Citrus Sinensis ID: 041028

---

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---
Protein Sequence
MGGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKLGLKFDEESESGRTRSPWSRLKKEKLQIICGKKMEGDYAEGSELKWLAMDVAKECAGLPVSIVTGIKEQELFEWKDALEQLRRPSSTNFKDVQPAAYKAMELGYNKLEGDELKSTFLLIGYTAIASIDDLLMYGMGLGLFQGVNKMEAARARVHTLVHKLKASCMLLDHTSKNEKLFSIHDVVRDVAISIASGEQNVFSATNEQVDGCTEWSDESAVILYTSIVLRDIKTNVLPDR
Secondary Structure (PSIPRED)
cccccHHHHHHHHHHHHHccccccEEEEEEEcccccHHHHHHHHHHHHcccccccccccccccccHHHHHHHHHHHHccccccccccccHHHHHHHHHHHHcccccccEEcccccccHHHHHHHHHHHcccccccccccHHHHHHHHHHHHHcccccHHHHHHHcccccccccHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHcccccccccccccEEEEcHHHHHHHHHHHHccccEEEEEcccccccccccccccEEccEEEEEccccccccccc
Secondary Structure Prediction (SSPRO)
cccccHHHHHHHHHHHHHHcccccEEEEEEEcccccHHHHHHEEEEcccccEEEEcccccHHHHHHHccHHHcccccHHHccccccccccHHHHHHHHHHHHccccEEEEEEcccccHHHHHHHHHHHHccccccccccHHHHHHHHHccHHccccHHHHHHHHHHHHcccccHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHccccccccEEEHHHHHHHHHHHHHHcccccEEEEEEcccccEEcccHHHHccEEEEEcccccccccccc
Coil and Loop (DISEMBL)
MGGIGKTTLAKEVARKAKNGKLFDQIVFTEvsqnpnikkIQGEIAFKLGlkfdeesesgrtrspwsrlKKEKLQIICGKkmegdyaegsELKWLAMDVAKecaglpvsivtgikeqELFEWKDALEqlrrpsstnfkdvqPAAYKAMELGYnklegdelkSTFLLIGYTAIASIDDLLMYGMGLGLFQGVNKMEAARARVHTLVHKLKASCMlldhtskneklfsIHDVVRDVAISIASgeqnvfsatneqvdgctewsdeSAVILYTSIVLRdiktnvlpdr
Flexible Loop (DISEMBL)
mggigkttlAKEVArkakngklfdQIVFtevsqnpnikkiQGEIAFKlglkfdeesesgrtrspwsrlkkekLQIICGKKMEGDYAEGSELKWLAMDVAKECAGLPVSIVTGIKEQELFEWKDALeqlrrpsstnfkdvqpAAYKAMELGYNKLEGDELKSTFLLIGYTAIASIDDLLMYGMGLGLFQGVNKMEAARARVHTLVHKLKASCMLLDHTSKNEKLFSIHDVVRDVAISIASGEQNVFSATNEQVDGCTEWSDESAVILYtsivlrdiktnvlpdr
Low Complexity Region (SEG)
MGGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKLGLKFDEESESGRTRSPWSRLKKEKLQIICGKKMEGDYAEGSELKWLAMDVAKECAGLPVSIVTGIKEQELFEWKDALEQLRRPSSTNFKDVQPAAYKAMELGYNKLEGDELKSTFLLIGYTAIASIDDllmygmglglFQGVNKMEAARARVHTLVHKLKASCMLLDHTSKNEKLFSIHDVVRDVAISIASGEQNVFSATNEQVDGCTEWSDESAVILYTSIVLRDIKTNVLPDR
Disordered region (IsUnstruct)
******************NGKLFDQIVFTEVSQNPNIKKIQGEIAFKLGLKF*******************KLQIICGKKMEGDYAEGSELKWLAMDVAKECAGLPVSIVTGIKEQELFEWKDALEQL*********DVQPAAYKAMELGYNKLEGDELKSTFLLIGYTAIASIDDLLMYGMGLGLFQGVNKMEAARARVHTLVHKLKASCMLLDHTSKNEKLFSIHDVVRDVAISIASGEQNVFSATNEQVDGCTEWSDESAVILYTSIVLRDIKTNV****
Disordered Region (DISOPRED)
MGGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKLGLKFDEESESGRTRSPWSRLKKEKLQIICGKKMEGDYAEGSELKWLAMDVAKECAGLPVSIVTGIKEQELFEWKDALEQLRRPSSTNFKDVQPAAYKAMELGYNKLEGDELKSTFLLIGYTAIASIDDLLMYGMGLGLFQGVNKMEAARARVHTLVHKLKASCMLLDHTSKNEKLFSIHDVVRDVAISIASGEQNVFSATNEQVDGCTEWSDESAVILYTSIVLRDIKTNVLP**
Disordered Region (DISEMBL)
MGGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKLGLKFD**************LKKEKLQIICGKKMEGDYAEGSELKWLAMDVAKECAGLPVSIVTGIKEQELFEWKDALEQLRRPSSTNFKDVQPAAYKAMELGYNKLEGDELKSTFLLIGYTAIASIDDLLMYGMGLGLFQGVNKMEAARARVHTLVHKLKASCMLLDHTSKNEKLFSIHDVVRDVAISIASGEQNVFSATNEQVDGCTEWSDESAVILYTSIVLRDIKTNVLPDR
Disordered Region (DISPRO)
**GIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKLGLKFDEESESGRTRSPWSRLKKEKLQIICGKKMEGDYAEGSELKWLAMDVAKECAGLPVSIVTGIKEQELFEWKDALEQLRRPSSTNFKDVQPAAYKAMELGYNKLEGDELKSTFLLIGYTAIASIDDLLMYGMGLGLFQGVNKMEAARARVHTLVHKLKASCMLLDHTSKNEKLFSIHDVVRDVAISIASGEQNVFSATNEQVDGCTEWSDESAVILYTSIVLRDIKTNV****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MGGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKLGLKFDEESESGRTRSPWSRLKKEKLQIICGKKMEGDYAEGSELKWLAMDVAKECAGLPVSIVTGIKEQELFEWKDALEQLRRPSSTNFKDVQPAAYKAMELGYNKLEGDELKSTFLLIGYTAIASIDDLLMYGMGLGLFQGVNKMEAARARVHTLVHKLKASCMLLDHTSKNEKLFSIHDVVRDVAISIASGEQNVFSATNEQVDGCTEWSDESAVILYTSIVLRDIKTNVLPDR
Positional Conservation
no confident homologs detected

---

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	283	2.2.26 [Sep-21-2011]
O81825	919	Probable disease resistan	yes	no	0.971	0.299	0.252	7e-16
Q8L3R3	885	Disease resistance protei	no	no	0.819	0.262	0.258	1e-11
Q8RXS5	888	Probable disease resistan	no	no	0.812	0.259	0.256	4e-10
Q9FLB4	874	Putative disease resistan	no	no	0.886	0.287	0.236	8e-10
Q9T048	985	Disease resistance protei	no	no	0.593	0.170	0.297	2e-09
O64973	889	Disease resistance protei	no	no	0.837	0.266	0.233	3e-09
Q42484	909	Disease resistance protei	no	no	0.575	0.179	0.296	5e-09
P60838	894	Probable disease resistan	no	no	0.823	0.260	0.233	5e-09
Q9LVT4	843	Probable disease resistan	no	no	0.932	0.313	0.225	8e-07
P60839	884	Probable disease resistan	no	no	0.830	0.265	0.226	2e-06

>sp|O81825|DRL28_ARATH Probable disease resistance protein At4g27220 OS=Arabidopsis thaliana GN=At4g27220 PE=2 SV=1

 Score = 84.7 bits (208), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 89/353 (25%), Positives = 145/353 (41%), Gaps = 78/353 (22%)

Query: 1   MGGIGKTTLAKEVAR---KAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKLGLKFDEES- 56
           MGG+GKTTL + +     K    + F  +++  VS++ ++K++Q +IA +LG +F  E  
Sbjct: 142 MGGVGKTTLVRTLNNDLLKYAATQQFALVIWVTVSKDFDLKRVQMDIAKRLGKRFTREQM 201

Query: 57  -------------------------------------------------ESGRTRSPWSR 67
                                                             S R       
Sbjct: 202 NQLGLTICERLIDLKNFLLILDDVWHPIDLDQLGIPLALERSKDSKVVLTSRRLEVCQQM 261

Query: 68  LKKEKLQIICGKKME---------GDYAEGSELKWLAMDVAKECAGLPVSIVT------G 112
           +  E +++ C ++ E         G+ A    +K +A DV+ EC GLP++I+T      G
Sbjct: 262 MTNENIKVACLQEKEAWELFCHNVGEVANSDNVKPIAKDVSHECCGLPLAIITIGRTLRG 321

Query: 113 IKEQELFEWKDALEQLRRPSSTNFKDVQPAAYKAMELGYNKLEGDELKSTFL---LIGYT 169
             + E+  WK  L  L+R + +   D +   +  ++L Y+ L+ D +KS FL   L    
Sbjct: 322 KPQVEV--WKHTLNLLKRSAPS--IDTEEKIFGTLKLSYDFLQ-DNMKSCFLFCALFPED 376

Query: 170 AIASIDDLLMYGMGLGLFQGVNKMEAARARVHTLVHKLKASCMLLDHTSKNEKLFSIHDV 229
               + +L+MY +  GL  G +  E       TLV +LK SC+L D  S +     +HDV
Sbjct: 377 YSIKVSELIMYWVAEGLLDGQHHYEDMMNEGVTLVERLKDSCLLEDGDSCDT--VKMHDV 434

Query: 230 VRDVAISIASGEQNVFSATNEQVDGCTEWSDESAVILYTSIVLRDIKTNVLPD 282
           VRD AI   S +   F +      G  E+  +  V     + L   K   LP+
Sbjct: 435 VRDFAIWFMSSQGEGFHSLVMAGRGLIEFPQDKFVSSVQRVSLMANKLERLPN 487

Probable disease resistance protein.
Arabidopsis thaliana (taxid: 3702)

>sp|Q8L3R3|RFL1_ARATH Disease resistance protein RFL1 OS=Arabidopsis thaliana GN=RFL1 PE=3 SV=2

 Score = 70.9 bits (172), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 81/313 (25%), Positives = 140/313 (44%), Gaps = 81/313 (25%)

Query: 1   MGGIGKTTLAKEVARK-AKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKLGL---KFDEES 56
           MGG+GKTTL  ++  K +K G  FD +++  VS+N  + KIQ  I  KLGL    +DE++
Sbjct: 184 MGGVGKTTLLTQINNKFSKLGGGFDVVIWVVVSKNATVHKIQKSIGEKLGLVGKNWDEKN 243

Query: 57  ESGRTRSPWSRLKKEKLQI-----------------------------------ICG--- 78
           ++ R     + L+++K  +                                   +CG   
Sbjct: 244 KNQRALDIHNVLRRKKFVLLLDDIWEKVELKVIGVPYPSGENGCKVAFTTHSKEVCGRMG 303

Query: 79  -------------------KKMEGDYAEGS--ELKWLAMDVAKECAGLPVSIVTGIKEQE 117
                              KK  G+   GS  ++  LA  V+++C GLP+++   I E  
Sbjct: 304 VDNPMEISCLDTGNAWDLLKKKVGENTLGSHPDIPQLARKVSEKCCGLPLAL-NVIGETM 362

Query: 118 LF-----EWKDALEQLRRPSSTNFKDVQPAAYKAMELGYNKLEGDELKSTFLLIGYTAIA 172
            F     EW+ A E L   S+T+F  ++      ++  Y+ L G++ KS FL   Y ++ 
Sbjct: 363 SFKRTIQEWRHATEVL--TSATDFSGMEDEILPILKYSYDSLNGEDAKSCFL---YCSLF 417

Query: 173 SID------DLLMYGMGLGLFQGVNKMEAARARVHTLVHKLKASCMLLDHTSKNEKLFSI 226
             D       L+ Y +  G  +     E A  + + ++  L  S +LL+  +K++ + S+
Sbjct: 418 PEDFEIRKEMLIEYWICEGFIKEKQGREKAFNQGYDILGTLVRSSLLLE-GAKDKDVVSM 476

Query: 227 HDVVRDVAISIAS 239
           HD+VR++A+ I S
Sbjct: 477 HDMVREMALWIFS 489

Disease resistance (R) protein.

Arabidopsis thaliana (taxid: 3702)

>sp|Q8RXS5|DRL40_ARATH Probable disease resistance protein At5g63020 OS=Arabidopsis thaliana GN=At5g63020 PE=2 SV=2

 Score = 65.5 bits (158), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 80/312 (25%), Positives = 142/312 (45%), Gaps = 82/312 (26%)

Query: 1   MGGIGKTTLAKEVA-RKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKL---GLKFDEES 56
           MGG+GKTTL   +  R ++ G  FD +++  VS+   I++IQ EI  KL     K+ +++
Sbjct: 182 MGGVGKTTLLSHINNRFSRVGGEFDIVIWIVVSKELQIQRIQDEIWEKLRSDNEKWKQKT 241

Query: 57  ESGRTRSPWSRLKKEK-----------------------------------LQIICGK-- 79
           E  +  + ++ LK ++                                   L+ ICG+  
Sbjct: 242 EDIKASNIYNVLKHKRFVLLLDDIWSKVDLTEVGVPFPSRENGCKIVFTTRLKEICGRMG 301

Query: 80  --------------------KMEGDYAEGS--ELKWLAMDVAKECAGLPVSIV----TGI 113
                               K  G+   GS  E+  +A  VAK+C GLP+++     T  
Sbjct: 302 VDSDMEVRCLAPDDAWDLFTKKVGEITLGSHPEIPTVARTVAKKCRGLPLALNVIGETMA 361

Query: 114 KEQELFEWKDALEQLRRPSSTNFKDVQPAAYKAMELGYNKLEGDELKSTFLLIGYTAIAS 173
            ++ + EW+ A++ L   S+  F  ++      ++  Y+ L+ ++LK  F    Y A+  
Sbjct: 362 YKRTVQEWRSAIDVLTS-SAAEFSGMEDEILPILKYSYDNLKSEQLKLCF---QYCALFP 417

Query: 174 ID------DLLMYGMGLGLFQGVNKMEAARARVHTLVHKLKASCMLLDHTSKNEKLFSIH 227
            D      DL+ Y +G G F   NK +A   + + ++  L  SC+L++   +N++   +H
Sbjct: 418 EDHNIEKNDLVDYWIGEG-FIDRNKGKAEN-QGYEIIGILVRSCLLME---ENQETVKMH 472

Query: 228 DVVRDVAISIAS 239
           DVVR++A+ IAS
Sbjct: 473 DVVREMALWIAS 484

Probable disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FLB4|DRL31_ARATH Putative disease resistance protein At5g05400 OS=Arabidopsis thaliana GN=At5g05400 PE=2 SV=1

 Score = 64.7 bits (156), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 80/338 (23%), Positives = 141/338 (41%), Gaps = 87/338 (25%)

Query: 1   MGGIGKTTLAKEVARKAKN-GKLFDQIVFTEVSQNPNIKKIQGEIAFKLGL-------KF 52
           MGG+GKTTL  ++  K +     FD  ++  VS+NP +K+IQ +I  +L L       K 
Sbjct: 183 MGGVGKTTLLSQINNKFRTVSNDFDIAIWVVVSKNPTVKRIQEDIGKRLDLYNEGWEQKT 242

Query: 53  DEESESGRTRS------------PWSRLKKEKLQI------------------ICGKKME 82
           + E  S   RS             W+++    + I                  +CGK   
Sbjct: 243 ENEIASTIKRSLENKKYMLLLDDMWTKVDLANIGIPVPKRNGSKIAFTSRSNEVCGKMGV 302

Query: 83  GDYAEGSELKW-----------------------LAMDVAKECAGLPVSIV----TGIKE 115
               E + L W                       +A  +A++C GLP+++     T  ++
Sbjct: 303 DKEIEVTCLMWDDAWDLFTRNMKETLESHPKIPEVAKSIARKCNGLPLALNVIGETMARK 362

Query: 116 QELFEWKDALEQLRRPSSTNFKDVQPAAYKAMELGYNKLEGDELKSTFL---LIGYTAIA 172
           + + EW DA+          F  ++      ++  Y+ L+ ++ KS FL   L       
Sbjct: 363 KSIEEWHDAV--------GVFSGIEADILSILKFSYDDLKCEKTKSCFLFSALFPEDYEI 414

Query: 173 SIDDLLMYGMGLGLFQGVNKMEAARARVHTLVHKLKASCMLLDHTSKNEKLFSIHDVVRD 232
             DDL+ Y +G G+  G    +    + +T++  L  + +L +  +K +    +HDVVR+
Sbjct: 415 GKDDLIEYWVGQGIILG---SKGINYKGYTIIGTLTRAYLLKESETKEK--VKMHDVVRE 469

Query: 233 VAISIASG-----EQNVFSA-TNEQVDGCTEWSDESAV 264
           +A+ I+SG     ++NV     N Q+    +  D+ AV
Sbjct: 470 MALWISSGCGDQKQKNVLVVEANAQLRDIPKIEDQKAV 507

Potential disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9T048|DRL27_ARATH Disease resistance protein At4g27190 OS=Arabidopsis thaliana GN=At4g27190 PE=2 SV=1

 Score = 63.5 bits (153), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 55/185 (29%), Positives = 92/185 (49%), Gaps = 17/185 (9%)

Query: 68  LKKEKLQIICGKKMEGDYAEGSELKWLAMDVAKECAGLPVSIVT------GIKEQELFEW 121
           L+++  ++ C  K  GD      ++ +A  V++EC GLP++I+T      G K  +L  W
Sbjct: 303 LEEDAWELFC--KNAGDVVRSDHVRKIAKAVSQECGGLPLAIITVGTAMRGKKNVKL--W 358

Query: 122 KDALEQLRRPSSTNFKDVQPAAYKAMELGYNKLEGDELKSTFLLIG-YTAIASID--DLL 178
              L +L + S    K ++   ++ ++L Y+ LE D+ K  FLL   +    SI+  +++
Sbjct: 359 NHVLSKLSK-SVPWIKSIEEKIFQPLKLSYDFLE-DKAKFCFLLCALFPEDYSIEVTEVV 416

Query: 179 MYGMGLGLFQGVNKMEAARARVHTLVHKLKASCMLLDHTSKNEKLFSIHDVVRDVAISIA 238
            Y M  G  + +   E +     T V  LK  C+L D   ++     +HDVVRD AI I 
Sbjct: 417 RYWMAEGFMEELGSQEDSMNEGITTVESLKDYCLLEDGDRRDT--VKMHDVVRDFAIWIM 474

Query: 239 SGEQN 243
           S  Q+
Sbjct: 475 SSSQD 479

Disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|O64973|RPS5_ARATH Disease resistance protein RPS5 OS=Arabidopsis thaliana GN=RPS5 PE=1 SV=2

 Score = 62.8 bits (151), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 72/309 (23%), Positives = 136/309 (44%), Gaps = 72/309 (23%)

Query: 1   MGGIGKTTLAKEVARK-AKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKL---GLKFDEES 56
           MGG+GKTTL  ++  K +K    FD +++  VS++  ++KIQ +IA K+   G+++ E++
Sbjct: 184 MGGVGKTTLLTKINNKFSKIDDRFDVVIWVVVSRSSTVRKIQRDIAEKVGLGGMEWSEKN 243

Query: 57  ESGRTRSPWSRLKKEKLQI-----------------------------------ICGKKM 81
           ++       + L++ K  +                                   +CG+  
Sbjct: 244 DNQIAVDIHNVLRRRKFVLLLDDIWEKVNLKAVGVPYPSKDNGCKVAFTTRSRDVCGRMG 303

Query: 82  EGDYAEGSELK----W--------------------LAMDVAKECAGLPVSI-VTG---I 113
             D  E S L+    W                    LA  VA++C GLP+++ V G    
Sbjct: 304 VDDPMEVSCLQPEESWDLFQMKVGKNTLGSHPDIPGLARKVARKCRGLPLALNVIGEAMA 363

Query: 114 KEQELFEWKDALEQLRRPSSTNFKDVQPAAYKAMELGYNKLEGDELKSTFL---LIGYTA 170
            ++ + EW  A++ L   S+ +F  ++      ++  Y+ L G+ +KS FL   L     
Sbjct: 364 CKRTVHEWCHAIDVLT-SSAIDFSGMEDEILHVLKYSYDNLNGELMKSCFLYCSLFPEDY 422

Query: 171 IASIDDLLMYGMGLGLFQGVNKMEAARARVHTLVHKLKASCMLLDHTSKNEKLFSIHDVV 230
           +   + L+ Y +  G        E    + + ++  L  +C+LL+   +N+    +HDVV
Sbjct: 423 LIDKEGLVDYWISEGFINEKEGRERNINQGYEIIGTLVRACLLLEE-ERNKSNVKMHDVV 481

Query: 231 RDVAISIAS 239
           R++A+ I+S
Sbjct: 482 REMALWISS 490

Disease resistance (R) protein that specifically recognizes the avrPphB type III effector avirulence protein from Pseudomonas syringae. Also confers resistance against Hyaloperonospora parasitica (downy mildew). Resistance proteins guard the plant against pathogens that contain an appropriate avirulence protein via an indirect interaction with this avirulence protein. That triggers a defense system including the hypersensitive response, which restricts the pathogen growth. Requires PBS1 to trigger the defense reaction against avrPphB. Probably triggers the defense mechanism when PBS1 is cleaved by avrPphB, suggesting that it detects indirectly the protease activity of avrPphB, and possibly binds to the cleaved RPS5.

Arabidopsis thaliana (taxid: 3702)

>sp|Q42484|RPS2_ARATH Disease resistance protein RPS2 OS=Arabidopsis thaliana GN=RPS2 PE=1 SV=1

 Score = 62.0 bits (149), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 57/192 (29%), Positives = 90/192 (46%), Gaps = 29/192 (15%)

Query: 69  KKEKLQIICGKKMEGDYAEGSELKWLAMDVAKECAGLPVSIVT-----GIKEQELFEWKD 123
           KK   ++ C K    D  E S ++ LA  +  +C GLP++++T       +E E  EW  
Sbjct: 312 KKHAWELFCSKVWRKDLLESSSIRRLAEIIVSKCGGLPLALITLGGAMAHRETE-EEWIH 370

Query: 124 ALEQLRR-PSSTNFKDVQPAAYKAMELGYNKLEGDELKSTFLLIGYTAI------ASIDD 176
           A E L R P+     +     +  ++  Y+ LE D L+S FL   Y A+        I+ 
Sbjct: 371 ASEVLTRFPAEMKGMNY---VFALLKFSYDNLESDLLRSCFL---YCALFPEEHSIEIEQ 424

Query: 177 LLMYGMGLGLF---QGVNKMEAARARVHTLVHKLKASCMLLDHTSKNEKLFSIHDVVRDV 233
           L+ Y +G G      GVN +       + L+  LKA+C+L   T   +    +H+VVR  
Sbjct: 425 LVEYWVGEGFLTSSHGVNTIYKG----YFLIGDLKAACLL--ETGDEKTQVKMHNVVRSF 478

Query: 234 AISIASGEQNVF 245
           A+ +AS EQ  +
Sbjct: 479 ALWMAS-EQGTY 489

Disease resistance (R) protein that specifically recognizes the AvrRpt2 type III effector avirulence protein from Pseudomonas syringae. Resistance proteins guard the plant against pathogens that contain an appropriate avirulence protein via an indirect interaction with this avirulence protein. That triggers a defense system including the hypersensitive response, which restricts the pathogen growth. Acts via its interaction with RIN4, and probably triggers the plant resistance when RIN4 is degraded by AvrRpt2.

Arabidopsis thaliana (taxid: 3702)

>sp|P60838|DRL1_ARATH Probable disease resistance protein At1g12280 OS=Arabidopsis thaliana GN=At1g12280 PE=3 SV=1

 Score = 61.6 bits (148), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 73/312 (23%), Positives = 135/312 (43%), Gaps = 79/312 (25%)

Query: 1   MGGIGKTTLAKEVARK-AKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKLGL---KFDEES 56
           MGG+GKTTL   +  K ++    F  +++  VS++P+I +IQG+I  +L L   ++D  +
Sbjct: 184 MGGVGKTTLLTRINNKFSEKCSGFGVVIWVVVSKSPDIHRIQGDIGKRLDLGGEEWDNVN 243

Query: 57  ESGRTRSPWSRLKKEKLQI-----------------------------------ICGKKM 81
           E+ R    ++ L K+K  +                                   +CG+  
Sbjct: 244 ENQRALDIYNVLGKQKFVLLLDDIWEKVNLEVLGVPYPSRQNGCKVVFTTRSRDVCGRMR 303

Query: 82  EGDYAEGSELK----W--------------------LAMDVAKECAGLPVSI----VTGI 113
             D  E S L+    W                    LA  VA +C GLP+++     T  
Sbjct: 304 VDDPMEVSCLEPNEAWELFQMKVGENTLKGHPDIPELARKVAGKCCGLPLALNVIGETMA 363

Query: 114 KEQELFEWKDALEQLRRPSSTNFKDVQPAAYKAMELGYNKLEGDELKSTFLLIGYTAIAS 173
            ++ + EW++A++ L    +  F  ++      ++  Y+ L  +++K  FL   Y ++  
Sbjct: 364 CKRMVQEWRNAIDVLS-SYAAEFPGME-QILPILKYSYDNLNKEQVKPCFL---YCSLFP 418

Query: 174 ID------DLLMYGMGLGLFQGVNKMEAARARVHTLVHKLKASCMLLDHTSKNEKLFSIH 227
            D       L+ Y +  G        E A ++ + ++  L  +C+LL+     E++  +H
Sbjct: 419 EDYRMEKERLIDYWICEGFIDENESRERALSQGYEIIGILVRACLLLEEAINKEQV-KMH 477

Query: 228 DVVRDVAISIAS 239
           DVVR++A+ IAS
Sbjct: 478 DVVREMALWIAS 489

Probable disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LVT4|DRL37_ARATH Probable disease resistance protein At5g47250 OS=Arabidopsis thaliana GN=At5g47250 PE=2 SV=1

 Score = 54.7 bits (130), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 77/341 (22%), Positives = 142/341 (41%), Gaps = 77/341 (22%)

Query: 1   MGGIGKTTLAKEVARK-AKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKL----------- 48
           MGG+GKTTL   +  K  +    +D +++ E S++ ++ KIQ  I  +L           
Sbjct: 184 MGGVGKTTLLTLINNKFVEVSDDYDVVIWVESSKDADVGKIQDAIGERLHICDNNWSTYS 243

Query: 49  -GLKFDEESESGRTRSP---------WSRLKKEKLQI-ICGKKM---------------- 81
            G K  E S   R   P         W  +    + I + GKK                 
Sbjct: 244 RGKKASEISRVLRDMKPRFVLLLDDLWEDVSLTAIGIPVLGKKYKVVFTTRSKDVCSVMR 303

Query: 82  -----------EGD---------YAEG-SELKWLAMDVAKECAGLPVSI----VTGIKEQ 116
                      E D         + +G +E+  +A  +  +C GLP+++     T   + 
Sbjct: 304 ANEDIEVQCLSENDAWDLFDMKVHCDGLNEISDIAKKIVAKCCGLPLALEVIRKTMASKS 363

Query: 117 ELFEWKDALEQLRRPSSTNFKDVQPAAYKAMELGYNKLEGDELKSTFLLIGYTAIASI-- 174
            + +W+ AL+ L    S   K  +   ++ ++L Y+ L+    K       +     I  
Sbjct: 364 TVIQWRRALDTLESYRS-EMKGTEKGIFQVLKLSYDYLKTKNAKCFLYCALFPKAYYIKQ 422

Query: 175 DDLLMYGMGLGLFQGVNKMEAARARVHTLVHKLKASCMLLDHTSKNEKLFSIHDVVRDVA 234
           D+L+ Y +G G     +  E A+ R + ++  L  + +LL+    N+K++ +HD++RD+A
Sbjct: 423 DELVEYWIGEGFIDEKDGRERAKDRGYEIIDNLVGAGLLLE---SNKKVY-MHDMIRDMA 478

Query: 235 ISIAS----GEQNVF--SATNEQVDGCTEWSDESAVILYTS 269
           + I S    GE+ V    A   Q+   T+W+  + + L+ +
Sbjct: 479 LWIVSEFRDGERYVVKTDAGLSQLPDVTDWTTVTKMSLFNN 519

Probable disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|P60839|DRL2_ARATH Probable disease resistance protein At1g12290 OS=Arabidopsis thaliana GN=At1g12290 PE=2 SV=1

 Score = 53.5 bits (127), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 71/313 (22%), Positives = 129/313 (41%), Gaps = 78/313 (24%)

Query: 1   MGGIGKTTLAKEVA-RKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKLG---LKFDEES 56
           MGG+GKTTL  ++  R        + +++  VS +  I KIQ EI  K+G   ++++++S
Sbjct: 183 MGGVGKTTLLTQINNRFCDTDDGVEIVIWVVVSGDLQIHKIQKEIGEKIGFIGVEWNQKS 242

Query: 57  ESGRT----------------RSPWSRLK-------------------KEKLQIICG--- 78
           E+ +                    W R++                     + Q +C    
Sbjct: 243 ENQKAVDILNFLSKKRFVLLLDDIWKRVELTEIGIPNPTSENGCKIAFTTRCQSVCASMG 302

Query: 79  -------------------KKMEGDYAEGS--ELKWLAMDVAKECAGLPVSIV----TGI 113
                              KK  GD    S  ++  +A  VA+ C GLP+++     T  
Sbjct: 303 VHDPMEVRCLGADDAWDLFKKKVGDITLSSHPDIPEIARKVAQACCGLPLALNVIGETMA 362

Query: 114 KEQELFEWKDALEQLRRPSSTNFKDVQPAAYKAMELGYNKLEGDELKSTFLLIGYTAIAS 173
            ++   EW  A++ +    + NF  V+      ++  Y+ LE + +K+ FL   Y ++  
Sbjct: 363 CKKTTQEWDRAVD-VSTTYAANFGAVKERILPILKYSYDNLESESVKTCFL---YCSLFP 418

Query: 174 IDDLLM------YGMGLGLFQGVNKMEAARARVHTLVHKLKASCMLLDHTSKNEKLF-SI 226
            DDL+       Y +  G   G    + A    + ++  L  + +L++    N K +  +
Sbjct: 419 EDDLIEKERLIDYWICEGFIDGDENKKGAVGEGYEILGTLVCASLLVEGGKFNNKSYVKM 478

Query: 227 HDVVRDVAISIAS 239
           HDVVR++A+ IAS
Sbjct: 479 HDVVREMALWIAS 491

Probable disease resistance protein.

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	283
224083434	1144	cc-nbs-lrr resistance protein [Populus t	0.851	0.210	0.461	4e-56
359488288	1340	PREDICTED: LOW QUALITY PROTEIN: probable	0.978	0.206	0.387	4e-51
147802546	1409	hypothetical protein VITISV_007222 [Viti	0.946	0.190	0.400	2e-49
296087872	1152	unnamed protein product [Vitis vinifera]	0.946	0.232	0.400	2e-49
359488027	1520	PREDICTED: disease resistance protein At	0.946	0.176	0.400	2e-49
147865073	1694	hypothetical protein VITISV_021876 [Viti	0.893	0.149	0.387	2e-46
255563252	1603	Disease resistance protein RPS5, putativ	0.950	0.167	0.387	2e-46
147833354	1494	hypothetical protein VITISV_041837 [Viti	0.975	0.184	0.365	2e-44
359488095	1347	PREDICTED: probable disease resistance p	0.975	0.204	0.365	3e-44
359488103	1530	PREDICTED: disease resistance protein At	0.904	0.167	0.375	4e-44

>gi|224083434|ref|XP_002307025.1| cc-nbs-lrr resistance protein [Populus trichocarpa] gi|222856474|gb|EEE94021.1| cc-nbs-lrr resistance protein [Populus trichocarpa]

 Score =  224 bits (570), Expect = 4e-56,   Method: Compositional matrix adjust.
 Identities = 143/310 (46%), Positives = 178/310 (57%), Gaps = 69/310 (22%)

Query: 6   KTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKLGLKFDEESESGRTRSPW 65
           KTTL KE AR+A   KLF+Q+VF  ++Q  +IKKIQG+IA +L LKFDEESE GR     
Sbjct: 189 KTTLVKEAARQAIQEKLFNQVVFATITQTQDIKKIQGQIADQLSLKFDEESECGRAGRLR 248

Query: 66  SRLKKE-KLQII-------------------------------------CG--------- 78
            RLK+E K+ II                                     CG         
Sbjct: 249 QRLKQEQKILIILDDLWKSLDLEAVGIPLKDEHEGCKMLVTSREFDVLSCGMDIQKNFPI 308

Query: 79  ------------KKMEGDYAEGSELKWLAMDVAKECAGLPVSIVT---GIKEQELFEWKD 123
                       KKM GD+ E  +L+ LA++VAK CAGLPV+IVT    +K + L +WK+
Sbjct: 309 NALSEEETWELFKKMAGDHVEHPDLQSLAIEVAKMCAGLPVAIVTVARALKNKNLSQWKN 368

Query: 124 ALEQLRRPSSTNFKDVQPAAYKAMELGYNKLEGDELKSTFLL---IGYTAIASIDDLLMY 180
           AL +L+RPS  NF  VQ   Y A+EL YN LE  ELKSTFLL   +GY   AS  DLL Y
Sbjct: 369 ALRELKRPSPRNFAGVQEDVYAAIELSYNHLESKELKSTFLLCSRMGYN--ASTRDLLKY 426

Query: 181 GMGLGLFQGVNKMEAARARVHTLVHKLKASCMLLDHTSKNEKLFSIHDVVRDVAISIASG 240
           GMGLGLF G   +E A+ RVH+LVHKLKAS +LL++ S  +  FS+HD VRDVAISIA  
Sbjct: 427 GMGLGLFSGFVTVEEAQDRVHSLVHKLKASGLLLENHSDWQ--FSMHDAVRDVAISIAFR 484

Query: 241 EQNVFSATNE 250
           + +VF   +E
Sbjct: 485 DCHVFVGGDE 494

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359488288|ref|XP_003633735.1| PREDICTED: LOW QUALITY PROTEIN: probable disease resistance protein At1g61310-like [Vitis vinifera]

 Score =  207 bits (527), Expect = 4e-51,   Method: Compositional matrix adjust.
 Identities = 134/346 (38%), Positives = 183/346 (52%), Gaps = 69/346 (19%)

Query: 1   MGGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKLGLKFDEESESGR 60
           MGG+GK TL K+VA +A   KLFD++V T V Q P+ ++IQGEIA  LG+KF+EESE GR
Sbjct: 181 MGGVGKNTLVKQVAEQAAQEKLFDKVVMTSVFQTPDFRRIQGEIADMLGMKFEEESEQGR 240

Query: 61  TR-----------------SPWSRLKKEKLQI---------------------------- 75
                                W+ L+ EK+ I                            
Sbjct: 241 AARLHRKINEEKTILIILDDIWAELELEKIGIPSPDNHKGCKLVLTSRNKHVLSNEMSTQ 300

Query: 76  --------------ICGKKMEGDYAEGSELKWLAMDVAKECAGLPVSIVT---GIKEQEL 118
                         I  K M GD  E  +L  +A DVAKEC GLP++IVT    +K + +
Sbjct: 301 KDFGVEHLQGDEAWILFKNMVGDSIENPDLLLIATDVAKECTGLPIAIVTVAKALKNKNV 360

Query: 119 FEWKDALEQLRRPSSTNFKDVQPAAYKAMELGYNKLEGDELKSTFLLIG-YTAIASIDDL 177
             WKDAL+QL+  +STN   +    Y  ++L Y  LEGDE+KS FLL G ++    I DL
Sbjct: 361 SIWKDALKQLKTQTSTNITGMGTKVYSTLKLSYKHLEGDEVKSLFLLCGLFSNYIDIRDL 420

Query: 178 LMYGMGLGLFQGVNKMEAARARVHTLVHKLKASCMLLDHTSKNEKLFSIHDVVRDVAISI 237
           L YGMGL LFQG N +E A+ R+ TLV  LKAS +LL+  ++   +F +HDVV++VAI I
Sbjct: 421 LKYGMGLRLFQGTNTLEEAKNRIETLVDNLKASNLLLE--TRYNAVFRMHDVVQNVAIEI 478

Query: 238 ASGEQNVFS-ATNEQVDGCTEWSDESAVILYTSIVLRDIKTNVLPD 282
           AS E +VF+  T  +++   EW +   +  +T I L       LP+
Sbjct: 479 ASKEHHVFTFQTGVRME---EWPNMDELQKFTMIYLDCCDIRELPE 521

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147802546|emb|CAN77665.1| hypothetical protein VITISV_007222 [Vitis vinifera]

 Score =  202 bits (514), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 137/342 (40%), Positives = 176/342 (51%), Gaps = 74/342 (21%)

Query: 1   MGGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKLGLKFDEESESGR 60
           M G+GKTTL K+VA++ +  KLFD++V   +S  P +KKIQGE+A  LGLKF  E ES  
Sbjct: 181 MAGVGKTTLMKQVAKQVEEEKLFDKVVMAYISSTPELKKIQGELADMLGLKF--EEESEM 238

Query: 61  TRSP-------------------WSRLKKEKLQIICG----------------------- 78
            R+                    W+ L  EK+ I  G                       
Sbjct: 239 GRAARLCERLKKVKKILIILDDIWTELDLEKVGIPFGDDHKGCKMVLTSRNKHVLSNEMG 298

Query: 79  -------------------KKMEGDYAEGSELKWLAMDVAKECAGLPVSIVT---GIKEQ 116
                              KKM GD  E  +L+ +A+DVAKECAGLP++IVT    +K +
Sbjct: 299 TQKDFPVEHLQEEEALILFKKMAGDSIEEPDLQSIAIDVAKECAGLPIAIVTVAKALKNK 358

Query: 117 ELFEWKDALEQLRRPSSTNFKDVQPAAYKAMELGYNKLEGDELKSTFLLIGYTA-IASID 175
            L  W+DAL QL+R   TN K +    Y  +EL YN LEGDE+KS FLL G  +    ID
Sbjct: 359 GLSIWEDALRQLKRSIPTNIKGMDAMVYSTLELSYNHLEGDEVKSLFLLCGLMSNKIYID 418

Query: 176 DLLMYGMGLGLFQGVNKMEAARARVHTLVHKLKASCMLLDHTSKNEKLFSIHDVVRDVAI 235
           DLL YGMGL LFQG N +E A+ R+ TLV  LKAS +LLD  + +     +HDVVRDVAI
Sbjct: 419 DLLKYGMGLRLFQGTNTLEEAKNRIDTLVDSLKASKLLLD--TGHNSFVRMHDVVRDVAI 476

Query: 236 SIASGEQNVFSATNEQVDGCTEWS--DESAVILYTSIVLRDI 275
           +I S    VFS   +++    EW   DE       S+   DI
Sbjct: 477 AIVSKVHCVFSLREDEL---AEWPKMDELQTCTKMSLAYNDI 515

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|296087872|emb|CBI35155.3| unnamed protein product [Vitis vinifera]

 Score =  202 bits (513), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 137/342 (40%), Positives = 176/342 (51%), Gaps = 74/342 (21%)

Query: 1   MGGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKLGLKFDEESESGR 60
           M G+GKTTL K+VA++A+  KLFD++V   +S  P +KKIQGE+A  LGLKF  E ES  
Sbjct: 1   MAGVGKTTLMKQVAKQAEEEKLFDKVVMAYISSTPELKKIQGELADMLGLKF--EEESEM 58

Query: 61  TRSP-------------------WSRLKKEKLQIICG----------------------- 78
            R+                    W+ L  EK+ I  G                       
Sbjct: 59  GRAARLCERLKKVKKILIILDDIWTELDLEKVGIPFGDDHKGCKMVLTSRNKHILSNEMG 118

Query: 79  -------------------KKMEGDYAEGSELKWLAMDVAKECAGLPVSIVT---GIKEQ 116
                              KKM GD  E  +L+ +A+DVAKECAGLP++IVT    +K +
Sbjct: 119 TQKDFPVEHLQEEEALILFKKMAGDSIEEPDLQSIAIDVAKECAGLPIAIVTVAKALKNK 178

Query: 117 ELFEWKDALEQLRRPSSTNFKDVQPAAYKAMELGYNKLEGDELKSTFLLIGYTA-IASID 175
            L  W+DAL QL+R   TN K +    Y  +EL Y  LEGDE+KS FLL G  +    ID
Sbjct: 179 GLSIWEDALRQLKRSIPTNIKGMDAMVYSTLELSYKHLEGDEVKSLFLLCGLMSNKIYID 238

Query: 176 DLLMYGMGLGLFQGVNKMEAARARVHTLVHKLKASCMLLDHTSKNEKLFSIHDVVRDVAI 235
           DLL YGMGL LFQG N +E A+ R+ TLV  LKAS +LLD  + +     +HDVVRDVAI
Sbjct: 239 DLLKYGMGLRLFQGTNTLEEAKNRIDTLVDSLKASKLLLD--TGHNSFVRMHDVVRDVAI 296

Query: 236 SIASGEQNVFSATNEQVDGCTEWS--DESAVILYTSIVLRDI 275
           +I S    VFS   +++    EW   DE       S+   DI
Sbjct: 297 AIVSKVHRVFSLREDEL---VEWPKMDELQTCTKMSLAYNDI 335

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359488027|ref|XP_002269288.2| PREDICTED: disease resistance protein At4g27190-like [Vitis vinifera]

 Score =  202 bits (513), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 137/342 (40%), Positives = 176/342 (51%), Gaps = 74/342 (21%)

Query: 1   MGGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKLGLKFDEESESGR 60
           M G+GKTTL K+VA++A+  KLFD++V   +S  P +KKIQGE+A  LGLKF  E ES  
Sbjct: 181 MAGVGKTTLMKQVAKQAEEEKLFDKVVMAYISSTPELKKIQGELADMLGLKF--EEESEM 238

Query: 61  TRSP-------------------WSRLKKEKLQIICG----------------------- 78
            R+                    W+ L  EK+ I  G                       
Sbjct: 239 GRAARLCERLKKVKKILIILDDIWTELDLEKVGIPFGDDHKGCKMVLTSRNKHILSNEMG 298

Query: 79  -------------------KKMEGDYAEGSELKWLAMDVAKECAGLPVSIVT---GIKEQ 116
                              KKM GD  E  +L+ +A+DVAKECAGLP++IVT    +K +
Sbjct: 299 TQKDFPVEHLQEEEALILFKKMAGDSIEEPDLQSIAIDVAKECAGLPIAIVTVAKALKNK 358

Query: 117 ELFEWKDALEQLRRPSSTNFKDVQPAAYKAMELGYNKLEGDELKSTFLLIGYTA-IASID 175
            L  W+DAL QL+R   TN K +    Y  +EL Y  LEGDE+KS FLL G  +    ID
Sbjct: 359 GLSIWEDALRQLKRSIPTNIKGMDAMVYSTLELSYKHLEGDEVKSLFLLCGLMSNKIYID 418

Query: 176 DLLMYGMGLGLFQGVNKMEAARARVHTLVHKLKASCMLLDHTSKNEKLFSIHDVVRDVAI 235
           DLL YGMGL LFQG N +E A+ R+ TLV  LKAS +LLD  + +     +HDVVRDVAI
Sbjct: 419 DLLKYGMGLRLFQGTNTLEEAKNRIDTLVDSLKASKLLLD--TGHNSFVRMHDVVRDVAI 476

Query: 236 SIASGEQNVFSATNEQVDGCTEWS--DESAVILYTSIVLRDI 275
           +I S    VFS   +++    EW   DE       S+   DI
Sbjct: 477 AIVSKVHRVFSLREDEL---VEWPKMDELQTCTKMSLAYNDI 515

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147865073|emb|CAN83232.1| hypothetical protein VITISV_021876 [Vitis vinifera]

 Score =  192 bits (487), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 124/320 (38%), Positives = 171/320 (53%), Gaps = 67/320 (20%)

Query: 1   MGGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKLGLKFDEESESGR 60
           MGG+GK+TL K+VA +A+  KLF ++V   V Q P+ K IQ +IA KLG+KF+E SE GR
Sbjct: 178 MGGVGKSTLVKQVAEQAEQEKLFRKVVMVPVIQTPDFKGIQQQIADKLGMKFEEVSEQGR 237

Query: 61  TR-----------------SPWSRLKKEKLQI---------------------------- 75
                                W+ L+ EK+ I                            
Sbjct: 238 ADRLHQRIKQENTILIILDDLWAELELEKVGIPSPDDHKGCKLVLTSRNKQVLSNEMSTQ 297

Query: 76  --------------ICGKKMEGDYAEGSELKWLAMDVAKECAGLPVSIVT---GIKEQEL 118
                         I  K   GD  E  EL+ +A+DVAKECAGLP++IVT    +K + +
Sbjct: 298 KDFRVQHLQEDETWILFKNTAGDSIENPELQPIAVDVAKECAGLPIAIVTVAKALKNKNV 357

Query: 119 FEWKDALEQLRRPSSTNFKDVQPAAYKAMELGYNKLEGDELKSTFLLIG-YTAIASIDDL 177
             WKDAL+QL   +STN   ++   Y +++L Y  LEGDE+KS FLL G ++    I DL
Sbjct: 358 SIWKDALQQLNSQTSTNITGMETKVYSSLKLSYEHLEGDEVKSLFLLCGLFSNYIYIRDL 417

Query: 178 LMYGMGLGLFQGVNKMEAARARVHTLVHKLKASCMLLDHTSKNEKLFSIHDVVRDVAISI 237
           L YGMGL LFQG N +E A+ R+ TLV  LK+S +LL+  + +  +  +HDVVR VA+ I
Sbjct: 418 LKYGMGLRLFQGTNTLEEAKNRIDTLVDNLKSSNLLLE--TGHNAVVRMHDVVRSVALDI 475

Query: 238 ASGEQNVFSATNEQVDGCTE 257
           +S + +VF  T +Q  G  E
Sbjct: 476 SSKDHHVF--TLQQTTGRVE 493

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255563252|ref|XP_002522629.1| Disease resistance protein RPS5, putative [Ricinus communis] gi|223538105|gb|EEF39716.1| Disease resistance protein RPS5, putative [Ricinus communis]

 Score =  192 bits (487), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 132/341 (38%), Positives = 179/341 (52%), Gaps = 72/341 (21%)

Query: 6   KTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKLGLKFDEESESGRTR--- 62
           KTTLAKEV ++    KLFD +V   VS+ P+I+KIQG IA  LGLKFDEE+E+GR     
Sbjct: 188 KTTLAKEVHQQVIEEKLFDIVVMATVSEKPDIRKIQGNIADVLGLKFDEETETGRAYRLR 247

Query: 63  --------------SPWSRLKKEKLQIICG------------------------------ 78
                         + W++L+ E++ I CG                              
Sbjct: 248 QRLMTEKKILVILDNIWAQLELEEVGIPCGVDHKGCKILLTSRSRDLLSCDMGVQKVFRL 307

Query: 79  ------------KKMEGDYAEGSELKWLAMDVAKECAGLPVSIVT---GIKEQELFEWKD 123
                       + M GD  +G E +  A +V K+CAGLPV IVT    +K ++L+ WKD
Sbjct: 308 EVLQEEEALSLFEMMVGD-VKGGEFQSAASEVTKKCAGLPVLIVTIARALKNKDLYVWKD 366

Query: 124 ALEQLRRPSSTNFKDVQPAAYKAMELGYNKLEGDELKSTFLLIGYTAIASID--DLLMYG 181
           A++QL R    + +++Q   Y A+EL YN L G E+KS FLL G    + I   DLLMY 
Sbjct: 367 AVKQLSR---CDNEEIQEKVYSALELSYNHLIGAEVKSLFLLCGLLGKSDIAILDLLMYS 423

Query: 182 MGLGLFQGVNKMEAARARVHTLVHKLKASCMLLDHTSKNEKLFSIHDVVRDVAISIASGE 241
            GLGLF+G++ +  AR RVH L+  LKA+C+LLD   K      IHDVVRDVAISIAS  
Sbjct: 424 TGLGLFKGIDTLGDARNRVHKLISDLKAACLLLDSDIKGR--VKIHDVVRDVAISIASRM 481

Query: 242 QNVFSATNEQVDGCTEWSDESAVILYTSIVLRDIKTNVLPD 282
           Q++F+  N  +    EW ++      T I L     + LP+
Sbjct: 482 QHLFTVRNGAL--LKEWPNKDVCKSCTRISLPYNDIHGLPE 520

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147833354|emb|CAN66237.1| hypothetical protein VITISV_041837 [Vitis vinifera]

 Score =  185 bits (469), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 127/347 (36%), Positives = 180/347 (51%), Gaps = 71/347 (20%)

Query: 1   MGGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKLGLKFDEESESGR 60
           MGG+GK+TL K +A +A   KLFD++V   V Q P++++IQ E+A  LG+KF+EESE GR
Sbjct: 178 MGGVGKSTLVKHLAEQANQEKLFDKVVKVSVLQTPDLERIQRELADGLGMKFEEESEQGR 237

Query: 61  TR-----------------SPWSRLKKEKLQI---------------------------- 75
                                W+ L+ EK+ I                            
Sbjct: 238 AARLLQRMEAEKTILIILDDLWAELELEKVGIPSPDDHKGCKLVLTSRNKQVLSNEMSTQ 297

Query: 76  --------------ICGKKMEGDYAEGSELKWLAMDVAKECAGLPVSIVT---GIKEQEL 118
                         I  K   GD  E  EL+ +A+DVAKECAGLP++IVT    +K + +
Sbjct: 298 KDFRVRHLQEDETWILFKNTAGDSIENPELQPIAVDVAKECAGLPLAIVTVAKALKNKNV 357

Query: 119 FEWKDALEQLRRPSSTNFKDVQPAAYKAMELGYNKLEGDELKSTFLLIG-YTAIASIDDL 177
             WKDAL+QL+  +STN   ++   Y +++L Y  LEGDE+KS  LL G +++   I DL
Sbjct: 358 SIWKDALQQLKSQTSTNITGIETKVYSSLKLSYEHLEGDEVKSLCLLCGLFSSYIHIRDL 417

Query: 178 LMYGMGLGLFQGVNKMEAARARVHTLVHKLKASCMLLDHTSKNEKLFSIHDVVRDVAISI 237
           L YG+GL LFQG N +E A+ R+ TLV  LK+S  LL+    +  +  +HD+VR  A  I
Sbjct: 418 LKYGVGLRLFQGTNTLEEAKNRIDTLVDNLKSSNFLLE--IGHNAVVRMHDLVRSTARKI 475

Query: 238 ASGEQNVFSATNEQVDGCTEWS--DESAVILYTSIVLRDIKTNVLPD 282
            S +++VF+     V    EWS  DE  V   T + L D   + LP+
Sbjct: 476 TSKQRHVFTHQKTTVR-VEEWSRIDELQV---TWVKLHDCDIHELPE 518

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359488095|ref|XP_002270726.2| PREDICTED: probable disease resistance protein At4g27220-like [Vitis vinifera]

 Score =  184 bits (467), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 127/347 (36%), Positives = 180/347 (51%), Gaps = 71/347 (20%)

Query: 1   MGGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKLGLKFDEESESGR 60
           +GG+GK+TL K+VA +A+  KLF ++V   V Q P+ K IQ +IA KLG+KF+E SE GR
Sbjct: 178 LGGVGKSTLVKQVAEQAEQEKLFRKVVMVPVFQTPDFKGIQQQIADKLGMKFEEVSEQGR 237

Query: 61  TR-----------------SPWSRLKKEKLQI---------------------------- 75
                                W+ L+ EK+ I                            
Sbjct: 238 ADRLHQRIKQENTILIILDDLWAELELEKVGIPSPDDHKGCKLVLTSRNKQVLSNEMSTQ 297

Query: 76  --------------ICGKKMEGDYAEGSELKWLAMDVAKECAGLPVSIVT---GIKEQEL 118
                         I  K   GD  +  EL+ +A+DVAKECAGLP++IVT    +K + +
Sbjct: 298 KDFRVQHLQEDETWILFKNTAGDSIKNPELQPIAVDVAKECAGLPIAIVTVAKALKNKNV 357

Query: 119 FEWKDALEQLRRPSSTNFKDVQPAAYKAMELGYNKLEGDELKSTFLLIG-YTAIASIDDL 177
             WKDAL+QL+  +STN   ++   Y +++L Y  LEGDE+KS  LL G +++   I DL
Sbjct: 358 SIWKDALQQLKSQTSTNITGMETKVYSSLKLSYEHLEGDEVKSLCLLCGLFSSDIHIGDL 417

Query: 178 LMYGMGLGLFQGVNKMEAARARVHTLVHKLKASCMLLDHTSKNEKLFSIHDVVRDVAISI 237
           L YG+GL LFQG N +E A+ R+ TLV  LK+S  LL+  + +     +HD+VR  A  I
Sbjct: 418 LKYGVGLRLFQGTNTLEEAKNRIDTLVDNLKSSNFLLE--TDHNAYVRMHDLVRSTARKI 475

Query: 238 ASGEQNVFSATNEQVDGCTEWS--DESAVILYTSIVLRDIKTNVLPD 282
           AS +++VF+     V    EWS  DE  V   T + L D   + LP+
Sbjct: 476 ASEQRHVFTHQKTTVR-VEEWSRIDELQV---TWVKLHDCDIHELPE 518

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359488103|ref|XP_002263579.2| PREDICTED: disease resistance protein At4g27190-like [Vitis vinifera]

 Score =  184 bits (467), Expect = 4e-44,   Method: Compositional matrix adjust.
 Identities = 121/322 (37%), Positives = 170/322 (52%), Gaps = 66/322 (20%)

Query: 1   MGGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKLGLKFDEESESGR 60
           MGG+GK+TL K+VA +A   KLF+++V   V Q P++++IQ E+A  LG+KF+EESE GR
Sbjct: 178 MGGVGKSTLVKQVAEQANQEKLFEKVVNVSVLQTPDLERIQRELADWLGMKFEEESEQGR 237

Query: 61  TR-----------------SPWSRLKKEKLQI---------------------------- 75
                                W+ L+ EK+ I                            
Sbjct: 238 AARLHQRMKAEKTILIILDDLWAELELEKVGIPSPDDHKGCKLVLTSRNKQVLSNEMSTQ 297

Query: 76  --------------ICGKKMEGDYAEGSELKWLAMDVAKECAGLPVSIVT---GIKEQEL 118
                         I  K   GD  E  EL+ +A+DVAKECAGLP++IVT    +K + +
Sbjct: 298 KDFRVRHLQEDETWILFKNTAGDSIENPELQPIAVDVAKECAGLPIAIVTVAKALKNKNV 357

Query: 119 FEWKDALEQLRRPSSTNFKDVQPAAYKAMELGYNKLEGDELKSTFLLIG-YTAIASIDDL 177
             WKDAL+QL+  +STN   ++   Y +++L Y  LEGDE+KS  LL G ++    I DL
Sbjct: 358 SIWKDALQQLKSQTSTNITGMETKVYSSLKLSYEHLEGDEVKSLCLLCGLFSRYIHIRDL 417

Query: 178 LMYGMGLGLFQGVNKMEAARARVHTLVHKLKASCMLLDHTSKNEKLFSIHDVVRDVAISI 237
           L YG+GL LFQG N +E  + R+ TLV  LK+S  LL+ T +N  +  +HD+VR  A  I
Sbjct: 418 LKYGVGLRLFQGTNTLEEVKNRIDTLVDNLKSSNFLLE-TGRN-AVVRMHDLVRSTARKI 475

Query: 238 ASGEQNVFSATNEQVDGCTEWS 259
           AS + +VF+     V    EWS
Sbjct: 476 ASEQHHVFTHQKTTVR-VEEWS 496

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

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	283
TAIR|locus:2131689	919	AT4G27220 [Arabidopsis thalian	0.731	0.225	0.285	1.5e-14
TAIR|locus:2201996	889	RPS5 "AT1G12220" [Arabidopsis	0.579	0.184	0.252	1.8e-12
TAIR|locus:2136447	985	AT4G27190 [Arabidopsis thalian	0.731	0.210	0.258	2.1e-12
TAIR|locus:2203881	893	AT1G62630 [Arabidopsis thalian	0.565	0.179	0.263	8.4e-12
TAIR|locus:2031356	884	AT1G63360 [Arabidopsis thalian	0.565	0.180	0.257	1.9e-11
TAIR|locus:2005517	909	RPS2 "RESISTANT TO P. SYRINGAE	0.590	0.183	0.281	2.7e-11
TAIR|locus:2166320	888	AT5G63020 [Arabidopsis thalian	0.551	0.175	0.262	8e-11
TAIR|locus:2153474	874	AT5G05400 [Arabidopsis thalian	0.363	0.117	0.321	3.5e-09
TAIR|locus:2034770	894	SUMM2 "AT1G12280" [Arabidopsis	0.268	0.085	0.325	9.7e-09
TAIR|locus:2031366	898	AT1G63350 "AT1G63350" [Arabido	0.579	0.182	0.237	1.6e-08

TAIR|locus:2131689 AT4G27220 [Arabidopsis thaliana (taxid:3702)]

 Score = 168 (64.2 bits), Expect = 1.5e-14, Sum P(2) = 1.5e-14
 Identities = 63/221 (28%), Positives = 99/221 (44%)

Query:    69 KKEKLQIICGKKMEGDYAEGSELKWLAMDVAKECAGLPVSIVT-G--IKEQELFE-WKDA 124
             +KE  ++ C     G+ A    +K +A DV+ EC GLP++I+T G  ++ +   E WK  
Sbjct:   274 EKEAWELFCHNV--GEVANSDNVKPIAKDVSHECCGLPLAIITIGRTLRGKPQVEVWKHT 331

Query:   125 LEQLRRPSSTNFKDVQPAAYKAMELGYNKLEGDELKSTFL---LIGYTAIASIDDXXXXX 181
             L  L+R S+ +  D +   +  ++L Y+ L+ D +KS FL   L        + +     
Sbjct:   332 LNLLKR-SAPSI-DTEEKIFGTLKLSYDFLQ-DNMKSCFLFCALFPEDYSIKVSELIMYW 388

Query:   182 XXXXXFQGVNKMEAARARVHTLVHKLKASCMLLDHTSKNEKLFSIHDVVRDVAISIASGE 241
                    G +  E       TLV +LK SC+L D  S +     +HDVVRD AI   S +
Sbjct:   389 VAEGLLDGQHHYEDMMNEGVTLVERLKDSCLLEDGDSCDT--VKMHDVVRDFAIWFMSSQ 446

Query:   242 QNVFSATNEQVDGCTEWSDESAVILYTSIVLRDIKTNVLPD 282
                F +      G  E+  +  V     + L   K   LP+
Sbjct:   447 GEGFHSLVMAGRGLIEFPQDKFVSSVQRVSLMANKLERLPN 487

GO:0005634 "nucleus" evidence=ISM

GO:0006952 "defense response" evidence=IEA;ISS

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2201996 RPS5 "AT1G12220" [Arabidopsis thaliana (taxid:3702)]

 Score = 134 (52.2 bits), Expect = 1.8e-12, Sum P(2) = 1.8e-12
 Identities = 45/178 (25%), Positives = 86/178 (48%)

Query:    74 QIICGKKMEGDYAEGSELKWLAMDVAKECAGLPVSI-VTGIK---EQELFEWKDALEQLR 129
             Q+  GK   G + +   +  LA  VA++C GLP+++ V G     ++ + EW  A++ L 
Sbjct:   323 QMKVGKNTLGSHPD---IPGLARKVARKCRGLPLALNVIGEAMACKRTVHEWCHAIDVLT 379

Query:   130 RPSSTNFKDVQPAAYKAMELGYNKLEGDELKSTFLLIGYTAIASIDDXXXXXXXXXXFQG 189
               S+ +F  ++      ++  Y+ L G+ +KS FL         + D             
Sbjct:   380 S-SAIDFSGMEDEILHVLKYSYDNLNGELMKSCFLYCSLFPEDYLIDKEGLVDYWISEGF 438

Query:   190 VNKMEAARARV---HTLVHKLKASCMLLDHTSKNEKLFSIHDVVRDVAISIAS--GEQ 242
             +N+ E     +   + ++  L  +C+LL+   +N+    +HDVVR++A+ I+S  G+Q
Sbjct:   439 INEKEGRERNINQGYEIIGTLVRACLLLEE-ERNKSNVKMHDVVREMALWISSDLGKQ 495

GO:0009626 "plant-type hypersensitive response" evidence=IMP

GO:0006952 "defense response" evidence=IMP;TAS

GO:0009816 "defense response to bacterium, incompatible interaction" evidence=IDA

GO:0005886 "plasma membrane" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0008219 "cell death" evidence=IMP

GO:0038023 "signaling receptor activity" evidence=IMP

GO:0000166 "nucleotide binding" evidence=IMP

GO:0005622 "intracellular" evidence=ISS

TAIR|locus:2136447 AT4G27190 [Arabidopsis thaliana (taxid:3702)]

 Score = 149 (57.5 bits), Expect = 2.1e-12, Sum P(2) = 2.1e-12
 Identities = 58/224 (25%), Positives = 98/224 (43%)

Query:    68 LKKEKLQIICGKKMEGDYAEGSELKWLAMDVAKECAGLPVSIVT------GIKEQELFEW 121
             L+++  ++ C  K  GD      ++ +A  V++EC GLP++I+T      G K  +L  W
Sbjct:   303 LEEDAWELFC--KNAGDVVRSDHVRKIAKAVSQECGGLPLAIITVGTAMRGKKNVKL--W 358

Query:   122 KDALEQLRRPSSTNFKDVQPAAYKAMELGYNKLEGDELKSTFLLIG-YTAIASID--DXX 178
                L +L + S    K ++   ++ ++L Y+ LE D+ K  FLL   +    SI+  +  
Sbjct:   359 NHVLSKLSK-SVPWIKSIEEKIFQPLKLSYDFLE-DKAKFCFLLCALFPEDYSIEVTEVV 416

Query:   179 XXXXXXXXFQGVNKMEAARARVHTLVHKLKASCMLLDHTSKNEKLFSIHDVVRDVAISIA 238
                      + +   E +     T V  LK  C+L D   ++     +HDVVRD AI I 
Sbjct:   417 RYWMAEGFMEELGSQEDSMNEGITTVESLKDYCLLEDGDRRDT--VKMHDVVRDFAIWIM 474

Query:   239 SGEQNVFSATNEQVDGCTEWSDESAVILYTSIVLRDIKTNVLPD 282
             S  Q+   +      G  +   +        + L + K   LPD
Sbjct:   475 SSSQDDSHSLVMSGTGLQDIRQDKLAPSLRRVSLMNNKLESLPD 518

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005739 "mitochondrion" evidence=ISM

GO:0006952 "defense response" evidence=IEA;ISS

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

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2203881 AT1G62630 [Arabidopsis thaliana (taxid:3702)]

 Score = 130 (50.8 bits), Expect = 8.4e-12, Sum P(2) = 8.4e-12
 Identities = 45/171 (26%), Positives = 84/171 (49%)

Query:    79 KKMEGDYAEGSE--LKWLAMDVAKECAGLPVSI-VTGIK---EQELFEWKDALEQLRRPS 132
             +K  G    GS+  +  LA  VAK+C GLP+++ V G     ++ + EW++A+  L   +
Sbjct:   319 QKKVGQKTLGSDPGIPQLARIVAKKCCGLPLALNVIGETMSCKRTIQEWRNAIHVLNSYA 378

Query:   133 STNFKDVQPAAYKAMELGYNKLEGDELKSTFLLIG-YTAIASI--DDXXXXXXXXXXFQG 189
             +  F  ++      ++  Y+ L+G+ +KS+ L    Y   A I  +D            G
Sbjct:   379 A-EFIGMEDKILPLLKYSYDNLKGEHVKSSLLYCALYPEDAKIRKEDLIEHWICEEIIDG 437

Query:   190 VNKMEAARARVHTLVHKLKASCMLLDHTS-KNEKLFSIHDVVRDVAISIAS 239
                +E A  + + ++  L  + +L++    K +    +HDVVR++A+ IAS
Sbjct:   438 SEGIEKAEDKGYDIIGSLVRASLLMECVDLKGKSSVIMHDVVREMALWIAS 488

GO:0005634 "nucleus" evidence=ISM

GO:0006952 "defense response" evidence=IEA;ISS

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2031356 AT1G63360 [Arabidopsis thaliana (taxid:3702)]

 Score = 126 (49.4 bits), Expect = 1.9e-11, Sum P(2) = 1.9e-11
 Identities = 44/171 (25%), Positives = 83/171 (48%)

Query:    79 KKMEGDYAEGSE--LKWLAMDVAKECAGLPVSI-VTGIK---EQELFEWKDALEQLRRPS 132
             +K  G    GS+  +  LA  VAK+C GLP+++ V G     ++ + EW+ A+  L   +
Sbjct:   319 QKKVGQTTLGSDPGIPQLARIVAKKCCGLPLALNVIGETMSCKRTIQEWRHAIHVLNSYA 378

Query:   133 STNFKDVQPAAYKAMELGYNKLEGDELKSTFLLIG-YTAIASI--DDXXXXXXXXXXFQG 189
             +  F  ++      ++  Y+ L+G+++KS+ L    Y   A I  +D            G
Sbjct:   379 A-EFIGMEDKVLPLLKYSYDNLKGEQVKSSLLYCALYPEDAKILKEDLIEHWICEEIIDG 437

Query:   190 VNKMEAARARVHTLVHKLKASCMLLD-HTSKNEKLFSIHDVVRDVAISIAS 239
                +E A  + + ++  L  + +L++       +   +HDVVR++A+ IAS
Sbjct:   438 SEGIEKAEDKGYEIIGCLVRASLLMEWDDGDGRRAVCMHDVVREMALWIAS 488

GO:0005634 "nucleus" evidence=ISM

GO:0006952 "defense response" evidence=IEA;ISS

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2005517 RPS2 "RESISTANT TO P. SYRINGAE 2" [Arabidopsis thaliana (taxid:3702)]

 Score = 140 (54.3 bits), Expect = 2.7e-11, Sum P(2) = 2.7e-11
 Identities = 53/188 (28%), Positives = 86/188 (45%)

Query:    69 KKEKLQIICGKKMEGDYAEGSELKWLAMDVAKECAGLPVSIVT--GI---KEQELFEWKD 123
             KK   ++ C K    D  E S ++ LA  +  +C GLP++++T  G    +E E  EW  
Sbjct:   312 KKHAWELFCSKVWRKDLLESSSIRRLAEIIVSKCGGLPLALITLGGAMAHRETEE-EWIH 370

Query:   124 ALEQLRRPSSTNFKDVQPAAYKAMELGYNKLEGDELKSTFLLIGYTAIASIDDXXXXXXX 183
             A E L R      K +    +  ++  Y+ LE D L+S FL   Y A+   +        
Sbjct:   371 ASEVLTR-FPAEMKGMN-YVFALLKFSYDNLESDLLRSCFL---YCALFPEEHSIEIEQL 425

Query:   184 XXXFQGVNKMEAARARVHT------LVHKLKASCMLLDHTSKNEKLFSIHDVVRDVAISI 237
                + G   + ++   V+T      L+  LKA+C+L   T   +    +H+VVR  A+ +
Sbjct:   426 VEYWVGEGFLTSSHG-VNTIYKGYFLIGDLKAACLL--ETGDEKTQVKMHNVVRSFALWM 482

Query:   238 ASGEQNVF 245
             AS EQ  +
Sbjct:   483 AS-EQGTY 489

GO:0000166 "nucleotide binding" evidence=IEA

GO:0006952 "defense response" evidence=ISS;TAS

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

GO:0043531 "ADP binding" evidence=IEA

GO:0009626 "plant-type hypersensitive response" evidence=IMP

GO:0016045 "detection of bacterium" evidence=RCA;IMP

GO:0005515 "protein binding" evidence=IPI

GO:0005886 "plasma membrane" evidence=IDA

GO:0042742 "defense response to bacterium" evidence=RCA;IMP

GO:0000165 "MAPK cascade" evidence=RCA

GO:0006612 "protein targeting to membrane" evidence=RCA

GO:0009595 "detection of biotic stimulus" evidence=RCA

GO:0009617 "response to bacterium" evidence=RCA

GO:0009697 "salicylic acid biosynthetic process" evidence=RCA

GO:0009862 "systemic acquired resistance, salicylic acid mediated signaling pathway" evidence=RCA

GO:0009863 "salicylic acid mediated signaling pathway" evidence=RCA

GO:0009867 "jasmonic acid mediated signaling pathway" evidence=RCA

GO:0009963 "positive regulation of flavonoid biosynthetic process" evidence=RCA

GO:0010200 "response to chitin" evidence=RCA

GO:0010310 "regulation of hydrogen peroxide metabolic process" evidence=RCA

GO:0010363 "regulation of plant-type hypersensitive response" evidence=RCA

GO:0031347 "regulation of defense response" evidence=RCA

GO:0031348 "negative regulation of defense response" evidence=RCA

GO:0043069 "negative regulation of programmed cell death" evidence=RCA

GO:0043900 "regulation of multi-organism process" evidence=RCA

GO:0045087 "innate immune response" evidence=RCA

GO:0050776 "regulation of immune response" evidence=RCA

GO:0050832 "defense response to fungus" evidence=RCA

GO:0051707 "response to other organism" evidence=RCA

TAIR|locus:2166320 AT5G63020 [Arabidopsis thaliana (taxid:3702)]

 Score = 134 (52.2 bits), Expect = 8.0e-11, Sum P(2) = 8.0e-11
 Identities = 46/175 (26%), Positives = 88/175 (50%)

Query:    80 KMEGDYAEGS--ELKWLAMDVAKECAGLPVSI-VTG---IKEQELFEWKDALEQLRRPSS 133
             K  G+   GS  E+  +A  VAK+C GLP+++ V G     ++ + EW+ A++ L   S+
Sbjct:   322 KKVGEITLGSHPEIPTVARTVAKKCRGLPLALNVIGETMAYKRTVQEWRSAIDVLTS-SA 380

Query:   134 TNFKDVQPAAYKAMELGYNKLEGDELKSTFLLIGYTAIASIDDXXXXXXXXXXFQGVNKM 193
               F  ++      ++  Y+ L+ ++LK  F    Y A+   D           + G   +
Sbjct:   381 AEFSGMEDEILPILKYSYDNLKSEQLKLCFQ---YCALFPEDHNIEKNDLVDYWIGEGFI 437

Query:   194 EAARARV----HTLVHKLKASCMLLDHTSKNEKLFSIHDVVRDVAISIAS--GEQ 242
             +  + +     + ++  L  SC+L++   +N++   +HDVVR++A+ IAS  G+Q
Sbjct:   438 DRNKGKAENQGYEIIGILVRSCLLME---ENQETVKMHDVVREMALWIASDFGKQ 489

GO:0005634 "nucleus" evidence=ISM

GO:0006952 "defense response" evidence=IEA;ISS

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2153474 AT5G05400 [Arabidopsis thaliana (taxid:3702)]

 Score = 108 (43.1 bits), Expect = 3.5e-09, Sum P(2) = 3.5e-09
 Identities = 37/115 (32%), Positives = 58/115 (50%)

Query:     1 MGGIGKTTLAKEVARKAKN-GKLFDQIVFTEVSQNPNIKKIQGEIAFKLGLKFDEESESG 59
             MGG+GKTTL  ++  K +     FD  ++  VS+NP +K+IQ +I  +L L ++E  E  
Sbjct:   183 MGGVGKTTLLSQINNKFRTVSNDFDIAIWVVVSKNPTVKRIQEDIGKRLDL-YNEGWEQ- 240

Query:    60 RTRSPWSRLKKEKLQIICGKKMEGDYAEGSELKWLAMDVAKECAGLPVSIVTGIK 114
             +T +  +   K  L+    KK    Y    +  W  +D+A    G+PV    G K
Sbjct:   241 KTENEIASTIKRSLE---NKK----YMLLLDDMWTKVDLAN--IGIPVPKRNGSK 286

GO:0005634 "nucleus" evidence=ISM

GO:0006952 "defense response" evidence=IEA;ISS

GO:0043531 "ADP binding" evidence=IEA

GO:0006826 "iron ion transport" evidence=RCA

GO:0010106 "cellular response to iron ion starvation" evidence=RCA

GO:0010167 "response to nitrate" evidence=RCA

GO:0015706 "nitrate transport" evidence=RCA

TAIR|locus:2034770 SUMM2 "AT1G12280" [Arabidopsis thaliana (taxid:3702)]

 Score = 107 (42.7 bits), Expect = 9.7e-09, Sum P(2) = 9.7e-09
 Identities = 26/80 (32%), Positives = 48/80 (60%)

Query:     1 MGGIGKTTLAKEVARK-AKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKLGL---KFDEES 56
             MGG+GKTTL   +  K ++    F  +++  VS++P+I +IQG+I  +L L   ++D  +
Sbjct:   184 MGGVGKTTLLTRINNKFSEKCSGFGVVIWVVVSKSPDIHRIQGDIGKRLDLGGEEWDNVN 243

Query:    57 ESGRTRSPWSRLKKEKLQII 76
             E+ R    ++ L K+K  ++
Sbjct:   244 ENQRALDIYNVLGKQKFVLL 263

GO:0006952 "defense response" evidence=IGI;ISS

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2031366 AT1G63350 "AT1G63350" [Arabidopsis thaliana (taxid:3702)]

 Score = 116 (45.9 bits), Expect = 1.6e-08, Sum P(2) = 1.6e-08
 Identities = 42/177 (23%), Positives = 85/177 (48%)

Query:    79 KKMEGDYAEGS--ELKWLAMDVAKECAGLPVSI----VTGIKEQELFEWKDALEQLRRPS 132
             +K  G    GS  E++ L+  VAK+C GLP+++     T   ++ + EW+ A+  L   +
Sbjct:   319 QKKVGQITLGSDPEIRELSRVVAKKCCGLPLALNVVSETMSCKRTVQEWRHAIYVLNSYA 378

Query:   133 STNFKDVQPAAYKAMELGYNKLEGDELKSTFLLIG-YTAIASI--DDXXXXXXXXXXFQG 189
             +  F  +       ++  Y+ L+G+++K   L    +   A I  ++            G
Sbjct:   379 A-KFSGMDDKILPLLKYSYDSLKGEDVKMCLLYCALFPEDAKIRKENLIEYWICEEIIDG 437

Query:   190 VNKMEAARARVHTLVHKLKASCMLLDHTSKN-EKLFSIHDVVRDVAISIAS--GEQN 243
                ++ A  + + ++  L  + +L++    +   +  +HDVVR++A+ IAS  G+QN
Sbjct:   438 SEGIDKAENQGYEIIGSLVRASLLMEEVELDGANIVCLHDVVREMALWIASDLGKQN 494

GO:0005575 "cellular_component" evidence=ND

GO:0006952 "defense response" evidence=IEA;ISS

GO:0043531 "ADP binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

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: eugene3.00050016 cc-nbs-lrr resistance protein (1144 aa) (Populus trichocarpa)

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	283
pfam00931	285	pfam00931, NB-ARC, NB-ARC domain	4e-06
pfam00931	285	pfam00931, NB-ARC, NB-ARC domain	5e-06

>gnl|CDD|216202 pfam00931, NB-ARC, NB-ARC domain

 Score = 46.9 bits (112), Expect = 4e-06
 Identities = 24/101 (23%), Positives = 43/101 (42%), Gaps = 9/101 (8%)

Query: 69  KKEKLQIICGKKMEGDYAEGSELKWLAMDVAKECAGLPVSIVTGIKE-----QELFEWKD 123
            +E  ++   K  E +     EL+ +A ++ ++C GLP+++   +         + EW+ 
Sbjct: 158 PEESWELFSNKVFEKELPPCPELEEVAKEIVEKCKGLPLALKV-LGGLLAFKSTVQEWEH 216

Query: 124 ALEQLRRPSSTNFKDVQPAAYKAMELGYNKLEGDELKSTFL 164
            LEQL        +D        + L Y+ L    LK  FL
Sbjct: 217 VLEQLNN--ELAGRDGLNEVLSILSLSYDNLP-MHLKRCFL 254

Length = 285

>gnl|CDD|216202 pfam00931, NB-ARC, NB-ARC domain

 Score = 46.6 bits (111), Expect = 5e-06
 Identities = 23/62 (37%), Positives = 33/62 (53%), Gaps = 5/62 (8%)

Query: 1  MGGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKLGL-----KFDEE 55
          MGG+GKTTLAK++      G  FD + +  VS+     ++Q +I  +LGL         E
Sbjct: 27 MGGVGKTTLAKQIYNDDSVGGHFDSVAWVVVSKTYTEFRLQKDILQELGLDDSDWVEKNE 86

Query: 56 SE 57
          SE
Sbjct: 87 SE 88

Length = 285

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	283
KOG4658	889	consensus Apoptotic ATPase [Signal transduction me	100.0
PF00931	287	NB-ARC: NB-ARC domain; InterPro: IPR002182 This is	99.97
PLN03210	1153	Resistant to P. syringae 6; Provisional	99.96
PRK04841	903	transcriptional regulator MalT; Provisional	98.96
COG3903	414	Predicted ATPase [General function prediction only	98.37
COG2909	894	MalT ATP-dependent transcriptional regulator [Tran	98.21
cd01128	249	rho_factor Transcription termination factor rho is	98.07
PRK09376	416	rho transcription termination factor Rho; Provisio	98.04
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	97.86
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	97.67
TIGR00767	415	rho transcription termination factor Rho. Members	97.47
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	97.21
PRK08118	167	topology modulation protein; Reviewed	97.16
PF05621	302	TniB: Bacterial TniB protein; InterPro: IPR008868	97.14
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	97.05
PRK00411	394	cdc6 cell division control protein 6; Reviewed	97.04
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	96.69
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	96.64
PF05729	166	NACHT: NACHT domain	96.58
PTZ00202	550	tuzin; Provisional	96.57
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	96.14
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	96.08
PRK07261	171	topology modulation protein; Provisional	95.95
PF13207	121	AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6	95.42
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	95.39
PRK12608	380	transcription termination factor Rho; Provisional	95.18
COG1618	179	Predicted nucleotide kinase [Nucleotide transport	95.04
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	95.0
PF13238	129	AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB	94.86
PRK08233	182	hypothetical protein; Provisional	94.66
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	94.64
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	94.51
smart00382	148	AAA ATPases associated with a variety of cellular	94.47
PHA02518	211	ParA-like protein; Provisional	94.44
cd00983	325	recA RecA is a bacterial enzyme which has roles in	94.29
PRK12727	559	flagellar biosynthesis regulator FlhF; Provisional	94.26
PRK03839	180	putative kinase; Provisional	94.26
PRK05541	176	adenylylsulfate kinase; Provisional	94.25
PF13191	185	AAA_16: AAA ATPase domain; PDB: 2V1U_A.	94.17
COG0003	322	ArsA Predicted ATPase involved in chromosome parti	94.08
PF02374	305	ArsA_ATPase: Anion-transporting ATPase; PDB: 2WOO_	94.06
PRK06217	183	hypothetical protein; Validated	94.05
PF07728	139	AAA_5: AAA domain (dynein-related subfamily); Inte	94.01
TIGR02012	321	tigrfam_recA protein RecA. This model describes or	93.99
TIGR02237	209	recomb_radB DNA repair and recombination protein R	93.95
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	93.92
COG1428	216	Deoxynucleoside kinases [Nucleotide transport and	93.83
PRK00625	173	shikimate kinase; Provisional	93.83
cd01393	226	recA_like RecA is a bacterial enzyme which has rol	93.82
COG1192	259	Soj ATPases involved in chromosome partitioning [C	93.81
COG1484	254	DnaC DNA replication protein [DNA replication, rec	93.81
PRK09354	349	recA recombinase A; Provisional	93.76
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	93.69
PF07726	131	AAA_3: ATPase family associated with various cellu	93.68
PF13173	128	AAA_14: AAA domain	93.59
PF01583	156	APS_kinase: Adenylylsulphate kinase; InterPro: IPR	93.58
cd01133	274	F1-ATPase_beta F1 ATP synthase beta subunit, nucle	93.5
PF01656	195	CbiA: CobQ/CobB/MinD/ParA nucleotide binding domai	93.4
PF13671	143	AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1	93.38
COG1102	179	Cmk Cytidylate kinase [Nucleotide transport and me	93.37
COG3640	255	CooC CO dehydrogenase maturation factor [Cell divi	93.36
cd01123	235	Rad51_DMC1_radA Rad51_DMC1_radA,B. This group of r	93.32
COG3899	849	Predicted ATPase [General function prediction only	93.3
PRK08116	268	hypothetical protein; Validated	93.28
cd02040	270	NifH NifH gene encodes component II (iron protein)	93.15
PF00004	132	AAA: ATPase family associated with various cellula	93.15
COG2256	436	MGS1 ATPase related to the helicase subunit of the	93.14
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	93.13
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	93.11
PRK07952	244	DNA replication protein DnaC; Validated	93.11
KOG2028	554	consensus ATPase related to the helicase subunit o	93.08
cd01122	271	GP4d_helicase GP4d_helicase is a homohexameric 5'-	93.06
KOG3347	176	consensus Predicted nucleotide kinase/nuclear prot	92.99
TIGR02238	313	recomb_DMC1 meiotic recombinase Dmc1. This model d	92.95
PRK13947	171	shikimate kinase; Provisional	92.94
PRK13849	231	putative crown gall tumor protein VirC1; Provision	92.91
PRK09361	225	radB DNA repair and recombination protein RadB; Pr	92.91
PRK12377	248	putative replication protein; Provisional	92.9
PRK06762	166	hypothetical protein; Provisional	92.87
PRK06893	229	DNA replication initiation factor; Validated	92.86
cd01394	218	radB RadB. The archaeal protein radB shares simila	92.84
PRK14721	420	flhF flagellar biosynthesis regulator FlhF; Provis	92.8
PRK00771	437	signal recognition particle protein Srp54; Provisi	92.69
PRK06995	484	flhF flagellar biosynthesis regulator FlhF; Valida	92.64
cd02042	104	ParA ParA and ParB of Caulobacter crescentus belon	92.64
PF00910	107	RNA_helicase: RNA helicase; InterPro: IPR000605 He	92.6
cd02019	69	NK Nucleoside/nucleotide kinase (NK) is a protein	92.58
PRK00131	175	aroK shikimate kinase; Reviewed	92.56
PRK13231	264	nitrogenase reductase-like protein; Reviewed	92.55
cd02036	179	MinD Bacterial cell division requires the formatio	92.4
PHA00729	226	NTP-binding motif containing protein	92.33
cd00544	169	CobU Adenosylcobinamide kinase / adenosylcobinamid	92.27
cd02025	220	PanK Pantothenate kinase (PanK) catalyzes the phos	92.27
PF03029	238	ATP_bind_1: Conserved hypothetical ATP binding pro	92.13
cd02037	169	MRP-like MRP (Multiple Resistance and pH adaptatio	92.05
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	91.94
PRK12724	432	flagellar biosynthesis regulator FlhF; Provisional	91.92
PF00485	194	PRK: Phosphoribulokinase / Uridine kinase family;	91.87
PRK10037	250	cell division protein; Provisional	91.84
cd02021	150	GntK Gluconate kinase (GntK) catalyzes the phospho	91.82
TIGR01281	268	DPOR_bchL light-independent protochlorophyllide re	91.81
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	91.77
COG2255	332	RuvB Holliday junction resolvasome, helicase subun	91.75
COG3265	161	GntK Gluconate kinase [Carbohydrate transport and	91.75
PRK13185	270	chlL protochlorophyllide reductase iron-sulfur ATP	91.73
TIGR01287	275	nifH nitrogenase iron protein. This model describe	91.71
PRK14723	767	flhF flagellar biosynthesis regulator FlhF; Provis	91.67
COG0703	172	AroK Shikimate kinase [Amino acid transport and me	91.55
COG0467	260	RAD55 RecA-superfamily ATPases implicated in signa	91.54
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	91.48
PRK13230	279	nitrogenase reductase-like protein; Reviewed	91.45
cd00227	175	CPT Chloramphenicol (Cm) phosphotransferase (CPT).	91.4
PRK13949	169	shikimate kinase; Provisional	91.32
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	91.31
PRK13975	196	thymidylate kinase; Provisional	91.28
TIGR02236	310	recomb_radA DNA repair and recombination protein R	91.22
TIGR01969	251	minD_arch cell division ATPase MinD, archaeal. Thi	91.21
PTZ00301	210	uridine kinase; Provisional	91.19
cd02032	267	Bchl_like This family of proteins contains bchL an	91.18
PLN03187	344	meiotic recombination protein DMC1 homolog; Provis	91.17
COG0563	178	Adk Adenylate kinase and related kinases [Nucleoti	91.17
PRK04301	317	radA DNA repair and recombination protein RadA; Va	91.16
PRK13233	275	nifH nitrogenase reductase; Reviewed	91.15
PRK13946	184	shikimate kinase; Provisional	91.09
PF02367	123	UPF0079: Uncharacterised P-loop hydrolase UPF0079;	91.07
cd03115	173	SRP The signal recognition particle (SRP) mediates	91.07
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	91.06
PTZ00088	229	adenylate kinase 1; Provisional	91.05
KOG1969	877	consensus DNA replication checkpoint protein CHL12	90.96
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	90.93
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	90.93
TIGR01359	183	UMP_CMP_kin_fam UMP-CMP kinase family. This subfam	90.88
PRK05480	209	uridine/cytidine kinase; Provisional	90.85
PRK12726	407	flagellar biosynthesis regulator FlhF; Provisional	90.85
cd01983	99	Fer4_NifH The Fer4_NifH superfamily contains a var	90.84
PRK13235	274	nifH nitrogenase reductase; Reviewed	90.82
PRK06547	172	hypothetical protein; Provisional	90.79
PRK13232	273	nifH nitrogenase reductase; Reviewed	90.79
COG0125	208	Tmk Thymidylate kinase [Nucleotide transport and m	90.76
PRK04040	188	adenylate kinase; Provisional	90.73
PF07015	231	VirC1: VirC1 protein; InterPro: IPR009744 This fam	90.7
PRK13342	413	recombination factor protein RarA; Reviewed	90.69
COG0529	197	CysC Adenylylsulfate kinase and related kinases [I	90.68
PF03266	168	NTPase_1: NTPase; InterPro: IPR004948 This entry r	90.67
PF01202	158	SKI: Shikimate kinase; InterPro: IPR000623 Shikima	90.54
cd03110	179	Fer4_NifH_child This protein family's function is	90.51
PRK05973	237	replicative DNA helicase; Provisional	90.48
PRK06921	266	hypothetical protein; Provisional	90.46
PRK08727	233	hypothetical protein; Validated	90.45
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	90.44
PRK13948	182	shikimate kinase; Provisional	90.43
cd02024	187	NRK1 Nicotinamide riboside kinase (NRK) is an enzy	90.42
PRK06696	223	uridine kinase; Validated	90.39
cd00464	154	SK Shikimate kinase (SK) is the fifth enzyme in th	90.36
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	90.35
PRK05564	313	DNA polymerase III subunit delta'; Validated	90.34
cd01672	200	TMPK Thymidine monophosphate kinase (TMPK), also k	90.33
PRK14087	450	dnaA chromosomal replication initiation protein; P	90.26
PRK08939	306	primosomal protein DnaI; Reviewed	90.23
PLN03186	342	DNA repair protein RAD51 homolog; Provisional	90.14
cd02117	212	NifH_like This family contains the NifH (iron prot	90.11
PRK00889	175	adenylylsulfate kinase; Provisional	90.06
TIGR01313	163	therm_gnt_kin carbohydrate kinase, thermoresistant	90.05
PF08423	256	Rad51: Rad51; InterPro: IPR013632 This domain is f	90.04
TIGR02322	179	phosphon_PhnN phosphonate metabolism protein/1,5-b	90.03
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	89.97
PF02223	186	Thymidylate_kin: Thymidylate kinase; InterPro: IPR	89.94
PF06564	243	YhjQ: YhjQ protein; InterPro: IPR017746 The YhjQ p	89.85
PF13481	193	AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C.	89.82
COG1066	456	Sms Predicted ATP-dependent serine protease [Postt	89.8
TIGR03371	246	cellulose_yhjQ cellulose synthase operon protein Y	89.79
TIGR00150	133	HI0065_YjeE ATPase, YjeE family. Members of this f	89.78
TIGR00959	428	ffh signal recognition particle protein. This mode	89.77
PF08303	168	tRNA_lig_kinase: tRNA ligase kinase domain; InterP	89.76
COG4088	261	Predicted nucleotide kinase [Nucleotide transport	89.73
CHL00181	287	cbbX CbbX; Provisional	89.73
TIGR00235	207	udk uridine kinase. Model contains a number of lon	89.72
PRK08903	227	DnaA regulatory inactivator Hda; Validated	89.68
TIGR03453	387	partition_RepA plasmid partitioning protein RepA.	89.65
PRK12422	445	chromosomal replication initiation protein; Provis	89.64
PRK14532	188	adenylate kinase; Provisional	89.59
PRK12339	197	2-phosphoglycerate kinase; Provisional	89.59
PRK03731	171	aroL shikimate kinase II; Reviewed	89.59
TIGR03574	249	selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal. Mem	89.54
PRK10646	153	ADP-binding protein; Provisional	89.47
PRK08084	235	DNA replication initiation factor; Provisional	89.41
cd02020	147	CMPK Cytidine monophosphate kinase (CMPK) catalyze	89.4
PRK05057	172	aroK shikimate kinase I; Reviewed	89.4
TIGR01360	188	aden_kin_iso1 adenylate kinase, isozyme 1 subfamil	89.38
PF13521	163	AAA_28: AAA domain; PDB: 1LW7_A.	89.37
CHL00072	290	chlL photochlorophyllide reductase subunit L	89.37
PRK13695	174	putative NTPase; Provisional	89.34
PRK11545	163	gntK gluconate kinase 1; Provisional	89.34
PRK14529	223	adenylate kinase; Provisional	89.33
PRK05642	234	DNA replication initiation factor; Validated	89.19
PRK13869	405	plasmid-partitioning protein RepA; Provisional	89.18
TIGR01968	261	minD_bact septum site-determining protein MinD. Th	89.16
cd00984	242	DnaB_C DnaB helicase C terminal domain. The hexame	89.1
PLN03025	319	replication factor C subunit; Provisional	89.07
cd02023	198	UMPK Uridine monophosphate kinase (UMPK, EC 2.7.1.	89.02
PRK07004	460	replicative DNA helicase; Provisional	89.01
TIGR00041	195	DTMP_kinase thymidylate kinase. Function: phosphor	89.01
PRK09519	790	recA DNA recombination protein RecA; Reviewed	88.95
PRK14530	215	adenylate kinase; Provisional	88.95
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	88.87
KOG1532	366	consensus GTPase XAB1, interacts with DNA repair p	88.82
COG1149	284	MinD superfamily P-loop ATPase containing an inser	88.79
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	88.71
cd02028	179	UMPK_like Uridine monophosphate kinase_like (UMPK_	88.7
PRK13973	213	thymidylate kinase; Provisional	88.66
TIGR03881	229	KaiC_arch_4 KaiC domain protein, PAE1156 family. M	88.64
PRK08533	230	flagellar accessory protein FlaH; Reviewed	88.63
COG0468	279	RecA RecA/RadA recombinase [DNA replication, recom	88.6
PF08477	119	Miro: Miro-like protein; InterPro: IPR013684 Mitoc	88.59
PRK00149	450	dnaA chromosomal replication initiation protein; R	88.53
cd02034	116	CooC The accessory protein CooC, which contains a	88.53
PF03796	259	DnaB_C: DnaB-like helicase C terminal domain; Inte	88.51
COG0572	218	Udk Uridine kinase [Nucleotide transport and metab	88.47
PRK10818	270	cell division inhibitor MinD; Provisional	88.45
cd03111	106	CpaE_like This protein family consists of proteins	88.38
PRK07667	193	uridine kinase; Provisional	88.33
COG1936	180	Predicted nucleotide kinase (related to CMP and AM	88.28
cd02027	149	APSK Adenosine 5'-phosphosulfate kinase (APSK) cat	88.28
TIGR02239	316	recomb_RAD51 DNA repair protein RAD51. This eukary	88.28
CHL00175	281	minD septum-site determining protein; Validated	88.24
cd01428	194	ADK Adenylate kinase (ADK) catalyzes the reversibl	88.22
cd00550	254	ArsA_ATPase Oxyanion-translocating ATPase (ArsA).	88.17
PRK03846	198	adenylylsulfate kinase; Provisional	88.14
KOG2543	438	consensus Origin recognition complex, subunit 5 [R	88.12
PRK13976	209	thymidylate kinase; Provisional	88.1
KOG0744	423	consensus AAA+-type ATPase [Posttranslational modi	88.07
COG1222	406	RPT1 ATP-dependent 26S proteasome regulatory subun	87.94
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	87.94
TIGR00764	608	lon_rel lon-related putative ATP-dependent proteas	87.93
PRK10867	433	signal recognition particle protein; Provisional	87.86
PF04665	241	Pox_A32: Poxvirus A32 protein; InterPro: IPR006758	87.85
PF00406	151	ADK: Adenylate kinase; InterPro: IPR000850 Adenyla	87.75
PHA02519	387	plasmid partition protein SopA; Reviewed	87.67
PRK06761	282	hypothetical protein; Provisional	87.65
PLN02924	220	thymidylate kinase	87.62
TIGR00390	441	hslU ATP-dependent protease HslVU, ATPase subunit.	87.61
PRK06835	329	DNA replication protein DnaC; Validated	87.59
PRK04182	180	cytidylate kinase; Provisional	87.57
PRK06620	214	hypothetical protein; Validated	87.57
PF13245	76	AAA_19: Part of AAA domain	87.52
COG0470	325	HolB ATPase involved in DNA replication [DNA repli	87.39
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	87.38
PF09140	261	MipZ: ATPase MipZ; InterPro: IPR015223 Cell divisi	87.33
PRK10078	186	ribose 1,5-bisphosphokinase; Provisional	87.27
PRK13705	388	plasmid-partitioning protein SopA; Provisional	87.27
PRK13236	296	nitrogenase reductase; Reviewed	87.24
PRK00698	205	tmk thymidylate kinase; Validated	87.17
PRK04328	249	hypothetical protein; Provisional	87.12
COG0714	329	MoxR-like ATPases [General function prediction onl	87.0
PRK14528	186	adenylate kinase; Provisional	86.99
PHA02530	300	pseT polynucleotide kinase; Provisional	86.98
PRK06067	234	flagellar accessory protein FlaH; Validated	86.91
TIGR03575	340	selen_PSTK_euk L-seryl-tRNA(Sec) kinase, eukaryoti	86.9
TIGR02016	296	BchX chlorophyllide reductase iron protein subunit	86.89
PRK04296	190	thymidine kinase; Provisional	86.84
PRK09183	259	transposase/IS protein; Provisional	86.79
PF06745	226	KaiC: KaiC; InterPro: IPR014774 This entry represe	86.72
TIGR01242	364	26Sp45 26S proteasome subunit P45 family. Many pro	86.66
PRK13768	253	GTPase; Provisional	86.58
COG0802	149	Predicted ATPase or kinase [General function predi	86.53
PF13504	17	LRR_7: Leucine rich repeat; PDB: 3OJA_B 3G06_A 1OO	86.49
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	86.44
PRK06526	254	transposase; Provisional	86.4
PF03205	140	MobB: Molybdopterin guanine dinucleotide synthesis	86.36
PF00693	281	Herpes_TK: Thymidine kinase from herpesvirus; Inte	86.33
PRK13765	637	ATP-dependent protease Lon; Provisional	86.32
PTZ00112	1164	origin recognition complex 1 protein; Provisional	86.25
PRK05201	443	hslU ATP-dependent protease ATP-binding subunit Hs	86.22
PF10662	143	PduV-EutP: Ethanolamine utilisation - propanediol	86.16
PRK14957	546	DNA polymerase III subunits gamma and tau; Provisi	86.15
PRK14088	440	dnaA chromosomal replication initiation protein; P	86.13
PRK14958	509	DNA polymerase III subunits gamma and tau; Provisi	86.09
cd00880	163	Era_like Era (E. coli Ras-like protein)-like. This	86.06
PRK05800	170	cobU adenosylcobinamide kinase/adenosylcobinamide-	86.01
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	85.92
PRK08181	269	transposase; Validated	85.86
PRK14527	191	adenylate kinase; Provisional	85.83
TIGR03263	180	guanyl_kin guanylate kinase. Members of this famil	85.8
COG4778	235	PhnL ABC-type phosphonate transport system, ATPase	85.79
TIGR00064	272	ftsY signal recognition particle-docking protein F	85.78
TIGR03815	322	CpaE_hom_Actino helicase/secretion neighborhood Cp	85.68
PRK05439	311	pantothenate kinase; Provisional	85.65
TIGR00176	155	mobB molybdopterin-guanine dinucleotide biosynthes	85.57
COG1100	219	GTPase SAR1 and related small G proteins [General	85.55
cd01673	193	dNK Deoxyribonucleoside kinase (dNK) catalyzes the	85.48
TIGR03878	259	thermo_KaiC_2 KaiC domain protein, AF_0795 family.	85.47
PRK14526	211	adenylate kinase; Provisional	85.45
PTZ00035	337	Rad51 protein; Provisional	85.44
TIGR02173	171	cyt_kin_arch cytidylate kinase, putative. Proteins	85.39
TIGR00554	290	panK_bact pantothenate kinase, bacterial type. Sho	85.38
PRK13234	295	nifH nitrogenase reductase; Reviewed	85.35
PLN02200	234	adenylate kinase family protein	85.33
PRK03992	389	proteasome-activating nucleotidase; Provisional	85.26
PRK08840	464	replicative DNA helicase; Provisional	85.16
PRK13341	725	recombination factor protein RarA/unknown domain f	85.14
PRK00279	215	adk adenylate kinase; Reviewed	85.12
PRK14531	183	adenylate kinase; Provisional	85.06
PRK12402	337	replication factor C small subunit 2; Reviewed	85.01
smart00173	164	RAS Ras subfamily of RAS small GTPases. Similar in	85.01
PRK10536	262	hypothetical protein; Provisional	85.0
PRK04195	482	replication factor C large subunit; Provisional	84.9
PRK02496	184	adk adenylate kinase; Provisional	84.85
TIGR01425	429	SRP54_euk signal recognition particle protein SRP5	84.78
TIGR03880	224	KaiC_arch_3 KaiC domain protein, AF_0351 family. T	84.74
TIGR03018	207	pepcterm_TyrKin exopolysaccharide/PEPCTERM locus t	84.74
COG1124	252	DppF ABC-type dipeptide/oligopeptide/nickel transp	84.72
PRK09087	226	hypothetical protein; Validated	84.72
TIGR01351	210	adk adenylate kinases. Adenylate kinase (EC 2.7.4.	84.69
smart00763	361	AAA_PrkA PrkA AAA domain. This is a family of PrkA	84.66
cd04139	164	RalA_RalB RalA/RalB subfamily. The Ral (Ras-like)	84.63
PRK09280	463	F0F1 ATP synthase subunit beta; Validated	84.61
cd03114	148	ArgK-like The function of this protein family is u	84.59
KOG3354	191	consensus Gluconate kinase [Carbohydrate transport	84.54
PRK08006	471	replicative DNA helicase; Provisional	84.5
COG0194	191	Gmk Guanylate kinase [Nucleotide transport and met	84.45
cd02030	219	NDUO42 NADH:Ubiquinone oxioreductase, 42 kDa (NDUO	84.4
PRK09270	229	nucleoside triphosphate hydrolase domain-containin	84.37
PRK12338	319	hypothetical protein; Provisional	84.35
PF09848	352	DUF2075: Uncharacterized conserved protein (DUF207	84.33
PRK06904	472	replicative DNA helicase; Validated	84.33
PF07724	171	AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR	84.32
cd01135	276	V_A-ATPase_B V/A-type ATP synthase (non-catalytic)	84.24
cd00071	137	GMPK Guanosine monophosphate kinase (GMPK, EC 2.7.	84.18
cd04138	162	H_N_K_Ras_like H-Ras/N-Ras/K-Ras subfamily. H-Ras,	84.17
cd01125	239	repA Hexameric Replicative Helicase RepA. RepA is	84.16
PRK14974	336	cell division protein FtsY; Provisional	84.13
PRK07933	213	thymidylate kinase; Validated	84.02
PRK00300	205	gmk guanylate kinase; Provisional	83.99
COG2074	299	2-phosphoglycerate kinase [Carbohydrate transport	83.87
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	83.86
cd04119	168	RJL RJL (RabJ-Like) subfamily. RJLs are found in m	83.82
COG1157	441	FliI Flagellar biosynthesis/type III secretory pat	83.77
cd02029	277	PRK_like Phosphoribulokinase-like (PRK-like) is a	83.71
PRK11670	369	antiporter inner membrane protein; Provisional	83.64
TIGR01650	327	PD_CobS cobaltochelatase, CobS subunit. This model	83.63
PRK09302	509	circadian clock protein KaiC; Reviewed	83.55
PF00154	322	RecA: recA bacterial DNA recombination protein; In	83.5
PRK05748	448	replicative DNA helicase; Provisional	83.5
KOG0735	952	consensus AAA+-type ATPase [Posttranslational modi	83.5
PF13614	157	AAA_31: AAA domain; PDB: 2VED_B 2PH1_A 3EA0_B 3FKQ	83.46
TIGR03600	421	phage_DnaB phage replicative helicase, DnaB family	83.44
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	83.36
PRK05636	505	replicative DNA helicase; Provisional	83.27
PRK13531	498	regulatory ATPase RavA; Provisional	83.17
PRK08760	476	replicative DNA helicase; Provisional	83.16
cd00820	107	PEPCK_HprK Phosphoenolpyruvate carboxykinase (PEPC	83.13
cd04124	161	RabL2 RabL2 subfamily. RabL2 (Rab-like2) subfamily	83.09
PRK14493	274	putative bifunctional molybdopterin-guanine dinucl	83.05
PRK09825	176	idnK D-gluconate kinase; Provisional	82.99
PF01926	116	MMR_HSR1: 50S ribosome-binding GTPase; InterPro: I	82.85
COG0645	170	Predicted kinase [General function prediction only	82.76
PTZ00361	438	26 proteosome regulatory subunit 4-like protein; P	82.69
cd02038	139	FleN-like FleN is a member of the Fer4_NifH superf	82.68
cd04113	161	Rab4 Rab4 subfamily. Rab4 has been implicated in n	82.64
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	82.59
PRK05595	444	replicative DNA helicase; Provisional	82.56
TIGR01618	220	phage_P_loop phage nucleotide-binding protein. Thi	82.53
cd01862	172	Rab7 Rab7 subfamily. Rab7 is a small Rab GTPase th	82.48
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	82.44
TIGR00455	184	apsK adenylylsulfate kinase (apsK). Important resi	82.41
cd01918	149	HprK_C HprK/P, the bifunctional histidine-containi	82.41
cd04136	163	Rap_like Rap-like subfamily. The Rap subfamily con	82.39
KOG0991	333	consensus Replication factor C, subunit RFC2 [Repl	82.34
TIGR02903	615	spore_lon_C ATP-dependent protease, Lon family. Me	82.27
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	82.26
cd01131	198	PilT Pilus retraction ATPase PilT. PilT is a nucle	82.06
PRK10751	173	molybdopterin-guanine dinucleotide biosynthesis pr	81.81
TIGR00231	161	small_GTP small GTP-binding protein domain. This m	81.79
PRK14086	617	dnaA chromosomal replication initiation protein; P	81.79
COG0541	451	Ffh Signal recognition particle GTPase [Intracellu	81.77
PRK04220	301	2-phosphoglycerate kinase; Provisional	81.74
PRK13974	212	thymidylate kinase; Provisional	81.72
PRK08506	472	replicative DNA helicase; Provisional	81.67
cd00882	157	Ras_like_GTPase Ras-like GTPase superfamily. The R	81.67
TIGR02528	142	EutP ethanolamine utilization protein, EutP. This	81.59
PHA02544	316	44 clamp loader, small subunit; Provisional	81.25
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	81.25
PF00071	162	Ras: Ras family; InterPro: IPR001806 Small GTPases	81.18
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	81.14
cd04137	180	RheB Rheb (Ras Homolog Enriched in Brain) subfamil	81.02
smart00175	164	RAB Rab subfamily of small GTPases. Rab GTPases ar	81.01
PHA02244	383	ATPase-like protein	80.94
PF08433	270	KTI12: Chromatin associated protein KTI12 ; InterP	80.92
cd02022	179	DPCK Dephospho-coenzyme A kinase (DPCK, EC 2.7.1.2	80.89
PRK00440	319	rfc replication factor C small subunit; Reviewed	80.77
TIGR00665	434	DnaB replicative DNA helicase. This model describe	80.75
COG3598	402	RepA RecA-family ATPase [DNA replication, recombin	80.74
PF00625	183	Guanylate_kin: Guanylate kinase; InterPro: IPR0081	80.59
PRK14737	186	gmk guanylate kinase; Provisional	80.58
PRK05342	412	clpX ATP-dependent protease ATP-binding subunit Cl	80.55
PRK08356	195	hypothetical protein; Provisional	80.45
PRK14738	206	gmk guanylate kinase; Provisional	80.44
PRK06321	472	replicative DNA helicase; Provisional	80.42
PRK13886	241	conjugal transfer protein TraL; Provisional	80.29
PRK12597	461	F0F1 ATP synthase subunit beta; Provisional	80.24
KOG0726	440	consensus 26S proteasome regulatory complex, ATPas	80.2
cd01864	165	Rab19 Rab19 subfamily. Rab19 proteins are associat	80.18
PF01637	234	Arch_ATPase: Archaeal ATPase; InterPro: IPR011579	80.17
TIGR00416	454	sms DNA repair protein RadA. The gene protuct code	80.16
cd00046	144	DEXDc DEAD-like helicases superfamily. A diverse f	80.14
PRK08154	309	anaerobic benzoate catabolism transcriptional regu	80.13
cd00154	159	Rab Rab family. Rab GTPases form the largest famil	80.11
PRK11823	446	DNA repair protein RadA; Provisional	80.11
TIGR01007	204	eps_fam capsular exopolysaccharide family. This mo	80.05
PRK08099	399	bifunctional DNA-binding transcriptional repressor	80.05

>KOG4658 consensus Apoptotic ATPase [Signal transduction mechanisms]

Probab=100.00  E-value=7e-50  Score=383.86  Aligned_cols=277  Identities=25%  Similarity=0.414  Sum_probs=235.7

Q ss_pred             CCCCcHHHHHHHHHhhhc-cCCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCcC---CHhhhHHhHHHHccCCcEEEE
Q 041028            1 MGGIGKTTLAKEVARKAK-NGKLFDQIVFTEVSQNPNIKKIQGEIAFKLGLKFDEE---SESGRTRSPWSRLKKEKLQII   76 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~-~~~~Fd~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~---~~~~~~~~l~~~L~~kr~LlV   76 (283)
                      |||+||||||+.++|+.. +..+||.++||.||+.++...++.+|++.++.....+   +..+.+..|.+.|++||||||
T Consensus       187 MGGvGKTTL~~qi~N~~~~v~~~Fd~~iWV~VSk~f~~~~iq~~Il~~l~~~~~~~~~~~~~~~~~~i~~~L~~krfllv  266 (889)
T KOG4658|consen  187 MGGVGKTTLARQIFNKFDEVGNHFDGVIWVVVSKEFTTRKIQQTILERLGLLDEEWEDKEEDELASKLLNLLEGKRFLLV  266 (889)
T ss_pred             CCcccHHHHHHHHhcccchhcccCceEEEEEEcccccHHhHHHHHHHHhccCCcccchhhHHHHHHHHHHHhccCceEEE
Confidence            999999999999999987 8899999999999999999999999999998854433   335678899999999999999


Q ss_pred             ---------------------cC--------------------------------------eecCCC-CCCCcchHHHHH
Q 041028           77 ---------------------CG--------------------------------------KKMEGD-YAEGSELKWLAM   96 (283)
Q Consensus        77 ---------------------~G--------------------------------------~~~~~~-~~~~~~~~~~~~   96 (283)
                                           +|                                      +.++.. ....+.++++|+
T Consensus       267 LDDIW~~~dw~~I~~~~p~~~~g~KvvlTTRs~~V~~~~m~~~~~~~v~~L~~~eaW~LF~~~v~~~~~~~~~~i~~lak  346 (889)
T KOG4658|consen  267 LDDIWEEVDWDKIGVPFPSRENGSKVVLTTRSEEVCGRAMGVDYPIEVECLTPEEAWDLFQKKVGPNTLGSHPDIEELAK  346 (889)
T ss_pred             EecccccccHHhcCCCCCCccCCeEEEEEeccHhhhhccccCCccccccccCccccHHHHHHhhccccccccccHHHHHH
Confidence                                 22                                      233332 223344899999


Q ss_pred             HHHHhcCCchHHHHH---hhc-cCChHHHHHHHHHhcCCCCCCCCCchhHHHHHHhhhhccCCCCcHHHHHHHHhhCc--
Q 041028           97 DVAKECAGLPVSIVT---GIK-EQELFEWKDALEQLRRPSSTNFKDVQPAAYKAMELGYNKLEGDELKSTFLLIGYTA--  170 (283)
Q Consensus        97 ~i~~~c~glPLal~~---~l~-~~~~~~w~~~l~~l~~~~~~~~~~~~~~~~~~l~~sy~~L~~~~~k~~fl~~s~fp--  170 (283)
                      +|+++|+|+|||+.+   .|+ +.+..+|+++.+.+.+....+.+++...+..++++||+.||++ +|.||+|||+||  
T Consensus       347 ~v~~kC~GLPLAl~viG~~ma~K~t~~eW~~~~~~l~s~~~~~~~~~~~~i~~iLklSyd~L~~~-lK~CFLycalFPED  425 (889)
T KOG4658|consen  347 EVAEKCGGLPLALNVLGGLLACKKTVQEWRRALNVLKSSLAADFSGMEESILPILKLSYDNLPEE-LKSCFLYCALFPED  425 (889)
T ss_pred             HHHHHhCChHHHHHHHHHHhcCCCcHHHHHHHHccccccccCCCCchhhhhHHhhhccHhhhhHH-HHHHHHhhccCCcc
Confidence            999999999999999   777 8888899999999988866666677889999999999999987 999999999999  


Q ss_pred             -CCCHHHHHHHHhhccccCCCchHHHHHHHHHHHHHHHHhccccccccC-CCcceEEechhHHHHHHHHHc-----cCCc
Q 041028          171 -IASIDDLLMYGMGLGLFQGVNKMEAARARVHTLVHKLKASCMLLDHTS-KNEKLFSIHDVVRDVAISIAS-----GEQN  243 (283)
Q Consensus       171 -~i~~~~l~~~w~aeg~~~~~~~~~~~~~~~~~~~~~L~~~sLl~~~~~-~~~~~~~mH~lv~~~a~~~~~-----~~~~  243 (283)
                       .|+++.|+.+|+||||+.+....+.+++.+++++.+|+++||++.... .+..+|+|||+||++|.++++     ++++
T Consensus       426 ~~I~~e~Li~yWiaEGfi~~~~~~~~~~d~G~~~i~~LV~~~Ll~~~~~~~~~~~~kmHDvvRe~al~ias~~~~~~e~~  505 (889)
T KOG4658|consen  426 YEIKKEKLIEYWIAEGFIDPLDGGETAEDVGYDYIEELVRASLLIEERDEGRKETVKMHDVVREMALWIASDFGKQEENQ  505 (889)
T ss_pred             cccchHHHHHHHHhccCcCccccccchhcchHHHHHHHHHHHHHhhcccccceeEEEeeHHHHHHHHHHhccccccccce
Confidence             899999999999999998866666689999999999999999976653 244799999999999999999     6663


Q ss_pred             eeeeccccccCCCcCCcccccccccEEEEeCCCCCCCCC
Q 041028          244 VFSATNEQVDGCTEWSDESAVILYTSIVLRDIKTNVLPD  282 (283)
Q Consensus       244 ~~~~~~~~~~~~~~~~~~~~~~~~r~lsl~~~~~~~lp~  282 (283)
                      + +..+.++   .+.|....|..+||+|+++|++..+|.
T Consensus       506 i-v~~~~~~---~~~~~~~~~~~~rr~s~~~~~~~~~~~  540 (889)
T KOG4658|consen  506 I-VSDGVGL---SEIPQVKSWNSVRRMSLMNNKIEHIAG  540 (889)
T ss_pred             E-EECCcCc---cccccccchhheeEEEEeccchhhccC
Confidence            3 3333233   456777888999999999999988774

>PF00931 NB-ARC: NB-ARC domain; InterPro: IPR002182 This is the NB-ARC domain, a novel signalling motif found in bacteria and eukaryotes, shared by plant resistance gene products and regulators of cell death in animals []

Probab=99.97  E-value=2.9e-31  Score=229.30  Aligned_cols=187  Identities=26%  Similarity=0.475  Sum_probs=149.7

Q ss_pred             CCCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCC----cCCHhhhHHhHHHHccCCcEEEE
Q 041028            1 MGGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKLGLKFD----EESESGRTRSPWSRLKKEKLQII   76 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~~l~~~~~----~~~~~~~~~~l~~~L~~kr~LlV   76 (283)
                      |||+||||||.+++++...+.+|++++||++++..+..+++..|+.+++....    ..+..+....+++.|.++++|||
T Consensus        27 ~~G~GKT~LA~~~~~~~~~~~~f~~v~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~l~~~L~~~~~LlV  106 (287)
T PF00931_consen   27 MGGIGKTTLARQVARDLRIKNRFDGVIWVSLSKNPSLEQLLEQILRQLGEPDSSISDPKDIEELQDQLRELLKDKRCLLV  106 (287)
T ss_dssp             STTSSHHHHHHHHHCHHHHCCCCTEEEEEEEES-SCCHHHHHHHHHHHTCC-STSSCCSSHHHHHHHHHHHHCCTSEEEE
T ss_pred             CCcCCcceeeeecccccccccccccccccccccccccccccccccccccccccccccccccccccccchhhhccccceee
Confidence            79999999999999996677889999999999999999999999999988743    34667788999999999999999


Q ss_pred             -c--------------------C--------------------------------------eecCCCC-CCCcchHHHHH
Q 041028           77 -C--------------------G--------------------------------------KKMEGDY-AEGSELKWLAM   96 (283)
Q Consensus        77 -~--------------------G--------------------------------------~~~~~~~-~~~~~~~~~~~   96 (283)
                       +                    |                                      +.++... .......+.++
T Consensus       107 lDdv~~~~~~~~l~~~~~~~~~~~kilvTTR~~~v~~~~~~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~~~~~~~~~~~  186 (287)
T PF00931_consen  107 LDDVWDEEDLEELREPLPSFSSGSKILVTTRDRSVAGSLGGTDKVIELEPLSEEEALELFKKRAGRKESESPEDLEDLAK  186 (287)
T ss_dssp             EEEE-SHHHH-------HCHHSS-EEEEEESCGGGGTTHHSCEEEEECSS--HHHHHHHHHHHHTSHS----TTSCTHHH
T ss_pred             eeeecccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Confidence             0                    1                                      1122211 23345567899


Q ss_pred             HHHHhcCCchHHHHH---hhc-cCChHHHHHHHHHhcCCCCCCCCCchhHHHHHHhhhhccCCCCcHHHHHHHHhhCc--
Q 041028           97 DVAKECAGLPVSIVT---GIK-EQELFEWKDALEQLRRPSSTNFKDVQPAAYKAMELGYNKLEGDELKSTFLLIGYTA--  170 (283)
Q Consensus        97 ~i~~~c~glPLal~~---~l~-~~~~~~w~~~l~~l~~~~~~~~~~~~~~~~~~l~~sy~~L~~~~~k~~fl~~s~fp--  170 (283)
                      +|++.|+|+||||++   .++ ..+..+|..+++++....... .+...++..++.+||+.||++ +|+||+|||+||  
T Consensus       187 ~i~~~c~glPLal~~~a~~l~~~~~~~~w~~~~~~l~~~~~~~-~~~~~~~~~~l~~s~~~L~~~-~~~~f~~L~~f~~~  264 (287)
T PF00931_consen  187 EIVEKCGGLPLALKLIASYLRSKSTVDEWEEALEELENSLRES-RDYDRSVFSALELSYDSLPDE-LRRCFLYLSIFPEG  264 (287)
T ss_dssp             HHHHHTTT-HHHHHHHHHHHHHHHSSSSHHHHHHHHHHCHTCS-SGSCHHHHHHHHHHHHSSHTC-CHHHHHHGGGSGTT
T ss_pred             ccccccccccccccccccccccccccccccccccccccccccc-ccccccccccceechhcCCcc-HHHHHhhCcCCCCC
Confidence            999999999999999   564 447899999998887664322 124688999999999999998 999999999999  


Q ss_pred             -CCCHHHHHHHHhhccccCC
Q 041028          171 -IASIDDLLMYGMGLGLFQG  189 (283)
Q Consensus       171 -~i~~~~l~~~w~aeg~~~~  189 (283)
                       .|+.+.|+++|+++|+++.
T Consensus       265 ~~i~~~~li~lW~~e~~i~~  284 (287)
T PF00931_consen  265 VPIPRERLIRLWVAEGFISS  284 (287)
T ss_dssp             S-EEHHHHHHHHTT-HHTC-
T ss_pred             ceECHHHHHHHHHHCCCCcc
Confidence             7899999999999999975

This domain has been structurally characterised in the human protein apoptotic protease-activating factor 1 (Apaf-1) []. It contains the three-layered alpha-beta fold and subsequent short alpha-helical region characteristic of the AAA+ ATPase domain superfamily. While this domain is thought to bind and hyrolyse ATP, only ADP binding has been experimentally verified. It is proposed that binding and hydrolysis of ATP by this domain induces conformational changes the the overall protein, leading to formation of the apoptosome.; GO: 0043531 ADP binding; PDB: 3IZA_E 1Z6T_D 3SFZ_A 3SHF_A 1VT4_M 3IZ8_G 3LQR_A 2A5Y_C 3LQQ_A.

>PLN03210 Resistant to P

Probab=99.96  E-value=2e-28  Score=245.57  Aligned_cols=251  Identities=19%  Similarity=0.227  Sum_probs=171.4

Q ss_pred             CCCCcHHHHHHHHHhhhccCCCCCeEEEEEe---CCC-----------CC-HHHHHHHHHHHhCCCCCcCCHhhhHHhHH
Q 041028            1 MGGIGKTTLAKEVARKAKNGKLFDQIVFTEV---SQN-----------PN-IKKIQGEIAFKLGLKFDEESESGRTRSPW   65 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v---~~~-----------~~-~~~l~~~i~~~l~~~~~~~~~~~~~~~l~   65 (283)
                      ||||||||||+++|++...  .|++.+|+..   +..           ++ ...++++++..+...... .. .....++
T Consensus       215 ~gGiGKTTLA~~l~~~l~~--~F~g~vfv~~~~v~~~~~~~~~~~~~~~~~~~~l~~~~l~~il~~~~~-~~-~~~~~~~  290 (1153)
T PLN03210        215 SSGIGKTTIARALFSRLSR--QFQSSVFIDRAFISKSMEIYSSANPDDYNMKLHLQRAFLSEILDKKDI-KI-YHLGAME  290 (1153)
T ss_pred             CCCCchHHHHHHHHHHHhh--cCCeEEEeeccccccchhhcccccccccchhHHHHHHHHHHHhCCCCc-cc-CCHHHHH
Confidence            8999999999999998764  4999888742   111           11 234555555554322111 00 1124577


Q ss_pred             HHccCCcEEEE---------------------cC-------------------------------------eecCCCCCC
Q 041028           66 SRLKKEKLQII---------------------CG-------------------------------------KKMEGDYAE   87 (283)
Q Consensus        66 ~~L~~kr~LlV---------------------~G-------------------------------------~~~~~~~~~   87 (283)
                      +.|+++|+|||                     .|                                     +.+|+...+
T Consensus       291 ~~L~~krvLLVLDdv~~~~~l~~L~~~~~~~~~GsrIIiTTrd~~vl~~~~~~~~~~v~~l~~~ea~~LF~~~Af~~~~~  370 (1153)
T PLN03210        291 ERLKHRKVLIFIDDLDDQDVLDALAGQTQWFGSGSRIIVITKDKHFLRAHGIDHIYEVCLPSNELALEMFCRSAFKKNSP  370 (1153)
T ss_pred             HHHhCCeEEEEEeCCCCHHHHHHHHhhCccCCCCcEEEEEeCcHHHHHhcCCCeEEEecCCCHHHHHHHHHHHhcCCCCC
Confidence            78889999998                     12                                     345555555


Q ss_pred             CcchHHHHHHHHHhcCCchHHHHH---hhccCChHHHHHHHHHhcCCCCCCCCCchhHHHHHHhhhhccCCCCcHHHHHH
Q 041028           88 GSELKWLAMDVAKECAGLPVSIVT---GIKEQELFEWKDALEQLRRPSSTNFKDVQPAAYKAMELGYNKLEGDELKSTFL  164 (283)
Q Consensus        88 ~~~~~~~~~~i~~~c~glPLal~~---~l~~~~~~~w~~~l~~l~~~~~~~~~~~~~~~~~~l~~sy~~L~~~~~k~~fl  164 (283)
                      +.++.+++++|+++|+|+||||++   .|+.++..+|..+++++....       ...+..+|++||+.|+++..|.||+
T Consensus       371 ~~~~~~l~~~iv~~c~GLPLAl~vlgs~L~~k~~~~W~~~l~~L~~~~-------~~~I~~~L~~SYd~L~~~~~k~~Fl  443 (1153)
T PLN03210        371 PDGFMELASEVALRAGNLPLGLNVLGSYLRGRDKEDWMDMLPRLRNGL-------DGKIEKTLRVSYDGLNNKKDKAIFR  443 (1153)
T ss_pred             cHHHHHHHHHHHHHhCCCcHHHHHHHHHHcCCCHHHHHHHHHHHHhCc-------cHHHHHHHHHhhhccCccchhhhhh
Confidence            667899999999999999999999   677888999999999987532       4578999999999998644899999


Q ss_pred             HHhhCc-CCCHHHHHHHHhhccccCCCchHHHHHHHHHHHHHHHHhccccccccCCCcceEEechhHHHHHHHHHccCCc
Q 041028          165 LIGYTA-IASIDDLLMYGMGLGLFQGVNKMEAARARVHTLVHKLKASCMLLDHTSKNEKLFSIHDVVRDVAISIASGEQN  243 (283)
Q Consensus       165 ~~s~fp-~i~~~~l~~~w~aeg~~~~~~~~~~~~~~~~~~~~~L~~~sLl~~~~~~~~~~~~mH~lv~~~a~~~~~~~~~  243 (283)
                      ++|+|| +.+.+. +..|.+.+....           ...++.|+++||++...    .+++||||+|+||+.++.++..
T Consensus       444 ~ia~ff~~~~~~~-v~~~l~~~~~~~-----------~~~l~~L~~ksLi~~~~----~~~~MHdLl~~~~r~i~~~~~~  507 (1153)
T PLN03210        444 HIACLFNGEKVND-IKLLLANSDLDV-----------NIGLKNLVDKSLIHVRE----DIVEMHSLLQEMGKEIVRAQSN  507 (1153)
T ss_pred             eehhhcCCCCHHH-HHHHHHhcCCCc-----------hhChHHHHhcCCEEEcC----CeEEhhhHHHHHHHHHHHhhcC
Confidence            999998 776665 445555543321           23467788899996543    4799999999999999987642


Q ss_pred             eeeeccccccCCCc----CCcccccccccEEEEeCCCCCC
Q 041028          244 VFSATNEQVDGCTE----WSDESAVILYTSIVLRDIKTNV  279 (283)
Q Consensus       244 ~~~~~~~~~~~~~~----~~~~~~~~~~r~lsl~~~~~~~  279 (283)
                       ...+...+++..+    ...+...++++.|++..+++.+
T Consensus       508 -~~~~r~~l~~~~di~~vl~~~~g~~~v~~i~l~~~~~~~  546 (1153)
T PLN03210        508 -EPGEREFLVDAKDICDVLEDNTGTKKVLGITLDIDEIDE  546 (1153)
T ss_pred             -CCCcceeEeCHHHHHHHHHhCcccceeeEEEeccCccce
Confidence             1111111110000    0122344677777777666554

syringae 6; Provisional

>PRK04841 transcriptional regulator MalT; Provisional

Probab=98.96  E-value=2.7e-08  Score=99.12  Aligned_cols=127  Identities=7%  Similarity=0.064  Sum_probs=77.6

Q ss_pred             HHHHHHHHHhcCCchHHHHH-h--hccCChHHHHHHHHHhcCCCCCCCCCchhHHHHHHhh-hhccCCCCcHHHHHHHHh
Q 041028           92 KWLAMDVAKECAGLPVSIVT-G--IKEQELFEWKDALEQLRRPSSTNFKDVQPAAYKAMEL-GYNKLEGDELKSTFLLIG  167 (283)
Q Consensus        92 ~~~~~~i~~~c~glPLal~~-~--l~~~~~~~w~~~l~~l~~~~~~~~~~~~~~~~~~l~~-sy~~L~~~~~k~~fl~~s  167 (283)
                      .+.+.+|.+.|+|+|+++.. +  +..... ........+...       ....+...+.- .++.||++ .+..++.+|
T Consensus       205 ~~~~~~l~~~t~Gwp~~l~l~~~~~~~~~~-~~~~~~~~~~~~-------~~~~~~~~l~~~v~~~l~~~-~~~~l~~~a  275 (903)
T PRK04841        205 AAESSRLCDDVEGWATALQLIALSARQNNS-SLHDSARRLAGI-------NASHLSDYLVEEVLDNVDLE-TRHFLLRCS  275 (903)
T ss_pred             HHHHHHHHHHhCChHHHHHHHHHHHhhCCC-chhhhhHhhcCC-------CchhHHHHHHHHHHhcCCHH-HHHHHHHhc
Confidence            34567899999999999988 3  322111 011111111100       01234444333 47899997 999999999


Q ss_pred             hCcCCCHHHHHHHHhhccccCCCchHHHHHHHHHHHHHHHHhccccccccCCCcceEEechhHHHHHHHHHccC
Q 041028          168 YTAIASIDDLLMYGMGLGLFQGVNKMEAARARVHTLVHKLKASCMLLDHTSKNEKLFSIHDVVRDVAISIASGE  241 (283)
Q Consensus       168 ~fp~i~~~~l~~~w~aeg~~~~~~~~~~~~~~~~~~~~~L~~~sLl~~~~~~~~~~~~mH~lv~~~a~~~~~~~  241 (283)
                      +++.|+.+.+-...   |   .        ......++.|.+.+++....++...+|+.|++++++++.....+
T Consensus       276 ~~~~~~~~l~~~l~---~---~--------~~~~~~L~~l~~~~l~~~~~~~~~~~yr~H~L~r~~l~~~l~~~  335 (903)
T PRK04841        276 VLRSMNDALIVRVT---G---E--------ENGQMRLEELERQGLFIQRMDDSGEWFRYHPLFASFLRHRCQWE  335 (903)
T ss_pred             ccccCCHHHHHHHc---C---C--------CcHHHHHHHHHHCCCeeEeecCCCCEEehhHHHHHHHHHHHHhc
Confidence            99988865544322   1   0        12246777788899974332221258999999999999876433

>COG3903 Predicted ATPase [General function prediction only]

Probab=98.37  E-value=9.7e-07  Score=77.57  Aligned_cols=226  Identities=16%  Similarity=0.218  Sum_probs=138.4

Q ss_pred             CCCcHHHHHHHHHhhhccCCCC-CeEEEEEeCCCCCHHHHHHHHHHHhCCCCCcCCHhhhHHhHHHHccCCcEEEE----
Q 041028            2 GGIGKTTLAKEVARKAKNGKLF-DQIVFTEVSQNPNIKKIQGEIAFKLGLKFDEESESGRTRSPWSRLKKEKLQII----   76 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~F-d~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~kr~LlV----   76 (283)
                      |||||||++-.+.+ .+..  | ++++++...+-.+...+.--....++.....  -+.....+.....++|.++|    
T Consensus        23 ggvgkttl~~~~a~-~~~~--~~~~v~~vdl~pitD~~~v~~~~ag~~gl~~~~--g~~~~~~~~~~~~~rr~llvldnc   97 (414)
T COG3903          23 GGVGKTTLALQAAH-AASE--YADGVAFVDLAPITDPALVFPTLAGALGLHVQP--GDSAVDTLVRRIGDRRALLVLDNC   97 (414)
T ss_pred             CccceehhhhhhHh-Hhhh--cccceeeeeccccCchhHhHHHHHhhccccccc--chHHHHHHHHHHhhhhHHHHhcCc
Confidence            89999999999999 5544  8 7788887776666666666666667665432  11223345555566666666    


Q ss_pred             -----------------c----------------C---e-----ecCC---------------CCCCCcchHHHHHHHHH
Q 041028           77 -----------------C----------------G---K-----KMEG---------------DYAEGSELKWLAMDVAK  100 (283)
Q Consensus        77 -----------------~----------------G---~-----~~~~---------------~~~~~~~~~~~~~~i~~  100 (283)
                                       +                |   +     ..++               .-............|++
T Consensus        98 ehl~~~~a~~i~all~~~~~~~~~atsre~~l~~ge~~~~~~~L~~~d~a~~lf~~ra~~~~~~f~l~~~~~a~v~~icr  177 (414)
T COG3903          98 EHLLDACAALIVALLGACPRLAILATSREAILVAGEVHRRVPSLSLFDEAIELFVCRAVLVALSFWLTDDNAAAVAEICR  177 (414)
T ss_pred             HHHHHHHHHHHHHHHccchhhhhHHHhHhhhcccccccccCCccccCCchhHHHHHHHHHhccceeecCCchHHHHHHHH
Confidence                             0                1   0     0000               01112233456778999


Q ss_pred             hcCCchHHHHH------hhc-cCChHHHHHHHHHhcCCCCCCCCCchhHHHHHHhhhhccCCCCcHHHHHHHHhhCc-CC
Q 041028          101 ECAGLPVSIVT------GIK-EQELFEWKDALEQLRRPSSTNFKDVQPAAYKAMELGYNKLEGDELKSTFLLIGYTA-IA  172 (283)
Q Consensus       101 ~c~glPLal~~------~l~-~~~~~~w~~~l~~l~~~~~~~~~~~~~~~~~~l~~sy~~L~~~~~k~~fl~~s~fp-~i  172 (283)
                      +..|.||+|..      ++. ..-.....+-...+... .....--.......+.+||.-|..- .+-.|.-++.|. .|
T Consensus       178 ~ldg~~laielaaarv~sl~~~~i~~~L~drf~ll~~~-~r~a~~~~qtl~asl~ws~~lLtgw-e~~~~~rLa~~~g~f  255 (414)
T COG3903         178 RLDGIPLAIELAAARVRSLSPDEIAAGLRDRFRLLTGG-ARLAVLRQQTLRASLDWSYALLTGW-ERALFGRLAVFVGGF  255 (414)
T ss_pred             HhhcchHHHHHHHHHHHhcCHHHHHHHHhhHHHHHhcc-cccchhHHHhccchhhhhhHhhhhH-HHHHhcchhhhhhhh
Confidence            99999999998      222 22223333333444333 2222222567889999999999997 999999999998 78


Q ss_pred             CHHHHHHHHhhccccCCCchHHHHHHHHHHHHHHHHhccccccccCCCcceEEechhHHHHHHHHHccC
Q 041028          173 SIDDLLMYGMGLGLFQGVNKMEAARARVHTLVHKLKASCMLLDHTSKNEKLFSIHDVVRDVAISIASGE  241 (283)
Q Consensus       173 ~~~~l~~~w~aeg~~~~~~~~~~~~~~~~~~~~~L~~~sLl~~~~~~~~~~~~mH~lv~~~a~~~~~~~  241 (283)
                      +.+  ...|.+.|-.-.    . ..-.....+..|+++|++...+......|+.-+-++.|+..+..+.
T Consensus       256 ~~~--l~~~~a~g~~~~----~-~~y~~~~a~~ll~~kslv~a~~~~~~a~~Rl~eT~r~YalaeL~r~  317 (414)
T COG3903         256 DLG--LALAVAAGADVD----V-PRYLVLLALTLLVDKSLVVALDLLGRARYRLLETGRRYALAELHRS  317 (414)
T ss_pred             ccc--HHHHHhcCCccc----c-chHHHHHHHHHHhhccchhhhhhhhHHHHHHHHHHHHHHHHHHHhh
Confidence            776  345555443210    0 1112233455788899985444333356777777888877665543

>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]

Probab=98.21  E-value=4.6e-05  Score=72.69  Aligned_cols=211  Identities=11%  Similarity=0.078  Sum_probs=123.4

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCC-CCCHHHHHHHHHHHhCCCCCc--C------------CHhhhHHhHHH
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQ-NPNIKKIQGEIAFKLGLKFDE--E------------SESGRTRSPWS   66 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~-~~~~~~l~~~i~~~l~~~~~~--~------------~~~~~~~~l~~   66 (283)
                      +|.|||||+........ .  =..+.|.+++. +-++......++..++.-.+.  +            +.......+..
T Consensus        46 AGfGKttl~aq~~~~~~-~--~~~v~Wlslde~dndp~rF~~yLi~al~~~~p~~~~~a~~l~q~~~~~~l~~l~~~L~~  122 (894)
T COG2909          46 AGFGKTTLLAQWRELAA-D--GAAVAWLSLDESDNDPARFLSYLIAALQQATPTLGDEAQTLLQKHQYVSLESLLSSLLN  122 (894)
T ss_pred             CCCcHHHHHHHHHHhcC-c--ccceeEeecCCccCCHHHHHHHHHHHHHHhCccccHHHHHHHHhcccccHHHHHHHHHH
Confidence            69999999999987322 2  24689999975 567888888899888732221  1            12223333333


Q ss_pred             HccC--CcEEEE-cC--------------------------------------------------------------eec
Q 041028           67 RLKK--EKLQII-CG--------------------------------------------------------------KKM   81 (283)
Q Consensus        67 ~L~~--kr~LlV-~G--------------------------------------------------------------~~~   81 (283)
                      -+..  +.+.|| +.                                                              ...
T Consensus       123 Ela~~~~pl~LVlDDyHli~~~~l~~~l~fLl~~~P~~l~lvv~SR~rP~l~la~lRlr~~llEi~~~~Lrf~~eE~~~f  202 (894)
T COG2909         123 ELASYEGPLYLVLDDYHLISDPALHEALRFLLKHAPENLTLVVTSRSRPQLGLARLRLRDELLEIGSEELRFDTEEAAAF  202 (894)
T ss_pred             HHHhhcCceEEEeccccccCcccHHHHHHHHHHhCCCCeEEEEEeccCCCCcccceeehhhHHhcChHhhcCChHHHHHH
Confidence            3332  354444 10                                                              011


Q ss_pred             CCCCCCCcchHHHHHHHHHhcCCchHHHHH-hhc-c--CChHHHHHHHHHhcCCCCCCCCCchhHHHH-HHhhhhccCCC
Q 041028           82 EGDYAEGSELKWLAMDVAKECAGLPVSIVT-GIK-E--QELFEWKDALEQLRRPSSTNFKDVQPAAYK-AMELGYNKLEG  156 (283)
Q Consensus        82 ~~~~~~~~~~~~~~~~i~~~c~glPLal~~-~l~-~--~~~~~w~~~l~~l~~~~~~~~~~~~~~~~~-~l~~sy~~L~~  156 (283)
                      +.+....+-...-++.+.+..+|.+-|+.. +|. .  .+...-...+.           +...-+.. ...--++.||+
T Consensus       203 l~~~~~l~Ld~~~~~~L~~~teGW~~al~L~aLa~~~~~~~~q~~~~Ls-----------G~~~~l~dYL~eeVld~Lp~  271 (894)
T COG2909         203 LNDRGSLPLDAADLKALYDRTEGWAAALQLIALALRNNTSAEQSLRGLS-----------GAASHLSDYLVEEVLDRLPP  271 (894)
T ss_pred             HHHcCCCCCChHHHHHHHhhcccHHHHHHHHHHHccCCCcHHHHhhhcc-----------chHHHHHHHHHHHHHhcCCH
Confidence            111111222333466777777888877777 443 2  22222211111           00111111 22344688999


Q ss_pred             CcHHHHHHHHhhCcCCCHHHHHHHHhhccccCCCchHHHHHHHHHHHHHHHHhccccccccCCCcceEEechhHHHHHHH
Q 041028          157 DELKSTFLLIGYTAIASIDDLLMYGMGLGLFQGVNKMEAARARVHTLVHKLKASCMLLDHTSKNEKLFSIHDVVRDVAIS  236 (283)
Q Consensus       157 ~~~k~~fl~~s~fp~i~~~~l~~~w~aeg~~~~~~~~~~~~~~~~~~~~~L~~~sLl~~~~~~~~~~~~mH~lv~~~a~~  236 (283)
                      + +|..++-||+++.|..+-.-++-              .++.+..++++|.+++|+...=++....|+.|.|..+|.+.
T Consensus       272 ~-l~~FLl~~svl~~f~~eL~~~Lt--------------g~~ng~amLe~L~~~gLFl~~Ldd~~~WfryH~LFaeFL~~  336 (894)
T COG2909         272 E-LRDFLLQTSVLSRFNDELCNALT--------------GEENGQAMLEELERRGLFLQRLDDEGQWFRYHHLFAEFLRQ  336 (894)
T ss_pred             H-HHHHHHHHHhHHHhhHHHHHHHh--------------cCCcHHHHHHHHHhCCCceeeecCCCceeehhHHHHHHHHh
Confidence            8 99999999999866554433221              22345677888888999853323333899999999999988


Q ss_pred             HHccC
Q 041028          237 IASGE  241 (283)
Q Consensus       237 ~~~~~  241 (283)
                      ....+
T Consensus       337 r~~~~  341 (894)
T COG2909         337 RLQRE  341 (894)
T ss_pred             hhccc
Confidence            77653

>cd01128 rho_factor Transcription termination factor rho is a bacterial ATP-dependent RNA/DNA helicase

Probab=98.07  E-value=1.4e-05  Score=67.39  Aligned_cols=44  Identities=16%  Similarity=0.207  Sum_probs=38.4

Q ss_pred             CCCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCC--CCHHHHHHHHH
Q 041028            1 MGGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQN--PNIKKIQGEIA   45 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~--~~~~~l~~~i~   45 (283)
                      .+|+|||||++.+|++.... +|+.++|+.+.+.  +++.++++.+.
T Consensus        24 ~~G~GKTTLlr~I~n~l~~~-~fdv~~~v~vI~er~~ev~el~~~I~   69 (249)
T cd01128          24 PPKAGKTTLLQSIANAITKN-HPEVYLIVLLIDERPEEVTDMQRSVK   69 (249)
T ss_pred             CCCCCHHHHHHHHHhccccc-cCCeEEEEEEccCCCccHHHHHHHhc
Confidence            37999999999999987665 8999999997766  89999999993

It is a homohexamer. Each monomer consists of an N-terminal domain of the OB fold, which is responsible for binding to cysteine rich nucleotides. This alignment is of the C-terminal ATP binding domain.

>PRK09376 rho transcription termination factor Rho; Provisional

Probab=98.04  E-value=1.1e-05  Score=71.37  Aligned_cols=45  Identities=13%  Similarity=0.138  Sum_probs=39.3

Q ss_pred             CCCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCC--CHHHHHHHHHH
Q 041028            1 MGGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNP--NIKKIQGEIAF   46 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~--~~~~l~~~i~~   46 (283)
                      .+|+||||||+.+|+..... +|+.++||.+.+.+  .+.++++.|..
T Consensus       177 ppGvGKTTLaK~Ian~I~~n-hFDv~~~VvLIgER~~EVtdiqrsIlg  223 (416)
T PRK09376        177 PPKAGKTVLLQNIANSITTN-HPEVHLIVLLIDERPEEVTDMQRSVKG  223 (416)
T ss_pred             CCCCChhHHHHHHHHHHHhh-cCCeEEEEEEeCCchhHHHHHHHHhcC
Confidence            37999999999999998765 89999999998887  78888888863

>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily

Probab=97.86  E-value=0.00035  Score=59.59  Aligned_cols=73  Identities=16%  Similarity=0.230  Sum_probs=45.2

Q ss_pred             CCCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCcCCHhhhHHhHHHHc-----cCCcEEE
Q 041028            1 MGGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKLGLKFDEESESGRTRSPWSRL-----KKEKLQI   75 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~L-----~~kr~Ll   75 (283)
                      .+|+|||||++.+++...... + ..+|+ +....+..+++..|+..+|.+....+.......+.+.+     .+++.+|
T Consensus        51 ~~G~GKTtl~~~l~~~l~~~~-~-~~~~~-~~~~~~~~~~l~~i~~~lG~~~~~~~~~~~~~~l~~~l~~~~~~~~~~vl  127 (269)
T TIGR03015        51 EVGAGKTTLIRNLLKRLDQER-V-VAAKL-VNTRVDAEDLLRMVAADFGLETEGRDKAALLRELEDFLIEQFAAGKRALL  127 (269)
T ss_pred             CCCCCHHHHHHHHHHhcCCCC-e-EEeee-eCCCCCHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHHHHHHHhCCCCeEE
Confidence            379999999999998865321 1 22333 23345778899999999988655443333333443322     4555555


Q ss_pred             E
Q 041028           76 I   76 (283)
Q Consensus        76 V   76 (283)
                      |
T Consensus       128 i  128 (269)
T TIGR03015       128 V  128 (269)
T ss_pred             E
Confidence            5

Members of this protein are marked as probable ATPases by the nucleotide binding P-loop motif GXXGXGKTT, a motif DEAQ similar to the DEAD/H box of helicases, and extensive homology to ATPases of MSHA-type pilus systems and to GspA proteins associated with type II protein secretion systems.

>PF13401 AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S_B

Probab=97.67  E-value=0.00011  Score=55.35  Aligned_cols=76  Identities=24%  Similarity=0.340  Sum_probs=56.0

Q ss_pred             CCCcHHHHHHHHHhhhccC---CCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCc-CCHhhhHHhHHHHccCCc--EEE
Q 041028            2 GGIGKTTLAKEVARKAKNG---KLFDQIVFTEVSQNPNIKKIQGEIAFKLGLKFDE-ESESGRTRSPWSRLKKEK--LQI   75 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~---~~Fd~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~-~~~~~~~~~l~~~L~~kr--~Ll   75 (283)
                      +|+|||++++++.+.....   ..-..++|+++....+...+...|+.+++.+... .+..+..+.+.+.+...+  +++
T Consensus        13 ~G~GKT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~l~~~~~~~l~~~~~~~lv   92 (131)
T PF13401_consen   13 PGSGKTTLIKRLARQLNAEAEIKNHPDVIYVNCPSSRTPRDFAQEILEALGLPLKSRQTSDELRSLLIDALDRRRVVLLV   92 (131)
T ss_dssp             TTSSHHHHHHHHHHHHHHHHHHCCCEEEEEEEHHHHSSHHHHHHHHHHHHT-SSSSTS-HHHHHHHHHHHHHHCTEEEEE
T ss_pred             CCCCHHHHHHHHHHHhHHhhhccCCCcEEEEEeCCCCCHHHHHHHHHHHhCccccccCCHHHHHHHHHHHHHhcCCeEEE
Confidence            6999999999999875321   0023567999988779999999999999987665 566777788888886654  444


Q ss_pred             Ec
Q 041028           76 IC   77 (283)
Q Consensus        76 V~   77 (283)
                      |+
T Consensus        93 iD   94 (131)
T PF13401_consen   93 ID   94 (131)
T ss_dssp             EE
T ss_pred             Ee
Confidence            44

>TIGR00767 rho transcription termination factor Rho

Probab=97.47  E-value=0.00049  Score=61.40  Aligned_cols=46  Identities=13%  Similarity=0.180  Sum_probs=39.0

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCC--CCHHHHHHHHHHHh
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQN--PNIKKIQGEIAFKL   48 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~--~~~~~l~~~i~~~l   48 (283)
                      +|+|||||++.+++..... +|+..+||.+.+.  ..+.++++.++..+
T Consensus       177 ~g~GKTtL~~~i~~~I~~n-hfdv~v~VlLIgER~~EVtDLqrsIlg~V  224 (415)
T TIGR00767       177 PKAGKTVLLQKIAQAITRN-HPEVELIVLLIDERPEEVTDMQRSVKGEV  224 (415)
T ss_pred             CCCChhHHHHHHHHhhccc-CCceEEEEEEcCCCCccHHHHHHHhhceE
Confidence            6999999999999987654 8999999999855  78999999995433

Members of this family differ in the specificity of RNA binding.

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=97.21  E-value=0.013  Score=51.72  Aligned_cols=105  Identities=10%  Similarity=0.091  Sum_probs=55.6

Q ss_pred             HHHHHHHHhcCCchHHHHHhhccCChHHHHHHHHHhcCCCCCCCC-CchhHHHHHHhhhhccCCCCcHHHHHH-HHhhCc
Q 041028           93 WLAMDVAKECAGLPVSIVTGIKEQELFEWKDALEQLRRPSSTNFK-DVQPAAYKAMELGYNKLEGDELKSTFL-LIGYTA  170 (283)
Q Consensus        93 ~~~~~i~~~c~glPLal~~~l~~~~~~~w~~~l~~l~~~~~~~~~-~~~~~~~~~l~~sy~~L~~~~~k~~fl-~~s~fp  170 (283)
                      +.+..|++.|+|.|-.+...+.  ....|....    ..  ..+. ..-......+...+..|++. .+..+. .+..|+
T Consensus       203 ~~~~~ia~~~~G~pR~a~~~l~--~~~~~a~~~----~~--~~I~~~~v~~~l~~~~~~~~~l~~~-~~~~l~~~~~~~~  273 (328)
T PRK00080        203 EGALEIARRSRGTPRIANRLLR--RVRDFAQVK----GD--GVITKEIADKALDMLGVDELGLDEM-DRKYLRTIIEKFG  273 (328)
T ss_pred             HHHHHHHHHcCCCchHHHHHHH--HHHHHHHHc----CC--CCCCHHHHHHHHHHhCCCcCCCCHH-HHHHHHHHHHHcC
Confidence            4567788888888843333221  111111110    00  1110 11233445567778889886 777775 777776


Q ss_pred             --CCCHHHHHHHHhhccccCCCchHHHHHHHHHHHHH-HHHhccccccccC
Q 041028          171 --IASIDDLLMYGMGLGLFQGVNKMEAARARVHTLVH-KLKASCMLLDHTS  218 (283)
Q Consensus       171 --~i~~~~l~~~w~aeg~~~~~~~~~~~~~~~~~~~~-~L~~~sLl~~~~~  218 (283)
                        ++..+.+...+   |.     +.    ..+++.++ .|++.+|++....
T Consensus       274 ~~~~~~~~~a~~l---g~-----~~----~~~~~~~e~~Li~~~li~~~~~  312 (328)
T PRK00080        274 GGPVGLDTLAAAL---GE-----ER----DTIEDVYEPYLIQQGFIQRTPR  312 (328)
T ss_pred             CCceeHHHHHHHH---CC-----Cc----chHHHHhhHHHHHcCCcccCCc
Confidence              77777765544   21     11    12333444 6677999964443

>PRK08118 topology modulation protein; Reviewed

Probab=97.16  E-value=0.00018  Score=56.94  Aligned_cols=28  Identities=32%  Similarity=0.565  Sum_probs=22.6

Q ss_pred             CCCCcHHHHHHHHHhhhccC-CCCCeEEE
Q 041028            1 MGGIGKTTLAKEVARKAKNG-KLFDQIVF   28 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~-~~Fd~~~w   28 (283)
                      .+|+||||||+.+++..... -+||..+|
T Consensus         9 ~~GsGKSTlak~L~~~l~~~~~~lD~l~~   37 (167)
T PRK08118          9 SGGSGKSTLARQLGEKLNIPVHHLDALFW   37 (167)
T ss_pred             CCCCCHHHHHHHHHHHhCCCceecchhhc
Confidence            47999999999999986654 35677776

>PF05621 TniB: Bacterial TniB protein; InterPro: IPR008868 This family consists of several bacterial TniB NTP-binding proteins

Probab=97.14  E-value=0.0085  Score=51.49  Aligned_cols=75  Identities=17%  Similarity=0.282  Sum_probs=55.2

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCC----eEEEEEeCCCCCHHHHHHHHHHHhCCCCCc-CCHhhhHHhHHHHccC--CcEE
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFD----QIVFTEVSQNPNIKKIQGEIAFKLGLKFDE-ESESGRTRSPWSRLKK--EKLQ   74 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd----~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~-~~~~~~~~~l~~~L~~--kr~L   74 (283)
                      +|.|||++++++....-....=+    .++.|.+...++...+...|+.+++.+... .+...........|+.  -|+|
T Consensus        70 snnGKT~Ii~rF~~~hp~~~d~~~~~~PVv~vq~P~~p~~~~~Y~~IL~~lgaP~~~~~~~~~~~~~~~~llr~~~vrmL  149 (302)
T PF05621_consen   70 SNNGKTMIIERFRRLHPPQSDEDAERIPVVYVQMPPEPDERRFYSAILEALGAPYRPRDRVAKLEQQVLRLLRRLGVRML  149 (302)
T ss_pred             CCCcHHHHHHHHHHHCCCCCCCCCccccEEEEecCCCCChHHHHHHHHHHhCcccCCCCCHHHHHHHHHHHHHHcCCcEE
Confidence            58999999999997754331011    467778888999999999999999998754 3444445555566654  4899


Q ss_pred             EE
Q 041028           75 II   76 (283)
Q Consensus        75 lV   76 (283)
                      ||
T Consensus       150 II  151 (302)
T PF05621_consen  150 II  151 (302)
T ss_pred             Ee
Confidence            99

TniB is a probable ATP-binding protein [] which is involved in Tn5053 mercury resistance transposition [].

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=97.05  E-value=0.02  Score=49.85  Aligned_cols=62  Identities=11%  Similarity=-0.005  Sum_probs=36.7

Q ss_pred             HHHHhhhhccCCCCcHHHHHH-HHhhCc--CCCHHHHHHHHhhccccCCCchHHHHHHHHHHHHH-HHHhccccccccC
Q 041028          144 YKAMELGYNKLEGDELKSTFL-LIGYTA--IASIDDLLMYGMGLGLFQGVNKMEAARARVHTLVH-KLKASCMLLDHTS  218 (283)
Q Consensus       144 ~~~l~~sy~~L~~~~~k~~fl-~~s~fp--~i~~~~l~~~w~aeg~~~~~~~~~~~~~~~~~~~~-~L~~~sLl~~~~~  218 (283)
                      ...+..+|..|++. .+..+. .++.++  +++.+.+....   |.-         .......++ .|++++|+.....
T Consensus       226 l~~l~~~~~~l~~~-~~~~L~al~~~~~~~~~~~~~ia~~l---g~~---------~~~~~~~~e~~Li~~~li~~~~~  291 (305)
T TIGR00635       226 LEMLMIDELGLDEI-DRKLLSVLIEQFQGGPVGLKTLAAAL---GED---------ADTIEDVYEPYLLQIGFLQRTPR  291 (305)
T ss_pred             HHHhCCCCCCCCHH-HHHHHHHHHHHhCCCcccHHHHHHHh---CCC---------cchHHHhhhHHHHHcCCcccCCc
Confidence            33366778888886 666565 556675  56666655443   221         123334555 4777999964443

RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=97.04  E-value=0.0042  Score=56.09  Aligned_cols=70  Identities=21%  Similarity=0.029  Sum_probs=47.4

Q ss_pred             CCCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCC-C--CcCCHhhhHHhHHHHccC
Q 041028            1 MGGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKLGLK-F--DEESESGRTRSPWSRLKK   70 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~~l~~~-~--~~~~~~~~~~~l~~~L~~   70 (283)
                      .+|+|||++++.++++.......-..++++.....+...++.+|+.++... .  ...+..+..+.+.+.+..
T Consensus        63 ~~GtGKT~l~~~v~~~l~~~~~~~~~v~in~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~l~~  135 (394)
T PRK00411         63 PPGTGKTTTVKKVFEELEEIAVKVVYVYINCQIDRTRYAIFSEIARQLFGHPPPSSGLSFDELFDKIAEYLDE  135 (394)
T ss_pred             CCCCCHHHHHHHHHHHHHHhcCCcEEEEEECCcCCCHHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHHHHh
Confidence            379999999999999876542123456666666677888999999988652 1  122444555666666653

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=96.69  E-value=0.011  Score=52.83  Aligned_cols=76  Identities=22%  Similarity=0.243  Sum_probs=47.8

Q ss_pred             CCCCcHHHHHHHHHhhhccC-CCC---CeEEEEEeCCCCCHHHHHHHHHHHh---CCCCC--cCCHhhhHHhHHHHcc--
Q 041028            1 MGGIGKTTLAKEVARKAKNG-KLF---DQIVFTEVSQNPNIKKIQGEIAFKL---GLKFD--EESESGRTRSPWSRLK--   69 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~-~~F---d~~~wv~v~~~~~~~~l~~~i~~~l---~~~~~--~~~~~~~~~~l~~~L~--   69 (283)
                      .+|+|||++++.++++.... ...   -..+|++.....+...++.+|+.++   +...+  ..+..+....+.+.+.  
T Consensus        48 ~~GtGKT~l~~~~~~~l~~~~~~~~~~~~~v~in~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~~  127 (365)
T TIGR02928        48 KTGTGKTAVTKYVMKELEEAAEDRDVRVVTVYVNCQILDTLYQVLVELANQLRGSGEEVPTTGLSTSEVFRRLYKELNER  127 (365)
T ss_pred             CCCCCHHHHHHHHHHHHHHHhhccCCceEEEEEECCCCCCHHHHHHHHHHHHhhcCCCCCCCCCCHHHHHHHHHHHHHhc
Confidence            37999999999999875422 111   1356777777677888999999988   33322  2233444555555553  


Q ss_pred             CCcEEEE
Q 041028           70 KEKLQII   76 (283)
Q Consensus        70 ~kr~LlV   76 (283)
                      ++.++||
T Consensus       128 ~~~~vlv  134 (365)
T TIGR02928       128 GDSLIIV  134 (365)
T ss_pred             CCeEEEE
Confidence            3344444

Members of this protein family are found exclusively in the archaea. This set of DNA binding proteins shows homology to the origin recognition complex subunit 1/cell division control protein 6 family in eukaryotes. Several members may be found in genome and interact with each other.

>PRK11331 5-methylcytosine-specific restriction enzyme subunit McrB; Provisional

Probab=96.64  E-value=0.0029  Score=57.46  Aligned_cols=42  Identities=19%  Similarity=0.217  Sum_probs=36.0

Q ss_pred             CCCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHH
Q 041028            1 MGGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQG   42 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~   42 (283)
                      ++|+|||++|+.+++.......|+.+.||++++.++..+...
T Consensus       202 ppGtGKT~lA~~la~~l~~~~~~~~v~~VtFHpsySYeDFI~  243 (459)
T PRK11331        202 PPGVGKTFVARRLAYLLTGEKAPQRVNMVQFHQSYSYEDFIQ  243 (459)
T ss_pred             CCCCCHHHHHHHHHHHhcCCcccceeeEEeecccccHHHHhc
Confidence            689999999999999876656688899999999988777654

>PF05729 NACHT: NACHT domain

Probab=96.58  E-value=0.0049  Score=48.06  Aligned_cols=33  Identities=24%  Similarity=0.356  Sum_probs=24.6

Q ss_pred             CCCcHHHHHHHHHhhhccCCC----CCeEEEEEeCCC
Q 041028            2 GGIGKTTLAKEVARKAKNGKL----FDQIVFTEVSQN   34 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~----Fd~~~wv~v~~~   34 (283)
                      +|+||||+++.++.+......    +...+|++.+..
T Consensus         9 ~G~GKStll~~~~~~~~~~~~~~~~~~~~~~~~~~~~   45 (166)
T PF05729_consen    9 PGSGKSTLLRKLAQQLAEEEPPPSKFPYPFFFSLRDI   45 (166)
T ss_pred             CCCChHHHHHHHHHHHHhcCcccccceEEEEEeehhh
Confidence            799999999999988665543    345677776644

>PTZ00202 tuzin; Provisional

Probab=96.57  E-value=0.012  Score=53.17  Aligned_cols=67  Identities=19%  Similarity=0.226  Sum_probs=42.7

Q ss_pred             CCCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCcCCHhhhHHhHHHHc-----c-CCcEE
Q 041028            1 MGGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKLGLKFDEESESGRTRSPWSRL-----K-KEKLQ   74 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~L-----~-~kr~L   74 (283)
                      ++|+|||||++.+.....    + ..++++..   +..++++.|+.+||.+.. ....++...|.+.|     . +++.+
T Consensus       294 ~~G~GKTTLlR~~~~~l~----~-~qL~vNpr---g~eElLr~LL~ALGV~p~-~~k~dLLrqIqeaLl~~~~e~GrtPV  364 (550)
T PTZ00202        294 FRGCGKSSLCRSAVRKEG----M-PAVFVDVR---GTEDTLRSVVKALGVPNV-EACGDLLDFISEACRRAKKMNGETPL  364 (550)
T ss_pred             CCCCCHHHHHHHHHhcCC----c-eEEEECCC---CHHHHHHHHHHHcCCCCc-ccHHHHHHHHHHHHHHHHHhCCCCEE
Confidence            479999999999986543    1 24444443   679999999999998433 22233444444433     2 55555


Q ss_pred             EE
Q 041028           75 II   76 (283)
Q Consensus        75 lV   76 (283)
                      ||
T Consensus       365 LI  366 (550)
T PTZ00202        365 LV  366 (550)
T ss_pred             EE
Confidence            55

>PF05496 RuvB_N: Holliday junction DNA helicase ruvB N-terminus; InterPro: IPR008824 The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair

Probab=96.14  E-value=0.011  Score=48.65  Aligned_cols=69  Identities=25%  Similarity=0.250  Sum_probs=34.3

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCC----CcC--CHhhhHHhHHHHccCCcEEE
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKLGLKF----DEE--SESGRTRSPWSRLKKEKLQI   75 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~~l~~~~----~~~--~~~~~~~~l~~~L~~kr~Ll   75 (283)
                      +|+||||||.-+++.....  |.   +++...--...+ +..++..+....    ++.  =.....+.|-..+.+-++-|
T Consensus        59 PG~GKTTLA~IIA~e~~~~--~~---~~sg~~i~k~~d-l~~il~~l~~~~ILFIDEIHRlnk~~qe~LlpamEd~~idi  132 (233)
T PF05496_consen   59 PGLGKTTLARIIANELGVN--FK---ITSGPAIEKAGD-LAAILTNLKEGDILFIDEIHRLNKAQQEILLPAMEDGKIDI  132 (233)
T ss_dssp             TTSSHHHHHHHHHHHCT----EE---EEECCC--SCHH-HHHHHHT--TT-EEEECTCCC--HHHHHHHHHHHHCSEEEE
T ss_pred             CccchhHHHHHHHhccCCC--eE---eccchhhhhHHH-HHHHHHhcCCCcEEEEechhhccHHHHHHHHHHhccCeEEE
Confidence            7999999999999987754  42   222211111222 234445554321    111  12234556777777777644


Q ss_pred             E
Q 041028           76 I   76 (283)
Q Consensus        76 V   76 (283)
                      |
T Consensus       133 i  133 (233)
T PF05496_consen  133 I  133 (233)
T ss_dssp             E
T ss_pred             E
Confidence            4

Branch migration is catalysed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein []. This group of sequences contain this signature which is located in the N-terminal region of the proteins.; GO: 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 1IQP_B 3PFI_B 1IXR_C 1HQC_B 1IXS_B.

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

Probab=96.08  E-value=0.034  Score=49.72  Aligned_cols=75  Identities=21%  Similarity=0.249  Sum_probs=55.7

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHHHhCC-CCCcCCHhhhHHhHHHHccCC-cEEEE
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKLGL-KFDEESESGRTRSPWSRLKKE-KLQII   76 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~~l~~-~~~~~~~~~~~~~l~~~L~~k-r~LlV   76 (283)
                      .|+|||+.++.+....+....=..+++|+.-...+..+++.+|+++++. +..+....+..+.+.+.+..+ +.+||
T Consensus        51 ~GTGKT~~~~~v~~~l~~~~~~~~~~yINc~~~~t~~~i~~~i~~~~~~~p~~g~~~~~~~~~l~~~~~~~~~~~Iv  127 (366)
T COG1474          51 TGTGKTATVKFVMEELEESSANVEVVYINCLELRTPYQVLSKILNKLGKVPLTGDSSLEILKRLYDNLSKKGKTVIV  127 (366)
T ss_pred             CCCCHhHHHHHHHHHHHhhhccCceEEEeeeeCCCHHHHHHHHHHHcCCCCCCCCchHHHHHHHHHHHHhcCCeEEE
Confidence            6999999999999987654111227889888999999999999999963 333456667777788887653 34444

>PRK07261 topology modulation protein; Provisional

Probab=95.95  E-value=0.014  Score=46.41  Aligned_cols=28  Identities=29%  Similarity=0.475  Sum_probs=19.8

Q ss_pred             CCCCcHHHHHHHHHhhhccC-CCCCeEEE
Q 041028            1 MGGIGKTTLAKEVARKAKNG-KLFDQIVF   28 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~-~~Fd~~~w   28 (283)
                      ++|+||||||+.+....... -+.|...|
T Consensus         8 ~~GsGKSTla~~l~~~~~~~~i~~D~~~~   36 (171)
T PRK07261          8 YSGSGKSTLARKLSQHYNCPVLHLDTLHF   36 (171)
T ss_pred             CCCCCHHHHHHHHHHHhCCCeEecCCEEe
Confidence            57999999999998765432 12455555

>PF13207 AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6_G 2QT1_A 2QSZ_A 2QSY_A 2QT0_A 2QG6_A 2P0E_A

Probab=95.42  E-value=0.011  Score=43.74  Aligned_cols=17  Identities=53%  Similarity=0.665  Sum_probs=15.3

Q ss_pred             CCCCcHHHHHHHHHhhh
Q 041028            1 MGGIGKTTLAKEVARKA   17 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (283)
                      .+|+||||+|+.+.+..
T Consensus         7 ~~gsGKST~a~~La~~~   23 (121)
T PF13207_consen    7 PPGSGKSTLAKELAERL   23 (121)
T ss_dssp             STTSSHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHH
Confidence            47999999999999975

...

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=95.39  E-value=0.071  Score=47.63  Aligned_cols=74  Identities=14%  Similarity=0.141  Sum_probs=46.1

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCC-CCCHHHHHHHHHHHhCCCCCcC-CHhhhHHhHHHHccCCcEEEE
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQ-NPNIKKIQGEIAFKLGLKFDEE-SESGRTRSPWSRLKKEKLQII   76 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~-~~~~~~l~~~i~~~l~~~~~~~-~~~~~~~~l~~~L~~kr~LlV   76 (283)
                      .|+||||++..++...........+..++... .....+-++...+.++.+.... +..+... ....+.++.++||
T Consensus       146 tGvGKTTtiakLA~~~~~~~G~~~V~lit~D~~R~ga~EqL~~~a~~~gv~~~~~~~~~~l~~-~l~~l~~~DlVLI  221 (374)
T PRK14722        146 TGVGKTTTTAKLAARCVMRFGASKVALLTTDSYRIGGHEQLRIFGKILGVPVHAVKDGGDLQL-ALAELRNKHMVLI  221 (374)
T ss_pred             CCCCHHHHHHHHHHHHHHhcCCCeEEEEecccccccHHHHHHHHHHHcCCceEecCCcccHHH-HHHHhcCCCEEEE
Confidence            59999999999998764331123456665432 2345666777778888765432 2223333 3345677889988

>PRK12608 transcription termination factor Rho; Provisional

Probab=95.18  E-value=0.15  Score=45.42  Aligned_cols=50  Identities=10%  Similarity=0.135  Sum_probs=37.3

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCe-EEEEEeCC-CCCHHHHHHHHHHHhCCCC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQ-IVFTEVSQ-NPNIKKIQGEIAFKLGLKF   52 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~-~~wv~v~~-~~~~~~l~~~i~~~l~~~~   52 (283)
                      +|+|||||++.+++..... +-+. ++|+.+++ ...+.++++.+...+....
T Consensus       142 pGtGKTTLl~~la~~i~~~-~~dv~~vv~lIgER~~EV~df~~~i~~~Vvast  193 (380)
T PRK12608        142 PRAGKTVLLQQIAAAVAAN-HPEVHLMVLLIDERPEEVTDMRRSVKGEVYAST  193 (380)
T ss_pred             CCCCHHHHHHHHHHHHHhc-CCCceEEEEEecCCCCCHHHHHHHHhhhEEeec
Confidence            5999999999999976543 2344 46777775 4578889999888777654

>COG1618 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=95.04  E-value=0.027  Score=43.77  Aligned_cols=24  Identities=33%  Similarity=0.526  Sum_probs=19.9

Q ss_pred             CCCCcHHHHHHHHHhhhccCCCCCe
Q 041028            1 MGGIGKTTLAKEVARKAKNGKLFDQ   25 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~~~Fd~   25 (283)
                      |+|||||||++.+.+..+..+ |..
T Consensus        13 ~PGvGKtTl~~ki~e~L~~~g-~kv   36 (179)
T COG1618          13 RPGVGKTTLVLKIAEKLREKG-YKV   36 (179)
T ss_pred             CCCccHHHHHHHHHHHHHhcC-cee
Confidence            789999999999999887654 643

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=95.00  E-value=0.12  Score=44.65  Aligned_cols=73  Identities=18%  Similarity=0.151  Sum_probs=41.8

Q ss_pred             CCCcHHHHHHHHHhhhccC-CCCCeEEEEEeCCC-CCHHHHHHHHHHHhCCCCCc-CCHhhhHHhHHHHccCCcEEEE
Q 041028            2 GGIGKTTLAKEVARKAKNG-KLFDQIVFTEVSQN-PNIKKIQGEIAFKLGLKFDE-ESESGRTRSPWSRLKKEKLQII   76 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~-~~Fd~~~wv~v~~~-~~~~~l~~~i~~~l~~~~~~-~~~~~~~~~l~~~L~~kr~LlV   76 (283)
                      +|+||||++..++.....+ +.+ .+..|+.... ....+.+....+.++.+... .+..+....+. .+.+..++||
T Consensus       203 tGvGKTTt~~kLa~~~~~~~g~~-~V~li~~D~~r~~a~eql~~~~~~~~~p~~~~~~~~~l~~~l~-~~~~~d~vli  278 (282)
T TIGR03499       203 TGVGKTTTLAKLAARFVLEHGNK-KVALITTDTYRIGAVEQLKTYAKILGVPVKVARDPKELRKALD-RLRDKDLILI  278 (282)
T ss_pred             CCCCHHHHHHHHHHHHHHHcCCC-eEEEEECCccchhHHHHHHHHHHHhCCceeccCCHHHHHHHHH-HccCCCEEEE
Confidence            6999999999998776533 112 4555665432 22344555566666765432 23334433343 3455677776

>PF13238 AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB_A 3IIM_A 2AXP_A 3KB2_A 1KHT_A 1NKS_A 3H86_C

Probab=94.86  E-value=0.02  Score=42.57  Aligned_cols=17  Identities=53%  Similarity=0.757  Sum_probs=15.0

Q ss_pred             CCCCcHHHHHHHHHhhh
Q 041028            1 MGGIGKTTLAKEVARKA   17 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (283)
                      ..|+||||+|+++....
T Consensus         6 ~~GsGKtTia~~L~~~~   22 (129)
T PF13238_consen    6 IPGSGKTTIAKELAERL   22 (129)
T ss_dssp             STTSSHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHH
Confidence            36999999999999875

...

>PRK08233 hypothetical protein; Provisional

Probab=94.66  E-value=0.096  Score=41.58  Aligned_cols=18  Identities=44%  Similarity=0.617  Sum_probs=15.3

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      .+|+||||||..++....
T Consensus        11 ~~GsGKtTla~~L~~~l~   28 (182)
T PRK08233         11 VSGGGKTTLTERLTHKLK   28 (182)
T ss_pred             CCCCCHHHHHHHHHhhCC
Confidence            369999999999998754

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.64  E-value=0.44  Score=45.65  Aligned_cols=18  Identities=39%  Similarity=0.619  Sum_probs=15.2

Q ss_pred             CCCcHHHHHHHHHhhhcc
Q 041028            2 GGIGKTTLAKEVARKAKN   19 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~   19 (283)
                      .|+||||+|+.+.+....
T Consensus        47 ~GvGKTTLAriLAkaLnC   64 (700)
T PRK12323         47 RGVGKTTLSRILAKSLNC   64 (700)
T ss_pred             CCCCHHHHHHHHHHHhcC
Confidence            599999999999887643

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

Probab=94.51  E-value=0.059  Score=40.48  Aligned_cols=32  Identities=28%  Similarity=0.306  Sum_probs=22.9

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNP   35 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~   35 (283)
                      +|+|||+||+.+++.....  -..+++++.++..
T Consensus        28 ~G~GKT~l~~~i~~~~~~~--~~~v~~~~~~~~~   59 (151)
T cd00009          28 PGTGKTTLARAIANELFRP--GAPFLYLNASDLL   59 (151)
T ss_pred             CCCCHHHHHHHHHHHhhcC--CCCeEEEehhhhh
Confidence            6999999999999987522  2345666665443

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

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=94.47  E-value=0.14  Score=37.98  Aligned_cols=31  Identities=29%  Similarity=0.374  Sum_probs=22.0

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQN   34 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~   34 (283)
                      +|+||||+|+.+++.....  ...+++++.+..
T Consensus        11 ~G~GKTtl~~~l~~~~~~~--~~~~~~~~~~~~   41 (148)
T smart00382       11 PGSGKTTLARALARELGPP--GGGVIYIDGEDI   41 (148)
T ss_pred             CCCcHHHHHHHHHhccCCC--CCCEEEECCEEc
Confidence            6999999999999876543  224566655543

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

>PHA02518 ParA-like protein; Provisional

Probab=94.44  E-value=0.19  Score=40.87  Aligned_cols=36  Identities=22%  Similarity=0.403  Sum_probs=25.0

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHH
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKK   39 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~   39 (283)
                      ||+||||+|..++.....++  ..++-|+.....+...
T Consensus        10 GGvGKTT~a~~la~~la~~g--~~vlliD~D~q~~~~~   45 (211)
T PHA02518         10 GGAGKTTVATNLASWLHADG--HKVLLVDLDPQGSSTD   45 (211)
T ss_pred             CCCCHHHHHHHHHHHHHhCC--CeEEEEeCCCCCChHH
Confidence            89999999999888665332  2456677765555444

>cd00983 recA RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=94.29  E-value=0.18  Score=44.21  Aligned_cols=70  Identities=21%  Similarity=0.223  Sum_probs=44.2

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCC------cCCHhhhHHhHHHHccCC--cE
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKLGLKFD------EESESGRTRSPWSRLKKE--KL   73 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~~l~~~~~------~~~~~~~~~~l~~~L~~k--r~   73 (283)
                      +|+||||||.+++-.....  -..++||+....++..     .+++++.+.+      ..+.++....+...++..  +.
T Consensus        64 ~GsGKTtLal~~~~~~~~~--g~~~vyId~E~~~~~~-----~a~~lGvd~~~l~v~~p~~~eq~l~i~~~li~s~~~~l  136 (325)
T cd00983          64 ESSGKTTLALHAIAEAQKL--GGTVAFIDAEHALDPV-----YAKKLGVDLDNLLISQPDTGEQALEIADSLVRSGAVDL  136 (325)
T ss_pred             CCCCHHHHHHHHHHHHHHc--CCCEEEECccccHHHH-----HHHHcCCCHHHheecCCCCHHHHHHHHHHHHhccCCCE
Confidence            6999999999987665433  3567899888777753     4555555321      224455555555555443  56


Q ss_pred             EEEcC
Q 041028           74 QIICG   78 (283)
Q Consensus        74 LlV~G   78 (283)
                      ++|+.
T Consensus       137 IVIDS  141 (325)
T cd00983         137 IVVDS  141 (325)
T ss_pred             EEEcc
Confidence            66654

RecA couples ATP hydrolysis to DNA strand exchange.

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional

Probab=94.26  E-value=0.17  Score=47.20  Aligned_cols=75  Identities=20%  Similarity=0.220  Sum_probs=40.8

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCC-CCCHHHHHHHHHHHhCCCCCc-CCHhhhHHhHHHHccCCcEEEEc
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQ-NPNIKKIQGEIAFKLGLKFDE-ESESGRTRSPWSRLKKEKLQIIC   77 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~-~~~~~~l~~~i~~~l~~~~~~-~~~~~~~~~l~~~L~~kr~LlV~   77 (283)
                      +|+||||++..++...........+..++... .....+.++.....++..... .+..+....+ +.+.++.++||+
T Consensus       359 tGvGKTTtaakLAa~la~~~~gkkVaLIdtDtyRigA~EQLk~ya~iLgv~v~~a~d~~~L~~aL-~~l~~~DLVLID  435 (559)
T PRK12727        359 TGAGKTTTIAKLAQRFAAQHAPRDVALVTTDTQRVGGREQLHSYGRQLGIAVHEADSAESLLDLL-ERLRDYKLVLID  435 (559)
T ss_pred             CCCCHHHHHHHHHHHHHHhcCCCceEEEecccccccHHHHHHHhhcccCceeEecCcHHHHHHHH-HHhccCCEEEec
Confidence            69999999999887654332123455555432 122233344444555554332 2233333333 345677888883

>PRK03839 putative kinase; Provisional

Probab=94.26  E-value=0.03  Score=44.68  Aligned_cols=19  Identities=42%  Similarity=0.522  Sum_probs=16.7

Q ss_pred             CCCCcHHHHHHHHHhhhcc
Q 041028            1 MGGIGKTTLAKEVARKAKN   19 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~   19 (283)
                      |+|+||||+|+.+++....
T Consensus         8 ~pGsGKsT~~~~La~~~~~   26 (180)
T PRK03839          8 TPGVGKTTVSKLLAEKLGY   26 (180)
T ss_pred             CCCCCHHHHHHHHHHHhCC
Confidence            6899999999999998653

>PRK05541 adenylylsulfate kinase; Provisional

Probab=94.25  E-value=0.052  Score=43.12  Aligned_cols=28  Identities=29%  Similarity=0.606  Sum_probs=21.6

Q ss_pred             CCCCcHHHHHHHHHhhhccCCCCCeEEEEE
Q 041028            1 MGGIGKTTLAKEVARKAKNGKLFDQIVFTE   30 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~~~Fd~~~wv~   30 (283)
                      +.|+||||+|+.+++.....  +...+++.
T Consensus        15 ~~GsGKst~a~~l~~~l~~~--~~~~~~~~   42 (176)
T PRK05541         15 LAGSGKTTIAKALYERLKLK--YSNVIYLD   42 (176)
T ss_pred             CCCCCHHHHHHHHHHHHHHc--CCcEEEEe
Confidence            47999999999999987643  65666553

>PF13191 AAA_16: AAA ATPase domain; PDB: 2V1U_A

Probab=94.17  E-value=0.04  Score=43.77  Aligned_cols=20  Identities=25%  Similarity=0.398  Sum_probs=16.7

Q ss_pred             CCCCcHHHHHHHHHhhhccC
Q 041028            1 MGGIGKTTLAKEVARKAKNG   20 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~   20 (283)
                      .+|+|||+|.++++......
T Consensus        32 ~~G~GKT~ll~~~~~~~~~~   51 (185)
T PF13191_consen   32 ESGSGKTSLLRALLDRLAER   51 (185)
T ss_dssp             -TTSSHHHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHhc
Confidence            37999999999999887655

>COG0003 ArsA Predicted ATPase involved in chromosome partitioning [Cell division and chromosome partitioning]

Probab=94.08  E-value=0.078  Score=46.41  Aligned_cols=41  Identities=22%  Similarity=0.339  Sum_probs=28.7

Q ss_pred             CCCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHH
Q 041028            1 MGGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGE   43 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~   43 (283)
                      .|||||||+|.+.+-.....  ...++=|+.....++.+++..
T Consensus        10 KGGVGKTT~aaA~A~~lA~~--g~kvLlvStDPAhsL~d~f~~   50 (322)
T COG0003          10 KGGVGKTTIAAATAVKLAES--GKKVLLVSTDPAHSLGDVFDL   50 (322)
T ss_pred             CCcccHHHHHHHHHHHHHHc--CCcEEEEEeCCCCchHhhhcc
Confidence            48999999999976665544  344777777766666665554

>PF02374 ArsA_ATPase: Anion-transporting ATPase; PDB: 2WOO_A 3IBG_B 3SJA_A 3H84_B 3SJD_A 3ZS9_A 3A37_A 2WOJ_A 3SJC_B 3A36_B

Probab=94.06  E-value=0.069  Score=46.55  Aligned_cols=40  Identities=23%  Similarity=0.430  Sum_probs=26.3

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHH
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGE   43 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~   43 (283)
                      |||||||+|.+.+-....++  ..++-|+.....++.+++..
T Consensus        10 GGVGKTT~aaA~A~~~A~~G--~rtLlvS~Dpa~~L~d~l~~   49 (305)
T PF02374_consen   10 GGVGKTTVAAALALALARRG--KRTLLVSTDPAHSLSDVLGQ   49 (305)
T ss_dssp             TTSSHHHHHHHHHHHHHHTT--S-EEEEESSTTTHHHHHHTS
T ss_pred             CCCCcHHHHHHHHHHHhhCC--CCeeEeecCCCccHHHHhCC
Confidence            89999999988776544332  23566676666666555543

...

>PRK06217 hypothetical protein; Validated

Probab=94.05  E-value=0.1  Score=41.82  Aligned_cols=28  Identities=25%  Similarity=0.357  Sum_probs=20.7

Q ss_pred             CCCCcHHHHHHHHHhhhccCCCC--CeEEEE
Q 041028            1 MGGIGKTTLAKEVARKAKNGKLF--DQIVFT   29 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~~~F--d~~~wv   29 (283)
                      ++|+||||||+.+....... +|  |..+|.
T Consensus         9 ~~GsGKSTla~~L~~~l~~~-~~~~D~~~~~   38 (183)
T PRK06217          9 ASGSGTTTLGAALAERLDIP-HLDTDDYFWL   38 (183)
T ss_pred             CCCCCHHHHHHHHHHHcCCc-EEEcCceeec
Confidence            47999999999999886543 34  556664

>PF07728 AAA_5: AAA domain (dynein-related subfamily); InterPro: IPR011704 The ATPases Associated to a variety of cellular Activities (AAA) are a family distinguished by a highly conserved module of 230 amino acids []

Probab=94.01  E-value=0.11  Score=39.42  Aligned_cols=37  Identities=30%  Similarity=0.419  Sum_probs=27.0

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHH
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGE   43 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~   43 (283)
                      +|+|||+||+.+++....     ...-+.++...+..++...
T Consensus         8 ~G~GKt~l~~~la~~~~~-----~~~~i~~~~~~~~~dl~g~   44 (139)
T PF07728_consen    8 PGTGKTTLARELAALLGR-----PVIRINCSSDTTEEDLIGS   44 (139)
T ss_dssp             SSSSHHHHHHHHHHHHTC-----EEEEEE-TTTSTHHHHHCE
T ss_pred             CCCCHHHHHHHHHHHhhc-----ceEEEEeccccccccceee
Confidence            699999999999997621     2344677788888777654

The highly conserved nature of this module across taxa suggests that it has a key cellular role. Members of the family are involved in diverse cellular functions including gene expression, peroxisome assembly and vesicle mediated transport. Although the role of this ATPase AAA domain is not, as yet, clear, the AAA+ superfamily of proteins to which the AAA ATPases belong has a chaperone-like function in the assembly, operation or disassembly of proteins []. This ATPase domain includes some proteins not detected by the IPR003959 from INTERPRO model.; GO: 0005524 ATP binding, 0016887 ATPase activity; PDB: 3NBX_X 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A.

>TIGR02012 tigrfam_recA protein RecA

Probab=93.99  E-value=0.22  Score=43.61  Aligned_cols=70  Identities=19%  Similarity=0.213  Sum_probs=43.6

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCC------cCCHhhhHHhHHHHccC--CcE
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKLGLKFD------EESESGRTRSPWSRLKK--EKL   73 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~~l~~~~~------~~~~~~~~~~l~~~L~~--kr~   73 (283)
                      +|+||||||.++.......  =..++|++..+.++..     .+++++.+.+      ..+.++....+...++.  -+.
T Consensus        64 ~GsGKTtLaL~~~~~~~~~--g~~v~yId~E~~~~~~-----~a~~lGvd~~~l~v~~p~~~eq~l~~~~~li~~~~~~l  136 (321)
T TIGR02012        64 ESSGKTTLALHAIAEAQKA--GGTAAFIDAEHALDPV-----YARKLGVDIDNLLVSQPDTGEQALEIAETLVRSGAVDI  136 (321)
T ss_pred             CCCCHHHHHHHHHHHHHHc--CCcEEEEcccchhHHH-----HHHHcCCCHHHeEEecCCCHHHHHHHHHHHhhccCCcE
Confidence            6999999999987765433  3467899887776653     4566665421      22444455555555543  256


Q ss_pred             EEEcC
Q 041028           74 QIICG   78 (283)
Q Consensus        74 LlV~G   78 (283)
                      ++|++
T Consensus       137 IVIDS  141 (321)
T TIGR02012       137 IVVDS  141 (321)
T ss_pred             EEEcc
Confidence            66654

This model describes orthologs of the recA protein. RecA promotes hybridization of homolgous regions of DNA. A segment of ssDNA can be hybridized to another ssDNA region, or to a dsDNA region. ATP is hydrolyzed in the process. Part of the SOS respones, it is regulated by LexA via autocatalytic cleavage.

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=93.95  E-value=0.11  Score=42.37  Aligned_cols=38  Identities=18%  Similarity=0.270  Sum_probs=28.4

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHH
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQG   42 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~   42 (283)
                      +|+|||+||.+++......  -..++|++... ++...+.+
T Consensus        21 ~GsGKT~l~~~~~~~~~~~--g~~v~yi~~e~-~~~~rl~~   58 (209)
T TIGR02237        21 PGSGKTNICMILAVNAARQ--GKKVVYIDTEG-LSPERFKQ   58 (209)
T ss_pred             CCCCHHHHHHHHHHHHHhC--CCeEEEEECCC-CCHHHHHH
Confidence            7999999999988765433  46789999876 66655443

This family consists exclusively of archaeal RadB protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and archaeal RadA (TIGR02236).

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=93.92  E-value=2.6  Score=41.30  Aligned_cols=17  Identities=41%  Similarity=0.647  Sum_probs=14.5

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      .|+||||+|+.+.+...
T Consensus        47 pGvGKTTlAriLAKaLn   63 (830)
T PRK07003         47 RGVGKTTLSRIFAKALN   63 (830)
T ss_pred             CCCCHHHHHHHHHHHhc
Confidence            59999999999888654

>COG1428 Deoxynucleoside kinases [Nucleotide transport and metabolism]

Probab=93.83  E-value=0.041  Score=44.73  Aligned_cols=39  Identities=28%  Similarity=0.377  Sum_probs=25.5

Q ss_pred             CCCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHH
Q 041028            1 MGGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEI   44 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i   44 (283)
                      |=|+||||||+.++++....     +++-.+.+++=+.....++
T Consensus        12 ~IG~GKSTLa~~La~~l~~~-----~~~E~vednp~L~~FY~d~   50 (216)
T COG1428          12 MIGAGKSTLAQALAEHLGFK-----VFYELVEDNPFLDLFYEDP   50 (216)
T ss_pred             ccccCHHHHHHHHHHHhCCc-----eeeecccCChHHHHHHHhH
Confidence            45999999999999988733     2334455554444444443

>PRK00625 shikimate kinase; Provisional

Probab=93.83  E-value=0.044  Score=43.58  Aligned_cols=18  Identities=28%  Similarity=0.468  Sum_probs=16.2

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      |+|+||||+++.+.++..
T Consensus         8 ~pGsGKTT~~k~La~~l~   25 (173)
T PRK00625          8 LPTVGKTSFGKALAKFLS   25 (173)
T ss_pred             CCCCCHHHHHHHHHHHhC
Confidence            789999999999998765

>cd01393 recA_like RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=93.82  E-value=0.4  Score=39.57  Aligned_cols=46  Identities=22%  Similarity=0.298  Sum_probs=30.5

Q ss_pred             CCCcHHHHHHHHHhhhccCC----CCCeEEEEEeCCCCCHHHHHHHHHHHh
Q 041028            2 GGIGKTTLAKEVARKAKNGK----LFDQIVFTEVSQNPNIKKIQGEIAFKL   48 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~----~Fd~~~wv~v~~~~~~~~l~~~i~~~l   48 (283)
                      +|+|||+||..++......+    .=..++|++....++...+ .++.+..
T Consensus        28 ~GsGKT~l~~~ia~~~~~~~~~~g~~~~v~yi~~e~~~~~~rl-~~~~~~~   77 (226)
T cd01393          28 FGSGKTQLCLQLAVEAQLPGELGGLEGKVVYIDTEGAFRPERL-VQLAVRF   77 (226)
T ss_pred             CCCChhHHHHHHHHHhhcccccCCCcceEEEEecCCCCCHHHH-HHHHHHh
Confidence            69999999999876643221    0056789988877776554 3444443

RecA couples ATP hydrolysis to DNA strand exchange. While prokaryotes have a single RecA protein, eukaryotes have multiple RecA homologs such as Rad51, DMC1 and Rad55/57. Archaea have the RecA-like homologs radA and radB.

>COG1192 Soj ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]

Probab=93.81  E-value=0.079  Score=44.90  Aligned_cols=32  Identities=25%  Similarity=0.421  Sum_probs=23.3

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQN   34 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~   34 (283)
                      |||||||+|.+++......+ -..++-|+....
T Consensus        12 GGvGKTT~a~nLa~~La~~~-~~kVLliDlDpQ   43 (259)
T COG1192          12 GGVGKTTTAVNLAAALAKRG-GKKVLLIDLDPQ   43 (259)
T ss_pred             CCccHHHHHHHHHHHHHHhc-CCcEEEEeCCCc
Confidence            89999999999998876221 145777776544

>COG1484 DnaC DNA replication protein [DNA replication, recombination, and repair]

Probab=93.81  E-value=0.19  Score=42.57  Aligned_cols=61  Identities=21%  Similarity=0.249  Sum_probs=40.4

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCcCCHhhhHHhHHHHccCCcEEEEc
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKLGLKFDEESESGRTRSPWSRLKKEKLQIIC   77 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~kr~LlV~   77 (283)
                      +|+|||.||.++.+... +.-+ .+.++      +..+++.++......       ......+...+..-.+||++
T Consensus       114 ~G~GKThLa~Ai~~~l~-~~g~-sv~f~------~~~el~~~Lk~~~~~-------~~~~~~l~~~l~~~dlLIiD  174 (254)
T COG1484         114 PGVGKTHLAIAIGNELL-KAGI-SVLFI------TAPDLLSKLKAAFDE-------GRLEEKLLRELKKVDLLIID  174 (254)
T ss_pred             CCCcHHHHHHHHHHHHH-HcCC-eEEEE------EHHHHHHHHHHHHhc-------CchHHHHHHHhhcCCEEEEe
Confidence            59999999999999987 4223 34444      455666666655543       11334566667777888883

>PRK09354 recA recombinase A; Provisional

Probab=93.76  E-value=0.27  Score=43.49  Aligned_cols=70  Identities=20%  Similarity=0.219  Sum_probs=45.1

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCC------cCCHhhhHHhHHHHccCC--cE
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKLGLKFD------EESESGRTRSPWSRLKKE--KL   73 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~~l~~~~~------~~~~~~~~~~l~~~L~~k--r~   73 (283)
                      +|+||||||.++.......  =..++||+....++.     ..++++|.+.+      ..+.++....+...++..  +.
T Consensus        69 ~GsGKTtLal~~~~~~~~~--G~~~~yId~E~s~~~-----~~a~~lGvdld~lli~qp~~~Eq~l~i~~~li~s~~~~l  141 (349)
T PRK09354         69 ESSGKTTLALHAIAEAQKA--GGTAAFIDAEHALDP-----VYAKKLGVDIDNLLVSQPDTGEQALEIADTLVRSGAVDL  141 (349)
T ss_pred             CCCCHHHHHHHHHHHHHHc--CCcEEEECCccchHH-----HHHHHcCCCHHHeEEecCCCHHHHHHHHHHHhhcCCCCE
Confidence            6999999999988765533  356789998887775     34566665421      224455555555555443  56


Q ss_pred             EEEcC
Q 041028           74 QIICG   78 (283)
Q Consensus        74 LlV~G   78 (283)
                      ++|+.
T Consensus       142 IVIDS  146 (349)
T PRK09354        142 IVVDS  146 (349)
T ss_pred             EEEeC
Confidence            66654

>PF00448 SRP54: SRP54-type protein, GTPase domain; InterPro: IPR000897 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]

Probab=93.69  E-value=0.33  Score=39.45  Aligned_cols=73  Identities=22%  Similarity=0.262  Sum_probs=45.7

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCC-CCCHHHHHHHHHHHhCCCCC----cCCHhhhHHhHHHHccC--CcEE
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQ-NPNIKKIQGEIAFKLGLKFD----EESESGRTRSPWSRLKK--EKLQ   74 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~-~~~~~~l~~~i~~~l~~~~~----~~~~~~~~~~l~~~L~~--kr~L   74 (283)
                      .|+||||.+..++.....+  =..+..++... .....+-++..++.++.+..    ..+..+......+.+..  ..++
T Consensus        10 tGvGKTTt~aKLAa~~~~~--~~~v~lis~D~~R~ga~eQL~~~a~~l~vp~~~~~~~~~~~~~~~~~l~~~~~~~~D~v   87 (196)
T PF00448_consen   10 TGVGKTTTIAKLAARLKLK--GKKVALISADTYRIGAVEQLKTYAEILGVPFYVARTESDPAEIAREALEKFRKKGYDLV   87 (196)
T ss_dssp             TTSSHHHHHHHHHHHHHHT--T--EEEEEESTSSTHHHHHHHHHHHHHTEEEEESSTTSCHHHHHHHHHHHHHHTTSSEE
T ss_pred             CCCchHhHHHHHHHHHhhc--cccceeecCCCCCccHHHHHHHHHHHhccccchhhcchhhHHHHHHHHHHHhhcCCCEE
Confidence            5999999888888776654  34567777753 34567788899999998732    12333433332333333  3578


Q ss_pred             EE
Q 041028           75 II   76 (283)
Q Consensus        75 lV   76 (283)
                      +|
T Consensus        88 lI   89 (196)
T PF00448_consen   88 LI   89 (196)
T ss_dssp             EE
T ss_pred             EE
Confidence            87

SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. This entry represents the GTPase domain of the 54 kDa SRP54 component, a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 of the signal recognition particle has a three-domain structure: an N-terminal helical bundle domain, a GTPase domain, and the M-domain that binds the 7s RNA and also binds the signal sequence. The extreme C-terminal region is glycine-rich and lower in complexity and poorly conserved between species. The GTPase domain is evolutionary related to P-loop NTPase domains found in a variety of other proteins []. These proteins include Escherichia coli and Bacillus subtilis ffh protein (P48), which seems to be the prokaryotic counterpart of SRP54; signal recognition particle receptor alpha subunit (docking protein), an integral membrane GTP-binding protein which ensures, in conjunction with SRP, the correct targeting of nascent secretory proteins to the endoplasmic reticulum membrane; bacterial FtsY protein, which is believed to play a similar role to that of the docking protein in eukaryotes; the pilA protein from Neisseria gonorrhoeae, the homologue of ftsY; and bacterial flagellar biosynthesis protein flhF.; GO: 0005525 GTP binding, 0006614 SRP-dependent cotranslational protein targeting to membrane; PDB: 2OG2_A 3B9Q_A 3DM9_B 3DMD_B 3E70_C 3DM5_B 2XXA_C 2J28_9 1ZU5_B 1ZU4_A ....

>PF07726 AAA_3: ATPase family associated with various cellular activities (AAA); InterPro: IPR011703 This entry includes some of the AAA proteins not detected by the IPR003959 from INTERPRO model

Probab=93.68  E-value=0.053  Score=40.62  Aligned_cols=21  Identities=52%  Similarity=0.700  Sum_probs=15.1

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFD   24 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd   24 (283)
                      +|+||||+|+.++......  |.
T Consensus         8 PG~GKT~la~~lA~~~~~~--f~   28 (131)
T PF07726_consen    8 PGVGKTTLAKALARSLGLS--FK   28 (131)
T ss_dssp             --HHHHHHHHHHHHHTT----EE
T ss_pred             CccHHHHHHHHHHHHcCCc--ee
Confidence            6999999999999987644  63

AAA ATPases form a large, functionally diverse protein family belonging to the AAA+ superfamily of ring-shaped P-loop NTPases, which exert their activity through the energy-dependent unfolding of macromolecules. AAA ATPases contain a P-loop NTPase domain, which is the most abundant class of NTP-binding protein fold, and is found throughout all kingdoms of life []. P-loop NTPase domains act to hydrolyse the beta-gamma phosphate bond of bound nucleoside triphosphate. There are two classes of P-loop domains: the KG (kinase-GTPase) division, and the ASCE division, the latter including the AAA+ group as well as several other ATPases. There are at least six major clades of AAA domains (metalloproteases, meiotic proteins, D1 and D2 domains of ATPases with two AAA domains, proteasome subunits, and BSC1), as well as several minor clades, some of which consist of hypothetical proteins []. The domain organisation of AAA ATPases consists of a non-ATPase N-terminal domain that acts in substrate recognition, followed by one or two AAA domains (D1 and D2), one of which may be degenerate.; GO: 0005524 ATP binding, 0016887 ATPase activity; PDB: 2R44_A.

>PF13173 AAA_14: AAA domain

Probab=93.59  E-value=0.068  Score=40.08  Aligned_cols=30  Identities=30%  Similarity=0.494  Sum_probs=22.7

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQN   34 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~   34 (283)
                      .|+|||||+++++.+..   ....+++++..+.
T Consensus        11 R~vGKTtll~~~~~~~~---~~~~~~yi~~~~~   40 (128)
T PF13173_consen   11 RGVGKTTLLKQLAKDLL---PPENILYINFDDP   40 (128)
T ss_pred             CCCCHHHHHHHHHHHhc---ccccceeeccCCH
Confidence            48999999999998765   2356677776654

>PF01583 APS_kinase: Adenylylsulphate kinase; InterPro: IPR002891 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases

Probab=93.58  E-value=0.091  Score=40.92  Aligned_cols=28  Identities=29%  Similarity=0.396  Sum_probs=20.9

Q ss_pred             CCCCcHHHHHHHHHhhhccCCCCCeEEEEE
Q 041028            1 MGGIGKTTLAKEVARKAKNGKLFDQIVFTE   30 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~~~Fd~~~wv~   30 (283)
                      ++|.||||||+++.+.....  -..+++++
T Consensus        10 lsGsGKtTlA~~L~~~L~~~--g~~~~~LD   37 (156)
T PF01583_consen   10 LSGSGKTTLARALERRLFAR--GIKVYLLD   37 (156)
T ss_dssp             STTSSHHHHHHHHHHHHHHT--TS-EEEEE
T ss_pred             CCCCCHHHHHHHHHHHHHHc--CCcEEEec
Confidence            47999999999999998755  33455553

Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. This domain contains an ATP binding P-loop motif [].; GO: 0005524 ATP binding, 0016301 kinase activity, 0016772 transferase activity, transferring phosphorus-containing groups, 0000103 sulfate assimilation; PDB: 1M7H_B 1M7G_B 3CR7_B 1D6J_A 2OFW_G 1X6V_B 1XNJ_A 1XJQ_B 2PEY_A 2PEZ_B ....

>cd01133 F1-ATPase_beta F1 ATP synthase beta subunit, nucleotide-binding domain

Probab=93.50  E-value=0.12  Score=44.11  Aligned_cols=43  Identities=23%  Similarity=0.326  Sum_probs=31.8

Q ss_pred             CCCcHHHHHHHHHhhhccCCCC-CeEEEEEeCCCC-CHHHHHHHHHH
Q 041028            2 GGIGKTTLAKEVARKAKNGKLF-DQIVFTEVSQNP-NIKKIQGEIAF   46 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~F-d~~~wv~v~~~~-~~~~l~~~i~~   46 (283)
                      +|+||||||+.+++....+  | +.++++-+++.. .+.++..++..
T Consensus        78 ~G~GKTtLa~~i~~~i~~~--~~~~~V~~~iGer~~Ev~e~~~~~~~  122 (274)
T cd01133          78 AGVGKTVLIMELINNIAKA--HGGYSVFAGVGERTREGNDLYHEMKE  122 (274)
T ss_pred             CCCChhHHHHHHHHHHHhc--CCCEEEEEEeccCcHHHHHHHHHHHh
Confidence            5999999999999987754  6 566777777654 45666666654

The F-ATPase is found in bacterial plasma membranes, mitochondrial inner membranes and in chloroplast thylakoid membranes. It has also been found in the archaea Methanosarcina barkeri. It uses a proton gradient to drive ATP synthesis and hydrolyzes ATP to build the proton gradient. The extrinisic membrane domain, F1, is composed of alpha, beta, gamma, delta and epsilon subunits with a stoichiometry of 3:3:1:1:1. The beta subunit of ATP synthase is catalytic.

>PF01656 CbiA: CobQ/CobB/MinD/ParA nucleotide binding domain; InterPro: IPR002586 This entry consists of various cobyrinic acid a,c-diamide synthases

Probab=93.40  E-value=0.13  Score=41.18  Aligned_cols=38  Identities=24%  Similarity=0.400  Sum_probs=25.4

Q ss_pred             CCCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHH
Q 041028            1 MGGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKI   40 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l   40 (283)
                      .||+||||+|..++......  =..++-++.....+....
T Consensus         7 kGG~GKTt~a~~la~~la~~--g~~VlliD~D~~~~~~~~   44 (195)
T PF01656_consen    7 KGGVGKTTIAANLAQALARK--GKKVLLIDLDPQAPNLSI   44 (195)
T ss_dssp             STTSSHHHHHHHHHHHHHHT--TS-EEEEEESTTSHHHHH
T ss_pred             CCCccHHHHHHHHHhccccc--cccccccccCcccccHHH
Confidence            38999999999998876653  235566776554444333

These include CbiA and CbiP from Salmonella typhimurium []., and CobQ from Rhodobacter capsulatus []. These amidases catalyse amidations to various side chains of hydrogenobyrinic acid or cobyrinic acid a,c-diamide in the biosynthesis of cobalamin (vitamin B12) from uroporphyrinogen III. Vitamin B12 is an important cofactor and an essential nutrient for many plants and animals and is primarily produced by bacteria [].; PDB: 3K9G_A 3K9H_B 3EZ9_B 3EZF_A 3EZ2_B 3EZ6_A 3EZ7_A 1G3Q_A 1G3R_A 1DTS_A ....

>PF13671 AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1_A 1RRC_A 1RPZ_A 3ZVM_A 1YJ5_A 3ZVL_A 3U7E_B

Probab=93.38  E-value=0.059  Score=40.95  Aligned_cols=18  Identities=44%  Similarity=0.591  Sum_probs=15.0

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      ++|+||||+|+.+.....
T Consensus         7 ~pgsGKSt~a~~l~~~~~   24 (143)
T PF13671_consen    7 PPGSGKSTLAKRLAKRLG   24 (143)
T ss_dssp             STTSSHHHHHHHHHHHST
T ss_pred             CCCCCHHHHHHHHHHHCC
Confidence            479999999999986543

...

>COG1102 Cmk Cytidylate kinase [Nucleotide transport and metabolism]

Probab=93.37  E-value=0.1  Score=40.68  Aligned_cols=38  Identities=32%  Similarity=0.377  Sum_probs=30.3

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKLGLKF   52 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~~l~~~~   52 (283)
                      +|+||||+|+.++++..-.  |           .+...+++++++..|.+.
T Consensus         9 pGsG~TTva~~lAe~~gl~--~-----------vsaG~iFR~~A~e~gmsl   46 (179)
T COG1102           9 PGSGKTTVARELAEHLGLK--L-----------VSAGTIFREMARERGMSL   46 (179)
T ss_pred             CCCChhHHHHHHHHHhCCc--e-----------eeccHHHHHHHHHcCCCH
Confidence            7999999999999987644  1           244578899999998763

>COG3640 CooC CO dehydrogenase maturation factor [Cell division and chromosome partitioning]

Probab=93.36  E-value=0.13  Score=42.61  Aligned_cols=35  Identities=23%  Similarity=0.508  Sum_probs=23.4

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCH
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNI   37 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~   37 (283)
                      ||+||||+|..+......++-| .++=|+...++++
T Consensus         9 GG~GKTtiaalll~~l~~~~~~-~VLvVDaDpd~nL   43 (255)
T COG3640           9 GGVGKTTIAALLLKRLLSKGGY-NVLVVDADPDSNL   43 (255)
T ss_pred             CCccHHHHHHHHHHHHHhcCCc-eEEEEeCCCCCCh
Confidence            8999999999977765544323 3444666666554

>cd01123 Rad51_DMC1_radA Rad51_DMC1_radA,B

Probab=93.32  E-value=0.16  Score=42.23  Aligned_cols=48  Identities=23%  Similarity=0.259  Sum_probs=31.9

Q ss_pred             CCCcHHHHHHHHHhhhccCCC----CCeEEEEEeCCCCCHHHHHHHHHHHhCC
Q 041028            2 GGIGKTTLAKEVARKAKNGKL----FDQIVFTEVSQNPNIKKIQGEIAFKLGL   50 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~----Fd~~~wv~v~~~~~~~~l~~~i~~~l~~   50 (283)
                      +|+|||+||.+++-.......    -..++|++....++...+ .++++..+.
T Consensus        28 ~GsGKT~l~~~l~~~~~~~~~~~g~~~~viyi~~e~~~~~~rl-~~~~~~~~~   79 (235)
T cd01123          28 FGSGKTQLCHQLAVTVQLPIELGGLEGKAVYIDTEGTFRPERL-VQIAERFGL   79 (235)
T ss_pred             CCCCHHHHHHHHHHHeeCccccCCCCccEEEEeCCCCcCHHHH-HHHHHHhcc
Confidence            699999999999755332211    257899998887775444 444554443

This group of recombinases includes the eukaryotic proteins RAD51, RAD55/57 and the meiosis-specific protein DMC1, and the archaeal proteins radA and radB. They are closely related to the bacterial RecA group. Rad51 proteins catalyze a similiar recombination reaction as RecA, using ATP-dependent DNA binding activity and a DNA-dependent ATPase. However, this reaction is less efficient and requires accessory proteins such as RAD55/57 .

>COG3899 Predicted ATPase [General function prediction only]

Probab=93.30  E-value=1.5  Score=43.93  Aligned_cols=132  Identities=15%  Similarity=0.154  Sum_probs=81.6

Q ss_pred             chHHHHHHHHHhcCCchHHHHH---hhc-------cCChHHHHHHHHHhcCCCCCCCCCchhHHHHHHhhhhccCCCCcH
Q 041028           90 ELKWLAMDVAKECAGLPVSIVT---GIK-------EQELFEWKDALEQLRRPSSTNFKDVQPAAYKAMELGYNKLEGDEL  159 (283)
Q Consensus        90 ~~~~~~~~i~~~c~glPLal~~---~l~-------~~~~~~w~~~l~~l~~~~~~~~~~~~~~~~~~l~~sy~~L~~~~~  159 (283)
                      ...+....|.++-.|.|+-+.-   ++.       +.+...|..-...+...      .....+.+.+..-.+.||+. .
T Consensus       238 ~~~p~~~~i~~kt~GnPfFi~e~lk~l~~~~~i~f~~~~~~w~~~~~~i~~~------~~~~~vv~~l~~rl~kL~~~-t  310 (849)
T COG3899         238 LPAPLLELIFEKTKGNPFFIEEFLKALYEEGLLVFNFDTGAWQCSIASLGIL------ATTDAVVEFLAARLQKLPGT-T  310 (849)
T ss_pred             ccchHHHHHHHHhcCCCccHHHHHHHHHhCCeeEecCCCcceeccHHhcCCc------hhhHHHHHHHHHHHhcCCHH-H
Confidence            3456688899999999998887   222       34555555444333221      11233566788889999997 9


Q ss_pred             HHHHHHHhhCc-CCCHHHHHHHHhhccccCCCchHHHHHHHHHHHHHHHHhccccccccC----C-CcceE---EechhH
Q 041028          160 KSTFLLIGYTA-IASIDDLLMYGMGLGLFQGVNKMEAARARVHTLVHKLKASCMLLDHTS----K-NEKLF---SIHDVV  230 (283)
Q Consensus       160 k~~fl~~s~fp-~i~~~~l~~~w~aeg~~~~~~~~~~~~~~~~~~~~~L~~~sLl~~~~~----~-~~~~~---~mH~lv  230 (283)
                      |..+...|++- .|+.+.|...+...           ....+..+.+.|....++ +.+.    . .....   -.|+++
T Consensus       311 ~~Vl~~AA~iG~~F~l~~La~l~~~~-----------~~~~a~~l~~al~e~lI~-~~~~~yr~~~~~~~~~Y~F~H~~v  378 (849)
T COG3899         311 REVLKAAACIGNRFDLDTLAALAEDS-----------PALEAAALLDALQEGLIL-PLSETYRFGSNVDIATYKFLHDRV  378 (849)
T ss_pred             HHHHHHHHHhCccCCHHHHHHHHhhc-----------hHHHHHHHHHHhHhhcee-ccccccccccccchhhHHhhHHHH
Confidence            99999999996 99998888776321           222333444444444443 4221    0 11112   568888


Q ss_pred             HHHHHHHHcc
Q 041028          231 RDVAISIASG  240 (283)
Q Consensus       231 ~~~a~~~~~~  240 (283)
                      ++.|-....+
T Consensus       379 qqaaY~~i~~  388 (849)
T COG3899         379 QQAAYNLIPE  388 (849)
T ss_pred             HHHHhccCch
Confidence            8888654443

>PRK08116 hypothetical protein; Validated

Probab=93.28  E-value=0.42  Score=40.85  Aligned_cols=63  Identities=21%  Similarity=0.173  Sum_probs=37.8

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCcCCHhhhHHhHHHHccCCcEEEEc
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKLGLKFDEESESGRTRSPWSRLKKEKLQIIC   77 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~kr~LlV~   77 (283)
                      .|+|||.||.++++....+  -..+++++      ..+++..+........ ..+    ...+.+.+.+-.+|+++
T Consensus       123 ~GtGKThLa~aia~~l~~~--~~~v~~~~------~~~ll~~i~~~~~~~~-~~~----~~~~~~~l~~~dlLviD  185 (268)
T PRK08116        123 VGTGKTYLAACIANELIEK--GVPVIFVN------FPQLLNRIKSTYKSSG-KED----ENEIIRSLVNADLLILD  185 (268)
T ss_pred             CCCCHHHHHHHHHHHHHHc--CCeEEEEE------HHHHHHHHHHHHhccc-ccc----HHHHHHHhcCCCEEEEe
Confidence            5999999999999987644  33456664      4445555555443211 111    22344556666788874

>cd02040 NifH NifH gene encodes component II (iron protein) of nitrogenase

Probab=93.15  E-value=0.14  Score=43.65  Aligned_cols=31  Identities=19%  Similarity=0.374  Sum_probs=21.1

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQN   34 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~   34 (283)
                      |||||||+|..++.-....++  .++=|+....
T Consensus        10 GGvGKTT~~~nLA~~La~~G~--kVlliD~Dpq   40 (270)
T cd02040          10 GGIGKSTTTQNLSAALAEMGK--KVMIVGCDPK   40 (270)
T ss_pred             CcCCHHHHHHHHHHHHHhCCC--eEEEEEcCCC
Confidence            899999999998887653321  3444555433

Nitrogenase is responsible for the biological nitrogen fixation, i.e. reduction of molecular nitrogen to ammonia. NifH consists of two oxygen-sensitive metallosulfur proteins: the mollybdenum-iron (alternatively, vanadium-iron or iron-iron) protein (commonly referred to as component 1), and the iron protein (commonly referred to as component 2). The iron protein is a homodimer, with an Fe4S4 cluster bound between the subunits and two ATP-binding domains. It supplies energy by ATP hydrolysis, and transfers electrons from reduced ferredoxin or flavodoxin to component 1 for the reduction of molecular nitrogen to ammonia.

>PF00004 AAA: ATPase family associated with various cellular activities (AAA); InterPro: IPR003959 AAA ATPases (ATPases Associated with diverse cellular Activities) form a large protein family and play a number of roles in the cell including cell-cycle regulation, protein proteolysis and disaggregation, organelle biogenesis and intracellular transport

Probab=93.15  E-value=0.065  Score=39.87  Aligned_cols=17  Identities=47%  Similarity=0.581  Sum_probs=15.5

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      +|+||||+|+.+++...
T Consensus         7 ~G~GKT~l~~~la~~l~   23 (132)
T PF00004_consen    7 PGTGKTTLARALAQYLG   23 (132)
T ss_dssp             TTSSHHHHHHHHHHHTT
T ss_pred             CCCCeeHHHHHHHhhcc
Confidence            69999999999999874

Some of them function as molecular chaperones, subunits of proteolytic complexes or independent proteases (FtsH, Lon). They also act as DNA helicases and transcription factors []. AAA ATPases belong to the AAA+ superfamily of ringshaped P-loop NTPases, which act via the energy-dependent unfolding of macromolecules [, ]. There are six major clades of AAA domains (proteasome subunits, metalloproteases, domains D1 and D2 of ATPases with two AAA domains, the MSP1/katanin/spastin group and BCS1 and it homologues), as well as a number of deeply branching minor clades []. They assemble into oligomeric assemblies (often hexamers) that form a ring-shaped structure with a central pore. These proteins produce a molecular motor that couples ATP binding and hydrolysis to changes in conformational states that act upon a target substrate, either translocating or remodelling it []. They are found in all living organisms and share the common feature of the presence of a highly conserved AAA domain called the AAA module. This domain is responsible for ATP binding and hydrolysis. It contains 200-250 residues, among them there are two classical motifs, Walker A (GX4GKT) and Walker B (HyDE) []. The functional variety seen between AAA ATPases is in part due to their extensive number of accessory domains and factors, and to their variable organisation within oligomeric assemblies, in addition to changes in key functional residues within the ATPase domain itself. More information about these proteins can be found at Protein of the Month: AAA ATPases [].; GO: 0005524 ATP binding; PDB: 3H4M_A 1NSF_A 1D2N_A 1HQY_E 1DO0_E 1DO2_C 1G4B_E 1HT1_F 1G4A_F 1HT2_G ....

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

Probab=93.14  E-value=0.16  Score=45.29  Aligned_cols=19  Identities=42%  Similarity=0.557  Sum_probs=16.1

Q ss_pred             CCCcHHHHHHHHHhhhccC
Q 041028            2 GGIGKTTLAKEVARKAKNG   20 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~   20 (283)
                      +|+||||||+.+.......
T Consensus        57 PG~GKTTlA~liA~~~~~~   75 (436)
T COG2256          57 PGTGKTTLARLIAGTTNAA   75 (436)
T ss_pred             CCCCHHHHHHHHHHhhCCc
Confidence            7999999999999966543

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=93.13  E-value=0.29  Score=44.75  Aligned_cols=74  Identities=14%  Similarity=0.112  Sum_probs=43.1

Q ss_pred             CCCcHHHHHHHHHhhhc-cCCCCCeEEEEEeCCCC-CHHHHHHHHHHHhCCCCCc-CCHhhhHHhHHHHccCCcEEEEc
Q 041028            2 GGIGKTTLAKEVARKAK-NGKLFDQIVFTEVSQNP-NIKKIQGEIAFKLGLKFDE-ESESGRTRSPWSRLKKEKLQIIC   77 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~-~~~~Fd~~~wv~v~~~~-~~~~l~~~i~~~l~~~~~~-~~~~~~~~~l~~~L~~kr~LlV~   77 (283)
                      +|+||||++..++.... ... -..+..|+..... ...+-++...+.++.+... .+..+....+.. +.+..++||+
T Consensus       230 tGvGKTTt~~kLA~~~~~~~~-g~~V~li~~D~~r~~a~eqL~~~a~~~~vp~~~~~~~~~l~~~l~~-~~~~DlVlID  306 (424)
T PRK05703        230 TGVGKTTTLAKLAARYALLYG-KKKVALITLDTYRIGAVEQLKTYAKIMGIPVEVVYDPKELAKALEQ-LRDCDVILID  306 (424)
T ss_pred             CCCCHHHHHHHHHHHHHHhcC-CCeEEEEECCccHHHHHHHHHHHHHHhCCceEccCCHHhHHHHHHH-hCCCCEEEEe
Confidence            69999999999877654 221 2356667654321 1234455556667765432 233444444443 4567888884

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=93.11  E-value=0.077  Score=43.83  Aligned_cols=29  Identities=17%  Similarity=0.319  Sum_probs=20.9

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVS   32 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~   32 (283)
                      +|+|||+||+.+++.....  ....++++++
T Consensus        47 ~G~GKT~la~~~~~~~~~~--~~~~~~i~~~   75 (226)
T TIGR03420        47 SGSGKSHLLQAACAAAEER--GKSAIYLPLA   75 (226)
T ss_pred             CCCCHHHHHHHHHHHHHhc--CCcEEEEeHH
Confidence            6999999999999876533  3345566543

Members of this protein family are Hda (Homologous to DnaA). These proteins are about half the length of DnaA and homologous over length of Hda. In the model species Escherichia coli, the initiation of DNA replication requires DnaA bound to ATP rather than ADP; Hda helps facilitate the conversion of DnaA-ATP to DnaA-ADP.

>PRK07952 DNA replication protein DnaC; Validated

Probab=93.11  E-value=0.43  Score=40.14  Aligned_cols=62  Identities=18%  Similarity=0.199  Sum_probs=36.8

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCcCCHhhhHHhHHHHccCCcEEEEc
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKLGLKFDEESESGRTRSPWSRLKKEKLQIIC   77 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~kr~LlV~   77 (283)
                      +|+|||+||.++++.....  -..+++++      ..+++..+-.....  ...+    ...+.+.+..-.+|+|+
T Consensus       108 ~GtGKThLa~aia~~l~~~--g~~v~~it------~~~l~~~l~~~~~~--~~~~----~~~~l~~l~~~dlLvID  169 (244)
T PRK07952        108 PGTGKNHLAAAICNELLLR--GKSVLIIT------VADIMSAMKDTFSN--SETS----EEQLLNDLSNVDLLVID  169 (244)
T ss_pred             CCCCHHHHHHHHHHHHHhc--CCeEEEEE------HHHHHHHHHHHHhh--cccc----HHHHHHHhccCCEEEEe
Confidence            6999999999999987543  23456654      44555554443321  1111    22344456667888884

>KOG2028 consensus ATPase related to the helicase subunit of the Holliday junction resolvase [Replication, recombination and repair]

Probab=93.08  E-value=0.18  Score=44.56  Aligned_cols=29  Identities=41%  Similarity=0.541  Sum_probs=22.5

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQN   34 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~   34 (283)
                      +|+||||||+.+.+..+..    ...||..|..
T Consensus       171 pG~GKTtlArlia~tsk~~----SyrfvelSAt  199 (554)
T KOG2028|consen  171 PGTGKTTLARLIASTSKKH----SYRFVELSAT  199 (554)
T ss_pred             CCCchHHHHHHHHhhcCCC----ceEEEEEecc
Confidence            6999999999999976643    2567877744

>cd01122 GP4d_helicase GP4d_helicase is a homohexameric 5'-3' helicases

Probab=93.06  E-value=0.73  Score=39.21  Aligned_cols=43  Identities=16%  Similarity=0.145  Sum_probs=29.4

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHHH
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFK   47 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~~   47 (283)
                      +|+|||||+.+++...... +=..++|+++..+  ..++...+...
T Consensus        39 ~G~GKT~l~~~~~~~~~~~-~g~~vl~iS~E~~--~~~~~~r~~~~   81 (271)
T cd01122          39 TGVGKTTFLREYALDLITQ-HGVRVGTISLEEP--VVRTARRLLGQ   81 (271)
T ss_pred             CCCCHHHHHHHHHHHHHHh-cCceEEEEEcccC--HHHHHHHHHHH
Confidence            6999999999988765432 1146788887663  45566666554

Helicases couple NTP hydrolysis to the unwinding of nucleic acid duplexes into their component strands.

>KOG3347 consensus Predicted nucleotide kinase/nuclear protein involved oxidative stress response [Nucleotide transport and metabolism]

Probab=92.99  E-value=0.14  Score=39.28  Aligned_cols=17  Identities=47%  Similarity=0.657  Sum_probs=14.5

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      +|+||||||..++....
T Consensus        16 PG~GKstl~~~lae~~~   32 (176)
T KOG3347|consen   16 PGTGKSTLAERLAEKTG   32 (176)
T ss_pred             CCCCchhHHHHHHHHhC
Confidence            79999999999996543

>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1

Probab=92.95  E-value=0.46  Score=41.60  Aligned_cols=49  Identities=18%  Similarity=0.220  Sum_probs=34.7

Q ss_pred             CCCcHHHHHHHHHhhhccC---CC-CCeEEEEEeCCCCCHHHHHHHHHHHhCCC
Q 041028            2 GGIGKTTLAKEVARKAKNG---KL-FDQIVFTEVSQNPNIKKIQGEIAFKLGLK   51 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~---~~-Fd~~~wv~v~~~~~~~~l~~~i~~~l~~~   51 (283)
                      +|+|||+|+..++-.....   .. =..++||+....|++..+. ++++.++..
T Consensus       105 ~GsGKTql~lqla~~~~~~~~~gg~~~~vvYIdtE~~f~~eRi~-~~a~~~g~d  157 (313)
T TIGR02238       105 FRCGKTQLSHTLCVTAQLPREMGGGNGKVAYIDTEGTFRPDRIR-AIAERFGVD  157 (313)
T ss_pred             CCCCcCHHHHHHHHHHhcchhhcCCCCeEEEEEcCCCCCHHHHH-HHHHHcCCC
Confidence            6999999999876432211   11 1468999999999988875 467777654

This model describes DMC1, a subfamily of a larger family of DNA repair and recombination proteins. It is eukaryotic only and most closely related to eukaryotic RAD51. It also resembles archaeal RadA (TIGR02236) and RadB (TIGR02237) and bacterial RecA (TIGR02012). It has been characterized for human as a recombinase active only in meiosis.

>PRK13947 shikimate kinase; Provisional

Probab=92.94  E-value=0.072  Score=41.96  Aligned_cols=20  Identities=45%  Similarity=0.549  Sum_probs=17.1

Q ss_pred             CCCCcHHHHHHHHHhhhccC
Q 041028            1 MGGIGKTTLAKEVARKAKNG   20 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~   20 (283)
                      |+|+||||+|+.+++.....
T Consensus         9 ~~GsGKst~a~~La~~lg~~   28 (171)
T PRK13947          9 FMGTGKTTVGKRVATTLSFG   28 (171)
T ss_pred             CCCCCHHHHHHHHHHHhCCC
Confidence            68999999999999986543

>PRK13849 putative crown gall tumor protein VirC1; Provisional

Probab=92.91  E-value=0.2  Score=41.81  Aligned_cols=38  Identities=21%  Similarity=0.323  Sum_probs=26.0

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHH
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQ   41 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~   41 (283)
                      ||+||||+|..++.....++ + .++-|+....-+.....
T Consensus        11 GGvGKTT~a~nLA~~la~~G-~-~VlliD~DpQ~s~~~w~   48 (231)
T PRK13849         11 GGAGKTTALMGLCAALASDG-K-RVALFEADENRPLTRWK   48 (231)
T ss_pred             CCccHHHHHHHHHHHHHhCC-C-cEEEEeCCCCCCHHHHH
Confidence            89999999999988765442 2 44556776555554443

>PRK09361 radB DNA repair and recombination protein RadB; Provisional

Probab=92.91  E-value=0.2  Score=41.42  Aligned_cols=36  Identities=17%  Similarity=0.346  Sum_probs=27.1

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHH
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKI   40 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l   40 (283)
                      +|+|||+||.+++......  -..++|++.. .++...+
T Consensus        32 ~GsGKT~l~~~la~~~~~~--~~~v~yi~~e-~~~~~r~   67 (225)
T PRK09361         32 PGSGKTNICLQLAVEAAKN--GKKVIYIDTE-GLSPERF   67 (225)
T ss_pred             CCCCHHHHHHHHHHHHHHC--CCeEEEEECC-CCCHHHH
Confidence            7999999999998876433  4678999887 5555443

>PRK12377 putative replication protein; Provisional

Probab=92.90  E-value=0.39  Score=40.50  Aligned_cols=61  Identities=16%  Similarity=0.174  Sum_probs=37.1

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCcCCHhhhHHhHHHHccCCcEEEEc
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKLGLKFDEESESGRTRSPWSRLKKEKLQIIC   77 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~kr~LlV~   77 (283)
                      +|+|||+||.++++....+  .-.++++++      .+++..|-.....   ..+    ...+.+.+..-.+|+|+
T Consensus       110 ~GtGKThLa~AIa~~l~~~--g~~v~~i~~------~~l~~~l~~~~~~---~~~----~~~~l~~l~~~dLLiID  170 (248)
T PRK12377        110 PGTGKNHLAAAIGNRLLAK--GRSVIVVTV------PDVMSRLHESYDN---GQS----GEKFLQELCKVDLLVLD  170 (248)
T ss_pred             CCCCHHHHHHHHHHHHHHc--CCCeEEEEH------HHHHHHHHHHHhc---cch----HHHHHHHhcCCCEEEEc
Confidence            5999999999999987644  334566654      3455555443321   111    12344556677888884

>PRK06762 hypothetical protein; Provisional

Probab=92.87  E-value=0.074  Score=41.71  Aligned_cols=17  Identities=41%  Similarity=0.616  Sum_probs=15.1

Q ss_pred             CCCCcHHHHHHHHHhhh
Q 041028            1 MGGIGKTTLAKEVARKA   17 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (283)
                      ++|+||||+|+.+.+..
T Consensus        10 ~~GsGKST~A~~L~~~l   26 (166)
T PRK06762         10 NSGSGKTTIAKQLQERL   26 (166)
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            47999999999999875

>PRK06893 DNA replication initiation factor; Validated

Probab=92.86  E-value=0.091  Score=43.78  Aligned_cols=29  Identities=21%  Similarity=0.236  Sum_probs=22.4

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVS   32 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~   32 (283)
                      +|+|||+||+.+++....+  ...+.|+++.
T Consensus        48 ~G~GKThL~~ai~~~~~~~--~~~~~y~~~~   76 (229)
T PRK06893         48 KSSGKSHLLKAVSNHYLLN--QRTAIYIPLS   76 (229)
T ss_pred             CCCCHHHHHHHHHHHHHHc--CCCeEEeeHH
Confidence            6999999999999986544  3355777764

>cd01394 radB RadB

Probab=92.84  E-value=0.22  Score=40.91  Aligned_cols=33  Identities=18%  Similarity=0.302  Sum_probs=24.1

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPN   36 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~   36 (283)
                      +|+||||||.+++.....+  =..++|++....+.
T Consensus        28 ~GsGKT~l~~~~a~~~~~~--g~~v~yi~~e~~~~   60 (218)
T cd01394          28 PGTGKTNIAIQLAVETAGQ--GKKVAYIDTEGLSS   60 (218)
T ss_pred             CCCCHHHHHHHHHHHHHhc--CCeEEEEECCCCCH
Confidence            7999999999998775432  24677887665554

The archaeal protein radB shares similarity radA, the archaeal functional homologue to the bacterial RecA. The precise function of radB is unclear.

>PRK14721 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=92.80  E-value=0.64  Score=42.33  Aligned_cols=75  Identities=16%  Similarity=0.143  Sum_probs=43.7

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCC-CCCHHHHHHHHHHHhCCCCCc-CCHhhhHHhHHHHccCCcEEEEc
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQ-NPNIKKIQGEIAFKLGLKFDE-ESESGRTRSPWSRLKKEKLQIIC   77 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~-~~~~~~l~~~i~~~l~~~~~~-~~~~~~~~~l~~~L~~kr~LlV~   77 (283)
                      .|+||||+...++........-+.+..++... .....+-+....+.++.+... .+..+.. .....+.++..++|+
T Consensus       200 nG~GKTTtlakLA~~~~~~~~~~~v~~i~~d~~rigalEQL~~~a~ilGvp~~~v~~~~dl~-~al~~l~~~d~VLID  276 (420)
T PRK14721        200 TGVGKTTTTAKLAARAVIRHGADKVALLTTDSYRIGGHEQLRIYGKLLGVSVRSIKDIADLQ-LMLHELRGKHMVLID  276 (420)
T ss_pred             CCCCHHHHHHHHHHHHHHhcCCCeEEEEecCCcchhHHHHHHHHHHHcCCceecCCCHHHHH-HHHHHhcCCCEEEec
Confidence            49999999998887542221123444444332 233444466677777776543 2333433 334457888888883

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=92.69  E-value=0.71  Score=42.31  Aligned_cols=73  Identities=23%  Similarity=0.326  Sum_probs=43.0

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCC-CCCHHHHHHHHHHHhCCCCCc----CCHhhhHHhHHHHccCCcEEEE
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQ-NPNIKKIQGEIAFKLGLKFDE----ESESGRTRSPWSRLKKEKLQII   76 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~-~~~~~~l~~~i~~~l~~~~~~----~~~~~~~~~l~~~L~~kr~LlV   76 (283)
                      +|+||||+|..++......+ + .+.-|+... .+...+.++.+..+++.+.-.    .+.........+.+.+..++||
T Consensus       104 ~GsGKTTtaakLA~~L~~~g-~-kV~lV~~D~~R~aa~eQL~~la~~~gvp~~~~~~~~d~~~i~~~al~~~~~~DvVII  181 (437)
T PRK00771        104 QGSGKTTTAAKLARYFKKKG-L-KVGLVAADTYRPAAYDQLKQLAEKIGVPFYGDPDNKDAVEIAKEGLEKFKKADVIIV  181 (437)
T ss_pred             CCCcHHHHHHHHHHHHHHcC-C-eEEEecCCCCCHHHHHHHHHHHHHcCCcEEecCCccCHHHHHHHHHHHhhcCCEEEE
Confidence            69999999999998776432 3 344454432 223456677788888775322    1222223333334445578887

>PRK06995 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=92.64  E-value=0.56  Score=43.45  Aligned_cols=75  Identities=15%  Similarity=0.156  Sum_probs=43.3

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCC-CCCHHHHHHHHHHHhCCCCCc-CCHhhhHHhHHHHccCCcEEEEc
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQ-NPNIKKIQGEIAFKLGLKFDE-ESESGRTRSPWSRLKKEKLQIIC   77 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~-~~~~~~l~~~i~~~l~~~~~~-~~~~~~~~~l~~~L~~kr~LlV~   77 (283)
                      .|+||||++..++.....+..-..+..|+... .....+-++.+.+.++.+... .+..+....+ ..+.++.+.+|+
T Consensus       265 nGvGKTTTiaKLA~~~~~~~G~~kV~LI~~Dt~RigA~EQLr~~AeilGVpv~~~~~~~Dl~~aL-~~L~d~d~VLID  341 (484)
T PRK06995        265 TGVGKTTTTAKLAARCVMRHGASKVALLTTDSYRIGGHEQLRIYGKILGVPVHAVKDAADLRLAL-SELRNKHIVLID  341 (484)
T ss_pred             CCccHHHHHHHHHHHHHHhcCCCeEEEEeCCccchhHHHHHHHHHHHhCCCeeccCCchhHHHHH-HhccCCCeEEeC
Confidence            49999999999998764331112345555432 234455566677777765432 2222222222 456677888883

>cd02042 ParA ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation

Probab=92.64  E-value=0.079  Score=37.98  Aligned_cols=17  Identities=47%  Similarity=0.647  Sum_probs=14.8

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      ||+||||+|..++....
T Consensus         9 gG~Gkst~~~~la~~~~   25 (104)
T cd02042           9 GGVGKTTTAVNLAAALA   25 (104)
T ss_pred             CCcCHHHHHHHHHHHHH
Confidence            89999999999887654

ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the initiation of DNA replication. ParB regulates the ParA ATPase activity by promoting nucleotide exchange in a fashion reminiscent of the exchange factors of eukaryotic G proteins. ADP-bound ParA binds single-stranded DNA, whereas the ATP-bound form dissociates ParB from its DNA binding sites. Increasing the fraction of ParA-ADP in the cell inhibits cell division, suggesting that this simple nucleotide switch may regulate cytokinesis. ParA shares sequence similarity to a conserved and widespread family of ATPases which includes the repA protein of the repABC operon in R. etli Sym plasmid. This operon is involved in the plasmid replication and partition.

>PF00910 RNA_helicase: RNA helicase; InterPro: IPR000605 Helicases have been classified in 5 superfamilies (SF1-SF5)

Probab=92.60  E-value=0.087  Score=38.21  Aligned_cols=17  Identities=59%  Similarity=0.786  Sum_probs=14.8

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      +|+|||+||+.++.+..
T Consensus         7 ~G~GKS~l~~~l~~~l~   23 (107)
T PF00910_consen    7 PGIGKSTLAKELAKDLL   23 (107)
T ss_pred             CCCCHHHHHHHHHHHHH
Confidence            69999999999887754

All of the proteins bind ATP and, consequently, all of them carry the classical Walker A (phosphate-binding loop or P-loop) and Walker B (Mg2+-binding aspartic acid) motifs. Superfamily 3 consists of helicases encoded mainly by small DNA viruses and some large nucleocytoplasmic DNA viruses [, ]. Small viruses are very dependent on the host-cell machinery to replicate. SF3 helicase in small viruses is associated with an origin-binding domain. By pairing a domain that recognises the ori with a helicase, the virus can bypass the host-cell-based regulation pathway and initiate its own replication. The protein binds to the viral ori leading to origin unwinding. Cellular replication proteins are then recruited to the ori and the viral DNA is replicated. In SF3 helicases the Walker A and Walker B motifs are separated by spacers of rather uniform, and relatively short, length. In addition to the A and B motifs this family is characterised by a third motif (C) which resides between the B motif and the C terminus of the conserved region. This motif consists of an Asn residue preceded by a run of hydrophobic residues []. Several structures of SF3 helicases have been solved []. They all possess the same core alpha/beta fold, consisting of a five-stranded parallel beta sheet flanked on both sides by several alpha helices. In contrast to SF1 and SF2 helicases, which have RecA-like core folds, the strand connectivity within the alpha/beta core domain is that of AAA+ proteins []. The SF3 helicase proteins assemble into a hexameric ring. Some proteins known to contain an SF3 helicase domain are listed below: Polyomavirus large T antigen. It initiates DNA unwinding and replication via interactions with the viral origin of replication. Papillomavirus E1 protein. An ATP-dependent DNA helicase required for initiation of viral DNA replication. Parvovirus Rep/NS1 protein, which is also required for the initiation of viral replication. Poxviridae and other large DNA viruses D5 protein. Bacteriophage DNA primase/helicase protein. Bacterial prophage DNA primase/helicase protein. The entry represents the core alpha/beta fold of the SF3 helicase domain found predominantly in DNA viruses.; GO: 0003723 RNA binding, 0003724 RNA helicase activity

>cd02019 NK Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars

Probab=92.58  E-value=0.1  Score=34.55  Aligned_cols=16  Identities=44%  Similarity=0.677  Sum_probs=14.4

Q ss_pred             CCCcHHHHHHHHHhhh
Q 041028            2 GGIGKTTLAKEVARKA   17 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~   17 (283)
                      .|+||||+|+.+.+..
T Consensus         8 ~gsGKst~~~~l~~~l   23 (69)
T cd02019           8 SGSGKSTVAKKLAEQL   23 (69)
T ss_pred             CCCCHHHHHHHHHHHh
Confidence            6999999999999874

Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of coenzymes and aromatic compounds, as well as the metabolism of sugar and sulfate.

>PRK00131 aroK shikimate kinase; Reviewed

Probab=92.56  E-value=0.086  Score=41.43  Aligned_cols=18  Identities=28%  Similarity=0.523  Sum_probs=16.1

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      ++|+||||+|+.++....
T Consensus        12 ~~GsGKstla~~La~~l~   29 (175)
T PRK00131         12 FMGAGKSTIGRLLAKRLG   29 (175)
T ss_pred             CCCCCHHHHHHHHHHHhC
Confidence            589999999999999864

>PRK13231 nitrogenase reductase-like protein; Reviewed

Probab=92.55  E-value=0.15  Score=43.32  Aligned_cols=30  Identities=27%  Similarity=0.472  Sum_probs=21.7

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQN   34 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~   34 (283)
                      |||||||+|..++......+   .++-++....
T Consensus        11 GGvGKTT~a~nLA~~La~~G---rVLliD~Dpq   40 (264)
T PRK13231         11 GGIGKSTTVSNMAAAYSNDH---RVLVIGCDPK   40 (264)
T ss_pred             CCCcHHHHHHHHhcccCCCC---EEEEEeEccC
Confidence            89999999999998766432   3555655433

>cd02036 MinD Bacterial cell division requires the formation of a septum at mid-cell

Probab=92.40  E-value=0.095  Score=41.39  Aligned_cols=31  Identities=23%  Similarity=0.442  Sum_probs=21.7

Q ss_pred             CCCCcHHHHHHHHHhhhccCCCCCeEEEEEeCC
Q 041028            1 MGGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQ   33 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~   33 (283)
                      .||+||||+|..++.....++ + .++-|+...
T Consensus         8 kgG~GKtt~a~~la~~l~~~g-~-~vllvD~D~   38 (179)
T cd02036           8 KGGVGKTTTTANLGTALAQLG-Y-KVVLIDADL   38 (179)
T ss_pred             CCCCCHHHHHHHHHHHHHhCC-C-eEEEEeCCC
Confidence            489999999999988765432 2 445555543

The site is determined by the min operon products MinC, MinD and MinE. MinC is a nonspecific inhibitor of the septum protein FtsZ. MinE is the supressor of MinC. MinD plays a pivotal role, selecting the mid-cell over other sites through the activation and regulation of MinC and MinE. MinD is a membrane-associated ATPase, related to nitrogenase iron protein. More distantly related proteins include flagellar biosynthesis proteins and ParA chromosome partitioning proteins. MinD is a monomer.

>PHA00729 NTP-binding motif containing protein

Probab=92.33  E-value=0.091  Score=43.50  Aligned_cols=16  Identities=56%  Similarity=0.650  Sum_probs=14.7

Q ss_pred             CCCcHHHHHHHHHhhh
Q 041028            2 GGIGKTTLAKEVARKA   17 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~   17 (283)
                      +|+||||||..+.+..
T Consensus        26 pGvGKT~LA~aLa~~l   41 (226)
T PHA00729         26 QGSGKTTYALKVARDV   41 (226)
T ss_pred             CCCCHHHHHHHHHHHH
Confidence            7999999999999875

>cd00544 CobU Adenosylcobinamide kinase / adenosylcobinamide phosphate guanyltransferase (CobU)

Probab=92.27  E-value=0.77  Score=36.32  Aligned_cols=70  Identities=14%  Similarity=0.099  Sum_probs=38.9

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCcCCHhhhHHhHHHHc---cCCcEEEEc
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKLGLKFDEESESGRTRSPWSRL---KKEKLQIIC   77 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~L---~~kr~LlV~   77 (283)
                      +|+|||++|.++....     ...++++.-.+.++. ++.+.|.+....+.......+....+.+.+   .+...+||+
T Consensus         8 ~~sGKS~~a~~~~~~~-----~~~~~y~at~~~~d~-em~~rI~~H~~~R~~~w~t~E~~~~l~~~l~~~~~~~~VLID   80 (169)
T cd00544           8 ARSGKSRFAERLAAEL-----GGPVTYIATAEAFDD-EMAERIARHRKRRPAHWRTIETPRDLVSALKELDPGDVVLID   80 (169)
T ss_pred             CCCCHHHHHHHHHHhc-----CCCeEEEEccCcCCH-HHHHHHHHHHHhCCCCceEeecHHHHHHHHHhcCCCCEEEEE
Confidence            5899999999987651     235677766676655 355555553333333332223333344444   233466663

CobU is bifunctional cobalbumin biosynthesis enzymes which display adenosylcobinamide kinase and adenosylcobinamide phosphate guanyltransferase activity. This enzyme is a homotrimer with a propeller-like shape.

>cd02025 PanK Pantothenate kinase (PanK) catalyzes the phosphorylation of pantothenic acid to form 4'-phosphopantothenic, which is the first of five steps in coenzyme A (CoA) biosynthetic pathway

Probab=92.27  E-value=0.91  Score=37.57  Aligned_cols=33  Identities=12%  Similarity=0.002  Sum_probs=21.4

Q ss_pred             CCCcHHHHHHHHHhhhccCCCC-CeEEEEEeCCCC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLF-DQIVFTEVSQNP   35 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~F-d~~~wv~v~~~~   35 (283)
                      .|+||||||+.+....... .. ..+..|+...-+
T Consensus         8 sGSGKTTla~~L~~~l~~~-~~~~~v~vi~~D~f~   41 (220)
T cd02025           8 VAVGKSTTARVLQALLSRW-PDHPNVELITTDGFL   41 (220)
T ss_pred             CCCCHHHHHHHHHHHHhhc-CCCCcEEEEecCccc
Confidence            5999999999999876431 01 234555555443

The reaction carried out by this enzyme is a key regulatory point in CoA biosynthesis.

>PF03029 ATP_bind_1: Conserved hypothetical ATP binding protein; InterPro: IPR004130 Members of this family are found in a range of archaea and eukaryotes and have hypothesised ATP binding activity

Probab=92.13  E-value=0.22  Score=41.80  Aligned_cols=32  Identities=19%  Similarity=0.260  Sum_probs=21.7

Q ss_pred             CCCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCC
Q 041028            1 MGGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQN   34 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~   34 (283)
                      ++|+||||+++.+.+.....  -..++-|++...
T Consensus         4 paGSGKTT~~~~~~~~~~~~--~~~~~~vNLDPa   35 (238)
T PF03029_consen    4 PAGSGKTTFCKGLSEWLESN--GRDVYIVNLDPA   35 (238)
T ss_dssp             STTSSHHHHHHHHHHHHTTT---S-EEEEE--TT
T ss_pred             CCCCCHHHHHHHHHHHHHhc--cCCceEEEcchH
Confidence            68999999999999987654  334556666543

; GO: 0000166 nucleotide binding; PDB: 1YR7_A 1YRA_B 1YR8_A 1YR6_A 1YR9_A 1YRB_A 2OXR_A.

>cd02037 MRP-like MRP (Multiple Resistance and pH adaptation) is a homologue of the Fer4_NifH superfamily

Probab=92.05  E-value=0.11  Score=41.05  Aligned_cols=29  Identities=24%  Similarity=0.452  Sum_probs=20.2

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVS   32 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~   32 (283)
                      ||+||||+|..++......+ + .++-|+..
T Consensus         9 gG~GKTt~a~~LA~~la~~g-~-~vllvD~D   37 (169)
T cd02037           9 GGVGKSTVAVNLALALAKLG-Y-KVGLLDAD   37 (169)
T ss_pred             CcCChhHHHHHHHHHHHHcC-C-cEEEEeCC
Confidence            89999999999988765432 2 34445544

Like the other members of the superfamily, MRP contains a ATP-binding domain at the N-termini. It is found in bacteria as a membrane-spanning protein and functions as a Na+/H+ antiporter.

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=91.94  E-value=0.21  Score=38.36  Aligned_cols=33  Identities=27%  Similarity=0.409  Sum_probs=24.9

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPN   36 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~   36 (283)
                      +|+||||++..+.......  -..++|++......
T Consensus         8 ~G~GKT~l~~~i~~~~~~~--~~~v~~~~~e~~~~   40 (165)
T cd01120           8 TGSGKTTLALQLALNIATK--GGKVVYVDIEEEIE   40 (165)
T ss_pred             CCCCHHHHHHHHHHHHHhc--CCEEEEEECCcchH
Confidence            6999999999998876532  35678888766543

This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.

>PRK12724 flagellar biosynthesis regulator FlhF; Provisional

Probab=91.92  E-value=0.56  Score=42.62  Aligned_cols=72  Identities=18%  Similarity=0.074  Sum_probs=38.8

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCC-CCCHHHHHHHHHHHhCCCCCcCCHhhhHHhHHHHc--cCCcEEEEc
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQ-NPNIKKIQGEIAFKLGLKFDEESESGRTRSPWSRL--KKEKLQIIC   77 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~-~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~L--~~kr~LlV~   77 (283)
                      +|+||||++..++........+ .+..++... .....+.++..++.++.+.....  + ...+.+.+  .+..++||+
T Consensus       232 tGvGKTTtaaKLA~~~~~~~G~-~V~Lit~Dt~R~aA~eQLk~yAe~lgvp~~~~~--~-~~~l~~~l~~~~~D~VLID  306 (432)
T PRK12724        232 TGSGKTTSIAKLAAKYFLHMGK-SVSLYTTDNYRIAAIEQLKRYADTMGMPFYPVK--D-IKKFKETLARDGSELILID  306 (432)
T ss_pred             CCCCHHHHHHHHHHHHHHhcCC-eEEEecccchhhhHHHHHHHHHHhcCCCeeehH--H-HHHHHHHHHhCCCCEEEEe
Confidence            6999999999998754322112 233344332 22334555666677776543211  1 12233333  355888885

>PF00485 PRK: Phosphoribulokinase / Uridine kinase family; InterPro: IPR006083 Phosphoribulokinase (PRK) 2

Probab=91.87  E-value=0.13  Score=41.57  Aligned_cols=18  Identities=50%  Similarity=0.630  Sum_probs=16.0

Q ss_pred             CCCcHHHHHHHHHhhhcc
Q 041028            2 GGIGKTTLAKEVARKAKN   19 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~   19 (283)
                      +|+||||||+.+......
T Consensus         8 sgSGKTTla~~L~~~L~~   25 (194)
T PF00485_consen    8 SGSGKTTLAKRLAQILNK   25 (194)
T ss_dssp             TTSSHHHHHHHHHHHHTT
T ss_pred             CCCCHHHHHHHHHHHhCc
Confidence            699999999999998764

7.1.19 from EC catalyses the ATP-dependent phosphorylation of ribulose-5-phosphate to ribulose-1,5-phosphate, a key step in the pentose phosphate pathway where carbon dioxide is assimilated by autotrophic organisms []. In general, plant enzymes are light-activated by the thioredoxin/ferredoxin system, while those from photosynthetic bacteria are regulated by a system that has an absolute requirement for NADH. Thioredoxin/ferredoxin regulation is mediated by the reversible oxidation/reduction of sulphydryl and disulphide groups. Uridine kinase (pyrimidine ribonucleoside kinase) is the rate-limiting enzyme in the pyrimidine salvage pathway. It catalyzes the following reaction: ATP + Uridine = ADP + UMP Pantothenate kinase (2.7.1.33 from EC) catalyzes the rate-limiting step in the biosynthesis of coenzyme A, the conversion of pantothenate to D-4'-phosphopantothenate in the presence of ATP. ; GO: 0005524 ATP binding, 0016301 kinase activity, 0008152 metabolic process; PDB: 2ZSE_A 2ZS7_A 3AF0_A 3AVP_A 2ZS9_A 2ZS8_A 3AEZ_A 2ZSB_A 2ZSD_A 2GEV_A ....

>PRK10037 cell division protein; Provisional

Probab=91.84  E-value=0.12  Score=43.72  Aligned_cols=30  Identities=17%  Similarity=0.338  Sum_probs=20.9

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQ   33 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~   33 (283)
                      |||||||+|..++.....+++  .++-|+...
T Consensus        11 GGvGKTT~a~nLA~~La~~G~--rVLlID~D~   40 (250)
T PRK10037         11 GGVGTTSITAALAWSLQMLGE--NVLVIDACP   40 (250)
T ss_pred             CCccHHHHHHHHHHHHHhcCC--cEEEEeCCh
Confidence            899999999999887654322  345455543

>cd02021 GntK Gluconate kinase (GntK) catalyzes the phosphoryl transfer from ATP to gluconate

Probab=91.82  E-value=0.12  Score=39.77  Aligned_cols=17  Identities=35%  Similarity=0.632  Sum_probs=14.7

Q ss_pred             CCCCcHHHHHHHHHhhh
Q 041028            1 MGGIGKTTLAKEVARKA   17 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (283)
                      .+|+||||+|+.+....
T Consensus         7 ~~GsGKST~a~~l~~~~   23 (150)
T cd02021           7 VSGSGKSTVGKALAERL   23 (150)
T ss_pred             CCCCCHHHHHHHHHhhc
Confidence            47999999999998863

The resulting product gluconate-6-phoshate is an important precursor of gluconate metabolism. GntK acts as a dimmer composed of two identical subunits.

>TIGR01281 DPOR_bchL light-independent protochlorophyllide reductase, iron-sulfur ATP-binding protein

Probab=91.81  E-value=0.12  Score=44.13  Aligned_cols=17  Identities=35%  Similarity=0.581  Sum_probs=14.2

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      |||||||+|..++....
T Consensus         9 GGVGKTT~~~nLA~~La   25 (268)
T TIGR01281         9 GGIGKSTTSSNLSVAFA   25 (268)
T ss_pred             CcCcHHHHHHHHHHHHH
Confidence            89999999988877654

The BchL peptide (ChlL in chloroplast and cyanobacteria) is an ATP-binding iron-sulfur protein of the dark form protochlorophyllide reductase, an enzyme similar to nitrogenase. This subunit resembles the nitrogenase NifH subunit.

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=91.77  E-value=0.69  Score=41.72  Aligned_cols=75  Identities=19%  Similarity=0.079  Sum_probs=44.7

Q ss_pred             CCCcHHHHHHHHHhhhccCC--CCCeEEEEEeCCC-CCHHHHHHHHHHHhCCCCCc-CCHhhhHHhHHHHccCCcEEEEc
Q 041028            2 GGIGKTTLAKEVARKAKNGK--LFDQIVFTEVSQN-PNIKKIQGEIAFKLGLKFDE-ESESGRTRSPWSRLKKEKLQIIC   77 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~--~Fd~~~wv~v~~~-~~~~~l~~~i~~~l~~~~~~-~~~~~~~~~l~~~L~~kr~LlV~   77 (283)
                      .|+||||.+..++.......  .=..+..|+.... ....+-++..++.++.+... .+..+....+.. +.+..++||+
T Consensus       183 tGvGKTTT~aKLA~~~~~~~~~~g~~V~lit~Dt~R~aa~eQL~~~a~~lgvpv~~~~~~~~l~~~L~~-~~~~DlVLID  261 (388)
T PRK12723        183 TGVGKTTTIAKLAAIYGINSDDKSLNIKIITIDNYRIGAKKQIQTYGDIMGIPVKAIESFKDLKEEITQ-SKDFDLVLVD  261 (388)
T ss_pred             CCCCHHHHHHHHHHHHHhhhccCCCeEEEEeccCccHHHHHHHHHHhhcCCcceEeeCcHHHHHHHHHH-hCCCCEEEEc
Confidence            59999999999987654321  1134555665532 22344477777778876443 233444444444 4667888883

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

Probab=91.75  E-value=0.13  Score=43.90  Aligned_cols=19  Identities=42%  Similarity=0.524  Sum_probs=17.2

Q ss_pred             CCCcHHHHHHHHHhhhccC
Q 041028            2 GGIGKTTLAKEVARKAKNG   20 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~   20 (283)
                      +|.||||||.-+++...+.
T Consensus        61 PGlGKTTLA~IIA~Emgvn   79 (332)
T COG2255          61 PGLGKTTLAHIIANELGVN   79 (332)
T ss_pred             CCCcHHHHHHHHHHHhcCC
Confidence            7999999999999988765

>COG3265 GntK Gluconate kinase [Carbohydrate transport and metabolism]

Probab=91.75  E-value=0.52  Score=36.22  Aligned_cols=40  Identities=20%  Similarity=0.295  Sum_probs=26.6

Q ss_pred             CCCcHHHHHHHHHhhhccCCCC-CeEEEEEeCCCCCHHHHHHHHHHHhCC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLF-DQIVFTEVSQNPNIKKIQGEIAFKLGL   50 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~F-d~~~wv~v~~~~~~~~l~~~i~~~l~~   50 (283)
                      +|.||||++..+++.....  | |+       ..+.+.+-..++.+.+-+
T Consensus         4 sG~GKStvg~~lA~~lg~~--fidG-------DdlHp~aNi~KM~~GiPL   44 (161)
T COG3265           4 SGSGKSTVGSALAERLGAK--FIDG-------DDLHPPANIEKMSAGIPL   44 (161)
T ss_pred             CccCHHHHHHHHHHHcCCc--eecc-------cccCCHHHHHHHhCCCCC
Confidence            4999999999999987754  4 32       344555555556554433

>PRK13185 chlL protochlorophyllide reductase iron-sulfur ATP-binding protein; Provisional

Probab=91.73  E-value=0.24  Score=42.21  Aligned_cols=18  Identities=33%  Similarity=0.589  Sum_probs=15.2

Q ss_pred             CCCcHHHHHHHHHhhhcc
Q 041028            2 GGIGKTTLAKEVARKAKN   19 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~   19 (283)
                      |||||||++..++.....
T Consensus        11 GGVGKTT~~~nLA~~la~   28 (270)
T PRK13185         11 GGIGKSTTSSNLSAAFAK   28 (270)
T ss_pred             CCCCHHHHHHHHHHHHHH
Confidence            899999999998887643

>TIGR01287 nifH nitrogenase iron protein

Probab=91.71  E-value=0.19  Score=42.99  Aligned_cols=29  Identities=24%  Similarity=0.409  Sum_probs=19.9

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVS   32 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~   32 (283)
                      |||||||+|..++.....++ + .++-|+..
T Consensus         9 GGVGKTT~a~nLA~~La~~G-~-~VlliD~D   37 (275)
T TIGR01287         9 GGIGKSTTTQNIAAALAEMG-K-KVMIVGCD   37 (275)
T ss_pred             CcCcHHHHHHHHHHHHHHCC-C-eEEEEeCC
Confidence            89999999999888765443 2 34444444

This model describes nitrogenase (EC 1.18.6.1) iron protein, also called nitrogenase reductase or nitrogenase component II. This model includes molybdenum-iron nitrogenase reductase (nifH), vanadium-iron nitrogenase reductase (vnfH), and iron-iron nitrogenase reductase (anfH). The model excludes the homologous protein from the light-independent protochlorophyllide reductase.

>PRK14723 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=91.67  E-value=0.8  Score=44.76  Aligned_cols=75  Identities=17%  Similarity=0.147  Sum_probs=47.1

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCC-CCCHHHHHHHHHHHhCCCCCc-CCHhhhHHhHHHHccCCcEEEEc
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQ-NPNIKKIQGEIAFKLGLKFDE-ESESGRTRSPWSRLKKEKLQIIC   77 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~-~~~~~~l~~~i~~~l~~~~~~-~~~~~~~~~l~~~L~~kr~LlV~   77 (283)
                      .|+||||++..++........-..+..++... .....+-++...+.++.+... .+..+..+.+. .++++.++||+
T Consensus       194 nGvGKTTTiaKLA~~~~~~~G~kkV~lit~Dt~RigA~eQL~~~a~~~gvpv~~~~~~~~l~~al~-~~~~~D~VLID  270 (767)
T PRK14723        194 TGVGKTTTTAKLAARCVAREGADQLALLTTDSFRIGALEQLRIYGRILGVPVHAVKDAADLRFALA-ALGDKHLVLID  270 (767)
T ss_pred             CCCcHHHHHHHHHhhHHHHcCCCeEEEecCcccchHHHHHHHHHHHhCCCCccccCCHHHHHHHHH-HhcCCCEEEEe
Confidence            59999999999887653221113455555442 223566777788888876542 35555544444 56777899983

>COG0703 AroK Shikimate kinase [Amino acid transport and metabolism]

Probab=91.55  E-value=0.15  Score=40.30  Aligned_cols=20  Identities=25%  Similarity=0.421  Sum_probs=17.5

Q ss_pred             CCCCcHHHHHHHHHhhhccC
Q 041028            1 MGGIGKTTLAKEVARKAKNG   20 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~   20 (283)
                      |.|+||||+.++++......
T Consensus        10 ~mGaGKSTIGr~LAk~L~~~   29 (172)
T COG0703          10 FMGAGKSTIGRALAKALNLP   29 (172)
T ss_pred             CCCCCHhHHHHHHHHHcCCC
Confidence            67999999999999987754

>COG0467 RAD55 RecA-superfamily ATPases implicated in signal transduction [Signal transduction mechanisms]

Probab=91.54  E-value=0.2  Score=42.50  Aligned_cols=31  Identities=16%  Similarity=0.306  Sum_probs=26.2

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQN   34 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~   34 (283)
                      +|+|||++|.++.......  ...++||+.++.
T Consensus        32 pGsGKT~f~~qfl~~~~~~--ge~vlyvs~~e~   62 (260)
T COG0467          32 PGTGKTIFALQFLYEGARE--GEPVLYVSTEES   62 (260)
T ss_pred             CCCcHHHHHHHHHHHHHhc--CCcEEEEEecCC
Confidence            6999999999998876644  788999998765

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=91.48  E-value=0.33  Score=41.31  Aligned_cols=36  Identities=33%  Similarity=0.445  Sum_probs=23.5

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHH
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQG   42 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~   42 (283)
                      +|+|||+||+.+++...    . ..+.++.....+..+++.
T Consensus        30 ~GtGKT~lA~~la~~lg----~-~~~~i~~~~~~~~~dllg   65 (262)
T TIGR02640        30 AGTGKTTLAMHVARKRD----R-PVMLINGDAELTTSDLVG   65 (262)
T ss_pred             CCCCHHHHHHHHHHHhC----C-CEEEEeCCccCCHHHHhh
Confidence            69999999999987432    1 234555555555555543

Members of this family are the GvpN protein associated with the production of gas vesicles produced in some prokaryotes to give cells buoyancy. This family belongs to a larger family of ATPases (pfam07728).

>PRK13230 nitrogenase reductase-like protein; Reviewed

Probab=91.45  E-value=0.13  Score=44.08  Aligned_cols=19  Identities=37%  Similarity=0.564  Sum_probs=15.9

Q ss_pred             CCCcHHHHHHHHHhhhccC
Q 041028            2 GGIGKTTLAKEVARKAKNG   20 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~   20 (283)
                      |||||||+|..++......
T Consensus        10 GGVGKTT~a~nLA~~La~~   28 (279)
T PRK13230         10 GGIGKSTTVCNIAAALAES   28 (279)
T ss_pred             CCCcHHHHHHHHHHHHHhC
Confidence            8999999999988876543

>cd00227 CPT Chloramphenicol (Cm) phosphotransferase (CPT)

Probab=91.40  E-value=0.14  Score=40.64  Aligned_cols=17  Identities=18%  Similarity=0.309  Sum_probs=14.9

Q ss_pred             CCCCcHHHHHHHHHhhh
Q 041028            1 MGGIGKTTLAKEVARKA   17 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (283)
                      ++|+||||+|+.+....
T Consensus        10 ~~gsGKst~a~~l~~~~   26 (175)
T cd00227          10 GSSAGKSSIARALQSVL   26 (175)
T ss_pred             CCCCCHHHHHHHHHHhh
Confidence            47999999999998764

Cm-inactivating enzyme; modifies the primary (C-3) hydroxyl of the antibiotic. Related structurally to shikimate kinase II.

>PRK13949 shikimate kinase; Provisional

Probab=91.32  E-value=0.15  Score=40.31  Aligned_cols=18  Identities=50%  Similarity=0.601  Sum_probs=16.1

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      |+|+|||||++.+++...
T Consensus         9 ~~GsGKstl~~~La~~l~   26 (169)
T PRK13949          9 YMGAGKTTLGKALARELG   26 (169)
T ss_pred             CCCCCHHHHHHHHHHHcC
Confidence            579999999999999765

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=91.31  E-value=1  Score=40.62  Aligned_cols=74  Identities=18%  Similarity=0.156  Sum_probs=42.7

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCC-CCHHHHHHHHHHHhCCCCC-cCCHhhhHHhHHHHcc--CCcEEEEc
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQN-PNIKKIQGEIAFKLGLKFD-EESESGRTRSPWSRLK--KEKLQIIC   77 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~-~~~~~l~~~i~~~l~~~~~-~~~~~~~~~~l~~~L~--~kr~LlV~   77 (283)
                      +|+||||++..++.....++ + .+..++.... ....+-++.....++.+.. ..+..+..+.+...-.  +..++||+
T Consensus       250 tGvGKTTTiaKLA~~L~~~G-k-kVglI~aDt~RiaAvEQLk~yae~lgipv~v~~d~~~L~~aL~~lk~~~~~DvVLID  327 (436)
T PRK11889        250 TGVGKTTTLAKMAWQFHGKK-K-TVGFITTDHSRIGTVQQLQDYVKTIGFEVIAVRDEAAMTRALTYFKEEARVDYILID  327 (436)
T ss_pred             CCCcHHHHHHHHHHHHHHcC-C-cEEEEecCCcchHHHHHHHHHhhhcCCcEEecCCHHHHHHHHHHHHhccCCCEEEEe
Confidence            69999999999988765332 2 3445554422 2234444555566666543 2345555555544432  45888883

>PRK13975 thymidylate kinase; Provisional

Probab=91.28  E-value=0.15  Score=41.15  Aligned_cols=19  Identities=47%  Similarity=0.536  Sum_probs=16.4

Q ss_pred             CCCCcHHHHHHHHHhhhcc
Q 041028            1 MGGIGKTTLAKEVARKAKN   19 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~   19 (283)
                      +.|+||||+|+.+++....
T Consensus        10 ~~GsGKtT~~~~L~~~l~~   28 (196)
T PRK13975         10 IDGSGKTTQAKLLAEKLNA   28 (196)
T ss_pred             CCCCCHHHHHHHHHHHhCC
Confidence            4699999999999998753

>TIGR02236 recomb_radA DNA repair and recombination protein RadA

Probab=91.22  E-value=0.49  Score=41.31  Aligned_cols=48  Identities=21%  Similarity=0.245  Sum_probs=34.1

Q ss_pred             CCCcHHHHHHHHHhhhccCCC----CCeEEEEEeCCCCCHHHHHHHHHHHhCC
Q 041028            2 GGIGKTTLAKEVARKAKNGKL----FDQIVFTEVSQNPNIKKIQGEIAFKLGL   50 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~----Fd~~~wv~v~~~~~~~~l~~~i~~~l~~   50 (283)
                      +|+|||||+.+++-.......    =..++||+....|+...+. ++++.++.
T Consensus       104 ~g~GKT~l~~~~~~~~~~~~~~g~~~~~~~yi~te~~f~~~rl~-~~~~~~gl  155 (310)
T TIGR02236       104 FGSGKTQICHQLAVNVQLPEEKGGLGGKAVYIDTENTFRPERIM-QMAEARGL  155 (310)
T ss_pred             CCCCHHHHHHHHHHHhcCCcccCCCcceEEEEECCCCCCHHHHH-HHHHHcCC
Confidence            699999999999876432110    1378999999888887654 55666554

This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239), and archaeal RadB (TIGR02237). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein.

>TIGR01969 minD_arch cell division ATPase MinD, archaeal

Probab=91.21  E-value=0.15  Score=42.82  Aligned_cols=17  Identities=35%  Similarity=0.581  Sum_probs=14.7

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      |||||||+|..++....
T Consensus        10 GGvGKTt~a~~LA~~la   26 (251)
T TIGR01969        10 GGTGKTTITANLGVALA   26 (251)
T ss_pred             CCCcHHHHHHHHHHHHH
Confidence            89999999999887654

This model represents the archaeal branch of the MinD family. MinD, a weak ATPase, works in bacteria with MinC as a generalized cell division inhibitor and, through interaction with MinE, prevents septum placement inappropriate sites. Often several members of this family are found in archaeal genomes, and the function is uncharacterized. More distantly related proteins include flagellar biosynthesis proteins and ParA chromosome partitioning proteins. The exact roles of the various archaeal MinD homologs are unknown.

>PTZ00301 uridine kinase; Provisional

Probab=91.19  E-value=0.14  Score=42.04  Aligned_cols=17  Identities=24%  Similarity=0.505  Sum_probs=14.6

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      +|+||||||+.+.....
T Consensus        12 SgSGKTTla~~l~~~l~   28 (210)
T PTZ00301         12 SGSGKSSLSTNIVSELM   28 (210)
T ss_pred             CcCCHHHHHHHHHHHHH
Confidence            69999999999987754

>cd02032 Bchl_like This family of proteins contains bchL and chlL

Probab=91.18  E-value=0.15  Score=43.44  Aligned_cols=18  Identities=33%  Similarity=0.584  Sum_probs=15.3

Q ss_pred             CCCcHHHHHHHHHhhhcc
Q 041028            2 GGIGKTTLAKEVARKAKN   19 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~   19 (283)
                      |||||||+|..++.....
T Consensus         9 GGvGKTT~a~nLA~~la~   26 (267)
T cd02032           9 GGIGKSTTSSNLSVALAK   26 (267)
T ss_pred             CCCCHHHHHHHHHHHHHH
Confidence            899999999998887654

Protochlorophyllide reductase catalyzes the reductive formation of chlorophyllide from protochlorophyllide during biosynthesis of chlorophylls and bacteriochlorophylls. Three genes, bchL, bchN and bchB, are involved in light-independent protochlorophyllide reduction in bacteriochlorophyll biosynthesis. In cyanobacteria, algae, and gymnosperms, three similar genes, chlL, chlN and chlB are involved in protochlorophyllide reduction during chlorophylls biosynthesis. BchL/chlL, bchN/chlN and bchB/chlB exhibit significant sequence similarity to the nifH, nifD and nifK subunits of nitrogenase, respectively. Nitrogenase catalyzes the reductive formation of ammonia from dinitrogen.

>PLN03187 meiotic recombination protein DMC1 homolog; Provisional

Probab=91.17  E-value=0.54  Score=41.69  Aligned_cols=49  Identities=18%  Similarity=0.175  Sum_probs=34.8

Q ss_pred             CCCcHHHHHHHHHhhhcc---CCC-CCeEEEEEeCCCCCHHHHHHHHHHHhCCC
Q 041028            2 GGIGKTTLAKEVARKAKN---GKL-FDQIVFTEVSQNPNIKKIQGEIAFKLGLK   51 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~---~~~-Fd~~~wv~v~~~~~~~~l~~~i~~~l~~~   51 (283)
                      +|+|||+|+..++-....   .+- -..++||+-...|++..+.+ +++.++.+
T Consensus       135 ~GsGKTql~lqlav~~qlp~~~gg~~~~vvyIdTE~tF~peRl~~-ia~~~g~d  187 (344)
T PLN03187        135 FRSGKTQLAHTLCVTTQLPTEMGGGNGKVAYIDTEGTFRPDRIVP-IAERFGMD  187 (344)
T ss_pred             CCCChhHHHHHHHHHHhcchhhCCCCceEEEEEcCCCCCHHHHHH-HHHHcCCC
Confidence            699999999988643321   111 24689999999999888744 67777654

>COG0563 Adk Adenylate kinase and related kinases [Nucleotide transport and metabolism]

Probab=91.17  E-value=0.14  Score=40.84  Aligned_cols=18  Identities=50%  Similarity=0.623  Sum_probs=15.8

Q ss_pred             CCCcHHHHHHHHHhhhcc
Q 041028            2 GGIGKTTLAKEVARKAKN   19 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~   19 (283)
                      +|+||||+|+.+.+....
T Consensus         9 pGaGK~T~A~~La~~~~i   26 (178)
T COG0563           9 PGAGKSTLAKKLAKKLGL   26 (178)
T ss_pred             CCCCHHHHHHHHHHHhCC
Confidence            699999999999998543

>PRK04301 radA DNA repair and recombination protein RadA; Validated

Probab=91.16  E-value=0.47  Score=41.60  Aligned_cols=48  Identities=23%  Similarity=0.308  Sum_probs=34.1

Q ss_pred             CCCcHHHHHHHHHhhhccCCCC----CeEEEEEeCCCCCHHHHHHHHHHHhCC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLF----DQIVFTEVSQNPNIKKIQGEIAFKLGL   50 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~F----d~~~wv~v~~~~~~~~l~~~i~~~l~~   50 (283)
                      +|+|||+||.+++-.......+    ..++||+....|++..+. ++++.++.
T Consensus       111 ~GsGKT~l~~~~~~~~~~~~~~gg~~~~~~yi~te~~f~~~rl~-~~~~~~g~  162 (317)
T PRK04301        111 FGSGKTQICHQLAVNVQLPEEKGGLEGKAVYIDTEGTFRPERIE-QMAEALGL  162 (317)
T ss_pred             CCCCHhHHHHHHHHHhccccccCCCCceEEEEeCCCCcCHHHHH-HHHHHcCC
Confidence            6999999999998664322111    478999999988887764 45555553

>PRK13233 nifH nitrogenase reductase; Reviewed

Probab=91.15  E-value=0.13  Score=44.07  Aligned_cols=17  Identities=41%  Similarity=0.647  Sum_probs=14.6

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      |||||||+|..++.-..
T Consensus        11 GGVGKTT~a~nLA~~La   27 (275)
T PRK13233         11 GGIGKSTTTQNTAAAMA   27 (275)
T ss_pred             CCCcHHHHHHHHHHHHH
Confidence            89999999998877654

>PRK13946 shikimate kinase; Provisional

Probab=91.09  E-value=0.16  Score=40.64  Aligned_cols=19  Identities=26%  Similarity=0.380  Sum_probs=16.7

Q ss_pred             CCCCcHHHHHHHHHhhhcc
Q 041028            1 MGGIGKTTLAKEVARKAKN   19 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~   19 (283)
                      |+|+||||+|+.+++....
T Consensus        18 ~~GsGKsti~~~LA~~Lg~   36 (184)
T PRK13946         18 LMGAGKSTVGRRLATMLGL   36 (184)
T ss_pred             CCCCCHHHHHHHHHHHcCC
Confidence            6799999999999998753

>PF02367 UPF0079: Uncharacterised P-loop hydrolase UPF0079; InterPro: IPR003442 This group consists of bacterial proteins, which contain a P-loop

Probab=91.07  E-value=0.17  Score=37.78  Aligned_cols=17  Identities=41%  Similarity=0.550  Sum_probs=14.4

Q ss_pred             CCcHHHHHHHHHhhhcc
Q 041028            3 GIGKTTLAKEVARKAKN   19 (283)
Q Consensus         3 GiGKTtLA~~v~~~~~~   19 (283)
                      |.|||||++.++.....
T Consensus        25 GaGKTtf~r~l~~~lg~   41 (123)
T PF02367_consen   25 GAGKTTFVRGLARALGI   41 (123)
T ss_dssp             TSSHHHHHHHHHHHTT-
T ss_pred             CCCHHHHHHHHHHHcCC
Confidence            89999999999987644

They are probably essential to bacteria as members are found in all genomes so far sequenced and no equivalent genes have been found in the archaea and eukaryotes, suggesting the protein may be involved in cell wall biosynthesis. The sequence of YjeE, from Haemophilus influenzae, has been determined to 1.7-A resolution. The protein has a nucleotide-binding fold with a four-stranded parallel beta-sheet flanked by antiparallel beta-strands on each side. The topology of the beta-sheet is unique among P-loop proteins and has features of different families of enzymes. ADP has been shown to bind to the P-loop in the presence of Mg2+ and ATPase activity has been confirmed by kinetic measurements [].; PDB: 1HTW_A 1FL9_A.

>cd03115 SRP The signal recognition particle (SRP) mediates the transport to or across the plasma membrane in bacteria and the endoplasmic reticulum in eukaryotes

Probab=91.07  E-value=1.1  Score=35.23  Aligned_cols=74  Identities=16%  Similarity=0.182  Sum_probs=37.9

Q ss_pred             CCCCcHHHHHHHHHhhhccCCCCCeEEEEEeCC-CCCHHHHHHHHHHHhCCCCC----cCCHhhhH-HhHHHHcc-CCcE
Q 041028            1 MGGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQ-NPNIKKIQGEIAFKLGLKFD----EESESGRT-RSPWSRLK-KEKL   73 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~-~~~~~~l~~~i~~~l~~~~~----~~~~~~~~-~~l~~~L~-~kr~   73 (283)
                      ++|+||||++..++......+ + .++.++... .....+.+..++...+.+..    ..+..+.. +.+...+. +..+
T Consensus         8 ~~G~GKTt~~~~la~~~~~~g-~-~v~~i~~D~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~   85 (173)
T cd03115           8 LQGVGKTTTAAKLALYLKKKG-K-KVLLVAADTYRPAAIEQLRVLGEQVGVPVFEEGEGKDPVSIAKRAIEHAREENFDV   85 (173)
T ss_pred             CCCCCHHHHHHHHHHHHHHCC-C-cEEEEEcCCCChHHHHHHHHhcccCCeEEEecCCCCCHHHHHHHHHHHHHhCCCCE
Confidence            479999999999988765331 2 234444332 12333445555555554311    11222222 33444443 4467


Q ss_pred             EEE
Q 041028           74 QII   76 (283)
Q Consensus        74 LlV   76 (283)
                      +||
T Consensus        86 vii   88 (173)
T cd03115          86 VIV   88 (173)
T ss_pred             EEE
Confidence            777

SRP recognizes N-terminal sighnal sequences of newly synthesized polypeptides at the ribosome. The SRP-polypeptide complex is then targeted to the membrane by an interaction between SRP and its cognated receptor (SR). In mammals, SRP consists of six protein subunits and a 7SL RNA. One of these subunits is a 54 kd protein (SRP54), which is a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 is a multidomain protein that consists of an N-terminal domain, followed by a central G (GTPase) domain and a C-terminal M domain.

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=91.06  E-value=0.76  Score=41.24  Aligned_cols=45  Identities=29%  Similarity=0.442  Sum_probs=29.2

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKLGLK   51 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~~l~~~   51 (283)
                      +|+|||||+.+++......  -..++|++..+..  .++ +.-++.++..
T Consensus        91 pG~GKStLllq~a~~~a~~--g~~VlYvs~EEs~--~qi-~~Ra~rlg~~  135 (372)
T cd01121          91 PGIGKSTLLLQVAARLAKR--GGKVLYVSGEESP--EQI-KLRADRLGIS  135 (372)
T ss_pred             CCCCHHHHHHHHHHHHHhc--CCeEEEEECCcCH--HHH-HHHHHHcCCC
Confidence            6999999999998776533  3467888765543  232 2234556653

This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.

>PTZ00088 adenylate kinase 1; Provisional

Probab=91.05  E-value=0.19  Score=41.95  Aligned_cols=18  Identities=33%  Similarity=0.577  Sum_probs=15.8

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      ++|+||||+|+.+++...
T Consensus        14 ~PGsGK~T~a~~La~~~g   31 (229)
T PTZ00088         14 APGVGKGTFAEILSKKEN   31 (229)
T ss_pred             CCCCCHHHHHHHHHHHhC
Confidence            479999999999998764

>KOG1969 consensus DNA replication checkpoint protein CHL12/CTF18 [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=90.96  E-value=0.38  Score=46.17  Aligned_cols=43  Identities=28%  Similarity=0.420  Sum_probs=34.1

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHHHhC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKLG   49 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~~l~   49 (283)
                      +|.||||||.-++++..    | .++=|+.|...+...+-..|...+.
T Consensus       335 pGlGKTTLAHViAkqaG----Y-sVvEINASDeRt~~~v~~kI~~avq  377 (877)
T KOG1969|consen  335 PGLGKTTLAHVIAKQAG----Y-SVVEINASDERTAPMVKEKIENAVQ  377 (877)
T ss_pred             CCCChhHHHHHHHHhcC----c-eEEEecccccccHHHHHHHHHHHHh
Confidence            79999999999999754    3 3566888888888877777776663

>PF01695 IstB_IS21: IstB-like ATP binding protein; InterPro: IPR002611 Proteins in this entry contain an ATP/GTP binding P-loop motif

Probab=90.93  E-value=0.51  Score=37.65  Aligned_cols=60  Identities=27%  Similarity=0.357  Sum_probs=34.6

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCcCCHhhhHHhHHHHccCCcEEEEc
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKLGLKFDEESESGRTRSPWSRLKKEKLQIIC   77 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~kr~LlV~   77 (283)
                      .|+|||.||..+.+....++ + .+.|++      ..+++..+-.    ......    ...+.+.+.+-.+||++
T Consensus        56 ~G~GKThLa~ai~~~~~~~g-~-~v~f~~------~~~L~~~l~~----~~~~~~----~~~~~~~l~~~dlLilD  115 (178)
T PF01695_consen   56 PGTGKTHLAVAIANEAIRKG-Y-SVLFIT------ASDLLDELKQ----SRSDGS----YEELLKRLKRVDLLILD  115 (178)
T ss_dssp             TTSSHHHHHHHHHHHHHHTT----EEEEE------HHHHHHHHHC----CHCCTT----HCHHHHHHHTSSCEEEE
T ss_pred             HhHHHHHHHHHHHHHhccCC-c-ceeEee------cCceeccccc----cccccc----hhhhcCccccccEeccc
Confidence            69999999999998765432 3 345554      3444444432    211111    12334556667889884

They are found associated with IS21 family insertion sequences []. Functionally they have not been characterised, but they may be involved in transposition [].; GO: 0005524 ATP binding; PDB: 3EC2_A 3ECC_A 2W58_A 2QGZ_A.

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=90.93  E-value=0.76  Score=41.75  Aligned_cols=29  Identities=21%  Similarity=0.385  Sum_probs=20.3

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEE
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTE   30 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~   30 (283)
                      .|+|||+|++++++.......=-.+++++
T Consensus       145 ~G~GKThL~~ai~~~l~~~~~~~~v~yi~  173 (405)
T TIGR00362       145 VGLGKTHLLHAIGNEILENNPNAKVVYVS  173 (405)
T ss_pred             CCCcHHHHHHHHHHHHHHhCCCCcEEEEE
Confidence            69999999999999875431112455664

DnaA is involved in DNA biosynthesis; initiation of chromosome replication and can also be transcription regulator. The C-terminal of the family hits the pfam bacterial DnaA (bac_dnaA) domain family. For a review, see Kaguni (2006).

>TIGR01359 UMP_CMP_kin_fam UMP-CMP kinase family

Probab=90.88  E-value=0.17  Score=40.34  Aligned_cols=18  Identities=22%  Similarity=0.217  Sum_probs=15.5

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      ++|+||||+|+.++....
T Consensus         7 ~pGsGKst~a~~la~~~~   24 (183)
T TIGR01359         7 GPGSGKGTQCAKIVENFG   24 (183)
T ss_pred             CCCCCHHHHHHHHHHHcC
Confidence            479999999999988653

This subfamily of the adenylate kinase superfamily contains examples of UMP-CMP kinase, as well as others proteins with unknown specificity, some currently designated adenylate kinase. All known members are eukaryotic.

>PRK05480 uridine/cytidine kinase; Provisional

Probab=90.85  E-value=0.16  Score=41.54  Aligned_cols=16  Identities=38%  Similarity=0.532  Sum_probs=14.5

Q ss_pred             CCCcHHHHHHHHHhhh
Q 041028            2 GGIGKTTLAKEVARKA   17 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~   17 (283)
                      +|+||||||+.++...
T Consensus        15 sGsGKTTl~~~l~~~l   30 (209)
T PRK05480         15 SGSGKTTVASTIYEEL   30 (209)
T ss_pred             CCCCHHHHHHHHHHHh
Confidence            6999999999999875

>PRK12726 flagellar biosynthesis regulator FlhF; Provisional

Probab=90.85  E-value=1.4  Score=39.60  Aligned_cols=74  Identities=15%  Similarity=0.048  Sum_probs=46.1

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCC-CCHHHHHHHHHHHhCCCCC-cCCHhhhHHhHHHHc--cCCcEEEEc
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQN-PNIKKIQGEIAFKLGLKFD-EESESGRTRSPWSRL--KKEKLQIIC   77 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~-~~~~~l~~~i~~~l~~~~~-~~~~~~~~~~l~~~L--~~kr~LlV~   77 (283)
                      .|+||||++..++.....++  ..+.+|+.... ....+-++...+.++.+.. ..+..+..+.+...-  .+..++||+
T Consensus       215 tGvGKTTt~akLA~~l~~~g--~~V~lItaDtyR~gAveQLk~yae~lgvpv~~~~dp~dL~~al~~l~~~~~~D~VLID  292 (407)
T PRK12726        215 TGVGKTTTLVKLGWQLLKQN--RTVGFITTDTFRSGAVEQFQGYADKLDVELIVATSPAELEEAVQYMTYVNCVDHILID  292 (407)
T ss_pred             CCCCHHHHHHHHHHHHHHcC--CeEEEEeCCccCccHHHHHHHHhhcCCCCEEecCCHHHHHHHHHHHHhcCCCCEEEEE
Confidence            59999999999987664332  34666776532 2345566777777776643 234555544454332  356888883

>cd01983 Fer4_NifH The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain

Probab=90.84  E-value=0.19  Score=34.83  Aligned_cols=18  Identities=50%  Similarity=0.748  Sum_probs=15.6

Q ss_pred             CCCcHHHHHHHHHhhhcc
Q 041028            2 GGIGKTTLAKEVARKAKN   19 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~   19 (283)
                      +|+||||++..+......
T Consensus         8 ~G~Gktt~~~~l~~~l~~   25 (99)
T cd01983           8 GGVGKTTLAANLAAALAK   25 (99)
T ss_pred             CCCCHHHHHHHHHHHHHH
Confidence            699999999999987653

Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion.

>PRK13235 nifH nitrogenase reductase; Reviewed

Probab=90.82  E-value=0.15  Score=43.73  Aligned_cols=18  Identities=33%  Similarity=0.564  Sum_probs=15.1

Q ss_pred             CCCcHHHHHHHHHhhhcc
Q 041028            2 GGIGKTTLAKEVARKAKN   19 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~   19 (283)
                      |||||||+|..++.-...
T Consensus        10 GGVGKTT~~~nLA~~La~   27 (274)
T PRK13235         10 GGIGKSTTTQNTVAGLAE   27 (274)
T ss_pred             CCccHHHHHHHHHHHHHH
Confidence            899999999998876543

>PRK06547 hypothetical protein; Provisional

Probab=90.79  E-value=0.18  Score=40.09  Aligned_cols=18  Identities=44%  Similarity=0.545  Sum_probs=15.3

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      .+|+||||||+.+.+...
T Consensus        23 ~~GsGKTt~a~~l~~~~~   40 (172)
T PRK06547         23 RSGSGKTTLAGALAARTG   40 (172)
T ss_pred             CCCCCHHHHHHHHHHHhC
Confidence            369999999999998754

>PRK13232 nifH nitrogenase reductase; Reviewed

Probab=90.79  E-value=0.15  Score=43.63  Aligned_cols=17  Identities=35%  Similarity=0.647  Sum_probs=14.6

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      |||||||+|..++.-..
T Consensus        10 GGVGKTT~a~nLA~~La   26 (273)
T PRK13232         10 GGIGKSTTTQNLTAALS   26 (273)
T ss_pred             CCCcHHHHHHHHHHHHH
Confidence            89999999999887654

>COG0125 Tmk Thymidylate kinase [Nucleotide transport and metabolism]

Probab=90.76  E-value=0.54  Score=38.55  Aligned_cols=43  Identities=23%  Similarity=0.329  Sum_probs=27.9

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHH
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAF   46 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~   46 (283)
                      -|+||||.++.++...+.++.  .++|..-.....+.+..++++.
T Consensus        12 DGaGKTT~~~~L~~~l~~~g~--~v~~trEP~~~~ige~iR~~ll   54 (208)
T COG0125          12 DGAGKTTQAELLKERLEERGI--KVVLTREPGGTPIGEKIRELLL   54 (208)
T ss_pred             CCCCHHHHHHHHHHHHHHcCC--eEEEEeCCCCChHHHHHHHHHc
Confidence            499999999999999876632  4454443333444555555443

>PRK04040 adenylate kinase; Provisional

Probab=90.73  E-value=0.18  Score=40.72  Aligned_cols=39  Identities=31%  Similarity=0.454  Sum_probs=25.9

Q ss_pred             CCCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHHHhCC
Q 041028            1 MGGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKLGL   50 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~~l~~   50 (283)
                      ++|+||||+++.+.......  |..   +      +..+++..++...|.
T Consensus        10 ~pG~GKtt~~~~l~~~l~~~--~~~---~------~~g~~~~~~a~~~g~   48 (188)
T PRK04040         10 VPGVGKTTVLNKALEKLKED--YKI---V------NFGDVMLEVAKEEGL   48 (188)
T ss_pred             CCCCCHHHHHHHHHHHhccC--CeE---E------ecchHHHHHHHHcCC
Confidence            57999999999999876311  322   2      334566666666664

>PF07015 VirC1: VirC1 protein; InterPro: IPR009744 This family consists of several bacterial VirC1 proteins

Probab=90.70  E-value=0.45  Score=39.43  Aligned_cols=35  Identities=26%  Similarity=0.403  Sum_probs=24.7

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHH
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIK   38 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~   38 (283)
                      ||.||||++..++.....++  ..+.-++...+-.+.
T Consensus        11 GGaGKTT~~~~LAs~la~~G--~~V~lIDaDpn~pl~   45 (231)
T PF07015_consen   11 GGAGKTTAAMALASELAARG--ARVALIDADPNQPLA   45 (231)
T ss_pred             CCCcHHHHHHHHHHHHHHCC--CeEEEEeCCCCCcHH
Confidence            89999999999998875442  245556665554444

In Agrobacterium tumefaciens, a cis-active 24-base-pair sequence adjacent to the right border of the T-DNA, called overdrive, stimulates tumour formation by increasing the level of T-DNA processing. It is thought that the virC operon, which enhances T-DNA processing probably, does so because the VirC1 protein interacts with overdrive. It has now been shown that the virC1 gene product binds to overdrive but not to the right border of T-DNA [].

>PRK13342 recombination factor protein RarA; Reviewed

Probab=90.69  E-value=0.44  Score=43.45  Aligned_cols=17  Identities=47%  Similarity=0.604  Sum_probs=15.2

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      +|+||||||+.+++...
T Consensus        45 pGtGKTtLA~~ia~~~~   61 (413)
T PRK13342         45 PGTGKTTLARIIAGATD   61 (413)
T ss_pred             CCCCHHHHHHHHHHHhC
Confidence            79999999999998754

>COG0529 CysC Adenylylsulfate kinase and related kinases [Inorganic ion transport and metabolism]

Probab=90.68  E-value=0.2  Score=39.66  Aligned_cols=20  Identities=30%  Similarity=0.456  Sum_probs=17.0

Q ss_pred             CCCCcHHHHHHHHHhhhccC
Q 041028            1 MGGIGKTTLAKEVARKAKNG   20 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~   20 (283)
                      .+|.||||+|.+++......
T Consensus        31 LSGsGKSTiA~ale~~L~~~   50 (197)
T COG0529          31 LSGSGKSTIANALEEKLFAK   50 (197)
T ss_pred             CCCCCHHHHHHHHHHHHHHc
Confidence            47999999999999987544

>PF03266 NTPase_1: NTPase; InterPro: IPR004948 This entry represents a family of nucleoside-triphosphatases which have activity towards ATP, GTP, CTP, TTP and UTP and may hydrolyse nucleoside diphosphates with lower efficiency []

Probab=90.67  E-value=0.18  Score=39.89  Aligned_cols=17  Identities=53%  Similarity=0.712  Sum_probs=15.3

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      +|+|||||.+.+.+..+
T Consensus         8 pG~GKTTll~k~i~~l~   24 (168)
T PF03266_consen    8 PGVGKTTLLKKVIEELK   24 (168)
T ss_dssp             TTSSHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHhh
Confidence            69999999999998874

It includes proteins from bacteria to human, and the function was determined first in a hyperthermophilic bacterium to be an NTPase []. The structure of one member-sequence represents a variation of the RecA fold, and implies that the function might be that of a DNA/RNA modifying enzyme []. The sequence carries both a Walker A and Walker B motif which together are characteristic of ATPases or GTPases. The protein exhibits an increased expression profile in human liver cholangiocarcinoma when compared to normal tissue [].; GO: 0005524 ATP binding, 0016740 transferase activity, 0019204 nucleotide phosphatase activity; PDB: 1YE8_A 2I3B_A.

>PF01202 SKI: Shikimate kinase; InterPro: IPR000623 Shikimate kinase (2

Probab=90.54  E-value=0.16  Score=39.68  Aligned_cols=19  Identities=32%  Similarity=0.419  Sum_probs=16.6

Q ss_pred             CCCcHHHHHHHHHhhhccC
Q 041028            2 GGIGKTTLAKEVARKAKNG   20 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~   20 (283)
                      .|+||||+++.++......
T Consensus         1 ~GsGKStvg~~lA~~L~~~   19 (158)
T PF01202_consen    1 MGSGKSTVGKLLAKRLGRP   19 (158)
T ss_dssp             TTSSHHHHHHHHHHHHTSE
T ss_pred             CCCcHHHHHHHHHHHhCCC
Confidence            5999999999999987754

7.1.71 from EC) catalyses the fifth step in the biosynthesis of aromatic amino acids from chorismate (the so-called shikimate pathway) []. The enzyme catalyses the following reaction: ATP + shikimate = ADP + shikimate-3-phosphate The protein is found in bacteria (gene aroK or aroL), plants and fungi (where it is part of a multifunctional enzyme that catalyses five consecutive steps in this pathway). In 1994, the 3D structure of shikimate kinase was predicted to be very close to that of adenylate kinase, suggesting a functional similarity as well as an evolutionary relationship []. This prediction has since been confirmed experimentally. The protein is reported to possess an alpha/beta fold, consisting of a central sheet of five parallel beta-strands flanked by alpha-helices. Such a topology is very similar to that of adenylate kinase [].; GO: 0004765 shikimate kinase activity, 0005524 ATP binding; PDB: 3VAA_C 1KO8_B 1KO4_B 1KO1_A 1KOF_A 1KNQ_A 1KO5_A 1KAG_A 2PT5_D 1SHK_A ....

>cd03110 Fer4_NifH_child This protein family's function is unkown

Probab=90.51  E-value=0.17  Score=40.26  Aligned_cols=16  Identities=44%  Similarity=0.619  Sum_probs=14.5

Q ss_pred             CCCcHHHHHHHHHhhh
Q 041028            2 GGIGKTTLAKEVARKA   17 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~   17 (283)
                      ||+||||+|..++...
T Consensus         9 gG~GKSt~a~nLA~~l   24 (179)
T cd03110           9 GGTGKTTVTAALAALL   24 (179)
T ss_pred             CCCCHHHHHHHHHHHH
Confidence            8999999999988766

It contains nucleotide binding site. It uses NTP as energy source to transfer electron or ion.

>PRK05973 replicative DNA helicase; Provisional

Probab=90.48  E-value=0.7  Score=38.70  Aligned_cols=39  Identities=26%  Similarity=0.271  Sum_probs=26.0

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHH
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEI   44 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i   44 (283)
                      +|+|||+||.++......+  =..+++++....  ..++...+
T Consensus        73 PG~GKT~lalqfa~~~a~~--Ge~vlyfSlEes--~~~i~~R~  111 (237)
T PRK05973         73 PGHGKTLLGLELAVEAMKS--GRTGVFFTLEYT--EQDVRDRL  111 (237)
T ss_pred             CCCCHHHHHHHHHHHHHhc--CCeEEEEEEeCC--HHHHHHHH
Confidence            7999999999987665432  235677776655  44555553

>PRK06921 hypothetical protein; Provisional

Probab=90.46  E-value=1.1  Score=38.28  Aligned_cols=29  Identities=24%  Similarity=0.243  Sum_probs=20.8

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEe
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEV   31 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v   31 (283)
                      .|+|||+||.++++....+. -..++|++.
T Consensus       126 ~G~GKThLa~aia~~l~~~~-g~~v~y~~~  154 (266)
T PRK06921        126 PGSGKTHLLTAAANELMRKK-GVPVLYFPF  154 (266)
T ss_pred             CCCcHHHHHHHHHHHHhhhc-CceEEEEEH
Confidence            59999999999999865331 234566664

>PRK08727 hypothetical protein; Validated

Probab=90.45  E-value=0.21  Score=41.71  Aligned_cols=29  Identities=24%  Similarity=0.314  Sum_probs=21.5

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVS   32 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~   32 (283)
                      .|+|||+|++++++.....  ...+.|+++.
T Consensus        50 ~G~GKThL~~a~~~~~~~~--~~~~~y~~~~   78 (233)
T PRK08727         50 AGTGKTHLALALCAAAEQA--GRSSAYLPLQ   78 (233)
T ss_pred             CCCCHHHHHHHHHHHHHHc--CCcEEEEeHH
Confidence            5999999999999986544  3355667643

>cd01124 KaiC KaiC is a circadian clock protein primarily found in cyanobacteria KaiC is a RecA-like ATPase, having both Walker A and Walker B motifs

Probab=90.44  E-value=0.35  Score=38.50  Aligned_cols=38  Identities=16%  Similarity=0.195  Sum_probs=25.4

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHH
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGE   43 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~   43 (283)
                      +|+|||+||.++.......  =..++|++....  ..++.+.
T Consensus         8 ~G~GKT~l~~~~~~~~~~~--g~~v~~~s~e~~--~~~~~~~   45 (187)
T cd01124           8 PGTGKTTFALQFLYAGLAR--GEPGLYVTLEES--PEELIEN   45 (187)
T ss_pred             CCCCHHHHHHHHHHHHHHC--CCcEEEEECCCC--HHHHHHH
Confidence            6999999999987765422  145778877554  4444443

A related protein is found in archaea.

>PRK13948 shikimate kinase; Provisional

Probab=90.43  E-value=0.19  Score=40.26  Aligned_cols=18  Identities=28%  Similarity=0.431  Sum_probs=16.0

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      |.|+||||+++.+.+...
T Consensus        18 ~~GsGKSTvg~~La~~lg   35 (182)
T PRK13948         18 FMGTGKSRIGWELSRALM   35 (182)
T ss_pred             CCCCCHHHHHHHHHHHcC
Confidence            679999999999998764

>cd02024 NRK1 Nicotinamide riboside kinase (NRK) is an enzyme involved in the metabolism of nicotinamide adenine dinucleotide (NAD+)

Probab=90.42  E-value=0.19  Score=40.51  Aligned_cols=16  Identities=50%  Similarity=0.461  Sum_probs=14.5

Q ss_pred             CCCcHHHHHHHHHhhh
Q 041028            2 GGIGKTTLAKEVARKA   17 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~   17 (283)
                      +|+||||||+.+....
T Consensus         8 sgsGKTtla~~l~~~~   23 (187)
T cd02024           8 TNSGKTTLAKLLQRIL   23 (187)
T ss_pred             CCCCHHHHHHHHHHHc
Confidence            6999999999999875

This enzyme catalyzes the phosphorylation of nicotinamide riboside (NR) to form nicotinamide mononucleotide (NMN). It defines the NR salvage pathway of NAD+ biosynthesis in addition to the pathways through nicotinic acid mononucleotide (NaMN). This enzyme can also phosphorylate the anticancer drug tiazofurin, which is an analog of nicotinamide riboside.

>PRK06696 uridine kinase; Validated

Probab=90.39  E-value=0.18  Score=41.72  Aligned_cols=18  Identities=44%  Similarity=0.554  Sum_probs=15.7

Q ss_pred             CCCcHHHHHHHHHhhhcc
Q 041028            2 GGIGKTTLAKEVARKAKN   19 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~   19 (283)
                      +|+||||||+.+......
T Consensus        31 sgsGKSTlA~~L~~~l~~   48 (223)
T PRK06696         31 TASGKTTFADELAEEIKK   48 (223)
T ss_pred             CCCCHHHHHHHHHHHHHH
Confidence            699999999999987653

>cd00464 SK Shikimate kinase (SK) is the fifth enzyme in the shikimate pathway, a seven-step biosynthetic pathway which converts erythrose-4-phosphate to chorismic acid, found in bacteria, fungi and plants

Probab=90.36  E-value=0.21  Score=38.43  Aligned_cols=18  Identities=39%  Similarity=0.516  Sum_probs=15.7

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      ++|+||||+|+.+.....
T Consensus         7 ~~GsGKstla~~la~~l~   24 (154)
T cd00464           7 MMGAGKTTVGRLLAKALG   24 (154)
T ss_pred             CCCCCHHHHHHHHHHHhC
Confidence            579999999999988764

Chorismic acid is a important intermediate in the synthesis of aromatic compounds, such as aromatic amino acids, p-aminobenzoic acid, folate and ubiquinone. Shikimate kinase catalyses the phosphorylation of the 3-hydroxyl group of shikimic acid using ATP.

>PF00308 Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013317 This entry represents the central domain of bacterial DnaA proteins [, , ] that play an important role in initiating and regulating chromosomal replication

Probab=90.35  E-value=0.93  Score=37.47  Aligned_cols=62  Identities=27%  Similarity=0.338  Sum_probs=37.4

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCcCCHhhhHHhHHHHccCCcEEEEc
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKLGLKFDEESESGRTRSPWSRLKKEKLQIIC   77 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~kr~LlV~   77 (283)
                      .|+|||.|.+++++.......=..+++++      ..+....+...+..        .....+++.+++-.+|+|+
T Consensus        43 ~G~GKTHLL~Ai~~~~~~~~~~~~v~y~~------~~~f~~~~~~~~~~--------~~~~~~~~~~~~~DlL~iD  104 (219)
T PF00308_consen   43 SGLGKTHLLQAIANEAQKQHPGKRVVYLS------AEEFIREFADALRD--------GEIEEFKDRLRSADLLIID  104 (219)
T ss_dssp             TTSSHHHHHHHHHHHHHHHCTTS-EEEEE------HHHHHHHHHHHHHT--------TSHHHHHHHHCTSSEEEEE
T ss_pred             CCCCHHHHHHHHHHHHHhccccccceeec------HHHHHHHHHHHHHc--------ccchhhhhhhhcCCEEEEe
Confidence            59999999999999865431112355554      44555555554432        1234566666677777774

DnaA is an ATP- and DNA-binding protein. It binds specifically to 9 bp nucleotide repeats known as dnaA boxes which are found in the chromosome origin of replication (oriC). DnaA is a protein of about 50 kDa that contains two conserved regions: the first is located in the N-terminal half and corresponds to the ATP-binding domain, the second is located in the C-terminal half and could be involved in DNA-binding. The protein may also bind the RNA polymerase beta subunit, the dnaB and dnaZ proteins, and the groE gene products (chaperonins) [].; PDB: 2KJQ_A 2Z4S_A 2Z4R_C 2HCB_B 3R8F_C 1L8Q_A 3SC3_B 3BOS_A.

>PRK05564 DNA polymerase III subunit delta'; Validated

Probab=90.34  E-value=1.1  Score=39.13  Aligned_cols=47  Identities=32%  Similarity=0.454  Sum_probs=31.0

Q ss_pred             CCCcHHHHHHHHHhhhcc----CCCCCeEEEEEe-CCCCCHHHHHHHHHHHhC
Q 041028            2 GGIGKTTLAKEVARKAKN----GKLFDQIVFTEV-SQNPNIKKIQGEIAFKLG   49 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~----~~~Fd~~~wv~v-~~~~~~~~l~~~i~~~l~   49 (283)
                      .|+||||+|+.++...-.    ..|+|...|... +....+.++ +++...+.
T Consensus        35 ~G~Gk~~la~~~a~~l~c~~~~~~h~D~~~~~~~~~~~i~v~~i-r~~~~~~~   86 (313)
T PRK05564         35 DGIGKSLLAKEIALKILGKSQQREYVDIIEFKPINKKSIGVDDI-RNIIEEVN   86 (313)
T ss_pred             CCCCHHHHHHHHHHHHcCCCCCCCCCCeEEeccccCCCCCHHHH-HHHHHHHh
Confidence            599999999999986422    346687777663 444555554 45555543

>cd01672 TMPK Thymidine monophosphate kinase (TMPK), also known as thymidylate kinase, catalyzes the phosphorylation of thymidine monophosphate (TMP) to thymidine diphosphate (TDP) utilizing ATP as its preferred phophoryl donor

Probab=90.33  E-value=0.72  Score=36.91  Aligned_cols=18  Identities=39%  Similarity=0.543  Sum_probs=15.7

Q ss_pred             CCCcHHHHHHHHHhhhcc
Q 041028            2 GGIGKTTLAKEVARKAKN   19 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~   19 (283)
                      .|+||||+++.+++....
T Consensus         9 ~GsGKtT~~~~L~~~l~~   26 (200)
T cd01672           9 DGAGKTTLIELLAERLEA   26 (200)
T ss_pred             CCCCHHHHHHHHHHHHHH
Confidence            599999999999988753

TMPK represents the rate-limiting step in either de novo or salvage biosynthesis of thymidine triphosphate (TTP).

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=90.26  E-value=0.93  Score=41.84  Aligned_cols=30  Identities=20%  Similarity=0.204  Sum_probs=19.8

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEe
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEV   31 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v   31 (283)
                      .|+|||+|++++++.......=-.+++++.
T Consensus       150 ~G~GKTHLl~Ai~~~l~~~~~~~~v~yv~~  179 (450)
T PRK14087        150 SGMGKTHLLKAAKNYIESNFSDLKVSYMSG  179 (450)
T ss_pred             CCCcHHHHHHHHHHHHHHhCCCCeEEEEEH
Confidence            599999999999996543211123455543

>PRK08939 primosomal protein DnaI; Reviewed

Probab=90.23  E-value=1  Score=39.25  Aligned_cols=60  Identities=13%  Similarity=0.154  Sum_probs=37.6

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCcCCHhhhHHhHHHHccCCcEEEEc
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKLGLKFDEESESGRTRSPWSRLKKEKLQIIC   77 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~kr~LlV~   77 (283)
                      .|+|||.||.++++..... .+. +.++++      .+++.++-...+..    +    .....+.+..-.+|+++
T Consensus       165 ~G~GKThLa~Aia~~l~~~-g~~-v~~~~~------~~l~~~lk~~~~~~----~----~~~~l~~l~~~dlLiID  224 (306)
T PRK08939        165 FGVGKSYLLAAIANELAKK-GVS-STLLHF------PEFIRELKNSISDG----S----VKEKIDAVKEAPVLMLD  224 (306)
T ss_pred             CCCCHHHHHHHHHHHHHHc-CCC-EEEEEH------HHHHHHHHHHHhcC----c----HHHHHHHhcCCCEEEEe
Confidence            5999999999999997643 233 455544      35556665554321    1    22334456777889883

>PLN03186 DNA repair protein RAD51 homolog; Provisional

Probab=90.14  E-value=0.6  Score=41.38  Aligned_cols=49  Identities=16%  Similarity=0.171  Sum_probs=34.8

Q ss_pred             CCCcHHHHHHHHHhhhccC---C-CCCeEEEEEeCCCCCHHHHHHHHHHHhCCC
Q 041028            2 GGIGKTTLAKEVARKAKNG---K-LFDQIVFTEVSQNPNIKKIQGEIAFKLGLK   51 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~---~-~Fd~~~wv~v~~~~~~~~l~~~i~~~l~~~   51 (283)
                      +|+|||+||..++-.....   + .-..++|++....|++..+ .+|++.++..
T Consensus       132 ~g~GKT~l~~~l~~~~~~~~~~gg~~g~vlyIdtE~~f~~eRl-~qia~~~~~~  184 (342)
T PLN03186        132 FRTGKTQLCHTLCVTCQLPLDQGGGEGKAMYIDTEGTFRPQRL-IQIAERFGLN  184 (342)
T ss_pred             CCCCccHHHHHHHHHhhcchhhCCCCceEEEEECCCCccHHHH-HHHHHHcCCC
Confidence            6999999999887543211   1 1136899999999988776 5667777653

>cd02117 NifH_like This family contains the NifH (iron protein) of nitrogenase, L subunit (BchL/ChlL) of the protochlorophyllide reductase and the BchX subunit of the Chlorophyllide reductase

Probab=90.11  E-value=0.21  Score=40.93  Aligned_cols=19  Identities=32%  Similarity=0.543  Sum_probs=15.7

Q ss_pred             CCCcHHHHHHHHHhhhccC
Q 041028            2 GGIGKTTLAKEVARKAKNG   20 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~   20 (283)
                      |||||||++..++.-....
T Consensus         9 GGvGKTt~~~nLA~~la~~   27 (212)
T cd02117           9 GGIGKSTTSQNLSAALAEM   27 (212)
T ss_pred             CcCcHHHHHHHHHHHHHHC
Confidence            8999999999988876543

Members of this family use energey from ATP hydrolysis and transfer electrons through a Fe4-S4 cluster to other subunit for reduction of substrate.

>PRK00889 adenylylsulfate kinase; Provisional

Probab=90.06  E-value=0.22  Score=39.42  Aligned_cols=19  Identities=42%  Similarity=0.735  Sum_probs=16.2

Q ss_pred             CCCCcHHHHHHHHHhhhcc
Q 041028            1 MGGIGKTTLAKEVARKAKN   19 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~   19 (283)
                      ++|+||||+|+.++.....
T Consensus        12 ~~GsGKST~a~~la~~l~~   30 (175)
T PRK00889         12 LSGAGKTTIARALAEKLRE   30 (175)
T ss_pred             CCCCCHHHHHHHHHHHHHH
Confidence            4799999999999987653

>TIGR01313 therm_gnt_kin carbohydrate kinase, thermoresistant glucokinase family

Probab=90.05  E-value=0.22  Score=38.86  Aligned_cols=16  Identities=38%  Similarity=0.640  Sum_probs=14.4

Q ss_pred             CCCcHHHHHHHHHhhh
Q 041028            2 GGIGKTTLAKEVARKA   17 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~   17 (283)
                      +|+||||+|+.+.+..
T Consensus         7 ~GsGKSTla~~l~~~l   22 (163)
T TIGR01313         7 AGSGKSTIASALAHRL   22 (163)
T ss_pred             CCCCHHHHHHHHHHhc
Confidence            6999999999999865

This model represents a subfamily of proteins that includes thermoresistant and thermosensitve isozymes of gluconate kinase (gluconokinase) in E. coli and other related proteins; members of this family are often named by similarity to the thermostable isozyme. These proteins show homology to shikimate kinases and adenylate kinases but not to gluconate kinases from the FGGY family of carbohydrate kinases.

>PF08423 Rad51: Rad51; InterPro: IPR013632 This domain is found at the C terminus of the DNA repair and recombination protein Rad51

Probab=90.04  E-value=0.59  Score=39.68  Aligned_cols=47  Identities=23%  Similarity=0.374  Sum_probs=32.7

Q ss_pred             CCCcHHHHHHHHHhhhccC---CCC-CeEEEEEeCCCCCHHHHHHHHHHHhC
Q 041028            2 GGIGKTTLAKEVARKAKNG---KLF-DQIVFTEVSQNPNIKKIQGEIAFKLG   49 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~---~~F-d~~~wv~v~~~~~~~~l~~~i~~~l~   49 (283)
                      +|+|||.|+..++-.....   +.. ..++|++-...|+...+. +|++..+
T Consensus        47 ~gsGKTql~l~l~~~~~l~~~~~g~~~~vvyidTe~~f~~~Rl~-~i~~~~~   97 (256)
T PF08423_consen   47 SGSGKTQLCLQLAVNVQLPEEIGGLGGKVVYIDTEGTFSPERLQ-QIAERFG   97 (256)
T ss_dssp             TTSSHHHHHHHHHHHTTSGGCTTSSSSEEEEEESSSSS-HHHHH-HHHHHTT
T ss_pred             cccccchHHHHHHHHhhcccccccCCCceEEEeCCCCCCHHHHH-HHhhccc
Confidence            6999999999887553321   112 468999998889887774 5676654

It is critical for DNA binding []. Rad51 is a homologue of the bacterial RecA protein. Rad51 and RecA share a core ATPase domain.; PDB: 2ZUC_A 2Z43_C 2ZUD_B 2DFL_A 2ZUB_A 2BKE_A 2KZ3_A 2CVH_B 2CVF_B 1SZP_D ....

>TIGR02322 phosphon_PhnN phosphonate metabolism protein/1,5-bisphosphokinase (PRPP-forming) PhnN

Probab=90.03  E-value=0.22  Score=39.54  Aligned_cols=18  Identities=28%  Similarity=0.311  Sum_probs=15.2

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      +.|+|||||++.+.....
T Consensus         9 ~sGsGKttl~~~l~~~~~   26 (179)
T TIGR02322         9 PSGAGKDTLLDYARARLA   26 (179)
T ss_pred             CCCCCHHHHHHHHHHHcC
Confidence            479999999999988753

Members of this family resemble PhnN of phosphonate utilization operons, where different such operons confer the ability to use somewhat different profiles of C-P bond-containing compounds (see PubMed:15231805), including phosphites as well as phosphonates. PhnN in E. coli shows considerable homology to guanylate kinases (EC 2.7.4.8), and has actually been shown to act as a ribose 1,5-bisphosphokinase (PRPP forming). This suggests an analogous kinase reaction for phosphonate metabolism, converting 5-phosphoalpha-1-(methylphosphono)ribose to methylphosphono-PRPP.

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=89.97  E-value=0.2  Score=42.53  Aligned_cols=16  Identities=38%  Similarity=0.501  Sum_probs=14.4

Q ss_pred             CCCcHHHHHHHHHhhh
Q 041028            2 GGIGKTTLAKEVARKA   17 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~   17 (283)
                      +|+||||+|+.+++..
T Consensus        51 pGtGKTtlA~~ia~~l   66 (261)
T TIGR02881        51 PGTGKTTVARILGKLF   66 (261)
T ss_pred             CCCCHHHHHHHHHHHH
Confidence            7999999999998864

Members of this protein family are the stage V sporulation protein K (SpoVK), a close homolog of the Rubisco expression protein CbbX (TIGR02880) and a members of the ATPase family associated with various cellular activities (pfam00004). Members are strictly limited to bacterial endospore-forming species, but are not universal in this group and are missing from the Clostridium group.

>PF02223 Thymidylate_kin: Thymidylate kinase; InterPro: IPR018094 Thymidylate kinase (2

Probab=89.94  E-value=0.47  Score=37.92  Aligned_cols=42  Identities=24%  Similarity=0.261  Sum_probs=27.1

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCC-CCCHHHHHHHHHH
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQ-NPNIKKIQGEIAF   46 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~-~~~~~~l~~~i~~   46 (283)
                      -|+||||+++.+++.....+. .  +.++... .....+.+++++.
T Consensus         5 DGsGKtT~~~~L~~~l~~~~~-~--~~~~~~~~~~~~g~~ir~~l~   47 (186)
T PF02223_consen    5 DGSGKTTQIRLLAEALKEKGY-K--VIITFPPGSTPIGELIRELLR   47 (186)
T ss_dssp             TTSSHHHHHHHHHHHHHHTTE-E--EEEEESSTSSHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHcCC-c--ccccCCCCCChHHHHHHHHHh
Confidence            599999999999999876522 2  2233322 2334566666666

7.4.9 from EC; dTMP kinase) catalyzes the phosphorylation of thymidine 5'-monophosphate (dTMP) to form thymidine 5'-diphosphate (dTDP) in the presence of ATP and magnesium: ATP + thymidine 5'-phosphate = ADP + thymidine 5'-diphosphate Thymidylate kinase is an ubiquitous enzyme of about 25 Kd and is important in the dTTP synthesis pathway for DNA synthesis. The function of dTMP kinase in eukaryotes comes from the study of a cell cycle mutant, cdc8, in Saccharomyces cerevisiae. Structural and functional analyses suggest that the cDNA codes for authentic human dTMP kinase. The mRNA levels and enzyme activities corresponded to cell cycle progression and cell growth stages[]. ; GO: 0004798 thymidylate kinase activity, 0005524 ATP binding, 0006233 dTDP biosynthetic process; PDB: 2PLR_B 1NMX_A 1NN0_A 2XX3_A 1NN3_A 1E9F_A 1E2Q_A 1E2D_A 1E9A_A 1E99_A ....

>PF06564 YhjQ: YhjQ protein; InterPro: IPR017746 The YhjQ protein is encoded immediately upstream of bacterial cellulose synthase (bcs) genes in a broad range of bacteria, including both copies of the bcs locus in Klebsiella pneumoniae, and in several species is clearly part of the bcs operon

Probab=89.85  E-value=0.24  Score=41.57  Aligned_cols=28  Identities=29%  Similarity=0.424  Sum_probs=20.5

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEe
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEV   31 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v   31 (283)
                      ||+|||||+..++.-....+.  .++=|+.
T Consensus        11 GGvG~TTltAnLA~aL~~~G~--~VlaID~   38 (243)
T PF06564_consen   11 GGVGKTTLTANLAWALARLGE--SVLAIDL   38 (243)
T ss_pred             CCCCHHHHHHHHHHHHHHCCC--cEEEEeC
Confidence            899999999999987665432  3554554

It is identified as a probable component of the bacterial cellulose metabolic process not only by gene location, but also by partial phylogenetic profiling, or Haft-Selengut algorithm [], based on a bacterial cellulose biosynthesis genome property profile. Cellulose plays an important role in biofilm formation and structural integrity in some bacteria. Mutants in yhjQ in Escherichia coli, show altered morphology an growth, but the function of YhjQ has not yet been determined.

>PF13481 AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C

Probab=89.82  E-value=0.9  Score=36.36  Aligned_cols=42  Identities=26%  Similarity=0.472  Sum_probs=25.5

Q ss_pred             CCCcHHHHHHHHHhhhccCCCC--------CeEEEEEeCCCCCHHHHHHHHH
Q 041028            2 GGIGKTTLAKEVARKAKNGKLF--------DQIVFTEVSQNPNIKKIQGEIA   45 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~F--------d~~~wv~v~~~~~~~~l~~~i~   45 (283)
                      +|+||||++..+.........|        ..++|++...+  ..++.+.+.
T Consensus        41 ~g~GKT~~~~~l~~~~~~g~~~~g~~~~~~~~Vl~i~~E~~--~~~~~~rl~   90 (193)
T PF13481_consen   41 PGSGKTTLALQLAAALATGRPFLGELPPRPGRVLYISLEDS--ESQIARRLR   90 (193)
T ss_dssp             STSSHHHHHHHHHHHHHT---TT---------EEEEESSS---HHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHhCCccCCcccccCceEEEEeccCC--HHHHHHHHH
Confidence            7999999999998876543223        25788887766  333444443

>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]

Probab=89.80  E-value=0.86  Score=40.97  Aligned_cols=45  Identities=29%  Similarity=0.385  Sum_probs=32.0

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKLGLKF   52 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~~l~~~~   52 (283)
                      +|||||||..+++.+...+.   .+++|+-.+...-..+   -++.|+.+.
T Consensus       102 PGIGKSTLLLQva~~lA~~~---~vLYVsGEES~~Qikl---RA~RL~~~~  146 (456)
T COG1066         102 PGIGKSTLLLQVAARLAKRG---KVLYVSGEESLQQIKL---RADRLGLPT  146 (456)
T ss_pred             CCCCHHHHHHHHHHHHHhcC---cEEEEeCCcCHHHHHH---HHHHhCCCc
Confidence            69999999999999876553   6788877666444333   345676544

>TIGR03371 cellulose_yhjQ cellulose synthase operon protein YhjQ

Probab=89.79  E-value=0.24  Score=41.46  Aligned_cols=30  Identities=30%  Similarity=0.401  Sum_probs=21.3

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQ   33 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~   33 (283)
                      ||+||||+|..++......+ + .++-|+...
T Consensus        11 GGvGKTt~a~nla~~la~~g-~-~VlliD~D~   40 (246)
T TIGR03371        11 GGVGKTTLTANLASALKLLG-E-PVLAIDLDP   40 (246)
T ss_pred             CCccHHHHHHHHHHHHHhCC-C-cEEEEeCCC
Confidence            89999999999988765332 1 355666543

Members of this family are the YhjQ protein, found immediately upsteam of bacterial cellulose synthase (bcs) genes in a broad range of bacteria, including both copies of the bcs locus in Klebsiella pneumoniae. In several species it is seen clearly as part of the bcs operon. It is identified as a probable component of the bacterial cellulose metabolic process not only by gene location, but also by partial phylogenetic profiling, or Haft-Selengut algorithm (PubMed:16930487), based on a bacterial cellulose biosynthesis genome property profile. Cellulose plays an important role in biofilm formation and structural integrity in some bacteria. Mutants in yhjQ in Escherichia coli, show altered morphology an growth, but the function of YhjQ has not yet been determined.

>TIGR00150 HI0065_YjeE ATPase, YjeE family

Probab=89.78  E-value=0.25  Score=37.40  Aligned_cols=18  Identities=33%  Similarity=0.314  Sum_probs=15.4

Q ss_pred             CCCcHHHHHHHHHhhhcc
Q 041028            2 GGIGKTTLAKEVARKAKN   19 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~   19 (283)
                      -|.|||||++.+++....
T Consensus        31 lGaGKTtl~~~l~~~lg~   48 (133)
T TIGR00150        31 LGAGKTTLVQGLLQGLGI   48 (133)
T ss_pred             CCCCHHHHHHHHHHHcCC
Confidence            499999999999997654

Members of this family have a conserved nucleotide-binding motif GXXGXGKT and a nucleotide-binding fold. Member protein YjeE of Haemophilus influenzae (HI0065) was shown to have ATPase activity.

>TIGR00959 ffh signal recognition particle protein

Probab=89.77  E-value=1.5  Score=40.08  Aligned_cols=74  Identities=16%  Similarity=0.109  Sum_probs=39.1

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCC-CCCHHHHHHHHHHHhCCCCC----cCCHhhhHHh-HHHHc-cCCcEE
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQ-NPNIKKIQGEIAFKLGLKFD----EESESGRTRS-PWSRL-KKEKLQ   74 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~-~~~~~~l~~~i~~~l~~~~~----~~~~~~~~~~-l~~~L-~~kr~L   74 (283)
                      +|+||||.|..++.....+..+ .+.-|+... .+...+-+......++.+.-    ..+..+.... +.... .+..++
T Consensus       108 ~GsGKTTtaakLA~~l~~~~g~-kV~lV~~D~~R~~a~~QL~~~a~~~gvp~~~~~~~~~P~~i~~~al~~~~~~~~DvV  186 (428)
T TIGR00959       108 QGSGKTTTCGKLAYYLKKKQGK-KVLLVACDLYRPAAIEQLKVLGQQVGVPVFALGKGQSPVEIARRALEYAKENGFDVV  186 (428)
T ss_pred             CCCcHHHHHHHHHHHHHHhCCC-eEEEEeccccchHHHHHHHHHHHhcCCceEecCCCCCHHHHHHHHHHHHHhcCCCEE
Confidence            6999999999988775422112 334444432 22334455666777776522    1233333332 33322 233577


Q ss_pred             EE
Q 041028           75 II   76 (283)
Q Consensus        75 lV   76 (283)
                      ||
T Consensus       187 II  188 (428)
T TIGR00959       187 IV  188 (428)
T ss_pred             EE
Confidence            77

This model represents Ffh (Fifty-Four Homolog), the protein component that forms the bacterial (and organellar) signal recognition particle together with a 4.5S RNA. Ffh is a GTPase homologous to eukaryotic SRP54 and also to the GTPase FtsY (TIGR00064) that is the receptor for the signal recognition particle.

>PF08303 tRNA_lig_kinase: tRNA ligase kinase domain; InterPro: IPR015966 This entry represents a kinase domain found in fungal tRNA ligases []

Probab=89.76  E-value=0.21  Score=39.02  Aligned_cols=38  Identities=26%  Similarity=0.301  Sum_probs=25.7

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEe-----CCCCCHHHHHHHHHHHh
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEV-----SQNPNIKKIQGEIAFKL   48 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v-----~~~~~~~~l~~~i~~~l   48 (283)
                      -|.||||+|.++.+-      |..  |-.+     +.. ....+.+.+++.|
T Consensus         8 iGCGKTTva~aL~~L------Fg~--wgHvQnDnI~~k-~~~~f~~~~l~~L   50 (168)
T PF08303_consen    8 IGCGKTTVALALSNL------FGE--WGHVQNDNITGK-RKPKFIKAVLELL   50 (168)
T ss_pred             CCcCHHHHHHHHHHH------cCC--CCccccCCCCCC-CHHHHHHHHHHHH
Confidence            499999999999874      432  4433     233 5666777777777

Please see the following relevant references: [, ].; GO: 0003972 RNA ligase (ATP) activity, 0005524 ATP binding, 0006388 tRNA splicing, via endonucleolytic cleavage and ligation

>COG4088 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=89.73  E-value=0.2  Score=40.73  Aligned_cols=20  Identities=45%  Similarity=0.642  Sum_probs=16.8

Q ss_pred             CCCCcHHHHHHHHHhhhccC
Q 041028            1 MGGIGKTTLAKEVARKAKNG   20 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~   20 (283)
                      .+|+||||+|++++...+.+
T Consensus         9 yPgsGKTtfakeLak~L~~~   28 (261)
T COG4088           9 YPGSGKTTFAKELAKELRQE   28 (261)
T ss_pred             CCCCCchHHHHHHHHHHHHh
Confidence            37999999999999876644

>CHL00181 cbbX CbbX; Provisional

Probab=89.73  E-value=0.31  Score=42.11  Aligned_cols=17  Identities=41%  Similarity=0.409  Sum_probs=14.8

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      +|+||||+|+.+++...
T Consensus        68 pGtGKT~lAr~la~~~~   84 (287)
T CHL00181         68 PGTGKTTVALKMADILY   84 (287)
T ss_pred             CCCCHHHHHHHHHHHHH
Confidence            69999999999988643

>TIGR00235 udk uridine kinase

Probab=89.72  E-value=0.23  Score=40.61  Aligned_cols=17  Identities=35%  Similarity=0.562  Sum_probs=14.8

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      +|+||||||+.+.....
T Consensus        15 sGsGKSTl~~~l~~~l~   31 (207)
T TIGR00235        15 SGSGKTTVARKIYEQLG   31 (207)
T ss_pred             CCCCHHHHHHHHHHHhc
Confidence            69999999999998654

Model contains a number of longer eukaryotic proteins and starts bringing in phosphoribulokinase hits at scores of 160 and below

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=89.68  E-value=0.23  Score=41.19  Aligned_cols=17  Identities=24%  Similarity=0.479  Sum_probs=15.1

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      .|+|||+||+.+++...
T Consensus        51 ~G~GKT~La~ai~~~~~   67 (227)
T PRK08903         51 AGSGRSHLLQALVADAS   67 (227)
T ss_pred             CCCCHHHHHHHHHHHHH
Confidence            59999999999999763

>TIGR03453 partition_RepA plasmid partitioning protein RepA

Probab=89.65  E-value=0.48  Score=42.80  Aligned_cols=35  Identities=23%  Similarity=0.357  Sum_probs=23.7

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHH
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIK   38 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~   38 (283)
                      ||+||||+|..++......++  .++-|+.....++.
T Consensus       114 GGvGKTT~a~nLA~~La~~G~--rVLlID~DpQ~~ls  148 (387)
T TIGR03453       114 GGSGKTTTAAHLAQYLALRGY--RVLAIDLDPQASLS  148 (387)
T ss_pred             CCcCHHHHHHHHHHHHHhcCC--CEEEEecCCCCCHH
Confidence            899999999999887654321  35566665444433

Members of this family are the RepA (or ParA) protein involved in replicon partitioning. All known examples occur in bacterial species with two or more replicons, on a plasmid or the smaller chromosome. Note that an apparent exception may be seen as a pseudomolecule from assembly of an incompletely sequenced genome. Members of this family belong to a larger family that also includes the enzyme cobyrinic acid a,c-diamide synthase, but assignment of that name to members of this family would be in error.

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=89.64  E-value=1.4  Score=40.63  Aligned_cols=28  Identities=21%  Similarity=0.367  Sum_probs=20.3

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEe
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEV   31 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v   31 (283)
                      .|+|||+|++++++.....  --.+++++.
T Consensus       150 ~G~GKTHLl~Ai~~~l~~~--~~~v~yi~~  177 (445)
T PRK12422        150 EGSGKTHLMQAAVHALRES--GGKILYVRS  177 (445)
T ss_pred             CCCCHHHHHHHHHHHHHHc--CCCEEEeeH
Confidence            6999999999999987543  233456553

>PRK14532 adenylate kinase; Provisional

Probab=89.59  E-value=0.25  Score=39.64  Aligned_cols=17  Identities=29%  Similarity=0.280  Sum_probs=14.8

Q ss_pred             CCCCcHHHHHHHHHhhh
Q 041028            1 MGGIGKTTLAKEVARKA   17 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (283)
                      ++|+||||+|+.++...
T Consensus         8 ~pGsGKsT~a~~la~~~   24 (188)
T PRK14532          8 PPAAGKGTQAKRLVEER   24 (188)
T ss_pred             CCCCCHHHHHHHHHHHc
Confidence            47999999999998755

>PRK12339 2-phosphoglycerate kinase; Provisional

Probab=89.59  E-value=0.25  Score=40.17  Aligned_cols=17  Identities=35%  Similarity=0.681  Sum_probs=15.1

Q ss_pred             CCCCcHHHHHHHHHhhh
Q 041028            1 MGGIGKTTLAKEVARKA   17 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (283)
                      .+|+||||+|+.++.+.
T Consensus        11 ~~G~GKst~a~~l~~~~   27 (197)
T PRK12339         11 IPGVGKTSISGYIARHR   27 (197)
T ss_pred             CCCCCHHHHHHHHHHhc
Confidence            47999999999999874

>PRK03731 aroL shikimate kinase II; Reviewed

Probab=89.59  E-value=0.26  Score=38.83  Aligned_cols=18  Identities=33%  Similarity=0.418  Sum_probs=15.9

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      |.|+||||+|+.+.+...
T Consensus        10 ~~GsGKst~~~~la~~lg   27 (171)
T PRK03731         10 ARGCGKTTVGMALAQALG   27 (171)
T ss_pred             CCCCCHHHHHHHHHHHhC
Confidence            579999999999998764

>TIGR03574 selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal

Probab=89.54  E-value=0.24  Score=41.70  Aligned_cols=19  Identities=42%  Similarity=0.781  Sum_probs=16.2

Q ss_pred             CCCCcHHHHHHHHHhhhcc
Q 041028            1 MGGIGKTTLAKEVARKAKN   19 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~   19 (283)
                      ++|+||||+|+.+......
T Consensus         7 ~pGSGKST~a~~La~~l~~   25 (249)
T TIGR03574         7 LPGVGKSTFSKELAKKLSE   25 (249)
T ss_pred             CCCCCHHHHHHHHHHHHHH
Confidence            4799999999999987653

Members of this protein are L-seryl-tRNA(Sec) kinase. This enzyme is part of a two-step pathway in Eukaryota and Archaea for performing selenocysteine biosynthesis by changing serine misacylated on selenocysteine-tRNA to selenocysteine. This enzyme performs the first step, phosphorylation of the OH group of the serine side chain. This family represents archaeal proteins with this activity.

>PRK10646 ADP-binding protein; Provisional

Probab=89.47  E-value=0.23  Score=38.49  Aligned_cols=18  Identities=28%  Similarity=0.436  Sum_probs=15.5

Q ss_pred             CCcHHHHHHHHHhhhccC
Q 041028            3 GIGKTTLAKEVARKAKNG   20 (283)
Q Consensus         3 GiGKTtLA~~v~~~~~~~   20 (283)
                      |.|||||++.++....+.
T Consensus        38 GaGKTtf~rgl~~~Lg~~   55 (153)
T PRK10646         38 GAGKTTFSRGFLQALGHQ   55 (153)
T ss_pred             CCCHHHHHHHHHHHcCCC
Confidence            899999999999976543

>PRK08084 DNA replication initiation factor; Provisional

Probab=89.41  E-value=0.39  Score=40.14  Aligned_cols=30  Identities=10%  Similarity=0.237  Sum_probs=22.3

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQ   33 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~   33 (283)
                      .|+|||+|++.+++.....  -..+.++++..
T Consensus        54 ~G~GKThLl~a~~~~~~~~--~~~v~y~~~~~   83 (235)
T PRK08084         54 EGAGRSHLLHAACAELSQR--GRAVGYVPLDK   83 (235)
T ss_pred             CCCCHHHHHHHHHHHHHhC--CCeEEEEEHHH
Confidence            6999999999999876543  23566777654

>cd02020 CMPK Cytidine monophosphate kinase (CMPK) catalyzes the reversible phosphorylation of cytidine monophosphate (CMP) to produce cytidine diphosphate (CDP), using ATP as the preferred phosphoryl donor

Probab=89.40  E-value=0.27  Score=37.34  Aligned_cols=18  Identities=44%  Similarity=0.540  Sum_probs=15.5

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      .+|+||||+|+.+.....
T Consensus         7 ~~GsGKst~a~~la~~~~   24 (147)
T cd02020           7 PAGSGKSTVAKLLAKKLG   24 (147)
T ss_pred             CCCCCHHHHHHHHHHHhC
Confidence            379999999999998754

>PRK05057 aroK shikimate kinase I; Reviewed

Probab=89.40  E-value=0.26  Score=39.04  Aligned_cols=18  Identities=28%  Similarity=0.523  Sum_probs=15.6

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      +.|+||||||+.+.+...
T Consensus        12 ~~GaGKStl~~~La~~l~   29 (172)
T PRK05057         12 PMGAGKSTIGRQLAQQLN   29 (172)
T ss_pred             CCCcCHHHHHHHHHHHcC
Confidence            579999999999998754

>TIGR01360 aden_kin_iso1 adenylate kinase, isozyme 1 subfamily

Probab=89.38  E-value=0.26  Score=39.27  Aligned_cols=17  Identities=29%  Similarity=0.331  Sum_probs=14.6

Q ss_pred             CCCCcHHHHHHHHHhhh
Q 041028            1 MGGIGKTTLAKEVARKA   17 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (283)
                      .+|+||||+|+.+....
T Consensus        11 ~~GsGKsTl~~~l~~~~   27 (188)
T TIGR01360        11 GPGSGKGTQCEKIVEKY   27 (188)
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            36999999999998764

Members of this family are adenylate kinase, EC 2.7.4.3. This clade is found only in eukaryotes and includes human adenylate kinase isozyme 1 (myokinase). Within the adenylate kinase superfamily, this set appears specifically closely related to a subfamily of eukaryotic UMP-CMP kinases (TIGR01359), rather than to the large clade of bacterial, archaeal, and eukaryotic adenylate kinase family members in TIGR01351.

>PF13521 AAA_28: AAA domain; PDB: 1LW7_A

Probab=89.37  E-value=0.24  Score=38.67  Aligned_cols=15  Identities=40%  Similarity=0.527  Sum_probs=13.6

Q ss_pred             CCCcHHHHHHHHHhh
Q 041028            2 GGIGKTTLAKEVARK   16 (283)
Q Consensus         2 gGiGKTtLA~~v~~~   16 (283)
                      .|+|||||++.+...
T Consensus         8 ~stGKTTL~~~L~~~   22 (163)
T PF13521_consen    8 PSTGKTTLIEALAAR   22 (163)
T ss_dssp             TTSHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHc
Confidence            489999999999986

>CHL00072 chlL photochlorophyllide reductase subunit L

Probab=89.37  E-value=0.26  Score=42.64  Aligned_cols=18  Identities=33%  Similarity=0.538  Sum_probs=15.4

Q ss_pred             CCCcHHHHHHHHHhhhcc
Q 041028            2 GGIGKTTLAKEVARKAKN   19 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~   19 (283)
                      |||||||+|..++.....
T Consensus         9 GGVGKTTta~nLA~~La~   26 (290)
T CHL00072          9 GGIGKSTTSCNISIALAR   26 (290)
T ss_pred             CCCcHHHHHHHHHHHHHH
Confidence            899999999998887653

>PRK13695 putative NTPase; Provisional

Probab=89.34  E-value=0.44  Score=37.67  Aligned_cols=27  Identities=33%  Similarity=0.359  Sum_probs=19.2

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEE
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFT   29 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv   29 (283)
                      +|+|||||++.+++..... .|....|+
T Consensus         9 ~G~GKTTll~~i~~~l~~~-G~~~~g~~   35 (174)
T PRK13695          9 PGVGKTTLVLKIAELLKEE-GYKVGGFY   35 (174)
T ss_pred             CCCCHHHHHHHHHHHHHHC-CCeEEEEE
Confidence            7999999999998876542 24444444

>PRK11545 gntK gluconate kinase 1; Provisional

Probab=89.34  E-value=0.27  Score=38.56  Aligned_cols=17  Identities=41%  Similarity=0.634  Sum_probs=15.0

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      +|.||||||+.++....
T Consensus         4 sGsGKSTla~~la~~l~   20 (163)
T PRK11545          4 SGSGKSAVASEVAHQLH   20 (163)
T ss_pred             CCCcHHHHHHHHHHHhC
Confidence            69999999999998763

>PRK14529 adenylate kinase; Provisional

Probab=89.33  E-value=0.84  Score=37.84  Aligned_cols=19  Identities=32%  Similarity=0.246  Sum_probs=16.4

Q ss_pred             CCCCcHHHHHHHHHhhhcc
Q 041028            1 MGGIGKTTLAKEVARKAKN   19 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~   19 (283)
                      .+|+||||+|+.++.....
T Consensus         8 ~PGsGK~T~a~~La~~~~~   26 (223)
T PRK14529          8 PNGSGKGTQGALVKKKYDL   26 (223)
T ss_pred             CCCCCHHHHHHHHHHHHCC
Confidence            4799999999999988764

>PRK05642 DNA replication initiation factor; Validated

Probab=89.19  E-value=0.43  Score=39.90  Aligned_cols=29  Identities=14%  Similarity=0.351  Sum_probs=21.5

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVS   32 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~   32 (283)
                      .|+|||.|++.+++....+  -..++|++..
T Consensus        54 ~G~GKTHLl~a~~~~~~~~--~~~v~y~~~~   82 (234)
T PRK05642         54 DGVGRSHLLQAACLRFEQR--GEPAVYLPLA   82 (234)
T ss_pred             CCCCHHHHHHHHHHHHHhC--CCcEEEeeHH
Confidence            5999999999999876533  2356777654

>PRK13869 plasmid-partitioning protein RepA; Provisional

Probab=89.18  E-value=0.52  Score=42.86  Aligned_cols=35  Identities=20%  Similarity=0.398  Sum_probs=23.2

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHH
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIK   38 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~   38 (283)
                      |||||||+|.+++......+ + .++-|+.....++.
T Consensus       131 GGvGKTTta~nLA~~LA~~G-~-rVLlIDlDpQ~~lt  165 (405)
T PRK13869        131 GGSGKTTTSAHLAQYLALQG-Y-RVLAVDLDPQASLS  165 (405)
T ss_pred             CCCCHHHHHHHHHHHHHhcC-C-ceEEEcCCCCCCHH
Confidence            89999999999988765432 2 34555655444433

>TIGR01968 minD_bact septum site-determining protein MinD

Probab=89.16  E-value=0.27  Score=41.41  Aligned_cols=18  Identities=33%  Similarity=0.580  Sum_probs=15.3

Q ss_pred             CCCcHHHHHHHHHhhhcc
Q 041028            2 GGIGKTTLAKEVARKAKN   19 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~   19 (283)
                      ||+||||+|..++.....
T Consensus        11 GGvGKTt~a~~lA~~la~   28 (261)
T TIGR01968        11 GGVGKTTTTANLGTALAR   28 (261)
T ss_pred             CCccHHHHHHHHHHHHHH
Confidence            899999999998876543

This model describes the bacterial and chloroplast form of MinD, a multifunctional cell division protein that guides correct placement of the septum. The homologous archaeal MinD proteins, with many archaeal genomes having two or more forms, are described by a separate model.

>cd00984 DnaB_C DnaB helicase C terminal domain

Probab=89.10  E-value=0.84  Score=38.07  Aligned_cols=43  Identities=14%  Similarity=0.253  Sum_probs=29.2

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHHH
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFK   47 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~~   47 (283)
                      +|+|||++|..++.+...... ..++|++...  +..++..+++..
T Consensus        22 ~G~GKT~~~~~~~~~~~~~~g-~~vly~s~E~--~~~~~~~r~~~~   64 (242)
T cd00984          22 PSMGKTAFALNIAENIAKKQG-KPVLFFSLEM--SKEQLLQRLLAS   64 (242)
T ss_pred             CCCCHHHHHHHHHHHHHHhCC-CceEEEeCCC--CHHHHHHHHHHH
Confidence            699999999998776544311 3567777655  455667776543

The hexameric helicase DnaB unwinds the DNA duplex at the chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis.

>PLN03025 replication factor C subunit; Provisional

Probab=89.07  E-value=0.67  Score=40.64  Aligned_cols=17  Identities=35%  Similarity=0.333  Sum_probs=15.2

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      +|+||||+|..+++...
T Consensus        43 ~G~GKTtla~~la~~l~   59 (319)
T PLN03025         43 PGTGKTTSILALAHELL   59 (319)
T ss_pred             CCCCHHHHHHHHHHHHh
Confidence            69999999999998864

>cd02023 UMPK Uridine monophosphate kinase (UMPK, EC 2

Probab=89.02  E-value=0.26  Score=39.84  Aligned_cols=16  Identities=44%  Similarity=0.667  Sum_probs=14.2

Q ss_pred             CCCcHHHHHHHHHhhh
Q 041028            2 GGIGKTTLAKEVARKA   17 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~   17 (283)
                      +|+||||||+.+....
T Consensus         8 ~GsGKSTl~~~l~~~l   23 (198)
T cd02023           8 SGSGKTTVAEEIIEQL   23 (198)
T ss_pred             CCCCHHHHHHHHHHHh
Confidence            6999999999998865

7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK), catalyzes the reversible phosphoryl transfer from ATP to uridine or cytidine to yield UMP or CMP. In the primidine nucleotide-salvage pathway, this enzyme combined with nucleoside diphosphate kinases further phosphorylates UMP and CMP to form UTP and CTP. This kinase also catalyzes the phosphorylation of several cytotoxic ribonucleoside analogs such as 5-flurrouridine and cyclopentenyl-cytidine.

>PRK07004 replicative DNA helicase; Provisional

Probab=89.01  E-value=2.5  Score=39.14  Aligned_cols=98  Identities=13%  Similarity=0.126  Sum_probs=52.5

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHHHhCC-CCC-----cCCHhh--hHHhHHHHccCCcE
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKLGL-KFD-----EESESG--RTRSPWSRLKKEKL   73 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~~l~~-~~~-----~~~~~~--~~~~l~~~L~~kr~   73 (283)
                      +|+|||++|..++.+....... .++|+  |-..+..++..+++...+. +..     ..+.++  ........+.+..+
T Consensus       222 pg~GKT~~al~ia~~~a~~~~~-~v~~f--SlEM~~~ql~~R~la~~~~v~~~~i~~g~l~~~e~~~~~~a~~~l~~~~l  298 (460)
T PRK07004        222 PSMGKTAFSMNIGEYVAVEYGL-PVAVF--SMEMPGTQLAMRMLGSVGRLDQHRMRTGRLTDEDWPKLTHAVQKMSEAQL  298 (460)
T ss_pred             CCCCccHHHHHHHHHHHHHcCC-eEEEE--eCCCCHHHHHHHHHHhhcCCCHHHHhcCCCCHHHHHHHHHHHHHHhcCCE
Confidence            6999999999988765433222 34454  4456677888888765432 111     112222  22233344555555


Q ss_pred             EEEcCeecCCCCCCCcchHHHHHHHHHhcCCchH
Q 041028           74 QIICGKKMEGDYAEGSELKWLAMDVAKECAGLPV  107 (283)
Q Consensus        74 LlV~G~~~~~~~~~~~~~~~~~~~i~~~c~glPL  107 (283)
                      .|.+.     ......++...++++.++++++.+
T Consensus       299 ~I~d~-----~~~~~~~i~~~~r~l~~~~~~~~l  327 (460)
T PRK07004        299 FIDET-----GGLNPMELRSRARRLARQCGKLGL  327 (460)
T ss_pred             EEECC-----CCCCHHHHHHHHHHHHHhCCCCCE
Confidence            54410     011223455666777777766654

>TIGR00041 DTMP_kinase thymidylate kinase

Probab=89.01  E-value=0.99  Score=36.23  Aligned_cols=19  Identities=32%  Similarity=0.407  Sum_probs=16.2

Q ss_pred             CCCcHHHHHHHHHhhhccC
Q 041028            2 GGIGKTTLAKEVARKAKNG   20 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~   20 (283)
                      .|+||||+|+.+++.....
T Consensus        12 ~GsGKsT~~~~L~~~l~~~   30 (195)
T TIGR00041        12 DGAGKTTQANLLKKLLQEN   30 (195)
T ss_pred             CCCCHHHHHHHHHHHHHHc
Confidence            5999999999999886643

Function: phosphorylation of DTMP to form DTDP in both de novo and salvage pathways of DTTP synthesis. Catalytic activity: ATP + thymidine 5'-phosphate = ADP + thymidine 5'-diphosphate.

>PRK09519 recA DNA recombination protein RecA; Reviewed

Probab=88.95  E-value=1.5  Score=43.09  Aligned_cols=70  Identities=19%  Similarity=0.196  Sum_probs=44.9

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCC------cCCHhhhHHhHHHHccCC--cE
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKLGLKFD------EESESGRTRSPWSRLKKE--KL   73 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~~l~~~~~------~~~~~~~~~~l~~~L~~k--r~   73 (283)
                      +|+||||||.+++......  =..++|++....++.     ..++++|.+.+      ..+.+.....+...++..  +.
T Consensus        69 ~GsGKTtLal~~~~~a~~~--G~~v~yId~E~t~~~-----~~A~~lGvDl~~llv~~~~~~E~~l~~i~~lv~~~~~~L  141 (790)
T PRK09519         69 ESSGKTTVALHAVANAQAA--GGVAAFIDAEHALDP-----DYAKKLGVDTDSLLVSQPDTGEQALEIADMLIRSGALDI  141 (790)
T ss_pred             CCCCHHHHHHHHHHHHHHc--CCcEEEECCccchhH-----HHHHHcCCChhHeEEecCCCHHHHHHHHHHHhhcCCCeE
Confidence            6999999998866554322  246799988887774     36777777533      224445555666666543  56


Q ss_pred             EEEcC
Q 041028           74 QIICG   78 (283)
Q Consensus        74 LlV~G   78 (283)
                      +||++
T Consensus       142 VVIDS  146 (790)
T PRK09519        142 VVIDS  146 (790)
T ss_pred             EEEcc
Confidence            66643

>PRK14530 adenylate kinase; Provisional

Probab=88.95  E-value=0.3  Score=40.19  Aligned_cols=18  Identities=28%  Similarity=0.327  Sum_probs=15.5

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      ++|+||||+|+.++....
T Consensus        11 ~pGsGKsT~~~~La~~~~   28 (215)
T PRK14530         11 APGAGKGTQSSNLAEEFG   28 (215)
T ss_pred             CCCCCHHHHHHHHHHHhC
Confidence            479999999999988764

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family

Probab=88.87  E-value=1  Score=37.66  Aligned_cols=43  Identities=9%  Similarity=0.258  Sum_probs=27.8

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHHHhC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKLG   49 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~~l~   49 (283)
                      +|+|||+||.++....-.+  -..++||+...  ++.++.+.+ .+++
T Consensus        30 pGsGKT~la~~~l~~~~~~--ge~~lyvs~ee--~~~~i~~~~-~~~g   72 (237)
T TIGR03877        30 PGTGKSIFSQQFLWNGLQM--GEPGIYVALEE--HPVQVRRNM-AQFG   72 (237)
T ss_pred             CCCCHHHHHHHHHHHHHHc--CCcEEEEEeeC--CHHHHHHHH-HHhC
Confidence            6999999999876543222  35788888765  444555553 3444

Members of this family contain a single copy of the KaiC domain (pfam06745) that occurs in two copies of the circadian clock protein kinase KaiC itself. Members occur primarily in thermophilic archaea and in Thermotoga.

>KOG1532 consensus GTPase XAB1, interacts with DNA repair protein XPA [Replication, recombination and repair]

Probab=88.82  E-value=0.37  Score=40.93  Aligned_cols=74  Identities=16%  Similarity=0.116  Sum_probs=42.4

Q ss_pred             CCCCcHHHHHHHHHhhhccCCCCCeEEEEEeC---------CCCCHHH--HHHHHHHHhCCCCCcC--C--------Hhh
Q 041028            1 MGGIGKTTLAKEVARKAKNGKLFDQIVFTEVS---------QNPNIKK--IQGEIAFKLGLKFDEE--S--------ESG   59 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~---------~~~~~~~--l~~~i~~~l~~~~~~~--~--------~~~   59 (283)
                      |+|.||||+.+.++.+...+  +..-+-|++.         -+.++.+  -.++...+.+....+.  +        ..+
T Consensus        27 MAGSGKTTF~QrL~~hl~~~--~~ppYviNLDPAv~~vpy~aniDIRDtVkYkEvMkqY~LGPNGgI~TsLNLF~tk~dq  104 (366)
T KOG1532|consen   27 MAGSGKTTFMQRLNSHLHAK--KTPPYVINLDPAVRNVPYPANIDIRDTVKYKEVMKQYQLGPNGGIVTSLNLFATKFDQ  104 (366)
T ss_pred             cCCCCchhHHHHHHHHHhhc--cCCCeEEeCCHHHhcCCCccCCchhhhhhHHHHHHHhCCCCCcchhhhHHHHHHHHHH
Confidence            89999999999999887655  4322333332         2234433  3566777776655432  1        122


Q ss_pred             hHHhHHHHccCCcEEEE
Q 041028           60 RTRSPWSRLKKEKLQII   76 (283)
Q Consensus        60 ~~~~l~~~L~~kr~LlV   76 (283)
                      ....+...-..-.|.||
T Consensus       105 v~~~iek~~~~~~~~li  121 (366)
T KOG1532|consen  105 VIELIEKRAEEFDYVLI  121 (366)
T ss_pred             HHHHHHHhhcccCEEEE
Confidence            23333333333478888

>COG1149 MinD superfamily P-loop ATPase containing an inserted ferredoxin domain [Energy production and conversion]

Probab=88.79  E-value=0.35  Score=40.91  Aligned_cols=24  Identities=33%  Similarity=0.555  Sum_probs=18.7

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEE
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIV   27 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~   27 (283)
                      ||+||||+|..++--....  |..++
T Consensus        11 GGtGKTTva~~la~~l~~~--~~~~l   34 (284)
T COG1149          11 GGTGKTTVAANLAVLLGDK--YKLVL   34 (284)
T ss_pred             CCCChhhHHHHHHHHhccc--cceEE
Confidence            8999999999988776644  65543

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=88.71  E-value=0.46  Score=40.99  Aligned_cols=17  Identities=41%  Similarity=0.481  Sum_probs=14.2

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      +|+||||+|+.+++...
T Consensus        67 pGTGKT~lA~~ia~~l~   83 (284)
T TIGR02880        67 PGTGKTTVALRMAQILH   83 (284)
T ss_pred             CCCCHHHHHHHHHHHHH
Confidence            69999999988877653

Proteins in this family are now designated CbbX. Some previously were CfxQ (carbon fixation Q). Its gene is often found immmediately downstream of the Rubisco large and small chain genes, and it is suggested to be necessary for Rubisco expression. CbbX has been shown to be necessary for photoautotrophic growth. This protein belongs to the larger family of pfam00004, ATPase family Associated with various cellular Activities. Within that larger family, members of this family are most closely related to the stage V sporulation protein K, or SpoVK, in endospore-forming bacteria such as Bacillus subtilis.

>cd02028 UMPK_like Uridine monophosphate kinase_like (UMPK_like) is a family of proteins highly similar to the uridine monophosphate kinase (UMPK, EC 2

Probab=88.70  E-value=0.29  Score=39.09  Aligned_cols=17  Identities=41%  Similarity=0.687  Sum_probs=15.0

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      +|+||||||+.+.....
T Consensus         8 sgsGKttla~~l~~~l~   24 (179)
T cd02028           8 SGSGKTTFAKKLSNQLR   24 (179)
T ss_pred             CCCCHHHHHHHHHHHHH
Confidence            69999999999998764

7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK).

>PRK13973 thymidylate kinase; Provisional

Probab=88.66  E-value=1.2  Score=36.59  Aligned_cols=43  Identities=16%  Similarity=0.247  Sum_probs=25.4

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHH
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAF   46 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~   46 (283)
                      .|+||||+++.+++.....+ +.. +...-.......+.+++++.
T Consensus        12 dGsGKtTq~~~l~~~l~~~g-~~~-~~~~~p~~~~~g~~ir~~l~   54 (213)
T PRK13973         12 EGAGKSTQIRLLAERLRAAG-YDV-LVTREPGGSPGAEAIRHVLL   54 (213)
T ss_pred             CCCCHHHHHHHHHHHHHHCC-CeE-EEEECCCCCchHHHHHHHHc
Confidence            59999999999999876542 322 22222222334555555543

>TIGR03881 KaiC_arch_4 KaiC domain protein, PAE1156 family

Probab=88.64  E-value=1.3  Score=36.60  Aligned_cols=44  Identities=23%  Similarity=0.373  Sum_probs=27.9

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHHHhCC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKLGL   50 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~~l~~   50 (283)
                      +|.||||||.++......+  -..++|++.....  .++... +++++.
T Consensus        29 ~G~GKT~l~~~~~~~~~~~--g~~~~~is~e~~~--~~i~~~-~~~~g~   72 (229)
T TIGR03881        29 PGTGKTIFCLHFAYKGLRD--GDPVIYVTTEESR--ESIIRQ-AAQFGM   72 (229)
T ss_pred             CCCChHHHHHHHHHHHHhc--CCeEEEEEccCCH--HHHHHH-HHHhCC
Confidence            6999999999876553322  3577888875443  444433 455553

Members of this protein family are archaeal single-domain KaiC_related proteins, homologous to the Cyanobacterial circadian clock cycle protein KaiC, an autokinase/autophosphorylase that has two copies of the domain.

>PRK08533 flagellar accessory protein FlaH; Reviewed

Probab=88.63  E-value=1.2  Score=37.12  Aligned_cols=44  Identities=14%  Similarity=0.249  Sum_probs=26.5

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHHHhCC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKLGL   50 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~~l~~   50 (283)
                      +|+||||||.++......++  ..+++++...  +..++++.+ .+++.
T Consensus        33 ~G~GKTtl~~~~~~~~~~~g--~~~~yi~~e~--~~~~~~~~~-~~~g~   76 (230)
T PRK08533         33 ESTGKSILSQRLAYGFLQNG--YSVSYVSTQL--TTTEFIKQM-MSLGY   76 (230)
T ss_pred             CCCCHHHHHHHHHHHHHhCC--CcEEEEeCCC--CHHHHHHHH-HHhCC
Confidence            69999999877655442221  3456666333  456666665 44554

>COG0468 RecA RecA/RadA recombinase [DNA replication, recombination, and repair]

Probab=88.60  E-value=0.91  Score=38.94  Aligned_cols=43  Identities=19%  Similarity=0.269  Sum_probs=32.8

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHHH
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFK   47 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~~   47 (283)
                      .|.||||||.+++-..+..  -..++|++....+++..+.. ++..
T Consensus        69 ~gsGKT~lal~~~~~aq~~--g~~a~fIDtE~~l~p~r~~~-l~~~  111 (279)
T COG0468          69 ESSGKTTLALQLVANAQKP--GGKAAFIDTEHALDPERAKQ-LGVD  111 (279)
T ss_pred             CCcchhhHHHHHHHHhhcC--CCeEEEEeCCCCCCHHHHHH-HHHh
Confidence            5899999999988765544  44889999999999877643 4433

>PF08477 Miro: Miro-like protein; InterPro: IPR013684 Mitochondrial Rho proteins (Miro-1, Q8IXI2 from SWISSPROT and Miro-2, Q8IXI1 from SWISSPROT) are atypical Rho GTPases

Probab=88.59  E-value=0.32  Score=35.42  Aligned_cols=17  Identities=29%  Similarity=0.532  Sum_probs=14.1

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      .|+|||||.+.+.+...
T Consensus         8 ~g~GKTsLi~~l~~~~~   24 (119)
T PF08477_consen    8 SGVGKTSLIRRLCGGEF   24 (119)
T ss_dssp             TTSSHHHHHHHHHHSS-
T ss_pred             CCCCHHHHHHHHhcCCC
Confidence            59999999999987643

They have a unique domain organisation, with tandem GTP-binding domains and two EF hand domains (IPR002048 from INTERPRO), that may bind calcium. They are also larger than classical small GTPases. It has been proposed that they are involved in mitochondrial homeostasis and apoptosis []. ; GO: 0005525 GTP binding, 0007264 small GTPase mediated signal transduction, 0005622 intracellular; PDB: 2IWR_A 2BMJ_A 3IHW_A 2ZEJ_A 3D6T_B 3DPU_A.

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=88.53  E-value=1.7  Score=40.13  Aligned_cols=30  Identities=20%  Similarity=0.305  Sum_probs=20.9

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEe
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEV   31 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v   31 (283)
                      .|+|||+|++++++.......--.+++++.
T Consensus       157 ~G~GKThL~~ai~~~~~~~~~~~~v~yi~~  186 (450)
T PRK00149        157 VGLGKTHLLHAIGNYILEKNPNAKVVYVTS  186 (450)
T ss_pred             CCCCHHHHHHHHHHHHHHhCCCCeEEEEEH
Confidence            699999999999998764311123556654

>cd02034 CooC The accessory protein CooC, which contains a nucleotide-binding domain (P-loop) near the N-terminus, participates in the maturation of the nickel center of carbon monoxide dehydrogenase (CODH)

Probab=88.53  E-value=0.37  Score=35.53  Aligned_cols=19  Identities=47%  Similarity=0.663  Sum_probs=16.1

Q ss_pred             CCCCcHHHHHHHHHhhhcc
Q 041028            1 MGGIGKTTLAKEVARKAKN   19 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~   19 (283)
                      .||+||||++..+++....
T Consensus         7 kgG~GKTt~a~~la~~l~~   25 (116)
T cd02034           7 KGGVGKTTIAALLARYLAE   25 (116)
T ss_pred             CCCCCHHHHHHHHHHHHHH
Confidence            3899999999999887654

CODH from Rhodospirillum rubrum catalyzes the reversible oxidation of CO to CO2. CODH contains a nickel-iron-sulfur cluster (C-center) and an iron-sulfur cluster (B-center). CO oxidation occurs at the C-center. Three accessory proteins encoded by cooCTJ genes are involved in nickel incorporation into a nickel site. CooC functions as a nickel insertase that mobilizes nickel to apoCODH using energy released from ATP hydrolysis. CooC is a homodimer and has NTPase activities. Mutation at the P-loop abolishs its function.

>PF03796 DnaB_C: DnaB-like helicase C terminal domain; InterPro: IPR007694 The hexameric helicase DnaB unwinds the DNA duplex at the Escherichia coli chromosome replication fork

Probab=88.51  E-value=1.2  Score=37.60  Aligned_cols=44  Identities=18%  Similarity=0.287  Sum_probs=31.4

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHHHh
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKL   48 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~~l   48 (283)
                      +|+|||++|..++.+...... ..++|++..  .+..++..+++..+
T Consensus        28 pg~GKT~~~l~ia~~~a~~~~-~~vly~SlE--m~~~~l~~R~la~~   71 (259)
T PF03796_consen   28 PGVGKTAFALQIALNAALNGG-YPVLYFSLE--MSEEELAARLLARL   71 (259)
T ss_dssp             TTSSHHHHHHHHHHHHHHTTS-SEEEEEESS--S-HHHHHHHHHHHH
T ss_pred             ccCCchHHHHHHHHHHHHhcC-CeEEEEcCC--CCHHHHHHHHHHHh
Confidence            699999999999998765422 567776654  45566777777655

Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis. ; GO: 0003678 DNA helicase activity, 0005524 ATP binding, 0006260 DNA replication; PDB: 1Q57_E 1E0K_D 1E0J_B 1CR2_A 1CR4_A 1CR1_A 1CR0_A 1MI8_A 2R6D_B 2R6C_C ....

>COG0572 Udk Uridine kinase [Nucleotide transport and metabolism]

Probab=88.47  E-value=0.34  Score=39.77  Aligned_cols=19  Identities=42%  Similarity=0.536  Sum_probs=16.2

Q ss_pred             CCCcHHHHHHHHHhhhccC
Q 041028            2 GGIGKTTLAKEVARKAKNG   20 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~   20 (283)
                      +|.||||+|+.++......
T Consensus        17 SgSGKTTva~~l~~~~~~~   35 (218)
T COG0572          17 SGSGKTTVAKELSEQLGVE   35 (218)
T ss_pred             CCCCHHHHHHHHHHHhCcC
Confidence            5899999999999987643

>PRK10818 cell division inhibitor MinD; Provisional

Probab=88.45  E-value=0.29  Score=41.70  Aligned_cols=30  Identities=27%  Similarity=0.407  Sum_probs=21.0

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQ   33 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~   33 (283)
                      |||||||+|..++......+  ..++-|+...
T Consensus        12 GGvGKTt~a~nlA~~la~~g--~~vllvD~D~   41 (270)
T PRK10818         12 GGVGKTTSSAAIATGLAQKG--KKTVVIDFDI   41 (270)
T ss_pred             CCCcHHHHHHHHHHHHHHCC--CeEEEEECCC
Confidence            89999999999988654332  2355565543

>cd03111 CpaE_like This protein family consists of proteins similar to the cpaE protein of the Caulobacter pilus assembly and the orf4 protein of Actinobacillus pilus formation gene cluster

Probab=88.38  E-value=0.31  Score=35.19  Aligned_cols=18  Identities=44%  Similarity=0.656  Sum_probs=15.0

Q ss_pred             CCCcHHHHHHHHHhhhcc
Q 041028            2 GGIGKTTLAKEVARKAKN   19 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~   19 (283)
                      ||+||||+|..+......
T Consensus         9 gg~gkt~~~~~la~~~~~   26 (106)
T cd03111           9 GGVGATTLAANLAVALAK   26 (106)
T ss_pred             CCCcHHHHHHHHHHHHHh
Confidence            899999999998876553

The function of these proteins are unkown. The Caulobacter pilus assembly contains 7 genes: pilA, cpaA, cpaB, cpaC, cpaD, cpaE and cpaF. These genes are clustered together on chromosome.

>PRK07667 uridine kinase; Provisional

Probab=88.33  E-value=0.33  Score=39.23  Aligned_cols=18  Identities=28%  Similarity=0.425  Sum_probs=15.5

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      .+|+||||+|+.+.....
T Consensus        25 ~~gsGKStla~~L~~~l~   42 (193)
T PRK07667         25 LSRSGKTTFVANLKENMK   42 (193)
T ss_pred             CCCCCHHHHHHHHHHHHH
Confidence            369999999999998764

>COG1936 Predicted nucleotide kinase (related to CMP and AMP kinases) [Nucleotide transport and metabolism]

Probab=88.28  E-value=0.28  Score=38.62  Aligned_cols=13  Identities=46%  Similarity=0.687  Sum_probs=12.3

Q ss_pred             CCCcHHHHHHHHH
Q 041028            2 GGIGKTTLAKEVA   14 (283)
Q Consensus         2 gGiGKTtLA~~v~   14 (283)
                      +|+||||++..+.
T Consensus         9 PGvGKTT~~~~L~   21 (180)
T COG1936           9 PGVGKTTVCKLLR   21 (180)
T ss_pred             CCCchHHHHHHHH
Confidence            7999999999988

>cd02027 APSK Adenosine 5'-phosphosulfate kinase (APSK) catalyzes the phosphorylation of adenosine 5'-phosphosulfate to form 3'-phosphoadenosine 5'-phosphosulfate (PAPS)

Probab=88.28  E-value=0.35  Score=37.35  Aligned_cols=17  Identities=35%  Similarity=0.546  Sum_probs=15.0

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      +|+||||||+.+.....
T Consensus         8 ~GsGKSTla~~L~~~l~   24 (149)
T cd02027           8 SGSGKSTIARALEEKLF   24 (149)
T ss_pred             CCCCHHHHHHHHHHHHH
Confidence            69999999999988764

The end-product PAPS is a biologically "activated" sulfate form important for the assimilation of inorganic sulfate.

>TIGR02239 recomb_RAD51 DNA repair protein RAD51

Probab=88.28  E-value=0.97  Score=39.63  Aligned_cols=48  Identities=19%  Similarity=0.126  Sum_probs=32.3

Q ss_pred             CCCcHHHHHHHHHhhhccC---C-CCCeEEEEEeCCCCCHHHHHHHHHHHhCC
Q 041028            2 GGIGKTTLAKEVARKAKNG---K-LFDQIVFTEVSQNPNIKKIQGEIAFKLGL   50 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~---~-~Fd~~~wv~v~~~~~~~~l~~~i~~~l~~   50 (283)
                      +|+|||||+..++......   + .-..++|++-...++... +.++++.++.
T Consensus       105 ~g~GKT~l~~~~~~~~~~~~~~Gg~~~~vvyIdtE~~f~~~R-l~~ia~~~~~  156 (316)
T TIGR02239       105 FRTGKTQLCHTLAVTCQLPIDQGGGEGKALYIDTEGTFRPER-LLAIAERYGL  156 (316)
T ss_pred             CCCCcCHHHHHHHHHHhhhhhcCCCCceEEEEECCCCCCHHH-HHHHHHHcCC
Confidence            6999999999987643211   1 113579999888888776 4556666654

This eukaryotic sequence family consists of RAD51, a protein involved in DNA homologous recombination and repair. It is similar in sequence the exclusively meiotic recombinase DMC1 (TIGR02238), to archaeal families RadA (TIGR02236) and RadB (TIGR02237), and to bacterial RecA (TIGR02012).

>CHL00175 minD septum-site determining protein; Validated

Probab=88.24  E-value=0.3  Score=41.90  Aligned_cols=30  Identities=20%  Similarity=0.334  Sum_probs=20.5

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQ   33 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~   33 (283)
                      |||||||+|..++.-....+  ..++-|+...
T Consensus        25 GGvGKTt~a~nLA~~La~~g--~~vlliD~D~   54 (281)
T CHL00175         25 GGVGKTTTTANLGMSIARLG--YRVALIDADI   54 (281)
T ss_pred             CCCcHHHHHHHHHHHHHhCC--CeEEEEeCCC
Confidence            89999999999887655332  1355555543

>cd01428 ADK Adenylate kinase (ADK) catalyzes the reversible phosphoryl transfer from adenosine triphosphates (ATP) to adenosine monophosphates (AMP) and to yield adenosine diphosphates (ADP)

Probab=88.22  E-value=0.35  Score=38.76  Aligned_cols=17  Identities=41%  Similarity=0.438  Sum_probs=15.0

Q ss_pred             CCCCcHHHHHHHHHhhh
Q 041028            1 MGGIGKTTLAKEVARKA   17 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (283)
                      ++|+||||+|+.++...
T Consensus         7 ~pGsGKst~a~~La~~~   23 (194)
T cd01428           7 PPGSGKGTQAERLAKKY   23 (194)
T ss_pred             CCCCCHHHHHHHHHHHc
Confidence            47999999999998874

This enzyme is required for the biosynthesis of ADP and is essential for homeostasis of adenosine phosphates.

>cd00550 ArsA_ATPase Oxyanion-translocating ATPase (ArsA)

Probab=88.17  E-value=0.69  Score=39.19  Aligned_cols=38  Identities=18%  Similarity=0.377  Sum_probs=26.5

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHH
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQ   41 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~   41 (283)
                      ||+||||+|..++......+  ..++-|+.....++.+++
T Consensus         9 gG~GKtt~a~~la~~~a~~g--~~vLlvd~D~~~sl~~~~   46 (254)
T cd00550           9 GGVGKTTISAATAVRLAEQG--KKVLLVSTDPAHSLSDSF   46 (254)
T ss_pred             CCchHHHHHHHHHHHHHHCC--CCceEEeCCCcccHHHHh
Confidence            89999999999988765442  346667765555555444

This ATPase is involved in transport of arsenite, antimonite or other oxyanions across biological membranes in all three kingdoms of life. ArsA contains a highly conserved AAA motif present in the AAA+ ATPase superfamily associated with a variety of cellular activities. To form a functional ATP-driven pump, ArsA interacts with the permease ArsB, which is a channel-forming integral membrane protein. One of the most interesting features of ArsA is the allosteric activation by its transport substrates. A divalent cation, typically Mg2+, is required for its enzymatic activity.

>PRK03846 adenylylsulfate kinase; Provisional

Probab=88.14  E-value=0.34  Score=39.25  Aligned_cols=18  Identities=28%  Similarity=0.484  Sum_probs=15.3

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      ++|+||||||+.+.....
T Consensus        32 ~~GsGKSTla~~l~~~l~   49 (198)
T PRK03846         32 LSGSGKSTVAGALEEALH   49 (198)
T ss_pred             CCCCCHHHHHHHHHHHHH
Confidence            359999999999998653

>KOG2543 consensus Origin recognition complex, subunit 5 [Replication, recombination and repair]

Probab=88.12  E-value=1.3  Score=39.55  Aligned_cols=43  Identities=23%  Similarity=0.232  Sum_probs=38.1

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHHHhC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKLG   49 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~~l~   49 (283)
                      .|.|||.+.+.+.+....     ..+|+++-+.++...++.+|+.+++
T Consensus        39 sgTGKT~~~r~~l~~~n~-----~~vw~n~~ecft~~~lle~IL~~~~   81 (438)
T KOG2543|consen   39 SGTGKTYLVRQLLRKLNL-----ENVWLNCVECFTYAILLEKILNKSQ   81 (438)
T ss_pred             CCCchhHHHHHHHhhcCC-----cceeeehHHhccHHHHHHHHHHHhc
Confidence            599999999999997733     3589999999999999999999996

>PRK13976 thymidylate kinase; Provisional

Probab=88.10  E-value=1  Score=36.94  Aligned_cols=18  Identities=33%  Similarity=0.422  Sum_probs=16.1

Q ss_pred             CCCcHHHHHHHHHhhhcc
Q 041028            2 GGIGKTTLAKEVARKAKN   19 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~   19 (283)
                      -|+||||+++.+++..+.
T Consensus         9 DGsGKsTq~~~L~~~L~~   26 (209)
T PRK13976          9 DGSGKTTQSRLLAEYLSD   26 (209)
T ss_pred             CCCCHHHHHHHHHHHHHH
Confidence            599999999999998764

>KOG0744 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=88.07  E-value=0.69  Score=40.30  Aligned_cols=65  Identities=17%  Similarity=0.120  Sum_probs=38.3

Q ss_pred             CCCcHHHHHHHHHhhhccC--CCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCcCCHhhhHHhHHHHccCCcEEE
Q 041028            2 GGIGKTTLAKEVARKAKNG--KLFDQIVFTEVSQNPNIKKIQGEIAFKLGLKFDEESESGRTRSPWSRLKKEKLQI   75 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~--~~Fd~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~kr~Ll   75 (283)
                      +|.|||+|.++++++..++  +.|....-+.+    +...++.++...-|.     .....-+++.+.+.++..|+
T Consensus       186 PGTGKTSLCKaLaQkLSIR~~~~y~~~~liEi----nshsLFSKWFsESgK-----lV~kmF~kI~ELv~d~~~lV  252 (423)
T KOG0744|consen  186 PGTGKTSLCKALAQKLSIRTNDRYYKGQLIEI----NSHSLFSKWFSESGK-----LVAKMFQKIQELVEDRGNLV  252 (423)
T ss_pred             CCCChhHHHHHHHHhheeeecCccccceEEEE----ehhHHHHHHHhhhhh-----HHHHHHHHHHHHHhCCCcEE
Confidence            7999999999999986654  33433333433    333444444433221     23345567777777775443

>COG1222 RPT1 ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones]

Probab=87.94  E-value=0.28  Score=43.18  Aligned_cols=19  Identities=47%  Similarity=0.567  Sum_probs=16.8

Q ss_pred             CCCcHHHHHHHHHhhhccC
Q 041028            2 GGIGKTTLAKEVARKAKNG   20 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~   20 (283)
                      +|.|||-||++|+|+....
T Consensus       194 PGTGKTLLAkAVA~~T~At  212 (406)
T COG1222         194 PGTGKTLLAKAVANQTDAT  212 (406)
T ss_pred             CCCcHHHHHHHHHhccCce
Confidence            7999999999999987654

>PF02562 PhoH: PhoH-like protein; InterPro: IPR003714 PhoH is a cytoplasmic protein and predicted ATPase that is induced by phosphate starvation and belongings to the phosphate regulon (pho) in Escherichia coli []

Probab=87.94  E-value=0.52  Score=38.52  Aligned_cols=29  Identities=34%  Similarity=0.437  Sum_probs=22.7

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEE
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTE   30 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~   30 (283)
                      +|.|||.||.+.+-+.-..+.|+.++++.
T Consensus        28 AGTGKT~LA~a~Al~~v~~g~~~kiii~R   56 (205)
T PF02562_consen   28 AGTGKTFLALAAALELVKEGEYDKIIITR   56 (205)
T ss_dssp             TTSSTTHHHHHHHHHHHHTTS-SEEEEEE
T ss_pred             CCCcHHHHHHHHHHHHHHhCCCcEEEEEe
Confidence            69999999999887654557788888873

; GO: 0005524 ATP binding; PDB: 3B85_A.

>TIGR00764 lon_rel lon-related putative ATP-dependent protease

Probab=87.93  E-value=0.84  Score=43.78  Aligned_cols=48  Identities=21%  Similarity=0.171  Sum_probs=30.6

Q ss_pred             CCCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHHHhCC
Q 041028            1 MGGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKLGL   50 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~~l~~   50 (283)
                      ++|+||||||+.+.+..... .|...+++.- ...+..++++.++..++.
T Consensus        45 ~pG~GKT~la~~la~~l~~~-~~~~~~~~~n-~~~~~~~~~~~v~~~~g~   92 (608)
T TIGR00764        45 EPGVGKSMLAKAMAELLPDE-ELEDILVYPN-PEDPNMPRIVEVPAGEGR   92 (608)
T ss_pred             CCCCCHHHHHHHHHHHcCch-hheeEEEEeC-CCCCchHHHHHHHHhhch
Confidence            47999999999999876433 3433333322 223455667777777764

Members of this family from Pyrococcus horikoshii and Pyrococcus abyssi each contain a predicted intein.

>PRK10867 signal recognition particle protein; Provisional

Probab=87.86  E-value=2.5  Score=38.76  Aligned_cols=74  Identities=18%  Similarity=0.241  Sum_probs=39.9

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCC-CCCHHHHHHHHHHHhCCCCC----cCCHhhhHHhHHHHcc--CCcEE
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQ-NPNIKKIQGEIAFKLGLKFD----EESESGRTRSPWSRLK--KEKLQ   74 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~-~~~~~~l~~~i~~~l~~~~~----~~~~~~~~~~l~~~L~--~kr~L   74 (283)
                      +|+||||.|..++.....+.. ..++.|+... .+...+-++.+....+.+.-    ..+..+......+..+  +..++
T Consensus       109 ~GsGKTTtaakLA~~l~~~~G-~kV~lV~~D~~R~aa~eQL~~~a~~~gv~v~~~~~~~dp~~i~~~a~~~a~~~~~DvV  187 (433)
T PRK10867        109 QGAGKTTTAGKLAKYLKKKKK-KKVLLVAADVYRPAAIEQLKTLGEQIGVPVFPSGDGQDPVDIAKAALEEAKENGYDVV  187 (433)
T ss_pred             CCCcHHHHHHHHHHHHHHhcC-CcEEEEEccccchHHHHHHHHHHhhcCCeEEecCCCCCHHHHHHHHHHHHHhcCCCEE
Confidence            699999999888876653311 2344454432 22234455666777776522    2244444433333332  34677


Q ss_pred             EE
Q 041028           75 II   76 (283)
Q Consensus        75 lV   76 (283)
                      ||
T Consensus       188 II  189 (433)
T PRK10867        188 IV  189 (433)
T ss_pred             EE
Confidence            77

>PF04665 Pox_A32: Poxvirus A32 protein; InterPro: IPR006758 This entry contains uncharacterised proteins belonging to the B354L family which include the pox virus A32 protein

Probab=87.85  E-value=0.67  Score=38.82  Aligned_cols=28  Identities=36%  Similarity=0.494  Sum_probs=22.7

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEe
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEV   31 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v   31 (283)
                      .|.|||||...+.......  |+.+++++-
T Consensus        22 sGSGKT~li~~lL~~~~~~--f~~I~l~t~   49 (241)
T PF04665_consen   22 SGSGKTTLIKSLLYYLRHK--FDHIFLITP   49 (241)
T ss_pred             CCCCHHHHHHHHHHhhccc--CCEEEEEec
Confidence            6999999999999876644  988777754

This is thought to be an ATPase involved in viral DNA packaging [].

>PF00406 ADK: Adenylate kinase; InterPro: IPR000850 Adenylate kinases (ADK) are phosphotransferases that catalyse the reversible reaction AMP + MgATP = ADP + MgADP an essential reaction for many processes in living cells

Probab=87.75  E-value=0.4  Score=36.90  Aligned_cols=17  Identities=41%  Similarity=0.493  Sum_probs=15.4

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      +|+||||+|+.++.+..
T Consensus         5 PgsGK~t~~~~la~~~~   21 (151)
T PF00406_consen    5 PGSGKGTQAKRLAKRYG   21 (151)
T ss_dssp             TTSSHHHHHHHHHHHHT
T ss_pred             CCCChHHHHHHHHHhcC
Confidence            79999999999999764

Two ADK isozymes have been identified in mammalian cells. These specifically bind AMP and favour binding to ATP over other nucleotide triphosphates (AK1 is cytosolic and AK2 is located in the mitochondria). A third ADK has been identified in bovine heart and human cells [], this is a mitochondrial GTP:AMP phosphotransferase, also specific for the phosphorylation of AMP, but can only use GTP or ITP as a substrate []. ADK has also been identified in different bacterial species and in yeast []. Two further enzymes are known to be related to the ADK family, i.e. yeast uridine monophosphokinase and slime mold UMP-CMP kinase. Within the ADK family there are several conserved regions, including the ATP-binding domains. One of the most conserved areas includes an Arg residue, whose modification inactivates the enzyme, together with an Asp that resides in the catalytic cleft of the enzyme and participates in a salt bridge.; GO: 0005524 ATP binding, 0019205 nucleobase-containing compound kinase activity, 0006139 nucleobase-containing compound metabolic process; PDB: 1ZD8_A 3TLX_D 1TEV_A 1ZAK_B 3CM0_A 3ADK_A 1ZIP_A 1ZIO_A 1ZIN_A 3NDP_A ....

>PHA02519 plasmid partition protein SopA; Reviewed

Probab=87.67  E-value=0.4  Score=43.32  Aligned_cols=33  Identities=21%  Similarity=0.205  Sum_probs=22.8

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEe-CCCCC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEV-SQNPN   36 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v-~~~~~   36 (283)
                      |||||||+|.+++......+ + .++-|+. ....+
T Consensus       116 GGVGKTTta~nLA~~LA~~G-~-rVLlIDl~DpQ~n  149 (387)
T PHA02519        116 GGVYKTSSAVHTAQWLALQG-H-RVLLIEGNDPQGT  149 (387)
T ss_pred             CCCcHHHHHHHHHHHHHhCC-C-cEEEEeCCCCCCC
Confidence            89999999999988765433 2 4566664 44333

>PRK06761 hypothetical protein; Provisional

Probab=87.65  E-value=0.92  Score=39.02  Aligned_cols=27  Identities=22%  Similarity=0.322  Sum_probs=19.6

Q ss_pred             CCCCcHHHHHHHHHhhhccCCCCCeEEE
Q 041028            1 MGGIGKTTLAKEVARKAKNGKLFDQIVF   28 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~~~Fd~~~w   28 (283)
                      .+|+||||+|+.+++..... .++...+
T Consensus        11 ~~GsGKTTla~~L~~~L~~~-g~~v~~~   37 (282)
T PRK06761         11 LPGFGKSTTAKMLNDILSQN-GIEVELY   37 (282)
T ss_pred             CCCCCHHHHHHHHHHhcCcC-ceEEEEE
Confidence            37999999999999987543 3344443

>PLN02924 thymidylate kinase

Probab=87.62  E-value=1.2  Score=36.76  Aligned_cols=44  Identities=9%  Similarity=0.021  Sum_probs=27.8

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHH
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAF   46 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~   46 (283)
                      .|+||||+|+.+++..... .+....+=..+......+..++++.
T Consensus        25 DGsGKsTq~~~L~~~l~~~-g~~v~~~~ep~~~~~~g~~ir~~l~   68 (220)
T PLN02924         25 DRSGKSTQCAKLVSFLKGL-GVAAELWRFPDRTTSVGQMISAYLS   68 (220)
T ss_pred             CCCCHHHHHHHHHHHHHhc-CCCceeeeCCCCCChHHHHHHHHHh
Confidence            5999999999999988754 3444333222223445566666554

>TIGR00390 hslU ATP-dependent protease HslVU, ATPase subunit

Probab=87.61  E-value=0.92  Score=41.21  Aligned_cols=19  Identities=37%  Similarity=0.618  Sum_probs=16.3

Q ss_pred             CCCcHHHHHHHHHhhhccC
Q 041028            2 GGIGKTTLAKEVARKAKNG   20 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~   20 (283)
                      +|+|||+||+.++......
T Consensus        56 pG~GKT~lAraLA~~l~~~   74 (441)
T TIGR00390        56 TGVGKTEIARRLAKLANAP   74 (441)
T ss_pred             CCCCHHHHHHHHHHHhCCe
Confidence            6999999999999986543

This model represents the ATPase subunit of HslVU, while the proteasome-related peptidase subunit is HslV. Residues 54-61 of the model contain a P-loop ATP-binding motif. Cys-287 of E. coli (position 308 in the seed alignment), studied in PubMed:98389714, is Ser in other members of the seed alignment.

>PRK06835 DNA replication protein DnaC; Validated

Probab=87.59  E-value=0.58  Score=41.23  Aligned_cols=28  Identities=21%  Similarity=0.428  Sum_probs=20.9

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEe
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEV   31 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v   31 (283)
                      .|+|||.||.++++....++  -.++|+++
T Consensus       192 ~GtGKThLa~aIa~~l~~~g--~~V~y~t~  219 (329)
T PRK06835        192 TGTGKTFLSNCIAKELLDRG--KSVIYRTA  219 (329)
T ss_pred             CCCcHHHHHHHHHHHHHHCC--CeEEEEEH
Confidence            59999999999999875442  24566654

>PRK04182 cytidylate kinase; Provisional

Probab=87.57  E-value=0.41  Score=37.77  Aligned_cols=18  Identities=44%  Similarity=0.468  Sum_probs=15.7

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      +.|+||||+|+.+++...
T Consensus         8 ~~GsGKstia~~la~~lg   25 (180)
T PRK04182          8 PPGSGKTTVARLLAEKLG   25 (180)
T ss_pred             CCCCCHHHHHHHHHHHcC
Confidence            479999999999998764

>PRK06620 hypothetical protein; Validated

Probab=87.57  E-value=0.35  Score=39.84  Aligned_cols=16  Identities=31%  Similarity=0.231  Sum_probs=14.0

Q ss_pred             CCCcHHHHHHHHHhhh
Q 041028            2 GGIGKTTLAKEVARKA   17 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~   17 (283)
                      +|+|||+|++.+++..
T Consensus        53 ~G~GKThLl~a~~~~~   68 (214)
T PRK06620         53 SSSGKTYLTKIWQNLS   68 (214)
T ss_pred             CCCCHHHHHHHHHhcc
Confidence            6999999999987764

>PF13245 AAA_19: Part of AAA domain

Probab=87.52  E-value=0.99  Score=30.48  Aligned_cols=16  Identities=50%  Similarity=0.588  Sum_probs=10.6

Q ss_pred             CCCcHHH-HHHHHHhhh
Q 041028            2 GGIGKTT-LAKEVARKA   17 (283)
Q Consensus         2 gGiGKTt-LA~~v~~~~   17 (283)
                      +|.|||+ ++..+.+-.
T Consensus        19 pGtGKT~~~~~~i~~l~   35 (76)
T PF13245_consen   19 PGTGKTTTLAARIAELL   35 (76)
T ss_pred             CCCCHHHHHHHHHHHHH
Confidence            7999995 444455544

>COG0470 HolB ATPase involved in DNA replication [DNA replication, recombination, and repair]

Probab=87.39  E-value=2.5  Score=36.75  Aligned_cols=50  Identities=24%  Similarity=0.143  Sum_probs=35.0

Q ss_pred             CCCcHHHHHHHHHhhhccCC-------------------CCCeEEEEEeCCCCC---HHHHHHHHHHHhCCC
Q 041028            2 GGIGKTTLAKEVARKAKNGK-------------------LFDQIVFTEVSQNPN---IKKIQGEIAFKLGLK   51 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~-------------------~Fd~~~wv~v~~~~~---~~~l~~~i~~~l~~~   51 (283)
                      +|+||||+|.++++......                   ....+..++.+....   ..+..+++.+.....
T Consensus        33 ~G~Gktt~a~~lA~~l~~~~~~~~~~~~~~~~~~~~~~~~~~d~lel~~s~~~~~~i~~~~vr~~~~~~~~~  104 (325)
T COG0470          33 PGVGKTTAALALAKELLCENPTGLLPCGHCRSCKLIPAGNHPDFLELNPSDLRKIDIIVEQVRELAEFLSES  104 (325)
T ss_pred             CCCCHHHHHHHHHHHHhCCCcccCCcccchhhhhHHhhcCCCceEEecccccCCCcchHHHHHHHHHHhccC
Confidence            59999999999999865332                   234566666666555   577778888776543

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=87.38  E-value=29  Score=33.90  Aligned_cols=16  Identities=44%  Similarity=0.719  Sum_probs=14.1

Q ss_pred             CCCcHHHHHHHHHhhh
Q 041028            2 GGIGKTTLAKEVARKA   17 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~   17 (283)
                      .|+||||+|+.+++..
T Consensus        47 ~GvGKTTlAriLAk~L   62 (709)
T PRK08691         47 RGVGKTTIARILAKSL   62 (709)
T ss_pred             CCCcHHHHHHHHHHHh
Confidence            5999999999998864

>PF09140 MipZ: ATPase MipZ; InterPro: IPR015223 Cell division in bacteria is facilitated by a polymeric ring structure, the Z ring, composed of tubulin-like FtsZ protofilaments

Probab=87.33  E-value=0.38  Score=40.30  Aligned_cols=20  Identities=35%  Similarity=0.491  Sum_probs=16.5

Q ss_pred             CCCcHHHHHHHHHhhhccCC
Q 041028            2 GGIGKTTLAKEVARKAKNGK   21 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~   21 (283)
                      ||+||||.|.+++-.....+
T Consensus        10 GGvGKSTva~~lA~aLa~~G   29 (261)
T PF09140_consen   10 GGVGKSTVAVNLAVALARMG   29 (261)
T ss_dssp             TTTTHHHHHHHHHHHHHCTT
T ss_pred             CCCcHHHHHHHHHHHHHHCC
Confidence            89999999999988765443

Correct positioning of the division plane is a prerequisite for the generation of daughter cells with a normal chromosome complement. In Caulobacter crescentus MipZ, an essential protein, coordinates and regulates the assembly of the FtsZ cytokinetic ring during cell division. MipZ, forms a complex with the partitioning protein ParB near the origin of replication and localizes with the duplicated origin regions to the cell poles. MipZ also directly interferes with FtsZ polymerisation, thereby restricting FtsZ ring formation to mid-cell, the region of lowest MipZ concentration. In eukaryotes members of this entry belong to the Mrp/NBP35 ATP-binding protein family, and specifically the NUBP2/CFD1 subfamily. This includes the cytosolic Fe-S cluster assembly factor Cfd1, which is a component of the cytosolic iron-sulphur (Fe/S) protein assembly machinery. This protein is required for maturation of extra-mitochondrial Fe/S proteins. It may bind and transfer a labile 4Fe-4S cluster to target apoproteins. Cfd1 is also required for biogenesis and export of both ribosomal subunits, suggesting a role in assembly of the Fe/S clusters in RLI1, a protein which performs rRNA processing and ribosome export. ; PDB: 2XIT_B 2XJ4_A 2XJ9_A.

>PRK10078 ribose 1,5-bisphosphokinase; Provisional

Probab=87.27  E-value=0.39  Score=38.52  Aligned_cols=17  Identities=24%  Similarity=0.430  Sum_probs=14.5

Q ss_pred             CCCCcHHHHHHHHHhhh
Q 041028            1 MGGIGKTTLAKEVARKA   17 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (283)
                      +.|+|||||++.++...
T Consensus        10 ~sGsGKsTl~~~l~~~~   26 (186)
T PRK10078         10 PSGSGKDSLLAALRQRE   26 (186)
T ss_pred             CCCCCHHHHHHHHhccC
Confidence            46999999999997754

>PRK13705 plasmid-partitioning protein SopA; Provisional

Probab=87.27  E-value=0.41  Score=43.28  Aligned_cols=33  Identities=18%  Similarity=0.316  Sum_probs=22.1

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEe-CCCCC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEV-SQNPN   36 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v-~~~~~   36 (283)
                      |||||||+|.+++......+ + .++-|+. ....+
T Consensus       116 GGVGKTT~a~nLA~~LA~~G-~-rVLlID~~DpQ~n  149 (388)
T PRK13705        116 GGVYKTSVSVHLAQDLALKG-L-RVLLVEGNDPQGT  149 (388)
T ss_pred             CCchHHHHHHHHHHHHHhcC-C-CeEEEcCCCCCCc
Confidence            89999999999988765432 2 3455663 44333

>PRK13236 nitrogenase reductase; Reviewed

Probab=87.24  E-value=0.68  Score=40.17  Aligned_cols=18  Identities=33%  Similarity=0.571  Sum_probs=14.5

Q ss_pred             CCCcHHHHHHHHHhhhcc
Q 041028            2 GGIGKTTLAKEVARKAKN   19 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~   19 (283)
                      |||||||+|..++.-...
T Consensus        15 GGVGKTt~a~NLA~~La~   32 (296)
T PRK13236         15 GGIGKSTTSQNTLAAMAE   32 (296)
T ss_pred             CcCCHHHHHHHHHHHHHH
Confidence            899999988887776543

>PRK00698 tmk thymidylate kinase; Validated

Probab=87.17  E-value=1.4  Score=35.57  Aligned_cols=18  Identities=22%  Similarity=0.300  Sum_probs=15.6

Q ss_pred             CCCcHHHHHHHHHhhhcc
Q 041028            2 GGIGKTTLAKEVARKAKN   19 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~   19 (283)
                      .|+||||+++.+.+....
T Consensus        12 ~gsGKsT~~~~L~~~l~~   29 (205)
T PRK00698         12 DGAGKSTQIELLKELLEQ   29 (205)
T ss_pred             CCCCHHHHHHHHHHHHHH
Confidence            599999999999987654

>PRK04328 hypothetical protein; Provisional

Probab=87.12  E-value=1.1  Score=37.77  Aligned_cols=44  Identities=14%  Similarity=0.259  Sum_probs=28.4

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHHHhCC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKLGL   50 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~~l~~   50 (283)
                      +|+|||+||.++......+  -..++|++..+.+  .++ .+.+++++.
T Consensus        32 pGsGKT~l~~~fl~~~~~~--ge~~lyis~ee~~--~~i-~~~~~~~g~   75 (249)
T PRK04328         32 PGTGKSIFSQQFLWNGLQM--GEPGVYVALEEHP--VQV-RRNMRQFGW   75 (249)
T ss_pred             CCCCHHHHHHHHHHHHHhc--CCcEEEEEeeCCH--HHH-HHHHHHcCC
Confidence            6999999999976653222  3567888887643  333 334555554

>COG0714 MoxR-like ATPases [General function prediction only]

Probab=87.00  E-value=0.92  Score=39.98  Aligned_cols=39  Identities=28%  Similarity=0.324  Sum_probs=27.1

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHH
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIA   45 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~   45 (283)
                      +|+|||+||+.++......     ..+|.........++.....
T Consensus        52 PG~gKT~la~~lA~~l~~~-----~~~i~~t~~l~p~d~~G~~~   90 (329)
T COG0714          52 PGVGKTLLARALARALGLP-----FVRIQCTPDLLPSDLLGTYA   90 (329)
T ss_pred             CCccHHHHHHHHHHHhCCC-----eEEEecCCCCCHHHhcCchh
Confidence            7999999999999876532     34555666666666555443

>PRK14528 adenylate kinase; Provisional

Probab=86.99  E-value=0.35  Score=38.87  Aligned_cols=17  Identities=35%  Similarity=0.413  Sum_probs=14.9

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      +|+||||+|+.+.....
T Consensus        10 pGsGKtt~a~~la~~~~   26 (186)
T PRK14528         10 PGAGKGTQAKILCERLS   26 (186)
T ss_pred             CCCCHHHHHHHHHHHhC
Confidence            79999999999987654

>PHA02530 pseT polynucleotide kinase; Provisional

Probab=86.98  E-value=0.43  Score=41.28  Aligned_cols=17  Identities=47%  Similarity=0.616  Sum_probs=14.6

Q ss_pred             CCCCcHHHHHHHHHhhh
Q 041028            1 MGGIGKTTLAKEVARKA   17 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (283)
                      .+|+||||+|+.+..+.
T Consensus        10 ~pGSGKSTla~~L~~~~   26 (300)
T PHA02530         10 VPGSGKSTWAREFAAKN   26 (300)
T ss_pred             CCCCCHHHHHHHHHHHC
Confidence            37999999999998764

>PRK06067 flagellar accessory protein FlaH; Validated

Probab=86.91  E-value=1.4  Score=36.66  Aligned_cols=43  Identities=14%  Similarity=0.160  Sum_probs=28.2

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHHHhC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKLG   49 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~~l~   49 (283)
                      +|+|||+||.++......+  =..++|++..+.  ..++.+++ .+++
T Consensus        34 ~GsGKt~l~~~~~~~~~~~--g~~~~y~~~e~~--~~~~~~~~-~~~g   76 (234)
T PRK06067         34 HGTGKSVLSQQFVYGALKQ--GKKVYVITTENT--SKSYLKQM-ESVK   76 (234)
T ss_pred             CCCChHHHHHHHHHHHHhC--CCEEEEEEcCCC--HHHHHHHH-HHCC
Confidence            6999999999986553222  246888888754  34555543 3444

>TIGR03575 selen_PSTK_euk L-seryl-tRNA(Sec) kinase, eukaryotic

Probab=86.90  E-value=0.77  Score=40.61  Aligned_cols=18  Identities=28%  Similarity=0.517  Sum_probs=15.8

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      ++|.||||+++.+.+...
T Consensus         7 l~GaGKST~~~~l~~~l~   24 (340)
T TIGR03575         7 LPAAGKSTLARSLSATLR   24 (340)
T ss_pred             CCCCCHHHHHHHHHHHHH
Confidence            479999999999998765

Members of this protein are L-seryl-tRNA(Sec) kinase. This enzyme is part of a two-step pathway in Eukaryota and Archaea for performing selenocysteine biosynthesis by changing serine misacylated on selenocysteine-tRNA to selenocysteine. This enzyme performs the first step, phosphorylation of the OH group of the serine side chain. This family represents eukaryotic proteins with this activity.

>TIGR02016 BchX chlorophyllide reductase iron protein subunit X

Probab=86.89  E-value=0.85  Score=39.58  Aligned_cols=18  Identities=22%  Similarity=0.422  Sum_probs=15.5

Q ss_pred             CCCcHHHHHHHHHhhhcc
Q 041028            2 GGIGKTTLAKEVARKAKN   19 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~   19 (283)
                      |||||||+|..++.-...
T Consensus         9 GGvGKTT~a~nLA~~La~   26 (296)
T TIGR02016         9 GGSGKSFTTTNLSHMMAE   26 (296)
T ss_pred             CCCCHHHHHHHHHHHHHH
Confidence            899999999999886554

This model represents the X subunit of the three-subunit enzyme, (bacterio)chlorophyllide reductase. This enzyme is responsible for the reduction of the chlorin B-ring and is closely related to the protochlorophyllide reductase complex which reduces the D-ring. Both of these complexes in turn are homologous to nitrogenase. This subunit is homologous to the nitrogenase component II, or "iron" protein.

>PRK04296 thymidine kinase; Provisional

Probab=86.84  E-value=0.64  Score=37.46  Aligned_cols=71  Identities=13%  Similarity=0.051  Sum_probs=36.0

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCc---CCHhhhHHhHHHHccCC-cEEEEc
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKLGLKFDE---ESESGRTRSPWSRLKKE-KLQIIC   77 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~---~~~~~~~~~l~~~L~~k-r~LlV~   77 (283)
                      .|.||||+|..++.+....  -..++.+.  ..++.......++++++.....   ....+....+.+ ..++ .+++|+
T Consensus        11 ~GsGKTT~~l~~~~~~~~~--g~~v~i~k--~~~d~~~~~~~i~~~lg~~~~~~~~~~~~~~~~~~~~-~~~~~dvviID   85 (190)
T PRK04296         11 MNSGKSTELLQRAYNYEER--GMKVLVFK--PAIDDRYGEGKVVSRIGLSREAIPVSSDTDIFELIEE-EGEKIDCVLID   85 (190)
T ss_pred             CCCHHHHHHHHHHHHHHHc--CCeEEEEe--ccccccccCCcEecCCCCcccceEeCChHHHHHHHHh-hCCCCCEEEEE
Confidence            3999999999998876543  22333331  1122222234456666644322   123334444444 2223 456664

>PRK09183 transposase/IS protein; Provisional

Probab=86.79  E-value=0.74  Score=39.15  Aligned_cols=18  Identities=39%  Similarity=0.540  Sum_probs=15.3

Q ss_pred             CCCcHHHHHHHHHhhhcc
Q 041028            2 GGIGKTTLAKEVARKAKN   19 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~   19 (283)
                      +|+|||+||..+++....
T Consensus       111 ~GtGKThLa~al~~~a~~  128 (259)
T PRK09183        111 SGVGKTHLAIALGYEAVR  128 (259)
T ss_pred             CCCCHHHHHHHHHHHHHH
Confidence            699999999999887543

>PF06745 KaiC: KaiC; InterPro: IPR014774 This entry represents a domain within bacterial and archaeal proteins, most of which are hypothetical

Probab=86.72  E-value=0.64  Score=38.45  Aligned_cols=32  Identities=28%  Similarity=0.538  Sum_probs=20.5

Q ss_pred             CCCcHHHHHHHHHhhhccCCCC-CeEEEEEeCCCC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLF-DQIVFTEVSQNP   35 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~F-d~~~wv~v~~~~   35 (283)
                      +|+|||+||.++......+  + ..++||+..+++
T Consensus        28 ~GsGKT~l~~q~l~~~~~~--~ge~vlyvs~ee~~   60 (226)
T PF06745_consen   28 PGSGKTTLALQFLYNGLKN--FGEKVLYVSFEEPP   60 (226)
T ss_dssp             TTSSHHHHHHHHHHHHHHH--HT--EEEEESSS-H
T ss_pred             CCCCcHHHHHHHHHHhhhh--cCCcEEEEEecCCH
Confidence            6999999999866443222  1 357888876654

More than one copy is sometimes found in each protein in this entry. These include KaiC, which is one of the Kai proteins among which direct protein-protein association may be a critical process in the generation of circadian rhythms in cyanobacteria []. The circadian clock protein KaiC, is encoded in the kaiABC operon that controls circadian rhythms and may be universal in Cyanobacteria. Each member contains two copies of this domain, which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor. RadA/Sms is a highly conserved eubacterial protein that shares sequence similarity with both RecA strand transferase and lon protease. The RadA/Sms family are probable ATP-dependent proteases involved in both DNA repair and degradation of proteins, peptides, glycopeptides. They are classified in as non-peptidase homologues and unassigned peptidases in MEROPS peptidase family S16 (lon protease family, clan SJ). RadA/Sms is involved in recombination and recombinational repair, most likely involving the stabilisation or processing of branched DNA molecules or blocked replication forks because of its genetic redundancy with RecG and RuvABC [].; PDB: 2W0M_A 2ZTS_C 4DUG_B 3K0E_B 3K09_B 3S1A_E 3JZM_E 2GBL_B 3DVL_A 1TF7_C ....

>TIGR01242 26Sp45 26S proteasome subunit P45 family

Probab=86.66  E-value=0.44  Score=42.62  Aligned_cols=18  Identities=50%  Similarity=0.625  Sum_probs=15.8

Q ss_pred             CCCcHHHHHHHHHhhhcc
Q 041028            2 GGIGKTTLAKEVARKAKN   19 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~   19 (283)
                      +|+|||+||+++++....
T Consensus       165 pGtGKT~lakaia~~l~~  182 (364)
T TIGR01242       165 PGTGKTLLAKAVAHETNA  182 (364)
T ss_pred             CCCCHHHHHHHHHHhCCC
Confidence            699999999999997653

Many proteins may score above the trusted cutoff because an internal

>PRK13768 GTPase; Provisional

Probab=86.58  E-value=0.86  Score=38.58  Aligned_cols=29  Identities=24%  Similarity=0.349  Sum_probs=19.6

Q ss_pred             CCCCcHHHHHHHHHhhhccCCCCCeEEEEEe
Q 041028            1 MGGIGKTTLAKEVARKAKNGKLFDQIVFTEV   31 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v   31 (283)
                      .||+||||++..+.......+  ..++.|+.
T Consensus        10 ~~G~GKTt~~~~~~~~l~~~g--~~v~~i~~   38 (253)
T PRK13768         10 TAGSGKTTLTKALSDWLEEQG--YDVAIVNL   38 (253)
T ss_pred             CCCccHHHHHHHHHHHHHhcC--CceEEEEC
Confidence            389999999999887765432  23444444

>COG0802 Predicted ATPase or kinase [General function prediction only]

Probab=86.53  E-value=0.45  Score=36.57  Aligned_cols=18  Identities=39%  Similarity=0.543  Sum_probs=15.4

Q ss_pred             CCcHHHHHHHHHhhhccC
Q 041028            3 GIGKTTLAKEVARKAKNG   20 (283)
Q Consensus         3 GiGKTtLA~~v~~~~~~~   20 (283)
                      |.|||||++.+..-....
T Consensus        35 GAGKTtf~rgi~~~Lg~~   52 (149)
T COG0802          35 GAGKTTLVRGIAKGLGVD   52 (149)
T ss_pred             cCChHHHHHHHHHHcCCC
Confidence            899999999999876643

>PF13504 LRR_7: Leucine rich repeat; PDB: 3OJA_B 3G06_A 1OOK_G 1QYY_G 1SQ0_B 1P9A_G 1GWB_A 1P8V_A 1M0Z_A 1U0N_D

Probab=86.49  E-value=0.41  Score=22.22  Aligned_cols=16  Identities=19%  Similarity=0.291  Sum_probs=10.9

Q ss_pred             cccEEEEeCCCCCCCC
Q 041028          266 LYTSIVLRDIKTNVLP  281 (283)
Q Consensus       266 ~~r~lsl~~~~~~~lp  281 (283)
                      +.+.|+|.+|++++||
T Consensus         2 ~L~~L~l~~n~L~~lP   17 (17)
T PF13504_consen    2 NLRTLDLSNNRLTSLP   17 (17)
T ss_dssp             T-SEEEETSS--SSE-
T ss_pred             ccCEEECCCCCCCCCc
Confidence            5788999999999998

...

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=86.44  E-value=0.39  Score=44.93  Aligned_cols=18  Identities=39%  Similarity=0.501  Sum_probs=15.7

Q ss_pred             CCCcHHHHHHHHHhhhcc
Q 041028            2 GGIGKTTLAKEVARKAKN   19 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~   19 (283)
                      +|+||||+|+.+++....
T Consensus        45 pGtGKTTlA~~lA~~l~c   62 (504)
T PRK14963         45 RGVGKTTTARLIAMAVNC   62 (504)
T ss_pred             CCCCHHHHHHHHHHHHhc
Confidence            699999999999988653

>PRK06526 transposase; Provisional

Probab=86.40  E-value=0.5  Score=40.04  Aligned_cols=18  Identities=39%  Similarity=0.423  Sum_probs=15.6

Q ss_pred             CCCcHHHHHHHHHhhhcc
Q 041028            2 GGIGKTTLAKEVARKAKN   19 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~   19 (283)
                      +|+|||+||..+.+....
T Consensus       107 ~GtGKThLa~al~~~a~~  124 (254)
T PRK06526        107 PGTGKTHLAIGLGIRACQ  124 (254)
T ss_pred             CCCchHHHHHHHHHHHHH
Confidence            699999999999887653

>PF03205 MobB: Molybdopterin guanine dinucleotide synthesis protein B; PDB: 2F1R_B 1P9N_A 1NP6_B 2NPI_A 1XJC_A

Probab=86.36  E-value=0.52  Score=36.03  Aligned_cols=31  Identities=23%  Similarity=0.302  Sum_probs=21.5

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQ   33 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~   33 (283)
                      .|+|||||++.+.+....+ .+...+..+...
T Consensus         9 ~~sGKTTl~~~Li~~l~~~-g~~v~~ik~~~~   39 (140)
T PF03205_consen    9 KNSGKTTLIRKLINELKRR-GYRVAVIKHTDH   39 (140)
T ss_dssp             TTSSHHHHHHHHHHHHHHT-T--EEEEEE-ST
T ss_pred             CCCCHHHHHHHHHHHHhHc-CCceEEEEEccC
Confidence            4899999999999987654 355555666655

>PF00693 Herpes_TK: Thymidine kinase from herpesvirus; InterPro: IPR001889 The thymidine kinase from Herpesviridae catalyses the reaction: ATP + THYMIDINE = ADP + THYMIDINE 5'-PHOSPHATE

Probab=86.33  E-value=0.47  Score=40.48  Aligned_cols=16  Identities=44%  Similarity=0.576  Sum_probs=14.3

Q ss_pred             CCcHHHHHHHHHhhhc
Q 041028            3 GIGKTTLAKEVARKAK   18 (283)
Q Consensus         3 GiGKTtLA~~v~~~~~   18 (283)
                      ||||||+++++.+...
T Consensus         4 GvGKTT~~~~l~~~~~   19 (281)
T PF00693_consen    4 GVGKTTTLKALAEALP   19 (281)
T ss_dssp             TSSHHHHHHHHHHCCT
T ss_pred             CcCHHHHHHHHHHccC
Confidence            9999999999998654

The enzyme is not subject to feedback inhibition by its product and the crystal structure of the enzyme from Human herpesvirus 1 (HHV-1) has been reported [].; GO: 0004797 thymidine kinase activity, 0005524 ATP binding, 0006230 TMP biosynthetic process; PDB: 1P73_B 1P75_C 1P6X_A 1P72_A 1OSN_D 1E2J_B 1KI3_A 3RDP_B 1P7C_A 3F0T_A ....

>PRK13765 ATP-dependent protease Lon; Provisional

Probab=86.32  E-value=0.81  Score=44.01  Aligned_cols=47  Identities=19%  Similarity=0.167  Sum_probs=34.5

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHHHhCC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKLGL   50 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~~l~~   50 (283)
                      +|+||||+|+.+.+.... .+|+..+|..- ..-+...+++.++..+|.
T Consensus        59 ~G~GKttla~~l~~~l~~-~~~~~~~~~~n-p~~~~~~~~~~v~~~~G~  105 (637)
T PRK13765         59 PGTGKSMLAKAMAELLPK-EELQDILVYPN-PEDPNNPKIRTVPAGKGK  105 (637)
T ss_pred             CCCcHHHHHHHHHHHcCh-HhHHHheEeeC-CCcchHHHHHHHHHhcCH
Confidence            699999999999987532 34577788655 334677778888877765

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=86.25  E-value=4  Score=40.85  Aligned_cols=50  Identities=18%  Similarity=0.068  Sum_probs=35.1

Q ss_pred             CCCCcHHHHHHHHHhhhccC---CCCC--eEEEEEeCCCCCHHHHHHHHHHHhCC
Q 041028            1 MGGIGKTTLAKEVARKAKNG---KLFD--QIVFTEVSQNPNIKKIQGEIAFKLGL   50 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~---~~Fd--~~~wv~v~~~~~~~~l~~~i~~~l~~   50 (283)
                      .+|+|||+.++.|.+.....   ....  .+++|+...-.+...++..|.++|..
T Consensus       789 ~PGTGKTATVK~VLrELqeeaeqk~lp~f~vVYINCm~Lstp~sIYqvI~qqL~g  843 (1164)
T PTZ00112        789 MPGTGKTATVYSVIQLLQHKTKQKLLPSFNVFEINGMNVVHPNAAYQVLYKQLFN  843 (1164)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHhhccCCCceEEEEeCCccCCHHHHHHHHHHHHcC
Confidence            47999999999998775321   1122  24666666666788888888888843

>PRK05201 hslU ATP-dependent protease ATP-binding subunit HslU; Provisional

Probab=86.22  E-value=0.94  Score=41.18  Aligned_cols=18  Identities=39%  Similarity=0.682  Sum_probs=15.7

Q ss_pred             CCCcHHHHHHHHHhhhcc
Q 041028            2 GGIGKTTLAKEVARKAKN   19 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~   19 (283)
                      +|+|||+||+.+......
T Consensus        59 ~G~GKT~LAr~LAk~l~~   76 (443)
T PRK05201         59 TGVGKTEIARRLAKLANA   76 (443)
T ss_pred             CCCCHHHHHHHHHHHhCC
Confidence            699999999999987654

>PF10662 PduV-EutP: Ethanolamine utilisation - propanediol utilisation; InterPro: IPR012381 Members of this family function in ethanolamine [] and propanediol [] degradation pathways

Probab=86.16  E-value=0.46  Score=36.40  Aligned_cols=16  Identities=44%  Similarity=0.617  Sum_probs=13.7

Q ss_pred             CCCcHHHHHHHHHhhh
Q 041028            2 GGIGKTTLAKEVARKA   17 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~   17 (283)
                      .|+|||||++.+-...
T Consensus        10 ~g~GKTTL~q~L~~~~   25 (143)
T PF10662_consen   10 SGSGKTTLAQALNGEE   25 (143)
T ss_pred             CCCCHHHHHHHHcCCC
Confidence            4999999999998753

Both pathways require coenzyme B12 (adenosylcobalamin, AdoCbl). Bacteria that harbour these pathways can use ethanolamine as a source of carbon and nitrogen, or propanediol as a sole carbon and energy source, respectively. The exact roles of the EutP and PduV proteins in these respective pathways are not yet determined. Members of this family contain P-loop consensus motifs in the N-terminal part, and are distantly related to various GTPases and ATPases, including ATPase components of transport systems. Propanediol degradation is thought to be important for the natural Salmonella populations, since propanediol is produced by the fermentation of the common plant sugars rhamnose and fucose [, ]. More than 1% of the Salmonella enterica genome is devoted to the utilisation of propanediol and cobalamin biosynthesis. In vivo expression technology has indicated that propanediol utilisation (pdu) genes may be important for growth in host tissues, and competitive index studies with mice have shown that pdu mutations confer a virulence defect [, ]. The pdu operon is contiguous and co-regulated with the cobalamin (B12) biosynthesis cob operon, indicating that propanediol catabolism may be the primary reason for de novo B12 synthesis in Salmonella [, , ]. Please see IPR003207 from INTERPRO, IPR003208 from INTERPRO, IPR009204 from INTERPRO, IPR009191 from INTERPRO, IPR009192 from INTERPRO for more details on the propanediol utilisation pathway and the pdu operon.; GO: 0005524 ATP binding, 0006576 cellular biogenic amine metabolic process

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional

Probab=86.15  E-value=1.8  Score=40.90  Aligned_cols=17  Identities=41%  Similarity=0.620  Sum_probs=14.8

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      .|+||||+|+.+++...
T Consensus        47 ~GvGKTTlAr~lAk~L~   63 (546)
T PRK14957         47 RGVGKTTLGRLLAKCLN   63 (546)
T ss_pred             CCCCHHHHHHHHHHHhC
Confidence            69999999999998653

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=86.13  E-value=0.82  Score=42.06  Aligned_cols=29  Identities=17%  Similarity=0.265  Sum_probs=21.3

Q ss_pred             CCCcHHHHHHHHHhhhccCCCC-CeEEEEEe
Q 041028            2 GGIGKTTLAKEVARKAKNGKLF-DQIVFTEV   31 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~F-d~~~wv~v   31 (283)
                      +|+|||+||+++++..... +. ..++|++.
T Consensus       139 ~G~GKTHLl~ai~~~l~~~-~~~~~v~yi~~  168 (440)
T PRK14088        139 VGLGKTHLLQSIGNYVVQN-EPDLRVMYITS  168 (440)
T ss_pred             CCCcHHHHHHHHHHHHHHh-CCCCeEEEEEH
Confidence            5999999999999986543 22 24667654

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional

Probab=86.09  E-value=1.8  Score=40.68  Aligned_cols=46  Identities=20%  Similarity=0.353  Sum_probs=29.3

Q ss_pred             CCCcHHHHHHHHHhhhccCC-------------------CCCeEEEEEeCCCCCHHHHHHHHHHHh
Q 041028            2 GGIGKTTLAKEVARKAKNGK-------------------LFDQIVFTEVSQNPNIKKIQGEIAFKL   48 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~-------------------~Fd~~~wv~v~~~~~~~~l~~~i~~~l   48 (283)
                      .|+||||+|+.+++..-...                   .|..++.++.+....+.++ ++++..+
T Consensus        47 ~G~GKTt~A~~lAk~l~c~~~~~~~pCg~C~~C~~i~~g~~~d~~eidaas~~~v~~i-R~l~~~~  111 (509)
T PRK14958         47 RGVGKTTISRILAKCLNCEKGVSANPCNDCENCREIDEGRFPDLFEVDAASRTKVEDT-RELLDNI  111 (509)
T ss_pred             CCCCHHHHHHHHHHHhcCCCCCCcccCCCCHHHHHHhcCCCceEEEEcccccCCHHHH-HHHHHHH
Confidence            69999999999998754321                   2323455555555556654 5566654

>cd00880 Era_like Era (E

Probab=86.06  E-value=0.48  Score=35.77  Aligned_cols=16  Identities=19%  Similarity=0.300  Sum_probs=14.0

Q ss_pred             CCCCcHHHHHHHHHhh
Q 041028            1 MGGIGKTTLAKEVARK   16 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~   16 (283)
                      .+|+|||||++.+++.
T Consensus         4 ~~gsGKstl~~~l~~~   19 (163)
T cd00880           4 RTNAGKSSLLNALLGQ   19 (163)
T ss_pred             CCCCCHHHHHHHHhCc
Confidence            3699999999999875

coli Ras-like protein)-like. This family includes several distinct subfamilies (TrmE/ThdF, FeoB, YihA (EngG), Era, and EngA/YfgK) that generally show sequence conservation in the region between the Walker A and B motifs (G1 and G3 box motifs), to the exclusion of other GTPases. TrmE is ubiquitous in bacteria and is a widespread mitochondrial protein in eukaryotes, but is absent from archaea. The yeast member of TrmE family, MSS1, is involved in mitochondrial translation; bacterial members are often present in translation-related operons. FeoB represents an unusual adaptation of GTPases for high-affinity iron (II) transport. YihA (EngB) family of GTPases is typified by the E. coli YihA, which is an essential protein involved in cell division control. Era is characterized by a distinct derivative of the KH domain (the pseudo-KH domain) which is located C-terminal to the GTPase domain. EngA and its orthologs are composed of two GTPase domains and, since the se

>PRK05800 cobU adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase; Validated

Probab=86.01  E-value=4.1  Score=32.17  Aligned_cols=42  Identities=19%  Similarity=0.268  Sum_probs=24.5

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHHHhC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKLG   49 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~~l~   49 (283)
                      +|+||||+|..+......     ..+++.-... .-.+..++|.....
T Consensus        10 ~~sGKS~~a~~l~~~~~~-----~~~~iat~~~-~~~e~~~ri~~h~~   51 (170)
T PRK05800         10 ARSGKSRFAERLAAQSGL-----QVLYIATAQP-FDDEMAARIAHHRQ   51 (170)
T ss_pred             CCccHHHHHHHHHHHcCC-----CcEeCcCCCC-ChHHHHHHHHHHHh
Confidence            589999999999876421     1233333333 33455566655443

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=85.92  E-value=1.7  Score=43.32  Aligned_cols=18  Identities=39%  Similarity=0.569  Sum_probs=15.6

Q ss_pred             CCCcHHHHHHHHHhhhcc
Q 041028            2 GGIGKTTLAKEVARKAKN   19 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~   19 (283)
                      .|+||||+|+.+++....
T Consensus        47 pGtGKTTLARiLAk~Lnc   64 (944)
T PRK14949         47 RGVGKTSLARLFAKGLNC   64 (944)
T ss_pred             CCCCHHHHHHHHHHhccC
Confidence            599999999999987644

>PRK08181 transposase; Validated

Probab=85.86  E-value=0.67  Score=39.61  Aligned_cols=60  Identities=22%  Similarity=0.212  Sum_probs=34.5

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCcCCHhhhHHhHHHHccCCcEEEEc
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKLGLKFDEESESGRTRSPWSRLKKEKLQIIC   77 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~kr~LlV~   77 (283)
                      +|+|||.||..+.+.....  .-.++|++      ..+++..+.....    ..+    ...+.+.+..-.+|||+
T Consensus       115 ~GtGKTHLa~Aia~~a~~~--g~~v~f~~------~~~L~~~l~~a~~----~~~----~~~~l~~l~~~dLLIID  174 (269)
T PRK08181        115 PGGGKSHLAAAIGLALIEN--GWRVLFTR------TTDLVQKLQVARR----ELQ----LESAIAKLDKFDLLILD  174 (269)
T ss_pred             CCCcHHHHHHHHHHHHHHc--CCceeeee------HHHHHHHHHHHHh----CCc----HHHHHHHHhcCCEEEEe
Confidence            6999999999999876533  23445554      3455555543321    111    22233445556777773

>PRK14527 adenylate kinase; Provisional

Probab=85.83  E-value=0.55  Score=37.78  Aligned_cols=18  Identities=33%  Similarity=0.361  Sum_probs=15.5

Q ss_pred             CCCcHHHHHHHHHhhhcc
Q 041028            2 GGIGKTTLAKEVARKAKN   19 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~   19 (283)
                      +|+||||+|+.+++....
T Consensus        15 pGsGKsT~a~~La~~~~~   32 (191)
T PRK14527         15 PGAGKGTQAERLAQELGL   32 (191)
T ss_pred             CCCCHHHHHHHHHHHhCC
Confidence            799999999999887653

>TIGR03263 guanyl_kin guanylate kinase

Probab=85.80  E-value=0.49  Score=37.51  Aligned_cols=16  Identities=38%  Similarity=0.690  Sum_probs=14.1

Q ss_pred             CCCcHHHHHHHHHhhh
Q 041028            2 GGIGKTTLAKEVARKA   17 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~   17 (283)
                      .|+||||||+.++...
T Consensus        10 ~GsGKsTl~~~L~~~~   25 (180)
T TIGR03263        10 SGVGKSTLVKALLEED   25 (180)
T ss_pred             CCCCHHHHHHHHHccC
Confidence            6999999999998853

Members of this family are the enzyme guanylate kinase, also called GMP kinase. This enzyme transfers a phosphate from ATP to GMP, yielding ADP and GDP.

>COG4778 PhnL ABC-type phosphonate transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=85.79  E-value=0.85  Score=36.12  Aligned_cols=27  Identities=19%  Similarity=0.282  Sum_probs=22.2

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEe
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEV   31 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v   31 (283)
                      +|+|||||.+.+|.++...   .+.+||.-
T Consensus        46 SG~GKStllr~LYaNY~~d---~G~I~v~H   72 (235)
T COG4778          46 SGSGKSTLLRSLYANYLPD---EGQILVRH   72 (235)
T ss_pred             CCCcHHHHHHHHHhccCCC---CceEEEEe
Confidence            6999999999999987653   57888853

>TIGR00064 ftsY signal recognition particle-docking protein FtsY

Probab=85.78  E-value=1.8  Score=37.07  Aligned_cols=74  Identities=18%  Similarity=0.157  Sum_probs=40.4

Q ss_pred             CCCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCH--HHHHHHHHHHhCCCCC----cCCHhh-hHHhHHHHc-cCCc
Q 041028            1 MGGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNI--KKIQGEIAFKLGLKFD----EESESG-RTRSPWSRL-KKEK   72 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~--~~l~~~i~~~l~~~~~----~~~~~~-~~~~l~~~L-~~kr   72 (283)
                      .+|+||||++..++......  -..+..++... +..  .+-++..++..+.+.-    ..+... ....+.... ++..
T Consensus        80 ~~G~GKTTt~akLA~~l~~~--g~~V~li~~D~-~r~~a~~ql~~~~~~~~i~~~~~~~~~dp~~~~~~~l~~~~~~~~D  156 (272)
T TIGR00064        80 VNGVGKTTTIAKLANKLKKQ--GKSVLLAAGDT-FRAAAIEQLEEWAKRLGVDVIKQKEGADPAAVAFDAIQKAKARNID  156 (272)
T ss_pred             CCCCcHHHHHHHHHHHHHhc--CCEEEEEeCCC-CCHHHHHHHHHHHHhCCeEEEeCCCCCCHHHHHHHHHHHHHHCCCC
Confidence            37999999999998776533  23456666543 322  3444556666664421    112222 223343333 4457


Q ss_pred             EEEEc
Q 041028           73 LQIIC   77 (283)
Q Consensus        73 ~LlV~   77 (283)
                      ++||+
T Consensus       157 ~ViID  161 (272)
T TIGR00064       157 VVLID  161 (272)
T ss_pred             EEEEe
Confidence            88883

There is a weak division between FtsY and SRP54; both are GTPases. In E.coli, ftsY is an essential gene located in an operon with cell division genes ftsE and ftsX, but its apparent function is as the signal recognition particle docking protein.

>TIGR03815 CpaE_hom_Actino helicase/secretion neighborhood CpaE-like protein

Probab=85.68  E-value=0.5  Score=41.47  Aligned_cols=17  Identities=47%  Similarity=0.632  Sum_probs=14.9

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      ||+||||+|..++....
T Consensus       103 GGvGkTT~a~nLA~~la  119 (322)
T TIGR03815       103 GGAGASTLAAALALAAA  119 (322)
T ss_pred             CCCcHHHHHHHHHHHHH
Confidence            89999999999887654

Members of this protein family belong to the MinD/ParA family of P-loop NTPases, and in particular show homology to the CpaE family of pilus assembly proteins (see PubMed:12370432). Nearly all members are found, not only in a gene context consistent with pilus biogenesis or a pilus-like secretion apparatus, but also near a DEAD/DEAH-box helicase, suggesting an involvement in DNA transfer activity. The model describes a clade restricted to the Actinobacteria.

>PRK05439 pantothenate kinase; Provisional

Probab=85.65  E-value=3.3  Score=36.15  Aligned_cols=17  Identities=24%  Similarity=0.255  Sum_probs=14.4

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      +|+||||+|+.+.....
T Consensus        95 ~gsGKSTla~~L~~~l~  111 (311)
T PRK05439         95 VAVGKSTTARLLQALLS  111 (311)
T ss_pred             CCCCHHHHHHHHHHHHH
Confidence            59999999999887553

>TIGR00176 mobB molybdopterin-guanine dinucleotide biosynthesis protein MobB

Probab=85.57  E-value=0.69  Score=35.99  Aligned_cols=26  Identities=23%  Similarity=0.272  Sum_probs=19.0

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEE
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVF   28 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~w   28 (283)
                      .|+|||||+.++....+.+ .+...+.
T Consensus         8 ~gsGKTtl~~~l~~~l~~~-G~~V~vi   33 (155)
T TIGR00176         8 KNSGKTTLIERLVKALKAR-GYRVATI   33 (155)
T ss_pred             CCCCHHHHHHHHHHHHHhc-CCeEEEE
Confidence            5999999999999987643 3444443

This molybdenum cofactor biosynthesis enzyme is similar to the urease accessory protein UreG and to the hydrogenase accessory protein HypB, both GTP hydrolases involved in loading nickel into the metallocenters of their respective target enzymes.

>COG1100 GTPase SAR1 and related small G proteins [General function prediction only]

Probab=85.55  E-value=0.49  Score=38.67  Aligned_cols=19  Identities=37%  Similarity=0.515  Sum_probs=15.8

Q ss_pred             CCCCcHHHHHHHHHhhhcc
Q 041028            1 MGGIGKTTLAKEVARKAKN   19 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~   19 (283)
                      .+|+|||||...+.++.-.
T Consensus        13 ~~g~GKTtl~~~l~~~~~~   31 (219)
T COG1100          13 DGGVGKTTLLNRLVGDEFP   31 (219)
T ss_pred             CCCccHHHHHHHHhcCcCc
Confidence            4899999999999887543

>cd01673 dNK Deoxyribonucleoside kinase (dNK) catalyzes the phosphorylation of deoxyribonucleosides to yield corresponding monophosphates (dNMPs)

Probab=85.48  E-value=0.61  Score=37.45  Aligned_cols=17  Identities=53%  Similarity=0.591  Sum_probs=14.5

Q ss_pred             CCCCcHHHHHHHHHhhh
Q 041028            1 MGGIGKTTLAKEVARKA   17 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (283)
                      +.|+||||+++.+.+..
T Consensus         7 ~~GsGKSTl~~~L~~~~   23 (193)
T cd01673           7 NIGAGKSTLAKELAEHL   23 (193)
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            35999999999998863

This family consists of various deoxynucleoside kinases including deoxyribo- cytidine (EC 2.7.1.74), guanosine (EC 2.7.1.113), adenosine (EC 2.7.1.76), and thymidine (EC 2.7.1.21) kinases. They are key enzymes in the salvage of deoxyribonucleosides originating from extra- or intracellular breakdown of DNA.

>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family

Probab=85.47  E-value=1.1  Score=37.96  Aligned_cols=31  Identities=16%  Similarity=0.293  Sum_probs=22.3

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQN   34 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~   34 (283)
                      +|+|||+||.+++.....+  =..++|++...+
T Consensus        45 pGtGKT~l~~qf~~~~a~~--Ge~vlyis~Ee~   75 (259)
T TIGR03878        45 SDTGKSLMVEQFAVTQASR--GNPVLFVTVESP   75 (259)
T ss_pred             CCCCHHHHHHHHHHHHHhC--CCcEEEEEecCC
Confidence            6999999999976654322  246788888753

This KaiC domain-containing protein family occurs sporadically across a broad taxonomic range (Euryarchaeota, Aquificae, Dictyoglomi, Epsilonproteobacteria, and Firmicutes), but exclusively in thermophiles.

>PRK14526 adenylate kinase; Provisional

Probab=85.45  E-value=0.74  Score=37.84  Aligned_cols=18  Identities=33%  Similarity=0.403  Sum_probs=15.0

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      .+|+||||+|+.++....
T Consensus         8 ~pGsGKsT~a~~La~~~~   25 (211)
T PRK14526          8 PPGSGKGTIAKILSNELN   25 (211)
T ss_pred             CCCCCHHHHHHHHHHHhC
Confidence            479999999999987653

>PTZ00035 Rad51 protein; Provisional

Probab=85.44  E-value=2.7  Score=37.27  Aligned_cols=48  Identities=17%  Similarity=0.176  Sum_probs=32.2

Q ss_pred             CCCcHHHHHHHHHhhhcc---CC-CCCeEEEEEeCCCCCHHHHHHHHHHHhCC
Q 041028            2 GGIGKTTLAKEVARKAKN---GK-LFDQIVFTEVSQNPNIKKIQGEIAFKLGL   50 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~---~~-~Fd~~~wv~v~~~~~~~~l~~~i~~~l~~   50 (283)
                      +|+|||||+..++-....   .. .=..++|++-...|+... +.++++.++.
T Consensus       127 ~GsGKT~l~~~l~~~~qlp~~~gg~~g~vvyIdtE~~f~~er-i~~ia~~~g~  178 (337)
T PTZ00035        127 FRTGKTQLCHTLCVTCQLPIEQGGGEGKVLYIDTEGTFRPER-IVQIAERFGL  178 (337)
T ss_pred             CCCchhHHHHHHHHHhccccccCCCCceEEEEEccCCCCHHH-HHHHHHHhCC
Confidence            699999999988754331   11 113567999888788776 3555666654

>TIGR02173 cyt_kin_arch cytidylate kinase, putative

Probab=85.39  E-value=0.63  Score=36.36  Aligned_cols=18  Identities=50%  Similarity=0.501  Sum_probs=15.2

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      ..|+||||+|+.+.+...
T Consensus         8 ~~GSGKstia~~la~~lg   25 (171)
T TIGR02173         8 PPGSGKTTVAKILAEKLS   25 (171)
T ss_pred             CCCCCHHHHHHHHHHHcC
Confidence            469999999999988653

Proteins in this family are believed to be cytidylate kinase. Members of this family are found in the archaea and in spirochaetes, and differ considerably from the common bacterial form of cytidylate kinase described by TIGR00017.

>TIGR00554 panK_bact pantothenate kinase, bacterial type

Probab=85.38  E-value=2.8  Score=36.22  Aligned_cols=17  Identities=24%  Similarity=0.257  Sum_probs=13.4

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      .|+||||||+.+..-..
T Consensus        71 ~GSGKSTlar~L~~ll~   87 (290)
T TIGR00554        71 VAVGKSTTARILQALLS   87 (290)
T ss_pred             CCCCHHHHHHHHHHHHh
Confidence            59999999988765543

Shown to be a homodimer in E. coli. This enzyme catalyzes the rate-limiting step in the biosynthesis of coenzyme A. It is very well conserved from E. coli to B. subtilis, but differs considerably from known eukaryotic forms, described in a separate model.

>PRK13234 nifH nitrogenase reductase; Reviewed

Probab=85.35  E-value=0.61  Score=40.43  Aligned_cols=17  Identities=35%  Similarity=0.552  Sum_probs=14.0

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      |||||||++..+.....
T Consensus        13 GGvGKTt~~~nLa~~la   29 (295)
T PRK13234         13 GGIGKSTTSQNTLAALV   29 (295)
T ss_pred             CCccHHHHHHHHHHHHH
Confidence            89999999888776544

>PLN02200 adenylate kinase family protein

Probab=85.33  E-value=0.62  Score=38.95  Aligned_cols=18  Identities=22%  Similarity=0.233  Sum_probs=15.2

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      ++|+||||+|+.++....
T Consensus        51 ~PGSGKsT~a~~La~~~g   68 (234)
T PLN02200         51 GPGSGKGTQCEKIVETFG   68 (234)
T ss_pred             CCCCCHHHHHHHHHHHhC
Confidence            479999999999987653

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=85.26  E-value=0.57  Score=42.37  Aligned_cols=17  Identities=53%  Similarity=0.667  Sum_probs=15.3

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      +|+|||+||+++++...
T Consensus       174 pGtGKT~lAkaia~~~~  190 (389)
T PRK03992        174 PGTGKTLLAKAVAHETN  190 (389)
T ss_pred             CCCChHHHHHHHHHHhC
Confidence            69999999999999765

>PRK08840 replicative DNA helicase; Provisional

Probab=85.16  E-value=1.6  Score=40.43  Aligned_cols=45  Identities=16%  Similarity=0.208  Sum_probs=31.2

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHHHhC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKLG   49 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~~l~   49 (283)
                      +|+|||++|..++.....+.. ..++|.++.  .+..++..+++....
T Consensus       226 Pg~GKTafalnia~~~a~~~~-~~v~~fSlE--Ms~~ql~~Rlla~~s  270 (464)
T PRK08840        226 PSMGKTTFAMNLCENAAMDQD-KPVLIFSLE--MPAEQLMMRMLASLS  270 (464)
T ss_pred             CCCchHHHHHHHHHHHHHhCC-CeEEEEecc--CCHHHHHHHHHHhhC
Confidence            799999999988877543222 245555544  678888888887654

>PRK13341 recombination factor protein RarA/unknown domain fusion protein; Reviewed

Probab=85.14  E-value=0.62  Score=45.54  Aligned_cols=18  Identities=44%  Similarity=0.678  Sum_probs=15.7

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      .+|+||||||+.+++...
T Consensus        60 PpGtGKTTLA~aIA~~~~   77 (725)
T PRK13341         60 PPGVGKTTLARIIANHTR   77 (725)
T ss_pred             CCCCCHHHHHHHHHHHhc
Confidence            379999999999998765

>PRK00279 adk adenylate kinase; Reviewed

Probab=85.12  E-value=0.65  Score=38.15  Aligned_cols=18  Identities=44%  Similarity=0.351  Sum_probs=15.3

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      .+|+||||+|+.++....
T Consensus         8 ~pGsGKsT~a~~la~~~~   25 (215)
T PRK00279          8 PPGAGKGTQAKFIAEKYG   25 (215)
T ss_pred             CCCCCHHHHHHHHHHHhC
Confidence            479999999999987654

>PRK14531 adenylate kinase; Provisional

Probab=85.06  E-value=0.67  Score=37.02  Aligned_cols=18  Identities=28%  Similarity=0.246  Sum_probs=15.5

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      .+|+||||+++.++....
T Consensus        10 ~pGsGKsT~~~~la~~~g   27 (183)
T PRK14531         10 PPGAGKGTQAARLCAAHG   27 (183)
T ss_pred             CCCCCHHHHHHHHHHHhC
Confidence            379999999999988764

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=85.01  E-value=0.86  Score=40.01  Aligned_cols=17  Identities=35%  Similarity=0.481  Sum_probs=15.0

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      +|+||||+|+.+++...
T Consensus        45 ~GtGKT~la~~~~~~l~   61 (337)
T PRK12402         45 PGSGKTAAVRALARELY   61 (337)
T ss_pred             CCCCHHHHHHHHHHHhc
Confidence            69999999999998764

>smart00173 RAS Ras subfamily of RAS small GTPases

Probab=85.01  E-value=0.58  Score=36.16  Aligned_cols=15  Identities=33%  Similarity=0.733  Sum_probs=13.2

Q ss_pred             CCCcHHHHHHHHHhh
Q 041028            2 GGIGKTTLAKEVARK   16 (283)
Q Consensus         2 gGiGKTtLA~~v~~~   16 (283)
                      +|+|||||+..+.+.
T Consensus         9 ~~~GKTsli~~~~~~   23 (164)
T smart00173        9 GGVGKSALTIQFVQG   23 (164)
T ss_pred             CCCCHHHHHHHHHhC
Confidence            699999999998764

Similar in fold and function to the bacterial EF-Tu GTPase. p21Ras couples receptor Tyr kinases and G protein receptors to protein kinase cascades

>PRK10536 hypothetical protein; Provisional

Probab=85.00  E-value=1  Score=38.08  Aligned_cols=27  Identities=33%  Similarity=0.352  Sum_probs=18.5

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEE
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVF   28 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~w   28 (283)
                      +|.|||+||.+++.+.-..+.|+.++-
T Consensus        83 aGTGKT~La~a~a~~~l~~~~~~kIiI  109 (262)
T PRK10536         83 AGCGKTWISAAKAAEALIHKDVDRIIV  109 (262)
T ss_pred             CCCCHHHHHHHHHHHHHhcCCeeEEEE
Confidence            699999999998886332233554443

>PRK04195 replication factor C large subunit; Provisional

Probab=84.90  E-value=1.8  Score=40.42  Aligned_cols=17  Identities=41%  Similarity=0.601  Sum_probs=15.3

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      +|+||||+|+.++++..
T Consensus        48 pG~GKTtla~ala~el~   64 (482)
T PRK04195         48 PGVGKTSLAHALANDYG   64 (482)
T ss_pred             CCCCHHHHHHHHHHHcC
Confidence            69999999999999764

>PRK02496 adk adenylate kinase; Provisional

Probab=84.85  E-value=0.69  Score=36.87  Aligned_cols=18  Identities=33%  Similarity=0.276  Sum_probs=15.3

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      .+|+||||+|+.+.....
T Consensus         9 ~pGsGKst~a~~la~~~~   26 (184)
T PRK02496          9 PPGAGKGTQAVVLAEHLH   26 (184)
T ss_pred             CCCCCHHHHHHHHHHHhC
Confidence            379999999999988654

>TIGR01425 SRP54_euk signal recognition particle protein SRP54

Probab=84.78  E-value=2.7  Score=38.43  Aligned_cols=48  Identities=19%  Similarity=0.123  Sum_probs=29.6

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCC-CCCHHHHHHHHHHHhCCC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQ-NPNIKKIQGEIAFKLGLK   51 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~-~~~~~~l~~~i~~~l~~~   51 (283)
                      .|+||||+|..++...+..+ + .++.|+... .+...+-++......+.+
T Consensus       109 ~GvGKTTtaaKLA~~l~~~G-~-kV~lV~~D~~R~aA~eQLk~~a~~~~vp  157 (429)
T TIGR01425       109 QGSGKTTTCTKLAYYYQRKG-F-KPCLVCADTFRAGAFDQLKQNATKARIP  157 (429)
T ss_pred             CCCCHHHHHHHHHHHHHHCC-C-CEEEEcCcccchhHHHHHHHHhhccCCe
Confidence            69999999999988765432 2 445555432 223344445566666665

This model represents examples from the eukaryotic cytosol of the signal recognition particle protein component, SRP54. This GTP-binding protein is a component of the eukaryotic signal recognition particle, along with several other protein subunits and a 7S RNA. Some species, including Arabidopsis, have several closely related forms. The extreme C-terminal region is glycine-rich and lower in complexity, poorly conserved between species, and excluded from this model.

>TIGR03880 KaiC_arch_3 KaiC domain protein, AF_0351 family

Probab=84.74  E-value=2.5  Score=34.88  Aligned_cols=31  Identities=16%  Similarity=0.283  Sum_probs=22.5

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQN   34 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~   34 (283)
                      +|+|||++|.+++.....+  =..++|++...+
T Consensus        25 ~G~GKt~~~~~~~~~~~~~--g~~~~y~s~e~~   55 (224)
T TIGR03880        25 YGTGKTTFSLQFLYQGLKN--GEKAMYISLEER   55 (224)
T ss_pred             CCCCHHHHHHHHHHHHHhC--CCeEEEEECCCC
Confidence            6999999999987654322  146788888764

This model represents a rather narrowly distributed archaeal protein family in which members have a single copy of the KaiC domain. This stands in contrast to the circadian clock protein KaiC itself, with two copies of the domain. Members are expected to have weak ATPase activity, by homology to the autokinase/autophosphorylase KaiC itself.

>TIGR03018 pepcterm_TyrKin exopolysaccharide/PEPCTERM locus tyrosine autokinase

Probab=84.74  E-value=0.63  Score=38.02  Aligned_cols=30  Identities=17%  Similarity=0.174  Sum_probs=20.0

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVS   32 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~   32 (283)
                      ||+||||+|..++........ ..++.|+..
T Consensus        45 gG~GkSt~a~nLA~~la~~~g-~~VLlvD~D   74 (207)
T TIGR03018        45 PGEGKSFTAINLAISLAQEYD-KTVLLIDAD   74 (207)
T ss_pred             CCCCHHHHHHHHHHHHHHhcC-CeEEEEECC
Confidence            899999999998876542100 245666554

Members of this protein family are related to a known protein-tyrosine autokinase and to numerous homologs from exopolysaccharide biosynthesis region proteins, many of which are designated as chain length determinants. Most members of this family contain a short region, immediately C-terminal to the region modeled here, with an abundance of Tyr residues. These C-terminal tyrosine residues are likely to be autophosphorylation sites. Some members of this family are fusion proteins.

>COG1124 DppF ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]

Probab=84.72  E-value=0.91  Score=37.88  Aligned_cols=17  Identities=47%  Similarity=0.581  Sum_probs=14.4

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      .|.|||||++.+.--.+
T Consensus        42 SGsGKSTL~r~l~Gl~~   58 (252)
T COG1124          42 SGSGKSTLARLLAGLEK   58 (252)
T ss_pred             CCCCHHHHHHHHhcccC
Confidence            59999999999987544

>PRK09087 hypothetical protein; Validated

Probab=84.72  E-value=0.67  Score=38.55  Aligned_cols=16  Identities=44%  Similarity=0.393  Sum_probs=14.0

Q ss_pred             CCCcHHHHHHHHHhhh
Q 041028            2 GGIGKTTLAKEVARKA   17 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~   17 (283)
                      .|+|||+|++.+++..
T Consensus        53 ~GsGKThLl~~~~~~~   68 (226)
T PRK09087         53 VGSGKTHLASIWREKS   68 (226)
T ss_pred             CCCCHHHHHHHHHHhc
Confidence            5999999999988764

>TIGR01351 adk adenylate kinases

Probab=84.69  E-value=0.69  Score=37.84  Aligned_cols=18  Identities=44%  Similarity=0.412  Sum_probs=15.2

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      .+|+||||+|+.+.....
T Consensus         7 ~pGsGKsT~a~~La~~~g   24 (210)
T TIGR01351         7 PPGSGKGTQAKRIAEKYG   24 (210)
T ss_pred             CCCCCHHHHHHHHHHHcC
Confidence            479999999999987654

Adenylate kinase (EC 2.7.4.3) converts ATP + AMP to ADP + ADP, that is, uses ATP as a phosphate donor for AMP. Most members of this family are known or believed to be adenylate kinase. However, some members accept other nucleotide triphosphates as donors, may be unable to use ATP, and may fail to complement adenylate kinase mutants. An example of a nucleoside-triphosphate--adenylate kinase (EC 2.7.4.10) is a GTP:AMP phosphotransferase. This family is designated subfamily rather than equivalog for this reason.

>smart00763 AAA_PrkA PrkA AAA domain

Probab=84.66  E-value=0.64  Score=41.31  Aligned_cols=50  Identities=14%  Similarity=0.242  Sum_probs=30.0

Q ss_pred             CCCcHHHHHHHHHhhhcc-----CCCCCeEEEE----EeCCCC---CHHHHHHHHHHHhCCC
Q 041028            2 GGIGKTTLAKEVARKAKN-----GKLFDQIVFT----EVSQNP---NIKKIQGEIAFKLGLK   51 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~-----~~~Fd~~~wv----~v~~~~---~~~~l~~~i~~~l~~~   51 (283)
                      +|+||||||..+++....     ++.|-..-|.    .+-+.+   -..+.-..+.+.++.+
T Consensus        87 PGsGKStla~~La~~l~~ys~t~eG~~Y~~~~~~~~sp~~e~Pl~l~p~~~r~~~~~~~~~~  148 (361)
T smart00763       87 VGGGKSSLVECLKRGLEEYSKTPEGRRYTFKWNGEESPMHEDPLHLFPDELREDLEDEYGIP  148 (361)
T ss_pred             CCCCHHHHHHHHHHHHhhhcccccCceEEEEecCCCCCCccCCcccCCHHHHHHHHHHhCCC
Confidence            699999999999988654     1234344452    222221   2455566666777653

This is a family of PrkA bacterial and archaeal serine kinases approximately 630 residues long. This is the N-terminal AAA domain.

>cd04139 RalA_RalB RalA/RalB subfamily

Probab=84.63  E-value=0.6  Score=35.87  Aligned_cols=16  Identities=31%  Similarity=0.636  Sum_probs=13.8

Q ss_pred             CCCcHHHHHHHHHhhh
Q 041028            2 GGIGKTTLAKEVARKA   17 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~   17 (283)
                      +|+|||||+..+.+..
T Consensus         9 ~~~GKTsl~~~l~~~~   24 (164)
T cd04139           9 GGVGKSALTLQFMYDE   24 (164)
T ss_pred             CCCCHHHHHHHHHhCC
Confidence            7999999999998653

The Ral (Ras-like) subfamily consists of the highly homologous RalA and RalB. Ral proteins are believed to play a crucial role in tumorigenesis, metastasis, endocytosis, and actin cytoskeleton dynamics. Despite their high sequence similarity (80% sequence identity), nonoverlapping and opposing functions have been assigned to RalA and RalBs in tumor migration. In human bladder and prostate cancer cells, RalB promotes migration while RalA inhibits it. A Ral-specific set of GEFs has been identified that are activated by Ras binding. This RalGEF activity is enhanced by Ras binding to another of its target proteins, phosphatidylinositol 3-kinase (PI3K). Ral effectors include RLIP76/RalBP1, a Rac/cdc42 GAP, and the exocyst (Sec6/8) complex, a heterooctomeric protein complex that is involved in tethering vesicles to specific sites on the plasma membrane prior to exocytosis. In rat kidney cells, RalB is required for functional assembly of the exo

>PRK09280 F0F1 ATP synthase subunit beta; Validated

Probab=84.61  E-value=5.9  Score=36.58  Aligned_cols=45  Identities=22%  Similarity=0.284  Sum_probs=31.7

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCC-CCHHHHHHHHHHH
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQN-PNIKKIQGEIAFK   47 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~-~~~~~l~~~i~~~   47 (283)
                      +|+|||||+..+........ =+.++++-+++. ..+.+++.++...
T Consensus       153 ~GvGKt~Ll~~i~~~~~~~~-~~v~V~~liGER~rEv~efi~~~~~~  198 (463)
T PRK09280        153 AGVGKTVLIQELINNIAKEH-GGYSVFAGVGERTREGNDLYHEMKES  198 (463)
T ss_pred             CCCChhHHHHHHHHHHHhcC-CCEEEEEEeccCcHHHHHHHHHHHhc
Confidence            59999999999877655331 156778878755 4567777777654

>cd03114 ArgK-like The function of this protein family is unkown

Probab=84.59  E-value=1  Score=34.70  Aligned_cols=19  Identities=26%  Similarity=0.392  Sum_probs=15.8

Q ss_pred             CCCcHHHHHHHHHhhhccC
Q 041028            2 GGIGKTTLAKEVARKAKNG   20 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~   20 (283)
                      +|+||||++..+.......
T Consensus         8 ~GsGKTt~~~~l~~~~~~~   26 (148)
T cd03114           8 PGAGKSTLIDALITALRAR   26 (148)
T ss_pred             CCCcHHHHHHHHHHHHHHC
Confidence            7999999999998876443

The protein sequences are similar to the ArgK protein in E. coli. ArgK protein is a membrane ATPase which is required for transporting arginine, ornithine and lysine into the cells by the arginine and ornithine (AO system) and lysine, arginine and ornithine (LAO) transport systems.

>KOG3354 consensus Gluconate kinase [Carbohydrate transport and metabolism]

Probab=84.54  E-value=3.5  Score=32.12  Aligned_cols=41  Identities=20%  Similarity=0.280  Sum_probs=27.7

Q ss_pred             CCCcHHHHHHHHHhhhccCCCC-CeEEEEEeCCCCCHHHHHHHHHHHhCCC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLF-DQIVFTEVSQNPNIKKIQGEIAFKLGLK   51 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~F-d~~~wv~v~~~~~~~~l~~~i~~~l~~~   51 (283)
                      +|.||||+++++.+.....  | |+       ..+...+-..++-+.+..+
T Consensus        21 sGsGKSTigk~L~~~l~~~--F~dg-------Dd~Hp~~NveKM~~GipLn   62 (191)
T KOG3354|consen   21 SGSGKSTIGKALSEELGLK--FIDG-------DDLHPPANVEKMTQGIPLN   62 (191)
T ss_pred             CCCChhhHHHHHHHHhCCc--cccc-------ccCCCHHHHHHHhcCCCCC
Confidence            5999999999999988754  5 43       4455555555555544443

>PRK08006 replicative DNA helicase; Provisional

Probab=84.50  E-value=1.9  Score=40.00  Aligned_cols=44  Identities=18%  Similarity=0.163  Sum_probs=30.6

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHHHh
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKL   48 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~~l   48 (283)
                      +|+|||++|..++.+...... ..++++++  ..+..++..+++...
T Consensus       233 PgmGKTafalnia~~~a~~~g-~~V~~fSl--EM~~~ql~~Rlla~~  276 (471)
T PRK08006        233 PSMGKTTFAMNLCENAAMLQD-KPVLIFSL--EMPGEQIMMRMLASL  276 (471)
T ss_pred             CCCCHHHHHHHHHHHHHHhcC-CeEEEEec--cCCHHHHHHHHHHHh
Confidence            799999999998877543211 23445444  467788888888765

>COG0194 Gmk Guanylate kinase [Nucleotide transport and metabolism]

Probab=84.45  E-value=0.69  Score=36.97  Aligned_cols=16  Identities=38%  Similarity=0.675  Sum_probs=14.7

Q ss_pred             CCCcHHHHHHHHHhhh
Q 041028            2 GGIGKTTLAKEVARKA   17 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~   17 (283)
                      +|+|||||+++++.+.
T Consensus        13 SG~GKsTl~k~L~~~~   28 (191)
T COG0194          13 SGVGKSTLVKALLEDD   28 (191)
T ss_pred             CCCCHHHHHHHHHhhc
Confidence            6999999999999876

>cd02030 NDUO42 NADH:Ubiquinone oxioreductase, 42 kDa (NDUO42) is a family of proteins that are highly similar to deoxyribonucleoside kinases (dNK)

Probab=84.40  E-value=0.73  Score=38.03  Aligned_cols=17  Identities=47%  Similarity=0.427  Sum_probs=15.0

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      -|+||||+|+.+.....
T Consensus         8 ~GsGKSTl~~~L~~~l~   24 (219)
T cd02030           8 IASGKGKLAKELAEKLG   24 (219)
T ss_pred             CCCCHHHHHHHHHHHhC
Confidence            59999999999998764

Members of this family have been identified as one of the subunits of NADH:Ubiquinone oxioreductase (complex I), a multi-protein complex located in the inner mitochondrial membrane. The main function of the complex is to transport electrons from NADH to ubiquinone, which is accompanied by the translocation of protons from the mitochondrial matrix to the inter membrane space.

>PRK09270 nucleoside triphosphate hydrolase domain-containing protein; Reviewed

Probab=84.37  E-value=0.7  Score=38.41  Aligned_cols=18  Identities=33%  Similarity=0.405  Sum_probs=15.6

Q ss_pred             CCCcHHHHHHHHHhhhcc
Q 041028            2 GGIGKTTLAKEVARKAKN   19 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~   19 (283)
                      .|.|||||++.+......
T Consensus        42 ~GsGKTTl~~~L~~~l~~   59 (229)
T PRK09270         42 PGAGKSTLAEFLEALLQQ   59 (229)
T ss_pred             CCCCHHHHHHHHHHHhhh
Confidence            699999999999987654

>PRK12338 hypothetical protein; Provisional

Probab=84.35  E-value=0.68  Score=40.49  Aligned_cols=17  Identities=53%  Similarity=0.829  Sum_probs=15.1

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      +|+||||+|+.++....
T Consensus        13 sGsGKST~a~~la~~l~   29 (319)
T PRK12338         13 SGIGKSTIASELARTLN   29 (319)
T ss_pred             CCCCHHHHHHHHHHHCC
Confidence            69999999999998754

>PF09848 DUF2075: Uncharacterized conserved protein (DUF2075); InterPro: IPR018647 This domain, found in putative ATP/GTP binding proteins, has no known function

Probab=84.33  E-value=4  Score=36.33  Aligned_cols=34  Identities=24%  Similarity=0.314  Sum_probs=23.9

Q ss_pred             CCCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCC
Q 041028            1 MGGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQN   34 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~   34 (283)
                      .+|.|||.||..++.+...........+++....
T Consensus         9 ~aGTGKTvla~~l~~~l~~~~~~~~~~~l~~n~~   42 (352)
T PF09848_consen    9 GAGTGKTVLALNLAKELQNSEEGKKVLYLCGNHP   42 (352)
T ss_pred             cCCcCHHHHHHHHHHHhhccccCCceEEEEecch
Confidence            3799999999999998721223556666665544

It is found in some proteins described as Schlafen family members, which may have a role in hematopoeitic cell differentiation [].

>PRK06904 replicative DNA helicase; Validated

Probab=84.33  E-value=2  Score=39.98  Aligned_cols=45  Identities=18%  Similarity=0.209  Sum_probs=31.5

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHHHhC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKLG   49 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~~l~   49 (283)
                      +|+|||++|..++....... =..++|+++  ..+..++..+++....
T Consensus       230 Pg~GKTafalnia~~~a~~~-g~~Vl~fSl--EMs~~ql~~Rlla~~s  274 (472)
T PRK06904        230 PSMGKTTFAMNLCENAAMAS-EKPVLVFSL--EMPAEQIMMRMLASLS  274 (472)
T ss_pred             CCCChHHHHHHHHHHHHHhc-CCeEEEEec--cCCHHHHHHHHHHhhC
Confidence            79999999998887654321 124555544  4778888888887763

>PF07724 AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR013093 ATPases Associated to a variety of cellular Activities (AAA) are a family distinguished by a highly conserved module of 230 amino acids []

Probab=84.32  E-value=0.72  Score=36.55  Aligned_cols=31  Identities=29%  Similarity=0.328  Sum_probs=21.4

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQ   33 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~   33 (283)
                      .|+|||.||+.++..... +.....+-++.+.
T Consensus        12 sGvGKT~la~~la~~l~~-~~~~~~~~~d~s~   42 (171)
T PF07724_consen   12 SGVGKTELAKALAELLFV-GSERPLIRIDMSE   42 (171)
T ss_dssp             TTSSHHHHHHHHHHHHT--SSCCEEEEEEGGG
T ss_pred             CCCCHHHHHHHHHHHhcc-CCccchHHHhhhc
Confidence            599999999999998763 1144555555553

The highly conserved nature of this module across taxa suggests that it has a key cellular role. Members of the family are involved in diverse cellular functions including gene expression, peroxisome assembly and vesicle mediated transport. Although the role of ATPase AAA-2 domain is not, as yet, clear, the AAA+ superfamily of proteins to which the AAA ATPases belong has a chaperone-like function in the assembly, operation or disassembly of proteins []. Some of these ATPases function as a chaperone subunit of a proteasome-like degradation complex. This ATPase family includes some proteins not detected by IPR003959 from INTERPRO.; GO: 0005524 ATP binding; PDB: 1R6B_X 1KSF_X 3PXI_C 1KYI_T 1G3I_S 1OFH_B 1OFI_A 1G41_A 1IM2_A 1HQY_E ....

>cd01135 V_A-ATPase_B V/A-type ATP synthase (non-catalytic) subunit B

Probab=84.24  E-value=2.4  Score=36.33  Aligned_cols=46  Identities=17%  Similarity=0.255  Sum_probs=32.7

Q ss_pred             CCCcHHHHHHHHHhhhcc--CCCCCeEEEEEeCCC-CCHHHHHHHHHHH
Q 041028            2 GGIGKTTLAKEVARKAKN--GKLFDQIVFTEVSQN-PNIKKIQGEIAFK   47 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~--~~~Fd~~~wv~v~~~-~~~~~l~~~i~~~   47 (283)
                      .|+|||+|+..+.++...  ++.-+.++++-+++. ..+.++..++...
T Consensus        78 ~GvGKt~L~~~i~~~~~~~~~~~~~v~V~~~IGeR~rev~e~~~~~~~~  126 (276)
T cd01135          78 SGLPHNELAAQIARQAGVVGEEENFAVVFAAMGITMEDARFFKDDFEET  126 (276)
T ss_pred             CCCChhHHHHHHHHhhhccccCCCCEEEEEEeccccHHHHHHHHHhhhc
Confidence            589999999999887541  122478889988865 4566676666553

These ATPases couple ATP hydrolysis to the build up of a H+ gradient, but V-type ATPases do not catalyze the reverse reaction. The Vacuolar (V-type) ATPase is found in the membranes of vacuoles, the golgi apparatus and in other coated vesicles in eukaryotes. Archaea have a protein which is similar in sequence to V-ATPases, but functions like an F-ATPase (called A-ATPase). A similar protein is also found in a few bacteria. This subfamily consists of the non-catalytic beta subunit.

>cd00071 GMPK Guanosine monophosphate kinase (GMPK, EC 2

Probab=84.18  E-value=0.7  Score=35.09  Aligned_cols=16  Identities=38%  Similarity=0.630  Sum_probs=14.2

Q ss_pred             CCCcHHHHHHHHHhhh
Q 041028            2 GGIGKTTLAKEVARKA   17 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~   17 (283)
                      .|+|||||++.+....
T Consensus         8 sGsGKstl~~~L~~~~   23 (137)
T cd00071           8 SGVGKSTLLKRLLEEF   23 (137)
T ss_pred             CCCCHHHHHHHHHhcC
Confidence            5999999999998764

7.4.8), also known as guanylate kinase (GKase), catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to guanosine monophosphate (GMP) to yield adenosine diphosphate (ADP) and guanosine diphosphate (GDP). It plays an essential role in the biosynthesis of guanosine triphosphate (GTP). This enzyme is also important for the activation of some antiviral and anticancer agents, such as acyclovir, ganciclovir, carbovir, and thiopurines.

>cd04138 H_N_K_Ras_like H-Ras/N-Ras/K-Ras subfamily

Probab=84.17  E-value=0.66  Score=35.52  Aligned_cols=15  Identities=33%  Similarity=0.793  Sum_probs=13.3

Q ss_pred             CCCcHHHHHHHHHhh
Q 041028            2 GGIGKTTLAKEVARK   16 (283)
Q Consensus         2 gGiGKTtLA~~v~~~   16 (283)
                      +|+|||||...+.+.
T Consensus        10 ~~vGKTsl~~~~~~~   24 (162)
T cd04138          10 GGVGKSALTIQLIQN   24 (162)
T ss_pred             CCCCHHHHHHHHHhC
Confidence            699999999998864

H-Ras, N-Ras, and K-Ras4A/4B are the prototypical members of the Ras family. These isoforms generate distinct signal outputs despite interacting with a common set of activators and effectors, and are strongly associated with oncogenic progression in tumor initiation. Mutated versions of Ras that are insensitive to GAP stimulation (and are therefore constitutively active) are found in a significant fraction of human cancers. Many Ras guanine nucleotide exchange factors (GEFs) have been identified. They are sequestered in the cytosol until activation by growth factors triggers recruitment to the plasma membrane or Golgi, where the GEF colocalizes with Ras. Active (GTP-bound) Ras interacts with several effector proteins that stimulate a variety of diverse cytoplasmic signaling activities. Some are known to positively mediate the oncogenic properties of Ras, including Raf, phosphatidylinositol 3-kinase (PI3K), RalGEFs, and Tiam1.

>cd01125 repA Hexameric Replicative Helicase RepA

Probab=84.16  E-value=2.2  Score=35.65  Aligned_cols=18  Identities=33%  Similarity=0.414  Sum_probs=15.0

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      .||+|||+||..++-...
T Consensus         9 ~~G~GKS~lal~la~~va   26 (239)
T cd01125           9 PGGTGKSSLLLVLALAMA   26 (239)
T ss_pred             CCCCCHHHHHHHHHHHHh
Confidence            489999999999987643

RepA is encoded by a plasmid, which is found in most Gram negative bacteria. RepA is a 5'-3' DNA helicase which can utilize ATP, GTP and CTP to a lesser extent.

>PRK14974 cell division protein FtsY; Provisional

Probab=84.13  E-value=2.2  Score=37.73  Aligned_cols=49  Identities=29%  Similarity=0.293  Sum_probs=29.9

Q ss_pred             CCCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCC--CHHHHHHHHHHHhCCCC
Q 041028            1 MGGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNP--NIKKIQGEIAFKLGLKF   52 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~--~~~~l~~~i~~~l~~~~   52 (283)
                      ++|+||||++..+++..... .+ .++.+.. ..+  ...+-++..+..++.+.
T Consensus       148 ~~GvGKTTtiakLA~~l~~~-g~-~V~li~~-Dt~R~~a~eqL~~~a~~lgv~v  198 (336)
T PRK14974        148 VNGTGKTTTIAKLAYYLKKN-GF-SVVIAAG-DTFRAGAIEQLEEHAERLGVKV  198 (336)
T ss_pred             CCCCCHHHHHHHHHHHHHHc-CC-eEEEecC-CcCcHHHHHHHHHHHHHcCCce
Confidence            47999999888888766533 23 2333432 223  23345666777887653

>PRK07933 thymidylate kinase; Validated

Probab=84.02  E-value=0.84  Score=37.56  Aligned_cols=20  Identities=25%  Similarity=0.406  Sum_probs=17.1

Q ss_pred             CCCCcHHHHHHHHHhhhccC
Q 041028            1 MGGIGKTTLAKEVARKAKNG   20 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~   20 (283)
                      +-|+||||+++.+.+....+
T Consensus         8 ~dGsGKST~~~~L~~~L~~~   27 (213)
T PRK07933          8 VDGAGKRTLTEALRAALEAR   27 (213)
T ss_pred             CCCCCHHHHHHHHHHHHHHC
Confidence            35999999999999987654

>PRK00300 gmk guanylate kinase; Provisional

Probab=83.99  E-value=0.71  Score=37.44  Aligned_cols=16  Identities=38%  Similarity=0.640  Sum_probs=14.3

Q ss_pred             CCCcHHHHHHHHHhhh
Q 041028            2 GGIGKTTLAKEVARKA   17 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~   17 (283)
                      .|+||||||+.++...
T Consensus        14 sGsGKstl~~~l~~~~   29 (205)
T PRK00300         14 SGAGKSTLVKALLERD   29 (205)
T ss_pred             CCCCHHHHHHHHHhhC
Confidence            6999999999999864

>COG2074 2-phosphoglycerate kinase [Carbohydrate transport and metabolism]

Probab=83.87  E-value=0.76  Score=38.60  Aligned_cols=19  Identities=42%  Similarity=0.651  Sum_probs=17.2

Q ss_pred             CCCcHHHHHHHHHhhhccC
Q 041028            2 GGIGKTTLAKEVARKAKNG   20 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~   20 (283)
                      +||||||+|..++++..+.
T Consensus        98 sGVGkStIA~ElA~rLgI~  116 (299)
T COG2074          98 SGVGKSTIAGELARRLGIR  116 (299)
T ss_pred             CCCChhHHHHHHHHHcCCc
Confidence            6999999999999998765

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=83.86  E-value=0.72  Score=41.30  Aligned_cols=17  Identities=41%  Similarity=0.690  Sum_probs=15.0

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      .|+||||+|+.+++...
T Consensus        47 ~G~GKTtla~~la~~l~   63 (363)
T PRK14961         47 RGVGKTTIARLLAKSLN   63 (363)
T ss_pred             CCCCHHHHHHHHHHHhc
Confidence            69999999999998764

>cd04119 RJL RJL (RabJ-Like) subfamily

Probab=83.82  E-value=0.68  Score=35.68  Aligned_cols=16  Identities=25%  Similarity=0.513  Sum_probs=13.9

Q ss_pred             CCCcHHHHHHHHHhhh
Q 041028            2 GGIGKTTLAKEVARKA   17 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~   17 (283)
                      +|+|||||...+.+..
T Consensus         9 ~~vGKTsli~~l~~~~   24 (168)
T cd04119           9 SGVGKSCIIKRYCEGR   24 (168)
T ss_pred             CCCCHHHHHHHHHhCC
Confidence            6999999999998754

RJLs are found in many protists and as chimeras with C-terminal DNAJ domains in deuterostome metazoa. They are not found in plants, fungi, and protostome metazoa, suggesting a horizontal gene transfer between protists and deuterostome metazoa. RJLs lack any known membrane targeting signal and contain a degenerate phosphate/magnesium-binding 3 (PM3) motif, suggesting an impaired ability to hydrolyze GTP. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization.

>COG1157 FliI Flagellar biosynthesis/type III secretory pathway ATPase [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=83.77  E-value=4.3  Score=36.68  Aligned_cols=71  Identities=21%  Similarity=0.272  Sum_probs=47.1

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeC-CCCCHHHHHHHHHHHhCCCC-------CcCCHh------hhHHhHHHH
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVS-QNPNIKKIQGEIAFKLGLKF-------DEESES------GRTRSPWSR   67 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~-~~~~~~~l~~~i~~~l~~~~-------~~~~~~------~~~~~l~~~   67 (283)
                      +|||||||.-.+++..+    +|.++-.-++ +..-+.+...+.+..-+...       ++++..      ..+-.+.++
T Consensus       172 sGVGKStLLgMiar~t~----aDv~ViaLIGERGREVrEFIE~~Lg~egl~rsViVvATSD~s~l~R~~aa~~At~IAEy  247 (441)
T COG1157         172 SGVGKSTLLGMIARNTE----ADVNVIALIGERGREVREFIEKDLGEEGLKRSVVVVATSDESALMRLKAAFTATTIAEY  247 (441)
T ss_pred             CCCcHHHHHHHHhcccc----CCEEEEEEeeccchhHHHHHHHhcchhhccceEEEEECCCCCHHHHHHHHHHHHHHHHH
Confidence            59999999999998554    7777665555 45667888887776665542       122211      123356777


Q ss_pred             cc--CCcEEEE
Q 041028           68 LK--KEKLQII   76 (283)
Q Consensus        68 L~--~kr~LlV   76 (283)
                      ++  +|++|++
T Consensus       248 FRDqG~~VLL~  258 (441)
T COG1157         248 FRDQGKRVLLI  258 (441)
T ss_pred             HHhCCCeEEEE
Confidence            75  5688888

>cd02029 PRK_like Phosphoribulokinase-like (PRK-like) is a family of proteins similar to phosphoribulokinase (PRK), the enzyme involved in the Benson-Calvin cycle in chloroplasts or photosynthetic prokaryotes

Probab=83.71  E-value=5  Score=34.28  Aligned_cols=17  Identities=24%  Similarity=0.352  Sum_probs=14.6

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      +|+||||+|+.+.+...
T Consensus         8 SGSGKTTv~~~l~~~l~   24 (277)
T cd02029           8 SGAGTTTVKRAFEHIFA   24 (277)
T ss_pred             CCCCHHHHHHHHHHHHH
Confidence            59999999999887654

PRK catalyzes the phosphorylation of D-ribulose 5-phosphate to form D-ribulose 1, 5-biphosphate, using ATP and NADPH produced by the primary reactions of photosynthesis.

>PRK11670 antiporter inner membrane protein; Provisional

Probab=83.64  E-value=0.81  Score=41.06  Aligned_cols=17  Identities=35%  Similarity=0.577  Sum_probs=14.9

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      ||+||||+|..++....
T Consensus       117 GGVGKTT~avNLA~aLA  133 (369)
T PRK11670        117 GGVGKSSTAVNLALALA  133 (369)
T ss_pred             CCCCHHHHHHHHHHHHH
Confidence            89999999999887654

>TIGR01650 PD_CobS cobaltochelatase, CobS subunit

Probab=83.63  E-value=1.4  Score=38.76  Aligned_cols=17  Identities=29%  Similarity=0.507  Sum_probs=15.3

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      +|+||||+|+.++....
T Consensus        73 pGtGKTtla~~lA~~l~   89 (327)
T TIGR01650        73 HGTGKSTHIEQIAARLN   89 (327)
T ss_pred             CCChHHHHHHHHHHHHC
Confidence            69999999999998765

This model describes the aerobic cobalamin pathway Pseudomonas denitrificans CobS gene product, which is a cobalt chelatase subunit, with a MW ~37 kDa. The aerobic pathway cobalt chelatase is a heterotrimeric, ATP-dependent enzyme that catalyzes cobalt insertion during cobalamin biosynthesis. The other two subunits are the P. denitrificans CobT (TIGR01651) and CobN (pfam02514 CobN/Magnesium Chelatase) proteins. To avoid potential confusion with the nonhomologous Salmonella typhimurium/E.coli cobS gene product, the P. denitrificans gene symbol is not used in the name of this model.

>PRK09302 circadian clock protein KaiC; Reviewed

Probab=83.55  E-value=2.1  Score=40.23  Aligned_cols=31  Identities=26%  Similarity=0.384  Sum_probs=22.9

Q ss_pred             CCCcHHHHHHHHHhhhccCCCC-CeEEEEEeCCC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLF-DQIVFTEVSQN   34 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~F-d~~~wv~v~~~   34 (283)
                      +|+|||+||.++......+  + ..++|++....
T Consensus        40 pGsGKT~l~~qf~~~~~~~--~ge~~lyis~ee~   71 (509)
T PRK09302         40 AGTGKTLFALQFLVNGIKR--FDEPGVFVTFEES   71 (509)
T ss_pred             CCCCHHHHHHHHHHHHHHh--cCCCEEEEEccCC
Confidence            6999999999987654332  3 46788887764

>PF00154 RecA: recA bacterial DNA recombination protein; InterPro: IPR013765 The recA gene product is a multifunctional enzyme that plays a role in homologous recombination, DNA repair and induction of the SOS response []

Probab=83.50  E-value=2.1  Score=37.54  Aligned_cols=63  Identities=19%  Similarity=0.186  Sum_probs=37.9

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCC------cCCHhhhHHhHHHHccCC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKLGLKFD------EESESGRTRSPWSRLKKE   71 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~~l~~~~~------~~~~~~~~~~l~~~L~~k   71 (283)
                      .|+||||||.++.......  -..++||+....++..     .+..+|.+.+      ..+.++....+.+.++..
T Consensus        62 ~ssGKttLaL~~ia~~q~~--g~~~a~ID~e~~ld~~-----~a~~lGvdl~rllv~~P~~~E~al~~~e~lirsg  130 (322)
T PF00154_consen   62 ESSGKTTLALHAIAEAQKQ--GGICAFIDAEHALDPE-----YAESLGVDLDRLLVVQPDTGEQALWIAEQLIRSG  130 (322)
T ss_dssp             TTSSHHHHHHHHHHHHHHT--T-EEEEEESSS---HH-----HHHHTT--GGGEEEEE-SSHHHHHHHHHHHHHTT
T ss_pred             CCCchhhhHHHHHHhhhcc--cceeEEecCcccchhh-----HHHhcCccccceEEecCCcHHHHHHHHHHHhhcc
Confidence            4789999999988776543  4578999988877653     4455666532      224455556666666554

In homologous recombination, the protein functions as a DNA-dependent ATPase, promoting synapsis, heteroduplex formation and strand exchange between homologous DNAs []. RecA also acts as a protease cofactor that promotes autodigestion of the lexA product and phage repressors. The proteolytic inactivation of the lexA repressor by an activated form of recA may cause a derepression of the 20 or so genes involved in the SOS response, which regulates DNA repair, induced mutagenesis, delayed cell division and prophage induction in response to DNA damage []. RecA is a protein of about 350 amino-acid residues. Its sequence is very well conserved [, , ] among eubacterial species. It is also found in the chloroplast of plants []. RecA-like proteins are found in archaea and diverse eukaryotic organisms, like fission yeast, mouse or human. In the filament visualised by X-ray crystallography, beta-strand 3, the loop C-terminal to beta-strand 2, and alpha-helix D of the core domain form one surface that packs against alpha-helix A and beta-strand 0 (the N-terminal domain) of an adjacent monomer during polymerisation []. The core ATP-binding site domain is well conserved, with 14 invariant residues. It contains the nucleotide binding loop between beta-strand 1 and alpha-helix C. The Escherichia coli sequence GPESSGKT matches the consensus sequence of amino acids (G/A)XXXXGK(T/S) for the Walker A box (also referred to as the P-loop) found in a number of nucleoside triphosphate (NTP)-binding proteins. Another nucleotide binding motif, the Walker B box is found at beta-strand 4 in the RecA structure. The Walker B box is characterised by four hydrophobic amino acids followed by an acidic residue (usually aspartate). Nucleotide specificity and additional ATP binding interactions are contributed by the amino acid residues at beta-strand 2 and the loop C-terminal to that strand, all of which are greater than 90% conserved among bacterial RecA proteins.; GO: 0003697 single-stranded DNA binding, 0005524 ATP binding, 0006281 DNA repair; PDB: 2IN0_A 1MO3_A 3IFJ_A 2IN8_A 2IMZ_B 1G18_A 1MO4_A 3IGD_A 2L8L_A 2IN9_A ....

>PRK05748 replicative DNA helicase; Provisional

Probab=83.50  E-value=2.2  Score=39.38  Aligned_cols=45  Identities=13%  Similarity=0.207  Sum_probs=30.4

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHHHhC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKLG   49 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~~l~   49 (283)
                      +|+|||+||..+..+...+.. ..++++++  .-+..++..+++...+
T Consensus       212 pg~GKT~~al~ia~~~a~~~g-~~v~~fSl--Ems~~~l~~R~l~~~~  256 (448)
T PRK05748        212 PSVGKTAFALNIAQNVATKTD-KNVAIFSL--EMGAESLVMRMLCAEG  256 (448)
T ss_pred             CCCCchHHHHHHHHHHHHhCC-CeEEEEeC--CCCHHHHHHHHHHHhc
Confidence            799999999999877543311 24556544  4466778888876554

>KOG0735 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=83.50  E-value=2.4  Score=40.98  Aligned_cols=44  Identities=25%  Similarity=0.302  Sum_probs=28.4

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeC--CCCCHHHHHHHHHH
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVS--QNPNIKKIQGEIAF   46 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~--~~~~~~~l~~~i~~   46 (283)
                      .|+|||+||+++++... +++.-.+.+|+.+  +.-....+++.+-.
T Consensus       440 ~GsGKT~L~kal~~~~~-k~~~~hv~~v~Cs~l~~~~~e~iQk~l~~  485 (952)
T KOG0735|consen  440 KGSGKTNLVKALFDYYS-KDLIAHVEIVSCSTLDGSSLEKIQKFLNN  485 (952)
T ss_pred             CCCCHhHHHHHHHHHhc-cccceEEEEEechhccchhHHHHHHHHHH
Confidence            49999999999999876 3344445556554  23345555555443

>PF13614 AAA_31: AAA domain; PDB: 2VED_B 2PH1_A 3EA0_B 3FKQ_A 3KB1_B 1ION_A 3LA6_H 3BFV_B 3CIO_D

Probab=83.46  E-value=2.4  Score=32.55  Aligned_cols=32  Identities=28%  Similarity=0.442  Sum_probs=22.9

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNP   35 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~   35 (283)
                      ||+||||+|..++......+  ..++.|+.....
T Consensus        10 ~g~G~t~~a~~lA~~la~~~--~~Vllid~~~~~   41 (157)
T PF13614_consen   10 GGVGKTTLALNLAAALARKG--KKVLLIDFDFFS   41 (157)
T ss_dssp             TTSSHHHHHHHHHHHHHHTT--T-EEEEE--SSS
T ss_pred             CCCCHHHHHHHHHHHHHhcC--CCeEEEECCCCC
Confidence            79999999999999876552  228888876543

>TIGR03600 phage_DnaB phage replicative helicase, DnaB family, HK022 subfamily

Probab=83.44  E-value=2.4  Score=38.72  Aligned_cols=44  Identities=18%  Similarity=0.243  Sum_probs=30.6

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHHHh
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKL   48 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~~l   48 (283)
                      +|+|||++|..++.+...+.. ..++|++..  .+..++..+++...
T Consensus       203 pg~GKT~~al~ia~~~a~~~g-~~v~~fSlE--m~~~~l~~Rl~~~~  246 (421)
T TIGR03600       203 PSMGKTTLALNIAENVALREG-KPVLFFSLE--MSAEQLGERLLASK  246 (421)
T ss_pred             CCCCHHHHHHHHHHHHHHhCC-CcEEEEECC--CCHHHHHHHHHHHH
Confidence            799999999999866543222 346666654  47777888877654

Members of this family are phage (or prophage-region) homologs of the bacterial homohexameric replicative helicase DnaB. Some phage may rely on host DnaB, while others encode their own verions. This model describes the largest phage-specific clade among the close homologs of DnaB, but there are, or course, other DnaB homologs from phage that fall outside the scope of this model.

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=83.36  E-value=1.2  Score=41.49  Aligned_cols=30  Identities=23%  Similarity=0.329  Sum_probs=20.0

Q ss_pred             CCCcHHHHHHHHHhhhccCCCC-CeEEEEEeCC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLF-DQIVFTEVSQ   33 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~F-d~~~wv~v~~   33 (283)
                      +|+||||||.++..+-..+  + ...+||+..+
T Consensus        30 pGsGKT~la~qfl~~g~~~--~ge~~lyvs~eE   60 (484)
T TIGR02655        30 SGTGKTLFSIQFLYNGIIH--FDEPGVFVTFEE   60 (484)
T ss_pred             CCCCHHHHHHHHHHHHHHh--CCCCEEEEEEec
Confidence            7999999999975543222  3 3566776653

Members of this family are the circadian clock protein KaiC, part of the kaiABC operon that controls circadian rhythm. It may be universal in Cyanobacteria. Each member has two copies of the KaiC domain (Pfam model pfam06745), which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor.

>PRK05636 replicative DNA helicase; Provisional

Probab=83.27  E-value=2  Score=40.27  Aligned_cols=44  Identities=25%  Similarity=0.157  Sum_probs=29.4

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHHHh
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKL   48 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~~l   48 (283)
                      +|+|||+||..++.....+... .++++  |-..+..++..+++...
T Consensus       274 pg~GKT~~al~~a~~~a~~~g~-~v~~f--SlEMs~~ql~~R~ls~~  317 (505)
T PRK05636        274 PGVGKSTLALDFMRSASIKHNK-ASVIF--SLEMSKSEIVMRLLSAE  317 (505)
T ss_pred             CCCCHHHHHHHHHHHHHHhCCC-eEEEE--EeeCCHHHHHHHHHHHh
Confidence            6999999999988765433222 33333  44556777777777654

>PRK13531 regulatory ATPase RavA; Provisional

Probab=83.17  E-value=0.97  Score=41.83  Aligned_cols=23  Identities=26%  Similarity=0.489  Sum_probs=17.5

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFD   24 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd   24 (283)
                      +|+|||+||+.+.........|.
T Consensus        48 PGTGKT~LAraLa~~~~~~~~F~   70 (498)
T PRK13531         48 PGIAKSLIARRLKFAFQNARAFE   70 (498)
T ss_pred             CChhHHHHHHHHHHHhcccCcce
Confidence            79999999999998654333453

>PRK08760 replicative DNA helicase; Provisional

Probab=83.16  E-value=2.3  Score=39.64  Aligned_cols=44  Identities=16%  Similarity=0.088  Sum_probs=28.6

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHHHh
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKL   48 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~~l   48 (283)
                      +|+|||++|..++.....+... .+++++  -.-+..++..+++...
T Consensus       238 Pg~GKTafal~iA~~~a~~~g~-~V~~fS--lEMs~~ql~~Rl~a~~  281 (476)
T PRK08760        238 PAMGKTTFALNIAEYAAIKSKK-GVAVFS--MEMSASQLAMRLISSN  281 (476)
T ss_pred             CCCChhHHHHHHHHHHHHhcCC-ceEEEe--ccCCHHHHHHHHHHhh
Confidence            7999999999998775433222 344444  3445567777776654

>cd00820 PEPCK_HprK Phosphoenolpyruvate carboxykinase (PEPCK), a critical gluconeogenic enzyme, catalyzes the first committed step in the diversion of tricarboxylic acid cycle intermediates toward gluconeogenesis

Probab=83.13  E-value=0.75  Score=33.37  Aligned_cols=13  Identities=62%  Similarity=0.823  Sum_probs=11.8

Q ss_pred             CCCcHHHHHHHHH
Q 041028            2 GGIGKTTLAKEVA   14 (283)
Q Consensus         2 gGiGKTtLA~~v~   14 (283)
                      .|.|||||++.+.
T Consensus        24 SGsGKSTLl~~l~   36 (107)
T cd00820          24 SGIGKTELALELI   36 (107)
T ss_pred             CCCCHHHHHHHhh
Confidence            5999999999976

It catalyzes the reversible decarboxylation and phosphorylation of oxaloacetate to yield phosphoenolpyruvate and carbon dioxide, using a nucleotide molecule (ATP or GTP) for the phosphoryl transfer, and has a strict requirement for divalent metal ions for activity. PEPCK's separate into two phylogenetic groups based on their nucleotide substrate specificity (the ATP-, and GTP-dependent groups).HprK/P, the bifunctional histidine-containing protein kinase/phosphatase, controls the phosphorylation state of the phosphocarrier protein HPr and regulates the utilization of carbon sources by gram-positive bacteria. It catalyzes both the ATP-dependent phosphorylation of HPr and its dephosphorylation by phosphorolysis. PEPCK and the C-terminal catalytic domain of HprK/P are structural

>cd04124 RabL2 RabL2 subfamily

Probab=83.09  E-value=0.77  Score=35.57  Aligned_cols=15  Identities=20%  Similarity=0.419  Sum_probs=12.8

Q ss_pred             CCCcHHHHHHHHHhh
Q 041028            2 GGIGKTTLAKEVARK   16 (283)
Q Consensus         2 gGiGKTtLA~~v~~~   16 (283)
                      +|+|||||+..+.+.
T Consensus         9 ~~vGKTsli~~~~~~   23 (161)
T cd04124           9 SAVGKSKLVERFLMD   23 (161)
T ss_pred             CCCCHHHHHHHHHhC
Confidence            699999999987754

RabL2 (Rab-like2) subfamily. RabL2s are novel Rab proteins identified recently which display features that are distinct from other Rabs, and have been termed Rab-like. RabL2 contains RabL2a and RabL2b, two very similar Rab proteins that share 98% sequence identity in humans. RabL2b maps to the subtelomeric region of chromosome 22q13.3 and RabL2a maps to 2q13, a region that suggests it is also a subtelomeric gene. Both genes are believed to be expressed ubiquitously, suggesting that RabL2s are the first example of duplicated genes in human proximal subtelomeric regions that are both expressed actively. Like other Rab-like proteins, RabL2s lack a prenylation site at the C-terminus. The specific functions of RabL2a and RabL2b remain unknown. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-b

>PRK14493 putative bifunctional molybdopterin-guanine dinucleotide biosynthesis protein MobB/MoaE; Provisional

Probab=83.05  E-value=0.9  Score=38.97  Aligned_cols=27  Identities=19%  Similarity=0.238  Sum_probs=20.6

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEe
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEV   31 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v   31 (283)
                      +|+|||||+..+......++   .+.-|..
T Consensus        10 ~gSGKTTLi~~Li~~L~~~G---~V~~IKh   36 (274)
T PRK14493         10 KATGKTTLVERLVDRLSGRG---RVGTVKH   36 (274)
T ss_pred             CCCCHHHHHHHHHHHHHhCC---CEEEEEE
Confidence            69999999999999887653   2555544

>PRK09825 idnK D-gluconate kinase; Provisional

Probab=82.99  E-value=0.89  Score=36.18  Aligned_cols=17  Identities=24%  Similarity=0.401  Sum_probs=15.0

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      .|.|||||++.++....
T Consensus        12 sGsGKSTl~~~la~~l~   28 (176)
T PRK09825         12 SGSGKSLIGSKIAALFS   28 (176)
T ss_pred             CCCCHHHHHHHHHHhcC
Confidence            69999999999998754

>PF01926 MMR_HSR1: 50S ribosome-binding GTPase; InterPro: IPR002917 Human HSR1, has been localized to the human MHC class I region and is highly homologous to a putative GTP-binding protein, MMR1 from mouse

Probab=82.85  E-value=0.92  Score=33.01  Aligned_cols=16  Identities=31%  Similarity=0.472  Sum_probs=14.2

Q ss_pred             CCCCcHHHHHHHHHhh
Q 041028            1 MGGIGKTTLAKEVARK   16 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~   16 (283)
                      +.|+|||||...+.+.
T Consensus         7 ~~~~GKSTlin~l~~~   22 (116)
T PF01926_consen    7 RPNVGKSTLINALTGK   22 (116)
T ss_dssp             STTSSHHHHHHHHHTS
T ss_pred             CCCCCHHHHHHHHhcc
Confidence            4699999999999974

These proteins represent a new subfamily of GTP-binding proteins that has both prokaryote and eukaryote members [].; GO: 0005525 GTP binding, 0005622 intracellular; PDB: 2DWQ_B 2DBY_A 3CNN_A 3CNO_A 3CNL_A 3IBY_A 1PUI_B 1WXQ_A 1LNZ_A 3GEE_A ....

>COG0645 Predicted kinase [General function prediction only]

Probab=82.76  E-value=0.86  Score=35.80  Aligned_cols=17  Identities=41%  Similarity=0.501  Sum_probs=14.9

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      .|+||||||+.+.....
T Consensus        10 ~GsGKstlA~~l~~~lg   26 (170)
T COG0645          10 PGSGKSTLARGLAELLG   26 (170)
T ss_pred             CCccHhHHHHHHHhhcC
Confidence            69999999999988754

>PTZ00361 26 proteosome regulatory subunit 4-like protein; Provisional

Probab=82.69  E-value=0.86  Score=41.81  Aligned_cols=17  Identities=53%  Similarity=0.647  Sum_probs=15.4

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      +|+|||+||+.+++...
T Consensus       226 PGTGKT~LAraIA~el~  242 (438)
T PTZ00361        226 PGTGKTLLAKAVANETS  242 (438)
T ss_pred             CCCCHHHHHHHHHHhhC
Confidence            69999999999999765

>cd02038 FleN-like FleN is a member of the Fer4_NifH superfamily

Probab=82.68  E-value=1  Score=34.20  Aligned_cols=18  Identities=33%  Similarity=0.636  Sum_probs=15.3

Q ss_pred             CCCcHHHHHHHHHhhhcc
Q 041028            2 GGIGKTTLAKEVARKAKN   19 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~   19 (283)
                      ||+||||+|..+......
T Consensus         9 gg~gkt~~~~~~a~~~~~   26 (139)
T cd02038           9 GGVGKTNISANLALALAK   26 (139)
T ss_pred             CCCcHHHHHHHHHHHHHH
Confidence            899999999998887553

It shares the common function as an ATPase, with the ATP-binding domain at the N-terminus. In Pseudomonas aeruginosa, FleN gene is involved in regulating the number of flagella and chemotactic motility by influencing FleQ activity.

>cd04113 Rab4 Rab4 subfamily

Probab=82.64  E-value=0.85  Score=35.10  Aligned_cols=15  Identities=27%  Similarity=0.499  Sum_probs=13.3

Q ss_pred             CCCcHHHHHHHHHhh
Q 041028            2 GGIGKTTLAKEVARK   16 (283)
Q Consensus         2 gGiGKTtLA~~v~~~   16 (283)
                      +|+|||||...+.+.
T Consensus         9 ~~vGKTsli~~l~~~   23 (161)
T cd04113           9 SGTGKSCLLHRFVEN   23 (161)
T ss_pred             CCCCHHHHHHHHHhC
Confidence            699999999998765

Rab4 has been implicated in numerous functions within the cell. It helps regulate endocytosis through the sorting, recycling, and degradation of early endosomes. Mammalian Rab4 is involved in the regulation of many surface proteins including G-protein-coupled receptors, transferrin receptor, integrins, and surfactant protein A. Experimental data implicate Rab4 in regulation of the recycling of internalized receptors back to the plasma membrane. It is also believed to influence receptor-mediated antigen processing in B-lymphocytes, in calcium-dependent exocytosis in platelets, in alpha-amylase secretion in pancreatic cells, and in insulin-induced translocation of Glut4 from internal vesicles to the cell surface. Rab4 is known to share effector proteins with Rab5 and Rab11. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to p

>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional

Probab=82.59  E-value=0.85  Score=41.34  Aligned_cols=17  Identities=53%  Similarity=0.655  Sum_probs=15.3

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      +|+|||+||+++++...
T Consensus       188 pGTGKT~LAkalA~~l~  204 (398)
T PTZ00454        188 PGTGKTMLAKAVAHHTT  204 (398)
T ss_pred             CCCCHHHHHHHHHHhcC
Confidence            69999999999999764

>PRK05595 replicative DNA helicase; Provisional

Probab=82.56  E-value=2.6  Score=38.90  Aligned_cols=44  Identities=16%  Similarity=0.157  Sum_probs=29.8

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHHHh
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKL   48 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~~l   48 (283)
                      +|+|||++|..+..+...+.. ..++|++.  ..+..++..+++...
T Consensus       210 pg~GKT~~al~ia~~~a~~~g-~~vl~fSl--Ems~~~l~~R~~a~~  253 (444)
T PRK05595        210 PSMGKTTFALNIAEYAALREG-KSVAIFSL--EMSKEQLAYKLLCSE  253 (444)
T ss_pred             CCCChHHHHHHHHHHHHHHcC-CcEEEEec--CCCHHHHHHHHHHHh
Confidence            699999999999876432222 23556554  446777888877655

>TIGR01618 phage_P_loop phage nucleotide-binding protein

Probab=82.53  E-value=0.66  Score=38.38  Aligned_cols=14  Identities=36%  Similarity=0.423  Sum_probs=12.3

Q ss_pred             CCCcHHHHHHHHHh
Q 041028            2 GGIGKTTLAKEVAR   15 (283)
Q Consensus         2 gGiGKTtLA~~v~~   15 (283)
                      +|+||||+|+.+.+
T Consensus        21 ~G~GKtt~a~~~~~   34 (220)
T TIGR01618        21 PGTGKTSTIKYLPG   34 (220)
T ss_pred             CCCCHHHHHHhcCC
Confidence            79999999998853

This model represents an uncharacterized family of proteins from a number of phage of Gram-positive bacteria. This protein contains a P-loop motif, G/A-X-X-G-X-G-K-T near its amino end. The function of this protein is unknown.

>cd01862 Rab7 Rab7 subfamily

Probab=82.48  E-value=0.78  Score=35.65  Aligned_cols=15  Identities=40%  Similarity=0.716  Sum_probs=13.4

Q ss_pred             CCCcHHHHHHHHHhh
Q 041028            2 GGIGKTTLAKEVARK   16 (283)
Q Consensus         2 gGiGKTtLA~~v~~~   16 (283)
                      +|+|||||+..+.+.
T Consensus         9 ~~~GKSsl~~~l~~~   23 (172)
T cd01862           9 SGVGKTSLMNQYVNK   23 (172)
T ss_pred             CCCCHHHHHHHHhcC
Confidence            699999999998775

Rab7 is a small Rab GTPase that regulates vesicular traffic from early to late endosomal stages of the endocytic pathway. The yeast Ypt7 and mammalian Rab7 are both involved in transport to the vacuole/lysosome, whereas Ypt7 is also required for homotypic vacuole fusion. Mammalian Rab7 is an essential participant in the autophagic pathway for sequestration and targeting of cytoplasmic components to the lytic compartment. Mammalian Rab7 is also proposed to function as a tumor suppressor. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-

>PF13086 AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV_A 2XZP_A 2GK6_A 2GK7_A 2GJK_A

Probab=82.44  E-value=1.5  Score=35.82  Aligned_cols=45  Identities=16%  Similarity=0.161  Sum_probs=25.3

Q ss_pred             CCCcHHHHHHHHHhhhcc-----CCCCCeEEEEEeCCCCCHHHHHHHHHH
Q 041028            2 GGIGKTTLAKEVARKAKN-----GKLFDQIVFTEVSQNPNIKKIQGEIAF   46 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~-----~~~Fd~~~wv~v~~~~~~~~l~~~i~~   46 (283)
                      +|.||||++..+......     ...-+..+-+....+..+..++..+..
T Consensus        26 PGTGKT~~l~~~i~~~~~~~~~~~~~~~~~il~~~~sN~avd~~~~~l~~   75 (236)
T PF13086_consen   26 PGTGKTTTLASIIAQLLQRFKSRSADRGKKILVVSPSNAAVDNILERLKK   75 (236)
T ss_dssp             TTSSHHHHHHHHHHHH-------HCCCSS-EEEEESSHHHHHHHHHHHHC
T ss_pred             CCCChHHHHHHHHHHhccchhhhhhhccccceeecCCchhHHHHHHHHHh
Confidence            699999877776665511     112344444544455555666666555

>TIGR00455 apsK adenylylsulfate kinase (apsK)

Probab=82.41  E-value=1  Score=35.95  Aligned_cols=17  Identities=35%  Similarity=0.642  Sum_probs=15.0

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      +|+||||+|+.+.....
T Consensus        27 ~GsGKstla~~l~~~l~   43 (184)
T TIGR00455        27 SGSGKSTIANALEKKLE   43 (184)
T ss_pred             CCCCHHHHHHHHHHHHH
Confidence            59999999999998764

Important residue (active site in E.coli) is residue 100 of the seed alignment.

>cd01918 HprK_C HprK/P, the bifunctional histidine-containing protein kinase/phosphatase, controls the phosphorylation state of the phosphocarrier protein HPr and regulates the utilization of carbon sources by gram-positive bacteria

Probab=82.41  E-value=0.93  Score=35.02  Aligned_cols=15  Identities=47%  Similarity=0.811  Sum_probs=13.3

Q ss_pred             CCCcHHHHHHHHHhh
Q 041028            2 GGIGKTTLAKEVARK   16 (283)
Q Consensus         2 gGiGKTtLA~~v~~~   16 (283)
                      +|+||||||..+..+
T Consensus        23 sG~GKStlal~L~~~   37 (149)
T cd01918          23 SGIGKSELALELIKR   37 (149)
T ss_pred             CCCCHHHHHHHHHHc
Confidence            699999999988775

It catalyzes both the ATP-dependent phosphorylation of Ser-46 of HPr and its dephosphorylation by phosphorolysis. The latter reaction uses inorganic phosphate as substrate and produces pyrophosphate. Phosphoenolpyruvate carboxykinase (PEPCK) and the C-terminal catalytic domain of HprK/P are structurally similar with conserved active site residues suggesting these two phosphotransferases have related functions. The HprK/P N-terminal domain is structurally similar to the N-terminal domains of the MurE and MurF amino acid ligases.

>cd04136 Rap_like Rap-like subfamily

Probab=82.39  E-value=0.85  Score=35.07  Aligned_cols=15  Identities=33%  Similarity=0.742  Sum_probs=12.8

Q ss_pred             CCCcHHHHHHHHHhh
Q 041028            2 GGIGKTTLAKEVARK   16 (283)
Q Consensus         2 gGiGKTtLA~~v~~~   16 (283)
                      +|+|||||+..+.+.
T Consensus        10 ~~vGKTsl~~~~~~~   24 (163)
T cd04136          10 GGVGKSALTVQFVQG   24 (163)
T ss_pred             CCCCHHHHHHHHHhC
Confidence            699999999988754

The Rap subfamily consists of the Rap1, Rap2, and RSR1. Rap subfamily proteins perform different cellular functions, depending on the isoform and its subcellular localization. For example, in rat salivary gland, neutrophils, and platelets, Rap1 localizes to secretory granules and is believed to regulate exocytosis or the formation of secretory granules. Rap1 has also been shown to localize in the Golgi of rat fibroblasts, zymogen granules, plasma membrane, and microsomal membrane of the pancreatic acini, as well as in the endocytic compartment of skeletal muscle cells and fibroblasts. Rap1 localizes in the nucleus of human oropharyngeal squamous cell carcinomas (SCCs) and cell lines. Rap1 plays a role in phagocytosis by controlling the binding of adhesion receptors (typically integrins) to their ligands. In yeast, Rap1 has been implicated in multiple functions, including activation and silencing of transcription and maintenance of telomeres.

>KOG0991 consensus Replication factor C, subunit RFC2 [Replication, recombination and repair]

Probab=82.34  E-value=1  Score=37.45  Aligned_cols=44  Identities=23%  Similarity=0.249  Sum_probs=31.7

Q ss_pred             CCCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHH
Q 041028            1 MGGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEI   44 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i   44 (283)
                      |+|+||||=+..+++..-...+=++++=++.|....+.-+-.+|
T Consensus        56 pPG~GKTTsi~~LAr~LLG~~~ke~vLELNASdeRGIDvVRn~I   99 (333)
T KOG0991|consen   56 PPGTGKTTSILCLARELLGDSYKEAVLELNASDERGIDVVRNKI   99 (333)
T ss_pred             CCCCchhhHHHHHHHHHhChhhhhHhhhccCccccccHHHHHHH
Confidence            68999999888888876543333788888888776665554444

>TIGR02903 spore_lon_C ATP-dependent protease, Lon family

Probab=82.27  E-value=1.1  Score=43.06  Aligned_cols=18  Identities=44%  Similarity=0.573  Sum_probs=15.5

Q ss_pred             CCCcHHHHHHHHHhhhcc
Q 041028            2 GGIGKTTLAKEVARKAKN   19 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~   19 (283)
                      +|+||||||+.+++....
T Consensus       184 ~GtGKTTLAr~i~~~~~~  201 (615)
T TIGR02903       184 PGVGKTTAARLALEEAKK  201 (615)
T ss_pred             CCCCHHHHHHHHHHhhhh
Confidence            699999999999887643

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

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=82.26  E-value=2.6  Score=40.61  Aligned_cols=18  Identities=39%  Similarity=0.597  Sum_probs=15.2

Q ss_pred             CCCcHHHHHHHHHhhhcc
Q 041028            2 GGIGKTTLAKEVARKAKN   19 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~   19 (283)
                      .|+||||+|+.+++..-.
T Consensus        47 ~GvGKTTlAr~lAk~L~c   64 (647)
T PRK07994         47 RGVGKTTIARLLAKGLNC   64 (647)
T ss_pred             CCCCHHHHHHHHHHhhhh
Confidence            599999999999887544

>cd01131 PilT Pilus retraction ATPase PilT

Probab=82.06  E-value=1.6  Score=35.38  Aligned_cols=17  Identities=24%  Similarity=0.257  Sum_probs=14.3

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      .|.||||++..+.....
T Consensus        10 tGSGKTTll~~ll~~~~   26 (198)
T cd01131          10 TGSGKSTTLAAMIDYIN   26 (198)
T ss_pred             CCCCHHHHHHHHHHHhh
Confidence            59999999998887654

PilT is a nucleotide binding protein responsible for the retraction of type IV pili, likely by pili disassembly. This retraction provides the force required for travel of bacteria in low water environments by a mechanism known as twitching motility.

>PRK10751 molybdopterin-guanine dinucleotide biosynthesis protein B; Provisional

Probab=81.81  E-value=1  Score=35.77  Aligned_cols=18  Identities=39%  Similarity=0.442  Sum_probs=15.5

Q ss_pred             CCCcHHHHHHHHHhhhcc
Q 041028            2 GGIGKTTLAKEVARKAKN   19 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~   19 (283)
                      .|+|||||++.+......
T Consensus        15 sgsGKTTLi~~li~~l~~   32 (173)
T PRK10751         15 SGTGKTTLLKKLIPALCA   32 (173)
T ss_pred             CCChHHHHHHHHHHHHhh
Confidence            599999999999987654

>TIGR00231 small_GTP small GTP-binding protein domain

Probab=81.79  E-value=0.89  Score=34.19  Aligned_cols=17  Identities=24%  Similarity=0.329  Sum_probs=14.5

Q ss_pred             CCCCcHHHHHHHHHhhh
Q 041028            1 MGGIGKTTLAKEVARKA   17 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (283)
                      .+|+|||||...+....
T Consensus         9 ~~~~GKstl~~~l~~~~   25 (161)
T TIGR00231         9 DPNVGKSTLLNRLLGNK   25 (161)
T ss_pred             CCCCCHHHHHHHHhCCC
Confidence            36999999999998765

This model recognizes a large number of small GTP-binding proteins and related domains in larger proteins. Note that the alpha chains of heterotrimeric G proteins are larger proteins in which the NKXD motif is separated from the GxxxxGK[ST] motif (P-loop) by a long insert and are not easily detected by this model.

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=81.79  E-value=6.2  Score=37.80  Aligned_cols=30  Identities=20%  Similarity=0.286  Sum_probs=20.6

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEe
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEV   31 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v   31 (283)
                      .|+|||.|++++++.......--.++|++.
T Consensus       323 sGsGKTHLL~AIa~~a~~~~~g~~V~Yita  352 (617)
T PRK14086        323 SGLGKTHLLHAIGHYARRLYPGTRVRYVSS  352 (617)
T ss_pred             CCCCHHHHHHHHHHHHHHhCCCCeEEEeeH
Confidence            499999999999998653211124566654

>COG0541 Ffh Signal recognition particle GTPase [Intracellular trafficking and secretion]

Probab=81.77  E-value=8.3  Score=35.10  Aligned_cols=48  Identities=25%  Similarity=0.344  Sum_probs=33.1

Q ss_pred             CCcHHHHHHHHHhhhccCCCCCeEEEEEeC-CCCCHHHHHHHHHHHhCCCC
Q 041028            3 GIGKTTLAKEVARKAKNGKLFDQIVFTEVS-QNPNIKKIQGEIAFKLGLKF   52 (283)
Q Consensus         3 GiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~-~~~~~~~l~~~i~~~l~~~~   52 (283)
                      |.||||-|-.+++..+.+ .+ .+.-|... ..+-..+-++.+..+++.+.
T Consensus       110 GsGKTTt~~KLA~~lkk~-~~-kvllVaaD~~RpAA~eQL~~La~q~~v~~  158 (451)
T COG0541         110 GSGKTTTAGKLAKYLKKK-GK-KVLLVAADTYRPAAIEQLKQLAEQVGVPF  158 (451)
T ss_pred             CCChHhHHHHHHHHHHHc-CC-ceEEEecccCChHHHHHHHHHHHHcCCce
Confidence            899999999998887653 22 23334333 34556677888999998874

>PRK04220 2-phosphoglycerate kinase; Provisional

Probab=81.74  E-value=1  Score=39.06  Aligned_cols=17  Identities=35%  Similarity=0.602  Sum_probs=15.1

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      +|+||||+|..++++..
T Consensus       101 sgsGKStlA~~La~~l~  117 (301)
T PRK04220        101 SGVGTSTIAFELASRLG  117 (301)
T ss_pred             CCCCHHHHHHHHHHHhC
Confidence            69999999999998763

>PRK13974 thymidylate kinase; Provisional

Probab=81.72  E-value=3.8  Score=33.54  Aligned_cols=45  Identities=20%  Similarity=0.285  Sum_probs=26.9

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCC---eEEEEEeCCCCCHHHHHHHHHH
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFD---QIVFTEVSQNPNIKKIQGEIAF   46 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd---~~~wv~v~~~~~~~~l~~~i~~   46 (283)
                      .|+||||+++.++......+...   .++...........+..++++.
T Consensus        12 dGsGKsT~~~~l~~~l~~~g~~~~~~~~~~~~~p~~~~~g~~ir~~l~   59 (212)
T PRK13974         12 DGCGKTTQIDHLSKWLPSSGLMPKGAKLIITREPGGTLLGKSLRELLL   59 (212)
T ss_pred             CCCCHHHHHHHHHHHHHhcCccccCCeeeeeeCCCCCchHHHHHHHHc
Confidence            59999999999998876443321   2222223233345566666654

>PRK08506 replicative DNA helicase; Provisional

Probab=81.67  E-value=3.4  Score=38.41  Aligned_cols=43  Identities=23%  Similarity=0.176  Sum_probs=30.5

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHHHh
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKL   48 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~~l   48 (283)
                      +|+|||+||..++.+.... .. .++++++  ..+..++..+++...
T Consensus       201 pg~GKT~fal~ia~~~~~~-g~-~V~~fSl--EMs~~ql~~Rlla~~  243 (472)
T PRK08506        201 PSMGKTTLCLNMALKALNQ-DK-GVAFFSL--EMPAEQLMLRMLSAK  243 (472)
T ss_pred             CCCChHHHHHHHHHHHHhc-CC-cEEEEeC--cCCHHHHHHHHHHHh
Confidence            6999999999998876422 22 4555544  467788888887655

>cd00882 Ras_like_GTPase Ras-like GTPase superfamily

Probab=81.67  E-value=0.95  Score=33.56  Aligned_cols=17  Identities=29%  Similarity=0.454  Sum_probs=14.6

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      .|+|||||...+.....
T Consensus         5 ~~~GKStl~~~l~~~~~   21 (157)
T cd00882           5 SGVGKTSLLNRLLGGEF   21 (157)
T ss_pred             CCCcHHHHHHHHHhCCc
Confidence            69999999999987644

The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulate initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Memb

>TIGR02528 EutP ethanolamine utilization protein, EutP

Probab=81.59  E-value=0.81  Score=34.47  Aligned_cols=15  Identities=40%  Similarity=0.554  Sum_probs=13.2

Q ss_pred             CCCcHHHHHHHHHhh
Q 041028            2 GGIGKTTLAKEVARK   16 (283)
Q Consensus         2 gGiGKTtLA~~v~~~   16 (283)
                      +|+|||||...+.+.
T Consensus         9 ~~vGKSsL~~~l~~~   23 (142)
T TIGR02528         9 VGCGKTTLTQALQGE   23 (142)
T ss_pred             CCCCHHHHHHHHcCC
Confidence            699999999998765

This protein is found within operons which code for polyhedral organelles containing the enzyme ethanolamine ammonia lyase. The function of this gene is unknown, although the presence of an N-terminal GxxGxGK motif implies a GTP-binding site.

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=81.25  E-value=1  Score=39.22  Aligned_cols=16  Identities=44%  Similarity=0.636  Sum_probs=14.6

Q ss_pred             CCCcHHHHHHHHHhhh
Q 041028            2 GGIGKTTLAKEVARKA   17 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~   17 (283)
                      +|+||||+|+.+++..
T Consensus        52 ~G~GKT~la~~l~~~~   67 (316)
T PHA02544         52 PGTGKTTVAKALCNEV   67 (316)
T ss_pred             CCCCHHHHHHHHHHHh
Confidence            6999999999999875

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=81.25  E-value=3  Score=40.27  Aligned_cols=17  Identities=41%  Similarity=0.636  Sum_probs=14.8

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      .|+||||+|+.+++...
T Consensus        46 pGvGKTTlAriLAK~Ln   62 (702)
T PRK14960         46 RGVGKTTIARILAKCLN   62 (702)
T ss_pred             CCCCHHHHHHHHHHHhC
Confidence            59999999999988754

>PF00071 Ras: Ras family; InterPro: IPR001806 Small GTPases form an independent superfamily within the larger class of regulatory GTP hydrolases

Probab=81.18  E-value=1.1  Score=34.41  Aligned_cols=16  Identities=31%  Similarity=0.594  Sum_probs=13.9

Q ss_pred             CCCcHHHHHHHHHhhh
Q 041028            2 GGIGKTTLAKEVARKA   17 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~   17 (283)
                      +|+|||||...+.+..
T Consensus         8 ~~vGKtsl~~~~~~~~   23 (162)
T PF00071_consen    8 SGVGKTSLINRLINGE   23 (162)
T ss_dssp             TTSSHHHHHHHHHHSS
T ss_pred             CCCCHHHHHHHHHhhc
Confidence            6999999999988753

This superfamily contains proteins that control a vast number of important processes and possess a common, structurally preserved GTP-binding domain [, ]. Sequence comparisons of small G proteins from various species have revealed that they are conserved in primary structures at the level of 30-55% similarity []. Crystallographic analysis of various small G proteins revealed the presence of a 20 kDa catalytic domain that is unique for the whole superfamily [, ]. The domain is built of five alpha helices (A1-A5), six beta-strands (B1-B6) and five polypeptide loops (G1-G5). A structural comparison of the GTP- and GDP-bound form, allows one to distinguish two functional loop regions: switch I and switch II that surround the gamma-phosphate group of the nucleotide. The G1 loop (also called the P-loop) that connects the B1 strand and the A1 helix is responsible for the binding of the phosphate groups. The G3 loop provides residues for Mg(2+) and phosphate binding and is located at the N terminus of the A2 helix. The G1 and G3 loops are sequentially similar to Walker A and Walker B boxes that are found in other nucleotide binding motifs. The G2 loop connects the A1 helix and the B2 strand and contains a conserved Thr residue responsible for Mg(2+) binding. The guanine base is recognised by the G4 and G5 loops. The consensus sequence NKXD of the G4 loop contains Lys and Asp residues directly interacting with the nucleotide. Part of the G5 loop located between B6 and A5 acts as a recognition site for the guanine base []. The small GTPase superfamily can be divided into at least 8 different families, including: Arf small GTPases. GTP-binding proteins involved in protein trafficking by modulating vesicle budding and uncoating within the Golgi apparatus. Ran small GTPases. GTP-binding proteins involved in nucleocytoplasmic transport. Required for the import of proteins into the nucleus and also for RNA export. Rab small GTPases. GTP-binding proteins involved in vesicular traffic. Rho small GTPases. GTP-binding proteins that control cytoskeleton reorganisation. Ras small GTPases. GTP-binding proteins involved in signalling pathways. Sar1 small GTPases. Small GTPase component of the coat protein complex II (COPII) which promotes the formation of transport vesicles from the endoplasmic reticulum (ER). Mitochondrial Rho (Miro). Small GTPase domain found in mitochondrial proteins involved in mitochondrial trafficking. Roc small GTPases domain. Small GTPase domain always found associated with the COR domain. ; GO: 0005525 GTP binding, 0007264 small GTPase mediated signal transduction; PDB: 1M7B_A 2V55_B 3EG5_C 3LAW_A 1YHN_A 1T91_B 1HE8_B 3SEA_B 3T5G_A 1XTS_A ....

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=81.14  E-value=1  Score=41.77  Aligned_cols=17  Identities=41%  Similarity=0.601  Sum_probs=14.9

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      +|+||||+|+.+++...
T Consensus        45 pGtGKTTlA~~lA~~l~   61 (472)
T PRK14962         45 RGTGKTTVARILAKSLN   61 (472)
T ss_pred             CCCCHHHHHHHHHHHhc
Confidence            69999999999988754

>cd04137 RheB Rheb (Ras Homolog Enriched in Brain) subfamily

Probab=81.02  E-value=1  Score=35.42  Aligned_cols=15  Identities=20%  Similarity=0.432  Sum_probs=13.0

Q ss_pred             CCCcHHHHHHHHHhh
Q 041028            2 GGIGKTTLAKEVARK   16 (283)
Q Consensus         2 gGiGKTtLA~~v~~~   16 (283)
                      +|+|||||+..+.+.
T Consensus        10 ~g~GKTtl~~~~~~~   24 (180)
T cd04137          10 RSVGKSSLTVQFVEG   24 (180)
T ss_pred             CCCCHHHHHHHHHhC
Confidence            699999999998754

Rheb was initially identified in rat brain, where its expression is elevated by seizures or by long-term potentiation. It is expressed ubiquitously, with elevated levels in muscle and brain. Rheb functions as an important mediator between the tuberous sclerosis complex proteins, TSC1 and TSC2, and the mammalian target of rapamycin (TOR) kinase to stimulate cell growth. TOR kinase regulates cell growth by controlling nutrient availability, growth factors, and the energy status of the cell. TSC1 and TSC2 form a dimeric complex that has tumor suppressor activity, and TSC2 is a GTPase activating protein (GAP) for Rheb. The TSC1/TSC2 complex inhibits the activation of TOR kinase through Rheb. Rheb has also been shown to induce the formation of large cytoplasmic vacuoles in a process that is dependent on the GTPase cycle of Rheb, but independent of the TOR kinase, suggesting Rheb plays a role in endocytic trafficking that le

>smart00175 RAB Rab subfamily of small GTPases

Probab=81.01  E-value=0.96  Score=34.76  Aligned_cols=16  Identities=25%  Similarity=0.524  Sum_probs=13.8

Q ss_pred             CCCcHHHHHHHHHhhh
Q 041028            2 GGIGKTTLAKEVARKA   17 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~   17 (283)
                      +|+|||||.+.+.+..
T Consensus         9 ~~~GKTtli~~l~~~~   24 (164)
T smart00175        9 SGVGKSSLLSRFTDGK   24 (164)
T ss_pred             CCCCHHHHHHHHhcCC
Confidence            6999999999998653

Rab GTPases are implicated in vesicle trafficking.

>PHA02244 ATPase-like protein

Probab=80.94  E-value=1.1  Score=39.94  Aligned_cols=17  Identities=29%  Similarity=0.554  Sum_probs=15.1

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      +|+|||+||+++++...
T Consensus       128 pGtGKTtLA~aLA~~lg  144 (383)
T PHA02244        128 AGSGKNHIAEQIAEALD  144 (383)
T ss_pred             CCCCHHHHHHHHHHHhC
Confidence            69999999999998754

>PF08433 KTI12: Chromatin associated protein KTI12 ; InterPro: IPR013641 This is a family of chromatin associated proteins which interact with the Elongator complex, a component of the elongating form of RNA polymerase II []

Probab=80.92  E-value=1.1  Score=38.26  Aligned_cols=19  Identities=37%  Similarity=0.389  Sum_probs=15.8

Q ss_pred             CCCCcHHHHHHHHHhhhcc
Q 041028            1 MGGIGKTTLAKEVARKAKN   19 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~   19 (283)
                      .+|+||||+|+.+......
T Consensus         9 ~P~SGKTt~a~~L~~~~~~   27 (270)
T PF08433_consen    9 LPCSGKTTRAKELKKYLEE   27 (270)
T ss_dssp             -TTSSHHHHHHHHHHHHHH
T ss_pred             CCCCcHHHHHHHHHHHHHh
Confidence            3799999999999987654

The Elongator complex has histone acetyltransferase activity. ; PDB: 3ADB_B 3ADC_B 3A4M_B 3A4N_B 3AM1_A 3A4L_B 3ADD_A.

>cd02022 DPCK Dephospho-coenzyme A kinase (DPCK, EC 2

Probab=80.89  E-value=1.2  Score=35.50  Aligned_cols=15  Identities=40%  Similarity=0.379  Sum_probs=13.4

Q ss_pred             CCCCcHHHHHHHHHh
Q 041028            1 MGGIGKTTLAKEVAR   15 (283)
Q Consensus         1 mgGiGKTtLA~~v~~   15 (283)
                      +.|+||||+|+.+.+
T Consensus         7 ~~gsGKst~~~~l~~   21 (179)
T cd02022           7 GIGSGKSTVAKLLKE   21 (179)
T ss_pred             CCCCCHHHHHHHHHH
Confidence            469999999999987

7.1.24) catalyzes the phosphorylation of dephosphocoenzyme A (dCoA) to yield CoA, which is the final step in CoA biosynthesis.

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=80.77  E-value=3.7  Score=35.60  Aligned_cols=18  Identities=44%  Similarity=0.473  Sum_probs=15.5

Q ss_pred             CCCcHHHHHHHHHhhhcc
Q 041028            2 GGIGKTTLAKEVARKAKN   19 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~   19 (283)
                      .|+||||+|+.+++....
T Consensus        47 ~G~GKt~~~~~l~~~l~~   64 (319)
T PRK00440         47 PGTGKTTAALALARELYG   64 (319)
T ss_pred             CCCCHHHHHHHHHHHHcC
Confidence            599999999999988643

>TIGR00665 DnaB replicative DNA helicase

Probab=80.75  E-value=3.3  Score=38.00  Aligned_cols=44  Identities=16%  Similarity=0.203  Sum_probs=29.8

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHHHh
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKL   48 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~~l   48 (283)
                      +|+|||++|..+..+...... ..++|+++..  +..++..+++...
T Consensus       204 pg~GKT~~~l~~a~~~a~~~g-~~vl~~SlEm--~~~~i~~R~~~~~  247 (434)
T TIGR00665       204 PSMGKTAFALNIAENAAIKEG-KPVAFFSLEM--SAEQLAMRMLSSE  247 (434)
T ss_pred             CCCChHHHHHHHHHHHHHhCC-CeEEEEeCcC--CHHHHHHHHHHHh
Confidence            699999999998877543211 2566766544  5667777776554

This model describes the helicase DnaB, a homohexameric protein required for DNA replication. The homohexamer can form a ring around a single strand of DNA near a replication fork. An intein of 400 residues is found at a conserved location in DnaB of Synechocystis PCC6803, Rhodothermus marinus (both experimentally confirmed), and Mycobacterium tuberculosis. The intein removes itself by a self-splicing reaction. The seed alignment contains inteins so that the model built from the seed alignment will model a low cost at common intein insertion sites.

>COG3598 RepA RecA-family ATPase [DNA replication, recombination, and repair]

Probab=80.74  E-value=2.8  Score=36.65  Aligned_cols=51  Identities=22%  Similarity=0.371  Sum_probs=34.6

Q ss_pred             CCCcHHHHHHHHHhhh-ccCCCCC-------eEEEEEeCC-CCCHHHHHHHHHHHhCCCC
Q 041028            2 GGIGKTTLAKEVARKA-KNGKLFD-------QIVFTEVSQ-NPNIKKIQGEIAFKLGLKF   52 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~-~~~~~Fd-------~~~wv~v~~-~~~~~~l~~~i~~~l~~~~   52 (283)
                      ||+|||||+..++=.. .-++.|.       .+++|+... ..++.+-++.+..+++.+.
T Consensus        98 sg~GKttllL~l~IalaaG~~lfG~~v~epGkvlyvslEl~re~~L~Rl~~v~a~mgLsP  157 (402)
T COG3598          98 SGVGKTTLLLYLCIALAAGKNLFGNKVKEPGKVLYVSLELYREDILERLEPVRARMGLSP  157 (402)
T ss_pred             CcccHhHHHHHHHHHHHhhHHHhcccccCCCeEEEEEeccChHHHHHHHHHHHHHcCCCh
Confidence            7999999998865432 2223343       567787764 3466777788888888763

>PF00625 Guanylate_kin: Guanylate kinase; InterPro: IPR008144 Guanylate kinase (2

Probab=80.59  E-value=1.9  Score=34.40  Aligned_cols=27  Identities=33%  Similarity=0.529  Sum_probs=19.9

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEE
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTE   30 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~   30 (283)
                      .|+|||||++.+.......  |...+.-+
T Consensus        11 sg~GK~~l~~~L~~~~~~~--~~~~v~~T   37 (183)
T PF00625_consen   11 SGSGKSTLAKRLIQEFPDK--FGRVVSHT   37 (183)
T ss_dssp             TTSSHHHHHHHHHHHSTTT--EEEEEEEE
T ss_pred             CCCCHHHHHHHHHHhcccc--cccceeec
Confidence            5999999999999976633  75444443

7.4.8 from EC) (GK) [] catalyzes the ATP-dependent phosphorylation of GMP into GDP. It is essential for recycling GMP and indirectly, cGMP. In prokaryotes (such as Escherichia coli), lower eukaryotes (such as yeast) and in vertebrates, GK is a highly conserved monomeric protein of about 200 amino acids. GK has been shown [, , ] to be structurally similar to protein A57R (or SalG2R) from various strains of Vaccinia virus. Proteins containing one or more copies of the DHR domain, an SH3 domain as well as a C-terminal GK-like domain, are collectively termed MAGUKs (membrane-associated guanylate kinase homologs) [], and include Drosophila lethal(1)discs large-1 tumor suppressor protein (gene dlg1); mammalian tight junction protein Zo-1; a family of mammalian synaptic proteins that seem to interact with the cytoplasmic tail of NMDA receptor subunits (SAP90/PSD-95, CHAPSYN-110/PSD-93, SAP97/DLG1 and SAP102); vertebrate 55kDa erythrocyte membrane protein (p55); Caenorhabditis elegans protein lin-2; rat protein CASK; and human proteins DLG2 and DLG3. There is an ATP-binding site (P-loop) in the N-terminal section of GK, which is not conserved in the GK-like domain of the above proteins. However these proteins retain the residues known, in GK, to be involved in the binding of GMP.; GO: 0005515 protein binding; PDB: 3UAT_A 3KFV_A 2ANC_F 2F3T_E 2ANB_A 2AN9_A 1S96_A 2F3R_B 3TR0_A 1LVG_A ....

>PRK14737 gmk guanylate kinase; Provisional

Probab=80.58  E-value=1.1  Score=36.01  Aligned_cols=16  Identities=25%  Similarity=0.445  Sum_probs=14.1

Q ss_pred             CCCcHHHHHHHHHhhh
Q 041028            2 GGIGKTTLAKEVARKA   17 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~   17 (283)
                      +|+|||||++.+....
T Consensus        13 sG~GK~tl~~~l~~~~   28 (186)
T PRK14737         13 AGGGKSTIIQALLEEH   28 (186)
T ss_pred             CCCCHHHHHHHHHhcC
Confidence            6999999999998753

>PRK05342 clpX ATP-dependent protease ATP-binding subunit ClpX; Provisional

Probab=80.55  E-value=1.2  Score=40.46  Aligned_cols=17  Identities=47%  Similarity=0.561  Sum_probs=14.9

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      +|+|||+||+.++....
T Consensus       117 ~GtGKT~lAr~lA~~l~  133 (412)
T PRK05342        117 TGSGKTLLAQTLARILD  133 (412)
T ss_pred             CCCCHHHHHHHHHHHhC
Confidence            59999999999997654

>PRK08356 hypothetical protein; Provisional

Probab=80.45  E-value=1.1  Score=36.19  Aligned_cols=14  Identities=43%  Similarity=0.292  Sum_probs=12.3

Q ss_pred             CCCCcHHHHHHHHH
Q 041028            1 MGGIGKTTLAKEVA   14 (283)
Q Consensus         1 mgGiGKTtLA~~v~   14 (283)
                      ++|+||||+|+.+.
T Consensus        13 ~~gsGK~t~a~~l~   26 (195)
T PRK08356         13 KIAAGKTTVAKFFE   26 (195)
T ss_pred             CCCCCHHHHHHHHH
Confidence            47999999999993

>PRK14738 gmk guanylate kinase; Provisional

Probab=80.44  E-value=1.1  Score=36.63  Aligned_cols=15  Identities=20%  Similarity=0.561  Sum_probs=13.2

Q ss_pred             CCCcHHHHHHHHHhh
Q 041028            2 GGIGKTTLAKEVARK   16 (283)
Q Consensus         2 gGiGKTtLA~~v~~~   16 (283)
                      +|+|||||++.+...
T Consensus        22 sG~GK~tl~~~L~~~   36 (206)
T PRK14738         22 SGVGKDAVLARMRER   36 (206)
T ss_pred             CCCCHHHHHHHHHhc
Confidence            699999999999754

>PRK06321 replicative DNA helicase; Provisional

Probab=80.42  E-value=3.1  Score=38.68  Aligned_cols=44  Identities=16%  Similarity=0.126  Sum_probs=29.2

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHHHh
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKL   48 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~~l   48 (283)
                      +|+|||++|..++.....+.. ..++|+++  ..+..++..+++...
T Consensus       235 PgmGKTafal~ia~~~a~~~g-~~v~~fSL--EMs~~ql~~Rlla~~  278 (472)
T PRK06321        235 PAMGKTALALNIAENFCFQNR-LPVGIFSL--EMTVDQLIHRIICSR  278 (472)
T ss_pred             CCCChHHHHHHHHHHHHHhcC-CeEEEEec--cCCHHHHHHHHHHhh
Confidence            699999999999887643211 24556554  345667777776543

>PRK13886 conjugal transfer protein TraL; Provisional

Probab=80.29  E-value=1.3  Score=37.07  Aligned_cols=19  Identities=32%  Similarity=0.592  Sum_probs=15.4

Q ss_pred             CCCCcHHHHHHHHHhhhcc
Q 041028            1 MGGIGKTTLAKEVARKAKN   19 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~   19 (283)
                      -||+||||.|..++.....
T Consensus        11 KGGvGKSt~a~~la~~l~~   29 (241)
T PRK13886         11 KGGVGKSFIAATIAQYKAS   29 (241)
T ss_pred             CCCCcHHHHHHHHHHHHHh
Confidence            3899999999998876543

>PRK12597 F0F1 ATP synthase subunit beta; Provisional

Probab=80.24  E-value=2.8  Score=38.74  Aligned_cols=45  Identities=22%  Similarity=0.256  Sum_probs=33.2

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCC-CCHHHHHHHHHHH
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQN-PNIKKIQGEIAFK   47 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~-~~~~~l~~~i~~~   47 (283)
                      +|+|||||+..+.+..... +-+.++++-+++. ..+.++..++...
T Consensus       152 ~G~GKt~Ll~~~~~~~~~~-~~dv~V~~liGER~rEv~ef~~~~~~~  197 (461)
T PRK12597        152 AGVGKTVLMMELIFNISKQ-HSGSSVFAGVGERSREGHELYHEMKES  197 (461)
T ss_pred             CCCChhHHHHHHHHHHHhh-CCCEEEEEcCCcchHHHHHHHHHHHhc
Confidence            5999999999988876543 4588888888755 4566677766653

>KOG0726 consensus 26S proteasome regulatory complex, ATPase RPT2 [Posttranslational modification, protein turnover, chaperones]

Probab=80.20  E-value=0.91  Score=39.03  Aligned_cols=19  Identities=47%  Similarity=0.560  Sum_probs=16.7

Q ss_pred             CCCcHHHHHHHHHhhhccC
Q 041028            2 GGIGKTTLAKEVARKAKNG   20 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~   20 (283)
                      +|.|||-||++|+|+....
T Consensus       228 PGTGKTLLAKAVANqTSAT  246 (440)
T KOG0726|consen  228 PGTGKTLLAKAVANQTSAT  246 (440)
T ss_pred             CCCchhHHHHHHhcccchh
Confidence            6999999999999987654

>cd01864 Rab19 Rab19 subfamily

Probab=80.18  E-value=1.1  Score=34.69  Aligned_cols=15  Identities=20%  Similarity=0.399  Sum_probs=12.8

Q ss_pred             CCCcHHHHHHHHHhh
Q 041028            2 GGIGKTTLAKEVARK   16 (283)
Q Consensus         2 gGiGKTtLA~~v~~~   16 (283)
                      +|+|||||+..+.+.
T Consensus        12 ~~~GKTsli~~l~~~   26 (165)
T cd01864          12 SNVGKTCVVQRFKSG   26 (165)
T ss_pred             CCCCHHHHHHHHhhC
Confidence            699999999998653

Rab19 proteins are associated with Golgi stacks. Similarity analysis indicated that Rab41 is closely related to Rab19. However, the function of these Rabs is not yet chracterized. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.

>PF01637 Arch_ATPase: Archaeal ATPase; InterPro: IPR011579 This domain has been found in a number of bacterial and archaeal proteins, all of which contain a conserved P-loop motif that is involved in binding ATP

Probab=80.17  E-value=1.3  Score=36.25  Aligned_cols=17  Identities=47%  Similarity=0.589  Sum_probs=15.2

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      .|+|||+|++++.+..+
T Consensus        29 rg~GKTsLl~~~~~~~~   45 (234)
T PF01637_consen   29 RGSGKTSLLKEFINELK   45 (234)
T ss_dssp             TTSSHHHHHHHHHHHCT
T ss_pred             CcCCHHHHHHHHHHHhh
Confidence            59999999999999774

; GO: 0005524 ATP binding; PDB: 2FNA_A 2QEN_A.

>TIGR00416 sms DNA repair protein RadA

Probab=80.16  E-value=2  Score=39.67  Aligned_cols=31  Identities=26%  Similarity=0.427  Sum_probs=22.6

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQN   34 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~   34 (283)
                      +|+|||||+..+.......+  ..++|++..+.
T Consensus       103 pGsGKTTL~lq~a~~~a~~g--~kvlYvs~EEs  133 (454)
T TIGR00416       103 PGIGKSTLLLQVACQLAKNQ--MKVLYVSGEES  133 (454)
T ss_pred             CCCCHHHHHHHHHHHHHhcC--CcEEEEECcCC
Confidence            69999999999977654321  35788876654

The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).

>cd00046 DEXDc DEAD-like helicases superfamily

Probab=80.14  E-value=2.2  Score=31.29  Aligned_cols=29  Identities=21%  Similarity=0.046  Sum_probs=20.4

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEE
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTE   30 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~   30 (283)
                      .|.|||+.+..+............++|+.
T Consensus         9 ~G~GKT~~~~~~~~~~~~~~~~~~~lv~~   37 (144)
T cd00046           9 TGSGKTLAALLPILELLDSLKGGQVLVLA   37 (144)
T ss_pred             CCCchhHHHHHHHHHHHhcccCCCEEEEc
Confidence            59999999998877655432345666664

A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.

>PRK08154 anaerobic benzoate catabolism transcriptional regulator; Reviewed

Probab=80.13  E-value=1.2  Score=38.85  Aligned_cols=18  Identities=33%  Similarity=0.567  Sum_probs=15.8

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      |.|+||||+++.++....
T Consensus       141 ~~GsGKStvg~~La~~Lg  158 (309)
T PRK08154        141 LRGAGKSTLGRMLAARLG  158 (309)
T ss_pred             CCCCCHHHHHHHHHHHcC
Confidence            679999999999998764

>cd00154 Rab Rab family

Probab=80.11  E-value=1.2  Score=33.64  Aligned_cols=17  Identities=29%  Similarity=0.401  Sum_probs=14.4

Q ss_pred             CCCCcHHHHHHHHHhhh
Q 041028            1 MGGIGKTTLAKEVARKA   17 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (283)
                      .+|+|||||...+.+..
T Consensus         8 ~~~~GKStl~~~l~~~~   24 (159)
T cd00154           8 DSGVGKTSLLLRFVDGK   24 (159)
T ss_pred             CCCCCHHHHHHHHHhCc
Confidence            36999999999998764

Rab GTPases form the largest family within the Ras superfamily. There are at least 60 Rab genes in the human genome, and a number of Rab GTPases are conserved from yeast to humans. Rab GTPases are small, monomeric proteins that function as molecular switches to regulate vesicle trafficking pathways. The different Rab GTPases are localized to the cytosolic face of specific intracellular membranes, where they regulate distinct steps in membrane traffic pathways. In the GTP-bound form, Rab GTPases recruit specific sets of effector proteins onto membranes. Through their effectors, Rab GTPases regulate vesicle formation, actin- and tubulin-dependent vesicle movement, and membrane fusion. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide di

>PRK11823 DNA repair protein RadA; Provisional

Probab=80.11  E-value=2  Score=39.61  Aligned_cols=44  Identities=30%  Similarity=0.412  Sum_probs=28.4

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHHHhCC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKLGL   50 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~~l~~   50 (283)
                      +|+|||||+.+++......  =..++|++..+.+  .++.. -++.++.
T Consensus        89 pG~GKTtL~lq~a~~~a~~--g~~vlYvs~Ees~--~qi~~-ra~rlg~  132 (446)
T PRK11823         89 PGIGKSTLLLQVAARLAAA--GGKVLYVSGEESA--SQIKL-RAERLGL  132 (446)
T ss_pred             CCCCHHHHHHHHHHHHHhc--CCeEEEEEccccH--HHHHH-HHHHcCC
Confidence            6999999999998876422  2357888776543  23322 2455654

>TIGR01007 eps_fam capsular exopolysaccharide family

Probab=80.05  E-value=1.4  Score=35.76  Aligned_cols=29  Identities=17%  Similarity=0.242  Sum_probs=21.1

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVS   32 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~   32 (283)
                      ||+||||+|..++......+.  .++-|+..
T Consensus        27 gG~GKTt~a~~LA~~la~~G~--rVllID~D   55 (204)
T TIGR01007        27 PGEGKSTTSANIAVAFAQAGY--KTLLIDGD   55 (204)
T ss_pred             CCCCHHHHHHHHHHHHHhCCC--eEEEEeCC
Confidence            899999999999887654321  35666665

This model describes the capsular exopolysaccharide proteins in bacteria. The exopolysaccharide gene cluster consists of several genes which encode a number of proteins which regulate the exoploysaccharide biosynthesis(EPS). Atleast 13 genes espA to espM in streptococcus species seem to direct the EPS proteins and all of which share high homology. Functional roles were characterized by gene disruption experiments which resulted in exopolysaccharide-deficient phenotypes.

>PRK08099 bifunctional DNA-binding transcriptional repressor/ NMN adenylyltransferase; Provisional

Probab=80.05  E-value=1.2  Score=40.42  Aligned_cols=17  Identities=29%  Similarity=0.366  Sum_probs=14.6

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      .|.||||||+.+++...
T Consensus       228 ~gsGKTTL~~~La~~~g  244 (399)
T PRK08099        228 ESSGKSTLVNKLANIFN  244 (399)
T ss_pred             CCCCHHHHHHHHHHHhC
Confidence            59999999999998643

---

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	283
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-13
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	9e-10
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	1e-08
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	3e-05
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	5e-04

>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 = 70.3 bits (171), Expect = 1e-13
 Identities = 33/299 (11%), Positives = 86/299 (28%), Gaps = 79/299 (26%)

Query: 1   MGGIGKTTLAKEVARKAKNGKLFDQIVF----TEVSQNPNIKKIQGEIAFKLGLKFDEES 56
           + G GKT +A +V    K     D  +F       +    + ++  ++ +++   +   S
Sbjct: 158 VLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRS 217

Query: 57  E-SGRTRSPWSRLKKEKLQIICGKKMEGDYAEG---------SELKWLAMDVAKEC---- 102
           + S   +     ++ E  +++  K     Y            ++  W A ++   C    
Sbjct: 218 DHSSNIKLRIHSIQAELRRLLKSK----PYENCLLVLLNVQNAKA-WNAFNL--SCKILL 270

Query: 103 -----------AGLPVSIVTGIKEQELFEWKDALEQLRRPSSTNFKDVQPAAYKAMEL-- 149
                      +    + ++           +    L +      +D+            
Sbjct: 271 TTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRL 330

Query: 150 ---------------GYNKLEGDELKSTFLLIGYTAIASIDDLL------MYGMGLGLFQ 188
                           +  +  D+L +          +S++ L       M+   L +F 
Sbjct: 331 SIIAESIRDGLATWDNWKHVNCDKLTTIIE-------SSLNVLEPAEYRKMFDR-LSVFP 382

Query: 189 -GVNKMEAARAR---------VHTLVHKLKASCMLLDHTSKNEKLFSIHDVVRDVAISI 237
              +      +          V  +V+KL    ++       E   SI  +  ++ + +
Sbjct: 383 PSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQ--PKESTISIPSIYLELKVKL 439

>2a5y_B CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis elegans} SCOP: a.4.5.80 a.77.1.3 c.37.1.20 PDB: 3lqq_A* 3lqr_A* Length = 549

 Score = 58.1 bits (140), Expect = 9e-10
 Identities = 21/175 (12%), Positives = 52/175 (29%), Gaps = 18/175 (10%)

Query: 79  KKMEGDYAEGSELKWLAMDVAKECAGLPVSIVT---GIKEQELFEWKDALEQLRRPSSTN 135
           +        G + + +     +  +G P +++      + +   +      +L       
Sbjct: 303 EAYGMPMPVGEKEEDVLNKTIELSSGNPATLMMFFKSCEPKTFEKMAQLNNKLESRGLVG 362

Query: 136 FKDVQPAAY----KAMELGYNKLEGDELKSTFLLIGYTAI----ASID-DLLMYGMGLGL 186
            + + P +Y     A++     L  DE +S      +  +      I   L    + + +
Sbjct: 363 VECITPYSYKSLAMALQRCVEVLS-DEDRSALA---FAVVMPPGVDIPVKLWSCVIPVDI 418

Query: 187 FQGVNKMEAARARVHTLVHKLKASCMLLDHTSKNEKLFSIHDVVRDVAISIASGE 241
               N+ E     V   + +L     LL         F I  ++      +   +
Sbjct: 419 CS--NEEEQLDDEVADRLKRLSKRGALLSGKRMPVLTFKIDHIIHMFLKHVVDAQ 471

>2a5y_B CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis elegans} SCOP: a.4.5.80 a.77.1.3 c.37.1.20 PDB: 3lqq_A* 3lqr_A* Length = 549

 Score = 54.6 bits (131), Expect = 1e-08
 Identities = 15/84 (17%), Positives = 30/84 (35%), Gaps = 4/84 (4%)

Query: 1   MGGIGKTTLAKEVARKAKN--GKLFDQIVFTEVSQN--PNIKKIQGEIAFKLGLKFDEES 56
             G GK+ +A +   K+    G  +D IV+ + S     +   +  +I   L  + D  +
Sbjct: 160 RAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKSTFDLFTDILLMLKSEDDLLN 219

Query: 57  ESGRTRSPWSRLKKEKLQIICGKK 80
                      LK+     +  + 
Sbjct: 220 FPSVEHVTSVVLKRMICNALIDRP 243

>1z6t_A APAF-1, apoptotic protease activating factor 1; caspase activation, ADP, nucleotide binding, CARD, apoptosis; HET: ADP; 2.21A {Homo sapiens} Length = 591

 Score = 44.1 bits (104), Expect = 3e-05
 Identities = 15/82 (18%), Positives = 30/82 (36%), Gaps = 4/82 (4%)

Query: 1   MGGIGKTTLAKEVARKAKNGKLF--DQIVFTEVSQNPNIKKIQGEIAFKLGLKFDEESES 58
           M G GK+ LA E  R     +      + +  V +      +       L  + D++   
Sbjct: 155 MAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVSVGKQDKSGLLM--KLQNLCTRLDQDESF 212

Query: 59  GRTRSPWSRLKKEKLQIICGKK 80
            +         K++L+I+  +K
Sbjct: 213 SQRLPLNIEEAKDRLRILMLRK 234

>1z6t_A APAF-1, apoptotic protease activating factor 1; caspase activation, ADP, nucleotide binding, CARD, apoptosis; HET: ADP; 2.21A {Homo sapiens} Length = 591

 Score = 40.2 bits (94), Expect = 5e-04
 Identities = 24/169 (14%), Positives = 54/169 (31%), Gaps = 36/169 (21%)

Query: 89  SELKWLAMDVAKECAGLPVSIVT--GI---KEQELFEWKDAL-----EQLRRPSSTNFKD 138
           ++L   A  + KEC G P+ +     +          +   L     +++R+ SS +++ 
Sbjct: 304 ADLPEQAHSIIKECKGSPLVVSLIGALLRDFPNRWEYYLKQLQNKQFKRIRKSSSYDYEA 363

Query: 139 VQPAAYKAMELGYNKLEGDELKSTFLLIGYTAI------ASIDDLLMYGMGLGLFQGVNK 192
           +      AM +    L  +++K  +      +I           L +             
Sbjct: 364 LDE----AMSISVEMLR-EDIKDYYT---DLSILQKDVKVPTKVLCILWDMET------- 408

Query: 193 MEAARARVHTLVHKLKASCMLLDHTSKNEKLFSIHDVVRDVAISIASGE 241
            E     +   V+K     +L    +     + +HD+  D        +
Sbjct: 409 -EEVEDILQEFVNK----SLLFCDRNGKSFRYYLHDLQVDFLTEKNCSQ 452

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	283
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	100.0
3sfz_A	1249	APAF-1, apoptotic peptidase activating factor 1; a	99.96
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	99.94
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	99.93
2qen_A	350	Walker-type ATPase; unknown function; HET: ADP; 2.	98.04
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	97.61
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	96.94
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	96.92
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	96.78
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	96.67
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	96.48
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	95.77
2fna_A	357	Conserved hypothetical protein; structural genomic	94.33
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	94.27
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	94.07
2cvh_A	220	DNA repair and recombination protein RADB; filamen	94.03
1qhx_A	178	CPT, protein (chloramphenicol phosphotransferase);	93.8
1xp8_A	366	RECA protein, recombinase A; recombination, radior	93.78
3hr8_A	356	Protein RECA; alpha and beta proteins (A/B, A+B),	93.72
2chg_A	226	Replication factor C small subunit; DNA-binding pr	93.53
3io5_A	333	Recombination and repair protein; storage dimer, i	93.5
3cwq_A	209	Para family chromosome partitioning protein; alpha	93.47
3bos_A	242	Putative DNA replication factor; P-loop containing	93.19
2zr9_A	349	Protein RECA, recombinase A; recombination, RECA m	93.14
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	93.11
3hjn_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	93.09
2px0_A	296	Flagellar biosynthesis protein FLHF; SRP GTPase, f	93.04
1u94_A	356	RECA protein, recombinase A; homologous recombinat	92.96
3kb2_A	173	SPBC2 prophage-derived uncharacterized protein YOR	92.94
3kjh_A	254	CO dehydrogenase/acetyl-COA synthase complex, acce	92.33
4dzz_A	206	Plasmid partitioning protein PARF; deviant walker	92.33
3trf_A	185	Shikimate kinase, SK; amino acid biosynthesis, tra	92.32
1ly1_A	181	Polynucleotide kinase; PNK, phosphatase, transfera	92.26
2vhj_A	331	Ntpase P4, P4; non- hydrolysable ATP analogue, hyd	92.25
1nks_A	194	Adenylate kinase; thermophilic, transferase; HET:	92.16
3vaa_A	199	Shikimate kinase, SK; structural genomics, center	92.15
3lw7_A	179	Adenylate kinase related protein (ADKA-like); AMP,	92.12
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	92.1
2r8r_A	228	Sensor protein; KDPD, PFAM02702, MCSG, structural	92.06
1kht_A	192	Adenylate kinase; phosphotransferase, signaling pr	91.86
1via_A	175	Shikimate kinase; structural genomics, transferase	91.8
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	91.74
2rhm_A	193	Putative kinase; P-loop containing nucleoside trip	91.74
2i1q_A	322	DNA repair and recombination protein RADA; ATPase,	91.73
2jaq_A	205	Deoxyguanosine kinase; transferase, deoxyribonucle	91.63
3iij_A	180	Coilin-interacting nuclear ATPase protein; alpha a	91.61
3k9g_A	267	PF-32 protein; ssgcid, SBRI, decode biostructures,	91.43
1kag_A	173	SKI, shikimate kinase I; transferase, structural g	91.42
2z43_A	324	DNA repair and recombination protein RADA; archaea	91.26
3t61_A	202	Gluconokinase; PSI-biology, structural genomics, p	91.18
1zuh_A	168	Shikimate kinase; alpha-beta protein, transferase;	91.15
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	91.11
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	91.02
1zp6_A	191	Hypothetical protein ATU3015; alpha-beta protein.,	90.98
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	90.95
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	90.82
3zq6_A	324	Putative arsenical pump-driving ATPase; tail-ancho	90.77
3cm0_A	186	Adenylate kinase; ATP-binding, cytoplasm, nucleoti	90.72
1e6c_A	173	Shikimate kinase; phosphoryl transfer, ADP, shikim	90.68
1cp2_A	269	CP2, nitrogenase iron protein; oxidoreductase; 1.9	90.67
2yvu_A	186	Probable adenylyl-sulfate kinase; transferase, str	90.58
2plr_A	213	DTMP kinase, probable thymidylate kinase; TMP-bind	90.5
2iyv_A	184	Shikimate kinase, SK; transferase, aromatic amino	90.49
2ze6_A	253	Isopentenyl transferase; crown GALL tumor, cytokin	90.47
2pt5_A	168	Shikimate kinase, SK; aromatic amino acid biosynth	90.45
1y63_A	184	LMAJ004144AAA protein; structural genomics, protei	90.38
2vli_A	183	Antibiotic resistance protein; transferase, tunica	90.37
1tev_A	196	UMP-CMP kinase; ploop, NMP binding region, LID reg	90.35
2qor_A	204	Guanylate kinase; phosphotransferase, purine metab	90.3
1yrb_A	262	ATP(GTP)binding protein; GTPase, P-loop, rossman f	90.22
1j8m_F	297	SRP54, signal recognition 54 kDa protein; signalin	90.21
3iqw_A	334	Tail-anchored protein targeting factor GET3; ATPas	90.18
3a4m_A	260	L-seryl-tRNA(SEC) kinase; P-loop motif, walker A m	90.11
1knq_A	175	Gluconate kinase; ALFA/beta structure, transferase	90.04
2afh_E	289	Nitrogenase iron protein 1; nitrogen fixation, iro	90.04
1v5w_A	343	DMC1, meiotic recombination protein DMC1/LIM15 hom	89.97
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	89.95
3ea0_A	245	ATPase, para family; alpha-beta-alpha sandwich, st	89.92
2cdn_A	201	Adenylate kinase; phosphoryl transfer, associative	89.91
3end_A	307	Light-independent protochlorophyllide reductase ir	89.9
3q9l_A	260	Septum site-determining protein MIND; ATPase, bact	89.89
2c95_A	196	Adenylate kinase 1; transferase, AP4A, nucleotide	89.84
3ug7_A	349	Arsenical pump-driving ATPase; tail-anchored, memb	89.84
3uie_A	200	Adenylyl-sulfate kinase 1, chloroplastic; rossmann	89.79
2xj4_A	286	MIPZ; replication, cell division, ATPase, WACA; 1.	89.75
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	89.72
1aky_A	220	Adenylate kinase; ATP:AMP phosphotransferase, myok	89.63
2bwj_A	199	Adenylate kinase 5; phosphoryl transfer reaction,	89.62
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	89.54
4eun_A	200	Thermoresistant glucokinase; putative sugar kinase	89.43
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	89.39
2ph1_A	262	Nucleotide-binding protein; alpha-beta protein, st	89.37
1g3q_A	237	MIND ATPase, cell division inhibitor; alpha-beta-a	89.34
1zd8_A	227	GTP:AMP phosphotransferase mitochondrial; ATP:AMP	89.3
2pbr_A	195	DTMP kinase, thymidylate kinase; transferase, nucl	89.29
1zak_A	222	Adenylate kinase; ATP:AMP-phosphotransferase, tran	89.27
2z0h_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	89.18
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	89.08
3fb4_A	216	Adenylate kinase; psychrophIle, phosphotransferase	89.03
2wwf_A	212	Thymidilate kinase, putative; transferase, malaria	88.98
1qf9_A	194	UMP/CMP kinase, protein (uridylmonophosphate/cytid	88.91
2bdt_A	189	BH3686; alpha-beta protein, structural genomics, P	88.9
2woo_A	329	ATPase GET3; tail-anchored, membrane protein, targ	88.89
2oze_A	298	ORF delta'; para, walker type atpases, DNA segrega	88.79
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	88.77
3be4_A	217	Adenylate kinase; malaria, cryptosporidium parvum	88.76
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	88.71
1ukz_A	203	Uridylate kinase; transferase; HET: ADP AMP; 1.90A	88.7
1byi_A	224	Dethiobiotin synthase; biotin synthesis, cyclo-lig	88.63
3dl0_A	216	Adenylate kinase; phosphotransferase, zinc coordin	88.6
1nn5_A	215	Similar to deoxythymidylate kinase (thymidylate K;	88.59
3lda_A	400	DNA repair protein RAD51; DNA binding protein, ATP	88.59
3pg5_A	361	Uncharacterized protein; structural genomics, PSI-	88.56
2if2_A	204	Dephospho-COA kinase; alpha-beta protein, structur	88.51
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	88.5
3fkq_A	373	NTRC-like two-domain protein; RER070207001320, str	88.44
2woj_A	354	ATPase GET3; tail-anchored, membrane protein, targ	88.43
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	88.39
1gvn_B	287	Zeta; postsegregational killing system, plasmid; 1	88.38
3io3_A	348	DEHA2D07832P; chaperone, membrane traffic, ATPase;	88.38
1e4v_A	214	Adenylate kinase; transferase(phosphotransferase);	88.34
4a74_A	231	DNA repair and recombination protein RADA; hydrola	88.34
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	88.29
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	88.23
2xxa_A	433	Signal recognition particle protein; protein trans	88.21
1ls1_A	295	Signal recognition particle protein; FFH, SRP54, S	88.2
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	88.18
1ak2_A	233	Adenylate kinase isoenzyme-2; nucleoside monophosp	88.17
1hyq_A	263	MIND, cell division inhibitor (MIND-1); MINC, FTSZ	88.12
3gmt_A	230	Adenylate kinase; ssgcid, ATP-BIN cytoplasm, nucle	88.08
1cr0_A	296	DNA primase/helicase; RECA-type protein fold, tran	88.07
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	88.03
2v54_A	204	DTMP kinase, thymidylate kinase; nucleotide biosyn	88.01
2qgz_A	308	Helicase loader, putative primosome component; str	87.96
3fwy_A	314	Light-independent protochlorophyllide reductase I	87.96
2xb4_A	223	Adenylate kinase; ATP-binding, nucleotide-binding,	87.93
1kgd_A	180	CASK, peripheral plasma membrane CASK; maguk, guan	87.85
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	87.84
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	87.75
1m7g_A	211	Adenylylsulfate kinase; APS kinase, transferase, s	87.58
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	87.55
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	87.55
1ye8_A	178	Protein THEP1, hypothetical UPF0334 kinase-like pr	87.49
2pez_A	179	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	87.46
1wcv_1	257	SOJ, segregation protein; ATPase, bacterial, chrom	87.45
3lv8_A	236	DTMP kinase, thymidylate kinase; structural genomi	87.42
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	87.32
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	87.3
4tmk_A	213	Protein (thymidylate kinase); ATP:DTMP phosphotran	87.23
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	87.21
1cke_A	227	CK, MSSA, protein (cytidine monophosphate kinase);	87.07
3co5_A	143	Putative two-component system transcriptional RES	87.03
2j41_A	207	Guanylate kinase; GMP, GMK, transferase, ATP-bindi	87.02
2bbw_A	246	Adenylate kinase 4, AK4; nucleotide kinase, nucleo	86.95
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	86.94
4eaq_A	229	DTMP kinase, thymidylate kinase; structural genomi	86.76
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	86.72
2ffh_A	425	Protein (FFH); SRP54, signal recognition particle,	86.69
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	86.67
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	86.61
1jjv_A	206	Dephospho-COA kinase; P-loop nucleotide-binding fo	86.59
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	86.53
1uf9_A	203	TT1252 protein; P-loop, nucleotide binding domain,	86.43
3tlx_A	243	Adenylate kinase 2; structural genomics, structura	86.37
2q6t_A	444	DNAB replication FORK helicase; hydrolase; 2.90A {	86.33
4edh_A	213	DTMP kinase, thymidylate kinase; structural genomi	86.31
3tr0_A	205	Guanylate kinase, GMP kinase; purines, pyrimidines	86.31
3c8u_A	208	Fructokinase; YP_612366.1, putative fructose trans	86.23
1xjc_A	169	MOBB protein homolog; structural genomics, midwest	86.13
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	86.11
3ez2_A	398	Plasmid partition protein A; type IA, DNA binding,	86.08
3nwj_A	250	ATSK2; P loop, shikimate, nucleoside monophosphate	86.07
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	86.01
2p5t_B	253	PEZT; postsegregational killing system, phosphoryl	85.96
2qt1_A	207	Nicotinamide riboside kinase 1; non-protein kinase	85.94
1ltq_A	301	Polynucleotide kinase; phosphatase, alpha/beta, P-	85.73
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	85.66
2hf9_A	226	Probable hydrogenase nickel incorporation protein	85.47
1ihu_A	589	Arsenical pump-driving ATPase; aluminum fluoride,	85.46
2grj_A	192	Dephospho-COA kinase; TM1387, EC 2.7.1.24, dephosp	85.46
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	85.39
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	85.32
2fna_A	357	Conserved hypothetical protein; structural genomic	85.27
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	85.26
3asz_A	211	Uridine kinase; cytidine phosphorylation, transfer	85.26
3tau_A	208	Guanylate kinase, GMP kinase; structural genomics,	85.19
4hlc_A	205	DTMP kinase, thymidylate kinase; TMK, MRSA, pipiri	85.16
1gtv_A	214	TMK, thymidylate kinase; transferase, transferase	85.0
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	84.96
2zts_A	251	Putative uncharacterized protein PH0186; KAIC like	84.81
3bgw_A	444	DNAB-like replicative helicase; ATPase, replicatio	84.77
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	84.74
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	84.64
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	84.58
1vht_A	218	Dephospho-COA kinase; structural genomics, transfe	84.5
3ake_A	208	Cytidylate kinase; CMP kinase, CMP complex, open c	84.48
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	84.48
1uj2_A	252	Uridine-cytidine kinase 2; alpha/beta mononucleoti	84.37
3a00_A	186	Guanylate kinase, GMP kinase; domain movement, dim	84.35
3ld9_A	223	DTMP kinase, thymidylate kinase; ssgcid, NIH, niai	84.27
1rz3_A	201	Hypothetical protein rbstp0775; MCSG, structural g	84.27
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	84.2
3pvs_A	447	Replication-associated recombination protein A; ma	84.18
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	84.06
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	83.95
1htw_A	158	HI0065; nucleotide-binding fold, structural genomi	83.9
2j37_W	504	Signal recognition particle 54 kDa protein (SRP54)	83.87
2ce2_X	166	GTPase HRAS; signaling protein, guanine nucleotide	83.86
4e22_A	252	Cytidylate kinase; P-loop, CMP/ATP binding, transf	83.85
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	83.83
3igf_A	374	ALL4481 protein; two-domained protein consisting o	83.75
2ocp_A	241	DGK, deoxyguanosine kinase; protein-nucleotide com	83.72
1ex7_A	186	Guanylate kinase; substrate-induced FIT, domain mo	83.72
2r6a_A	454	DNAB helicase, replicative helicase; replication,	83.49
2wsm_A	221	Hydrogenase expression/formation protein (HYPB); m	83.45
4gp7_A	171	Metallophosphoesterase; polynucleotide kinase phos	83.25
1q57_A	503	DNA primase/helicase; dntpase, DNA replication, tr	83.07
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	83.03
2ehv_A	251	Hypothetical protein PH0186; KAIC, RECA ATPase, un	82.98
1lvg_A	198	Guanylate kinase, GMP kinase; transferase; HET: AD	82.93
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	82.86
2ga8_A	359	Hypothetical 39.9 kDa protein; YFR007W, YFH7, unkn	82.72
1odf_A	290	YGR205W, hypothetical 33.3 kDa protein in ADE3-Ser	82.64
3r20_A	233	Cytidylate kinase; structural genomics, seattle st	82.64
1pzn_A	349	RAD51, DNA repair and recombination protein RAD51,	82.53
2r44_A	331	Uncharacterized protein; putative ATPase, structur	82.52
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	82.52
2jeo_A	245	Uridine-cytidine kinase 1; UCK, transferase, ATP-b	82.51
1znw_A	207	Guanylate kinase, GMP kinase; ATP:GMP-phosphotrans	82.49
2dyk_A	161	GTP-binding protein; GTPase, ribosome-binding prot	82.47
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	82.4
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	82.38
1vma_A	306	Cell division protein FTSY; TM0570, structural gen	82.34
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	82.27
3crm_A	323	TRNA delta(2)-isopentenylpyrophosphate transferase	82.23
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	82.17
1tue_A	212	Replication protein E1; helicase, replication, E1E	82.16
3tmk_A	216	Thymidylate kinase; phosphotransferase; HET: T5A;	82.02
3aez_A	312	Pantothenate kinase; transferase, homodimer, COA b	82.01
3ney_A	197	55 kDa erythrocyte membrane protein; structural ge	81.99
3zvl_A	416	Bifunctional polynucleotide phosphatase/kinase; hy	81.99
1oix_A	191	RAS-related protein RAB-11A; small G protein, intr	81.98
2i3b_A	189	HCR-ntpase, human cancer-related ntpase; AAA, ross	81.89
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	81.88
3con_A	190	GTPase NRAS; structural genomics consortium, SGC,	81.86
2f6r_A	281	COA synthase, bifunctional coenzyme A synthase; 18	81.82
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	81.81
3sr0_A	206	Adenylate kinase; phosphoryl transfer analogue, AL	81.72
1z6g_A	218	Guanylate kinase; structural genomics, SGC, struct	81.6
1np6_A	174	Molybdopterin-guanine dinucleotide biosynthesis pr	81.57
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	81.52
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	81.29
1g8f_A	511	Sulfate adenylyltransferase; alpha-beta protein, b	81.29
3ez9_A	403	Para; DNA binding, winged-HTH, partition, biosynth	81.27
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	81.21
2f9l_A	199	RAB11B, member RAS oncogene family; RAB11B GTPase,	81.08
1nlf_A	279	Regulatory protein REPA; replicative DNA helicase	81.06
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	81.03
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	80.97
2zej_A	184	Dardarin, leucine-rich repeat kinase 2; parkinson'	80.91
1p6x_A	334	Thymidine kinase; P-loop, LID, transferase; HET: T	80.87
1g8p_A	350	Magnesium-chelatase 38 kDa subunit; parallel beta	80.72
1z2a_A	168	RAS-related protein RAB-23; RAB GTPase, vesicular	80.67
3pxg_A	468	Negative regulator of genetic competence CLPC/MEC;	80.64
2wji_A	165	Ferrous iron transport protein B homolog; membrane	80.6
2axn_A	520	6-phosphofructo-2-kinase/fructose-2,6- biphosphata	80.58
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	80.56
2chq_A	319	Replication factor C small subunit; DNA-binding pr	80.3

>2a5y_B CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis elegans} SCOP: a.4.5.80 a.77.1.3 c.37.1.20 PDB: 3lqq_A* 3lqr_A*

Probab=100.00  E-value=3.7e-37  Score=287.16  Aligned_cols=231  Identities=13%  Similarity=0.056  Sum_probs=166.8

Q ss_pred             CCCCcHHHHHHHHHh--hhccCCCCCeEEEEEeCCCC--CHHHHHHHHHHHhCCCCC--------cCCHhhhHHhHHHHc
Q 041028            1 MGGIGKTTLAKEVAR--KAKNGKLFDQIVFTEVSQNP--NIKKIQGEIAFKLGLKFD--------EESESGRTRSPWSRL   68 (283)
Q Consensus         1 mgGiGKTtLA~~v~~--~~~~~~~Fd~~~wv~v~~~~--~~~~l~~~i~~~l~~~~~--------~~~~~~~~~~l~~~L   68 (283)
                      ||||||||||+++|+  +.++..+|++++||++++.+  ++..+++.|+.+++....        ..+...+...+++.|
T Consensus       160 ~gGvGKTtLA~~v~~~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~~~~l~~~l~~~L  239 (549)
T 2a5y_B          160 RAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKSTFDLFTDILLMLKSEDDLLNFPSVEHVTSVVLKRMICNAL  239 (549)
T ss_dssp             STTSSHHHHHHHHHHHCSSTBTTTBSEEEEEECCCCSTTHHHHHHHHHHHHHTTTSCCTTCCCCTTCCHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHhhhHHHhccCCcEEEEEECCCCCCCHHHHHHHHHHHHhcCcccccccccccccHHHHHHHHHHHH
Confidence            899999999999998  56677889999999999885  899999999999986522        113445678999999


Q ss_pred             cCC-cEEEE---------------cC--------------------------------------eecCCCCCCCcchHHH
Q 041028           69 KKE-KLQII---------------CG--------------------------------------KKMEGDYAEGSELKWL   94 (283)
Q Consensus        69 ~~k-r~LlV---------------~G--------------------------------------~~~~~~~~~~~~~~~~   94 (283)
                      +++ |||||               .|                                      +.+++.. ..+.+.++
T Consensus       240 ~~~kr~LlVLDdv~~~~~~~~~~~~gs~ilvTTR~~~v~~~~~~~~~~~~l~~L~~~ea~~Lf~~~a~~~~-~~~~~~~~  318 (549)
T 2a5y_B          240 IDRPNTLFVFDDVVQEETIRWAQELRLRCLVTTRDVEISNAASQTCEFIEVTSLEIDECYDFLEAYGMPMP-VGEKEEDV  318 (549)
T ss_dssp             TTSTTEEEEEEEECCHHHHHHHHHTTCEEEEEESBGGGGGGCCSCEEEEECCCCCHHHHHHHHHHTSCCCC---CHHHHH
T ss_pred             cCCCcEEEEEECCCCchhhcccccCCCEEEEEcCCHHHHHHcCCCCeEEECCCCCHHHHHHHHHHHhcCCC-CchhHHHH
Confidence            996 99999               11                                      1223221 23677889


Q ss_pred             HHHHHHhcCCchHHHHH---hhccCChHHHHHHHHHhcCCCCCCCCCchhHHHHHHhhhhccCCCCcHHHHHH-------
Q 041028           95 AMDVAKECAGLPVSIVT---GIKEQELFEWKDALEQLRRPSSTNFKDVQPAAYKAMELGYNKLEGDELKSTFL-------  164 (283)
Q Consensus        95 ~~~i~~~c~glPLal~~---~l~~~~~~~w~~~l~~l~~~~~~~~~~~~~~~~~~l~~sy~~L~~~~~k~~fl-------  164 (283)
                      +++|+++|+|+||||++   .++.+ .++|...+.......   .   ...+..++.+||+.||++ +|.||+       
T Consensus       319 ~~~I~~~c~GlPLAl~~~g~~l~~~-~w~~~~~l~~~l~~~---~---~~~i~~~l~~Sy~~L~~~-lk~~f~~Ls~~er  390 (549)
T 2a5y_B          319 LNKTIELSSGNPATLMMFFKSCEPK-TFEKMAQLNNKLESR---G---LVGVECITPYSYKSLAMA-LQRCVEVLSDEDR  390 (549)
T ss_dssp             HHHHHHHHTTCHHHHHHHHTTCCSS-SHHHHHHHHHHHHHH---C---SSTTCCCSSSSSSSHHHH-HHHHHHTSCHHHH
T ss_pred             HHHHHHHhCCChHHHHHHHHHhccc-hHHHHHHhHHHhhcc---c---HHHHHHHHhcccccccHH-HHHHHhccchhhh
Confidence            99999999999999999   34444 233433332211110   0   234678899999999998 999999       


Q ss_pred             ----HHhhCc-CCCHHHHHHHHhhc--cccCCCchHHHHHHHHHHHHHHHHhccccccccCCCcceEEechhHHHHHHHH
Q 041028          165 ----LIGYTA-IASIDDLLMYGMGL--GLFQGVNKMEAARARVHTLVHKLKASCMLLDHTSKNEKLFSIHDVVRDVAISI  237 (283)
Q Consensus       165 ----~~s~fp-~i~~~~l~~~w~ae--g~~~~~~~~~~~~~~~~~~~~~L~~~sLl~~~~~~~~~~~~mH~lv~~~a~~~  237 (283)
                          |||+|| +.+..  +++|+|+  ||+.........++.++ ++++|+++||+++...++..+|+|||+||+||+++
T Consensus       391 ~l~~~ls~fp~~~~i~--i~~w~a~~~G~i~~~~~~~~~~~~~~-~l~~L~~rsLl~~~~~~~~~~~~mHdlv~~~a~~~  467 (549)
T 2a5y_B          391 SALAFAVVMPPGVDIP--VKLWSCVIPVDICSNEEEQLDDEVAD-RLKRLSKRGALLSGKRMPVLTFKIDHIIHMFLKHV  467 (549)
T ss_dssp             HHTTGGGSSCTTCCEE--HHHHHHHSCC-------CCCTHHHHH-HHHHTTTBSSCSEEECSSSCEEECCHHHHHHHHTT
T ss_pred             hHhhheeeeCCCCeee--eeeeeeeccceeccCCCCCCHHHHHH-HHHHHHHcCCeeEecCCCceEEEeChHHHHHHHHH
Confidence                999998 33333  7899999  99965321111223334 88899999999877654446899999999999998


Q ss_pred             HccCCc
Q 041028          238 ASGEQN  243 (283)
Q Consensus       238 ~~~~~~  243 (283)
                      +.+++.
T Consensus       468 ~~~~~~  473 (549)
T 2a5y_B          468 VDAQTI  473 (549)
T ss_dssp             SCTHHH
T ss_pred             HHHHHH
Confidence            877654

>3sfz_A APAF-1, apoptotic peptidase activating factor 1; apoptosis, caspase activation, cytochrome C, procaspase-9, A nucleotide, cytosol; HET: ADP; 3.00A {Mus musculus} PDB: 3shf_A* 3iyt_A* 3iza_A*

Probab=99.96  E-value=4.6e-29  Score=251.74  Aligned_cols=227  Identities=16%  Similarity=0.198  Sum_probs=170.6

Q ss_pred             CCCCcHHHHHHHHHhhhcc-CCCC-CeEEEEEeCCCCC--HHHHHHHHHHHhCCCCC-----cCCHhhhHHhHHHHccCC
Q 041028            1 MGGIGKTTLAKEVARKAKN-GKLF-DQIVFTEVSQNPN--IKKIQGEIAFKLGLKFD-----EESESGRTRSPWSRLKKE   71 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~-~~~F-d~~~wv~v~~~~~--~~~l~~~i~~~l~~~~~-----~~~~~~~~~~l~~~L~~k   71 (283)
                      ||||||||||+++|++.+. ..+| +.++||++++..+  ....+..++..++....     ..+..+..+.++..|.++
T Consensus       155 ~gG~GKTtLa~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~~  234 (1249)
T 3sfz_A          155 MAGCGKSVLAAEAVRDHSLLEGCFSGGVHWVSIGKQDKSGLLMKLQNLCMRLDQEESFSQRLPLNIEEAKDRLRVLMLRK  234 (1249)
T ss_dssp             STTSSHHHHHHHHTCCHHHHTTTSTTCEEEEECCSCCHHHHHHHHHHHHHHHTTTCTTCSSCCSSHHHHHHHHHHHTSSS
T ss_pred             CCCCCHHHHHHHHhcChhHHHhhCCCeEEEEEECCcCchHHHHHHHHHHHHhhhhcccccCCCCCHHHHHHHHHHHHhcc
Confidence            8999999999999998543 3445 8899999998543  45557778888865432     235667788899999877


Q ss_pred             --cEEEE--------------cC---------eec----CCC-----------------------CCCCcchHHHHHHHH
Q 041028           72 --KLQII--------------CG---------KKM----EGD-----------------------YAEGSELKWLAMDVA   99 (283)
Q Consensus        72 --r~LlV--------------~G---------~~~----~~~-----------------------~~~~~~~~~~~~~i~   99 (283)
                        |+|||              .|         ..+    .+.                       ....+.+.+.+++|+
T Consensus       235 ~~~~LlvlDd~~~~~~~~~~~~~~~ilvTtR~~~~~~~~~~~~~~~~~~~~l~~~~a~~l~~~~~~~~~~~~~~~~~~i~  314 (1249)
T 3sfz_A          235 HPRSLLILDDVWDPWVLKAFDNQCQILLTTRDKSVTDSVMGPKHVVPVESGLGREKGLEILSLFVNMKKEDLPAEAHSII  314 (1249)
T ss_dssp             SCSCEEEEESCCCHHHHTTTCSSCEEEEEESSTTTTTTCCSCBCCEECCSSCCHHHHHHHHHHHHTSCSTTCCTHHHHHH
T ss_pred             CCCEEEEEecCCCHHHHHhhcCCCEEEEEcCCHHHHHhhcCCceEEEecCCCCHHHHHHHHHHhhCCChhhCcHHHHHHH
Confidence              99999              11         000    000                       011233456789999


Q ss_pred             HhcCCchHHHHH---hhccCChHHHHHHHHHhcCCCCCCC----CCchhHHHHHHhhhhccCCCCcHHHHHHHHhhCc--
Q 041028          100 KECAGLPVSIVT---GIKEQELFEWKDALEQLRRPSSTNF----KDVQPAAYKAMELGYNKLEGDELKSTFLLIGYTA--  170 (283)
Q Consensus       100 ~~c~glPLal~~---~l~~~~~~~w~~~l~~l~~~~~~~~----~~~~~~~~~~l~~sy~~L~~~~~k~~fl~~s~fp--  170 (283)
                      ++|+|+||||++   .++... ..|...++.+.......+    .....++..+|.+||+.||++ +|.||+|||+||  
T Consensus       315 ~~~~glPLal~~~~~~l~~~~-~~~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~l~~s~~~L~~~-~~~~~~~l~~f~~~  392 (1249)
T 3sfz_A          315 KECKGSPLVVSLIGALLRDFP-NRWAYYLRQLQNKQFKRIRKSSSYDYEALDEAMSISVEMLRED-IKDYYTDLSILQKD  392 (1249)
T ss_dssp             HHTTTCHHHHHHHHHHHHHSS-SCHHHHHHHHHSCCCCCSSCTTCTTHHHHHHHHHHHHHTSCTT-THHHHHHGGGSCTT
T ss_pred             HHhCCCHHHHHHHHHHhhcCh-hHHHHHHHHHhhhhhhhcccccccchHHHHHHHHHHHHhCCHH-HHHHHHHhCccCCC
Confidence            999999999999   444333 579999998876543222    122467999999999999998 999999999998  


Q ss_pred             -CCCHHHHHHHHhhccccCCCchHHHHHHHHHHHHHHHHhccccccccCCCcceEEechhHHHHHHHHHccC
Q 041028          171 -IASIDDLLMYGMGLGLFQGVNKMEAARARVHTLVHKLKASCMLLDHTSKNEKLFSIHDVVRDVAISIASGE  241 (283)
Q Consensus       171 -~i~~~~l~~~w~aeg~~~~~~~~~~~~~~~~~~~~~L~~~sLl~~~~~~~~~~~~mH~lv~~~a~~~~~~~  241 (283)
                       .|+.+.++.+|.+++            +.+..++++|+++||++....++..+|+||++||+|++..+.++
T Consensus       393 ~~i~~~~~~~~~~~~~------------~~~~~~l~~L~~~sl~~~~~~~~~~~~~~h~l~~~~~~~~~~~~  452 (1249)
T 3sfz_A          393 VKVPTKVLCVLWDLET------------EEVEDILQEFVNKSLLFCNRNGKSFCYYLHDLQVDFLTEKNRSQ  452 (1249)
T ss_dssp             CCEEHHHHHHHHTCCH------------HHHHHHHHHHHHTTSCEEEESSSSEEEECCHHHHHHHHHHTGGG
T ss_pred             CeeCHHHHHHHhCCCH------------HHHHHHHHHHHhccceEEecCCCceEEEecHHHHHHHHhhhhHH
Confidence             789999999996552            34457788888899998766554457999999999999997765

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A*

Probab=99.94  E-value=4.4e-27  Score=226.30  Aligned_cols=206  Identities=16%  Similarity=0.102  Sum_probs=146.4

Q ss_pred             CCCCcHHHHHHHHHhhhccCCCCCe-EEEEEeCCCCCHHHHHHHHHHHhCC---CCC--c-------CCHhhhHHhHHHH
Q 041028            1 MGGIGKTTLAKEVARKAKNGKLFDQ-IVFTEVSQNPNIKKIQGEIAFKLGL---KFD--E-------ESESGRTRSPWSR   67 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~~~Fd~-~~wv~v~~~~~~~~l~~~i~~~l~~---~~~--~-------~~~~~~~~~l~~~   67 (283)
                      ||||||||||+++|++.++..+|+. ++||++++.++...++..|++.++.   ...  .       .+.++..+.+++.
T Consensus       158 mGGIGKTTLAk~Vy~d~rV~~~Fd~gV~WVsVs~~~d~~~IL~~Ll~lL~~i~~~~~~~~d~~~~ip~~leeL~e~Lr~l  237 (1221)
T 1vt4_I          158 VLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRL  237 (1221)
T ss_dssp             STTSSHHHHHHHHHHHCHHHHHHSSCEEEEECCCSSSHHHHHHHHHHHHHHHCSSSTTTSCCCSSHHHHHHHHHHHHHHH
T ss_pred             CCCccHHHHHHHHHHhhHHHHhCCCcEEEEEeCCCCCHHHHHHHHHHHHhhcCcccccccccccCCCCCHHHHHHHHHHH
Confidence            8999999999999998766667965 9999999999998888888875432   111  0       0223445667776


Q ss_pred             c---cCCcEEEE--------------cC---------ee----cCCC-----C------CCC-cchHHHH---------H
Q 041028           68 L---KKEKLQII--------------CG---------KK----MEGD-----Y------AEG-SELKWLA---------M   96 (283)
Q Consensus        68 L---~~kr~LlV--------------~G---------~~----~~~~-----~------~~~-~~~~~~~---------~   96 (283)
                      |   .+||+|||              .|         ..    ..+.     .      ..+ .+-.++-         .
T Consensus       238 L~~l~~KRvLLVLDDVwd~eqLe~f~pGSRILVTTRd~~Va~~l~g~~vy~LeL~d~dL~LS~eEA~eLF~~~~g~~~ee  317 (1221)
T 1vt4_I          238 LKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQD  317 (1221)
T ss_dssp             HHHSTTSSCEEEEESCCCHHHHHHHHSSCCEEEECSCSHHHHHHHHHSSCEEEECSSSSCCCHHHHHHHHHHHHCCCTTT
T ss_pred             HHhhcCCCEEEEEeCcChHHHHHhhCCCeEEEEeccChHHHHhcCCCeEEEecCccccCCcCHHHHHHHHHHHcCCCHHH
Confidence            6   67899999              12         00    0000     0      000 0000000         1


Q ss_pred             HHHHhcCCchHHHHH---hhccC--ChHHHHHHHHHhcCCCCCCCCCchhHHHHHHhhhhccCCCCcH-HHHHHHHhhCc
Q 041028           97 DVAKECAGLPVSIVT---GIKEQ--ELFEWKDALEQLRRPSSTNFKDVQPAAYKAMELGYNKLEGDEL-KSTFLLIGYTA  170 (283)
Q Consensus        97 ~i~~~c~glPLal~~---~l~~~--~~~~w~~~l~~l~~~~~~~~~~~~~~~~~~l~~sy~~L~~~~~-k~~fl~~s~fp  170 (283)
                      ...+.|+|+||||++   .|+..  +...|...          +    ...+..+|++||+.||++ . |.||+|||+||
T Consensus       318 L~~eICgGLPLALkLaGs~Lr~k~~s~eeW~~~----------~----~~~I~aaLelSYd~Lp~e-elK~cFL~LAIFP  382 (1221)
T 1vt4_I          318 LPREVLTTNPRRLSIIAESIRDGLATWDNWKHV----------N----CDKLTTIIESSLNVLEPA-EYRKMFDRLSVFP  382 (1221)
T ss_dssp             HHHHHCCCCHHHHHHHHHHHHHSCSSHHHHHHC----------S----CHHHHHHHHHHHHHSCTT-HHHHHHHHTTSSC
T ss_pred             HHHHHhCCCHHHHHHHHHHHhCCCCCHHHHhcC----------C----hhHHHHHHHHHHHhCCHH-HHHHHHHHHhCCC
Confidence            122459999999999   45533  67788642          1    467899999999999998 8 99999999999


Q ss_pred             ---CCCHHHHHHHHhhccccCCCchHHHHHHHHHHHHHHHHhccccccccCCCcceEEechhHHHHH
Q 041028          171 ---IASIDDLLMYGMGLGLFQGVNKMEAARARVHTLVHKLKASCMLLDHTSKNEKLFSIHDVVRDVA  234 (283)
Q Consensus       171 ---~i~~~~l~~~w~aeg~~~~~~~~~~~~~~~~~~~~~L~~~sLl~~~~~~~~~~~~mH~lv~~~a  234 (283)
                         .|+.+.++.+|+++|.           +.+..++++|+++||++.....  .+|+||||+++++
T Consensus       383 ed~~I~~elLa~LW~aeGe-----------edAe~~L~eLvdRSLLq~d~~~--~rYrMHDLllELr  436 (1221)
T 1vt4_I          383 PSAHIPTILLSLIWFDVIK-----------SDVMVVVNKLHKYSLVEKQPKE--STISIPSIYLELK  436 (1221)
T ss_dssp             TTSCEEHHHHHHHHCSSCS-----------HHHHHHHHHHHTSSSSSBCSSS--SEEBCCCHHHHHH
T ss_pred             CCCCCCHHHHHHHhcCCCH-----------HHHHHHHHHHHhhCCEEEeCCC--CEEEehHHHHHHh
Confidence               6889999999998871           1355788889999999875333  6899999999865

>1z6t_A APAF-1, apoptotic protease activating factor 1; caspase activation, ADP, nucleotide binding, CARD, apoptosis; HET: ADP; 2.21A {Homo sapiens}

Probab=99.93  E-value=7.9e-26  Score=212.53  Aligned_cols=224  Identities=17%  Similarity=0.190  Sum_probs=158.5

Q ss_pred             CCCCcHHHHHHHHHhhhcc-CCCC-CeEEEEEeCCCCCHHHHHH---HHHHHhCCC-----CCcCCHhhhHHhHHHHccC
Q 041028            1 MGGIGKTTLAKEVARKAKN-GKLF-DQIVFTEVSQNPNIKKIQG---EIAFKLGLK-----FDEESESGRTRSPWSRLKK   70 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~-~~~F-d~~~wv~v~~~~~~~~l~~---~i~~~l~~~-----~~~~~~~~~~~~l~~~L~~   70 (283)
                      ||||||||||.++|++... ..+| ++++|++++.. +...++.   .++..++..     ....+.......++..+.+
T Consensus       155 ~~GiGKTtLa~~~~~~~~~~~~~f~~~v~wv~~~~~-~~~~~~~~l~~l~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~  233 (591)
T 1z6t_A          155 MAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVSVGKQ-DKSGLLMKLQNLCTRLDQDESFSQRLPLNIEEAKDRLRILMLR  233 (591)
T ss_dssp             CTTSSHHHHHHHHHCCHHHHHHHCTTCEEEEEEESC-CHHHHHHHHHHHHHHHCSSCCSCSSCCCSHHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHhchhHHHhhCCCceEEEECCCC-chHHHHHHHHHHHHHhccccccccCCCCCHHHHHHHHHHHHcc
Confidence            7999999999999987643 4569 68999999876 3333333   344566531     1223555677788888876


Q ss_pred             --CcEEEE--------------cC---------e-----------ec-----CCC-----------CCCCcchHHHHHHH
Q 041028           71 --EKLQII--------------CG---------K-----------KM-----EGD-----------YAEGSELKWLAMDV   98 (283)
Q Consensus        71 --kr~LlV--------------~G---------~-----------~~-----~~~-----------~~~~~~~~~~~~~i   98 (283)
                        +++|||              .|         .           .+     +..           ........+.+.+|
T Consensus       234 ~~~~~LLVLDdv~~~~~l~~l~~~~~ilvTsR~~~~~~~~~~~~~~v~~l~~L~~~ea~~L~~~~~~~~~~~~~~~~~~i  313 (591)
T 1z6t_A          234 KHPRSLLILDDVWDSWVLKAFDSQCQILLTTRDKSVTDSVMGPKYVVPVESSLGKEKGLEILSLFVNMKKADLPEQAHSI  313 (591)
T ss_dssp             TCTTCEEEEEEECCHHHHHTTCSSCEEEEEESCGGGGTTCCSCEEEEECCSSCCHHHHHHHHHHHHTSCGGGSCTHHHHH
T ss_pred             CCCCeEEEEeCCCCHHHHHHhcCCCeEEEECCCcHHHHhcCCCceEeecCCCCCHHHHHHHHHHHhCCCcccccHHHHHH
Confidence              688888              11         0           00     000           00112234578899


Q ss_pred             HHhcCCchHHHHH---hhccCChHHHHHHHHHhcCCCCCCC----CCchhHHHHHHhhhhccCCCCcHHHHHHHHhhCc-
Q 041028           99 AKECAGLPVSIVT---GIKEQELFEWKDALEQLRRPSSTNF----KDVQPAAYKAMELGYNKLEGDELKSTFLLIGYTA-  170 (283)
Q Consensus        99 ~~~c~glPLal~~---~l~~~~~~~w~~~l~~l~~~~~~~~----~~~~~~~~~~l~~sy~~L~~~~~k~~fl~~s~fp-  170 (283)
                      +++|+|+||||++   .++.. ...|...++.+.......+    .....++..++.+||+.||++ .|.||++||+|| 
T Consensus       314 ~~~~~G~PLal~~~a~~l~~~-~~~w~~~l~~l~~~~~~~~~~~~~~~~~~l~~~l~~s~~~L~~~-~~~~l~~la~f~~  391 (591)
T 1z6t_A          314 IKECKGSPLVVSLIGALLRDF-PNRWEYYLKQLQNKQFKRIRKSSSYDYEALDEAMSISVEMLRED-IKDYYTDLSILQK  391 (591)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHS-TTCHHHHHHHHHSCCCCCSSCCCSSCCHHHHHHHHHHHHTSCTT-THHHHHHGGGCCT
T ss_pred             HHHhCCCcHHHHHHHHHHhcC-chhHHHHHHHHHHhHHHHhhhccccchHHHHHHHHHHHHhCCHH-HHHHHHHccccCC
Confidence            9999999999999   34433 3479988888876542211    122468999999999999998 999999999998 


Q ss_pred             --CCCHHHHHHHHhhccccCCCchHHHHHHHHHHHHHHHHhccccccccCCCcceEEechhHHHHHHHHHc
Q 041028          171 --IASIDDLLMYGMGLGLFQGVNKMEAARARVHTLVHKLKASCMLLDHTSKNEKLFSIHDVVRDVAISIAS  239 (283)
Q Consensus       171 --~i~~~~l~~~w~aeg~~~~~~~~~~~~~~~~~~~~~L~~~sLl~~~~~~~~~~~~mH~lv~~~a~~~~~  239 (283)
                        .|+.+.+..+|.+++            ..+..+++.|+++||++...++...+|+||+++|++++....
T Consensus       392 ~~~i~~~~l~~l~~~~~------------~~~~~~l~~L~~~~Ll~~~~~~~~~~~~~H~lv~~~~~~~~~  450 (591)
T 1z6t_A          392 DVKVPTKVLCILWDMET------------EEVEDILQEFVNKSLLFCDRNGKSFRYYLHDLQVDFLTEKNC  450 (591)
T ss_dssp             TCCEEHHHHHHHHTCCH------------HHHHHHHHHHHHTTSSEEEEETTEEEEECCHHHHHHHHHHTG
T ss_pred             CCccCHHHHHHHhccCH------------HHHHHHHHHHHhCcCeEEecCCCccEEEEcHHHHHHHHhhhh
Confidence              589999999995431            234577888888999976554434689999999999998843

>2qen_A Walker-type ATPase; unknown function; HET: ADP; 2.25A {Pyrococcus abyssi}

Probab=98.04  E-value=0.00014  Score=62.82  Aligned_cols=116  Identities=15%  Similarity=0.088  Sum_probs=61.9

Q ss_pred             HHHHHHHHhcCCchHHHHH-h--hc-cCChHHHHHHHHHhcCCCCCCCCCchhHHHHHHhhhhccC---CCCcHHHHHHH
Q 041028           93 WLAMDVAKECAGLPVSIVT-G--IK-EQELFEWKDALEQLRRPSSTNFKDVQPAAYKAMELGYNKL---EGDELKSTFLL  165 (283)
Q Consensus        93 ~~~~~i~~~c~glPLal~~-~--l~-~~~~~~w~~~l~~l~~~~~~~~~~~~~~~~~~l~~sy~~L---~~~~~k~~fl~  165 (283)
                      +.+..|...|+|+|+++.. .  +. ..+...+.   ..+           ...+...+.-.+..+   ++. .+..+..
T Consensus       226 ~~~~~i~~~tgG~P~~l~~~~~~~~~~~~~~~~~---~~~-----------~~~~~~~~~~~l~~l~~~~~~-~~~~l~~  290 (350)
T 2qen_A          226 NEIEEAVELLDGIPGWLVVFGVEYLRNGDFGRAM---KRT-----------LEVAKGLIMGELEELRRRSPR-YVDILRA  290 (350)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHCCHHHHH---HHH-----------HHHHHHHHHHHHHHHHHHCHH-HHHHHHH
T ss_pred             HHHHHHHHHhCCCHHHHHHHHHHHhccccHhHHH---HHH-----------HHHHHHHHHHHHHHHHhCChh-HHHHHHH
Confidence            3566788999999999987 2  11 22222221   111           001111111112222   565 8888888


Q ss_pred             HhhCcCCCHHHHHHHHhhccccCCCchHHHHHHHHHHHHHHHHhccccccccCCCcceEEe-chhHHHHHH
Q 041028          166 IGYTAIASIDDLLMYGMGLGLFQGVNKMEAARARVHTLVHKLKASCMLLDHTSKNEKLFSI-HDVVRDVAI  235 (283)
Q Consensus       166 ~s~fp~i~~~~l~~~w~aeg~~~~~~~~~~~~~~~~~~~~~L~~~sLl~~~~~~~~~~~~m-H~lv~~~a~  235 (283)
                      +|. ..++...+........ - . .+    ......+++.|.+.+||...+    ..|++ |++++.+.+
T Consensus       291 la~-g~~~~~~l~~~~~~~~-~-~-~~----~~~~~~~l~~L~~~gli~~~~----~~y~~~~p~~~~~~~  349 (350)
T 2qen_A          291 IAL-GYNRWSLIRDYLAVKG-T-K-IP----EPRLYALLENLKKMNWIVEED----NTYKIADPVVATVLR  349 (350)
T ss_dssp             HHT-TCCSHHHHHHHHHHTT-C-C-CC----HHHHHHHHHHHHHTTSEEEET----TEEEESSHHHHHHHT
T ss_pred             HHh-CCCCHHHHHHHHHHHh-C-C-CC----HHHHHHHHHHHHhCCCEEecC----CEEEEecHHHHHHHc
Confidence            887 3345556554432211 0 0 11    123456778888899996542    35665 668887653

>1w5s_A Origin recognition complex subunit 2 ORC2; replication, CDC6, DNA replication initiation, DNA BIND protein, AAA+ ATPase; HET: ADP; 2.4A {Aeropyrum pernix} SCOP: a.4.5.11 c.37.1.20 PDB: 1w5t_A*

Probab=97.61  E-value=0.00013  Score=64.61  Aligned_cols=76  Identities=22%  Similarity=0.268  Sum_probs=52.5

Q ss_pred             CCCCcHHHHHHHHHhhhccC---CCCC-eEEEEEeCCCCCHHHHHHHHHHHhCCCCC--cCCHhhhHHhHHHHcc--CCc
Q 041028            1 MGGIGKTTLAKEVARKAKNG---KLFD-QIVFTEVSQNPNIKKIQGEIAFKLGLKFD--EESESGRTRSPWSRLK--KEK   72 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~---~~Fd-~~~wv~v~~~~~~~~l~~~i~~~l~~~~~--~~~~~~~~~~l~~~L~--~kr   72 (283)
                      ++|+||||||+++++.....   ..|+ .++|++.....+...++..++.+++....  ..+..+....+.+.+.  +++
T Consensus        60 ~~G~GKT~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~  139 (412)
T 1w5s_A           60 RVGIGKTTLAKFTVKRVSEAAAKEGLTVKQAYVNAFNAPNLYTILSLIVRQTGYPIQVRGAPALDILKALVDNLYVENHY  139 (412)
T ss_dssp             CCSSSHHHHHHHHHHHHHHHHHHTTCCEEEEEEEGGGCCSHHHHHHHHHHHHTCCCCCTTCCHHHHHHHHHHHHHHHTCE
T ss_pred             cCCCCHHHHHHHHHHHHHHHHhccCCceeEEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHHHhcCCe
Confidence            47999999999999876431   1132 35788877777889999999999976533  2234455566666664  556


Q ss_pred             EEEE
Q 041028           73 LQII   76 (283)
Q Consensus        73 ~LlV   76 (283)
                      ++||
T Consensus       140 ~llv  143 (412)
T 1w5s_A          140 LLVI  143 (412)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            6555

>2qby_B CDC6 homolog 3, cell division control protein 6 homolog 3; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus}

Probab=96.94  E-value=0.0011  Score=58.11  Aligned_cols=48  Identities=17%  Similarity=0.170  Sum_probs=34.0

Q ss_pred             CCCCcHHHHHHHHHhhhccC----CC--CCeEEEEEeCCCC-CHHHHHHHHHHHh
Q 041028            1 MGGIGKTTLAKEVARKAKNG----KL--FDQIVFTEVSQNP-NIKKIQGEIAFKL   48 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~----~~--Fd~~~wv~v~~~~-~~~~l~~~i~~~l   48 (283)
                      .+|+||||||+.+++.....    ..  ....+|++..... +...++..++..+
T Consensus        53 ~~G~GKT~la~~l~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~l~~~l  107 (384)
T 2qby_B           53 LTGTGKTFVSKYIFNEIEEVKKEDEEYKDVKQAYVNCREVGGTPQAVLSSLAGKL  107 (384)
T ss_dssp             CTTSSHHHHHHHHHHHHHHHHHHSSSSTTCEEEEEEHHHHCSCHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHhhhhcCCCCceEEEEECccCCCCHHHHHHHHHHHh
Confidence            47999999999999875321    11  2346777776655 7777777777776

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=96.92  E-value=0.0039  Score=54.34  Aligned_cols=68  Identities=19%  Similarity=0.268  Sum_probs=43.9

Q ss_pred             CCCCcHHHHHHHHHhhhccC----CCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCC--cCCHhhhHHhHHHHc
Q 041028            1 MGGIGKTTLAKEVARKAKNG----KLFDQIVFTEVSQNPNIKKIQGEIAFKLGLKFD--EESESGRTRSPWSRL   68 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~----~~Fd~~~wv~v~~~~~~~~l~~~i~~~l~~~~~--~~~~~~~~~~l~~~L   68 (283)
                      .+|+||||||+.+++.....    +.--..+|++.....+...++..++.+++....  ..+..+....+.+.+
T Consensus        52 ~~G~GKT~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l  125 (387)
T 2v1u_A           52 LTGTGKTAVARLVLRRLEARASSLGVLVKPIYVNARHRETPYRVASAIAEAVGVRVPFTGLSVGEVYERLVKRL  125 (387)
T ss_dssp             CTTSSHHHHHHHHHHHHHHHHHHHTCCEEEEEEETTTSCSHHHHHHHHHHHHSCCCCSSCCCHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHHhccCCCeEEEEEECCcCCCHHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHH
Confidence            37999999999999876321    001245777777777888888888888765432  123344444555555

>1fnn_A CDC6P, cell division control protein 6; ORC1, AAA protein, DNA replication initation factor, cell cycle control factor; HET: ADP; 2.00A {Pyrobaculum aerophilum} SCOP: a.4.5.11 c.37.1.20

Probab=96.78  E-value=0.0077  Score=52.53  Aligned_cols=49  Identities=27%  Similarity=0.293  Sum_probs=37.7

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKLGLK   51 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~~l~~~   51 (283)
                      +|+||||||+.+++....... -..+|++.+...+...++..++..++..
T Consensus        53 ~G~GKTtl~~~l~~~~~~~~~-~~~~~i~~~~~~~~~~~~~~l~~~l~~~  101 (389)
T 1fnn_A           53 PGTGKTVTLRKLWELYKDKTT-ARFVYINGFIYRNFTAIIGEIARSLNIP  101 (389)
T ss_dssp             TTSSHHHHHHHHHHHHTTSCC-CEEEEEETTTCCSHHHHHHHHHHHTTCC
T ss_pred             CCCCHHHHHHHHHHHHhhhcC-eeEEEEeCccCCCHHHHHHHHHHHhCcc
Confidence            699999999999988654311 2467777777778888888888888654

>2qby_A CDC6 homolog 1, cell division control protein 6 homolog 1; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus}

Probab=96.67  E-value=0.0025  Score=55.50  Aligned_cols=50  Identities=22%  Similarity=0.222  Sum_probs=33.2

Q ss_pred             CCCCcHHHHHHHHHhhhccCCC-CCeEEEEEeCCCCCHHHHHHHHHHHhCC
Q 041028            1 MGGIGKTTLAKEVARKAKNGKL-FDQIVFTEVSQNPNIKKIQGEIAFKLGL   50 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~~~-Fd~~~wv~v~~~~~~~~l~~~i~~~l~~   50 (283)
                      .+|+||||||+.+++....... -...+|++.....+...++..++..++.
T Consensus        53 ~~G~GKTtl~~~l~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~i~~~l~~  103 (386)
T 2qby_A           53 LTGTGKTAVVKFVLSKLHKKFLGKFKHVYINTRQIDTPYRVLADLLESLDV  103 (386)
T ss_dssp             CTTSSHHHHHHHHHHHHHHHTCSSCEEEEEEHHHHCSHHHHHHHHTTTTSC
T ss_pred             CCCCCHHHHHHHHHHHHHHHhcCCceEEEEECCCCCCHHHHHHHHHHHhCC
Confidence            4799999999999987653310 1245777765555666666666666654

>1hqc_A RUVB; extended AAA-ATPase domain, complex with nucleotide, hydrolase; HET: ADE; 3.20A {Thermus thermophilus} SCOP: a.4.5.11 c.37.1.20 PDB: 1ixs_B* 1ixr_C*

Probab=96.48  E-value=0.0083  Score=51.10  Aligned_cols=36  Identities=25%  Similarity=0.271  Sum_probs=22.9

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHH
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQG   42 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~   42 (283)
                      +|+|||+||+.+++....     ..++++.+......++..
T Consensus        47 ~GtGKT~la~~i~~~~~~-----~~~~~~~~~~~~~~~l~~   82 (324)
T 1hqc_A           47 PGLGKTTLAHVIAHELGV-----NLRVTSGPAIEKPGDLAA   82 (324)
T ss_dssp             TTCCCHHHHHHHHHHHTC-----CEEEECTTTCCSHHHHHH
T ss_pred             CCCCHHHHHHHHHHHhCC-----CEEEEeccccCChHHHHH
Confidence            699999999999987642     123454444444444443

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=95.77  E-value=0.036  Score=47.37  Aligned_cols=49  Identities=10%  Similarity=0.153  Sum_probs=34.3

Q ss_pred             CCCcHHHHHHHHHhhhccCCC---CC--eEEEEEeCCCCCHHHHHHHHHHHhCC
Q 041028            2 GGIGKTTLAKEVARKAKNGKL---FD--QIVFTEVSQNPNIKKIQGEIAFKLGL   50 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~---Fd--~~~wv~v~~~~~~~~l~~~i~~~l~~   50 (283)
                      +|+|||++++++++.......   ..  ..+.|+...-.+...++..|++++..
T Consensus        54 PGTGKT~~v~~v~~~L~~~~~~~~~~~~~~v~INc~~~~t~~~~~~~I~~~L~g  107 (318)
T 3te6_A           54 DDSTKFQLVNDVMDELITSSARKELPIFDYIHIDALELAGMDALYEKIWFAISK  107 (318)
T ss_dssp             CSHHHHHHHHHHHHHHHHTTTTTSSCCEEEEEEETTCCC--HHHHHHHHHHHSC
T ss_pred             CCCCHHHHHHHHHHHHHHHhhhccCCceEEEEEeccccCCHHHHHHHHHHHhcC
Confidence            799999999999998753211   11  23555555667888999999999954

>2fna_A Conserved hypothetical protein; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2; HET: MSE ADP; 2.00A {Sulfolobus solfataricus} SCOP: a.4.5.11 c.37.1.20

Probab=94.33  E-value=0.052  Score=46.40  Aligned_cols=114  Identities=10%  Similarity=0.027  Sum_probs=61.4

Q ss_pred             HHHHHhcCCchHHHHH---hhc-cCChHHHHHH-HHHhcCCCCCCCCCchhHHHHHHh-hhh--ccCCCCcHHHHHHHHh
Q 041028           96 MDVAKECAGLPVSIVT---GIK-EQELFEWKDA-LEQLRRPSSTNFKDVQPAAYKAME-LGY--NKLEGDELKSTFLLIG  167 (283)
Q Consensus        96 ~~i~~~c~glPLal~~---~l~-~~~~~~w~~~-l~~l~~~~~~~~~~~~~~~~~~l~-~sy--~~L~~~~~k~~fl~~s  167 (283)
                      ..|...|+|+|+++..   .+. ..+...|..- .+..           ...+...+. +.+  ..|++. .+..+..+|
T Consensus       233 ~~i~~~t~G~P~~l~~~~~~~~~~~~~~~~~~~~~~~~-----------~~~~~~~l~~~~~~~~~l~~~-~~~~l~~la  300 (357)
T 2fna_A          233 EVVYEKIGGIPGWLTYFGFIYLDNKNLDFAINQTLEYA-----------KKLILKEFENFLHGREIARKR-YLNIMRTLS  300 (357)
T ss_dssp             HHHHHHHCSCHHHHHHHHHHHHHHCCHHHHHHHHHHHH-----------HHHHHHHHHHHHTTCGGGHHH-HHHHHHHHT
T ss_pred             HHHHHHhCCCHHHHHHHHHHHccccchHHHHHHHHHHH-----------HHHHHHHHHHHhhccccccHH-HHHHHHHHH
Confidence            4678899999999987   222 2333333211 1110           111122222 111  157776 899999888


Q ss_pred             hCcCCCHHHHHHHHh-hccccCCCchHHHHHHHHHHHHHHHHhccccccccCCCcceEEe-chhHHHHH
Q 041028          168 YTAIASIDDLLMYGM-GLGLFQGVNKMEAARARVHTLVHKLKASCMLLDHTSKNEKLFSI-HDVVRDVA  234 (283)
Q Consensus       168 ~fp~i~~~~l~~~w~-aeg~~~~~~~~~~~~~~~~~~~~~L~~~sLl~~~~~~~~~~~~m-H~lv~~~a  234 (283)
                      .-+  +...+..... ..|.  + .    .......+++.|++.+||...+    ..|++ |++++++.
T Consensus       301 ~g~--~~~~l~~~~~~~~g~--~-~----~~~~~~~~L~~L~~~gli~~~~----~~y~f~~~~~~~~l  356 (357)
T 2fna_A          301 KCG--KWSDVKRALELEEGI--E-I----SDSEIYNYLTQLTKHSWIIKEG----EKYCPSEPLISLAF  356 (357)
T ss_dssp             TCB--CHHHHHHHHHHHHCS--C-C----CHHHHHHHHHHHHHTTSEEESS----SCEEESSHHHHHHT
T ss_pred             cCC--CHHHHHHHHHHhcCC--C-C----CHHHHHHHHHHHHhCCCEEecC----CEEEecCHHHHHhh
Confidence            833  5555543221 1121  0 0    1123456778888899996543    35764 67888764

>3ec2_A DNA replication protein DNAC; helicase loader, replication initiation factor, ATP-binding, nucleotide-binding; HET: DNA ADP; 2.70A {Aquifex aeolicus} PDB: 3ecc_A*

Probab=94.27  E-value=0.043  Score=42.39  Aligned_cols=17  Identities=35%  Similarity=0.452  Sum_probs=15.3

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      +|+||||||+.+++...
T Consensus        47 ~G~GKTtL~~~i~~~~~   63 (180)
T 3ec2_A           47 PGVGKTHLAVATLKAIY   63 (180)
T ss_dssp             SSSSHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHH
Confidence            59999999999998864

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=94.07  E-value=0.035  Score=43.72  Aligned_cols=28  Identities=25%  Similarity=0.221  Sum_probs=20.9

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEe
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEV   31 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v   31 (283)
                      +|+|||+||+.+++.....  ...++|++.
T Consensus        63 ~GtGKT~la~~i~~~~~~~--~~~~~~~~~   90 (202)
T 2w58_A           63 FGVGKTYLLAAIANELAKR--NVSSLIVYV   90 (202)
T ss_dssp             TTSSHHHHHHHHHHHHHTT--TCCEEEEEH
T ss_pred             CCCCHHHHHHHHHHHHHHc--CCeEEEEEh
Confidence            6999999999999987643  334566654

>2cvh_A DNA repair and recombination protein RADB; filament formation, homologous recombination, ATPase domain, hyperthermophIle; HET: DNA; 2.20A {Thermococcus kodakarensis} PDB: 2cvf_A*

Probab=94.03  E-value=0.16  Score=40.19  Aligned_cols=41  Identities=17%  Similarity=0.146  Sum_probs=28.5

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHHHh
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKL   48 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~~l   48 (283)
                      +|+||||||..++. ..    -..++|++....++...+.. +.+.+
T Consensus        29 ~GsGKTtl~~~l~~-~~----~~~v~~i~~~~~~~~~~~~~-~~~~~   69 (220)
T 2cvh_A           29 YASGKTTLALQTGL-LS----GKKVAYVDTEGGFSPERLVQ-MAETR   69 (220)
T ss_dssp             TTSSHHHHHHHHHH-HH----CSEEEEEESSCCCCHHHHHH-HHHTT
T ss_pred             CCCCHHHHHHHHHH-Hc----CCcEEEEECCCCCCHHHHHH-HHHhc
Confidence            69999999999988 21    24688888877666655443 44433

>1qhx_A CPT, protein (chloramphenicol phosphotransferase); kinase, antibiotic resistance, phosphorylation, mononucleoti binding fold; HET: ATP; 2.50A {Streptomyces venezuelae} SCOP: c.37.1.3 PDB: 1grr_A* 1grq_A 1qhs_A* 1qhn_A* 1qhy_A*

Probab=93.80  E-value=0.028  Score=43.19  Aligned_cols=18  Identities=11%  Similarity=0.135  Sum_probs=15.7

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      ++|+||||+|+.+.....
T Consensus        11 ~~GsGKST~a~~La~~l~   28 (178)
T 1qhx_A           11 GSSAGKSGIVRCLQSVLP   28 (178)
T ss_dssp             CTTSSHHHHHHHHHHHSS
T ss_pred             CCCCCHHHHHHHHHHhcC
Confidence            579999999999998754

>1xp8_A RECA protein, recombinase A; recombination, radioresistance, DNA-repair, ATPase, DNA-BIND protein, DNA binding protein; HET: AGS; 2.50A {Deinococcus radiodurans} SCOP: c.37.1.11 d.48.1.1

Probab=93.78  E-value=0.24  Score=43.08  Aligned_cols=70  Identities=17%  Similarity=0.147  Sum_probs=45.1

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCC------cCCHhhhHHhHHHHccC--CcE
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKLGLKFD------EESESGRTRSPWSRLKK--EKL   73 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~~l~~~~~------~~~~~~~~~~l~~~L~~--kr~   73 (283)
                      +|+||||||.+++......  =..++|++....++..     .++.++.+.+      ..+.++..+.+....+.  -.+
T Consensus        83 pGsGKTtlal~la~~~~~~--g~~vlyi~~E~s~~~~-----~a~~~g~d~~~l~i~~~~~~e~~l~~l~~l~~~~~~~l  155 (366)
T 1xp8_A           83 ESGGKTTLALAIVAQAQKA--GGTCAFIDAEHALDPV-----YARALGVNTDELLVSQPDNGEQALEIMELLVRSGAIDV  155 (366)
T ss_dssp             TTSSHHHHHHHHHHHHHHT--TCCEEEEESSCCCCHH-----HHHHTTCCGGGCEEECCSSHHHHHHHHHHHHTTTCCSE
T ss_pred             CCCChHHHHHHHHHHHHHC--CCeEEEEECCCChhHH-----HHHHcCCCHHHceeecCCcHHHHHHHHHHHHhcCCCCE
Confidence            6999999999988765433  2368999998877654     2456665422      12445555566655543  367


Q ss_pred             EEEcC
Q 041028           74 QIICG   78 (283)
Q Consensus        74 LlV~G   78 (283)
                      +||+.
T Consensus       156 VVIDs  160 (366)
T 1xp8_A          156 VVVDS  160 (366)
T ss_dssp             EEEEC
T ss_pred             EEEeC
Confidence            77743

>3hr8_A Protein RECA; alpha and beta proteins (A/B, A+B), ATP-binding, cytoplasm, damage, DNA recombination, DNA repair, DNA-binding; 1.95A {Thermotoga maritima}

Probab=93.72  E-value=0.21  Score=43.30  Aligned_cols=69  Identities=17%  Similarity=0.157  Sum_probs=44.3

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCC------cCCHhhhHHhHHHHccC--CcE
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKLGLKFD------EESESGRTRSPWSRLKK--EKL   73 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~~l~~~~~------~~~~~~~~~~l~~~L~~--kr~   73 (283)
                      +|+||||||.+++......+  ..++|++....++..     .++.++...+      ..+.++....+...++.  -.+
T Consensus        70 pGsGKSTLal~la~~~~~~g--g~VlyId~E~s~~~~-----ra~rlgv~~~~l~i~~~~~~e~~l~~~~~l~~~~~~dl  142 (356)
T 3hr8_A           70 ESSGKTTLALHAIAEAQKMG--GVAAFIDAEHALDPV-----YAKNLGVDLKSLLISQPDHGEQALEIVDELVRSGVVDL  142 (356)
T ss_dssp             TTSSHHHHHHHHHHHHHHTT--CCEEEEESSCCCCHH-----HHHHHTCCGGGCEEECCSSHHHHHHHHHHHHHTSCCSE
T ss_pred             CCCCHHHHHHHHHHHHHhcC--CeEEEEecccccchH-----HHHHcCCchhhhhhhhccCHHHHHHHHHHHhhhcCCCe
Confidence            69999999999988755331  347888887777754     5566665432      22445555555555532  367


Q ss_pred             EEEc
Q 041028           74 QIIC   77 (283)
Q Consensus        74 LlV~   77 (283)
                      ++|+
T Consensus       143 vVID  146 (356)
T 3hr8_A          143 IVVD  146 (356)
T ss_dssp             EEEE
T ss_pred             EEeh
Confidence            7774

>2chg_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATPase, ATP-binding, nucleotide-binding; HET: ANP; 2.1A {Archaeoglobus fulgidus}

Probab=93.53  E-value=0.085  Score=41.52  Aligned_cols=38  Identities=26%  Similarity=0.324  Sum_probs=23.0

Q ss_pred             CCCcHHHHHHHHHhhhccCCCC-CeEEEEEeCCCCCHHHH
Q 041028            2 GGIGKTTLAKEVARKAKNGKLF-DQIVFTEVSQNPNIKKI   40 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~F-d~~~wv~v~~~~~~~~l   40 (283)
                      +|+|||+||+.+++..... .+ ...+.++.+.......+
T Consensus        47 ~G~GKT~l~~~l~~~~~~~-~~~~~~~~~~~~~~~~~~~~   85 (226)
T 2chg_A           47 PGTGKTATAIALARDLFGE-NWRDNFIEMNASDERGIDVV   85 (226)
T ss_dssp             TTSSHHHHHHHHHHHHHGG-GGGGGEEEEETTCTTCHHHH
T ss_pred             CCCCHHHHHHHHHHHHhcc-ccccceEEeccccccChHHH
Confidence            6999999999999875332 12 22344444444444333

>3io5_A Recombination and repair protein; storage dimer, inactive conformation, RECA like core domain, binding, DNA damage, DNA recombination; 2.40A {Enterobacteria phage T4}

Probab=93.50  E-value=0.24  Score=42.25  Aligned_cols=46  Identities=7%  Similarity=-0.086  Sum_probs=33.2

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKLGLKF   52 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~~l~~~~   52 (283)
                      +|+||||||.+++........=..++||+....++..     .++++|.+.
T Consensus        37 pGsGKTtL~Lq~~~~~~~~g~g~~vlyId~E~s~~~~-----ra~~lGvd~   82 (333)
T 3io5_A           37 SKSFKSNFGLTMVSSYMRQYPDAVCLFYDSEFGITPA-----YLRSMGVDP   82 (333)
T ss_dssp             SSSSHHHHHHHHHHHHHHHCTTCEEEEEESSCCCCHH-----HHHHTTCCG
T ss_pred             CCCCHHHHHHHHHHHHHhcCCCceEEEEeccchhhHH-----HHHHhCCCH
Confidence            6999999999987765432101467999988888764     377888764

>3cwq_A Para family chromosome partitioning protein; alpha-beta protein, structural genomics, PSI-2, protein STRU initiative; HET: ADP; 2.47A {Synechocystis SP}

Probab=93.47  E-value=0.089  Score=41.86  Aligned_cols=37  Identities=22%  Similarity=0.250  Sum_probs=27.2

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHH
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQ   41 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~   41 (283)
                      ||+||||+|..++......+   .++-|+.....+....+
T Consensus        10 GGvGKTT~a~~LA~~la~~g---~VlliD~D~q~~~~~~~   46 (209)
T 3cwq_A           10 GGVGKTTTAVHLSAYLALQG---ETLLIDGDPNRSATGWG   46 (209)
T ss_dssp             TTSSHHHHHHHHHHHHHTTS---CEEEEEECTTCHHHHHH
T ss_pred             CCCcHHHHHHHHHHHHHhcC---CEEEEECCCCCCHHHHh
Confidence            89999999999998876542   57777777655544433

>3bos_A Putative DNA replication factor; P-loop containing nucleoside triphosphate hydrolases, struct genomics; HET: MSE CDP; 1.75A {Shewanella amazonensis} PDB: 3sc3_A

Probab=93.19  E-value=0.052  Score=43.59  Aligned_cols=29  Identities=14%  Similarity=0.155  Sum_probs=21.7

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVS   32 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~   32 (283)
                      +|+||||||+.+++.....  ...+.|++.+
T Consensus        61 ~G~GKT~la~~l~~~~~~~--~~~~~~~~~~   89 (242)
T 3bos_A           61 VKSGRTHLIHAACARANEL--ERRSFYIPLG   89 (242)
T ss_dssp             TTSSHHHHHHHHHHHHHHT--TCCEEEEEGG
T ss_pred             CCCCHHHHHHHHHHHHHHc--CCeEEEEEHH
Confidence            6999999999999886544  3345666654

>2zr9_A Protein RECA, recombinase A; recombination, RECA mutants, DNA-repair, ATP-binding, DNA DA recombination, DNA repair, DNA-binding; HET: DTP; 2.50A {Mycobacterium smegmatis str} PDB: 2zr0_A* 2zra_A* 2zrb_A 2zrm_A* 1ubc_A* 1ubf_A* 1ubg_A* 1ube_A* 2g88_A* 2odw_A* 2oe2_A 2oep_A* 2oes_A 2ofo_A 2zr7_A 2odn_A* 2zrn_A 2zro_A* 2zrp_A* 2zre_A* ...

Probab=93.14  E-value=0.36  Score=41.66  Aligned_cols=70  Identities=19%  Similarity=0.171  Sum_probs=44.0

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCC------cCCHhhhHHhHHHHccC--CcE
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKLGLKFD------EESESGRTRSPWSRLKK--EKL   73 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~~l~~~~~------~~~~~~~~~~l~~~L~~--kr~   73 (283)
                      +|+||||||.+++......  =..++|++....++..     .++.++...+      ..+.++..+.+....+.  -++
T Consensus        70 pGsGKTtLal~la~~~~~~--g~~vlyi~~E~~~~~~-----~a~~lG~~~~~l~i~~~~~~e~~l~~~~~l~~~~~~~l  142 (349)
T 2zr9_A           70 ESSGKTTVALHAVANAQAA--GGIAAFIDAEHALDPE-----YAKKLGVDTDSLLVSQPDTGEQALEIADMLVRSGALDI  142 (349)
T ss_dssp             TTSSHHHHHHHHHHHHHHT--TCCEEEEESSCCCCHH-----HHHHTTCCGGGCEEECCSSHHHHHHHHHHHHTTTCCSE
T ss_pred             CCCCHHHHHHHHHHHHHhC--CCeEEEEECCCCcCHH-----HHHHcCCCHHHeEEecCCCHHHHHHHHHHHHhcCCCCE
Confidence            6999999999998765433  2367899988777653     3556665422      12344445555555443  367


Q ss_pred             EEEcC
Q 041028           74 QIICG   78 (283)
Q Consensus        74 LlV~G   78 (283)
                      +||+.
T Consensus       143 IVIDs  147 (349)
T 2zr9_A          143 IVIDS  147 (349)
T ss_dssp             EEEEC
T ss_pred             EEEcC
Confidence            77743

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=93.11  E-value=0.17  Score=43.00  Aligned_cols=43  Identities=16%  Similarity=0.223  Sum_probs=31.9

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHHHh
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKL   48 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~~l   48 (283)
                      +|+||||||..++.....++  ..++|++..  .+..++..+++...
T Consensus        77 pG~GKTtl~l~ia~~~a~~g--~~vl~~slE--~s~~~l~~R~~~~~  119 (315)
T 3bh0_A           77 PSMGKTAFALKQAKNMSDND--DVVNLHSLE--MGKKENIKRLIVTA  119 (315)
T ss_dssp             TTSSHHHHHHHHHHHHHTTT--CEEEEEESS--SCHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHcC--CeEEEEECC--CCHHHHHHHHHHHH
Confidence            79999999999987765443  578888766  55677777776543

>3hjn_A DTMP kinase, thymidylate kinase; ATP-binding, nucleotide biosynth nucleotide-binding, transferase, structural genomics; HET: ADP TYD; 2.10A {Thermotoga maritima}

Probab=93.09  E-value=0.17  Score=39.95  Aligned_cols=73  Identities=12%  Similarity=0.080  Sum_probs=39.2

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCcC------CHhhhHHhHHHHccCCcEEE
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKLGLKFDEE------SESGRTRSPWSRLKKEKLQI   75 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~~------~~~~~~~~l~~~L~~kr~Ll   75 (283)
                      -|+||||.++.+++..+..+ .+ +++..-.......+..++++..-.......      +-.+....+...|...+++|
T Consensus         9 DGsGKsTq~~~L~~~L~~~g-~~-v~~treP~~t~~~~~ir~~l~~~~~~~~~~~ll~~a~r~~~~~~I~~~L~~g~~Vi   86 (197)
T 3hjn_A            9 DGSGKSTQIQLLAQYLEKRG-KK-VILKREPGGTETGEKIRKILLEEEVTPKAELFLFLASRNLLVTEIKQYLSEGYAVL   86 (197)
T ss_dssp             TTSSHHHHHHHHHHHHHHTT-CC-EEEEESSCSSHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHHHHHHHTTTCEEE
T ss_pred             CCCCHHHHHHHHHHHHHHCC-Cc-EEEEECCCCCcHHHHHHHHhhcccCChHHHHHHHHHHHHHHHHHHHHHHHCCCeEE
Confidence            49999999999999876542 23 333333333345555666554322211000      11223345666666666655


Q ss_pred             E
Q 041028           76 I   76 (283)
Q Consensus        76 V   76 (283)
                      .
T Consensus        87 ~   87 (197)
T 3hjn_A           87 L   87 (197)
T ss_dssp             E
T ss_pred             e
Confidence            5

>2px0_A Flagellar biosynthesis protein FLHF; SRP GTPase, flagellum, protein transport, biosynthetic protein; HET: GNP; 3.00A {Bacillus subtilis} PDB: 2px3_A* 3syn_A*

Probab=93.04  E-value=0.41  Score=40.34  Aligned_cols=74  Identities=15%  Similarity=0.051  Sum_probs=41.0

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCC-CCCHHHHHHHHHHHhCCCCCc-CCHhhhHHhHHHHccCCcEEEEc
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQ-NPNIKKIQGEIAFKLGLKFDE-ESESGRTRSPWSRLKKEKLQIIC   77 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~-~~~~~~l~~~i~~~l~~~~~~-~~~~~~~~~l~~~L~~kr~LlV~   77 (283)
                      +|+||||++..++.......- ..+..+.... .....+.+....+..+.+... .+..+....+. .+.+..++|++
T Consensus       114 ~GsGKTTl~~~LA~~l~~~~G-~~V~lv~~D~~r~~a~eqL~~~~~~~gl~~~~~~~~~~l~~al~-~~~~~dlvIiD  189 (296)
T 2px0_A          114 TGAGKTTTLAKLAAISMLEKH-KKIAFITTDTYRIAAVEQLKTYAELLQAPLEVCYTKEEFQQAKE-LFSEYDHVFVD  189 (296)
T ss_dssp             TTSSHHHHHHHHHHHHHHTTC-CCEEEEECCCSSTTHHHHHHHHHTTTTCCCCBCSSHHHHHHHHH-HGGGSSEEEEE
T ss_pred             CCCCHHHHHHHHHHHHHHhcC-CEEEEEecCcccchHHHHHHHHHHhcCCCeEecCCHHHHHHHHH-HhcCCCEEEEe
Confidence            699999999999887653211 1345555432 233444455555555554321 23333333343 34666888884

>1u94_A RECA protein, recombinase A; homologous recombination, ATPase, DNA repair, DNA binding protein; 1.90A {Escherichia coli} SCOP: c.37.1.11 d.48.1.1 PDB: 1u98_A 1u99_A 1xms_A* 1xmv_A* 2rec_A 2reb_A 1n03_A* 1rea_A 1aa3_A

Probab=92.96  E-value=0.28  Score=42.53  Aligned_cols=70  Identities=19%  Similarity=0.191  Sum_probs=42.9

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCc------CCHhhhHHhHHHHcc--CCcE
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKLGLKFDE------ESESGRTRSPWSRLK--KEKL   73 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~------~~~~~~~~~l~~~L~--~kr~   73 (283)
                      +|+||||||.+++......+  ..++|++....++..     .+..++...+.      .+.++..+.++...+  +-++
T Consensus        72 pGsGKTtLal~la~~~~~~g--~~vlyid~E~s~~~~-----~a~~~g~~~~~l~i~~~~~~e~~~~~~~~l~~~~~~~l  144 (356)
T 1u94_A           72 ESSGKTTLTLQVIAAAQREG--KTCAFIDAEHALDPI-----YARKLGVDIDNLLCSQPDTGEQALEICDALARSGAVDV  144 (356)
T ss_dssp             TTSSHHHHHHHHHHHHHHTT--CCEEEEESSCCCCHH-----HHHHTTCCGGGCEEECCSSHHHHHHHHHHHHHHTCCSE
T ss_pred             CCCCHHHHHHHHHHHHHHCC--CeEEEEeCCCCccHH-----HHHHcCCChhheeeeCCCCHHHHHHHHHHHHhccCCCE
Confidence            69999999999887754332  368899998877754     24556654221      233444444444432  3367


Q ss_pred             EEEcC
Q 041028           74 QIICG   78 (283)
Q Consensus        74 LlV~G   78 (283)
                      +||+.
T Consensus       145 VVIDs  149 (356)
T 1u94_A          145 IVVDS  149 (356)
T ss_dssp             EEEEC
T ss_pred             EEEcC
Confidence            77743

>3kb2_A SPBC2 prophage-derived uncharacterized protein YORR; alpha-beta protein., structural genomics, PSI-2, protein structure initiative; HET: G3D; 2.20A {Bacillus subtilis} SCOP: c.37.1.1 PDB: 2axp_A*

Probab=92.94  E-value=0.046  Score=41.57  Aligned_cols=18  Identities=22%  Similarity=0.194  Sum_probs=15.5

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      +.|+||||+|+.+.....
T Consensus         9 ~~GsGKsT~~~~L~~~l~   26 (173)
T 3kb2_A            9 PDCCFKSTVAAKLSKELK   26 (173)
T ss_dssp             SSSSSHHHHHHHHHHHHC
T ss_pred             CCCCCHHHHHHHHHHHhC
Confidence            479999999999988754

>3kjh_A CO dehydrogenase/acetyl-COA synthase complex, accessory protein COOC; Zn-bound dimer, nickel binding protein, ATPase; 1.90A {Carboxydothermus hydrogenoformans} PDB: 3kjg_A* 3kje_A 3kji_A*

Probab=92.33  E-value=0.12  Score=41.83  Aligned_cols=36  Identities=25%  Similarity=0.409  Sum_probs=26.1

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHH
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKK   39 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~   39 (283)
                      ||+||||+|..++......+  ..++-|+.....++..
T Consensus         9 GGvGKTt~a~~LA~~la~~g--~~VlliD~D~~~~l~~   44 (254)
T 3kjh_A            9 GGVGKTTVAAGLIKIMASDY--DKIYAVDGDPDSCLGQ   44 (254)
T ss_dssp             SSHHHHHHHHHHHHHHTTTC--SCEEEEEECTTSCHHH
T ss_pred             CCCCHHHHHHHHHHHHHHCC--CeEEEEeCCCCcChHH
Confidence            89999999999998876443  3466677765555443

>4dzz_A Plasmid partitioning protein PARF; deviant walker BOX, DNA segregation, unknown function; HET: ADP; 1.80A {Escherichia coli} PDB: 4e03_A* 4e07_A* 4e09_A*

Probab=92.33  E-value=0.13  Score=40.39  Aligned_cols=35  Identities=23%  Similarity=0.330  Sum_probs=24.7

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHH
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIK   38 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~   38 (283)
                      ||+||||+|..++......+  ..++-|+.....+..
T Consensus        11 gG~GKTt~a~~la~~la~~g--~~vlliD~D~~~~~~   45 (206)
T 4dzz_A           11 GGSGKTTAVINIATALSRSG--YNIAVVDTDPQMSLT   45 (206)
T ss_dssp             TTSSHHHHHHHHHHHHHHTT--CCEEEEECCTTCHHH
T ss_pred             CCccHHHHHHHHHHHHHHCC--CeEEEEECCCCCCHH
Confidence            89999999999988765432  246667776554443

>3trf_A Shikimate kinase, SK; amino acid biosynthesis, transferase; 2.60A {Coxiella burnetii}

Probab=92.32  E-value=0.062  Score=41.54  Aligned_cols=18  Identities=33%  Similarity=0.586  Sum_probs=15.6

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      +.|+||||+|+.+.....
T Consensus        13 ~~GsGKst~a~~La~~l~   30 (185)
T 3trf_A           13 LMGAGKTSVGSQLAKLTK   30 (185)
T ss_dssp             STTSSHHHHHHHHHHHHC
T ss_pred             CCCCCHHHHHHHHHHHhC
Confidence            479999999999998764

>1ly1_A Polynucleotide kinase; PNK, phosphatase, transferase; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.1

Probab=92.26  E-value=0.062  Score=41.15  Aligned_cols=15  Identities=40%  Similarity=0.508  Sum_probs=13.7

Q ss_pred             CCCCcHHHHHHHHHh
Q 041028            1 MGGIGKTTLAKEVAR   15 (283)
Q Consensus         1 mgGiGKTtLA~~v~~   15 (283)
                      ++|+||||+|+.+..
T Consensus        10 ~~GsGKST~a~~L~~   24 (181)
T 1ly1_A           10 CPGSGKSTWAREFIA   24 (181)
T ss_dssp             CTTSSHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHh
Confidence            479999999999987

>2vhj_A Ntpase P4, P4; non- hydrolysable ATP analogue, hydrolase, virus dsRNA, molecular motor, packaging ATPase, hexameric helicase; HET: ADP; 1.80A {Pseudomonas phage PHI12} PDB: 2vhq_A* 1w44_A* 1w46_A* 1w47_A* 1w48_A* 1w49_A* 1w4a_A* 1w4b_A* 1w4c_A 2vht_A* 2vhu_A* 2vhc_A*

Probab=92.25  E-value=0.051  Score=46.46  Aligned_cols=58  Identities=12%  Similarity=0.077  Sum_probs=33.4

Q ss_pred             CCCCcHHHHHHHHHhhhccCCCCCeEEEEEe--CCCCCHHHHHHHHHHHhCCCCCcCCHhhhHHhHHHHccCCcEEEEcC
Q 041028            1 MGGIGKTTLAKEVARKAKNGKLFDQIVFTEV--SQNPNIKKIQGEIAFKLGLKFDEESESGRTRSPWSRLKKEKLQIICG   78 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v--~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~l~~~L~~kr~LlV~G   78 (283)
                      .+|+||||||.+++....     ..++|+++  ++..+.               ...+.+...+.+.+.+...+.++|+.
T Consensus       131 pPGsGKTtLAlqlA~~~G-----~~VlyIs~~~eE~v~~---------------~~~~le~~l~~i~~~l~~~~LLVIDs  190 (331)
T 2vhj_A          131 KGNSGKTPLVHALGEALG-----GKDKYATVRFGEPLSG---------------YNTDFNVFVDDIARAMLQHRVIVIDS  190 (331)
T ss_dssp             SCSSSHHHHHHHHHHHHH-----TTSCCEEEEBSCSSTT---------------CBCCHHHHHHHHHHHHHHCSEEEEEC
T ss_pred             CCCCCHHHHHHHHHHhCC-----CCEEEEEecchhhhhh---------------hhcCHHHHHHHHHHHHhhCCEEEEec
Confidence            479999999999988611     12456666  333111               01334445555666665555555543

>1nks_A Adenylate kinase; thermophilic, transferase; HET: AMP ADP; 2.57A {Sulfolobus acidocaldarius} SCOP: c.37.1.1

Probab=92.16  E-value=0.068  Score=41.40  Aligned_cols=18  Identities=28%  Similarity=0.490  Sum_probs=15.9

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      ++|+||||+|+.+.....
T Consensus         9 ~~GsGKsT~~~~L~~~l~   26 (194)
T 1nks_A            9 IPGVGKSTVLAKVKEILD   26 (194)
T ss_dssp             CTTSCHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHH
Confidence            479999999999998765

>3vaa_A Shikimate kinase, SK; structural genomics, center for structural genomics of infec diseases, csgid, metal binding, transferase; 1.70A {Bacteroides thetaiotaomicron}

Probab=92.15  E-value=0.068  Score=42.07  Aligned_cols=18  Identities=56%  Similarity=0.641  Sum_probs=15.7

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      +.|+||||+|+.+.....
T Consensus        33 ~~GsGKsTl~~~La~~l~   50 (199)
T 3vaa_A           33 YMGAGKTTLGKAFARKLN   50 (199)
T ss_dssp             CTTSCHHHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHHHcC
Confidence            579999999999998764

>3lw7_A Adenylate kinase related protein (ADKA-like); AMP, PSI, MCSG, structural genomics, midwest center for structural genomics; HET: AMP; 2.30A {Sulfolobus solfataricus} PDB: 3h0k_A

Probab=92.12  E-value=0.059  Score=40.89  Aligned_cols=13  Identities=46%  Similarity=0.649  Sum_probs=12.1

Q ss_pred             CCCCcHHHHHHHH
Q 041028            1 MGGIGKTTLAKEV   13 (283)
Q Consensus         1 mgGiGKTtLA~~v   13 (283)
                      ++|+||||+|+.+
T Consensus         9 ~~GsGKsT~a~~L   21 (179)
T 3lw7_A            9 MPGSGKSEFAKLL   21 (179)
T ss_dssp             CTTSCHHHHHHHH
T ss_pred             CCCCCHHHHHHHH
Confidence            5799999999999

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=92.10  E-value=0.065  Score=41.10  Aligned_cols=17  Identities=29%  Similarity=0.585  Sum_probs=15.1

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      +|+|||+||+.+++...
T Consensus        52 ~G~GKT~l~~~~~~~~~   68 (195)
T 1jbk_A           52 PGVGKTAIVEGLAQRII   68 (195)
T ss_dssp             TTSCHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHH
Confidence            69999999999998754

>2r8r_A Sensor protein; KDPD, PFAM02702, MCSG, structural genomics, protein structure initiative, midwest center for structural genomics, kinase; 2.30A {Pseudomonas syringae PV}

Probab=92.06  E-value=0.07  Score=43.14  Aligned_cols=30  Identities=20%  Similarity=0.197  Sum_probs=21.4

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQ   33 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~   33 (283)
                      ||+||||+|..++.....++ ++ ++.+.+..
T Consensus        15 gGvGKTt~a~~la~~l~~~G-~~-V~v~d~D~   44 (228)
T 2r8r_A           15 PGVGKTYAMLQAAHAQLRQG-VR-VMAGVVET   44 (228)
T ss_dssp             TTSSHHHHHHHHHHHHHHTT-CC-EEEEECCC
T ss_pred             CCCcHHHHHHHHHHHHHHCC-CC-EEEEEeCC
Confidence            89999999999998865443 33 44555544

>1kht_A Adenylate kinase; phosphotransferase, signaling protein, transferase; HET: AMP; 2.50A {Methanococcus voltae} SCOP: c.37.1.1 PDB: 3h86_B* 1ki9_A

Probab=91.86  E-value=0.077  Score=41.04  Aligned_cols=18  Identities=22%  Similarity=0.381  Sum_probs=15.7

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      ++|+||||+|+.+.....
T Consensus        11 ~~GsGKsT~~~~L~~~l~   28 (192)
T 1kht_A           11 VPGVGSTTSSQLAMDNLR   28 (192)
T ss_dssp             CTTSCHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHH
Confidence            479999999999998765

>1via_A Shikimate kinase; structural genomics, transferase; HET: MSE; 1.57A {Campylobacter jejuni} SCOP: c.37.1.2

Probab=91.80  E-value=0.08  Score=40.60  Aligned_cols=18  Identities=39%  Similarity=0.602  Sum_probs=15.6

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      ++|+||||+|+.++....
T Consensus        12 ~~GsGKsTla~~La~~l~   29 (175)
T 1via_A           12 FMGSGKSTLARALAKDLD   29 (175)
T ss_dssp             CTTSCHHHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHHHcC
Confidence            479999999999998754

>1n0w_A DNA repair protein RAD51 homolog 1; DNA repair, homologous recombination, breast cancer susceptibility, RECA-like ATPase, protein complex; HET: DNA MSE; 1.70A {Homo sapiens} SCOP: c.37.1.11

Probab=91.74  E-value=0.36  Score=38.76  Aligned_cols=48  Identities=15%  Similarity=0.134  Sum_probs=31.9

Q ss_pred             CCCcHHHHHHHHHhhhccCC----CCCeEEEEEeCCCCCHHHHHHHHHHHhCC
Q 041028            2 GGIGKTTLAKEVARKAKNGK----LFDQIVFTEVSQNPNIKKIQGEIAFKLGL   50 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~----~Fd~~~wv~v~~~~~~~~l~~~i~~~l~~   50 (283)
                      +|+|||||+..++.......    .-..++|++....++...+ .++++.++.
T Consensus        33 ~GsGKTtl~~~l~~~~~~~~~~g~~~~~~~~i~~~~~~~~~~~-~~~~~~~g~   84 (243)
T 1n0w_A           33 FRTGKTQICHTLAVTCQLPIDRGGGEGKAMYIDTEGTFRPERL-LAVAERYGL   84 (243)
T ss_dssp             TTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEESSSCCCHHHH-HHHHHHTTC
T ss_pred             CCCcHHHHHHHHHHHHhCchhcCCCCCeEEEEECCCCcCHHHH-HHHHHHcCC
Confidence            69999999999987532211    1257899988776665544 345555654

>2rhm_A Putative kinase; P-loop containing nucleoside triphosphate hydrolases fold, S genomics, joint center for structural genomics, JCSG; HET: MSE; 1.70A {Chloroflexus aurantiacus}

Probab=91.74  E-value=0.079  Score=41.11  Aligned_cols=18  Identities=33%  Similarity=0.423  Sum_probs=15.4

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      ++|+||||+|+.+.....
T Consensus        13 ~~GsGKST~~~~L~~~l~   30 (193)
T 2rhm_A           13 HPATGKTTLSQALATGLR   30 (193)
T ss_dssp             STTSSHHHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHHHcC
Confidence            479999999999988653

>2i1q_A DNA repair and recombination protein RADA; ATPase, recombinase, ATP complex, calcium stimulation, RECA, DMC1; HET: DNA ANP; 1.90A {Methanococcus voltae} SCOP: a.60.4.1 c.37.1.11 PDB: 1xu4_A* 2b21_A* 2fpk_A* 2fpl_A* 2fpm_A* 1t4g_A* 3fyh_A* 2f1j_A* 2f1i_A* 2f1h_A* 3ntu_A* 3ewa_A* 3ew9_A* 3etl_A* 4dc9_A* 2gdj_A*

Probab=91.73  E-value=0.32  Score=41.35  Aligned_cols=48  Identities=19%  Similarity=0.230  Sum_probs=33.5

Q ss_pred             CCCcHHHHHHHHHhhhccCC---------CC-----CeEEEEEeCCCCCHHHHHHHHHHHhCC
Q 041028            2 GGIGKTTLAKEVARKAKNGK---------LF-----DQIVFTEVSQNPNIKKIQGEIAFKLGL   50 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~---------~F-----d~~~wv~v~~~~~~~~l~~~i~~~l~~   50 (283)
                      +|+||||||..++.......         ..     ..++|++....++...+.. +++.++.
T Consensus       107 ~gsGKT~la~~la~~~~l~~~~~~~~~~~~~gg~~~~~v~yi~~e~~~~~~~l~~-~~~~~g~  168 (322)
T 2i1q_A          107 FGSGKTQIMHQSCVNLQNPEFLFYDEEAVSKGEVAQPKAVYIDTEGTFRPERIMQ-MAEHAGI  168 (322)
T ss_dssp             TTSSHHHHHHHHHHHTTCGGGEECCTTTSCTTTTSSEEEEEEESSSCCCHHHHHH-HHHHHTC
T ss_pred             CCCCHHHHHHHHHHHHhccccccccccccccCCCCCceEEEEECCCCCCHHHHHH-HHHHcCC
Confidence            69999999999887532110         11     4689999988888777664 4566665

>2jaq_A Deoxyguanosine kinase; transferase, deoxyribonucleoside kinase; HET: DCP; 2.3A {Mycoplasma mycoides subsp} PDB: 2jat_A* 2jas_A*

Probab=91.63  E-value=0.084  Score=41.29  Aligned_cols=18  Identities=33%  Similarity=0.567  Sum_probs=15.7

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      +.|+||||+|+.+.....
T Consensus         8 ~~GsGKsT~~~~L~~~l~   25 (205)
T 2jaq_A            8 TVGAGKSTISAEISKKLG   25 (205)
T ss_dssp             CTTSCHHHHHHHHHHHHC
T ss_pred             CCccCHHHHHHHHHHhcC
Confidence            479999999999998764

>3iij_A Coilin-interacting nuclear ATPase protein; alpha and beta proteins (A/B), protein binding, transferase, phosphotransferase; HET: ADP; 1.76A {Homo sapiens} SCOP: c.37.1.1 PDB: 3iik_A 3iil_A* 3iim_A* 1rkb_A

Probab=91.61  E-value=0.084  Score=40.65  Aligned_cols=18  Identities=56%  Similarity=0.756  Sum_probs=15.5

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      ++|+||||+|+.+.....
T Consensus        19 ~~GsGKst~~~~l~~~~~   36 (180)
T 3iij_A           19 TPGVGKTTLGKELASKSG   36 (180)
T ss_dssp             STTSSHHHHHHHHHHHHC
T ss_pred             CCCCCHHHHHHHHHHHhC
Confidence            579999999999998753

>3k9g_A PF-32 protein; ssgcid, SBRI, decode biostructures, UW, NIH, niaid, borellia burgdorferi, plasmid partition protein, iodide; 2.25A {Borrelia burgdorferi} PDB: 3k9h_A

Probab=91.43  E-value=0.47  Score=38.91  Aligned_cols=37  Identities=22%  Similarity=0.395  Sum_probs=26.6

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHH
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQ   41 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~   41 (283)
                      ||+||||+|..++.... ++  ..++-|+.....+....+
T Consensus        37 GGvGKTT~a~~LA~~la-~g--~~VlliD~D~~~~~~~~~   73 (267)
T 3k9g_A           37 GGVGKSTSAIILATLLS-KN--NKVLLIDMDTQASITSYF   73 (267)
T ss_dssp             SSSCHHHHHHHHHHHHT-TT--SCEEEEEECTTCHHHHHT
T ss_pred             CCchHHHHHHHHHHHHH-CC--CCEEEEECCCCCCHHHHh
Confidence            89999999999998876 43  356677776554444433

>1kag_A SKI, shikimate kinase I; transferase, structural genomics, PSI, protein structure initiative; 2.05A {Escherichia coli} SCOP: c.37.1.2

Probab=91.42  E-value=0.092  Score=39.99  Aligned_cols=18  Identities=28%  Similarity=0.523  Sum_probs=15.3

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      +.|+|||||++.+.....
T Consensus        12 ~~GsGKSTl~~~La~~l~   29 (173)
T 1kag_A           12 PMGAGKSTIGRQLAQQLN   29 (173)
T ss_dssp             CTTSCHHHHHHHHHHHTT
T ss_pred             CCCCCHHHHHHHHHHHhC
Confidence            469999999999988654

>2z43_A DNA repair and recombination protein RADA; archaea, filament, DNA binding, molecular SWI RECA, DMC1; HET: DNA; 1.93A {Sulfolobus solfataricus} PDB: 2bke_A* 2dfl_A* 2zub_A* 2zuc_A* 2zud_A*

Probab=91.26  E-value=0.47  Score=40.37  Aligned_cols=48  Identities=23%  Similarity=0.291  Sum_probs=33.9

Q ss_pred             CCCcHHHHHHHHHhhhccCC---C-CCeEEEEEeCCCCCHHHHHHHHHHHhCC
Q 041028            2 GGIGKTTLAKEVARKAKNGK---L-FDQIVFTEVSQNPNIKKIQGEIAFKLGL   50 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~---~-Fd~~~wv~v~~~~~~~~l~~~i~~~l~~   50 (283)
                      +|+||||||..++.......   - =..++|++....++...+. ++++.++.
T Consensus       116 ~GsGKT~la~~la~~~~~~~~~gg~~~~vlyi~~e~~~~~~~l~-~~~~~~g~  167 (324)
T 2z43_A          116 FGSGKTQLCHQLSVNVQLPPEKGGLSGKAVYIDTEGTFRWERIE-NMAKALGL  167 (324)
T ss_dssp             TTSSHHHHHHHHHHHTTSCGGGTCCSCEEEEEESSSCCCHHHHH-HHHHHTTC
T ss_pred             CCCCHhHHHHHHHHHHhcccccCCCCCeEEEEECCCCCCHHHHH-HHHHHhCC
Confidence            69999999999987643211   0 1468999998888877665 44566654

>3t61_A Gluconokinase; PSI-biology, structural genomics, protein structure initiati YORK structural genomics research consortium, nysgrc; 2.20A {Sinorhizobium meliloti}

Probab=91.18  E-value=0.097  Score=41.16  Aligned_cols=17  Identities=24%  Similarity=0.571  Sum_probs=14.9

Q ss_pred             CCCCcHHHHHHHHHhhh
Q 041028            1 MGGIGKTTLAKEVARKA   17 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (283)
                      +.|+||||||+.+....
T Consensus        26 ~~GsGKSTla~~L~~~l   42 (202)
T 3t61_A           26 VSGSGKSSVGEAIAEAC   42 (202)
T ss_dssp             STTSCHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            36999999999998875

>1zuh_A Shikimate kinase; alpha-beta protein, transferase; 1.80A {Helicobacter pylori} PDB: 1zui_A* 3hr7_A 3muf_A* 3mrs_A 3n2e_A*

Probab=91.15  E-value=0.1  Score=39.62  Aligned_cols=18  Identities=39%  Similarity=0.536  Sum_probs=15.7

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      +.|+||||+|+.+.....
T Consensus        15 ~~GsGKSTva~~La~~lg   32 (168)
T 1zuh_A           15 FMGSGKSSLAQELGLALK   32 (168)
T ss_dssp             CTTSSHHHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHHHhC
Confidence            579999999999998764

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=91.11  E-value=0.074  Score=40.71  Aligned_cols=17  Identities=35%  Similarity=0.526  Sum_probs=15.0

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      +|+|||+||+.+++...
T Consensus        52 ~G~GKT~la~~~~~~~~   68 (187)
T 2p65_A           52 PGVGKTAIVEGLAIKIV   68 (187)
T ss_dssp             GGGCHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHH
Confidence            59999999999998754

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=91.02  E-value=0.099  Score=38.87  Aligned_cols=16  Identities=25%  Similarity=0.279  Sum_probs=14.4

Q ss_pred             CCCcHHHHHHHHHhhh
Q 041028            2 GGIGKTTLAKEVARKA   17 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~   17 (283)
                      +|+|||+||+.+++..
T Consensus        33 ~GtGKt~lA~~i~~~~   48 (145)
T 3n70_A           33 PGTGRMTGARYLHQFG   48 (145)
T ss_dssp             TTSSHHHHHHHHHHSS
T ss_pred             CCCCHHHHHHHHHHhC
Confidence            6999999999999864

>1zp6_A Hypothetical protein ATU3015; alpha-beta protein., structural genomics, PSI, protein struc initiative; 3.20A {Agrobacterium tumefaciens str} SCOP: c.37.1.25

Probab=90.98  E-value=0.096  Score=40.63  Aligned_cols=16  Identities=38%  Similarity=0.511  Sum_probs=14.1

Q ss_pred             CCCCcHHHHHHHHHhh
Q 041028            1 MGGIGKTTLAKEVARK   16 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~   16 (283)
                      +.|+|||||++.+...
T Consensus        17 ~~GsGKSTl~~~La~~   32 (191)
T 1zp6_A           17 HPGSGKSTIAEALANL   32 (191)
T ss_dssp             CTTSCHHHHHHHHHTC
T ss_pred             CCCCCHHHHHHHHHhc
Confidence            4799999999999875

>1njg_A DNA polymerase III subunit gamma; rossman-like fold, AAA+ ATPase domains, sensor 1, sensor 2, transferase; HET: DNA; 2.20A {Escherichia coli} SCOP: c.37.1.20 PDB: 1njf_A*

Probab=90.95  E-value=0.099  Score=41.65  Aligned_cols=18  Identities=33%  Similarity=0.578  Sum_probs=15.7

Q ss_pred             CCCcHHHHHHHHHhhhcc
Q 041028            2 GGIGKTTLAKEVARKAKN   19 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~   19 (283)
                      +|+||||||+.+++....
T Consensus        54 ~G~GKT~l~~~~~~~~~~   71 (250)
T 1njg_A           54 RGVGKTSIARLLAKGLNC   71 (250)
T ss_dssp             TTSCHHHHHHHHHHHHHC
T ss_pred             CCCCHHHHHHHHHHHhcC
Confidence            699999999999987654

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A

Probab=90.82  E-value=0.12  Score=43.52  Aligned_cols=17  Identities=35%  Similarity=0.339  Sum_probs=15.7

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      +|+|||+||+.+++...
T Consensus        45 pGtGKT~la~aiA~~l~   61 (293)
T 3t15_A           45 KGQGKSFQCELVFRKMG   61 (293)
T ss_dssp             TTSCHHHHHHHHHHHHT
T ss_pred             CCCCHHHHHHHHHHHhC
Confidence            79999999999999875

>3zq6_A Putative arsenical pump-driving ATPase; tail-anchored, membrane protein; HET: ADP; 2.11A {Methanothermobacter thermautotrophicusorganism_taxid}

Probab=90.77  E-value=0.27  Score=41.96  Aligned_cols=37  Identities=19%  Similarity=0.309  Sum_probs=24.6

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHH
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKI   40 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l   40 (283)
                      ||+||||+|..++......+  ..++-|+.....++...
T Consensus        23 GGvGKTTvA~~LA~~lA~~G--~rVLlvD~D~~~~l~~~   59 (324)
T 3zq6_A           23 GGVGKTTISAATALWMARSG--KKTLVISTDPAHSLSDS   59 (324)
T ss_dssp             TTSSHHHHHHHHHHHHHHTT--CCEEEEECCSSCCHHHH
T ss_pred             CCchHHHHHHHHHHHHHHCC--CcEEEEeCCCCcCHHHH
Confidence            89999999999887755432  24555666554454443

>3cm0_A Adenylate kinase; ATP-binding, cytoplasm, nucleotide biosynthesis, nucleotide-binding, transferase, structural genomics; 1.80A {Thermus thermophilus}

Probab=90.72  E-value=0.12  Score=39.91  Aligned_cols=18  Identities=33%  Similarity=0.351  Sum_probs=15.2

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      +.|+||||+|+.+.....
T Consensus        12 ~~GsGKST~~~~La~~l~   29 (186)
T 3cm0_A           12 PPGAGKGTQASRLAQELG   29 (186)
T ss_dssp             CTTSCHHHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHHHhC
Confidence            479999999999987653

>1e6c_A Shikimate kinase; phosphoryl transfer, ADP, shikimate pathway, P-loop protein, transferase; 1.8A {Erwinia chrysanthemi} SCOP: c.37.1.2 PDB: 1shk_A 2shk_A*

Probab=90.68  E-value=0.12  Score=39.28  Aligned_cols=18  Identities=39%  Similarity=0.534  Sum_probs=15.4

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      +.|+||||+|+.+.....
T Consensus        10 ~~GsGKsT~a~~La~~lg   27 (173)
T 1e6c_A           10 ARGCGMTTVGRELARALG   27 (173)
T ss_dssp             CTTSSHHHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHHHhC
Confidence            479999999999998654

>1cp2_A CP2, nitrogenase iron protein; oxidoreductase; 1.93A {Clostridium pasteurianum} SCOP: c.37.1.10

Probab=90.67  E-value=0.13  Score=42.43  Aligned_cols=30  Identities=23%  Similarity=0.379  Sum_probs=21.8

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQ   33 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~   33 (283)
                      ||+||||+|..++......+  ..++-|+...
T Consensus        10 GGvGKTT~a~nLA~~la~~G--~~VlliD~D~   39 (269)
T 1cp2_A           10 GGIGKSTTTQNLTSGLHAMG--KTIMVVGCDP   39 (269)
T ss_dssp             TTSSHHHHHHHHHHHHHTTT--CCEEEEEECT
T ss_pred             CCCcHHHHHHHHHHHHHHCC--CcEEEEcCCC
Confidence            89999999999998765432  2456666653

>2yvu_A Probable adenylyl-sulfate kinase; transferase, structural genomics, NPPSFA, national P protein structural and functional analyses; 2.10A {Aeropyrum pernix}

Probab=90.58  E-value=0.12  Score=39.94  Aligned_cols=19  Identities=37%  Similarity=0.517  Sum_probs=16.3

Q ss_pred             CCCCcHHHHHHHHHhhhcc
Q 041028            1 MGGIGKTTLAKEVARKAKN   19 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~   19 (283)
                      ++|+||||+|+.++.....
T Consensus        21 ~~GsGKsT~~~~L~~~l~~   39 (186)
T 2yvu_A           21 LPGSGKTTIATRLADLLQK   39 (186)
T ss_dssp             CTTSSHHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHh
Confidence            4799999999999987654

>2plr_A DTMP kinase, probable thymidylate kinase; TMP-binding, ATP-binding, structural GEN NPPSFA; HET: 1PE PGE EPE PG4; 1.60A {Sulfolobus tokodaii}

Probab=90.50  E-value=0.13  Score=40.52  Aligned_cols=20  Identities=20%  Similarity=0.205  Sum_probs=16.7

Q ss_pred             CCCCcHHHHHHHHHhhhccC
Q 041028            1 MGGIGKTTLAKEVARKAKNG   20 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~   20 (283)
                      ++|+||||+|+.+.......
T Consensus        12 ~~GsGKsT~~~~L~~~l~~~   31 (213)
T 2plr_A           12 IDGSGKSSQATLLKDWIELK   31 (213)
T ss_dssp             CTTSSHHHHHHHHHHHHTTT
T ss_pred             CCCCCHHHHHHHHHHHHhhc
Confidence            46999999999999876543

>2iyv_A Shikimate kinase, SK; transferase, aromatic amino acid biosynthesis, P-loop kinase, metal- binding, shikimate pathway; HET: ADP; 1.35A {Mycobacterium tuberculosis} SCOP: c.37.1.2 PDB: 2iyr_A* 2iyq_A* 2iyt_A 2iyu_A* 2iys_A* 2iyw_A* 2iyx_A* 2iyy_A* 2iyz_A* 2g1k_A* 1l4y_A* 1u8a_A* 1we2_A* 1zyu_A* 2dfn_A* 2dft_A* 2g1j_A 1l4u_A* 3baf_A*

Probab=90.49  E-value=0.12  Score=39.77  Aligned_cols=18  Identities=28%  Similarity=0.564  Sum_probs=15.5

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      ++|+||||+|+.+.....
T Consensus        10 ~~GsGKsT~a~~La~~lg   27 (184)
T 2iyv_A           10 LPGSGKSTIGRRLAKALG   27 (184)
T ss_dssp             STTSSHHHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHHHcC
Confidence            479999999999998754

>2ze6_A Isopentenyl transferase; crown GALL tumor, cytokinin biosynthesis; HET: DST AMP; 2.10A {Agrobacterium tumefaciens} PDB: 2ze5_A* 2ze7_A* 2ze8_A

Probab=90.47  E-value=0.12  Score=42.40  Aligned_cols=18  Identities=28%  Similarity=0.326  Sum_probs=15.4

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      +.|+||||||+.++....
T Consensus         9 ~~GSGKSTla~~La~~~~   26 (253)
T 2ze6_A            9 PTCSGKTDMAIQIAQETG   26 (253)
T ss_dssp             CTTSSHHHHHHHHHHHHC
T ss_pred             CCCcCHHHHHHHHHhcCC
Confidence            469999999999998754

>2pt5_A Shikimate kinase, SK; aromatic amino acid biosynthesis, P-loop kinase, SHI kinase, shikimate pathway; 2.10A {Aquifex aeolicus}

Probab=90.45  E-value=0.13  Score=38.92  Aligned_cols=18  Identities=22%  Similarity=0.279  Sum_probs=15.5

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      +.|+||||+|+.+.+...
T Consensus         8 ~~GsGKsT~a~~L~~~l~   25 (168)
T 2pt5_A            8 FMCSGKSTVGSLLSRSLN   25 (168)
T ss_dssp             CTTSCHHHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHHHhC
Confidence            479999999999998654

>1y63_A LMAJ004144AAA protein; structural genomics, protein structure initiative, PSI, SGPP structural genomics of pathogenic protozoa consortium; HET: ADP; 1.70A {Leishmania major} SCOP: c.37.1.1

Probab=90.38  E-value=0.13  Score=39.88  Aligned_cols=16  Identities=38%  Similarity=0.586  Sum_probs=14.4

Q ss_pred             CCCCcHHHHHHHHHhh
Q 041028            1 MGGIGKTTLAKEVARK   16 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~   16 (283)
                      +.|+||||+|+.+...
T Consensus        18 ~~GsGKSTv~~~La~~   33 (184)
T 1y63_A           18 TPGTGKTSMAEMIAAE   33 (184)
T ss_dssp             STTSSHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHh
Confidence            5799999999999886

>2vli_A Antibiotic resistance protein; transferase, tunicamycin, phosphotransferase; 1.95A {Deinococcus radiodurans}

Probab=90.37  E-value=0.089  Score=40.46  Aligned_cols=18  Identities=28%  Similarity=0.335  Sum_probs=11.5

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      +.|+||||+|+.+.....
T Consensus        13 ~~GsGKST~a~~La~~l~   30 (183)
T 2vli_A           13 PFGVGKTHTAHTLHERLP   30 (183)
T ss_dssp             CC----CHHHHHHHHHST
T ss_pred             CCCCCHHHHHHHHHHhcC
Confidence            479999999999987654

>1tev_A UMP-CMP kinase; ploop, NMP binding region, LID region, conformational changes, transferase; 2.10A {Homo sapiens} SCOP: c.37.1.1

Probab=90.35  E-value=0.13  Score=39.78  Aligned_cols=18  Identities=28%  Similarity=0.266  Sum_probs=15.1

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      ++|+||||+|+.+.....
T Consensus        11 ~~GsGKsT~a~~L~~~~~   28 (196)
T 1tev_A           11 GPGAGKGTQCARIVEKYG   28 (196)
T ss_dssp             CTTSSHHHHHHHHHHHHC
T ss_pred             CCCCCHHHHHHHHHHHhC
Confidence            479999999999987653

>2qor_A Guanylate kinase; phosphotransferase, purine metabolism, structural genomics, structural genomics of pathogenic protozoa consortium; HET: 5GP POP; 1.80A {Plasmodium vivax}

Probab=90.30  E-value=0.13  Score=40.51  Aligned_cols=17  Identities=41%  Similarity=0.538  Sum_probs=15.0

Q ss_pred             CCCCcHHHHHHHHHhhh
Q 041028            1 MGGIGKTTLAKEVARKA   17 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (283)
                      ++|+|||||++.+....
T Consensus        20 ~sGsGKsTl~~~L~~~~   36 (204)
T 2qor_A           20 PSGVGKGTLIKKVLSEF   36 (204)
T ss_dssp             CTTSCHHHHHHHHHHHC
T ss_pred             CCCCCHHHHHHHHHHhC
Confidence            47999999999998865

>1yrb_A ATP(GTP)binding protein; GTPase, P-loop, rossman fold, GDP, HYDR; HET: GDP; 1.75A {Pyrococcus abyssi} SCOP: c.37.1.10 PDB: 1yr6_A* 1yr8_A* 1yr9_A* 1yra_A* 1yr7_A* 2oxr_A*

Probab=90.22  E-value=0.14  Score=41.80  Aligned_cols=18  Identities=44%  Similarity=0.553  Sum_probs=15.5

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      .||+|||||+..++....
T Consensus        22 kgGvGKTTl~~~La~~l~   39 (262)
T 1yrb_A           22 TAGSGKTTLTGEFGRYLE   39 (262)
T ss_dssp             STTSSHHHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHHHHH
Confidence            389999999999987655

>1j8m_F SRP54, signal recognition 54 kDa protein; signaling protein; 2.00A {Acidianus ambivalens} SCOP: a.24.13.1 c.37.1.10 PDB: 1j8y_F

Probab=90.21  E-value=1.2  Score=37.52  Aligned_cols=74  Identities=19%  Similarity=0.235  Sum_probs=41.2

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCC-CCCHHHHHHHHHHHhCCCC----CcCCHhhhHHhHHHHc--cCCcEE
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQ-NPNIKKIQGEIAFKLGLKF----DEESESGRTRSPWSRL--KKEKLQ   74 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~-~~~~~~l~~~i~~~l~~~~----~~~~~~~~~~~l~~~L--~~kr~L   74 (283)
                      +|+||||++..++......+  ..+.++.... .....+.++.+....+.+.    ...+..+......+.+  .+..++
T Consensus       107 ~G~GKTT~~~~la~~~~~~g--~~v~l~~~D~~r~~a~~ql~~~~~~~~v~v~~~~~~~~p~~~~~~~l~~~~~~~~D~V  184 (297)
T 1j8m_F          107 QGTGKTTTAGKLAYFYKKKG--FKVGLVGADVYRPAALEQLQQLGQQIGVPVYGEPGEKDVVGIAKRGVEKFLSEKMEII  184 (297)
T ss_dssp             SCSSTTHHHHHHHHHHHHTT--CCEEEEECCCSSSHHHHHHHHHHHHHTCCEECCTTCCCHHHHHHHHHHHHHHTTCSEE
T ss_pred             CCCCHHHHHHHHHHHHHHCC--CeEEEEecCCCCHHHHHHHHHHhccCCeEEEecCCCCCHHHHHHHHHHHHHhCCCCEE
Confidence            79999999999988765432  2455565542 2333444555566666542    1123444433333333  345788


Q ss_pred             EEc
Q 041028           75 IIC   77 (283)
Q Consensus        75 lV~   77 (283)
                      ||+
T Consensus       185 iID  187 (297)
T 1j8m_F          185 IVD  187 (297)
T ss_dssp             EEE
T ss_pred             EEe
Confidence            883

>3iqw_A Tail-anchored protein targeting factor GET3; ATPase, Zn binding, protein transport; HET: ANP; 3.00A {Chaetomium thermophilum} PDB: 3iqx_A* 3ibg_A*

Probab=90.18  E-value=0.29  Score=42.05  Aligned_cols=37  Identities=22%  Similarity=0.373  Sum_probs=24.7

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHH
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKI   40 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l   40 (283)
                      ||+||||+|..++......+  ..++-|+.....++...
T Consensus        25 GGvGKTt~a~~lA~~la~~g--~~vllid~D~~~~l~~~   61 (334)
T 3iqw_A           25 GGVGKTTTSCSLAIQLAKVR--RSVLLLSTDPAHNLSDA   61 (334)
T ss_dssp             TTSSHHHHHHHHHHHHTTSS--SCEEEEECCSSCHHHHH
T ss_pred             CCccHHHHHHHHHHHHHhCC--CcEEEEECCCCCChhHH
Confidence            89999999999988765432  24566666654444433

>3a4m_A L-seryl-tRNA(SEC) kinase; P-loop motif, walker A motif, ATP binding motif, ATP- binding, nucleotide-binding, transferase; HET: ADP; 1.79A {Methanocaldococcus jannaschii} PDB: 3a4l_A* 3a4n_A 3am1_A* 3add_A* 3adc_A* 3adb_A*

Probab=90.11  E-value=0.14  Score=42.26  Aligned_cols=18  Identities=33%  Similarity=0.660  Sum_probs=15.4

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      ++|+||||+|+.+.....
T Consensus        12 ~pGSGKSTla~~La~~L~   29 (260)
T 3a4m_A           12 LPGVGKSTFSKNLAKILS   29 (260)
T ss_dssp             CTTSSHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHH
Confidence            579999999999998743

>1knq_A Gluconate kinase; ALFA/beta structure, transferase; 2.00A {Escherichia coli} SCOP: c.37.1.17 PDB: 1ko1_A 1ko4_A 1ko5_A* 1ko8_A* 1kof_A*

Probab=90.04  E-value=0.14  Score=39.04  Aligned_cols=17  Identities=41%  Similarity=0.653  Sum_probs=14.6

Q ss_pred             CCCCcHHHHHHHHHhhh
Q 041028            1 MGGIGKTTLAKEVARKA   17 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (283)
                      +.|+||||||+.+....
T Consensus        16 ~~GsGKSTl~~~l~~~~   32 (175)
T 1knq_A           16 VSGSGKSAVASEVAHQL   32 (175)
T ss_dssp             STTSCHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHhh
Confidence            46999999999998764

>2afh_E Nitrogenase iron protein 1; nitrogen fixation, iron-sulfur, metal-binding, molybdenum, oxidoreductase; HET: HCA CFN CLF PGE PG4 P6G 1PE; 2.10A {Azotobacter vinelandii} SCOP: c.37.1.10 PDB: 1g1m_A 1g5p_A 1m1y_E* 1m34_E* 1n2c_E* 1nip_A* 1fp6_A* 2afi_E* 2afk_E* 2nip_A 1de0_A 1xcp_A* 1xdb_A 1xd8_A 1xd9_A* 1g20_E* 1g21_E* 2c8v_A* 1rw4_A

Probab=90.04  E-value=0.25  Score=41.24  Aligned_cols=30  Identities=20%  Similarity=0.396  Sum_probs=21.6

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQ   33 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~   33 (283)
                      ||+||||+|..++......+  ..++-|+...
T Consensus        11 GGvGKTT~a~nLA~~La~~G--~rVlliD~D~   40 (289)
T 2afh_E           11 GGIGKSTTTQNLVAALAEMG--KKVMIVGCDP   40 (289)
T ss_dssp             TTSSHHHHHHHHHHHHHHTT--CCEEEEEECS
T ss_pred             CcCcHHHHHHHHHHHHHHCC--CeEEEEecCC
Confidence            89999999999988765432  2456666653

>1v5w_A DMC1, meiotic recombination protein DMC1/LIM15 homolog; DNA-binding protein, ring protein, octamer, AAA ATPase; 3.20A {Homo sapiens} SCOP: c.37.1.11 PDB: 2zjb_A

Probab=89.97  E-value=0.6  Score=40.13  Aligned_cols=48  Identities=19%  Similarity=0.240  Sum_probs=33.7

Q ss_pred             CCCcHHHHHHHHHhhhccCC----CCCeEEEEEeCCCCCHHHHHHHHHHHhCC
Q 041028            2 GGIGKTTLAKEVARKAKNGK----LFDQIVFTEVSQNPNIKKIQGEIAFKLGL   50 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~----~Fd~~~wv~v~~~~~~~~l~~~i~~~l~~   50 (283)
                      +|+||||||..++.......    .=..++|++....++...+. +++..++.
T Consensus       131 ~GsGKTtla~~la~~~~~~~~~gg~~~~vlyi~~E~~~~~~~l~-~~~~~~g~  182 (343)
T 1v5w_A          131 FRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDTENTFRPDRLR-DIADRFNV  182 (343)
T ss_dssp             TTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEEESSSCCCHHHHH-HHHHHTTC
T ss_pred             CCCCHHHHHHHHHHHHhcccccCCCCCeEEEEECCCCCCHHHHH-HHHHHcCC
Confidence            69999999999987643211    12478999998888877654 44556654

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=89.95  E-value=0.16  Score=42.71  Aligned_cols=18  Identities=39%  Similarity=0.429  Sum_probs=15.4

Q ss_pred             CCCcHHHHHHHHHhhhcc
Q 041028            2 GGIGKTTLAKEVARKAKN   19 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~   19 (283)
                      +|+|||+||+.+++....
T Consensus        76 ~GtGKT~la~~la~~l~~   93 (309)
T 3syl_A           76 PGTGKTTVALKMAGLLHR   93 (309)
T ss_dssp             TTSSHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHh
Confidence            699999999998887644

>3ea0_A ATPase, para family; alpha-beta-alpha sandwich, structural genomics, PSI-2, prote structure initiative; HET: ATP; 2.20A {Chlorobium tepidum}

Probab=89.92  E-value=0.17  Score=40.88  Aligned_cols=31  Identities=19%  Similarity=0.229  Sum_probs=22.0

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQ   33 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~   33 (283)
                      ||+||||+|..++........ ..++-|+...
T Consensus        14 GGvGKTt~a~~LA~~la~~~g-~~VlliD~D~   44 (245)
T 3ea0_A           14 GGDGGSCIAANFAFALSQEPD-IHVLAVDISL   44 (245)
T ss_dssp             TTSSHHHHHHHHHHHHTTSTT-CCEEEEECCT
T ss_pred             CCcchHHHHHHHHHHHHhCcC-CCEEEEECCC
Confidence            899999999999987654301 2456666653

>2cdn_A Adenylate kinase; phosphoryl transfer, associative mechanism, ATP-binding, nucleotide biosynthesis, nucleotide-binding, transferase; HET: ADP; 1.9A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1p4s_A

Probab=89.91  E-value=0.15  Score=39.99  Aligned_cols=18  Identities=39%  Similarity=0.350  Sum_probs=15.5

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      ++|+||||+|+.+.....
T Consensus        28 ~~GsGKST~a~~La~~l~   45 (201)
T 2cdn_A           28 PPGAGKGTQAVKLAEKLG   45 (201)
T ss_dssp             CTTSSHHHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHHHhC
Confidence            479999999999988653

>3q9l_A Septum site-determining protein MIND; ATPase, bacterial cell division inhibitor, MINC, MINE, cell hydrolase; HET: ATP; 2.34A {Escherichia coli} PDB: 3r9i_A* 3r9j_A*

Probab=89.89  E-value=0.31  Score=39.62  Aligned_cols=30  Identities=27%  Similarity=0.385  Sum_probs=22.0

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQ   33 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~   33 (283)
                      ||+||||+|..++......+.  .++-|+...
T Consensus        12 gGvGKTt~a~~LA~~la~~g~--~VlliD~D~   41 (260)
T 3q9l_A           12 GGVGKTTSSAAIATGLAQKGK--KTVVIDFAI   41 (260)
T ss_dssp             TTSSHHHHHHHHHHHHHHTTC--CEEEEECCC
T ss_pred             CCCcHHHHHHHHHHHHHhCCC--cEEEEECCC
Confidence            899999999999887654322  456666664

>2c95_A Adenylate kinase 1; transferase, AP4A, nucleotide kinase, transferase ATP-bindi; HET: B4P; 1.71A {Homo sapiens} PDB: 1z83_A* 3adk_A

Probab=89.84  E-value=0.15  Score=39.52  Aligned_cols=18  Identities=28%  Similarity=0.313  Sum_probs=15.3

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      +.|+||||+|+.+.....
T Consensus        17 ~~GsGKsT~~~~La~~l~   34 (196)
T 2c95_A           17 GPGSGKGTQCEKIVQKYG   34 (196)
T ss_dssp             CTTSSHHHHHHHHHHHHC
T ss_pred             CCCCCHHHHHHHHHHHhC
Confidence            479999999999988653

>3ug7_A Arsenical pump-driving ATPase; tail-anchored, membrane protein, targeting factor, ATP-bindi TRC40, ARSA, nucleotide-binding; HET: ADP; 2.90A {Methanocaldococcus jannaschii} PDB: 3ug6_A*

Probab=89.84  E-value=0.28  Score=42.39  Aligned_cols=30  Identities=27%  Similarity=0.463  Sum_probs=20.3

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQ   33 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~   33 (283)
                      ||+||||+|..++......+.  .++-|+...
T Consensus        35 GGvGKTTvA~~LA~~lA~~G~--rVLlvD~D~   64 (349)
T 3ug7_A           35 GGVGKTTMSAATGVYLAEKGL--KVVIVSTDP   64 (349)
T ss_dssp             SSTTHHHHHHHHHHHHHHSSC--CEEEEECCT
T ss_pred             CCccHHHHHHHHHHHHHHCCC--eEEEEeCCC
Confidence            899999999998877544321  345555443

>3uie_A Adenylyl-sulfate kinase 1, chloroplastic; rossmann fold, transferase-transferase complex; HET: ADX ANP; 1.79A {Arabidopsis thaliana} SCOP: c.37.1.0 PDB: 4fxp_A*

Probab=89.79  E-value=0.15  Score=40.00  Aligned_cols=18  Identities=33%  Similarity=0.440  Sum_probs=15.6

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      +.|.||||||+.+.....
T Consensus        33 ~sGsGKSTl~~~La~~l~   50 (200)
T 3uie_A           33 LSGSGKSTLACALNQMLY   50 (200)
T ss_dssp             STTSSHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHH
Confidence            469999999999998765

>2xj4_A MIPZ; replication, cell division, ATPase, WACA; 1.60A {Caulobacter vibrioides} PDB: 2xj9_A* 2xit_A

Probab=89.75  E-value=0.31  Score=40.68  Aligned_cols=38  Identities=18%  Similarity=0.341  Sum_probs=26.1

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCC-CCCHHHHH
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQ-NPNIKKIQ   41 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~-~~~~~~l~   41 (283)
                      ||+||||+|..++......+  ..++-|+... ..+....+
T Consensus        14 GGvGKTT~a~nLA~~La~~G--~~VlliD~D~~q~~l~~~l   52 (286)
T 2xj4_A           14 GGAGKSTIAVHLVTALLYGG--AKVAVIDLDLRQRTSARFF   52 (286)
T ss_dssp             SCTTHHHHHHHHHHHHHHTT--CCEEEEECCTTTCHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHCC--CcEEEEECCCCCCCHHHHh
Confidence            89999999999988765432  2456677765 55554443

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=89.72  E-value=0.14  Score=42.45  Aligned_cols=17  Identities=53%  Similarity=0.651  Sum_probs=15.2

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      +|+|||+||+.+++...
T Consensus        60 ~GtGKT~la~~la~~~~   76 (285)
T 3h4m_A           60 PGTGKTLLAKAVATETN   76 (285)
T ss_dssp             SSSSHHHHHHHHHHHTT
T ss_pred             CCCcHHHHHHHHHHHhC
Confidence            69999999999998754

>1aky_A Adenylate kinase; ATP:AMP phosphotransferase, myokinase, transferase (phosphotransferase); HET: AP5; 1.63A {Saccharomyces cerevisiae} SCOP: c.37.1.1 g.41.2.1 PDB: 2aky_A* 3aky_A* 1dvr_A*

Probab=89.63  E-value=0.16  Score=40.49  Aligned_cols=18  Identities=28%  Similarity=0.318  Sum_probs=15.5

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      ++|+||||+|+.++....
T Consensus        12 ~~GsGKsT~a~~La~~l~   29 (220)
T 1aky_A           12 PPGAGKGTQAPNLQERFH   29 (220)
T ss_dssp             CTTSSHHHHHHHHHHHHC
T ss_pred             CCCCCHHHHHHHHHHHcC
Confidence            479999999999988654

>2bwj_A Adenylate kinase 5; phosphoryl transfer reaction, transferase; HET: AMP; 2.3A {Homo sapiens}

Probab=89.62  E-value=0.16  Score=39.47  Aligned_cols=18  Identities=28%  Similarity=0.268  Sum_probs=15.4

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      ++|+||||+|+.+.....
T Consensus        20 ~~GsGKsT~a~~L~~~l~   37 (199)
T 2bwj_A           20 GPGSGKGTQCEKLVEKYG   37 (199)
T ss_dssp             CTTSSHHHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHHHhC
Confidence            479999999999998653

>2qz4_A Paraplegin; AAA+, SPG7, protease, ADP, structural genomics, structural G consortium, SGC, ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.22A {Homo sapiens}

Probab=89.54  E-value=0.15  Score=41.58  Aligned_cols=17  Identities=59%  Similarity=0.690  Sum_probs=15.2

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      +|+|||+||+.+++...
T Consensus        48 ~GtGKT~la~~la~~~~   64 (262)
T 2qz4_A           48 PGCGKTLLAKAVATEAQ   64 (262)
T ss_dssp             TTSSHHHHHHHHHHHHT
T ss_pred             CCCCHHHHHHHHHHHhC
Confidence            69999999999999764

>4eun_A Thermoresistant glucokinase; putative sugar kinase, enzyme function initiative, EFI, STRU genomics, transferase; 1.60A {Janibacter SP}

Probab=89.43  E-value=0.17  Score=39.71  Aligned_cols=17  Identities=47%  Similarity=0.665  Sum_probs=14.8

Q ss_pred             CCCCcHHHHHHHHHhhh
Q 041028            1 MGGIGKTTLAKEVARKA   17 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (283)
                      +.|+|||||++.+....
T Consensus        37 ~~GsGKSTl~~~L~~~~   53 (200)
T 4eun_A           37 VSGSGKTTIAHGVADET   53 (200)
T ss_dssp             CTTSCHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHhh
Confidence            36999999999998765

>2r62_A Cell division protease FTSH homolog; ATPase domain, ATP-binding, cell CELL division, hydrolase, membrane, metal-binding; 3.30A {Helicobacter pylori} PDB: 2r65_A*

Probab=89.39  E-value=0.18  Score=41.42  Aligned_cols=18  Identities=56%  Similarity=0.589  Sum_probs=15.7

Q ss_pred             CCCcHHHHHHHHHhhhcc
Q 041028            2 GGIGKTTLAKEVARKAKN   19 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~   19 (283)
                      +|+|||+||+.+++....
T Consensus        53 ~GtGKT~la~~la~~~~~   70 (268)
T 2r62_A           53 PGTGKTLLAKAVAGEAHV   70 (268)
T ss_dssp             SCSSHHHHHHHHHHHHTC
T ss_pred             CCCcHHHHHHHHHHHhCC
Confidence            699999999999997653

>2ph1_A Nucleotide-binding protein; alpha-beta protein, structural genomics, PSI-2, protein STRU initiative; 2.70A {Archaeoglobus fulgidus dsm 4304} PDB: 3kb1_A*

Probab=89.37  E-value=0.16  Score=41.72  Aligned_cols=31  Identities=19%  Similarity=0.291  Sum_probs=21.9

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQN   34 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~   34 (283)
                      ||+||||+|..++......+  ..++-|+....
T Consensus        28 GGvGKTT~a~nLA~~la~~G--~~VlliD~D~~   58 (262)
T 2ph1_A           28 GGVGKSTVTALLAVHYARQG--KKVGILDADFL   58 (262)
T ss_dssp             SCTTHHHHHHHHHHHHHHTT--CCEEEEECCSS
T ss_pred             CCCCHHHHHHHHHHHHHHCC--CeEEEEeCCCC
Confidence            89999999999988765432  23566666543

>1g3q_A MIND ATPase, cell division inhibitor; alpha-beta-alpha layered, protein-ADP complex, cell cycle, hydrolase; HET: ADP; 2.00A {Pyrococcus furiosus} SCOP: c.37.1.10 PDB: 1g3r_A* 1ion_A*

Probab=89.34  E-value=0.37  Score=38.63  Aligned_cols=30  Identities=20%  Similarity=0.343  Sum_probs=22.4

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQ   33 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~   33 (283)
                      ||+||||+|..++......+  ..++.|+...
T Consensus        12 gGvGKTt~a~~LA~~la~~g--~~VlliD~D~   41 (237)
T 1g3q_A           12 GGTGKTTVTANLSVALGDRG--RKVLAVDGDL   41 (237)
T ss_dssp             TTSSHHHHHHHHHHHHHHTT--CCEEEEECCT
T ss_pred             CCCCHHHHHHHHHHHHHhcC--CeEEEEeCCC
Confidence            89999999999998765432  2466677654

>1zd8_A GTP:AMP phosphotransferase mitochondrial; ATP:AMP phosphotransferase, myokinase, structural genomics, structural genomics consortium, SGC; 1.48A {Homo sapiens} PDB: 2ak3_A*

Probab=89.30  E-value=0.17  Score=40.51  Aligned_cols=17  Identities=24%  Similarity=0.372  Sum_probs=14.9

Q ss_pred             CCCCcHHHHHHHHHhhh
Q 041028            1 MGGIGKTTLAKEVARKA   17 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (283)
                      ++|+||||+|+.+....
T Consensus        15 ~~GsGKsT~a~~La~~l   31 (227)
T 1zd8_A           15 APGSGKGTVSSRITTHF   31 (227)
T ss_dssp             CTTSSHHHHHHHHHHHS
T ss_pred             CCCCCHHHHHHHHHHHc
Confidence            47999999999998865

>2pbr_A DTMP kinase, thymidylate kinase; transferase, nucleotide biosynthesis, TMP-binding, A binding, structural genomics, NPPSFA; 1.96A {Aquifex aeolicus}

Probab=89.29  E-value=0.18  Score=39.05  Aligned_cols=18  Identities=44%  Similarity=0.506  Sum_probs=15.5

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      +.|+||||+|+.+.+...
T Consensus         8 ~~GsGKsT~~~~L~~~l~   25 (195)
T 2pbr_A            8 IDGSGKTTQAKKLYEYLK   25 (195)
T ss_dssp             STTSCHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHH
Confidence            469999999999998763

>1zak_A Adenylate kinase; ATP:AMP-phosphotransferase, transferase; HET: AP5; 3.50A {Zea mays} SCOP: c.37.1.1 g.41.2.1

Probab=89.27  E-value=0.17  Score=40.33  Aligned_cols=18  Identities=22%  Similarity=0.185  Sum_probs=15.7

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      ++|+||||+|+.++....
T Consensus        13 ~~GsGKsT~~~~La~~l~   30 (222)
T 1zak_A           13 APASGKGTQCELIKTKYQ   30 (222)
T ss_dssp             STTSSHHHHHHHHHHHHC
T ss_pred             CCCCCHHHHHHHHHHHhC
Confidence            479999999999998764

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20

Probab=89.08  E-value=0.17  Score=41.34  Aligned_cols=17  Identities=59%  Similarity=0.712  Sum_probs=15.2

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      +|+||||||+.+++...
T Consensus        54 ~GtGKT~la~~la~~~~   70 (257)
T 1lv7_A           54 PGTGKTLLAKAIAGEAK   70 (257)
T ss_dssp             TTSCHHHHHHHHHHHHT
T ss_pred             CCCCHHHHHHHHHHHcC
Confidence            69999999999998764

>3fb4_A Adenylate kinase; psychrophIle, phosphotransferase, ATP-binding, nucleotide-binding, transferase; HET: AP5; 2.00A {Marinibacillus marinus}

Probab=89.03  E-value=0.19  Score=39.86  Aligned_cols=18  Identities=33%  Similarity=0.497  Sum_probs=15.2

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      ++|+||||+|+.+.....
T Consensus         8 ~~GsGKsT~a~~L~~~~~   25 (216)
T 3fb4_A            8 LPGAGKGTQAEQIIEKYE   25 (216)
T ss_dssp             STTSSHHHHHHHHHHHHC
T ss_pred             CCCCCHHHHHHHHHHHhC
Confidence            469999999999987653

>2wwf_A Thymidilate kinase, putative; transferase, malaria; HET: TMP ADP; 1.89A {Plasmodium falciparum} PDB: 2wwg_A* 2wwh_A* 2wwi_A*

Probab=88.98  E-value=0.19  Score=39.59  Aligned_cols=24  Identities=25%  Similarity=0.259  Sum_probs=18.4

Q ss_pred             CCCCcHHHHHHHHHhhhccCCCCCe
Q 041028            1 MGGIGKTTLAKEVARKAKNGKLFDQ   25 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~~~Fd~   25 (283)
                      +.|+||||+|+.+....... +++.
T Consensus        18 ~~GsGKST~~~~L~~~l~~~-~~~~   41 (212)
T 2wwf_A           18 LDRSGKSTQSKLLVEYLKNN-NVEV   41 (212)
T ss_dssp             STTSSHHHHHHHHHHHHHHT-TCCE
T ss_pred             CCCCCHHHHHHHHHHHHHHc-CCcE
Confidence            36999999999999876543 3455

>1qf9_A UMP/CMP kinase, protein (uridylmonophosphate/cytidylmonophosphate kinase); nucleoside monophosphate kinase, NMP kinase; HET: ADP C5P; 1.70A {Dictyostelium discoideum} SCOP: c.37.1.1 PDB: 1uke_A* 2ukd_A* 3ukd_A* 4ukd_A* 5ukd_A*

Probab=88.91  E-value=0.19  Score=38.71  Aligned_cols=18  Identities=28%  Similarity=0.285  Sum_probs=15.2

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      +.|+||||+|+.+.....
T Consensus        14 ~~GsGKsT~~~~L~~~l~   31 (194)
T 1qf9_A           14 GPGSGKGTQCANIVRDFG   31 (194)
T ss_dssp             STTSSHHHHHHHHHHHHC
T ss_pred             CCCCCHHHHHHHHHHHhC
Confidence            479999999999988653

>2bdt_A BH3686; alpha-beta protein, structural genomics, PSI, protein struct initiative, northeast structural genomics consortium, NESG, function; 2.40A {Bacillus halodurans} SCOP: c.37.1.25

Probab=88.90  E-value=0.19  Score=38.97  Aligned_cols=15  Identities=40%  Similarity=0.623  Sum_probs=13.3

Q ss_pred             CCCCcHHHHHHHHHh
Q 041028            1 MGGIGKTTLAKEVAR   15 (283)
Q Consensus         1 mgGiGKTtLA~~v~~   15 (283)
                      ..|+|||||++.+..
T Consensus        10 ~~GaGKSTl~~~L~~   24 (189)
T 2bdt_A           10 PAGVGKSTTCKRLAA   24 (189)
T ss_dssp             STTSSHHHHHHHHHH
T ss_pred             CCCCcHHHHHHHHhc
Confidence            369999999999976

>2woo_A ATPase GET3; tail-anchored, membrane protein, targeting factor, endoplasmic reticulum, TRC40, ATP-binding, golgi apparatus; 3.01A {Schizosaccharomyces pombe}

Probab=88.89  E-value=0.39  Score=41.02  Aligned_cols=30  Identities=23%  Similarity=0.395  Sum_probs=20.9

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQ   33 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~   33 (283)
                      ||+||||+|..++......+ + .++-|+...
T Consensus        28 GGvGKTTva~~LA~~lA~~G-~-rVllvD~D~   57 (329)
T 2woo_A           28 GGVGKTTTSCSLAIQMSKVR-S-SVLLISTDP   57 (329)
T ss_dssp             SSSSHHHHHHHHHHHHHTSS-S-CEEEEECCT
T ss_pred             CCCcHHHHHHHHHHHHHHCC-C-eEEEEECCC
Confidence            89999999999988765432 2 345555543

>2oze_A ORF delta'; para, walker type atpases, DNA segregation, PSM19035, plasmid, DNA binding protein; HET: AGS EPE; 1.83A {Streptococcus pyogenes}

Probab=88.79  E-value=0.19  Score=42.05  Aligned_cols=31  Identities=19%  Similarity=0.343  Sum_probs=21.6

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQN   34 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~   34 (283)
                      ||+||||+|..++......+  ..++-|+....
T Consensus        46 GGvGKTT~a~nLA~~la~~G--~rVlliD~D~q   76 (298)
T 2oze_A           46 GGVGKSKLSTMFAYLTDKLN--LKVLMIDKDLQ   76 (298)
T ss_dssp             SSSSHHHHHHHHHHHHHHTT--CCEEEEEECTT
T ss_pred             CCchHHHHHHHHHHHHHhCC--CeEEEEeCCCC
Confidence            89999999999988765332  23555665543

>1d2n_A N-ethylmaleimide-sensitive fusion protein; hexamerization domain, ATPase, transport; HET: ANP; 1.75A {Cricetulus griseus} SCOP: c.37.1.20 PDB: 1nsf_A*

Probab=88.77  E-value=0.19  Score=41.56  Aligned_cols=17  Identities=35%  Similarity=0.477  Sum_probs=15.1

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      +|+|||+||+.+++...
T Consensus        73 ~GtGKT~la~~ia~~~~   89 (272)
T 1d2n_A           73 PHSGKTALAAKIAEESN   89 (272)
T ss_dssp             TTSSHHHHHHHHHHHHT
T ss_pred             CCCcHHHHHHHHHHHhC
Confidence            69999999999999753

>3be4_A Adenylate kinase; malaria, cryptosporidium parvum nonprotein inhibitors, nucleotide-binding, transferase; HET: AP5; 1.60A {Cryptosporidium parvum iowa II}

Probab=88.76  E-value=0.2  Score=39.86  Aligned_cols=18  Identities=22%  Similarity=0.246  Sum_probs=15.6

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      ++|+||||+|+.+.....
T Consensus        13 ~~GsGKsT~a~~La~~l~   30 (217)
T 3be4_A           13 APGSGKGTQCEFIKKEYG   30 (217)
T ss_dssp             CTTSSHHHHHHHHHHHHC
T ss_pred             CCCCCHHHHHHHHHHHhC
Confidence            479999999999998763

>3kl4_A SRP54, signal recognition 54 kDa protein; signal recognition particle, SRP, SRP54, FFH, signal sequenc peptide; 3.50A {Sulfolobus solfataricus} PDB: 1qzx_A 1qzw_A

Probab=88.71  E-value=1.8  Score=38.53  Aligned_cols=74  Identities=16%  Similarity=0.161  Sum_probs=40.3

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeC-CCCCHHHHHHHHHHHhCCCCC----cCCHhhhHH-hHHHHc-cCCcEE
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVS-QNPNIKKIQGEIAFKLGLKFD----EESESGRTR-SPWSRL-KKEKLQ   74 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~-~~~~~~~l~~~i~~~l~~~~~----~~~~~~~~~-~l~~~L-~~kr~L   74 (283)
                      +|+||||++..++......+ . .++.+... ..+...+-+......++.+..    ..+...... .+.... .+..++
T Consensus       106 ~GsGKTTt~~kLA~~l~~~G-~-kVllv~~D~~r~~a~eqL~~~~~~~gv~~~~~~~~~dp~~i~~~al~~a~~~~~Dvv  183 (433)
T 3kl4_A          106 QGSGKTTTAGKLAYFYKKRG-Y-KVGLVAADVYRPAAYDQLLQLGNQIGVQVYGEPNNQNPIEIAKKGVDIFVKNKMDII  183 (433)
T ss_dssp             TTSCHHHHHHHHHHHHHHTT-C-CEEEEEECCSCHHHHHHHHHHHHTTTCCEECCTTCSCHHHHHHHHHHHTTTTTCSEE
T ss_pred             CCCCHHHHHHHHHHHHHHcC-C-eEEEEecCccchhHHHHHHHHHHhcCCceeeccccCCHHHHHHHHHHHHHhcCCCEE
Confidence            69999999999988765432 2 34444443 222334455556666666422    123333332 333332 245788


Q ss_pred             EEc
Q 041028           75 IIC   77 (283)
Q Consensus        75 lV~   77 (283)
                      ||+
T Consensus       184 IID  186 (433)
T 3kl4_A          184 IVD  186 (433)
T ss_dssp             EEE
T ss_pred             EEE
Confidence            883

>1ukz_A Uridylate kinase; transferase; HET: ADP AMP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1uky_A*

Probab=88.70  E-value=0.2  Score=39.20  Aligned_cols=17  Identities=24%  Similarity=0.317  Sum_probs=14.7

Q ss_pred             CCCCcHHHHHHHHHhhh
Q 041028            1 MGGIGKTTLAKEVARKA   17 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (283)
                      +.|+||||+|+.+.+..
T Consensus        23 ~~GsGKsT~~~~L~~~~   39 (203)
T 1ukz_A           23 GPGAGKGTQCEKLVKDY   39 (203)
T ss_dssp             STTSSHHHHHHHHHHHS
T ss_pred             CCCCCHHHHHHHHHHHc
Confidence            46999999999998764

>1byi_A Dethiobiotin synthase; biotin synthesis, cyclo-ligase, ligase; 0.97A {Escherichia coli} SCOP: c.37.1.10 PDB: 1bs1_A* 1a82_A 1dad_A* 1dae_A* 1daf_A* 1dag_A* 1dah_A* 1dai_A* 1dak_A* 1dam_A* 1dbs_A 1dts_A

Probab=88.63  E-value=0.21  Score=39.80  Aligned_cols=19  Identities=26%  Similarity=0.319  Sum_probs=15.9

Q ss_pred             CCCcHHHHHHHHHhhhccC
Q 041028            2 GGIGKTTLAKEVARKAKNG   20 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~   20 (283)
                      ||+||||+|..++.....+
T Consensus        11 gGvGKTt~a~nLa~~la~~   29 (224)
T 1byi_A           11 TEVGKTVASCALLQAAKAA   29 (224)
T ss_dssp             TTSCHHHHHHHHHHHHHHT
T ss_pred             CCCCHHHHHHHHHHHHHHC
Confidence            8999999999998876543

>3dl0_A Adenylate kinase; phosphotransferase, zinc coordination, ATP-binding, binding, nucleotide biosynthesis, nucleotide-binding, trans; HET: AP5; 1.58A {Bacillus subtilis} PDB: 1p3j_A* 2ori_A* 2eu8_A* 2oo7_A* 2p3s_A* 2qaj_A* 2osb_A* 3dkv_A* 1zin_A* 1zio_A* 1zip_A* 1s3g_A*

Probab=88.60  E-value=0.21  Score=39.64  Aligned_cols=17  Identities=29%  Similarity=0.458  Sum_probs=14.7

Q ss_pred             CCCCcHHHHHHHHHhhh
Q 041028            1 MGGIGKTTLAKEVARKA   17 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (283)
                      .+|+||||+|+.+....
T Consensus         8 ~~GsGKsT~a~~L~~~~   24 (216)
T 3dl0_A            8 LPGAGKGTQGERIVEKY   24 (216)
T ss_dssp             STTSSHHHHHHHHHHHS
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            46999999999998765

>1nn5_A Similar to deoxythymidylate kinase (thymidylate K; P-loop, D4TMP, transferase; HET: 2DT ANP; 1.50A {Homo sapiens} SCOP: c.37.1.1 PDB: 1e2e_A* 1e2d_A* 1e2g_A* 1e2q_A* 1e99_A* 1e9a_A* 1e9b_A* 1nmx_A* 1nmz_A* 1nn0_A* 1nn1_A* 1e2f_A* 1nn3_A* 2xx3_A* 1e9c_A* 1e9d_A* 1e9e_A* 1e98_A* 1nmy_A* 1e9f_A*

Probab=88.59  E-value=0.21  Score=39.40  Aligned_cols=24  Identities=13%  Similarity=0.144  Sum_probs=18.3

Q ss_pred             CCCCcHHHHHHHHHhhhccCCCCCe
Q 041028            1 MGGIGKTTLAKEVARKAKNGKLFDQ   25 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~~~Fd~   25 (283)
                      +.|+||||+|+.+....... .++.
T Consensus        17 ~~GsGKsT~~~~L~~~l~~~-~~~v   40 (215)
T 1nn5_A           17 VDRAGKSTQSRKLVEALCAA-GHRA   40 (215)
T ss_dssp             STTSSHHHHHHHHHHHHHHT-TCCE
T ss_pred             CCCCCHHHHHHHHHHHHHHc-CCcE
Confidence            46999999999999876543 3454

>3lda_A DNA repair protein RAD51; DNA binding protein, ATP-binding, DNA damage, DNA recombinat repair, nucleotide-binding; HET: DNA; 2.50A {Saccharomyces cerevisiae} PDB: 1szp_A*

Probab=88.59  E-value=0.98  Score=39.73  Aligned_cols=48  Identities=17%  Similarity=0.161  Sum_probs=31.6

Q ss_pred             CCCcHHHHHHHHHhhhccC----CCCCeEEEEEeCCCCCHHHHHHHHHHHhCC
Q 041028            2 GGIGKTTLAKEVARKAKNG----KLFDQIVFTEVSQNPNIKKIQGEIAFKLGL   50 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~----~~Fd~~~wv~v~~~~~~~~l~~~i~~~l~~   50 (283)
                      +|+|||||+..++-.....    ..-..++|++....++...+ ..+++.++.
T Consensus       187 sGsGKTTLl~~la~~~~~p~~~Gg~~~~viyid~E~~~~~~rl-~~~a~~~gl  238 (400)
T 3lda_A          187 FRTGKSQLCHTLAVTCQIPLDIGGGEGKCLYIDTEGTFRPVRL-VSIAQRFGL  238 (400)
T ss_dssp             TTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEESSSCCCHHHH-HHHHHHTTC
T ss_pred             CCCChHHHHHHHHHHhccCcccCCCCCcEEEEeCCCccCHHHH-HHHHHHcCC
Confidence            6999999999876432211    01246889988777666554 446677765

>3pg5_A Uncharacterized protein; structural genomics, PSI-biology, protein structure initiati northeast structural genomics consortium, NESG; 3.30A {Corynebacterium diphtheriae}

Probab=88.56  E-value=0.33  Score=42.06  Aligned_cols=37  Identities=27%  Similarity=0.485  Sum_probs=25.7

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHH
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKI   40 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l   40 (283)
                      ||+||||+|..++......+  ..++-|+.....+....
T Consensus        11 GGvGKTT~a~nLA~~LA~~G--~rVLlID~D~q~~~~~~   47 (361)
T 3pg5_A           11 GGVGKTTLSTNVAHYFALQG--KRVLYVDCDPQCNATQL   47 (361)
T ss_dssp             CCHHHHHHHHHHHHHHHHTT--CCEEEEECCTTCTTHHH
T ss_pred             CCCcHHHHHHHHHHHHHhCC--CcEEEEEcCCCCChhhh
Confidence            89999999999988765332  25677777755444433

>2if2_A Dephospho-COA kinase; alpha-beta protein, structural genomics, PSI-2, protein STRU initiative, northeast structural genomics consortium, NESG; 3.00A {Aquifex aeolicus}

Probab=88.51  E-value=0.21  Score=39.19  Aligned_cols=15  Identities=33%  Similarity=0.361  Sum_probs=13.6

Q ss_pred             CCCCcHHHHHHHHHh
Q 041028            1 MGGIGKTTLAKEVAR   15 (283)
Q Consensus         1 mgGiGKTtLA~~v~~   15 (283)
                      +.|+||||+++.+..
T Consensus         9 ~~GsGKSTl~~~L~~   23 (204)
T 2if2_A            9 NIGCGKSTVAQMFRE   23 (204)
T ss_dssp             CTTSSHHHHHHHHHH
T ss_pred             CCCcCHHHHHHHHHH
Confidence            369999999999987

>1in4_A RUVB, holliday junction DNA helicase RUVB; AAA+-class ATPase, winged-helix domain, ATP hydrolysis, walker A, walker B, sensor 1, sensor 2; HET: ADP; 1.60A {Thermotoga maritima} SCOP: a.4.5.11 c.37.1.20 PDB: 1in5_A* 1in6_A* 1in8_A* 1in7_A* 1j7k_A*

Probab=88.50  E-value=0.19  Score=43.11  Aligned_cols=17  Identities=47%  Similarity=0.661  Sum_probs=15.2

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      +|+||||||+.+++...
T Consensus        60 ~G~GKTTLa~~ia~~l~   76 (334)
T 1in4_A           60 PGLGKTTLAHIIASELQ   76 (334)
T ss_dssp             TTSSHHHHHHHHHHHHT
T ss_pred             CCCcHHHHHHHHHHHhC
Confidence            69999999999999763

>3fkq_A NTRC-like two-domain protein; RER070207001320, structural GE joint center for structural genomics, JCSG, protein structu initiative, PSI-2; HET: ATP 2PE; 2.10A {Eubacterium rectale}

Probab=88.44  E-value=0.31  Score=42.39  Aligned_cols=33  Identities=24%  Similarity=0.419  Sum_probs=23.1

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPN   36 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~   36 (283)
                      ||+||||+|..++......+  ..++-|+.....+
T Consensus       153 GGvGKTT~a~nLA~~La~~g--~rVlliD~D~~~~  185 (373)
T 3fkq_A          153 GGVGTSTVAAACAIAHANMG--KKVFYLNIEQCGT  185 (373)
T ss_dssp             TTSSHHHHHHHHHHHHHHHT--CCEEEEECCTTCC
T ss_pred             CCChHHHHHHHHHHHHHhCC--CCEEEEECCCCCC
Confidence            89999999999887754331  2467777663333

>2woj_A ATPase GET3; tail-anchored, membrane protein, targeting factor, endoplasmic reticulum, TRC40, ATP-binding, golgi apparatus; HET: ADP; 1.99A {Saccharomyces cerevisiae} PDB: 3h84_A 3zs8_A 3zs9_A* 3sja_A 3sjb_A 3sjc_A 3sjd_A* 3idq_A 3a36_A 3a37_A*

Probab=88.43  E-value=0.56  Score=40.54  Aligned_cols=38  Identities=24%  Similarity=0.363  Sum_probs=25.7

Q ss_pred             CCCcHHHHHHHHHhhhc--cCCCCCeEEEEEeCCCCCHHHHH
Q 041028            2 GGIGKTTLAKEVARKAK--NGKLFDQIVFTEVSQNPNIKKIQ   41 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~--~~~~Fd~~~wv~v~~~~~~~~l~   41 (283)
                      ||+||||+|..++....  ..+  ..++-|+.....++..++
T Consensus        27 GGvGKTTvaanLA~~lA~~~~G--~rVLLvD~D~~~~l~~~l   66 (354)
T 2woj_A           27 GGVGKTTSSCSIAIQMALSQPN--KQFLLISTDPAHNLSDAF   66 (354)
T ss_dssp             TTSSHHHHHHHHHHHHHHHCTT--SCEEEEECCSSCCHHHHH
T ss_pred             CCCcHHHHHHHHHHHHHHhcCC--CeEEEEECCCCCCHHHHh
Confidence            89999999999887765  332  245666665555555443

>1l8q_A Chromosomal replication initiator protein DNAA; AAA+, helix-turn-helix, nucleotide-binding, DNA binding, REP initiation, DNA binding protein; HET: ADP; 2.70A {Aquifex aeolicus} SCOP: a.4.12.2 c.37.1.20 PDB: 3r8f_A* 2hcb_A*

Probab=88.39  E-value=0.2  Score=42.54  Aligned_cols=18  Identities=39%  Similarity=0.510  Sum_probs=15.7

Q ss_pred             CCCcHHHHHHHHHhhhcc
Q 041028            2 GGIGKTTLAKEVARKAKN   19 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~   19 (283)
                      +|+||||||+.+++....
T Consensus        46 ~GtGKT~la~~i~~~~~~   63 (324)
T 1l8q_A           46 VGTGKTHLLQAAGNEAKK   63 (324)
T ss_dssp             SSSSHHHHHHHHHHHHHH
T ss_pred             CCCcHHHHHHHHHHHHHH
Confidence            699999999999997643

>1gvn_B Zeta; postsegregational killing system, plasmid; 1.95A {Streptococcus pyogenes} SCOP: c.37.1.21 PDB: 3q8x_B*

Probab=88.38  E-value=0.18  Score=42.33  Aligned_cols=17  Identities=29%  Similarity=0.442  Sum_probs=14.7

Q ss_pred             CCCCcHHHHHHHHHhhh
Q 041028            1 MGGIGKTTLAKEVARKA   17 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (283)
                      ++|+||||+|+.+....
T Consensus        41 ~sGsGKSTla~~L~~~~   57 (287)
T 1gvn_B           41 QPGSGKTSLRSAIFEET   57 (287)
T ss_dssp             CTTSCTHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            47999999999998754

>3io3_A DEHA2D07832P; chaperone, membrane traffic, ATPase; HET: ADP; 1.80A {Debaryomyces hansenii}

Probab=88.38  E-value=0.45  Score=41.08  Aligned_cols=35  Identities=29%  Similarity=0.479  Sum_probs=22.8

Q ss_pred             CCCcHHHHHHHHHhhhc--cCCCCCeEEEEEeCCCCCHH
Q 041028            2 GGIGKTTLAKEVARKAK--NGKLFDQIVFTEVSQNPNIK   38 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~--~~~~Fd~~~wv~v~~~~~~~   38 (283)
                      ||+||||+|..++....  ..+  ..++-|+.....++.
T Consensus        27 GGvGKTt~a~~lA~~la~~~~g--~~vllid~D~~~~l~   63 (348)
T 3io3_A           27 GGVGKTTTSSSVAVQLALAQPN--EQFLLISTDPAHNLS   63 (348)
T ss_dssp             TTSSHHHHHHHHHHHHHHHCTT--SCEEEEECCSSCHHH
T ss_pred             CCCcHHHHHHHHHHHHHHhcCC--CeEEEEECCCCCChH
Confidence            89999999999887655  321  235556655443333

>1e4v_A Adenylate kinase; transferase(phosphotransferase); HET: AP5; 1.85A {Escherichia coli} SCOP: c.37.1.1 g.41.2.1 PDB: 1e4y_A* 1ake_A* 1ank_A* 2eck_A* 3hpq_A* 4ake_A 3hpr_A*

Probab=88.34  E-value=0.22  Score=39.48  Aligned_cols=17  Identities=29%  Similarity=0.139  Sum_probs=15.1

Q ss_pred             CCCCcHHHHHHHHHhhh
Q 041028            1 MGGIGKTTLAKEVARKA   17 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (283)
                      ++|+||||+|+.+....
T Consensus         8 ~~GsGKsT~a~~L~~~~   24 (214)
T 1e4v_A            8 APVAGKGTQAQFIMEKY   24 (214)
T ss_dssp             STTSSHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            47999999999998865

>4a74_A DNA repair and recombination protein RADA; hydrolase, recombinase; HET: DNA ANP; 1.48A {Pyrococcus furiosus} PDB: 4a6x_A* 4a6p_A* 4a7o_A*

Probab=88.34  E-value=0.79  Score=36.27  Aligned_cols=47  Identities=26%  Similarity=0.268  Sum_probs=28.4

Q ss_pred             CCCcHHHHHHHHHhhhccC---C-CCCeEEEEEeCCCCCHHHHHHHHHHHhC
Q 041028            2 GGIGKTTLAKEVARKAKNG---K-LFDQIVFTEVSQNPNIKKIQGEIAFKLG   49 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~---~-~Fd~~~wv~v~~~~~~~~l~~~i~~~l~   49 (283)
                      .|+|||||++.++......   . .-..++|+.-...+.... ...+.+..+
T Consensus        34 nGsGKSTll~~l~g~~~~~~~~g~~~~~~i~~~~~~~~~~~~-i~~~~~~~~   84 (231)
T 4a74_A           34 FGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDTENTFRPER-IREIAQNRG   84 (231)
T ss_dssp             TTSSHHHHHHHHHHHTTSCGGGTCCSCEEEEEESSSCCCHHH-HHHHHHHTT
T ss_pred             CCCCHHHHHHHHHHHHhcccccCCCCCEEEEEECCCCCCHHH-HHHHHHHcC
Confidence            5999999999998743321   1 124678887655444333 334445444

>1ixz_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 2.20A {Thermus thermophilus} SCOP: c.37.1.20 PDB: 1iy0_A* 1iy1_A*

Probab=88.29  E-value=0.21  Score=40.73  Aligned_cols=17  Identities=53%  Similarity=0.790  Sum_probs=15.1

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      +|+||||||+.+++...
T Consensus        58 ~G~GKTtl~~~i~~~~~   74 (254)
T 1ixz_A           58 PGVGKTHLARAVAGEAR   74 (254)
T ss_dssp             TTSSHHHHHHHHHHHTT
T ss_pred             CCCCHHHHHHHHHHHhC
Confidence            69999999999998764

>1sxj_B Activator 1 37 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=88.23  E-value=0.2  Score=42.20  Aligned_cols=38  Identities=26%  Similarity=0.276  Sum_probs=23.2

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHH
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKK   39 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~   39 (283)
                      +|+||||+|+.+++.......-...++++.+.......
T Consensus        51 ~G~GKt~la~~l~~~l~~~~~~~~~~~~~~~~~~~~~~   88 (323)
T 1sxj_B           51 PGIGKTTSVHCLAHELLGRSYADGVLELNASDDRGIDV   88 (323)
T ss_dssp             TTSSHHHHHHHHHHHHHGGGHHHHEEEECTTSCCSHHH
T ss_pred             CCCCHHHHHHHHHHHhcCCcccCCEEEecCccccChHH
Confidence            69999999999998754321112345555554444433

>2xxa_A Signal recognition particle protein; protein transport, RNA/RNA binding protein, hydrolase, gtpas; HET: GCP; 3.94A {Escherichia coli} PDB: 2j28_9

Probab=88.21  E-value=2.4  Score=37.65  Aligned_cols=75  Identities=15%  Similarity=0.177  Sum_probs=40.3

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCC-CCCHHHHHHHHHHHhCCCCC----cCCHhhhHHhHHHHc--cCCcEE
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQ-NPNIKKIQGEIAFKLGLKFD----EESESGRTRSPWSRL--KKEKLQ   74 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~-~~~~~~l~~~i~~~l~~~~~----~~~~~~~~~~l~~~L--~~kr~L   74 (283)
                      +|+||||++..++.....+... .++-|+... .....+.+.......+.+.-    ..+..+.....-..+  .+-.++
T Consensus       109 ~GvGKTT~a~~LA~~l~~~~G~-kVllvd~D~~r~~a~~ql~~~~~~~~l~v~~~~~~~dp~~i~~~~l~~~~~~~~D~V  187 (433)
T 2xxa_A          109 QGAGKTTSVGKLGKFLREKHKK-KVLVVSADVYRPAAIKQLETLAEQVGVDFFPSDVGQKPVDIVNAALKEAKLKFYDVL  187 (433)
T ss_dssp             TTSSHHHHHHHHHHHHHHTSCC-CEEEEECCCSSTTHHHHHHHHHHHHTCEECCCCSSSCHHHHHHHHHHHHHHTTCSEE
T ss_pred             CCCCHHHHHHHHHHHHHHhcCC-eEEEEecCCCCccHHHHHHhhcccCCeeEEeCCCCCCHHHHHHHHHHHHHhCCCCEE
Confidence            7999999999999876644112 345555542 33444444444555554311    123333322222233  345788


Q ss_pred             EEc
Q 041028           75 IIC   77 (283)
Q Consensus        75 lV~   77 (283)
                      ||+
T Consensus       188 IID  190 (433)
T 2xxa_A          188 LVD  190 (433)
T ss_dssp             EEE
T ss_pred             EEE
Confidence            884

>1ls1_A Signal recognition particle protein; FFH, SRP54, SRP, GTPase, ultrahigh resolution, protein transport; 1.10A {Thermus aquaticus} SCOP: a.24.13.1 c.37.1.10 PDB: 1jpn_B* 1jpj_A* 1ry1_U* 2j45_A* 1o87_A* 2c04_A* 2j46_A* 1rj9_B* 2c03_A* 2j7p_A* 1okk_A* 2cnw_A* 1ng1_A* 2xkv_A 3ng1_A 1ffh_A 2ng1_A*

Probab=88.20  E-value=2  Score=35.98  Aligned_cols=74  Identities=19%  Similarity=0.144  Sum_probs=39.7

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCC-CHHHHHHHHHHHhCCCCC----cCCHhhhH-HhHHHHc-cCCcEE
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNP-NIKKIQGEIAFKLGLKFD----EESESGRT-RSPWSRL-KKEKLQ   74 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~-~~~~l~~~i~~~l~~~~~----~~~~~~~~-~~l~~~L-~~kr~L   74 (283)
                      +|+||||++..++......+  ..+.++...-.. .....+..+....+.+.-    ..+..+.. ..+.... .+..++
T Consensus       107 ~G~GKTT~~~~la~~~~~~~--~~v~l~~~d~~~~~~~~ql~~~~~~~~l~~~~~~~~~~p~~l~~~~l~~~~~~~~D~v  184 (295)
T 1ls1_A          107 QGSGKTTTAAKLALYYKGKG--RRPLLVAADTQRPAAREQLRLLGEKVGVPVLEVMDGESPESIRRRVEEKARLEARDLI  184 (295)
T ss_dssp             TTTTHHHHHHHHHHHHHHTT--CCEEEEECCSSCHHHHHHHHHHHHHHTCCEEECCTTCCHHHHHHHHHHHHHHHTCCEE
T ss_pred             CCCCHHHHHHHHHHHHHHcC--CeEEEecCCcccHhHHHHHHHhcccCCeEEEEcCCCCCHHHHHHHHHHHHHhCCCCEE
Confidence            79999999999988765431  234555443221 122223445555555421    12333333 2444443 566888


Q ss_pred             EEc
Q 041028           75 IIC   77 (283)
Q Consensus        75 lV~   77 (283)
                      ||+
T Consensus       185 iiD  187 (295)
T 1ls1_A          185 LVD  187 (295)
T ss_dssp             EEE
T ss_pred             EEe
Confidence            883

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=88.18  E-value=0.14  Score=38.39  Aligned_cols=30  Identities=17%  Similarity=0.275  Sum_probs=21.0

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQ   33 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~   33 (283)
                      .|+|||||++.+++.....+ + .+++++...
T Consensus        45 ~G~GKTtL~~~i~~~~~~~g-~-~~~~~~~~~   74 (149)
T 2kjq_A           45 EGAGKSHLLQAWVAQALEAG-K-NAAYIDAAS   74 (149)
T ss_dssp             STTTTCHHHHHHHHHHHTTT-C-CEEEEETTT
T ss_pred             CCCCHHHHHHHHHHHHHhcC-C-cEEEEcHHH
Confidence            59999999999999765321 2 256666543

>1ak2_A Adenylate kinase isoenzyme-2; nucleoside monophosphate kinase, phosphotransferase; 1.92A {Bos taurus} SCOP: c.37.1.1 g.41.2.1 PDB: 2ak2_A 2c9y_A*

Probab=88.17  E-value=0.23  Score=40.02  Aligned_cols=18  Identities=33%  Similarity=0.316  Sum_probs=15.6

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      +.|+||||+|+.+.+...
T Consensus        24 ~~GsGKsT~a~~La~~l~   41 (233)
T 1ak2_A           24 PPGAGKGTQAPKLAKNFC   41 (233)
T ss_dssp             CTTSSHHHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHHHhC
Confidence            479999999999998764

>1hyq_A MIND, cell division inhibitor (MIND-1); MINC, FTSZ, bacterial cell division, cell cycle; 2.60A {Archaeoglobus fulgidus} SCOP: c.37.1.10

Probab=88.12  E-value=0.48  Score=38.68  Aligned_cols=30  Identities=20%  Similarity=0.353  Sum_probs=22.1

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQ   33 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~   33 (283)
                      ||+||||+|..++......+  ..++-|+...
T Consensus        12 gGvGKTt~a~~LA~~la~~g--~~VlliD~D~   41 (263)
T 1hyq_A           12 GGTGKTTITANLGVALAQLG--HDVTIVDADI   41 (263)
T ss_dssp             SCSCHHHHHHHHHHHHHHTT--CCEEEEECCC
T ss_pred             CCCCHHHHHHHHHHHHHhCC--CcEEEEECCC
Confidence            89999999999988765432  2456677654

>3gmt_A Adenylate kinase; ssgcid, ATP-BIN cytoplasm, nucleotide biosynthesis, nucleotide-BIND transferase, structural genomics; 2.10A {Burkholderia pseudomallei 1710B}

Probab=88.08  E-value=1.3  Score=35.80  Aligned_cols=18  Identities=33%  Similarity=0.285  Sum_probs=15.7

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      ++|+||||+|+.+.....
T Consensus        16 ~pGsGKsT~a~~L~~~~g   33 (230)
T 3gmt_A           16 APGAGKGTQANFIKEKFG   33 (230)
T ss_dssp             CTTSCHHHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHHHhC
Confidence            479999999999998764

>1cr0_A DNA primase/helicase; RECA-type protein fold, transferase; HET: DNA; 2.30A {Enterobacteria phage T7} SCOP: c.37.1.11 PDB: 1cr1_A* 1cr2_A* 1cr4_A* 1e0j_A* 1e0k_A*

Probab=88.07  E-value=0.76  Score=38.34  Aligned_cols=43  Identities=12%  Similarity=0.265  Sum_probs=27.8

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCC-eEEEEEeCCCCCHHHHHHHHHHHh
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFD-QIVFTEVSQNPNIKKIQGEIAFKL   48 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd-~~~wv~v~~~~~~~~l~~~i~~~l   48 (283)
                      +|+|||||++.++......  -. .++|++...  +..++...++...
T Consensus        44 ~G~GKTTl~~~ia~~~~~~--~G~~v~~~~~e~--~~~~~~~r~~~~~   87 (296)
T 1cr0_A           44 SGMGKSTFVRQQALQWGTA--MGKKVGLAMLEE--SVEETAEDLIGLH   87 (296)
T ss_dssp             TTSSHHHHHHHHHHHHHHT--SCCCEEEEESSS--CHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHH--cCCeEEEEeCcC--CHHHHHHHHHHHH
Confidence            6999999999998876543  22 466766543  4455555555443

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=88.03  E-value=0.22  Score=41.61  Aligned_cols=17  Identities=47%  Similarity=0.583  Sum_probs=15.1

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      +|+||||||+.+++...
T Consensus        63 ~GtGKT~la~~la~~~~   79 (297)
T 3b9p_A           63 PGNGKTLLARAVATECS   79 (297)
T ss_dssp             SSSCHHHHHHHHHHHTT
T ss_pred             CCCCHHHHHHHHHHHhC
Confidence            69999999999998754

>2v54_A DTMP kinase, thymidylate kinase; nucleotide biosynthesis, ATP-binding, nucleotide-binding, poxvirus, transferase; HET: TYD POP; 2.4A {Vaccinia virus copenhagen} PDB: 2w0s_A*

Probab=88.01  E-value=0.23  Score=38.81  Aligned_cols=17  Identities=24%  Similarity=0.302  Sum_probs=14.9

Q ss_pred             CCCCcHHHHHHHHHhhh
Q 041028            1 MGGIGKTTLAKEVARKA   17 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (283)
                      +.|+||||+++.+....
T Consensus        12 ~~GsGKsT~~~~L~~~l   28 (204)
T 2v54_A           12 LDKSGKTTQCMNIMESI   28 (204)
T ss_dssp             CTTSSHHHHHHHHHHTS
T ss_pred             CCCCCHHHHHHHHHHHH
Confidence            46999999999998865

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=87.96  E-value=0.32  Score=41.19  Aligned_cols=28  Identities=21%  Similarity=0.277  Sum_probs=20.0

Q ss_pred             CCCcHHHHHHHHHhhhc-cCCCCCeEEEEEe
Q 041028            2 GGIGKTTLAKEVARKAK-NGKLFDQIVFTEV   31 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~-~~~~Fd~~~wv~v   31 (283)
                      +|+|||+||..+++... ..+ + .+.++++
T Consensus       161 ~GtGKT~La~aia~~~~~~~g-~-~v~~~~~  189 (308)
T 2qgz_A          161 MGIGKSYLLAAMAHELSEKKG-V-STTLLHF  189 (308)
T ss_dssp             TTSSHHHHHHHHHHHHHHHSC-C-CEEEEEH
T ss_pred             CCCCHHHHHHHHHHHHHHhcC-C-cEEEEEH
Confidence            59999999999999765 432 2 3445544

>3fwy_A Light-independent protochlorophyllide reductase I ATP-binding protein; BCHL, electron donor, DPOR, Fe protein, nitrogenase; HET: ADP; 1.63A {Rhodobacter sphaeroides 2}

Probab=87.96  E-value=0.2  Score=42.60  Aligned_cols=30  Identities=20%  Similarity=0.266  Sum_probs=21.2

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQ   33 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~   33 (283)
                      |||||||.|..++--....+.  .++-|....
T Consensus        57 GGVGKTTtavNLA~aLA~~Gk--kVllID~Dp   86 (314)
T 3fwy_A           57 GGIGKSTTSSNLSAAFSILGK--RVLQIGCDP   86 (314)
T ss_dssp             TTSSHHHHHHHHHHHHHHTTC--CEEEEEESS
T ss_pred             CccCHHHHHHHHHHHHHHCCC--eEEEEecCC
Confidence            899999999988776554322  456666664

>2xb4_A Adenylate kinase; ATP-binding, nucleotide-binding, transferase; HET: SRT; 1.80A {Desulfovibrio gigas} PDB: 3l0s_A* 3l0p_A*

Probab=87.93  E-value=0.25  Score=39.62  Aligned_cols=17  Identities=35%  Similarity=0.288  Sum_probs=15.0

Q ss_pred             CCCCcHHHHHHHHHhhh
Q 041028            1 MGGIGKTTLAKEVARKA   17 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (283)
                      ++|+||||+|+.+....
T Consensus         8 ~~GsGKsT~a~~La~~l   24 (223)
T 2xb4_A            8 PNGSGKGTQGNLVKDKY   24 (223)
T ss_dssp             CTTSCHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            47999999999998865

>1kgd_A CASK, peripheral plasma membrane CASK; maguk, guanylate kinase like domain, protein binding; 1.31A {Homo sapiens} SCOP: c.37.1.1

Probab=87.85  E-value=0.23  Score=38.27  Aligned_cols=16  Identities=19%  Similarity=0.488  Sum_probs=14.2

Q ss_pred             CCCcHHHHHHHHHhhh
Q 041028            2 GGIGKTTLAKEVARKA   17 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~   17 (283)
                      .|+|||||++.+....
T Consensus        14 sGsGKSTL~~~L~~~~   29 (180)
T 1kgd_A           14 HGVGRRHIKNTLITKH   29 (180)
T ss_dssp             TTSSHHHHHHHHHHHC
T ss_pred             CCCCHHHHHHHHHhhC
Confidence            6999999999998764

>3cf0_A Transitional endoplasmic reticulum ATPase; AAA, P97/VCP, ERAD, CDC48, ATP-binding, lipid-binding, nucle binding, nucleus, phosphoprotein, transport; HET: ADP; 3.00A {Mus musculus}

Probab=87.84  E-value=0.23  Score=41.84  Aligned_cols=17  Identities=47%  Similarity=0.657  Sum_probs=15.2

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      +|+|||+||+.+++...
T Consensus        58 ~GtGKT~la~ala~~~~   74 (301)
T 3cf0_A           58 PGCGKTLLAKAIANECQ   74 (301)
T ss_dssp             SSSSHHHHHHHHHHHTT
T ss_pred             CCcCHHHHHHHHHHHhC
Confidence            69999999999998764

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens}

Probab=87.75  E-value=0.24  Score=41.14  Aligned_cols=17  Identities=53%  Similarity=0.624  Sum_probs=15.1

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      +|+||||||+.++....
T Consensus        53 ~GtGKTtLakala~~~~   69 (274)
T 2x8a_A           53 PGCGKTLLAKAVANESG   69 (274)
T ss_dssp             TTSCHHHHHHHHHHHTT
T ss_pred             CCCcHHHHHHHHHHHcC
Confidence            69999999999998654

>1m7g_A Adenylylsulfate kinase; APS kinase, transferase, sulfate Met nucleotide 2 kinase; HET: AV2 ADX ADP; 1.43A {Penicillium chrysogenum} SCOP: c.37.1.4 PDB: 1d6j_A* 1m7h_A* 3cr7_A*

Probab=87.58  E-value=0.26  Score=38.96  Aligned_cols=18  Identities=33%  Similarity=0.464  Sum_probs=15.4

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      +.|+||||+|+.+.....
T Consensus        33 ~~GsGKsT~~~~l~~~l~   50 (211)
T 1m7g_A           33 LSASGKSTLAVELEHQLV   50 (211)
T ss_dssp             STTSSHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHhc
Confidence            479999999999988754

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori}

Probab=87.55  E-value=0.94  Score=38.87  Aligned_cols=43  Identities=16%  Similarity=0.141  Sum_probs=30.6

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHHHh
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKL   48 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~~l   48 (283)
                      +|+||||||..++......  =..++|++..  .+..++..+++...
T Consensus        55 pG~GKTt~al~ia~~~a~~--g~~Vl~fSlE--ms~~ql~~Rlls~~   97 (338)
T 4a1f_A           55 PSMGKTSLMMNMVLSALND--DRGVAVFSLE--MSAEQLALRALSDL   97 (338)
T ss_dssp             TTSCHHHHHHHHHHHHHHT--TCEEEEEESS--SCHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHc--CCeEEEEeCC--CCHHHHHHHHHHHh
Confidence            6999999999998876542  1356777664  45677777776543

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=87.55  E-value=0.26  Score=42.52  Aligned_cols=18  Identities=33%  Similarity=0.412  Sum_probs=16.0

Q ss_pred             CCCcHHHHHHHHHhhhcc
Q 041028            2 GGIGKTTLAKEVARKAKN   19 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~   19 (283)
                      +|+|||+||+.+++....
T Consensus        79 pGtGKT~la~~la~~l~~   96 (368)
T 3uk6_A           79 PGTGKTAIAMGMAQALGP   96 (368)
T ss_dssp             TTSSHHHHHHHHHHHHCS
T ss_pred             CCCCHHHHHHHHHHHhcc
Confidence            699999999999998753

>1ye8_A Protein THEP1, hypothetical UPF0334 kinase-like protein AQ_1292; mixed alpha-beta protein, rossman fold, signaling protein, transferase; 1.40A {Aquifex aeolicus} SCOP: c.37.1.11

Probab=87.49  E-value=0.25  Score=38.21  Aligned_cols=18  Identities=39%  Similarity=0.671  Sum_probs=15.5

Q ss_pred             CCCcHHHHHHHHHhhhcc
Q 041028            2 GGIGKTTLAKEVARKAKN   19 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~   19 (283)
                      .|+|||||++.++....+
T Consensus         9 nGsGKTTLl~~l~g~l~i   26 (178)
T 1ye8_A            9 PGVGKTTLVKKIVERLGK   26 (178)
T ss_dssp             TTSSHHHHHHHHHHHHGG
T ss_pred             CCCCHHHHHHHHHHHhCC
Confidence            599999999999987653

>2pez_A Bifunctional 3'-phosphoadenosine 5'- phosphosulfate synthetase 1 (PAPS synthetase...; NMP-kinase fold, protein in complex with nucleic acid; HET: GGZ DAT; 1.40A {Homo sapiens} PDB: 2pey_A* 2ax4_A*

Probab=87.46  E-value=0.27  Score=37.71  Aligned_cols=18  Identities=28%  Similarity=0.418  Sum_probs=15.4

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      +.|+||||+++.+.....
T Consensus        13 ~~GsGKST~~~~L~~~l~   30 (179)
T 2pez_A           13 LSGAGKTTVSMALEEYLV   30 (179)
T ss_dssp             CTTSSHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHh
Confidence            469999999999988653

>1wcv_1 SOJ, segregation protein; ATPase, bacterial, chromosome segregation; 1.6A {Thermus thermophilus} PDB: 2bej_A* 2bek_A*

Probab=87.45  E-value=0.32  Score=39.77  Aligned_cols=30  Identities=27%  Similarity=0.439  Sum_probs=21.6

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQ   33 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~   33 (283)
                      ||+||||+|..++......+  ..++-|+...
T Consensus        16 GGvGKTt~a~~LA~~la~~g--~~VlliD~D~   45 (257)
T 1wcv_1           16 GGVGKTTTAINLAAYLARLG--KRVLLVDLDP   45 (257)
T ss_dssp             CCHHHHHHHHHHHHHHHHTT--CCEEEEECCT
T ss_pred             CCchHHHHHHHHHHHHHHCC--CCEEEEECCC
Confidence            89999999999988765432  2455666554

>3lv8_A DTMP kinase, thymidylate kinase; structural genomics, in diseases, center for structural genomics of infectious DISE ATP-binding; HET: ADP TMP TYD; 1.80A {Vibrio cholerae o1 biovar eltor} PDB: 3n2i_A*

Probab=87.42  E-value=0.83  Score=37.05  Aligned_cols=43  Identities=19%  Similarity=0.194  Sum_probs=26.4

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHH
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIA   45 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~   45 (283)
                      .|+||||+++.+....... .+..+....-.....+.+.+++++
T Consensus        36 ~GsGKsT~~~~l~~~l~~~-~~~~~~~~rep~~t~~g~~ir~~l   78 (236)
T 3lv8_A           36 EGAGKSTAIQVVVETLQQN-GIDHITRTREPGGTLLAEKLRALV   78 (236)
T ss_dssp             TTSCHHHHHHHHHHHHHHT-TCCCEEEEESSCSSHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHhc-CCCeeeeecCCCCCHHHHHHHHHH
Confidence            6999999999999887653 355344443222223344445544

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=87.32  E-value=0.46  Score=38.12  Aligned_cols=44  Identities=11%  Similarity=0.255  Sum_probs=26.9

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHHHhCC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKLGL   50 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~~l~~   50 (283)
                      +|+||||||..++......  =..++|++....  ..++...+ ..++.
T Consensus        32 ~GsGKTtl~~~~~~~~~~~--~~~v~~~~~e~~--~~~~~~~~-~~~g~   75 (247)
T 2dr3_A           32 PGTGKTIFSQQFLWNGLKM--GEPGIYVALEEH--PVQVRQNM-AQFGW   75 (247)
T ss_dssp             TTSSHHHHHHHHHHHHHHT--TCCEEEEESSSC--HHHHHHHH-HTTTC
T ss_pred             CCCCHHHHHHHHHHHHHhc--CCeEEEEEccCC--HHHHHHHH-HHcCC
Confidence            6999999999887654322  235778776543  34444433 34443

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=87.30  E-value=0.25  Score=42.06  Aligned_cols=16  Identities=56%  Similarity=0.679  Sum_probs=14.8

Q ss_pred             CCCcHHHHHHHHHhhh
Q 041028            2 GGIGKTTLAKEVARKA   17 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~   17 (283)
                      +|+|||+||+.+++..
T Consensus        54 pGtGKT~la~ala~~~   69 (322)
T 1xwi_A           54 PGTGKSYLAKAVATEA   69 (322)
T ss_dssp             SSSCHHHHHHHHHHHT
T ss_pred             CCccHHHHHHHHHHHc
Confidence            6999999999999875

>4tmk_A Protein (thymidylate kinase); ATP:DTMP phosphotransferase, transferase; HET: T5A; 1.98A {Escherichia coli} SCOP: c.37.1.1 PDB: 5tmp_A*

Probab=87.23  E-value=0.9  Score=36.17  Aligned_cols=44  Identities=20%  Similarity=0.241  Sum_probs=27.8

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHH
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAF   46 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~   46 (283)
                      .|+||||+++.+.+..... .+..+.+..-.....+.+.+++++.
T Consensus        12 ~gsGKsT~~~~l~~~l~~~-~~~~v~~~rep~~t~~g~~ir~~l~   55 (213)
T 4tmk_A           12 EGAGKTTARNVVVETLEQL-GIRDMVFTREPGGTQLAEKLRSLLL   55 (213)
T ss_dssp             TTSCHHHHHHHHHHHHHHT-TCCCEEEEESSCSSHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHc-CCCcceeeeCCCCCHHHHHHHHHHh
Confidence            6999999999999887654 3433333332233345566666665

>3eie_A Vacuolar protein sorting-associated protein 4; AAA ATPase, ATP-binding cassette, ATP-binding, endosome, MEM nucleotide-binding; 2.70A {Saccharomyces cerevisiae} PDB: 3eih_A* 2rko_A 3mhv_C

Probab=87.21  E-value=0.26  Score=41.91  Aligned_cols=17  Identities=53%  Similarity=0.655  Sum_probs=15.2

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      +|+|||+||+.+++...
T Consensus        60 pGtGKT~la~aia~~~~   76 (322)
T 3eie_A           60 PGTGKSYLAKAVATEAN   76 (322)
T ss_dssp             SSSCHHHHHHHHHHHHT
T ss_pred             CCCcHHHHHHHHHHHHC
Confidence            69999999999999754

>1cke_A CK, MSSA, protein (cytidine monophosphate kinase); nucleotide monophosphate kinase,, transferase; 1.75A {Escherichia coli} SCOP: c.37.1.1 PDB: 1kdo_A* 1kdp_A* 1kdr_A* 1kdt_A* 2cmk_A* 2fem_A 2feo_A*

Probab=87.07  E-value=0.3  Score=38.91  Aligned_cols=18  Identities=39%  Similarity=0.501  Sum_probs=15.1

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      ..|+||||+|+.+.....
T Consensus        13 ~~GsGKSTl~~~L~~~~g   30 (227)
T 1cke_A           13 PSGAGKGTLCKAMAEALQ   30 (227)
T ss_dssp             CTTSSHHHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHHHhC
Confidence            369999999999988653

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=87.03  E-value=0.11  Score=38.60  Aligned_cols=16  Identities=19%  Similarity=0.216  Sum_probs=13.9

Q ss_pred             CCCcHHHHHHHHHhhh
Q 041028            2 GGIGKTTLAKEVARKA   17 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~   17 (283)
                      +|+|||++|+.+++..
T Consensus        36 ~GtGKt~lA~~i~~~~   51 (143)
T 3co5_A           36 AGSPFETVARYFHKNG   51 (143)
T ss_dssp             TTCCHHHHHGGGCCTT
T ss_pred             CCccHHHHHHHHHHhC
Confidence            6999999999998754

>2j41_A Guanylate kinase; GMP, GMK, transferase, ATP-binding, nucleotide- binding; HET: 5GP; 1.9A {Staphylococcus aureus}

Probab=87.02  E-value=0.28  Score=38.34  Aligned_cols=16  Identities=31%  Similarity=0.586  Sum_probs=14.2

Q ss_pred             CCCcHHHHHHHHHhhh
Q 041028            2 GGIGKTTLAKEVARKA   17 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~   17 (283)
                      .|+|||||++.+....
T Consensus        15 ~GsGKSTl~~~L~~~~   30 (207)
T 2j41_A           15 SGVGKGTVRKRIFEDP   30 (207)
T ss_dssp             TTSCHHHHHHHHHHCT
T ss_pred             CCCCHHHHHHHHHHhh
Confidence            6999999999998765

>2bbw_A Adenylate kinase 4, AK4; nucleotide kinase, nucleotide binding, human, structura genomics, structural genomics consortium, SGC, transferase; HET: GP5; 2.05A {Homo sapiens} PDB: 2ar7_A* 3ndp_A

Probab=86.95  E-value=0.3  Score=39.65  Aligned_cols=18  Identities=28%  Similarity=0.383  Sum_probs=15.2

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      ..|+|||||++.++....
T Consensus        35 ~~GsGKSTl~k~La~~lg   52 (246)
T 2bbw_A           35 PPGSGKGTVCQRIAQNFG   52 (246)
T ss_dssp             CTTSSHHHHHHHHHHHHC
T ss_pred             CCCCCHHHHHHHHHHHhC
Confidence            369999999999997654

>2b8t_A Thymidine kinase; deoxyribonucleoside kinase, zinc-binding domain, TK1, UU-TK, transferase; HET: THM; 2.00A {Ureaplasma parvum} SCOP: c.37.1.24 g.39.1.14 PDB: 2uz3_A*

Probab=86.94  E-value=0.25  Score=39.84  Aligned_cols=71  Identities=14%  Similarity=-0.034  Sum_probs=37.5

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCc---CCHhhhHHhHHHHccCC--cEEEE
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKLGLKFDE---ESESGRTRSPWSRLKKE--KLQII   76 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~---~~~~~~~~~l~~~L~~k--r~LlV   76 (283)
                      .|+||||++..+.++....  -..++.+.......   ....+++.+|.....   ....+..+.+.+.+.+.  .+++|
T Consensus        21 mGsGKTT~ll~~~~r~~~~--g~kVli~~~~~d~r---~~~~i~srlG~~~~~~~~~~~~~i~~~i~~~~~~~~~dvViI   95 (223)
T 2b8t_A           21 MFAGKTAELIRRLHRLEYA--DVKYLVFKPKIDTR---SIRNIQSRTGTSLPSVEVESAPEILNYIMSNSFNDETKVIGI   95 (223)
T ss_dssp             TTSCHHHHHHHHHHHHHHT--TCCEEEEEECCCGG---GCSSCCCCCCCSSCCEEESSTHHHHHHHHSTTSCTTCCEEEE
T ss_pred             CCCcHHHHHHHHHHHHHhc--CCEEEEEEeccCch---HHHHHHHhcCCCccccccCCHHHHHHHHHHHhhCCCCCEEEE
Confidence            4999999999998887644  22344444333211   223455556654332   12333444555544333  46666


Q ss_pred             c
Q 041028           77 C   77 (283)
Q Consensus        77 ~   77 (283)
                      +
T Consensus        96 D   96 (223)
T 2b8t_A           96 D   96 (223)
T ss_dssp             C
T ss_pred             e
Confidence            3

>4eaq_A DTMP kinase, thymidylate kinase; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, MTBI, transferase; HET: ATM; 1.85A {Staphylococcus aureus subsp} PDB: 4dwj_A* 4f4i_A

Probab=86.76  E-value=0.65  Score=37.38  Aligned_cols=19  Identities=37%  Similarity=0.426  Sum_probs=16.4

Q ss_pred             CCCCcHHHHHHHHHhhhcc
Q 041028            1 MGGIGKTTLAKEVARKAKN   19 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~   19 (283)
                      ..|+||||+++.+......
T Consensus        34 ~~GsGKsT~~~~l~~~l~~   52 (229)
T 4eaq_A           34 PEGSGKTTVINEVYHRLVK   52 (229)
T ss_dssp             CTTSCHHHHHHHHHHHHTT
T ss_pred             CCCCCHHHHHHHHHHHHhc
Confidence            3699999999999998764

>3dm5_A SRP54, signal recognition 54 kDa protein; protein-RNA, signal recognition particle, SRP-GTPase, protein targeting, cytoplasm, GTP-binding; HET: GDP; 2.51A {Pyrococcus furiosus}

Probab=86.72  E-value=1.8  Score=38.54  Aligned_cols=74  Identities=14%  Similarity=0.078  Sum_probs=40.5

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCC-CCCHHHHHHHHHHHhCCCCC----cCCHhhhH-HhHHHHcc-CCcEE
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQ-NPNIKKIQGEIAFKLGLKFD----EESESGRT-RSPWSRLK-KEKLQ   74 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~-~~~~~~l~~~i~~~l~~~~~----~~~~~~~~-~~l~~~L~-~kr~L   74 (283)
                      +|+||||++..++.....++ . .++-|.... .+...+-++......+.+..    ..+..+.. +.+...-. +..++
T Consensus       109 ~G~GKTTt~~kLA~~l~~~G-~-kVllv~~D~~R~aa~eqL~~~~~~~gvpv~~~~~~~dp~~i~~~al~~a~~~~~DvV  186 (443)
T 3dm5_A          109 QGSGKTTTVAKLARYFQKRG-Y-KVGVVCSDTWRPGAYHQLRQLLDRYHIEVFGNPQEKDAIKLAKEGVDYFKSKGVDII  186 (443)
T ss_dssp             TTSSHHHHHHHHHHHHHTTT-C-CEEEEECCCSSTHHHHHHHHHHGGGTCEEECCTTCCCHHHHHHHHHHHHHHTTCSEE
T ss_pred             CCCCHHHHHHHHHHHHHHCC-C-eEEEEeCCCcchhHHHHHHHHHHhcCCcEEecCCCCCHHHHHHHHHHHHHhCCCCEE
Confidence            79999999999988766432 2 334444432 23344555566666666421    12333332 22333322 35788


Q ss_pred             EEc
Q 041028           75 IIC   77 (283)
Q Consensus        75 lV~   77 (283)
                      ||+
T Consensus       187 IID  189 (443)
T 3dm5_A          187 IVD  189 (443)
T ss_dssp             EEE
T ss_pred             EEE
Confidence            884

>2ffh_A Protein (FFH); SRP54, signal recognition particle, GTPase, M domain, RNA-binding, signal sequence-binding, helix-turn-helix, protein targeting; 3.20A {Thermus aquaticus} SCOP: a.24.13.1 a.36.1.1 c.37.1.10 PDB: 2iy3_A

Probab=86.69  E-value=3  Score=36.89  Aligned_cols=73  Identities=21%  Similarity=0.187  Sum_probs=39.7

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHH--HHHHHHHHHhCCCC----CcCCHhhhHHhHHHHc--cCCcE
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIK--KIQGEIAFKLGLKF----DEESESGRTRSPWSRL--KKEKL   73 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~--~l~~~i~~~l~~~~----~~~~~~~~~~~l~~~L--~~kr~   73 (283)
                      +|+||||++..++......+  ..+..+.. ..+...  +.++......+.+.    ...+..+......+.+  .+..+
T Consensus       107 ~GsGKTT~~~~LA~~l~~~g--~~Vllvd~-D~~r~aa~~qL~~~~~~~gv~v~~~~~~~~p~~i~~~~l~~~~~~~~Dv  183 (425)
T 2ffh_A          107 QGSGKTTTAAKLALYYKGKG--RRPLLVAA-DTQRPAAREQLRLLGEKVGVPVLEVMDGESPESIRRRVEEKARLEARDL  183 (425)
T ss_dssp             TTSSHHHHHHHHHHHHHTTT--CCEEEEEC-CSSCHHHHHHHHHHHHHHTCCEEECCTTCCHHHHHHHHHHHHHHTTCSE
T ss_pred             CCCCHHHHHHHHHHHHHHcC--CeEEEeec-cccCchhHHHHHHhcccCCccEEecCCCCCHHHHHHHHHHHHHHCCCCE
Confidence            79999999999998766432  23444544 333332  23455556666542    1123333333222333  44578


Q ss_pred             EEEc
Q 041028           74 QIIC   77 (283)
Q Consensus        74 LlV~   77 (283)
                      +||+
T Consensus       184 VIID  187 (425)
T 2ffh_A          184 ILVD  187 (425)
T ss_dssp             EEEE
T ss_pred             EEEc
Confidence            8884

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=86.67  E-value=0.28  Score=41.77  Aligned_cols=17  Identities=41%  Similarity=0.632  Sum_probs=15.0

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      +|+|||+||+.+++...
T Consensus        64 ~GtGKT~la~~ia~~~~   80 (338)
T 3pfi_A           64 AGLGKTTLANIISYEMS   80 (338)
T ss_dssp             TTSSHHHHHHHHHHHTT
T ss_pred             CCCCHHHHHHHHHHHhC
Confidence            69999999999988754

>1ofh_A ATP-dependent HSL protease ATP-binding subunit HSLU; chaperone, hydrolase, ATP-binding; HET: ADP; 2.5A {Haemophilus influenzae} SCOP: c.37.1.20 PDB: 1ofi_A*

Probab=86.61  E-value=0.29  Score=40.85  Aligned_cols=17  Identities=41%  Similarity=0.728  Sum_probs=15.1

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      +|+|||+||+.+++...
T Consensus        59 ~GtGKT~la~~la~~l~   75 (310)
T 1ofh_A           59 TGVGKTEIARRLAKLAN   75 (310)
T ss_dssp             TTSSHHHHHHHHHHHHT
T ss_pred             CCCCHHHHHHHHHHHhC
Confidence            69999999999998763

>1jjv_A Dephospho-COA kinase; P-loop nucleotide-binding fold, structure 2 function project, S2F, structural genomics, transferase; HET: ATP; 2.00A {Haemophilus influenzae} SCOP: c.37.1.1

Probab=86.59  E-value=0.29  Score=38.44  Aligned_cols=15  Identities=40%  Similarity=0.339  Sum_probs=13.3

Q ss_pred             CCCCcHHHHHHHHHh
Q 041028            1 MGGIGKTTLAKEVAR   15 (283)
Q Consensus         1 mgGiGKTtLA~~v~~   15 (283)
                      +.|+||||+++.+..
T Consensus        10 ~~GsGKST~~~~La~   24 (206)
T 1jjv_A           10 GIGSGKTTIANLFTD   24 (206)
T ss_dssp             STTSCHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHH
Confidence            369999999999976

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20

Probab=86.53  E-value=0.3  Score=40.44  Aligned_cols=17  Identities=53%  Similarity=0.790  Sum_probs=15.1

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      +|+||||||+.+++...
T Consensus        82 ~GtGKTtl~~~i~~~~~   98 (278)
T 1iy2_A           82 PGVGKTHLARAVAGEAR   98 (278)
T ss_dssp             TTSSHHHHHHHHHHHTT
T ss_pred             CcChHHHHHHHHHHHcC
Confidence            69999999999998764

>1uf9_A TT1252 protein; P-loop, nucleotide binding domain, structural genomics, riken structural genomics/proteomics initiative, RSGI; HET: ATP; 2.80A {Thermus thermophilus} SCOP: c.37.1.1

Probab=86.43  E-value=0.32  Score=37.84  Aligned_cols=16  Identities=31%  Similarity=0.219  Sum_probs=14.2

Q ss_pred             CCCCcHHHHHHHHHhh
Q 041028            1 MGGIGKTTLAKEVARK   16 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~   16 (283)
                      +.|+||||+|+.+...
T Consensus        16 ~~GsGKST~~~~La~~   31 (203)
T 1uf9_A           16 NIGSGKSTVAALLRSW   31 (203)
T ss_dssp             CTTSCHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHHC
Confidence            4699999999999885

>3tlx_A Adenylate kinase 2; structural genomics, structural genomics consortium, SGC, RO fold, transferase, ATP binding, phosphorylation; HET: ADP ATP AMP; 2.75A {Plasmodium falciparum}

Probab=86.37  E-value=0.34  Score=39.41  Aligned_cols=17  Identities=24%  Similarity=0.304  Sum_probs=14.8

Q ss_pred             CCCCcHHHHHHHHHhhh
Q 041028            1 MGGIGKTTLAKEVARKA   17 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (283)
                      .+|+||||+|+.+.+..
T Consensus        37 ~~GsGKsT~a~~L~~~~   53 (243)
T 3tlx_A           37 APGSGKGTQSLNLKKSH   53 (243)
T ss_dssp             CTTSSHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            47999999999998765

>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus}

Probab=86.33  E-value=1.1  Score=40.03  Aligned_cols=43  Identities=14%  Similarity=0.098  Sum_probs=29.9

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHHH
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFK   47 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~~   47 (283)
                      +|+||||||..++....... =..++|++..  .+..++..+++..
T Consensus       209 pg~GKT~lal~ia~~~a~~~-g~~vl~~slE--~~~~~l~~R~~~~  251 (444)
T 2q6t_A          209 PAMGKTAFALTIAQNAALKE-GVGVGIYSLE--MPAAQLTLRMMCS  251 (444)
T ss_dssp             TTSCHHHHHHHHHHHHHHTT-CCCEEEEESS--SCHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHhC-CCeEEEEECC--CCHHHHHHHHHHH
Confidence            69999999999988765321 1357777765  4456777776643

>4edh_A DTMP kinase, thymidylate kinase; structural genomics, PSI-biology; HET: TMP ADP; 1.32A {Pseudomonas aeruginosa PAO1} PDB: 4e5u_A* 4esh_A* 4gmd_A* 3uwk_A* 3uwo_A* 3uxm_A*

Probab=86.31  E-value=1.1  Score=35.61  Aligned_cols=43  Identities=16%  Similarity=0.195  Sum_probs=25.6

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHH
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAF   46 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~   46 (283)
                      .|+||||+++.+.+..... .+..+. ..-.....+.+.+++++.
T Consensus        15 ~gsGKsT~~~~l~~~l~~~-~~~v~~-~~~p~~~~~g~~i~~~l~   57 (213)
T 4edh_A           15 EGAGKSTNRDYLAERLRER-GIEVQL-TREPGGTPLAERIRELLL   57 (213)
T ss_dssp             TTSSHHHHHHHHHHHHHTT-TCCEEE-EESSCSSHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHc-CCCccc-ccCCCCCHHHHHHHHHHh
Confidence            6999999999999887643 355432 222222223444555554

>3tr0_A Guanylate kinase, GMP kinase; purines, pyrimidines, nucleosides, nucleotides, transferase; HET: 5GP; 1.85A {Coxiella burnetii}

Probab=86.31  E-value=0.31  Score=38.05  Aligned_cols=16  Identities=31%  Similarity=0.621  Sum_probs=14.0

Q ss_pred             CCCcHHHHHHHHHhhh
Q 041028            2 GGIGKTTLAKEVARKA   17 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~   17 (283)
                      .|+|||||++.+....
T Consensus        16 ~GsGKSTl~~~L~~~~   31 (205)
T 3tr0_A           16 SGAGKTSLVRALVKAL   31 (205)
T ss_dssp             TTSCHHHHHHHHHHHS
T ss_pred             CCCCHHHHHHHHHhhC
Confidence            5999999999998764

>3c8u_A Fructokinase; YP_612366.1, putative fructose transport system kinase, STRU genomics, joint center for structural genomics, JCSG; 1.95A {Silicibacter SP}

Probab=86.23  E-value=0.26  Score=38.94  Aligned_cols=17  Identities=35%  Similarity=0.481  Sum_probs=14.9

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      .|.|||||++.+.....
T Consensus        31 sGsGKSTl~~~l~~~~~   47 (208)
T 3c8u_A           31 PGSGKSTLSNPLAAALS   47 (208)
T ss_dssp             TTSCTHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHh
Confidence            59999999999988765

>1xjc_A MOBB protein homolog; structural genomics, midwest center for structural GEN PSI, protein structure initiative, MCSG; 2.10A {Geobacillus stearothermophilus} SCOP: c.37.1.10

Probab=86.13  E-value=0.4  Score=36.83  Aligned_cols=18  Identities=33%  Similarity=0.255  Sum_probs=15.4

Q ss_pred             CCCcHHHHHHHHHhhhcc
Q 041028            2 GGIGKTTLAKEVARKAKN   19 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~   19 (283)
                      .|+|||||+..+......
T Consensus        13 sGsGKTTl~~~L~~~l~~   30 (169)
T 1xjc_A           13 KHSGKTTLMEKWVAAAVR   30 (169)
T ss_dssp             TTSSHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHhhHh
Confidence            699999999999987653

>2z4s_A Chromosomal replication initiator protein DNAA; AAA+ ATPase, domain III (ATPase domain), ATP-binding, cytoplasm, DNA replication; HET: ADP; 3.00A {Thermotoga maritima} PDB: 2z4r_A*

Probab=86.11  E-value=0.31  Score=43.48  Aligned_cols=18  Identities=28%  Similarity=0.436  Sum_probs=15.7

Q ss_pred             CCCcHHHHHHHHHhhhcc
Q 041028            2 GGIGKTTLAKEVARKAKN   19 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~   19 (283)
                      +|+||||||+.+++....
T Consensus       139 ~G~GKTtLa~aia~~l~~  156 (440)
T 2z4s_A          139 VGLGKTHLLQSIGNYVVQ  156 (440)
T ss_dssp             SSSSHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHH
Confidence            699999999999997643

>3ez2_A Plasmid partition protein A; type IA, DNA binding, winged-HTH, DNA bindin; HET: ADP EPE; 2.05A {Escherichia coli} PDB: 3ez6_A* 3ez7_A

Probab=86.08  E-value=0.3  Score=42.82  Aligned_cols=34  Identities=18%  Similarity=0.306  Sum_probs=22.1

Q ss_pred             CCCcHHHHHHHHHhhhccCC---CC-CeEEEEEeCCCC
Q 041028            2 GGIGKTTLAKEVARKAKNGK---LF-DQIVFTEVSQNP   35 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~---~F-d~~~wv~v~~~~   35 (283)
                      ||+||||+|..++......+   .- ..++-|+.....
T Consensus       118 GGvGKTT~a~nLA~~La~~~~~~~~g~rVlliD~D~q~  155 (398)
T 3ez2_A          118 GGVSKTVSTVSLAHAMRAHPHLLMEDLRILVIDLDPQS  155 (398)
T ss_dssp             SSSSHHHHHHHHHHHHHHCTTTGGGCCCEEEEEECTTC
T ss_pred             CCccHHHHHHHHHHHHHhcchhhcCCCeEEEEeCCCCC
Confidence            89999999999987754200   01 245667766443

>3nwj_A ATSK2; P loop, shikimate, nucleoside monophosphate kinase, shikimat ATP binding, chloroplast, transferase; 2.35A {Arabidopsis thaliana}

Probab=86.07  E-value=0.33  Score=39.80  Aligned_cols=18  Identities=50%  Similarity=0.551  Sum_probs=15.7

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      |.|+||||+++.+.....
T Consensus        56 ~~GsGKSTl~~~La~~lg   73 (250)
T 3nwj_A           56 MMGSGKTTVGKIMARSLG   73 (250)
T ss_dssp             STTSCHHHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHHhcC
Confidence            579999999999998654

>2bjv_A PSP operon transcriptional activator; AAA, transcription activation, gene regulation, sigma54 activator, enhancer binding protein, PSPF; 1.7A {Escherichia coli} PDB: 2bjw_A 2c96_A* 2c98_A* 2c99_A* 2c9c_A* 2vii_A*

Probab=86.01  E-value=0.32  Score=39.88  Aligned_cols=17  Identities=24%  Similarity=0.343  Sum_probs=14.8

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      +|+|||+||+.+++...
T Consensus        38 ~GtGKt~la~~i~~~~~   54 (265)
T 2bjv_A           38 RGTGKELIASRLHYLSS   54 (265)
T ss_dssp             TTSCHHHHHHHHHHTST
T ss_pred             CCCcHHHHHHHHHHhcC
Confidence            69999999999998653

>2p5t_B PEZT; postsegregational killing system, phosphoryltransferase, HEL helix motif, transcription regulator; 3.20A {Streptococcus pneumoniae}

Probab=85.96  E-value=0.23  Score=40.63  Aligned_cols=18  Identities=28%  Similarity=0.431  Sum_probs=15.2

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      ++|+||||+|+.+.....
T Consensus        40 ~~GsGKSTla~~L~~~l~   57 (253)
T 2p5t_B           40 QSGAGKTTIHRIKQKEFQ   57 (253)
T ss_dssp             CGGGTTHHHHHHHHHHTT
T ss_pred             CCCCCHHHHHHHHHHhcC
Confidence            469999999999988653

>2qt1_A Nicotinamide riboside kinase 1; non-protein kinase, NAD+, NRK1, nicotinic acid riboside kinase activity, NAD biosynthesis; HET: NNR; 1.32A {Homo sapiens} PDB: 2qsy_A* 2qsz_A* 2qt0_A* 2p0e_A* 2qg6_A* 2ql6_A*

Probab=85.94  E-value=0.33  Score=38.19  Aligned_cols=15  Identities=47%  Similarity=0.616  Sum_probs=13.4

Q ss_pred             CCCcHHHHHHHHHhh
Q 041028            2 GGIGKTTLAKEVARK   16 (283)
Q Consensus         2 gGiGKTtLA~~v~~~   16 (283)
                      .|+||||||+.+...
T Consensus        30 ~GsGKSTl~~~L~~~   44 (207)
T 2qt1_A           30 TNSGKTTLAKNLQKH   44 (207)
T ss_dssp             TTSSHHHHHHHHHTT
T ss_pred             CCCCHHHHHHHHHHh
Confidence            699999999999874

>1ltq_A Polynucleotide kinase; phosphatase, alpha/beta, P-loop, transferase; HET: ADP; 2.33A {Enterobacteria phage T4} SCOP: c.108.1.9 c.37.1.1 PDB: 1rc8_A* 1rpz_A* 1rrc_A* 2ia5_A

Probab=85.73  E-value=0.35  Score=40.43  Aligned_cols=16  Identities=44%  Similarity=0.542  Sum_probs=14.1

Q ss_pred             CCCCcHHHHHHHHHhh
Q 041028            1 MGGIGKTTLAKEVARK   16 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~   16 (283)
                      ++|+||||+|+.+...
T Consensus        10 ~~GsGKST~a~~L~~~   25 (301)
T 1ltq_A           10 CPGSGKSTWAREFIAK   25 (301)
T ss_dssp             CTTSSHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHh
Confidence            4799999999999874

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=85.66  E-value=0.29  Score=43.08  Aligned_cols=18  Identities=44%  Similarity=0.571  Sum_probs=16.1

Q ss_pred             CCCcHHHHHHHHHhhhcc
Q 041028            2 GGIGKTTLAKEVARKAKN   19 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~   19 (283)
                      +|.|||.||+++++....
T Consensus       191 PGTGKTllAkAiA~e~~~  208 (405)
T 4b4t_J          191 PGTGKTLLARAVAHHTDC  208 (405)
T ss_dssp             SSSSHHHHHHHHHHHHTC
T ss_pred             CCCCHHHHHHHHHHhhCC
Confidence            799999999999998764

>2hf9_A Probable hydrogenase nickel incorporation protein HYPB; alpha and beta protein; HET: GSP; 1.90A {Methanocaldococcus jannaschii} PDB: 2hf8_A*

Probab=85.47  E-value=0.38  Score=38.21  Aligned_cols=17  Identities=35%  Similarity=0.401  Sum_probs=14.7

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      +|+|||||+..+.....
T Consensus        47 ~gvGKTtl~~~l~~~~~   63 (226)
T 2hf9_A           47 IGSGKTLLIEKLIDNLK   63 (226)
T ss_dssp             TTSSHHHHHHHHHHHHT
T ss_pred             CCCCHHHHHHHHHHHhc
Confidence            79999999999987653

>1ihu_A Arsenical pump-driving ATPase; aluminum fluoride, ADP, ARSA ATPase, ATP binding site, hydro; HET: ADP; 2.15A {Escherichia coli} SCOP: c.37.1.10 c.37.1.10 PDB: 1f48_A* 1ii0_A* 1ii9_A*

Probab=85.46  E-value=0.73  Score=42.68  Aligned_cols=29  Identities=21%  Similarity=0.469  Sum_probs=20.7

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVS   32 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~   32 (283)
                      ||+||||+|..++......+  ..++.|+..
T Consensus        17 GGvGKTT~a~~lA~~lA~~G--~rVLlvd~D   45 (589)
T 1ihu_A           17 GGVGKTSISCATAIRLAEQG--KRVLLVSTD   45 (589)
T ss_dssp             TTSSHHHHHHHHHHHHHHTT--CCEEEEECC
T ss_pred             CcCHHHHHHHHHHHHHHHCC--CcEEEEECC
Confidence            89999999999887755432  235666655

>2grj_A Dephospho-COA kinase; TM1387, EC 2.7.1.24, dephosphocoenzyme kinase, structural genomics, joint center for structural GE JCSG; HET: ADP COD; 2.60A {Thermotoga maritima}

Probab=85.46  E-value=0.4  Score=37.56  Aligned_cols=17  Identities=29%  Similarity=0.343  Sum_probs=14.5

Q ss_pred             CCCCcHHHHHHHHHhhh
Q 041028            1 MGGIGKTTLAKEVARKA   17 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (283)
                      +.|+||||+|+.+....
T Consensus        20 ~~GSGKSTva~~L~~~l   36 (192)
T 2grj_A           20 KIGTGKSTVCEILKNKY   36 (192)
T ss_dssp             STTSSHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHhc
Confidence            46999999999998863

>2qp9_X Vacuolar protein sorting-associated protein 4; ATPase domain, beta domain, C-terminal helix, ATP-binding, E nucleotide-binding; 2.90A {Saccharomyces cerevisiae} PDB: 2qpa_A*

Probab=85.39  E-value=0.36  Score=41.69  Aligned_cols=17  Identities=53%  Similarity=0.655  Sum_probs=15.3

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      +|+|||+||+.+++...
T Consensus        93 pGtGKT~la~ala~~~~  109 (355)
T 2qp9_X           93 PGTGKSYLAKAVATEAN  109 (355)
T ss_dssp             TTSCHHHHHHHHHHHHT
T ss_pred             CCCcHHHHHHHHHHHhC
Confidence            69999999999999764

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=85.32  E-value=0.3  Score=43.38  Aligned_cols=18  Identities=50%  Similarity=0.613  Sum_probs=16.1

Q ss_pred             CCCcHHHHHHHHHhhhcc
Q 041028            2 GGIGKTTLAKEVARKAKN   19 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~   19 (283)
                      +|+|||+||+++++....
T Consensus       215 PGtGKT~lakAiA~~~~~  232 (428)
T 4b4t_K          215 PGTGKTMLVKAVANSTKA  232 (428)
T ss_dssp             TTTTHHHHHHHHHHHHTC
T ss_pred             CCCCHHHHHHHHHHHhCC
Confidence            799999999999998753

>2fna_A Conserved hypothetical protein; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2; HET: MSE ADP; 2.00A {Sulfolobus solfataricus} SCOP: a.4.5.11 c.37.1.20

Probab=85.27  E-value=5  Score=33.73  Aligned_cols=28  Identities=11%  Similarity=0.255  Sum_probs=21.6

Q ss_pred             CCCCcHHHHHHHHHhhhccCCCCCeEEEEEeCC
Q 041028            1 MGGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQ   33 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~   33 (283)
                      ++|+|||||++++++....     ..+|++...
T Consensus        38 ~~G~GKT~L~~~~~~~~~~-----~~~~~~~~~   65 (357)
T 2fna_A           38 LRRTGKSSIIKIGINELNL-----PYIYLDLRK   65 (357)
T ss_dssp             STTSSHHHHHHHHHHHHTC-----CEEEEEGGG
T ss_pred             CCCCCHHHHHHHHHHhcCC-----CEEEEEchh
Confidence            4799999999999987542     257887753

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=85.26  E-value=0.56  Score=37.18  Aligned_cols=44  Identities=16%  Similarity=0.209  Sum_probs=25.7

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHHHhCC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKLGL   50 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~~l~~   50 (283)
                      +|+|||||++.++......  =..++|+....  ...++...+ ..++.
T Consensus        32 ~GsGKTtl~~~l~~~~~~~--~~~v~~~~~~~--~~~~~~~~~-~~~~~   75 (235)
T 2w0m_A           32 PGTGKTIFSLHFIAKGLRD--GDPCIYVTTEE--SRDSIIRQA-KQFNW   75 (235)
T ss_dssp             TTSSHHHHHHHHHHHHHHH--TCCEEEEESSS--CHHHHHHHH-HHTTC
T ss_pred             CCCCHHHHHHHHHHHHHHC--CCeEEEEEccc--CHHHHHHHH-HHhcc
Confidence            5999999999998654322  12456665443  344444333 34443

>3asz_A Uridine kinase; cytidine phosphorylation, transferase; HET: C5P; 2.25A {Thermus thermophilus} PDB: 3asy_A*

Probab=85.26  E-value=0.38  Score=37.87  Aligned_cols=17  Identities=47%  Similarity=0.530  Sum_probs=14.6

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      .|+|||||++.+.....
T Consensus        15 ~GsGKSTl~~~l~~~~~   31 (211)
T 3asz_A           15 TASGKTTLAQALARTLG   31 (211)
T ss_dssp             TTSSHHHHHHHHHHHHG
T ss_pred             CCCCHHHHHHHHHHHhC
Confidence            59999999999988644

>3tau_A Guanylate kinase, GMP kinase; structural genomics, center for structural genomics of infec diseases, csgid, putative guanylate kinase; HET: MSE; 2.05A {Listeria monocytogenes}

Probab=85.19  E-value=0.38  Score=38.00  Aligned_cols=17  Identities=29%  Similarity=0.579  Sum_probs=14.7

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      .|+|||||++.+.....
T Consensus        17 sGsGKsTl~~~L~~~~~   33 (208)
T 3tau_A           17 SGVGKGTVREAVFKDPE   33 (208)
T ss_dssp             TTSCHHHHHHHHHHSTT
T ss_pred             CCCCHHHHHHHHHhhCC
Confidence            69999999999988653

>4hlc_A DTMP kinase, thymidylate kinase; TMK, MRSA, pipiridine, transfera transferase inhibitor complex; HET: T05; 1.55A {Staphylococcus aureus subsp} PDB: 2cck_A 4gfd_A* 4gsy_A* 4hdc_A* 4hej_A* 2ccj_A* 4hld_A* 2ccg_A*

Probab=85.16  E-value=0.66  Score=36.70  Aligned_cols=42  Identities=26%  Similarity=0.286  Sum_probs=24.7

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHH
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAF   46 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~   46 (283)
                      -|+||||+++.+++....  .++.+. ..-.......+.+++++.
T Consensus        11 dGsGKsTq~~~L~~~L~~--~~~v~~-~~eP~~t~~g~~ir~~l~   52 (205)
T 4hlc_A           11 EGSGKTTVINEVYHRLVK--DYDVIM-TREPGGVPTGEEIRKIVL   52 (205)
T ss_dssp             TTSCHHHHHHHHHHHHTT--TSCEEE-EESSTTCHHHHHHHHHHH
T ss_pred             CCCcHHHHHHHHHHHHHC--CCCEEE-eeCCCCChHHHHHHHHHh
Confidence            599999999999998752  354432 221222234445555443

>1gtv_A TMK, thymidylate kinase; transferase, transferase (ATP:TMP phosphotransferase); HET: TYD TMP; 1.55A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1g3u_A* 1gsi_A* 1mrn_A* 1mrs_A* 1n5i_A* 1n5j_A* 1n5k_A* 1n5l_A* 1w2g_A* 1w2h_A*

Probab=85.00  E-value=0.28  Score=38.59  Aligned_cols=17  Identities=29%  Similarity=0.518  Sum_probs=14.8

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      .|+||||+|+.+.....
T Consensus         9 ~GsGKsTl~~~L~~~l~   25 (214)
T 1gtv_A            9 DGAGKRTLVEKLSGAFR   25 (214)
T ss_dssp             EEEEHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHH
Confidence            59999999999988764

>3d8b_A Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, structural genomics consortium, ATP- hydrolase, magnesium, metal-binding, nucleotide-binding; HET: ADP; 2.00A {Homo sapiens}

Probab=84.96  E-value=0.39  Score=41.49  Aligned_cols=17  Identities=35%  Similarity=0.505  Sum_probs=15.0

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      +|+|||+||+.+++...
T Consensus       126 pGtGKT~la~aia~~~~  142 (357)
T 3d8b_A          126 PGTGKTLIGKCIASQSG  142 (357)
T ss_dssp             TTSSHHHHHHHHHHHTT
T ss_pred             CCCCHHHHHHHHHHHcC
Confidence            69999999999998753

>2zts_A Putative uncharacterized protein PH0186; KAIC like protein, ATP-binding, nucleotide-binding, ATP- binding protein; HET: ADP; 2.07A {Pyrococcus horikoshii}

Probab=84.81  E-value=0.46  Score=38.24  Aligned_cols=40  Identities=25%  Similarity=0.378  Sum_probs=24.2

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHH
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEI   44 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i   44 (283)
                      +|+|||+||.+++.+...+ .-..+++++...  +..++.+.+
T Consensus        39 pG~GKT~l~l~~~~~~~~~-~~~~v~~~s~E~--~~~~~~~~~   78 (251)
T 2zts_A           39 TGTGKTTFAAQFIYKGAEE-YGEPGVFVTLEE--RARDLRREM   78 (251)
T ss_dssp             TTSSHHHHHHHHHHHHHHH-HCCCEEEEESSS--CHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHh-cCCCceeecccC--CHHHHHHHH
Confidence            6999999999876543221 123566776654  345554443

>3bgw_A DNAB-like replicative helicase; ATPase, replication; 3.91A {Bacillus phage SPP1}

Probab=84.77  E-value=1  Score=40.16  Aligned_cols=42  Identities=17%  Similarity=0.249  Sum_probs=28.6

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHHH
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFK   47 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~~   47 (283)
                      +|+||||||..++.+...++  ..++|++...  +..++..+++..
T Consensus       206 pG~GKTtlal~ia~~~a~~g--~~vl~fSlEm--s~~ql~~R~~~~  247 (444)
T 3bgw_A          206 PSMGKTAFALKQAKNMSDND--DVVNLHSLEM--GKKENIKRLIVT  247 (444)
T ss_dssp             SSSSHHHHHHHHHHHHHHTT--CEEEEECSSS--CTTHHHHHHHHH
T ss_pred             CCCChHHHHHHHHHHHHHcC--CEEEEEECCC--CHHHHHHHHHHH
Confidence            79999999999988765442  3577776654  344555555543

>4fcw_A Chaperone protein CLPB; AAA domain; HET: ADP; 2.35A {Thermus thermophilus} PDB: 4fcv_A* 4fd2_A* 4fct_A*

Probab=84.74  E-value=0.39  Score=40.20  Aligned_cols=29  Identities=28%  Similarity=0.424  Sum_probs=19.7

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVS   32 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~   32 (283)
                      +|+|||+||+.+++.....  -...+.++.+
T Consensus        56 ~GtGKt~la~~la~~~~~~--~~~~~~~~~~   84 (311)
T 4fcw_A           56 TGVGKTELAKTLAATLFDT--EEAMIRIDMT   84 (311)
T ss_dssp             SSSSHHHHHHHHHHHHHSC--GGGEEEEEGG
T ss_pred             CCcCHHHHHHHHHHHHcCC--CcceEEeecc
Confidence            6999999999999876432  1224455544

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=84.64  E-value=0.35  Score=43.10  Aligned_cols=18  Identities=39%  Similarity=0.536  Sum_probs=16.1

Q ss_pred             CCCcHHHHHHHHHhhhcc
Q 041028            2 GGIGKTTLAKEVARKAKN   19 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~   19 (283)
                      +|.|||.||+++++....
T Consensus       224 PGTGKTllAkAiA~e~~~  241 (434)
T 4b4t_M          224 PGTGKTLLARACAAQTNA  241 (434)
T ss_dssp             TTSSHHHHHHHHHHHHTC
T ss_pred             CCCCHHHHHHHHHHHhCC
Confidence            799999999999998653

>1iqp_A RFCS; clamp loader, extended AAA-ATPase domain, complex with ADP, replication; HET: ADP; 2.80A {Pyrococcus furiosus} SCOP: a.80.1.1 c.37.1.20

Probab=84.58  E-value=0.42  Score=40.17  Aligned_cols=17  Identities=47%  Similarity=0.542  Sum_probs=15.1

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      +|+||||+|+.+++...
T Consensus        55 ~G~GKT~la~~l~~~l~   71 (327)
T 1iqp_A           55 PGVGKTTAALALARELF   71 (327)
T ss_dssp             TTSSHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHhc
Confidence            69999999999998753

>1vht_A Dephospho-COA kinase; structural genomics, transferase; HET: BA3; 1.59A {Escherichia coli} SCOP: c.37.1.1 PDB: 1vhl_A* 1viy_A 1t3h_A 1n3b_A

Probab=84.50  E-value=0.45  Score=37.69  Aligned_cols=15  Identities=40%  Similarity=0.397  Sum_probs=13.2

Q ss_pred             CCCCcHHHHHHHHHh
Q 041028            1 MGGIGKTTLAKEVAR   15 (283)
Q Consensus         1 mgGiGKTtLA~~v~~   15 (283)
                      +.|+||||+++.+..
T Consensus        12 ~~GSGKST~~~~L~~   26 (218)
T 1vht_A           12 GIGSGKSTVANAFAD   26 (218)
T ss_dssp             CTTSCHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHH
Confidence            469999999999976

>3ake_A Cytidylate kinase; CMP kinase, CMP complex, open conformation, nucleotide metab transferase; HET: C5P; 1.50A {Thermus thermophilus} PDB: 3akc_A* 3akd_A*

Probab=84.48  E-value=0.47  Score=37.05  Aligned_cols=18  Identities=28%  Similarity=0.359  Sum_probs=15.3

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      ..|+||||+|+.+.....
T Consensus        10 ~~GsGKst~~~~la~~lg   27 (208)
T 3ake_A           10 PSASGKSSVARRVAAALG   27 (208)
T ss_dssp             STTSSHHHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHHhcC
Confidence            369999999999988654

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=84.48  E-value=0.35  Score=43.07  Aligned_cols=18  Identities=50%  Similarity=0.521  Sum_probs=16.1

Q ss_pred             CCCcHHHHHHHHHhhhcc
Q 041028            2 GGIGKTTLAKEVARKAKN   19 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~   19 (283)
                      +|+|||+||+++++....
T Consensus       224 PGtGKTllAkAiA~e~~~  241 (437)
T 4b4t_L          224 PGTGKTLLAKAVAATIGA  241 (437)
T ss_dssp             TTSSHHHHHHHHHHHHTC
T ss_pred             CCCcHHHHHHHHHHHhCC
Confidence            799999999999998764

>1uj2_A Uridine-cytidine kinase 2; alpha/beta mononucleotide-binding HOLD, transferase; HET: C5P ADP; 1.80A {Homo sapiens} SCOP: c.37.1.6 PDB: 1uei_A* 1uej_A* 1udw_A 1ufq_A* 1xrj_A*

Probab=84.37  E-value=0.46  Score=38.71  Aligned_cols=18  Identities=11%  Similarity=0.193  Sum_probs=15.1

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      +.|+||||+|+.+.....
T Consensus        30 ~~GSGKST~a~~L~~~lg   47 (252)
T 1uj2_A           30 GTASGKSSVCAKIVQLLG   47 (252)
T ss_dssp             STTSSHHHHHHHHHHHTT
T ss_pred             CCCCCHHHHHHHHHHHhh
Confidence            369999999999988644

>3ld9_A DTMP kinase, thymidylate kinase; ssgcid, NIH, niaid, SBRI, UW, emerald biostructures, ehrlich chaffeensis; 2.15A {Ehrlichia chaffeensis}

Probab=84.27  E-value=0.74  Score=37.01  Aligned_cols=45  Identities=20%  Similarity=0.245  Sum_probs=26.9

Q ss_pred             CCCCcHHHHHHHHHhhhcc-CCCCCeEEEEEeCCCCCHHHHHHHHHH
Q 041028            1 MGGIGKTTLAKEVARKAKN-GKLFDQIVFTEVSQNPNIKKIQGEIAF   46 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~-~~~Fd~~~wv~v~~~~~~~~l~~~i~~   46 (283)
                      ..|+||||+++.+.+.... . .++.++...-.......+.+++++.
T Consensus        29 ~~g~GKst~~~~l~~~l~~~~-g~~v~~~treP~~t~~g~~ir~~l~   74 (223)
T 3ld9_A           29 IDGSGKTTQSHLLAEYLSEIY-GVNNVVLTREPGGTLLNESVRNLLF   74 (223)
T ss_dssp             STTSSHHHHHHHHHHHHHHHH-CGGGEEEEESSCSSHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHhhcc-CceeeEeeeCCCCChHHHHHHHHHh
Confidence            3699999999999988654 3 2444432222222234555566655

>1rz3_A Hypothetical protein rbstp0775; MCSG, structural genomics, PSI, protein structure initiative; 1.90A {Geobacillus stearothermophilus} SCOP: c.37.1.6

Probab=84.27  E-value=0.45  Score=37.34  Aligned_cols=17  Identities=35%  Similarity=0.536  Sum_probs=14.7

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      .|+|||||++.+.....
T Consensus        31 ~GsGKstl~~~l~~~~~   47 (201)
T 1rz3_A           31 SRSGKTTLANQLSQTLR   47 (201)
T ss_dssp             TTSSHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHh
Confidence            69999999999987654

>1sxj_D Activator 1 41 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=84.20  E-value=0.44  Score=40.60  Aligned_cols=16  Identities=25%  Similarity=0.399  Sum_probs=14.5

Q ss_pred             CCCcHHHHHHHHHhhh
Q 041028            2 GGIGKTTLAKEVARKA   17 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~   17 (283)
                      +|+||||||+.+++..
T Consensus        67 ~G~GKT~la~~la~~l   82 (353)
T 1sxj_D           67 PGTGKTSTILALTKEL   82 (353)
T ss_dssp             TTSSHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHh
Confidence            6999999999999874

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=84.18  E-value=0.44  Score=42.65  Aligned_cols=17  Identities=59%  Similarity=0.710  Sum_probs=15.2

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      +|+||||||+.+++...
T Consensus        59 pGtGKTtlAr~ia~~~~   75 (447)
T 3pvs_A           59 PGTGKTTLAEVIARYAN   75 (447)
T ss_dssp             TTSSHHHHHHHHHHHTT
T ss_pred             CCCcHHHHHHHHHHHhC
Confidence            69999999999998764

>1um8_A ATP-dependent CLP protease ATP-binding subunit CL; CLPP binding loop, chaperone; HET: ADP; 2.60A {Helicobacter pylori} SCOP: c.37.1.20

Probab=84.06  E-value=0.46  Score=41.22  Aligned_cols=17  Identities=35%  Similarity=0.552  Sum_probs=15.1

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      +|+|||+||+.+++...
T Consensus        81 ~GtGKT~la~~la~~l~   97 (376)
T 1um8_A           81 TGSGKTLMAQTLAKHLD   97 (376)
T ss_dssp             TTSSHHHHHHHHHHHTT
T ss_pred             CCCCHHHHHHHHHHHhC
Confidence            69999999999998763

>3hws_A ATP-dependent CLP protease ATP-binding subunit CL; CLPXP, AAA+ molecular machine, hexamer, asymmetric,, ATP-BIN chaperone, metal-binding; HET: ADP; 3.25A {Escherichia coli} PDB: 3hte_A

Probab=83.95  E-value=0.46  Score=41.03  Aligned_cols=17  Identities=47%  Similarity=0.556  Sum_probs=15.2

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      +|+|||++|+.+++...
T Consensus        60 pGtGKT~la~~ia~~~~   76 (363)
T 3hws_A           60 TGSGKTLLAETLARLLD   76 (363)
T ss_dssp             TTSSHHHHHHHHHHHTT
T ss_pred             CCCCHHHHHHHHHHHcC
Confidence            69999999999998763

>1htw_A HI0065; nucleotide-binding fold, structural genomics, structure 2 function project, S2F, unknown function; HET: ADP; 1.70A {Haemophilus influenzae} SCOP: c.37.1.18 PDB: 1fl9_A

Probab=83.90  E-value=0.47  Score=35.92  Aligned_cols=16  Identities=38%  Similarity=0.474  Sum_probs=14.0

Q ss_pred             CCCcHHHHHHHHHhhh
Q 041028            2 GGIGKTTLAKEVARKA   17 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~   17 (283)
                      .|.|||||.+.++.-.
T Consensus        42 nGaGKTTLlr~l~g~l   57 (158)
T 1htw_A           42 LGAGKTTLTRGMLQGI   57 (158)
T ss_dssp             TTSSHHHHHHHHHHHT
T ss_pred             CCCCHHHHHHHHHHhC
Confidence            4999999999998865

>2j37_W Signal recognition particle 54 kDa protein (SRP54); ribosome, SRP, translation/RNA; 8.00A {Canis SP} PDB: 1wgw_A

Probab=83.87  E-value=6.1  Score=35.77  Aligned_cols=48  Identities=17%  Similarity=0.109  Sum_probs=27.1

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCC-CCCHHHHHHHHHHHhCCC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQ-NPNIKKIQGEIAFKLGLK   51 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~-~~~~~~l~~~i~~~l~~~   51 (283)
                      +|+||||++..++......+ . .+.-|+... .+...+.++......+.+
T Consensus       110 ~GvGKTTl~~kLA~~l~~~G-~-kVllVd~D~~r~aa~~qL~~~~~~~~i~  158 (504)
T 2j37_W          110 QGSGKTTTCSKLAYYYQRKG-W-KTCLICADTFRAGAFDQLKQNATKARIP  158 (504)
T ss_dssp             TTSSHHHHHHHHHHHHHHTT-C-CEEEEEECCSSSHHHHHHHHHHHHHTCC
T ss_pred             CCCCHHHHHHHHHHHHHhCC-C-eEEEEeccccchhHHHHHHHHhhccCce
Confidence            69999999999987765432 2 244455432 222333334444444543

>2ce2_X GTPase HRAS; signaling protein, guanine nucleotide binding protein, fluor membrane, lipoprotein, palmitate, prenylation; HET: GDP XY2; 1.0A {Homo sapiens} PDB: 2cl0_X* 2cl6_X* 2cl7_X* 2clc_X* 2evw_X* 2cld_X* 1aa9_A* 1ioz_A* 1q21_A* 6q21_A* 3k9l_A* 3k9n_A* 1ctq_A* 1bkd_R 1crp_A* 1crq_A* 1crr_A* 121p_A* 1gnp_A* 1gnq_A* ...

Probab=83.86  E-value=0.46  Score=35.12  Aligned_cols=16  Identities=31%  Similarity=0.727  Sum_probs=13.8

Q ss_pred             CCCcHHHHHHHHHhhh
Q 041028            2 GGIGKTTLAKEVARKA   17 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~   17 (283)
                      +|+|||||...+.+..
T Consensus        12 ~~~GKssl~~~l~~~~   27 (166)
T 2ce2_X           12 GGVGKSALTIQLIQNH   27 (166)
T ss_dssp             TTSSHHHHHHHHHHSS
T ss_pred             CCCCHHHHHHHHHhCc
Confidence            6999999999998653

>4e22_A Cytidylate kinase; P-loop, CMP/ATP binding, transferase; 2.32A {Yersinia pseudotuberculosis}

Probab=83.85  E-value=0.51  Score=38.53  Aligned_cols=18  Identities=39%  Similarity=0.501  Sum_probs=15.4

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      +.|+|||||++.+.....
T Consensus        35 ~~GsGKSTl~k~La~~Lg   52 (252)
T 4e22_A           35 PSGAGKGTLCKALAESLN   52 (252)
T ss_dssp             CTTSSHHHHHHHHHHHTT
T ss_pred             CCCCCHHHHHHHHHHhcC
Confidence            469999999999997654

>4b4t_H 26S protease regulatory subunit 7 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=83.83  E-value=0.39  Score=43.00  Aligned_cols=18  Identities=39%  Similarity=0.530  Sum_probs=16.1

Q ss_pred             CCCcHHHHHHHHHhhhcc
Q 041028            2 GGIGKTTLAKEVARKAKN   19 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~   19 (283)
                      +|+|||+||+++++....
T Consensus       252 PGTGKTlLAkAiA~e~~~  269 (467)
T 4b4t_H          252 PGTGKTLCARAVANRTDA  269 (467)
T ss_dssp             TTSSHHHHHHHHHHHHTC
T ss_pred             CCCcHHHHHHHHHhccCC
Confidence            699999999999998764

>3igf_A ALL4481 protein; two-domained protein consisting of the N-terminal alpha-beta the C-terminal all beta domain., structural genomics; 2.00A {Nostoc SP}

Probab=83.75  E-value=0.52  Score=41.13  Aligned_cols=34  Identities=15%  Similarity=0.375  Sum_probs=22.5

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHH
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIK   38 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~   38 (283)
                      ||+||||+|..++......+  ..++-|+. ...++.
T Consensus        11 GG~GKTt~a~~la~~la~~g--~~vllvd~-~~~~l~   44 (374)
T 3igf_A           11 SGVARTKIAIAAAKLLASQG--KRVLLAGL-AEPVLP   44 (374)
T ss_dssp             BHHHHHHHHHHHHHHHHHTT--CCEEEEEC-SCSHHH
T ss_pred             CCCcHHHHHHHHHHHHHHCC--CCeEEEeC-CCCChH
Confidence            89999999999887654432  23556666 444333

>2ocp_A DGK, deoxyguanosine kinase; protein-nucleotide complex, transferase; HET: DTP; 2.80A {Homo sapiens} SCOP: c.37.1.1

Probab=83.72  E-value=0.53  Score=38.03  Aligned_cols=17  Identities=24%  Similarity=0.350  Sum_probs=14.9

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      .|+||||+++.+++...
T Consensus        11 ~g~GKtt~~~~l~~~l~   27 (241)
T 2ocp_A           11 IAVGKSTFVKLLTKTYP   27 (241)
T ss_dssp             TTSSHHHHHHHHHHHCT
T ss_pred             CCCCHHHHHHHHHHHcC
Confidence            69999999999998753

>1ex7_A Guanylate kinase; substrate-induced FIT, domain movement, GMP, ATP, substrate specificity, X-RAY diffraction, transferase; HET: 5GP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1ex6_A* 1gky_A* 3sqk_A 4f4j_A

Probab=83.72  E-value=0.52  Score=36.76  Aligned_cols=16  Identities=38%  Similarity=0.528  Sum_probs=14.0

Q ss_pred             CCCcHHHHHHHHHhhh
Q 041028            2 GGIGKTTLAKEVARKA   17 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~   17 (283)
                      +|+|||||++.+..+.
T Consensus        10 SG~GK~Tl~~~L~~~~   25 (186)
T 1ex7_A           10 SGTGKSTLLKKLFAEY   25 (186)
T ss_dssp             TTSSHHHHHHHHHHHC
T ss_pred             CCCCHHHHHHHHHHhC
Confidence            6999999999998764

>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A 2r6e_A 2vyf_A 2vye_A

Probab=83.49  E-value=1  Score=40.22  Aligned_cols=41  Identities=12%  Similarity=0.255  Sum_probs=28.0

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHH
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIA   45 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~   45 (283)
                      +|+||||||..++....... =..++|++...  +..++...++
T Consensus       212 pG~GKTtl~l~ia~~~~~~~-g~~Vl~~s~E~--s~~~l~~r~~  252 (454)
T 2r6a_A          212 PSVGKTAFALNIAQNVATKT-NENVAIFSLEM--SAQQLVMRML  252 (454)
T ss_dssp             TTSCHHHHHHHHHHHHHHHS-SCCEEEEESSS--CHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHhC-CCcEEEEECCC--CHHHHHHHHH
Confidence            69999999999988765321 12577777654  4466666664

>2wsm_A Hydrogenase expression/formation protein (HYPB); metal binding protein; 2.30A {Archaeoglobus fulgidus}

Probab=83.45  E-value=0.52  Score=37.20  Aligned_cols=17  Identities=29%  Similarity=0.325  Sum_probs=14.7

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      +|+|||||+..+.....
T Consensus        39 ~g~GKTTl~~~l~~~~~   55 (221)
T 2wsm_A           39 IGSGKTLLIERTIERIG   55 (221)
T ss_dssp             TTSCHHHHHHHHHHHHT
T ss_pred             CCCCHHHHHHHHHHHhc
Confidence            69999999999988753

>4gp7_A Metallophosphoesterase; polynucleotide kinase phosphatase, RNA repair, transferase; HET: ATP CIT; 2.00A {Clostridium thermocellum} PDB: 4gp6_A*

Probab=83.25  E-value=0.41  Score=36.52  Aligned_cols=13  Identities=46%  Similarity=0.603  Sum_probs=11.3

Q ss_pred             CCCcHHHHHHHHH
Q 041028            2 GGIGKTTLAKEVA   14 (283)
Q Consensus         2 gGiGKTtLA~~v~   14 (283)
                      .|.|||||++.++
T Consensus        18 nGsGKSTl~~~~~   30 (171)
T 4gp7_A           18 SGSGKSTFAKKHF   30 (171)
T ss_dssp             TTSCHHHHHHHHS
T ss_pred             CCCCHHHHHHHHc
Confidence            5999999999854

>1q57_A DNA primase/helicase; dntpase, DNA replication, transferase; HET: DNA; 3.45A {Enterobacteria phage T7} SCOP: c.37.1.11 e.13.1.2

Probab=83.07  E-value=1.4  Score=39.94  Aligned_cols=43  Identities=7%  Similarity=0.107  Sum_probs=30.2

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHHH
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFK   47 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~~   47 (283)
                      +|+||||||..++.+...+. =..++|++...  +..++...++..
T Consensus       251 pG~GKT~lal~~a~~~a~~~-g~~vl~~s~E~--s~~~l~~r~~~~  293 (503)
T 1q57_A          251 SGMVMSTFVRQQALQWGTAM-GKKVGLAMLEE--SVEETAEDLIGL  293 (503)
T ss_dssp             SCHHHHHHHHHHHHHHTTTS-CCCEEEEESSS--CHHHHHHHHHHH
T ss_pred             CCCCchHHHHHHHHHHHHhc-CCcEEEEeccC--CHHHHHHHHHHH
Confidence            69999999999988765431 13577877655  456777776543

>1sxj_A Activator 1 95 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=83.03  E-value=0.51  Score=42.99  Aligned_cols=16  Identities=56%  Similarity=0.628  Sum_probs=14.8

Q ss_pred             CCCcHHHHHHHHHhhh
Q 041028            2 GGIGKTTLAKEVARKA   17 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~   17 (283)
                      +|+||||||+.+++..
T Consensus        86 pGtGKTtla~~la~~l  101 (516)
T 1sxj_A           86 PGIGKTTAAHLVAQEL  101 (516)
T ss_dssp             TTSSHHHHHHHHHHHT
T ss_pred             CCCCHHHHHHHHHHHc
Confidence            6999999999999876

>1lvg_A Guanylate kinase, GMP kinase; transferase; HET: ADP 5GP; 2.10A {Mus musculus} SCOP: c.37.1.1

Probab=82.93  E-value=0.55  Score=36.79  Aligned_cols=16  Identities=38%  Similarity=0.596  Sum_probs=14.0

Q ss_pred             CCCcHHHHHHHHHhhh
Q 041028            2 GGIGKTTLAKEVARKA   17 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~   17 (283)
                      .|+|||||++.+....
T Consensus        13 sGaGKSTLl~~L~~~~   28 (198)
T 1lvg_A           13 SGAGKSTLLKKLFQEH   28 (198)
T ss_dssp             TTSSHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHhhC
Confidence            5999999999998754

>3u61_B DNA polymerase accessory protein 44; AAA+, ATP hydrolase, clamp loader, sliding clamp, primer-TEM DNA, DNA binding protein-DNA complex; HET: DNA ADP 08T; 3.20A {Enterobacteria phage T4} PDB: 3u5z_B* 3u60_B*

Probab=82.86  E-value=0.55  Score=39.69  Aligned_cols=17  Identities=41%  Similarity=0.606  Sum_probs=15.0

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      +|+|||++|+.+++...
T Consensus        57 ~G~GKT~la~~la~~l~   73 (324)
T 3u61_B           57 PGTGKTTVAKALCHDVN   73 (324)
T ss_dssp             TTSSHHHHHHHHHHHTT
T ss_pred             CCCCHHHHHHHHHHHhC
Confidence            69999999999998763

>2ga8_A Hypothetical 39.9 kDa protein; YFR007W, YFH7, unknown function; HET: CME; 1.77A {Saccharomyces cerevisiae} PDB: 2gaa_A*

Probab=82.72  E-value=0.6  Score=40.36  Aligned_cols=18  Identities=33%  Similarity=0.506  Sum_probs=15.4

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      ++|+||||+++.++....
T Consensus        32 ~~G~GKTTl~~~la~~l~   49 (359)
T 2ga8_A           32 SPGSGKSTIAEELCQIIN   49 (359)
T ss_dssp             CTTSSHHHHHHHHHHHHH
T ss_pred             CCCCcHHHHHHHHHHHhC
Confidence            579999999999988654

>1odf_A YGR205W, hypothetical 33.3 kDa protein in ADE3-Ser2 intergenic region; yeast protein, ATP binding protein; 2.25A {Saccharomyces cerevisiae} SCOP: c.37.1.6

Probab=82.64  E-value=0.55  Score=39.40  Aligned_cols=44  Identities=11%  Similarity=0.024  Sum_probs=24.7

Q ss_pred             CCCcHHHHHHHHHhhhccCC-CCCeEEEEEeCCCCCHHHHHHHHH
Q 041028            2 GGIGKTTLAKEVARKAKNGK-LFDQIVFTEVSQNPNIKKIQGEIA   45 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~-~Fd~~~wv~v~~~~~~~~l~~~i~   45 (283)
                      .|+||||||+.+........ ....+..|+...-+-.......+.
T Consensus        40 sGsGKSTla~~L~~~l~~~g~~~~~~~iv~~D~f~~~~~~~~~l~   84 (290)
T 1odf_A           40 QGSGKSFTSIQIYNHLMEKYGGEKSIGYASIDDFYLTHEDQLKLN   84 (290)
T ss_dssp             TTSSHHHHHHHHHHHHHHHHGGGSCEEEEEGGGGBCCHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHhhhcCCCCceEEEeccccccCChHHHHHHh
Confidence            59999999999887654321 022344445544333334444443

>3r20_A Cytidylate kinase; structural genomics, seattle structural genomics center for infectious disease, ssgcid, ADP, DCMP, D transferase; 2.00A {Mycobacterium smegmatis} SCOP: c.37.1.0 PDB: 3r8c_A 4die_A*

Probab=82.64  E-value=0.63  Score=37.70  Aligned_cols=18  Identities=28%  Similarity=0.517  Sum_probs=15.3

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      .+|+||||+|+.+.....
T Consensus        17 ~~GsGKsTla~~la~~lg   34 (233)
T 3r20_A           17 PAGTGKSSVSRGLARALG   34 (233)
T ss_dssp             CTTSSHHHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHHHhC
Confidence            369999999999988754

>1pzn_A RAD51, DNA repair and recombination protein RAD51, RADA; heptameric ring, heptamer, ring, oligomer, RAD51 polymerizat motif; HET: DNA; 2.85A {Pyrococcus furiosus} SCOP: a.60.4.1 c.37.1.11

Probab=82.53  E-value=1.4  Score=37.91  Aligned_cols=47  Identities=23%  Similarity=0.259  Sum_probs=28.8

Q ss_pred             CCCcHHHHHHHHHhhhccC---CCCC-eEEEEEeCCCCCHHHHHHHHHHHhC
Q 041028            2 GGIGKTTLAKEVARKAKNG---KLFD-QIVFTEVSQNPNIKKIQGEIAFKLG   49 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~---~~Fd-~~~wv~v~~~~~~~~l~~~i~~~l~   49 (283)
                      .|+|||||+..++......   +... .++|++....+.... +..+++..+
T Consensus       140 ~GsGKTTL~~~l~~~~~~~~~~Gg~~G~vi~i~~e~~~~~~~-i~~i~q~~~  190 (349)
T 1pzn_A          140 FGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDTENTFRPER-IREIAQNRG  190 (349)
T ss_dssp             TTSSHHHHHHHHHHHTTSCGGGTSCSCEEEEEESSSCCCHHH-HHHHHHTTT
T ss_pred             CCCCHHHHHHHHHHHhccchhcCCCCCeEEEEeCCCCCCHHH-HHHHHHHcC
Confidence            6999999999998765211   1112 348888766654433 334555444

>2r44_A Uncharacterized protein; putative ATPase, structural genomics, joint center for struc genomics, JCSG; HET: MSE PG4; 2.00A {Cytophaga hutchinsonii atcc 33406}

Probab=82.52  E-value=0.41  Score=40.68  Aligned_cols=17  Identities=24%  Similarity=0.358  Sum_probs=15.0

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      +|+|||+||+.+++...
T Consensus        55 pGtGKT~la~~la~~~~   71 (331)
T 2r44_A           55 PGLAKTLSVNTLAKTMD   71 (331)
T ss_dssp             CCHHHHHHHHHHHHHTT
T ss_pred             CCCcHHHHHHHHHHHhC
Confidence            69999999999998654

>2c9o_A RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-binding, chromatin regulator, growth regulation, hydrolase, nuclear protein, DNA recombination; HET: ADP; 2.2A {Homo sapiens} PDB: 2xsz_A*

Probab=82.52  E-value=0.58  Score=41.89  Aligned_cols=17  Identities=41%  Similarity=0.540  Sum_probs=15.6

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      +|+|||+||+.+++...
T Consensus        72 pGtGKT~la~ala~~l~   88 (456)
T 2c9o_A           72 PGTGKTALALAIAQELG   88 (456)
T ss_dssp             TTSSHHHHHHHHHHHHC
T ss_pred             CcCCHHHHHHHHHHHhC
Confidence            69999999999999865

>2jeo_A Uridine-cytidine kinase 1; UCK, transferase, ATP-binding, nucleoside kinase, nucleotide-binding; 2.50A {Homo sapiens} PDB: 2uvq_A*

Probab=82.51  E-value=0.57  Score=38.00  Aligned_cols=16  Identities=19%  Similarity=0.327  Sum_probs=13.8

Q ss_pred             CCCcHHHHHHHHHhhh
Q 041028            2 GGIGKTTLAKEVARKA   17 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~   17 (283)
                      .|+|||||++.+....
T Consensus        34 ~GsGKSTl~k~L~~~l   49 (245)
T 2jeo_A           34 TASGKSTVCEKIMELL   49 (245)
T ss_dssp             TTSSHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHh
Confidence            5999999999998754

>1znw_A Guanylate kinase, GMP kinase; ATP:GMP-phosphotransferase, TR; 2.10A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1znx_A* 1zny_A* 1znz_A* 1s4q_A 1z8f_A

Probab=82.49  E-value=0.58  Score=36.83  Aligned_cols=16  Identities=19%  Similarity=0.478  Sum_probs=14.2

Q ss_pred             CCCcHHHHHHHHHhhh
Q 041028            2 GGIGKTTLAKEVARKA   17 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~   17 (283)
                      .|+|||||++.+..-.
T Consensus        29 nGsGKSTLl~~l~gl~   44 (207)
T 1znw_A           29 SAVGKSTVVRCLRERI   44 (207)
T ss_dssp             TTSSHHHHHHHHHHHS
T ss_pred             CCCCHHHHHHHHHhhC
Confidence            5999999999998765

>2dyk_A GTP-binding protein; GTPase, ribosome-binding protein, structural genomics; HET: GDP; 1.96A {Thermus thermophilus}

Probab=82.47  E-value=0.55  Score=34.64  Aligned_cols=16  Identities=25%  Similarity=0.490  Sum_probs=13.7

Q ss_pred             CCCcHHHHHHHHHhhh
Q 041028            2 GGIGKTTLAKEVARKA   17 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~   17 (283)
                      +|+|||||...+.+..
T Consensus        10 ~~~GKSsli~~l~~~~   25 (161)
T 2dyk_A           10 PNVGKSSLFNRLLKKR   25 (161)
T ss_dssp             TTSSHHHHHHHHHHCC
T ss_pred             CCCCHHHHHHHHhCCC
Confidence            6999999999998753

>4b4t_I 26S protease regulatory subunit 4 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=82.40  E-value=0.48  Score=42.03  Aligned_cols=18  Identities=50%  Similarity=0.612  Sum_probs=16.2

Q ss_pred             CCCcHHHHHHHHHhhhcc
Q 041028            2 GGIGKTTLAKEVARKAKN   19 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~   19 (283)
                      +|.|||.||+++++....
T Consensus       225 PGTGKTlLAkAiA~e~~~  242 (437)
T 4b4t_I          225 PGTGKTLLAKAVANQTSA  242 (437)
T ss_dssp             TTTTHHHHHHHHHHHHTC
T ss_pred             CCchHHHHHHHHHHHhCC
Confidence            799999999999998764

>1jr3_A DNA polymerase III subunit gamma; processivity, processivity clamp, clamp loader, AAA+ ATPase, transferase; HET: DNA; 2.70A {Escherichia coli} SCOP: a.80.1.1 c.37.1.20 PDB: 1xxh_B* 3glh_B* 3glf_B* 3gli_B* 3glg_B* 1xxi_B*

Probab=82.38  E-value=0.58  Score=40.21  Aligned_cols=18  Identities=33%  Similarity=0.578  Sum_probs=15.5

Q ss_pred             CCCcHHHHHHHHHhhhcc
Q 041028            2 GGIGKTTLAKEVARKAKN   19 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~   19 (283)
                      +|+||||+|+.+++....
T Consensus        47 ~G~GKT~la~~la~~l~~   64 (373)
T 1jr3_A           47 RGVGKTSIARLLAKGLNC   64 (373)
T ss_dssp             TTSSHHHHHHHHHHHHSC
T ss_pred             CCCCHHHHHHHHHHHhCC
Confidence            699999999999987643

>1vma_A Cell division protein FTSY; TM0570, structural genomics, JCS protein structure initiative, PSI, joint center for structu genomics; HET: CIT; 1.60A {Thermotoga maritima} SCOP: a.24.13.1 c.37.1.10

Probab=82.34  E-value=1.5  Score=36.96  Aligned_cols=47  Identities=17%  Similarity=0.177  Sum_probs=27.7

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCH--HHHHHHHHHHhCCC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNI--KKIQGEIAFKLGLK   51 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~--~~l~~~i~~~l~~~   51 (283)
                      +|+||||++..++......+  ..+.++... .+..  .+-+..+++.++.+
T Consensus       113 ~GsGKTTl~~~LA~~l~~~g--~kV~lv~~D-~~r~~a~eqL~~~~~~~gl~  161 (306)
T 1vma_A          113 NGTGKTTSCGKLAKMFVDEG--KSVVLAAAD-TFRAAAIEQLKIWGERVGAT  161 (306)
T ss_dssp             TTSSHHHHHHHHHHHHHHTT--CCEEEEEEC-TTCHHHHHHHHHHHHHHTCE
T ss_pred             CCChHHHHHHHHHHHHHhcC--CEEEEEccc-cccHHHHHHHHHHHHHcCCc
Confidence            69999999999998765431  234555443 2222  22334555665543

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=82.27  E-value=3  Score=44.18  Aligned_cols=69  Identities=19%  Similarity=0.181  Sum_probs=44.0

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCC------cCCHhhhHHhHHHHccC--CcE
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKLGLKFD------EESESGRTRSPWSRLKK--EKL   73 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~~l~~~~~------~~~~~~~~~~l~~~L~~--kr~   73 (283)
                      +|+|||+||.++.......+  ..++|+++...++...     ++.+|.+.+      ....++..+.++...+.  -+.
T Consensus      1436 pGtGKT~LA~ala~ea~~~G--~~v~Fi~~e~~~~~l~-----a~~~G~dl~~l~v~~~~~~E~~l~~~~~lvr~~~~~l 1508 (2050)
T 3cmu_A         1436 ESSGKTTLTLQVIAAAQREG--KTCAFIDAEHALDPIY-----ARKLGVDIDNLLCSQPDTGEQALEICDALARSGAVDV 1508 (2050)
T ss_dssp             TTSSHHHHHHHHHHHHHTTT--CCEEEECTTSCCCHHH-----HHHTTCCTTTCEEECCSSHHHHHHHHHHHHHHTCCSE
T ss_pred             CCCCHHHHHHHHHHHHHHcC--CcEEEEEcccccCHHH-----HHHcCCCchhceeecCChHHHHHHHHHHHHhcCCCCE
Confidence            69999999999988765432  3578888888877766     556664322      12334445555555432  267


Q ss_pred             EEEc
Q 041028           74 QIIC   77 (283)
Q Consensus        74 LlV~   77 (283)
                      ++|+
T Consensus      1509 VVID 1512 (2050)
T 3cmu_A         1509 IVVD 1512 (2050)
T ss_dssp             EEES
T ss_pred             EEEc
Confidence            7773

>3crm_A TRNA delta(2)-isopentenylpyrophosphate transferase; ATP-binding, nucleotide-binding, nucleotidyltransferase, tRNA processing; 1.90A {Pseudomonas aeruginosa} PDB: 3crq_A 3crr_A

Probab=82.23  E-value=0.64  Score=39.63  Aligned_cols=17  Identities=35%  Similarity=0.311  Sum_probs=14.7

Q ss_pred             CCCCcHHHHHHHHHhhh
Q 041028            1 MGGIGKTTLAKEVARKA   17 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (283)
                      ..|+||||||..++...
T Consensus        13 ptGsGKTtla~~La~~l   29 (323)
T 3crm_A           13 PTAAGKTDLAMALADAL   29 (323)
T ss_dssp             CTTSCHHHHHHHHHHHS
T ss_pred             CCCCCHHHHHHHHHHHc
Confidence            36999999999999864

>2zan_A Vacuolar protein sorting-associating protein 4B; SKD1, VPS4B, AAA ATPase, ATP-binding, coiled coil, membrane, nucleotide-binding, phosphorylation; HET: ATP; 3.00A {Mus musculus} PDB: 2zam_A* 2zao_A* 2jqh_A 2jqk_A 1wr0_A 2jq9_A 2k3w_A 1yxr_A

Probab=82.17  E-value=0.59  Score=41.74  Aligned_cols=16  Identities=56%  Similarity=0.679  Sum_probs=14.8

Q ss_pred             CCCcHHHHHHHHHhhh
Q 041028            2 GGIGKTTLAKEVARKA   17 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~   17 (283)
                      +|+|||+||+.+++..
T Consensus       176 pGtGKT~lA~aia~~~  191 (444)
T 2zan_A          176 PGTGKSYLAKAVATEA  191 (444)
T ss_dssp             TTSSHHHHHHHHHHHC
T ss_pred             CCCCHHHHHHHHHHHc
Confidence            6999999999999975

>1tue_A Replication protein E1; helicase, replication, E1E2 complex, AAA+ protein; 2.10A {Human papillomavirus type 18} SCOP: c.37.1.20

Probab=82.16  E-value=0.49  Score=37.61  Aligned_cols=17  Identities=12%  Similarity=0.165  Sum_probs=14.8

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      +|+||||+|..+++...
T Consensus        67 PGtGKTt~a~ala~~l~   83 (212)
T 1tue_A           67 ANTGKSYFGMSFIHFIQ   83 (212)
T ss_dssp             GGGCHHHHHHHHHHHHT
T ss_pred             CCCCHHHHHHHHHHHhC
Confidence            69999999999998753

>3tmk_A Thymidylate kinase; phosphotransferase; HET: T5A; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 2tmk_A* 1tmk_A*

Probab=82.02  E-value=1.9  Score=34.37  Aligned_cols=19  Identities=26%  Similarity=0.317  Sum_probs=16.3

Q ss_pred             CCCCcHHHHHHHHHhhhcc
Q 041028            1 MGGIGKTTLAKEVARKAKN   19 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~   19 (283)
                      ..|+||||+++.+.+....
T Consensus        13 ~~g~GKst~~~~l~~~l~~   31 (216)
T 3tmk_A           13 LDRTGKTTQCNILYKKLQP   31 (216)
T ss_dssp             CSSSSHHHHHHHHHHHHCS
T ss_pred             CCCCCHHHHHHHHHHHhcc
Confidence            3699999999999998763

>3aez_A Pantothenate kinase; transferase, homodimer, COA biosynthesis, nucleotide binding binding, cytoplasm, nucleotide-binding; HET: GDP PAZ; 2.20A {Mycobacterium tuberculosis} PDB: 2ges_A* 2geu_A* 2gev_A* 2zs7_A* 2zs8_A* 2zs9_A* 2zsa_A* 2zsb_A* 2zsd_A* 2zse_A* 2zsf_A* 2get_A* 3af0_A* 3af1_A* 3af2_A* 3af3_A* 3af4_A* 3avp_A* 3avo_A* 3avq_A*

Probab=82.01  E-value=0.59  Score=39.63  Aligned_cols=32  Identities=13%  Similarity=0.112  Sum_probs=20.4

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQ   33 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~   33 (283)
                      .|+|||||++.+..-......-..+.+|....
T Consensus        99 sGsGKSTL~~~L~gll~~~~G~~~v~~v~qd~  130 (312)
T 3aez_A           99 VAVGKSTTARVLQALLARWDHHPRVDLVTTDG  130 (312)
T ss_dssp             TTSCHHHHHHHHHHHHHTSTTCCCEEEEEGGG
T ss_pred             CCchHHHHHHHHHhhccccCCCCeEEEEecCc
Confidence            59999999999988654320002355665543

>3ney_A 55 kDa erythrocyte membrane protein; structural genomics consortium, SGC, 55 kDa erythrocyte MEMB protein; 2.26A {Homo sapiens} SCOP: c.37.1.0

Probab=81.99  E-value=0.66  Score=36.53  Aligned_cols=17  Identities=12%  Similarity=0.487  Sum_probs=14.5

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      .|+|||||++.+.....
T Consensus        28 SGaGKsTL~~~L~~~~~   44 (197)
T 3ney_A           28 SGVGRSHIKNALLSQNP   44 (197)
T ss_dssp             TTSSHHHHHHHHHHHCT
T ss_pred             CCCCHHHHHHHHHhhCC
Confidence            59999999999987643

>3zvl_A Bifunctional polynucleotide phosphatase/kinase; hydrolase-transferase complex, base excision repair, BER, non-homologous END-joining, NHEJ; 1.65A {Mus musculus} PDB: 3zvm_A* 3zvn_A* 1yj5_A 3u7e_B* 3u7f_B* 3u7h_B* 3u7g_A*

Probab=81.99  E-value=0.55  Score=41.56  Aligned_cols=17  Identities=35%  Similarity=0.456  Sum_probs=14.7

Q ss_pred             CCCCcHHHHHHHHHhhh
Q 041028            1 MGGIGKTTLAKEVARKA   17 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (283)
                      ++|+||||+|+.+..+.
T Consensus       266 ~pGSGKSTla~~L~~~~  282 (416)
T 3zvl_A          266 FPGAGKSTFIQEHLVSA  282 (416)
T ss_dssp             CTTSSHHHHHHHHTGGG
T ss_pred             CCCCCHHHHHHHHHHhc
Confidence            57999999999998754

>1oix_A RAS-related protein RAB-11A; small G protein, intracellular trafficking, GTP-binding, lipoprotein, prenylation, protein transport; HET: GDP; 1.7A {Homo sapiens} SCOP: c.37.1.8 PDB: 1oiw_A* 1oiv_A* 3rwo_B* 3rwm_B*

Probab=81.98  E-value=0.63  Score=35.97  Aligned_cols=16  Identities=31%  Similarity=0.655  Sum_probs=13.9

Q ss_pred             CCCcHHHHHHHHHhhh
Q 041028            2 GGIGKTTLAKEVARKA   17 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~   17 (283)
                      .|+|||||.+.+....
T Consensus        38 ~g~GKSTLl~~l~~~~   53 (191)
T 1oix_A           38 SGVGKSNLLSRFTRNE   53 (191)
T ss_dssp             TTSSHHHHHHHHHHSC
T ss_pred             CCCCHHHHHHHHhcCC
Confidence            6999999999998753

>2i3b_A HCR-ntpase, human cancer-related ntpase; AAA, rossmann, hydrolase; NMR {Homo sapiens} SCOP: c.37.1.11

Probab=81.89  E-value=0.67  Score=36.17  Aligned_cols=17  Identities=41%  Similarity=0.585  Sum_probs=14.7

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      .|+|||||++.++....
T Consensus        10 nG~GKTTll~~l~g~~~   26 (189)
T 2i3b_A           10 PGVGKTTLIHKASEVLK   26 (189)
T ss_dssp             CSSCHHHHHHHHHHHHH
T ss_pred             CCChHHHHHHHHHhhcc
Confidence            59999999999988654

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=81.88  E-value=0.62  Score=40.69  Aligned_cols=17  Identities=53%  Similarity=0.624  Sum_probs=14.8

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      +|+|||+||+.+++...
T Consensus       157 pGtGKT~la~aia~~~~  173 (389)
T 3vfd_A          157 PGNGKTMLAKAVAAESN  173 (389)
T ss_dssp             TTSCHHHHHHHHHHHTT
T ss_pred             CCCCHHHHHHHHHHhhc
Confidence            69999999999988743

>3con_A GTPase NRAS; structural genomics consortium, SGC, GDP, oncogene, disease mutation, golgi apparatus, GTP-binding, lipoprotein membrane, methylation; HET: GDP; 1.65A {Homo sapiens} PDB: 2pmx_A* 3gft_A* 4q21_A*

Probab=81.86  E-value=0.59  Score=35.75  Aligned_cols=16  Identities=31%  Similarity=0.727  Sum_probs=13.9

Q ss_pred             CCCcHHHHHHHHHhhh
Q 041028            2 GGIGKTTLAKEVARKA   17 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~   17 (283)
                      +|+|||||+..+....
T Consensus        30 ~~~GKSsli~~l~~~~   45 (190)
T 3con_A           30 GGVGKSALTIQLIQNH   45 (190)
T ss_dssp             TTSSHHHHHHHHHHSS
T ss_pred             CCCCHHHHHHHHHcCC
Confidence            6999999999998753

>2f6r_A COA synthase, bifunctional coenzyme A synthase; 18044849, bifunctional coenzyme A synthase (COA synthase), S genomics; HET: ACO UNL; 1.70A {Mus musculus}

Probab=81.82  E-value=0.62  Score=38.79  Aligned_cols=15  Identities=27%  Similarity=0.629  Sum_probs=13.2

Q ss_pred             CCCCcHHHHHHHHHh
Q 041028            1 MGGIGKTTLAKEVAR   15 (283)
Q Consensus         1 mgGiGKTtLA~~v~~   15 (283)
                      +.|+||||+|+.+..
T Consensus        83 ~~GSGKSTva~~La~   97 (281)
T 2f6r_A           83 ISGSGKSSVAQRLKN   97 (281)
T ss_dssp             CTTSCHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHH
Confidence            479999999999983

>1sxj_C Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=81.81  E-value=0.63  Score=39.73  Aligned_cols=17  Identities=35%  Similarity=0.425  Sum_probs=15.0

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      .|+||||+|+.+++...
T Consensus        55 ~G~GKTtla~~la~~l~   71 (340)
T 1sxj_C           55 PGTGKTSTIVALAREIY   71 (340)
T ss_dssp             SSSSHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHc
Confidence            59999999999998754

>3sr0_A Adenylate kinase; phosphoryl transfer analogue, ALF4, transferase (phosphotran phosphoryl transfer, nucleotide-binding; HET: ADP AMP; 1.56A {Aquifex aeolicus} PDB: 2rh5_A 2rgx_A*

Probab=81.72  E-value=0.68  Score=36.67  Aligned_cols=17  Identities=41%  Similarity=0.519  Sum_probs=15.2

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      +|+||||.|+.++.+..
T Consensus         9 PGsGKgTqa~~La~~~g   25 (206)
T 3sr0_A            9 PGAGKGTQAKRLAKEKG   25 (206)
T ss_dssp             TTSSHHHHHHHHHHHHC
T ss_pred             CCCCHHHHHHHHHHHHC
Confidence            79999999999998764

>1z6g_A Guanylate kinase; structural genomics, SGC, structural genom consortium, transferase; HET: EPE; 2.18A {Plasmodium falciparum}

Probab=81.60  E-value=0.65  Score=36.99  Aligned_cols=16  Identities=38%  Similarity=0.598  Sum_probs=14.0

Q ss_pred             CCCcHHHHHHHHHhhh
Q 041028            2 GGIGKTTLAKEVARKA   17 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~   17 (283)
                      .|+|||||++.+....
T Consensus        32 sGsGKSTLl~~L~g~~   47 (218)
T 1z6g_A           32 SGVGKGTLIKKLLNEF   47 (218)
T ss_dssp             TTSSHHHHHHHHHHHS
T ss_pred             CCCCHHHHHHHHHhhC
Confidence            5999999999998754

>1np6_A Molybdopterin-guanine dinucleotide biosynthesis protein B; mixed alpha-beta fold, elongated beta-sheet, walker A motif, P-loop structural motif; 1.90A {Escherichia coli} SCOP: c.37.1.10 PDB: 1p9n_A

Probab=81.57  E-value=0.71  Score=35.53  Aligned_cols=17  Identities=41%  Similarity=0.474  Sum_probs=14.7

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      .|+|||||+..+.....
T Consensus        15 sGsGKTTl~~~l~~~l~   31 (174)
T 1np6_A           15 SGTGKTTLLKKLIPALC   31 (174)
T ss_dssp             TTSCHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHhcc
Confidence            59999999999988754

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=81.52  E-value=3.3  Score=43.84  Aligned_cols=70  Identities=19%  Similarity=0.178  Sum_probs=45.7

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCC------cCCHhhhHHhHHHHcc--CCcE
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKLGLKFD------EESESGRTRSPWSRLK--KEKL   73 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~~l~~~~~------~~~~~~~~~~l~~~L~--~kr~   73 (283)
                      +|+||||||.+++......+  ..++|++....++...     ++.++.+.+      ..+.++..+.++...+  +-++
T Consensus       392 pGsGKTtLaLqia~~~a~~G--~~vlyis~E~s~~~~~-----a~~lGvd~~~L~I~~~~~~e~il~~~~~lv~~~~~~l  464 (2050)
T 3cmu_A          392 ESSGKTTLTLQVIAAAQREG--KTCAFIDAEHALDPIY-----ARKLGVDIDNLLCSQPDTGEQALEICDALARSGAVDV  464 (2050)
T ss_dssp             TTSSHHHHHHHHHHHHHTTT--CCEEEECTTSCCCHHH-----HHHTTCCTTTCEEECCSSHHHHHHHHHHHHHHTCCSE
T ss_pred             CCCCHHHHHHHHHHHHHhcC--CeEEEEEcCCCHHHHH-----HHHcCCCHHHeEEeCCCCHHHHHHHHHHHHHhcCCcE
Confidence            69999999999988765432  3689999888877642     566776432      2344555555554443  2367


Q ss_pred             EEEcC
Q 041028           74 QIICG   78 (283)
Q Consensus        74 LlV~G   78 (283)
                      ++|+.
T Consensus       465 IVIDS  469 (2050)
T 3cmu_A          465 IVVDS  469 (2050)
T ss_dssp             EEESC
T ss_pred             EEECC
Confidence            77743

>3cmw_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 2.80A {Escherichia coli} PDB: 3cmt_A* 3cmx_A* 3cmv_A*

Probab=81.29  E-value=2.8  Score=43.75  Aligned_cols=69  Identities=19%  Similarity=0.186  Sum_probs=43.6

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCC------cCCHhhhHHhHHHHcc--CCcE
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKLGLKFD------EESESGRTRSPWSRLK--KEKL   73 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~~l~~~~~------~~~~~~~~~~l~~~L~--~kr~   73 (283)
                      +|+||||||.+++......+  ..++|++........     .++.++.+.+      ..+.++..+.++...+  +-++
T Consensus       741 PG~GKTtLal~lA~~aa~~g--~~VlyiS~Ees~~ql-----~A~~lGvd~~~L~i~~~~~leei~~~l~~lv~~~~~~l  813 (1706)
T 3cmw_A          741 ESSGKTTLTLQVIAAAQREG--KTCAFIDAEHALDPI-----YARKLGVDIDNLLCSQPDTGEQALEICDALARSGAVDV  813 (1706)
T ss_dssp             TTSSHHHHHHHHHHHHHHTT--CCEEEECTTSCCCHH-----HHHHTTCCGGGCEEECCSSHHHHHHHHHHHHHHTCCSE
T ss_pred             CCCCcHHHHHHHHHHHHHcC--CCeEEEeccchHHHH-----HHHHcCCChhheEEecCCcHHHHHHHHHHHHHccCCCE
Confidence            69999999999988765432  357888887776653     1566665421      2244455555554443  2367


Q ss_pred             EEEc
Q 041028           74 QIIC   77 (283)
Q Consensus        74 LlV~   77 (283)
                      ++|+
T Consensus       814 VVID  817 (1706)
T 3cmw_A          814 IVVD  817 (1706)
T ss_dssp             EEES
T ss_pred             EEEe
Confidence            7774

>1g8f_A Sulfate adenylyltransferase; alpha-beta protein, beta-barrel, rossmann-fold, kinase fold; 1.95A {Saccharomyces cerevisiae} SCOP: b.122.1.3 c.26.1.5 c.37.1.15 PDB: 1g8g_A* 1g8h_A* 1j70_A 1jec_A 1jed_A* 1jee_A*

Probab=81.29  E-value=0.7  Score=42.05  Aligned_cols=19  Identities=5%  Similarity=-0.015  Sum_probs=16.5

Q ss_pred             CCCCcHHHHHHHHHhhhcc
Q 041028            1 MGGIGKTTLAKEVARKAKN   19 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~   19 (283)
                      +.|+||||+|+.++.....
T Consensus       403 lsGsGKSTIa~~La~~L~~  421 (511)
T 1g8f_A          403 SLTVSREQLSIALLSTFLQ  421 (511)
T ss_dssp             TCCSCHHHHHHHHHHHHTT
T ss_pred             cCCCCHHHHHHHHHHHHHH
Confidence            4699999999999998753

>3ez9_A Para; DNA binding, winged-HTH, partition, biosynthetic protein; 2.80A {Salmonella enterica subsp} PDB: 3ezf_A

Probab=81.27  E-value=0.35  Score=42.56  Aligned_cols=17  Identities=29%  Similarity=0.491  Sum_probs=8.0

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      ||+||||+|..++....
T Consensus       121 GGvGKTT~a~nLA~~LA  137 (403)
T 3ez9_A          121 GGVSKTVSTVTLAHALR  137 (403)
T ss_dssp             -------CHHHHHHHHH
T ss_pred             CCchHHHHHHHHHHHHH
Confidence            89999999999887654

>2ce7_A Cell division protein FTSH; metalloprotease; HET: ADP; 2.44A {Thermotoga maritima} SCOP: a.269.1.1 c.37.1.20 PDB: 2cea_A* 3kds_E*

Probab=81.21  E-value=0.64  Score=41.93  Aligned_cols=17  Identities=53%  Similarity=0.661  Sum_probs=15.3

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      +|+|||+||+.+++...
T Consensus        58 pGtGKT~Laraia~~~~   74 (476)
T 2ce7_A           58 PGTGKTLLARAVAGEAN   74 (476)
T ss_dssp             TTSSHHHHHHHHHHHHT
T ss_pred             CCCCHHHHHHHHHHHcC
Confidence            69999999999999764

>2f9l_A RAB11B, member RAS oncogene family; RAB11B GTPase, vesicle transport, hydrolase; HET: GDP; 1.55A {Homo sapiens} SCOP: c.37.1.8 PDB: 2f9m_A* 1yzk_A* 2hv8_A* 2gzd_A* 2gzh_A* 2d7c_A* 3bfk_A*

Probab=81.08  E-value=0.7  Score=35.84  Aligned_cols=15  Identities=33%  Similarity=0.698  Sum_probs=13.5

Q ss_pred             CCCcHHHHHHHHHhh
Q 041028            2 GGIGKTTLAKEVARK   16 (283)
Q Consensus         2 gGiGKTtLA~~v~~~   16 (283)
                      .|+|||||.+.+...
T Consensus        14 ~g~GKSTLl~~l~~~   28 (199)
T 2f9l_A           14 SGVGKSNLLSRFTRN   28 (199)
T ss_dssp             TTSSHHHHHHHHHHS
T ss_pred             CCCCHHHHHHHHhcC
Confidence            599999999999875

>1nlf_A Regulatory protein REPA; replicative DNA helicase structural changes, replication; 1.95A {Escherichia coli} SCOP: c.37.1.11 PDB: 1g8y_A 1olo_A

Probab=81.06  E-value=0.65  Score=38.44  Aligned_cols=33  Identities=27%  Similarity=0.515  Sum_probs=21.4

Q ss_pred             CCCcHHHHHHHHHhhhccCC-C-------CCeEEEEEeCCC
Q 041028            2 GGIGKTTLAKEVARKAKNGK-L-------FDQIVFTEVSQN   34 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~-~-------Fd~~~wv~v~~~   34 (283)
                      +|+||||||..++....... .       -..+++++....
T Consensus        39 ~GsGKTtl~~~l~~~~~~g~~~~g~~~~~~~~v~~~~~e~~   79 (279)
T 1nlf_A           39 GGAGKSMLALQLAAQIAGGPDLLEVGELPTGPVIYLPAEDP   79 (279)
T ss_dssp             TTSSHHHHHHHHHHHHHTCCCTTCCCCCCCCCEEEEESSSC
T ss_pred             CCCCHHHHHHHHHHHHhcCCCcCCCccCCCccEEEEECCCC
Confidence            69999999999886543210 0       124567776654

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli}

Probab=81.03  E-value=0.47  Score=43.09  Aligned_cols=17  Identities=24%  Similarity=0.358  Sum_probs=15.1

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      +|+|||+||+.+++...
T Consensus        50 PGtGKT~LAraLa~~l~   66 (500)
T 3nbx_X           50 PGIAKSLIARRLKFAFQ   66 (500)
T ss_dssp             SSSSHHHHHHHGGGGBS
T ss_pred             chHHHHHHHHHHHHHHh
Confidence            69999999999998663

>3cmw_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 2.80A {Escherichia coli} PDB: 3cmt_A* 3cmx_A* 3cmv_A*

Probab=80.97  E-value=2.9  Score=43.62  Aligned_cols=70  Identities=19%  Similarity=0.168  Sum_probs=44.9

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCC------cCCHhhhHHhHHHHccC--CcE
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKLGLKFD------EESESGRTRSPWSRLKK--EKL   73 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~~l~~~~~------~~~~~~~~~~l~~~L~~--kr~   73 (283)
                      +|+||||||.+++......  =..++|++....++..     .++.++.+.+      ..+.++..+.++...+.  -+.
T Consensus       392 pGsGKTtLaLq~a~~~~~~--G~~vlyis~E~s~~~~-----~a~~lGvd~~~L~i~~~~~~e~~l~~l~~lv~~~~~~l  464 (1706)
T 3cmw_A          392 ESSGKTTLTLQVIAAAQRE--GKTCAFIDAEHALDPI-----YARKLGVDIDNLLCSQPDTGEQALEICDALARSGAVDV  464 (1706)
T ss_dssp             TTSSHHHHHHHHHHHHHHT--TCCEEEECTTSCCCHH-----HHHHTTCCGGGCEEECCSSHHHHHHHHHHHHHHTCCSE
T ss_pred             CCCCHHHHHHHHHHHHHHh--CCCeEEEEccCchHHH-----HHHHcCCCHHHeEEcCCCCHHHHHHHHHHHHHhcCCCE
Confidence            6999999999998775543  2468999988887764     2566766432      12444455555544432  367


Q ss_pred             EEEcC
Q 041028           74 QIICG   78 (283)
Q Consensus        74 LlV~G   78 (283)
                      ++|+.
T Consensus       465 VVIDS  469 (1706)
T 3cmw_A          465 IVVDS  469 (1706)
T ss_dssp             EEESC
T ss_pred             EEECC
Confidence            77743

>2zej_A Dardarin, leucine-rich repeat kinase 2; parkinson'S disease, LRRK2, ROC, GTPase, ROCO, ATP-B disease mutation, GTP-binding, GTPase activation; HET: GDP; 2.00A {Homo sapiens} PDB: 3d6t_B*

Probab=80.91  E-value=0.52  Score=36.10  Aligned_cols=15  Identities=40%  Similarity=0.632  Sum_probs=13.2

Q ss_pred             CCCcHHHHHHHHHhh
Q 041028            2 GGIGKTTLAKEVARK   16 (283)
Q Consensus         2 gGiGKTtLA~~v~~~   16 (283)
                      +|+|||||.+.+...
T Consensus        11 ~gvGKStLl~~l~~~   25 (184)
T 2zej_A           11 TGSGKTTLLQQLMKT   25 (184)
T ss_dssp             TTSSHHHHHHHHTCC
T ss_pred             CCCCHHHHHHHHhcC
Confidence            699999999998763

>1p6x_A Thymidine kinase; P-loop, LID, transferase; HET: THM; 2.00A {Equid herpesvirus 4} SCOP: c.37.1.1 PDB: 1p72_A* 1p73_A* 1p75_A*

Probab=80.87  E-value=0.67  Score=39.73  Aligned_cols=18  Identities=39%  Similarity=0.495  Sum_probs=15.6

Q ss_pred             CCCcHHHHHHHHHhhhcc
Q 041028            2 GGIGKTTLAKEVARKAKN   19 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~   19 (283)
                      -|+||||+++.+.+....
T Consensus        16 dGaGKTT~~~~La~~L~~   33 (334)
T 1p6x_A           16 YGIGKSTTGRVMASAASG   33 (334)
T ss_dssp             TTSSHHHHHHHHHSGGGC
T ss_pred             CCCCHHHHHHHHHHHhcc
Confidence            399999999999988764

>1g8p_A Magnesium-chelatase 38 kDa subunit; parallel beta sheet, P-loop, rossman fold, AAA+, photosynthesis, metal transport; 2.10A {Rhodobacter capsulatus} SCOP: c.37.1.20 PDB: 2x31_G

Probab=80.72  E-value=0.41  Score=40.77  Aligned_cols=17  Identities=29%  Similarity=0.395  Sum_probs=14.9

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      +|+|||+||+.+++...
T Consensus        54 ~GtGKT~la~~la~~~~   70 (350)
T 1g8p_A           54 RGTGKSTAVRALAALLP   70 (350)
T ss_dssp             GGGCTTHHHHHHHHHSC
T ss_pred             CCccHHHHHHHHHHhCc
Confidence            59999999999998754

>1z2a_A RAS-related protein RAB-23; RAB GTPase, vesicular trafficking, protein transport; HET: GDP; 1.90A {Mus musculus} SCOP: c.37.1.8 PDB: 1z22_A*

Probab=80.67  E-value=0.76  Score=34.08  Aligned_cols=15  Identities=20%  Similarity=0.620  Sum_probs=13.5

Q ss_pred             CCCcHHHHHHHHHhh
Q 041028            2 GGIGKTTLAKEVARK   16 (283)
Q Consensus         2 gGiGKTtLA~~v~~~   16 (283)
                      +|+|||||...+.+.
T Consensus        14 ~~~GKssl~~~l~~~   28 (168)
T 1z2a_A           14 GAVGKSSMIQRYCKG   28 (168)
T ss_dssp             TTSSHHHHHHHHHHC
T ss_pred             CCCCHHHHHHHHHcC
Confidence            699999999999875

>3pxg_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 3.65A {Bacillus subtilis}

Probab=80.64  E-value=0.59  Score=42.04  Aligned_cols=16  Identities=38%  Similarity=0.688  Sum_probs=14.8

Q ss_pred             CCCcHHHHHHHHHhhh
Q 041028            2 GGIGKTTLAKEVARKA   17 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~   17 (283)
                      +|+|||+||+.+++..
T Consensus       210 pG~GKT~la~~la~~l  225 (468)
T 3pxg_A          210 PGVGKTAIAEGLAQQI  225 (468)
T ss_dssp             TTTTTHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHH
Confidence            6999999999999885

>2wji_A Ferrous iron transport protein B homolog; membrane G-proteins, cell membrane, ION transport, transmembrane; HET: GNP; 1.90A {Methanocaldococcus jannaschii} PDB: 2wjj_A* 2wjh_A*

Probab=80.60  E-value=0.67  Score=34.74  Aligned_cols=15  Identities=20%  Similarity=0.437  Sum_probs=13.3

Q ss_pred             CCCcHHHHHHHHHhh
Q 041028            2 GGIGKTTLAKEVARK   16 (283)
Q Consensus         2 gGiGKTtLA~~v~~~   16 (283)
                      +|+|||||...+...
T Consensus        12 ~gvGKStL~~~l~~~   26 (165)
T 2wji_A           12 PNVGKSTIFNALTGE   26 (165)
T ss_dssp             TTSSHHHHHHHHHCC
T ss_pred             CCCCHHHHHHHHhCC
Confidence            699999999999864

>2axn_A 6-phosphofructo-2-kinase/fructose-2,6- biphosphatase 3 (6PF-2-K/FRU- 2,6-P2ASE brain/placenta-type...; bifunctional enzyme, EDTA complex; HET: F6P EDT ADP; 2.10A {Homo sapiens} PDB: 2dwo_A* 2dwp_A* 2i1v_B* 3qpu_A* 3qpv_A* 3qpw_A*

Probab=80.58  E-value=1.1  Score=40.95  Aligned_cols=19  Identities=26%  Similarity=0.335  Sum_probs=16.1

Q ss_pred             CCCCcHHHHHHHHHhhhcc
Q 041028            1 MGGIGKTTLAKEVARKAKN   19 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~   19 (283)
                      ++|.||||+|+.+......
T Consensus        43 lpGSGKSTia~~La~~L~~   61 (520)
T 2axn_A           43 LPARGKTYISKKLTRYLNW   61 (520)
T ss_dssp             CTTSSHHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHhh
Confidence            5799999999999887643

>1sxj_E Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=80.56  E-value=0.58  Score=39.96  Aligned_cols=15  Identities=27%  Similarity=0.375  Sum_probs=13.7

Q ss_pred             CCCcHHHHHHHHHhh
Q 041028            2 GGIGKTTLAKEVARK   16 (283)
Q Consensus         2 gGiGKTtLA~~v~~~   16 (283)
                      .|+||||||+.+++.
T Consensus        45 ~G~GKTtl~~~la~~   59 (354)
T 1sxj_E           45 NGTGKKTRCMALLES   59 (354)
T ss_dssp             TTSSHHHHHHTHHHH
T ss_pred             CCCCHHHHHHHHHHH
Confidence            599999999999885

>2chq_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATP ATP-binding, nucleotide-binding; HET: ANP; 3.5A {Archaeoglobus fulgidus} PDB: 2chv_A

Probab=80.30  E-value=0.77  Score=38.36  Aligned_cols=16  Identities=44%  Similarity=0.511  Sum_probs=14.6

Q ss_pred             CCCcHHHHHHHHHhhh
Q 041028            2 GGIGKTTLAKEVARKA   17 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~   17 (283)
                      +|+|||++|+.+++..
T Consensus        47 ~G~GKt~la~~l~~~l   62 (319)
T 2chq_A           47 PGTGKTATAIALARDL   62 (319)
T ss_dssp             SSSSHHHHHHHHHHHH
T ss_pred             CCcCHHHHHHHHHHHh
Confidence            6999999999999875

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	283
d2a5yb3	277	c.37.1.20 (B:109-385) CED-4, NB-ARC domain {Caenor	5e-06

>d2a5yb3 c.37.1.20 (B:109-385) CED-4, NB-ARC domain {Caenorhabditis elegans [TaxId: 6239]} Length = 277

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CED-4, NB-ARC domain
species: Caenorhabditis elegans [TaxId: 6239]

 Score = 44.4 bits (104), Expect = 5e-06
 Identities = 13/60 (21%), Positives = 24/60 (40%), Gaps = 2/60 (3%)

Query: 1   MGGIGKTTLAKEVARKAKN--GKLFDQIVFTEVSQNPNIKKIQGEIAFKLGLKFDEESES 58
             G GK+ +A +   K+    G  +D IV+ + S               L LK +++  +
Sbjct: 52  RAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKSTFDLFTDILLMLKSEDDLLN 111

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	283
d2a5yb3	277	CED-4, NB-ARC domain {Caenorhabditis elegans [TaxI	99.92
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	96.18
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	95.97
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	95.91
d2iyva1	165	Shikimate kinase (AroK) {Mycobacterium tuberculosi	95.6
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	95.38
d1x6va3	195	Adenosine-5'phosphosulfate kinase (APS kinase) {Hu	95.22
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	95.16
d1viaa_	161	Shikimate kinase (AroK) {Campylobacter jejuni [Tax	95.1
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	95.06
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	94.79
d1e6ca_	170	Shikimate kinase (AroK) {Erwinia chrysanthemi [Tax	94.77
d1ihua1	296	Arsenite-translocating ATPase ArsA {Escherichia co	94.74
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	94.63
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	94.61
d1xp8a1	268	RecA protein, ATPase-domain {Deinococcus radiodura	94.52
d1np6a_	170	Molybdopterin-guanine dinucleotide biosynthesis pr	94.42
d1mo6a1	269	RecA protein, ATPase-domain {Mycobacterium tubercu	94.35
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	94.22
d1bifa1	213	6-phosphofructo-2-kinase/fructose-2,6-bisphosphata	94.14
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	93.87
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	93.61
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	93.57
d1hyqa_	232	Cell division regulator MinD {Archaeon Archaeoglob	93.53
d1okkd2	207	GTPase domain of the signal recognition particle r	93.47
d1qhxa_	178	Chloramphenicol phosphotransferase {Streptomyces v	93.32
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	93.26
d1ihua2	279	Arsenite-translocating ATPase ArsA {Escherichia co	93.14
d1ls1a2	207	GTPase domain of the signal sequence recognition p	93.06
d1g3qa_	237	Cell division regulator MinD {Archaeon Pyrococcus	93.04
d1m7ga_	208	Adenosine-5'phosphosulfate kinase (APS kinase) {Fu	93.01
d1u94a1	263	RecA protein, ATPase-domain {Escherichia coli [Tax	92.98
d1nksa_	194	Adenylate kinase {Archaeon Sulfolobus acidocaldari	92.97
d1khta_	190	Adenylate kinase {Archaeon Methanococcus voltae [T	92.92
d1cp2a_	269	Nitrogenase iron protein {Clostridium pasteurianum	92.86
d2afhe1	289	Nitrogenase iron protein {Azotobacter vinelandii [	92.78
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	92.59
d1rz3a_	198	Hypothetical protein rbstp0775 {Bacillus stearothe	92.57
d1yj5a2	172	5' polynucleotide kinase-3' phosphatase, C-termina	92.46
d2ak3a1	189	Adenylate kinase {Cow (Bos taurus), mitochondrial	92.44
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	92.43
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	92.41
d1xjca_	165	Molybdopterin-guanine dinucleotide biosynthesis pr	92.2
d1zina1	182	Adenylate kinase {Bacillus stearothermophilus [Tax	92.14
d2cdna1	181	Adenylate kinase {Mycobacterium tuberculosis [TaxI	92.1
d1zaka1	189	Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}	92.01
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	91.96
d2qy9a2	211	GTPase domain of the signal recognition particle r	91.81
d1nn5a_	209	Thymidylate kinase {Human (Homo sapiens) [TaxId: 9	91.79
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	91.64
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	91.61
d1qf9a_	194	UMP/CMP kinase {Dictyostelium discoideum [TaxId: 4	91.58
d1s3ga1	182	Adenylate kinase {Bacillus globisporus [TaxId: 145	91.52
d2fnaa2	283	Archaeal ATPase SSO1545 {Sulfolobus solfataricus [	91.34
d1akya1	180	Adenylate kinase {Baker's yeast (Saccharomyces cer	91.2
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	91.17
d1htwa_	158	Hypothetical protein HI0065 {Haemophilus influenza	91.15
d1tmka_	214	Thymidylate kinase {Baker's yeast (Saccharomyces c	91.09
d1j8yf2	211	GTPase domain of the signal sequence recognition p	91.03
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	90.78
d1ukza_	196	Uridylate kinase {Baker's yeast (Saccharomyces cer	90.75
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	90.67
d1vmaa2	213	GTPase domain of the signal recognition particle r	90.62
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	90.56
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	90.54
d1ak2a1	190	Adenylate kinase {Cow (Bos taurus), mitochondrial	90.41
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	90.31
d1e4va1	179	Adenylate kinase {Escherichia coli [TaxId: 562]}	90.28
d1q3ta_	223	CMP kinase {Streptococcus pneumoniae [TaxId: 1313]	89.98
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	89.73
d1ckea_	225	CMP kinase {Escherichia coli [TaxId: 562]}	89.6
d1pzna2	254	DNA repair protein Rad51, catalytic domain {Archae	89.59
d1teva_	194	UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]	89.54
d2vp4a1	197	Deoxyribonucleoside kinase {Fruit fly (Drosophila	89.44
d1uj2a_	213	Uridine-cytidine kinase 2 {Human (Homo sapiens) [T	89.22
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	88.44
d2ocpa1	241	Deoxyguanosine kinase {Human (Homo sapiens) [TaxId	88.05
d3adka_	194	Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}	87.77
d1byia_	224	Dethiobiotin synthetase {Escherichia coli [TaxId:	87.64
d1gsia_	208	Thymidylate kinase {Mycobacterium tuberculosis [Ta	87.57
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	87.35
d1n0wa_	242	DNA repair protein Rad51, catalytic domain {Human	87.01
d4tmka_	210	Thymidylate kinase {Escherichia coli [TaxId: 562]}	86.8
d1r8sa_	160	ADP-ribosylation factor {Human (Homo sapiens), ARF	86.27
d1gkya_	186	Guanylate kinase {Baker's yeast (Saccharomyces cer	86.05
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	86.02
d1sq5a_	308	Pantothenate kinase PanK {Escherichia coli [TaxId:	86.01
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	85.91
d1p6xa_	333	Thymidine kinase {Equine herpesvirus type 4 [TaxId	85.87
d1w44a_	321	NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}	85.78
d1lvga_	190	Guanylate kinase {Mouse (Mus musculus) [TaxId: 100	85.73
d1odfa_	286	Hypothetical protein Ygr205W {Baker's yeast (Sacch	85.59
d1v5wa_	258	Meiotic recombination protein DMC1/LIM15 homolog {	85.5
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	84.23
d2i1qa2	258	DNA repair protein Rad51, catalytic domain {Archae	84.14
d1z0fa1	166	Rab14 {Human (Homo sapiens) [TaxId: 9606]}	83.89
d1znwa1	182	Guanylate kinase {Mycobacterium tuberculosis [TaxI	83.85
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	83.81
d1upta_	169	ADP-ribosylation factor {Human (Homo sapiens), ARL	83.8
d1z06a1	165	Rab-33b {Mouse (Mus musculus) [TaxId: 10090]}	83.67
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	83.66
d1kaoa_	167	Rap2a {Human (Homo sapiens) [TaxId: 9606]}	83.44
d1p5zb_	241	Deoxycytidine kinase {Human (Homo sapiens) [TaxId:	83.09
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	83.09
d1z2aa1	164	Rab23 {Mouse (Mus musculus) [TaxId: 10090]}	83.02
d1z08a1	167	Rab21 {Human (Homo sapiens) [TaxId: 9606]}	82.84
d2a5ja1	173	Rab2b {Human (Homo sapiens) [TaxId: 9606]}	82.83
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	82.73
d3raba_	169	Rab3a {Rat (Rattus norvegicus) [TaxId: 10116]}	82.54
d2erxa1	171	di-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	82.52
d1yzqa1	164	Rab6 {Human (Homo sapiens) [TaxId: 9606]}	82.4
d1yrba1	244	ATP(GTP)-binding protein PAB0955 {Pyrococcus abyss	82.4
d1uf9a_	191	Dephospho-CoA kinase {Thermus thermophilus [TaxId:	82.28
d1z0ja1	167	Rab-22a {Mouse (Mus musculus) [TaxId: 10090]}	82.2
d2ew1a1	171	Rab30 {Human (Homo sapiens) [TaxId: 9606]}	81.93
d2f7sa1	186	Rab27b {Human (Homo sapiens) [TaxId: 9606]}	81.74
d1r2qa_	170	Rab5a {Human (Homo sapiens) [TaxId: 9606]}	81.51
d1g8pa_	333	ATPase subunit of magnesium chelatase, BchI {Rhodo	81.28
d2fn4a1	173	r-Ras {Human (Homo sapiens) [TaxId: 9606]}	81.2
d2bmea1	174	Rab4a {Human (Homo sapiens) [TaxId: 9606]}	81.19
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	81.04
d1ctqa_	166	cH-p21 Ras protein {Human (Homo sapiens) [TaxId: 9	80.87
d1g16a_	166	Rab-related protein Sec4 {Baker's yeast (Saccharom	80.84
d1nlfa_	274	Hexameric replicative helicase repA {Escherichia c	80.8
d2gjsa1	168	Rad {Human (Homo sapiens) [TaxId: 9606]}	80.68
d1e2ka_	329	Thymidine kinase {Herpes simplex virus type 1, dif	80.51
d1svsa1	195	Transducin (alpha subunit) {Rat (Rattus norvegicus	80.42
d2atva1	168	Ras-like estrogen-regulated growth inhibitor, RERG	80.34
d1osna_	331	Thymidine kinase {Varicella-zoster virus [TaxId: 1	80.04

>d2a5yb3 c.37.1.20 (B:109-385) CED-4, NB-ARC domain {Caenorhabditis elegans [TaxId: 6239]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CED-4, NB-ARC domain
species: Caenorhabditis elegans [TaxId: 6239]

Probab=99.92  E-value=8.8e-26  Score=190.68  Aligned_cols=157  Identities=12%  Similarity=0.054  Sum_probs=117.2

Q ss_pred             CCCCcHHHHHHHHHhhhc--cCCCCCeEEEEEeCCCCCHHHHHHHHHH---HhCCCCC------c--CCHhhhHHhHHHH
Q 041028            1 MGGIGKTTLAKEVARKAK--NGKLFDQIVFTEVSQNPNIKKIQGEIAF---KLGLKFD------E--ESESGRTRSPWSR   67 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~--~~~~Fd~~~wv~v~~~~~~~~l~~~i~~---~l~~~~~------~--~~~~~~~~~l~~~   67 (283)
                      ||||||||||+++|++..  ...+|++++||++++.++...+...+..   .++....      .  .........+.+.
T Consensus        52 mgGiGKTtLA~~v~~~~~~~~~~~f~~~~Wv~vs~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  131 (277)
T d2a5yb3          52 RAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKSTFDLFTDILLMLKSEDDLLNFPSVEHVTSVVLKRMICNAL  131 (277)
T ss_dssp             STTSSHHHHHHHHHHHCSSTBTTTBSEEEEEECCCCSTTHHHHHHHHHHHHHTTTSCCTTCCCCTTCCHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHhhhhhhhhcCceEEEEEecCCCCHHHHHHHHHHHHHHhcchhhcCCccchhhhhHHHHHHHHHHH
Confidence            899999999999999854  5567899999999999887776665544   3332211      1  1222344467888


Q ss_pred             ccCCcEEEE---------------cC--------------------------------------eecCCCCCCCcchHHH
Q 041028           68 LKKEKLQII---------------CG--------------------------------------KKMEGDYAEGSELKWL   94 (283)
Q Consensus        68 L~~kr~LlV---------------~G--------------------------------------~~~~~~~~~~~~~~~~   94 (283)
                      |.++|+|+|               .|                                      +..+.. ...+..+++
T Consensus       132 L~~kr~LlVLDDv~~~~~~~~~~~~~srilvTTR~~~v~~~~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~-~~~~~~~~~  210 (277)
T d2a5yb3         132 IDRPNTLFVFDDVVQEETIRWAQELRLRCLVTTRDVEISNAASQTCEFIEVTSLEIDECYDFLEAYGMPM-PVGEKEEDV  210 (277)
T ss_dssp             TTSTTEEEEEEEECCHHHHHHHHHTTCEEEEEESBGGGGGGCCSCEEEEECCCCCHHHHHHHHHHTSCCC-C--CHHHHH
T ss_pred             hccCCeeEecchhhHHhhhhhhcccCceEEEEeehHHHHHhcCCCCceEECCCCCHHHHHHHHHHHhCCc-cCchhhHHH
Confidence            999999999               01                                      223332 234456888


Q ss_pred             HHHHHHhcCCchHHHHH---hhccCChHHHHHHHHHhcCCCCCCCCCchhHHHHHHhhhhccCCCCcHHHHHHHH
Q 041028           95 AMDVAKECAGLPVSIVT---GIKEQELFEWKDALEQLRRPSSTNFKDVQPAAYKAMELGYNKLEGDELKSTFLLI  166 (283)
Q Consensus        95 ~~~i~~~c~glPLal~~---~l~~~~~~~w~~~l~~l~~~~~~~~~~~~~~~~~~l~~sy~~L~~~~~k~~fl~~  166 (283)
                      +++|+++|+|+||||++   .++.++.+.|.+...+|....       ...+..++.+||++||++ +|.||.++
T Consensus       211 ~~~iv~~c~GlPLAl~~ig~~l~~k~~~~~~~~~~~L~~~~-------~~~v~~il~~sY~~L~~~-lk~c~~~l  277 (277)
T d2a5yb3         211 LNKTIELSSGNPATLMMFFKSCEPKTFEKMAQLNNKLESRG-------LVGVECITPYSYKSLAMA-LQRCVEVL  277 (277)
T ss_dssp             HHHHHHHHTTCHHHHHHHHTTCCSSSHHHHHHHHHHHHHHC-------SSTTCCCSSSSSSSHHHH-HHHHHHTS
T ss_pred             HHHHHHHhCCCHHHHHHHHHHhccCCHHHHHHHHHHHhcCc-------HHHHHHHHHHHHhcccHH-HHHHHHhC
Confidence            99999999999999999   566888999999988886543       234688899999999998 99999864

>d1fnna2 c.37.1.20 (A:1-276) CDC6, N-domain {Archaeon Pyrobaculum aerophilum [TaxId: 13773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6, N-domain
species: Archaeon Pyrobaculum aerophilum [TaxId: 13773]

Probab=96.18  E-value=0.012  Score=46.33  Aligned_cols=67  Identities=24%  Similarity=0.201  Sum_probs=46.8

Q ss_pred             CCCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCc--CCHhhhHHhHHHHc
Q 041028            1 MGGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKLGLKFDE--ESESGRTRSPWSRL   68 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~--~~~~~~~~~l~~~L   68 (283)
                      .+|+||||+|+.+++....... ...+|+..............+....+.....  .........+.+.+
T Consensus        51 ppGtGKT~l~~~l~~~l~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  119 (276)
T d1fnna2          51 RPGTGKTVTLRKLWELYKDKTT-ARFVYINGFIYRNFTAIIGEIARSLNIPFPRRGLSRDEFLALLVEHL  119 (276)
T ss_dssp             CTTSSHHHHHHHHHHHHTTSCC-CEEEEEETTTCCSHHHHHHHHHHHTTCCCCSSCCCHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHhcccC-CcEEEecchhhhhhhhhhhhhHHhhhhhhhhhccchhHHHHHHHHHH
Confidence            3799999999999998764422 3456777778888889999999888765432  24444444444444

>d1m8pa3 c.37.1.15 (A:391-573) ATP sulfurylase C-terminal domain {Fungus (Penicillium chrysogenum) [TaxId: 5076]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ATP sulfurylase C-terminal domain
domain: ATP sulfurylase C-terminal domain
species: Fungus (Penicillium chrysogenum) [TaxId: 5076]

Probab=95.97  E-value=0.0018  Score=47.97  Aligned_cols=28  Identities=11%  Similarity=0.065  Sum_probs=21.2

Q ss_pred             CCCCcHHHHHHHHHhhhccCCCCCeEEEE
Q 041028            1 MGGIGKTTLAKEVARKAKNGKLFDQIVFT   29 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~~~Fd~~~wv   29 (283)
                      ++|+||||+|+.++...... +++...++
T Consensus        14 ~~GsGKTTia~~La~~L~~~-~~~~~~~~   41 (183)
T d1m8pa3          14 YMNSGKDAIARALQVTLNQQ-GGRSVSLL   41 (183)
T ss_dssp             STTSSHHHHHHHHHHHHHHH-CSSCEEEE
T ss_pred             CCCCCHHHHHHHHHHHHhhc-CCCchhhh
Confidence            68999999999999987543 24555554

>d1kaga_ c.37.1.2 (A:) Shikimate kinase (AroK) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Escherichia coli [TaxId: 562]

Probab=95.91  E-value=0.0016  Score=47.38  Aligned_cols=18  Identities=28%  Similarity=0.523  Sum_probs=16.0

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      ++|+||||+|+.++....
T Consensus        10 ~~GsGKSTvak~La~~L~   27 (169)
T d1kaga_          10 PMGAGKSTIGRQLAQQLN   27 (169)
T ss_dssp             CTTSCHHHHHHHHHHHTT
T ss_pred             CCCCCHHHHHHHHHHHhC
Confidence            689999999999999764

>d2iyva1 c.37.1.2 (A:2-166) Shikimate kinase (AroK) {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=95.60  E-value=0.0023  Score=47.23  Aligned_cols=20  Identities=30%  Similarity=0.581  Sum_probs=17.4

Q ss_pred             CCCCcHHHHHHHHHhhhccC
Q 041028            1 MGGIGKTTLAKEVARKAKNG   20 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~   20 (283)
                      |+|+||||+|+.+++.....
T Consensus         9 ~~G~GKSTig~~La~~l~~~   28 (165)
T d2iyva1           9 LPGSGKSTIGRRLAKALGVG   28 (165)
T ss_dssp             STTSSHHHHHHHHHHHHTCC
T ss_pred             CCCCCHHHHHHHHHHHhCCC
Confidence            68999999999999987643

>d1rkba_ c.37.1.1 (A:) Adenylate kinase {Human (Homo sapiens), isoenzyme 6 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Human (Homo sapiens), isoenzyme 6 [TaxId: 9606]

Probab=95.38  E-value=0.0032  Score=46.26  Aligned_cols=18  Identities=56%  Similarity=0.756  Sum_probs=15.7

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      ++|+||||+|+.++....
T Consensus        12 ~pGsGKTTia~~La~~l~   29 (173)
T d1rkba_          12 TPGVGKTTLGKELASKSG   29 (173)
T ss_dssp             STTSSHHHHHHHHHHHHC
T ss_pred             CCCCCHHHHHHHHHHHHC
Confidence            579999999999998754

>d1x6va3 c.37.1.4 (A:34-228) Adenosine-5'phosphosulfate kinase (APS kinase) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Adenosine-5'phosphosulfate kinase (APS kinase)
domain: Adenosine-5'phosphosulfate kinase (APS kinase)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.22  E-value=0.0032  Score=47.34  Aligned_cols=20  Identities=25%  Similarity=0.323  Sum_probs=17.2

Q ss_pred             CCCCcHHHHHHHHHhhhccC
Q 041028            1 MGGIGKTTLAKEVARKAKNG   20 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~   20 (283)
                      ++|+||||+|+.++......
T Consensus        27 ~pGSGKTTiAk~La~~l~~~   46 (195)
T d1x6va3          27 LSGAGKTTVSMALEEYLVCH   46 (195)
T ss_dssp             SCHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHHHHHhc
Confidence            57999999999999887654

>d1lw7a2 c.37.1.1 (A:220-411) Transcriptional regulator NadR, ribosylnicotinamide kinase domain {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Transcriptional regulator NadR, ribosylnicotinamide kinase domain
species: Haemophilus influenzae [TaxId: 727]

Probab=95.16  E-value=0.0038  Score=46.30  Aligned_cols=18  Identities=22%  Similarity=0.226  Sum_probs=15.4

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      ..|+||||||+.+++...
T Consensus        15 ~~GsGKTTla~~La~~~~   32 (192)
T d1lw7a2          15 GESSGKSVLVNKLAAVFN   32 (192)
T ss_dssp             CTTSHHHHHHHHHHHHTT
T ss_pred             CCCCCHHHHHHHHHHHhC
Confidence            369999999999998653

>d1viaa_ c.37.1.2 (A:) Shikimate kinase (AroK) {Campylobacter jejuni [TaxId: 197]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Campylobacter jejuni [TaxId: 197]

Probab=95.10  E-value=0.0038  Score=45.95  Aligned_cols=19  Identities=37%  Similarity=0.518  Sum_probs=16.9

Q ss_pred             CCCCcHHHHHHHHHhhhcc
Q 041028            1 MGGIGKTTLAKEVARKAKN   19 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~   19 (283)
                      |+|+||||+|+.++.+...
T Consensus         8 ~~GsGKsTi~k~La~~l~~   26 (161)
T d1viaa_           8 FMGSGKSTLARALAKDLDL   26 (161)
T ss_dssp             CTTSCHHHHHHHHHHHHTC
T ss_pred             CCCCCHHHHHHHHHHHhCC
Confidence            7899999999999998753

>d1ly1a_ c.37.1.1 (A:) Polynucleotide kinase, kinase domain {Bacteriophage T4 [TaxId: 10665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Polynucleotide kinase, kinase domain
species: Bacteriophage T4 [TaxId: 10665]

Probab=95.06  E-value=0.0048  Score=44.44  Aligned_cols=16  Identities=44%  Similarity=0.542  Sum_probs=13.7

Q ss_pred             CCCCcHHHHHHHHHhh
Q 041028            1 MGGIGKTTLAKEVARK   16 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~   16 (283)
                      ++|+||||||+++..+
T Consensus        10 ~pGsGKTTla~~L~~~   25 (152)
T d1ly1a_          10 CPGSGKSTWAREFIAK   25 (152)
T ss_dssp             CTTSSHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHh
Confidence            4799999999998764

>d2bdta1 c.37.1.25 (A:1-176) Hypothetical protein BH3686 {Bacillus halodurans [TaxId: 86665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Atu3015-like
domain: Hypothetical protein BH3686
species: Bacillus halodurans [TaxId: 86665]

Probab=94.79  E-value=0.006  Score=44.62  Aligned_cols=17  Identities=35%  Similarity=0.555  Sum_probs=14.7

Q ss_pred             CCCCcHHHHHHHHHhhh
Q 041028            1 MGGIGKTTLAKEVARKA   17 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (283)
                      ++|+||||+|+.+....
T Consensus        10 ~~GsGKTTva~~L~~~~   26 (176)
T d2bdta1          10 PAGVGKSTTCKRLAAQL   26 (176)
T ss_dssp             STTSSHHHHHHHHHHHS
T ss_pred             CCCCCHHHHHHHHHHHc
Confidence            47999999999998754

>d1e6ca_ c.37.1.2 (A:) Shikimate kinase (AroK) {Erwinia chrysanthemi [TaxId: 556]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Erwinia chrysanthemi [TaxId: 556]

Probab=94.77  E-value=0.0051  Score=45.51  Aligned_cols=19  Identities=37%  Similarity=0.482  Sum_probs=16.8

Q ss_pred             CCCCcHHHHHHHHHhhhcc
Q 041028            1 MGGIGKTTLAKEVARKAKN   19 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~   19 (283)
                      |+|+||||+|+.+++....
T Consensus        10 ~~GsGKSTia~~LA~~Lg~   28 (170)
T d1e6ca_          10 ARGCGMTTVGRELARALGY   28 (170)
T ss_dssp             CTTSSHHHHHHHHHHHHTC
T ss_pred             CCCCCHHHHHHHHHHHhCC
Confidence            6899999999999998753

>d1ihua1 c.37.1.10 (A:1-296) Arsenite-translocating ATPase ArsA {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Arsenite-translocating ATPase ArsA
species: Escherichia coli [TaxId: 562]

Probab=94.74  E-value=0.013  Score=47.12  Aligned_cols=38  Identities=18%  Similarity=0.403  Sum_probs=26.9

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHH
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQ   41 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~   41 (283)
                      |||||||+|..++.....++.  .++-|+.....++..++
T Consensus        17 GGVGKTTvaa~lA~~lA~~G~--rVLlvD~Dp~~~l~~~l   54 (296)
T d1ihua1          17 GGVGKTSISCATAIRLAEQGK--RVLLVSTDPASNVGQVF   54 (296)
T ss_dssp             TTSSHHHHHHHHHHHHHHTTC--CEEEEECCTTCCHHHHT
T ss_pred             CcChHHHHHHHHHHHHHHCCC--CEEEEeCCCCCCHHHHh
Confidence            899999999998887654432  46777777666655443

>d1w5sa2 c.37.1.20 (A:7-293) CDC6-like protein APE0152, N-terminal domain {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6-like protein APE0152, N-terminal domain
species: Aeropyrum pernix [TaxId: 56636]

Probab=94.63  E-value=0.046  Score=43.03  Aligned_cols=68  Identities=24%  Similarity=0.256  Sum_probs=45.4

Q ss_pred             CCCCcHHHHHHHHHhhhcc----CCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCC--cCCHhhhHHhHHHHc
Q 041028            1 MGGIGKTTLAKEVARKAKN----GKLFDQIVFTEVSQNPNIKKIQGEIAFKLGLKFD--EESESGRTRSPWSRL   68 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~----~~~Fd~~~wv~v~~~~~~~~l~~~i~~~l~~~~~--~~~~~~~~~~l~~~L   68 (283)
                      .+|+|||++++.+++....    ........+++.............+...++....  ..........+....
T Consensus        54 ppGtGKT~l~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~  127 (287)
T d1w5sa2          54 RVGIGKTTLAKFTVKRVSEAAAKEGLTVKQAYVNAFNAPNLYTILSLIVRQTGYPIQVRGAPALDILKALVDNL  127 (287)
T ss_dssp             CCSSSHHHHHHHHHHHHHHHHHHTTCCEEEEEEEGGGCCSHHHHHHHHHHHHTCCCCCTTCCHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHhhcccccCCceeeeeccccccchhhHHHHHhhhcccccccccchHHHHHHHHHHHH
Confidence            3799999999999987432    1112445677878888888888888888876543  234444444555444

>d1y63a_ c.37.1.1 (A:) Probable kinase LmjF30.1890 {Leishmania major [TaxId: 5664]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Probable kinase LmjF30.1890
species: Leishmania major [TaxId: 5664]

Probab=94.61  E-value=0.0071  Score=44.43  Aligned_cols=17  Identities=35%  Similarity=0.528  Sum_probs=15.1

Q ss_pred             CCCCcHHHHHHHHHhhh
Q 041028            1 MGGIGKTTLAKEVARKA   17 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (283)
                      ++|+||||+|+.+++..
T Consensus        13 ~~GsGKTT~~~~La~~l   29 (174)
T d1y63a_          13 TPGTGKTSMAEMIAAEL   29 (174)
T ss_dssp             STTSSHHHHHHHHHHHS
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            57999999999999864

>d1xp8a1 c.37.1.11 (A:15-282) RecA protein, ATPase-domain {Deinococcus radiodurans [TaxId: 1299]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Deinococcus radiodurans [TaxId: 1299]

Probab=94.52  E-value=0.069  Score=42.42  Aligned_cols=69  Identities=19%  Similarity=0.196  Sum_probs=47.8

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCc------CCHhhhHHhHHHHccCC--cE
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKLGLKFDE------ESESGRTRSPWSRLKKE--KL   73 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~------~~~~~~~~~l~~~L~~k--r~   73 (283)
                      +|+||||||..++......+  ..++|++....++..     +++.+|...+.      .+.++..+.+...++..  .+
T Consensus        66 ~~sGKT~l~l~~~~~aqk~g--~~v~yiDtE~~~~~~-----~a~~~Gvd~d~i~~~~~~~~E~~~~~~~~l~~~~~~~l  138 (268)
T d1xp8a1          66 ESGGKTTLALAIVAQAQKAG--GTCAFIDAEHALDPV-----YARALGVNTDELLVSQPDNGEQALEIMELLVRSGAIDV  138 (268)
T ss_dssp             TTSSHHHHHHHHHHHHHHTT--CCEEEEESSCCCCHH-----HHHHTTCCGGGCEEECCSSHHHHHHHHHHHHTTTCCSE
T ss_pred             CccchHHHHHHHHHHHHhCC--CEEEEEECCccCCHH-----HHHHhCCCchhEEEEcCCCHHHHHHHHHHHHhcCCCcE
Confidence            58999999999887765443  358999999999884     67788876432      34555556666555443  55


Q ss_pred             EEEc
Q 041028           74 QIIC   77 (283)
Q Consensus        74 LlV~   77 (283)
                      +||+
T Consensus       139 iIiD  142 (268)
T d1xp8a1         139 VVVD  142 (268)
T ss_dssp             EEEE
T ss_pred             EEEe
Confidence            6653

>d1np6a_ c.37.1.10 (A:) Molybdopterin-guanine dinucleotide biosynthesis protein MobB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Molybdopterin-guanine dinucleotide biosynthesis protein MobB
species: Escherichia coli [TaxId: 562]

Probab=94.42  E-value=0.0089  Score=43.60  Aligned_cols=19  Identities=37%  Similarity=0.401  Sum_probs=16.1

Q ss_pred             CCCcHHHHHHHHHhhhccC
Q 041028            2 GGIGKTTLAKEVARKAKNG   20 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~   20 (283)
                      .|+|||||++++.+....+
T Consensus        11 ~GSGKTTL~~~L~~~l~~~   29 (170)
T d1np6a_          11 SGTGKTTLLKKLIPALCAR   29 (170)
T ss_dssp             TTSCHHHHHHHHHHHHHHT
T ss_pred             CCCCHHHHHHHHHHHHHHC
Confidence            6999999999999876543

>d1mo6a1 c.37.1.11 (A:1-269) RecA protein, ATPase-domain {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=94.35  E-value=0.087  Score=41.82  Aligned_cols=63  Identities=19%  Similarity=0.192  Sum_probs=43.6

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCc------CCHhhhHHhHHHHccCC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKLGLKFDE------ESESGRTRSPWSRLKKE   71 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~------~~~~~~~~~l~~~L~~k   71 (283)
                      +|+||||||..++...+..+  ..++|++....++...     ++++|...+.      .+.++..+.+....+.+
T Consensus        69 ~~~GKT~l~l~~~~~~q~~g--~~~vyIDtE~~~~~e~-----a~~~GvD~d~il~~~~~~~E~~~~~~~~l~~~~  137 (269)
T d1mo6a1          69 ESSGKTTVALHAVANAQAAG--GVAAFIDAEHALDPDY-----AKKLGVDTDSLLVSQPDTGEQALEIADMLIRSG  137 (269)
T ss_dssp             SSSSHHHHHHHHHHHHHHTT--CEEEEEESSCCCCHHH-----HHHHTCCGGGCEEECCSSHHHHHHHHHHHHHTT
T ss_pred             CCcHHHHHHHHHHHHHhcCC--CEEEEEECCccCCHHH-----HHHhCCCHHHeEEecCCCHHHHHHHHHHHHhcC
Confidence            58999999998887766543  4689999999998754     5666775432      34555555555555544

>d2i3ba1 c.37.1.11 (A:1-189) Cancer-related NTPase, C1orf57 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Cancer-related NTPase, C1orf57
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.22  E-value=0.0092  Score=43.98  Aligned_cols=20  Identities=35%  Similarity=0.479  Sum_probs=16.7

Q ss_pred             CCCCcHHHHHHHHHhhhccC
Q 041028            1 MGGIGKTTLAKEVARKAKNG   20 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~   20 (283)
                      .+|+|||||+++++......
T Consensus         9 ~~GtGKTtl~~~i~~~l~~~   28 (189)
T d2i3ba1           9 PPGVGKTTLIHKASEVLKSS   28 (189)
T ss_dssp             CCSSCHHHHHHHHHHHHHHT
T ss_pred             CCCCcHHHHHHHHHHHHHHC
Confidence            37999999999999886543

>d1bifa1 c.37.1.7 (A:37-249) 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain
domain: 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=94.14  E-value=0.01  Score=45.09  Aligned_cols=19  Identities=26%  Similarity=0.344  Sum_probs=16.1

Q ss_pred             CCCCcHHHHHHHHHhhhcc
Q 041028            1 MGGIGKTTLAKEVARKAKN   19 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~   19 (283)
                      .+|+||||||++++.....
T Consensus        10 lpgsGKSTla~~L~~~l~~   28 (213)
T d1bifa1          10 LPARGKTYISKKLTRYLNF   28 (213)
T ss_dssp             CTTSSHHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHh
Confidence            4799999999999987654

>d1in4a2 c.37.1.20 (A:17-254) Holliday junction helicase RuvB {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Holliday junction helicase RuvB
species: Thermotoga maritima [TaxId: 2336]

Probab=93.87  E-value=0.039  Score=42.71  Aligned_cols=17  Identities=47%  Similarity=0.661  Sum_probs=15.5

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      +|+||||+|+.+++...
T Consensus        44 pGtGKT~lA~~la~~~~   60 (238)
T d1in4a2          44 PGLGKTTLAHIIASELQ   60 (238)
T ss_dssp             TTSSHHHHHHHHHHHHT
T ss_pred             CCCcHHHHHHHHHhccC
Confidence            79999999999999765

>d1ixsb2 c.37.1.20 (B:4-242) Holliday junction helicase RuvB {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Holliday junction helicase RuvB
species: Thermus thermophilus [TaxId: 274]

Probab=93.61  E-value=0.014  Score=45.51  Aligned_cols=18  Identities=44%  Similarity=0.562  Sum_probs=15.8

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      .+|+||||+|+.+++...
T Consensus        43 PpG~GKTtla~~la~~~~   60 (239)
T d1ixsb2          43 PPGLGKTTLAHVIAHELG   60 (239)
T ss_dssp             CTTSCHHHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHHHhC
Confidence            379999999999998765

>d1knqa_ c.37.1.17 (A:) Gluconate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Gluconate kinase
domain: Gluconate kinase
species: Escherichia coli [TaxId: 562]

Probab=93.57  E-value=0.015  Score=42.39  Aligned_cols=18  Identities=39%  Similarity=0.628  Sum_probs=15.6

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      .+|+||||+|+.+.....
T Consensus        14 ~~GsGKsT~a~~La~~l~   31 (171)
T d1knqa_          14 VSGSGKSAVASEVAHQLH   31 (171)
T ss_dssp             STTSCHHHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHHHhC
Confidence            379999999999998764

>d1hyqa_ c.37.1.10 (A:) Cell division regulator MinD {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Cell division regulator MinD
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=93.53  E-value=0.024  Score=43.69  Aligned_cols=29  Identities=21%  Similarity=0.339  Sum_probs=22.9

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVS   32 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~   32 (283)
                      ||+||||+|..++......  =..++.|+..
T Consensus        11 GGvGKTtia~nlA~~la~~--g~~VlliD~D   39 (232)
T d1hyqa_          11 GGTGKTTITANLGVALAQL--GHDVTIVDAD   39 (232)
T ss_dssp             SCSCHHHHHHHHHHHHHHT--TCCEEEEECC
T ss_pred             CCChHHHHHHHHHHHHHhC--CCCEEEEeCC
Confidence            8999999999998876644  2357788775

>d1okkd2 c.37.1.10 (D:97-303) GTPase domain of the signal recognition particle receptor FtsY {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Thermus aquaticus [TaxId: 271]

Probab=93.47  E-value=0.15  Score=38.70  Aligned_cols=73  Identities=15%  Similarity=0.196  Sum_probs=48.2

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCC-CCCHHHHHHHHHHHhCCCCCc-CCHhhhHHhHH-----HHccCCcEE
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQ-NPNIKKIQGEIAFKLGLKFDE-ESESGRTRSPW-----SRLKKEKLQ   74 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~-~~~~~~l~~~i~~~l~~~~~~-~~~~~~~~~l~-----~~L~~kr~L   74 (283)
                      .|+||||.+..++......+  ..+..|+... .....+-++..++.++.+... .+..+....++     ...++..++
T Consensus        15 tGvGKTTTiaKLA~~~~~~g--~kV~lit~Dt~R~gA~eQL~~~a~~l~i~~~~~~~~~d~~~~~~~~~~~~~~~~~d~i   92 (207)
T d1okkd2          15 NGVGKTTTIAKLGRYYQNLG--KKVMFCAGDTFRAAGGTQLSEWGKRLSIPVIQGPEGTDPAALAYDAVQAMKARGYDLL   92 (207)
T ss_dssp             TTSSHHHHHHHHHHHHHTTT--CCEEEECCCCSSTTHHHHHHHHHHHHTCCEECCCTTCCHHHHHHHHHHHHHHHTCSEE
T ss_pred             CCCCHHHHHHHHHHHHHHCC--CcEEEEEeccccccchhhHhhcccccCceEEeccCCccHHHHHHHHHHHHHHCCCCEE
Confidence            59999998888887765432  3577777763 466778888999999987422 22222333332     234677889


Q ss_pred             EE
Q 041028           75 II   76 (283)
Q Consensus        75 lV   76 (283)
                      ||
T Consensus        93 lI   94 (207)
T d1okkd2          93 FV   94 (207)
T ss_dssp             EE
T ss_pred             Ec
Confidence            88

>d1qhxa_ c.37.1.3 (A:) Chloramphenicol phosphotransferase {Streptomyces venezuelae [TaxId: 54571]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Chloramphenicol phosphotransferase
domain: Chloramphenicol phosphotransferase
species: Streptomyces venezuelae [TaxId: 54571]

Probab=93.32  E-value=0.018  Score=42.06  Aligned_cols=17  Identities=12%  Similarity=0.212  Sum_probs=15.1

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      +|+||||+|+.+++...
T Consensus        12 ~GsGKsTva~~L~~~l~   28 (178)
T d1qhxa_          12 SSAGKSGIVRCLQSVLP   28 (178)
T ss_dssp             TTSSHHHHHHHHHHHSS
T ss_pred             CCCCHHHHHHHHHHHcC
Confidence            69999999999998754

>d1zp6a1 c.37.1.25 (A:6-181) Hypothetical protein Atu3015 {Agrobacterium tumefaciens [TaxId: 358]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Atu3015-like
domain: Hypothetical protein Atu3015
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=93.26  E-value=0.015  Score=42.53  Aligned_cols=17  Identities=35%  Similarity=0.487  Sum_probs=14.5

Q ss_pred             CCCCcHHHHHHHHHhhh
Q 041028            1 MGGIGKTTLAKEVARKA   17 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (283)
                      ++|+||||+|+.+.+..
T Consensus        12 ~~GsGKSTia~~La~~l   28 (176)
T d1zp6a1          12 HPGSGKSTIAEALANLP   28 (176)
T ss_dssp             CTTSCHHHHHHHHHTCS
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            57999999999997754

>d1ihua2 c.37.1.10 (A:308-586) Arsenite-translocating ATPase ArsA {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Arsenite-translocating ATPase ArsA
species: Escherichia coli [TaxId: 562]

Probab=93.14  E-value=0.031  Score=44.39  Aligned_cols=33  Identities=27%  Similarity=0.476  Sum_probs=22.2

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPN   36 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~   36 (283)
                      |||||||+|..++.....+++  .++-|+.....+
T Consensus        29 GGVGKTT~a~nLA~~lA~~G~--rVllvD~Dp~~~   61 (279)
T d1ihua2          29 GGVGKTTMAAAIAVRLADMGF--DVHLTTSDPAAH   61 (279)
T ss_dssp             TTSSHHHHHHHHHHHHHHTTC--CEEEEESCCC--
T ss_pred             CCCCHHHHHHHHHHHHHHCCC--cEEEEeCCCCCC
Confidence            899999998888877654432  466676664433

>d1ls1a2 c.37.1.10 (A:89-295) GTPase domain of the signal sequence recognition protein Ffh {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal sequence recognition protein Ffh
species: Thermus aquaticus [TaxId: 271]

Probab=93.06  E-value=0.086  Score=40.12  Aligned_cols=73  Identities=25%  Similarity=0.262  Sum_probs=45.4

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCC-CCCHHHHHHHHHHHhCCCCCc----CCHhhhHHh--HHHHccCCcEE
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQ-NPNIKKIQGEIAFKLGLKFDE----ESESGRTRS--PWSRLKKEKLQ   74 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~-~~~~~~l~~~i~~~l~~~~~~----~~~~~~~~~--l~~~L~~kr~L   74 (283)
                      .|+||||.+..++.....+  -..+..++... .....+-++...+.++.+...    .+..+....  ....+.+..++
T Consensus        19 ~GvGKTTTiaKLA~~~~~~--g~kV~lit~Dt~R~gA~eQL~~~a~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~d~v   96 (207)
T d1ls1a2          19 QGSGKTTTAAKLALYYKGK--GRRPLLVAADTQRPAAREQLRLLGEKVGVPVLEVMDGESPESIRRRVEEKARLEARDLI   96 (207)
T ss_dssp             TTTTHHHHHHHHHHHHHHT--TCCEEEEECCSSCHHHHHHHHHHHHHHTCCEEECCTTCCHHHHHHHHHHHHHHHTCCEE
T ss_pred             CCCCHHHHHHHHHHHHHHC--CCcEEEEecccccchHHHHHHHHHHhcCCccccccccchhhHHHHHHHHHHhhccCcce
Confidence            6999999888877776544  23455666542 234567778888888887432    233333222  23346777888


Q ss_pred             EE
Q 041028           75 II   76 (283)
Q Consensus        75 lV   76 (283)
                      ||
T Consensus        97 lI   98 (207)
T d1ls1a2          97 LV   98 (207)
T ss_dssp             EE
T ss_pred             ee
Confidence            88

>d1g3qa_ c.37.1.10 (A:) Cell division regulator MinD {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Cell division regulator MinD
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=93.04  E-value=0.043  Score=42.18  Aligned_cols=29  Identities=21%  Similarity=0.326  Sum_probs=22.3

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVS   32 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~   32 (283)
                      ||+||||+|..++......  -..++-|+..
T Consensus        12 GGvGKTtia~nLA~~la~~--g~~VlliD~D   40 (237)
T d1g3qa_          12 GGTGKTTVTANLSVALGDR--GRKVLAVDGD   40 (237)
T ss_dssp             TTSSHHHHHHHHHHHHHHT--TCCEEEEECC
T ss_pred             CCCcHHHHHHHHHHHHHhC--CCCEEEEeCC
Confidence            8999999999999876644  2356777765

>d1m7ga_ c.37.1.4 (A:) Adenosine-5'phosphosulfate kinase (APS kinase) {Fungus (Penicillium chrysogenum) [TaxId: 5076]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Adenosine-5'phosphosulfate kinase (APS kinase)
domain: Adenosine-5'phosphosulfate kinase (APS kinase)
species: Fungus (Penicillium chrysogenum) [TaxId: 5076]

Probab=93.01  E-value=0.021  Score=43.78  Aligned_cols=18  Identities=33%  Similarity=0.464  Sum_probs=15.4

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      ++|+||||||+++.....
T Consensus        32 lsGsGKTTia~~L~~~l~   49 (208)
T d1m7ga_          32 LSASGKSTLAVELEHQLV   49 (208)
T ss_dssp             STTSSHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHH
Confidence            579999999999987653

>d1u94a1 c.37.1.11 (A:6-268) RecA protein, ATPase-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Escherichia coli [TaxId: 562]

Probab=92.98  E-value=0.13  Score=40.58  Aligned_cols=69  Identities=19%  Similarity=0.195  Sum_probs=45.0

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHHHhCCCCCc------CCHhhhHHhHHHHccC--CcE
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKLGLKFDE------ESESGRTRSPWSRLKK--EKL   73 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~~l~~~~~~------~~~~~~~~~l~~~L~~--kr~   73 (283)
                      +|+||||||.+++......+  ..++|++....++..     .++.+|.+.+.      .+.++..+.+....+.  .++
T Consensus        63 ~gsGKTtl~l~~~~~~q~~g--~~~vyidtE~~~~~~-----~a~~~Gvd~d~v~~~~~~~~E~~~~~i~~l~~~~~~~l  135 (263)
T d1u94a1          63 ESSGKTTLTLQVIAAAQREG--KTCAFIDAEHALDPI-----YARKLGVDIDNLLCSQPDTGEQALEICDALARSGAVDV  135 (263)
T ss_dssp             TTSSHHHHHHHHHHHHHHTT--CCEEEEESSCCCCHH-----HHHHTTCCGGGCEEECCSSHHHHHHHHHHHHHHTCCSE
T ss_pred             CCcHHHHHHHHHHHHHHcCC--CEEEEEccccccCHH-----HHHHhCCCHHHEEEecCCCHHHHHHHHHHHHhcCCCCE
Confidence            58999999999988766543  357999999888864     46677775332      2344455555544432  255


Q ss_pred             EEEc
Q 041028           74 QIIC   77 (283)
Q Consensus        74 LlV~   77 (283)
                      +||+
T Consensus       136 iViD  139 (263)
T d1u94a1         136 IVVD  139 (263)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            5553

>d1nksa_ c.37.1.1 (A:) Adenylate kinase {Archaeon Sulfolobus acidocaldarius [TaxId: 2285]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Archaeon Sulfolobus acidocaldarius [TaxId: 2285]

Probab=92.97  E-value=0.025  Score=41.78  Aligned_cols=20  Identities=30%  Similarity=0.488  Sum_probs=17.0

Q ss_pred             CCCCcHHHHHHHHHhhhccC
Q 041028            1 MGGIGKTTLAKEVARKAKNG   20 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~   20 (283)
                      ++|+||||+|+.+.......
T Consensus         9 ~~GsGKTT~~~~La~~L~~~   28 (194)
T d1nksa_           9 IPGVGKSTVLAKVKEILDNQ   28 (194)
T ss_dssp             CTTSCHHHHHHHHHHHHHTT
T ss_pred             CCCCCHHHHHHHHHHHHHHc
Confidence            57999999999999887643

>d1khta_ c.37.1.1 (A:) Adenylate kinase {Archaeon Methanococcus voltae [TaxId: 2188]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Archaeon Methanococcus voltae [TaxId: 2188]

Probab=92.92  E-value=0.023  Score=41.77  Aligned_cols=20  Identities=20%  Similarity=0.343  Sum_probs=16.9

Q ss_pred             CCCCcHHHHHHHHHhhhccC
Q 041028            1 MGGIGKTTLAKEVARKAKNG   20 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~   20 (283)
                      +.|+||||+++.+.......
T Consensus         9 ~~GsGKsT~~~~L~~~l~~~   28 (190)
T d1khta_           9 VPGVGSTTSSQLAMDNLRKE   28 (190)
T ss_dssp             CTTSCHHHHHHHHHHHHHTT
T ss_pred             CCCCCHHHHHHHHHHHHHHc
Confidence            57999999999999886543

>d1cp2a_ c.37.1.10 (A:) Nitrogenase iron protein {Clostridium pasteurianum [TaxId: 1501]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Nitrogenase iron protein
species: Clostridium pasteurianum [TaxId: 1501]

Probab=92.86  E-value=0.024  Score=44.95  Aligned_cols=29  Identities=24%  Similarity=0.351  Sum_probs=21.8

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVS   32 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~   32 (283)
                      |||||||+|..++......+ + .++-|+..
T Consensus        10 GGvGKTT~a~nLA~~LA~~G-~-rVllID~D   38 (269)
T d1cp2a_          10 GGIGKSTTTQNLTSGLHAMG-K-TIMVVGCD   38 (269)
T ss_dssp             TTSSHHHHHHHHHHHHHTTT-C-CEEEEEEC
T ss_pred             CcCCHHHHHHHHHHHHHhCC-C-cEEEEecC
Confidence            89999999999988876543 2 45556665

>d2afhe1 c.37.1.10 (E:1-289) Nitrogenase iron protein {Azotobacter vinelandii [TaxId: 354]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Nitrogenase iron protein
species: Azotobacter vinelandii [TaxId: 354]

Probab=92.78  E-value=0.022  Score=45.72  Aligned_cols=30  Identities=20%  Similarity=0.354  Sum_probs=21.5

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQ   33 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~   33 (283)
                      |||||||+|..++......+ + .++-|+...
T Consensus        11 GGVGKTT~a~NLA~~LA~~G-~-rVLlID~Dp   40 (289)
T d2afhe1          11 GGIGKSTTTQNLVAALAEMG-K-KVMIVGCDP   40 (289)
T ss_dssp             TTSSHHHHHHHHHHHHHHTT-C-CEEEEEECS
T ss_pred             CCCCHHHHHHHHHHHHHHCC-C-CEEEEecCC
Confidence            89999999999887665432 2 366666654

>d1sxja2 c.37.1.20 (A:295-547) Replication factor C1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=92.59  E-value=0.046  Score=42.57  Aligned_cols=34  Identities=32%  Similarity=0.305  Sum_probs=23.7

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHH
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKI   40 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l   40 (283)
                      +|+||||+|+.+++....     ..++++.+...+...+
T Consensus        61 pG~GKTt~a~~la~~~~~-----~~~~~~~~~~~~~~~~   94 (253)
T d1sxja2          61 PGIGKTTAAHLVAQELGY-----DILEQNASDVRSKTLL   94 (253)
T ss_dssp             TTSSHHHHHHHHHHHTTC-----EEEEECTTSCCCHHHH
T ss_pred             CCCCHHHHHHHHHHHHHh-----hhhccccccchhhHHH
Confidence            699999999999997542     2456666655554443

>d1rz3a_ c.37.1.6 (A:) Hypothetical protein rbstp0775 {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Hypothetical protein rbstp0775
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=92.57  E-value=0.04  Score=40.93  Aligned_cols=19  Identities=32%  Similarity=0.478  Sum_probs=16.3

Q ss_pred             CCCcHHHHHHHHHhhhccC
Q 041028            2 GGIGKTTLAKEVARKAKNG   20 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~   20 (283)
                      +|+||||||+.+.+.....
T Consensus        31 ~GSGKSTla~~L~~~l~~~   49 (198)
T d1rz3a_          31 SRSGKTTLANQLSQTLREQ   49 (198)
T ss_dssp             TTSSHHHHHHHHHHHHHHT
T ss_pred             CCCCHHHHHHHHHHHhccc
Confidence            6999999999999876654

>d1yj5a2 c.37.1.1 (A:351-522) 5' polynucleotide kinase-3' phosphatase, C-terminal domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: 5' polynucleotide kinase-3' phosphatase, C-terminal domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=92.46  E-value=0.023  Score=42.09  Aligned_cols=16  Identities=31%  Similarity=0.434  Sum_probs=13.5

Q ss_pred             CCCCcHHHHHHHHHhh
Q 041028            1 MGGIGKTTLAKEVARK   16 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~   16 (283)
                      ++|+||||+|+.+...
T Consensus        22 ~pGsGKST~a~~l~~~   37 (172)
T d1yj5a2          22 FPGAGKSTFIQEHLVS   37 (172)
T ss_dssp             CTTSSHHHHHHHHTGG
T ss_pred             CCCCCHHHHHHHHHHh
Confidence            5799999999988654

>d2ak3a1 c.37.1.1 (A:0-124,A:162-225) Adenylate kinase {Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]

Probab=92.44  E-value=0.028  Score=42.18  Aligned_cols=18  Identities=22%  Similarity=0.427  Sum_probs=15.9

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      ++|+||||+|+.++.+..
T Consensus        14 ~PGSGKtT~a~~La~~~g   31 (189)
T d2ak3a1          14 APGSGKGTVSSRITKHFE   31 (189)
T ss_dssp             CTTSSHHHHHHHHHHHBC
T ss_pred             CCCCCHHHHHHHHHHHHC
Confidence            689999999999998753

>d1ye8a1 c.37.1.11 (A:1-178) Hypothetical kinase-like protein Aq_1292 {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hypothetical kinase-like protein Aq 1292
species: Aquifex aeolicus [TaxId: 63363]

Probab=92.43  E-value=0.028  Score=41.20  Aligned_cols=18  Identities=39%  Similarity=0.671  Sum_probs=15.6

Q ss_pred             CCCcHHHHHHHHHhhhcc
Q 041028            2 GGIGKTTLAKEVARKAKN   19 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~   19 (283)
                      .|+|||||++.+......
T Consensus         9 ~G~GKSTLl~~i~~~l~~   26 (178)
T d1ye8a1           9 PGVGKTTLVKKIVERLGK   26 (178)
T ss_dssp             TTSSHHHHHHHHHHHHGG
T ss_pred             CCcHHHHHHHHHHhcCCC
Confidence            699999999999987653

>d1gvnb_ c.37.1.21 (B:) Plasmid maintenance system epsilon/zeta, toxin zeta subunit {Streptococcus pyogenes [TaxId: 1314]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
domain: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
species: Streptococcus pyogenes [TaxId: 1314]

Probab=92.41  E-value=0.025  Score=44.57  Aligned_cols=17  Identities=29%  Similarity=0.491  Sum_probs=15.5

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      +|+||||||+.+++...
T Consensus        41 PGtGKT~la~~la~~~~   57 (273)
T d1gvnb_          41 PGSGKTSLRSAIFEETQ   57 (273)
T ss_dssp             TTSCTHHHHHHHHHHTT
T ss_pred             CCCCHHHHHHHHHHHhh
Confidence            79999999999999765

>d1xjca_ c.37.1.10 (A:) Molybdopterin-guanine dinucleotide biosynthesis protein MobB {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Molybdopterin-guanine dinucleotide biosynthesis protein MobB
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=92.20  E-value=0.032  Score=40.67  Aligned_cols=19  Identities=32%  Similarity=0.228  Sum_probs=16.4

Q ss_pred             CCCcHHHHHHHHHhhhccC
Q 041028            2 GGIGKTTLAKEVARKAKNG   20 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~   20 (283)
                      .|+|||||+.++....+.+
T Consensus        10 ~gSGKTTli~~l~~~L~~~   28 (165)
T d1xjca_          10 KHSGKTTLMEKWVAAAVRE   28 (165)
T ss_dssp             TTSSHHHHHHHHHHHHHHT
T ss_pred             CCCCHHHHHHHHHHHHHhC
Confidence            6999999999999887654

>d1zina1 c.37.1.1 (A:1-125,A:161-217) Adenylate kinase {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=92.14  E-value=0.032  Score=41.15  Aligned_cols=18  Identities=28%  Similarity=0.377  Sum_probs=15.8

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      ++|+||||+|+.++....
T Consensus         8 ~pGSGKsT~a~~La~~~~   25 (182)
T d1zina1           8 LPGAGKGTQAEKIVAAYG   25 (182)
T ss_dssp             STTSSHHHHHHHHHHHHC
T ss_pred             CCCCCHHHHHHHHHHHHC
Confidence            479999999999998764

>d2cdna1 c.37.1.1 (A:1-181) Adenylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=92.10  E-value=0.033  Score=41.20  Aligned_cols=18  Identities=39%  Similarity=0.350  Sum_probs=16.0

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      ++|+||||+|+.+++...
T Consensus         8 ~pGsGKsT~a~~La~~~g   25 (181)
T d2cdna1           8 PPGAGKGTQAVKLAEKLG   25 (181)
T ss_dssp             CTTSSHHHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHHHHC
Confidence            479999999999998874

>d1zaka1 c.37.1.1 (A:3-127,A:159-222) Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Maize (Zea mays) [TaxId: 4577]

Probab=92.01  E-value=0.033  Score=41.52  Aligned_cols=18  Identities=22%  Similarity=0.185  Sum_probs=15.8

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      ++|+||||+|+.+++...
T Consensus        11 ppGsGKsT~a~~La~~~~   28 (189)
T d1zaka1          11 APASGKGTQCELIKTKYQ   28 (189)
T ss_dssp             STTSSHHHHHHHHHHHHC
T ss_pred             CCCCCHHHHHHHHHHHHC
Confidence            479999999999998764

>d1tf7a2 c.37.1.11 (A:256-497) Circadian clock protein KaiC {Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Circadian clock protein KaiC
species: Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]

Probab=91.96  E-value=0.062  Score=41.46  Aligned_cols=31  Identities=19%  Similarity=0.284  Sum_probs=24.8

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCC
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQN   34 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~   34 (283)
                      +|+|||+||.+++.+....  ...++|++...+
T Consensus        35 pGsGKT~l~~qia~~~~~~--~~~~~~is~e~~   65 (242)
T d1tf7a2          35 TGTGKTLLVSRFVENACAN--KERAILFAYEES   65 (242)
T ss_dssp             TTSSHHHHHHHHHHHHHTT--TCCEEEEESSSC
T ss_pred             CCCCHHHHHHHHHHHHHHh--ccccceeeccCC
Confidence            6999999999999886533  667888887654

>d2qy9a2 c.37.1.10 (A:285-495) GTPase domain of the signal recognition particle receptor FtsY {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Escherichia coli [TaxId: 562]

Probab=91.81  E-value=0.58  Score=35.35  Aligned_cols=72  Identities=13%  Similarity=0.120  Sum_probs=42.9

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCH--HHHHHHHHHHhCCCCCc-CCHhhhHHhHHHH-----ccCCcE
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNI--KKIQGEIAFKLGLKFDE-ESESGRTRSPWSR-----LKKEKL   73 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~--~~l~~~i~~~l~~~~~~-~~~~~~~~~l~~~-----L~~kr~   73 (283)
                      .|+||||.+..++.....++   ..+.+-..+.+.+  .+-++...+.++.+... .+..+....+++.     .++..+
T Consensus        18 tGvGKTTTiAKLA~~~~~~g---~kV~lit~Dt~R~gA~eQL~~~a~~l~v~~~~~~~~~d~~~~l~~~~~~a~~~~~d~   94 (211)
T d2qy9a2          18 NGVGKTTTIGKLARQFEQQG---KSVMLAAGDTFRAAAVEQLQVWGQRNNIPVIAQHTGADSASVIFDAIQAAKARNIDV   94 (211)
T ss_dssp             TTSCHHHHHHHHHHHHHTTT---CCEEEECCCTTCHHHHHHHHHHHHHTTCCEECCSTTCCHHHHHHHHHHHHHHTTCSE
T ss_pred             CCCCHHHHHHHHHHHHHHCC---CcEEEEecccccccchhhhhhhhhhcCCcccccccCCCHHHHHHHHHHHHHHcCCCE
Confidence            59999998877787765332   2344433344544  66778888999887432 2333333333332     345577


Q ss_pred             EEE
Q 041028           74 QII   76 (283)
Q Consensus        74 LlV   76 (283)
                      +||
T Consensus        95 ilI   97 (211)
T d2qy9a2          95 LIA   97 (211)
T ss_dssp             EEE
T ss_pred             EEe
Confidence            888

>d1nn5a_ c.37.1.1 (A:) Thymidylate kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.79  E-value=0.11  Score=39.43  Aligned_cols=19  Identities=16%  Similarity=0.240  Sum_probs=16.5

Q ss_pred             CCCcHHHHHHHHHhhhccC
Q 041028            2 GGIGKTTLAKEVARKAKNG   20 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~   20 (283)
                      .|+||||+|+.+.+.....
T Consensus        12 dGsGKsT~~~~L~~~L~~~   30 (209)
T d1nn5a_          12 DRAGKSTQSRKLVEALCAA   30 (209)
T ss_dssp             TTSSHHHHHHHHHHHHHHT
T ss_pred             CCCCHHHHHHHHHHHHHHC
Confidence            5999999999999987654

>d1sxje2 c.37.1.20 (E:4-255) Replication factor C5 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C5
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=91.64  E-value=0.031  Score=43.60  Aligned_cols=17  Identities=24%  Similarity=0.268  Sum_probs=15.0

Q ss_pred             CCCCcHHHHHHHHHhhh
Q 041028            1 MGGIGKTTLAKEVARKA   17 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (283)
                      .+|+||||+|+++++..
T Consensus        41 p~G~GKTt~~~~la~~l   57 (252)
T d1sxje2          41 PNGTGKKTRCMALLESI   57 (252)
T ss_dssp             STTSSHHHHHHTHHHHH
T ss_pred             CCCCCHHHHHHHHHHhh
Confidence            37999999999999874

>d1sxjb2 c.37.1.20 (B:7-230) Replication factor C4 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C4
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=91.61  E-value=0.041  Score=42.25  Aligned_cols=44  Identities=25%  Similarity=0.317  Sum_probs=26.6

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHH
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIA   45 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~   45 (283)
                      +|+||||+|+.+++....+..-..++-++.+.......+...+.
T Consensus        45 ~G~GKTt~a~~la~~l~~~~~~~~~~~~n~~~~~~~~~i~~~~~   88 (224)
T d1sxjb2          45 PGIGKTTSVHCLAHELLGRSYADGVLELNASDDRGIDVVRNQIK   88 (224)
T ss_dssp             TTSSHHHHHHHHHHHHHGGGHHHHEEEECTTSCCSHHHHHTHHH
T ss_pred             CCCCchhhHHHHHHHHhccccccccccccccccCCceehhhHHH
Confidence            69999999999998765431112344455555555554444433

>d1qf9a_ c.37.1.1 (A:) UMP/CMP kinase {Dictyostelium discoideum [TaxId: 44689]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: UMP/CMP kinase
species: Dictyostelium discoideum [TaxId: 44689]

Probab=91.58  E-value=0.04  Score=41.20  Aligned_cols=18  Identities=28%  Similarity=0.285  Sum_probs=15.7

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      .+|+||||+|+.++++..
T Consensus        14 ~pGSGKsT~a~~La~~~g   31 (194)
T d1qf9a_          14 GPGSGKGTQCANIVRDFG   31 (194)
T ss_dssp             STTSSHHHHHHHHHHHHC
T ss_pred             CCCCCHHHHHHHHHHHHC
Confidence            479999999999998764

>d1s3ga1 c.37.1.1 (A:1-125,A:161-217) Adenylate kinase {Bacillus globisporus [TaxId: 1459]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Bacillus globisporus [TaxId: 1459]

Probab=91.52  E-value=0.041  Score=40.73  Aligned_cols=18  Identities=33%  Similarity=0.434  Sum_probs=16.0

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      ++|+||||+|+.++.+..
T Consensus         8 ~pGSGKsT~a~~La~~~g   25 (182)
T d1s3ga1           8 LPGAGKGTQADRIVEKYG   25 (182)
T ss_dssp             STTSSHHHHHHHHHHHHC
T ss_pred             CCCCCHHHHHHHHHHHHC
Confidence            479999999999999874

>d2fnaa2 c.37.1.20 (A:1-283) Archaeal ATPase SSO1545 {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Archaeal ATPase SSO1545
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=91.34  E-value=0.058  Score=42.18  Aligned_cols=18  Identities=17%  Similarity=0.233  Sum_probs=15.5

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      .+|+|||+|++++.++..
T Consensus        37 ~~G~GKTsLl~~~~~~~~   54 (283)
T d2fnaa2          37 LRRTGKSSIIKIGINELN   54 (283)
T ss_dssp             STTSSHHHHHHHHHHHHT
T ss_pred             CCCCcHHHHHHHHHHHCC
Confidence            379999999999988764

>d1akya1 c.37.1.1 (A:3-130,A:169-220) Adenylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=91.20  E-value=0.047  Score=40.35  Aligned_cols=18  Identities=28%  Similarity=0.318  Sum_probs=15.7

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      ++|+||||+|+.++....
T Consensus        10 ~pGSGKtT~a~~La~~~g   27 (180)
T d1akya1          10 PPGAGKGTQAPNLQERFH   27 (180)
T ss_dssp             CTTSSHHHHHHHHHHHHC
T ss_pred             CCCCCHHHHHHHHHHHhC
Confidence            479999999999998764

>d1iqpa2 c.37.1.20 (A:2-232) Replication factor C {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=91.17  E-value=0.043  Score=42.25  Aligned_cols=17  Identities=47%  Similarity=0.542  Sum_probs=15.0

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      +|+||||+|+.+++...
T Consensus        54 ~G~GKTtla~~iak~l~   70 (231)
T d1iqpa2          54 PGVGKTTAALALARELF   70 (231)
T ss_dssp             TTSSHHHHHHHHHHHHH
T ss_pred             CCCcHHHHHHHHHHHHH
Confidence            69999999999998754

>d1htwa_ c.37.1.18 (A:) Hypothetical protein HI0065 {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: YjeE-like
domain: Hypothetical protein HI0065
species: Haemophilus influenzae [TaxId: 727]

Probab=91.15  E-value=0.056  Score=39.28  Aligned_cols=18  Identities=33%  Similarity=0.486  Sum_probs=15.7

Q ss_pred             CCcHHHHHHHHHhhhccC
Q 041028            3 GIGKTTLAKEVARKAKNG   20 (283)
Q Consensus         3 GiGKTtLA~~v~~~~~~~   20 (283)
                      |+||||+++.+++...+.
T Consensus        43 GaGKTtfvr~~~~~lg~~   60 (158)
T d1htwa_          43 GAGKTTLTRGMLQGIGHQ   60 (158)
T ss_dssp             TSSHHHHHHHHHHHTTCC
T ss_pred             CccHHHHHHHHHhhcccc
Confidence            899999999999986554

>d1tmka_ c.37.1.1 (A:) Thymidylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=91.09  E-value=0.21  Score=37.86  Aligned_cols=18  Identities=28%  Similarity=0.283  Sum_probs=15.5

Q ss_pred             CCCcHHHHHHHHHhhhcc
Q 041028            2 GGIGKTTLAKEVARKAKN   19 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~   19 (283)
                      -|+||||+++.+.+..+.
T Consensus        12 DGsGKST~~~~L~~~L~~   29 (214)
T d1tmka_          12 DRTGKTTQCNILYKKLQP   29 (214)
T ss_dssp             TTSSHHHHHHHHHHHTTT
T ss_pred             CCCcHHHHHHHHHHHHHh
Confidence            599999999999987653

>d1j8yf2 c.37.1.10 (F:87-297) GTPase domain of the signal sequence recognition protein Ffh {Archaeon Acidianus ambivalens [TaxId: 2283]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal sequence recognition protein Ffh
species: Archaeon Acidianus ambivalens [TaxId: 2283]

Probab=91.03  E-value=0.24  Score=37.60  Aligned_cols=73  Identities=18%  Similarity=0.180  Sum_probs=40.3

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCC-CCCHHHHHHHHHHHhCCCCCc-CCHhhhHHhHH-----HHccCCcEE
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQ-NPNIKKIQGEIAFKLGLKFDE-ESESGRTRSPW-----SRLKKEKLQ   74 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~-~~~~~~l~~~i~~~l~~~~~~-~~~~~~~~~l~-----~~L~~kr~L   74 (283)
                      .|+||||.+..++...+.++ . .+..|+... .....+-++..++.++.+... .+..+....+.     ....+..++
T Consensus        21 tGvGKTTTiAKLA~~~~~~g-~-kV~lit~Dt~R~ga~eQL~~~a~~l~v~~~~~~~~~~~~~~~~~a~~~~~~~~~d~I   98 (211)
T d1j8yf2          21 QGTGKATTAGKLAYFYKKKG-F-KVGLVGADVYRPAALEQLQQLGQQIGVPVYGEPGEKDVVGIAKRGVEKFLSEKMEII   98 (211)
T ss_dssp             CCC----HHHHHHHHHHHTT-C-CEEEEECCCSSHHHHHHHHHHHHHHTCCEECCTTCCCHHHHHHHHHHHHHHTTCSEE
T ss_pred             CCCCHHHHHHHHHHHHHHCC-C-ceEEEEeeccccchhHHHHHhccccCcceeecccchhhhHHHHHHHHHhhccCCceE
Confidence            59999997777776665432 2 466666653 334456677888888887432 22222322222     235667888


Q ss_pred             EE
Q 041028           75 II   76 (283)
Q Consensus        75 lV   76 (283)
                      ||
T Consensus        99 lI  100 (211)
T d1j8yf2          99 IV  100 (211)
T ss_dssp             EE
T ss_pred             EE
Confidence            88

>d1d2na_ c.37.1.20 (A:) Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein {Chinese hamster (Cricetulus griseus) [TaxId: 10029]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein
species: Chinese hamster (Cricetulus griseus) [TaxId: 10029]

Probab=90.78  E-value=0.048  Score=42.79  Aligned_cols=17  Identities=35%  Similarity=0.477  Sum_probs=15.4

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      +|+|||+||+++++...
T Consensus        49 pGtGKT~la~alA~~~~   65 (246)
T d1d2na_          49 PHSGKTALAAKIAEESN   65 (246)
T ss_dssp             TTSSHHHHHHHHHHHHT
T ss_pred             CCCCHHHHHHHHhhccc
Confidence            69999999999999765

>d1ukza_ c.37.1.1 (A:) Uridylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Uridylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=90.75  E-value=0.053  Score=40.58  Aligned_cols=18  Identities=22%  Similarity=0.302  Sum_probs=15.6

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      .+|+||||+|+.++....
T Consensus        16 ppGSGKsT~a~~La~~~g   33 (196)
T d1ukza_          16 GPGAGKGTQCEKLVKDYS   33 (196)
T ss_dssp             STTSSHHHHHHHHHHHSS
T ss_pred             CCCCCHHHHHHHHHHHhC
Confidence            379999999999998764

>d1sxjc2 c.37.1.20 (C:12-238) Replication factor C3 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C3
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=90.67  E-value=0.067  Score=40.93  Aligned_cols=18  Identities=33%  Similarity=0.409  Sum_probs=15.7

Q ss_pred             CCCcHHHHHHHHHhhhcc
Q 041028            2 GGIGKTTLAKEVARKAKN   19 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~   19 (283)
                      +|+||||+|+.+++....
T Consensus        44 ~G~GKttl~~~la~~l~~   61 (227)
T d1sxjc2          44 PGTGKTSTIVALAREIYG   61 (227)
T ss_dssp             SSSSHHHHHHHHHHHHHT
T ss_pred             CCCChhHHHHHHHHHhhc
Confidence            699999999999998653

>d1vmaa2 c.37.1.10 (A:82-294) GTPase domain of the signal recognition particle receptor FtsY {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Thermotoga maritima [TaxId: 2336]

Probab=90.62  E-value=0.54  Score=35.62  Aligned_cols=73  Identities=14%  Similarity=0.151  Sum_probs=45.3

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCC-CCCHHHHHHHHHHHhCCCCCc----CCHhhhHHh--HHHHccCCcEE
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQ-NPNIKKIQGEIAFKLGLKFDE----ESESGRTRS--PWSRLKKEKLQ   74 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~-~~~~~~l~~~i~~~l~~~~~~----~~~~~~~~~--l~~~L~~kr~L   74 (283)
                      .|+||||.+..++.+...++  ..+..|+... .....+-++..++.++.+...    .+.......  .....++..++
T Consensus        20 tGvGKTTTiAKLAa~~~~~~--~kV~lit~Dt~R~gA~eQL~~~a~~l~i~~~~~~~~~d~~~~~~~~~~~~~~~~~d~i   97 (213)
T d1vmaa2          20 NGTGKTTSCGKLAKMFVDEG--KSVVLAAADTFRAAAIEQLKIWGERVGATVISHSEGADPAAVAFDAVAHALARNKDVV   97 (213)
T ss_dssp             TTSSHHHHHHHHHHHHHHTT--CCEEEEEECTTCHHHHHHHHHHHHHHTCEEECCSTTCCHHHHHHHHHHHHHHTTCSEE
T ss_pred             CCCCHHHHHHHHHHHHHHCC--CceEEEeecccccchhHHHHHHhhhcCccccccCCCCcHHHHHHHHHHHHHHcCCCEE
Confidence            59999997777777665432  3567777653 344566778888888876432    233222222  23345677888


Q ss_pred             EE
Q 041028           75 II   76 (283)
Q Consensus        75 lV   76 (283)
                      ||
T Consensus        98 lI   99 (213)
T d1vmaa2          98 II   99 (213)
T ss_dssp             EE
T ss_pred             EE
Confidence            88

>d1ofha_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: HslU
species: Haemophilus influenzae [TaxId: 727]

Probab=90.56  E-value=0.05  Score=44.23  Aligned_cols=17  Identities=41%  Similarity=0.728  Sum_probs=15.1

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      +|+|||.||+.+++...
T Consensus        58 pG~GKT~lAkalA~~~~   74 (309)
T d1ofha_          58 TGVGKTEIARRLAKLAN   74 (309)
T ss_dssp             TTSSHHHHHHHHHHHHT
T ss_pred             CCCCHHHHHHHHhhccc
Confidence            69999999999998753

>d1l8qa2 c.37.1.20 (A:77-289) Chromosomal replication initiation factor DnaA {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Chromosomal replication initiation factor DnaA
species: Aquifex aeolicus [TaxId: 63363]

Probab=90.54  E-value=0.078  Score=40.51  Aligned_cols=28  Identities=25%  Similarity=0.395  Sum_probs=21.8

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEe
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEV   31 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v   31 (283)
                      .|+|||.|++++++.....  ...+++++.
T Consensus        45 ~G~GKTHLl~A~~~~~~~~--~~~~~~~~~   72 (213)
T d1l8qa2          45 VGTGKTHLLQAAGNEAKKR--GYRVIYSSA   72 (213)
T ss_dssp             SSSSHHHHHHHHHHHHHHT--TCCEEEEEH
T ss_pred             CCCcHHHHHHHHHHHhccC--ccceEEech
Confidence            6999999999999987755  445666643

>d1ak2a1 c.37.1.1 (A:14-146,A:177-233) Adenylate kinase {Cow (Bos taurus), mitochondrial izozyme-2 [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Cow (Bos taurus), mitochondrial izozyme-2 [TaxId: 9913]

Probab=90.41  E-value=0.061  Score=39.98  Aligned_cols=18  Identities=33%  Similarity=0.316  Sum_probs=15.6

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      ++|+||||+|+.++....
T Consensus        11 ~pGSGKsT~a~~La~~~g   28 (190)
T d1ak2a1          11 PPGAGKGTQAPKLAKNFC   28 (190)
T ss_dssp             CTTSSHHHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHHHhC
Confidence            479999999999998753

>d1sxjd2 c.37.1.20 (D:26-262) Replication factor C2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=90.31  E-value=0.058  Score=41.49  Aligned_cols=39  Identities=18%  Similarity=0.241  Sum_probs=23.0

Q ss_pred             CCCcHHHHHHHHHhhhccCC-CCCeEEEEEeCCCCCHHHH
Q 041028            2 GGIGKTTLAKEVARKAKNGK-LFDQIVFTEVSQNPNIKKI   40 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~-~Fd~~~wv~v~~~~~~~~l   40 (283)
                      +|+||||+|+.+++...... .....+.++.+........
T Consensus        42 ~G~GKTtl~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~   81 (237)
T d1sxjd2          42 PGTGKTSTILALTKELYGPDLMKSRILELNASDERGISIV   81 (237)
T ss_dssp             TTSSHHHHHHHHHHHHHHHHHHTTSEEEECSSSCCCHHHH
T ss_pred             CCCChHHHHHHHHHHHcCCcccccchhheeccccccchHH
Confidence            69999999999998742211 1223344455555444433

>d1e4va1 c.37.1.1 (A:1-121,A:157-214) Adenylate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Escherichia coli [TaxId: 562]

Probab=90.28  E-value=0.063  Score=39.48  Aligned_cols=18  Identities=28%  Similarity=0.111  Sum_probs=15.8

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      ++|+||||+|+.++.+..
T Consensus         8 ~pGSGKsT~~~~La~~~~   25 (179)
T d1e4va1           8 APVAGKGTQAQFIMEKYG   25 (179)
T ss_dssp             STTSSHHHHHHHHHHHHC
T ss_pred             CCCCCHHHHHHHHHHHhC
Confidence            479999999999998764

>d1q3ta_ c.37.1.1 (A:) CMP kinase {Streptococcus pneumoniae [TaxId: 1313]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: CMP kinase
species: Streptococcus pneumoniae [TaxId: 1313]

Probab=89.98  E-value=0.064  Score=40.83  Aligned_cols=34  Identities=18%  Similarity=0.168  Sum_probs=25.7

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHHHh
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKL   48 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~~l   48 (283)
                      +|+||||+|+.++.+....    .         .+..++++.++...
T Consensus        12 ~GsGKgT~ak~La~~lg~~----~---------istGdl~R~~a~~~   45 (223)
T d1q3ta_          12 ASSGKSTVAKIIAKDFGFT----Y---------LDTGAMYRAATYMA   45 (223)
T ss_dssp             SCSSHHHHHHHHHHHHCCE----E---------EEHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHhCCc----E---------ECHHHHHHHHHHHH
Confidence            6999999999999987532    1         36678888776543

>d1szpa2 c.37.1.11 (A:145-395) DNA repair protein Rad51, catalytic domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=89.73  E-value=0.14  Score=39.15  Aligned_cols=38  Identities=11%  Similarity=0.076  Sum_probs=25.9

Q ss_pred             CCCcHHHHHHHHHhhhccCCCC----CeEEEEEeCCCCCHHH
Q 041028            2 GGIGKTTLAKEVARKAKNGKLF----DQIVFTEVSQNPNIKK   39 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~F----d~~~wv~v~~~~~~~~   39 (283)
                      +|+||||||.++.........+    ..++|++....++...
T Consensus        43 pGsGKT~l~lq~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~   84 (251)
T d1szpa2          43 FRTGKSQLCHTLAVTCQIPLDIGGGEGKCLYIDTEGTFRPVR   84 (251)
T ss_dssp             TTSSHHHHHHHHTTTTTSCTTTTCCSCEEEEEESSSCCCGGG
T ss_pred             CCCCHHHHHHHHHHHhhhhhhhccCCceEEEEeecchHHHHH
Confidence            6999999999987654322112    4678888777765443

>d1ckea_ c.37.1.1 (A:) CMP kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: CMP kinase
species: Escherichia coli [TaxId: 562]

Probab=89.60  E-value=0.076  Score=40.21  Aligned_cols=34  Identities=26%  Similarity=0.317  Sum_probs=26.0

Q ss_pred             CCCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHHH
Q 041028            1 MGGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFK   47 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~~   47 (283)
                      ++|+||||+|+.+.++..    |..         .+..+++++++..
T Consensus        11 ppGSGKgT~ak~La~~~g----l~~---------iStGdLlR~~a~~   44 (225)
T d1ckea_          11 PSGAGKGTLCKAMAEALQ----WHL---------LDSGAIYRVLALA   44 (225)
T ss_dssp             CTTSSHHHHHHHHHHHHT----CEE---------EEHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHhC----CcE---------ECHHHHHHHHHHH
Confidence            479999999999999876    322         3667888877653

>d1pzna2 c.37.1.11 (A:96-349) DNA repair protein Rad51, catalytic domain {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=89.59  E-value=0.35  Score=37.00  Aligned_cols=39  Identities=23%  Similarity=0.273  Sum_probs=27.3

Q ss_pred             CCCcHHHHHHHHHhhhccC----CCCCeEEEEEeCCCCCHHHH
Q 041028            2 GGIGKTTLAKEVARKAKNG----KLFDQIVFTEVSQNPNIKKI   40 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~----~~Fd~~~wv~v~~~~~~~~l   40 (283)
                      +|+||||||.++..+....    ......+|+......+...+
T Consensus        45 pGsGKT~~~lq~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   87 (254)
T d1pzna2          45 FGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDTENTFRPERI   87 (254)
T ss_dssp             TTSSHHHHHHHHHHHTTSCGGGTSCSCEEEEEESSSCCCHHHH
T ss_pred             CCCCHHHHHHHHHHHhhchHHhcCCCceEEEEeccchhHHHHH
Confidence            6999999999988764322    12356788887777665444

>d1teva_ c.37.1.1 (A:) UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: UMP/CMP kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.54  E-value=0.079  Score=39.41  Aligned_cols=18  Identities=28%  Similarity=0.266  Sum_probs=15.6

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      .+|+||||+|+.+++...
T Consensus         9 ppGSGKsT~a~~La~~~g   26 (194)
T d1teva_           9 GPGAGKGTQCARIVEKYG   26 (194)
T ss_dssp             CTTSSHHHHHHHHHHHHC
T ss_pred             CCCCCHHHHHHHHHHHhC
Confidence            379999999999998763

>d2vp4a1 c.37.1.1 (A:12-208) Deoxyribonucleoside kinase {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Deoxyribonucleoside kinase
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=89.44  E-value=0.04  Score=41.20  Aligned_cols=16  Identities=31%  Similarity=0.322  Sum_probs=13.5

Q ss_pred             CCCcHHHHHHHHHhhh
Q 041028            2 GGIGKTTLAKEVARKA   17 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~   17 (283)
                      -|+||||+|+.+.+..
T Consensus        18 ~GsGKTTl~~~L~~~l   33 (197)
T d2vp4a1          18 IGSGKTTYLNHFEKYK   33 (197)
T ss_dssp             TTSCHHHHHHTTGGGT
T ss_pred             CCCCHHHHHHHHHHHh
Confidence            5999999999987654

>d1uj2a_ c.37.1.6 (A:) Uridine-cytidine kinase 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Uridine-cytidine kinase 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.22  E-value=0.08  Score=40.11  Aligned_cols=17  Identities=12%  Similarity=0.272  Sum_probs=14.7

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      .|+||||||+.+.+...
T Consensus        11 ~gSGKSTla~~L~~~l~   27 (213)
T d1uj2a_          11 TASGKSSVCAKIVQLLG   27 (213)
T ss_dssp             TTSSHHHHHHHHHHHTT
T ss_pred             CCCCHHHHHHHHHHHhc
Confidence            59999999999988754

>d1ixza_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Thermus thermophilus [TaxId: 274]

Probab=88.44  E-value=0.094  Score=41.07  Aligned_cols=17  Identities=53%  Similarity=0.790  Sum_probs=15.3

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      +|+|||+||+.+++...
T Consensus        51 pGtGKT~la~aia~~~~   67 (247)
T d1ixza_          51 PGVGKTHLARAVAGEAR   67 (247)
T ss_dssp             TTSSHHHHHHHHHHHTT
T ss_pred             CCCChhHHHHHHHHHcC
Confidence            69999999999998764

>d2ocpa1 c.37.1.1 (A:37-277) Deoxyguanosine kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Deoxyguanosine kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.05  E-value=0.1  Score=40.27  Aligned_cols=17  Identities=24%  Similarity=0.350  Sum_probs=14.8

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      -|+||||+++.+.+...
T Consensus        11 ~GsGKST~~~~L~~~l~   27 (241)
T d2ocpa1          11 IAVGKSTFVKLLTKTYP   27 (241)
T ss_dssp             TTSSHHHHHHHHHHHCT
T ss_pred             CCCcHHHHHHHHHHHHh
Confidence            59999999999998754

>d3adka_ c.37.1.1 (A:) Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Pig (Sus scrofa) [TaxId: 9823]

Probab=87.77  E-value=0.12  Score=38.37  Aligned_cols=18  Identities=28%  Similarity=0.313  Sum_probs=15.6

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      .+|+||||+|+.++....
T Consensus        16 ~pGSGKsT~a~~La~~~g   33 (194)
T d3adka_          16 GPGSGKGTQCEKIVQKYG   33 (194)
T ss_dssp             CTTSSHHHHHHHHHHHTC
T ss_pred             CCCCCHHHHHHHHHHHhC
Confidence            479999999999998653

>d1byia_ c.37.1.10 (A:) Dethiobiotin synthetase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Dethiobiotin synthetase
species: Escherichia coli [TaxId: 562]

Probab=87.64  E-value=0.12  Score=38.84  Aligned_cols=20  Identities=25%  Similarity=0.285  Sum_probs=16.4

Q ss_pred             CCCcHHHHHHHHHhhhccCC
Q 041028            2 GGIGKTTLAKEVARKAKNGK   21 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~   21 (283)
                      .||||||++..++.....++
T Consensus        11 ~GVGKTtvs~~La~aLa~~G   30 (224)
T d1byia_          11 TEVGKTVASCALLQAAKAAG   30 (224)
T ss_dssp             TTSCHHHHHHHHHHHHHHTT
T ss_pred             CCccHHHHHHHHHHHHHHCC
Confidence            39999999999998876553

>d1gsia_ c.37.1.1 (A:) Thymidylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=87.57  E-value=0.22  Score=37.18  Aligned_cols=19  Identities=26%  Similarity=0.468  Sum_probs=16.1

Q ss_pred             CCCcHHHHHHHHHhhhccC
Q 041028            2 GGIGKTTLAKEVARKAKNG   20 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~   20 (283)
                      -|+||||+++.+.+....+
T Consensus         9 dGsGKST~~~~L~~~l~~~   27 (208)
T d1gsia_           9 DGAGKRTLVEKLSGAFRAA   27 (208)
T ss_dssp             TTSSHHHHHHHHHHHHHHT
T ss_pred             CCCCHHHHHHHHHHHHHHC
Confidence            5999999999999876544

>d1jbka_ c.37.1.20 (A:) ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=87.35  E-value=0.13  Score=38.64  Aligned_cols=17  Identities=29%  Similarity=0.585  Sum_probs=14.5

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      +|||||+++..++.+..
T Consensus        52 pGVGKTalv~~LA~ri~   68 (195)
T d1jbka_          52 PGVGKTAIVEGLAQRII   68 (195)
T ss_dssp             TTSCHHHHHHHHHHHHH
T ss_pred             CCcccHHHHHHHHHHHH
Confidence            69999999999888643

>d1n0wa_ c.37.1.11 (A:) DNA repair protein Rad51, catalytic domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=87.01  E-value=0.75  Score=33.77  Aligned_cols=39  Identities=10%  Similarity=0.075  Sum_probs=24.3

Q ss_pred             CCCcHHHHHHHHHhhhccCC----CCCeEEEEEeCCCCCHHHH
Q 041028            2 GGIGKTTLAKEVARKAKNGK----LFDQIVFTEVSQNPNIKKI   40 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~----~Fd~~~wv~v~~~~~~~~l   40 (283)
                      +|+|||+||.+++.+.....    .+....++..........+
T Consensus        32 ~GsGKT~l~l~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   74 (242)
T d1n0wa_          32 FRTGKTQICHTLAVTCQLPIDRGGGEGKAMYIDTEGTFRPERL   74 (242)
T ss_dssp             TTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEESSSCCCHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHhhccccccceehhhhhhhhhHHHHH
Confidence            69999999999887643321    1234555555555554433

>d4tmka_ c.37.1.1 (A:) Thymidylate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Escherichia coli [TaxId: 562]

Probab=86.80  E-value=0.46  Score=35.54  Aligned_cols=27  Identities=33%  Similarity=0.410  Sum_probs=19.4

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEE
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFT   29 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv   29 (283)
                      .|+||||+++.+.+.....+ +..+.+.
T Consensus        11 dGsGKsT~~~~L~~~L~~~g-~~~~~~~   37 (210)
T d4tmka_          11 EGAGKTTARNVVVETLEQLG-IRDMVFT   37 (210)
T ss_dssp             TTSCHHHHHHHHHHHHHHTT-CCCEEEE
T ss_pred             CCCCHHHHHHHHHHHHHhCC-CCeEEEe
Confidence            59999999999998765432 3444443

>d1r8sa_ c.37.1.8 (A:) ADP-ribosylation factor {Human (Homo sapiens), ARF1 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARF1 [TaxId: 9606]

Probab=86.27  E-value=0.17  Score=35.79  Aligned_cols=17  Identities=24%  Similarity=0.319  Sum_probs=14.3

Q ss_pred             CCCCcHHHHHHHHHhhh
Q 041028            1 MGGIGKTTLAKEVARKA   17 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~   17 (283)
                      .+|+|||||...+.++.
T Consensus         8 ~~~vGKSsLi~~l~~~~   24 (160)
T d1r8sa_           8 LDAAGKTTILYKLKLGE   24 (160)
T ss_dssp             STTSSHHHHHHHHHHHC
T ss_pred             CCCCCHHHHHHHHhcCC
Confidence            36999999999987664

>d1gkya_ c.37.1.1 (A:) Guanylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=86.05  E-value=0.16  Score=37.53  Aligned_cols=17  Identities=35%  Similarity=0.485  Sum_probs=14.9

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      +|+|||||++.+.++..
T Consensus        10 sG~GK~tl~~~L~~~~~   26 (186)
T d1gkya_          10 SGTGKSTLLKKLFAEYP   26 (186)
T ss_dssp             TTSSHHHHHHHHHHHCT
T ss_pred             CCCCHHHHHHHHHHhCC
Confidence            59999999999988754

>d1lv7a_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Escherichia coli [TaxId: 562]

Probab=86.02  E-value=0.16  Score=39.91  Aligned_cols=17  Identities=59%  Similarity=0.712  Sum_probs=15.4

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      +|+|||+||+.+++...
T Consensus        54 pGtGKT~la~~iA~~~~   70 (256)
T d1lv7a_          54 PGTGKTLLAKAIAGEAK   70 (256)
T ss_dssp             TTSCHHHHHHHHHHHHT
T ss_pred             CCCCccHHHHHHHHHcC
Confidence            69999999999998765

>d1sq5a_ c.37.1.6 (A:) Pantothenate kinase PanK {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Pantothenate kinase PanK
species: Escherichia coli [TaxId: 562]

Probab=86.01  E-value=1  Score=36.05  Aligned_cols=67  Identities=10%  Similarity=-0.068  Sum_probs=35.5

Q ss_pred             CCCcHHHHHHHHHhhhccCCCC--CeEEEEEeCCCCCHHHHHHHHHHHhCCCC---CcCCHhhhHHhHHHHccCCc
Q 041028            2 GGIGKTTLAKEVARKAKNGKLF--DQIVFTEVSQNPNIKKIQGEIAFKLGLKF---DEESESGRTRSPWSRLKKEK   72 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~F--d~~~wv~v~~~~~~~~l~~~i~~~l~~~~---~~~~~~~~~~~l~~~L~~kr   72 (283)
                      .|+||||+|+.+.......  +  ..+.-|+...-+...+.+.+  +.+....   +.-+.+.+.+.+.....++.
T Consensus        89 sgSGKSTla~~L~~lL~~~--~~~~~v~~Is~D~F~~~~~~l~~--~~~~~~~g~Pes~D~~~L~~~L~~lk~g~~  160 (308)
T d1sq5a_          89 VAVGKSTTARVLQALLSRW--PEHRRVELITTDGFLHPNQVLKE--RGLMKKKGFPESYDMHRLVKFVSDLKSGVP  160 (308)
T ss_dssp             TTSSHHHHHHHHHHHHTTS--TTCCCEEEEEGGGGBCCHHHHHH--HTCTTCTTSGGGBCHHHHHHHHHHHTTTCS
T ss_pred             CCCCCcHHHHHHHHHHhhh--cCCCceEEEeeeeeECCchHHHH--hcCCccCCchHhhhHHHHHHHHHHHHcCCC
Confidence            5999999999998876532  3  23444555544333333221  1111111   12345556666666665554

>d1g41a_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: HslU
species: Haemophilus influenzae [TaxId: 727]

Probab=85.91  E-value=0.11  Score=44.29  Aligned_cols=43  Identities=30%  Similarity=0.504  Sum_probs=25.9

Q ss_pred             CCCcHHHHHHHHHhhhccCCCC---CeEEEEEeC-CCCCHHHHHHHHHH
Q 041028            2 GGIGKTTLAKEVARKAKNGKLF---DQIVFTEVS-QNPNIKKIQGEIAF   46 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~F---d~~~wv~v~-~~~~~~~l~~~i~~   46 (283)
                      .|+|||.||+.++.-..+-  |   |+.-+..++ -.-++..+.+++++
T Consensus        58 TGvGKTlLAr~LAk~l~VP--Fv~~daT~fTeaGYvG~DVesii~~L~~  104 (443)
T d1g41a_          58 TGVGKTEIARRLAKLANAP--FIKVEATKFTEVGYVGKEVDSIIRDLTD  104 (443)
T ss_dssp             TTSSHHHHHHHHHHHTTCC--EEEEEGGGGC----CCCCTHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHhCCC--EEEeecceeeecceeecchhHHHHHHHH
Confidence            5999999999999866543  3   111122221 23467777777664

>d1p6xa_ c.37.1.1 (A:) Thymidine kinase {Equine herpesvirus type 4 [TaxId: 10331]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidine kinase
species: Equine herpesvirus type 4 [TaxId: 10331]

Probab=85.87  E-value=0.24  Score=40.39  Aligned_cols=19  Identities=42%  Similarity=0.585  Sum_probs=16.0

Q ss_pred             CCCcHHHHHHHHHhhhccC
Q 041028            2 GGIGKTTLAKEVARKAKNG   20 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~   20 (283)
                      -|+||||+++.+.+.....
T Consensus        15 iGsGKSTl~~~L~~~l~~~   33 (333)
T d1p6xa_          15 YGIGKSTTGRVMASAASGG   33 (333)
T ss_dssp             TTSSHHHHHHHHHSGGGCS
T ss_pred             ccCCHHHHHHHHHHHhccC
Confidence            3999999999999986543

>d1w44a_ c.37.1.11 (A:) NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: NTPase P4
species: Bacteriophage phi-12 [TaxId: 161736]

Probab=85.78  E-value=0.2  Score=40.69  Aligned_cols=19  Identities=26%  Similarity=0.380  Sum_probs=16.3

Q ss_pred             CCCcHHHHHHHHHhhhccC
Q 041028            2 GGIGKTTLAKEVARKAKNG   20 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~   20 (283)
                      +|+|||.||+.++.....+
T Consensus       132 pG~GKT~la~ala~~~~~~  150 (321)
T d1w44a_         132 GNSGKTPLVHALGEALGGK  150 (321)
T ss_dssp             SSSCHHHHHHHHHHHHHTT
T ss_pred             CCccHHHHHHHHHHHhcCC
Confidence            7999999999999986533

>d1lvga_ c.37.1.1 (A:) Guanylate kinase {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=85.73  E-value=0.17  Score=37.58  Aligned_cols=17  Identities=35%  Similarity=0.563  Sum_probs=14.9

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      +|+|||||++++.....
T Consensus         9 sGsGK~tl~~~L~~~~~   25 (190)
T d1lvga_           9 SGAGKSTLLKKLFQEHS   25 (190)
T ss_dssp             TTSSHHHHHHHHHHHHT
T ss_pred             CCCCHHHHHHHHHHhCC
Confidence            69999999999988754

>d1odfa_ c.37.1.6 (A:) Hypothetical protein Ygr205W {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Hypothetical protein Ygr205W
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=85.59  E-value=0.59  Score=37.13  Aligned_cols=47  Identities=11%  Similarity=0.011  Sum_probs=27.8

Q ss_pred             CCCcHHHHHHHHHhhhccCCCC-CeEEEEEeCCCCCHHHHHHHHHHHh
Q 041028            2 GGIGKTTLAKEVARKAKNGKLF-DQIVFTEVSQNPNIKKIQGEIAFKL   48 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~F-d~~~wv~v~~~~~~~~l~~~i~~~l   48 (283)
                      .|+||||||..+......+..+ ..+.-+++..-+-..+=...+.+..
T Consensus        36 qGSGKSTl~~~l~~~L~~~~~~~~~v~~iS~DdfY~t~~~r~~L~~~~   83 (286)
T d1odfa_          36 QGSGKSFTSIQIYNHLMEKYGGEKSIGYASIDDFYLTHEDQLKLNEQF   83 (286)
T ss_dssp             TTSSHHHHHHHHHHHHHHHHGGGSCEEEEEGGGGBCCHHHHHHHHHHT
T ss_pred             CCCCHHHHHHHHHHHHHHHhCCCcceEeeccCCCCCCHHHHHHHhhhc
Confidence            5999999999987765432112 3455666655444333344455544

>d1v5wa_ c.37.1.11 (A:) Meiotic recombination protein DMC1/LIM15 homolog {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Meiotic recombination protein DMC1/LIM15 homolog
species: Human (Homo sapiens) [TaxId: 9606]

Probab=85.50  E-value=0.66  Score=35.28  Aligned_cols=39  Identities=21%  Similarity=0.245  Sum_probs=27.2

Q ss_pred             CCCcHHHHHHHHHhhhcc----CCCCCeEEEEEeCCCCCHHHH
Q 041028            2 GGIGKTTLAKEVARKAKN----GKLFDQIVFTEVSQNPNIKKI   40 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~----~~~Fd~~~wv~v~~~~~~~~l   40 (283)
                      +|+|||+||.+++.....    ...+..+.|+.....+.....
T Consensus        46 ~GsGKT~lalq~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   88 (258)
T d1v5wa_          46 FRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDTENTFRPDRL   88 (258)
T ss_dssp             TTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEEESSSCCCHHHH
T ss_pred             CCCCHHHHHHHHHHHHHhhhhcccccceEEEechHHHHHHHHH
Confidence            699999999998865322    123467888887777665433

>d1e32a2 c.37.1.20 (A:201-458) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=84.23  E-value=0.22  Score=39.07  Aligned_cols=17  Identities=41%  Similarity=0.591  Sum_probs=15.2

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      +|+|||+||+++++...
T Consensus        47 pGtGKT~l~~ala~~~~   63 (258)
T d1e32a2          47 PGTGKTLIARAVANETG   63 (258)
T ss_dssp             TTSSHHHHHHHHHHHTT
T ss_pred             CCCCchHHHHHHHHHhC
Confidence            69999999999999754

>d2i1qa2 c.37.1.11 (A:65-322) DNA repair protein Rad51, catalytic domain {Archaeon Methanococcus voltae [TaxId: 2188]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Archaeon Methanococcus voltae [TaxId: 2188]

Probab=84.14  E-value=0.43  Score=36.14  Aligned_cols=47  Identities=17%  Similarity=0.150  Sum_probs=28.7

Q ss_pred             CCCcHHHHHHHHHhhhccCC--------------CCCeEEEEEeCCCCCHHHHHHHHHHHhC
Q 041028            2 GGIGKTTLAKEVARKAKNGK--------------LFDQIVFTEVSQNPNIKKIQGEIAFKLG   49 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~--------------~Fd~~~wv~v~~~~~~~~l~~~i~~~l~   49 (283)
                      +|+|||+||..++.+....+              .-..++|++....++.. ....+...+.
T Consensus        43 ~G~GKT~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~e~~~~~~-~~~~~~~~~~  103 (258)
T d2i1qa2          43 FGSGKTQIMHQSCVNLQNPEFLFYDEEAVSKGEVAQPKAVYIDTEGTFRPE-RIMQMAEHAG  103 (258)
T ss_dssp             TTSSHHHHHHHHHHHTTCGGGEECCTTTSCTTTTSSEEEEEEESSSCCCHH-HHHHHHHHHT
T ss_pred             CCCCHHHHHHHHHHHHHhcCCCceEEeecccchhcCceEEEEEecCCcCHH-HHHHHHhhcc
Confidence            69999999999987643211              01246788776655543 3344455443

>d1z0fa1 c.37.1.8 (A:8-173) Rab14 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab14
species: Human (Homo sapiens) [TaxId: 9606]

Probab=83.89  E-value=0.21  Score=35.90  Aligned_cols=15  Identities=33%  Similarity=0.587  Sum_probs=13.1

Q ss_pred             CCCcHHHHHHHHHhh
Q 041028            2 GGIGKTTLAKEVARK   16 (283)
Q Consensus         2 gGiGKTtLA~~v~~~   16 (283)
                      +|+|||+|+..+.+.
T Consensus        13 ~~vGKTsli~~~~~~   27 (166)
T d1z0fa1          13 MGVGKSCLLHQFTEK   27 (166)
T ss_dssp             TTSSHHHHHHHHHHS
T ss_pred             CCcCHHHHHHHHHhC
Confidence            699999999998764

>d1znwa1 c.37.1.1 (A:20-201) Guanylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=83.85  E-value=0.24  Score=36.32  Aligned_cols=16  Identities=19%  Similarity=0.478  Sum_probs=14.1

Q ss_pred             CCCcHHHHHHHHHhhh
Q 041028            2 GGIGKTTLAKEVARKA   17 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~   17 (283)
                      +|+|||||++.+..+.
T Consensus        11 sG~GK~tl~~~L~~~~   26 (182)
T d1znwa1          11 SAVGKSTVVRCLRERI   26 (182)
T ss_dssp             TTSSHHHHHHHHHHHS
T ss_pred             CCCCHHHHHHHHHhhC
Confidence            5999999999998764

>d1r6bx2 c.37.1.20 (X:169-436) ClpA, an Hsp100 chaperone, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpA, an Hsp100 chaperone, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=83.81  E-value=0.23  Score=39.20  Aligned_cols=16  Identities=38%  Similarity=0.690  Sum_probs=14.2

Q ss_pred             CCCcHHHHHHHHHhhh
Q 041028            2 GGIGKTTLAKEVARKA   17 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~   17 (283)
                      +|||||+|+..++.+.
T Consensus        48 ~GvGKTalv~~la~ri   63 (268)
T d1r6bx2          48 SGVGKTAIAEGLAWRI   63 (268)
T ss_dssp             TTSSHHHHHHHHHHHH
T ss_pred             CCCcHHHHHHHHHHHH
Confidence            7999999999988874

>d1upta_ c.37.1.8 (A:) ADP-ribosylation factor {Human (Homo sapiens), ARL1 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARL1 [TaxId: 9606]

Probab=83.80  E-value=0.21  Score=35.44  Aligned_cols=16  Identities=31%  Similarity=0.399  Sum_probs=13.8

Q ss_pred             CCCcHHHHHHHHHhhh
Q 041028            2 GGIGKTTLAKEVARKA   17 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~   17 (283)
                      +|+|||||.+.+.++.
T Consensus        14 ~~vGKSSLi~~~~~~~   29 (169)
T d1upta_          14 DGAGKTTILYRLQVGE   29 (169)
T ss_dssp             TTSSHHHHHHHHHHSS
T ss_pred             CCCCHHHHHHHHhCCC
Confidence            6999999999987753

>d1z06a1 c.37.1.8 (A:32-196) Rab-33b {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-33b
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=83.67  E-value=0.23  Score=35.52  Aligned_cols=16  Identities=25%  Similarity=0.304  Sum_probs=13.8

Q ss_pred             CCCCcHHHHHHHHHhh
Q 041028            1 MGGIGKTTLAKEVARK   16 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~   16 (283)
                      .+|+|||||...+.+.
T Consensus        10 ~~~vGKTsLl~~~~~~   25 (165)
T d1z06a1          10 DSNVGKTCLTYRFCAG   25 (165)
T ss_dssp             CTTSSHHHHHHHHHHS
T ss_pred             CCCcCHHHHHHHHHhC
Confidence            3699999999998875

>d1cr2a_ c.37.1.11 (A:) Gene 4 protein (g4p, DNA primase), helicase domain {Bacteriophage T7 [TaxId: 10760]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Gene 4 protein (g4p, DNA primase), helicase domain
species: Bacteriophage T7 [TaxId: 10760]

Probab=83.66  E-value=0.38  Score=37.65  Aligned_cols=44  Identities=11%  Similarity=0.160  Sum_probs=28.8

Q ss_pred             CCCcHHHHHHHHHhhhccCCCCCeEEEEEeCCCCCHHHHHHHHHHHh
Q 041028            2 GGIGKTTLAKEVARKAKNGKLFDQIVFTEVSQNPNIKKIQGEIAFKL   48 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~~~~Fd~~~wv~v~~~~~~~~l~~~i~~~l   48 (283)
                      +|+||||||..++.+......+ .+++++..  .+..++..+++...
T Consensus        44 ~G~GKT~~~~~la~~~a~~~g~-~v~~~s~E--~~~~~~~~r~~~~~   87 (277)
T d1cr2a_          44 SGMGKSTFVRQQALQWGTAMGK-KVGLAMLE--ESVEETAEDLIGLH   87 (277)
T ss_dssp             TTSSHHHHHHHHHHHHHHTSCC-CEEEEESS--SCHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHhhhhhccc-ceeEeeec--cchhhHHhHHHHHh
Confidence            6999999999998765433222 35565554  45666666766544

>d1kaoa_ c.37.1.8 (A:) Rap2a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rap2a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=83.44  E-value=0.23  Score=35.74  Aligned_cols=15  Identities=33%  Similarity=0.705  Sum_probs=13.3

Q ss_pred             CCCcHHHHHHHHHhh
Q 041028            2 GGIGKTTLAKEVARK   16 (283)
Q Consensus         2 gGiGKTtLA~~v~~~   16 (283)
                      +|||||+|..++.++
T Consensus        12 ~~vGKTsLi~r~~~~   26 (167)
T d1kaoa_          12 GGVGKSALTVQFVTG   26 (167)
T ss_dssp             TTSSHHHHHHHHHHS
T ss_pred             CCcCHHHHHHHHHhC
Confidence            599999999998875

>d1p5zb_ c.37.1.1 (B:) Deoxycytidine kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Deoxycytidine kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=83.09  E-value=0.12  Score=39.52  Aligned_cols=16  Identities=19%  Similarity=0.221  Sum_probs=14.0

Q ss_pred             CCCcHHHHHHHHHhhh
Q 041028            2 GGIGKTTLAKEVARKA   17 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~   17 (283)
                      -|+||||+|+.+.+..
T Consensus        11 dGsGKST~~~~L~~~l   26 (241)
T d1p5zb_          11 IAAGKSTFVNILKQLC   26 (241)
T ss_dssp             TTSSHHHHHTTTGGGC
T ss_pred             CCCCHHHHHHHHHHHH
Confidence            5999999999988764

>d1r7ra3 c.37.1.20 (A:471-735) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=83.09  E-value=0.26  Score=38.82  Aligned_cols=18  Identities=44%  Similarity=0.615  Sum_probs=15.8

Q ss_pred             CCCcHHHHHHHHHhhhcc
Q 041028            2 GGIGKTTLAKEVARKAKN   19 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~~   19 (283)
                      +|+|||+||+++++....
T Consensus        50 ~GtGKT~l~~ala~~~~~   67 (265)
T d1r7ra3          50 PGCGKTLLAKAIANECQA   67 (265)
T ss_dssp             TTSSHHHHHHHHHHHTTC
T ss_pred             CCCcchhHHHHHHHHhCC
Confidence            699999999999998753

>d1z2aa1 c.37.1.8 (A:8-171) Rab23 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab23
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=83.02  E-value=0.26  Score=35.31  Aligned_cols=15  Identities=20%  Similarity=0.620  Sum_probs=13.0

Q ss_pred             CCCcHHHHHHHHHhh
Q 041028            2 GGIGKTTLAKEVARK   16 (283)
Q Consensus         2 gGiGKTtLA~~v~~~   16 (283)
                      +|+|||||...+.+.
T Consensus        11 ~~vGKSsLi~rl~~~   25 (164)
T d1z2aa1          11 GAVGKSSMIQRYCKG   25 (164)
T ss_dssp             TTSSHHHHHHHHHHC
T ss_pred             CCcCHHHHHHHHHhC
Confidence            699999999988764

>d1z08a1 c.37.1.8 (A:17-183) Rab21 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab21
species: Human (Homo sapiens) [TaxId: 9606]

Probab=82.84  E-value=0.24  Score=35.59  Aligned_cols=15  Identities=33%  Similarity=0.545  Sum_probs=13.1

Q ss_pred             CCCcHHHHHHHHHhh
Q 041028            2 GGIGKTTLAKEVARK   16 (283)
Q Consensus         2 gGiGKTtLA~~v~~~   16 (283)
                      +|+|||+|...+.+.
T Consensus        12 ~~vGKTsLi~r~~~~   26 (167)
T d1z08a1          12 GCVGKTSLVLRYCEN   26 (167)
T ss_dssp             TTSCHHHHHHHHHHC
T ss_pred             CCcCHHHHHHHHHhC
Confidence            699999999998764

>d2a5ja1 c.37.1.8 (A:9-181) Rab2b {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab2b
species: Human (Homo sapiens) [TaxId: 9606]

Probab=82.83  E-value=0.25  Score=35.83  Aligned_cols=15  Identities=33%  Similarity=0.565  Sum_probs=13.2

Q ss_pred             CCCcHHHHHHHHHhh
Q 041028            2 GGIGKTTLAKEVARK   16 (283)
Q Consensus         2 gGiGKTtLA~~v~~~   16 (283)
                      +|+|||||+..+.+.
T Consensus        12 ~~vGKTsli~r~~~~   26 (173)
T d2a5ja1          12 TGVGKSCLLLQFTDK   26 (173)
T ss_dssp             TTSSHHHHHHHHHHS
T ss_pred             CCcCHHHHHHHHhcC
Confidence            699999999998765

>d1a5ta2 c.37.1.20 (A:1-207) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=82.73  E-value=0.28  Score=36.98  Aligned_cols=16  Identities=25%  Similarity=0.430  Sum_probs=14.1

Q ss_pred             CCCcHHHHHHHHHhhh
Q 041028            2 GGIGKTTLAKEVARKA   17 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~   17 (283)
                      .|+||||+|+.+++..
T Consensus        33 ~G~GKtt~a~~~a~~l   48 (207)
T d1a5ta2          33 PGMGDDALIYALSRYL   48 (207)
T ss_dssp             TTSCHHHHHHHHHHHH
T ss_pred             CCCcHHHHHHHHHHhc
Confidence            6999999999998864

>d3raba_ c.37.1.8 (A:) Rab3a {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab3a
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=82.54  E-value=0.26  Score=35.57  Aligned_cols=15  Identities=27%  Similarity=0.381  Sum_probs=13.1

Q ss_pred             CCCcHHHHHHHHHhh
Q 041028            2 GGIGKTTLAKEVARK   16 (283)
Q Consensus         2 gGiGKTtLA~~v~~~   16 (283)
                      +|+|||||...+.+.
T Consensus        14 ~~vGKTsLi~~l~~~   28 (169)
T d3raba_          14 SSVGKTSFLFRYADD   28 (169)
T ss_dssp             TTSSHHHHHHHHHHS
T ss_pred             CCcCHHHHHHHHHcC
Confidence            699999999998764

>d2erxa1 c.37.1.8 (A:6-176) di-Ras2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: di-Ras2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=82.52  E-value=0.24  Score=35.73  Aligned_cols=15  Identities=33%  Similarity=0.740  Sum_probs=13.1

Q ss_pred             CCCcHHHHHHHHHhh
Q 041028            2 GGIGKTTLAKEVARK   16 (283)
Q Consensus         2 gGiGKTtLA~~v~~~   16 (283)
                      +|||||||...+.+.
T Consensus        11 ~~vGKTsLi~r~~~~   25 (171)
T d2erxa1          11 GGVGKSSLVLRFVKG   25 (171)
T ss_dssp             TTSSHHHHHHHHHTC
T ss_pred             CCCCHHHHHHHHHhC
Confidence            699999999988764

>d1yzqa1 c.37.1.8 (A:14-177) Rab6 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab6
species: Human (Homo sapiens) [TaxId: 9606]

Probab=82.40  E-value=0.26  Score=35.20  Aligned_cols=15  Identities=27%  Similarity=0.403  Sum_probs=13.2

Q ss_pred             CCCcHHHHHHHHHhh
Q 041028            2 GGIGKTTLAKEVARK   16 (283)
Q Consensus         2 gGiGKTtLA~~v~~~   16 (283)
                      +|+|||+|...+.+.
T Consensus         9 ~~vGKTsLi~r~~~~   23 (164)
T d1yzqa1           9 QSVGKTSLITRFMYD   23 (164)
T ss_dssp             TTSSHHHHHHHHHHS
T ss_pred             CCcCHHHHHHHHHhC
Confidence            699999999998764

>d1yrba1 c.37.1.10 (A:1-244) ATP(GTP)-binding protein PAB0955 {Pyrococcus abyssi [TaxId: 29292]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: ATP(GTP)-binding protein PAB0955
species: Pyrococcus abyssi [TaxId: 29292]

Probab=82.40  E-value=0.29  Score=37.25  Aligned_cols=18  Identities=44%  Similarity=0.553  Sum_probs=14.9

Q ss_pred             CCCCcHHHHHHHHHhhhc
Q 041028            1 MGGIGKTTLAKEVARKAK   18 (283)
Q Consensus         1 mgGiGKTtLA~~v~~~~~   18 (283)
                      +.|.|||||..++.++..
T Consensus         8 ~~GsGKTTLl~~ll~~~~   25 (244)
T d1yrba1           8 TAGSGKTTLTGEFGRYLE   25 (244)
T ss_dssp             STTSSHHHHHHHHHHHHT
T ss_pred             CCCCcHHHHHHHHHHHHh
Confidence            469999999999987654

>d1uf9a_ c.37.1.1 (A:) Dephospho-CoA kinase {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Dephospho-CoA kinase
species: Thermus thermophilus [TaxId: 274]

Probab=82.28  E-value=0.27  Score=36.26  Aligned_cols=14  Identities=36%  Similarity=0.337  Sum_probs=11.9

Q ss_pred             CCCCcHHHHHHHHH
Q 041028            1 MGGIGKTTLAKEVA   14 (283)
Q Consensus         1 mgGiGKTtLA~~v~   14 (283)
                      +.|+||||+|..+-
T Consensus        11 ~~gSGKstva~~l~   24 (191)
T d1uf9a_          11 NIGSGKSTVAALLR   24 (191)
T ss_dssp             CTTSCHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHH
Confidence            46999999999874

>d1z0ja1 c.37.1.8 (A:2-168) Rab-22a {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-22a
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=82.20  E-value=0.27  Score=35.33  Aligned_cols=16  Identities=19%  Similarity=0.472  Sum_probs=13.7

Q ss_pred             CCCcHHHHHHHHHhhh
Q 041028            2 GGIGKTTLAKEVARKA   17 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~   17 (283)
                      +|||||||...+.++.
T Consensus        13 ~~vGKTsli~rl~~~~   28 (167)
T d1z0ja1          13 TGVGKSSIMWRFVEDS   28 (167)
T ss_dssp             TTSSHHHHHHHHHHSC
T ss_pred             CCcCHHHHHHHHHhCC
Confidence            6999999999988753

>d2ew1a1 c.37.1.8 (A:4-174) Rab30 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab30
species: Human (Homo sapiens) [TaxId: 9606]

Probab=81.93  E-value=0.28  Score=35.40  Aligned_cols=15  Identities=33%  Similarity=0.674  Sum_probs=13.3

Q ss_pred             CCCcHHHHHHHHHhh
Q 041028            2 GGIGKTTLAKEVARK   16 (283)
Q Consensus         2 gGiGKTtLA~~v~~~   16 (283)
                      +|+|||||.+.+.+.
T Consensus        14 ~~vGKTsLi~~l~~~   28 (171)
T d2ew1a1          14 AGVGKTCLVRRFTQG   28 (171)
T ss_dssp             TTSSHHHHHHHHHHS
T ss_pred             CCcCHHHHHHHHHhC
Confidence            699999999998874

>d2f7sa1 c.37.1.8 (A:5-190) Rab27b {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab27b
species: Human (Homo sapiens) [TaxId: 9606]

Probab=81.74  E-value=0.27  Score=36.04  Aligned_cols=15  Identities=33%  Similarity=0.534  Sum_probs=12.9

Q ss_pred             CCCcHHHHHHHHHhh
Q 041028            2 GGIGKTTLAKEVARK   16 (283)
Q Consensus         2 gGiGKTtLA~~v~~~   16 (283)
                      +|+|||||+..+.+.
T Consensus        14 ~~vGKTsLi~~l~~~   28 (186)
T d2f7sa1          14 SGVGKTTFLYRYTDN   28 (186)
T ss_dssp             TTSSHHHHHHHHHCS
T ss_pred             CCcCHHHHHHHHhcC
Confidence            599999999998764

>d1r2qa_ c.37.1.8 (A:) Rab5a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab5a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=81.51  E-value=0.3  Score=35.22  Aligned_cols=15  Identities=20%  Similarity=0.468  Sum_probs=13.2

Q ss_pred             CCCcHHHHHHHHHhh
Q 041028            2 GGIGKTTLAKEVARK   16 (283)
Q Consensus         2 gGiGKTtLA~~v~~~   16 (283)
                      +|+|||||+..+.+.
T Consensus        15 ~~vGKTsLi~~l~~~   29 (170)
T d1r2qa_          15 SAVGKSSLVLRFVKG   29 (170)
T ss_dssp             TTSSHHHHHHHHHHS
T ss_pred             CCcCHHHHHHHHHhC
Confidence            699999999998865

>d1g8pa_ c.37.1.20 (A:) ATPase subunit of magnesium chelatase, BchI {Rhodobacter capsulatus [TaxId: 1061]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ATPase subunit of magnesium chelatase, BchI
species: Rhodobacter capsulatus [TaxId: 1061]

Probab=81.28  E-value=0.17  Score=41.12  Aligned_cols=14  Identities=36%  Similarity=0.572  Sum_probs=12.6

Q ss_pred             CCCcHHHHHHHHHh
Q 041028            2 GGIGKTTLAKEVAR   15 (283)
Q Consensus         2 gGiGKTtLA~~v~~   15 (283)
                      +|+||||||+.+..
T Consensus        37 pG~GKT~lar~~~~   50 (333)
T d1g8pa_          37 RGTGKSTAVRALAA   50 (333)
T ss_dssp             GGGCTTHHHHHHHH
T ss_pred             CCccHHHHHHHHHH
Confidence            59999999999875

>d2fn4a1 c.37.1.8 (A:24-196) r-Ras {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: r-Ras
species: Human (Homo sapiens) [TaxId: 9606]

Probab=81.20  E-value=0.31  Score=35.31  Aligned_cols=15  Identities=33%  Similarity=0.740  Sum_probs=13.1

Q ss_pred             CCCcHHHHHHHHHhh
Q 041028            2 GGIGKTTLAKEVARK   16 (283)
Q Consensus         2 gGiGKTtLA~~v~~~   16 (283)
                      +|||||+|...+.+.
T Consensus        15 ~~vGKTsLi~r~~~~   29 (173)
T d2fn4a1          15 GGVGKSALTIQFIQS   29 (173)
T ss_dssp             TTSSHHHHHHHHHHS
T ss_pred             CCcCHHHHHHHHHhC
Confidence            699999999998764

>d2bmea1 c.37.1.8 (A:6-179) Rab4a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab4a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=81.19  E-value=0.31  Score=35.25  Aligned_cols=15  Identities=33%  Similarity=0.563  Sum_probs=12.9

Q ss_pred             CCCcHHHHHHHHHhh
Q 041028            2 GGIGKTTLAKEVARK   16 (283)
Q Consensus         2 gGiGKTtLA~~v~~~   16 (283)
                      +|+|||||+..+...
T Consensus        14 ~~vGKTsll~~~~~~   28 (174)
T d2bmea1          14 AGTGKSCLLHQFIEK   28 (174)
T ss_dssp             TTSSHHHHHHHHHHS
T ss_pred             CCcCHHHHHHHHHhC
Confidence            699999999998754

>d1njfa_ c.37.1.20 (A:) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=81.04  E-value=0.34  Score=37.25  Aligned_cols=17  Identities=35%  Similarity=0.647  Sum_probs=14.5

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      +|+||||+|+.+++...
T Consensus        43 ~G~GKtt~a~~~~~~l~   59 (239)
T d1njfa_          43 RGVGKTSIARLLAKGLN   59 (239)
T ss_dssp             TTSSHHHHHHHHHHHHH
T ss_pred             CCCcHHHHHHHHHHHhc
Confidence            69999999999887653

>d1ctqa_ c.37.1.8 (A:) cH-p21 Ras protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: cH-p21 Ras protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=80.87  E-value=0.32  Score=34.88  Aligned_cols=15  Identities=33%  Similarity=0.793  Sum_probs=13.3

Q ss_pred             CCCcHHHHHHHHHhh
Q 041028            2 GGIGKTTLAKEVARK   16 (283)
Q Consensus         2 gGiGKTtLA~~v~~~   16 (283)
                      +|+|||||...+.++
T Consensus        12 ~~vGKTsli~~l~~~   26 (166)
T d1ctqa_          12 GGVGKSALTIQLIQN   26 (166)
T ss_dssp             TTSSHHHHHHHHHHC
T ss_pred             CCCCHHHHHHHHHhC
Confidence            699999999998875

>d1g16a_ c.37.1.8 (A:) Rab-related protein Sec4 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-related protein Sec4
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=80.84  E-value=0.32  Score=34.84  Aligned_cols=15  Identities=27%  Similarity=0.523  Sum_probs=13.2

Q ss_pred             CCCcHHHHHHHHHhh
Q 041028            2 GGIGKTTLAKEVARK   16 (283)
Q Consensus         2 gGiGKTtLA~~v~~~   16 (283)
                      +|+|||||...+.+.
T Consensus        11 ~~vGKTSli~~l~~~   25 (166)
T d1g16a_          11 SGVGKSCLLVRFVED   25 (166)
T ss_dssp             TTSSHHHHHHHHHHC
T ss_pred             CCcCHHHHHHHHHhC
Confidence            699999999998764

>d1nlfa_ c.37.1.11 (A:) Hexameric replicative helicase repA {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hexameric replicative helicase repA
species: Escherichia coli [TaxId: 562]

Probab=80.80  E-value=0.43  Score=37.20  Aligned_cols=17  Identities=41%  Similarity=0.647  Sum_probs=14.2

Q ss_pred             CCCcHHHHHHHHHhhhc
Q 041028            2 GGIGKTTLAKEVARKAK   18 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~~   18 (283)
                      +|+||||||..++-...
T Consensus        38 ~G~GKS~l~l~la~~ia   54 (274)
T d1nlfa_          38 GGAGKSMLALQLAAQIA   54 (274)
T ss_dssp             TTSSHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHH
Confidence            79999999999877643

>d2gjsa1 c.37.1.8 (A:91-258) Rad {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rad
species: Human (Homo sapiens) [TaxId: 9606]

Probab=80.68  E-value=0.33  Score=34.92  Aligned_cols=15  Identities=33%  Similarity=0.541  Sum_probs=12.9

Q ss_pred             CCCcHHHHHHHHHhh
Q 041028            2 GGIGKTTLAKEVARK   16 (283)
Q Consensus         2 gGiGKTtLA~~v~~~   16 (283)
                      +|||||+|++.+.+.
T Consensus        10 ~~vGKTsLi~~~~~~   24 (168)
T d2gjsa1          10 PGVGKSALARIFGGV   24 (168)
T ss_dssp             TTSSHHHHHHHHHTC
T ss_pred             CCcCHHHHHHHHhCC
Confidence            699999999998664

>d1e2ka_ c.37.1.1 (A:) Thymidine kinase {Herpes simplex virus type 1, different strains [TaxId: 10298]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidine kinase
species: Herpes simplex virus type 1, different strains [TaxId: 10298]

Probab=80.51  E-value=0.24  Score=40.39  Aligned_cols=15  Identities=33%  Similarity=0.481  Sum_probs=12.1

Q ss_pred             CCcHHHHHHHHHhhh
Q 041028            3 GIGKTTLAKEVARKA   17 (283)
Q Consensus         3 GiGKTtLA~~v~~~~   17 (283)
                      |+||||+++.+.+..
T Consensus        14 GsGKTTl~~~La~~l   28 (329)
T d1e2ka_          14 GMGKTTTTQLLVALG   28 (329)
T ss_dssp             TSSHHHHHHHHTC--
T ss_pred             CCCHHHHHHHHHHHh
Confidence            999999999997654

>d1svsa1 c.37.1.8 (A:32-60,A:182-347) Transducin (alpha subunit) {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Transducin (alpha subunit)
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=80.42  E-value=0.38  Score=35.11  Aligned_cols=16  Identities=31%  Similarity=0.449  Sum_probs=13.3

Q ss_pred             CCCcHHHHHHHHHhhh
Q 041028            2 GGIGKTTLAKEVARKA   17 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~   17 (283)
                      +|||||+|...+-...
T Consensus        11 ~~vGKTsl~~r~~~~~   26 (195)
T d1svsa1          11 GESGKSTIVKQMKIIH   26 (195)
T ss_dssp             TTSSHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHhhCC
Confidence            7999999999876553

>d2atva1 c.37.1.8 (A:5-172) Ras-like estrogen-regulated growth inhibitor, RERG {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ras-like estrogen-regulated growth inhibitor, RERG
species: Human (Homo sapiens) [TaxId: 9606]

Probab=80.34  E-value=0.34  Score=34.84  Aligned_cols=16  Identities=31%  Similarity=0.547  Sum_probs=13.8

Q ss_pred             CCCcHHHHHHHHHhhh
Q 041028            2 GGIGKTTLAKEVARKA   17 (283)
Q Consensus         2 gGiGKTtLA~~v~~~~   17 (283)
                      +|+|||+|...+.+..
T Consensus        11 ~~vGKTsli~r~~~~~   26 (168)
T d2atva1          11 AGVGKSALVVRFLTKR   26 (168)
T ss_dssp             TTSSHHHHHHHHHHSC
T ss_pred             CCCCHHHHHHHHHhCC
Confidence            6999999999988753

>d1osna_ c.37.1.1 (A:) Thymidine kinase {Varicella-zoster virus [TaxId: 10335]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidine kinase
species: Varicella-zoster virus [TaxId: 10335]

Probab=80.04  E-value=0.28  Score=39.99  Aligned_cols=17  Identities=47%  Similarity=0.511  Sum_probs=14.8

Q ss_pred             CCcHHHHHHHHHhhhcc
Q 041028            3 GIGKTTLAKEVARKAKN   19 (283)
Q Consensus         3 GiGKTtLA~~v~~~~~~   19 (283)
                      |+||||+++.+.+....
T Consensus        15 GsGKSTl~~~L~~~l~~   31 (331)
T d1osna_          15 GIGKTTAAEEFLHHFAI   31 (331)
T ss_dssp             SSCTTHHHHHHHHTTTT
T ss_pred             CCCHHHHHHHHHHHHhh
Confidence            99999999999987653