889999998875  677888888888775       35775       888999988887312236678888888888


Q ss_pred             hcCCHHHHHHHHHHhhcCCCCCCC-HH-HHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHH-ccCCHH
Q 012111          161 QSGLLDEAFSTINDMKSVSDCKPD-VY-TYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYG-KAKKFE  237 (471)
Q Consensus       161 ~~~~~~~a~~~~~~~~~~~~~~~~-~~-~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~-~~~~~~  237 (471)
                      ..|++++|..+|++..+.   .|+ .. .|..+...+.+.|++++|..+|++..+.. +.+...|........ ..|+++
T Consensus       111 ~~~~~~~A~~~~~~al~~---~p~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~-p~~~~~~~~~a~~~~~~~~~~~  186 (308)
T 2ond_A          111 SRMKYEKVHSIYNRLLAI---EDIDPTLVYIQYMKFARRAEGIKSGRMIFKKAREDA-RTRHHVYVTAALMEYYCSKDKS  186 (308)
T ss_dssp             HTTCHHHHHHHHHHHHTS---SSSCTHHHHHHHHHHHHHHHCHHHHHHHHHHHHTST-TCCTHHHHHHHHHHHHTSCCHH
T ss_pred             hcCCHHHHHHHHHHHHhc---cccCccHHHHHHHHHHHHhcCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHHcCCHH
Confidence            889999999999888863   343 33 67777888888888888888888887664 334444443333322 257788


Q ss_pred             HHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCC-CCC--CHHHHHHHHHHHHHcCCHHHHHHHH
Q 012111          238 EMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMG-VKA--DIQTLNILTKSYGRAGMYDKMRSVM  314 (471)
Q Consensus       238 ~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-~~~--~~~~~~~ll~~~~~~~~~~~a~~~~  314 (471)
                      +|..+|+...+..  +.+...|..++..+.+.|++++|..+|++..... ++|  ....|..++....+.|+.+.|..++
T Consensus       187 ~A~~~~~~al~~~--p~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~~l~p~~~~~l~~~~~~~~~~~g~~~~a~~~~  264 (308)
T 2ond_A          187 VAFKIFELGLKKY--GDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSGEIWARFLAFESNIGDLASILKVE  264 (308)
T ss_dssp             HHHHHHHHHHHHH--TTCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSSSSCGGGCHHHHHHHHHHHHHHSCHHHHHHHH
T ss_pred             HHHHHHHHHHHhC--CCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHH
Confidence            8888887776653  3456667777777777777777777777777652 233  3556666667777777777777777


Q ss_pred             HHHHhC
Q 012111          315 DFMQKR  320 (471)
Q Consensus       315 ~~~~~~  320 (471)
                      +++.+.
T Consensus       265 ~~a~~~  270 (308)
T 2ond_A          265 KRRFTA  270 (308)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            766654

>3vtx_A MAMA; tetratricopeptide repeats (TPR) containing protein, peptide protein, protein binding; 1.75A {Candidatus magnetobacterium bavaricum} PDB: 3vty_A

Probab=99.53  E-value=5.3e-12  Score=103.11  Aligned_cols=165  Identities=13%  Similarity=0.038  Sum_probs=97.6

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHH
Q 012111          256 IFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIET  335 (471)
Q Consensus       256 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~  335 (471)
                      ...|..+...+...|++++|+..|++..+.. +-+..++..+..+|.+.|++++|...+......... +...+..+...
T Consensus         5 ~~iy~~lG~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~~~~~   82 (184)
T 3vtx_A            5 TTIYMDIGDKKRTKGDFDGAIRAYKKVLKAD-PNNVETLLKLGKTYMDIGLPNDAIESLKKFVVLDTT-SAEAYYILGSA   82 (184)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCC-CHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCch-hHHHHHHHHHH
Confidence            3445555555555555555555555555443 334555555555555556666665555555544222 34445555555


Q ss_pred             HHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHH
Q 012111          336 FGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKM  415 (471)
Q Consensus       336 ~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a  415 (471)
                      +...++++.|...+.+..... +-+...+..+...+...|++++|.+.|++..+.++. +..+|..+..+|.+.|++++|
T Consensus        83 ~~~~~~~~~a~~~~~~a~~~~-~~~~~~~~~lg~~~~~~g~~~~A~~~~~~~l~~~p~-~~~~~~~lg~~~~~~g~~~~A  160 (184)
T 3vtx_A           83 NFMIDEKQAAIDALQRAIALN-TVYADAYYKLGLVYDSMGEHDKAIEAYEKTISIKPG-FIRAYQSIGLAYEGKGLRDEA  160 (184)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHcCCHHHHHHHHHHHHHhC-ccchHHHHHHHHHHHHhCCchhHHHHHHHHHHhcch-hhhHHHHHHHHHHHCCCHHHH
Confidence            666666666666666665542 234556666666666667777777666666665544 566666667777777777777


Q ss_pred             HHHHHHHHh
Q 012111          416 GELFLTMKE  424 (471)
Q Consensus       416 ~~~~~~~~~  424 (471)
                      ++.|++..+
T Consensus       161 ~~~~~~al~  169 (184)
T 3vtx_A          161 VKYFKKALE  169 (184)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHh
Confidence            777776665

>3ulq_A Response regulator aspartate phosphatase F; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis}

Probab=99.51  E-value=4.6e-12  Score=116.67  Aligned_cols=228  Identities=13%  Similarity=0.031  Sum_probs=131.0

Q ss_pred             HHHhcCCHHHHHHHHHHHHHC----CCCC-CHHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCC-----HHHHHHHH
Q 012111          194 SCTKFHRFDLIEKILAEMSYL----GIEC-SAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPD-----IFTLNSMI  263 (471)
Q Consensus       194 ~~~~~~~~~~a~~~~~~~~~~----g~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~-----~~~~~~l~  263 (471)
                      .+...|++++|...+++..+.    +-.+ ...++..+...|...|+++.|...+.+..+...-.++     ..++..+.
T Consensus       112 ~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg  191 (383)
T 3ulq_A          112 YELDQREYLSAIKFFKKAESKLIFVKDRIEKAEFFFKMSESYYYMKQTYFSMDYARQAYEIYKEHEAYNIRLLQCHSLFA  191 (383)
T ss_dssp             HHHHTTCHHHHHHHHHHHHTTGGGCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTCSTTHHHHHHHHHHHH
T ss_pred             HHHHhcCHHHHHHHHHHHHHHHhhCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCccchHHHHHHHHHHH
Confidence            344555555555555555432    1011 1344555556666666666666666555432111111     23555666


Q ss_pred             HHHHhcCCHHHHHHHHHHHHhCCC-CCC----HHHHHHHHHHHHHcCCHHHHHHHHHHHHhC----CC-CCCHHHHHHHH
Q 012111          264 SAYGNSGNIEKMEKWYNEFNLMGV-KAD----IQTLNILTKSYGRAGMYDKMRSVMDFMQKR----FF-FPTVVTYNIVI  333 (471)
Q Consensus       264 ~~~~~~~~~~~a~~~~~~~~~~~~-~~~----~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~----~~-~~~~~~~~~li  333 (471)
                      ..|...|++++|...+++...... ..+    ..++..+..+|...|++++|...+++..+.    +. +....++..+.
T Consensus       192 ~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~  271 (383)
T 3ulq_A          192 TNFLDLKQYEDAISHFQKAYSMAEAEKQPQLMGRTLYNIGLCKNSQSQYEDAIPYFKRAIAVFEESNILPSLPQAYFLIT  271 (383)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCGGGHHHHHHHHH
T ss_pred             HHHHHhcCHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhccchhHHHHHHHHH
Confidence            666667777777766666543210 011    235666677777777777777777766551    22 22345667777


Q ss_pred             HHHHhcCCHHHHHHHHHHHHHc----CCCCCHHHHHHHHHHHHhcCC---HHHHHHHHHHHHhCCCCc-CHHHHHHHHHH
Q 012111          334 ETFGKAGHIEKMEEYFKKMKHR----GMKPNSITYCSLVSAYSKAGL---IMKVDSILRQVENSDVIL-DTPFFNCIISA  405 (471)
Q Consensus       334 ~~~~~~g~~~~a~~~~~~m~~~----~~~p~~~~~~~li~~~~~~g~---~~~a~~~~~~~~~~~~~~-~~~~~~~l~~~  405 (471)
                      ..+...|++++|...+++....    +-+.....+..+...+...|+   +++|..+++..   +..+ ....+..+...
T Consensus       272 ~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~al~~~~~~---~~~~~~~~~~~~la~~  348 (383)
T 3ulq_A          272 QIHYKLGKIDKAHEYHSKGMAYSQKAGDVIYLSEFEFLKSLYLSGPDEEAIQGFFDFLESK---MLYADLEDFAIDVAKY  348 (383)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTSSCCHHHHHHHHHHHHHT---TCHHHHHHHHHHHHHH
T ss_pred             HHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHC---cCHHHHHHHHHHHHHH
Confidence            7777778888887777776543    111112234556667777777   56666666554   2222 23456677888


Q ss_pred             HHhcCCHHHHHHHHHHHHh
Q 012111          406 YGQAGDVEKMGELFLTMKE  424 (471)
Q Consensus       406 ~~~~g~~~~a~~~~~~~~~  424 (471)
                      |...|++++|...|++..+
T Consensus       349 y~~~g~~~~A~~~~~~al~  367 (383)
T 3ulq_A          349 YHERKNFQKASAYFLKVEQ  367 (383)
T ss_dssp             HHHTTCHHHHHHHHHHHHH
T ss_pred             HHHCCCHHHHHHHHHHHHH
Confidence            8888888888888887764

>4abn_A Tetratricopeptide repeat protein 5; P53 cofactor, stress-response, DNA repair, gene regulation; 2.05A {Mus musculus}

Probab=99.51  E-value=1.6e-12  Score=122.94  Aligned_cols=212  Identities=8%  Similarity=-0.064  Sum_probs=122.8

Q ss_pred             HHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCH-HHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHH
Q 012111          201 FDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKF-EEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWY  279 (471)
Q Consensus       201 ~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~-~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~  279 (471)
                      ++.+.+.++...... +.+...+..+...+...|++ ++|++.|++..+..  +.+...|..+..+|...|++++|...|
T Consensus        84 ~~~al~~l~~~~~~~-~~~a~~~~~lg~~~~~~g~~~~~A~~~~~~al~~~--p~~~~a~~~lg~~~~~~g~~~~A~~~~  160 (474)
T 4abn_A           84 MEKTLQQMEEVLGSA-QVEAQALMLKGKALNVTPDYSPEAEVLLSKAVKLE--PELVEAWNQLGEVYWKKGDVTSAHTCF  160 (474)
T ss_dssp             HHHHHHHHHHHHTTC-CCCHHHHHHHHHHHTSSSSCCHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHTCHHHHHHHH
T ss_pred             HHHHHHHHHHHhccC-chhHHHHHHHHHHHHhccccHHHHHHHHHHHHhhC--CCCHHHHHHHHHHHHHcCCHHHHHHHH
Confidence            555555665554432 33566666666777777777 77777777666653  334566666666666677777777777


Q ss_pred             HHHHhCCCCCCHHHHHHHHHHHHHc---------CCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhc--------CCH
Q 012111          280 NEFNLMGVKADIQTLNILTKSYGRA---------GMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKA--------GHI  342 (471)
Q Consensus       280 ~~~~~~~~~~~~~~~~~ll~~~~~~---------~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~--------g~~  342 (471)
                      ++..+.  .|+...+..+...+...         |++++|...+++..+.... +...|..+..+|...        |++
T Consensus       161 ~~al~~--~p~~~~~~~lg~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~lg~~~~~~~~~~~~~~g~~  237 (474)
T 4abn_A          161 SGALTH--CKNKVSLQNLSMVLRQLQTDSGDEHSRHVMDSVRQAKLAVQMDVL-DGRSWYILGNAYLSLYFNTGQNPKIS  237 (474)
T ss_dssp             HHHHTT--CCCHHHHHHHHHHHTTCCCSCHHHHHHHHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHHHHTTCCHHHH
T ss_pred             HHHHhh--CCCHHHHHHHHHHHHHhccCChhhhhhhHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHHHHhhccccchH
Confidence            666654  34455666666666666         6666666666665554322 445555555555555        556


Q ss_pred             HHHHHHHHHHHHcCCC--CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHH
Q 012111          343 EKMEEYFKKMKHRGMK--PNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELF  419 (471)
Q Consensus       343 ~~a~~~~~~m~~~~~~--p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~  419 (471)
                      ++|...|++..+....  -+...|..+..+|...|++++|.+.|++..+..+. +...+..+..++...|++++|++.+
T Consensus       238 ~~A~~~~~~al~~~p~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~p~-~~~a~~~l~~~~~~lg~~~eAi~~~  315 (474)
T 4abn_A          238 QQALSAYAQAEKVDRKASSNPDLHLNRATLHKYEESYGEALEGFSQAAALDPA-WPEPQQREQQLLEFLSRLTSLLESK  315 (474)
T ss_dssp             HHHHHHHHHHHHHCGGGGGCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHhCCCcccCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            6666666655554210  24555555555555666666666666555554433 4445555555555555555555443

>1hz4_A MALT regulatory protein; two-helix bundles, helix repeats, protein superhelix, transc activator; 1.45A {Escherichia coli} SCOP: a.118.8.2

Probab=99.49  E-value=6.6e-11  Score=108.46  Aligned_cols=302  Identities=10%  Similarity=0.003  Sum_probs=185.1

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCH----HHHHHHHHHHHhcCCHHHHHHHHHHHHHCCC-CCCH----HH
Q 012111          152 YTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDV----YTYSILIKSCTKFHRFDLIEKILAEMSYLGI-ECSA----VT  222 (471)
Q Consensus       152 ~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~----~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~-~~~~----~~  222 (471)
                      +......+...|++++|...+++...... ..+.    .+++.+...+...|+++.|.+.+++...... ..+.    .+
T Consensus        17 ~~~~a~~~~~~g~~~~A~~~~~~al~~~~-~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~   95 (373)
T 1hz4_A           17 NALRAQVAINDGNPDEAERLAKLALEELP-PGWFYSRIVATSVLGEVLHCKGELTRSLALMQQTEQMARQHDVWHYALWS   95 (373)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHTCC-TTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHcCC-CCchhHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHhcCcHHHHHHH
Confidence            34445566778889999998888776332 1222    2455666677788888888888887754311 1122    23


Q ss_pred             HHHHHHHHHccCCHHHHHHHHHHHHHcC---CCC--C-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCC----CCHH
Q 012111          223 YNTIIDGYGKAKKFEEMESSFSAMVESG---GCH--P-DIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVK----ADIQ  292 (471)
Q Consensus       223 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~---~~~--~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~----~~~~  292 (471)
                      +..+...+...|++++|...+++..+..   +..  | ....+..+...+...|++++|...+++.......    ....
T Consensus        96 ~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~  175 (373)
T 1hz4_A           96 LIQQSEILFAQGFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLWAWARLDEAEASARSGIEVLSSYQPQQQLQ  175 (373)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTSCGGGGHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhccccCcHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHhhccCcHHHHH
Confidence            5566777888888888888888776431   111  2 2345566777788888888888888877653211    1234


Q ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCC--HHHHH----HHHHHHHhcCCHHHHHHHHHHHHHcCCCC---CHHH
Q 012111          293 TLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPT--VVTYN----IVIETFGKAGHIEKMEEYFKKMKHRGMKP---NSIT  363 (471)
Q Consensus       293 ~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~~~----~li~~~~~~g~~~~a~~~~~~m~~~~~~p---~~~~  363 (471)
                      ++..+...+...|++++|...++........++  .....    ..+..+...|++++|...+++.......+   ....
T Consensus       176 ~~~~la~~~~~~g~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~  255 (373)
T 1hz4_A          176 CLAMLIQCSLARGDLDNARSQLNRLENLLGNGKYHSDWISNANKVRVIYWQMTGDKAAAANWLRHTAKPEFANNHFLQGQ  255 (373)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHSCCCCCTTCGGGHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHhccCcchhHHHHHHHHHHHHHHHCCCHHHHHHHHHhCCCCCCCcchhhHHH
Confidence            566777778888888888888877754321111  11111    22234667788888888887766542211   1234


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHhC----CCCcCH-HHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHH
Q 012111          364 YCSLVSAYSKAGLIMKVDSILRQVENS----DVILDT-PFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMI  438 (471)
Q Consensus       364 ~~~li~~~~~~g~~~~a~~~~~~~~~~----~~~~~~-~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~  438 (471)
                      +..+...+...|++++|...++.....    +..++. ..+..+..++...|+.++|...+++.....  +.    .-.+
T Consensus       256 ~~~la~~~~~~g~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~al~~~--~~----~g~~  329 (373)
T 1hz4_A          256 WRNIARAQILLGEFEPAEIVLEELNENARSLRLMSDLNRNLLLLNQLYWQAGRKSDAQRVLLDALKLA--NR----TGFI  329 (373)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHH--HH----HCCC
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCcchhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHh--cc----ccHH
Confidence            566677777888888888887776532    222122 255566677777888888888887776421  00    1122


Q ss_pred             HHHHhcCCHHHHHHHHHHHHHhhh
Q 012111          439 QAYNALGMTEAAQNLENKMIAMKE  462 (471)
Q Consensus       439 ~~~~~~g~~~~A~~~~~~m~~~~~  462 (471)
                      ..+...|  +....+++.+....+
T Consensus       330 ~~~~~~g--~~~~~ll~~~~~~~~  351 (373)
T 1hz4_A          330 SHFVIEG--EAMAQQLRQLIQLNT  351 (373)
T ss_dssp             HHHHTTH--HHHHHHHHHHHHTTC
T ss_pred             HHHHHcc--HHHHHHHHHHHhCCC
Confidence            3444555  566667776666555

>3nf1_A KLC 1, kinesin light chain 1; TPR, structural genomics consortium (SGC), motor PR transport protein; 2.80A {Homo sapiens}

Probab=99.49  E-value=1.3e-12  Score=116.40  Aligned_cols=244  Identities=17%  Similarity=0.177  Sum_probs=172.8

Q ss_pred             CHHHHHHHHHHHHccCCHHHHHHHHHHHHHcC------CCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhC------C
Q 012111          219 SAVTYNTIIDGYGKAKKFEEMESSFSAMVESG------GCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLM------G  286 (471)
Q Consensus       219 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~------~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~------~  286 (471)
                      +..++..+...+...|++++|..+++++.+..      ........+..+...+...|++++|...+++....      +
T Consensus        26 ~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~  105 (311)
T 3nf1_A           26 RLRTLHNLVIQYASQGRYEVAVPLCKQALEDLEKTSGHDHPDVATMLNILALVYRDQNKYKDAANLLNDALAIREKTLGK  105 (311)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHCSSSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHCT
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhCC
Confidence            46778889999999999999999999987630      02334567888899999999999999999998754      2


Q ss_pred             -CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhC------CCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc---
Q 012111          287 -VKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKR------FFFP-TVVTYNIVIETFGKAGHIEKMEEYFKKMKHR---  355 (471)
Q Consensus       287 -~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~------~~~~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~---  355 (471)
                       .+....++..+...|...|++++|...++.+.+.      +..| ....+..+...+...|++++|..+++++...   
T Consensus       106 ~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~  185 (311)
T 3nf1_A          106 DHPAVAATLNNLAVLYGKRGKYKEAEPLCKRALEIREKVLGKDHPDVAKQLNNLALLCQNQGKYEEVEYYYQRALEIYQT  185 (311)
T ss_dssp             TCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHH
T ss_pred             CChHHHHHHHHHHHHHHHcCcHHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHH
Confidence             1334567888899999999999999999988764      2222 3456788888999999999999999998764   


Q ss_pred             ---CCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCC-------CCcCH-------HHHHHHHHHHHhcCCHHHHHH
Q 012111          356 ---GMKP-NSITYCSLVSAYSKAGLIMKVDSILRQVENSD-------VILDT-------PFFNCIISAYGQAGDVEKMGE  417 (471)
Q Consensus       356 ---~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~-------~~~~~-------~~~~~l~~~~~~~g~~~~a~~  417 (471)
                         +..| ...++..+...+...|++++|...++++.+..       ..+..       ..+..+...+...+.+.++..
T Consensus       186 ~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~  265 (311)
T 3nf1_A          186 KLGPDDPNVAKTKNNLASCYLKQGKFKQAETLYKEILTRAHEREFGSVDDENKPIWMHAEEREECKGKQKDGTSFGEYGG  265 (311)
T ss_dssp             TSCTTCHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHC------CCHHHHHHHHHHC-------CCSCCCC-
T ss_pred             HhCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCCCcchHHHHHHHHHHHHhcCchhhHHHHHHHHH
Confidence               2123 34578888999999999999999999887531       11111       122223333444555666666


Q ss_pred             HHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhhhc
Q 012111          418 LFLTMKERHCVPDNITFATMIQAYNALGMTEAAQNLENKMIAMKEN  463 (471)
Q Consensus       418 ~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~  463 (471)
                      .++..... .+.+..++..+..+|.+.|++++|.++++++++..+.
T Consensus       266 ~~~~~~~~-~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~l~~~  310 (311)
T 3nf1_A          266 WYKACKVD-SPTVTTTLKNLGALYRRQGKFEAAETLEEAAMRSRKQ  310 (311)
T ss_dssp             ---------CHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHC-
T ss_pred             HHhhcCCC-CchHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHhhc
Confidence            66666543 1234567888899999999999999999999988764

>3q15_A PSP28, response regulator aspartate phosphatase H; tetratricopeptide repeat, 3-helix bundle, phosphorelay signa transduction, phosphatase; 2.19A {Bacillus subtilis}

Probab=99.48  E-value=1.5e-11  Score=112.88  Aligned_cols=234  Identities=12%  Similarity=0.033  Sum_probs=168.3

Q ss_pred             HHHHHHHccCCHHHHHHHHHHHHHcCCCCCC----HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCC--C---C-CCHHHH
Q 012111          225 TIIDGYGKAKKFEEMESSFSAMVESGGCHPD----IFTLNSMISAYGNSGNIEKMEKWYNEFNLMG--V---K-ADIQTL  294 (471)
Q Consensus       225 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~--~---~-~~~~~~  294 (471)
                      .....+...|++++|...|++..+.....++    ...+..+...|...|+++.|...+.+.....  .   . ....++
T Consensus       106 ~~g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~  185 (378)
T 3q15_A          106 FRGMYEFDQKEYVEAIGYYREAEKELPFVSDDIEKAEFHFKVAEAYYHMKQTHVSMYHILQALDIYQNHPLYSIRTIQSL  185 (378)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHTTGGGCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTSTTCHHHHHHHH
T ss_pred             HHHHHHHHHCCHHHHHHHHHHHHHHHhhCCChHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHhCCCchhhHHHHH
Confidence            3445567788999999988887654211222    4567778888888999999988888875421  0   1 124567


Q ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHhC----CCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHH-----cCCCCCHHHH
Q 012111          295 NILTKSYGRAGMYDKMRSVMDFMQKR----FFFP-TVVTYNIVIETFGKAGHIEKMEEYFKKMKH-----RGMKPNSITY  364 (471)
Q Consensus       295 ~~ll~~~~~~~~~~~a~~~~~~~~~~----~~~~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~-----~~~~p~~~~~  364 (471)
                      +.+...|...|++++|...+....+.    +..+ ...++..+...|...|++++|...+++...     .. +....++
T Consensus       186 ~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~-~~~~~~~  264 (378)
T 3q15_A          186 FVIAGNYDDFKHYDKALPHLEAALELAMDIQNDRFIAISLLNIANSYDRSGDDQMAVEHFQKAAKVSREKVP-DLLPKVL  264 (378)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHCG-GGHHHHH
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCC-hhHHHHH
Confidence            78888889999999999988876652    1111 234677788889999999999999998876     32 2236778


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHhCCC----CcCHHHHHHHHHHHHhcCC---HHHHHHHHHHHHhCCCCCC-HHHHHH
Q 012111          365 CSLVSAYSKAGLIMKVDSILRQVENSDV----ILDTPFFNCIISAYGQAGD---VEKMGELFLTMKERHCVPD-NITFAT  436 (471)
Q Consensus       365 ~~li~~~~~~g~~~~a~~~~~~~~~~~~----~~~~~~~~~l~~~~~~~g~---~~~a~~~~~~~~~~~~~p~-~~~~~~  436 (471)
                      ..+...+.+.|++++|...+++..+...    ......+..+...+...|+   +.+|+..+++.   +..|+ ...+..
T Consensus       265 ~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~ly~~~~~~~~~~~al~~~~~~---~~~~~~~~~~~~  341 (378)
T 3q15_A          265 FGLSWTLCKAGQTQKAFQFIEEGLDHITARSHKFYKELFLFLQAVYKETVDERKIHDLLSYFEKK---NLHAYIEACARS  341 (378)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHCCTTCCSCHHHHHHHHHHHHSSSCCHHHHHHHHHHHHHT---TCHHHHHHHHHH
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHhC---CChhHHHHHHHH
Confidence            8899999999999999999998875321    1123345666666777788   77777777763   22333 345567


Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHHhhh
Q 012111          437 MIQAYNALGMTEAAQNLENKMIAMKE  462 (471)
Q Consensus       437 l~~~~~~~g~~~~A~~~~~~m~~~~~  462 (471)
                      +...|...|++++|.+.++++++...
T Consensus       342 la~~y~~~g~~~~A~~~~~~al~~~~  367 (378)
T 3q15_A          342 AAAVFESSCHFEQAAAFYRKVLKAQE  367 (378)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence            88999999999999999999987654

>3nf1_A KLC 1, kinesin light chain 1; TPR, structural genomics consortium (SGC), motor PR transport protein; 2.80A {Homo sapiens}

Probab=99.48  E-value=3.7e-13  Score=120.00  Aligned_cols=246  Identities=15%  Similarity=0.100  Sum_probs=111.8

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHhhcCC------CCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHC------CC
Q 012111          149 VDVYTALVSAYGQSGLLDEAFSTINDMKSVS------DCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYL------GI  216 (471)
Q Consensus       149 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~------~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~------g~  216 (471)
                      ..++..+...+...|++++|+.+|+++.+..      .......++..+...+...|++++|...+++....      +-
T Consensus        27 ~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~  106 (311)
T 3nf1_A           27 LRTLHNLVIQYASQGRYEVAVPLCKQALEDLEKTSGHDHPDVATMLNILALVYRDQNKYKDAANLLNDALAIREKTLGKD  106 (311)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHCSSSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHCTT
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhCCC
Confidence            3455555566666666666666666555410      11122334445555555555555555555554432      11


Q ss_pred             -CCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHH
Q 012111          217 -ECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLN  295 (471)
Q Consensus       217 -~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~  295 (471)
                       +....++..+...|...|++++|...++++.+.....                             .....+.....+.
T Consensus       107 ~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~-----------------------------~~~~~~~~~~~~~  157 (311)
T 3nf1_A          107 HPAVAATLNNLAVLYGKRGKYKEAEPLCKRALEIREKV-----------------------------LGKDHPDVAKQLN  157 (311)
T ss_dssp             CHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHH-----------------------------HCTTCHHHHHHHH
T ss_pred             ChHHHHHHHHHHHHHHHcCcHHHHHHHHHHHHHHHHHh-----------------------------cCCCChHHHHHHH
Confidence             1123344444445555555555555554443320000                             0000011223344


Q ss_pred             HHHHHHHHcCCHHHHHHHHHHHHhC------CCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc-------CCCCC-
Q 012111          296 ILTKSYGRAGMYDKMRSVMDFMQKR------FFFP-TVVTYNIVIETFGKAGHIEKMEEYFKKMKHR-------GMKPN-  360 (471)
Q Consensus       296 ~ll~~~~~~~~~~~a~~~~~~~~~~------~~~~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~-------~~~p~-  360 (471)
                      .+...+...|++++|..+++.+.+.      +..| ....+..+...+...|++++|...++++.+.       ...+. 
T Consensus       158 ~la~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~  237 (311)
T 3nf1_A          158 NLALLCQNQGKYEEVEYYYQRALEIYQTKLGPDDPNVAKTKNNLASCYLKQGKFKQAETLYKEILTRAHEREFGSVDDEN  237 (311)
T ss_dssp             HHHHHHHTTTCHHHHHHHHHHHHHHHHHTSCTTCHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHC------
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCCCcch
Confidence            4445555555555555555544332      1111 1234555556666666666666666665532       01111 


Q ss_pred             ------HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 012111          361 ------SITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKE  424 (471)
Q Consensus       361 ------~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~  424 (471)
                            ...+..+...+...+.+.++...++......+. ...++..+..+|...|++++|.++|++..+
T Consensus       238 ~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~la~~~~~~g~~~~A~~~~~~al~  306 (311)
T 3nf1_A          238 KPIWMHAEEREECKGKQKDGTSFGEYGGWYKACKVDSPT-VTTTLKNLGALYRRQGKFEAAETLEEAAMR  306 (311)
T ss_dssp             CCHHHHHHHHHHC-------CCSCCCC---------CHH-HHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCchhhHHHHHHHHHHHhhcCCCCch-HHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence                  111222223333445555555566655544322 556778888888888888888888887765

>3as5_A MAMA; tetratricopeptide repeats (TPR) containing protein, TPR PROT protein-protein interactions, protein binding; 2.00A {Magnetospirillum magnetotacticum} PDB: 3as4_A 3asd_A 3asg_A 3ash_A 3as8_A 3asf_A

Probab=99.47  E-value=1.6e-11  Score=100.05  Aligned_cols=171  Identities=13%  Similarity=0.061  Sum_probs=132.9

Q ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Q 012111          292 QTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAY  371 (471)
Q Consensus       292 ~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~  371 (471)
                      ..+..+...+...|++++|...++.+.+... .+...+..+...+...|++++|...++++.+.. +.+...+..+...+
T Consensus         9 ~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~   86 (186)
T 3as5_A            9 VYYRDKGISHAKAGRYSQAVMLLEQVYDADA-FDVDVALHLGIAYVKTGAVDRGTELLERSLADA-PDNVKVATVLGLTY   86 (186)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHTTTCCTTS-CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHHhCc-cChHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHH
Confidence            3455566667777777777777777665432 256677777778888888888888888877653 34667778888888


Q ss_pred             HhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHH
Q 012111          372 SKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAYNALGMTEAAQ  451 (471)
Q Consensus       372 ~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~  451 (471)
                      ...|++++|.+.++.+.+..+. +...+..+...+...|++++|.+.++++.+.. +.+...+..+...+...|++++|.
T Consensus        87 ~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~  164 (186)
T 3as5_A           87 VQVQKYDLAVPLLIKVAEANPI-NFNVRFRLGVALDNLGRFDEAIDSFKIALGLR-PNEGKVHRAIAFSYEQMGRHEEAL  164 (186)
T ss_dssp             HHHTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHhcCHHHHHHHHHHHHhcCcH-hHHHHHHHHHHHHHcCcHHHHHHHHHHHHhcC-ccchHHHHHHHHHHHHcCCHHHHH
Confidence            8888888888888888776544 67788888888999999999999999888752 346778888889999999999999


Q ss_pred             HHHHHHHHhhhcCCC
Q 012111          452 NLENKMIAMKENSGK  466 (471)
Q Consensus       452 ~~~~~m~~~~~~~~~  466 (471)
                      +.++++++..|+...
T Consensus       165 ~~~~~~~~~~~~~~~  179 (186)
T 3as5_A          165 PHFKKANELDEGASV  179 (186)
T ss_dssp             HHHHHHHHHHHCCCG
T ss_pred             HHHHHHHHcCCCchh
Confidence            999999998887654

>4e6h_A MRNA 3'-END-processing protein RNA14; HAT domain, heat repeat, CLP1, PCF11, structural protein; 2.30A {Kluyveromyces lactis} PDB: 4e85_A 4eba_A

Probab=99.47  E-value=7.8e-10  Score=107.56  Aligned_cols=362  Identities=9%  Similarity=0.012  Sum_probs=242.3

Q ss_pred             HHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCC---HHHHHHH
Q 012111           95 QLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGL---LDEAFST  171 (471)
Q Consensus        95 ~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~---~~~a~~~  171 (471)
                      .+.+..|+.....+  +-|...|..++..+.+.+.++.+..+|+.+... ++.....|...+..-.+.+.   ++.+..+
T Consensus        49 ~d~i~~lE~~l~~n--p~d~~~W~~yi~~~~~~~~~~~aR~vyEraL~~-fP~~~~lW~~Yi~~E~~~~~~~~~~~v~~l  125 (679)
T 4e6h_A           49 SDVIGKLNDMIEEQ--PTDIFLYVKLLKHHVSLKQWKQVYETFDKLHDR-FPLMANIWCMRLSLEFDKMEELDAAVIEPV  125 (679)
T ss_dssp             SCHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-CTTCHHHHHHHHHHHHTC--CCCHHHHHHH
T ss_pred             HHHHHHHHHHHHHC--cCCHHHHHHHHHHHHhcCcHHHHHHHHHHHHHH-CCCCHHHHHHHHHHHHhhCCcchHHHHHHH
Confidence            34555666666665  779999999999999999999999999999987 45578889999998888888   9999999


Q ss_pred             HHHhhcCCCCCCCHHHHHHHHHHHHhcCCH--------HHHHHHHHHHHH-CCC-CC-CHHHHHHHHHHHHc--------
Q 012111          172 INDMKSVSDCKPDVYTYSILIKSCTKFHRF--------DLIEKILAEMSY-LGI-EC-SAVTYNTIIDGYGK--------  232 (471)
Q Consensus       172 ~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~--------~~a~~~~~~~~~-~g~-~~-~~~~~~~l~~~~~~--------  232 (471)
                      |++........|++..|...+....+.++.        +.+.++|+.... .|. .+ +...|...+.....        
T Consensus       126 feRal~~~~~~~sv~LW~~Yl~f~~~~~~~~~~~~~~r~~vr~~FErAl~~vG~~d~~s~~iW~~Yi~f~~~~~~~~~~e  205 (679)
T 4e6h_A          126 LARCLSKELGNNDLSLWLSYITYVRKKNDIITGGEEARNIVIQAFQVVVDKCAIFEPKSIQFWNEYLHFLEHWKPVNKFE  205 (679)
T ss_dssp             HHHHTCSSSCCCCHHHHHHHHHHHHHHSCSTTTHHHHHHHHHHHHHHHHHHTTTTCSSCHHHHHHHHHHHHTCCCCSHHH
T ss_pred             HHHHHHhcCCCCCHHHHHHHHHHHHHhcccccccchhHHHHHHHHHHHHHHhCcccccchHHHHHHHHHHHhccccCcHH
Confidence            999987322248999998888876665543        345577776553 466 44 45677777765432        


Q ss_pred             -cCCHHHHHHHHHHHHHcCCCCCCHHHHH---HHHHHH----------HhcCCHHHH-----------------------
Q 012111          233 -AKKFEEMESSFSAMVESGGCHPDIFTLN---SMISAY----------GNSGNIEKM-----------------------  275 (471)
Q Consensus       233 -~~~~~~a~~~~~~~~~~~~~~~~~~~~~---~l~~~~----------~~~~~~~~a-----------------------  275 (471)
                       .++++.+..+|+.++... ...-..+|.   .+....          ....+++.|                       
T Consensus       206 eq~~~~~~R~iy~raL~iP-~~~~~~~w~~Y~~fe~~~~~~~a~~~~~e~~~~y~~Ar~~~~e~~~~~~~l~r~~p~~~~  284 (679)
T 4e6h_A          206 EQQRVQYIRKLYKTLLCQP-MDCLESMWQRYTQWEQDVNQLTARRHIGELSAQYMNARSLYQDWLNITKGLKRNLPITLN  284 (679)
T ss_dssp             HHHHHHHHHHHHHHHTTSC-CSSHHHHHHHHHHHHHHHCTTTHHHHHHHHHHHHHHHHHHHHHHHHHTTTCCCCCCSSST
T ss_pred             HHhHHHHHHHHHHHHHhCc-cHHHHHHHHHHHHHHHhcCcchHHHHHHHhhHHHHHHHHHHHHHHHHHHhHhhccccccc
Confidence             334667777887776421 111112221   111110          000011112                       


Q ss_pred             --------------------------------------------HHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHH
Q 012111          276 --------------------------------------------EKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMR  311 (471)
Q Consensus       276 --------------------------------------------~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~  311 (471)
                                                                  ..+|++.... ++.....|...+..+...|+.++|.
T Consensus       285 ~~~~~~~p~~~~~~~~ql~lW~~yi~fEk~~~~~l~~~~~~~Rv~~~Ye~aL~~-~p~~~~lW~~ya~~~~~~~~~~~a~  363 (679)
T 4e6h_A          285 QATESNLPKPNEYDVQQLLIWLEWIRWESDNKLELSDDLHKARMTYVYMQAAQH-VCFAPEIWFNMANYQGEKNTDSTVI  363 (679)
T ss_dssp             TCCTTTSCCTTCCCHHHHHHHHHHHHHHHTCTTCCCHHHHHHHHHHHHHHHHHH-TTTCHHHHHHHHHHHHHHSCCTTHH
T ss_pred             cchhccCCCCchhHHHHHHHHHHHHHHHHhCCccccchhhHHHHHHHHHHHHHH-cCCCHHHHHHHHHHHHhcCcHHHHH
Confidence                                                        2223333222 1233444455555566778888886


Q ss_pred             -HHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC---------CCCC------------HHHHHHHHH
Q 012111          312 -SVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRG---------MKPN------------SITYCSLVS  369 (471)
Q Consensus       312 -~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~---------~~p~------------~~~~~~li~  369 (471)
                       .+|+..... ++.+...|-..+....+.|++++|.++|+++....         -.|+            ..+|...+.
T Consensus       364 r~il~rAi~~-~P~s~~Lwl~~a~~ee~~~~~e~aR~iyek~l~~l~~~~~~~~~~~p~~~~~~~~~~~~~~~vWi~y~~  442 (679)
T 4e6h_A          364 TKYLKLGQQC-IPNSAVLAFSLSEQYELNTKIPEIETTILSCIDRIHLDLAALMEDDPTNESAINQLKSKLTYVYCVYMN  442 (679)
T ss_dssp             HHHHHHHHHH-CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHh-CCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHhhhhhhccCcchhhhhhhccchHHHHHHHHH
Confidence             899888765 33456667777888888999999999999888641         0132            346777888


Q ss_pred             HHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhc-CCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHH
Q 012111          370 AYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQA-GDVEKMGELFLTMKERHCVPDNITFATMIQAYNALGMTE  448 (471)
Q Consensus       370 ~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~  448 (471)
                      ...+.|+.+.|..+|.++.+.........|...+..-.+. ++.+.|.++|+...+. ++-+...|...+......|+.+
T Consensus       443 ~erR~~~l~~AR~vf~~A~~~~~~~~~~lyi~~A~lE~~~~~d~e~Ar~ife~~Lk~-~p~~~~~w~~y~~fe~~~~~~~  521 (679)
T 4e6h_A          443 TMKRIQGLAASRKIFGKCRRLKKLVTPDIYLENAYIEYHISKDTKTACKVLELGLKY-FATDGEYINKYLDFLIYVNEES  521 (679)
T ss_dssp             HHHHHHCHHHHHHHHHHHHHTGGGSCTHHHHHHHHHHHTTTSCCHHHHHHHHHHHHH-HTTCHHHHHHHHHHHHHHTCHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHhCCCHHHHHHHHHHHHHH-CCCchHHHHHHHHHHHhCCCHH
Confidence            8888899999999999988761122334444333333344 4589999999998876 4446677778888888899999


Q ss_pred             HHHHHHHHHHHhhhc
Q 012111          449 AAQNLENKMIAMKEN  463 (471)
Q Consensus       449 ~A~~~~~~m~~~~~~  463 (471)
                      .|+.+|++++...++
T Consensus       522 ~AR~lferal~~~~~  536 (679)
T 4e6h_A          522 QVKSLFESSIDKISD  536 (679)
T ss_dssp             HHHHHHHHHTTTSSS
T ss_pred             HHHHHHHHHHHhcCC
Confidence            999999999887663

>3q15_A PSP28, response regulator aspartate phosphatase H; tetratricopeptide repeat, 3-helix bundle, phosphorelay signa transduction, phosphatase; 2.19A {Bacillus subtilis}

Probab=99.41  E-value=8.8e-11  Score=107.83  Aligned_cols=226  Identities=12%  Similarity=0.007  Sum_probs=134.7

Q ss_pred             HHhcCCHHHHHHHHHHHHHCCC-CC----CHHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCC-----CHHHHHHHHH
Q 012111          195 CTKFHRFDLIEKILAEMSYLGI-EC----SAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHP-----DIFTLNSMIS  264 (471)
Q Consensus       195 ~~~~~~~~~a~~~~~~~~~~g~-~~----~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~-----~~~~~~~l~~  264 (471)
                      +...|+++.|...+++..+... .+    ...++..+...|...|+++.|...+++..+...-.+     ...+++.+..
T Consensus       111 ~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~  190 (378)
T 3q15_A          111 EFDQKEYVEAIGYYREAEKELPFVSDDIEKAEFHFKVAEAYYHMKQTHVSMYHILQALDIYQNHPLYSIRTIQSLFVIAG  190 (378)
T ss_dssp             HHHTTCHHHHHHHHHHHHTTGGGCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTSTTCHHHHHHHHHHHHH
T ss_pred             HHHHCCHHHHHHHHHHHHHHHhhCCChHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHhCCCchhhHHHHHHHHHH
Confidence            4455666666666666554310 01    134555666666666676666666666544211111     1345566666


Q ss_pred             HHHhcCCHHHHHHHHHHHHhC----CCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHh-----CCCCCCHHHHHHHHH
Q 012111          265 AYGNSGNIEKMEKWYNEFNLM----GVK-ADIQTLNILTKSYGRAGMYDKMRSVMDFMQK-----RFFFPTVVTYNIVIE  334 (471)
Q Consensus       265 ~~~~~~~~~~a~~~~~~~~~~----~~~-~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~-----~~~~~~~~~~~~li~  334 (471)
                      .|...|++++|...+++..+.    +.. ....++..+..+|...|++++|...+++..+     .... ...++..+..
T Consensus       191 ~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~-~~~~~~~la~  269 (378)
T 3q15_A          191 NYDDFKHYDKALPHLEAALELAMDIQNDRFIAISLLNIANSYDRSGDDQMAVEHFQKAAKVSREKVPDL-LPKVLFGLSW  269 (378)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHCGGG-HHHHHHHHHH
T ss_pred             HHHHhCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCChh-HHHHHHHHHH
Confidence            777777777777777665442    111 1123566677777777777777777776665     3222 2556777777


Q ss_pred             HHHhcCCHHHHHHHHHHHHHcCC---CC-CHHHHHHHHHHHHhcCC---HHHHHHHHHHHHhCCCCc-CHHHHHHHHHHH
Q 012111          335 TFGKAGHIEKMEEYFKKMKHRGM---KP-NSITYCSLVSAYSKAGL---IMKVDSILRQVENSDVIL-DTPFFNCIISAY  406 (471)
Q Consensus       335 ~~~~~g~~~~a~~~~~~m~~~~~---~p-~~~~~~~li~~~~~~g~---~~~a~~~~~~~~~~~~~~-~~~~~~~l~~~~  406 (471)
                      .+...|++++|...+++......   .+ ....+..+...+...++   +.+|...++.   .+..+ ....+..+...|
T Consensus       270 ~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~ly~~~~~~~~~~~al~~~~~---~~~~~~~~~~~~~la~~y  346 (378)
T 3q15_A          270 TLCKAGQTQKAFQFIEEGLDHITARSHKFYKELFLFLQAVYKETVDERKIHDLLSYFEK---KNLHAYIEACARSAAAVF  346 (378)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHCCTTCCSCHHHHHHHHHHHHSSSCCHHHHHHHHHHHHH---TTCHHHHHHHHHHHHHHH
T ss_pred             HHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHh---CCChhHHHHHHHHHHHHH
Confidence            88888888888888887765421   12 23345555556666677   5666666654   22222 234566778888


Q ss_pred             HhcCCHHHHHHHHHHHHh
Q 012111          407 GQAGDVEKMGELFLTMKE  424 (471)
Q Consensus       407 ~~~g~~~~a~~~~~~~~~  424 (471)
                      ...|++++|...|++..+
T Consensus       347 ~~~g~~~~A~~~~~~al~  364 (378)
T 3q15_A          347 ESSCHFEQAAAFYRKVLK  364 (378)
T ss_dssp             HHTTCHHHHHHHHHHHHH
T ss_pred             HHCCCHHHHHHHHHHHHH
Confidence            888888888888887764

>1hz4_A MALT regulatory protein; two-helix bundles, helix repeats, protein superhelix, transc activator; 1.45A {Escherichia coli} SCOP: a.118.8.2

Probab=99.41  E-value=3e-10  Score=104.05  Aligned_cols=267  Identities=10%  Similarity=0.039  Sum_probs=144.7

Q ss_pred             HHhcCCCHHHHHHHHHHHHhCCCCCCHH----HHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCC----HHHHHHHHHH
Q 012111          123 MLGKCKQPEQASLLFEVMLSDGLKPSVD----VYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPD----VYTYSILIKS  194 (471)
Q Consensus       123 ~~~~~~~~~~a~~~~~~m~~~~~~~~~~----~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~----~~~~~~ll~~  194 (471)
                      .+...|++++|...+++........+..    +++.+...+...|++++|...+++......-..+    ..++..+...
T Consensus        23 ~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~  102 (373)
T 1hz4_A           23 VAINDGNPDEAERLAKLALEELPPGWFYSRIVATSVLGEVLHCKGELTRSLALMQQTEQMARQHDVWHYALWSLIQQSEI  102 (373)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHTCCTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHCCCHHHHHHHHHHHHHcCCCCchhHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHH
Confidence            3344455555555555544432111111    3344444555555555555555554331000111    1223444555


Q ss_pred             HHhcCCHHHHHHHHHHHHHC----CCC--C-CHHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCC---CCCHHHHHHHHH
Q 012111          195 CTKFHRFDLIEKILAEMSYL----GIE--C-SAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGC---HPDIFTLNSMIS  264 (471)
Q Consensus       195 ~~~~~~~~~a~~~~~~~~~~----g~~--~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~---~~~~~~~~~l~~  264 (471)
                      +...|++++|...+++..+.    +..  | ....+..+...+...|++++|...+++..+...-   ......+..+..
T Consensus       103 ~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~la~  182 (373)
T 1hz4_A          103 LFAQGFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLWAWARLDEAEASARSGIEVLSSYQPQQQLQCLAMLIQ  182 (373)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTSCGGGGHHHHHHHHH
T ss_pred             HHHCCCHHHHHHHHHHHHHHHHHhccccCcHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHhhccCcHHHHHHHHHHHH
Confidence            55666666666666555432    211  1 2334455666666777777777777766543210   012345666667


Q ss_pred             HHHhcCCHHHHHHHHHHHHhCCCCC--CHHHHH----HHHHHHHHcCCHHHHHHHHHHHHhCCCCC---CHHHHHHHHHH
Q 012111          265 AYGNSGNIEKMEKWYNEFNLMGVKA--DIQTLN----ILTKSYGRAGMYDKMRSVMDFMQKRFFFP---TVVTYNIVIET  335 (471)
Q Consensus       265 ~~~~~~~~~~a~~~~~~~~~~~~~~--~~~~~~----~ll~~~~~~~~~~~a~~~~~~~~~~~~~~---~~~~~~~li~~  335 (471)
                      .+...|++++|...+++.......+  ......    ..+..+...|++++|...+.........+   ....+..+...
T Consensus       183 ~~~~~g~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~la~~  262 (373)
T 1hz4_A          183 CSLARGDLDNARSQLNRLENLLGNGKYHSDWISNANKVRVIYWQMTGDKAAAANWLRHTAKPEFANNHFLQGQWRNIARA  262 (373)
T ss_dssp             HHHHHTCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHSCCCCCTTCGGGHHHHHHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHHHhccCcchhHHHHHHHHHHHHHHHCCCHHHHHHHHHhCCCCCCCcchhhHHHHHHHHHH
Confidence            7777777777777777664421111  111111    22334667788888888777765543221   12245566777


Q ss_pred             HHhcCCHHHHHHHHHHHHHc----CCCCCH-HHHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 012111          336 FGKAGHIEKMEEYFKKMKHR----GMKPNS-ITYCSLVSAYSKAGLIMKVDSILRQVEN  389 (471)
Q Consensus       336 ~~~~g~~~~a~~~~~~m~~~----~~~p~~-~~~~~li~~~~~~g~~~~a~~~~~~~~~  389 (471)
                      +...|++++|...+++....    |..++. ..+..+..++...|+.++|...+++...
T Consensus       263 ~~~~g~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~al~  321 (373)
T 1hz4_A          263 QILLGEFEPAEIVLEELNENARSLRLMSDLNRNLLLLNQLYWQAGRKSDAQRVLLDALK  321 (373)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHcCCHHHHHHHHHHHHHHHHhCcchhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence            88888888888888877543    211122 2556667778888999999988887764

>4i17_A Hypothetical protein; TPR repeats protein, structural genomics, joint center for S genomics, JCSG, protein structure initiative; HET: MSE; 1.83A {Bacteroides fragilis}

Probab=99.39  E-value=9.6e-11  Score=99.22  Aligned_cols=203  Identities=12%  Similarity=0.062  Sum_probs=156.4

Q ss_pred             CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHH
Q 012111          253 HPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIV  332 (471)
Q Consensus       253 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  332 (471)
                      ..|...+......+...|++++|...|++.......++...+..+..++...|++++|...++...+.... +...+..+
T Consensus         4 ~~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~p~-~~~~~~~l   82 (228)
T 4i17_A            4 TTDPNQLKNEGNDALNAKNYAVAFEKYSEYLKLTNNQDSVTAYNCGVCADNIKKYKEAADYFDIAIKKNYN-LANAYIGK   82 (228)
T ss_dssp             CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCS-HHHHHHHH
T ss_pred             ccCHHHHHHHHHHHHHccCHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHHhhcHHHHHHHHHHHHHhCcc-hHHHHHHH
Confidence            34567888889999999999999999999988763377888888999999999999999999999886443 56678888


Q ss_pred             HHHHHhcCCHHHHHHHHHHHHHcCCCCCH-------HHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCc-CHHHHHHHHH
Q 012111          333 IETFGKAGHIEKMEEYFKKMKHRGMKPNS-------ITYCSLVSAYSKAGLIMKVDSILRQVENSDVIL-DTPFFNCIIS  404 (471)
Q Consensus       333 i~~~~~~g~~~~a~~~~~~m~~~~~~p~~-------~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~-~~~~~~~l~~  404 (471)
                      ...+...|++++|...+++..+.. +.+.       ..|..+...+...|++++|.+.++++.+.++.. +...+..+..
T Consensus        83 ~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~~l~~  161 (228)
T 4i17_A           83 SAAYRDMKNNQEYIATLTEGIKAV-PGNATIEKLYAIYYLKEGQKFQQAGNIEKAEENYKHATDVTSKKWKTDALYSLGV  161 (228)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSSCHHHHHHHHHHHHH
T ss_pred             HHHHHHcccHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHHHhHHHHHhccHHHHHHHHHHHHhcCCCcccHHHHHHHHH
Confidence            999999999999999999998863 2244       457788888899999999999999998864320 2466777777


Q ss_pred             HHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhhhcCC
Q 012111          405 AYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAYNALGMTEAAQNLENKMIAMKENSG  465 (471)
Q Consensus       405 ~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~~~  465 (471)
                      +|...|     ..+++++...+ ..+...|....  ....+.+++|...++++++..|+..
T Consensus       162 ~~~~~~-----~~~~~~a~~~~-~~~~~~~~~~~--~~~~~~~~~A~~~~~~a~~l~p~~~  214 (228)
T 4i17_A          162 LFYNNG-----ADVLRKATPLA-SSNKEKYASEK--AKADAAFKKAVDYLGEAVTLSPNRT  214 (228)
T ss_dssp             HHHHHH-----HHHHHHHGGGT-TTCHHHHHHHH--HHHHHHHHHHHHHHHHHHHHCTTCH
T ss_pred             HHHHHH-----HHHHHHHHhcc-cCCHHHHHHHH--HHHHHHHHHHHHHHHHHhhcCCCCH
Confidence            776544     34456655542 23455554443  3445678999999999999988753

>3as5_A MAMA; tetratricopeptide repeats (TPR) containing protein, TPR PROT protein-protein interactions, protein binding; 2.00A {Magnetospirillum magnetotacticum} PDB: 3as4_A 3asd_A 3asg_A 3ash_A 3as8_A 3asf_A

Probab=99.38  E-value=1.2e-10  Score=94.87  Aligned_cols=163  Identities=12%  Similarity=0.039  Sum_probs=94.1

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHH
Q 012111          258 TLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFG  337 (471)
Q Consensus       258 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~  337 (471)
                      .+..+...+...|++++|...++++.... +.+...+..+...+...|++++|...++.+.+... .+...+..+...+.
T Consensus        10 ~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~~a~~~~   87 (186)
T 3as5_A           10 YYRDKGISHAKAGRYSQAVMLLEQVYDAD-AFDVDVALHLGIAYVKTGAVDRGTELLERSLADAP-DNVKVATVLGLTYV   87 (186)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHTTTCCTT-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHHHHhC-ccChHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCC-CCHHHHHHHHHHHH
Confidence            34444455555555555555555554332 33445555555555555666666655555554422 24455555566666


Q ss_pred             hcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHH
Q 012111          338 KAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGE  417 (471)
Q Consensus       338 ~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~  417 (471)
                      ..|++++|...++++.... +.+...+..+...+...|++++|...++.+.+..+. +...+..+...+...|++++|.+
T Consensus        88 ~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~la~~~~~~~~~~~A~~  165 (186)
T 3as5_A           88 QVQKYDLAVPLLIKVAEAN-PINFNVRFRLGVALDNLGRFDEAIDSFKIALGLRPN-EGKVHRAIAFSYEQMGRHEEALP  165 (186)
T ss_dssp             HHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HhcCHHHHHHHHHHHHhcC-cHhHHHHHHHHHHHHHcCcHHHHHHHHHHHHhcCcc-chHHHHHHHHHHHHcCCHHHHHH
Confidence            6666666666666665542 334556666666666666666666666666655433 45666666666777777777777


Q ss_pred             HHHHHHh
Q 012111          418 LFLTMKE  424 (471)
Q Consensus       418 ~~~~~~~  424 (471)
                      .++++.+
T Consensus       166 ~~~~~~~  172 (186)
T 3as5_A          166 HFKKANE  172 (186)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            7666654

>4gyw_A UDP-N-acetylglucosamine--peptide N- acetylglucosaminyltransferase 110 kDa subunit...; GT-B, glycosyltransferase, glcnacylation, transferase-peptid; HET: UDP NAG; 1.70A {Homo sapiens} PDB: 3pe3_A* 3pe4_A* 4ay5_A* 4ay6_A* 3tax_A* 4gyy_A* 4gz3_A* 4gz5_A* 4gz6_A*

Probab=99.38  E-value=3.6e-11  Score=118.29  Aligned_cols=167  Identities=8%  Similarity=0.034  Sum_probs=94.2

Q ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Q 012111          291 IQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSA  370 (471)
Q Consensus       291 ~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~  370 (471)
                      ..+++.|...|.+.|++++|+..|++..+.... +...|..+..+|.+.|++++|+..|++.++.. +-+...|..+..+
T Consensus         9 a~al~nLG~~~~~~G~~~eAi~~~~kAl~l~P~-~~~a~~nLg~~l~~~g~~~eA~~~~~~Al~l~-P~~~~a~~nLg~~   86 (723)
T 4gyw_A            9 ADSLNNLANIKREQGNIEEAVRLYRKALEVFPE-FAAAHSNLASVLQQQGKLQEALMHYKEAIRIS-PTFADAYSNMGNT   86 (723)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSC-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHH
Confidence            344555555555555555555555555544222 34455555555666666666666666555542 1235555666666


Q ss_pred             HHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC-CHHHHHHHHHHHHhcCCHHH
Q 012111          371 YSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVP-DNITFATMIQAYNALGMTEA  449 (471)
Q Consensus       371 ~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~  449 (471)
                      +...|++++|.+.|++..+.++. +...|+.+..+|...|++++|++.|++..+.  .| +...+..+..++...|++++
T Consensus        87 l~~~g~~~~A~~~~~kAl~l~P~-~~~a~~~Lg~~~~~~g~~~eAi~~~~~Al~l--~P~~~~a~~~L~~~l~~~g~~~~  163 (723)
T 4gyw_A           87 LKEMQDVQGALQCYTRAIQINPA-FADAHSNLASIHKDSGNIPEAIASYRTALKL--KPDFPDAYCNLAHCLQIVCDWTD  163 (723)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CSCCHHHHHHHHHHHHHTTCCTT
T ss_pred             HHHcCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCChHHHhhhhhHHHhcccHHH
Confidence            66666666666666666555444 5556666666666666666666666666553  33 34555566666666666666


Q ss_pred             HHHHHHHHHHhhh
Q 012111          450 AQNLENKMIAMKE  462 (471)
Q Consensus       450 A~~~~~~m~~~~~  462 (471)
                      |.+.++++++..+
T Consensus       164 A~~~~~kal~l~~  176 (723)
T 4gyw_A          164 YDERMKKLVSIVA  176 (723)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCh
Confidence            6666666655544

>4gyw_A UDP-N-acetylglucosamine--peptide N- acetylglucosaminyltransferase 110 kDa subunit...; GT-B, glycosyltransferase, glcnacylation, transferase-peptid; HET: UDP NAG; 1.70A {Homo sapiens} PDB: 3pe3_A* 3pe4_A* 4ay5_A* 4ay6_A* 3tax_A* 4gyy_A* 4gz3_A* 4gz5_A* 4gz6_A*

Probab=99.35  E-value=7.1e-11  Score=116.21  Aligned_cols=164  Identities=11%  Similarity=0.008  Sum_probs=92.1

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHH
Q 012111          256 IFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIET  335 (471)
Q Consensus       256 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~  335 (471)
                      ...|+.|..++.+.|++++|++.|++..+.. +-+..++..+..+|.+.|++++|...|++..+.... +...|..+..+
T Consensus         9 a~al~nLG~~~~~~G~~~eAi~~~~kAl~l~-P~~~~a~~nLg~~l~~~g~~~eA~~~~~~Al~l~P~-~~~a~~nLg~~   86 (723)
T 4gyw_A            9 ADSLNNLANIKREQGNIEEAVRLYRKALEVF-PEFAAAHSNLASVLQQQGKLQEALMHYKEAIRISPT-FADAYSNMGNT   86 (723)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHH
Confidence            3445555555555555555555555554432 333445555555555555555555555555544222 34455556666


Q ss_pred             HHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHH
Q 012111          336 FGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKM  415 (471)
Q Consensus       336 ~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a  415 (471)
                      |...|++++|++.|++..+.. +-+...|..+..++...|++++|++.|++..+.++. +...+..+..++...|++++|
T Consensus        87 l~~~g~~~~A~~~~~kAl~l~-P~~~~a~~~Lg~~~~~~g~~~eAi~~~~~Al~l~P~-~~~a~~~L~~~l~~~g~~~~A  164 (723)
T 4gyw_A           87 LKEMQDVQGALQCYTRAIQIN-PAFADAHSNLASIHKDSGNIPEAIASYRTALKLKPD-FPDAYCNLAHCLQIVCDWTDY  164 (723)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSC-CHHHHHHHHHHHHHTTCCTTH
T ss_pred             HHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-ChHHHhhhhhHHHhcccHHHH
Confidence            666666666666666665542 224556666666666666666666666666655544 555666666666666666666


Q ss_pred             HHHHHHHH
Q 012111          416 GELFLTMK  423 (471)
Q Consensus       416 ~~~~~~~~  423 (471)
                      .+.++++.
T Consensus       165 ~~~~~kal  172 (723)
T 4gyw_A          165 DERMKKLV  172 (723)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            66665554

>3edt_B KLC 2, kinesin light chain 2; superhelical, structural genomics, structural genomics conso SGC, microtubule, motor protein, phosphoprotein; 2.70A {Homo sapiens} PDB: 3ceq_A

Probab=99.30  E-value=3.7e-11  Score=105.24  Aligned_cols=229  Identities=17%  Similarity=0.163  Sum_probs=157.4

Q ss_pred             HccCCHHHHHHHHHHHHHcC------CCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhC------CC-CCCHHHHHHH
Q 012111          231 GKAKKFEEMESSFSAMVESG------GCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLM------GV-KADIQTLNIL  297 (471)
Q Consensus       231 ~~~~~~~~a~~~~~~~~~~~------~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~------~~-~~~~~~~~~l  297 (471)
                      ...|++++|+..|++..+..      ..+....++..+...+...|++++|...++++...      +- +....++..+
T Consensus        12 ~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~l   91 (283)
T 3edt_B           12 SGLVPRGSAVPLCKQALEDLEKTSGHDHPDVATMLNILALVYRDQNKYKEAAHLLNDALAIREKTLGKDHPAVAATLNNL   91 (283)
T ss_dssp             -CCSCSSSHHHHHHHHHHHHHHHHCSSSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTCHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHcCCcchHHHHHHHHH
Confidence            45678788887777765421      11224567888999999999999999999998754      21 2345678889


Q ss_pred             HHHHHHcCCHHHHHHHHHHHHhCC------C-CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc------CCCC-CHHH
Q 012111          298 TKSYGRAGMYDKMRSVMDFMQKRF------F-FPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHR------GMKP-NSIT  363 (471)
Q Consensus       298 l~~~~~~~~~~~a~~~~~~~~~~~------~-~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~------~~~p-~~~~  363 (471)
                      ...|...|++++|...+.+..+..      . +.....+..+...+...|++++|...++++.+.      +-.| ...+
T Consensus        92 ~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~  171 (283)
T 3edt_B           92 AVLYGKRGKYKEAEPLCKRALEIREKVLGKFHPDVAKQLNNLALLCQNQGKAEEVEYYYRRALEIYATRLGPDDPNVAKT  171 (283)
T ss_dssp             HHHHHTTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHSCTTCHHHHHH
T ss_pred             HHHHHHhccHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHH
Confidence            999999999999999999887641      1 223557888889999999999999999998865      1123 3567


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHhC-------CCCc-CHHHHHHHHHHHHhcCC------HHHHHHHHHHHHhCCCCC
Q 012111          364 YCSLVSAYSKAGLIMKVDSILRQVENS-------DVIL-DTPFFNCIISAYGQAGD------VEKMGELFLTMKERHCVP  429 (471)
Q Consensus       364 ~~~li~~~~~~g~~~~a~~~~~~~~~~-------~~~~-~~~~~~~l~~~~~~~g~------~~~a~~~~~~~~~~~~~p  429 (471)
                      +..+...+...|++++|..+++++.+.       ...+ ....+..+...+...+.      +..+...++..... ...
T Consensus       172 ~~~la~~~~~~g~~~~A~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~  250 (283)
T 3edt_B          172 KNNLASCYLKQGKYQDAETLYKEILTRAHEKEFGSVNGDNKPIWMHAEEREESKDKRRDSAPYGEYGSWYKACKVD-SPT  250 (283)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHSSSCCSSCCCHHHHHHHHHHTTCCCCC------------CCCCC-CHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCcchhHHHHHHHHHHHHhcCCchhHHHHHHHHHHHHHhcCCC-CHH
Confidence            888999999999999999999988753       1111 22333333333333333      22222222222111 112


Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHh
Q 012111          430 DNITFATMIQAYNALGMTEAAQNLENKMIAM  460 (471)
Q Consensus       430 ~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~  460 (471)
                      ...++..+...|...|++++|..+++++++.
T Consensus       251 ~~~~~~~la~~~~~~g~~~~A~~~~~~al~~  281 (283)
T 3edt_B          251 VNTTLRSLGALYRRQGKLEAAHTLEDCASRN  281 (283)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            3456778889999999999999999998864

>4i17_A Hypothetical protein; TPR repeats protein, structural genomics, joint center for S genomics, JCSG, protein structure initiative; HET: MSE; 1.83A {Bacteroides fragilis}

Probab=99.29  E-value=1e-09  Score=92.84  Aligned_cols=193  Identities=12%  Similarity=0.044  Sum_probs=97.7

Q ss_pred             HHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHH
Q 012111          220 AVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTK  299 (471)
Q Consensus       220 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~  299 (471)
                      +..+......+...|++++|...|++..+.. ..++...+..+..++...|++++|...+++..... +.+...+..+..
T Consensus         7 ~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l~~   84 (228)
T 4i17_A            7 PNQLKNEGNDALNAKNYAVAFEKYSEYLKLT-NNQDSVTAYNCGVCADNIKKYKEAADYFDIAIKKN-YNLANAYIGKSA   84 (228)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT-TTCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTT-CSHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHccCHHHHHHHHHHHHhcc-CCCCcHHHHHHHHHHHHhhcHHHHHHHHHHHHHhC-cchHHHHHHHHH
Confidence            3444455555555555555555555554442 11344444445555555555555555555555432 223444555555


Q ss_pred             HHHHcCCHHHHHHHHHHHHhCCCCCCH-------HHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCC---HHHHHHHHH
Q 012111          300 SYGRAGMYDKMRSVMDFMQKRFFFPTV-------VTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPN---SITYCSLVS  369 (471)
Q Consensus       300 ~~~~~~~~~~a~~~~~~~~~~~~~~~~-------~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~---~~~~~~li~  369 (471)
                      ++...|++++|...++...+.... +.       ..|..+...+...|++++|...|++..+.  .|+   ...+..+..
T Consensus        85 ~~~~~~~~~~A~~~~~~al~~~p~-~~~~~~~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~~~l~~  161 (228)
T 4i17_A           85 AYRDMKNNQEYIATLTEGIKAVPG-NATIEKLYAIYYLKEGQKFQQAGNIEKAEENYKHATDV--TSKKWKTDALYSLGV  161 (228)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHSTT-CHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHTTS--SCHHHHHHHHHHHHH
T ss_pred             HHHHcccHHHHHHHHHHHHHHCCC-cHHHHHHHHHHHHHHhHHHHHhccHHHHHHHHHHHHhc--CCCcccHHHHHHHHH
Confidence            555555555555555555543221 22       23555555566666777777777666654  333   344555555


Q ss_pred             HHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhC
Q 012111          370 AYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKER  425 (471)
Q Consensus       370 ~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~  425 (471)
                      ++...|     ..+++.+...+.. +...|....  ....+.+++|+..|++..+.
T Consensus       162 ~~~~~~-----~~~~~~a~~~~~~-~~~~~~~~~--~~~~~~~~~A~~~~~~a~~l  209 (228)
T 4i17_A          162 LFYNNG-----ADVLRKATPLASS-NKEKYASEK--AKADAAFKKAVDYLGEAVTL  209 (228)
T ss_dssp             HHHHHH-----HHHHHHHGGGTTT-CHHHHHHHH--HHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHH-----HHHHHHHHhcccC-CHHHHHHHH--HHHHHHHHHHHHHHHHHhhc
Confidence            554332     3334444443322 333333332  22345577777777777763

>3edt_B KLC 2, kinesin light chain 2; superhelical, structural genomics, structural genomics conso SGC, microtubule, motor protein, phosphoprotein; 2.70A {Homo sapiens} PDB: 3ceq_A

Probab=99.27  E-value=9.7e-11  Score=102.54  Aligned_cols=135  Identities=15%  Similarity=0.136  Sum_probs=69.9

Q ss_pred             ChhHHHHHHHHHhcCCCHHHHHHHHHHHHhC------CC-CCCHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCC-----C
Q 012111          113 RCQTFTKLMVMLGKCKQPEQASLLFEVMLSD------GL-KPSVDVYTALVSAYGQSGLLDEAFSTINDMKSVS-----D  180 (471)
Q Consensus       113 ~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~------~~-~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~-----~  180 (471)
                      ...++..+...+...|++++|...+++..+.      +. +....++..+..++...|++++|++.|++.....     .
T Consensus        42 ~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~  121 (283)
T 3edt_B           42 VATMLNILALVYRDQNKYKEAAHLLNDALAIREKTLGKDHPAVAATLNNLAVLYGKRGKYKEAEPLCKRALEIREKVLGK  121 (283)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHCT
T ss_pred             HHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHcCCcchHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHHcCC
Confidence            3456666777777777777777777766543      11 1123456666666666666666666666655420     0


Q ss_pred             -CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHC------C-CCCCHHHHHHHHHHHHccCCHHHHHHHHHHHH
Q 012111          181 -CKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYL------G-IECSAVTYNTIIDGYGKAKKFEEMESSFSAMV  247 (471)
Q Consensus       181 -~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~------g-~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  247 (471)
                       .+....++..+...+...|++++|..++++..+.      + .+....++..+...|...|++++|...++++.
T Consensus       122 ~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~l  196 (283)
T 3edt_B          122 FHPDVAKQLNNLALLCQNQGKAEEVEYYYRRALEIYATRLGPDDPNVAKTKNNLASCYLKQGKYQDAETLYKEIL  196 (283)
T ss_dssp             TCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHSCTTCHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             CChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence             0112334444555555555555555555554432      0 01113344444444445555555555544443

>2fo7_A Synthetic consensus TPR protein; tetratricopeptide repeat, consensus protein, superhelix, de novo protein; 2.30A {Synthetic} SCOP: k.38.1.1 PDB: 2hyz_A

Probab=99.26  E-value=8.3e-10  Score=84.46  Aligned_cols=133  Identities=17%  Similarity=0.187  Sum_probs=102.9

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHH
Q 012111          328 TYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYG  407 (471)
Q Consensus       328 ~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  407 (471)
                      .|..+...+...|++++|..+++++.+.. +.+...+..+...+...|++++|..+++++.+.++. +...+..+...+.
T Consensus         3 ~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~l~~~~~   80 (136)
T 2fo7_A            3 AWYNLGNAYYKQGDYDEAIEYYQKALELD-PRSAEAWYNLGNAYYKQGDYDEAIEYYQKALELDPR-SAEAWYNLGNAYY   80 (136)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCcHHHHHHHHHHHHHcC-CcchhHHHHHHHHHHHhcCHHHHHHHHHHHHHHCCC-chHHHHHHHHHHH
Confidence            45566777777888888888888877653 335667777788888888888888888887776544 5677778888888


Q ss_pred             hcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhhhc
Q 012111          408 QAGDVEKMGELFLTMKERHCVPDNITFATMIQAYNALGMTEAAQNLENKMIAMKEN  463 (471)
Q Consensus       408 ~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~  463 (471)
                      ..|++++|.++++++.+.. +.+...+..+...+...|++++|...++++++..|.
T Consensus        81 ~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~  135 (136)
T 2fo7_A           81 KQGDYDEAIEYYQKALELD-PRSAEAWYNLGNAYYKQGDYDEAIEYYQKALELDPR  135 (136)
T ss_dssp             TTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHSTT
T ss_pred             HhcCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHHccHHHHHHHHHHHHccCCC
Confidence            8888888888888887752 335777778888888899999999999888887764

>1qqe_A Vesicular transport protein SEC17; helix-turn-helix TPR-like repeat, protein transport; 2.90A {Saccharomyces cerevisiae} SCOP: a.118.8.1

Probab=99.21  E-value=5e-10  Score=98.68  Aligned_cols=197  Identities=9%  Similarity=-0.008  Sum_probs=122.3

Q ss_pred             HHHhcCCHHHHHHHHHHHHhC----CCCCC-HHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCC---CC--CHHHHHHHHH
Q 012111          265 AYGNSGNIEKMEKWYNEFNLM----GVKAD-IQTLNILTKSYGRAGMYDKMRSVMDFMQKRFF---FP--TVVTYNIVIE  334 (471)
Q Consensus       265 ~~~~~~~~~~a~~~~~~~~~~----~~~~~-~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~---~~--~~~~~~~li~  334 (471)
                      .|...|++++|...|.+....    +-+++ ..+|+.+..+|...|++++|...+++..+...   .+  -..++..+..
T Consensus        46 ~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~~~~g~~~~~a~~~~~lg~  125 (292)
T 1qqe_A           46 IYRLRKELNLAGDSFLKAADYQKKAGNEDEAGNTYVEAYKCFKSGGNSVNAVDSLENAIQIFTHRGQFRRGANFKFELGE  125 (292)
T ss_dssp             HHHHTTCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            455667777777777665432    21111 34666677777777777777777766554211   00  1245677777


Q ss_pred             HHHhc-CCHHHHHHHHHHHHHcCCC-CC----HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCH------HHHHHH
Q 012111          335 TFGKA-GHIEKMEEYFKKMKHRGMK-PN----SITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDT------PFFNCI  402 (471)
Q Consensus       335 ~~~~~-g~~~~a~~~~~~m~~~~~~-p~----~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~------~~~~~l  402 (471)
                      .|... |++++|+..|++..+.... .+    ..++..+...+...|++++|...|+++.+..+....      ..|..+
T Consensus       126 ~~~~~lg~~~~A~~~~~~Al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~l  205 (292)
T 1qqe_A          126 ILENDLHDYAKAIDCYELAGEWYAQDQSVALSNKCFIKCADLKALDGQYIEASDIYSKLIKSSMGNRLSQWSLKDYFLKK  205 (292)
T ss_dssp             HHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTSSCTTTGGGHHHHHHHH
T ss_pred             HHHHhhcCHHHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHH
Confidence            77775 8888888888877653110 01    345777788888888888888888888776544222      146667


Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhCCCCCCHH------HHHHHHHHHH--hcCCHHHHHHHHHHHHHhhhc
Q 012111          403 ISAYGQAGDVEKMGELFLTMKERHCVPDNI------TFATMIQAYN--ALGMTEAAQNLENKMIAMKEN  463 (471)
Q Consensus       403 ~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~------~~~~l~~~~~--~~g~~~~A~~~~~~m~~~~~~  463 (471)
                      ..++...|++++|+..|++..+.  .|+..      .+..++.++.  ..+++++|...+++++..+|.
T Consensus       206 g~~~~~~g~~~~A~~~~~~al~l--~p~~~~~~~~~~l~~l~~~~~~~~~~~~~~A~~~~~~~~~l~~~  272 (292)
T 1qqe_A          206 GLCQLAATDAVAAARTLQEGQSE--DPNFADSRESNFLKSLIDAVNEGDSEQLSEHCKEFDNFMRLDKW  272 (292)
T ss_dssp             HHHHHHTTCHHHHHHHHHGGGCC-----------HHHHHHHHHHHHTTCTTTHHHHHHHHTTSSCCCHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHhh--CCCCCCcHHHHHHHHHHHHHHcCCHHHHHHHHHHhccCCccHHH
Confidence            77788888888888888887753  33321      2334455554  346688888877776655553

>3mv2_B Coatomer subunit epsilon; vesicular membrane coat COAT protein complex I, protein TRAN; 2.90A {Saccharomyces cerevisiae} PDB: 3mv3_B

Probab=99.21  E-value=7e-09  Score=89.66  Aligned_cols=60  Identities=10%  Similarity=-0.042  Sum_probs=26.0

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHhCCC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Q 012111          260 NSMISAYGNSGNIEKMEKWYNEFNLMGV-KADIQTLNILTKSYGRAGMYDKMRSVMDFMQK  319 (471)
Q Consensus       260 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~  319 (471)
                      ..+..++...|++++|++++.+.+..+- .-+...+..++..+.+.|+.+.|.+.++.|.+
T Consensus       104 ~~la~i~~~~g~~eeAL~~l~~~i~~~~~~~~lea~~l~vqi~L~~~r~d~A~k~l~~~~~  164 (310)
T 3mv2_B          104 YLLATAQAILGDLDKSLETCVEGIDNDEAEGTTELLLLAIEVALLNNNVSTASTIFDNYTN  164 (310)
T ss_dssp             HHHHHHHHHHTCHHHHHHHHHHHHTSSCSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHhccCCCcCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHh
Confidence            3444444444444444444444433221 12333444444444444444444444444443

>3mv2_B Coatomer subunit epsilon; vesicular membrane coat COAT protein complex I, protein TRAN; 2.90A {Saccharomyces cerevisiae} PDB: 3mv3_B

Probab=99.21  E-value=6.2e-09  Score=89.97  Aligned_cols=243  Identities=7%  Similarity=-0.053  Sum_probs=167.8

Q ss_pred             hcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHH
Q 012111          197 KFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKME  276 (471)
Q Consensus       197 ~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~  276 (471)
                      -.|.+..++.-.   .+............+.++|...|++....          .-.|....+..+...+ ..+    |+
T Consensus        25 y~G~yq~~i~e~---~~~~~~~~~~~~~~~~Rs~iAlg~~~~~~----------~~~~~~~a~~~la~~~-~~~----a~   86 (310)
T 3mv2_B           25 YTGNFVQCLQEI---EKFSKVTDNTLLFYKAKTLLALGQYQSQD----------PTSKLGKVLDLYVQFL-DTK----NI   86 (310)
T ss_dssp             TTTCHHHHTHHH---HTSSCCCCHHHHHHHHHHHHHTTCCCCCC----------SSSTTHHHHHHHHHHH-TTT----CC
T ss_pred             HhhHHHHHHHHH---HhcCccchHHHHHHHHHHHHHcCCCccCC----------CCCHHHHHHHHHHHHh-ccc----HH
Confidence            346666666522   22211222334444567777777765310          1234444444444433 322    67


Q ss_pred             HHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCC-CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 012111          277 KWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFF-FPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHR  355 (471)
Q Consensus       277 ~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  355 (471)
                      ..+++....+ .++..++..+..++...|++++|++++......+. .-+...+..++..+.+.|+.+.|.+.+++|.+.
T Consensus        87 ~~l~~l~~~~-~~~~~~~~~la~i~~~~g~~eeAL~~l~~~i~~~~~~~~lea~~l~vqi~L~~~r~d~A~k~l~~~~~~  165 (310)
T 3mv2_B           87 EELENLLKDK-QNSPYELYLLATAQAILGDLDKSLETCVEGIDNDEAEGTTELLLLAIEVALLNNNVSTASTIFDNYTNA  165 (310)
T ss_dssp             HHHHHTTTTS-CCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTSSCSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhcC-CCCcHHHHHHHHHHHHcCCHHHHHHHHHHHhccCCCcCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc
Confidence            8888877655 56667777889999999999999999999877654 235678888899999999999999999999885


Q ss_pred             CCCC-----CHHHHHHHHHH--HHhcC--CHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhC-
Q 012111          356 GMKP-----NSITYCSLVSA--YSKAG--LIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKER-  425 (471)
Q Consensus       356 ~~~p-----~~~~~~~li~~--~~~~g--~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~-  425 (471)
                        .|     +..+...++.+  ....|  +.++|..+|+++.+..  |+...-..++.++.+.|++++|.+.++.+.+. 
T Consensus       166 --~~d~~~~~d~~l~~Laea~v~l~~g~~~~q~A~~~f~El~~~~--p~~~~~~lLln~~~~~g~~~eAe~~L~~l~~~~  241 (310)
T 3mv2_B          166 --IEDTVSGDNEMILNLAESYIKFATNKETATSNFYYYEELSQTF--PTWKTQLGLLNLHLQQRNIAEAQGIVELLLSDY  241 (310)
T ss_dssp             --SCHHHHHHHHHHHHHHHHHHHHHHTCSTTTHHHHHHHHHHTTS--CSHHHHHHHHHHHHHHTCHHHHHHHHHHHHSHH
T ss_pred             --CccccccchHHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHhC--CCcccHHHHHHHHHHcCCHHHHHHHHHHHHHhc
Confidence              56     35666666666  33334  8999999999997764  34233344444899999999999999976642 


Q ss_pred             ----CC----CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhhhcC
Q 012111          426 ----HC----VPDNITFATMIQAYNALGMTEAAQNLENKMIAMKENS  464 (471)
Q Consensus       426 ----~~----~p~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~~  464 (471)
                          +.    +-|+.++..+|......|+  +|.++++++.+..|+.
T Consensus       242 p~~~~k~~~~p~~~~~LaN~i~l~~~lgk--~a~~l~~qL~~~~P~h  286 (310)
T 3mv2_B          242 YSVEQKENAVLYKPTFLANQITLALMQGL--DTEDLTNQLVKLDHEH  286 (310)
T ss_dssp             HHTTTCHHHHSSHHHHHHHHHHHHHHTTC--TTHHHHHHHHHTTCCC
T ss_pred             ccccccccCCCCCHHHHHHHHHHHHHhCh--HHHHHHHHHHHhCCCC
Confidence                01    3356677677777777887  8999999999988865

>3qky_A Outer membrane assembly lipoprotein YFIO; membrane protein; 2.15A {Rhodothermus marinus}

Probab=99.17  E-value=3.7e-09  Score=91.46  Aligned_cols=188  Identities=14%  Similarity=0.127  Sum_probs=114.4

Q ss_pred             CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCC---HHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCC-CC-HHH
Q 012111          254 PDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKAD---IQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFF-PT-VVT  328 (471)
Q Consensus       254 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~---~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~-~~-~~~  328 (471)
                      .+...+..+...+.+.|++++|...|+++.... +.+   ...+..+..+|.+.|++++|...|+.+.+..+. |. ...
T Consensus        13 ~~~~~~~~~a~~~~~~g~~~~A~~~~~~~l~~~-p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a   91 (261)
T 3qky_A           13 SSPQEAFERAMEFYNQGKYDRAIEYFKAVFTYG-RTHEWAADAQFYLARAYYQNKEYLLAASEYERFIQIYQIDPRVPQA   91 (261)
T ss_dssp             SSHHHHHHHHHHHHHTTCHHHHHHHHHHHGGGC-SCSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTTHHHH
T ss_pred             CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhC-CCCcchHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHCCCCchhHHH
Confidence            345666667777778888888888888877653 223   566677777777888888888888777765321 12 345


Q ss_pred             HHHHHHHHHh--------cCCHHHHHHHHHHHHHcCCCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHH
Q 012111          329 YNIVIETFGK--------AGHIEKMEEYFKKMKHRGMKPN-SITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFF  399 (471)
Q Consensus       329 ~~~li~~~~~--------~g~~~~a~~~~~~m~~~~~~p~-~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~  399 (471)
                      +..+..++..        .|++++|...|+++.+..  |+ ......+..              +..+...    -...+
T Consensus        92 ~~~lg~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~--p~~~~~~~a~~~--------------~~~~~~~----~~~~~  151 (261)
T 3qky_A           92 EYERAMCYYKLSPPYELDQTDTRKAIEAFQLFIDRY--PNHELVDDATQK--------------IRELRAK----LARKQ  151 (261)
T ss_dssp             HHHHHHHHHHHCCCTTSCCHHHHHHHHHHHHHHHHC--TTCTTHHHHHHH--------------HHHHHHH----HHHHH
T ss_pred             HHHHHHHHHHhcccccccchhHHHHHHHHHHHHHHC--cCchhHHHHHHH--------------HHHHHHH----HHHHH
Confidence            5566666666        777777777777777652  32 112211100              0000000    01113


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHhCCCCCC----HHHHHHHHHHHHhc----------CCHHHHHHHHHHHHHhhhcC
Q 012111          400 NCIISAYGQAGDVEKMGELFLTMKERHCVPD----NITFATMIQAYNAL----------GMTEAAQNLENKMIAMKENS  464 (471)
Q Consensus       400 ~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~----~~~~~~l~~~~~~~----------g~~~~A~~~~~~m~~~~~~~  464 (471)
                      ..+...|...|++++|+..|+++.+.  .|+    ...+..+..+|...          |++++|...++++++..|+.
T Consensus       152 ~~la~~~~~~g~~~~A~~~~~~~l~~--~p~~~~~~~a~~~l~~~~~~~g~~~~~~~~~~~~~~A~~~~~~~~~~~p~~  228 (261)
T 3qky_A          152 YEAARLYERRELYEAAAVTYEAVFDA--YPDTPWADDALVGAMRAYIAYAEQSVRARQPERYRRAVELYERLLQIFPDS  228 (261)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHH--CTTSTTHHHHHHHHHHHHHHHHHTSCGGGHHHHHHHHHHHHHHHHHHCTTC
T ss_pred             HHHHHHHHHccCHHHHHHHHHHHHHH--CCCCchHHHHHHHHHHHHHHhcccchhhcccchHHHHHHHHHHHHHHCCCC
Confidence            45566677777777777777777664  233    34555666666655          77777777777777777654

>2uy1_A Cleavage stimulation factor 77; RNA-binding protein; 2.0A {Encephalitozoon cuniculi} PDB: 2uy1_B

Probab=99.15  E-value=3.5e-07  Score=86.30  Aligned_cols=347  Identities=12%  Similarity=0.002  Sum_probs=222.2

Q ss_pred             hhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCC-HHHHHHHHHHHHhC-CC-CCCHHHHHHHHHHHH----hcC
Q 012111           91 QKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQ-PEQASLLFEVMLSD-GL-KPSVDVYTALVSAYG----QSG  163 (471)
Q Consensus        91 ~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~-~~~a~~~~~~m~~~-~~-~~~~~~~~~li~~~~----~~~  163 (471)
                      .|+++.+.++|+.....   .|+...|...+....+.+. .+....+|+..... |. ..+...|...+..+.    ..+
T Consensus        27 ~~~~e~~~~iferal~~---~ps~~LW~~Y~~f~~~~~~~~~~i~~~fe~al~~vg~d~~s~~iW~~Yi~f~~~~~~~~~  103 (493)
T 2uy1_A           27 SKDYRSLESLFGRCLKK---SYNLDLWMLYIEYVRKVSQKKFKLYEVYEFTLGQFENYWDSYGLYKEYIEEEGKIEDEQT  103 (493)
T ss_dssp             TTCHHHHHHHHHHHSTT---CCCHHHHHHHHHHHHHHC----CTHHHHHHHHHHSTTCTTCHHHHHHHHHHTSSCSSHHH
T ss_pred             CCCHHHHHHHHHHHhcc---CCCHHHHHHHHHHHHHhCchHHHHHHHHHHHHHHcCCCcccHHHHHHHHHHHHhchhhhH
Confidence            38899999999999985   4699999888888777663 45677788877654 43 337788888887654    246


Q ss_pred             CHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHh-------------cCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHH
Q 012111          164 LLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTK-------------FHRFDLIEKILAEMSYLGIECSAVTYNTIIDGY  230 (471)
Q Consensus       164 ~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~-------------~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~  230 (471)
                      +.+.+..+|++... .+...-...|......-..             .+.+..|..+++.+...--..+...|...+..-
T Consensus       104 ~~~~vR~iy~rAL~-~P~~~~~~lw~~Y~~fE~~~~~~~~~~~~~~~~~~y~~ar~~y~~~~~~~~~~s~~~W~~y~~~E  182 (493)
T 2uy1_A          104 RIEKIRNGYMRALQ-TPMGSLSELWKDFENFELELNKITGKKIVGDTLPIFQSSFQRYQQIQPLIRGWSVKNAARLIDLE  182 (493)
T ss_dssp             HHHHHHHHHHHHHT-SCCTTHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHh-ChhhhHHHHHHHHHHHHHHhccccHHHHHHHHhHHHHHHHHHHHHHHHHHhhccHHHHHHHHHHH
Confidence            78889999999987 2222122233322221111             112233444444443210011344565555543


Q ss_pred             HccC--C-----HHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHH
Q 012111          231 GKAK--K-----FEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGR  303 (471)
Q Consensus       231 ~~~~--~-----~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~  303 (471)
                      ...+  -     .+.+..+|+++....  +.+...|...+..+.+.|+.+.|..++++....  +.+...+.    .|..
T Consensus       183 ~~~~~~~~~~~~~~Rv~~~ye~al~~~--p~~~~lW~~ya~~~~~~~~~~~ar~i~erAi~~--P~~~~l~~----~y~~  254 (493)
T 2uy1_A          183 MENGMKLGGRPHESRMHFIHNYILDSF--YYAEEVYFFYSEYLIGIGQKEKAKKVVERGIEM--SDGMFLSL----YYGL  254 (493)
T ss_dssp             HTCTTCCCHHHHHHHHHHHHHHHHHHT--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CCSSHHHH----HHHH
T ss_pred             hcCCccCcchhhHHHHHHHHHHHHHcC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhC--CCcHHHHH----HHHh
Confidence            3221  1     345678899988763  556778888888889999999999999999876  33332222    2332


Q ss_pred             cCCHHHHHHHHHHHHhCC---------C---CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Q 012111          304 AGMYDKMRSVMDFMQKRF---------F---FPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAY  371 (471)
Q Consensus       304 ~~~~~~a~~~~~~~~~~~---------~---~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~  371 (471)
                      ..+.++.   ++.+.+.-         .   ......|...+....+.++.+.|..+|++. .. ...+...|...+..-
T Consensus       255 ~~e~~~~---~~~l~~~~~~~~~~~~~~~~~~~~~~lw~~y~~~~~r~~~~~~AR~i~~~A-~~-~~~~~~v~i~~A~lE  329 (493)
T 2uy1_A          255 VMDEEAV---YGDLKRKYSMGEAESAEKVFSKELDLLRINHLNYVLKKRGLELFRKLFIEL-GN-EGVGPHVFIYCAFIE  329 (493)
T ss_dssp             HTTCTHH---HHHHHHHTC----------CHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHH-TT-SCCCHHHHHHHHHHH
T ss_pred             hcchhHH---HHHHHHHHHhhccchhhhhcccccHHHHHHHHHHHHHcCCHHHHHHHHHHh-hC-CCCChHHHHHHHHHH
Confidence            2222222   22222210         0   011245666677777788899999999999 32 123455554333332


Q ss_pred             Hhc-CCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHH
Q 012111          372 SKA-GLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAYNALGMTEAA  450 (471)
Q Consensus       372 ~~~-g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A  450 (471)
                      ... ++.+.|..+|+...+..+. +...+...+......|+.+.|..+|+++.     .....|...+..-...|+.+.+
T Consensus       330 ~~~~~d~~~ar~ife~al~~~~~-~~~~~~~yid~e~~~~~~~~aR~l~er~~-----k~~~lw~~~~~fE~~~G~~~~~  403 (493)
T 2uy1_A          330 YYATGSRATPYNIFSSGLLKHPD-STLLKEEFFLFLLRIGDEENARALFKRLE-----KTSRMWDSMIEYEFMVGSMELF  403 (493)
T ss_dssp             HHHHCCSHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHTCHHHHHHHHHHSC-----CBHHHHHHHHHHHHHHSCHHHH
T ss_pred             HHHCCChHHHHHHHHHHHHHCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHH-----HHHHHHHHHHHHHHHCCCHHHH
Confidence            233 3699999999998875433 45566777888888999999999999983     2577888888877888999999


Q ss_pred             HHHHHHHHHh
Q 012111          451 QNLENKMIAM  460 (471)
Q Consensus       451 ~~~~~~m~~~  460 (471)
                      .++++++...
T Consensus       404 r~v~~~~~~~  413 (493)
T 2uy1_A          404 RELVDQKMDA  413 (493)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            9999988863

>3urz_A Uncharacterized protein; tetratricopeptide repeats (TPR) containing protein, structur genomics, joint center for structural genomics, JCSG; HET: PG4; 2.19A {Bacteroides ovatus}

Probab=99.13  E-value=2.8e-09  Score=88.64  Aligned_cols=96  Identities=17%  Similarity=0.195  Sum_probs=56.4

Q ss_pred             hHHHHHHHHHHHhhcHHHHHHHHHHhhhccCccCChhHHHH----------------HHHHHhcCCCHHHHHHHHHHHHh
Q 012111           79 KPVLEALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTK----------------LMVMLGKCKQPEQASLLFEVMLS  142 (471)
Q Consensus        79 ~~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~----------------l~~~~~~~~~~~~a~~~~~~m~~  142 (471)
                      +.+......+...|++++|+..|+.+.+..  |.+...+..                +..++.+.|++++|...|+...+
T Consensus         5 ~~~~~~g~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~   82 (208)
T 3urz_A            5 DEMLQKVSAAIEAGQNGQAVSYFRQTIALN--IDRTEMYYWTNVDKNSEISSKLATELALAYKKNRNYDKAYLFYKELLQ   82 (208)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--HHHHHHHHHHHSCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHhC--CCChHHHHHhhhcchhhhhHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            344555566778999999999999998864  444555555                45555555555555555555544


Q ss_pred             CCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHhhc
Q 012111          143 DGLKPSVDVYTALVSAYGQSGLLDEAFSTINDMKS  177 (471)
Q Consensus       143 ~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~  177 (471)
                      .... +...+..+..++...|++++|+..|++..+
T Consensus        83 ~~p~-~~~~~~~lg~~~~~~g~~~~A~~~~~~al~  116 (208)
T 3urz_A           83 KAPN-NVDCLEACAEMQVCRGQEKDALRMYEKILQ  116 (208)
T ss_dssp             HCTT-CHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            4322 444555555555555555555555555544

>1qqe_A Vesicular transport protein SEC17; helix-turn-helix TPR-like repeat, protein transport; 2.90A {Saccharomyces cerevisiae} SCOP: a.118.8.1

Probab=99.13  E-value=2.8e-09  Score=93.83  Aligned_cols=210  Identities=10%  Similarity=0.063  Sum_probs=148.2

Q ss_pred             CHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHcC---CCCC-CHHHHHHHHHHHHhcCCHHHH
Q 012111          200 RFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESG---GCHP-DIFTLNSMISAYGNSGNIEKM  275 (471)
Q Consensus       200 ~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~---~~~~-~~~~~~~l~~~~~~~~~~~~a  275 (471)
                      ++++|...+++.               ...|...|++++|.+.|.+..+..   +..+ ...+|+.+..+|...|++++|
T Consensus        32 ~~~~A~~~~~~a---------------~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A   96 (292)
T 1qqe_A           32 KFEEAADLCVQA---------------ATIYRLRKELNLAGDSFLKAADYQKKAGNEDEAGNTYVEAYKCFKSGGNSVNA   96 (292)
T ss_dssp             HHHHHHHHHHHH---------------HHHHHHTTCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHH
T ss_pred             cHHHHHHHHHHH---------------HHHHHHcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHCCCHHHH
Confidence            477777777766               345677889999998888776531   1111 145788888899999999999


Q ss_pred             HHHHHHHHhCCC---CC--CHHHHHHHHHHHHHc-CCHHHHHHHHHHHHhCCCCC-C----HHHHHHHHHHHHhcCCHHH
Q 012111          276 EKWYNEFNLMGV---KA--DIQTLNILTKSYGRA-GMYDKMRSVMDFMQKRFFFP-T----VVTYNIVIETFGKAGHIEK  344 (471)
Q Consensus       276 ~~~~~~~~~~~~---~~--~~~~~~~ll~~~~~~-~~~~~a~~~~~~~~~~~~~~-~----~~~~~~li~~~~~~g~~~~  344 (471)
                      +..+++......   .+  ...++..+..+|... |++++|...|++..+..... +    ..++..+...+...|++++
T Consensus        97 ~~~~~~Al~l~~~~g~~~~~a~~~~~lg~~~~~~lg~~~~A~~~~~~Al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~  176 (292)
T 1qqe_A           97 VDSLENAIQIFTHRGQFRRGANFKFELGEILENDLHDYAKAIDCYELAGEWYAQDQSVALSNKCFIKCADLKALDGQYIE  176 (292)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHHHHhCCHHH
Confidence            998888755311   11  135778888889986 99999999998876642111 1    3467888899999999999


Q ss_pred             HHHHHHHHHHcCCCCCH------HHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcC----HHHHHHHHHHHH--hcCCH
Q 012111          345 MEEYFKKMKHRGMKPNS------ITYCSLVSAYSKAGLIMKVDSILRQVENSDVILD----TPFFNCIISAYG--QAGDV  412 (471)
Q Consensus       345 a~~~~~~m~~~~~~p~~------~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~----~~~~~~l~~~~~--~~g~~  412 (471)
                      |+..|++..........      ..|..+..++...|++++|...+++..+..+...    ...+..++.++.  ..+++
T Consensus       177 A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~p~~~~~~~~~~l~~l~~~~~~~~~~~~  256 (292)
T 1qqe_A          177 ASDIYSKLIKSSMGNRLSQWSLKDYFLKKGLCQLAATDAVAAARTLQEGQSEDPNFADSRESNFLKSLIDAVNEGDSEQL  256 (292)
T ss_dssp             HHHHHHHHHHTTSSCTTTGGGHHHHHHHHHHHHHHTTCHHHHHHHHHGGGCC---------HHHHHHHHHHHHTTCTTTH
T ss_pred             HHHHHHHHHHHHhcCCcccHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCCCcHHHHHHHHHHHHHHcCCHHHH
Confidence            99999999886432221      2567788889999999999999999886543211    123445566664  45678


Q ss_pred             HHHHHHHHHHHh
Q 012111          413 EKMGELFLTMKE  424 (471)
Q Consensus       413 ~~a~~~~~~~~~  424 (471)
                      ++|+..|+.+..
T Consensus       257 ~~A~~~~~~~~~  268 (292)
T 1qqe_A          257 SEHCKEFDNFMR  268 (292)
T ss_dssp             HHHHHHHTTSSC
T ss_pred             HHHHHHhccCCc
Confidence            888888877654

>3dra_A Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha; geranylgeranyltrasferase, ggtase, ggtase-I, PGGT, prenyltransferase, farnesyltransferase; HET: B3P GRG; 1.80A {Candida albicans}

Probab=99.11  E-value=1.1e-07  Score=83.01  Aligned_cols=227  Identities=13%  Similarity=0.050  Sum_probs=158.5

Q ss_pred             HHHHHHhhcH-HHHHHHHHHhhhccCccCChhHHHHHHHHHhcCC--CHHHHHHHHHHHHhCCCCCCHHHHHHHHHHH--
Q 012111           85 LDEAIKQKKW-QLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCK--QPEQASLLFEVMLSDGLKPSVDVYTALVSAY--  159 (471)
Q Consensus        85 l~~~~~~~~~-~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~--~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~--  159 (471)
                      +++..+.|.+ ++|+++++.+...+  |.+..+|+.-..++...+  ++++++++++.+...+.+ +..+|+.-...+  
T Consensus        39 ~~a~~~~~e~s~~aL~~t~~~L~~n--P~~~taWn~R~~~L~~l~~~~~~eeL~~~~~~L~~nPk-~y~aW~~R~~iL~~  115 (306)
T 3dra_A           39 LLALMKAEEYSERALHITELGINEL--ASHYTIWIYRFNILKNLPNRNLYDELDWCEEIALDNEK-NYQIWNYRQLIIGQ  115 (306)
T ss_dssp             HHHHHHTTCCSHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHTCTTSCHHHHHHHHHHHHHHCTT-CCHHHHHHHHHHHH
T ss_pred             HHHHHHcCCCCHHHHHHHHHHHHHC--cHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHCcc-cHHHHHHHHHHHHH
Confidence            4444455554 68999999999875  666778888888888888  999999999999987655 666777655554  


Q ss_pred             --Hhc---CCHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHH--HHHHHHHHHHHCCCCCCHHHHHHHHHHHHc
Q 012111          160 --GQS---GLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFD--LIEKILAEMSYLGIECSAVTYNTIIDGYGK  232 (471)
Q Consensus       160 --~~~---~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~--~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~  232 (471)
                        ...   +++++++.+++++.+.  .+-+..+|+.-.-.+.+.+.++  ++++.++.+.+.. +-|...|+.-...+..
T Consensus       116 ~~~~l~~~~~~~~EL~~~~~~l~~--~pkny~aW~~R~~vl~~l~~~~~~~EL~~~~~~i~~d-~~N~sAW~~R~~ll~~  192 (306)
T 3dra_A          116 IMELNNNDFDPYREFDILEAMLSS--DPKNHHVWSYRKWLVDTFDLHNDAKELSFVDKVIDTD-LKNNSAWSHRFFLLFS  192 (306)
T ss_dssp             HHHHTTTCCCTHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHS
T ss_pred             HHHhccccCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHhcccChHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHh
Confidence              444   7888888888888873  2567777877777777778777  8888888888765 4477777766666666


Q ss_pred             cCC------HHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHH-HHHHHHHHHhCC--CCCCHHHHHHHHHHHHH
Q 012111          233 AKK------FEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEK-MEKWYNEFNLMG--VKADIQTLNILTKSYGR  303 (471)
Q Consensus       233 ~~~------~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~-a~~~~~~~~~~~--~~~~~~~~~~ll~~~~~  303 (471)
                      .+.      ++++++.++.+....  +-|...|+.+...+.+.|+... +..+..++...+  -+.+...+..+..+|.+
T Consensus       193 l~~~~~~~~~~eEl~~~~~aI~~~--p~n~SaW~y~~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~s~~al~~la~~~~~  270 (306)
T 3dra_A          193 KKHLATDNTIDEELNYVKDKIVKC--PQNPSTWNYLLGIHERFDRSITQLEEFSLQFVDLEKDQVTSSFALETLAKIYTQ  270 (306)
T ss_dssp             SGGGCCHHHHHHHHHHHHHHHHHC--SSCHHHHHHHHHHHHHTTCCGGGGHHHHHTTEEGGGTEESCHHHHHHHHHHHHH
T ss_pred             ccccchhhhHHHHHHHHHHHHHhC--CCCccHHHHHHHHHHhcCCChHHHHHHHHHHHhccCCCCCCHHHHHHHHHHHHc
Confidence            665      777777777777663  5566777777777766666333 444555544321  13455666666666666


Q ss_pred             cCCHHHHHHHHHHHHh
Q 012111          304 AGMYDKMRSVMDFMQK  319 (471)
Q Consensus       304 ~~~~~~a~~~~~~~~~  319 (471)
                      .|+.++|.++++.+.+
T Consensus       271 ~~~~~~A~~~~~~l~~  286 (306)
T 3dra_A          271 QKKYNESRTVYDLLKS  286 (306)
T ss_dssp             TTCHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHh
Confidence            6666666666666654

>2fo7_A Synthetic consensus TPR protein; tetratricopeptide repeat, consensus protein, superhelix, de novo protein; 2.30A {Synthetic} SCOP: k.38.1.1 PDB: 2hyz_A

Probab=99.10  E-value=1.2e-08  Score=77.88  Aligned_cols=128  Identities=17%  Similarity=0.170  Sum_probs=77.0

Q ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHh
Q 012111          294 LNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSK  373 (471)
Q Consensus       294 ~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~  373 (471)
                      +..+...+...|++++|..+++.+.+... .+...+..+...+...|++++|..+++++...+ +.+...+..+...+..
T Consensus         4 ~~~l~~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~   81 (136)
T 2fo7_A            4 WYNLGNAYYKQGDYDEAIEYYQKALELDP-RSAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PRSAEAWYNLGNAYYK   81 (136)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHcCcHHHHHHHHHHHHHcCC-cchhHHHHHHHHHHHhcCHHHHHHHHHHHHHHC-CCchHHHHHHHHHHHH
Confidence            34445555555666666666655554422 244455555666666666666666666665543 2345556666666666


Q ss_pred             cCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 012111          374 AGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKE  424 (471)
Q Consensus       374 ~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~  424 (471)
                      .|++++|.++++.+.+..+. +...+..+...+...|++++|.+.++++.+
T Consensus        82 ~~~~~~A~~~~~~~~~~~~~-~~~~~~~la~~~~~~~~~~~A~~~~~~~~~  131 (136)
T 2fo7_A           82 QGDYDEAIEYYQKALELDPR-SAEAWYNLGNAYYKQGDYDEAIEYYQKALE  131 (136)
T ss_dssp             TTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHTTTCHHHHHHHHHHHHH
T ss_pred             hcCHHHHHHHHHHHHHhCCC-ChHHHHHHHHHHHHHccHHHHHHHHHHHHc
Confidence            66777777666666655433 455666666677777777777777776655

>3urz_A Uncharacterized protein; tetratricopeptide repeats (TPR) containing protein, structur genomics, joint center for structural genomics, JCSG; HET: PG4; 2.19A {Bacteroides ovatus}

Probab=99.10  E-value=1.1e-08  Score=85.03  Aligned_cols=136  Identities=13%  Similarity=-0.024  Sum_probs=84.8

Q ss_pred             HHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcC
Q 012111          296 ILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAG  375 (471)
Q Consensus       296 ~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g  375 (471)
                      .+..+|.+.|++++|...|+...+..+. +...+..+...+...|++++|...|++..+.. +-+..++..+...+...|
T Consensus        59 ~lg~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~lg~~~~~~~  136 (208)
T 3urz_A           59 ELALAYKKNRNYDKAYLFYKELLQKAPN-NVDCLEACAEMQVCRGQEKDALRMYEKILQLE-ADNLAANIFLGNYYYLTA  136 (208)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHHh
Confidence            3667777777777777777777765433 56677777777777888888888888777753 235666777776665554


Q ss_pred             C--HHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHH
Q 012111          376 L--IMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATM  437 (471)
Q Consensus       376 ~--~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l  437 (471)
                      .  ...+...++.+..  +.|....+..+..++...|++++|+..|++..+  +.|+......+
T Consensus       137 ~~~~~~~~~~~~~~~~--~~~~~~a~~~~g~~~~~~~~~~~A~~~~~~al~--l~P~~~~~~~l  196 (208)
T 3urz_A          137 EQEKKKLETDYKKLSS--PTKMQYARYRDGLSKLFTTRYEKARNSLQKVIL--RFPSTEAQKTL  196 (208)
T ss_dssp             HHHHHHHHHHHC---C--CCHHHHHHHHHHHHHHHHHTHHHHHHHHHHHTT--TSCCHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhC--CCchhHHHHHHHHHHHHccCHHHHHHHHHHHHH--hCCCHHHHHHH
Confidence            3  3334444444432  222223334445556667888888888888876  46776544443

>2yhc_A BAMD, UPF0169 lipoprotein YFIO; essential BAM component, membrane protein; 1.80A {Escherichia coli} PDB: 3tgo_A 3q5m_A

Probab=99.09  E-value=3.3e-08  Score=83.23  Aligned_cols=190  Identities=11%  Similarity=-0.027  Sum_probs=116.3

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCC-C-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCH--HHHHH
Q 012111          256 IFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVK-A-DIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTV--VTYNI  331 (471)
Q Consensus       256 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~-~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~--~~~~~  331 (471)
                      ...+..+...+...|++++|...|+++...... + ....+..+..++.+.|++++|...|+.+.+..+....  ..+..
T Consensus         4 ~~~~~~~a~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~P~~~~~~~a~~~   83 (225)
T 2yhc_A            4 PNEIYATAQQKLQDGNWRQAITQLEALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPNIDYVMYM   83 (225)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTTHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCCcHHHHHHH
Confidence            445566677788888888888888888764311 1 1356777788888888888888888888776433221  13333


Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHH--------------
Q 012111          332 VIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTP--------------  397 (471)
Q Consensus       332 li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~--------------  397 (471)
                      +..++...|..     .+            ..|..+...+...|+.++|...|+++.+..+. +..              
T Consensus        84 ~g~~~~~~~~~-----~~------------~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~P~-~~~a~~a~~~l~~~~~~  145 (225)
T 2yhc_A           84 RGLTNMALDDS-----AL------------QGFFGVDRSDRDPQQARAAFSDFSKLVRGYPN-SQYTTDATKRLVFLKDR  145 (225)
T ss_dssp             HHHHHHHHHC-------------------------------CCHHHHHHHHHHHHHHTTCTT-CTTHHHHHHHHHHHHHH
T ss_pred             HHHHHHhhhhh-----hh------------hhhhccchhhcCcHHHHHHHHHHHHHHHHCcC-ChhHHHHHHHHHHHHHH
Confidence            44444431100     00            00111111122233444444444444433222 111              


Q ss_pred             ---HHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCH----HHHHHHHHHHHhcCCHHHHHHHHHHHHHhhhcCC
Q 012111          398 ---FFNCIISAYGQAGDVEKMGELFLTMKERHCVPDN----ITFATMIQAYNALGMTEAAQNLENKMIAMKENSG  465 (471)
Q Consensus       398 ---~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~----~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~~~  465 (471)
                         ....+...|.+.|++++|+..|+++.+.  .|+.    ..+..+..++.+.|++++|.+.++.+....|...
T Consensus       146 ~~~~~~~~a~~~~~~~~~~~A~~~~~~~l~~--~p~~~~~~~a~~~l~~~~~~~g~~~~A~~~~~~l~~~~~~~~  218 (225)
T 2yhc_A          146 LAKYEYSVAEYYTERGAWVAVVNRVEGMLRD--YPDTQATRDALPLMENAYRQMQMNAQAEKVAKIIAANSSNTL  218 (225)
T ss_dssp             HHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--STTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHCCSCCC
T ss_pred             HHHHHHHHHHHHHHcCcHHHHHHHHHHHHHH--CcCCCccHHHHHHHHHHHHHcCCcHHHHHHHHHHHhhCCCch
Confidence               1134567788999999999999999875  3442    4677888999999999999999999988777643

>2pzi_A Probable serine/threonine-protein kinase PKNG; ATP-recognition, kinase-INH complex, rubredoxin fold, TPR domain, transferase; HET: AXX; 2.40A {Mycobacterium tuberculosis}

Probab=99.08  E-value=1.3e-09  Score=107.72  Aligned_cols=171  Identities=12%  Similarity=-0.056  Sum_probs=93.9

Q ss_pred             hcCCCHHHHHHHHHHHH--------hCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHH
Q 012111          125 GKCKQPEQASLLFEVML--------SDGLKPSVDVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCT  196 (471)
Q Consensus       125 ~~~~~~~~a~~~~~~m~--------~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~  196 (471)
                      ...|++++|.+.+++..        +.. +.+...+..+..++...|++++|++.|++..+..  +.+...|..+..++.
T Consensus       402 ~~~~~~~~A~~~~~~al~~~~~~~~~~~-p~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~--p~~~~a~~~lg~~~~  478 (681)
T 2pzi_A          402 TVLSQPVQTLDSLRAARHGALDADGVDF-SESVELPLMEVRALLDLGDVAKATRKLDDLAERV--GWRWRLVWYRAVAEL  478 (681)
T ss_dssp             TTTCCHHHHHHHHHHHHTC-------CC-TTCSHHHHHHHHHHHHHTCHHHHHHHHHHHHHHH--CCCHHHHHHHHHHHH
T ss_pred             ccccCHHHHHHHHHHhhhhccccccccc-ccchhHHHHHHHHHHhcCCHHHHHHHHHHHhccC--cchHHHHHHHHHHHH
Confidence            45566666666666655        221 2244555555666666666666666666655421  234455555566666


Q ss_pred             hcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHH
Q 012111          197 KFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKME  276 (471)
Q Consensus       197 ~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~  276 (471)
                      ..|++++|.+.|++..+.. +-+...+..+..++.+.|++++ ++.|++..+..  +.+...|..+..++.+.|++++|.
T Consensus       479 ~~g~~~~A~~~~~~al~l~-P~~~~~~~~lg~~~~~~g~~~~-~~~~~~al~~~--P~~~~a~~~lg~~~~~~g~~~~A~  554 (681)
T 2pzi_A          479 LTGDYDSATKHFTEVLDTF-PGELAPKLALAATAELAGNTDE-HKFYQTVWSTN--DGVISAAFGLARARSAEGDRVGAV  554 (681)
T ss_dssp             HHTCHHHHHHHHHHHHHHS-TTCSHHHHHHHHHHHHHTCCCT-TCHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HcCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHcCChHH-HHHHHHHHHhC--CchHHHHHHHHHHHHHcCCHHHHH
Confidence            6666666666666665543 2245555566666666666666 66666665542  334555666666666666666666


Q ss_pred             HHHHHHHhCCCCCCHHHHHHHHHHHHH
Q 012111          277 KWYNEFNLMGVKADIQTLNILTKSYGR  303 (471)
Q Consensus       277 ~~~~~~~~~~~~~~~~~~~~ll~~~~~  303 (471)
                      ..|++..+.+ +.+...+..+..++..
T Consensus       555 ~~~~~al~l~-P~~~~a~~~~~~~~~~  580 (681)
T 2pzi_A          555 RTLDEVPPTS-RHFTTARLTSAVTLLS  580 (681)
T ss_dssp             HHHHTSCTTS-TTHHHHHHHHHHHTC-
T ss_pred             HHHHhhcccC-cccHHHHHHHHHHHHc
Confidence            6666655432 2223444444444433

>3qky_A Outer membrane assembly lipoprotein YFIO; membrane protein; 2.15A {Rhodothermus marinus}

Probab=99.07  E-value=1.9e-08  Score=86.96  Aligned_cols=210  Identities=13%  Similarity=0.051  Sum_probs=132.9

Q ss_pred             CCchHHHHHHHHHHHhhcHHHHHHHHHHhhhccCccCC---hhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCC-CC-CHH
Q 012111           76 LWPKPVLEALDEAIKQKKWQLALKIFGLLRQQQWYQAR---CQTFTKLMVMLGKCKQPEQASLLFEVMLSDGL-KP-SVD  150 (471)
Q Consensus        76 ~~~~~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~---~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~-~~-~~~  150 (471)
                      ..+..+......+.+.|++++|++.|+.+.+..  |.+   ..++..+..++.+.|++++|...|+...+... .+ ...
T Consensus        13 ~~~~~~~~~a~~~~~~g~~~~A~~~~~~~l~~~--p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~   90 (261)
T 3qky_A           13 SSPQEAFERAMEFYNQGKYDRAIEYFKAVFTYG--RTHEWAADAQFYLARAYYQNKEYLLAASEYERFIQIYQIDPRVPQ   90 (261)
T ss_dssp             SSHHHHHHHHHHHHHTTCHHHHHHHHHHHGGGC--SCSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTTHHH
T ss_pred             CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhC--CCCcchHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHCCCCchhHH
Confidence            445666677777888999999999999998864  444   67888889999999999999999999988632 11 245


Q ss_pred             HHHHHHHHHHh--------cCCHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHH
Q 012111          151 VYTALVSAYGQ--------SGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVT  222 (471)
Q Consensus       151 ~~~~li~~~~~--------~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~  222 (471)
                      .+..+..++..        .|++++|+..|+++....+-  +......+..              +..+...    ....
T Consensus        91 a~~~lg~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~p~--~~~~~~a~~~--------------~~~~~~~----~~~~  150 (261)
T 3qky_A           91 AEYERAMCYYKLSPPYELDQTDTRKAIEAFQLFIDRYPN--HELVDDATQK--------------IRELRAK----LARK  150 (261)
T ss_dssp             HHHHHHHHHHHHCCCTTSCCHHHHHHHHHHHHHHHHCTT--CTTHHHHHHH--------------HHHHHHH----HHHH
T ss_pred             HHHHHHHHHHHhcccccccchhHHHHHHHHHHHHHHCcC--chhHHHHHHH--------------HHHHHHH----HHHH
Confidence            67778888888        89999999999998874321  2222211110              0000000    0112


Q ss_pred             HHHHHHHHHccCCHHHHHHHHHHHHHcCCCCC-CHHHHHHHHHHHHhc----------CCHHHHHHHHHHHHhCCCCCC-
Q 012111          223 YNTIIDGYGKAKKFEEMESSFSAMVESGGCHP-DIFTLNSMISAYGNS----------GNIEKMEKWYNEFNLMGVKAD-  290 (471)
Q Consensus       223 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~----------~~~~~a~~~~~~~~~~~~~~~-  290 (471)
                      +..+...|.+.|++++|+..|+.+.+...-.+ ....+..+..+|...          |++++|...|+++.+.. +-+ 
T Consensus       151 ~~~la~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~a~~~l~~~~~~~g~~~~~~~~~~~~~~A~~~~~~~~~~~-p~~~  229 (261)
T 3qky_A          151 QYEAARLYERRELYEAAAVTYEAVFDAYPDTPWADDALVGAMRAYIAYAEQSVRARQPERYRRAVELYERLLQIF-PDSP  229 (261)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHHHHTSCGGGHHHHHHHHHHHHHHHHHHC-TTCT
T ss_pred             HHHHHHHHHHccCHHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHhcccchhhcccchHHHHHHHHHHHHHHC-CCCh
Confidence            44566667777777777777777766531111 234566666666654          77777777777776542 112 


Q ss_pred             --HHHHHHHHHHHHHcCCHH
Q 012111          291 --IQTLNILTKSYGRAGMYD  308 (471)
Q Consensus       291 --~~~~~~ll~~~~~~~~~~  308 (471)
                        ......+-..+...++++
T Consensus       230 ~~~~a~~~l~~~~~~~~~~~  249 (261)
T 3qky_A          230 LLRTAEELYTRARQRLTELE  249 (261)
T ss_dssp             HHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHhh
Confidence              233444444444444443

>3dra_A Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha; geranylgeranyltrasferase, ggtase, ggtase-I, PGGT, prenyltransferase, farnesyltransferase; HET: B3P GRG; 1.80A {Candida albicans}

Probab=99.07  E-value=2.1e-07  Score=81.35  Aligned_cols=219  Identities=7%  Similarity=-0.057  Sum_probs=112.4

Q ss_pred             CHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccC--CHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHH----Hhc---C
Q 012111          200 RFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAK--KFEEMESSFSAMVESGGCHPDIFTLNSMISAY----GNS---G  270 (471)
Q Consensus       200 ~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~--~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~----~~~---~  270 (471)
                      ..++|+++++.++..+ +-+..+|+.--.++...|  .++++++.++.+....  +.+..+|+.-...+    ...   +
T Consensus        48 ~s~~aL~~t~~~L~~n-P~~~taWn~R~~~L~~l~~~~~~eeL~~~~~~L~~n--Pk~y~aW~~R~~iL~~~~~~l~~~~  124 (306)
T 3dra_A           48 YSERALHITELGINEL-ASHYTIWIYRFNILKNLPNRNLYDELDWCEEIALDN--EKNYQIWNYRQLIIGQIMELNNNDF  124 (306)
T ss_dssp             CSHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTCTTSCHHHHHHHHHHHHHHC--TTCCHHHHHHHHHHHHHHHHTTTCC
T ss_pred             CCHHHHHHHHHHHHHC-cHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHC--cccHHHHHHHHHHHHHHHHhccccC
Confidence            3356777777766654 335556666666666666  6777777777766653  33344454443333    333   5


Q ss_pred             CHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHH--HHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCC------H
Q 012111          271 NIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYD--KMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGH------I  342 (471)
Q Consensus       271 ~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~--~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~------~  342 (471)
                      ++++++.+++.+.+.. +-+..+|+.-.-.+.+.|.++  ++...++.+.+..+. +...|+.-...+...++      +
T Consensus       125 ~~~~EL~~~~~~l~~~-pkny~aW~~R~~vl~~l~~~~~~~EL~~~~~~i~~d~~-N~sAW~~R~~ll~~l~~~~~~~~~  202 (306)
T 3dra_A          125 DPYREFDILEAMLSSD-PKNHHVWSYRKWLVDTFDLHNDAKELSFVDKVIDTDLK-NNSAWSHRFFLLFSKKHLATDNTI  202 (306)
T ss_dssp             CTHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHSSGGGCCHHHH
T ss_pred             CHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhcccChHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHhccccchhhhH
Confidence            5666666666665543 445555555555555555555  555555555554333 44455544444444443      4


Q ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHH-HHHHHHHHHhCC--CCcCHHHHHHHHHHHHhcCCHHHHHHHH
Q 012111          343 EKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMK-VDSILRQVENSD--VILDTPFFNCIISAYGQAGDVEKMGELF  419 (471)
Q Consensus       343 ~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~-a~~~~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~  419 (471)
                      +++++.+++++... +-|...|+.+...+.+.|+... +..+...+.+.+  -..+...+..+..+|.+.|+.++|.+++
T Consensus       203 ~eEl~~~~~aI~~~-p~n~SaW~y~~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~s~~al~~la~~~~~~~~~~~A~~~~  281 (306)
T 3dra_A          203 DEELNYVKDKIVKC-PQNPSTWNYLLGIHERFDRSITQLEEFSLQFVDLEKDQVTSSFALETLAKIYTQQKKYNESRTVY  281 (306)
T ss_dssp             HHHHHHHHHHHHHC-SSCHHHHHHHHHHHHHTTCCGGGGHHHHHTTEEGGGTEESCHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HHHHHHHHHHHHhC-CCCccHHHHHHHHHHhcCCChHHHHHHHHHHHhccCCCCCCHHHHHHHHHHHHccCCHHHHHHHH
Confidence            55555555555442 2244455555444544444222 333444333322  0114444555555555555555555555


Q ss_pred             HHHHh
Q 012111          420 LTMKE  424 (471)
Q Consensus       420 ~~~~~  424 (471)
                      +.+.+
T Consensus       282 ~~l~~  286 (306)
T 3dra_A          282 DLLKS  286 (306)
T ss_dssp             HHHHH
T ss_pred             HHHHh
Confidence            55543

>2pzi_A Probable serine/threonine-protein kinase PKNG; ATP-recognition, kinase-INH complex, rubredoxin fold, TPR domain, transferase; HET: AXX; 2.40A {Mycobacterium tuberculosis}

Probab=99.05  E-value=5.5e-09  Score=103.24  Aligned_cols=173  Identities=8%  Similarity=-0.103  Sum_probs=133.0

Q ss_pred             HhcCCHHHHHHHHHHHH--------hCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHh
Q 012111          267 GNSGNIEKMEKWYNEFN--------LMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGK  338 (471)
Q Consensus       267 ~~~~~~~~a~~~~~~~~--------~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~  338 (471)
                      ...|++++|++.+++..        ... +.+...+..+...+...|++++|...|+.+.+.... +...|..+..++..
T Consensus       402 ~~~~~~~~A~~~~~~al~~~~~~~~~~~-p~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~p~-~~~a~~~lg~~~~~  479 (681)
T 2pzi_A          402 TVLSQPVQTLDSLRAARHGALDADGVDF-SESVELPLMEVRALLDLGDVAKATRKLDDLAERVGW-RWRLVWYRAVAELL  479 (681)
T ss_dssp             TTTCCHHHHHHHHHHHHTC-------CC-TTCSHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHCC-CHHHHHHHHHHHHH
T ss_pred             ccccCHHHHHHHHHHhhhhccccccccc-ccchhHHHHHHHHHHhcCCHHHHHHHHHHHhccCcc-hHHHHHHHHHHHHH
Confidence            67888889998888887        332 455677888888888889999999988888776433 66778888888888


Q ss_pred             cCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHH
Q 012111          339 AGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGEL  418 (471)
Q Consensus       339 ~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~  418 (471)
                      .|++++|...|++..+.. +-+...+..+..++...|++++ .+.|+++.+.++. +...|..+..++.+.|++++|+..
T Consensus       480 ~g~~~~A~~~~~~al~l~-P~~~~~~~~lg~~~~~~g~~~~-~~~~~~al~~~P~-~~~a~~~lg~~~~~~g~~~~A~~~  556 (681)
T 2pzi_A          480 TGDYDSATKHFTEVLDTF-PGELAPKLALAATAELAGNTDE-HKFYQTVWSTNDG-VISAAFGLARARSAEGDRVGAVRT  556 (681)
T ss_dssp             HTCHHHHHHHHHHHHHHS-TTCSHHHHHHHHHHHHHTCCCT-TCHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHcCChHH-HHHHHHHHHhCCc-hHHHHHHHHHHHHHcCCHHHHHHH
Confidence            899999999998888763 2356778888888888899988 8888888887665 777888888888899999999999


Q ss_pred             HHHHHhCCCCCC-HHHHHHHHHHHHhcCC
Q 012111          419 FLTMKERHCVPD-NITFATMIQAYNALGM  446 (471)
Q Consensus       419 ~~~~~~~~~~p~-~~~~~~l~~~~~~~g~  446 (471)
                      |++..+.  .|+ ...+..+..++...|+
T Consensus       557 ~~~al~l--~P~~~~a~~~~~~~~~~~~~  583 (681)
T 2pzi_A          557 LDEVPPT--SRHFTTARLTSAVTLLSGRS  583 (681)
T ss_dssp             HHTSCTT--STTHHHHHHHHHHHTC----
T ss_pred             HHhhccc--CcccHHHHHHHHHHHHccCC
Confidence            8888763  565 4566666666655554

>2vsy_A XCC0866; transferase, glycosyl transferase, GT-B, OGT, protein O-GLCN; HET: NHE; 2.10A {Xanthomonas campestris PV} PDB: 2jlb_A* 2xgm_A* 2xgo_A* 2xgs_A* 2vsn_A*

Probab=99.05  E-value=9.2e-09  Score=99.80  Aligned_cols=153  Identities=5%  Similarity=-0.145  Sum_probs=110.4

Q ss_pred             cCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHH
Q 012111          269 SGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEY  348 (471)
Q Consensus       269 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~  348 (471)
                      .|++++|...+++..+.. +.+...+..+...+...|++++|...+++..+.... +...+..+...|...|++++|.+.
T Consensus         2 ~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~lg~~~~~~g~~~~A~~~   79 (568)
T 2vsy_A            2 TADGPRELLQLRAAVRHR-PQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPG-HPEAVARLGRVRWTQQRHAEAAVL   79 (568)
T ss_dssp             --------------------CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTTSTT-CHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             CccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHCCCHHHHHHH
Confidence            477888888888887653 456778888888888999999999999888876433 567788888888889999999999


Q ss_pred             HHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhc---CCHHHHHHHHHHHHhC
Q 012111          349 FKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQA---GDVEKMGELFLTMKER  425 (471)
Q Consensus       349 ~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~---g~~~~a~~~~~~~~~~  425 (471)
                      +++..+.. +.+...+..+..++...|++++|.+.+++..+..+. +...+..+..++...   |++++|.+.+++..+.
T Consensus        80 ~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~l~~~~~~~~~~g~~~~A~~~~~~al~~  157 (568)
T 2vsy_A           80 LQQASDAA-PEHPGIALWLGHALEDAGQAEAAAAAYTRAHQLLPE-EPYITAQLLNWRRRLCDWRALDVLSAQVRAAVAQ  157 (568)
T ss_dssp             HHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCCTTHHHHHHHHHHHHHH
T ss_pred             HHHHHhcC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHhhccccHHHHHHHHHHHHhc
Confidence            98888763 335778888888889999999999999888877654 677888888888888   8899999998888775

>3rjv_A Putative SEL1 repeat protein; alpha-alpha superhelix, structural genomics, joint center FO structural genomics, JCSG; HET: MSE; 1.65A {Klebsiella pneumoniae subsp}

Probab=99.03  E-value=9.2e-08  Score=79.60  Aligned_cols=162  Identities=10%  Similarity=-0.028  Sum_probs=74.6

Q ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcC----CHHHHHHHHHHHHHcCCCCCHHHHHH
Q 012111          291 IQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAG----HIEKMEEYFKKMKHRGMKPNSITYCS  366 (471)
Q Consensus       291 ~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g----~~~~a~~~~~~m~~~~~~p~~~~~~~  366 (471)
                      ...+..+...|...+++++|...|++..+.+   +...+..+...|.. +    ++++|..+|++..+.|   +...+..
T Consensus        18 ~~a~~~lg~~~~~~~~~~~A~~~~~~a~~~g---~~~a~~~lg~~y~~-~g~~~~~~~A~~~~~~A~~~g---~~~a~~~   90 (212)
T 3rjv_A           18 RRAQYYLADTWVSSGDYQKAEYWAQKAAAQG---DGDALALLAQLKIR-NPQQADYPQARQLAEKAVEAG---SKSGEIV   90 (212)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHTT---CHHHHHHHHHHTTS-STTSCCHHHHHHHHHHHHHTT---CHHHHHH
T ss_pred             HHHHHHHHHHHhcCCCHHHHHHHHHHHHHcC---CHHHHHHHHHHHHc-CCCCCCHHHHHHHHHHHHHCC---CHHHHHH
Confidence            3344444444444444444444444444432   23333334444433 3    4555555555554433   3344444


Q ss_pred             HHHHHHh----cCCHHHHHHHHHHHHhCCCC-cCHHHHHHHHHHHHh----cCCHHHHHHHHHHHHhCCCCCCHHHHHHH
Q 012111          367 LVSAYSK----AGLIMKVDSILRQVENSDVI-LDTPFFNCIISAYGQ----AGDVEKMGELFLTMKERHCVPDNITFATM  437 (471)
Q Consensus       367 li~~~~~----~g~~~~a~~~~~~~~~~~~~-~~~~~~~~l~~~~~~----~g~~~~a~~~~~~~~~~~~~p~~~~~~~l  437 (471)
                      |...|..    .+++++|..+|++..+.+.. .+...+..|...|..    .+++++|+.+|++..+.  ..+...+..|
T Consensus        91 Lg~~y~~g~g~~~d~~~A~~~~~~A~~~~~~~~~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~A~~~--~~~~~a~~~L  168 (212)
T 3rjv_A           91 LARVLVNRQAGATDVAHAITLLQDAARDSESDAAVDAQMLLGLIYASGVHGPEDDVKASEYFKGSSSL--SRTGYAEYWA  168 (212)
T ss_dssp             HHHHHTCGGGSSCCHHHHHHHHHHHTSSTTSHHHHHHHHHHHHHHHHTSSSSCCHHHHHHHHHHHHHT--SCTTHHHHHH
T ss_pred             HHHHHHcCCCCccCHHHHHHHHHHHHHcCCCcchHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHc--CCCHHHHHHH
Confidence            4444444    45555555555555544321 013444555555554    45555555555555543  1233344444


Q ss_pred             HHHHHhc-C-----CHHHHHHHHHHHHHhh
Q 012111          438 IQAYNAL-G-----MTEAAQNLENKMIAMK  461 (471)
Q Consensus       438 ~~~~~~~-g-----~~~~A~~~~~~m~~~~  461 (471)
                      ...|... |     +.++|.+++++..+.+
T Consensus       169 g~~y~~g~gg~~~~d~~~A~~~~~~A~~~g  198 (212)
T 3rjv_A          169 GMMFQQGEKGFIEPNKQKALHWLNVSCLEG  198 (212)
T ss_dssp             HHHHHHCBTTTBCCCHHHHHHHHHHHHHHT
T ss_pred             HHHHHcCCCCCCCCCHHHHHHHHHHHHHcC
Confidence            4444332 2     5555555555555544

>2r5s_A Uncharacterized protein VP0806; APC090868.1, vibrio parahaemolyticus RIMD 22 structural genomics, PSI-2, protein structure initiative; HET: MES; 2.14A {Vibrio parahaemolyticus}

Probab=99.02  E-value=6.9e-09  Score=83.71  Aligned_cols=159  Identities=11%  Similarity=0.027  Sum_probs=81.7

Q ss_pred             HHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHH-HHhcC
Q 012111          297 LTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSA-YSKAG  375 (471)
Q Consensus       297 ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~-~~~~g  375 (471)
                      +...+...|++++|...++...+..+. +...+..+...+...|++++|...+++.....  |+...+..+... +...+
T Consensus        12 ~a~~~~~~g~~~~A~~~~~~al~~~P~-~~~a~~~la~~~~~~g~~~~A~~~~~~a~~~~--p~~~~~~~~~~~~~~~~~   88 (176)
T 2r5s_A           12 QVSELLQQGEHAQALNVIQTLSDELQS-RGDVKLAKADCLLETKQFELAQELLATIPLEY--QDNSYKSLIAKLELHQQA   88 (176)
T ss_dssp             HHHHHHHTTCHHHHHHHHHTSCHHHHT-SHHHHHHHHHHHHHTTCHHHHHHHHTTCCGGG--CCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHCCC-cHHHHHHHHHHHHHCCCHHHHHHHHHHhhhcc--CChHHHHHHHHHHHHhhc
Confidence            334444555555555555544433111 34445555555555555555555555544432  233222211111 11112


Q ss_pred             CHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC-CHHHHHHHHHHHHhcCCHHHHHHHH
Q 012111          376 LIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVP-DNITFATMIQAYNALGMTEAAQNLE  454 (471)
Q Consensus       376 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~  454 (471)
                      ....|...+++..+..+. +...+..+..++...|++++|...|+++.+..-.+ +...+..+...+...|+.++|...+
T Consensus        89 ~~~~a~~~~~~al~~~P~-~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~a~~~l~~~~~~~g~~~~A~~~y  167 (176)
T 2r5s_A           89 AESPELKRLEQELAANPD-NFELACELAVQYNQVGRDEEALELLWNILKVNLGAQDGEVKKTFMDILSALGQGNAIASKY  167 (176)
T ss_dssp             TSCHHHHHHHHHHHHSTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTTTTTHHHHHHHHHHHHHCSSCHHHHHH
T ss_pred             ccchHHHHHHHHHHhCCC-CHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccChHHHHHHHHHHHHHhCCCCcHHHHH
Confidence            223355666666655443 55666666666667777777777776666542111 2445666666666677777776666


Q ss_pred             HHHHH
Q 012111          455 NKMIA  459 (471)
Q Consensus       455 ~~m~~  459 (471)
                      ++.+.
T Consensus       168 ~~al~  172 (176)
T 2r5s_A          168 RRQLY  172 (176)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            66554

>3qou_A Protein YBBN; thioredoxin-like fold, tetratricopeptide repeat, lysine dimethylation, protein binding; HET: MLY; 1.80A {Escherichia coli} PDB: 3qdn_A*

Probab=99.01  E-value=1.3e-08  Score=89.16  Aligned_cols=163  Identities=12%  Similarity=-0.026  Sum_probs=86.5

Q ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHH-HHH
Q 012111          291 IQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCS-LVS  369 (471)
Q Consensus       291 ~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~-li~  369 (471)
                      ...+..+...+...|++++|...|+...+.... +...+..+...+...|++++|...++++...  .|+...... ...
T Consensus       117 ~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~P~-~~~a~~~la~~~~~~g~~~~A~~~l~~~~~~--~p~~~~~~~~~~~  193 (287)
T 3qou_A          117 EELXAQQAMQLMQESNYTDALPLLXDAWQLSNQ-NGEIGLLLAETLIALNRSEDAEAVLXTIPLQ--DQDTRYQGLVAQI  193 (287)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTS-CHHHHHHHHHHHHHTTCHHHHHHHHTTSCGG--GCSHHHHHHHHHH
T ss_pred             hhhHHHHHHHHHhCCCHHHHHHHHHHHHHhCCc-chhHHHHHHHHHHHCCCHHHHHHHHHhCchh--hcchHHHHHHHHH
Confidence            334444555555555555555555555544222 3445555555555666666666666555443  233322211 122


Q ss_pred             HHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCC---HHHHHHHHHHHHhcCC
Q 012111          370 AYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPD---NITFATMIQAYNALGM  446 (471)
Q Consensus       370 ~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~---~~~~~~l~~~~~~~g~  446 (471)
                      .+...++.+.|...+++.....+. +...+..+...+...|++++|+..|+++.+.  .|+   ...+..++..+...|+
T Consensus       194 ~l~~~~~~~~a~~~l~~al~~~P~-~~~~~~~la~~l~~~g~~~~A~~~l~~~l~~--~p~~~~~~a~~~l~~~~~~~g~  270 (287)
T 3qou_A          194 ELLXQAADTPEIQQLQQQVAENPE-DAALATQLALQLHQVGRNEEALELLFGHLRX--DLTAADGQTRXTFQEILAALGT  270 (287)
T ss_dssp             HHHHHHTSCHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTGGGGHHHHHHHHHHHHHCT
T ss_pred             HHHhhcccCccHHHHHHHHhcCCc-cHHHHHHHHHHHHHcccHHHHHHHHHHHHhc--ccccccchHHHHHHHHHHHcCC
Confidence            244445555556666665555443 5555666666666666666666666666553  232   3455566666666666


Q ss_pred             HHHHHHHHHHHHH
Q 012111          447 TEAAQNLENKMIA  459 (471)
Q Consensus       447 ~~~A~~~~~~m~~  459 (471)
                      .++|...+++.+.
T Consensus       271 ~~~a~~~~r~al~  283 (287)
T 3qou_A          271 GDALASXYRRQLY  283 (287)
T ss_dssp             TCHHHHHHHHHHH
T ss_pred             CCcHHHHHHHHHH
Confidence            6666666655543

>2uy1_A Cleavage stimulation factor 77; RNA-binding protein; 2.0A {Encephalitozoon cuniculi} PDB: 2uy1_B

Probab=99.01  E-value=2.3e-07  Score=87.56  Aligned_cols=335  Identities=9%  Similarity=-0.033  Sum_probs=206.2

Q ss_pred             Hhh-cHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCC-HHH
Q 012111           90 KQK-KWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGL-LDE  167 (471)
Q Consensus        90 ~~~-~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~-~~~  167 (471)
                      +.| +++.|..+|+.+...-   |.              |+++.+..+|+.....  .|+...|...+....+.+. .+.
T Consensus         6 ~~~~~i~~aR~vyer~l~~~---P~--------------~~~e~~~~iferal~~--~ps~~LW~~Y~~f~~~~~~~~~~   66 (493)
T 2uy1_A            6 KMGVELSSPSAIMEHARRLY---MS--------------KDYRSLESLFGRCLKK--SYNLDLWMLYIEYVRKVSQKKFK   66 (493)
T ss_dssp             ------CCHHHHHHHHHHHH---HT--------------TCHHHHHHHHHHHSTT--CCCHHHHHHHHHHHHHHC----C
T ss_pred             HcCcchHHHHHHHHHHHHHC---CC--------------CCHHHHHHHHHHHhcc--CCCHHHHHHHHHHHHHhCchHHH
Confidence            345 3777888888877642   32              8899999999999985  5799999999888777663 456


Q ss_pred             HHHHHHHhhcCCCC-CCCHHHHHHHHHHHH----hcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHH-----------
Q 012111          168 AFSTINDMKSVSDC-KPDVYTYSILIKSCT----KFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYG-----------  231 (471)
Q Consensus       168 a~~~~~~~~~~~~~-~~~~~~~~~ll~~~~----~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~-----------  231 (471)
                      ...+|+.....-|. ..+...|...+..+.    ..++.+.+.++|+..+.....--...|......-.           
T Consensus        67 i~~~fe~al~~vg~d~~s~~iW~~Yi~f~~~~~~~~~~~~~vR~iy~rAL~~P~~~~~~lw~~Y~~fE~~~~~~~~~~~~  146 (493)
T 2uy1_A           67 LYEVYEFTLGQFENYWDSYGLYKEYIEEEGKIEDEQTRIEKIRNGYMRALQTPMGSLSELWKDFENFELELNKITGKKIV  146 (493)
T ss_dssp             THHHHHHHHHHSTTCTTCHHHHHHHHHHTSSCSSHHHHHHHHHHHHHHHHTSCCTTHHHHHHHHHHHHHHHCHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCcccHHHHHHHHHHHHhchhhhHHHHHHHHHHHHHHhChhhhHHHHHHHHHHHHHHhccccHHHHH
Confidence            67788887764443 346677888877654    24578889999999987422111222322222111           


Q ss_pred             --ccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcC--C-----HHHHHHHHHHHHhCCCCCCHHHHHHHHHHHH
Q 012111          232 --KAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSG--N-----IEKMEKWYNEFNLMGVKADIQTLNILTKSYG  302 (471)
Q Consensus       232 --~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~--~-----~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~  302 (471)
                        ..+.+..|..+++.+.... ...+...|...+..-...+  -     .+.+..+|+++.... +.+...|...+..+.
T Consensus       147 ~~~~~~y~~ar~~y~~~~~~~-~~~s~~~W~~y~~~E~~~~~~~~~~~~~~Rv~~~ye~al~~~-p~~~~lW~~ya~~~~  224 (493)
T 2uy1_A          147 GDTLPIFQSSFQRYQQIQPLI-RGWSVKNAARLIDLEMENGMKLGGRPHESRMHFIHNYILDSF-YYAEEVYFFYSEYLI  224 (493)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHH-HTCSHHHHHHHHHHHHTCTTCCCHHHHHHHHHHHHHHHHHHT-TTCHHHHHHHHHHHH
T ss_pred             HHHhHHHHHHHHHHHHHHHHH-hhccHHHHHHHHHHHhcCCccCcchhhHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHH
Confidence              1122334444454443211 0113345655555432221  1     345678898887753 667888888899999


Q ss_pred             HcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC---------CCC---CHHHHHHHHHH
Q 012111          303 RAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRG---------MKP---NSITYCSLVSA  370 (471)
Q Consensus       303 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~---------~~p---~~~~~~~li~~  370 (471)
                      +.|+.+.|..++++....  +.+...+.    .|....+.++.   ++.+.+.-         ..+   ....|...+..
T Consensus       225 ~~~~~~~ar~i~erAi~~--P~~~~l~~----~y~~~~e~~~~---~~~l~~~~~~~~~~~~~~~~~~~~~~lw~~y~~~  295 (493)
T 2uy1_A          225 GIGQKEKAKKVVERGIEM--SDGMFLSL----YYGLVMDEEAV---YGDLKRKYSMGEAESAEKVFSKELDLLRINHLNY  295 (493)
T ss_dssp             HTTCHHHHHHHHHHHHHH--CCSSHHHH----HHHHHTTCTHH---HHHHHHHTC----------CHHHHHHHHHHHHHH
T ss_pred             HcCCHHHHHHHHHHHHhC--CCcHHHHH----HHHhhcchhHH---HHHHHHHHHhhccchhhhhcccccHHHHHHHHHH
Confidence            999999999999999987  33333332    22222111121   22222210         001   12456777777


Q ss_pred             HHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHh-cCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHH
Q 012111          371 YSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQ-AGDVEKMGELFLTMKERHCVPDNITFATMIQAYNALGMTEA  449 (471)
Q Consensus       371 ~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~-~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~  449 (471)
                      ..+.++.+.|..+|+++ +. ...+..+|......-.. .++.+.|..+|+...+. +.-++..+...++...+.|+.+.
T Consensus       296 ~~r~~~~~~AR~i~~~A-~~-~~~~~~v~i~~A~lE~~~~~d~~~ar~ife~al~~-~~~~~~~~~~yid~e~~~~~~~~  372 (493)
T 2uy1_A          296 VLKKRGLELFRKLFIEL-GN-EGVGPHVFIYCAFIEYYATGSRATPYNIFSSGLLK-HPDSTLLKEEFFLFLLRIGDEEN  372 (493)
T ss_dssp             HHHHHCHHHHHHHHHHH-TT-SCCCHHHHHHHHHHHHHHHCCSHHHHHHHHHHHHH-CTTCHHHHHHHHHHHHHHTCHHH
T ss_pred             HHHcCCHHHHHHHHHHh-hC-CCCChHHHHHHHHHHHHHCCChHHHHHHHHHHHHH-CCCCHHHHHHHHHHHHHcCCHHH
Confidence            77888999999999999 32 22344455433332222 34799999999999875 32245566777887888999999


Q ss_pred             HHHHHHHH
Q 012111          450 AQNLENKM  457 (471)
Q Consensus       450 A~~~~~~m  457 (471)
                      |+.+|+++
T Consensus       373 aR~l~er~  380 (493)
T 2uy1_A          373 ARALFKRL  380 (493)
T ss_dssp             HHHHHHHS
T ss_pred             HHHHHHHH
Confidence            99888875

>2r5s_A Uncharacterized protein VP0806; APC090868.1, vibrio parahaemolyticus RIMD 22 structural genomics, PSI-2, protein structure initiative; HET: MES; 2.14A {Vibrio parahaemolyticus}

Probab=99.00  E-value=6.8e-09  Score=83.75  Aligned_cols=160  Identities=13%  Similarity=0.082  Sum_probs=83.2

Q ss_pred             HHHHHHHHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHH-H
Q 012111           81 VLEALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSA-Y  159 (471)
Q Consensus        81 ~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~-~  159 (471)
                      .......+.+.|++++|+..|+.+.+..  |.+...+..+..++...|++++|...++......  |+...+..+... +
T Consensus         9 ~~~~a~~~~~~g~~~~A~~~~~~al~~~--P~~~~a~~~la~~~~~~g~~~~A~~~~~~a~~~~--p~~~~~~~~~~~~~   84 (176)
T 2r5s_A            9 LLKQVSELLQQGEHAQALNVIQTLSDEL--QSRGDVKLAKADCLLETKQFELAQELLATIPLEY--QDNSYKSLIAKLEL   84 (176)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHTSCHHH--HTSHHHHHHHHHHHHHTTCHHHHHHHHTTCCGGG--CCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHC--CCcHHHHHHHHHHHHHCCCHHHHHHHHHHhhhcc--CChHHHHHHHHHHH
Confidence            4444555667777777777777776654  5566667777777777777777777777665542  233332222111 1


Q ss_pred             HhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCC-CHHHHHHHHHHHHccCCHHH
Q 012111          160 GQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIEC-SAVTYNTIIDGYGKAKKFEE  238 (471)
Q Consensus       160 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~-~~~~~~~l~~~~~~~~~~~~  238 (471)
                      ...++...|+..+++..+..  +-+...+..+...+...|++++|...|+++.+....+ +...+..+..++...|+.++
T Consensus        85 ~~~~~~~~a~~~~~~al~~~--P~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~a~~~l~~~~~~~g~~~~  162 (176)
T 2r5s_A           85 HQQAAESPELKRLEQELAAN--PDNFELACELAVQYNQVGRDEEALELLWNILKVNLGAQDGEVKKTFMDILSALGQGNA  162 (176)
T ss_dssp             HHHHTSCHHHHHHHHHHHHS--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTTTTTHHHHHHHHHHHHHCSSCH
T ss_pred             HhhcccchHHHHHHHHHHhC--CCCHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccChHHHHHHHHHHHHHhCCCCc
Confidence            11112223445555544411  2234445555555555555555555555555442211 13344455555555555555


Q ss_pred             HHHHHHHH
Q 012111          239 MESSFSAM  246 (471)
Q Consensus       239 a~~~~~~~  246 (471)
                      |...|++.
T Consensus       163 A~~~y~~a  170 (176)
T 2r5s_A          163 IASKYRRQ  170 (176)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            55555444

>3qou_A Protein YBBN; thioredoxin-like fold, tetratricopeptide repeat, lysine dimethylation, protein binding; HET: MLY; 1.80A {Escherichia coli} PDB: 3qdn_A*

Probab=98.99  E-value=2.7e-08  Score=87.20  Aligned_cols=164  Identities=9%  Similarity=-0.053  Sum_probs=76.6

Q ss_pred             ChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHH
Q 012111          113 RCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILI  192 (471)
Q Consensus       113 ~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll  192 (471)
                      +...+..+...+.+.|++++|...|++..+.... +...+..+..++...|++++|...++++...   .|+........
T Consensus       116 ~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~P~-~~~a~~~la~~~~~~g~~~~A~~~l~~~~~~---~p~~~~~~~~~  191 (287)
T 3qou_A          116 EEELXAQQAMQLMQESNYTDALPLLXDAWQLSNQ-NGEIGLLLAETLIALNRSEDAEAVLXTIPLQ---DQDTRYQGLVA  191 (287)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTS-CHHHHHHHHHHHHHTTCHHHHHHHHTTSCGG---GCSHHHHHHHH
T ss_pred             chhhHHHHHHHHHhCCCHHHHHHHHHHHHHhCCc-chhHHHHHHHHHHHCCCHHHHHHHHHhCchh---hcchHHHHHHH
Confidence            3344445555555555555555555555544222 4445555555555555555555555555431   23322221111


Q ss_pred             H-HHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCC
Q 012111          193 K-SCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGN  271 (471)
Q Consensus       193 ~-~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  271 (471)
                      . .+...++.+.|...+++..... +.+...+..+...+...|++++|...|.++.+...-..+...+..++..+...|+
T Consensus       192 ~~~l~~~~~~~~a~~~l~~al~~~-P~~~~~~~~la~~l~~~g~~~~A~~~l~~~l~~~p~~~~~~a~~~l~~~~~~~g~  270 (287)
T 3qou_A          192 QIELLXQAADTPEIQQLQQQVAEN-PEDAALATQLALQLHQVGRNEEALELLFGHLRXDLTAADGQTRXTFQEILAALGT  270 (287)
T ss_dssp             HHHHHHHHTSCHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTGGGGHHHHHHHHHHHHHCT
T ss_pred             HHHHHhhcccCccHHHHHHHHhcC-CccHHHHHHHHHHHHHcccHHHHHHHHHHHHhcccccccchHHHHHHHHHHHcCC
Confidence            1 2334444444555555544432 3344455555555555555555555555554432111113444555555555555


Q ss_pred             HHHHHHHHHH
Q 012111          272 IEKMEKWYNE  281 (471)
Q Consensus       272 ~~~a~~~~~~  281 (471)
                      .++|...|++
T Consensus       271 ~~~a~~~~r~  280 (287)
T 3qou_A          271 GDALASXYRR  280 (287)
T ss_dssp             TCHHHHHHHH
T ss_pred             CCcHHHHHHH
Confidence            5555544444

>4ga2_A E3 SUMO-protein ligase ranbp2; TPR motif, nuclear pore complex component nucleocytoplasmic transport, transport protein; 0.95A {Pan troglodytes} PDB: 4ga0_A 4ga1_A*

Probab=98.98  E-value=9.9e-09  Score=80.22  Aligned_cols=140  Identities=9%  Similarity=-0.084  Sum_probs=98.9

Q ss_pred             HhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHH
Q 012111           90 KQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAF  169 (471)
Q Consensus        90 ~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~  169 (471)
                      ..|++++|++.++.+....  +.+...+..+..+|.+.|++++|.+.|++..+.... +..+|..+..+|...|++++|+
T Consensus         9 ~~~~~e~ai~~~~~a~~~~--p~~~~~~~~la~~y~~~~~~~~A~~~~~~al~~~p~-~~~a~~~lg~~~~~~~~~~~A~   85 (150)
T 4ga2_A            9 SKADVERYIASVQGSTPSP--RQKSIKGFYFAKLYYEAKEYDLAKKYICTYINVQER-DPKAHRFLGLLYELEENTDKAV   85 (150)
T ss_dssp             CHHHHHHHHHHHHHHSCSH--HHHHTTHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HcChHHHHHHHHHHhcccC--cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHcCchHHHH
Confidence            4677888888888877653  444556677788888888888888888888776433 6778888888888888888888


Q ss_pred             HHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHH-HHHHHHCCCCCCHHHHHHHHHHHHccCC
Q 012111          170 STINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKI-LAEMSYLGIECSAVTYNTIIDGYGKAKK  235 (471)
Q Consensus       170 ~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~-~~~~~~~g~~~~~~~~~~l~~~~~~~~~  235 (471)
                      ..|++..+..  +-+...|..+...+.+.|+++++.+. +++..+.. +-++.+|......+...|+
T Consensus        86 ~~~~~al~~~--p~~~~~~~~la~~~~~~~~~~~aa~~~~~~al~l~-P~~~~~~~l~~~ll~~~G~  149 (150)
T 4ga2_A           86 ECYRRSVELN--PTQKDLVLKIAELLCKNDVTDGRAKYWVERAAKLF-PGSPAVYKLKEQLLDCEGE  149 (150)
T ss_dssp             HHHHHHHHHC--TTCHHHHHHHHHHHHHHCSSSSHHHHHHHHHHHHS-TTCHHHHHHHHHHHHTCCC
T ss_pred             HHHHHHHHhC--CCCHHHHHHHHHHHHHcCChHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHhCc
Confidence            8888877632  33566777777777777777655544 46666553 3456666666666655553

>2ifu_A Gamma-SNAP; membrane fusion, snare complex disassembly, protein structure initiative, PSI, center for eukaryotic structural genomics, CESG; HET: MSE; 2.60A {Danio rerio}

Probab=98.98  E-value=3.7e-08  Score=87.33  Aligned_cols=202  Identities=6%  Similarity=-0.055  Sum_probs=113.4

Q ss_pred             HhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHH
Q 012111           90 KQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAF  169 (471)
Q Consensus        90 ~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~  169 (471)
                      ..|++++|.++++.+.+..  +..         .+...++++.|...|...               ...|...|++++|.
T Consensus         3 ~~~~~~eA~~~~~~a~k~~--~~~---------~~~~~~~~~~A~~~~~~a---------------~~~~~~~g~~~~A~   56 (307)
T 2ifu_A            3 AAQKISEAHEHIAKAEKYL--KTS---------FMKWKPDYDSAASEYAKA---------------AVAFKNAKQLEQAK   56 (307)
T ss_dssp             CHHHHHHHHHHHHHHHHHH--CCC---------SSSCSCCHHHHHHHHHHH---------------HHHHHHTTCHHHHH
T ss_pred             ccchHHHHHHHHHHHHHHc--ccc---------ccCCCCCHHHHHHHHHHH---------------HHHHHHcCCHHHHH
Confidence            5788899999999888653  221         111157888888887765               34667788888888


Q ss_pred             HHHHHhhcCC---CCC-CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHC----CCCC-CHHHHHHHHHHHHccCCHHHHH
Q 012111          170 STINDMKSVS---DCK-PDVYTYSILIKSCTKFHRFDLIEKILAEMSYL----GIEC-SAVTYNTIIDGYGKAKKFEEME  240 (471)
Q Consensus       170 ~~~~~~~~~~---~~~-~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~----g~~~-~~~~~~~l~~~~~~~~~~~~a~  240 (471)
                      ..|.+.....   +.. .-..+|+.+...|...|++++|...+++..+.    |-.. ...++..+...|.. |++++|+
T Consensus        57 ~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~~~~g~~~~~a~~~~~lg~~~~~-g~~~~A~  135 (307)
T 2ifu_A           57 DAYLQEAEAHANNRSLFHAAKAFEQAGMMLKDLQRMPEAVQYIEKASVMYVENGTPDTAAMALDRAGKLMEP-LDLSKAV  135 (307)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCGGGGHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHTT-TCHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHc-CCHHHHH
Confidence            8887765421   100 01335666667777777777777777665432    1110 13455566666666 7777777


Q ss_pred             HHHHHHHHcCCCCC----CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhC----CCCCC-HHHHHHHHHHHHHcCCHHHHH
Q 012111          241 SSFSAMVESGGCHP----DIFTLNSMISAYGNSGNIEKMEKWYNEFNLM----GVKAD-IQTLNILTKSYGRAGMYDKMR  311 (471)
Q Consensus       241 ~~~~~~~~~~~~~~----~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~~~-~~~~~~ll~~~~~~~~~~~a~  311 (471)
                      ..|++..+...-..    ...++..+...+...|++++|+..|++....    +..+. ...+..+..++...|++++|.
T Consensus       136 ~~~~~Al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~g~~~~~~g~~~~A~  215 (307)
T 2ifu_A          136 HLYQQAAAVFENEERLRQAAELIGKASRLLVRQQKFDEAAASLQKEKSMYKEMENYPTCYKKCIAQVLVQLHRADYVAAQ  215 (307)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCChhHHHHHHHHHHHHHHHcCCHHHHH
Confidence            77666554210000    1234555556666666666666666655432    10000 113333444444445555555


Q ss_pred             HHHHHHH
Q 012111          312 SVMDFMQ  318 (471)
Q Consensus       312 ~~~~~~~  318 (471)
                      ..|++..
T Consensus       216 ~~~~~al  222 (307)
T 2ifu_A          216 KCVRESY  222 (307)
T ss_dssp             HHHHHHT
T ss_pred             HHHHHHh
Confidence            5555544

>2ifu_A Gamma-SNAP; membrane fusion, snare complex disassembly, protein structure initiative, PSI, center for eukaryotic structural genomics, CESG; HET: MSE; 2.60A {Danio rerio}

Probab=98.98  E-value=1.4e-08  Score=90.14  Aligned_cols=224  Identities=7%  Similarity=0.022  Sum_probs=155.8

Q ss_pred             cCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHc-cCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHH
Q 012111          198 FHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGK-AKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKME  276 (471)
Q Consensus       198 ~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~-~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~  276 (471)
                      .|++++|.+++++..+.. + .         .+.+ .++++.|...|.+.                ...|...|++++|.
T Consensus         4 ~~~~~eA~~~~~~a~k~~-~-~---------~~~~~~~~~~~A~~~~~~a----------------~~~~~~~g~~~~A~   56 (307)
T 2ifu_A            4 AQKISEAHEHIAKAEKYL-K-T---------SFMKWKPDYDSAASEYAKA----------------AVAFKNAKQLEQAK   56 (307)
T ss_dssp             HHHHHHHHHHHHHHHHHH-C-C---------CSSSCSCCHHHHHHHHHHH----------------HHHHHHTTCHHHHH
T ss_pred             cchHHHHHHHHHHHHHHc-c-c---------cccCCCCCHHHHHHHHHHH----------------HHHHHHcCCHHHHH
Confidence            456677777777766532 1 1         1222 46777777766654                45677899999999


Q ss_pred             HHHHHHHhCCC---CC--CHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCC---CCCC--HHHHHHHHHHHHhcCCHHHHH
Q 012111          277 KWYNEFNLMGV---KA--DIQTLNILTKSYGRAGMYDKMRSVMDFMQKRF---FFPT--VVTYNIVIETFGKAGHIEKME  346 (471)
Q Consensus       277 ~~~~~~~~~~~---~~--~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~---~~~~--~~~~~~li~~~~~~g~~~~a~  346 (471)
                      ..|.+......   .+  -..+|+.+..+|...|++++|...|++..+..   -.+.  ..++..+...|.. |++++|+
T Consensus        57 ~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~~~~g~~~~~a~~~~~lg~~~~~-g~~~~A~  135 (307)
T 2ifu_A           57 DAYLQEAEAHANNRSLFHAAKAFEQAGMMLKDLQRMPEAVQYIEKASVMYVENGTPDTAAMALDRAGKLMEP-LDLSKAV  135 (307)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCGGGGHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHTT-TCHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHc-CCHHHHH
Confidence            99988754311   11  14578888999999999999999999876531   1111  3467778888888 9999999


Q ss_pred             HHHHHHHHcCCC---C--CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhC----CCCcC-HHHHHHHHHHHHhcCCHHHHH
Q 012111          347 EYFKKMKHRGMK---P--NSITYCSLVSAYSKAGLIMKVDSILRQVENS----DVILD-TPFFNCIISAYGQAGDVEKMG  416 (471)
Q Consensus       347 ~~~~~m~~~~~~---p--~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~----~~~~~-~~~~~~l~~~~~~~g~~~~a~  416 (471)
                      ..|++.......   +  ...++..+...+...|++++|...|++..+.    +..+. ...+..++.++...|++++|.
T Consensus       136 ~~~~~Al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~g~~~~~~g~~~~A~  215 (307)
T 2ifu_A          136 HLYQQAAAVFENEERLRQAAELIGKASRLLVRQQKFDEAAASLQKEKSMYKEMENYPTCYKKCIAQVLVQLHRADYVAAQ  215 (307)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCChhHHHHHHHHHHHHHHHcCCHHHHH
Confidence            999988764111   1  1457888999999999999999999988753    22111 235667777888889999999


Q ss_pred             HHHHHHHhCCCCCC---H---HHHHHHHHHHHhcCCHHHHHHH
Q 012111          417 ELFLTMKERHCVPD---N---ITFATMIQAYNALGMTEAAQNL  453 (471)
Q Consensus       417 ~~~~~~~~~~~~p~---~---~~~~~l~~~~~~~g~~~~A~~~  453 (471)
                      ..|++.. .  .|+   .   .....++.++ ..|+.+.+..+
T Consensus       216 ~~~~~al-~--~p~~~~~~e~~~l~~l~~~~-~~~d~~~~~~~  254 (307)
T 2ifu_A          216 KCVRESY-S--IPGFSGSEDCAALEDLLQAY-DEQDEEQLLRV  254 (307)
T ss_dssp             HHHHHHT-T--STTSTTSHHHHHHHHHHHHH-HTTCHHHHHHH
T ss_pred             HHHHHHh-C--CCCCCCCHHHHHHHHHHHHH-HhcCHHHHHHH
Confidence            9999988 4  232   1   2344555555 67887766653

>3rjv_A Putative SEL1 repeat protein; alpha-alpha superhelix, structural genomics, joint center FO structural genomics, JCSG; HET: MSE; 1.65A {Klebsiella pneumoniae subsp}

Probab=98.97  E-value=1.2e-07  Score=78.98  Aligned_cols=28  Identities=7%  Similarity=0.033  Sum_probs=11.5

Q ss_pred             HHHHHHHHHHHHccCCHHHHHHHHHHHH
Q 012111          220 AVTYNTIIDGYGKAKKFEEMESSFSAMV  247 (471)
Q Consensus       220 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~  247 (471)
                      ...+..+...|...+++++|.+.|++..
T Consensus        18 ~~a~~~lg~~~~~~~~~~~A~~~~~~a~   45 (212)
T 3rjv_A           18 RRAQYYLADTWVSSGDYQKAEYWAQKAA   45 (212)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCCCHHHHHHHHHHHH
Confidence            3333334444444444444444444443

>4ga2_A E3 SUMO-protein ligase ranbp2; TPR motif, nuclear pore complex component nucleocytoplasmic transport, transport protein; 0.95A {Pan troglodytes} PDB: 4ga0_A 4ga1_A*

Probab=98.97  E-value=4.4e-09  Score=82.25  Aligned_cols=112  Identities=9%  Similarity=0.003  Sum_probs=54.6

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhc
Q 012111          330 NIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQA  409 (471)
Q Consensus       330 ~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  409 (471)
                      -.+...|...|++++|.+.|++.++.. +-+..+|..+..++...|++++|...|++..+.++. +..+|..+...|.+.
T Consensus        35 ~~la~~y~~~~~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~p~-~~~~~~~la~~~~~~  112 (150)
T 4ga2_A           35 FYFAKLYYEAKEYDLAKKYICTYINVQ-ERDPKAHRFLGLLYELEENTDKAVECYRRSVELNPT-QKDLVLKIAELLCKN  112 (150)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCchHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHc
Confidence            344455555555555555555555432 223445555555555555555555555555554433 445555555555555


Q ss_pred             CCHHHHHHH-HHHHHhCCCCC-CHHHHHHHHHHHHhcC
Q 012111          410 GDVEKMGEL-FLTMKERHCVP-DNITFATMIQAYNALG  445 (471)
Q Consensus       410 g~~~~a~~~-~~~~~~~~~~p-~~~~~~~l~~~~~~~g  445 (471)
                      |++++|.+. +++..+.  .| ++.+|......+...|
T Consensus       113 ~~~~~aa~~~~~~al~l--~P~~~~~~~l~~~ll~~~G  148 (150)
T 4ga2_A          113 DVTDGRAKYWVERAAKL--FPGSPAVYKLKEQLLDCEG  148 (150)
T ss_dssp             CSSSSHHHHHHHHHHHH--STTCHHHHHHHHHHHHTCC
T ss_pred             CChHHHHHHHHHHHHHh--CcCCHHHHHHHHHHHHHhC
Confidence            555444433 3444442  23 3344444444444444

>2vsy_A XCC0866; transferase, glycosyl transferase, GT-B, OGT, protein O-GLCN; HET: NHE; 2.10A {Xanthomonas campestris PV} PDB: 2jlb_A* 2xgm_A* 2xgo_A* 2xgs_A* 2vsn_A*

Probab=98.96  E-value=3.4e-08  Score=95.80  Aligned_cols=154  Identities=7%  Similarity=-0.060  Sum_probs=111.3

Q ss_pred             hhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHH
Q 012111           91 QKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAFS  170 (471)
Q Consensus        91 ~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~  170 (471)
                      .|++++|++.|+.+.+..  +.+...+..+...+...|++++|...|++..+.... +...+..+..+|...|++++|.+
T Consensus         2 ~g~~~~A~~~~~~al~~~--p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~lg~~~~~~g~~~~A~~   78 (568)
T 2vsy_A            2 TADGPRELLQLRAAVRHR--PQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPG-HPEAVARLGRVRWTQQRHAEAAV   78 (568)
T ss_dssp             ---------------------CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTTSTT-CHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             CccHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHCCCHHHHHH
Confidence            467888888888888764  566788888888888899999999999988876433 67888888888999999999999


Q ss_pred             HHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHcc---CCHHHHHHHHHHHH
Q 012111          171 TINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKA---KKFEEMESSFSAMV  247 (471)
Q Consensus       171 ~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~---~~~~~a~~~~~~~~  247 (471)
                      .|++..+..  +.+...+..+..++...|++++|.+.+++..+.. +.+...+..+...+...   |++++|.+.+++..
T Consensus        79 ~~~~al~~~--p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~~~~g~~~~A~~~~~~al  155 (568)
T 2vsy_A           79 LLQQASDAA--PEHPGIALWLGHALEDAGQAEAAAAAYTRAHQLL-PEEPYITAQLLNWRRRLCDWRALDVLSAQVRAAV  155 (568)
T ss_dssp             HHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCCTTHHHHHHHHHHHH
T ss_pred             HHHHHHhcC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhhccccHHHHHHHHHHHH
Confidence            998887732  4457788888888889999999999998888764 44677888888888888   88999999998888


Q ss_pred             HcC
Q 012111          248 ESG  250 (471)
Q Consensus       248 ~~~  250 (471)
                      +.+
T Consensus       156 ~~~  158 (568)
T 2vsy_A          156 AQG  158 (568)
T ss_dssp             HHT
T ss_pred             hcC
Confidence            765

>3u3w_A Transcriptional activator PLCR protein; ternary complex, PLCR-PAPR7-DNA, HTH DNA-binding domain, QUO sensing; 2.40A {Bacillus thuringiensis} PDB: 2qfc_A

Probab=98.93  E-value=1.5e-06  Score=76.25  Aligned_cols=170  Identities=11%  Similarity=-0.049  Sum_probs=121.3

Q ss_pred             HHHHHHHcCCHHHHHHHHHHHHhCCC-CCCHH----HHHHHHHHHHhcCCHHHHHHHHHHHHHcCCC-CC----HHHHHH
Q 012111          297 LTKSYGRAGMYDKMRSVMDFMQKRFF-FPTVV----TYNIVIETFGKAGHIEKMEEYFKKMKHRGMK-PN----SITYCS  366 (471)
Q Consensus       297 ll~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~----~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~-p~----~~~~~~  366 (471)
                      .+..+...|++++|..+++...+... .|+..    .+..+...+...|++++|...+++....... ++    ..+++.
T Consensus        81 ~i~~~~~~~~y~~a~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~Ai~~~~~al~~~~~~~~~~~~~~~~~~  160 (293)
T 3u3w_A           81 QVIMLCKQKRYKEIYNKVWNELKKEEYHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQNLYIENA  160 (293)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHHHHTTSSCHHHHHHHHHHHHHTCCCCSCTTHHHHHHHH
T ss_pred             HHHHHHHHhhHHHHHHHHHHHhccccCChHHHHHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHhcccccHHHHHHHHHH
Confidence            35667788888888888888776432 22211    2334556666777899999999988874222 22    336888


Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHh----C-CCCc-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhC----CCCCC-HHHHH
Q 012111          367 LVSAYSKAGLIMKVDSILRQVEN----S-DVIL-DTPFFNCIISAYGQAGDVEKMGELFLTMKER----HCVPD-NITFA  435 (471)
Q Consensus       367 li~~~~~~g~~~~a~~~~~~~~~----~-~~~~-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~----~~~p~-~~~~~  435 (471)
                      +...|...|++++|...++++.+    . +..+ ...++..+...|...|++++|+..+++..+.    +..+. ..+|.
T Consensus       161 lg~~y~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~A~~~~~~al~~~~~~~~~~~~~~~~~  240 (293)
T 3u3w_A          161 IANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAIEISCRINSMALIGQLYY  240 (293)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTBCTTHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHcCcHHHHHHHHH
Confidence            88889999999999999888773    1 1111 2347788889999999999999999887642    22233 57788


Q ss_pred             HHHHHHHhcC-CHHHHHHHHHHHHHhhhcCCC
Q 012111          436 TMIQAYNALG-MTEAAQNLENKMIAMKENSGK  466 (471)
Q Consensus       436 ~l~~~~~~~g-~~~~A~~~~~~m~~~~~~~~~  466 (471)
                      .+..++.+.| .+++|.+.+++++......++
T Consensus       241 ~lg~~~~~~g~~~~~A~~~~~~Al~i~~~~~~  272 (293)
T 3u3w_A          241 QRGECLRKLEYEEAEIEDAYKKASFFFDILEM  272 (293)
T ss_dssp             HHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHhCCcHHHHHHHHHHHHHHHHHhCC
Confidence            8889999999 469999999999887665443

>1hh8_A P67PHOX, NCF-2, neutrophil cytosol factor 2; cell cycle, phagocyte oxidase factor, SH3 domain, repeat, TPR repeat cell cycle; HET: FLC; 1.8A {Homo sapiens} SCOP: a.118.8.1 PDB: 1wm5_A 1e96_B*

Probab=98.92  E-value=5.2e-08  Score=81.18  Aligned_cols=131  Identities=11%  Similarity=-0.008  Sum_probs=91.2

Q ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Q 012111          293 TLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYS  372 (471)
Q Consensus       293 ~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~  372 (471)
                      .+..+...+...|++++|...|+...    .|+...+..+...+...|++++|...+++..... +.+...+..+..++.
T Consensus         8 ~~~~~g~~~~~~~~~~~A~~~~~~a~----~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~lg~~~~   82 (213)
T 1hh8_A            8 SLWNEGVLAADKKDWKGALDAFSAVQ----DPHSRICFNIGCMYTILKNMTEAEKAFTRSINRD-KHLAVAYFQRGMLYY   82 (213)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHTSS----SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHHc----CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-ccchHHHHHHHHHHH
Confidence            34455666777778888877777663    4466777777777777788888888777777653 335667777777777


Q ss_pred             hcCCHHHHHHHHHHHHhCCCCcCH----------------HHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCH
Q 012111          373 KAGLIMKVDSILRQVENSDVILDT----------------PFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDN  431 (471)
Q Consensus       373 ~~g~~~~a~~~~~~~~~~~~~~~~----------------~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~  431 (471)
                      ..|++++|...++.+.+..+. +.                ..+..+..++...|++++|.+.|++..+.  .|+.
T Consensus        83 ~~~~~~~A~~~~~~al~~~~~-~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~--~p~~  154 (213)
T 1hh8_A           83 QTEKYDLAIKDLKEALIQLRG-NQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATSM--KSEP  154 (213)
T ss_dssp             HTTCHHHHHHHHHHHHHTTTT-CSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT--CCSG
T ss_pred             HcccHHHHHHHHHHHHHhCCC-ccHHHHHHhccccCccchHHHHHHHHHHHHccCHHHHHHHHHHHHHc--Cccc
Confidence            778888887777777765433 22                56667777777777777777777777763  4543

>2yhc_A BAMD, UPF0169 lipoprotein YFIO; essential BAM component, membrane protein; 1.80A {Escherichia coli} PDB: 3tgo_A 3q5m_A

Probab=98.92  E-value=3.8e-07  Score=76.71  Aligned_cols=207  Identities=9%  Similarity=-0.021  Sum_probs=107.4

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCC-CC-HHHHH
Q 012111          148 SVDVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPD-VYTYSILIKSCTKFHRFDLIEKILAEMSYLGIE-CS-AVTYN  224 (471)
Q Consensus       148 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~-~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~-~~-~~~~~  224 (471)
                      +...+..+...+...|++++|+..|+++....+..+. ...+..+..++.+.|++++|...|+++.+.... +. ...+.
T Consensus         3 ~~~~~~~~a~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~P~~~~~~~a~~   82 (225)
T 2yhc_A            3 PPNEIYATAQQKLQDGNWRQAITQLEALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPNIDYVMY   82 (225)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTTHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCCcHHHHHH
Confidence            3444555566666677777777777776653221121 244555666666667777777777666654211 11 11333


Q ss_pred             HHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHc
Q 012111          225 TIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRA  304 (471)
Q Consensus       225 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~  304 (471)
                      .+..++...+..     .+             ..|..+...+...|++++|...|+++.+.. +-+...........   
T Consensus        83 ~~g~~~~~~~~~-----~~-------------~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~-P~~~~a~~a~~~l~---  140 (225)
T 2yhc_A           83 MRGLTNMALDDS-----AL-------------QGFFGVDRSDRDPQQARAAFSDFSKLVRGY-PNSQYTTDATKRLV---  140 (225)
T ss_dssp             HHHHHHHHHHC--------------------------------CCHHHHHHHHHHHHHHTTC-TTCTTHHHHHHHHH---
T ss_pred             HHHHHHHhhhhh-----hh-------------hhhhccchhhcCcHHHHHHHHHHHHHHHHC-cCChhHHHHHHHHH---
Confidence            333333322110     00             011122223334567777777777776542 22222221111000   


Q ss_pred             CCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCC----HHHHHHHHHHHHhcCCHHHH
Q 012111          305 GMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPN----SITYCSLVSAYSKAGLIMKV  380 (471)
Q Consensus       305 ~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~----~~~~~~li~~~~~~g~~~~a  380 (471)
                             .+...+        ......+...|.+.|++++|...|+++.+.  .|+    ...+..+..++.+.|+.++|
T Consensus       141 -------~~~~~~--------~~~~~~~a~~~~~~~~~~~A~~~~~~~l~~--~p~~~~~~~a~~~l~~~~~~~g~~~~A  203 (225)
T 2yhc_A          141 -------FLKDRL--------AKYEYSVAEYYTERGAWVAVVNRVEGMLRD--YPDTQATRDALPLMENAYRQMQMNAQA  203 (225)
T ss_dssp             -------HHHHHH--------HHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--STTSHHHHHHHHHHHHHHHHTTCHHHH
T ss_pred             -------HHHHHH--------HHHHHHHHHHHHHcCcHHHHHHHHHHHHHH--CcCCCccHHHHHHHHHHHHHcCCcHHH
Confidence                   000000        011124556777888888888888888875  232    24677788888888888888


Q ss_pred             HHHHHHHHhCCCC
Q 012111          381 DSILRQVENSDVI  393 (471)
Q Consensus       381 ~~~~~~~~~~~~~  393 (471)
                      .+.++.+...++.
T Consensus       204 ~~~~~~l~~~~~~  216 (225)
T 2yhc_A          204 EKVAKIIAANSSN  216 (225)
T ss_dssp             HHHHHHHHHCCSC
T ss_pred             HHHHHHHHhhCCC
Confidence            8888888776543

>3u3w_A Transcriptional activator PLCR protein; ternary complex, PLCR-PAPR7-DNA, HTH DNA-binding domain, QUO sensing; 2.40A {Bacillus thuringiensis} PDB: 2qfc_A

Probab=98.86  E-value=8.4e-07  Score=77.95  Aligned_cols=161  Identities=11%  Similarity=0.007  Sum_probs=79.3

Q ss_pred             HHHHHccCCHHHHHHHHHHHHHcCCCCCCH----HHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCC-CC----HHHHHHH
Q 012111          227 IDGYGKAKKFEEMESSFSAMVESGGCHPDI----FTLNSMISAYGNSGNIEKMEKWYNEFNLMGVK-AD----IQTLNIL  297 (471)
Q Consensus       227 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~----~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~~----~~~~~~l  297 (471)
                      +..+...|++++|...+++..+.....++.    ..+..+...+...|++++|...+++....... .+    ..+++.+
T Consensus        82 i~~~~~~~~y~~a~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~Ai~~~~~al~~~~~~~~~~~~~~~~~~l  161 (293)
T 3u3w_A           82 VIMLCKQKRYKEIYNKVWNELKKEEYHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQNLYIENAI  161 (293)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHHHHTTSSCHHHHHHHHHHHHHTCCCCSCTTHHHHHHHHH
T ss_pred             HHHHHHHhhHHHHHHHHHHHhccccCChHHHHHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHhcccccHHHHHHHHHHH
Confidence            455666677777777777765543222221    12223445555556666666666666553211 11    2245555


Q ss_pred             HHHHHHcCCHHHHHHHHHHHHhC-----CCCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHHc----CCCCC-HHHHHH
Q 012111          298 TKSYGRAGMYDKMRSVMDFMQKR-----FFFPT-VVTYNIVIETFGKAGHIEKMEEYFKKMKHR----GMKPN-SITYCS  366 (471)
Q Consensus       298 l~~~~~~~~~~~a~~~~~~~~~~-----~~~~~-~~~~~~li~~~~~~g~~~~a~~~~~~m~~~----~~~p~-~~~~~~  366 (471)
                      ..+|...|++++|...++.+.+.     +..+. ..+|..+...|...|++++|...+++..+.    +..+. ..+|..
T Consensus       162 g~~y~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~A~~~~~~al~~~~~~~~~~~~~~~~~~  241 (293)
T 3u3w_A          162 ANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAIEISCRINSMALIGQLYYQ  241 (293)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTBCTTHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHcCcHHHHHHHHHH
Confidence            66666666666666666555421     11111 124445555555555555555555554432    11111 344455


Q ss_pred             HHHHHHhcCC-HHHHHHHHHHH
Q 012111          367 LVSAYSKAGL-IMKVDSILRQV  387 (471)
Q Consensus       367 li~~~~~~g~-~~~a~~~~~~~  387 (471)
                      +..++.+.|+ +++|.+.+++.
T Consensus       242 lg~~~~~~g~~~~~A~~~~~~A  263 (293)
T 3u3w_A          242 RGECLRKLEYEEAEIEDAYKKA  263 (293)
T ss_dssp             HHHHHHHTTCCHHHHHHHHHHH
T ss_pred             HHHHHHHhCCcHHHHHHHHHHH
Confidence            5555555552 35555554443

>3gyz_A Chaperone protein IPGC; asymmetric homodimer, tetratricopeptide repeat, TPR, chapero virulence; 2.15A {Shigella flexneri} PDB: 3gz1_A 3gz2_A 3ks2_A

Probab=98.86  E-value=6.1e-08  Score=75.38  Aligned_cols=94  Identities=14%  Similarity=-0.017  Sum_probs=44.1

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHh
Q 012111          329 YNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQ  408 (471)
Q Consensus       329 ~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  408 (471)
                      +..+...+.+.|++++|...|++..... +-+...|..+..++...|++++|...|+++.+.++. +...|..+..+|..
T Consensus        39 ~~~lg~~~~~~g~~~eA~~~~~~al~~~-P~~~~~~~~lg~~~~~~g~~~~Ai~~~~~al~l~P~-~~~~~~~lg~~~~~  116 (151)
T 3gyz_A           39 IYSYAYDFYNKGRIEEAEVFFRFLCIYD-FYNVDYIMGLAAIYQIKEQFQQAADLYAVAFALGKN-DYTPVFHTGQCQLR  116 (151)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSSS-CCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHccHHHHHHHHHHHHhhCCC-CcHHHHHHHHHHHH
Confidence            3344444444555555555555444432 223444444444455555555555555544444433 34444444444555


Q ss_pred             cCCHHHHHHHHHHHHh
Q 012111          409 AGDVEKMGELFLTMKE  424 (471)
Q Consensus       409 ~g~~~~a~~~~~~~~~  424 (471)
                      .|++++|+..|++..+
T Consensus       117 lg~~~eA~~~~~~al~  132 (151)
T 3gyz_A          117 LKAPLKAKECFELVIQ  132 (151)
T ss_dssp             TTCHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHH
Confidence            5555555555544444

>1a17_A Serine/threonine protein phosphatase 5; hydrolase, protein-protein interactions, TPR, S helix; 2.45A {Homo sapiens} SCOP: a.118.8.1 PDB: 2bug_A

Probab=98.86  E-value=3.2e-07  Score=72.80  Aligned_cols=136  Identities=10%  Similarity=-0.034  Sum_probs=102.4

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHH
Q 012111          327 VTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAY  406 (471)
Q Consensus       327 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  406 (471)
                      ..+..+...+...|++++|...|++..... +.+..++..+...+...|++++|...+++..+..+. +...+..+..++
T Consensus        14 ~~~~~~a~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~~~-~~~~~~~~a~~~   91 (166)
T 1a17_A           14 EELKTQANDYFKAKDYENAIKFYSQAIELN-PSNAIYYGNRSLAYLRTECYGYALGDATRAIELDKK-YIKGYYRRAASN   91 (166)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcc-cHHHHHHHHHHH
Confidence            356666777788888888888888887753 336777888888888888999998888888876554 677888888888


Q ss_pred             HhcCCHHHHHHHHHHHHhCCCCCCHHHHHH--HHHHHHhcCCHHHHHHHHHHHHHhhhcCC
Q 012111          407 GQAGDVEKMGELFLTMKERHCVPDNITFAT--MIQAYNALGMTEAAQNLENKMIAMKENSG  465 (471)
Q Consensus       407 ~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~--l~~~~~~~g~~~~A~~~~~~m~~~~~~~~  465 (471)
                      ...|++++|...|+++.+.. +.+...+..  +...+...|++++|.+.+++....-...+
T Consensus        92 ~~~~~~~~A~~~~~~a~~~~-p~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~  151 (166)
T 1a17_A           92 MALGKFRAALRDYETVVKVK-PHDKDAKMKYQECNKIVKQKAFERAIAGDEHKRSVVDSLD  151 (166)
T ss_dssp             HHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_pred             HHhccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHHHHHHHHHHHcccchHHHhcccc
Confidence            89999999999998888752 224445533  33447778899999998888776655433

>3q7a_A Farnesyltransferase alpha subunit; protein prenyltransferase, transferase-transferase inhibitor; HET: SUC 3FX FPP 778; 2.00A {Cryptococcus neoformans} PDB: 3q73_A* 3q78_A* 3q79_A* 3q75_A* 3q7f_A* 3sfx_A* 3sfy_A*

Probab=98.85  E-value=4.6e-06  Score=73.61  Aligned_cols=172  Identities=10%  Similarity=-0.013  Sum_probs=131.5

Q ss_pred             hcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCC-CHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhc-C-CHHHH
Q 012111           92 KKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCK-QPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQS-G-LLDEA  168 (471)
Q Consensus        92 ~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~-~-~~~~a  168 (471)
                      +..++|+++++.+...+  |.+..+|+..-.++...| .+++++.+++.+.....+ +..+|+.-..++... + +++++
T Consensus        68 e~se~AL~lt~~~L~~n--P~~ytaWn~R~~iL~~l~~~l~eEL~~~~~~L~~nPK-ny~aW~hR~wlL~~l~~~~~~~E  144 (349)
T 3q7a_A           68 EKSERALELTEIIVRMN--PAHYTVWQYRFSLLTSLNKSLEDELRLMNEFAVQNLK-SYQVWHHRLLLLDRISPQDPVSE  144 (349)
T ss_dssp             CCSHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHTTCC-CHHHHHHHHHHHHHHCCSCCHHH
T ss_pred             CCCHHHHHHHHHHHHhC--chhHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHhCCC-cHHHHHHHHHHHHHhcCCChHHH
Confidence            34468999999999876  667778888888888888 599999999999988665 888888877777776 6 88999


Q ss_pred             HHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHH--------HHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCC-----
Q 012111          169 FSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFD--------LIEKILAEMSYLGIECSAVTYNTIIDGYGKAKK-----  235 (471)
Q Consensus       169 ~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~--------~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~-----  235 (471)
                      +++++++.+.  .+-|..+|+.-.-.+.+.+.++        ++++.++++++.. +-|...|+.....+.+.+.     
T Consensus       145 L~~~~k~L~~--dpkNy~AW~~R~wvl~~l~~~~~~~~~~~~eELe~~~k~I~~d-p~N~SAW~~R~~lL~~l~~~~~~~  221 (349)
T 3q7a_A          145 IEYIHGSLLP--DPKNYHTWAYLHWLYSHFSTLGRISEAQWGSELDWCNEMLRVD-GRNNSAWGWRWYLRVSRPGAETSS  221 (349)
T ss_dssp             HHHHHHHTSS--CTTCHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHTTSTTCCCCH
T ss_pred             HHHHHHHHHh--CCCCHHHHHHHHHHHHHhccccccchhhHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHhccccccch
Confidence            9999999873  3567777777666666655555        7888888888765 4478888887777777765     


Q ss_pred             --HHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCC
Q 012111          236 --FEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGN  271 (471)
Q Consensus       236 --~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  271 (471)
                        ++++++.+++.....  +-|...|+.+-..+.+.|.
T Consensus       222 ~~~~eELe~~~~aI~~~--P~n~SaW~Ylr~Ll~~~~~  257 (349)
T 3q7a_A          222 RSLQDELIYILKSIHLI--PHNVSAWNYLRGFLKHFSL  257 (349)
T ss_dssp             HHHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHhcCC
Confidence              677888887777763  5566777776666665554

>4gco_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; 1.60A {Caenorhabditis elegans}

Probab=98.84  E-value=1.2e-07  Score=71.44  Aligned_cols=94  Identities=10%  Similarity=-0.026  Sum_probs=44.1

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHh
Q 012111          329 YNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQ  408 (471)
Q Consensus       329 ~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  408 (471)
                      +......|.+.|++++|++.|++.++.. +.+...|..+..++.+.|++++|...+++..+.++. +...|..+..++..
T Consensus        16 ~~~~G~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~p~-~~~a~~~lg~~~~~   93 (126)
T 4gco_A           16 EKNKGNEYFKKGDYPTAMRHYNEAVKRD-PENAILYSNRAACLTKLMEFQRALDDCDTCIRLDSK-FIKGYIRKAACLVA   93 (126)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHhhHHHhhccHHHHHHHHHHHHHhhhh-hhHHHHHHHHHHHH
Confidence            4444444445555555555555444432 223444444444444555555555555444444333 34444444444444


Q ss_pred             cCCHHHHHHHHHHHHh
Q 012111          409 AGDVEKMGELFLTMKE  424 (471)
Q Consensus       409 ~g~~~~a~~~~~~~~~  424 (471)
                      .|++++|++.|++..+
T Consensus        94 ~~~~~~A~~~~~~al~  109 (126)
T 4gco_A           94 MREWSKAQRAYEDALQ  109 (126)
T ss_dssp             TTCHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHH
Confidence            4555555544444444

>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovar ISRAELE35646}

Probab=98.83  E-value=7.4e-07  Score=78.30  Aligned_cols=166  Identities=11%  Similarity=-0.047  Sum_probs=83.9

Q ss_pred             HHHHHHHcCCHHHHHHHHHHHHhCCCCCCH-----HHHHHHHHHHHhcCCHHHHHHHHHHHHHcCC---CCC--HHHHHH
Q 012111          297 LTKSYGRAGMYDKMRSVMDFMQKRFFFPTV-----VTYNIVIETFGKAGHIEKMEEYFKKMKHRGM---KPN--SITYCS  366 (471)
Q Consensus       297 ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~-----~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~---~p~--~~~~~~  366 (471)
                      .+..+...|++++|...+....+.......     ..+..+...+...|++++|...+++......   .+.  ..+++.
T Consensus        81 ~~~~~~~~~~y~~A~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~  160 (293)
T 2qfc_A           81 QVIMLCKQKRYKEIYNKVWNELKKEEYHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQNLYIENA  160 (293)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHTCCCCHHHHHHHHHHHHHHHHHHTSSCHHHHHHHHHHHHTTCCCSSCTTHHHHHHHH
T ss_pred             HHHHHHHhhhHHHHHHHHHHHhccccCChhHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhcCCchHHHHHHHHH
Confidence            344445555555555555544443211110     1122233444555666666666666553211   111  335566


Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHh---CCCC-c--CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhC----CCCC-CHHHHH
Q 012111          367 LVSAYSKAGLIMKVDSILRQVEN---SDVI-L--DTPFFNCIISAYGQAGDVEKMGELFLTMKER----HCVP-DNITFA  435 (471)
Q Consensus       367 li~~~~~~g~~~~a~~~~~~~~~---~~~~-~--~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~----~~~p-~~~~~~  435 (471)
                      +...|...|++++|...++++.+   .... +  ...++..+...|...|++++|+..+++..+.    +... -..+|.
T Consensus       161 lg~~y~~~~~~~~A~~~~~kal~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~Al~~~~kal~~~~~~~~~~~~~~~~~  240 (293)
T 2qfc_A          161 IANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAIEISCRINSMALIGQLYY  240 (293)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTBCSSHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHHHhcCccccchHHHHHhHHHHHHHHhhHHHHHHHHHHHHHHHHhcCcHHHHHHHHH
Confidence            66666666666666666665541   1111 0  1135566666666666666666666665432    1111 144555


Q ss_pred             HHHHHHHhcCCHHHH-HHHHHHHHHhhh
Q 012111          436 TMIQAYNALGMTEAA-QNLENKMIAMKE  462 (471)
Q Consensus       436 ~l~~~~~~~g~~~~A-~~~~~~m~~~~~  462 (471)
                      .+..+|...|++++| ...+++++....
T Consensus       241 ~lg~~y~~~g~~~~Ai~~~~~~Al~~~~  268 (293)
T 2qfc_A          241 QRGECLRKLEYEEAEIEDAYKKASFFFD  268 (293)
T ss_dssp             HHHHHHHHTTCCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCcHHHHHHHHHHHHHHHH
Confidence            666666666666666 555666655443

>3q7a_A Farnesyltransferase alpha subunit; protein prenyltransferase, transferase-transferase inhibitor; HET: SUC 3FX FPP 778; 2.00A {Cryptococcus neoformans} PDB: 3q73_A* 3q78_A* 3q79_A* 3q75_A* 3q7f_A* 3sfx_A* 3sfy_A*

Probab=98.79  E-value=1e-05  Score=71.42  Aligned_cols=220  Identities=7%  Similarity=-0.037  Sum_probs=111.0

Q ss_pred             CHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccC-CHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhc-C-CHHHHH
Q 012111          200 RFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAK-KFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNS-G-NIEKME  276 (471)
Q Consensus       200 ~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~-~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-~-~~~~a~  276 (471)
                      ..++|+++++.++... +-+..+|+.--..+...| .++++++.++.+....  +.+..+|+.-..++... + ++++++
T Consensus        69 ~se~AL~lt~~~L~~n-P~~ytaWn~R~~iL~~l~~~l~eEL~~~~~~L~~n--PKny~aW~hR~wlL~~l~~~~~~~EL  145 (349)
T 3q7a_A           69 KSERALELTEIIVRMN-PAHYTVWQYRFSLLTSLNKSLEDELRLMNEFAVQN--LKSYQVWHHRLLLLDRISPQDPVSEI  145 (349)
T ss_dssp             CSHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHTT--CCCHHHHHHHHHHHHHHCCSCCHHHH
T ss_pred             CCHHHHHHHHHHHHhC-chhHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHhC--CCcHHHHHHHHHHHHHhcCCChHHHH
Confidence            3445666666665543 334455555555555555 3666666666665543  44455555555554444 4 556666


Q ss_pred             HHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHH--------HHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCC-------
Q 012111          277 KWYNEFNLMGVKADIQTLNILTKSYGRAGMYD--------KMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGH-------  341 (471)
Q Consensus       277 ~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~--------~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~-------  341 (471)
                      .+++.+.+.. +-+..+|+.-.-.+.+.|.++        +++..++.+.+..+. |...|+.....+.+.++       
T Consensus       146 ~~~~k~L~~d-pkNy~AW~~R~wvl~~l~~~~~~~~~~~~eELe~~~k~I~~dp~-N~SAW~~R~~lL~~l~~~~~~~~~  223 (349)
T 3q7a_A          146 EYIHGSLLPD-PKNYHTWAYLHWLYSHFSTLGRISEAQWGSELDWCNEMLRVDGR-NNSAWGWRWYLRVSRPGAETSSRS  223 (349)
T ss_dssp             HHHHHHTSSC-TTCHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHTTSTTCCCCHHH
T ss_pred             HHHHHHHHhC-CCCHHHHHHHHHHHHHhccccccchhhHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHhccccccchHH
Confidence            6666665543 344444444333333333333        556666666555333 55555555555555544       


Q ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCH--------------------HHHHHHHHHHHhCC-----CCcCH
Q 012111          342 IEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLI--------------------MKVDSILRQVENSD-----VILDT  396 (471)
Q Consensus       342 ~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~--------------------~~a~~~~~~~~~~~-----~~~~~  396 (471)
                      ++++++.+++++... +-|...|+.+-..+.+.|..                    .....+...+...+     -.++.
T Consensus       224 ~~eELe~~~~aI~~~-P~n~SaW~Ylr~Ll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~  302 (349)
T 3q7a_A          224 LQDELIYILKSIHLI-PHNVSAWNYLRGFLKHFSLPLVPILPAILPYTASKLNPDIETVEAFGFPMPSDPLPEDTPLPVP  302 (349)
T ss_dssp             HHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCCSGGGHHHHGGGTC--------------CCCCC-CCCSSCCSCCH
T ss_pred             HHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHhcCCCcccccccccccccccccccchhHHHHHHHHHhcccccccCCCcH
Confidence            456666666666542 22555555555545444432                    11222222222111     02355


Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhC
Q 012111          397 PFFNCIISAYGQAGDVEKMGELFLTMKER  425 (471)
Q Consensus       397 ~~~~~l~~~~~~~g~~~~a~~~~~~~~~~  425 (471)
                      ..+..|+..|...|+.++|.++++.+.+.
T Consensus       303 ~al~~l~d~~~~~~~~~~a~~~~~~l~~~  331 (349)
T 3q7a_A          303 LALEYLADSFIEQNRVDDAAKVFEKLSSE  331 (349)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhh
Confidence            56666666666666666666666666543

>3gw4_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, no structural genomics consortium, NESG, DRR162B; 2.49A {Deinococcus radiodurans R1}

Probab=98.79  E-value=1.2e-07  Score=78.10  Aligned_cols=139  Identities=7%  Similarity=-0.064  Sum_probs=67.9

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHHc----CCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhC----CCC--cC
Q 012111          327 VTYNIVIETFGKAGHIEKMEEYFKKMKHR----GMKP-NSITYCSLVSAYSKAGLIMKVDSILRQVENS----DVI--LD  395 (471)
Q Consensus       327 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~----~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~----~~~--~~  395 (471)
                      ..+..+...+...|++++|...+++....    +..+ ...++..+...+...|++++|...+++..+.    +-.  ..
T Consensus        27 ~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~  106 (203)
T 3gw4_A           27 GARFMLGYVYAFMDRFDEARASFQALQQQAQKSGDHTAEHRALHQVGMVERMAGNWDAARRCFLEERELLASLPEDPLAA  106 (203)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHH
T ss_pred             HHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCccHHHH
Confidence            34444445555555555555555544431    1111 2234455555555556666665555554332    101  11


Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCC-CCCC----HHHHHHHHHHHHhcCCHHHHHHHHHHHHHhhhcCC
Q 012111          396 TPFFNCIISAYGQAGDVEKMGELFLTMKERH-CVPD----NITFATMIQAYNALGMTEAAQNLENKMIAMKENSG  465 (471)
Q Consensus       396 ~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~-~~p~----~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~~~  465 (471)
                      ...+..+...+...|++++|...+++..+.. -..+    ..++..+...+...|++++|.+.++++++.....+
T Consensus       107 ~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~  181 (203)
T 3gw4_A          107 SANAYEVATVALHFGDLAGARQEYEKSLVYAQQADDQVAIACAFRGLGDLAQQEKNLLEAQQHWLRARDIFAELE  181 (203)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhccchHHHHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHcC
Confidence            2345555556666666666666665554210 0011    12334555566666666666666666665554443

>2vgx_A Chaperone SYCD; alternative dimer assembly, tetratricopeptide repeat, type III secretion; HET: MLY; 1.95A {Yersinia enterocolitica} SCOP: k.38.1.1 PDB: 2vgx_B* 2vgy_A*

Probab=98.78  E-value=3.9e-08  Score=76.55  Aligned_cols=96  Identities=11%  Similarity=0.017  Sum_probs=59.3

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHH
Q 012111          327 VTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAY  406 (471)
Q Consensus       327 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  406 (471)
                      ..+..+...+...|++++|...|++..... +.+...|..+..++...|++++|...|+++...++. +...+..+..+|
T Consensus        22 ~~~~~~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~p~-~~~~~~~lg~~~   99 (148)
T 2vgx_A           22 EQLYSLAFNQYQSGXYEDAHXVFQALCVLD-HYDSRFFLGLGACRQAMGQYDLAIHSYSYGAVMDIX-EPRFPFHAAECL   99 (148)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTT-CTHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCChHHHHHHHHHHHHcC-cccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCC-CchHHHHHHHHH
Confidence            344555556666666666666666666543 235556666666666666666666666666655444 455566666666


Q ss_pred             HhcCCHHHHHHHHHHHHh
Q 012111          407 GQAGDVEKMGELFLTMKE  424 (471)
Q Consensus       407 ~~~g~~~~a~~~~~~~~~  424 (471)
                      ...|++++|...|++..+
T Consensus       100 ~~~g~~~~A~~~~~~al~  117 (148)
T 2vgx_A          100 LQXGELAEAESGLFLAQE  117 (148)
T ss_dssp             HHTTCHHHHHHHHHHHHH
T ss_pred             HHcCCHHHHHHHHHHHHH
Confidence            666666666666666654

>1hh8_A P67PHOX, NCF-2, neutrophil cytosol factor 2; cell cycle, phagocyte oxidase factor, SH3 domain, repeat, TPR repeat cell cycle; HET: FLC; 1.8A {Homo sapiens} SCOP: a.118.8.1 PDB: 1wm5_A 1e96_B*

Probab=98.77  E-value=1.1e-06  Score=72.95  Aligned_cols=132  Identities=8%  Similarity=-0.074  Sum_probs=110.3

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHH
Q 012111          257 FTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETF  336 (471)
Q Consensus       257 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~  336 (471)
                      ..+..+...+...|++++|...|++..    .++...+..+...+...|++++|...++...+... .+...+..+..++
T Consensus         7 ~~~~~~g~~~~~~~~~~~A~~~~~~a~----~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~-~~~~~~~~lg~~~   81 (213)
T 1hh8_A            7 ISLWNEGVLAADKKDWKGALDAFSAVQ----DPHSRICFNIGCMYTILKNMTEAEKAFTRSINRDK-HLAVAYFQRGMLY   81 (213)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHTSS----SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCHHHHHHHHHHHc----CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCc-cchHHHHHHHHHH
Confidence            445667788889999999999998873    56888999999999999999999999999887643 3677888899999


Q ss_pred             HhcCCHHHHHHHHHHHHHcCCC--------------C-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCC
Q 012111          337 GKAGHIEKMEEYFKKMKHRGMK--------------P-NSITYCSLVSAYSKAGLIMKVDSILRQVENSDVI  393 (471)
Q Consensus       337 ~~~g~~~~a~~~~~~m~~~~~~--------------p-~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~  393 (471)
                      ...|++++|...|++..+....              | ....+..+..++...|++++|...++.+.+..+.
T Consensus        82 ~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~  153 (213)
T 1hh8_A           82 YQTEKYDLAIKDLKEALIQLRGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATSMKSE  153 (213)
T ss_dssp             HHTTCHHHHHHHHHHHHHTTTTCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCS
T ss_pred             HHcccHHHHHHHHHHHHHhCCCccHHHHHHhccccCccchHHHHHHHHHHHHccCHHHHHHHHHHHHHcCcc
Confidence            9999999999999999886311              1 1267888999999999999999999999987654

>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovar ISRAELE35646}

Probab=98.76  E-value=1.7e-06  Score=76.06  Aligned_cols=167  Identities=10%  Similarity=-0.014  Sum_probs=93.9

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCH----HHHHHHHHHHHhcCCHHHHHHHHHHHHHCCC---CCC--H
Q 012111          150 DVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDV----YTYSILIKSCTKFHRFDLIEKILAEMSYLGI---ECS--A  220 (471)
Q Consensus       150 ~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~----~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~---~~~--~  220 (471)
                      ..+...+..+...|++++|++.+.+..+.....++.    ..+..+...+...|++++|...+++..+...   .+.  .
T Consensus        76 ~~l~~~~~~~~~~~~y~~A~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~  155 (293)
T 2qfc_A           76 KQFKDQVIMLCKQKRYKEIYNKVWNELKKEEYHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQNL  155 (293)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHTCCCCHHHHHHHHHHHHHHHHHHTSSCHHHHHHHHHHHHTTCCCSSCTTHHH
T ss_pred             HHHHHHHHHHHHhhhHHHHHHHHHHHhccccCChhHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhcCCchHHHH
Confidence            345556667778888888888887766532211111    1233344455666677777777777664321   111  3


Q ss_pred             HHHHHHHHHHHccCCHHHHHHHHHHHH---HcCCCCC--CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCC----CCC-C
Q 012111          221 VTYNTIIDGYGKAKKFEEMESSFSAMV---ESGGCHP--DIFTLNSMISAYGNSGNIEKMEKWYNEFNLMG----VKA-D  290 (471)
Q Consensus       221 ~~~~~l~~~~~~~~~~~~a~~~~~~~~---~~~~~~~--~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~----~~~-~  290 (471)
                      .+++.+...|...|++++|...|++..   +..+..+  ...++..+...|...|++++|...+++.....    ... -
T Consensus       156 ~~~~~lg~~y~~~~~~~~A~~~~~kal~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~Al~~~~kal~~~~~~~~~~~~  235 (293)
T 2qfc_A          156 YIENAIANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAIEISCRINSMALI  235 (293)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTBCSSH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcCccccchHHHHHhHHHHHHHHhhHHHHHHHHHHHHHHHHhcCcHHHH
Confidence            466667777777777777777777665   2211111  11456666667777777777777776654321    011 1


Q ss_pred             HHHHHHHHHHHHHcCCHHHH-HHHHHH
Q 012111          291 IQTLNILTKSYGRAGMYDKM-RSVMDF  316 (471)
Q Consensus       291 ~~~~~~ll~~~~~~~~~~~a-~~~~~~  316 (471)
                      ..+|..+..+|.+.|++++| ...++.
T Consensus       236 ~~~~~~lg~~y~~~g~~~~Ai~~~~~~  262 (293)
T 2qfc_A          236 GQLYYQRGECLRKLEYEEAEIEDAYKK  262 (293)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCcHHHHHHHHHH
Confidence            34555556666666666666 444443

>3gyz_A Chaperone protein IPGC; asymmetric homodimer, tetratricopeptide repeat, TPR, chapero virulence; 2.15A {Shigella flexneri} PDB: 3gz1_A 3gz2_A 3ks2_A

Probab=98.74  E-value=1.1e-06  Score=68.33  Aligned_cols=102  Identities=12%  Similarity=0.073  Sum_probs=81.7

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHH
Q 012111          361 SITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQA  440 (471)
Q Consensus       361 ~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~  440 (471)
                      ...+..+...+.+.|++++|...|+++...++. +...|..+..+|...|++++|+..|++..+.. +-++..|..+..+
T Consensus        36 ~~~~~~lg~~~~~~g~~~eA~~~~~~al~~~P~-~~~~~~~lg~~~~~~g~~~~Ai~~~~~al~l~-P~~~~~~~~lg~~  113 (151)
T 3gyz_A           36 MDDIYSYAYDFYNKGRIEEAEVFFRFLCIYDFY-NVDYIMGLAAIYQIKEQFQQAADLYAVAFALG-KNDYTPVFHTGQC  113 (151)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-SSCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHHccHHHHHHHHHHHHhhC-CCCcHHHHHHHHH
Confidence            456777778888888888888888888887765 78888888888888888888888888888742 2256777788888


Q ss_pred             HHhcCCHHHHHHHHHHHHHhhhcC
Q 012111          441 YNALGMTEAAQNLENKMIAMKENS  464 (471)
Q Consensus       441 ~~~~g~~~~A~~~~~~m~~~~~~~  464 (471)
                      |...|++++|...|+++++..|++
T Consensus       114 ~~~lg~~~eA~~~~~~al~l~~~~  137 (151)
T 3gyz_A          114 QLRLKAPLKAKECFELVIQHSNDE  137 (151)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHCCCH
T ss_pred             HHHcCCHHHHHHHHHHHHHhCCCH
Confidence            888888888888888888887654

>2e2e_A Formate-dependent nitrite reductase complex NRFG; TPR, cytochrome C biogenesis, O157:H7 EDL933, formate- nitrite reductase complex, lyase; 2.05A {Escherichia coli}

Probab=98.73  E-value=1.4e-07  Score=75.94  Aligned_cols=121  Identities=8%  Similarity=0.022  Sum_probs=88.9

Q ss_pred             HHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHH-HHhcCCH--H
Q 012111          302 GRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSA-YSKAGLI--M  378 (471)
Q Consensus       302 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~-~~~~g~~--~  378 (471)
                      ...|++++|...++...+... .+...+..+...|...|++++|...|++..... +.+...+..+..+ +...|++  +
T Consensus        21 ~~~~~~~~A~~~~~~al~~~p-~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~la~~l~~~~~~~~~~   98 (177)
T 2e2e_A           21 ASQQNPEAQLQALQDKIRANP-QNSEQWALLGEYYLWQNDYSNSLLAYRQALQLR-GENAELYAALATVLYYQASQHMTA   98 (177)
T ss_dssp             C-----CCCCHHHHHHHHHCC-SCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH-CSCHHHHHHHHHHHHHHTTTCCCH
T ss_pred             hhccCHHHHHHHHHHHHHhCC-CcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHhcCCcchH
Confidence            456778888888887776533 356777888888888888888888888887753 3356677777777 6778887  8


Q ss_pred             HHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhC
Q 012111          379 KVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKER  425 (471)
Q Consensus       379 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~  425 (471)
                      +|...++.+.+.++. +...+..+...+...|++++|...|+++.+.
T Consensus        99 ~A~~~~~~al~~~p~-~~~~~~~la~~~~~~g~~~~A~~~~~~al~~  144 (177)
T 2e2e_A           99 QTRAMIDKALALDSN-EITALMLLASDAFMQANYAQAIELWQKVMDL  144 (177)
T ss_dssp             HHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHhCCC-cHHHHHHHHHHHHHcccHHHHHHHHHHHHhh
Confidence            888888888876654 6777778888888888888888888888774

>2c2l_A CHIP, carboxy terminus of HSP70-interacting protein; chaperone, E3 ligase, ubiquitinylation, TPR, heat-shock protein complex; 3.3A {Mus musculus} SCOP: a.118.8.1 g.44.1.2

Probab=98.73  E-value=1.1e-07  Score=82.96  Aligned_cols=98  Identities=9%  Similarity=-0.006  Sum_probs=58.8

Q ss_pred             CHHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHH
Q 012111          219 SAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILT  298 (471)
Q Consensus       219 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll  298 (471)
                      +...+..+...+.+.|++++|...|++..+..  +.+...|..+..++.+.|++++|...+++..+.. +.+...+..+.
T Consensus         3 ~a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg   79 (281)
T 2c2l_A            3 SAQELKEQGNRLFVGRKYPEAAACYGRAITRN--PLVAVYYTNRALCYLKMQQPEQALADCRRALELD-GQSVKAHFFLG   79 (281)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSC-TTCHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCCHHHHHHHH
Confidence            34455555666666666666666666665542  3355566666666666666666666666665543 34455566666


Q ss_pred             HHHHHcCCHHHHHHHHHHHHh
Q 012111          299 KSYGRAGMYDKMRSVMDFMQK  319 (471)
Q Consensus       299 ~~~~~~~~~~~a~~~~~~~~~  319 (471)
                      .++...|++++|...|....+
T Consensus        80 ~~~~~~g~~~~A~~~~~~al~  100 (281)
T 2c2l_A           80 QCQLEMESYDEAIANLQRAYS  100 (281)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHH
Confidence            666666666666666665544

>4gco_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; 1.60A {Caenorhabditis elegans}

Probab=98.72  E-value=5.1e-07  Score=67.92  Aligned_cols=101  Identities=8%  Similarity=-0.059  Sum_probs=73.8

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHH
Q 012111          362 ITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAY  441 (471)
Q Consensus       362 ~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~  441 (471)
                      ..+......+.+.|++++|.+.|++..+.++. +...|..+..+|...|++++|+..|++.++.+ +.+...|..+..++
T Consensus        14 ~~~~~~G~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~   91 (126)
T 4gco_A           14 QEEKNKGNEYFKKGDYPTAMRHYNEAVKRDPE-NAILYSNRAACLTKLMEFQRALDDCDTCIRLD-SKFIKGYIRKAACL   91 (126)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-CHHHHHHHhhHHHhhccHHHHHHHHHHHHHhh-hhhhHHHHHHHHHH
Confidence            45666677777778888888888777776654 67777777777777788888888777777642 23566777777777


Q ss_pred             HhcCCHHHHHHHHHHHHHhhhcC
Q 012111          442 NALGMTEAAQNLENKMIAMKENS  464 (471)
Q Consensus       442 ~~~g~~~~A~~~~~~m~~~~~~~  464 (471)
                      ...|++++|.+.|+++++.+|+.
T Consensus        92 ~~~~~~~~A~~~~~~al~l~P~~  114 (126)
T 4gco_A           92 VAMREWSKAQRAYEDALQVDPSN  114 (126)
T ss_dssp             HHTTCHHHHHHHHHHHHHHCTTC
T ss_pred             HHCCCHHHHHHHHHHHHHHCcCC
Confidence            77788888888888877777654

>1a17_A Serine/threonine protein phosphatase 5; hydrolase, protein-protein interactions, TPR, S helix; 2.45A {Homo sapiens} SCOP: a.118.8.1 PDB: 2bug_A

Probab=98.72  E-value=1.1e-06  Score=69.52  Aligned_cols=128  Identities=9%  Similarity=-0.105  Sum_probs=79.4

Q ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Q 012111          293 TLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYS  372 (471)
Q Consensus       293 ~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~  372 (471)
                      .+..+...+...|++++|...+....+.... +...+..+...+...|++++|...+++..... +.+...+..+..++.
T Consensus        15 ~~~~~a~~~~~~~~~~~A~~~~~~al~~~~~-~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~~a~~~~   92 (166)
T 1a17_A           15 ELKTQANDYFKAKDYENAIKFYSQAIELNPS-NAIYYGNRSLAYLRTECYGYALGDATRAIELD-KKYIKGYYRRAASNM   92 (166)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHSTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHccCHHHHHHHHHHHHHhCCC-ChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHH
Confidence            3444555566666666666666666554222 45566666666777777777777777766653 335666777777777


Q ss_pred             hcCCHHHHHHHHHHHHhCCCCcCHHHHHH--HHHHHHhcCCHHHHHHHHHHHH
Q 012111          373 KAGLIMKVDSILRQVENSDVILDTPFFNC--IISAYGQAGDVEKMGELFLTMK  423 (471)
Q Consensus       373 ~~g~~~~a~~~~~~~~~~~~~~~~~~~~~--l~~~~~~~g~~~~a~~~~~~~~  423 (471)
                      ..|++++|...++++.+..+. +...+..  ++..+...|++++|+..+....
T Consensus        93 ~~~~~~~A~~~~~~a~~~~p~-~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~  144 (166)
T 1a17_A           93 ALGKFRAALRDYETVVKVKPH-DKDAKMKYQECNKIVKQKAFERAIAGDEHKR  144 (166)
T ss_dssp             HTTCHHHHHHHHHHHHHHSTT-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HhccHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHHHHHHHHHHHHcccchH
Confidence            777777777777777665443 4444433  3333666677777777776554

>4f3v_A ESX-1 secretion system protein ECCA1; tetratricopeptide repeat, TPR domain, ATPase, protein secret protein transport; 2.00A {Mycobacterium tuberculosis}

Probab=98.72  E-value=9e-07  Score=75.50  Aligned_cols=186  Identities=7%  Similarity=-0.059  Sum_probs=82.9

Q ss_pred             ccCCHHHHHHHHHHHHHcCCCCCCHHHHHHH-------HHHHHhcCCHHHHHHHHHHHHhCCCCCC--------------
Q 012111          232 KAKKFEEMESSFSAMVESGGCHPDIFTLNSM-------ISAYGNSGNIEKMEKWYNEFNLMGVKAD--------------  290 (471)
Q Consensus       232 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l-------~~~~~~~~~~~~a~~~~~~~~~~~~~~~--------------  290 (471)
                      ..++...|.+.|.++.+..  +-....|..+       ..++...++..+++..+..-..  +.|+              
T Consensus        18 ~~~d~~~A~~~F~~a~~~d--P~~~Daw~g~~a~g~~~~~~L~~~~r~~~a~~~~~~~l~--l~p~~l~a~~~~~g~y~~   93 (282)
T 4f3v_A           18 LPMSEARSLDLFTEITNYD--ESACDAWIGRIRCGDTDRVTLFRAWYSRRNFGQLSGSVQ--ISMSTLNARIAIGGLYGD   93 (282)
T ss_dssp             TTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHTTCCCHHHHHHHHHTGGGTTHHHHTTT--CCGGGGCCEEECCTTTCC
T ss_pred             cCCCHHHHHHHHHHHHHhC--hhhhHHHHhHHHccCCcHHHHHHHHHHHHHHHHHHHHhc--CChhhhhhhhccCCcccc
Confidence            4677777777777776653  3344556555       3334333334444433333322  1111              


Q ss_pred             --------HHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCC--
Q 012111          291 --------IQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPN--  360 (471)
Q Consensus       291 --------~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~--  360 (471)
                              ......+...+...|++++|.++|+.+...+  |+......+...+.+.+++++|+..|+...... .|.  
T Consensus        94 ~~~~v~~r~dl~LayA~~L~~~g~y~eA~~~l~~~~~~~--p~~~~~~~~a~l~~~~~r~~dA~~~l~~a~~~~-d~~~~  170 (282)
T 4f3v_A           94 ITYPVTSPLAITMGFAACEAAQGNYADAMEALEAAPVAG--SEHLVAWMKAVVYGAAERWTDVIDQVKSAGKWP-DKFLA  170 (282)
T ss_dssp             CEEECSSHHHHHHHHHHHHHHHTCHHHHHHHHTSSCCTT--CHHHHHHHHHHHHHHTTCHHHHHHHHTTGGGCS-CHHHH
T ss_pred             cccccCCHhHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC--CchHHHHHHHHHHHHcCCHHHHHHHHHHhhccC-CcccH
Confidence                    1222334444555555555555555544432  222233333334455555555555554332210 010  


Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcC--HHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 012111          361 SITYCSLVSAYSKAGLIMKVDSILRQVENSDVILD--TPFFNCIISAYGQAGDVEKMGELFLTMKE  424 (471)
Q Consensus       361 ~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~--~~~~~~l~~~~~~~g~~~~a~~~~~~~~~  424 (471)
                      ...+..+..++...|++++|+..|++.......|.  .........++.+.|+.++|..+|+++..
T Consensus       171 ~~a~~~LG~al~~LG~~~eAl~~l~~a~~g~~~P~~~~da~~~~glaL~~lGr~deA~~~l~~a~a  236 (282)
T 4f3v_A          171 GAAGVAHGVAAANLALFTEAERRLTEANDSPAGEACARAIAWYLAMARRSQGNESAAVALLEWLQT  236 (282)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHTSTTTTTTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHhcCCCCccccHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            12344444455555555555555555443221121  12333344444455555555555555544

>2c2l_A CHIP, carboxy terminus of HSP70-interacting protein; chaperone, E3 ligase, ubiquitinylation, TPR, heat-shock protein complex; 3.3A {Mus musculus} SCOP: a.118.8.1 g.44.1.2

Probab=98.71  E-value=2.1e-07  Score=81.20  Aligned_cols=197  Identities=7%  Similarity=-0.064  Sum_probs=136.2

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHH
Q 012111          255 DIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIE  334 (471)
Q Consensus       255 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~  334 (471)
                      +...+..+...+...|++++|...|++..... +.+...+..+..+|.+.|++++|...++...+.... +...+..+..
T Consensus         3 ~a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~p~-~~~~~~~lg~   80 (281)
T 2c2l_A            3 SAQELKEQGNRLFVGRKYPEAAACYGRAITRN-PLVAVYYTNRALCYLKMQQPEQALADCRRALELDGQ-SVKAHFFLGQ   80 (281)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSCTT-CHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCC-CHHHHHHHHH
Confidence            45678888899999999999999999998764 557889999999999999999999999999886433 6778888999


Q ss_pred             HHHhcCCHHHHHHHHHHHHHcCCCCCH-HHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHH
Q 012111          335 TFGKAGHIEKMEEYFKKMKHRGMKPNS-ITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVE  413 (471)
Q Consensus       335 ~~~~~g~~~~a~~~~~~m~~~~~~p~~-~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~  413 (471)
                      ++...|++++|...|++..+..  |+. ..+...+....+   ...+. -+..........+......+.. + ..|+++
T Consensus        81 ~~~~~g~~~~A~~~~~~al~l~--p~~~~~~~~~~~~~~~---~~~~~-~~~~~~~~~~~~~~~i~~~l~~-l-~~~~~~  152 (281)
T 2c2l_A           81 CQLEMESYDEAIANLQRAYSLA--KEQRLNFGDDIPSALR---IAKKK-RWNSIEERRIHQESELHSYLTR-L-IAAERE  152 (281)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHH--HHTTCCCCSHHHHHHH---HHHHH-HHHHHHHTCCCCCCHHHHHHHH-H-HHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHhC--ccchhhHHHHHHHHHH---HHHHH-HHHHHHHHHHhhhHHHHHHHHH-H-HHHHHH
Confidence            9999999999999999887642  211 011111111111   11111 1222333334445555444433 2 368999


Q ss_pred             HHHHHHHHHHhCCCCCCHHHHH-HHHHHHHhc-CCHHHHHHHHHHHHHhhhc
Q 012111          414 KMGELFLTMKERHCVPDNITFA-TMIQAYNAL-GMTEAAQNLENKMIAMKEN  463 (471)
Q Consensus       414 ~a~~~~~~~~~~~~~p~~~~~~-~l~~~~~~~-g~~~~A~~~~~~m~~~~~~  463 (471)
                      +|++.+++..+.  .|+..... .+...+.+. +.+++|.++|+++.+..+.
T Consensus       153 ~A~~~~~~al~~--~p~~~~~~~~l~~~~~~~~~~~~~a~~~f~~a~~~~~~  202 (281)
T 2c2l_A          153 RELEECQRNHEG--HEDDGHIRAQQACIEAKHDKYMADMDELFSQVDEKRKK  202 (281)
T ss_dssp             HHHTTTSGGGTT--TSCHHHHTHHHHHHHHHHHHHHHHHHHHHHHSSCTTSC
T ss_pred             HHHHHHHhhhcc--ccchhhhhhHHHHHHHHHHHHHHHHHHHHHhhhccccC
Confidence            999999888864  56654443 333444444 6788999999988765443

>3dss_A Geranylgeranyl transferase type-2 subunit alpha; protein prenylation, metal-binding, prenyltransferase, zinc, phosphoprotein; 1.80A {Rattus norvegicus} PDB: 3dst_A* 3dsu_A* 3dsv_A* 3dsw_A* 3dsx_A* 3hxb_A* 3hxc_A* 3hxd_A* 3hxe_A* 3hxf_A* 3pz1_A* 3pz2_A* 3pz3_A* 3c72_A* 4gtv_A* 4gts_A* 4ehm_A* 4gtt_A*

Probab=98.70  E-value=1.9e-05  Score=69.36  Aligned_cols=232  Identities=9%  Similarity=0.023  Sum_probs=109.9

Q ss_pred             HHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCC----------HHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcC-
Q 012111          202 DLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKK----------FEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSG-  270 (471)
Q Consensus       202 ~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~----------~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-  270 (471)
                      ++|+++++.+...+ +-+..+|+.--..+...+.          +++++.+++.+....  +.+..+|+.-..++...+ 
T Consensus        47 ~eaL~~t~~~L~~n-P~~ytaWn~Rr~iL~~l~~~~~~~~~~~~l~~EL~~~~~~L~~~--PKny~aW~hR~wlL~~l~~  123 (331)
T 3dss_A           47 ESVLELTSQILGAN-PDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVN--PKSYGTWHHRCWLLSRLPE  123 (331)
T ss_dssp             HHHHHHHHHHHTTC-TTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHCSS
T ss_pred             HHHHHHHHHHHHHC-chhHHHHHHHHHHHHHhcccccchhhhHHHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHhccCc
Confidence            35666666666553 2344445443333332222          345555555555542  344555555554444444 


Q ss_pred             -CHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCC-HHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHH
Q 012111          271 -NIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGM-YDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEY  348 (471)
Q Consensus       271 -~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~-~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~  348 (471)
                       ++++++.+++.+.+.. +-+..+|+.-.-++...|. ++++...++.+.+..+. |...|+.....+...+....+-  
T Consensus       124 ~~~~~EL~~~~k~l~~d-prNy~AW~~R~~vl~~l~~~~~eel~~~~~~I~~~p~-N~SAW~~R~~ll~~l~~~~~~~--  199 (331)
T 3dss_A          124 PNWARELELCARFLEAD-ERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRNFS-NYSSWHYRSCLLPQLHPQPDSG--  199 (331)
T ss_dssp             CCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCSC-CHHHHHHHHHHHHHHSCCC-----
T ss_pred             ccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhCcCHHHHHHHHHHHHHHCCC-CHHHHHHHHHHHHHhhhccccc--
Confidence             2455555555555443 3344444444444444444 34455555544444322 4444444333333221000000  


Q ss_pred             HHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhc-----------CCHHHHHH
Q 012111          349 FKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQA-----------GDVEKMGE  417 (471)
Q Consensus       349 ~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-----------g~~~~a~~  417 (471)
                           ..+ .             ...+.++++.+.+.......+. |...|+-+-..+.+.           +.++++++
T Consensus       200 -----~~~-~-------------~~~~~~~eEle~~~~ai~~~P~-d~SaW~Y~r~ll~~~~~~~~~~~~~~~~l~~el~  259 (331)
T 3dss_A          200 -----PQG-R-------------LPENVLLKELELVQNAFFTDPN-DQSAWFYHRWLLGAGSGRCELSVEKSTVLQSELE  259 (331)
T ss_dssp             ---------C-------------CCHHHHHHHHHHHHHHHHHSTT-CHHHHHHHHHHHHSSSCGGGCCHHHHHHHHHHHH
T ss_pred             -----ccc-c-------------cchHHHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHhccCccccchHHHHHHHHHHH
Confidence                 000 0             0002345555556555555444 555555444444333           34677777


Q ss_pred             HHHHHHhCCCCCCHHHHHHHH-----HHHHhcCCHHHHHHHHHHHHHhhhc
Q 012111          418 LFLTMKERHCVPDNITFATMI-----QAYNALGMTEAAQNLENKMIAMKEN  463 (471)
Q Consensus       418 ~~~~~~~~~~~p~~~~~~~l~-----~~~~~~g~~~~A~~~~~~m~~~~~~  463 (471)
                      .++++.+.  .||. .|..+.     .+....|..+++...+.++++.+|-
T Consensus       260 ~~~elle~--~pd~-~w~l~~~~~~~~~~~~~~~~~~~~~~l~~l~~~Dp~  307 (331)
T 3dss_A          260 SCKELQEL--EPEN-KWCLLTIILLMRALDPLLYEKETLQYFSTLKAVDPM  307 (331)
T ss_dssp             HHHHHHHH--CTTC-HHHHHHHHHHHHHHCTTTTHHHHHHHHHHHHHHCGG
T ss_pred             HHHHHHhh--Cccc-chHHHHHHHHHHhhcccccHHHHHHHHHHHHHhCcc
Confidence            77777763  4553 232211     1222456777888888888877774

>1na0_A Designed protein CTPR3; de novo protein; HET: IPT; 1.60A {Unidentified} SCOP: k.38.1.1 PDB: 2wqh_A 3kd7_A

Probab=98.70  E-value=1.4e-06  Score=64.95  Aligned_cols=113  Identities=17%  Similarity=0.164  Sum_probs=66.3

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHH
Q 012111          327 VTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAY  406 (471)
Q Consensus       327 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  406 (471)
                      ..+..+...+...|++++|..+++++.... +.+..++..+...+...|++++|..+++++.+..+. +...+..+...+
T Consensus        10 ~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~la~~~   87 (125)
T 1na0_A           10 EAWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAWYNLGNAYYKQGDYDEAIEYYQKALELDPN-NAEAWYNLGNAY   87 (125)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHC-cCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhCCc-cHHHHHHHHHHH
Confidence            445555566666666666666666666542 234556666666666666666666666666655433 555666666666


Q ss_pred             HhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHH
Q 012111          407 GQAGDVEKMGELFLTMKERHCVPDNITFATMIQAYN  442 (471)
Q Consensus       407 ~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~  442 (471)
                      ...|++++|...++++.+.. +.+...+..+...+.
T Consensus        88 ~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~  122 (125)
T 1na0_A           88 YKQGDYDEAIEYYQKALELD-PNNAEAKQNLGNAKQ  122 (125)
T ss_dssp             HHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHH
T ss_pred             HHhcCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHH
Confidence            66677777777776666531 223444444444443

>1p5q_A FKBP52, FK506-binding protein 4; isomerase; 2.80A {Homo sapiens} SCOP: a.118.8.1 d.26.1.1 PDB: 1qz2_A

Probab=98.68  E-value=7.9e-07  Score=79.71  Aligned_cols=130  Identities=11%  Similarity=-0.057  Sum_probs=76.7

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCC--------------HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCC
Q 012111          328 TYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPN--------------SITYCSLVSAYSKAGLIMKVDSILRQVENSDVI  393 (471)
Q Consensus       328 ~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~--------------~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~  393 (471)
                      .+..+...+.+.|++++|...|++.........              ...|..+..++.+.|++++|...++++.+..+.
T Consensus       149 ~~~~~g~~~~~~g~~~~A~~~y~~Al~~~p~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~~~p~  228 (336)
T 1p5q_A          149 IVKERGTVYFKEGKYKQALLQYKKIVSWLEYESSFSNEEAQKAQALRLASHLNLAMCHLKLQAFSAAIESCNKALELDSN  228 (336)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHTTTCCCCCSHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHHhhccccCChHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC
Confidence            444455555555555555555555555421111              356666666666677777777777666665544


Q ss_pred             cCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHH-HHHHHHHHH
Q 012111          394 LDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAYNALGMTEAA-QNLENKMIA  459 (471)
Q Consensus       394 ~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A-~~~~~~m~~  459 (471)
                       +...|..+..+|...|++++|+..|+++.+.. +-+...+..+..++...|+.++| ..++++|..
T Consensus       229 -~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~-P~~~~a~~~l~~~~~~~~~~~~a~~~~~~~~~~  293 (336)
T 1p5q_A          229 -NEKGLSRRGEAHLAVNDFELARADFQKVLQLY-PNNKAAKTQLAVCQQRIRRQLAREKKLYANMFE  293 (336)
T ss_dssp             -CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             -cHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence             56666666667777777777777776666531 22455566666666666666666 445555543

>2xcb_A PCRH, regulatory protein PCRH; protein transport, bacterial toxin, type III secretion, protein binding; 1.85A {Pseudomonas aeruginosa} PDB: 2xcc_A

Probab=98.66  E-value=4.8e-07  Score=69.78  Aligned_cols=95  Identities=13%  Similarity=0.063  Sum_probs=60.6

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHH
Q 012111          328 TYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYG  407 (471)
Q Consensus       328 ~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  407 (471)
                      .+..+...+...|++++|...|++..... +.+...|..+..++...|++++|...|+.....++. +...+..+..+|.
T Consensus        20 ~~~~~a~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~lg~~~~   97 (142)
T 2xcb_A           20 QLYALGFNQYQAGKWDDAQKIFQALCMLD-HYDARYFLGLGACRQSLGLYEQALQSYSYGALMDIN-EPRFPFHAAECHL   97 (142)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CTHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHccHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCC-CcHHHHHHHHHHH
Confidence            44445556666677777777777666653 235566666666666777777777777666665544 5556666666666


Q ss_pred             hcCCHHHHHHHHHHHHh
Q 012111          408 QAGDVEKMGELFLTMKE  424 (471)
Q Consensus       408 ~~g~~~~a~~~~~~~~~  424 (471)
                      ..|++++|...|++..+
T Consensus        98 ~~g~~~~A~~~~~~al~  114 (142)
T 2xcb_A           98 QLGDLDGAESGFYSARA  114 (142)
T ss_dssp             HTTCHHHHHHHHHHHHH
T ss_pred             HcCCHHHHHHHHHHHHH
Confidence            67777777776666654

>2vyi_A SGTA protein; chaperone, TPR repeat, phosphoprotein, tetratricopeptide repeat protein, HOST-virus interaction; 2.4A {Homo sapiens} SCOP: k.38.1.1

Probab=98.66  E-value=1.1e-06  Score=66.20  Aligned_cols=118  Identities=13%  Similarity=0.041  Sum_probs=78.4

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHH
Q 012111          326 VVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISA  405 (471)
Q Consensus       326 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  405 (471)
                      ...+..+...+...|++++|...+++..... +.+...+..+...+...|++++|...++...+..+. +...+..+..+
T Consensus        12 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~~~~~   89 (131)
T 2vyi_A           12 AERLKTEGNEQMKVENFEAAVHFYGKAIELN-PANAVYFCNRAAAYSKLGNYAGAVQDCERAICIDPA-YSKAYGRMGLA   89 (131)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHccCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHhhchHHHHHHHHHHHhcCcc-CHHHHHHHHHH
Confidence            3455566666677777777777777766653 335666777777777777777777777777665443 56667777777


Q ss_pred             HHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCC
Q 012111          406 YGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAYNALGM  446 (471)
Q Consensus       406 ~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~  446 (471)
                      +...|++++|...|++..+.. +.+...+..+..++...|+
T Consensus        90 ~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~~l~~~~~~~~~  129 (131)
T 2vyi_A           90 LSSLNKHVEAVAYYKKALELD-PDNETYKSNLKIAELKLRE  129 (131)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHTT
T ss_pred             HHHhCCHHHHHHHHHHHHhcC-ccchHHHHHHHHHHHHHhc
Confidence            777777777777777776642 2255566666666666654

>1na0_A Designed protein CTPR3; de novo protein; HET: IPT; 1.60A {Unidentified} SCOP: k.38.1.1 PDB: 2wqh_A 3kd7_A

Probab=98.65  E-value=2.5e-06  Score=63.55  Aligned_cols=111  Identities=16%  Similarity=0.121  Sum_probs=55.8

Q ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Q 012111          293 TLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYS  372 (471)
Q Consensus       293 ~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~  372 (471)
                      .+..+...+...|++++|...++.+.+... .+...+..+...+...|++++|..+++++.... +.+..++..+...+.
T Consensus        11 ~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~   88 (125)
T 1na0_A           11 AWYNLGNAYYKQGDYDEAIEYYQKALELDP-NNAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAWYNLGNAYY   88 (125)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHCc-CcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhC-CccHHHHHHHHHHHH
Confidence            344444445555555555555555444321 134445555555555555555555555555442 224455555555566


Q ss_pred             hcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHH
Q 012111          373 KAGLIMKVDSILRQVENSDVILDTPFFNCIISAY  406 (471)
Q Consensus       373 ~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  406 (471)
                      ..|++++|...++++.+..+. +...+..+...+
T Consensus        89 ~~~~~~~A~~~~~~~~~~~~~-~~~~~~~l~~~~  121 (125)
T 1na0_A           89 KQGDYDEAIEYYQKALELDPN-NAEAKQNLGNAK  121 (125)
T ss_dssp             HTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHH
T ss_pred             HhcCHHHHHHHHHHHHHhCCC-cHHHHHHHHHHH
Confidence            666666666666655554332 344444444333

>3sz7_A HSC70 cochaperone (SGT); TPR domain, GET4, GET5, GET3, MDY2, SSA1, SSE1, chaperone regulator; 1.72A {Aspergillus fumigatus}

Probab=98.64  E-value=7.8e-07  Score=70.51  Aligned_cols=99  Identities=13%  Similarity=-0.013  Sum_probs=79.4

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHH
Q 012111          325 TVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIIS  404 (471)
Q Consensus       325 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  404 (471)
                      +...+..+...+...|++++|+..|++..... +-+...|..+..++...|++++|...+++..+.++. +...|..+..
T Consensus        10 ~a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~lg~   87 (164)
T 3sz7_A           10 ESDKLKSEGNAAMARKEYSKAIDLYTQALSIA-PANPIYLSNRAAAYSASGQHEKAAEDAELATVVDPK-YSKAWSRLGL   87 (164)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CcCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCC-CHHHHHHHHH
Confidence            45567777788888888888888888888763 336778888888888888888888888888877655 6778888888


Q ss_pred             HHHhcCCHHHHHHHHHHHHhC
Q 012111          405 AYGQAGDVEKMGELFLTMKER  425 (471)
Q Consensus       405 ~~~~~g~~~~a~~~~~~~~~~  425 (471)
                      +|...|++++|+..|++..+.
T Consensus        88 ~~~~~g~~~~A~~~~~~al~~  108 (164)
T 3sz7_A           88 ARFDMADYKGAKEAYEKGIEA  108 (164)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHccCHHHHHHHHHHHHHh
Confidence            888888888888888888764

>3q49_B STIP1 homology and U box-containing protein 1; E3 ubiquitin ligase, ligase-chaperone complex; 1.54A {Mus musculus} PDB: 3q47_B 3q4a_B*

Probab=98.63  E-value=1.8e-06  Score=65.94  Aligned_cols=96  Identities=6%  Similarity=-0.097  Sum_probs=46.0

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHH
Q 012111          326 VVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISA  405 (471)
Q Consensus       326 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  405 (471)
                      ...+..+...+...|++++|...|++..... +.+...+..+..++...|++++|...++...+.++. +...+..+..+
T Consensus         9 ~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~-~~~~~~~l~~~   86 (137)
T 3q49_B            9 AQELKEQGNRLFVGRKYPEAAACYGRAITRN-PLVAVYYTNRALCYLKMQQPEQALADCRRALELDGQ-SVKAHFFLGQC   86 (137)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCcHHHHHHHHHHHHhhC-cCcHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCch-hHHHHHHHHHH
Confidence            3444444455555555555555555544432 223444444455555555555555555554444332 34444444445


Q ss_pred             HHhcCCHHHHHHHHHHHH
Q 012111          406 YGQAGDVEKMGELFLTMK  423 (471)
Q Consensus       406 ~~~~g~~~~a~~~~~~~~  423 (471)
                      +...|++++|+..|++..
T Consensus        87 ~~~~~~~~~A~~~~~~a~  104 (137)
T 3q49_B           87 QLEMESYDEAIANLQRAY  104 (137)
T ss_dssp             HHHTTCHHHHHHHHHHHH
T ss_pred             HHHHhhHHHHHHHHHHHH
Confidence            555555555555554444

>3gw4_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, no structural genomics consortium, NESG, DRR162B; 2.49A {Deinococcus radiodurans R1}

Probab=98.63  E-value=1.7e-06  Score=71.17  Aligned_cols=133  Identities=12%  Similarity=0.037  Sum_probs=72.2

Q ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHh----CCCC-CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc----CCCC--C
Q 012111          292 QTLNILTKSYGRAGMYDKMRSVMDFMQK----RFFF-PTVVTYNIVIETFGKAGHIEKMEEYFKKMKHR----GMKP--N  360 (471)
Q Consensus       292 ~~~~~ll~~~~~~~~~~~a~~~~~~~~~----~~~~-~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~----~~~p--~  360 (471)
                      .++..+...+...|++++|...+++..+    .+.. .....+..+...+...|++++|...+++....    +-.+  .
T Consensus        27 ~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~  106 (203)
T 3gw4_A           27 GARFMLGYVYAFMDRFDEARASFQALQQQAQKSGDHTAEHRALHQVGMVERMAGNWDAARRCFLEERELLASLPEDPLAA  106 (203)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHH
T ss_pred             HHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCccHHHH
Confidence            3444444444444555554444444333    1111 12234555556666666766666666665442    1011  1


Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHhC----CCC-cCHHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 012111          361 SITYCSLVSAYSKAGLIMKVDSILRQVENS----DVI-LDTPFFNCIISAYGQAGDVEKMGELFLTMKE  424 (471)
Q Consensus       361 ~~~~~~li~~~~~~g~~~~a~~~~~~~~~~----~~~-~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~  424 (471)
                      ...+..+...+...|++++|...+++..+.    +.. .-..++..+...+...|++++|.+.+++..+
T Consensus       107 ~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  175 (203)
T 3gw4_A          107 SANAYEVATVALHFGDLAGARQEYEKSLVYAQQADDQVAIACAFRGLGDLAQQEKNLLEAQQHWLRARD  175 (203)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhccchHHHHHHHHHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            334566666777777777777777665431    111 1123356677778888888888888776654

>2e2e_A Formate-dependent nitrite reductase complex NRFG; TPR, cytochrome C biogenesis, O157:H7 EDL933, formate- nitrite reductase complex, lyase; 2.05A {Escherichia coli}

Probab=98.62  E-value=4.9e-07  Score=72.73  Aligned_cols=123  Identities=9%  Similarity=-0.026  Sum_probs=76.1

Q ss_pred             HhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHH-HHhcCCH--H
Q 012111          267 GNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIET-FGKAGHI--E  343 (471)
Q Consensus       267 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~-~~~~g~~--~  343 (471)
                      ...|++++|...+++..... +.+...+..+...|...|++++|...|+...+.... +...+..+..+ +...|++  +
T Consensus        21 ~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~-~~~~~~~la~~l~~~~~~~~~~   98 (177)
T 2e2e_A           21 ASQQNPEAQLQALQDKIRAN-PQNSEQWALLGEYYLWQNDYSNSLLAYRQALQLRGE-NAELYAALATVLYYQASQHMTA   98 (177)
T ss_dssp             C-----CCCCHHHHHHHHHC-CSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHCS-CHHHHHHHHHHHHHHTTTCCCH
T ss_pred             hhccCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCC-CHHHHHHHHHHHHHhcCCcchH
Confidence            34566677777776665543 445666677777777777777777777766654322 45555566666 5566776  7


Q ss_pred             HHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCC
Q 012111          344 KMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDV  392 (471)
Q Consensus       344 ~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~  392 (471)
                      +|...++++.... +-+...+..+...+...|++++|...++.+.+..+
T Consensus        99 ~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p  146 (177)
T 2e2e_A           99 QTRAMIDKALALD-SNEITALMLLASDAFMQANYAQAIELWQKVMDLNS  146 (177)
T ss_dssp             HHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTCC
T ss_pred             HHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcccHHHHHHHHHHHHhhCC
Confidence            7777777766653 22456666667777777777777777777666543

>4f3v_A ESX-1 secretion system protein ECCA1; tetratricopeptide repeat, TPR domain, ATPase, protein secret protein transport; 2.00A {Mycobacterium tuberculosis}

Probab=98.62  E-value=4.8e-06  Score=71.02  Aligned_cols=128  Identities=9%  Similarity=-0.010  Sum_probs=67.9

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCC--HHHHHHHHHHHHh
Q 012111          261 SMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPT--VVTYNIVIETFGK  338 (471)
Q Consensus       261 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~~~~li~~~~~  338 (471)
                      .+...+...|++++|.++|..+...+  |+......+...+.+.+++++|+..|+...... .|.  ...+..+..++..
T Consensus       107 ayA~~L~~~g~y~eA~~~l~~~~~~~--p~~~~~~~~a~l~~~~~r~~dA~~~l~~a~~~~-d~~~~~~a~~~LG~al~~  183 (282)
T 4f3v_A          107 GFAACEAAQGNYADAMEALEAAPVAG--SEHLVAWMKAVVYGAAERWTDVIDQVKSAGKWP-DKFLAGAAGVAHGVAAAN  183 (282)
T ss_dssp             HHHHHHHHHTCHHHHHHHHTSSCCTT--CHHHHHHHHHHHHHHTTCHHHHHHHHTTGGGCS-CHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHhcC--CchHHHHHHHHHHHHcCCHHHHHHHHHHhhccC-CcccHHHHHHHHHHHHHH
Confidence            34455556666666666666654432  322244444445566666666666665443321 110  1244455556666


Q ss_pred             cCCHHHHHHHHHHHHHcCCCCC--HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCC
Q 012111          339 AGHIEKMEEYFKKMKHRGMKPN--SITYCSLVSAYSKAGLIMKVDSILRQVENSD  391 (471)
Q Consensus       339 ~g~~~~a~~~~~~m~~~~~~p~--~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~  391 (471)
                      .|++++|+..|++.......|.  .........++.+.|+.++|..+|+++...+
T Consensus       184 LG~~~eAl~~l~~a~~g~~~P~~~~da~~~~glaL~~lGr~deA~~~l~~a~a~~  238 (282)
T 4f3v_A          184 LALFTEAERRLTEANDSPAGEACARAIAWYLAMARRSQGNESAAVALLEWLQTTH  238 (282)
T ss_dssp             TTCHHHHHHHHHHHHTSTTTTTTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHS
T ss_pred             CCCHHHHHHHHHHHhcCCCCccccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC
Confidence            6666666666666653322132  2344555555666666666666666666544

>2vyi_A SGTA protein; chaperone, TPR repeat, phosphoprotein, tetratricopeptide repeat protein, HOST-virus interaction; 2.4A {Homo sapiens} SCOP: k.38.1.1

Probab=98.61  E-value=2.5e-06  Score=64.21  Aligned_cols=89  Identities=11%  Similarity=0.060  Sum_probs=34.1

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCC
Q 012111          192 IKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGN  271 (471)
Q Consensus       192 l~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  271 (471)
                      ...+...|+++.|...+++..... +.+...+..+...+...|++++|.+.++...+..  +.+...+..+...+...|+
T Consensus        19 ~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~   95 (131)
T 2vyi_A           19 GNEQMKVENFEAAVHFYGKAIELN-PANAVYFCNRAAAYSKLGNYAGAVQDCERAICID--PAYSKAYGRMGLALSSLNK   95 (131)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHccCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHhhchHHHHHHHHHHHhcC--ccCHHHHHHHHHHHHHhCC
Confidence            333333344444444443333321 1233333334444444444444444444443321  2223333333444444444


Q ss_pred             HHHHHHHHHHHH
Q 012111          272 IEKMEKWYNEFN  283 (471)
Q Consensus       272 ~~~a~~~~~~~~  283 (471)
                      +++|...+++..
T Consensus        96 ~~~A~~~~~~~~  107 (131)
T 2vyi_A           96 HVEAVAYYKKAL  107 (131)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHH
Confidence            444444444433

>2lni_A Stress-induced-phosphoprotein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, chaperone; NMR {Homo sapiens}

Probab=98.60  E-value=1.8e-06  Score=65.30  Aligned_cols=93  Identities=9%  Similarity=-0.013  Sum_probs=37.4

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHh
Q 012111          329 YNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQ  408 (471)
Q Consensus       329 ~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  408 (471)
                      +..+...+...|++++|...+++..+.. +.+...+..+...+...|++++|...++++.+..+. +...+..+..++..
T Consensus        19 ~~~~~~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~-~~~~~~~la~~~~~   96 (133)
T 2lni_A           19 VKNKGNECFQKGDYPQAMKHYTEAIKRN-PKDAKLYSNRAACYTKLLEFQLALKDCEECIQLEPT-FIKGYTRKAAALEA   96 (133)
T ss_dssp             HHHHHHHHHHTTCSHHHHHHHHHHHTTC-TTCHHHHHHHHHHHTTTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCcHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCC-chHHHHHHHHHHHH
Confidence            3333333444444444444444433321 113333444444444444444444444444433222 33344444444444


Q ss_pred             cCCHHHHHHHHHHHH
Q 012111          409 AGDVEKMGELFLTMK  423 (471)
Q Consensus       409 ~g~~~~a~~~~~~~~  423 (471)
                      .|++++|.+.|++..
T Consensus        97 ~~~~~~A~~~~~~~~  111 (133)
T 2lni_A           97 MKDYTKAMDVYQKAL  111 (133)
T ss_dssp             TTCHHHHHHHHHHHH
T ss_pred             HhhHHHHHHHHHHHH
Confidence            444444444444443

>3upv_A Heat shock protein STI1; TPR-fold, adaptor protein for HSP70 and HSP90, C-terminal PA HSP70, peptide binding protein; 1.60A {Saccharomyces cerevisiae}

Probab=98.60  E-value=1.4e-06  Score=65.52  Aligned_cols=95  Identities=8%  Similarity=-0.035  Sum_probs=53.1

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHH
Q 012111          328 TYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYG  407 (471)
Q Consensus       328 ~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  407 (471)
                      .+..+...+...|++++|...|++..+.. +.+...|..+..++...|++++|...+++..+.++. +...|..+..++.
T Consensus         6 ~~~~~g~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~p~-~~~~~~~lg~~~~   83 (126)
T 3upv_A            6 EARLEGKEYFTKSDWPNAVKAYTEMIKRA-PEDARGYSNRAAALAKLMSFPEAIADCNKAIEKDPN-FVRAYIRKATAQI   83 (126)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCC-cHHHHHHHHHHHH
Confidence            44445555556666666666666555542 224555555555556666666666666555555433 4555555555555


Q ss_pred             hcCCHHHHHHHHHHHHh
Q 012111          408 QAGDVEKMGELFLTMKE  424 (471)
Q Consensus       408 ~~g~~~~a~~~~~~~~~  424 (471)
                      ..|++++|...|++..+
T Consensus        84 ~~~~~~~A~~~~~~al~  100 (126)
T 3upv_A           84 AVKEYASALETLDAART  100 (126)
T ss_dssp             HTTCHHHHHHHHHHHHH
T ss_pred             HHhCHHHHHHHHHHHHH
Confidence            55666666665555554

>2lni_A Stress-induced-phosphoprotein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, chaperone; NMR {Homo sapiens}

Probab=98.60  E-value=2.3e-06  Score=64.76  Aligned_cols=92  Identities=13%  Similarity=0.024  Sum_probs=36.7

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHH
Q 012111          188 YSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYG  267 (471)
Q Consensus       188 ~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~  267 (471)
                      +..+...+...|+++.|...+++..+.. +.+...+..+..++...|++++|...+++..+..  +.+...+..+..++.
T Consensus        19 ~~~~~~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~--~~~~~~~~~la~~~~   95 (133)
T 2lni_A           19 VKNKGNECFQKGDYPQAMKHYTEAIKRN-PKDAKLYSNRAACYTKLLEFQLALKDCEECIQLE--PTFIKGYTRKAAALE   95 (133)
T ss_dssp             HHHHHHHHHHTTCSHHHHHHHHHHHTTC-TTCHHHHHHHHHHHTTTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCcHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC--CCchHHHHHHHHHHH
Confidence            3333333444444444444444433322 1233334444444444444444444444443331  223333444444444


Q ss_pred             hcCCHHHHHHHHHHH
Q 012111          268 NSGNIEKMEKWYNEF  282 (471)
Q Consensus       268 ~~~~~~~a~~~~~~~  282 (471)
                      ..|++++|...|++.
T Consensus        96 ~~~~~~~A~~~~~~~  110 (133)
T 2lni_A           96 AMKDYTKAMDVYQKA  110 (133)
T ss_dssp             HTTCHHHHHHHHHHH
T ss_pred             HHhhHHHHHHHHHHH
Confidence            444444444444443

>1p5q_A FKBP52, FK506-binding protein 4; isomerase; 2.80A {Homo sapiens} SCOP: a.118.8.1 d.26.1.1 PDB: 1qz2_A

Probab=98.60  E-value=2.3e-06  Score=76.72  Aligned_cols=96  Identities=8%  Similarity=-0.124  Sum_probs=70.6

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHH
Q 012111          326 VVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISA  405 (471)
Q Consensus       326 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  405 (471)
                      ...|..+..+|.+.|++++|+..+++.++.. +.+...+..+..+|...|++++|...|+++.+..+. +..++..+..+
T Consensus       196 ~~~~~nla~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~P~-~~~a~~~l~~~  273 (336)
T 1p5q_A          196 LASHLNLAMCHLKLQAFSAAIESCNKALELD-SNNEKGLSRRGEAHLAVNDFELARADFQKVLQLYPN-NKAAKTQLAVC  273 (336)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSS-CHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCC-CHHHHHHHHHH
Confidence            3566777777778888888888888777763 336777777888888888888888888887776655 66777777778


Q ss_pred             HHhcCCHHHH-HHHHHHHH
Q 012111          406 YGQAGDVEKM-GELFLTMK  423 (471)
Q Consensus       406 ~~~~g~~~~a-~~~~~~~~  423 (471)
                      +...|+.++| ..+|+.|.
T Consensus       274 ~~~~~~~~~a~~~~~~~~~  292 (336)
T 1p5q_A          274 QQRIRRQLAREKKLYANMF  292 (336)
T ss_dssp             HHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHH
Confidence            8888887777 44555554

>4gcn_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; HET: PGE; 1.85A {Caenorhabditis elegans}

Probab=98.59  E-value=4.6e-07  Score=68.30  Aligned_cols=106  Identities=11%  Similarity=0.023  Sum_probs=64.4

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCc--C----HHHHH
Q 012111          327 VTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVIL--D----TPFFN  400 (471)
Q Consensus       327 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~--~----~~~~~  400 (471)
                      ..+..+...+.+.|++++|+..|++.++.. +-+...|..+..+|...|++++|++.+++..+.++..  +    ..+|.
T Consensus         9 ~a~~~lG~~~~~~~~~~~A~~~y~~Al~~~-p~~~~~~~nlg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~   87 (127)
T 4gcn_A            9 IAEKDLGNAAYKQKDFEKAHVHYDKAIELD-PSNITFYNNKAAVYFEEKKFAECVQFCEKAVEVGRETRADYKLIAKAMS   87 (127)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHhHHHHHHHhhhHHHHHHHHHHHHHhCcccchhhHHHHHHHH
Confidence            345566666777777777777777766642 2245666667777777777777777776665432211  1    12455


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHH
Q 012111          401 CIISAYGQAGDVEKMGELFLTMKERHCVPDNITFA  435 (471)
Q Consensus       401 ~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~  435 (471)
                      .+..++...|++++|++.|++..+  ..||+.+..
T Consensus        88 ~lg~~~~~~~~~~~A~~~~~kal~--~~~~~~~~~  120 (127)
T 4gcn_A           88 RAGNAFQKQNDLSLAVQWFHRSLS--EFRDPELVK  120 (127)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHH--HSCCHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHh--hCcCHHHHH
Confidence            566666666777777777666655  245655543

>2vgx_A Chaperone SYCD; alternative dimer assembly, tetratricopeptide repeat, type III secretion; HET: MLY; 1.95A {Yersinia enterocolitica} SCOP: k.38.1.1 PDB: 2vgx_B* 2vgy_A*

Probab=98.56  E-value=5.2e-07  Score=70.07  Aligned_cols=100  Identities=11%  Similarity=0.007  Sum_probs=54.8

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHH
Q 012111          362 ITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAY  441 (471)
Q Consensus       362 ~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~  441 (471)
                      ..+..+...+...|++++|...|+.+...++. +...|..+..+|...|++++|+..|++..... +.+...+..+..+|
T Consensus        22 ~~~~~~g~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~-p~~~~~~~~lg~~~   99 (148)
T 2vgx_A           22 EQLYSLAFNQYQSGXYEDAHXVFQALCVLDHY-DSRFFLGLGACRQAMGQYDLAIHSYSYGAVMD-IXEPRFPFHAAECL   99 (148)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCTHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCChHHHHHHHHHHHHcCcc-cHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-CCCchHHHHHHHHH
Confidence            34444555555556666666666555554443 55555555555555666666666665555431 12344555555555


Q ss_pred             HhcCCHHHHHHHHHHHHHhhhc
Q 012111          442 NALGMTEAAQNLENKMIAMKEN  463 (471)
Q Consensus       442 ~~~g~~~~A~~~~~~m~~~~~~  463 (471)
                      ...|++++|.+.++++++..|.
T Consensus       100 ~~~g~~~~A~~~~~~al~~~p~  121 (148)
T 2vgx_A          100 LQXGELAEAESGLFLAQELIAN  121 (148)
T ss_dssp             HHTTCHHHHHHHHHHHHHHHTT
T ss_pred             HHcCCHHHHHHHHHHHHHHCcC
Confidence            5666666666666665555543

>4b4t_Q 26S proteasome regulatory subunit RPN6; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.56  E-value=4.2e-06  Score=77.99  Aligned_cols=207  Identities=9%  Similarity=-0.040  Sum_probs=142.3

Q ss_pred             chHHHHHHHHHHHhhcHHHHHHHHHHhhhccCccCC---------------hhHHHHHHHHHhcCCCHHHHHHHHHHHHh
Q 012111           78 PKPVLEALDEAIKQKKWQLALKIFGLLRQQQWYQAR---------------CQTFTKLMVMLGKCKQPEQASLLFEVMLS  142 (471)
Q Consensus        78 ~~~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~---------------~~~~~~l~~~~~~~~~~~~a~~~~~~m~~  142 (471)
                      |...+...+.+.+.|++++|++.|..+.+...-..+               ...+..++..|...|++++|.+.+..+..
T Consensus         4 p~~~l~~a~~l~~~~~y~eA~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~al~~l~~~y~~~~~~~~a~~~~~~~~~   83 (434)
T 4b4t_Q            4 PGSKLEEARRLVNEKQYNEAEQVYLSLLDKDSSQSSAAAGASVDDKRRNEQETSILELGQLYVTMGAKDKLREFIPHSTE   83 (434)
T ss_dssp             TTHHHHHHHHHHHHTCHHHHHHHHHHHHHSCCCSSSBSSSSSBCSHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHTHH
T ss_pred             hHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCcccchhHHHHHHHHHHhhhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            445566677888999999999999999876421111               12477889999999999999999988765


Q ss_pred             CC-CCCCH----HHHHHHHHHHHhcCCHHHHHHHHHHhhcC----CCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 012111          143 DG-LKPSV----DVYTALVSAYGQSGLLDEAFSTINDMKSV----SDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSY  213 (471)
Q Consensus       143 ~~-~~~~~----~~~~~li~~~~~~~~~~~a~~~~~~~~~~----~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~  213 (471)
                      .- ..++.    .+.+.+...+...|+.+.|..+++.....    .....-..++..+...+...|++++|..+++++..
T Consensus        84 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~~~~  163 (434)
T 4b4t_Q           84 YMMQFAKSKTVKVLKTLIEKFEQVPDSLDDQIFVCEKSIEFAKREKRVFLKHSLSIKLATLHYQKKQYKDSLALINDLLR  163 (434)
T ss_dssp             HHHTSCHHHHHHHHHHHHHHHCSCCSCHHHHHHHHHHHHHHHHHSSCCSSHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHccchHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHhCccHHHHHHHHHHHHHHHHccChHHHHHHHHHHHH
Confidence            31 11122    12333334445568889998888776431    11222355678888899999999999999988754


Q ss_pred             C--CC---CCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHcCC-C-CC-C--HHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 012111          214 L--GI---ECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGG-C-HP-D--IFTLNSMISAYGNSGNIEKMEKWYNEFN  283 (471)
Q Consensus       214 ~--g~---~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-~-~~-~--~~~~~~l~~~~~~~~~~~~a~~~~~~~~  283 (471)
                      .  +.   +....++..++..|...|++++|...+++...... . .| .  ...+..+...+...|++++|...|.+..
T Consensus       164 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~g~~~~~~~~y~~A~~~~~~a~  243 (434)
T 4b4t_Q          164 EFKKLDDKPSLVDVHLLESKVYHKLRNLAKSKASLTAARTAANSIYCPTQTVAELDLMSGILHCEDKDYKTAFSYFFESF  243 (434)
T ss_dssp             HHTTSSCSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHTTSSSCHHHHHHHHHHHH
T ss_pred             HHHhcccchhHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHhhcCCCchHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHH
Confidence            3  11   11256788888999999999999999887754211 1 11 1  2456666777788899999988887764


Q ss_pred             h
Q 012111          284 L  284 (471)
Q Consensus       284 ~  284 (471)
                      .
T Consensus       244 ~  244 (434)
T 4b4t_Q          244 E  244 (434)
T ss_dssp             H
T ss_pred             H
Confidence            3

>3dss_A Geranylgeranyl transferase type-2 subunit alpha; protein prenylation, metal-binding, prenyltransferase, zinc, phosphoprotein; 1.80A {Rattus norvegicus} PDB: 3dst_A* 3dsu_A* 3dsv_A* 3dsw_A* 3dsx_A* 3hxb_A* 3hxc_A* 3hxd_A* 3hxe_A* 3hxf_A* 3pz1_A* 3pz2_A* 3pz3_A* 3c72_A* 4gtv_A* 4gts_A* 4ehm_A* 4gtt_A*

Probab=98.55  E-value=0.00011  Score=64.67  Aligned_cols=178  Identities=5%  Similarity=-0.120  Sum_probs=121.4

Q ss_pred             HHHHHHHhhcHH-HHHHHHHHhhhccCccCChhHHHHHHHHHhcCCC----------HHHHHHHHHHHHhCCCCCCHHHH
Q 012111           84 ALDEAIKQKKWQ-LALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQ----------PEQASLLFEVMLSDGLKPSVDVY  152 (471)
Q Consensus        84 ~l~~~~~~~~~~-~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~----------~~~a~~~~~~m~~~~~~~~~~~~  152 (471)
                      .+....+.|.++ +|+++++.+...+  |.+..+|+.--.++...+.          +++++.+++.+.....+ +..+|
T Consensus        35 ~~~~~~~~~e~s~eaL~~t~~~L~~n--P~~ytaWn~Rr~iL~~l~~~~~~~~~~~~l~~EL~~~~~~L~~~PK-ny~aW  111 (331)
T 3dss_A           35 AVFQKRQAGELDESVLELTSQILGAN--PDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVNPK-SYGTW  111 (331)
T ss_dssp             HHHHHHHTTCCSHHHHHHHHHHHTTC--TTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCTT-CHHHH
T ss_pred             HHHHHHHcCCCCHHHHHHHHHHHHHC--chhHHHHHHHHHHHHHhcccccchhhhHHHHHHHHHHHHHHHhCCC-CHHHH
Confidence            344444566654 7999999999875  5556667666555544443          67888888888876554 77888


Q ss_pred             HHHHHHHHhcC--CHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCC-HHHHHHHHHHHHHCCCCCCHHHHHHHHHH
Q 012111          153 TALVSAYGQSG--LLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHR-FDLIEKILAEMSYLGIECSAVTYNTIIDG  229 (471)
Q Consensus       153 ~~li~~~~~~~--~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~-~~~a~~~~~~~~~~g~~~~~~~~~~l~~~  229 (471)
                      +.-.-++...+  .+++++.+++++.+..  +-|..+|+.-.-.+...|. ++++++.++.+++.. +-|...|+.....
T Consensus       112 ~hR~wlL~~l~~~~~~~EL~~~~k~l~~d--prNy~AW~~R~~vl~~l~~~~~eel~~~~~~I~~~-p~N~SAW~~R~~l  188 (331)
T 3dss_A          112 HHRCWLLSRLPEPNWARELELCARFLEAD--ERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRN-FSNYSSWHYRSCL  188 (331)
T ss_dssp             HHHHHHHHHCSSCCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHC-SCCHHHHHHHHHH
T ss_pred             HHHHHHHhccCcccHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHhCcCHHHHHHHHHHHHHHC-CCCHHHHHHHHHH
Confidence            87777777777  4788888888888732  5677777777777777777 588888888888765 4477777766555


Q ss_pred             HHcc--------------CCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhc
Q 012111          230 YGKA--------------KKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNS  269 (471)
Q Consensus       230 ~~~~--------------~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  269 (471)
                      +...              +.++++++.+.......  +-|...|+-+-..+.+.
T Consensus       189 l~~l~~~~~~~~~~~~~~~~~~eEle~~~~ai~~~--P~d~SaW~Y~r~ll~~~  240 (331)
T 3dss_A          189 LPQLHPQPDSGPQGRLPENVLLKELELVQNAFFTD--PNDQSAWFYHRWLLGAG  240 (331)
T ss_dssp             HHHHSCCC------CCCHHHHHHHHHHHHHHHHHS--TTCHHHHHHHHHHHHSS
T ss_pred             HHHhhhccccccccccchHHHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHhc
Confidence            5443              34667777777776653  45566665544444333

>3upv_A Heat shock protein STI1; TPR-fold, adaptor protein for HSP70 and HSP90, C-terminal PA HSP70, peptide binding protein; 1.60A {Saccharomyces cerevisiae}

Probab=98.55  E-value=4e-06  Score=62.91  Aligned_cols=98  Identities=7%  Similarity=-0.156  Sum_probs=64.8

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHH
Q 012111          362 ITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAY  441 (471)
Q Consensus       362 ~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~  441 (471)
                      ..+..+...+.+.|++++|...|++..+..+. +...|..+..++...|++++|+..+++..+.. +.+...|..+..++
T Consensus         5 ~~~~~~g~~~~~~~~~~~A~~~~~~al~~~p~-~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~   82 (126)
T 3upv_A            5 EEARLEGKEYFTKSDWPNAVKAYTEMIKRAPE-DARGYSNRAAALAKLMSFPEAIADCNKAIEKD-PNFVRAYIRKATAQ   82 (126)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCC-ChHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHH
Confidence            34555666666777777777777776665544 56666667777777777777777777766541 22455666666677


Q ss_pred             HhcCCHHHHHHHHHHHHHhh
Q 012111          442 NALGMTEAAQNLENKMIAMK  461 (471)
Q Consensus       442 ~~~g~~~~A~~~~~~m~~~~  461 (471)
                      ...|++++|...++++++..
T Consensus        83 ~~~~~~~~A~~~~~~al~~~  102 (126)
T 3upv_A           83 IAVKEYASALETLDAARTKD  102 (126)
T ss_dssp             HHTTCHHHHHHHHHHHHHHH
T ss_pred             HHHhCHHHHHHHHHHHHHhC
Confidence            77777777777777777666

>2kck_A TPR repeat; tetratricopeptide repeat, structural genomics, unknown function, PSI-2, protein structure initiative; NMR {Methanococcus maripaludis}

Probab=98.55  E-value=6.6e-07  Score=65.40  Aligned_cols=103  Identities=11%  Similarity=0.006  Sum_probs=71.9

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC--CHHHHHHHH
Q 012111          361 SITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVP--DNITFATMI  438 (471)
Q Consensus       361 ~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p--~~~~~~~l~  438 (471)
                      ...+..+...+...|++++|...++++.+..+. +...+..+..++...|++++|...+++..+.. +.  +...+..+.
T Consensus         6 ~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~-~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~~~l~   83 (112)
T 2kck_A            6 PEEYYLEGVLQYDAGNYTESIDLFEKAIQLDPE-ESKYWLMKGKALYNLERYEEAVDCYNYVINVI-EDEYNKDVWAAKA   83 (112)
T ss_dssp             TTGGGGHHHHHHSSCCHHHHHHHHHHHHHHCCC-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTS-CCTTCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhhhHHHHHHHHHHHHHhCcC-CHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-cccchHHHHHHHH
Confidence            344556666677777777777777777665543 56667777777777788888888887777642 22  466777777


Q ss_pred             HHHHhc-CCHHHHHHHHHHHHHhhhcCC
Q 012111          439 QAYNAL-GMTEAAQNLENKMIAMKENSG  465 (471)
Q Consensus       439 ~~~~~~-g~~~~A~~~~~~m~~~~~~~~  465 (471)
                      ..+... |++++|.+.+++++...|.+.
T Consensus        84 ~~~~~~~~~~~~A~~~~~~~~~~~p~~~  111 (112)
T 2kck_A           84 DALRYIEGKEVEAEIAEARAKLEHHHHH  111 (112)
T ss_dssp             HHHTTCSSCSHHHHHHHHHHGGGCCCCC
T ss_pred             HHHHHHhCCHHHHHHHHHHHhhcccCCC
Confidence            777788 888888888888777766543

>1hxi_A PEX5, peroxisome targeting signal 1 receptor PEX5; alpha helical, transport protein; 1.60A {Trypanosoma brucei} SCOP: a.118.8.1

Probab=98.55  E-value=8.7e-07  Score=66.08  Aligned_cols=97  Identities=7%  Similarity=-0.098  Sum_probs=58.9

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC-CHHHHHHHHHHHHh
Q 012111          365 CSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVP-DNITFATMIQAYNA  443 (471)
Q Consensus       365 ~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p-~~~~~~~l~~~~~~  443 (471)
                      ..+...+.+.|++++|...++++.+..+. +...|..+..++...|++++|+..|++..+.  .| +...+..+..++..
T Consensus        21 ~~~g~~~~~~g~~~~A~~~~~~al~~~P~-~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l--~P~~~~~~~~la~~~~~   97 (121)
T 1hxi_A           21 MEEGLSMLKLANLAEAALAFEAVCQKEPE-REEAWRSLGLTQAENEKDGLAIIALNHARML--DPKDIAVHAALAVSHTN   97 (121)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHSTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHH
Confidence            34445566666666666666666665544 5666666666666677777777777666653  23 45556666666667


Q ss_pred             cCCHHHHHHHHHHHHHhhhcC
Q 012111          444 LGMTEAAQNLENKMIAMKENS  464 (471)
Q Consensus       444 ~g~~~~A~~~~~~m~~~~~~~  464 (471)
                      .|++++|...++++++..|..
T Consensus        98 ~g~~~~A~~~~~~al~~~P~~  118 (121)
T 1hxi_A           98 EHNANAALASLRAWLLSQPQY  118 (121)
T ss_dssp             HHHHHHHHHHHHHHHC-----
T ss_pred             cCCHHHHHHHHHHHHHhCcCC
Confidence            777777777777766666543

>1elw_A TPR1-domain of HOP; HOP, TPR-domain, peptide-complex, helical repeat, HSP70, protein binding, chaperone; 1.60A {Homo sapiens} SCOP: a.118.8.1

Probab=98.53  E-value=2.2e-06  Score=63.16  Aligned_cols=98  Identities=12%  Similarity=0.006  Sum_probs=71.7

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHH
Q 012111          326 VVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISA  405 (471)
Q Consensus       326 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  405 (471)
                      ...+..+...+...|++++|...+++..... +.+...+..+...+...|++++|...+++..+..+. +...+..+..+
T Consensus         4 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~~a~~   81 (118)
T 1elw_A            4 VNELKEKGNKALSVGNIDDALQCYSEAIKLD-PHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLKPD-WGKGYSRKAAA   81 (118)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcccHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHhhccHHHHHHHHHHHHHhCcc-cHHHHHHHHHH
Confidence            4456667777777888888888888777653 335667777777777788888888888777766544 56677777777


Q ss_pred             HHhcCCHHHHHHHHHHHHhC
Q 012111          406 YGQAGDVEKMGELFLTMKER  425 (471)
Q Consensus       406 ~~~~g~~~~a~~~~~~~~~~  425 (471)
                      +...|++++|.+.+++..+.
T Consensus        82 ~~~~~~~~~A~~~~~~~~~~  101 (118)
T 1elw_A           82 LEFLNRFEEAKRTYEEGLKH  101 (118)
T ss_dssp             HHHTTCHHHHHHHHHHHHTT
T ss_pred             HHHHhhHHHHHHHHHHHHHc
Confidence            77788888888888777764

>4gcn_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; HET: PGE; 1.85A {Caenorhabditis elegans}

Probab=98.51  E-value=4.1e-06  Score=63.00  Aligned_cols=101  Identities=13%  Similarity=0.032  Sum_probs=62.8

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCC--CCCC----HHHHH
Q 012111          362 ITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERH--CVPD----NITFA  435 (471)
Q Consensus       362 ~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~--~~p~----~~~~~  435 (471)
                      ..+..+...+.+.|++++|+..|++..+.++. +...|..+..+|...|++++|++.+++.++.+  ..++    ..+|.
T Consensus         9 ~a~~~lG~~~~~~~~~~~A~~~y~~Al~~~p~-~~~~~~nlg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~   87 (127)
T 4gcn_A            9 IAEKDLGNAAYKQKDFEKAHVHYDKAIELDPS-NITFYNNKAAVYFEEKKFAECVQFCEKAVEVGRETRADYKLIAKAMS   87 (127)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-CHHHHHhHHHHHHHhhhHHHHHHHHHHHHHhCcccchhhHHHHHHHH
Confidence            34555666667777777777777776666544 56666667777777777777777776665421  1111    13455


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHHhhhc
Q 012111          436 TMIQAYNALGMTEAAQNLENKMIAMKEN  463 (471)
Q Consensus       436 ~l~~~~~~~g~~~~A~~~~~~m~~~~~~  463 (471)
                      .+..++...|++++|.+.+++.++..++
T Consensus        88 ~lg~~~~~~~~~~~A~~~~~kal~~~~~  115 (127)
T 4gcn_A           88 RAGNAFQKQNDLSLAVQWFHRSLSEFRD  115 (127)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHSCC
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHhhCcC
Confidence            5666666777777777777776665543

>1elw_A TPR1-domain of HOP; HOP, TPR-domain, peptide-complex, helical repeat, HSP70, protein binding, chaperone; 1.60A {Homo sapiens} SCOP: a.118.8.1

Probab=98.49  E-value=1.1e-05  Score=59.24  Aligned_cols=97  Identities=13%  Similarity=-0.033  Sum_probs=47.6

Q ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Q 012111          293 TLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYS  372 (471)
Q Consensus       293 ~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~  372 (471)
                      .+..+...+...|++++|...++....... .+...+..+...+...|++++|...+++..... +.+...+..+..++.
T Consensus         6 ~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~   83 (118)
T 1elw_A            6 ELKEKGNKALSVGNIDDALQCYSEAIKLDP-HNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLK-PDWGKGYSRKAAALE   83 (118)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcccHHHHHHHHHHHHHHCC-CcHHHHHHHHHHHHhhccHHHHHHHHHHHHHhC-cccHHHHHHHHHHHH
Confidence            344444455555555555555555544322 134444445555555555555555555554432 223444555555555


Q ss_pred             hcCCHHHHHHHHHHHHhCC
Q 012111          373 KAGLIMKVDSILRQVENSD  391 (471)
Q Consensus       373 ~~g~~~~a~~~~~~~~~~~  391 (471)
                      ..|++++|.+.++...+.+
T Consensus        84 ~~~~~~~A~~~~~~~~~~~  102 (118)
T 1elw_A           84 FLNRFEEAKRTYEEGLKHE  102 (118)
T ss_dssp             HTTCHHHHHHHHHHHHTTC
T ss_pred             HHhhHHHHHHHHHHHHHcC
Confidence            5555555555555555443

>2fbn_A 70 kDa peptidylprolyl isomerase, putative; sulfur SAD, PFL2275C, TPR-containing domain, structural genomics; 1.63A {Plasmodium falciparum} SCOP: a.118.8.1

Probab=98.46  E-value=5.8e-06  Score=67.77  Aligned_cols=130  Identities=14%  Similarity=-0.034  Sum_probs=75.0

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHcCCC-C--------------CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCC
Q 012111          329 YNIVIETFGKAGHIEKMEEYFKKMKHRGMK-P--------------NSITYCSLVSAYSKAGLIMKVDSILRQVENSDVI  393 (471)
Q Consensus       329 ~~~li~~~~~~g~~~~a~~~~~~m~~~~~~-p--------------~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~  393 (471)
                      +..+...+...|++++|...|++....... |              ....+..+..++...|++++|...++...+..+.
T Consensus        41 ~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~p~  120 (198)
T 2fbn_A           41 IKEEGNEFFKKNEINEAIVKYKEALDFFIHTEEWDDQILLDKKKNIEISCNLNLATCYNKNKDYPKAIDHASKVLKIDKN  120 (198)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHTTTTCTTCCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTT
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHHhcccccchhhHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCcc
Confidence            444445555555666666666555543111 0              0256667777777777777777777777766543


Q ss_pred             cCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC-CHHHHHHHHHHHHhcCCHHHHH-HHHHHHHHhh
Q 012111          394 LDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVP-DNITFATMIQAYNALGMTEAAQ-NLENKMIAMK  461 (471)
Q Consensus       394 ~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~-~~~~~m~~~~  461 (471)
                       +...+..+..+|...|++++|++.|++..+.  .| +...+..+..++...|+.+++. ..+..|...+
T Consensus       121 -~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~f~~~  187 (198)
T 2fbn_A          121 -NVKALYKLGVANMYFGFLEEAKENLYKAASL--NPNNLDIRNSYELCVNKLKEARKKDKLTFGGMFDKG  187 (198)
T ss_dssp             -CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--STTCHHHHHHHHHHHHHHHHHHC-------------
T ss_pred             -cHHHHHHHHHHHHHcccHHHHHHHHHHHHHH--CCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence             6667777777777778888888888777764  33 4556666666666666666665 4555554443

>3sz7_A HSC70 cochaperone (SGT); TPR domain, GET4, GET5, GET3, MDY2, SSA1, SSE1, chaperone regulator; 1.72A {Aspergillus fumigatus}

Probab=98.44  E-value=4e-06  Score=66.34  Aligned_cols=96  Identities=13%  Similarity=0.003  Sum_probs=77.1

Q ss_pred             HHHHHHHHHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHH
Q 012111           80 PVLEALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAY  159 (471)
Q Consensus        80 ~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~  159 (471)
                      .+...-..+.+.|++++|++.|+.+.+..  +.+...|..+..++...|++++|+..|+...+.... +...|..+..++
T Consensus        13 ~~~~~g~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~lg~~~   89 (164)
T 3sz7_A           13 KLKSEGNAAMARKEYSKAIDLYTQALSIA--PANPIYLSNRAAAYSASGQHEKAAEDAELATVVDPK-YSKAWSRLGLAR   89 (164)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHS--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CcCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHH
Confidence            44455566678888999999998888765  567788888888888889999999888888876533 678888888888


Q ss_pred             HhcCCHHHHHHHHHHhhcC
Q 012111          160 GQSGLLDEAFSTINDMKSV  178 (471)
Q Consensus       160 ~~~~~~~~a~~~~~~~~~~  178 (471)
                      ...|++++|+..|++..+.
T Consensus        90 ~~~g~~~~A~~~~~~al~~  108 (164)
T 3sz7_A           90 FDMADYKGAKEAYEKGIEA  108 (164)
T ss_dssp             HHTTCHHHHHHHHHHHHHH
T ss_pred             HHccCHHHHHHHHHHHHHh
Confidence            8888999888888888764

>4b4t_Q 26S proteasome regulatory subunit RPN6; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.43  E-value=2.7e-05  Score=72.44  Aligned_cols=56  Identities=11%  Similarity=0.237  Sum_probs=29.8

Q ss_pred             HHHHHccCCHHHHHHHHHHHHHcCCCCCCH---------------HHHHHHHHHHHhcCCHHHHHHHHHHH
Q 012111          227 IDGYGKAKKFEEMESSFSAMVESGGCHPDI---------------FTLNSMISAYGNSGNIEKMEKWYNEF  282 (471)
Q Consensus       227 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~---------------~~~~~l~~~~~~~~~~~~a~~~~~~~  282 (471)
                      .+.+.+.|++++|++.|..+.+......+.               ..+..+...|...|++++|.+++..+
T Consensus        11 a~~l~~~~~y~eA~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~al~~l~~~y~~~~~~~~a~~~~~~~   81 (434)
T 4b4t_Q           11 ARRLVNEKQYNEAEQVYLSLLDKDSSQSSAAAGASVDDKRRNEQETSILELGQLYVTMGAKDKLREFIPHS   81 (434)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHHHSCCCSSSBSSSSSBCSHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHT
T ss_pred             HHHHHHCCCHHHHHHHHHHHHhhCcccchhHHHHHHHHHHhhhHHHHHHHHHHHHHHCCCHHHHHHHHHHH
Confidence            344566677777777777776653221111               12444555555555555555555544

>2xcb_A PCRH, regulatory protein PCRH; protein transport, bacterial toxin, type III secretion, protein binding; 1.85A {Pseudomonas aeruginosa} PDB: 2xcc_A

Probab=98.43  E-value=6e-06  Score=63.51  Aligned_cols=99  Identities=13%  Similarity=0.002  Sum_probs=55.7

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHH
Q 012111          363 TYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAYN  442 (471)
Q Consensus       363 ~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~  442 (471)
                      .+..+...+...|++++|...|+.+...++. +...|..+..+|...|++++|+..|++..+.. +-+...+..+..++.
T Consensus        20 ~~~~~a~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~   97 (142)
T 2xcb_A           20 QLYALGFNQYQAGKWDDAQKIFQALCMLDHY-DARYFLGLGACRQSLGLYEQALQSYSYGALMD-INEPRFPFHAAECHL   97 (142)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCTHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHccHHHHHHHHHHHHHhCCc-cHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-CCCcHHHHHHHHHHH
Confidence            3444455555666666666666665555443 55555555666666666666666666655531 223445555555666


Q ss_pred             hcCCHHHHHHHHHHHHHhhhc
Q 012111          443 ALGMTEAAQNLENKMIAMKEN  463 (471)
Q Consensus       443 ~~g~~~~A~~~~~~m~~~~~~  463 (471)
                      ..|++++|.+.++++++..|.
T Consensus        98 ~~g~~~~A~~~~~~al~~~p~  118 (142)
T 2xcb_A           98 QLGDLDGAESGFYSARALAAA  118 (142)
T ss_dssp             HTTCHHHHHHHHHHHHHHHHT
T ss_pred             HcCCHHHHHHHHHHHHHhCCC
Confidence            666666666666666655553

>1elr_A TPR2A-domain of HOP; HOP, TPR-domain, peptide-complex, helical repeat, protein binding, chaperone; 1.90A {Homo sapiens} SCOP: a.118.8.1 PDB: 3esk_A 3fwv_A

Probab=98.43  E-value=3.7e-06  Score=63.28  Aligned_cols=111  Identities=11%  Similarity=0.015  Sum_probs=72.1

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCC--cC----HHHHH
Q 012111          327 VTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVI--LD----TPFFN  400 (471)
Q Consensus       327 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~--~~----~~~~~  400 (471)
                      ..+..+...+...|++++|...+++..... +.+...+..+...+...|++++|...++.+.+..+.  ++    ..++.
T Consensus         5 ~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~   83 (131)
T 1elr_A            5 LKEKELGNDAYKKKDFDTALKHYDKAKELD-PTNMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENREDYRQIAKAYA   83 (131)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHhcC-CccHHHHHHHHHHHHHhccHHHHHHHHHHHHhhccccchhHHHHHHHHH
Confidence            345556666677777777777777766653 335666667777777777777777777776654321  11    55667


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHH
Q 012111          401 CIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQA  440 (471)
Q Consensus       401 ~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~  440 (471)
                      .+..++...|++++|.+.|+++.+.  .|+......+...
T Consensus        84 ~la~~~~~~~~~~~A~~~~~~~~~~--~~~~~~~~~l~~~  121 (131)
T 1elr_A           84 RIGNSYFKEEKYKDAIHFYNKSLAE--HRTPDVLKKCQQA  121 (131)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHH--CCCHHHHHHHHHH
T ss_pred             HHHHHHHHhccHHHHHHHHHHHHHh--CCCHHHHHHHHHH
Confidence            7777777788888888888777764  4565555444433

>2fbn_A 70 kDa peptidylprolyl isomerase, putative; sulfur SAD, PFL2275C, TPR-containing domain, structural genomics; 1.63A {Plasmodium falciparum} SCOP: a.118.8.1

Probab=98.42  E-value=9.1e-06  Score=66.55  Aligned_cols=96  Identities=14%  Similarity=0.023  Sum_probs=62.7

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHH
Q 012111          327 VTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAY  406 (471)
Q Consensus       327 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  406 (471)
                      ..+..+..++...|++++|...+++..... +.+...+..+..++...|++++|...|++..+..+. +..++..+..++
T Consensus        89 ~~~~~la~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~-~~~~~~~l~~~~  166 (198)
T 2fbn_A           89 SCNLNLATCYNKNKDYPKAIDHASKVLKID-KNNVKALYKLGVANMYFGFLEEAKENLYKAASLNPN-NLDIRNSYELCV  166 (198)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHSTT-CHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHcccHHHHHHHHHHHHHHCCC-cHHHHHHHHHHH
Confidence            556667777777888888888888777753 335677777888888888888888888887776544 566777777777


Q ss_pred             HhcCCHHHHH-HHHHHHHh
Q 012111          407 GQAGDVEKMG-ELFLTMKE  424 (471)
Q Consensus       407 ~~~g~~~~a~-~~~~~~~~  424 (471)
                      ...++..++. ..+..|..
T Consensus       167 ~~~~~~~~~~~~~~~~~f~  185 (198)
T 2fbn_A          167 NKLKEARKKDKLTFGGMFD  185 (198)
T ss_dssp             HHHHHHHC-----------
T ss_pred             HHHHHHHHHHHHHHHHHhc
Confidence            6666666555 44444443

>3q49_B STIP1 homology and U box-containing protein 1; E3 ubiquitin ligase, ligase-chaperone complex; 1.54A {Mus musculus} PDB: 3q47_B 3q4a_B*

Probab=98.41  E-value=2.1e-05  Score=59.76  Aligned_cols=102  Identities=5%  Similarity=-0.102  Sum_probs=62.9

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHH
Q 012111          360 NSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQ  439 (471)
Q Consensus       360 ~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~  439 (471)
                      +...+..+...+...|++++|...|+...+..+. +...+..+..++...|++++|...+++..+.. +.+...+..+..
T Consensus         8 ~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~-~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l~~   85 (137)
T 3q49_B            8 SAQELKEQGNRLFVGRKYPEAAACYGRAITRNPL-VAVYYTNRALCYLKMQQPEQALADCRRALELD-GQSVKAHFFLGQ   85 (137)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHhCcHHHHHHHHHHHHhhCcC-cHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-chhHHHHHHHHH
Confidence            4555666666666666666666666666655443 45566666666666666666666666666532 224555666666


Q ss_pred             HHHhcCCHHHHHHHHHHHHHhhhc
Q 012111          440 AYNALGMTEAAQNLENKMIAMKEN  463 (471)
Q Consensus       440 ~~~~~g~~~~A~~~~~~m~~~~~~  463 (471)
                      ++...|++++|...++++++..|+
T Consensus        86 ~~~~~~~~~~A~~~~~~a~~~~p~  109 (137)
T 3q49_B           86 CQLEMESYDEAIANLQRAYSLAKE  109 (137)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHhhHHHHHHHHHHHHHHChh
Confidence            666666666666666666666665

>2dba_A Smooth muscle cell associated protein-1, isoform 2; tetratricopeptide repeat, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.40  E-value=8.9e-06  Score=62.76  Aligned_cols=98  Identities=9%  Similarity=-0.066  Sum_probs=70.3

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCC----HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHH
Q 012111          325 TVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPN----SITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFN  400 (471)
Q Consensus       325 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~----~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~  400 (471)
                      +...+..+...+...|++++|...|++..+.  .|+    ...+..+..++...|++++|...++...+..+. +...+.
T Consensus        27 ~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~--~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~  103 (148)
T 2dba_A           27 SVEQLRKEGNELFKCGDYGGALAAYTQALGL--DATPQDQAVLHRNRAACHLKLEDYDKAETEASKAIEKDGG-DVKALY  103 (148)
T ss_dssp             CHHHHHHHHHHHHTTTCHHHHHHHHHHHHTS--CCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTSC-CHHHHH
T ss_pred             HHHHHHHHHHHHHHhCCHHHHHHHHHHHHHH--cccchHHHHHHHHHHHHHHHHccHHHHHHHHHHHHhhCcc-CHHHHH
Confidence            4556667777777778888888888777764  444    566677777777777777777777777765443 566677


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHhC
Q 012111          401 CIISAYGQAGDVEKMGELFLTMKER  425 (471)
Q Consensus       401 ~l~~~~~~~g~~~~a~~~~~~~~~~  425 (471)
                      .+..++...|++++|...|++..+.
T Consensus       104 ~~a~~~~~~~~~~~A~~~~~~al~~  128 (148)
T 2dba_A          104 RRSQALEKLGRLDQAVLDLQRCVSL  128 (148)
T ss_dssp             HHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHc
Confidence            7777777777777777777777663

>3ro3_A PINS homolog, G-protein-signaling modulator 2; asymmetric cell division, protein binding; 1.10A {Mus musculus}

Probab=98.38  E-value=3.2e-06  Score=66.38  Aligned_cols=137  Identities=15%  Similarity=0.107  Sum_probs=87.6

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHcCCC-CC----HHHHHHHHHHHHhcCCHHHHHHHHHHHHhC----CCC-cCHH
Q 012111          328 TYNIVIETFGKAGHIEKMEEYFKKMKHRGMK-PN----SITYCSLVSAYSKAGLIMKVDSILRQVENS----DVI-LDTP  397 (471)
Q Consensus       328 ~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~-p~----~~~~~~li~~~~~~g~~~~a~~~~~~~~~~----~~~-~~~~  397 (471)
                      ++..+...+...|++++|...+++....... ++    ..++..+...+...|++++|...+++..+.    +.. ....
T Consensus        11 ~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~   90 (164)
T 3ro3_A           11 AFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERIAYSNLGNAYIFLGEFETASEYYKKTLLLARQLKDRAVEAQ   90 (164)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhCCcHHHHH
Confidence            4455555666666666666666665543100 11    135666677777777777777777765532    111 1134


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhC----CCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhhhcC
Q 012111          398 FFNCIISAYGQAGDVEKMGELFLTMKER----HCVP-DNITFATMIQAYNALGMTEAAQNLENKMIAMKENS  464 (471)
Q Consensus       398 ~~~~l~~~~~~~g~~~~a~~~~~~~~~~----~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~~  464 (471)
                      ++..+...+...|++++|.+.+++..+.    +..+ ....+..+...+...|++++|.+.+++.++.....
T Consensus        91 ~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~~  162 (164)
T 3ro3_A           91 SCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELKDRIGEGRACWSLGNAYTALGNHDQAMHFAEKHLEISREV  162 (164)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHccchHhHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHHh
Confidence            5677777888888888888888877642    1111 13456677788889999999999999988776543

>2xev_A YBGF; tetratricopeptide, alpha-helical, metal binding; 1.57A {Xanthomonas campestris}

Probab=98.38  E-value=1e-05  Score=60.82  Aligned_cols=93  Identities=9%  Similarity=-0.042  Sum_probs=64.7

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHHcCCCCCH---HHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcC---HHHHHHHHH
Q 012111          331 IVIETFGKAGHIEKMEEYFKKMKHRGMKPNS---ITYCSLVSAYSKAGLIMKVDSILRQVENSDVILD---TPFFNCIIS  404 (471)
Q Consensus       331 ~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~---~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~---~~~~~~l~~  404 (471)
                      .+...+...|++++|...|+.+.+... .+.   ..+..+..++...|++++|...++.+.+..+. +   ...+..+..
T Consensus         7 ~~a~~~~~~~~~~~A~~~~~~~~~~~p-~~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~~~~~~p~-~~~~~~~~~~la~   84 (129)
T 2xev_A            7 NVAFDALKNGKYDDASQLFLSFLELYP-NGVYTPNALYWLGESYYATRNFQLAEAQFRDLVSRYPT-HDKAAGGLLKLGL   84 (129)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHCS-SSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-STTHHHHHHHHHH
T ss_pred             HHHHHHHHhCCHHHHHHHHHHHHHHCC-CCcccHHHHHHHHHHHHHhccHHHHHHHHHHHHHHCCC-CcccHHHHHHHHH
Confidence            455666777888888888887776531 122   46666777777788888888888777765543 3   455667777


Q ss_pred             HHHhcCCHHHHHHHHHHHHhC
Q 012111          405 AYGQAGDVEKMGELFLTMKER  425 (471)
Q Consensus       405 ~~~~~g~~~~a~~~~~~~~~~  425 (471)
                      ++...|++++|...|+++.+.
T Consensus        85 ~~~~~g~~~~A~~~~~~~~~~  105 (129)
T 2xev_A           85 SQYGEGKNTEAQQTLQQVATQ  105 (129)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHH
Confidence            777778888888888777764

>1elr_A TPR2A-domain of HOP; HOP, TPR-domain, peptide-complex, helical repeat, protein binding, chaperone; 1.90A {Homo sapiens} SCOP: a.118.8.1 PDB: 3esk_A 3fwv_A

Probab=98.36  E-value=5.7e-06  Score=62.21  Aligned_cols=102  Identities=17%  Similarity=0.090  Sum_probs=87.3

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCC--CCC----HHHH
Q 012111          361 SITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHC--VPD----NITF  434 (471)
Q Consensus       361 ~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~--~p~----~~~~  434 (471)
                      ...+..+...+...|++++|...+++..+..+. +...+..+...+...|++++|...++++.+...  .++    ..++
T Consensus         4 ~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~-~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~   82 (131)
T 1elr_A            4 ALKEKELGNDAYKKKDFDTALKHYDKAKELDPT-NMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENREDYRQIAKAY   82 (131)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSTTCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHhcCCc-cHHHHHHHHHHHHHhccHHHHHHHHHHHHhhccccchhHHHHHHHH
Confidence            456778888999999999999999999887654 788899999999999999999999999886421  122    6788


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHHhhhc
Q 012111          435 ATMIQAYNALGMTEAAQNLENKMIAMKEN  463 (471)
Q Consensus       435 ~~l~~~~~~~g~~~~A~~~~~~m~~~~~~  463 (471)
                      ..+..++...|++++|.+.++++++..++
T Consensus        83 ~~la~~~~~~~~~~~A~~~~~~~~~~~~~  111 (131)
T 1elr_A           83 ARIGNSYFKEEKYKDAIHFYNKSLAEHRT  111 (131)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHCCC
T ss_pred             HHHHHHHHHhccHHHHHHHHHHHHHhCCC
Confidence            88889999999999999999999998763

>2dba_A Smooth muscle cell associated protein-1, isoform 2; tetratricopeptide repeat, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.35  E-value=2.5e-05  Score=60.19  Aligned_cols=99  Identities=13%  Similarity=0.005  Sum_probs=59.7

Q ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCC----HHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHH
Q 012111          290 DIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPT----VVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYC  365 (471)
Q Consensus       290 ~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~----~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~  365 (471)
                      +...+..+...+...|++++|...|+...+..  |+    ...+..+...+...|++++|...+++..... +.+...+.
T Consensus        27 ~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~--~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~  103 (148)
T 2dba_A           27 SVEQLRKEGNELFKCGDYGGALAAYTQALGLD--ATPQDQAVLHRNRAACHLKLEDYDKAETEASKAIEKD-GGDVKALY  103 (148)
T ss_dssp             CHHHHHHHHHHHHTTTCHHHHHHHHHHHHTSC--CCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT-SCCHHHHH
T ss_pred             HHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHc--ccchHHHHHHHHHHHHHHHHccHHHHHHHHHHHHhhC-ccCHHHHH
Confidence            45555666666666666666666666666542  33    4455556666666666666666666665542 22455566


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHhCC
Q 012111          366 SLVSAYSKAGLIMKVDSILRQVENSD  391 (471)
Q Consensus       366 ~li~~~~~~g~~~~a~~~~~~~~~~~  391 (471)
                      .+..++...|++++|...|++..+..
T Consensus       104 ~~a~~~~~~~~~~~A~~~~~~al~~~  129 (148)
T 2dba_A          104 RRSQALEKLGRLDQAVLDLQRCVSLE  129 (148)
T ss_dssp             HHHHHHHHHTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHcC
Confidence            66666666666666666666666544

>1hxi_A PEX5, peroxisome targeting signal 1 receptor PEX5; alpha helical, transport protein; 1.60A {Trypanosoma brucei} SCOP: a.118.8.1

Probab=98.35  E-value=7.5e-06  Score=60.91  Aligned_cols=95  Identities=7%  Similarity=-0.100  Sum_probs=75.1

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHh
Q 012111          329 YNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQ  408 (471)
Q Consensus       329 ~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  408 (471)
                      +..+...+.+.|++++|...+++..+.. +-+...+..+..++...|++++|...+++..+.++. +...+..+..++..
T Consensus        20 ~~~~g~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~P~-~~~~~~~la~~~~~   97 (121)
T 1hxi_A           20 PMEEGLSMLKLANLAEAALAFEAVCQKE-PEREEAWRSLGLTQAENEKDGLAIIALNHARMLDPK-DIAVHAALAVSHTN   97 (121)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHH
Confidence            4455667778888888888888888763 336777888888888888888888888888887665 67788888888888


Q ss_pred             cCCHHHHHHHHHHHHhC
Q 012111          409 AGDVEKMGELFLTMKER  425 (471)
Q Consensus       409 ~g~~~~a~~~~~~~~~~  425 (471)
                      .|++++|+..+++..+.
T Consensus        98 ~g~~~~A~~~~~~al~~  114 (121)
T 1hxi_A           98 EHNANAALASLRAWLLS  114 (121)
T ss_dssp             HHHHHHHHHHHHHHHC-
T ss_pred             cCCHHHHHHHHHHHHHh
Confidence            88888888888888763

>2hr2_A Hypothetical protein; alpha-alpha superhelix fold, structural genomics, joint CENT structural genomics, JCSG, protein structure initiative; 2.54A {Chlorobium tepidum} SCOP: a.118.8.8

Probab=98.34  E-value=1.3e-05  Score=61.70  Aligned_cols=103  Identities=14%  Similarity=-0.006  Sum_probs=74.7

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHhCCCCc------C-----HHHHHHHHHHHHhcCCHHHHHHHHHHHHhC-----CC
Q 012111          364 YCSLVSAYSKAGLIMKVDSILRQVENSDVIL------D-----TPFFNCIISAYGQAGDVEKMGELFLTMKER-----HC  427 (471)
Q Consensus       364 ~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~------~-----~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~-----~~  427 (471)
                      +......+.+.|++++|...|++..+..+..      +     ...|..+..++.+.|++++|+..+++.++.     .+
T Consensus        14 ~~~~G~~l~~~g~~eeAi~~Y~kAL~l~p~~~~~~a~~~~~~~a~a~~n~g~al~~Lgr~~eAl~~~~kAL~l~n~~~e~   93 (159)
T 2hr2_A           14 ALSDAQRQLVAGEYDEAAANCRRAMEISHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKALHYFNRRGEL   93 (159)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHCCT
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHhhCCCCcchhhhhhccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhhhccccC
Confidence            3444455556666666666666665543321      2     237888888888899999999888888873     12


Q ss_pred             CCC-HHHH----HHHHHHHHhcCCHHHHHHHHHHHHHhhhcCCC
Q 012111          428 VPD-NITF----ATMIQAYNALGMTEAAQNLENKMIAMKENSGK  466 (471)
Q Consensus       428 ~p~-~~~~----~~l~~~~~~~g~~~~A~~~~~~m~~~~~~~~~  466 (471)
                      .|+ ...|    .....++...|++++|...|+++++..|+...
T Consensus        94 ~pd~~~A~~~~~~~rG~aL~~lgr~eEAl~~y~kAlel~p~d~~  137 (159)
T 2hr2_A           94 NQDEGKLWISAVYSRALALDGLGRGAEAMPEFKKVVEMIEERKG  137 (159)
T ss_dssp             TSTHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHCCS
T ss_pred             CCchHHHHHHHHHhHHHHHHHCCCHHHHHHHHHHHHhcCCCcHH
Confidence            565 4567    78889999999999999999999999988554

>2kck_A TPR repeat; tetratricopeptide repeat, structural genomics, unknown function, PSI-2, protein structure initiative; NMR {Methanococcus maripaludis}

Probab=98.32  E-value=8.5e-06  Score=59.27  Aligned_cols=93  Identities=8%  Similarity=-0.046  Sum_probs=39.2

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCC--CHHHHHHHHHH
Q 012111          188 YSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHP--DIFTLNSMISA  265 (471)
Q Consensus       188 ~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~~~~~l~~~  265 (471)
                      +..+...+...|++++|...+++..+.. +.+...+..+...+...|++++|.+.|++..+..  +.  +...+..+..+
T Consensus         9 ~~~~~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~--~~~~~~~~~~~l~~~   85 (112)
T 2kck_A            9 YYLEGVLQYDAGNYTESIDLFEKAIQLD-PEESKYWLMKGKALYNLERYEEAVDCYNYVINVI--EDEYNKDVWAAKADA   85 (112)
T ss_dssp             GGGHHHHHHSSCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTS--CCTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhhHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC--cccchHHHHHHHHHH
Confidence            3334444444444444444444444332 2233444444444444444444444444444332  11  23344444444


Q ss_pred             HHhc-CCHHHHHHHHHHHH
Q 012111          266 YGNS-GNIEKMEKWYNEFN  283 (471)
Q Consensus       266 ~~~~-~~~~~a~~~~~~~~  283 (471)
                      +... |++++|.+.+....
T Consensus        86 ~~~~~~~~~~A~~~~~~~~  104 (112)
T 2kck_A           86 LRYIEGKEVEAEIAEARAK  104 (112)
T ss_dssp             HTTCSSCSHHHHHHHHHHG
T ss_pred             HHHHhCCHHHHHHHHHHHh
Confidence            4444 44444444444443

>3rkv_A Putative peptidylprolyl isomerase; structural genomics, APC102156, PSI-biology, midwest center structural genomics, MCSG; 2.41A {Caenorhabditis elegans}

Probab=98.30  E-value=8.4e-06  Score=64.28  Aligned_cols=103  Identities=11%  Similarity=0.055  Sum_probs=75.1

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHHc--------C---------CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 012111          326 VVTYNIVIETFGKAGHIEKMEEYFKKMKHR--------G---------MKPNSITYCSLVSAYSKAGLIMKVDSILRQVE  388 (471)
Q Consensus       326 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~--------~---------~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~  388 (471)
                      ...+......+.+.|++++|+..|.+....        .         -+.+...|..+..++.+.|++++|...++.+.
T Consensus        11 a~~~~~~G~~~~~~~~~~~A~~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~~~~~~A~~~~~~al   90 (162)
T 3rkv_A           11 VEALRQKGNELFVQKDYKEAIDAYRDALTRLDTLILREKPGEPEWVELDRKNIPLYANMSQCYLNIGDLHEAEETSSEVL   90 (162)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHTSCTTSHHHHHHHHTHHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHH
Confidence            445677777888889999999988887764        0         01123567777777888888888888888877


Q ss_pred             hCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCH
Q 012111          389 NSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDN  431 (471)
Q Consensus       389 ~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~  431 (471)
                      +.++. +...|..+..+|...|++++|...|++..+.  .|+.
T Consensus        91 ~~~p~-~~~a~~~~g~~~~~~g~~~~A~~~~~~al~l--~p~~  130 (162)
T 3rkv_A           91 KREET-NEKALFRRAKARIAAWKLDEAEEDLKLLLRN--HPAA  130 (162)
T ss_dssp             HHSTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CGGG
T ss_pred             hcCCc-chHHHHHHHHHHHHHhcHHHHHHHHHHHHhc--CCCC
Confidence            76654 6777777888888888888888888877764  4543

>3k9i_A BH0479 protein; putative protein binding protein, structural genomics, joint for structural genomics, JCSG; 2.71A {Bacillus halodurans}

Probab=98.27  E-value=1.4e-06  Score=64.45  Aligned_cols=88  Identities=5%  Similarity=-0.083  Sum_probs=63.5

Q ss_pred             HhhcHHHHHHHHHHhhhccC-ccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHH
Q 012111           90 KQKKWQLALKIFGLLRQQQW-YQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEA  168 (471)
Q Consensus        90 ~~~~~~~A~~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a  168 (471)
                      ..|++++|++.|+.+.+.+. -+.+..++..+..++...|++++|...|++..+.... +...+..+..++...|++++|
T Consensus         2 ~~g~~~~A~~~~~~al~~~~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~-~~~~~~~l~~~~~~~g~~~~A   80 (117)
T 3k9i_A            2 VLGLEAQAVPYYEKAIASGLQGKDLAECYLGLGSTFRTLGEYRKAEAVLANGVKQFPN-HQALRVFYAMVLYNLGRYEQG   80 (117)
T ss_dssp             -----CCCHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHTCHHHH
T ss_pred             CCCcHHHHHHHHHHHHHcCCCCccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-chHHHHHHHHHHHHcCCHHHH
Confidence            35778888888888887520 0345567888888888888888888888888876543 577788888888888888888


Q ss_pred             HHHHHHhhcC
Q 012111          169 FSTINDMKSV  178 (471)
Q Consensus       169 ~~~~~~~~~~  178 (471)
                      +..|++....
T Consensus        81 ~~~~~~al~~   90 (117)
T 3k9i_A           81 VELLLKIIAE   90 (117)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHh
Confidence            8888887763

>1kt0_A FKBP51, 51 kDa FK506-binding protein; FKBP-like ppiase, TPR repeats, isomerase; 2.70A {Homo sapiens} SCOP: a.118.8.1 d.26.1.1 d.26.1.1 PDB: 1kt1_A 3o5d_A

Probab=98.27  E-value=1.6e-05  Score=74.44  Aligned_cols=131  Identities=10%  Similarity=-0.019  Sum_probs=77.3

Q ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCC--------------HHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC
Q 012111          291 IQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPT--------------VVTYNIVIETFGKAGHIEKMEEYFKKMKHRG  356 (471)
Q Consensus       291 ~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~--------------~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~  356 (471)
                      ...+..+...+.+.|++++|...|.+..+......              ...|..+..+|.+.|++++|+..+++.+...
T Consensus       268 a~~~~~~G~~~~~~g~~~~A~~~y~~Al~~~p~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~~~  347 (457)
T 1kt0_A          268 AAIVKEKGTVYFKGGKYMQAVIQYGKIVSWLEMEYGLSEKESKASESFLLAAFLNLAMCYLKLREYTKAVECCDKALGLD  347 (457)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTCCSCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHhcC
Confidence            44566666777777777777777777666422211              3556666666666666666666666666643


Q ss_pred             CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHH-HHHHHH
Q 012111          357 MKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGE-LFLTMK  423 (471)
Q Consensus       357 ~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~-~~~~~~  423 (471)
                       +.+...|..+..+|...|++++|...|+++.+..+. +..++..+..++.+.|+.+++.+ ++..|.
T Consensus       348 -p~~~~a~~~~g~a~~~~g~~~~A~~~~~~al~l~P~-~~~a~~~l~~~~~~~~~~~~a~~~~~~~~f  413 (457)
T 1kt0_A          348 -SANEKGLYRRGEAQLLMNEFESAKGDFEKVLEVNPQ-NKAARLQISMCQKKAKEHNERDRRIYANMF  413 (457)
T ss_dssp             -TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC-----CHHHHHHHHHHHHHHHHHHHHHHHHHC-
T ss_pred             -CccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence             234556666666666666666666666666665443 44556666666666666655543 334443

>2if4_A ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha, signaling protein; 2.85A {Arabidopsis thaliana}

Probab=98.26  E-value=3.1e-06  Score=75.91  Aligned_cols=154  Identities=9%  Similarity=0.032  Sum_probs=82.8

Q ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Q 012111          291 IQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSA  370 (471)
Q Consensus       291 ~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~  370 (471)
                      ...+..+...+.+.|++++|...|......  .|+...       +...|+.+++...+.          ...|..+..+
T Consensus       179 a~~~~~~g~~~~~~g~~~~A~~~y~~Al~~--~p~~~~-------~~~~~~~~~~~~~l~----------~~~~~nla~~  239 (338)
T 2if4_A          179 ADRRKMDGNSLFKEEKLEEAMQQYEMAIAY--MGDDFM-------FQLYGKYQDMALAVK----------NPCHLNIAAC  239 (338)
T ss_dssp             HHHHHHHHHHTCSSSCCHHHHHHHHHHHHH--SCHHHH-------HTCCHHHHHHHHHHH----------THHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHHH--hccchh-------hhhcccHHHHHHHHH----------HHHHHHHHHH
Confidence            445566666777777888888887776654  222221       122233333332221          1378888999


Q ss_pred             HHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCC-HHHHHHHHHH-HHhcCCHH
Q 012111          371 YSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPD-NITFATMIQA-YNALGMTE  448 (471)
Q Consensus       371 ~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~-~~~~~~l~~~-~~~~g~~~  448 (471)
                      +.+.|++++|...+++..+..+. +...|..+..+|...|++++|+..|++..+.  .|+ ...+..+... ....+..+
T Consensus       240 ~~~~g~~~~A~~~~~~al~~~p~-~~~a~~~lg~a~~~~g~~~~A~~~l~~al~l--~p~~~~a~~~L~~l~~~~~~~~~  316 (338)
T 2if4_A          240 LIKLKRYDEAIGHCNIVLTEEEK-NPKALFRRGKAKAELGQMDSARDDFRKAQKY--APDDKAIRRELRALAEQEKALYQ  316 (338)
T ss_dssp             HHTTTCCHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHTTTCHHHHHHHHHHTTC--------------------------
T ss_pred             HHHcCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH--CCCCHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999987655 7889999999999999999999999999864  454 3444444444 34456788


Q ss_pred             HHHHHHHHHHHhhhcCCC
Q 012111          449 AAQNLENKMIAMKENSGK  466 (471)
Q Consensus       449 ~A~~~~~~m~~~~~~~~~  466 (471)
                      .+.+++++|....|.+..
T Consensus       317 ~a~~~~~~~l~~~p~~~~  334 (338)
T 2if4_A          317 KQKEMYKGIFKGKDEGGA  334 (338)
T ss_dssp             ------------------
T ss_pred             HHHHHHHHhhCCCCCCCC
Confidence            889999999999887654

>3k9i_A BH0479 protein; putative protein binding protein, structural genomics, joint for structural genomics, JCSG; 2.71A {Bacillus halodurans}

Probab=98.23  E-value=3.2e-06  Score=62.52  Aligned_cols=87  Identities=18%  Similarity=0.161  Sum_probs=59.0

Q ss_pred             hcCCHHHHHHHHHHHHHcCC--CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHH
Q 012111          338 KAGHIEKMEEYFKKMKHRGM--KPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKM  415 (471)
Q Consensus       338 ~~g~~~~a~~~~~~m~~~~~--~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a  415 (471)
                      ..|++++|+..|++..+.+.  +-+...+..+..++...|++++|...++++.+..+. +...+..+..++...|++++|
T Consensus         2 ~~g~~~~A~~~~~~al~~~~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~-~~~~~~~l~~~~~~~g~~~~A   80 (117)
T 3k9i_A            2 VLGLEAQAVPYYEKAIASGLQGKDLAECYLGLGSTFRTLGEYRKAEAVLANGVKQFPN-HQALRVFYAMVLYNLGRYEQG   80 (117)
T ss_dssp             -----CCCHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHTCHHHH
T ss_pred             CCCcHHHHHHHHHHHHHcCCCCccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-chHHHHHHHHHHHHcCCHHHH
Confidence            35677778888887776431  223456677777777888888888888877776655 567777777777788888888


Q ss_pred             HHHHHHHHhC
Q 012111          416 GELFLTMKER  425 (471)
Q Consensus       416 ~~~~~~~~~~  425 (471)
                      +..|++..+.
T Consensus        81 ~~~~~~al~~   90 (117)
T 3k9i_A           81 VELLLKIIAE   90 (117)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHh
Confidence            8887777654

>2xev_A YBGF; tetratricopeptide, alpha-helical, metal binding; 1.57A {Xanthomonas campestris}

Probab=98.23  E-value=2.9e-05  Score=58.25  Aligned_cols=94  Identities=15%  Similarity=0.036  Sum_probs=72.1

Q ss_pred             HHHHHHHHHHhhcHHHHHHHHHHhhhccCccCCh---hHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCC---HHHHHH
Q 012111           81 VLEALDEAIKQKKWQLALKIFGLLRQQQWYQARC---QTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPS---VDVYTA  154 (471)
Q Consensus        81 ~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~---~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~---~~~~~~  154 (471)
                      +......+...|++++|++.|+.+.+..  +.+.   ..+..+..++...|++++|...|+...+.... +   ...+..
T Consensus         5 ~~~~a~~~~~~~~~~~A~~~~~~~~~~~--p~~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~~~~~~p~-~~~~~~~~~~   81 (129)
T 2xev_A            5 AYNVAFDALKNGKYDDASQLFLSFLELY--PNGVYTPNALYWLGESYYATRNFQLAEAQFRDLVSRYPT-HDKAAGGLLK   81 (129)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHC--SSSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-STTHHHHHHH
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHHHHC--CCCcccHHHHHHHHHHHHHhccHHHHHHHHHHHHHHCCC-CcccHHHHHH
Confidence            3444556678889999999999888764  3344   47778888888889999999988888876432 3   566777


Q ss_pred             HHHHHHhcCCHHHHHHHHHHhhc
Q 012111          155 LVSAYGQSGLLDEAFSTINDMKS  177 (471)
Q Consensus       155 li~~~~~~~~~~~a~~~~~~~~~  177 (471)
                      +..++...|++++|...|+++..
T Consensus        82 la~~~~~~g~~~~A~~~~~~~~~  104 (129)
T 2xev_A           82 LGLSQYGEGKNTEAQQTLQQVAT  104 (129)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHH
Confidence            88888888888888888888876

>1wao_1 Serine/threonine protein phosphatase 5; hydrolase, protein-protein interactions, TPR, super-helix,; 2.9A {Homo sapiens} SCOP: a.118.8.1 d.159.1.3

Probab=98.22  E-value=2.6e-06  Score=80.16  Aligned_cols=117  Identities=9%  Similarity=-0.127  Sum_probs=52.5

Q ss_pred             HHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHH
Q 012111          301 YGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKV  380 (471)
Q Consensus       301 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a  380 (471)
                      +.+.|++++|...+++..+.... +...|..+..+|.+.|++++|...+++..+.. +-+...+..+..+|...|++++|
T Consensus        16 ~~~~g~~~~A~~~~~~Al~~~p~-~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~-p~~~~~~~~lg~~~~~~g~~~eA   93 (477)
T 1wao_1           16 YFKAKDYENAIKFYSQAIELNPS-NAIYYGNRSLAYLRTECYGYALGDATRAIELD-KKYIKGYYRRAASNMALGKFRAA   93 (477)
T ss_dssp             TTTTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSC-TTCHHHHHHHHHHHHHHTCHHHH
T ss_pred             HHHhCCHHHHHHHHHHHHHhCCc-cHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHH
Confidence            34445555555555555443221 34445555555555555555555555555432 22344455555555555555555


Q ss_pred             HHHHHHHHhCCCCcCHHHHHHHHHH--HHhcCCHHHHHHHHH
Q 012111          381 DSILRQVENSDVILDTPFFNCIISA--YGQAGDVEKMGELFL  420 (471)
Q Consensus       381 ~~~~~~~~~~~~~~~~~~~~~l~~~--~~~~g~~~~a~~~~~  420 (471)
                      .+.++++.+..+. +...+..+..+  +.+.|++++|++.++
T Consensus        94 ~~~~~~al~~~p~-~~~~~~~l~~~~~~~~~g~~~~A~~~~~  134 (477)
T 1wao_1           94 LRDYETVVKVKPH-DKDAKMKYQECNKIVKQKAFERAIAGDE  134 (477)
T ss_dssp             HHHHHHHHHHSTT-CTTHHHHHHHHHHHHHHHHHCCC-----
T ss_pred             HHHHHHHHHhCCC-CHHHHHHHHHHHHHHHHHHHHHHhcccc
Confidence            5555555443322 22233333333  444455555555544

>1kt0_A FKBP51, 51 kDa FK506-binding protein; FKBP-like ppiase, TPR repeats, isomerase; 2.70A {Homo sapiens} SCOP: a.118.8.1 d.26.1.1 d.26.1.1 PDB: 1kt1_A 3o5d_A

Probab=98.20  E-value=3.1e-05  Score=72.49  Aligned_cols=125  Identities=13%  Similarity=-0.017  Sum_probs=88.8

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCC---------------HHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Q 012111          255 DIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKAD---------------IQTLNILTKSYGRAGMYDKMRSVMDFMQK  319 (471)
Q Consensus       255 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~---------------~~~~~~ll~~~~~~~~~~~a~~~~~~~~~  319 (471)
                      ....+..+...+.+.|++++|...|++..... +.+               ...|..+..+|.+.|++++|...++...+
T Consensus       267 ~a~~~~~~G~~~~~~g~~~~A~~~y~~Al~~~-p~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~  345 (457)
T 1kt0_A          267 QAAIVKEKGTVYFKGGKYMQAVIQYGKIVSWL-EMEYGLSEKESKASESFLLAAFLNLAMCYLKLREYTKAVECCDKALG  345 (457)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH-TTCCSCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHh-cccccCChHHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHh
Confidence            34567777778888888888888888876643 222               46777788888888888888888888877


Q ss_pred             CCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHH
Q 012111          320 RFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDS  382 (471)
Q Consensus       320 ~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~  382 (471)
                      .... +...|..+..+|...|++++|...|++..+.. +-+...+..+..++.+.++.+++.+
T Consensus       346 ~~p~-~~~a~~~~g~a~~~~g~~~~A~~~~~~al~l~-P~~~~a~~~l~~~~~~~~~~~~a~~  406 (457)
T 1kt0_A          346 LDSA-NEKGLYRRGEAQLLMNEFESAKGDFEKVLEVN-PQNKAARLQISMCQKKAKEHNERDR  406 (457)
T ss_dssp             HSTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC-----CHHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCc-cHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            6433 56677778888888888888888888877652 2244566777777777777766653

>3ro3_A PINS homolog, G-protein-signaling modulator 2; asymmetric cell division, protein binding; 1.10A {Mus musculus}

Probab=98.18  E-value=2.3e-05  Score=61.34  Aligned_cols=97  Identities=15%  Similarity=0.066  Sum_probs=61.3

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHcC----CCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhC----CCC-cCHH
Q 012111          328 TYNIVIETFGKAGHIEKMEEYFKKMKHRG----MKP-NSITYCSLVSAYSKAGLIMKVDSILRQVENS----DVI-LDTP  397 (471)
Q Consensus       328 ~~~~li~~~~~~g~~~~a~~~~~~m~~~~----~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~----~~~-~~~~  397 (471)
                      .+..+...+...|++++|...+++.....    ..+ ....+..+...+...|++++|...+++..+.    +.. ....
T Consensus        51 ~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~  130 (164)
T 3ro3_A           51 AYSNLGNAYIFLGEFETASEYYKKTLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELKDRIGEGR  130 (164)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhCCcHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHccchHhHHH
Confidence            45555666666677777776666655321    000 1345666677777778888877777765532    111 1234


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 012111          398 FFNCIISAYGQAGDVEKMGELFLTMKE  424 (471)
Q Consensus       398 ~~~~l~~~~~~~g~~~~a~~~~~~~~~  424 (471)
                      .+..+...+...|++++|.+.+++..+
T Consensus       131 ~~~~la~~~~~~g~~~~A~~~~~~a~~  157 (164)
T 3ro3_A          131 ACWSLGNAYTALGNHDQAMHFAEKHLE  157 (164)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHccCHHHHHHHHHHHHH
Confidence            567777888888999988888887764

>3rkv_A Putative peptidylprolyl isomerase; structural genomics, APC102156, PSI-biology, midwest center structural genomics, MCSG; 2.41A {Caenorhabditis elegans}

Probab=98.17  E-value=3.4e-05  Score=60.74  Aligned_cols=102  Identities=12%  Similarity=0.041  Sum_probs=80.3

Q ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHhC--------CC---------CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 012111          291 IQTLNILTKSYGRAGMYDKMRSVMDFMQKR--------FF---------FPTVVTYNIVIETFGKAGHIEKMEEYFKKMK  353 (471)
Q Consensus       291 ~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~--------~~---------~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~  353 (471)
                      ...+......+.+.|++++|...|......        ..         +.+...|..+..+|.+.|++++|+..+++.+
T Consensus        11 a~~~~~~G~~~~~~~~~~~A~~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~~~~~~A~~~~~~al   90 (162)
T 3rkv_A           11 VEALRQKGNELFVQKDYKEAIDAYRDALTRLDTLILREKPGEPEWVELDRKNIPLYANMSQCYLNIGDLHEAEETSSEVL   90 (162)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHTSCTTSHHHHHHHHTHHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHH
Confidence            456777788888999999999999887664        10         1123577788888889999999999999888


Q ss_pred             HcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCC
Q 012111          354 HRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVI  393 (471)
Q Consensus       354 ~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~  393 (471)
                      ... +.+...|..+..++...|++++|...|+...+..+.
T Consensus        91 ~~~-p~~~~a~~~~g~~~~~~g~~~~A~~~~~~al~l~p~  129 (162)
T 3rkv_A           91 KRE-ETNEKALFRRAKARIAAWKLDEAEEDLKLLLRNHPA  129 (162)
T ss_dssp             HHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCGG
T ss_pred             hcC-CcchHHHHHHHHHHHHHhcHHHHHHHHHHHHhcCCC
Confidence            864 346788888999999999999999999988877544

>1ihg_A Cyclophilin 40; ppiase immunophilin tetratricopeptide, isomerase; 1.80A {Bos taurus} SCOP: a.118.8.1 b.62.1.1 PDB: 1iip_A

Probab=98.16  E-value=3.6e-05  Score=69.73  Aligned_cols=90  Identities=8%  Similarity=-0.020  Sum_probs=69.5

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC-CHHHHHHHH
Q 012111          360 NSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVP-DNITFATMI  438 (471)
Q Consensus       360 ~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p-~~~~~~~l~  438 (471)
                      +..+|..+..+|.+.|++++|...++++.+..+. +...|..+..+|...|++++|++.|+++.+.  .| +...+..+.
T Consensus       272 ~~~~~~nla~~~~~~g~~~~A~~~~~~al~~~p~-~~~a~~~lg~~~~~~g~~~eA~~~l~~Al~l--~P~~~~~~~~l~  348 (370)
T 1ihg_A          272 ALSCVLNIGACKLKMSDWQGAVDSCLEALEIDPS-NTKALYRRAQGWQGLKEYDQALADLKKAQEI--APEDKAIQAELL  348 (370)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhccCHHHHHHHHHHHHHhCch-hHHHHHHHHHHHHHccCHHHHHHHHHHHHHh--CCCCHHHHHHHH
Confidence            4567778888888888888888888888887654 6778888888888888999998888888774  34 556666666


Q ss_pred             HHHHhcCCHHHHHH
Q 012111          439 QAYNALGMTEAAQN  452 (471)
Q Consensus       439 ~~~~~~g~~~~A~~  452 (471)
                      ..+...++.+++.+
T Consensus       349 ~~~~~~~~~~~a~k  362 (370)
T 1ihg_A          349 KVKQKIKAQKDKEK  362 (370)
T ss_dssp             HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHH
Confidence            77777777776643

>1wao_1 Serine/threonine protein phosphatase 5; hydrolase, protein-protein interactions, TPR, super-helix,; 2.9A {Homo sapiens} SCOP: a.118.8.1 d.159.1.3

Probab=98.14  E-value=8e-06  Score=76.88  Aligned_cols=116  Identities=11%  Similarity=-0.006  Sum_probs=85.8

Q ss_pred             HHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHH
Q 012111           89 IKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEA  168 (471)
Q Consensus        89 ~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a  168 (471)
                      .+.|++++|++.|+.+.+..  +.+..++..+..++.+.|++++|...+++..+.... +...|..+..+|...|++++|
T Consensus        17 ~~~g~~~~A~~~~~~Al~~~--p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~p~-~~~~~~~lg~~~~~~g~~~eA   93 (477)
T 1wao_1           17 FKAKDYENAIKFYSQAIELN--PSNAIYYGNRSLAYLRTECYGYALGDATRAIELDKK-YIKGYYRRAASNMALGKFRAA   93 (477)
T ss_dssp             TTTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSCTT-CHHHHHHHHHHHHHHTCHHHH
T ss_pred             HHhCCHHHHHHHHHHHHHhC--CccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHcCCHHHH
Confidence            46788999999999888864  566788888888999999999999999988887433 678888888889999999999


Q ss_pred             HHHHHHhhcCCCCCCCHHHHHHHHHH--HHhcCCHHHHHHHHH
Q 012111          169 FSTINDMKSVSDCKPDVYTYSILIKS--CTKFHRFDLIEKILA  209 (471)
Q Consensus       169 ~~~~~~~~~~~~~~~~~~~~~~ll~~--~~~~~~~~~a~~~~~  209 (471)
                      ++.|++..+...-  +...+..+..+  +.+.|++++|.+.++
T Consensus        94 ~~~~~~al~~~p~--~~~~~~~l~~~~~~~~~g~~~~A~~~~~  134 (477)
T 1wao_1           94 LRDYETVVKVKPH--DKDAKMKYQECNKIVKQKAFERAIAGDE  134 (477)
T ss_dssp             HHHHHHHHHHSTT--CTTHHHHHHHHHHHHHHHHHCCC-----
T ss_pred             HHHHHHHHHhCCC--CHHHHHHHHHHHHHHHHHHHHHHhcccc
Confidence            9999888764322  23344444444  777788888888877

>2kat_A Uncharacterized protein; NESG, structure, structural genomics, PSI-2, protein structure initiative; NMR {Bordetella parapertussis}

Probab=98.06  E-value=3.3e-05  Score=56.71  Aligned_cols=79  Identities=14%  Similarity=0.106  Sum_probs=57.6

Q ss_pred             HHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 012111          344 KMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMK  423 (471)
Q Consensus       344 ~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~  423 (471)
                      .|+..|++..+.. +.+...+..+...+...|++++|...+++..+.++. +...|..+..+|...|++++|...|++..
T Consensus         3 ~a~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~la~~~~~~g~~~~A~~~~~~al   80 (115)
T 2kat_A            3 AITERLEAMLAQG-TDNMLLRFTLGKTYAEHEQFDAALPHLRAALDFDPT-YSVAWKWLGKTLQGQGDRAGARQAWESGL   80 (115)
T ss_dssp             CHHHHHHHHHTTT-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhC-CCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHHCCC-cHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            4566777766643 335677777777888888888888888887776554 56677777778888888888888887776


Q ss_pred             h
Q 012111          424 E  424 (471)
Q Consensus       424 ~  424 (471)
                      +
T Consensus        81 ~   81 (115)
T 2kat_A           81 A   81 (115)
T ss_dssp             H
T ss_pred             H
Confidence            5

>1ihg_A Cyclophilin 40; ppiase immunophilin tetratricopeptide, isomerase; 1.80A {Bos taurus} SCOP: a.118.8.1 b.62.1.1 PDB: 1iip_A

Probab=98.03  E-value=8e-05  Score=67.43  Aligned_cols=91  Identities=4%  Similarity=-0.089  Sum_probs=71.1

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHH
Q 012111          325 TVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIIS  404 (471)
Q Consensus       325 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  404 (471)
                      +...|..+..+|.+.|++++|+..+++..+.. +-+...+..+..+|...|++++|...|+++.+..+. +...+..+..
T Consensus       272 ~~~~~~nla~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~g~~~eA~~~l~~Al~l~P~-~~~~~~~l~~  349 (370)
T 1ihg_A          272 ALSCVLNIGACKLKMSDWQGAVDSCLEALEID-PSNTKALYRRAQGWQGLKEYDQALADLKKAQEIAPE-DKAIQAELLK  349 (370)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhccCHHHHHHHHHHHHHhC-chhHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCC-CHHHHHHHHH
Confidence            34577778888888899999999998888753 336778888888899999999999999888877654 6777777777


Q ss_pred             HHHhcCCHHHHHH
Q 012111          405 AYGQAGDVEKMGE  417 (471)
Q Consensus       405 ~~~~~g~~~~a~~  417 (471)
                      ++...++.+++.+
T Consensus       350 ~~~~~~~~~~a~k  362 (370)
T 1ihg_A          350 VKQKIKAQKDKEK  362 (370)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHH
Confidence            7777777666654

>1klx_A Cysteine rich protein B; structural genomics, helix-turn-helix, right handed super helix, modular structure', hydrolase; 1.95A {Helicobacter pylori} SCOP: a.118.18.1

Probab=98.02  E-value=0.00032  Score=53.33  Aligned_cols=110  Identities=12%  Similarity=0.002  Sum_probs=54.6

Q ss_pred             CHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHh----cCCHHHHH
Q 012111          341 HIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQ----AGDVEKMG  416 (471)
Q Consensus       341 ~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~g~~~~a~  416 (471)
                      ++++|..+|++..+.| .++..    +...|...+.+++|.+.|++..+.+   +...+..|...|..    .+++++|.
T Consensus        10 d~~~A~~~~~~aa~~g-~~~a~----lg~~y~~g~~~~~A~~~~~~Aa~~g---~~~a~~~Lg~~y~~G~g~~~d~~~A~   81 (138)
T 1klx_A           10 DLKKAIQYYVKACELN-EMFGC----LSLVSNSQINKQKLFQYLSKACELN---SGNGCRFLGDFYENGKYVKKDLRKAA   81 (138)
T ss_dssp             HHHHHHHHHHHHHHTT-CTTHH----HHHHTCTTSCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHCSSSCCCHHHHH
T ss_pred             CHHHHHHHHHHHHcCC-CHhhh----HHHHHHcCCCHHHHHHHHHHHHcCC---CHHHHHHHHHHHHcCCCCCccHHHHH
Confidence            3445555555555544 22222    4444444445555555555555443   44444555555554    45555555


Q ss_pred             HHHHHHHhCCCCCCHHHHHHHHHHHHh----cCCHHHHHHHHHHHHHhh
Q 012111          417 ELFLTMKERHCVPDNITFATMIQAYNA----LGMTEAAQNLENKMIAMK  461 (471)
Q Consensus       417 ~~~~~~~~~~~~p~~~~~~~l~~~~~~----~g~~~~A~~~~~~m~~~~  461 (471)
                      ++|++..+.|   ++..+..|...|..    .++.++|.+++++..+.+
T Consensus        82 ~~~~~Aa~~g---~~~a~~~Lg~~y~~G~g~~~d~~~A~~~~~~Aa~~g  127 (138)
T 1klx_A           82 QYYSKACGLN---DQDGCLILGYKQYAGKGVVKNEKQAVKTFEKACRLG  127 (138)
T ss_dssp             HHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHcCC---CHHHHHHHHHHHHCCCCCCcCHHHHHHHHHHHHHCC
Confidence            5555555542   34444445555554    455555555555555543

>1dce_A Protein (RAB geranylgeranyltransferase alpha subunit); 2.0 A resolution, N-formylmethionine, alpha subunit; HET: FME; 2.00A {Rattus norvegicus} SCOP: a.118.6.1 b.7.4.1 c.10.2.2 PDB: 1ltx_A*

Probab=97.97  E-value=0.00081  Score=64.51  Aligned_cols=155  Identities=7%  Similarity=-0.054  Sum_probs=118.2

Q ss_pred             HHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCC----------HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcC-
Q 012111          307 YDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGH----------IEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAG-  375 (471)
Q Consensus       307 ~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~----------~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g-  375 (471)
                      .++|...++.+.+..+. +...|+.--..+...|+          ++++++.++.+.... +-+..+|..-...+.+.| 
T Consensus        45 ~eeal~~~~~~l~~nP~-~~taW~~R~~~l~~l~~~~~~~~~~~~~~~eL~~~~~~l~~~-pK~y~aW~hR~w~l~~l~~  122 (567)
T 1dce_A           45 DESVLELTSQILGANPD-FATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVN-PKSYGTWHHRCWLLSRLPE  122 (567)
T ss_dssp             SHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTCSS
T ss_pred             CHHHHHHHHHHHHHCch-hHHHHHHHHHHHHhcccccchhhhhhhHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHccc
Confidence            45677777777776443 45566665555555555          888999999888864 336778888788888888 


Q ss_pred             -CHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcC-CHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhc---------
Q 012111          376 -LIMKVDSILRQVENSDVILDTPFFNCIISAYGQAG-DVEKMGELFLTMKERHCVPDNITFATMIQAYNAL---------  444 (471)
Q Consensus       376 -~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g-~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~---------  444 (471)
                       +++++.+.++++.+.++. +..+|+.-..++.+.| .++++++.++++.+.. .-|...|+.....+.+.         
T Consensus       123 ~~~~~el~~~~k~l~~d~~-N~~aW~~R~~~l~~l~~~~~~el~~~~~~I~~~-p~n~saW~~r~~ll~~l~~~~~~~~~  200 (567)
T 1dce_A          123 PNWARELELCARFLEADER-NFHCWDYRRFVAAQAAVAPAEELAFTDSLITRN-FSNYSSWHYRSCLLPQLHPQPDSGPQ  200 (567)
T ss_dssp             CCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTCCCHHHHHHHHHTTTTTT-CCCHHHHHHHHHHHHHHSCCCCSSSC
T ss_pred             ccHHHHHHHHHHHHhhccc-cccHHHHHHHHHHHcCCChHHHHHHHHHHHHHC-CCCccHHHHHHHHHHhhccccccccc
Confidence             679999999999988877 8888888888888888 8899999999888753 23677777776666553         


Q ss_pred             -----CCHHHHHHHHHHHHHhhhcCC
Q 012111          445 -----GMTEAAQNLENKMIAMKENSG  465 (471)
Q Consensus       445 -----g~~~~A~~~~~~m~~~~~~~~  465 (471)
                           +.++++.+.+++++..+|+..
T Consensus       201 ~~~~~~~~~eel~~~~~ai~~~P~~~  226 (567)
T 1dce_A          201 GRLPENVLLKELELVQNAFFTDPNDQ  226 (567)
T ss_dssp             CSSCHHHHHHHHHHHHHHHHHCSSCS
T ss_pred             ccccHHHHHHHHHHHHHHHhhCCCCc
Confidence                 567999999999999988754

>2hr2_A Hypothetical protein; alpha-alpha superhelix fold, structural genomics, joint CENT structural genomics, JCSG, protein structure initiative; 2.54A {Chlorobium tepidum} SCOP: a.118.8.8

Probab=97.97  E-value=0.00019  Score=55.16  Aligned_cols=109  Identities=8%  Similarity=-0.020  Sum_probs=76.5

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHcCCCC------C-----HHHHHHHHHHHHhcCCHHHHHHHHHHHHhC-------
Q 012111          329 YNIVIETFGKAGHIEKMEEYFKKMKHRGMKP------N-----SITYCSLVSAYSKAGLIMKVDSILRQVENS-------  390 (471)
Q Consensus       329 ~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p------~-----~~~~~~li~~~~~~g~~~~a~~~~~~~~~~-------  390 (471)
                      +......+...|++++|+..|++.++.....      +     ...|..+..++.+.|++++|+..+++.++.       
T Consensus        14 ~~~~G~~l~~~g~~eeAi~~Y~kAL~l~p~~~~~~a~~~~~~~a~a~~n~g~al~~Lgr~~eAl~~~~kAL~l~n~~~e~   93 (159)
T 2hr2_A           14 ALSDAQRQLVAGEYDEAAANCRRAMEISHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKALHYFNRRGEL   93 (159)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHCCT
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHhhCCCCcchhhhhhccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhhhccccC
Confidence            3444555666777777777777776642110      2     237888888888888888888888888876       


Q ss_pred             CCCcCHHHH----HHHHHHHHhcCCHHHHHHHHHHHHh-----CCCCCCHHHHHHHH
Q 012111          391 DVILDTPFF----NCIISAYGQAGDVEKMGELFLTMKE-----RHCVPDNITFATMI  438 (471)
Q Consensus       391 ~~~~~~~~~----~~l~~~~~~~g~~~~a~~~~~~~~~-----~~~~p~~~~~~~l~  438 (471)
                      ++. +...|    .....++...|++++|+..|++..+     .|+.+........+
T Consensus        94 ~pd-~~~A~~~~~~~rG~aL~~lgr~eEAl~~y~kAlel~p~d~~~~~~~~~~~~~~  149 (159)
T 2hr2_A           94 NQD-EGKLWISAVYSRALALDGLGRGAEAMPEFKKVVEMIEERKGETPGKERMMEVA  149 (159)
T ss_dssp             TST-HHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHCCSCCTTHHHHHHHH
T ss_pred             CCc-hHHHHHHHHHhHHHHHHHCCCHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHH
Confidence            544 56677    8888899999999999999998875     35555544444333

>1dce_A Protein (RAB geranylgeranyltransferase alpha subunit); 2.0 A resolution, N-formylmethionine, alpha subunit; HET: FME; 2.00A {Rattus norvegicus} SCOP: a.118.6.1 b.7.4.1 c.10.2.2 PDB: 1ltx_A*

Probab=97.92  E-value=0.0013  Score=63.15  Aligned_cols=170  Identities=7%  Similarity=-0.122  Sum_probs=117.1

Q ss_pred             HHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCC----------HHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcC-
Q 012111          272 IEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGM----------YDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAG-  340 (471)
Q Consensus       272 ~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~----------~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g-  340 (471)
                      .++|++.++++.... +-+..+|+.--.++...|+          ++++...++.+.+...+ +..+|+.-.-.+.+.| 
T Consensus        45 ~eeal~~~~~~l~~n-P~~~taW~~R~~~l~~l~~~~~~~~~~~~~~~eL~~~~~~l~~~pK-~y~aW~hR~w~l~~l~~  122 (567)
T 1dce_A           45 DESVLELTSQILGAN-PDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVNPK-SYGTWHHRCWLLSRLPE  122 (567)
T ss_dssp             SHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHTCSS
T ss_pred             CHHHHHHHHHHHHHC-chhHHHHHHHHHHHHhcccccchhhhhhhHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHccc
Confidence            345666666666543 3344455544444444444          77777788777776444 6667777777777777 


Q ss_pred             -CHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcC-CHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhc---------
Q 012111          341 -HIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAG-LIMKVDSILRQVENSDVILDTPFFNCIISAYGQA---------  409 (471)
Q Consensus       341 -~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g-~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~---------  409 (471)
                       +++++++.++++.+.. +-+...|+.-...+.+.| .++++.+.++++++.++. |...|+.....+.+.         
T Consensus       123 ~~~~~el~~~~k~l~~d-~~N~~aW~~R~~~l~~l~~~~~~el~~~~~~I~~~p~-n~saW~~r~~ll~~l~~~~~~~~~  200 (567)
T 1dce_A          123 PNWARELELCARFLEAD-ERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRNFS-NYSSWHYRSCLLPQLHPQPDSGPQ  200 (567)
T ss_dssp             CCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTCCCHHHHHHHHHTTTTTTCC-CHHHHHHHHHHHHHHSCCCCSSSC
T ss_pred             ccHHHHHHHHHHHHhhc-cccccHHHHHHHHHHHcCCChHHHHHHHHHHHHHCCC-CccHHHHHHHHHHhhccccccccc
Confidence             6688888888888764 336777777777777777 788888888888887776 778887777766653         


Q ss_pred             -----CCHHHHHHHHHHHHhCCCCC-CHHHHHHHHHHHHhcCCH
Q 012111          410 -----GDVEKMGELFLTMKERHCVP-DNITFATMIQAYNALGMT  447 (471)
Q Consensus       410 -----g~~~~a~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~  447 (471)
                           +.++++++.++++...  .| |...|..+...+.+.++.
T Consensus       201 ~~~~~~~~~eel~~~~~ai~~--~P~~~saW~y~~~ll~~~~~~  242 (567)
T 1dce_A          201 GRLPENVLLKELELVQNAFFT--DPNDQSAWFYHRWLLGRAEPH  242 (567)
T ss_dssp             CSSCHHHHHHHHHHHHHHHHH--CSSCSHHHHHHHHHHSCCCCC
T ss_pred             ccccHHHHHHHHHHHHHHHhh--CCCCccHHHHHHHHHhcCCCc
Confidence                 5578899999888874  34 567777766666666653

>3n71_A Histone lysine methyltransferase SMYD1; heart development, transcription; HET: SFG MES; 2.30A {Mus musculus}

Probab=97.89  E-value=8.9e-05  Score=69.41  Aligned_cols=126  Identities=10%  Similarity=-0.074  Sum_probs=71.4

Q ss_pred             HHhcCCHHHHHHHHHHHHHcC---C---CC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHh-----CCCC-c-CHHHHHH
Q 012111          336 FGKAGHIEKMEEYFKKMKHRG---M---KP-NSITYCSLVSAYSKAGLIMKVDSILRQVEN-----SDVI-L-DTPFFNC  401 (471)
Q Consensus       336 ~~~~g~~~~a~~~~~~m~~~~---~---~p-~~~~~~~li~~~~~~g~~~~a~~~~~~~~~-----~~~~-~-~~~~~~~  401 (471)
                      +...|++++|..++++..+..   +   .| ...+++.|..+|...|++++|..++++..+     .|.. | ...+++.
T Consensus       319 ~~~qg~~~eA~~l~~~aL~~~~~~lg~~Hp~~a~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp~~a~~l~n  398 (490)
T 3n71_A          319 ARSEGLYHEVVKLCRECLEKQEPVFADTNLYVLRLLSIASEVLSYLQAYEEASHYARRMVDGYMKLYHHNNAQLGMAVMR  398 (490)
T ss_dssp             HHTTTCHHHHHHHHHHHHHHHTTTBCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCTTCHHHHHHHHH
T ss_pred             HHhCCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHH
Confidence            345566666666666655321   1   11 234566666677777777777766666542     2221 1 2335666


Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHh-----CCC-CCCH-HHHHHHHHHHHhcCCHHHHHHHHHHHHHhh
Q 012111          402 IISAYGQAGDVEKMGELFLTMKE-----RHC-VPDN-ITFATMIQAYNALGMTEAAQNLENKMIAMK  461 (471)
Q Consensus       402 l~~~~~~~g~~~~a~~~~~~~~~-----~~~-~p~~-~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~  461 (471)
                      |...|...|++++|+.++++..+     .|- .|+. .+...+-.++...|.+++|..+++++.+..
T Consensus       399 La~~~~~~G~~~eA~~~~~~Al~i~~~~lG~~Hp~~~~~~~~l~~~~~e~~~~~~ae~~~~~~~~~~  465 (490)
T 3n71_A          399 AGLTNWHAGHIEVGHGMICKAYAILLVTHGPSHPITKDLEAMRMQTEMELRMFRQNEFMYHKMREAA  465 (490)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            77777777777777777766553     121 1222 233344466666777777777777776544

>1klx_A Cysteine rich protein B; structural genomics, helix-turn-helix, right handed super helix, modular structure', hydrolase; 1.95A {Helicobacter pylori} SCOP: a.118.18.1

Probab=97.87  E-value=0.00096  Score=50.63  Aligned_cols=112  Identities=13%  Similarity=-0.028  Sum_probs=77.8

Q ss_pred             hhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHh----cCCHH
Q 012111           91 QKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQ----SGLLD  166 (471)
Q Consensus        91 ~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~----~~~~~  166 (471)
                      .+++++|++.|+.+.+.+  .+..  .  +...|...+.+++|.+.|++..+.|   +...+..|...|..    .++++
T Consensus         8 ~~d~~~A~~~~~~aa~~g--~~~a--~--lg~~y~~g~~~~~A~~~~~~Aa~~g---~~~a~~~Lg~~y~~G~g~~~d~~   78 (138)
T 1klx_A            8 KKDLKKAIQYYVKACELN--EMFG--C--LSLVSNSQINKQKLFQYLSKACELN---SGNGCRFLGDFYENGKYVKKDLR   78 (138)
T ss_dssp             HHHHHHHHHHHHHHHHTT--CTTH--H--HHHHTCTTSCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHCSSSCCCHH
T ss_pred             ccCHHHHHHHHHHHHcCC--CHhh--h--HHHHHHcCCCHHHHHHHHHHHHcCC---CHHHHHHHHHHHHcCCCCCccHH
Confidence            356778888888887765  3333  3  6667777777888888888877753   56677777777776    67777


Q ss_pred             HHHHHHHHhhcCCCCCCCHHHHHHHHHHHHh----cCCHHHHHHHHHHHHHCC
Q 012111          167 EAFSTINDMKSVSDCKPDVYTYSILIKSCTK----FHRFDLIEKILAEMSYLG  215 (471)
Q Consensus       167 ~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~----~~~~~~a~~~~~~~~~~g  215 (471)
                      +|++.|++..+ .   -+...+..|...|..    .++.++|.+.|+...+.|
T Consensus        79 ~A~~~~~~Aa~-~---g~~~a~~~Lg~~y~~G~g~~~d~~~A~~~~~~Aa~~g  127 (138)
T 1klx_A           79 KAAQYYSKACG-L---NDQDGCLILGYKQYAGKGVVKNEKQAVKTFEKACRLG  127 (138)
T ss_dssp             HHHHHHHHHHH-T---TCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHc-C---CCHHHHHHHHHHHHCCCCCCcCHHHHHHHHHHHHHCC
Confidence            78777777766 2   345566666666666    667777777777776665

>2if4_A ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha, signaling protein; 2.85A {Arabidopsis thaliana}

Probab=97.83  E-value=8.7e-05  Score=66.38  Aligned_cols=114  Identities=11%  Similarity=0.049  Sum_probs=61.1

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHH
Q 012111          149 VDVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIID  228 (471)
Q Consensus       149 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~  228 (471)
                      ...+..+...+.+.|++++|+..|++....   .|+...       +...++.+++...+.          ...|..+..
T Consensus       179 a~~~~~~g~~~~~~g~~~~A~~~y~~Al~~---~p~~~~-------~~~~~~~~~~~~~l~----------~~~~~nla~  238 (338)
T 2if4_A          179 ADRRKMDGNSLFKEEKLEEAMQQYEMAIAY---MGDDFM-------FQLYGKYQDMALAVK----------NPCHLNIAA  238 (338)
T ss_dssp             HHHHHHHHHHTCSSSCCHHHHHHHHHHHHH---SCHHHH-------HTCCHHHHHHHHHHH----------THHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHHH---hccchh-------hhhcccHHHHHHHHH----------HHHHHHHHH
Confidence            444555666666667777777777766542   233221       111222222221110          124555666


Q ss_pred             HHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 012111          229 GYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNL  284 (471)
Q Consensus       229 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  284 (471)
                      +|.+.|++++|+..+++..+..  +.+...|..+..+|...|++++|...|++...
T Consensus       239 ~~~~~g~~~~A~~~~~~al~~~--p~~~~a~~~lg~a~~~~g~~~~A~~~l~~al~  292 (338)
T 2if4_A          239 CLIKLKRYDEAIGHCNIVLTEE--EKNPKALFRRGKAKAELGQMDSARDDFRKAQK  292 (338)
T ss_dssp             HHHTTTCCHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHTTTCHHHHHHHHHHTTC
T ss_pred             HHHHcCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            6666666666666666666542  33455666666666666666666666666544

>2kat_A Uncharacterized protein; NESG, structure, structural genomics, PSI-2, protein structure initiative; NMR {Bordetella parapertussis}

Probab=97.82  E-value=9.4e-05  Score=54.19  Aligned_cols=79  Identities=10%  Similarity=-0.105  Sum_probs=61.0

Q ss_pred             HHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHh
Q 012111           96 LALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAFSTINDM  175 (471)
Q Consensus        96 ~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~  175 (471)
                      .|++.|+.+.+..  +.+...+..+...+...|++++|...|+...+.... +...|..+..++...|++++|...|++.
T Consensus         3 ~a~~~~~~al~~~--p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~la~~~~~~g~~~~A~~~~~~a   79 (115)
T 2kat_A            3 AITERLEAMLAQG--TDNMLLRFTLGKTYAEHEQFDAALPHLRAALDFDPT-YSVAWKWLGKTLQGQGDRAGARQAWESG   79 (115)
T ss_dssp             CHHHHHHHHHTTT--CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhC--CCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHHCCC-cHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            4667777777664  566778888888888888888888888888776432 5677888888888888888888888877


Q ss_pred             hc
Q 012111          176 KS  177 (471)
Q Consensus       176 ~~  177 (471)
                      ..
T Consensus        80 l~   81 (115)
T 2kat_A           80 LA   81 (115)
T ss_dssp             HH
T ss_pred             HH
Confidence            65

>2l6j_A TPR repeat-containing protein associated with HSP; tetratricopeptide repeat (TPR), HSP90 CO-factor, protein BIN; NMR {Saccharomyces cerevisiae}

Probab=97.82  E-value=8.1e-05  Score=53.95  Aligned_cols=87  Identities=10%  Similarity=-0.039  Sum_probs=49.5

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCC-------HHH
Q 012111          361 SITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPD-------NIT  433 (471)
Q Consensus       361 ~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~-------~~~  433 (471)
                      ...+..+...+...|++++|...+++..+..+. +...+..+..++...|++++|++.+++..+.  .|+       ...
T Consensus         4 ~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~p~-~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~~~~   80 (111)
T 2l6j_A            4 FEKQKEQGNSLFKQGLYREAVHCYDQLITAQPQ-NPVGYSNKAMALIKLGEYTQAIQMCQQGLRY--TSTAEHVAIRSKL   80 (111)
T ss_dssp             HHHHHHHHHHHHTTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHTS--CSSTTSHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCC-CHHHHHHHHHHHHHhcCHHHHHHHHHHHHHh--CCCccHHHHHHHH
Confidence            344555566666666666666666666655443 5556666666666666666666666666653  333       333


Q ss_pred             HHHHHHHHHhcCCHHHH
Q 012111          434 FATMIQAYNALGMTEAA  450 (471)
Q Consensus       434 ~~~l~~~~~~~g~~~~A  450 (471)
                      +..+..++...|+.+.|
T Consensus        81 ~~~~~~~~~~~~~~~~a   97 (111)
T 2l6j_A           81 QYRLELAQGAVGSVQIP   97 (111)
T ss_dssp             HHHHHHHHHHHHCCCCC
T ss_pred             HHHHHHHHHHHHhHhhh
Confidence            44444444444444433

>1zu2_A Mitochondrial import receptor subunit TOM20-3; TPR, tetratricopeptide repeat like, TPR-like, transport protein; NMR {Arabidopsis thaliana} SCOP: a.118.8.1

Probab=97.79  E-value=6.8e-05  Score=57.51  Aligned_cols=99  Identities=15%  Similarity=0.026  Sum_probs=72.9

Q ss_pred             HHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCH----------HHHHHHHHHHHhCCCCCCHHHHHHHHHH
Q 012111           89 IKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQP----------EQASLLFEVMLSDGLKPSVDVYTALVSA  158 (471)
Q Consensus        89 ~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~----------~~a~~~~~~m~~~~~~~~~~~~~~li~~  158 (471)
                      -+.+++++|++.++.+.+..  |.+...|..+..++...+++          ++|+..|++.++.... +..+|..+..+
T Consensus        13 ~r~~~feeA~~~~~~Ai~l~--P~~aea~~n~G~~l~~l~~~~~g~~al~~~~eAi~~le~AL~ldP~-~~~A~~~LG~a   89 (158)
T 1zu2_A           13 DRILLFEQIRQDAENTYKSN--PLDADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALLIDPK-KDEAVWCIGNA   89 (158)
T ss_dssp             HHHHHHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCTT-CHHHHHHHHHH
T ss_pred             HHHhHHHHHHHHHHHHHHHC--CCCHHHHHHHHHHHHHhcccchhhhhHhHHHHHHHHHHHHHHhCcC-cHHHHHHHHHH
Confidence            46778888999999888876  67788888888888877664          4888888888876544 67778888888


Q ss_pred             HHhcC-----------CHHHHHHHHHHhhcCCCCCCCHHHHHHHHH
Q 012111          159 YGQSG-----------LLDEAFSTINDMKSVSDCKPDVYTYSILIK  193 (471)
Q Consensus       159 ~~~~~-----------~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~  193 (471)
                      |...|           ++++|++.|++..+   +.|+...|...+.
T Consensus        90 y~~lg~l~P~~~~a~g~~~eA~~~~~kAl~---l~P~~~~y~~al~  132 (158)
T 1zu2_A           90 YTSFAFLTPDETEAKHNFDLATQFFQQAVD---EQPDNTHYLKSLE  132 (158)
T ss_dssp             HHHHHHHCCCHHHHHHHHHHHHHHHHHHHH---HCTTCHHHHHHHH
T ss_pred             HHHhcccCcchhhhhccHHHHHHHHHHHHH---hCCCCHHHHHHHH
Confidence            87664           77888888887776   2566555544433

>1zu2_A Mitochondrial import receptor subunit TOM20-3; TPR, tetratricopeptide repeat like, TPR-like, transport protein; NMR {Arabidopsis thaliana} SCOP: a.118.8.1

Probab=97.78  E-value=8.6e-05  Score=56.95  Aligned_cols=98  Identities=11%  Similarity=0.105  Sum_probs=65.8

Q ss_pred             hcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCC----------HHHHHHHHHHHHhCCCCcCHHHHHHHHHHHH
Q 012111          338 KAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGL----------IMKVDSILRQVENSDVILDTPFFNCIISAYG  407 (471)
Q Consensus       338 ~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~----------~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  407 (471)
                      +.+.+++|...+++..+.. +-+...|..+..++...++          +++|+..|++.++.++. +..+|..+..+|.
T Consensus        14 r~~~feeA~~~~~~Ai~l~-P~~aea~~n~G~~l~~l~~~~~g~~al~~~~eAi~~le~AL~ldP~-~~~A~~~LG~ay~   91 (158)
T 1zu2_A           14 RILLFEQIRQDAENTYKSN-PLDADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALLIDPK-KDEAVWCIGNAYT   91 (158)
T ss_dssp             HHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHH
T ss_pred             HHhHHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHhcccchhhhhHhHHHHHHHHHHHHHHhCcC-cHHHHHHHHHHHH
Confidence            3445666666666666653 3356666666666666554          45788888888777666 6777777888877


Q ss_pred             hcC-----------CHHHHHHHHHHHHhCCCCCCHHHHHHHHH
Q 012111          408 QAG-----------DVEKMGELFLTMKERHCVPDNITFATMIQ  439 (471)
Q Consensus       408 ~~g-----------~~~~a~~~~~~~~~~~~~p~~~~~~~l~~  439 (471)
                      ..|           ++++|++.|++..+  +.|+...|...+.
T Consensus        92 ~lg~l~P~~~~a~g~~~eA~~~~~kAl~--l~P~~~~y~~al~  132 (158)
T 1zu2_A           92 SFAFLTPDETEAKHNFDLATQFFQQAVD--EQPDNTHYLKSLE  132 (158)
T ss_dssp             HHHHHCCCHHHHHHHHHHHHHHHHHHHH--HCTTCHHHHHHHH
T ss_pred             HhcccCcchhhhhccHHHHHHHHHHHHH--hCCCCHHHHHHHH
Confidence            664           78888888888887  4677665544443

>3n71_A Histone lysine methyltransferase SMYD1; heart development, transcription; HET: SFG MES; 2.30A {Mus musculus}

Probab=97.77  E-value=0.0003  Score=65.86  Aligned_cols=125  Identities=10%  Similarity=0.058  Sum_probs=86.9

Q ss_pred             HHHHcCCHHHHHHHHHHHHhC---CCC---C-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc-----C-CCC-CHHHHH
Q 012111          300 SYGRAGMYDKMRSVMDFMQKR---FFF---P-TVVTYNIVIETFGKAGHIEKMEEYFKKMKHR-----G-MKP-NSITYC  365 (471)
Q Consensus       300 ~~~~~~~~~~a~~~~~~~~~~---~~~---~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~-----~-~~p-~~~~~~  365 (471)
                      .+...|++++|..++++..+.   -+.   | ...+++.|...|...|++++|..++++.+..     | -.| ...+++
T Consensus       318 ~~~~qg~~~eA~~l~~~aL~~~~~~lg~~Hp~~a~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp~~a~~l~  397 (490)
T 3n71_A          318 KARSEGLYHEVVKLCRECLEKQEPVFADTNLYVLRLLSIASEVLSYLQAYEEASHYARRMVDGYMKLYHHNNAQLGMAVM  397 (490)
T ss_dssp             HHHTTTCHHHHHHHHHHHHHHHTTTBCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCTTCHHHHHHHH
T ss_pred             HHHhCCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHH
Confidence            345678888888887766542   111   2 2346788888888888888888888876643     2 122 245788


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHh-----CCCC-c-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 012111          366 SLVSAYSKAGLIMKVDSILRQVEN-----SDVI-L-DTPFFNCIISAYGQAGDVEKMGELFLTMKE  424 (471)
Q Consensus       366 ~li~~~~~~g~~~~a~~~~~~~~~-----~~~~-~-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~  424 (471)
                      .|...|...|++++|..++++..+     .|.. | ...+.+.+..++...|.+++|..+|+++++
T Consensus       398 nLa~~~~~~G~~~eA~~~~~~Al~i~~~~lG~~Hp~~~~~~~~l~~~~~e~~~~~~ae~~~~~~~~  463 (490)
T 3n71_A          398 RAGLTNWHAGHIEVGHGMICKAYAILLVTHGPSHPITKDLEAMRMQTEMELRMFRQNEFMYHKMRE  463 (490)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            888889999999999988887653     3432 1 223455666777788889999999988876

>2l6j_A TPR repeat-containing protein associated with HSP; tetratricopeptide repeat (TPR), HSP90 CO-factor, protein BIN; NMR {Saccharomyces cerevisiae}

Probab=97.73  E-value=4.2e-05  Score=55.50  Aligned_cols=93  Identities=13%  Similarity=0.041  Sum_probs=61.9

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcC------HHH
Q 012111          325 TVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILD------TPF  398 (471)
Q Consensus       325 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~------~~~  398 (471)
                      +...+..+...+...|++++|...|++..+.. +.+...+..+..++...|++++|...+++..+..+. +      ...
T Consensus         3 ~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~~~~   80 (111)
T 2l6j_A            3 QFEKQKEQGNSLFKQGLYREAVHCYDQLITAQ-PQNPVGYSNKAMALIKLGEYTQAIQMCQQGLRYTST-AEHVAIRSKL   80 (111)
T ss_dssp             HHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSCSS-TTSHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCC-ccHHHHHHHH
Confidence            34556667777777888888888888777653 335677777778888888888888888887776543 2      444


Q ss_pred             HHHHHHHHHhcCCHHHHHHHH
Q 012111          399 FNCIISAYGQAGDVEKMGELF  419 (471)
Q Consensus       399 ~~~l~~~~~~~g~~~~a~~~~  419 (471)
                      +..+..++...|+++.|+..+
T Consensus        81 ~~~~~~~~~~~~~~~~a~~~~  101 (111)
T 2l6j_A           81 QYRLELAQGAVGSVQIPVVEV  101 (111)
T ss_dssp             HHHHHHHHHHHHCCCCCSSSS
T ss_pred             HHHHHHHHHHHHhHhhhHhHH
Confidence            555555555555555544433

>3ma5_A Tetratricopeptide repeat domain protein; NESG, structural genomics, PSI-2, protein structure initiative; 2.80A {Salinibacter ruber} PDB: 2kcl_A 2kcv_A

Probab=97.70  E-value=0.00024  Score=50.49  Aligned_cols=64  Identities=9%  Similarity=0.064  Sum_probs=48.2

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 012111          360 NSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKE  424 (471)
Q Consensus       360 ~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~  424 (471)
                      +...+..+...+...|++++|...|+++.+.++. +...|..+..+|...|++++|++.|++..+
T Consensus         6 ~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~-~~~a~~~lg~~~~~~g~~~~A~~~~~~al~   69 (100)
T 3ma5_A            6 DPFTRYALAQEHLKHDNASRALALFEELVETDPD-YVGTYYHLGKLYERLDRTDDAIDTYAQGIE   69 (100)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTT-CTHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-cHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            5667777777788888888888888877776655 566777777788888888888887777664

>1na3_A Designed protein CTPR2; de novo protein; HET: IPT; 1.55A {Unidentified} SCOP: k.38.1.1 PDB: 2avp_A

Probab=97.69  E-value=0.00064  Score=46.90  Aligned_cols=79  Identities=16%  Similarity=0.115  Sum_probs=39.7

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHH
Q 012111          362 ITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAY  441 (471)
Q Consensus       362 ~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~  441 (471)
                      ..+..+...+...|++++|...+++..+..+. +...+..+..++...|++++|...+++..+.. +-+...+..+..++
T Consensus        10 ~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~-~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-p~~~~~~~~l~~~~   87 (91)
T 1na3_A           10 EAWYNLGNAYYKQGDYDEAIEYYQKALELDPN-NAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAKQNLGNAK   87 (91)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHccCHHHHHHHHHHHHhcCCC-CHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-CCCHHHHHHHHHHH
Confidence            34444555555555555555555555544332 44455555555555666666666665555431 12334444444444


Q ss_pred             H
Q 012111          442 N  442 (471)
Q Consensus       442 ~  442 (471)
                      .
T Consensus        88 ~   88 (91)
T 1na3_A           88 Q   88 (91)
T ss_dssp             H
T ss_pred             H
Confidence            3

>1na3_A Designed protein CTPR2; de novo protein; HET: IPT; 1.55A {Unidentified} SCOP: k.38.1.1 PDB: 2avp_A

Probab=97.66  E-value=0.0009  Score=46.12  Aligned_cols=81  Identities=16%  Similarity=0.144  Sum_probs=51.1

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHH
Q 012111          326 VVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISA  405 (471)
Q Consensus       326 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  405 (471)
                      ...+..+...+...|++++|...+++..... +.+...+..+..++...|++++|...+++..+..+. +...+..+..+
T Consensus         9 ~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~p~-~~~~~~~l~~~   86 (91)
T 1na3_A            9 AEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAWYNLGNAYYKQGDYDEAIEYYQKALELDPN-NAEAKQNLGNA   86 (91)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHccCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCC-CHHHHHHHHHH
Confidence            3455556666667777777777777766653 234566667777777777777777777777665443 45555555555


Q ss_pred             HHh
Q 012111          406 YGQ  408 (471)
Q Consensus       406 ~~~  408 (471)
                      +..
T Consensus        87 ~~~   89 (91)
T 1na3_A           87 KQK   89 (91)
T ss_dssp             HHH
T ss_pred             HHh
Confidence            544

>3ma5_A Tetratricopeptide repeat domain protein; NESG, structural genomics, PSI-2, protein structure initiative; 2.80A {Salinibacter ruber} PDB: 2kcl_A 2kcv_A

Probab=97.55  E-value=0.00021  Score=50.73  Aligned_cols=66  Identities=21%  Similarity=0.113  Sum_probs=41.2

Q ss_pred             cCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHhhc
Q 012111          111 QARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAFSTINDMKS  177 (471)
Q Consensus       111 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~  177 (471)
                      |.+...+..+..++...|++++|...|+...+.... +...|..+..+|...|++++|++.|++..+
T Consensus         4 p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~-~~~a~~~lg~~~~~~g~~~~A~~~~~~al~   69 (100)
T 3ma5_A            4 PEDPFTRYALAQEHLKHDNASRALALFEELVETDPD-YVGTYYHLGKLYERLDRTDDAIDTYAQGIE   69 (100)
T ss_dssp             -CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTT-CTHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             ccCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-cHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            344556666666666666777776666666665432 455666666666666777766666666554

>2kc7_A BFR218_protein; tetratricopeptide repeat, all-alpha, GFT-structural genomics, PSI-2, protein structure initiative; NMR {Bacteroides fragilis}

Probab=97.41  E-value=0.00072  Score=47.67  Aligned_cols=87  Identities=18%  Similarity=0.157  Sum_probs=55.4

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhCCCCcCHH-HHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCH-HHHHHHHHHHHhcC
Q 012111          368 VSAYSKAGLIMKVDSILRQVENSDVILDTP-FFNCIISAYGQAGDVEKMGELFLTMKERHCVPDN-ITFATMIQAYNALG  445 (471)
Q Consensus       368 i~~~~~~g~~~~a~~~~~~~~~~~~~~~~~-~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~-~~~~~l~~~~~~~g  445 (471)
                      ...+...|++++|...++.+.+..+. +.. .+..+..+|...|++++|++.|++..+.  .|+. ..+..        +
T Consensus         7 a~~~~~~~~~~~A~~~~~~al~~~p~-~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~--------~   75 (99)
T 2kc7_A            7 IKELINQGDIENALQALEEFLQTEPV-GKDEAYYLMGNAYRKLGDWQKALNNYQSAIEL--NPDSPALQAR--------K   75 (99)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHHHHCSS-THHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--CTTSTHHHHH--------H
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHCCC-cHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc--CCCcHHHHHH--------H
Confidence            44556677777777777777765544 555 6777777777777777777777777764  3332 22211        5


Q ss_pred             CHHHHHHHHHHHHHhhhcCC
Q 012111          446 MTEAAQNLENKMIAMKENSG  465 (471)
Q Consensus       446 ~~~~A~~~~~~m~~~~~~~~  465 (471)
                      .+.++...+++.....|.+.
T Consensus        76 ~~~~a~~~~~~~~~~~p~~~   95 (99)
T 2kc7_A           76 MVMDILNFYNKDMYNQLEHH   95 (99)
T ss_dssp             HHHHHHHHHCCTTHHHHCCS
T ss_pred             HHHHHHHHHHHHhccCcccc
Confidence            56667777777666666544

>3ly7_A Transcriptional activator CADC; alpha/beta domain, alpha domain, DNA-binding, transcription regulation, transmembrane; 1.80A {Escherichia coli} PDB: 3lya_A 3ly8_A 3ly9_A

Probab=97.20  E-value=0.018  Score=50.93  Aligned_cols=74  Identities=16%  Similarity=0.037  Sum_probs=48.6

Q ss_pred             CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHH
Q 012111          182 KPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLN  260 (471)
Q Consensus       182 ~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  260 (471)
                      +.+..+|..+...+...|+++.|...++++...+  |+...|..+...+.-.|++++|.+.|++....   .|...+|.
T Consensus       274 ~~~a~~~~alal~~l~~gd~d~A~~~l~rAl~Ln--~s~~a~~llG~~~~~~G~~~eA~e~~~~AlrL---~P~~~t~~  347 (372)
T 3ly7_A          274 NNLSIIYQIKAVSALVKGKTDESYQAINTGIDLE--MSWLNYVLLGKVYEMKGMNREAADAYLTAFNL---RPGANTLY  347 (372)
T ss_dssp             TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH---SCSHHHHH
T ss_pred             CcCHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcC--CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc---CCCcChHH
Confidence            4566666666665666677777777777777664  56666666666777777777777777776654   45554443

>3ly7_A Transcriptional activator CADC; alpha/beta domain, alpha domain, DNA-binding, transcription regulation, transmembrane; 1.80A {Escherichia coli} PDB: 3lya_A 3ly8_A 3ly9_A

Probab=97.19  E-value=0.01  Score=52.45  Aligned_cols=68  Identities=9%  Similarity=0.074  Sum_probs=39.6

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhhhcC
Q 012111          395 DTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAYNALGMTEAAQNLENKMIAMKENS  464 (471)
Q Consensus       395 ~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~~  464 (471)
                      +..+|..+...+...|++++|...++++...+  |+...|..+...+.-.|++++|.+.+++++.++|..
T Consensus       276 ~a~~~~alal~~l~~gd~d~A~~~l~rAl~Ln--~s~~a~~llG~~~~~~G~~~eA~e~~~~AlrL~P~~  343 (372)
T 3ly7_A          276 LSIIYQIKAVSALVKGKTDESYQAINTGIDLE--MSWLNYVLLGKVYEMKGMNREAADAYLTAFNLRPGA  343 (372)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSCSH
T ss_pred             CHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcC--CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCc
Confidence            45555555555555566666666666666542  555555555555666666666666666666665543

>1pc2_A Mitochondria fission protein; unknown function; NMR {Homo sapiens} SCOP: a.118.8.1

Probab=97.11  E-value=0.0052  Score=46.58  Aligned_cols=82  Identities=13%  Similarity=0.056  Sum_probs=49.3

Q ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcC---CHHHHHHHHHHHHhCC-CCcCHHHHHHHHHHHHhcCCHHHHHH
Q 012111          342 IEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAG---LIMKVDSILRQVENSD-VILDTPFFNCIISAYGQAGDVEKMGE  417 (471)
Q Consensus       342 ~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g---~~~~a~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~g~~~~a~~  417 (471)
                      ...+.+-|.+....| .++..+...+..++++.+   +++++..+++.+.+.+ +.-+...+-.|.-+|.+.|++++|.+
T Consensus        14 l~~~~~~y~~e~~~~-~~~~~~~F~ya~~Lv~S~~~~~~~~gI~lLe~ll~~~~p~~~rd~lY~LAv~~~kl~~Y~~A~~   92 (152)
T 1pc2_A           14 LLKFEKKFQSEKAAG-SVSKSTQFEYAWCLVRSKYNDDIRKGIVLLEELLPKGSKEEQRDYVFYLAVGNYRLKEYEKALK   92 (152)
T ss_dssp             HHHHHHHHHHHHHTT-CCCHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHTSCHHHHHH
T ss_pred             HHHHHHHHHHHHccC-CCcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCCccchHHHHHHHHHHHHHccCHHHHHH
Confidence            445555565555554 356666666666677666   5556777777666654 21123444455556667777777777


Q ss_pred             HHHHHHh
Q 012111          418 LFLTMKE  424 (471)
Q Consensus       418 ~~~~~~~  424 (471)
                      .++.+.+
T Consensus        93 y~~~lL~   99 (152)
T 1pc2_A           93 YVRGLLQ   99 (152)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHh
Confidence            7777766

>3mkq_A Coatomer beta'-subunit; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae} PDB: 2ynp_A

Probab=96.96  E-value=0.033  Score=56.23  Aligned_cols=130  Identities=13%  Similarity=0.087  Sum_probs=70.1

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhc
Q 012111          260 NSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKA  339 (471)
Q Consensus       260 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~  339 (471)
                      ..++..+.+.|..+.|.++.+.-.            .-.......|+++.|.++.+.+      .+...|..+...+.+.
T Consensus       633 ~~~~~~l~~~~~~~~a~~~~~~~~------------~~f~~~l~~~~~~~A~~~~~~~------~~~~~W~~la~~al~~  694 (814)
T 3mkq_A          633 TKIARFLEGQEYYEEALNISPDQD------------QKFELALKVGQLTLARDLLTDE------SAEMKWRALGDASLQR  694 (814)
T ss_dssp             HHHHHHHHHTTCHHHHHHHCCCHH------------HHHHHHHHHTCHHHHHHHHTTC------CCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHhCCChHHheecCCCcc------------hheehhhhcCCHHHHHHHHHhh------CcHhHHHHHHHHHHHc
Confidence            555666666777776665542110            1122345567777777765432      2556777777777777


Q ss_pred             CCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHH
Q 012111          340 GHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELF  419 (471)
Q Consensus       340 g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~  419 (471)
                      |+++.|.++|.++..         |..+...+...|+.+...++.+.....|.      ++....+|.+.|++++|++++
T Consensus       695 ~~~~~A~~~y~~~~d---------~~~l~~l~~~~~~~~~~~~~~~~a~~~~~------~~~A~~~~~~~g~~~~a~~~~  759 (814)
T 3mkq_A          695 FNFKLAIEAFTNAHD---------LESLFLLHSSFNNKEGLVTLAKDAETTGK------FNLAFNAYWIAGDIQGAKDLL  759 (814)
T ss_dssp             TCHHHHHHHHHHHTC---------HHHHHHHHHHTTCHHHHHHHHHHHHHTTC------HHHHHHHHHHHTCHHHHHHHH
T ss_pred             CCHHHHHHHHHHccC---------hhhhHHHHHHcCCHHHHHHHHHHHHHcCc------hHHHHHHHHHcCCHHHHHHHH
Confidence            777777777776543         33344444445555555554444444331      123333444455555555555


Q ss_pred             HHH
Q 012111          420 LTM  422 (471)
Q Consensus       420 ~~~  422 (471)
                      .++
T Consensus       760 ~~~  762 (814)
T 3mkq_A          760 IKS  762 (814)
T ss_dssp             HHT
T ss_pred             HHc
Confidence            443

>2kc7_A BFR218_protein; tetratricopeptide repeat, all-alpha, GFT-structural genomics, PSI-2, protein structure initiative; NMR {Bacteroides fragilis}

Probab=96.94  E-value=0.0047  Score=43.31  Aligned_cols=64  Identities=20%  Similarity=0.181  Sum_probs=54.3

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHhCCCCCCHH-HHHHHHHHHHhcCCHHHHHHHHHHHHHhhhcCCC
Q 012111          402 IISAYGQAGDVEKMGELFLTMKERHCVPDNI-TFATMIQAYNALGMTEAAQNLENKMIAMKENSGK  466 (471)
Q Consensus       402 l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~-~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~~~~  466 (471)
                      ....+...|++++|++.|+++.+.. +.+.. .+..+..++...|++++|.+.++++++..|+...
T Consensus         6 ~a~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~   70 (99)
T 2kc7_A            6 TIKELINQGDIENALQALEEFLQTE-PVGKDEAYYLMGNAYRKLGDWQKALNNYQSAIELNPDSPA   70 (99)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHHHC-SSTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTSTH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCcHH
Confidence            4567888999999999999998852 23566 8888889999999999999999999999887653

>3qww_A SET and MYND domain-containing protein 2; methyltransferase, HSP90, transferase-transferase inhibitor; HET: SFG; 1.80A {Mus musculus} PDB: 3qwv_A* 3s7d_A* 3s7b_A* 3s7f_A* 3s7j_A* 3tg4_A* 3tg5_A* 3rib_A*

Probab=96.89  E-value=0.0034  Score=57.67  Aligned_cols=62  Identities=13%  Similarity=0.013  Sum_probs=29.4

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhC-----C-CCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 012111          398 FFNCIISAYGQAGDVEKMGELFLTMKER-----H-CVPD-NITFATMIQAYNALGMTEAAQNLENKMIA  459 (471)
Q Consensus       398 ~~~~l~~~~~~~g~~~~a~~~~~~~~~~-----~-~~p~-~~~~~~l~~~~~~~g~~~~A~~~~~~m~~  459 (471)
                      +++.|..+|...|++++|+.++++..+-     | -.|+ ..+++.|...|...|++++|..+++++++
T Consensus       342 ~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp~~a~~l~nLa~~~~~qg~~~eA~~~~~~Al~  410 (433)
T 3qww_A          342 MMYQAMGVCLYMQDWEGALKYGQKIIKPYSKHYPVYSLNVASMWLKLGRLYMGLENKAAGEKALKKAIA  410 (433)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCSSCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHHHHHHhccCHHHHHHHHHHHHH
Confidence            3445555555555555555555544321     1 1121 23444555555555555555555555543

>3mkq_A Coatomer beta'-subunit; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae} PDB: 2ynp_A

Probab=96.88  E-value=0.058  Score=54.44  Aligned_cols=154  Identities=13%  Similarity=0.071  Sum_probs=90.6

Q ss_pred             HHHHHhhcHHHHHH-HHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCC
Q 012111           86 DEAIKQKKWQLALK-IFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGL  164 (471)
Q Consensus        86 ~~~~~~~~~~~A~~-~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~  164 (471)
                      ......+++++|.+ ++..+.       +......++..+.+.|..++|.++.+.-.            .-.......|+
T Consensus       607 ~~~~~~~~~~~a~~~~l~~i~-------~~~~~~~~~~~l~~~~~~~~a~~~~~~~~------------~~f~~~l~~~~  667 (814)
T 3mkq_A          607 QTLTLRGEIEEAIENVLPNVE-------GKDSLTKIARFLEGQEYYEEALNISPDQD------------QKFELALKVGQ  667 (814)
T ss_dssp             HHHHHTTCHHHHHHHTGGGCC-------CHHHHHHHHHHHHHTTCHHHHHHHCCCHH------------HHHHHHHHHTC
T ss_pred             hHHHHhCCHHHHHHHHHhcCC-------chHHHHHHHHHHHhCCChHHheecCCCcc------------hheehhhhcCC
Confidence            34456777887766 442221       12223666777777788887776653211            11233456788


Q ss_pred             HHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHH
Q 012111          165 LDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFS  244 (471)
Q Consensus       165 ~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~a~~~~~  244 (471)
                      ++.|.++.+.+       .+...|..+...+.+.++++.|.+.|..+..         |..+...+...|+.+...++-+
T Consensus       668 ~~~A~~~~~~~-------~~~~~W~~la~~al~~~~~~~A~~~y~~~~d---------~~~l~~l~~~~~~~~~~~~~~~  731 (814)
T 3mkq_A          668 LTLARDLLTDE-------SAEMKWRALGDASLQRFNFKLAIEAFTNAHD---------LESLFLLHSSFNNKEGLVTLAK  731 (814)
T ss_dssp             HHHHHHHHTTC-------CCHHHHHHHHHHHHHTTCHHHHHHHHHHHTC---------HHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHHhh-------CcHhHHHHHHHHHHHcCCHHHHHHHHHHccC---------hhhhHHHHHHcCCHHHHHHHHH
Confidence            88887775433       3566788888888888888888888887642         3345555555666666555554


Q ss_pred             HHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHH
Q 012111          245 AMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNE  281 (471)
Q Consensus       245 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~  281 (471)
                      .....+       -++....+|.+.|++++|.+++.+
T Consensus       732 ~a~~~~-------~~~~A~~~~~~~g~~~~a~~~~~~  761 (814)
T 3mkq_A          732 DAETTG-------KFNLAFNAYWIAGDIQGAKDLLIK  761 (814)
T ss_dssp             HHHHTT-------CHHHHHHHHHHHTCHHHHHHHHHH
T ss_pred             HHHHcC-------chHHHHHHHHHcCCHHHHHHHHHH
Confidence            443332       123334445556666666555544

>3qwp_A SET and MYND domain-containing protein 3; SMYD3,SET and MYND domain, zinc finger MYND domain-containin 1, structural genomics; HET: SAM; 1.53A {Homo sapiens} PDB: 3mek_A* 3oxg_A* 3oxf_A* 3pdn_A* 3oxl_A* 3ru0_A*

Probab=96.87  E-value=0.0048  Score=56.76  Aligned_cols=98  Identities=11%  Similarity=0.049  Sum_probs=57.0

Q ss_pred             HHHHHHHHHHHhhcHHHHHHHHHHhhhcc--CccC----ChhHHHHHHHHHhcCCCHHHHHHHHHHHHhC-----CC-CC
Q 012111           80 PVLEALDEAIKQKKWQLALKIFGLLRQQQ--WYQA----RCQTFTKLMVMLGKCKQPEQASLLFEVMLSD-----GL-KP  147 (471)
Q Consensus        80 ~~~~~l~~~~~~~~~~~A~~~~~~~~~~~--~~~~----~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~-----~~-~~  147 (471)
                      .+...+..+.++|++++|+++++.+.+..  .+.+    ...+++.+..+|...|++++|..++++....     |. .|
T Consensus       289 ~ll~~ie~~~~~g~~~~a~~~~~~~L~~~~~~lg~~h~~~~~~~~~L~~~y~~~g~~~eA~~~~~~~L~i~~~~lg~~Hp  368 (429)
T 3qwp_A          289 ESLKKIEELKAHWKWEQVLAMCQAIISSNSERLPDINIYQLKVLDCAMDACINLGLLEEALFYGTRTMEPYRIFFPGSHP  368 (429)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHTCSSCCCCTTSHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHSCSSCH
T ss_pred             HHHHHHHHHHhhccHHHHHHHHHHHHHhccCcCCccchHHHHHHHHHHHHHHhhccHHHHHHHHHHHHHhHHHHcCCCCh
Confidence            33445566667777777777777776431  1112    1345666777777777777777776665431     21 12


Q ss_pred             C-HHHHHHHHHHHHhcCCHHHHHHHHHHhhc
Q 012111          148 S-VDVYTALVSAYGQSGLLDEAFSTINDMKS  177 (471)
Q Consensus       148 ~-~~~~~~li~~~~~~~~~~~a~~~~~~~~~  177 (471)
                      + ..+++.|...|...|++++|..++++..+
T Consensus       369 ~~a~~l~nLa~~~~~~g~~~eA~~~~~~Al~  399 (429)
T 3qwp_A          369 VRGVQVMKVGKLQLHQGMFPQAMKNLRLAFD  399 (429)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Confidence            2 23466666666666666666666665443

>3qwp_A SET and MYND domain-containing protein 3; SMYD3,SET and MYND domain, zinc finger MYND domain-containin 1, structural genomics; HET: SAM; 1.53A {Homo sapiens} PDB: 3mek_A* 3oxg_A* 3oxf_A* 3pdn_A* 3oxl_A* 3ru0_A*

Probab=96.86  E-value=0.0085  Score=55.13  Aligned_cols=92  Identities=8%  Similarity=-0.107  Sum_probs=49.0

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHHcC---CCC----CHHHHHHHHHHHHhcCCHHHHHHHHHHHHh-----CCCC-c-CHHH
Q 012111          333 IETFGKAGHIEKMEEYFKKMKHRG---MKP----NSITYCSLVSAYSKAGLIMKVDSILRQVEN-----SDVI-L-DTPF  398 (471)
Q Consensus       333 i~~~~~~g~~~~a~~~~~~m~~~~---~~p----~~~~~~~li~~~~~~g~~~~a~~~~~~~~~-----~~~~-~-~~~~  398 (471)
                      +..+...|++++|..++++..+..   +.|    ...+++.+..+|...|++++|+.+++++..     .|.. | ...+
T Consensus       294 ie~~~~~g~~~~a~~~~~~~L~~~~~~lg~~h~~~~~~~~~L~~~y~~~g~~~eA~~~~~~~L~i~~~~lg~~Hp~~a~~  373 (429)
T 3qwp_A          294 IEELKAHWKWEQVLAMCQAIISSNSERLPDINIYQLKVLDCAMDACINLGLLEEALFYGTRTMEPYRIFFPGSHPVRGVQ  373 (429)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHTCSSCCCCTTSHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHSCSSCHHHHHH
T ss_pred             HHHHHhhccHHHHHHHHHHHHHhccCcCCccchHHHHHHHHHHHHHHhhccHHHHHHHHHHHHHhHHHHcCCCChHHHHH
Confidence            344445566666666666665431   111    133555666666666666666666665442     1211 1 1234


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHh
Q 012111          399 FNCIISAYGQAGDVEKMGELFLTMKE  424 (471)
Q Consensus       399 ~~~l~~~~~~~g~~~~a~~~~~~~~~  424 (471)
                      ++.|...|...|++++|+.++++..+
T Consensus       374 l~nLa~~~~~~g~~~eA~~~~~~Al~  399 (429)
T 3qwp_A          374 VMKVGKLQLHQGMFPQAMKNLRLAFD  399 (429)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHH
Confidence            55566666666666666666666555

>2v5f_A Prolyl 4-hydroxylase subunit alpha-1; endoplasmic reticulum, metal-binding, oxidoreductase; 2.03A {Homo sapiens} PDB: 1tjc_A

Probab=96.84  E-value=0.0099  Score=42.26  Aligned_cols=71  Identities=15%  Similarity=0.060  Sum_probs=53.8

Q ss_pred             CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCC------CCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCH
Q 012111          359 PNSITYCSLVSAYSKAGLIMKVDSILRQVENSD------VILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDN  431 (471)
Q Consensus       359 p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~------~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~  431 (471)
                      .+...+..|...+...|+++.|...|+.+.+..      -.+...++..|..++.+.|+++.|..+++++.+.  .|+.
T Consensus         3 Lsa~dc~~lG~~~~~~~~y~~A~~W~~~Al~~~~~~~~~~~~~~~i~~~L~~~~~~~g~~~~A~~~~~~al~l--~P~~   79 (104)
T 2v5f_A            3 LTAEDCFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLEL--DPEH   79 (104)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTC
T ss_pred             CCHHHHHHHHHHHHHccchHHHHHHHHHHHHhhhccCCCcccHHHHHHHHHHHHHHccCHHHHHHHHHHHHhc--CCCC
Confidence            455667788888888999999999888876421      1235677888888888999999999998888873  5654

>3qww_A SET and MYND domain-containing protein 2; methyltransferase, HSP90, transferase-transferase inhibitor; HET: SFG; 1.80A {Mus musculus} PDB: 3qwv_A* 3s7d_A* 3s7b_A* 3s7f_A* 3s7j_A* 3tg4_A* 3tg5_A* 3rib_A*

Probab=96.80  E-value=0.0049  Score=56.68  Aligned_cols=86  Identities=5%  Similarity=-0.134  Sum_probs=59.1

Q ss_pred             cCCHHHHHHHHHHHHHc---CCCC----CHHHHHHHHHHHHhcCCHHHHHHHHHHHHh-----CCCC-c-CHHHHHHHHH
Q 012111          339 AGHIEKMEEYFKKMKHR---GMKP----NSITYCSLVSAYSKAGLIMKVDSILRQVEN-----SDVI-L-DTPFFNCIIS  404 (471)
Q Consensus       339 ~g~~~~a~~~~~~m~~~---~~~p----~~~~~~~li~~~~~~g~~~~a~~~~~~~~~-----~~~~-~-~~~~~~~l~~  404 (471)
                      .|++++|..++++..+.   -+.|    ...+++.|..+|...|++++|..++++..+     .|.. | ...+++.|..
T Consensus       311 ~g~~~eA~~~~~~~L~i~~~~lg~~Hp~~a~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp~~a~~l~nLa~  390 (433)
T 3qww_A          311 YKSPSELLEICELSQEKMSSVFEDSNVYMLHMMYQAMGVCLYMQDWEGALKYGQKIIKPYSKHYPVYSLNVASMWLKLGR  390 (433)
T ss_dssp             TSCHHHHHHHHHHHHHHHTTTBCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCSSCHHHHHHHHHHHH
T ss_pred             ccCHHHHHHHHHHHHHHhhCccChhchHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHHH
Confidence            46777888777776542   1112    245677888888888888888888877653     2322 1 2345788888


Q ss_pred             HHHhcCCHHHHHHHHHHHHh
Q 012111          405 AYGQAGDVEKMGELFLTMKE  424 (471)
Q Consensus       405 ~~~~~g~~~~a~~~~~~~~~  424 (471)
                      .|...|++++|+.++++..+
T Consensus       391 ~~~~qg~~~eA~~~~~~Al~  410 (433)
T 3qww_A          391 LYMGLENKAAGEKALKKAIA  410 (433)
T ss_dssp             HHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHhccCHHHHHHHHHHHHH
Confidence            88888888888888887764

>3bee_A Putative YFRE protein; putaive YFRE protein, structural GE PSI-2, protein structure initiative; 2.15A {Vibrio parahaemolyticus rimd 2210633}

Probab=96.70  E-value=0.019  Score=39.75  Aligned_cols=66  Identities=6%  Similarity=-0.019  Sum_probs=43.6

Q ss_pred             CCHHHHHHHHHHHHhcCC---HHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhC
Q 012111          359 PNSITYCSLVSAYSKAGL---IMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKER  425 (471)
Q Consensus       359 p~~~~~~~li~~~~~~g~---~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~  425 (471)
                      .++..+..+..++...++   .++|..++++..+.++. +......+...+...|++++|+..|+++.+.
T Consensus         4 ~~~~~~~~~a~al~~~~~~~~~~~A~~~l~~AL~~dp~-~~rA~~~lg~~~~~~g~y~~Ai~~w~~~l~~   72 (93)
T 3bee_A            4 VTATQLAAKATTLYYLHKQAMTDEVSLLLEQALQLEPY-NEAALSLIANDHFISFRFQEAIDTWVLLLDS   72 (93)
T ss_dssp             CCHHHHHHHHHHHHHTTTTCCCHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHTC
T ss_pred             CCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHCcC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            355566666666654443   56777777777766655 6666666777777777777777777777664

>4h7y_A Dual specificity protein kinase TTK; mitotic checkpoint kinase, chromosome instability, cancer, tetratricopeptide repeat (TPR) motif; 1.80A {Homo sapiens} PDB: 4h7x_A

Probab=96.61  E-value=0.018  Score=43.00  Aligned_cols=53  Identities=9%  Similarity=0.058  Sum_probs=24.0

Q ss_pred             CCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhhhc
Q 012111          410 GDVEKMGELFLTMKERHCVPDNITFATMIQAYNALGMTEAAQNLENKMIAMKEN  463 (471)
Q Consensus       410 g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~  463 (471)
                      +|.++|.++|+.++..+-.- ...|....+--.+.|+.+.|++++.+.+.++|.
T Consensus        74 ~D~d~aR~vy~~a~~~hKkF-AKiwi~~AqFEiRqgnl~kARkILg~AiG~~~k  126 (161)
T 4h7y_A           74 QEPDDARDYFQMARANCKKF-AFVHISFAQFELSQGNVKKSKQLLQKAVERGAV  126 (161)
T ss_dssp             HCGGGCHHHHHHHHHHCTTB-HHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCB
T ss_pred             cCHHHHHHHHHHHHHHhHHH-HHHHHHHHHHHHHcccHHHHHHHHHHHhccCCC
Confidence            44455555555444321111 444444444444555555555555555554443

>3mkq_B Coatomer subunit alpha; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae}

Probab=96.58  E-value=0.18  Score=39.23  Aligned_cols=104  Identities=10%  Similarity=-0.057  Sum_probs=66.5

Q ss_pred             HHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCC
Q 012111          121 MVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHR  200 (471)
Q Consensus       121 ~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~  200 (471)
                      .....+.|+++.|.++.+.+      .+...|..|.......|+++-|.+.|.+...          +..+.-.|.-.|+
T Consensus        12 F~LAL~lg~l~~A~e~a~~l------~~~~~Wk~Lg~~AL~~gn~~lAe~cy~~~~D----------~~~L~~Ly~~tg~   75 (177)
T 3mkq_B           12 FDLALEYGNLDAALDEAKKL------NDSITWERLIQEALAQGNASLAEMIYQTQHS----------FDKLSFLYLVTGD   75 (177)
T ss_dssp             HHHHHHTTCHHHHHHHHHHH------CCHHHHHHHHHHHHHTTCHHHHHHHHHHTTC----------HHHHHHHHHHHTC
T ss_pred             HHHHHhcCCHHHHHHHHHHh------CCHHHHHHHHHHHHHcCChHHHHHHHHHhCC----------HHHHHHHHHHhCC
Confidence            34455677777777776655      2567777777777777777777777777654          3445555666677


Q ss_pred             HHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHH
Q 012111          201 FDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAM  246 (471)
Q Consensus       201 ~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  246 (471)
                      .+...++-+.....|-      ++.....+...|+++++.++|.+.
T Consensus        76 ~e~L~kla~iA~~~g~------~n~af~~~l~lGdv~~~i~lL~~~  115 (177)
T 3mkq_B           76 VNKLSKMQNIAQTRED------FGSMLLNTFYNNSTKERSSIFAEG  115 (177)
T ss_dssp             HHHHHHHHHHHHHTTC------HHHHHHHHHHHTCHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHCcc------HHHHHHHHHHcCCHHHHHHHHHHC
Confidence            6666655555554441      344445555667777777776544

>3bee_A Putative YFRE protein; putaive YFRE protein, structural GE PSI-2, protein structure initiative; 2.15A {Vibrio parahaemolyticus rimd 2210633}

Probab=96.53  E-value=0.048  Score=37.64  Aligned_cols=66  Identities=15%  Similarity=0.027  Sum_probs=37.9

Q ss_pred             cCChhHHHHHHHHHhcCCC---HHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHhhc
Q 012111          111 QARCQTFTKLMVMLGKCKQ---PEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAFSTINDMKS  177 (471)
Q Consensus       111 ~~~~~~~~~l~~~~~~~~~---~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~  177 (471)
                      +.+...+..+..++...++   .++|..++++..+.... ++.....+...+...|++++|+..|+++.+
T Consensus         3 p~~~~~~~~~a~al~~~~~~~~~~~A~~~l~~AL~~dp~-~~rA~~~lg~~~~~~g~y~~Ai~~w~~~l~   71 (93)
T 3bee_A            3 AVTATQLAAKATTLYYLHKQAMTDEVSLLLEQALQLEPY-NEAALSLIANDHFISFRFQEAIDTWVLLLD   71 (93)
T ss_dssp             CCCHHHHHHHHHHHHHTTTTCCCHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             CCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHCcC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            3445555555555543332   46666666666655433 555666666666666666666666666665

>1pc2_A Mitochondria fission protein; unknown function; NMR {Homo sapiens} SCOP: a.118.8.1

Probab=96.51  E-value=0.031  Score=42.32  Aligned_cols=81  Identities=10%  Similarity=-0.049  Sum_probs=36.3

Q ss_pred             HHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcC---CHHHHHHHHHHHHHcCCCC--CHHHHHHHHHHHHhcCCHHHHHHH
Q 012111          309 KMRSVMDFMQKRFFFPTVVTYNIVIETFGKAG---HIEKMEEYFKKMKHRGMKP--NSITYCSLVSAYSKAGLIMKVDSI  383 (471)
Q Consensus       309 ~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g---~~~~a~~~~~~m~~~~~~p--~~~~~~~li~~~~~~g~~~~a~~~  383 (471)
                      .+.+-|....+.+. ++..+...+.-++++.+   +.++++.++++..+.. .|  ....+-.+.-++.+.|++++|.+.
T Consensus        16 ~~~~~y~~e~~~~~-~~~~~~F~ya~~Lv~S~~~~~~~~gI~lLe~ll~~~-~p~~~rd~lY~LAv~~~kl~~Y~~A~~y   93 (152)
T 1pc2_A           16 KFEKKFQSEKAAGS-VSKSTQFEYAWCLVRSKYNDDIRKGIVLLEELLPKG-SKEEQRDYVFYLAVGNYRLKEYEKALKY   93 (152)
T ss_dssp             HHHHHHHHHHHTTC-CCHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHS-CHHHHHHHHHHHHHHHHHTSCHHHHHHH
T ss_pred             HHHHHHHHHHccCC-CcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcC-CccchHHHHHHHHHHHHHccCHHHHHHH
Confidence            33444444333333 34444444444445444   3345555555555442 12  233334444444555555555555


Q ss_pred             HHHHHhCC
Q 012111          384 LRQVENSD  391 (471)
Q Consensus       384 ~~~~~~~~  391 (471)
                      ++.+.+..
T Consensus        94 ~~~lL~ie  101 (152)
T 1pc2_A           94 VRGLLQTE  101 (152)
T ss_dssp             HHHHHHHC
T ss_pred             HHHHHhcC
Confidence            55555443

>4ady_A RPN2, 26S proteasome regulatory subunit RPN2; protein binding, PC repeat; 2.70A {Saccharomyces cerevisiae} PDB: 4b4t_N

Probab=96.31  E-value=0.57  Score=46.98  Aligned_cols=87  Identities=14%  Similarity=0.098  Sum_probs=35.6

Q ss_pred             HHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHH--HHHHHHHHcCCH
Q 012111          230 YGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLN--ILTKSYGRAGMY  307 (471)
Q Consensus       230 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~--~ll~~~~~~~~~  307 (471)
                      +.-.|+.+....++..+.+..  ..+..-...+.-++...|+.+.+..+++.+.... .|....-.  .+.-+|+..|+.
T Consensus       500 ~vGTgn~~ai~~LL~~~~e~~--~e~vrR~aalgLGll~~g~~e~~~~li~~L~~~~-dp~vRygaa~alglAyaGTGn~  576 (963)
T 4ady_A          500 MLGTGKPEAIHDMFTYSQETQ--HGNITRGLAVGLALINYGRQELADDLITKMLASD-ESLLRYGGAFTIALAYAGTGNN  576 (963)
T ss_dssp             HTTCCCHHHHHHHHHHHHHCS--CHHHHHHHHHHHHHHTTTCGGGGHHHHHHHHHCS-CHHHHHHHHHHHHHHTTTSCCH
T ss_pred             hcccCCHHHHHHHHHHHhccC--cHHHHHHHHHHHHhhhCCChHHHHHHHHHHHhCC-CHHHHHHHHHHHHHHhcCCCCH
Confidence            334455555555555444321  1112222222233334555555555555554321 12221111  222334455555


Q ss_pred             HHHHHHHHHHHh
Q 012111          308 DKMRSVMDFMQK  319 (471)
Q Consensus       308 ~~a~~~~~~~~~  319 (471)
                      ....+++..+..
T Consensus       577 ~aIq~LL~~~~~  588 (963)
T 4ady_A          577 SAVKRLLHVAVS  588 (963)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcc
Confidence            555555555544

>3mkq_B Coatomer subunit alpha; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae}

Probab=96.29  E-value=0.2  Score=38.95  Aligned_cols=101  Identities=12%  Similarity=0.126  Sum_probs=58.1

Q ss_pred             HHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHH
Q 012111          301 YGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKV  380 (471)
Q Consensus       301 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a  380 (471)
                      ....|+++.|.++.+.+      .+...|..|.......|+++-|.+.|.+...         +..+.-.|.-.|+.+..
T Consensus        15 AL~lg~l~~A~e~a~~l------~~~~~Wk~Lg~~AL~~gn~~lAe~cy~~~~D---------~~~L~~Ly~~tg~~e~L   79 (177)
T 3mkq_B           15 ALEYGNLDAALDEAKKL------NDSITWERLIQEALAQGNASLAEMIYQTQHS---------FDKLSFLYLVTGDVNKL   79 (177)
T ss_dssp             HHHTTCHHHHHHHHHHH------CCHHHHHHHHHHHHHTTCHHHHHHHHHHTTC---------HHHHHHHHHHHTCHHHH
T ss_pred             HHhcCCHHHHHHHHHHh------CCHHHHHHHHHHHHHcCChHHHHHHHHHhCC---------HHHHHHHHHHhCCHHHH
Confidence            34556666666665544      2456677777777777777777777665442         34444445556666665


Q ss_pred             HHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 012111          381 DSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTM  422 (471)
Q Consensus       381 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~  422 (471)
                      .++-+.....|-      ++.....+...|+++++.++|.+.
T Consensus        80 ~kla~iA~~~g~------~n~af~~~l~lGdv~~~i~lL~~~  115 (177)
T 3mkq_B           80 SKMQNIAQTRED------FGSMLLNTFYNNSTKERSSIFAEG  115 (177)
T ss_dssp             HHHHHHHHHTTC------HHHHHHHHHHHTCHHHHHHHHHHT
T ss_pred             HHHHHHHHHCcc------HHHHHHHHHHcCCHHHHHHHHHHC
Confidence            555554444331      344444555667777777766443

>1wy6_A Hypothetical protein ST1625; helical repeat protein, structural genomics, unknown function; 2.20A {Sulfolobus tokodaii} SCOP: a.118.20.1

Probab=96.04  E-value=0.28  Score=35.89  Aligned_cols=139  Identities=14%  Similarity=0.047  Sum_probs=84.5

Q ss_pred             HcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHH
Q 012111          303 RAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDS  382 (471)
Q Consensus       303 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~  382 (471)
                      -.|..++..++..+....   .+..-||.+|--....-+-+-..++++.+-+.   .|.          ...|++.....
T Consensus        19 ldG~v~qGveii~k~~~s---sni~E~NW~ICNiiD~a~C~y~v~vLd~IGki---FDi----------s~C~NlKrVi~   82 (172)
T 1wy6_A           19 LDGYIDEGVKIVLEITKS---STKSEYNWFICNLLESIDCRYMFQVLDKIGSY---FDL----------DKCQNLKSVVE   82 (172)
T ss_dssp             HTTCHHHHHHHHHHHHHH---SCHHHHTHHHHHHHHHCCHHHHHHHHHHHGGG---SCG----------GGCSCTHHHHH
T ss_pred             HhhhHHHHHHHHHHHcCC---CCccccceeeeecchhhchhHHHHHHHHHhhh---cCc----------HhhhcHHHHHH
Confidence            345566666666555443   24445555555555555555555555544321   111          11222222222


Q ss_pred             HHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhhh
Q 012111          383 ILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAYNALGMTEAAQNLENKMIAMKE  462 (471)
Q Consensus       383 ~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~  462 (471)
                      .+-.+-     .+....+..+..+...|+-+.-.+++..+.. +-+|++.....+..+|.+.|+..+|.+++.++.+.|.
T Consensus        83 C~~~~n-----~~se~vd~ALd~lv~~~KkDqLdki~~~~l~-n~~~~~~~l~kia~Ay~Klg~~r~a~eLl~~AC~kG~  156 (172)
T 1wy6_A           83 CGVINN-----TLNEHVNKALDILVIQGKRDKLEEIGREILK-NNEVSASILVAIANALRRVGDERDATTLLIEACKKGE  156 (172)
T ss_dssp             HHHHTT-----CCCHHHHHHHHHHHHTTCHHHHHHHHHHHC---CCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHhc-----chHHHHHHHHHHHHHhccHhHHHHHHHHHhc-cCCCChHHHHHHHHHHHHhcchhhHHHHHHHHHHhhh
Confidence            222111     1445566777788888888888888888544 2567888888888999999999999999999988775


Q ss_pred             c
Q 012111          463 N  463 (471)
Q Consensus       463 ~  463 (471)
                      +
T Consensus       157 k  157 (172)
T 1wy6_A          157 K  157 (172)
T ss_dssp             H
T ss_pred             H
Confidence            4

>2v5f_A Prolyl 4-hydroxylase subunit alpha-1; endoplasmic reticulum, metal-binding, oxidoreductase; 2.03A {Homo sapiens} PDB: 1tjc_A

Probab=95.97  E-value=0.1  Score=36.85  Aligned_cols=69  Identities=10%  Similarity=-0.080  Sum_probs=49.0

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC------CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCC
Q 012111          325 TVVTYNIVIETFGKAGHIEKMEEYFKKMKHRG------MKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVI  393 (471)
Q Consensus       325 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~------~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~  393 (471)
                      +..-+..|...+...|++..|...|+...+.-      -.+....+..+..++.+.|+++.|...++++.+..+.
T Consensus         4 sa~dc~~lG~~~~~~~~y~~A~~W~~~Al~~~~~~~~~~~~~~~i~~~L~~~~~~~g~~~~A~~~~~~al~l~P~   78 (104)
T 2v5f_A            4 TAEDCFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLELDPE   78 (104)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT
T ss_pred             CHHHHHHHHHHHHHccchHHHHHHHHHHHHhhhccCCCcccHHHHHHHHHHHHHHccCHHHHHHHHHHHHhcCCC
Confidence            44455667777788888888888888766531      1234567777888888888888888888888776544

>4h7y_A Dual specificity protein kinase TTK; mitotic checkpoint kinase, chromosome instability, cancer, tetratricopeptide repeat (TPR) motif; 1.80A {Homo sapiens} PDB: 4h7x_A

Probab=95.88  E-value=0.22  Score=37.31  Aligned_cols=53  Identities=13%  Similarity=0.202  Sum_probs=33.0

Q ss_pred             CCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCC
Q 012111          340 GHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVI  393 (471)
Q Consensus       340 g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~  393 (471)
                      +++++|.++|+.+++.+-. -...|....+--.++|++..|.+++...+..++.
T Consensus        74 ~D~d~aR~vy~~a~~~hKk-FAKiwi~~AqFEiRqgnl~kARkILg~AiG~~~k  126 (161)
T 4h7y_A           74 QEPDDARDYFQMARANCKK-FAFVHISFAQFELSQGNVKKSKQLLQKAVERGAV  126 (161)
T ss_dssp             HCGGGCHHHHHHHHHHCTT-BHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCB
T ss_pred             cCHHHHHHHHHHHHHHhHH-HHHHHHHHHHHHHHcccHHHHHHHHHHHhccCCC
Confidence            5666667777666554222 2555555556566667777777777776666655

>1nzn_A CGI-135 protein, fission protein FIS1P; TPR, unknown function; 2.00A {Homo sapiens} SCOP: a.118.8.1 PDB: 1iyg_A

Probab=95.87  E-value=0.078  Score=38.57  Aligned_cols=86  Identities=10%  Similarity=0.025  Sum_probs=42.8

Q ss_pred             hcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHH---HHHHHHHHHhCC-CCcCHHHHHHHHHHHHhcCCHH
Q 012111          338 KAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMK---VDSILRQVENSD-VILDTPFFNCIISAYGQAGDVE  413 (471)
Q Consensus       338 ~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~---a~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~g~~~  413 (471)
                      .......+.+-|......| .++..+-..+..++.+..+...   ++.+++.+.+.+ +.-.....-.|.-++.+.|+++
T Consensus        13 ~~~~l~~~~~~y~~e~~~~-~~s~~~~F~yAw~Lv~S~~~~d~~~GI~lLe~l~~~~~p~~~Rd~lY~LAvg~yklg~Y~   91 (126)
T 1nzn_A           13 SVEDLLKFEKKFQSEKAAG-SVSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKGSKEEQRDYVFYLAVGNYRLKEYE   91 (126)
T ss_dssp             HHHHHHHHHHHHHHHHHHS-CCCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTSCHHHHHHHHHHHHHHHHHTTCHH
T ss_pred             CHHHHHHHHHHHHHHhccC-CCcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHHhhhHH
Confidence            3334444555555444444 2555555555555555554443   555555555543 1112233334444555666666


Q ss_pred             HHHHHHHHHHh
Q 012111          414 KMGELFLTMKE  424 (471)
Q Consensus       414 ~a~~~~~~~~~  424 (471)
                      +|.+.++.+.+
T Consensus        92 ~A~~~~~~lL~  102 (126)
T 1nzn_A           92 KALKYVRGLLQ  102 (126)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            66666665555

>1wy6_A Hypothetical protein ST1625; helical repeat protein, structural genomics, unknown function; 2.20A {Sulfolobus tokodaii} SCOP: a.118.20.1

Probab=95.72  E-value=0.39  Score=35.14  Aligned_cols=63  Identities=13%  Similarity=0.168  Sum_probs=33.2

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCC
Q 012111          329 YNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDV  392 (471)
Q Consensus       329 ~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~  392 (471)
                      ....+..+...|+-++..+++..+... .+|++.....+..+|.+.|+..++.+++.++-+.|+
T Consensus        94 vd~ALd~lv~~~KkDqLdki~~~~l~n-~~~~~~~l~kia~Ay~Klg~~r~a~eLl~~AC~kG~  156 (172)
T 1wy6_A           94 VNKALDILVIQGKRDKLEEIGREILKN-NEVSASILVAIANALRRVGDERDATTLLIEACKKGE  156 (172)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHC---CCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHhccHhHHHHHHHHHhcc-CCCChHHHHHHHHHHHHhcchhhHHHHHHHHHHhhh
Confidence            344445555555555555555554332 245555555555555555555555555555555554

>3u64_A Protein TP_0956; tetratrico peptide repeat, protein-prote interaction, syphilis, lipoprotein, transport protein; 2.30A {Treponema pallidum subsp} PDB: 4di3_A 4di4_A*

Probab=95.47  E-value=0.068  Score=45.30  Aligned_cols=106  Identities=12%  Similarity=0.099  Sum_probs=73.7

Q ss_pred             HHHHHHHHHHHHHcCCCCC---HHHHHHHHHHHHhc-----CCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhc-CCH
Q 012111          342 IEKMEEYFKKMKHRGMKPN---SITYCSLVSAYSKA-----GLIMKVDSILRQVENSDVILDTPFFNCIISAYGQA-GDV  412 (471)
Q Consensus       342 ~~~a~~~~~~m~~~~~~p~---~~~~~~li~~~~~~-----g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-g~~  412 (471)
                      ...|...+++.++.  .|+   ...|..+...|...     |+.++|.+.|++..+.++.-+..++..+...+++. |+.
T Consensus       179 l~~A~a~lerAleL--DP~~~~GsA~~~LG~lY~~vPp~~gGd~ekA~~~ferAL~LnP~~~id~~v~YA~~l~~~~gd~  256 (301)
T 3u64_A          179 VHAAVMMLERACDL--WPSYQEGAVWNVLTKFYAAAPESFGGGMEKAHTAFEHLTRYCSAHDPDHHITYADALCIPLNNR  256 (301)
T ss_dssp             HHHHHHHHHHHHHH--CTTHHHHHHHHHHHHHHHHSCTTTTCCHHHHHHHHHHHHHHCCTTCSHHHHHHHHHTTTTTTCH
T ss_pred             HHHHHHHHHHHHHh--CCCcccCHHHHHHHHHHHhCCCccCCCHHHHHHHHHHHHHhCCCCCchHHHHHHHHHHHhcCCH
Confidence            56777777777774  555   45778888888874     88888888888888876643577777778878774 888


Q ss_pred             HHHHHHHHHHHhCCCC--CCHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 012111          413 EKMGELFLTMKERHCV--PDNITFATMIQAYNALGMTEAAQNLENKM  457 (471)
Q Consensus       413 ~~a~~~~~~~~~~~~~--p~~~~~~~l~~~~~~~g~~~~A~~~~~~m  457 (471)
                      +++.+.+++.......  |+....+.+        .-++|..++.++
T Consensus       257 ~~a~~~L~kAL~a~p~~~P~~~lan~~--------~q~eA~~LL~~~  295 (301)
T 3u64_A          257 AGFDEALDRALAIDPESVPHNKLLVIL--------SQKRARWLKAHV  295 (301)
T ss_dssp             HHHHHHHHHHHHCCGGGCSSCHHHHHH--------HHHHHHHHHHTH
T ss_pred             HHHHHHHHHHHcCCCCCCCChhHHHHH--------HHHHHHHHHHHh
Confidence            8888888888876554  554333332        335555555544

>3u64_A Protein TP_0956; tetratrico peptide repeat, protein-prote interaction, syphilis, lipoprotein, transport protein; 2.30A {Treponema pallidum subsp} PDB: 4di3_A 4di4_A*

Probab=95.44  E-value=0.22  Score=42.20  Aligned_cols=107  Identities=11%  Similarity=0.108  Sum_probs=80.1

Q ss_pred             HHHHHHHHHHHHhCCCCCC---HHHHHHHHHHHHhc-----CCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhc-CCH
Q 012111          307 YDKMRSVMDFMQKRFFFPT---VVTYNIVIETFGKA-----GHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKA-GLI  377 (471)
Q Consensus       307 ~~~a~~~~~~~~~~~~~~~---~~~~~~li~~~~~~-----g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~-g~~  377 (471)
                      ...|...+++..+.  .|+   ...|..+...|.+.     |+.++|.+.|++.++.+..-+..++......++.. |+.
T Consensus       179 l~~A~a~lerAleL--DP~~~~GsA~~~LG~lY~~vPp~~gGd~ekA~~~ferAL~LnP~~~id~~v~YA~~l~~~~gd~  256 (301)
T 3u64_A          179 VHAAVMMLERACDL--WPSYQEGAVWNVLTKFYAAAPESFGGGMEKAHTAFEHLTRYCSAHDPDHHITYADALCIPLNNR  256 (301)
T ss_dssp             HHHHHHHHHHHHHH--CTTHHHHHHHHHHHHHHHHSCTTTTCCHHHHHHHHHHHHHHCCTTCSHHHHHHHHHTTTTTTCH
T ss_pred             HHHHHHHHHHHHHh--CCCcccCHHHHHHHHHHHhCCCccCCCHHHHHHHHHHHHHhCCCCCchHHHHHHHHHHHhcCCH
Confidence            56777788888775  444   55788888889884     99999999999999864222477888888888885 999


Q ss_pred             HHHHHHHHHHHhCCCC--cCHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 012111          378 MKVDSILRQVENSDVI--LDTPFFNCIISAYGQAGDVEKMGELFLTMK  423 (471)
Q Consensus       378 ~~a~~~~~~~~~~~~~--~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~  423 (471)
                      +++.+.+++.....+.  |+....+.+-        -.+|..++.+..
T Consensus       257 ~~a~~~L~kAL~a~p~~~P~~~lan~~~--------q~eA~~LL~~~~  296 (301)
T 3u64_A          257 AGFDEALDRALAIDPESVPHNKLLVILS--------QKRARWLKAHVQ  296 (301)
T ss_dssp             HHHHHHHHHHHHCCGGGCSSCHHHHHHH--------HHHHHHHHHTHH
T ss_pred             HHHHHHHHHHHcCCCCCCCChhHHHHHH--------HHHHHHHHHHhH
Confidence            9999999999998877  6655444433        345666655443

>1nzn_A CGI-135 protein, fission protein FIS1P; TPR, unknown function; 2.00A {Homo sapiens} SCOP: a.118.8.1 PDB: 1iyg_A

Probab=95.36  E-value=0.27  Score=35.74  Aligned_cols=90  Identities=14%  Similarity=0.094  Sum_probs=59.6

Q ss_pred             HHHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHH---HHHHHHHHHhCCCC-CCHHHHHHHHHHHHh
Q 012111           86 DEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQ---ASLLFEVMLSDGLK-PSVDVYTALVSAYGQ  161 (471)
Q Consensus        86 ~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~---a~~~~~~m~~~~~~-~~~~~~~~li~~~~~  161 (471)
                      +.-........+.+-|......+  .++..+-..+..++.+.++...   ++.+++.+...+.+ ......-.|.-++.+
T Consensus         9 ~~~~~~~~l~~~~~~y~~e~~~~--~~s~~~~F~yAw~Lv~S~~~~d~~~GI~lLe~l~~~~~p~~~Rd~lY~LAvg~yk   86 (126)
T 1nzn_A            9 NELVSVEDLLKFEKKFQSEKAAG--SVSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKGSKEEQRDYVFYLAVGNYR   86 (126)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHS--CCCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTSCHHHHHHHHHHHHHHHHH
T ss_pred             hccCCHHHHHHHHHHHHHHhccC--CCcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHH
Confidence            33344555556666666665554  4777777777778888776665   77788887765311 133444456667788


Q ss_pred             cCCHHHHHHHHHHhhc
Q 012111          162 SGLLDEAFSTINDMKS  177 (471)
Q Consensus       162 ~~~~~~a~~~~~~~~~  177 (471)
                      .|++++|.+.++.+.+
T Consensus        87 lg~Y~~A~~~~~~lL~  102 (126)
T 1nzn_A           87 LKEYEKALKYVRGLLQ  102 (126)
T ss_dssp             TTCHHHHHHHHHHHHH
T ss_pred             hhhHHHHHHHHHHHHH
Confidence            8888888888888876

>4ady_A RPN2, 26S proteasome regulatory subunit RPN2; protein binding, PC repeat; 2.70A {Saccharomyces cerevisiae} PDB: 4b4t_N

Probab=94.80  E-value=3.8  Score=41.22  Aligned_cols=303  Identities=8%  Similarity=-0.041  Sum_probs=166.3

Q ss_pred             HHHHHHHHhcCCCHHHH-H-HHHHHHHhCCCCCCHHHHHH-HHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHH--HHHHH
Q 012111          117 FTKLMVMLGKCKQPEQA-S-LLFEVMLSDGLKPSVDVYTA-LVSAYGQSGLLDEAFSTINDMKSVSDCKPDVY--TYSIL  191 (471)
Q Consensus       117 ~~~l~~~~~~~~~~~~a-~-~~~~~m~~~~~~~~~~~~~~-li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~--~~~~l  191 (471)
                      -..+..++...|--... . ...+++.+.  . +-.-+.+ .--+.+..|+.++++.++....... ...+..  .=..+
T Consensus       342 A~~f~Naf~naG~~~D~~l~~~~~Wl~k~--~-~~~k~sA~aSLGlIh~g~~~~gl~~L~~yL~~~-~s~~~~ik~GAll  417 (963)
T 4ady_A          342 AVSVANGFMHAGTTDNSFIKANLPWLGKA--Q-NWAKFTATASLGVIHKGNLLEGKKVMAPYLPGS-RASSRFIKGGSLY  417 (963)
T ss_dssp             HHHHHHHHHTTTTCCCHHHHHCHHHHHHC--C-THHHHHHHHHHHHHTSSCTTTHHHHHTTTSTTS-CCSCHHHHHHHHH
T ss_pred             HHHHHHHHHhCCCCcchhhhcchhhhhcc--c-hHHHHHHHHHhhhhccCchHHHHHHHHHhcccc-CCCcHHHHHHHHH
Confidence            34556666666633221 1 122344443  2 3333333 3345777899999998888766411 122333  33333


Q ss_pred             HHHHHhcCCHHHHHHHHHHHHHCCC-------CCCHHHHHHHHHHHHccCC-HHHHHHHHHHHHHcCCCCCCHH--HHHH
Q 012111          192 IKSCTKFHRFDLIEKILAEMSYLGI-------ECSAVTYNTIIDGYGKAKK-FEEMESSFSAMVESGGCHPDIF--TLNS  261 (471)
Q Consensus       192 l~~~~~~~~~~~a~~~~~~~~~~g~-------~~~~~~~~~l~~~~~~~~~-~~~a~~~~~~~~~~~~~~~~~~--~~~~  261 (471)
                      .-+....|..+.+..++.......-       .+....-..+.-+++-.|. -+++.+.+..+....  .....  .-..
T Consensus       418 aLGli~ag~~~~~~~lL~~~L~~~~~~~~~~~~~~ir~gAaLGLGla~~GS~~eev~e~L~~~L~dd--~~~~~~~AalA  495 (963)
T 4ady_A          418 GLGLIYAGFGRDTTDYLKNIIVENSGTSGDEDVDVLLHGASLGIGLAAMGSANIEVYEALKEVLYND--SATSGEAAALG  495 (963)
T ss_dssp             HHHHHTTTTTHHHHHHHHHHHHHHSSCCSCHHHHHHHHHHHHHHHHHSTTCCCHHHHHHHHHHHHTC--CHHHHHHHHHH
T ss_pred             HHHHhcCCCcHHHHHHHHHHHcCccccccccccHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHhcC--CHHHHHHHHHH
Confidence            3445566665678887776654321       0112223334344443443 245566666665532  11111  2223


Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHH--HHHcCCHHHHHHHHHHHHhCCCCCCHHHHH---HHHHHH
Q 012111          262 MISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKS--YGRAGMYDKMRSVMDFMQKRFFFPTVVTYN---IVIETF  336 (471)
Q Consensus       262 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~--~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~---~li~~~  336 (471)
                      |...+...|+.+....++..+.+.   .+..+...+..+  +...|+.+.+..+.+.+... ..|.. -|.   .+.-+|
T Consensus       496 LGli~vGTgn~~ai~~LL~~~~e~---~~e~vrR~aalgLGll~~g~~e~~~~li~~L~~~-~dp~v-Rygaa~alglAy  570 (963)
T 4ady_A          496 MGLCMLGTGKPEAIHDMFTYSQET---QHGNITRGLAVGLALINYGRQELADDLITKMLAS-DESLL-RYGGAFTIALAY  570 (963)
T ss_dssp             HHHHHTTCCCHHHHHHHHHHHHHC---SCHHHHHHHHHHHHHHTTTCGGGGHHHHHHHHHC-SCHHH-HHHHHHHHHHHT
T ss_pred             HhhhhcccCCHHHHHHHHHHHhcc---CcHHHHHHHHHHHHhhhCCChHHHHHHHHHHHhC-CCHHH-HHHHHHHHHHHh
Confidence            344566778888888888887653   233444444444  44678999999998888764 22222 233   233456


Q ss_pred             HhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCH-HHH
Q 012111          337 GKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDV-EKM  415 (471)
Q Consensus       337 ~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~-~~a  415 (471)
                      +..|+.....+++..+.... ..+..-...+.-++...|+.+.+.++++.+.+.+ .|....-..+.-+....|.. .+|
T Consensus       571 aGTGn~~aIq~LL~~~~~d~-~d~VRraAViaLGlI~~g~~e~v~rlv~~L~~~~-d~~VR~gAalALGli~aGn~~~~a  648 (963)
T 4ady_A          571 AGTGNNSAVKRLLHVAVSDS-NDDVRRAAVIALGFVLLRDYTTVPRIVQLLSKSH-NAHVRCGTAFALGIACAGKGLQSA  648 (963)
T ss_dssp             TTSCCHHHHHHHHHHHHHCS-CHHHHHHHHHHHHHHTSSSCSSHHHHTTTGGGCS-CHHHHHHHHHHHHHHTSSSCCHHH
T ss_pred             cCCCCHHHHHHHHHHhccCC-cHHHHHHHHHHHHhhccCCHHHHHHHHHHHHhcC-CHHHHHHHHHHHHHhccCCCcHHH
Confidence            77889888777999888752 2233333333344555777777777777666543 34444444444455555543 578


Q ss_pred             HHHHHHHHhCCCCCCHHHHH
Q 012111          416 GELFLTMKERHCVPDNITFA  435 (471)
Q Consensus       416 ~~~~~~~~~~~~~p~~~~~~  435 (471)
                      ++++..+...   +|..+-.
T Consensus       649 id~L~~L~~D---~d~~Vrq  665 (963)
T 4ady_A          649 IDVLDPLTKD---PVDFVRQ  665 (963)
T ss_dssp             HHHHHHHHTC---SSHHHHH
T ss_pred             HHHHHHHccC---CCHHHHH
Confidence            8888888752   4544433

>1v54_E Cytochrome C oxidase polypeptide VA; oxidoreductase; HET: FME TPO HEA TGL PGV CHD CDL PEK PSC DMU; 1.80A {Bos taurus} SCOP: a.118.11.1 PDB: 1oco_E* 1occ_E* 1ocz_E* 1ocr_E* 1v55_E* 2dyr_E* 2dys_E* 2eij_E* 2eik_E* 2eil_E* 2eim_E* 2ein_E* 2occ_E* 2ybb_P* 2zxw_E* 3abk_E* 3abl_E* 3abm_E* 3ag1_E* 3ag2_E* ...

Probab=94.22  E-value=0.53  Score=32.28  Aligned_cols=63  Identities=11%  Similarity=0.211  Sum_probs=38.0

Q ss_pred             CHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHH
Q 012111          376 LIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQ  439 (471)
Q Consensus       376 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~  439 (471)
                      +.-+..+-++.+...++.|++.+..+.+++|.+.+++..|.++|+..+.+ +.+...+|..+++
T Consensus        25 D~~e~rrglN~l~~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~iK~K-~~~~~~iY~~~lq   87 (109)
T 1v54_E           25 DAWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDK-AGPHKEIYPYVIQ   87 (109)
T ss_dssp             CHHHHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-TTTCTTHHHHHHH
T ss_pred             cHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHH-hcCchhhHHHHHH
Confidence            34455556666666666677777777777777777777777777666543 2233344554443

>2ff4_A Probable regulatory protein EMBR; winged-helix, tetratricopeptide repeat, beta-sandwich, trans; HET: DNA TPO; 1.90A {Mycobacterium tuberculosis} SCOP: a.4.6.1 a.118.8.3 b.26.1.2 PDB: 2fez_A*

Probab=94.06  E-value=0.9  Score=41.03  Aligned_cols=75  Identities=15%  Similarity=0.053  Sum_probs=51.5

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHh-----CCCCCCHHHHHHHH
Q 012111          364 YCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKE-----RHCVPDNITFATMI  438 (471)
Q Consensus       364 ~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~-----~~~~p~~~~~~~l~  438 (471)
                      ...++..+...|+.+++...+..+....+- +...|..+|.++.+.|+..+|++.|+++.+     .|+.|+..+-...-
T Consensus       174 ~~~~~~~~l~~g~~~~a~~~l~~~~~~~P~-~E~~~~~lm~al~~~Gr~~~Al~~y~~~r~~L~~eLG~~P~~~l~~l~~  252 (388)
T 2ff4_A          174 HTAKAEAEIACGRASAVIAELEALTFEHPY-REPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTLRALNE  252 (388)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHSTT-CHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHH
Confidence            344566667777777777777777666544 677777778888888888888777776643     47777776644433


Q ss_pred             H
Q 012111          439 Q  439 (471)
Q Consensus       439 ~  439 (471)
                      .
T Consensus       253 ~  253 (388)
T 2ff4_A          253 R  253 (388)
T ss_dssp             H
T ss_pred             H
Confidence            3

>3o48_A Mitochondria fission 1 protein; tetratricopeptide repeat fold, TPR, scaffold, peroxisome, membrane fission, protein binding; 1.75A {Saccharomyces cerevisiae} PDB: 2pqr_A 2pqn_A 3uux_A

Probab=93.98  E-value=0.65  Score=33.93  Aligned_cols=71  Identities=8%  Similarity=-0.048  Sum_probs=42.7

Q ss_pred             CCCHHHHHHHHHHHHhcCCH---HHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCC
Q 012111          358 KPNSITYCSLVSAYSKAGLI---MKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPD  430 (471)
Q Consensus       358 ~p~~~~~~~li~~~~~~g~~---~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~  430 (471)
                      .|+..+--.+..++.+..+.   .+++.+++.+.+.++.-....+-.|.-++.+.|++++|.+..+.+.+  +.|+
T Consensus        37 ~vs~qt~F~yAw~Lv~S~~~~d~~~GI~LLe~l~~~~~~~~Rd~LYyLAvg~yklgdY~~Ar~y~d~lL~--~eP~  110 (134)
T 3o48_A           37 TATIQSRFNYAWGLIKSTDVNDERLGVKILTDIYKEAESRRRECLYYLTIGCYKLGEYSMAKRYVDTLFE--HERN  110 (134)
T ss_dssp             GSCHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHHHHTCHHHHHHHHHHHHT--TCTT
T ss_pred             CCChhhHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcchhHHHHHHHHHHHHHhhhHHHHHHHHHHHHh--hCCC
Confidence            45666655666666666543   35666666666554322344455566667777777777777777766  3454

>4b4t_P 26S proteasome regulatory subunit RPN5; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=93.87  E-value=3.9  Score=37.62  Aligned_cols=51  Identities=12%  Similarity=0.121  Sum_probs=31.4

Q ss_pred             CCHHHHHHHHHHhhcC----CCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 012111          163 GLLDEAFSTINDMKSV----SDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSY  213 (471)
Q Consensus       163 ~~~~~a~~~~~~~~~~----~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~  213 (471)
                      |+++.|++.+..+.+.    .+..........++..|...++++...+.+.-+.+
T Consensus        30 ~~~~~a~e~ll~lEK~~r~~~d~~s~~r~l~~iv~l~~~~~~~~~l~e~i~~Lsk   84 (445)
T 4b4t_P           30 NDCNSALDQLLVLEKKTRQASDLASSKEVLAKIVDLLASRNKWDDLNEQLTLLSK   84 (445)
T ss_dssp             HHHHHHHHHHHHHHHHHSSSCSTTTCHHHHHHHHHHHHHHSCHHHHHHHHHHHHT
T ss_pred             CCHHHHHHHHHHHHHHhhhccchhhHHHHHHHHHHHHHHhccHHHHHHHHHHHHH
Confidence            5677777766554431    23344555667777777777777777666655543

>4fhn_B Nucleoporin NUP120; protein complex,structural protein,nuclear pore complex,mRNA transport,protein transport, WD repeat; 6.99A {Schizosaccharomyces pombe 972h-}

Probab=93.85  E-value=3.4  Score=43.41  Aligned_cols=131  Identities=7%  Similarity=0.003  Sum_probs=62.4

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCH----HHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHH
Q 012111          329 YNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNS----ITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIIS  404 (471)
Q Consensus       329 ~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~----~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  404 (471)
                      |..++..+.+.+.++.+.++-....+....-+.    ..|..+.+++...|++++|...+-.+.+...  -...+..|+.
T Consensus       902 Y~hv~~LFe~~~~~~~vi~fa~lAi~~~~~~~~~~~~~l~~~iFk~~L~l~~ye~Ay~aL~~~pd~~~--r~~cLr~LV~  979 (1139)
T 4fhn_B          902 YLHLSKKLFEESAYIDALEFSLLADASKETDDEDLSIAITHETLKTACAAGKFDAAHVALMVLSTTPL--KKSCLLDFVN  979 (1139)
T ss_dssp             HHHHHHHHHHTSCCHHHHHHHHHHHHHCCSCCHHHHHHHHHHHHHHHHHHCCSGGGGHHHHHHHHSSS--CHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHhccCCChhhHHHHHHHHHHHHHhhCCHHHHHHHHHhCCCHHH--HHHHHHHHHH
Confidence            455555566666666666555554443211111    1355566666666666666666655554432  2344555555


Q ss_pred             HHHhcCCH------------HHHHHHHHHHHh-C-CCCCCHHHHHHHHHHHHhcCCHHHH-HHHHHHHHHhh
Q 012111          405 AYGQAGDV------------EKMGELFLTMKE-R-HCVPDNITFATMIQAYNALGMTEAA-QNLENKMIAMK  461 (471)
Q Consensus       405 ~~~~~g~~------------~~a~~~~~~~~~-~-~~~p~~~~~~~l~~~~~~~g~~~~A-~~~~~~m~~~~  461 (471)
                      .++..|..            ++..+++..-.+ . .+...+.-|..|-.-+...|++..| .-+|+.+.+.+
T Consensus       980 ~lce~~~~~~L~~lpf~gl~~~Vd~IL~~kAr~~~~~~~~p~Yy~iLYs~ri~r~dyR~AA~vmYe~~~RL~ 1051 (1139)
T 4fhn_B          980 QLTKQGKINQLLNYSMPTLRQDVDNLLERKAFQMINVESQPCWYNILFSWRYKHQNYRDAAAIIYEKLSRYI 1051 (1139)
T ss_dssp             HHHHHCCHHHHHHHTTTSCHHHHHHHHHHHHHHHHHHCCSTHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHH
T ss_pred             HHHhCCChhhhhCCCCccHHHHHHHHHHHHHHhCCccccCCCHHHHhHhhhhccCChHHHHHHHHHHHHHhh
Confidence            55544433            333333322111 1 0111223344555555666666655 44555555544

>1y8m_A FIS1; mitochondria, unknown function; NMR {Saccharomyces cerevisiae} SCOP: a.118.8.1

Probab=93.58  E-value=1.6  Score=32.31  Aligned_cols=71  Identities=8%  Similarity=-0.048  Sum_probs=42.8

Q ss_pred             CCCHHHHHHHHHHHHhcCCH---HHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCC
Q 012111          358 KPNSITYCSLVSAYSKAGLI---MKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPD  430 (471)
Q Consensus       358 ~p~~~~~~~li~~~~~~g~~---~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~  430 (471)
                      .|+..+--.+..++.+..+.   .+++.+++.+.+.++.-.....-.|.-++.+.|++++|.++.+.+.+  +.|+
T Consensus        36 ~vs~~t~F~YAw~Lv~S~~~~di~~GI~LLe~l~~~~~~~~RdcLYyLAvg~ykl~~Y~~Ar~y~d~lL~--~eP~  109 (144)
T 1y8m_A           36 TATIQSRFNYAWGLIKSTDVNDERLGVKILTDIYKEAESRRRECLYYLTIGCYKLGEYSMAKRYVDTLFE--HERN  109 (144)
T ss_dssp             TSCHHHHHHHHHHHHHSSSHHHHHHHHHHHHHHHHHCCSTHHHHHHHHHHHHHTTTCHHHHHHHHHHHHH--TCCC
T ss_pred             CCcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCccchhHHHHHHHHHHHHhhhHHHHHHHHHHHHh--cCCC
Confidence            45666666666666666543   35666666666554432344444555667777777777777777776  3554

>4gns_B Protein CSD3, chitin biosynthesis protein CHS6; FN3, BRCT, tetratricopeptide repeat, cargo adaptor, transpor; HET: EPE; 2.75A {Saccharomyces cerevisiae}

Probab=93.57  E-value=0.51  Score=46.29  Aligned_cols=53  Identities=17%  Similarity=-0.054  Sum_probs=38.9

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhCCCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 012111          403 ISAYGQAGDVEKMGELFLTMKERHCVP-DNITFATMIQAYNALGMTEAAQNLENKM  457 (471)
Q Consensus       403 ~~~~~~~g~~~~a~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~m  457 (471)
                      ...|...|+++.|+++-++....  .| +..+|..|..+|...|+++.|+-.++.+
T Consensus       344 a~FLl~K~~~elAL~~Ak~AV~~--aPseF~tW~~La~vYi~l~d~e~ALLtLNSc  397 (754)
T 4gns_B          344 TNFLLNRGDYELALGVSNTSTEL--ALDSFESWYNLARCHIKKEEYEKALFAINSM  397 (754)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHH--CSSCHHHHHHHHHHHHHTTCHHHHHHHHHHS
T ss_pred             HHHHhccCcHHHHHHHHHHHHhc--CchhhHHHHHHHHHHHHhccHHHHHHHHhcC
Confidence            34456678888888888877764  44 4677888888888888888887777665

>2ff4_A Probable regulatory protein EMBR; winged-helix, tetratricopeptide repeat, beta-sandwich, trans; HET: DNA TPO; 1.90A {Mycobacterium tuberculosis} SCOP: a.4.6.1 a.118.8.3 b.26.1.2 PDB: 2fez_A*

Probab=93.08  E-value=0.43  Score=43.16  Aligned_cols=72  Identities=15%  Similarity=0.119  Sum_probs=48.3

Q ss_pred             HHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHhhc----CCCCCCCHHHHH
Q 012111          117 FTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAFSTINDMKS----VSDCKPDVYTYS  189 (471)
Q Consensus       117 ~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~----~~~~~~~~~~~~  189 (471)
                      ...++..+...|++++|...+..+.... +.+...|..+|.++.+.|+..+|++.|+.+..    ..|+.|...+-.
T Consensus       174 ~~~~~~~~l~~g~~~~a~~~l~~~~~~~-P~~E~~~~~lm~al~~~Gr~~~Al~~y~~~r~~L~~eLG~~P~~~l~~  249 (388)
T 2ff4_A          174 HTAKAEAEIACGRASAVIAELEALTFEH-PYREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTLRA  249 (388)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Confidence            4455666667777777777777766543 33666777777777777777777777766543    246777776543

>3ffl_A Anaphase-promoting complex subunit 7; tetratricopeptide repeat motif, helis-turn-helix, cell cycle division, mitosis, TPR repeat; 2.50A {Homo sapiens}

Probab=92.97  E-value=1.9  Score=32.98  Aligned_cols=64  Identities=13%  Similarity=-0.018  Sum_probs=47.4

Q ss_pred             chHHHHHHHHHHHhhcHHHHHHHHHHhhhccCccCCh-------hHHHHHHHHHhcCCCHHHHHHHHHHHH
Q 012111           78 PKPVLEALDEAIKQKKWQLALKIFGLLRQQQWYQARC-------QTFTKLMVMLGKCKQPEQASLLFEVML  141 (471)
Q Consensus        78 ~~~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~-------~~~~~l~~~~~~~~~~~~a~~~~~~m~  141 (471)
                      ...+.+-++.+...+.++.|+-+.+.+......+++.       .++..+.+++...|++..|...|++.+
T Consensus        20 ~~~l~dqik~L~d~~LY~sA~~La~lLlSl~~~~~~~~sp~~~~~~l~~ladalf~~~eyrrA~~~y~qAL   90 (167)
T 3ffl_A           20 HMNVIDHVRDMAAAGLHSNVRLLSSLLLTLSNNNPELFSPPQKYQLLVYHADSLFHDKEYRNAVSKYTMAL   90 (167)
T ss_dssp             -CCHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSTTSSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhhhHHHHHHHHHHHHHhhcCCcccccHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHH
Confidence            3466777888889999999988888766543123332       366778888899999999999998854

>1qsa_A Protein (soluble lytic transglycosylase SLT70); alpha-superhelix, transferase; HET: GOL; 1.65A {Escherichia coli} SCOP: a.118.5.1 d.2.1.6 PDB: 1qte_A* 1sly_A*

Probab=92.89  E-value=7  Score=37.60  Aligned_cols=80  Identities=9%  Similarity=0.001  Sum_probs=45.9

Q ss_pred             hhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHHH
Q 012111          114 CQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIK  193 (471)
Q Consensus       114 ~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~  193 (471)
                      ...-..-+..+.+.+++......+..     .+.+...-+....+....|+..+|......+-...  ......+..++.
T Consensus        72 ~~Lr~~~l~~l~~~~~w~~~l~~~~~-----~p~~~~~~c~~~~A~~~~G~~~~a~~~~~~lW~~~--~~~p~~c~~l~~  144 (618)
T 1qsa_A           72 RTLQSRFVNELARREDWRGLLAFSPE-----KPGTTEAQCNYYYAKWNTGQSEEAWQGAKELWLTG--KSQPNACDKLFS  144 (618)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHCCS-----CCSSHHHHHHHHHHHHHTTCHHHHHHHHHHHHSCS--SCCCTHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCHHHHHHhccC-----CCCCHHHHHHHHHHHHHcCChhHHHHHHHHHHhCC--CCCcHHHHHHHH
Confidence            33445555666667777666654432     13455666666777777787777766666655422  223344555666


Q ss_pred             HHHhcCC
Q 012111          194 SCTKFHR  200 (471)
Q Consensus       194 ~~~~~~~  200 (471)
                      .+.+.|.
T Consensus       145 ~~~~~g~  151 (618)
T 1qsa_A          145 VWRASGK  151 (618)
T ss_dssp             HHHHTTC
T ss_pred             HHHHCCC
Confidence            6665443

>2y69_E Cytochrome C oxidase subunit 5A; electron transport, complex IV, proton pumps, membrane prote; HET: TPO HEA CHD PEK PGV DMU; 1.95A {Bos taurus}

Probab=92.59  E-value=1.3  Score=32.20  Aligned_cols=63  Identities=11%  Similarity=0.211  Sum_probs=41.5

Q ss_pred             CHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHH
Q 012111          376 LIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQ  439 (471)
Q Consensus       376 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~  439 (471)
                      |.-+..+-++.+...++.|++.+..+.+++|.+.+|+..|.++|+-.+.+ +.+...+|..+++
T Consensus        68 D~wElrrglN~l~~~DlVPeP~Ii~AALrAcRRvNDfalAVR~lE~vK~K-~~~~~~iY~y~lq  130 (152)
T 2y69_E           68 DAWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDK-AGPHKEIYPYVIQ  130 (152)
T ss_dssp             CHHHHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-TTTCTTHHHHHHH
T ss_pred             cHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHh-cCCchhhHHHHHH
Confidence            33445566666667777777777777777777777777777777776654 3344445655554

>1v54_E Cytochrome C oxidase polypeptide VA; oxidoreductase; HET: FME TPO HEA TGL PGV CHD CDL PEK PSC DMU; 1.80A {Bos taurus} SCOP: a.118.11.1 PDB: 1oco_E* 1occ_E* 1ocz_E* 1ocr_E* 1v55_E* 2dyr_E* 2dys_E* 2eij_E* 2eik_E* 2eil_E* 2eim_E* 2ein_E* 2occ_E* 2ybb_P* 2zxw_E* 3abk_E* 3abl_E* 3abm_E* 3ag1_E* 3ag2_E* ...

Probab=92.37  E-value=1.7  Score=29.82  Aligned_cols=63  Identities=14%  Similarity=0.171  Sum_probs=48.6

Q ss_pred             CHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHHH
Q 012111          129 QPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIK  193 (471)
Q Consensus       129 ~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~  193 (471)
                      +.-+..+-++.+......|++.+..+.+++|-+.+++..|+++|+.++..-  .....+|..++.
T Consensus        25 D~~e~rrglN~l~~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~iK~K~--~~~~~iY~~~lq   87 (109)
T 1v54_E           25 DAWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDKA--GPHKEIYPYVIQ   87 (109)
T ss_dssp             CHHHHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT--TTCTTHHHHHHH
T ss_pred             cHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHh--cCchhhHHHHHH
Confidence            556778888888888888899999999999999999999999998887633  333445655554

>4fhn_B Nucleoporin NUP120; protein complex,structural protein,nuclear pore complex,mRNA transport,protein transport, WD repeat; 6.99A {Schizosaccharomyces pombe 972h-}

Probab=92.34  E-value=4.8  Score=42.28  Aligned_cols=87  Identities=7%  Similarity=-0.005  Sum_probs=61.0

Q ss_pred             HHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCC---HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHH
Q 012111          221 VTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPD---IFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNIL  297 (471)
Q Consensus       221 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~---~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  297 (471)
                      .-|..++..+.+.+.++.+.++-....+..+..++   ...|..+.+.+...|++++|...+-.+....  .-......|
T Consensus       900 ~YY~hv~~LFe~~~~~~~vi~fa~lAi~~~~~~~~~~~~~l~~~iFk~~L~l~~ye~Ay~aL~~~pd~~--~r~~cLr~L  977 (1139)
T 4fhn_B          900 CYYLHLSKKLFEESAYIDALEFSLLADASKETDDEDLSIAITHETLKTACAAGKFDAAHVALMVLSTTP--LKKSCLLDF  977 (1139)
T ss_dssp             HHHHHHHHHHHHTSCCHHHHHHHHHHHHHCCSCCHHHHHHHHHHHHHHHHHHCCSGGGGHHHHHHHHSS--SCHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHhccCCChhhHHHHHHHHHHHHHhhCCHHHHHHHHHhCCCHH--HHHHHHHHH
Confidence            45777888888888888888887777665322221   1257788888889999999988887776543  335567777


Q ss_pred             HHHHHHcCCHHH
Q 012111          298 TKSYGRAGMYDK  309 (471)
Q Consensus       298 l~~~~~~~~~~~  309 (471)
                      +...|..|..+.
T Consensus       978 V~~lce~~~~~~  989 (1139)
T 4fhn_B          978 VNQLTKQGKINQ  989 (1139)
T ss_dssp             HHHHHHHCCHHH
T ss_pred             HHHHHhCCChhh
Confidence            777777666543

>4gns_B Protein CSD3, chitin biosynthesis protein CHS6; FN3, BRCT, tetratricopeptide repeat, cargo adaptor, transpor; HET: EPE; 2.75A {Saccharomyces cerevisiae}

Probab=92.11  E-value=1.6  Score=42.95  Aligned_cols=130  Identities=11%  Similarity=0.058  Sum_probs=79.8

Q ss_pred             HHHHHHHHHhcCCC-HHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcC-CHHHHHHHHHHhhcC-----CCCCC-CH--
Q 012111          116 TFTKLMVMLGKCKQ-PEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSG-LLDEAFSTINDMKSV-----SDCKP-DV--  185 (471)
Q Consensus       116 ~~~~l~~~~~~~~~-~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~-~~~~a~~~~~~~~~~-----~~~~~-~~--  185 (471)
                      ....++..+.-.++ ++.|..+|+.+.......+......++..+...+ +--+|.+++.+..+.     ....+ +.  
T Consensus       250 L~~~Ll~~~~~t~~~~~~a~~~le~L~~~~p~~~~~~~~~~i~~~~~~~~~Ev~av~ll~~~l~~~~~~~~~l~~~~~~~  329 (754)
T 4gns_B          250 LMYSLKSFIAITPSLVDFTIDYLKGLTKKDPIHDIYYKTAMITILDHIETKELDMITILNETLDPLLSLLNDLPPRDADS  329 (754)
T ss_dssp             HHHHHHHHHHTCGGGHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHTTCGGGHHHHHHHHHHHHHHHHHHHHTCSSCCHHH
T ss_pred             HHHHHHHHHcccccHHHHHHHHHHHHHhhCCchhHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhhhhhhhhccccccc
Confidence            34556666666666 5789999999887632212222233333333333 223455555444320     01111 11  


Q ss_pred             --------HHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHH
Q 012111          186 --------YTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAM  246 (471)
Q Consensus       186 --------~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  246 (471)
                              .....=...|...|+++.|+++-++....- +-+-.+|..|..+|...|+++.|+-.++.+
T Consensus       330 ~~~~~~~~~LL~~Qa~FLl~K~~~elAL~~Ak~AV~~a-PseF~tW~~La~vYi~l~d~e~ALLtLNSc  397 (754)
T 4gns_B          330 ARLMNCMSDLLNIQTNFLLNRGDYELALGVSNTSTELA-LDSFESWYNLARCHIKKEEYEKALFAINSM  397 (754)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SSCHHHHHHHHHHHHHTTCHHHHHHHHHHS
T ss_pred             ccccCcchHHHHHHHHHHhccCcHHHHHHHHHHHHhcC-chhhHHHHHHHHHHHHhccHHHHHHHHhcC
Confidence                    112222334667899999999999988763 556889999999999999999999988877

>4b4t_P 26S proteasome regulatory subunit RPN5; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=90.88  E-value=9.6  Score=35.00  Aligned_cols=33  Identities=15%  Similarity=0.212  Sum_probs=21.4

Q ss_pred             CCchHHHHHHHHHHHhhcHHHHHHHHHHhhhcc
Q 012111           76 LWPKPVLEALDEAIKQKKWQLALKIFGLLRQQQ  108 (471)
Q Consensus        76 ~~~~~~~~~l~~~~~~~~~~~A~~~~~~~~~~~  108 (471)
                      .+...+...+..+...|+|+...+.+..+....
T Consensus        54 s~~r~l~~iv~l~~~~~~~~~l~e~i~~Lskkr   86 (445)
T 4b4t_P           54 SSKEVLAKIVDLLASRNKWDDLNEQLTLLSKKH   86 (445)
T ss_dssp             TCHHHHHHHHHHHHHHSCHHHHHHHHHHHHTTT
T ss_pred             hHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHh
Confidence            344556667777777777777766666665543

>3o48_A Mitochondria fission 1 protein; tetratricopeptide repeat fold, TPR, scaffold, peroxisome, membrane fission, protein binding; 1.75A {Saccharomyces cerevisiae} PDB: 2pqr_A 2pqn_A 3uux_A

Probab=90.84  E-value=3.1  Score=30.39  Aligned_cols=69  Identities=7%  Similarity=-0.084  Sum_probs=34.1

Q ss_pred             CCHHHHHHHHHHHHhcCC---HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCC
Q 012111          324 PTVVTYNIVIETFGKAGH---IEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDV  392 (471)
Q Consensus       324 ~~~~~~~~li~~~~~~g~---~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~  392 (471)
                      |+..+--.+.-++++..+   ..+++.+++++.+.+..-....+-.+.-++.+.|+++.|.+..+.+.+..+
T Consensus        38 vs~qt~F~yAw~Lv~S~~~~d~~~GI~LLe~l~~~~~~~~Rd~LYyLAvg~yklgdY~~Ar~y~d~lL~~eP  109 (134)
T 3o48_A           38 ATIQSRFNYAWGLIKSTDVNDERLGVKILTDIYKEAESRRRECLYYLTIGCYKLGEYSMAKRYVDTLFEHER  109 (134)
T ss_dssp             SCHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHHHHTCHHHHHHHHHHHHTTCT
T ss_pred             CChhhHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcchhHHHHHHHHHHHHHhhhHHHHHHHHHHHHhhCC
Confidence            444443334444444433   334555555555543111233444455556666666666666666665443

>2y69_E Cytochrome C oxidase subunit 5A; electron transport, complex IV, proton pumps, membrane prote; HET: TPO HEA CHD PEK PGV DMU; 1.95A {Bos taurus}

Probab=89.69  E-value=3.6  Score=30.02  Aligned_cols=63  Identities=14%  Similarity=0.171  Sum_probs=49.4

Q ss_pred             CHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHHH
Q 012111          129 QPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIK  193 (471)
Q Consensus       129 ~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~  193 (471)
                      +.-+..+-++.+....+.|++.+....+++|-+.+++..|+++|+.++..-  .+...+|..++.
T Consensus        68 D~wElrrglN~l~~~DlVPeP~Ii~AALrAcRRvNDfalAVR~lE~vK~K~--~~~~~iY~y~lq  130 (152)
T 2y69_E           68 DAWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDKA--GPHKEIYPYVIQ  130 (152)
T ss_dssp             CHHHHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT--TTCTTHHHHHHH
T ss_pred             cHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHhc--CCchhhHHHHHH
Confidence            455677888888888888999999999999999999999999999888633  344445665554

>3lvg_A Clathrin heavy chain 1; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} PDB: 3lvh_A

Probab=89.64  E-value=0.00013  Score=65.86  Aligned_cols=91  Identities=15%  Similarity=0.196  Sum_probs=54.2

Q ss_pred             CchHHHHHHHHHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHH
Q 012111           77 WPKPVLEALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALV  156 (471)
Q Consensus        77 ~~~~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li  156 (471)
                      +|..+.+++..+-+.|.+++-++.+..+++.   ..++..=+.|+-+|++.++..+..+++       -.|+..-...+.
T Consensus        82 Dps~y~eVi~~A~~~~~~edLv~yL~MaRk~---~ke~~IDteLi~ayAk~~rL~elEefl-------~~~N~A~iq~VG  151 (624)
T 3lvg_A           82 DPSSYMEVVQAANTSGNWEELVKYLQMARKK---ARESYVETELIFALAKTNRLAELEEFI-------NGPNNAHIQQVG  151 (624)
T ss_dssp             CCCSSSHHHHHTTTSSCCTTHHHHHHTTSTT---CCSTTTTHHHHHHHHTSCSSSTTTSTT-------SCCSSSCTHHHH
T ss_pred             ChHHHHHHHHHHHhCCCHHHHHHHHHHHHHH---hcccccHHHHHHHHHhhCcHHHHHHHH-------cCCCcccHHHHH
Confidence            4455666666666777777777777666654   233344456777777777655533322       124444455566


Q ss_pred             HHHHhcCCHHHHHHHHHHhhc
Q 012111          157 SAYGQSGLLDEAFSTINDMKS  177 (471)
Q Consensus       157 ~~~~~~~~~~~a~~~~~~~~~  177 (471)
                      +-|...|.++.|.-+|..+..
T Consensus       152 Drcf~e~lYeAAKilys~isN  172 (624)
T 3lvg_A          152 DRCYDEKMYDAAKLLYNNVSN  172 (624)
T ss_dssp             HHHHHSCCSTTSSTTGGGSCC
T ss_pred             HHHHHccCHHHHHHHHHhCcc
Confidence            666667777666666655443

>1zbp_A Hypothetical protein VPA1032; alpha-beta protein, structural genomics, PSI, protein struct initiative; 2.40A {Vibrio parahaemolyticus} SCOP: e.61.1.1

Probab=88.88  E-value=1.9  Score=35.97  Aligned_cols=117  Identities=12%  Similarity=0.082  Sum_probs=72.9

Q ss_pred             HHHHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCC--CCHHHHHHHHHHHHhc
Q 012111           85 LDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLK--PSVDVYTALVSAYGQS  162 (471)
Q Consensus        85 l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~--~~~~~~~~li~~~~~~  162 (471)
                      +..+.+.|++++|++....-.+..  |.|...-..++..+|-.|+++.|.+-++...+....  |....|..+|++=   
T Consensus         4 ~~~ll~~g~L~~al~~~~~~VR~~--P~da~~R~~LfqLLcv~G~w~RA~~QL~~~a~l~p~~~~~a~~yr~lI~aE---   78 (273)
T 1zbp_A            4 WKNALSEGQLQQALELLIEAIKAS--PKDASLRSSFIELLCIDGDFERADEQLMQSIKLFPEYLPGASQLRHLVKAA---   78 (273)
T ss_dssp             HHHHTTTTCHHHHHHHHHHHHHTC--TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHHH---
T ss_pred             HHHHHhCCCHHHHHHHHHHHHHhC--CcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCchhhHHHHHHHHHHHHH---
Confidence            345668899999999888888775  778888889999999999999999988888775322  1223444444431   


Q ss_pred             CCHHHHHHHHHHhhcCCCCCC-----CHHHHHHHHHHH--HhcCCHHHHHHHHHHHHHC
Q 012111          163 GLLDEAFSTINDMKSVSDCKP-----DVYTYSILIKSC--TKFHRFDLIEKILAEMSYL  214 (471)
Q Consensus       163 ~~~~~a~~~~~~~~~~~~~~~-----~~~~~~~ll~~~--~~~~~~~~a~~~~~~~~~~  214 (471)
                             ..=.++.. .+-.|     ...-...++.+.  ...|+.+.|..+-+++.+.
T Consensus        79 -------~~R~~vfa-G~~~P~~~g~~~~w~~~ll~Al~~~~~G~~~~A~~lr~~A~e~  129 (273)
T 1zbp_A           79 -------QARKDFAQ-GAATAKVLGENEELTKSLVSFNLSMVSQDYEQVSELALQIEEL  129 (273)
T ss_dssp             -------HHHHHHTT-SCCCEECCCSCHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             -------HHHHHHHc-CCCCCCCCCCCHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHhc
Confidence                   11111221 11111     122334444443  3457888877777776543

>3lvg_A Clathrin heavy chain 1; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} PDB: 3lvh_A

Probab=86.61  E-value=2.1e-05  Score=70.77  Aligned_cols=78  Identities=10%  Similarity=0.088  Sum_probs=35.1

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHH
Q 012111          255 DIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIE  334 (471)
Q Consensus       255 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~  334 (471)
                      ++.||..+-.+|...+.+.-|.-.--.++-..   |  -...++..|...|-+++.+.+++.-... -......|+-|.-
T Consensus       198 s~ktWKeV~~ACvd~~EfrLAqicGLniIvha---d--eL~elv~~YE~~G~f~ELIsLlEaglgl-ErAHmGmFTELaI  271 (624)
T 3lvg_A          198 STRTWKEVCFACVDGKEFRLAQMCGLHIVVHA---D--ELEELINYYQDRGYFEELITMLEAALGL-ERAHMGMFTELAI  271 (624)
T ss_dssp             SSCSHHHHTHHHHHSCTTTTTTHHHHHHHCCS---S--CCSGGGSSSSTTCCCTTSTTTHHHHTTS-TTCCHHHHHHHHH
T ss_pred             ChhHHHHHHHHHhCchHHHHHHHhcchhcccH---H--HHHHHHHHHHhCCCHHHHHHHHHHHhCC-CchhHHHHHHHHH
Confidence            33455555566666665554443333222111   0  1122444555555565555555544421 1124444555544


Q ss_pred             HHHh
Q 012111          335 TFGK  338 (471)
Q Consensus       335 ~~~~  338 (471)
                      .|++
T Consensus       272 LYsK  275 (624)
T 3lvg_A          272 LYSK  275 (624)
T ss_dssp             HHHS
T ss_pred             HHHh
Confidence            4444

>3ffl_A Anaphase-promoting complex subunit 7; tetratricopeptide repeat motif, helis-turn-helix, cell cycle division, mitosis, TPR repeat; 2.50A {Homo sapiens}

Probab=86.03  E-value=7.3  Score=29.77  Aligned_cols=25  Identities=8%  Similarity=0.117  Sum_probs=14.5

Q ss_pred             HHHHHHHHHHccCCHHHHHHHHHHH
Q 012111          222 TYNTIIDGYGKAKKFEEMESSFSAM  246 (471)
Q Consensus       222 ~~~~l~~~~~~~~~~~~a~~~~~~~  246 (471)
                      .-..+..+|.+.+++++|+.+++.+
T Consensus       124 lkykia~C~~~l~~~~~Ai~~Le~I  148 (167)
T 3ffl_A          124 VKYKLAECYTVLKQDKDAIAILDGI  148 (167)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHTS
T ss_pred             HHHHHHHHHHHHCCHHHHHHHHhcC
Confidence            3344556666666666666665554

>1y8m_A FIS1; mitochondria, unknown function; NMR {Saccharomyces cerevisiae} SCOP: a.118.8.1

Probab=85.90  E-value=8.9  Score=28.44  Aligned_cols=71  Identities=7%  Similarity=-0.105  Sum_probs=41.1

Q ss_pred             CCCHHHHHHHHHHHHhcCC---HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCC
Q 012111          323 FPTVVTYNIVIETFGKAGH---IEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVI  393 (471)
Q Consensus       323 ~~~~~~~~~li~~~~~~g~---~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~  393 (471)
                      .|+..+--.+.-++++..+   ..+++.+++.+...+..-.....-.|.-++.+.|++++|.++.+.+.+..+.
T Consensus        36 ~vs~~t~F~YAw~Lv~S~~~~di~~GI~LLe~l~~~~~~~~RdcLYyLAvg~ykl~~Y~~Ar~y~d~lL~~eP~  109 (144)
T 1y8m_A           36 TATIQSRFNYAWGLIKSTDVNDERLGVKILTDIYKEAESRRRECLYYLTIGCYKLGEYSMAKRYVDTLFEHERN  109 (144)
T ss_dssp             TSCHHHHHHHHHHHHHSSSHHHHHHHHHHHHHHHHHCCSTHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHTCCC
T ss_pred             CCcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCccchhHHHHHHHHHHHHhhhHHHHHHHHHHHHhcCCC
Confidence            4555554455555555543   3456667776666532223344455556677777777777777777765543

>3lpz_A GET4 (YOR164C homolog); protein targeting, tail-anchored protein biogenesis, GET PAT GET5 binding, protein transport; 1.98A {Chaetomium thermophilum}

Probab=84.78  E-value=19  Score=31.30  Aligned_cols=83  Identities=7%  Similarity=-0.008  Sum_probs=44.8

Q ss_pred             CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHH
Q 012111          359 PNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMI  438 (471)
Q Consensus       359 p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~  438 (471)
                      -|+.....+...|.+.+++.+|...|-  .  +-.+....|..++.-+...+...+              ++...-.++ 
T Consensus       134 Gdp~LH~~ig~~~~~e~~~~~Ae~H~i--l--g~~~s~~~~a~mL~ew~~~~~~~e--------------~dlfiaRaV-  194 (336)
T 3lpz_A          134 GDPELHHVVGTLYVEEGEFEAAEKHLV--L--GTKESPEVLARMEYEWYKQDESHT--------------APLYCARAV-  194 (336)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHT--T--SCTTHHHHHHHHHHHHHHTSCGGG--------------HHHHHHHHH-
T ss_pred             CCHHHHHHHHHHHHccCCHHHHHHHHH--h--cCCchHHHHHHHHHHHHHhcCCcc--------------HHHHHHHHH-
Confidence            366677777788888888877777662  1  222223455444443333322111              112222222 


Q ss_pred             HHHHhcCCHHHHHHHHHHHHHh
Q 012111          439 QAYNALGMTEAAQNLENKMIAM  460 (471)
Q Consensus       439 ~~~~~~g~~~~A~~~~~~m~~~  460 (471)
                      --|.-.++...|..+++...+.
T Consensus       195 L~yL~l~n~~~A~~~~~~f~~~  216 (336)
T 3lpz_A          195 LPYLLVANVRAANTAYRIFTSA  216 (336)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHhCCHHHHHHHHHHHHHH
Confidence            3456677888887777776653

>1zbp_A Hypothetical protein VPA1032; alpha-beta protein, structural genomics, PSI, protein struct initiative; 2.40A {Vibrio parahaemolyticus} SCOP: e.61.1.1

Probab=84.09  E-value=5.2  Score=33.44  Aligned_cols=120  Identities=8%  Similarity=0.053  Sum_probs=81.5

Q ss_pred             HHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCc--CHHHHHHHHHHHHhcCC
Q 012111          334 ETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVIL--DTPFFNCIISAYGQAGD  411 (471)
Q Consensus       334 ~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~--~~~~~~~l~~~~~~~g~  411 (471)
                      ....+.|++++++.....-++.. +-|...-..+++.+|-.|++++|.+-++...+.++..  ....|..+|.+      
T Consensus         5 ~~ll~~g~L~~al~~~~~~VR~~-P~da~~R~~LfqLLcv~G~w~RA~~QL~~~a~l~p~~~~~a~~yr~lI~a------   77 (273)
T 1zbp_A            5 KNALSEGQLQQALELLIEAIKAS-PKDASLRSSFIELLCIDGDFERADEQLMQSIKLFPEYLPGASQLRHLVKA------   77 (273)
T ss_dssp             HHHTTTTCHHHHHHHHHHHHHTC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHH------
T ss_pred             HHHHhCCCHHHHHHHHHHHHHhC-CcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCchhhHHHHHHHHHHHH------
Confidence            45678899999999999888874 5588888899999999999999999999988765431  12233333332      


Q ss_pred             HHHHHHHHHHHHhCCCCC-----CHHHHHHHHHHH--HhcCCHHHHHHHHHHHHHhhhcC
Q 012111          412 VEKMGELFLTMKERHCVP-----DNITFATMIQAY--NALGMTEAAQNLENKMIAMKENS  464 (471)
Q Consensus       412 ~~~a~~~~~~~~~~~~~p-----~~~~~~~l~~~~--~~~g~~~~A~~~~~~m~~~~~~~  464 (471)
                          +..=.+...-+-.|     ...-...++.++  ...|+.++|.++-..+.+..|..
T Consensus        78 ----E~~R~~vfaG~~~P~~~g~~~~w~~~ll~Al~~~~~G~~~~A~~lr~~A~e~ap~~  133 (273)
T 1zbp_A           78 ----AQARKDFAQGAATAKVLGENEELTKSLVSFNLSMVSQDYEQVSELALQIEELRQEK  133 (273)
T ss_dssp             ----HHHHHHHTTSCCCEECCCSCHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCCCC
T ss_pred             ----HHHHHHHHcCCCCCCCCCCCHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHhcCccc
Confidence                22112222222222     233344566655  45699999999999998886543

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	471
d1w3ba_	388	O-GlcNAc transferase p110 subunit, OGT {Human (Hom	99.94
d1w3ba_	388	O-GlcNAc transferase p110 subunit, OGT {Human (Hom	99.93
d1fcha_	323	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	99.69
d1fcha_	323	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	99.68
d2onda1	308	Cleavage stimulation factor 77 kDa subunit CSTF3 {	99.36
d1hz4a_	366	Transcription factor MalT domain III {Escherichia	99.32
d2h6fa1	315	Protein farnesyltransferase alpha-subunit {Human (	99.31
d2h6fa1	315	Protein farnesyltransferase alpha-subunit {Human (	99.31
d1hz4a_	366	Transcription factor MalT domain III {Escherichia	99.3
d2onda1	308	Cleavage stimulation factor 77 kDa subunit CSTF3 {	99.27
d1xnfa_	259	Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	99.16
d1dcea1	334	Rab geranylgeranyltransferase alpha-subunit, N-ter	99.14
d1dcea1	334	Rab geranylgeranyltransferase alpha-subunit, N-ter	99.12
d1xnfa_	259	Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	99.11
d1hh8a_	192	Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {H	98.77
d2c2la1	201	STIP1 homology and U box-containing protein 1, STU	98.74
d1qqea_	290	Vesicular transport protein sec17 {Baker's yeast (	98.73
d1elwa_	117	Hop {Human (Homo sapiens) [TaxId: 9606]}	98.68
d1qqea_	290	Vesicular transport protein sec17 {Baker's yeast (	98.65
d1hh8a_	192	Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {H	98.62
d1elwa_	117	Hop {Human (Homo sapiens) [TaxId: 9606]}	98.62
d1a17a_	159	Protein phosphatase 5 {Human (Homo sapiens) [TaxId	98.61
d1b89a_	336	Clathrin heavy chain proximal leg segment {Cow (Bo	98.59
d1a17a_	159	Protein phosphatase 5 {Human (Homo sapiens) [TaxId	98.58
d1nzna_	122	Mitochondria fission protein Fis1 {Human (Homo sap	98.54
d1ouva_	265	Cysteine rich protein C (HcpC) {Helicobacter pylor	98.48
d1ouva_	265	Cysteine rich protein C (HcpC) {Helicobacter pylor	98.47
d2c2la1	201	STIP1 homology and U box-containing protein 1, STU	98.46
d1nzna_	122	Mitochondria fission protein Fis1 {Human (Homo sap	98.41
d1hxia_	112	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	98.4
d1hxia_	112	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	98.4
d1b89a_	336	Clathrin heavy chain proximal leg segment {Cow (Bo	98.28
d1p5qa1	170	FKBP52 (FKBP4), C-terminal domain {Human (Homo sap	98.24
d1elra_	128	Hop {Human (Homo sapiens) [TaxId: 9606]}	98.22
d1p5qa1	170	FKBP52 (FKBP4), C-terminal domain {Human (Homo sap	98.15
d2fbna1	153	Putative 70 kda peptidylprolyl isomerase PFL2275c	98.11
d1elra_	128	Hop {Human (Homo sapiens) [TaxId: 9606]}	98.1
d1kt1a1	168	FKBP51, C-terminal domain {Monkey (Saimiri bolivie	98.07
d2fbna1	153	Putative 70 kda peptidylprolyl isomerase PFL2275c	98.05
d1zbpa1	264	Hypothetical protein VPA1032 {Vibrio parahaemolyti	98.0
d1ya0a1	497	SMG-7 {Human (Homo sapiens) [TaxId: 9606]}	97.98
d1ihga1	169	Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}	97.95
d2ff4a2	179	Probable regulatory protein EmbR, middle domain {M	97.94
d1kt1a1	168	FKBP51, C-terminal domain {Monkey (Saimiri bolivie	97.88
d1zbpa1	264	Hypothetical protein VPA1032 {Vibrio parahaemolyti	97.86
d1ihga1	169	Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}	97.86
d1ya0a1	497	SMG-7 {Human (Homo sapiens) [TaxId: 9606]}	97.84
d1zu2a1	145	Mitochondrial import receptor subunit tom20-3 {Tha	97.81
d2ff4a2	179	Probable regulatory protein EmbR, middle domain {M	97.77
d2hr2a1	156	Hypothetical protein CT2138 {Chlorobium tepidum [T	97.76
d1zu2a1	145	Mitochondrial import receptor subunit tom20-3 {Tha	97.66
d1tjca_	95	Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human	97.23
d2hr2a1	156	Hypothetical protein CT2138 {Chlorobium tepidum [T	97.19
d1tjca_	95	Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human	97.16
d1klxa_	133	Cysteine rich protein B (HcpB) {Helicobacter pylor	96.64
d1klxa_	133	Cysteine rich protein B (HcpB) {Helicobacter pylor	96.46
d1wy6a1	161	Hypothetical protein ST1625 {Archaeon Sulfolobus t	96.22
d1qsaa1	450	70 KDa soluble lytic transglycosylase (SLT70), sup	96.02
d2pqrb1	124	Mitochondria fission protein Fis1 {Baker's yeast (	95.69
d1wy6a1	161	Hypothetical protein ST1625 {Archaeon Sulfolobus t	95.59
d1v54e_	105	Cytochrome c oxidase subunit E {Cow (Bos taurus) [	94.16
d2pqrb1	124	Mitochondria fission protein Fis1 {Baker's yeast (	92.43
d1v54e_	105	Cytochrome c oxidase subunit E {Cow (Bos taurus) [	91.59
d1qsaa1	450	70 KDa soluble lytic transglycosylase (SLT70), sup	91.27

>d1w3ba_ a.118.8.1 (A:) O-GlcNAc transferase p110 subunit, OGT {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: O-GlcNAc transferase p110 subunit, OGT
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.94  E-value=1.5e-22  Score=184.90  Aligned_cols=368  Identities=11%  Similarity=0.096  Sum_probs=286.4

Q ss_pred             HHHHHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcC
Q 012111           84 ALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSG  163 (471)
Q Consensus        84 ~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~  163 (471)
                      ......+.|++++|++.|+.+.+..  |.+..++..+..++.+.|++++|...|+...+.... +..+|..+..+|...|
T Consensus         5 la~~~~~~G~~~~A~~~~~~~l~~~--p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~p~-~~~a~~~l~~~~~~~g   81 (388)
T d1w3ba_           5 LAHREYQAGDFEAAERHCMQLWRQE--PDNTGVLLLLSSIHFQCRRLDRSAHFSTLAIKQNPL-LAEAYSNLGNVYKERG   81 (388)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHhhhhc
Confidence            3455678999999999999998875  667888999999999999999999999999887533 6788999999999999


Q ss_pred             CHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHH
Q 012111          164 LLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSF  243 (471)
Q Consensus       164 ~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~a~~~~  243 (471)
                      ++++|+..+.......  +.+..............+....+........... .................+....+...+
T Consensus        82 ~~~~A~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~  158 (388)
T d1w3ba_          82 QLQEAIEHYRHALRLK--PDFIDGYINLAAALVAAGDMEGAVQAYVSALQYN-PDLYCVRSDLGNLLKALGRLEEAKACY  158 (388)
T ss_dssp             CHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHSCSSHHHHHHHHHHHHC-TTCTHHHHHHHHHHHTTSCHHHHHHHH
T ss_pred             cccccccccccccccc--cccccccccccccccccccccccccccccccccc-cccccccccccccccccchhhhhHHHH
Confidence            9999999999988732  3445555555555556666666666655555443 334445555666667778888888888


Q ss_pred             HHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCC
Q 012111          244 SAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFF  323 (471)
Q Consensus       244 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~  323 (471)
                      .......  +.+...+..+...+...|++++|...+++..... +-+...+..+...+...|++++|...+.........
T Consensus       159 ~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~  235 (388)
T d1w3ba_         159 LKAIETQ--PNFAVAWSNLGCVFNAQGEIWLAIHHFEKAVTLD-PNFLDAYINLGNVLKEARIFDRAVAAYLRALSLSPN  235 (388)
T ss_dssp             HHHHHHC--TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCTTHHHHHHHHHHHHCTT
T ss_pred             HHhhccC--cchhHHHHhhcccccccCcHHHHHHHHHHHHHhC-cccHHHHHHHhhhhhccccHHHHHHHHHHhHHHhhh
Confidence            7776653  4456777788888888899999998888887654 456677888888888889999998888888776433


Q ss_pred             CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHH
Q 012111          324 PTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCII  403 (471)
Q Consensus       324 ~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~  403 (471)
                       +...+..+...+...|++++|...|++..+.. +-+..++..+...+...|++++|.+.++......+. +...+..+.
T Consensus       236 -~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~l~  312 (388)
T d1w3ba_         236 -HAVVHGNLACVYYEQGLIDLAIDTYRRAIELQ-PHFPDAYCNLANALKEKGSVAEAEDCYNTALRLCPT-HADSLNNLA  312 (388)
T ss_dssp             -CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTC-SSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHCTT-CHHHHHHHH
T ss_pred             -HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHhhhccCCc-cchhhhHHH
Confidence             56677778888888899999999998888753 335678888888888889999999988888776544 777888888


Q ss_pred             HHHHhcCCHHHHHHHHHHHHhCCCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhhhcCC
Q 012111          404 SAYGQAGDVEKMGELFLTMKERHCVP-DNITFATMIQAYNALGMTEAAQNLENKMIAMKENSG  465 (471)
Q Consensus       404 ~~~~~~g~~~~a~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~~~  465 (471)
                      ..+...|++++|++.|++..+.  .| +..++..+..+|...|++++|.+.++++++..|+..
T Consensus       313 ~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~l~P~~~  373 (388)
T d1w3ba_         313 NIKREQGNIEEAVRLYRKALEV--FPEFAAAHSNLASVLQQQGKLQEALMHYKEAIRISPTFA  373 (388)
T ss_dssp             HHHHTTTCHHHHHHHHHHHTTS--CTTCHHHHHHHHHHHHTTTCCHHHHHHHHHHHTTCTTCH
T ss_pred             HHHHHCCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCH
Confidence            8888889999999999888774  44 466777888888889999999999998888877643

>d1w3ba_ a.118.8.1 (A:) O-GlcNAc transferase p110 subunit, OGT {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: O-GlcNAc transferase p110 subunit, OGT
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.93  E-value=6.2e-21  Score=174.05  Aligned_cols=381  Identities=10%  Similarity=-0.005  Sum_probs=313.2

Q ss_pred             HHHHHHHhhHHHHHHHHHhhhhhhccCCCchHHHHHHHHHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCC
Q 012111           49 KDLSKILRTEFAIKNIEKKVSSKKYKNLWPKPVLEALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCK  128 (471)
Q Consensus        49 ~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  128 (471)
                      ....+.+++..+.+.+++.+...|   ..+..+......+.+.|++++|++.|+.+.+..  |.+..++..+..++.+.|
T Consensus         7 ~~~~~~G~~~~A~~~~~~~l~~~p---~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~--p~~~~a~~~l~~~~~~~g   81 (388)
T d1w3ba_           7 HREYQAGDFEAAERHCMQLWRQEP---DNTGVLLLLSSIHFQCRRLDRSAHFSTLAIKQN--PLLAEAYSNLGNVYKERG   81 (388)
T ss_dssp             HHHHHHTCHHHHHHHHHHHHHHCT---TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHT
T ss_pred             HHHHHcCCHHHHHHHHHHHHHhCC---CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHhhhhc
Confidence            445667788888888888776543   345666777777889999999999999999875  667789999999999999


Q ss_pred             CHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHH
Q 012111          129 QPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKIL  208 (471)
Q Consensus       129 ~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~  208 (471)
                      ++++|...+......... +...+..........+....+..........  ..................+....+...+
T Consensus        82 ~~~~A~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~  158 (388)
T d1w3ba_          82 QLQEAIEHYRHALRLKPD-FIDGYINLAAALVAAGDMEGAVQAYVSALQY--NPDLYCVRSDLGNLLKALGRLEEAKACY  158 (388)
T ss_dssp             CHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHSCSSHHHHHHHHHHHH--CTTCTHHHHHHHHHHHTTSCHHHHHHHH
T ss_pred             cccccccccccccccccc-ccccccccccccccccccccccccccccccc--ccccccccccccccccccchhhhhHHHH
Confidence            999999999999887544 5555555555566666666665555555442  2344455555666677788888888888


Q ss_pred             HHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCC
Q 012111          209 AEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVK  288 (471)
Q Consensus       209 ~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~  288 (471)
                      ....... +-+...+..+...+...|++++|...+++..+..  +.+...+..+...+...|++++|...+.+....+ +
T Consensus       159 ~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~--p~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~  234 (388)
T d1w3ba_         159 LKAIETQ-PNFAVAWSNLGCVFNAQGEIWLAIHHFEKAVTLD--PNFLDAYINLGNVLKEARIFDRAVAAYLRALSLS-P  234 (388)
T ss_dssp             HHHHHHC-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHTTTCTTHHHHHHHHHHHHC-T
T ss_pred             HHhhccC-cchhHHHHhhcccccccCcHHHHHHHHHHHHHhC--cccHHHHHHHhhhhhccccHHHHHHHHHHhHHHh-h
Confidence            8877654 4467888889999999999999999999998864  4567789999999999999999999999988765 5


Q ss_pred             CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHH
Q 012111          289 ADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLV  368 (471)
Q Consensus       289 ~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li  368 (471)
                      .+...+..+...+.+.|++++|...|+...+.... +...+..+...+...|++++|...++...... +.+...+..+.
T Consensus       235 ~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~-~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~  312 (388)
T d1w3ba_         235 NHAVVHGNLACVYYEQGLIDLAIDTYRRAIELQPH-FPDAYCNLANALKEKGSVAEAEDCYNTALRLC-PTHADSLNNLA  312 (388)
T ss_dssp             TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTCSS-CHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHC-TTCHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHhhhccC-CccchhhhHHH
Confidence            67788888999999999999999999999886433 57788899999999999999999999988764 56788899999


Q ss_pred             HHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC-CHHHHHHHHHHHHhcCC
Q 012111          369 SAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVP-DNITFATMIQAYNALGM  446 (471)
Q Consensus       369 ~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~  446 (471)
                      ..+...|++++|...+++..+..+. +..++..+..+|...|++++|+..|++..+.  .| +...|..+..+|.+.||
T Consensus       313 ~~~~~~~~~~~A~~~~~~al~~~p~-~~~~~~~la~~~~~~g~~~~A~~~~~~al~l--~P~~~~a~~~lg~~~~~~~D  388 (388)
T d1w3ba_         313 NIKREQGNIEEAVRLYRKALEVFPE-FAAAHSNLASVLQQQGKLQEALMHYKEAIRI--SPTFADAYSNMGNTLKEMQD  388 (388)
T ss_dssp             HHHHTTTCHHHHHHHHHHHTTSCTT-CHHHHHHHHHHHHTTTCCHHHHHHHHHHHTT--CTTCHHHHHHHHHHHHHTCC
T ss_pred             HHHHHCCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCC
Confidence            9999999999999999999987665 7888999999999999999999999999874  56 57788899999988875

>d1fcha_ a.118.8.1 (A:) Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.69  E-value=1.9e-14  Score=127.24  Aligned_cols=249  Identities=8%  Similarity=-0.030  Sum_probs=161.0

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcC
Q 012111          191 LIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSG  270 (471)
Q Consensus       191 ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  270 (471)
                      ....+.+.|++++|...|+.+.+.. +-+..+|..+..++...|++++|...|.+..+..  +-+...+..+...+...|
T Consensus        25 ~g~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~--p~~~~~~~~la~~~~~~~  101 (323)
T d1fcha_          25 EGLRRLQEGDLPNAVLLFEAAVQQD-PKHMEAWQYLGTTQAENEQELLAISALRRCLELK--PDNQTALMALAVSFTNES  101 (323)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHSC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCChHHHHHHHHhhhccc--cccccccccccccccccc
Confidence            4555677788888888888887764 4457777778888888888888888888777653  445667777777788888


Q ss_pred             CHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHH
Q 012111          271 NIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFK  350 (471)
Q Consensus       271 ~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~  350 (471)
                      ++++|.+.++++....  |+.............                   ..+.......+..+...+.+.+|...+.
T Consensus       102 ~~~~A~~~~~~~~~~~--~~~~~~~~~~~~~~~-------------------~~~~~~~~~~~~~~~~~~~~~~a~~~~~  160 (323)
T d1fcha_         102 LQRQACEILRDWLRYT--PAYAHLVTPAEEGAG-------------------GAGLGPSKRILGSLLSDSLFLEVKELFL  160 (323)
T ss_dssp             CHHHHHHHHHHHHHTS--TTTGGGCC----------------------------------CTTHHHHHHHHHHHHHHHHH
T ss_pred             cccccccchhhHHHhc--cchHHHHHhhhhhhh-------------------hcccccchhhHHHHHHhhHHHHHHHHHH
Confidence            8888888887776532  221110000000000                   0000011111222334455666777777


Q ss_pred             HHHHcCC-CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC
Q 012111          351 KMKHRGM-KPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVP  429 (471)
Q Consensus       351 ~m~~~~~-~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p  429 (471)
                      +...... ..+..++..+...+...|++++|...++......+. +..+|..+..+|...|++++|++.|++..+.  .|
T Consensus       161 ~al~~~p~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~-~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~--~p  237 (323)
T d1fcha_         161 AAVRLDPTSIDPDVQCGLGVLFNLSGEYDKAVDCFTAALSVRPN-DYLLWNKLGATLANGNQSEEAVAAYRRALEL--QP  237 (323)
T ss_dssp             HHHHHSTTSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CT
T ss_pred             HHHHHhhcccccccchhhHHHHHHHHHHhhhhcccccccccccc-cccchhhhhhcccccccchhHHHHHHHHHHH--hh
Confidence            6665421 235666777777778888888888888887766554 6677777888888888888888888877764  34


Q ss_pred             -CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhhhcCCC
Q 012111          430 -DNITFATMIQAYNALGMTEAAQNLENKMIAMKENSGK  466 (471)
Q Consensus       430 -~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~~~~  466 (471)
                       +...|..+..+|.+.|++++|.+.|+++++..|+...
T Consensus       238 ~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~p~~~~  275 (323)
T d1fcha_         238 GYIRSRYNLGISCINLGAHREAVEHFLEALNMQRKSRG  275 (323)
T ss_dssp             TCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHTC--
T ss_pred             ccHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCcChh
Confidence             4666777778888888888888888888887776543

>d1fcha_ a.118.8.1 (A:) Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.68  E-value=5.6e-14  Score=124.10  Aligned_cols=247  Identities=13%  Similarity=0.021  Sum_probs=165.5

Q ss_pred             HHHHHHHHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHH
Q 012111           81 VLEALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYG  160 (471)
Q Consensus        81 ~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~  160 (471)
                      ....-..+.+.|++++|++.|+.+.+..  |.+..+|..+..++...|++++|...|++..+.... +...|..+..+|.
T Consensus        22 ~~~~g~~~~~~g~~~~A~~~~~~al~~~--P~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~p~-~~~~~~~la~~~~   98 (323)
T d1fcha_          22 PFEEGLRRLQEGDLPNAVLLFEAAVQQD--PKHMEAWQYLGTTQAENEQELLAISALRRCLELKPD-NQTALMALAVSFT   98 (323)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHSC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHcCChHHHHHHHHhhhccccc-ccccccccccccc
Confidence            3444555678999999999999998875  667888999999999999999999999998876533 6788888889999


Q ss_pred             hcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHH
Q 012111          161 QSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEME  240 (471)
Q Consensus       161 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~a~  240 (471)
                      ..|++++|.+.++.....   .|+.............                   ..+.......+..+...+.+.+|.
T Consensus        99 ~~~~~~~A~~~~~~~~~~---~~~~~~~~~~~~~~~~-------------------~~~~~~~~~~~~~~~~~~~~~~a~  156 (323)
T d1fcha_          99 NESLQRQACEILRDWLRY---TPAYAHLVTPAEEGAG-------------------GAGLGPSKRILGSLLSDSLFLEVK  156 (323)
T ss_dssp             HTTCHHHHHHHHHHHHHT---STTTGGGCC----------------------------------CTTHHHHHHHHHHHHH
T ss_pred             ccccccccccchhhHHHh---ccchHHHHHhhhhhhh-------------------hcccccchhhHHHHHHhhHHHHHH
Confidence            999999999999888763   2322111000000000                   000001111122233445566677


Q ss_pred             HHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhC
Q 012111          241 SSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKR  320 (471)
Q Consensus       241 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~  320 (471)
                      +.|.+..+......+...+..+...+...|++++|...+++..... +-+...+..+..+|...|++++|...|+...+.
T Consensus       157 ~~~~~al~~~p~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~  235 (323)
T d1fcha_         157 ELFLAAVRLDPTSIDPDVQCGLGVLFNLSGEYDKAVDCFTAALSVR-PNDYLLWNKLGATLANGNQSEEAVAAYRRALEL  235 (323)
T ss_dssp             HHHHHHHHHSTTSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhhcccccccchhhHHHHHHHHHHhhhhcccccccccc-cccccchhhhhhcccccccchhHHHHHHHHHHH
Confidence            7777766654344556667777777777888888888877776543 445666777777777777777777777777665


Q ss_pred             CCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 012111          321 FFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKH  354 (471)
Q Consensus       321 ~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  354 (471)
                      ... +...|..+..+|...|++++|+..|++.++
T Consensus       236 ~p~-~~~a~~~lg~~~~~~g~~~~A~~~~~~al~  268 (323)
T d1fcha_         236 QPG-YIRSRYNLGISCINLGAHREAVEHFLEALN  268 (323)
T ss_dssp             CTT-CHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             hhc-cHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            322 455677777777777777777777777665

>d2onda1 a.118.8.7 (A:242-549) Cleavage stimulation factor 77 kDa subunit CSTF3 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: HAT/Suf repeat
domain: Cleavage stimulation factor 77 kDa subunit CSTF3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.36  E-value=5.8e-10  Score=96.91  Aligned_cols=192  Identities=11%  Similarity=0.051  Sum_probs=128.6

Q ss_pred             CHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHH
Q 012111          271 NIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFK  350 (471)
Q Consensus       271 ~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~  350 (471)
                      ..++|..+|+...+...+.+...+...+......|+++.|..+|+.+.+.........|...+..+.+.|+.+.|.++|+
T Consensus        79 ~~~~a~~i~~ral~~~~p~~~~l~~~ya~~~~~~~~~~~a~~i~~~~l~~~~~~~~~~w~~~~~~~~~~~~~~~ar~i~~  158 (308)
T d2onda1          79 FSDEAANIYERAISTLLKKNMLLYFAYADYEESRMKYEKVHSIYNRLLAIEDIDPTLVYIQYMKFARRAEGIKSGRMIFK  158 (308)
T ss_dssp             HHHHHHHHHHHHHTTTTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSSSSCTHHHHHHHHHHHHHHHCHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHhcccHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHcCChHHHHHHHH
Confidence            34667777777765544555666677777777777888888888777765443334467777777777778888888887


Q ss_pred             HHHHcCCCCCHHHHHHHHHH-HHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCC-CC
Q 012111          351 KMKHRGMKPNSITYCSLVSA-YSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERH-CV  428 (471)
Q Consensus       351 ~m~~~~~~p~~~~~~~li~~-~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~-~~  428 (471)
                      ++...+ +.+...|...... +...|+.+.|..+|+.+.+..+. +...|...+..+...|+++.|..+|++..... ..
T Consensus       159 ~al~~~-~~~~~~~~~~a~~e~~~~~~~~~a~~i~e~~l~~~p~-~~~~w~~y~~~~~~~g~~~~aR~~fe~ai~~~~~~  236 (308)
T d2onda1         159 KAREDA-RTRHHVYVTAALMEYYCSKDKSVAFKIFELGLKKYGD-IPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLP  236 (308)
T ss_dssp             HHHTST-TCCTHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHTT-CHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSSSSC
T ss_pred             HHHHhC-CCcHHHHHHHHHHHHHhccCHHHHHHHHHHHHHhhhh-hHHHHHHHHHHHHHcCChHHHHHHHHHHHHhCCCC
Confidence            777654 2233344433332 33457778888888777765443 56777777777778888888888888776642 23


Q ss_pred             CC--HHHHHHHHHHHHhcCCHHHHHHHHHHHHHhhhcC
Q 012111          429 PD--NITFATMIQAYNALGMTEAAQNLENKMIAMKENS  464 (471)
Q Consensus       429 p~--~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~~  464 (471)
                      |+  ...|...+..-...|+.+.+..+.+++.+.-|..
T Consensus       237 ~~~~~~iw~~~~~fE~~~G~~~~~~~~~~r~~~~~~~~  274 (308)
T d2onda1         237 PEKSGEIWARFLAFESNIGDLASILKVEKRRFTAFREE  274 (308)
T ss_dssp             GGGCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHTTTT
T ss_pred             hHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCccc
Confidence            32  3467777776677788888888888777766543

>d1hz4a_ a.118.8.2 (A:) Transcription factor MalT domain III {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Transcription factor MalT domain III
domain: Transcription factor MalT domain III
species: Escherichia coli [TaxId: 562]

Probab=99.32  E-value=3e-09  Score=94.28  Aligned_cols=271  Identities=10%  Similarity=-0.009  Sum_probs=135.8

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCC---HHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCC-CCC----HHHHH
Q 012111          153 TALVSAYGQSGLLDEAFSTINDMKSVSDCKPD---VYTYSILIKSCTKFHRFDLIEKILAEMSYLGI-ECS----AVTYN  224 (471)
Q Consensus       153 ~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~---~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~-~~~----~~~~~  224 (471)
                      ......+...|++++|++++++.....+-.+.   ...+..+...+...|++++|...+++..+... .++    ...+.
T Consensus        16 ~lrA~~~~~~g~~~~A~~~~~~aL~~~~~~~~~~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~   95 (366)
T d1hz4a_          16 ALRAQVAINDGNPDEAERLAKLALEELPPGWFYSRIVATSVLGEVLHCKGELTRSLALMQQTEQMARQHDVWHYALWSLI   95 (366)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHTCCTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHhhCcCCCcHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhcchHHHHHHHH
Confidence            33445566777777777777776653211111   23455566667777777777777776654210 011    23344


Q ss_pred             HHHHHHHccCCHHHHHHHHHHHHHc---CCCC--CC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCC----CCCCHHHH
Q 012111          225 TIIDGYGKAKKFEEMESSFSAMVES---GGCH--PD-IFTLNSMISAYGNSGNIEKMEKWYNEFNLMG----VKADIQTL  294 (471)
Q Consensus       225 ~l~~~~~~~~~~~~a~~~~~~~~~~---~~~~--~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~----~~~~~~~~  294 (471)
                      .+...+...|++..+...+......   .+..  +. ...+..+...+...|+++.+...+.......    .......+
T Consensus        96 ~~~~~~~~~~~~~~a~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~  175 (366)
T d1hz4a_          96 QQSEILFAQGFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLWAWARLDEAEASARSGIEVLSSYQPQQQLQCL  175 (366)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTSCGGGGHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhHhcccchhhHHHHHHHHHHHHHHHhcchhhhHHHHHHHHHHhhhhhhhhHHHHH
Confidence            4555666667777777666655431   1011  11 1234445555666666666666666554321    11223344


Q ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHhC----CCCCC--HHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCC---CCHHHHH
Q 012111          295 NILTKSYGRAGMYDKMRSVMDFMQKR----FFFPT--VVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMK---PNSITYC  365 (471)
Q Consensus       295 ~~ll~~~~~~~~~~~a~~~~~~~~~~----~~~~~--~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~---p~~~~~~  365 (471)
                      ......+...++...+...+......    +..+.  ...+..+...+...|++++|...+.........   .....+.
T Consensus       176 ~~~~~~~~~~~~~~~a~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~  255 (366)
T d1hz4a_         176 AMLIQCSLARGDLDNARSQLNRLENLLGNGKYHSDWISNANKVRVIYWQMTGDKAAAANWLRHTAKPEFANNHFLQGQWR  255 (366)
T ss_dssp             HHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHSCCCCCTTCGGGHHHHH
T ss_pred             HHHHHHHHhhhhHHHHHHHHHHHHHHHHHhcccCchHHHHHHHHHHHHHhcccHHHHHHHHHHHHHhccccchHHHHHHH
Confidence            44455555566666666555544321    11110  112333444455556666666665554433211   1123344


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHh----CCCCcC-HHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 012111          366 SLVSAYSKAGLIMKVDSILRQVEN----SDVILD-TPFFNCIISAYGQAGDVEKMGELFLTMK  423 (471)
Q Consensus       366 ~li~~~~~~g~~~~a~~~~~~~~~----~~~~~~-~~~~~~l~~~~~~~g~~~~a~~~~~~~~  423 (471)
                      .+..++...|++++|...++.+..    .+..|+ ..++..+..+|...|++++|.+.+++..
T Consensus       256 ~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~Al  318 (366)
T d1hz4a_         256 NIARAQILLGEFEPAEIVLEELNENARSLRLMSDLNRNLLLLNQLYWQAGRKSDAQRVLLDAL  318 (366)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHHHhhcccChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            455555666666666666555432    122221 2344555555566666666666665554

>d2h6fa1 a.118.6.1 (A:55-369) Protein farnesyltransferase alpha-subunit {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Protein prenylyltransferase
family: Protein prenylyltransferase
domain: Protein farnesyltransferase alpha-subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.31  E-value=6.2e-10  Score=96.79  Aligned_cols=214  Identities=9%  Similarity=0.019  Sum_probs=135.3

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccC-CHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Q 012111          186 YTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAK-KFEEMESSFSAMVESGGCHPDIFTLNSMIS  264 (471)
Q Consensus       186 ~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~-~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~  264 (471)
                      ..++.+...+.+.+.+++|+++++.+++.. +-+...|+....++...| ++++|+..++...+..  +-+..+|..+..
T Consensus        44 ~a~~~~~~~~~~~e~~~~Al~~~~~ai~ln-P~~~~a~~~r~~~l~~l~~~~~eal~~~~~al~~~--p~~~~a~~~~~~  120 (315)
T d2h6fa1          44 DVYDYFRAVLQRDERSERAFKLTRDAIELN-AANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQ--PKNYQVWHHRRV  120 (315)
T ss_dssp             HHHHHHHHHHHHTCCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHC--TTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCchHHHHHHHHHHHHHC-CCChHHHHHHHHHHHHhCcCHHHHHHHHHHHHHHH--HhhhhHHHHHhH
Confidence            345556666667777788888887777764 445667777777776655 4777777777777663  456677777777


Q ss_pred             HHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCC---
Q 012111          265 AYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGH---  341 (471)
Q Consensus       265 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~---  341 (471)
                      .+.+.|++++|+..++++.+.. +.+...|..+...+...|++++|...++.+.+..+. +...|+.+...+.+.+.   
T Consensus       121 ~~~~l~~~~eAl~~~~kal~~d-p~n~~a~~~~~~~~~~~~~~~~Al~~~~~al~~~p~-n~~a~~~r~~~l~~~~~~~~  198 (315)
T d2h6fa1         121 LVEWLRDPSQELEFIADILNQD-AKNYHAWQHRQWVIQEFKLWDNELQYVDQLLKEDVR-NNSVWNQRYFVISNTTGYND  198 (315)
T ss_dssp             HHHHHTCCTTHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCSCS
T ss_pred             HHHhhccHHHHHHHHhhhhhhh-hcchHHHHHHHHHHHHHHhhHHHHHHHHHHHHHCCc-cHHHHHHHHHHHHHccccch
Confidence            7777777777777777777654 556777777777777777777777777777775433 55566665555555443   


Q ss_pred             ---HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCc-CHHHHHHHHHHH
Q 012111          342 ---IEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVIL-DTPFFNCIISAY  406 (471)
Q Consensus       342 ---~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~-~~~~~~~l~~~~  406 (471)
                         +++|++.+....... +-+...|..+...+.. ...+++.+.++...+..+.+ +...+..++..|
T Consensus       199 ~~~~~~ai~~~~~al~~~-P~~~~~~~~l~~ll~~-~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~y  265 (315)
T d2h6fa1         199 RAVLEREVQYTLEMIKLV-PHNESAWNYLKGILQD-RGLSKYPNLLNQLLDLQPSHSSPYLIAFLVDIY  265 (315)
T ss_dssp             HHHHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHTT-TCGGGCHHHHHHHHHHTTTCCCHHHHHHHHHHH
T ss_pred             hhhhHHhHHHHHHHHHhC-CCchHHHHHHHHHHHh-cChHHHHHHHHHHHHhCCCcCCHHHHHHHHHHH
Confidence               456666666666653 2245555555444333 33456666666655433322 233344444443

>d2h6fa1 a.118.6.1 (A:55-369) Protein farnesyltransferase alpha-subunit {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Protein prenylyltransferase
family: Protein prenylyltransferase
domain: Protein farnesyltransferase alpha-subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.31  E-value=1.6e-09  Score=94.22  Aligned_cols=216  Identities=6%  Similarity=-0.031  Sum_probs=169.2

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcC-CHHHHHHHHHHHHHCCCCCCHHHHHHHH
Q 012111          149 VDVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFH-RFDLIEKILAEMSYLGIECSAVTYNTII  227 (471)
Q Consensus       149 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~-~~~~a~~~~~~~~~~g~~~~~~~~~~l~  227 (471)
                      ...|+.+...+.+.+..++|+++++++.+..  +-+...|+....++...| ++++|+..++...+.. +-+..+|..+.
T Consensus        43 ~~a~~~~~~~~~~~e~~~~Al~~~~~ai~ln--P~~~~a~~~r~~~l~~l~~~~~eal~~~~~al~~~-p~~~~a~~~~~  119 (315)
T d2h6fa1          43 RDVYDYFRAVLQRDERSERAFKLTRDAIELN--AANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQ-PKNYQVWHHRR  119 (315)
T ss_dssp             HHHHHHHHHHHHHTCCCHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHC-TTCHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCchHHHHHHHHHHHHHC--CCChHHHHHHHHHHHHhCcCHHHHHHHHHHHHHHH-HhhhhHHHHHh
Confidence            4567778888889999999999999999842  456667888888888766 5899999999998775 55789999999


Q ss_pred             HHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCC-
Q 012111          228 DGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGM-  306 (471)
Q Consensus       228 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~-  306 (471)
                      ..+.+.|++++|++.++++.+..  +.+...|..+...+...|++++|+..++++.+.+ +.+...|+.+...+.+.+. 
T Consensus       120 ~~~~~l~~~~eAl~~~~kal~~d--p~n~~a~~~~~~~~~~~~~~~~Al~~~~~al~~~-p~n~~a~~~r~~~l~~~~~~  196 (315)
T d2h6fa1         120 VLVEWLRDPSQELEFIADILNQD--AKNYHAWQHRQWVIQEFKLWDNELQYVDQLLKED-VRNNSVWNQRYFVISNTTGY  196 (315)
T ss_dssp             HHHHHHTCCTTHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCS
T ss_pred             HHHHhhccHHHHHHHHhhhhhhh--hcchHHHHHHHHHHHHHHhhHHHHHHHHHHHHHC-CccHHHHHHHHHHHHHcccc
Confidence            99999999999999999998874  6678899999999999999999999999998875 5677788887777776665 


Q ss_pred             -----HHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHHH
Q 012111          307 -----YDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKP-NSITYCSLVSAYS  372 (471)
Q Consensus       307 -----~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~  372 (471)
                           +++|...+....+..+. +...|..+...+. ....+++.+.++...+....+ +...+..++..|.
T Consensus       197 ~~~~~~~~ai~~~~~al~~~P~-~~~~~~~l~~ll~-~~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~y~  266 (315)
T d2h6fa1         197 NDRAVLEREVQYTLEMIKLVPH-NESAWNYLKGILQ-DRGLSKYPNLLNQLLDLQPSHSSPYLIAFLVDIYE  266 (315)
T ss_dssp             CSHHHHHHHHHHHHHHHHHSTT-CHHHHHHHHHHHT-TTCGGGCHHHHHHHHHHTTTCCCHHHHHHHHHHHH
T ss_pred             chhhhhHHhHHHHHHHHHhCCC-chHHHHHHHHHHH-hcChHHHHHHHHHHHHhCCCcCCHHHHHHHHHHHH
Confidence                 57888888887776443 6777777665544 444677888888777653332 3555556665554

>d1hz4a_ a.118.8.2 (A:) Transcription factor MalT domain III {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Transcription factor MalT domain III
domain: Transcription factor MalT domain III
species: Escherichia coli [TaxId: 562]

Probab=99.30  E-value=1.3e-08  Score=90.09  Aligned_cols=276  Identities=10%  Similarity=0.025  Sum_probs=201.2

Q ss_pred             hhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCC----HHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCC----H
Q 012111          114 CQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPS----VDVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPD----V  185 (471)
Q Consensus       114 ~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~----~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~----~  185 (471)
                      ..........+...|++++|.+++++..+.....+    ..++..+..++...|++++|+..|++........++    .
T Consensus        12 ae~~~lrA~~~~~~g~~~~A~~~~~~aL~~~~~~~~~~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~   91 (366)
T d1hz4a_          12 AEFNALRAQVAINDGNPDEAERLAKLALEELPPGWFYSRIVATSVLGEVLHCKGELTRSLALMQQTEQMARQHDVWHYAL   91 (366)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHTCCTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCcCCCcHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhcchHHHH
Confidence            34555567778899999999999999887643322    346777888999999999999999987653211222    2


Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHH----CCCCCC---HHHHHHHHHHHHccCCHHHHHHHHHHHHHcCC---CCCC
Q 012111          186 YTYSILIKSCTKFHRFDLIEKILAEMSY----LGIECS---AVTYNTIIDGYGKAKKFEEMESSFSAMVESGG---CHPD  255 (471)
Q Consensus       186 ~~~~~ll~~~~~~~~~~~a~~~~~~~~~----~g~~~~---~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~---~~~~  255 (471)
                      ..+..+...+...|++..+...+.....    .+....   ...+..+...+...|+++.+...+........   ....
T Consensus        92 ~~~~~~~~~~~~~~~~~~a~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~  171 (366)
T d1hz4a_          92 WSLIQQSEILFAQGFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLWAWARLDEAEASARSGIEVLSSYQPQQQ  171 (366)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTSCGGGG
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhcccchhhHHHHHHHHHHHHHHHhcchhhhHHHHHHHHHHhhhhhhhhH
Confidence            3456666778889999999999987653    222221   23556677888999999999999998876431   1223


Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHhC--CCCCC----HHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCC---CH
Q 012111          256 IFTLNSMISAYGNSGNIEKMEKWYNEFNLM--GVKAD----IQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFP---TV  326 (471)
Q Consensus       256 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~--~~~~~----~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~---~~  326 (471)
                      ...+..+...+...++...+...+.+....  .....    ...+..+...+...|++++|...+..........   ..
T Consensus       172 ~~~~~~~~~~~~~~~~~~~a~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~  251 (366)
T d1hz4a_         172 LQCLAMLIQCSLARGDLDNARSQLNRLENLLGNGKYHSDWISNANKVRVIYWQMTGDKAAAANWLRHTAKPEFANNHFLQ  251 (366)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHSCCCCCTTCGGGH
T ss_pred             HHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHhcccCchHHHHHHHHHHHHHhcccHHHHHHHHHHHHHhccccchHHH
Confidence            456666777888999999999988876442  11221    2345666777889999999999998876653322   23


Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHHc----CCCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 012111          327 VTYNIVIETFGKAGHIEKMEEYFKKMKHR----GMKPN-SITYCSLVSAYSKAGLIMKVDSILRQVEN  389 (471)
Q Consensus       327 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~----~~~p~-~~~~~~li~~~~~~g~~~~a~~~~~~~~~  389 (471)
                      ..+..+...+...|++++|...++.....    +..|+ ..++..+...|...|++++|.+.+++..+
T Consensus       252 ~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~Al~  319 (366)
T d1hz4a_         252 GQWRNIARAQILLGEFEPAEIVLEELNENARSLRLMSDLNRNLLLLNQLYWQAGRKSDAQRVLLDALK  319 (366)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhhcccChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            45666788899999999999999987642    33343 45678888999999999999999988764

>d2onda1 a.118.8.7 (A:242-549) Cleavage stimulation factor 77 kDa subunit CSTF3 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: HAT/Suf repeat
domain: Cleavage stimulation factor 77 kDa subunit CSTF3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.27  E-value=2.8e-09  Score=92.51  Aligned_cols=220  Identities=10%  Similarity=-0.021  Sum_probs=116.0

Q ss_pred             HHHHHHHHHHhhhccCccCChhHHHHHHHHHhcC--------------CCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHH
Q 012111           94 WQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKC--------------KQPEQASLLFEVMLSDGLKPSVDVYTALVSAY  159 (471)
Q Consensus        94 ~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~--------------~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~  159 (471)
                      .+.+..+|+.+....  +.+...|...+..+...              +..++|..+|+...+...+.+...|...+...
T Consensus        32 ~~Rv~~vyerAl~~~--~~~~~lW~~y~~~~~~~~~~~~~~~~~~~~~~~~~~a~~i~~ral~~~~p~~~~l~~~ya~~~  109 (308)
T d2onda1          32 TKRVMFAYEQCLLVL--GHHPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANIYERAISTLLKKNMLLYFAYADYE  109 (308)
T ss_dssp             HHHHHHHHHHHHHHH--TTCHHHHHHHHHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHHHHTTTTTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHC--CCCHHHHHHHHHHHHHcCchHHHHHHHhhcccchHHHHHHHHHHHHHcCCCCHHHHHHHHHHH
Confidence            345666777777653  55556665555543222              23456666666666543344555666666666


Q ss_pred             HhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHH-HHccCCHHH
Q 012111          160 GQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDG-YGKAKKFEE  238 (471)
Q Consensus       160 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~-~~~~~~~~~  238 (471)
                      ...|+++.|..+|+++... ........|...+..+.+.|+.+.|.++|+.+.+.+ +.+...|...... +...|+.+.
T Consensus       110 ~~~~~~~~a~~i~~~~l~~-~~~~~~~~w~~~~~~~~~~~~~~~ar~i~~~al~~~-~~~~~~~~~~a~~e~~~~~~~~~  187 (308)
T d2onda1         110 ESRMKYEKVHSIYNRLLAI-EDIDPTLVYIQYMKFARRAEGIKSGRMIFKKAREDA-RTRHHVYVTAALMEYYCSKDKSV  187 (308)
T ss_dssp             HHTTCHHHHHHHHHHHHTS-SSSCTHHHHHHHHHHHHHHHCHHHHHHHHHHHHTST-TCCTHHHHHHHHHHHHTSCCHHH
T ss_pred             HhcccHHHHHHHHHHHHHH-hcCChHHHHHHHHHHHHHcCChHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHhccCHHH
Confidence            6666666666666666542 111123345666666666666666666666665543 2233333332222 223455666


Q ss_pred             HHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCC-CCC--CHHHHHHHHHHHHHcCCHHHHHHHHH
Q 012111          239 MESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMG-VKA--DIQTLNILTKSYGRAGMYDKMRSVMD  315 (471)
Q Consensus       239 a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-~~~--~~~~~~~ll~~~~~~~~~~~a~~~~~  315 (471)
                      |..+|+.+.+..  +.+...|...+..+.+.|+++.|..+|++..... ..|  ....|...+..-...|+.+.+..+++
T Consensus       188 a~~i~e~~l~~~--p~~~~~w~~y~~~~~~~g~~~~aR~~fe~ai~~~~~~~~~~~~iw~~~~~fE~~~G~~~~~~~~~~  265 (308)
T d2onda1         188 AFKIFELGLKKY--GDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSGEIWARFLAFESNIGDLASILKVEK  265 (308)
T ss_dssp             HHHHHHHHHHHH--TTCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSSSSCGGGCHHHHHHHHHHHHHHSCHHHHHHHHH
T ss_pred             HHHHHHHHHHhh--hhhHHHHHHHHHHHHHcCChHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence            666666665542  3344555555555556666666666666554432 122  12344444554445555555555555


Q ss_pred             HHHh
Q 012111          316 FMQK  319 (471)
Q Consensus       316 ~~~~  319 (471)
                      ++.+
T Consensus       266 r~~~  269 (308)
T d2onda1         266 RRFT  269 (308)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            4433

>d1xnfa_ a.118.8.1 (A:) Lipoprotein NlpI {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Lipoprotein NlpI
species: Escherichia coli [TaxId: 562]

Probab=99.16  E-value=1.2e-09  Score=92.24  Aligned_cols=151  Identities=13%  Similarity=-0.024  Sum_probs=88.4

Q ss_pred             cHHHHHHHHHHhhhccCcc--CChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHH
Q 012111           93 KWQLALKIFGLLRQQQWYQ--ARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAFS  170 (471)
Q Consensus        93 ~~~~A~~~~~~~~~~~~~~--~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~  170 (471)
                      +.+.|+.-++++.......  -...+|..+..+|.+.|++++|...|++.++.... ++.+|..+..++...|++++|+.
T Consensus        14 ~~e~al~~~~e~l~~~~~~~~~~a~~~~~~G~~y~~~g~~~~A~~~~~~al~l~p~-~~~a~~~lg~~~~~~g~~~~A~~   92 (259)
T d1xnfa_          14 QQEVILARMEQILASRALTDDERAQLLYERGVLYDSLGLRALARNDFSQALAIRPD-MPEVFNYLGIYLTQAGNFDAAYE   92 (259)
T ss_dssp             HHHHHHHHHHHHHTSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCC-CHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHhhccCCC-CHHHHhhhchHHHHHHHHHHhhh
Confidence            3444555555555432111  12345666677777777777777777777765433 56777777777777777777777


Q ss_pred             HHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHH
Q 012111          171 TINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMV  247 (471)
Q Consensus       171 ~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  247 (471)
                      .|++..+..  +-+..++..+..++...|+++.|...++...+.. +.+......+..++.+.+..+.+..+.....
T Consensus        93 ~~~~al~~~--p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  166 (259)
T d1xnfa_          93 AFDSVLELD--PTYNYAHLNRGIALYYGGRDKLAQDDLLAFYQDD-PNDPFRSLWLYLAEQKLDEKQAKEVLKQHFE  166 (259)
T ss_dssp             HHHHHHHHC--TTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHCHHHHHHHHHHHHH
T ss_pred             hhhHHHHHH--hhhhhhHHHHHHHHHHHhhHHHHHHHHHHHHhhc-cccHHHHHHHHHHHHHhhhHHHHHHHHHHhh
Confidence            777776632  2334556666666777777777777777766553 2344443334444444444444444444443

>d1dcea1 a.118.6.1 (A:1-241,A:351-443) Rab geranylgeranyltransferase alpha-subunit, N-terminal domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Protein prenylyltransferase
family: Protein prenylyltransferase
domain: Rab geranylgeranyltransferase alpha-subunit, N-terminal domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=99.14  E-value=3.8e-10  Score=99.43  Aligned_cols=275  Identities=6%  Similarity=-0.063  Sum_probs=177.4

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCC-HHHHHHHHHHHH---hc-------CCHHHHHHHHHHHHHCCCCCCH
Q 012111          152 YTALVSAYGQSGLLDEAFSTINDMKSVSDCKPD-VYTYSILIKSCT---KF-------HRFDLIEKILAEMSYLGIECSA  220 (471)
Q Consensus       152 ~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~-~~~~~~ll~~~~---~~-------~~~~~a~~~~~~~~~~g~~~~~  220 (471)
                      +..++......+..++|++++++..+.   .|+ ...|+..-..+.   ..       |.+++|+.+++...+.. +-+.
T Consensus        32 ~~~~~~~~~~~~~~~~al~~~~~~l~~---~P~~~~a~~~r~~~l~~l~~~~~~~~~~~~~~~al~~~~~~l~~~-pk~~  107 (334)
T d1dcea1          32 TQAVFQKRQAGELDESVLELTSQILGA---NPDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVN-PKSY  107 (334)
T ss_dssp             HHHHHHHHHTTCCSHHHHHHHHHHHHH---CTTCHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHC-TTCH
T ss_pred             HHHHHHHHhcccccHHHHHHHHHHHHH---CCCcHHHHHHHHHHHHHHhhhcchHHHHHHHHHHHHHHHHHHHhC-CCcH
Confidence            333444333444458899999888763   344 344544433333   32       23667888888877664 4467


Q ss_pred             HHHHHHHHHHHccC--CHHHHHHHHHHHHHcCCCCCCHHHHHH-HHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHH
Q 012111          221 VTYNTIIDGYGKAK--KFEEMESSFSAMVESGGCHPDIFTLNS-MISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNIL  297 (471)
Q Consensus       221 ~~~~~l~~~~~~~~--~~~~a~~~~~~~~~~~~~~~~~~~~~~-l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  297 (471)
                      ..|..+..++...+  ++++|...+..+.+..  +++...+.. ....+...+.++.|+..++.+...+ +-+...|..+
T Consensus       108 ~~~~~~~~~~~~~~~~~~~~a~~~~~~al~~~--~~~~~~~~~~~~~~~~~~~~~~~Al~~~~~~i~~~-p~~~~a~~~l  184 (334)
T d1dcea1         108 GTWHHRCWLLSRLPEPNWARELELCARFLEAD--ERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRN-FSNYSSWHYR  184 (334)
T ss_dssp             HHHHHHHHHHHTCSSCCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTCCCHHHHHHHHHTTTTTT-CCCHHHHHHH
T ss_pred             HHHHHhhHHHHHhccccHHHHHHHHHHHHhhC--chhhhhhhhHHHHHHHhccccHHHHHHHHHHHHcC-CCCHHHHHHH
Confidence            77777766666654  4788888888887763  445555543 4456667788888888888887765 5677788888


Q ss_pred             HHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCH
Q 012111          298 TKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLI  377 (471)
Q Consensus       298 l~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~  377 (471)
                      ..++.+.|++++|...+....+.    ... ...+...+...+..+++...+....... +++...+..+...+...|+.
T Consensus       185 ~~~~~~~~~~~~A~~~~~~~~~~----~~~-~~~~~~~~~~l~~~~~a~~~~~~~l~~~-~~~~~~~~~l~~~~~~~~~~  258 (334)
T d1dcea1         185 SCLLPQLHPQPDSGPQGRLPENV----LLK-ELELVQNAFFTDPNDQSAWFYHRWLLGR-AEPLFRCELSVEKSTVLQSE  258 (334)
T ss_dssp             HHHHHHHSCCCCSSSCCSSCHHH----HHH-HHHHHHHHHHHCSSCSHHHHHHHHHHSC-CCCSSSCCCCHHHHHHHHHH
T ss_pred             HHHHHHhcCHHHHHHHHHHhHHh----HHH-HHHHHHHHHHhcchhHHHHHHHHHHHhC-cchhhHHHHHHHHHHHHhhH
Confidence            88888888888776665544432    111 1223334455566667777777766653 33445566667777777888


Q ss_pred             HHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCC-HHHHHHHHHHHH
Q 012111          378 MKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPD-NITFATMIQAYN  442 (471)
Q Consensus       378 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~-~~~~~~l~~~~~  442 (471)
                      ++|...+.+..+.++. +..++..+..++...|++++|++.+++..+.  .|+ ...|..|...+.
T Consensus       259 ~~a~~~~~~~~~~~p~-~~~~~~~l~~~~~~~~~~~eA~~~~~~ai~l--dP~~~~y~~~L~~~~~  321 (334)
T d1dcea1         259 LESCKELQELEPENKW-CLLTIILLMRALDPLLYEKETLQYFSTLKAV--DPMRAAYLDDLRSKFL  321 (334)
T ss_dssp             HHHHHHHHHHCTTCHH-HHHHHHHHHHHHCTGGGHHHHHHHHHHHHHH--CGGGHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhCch-HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH--CcccHHHHHHHHHHHh
Confidence            8888888877776544 5667777788888888888888888888773  564 344444544443

>d1dcea1 a.118.6.1 (A:1-241,A:351-443) Rab geranylgeranyltransferase alpha-subunit, N-terminal domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Protein prenylyltransferase
family: Protein prenylyltransferase
domain: Rab geranylgeranyltransferase alpha-subunit, N-terminal domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=99.12  E-value=8.9e-10  Score=97.03  Aligned_cols=277  Identities=7%  Similarity=-0.073  Sum_probs=181.2

Q ss_pred             HHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHH---hcC-------CHHHHHHHHHHhhcCCCCCCCHH
Q 012111          117 FTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYG---QSG-------LLDEAFSTINDMKSVSDCKPDVY  186 (471)
Q Consensus       117 ~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~---~~~-------~~~~a~~~~~~~~~~~~~~~~~~  186 (471)
                      ...++......+..++|..+++...+..+. +...|+..-..+.   ..+       ++++|+.+++...+.  .+-+..
T Consensus        32 ~~~~~~~~~~~~~~~~al~~~~~~l~~~P~-~~~a~~~r~~~l~~l~~~~~~~~~~~~~~~al~~~~~~l~~--~pk~~~  108 (334)
T d1dcea1          32 TQAVFQKRQAGELDESVLELTSQILGANPD-FATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRV--NPKSYG  108 (334)
T ss_dssp             HHHHHHHHHTTCCSHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHH--CTTCHH
T ss_pred             HHHHHHHHhcccccHHHHHHHHHHHHHCCC-cHHHHHHHHHHHHHHhhhcchHHHHHHHHHHHHHHHHHHHh--CCCcHH
Confidence            344444444445568888888888876433 4556655444333   322       367788888887762  244666


Q ss_pred             HHHHHHHHHHhcC--CHHHHHHHHHHHHHCCCCCCHHHHH-HHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHH
Q 012111          187 TYSILIKSCTKFH--RFDLIEKILAEMSYLGIECSAVTYN-TIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMI  263 (471)
Q Consensus       187 ~~~~ll~~~~~~~--~~~~a~~~~~~~~~~g~~~~~~~~~-~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~  263 (471)
                      .|..+..++...+  +++++...+..+.+.. +.+...+. .....+...+.+++|+..++.+.+..  +-+...|..+.
T Consensus       109 ~~~~~~~~~~~~~~~~~~~a~~~~~~al~~~-~~~~~~~~~~~~~~~~~~~~~~~Al~~~~~~i~~~--p~~~~a~~~l~  185 (334)
T d1dcea1         109 TWHHRCWLLSRLPEPNWARELELCARFLEAD-ERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRN--FSNYSSWHYRS  185 (334)
T ss_dssp             HHHHHHHHHHTCSSCCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTCCCHHHHHHHHHTTTTTT--CCCHHHHHHHH
T ss_pred             HHHHhhHHHHHhccccHHHHHHHHHHHHhhC-chhhhhhhhHHHHHHHhccccHHHHHHHHHHHHcC--CCCHHHHHHHH
Confidence            6766666666554  4788888888887764 34555544 44466677888888888888887764  45677888888


Q ss_pred             HHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHH
Q 012111          264 SAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIE  343 (471)
Q Consensus       264 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~  343 (471)
                      .++.+.|++++|...+......  .|   ....+...+...+..+++...+........ ++...+..+...+...|+.+
T Consensus       186 ~~~~~~~~~~~A~~~~~~~~~~--~~---~~~~~~~~~~~l~~~~~a~~~~~~~l~~~~-~~~~~~~~l~~~~~~~~~~~  259 (334)
T d1dcea1         186 CLLPQLHPQPDSGPQGRLPENV--LL---KELELVQNAFFTDPNDQSAWFYHRWLLGRA-EPLFRCELSVEKSTVLQSEL  259 (334)
T ss_dssp             HHHHHHSCCCCSSSCCSSCHHH--HH---HHHHHHHHHHHHCSSCSHHHHHHHHHHSCC-CCSSSCCCCHHHHHHHHHHH
T ss_pred             HHHHHhcCHHHHHHHHHHhHHh--HH---HHHHHHHHHHHhcchhHHHHHHHHHHHhCc-chhhHHHHHHHHHHHHhhHH
Confidence            8888888888776655543321  11   112233445566777777777777666533 24445556667777778888


Q ss_pred             HHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHH
Q 012111          344 KMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYG  407 (471)
Q Consensus       344 ~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  407 (471)
                      +|...+.+..... +-+..++..+..++...|+.++|.+.++.+.+.++. +...|+.|...+.
T Consensus       260 ~a~~~~~~~~~~~-p~~~~~~~~l~~~~~~~~~~~eA~~~~~~ai~ldP~-~~~y~~~L~~~~~  321 (334)
T d1dcea1         260 ESCKELQELEPEN-KWCLLTIILLMRALDPLLYEKETLQYFSTLKAVDPM-RAAYLDDLRSKFL  321 (334)
T ss_dssp             HHHHHHHHHCTTC-HHHHHHHHHHHHHHCTGGGHHHHHHHHHHHHHHCGG-GHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhC-chHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCcc-cHHHHHHHHHHHh
Confidence            8888888776642 224566777888888888889999988888887543 4556666655554

>d1xnfa_ a.118.8.1 (A:) Lipoprotein NlpI {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Lipoprotein NlpI
species: Escherichia coli [TaxId: 562]

Probab=99.11  E-value=3.9e-09  Score=89.07  Aligned_cols=96  Identities=7%  Similarity=-0.130  Sum_probs=49.2

Q ss_pred             HHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHH
Q 012111          222 TYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSY  301 (471)
Q Consensus       222 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~  301 (471)
                      +|..+..+|.+.|++++|.+.|++..+..  +.+..+|..+..++...|++++|+..|+++.+.. +.+..++..+..++
T Consensus        39 ~~~~~G~~y~~~g~~~~A~~~~~~al~l~--p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~  115 (259)
T d1xnfa_          39 LLYERGVLYDSLGLRALARNDFSQALAIR--PDMPEVFNYLGIYLTQAGNFDAAYEAFDSVLELD-PTYNYAHLNRGIAL  115 (259)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC--CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCTHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHhhccC--CCCHHHHhhhchHHHHHHHHHHhhhhhhHHHHHH-hhhhhhHHHHHHHH
Confidence            34444455555555555555555555442  3344455555555555555555555555554432 23344455555555


Q ss_pred             HHcCCHHHHHHHHHHHHhC
Q 012111          302 GRAGMYDKMRSVMDFMQKR  320 (471)
Q Consensus       302 ~~~~~~~~a~~~~~~~~~~  320 (471)
                      ...|++++|...|+...+.
T Consensus       116 ~~~g~~~~A~~~~~~al~~  134 (259)
T d1xnfa_         116 YYGGRDKLAQDDLLAFYQD  134 (259)
T ss_dssp             HHTTCHHHHHHHHHHHHHH
T ss_pred             HHHhhHHHHHHHHHHHHhh
Confidence            5555555555555555443

>d1hh8a_ a.118.8.1 (A:) Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Neutrophil cytosolic factor 2 (NCF-2, p67-phox)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.77  E-value=1.8e-07  Score=74.18  Aligned_cols=123  Identities=11%  Similarity=-0.016  Sum_probs=78.0

Q ss_pred             HHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCH
Q 012111          298 TKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLI  377 (471)
Q Consensus       298 l~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~  377 (471)
                      ...+...|+++.|.+.|..+.    .|+..+|..+..+|...|++++|++.|++.++.. +-+...|..+..++.+.|++
T Consensus        12 g~~~~~~~d~~~Al~~~~~i~----~~~~~~~~nlG~~~~~~g~~~~A~~~~~kAl~ld-p~~~~a~~~~g~~~~~~g~~   86 (192)
T d1hh8a_          12 GVLAADKKDWKGALDAFSAVQ----DPHSRICFNIGCMYTILKNMTEAEKAFTRSINRD-KHLAVAYFQRGMLYYQTEKY   86 (192)
T ss_dssp             HHHHHHTTCHHHHHHHHHTSS----SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHCCCHHHHHHHHHhcC----CCCHHHHHHHHHHHHHcCCchhHHHHHHHHHHHh-hhhhhhHHHHHHHHHhhccH
Confidence            344566677777777776542    3456666677777777777777777777777653 33566677777777777777


Q ss_pred             HHHHHHHHHHHhCCCCc---------------CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhC
Q 012111          378 MKVDSILRQVENSDVIL---------------DTPFFNCIISAYGQAGDVEKMGELFLTMKER  425 (471)
Q Consensus       378 ~~a~~~~~~~~~~~~~~---------------~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~  425 (471)
                      ++|...|++........               ...++..+..++.+.|++++|.+.+......
T Consensus        87 ~~A~~~~~kAl~~~~~n~~~~~~~~~~~~~~~~~e~~~n~a~~~~~~~~~~~A~~~l~~A~~~  149 (192)
T d1hh8a_          87 DLAIKDLKEALIQLRGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATSM  149 (192)
T ss_dssp             HHHHHHHHHHHHTTTTCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHhCccCchHHHHHhhhhcccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc
Confidence            77777777765432110               0133445566666777777777777666653

>d2c2la1 a.118.8.1 (A:24-224) STIP1 homology and U box-containing protein 1, STUB1 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: STIP1 homology and U box-containing protein 1, STUB1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.74  E-value=1.9e-07  Score=74.90  Aligned_cols=99  Identities=7%  Similarity=-0.063  Sum_probs=54.3

Q ss_pred             CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHH
Q 012111          324 PTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCII  403 (471)
Q Consensus       324 ~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~  403 (471)
                      |+...+......+.+.|++++|+..|.+.+... +-+...|..+..+|.+.|++++|...|+.+.+.++. +..+|..+.
T Consensus         2 ~~a~~l~~~Gn~~~~~g~~~~Ai~~~~kal~~~-p~~~~~~~~lg~~y~~~~~~~~Ai~~~~~al~l~p~-~~~a~~~lg   79 (201)
T d2c2la1           2 PSAQELKEQGNRLFVGRKYPEAAACYGRAITRN-PLVAVYYTNRALCYLKMQQPEQALADCRRALELDGQ-SVKAHFFLG   79 (201)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSCTT-CHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHhHHHHHhhhhhhhhhhHHHHHHHHhCCC-cHHHHHHHH
Confidence            344444445555555666666666665555542 224555555555555666666666666555554433 455555555


Q ss_pred             HHHHhcCCHHHHHHHHHHHHh
Q 012111          404 SAYGQAGDVEKMGELFLTMKE  424 (471)
Q Consensus       404 ~~~~~~g~~~~a~~~~~~~~~  424 (471)
                      .+|...|++++|+..|+++.+
T Consensus        80 ~~~~~l~~~~~A~~~~~~al~  100 (201)
T d2c2la1          80 QCQLEMESYDEAIANLQRAYS  100 (201)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHCCCHHHHHHHHHHHHH
Confidence            555555666666555555543

>d1qqea_ a.118.8.1 (A:) Vesicular transport protein sec17 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Vesicular transport protein sec17
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.73  E-value=2.3e-07  Score=79.24  Aligned_cols=132  Identities=9%  Similarity=-0.039  Sum_probs=59.4

Q ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHhCC----C-CCCHHHHHHHHHHHHh-cCCHHHHHHHHHHHHHc----CCCC-CH
Q 012111          293 TLNILTKSYGRAGMYDKMRSVMDFMQKRF----F-FPTVVTYNIVIETFGK-AGHIEKMEEYFKKMKHR----GMKP-NS  361 (471)
Q Consensus       293 ~~~~ll~~~~~~~~~~~a~~~~~~~~~~~----~-~~~~~~~~~li~~~~~-~g~~~~a~~~~~~m~~~----~~~p-~~  361 (471)
                      +|..+..+|.+.|++++|...++...+..    . .....++..+...|.. .|++++|...+++..+.    +..+ ..
T Consensus        79 ~~~~~g~~y~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~A~~l~~~~~~~~~~~  158 (290)
T d1qqea_          79 TYVEAYKCFKSGGNSVNAVDSLENAIQIFTHRGQFRRGANFKFELGEILENDLHDYAKAIDCYELAGEWYAQDQSVALSN  158 (290)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHHHHHHhCCcHHHHHHHHHhhHHhhhcccchhHHHHHHHHHHhHhhHHHHHHHHHHHHHHHHHHHHhcCchhhhh
Confidence            34444444445555555544444332210    0 0011233333334432 35666666666554321    1111 12


Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCH------HHHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 012111          362 ITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDT------PFFNCIISAYGQAGDVEKMGELFLTMKE  424 (471)
Q Consensus       362 ~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~------~~~~~l~~~~~~~g~~~~a~~~~~~~~~  424 (471)
                      .++..+...+...|++++|.+.++++.........      ..+...+..+...|+++.|.+.++++.+
T Consensus       159 ~~~~~la~~~~~~g~y~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~d~~~A~~~~~~~~~  227 (290)
T d1qqea_         159 KCFIKCADLKALDGQYIEASDIYSKLIKSSMGNRLSQWSLKDYFLKKGLCQLAATDAVAAARTLQEGQS  227 (290)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHTTSSCTTTGGGHHHHHHHHHHHHHHTTCHHHHHHHHHGGGC
T ss_pred             hHHHHHHHHHHHcChHHHHHHHHHHHHHhCccchhhhhhHHHHHHHHHHHHHHhccHHHHHHHHHHHHH
Confidence            33455556666666666666666665543222111      1122333344555666666666666554

>d1elwa_ a.118.8.1 (A:) Hop {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Hop
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.68  E-value=2.4e-07  Score=66.77  Aligned_cols=91  Identities=12%  Similarity=0.007  Sum_probs=57.5

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCC
Q 012111          332 VIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGD  411 (471)
Q Consensus       332 li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~  411 (471)
                      -...+...|++++|+.+|.+.++.. +-+...|..+..++...|++++|+..+....+.++. +...|..+..++...|+
T Consensus         9 ~g~~~~~~g~~~eAi~~~~~al~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~p~-~~~~~~~~g~~~~~~~~   86 (117)
T d1elwa_           9 KGNKALSVGNIDDALQCYSEAIKLD-PHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLKPD-WGKGYSRKAAALEFLNR   86 (117)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHhcC-CcchhhhhcccccccccccccccchhhhhHHHhccc-hhhHHHHHHHHHHHccC
Confidence            3445566666666666666666553 335556666666666666666666666666665554 56666666666666666


Q ss_pred             HHHHHHHHHHHHh
Q 012111          412 VEKMGELFLTMKE  424 (471)
Q Consensus       412 ~~~a~~~~~~~~~  424 (471)
                      +++|+..|++..+
T Consensus        87 ~~~A~~~~~~a~~   99 (117)
T d1elwa_          87 FEEAKRTYEEGLK   99 (117)
T ss_dssp             HHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHH
Confidence            6666666666665

>d1qqea_ a.118.8.1 (A:) Vesicular transport protein sec17 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Vesicular transport protein sec17
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.65  E-value=1.8e-06  Score=73.47  Aligned_cols=198  Identities=12%  Similarity=0.071  Sum_probs=127.8

Q ss_pred             HHHHHccCCHHHHHHHHHHHHHcC---CCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhC----CC-CCCHHHHHHH
Q 012111          227 IDGYGKAKKFEEMESSFSAMVESG---GCHP-DIFTLNSMISAYGNSGNIEKMEKWYNEFNLM----GV-KADIQTLNIL  297 (471)
Q Consensus       227 ~~~~~~~~~~~~a~~~~~~~~~~~---~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~-~~~~~~~~~l  297 (471)
                      ...|...|++++|.+.|.+..+..   +..+ ...+|..+..+|.+.|++++|...+++....    +. .....++..+
T Consensus        44 a~~y~~~~~~~~A~~~y~kA~~~~~~~~~~~~~a~~~~~~g~~y~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l  123 (290)
T d1qqea_          44 ATIYRLRKELNLAGDSFLKAADYQKKAGNEDEAGNTYVEAYKCFKSGGNSVNAVDSLENAIQIFTHRGQFRRGANFKFEL  123 (290)
T ss_dssp             HHHHHHTTCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHCcCHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCCcHHHHHHHHHhhHHhhhcccchhHHHHHHHH
Confidence            456777788888888887765421   1111 2356777888888888888888888876442    10 1113445566


Q ss_pred             HHHHHH-cCCHHHHHHHHHHHHhC----CCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCC-----CH-HHHH
Q 012111          298 TKSYGR-AGMYDKMRSVMDFMQKR----FFFP-TVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKP-----NS-ITYC  365 (471)
Q Consensus       298 l~~~~~-~~~~~~a~~~~~~~~~~----~~~~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p-----~~-~~~~  365 (471)
                      ...|.. .|++++|...+....+.    +..+ -..++..+...+...|++++|..+|++........     .. ..+.
T Consensus       124 ~~~~~~~~~~~~~A~~~~~~A~~l~~~~~~~~~~~~~~~~la~~~~~~g~y~~A~~~~~~~~~~~~~~~~~~~~~~~~~~  203 (290)
T d1qqea_         124 GEILENDLHDYAKAIDCYELAGEWYAQDQSVALSNKCFIKCADLKALDGQYIEASDIYSKLIKSSMGNRLSQWSLKDYFL  203 (290)
T ss_dssp             HHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTSSCTTTGGGHHHHHH
T ss_pred             HHhHhhHHHHHHHHHHHHHHHHHHHHhcCchhhhhhHHHHHHHHHHHcChHHHHHHHHHHHHHhCccchhhhhhHHHHHH
Confidence            666644 58899999888776532    1111 13357778889999999999999999987753211     11 2334


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHhCCCCc-C---HHHHHHHHHHHHh--cCCHHHHHHHHHHHHh
Q 012111          366 SLVSAYSKAGLIMKVDSILRQVENSDVIL-D---TPFFNCIISAYGQ--AGDVEKMGELFLTMKE  424 (471)
Q Consensus       366 ~li~~~~~~g~~~~a~~~~~~~~~~~~~~-~---~~~~~~l~~~~~~--~g~~~~a~~~~~~~~~  424 (471)
                      ..+..+...|+++.|.+.+++..+..+.. +   ......++.++..  .+.+++|+..|+.+.+
T Consensus       204 ~~~~~~l~~~d~~~A~~~~~~~~~~~~~~~~sre~~~l~~l~~a~~~~d~e~~~eai~~y~~~~~  268 (290)
T d1qqea_         204 KKGLCQLAATDAVAAARTLQEGQSEDPNFADSRESNFLKSLIDAVNEGDSEQLSEHCKEFDNFMR  268 (290)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHGGGCC---------HHHHHHHHHHHHTTCTTTHHHHHHHHTTSSC
T ss_pred             HHHHHHHHhccHHHHHHHHHHHHHhCCCccchHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHhh
Confidence            55556778899999999999988764321 1   2345666666654  3458888888876553

>d1hh8a_ a.118.8.1 (A:) Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Neutrophil cytosolic factor 2 (NCF-2, p67-phox)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.62  E-value=2.4e-06  Score=67.52  Aligned_cols=27  Identities=15%  Similarity=0.076  Sum_probs=14.5

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 012111          329 YNIVIETFGKAGHIEKMEEYFKKMKHR  355 (471)
Q Consensus       329 ~~~li~~~~~~g~~~~a~~~~~~m~~~  355 (471)
                      +..+..++.+.|++++|.+.+......
T Consensus       123 ~~n~a~~~~~~~~~~~A~~~l~~A~~~  149 (192)
T d1hh8a_         123 LYNIAFMYAKKEEWKKAEEQLALATSM  149 (192)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHhc
Confidence            334444555566666666655555543

>d1elwa_ a.118.8.1 (A:) Hop {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Hop
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.62  E-value=9.9e-07  Score=63.42  Aligned_cols=92  Identities=11%  Similarity=-0.069  Sum_probs=79.2

Q ss_pred             HHHHHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcC
Q 012111           84 ALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSG  163 (471)
Q Consensus        84 ~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~  163 (471)
                      .-..+.+.|++++|+..|+.+.+..  |.+...|..+..++...|++++|+..++...+.+.. +...|..+..++...|
T Consensus         9 ~g~~~~~~g~~~eAi~~~~~al~~~--p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~p~-~~~~~~~~g~~~~~~~   85 (117)
T d1elwa_           9 KGNKALSVGNIDDALQCYSEAIKLD--PHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLKPD-WGKGYSRKAAALEFLN   85 (117)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHhcC--CcchhhhhcccccccccccccccchhhhhHHHhccc-hhhHHHHHHHHHHHcc
Confidence            3456678899999999999998875  777888999999999999999999999999887544 7888999999999999


Q ss_pred             CHHHHHHHHHHhhcC
Q 012111          164 LLDEAFSTINDMKSV  178 (471)
Q Consensus       164 ~~~~a~~~~~~~~~~  178 (471)
                      ++++|+..|++..+.
T Consensus        86 ~~~~A~~~~~~a~~~  100 (117)
T d1elwa_          86 RFEEAKRTYEEGLKH  100 (117)
T ss_dssp             CHHHHHHHHHHHHTT
T ss_pred             CHHHHHHHHHHHHHh
Confidence            999999999998873

>d1a17a_ a.118.8.1 (A:) Protein phosphatase 5 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Protein phosphatase 5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.61  E-value=5.7e-07  Score=68.95  Aligned_cols=90  Identities=11%  Similarity=0.049  Sum_probs=76.4

Q ss_pred             HHHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCH
Q 012111           86 DEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLL  165 (471)
Q Consensus        86 ~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~  165 (471)
                      ..+.+.|++++|+..|+.+.+.+  |.+...|..+..++...|++++|...|+..++.... +..+|..+..++...|++
T Consensus        18 n~~~~~~~y~~A~~~~~~al~~~--p~~~~~~~~lg~~~~~~~~~~~A~~~~~kal~~~p~-~~~a~~~~g~~~~~~g~~   94 (159)
T d1a17a_          18 NDYFKAKDYENAIKFYSQAIELN--PSNAIYYGNRSLAYLRTECYGYALGDATRAIELDKK-YIKGYYRRAASNMALGKF   94 (159)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHS--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHcCCHHHHHHHhhhccccc--hhhhhhhhhhHHHHHhccccchHHHHHHHHHHHccc-chHHHHHHHHHHHHcCCH
Confidence            44568899999999999998876  677888889999999999999999999998887533 678888899999999999


Q ss_pred             HHHHHHHHHhhcC
Q 012111          166 DEAFSTINDMKSV  178 (471)
Q Consensus       166 ~~a~~~~~~~~~~  178 (471)
                      ++|+..+++....
T Consensus        95 ~eA~~~~~~a~~~  107 (159)
T d1a17a_          95 RAALRDYETVVKV  107 (159)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHc
Confidence            9999999888873

>d1b89a_ a.118.1.3 (A:) Clathrin heavy chain proximal leg segment {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: ARM repeat
family: Clathrin heavy chain proximal leg segment
domain: Clathrin heavy chain proximal leg segment
species: Cow (Bos taurus) [TaxId: 9913]

Probab=98.59  E-value=0.00013  Score=62.13  Aligned_cols=282  Identities=12%  Similarity=0.086  Sum_probs=156.6

Q ss_pred             chHHHHHHHHHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHH
Q 012111           78 PKPVLEALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVS  157 (471)
Q Consensus        78 ~~~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~  157 (471)
                      +-....+.+.|.+.|.++.|..+|..+..          |..++..+.+.++++.|.+++...-      +..+|..+..
T Consensus        14 ~~d~~~i~~~c~~~~lye~A~~lY~~~~d----------~~rl~~~~v~l~~~~~avd~~~k~~------~~~~~k~~~~   77 (336)
T d1b89a_          14 NAHIQQVGDRCYDEKMYDAAKLLYNNVSN----------FGRLASTLVHLGEYQAAVDGARKAN------STRTWKEVCF   77 (336)
T ss_dssp             ---------------CTTTHHHHHHHTTC----------HHHHHHHHHTTTCHHHHHHHHHHHT------CHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHCCCHHHHHHHHHhCCC----------HHHHHHHHHhhccHHHHHHHHHHcC------CHHHHHHHHH
Confidence            34566777778899999999999986643          5778888899999999988887552      7789999999


Q ss_pred             HHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHH
Q 012111          158 AYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFE  237 (471)
Q Consensus       158 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~  237 (471)
                      ++.+......+.-     .. .....+......++..|-..|.++....+++...... ..+...++.++..|++.+ .+
T Consensus        78 ~l~~~~e~~la~i-----~~-~~~~~~~d~l~~~v~~ye~~~~~e~Li~~Le~~~~~~-~~~~~~~~~L~~lyak~~-~~  149 (336)
T d1b89a_          78 ACVDGKEFRLAQM-----CG-LHIVVHADELEELINYYQDRGYFEELITMLEAALGLE-RAHMGMFTELAILYSKFK-PQ  149 (336)
T ss_dssp             HHHHTTCHHHHHH-----TT-TTTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTST-TCCHHHHHHHHHHHHTTC-HH
T ss_pred             HHHhCcHHHHHHH-----HH-HHhhcCHHHHHHHHHHHHHcCChHHHHHHHHHHHcCC-ccchHHHHHHHHHHHHhC-hH
Confidence            9998877655422     12 2234566666789999999999999999999876432 557778889999998864 33


Q ss_pred             HHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCC--------CCCCHHHHHHHHHHHHHcCCHHH
Q 012111          238 EMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMG--------VKADIQTLNILTKSYGRAGMYDK  309 (471)
Q Consensus       238 ~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~--------~~~~~~~~~~ll~~~~~~~~~~~  309 (471)
                      +..+.+...   . ..-+   ...++..|...+-+.++.-++..+....        ..++..-....+..+.+..+.  
T Consensus       150 kl~e~l~~~---s-~~y~---~~k~~~~c~~~~l~~elv~Ly~~~~~~~~A~~~~i~~~~~~~~~~~f~e~~~k~~N~--  220 (336)
T d1b89a_         150 KMREHLELF---W-SRVN---IPKVLRAAEQAHLWAELVFLYDKYEEYDNAIITMMNHPTDAWKEGQFKDIITKVANV--  220 (336)
T ss_dssp             HHHHHHHHH---S-TTSC---HHHHHHHHHTTTCHHHHHHHHHHTTCHHHHHHHHHHSTTTTCCHHHHHHHHHHCSST--
T ss_pred             HHHHHHHhc---c-ccCC---HHHHHHHHHHcCChHHHHHHHHhcCCHHHHHHHHHHcchhhhhHHHHHHHHHccCCh--
Confidence            433333332   1 1122   2234455555555555444444332100        011111111222222333322  


Q ss_pred             HHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 012111          310 MRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVEN  389 (471)
Q Consensus       310 a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~  389 (471)
                                       ..|-.++..|... +++-...++..+... +  |   ...++..+.+.+++.....+++...+
T Consensus       221 -----------------e~~~~~i~~yL~~-~p~~i~~lL~~v~~~-~--d---~~r~V~~~~k~~~l~li~p~Le~v~~  276 (336)
T d1b89a_         221 -----------------ELYYRAIQFYLEF-KPLLLNDLLMVLSPR-L--D---HTRAVNYFSKVKQLPLVKPYLRSVQN  276 (336)
T ss_dssp             -----------------HHHHHHHHHHHHH-CGGGHHHHHHHHGGG-C--C---HHHHHHHHHHTTCTTTTHHHHHHHHT
T ss_pred             -----------------HHHHHHHHHHHHc-CHHHHHHHHHHhccC-C--C---HHHHHHHHHhcCCcHHHHHHHHHHHH
Confidence                             2333333333322 122222222222221 1  1   13344555566666667777777666


Q ss_pred             CCCCcCHHHHHHHHHHHHhcCCHHHHHHHH
Q 012111          390 SDVILDTPFFNCIISAYGQAGDVEKMGELF  419 (471)
Q Consensus       390 ~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~  419 (471)
                      .+   +..+.+++...|...+|++.-.+..
T Consensus       277 ~n---~~~vn~al~~lyie~~d~~~l~~~i  303 (336)
T d1b89a_         277 HN---NKSVNESLNNLFITEEDYQALRTSI  303 (336)
T ss_dssp             TC---CHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             cC---hHHHHHHHHHHHhCcchhHHHHHHH
Confidence            55   4568888888999888876544444

>d1a17a_ a.118.8.1 (A:) Protein phosphatase 5 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Protein phosphatase 5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.58  E-value=8.1e-07  Score=68.04  Aligned_cols=124  Identities=11%  Similarity=-0.012  Sum_probs=99.4

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHH
Q 012111          328 TYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYG  407 (471)
Q Consensus       328 ~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  407 (471)
                      .+......|.+.|++++|+..|++..+.. +-+...|..+..+|...|++++|...|+.+.+.++. +..+|..+..++.
T Consensus        12 ~l~~~gn~~~~~~~y~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~A~~~~~kal~~~p~-~~~a~~~~g~~~~   89 (159)
T d1a17a_          12 ELKTQANDYFKAKDYENAIKFYSQAIELN-PSNAIYYGNRSLAYLRTECYGYALGDATRAIELDKK-YIKGYYRRAASNM   89 (159)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHhhhccccc-hhhhhhhhhhHHHHHhccccchHHHHHHHHHHHccc-chHHHHHHHHHHH
Confidence            34555677899999999999999999875 447889999999999999999999999999988766 7889999999999


Q ss_pred             hcCCHHHHHHHHHHHHhCCCCCC-HHHHHHHHHH--HHhcCCHHHHHHHHH
Q 012111          408 QAGDVEKMGELFLTMKERHCVPD-NITFATMIQA--YNALGMTEAAQNLEN  455 (471)
Q Consensus       408 ~~g~~~~a~~~~~~~~~~~~~p~-~~~~~~l~~~--~~~~g~~~~A~~~~~  455 (471)
                      ..|++++|...+++....  .|+ ...+..+..+  ....+.+++|....+
T Consensus        90 ~~g~~~eA~~~~~~a~~~--~p~~~~~~~~l~~~~~~~~~~~~~~a~~~~~  138 (159)
T d1a17a_          90 ALGKFRAALRDYETVVKV--KPHDKDAKMKYQECNKIVKQKAFERAIAGDE  138 (159)
T ss_dssp             HTTCHHHHHHHHHHHHHH--STTCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HcCCHHHHHHHHHHHHHc--CCCCHHHHHHHHHHHHHHHHHHHHHHHhCcH
Confidence            999999999999999985  454 4554444433  334455666655433

>d1nzna_ a.118.8.1 (A:) Mitochondria fission protein Fis1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Mitochondria fission protein Fis1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.54  E-value=2.4e-07  Score=67.02  Aligned_cols=93  Identities=13%  Similarity=0.091  Sum_probs=50.8

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCC---HHHHHHHHHHHHhCCCCcCH-HHHHHHHHHH
Q 012111          331 IVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGL---IMKVDSILRQVENSDVILDT-PFFNCIISAY  406 (471)
Q Consensus       331 ~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~---~~~a~~~~~~~~~~~~~~~~-~~~~~l~~~~  406 (471)
                      .++..+...+++++|.+.|++....+ +.+..++..+..++.+.++   +++|+.+++++...++.|+. .++..+..+|
T Consensus         4 ~l~n~~~~~~~l~~Ae~~Y~~aL~~~-p~~~~~~~n~a~~L~~s~~~~d~~~Ai~~l~~~l~~~~~~~~~~~~~~Lg~~y   82 (122)
T d1nzna_           4 AVLNELVSVEDLLKFEKKFQSEKAAG-SVSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKGSKEEQRDYVFYLAVGN   82 (122)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHS-CCCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTSCHHHHHHHHHHHHHHH
T ss_pred             HHHHHhcCHHHHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHhccCCchHHHHHHHHHHHH
Confidence            44555555666666666666666543 3345555555555554333   33456666665554443332 2455555566


Q ss_pred             HhcCCHHHHHHHHHHHHh
Q 012111          407 GQAGDVEKMGELFLTMKE  424 (471)
Q Consensus       407 ~~~g~~~~a~~~~~~~~~  424 (471)
                      .+.|++++|++.|+++.+
T Consensus        83 ~~~g~~~~A~~~~~~aL~  100 (122)
T d1nzna_          83 YRLKEYEKALKYVRGLLQ  100 (122)
T ss_dssp             HHTTCHHHHHHHHHHHHH
T ss_pred             HHHhhhHHHHHHHHHHHH
Confidence            666666666666666655

>d1ouva_ a.118.18.1 (A:) Cysteine rich protein C (HcpC) {Helicobacter pylori [TaxId: 210]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: HCP-like
family: HCP-like
domain: Cysteine rich protein C (HcpC)
species: Helicobacter pylori [TaxId: 210]

Probab=98.48  E-value=0.00022  Score=59.18  Aligned_cols=15  Identities=0%  Similarity=-0.223  Sum_probs=6.9

Q ss_pred             CHHHHHHHHHHHHhC
Q 012111          376 LIMKVDSILRQVENS  390 (471)
Q Consensus       376 ~~~~a~~~~~~~~~~  390 (471)
                      +.+.|...|+...+.
T Consensus       197 d~~~A~~~~~~aa~~  211 (265)
T d1ouva_         197 NFKEALARYSKACEL  211 (265)
T ss_dssp             CHHHHHHHHHHHHHT
T ss_pred             chhhhhhhHhhhhcc
Confidence            444444444444443

>d1ouva_ a.118.18.1 (A:) Cysteine rich protein C (HcpC) {Helicobacter pylori [TaxId: 210]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: HCP-like
family: HCP-like
domain: Cysteine rich protein C (HcpC)
species: Helicobacter pylori [TaxId: 210]

Probab=98.47  E-value=0.00023  Score=59.08  Aligned_cols=224  Identities=12%  Similarity=0.007  Sum_probs=128.8

Q ss_pred             HHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHh----cCCHHHHHHHHHHHHhCCCCCCHHHHHHH
Q 012111          222 TYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGN----SGNIEKMEKWYNEFNLMGVKADIQTLNIL  297 (471)
Q Consensus       222 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  297 (471)
                      .+..|...+...+++++|++.|++..+.+    +...+..|...|..    ..+...|..++......+   +......+
T Consensus         4 ~~~~lG~~~~~~~d~~~A~~~~~kAa~~g----~~~A~~~Lg~~y~~G~~~~~d~~~a~~~~~~a~~~~---~~~a~~~l   76 (265)
T d1ouva_           4 ELVGLGAKSYKEKDFTQAKKYFEKACDLK----ENSGCFNLGVLYYQGQGVEKNLKKAASFYAKACDLN---YSNGCHLL   76 (265)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHTT----CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHCC----CHHHHHHHHHHHHcCCCcchhHHHHHHhhccccccc---ccchhhcc
Confidence            34444444444555555555555554432    33334344444433    335555555555554433   22222222


Q ss_pred             HHHHHH----cCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHH----hcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHH
Q 012111          298 TKSYGR----AGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFG----KAGHIEKMEEYFKKMKHRGMKPNSITYCSLVS  369 (471)
Q Consensus       298 l~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~----~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~  369 (471)
                      ...+..    ..+.+.|...+....+.|..   .....+...+.    .......+...+......   .+...+..+..
T Consensus        77 ~~~~~~~~~~~~~~~~a~~~~~~a~~~g~~---~a~~~l~~~~~~~~~~~~~~~~a~~~~~~~~~~---~~~~~~~~L~~  150 (265)
T d1ouva_          77 GNLYYSGQGVSQNTNKALQYYSKACDLKYA---EGCASLGGIYHDGKVVTRDFKKAVEYFTKACDL---NDGDGCTILGS  150 (265)
T ss_dssp             HHHHHHTSSSCCCHHHHHHHHHHHHHTTCH---HHHHHHHHHHHHCSSSCCCHHHHHHHHHHHHHT---TCHHHHHHHHH
T ss_pred             ccccccccccchhhHHHHHHHhhhhhhhhh---hHHHhhcccccCCCcccchhHHHHHHhhhhhcc---cccchhhhhhh
Confidence            222222    33455566666655554322   11222222222    234556666666665553   35566666666


Q ss_pred             HHHh----cCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHh----cCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHH
Q 012111          370 AYSK----AGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQ----AGDVEKMGELFLTMKERHCVPDNITFATMIQAY  441 (471)
Q Consensus       370 ~~~~----~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~  441 (471)
                      .+..    ..+...+...++...+.+   +......+...|..    ..++++|+.+|++..+.|   ++..+..|...|
T Consensus       151 ~~~~~~~~~~~~~~~~~~~~~a~~~g---~~~A~~~lg~~y~~g~~~~~d~~~A~~~~~~aa~~g---~~~a~~~LG~~y  224 (265)
T d1ouva_         151 LYDAGRGTPKDLKKALASYDKACDLK---DSPGCFNAGNMYHHGEGATKNFKEALARYSKACELE---NGGGCFNLGAMQ  224 (265)
T ss_dssp             HHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTCSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHH
T ss_pred             hhccCCCcccccccchhhhhcccccc---ccccccchhhhcccCcccccchhhhhhhHhhhhccc---CHHHHHHHHHHH
Confidence            6664    456677777787777765   56666666666665    578999999999999876   566777777777


Q ss_pred             Hh----cCCHHHHHHHHHHHHHhhhcC
Q 012111          442 NA----LGMTEAAQNLENKMIAMKENS  464 (471)
Q Consensus       442 ~~----~g~~~~A~~~~~~m~~~~~~~  464 (471)
                      .+    ..+.++|.++|+++.+.|..+
T Consensus       225 ~~G~g~~~n~~~A~~~~~kAa~~g~~~  251 (265)
T d1ouva_         225 YNGEGVTRNEKQAIENFKKGCKLGAKG  251 (265)
T ss_dssp             HTTSSSSCCSTTHHHHHHHHHHHTCHH
T ss_pred             HcCCCCccCHHHHHHHHHHHHHCcCHH
Confidence            64    347899999999999888654

>d2c2la1 a.118.8.1 (A:24-224) STIP1 homology and U box-containing protein 1, STUB1 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: STIP1 homology and U box-containing protein 1, STUB1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.46  E-value=2.3e-06  Score=68.33  Aligned_cols=99  Identities=10%  Similarity=-0.071  Sum_probs=87.6

Q ss_pred             CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCC-CHHHHHHH
Q 012111          289 ADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKP-NSITYCSL  367 (471)
Q Consensus       289 ~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p-~~~~~~~l  367 (471)
                      |+...+......+.+.|++++|+..|....+..+. +...|..+..+|.+.|++++|+..|++.++.  .| +..+|..+
T Consensus         2 ~~a~~l~~~Gn~~~~~g~~~~Ai~~~~kal~~~p~-~~~~~~~lg~~y~~~~~~~~Ai~~~~~al~l--~p~~~~a~~~l   78 (201)
T d2c2la1           2 PSAQELKEQGNRLFVGRKYPEAAACYGRAITRNPL-VAVYYTNRALCYLKMQQPEQALADCRRALEL--DGQSVKAHFFL   78 (201)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSC-CHHHHHHHHHHHHHTTCHHHHHHHHHHHTTS--CTTCHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-CHHHHHhHHHHHhhhhhhhhhhHHHHHHHHh--CCCcHHHHHHH
Confidence            67777888889999999999999999998887543 7888999999999999999999999999875  45 57889999


Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhC
Q 012111          368 VSAYSKAGLIMKVDSILRQVENS  390 (471)
Q Consensus       368 i~~~~~~g~~~~a~~~~~~~~~~  390 (471)
                      ..+|...|++++|...|+.+.+.
T Consensus        79 g~~~~~l~~~~~A~~~~~~al~l  101 (201)
T d2c2la1          79 GQCQLEMESYDEAIANLQRAYSL  101 (201)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHh
Confidence            99999999999999999988764

>d1nzna_ a.118.8.1 (A:) Mitochondria fission protein Fis1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Mitochondria fission protein Fis1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.41  E-value=1.9e-06  Score=62.16  Aligned_cols=94  Identities=15%  Similarity=0.089  Sum_probs=77.8

Q ss_pred             HHHHHHHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCH---HHHHHHHHHHHhCCCCCC-HHHHHHHHH
Q 012111           82 LEALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQP---EQASLLFEVMLSDGLKPS-VDVYTALVS  157 (471)
Q Consensus        82 ~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~---~~a~~~~~~m~~~~~~~~-~~~~~~li~  157 (471)
                      ..++..+...+++++|.+.|+.+...+  |.+..++..+..++.+.++.   ++|+.+|+.+...+..|+ ..+|..+..
T Consensus         3 ~~l~n~~~~~~~l~~Ae~~Y~~aL~~~--p~~~~~~~n~a~~L~~s~~~~d~~~Ai~~l~~~l~~~~~~~~~~~~~~Lg~   80 (122)
T d1nzna_           3 EAVLNELVSVEDLLKFEKKFQSEKAAG--SVSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKGSKEEQRDYVFYLAV   80 (122)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHS--CCCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTSCHHHHHHHHHHHHH
T ss_pred             HHHHHHhcCHHHHHHHHHHHHHHHhhC--CCCHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHhccCCchHHHHHHHHHH
Confidence            356677888999999999999999976  77889999999999876554   569999999887654433 347788899


Q ss_pred             HHHhcCCHHHHHHHHHHhhc
Q 012111          158 AYGQSGLLDEAFSTINDMKS  177 (471)
Q Consensus       158 ~~~~~~~~~~a~~~~~~~~~  177 (471)
                      +|.+.|++++|++.|+++.+
T Consensus        81 ~y~~~g~~~~A~~~~~~aL~  100 (122)
T d1nzna_          81 GNYRLKEYEKALKYVRGLLQ  100 (122)
T ss_dssp             HHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHhhhHHHHHHHHHHHH
Confidence            99999999999999999987

>d1hxia_ a.118.8.1 (A:) Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor) {Trypanosoma brucei [TaxId: 5691]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor)
species: Trypanosoma brucei [TaxId: 5691]

Probab=98.40  E-value=2.3e-06  Score=60.90  Aligned_cols=88  Identities=7%  Similarity=-0.121  Sum_probs=45.4

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCH
Q 012111          368 VSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAYNALGMT  447 (471)
Q Consensus       368 i~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~  447 (471)
                      ...+.+.|++++|...|+++...++. +..+|..+..++.+.|++++|+..|++..+.. +-+...|..+...|...|++
T Consensus        23 g~~~~~~g~~~~A~~~~~~al~~~p~-~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~a~~~la~~y~~~g~~  100 (112)
T d1hxia_          23 GLSMLKLANLAEAALAFEAVCQKEPE-REEAWRSLGLTQAENEKDGLAIIALNHARMLD-PKDIAVHAALAVSHTNEHNA  100 (112)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHSTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhhhHHHHHHHhhhcccccc-cchhhhhhhhhhhhhhhHHHhhcccccccccc-cccccchHHHHHHHHHCCCH
Confidence            33444555555555555555554433 45555555555555555555555555555431 12344555555555555555


Q ss_pred             HHHHHHHHHH
Q 012111          448 EAAQNLENKM  457 (471)
Q Consensus       448 ~~A~~~~~~m  457 (471)
                      ++|.+.+++.
T Consensus       101 ~~A~~~l~~~  110 (112)
T d1hxia_         101 NAALASLRAW  110 (112)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            5555555543

>d1hxia_ a.118.8.1 (A:) Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor) {Trypanosoma brucei [TaxId: 5691]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor)
species: Trypanosoma brucei [TaxId: 5691]

Probab=98.40  E-value=1.2e-06  Score=62.32  Aligned_cols=90  Identities=14%  Similarity=0.084  Sum_probs=67.3

Q ss_pred             HHHHHHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhc
Q 012111           83 EALDEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQS  162 (471)
Q Consensus        83 ~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~  162 (471)
                      ..-..+.+.|++++|+..|+.+....  |.+..+|..+..++.+.|++++|...|+...+.... +..+|..+..+|...
T Consensus        21 ~~g~~~~~~g~~~~A~~~~~~al~~~--p~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~p~-~~~a~~~la~~y~~~   97 (112)
T d1hxia_          21 EEGLSMLKLANLAEAALAFEAVCQKE--PEREEAWRSLGLTQAENEKDGLAIIALNHARMLDPK-DIAVHAALAVSHTNE   97 (112)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHS--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhhhHHHHHHHhhhcccc--cccchhhhhhhhhhhhhhhHHHhhcccccccccccc-cccchHHHHHHHHHC
Confidence            33445567788888888888887765  556777888888888888888888888887776433 677777788888888


Q ss_pred             CCHHHHHHHHHHh
Q 012111          163 GLLDEAFSTINDM  175 (471)
Q Consensus       163 ~~~~~a~~~~~~~  175 (471)
                      |++++|++.+++.
T Consensus        98 g~~~~A~~~l~~~  110 (112)
T d1hxia_          98 HNANAALASLRAW  110 (112)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHH
Confidence            8888888877765

>d1b89a_ a.118.1.3 (A:) Clathrin heavy chain proximal leg segment {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: ARM repeat
family: Clathrin heavy chain proximal leg segment
domain: Clathrin heavy chain proximal leg segment
species: Cow (Bos taurus) [TaxId: 9913]

Probab=98.28  E-value=0.00081  Score=57.14  Aligned_cols=285  Identities=12%  Similarity=0.138  Sum_probs=144.8

Q ss_pred             CChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHH
Q 012111          112 ARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSIL  191 (471)
Q Consensus       112 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l  191 (471)
                      |+..-...++..|.+.|.++.|..+|..+..         |..++..+.+.++++.|.+.+.+..       +..+|..+
T Consensus        12 ~n~~d~~~i~~~c~~~~lye~A~~lY~~~~d---------~~rl~~~~v~l~~~~~avd~~~k~~-------~~~~~k~~   75 (336)
T d1b89a_          12 PNNAHIQQVGDRCYDEKMYDAAKLLYNNVSN---------FGRLASTLVHLGEYQAAVDGARKAN-------STRTWKEV   75 (336)
T ss_dssp             C----------------CTTTHHHHHHHTTC---------HHHHHHHHHTTTCHHHHHHHHHHHT-------CHHHHHHH
T ss_pred             CCcCCHHHHHHHHHHCCCHHHHHHHHHhCCC---------HHHHHHHHHhhccHHHHHHHHHHcC-------CHHHHHHH
Confidence            4555556677777788888888888876542         5667777888888888888776542       45677777


Q ss_pred             HHHHHhcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCC
Q 012111          192 IKSCTKFHRFDLIEKILAEMSYLGIECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGN  271 (471)
Q Consensus       192 l~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  271 (471)
                      ...+.+......+     .+...+...+......++..|-..|.+++...+++.....  -..+...++.++..|++.+ 
T Consensus        76 ~~~l~~~~e~~la-----~i~~~~~~~~~d~l~~~v~~ye~~~~~e~Li~~Le~~~~~--~~~~~~~~~~L~~lyak~~-  147 (336)
T d1b89a_          76 CFACVDGKEFRLA-----QMCGLHIVVHADELEELINYYQDRGYFEELITMLEAALGL--ERAHMGMFTELAILYSKFK-  147 (336)
T ss_dssp             HHHHHHTTCHHHH-----HHTTTTTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTS--TTCCHHHHHHHHHHHHTTC-
T ss_pred             HHHHHhCcHHHHH-----HHHHHHhhcCHHHHHHHHHHHHHcCChHHHHHHHHHHHcC--CccchHHHHHHHHHHHHhC-
Confidence            7777776655442     2223334456666677888888888888888888876543  2556667778888777754 


Q ss_pred             HHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCC--------CCCCHHHHHHHHHHHHhcCCHH
Q 012111          272 IEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRF--------FFPTVVTYNIVIETFGKAGHIE  343 (471)
Q Consensus       272 ~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~--------~~~~~~~~~~li~~~~~~g~~~  343 (471)
                      .++..+.+....   ...+.   ..++..|.+.+-++++.-++..+....        ..++..-....+..+.+..+. 
T Consensus       148 ~~kl~e~l~~~s---~~y~~---~k~~~~c~~~~l~~elv~Ly~~~~~~~~A~~~~i~~~~~~~~~~~f~e~~~k~~N~-  220 (336)
T d1b89a_         148 PQKMREHLELFW---SRVNI---PKVLRAAEQAHLWAELVFLYDKYEEYDNAIITMMNHPTDAWKEGQFKDIITKVANV-  220 (336)
T ss_dssp             HHHHHHHHHHHS---TTSCH---HHHHHHHHTTTCHHHHHHHHHHTTCHHHHHHHHHHSTTTTCCHHHHHHHHHHCSST-
T ss_pred             hHHHHHHHHhcc---ccCCH---HHHHHHHHHcCChHHHHHHHHhcCCHHHHHHHHHHcchhhhhHHHHHHHHHccCCh-
Confidence            334333333321   11121   223344444444444433333322100        000111111122222222222 


Q ss_pred             HHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 012111          344 KMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMK  423 (471)
Q Consensus       344 ~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~  423 (471)
                                        ..+-.++..|... +.+-...++..+... +  |   ...++..+.+.+++.....+++...
T Consensus       221 ------------------e~~~~~i~~yL~~-~p~~i~~lL~~v~~~-~--d---~~r~V~~~~k~~~l~li~p~Le~v~  275 (336)
T d1b89a_         221 ------------------ELYYRAIQFYLEF-KPLLLNDLLMVLSPR-L--D---HTRAVNYFSKVKQLPLVKPYLRSVQ  275 (336)
T ss_dssp             ------------------HHHHHHHHHHHHH-CGGGHHHHHHHHGGG-C--C---HHHHHHHHHHTTCTTTTHHHHHHHH
T ss_pred             ------------------HHHHHHHHHHHHc-CHHHHHHHHHHhccC-C--C---HHHHHHHHHhcCCcHHHHHHHHHHH
Confidence                              2333333333321 122222222222221 1  1   1334555556666666667776665


Q ss_pred             hCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHH
Q 012111          424 ERHCVPDNITFATMIQAYNALGMTEAAQNLEN  455 (471)
Q Consensus       424 ~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~  455 (471)
                      +.|   +..+.+++...|...++++.-+...+
T Consensus       276 ~~n---~~~vn~al~~lyie~~d~~~l~~~i~  304 (336)
T d1b89a_         276 NHN---NKSVNESLNNLFITEEDYQALRTSID  304 (336)
T ss_dssp             TTC---CHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HcC---hHHHHHHHHHHHhCcchhHHHHHHHH
Confidence            544   45688899999999999766554443

>d1p5qa1 a.118.8.1 (A:258-427) FKBP52 (FKBP4), C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: FKBP52 (FKBP4), C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.24  E-value=4.4e-05  Score=58.67  Aligned_cols=81  Identities=10%  Similarity=-0.050  Sum_probs=62.5

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC-CHHHHHHHHHH
Q 012111          362 ITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVP-DNITFATMIQA  440 (471)
Q Consensus       362 ~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p-~~~~~~~l~~~  440 (471)
                      .+|+.+..+|.+.|++++|...++..++.++. +..+|..+..+|...|++++|+..|++..+.  .| |......+-..
T Consensus        63 ~~~~nla~~y~k~~~~~~A~~~~~~al~~~p~-~~~a~~~~g~~~~~~g~~~~A~~~~~~al~l--~P~n~~~~~~l~~~  139 (170)
T d1p5qa1          63 ASHLNLAMCHLKLQAFSAAIESCNKALELDSN-NEKGLSRRGEAHLAVNDFELARADFQKVLQL--YPNNKAAKTQLAVC  139 (170)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CSSCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhhhcccccchhhhhhhcccc-chhhhHHHHHHHHHhhhHHHHHHHHHHHHHh--CCCCHHHHHHHHHH
Confidence            35677888889999999999999999888766 7888889999999999999999999999874  45 44444444444


Q ss_pred             HHhcC
Q 012111          441 YNALG  445 (471)
Q Consensus       441 ~~~~g  445 (471)
                      ..+.+
T Consensus       140 ~~~~~  144 (170)
T d1p5qa1         140 QQRIR  144 (170)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            43333

>d1elra_ a.118.8.1 (A:) Hop {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Hop
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.22  E-value=5.5e-06  Score=60.47  Aligned_cols=103  Identities=9%  Similarity=-0.013  Sum_probs=70.1

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcC------HHHHHHH
Q 012111          329 YNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILD------TPFFNCI  402 (471)
Q Consensus       329 ~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~------~~~~~~l  402 (471)
                      +..+...+...|++++|+..|.+.++.+ +.+...+..+..+|...|++++|...++++++..+...      ..+|..+
T Consensus         7 ~k~~G~~~~~~~~y~~Ai~~y~~al~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~l~~~~~~~~~~~a~~~~~l   85 (128)
T d1elra_           7 EKELGNDAYKKKDFDTALKHYDKAKELD-PTNMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENREDYRQIAKAYARI   85 (128)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHhC-cccHHHHHhHHHHHHHcCchHHHHHHHHHHHHhCcccHHHHHHHHHHHHHH
Confidence            4456667777888888888888887764 33577777788888888888888888877765332211      1355666


Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHH
Q 012111          403 ISAYGQAGDVEKMGELFLTMKERHCVPDNITF  434 (471)
Q Consensus       403 ~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~  434 (471)
                      ...+...+++++|++.|+.....  .++....
T Consensus        86 g~~~~~~~~~~~A~~~~~kal~~--~~~~~~~  115 (128)
T d1elra_          86 GNSYFKEEKYKDAIHFYNKSLAE--HRTPDVL  115 (128)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHH--CCCHHHH
T ss_pred             HHHHHHhCCHHHHHHHHHHHHhc--CCCHHHH
Confidence            66777777888888888776653  3455443

>d1p5qa1 a.118.8.1 (A:258-427) FKBP52 (FKBP4), C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: FKBP52 (FKBP4), C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.15  E-value=8.8e-05  Score=56.89  Aligned_cols=128  Identities=7%  Similarity=-0.096  Sum_probs=84.5

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHH
Q 012111          258 TLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFG  337 (471)
Q Consensus       258 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~  337 (471)
                      .+......+.+.|++++|+..|.+.+...-...              +..+.-......+       ...+|+.+..+|.
T Consensus        15 ~l~~~G~~~~~~~~~~~Ai~~y~~al~~~~~~~--------------~~~~~~~~~~~~~-------~~~~~~nla~~y~   73 (170)
T d1p5qa1          15 IVKERGTVYFKEGKYKQALLQYKKIVSWLEYES--------------SFSNEEAQKAQAL-------RLASHLNLAMCHL   73 (170)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHTTTCC--------------CCCSHHHHHHHHH-------HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHhhhcc--------------ccchHHHhhhchh-------HHHHHHHHHHHHH
Confidence            344555667777788888877777654210000              0000000111111       1235677888899


Q ss_pred             hcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHh
Q 012111          338 KAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQ  408 (471)
Q Consensus       338 ~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  408 (471)
                      +.|++++|+..++..+... +-+..++..+..++...|++++|...|+.+.+.++. +..+...+..+..+
T Consensus        74 k~~~~~~A~~~~~~al~~~-p~~~~a~~~~g~~~~~~g~~~~A~~~~~~al~l~P~-n~~~~~~l~~~~~~  142 (170)
T d1p5qa1          74 KLQAFSAAIESCNKALELD-SNNEKGLSRRGEAHLAVNDFELARADFQKVLQLYPN-NKAAKTQLAVCQQR  142 (170)
T ss_dssp             HTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSS-CHHHHHHHHHHHHH
T ss_pred             hhhhcccccchhhhhhhcc-ccchhhhHHHHHHHHHhhhHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHH
Confidence            9999999999999998864 337888999999999999999999999999887655 66666555554433

>d2fbna1 a.118.8.1 (A:22-174) Putative 70 kda peptidylprolyl isomerase PFL2275c {Plasmodium falciparum [TaxId: 5833]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Putative 70 kda peptidylprolyl isomerase PFL2275c
species: Plasmodium falciparum [TaxId: 5833]

Probab=98.11  E-value=6.2e-05  Score=56.63  Aligned_cols=96  Identities=15%  Similarity=-0.015  Sum_probs=47.2

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHcCC----CCCH-----------HHHHHHHHHHHhcCCHHHHHHHHHHHHhCCC
Q 012111          328 TYNIVIETFGKAGHIEKMEEYFKKMKHRGM----KPNS-----------ITYCSLVSAYSKAGLIMKVDSILRQVENSDV  392 (471)
Q Consensus       328 ~~~~li~~~~~~g~~~~a~~~~~~m~~~~~----~p~~-----------~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~  392 (471)
                      .+..-...+.+.|++.+|+..|.+....-.    .++.           .+|..+..+|.+.|++++|++.++.+.+.++
T Consensus        19 ~~~~~G~~~f~~~~y~~A~~~Y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~Nla~~~~~l~~~~~Al~~~~~al~~~p   98 (153)
T d2fbna1          19 DIKEEGNEFFKKNEINEAIVKYKEALDFFIHTEEWDDQILLDKKKNIEISCNLNLATCYNKNKDYPKAIDHASKVLKIDK   98 (153)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHTTTTCTTCCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHST
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHhhCcchhhhhhHHHHHhhhhHHHHHHhhHHHHHHHhcccchhhhhhhccccccc
Confidence            444555677788888888888888775410    1111           1233333444444444444444444444333


Q ss_pred             CcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 012111          393 ILDTPFFNCIISAYGQAGDVEKMGELFLTMKE  424 (471)
Q Consensus       393 ~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~  424 (471)
                      . +..+|..+..++...|++++|+..|++..+
T Consensus        99 ~-~~ka~~~~g~~~~~lg~~~~A~~~~~~al~  129 (153)
T d2fbna1          99 N-NVKALYKLGVANMYFGFLEEAKENLYKAAS  129 (153)
T ss_dssp             T-CHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             h-hhhhhHHhHHHHHHcCCHHHHHHHHHHHHH
Confidence            2 344444444444444444444444444443

>d1elra_ a.118.8.1 (A:) Hop {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Hop
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.10  E-value=4.1e-05  Score=55.62  Aligned_cols=93  Identities=12%  Similarity=0.041  Sum_probs=45.4

Q ss_pred             HHHHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCC-CCC-----HHHHHHHHH
Q 012111          296 ILTKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGM-KPN-----SITYCSLVS  369 (471)
Q Consensus       296 ~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~-~p~-----~~~~~~li~  369 (471)
                      .+...+.+.|++++|+..|....+..+. +...+..+..+|.+.|++++|+..++++++... .+.     ..+|..+..
T Consensus         9 ~~G~~~~~~~~y~~Ai~~y~~al~~~p~-~~~~~~~~a~~~~~~~~~~~A~~~~~~al~l~~~~~~~~~~~a~~~~~lg~   87 (128)
T d1elra_           9 ELGNDAYKKKDFDTALKHYDKAKELDPT-NMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENREDYRQIAKAYARIGN   87 (128)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHhCcc-cHHHHHhHHHHHHHcCchHHHHHHHHHHHHhCcccHHHHHHHHHHHHHHHH
Confidence            3444555555555555555555554322 444555555555555555555555555443210 000     123444445


Q ss_pred             HHHhcCCHHHHHHHHHHHHh
Q 012111          370 AYSKAGLIMKVDSILRQVEN  389 (471)
Q Consensus       370 ~~~~~g~~~~a~~~~~~~~~  389 (471)
                      .+...+++++|...|+....
T Consensus        88 ~~~~~~~~~~A~~~~~kal~  107 (128)
T d1elra_          88 SYFKEEKYKDAIHFYNKSLA  107 (128)
T ss_dssp             HHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHhCCHHHHHHHHHHHHh
Confidence            55555555555555555443

>d1kt1a1 a.118.8.1 (A:254-421) FKBP51, C-terminal domain {Monkey (Saimiri boliviensis) [TaxId: 27679]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: FKBP51, C-terminal domain
species: Monkey (Saimiri boliviensis) [TaxId: 27679]

Probab=98.07  E-value=8.9e-05  Score=56.76  Aligned_cols=100  Identities=12%  Similarity=-0.002  Sum_probs=74.1

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC-CHHHHHHHHHH
Q 012111          362 ITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVP-DNITFATMIQA  440 (471)
Q Consensus       362 ~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p-~~~~~~~l~~~  440 (471)
                      .+|..+..+|.+.|++++|+..++.+.+.++. +..+|..+..++...|++++|...|+++.+.  .| +......+-..
T Consensus        65 ~~~~Nla~~~~~l~~~~~Ai~~~~~al~l~p~-~~~a~~~~~~~~~~l~~~~~A~~~~~~al~l--~P~n~~~~~~l~~~  141 (168)
T d1kt1a1          65 AAFLNLAMCYLKLREYTKAVECCDKALGLDSA-NEKGLYRRGEAQLLMNEFESAKGDFEKVLEV--NPQNKAARLQIFMC  141 (168)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHS--CTTCHHHHHHHHHH
T ss_pred             HHHHhHHHHHHHhhhcccchhhhhhhhhcccc-hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHH
Confidence            34666778888999999999999999887765 8888888999999999999999999999874  45 44444444444


Q ss_pred             HHhcCCH-HHHHHHHHHHHHhhhcC
Q 012111          441 YNALGMT-EAAQNLENKMIAMKENS  464 (471)
Q Consensus       441 ~~~~g~~-~~A~~~~~~m~~~~~~~  464 (471)
                      ....+.. +...+++.+|.+.-...
T Consensus       142 ~~~~~~~~e~~kk~~~~~f~~~~~~  166 (168)
T d1kt1a1         142 QKKAKEHNERDRRTYANMFKKFAEQ  166 (168)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHhHHHHHHHHHHHHHhhhhhc
Confidence            4444443 34577777777665543

>d2fbna1 a.118.8.1 (A:22-174) Putative 70 kda peptidylprolyl isomerase PFL2275c {Plasmodium falciparum [TaxId: 5833]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Putative 70 kda peptidylprolyl isomerase PFL2275c
species: Plasmodium falciparum [TaxId: 5833]

Probab=98.05  E-value=0.00013  Score=54.73  Aligned_cols=104  Identities=11%  Similarity=0.004  Sum_probs=55.9

Q ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHhCCCC----CC-----------HHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCC
Q 012111          295 NILTKSYGRAGMYDKMRSVMDFMQKRFFF----PT-----------VVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKP  359 (471)
Q Consensus       295 ~~ll~~~~~~~~~~~a~~~~~~~~~~~~~----~~-----------~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p  359 (471)
                      ..-...+.+.|++++|...|......-..    ++           ..+|..+..+|.+.|++++|++.+...+... +.
T Consensus        21 ~~~G~~~f~~~~y~~A~~~Y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~Nla~~~~~l~~~~~Al~~~~~al~~~-p~   99 (153)
T d2fbna1          21 KEEGNEFFKKNEINEAIVKYKEALDFFIHTEEWDDQILLDKKKNIEISCNLNLATCYNKNKDYPKAIDHASKVLKID-KN   99 (153)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHTTTTCTTCCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TT
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHhhCcchhhhhhHHHHHhhhhHHHHHHhhHHHHHHHhcccchhhhhhhcccccc-ch
Confidence            33444555666666666666655542110    01           1234445555666666666666666665543 23


Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHH
Q 012111          360 NSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFN  400 (471)
Q Consensus       360 ~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~  400 (471)
                      +..+|..+..++...|++++|...|+...+.++. +..+..
T Consensus       100 ~~ka~~~~g~~~~~lg~~~~A~~~~~~al~l~P~-n~~~~~  139 (153)
T d2fbna1         100 NVKALYKLGVANMYFGFLEEAKENLYKAASLNPN-NLDIRN  139 (153)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHSTT-CHHHHH
T ss_pred             hhhhhHHhHHHHHHcCCHHHHHHHHHHHHHhCCC-CHHHHH
Confidence            4556666666666666666666666666655443 343333

>d1zbpa1 e.61.1.1 (A:2-265) Hypothetical protein VPA1032 {Vibrio parahaemolyticus [TaxId: 670]}

class: Multi-domain proteins (alpha and beta)
fold: ImpE-like
superfamily: ImpE-like
family: ImpE-like
domain: Hypothetical protein VPA1032
species: Vibrio parahaemolyticus [TaxId: 670]

Probab=98.00  E-value=9.4e-06  Score=67.24  Aligned_cols=128  Identities=11%  Similarity=-0.020  Sum_probs=86.2

Q ss_pred             HHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHH
Q 012111          336 FGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKM  415 (471)
Q Consensus       336 ~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a  415 (471)
                      ..+.|++++|+..+++.++.. +-|...+..+...++..|++++|...++...+..+. +...+..+...+...+..+++
T Consensus         6 aL~~G~l~eAl~~l~~al~~~-P~d~~ar~~La~lL~~~G~~e~A~~~l~~a~~l~P~-~~~~~~~l~~ll~a~~~~~~a   83 (264)
T d1zbpa1           6 ALSEGQLQQALELLIEAIKAS-PKDASLRSSFIELLCIDGDFERADEQLMQSIKLFPE-YLPGASQLRHLVKAAQARKDF   83 (264)
T ss_dssp             HTTTTCHHHHHHHHHHHHHTC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCGG-GHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHCCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCC-cHHHHHHHHHHHHhccccHHH
Confidence            346789999999999988874 447788899999999999999999999998887654 445555555554443333332


Q ss_pred             HHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhhhcCC
Q 012111          416 GELFLTMKERHCVPDNITFATMIQAYNALGMTEAAQNLENKMIAMKENSG  465 (471)
Q Consensus       416 ~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~~~  465 (471)
                      ..-.......+-.++...+......+...|+.++|.+.++++.+..|..+
T Consensus        84 ~~~~~~~~~~~~p~~~~~~l~~a~~~~~~gd~~~A~~~~~~a~e~~p~~~  133 (264)
T d1zbpa1          84 AQGAATAKVLGENEELTKSLVSFNLSMVSQDYEQVSELALQIEELRQEKG  133 (264)
T ss_dssp             TTSCCCEECCCSCHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCCCCC
T ss_pred             HHHhhhhhcccCchHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcCCCCC
Confidence            22111111111112223334445677888999999999999999888754

>d1ya0a1 a.118.8.1 (A:1-497) SMG-7 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: SMG-7
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.98  E-value=8.1e-06  Score=75.12  Aligned_cols=228  Identities=11%  Similarity=-0.054  Sum_probs=116.5

Q ss_pred             HHHHHHHHhhhhhhccCCCchHHHHHHHHHHHhhcHHHHHHHHHHhhhccCccCC-hhHHHHHHHHHhcCCCHHHHHHHH
Q 012111           59 FAIKNIEKKVSSKKYKNLWPKPVLEALDEAIKQKKWQLALKIFGLLRQQQWYQAR-CQTFTKLMVMLGKCKQPEQASLLF  137 (471)
Q Consensus        59 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~~~~~~a~~~~  137 (471)
                      +|.+.+.+.+...+....   .....-..+..++++++|   |+.+...+   |+ ...++.....+  ...+..+.+.+
T Consensus         4 eA~q~~~qA~~l~p~~a~---a~~~la~~~~~~~~l~ea---ye~~i~~d---p~~a~~~~~e~~Lw--~~~y~~~ie~~   72 (497)
T d1ya0a1           4 QSAQYLRQAEVLKADMTD---SKLGPAEVWTSRQALQDL---YQKMLVTD---LEYALDKKVEQDLW--NHAFKNQITTL   72 (497)
T ss_dssp             HHHHHHHHHHHHHGGGTC---SSSCSSSSHHHHHHHHHH---HHHHHHHC---HHHHHHHTHHHHHH--HHHTHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCCHH---HHhhHHHHHHHHchHHHH---HHHHHHcC---hhhHHHHhHHHHHH--HHHHHHHHHHH
Confidence            445555555554443322   222333344566777765   66665432   22 11221111111  11245566667


Q ss_pred             HHHHhCCCCCCHHHHHHHHH--HHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCC
Q 012111          138 EVMLSDGLKPSVDVYTALVS--AYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLG  215 (471)
Q Consensus       138 ~~m~~~~~~~~~~~~~~li~--~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g  215 (471)
                      +...+....++..-....+.  .....+.++.|+..+......  ..++...+..+...+.+.|+.+.|...+.......
T Consensus        73 r~~~k~~~~~~~~~~~~~~~~~l~~a~~~Y~~ai~~l~~~~~l--~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~  150 (497)
T d1ya0a1          73 QGQAKNRANPNRSEVQANLSLFLEAASGFYTQLLQELCTVFNV--DLPCRVKSSQLGIISNKQTHTSAIVKPQSSSCSYI  150 (497)
T ss_dssp             HHHHSCSSCTTTTHHHHHHHHHHHHHHHHHHHHHHHHTC---------------------------------CCHHHHHH
T ss_pred             HHhcccccCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC--ChhhHHHHHHhHHHHHhCCCHHHHHHHHHHHhCCC
Confidence            66665543333322222221  222345556665555544321  13345566777777788888888887776665431


Q ss_pred             CCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHH
Q 012111          216 IECSAVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNLMGVKADIQTLN  295 (471)
Q Consensus       216 ~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~  295 (471)
                         ...++..+...+...|++++|...|++..+..  +.+...|+.|...+...|+..+|...|.+..... +|...++.
T Consensus       151 ---~~~~~~~LG~l~~~~~~~~~A~~~y~~A~~l~--P~~~~~~~~Lg~~~~~~~~~~~A~~~y~ral~~~-~~~~~a~~  224 (497)
T d1ya0a1         151 ---CQHCLVHLGDIARYRNQTSQAESYYRHAAQLV--PSNGQPYNQLAILASSKGDHLTTIFYYCRSIAVK-FPFPAAST  224 (497)
T ss_dssp             ---HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTBSHHHHHHHHHHHHTTCHHHHHHHHHHHHSSS-BCCHHHHH
T ss_pred             ---HHHHHHHHHHHHHHcccHHHHHHHHHHHHHHC--CCchHHHHHHHHHHHHcCCHHHHHHHHHHHHhCC-CCCHHHHH
Confidence               23566778888888899999999999888763  4556788999999999999999999998887765 67778888


Q ss_pred             HHHHHHHHcC
Q 012111          296 ILTKSYGRAG  305 (471)
Q Consensus       296 ~ll~~~~~~~  305 (471)
                      .|...+.+..
T Consensus       225 nL~~~~~~~~  234 (497)
T d1ya0a1         225 NLQKALSKAL  234 (497)
T ss_dssp             HHHHHHHHHT
T ss_pred             HHHHHHHHhh
Confidence            8877776544

>d1ihga1 a.118.8.1 (A:197-365) Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Cyclophilin 40
species: Cow (Bos taurus) [TaxId: 9913]

Probab=97.95  E-value=0.00013  Score=55.91  Aligned_cols=78  Identities=9%  Similarity=-0.040  Sum_probs=57.4

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC-CHHHHHHHHH
Q 012111          361 SITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVP-DNITFATMIQ  439 (471)
Q Consensus       361 ~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p-~~~~~~~l~~  439 (471)
                      ...|..+..++.+.|++++|+..+..+++.++. +...|..+..++...|++++|+..|+++.+.  .| +......+..
T Consensus        77 ~~~~~nla~~~~~~~~~~~Ai~~~~~al~~~p~-~~~a~~~~g~~~~~l~~~~~A~~~~~~al~l--~p~n~~~~~~l~~  153 (169)
T d1ihga1          77 LSCVLNIGACKLKMSDWQGAVDSCLEALEIDPS-NTKALYRRAQGWQGLKEYDQALADLKKAQEI--APEDKAIQAELLK  153 (169)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhcccchhhhhhhhhhhhhhh-hhhHHHhHHHHHHHccCHHHHHHHHHHHHHh--CCCCHHHHHHHHH
Confidence            445666777888888888888888888887765 7778888888888888888888888888874  34 4444444444


Q ss_pred             HH
Q 012111          440 AY  441 (471)
Q Consensus       440 ~~  441 (471)
                      +.
T Consensus       154 ~~  155 (169)
T d1ihga1         154 VK  155 (169)
T ss_dssp             HH
T ss_pred             HH
Confidence            33

>d2ff4a2 a.118.8.3 (A:105-283) Probable regulatory protein EmbR, middle domain {Mycobacterium tuberculosis [TaxId: 1773]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: BTAD-like
domain: Probable regulatory protein EmbR, middle domain
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=97.94  E-value=0.00024  Score=54.66  Aligned_cols=124  Identities=12%  Similarity=0.090  Sum_probs=84.9

Q ss_pred             HHHHHHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCH
Q 012111          298 TKSYGRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLI  377 (471)
Q Consensus       298 l~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~  377 (471)
                      .......|++++|...|.........  ...        ......+-+...-..+...    ....+..+...+...|++
T Consensus        18 g~~~~~~g~~e~A~~~~~~AL~l~rG--~~l--------~~~~~~~w~~~~r~~l~~~----~~~a~~~la~~~~~~g~~   83 (179)
T d2ff4a2          18 GVHAAAAGRFEQASRHLSAALREWRG--PVL--------DDLRDFQFVEPFATALVED----KVLAHTAKAEAEIACGRA   83 (179)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHTTCCS--STT--------GGGTTSTTHHHHHHHHHHH----HHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHCCCHHHHHHHHHHHHhhCcc--ccc--------ccCcchHHHHHHHHHHHHH----HHHHHHHHHHHHHHCCCc
Confidence            34567778888888888877764211  100        0000000011111111111    234677888999999999


Q ss_pred             HHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHH-----hCCCCCCHHHHHH
Q 012111          378 MKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMK-----ERHCVPDNITFAT  436 (471)
Q Consensus       378 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~-----~~~~~p~~~~~~~  436 (471)
                      ++|...++.+.+.++. +...|..++.+|...|+..+|++.|+++.     +.|+.|...+-..
T Consensus        84 ~~Al~~~~~al~~~P~-~e~~~~~l~~al~~~Gr~~eAl~~y~~~~~~L~~eLG~~P~~~l~~l  146 (179)
T d2ff4a2          84 SAVIAELEALTFEHPY-REPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTLRAL  146 (179)
T ss_dssp             HHHHHHHHHHHHHSTT-CHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHHHHH
T ss_pred             hHHHHHHHHHHHhCCc-cHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHhCCCcCHHHHHH
Confidence            9999999999998876 89999999999999999999999999875     3589999876443

>d1kt1a1 a.118.8.1 (A:254-421) FKBP51, C-terminal domain {Monkey (Saimiri boliviensis) [TaxId: 27679]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: FKBP51, C-terminal domain
species: Monkey (Saimiri boliviensis) [TaxId: 27679]

Probab=97.88  E-value=0.00059  Score=51.96  Aligned_cols=94  Identities=11%  Similarity=-0.026  Sum_probs=69.3

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHH
Q 012111          327 VTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIISAY  406 (471)
Q Consensus       327 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  406 (471)
                      ..|..+..+|.+.|++++|+..++..+... +.+..+|..+..++...|++++|...|+.+.+.++. +..+...+-.+.
T Consensus        65 ~~~~Nla~~~~~l~~~~~Ai~~~~~al~l~-p~~~~a~~~~~~~~~~l~~~~~A~~~~~~al~l~P~-n~~~~~~l~~~~  142 (168)
T d1kt1a1          65 AAFLNLAMCYLKLREYTKAVECCDKALGLD-SANEKGLYRRGEAQLLMNEFESAKGDFEKVLEVNPQ-NKAARLQIFMCQ  142 (168)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSCTT-CHHHHHHHHHHH
T ss_pred             HHHHhHHHHHHHhhhcccchhhhhhhhhcc-cchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHH
Confidence            356667788889999999999999988864 457888999999999999999999999999987765 666666655554


Q ss_pred             HhcCCHH-HHHHHHHHH
Q 012111          407 GQAGDVE-KMGELFLTM  422 (471)
Q Consensus       407 ~~~g~~~-~a~~~~~~~  422 (471)
                      ...+... ...++|..|
T Consensus       143 ~~~~~~~e~~kk~~~~~  159 (168)
T d1kt1a1         143 KKAKEHNERDRRTYANM  159 (168)
T ss_dssp             HHHHHHHHHHHHHHHHH
T ss_pred             HHHHhHHHHHHHHHHHH
Confidence            4444332 233444443

>d1zbpa1 e.61.1.1 (A:2-265) Hypothetical protein VPA1032 {Vibrio parahaemolyticus [TaxId: 670]}

class: Multi-domain proteins (alpha and beta)
fold: ImpE-like
superfamily: ImpE-like
family: ImpE-like
domain: Hypothetical protein VPA1032
species: Vibrio parahaemolyticus [TaxId: 670]

Probab=97.86  E-value=1.4e-05  Score=66.20  Aligned_cols=125  Identities=8%  Similarity=-0.008  Sum_probs=81.2

Q ss_pred             HHHHHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCH
Q 012111           86 DEAIKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLL  165 (471)
Q Consensus        86 ~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~  165 (471)
                      +...+.|++++|++.|+...+..  |.+...+..+...|+..|++++|...|+...+.... +...+..+...+...+..
T Consensus         4 ~~aL~~G~l~eAl~~l~~al~~~--P~d~~ar~~La~lL~~~G~~e~A~~~l~~a~~l~P~-~~~~~~~l~~ll~a~~~~   80 (264)
T d1zbpa1           4 KNALSEGQLQQALELLIEAIKAS--PKDASLRSSFIELLCIDGDFERADEQLMQSIKLFPE-YLPGASQLRHLVKAAQAR   80 (264)
T ss_dssp             HHHTTTTCHHHHHHHHHHHHHTC--TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCGG-GHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHCCCHHHHHHHHHHHHHHC--CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCC-cHHHHHHHHHHHHhcccc
Confidence            34557899999999999999876  778889999999999999999999999998876322 345555555554444333


Q ss_pred             HHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHC
Q 012111          166 DEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYL  214 (471)
Q Consensus       166 ~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~  214 (471)
                      +++..-+..... .+-+++...+......+...|+.++|.++++++.+.
T Consensus        81 ~~a~~~~~~~~~-~~~p~~~~~~l~~a~~~~~~gd~~~A~~~~~~a~e~  128 (264)
T d1zbpa1          81 KDFAQGAATAKV-LGENEELTKSLVSFNLSMVSQDYEQVSELALQIEEL  128 (264)
T ss_dssp             HHHTTSCCCEEC-CCSCHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHhhhhhc-ccCchHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhc
Confidence            333222111111 111222233444455566778888888888777654

>d1ihga1 a.118.8.1 (A:197-365) Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Cyclophilin 40
species: Cow (Bos taurus) [TaxId: 9913]

Probab=97.86  E-value=0.00022  Score=54.49  Aligned_cols=82  Identities=5%  Similarity=-0.087  Sum_probs=65.5

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHHHH
Q 012111          325 TVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCIIS  404 (471)
Q Consensus       325 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  404 (471)
                      ....|..+..++.+.|++++|+..+.+.++.. +-+...|..+..++...|++++|...|+.+.+..+. +..+...+..
T Consensus        76 ~~~~~~nla~~~~~~~~~~~Ai~~~~~al~~~-p~~~~a~~~~g~~~~~l~~~~~A~~~~~~al~l~p~-n~~~~~~l~~  153 (169)
T d1ihga1          76 ALSCVLNIGACKLKMSDWQGAVDSCLEALEID-PSNTKALYRRAQGWQGLKEYDQALADLKKAQEIAPE-DKAIQAELLK  153 (169)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHhhcccchhhhhhhhhhhhh-hhhhhHHHhHHHHHHHccCHHHHHHHHHHHHHhCCC-CHHHHHHHHH
Confidence            34467778888999999999999999998864 346888999999999999999999999999987655 6666666555


Q ss_pred             HHHh
Q 012111          405 AYGQ  408 (471)
Q Consensus       405 ~~~~  408 (471)
                      +..+
T Consensus       154 ~~~~  157 (169)
T d1ihga1         154 VKQK  157 (169)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            4433

>d1ya0a1 a.118.8.1 (A:1-497) SMG-7 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: SMG-7
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.84  E-value=9.6e-06  Score=74.58  Aligned_cols=227  Identities=8%  Similarity=-0.036  Sum_probs=118.7

Q ss_pred             HHHHHHHHhhcCCCCCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCH-HHHHHHHHHHHccCCHHHHHHHHH
Q 012111          167 EAFSTINDMKSVSDCKPD-VYTYSILIKSCTKFHRFDLIEKILAEMSYLGIECSA-VTYNTIIDGYGKAKKFEEMESSFS  244 (471)
Q Consensus       167 ~a~~~~~~~~~~~~~~~~-~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~-~~~~~l~~~~~~~~~~~~a~~~~~  244 (471)
                      +|.+.|++..+.   +|+ ...+..+..++...+++++|   +++++..  .|+. ..++.. ..+. ...+..+.+.++
T Consensus         4 eA~q~~~qA~~l---~p~~a~a~~~la~~~~~~~~l~ea---ye~~i~~--dp~~a~~~~~e-~~Lw-~~~y~~~ie~~r   73 (497)
T d1ya0a1           4 QSAQYLRQAEVL---KADMTDSKLGPAEVWTSRQALQDL---YQKMLVT--DLEYALDKKVE-QDLW-NHAFKNQITTLQ   73 (497)
T ss_dssp             HHHHHHHHHHHH---HGGGTCSSSCSSSSHHHHHHHHHH---HHHHHHH--CHHHHHHHTHH-HHHH-HHHTHHHHHHHH
T ss_pred             HHHHHHHHHHHc---CCCCHHHHhhHHHHHHHHchHHHH---HHHHHHc--ChhhHHHHhHH-HHHH-HHHHHHHHHHHH
Confidence            577888887652   444 33455566667677777665   6666544  2221 111111 1111 112345666666


Q ss_pred             HHHHcCCCCCCHHHHHHHH--HHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCC
Q 012111          245 AMVESGGCHPDIFTLNSMI--SAYGNSGNIEKMEKWYNEFNLMGVKADIQTLNILTKSYGRAGMYDKMRSVMDFMQKRFF  322 (471)
Q Consensus       245 ~~~~~~~~~~~~~~~~~l~--~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~  322 (471)
                      ...+.. ..++..-....+  ......+.++.++..+....... +++...+..+...+.+.|+.+.|...+....... 
T Consensus        74 ~~~k~~-~~~~~~~~~~~~~~~l~~a~~~Y~~ai~~l~~~~~l~-~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~-  150 (497)
T d1ya0a1          74 GQAKNR-ANPNRSEVQANLSLFLEAASGFYTQLLQELCTVFNVD-LPCRVKSSQLGIISNKQTHTSAIVKPQSSSCSYI-  150 (497)
T ss_dssp             HHHSCS-SCTTTTHHHHHHHHHHHHHHHHHHHHHHHHTC--------------------------------CCHHHHHH-
T ss_pred             Hhcccc-cCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC-hhhHHHHHHhHHHHHhCCCHHHHHHHHHHHhCCC-
Confidence            665433 222222121111  12223445555555554443322 3455667777888888899988888776655421 


Q ss_pred             CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcCHHHHHHH
Q 012111          323 FPTVVTYNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVILDTPFFNCI  402 (471)
Q Consensus       323 ~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l  402 (471)
                        ...++..+...+...|++++|...|++..... +-+...|+.+...+...|+..+|...|.+.....+ |...++..|
T Consensus       151 --~~~~~~~LG~l~~~~~~~~~A~~~y~~A~~l~-P~~~~~~~~Lg~~~~~~~~~~~A~~~y~ral~~~~-~~~~a~~nL  226 (497)
T d1ya0a1         151 --CQHCLVHLGDIARYRNQTSQAESYYRHAAQLV-PSNGQPYNQLAILASSKGDHLTTIFYYCRSIAVKF-PFPAASTNL  226 (497)
T ss_dssp             --HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTBSHHHHHHHHHHHHTTCHHHHHHHHHHHHSSSB-CCHHHHHHH
T ss_pred             --HHHHHHHHHHHHHHcccHHHHHHHHHHHHHHC-CCchHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCC-CCHHHHHHH
Confidence              13467778888889999999999999988863 33567899999999999999999999999887764 477788888


Q ss_pred             HHHHHhcC
Q 012111          403 ISAYGQAG  410 (471)
Q Consensus       403 ~~~~~~~g  410 (471)
                      ...+.+..
T Consensus       227 ~~~~~~~~  234 (497)
T d1ya0a1         227 QKALSKAL  234 (497)
T ss_dssp             HHHHHHHT
T ss_pred             HHHHHHhh
Confidence            77775543

>d1zu2a1 a.118.8.1 (A:1-145) Mitochondrial import receptor subunit tom20-3 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Mitochondrial import receptor subunit tom20-3
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=97.81  E-value=6.4e-05  Score=55.88  Aligned_cols=115  Identities=15%  Similarity=0.043  Sum_probs=73.4

Q ss_pred             HHhhcHHHHHHHHHHhhhccCccCChhHHHHHHHHHhcC----------CCHHHHHHHHHHHHhCCCCCCHHHHHHHHHH
Q 012111           89 IKQKKWQLALKIFGLLRQQQWYQARCQTFTKLMVMLGKC----------KQPEQASLLFEVMLSDGLKPSVDVYTALVSA  158 (471)
Q Consensus        89 ~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~----------~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~  158 (471)
                      -+.+.+++|++.|+.+.+..  |.+..++..+..++...          +.+++|+..|+...+.++. +..+|..+..+
T Consensus         8 ~r~~~fe~A~~~~e~al~~~--P~~~~~~~~~g~~l~~~~~~~~~~e~~~~~~~Ai~~~~kAl~l~P~-~~~a~~~lG~~   84 (145)
T d1zu2a1           8 DRILLFEQIRQDAENTYKSN--PLDADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALLIDPK-KDEAVWCIGNA   84 (145)
T ss_dssp             HHHHHHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCTT-CHHHHHHHHHH
T ss_pred             HHHccHHHHHHHHHHHHhhC--CcchHHHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHHHHHHhcch-hhHHHhhHHHH
Confidence            35677999999999998876  77788888888877644          4456788888887776433 66777777777


Q ss_pred             HHhcCC-----------HHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCC
Q 012111          159 YGQSGL-----------LDEAFSTINDMKSVSDCKPDVYTYSILIKSCTKFHRFDLIEKILAEMSYLG  215 (471)
Q Consensus       159 ~~~~~~-----------~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~g  215 (471)
                      |...|+           ++.|.+.|++..+   +.|+...|..-+..+      ..+.+++.+..+.|
T Consensus        85 y~~~g~~~~~~~~~~~~~~~A~~~~~kal~---l~P~~~~~~~~L~~~------~ka~~~~~e~~k~~  143 (145)
T d1zu2a1          85 YTSFAFLTPDETEAKHNFDLATQFFQQAVD---EQPDNTHYLKSLEMT------AKAPQLHAEAYKQG  143 (145)
T ss_dssp             HHHHHHHCCCHHHHHHHHHHHHHHHHHHHH---HCTTCHHHHHHHHHH------HTHHHHHHHHHHSS
T ss_pred             HHHcccchhhHHHHHHhHHHhhhhhhcccc---cCCCHHHHHHHHHHH------HHHHHHHHHHHHHh
Confidence            765542           4556666666654   244444444333332      23444554444443

>d2ff4a2 a.118.8.3 (A:105-283) Probable regulatory protein EmbR, middle domain {Mycobacterium tuberculosis [TaxId: 1773]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: BTAD-like
domain: Probable regulatory protein EmbR, middle domain
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=97.77  E-value=0.00065  Score=52.16  Aligned_cols=71  Identities=10%  Similarity=0.033  Sum_probs=48.8

Q ss_pred             HHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHh-----CCCCCCHHH
Q 012111          221 VTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNSMISAYGNSGNIEKMEKWYNEFNL-----MGVKADIQT  293 (471)
Q Consensus       221 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~-----~~~~~~~~~  293 (471)
                      ..+..+...+.+.|++++|+..++.+.+..  +-+...|..++.++...|+..+|++.|+++..     .|+.|+..+
T Consensus        68 ~a~~~la~~~~~~g~~~~Al~~~~~al~~~--P~~e~~~~~l~~al~~~Gr~~eAl~~y~~~~~~L~~eLG~~P~~~l  143 (179)
T d2ff4a2          68 LAHTAKAEAEIACGRASAVIAELEALTFEH--PYREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTL  143 (179)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHS--TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHH
T ss_pred             HHHHHHHHHHHHCCCchHHHHHHHHHHHhC--CccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHhCCCcCHHH
Confidence            445666777777777777777777777664  55666777777777777777777777777632     466666543

>d2hr2a1 a.118.8.8 (A:2-157) Hypothetical protein CT2138 {Chlorobium tepidum [TaxId: 1097]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: CT2138-like
domain: Hypothetical protein CT2138
species: Chlorobium tepidum [TaxId: 1097]

Probab=97.76  E-value=0.00046  Score=51.85  Aligned_cols=97  Identities=13%  Similarity=-0.022  Sum_probs=59.5

Q ss_pred             HHHhcCCHHHHHHHHHHHHhCCCC-c----------CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhC-----CCCCC---
Q 012111          370 AYSKAGLIMKVDSILRQVENSDVI-L----------DTPFFNCIISAYGQAGDVEKMGELFLTMKER-----HCVPD---  430 (471)
Q Consensus       370 ~~~~~g~~~~a~~~~~~~~~~~~~-~----------~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~-----~~~p~---  430 (471)
                      .+...|++++|+..|++..+.... |          ....|+.+..+|...|++++|...+++....     ...++   
T Consensus        18 ~~~~~g~y~~Ai~~y~~Al~i~~~~~~~~~~~~~~~~a~~~~nlg~~~~~lg~~~~A~~~~~~al~~~~~~~~~~~~~~~   97 (156)
T d2hr2a1          18 RQLVAGEYDEAAANCRRAMEISHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKALHYFNRRGELNQDEGK   97 (156)
T ss_dssp             HHHHHTCHHHHHHHHHHHHHHHTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHCCTTSTHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHhChhhhhhhhcccchhHHHHHHHHHHHHHHcCccchhhHhhhhhhhcccccccccccccc
Confidence            344556666666666555532111 1          1245667777777777777777777766531     11222   


Q ss_pred             --HHHHHHHHHHHHhcCCHHHHHHHHHHHHHhhhcCCC
Q 012111          431 --NITFATMIQAYNALGMTEAAQNLENKMIAMKENSGK  466 (471)
Q Consensus       431 --~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~~~~  466 (471)
                        ...+..+..+|...|++++|.+.|+++++..++...
T Consensus        98 ~~~~a~~~~g~~~~~lg~~eeA~~~~~~Al~l~~~~~~  135 (156)
T d2hr2a1          98 LWISAVYSRALALDGLGRGAEAMPEFKKVVEMIEERKG  135 (156)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHCCS
T ss_pred             hhHHHHhhhHHHHHHHHHHHHHHHHHHHHHHhhHHhhc
Confidence              124556677888888888888888888887776543

>d1zu2a1 a.118.8.1 (A:1-145) Mitochondrial import receptor subunit tom20-3 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Mitochondrial import receptor subunit tom20-3
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=97.66  E-value=0.00016  Score=53.57  Aligned_cols=111  Identities=12%  Similarity=0.103  Sum_probs=61.2

Q ss_pred             CCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhc----------CCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhc
Q 012111          340 GHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKA----------GLIMKVDSILRQVENSDVILDTPFFNCIISAYGQA  409 (471)
Q Consensus       340 g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~----------g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  409 (471)
                      +.+++|...|+...+.. +-++.++..+..++...          +.+++|...|+++.+.++. +..+|..+..+|...
T Consensus        11 ~~fe~A~~~~e~al~~~-P~~~~~~~~~g~~l~~~~~~~~~~e~~~~~~~Ai~~~~kAl~l~P~-~~~a~~~lG~~y~~~   88 (145)
T d1zu2a1          11 LLFEQIRQDAENTYKSN-PLDADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALLIDPK-KDEAVWCIGNAYTSF   88 (145)
T ss_dssp             HHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHhhC-CcchHHHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHHHHHHhcch-hhHHHhhHHHHHHHc
Confidence            34555555555555442 22344444444444322          3345666666666666554 566666666666554


Q ss_pred             C-----------CHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHh
Q 012111          410 G-----------DVEKMGELFLTMKERHCVPDNITFATMIQAYNALGMTEAAQNLENKMIAM  460 (471)
Q Consensus       410 g-----------~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~  460 (471)
                      |           .+++|.+.|++..+  +.|+...+..-+..+      ..|.+++.+..+.
T Consensus        89 g~~~~~~~~~~~~~~~A~~~~~kal~--l~P~~~~~~~~L~~~------~ka~~~~~e~~k~  142 (145)
T d1zu2a1          89 AFLTPDETEAKHNFDLATQFFQQAVD--EQPDNTHYLKSLEMT------AKAPQLHAEAYKQ  142 (145)
T ss_dssp             HHHCCCHHHHHHHHHHHHHHHHHHHH--HCTTCHHHHHHHHHH------HTHHHHHHHHHHS
T ss_pred             ccchhhHHHHHHhHHHhhhhhhcccc--cCCCHHHHHHHHHHH------HHHHHHHHHHHHH
Confidence            3           35778888888887  467766655444333      3455555555443

>d1tjca_ a.118.8.1 (A:) Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Prolyl 4-hydroxylase alpha-1 subunit, P4HA1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.23  E-value=0.0013  Score=44.34  Aligned_cols=63  Identities=16%  Similarity=0.058  Sum_probs=34.0

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhCC-----CCcC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 012111          362 ITYCSLVSAYSKAGLIMKVDSILRQVENSD-----VILD-TPFFNCIISAYGQAGDVEKMGELFLTMKE  424 (471)
Q Consensus       362 ~~~~~li~~~~~~g~~~~a~~~~~~~~~~~-----~~~~-~~~~~~l~~~~~~~g~~~~a~~~~~~~~~  424 (471)
                      ..+-.+...+.+.|++++|...|++..+..     ..++ ..+++.+..++.+.|++++|+..++++.+
T Consensus         6 ddc~~lG~~~~~~g~y~~A~~~~~~Al~~~~~~~~~~~~~~~~l~~Lg~~~~~~g~~~~A~~~y~~aL~   74 (95)
T d1tjca_           6 EDSFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLE   74 (95)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHHHhhhhccCccHHHHHHHHhhHHHhcCChHHHHHHHHHHHH
Confidence            334455556666666666666665554321     1111 34555566666666666666666666655

>d2hr2a1 a.118.8.8 (A:2-157) Hypothetical protein CT2138 {Chlorobium tepidum [TaxId: 1097]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: CT2138-like
domain: Hypothetical protein CT2138
species: Chlorobium tepidum [TaxId: 1097]

Probab=97.19  E-value=0.0052  Score=45.75  Aligned_cols=55  Identities=11%  Similarity=0.083  Sum_probs=28.1

Q ss_pred             HHHccCCHHHHHHHHHHHHHcCCCCCC----------HHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 012111          229 GYGKAKKFEEMESSFSAMVESGGCHPD----------IFTLNSMISAYGNSGNIEKMEKWYNEFN  283 (471)
Q Consensus       229 ~~~~~~~~~~a~~~~~~~~~~~~~~~~----------~~~~~~l~~~~~~~~~~~~a~~~~~~~~  283 (471)
                      .+...|++++|++.|++.++.....|+          ...|+.+..+|...|++++|...+++..
T Consensus        18 ~~~~~g~y~~Ai~~y~~Al~i~~~~~~~~~~~~~~~~a~~~~nlg~~~~~lg~~~~A~~~~~~al   82 (156)
T d2hr2a1          18 RQLVAGEYDEAAANCRRAMEISHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKAL   82 (156)
T ss_dssp             HHHHHTCHHHHHHHHHHHHHHHTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHhChhhhhhhhcccchhHHHHHHHHHHHHHHcCccchhhHhhhhhh
Confidence            344556666666666665543211111          2345555555555666655555555543

>d1tjca_ a.118.8.1 (A:) Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Prolyl 4-hydroxylase alpha-1 subunit, P4HA1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.16  E-value=0.0015  Score=44.04  Aligned_cols=67  Identities=12%  Similarity=-0.030  Sum_probs=37.8

Q ss_pred             CchHHHHHHHHHHHhhcHHHHHHHHHHhhhccCc----cC-ChhHHHHHHHHHhcCCCHHHHHHHHHHHHhC
Q 012111           77 WPKPVLEALDEAIKQKKWQLALKIFGLLRQQQWY----QA-RCQTFTKLMVMLGKCKQPEQASLLFEVMLSD  143 (471)
Q Consensus        77 ~~~~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~----~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~  143 (471)
                      +.++...+=..+.+.|++++|++.|+++.+....    .+ ...++..+..++.+.|++++|...++++++.
T Consensus         4 saddc~~lG~~~~~~g~y~~A~~~~~~Al~~~~~~~~~~~~~~~~l~~Lg~~~~~~g~~~~A~~~y~~aL~l   75 (95)
T d1tjca_           4 TAEDSFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLEL   75 (95)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHhhhhccCccHHHHHHHHhhHHHhcCChHHHHHHHHHHHHh
Confidence            3444445555556677777777777666543210    01 1345566666666666666666666666655

>d1klxa_ a.118.18.1 (A:) Cysteine rich protein B (HcpB) {Helicobacter pylori [TaxId: 210]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: HCP-like
family: HCP-like
domain: Cysteine rich protein B (HcpB)
species: Helicobacter pylori [TaxId: 210]

Probab=96.64  E-value=0.05  Score=38.77  Aligned_cols=82  Identities=11%  Similarity=-0.039  Sum_probs=39.8

Q ss_pred             CCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHh----cCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHh----cCC
Q 012111          375 GLIMKVDSILRQVENSDVILDTPFFNCIISAYGQ----AGDVEKMGELFLTMKERHCVPDNITFATMIQAYNA----LGM  446 (471)
Q Consensus       375 g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~----~g~  446 (471)
                      .+.++|.+++++..+.|   +...+..|...|..    ..+.++|.++|++..+.|   ++.....|...|..    ..+
T Consensus        37 ~~~~~a~~~~~~aa~~g---~~~a~~~Lg~~y~~g~~~~~d~~~A~~~~~~aa~~g---~~~a~~~Lg~~y~~G~gv~~d  110 (133)
T d1klxa_          37 INKQKLFQYLSKACELN---SGNGCRFLGDFYENGKYVKKDLRKAAQYYSKACGLN---DQDGCLILGYKQYAGKGVVKN  110 (133)
T ss_dssp             SCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHCSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCC
T ss_pred             cCHHHHHHHHhhhhccc---chhhhhhHHHhhhhccccchhhHHHHHHHhhhhccC---cchHHHHHHHHHHcCCccCCC
Confidence            34555555555555544   33333444444433    234556666666655543   23333334444433    235


Q ss_pred             HHHHHHHHHHHHHhhh
Q 012111          447 TEAAQNLENKMIAMKE  462 (471)
Q Consensus       447 ~~~A~~~~~~m~~~~~  462 (471)
                      .++|.+++++..+.+.
T Consensus       111 ~~~A~~~~~~Aa~~G~  126 (133)
T d1klxa_         111 EKQAVKTFEKACRLGS  126 (133)
T ss_dssp             HHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHCCC
Confidence            6666666666555543

>d1klxa_ a.118.18.1 (A:) Cysteine rich protein B (HcpB) {Helicobacter pylori [TaxId: 210]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: HCP-like
family: HCP-like
domain: Cysteine rich protein B (HcpB)
species: Helicobacter pylori [TaxId: 210]

Probab=96.46  E-value=0.078  Score=37.68  Aligned_cols=81  Identities=10%  Similarity=-0.061  Sum_probs=50.5

Q ss_pred             CCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHh----cCCHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHh----cCC
Q 012111          340 GHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSK----AGLIMKVDSILRQVENSDVILDTPFFNCIISAYGQ----AGD  411 (471)
Q Consensus       340 g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~----~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~g~  411 (471)
                      .+.++|+.++++..+.|   ++.....|...|..    ..+.++|.++|++..+.+   ++.....|...|..    ..+
T Consensus        37 ~~~~~a~~~~~~aa~~g---~~~a~~~Lg~~y~~g~~~~~d~~~A~~~~~~aa~~g---~~~a~~~Lg~~y~~G~gv~~d  110 (133)
T d1klxa_          37 INKQKLFQYLSKACELN---SGNGCRFLGDFYENGKYVKKDLRKAAQYYSKACGLN---DQDGCLILGYKQYAGKGVVKN  110 (133)
T ss_dssp             SCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHCSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCC
T ss_pred             cCHHHHHHHHhhhhccc---chhhhhhHHHhhhhccccchhhHHHHHHHhhhhccC---cchHHHHHHHHHHcCCccCCC
Confidence            45667777777666655   34444445544443    346777777777777765   44455556555554    356


Q ss_pred             HHHHHHHHHHHHhCC
Q 012111          412 VEKMGELFLTMKERH  426 (471)
Q Consensus       412 ~~~a~~~~~~~~~~~  426 (471)
                      ..+|.++|++..+.|
T Consensus       111 ~~~A~~~~~~Aa~~G  125 (133)
T d1klxa_         111 EKQAVKTFEKACRLG  125 (133)
T ss_dssp             HHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHCC
Confidence            777777777777665

>d1wy6a1 a.118.20.1 (A:7-167) Hypothetical protein ST1625 {Archaeon Sulfolobus tokodaii [TaxId: 111955]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Hypothetical protein ST1625
family: Hypothetical protein ST1625
domain: Hypothetical protein ST1625
species: Archaeon Sulfolobus tokodaii [TaxId: 111955]

Probab=96.22  E-value=0.094  Score=35.95  Aligned_cols=64  Identities=13%  Similarity=0.168  Sum_probs=36.9

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCC
Q 012111          329 YNIVIETFGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVENSDVI  393 (471)
Q Consensus       329 ~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~  393 (471)
                      ....++.+...|+-++..++++.+.+.+ +|++...-.+..+|.+.|...++.+++.++-+.|.+
T Consensus        89 vdlALd~lv~~~kkd~Ld~i~~~l~kn~-~i~~~~llkia~A~kkig~~re~nell~~ACe~G~K  152 (161)
T d1wy6a1          89 VNKALDILVIQGKRDKLEEIGREILKNN-EVSASILVAIANALRRVGDERDATTLLIEACKKGEK  152 (161)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHC--C-CSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHHHHHhccHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHhHH
Confidence            3444555566666666666666655543 555566666666666666666666666666655543

>d1qsaa1 a.118.5.1 (A:1-450) 70 KDa soluble lytic transglycosylase (SLT70), superhelical domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Bacterial muramidases
family: Bacterial muramidases
domain: 70 KDa soluble lytic transglycosylase (SLT70), superhelical domain
species: Escherichia coli [TaxId: 562]

Probab=96.02  E-value=0.45  Score=41.89  Aligned_cols=52  Identities=2%  Similarity=-0.188  Sum_probs=41.6

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 012111          403 ISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAYNALGMTEAAQNLENKM  457 (471)
Q Consensus       403 ~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~m  457 (471)
                      +..+...|....|.+.|..+.+.   .+......+.....+.|.++.|.....++
T Consensus       388 a~~L~~~g~~~~A~~e~~~l~~~---~~~~~~~~la~lA~~~g~~~~aI~a~~~~  439 (450)
T d1qsaa1         388 VRELMYWNLDNTARSEWANLVKS---KSKTEQAQLARYAFNNQWWDLSVQATIAG  439 (450)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHTT---CCHHHHHHHHHHHHHTTCHHHHHHHHHHT
T ss_pred             HHHHHHcCCchHHHHHHHHHHhC---CCHHHHHHHHHHHHHCCChhHHHHHHHHH
Confidence            55677889999999999988764   35667777788889999999998776554

>d2pqrb1 a.118.8.1 (B:5-128) Mitochondria fission protein Fis1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Mitochondria fission protein Fis1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=95.69  E-value=0.074  Score=36.80  Aligned_cols=51  Identities=8%  Similarity=0.041  Sum_probs=23.6

Q ss_pred             HHHHHHHHHHHHhCCCCCCH-HHHHHHHHHHHhcCCHHHHHHHHHHHHHhhhc
Q 012111          412 VEKMGELFLTMKERHCVPDN-ITFATMIQAYNALGMTEAAQNLENKMIAMKEN  463 (471)
Q Consensus       412 ~~~a~~~~~~~~~~~~~p~~-~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~  463 (471)
                      +++++.+|++....+ +.+. ..+..|.-+|.+.|++++|++.++++++.+|.
T Consensus        54 ~~~gI~lLe~~~~~~-p~~~rd~lY~Lav~yyklgdy~~A~~~~~~~L~ieP~  105 (124)
T d2pqrb1          54 ERLGVKILTDIYKEA-ESRRRECLYYLTIGCYKLGEYSMAKRYVDTLFEHERN  105 (124)
T ss_dssp             HHHHHHHHHHHHHHC-GGGHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTT
T ss_pred             HHHHHHHHHHHHhcC-chhHHHHHHHHHHHHHHHhhHHHHHHHHHHHHccCCC
Confidence            344555555544321 1122 23334444555555555555555555555554

>d1wy6a1 a.118.20.1 (A:7-167) Hypothetical protein ST1625 {Archaeon Sulfolobus tokodaii [TaxId: 111955]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Hypothetical protein ST1625
family: Hypothetical protein ST1625
domain: Hypothetical protein ST1625
species: Archaeon Sulfolobus tokodaii [TaxId: 111955]

Probab=95.59  E-value=0.19  Score=34.40  Aligned_cols=68  Identities=13%  Similarity=0.072  Sum_probs=53.9

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhhhc
Q 012111          395 DTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMIQAYNALGMTEAAQNLENKMIAMKEN  463 (471)
Q Consensus       395 ~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~  463 (471)
                      +...++..+..+...|+-+.-.++++.+.+. -.|++.....+..+|.+.|...++-+++.++.+.|.+
T Consensus        85 ~se~vdlALd~lv~~~kkd~Ld~i~~~l~kn-~~i~~~~llkia~A~kkig~~re~nell~~ACe~G~K  152 (161)
T d1wy6a1          85 LNEHVNKALDILVIQGKRDKLEEIGREILKN-NEVSASILVAIANALRRVGDERDATTLLIEACKKGEK  152 (161)
T ss_dssp             CCHHHHHHHHHHHHTTCHHHHHHHHHHHC---CCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCH
T ss_pred             hHHHHHHHHHHHHHhccHHHHHHHHHHHHhc-CCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHhHH
Confidence            3445666777888888888888888887664 4688888888889999999999999999999887754

>d1v54e_ a.118.11.1 (E:) Cytochrome c oxidase subunit E {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Cytochrome c oxidase subunit E
family: Cytochrome c oxidase subunit E
domain: Cytochrome c oxidase subunit E
species: Cow (Bos taurus) [TaxId: 9913]

Probab=94.16  E-value=0.32  Score=31.44  Aligned_cols=62  Identities=10%  Similarity=0.200  Sum_probs=38.2

Q ss_pred             CHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHH
Q 012111          376 LIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDNITFATMI  438 (471)
Q Consensus       376 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~  438 (471)
                      +.-++.+-+..+...+..|++.+..+.+++|.+.+|+..|.++|+..+.. +.++...|..++
T Consensus        21 D~we~rrgmN~l~~~DlVPeP~Ii~aALrAcRRvND~alAVR~lE~vK~K-~~~~k~~y~yil   82 (105)
T d1v54e_          21 DAWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDK-AGPHKEIYPYVI   82 (105)
T ss_dssp             CHHHHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-TTTCTTHHHHHH
T ss_pred             cHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHH-hcCcHHHHHHHH
Confidence            34455556666666667777777777777777777777777777666543 223344554444

>d2pqrb1 a.118.8.1 (B:5-128) Mitochondria fission protein Fis1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Mitochondria fission protein Fis1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=92.43  E-value=1.1  Score=30.79  Aligned_cols=71  Identities=10%  Similarity=-0.058  Sum_probs=39.2

Q ss_pred             CCHHHHHHHHHHHHhcC---CHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCH
Q 012111          359 PNSITYCSLVSAYSKAG---LIMKVDSILRQVENSDVILDTPFFNCIISAYGQAGDVEKMGELFLTMKERHCVPDN  431 (471)
Q Consensus       359 p~~~~~~~li~~~~~~g---~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~p~~  431 (471)
                      |...+--....++.+..   ++++++.+++.+.+.++.-....+-.|.-+|.+.|++++|.+.++.+.+  +.|+.
T Consensus        33 ~s~qt~F~YAw~Lv~S~~~~d~~~gI~lLe~~~~~~p~~~rd~lY~Lav~yyklgdy~~A~~~~~~~L~--ieP~n  106 (124)
T d2pqrb1          33 ATIQSRFNYAWGLIKSTDVNDERLGVKILTDIYKEAESRRRECLYYLTIGCYKLGEYSMAKRYVDTLFE--HERNN  106 (124)
T ss_dssp             SCHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH--HCTTC
T ss_pred             CCcchHHHHHHHHHcCCcHHHHHHHHHHHHHHHhcCchhHHHHHHHHHHHHHHHhhHHHHHHHHHHHHc--cCCCc
Confidence            44444444455555443   3456666666666543321124455566666677777777777777766  34543

>d1v54e_ a.118.11.1 (E:) Cytochrome c oxidase subunit E {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Cytochrome c oxidase subunit E
family: Cytochrome c oxidase subunit E
domain: Cytochrome c oxidase subunit E
species: Cow (Bos taurus) [TaxId: 9913]

Probab=91.59  E-value=1.1  Score=29.00  Aligned_cols=63  Identities=14%  Similarity=0.171  Sum_probs=47.2

Q ss_pred             CHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHHH
Q 012111          129 QPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIK  193 (471)
Q Consensus       129 ~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~  193 (471)
                      +.-++.+-++.+......|++.+..+.+++|-+.+++..|+++|+.++..-  ..+...|..++.
T Consensus        21 D~we~rrgmN~l~~~DlVPeP~Ii~aALrAcRRvND~alAVR~lE~vK~K~--~~~k~~y~yilq   83 (105)
T d1v54e_          21 DAWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDKA--GPHKEIYPYVIQ   83 (105)
T ss_dssp             CHHHHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT--TTCTTHHHHHHH
T ss_pred             cHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHh--cCcHHHHHHHHH
Confidence            555777788888888888889888999999989999999999988887633  233445555443

>d1qsaa1 a.118.5.1 (A:1-450) 70 KDa soluble lytic transglycosylase (SLT70), superhelical domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Bacterial muramidases
family: Bacterial muramidases
domain: 70 KDa soluble lytic transglycosylase (SLT70), superhelical domain
species: Escherichia coli [TaxId: 562]

Probab=91.27  E-value=4.2  Score=35.29  Aligned_cols=254  Identities=9%  Similarity=0.018  Sum_probs=113.4

Q ss_pred             HHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHH
Q 012111          116 TFTKLMVMLGKCKQPEQASLLFEVMLSDGLKPSVDVYTALVSAYGQSGLLDEAFSTINDMKSVSDCKPDVYTYSILIKSC  195 (471)
Q Consensus       116 ~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~  195 (471)
                      .....+..+.+.+++......+.     ..+.+...-.....+....|+.+.|...+..+-......|+  .+..+...+
T Consensus        74 lr~~~l~~L~~~~~w~~~~~~~~-----~~p~~~~~~c~~~~A~~~~g~~~~a~~~~~~lW~~~~~~p~--~c~~l~~~~  146 (450)
T d1qsaa1          74 LQSRFVNELARREDWRGLLAFSP-----EKPGTTEAQCNYYYAKWNTGQSEEAWQGAKELWLTGKSQPN--ACDKLFSVW  146 (450)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHCC-----SCCSSHHHHHHHHHHHHHTTCHHHHHHHHHHHHSCSSCCCT--HHHHHHHHH
T ss_pred             HHHHHHHHHHhccCHHHHHHhcc-----CCCCCHHHHHHHHHHHHHcCChHHHHHHHHHHHhcCCCCch--HHHHHHHHH
Confidence            34445566777777766444331     22345666667777788888888887777766552222332  333344444


Q ss_pred             HhcCCH--HHHHHHHHHHHHCC-----------CCCC-HHHHHHHHHHHHccCCHHHHHHHHHHHHHcCCCCCCHHHHHH
Q 012111          196 TKFHRF--DLIEKILAEMSYLG-----------IECS-AVTYNTIIDGYGKAKKFEEMESSFSAMVESGGCHPDIFTLNS  261 (471)
Q Consensus       196 ~~~~~~--~~a~~~~~~~~~~g-----------~~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~  261 (471)
                      ...|.+  +...+-++.+...|           ++++ .......+.....   ...+...   . ..  ...+......
T Consensus       147 ~~~~~lt~~~~~~R~~~~l~~~~~~~a~~l~~~l~~~~~~~~~a~~~l~~~---p~~~~~~---~-~~--~~~~~~~~~~  217 (450)
T d1qsaa1         147 RASGKQDPLAYLERIRLAMKAGNTGLVTVLAGQMPADYQTIASAIISLANN---PNTVLTF---A-RT--TGATDFTRQM  217 (450)
T ss_dssp             HHTTCSCHHHHHHHHHHHHHTTCHHHHHHHHHTCCGGGHHHHHHHHHHHHC---GGGHHHH---H-HH--SCCCHHHHHH
T ss_pred             HhcCCCCHHHHHHHHHHHHHcCChhhHHHHHhhCChhHHHHHHHHHHHHhC---hHhHHHH---H-hc--CCCChhhhHH
Confidence            333322  12222222222222           0001 0111111111111   1111110   0 11  1222222222


Q ss_pred             HHHHHHh--cCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHH----HHcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHH
Q 012111          262 MISAYGN--SGNIEKMEKWYNEFNLMGVKADIQTLNILTKSY----GRAGMYDKMRSVMDFMQKRFFFPTVVTYNIVIET  335 (471)
Q Consensus       262 l~~~~~~--~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~----~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~  335 (471)
                      +..++.+  ..+.+.+..++....... ..+......+-...    ...+..+.+...+......+.  +.......+..
T Consensus       218 ~~~~l~rla~~d~~~a~~~l~~~~~~~-~~~~~~~~~~~~~~a~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~w~~~~  294 (450)
T d1qsaa1         218 AAVAFASVARQDAENARLMIPSLAQAQ-QLNEDQIQELRDIVAWRLMGNDVTDEQAKWRDDAIMRSQ--STSLIERRVRM  294 (450)
T ss_dssp             HHHHHHHHHHHCHHHHHHHHHHHHHHT-TCCHHHHHHHHHHHHHTSCSTTCCHHHHHHHHHHHHTCC--CHHHHHHHHHH
T ss_pred             HHHHHHHHhccChhHHHHHHHhhhhcc-cccHHHHHHHHHHHHHHHHHcCchHHHHHHHHhhccccc--chHHHHHHHHH
Confidence            2222222  245666666666654432 22222222222222    233445566666655554432  33333334444


Q ss_pred             HHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 012111          336 FGKAGHIEKMEEYFKKMKHRGMKPNSITYCSLVSAYSKAGLIMKVDSILRQVEN  389 (471)
Q Consensus       336 ~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~  389 (471)
                      ....+++..+...+..|... ..-...-.--+..++...|+.+.|...|..+..
T Consensus       295 al~~~~~~~~~~~~~~l~~~-~~~~~r~~YW~gRa~~~~G~~~~A~~~~~~~a~  347 (450)
T d1qsaa1         295 ALGTGDRRGLNTWLARLPME-AKEKDEWRYWQADLLLERGREAEAKEILHQLMQ  347 (450)
T ss_dssp             HHHHTCHHHHHHHHHHSCTT-GGGSHHHHHHHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             HHHcCChHHHHHHHHhcCcc-cccHHHHHHHHHHHHHHcCChhhHHHHHHHHhc
Confidence            55566777776666665432 112234445566666777777777777776654