Psyllid ID: psy7268

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130----
Protein Sequence
MTMFALPSCCSSVLVFSKVLRNAYPTHRGYEAVSRIDLGTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIGQ
Secondary Structure (PSIPRED)
ccccccccccccccccHHHHHccccccccccccccccccccccccccHHHHHHHHHcccccccHHHHHHHHHHHccccEEEEcccccHHHHHHHHHHHHHHHcccccccccccccccEEEEEcccHHHHHHHcc
Secondary Structure Prediction (SSPRO)
cccccccccccccccHHHHHHccccccccHHcccccccccHHHccccHHHHHHHHHcccccccHHHHHHHHHHHccccEEEEcccccHHHHHHHHHHHHHHHcccccccccccccccEEEEEccHHHHHHHHHc
Coil and Loop (DISEMBL)
mtmfalpsccsSVLVFSKVLRnaypthrgyeavsridlgtfedtglapEIIDIFtkrglttpteiqkysiptllsgkSAILVAETGCGKTLSFLAPLVQQILtwksrpeykpelnaplaliitpgRELVFQIGQ
Flexible Loop (DISEMBL)
MTMFALPSCCSSVLVFSKVLRNAYPThrgyeavsridlgtfedtglAPEIIDIFtkrglttpteiQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNaplaliitpgRELVFQIGQ
Low Complexity Region (SEG)
MTMFALPSCCSSVLVFSKVLRNAYPTHRGYEAVSRIDLGTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIGQ
Disordered region (IsUnstruct)
***FALPSCCSSVLVFSKVLRNAYPTHRGYEAVSRIDLGTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQ***
Disordered Region (DISOPRED)
****************************************FEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQ*****************LALIITPGRELVFQIG*
Disordered Region (DISEMBL)
MTMFALPSCCSSVLVFSKVLRNAYPTHRGYEAVSRIDLGTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIGQ
Disordered Region (DISPRO)
***FALPSCCSSVLVFSKVLRNAYPTHRGYEAVSRIDLGTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSR******LNAPLALIITPGRELVFQIGQ
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
SSSSSSSSSSSSSSSSSSSSSooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
SSSSSSSSSSSSSSSSSSSSSSSSoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MTMFALPSCCSSVLVFSKVLRNAYPTHRGYEAVSRIDLGTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIGQ
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

No hits with e-value below 0.001 by BLAST

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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	134
UNIPROTKB|P25888	454	rhlE "ATP-dependent RNA helica	0.679	0.200	0.406	1.4e-12
TAIR|locus:2116920	626	AT4G34910 [Arabidopsis thalian	0.671	0.143	0.430	1.9e-12
UNIPROTKB|F1SLL4	232	LOC100626422 "Uncharacterized	0.761	0.439	0.384	3.1e-12
TIGR_CMR|CPS_4097	430	CPS_4097 "ATP-dependent RNA he	0.716	0.223	0.411	4.3e-12
TAIR|locus:2828586	505	AT3G02065 [Arabidopsis thalian	0.858	0.227	0.350	4.6e-12
ZFIN|ZDB-GENE-990415-272	716	vasa "vasa homolog" [Danio rer	0.694	0.129	0.376	4.9e-12
UNIPROTKB|Q9NUL7	540	DDX28 "Probable ATP-dependent	0.686	0.170	0.395	5.2e-12
UNIPROTKB|H0Y960	305	DDX4 "Probable ATP-dependent R	0.686	0.301	0.393	7.6e-12
UNIPROTKB|F1NSN3	233	DDX28 "Uncharacterized protein	0.694	0.399	0.376	8.2e-12
UNIPROTKB|Q0C4B9	536	HNE_0695 "Putative ATP-depende	0.664	0.166	0.4	8.4e-12

UNIPROTKB|P25888 rhlE "ATP-dependent RNA helicase" [Escherichia coli K-12 (taxid:83333)]

 Score = 175 (66.7 bits), Expect = 1.4e-12, P = 1.4e-12
 Identities = 39/96 (40%), Positives = 59/96 (61%)

Query:    40 TFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQ 99
             +F+  GL+P+I+    ++G   PT IQ+ +IP +L G+  +  A+TG GKT  F  PL+Q
Sbjct:     2 SFDSLGLSPDILRAVAEQGYREPTPIQQQAIPAVLEGRDLMASAQTGTGKTAGFTLPLLQ 61

Query:   100 QILTWKSRPEYKPELNAPL-ALIITPGRELVFQIGQ 134
              ++T   +P  K     P+ ALI+TP REL  QIG+
Sbjct:    62 HLIT--RQPHAKGR--RPVRALILTPTRELAAQIGE 93

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0042255 "ribosome assembly" evidence=IGI

GO:0004004 "ATP-dependent RNA helicase activity" evidence=IDA

GO:0005524 "ATP binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

TAIR|locus:2116920 AT4G34910 [Arabidopsis thaliana (taxid:3702)]

 Score = 176 (67.0 bits), Expect = 1.9e-12, P = 1.9e-12
 Identities = 40/93 (43%), Positives = 59/93 (63%)

Query:    40 TFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQ 99
             +FE+ GL   +I   TK+G+  PT IQ+ +IP +L GK  +  A+TG GKTL++L PL+Q
Sbjct:    47 SFEELGLDSRLIRALTKKGIEKPTLIQQSAIPYILEGKDVVARAKTGSGKTLAYLLPLLQ 106

Query:   100 QILTWKSRPEYKPELNAPLALIITPGRELVFQI 132
             ++ +  S    K +L AP A I+ P REL  Q+
Sbjct:   107 KLFSADSVS--KKKL-APSAFILVPSRELCQQV 136

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0008026 "ATP-dependent helicase activity" evidence=IEA;ISS

GO:0006606 "protein import into nucleus" evidence=RCA

UNIPROTKB|F1SLL4 LOC100626422 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 164 (62.8 bits), Expect = 3.1e-12, P = 3.1e-12
 Identities = 40/104 (38%), Positives = 56/104 (53%)

Query:    29 GYEAVSRIDLGTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCG 88
             G+EA   I L TFE+  L   +     K G T  T +QKYSIP +L G+  +  A+TG G
Sbjct:   121 GHEAPPAI-L-TFEEANLCQTLNSNIAKAGYTKLTPVQKYSIPIILGGRDLMACAQTGSG 178

Query:    89 KTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQI 132
             KT +FL P++  ++          EL  P  +I+ P REL+ QI
Sbjct:   179 KTAAFLLPILAHMMRDGITASRFKELQEPECIIVAPTRELINQI 222

GO:0008026 "ATP-dependent helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

TIGR_CMR|CPS_4097 CPS_4097 "ATP-dependent RNA helicase SrmB" [Colwellia psychrerythraea 34H (taxid:167879)]

 Score = 170 (64.9 bits), Expect = 4.3e-12, P = 4.3e-12
 Identities = 42/102 (41%), Positives = 55/102 (53%)

Query:    33 VSRIDLGTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLS 92
             +S + L  FE   L  E++    K G T PT IQ+  IP  + GK  +  A TG GKT +
Sbjct:     8 LSELSL-MFEQFDLDSELLASINKIGYTKPTSIQELVIPQAMVGKDVLASAPTGTGKTAA 66

Query:    93 FLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIGQ 134
             FL P+ Q +L +   P  KP    P  LI+TP REL  QIG+
Sbjct:    67 FLLPIAQHLLDY---PRTKPGF--PRVLILTPTRELAIQIGE 103

GO:0004004 "ATP-dependent RNA helicase activity" evidence=ISS

GO:0008186 "RNA-dependent ATPase activity" evidence=ISS

GO:0042254 "ribosome biogenesis" evidence=ISS

TAIR|locus:2828586 AT3G02065 [Arabidopsis thaliana (taxid:3702)]

 Score = 171 (65.3 bits), Expect = 4.6e-12, P = 4.6e-12
 Identities = 41/117 (35%), Positives = 62/117 (52%)

Query:    17 SKVLRNAYPTH-RGYEAVSRIDLGTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLS 75
             +++LR     H +G  +     + TF   GL P+++      G   PT IQ  +IP  L+
Sbjct:    87 AQLLRRKLDIHVQGQGSAVPPPVLTFTSCGLPPKLLLNLETAGYDFPTPIQMQAIPAALT 146

Query:    76 GKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQI 132
             GKS +  A+TG GKT SFL P++ +  T+ S        N PLA+++ P REL  Q+
Sbjct:   147 GKSLLASADTGSGKTASFLVPIISRCTTYHSEHPSDQRRN-PLAMVLAPTRELCVQV 202

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA;ISS

GO:0005634 "nucleus" evidence=ISM

GO:0008026 "ATP-dependent helicase activity" evidence=IEA;ISS

GO:0009507 "chloroplast" evidence=ISM

ZFIN|ZDB-GENE-990415-272 vasa "vasa homolog" [Danio rerio (taxid:7955)]

 Score = 173 (66.0 bits), Expect = 4.9e-12, P = 4.9e-12
 Identities = 35/93 (37%), Positives = 54/93 (58%)

Query:    40 TFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQ 99
             TFE+ GL   +    +K G   PT +QK+ IP + +G+  +  A+TG GKT +FL P++Q
Sbjct:   278 TFEEAGLCDSLSKNVSKSGYVKPTPVQKHGIPIISAGRDLMACAQTGSGKTAAFLLPILQ 337

Query:   100 QILTWKSRPEYKPELNAPLALIITPGRELVFQI 132
             + +T         E+  P A+I+ P REL+ QI
Sbjct:   338 RFMTDGVAASKFSEIQEPEAIIVAPTRELINQI 370

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0008026 "ATP-dependent helicase activity" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0043186 "P granule" evidence=IDA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

GO:0008406 "gonad development" evidence=IEP

UNIPROTKB|Q9NUL7 DDX28 "Probable ATP-dependent RNA helicase DDX28" [Homo sapiens (taxid:9606)]

 Score = 171 (65.3 bits), Expect = 5.2e-12, P = 5.2e-12
 Identities = 38/96 (39%), Positives = 56/96 (58%)

Query:    39 GTFEDTGLAPEIIDIFTKRG--LTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAP 96
             G+F D GL P ++    +    +  PT +Q  +IP+LL G+  +  AETG GKTLS+L P
Sbjct:   126 GSFADLGLEPRVLHALQEAAPEVVQPTTVQSSTIPSLLRGRHVVCAAETGSGKTLSYLLP 185

Query:    97 LVQQILTWKSRPEYKPELNAPLALIITPGRELVFQI 132
             L+Q++L   S     P + AP  L++ P REL  Q+
Sbjct:   186 LLQRLLGQPSLDSL-P-IPAPRGLVLVPSRELAQQV 219

GO:0008026 "ATP-dependent helicase activity" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005739 "mitochondrion" evidence=IDA

GO:0042645 "mitochondrial nucleoid" evidence=IDA

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

UNIPROTKB|H0Y960 DDX4 "Probable ATP-dependent RNA helicase DDX4" [Homo sapiens (taxid:9606)]

 Score = 164 (62.8 bits), Expect = 7.6e-12, P = 7.6e-12
 Identities = 37/94 (39%), Positives = 55/94 (58%)

Query:    40 TFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQ 99
             TFE+  L   + +   K G T  T +QKYSIP +L+G+  +  A+TG GKT +FL P++ 
Sbjct:   195 TFEEANLCQTLNNNIAKAGYTKLTPVQKYSIPIILAGRDLMACAQTGSGKTAAFLLPILA 254

Query:   100 QIL-TWKSRPEYKPELNAPLALIITPGRELVFQI 132
              ++    +   +K EL  P  +I+ P RELV QI
Sbjct:   255 HMMHDGITASRFK-ELQEPECIIVAPTRELVNQI 287

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0008026 "ATP-dependent helicase activity" evidence=IEA

UNIPROTKB|F1NSN3 DDX28 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 160 (61.4 bits), Expect = 8.2e-12, P = 8.2e-12
 Identities = 38/101 (37%), Positives = 56/101 (55%)

Query:    41 FEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQ 100
             F + GL   ++       +  PT +Q+ +IP L  G+SA+  AETG GKTL++L PL+ +
Sbjct:   133 FAEMGLQSALLTALQDLSIARPTAVQRLAIPALRRGRSALCAAETGSGKTLAYLLPLLDR 192

Query:   101 ILTWKSRPE---YKPELN-----APLALIITPGRELVFQIG 133
             +L     PE    KPE +     +P  L++ P RELV Q G
Sbjct:   193 LLARPPGPEPAVEKPEGSGPRSASPCGLVVLPSRELVAQGG 233

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0008026 "ATP-dependent helicase activity" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

UNIPROTKB|Q0C4B9 HNE_0695 "Putative ATP-dependent RNA helicase RhlE" [Hyphomonas neptunium ATCC 15444 (taxid:228405)]

 Score = 169 (64.5 bits), Expect = 8.4e-12, P = 8.4e-12
 Identities = 38/95 (40%), Positives = 55/95 (57%)

Query:    40 TFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQ 99
             TF D GLA  I+   T+ G T PT IQ+ +IP +L G     VA+TG GKT +F+ P++Q
Sbjct:     5 TFADFGLAENILKAVTESGYTIPTPIQREAIPHILMGGDVTGVAQTGTGKTAAFVLPMIQ 64

Query:   100 QILTWKSRPEYKPELNAPLALIITPGRELVFQIGQ 134
             ++ T ++R         P  LI+ P REL  Q+ +
Sbjct:    65 RLSTGRARARM------PRCLILCPTRELAAQVAE 93

GO:0006139 "nucleobase-containing compound metabolic process" evidence=ISS

GO:0008026 "ATP-dependent helicase activity" evidence=ISS

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Prediction of Enzyme Commission (EC) Number

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

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Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	134
cd00268	203	cd00268, DEADc, DEAD-box helicases	3e-25
COG0513	513	COG0513, SrmB, Superfamily II DNA and RNA helicase	3e-23
PTZ00110	545	PTZ00110, PTZ00110, helicase; Provisional	9e-17
PLN00206	518	PLN00206, PLN00206, DEAD-box ATP-dependent RNA hel	9e-17
PRK04837	423	PRK04837, PRK04837, ATP-dependent RNA helicase Rhl	4e-16
PRK11634	629	PRK11634, PRK11634, ATP-dependent RNA helicase Dea	5e-16
PRK10590	456	PRK10590, PRK10590, ATP-dependent RNA helicase Rhl	1e-15
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	1e-15
pfam00270	169	pfam00270, DEAD, DEAD/DEAH box helicase	3e-15
smart00487	201	smart00487, DEXDc, DEAD-like helicases superfamily	4e-13
PRK04537	572	PRK04537, PRK04537, ATP-dependent RNA helicase Rhl	2e-12
PRK01297	475	PRK01297, PRK01297, ATP-dependent RNA helicase Rhl	4e-12
COG1201	814	COG1201, Lhr, Lhr-like helicases [General function	9e-10
PRK11776	460	PRK11776, PRK11776, ATP-dependent RNA helicase Dbp	4e-07
PTZ00424	401	PTZ00424, PTZ00424, helicase 45; Provisional	4e-07
cd00046	144	cd00046, DEXDc, DEAD-like helicases superfamily	8e-07
TIGR04121	803	TIGR04121, DEXH_lig_assoc, DEXH box helicase, DNA	3e-05
PRK13767	876	PRK13767, PRK13767, ATP-dependent helicase; Provis	3e-04
COG1205	851	COG1205, COG1205, Distinct helicase family with a	4e-04
COG1199	654	COG1199, DinG, Rad3-related DNA helicases [Transcr	0.002

>gnl|CDD|238167 cd00268, DEADc, DEAD-box helicases

 Score = 94.5 bits (236), Expect = 3e-25
 Identities = 38/94 (40%), Positives = 55/94 (58%), Gaps = 7/94 (7%)

Query: 41  FEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQ 100
           FE+ GL+PE++      G   PT IQ  +IP LLSG+  I  A+TG GKT +FL P++++
Sbjct: 1   FEELGLSPELLRGIYALGFEKPTPIQARAIPPLLSGRDVIGQAQTGSGKTAAFLIPILEK 60

Query: 101 ILTWKSRPEYKPELNAPLALIITPGRELVFQIGQ 134
           +          P+ + P ALI+ P REL  QI +
Sbjct: 61  LD-------PSPKKDGPQALILAPTRELALQIAE 87

A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP- binding region. Length = 203

>gnl|CDD|223587 COG0513, SrmB, Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis]

 Score = 93.3 bits (232), Expect = 3e-23
 Identities = 37/93 (39%), Positives = 50/93 (53%), Gaps = 7/93 (7%)

Query: 40  TFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQ 99
            F   GL+PE++      G   PT IQ  +IP +L+G+  +  A+TG GKT +FL PL+Q
Sbjct: 30  EFASLGLSPELLQALKDLGFEEPTPIQLAAIPLILAGRDVLGQAQTGTGKTAAFLLPLLQ 89

Query: 100 QILTWKSRPEYKPELNAPLALIITPGRELVFQI 132
           +IL          E     ALI+ P REL  QI
Sbjct: 90  KILK-------SVERKYVSALILAPTRELAVQI 115

Length = 513

>gnl|CDD|240273 PTZ00110, PTZ00110, helicase; Provisional

 Score = 74.8 bits (184), Expect = 9e-17
 Identities = 36/95 (37%), Positives = 50/95 (52%), Gaps = 4/95 (4%)

Query: 40  TFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQ 99
           +FE T     I+      G T PT IQ    P  LSG+  I +AETG GKTL+FL P + 
Sbjct: 131 SFEYTSFPDYILKSLKNAGFTEPTPIQVQGWPIALSGRDMIGIAETGSGKTLAFLLPAIV 190

Query: 100 QILTWKSRPEYKPELNAPLALIITPGRELVFQIGQ 134
            I    ++P  +   + P+ L++ P REL  QI +
Sbjct: 191 HIN---AQPLLRYG-DGPIVLVLAPTRELAEQIRE 221

Length = 545

>gnl|CDD|215103 PLN00206, PLN00206, DEAD-box ATP-dependent RNA helicase; Provisional

 Score = 74.8 bits (184), Expect = 9e-17
 Identities = 37/93 (39%), Positives = 54/93 (58%), Gaps = 2/93 (2%)

Query: 40  TFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQ 99
           +F   GL P+++      G   PT IQ  +IP  LSG+S ++ A+TG GKT SFL P++ 
Sbjct: 122 SFSSCGLPPKLLLNLETAGYEFPTPIQMQAIPAALSGRSLLVSADTGSGKTASFLVPIIS 181

Query: 100 QILTWKSRPEYKPELNAPLALIITPGRELVFQI 132
           +  T   R  +  E   PLA+++TP REL  Q+
Sbjct: 182 RCCTI--RSGHPSEQRNPLAMVLTPTRELCVQV 212

Length = 518

>gnl|CDD|235314 PRK04837, PRK04837, ATP-dependent RNA helicase RhlB; Provisional

 Score = 72.7 bits (179), Expect = 4e-16
 Identities = 34/92 (36%), Positives = 52/92 (56%), Gaps = 2/92 (2%)

Query: 41  FEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQ 100
           F D  L P++++   K+G    T IQ  ++P  L+G+     A+TG GKT++FL      
Sbjct: 10  FSDFALHPQVVEALEKKGFHNCTPIQALALPLTLAGRDVAGQAQTGTGKTMAFLTATFHY 69

Query: 101 ILTWKSRPEYKPELNAPLALIITPGRELVFQI 132
           +L+    PE + ++N P ALI+ P REL  QI
Sbjct: 70  LLS-HPAPEDR-KVNQPRALIMAPTRELAVQI 99

Length = 423

>gnl|CDD|236941 PRK11634, PRK11634, ATP-dependent RNA helicase DeaD; Provisional

 Score = 73.0 bits (179), Expect = 5e-16
 Identities = 35/95 (36%), Positives = 50/95 (52%), Gaps = 9/95 (9%)

Query: 40  TFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQ 99
           TF D GL   I++     G   P+ IQ   IP LL+G+  + +A+TG GKT +F  PL+ 
Sbjct: 7   TFADLGLKAPILEALNDLGYEKPSPIQAECIPHLLNGRDVLGMAQTGSGKTAAFSLPLLH 66

Query: 100 QILTWKSRPEYKPELNAPLALIITPGRELVFQIGQ 134
            +          PEL AP  L++ P REL  Q+ +
Sbjct: 67  NL---------DPELKAPQILVLAPTRELAVQVAE 92

Length = 629

>gnl|CDD|236722 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional

 Score = 71.8 bits (176), Expect = 1e-15
 Identities = 36/95 (37%), Positives = 58/95 (61%), Gaps = 3/95 (3%)

Query: 40  TFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQ 99
           +F+  GL+P+I+    ++G   PT IQ+ +IP +L G+  +  A+TG GKT  F  PL+Q
Sbjct: 2   SFDSLGLSPDILRAVAEQGYREPTPIQQQAIPAVLEGRDLMASAQTGTGKTAGFTLPLLQ 61

Query: 100 QILTWKSRPEYKPELNAPLALIITPGRELVFQIGQ 134
            ++T +   + +  +    ALI+TP REL  QIG+
Sbjct: 62  HLITRQPHAKGRRPVR---ALILTPTRELAAQIGE 93

Length = 456

>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional

 Score = 71.9 bits (177), Expect = 1e-15
 Identities = 35/93 (37%), Positives = 49/93 (52%), Gaps = 5/93 (5%)

Query: 40  TFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQ 99
           TF +  L   +++    +G T PT IQ  +IP  L G+  +  A TG GKT +FL P +Q
Sbjct: 2   TFSELELDESLLEALQDKGYTRPTAIQAEAIPPALDGRDVLGSAPTGTGKTAAFLLPALQ 61

Query: 100 QILTWKSRPEYKPELNAPLALIITPGRELVFQI 132
            +L +   P  K     P  LI+TP REL  Q+
Sbjct: 62  HLLDF---PRRKS--GPPRILILTPTRELAMQV 89

Length = 434

>gnl|CDD|215832 pfam00270, DEAD, DEAD/DEAH box helicase

 Score = 68.1 bits (167), Expect = 3e-15
 Identities = 31/72 (43%), Positives = 43/72 (59%), Gaps = 9/72 (12%)

Query: 63  TEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALII 122
           T IQ  +IP +LSGK  ++ A TG GKTL+FL P++Q +L         P+   P AL++
Sbjct: 1   TPIQAQAIPAILSGKDVLVQAPTGSGKTLAFLLPILQALL---------PKKGGPQALVL 51

Query: 123 TPGRELVFQIGQ 134
            P REL  QI +
Sbjct: 52  APTRELAEQIYE 63

Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression. Length = 169

>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily

 Score = 62.9 bits (153), Expect = 4e-13
 Identities = 26/82 (31%), Positives = 35/82 (42%), Gaps = 11/82 (13%)

Query: 54  FTKRGLTTPTEIQKYSIPTLLSG-KSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKP 112
             K G       QK +I  LLSG +  IL A TG GKTL+ L P ++ +           
Sbjct: 1   IEKFGFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALK---------- 50

Query: 113 ELNAPLALIITPGRELVFQIGQ 134
                  L++ P REL  Q  +
Sbjct: 51  RGKGGRVLVLVPTRELAEQWAE 72

Length = 201

>gnl|CDD|235307 PRK04537, PRK04537, ATP-dependent RNA helicase RhlB; Provisional

 Score = 62.3 bits (151), Expect = 2e-12
 Identities = 35/93 (37%), Positives = 49/93 (52%), Gaps = 2/93 (2%)

Query: 40  TFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQ 99
           TF    L P ++      G T  T IQ  ++P  L G      A+TG GKTL+FL  ++ 
Sbjct: 10  TFSSFDLHPALLAGLESAGFTRCTPIQALTLPVALPGGDVAGQAQTGTGKTLAFLVAVMN 69

Query: 100 QILTWKSRPEYKPELNAPLALIITPGRELVFQI 132
           ++L+  +  + KPE   P ALI+ P REL  QI
Sbjct: 70  RLLSRPALADRKPE--DPRALILAPTRELAIQI 100

Length = 572

>gnl|CDD|234938 PRK01297, PRK01297, ATP-dependent RNA helicase RhlB; Provisional

 Score = 61.5 bits (149), Expect = 4e-12
 Identities = 37/92 (40%), Positives = 50/92 (54%), Gaps = 2/92 (2%)

Query: 41  FEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQ 100
           F D  LAPE++      G    T IQ   +   L+G  AI  A+TG GKT +FL  ++ Q
Sbjct: 89  FHDFNLAPELMHAIHDLGFPYCTPIQAQVLGYTLAGHDAIGRAQTGTGKTAAFLISIINQ 148

Query: 101 ILTWKSRPEYKPELNAPLALIITPGRELVFQI 132
           +L  ++ P  +  +  P ALII P RELV QI
Sbjct: 149 LL--QTPPPKERYMGEPRALIIAPTRELVVQI 178

Length = 475

>gnl|CDD|224122 COG1201, Lhr, Lhr-like helicases [General function prediction only]

 Score = 55.0 bits (133), Expect = 9e-10
 Identities = 27/83 (32%), Positives = 49/83 (59%), Gaps = 5/83 (6%)

Query: 46  LAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWK 105
           L P + + F ++  T+ T  Q+Y+IP + SG++ +++A TG GKT +   P++ ++L   
Sbjct: 8   LDPRVREWFKRKF-TSLTPPQRYAIPEIHSGENVLIIAPTGSGKTEAAFLPVINELL--- 63

Query: 106 SRPEYKPELNAPLALIITPGREL 128
           S  + K E +   AL I+P + L
Sbjct: 64  SLGKGKLE-DGIYALYISPLKAL 85

Length = 814

>gnl|CDD|236977 PRK11776, PRK11776, ATP-dependent RNA helicase DbpA; Provisional

 Score = 47.1 bits (113), Expect = 4e-07
 Identities = 30/94 (31%), Positives = 46/94 (48%), Gaps = 9/94 (9%)

Query: 41  FEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQ 100
           F    L P ++    + G T  T IQ  S+P +L+GK  I  A+TG GKT +F   L+Q+
Sbjct: 6   FSTLPLPPALLANLNELGYTEMTPIQAQSLPAILAGKDVIAQAKTGSGKTAAFGLGLLQK 65

Query: 101 ILTWKSRPEYKPELNAPLALIITPGRELVFQIGQ 134
           +           +     AL++ P REL  Q+ +
Sbjct: 66  L---------DVKRFRVQALVLCPTRELADQVAK 90

Length = 460

>gnl|CDD|185609 PTZ00424, PTZ00424, helicase 45; Provisional

 Score = 47.1 bits (112), Expect = 4e-07
 Identities = 30/93 (32%), Positives = 45/93 (48%), Gaps = 9/93 (9%)

Query: 40  TFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQ 99
           +F+   L  +++      G   P+ IQ+  I  +L G   I  A++G GKT +F+   +Q
Sbjct: 29  SFDALKLNEDLLRGIYSYGFEKPSAIQQRGIKPILDGYDTIGQAQSGTGKTATFVIAALQ 88

Query: 100 QILTWKSRPEYKPELNAPLALIITPGRELVFQI 132
            I           +LNA  ALI+ P REL  QI
Sbjct: 89  LI---------DYDLNACQALILAPTRELAQQI 112

Length = 401

>gnl|CDD|238005 cd00046, DEXDc, DEAD-like helicases superfamily

 Score = 45.0 bits (107), Expect = 8e-07
 Identities = 17/56 (30%), Positives = 28/56 (50%), Gaps = 10/56 (17%)

Query: 77  KSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQI 132
           +  +L A TG GKTL+ L P+++ + + K              L++ P REL  Q+
Sbjct: 1   RDVLLAAPTGSGKTLAALLPILELLDSLKGGQ----------VLVLAPTRELANQV 46

A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Length = 144

>gnl|CDD|234478 TIGR04121, DEXH_lig_assoc, DEXH box helicase, DNA ligase-associated

 Score = 41.8 bits (99), Expect = 3e-05
 Identities = 30/82 (36%), Positives = 37/82 (45%), Gaps = 9/82 (10%)

Query: 48  PEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLS-FLAPLVQQILTWKS 106
                 F  RG T P   Q       L G+S +L+A TG GKTL+ FL  L+   L    
Sbjct: 1   SPFEAWFAARGWT-PRPFQLEMWAAALEGRSGLLIAPTGSGKTLAGFLPSLID--LAGPE 57

Query: 107 RPEYKPELNAPLALIITPGREL 128
           +P  K  L+    L ITP R L
Sbjct: 58  KP--KKGLH---TLYITPLRAL 74

Members of this protein family are DEAD/DEAH box helicases found associated with a bacterial ATP-dependent DNA ligase, part of a four-gene system that occurs in about 12 % of prokaryotic reference genomes. The actual motif in this family is DE[VILW]H. Length = 803

>gnl|CDD|237497 PRK13767, PRK13767, ATP-dependent helicase; Provisional

 Score = 39.1 bits (92), Expect = 3e-04
 Identities = 21/55 (38%), Positives = 31/55 (56%), Gaps = 8/55 (14%)

Query: 49 EIIDIFT-------KRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLS-FLA 95
          EI+D+         K    T T  Q+Y+IP +  GK+ ++ + TG GKTL+ FLA
Sbjct: 13 EILDLLRPYVREWFKEKFGTFTPPQRYAIPLIHEGKNVLISSPTGSGKTLAAFLA 67

Length = 876

>gnl|CDD|224126 COG1205, COG1205, Distinct helicase family with a unique C-terminal domain including a metal-binding cysteine cluster [General function prediction only]

 Score = 38.5 bits (90), Expect = 4e-04
 Identities = 19/89 (21%), Positives = 33/89 (37%), Gaps = 10/89 (11%)

Query: 42  EDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQI 101
                   +     K G+      Q  ++  +  G++ ++   TG GKT SFL P++  +
Sbjct: 51  FPELRDESLKSALVKAGIERLYSHQVDALRLIREGRNVVVTTGTGSGKTESFLLPILDHL 110

Query: 102 LTWKSRPEYKPELNAPLALIITPGRELVF 130
           L   S            AL++ P   L  
Sbjct: 111 LRDPSAR----------ALLLYPTNALAN 129

Length = 851

>gnl|CDD|224120 COG1199, DinG, Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]

 Score = 36.3 bits (84), Expect = 0.002
 Identities = 17/63 (26%), Positives = 27/63 (42%), Gaps = 11/63 (17%)

Query: 72  TLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQ 131
            L  G+  ++ A TG GKTL++L P     L +      K        +I T  + L  Q
Sbjct: 30  ALKGGEGLLIEAPTGTGKTLAYLLP----ALAYAREEGKK-------VIISTRTKALQEQ 78

Query: 132 IGQ 134
           + +
Sbjct: 79  LLE 81

Length = 654

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	134
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	99.9
KOG0330|consensus	476		99.9
KOG0346|consensus	569		99.9
PTZ00110	545	helicase; Provisional	99.9
PLN00206	518	DEAD-box ATP-dependent RNA helicase; Provisional	99.9
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	99.89
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	99.88
KOG0331|consensus	519		99.88
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	99.88
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	99.88
KOG0348|consensus	708		99.88
KOG0345|consensus	567		99.87
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	99.86
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	99.86
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	99.86
KOG0340|consensus	442		99.85
PTZ00424	401	helicase 45; Provisional	99.85
KOG0338|consensus	691		99.85
KOG0343|consensus	758		99.84
KOG0334|consensus	997		99.84
KOG0333|consensus	673		99.83
KOG0342|consensus	543		99.83
KOG0335|consensus	482		99.83
TIGR03817	742	DECH_helic helicase/secretion neighborhood putativ	99.81
KOG0328|consensus	400		99.81
cd00268	203	DEADc DEAD-box helicases. A diverse family of prot	99.81
KOG0347|consensus	731		99.81
KOG0344|consensus	593		99.77
KOG0336|consensus	629		99.77
KOG0326|consensus	459		99.76
PRK02362	737	ski2-like helicase; Provisional	99.76
KOG0341|consensus	610		99.75
PRK00254	720	ski2-like helicase; Provisional	99.75
KOG0339|consensus	731		99.74
KOG0327|consensus	397		99.73
KOG0337|consensus	529		99.71
PRK13767	876	ATP-dependent helicase; Provisional	99.71
COG1201	814	Lhr Lhr-like helicases [General function predictio	99.69
PRK01172	674	ski2-like helicase; Provisional	99.69
KOG0350|consensus	620		99.68
KOG0332|consensus	477		99.65
KOG0329|consensus	387		99.61
KOG4284|consensus	980		99.6
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	99.59
PLN03137	1195	ATP-dependent DNA helicase; Q4-like; Provisional	99.56
PF00270	169	DEAD: DEAD/DEAH box helicase; InterPro: IPR011545	99.55
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	99.55
COG1205	851	Distinct helicase family with a unique C-terminal	99.52
PRK09401	1176	reverse gyrase; Reviewed	99.52
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	99.5
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	99.49
PRK14701	1638	reverse gyrase; Provisional	99.49
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	99.48
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	99.48
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	99.48
PRK12899	970	secA preprotein translocase subunit SecA; Reviewed	99.47
PRK10689	1147	transcription-repair coupling factor; Provisional	99.38
TIGR02621	844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	99.37
KOG0952|consensus	1230		99.33
PRK12898	656	secA preprotein translocase subunit SecA; Reviewed	99.31
COG1204	766	Superfamily II helicase [General function predicti	99.24
TIGR01407	850	dinG_rel DnaQ family exonuclease/DinG family helic	99.22
COG1202	830	Superfamily II helicase, archaea-specific [General	99.13
PRK05580	679	primosome assembly protein PriA; Validated	99.13
PHA02558	501	uvsW UvsW helicase; Provisional	99.12
TIGR03158	357	cas3_cyano CRISPR-associated helicase, Cyano-type.	99.09
smart00487	201	DEXDc DEAD-like helicases superfamily.	99.08
PRK09200	790	preprotein translocase subunit SecA; Reviewed	99.06
PRK07246	820	bifunctional ATP-dependent DNA helicase/DNA polyme	99.05
TIGR03117	636	cas_csf4 CRISPR-associated DEAD/DEAH-box helicase	99.02
KOG0349|consensus	725		99.02
PHA02653	675	RNA helicase NPH-II; Provisional	99.0
TIGR00963	745	secA preprotein translocase, SecA subunit. The pro	98.97
TIGR01587	358	cas3_core CRISPR-associated helicase Cas3. This mo	98.93
smart00489	289	DEXDc3 DEAD-like helicases superfamily.	98.92
smart00488	289	DEXDc2 DEAD-like helicases superfamily.	98.92
TIGR03714	762	secA2 accessory Sec system translocase SecA2. Memb	98.91
PF04851	184	ResIII: Type III restriction enzyme, res subunit;	98.87
PRK08074	928	bifunctional ATP-dependent DNA helicase/DNA polyme	98.85
COG4581	1041	Superfamily II RNA helicase [DNA replication, reco	98.82
PRK13766	773	Hef nuclease; Provisional	98.79
PRK09751	1490	putative ATP-dependent helicase Lhr; Provisional	98.79
PRK11747	697	dinG ATP-dependent DNA helicase DinG; Provisional	98.77
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	98.77
KOG0353|consensus	695		98.72
KOG0352|consensus	641		98.71
KOG0354|consensus	746		98.71
PRK11664	812	ATP-dependent RNA helicase HrpB; Provisional	98.69
COG0514	590	RecQ Superfamily II DNA helicase [DNA replication,	98.68
TIGR01970	819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	98.64
COG1199	654	DinG Rad3-related DNA helicases [Transcription / D	98.63
PRK13104	896	secA preprotein translocase subunit SecA; Reviewed	98.62
COG1061	442	SSL2 DNA or RNA helicases of superfamily II [Trans	98.58
KOG0951|consensus	1674		98.52
PRK09694	878	helicase Cas3; Provisional	98.45
cd00046	144	DEXDc DEAD-like helicases superfamily. A diverse f	98.45
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	98.39
PRK11448	1123	hsdR type I restriction enzyme EcoKI subunit R; Pr	98.36
KOG0351|consensus	941		98.33
TIGR00604	705	rad3 DNA repair helicase (rad3). All proteins in t	98.32
PRK12904	830	preprotein translocase subunit SecA; Reviewed	98.31
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	98.25
COG1111	542	MPH1 ERCC4-like helicases [DNA replication, recomb	98.23
PRK13107	908	preprotein translocase subunit SecA; Reviewed	98.15
PF13245	76	AAA_19: Part of AAA domain	98.15
TIGR00603	732	rad25 DNA repair helicase rad25. All proteins in t	98.09
KOG0947|consensus	1248		98.02
COG1198	730	PriA Primosomal protein N' (replication factor Y)	98.0
PF00580	315	UvrD-helicase: UvrD/REP helicase N-terminal domain	97.87
TIGR00348	667	hsdR type I site-specific deoxyribonuclease, HsdR	97.87
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	97.82
PRK12906	796	secA preprotein translocase subunit SecA; Reviewed	97.81
KOG0948|consensus	1041		97.76
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	97.69
PRK12326	764	preprotein translocase subunit SecA; Reviewed	97.68
TIGR00376	637	DNA helicase, putative. The gene product may repre	97.68
COG1203	733	CRISPR-associated helicase Cas3 [Defense mechanism	97.62
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	97.59
KOG1803|consensus	649		97.55
KOG0949|consensus	1330		97.42
KOG1802|consensus	935		97.41
COG0556	663	UvrB Helicase subunit of the DNA excision repair c	97.38
KOG0951|consensus	1674		97.29
PRK15483	986	type III restriction-modification system StyLTI en	97.26
PRK13103	913	secA preprotein translocase subunit SecA; Reviewed	97.25
PF07517	266	SecA_DEAD: SecA DEAD-like domain; InterPro: IPR011	97.22
PRK10536	262	hypothetical protein; Provisional	97.15
COG4096	875	HsdR Type I site-specific restriction-modification	97.1
CHL00122	870	secA preprotein translocase subunit SecA; Validate	97.03
PRK13889	988	conjugal transfer relaxase TraA; Provisional	97.0
PRK13894	319	conjugal transfer ATPase TrbB; Provisional	96.98
PF07652	148	Flavi_DEAD: Flavivirus DEAD domain ; InterPro: IPR	96.95
TIGR02782	299	TrbB_P P-type conjugative transfer ATPase TrbB. Th	96.94
PRK13833	323	conjugal transfer protein TrbB; Provisional	96.92
KOG1133|consensus	821		96.91
TIGR01448	720	recD_rel helicase, putative, RecD/TraA family. Thi	96.89
TIGR02768	744	TraA_Ti Ti-type conjugative transfer relaxase TraA	96.82
PRK11131	1294	ATP-dependent RNA helicase HrpA; Provisional	96.74
COG2805	353	PilT Tfp pilus assembly protein, pilus retraction	96.6
TIGR00631	655	uvrb excinuclease ABC, B subunit. This family is b	96.56
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	96.55
PRK10919	672	ATP-dependent DNA helicase Rep; Provisional	96.43
COG1484	254	DnaC DNA replication protein [DNA replication, rec	96.36
TIGR02525	372	plasmid_TraJ plasmid transfer ATPase TraJ. Members	96.34
PRK12902	939	secA preprotein translocase subunit SecA; Reviewed	96.33
PRK11054	684	helD DNA helicase IV; Provisional	96.31
PRK10875	615	recD exonuclease V subunit alpha; Provisional	96.22
TIGR01074	664	rep ATP-dependent DNA helicase Rep. Designed to id	96.18
PF05970	364	PIF1: PIF1-like helicase; InterPro: IPR010285 This	96.17
PRK05973	237	replicative DNA helicase; Provisional	96.16
KOG0950|consensus	1008		96.16
COG4889	1518	Predicted helicase [General function prediction on	96.14
COG2804	500	PulE Type II secretory pathway, ATPase PulE/Tfp pi	96.14
PRK13851	344	type IV secretion system protein VirB11; Provision	96.11
cd01129	264	PulE-GspE PulE/GspE The type II secretory pathway	96.07
PF00176	299	SNF2_N: SNF2 family N-terminal domain; InterPro: I	96.07
COG4962	355	CpaF Flp pilus assembly protein, ATPase CpaF [Intr	96.06
TIGR01447	586	recD exodeoxyribonuclease V, alpha subunit. This f	96.01
cd01130	186	VirB11-like_ATPase Type IV secretory pathway compo	95.96
PRK13900	332	type IV secretion system ATPase VirB11; Provisiona	95.96
KOG1132|consensus	945		95.89
PRK10436	462	hypothetical protein; Provisional	95.87
PRK13764	602	ATPase; Provisional	95.87
COG4098	441	comFA Superfamily II DNA/RNA helicase required for	95.86
PRK05298	652	excinuclease ABC subunit B; Provisional	95.85
COG3973	747	Superfamily I DNA and RNA helicases [General funct	95.79
TIGR01075	715	uvrD DNA helicase II. Designed to identify uvrD me	95.79
PRK04914	956	ATP-dependent helicase HepA; Validated	95.77
TIGR02538	564	type_IV_pilB type IV-A pilus assembly ATPase PilB.	95.76
TIGR02524	358	dot_icm_DotB Dot/Icm secretion system ATPase DotB.	95.68
TIGR02785	1232	addA_Gpos recombination helicase AddA, Firmicutes	95.63
PRK13826	1102	Dtr system oriT relaxase; Provisional	95.61
PF12340	229	DUF3638: Protein of unknown function (DUF3638); In	95.59
TIGR02533	486	type_II_gspE general secretory pathway protein E.	95.53
PRK08181	269	transposase; Validated	95.52
PRK11773	721	uvrD DNA-dependent helicase II; Provisional	95.47
PF12846	304	AAA_10: AAA-like domain	95.45
PRK06835	329	DNA replication protein DnaC; Validated	95.31
PRK06526	254	transposase; Provisional	95.28
PRK14873	665	primosome assembly protein PriA; Provisional	95.28
PF10412	386	TrwB_AAD_bind: Type IV secretion-system coupling p	95.23
PRK12903	925	secA preprotein translocase subunit SecA; Reviewed	95.2
COG0630	312	VirB11 Type IV secretory pathway, VirB11 component	95.17
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	95.15
COG1875	436	NYN ribonuclease and ATPase of PhoH family domains	95.15
PF09848	352	DUF2075: Uncharacterized conserved protein (DUF207	95.14
smart00382	148	AAA ATPases associated with a variety of cellular	95.04
PF00437	270	T2SE: Type II/IV secretion system protein; InterPr	94.98
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	94.98
TIGR03819	340	heli_sec_ATPase helicase/secretion neighborhood AT	94.97
cd01127	410	TrwB Bacterial conjugation protein TrwB, ATP bindi	94.93
PF06745	226	KaiC: KaiC; InterPro: IPR014774 This entry represe	94.78
PF02534	469	T4SS-DNA_transf: Type IV secretory system Conjugat	94.75
PRK06921	266	hypothetical protein; Provisional	94.74
TIGR01073	726	pcrA ATP-dependent DNA helicase PcrA. Designed to	94.69
TIGR01967	1283	DEAH_box_HrpA ATP-dependent helicase HrpA. This mo	94.69
KOG0952|consensus	1230		94.66
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	94.63
TIGR02760	1960	TraI_TIGR conjugative transfer relaxase protein Tr	94.58
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	94.52
COG5008	375	PilU Tfp pilus assembly protein, ATPase PilU [Cell	94.51
PRK07952	244	DNA replication protein DnaC; Validated	94.47
PRK12377	248	putative replication protein; Provisional	94.43
PF12775	272	AAA_7: P-loop containing dynein motor region D3; P	94.4
COG1219	408	ClpX ATP-dependent protease Clp, ATPase subunit [P	94.27
PRK13700	732	conjugal transfer protein TraD; Provisional	94.18
PRK09183	259	transposase/IS protein; Provisional	94.16
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	94.14
PRK13709	1747	conjugal transfer nickase/helicase TraI; Provision	94.12
PLN03142	1033	Probable chromatin-remodeling complex ATPase chain	94.06
cd01131	198	PilT Pilus retraction ATPase PilT. PilT is a nucle	94.04
KOG1805|consensus	1100		94.02
TIGR00595	505	priA primosomal protein N'. All proteins in this f	93.98
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	93.98
PRK14712	1623	conjugal transfer nickase/helicase TraI; Provision	93.91
PF04665	241	Pox_A32: Poxvirus A32 protein; InterPro: IPR006758	93.81
PF01580	205	FtsK_SpoIIIE: FtsK/SpoIIIE family; InterPro: IPR00	93.69
cd01122	271	GP4d_helicase GP4d_helicase is a homohexameric 5'-	93.62
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	93.59
PF02399	824	Herpes_ori_bp: Origin of replication binding prote	93.5
COG3587	985	Restriction endonuclease [Defense mechanisms]	93.48
PF00004	132	AAA: ATPase family associated with various cellula	93.44
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	93.42
PRK08116	268	hypothetical protein; Validated	93.39
PF01078	206	Mg_chelatase: Magnesium chelatase, subunit ChlI; I	93.39
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	93.31
PRK13531	498	regulatory ATPase RavA; Provisional	93.28
cd00984	242	DnaB_C DnaB helicase C terminal domain. The hexame	93.23
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	93.18
PF01935	229	DUF87: Domain of unknown function DUF87; InterPro:	93.18
cd01126	384	TraG_VirD4 The TraG/TraD/VirD4 family are bacteria	93.17
TIGR01420	343	pilT_fam pilus retraction protein PilT. This model	93.16
TIGR02759	566	TraD_Ftype type IV conjugative transfer system cou	93.14
COG0467	260	RAD55 RecA-superfamily ATPases implicated in signa	93.12
PF13555	62	AAA_29: P-loop containing region of AAA domain	93.08
TIGR03878	259	thermo_KaiC_2 KaiC domain protein, AF_0795 family.	93.07
TIGR02788	308	VirB11 P-type DNA transfer ATPase VirB11. The VirB	92.85
PF07728	139	AAA_5: AAA domain (dynein-related subfamily); Inte	92.81
PRK13897	606	type IV secretion system component VirD4; Provisio	92.76
TIGR02760	1960	TraI_TIGR conjugative transfer relaxase protein Tr	92.72
KOG1533|consensus	290		92.7
TIGR03881	229	KaiC_arch_4 KaiC domain protein, PAE1156 family. M	92.66
PTZ00361	438	26 proteosome regulatory subunit 4-like protein; P	92.63
PF13207	121	AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6	92.61
KOG0925|consensus	699		92.59
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	92.58
PF13671	143	AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1	92.46
TIGR02237	209	recomb_radB DNA repair and recombination protein R	92.42
KOG4150|consensus	1034		92.32
PRK04328	249	hypothetical protein; Provisional	92.32
PRK13880	636	conjugal transfer coupling protein TraG; Provision	92.29
PRK08727	233	hypothetical protein; Validated	92.25
PRK13850	670	type IV secretion system protein VirD4; Provisiona	92.23
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	92.22
PRK08084	235	DNA replication initiation factor; Provisional	92.15
PRK06893	229	DNA replication initiation factor; Validated	92.02
PRK12727	559	flagellar biosynthesis regulator FlhF; Provisional	91.98
PF09439	181	SRPRB: Signal recognition particle receptor beta s	91.94
TIGR03743	634	SXT_TraD conjugative coupling factor TraD, SXT/TOL	91.91
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	91.91
PRK08903	227	DnaA regulatory inactivator Hda; Validated	91.86
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	91.84
PF13238	129	AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB	91.73
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	91.72
PRK04296	190	thymidine kinase; Provisional	91.71
TIGR03744	893	traC_PFL_4706 conjugative transfer ATPase, PFL_470	91.69
COG0606	490	Predicted ATPase with chaperone activity [Posttran	91.68
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	91.63
PF13191	185	AAA_16: AAA ATPase domain; PDB: 2V1U_A.	91.63
KOG0744|consensus	423		91.46
TIGR03880	224	KaiC_arch_3 KaiC domain protein, AF_0351 family. T	91.44
PRK13876	663	conjugal transfer coupling protein TraG; Provision	91.42
TIGR02767	623	TraG-Ti Ti-type conjugative transfer system protie	91.41
KOG1807|consensus	1025		91.39
COG0714	329	MoxR-like ATPases [General function prediction onl	91.35
KOG0390|consensus	776		91.29
PRK06067	234	flagellar accessory protein FlaH; Validated	91.24
TIGR03689	512	pup_AAA proteasome ATPase. In the Actinobacteria,	91.17
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	91.15
PHA02244	383	ATPase-like protein	91.09
PRK12402	337	replication factor C small subunit 2; Reviewed	91.04
KOG0738|consensus	491		90.96
CHL00181	287	cbbX CbbX; Provisional	90.95
TIGR01242	364	26Sp45 26S proteasome subunit P45 family. Many pro	90.93
PRK08533	230	flagellar accessory protein FlaH; Reviewed	90.89
PRK03992	389	proteasome-activating nucleotidase; Provisional	90.87
TIGR01241	495	FtsH_fam ATP-dependent metalloprotease FtsH. HflB(	90.75
PRK13822	641	conjugal transfer coupling protein TraG; Provision	90.75
cd01394	218	radB RadB. The archaeal protein radB shares simila	90.73
PRK10078	186	ribose 1,5-bisphosphokinase; Provisional	90.71
PF14532	138	Sigma54_activ_2: Sigma-54 interaction domain; PDB:	90.66
PRK05642	234	DNA replication initiation factor; Validated	90.59
TIGR02746	797	TraC-F-type type-IV secretion system protein TraC.	90.57
COG1643	845	HrpA HrpA-like helicases [DNA replication, recombi	90.52
TIGR03754	643	conj_TOL_TraD conjugative coupling factor TraD, TO	90.51
KOG1131|consensus	755		90.43
PRK08939	306	primosomal protein DnaI; Reviewed	90.42
TIGR01650	327	PD_CobS cobaltochelatase, CobS subunit. This model	90.35
PF03193	161	DUF258: Protein of unknown function, DUF258; Inter	90.34
PRK12726	407	flagellar biosynthesis regulator FlhF; Provisional	90.32
cd01363	186	Motor_domain Myosin and Kinesin motor domain. Thes	90.32
KOG0745|consensus	564		90.31
KOG0733|consensus	802		90.24
KOG2340|consensus	698		90.11
PRK09361	225	radB DNA repair and recombination protein RadB; Pr	90.1
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	89.9
PF03205	140	MobB: Molybdopterin guanine dinucleotide synthesis	89.87
TIGR00176	155	mobB molybdopterin-guanine dinucleotide biosynthes	89.79
PF00625	183	Guanylate_kin: Guanylate kinase; InterPro: IPR0081	89.74
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	89.59
KOG0926|consensus	1172		89.57
TIGR02688	449	conserved hypothetical protein TIGR02688. Members	89.56
TIGR03238	504	dnd_assoc_3 dnd system-associated protein 3. cereu	89.52
cd00227	175	CPT Chloramphenicol (Cm) phosphotransferase (CPT).	89.42
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	89.37
COG1224	450	TIP49 DNA helicase TIP49, TBP-interacting protein	89.28
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	89.25
COG1419	407	FlhF Flagellar GTP-binding protein [Cell motility	89.22
PRK14530	215	adenylate kinase; Provisional	89.11
PF07724	171	AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR	89.04
COG1136	226	SalX ABC-type antimicrobial peptide transport syst	89.02
PF06068	398	TIP49: TIP49 C-terminus; InterPro: IPR010339 This	88.97
COG1222	406	RPT1 ATP-dependent 26S proteasome regulatory subun	88.95
KOG0989|consensus	346		88.95
COG1855	604	ATPase (PilT family) [General function prediction	88.89
PRK00131	175	aroK shikimate kinase; Reviewed	88.89
PRK14729	300	miaA tRNA delta(2)-isopentenylpyrophosphate transf	88.84
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	88.78
KOG1806|consensus	1320		88.73
PRK07261	171	topology modulation protein; Provisional	88.62
PRK08118	167	topology modulation protein; Reviewed	88.61
PF00225	335	Kinesin: Kinesin motor domain; InterPro: IPR001752	88.6
KOG0920|consensus	924		88.53
TIGR00390	441	hslU ATP-dependent protease HslVU, ATPase subunit.	88.52
PF13481	193	AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C.	88.52
PRK14087	450	dnaA chromosomal replication initiation protein; P	88.51
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	88.5
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	88.49
PRK14088	440	dnaA chromosomal replication initiation protein; P	88.47
cd03115	173	SRP The signal recognition particle (SRP) mediates	88.45
COG3451	796	VirB4 Type IV secretory pathway, VirB4 components	88.39
KOG0060|consensus	659		88.37
TIGR01313	163	therm_gnt_kin carbohydrate kinase, thermoresistant	88.36
PRK09302	509	circadian clock protein KaiC; Reviewed	88.35
TIGR00382	413	clpX endopeptidase Clp ATP-binding regulatory subu	88.19
PLN03025	319	replication factor C subunit; Provisional	88.18
PRK05342	412	clpX ATP-dependent protease ATP-binding subunit Cl	88.18
PF02374	305	ArsA_ATPase: Anion-transporting ATPase; PDB: 2WOO_	88.18
TIGR03600	421	phage_DnaB phage replicative helicase, DnaB family	88.12
PF14516	331	AAA_35: AAA-like domain	88.11
PF07088	484	GvpD: GvpD gas vesicle protein; InterPro: IPR00978	88.09
TIGR02322	179	phosphon_PhnN phosphonate metabolism protein/1,5-b	88.05
PRK00300	205	gmk guanylate kinase; Provisional	87.96
PRK06620	214	hypothetical protein; Validated	87.86
PF00005	137	ABC_tran: ABC transporter This structure is on hol	87.86
PLN02165	334	adenylate isopentenyltransferase	87.82
cd01370	338	KISc_KIP3_like Kinesin motor domain, KIP3-like sub	87.8
PRK12724	432	flagellar biosynthesis regulator FlhF; Provisional	87.79
PRK00149	450	dnaA chromosomal replication initiation protein; R	87.79
PF05729	166	NACHT: NACHT domain	87.78
cd03114	148	ArgK-like The function of this protein family is u	87.75
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	87.74
PRK12900	1025	secA preprotein translocase subunit SecA; Reviewed	87.64
cd00071	137	GMPK Guanosine monophosphate kinase (GMPK, EC 2.7.	87.54
cd01369	325	KISc_KHC_KIF5 Kinesin motor domain, kinesin heavy	87.46
PRK13873	811	conjugal transfer ATPase TrbE; Provisional	87.42
TIGR00764	608	lon_rel lon-related putative ATP-dependent proteas	87.4
PHA02533	534	17 large terminase protein; Provisional	87.36
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	87.35
cd01368	345	KISc_KIF23_like Kinesin motor domain, KIF23-like s	87.34
cd01365	356	KISc_KIF1A_KIF1B Kinesin motor domain, KIF1_like p	87.33
cd01376	319	KISc_KID_like Kinesin motor domain, KIF22/Kid-like	87.31
PRK14723	767	flhF flagellar biosynthesis regulator FlhF; Provis	87.29
KOG0733|consensus	802		87.26
TIGR00064	272	ftsY signal recognition particle-docking protein F	87.25
cd01367	322	KISc_KIF2_like Kinesin motor domain, KIF2-like gro	87.15
KOG1942|consensus	456		87.15
PRK00411	394	cdc6 cell division control protein 6; Reviewed	87.08
PRK04220	301	2-phosphoglycerate kinase; Provisional	86.98
TIGR02012	321	tigrfam_recA protein RecA. This model describes or	86.76
TIGR03263	180	guanyl_kin guanylate kinase. Members of this famil	86.72
PF00158	168	Sigma54_activat: Sigma-54 interaction domain; Inte	86.69
KOG0731|consensus	774		86.62
PRK09354	349	recA recombinase A; Provisional	86.59
cd01393	226	recA_like RecA is a bacterial enzyme which has rol	86.56
PRK00091	307	miaA tRNA delta(2)-isopentenylpyrophosphate transf	86.52
COG1126	240	GlnQ ABC-type polar amino acid transport system, A	86.5
PRK10416	318	signal recognition particle-docking protein FtsY;	86.42
PF13476	202	AAA_23: AAA domain; PDB: 3AV0_B 3AUY_B 3AUX_A 2O5V	86.42
PRK12422	445	chromosomal replication initiation protein; Provis	86.38
cd00983	325	recA RecA is a bacterial enzyme which has roles in	86.34
cd01373	337	KISc_KLP2_like Kinesin motor domain, KLP2-like sub	86.34
PRK12901	1112	secA preprotein translocase subunit SecA; Reviewed	86.3
PRK04195	482	replication factor C large subunit; Provisional	86.28
cd01375	334	KISc_KIF9_like Kinesin motor domain, KIF9-like sub	86.16
cd01374	321	KISc_CENP_E Kinesin motor domain, CENP-E/KIP2-like	86.14
COG1223	368	Predicted ATPase (AAA+ superfamily) [General funct	86.07
PRK11608	326	pspF phage shock protein operon transcriptional ac	86.07
KOG0736|consensus	953		86.05
PF03796	259	DnaB_C: DnaB-like helicase C terminal domain; Inte	85.83
smart00129	335	KISc Kinesin motor, catalytic domain. ATPase. Micr	85.63
KOG0991|consensus	333		85.58
PRK06762	166	hypothetical protein; Provisional	85.58
cd00820	107	PEPCK_HprK Phosphoenolpyruvate carboxykinase (PEPC	85.56
PRK11823	446	DNA repair protein RadA; Provisional	85.55
cd00106	328	KISc Kinesin motor domain. This catalytic (head) d	85.54
TIGR02974	329	phageshock_pspF psp operon transcriptional activat	85.5
CHL00195	489	ycf46 Ycf46; Provisional	85.48
TIGR01359	183	UMP_CMP_kin_fam UMP-CMP kinase family. This subfam	85.44
cd01123	235	Rad51_DMC1_radA Rad51_DMC1_radA,B. This group of r	85.31
PRK13891	852	conjugal transfer protein TrbE; Provisional	85.28
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	85.2
KOG0924|consensus	1042		85.19
PRK09825	176	idnK D-gluconate kinase; Provisional	85.19
TIGR00750	300	lao LAO/AO transport system ATPase. Mutations have	85.17
TIGR01360	188	aden_kin_iso1 adenylate kinase, isozyme 1 subfamil	85.16
PRK13765	637	ATP-dependent protease Lon; Provisional	84.98
TIGR00959	428	ffh signal recognition particle protein. This mode	84.93
TIGR00416	454	sms DNA repair protein RadA. The gene protuct code	84.92
cd02019	69	NK Nucleoside/nucleotide kinase (NK) is a protein	84.89
PRK06995	484	flhF flagellar biosynthesis regulator FlhF; Valida	84.85
PRK14086	617	dnaA chromosomal replication initiation protein; P	84.85
PRK00771	437	signal recognition particle protein Srp54; Provisi	84.78
COG0419	908	SbcC ATPase involved in DNA repair [DNA replicatio	84.76
smart00072	184	GuKc Guanylate kinase homologues. Active enzymes c	84.73
cd02020	147	CMPK Cytidine monophosphate kinase (CMPK) catalyze	84.66
PRK08233	182	hypothetical protein; Provisional	84.62
PRK09302	509	circadian clock protein KaiC; Reviewed	84.57
cd00464	154	SK Shikimate kinase (SK) is the fifth enzyme in th	84.53
PRK06547	172	hypothetical protein; Provisional	84.48
PRK14531	183	adenylate kinase; Provisional	84.46
PRK13768	253	GTPase; Provisional	84.46
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	84.36
PF02456	369	Adeno_IVa2: Adenovirus IVa2 protein; InterPro: IPR	84.32
PLN02796	347	D-glycerate 3-kinase	84.32
TIGR02784	1141	addA_alphas double-strand break repair helicase Ad	84.3
PRK08356	195	hypothetical protein; Provisional	84.29
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	84.2
PF10662	143	PduV-EutP: Ethanolamine utilisation - propanediol	84.19
PF08283	106	Gemini_AL1_M: Geminivirus rep protein central doma	84.18
cd01428	194	ADK Adenylate kinase (ADK) catalyzes the reversibl	84.14
cd02021	150	GntK Gluconate kinase (GntK) catalyzes the phospho	84.13
KOG0953|consensus	700		84.12
PRK10867	433	signal recognition particle protein; Provisional	84.05
cd01371	333	KISc_KIF3 Kinesin motor domain, kinesins II or KIF	84.0
PRK05541	176	adenylylsulfate kinase; Provisional	83.98
COG0210	655	UvrD Superfamily I DNA and RNA helicases [DNA repl	83.97
PF00485	194	PRK: Phosphoribulokinase / Uridine kinase family;	83.9
cd01372	341	KISc_KIF4 Kinesin motor domain, KIF4-like subfamil	83.85
PF03215	519	Rad17: Rad17 cell cycle checkpoint protein	83.81
cd03292	214	ABC_FtsE_transporter FtsE is a hydrophilic nucleot	83.81
cd03258	233	ABC_MetN_methionine_transporter MetN (also known a	83.8
KOG0732|consensus	1080		83.75
PRK14974	336	cell division protein FtsY; Provisional	83.7
PRK08506	472	replicative DNA helicase; Provisional	83.7
PRK14737	186	gmk guanylate kinase; Provisional	83.67
KOG0737|consensus	386		83.65
TIGR03783	829	Bac_Flav_CT_G Bacteroides conjugation system ATPas	83.62
KOG0729|consensus	435		83.49
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	83.43
KOG0240|consensus	607		83.35
PF02367	123	UPF0079: Uncharacterised P-loop hydrolase UPF0079;	83.34
TIGR00174	287	miaA tRNA isopentenyltransferase (miaA). Catalyzes	83.24
PRK01184	184	hypothetical protein; Provisional	83.23
PRK14721	420	flhF flagellar biosynthesis regulator FlhF; Provis	83.16
PF06414	199	Zeta_toxin: Zeta toxin; InterPro: IPR010488 This e	83.13
PHA00729	226	NTP-binding motif containing protein	83.13
TIGR01166	190	cbiO cobalt transport protein ATP-binding subunit.	83.06
PRK05480	209	uridine/cytidine kinase; Provisional	83.04
cd01983	99	Fer4_NifH The Fer4_NifH superfamily contains a var	83.02
PF03237	384	Terminase_6: Terminase-like family; InterPro: IPR0	83.02
cd01918	149	HprK_C HprK/P, the bifunctional histidine-containi	83.01
cd01125	239	repA Hexameric Replicative Helicase RepA. RepA is	82.82
cd01366	329	KISc_C_terminal Kinesin motor domain, KIFC2/KIFC3/	82.81
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	82.78
TIGR00665	434	DnaB replicative DNA helicase. This model describe	82.77
COG1074	1139	RecB ATP-dependent exoDNAse (exonuclease V) beta s	82.77
COG0324	308	MiaA tRNA delta(2)-isopentenylpyrophosphate transf	82.77
KOG0742|consensus	630		82.74
PF02463	220	SMC_N: RecF/RecN/SMC N terminal domain; InterPro:	82.62
cd03269	210	ABC_putative_ATPase This subfamily is involved in	82.59
TIGR01425	429	SRP54_euk signal recognition particle protein SRP5	82.57
cd03238	176	ABC_UvrA The excision repair protein UvrA; Nucleot	82.56
PRK14532	188	adenylate kinase; Provisional	82.49
PF03029	238	ATP_bind_1: Conserved hypothetical ATP binding pro	82.46
cd01364	352	KISc_BimC_Eg5 Kinesin motor domain, BimC/Eg5 spind	82.44
PRK06217	183	hypothetical protein; Validated	82.42
cd02023	198	UMPK Uridine monophosphate kinase (UMPK, EC 2.7.1.	82.41
TIGR02673	214	FtsE cell division ATP-binding protein FtsE. This	82.4
COG3839	338	MalK ABC-type sugar transport systems, ATPase comp	82.4
cd03259	213	ABC_Carb_Solutes_like ABC Carbohydrate and Solute	82.26
PF00910	107	RNA_helicase: RNA helicase; InterPro: IPR000605 He	82.26
TIGR01547	396	phage_term_2 phage terminase, large subunit, PBSX	82.23
PLN02199	303	shikimate kinase	82.22
PF08477	119	Miro: Miro-like protein; InterPro: IPR013684 Mitoc	82.13
TIGR01817	534	nifA Nif-specific regulatory protein. This model r	82.1
PRK13721	844	conjugal transfer ATP-binding protein TraC; Provis	81.99
PRK10247	225	putative ABC transporter ATP-binding protein YbbL;	81.96
PRK15429	686	formate hydrogenlyase transcriptional activator Fh	81.92
TIGR02562	1110	cas3_yersinia CRISPR-associated helicase Cas3. The	81.84

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.90  E-value=8.9e-24  Score=167.39  Aligned_cols=93  Identities=34%  Similarity=0.588  Sum_probs=82.6

Q ss_pred             CCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcE
Q psy7268          39 GTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPL  118 (134)
Q Consensus        39 ~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~  118 (134)
                      .+|++++|++.++++|.+.||+.||++|+++||.+++|+|++++||||||||++|++|+++.+.......  .....+++
T Consensus         8 ~~f~~~~l~~~l~~~l~~~g~~~pt~iQ~~aip~il~g~dvi~~ApTGsGKTla~llp~l~~l~~~~~~~--~~~~~~~~   85 (423)
T PRK04837          8 QKFSDFALHPQVVEALEKKGFHNCTPIQALALPLTLAGRDVAGQAQTGTGKTMAFLTATFHYLLSHPAPE--DRKVNQPR   85 (423)
T ss_pred             CCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCcEEEECCCCchHHHHHHHHHHHHHHhccccc--ccccCCce
Confidence            5899999999999999999999999999999999999999999999999999999999999997643211  11125689


Q ss_pred             EEEEcCcHHHHHHhc
Q psy7268         119 ALIITPGRELVFQIG  133 (134)
Q Consensus       119 ~lil~Pt~~La~Qi~  133 (134)
                      +||++||+|||.|++
T Consensus        86 ~lil~PtreLa~Qi~  100 (423)
T PRK04837         86 ALIMAPTRELAVQIH  100 (423)
T ss_pred             EEEECCcHHHHHHHH
Confidence            999999999999985

>KOG0330|consensus

Probab=99.90  E-value=3.5e-24  Score=164.96  Aligned_cols=93  Identities=38%  Similarity=0.596  Sum_probs=86.3

Q ss_pred             cccCCCCCCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCC
Q psy7268          32 AVSRIDLGTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYK  111 (134)
Q Consensus        32 ~~~~~~~~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~  111 (134)
                      ......+.+|.++++++++++++.+.||+.||+||+++||.++.|+|+|+.|.||||||.+|++|++++++.+.      
T Consensus        54 ~~~~e~~~sf~dLgv~~~L~~ac~~l~~~~PT~IQ~~aiP~~L~g~dvIglAeTGSGKT~afaLPIl~~LL~~p------  127 (476)
T KOG0330|consen   54 MQTDESFKSFADLGVHPELLEACQELGWKKPTKIQSEAIPVALGGRDVIGLAETGSGKTGAFALPILQRLLQEP------  127 (476)
T ss_pred             hhhhhhhcchhhcCcCHHHHHHHHHhCcCCCchhhhhhcchhhCCCcEEEEeccCCCchhhhHHHHHHHHHcCC------
Confidence            33456778999999999999999999999999999999999999999999999999999999999999998744      


Q ss_pred             CCCCCcEEEEEcCcHHHHHHhc
Q psy7268         112 PELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus       112 ~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                         ..++++|++||||||.||.
T Consensus       128 ---~~~~~lVLtPtRELA~QI~  146 (476)
T KOG0330|consen  128 ---KLFFALVLTPTRELAQQIA  146 (476)
T ss_pred             ---CCceEEEecCcHHHHHHHH
Confidence               4589999999999999985

>KOG0346|consensus

Probab=99.90  E-value=3.4e-24  Score=167.18  Aligned_cols=94  Identities=38%  Similarity=0.573  Sum_probs=87.0

Q ss_pred             CCCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCc
Q psy7268          38 LGTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAP  117 (134)
Q Consensus        38 ~~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~  117 (134)
                      ..+|++++|.+.+++++.++||++||-+|+.+||.++.|+|++..|.||||||.+|++|+++.+......   .....++
T Consensus        18 ~ktFe~~gLD~RllkAi~~lG~ekpTlIQs~aIplaLEgKDvvarArTGSGKT~AYliPllqkll~~k~t---~~~e~~~   94 (569)
T KOG0346|consen   18 EKTFEEFGLDSRLLKAITKLGWEKPTLIQSSAIPLALEGKDVVARARTGSGKTAAYLIPLLQKLLAEKKT---NDGEQGP   94 (569)
T ss_pred             hccHHHhCCCHHHHHHHHHhCcCCcchhhhcccchhhcCcceeeeeccCCCchHHHHHHHHHHHHHhhhc---ccccccc
Confidence            3799999999999999999999999999999999999999999999999999999999999999976543   2445799


Q ss_pred             EEEEEcCcHHHHHHhcC
Q psy7268         118 LALIITPGRELVFQIGQ  134 (134)
Q Consensus       118 ~~lil~Pt~~La~Qi~~  134 (134)
                      .++|++||||||+|+|+
T Consensus        95 sa~iLvPTkEL~qQvy~  111 (569)
T KOG0346|consen   95 SAVILVPTKELAQQVYK  111 (569)
T ss_pred             eeEEEechHHHHHHHHH
Confidence            99999999999999974

>PTZ00110 helicase; Provisional

Probab=99.90  E-value=1.6e-23  Score=170.70  Aligned_cols=97  Identities=36%  Similarity=0.478  Sum_probs=86.3

Q ss_pred             ccCCCCCCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCC
Q psy7268          33 VSRIDLGTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKP  112 (134)
Q Consensus        33 ~~~~~~~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~  112 (134)
                      ....|+.+|++++|++.++++|.+.||+.||++|.++||.+++|+|+++++|||||||++|++|++.++..+..    ..
T Consensus       124 ~~p~p~~~f~~~~l~~~l~~~l~~~g~~~pt~iQ~~aip~~l~G~dvI~~ApTGSGKTlaylLP~l~~i~~~~~----~~  199 (545)
T PTZ00110        124 NVPKPVVSFEYTSFPDYILKSLKNAGFTEPTPIQVQGWPIALSGRDMIGIAETGSGKTLAFLLPAIVHINAQPL----LR  199 (545)
T ss_pred             CCCcccCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCEEEEeCCCChHHHHHHHHHHHHHHhccc----cc
Confidence            34578899999999999999999999999999999999999999999999999999999999999999875321    11


Q ss_pred             CCCCcEEEEEcCcHHHHHHhc
Q psy7268         113 ELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus       113 ~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      ...++++|||+||||||.|++
T Consensus       200 ~~~gp~~LIL~PTreLa~Qi~  220 (545)
T PTZ00110        200 YGDGPIVLVLAPTRELAEQIR  220 (545)
T ss_pred             CCCCcEEEEECChHHHHHHHH
Confidence            225789999999999999986

>PLN00206 DEAD-box ATP-dependent RNA helicase; Provisional

Probab=99.90  E-value=2.2e-23  Score=169.13  Aligned_cols=99  Identities=37%  Similarity=0.597  Sum_probs=86.5

Q ss_pred             ccCCCCCCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCC
Q psy7268          33 VSRIDLGTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKP  112 (134)
Q Consensus        33 ~~~~~~~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~  112 (134)
                      ....|+.+|++++|++.++++|.+.||..|||+|.++||.++.|+|+++++|||||||++|++|++.++.......  ..
T Consensus       115 ~~p~pi~~f~~~~l~~~l~~~L~~~g~~~ptpiQ~~aip~il~g~dviv~ApTGSGKTlayllPil~~l~~~~~~~--~~  192 (518)
T PLN00206        115 AVPPPILSFSSCGLPPKLLLNLETAGYEFPTPIQMQAIPAALSGRSLLVSADTGSGKTASFLVPIISRCCTIRSGH--PS  192 (518)
T ss_pred             CCCchhcCHHhCCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCEEEEecCCCCccHHHHHHHHHHHHhhcccc--cc
Confidence            3347899999999999999999999999999999999999999999999999999999999999999886432111  11


Q ss_pred             CCCCcEEEEEcCcHHHHHHhc
Q psy7268         113 ELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus       113 ~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      ...++++||++||||||.|++
T Consensus       193 ~~~~~~aLIL~PTreLa~Qi~  213 (518)
T PLN00206        193 EQRNPLAMVLTPTRELCVQVE  213 (518)
T ss_pred             ccCCceEEEEeCCHHHHHHHH
Confidence            226789999999999999985

>COG0513 SrmB Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis]

Probab=99.89  E-value=1.2e-22  Score=164.70  Aligned_cols=89  Identities=40%  Similarity=0.636  Sum_probs=79.4

Q ss_pred             CCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcE
Q psy7268          39 GTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPL  118 (134)
Q Consensus        39 ~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~  118 (134)
                      ..|++++|++.+++++.+.||..|||||.++||.++.|+|++++|+||||||++|++|+++++.....       .....
T Consensus        29 ~~F~~l~l~~~ll~~l~~~gf~~pt~IQ~~~IP~~l~g~Dvi~~A~TGsGKT~Af~lP~l~~l~~~~~-------~~~~~  101 (513)
T COG0513          29 PEFASLGLSPELLQALKDLGFEEPTPIQLAAIPLILAGRDVLGQAQTGTGKTAAFLLPLLQKILKSVE-------RKYVS  101 (513)
T ss_pred             CCHhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHhcccc-------cCCCc
Confidence            68999999999999999999999999999999999999999999999999999999999999864210       01122


Q ss_pred             EEEEcCcHHHHHHhcC
Q psy7268         119 ALIITPGRELVFQIGQ  134 (134)
Q Consensus       119 ~lil~Pt~~La~Qi~~  134 (134)
                      +||++||||||.||++
T Consensus       102 aLil~PTRELA~Qi~~  117 (513)
T COG0513         102 ALILAPTRELAVQIAE  117 (513)
T ss_pred             eEEECCCHHHHHHHHH
Confidence            9999999999999973

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.88  E-value=2.2e-22  Score=164.85  Aligned_cols=93  Identities=34%  Similarity=0.535  Sum_probs=81.4

Q ss_pred             CcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEE
Q psy7268          40 TFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLA  119 (134)
Q Consensus        40 ~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~  119 (134)
                      +|++++|++.++++|.+.||+.||++|+++||.++.|+|+++++|||||||++|++|+++++.......  .....++++
T Consensus        10 ~f~~l~l~~~l~~~L~~~g~~~ptpiQ~~~ip~~l~G~Dvi~~ApTGSGKTlafllpil~~l~~~~~~~--~~~~~~~ra   87 (572)
T PRK04537         10 TFSSFDLHPALLAGLESAGFTRCTPIQALTLPVALPGGDVAGQAQTGTGKTLAFLVAVMNRLLSRPALA--DRKPEDPRA   87 (572)
T ss_pred             ChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEEcCCCCcHHHHHHHHHHHHHHhccccc--ccccCCceE
Confidence            699999999999999999999999999999999999999999999999999999999999987532110  111236899


Q ss_pred             EEEcCcHHHHHHhcC
Q psy7268         120 LIITPGRELVFQIGQ  134 (134)
Q Consensus       120 lil~Pt~~La~Qi~~  134 (134)
                      |||+||+||+.|+++
T Consensus        88 LIl~PTreLa~Qi~~  102 (572)
T PRK04537         88 LILAPTRELAIQIHK  102 (572)
T ss_pred             EEEeCcHHHHHHHHH
Confidence            999999999999863

>KOG0331|consensus

Probab=99.88  E-value=4.9e-23  Score=164.78  Aligned_cols=91  Identities=32%  Similarity=0.598  Sum_probs=82.9

Q ss_pred             CcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEE
Q psy7268          40 TFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLA  119 (134)
Q Consensus        40 ~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~  119 (134)
                      .|++++|++++...++..||..|||||+++||.++.|+|++..|.||||||++|++|++.++.....   ......+|++
T Consensus        92 ~f~~~~ls~~~~~~lk~~g~~~PtpIQaq~wp~~l~GrD~v~iA~TGSGKTLay~lP~i~~l~~~~~---~~~~~~~P~v  168 (519)
T KOG0331|consen   92 AFQELGLSEELMKALKEQGFEKPTPIQAQGWPIALSGRDLVGIARTGSGKTLAYLLPAIVHLNNEQG---KLSRGDGPIV  168 (519)
T ss_pred             hhhcccccHHHHHHHHhcCCCCCchhhhcccceeccCCceEEEeccCCcchhhhhhHHHHHHHhccc---cccCCCCCeE
Confidence            7899999999999999999999999999999999999999999999999999999999999986421   1333468999


Q ss_pred             EEEcCcHHHHHHhc
Q psy7268         120 LIITPGRELVFQIG  133 (134)
Q Consensus       120 lil~Pt~~La~Qi~  133 (134)
                      ||++||||||.||+
T Consensus       169 LVL~PTRELA~QV~  182 (519)
T KOG0331|consen  169 LVLAPTRELAVQVQ  182 (519)
T ss_pred             EEEcCcHHHHHHHH
Confidence            99999999999996

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=99.88  E-value=2.1e-22  Score=161.11  Aligned_cols=91  Identities=40%  Similarity=0.679  Sum_probs=80.6

Q ss_pred             CcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEE
Q psy7268          40 TFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLA  119 (134)
Q Consensus        40 ~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~  119 (134)
                      +|++++|++.++++|.++||..||++|.++||.+++|+|+++++|||+|||++|++|+++.+......   ......+++
T Consensus         2 ~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~ai~~il~g~dvlv~apTGsGKTla~~lpil~~l~~~~~~---~~~~~~~~a   78 (456)
T PRK10590          2 SFDSLGLSPDILRAVAEQGYREPTPIQQQAIPAVLEGRDLMASAQTGTGKTAGFTLPLLQHLITRQPH---AKGRRPVRA   78 (456)
T ss_pred             CHHHcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHhhhcccc---cccCCCceE
Confidence            69999999999999999999999999999999999999999999999999999999999998754321   111234689


Q ss_pred             EEEcCcHHHHHHhc
Q psy7268         120 LIITPGRELVFQIG  133 (134)
Q Consensus       120 lil~Pt~~La~Qi~  133 (134)
                      |||+||++||.|++
T Consensus        79 Lil~PtreLa~Qi~   92 (456)
T PRK10590         79 LILTPTRELAAQIG   92 (456)
T ss_pred             EEEeCcHHHHHHHH
Confidence            99999999999985

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=99.88  E-value=2.5e-22  Score=160.59  Aligned_cols=87  Identities=34%  Similarity=0.486  Sum_probs=80.3

Q ss_pred             CCCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCc
Q psy7268          38 LGTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAP  117 (134)
Q Consensus        38 ~~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~  117 (134)
                      ..+|++++|++.++++|.++||+.|||+|+++||.+++|+|++++||||+|||++|++|+++++....         ..+
T Consensus         3 ~~~f~~l~l~~~l~~~l~~~g~~~~t~iQ~~ai~~~l~g~dvi~~a~TGsGKT~a~~lpil~~l~~~~---------~~~   73 (460)
T PRK11776          3 MTAFSTLPLPPALLANLNELGYTEMTPIQAQSLPAILAGKDVIAQAKTGSGKTAAFGLGLLQKLDVKR---------FRV   73 (460)
T ss_pred             CCChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHhhhcc---------CCc
Confidence            35899999999999999999999999999999999999999999999999999999999999985322         456


Q ss_pred             EEEEEcCcHHHHHHhc
Q psy7268         118 LALIITPGRELVFQIG  133 (134)
Q Consensus       118 ~~lil~Pt~~La~Qi~  133 (134)
                      ++||++||+|||.|++
T Consensus        74 ~~lil~PtreLa~Q~~   89 (460)
T PRK11776         74 QALVLCPTRELADQVA   89 (460)
T ss_pred             eEEEEeCCHHHHHHHH
Confidence            8999999999999986

>KOG0348|consensus

Probab=99.88  E-value=1.4e-22  Score=161.13  Aligned_cols=93  Identities=38%  Similarity=0.696  Sum_probs=84.1

Q ss_pred             CCcccCCCCHHHHHHHHH-CCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCc
Q psy7268          39 GTFEDTGLAPEIIDIFTK-RGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAP  117 (134)
Q Consensus        39 ~~f~~~~l~~~i~~~l~~-~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~  117 (134)
                      ..|.++||++.+...|.. +++..||.+|+++||.++.|+|++|.++||||||++|++|+++.+.....+-+   ...|+
T Consensus       136 ~~f~~LGL~~~lv~~L~~~m~i~~pTsVQkq~IP~lL~grD~lV~aQTGSGKTLAYllPiVq~Lq~m~~ki~---Rs~G~  212 (708)
T KOG0348|consen  136 AAFASLGLHPHLVSHLNTKMKISAPTSVQKQAIPVLLEGRDALVRAQTGSGKTLAYLLPIVQSLQAMEPKIQ---RSDGP  212 (708)
T ss_pred             ccchhcCCCHHHHHHHHHHhccCccchHhhcchhhhhcCcceEEEcCCCCcccHHHHHHHHHHHHhcCcccc---ccCCc
Confidence            459999999999999988 59999999999999999999999999999999999999999999987654322   33689


Q ss_pred             EEEEEcCcHHHHHHhcC
Q psy7268         118 LALIITPGRELVFQIGQ  134 (134)
Q Consensus       118 ~~lil~Pt~~La~Qi~~  134 (134)
                      .+|||+||||||.|+|+
T Consensus       213 ~ALVivPTREL~~Q~y~  229 (708)
T KOG0348|consen  213 YALVIVPTRELALQIYE  229 (708)
T ss_pred             eEEEEechHHHHHHHHH
Confidence            99999999999999984

>KOG0345|consensus

Probab=99.87  E-value=6.3e-22  Score=155.42  Aligned_cols=91  Identities=35%  Similarity=0.545  Sum_probs=79.0

Q ss_pred             CCcccCC--CCHHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCC
Q psy7268          39 GTFEDTG--LAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNA  116 (134)
Q Consensus        39 ~~f~~~~--l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~  116 (134)
                      .+|++++  |++++++++.+.||+.+||+|..+||.+++++||.+.++||||||++|++|+++.+++......+    ..
T Consensus         4 ~~~~~l~~~L~~~l~~~l~~~GF~~mTpVQa~tIPlll~~KDVvveavTGSGKTlAFllP~le~i~rr~~~~~~----~~   79 (567)
T KOG0345|consen    4 KSFSSLAPPLSPWLLEALDESGFEKMTPVQAATIPLLLKNKDVVVEAVTGSGKTLAFLLPMLEIIYRREAKTPP----GQ   79 (567)
T ss_pred             cchhhcCCCccHHHHHHHHhcCCcccCHHHHhhhHHHhcCCceEEEcCCCCCchhhHHHHHHHHHHhhccCCCc----cc
Confidence            3677665  55999999999999999999999999999999999999999999999999999999765432111    14


Q ss_pred             cEEEEEcCcHHHHHHhc
Q psy7268         117 PLALIITPGRELVFQIG  133 (134)
Q Consensus       117 ~~~lil~Pt~~La~Qi~  133 (134)
                      .-+|||+||||||.||.
T Consensus        80 vgalIIsPTRELa~QI~   96 (567)
T KOG0345|consen   80 VGALIISPTRELARQIR   96 (567)
T ss_pred             eeEEEecCcHHHHHHHH
Confidence            57999999999999996

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.86  E-value=1.8e-21  Score=156.32  Aligned_cols=96  Identities=38%  Similarity=0.497  Sum_probs=83.3

Q ss_pred             CCCCCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCC
Q psy7268          36 IDLGTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELN  115 (134)
Q Consensus        36 ~~~~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~  115 (134)
                      ....+|.+++|++.++++|.+.||+.|+++|.++|+.+++|+|+++.+|||||||++|++|+++.+.......  .....
T Consensus        84 ~~~~~f~~~~l~~~l~~~l~~~g~~~~~~iQ~~ai~~~~~G~dvi~~apTGSGKTlay~lpil~~l~~~~~~~--~~~~~  161 (475)
T PRK01297         84 EGKTRFHDFNLAPELMHAIHDLGFPYCTPIQAQVLGYTLAGHDAIGRAQTGTGKTAAFLISIINQLLQTPPPK--ERYMG  161 (475)
T ss_pred             cCCCCHhHCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhcCccc--ccccC
Confidence            4456899999999999999999999999999999999999999999999999999999999999997643211  11113


Q ss_pred             CcEEEEEcCcHHHHHHhc
Q psy7268         116 APLALIITPGRELVFQIG  133 (134)
Q Consensus       116 ~~~~lil~Pt~~La~Qi~  133 (134)
                      .+++|||+||++||.|++
T Consensus       162 ~~~aLil~PtreLa~Q~~  179 (475)
T PRK01297        162 EPRALIIAPTRELVVQIA  179 (475)
T ss_pred             CceEEEEeCcHHHHHHHH
Confidence            579999999999999986

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=99.86  E-value=1.4e-21  Score=155.26  Aligned_cols=89  Identities=37%  Similarity=0.638  Sum_probs=80.2

Q ss_pred             CcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEE
Q psy7268          40 TFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLA  119 (134)
Q Consensus        40 ~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~  119 (134)
                      +|++++|++.+++.|.+.||..|+++|.++|+.+++|+|+++++|||+|||++|++|+++++.....     .....+++
T Consensus         2 ~f~~l~l~~~l~~~l~~~g~~~p~~iQ~~ai~~~~~g~d~l~~apTGsGKT~~~~lp~l~~l~~~~~-----~~~~~~~~   76 (434)
T PRK11192          2 TFSELELDESLLEALQDKGYTRPTAIQAEAIPPALDGRDVLGSAPTGTGKTAAFLLPALQHLLDFPR-----RKSGPPRI   76 (434)
T ss_pred             CHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHhhccc-----cCCCCceE
Confidence            6999999999999999999999999999999999999999999999999999999999999875321     11235789


Q ss_pred             EEEcCcHHHHHHhc
Q psy7268         120 LIITPGRELVFQIG  133 (134)
Q Consensus       120 lil~Pt~~La~Qi~  133 (134)
                      ||++||++||.|++
T Consensus        77 lil~Pt~eLa~Q~~   90 (434)
T PRK11192         77 LILTPTRELAMQVA   90 (434)
T ss_pred             EEECCcHHHHHHHH
Confidence            99999999999985

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=99.86  E-value=1.7e-21  Score=161.08  Aligned_cols=87  Identities=37%  Similarity=0.609  Sum_probs=80.4

Q ss_pred             CCCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCc
Q psy7268          38 LGTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAP  117 (134)
Q Consensus        38 ~~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~  117 (134)
                      ..+|++++|++.++++|.++||+.||++|.++||.++.|+|++++||||+|||++|++|+++.+....         .++
T Consensus         5 ~~~f~~l~L~~~ll~al~~~G~~~ptpiQ~~ai~~ll~g~dvl~~ApTGsGKT~af~lpll~~l~~~~---------~~~   75 (629)
T PRK11634          5 ETTFADLGLKAPILEALNDLGYEKPSPIQAECIPHLLNGRDVLGMAQTGSGKTAAFSLPLLHNLDPEL---------KAP   75 (629)
T ss_pred             cCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCcHHHHHHHHHHHHhhhcc---------CCC
Confidence            34799999999999999999999999999999999999999999999999999999999999985422         567


Q ss_pred             EEEEEcCcHHHHHHhc
Q psy7268         118 LALIITPGRELVFQIG  133 (134)
Q Consensus       118 ~~lil~Pt~~La~Qi~  133 (134)
                      ++||++||++||.|++
T Consensus        76 ~~LIL~PTreLa~Qv~   91 (629)
T PRK11634         76 QILVLAPTRELAVQVA   91 (629)
T ss_pred             eEEEEeCcHHHHHHHH
Confidence            9999999999999985

>KOG0340|consensus

Probab=99.85  E-value=1.2e-21  Score=149.67  Aligned_cols=89  Identities=35%  Similarity=0.574  Sum_probs=84.1

Q ss_pred             CCCCCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCC
Q psy7268          36 IDLGTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELN  115 (134)
Q Consensus        36 ~~~~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~  115 (134)
                      .....|+.+||.+++.+.++.+|.+.|||+|..|||.++.|+|++-+|.||||||.+|.+|+++++.+..         .
T Consensus         4 ~t~~~F~~LGl~~Wlve~l~~l~i~~pTpiQ~~cIpkILeGrdcig~AkTGsGKT~AFaLPil~rLsedP---------~   74 (442)
T KOG0340|consen    4 KTAKPFSILGLSPWLVEQLKALGIKKPTPIQQACIPKILEGRDCIGCAKTGSGKTAAFALPILNRLSEDP---------Y   74 (442)
T ss_pred             cccCchhhcCccHHHHHHHHHhcCCCCCchHhhhhHHHhcccccccccccCCCcchhhhHHHHHhhccCC---------C
Confidence            4457899999999999999999999999999999999999999999999999999999999999998755         7


Q ss_pred             CcEEEEEcCcHHHHHHhc
Q psy7268         116 APLALIITPGRELVFQIG  133 (134)
Q Consensus       116 ~~~~lil~Pt~~La~Qi~  133 (134)
                      +..++|++||||||.|+.
T Consensus        75 giFalvlTPTrELA~Qia   92 (442)
T KOG0340|consen   75 GIFALVLTPTRELALQIA   92 (442)
T ss_pred             cceEEEecchHHHHHHHH
Confidence            889999999999999985

>PTZ00424 helicase 45; Provisional

Probab=99.85  E-value=4e-21  Score=150.68  Aligned_cols=92  Identities=33%  Similarity=0.404  Sum_probs=82.9

Q ss_pred             ccCCCCCCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCC
Q psy7268          33 VSRIDLGTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKP  112 (134)
Q Consensus        33 ~~~~~~~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~  112 (134)
                      .......+|++++|++.+++++.+.||+.|+++|.++|+.+++|+|+++++|||+|||++|++|++..+...        
T Consensus        22 ~~~~~~~~~~~l~l~~~~~~~l~~~~~~~~~~~Q~~ai~~i~~~~d~ii~apTGsGKT~~~~l~~l~~~~~~--------   93 (401)
T PTZ00424         22 NYDEIVDSFDALKLNEDLLRGIYSYGFEKPSAIQQRGIKPILDGYDTIGQAQSGTGKTATFVIAALQLIDYD--------   93 (401)
T ss_pred             ccccccCCHhhCCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHhcCC--------
Confidence            334457899999999999999999999999999999999999999999999999999999999999987432        


Q ss_pred             CCCCcEEEEEcCcHHHHHHhc
Q psy7268         113 ELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus       113 ~~~~~~~lil~Pt~~La~Qi~  133 (134)
                       ..+.++||++|+++|+.|++
T Consensus        94 -~~~~~~lil~Pt~~L~~Q~~  113 (401)
T PTZ00424         94 -LNACQALILAPTRELAQQIQ  113 (401)
T ss_pred             -CCCceEEEECCCHHHHHHHH
Confidence             14678999999999999985

>KOG0338|consensus

Probab=99.85  E-value=6.5e-22  Score=156.82  Aligned_cols=91  Identities=31%  Similarity=0.514  Sum_probs=82.9

Q ss_pred             CCCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCc
Q psy7268          38 LGTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAP  117 (134)
Q Consensus        38 ~~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~  117 (134)
                      ..+|.+|+|+..+++++..+||..|||||..+||..+.|+|+..||.||||||.+|++|+|++++.....      -...
T Consensus       180 ~~sF~~mNLSRPlLka~~~lGy~~PTpIQ~a~IPvallgkDIca~A~TGsGKTAAF~lPiLERLlYrPk~------~~~T  253 (691)
T KOG0338|consen  180 NESFQSMNLSRPLLKACSTLGYKKPTPIQVATIPVALLGKDICACAATGSGKTAAFALPILERLLYRPKK------VAAT  253 (691)
T ss_pred             hhhHHhcccchHHHHHHHhcCCCCCCchhhhcccHHhhcchhhheecccCCchhhhHHHHHHHHhcCccc------Ccce
Confidence            4589999999999999999999999999999999999999999999999999999999999999975421      1356


Q ss_pred             EEEEEcCcHHHHHHhcC
Q psy7268         118 LALIITPGRELVFQIGQ  134 (134)
Q Consensus       118 ~~lil~Pt~~La~Qi~~  134 (134)
                      ++||++||||||.||++
T Consensus       254 RVLVL~PTRELaiQv~s  270 (691)
T KOG0338|consen  254 RVLVLVPTRELAIQVHS  270 (691)
T ss_pred             eEEEEeccHHHHHHHHH
Confidence            89999999999999974

>KOG0343|consensus

Probab=99.84  E-value=1.5e-21  Score=155.95  Aligned_cols=98  Identities=32%  Similarity=0.468  Sum_probs=89.2

Q ss_pred             ccccCCCCCCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCC
Q psy7268          31 EAVSRIDLGTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEY  110 (134)
Q Consensus        31 ~~~~~~~~~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~  110 (134)
                      +......+..|++++|+...++.|++.+|..||.+|+.+||..+.|+||+..|.||||||++|++|+|+.+++..     
T Consensus        61 ~ei~~~~~~kF~dlpls~~t~kgLke~~fv~~teiQ~~~Ip~aL~G~DvlGAAkTGSGKTLAFlvPvlE~L~r~k-----  135 (758)
T KOG0343|consen   61 AEIDSTTIKKFADLPLSQKTLKGLKEAKFVKMTEIQRDTIPMALQGHDVLGAAKTGSGKTLAFLVPVLEALYRLK-----  135 (758)
T ss_pred             HHhhhhhhhhHHhCCCchHHHHhHhhcCCccHHHHHHhhcchhccCcccccccccCCCceeeehHHHHHHHHHcC-----
Confidence            333446677899999999999999999999999999999999999999999999999999999999999999865     


Q ss_pred             CCCCCCcEEEEEcCcHHHHHHhc
Q psy7268         111 KPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus       111 ~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      |....|..||||+||||||.|++
T Consensus       136 Ws~~DGlGalIISPTRELA~QtF  158 (758)
T KOG0343|consen  136 WSPTDGLGALIISPTRELALQTF  158 (758)
T ss_pred             CCCCCCceeEEecchHHHHHHHH
Confidence            44557889999999999999986

>KOG0334|consensus

Probab=99.84  E-value=2.9e-21  Score=162.19  Aligned_cols=99  Identities=37%  Similarity=0.639  Sum_probs=88.5

Q ss_pred             cccCCCCCCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCC
Q psy7268          32 AVSRIDLGTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYK  111 (134)
Q Consensus        32 ~~~~~~~~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~  111 (134)
                      ..-..|+.+|.+.+++..+++.++++||.+|++||.+|||+++.|+|||.+|.||||||++|++|++.++..+..    .
T Consensus       358 ~~~pkpv~sW~q~gl~~~il~tlkkl~y~k~~~IQ~qAiP~ImsGrdvIgvakTgSGKT~af~LPmirhi~dQr~----~  433 (997)
T KOG0334|consen  358 KECPKPVTSWTQCGLSSKILETLKKLGYEKPTPIQAQAIPAIMSGRDVIGVAKTGSGKTLAFLLPMIRHIKDQRP----L  433 (997)
T ss_pred             CCCCcccchHhhCCchHHHHHHHHHhcCCCCcchhhhhcchhccCcceEEeeccCCccchhhhcchhhhhhcCCC----h
Confidence            344589999999999999999999999999999999999999999999999999999999999999977765433    3


Q ss_pred             CCCCCcEEEEEcCcHHHHHHhcC
Q psy7268         112 PELNAPLALIITPGRELVFQIGQ  134 (134)
Q Consensus       112 ~~~~~~~~lil~Pt~~La~Qi~~  134 (134)
                      ..+.||-+||++|||+|+.||++
T Consensus       434 ~~gdGPi~li~aPtrela~QI~r  456 (997)
T KOG0334|consen  434 EEGDGPIALILAPTRELAMQIHR  456 (997)
T ss_pred             hhCCCceEEEEcCCHHHHHHHHH
Confidence            33459999999999999999974

>KOG0333|consensus

Probab=99.83  E-value=8.7e-21  Score=150.75  Aligned_cols=99  Identities=36%  Similarity=0.576  Sum_probs=92.1

Q ss_pred             CCCCCCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCC
Q psy7268          35 RIDLGTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPEL  114 (134)
Q Consensus        35 ~~~~~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~  114 (134)
                      ..|+.+|++.+++.++++.+.+.||..|+|||+++||..++.+|+|..+.||||||.+|++|++..+.............
T Consensus       241 pnplrnwEE~~~P~e~l~~I~~~~y~eptpIqR~aipl~lQ~rD~igvaETgsGktaaf~ipLl~~IsslP~~~~~en~~  320 (673)
T KOG0333|consen  241 PNPLRNWEESGFPLELLSVIKKPGYKEPTPIQRQAIPLGLQNRDPIGVAETGSGKTAAFLIPLLIWISSLPPMARLENNI  320 (673)
T ss_pred             CccccChhhcCCCHHHHHHHHhcCCCCCchHHHhhccchhccCCeeeEEeccCCccccchhhHHHHHHcCCCcchhhhcc
Confidence            37899999999999999999999999999999999999999999999999999999999999999998876655555666


Q ss_pred             CCcEEEEEcCcHHHHHHhc
Q psy7268         115 NAPLALIITPGRELVFQIG  133 (134)
Q Consensus       115 ~~~~~lil~Pt~~La~Qi~  133 (134)
                      .+|.++|++|||+|++||+
T Consensus       321 ~gpyaiilaptReLaqqIe  339 (673)
T KOG0333|consen  321 EGPYAIILAPTRELAQQIE  339 (673)
T ss_pred             cCceeeeechHHHHHHHHH
Confidence            7999999999999999996

>KOG0342|consensus

Probab=99.83  E-value=5.4e-21  Score=150.64  Aligned_cols=94  Identities=38%  Similarity=0.553  Sum_probs=85.4

Q ss_pred             CCCCCCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCC
Q psy7268          35 RIDLGTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPEL  114 (134)
Q Consensus        35 ~~~~~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~  114 (134)
                      ...-..|++..|++..+++|.++||+.+|++|+.+|+.++.|+|+++.|.||+|||++|++|.++.+.+....+     .
T Consensus        78 ~~~~~~f~~~~LS~~t~kAi~~~GF~~MT~VQ~~ti~pll~gkDvl~~AKTGtGKTlAFLiPaie~l~k~~~~~-----r  152 (543)
T KOG0342|consen   78 ITTTFRFEEGSLSPLTLKAIKEMGFETMTPVQQKTIPPLLEGKDVLAAAKTGTGKTLAFLLPAIELLRKLKFKP-----R  152 (543)
T ss_pred             hhhhhHhhccccCHHHHHHHHhcCccchhHHHHhhcCccCCCccceeeeccCCCceeeehhHHHHHHHhcccCC-----C
Confidence            34456789999999999999999999999999999999999999999999999999999999999999866432     2


Q ss_pred             CCcEEEEEcCcHHHHHHhc
Q psy7268         115 NAPLALIITPGRELVFQIG  133 (134)
Q Consensus       115 ~~~~~lil~Pt~~La~Qi~  133 (134)
                      ++..+||++||||||.|++
T Consensus       153 ~~~~vlIi~PTRELA~Q~~  171 (543)
T KOG0342|consen  153 NGTGVLIICPTRELAMQIF  171 (543)
T ss_pred             CCeeEEEecccHHHHHHHH
Confidence            6788999999999999986

>KOG0335|consensus

Probab=99.83  E-value=5e-21  Score=151.58  Aligned_cols=101  Identities=35%  Similarity=0.505  Sum_probs=90.0

Q ss_pred             cCCCCCCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCC
Q psy7268          34 SRIDLGTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPE  113 (134)
Q Consensus        34 ~~~~~~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~  113 (134)
                      -..++.+|.+-.+.+.+..++...||..|||+|+.+||.+..|+|+++||+||||||.+|++|++.++++..........
T Consensus        69 ~p~~i~~f~~~~l~~~l~~ni~~~~~~~ptpvQk~sip~i~~Grdl~acAqTGsGKT~aFLiPii~~~~~~~~~~~~~~~  148 (482)
T KOG0335|consen   69 VPPHIPTFDEAILGEALAGNIKRSGYTKPTPVQKYSIPIISGGRDLMACAQTGSGKTAAFLIPIISYLLDEGPEDRGESG  148 (482)
T ss_pred             cCCCcccccccchhHHHhhccccccccCCCcceeeccceeecCCceEEEccCCCcchHHHHHHHHHHHHhcCcccCcccC
Confidence            34677799999999999999999999999999999999999999999999999999999999999999987664443333


Q ss_pred             C-CCcEEEEEcCcHHHHHHhcC
Q psy7268         114 L-NAPLALIITPGRELVFQIGQ  134 (134)
Q Consensus       114 ~-~~~~~lil~Pt~~La~Qi~~  134 (134)
                      . ..|+++|++||||||.||++
T Consensus       149 ~~~~P~~lIlapTReL~~Qi~n  170 (482)
T KOG0335|consen  149 GGVYPRALILAPTRELVDQIYN  170 (482)
T ss_pred             CCCCCceEEEeCcHHHhhHHHH
Confidence            3 47999999999999999984

>TIGR03817 DECH_helic helicase/secretion neighborhood putative DEAH-box helicase

Probab=99.81  E-value=1.3e-19  Score=152.21  Aligned_cols=78  Identities=18%  Similarity=0.341  Sum_probs=73.6

Q ss_pred             CCHHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCc
Q psy7268          46 LAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPG  125 (134)
Q Consensus        46 l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt  125 (134)
                      |++++.++|.+.||+.|+++|.++|+.+++|+|+++.+|||||||++|++|+++.+...          .+.++|||+||
T Consensus        21 l~~~l~~~L~~~g~~~p~~~Q~~ai~~il~G~nvvv~apTGSGKTla~~LPiL~~l~~~----------~~~~aL~l~Pt   90 (742)
T TIGR03817        21 AHPDVVAALEAAGIHRPWQHQARAAELAHAGRHVVVATGTASGKSLAYQLPVLSALADD----------PRATALYLAPT   90 (742)
T ss_pred             CCHHHHHHHHHcCCCcCCHHHHHHHHHHHCCCCEEEECCCCCcHHHHHHHHHHHHHhhC----------CCcEEEEEcCh
Confidence            89999999999999999999999999999999999999999999999999999999652          35789999999


Q ss_pred             HHHHHHhc
Q psy7268         126 RELVFQIG  133 (134)
Q Consensus       126 ~~La~Qi~  133 (134)
                      ||||.|++
T Consensus        91 raLa~q~~   98 (742)
T TIGR03817        91 KALAADQL   98 (742)
T ss_pred             HHHHHHHH
Confidence            99999985

A conserved gene neighborhood widely spread in the Actinobacteria contains this uncharacterized DEAH-box family helicase encoded convergently towards an operon of genes for protein homologous to type II secretion and pilus formation proteins. The context suggests that this helicase may play a role in conjugal transfer of DNA.

>KOG0328|consensus

Probab=99.81  E-value=5.8e-21  Score=142.70  Aligned_cols=92  Identities=33%  Similarity=0.522  Sum_probs=84.3

Q ss_pred             cCCCCCCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCC
Q psy7268          34 SRIDLGTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPE  113 (134)
Q Consensus        34 ~~~~~~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~  113 (134)
                      ...+..+|++++|.+++++.+..+||++|+.+|+++|+.+++|+|+++++.+|+|||.+|.+.+++.+.-..        
T Consensus        22 ~~~v~~~F~~Mgl~edlLrgiY~yGfekPS~IQqrAi~~IlkGrdViaQaqSGTGKTa~~si~vlq~~d~~~--------   93 (400)
T KOG0328|consen   22 KVKVIPTFDDMGLKEDLLRGIYAYGFEKPSAIQQRAIPQILKGRDVIAQAQSGTGKTATFSISVLQSLDISV--------   93 (400)
T ss_pred             CcccccchhhcCchHHHHHHHHHhccCCchHHHhhhhhhhhcccceEEEecCCCCceEEEEeeeeeeccccc--------
Confidence            346778999999999999999999999999999999999999999999999999999999999999885432        


Q ss_pred             CCCcEEEEEcCcHHHHHHhcC
Q psy7268         114 LNAPLALIITPGRELVFQIGQ  134 (134)
Q Consensus       114 ~~~~~~lil~Pt~~La~Qi~~  134 (134)
                       +..+++|++||||||.|+.+
T Consensus        94 -r~tQ~lilsPTRELa~Qi~~  113 (400)
T KOG0328|consen   94 -RETQALILSPTRELAVQIQK  113 (400)
T ss_pred             -ceeeEEEecChHHHHHHHHH
Confidence             56899999999999999863

>cd00268 DEADc DEAD-box helicases

Probab=99.81  E-value=3.1e-19  Score=128.08  Aligned_cols=86  Identities=43%  Similarity=0.704  Sum_probs=79.2

Q ss_pred             cccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEE
Q psy7268          41 FEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLAL  120 (134)
Q Consensus        41 f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~l  120 (134)
                      |+++++++.+.+.+.+.|++.|+++|+++++.+.+|+|+++++|||+|||++|++|++..+....       ..++++++
T Consensus         1 ~~~~~~~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~TG~GKT~~~~~~~l~~~~~~~-------~~~~~~vi   73 (203)
T cd00268           1 FEELGLSPELLRGIYALGFEKPTPIQARAIPPLLSGRDVIGQAQTGSGKTAAFLIPILEKLDPSP-------KKDGPQAL   73 (203)
T ss_pred             CCcCCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCcEEEECCCCCcHHHHHHHHHHHHHHhhc-------ccCCceEE
Confidence            78999999999999999999999999999999999999999999999999999999999987642       12578999


Q ss_pred             EEcCcHHHHHHhc
Q psy7268         121 IITPGRELVFQIG  133 (134)
Q Consensus       121 il~Pt~~La~Qi~  133 (134)
                      |++|+++|+.|+.
T Consensus        74 ii~p~~~L~~q~~   86 (203)
T cd00268          74 ILAPTRELALQIA   86 (203)
T ss_pred             EEcCCHHHHHHHH
Confidence            9999999999974

A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP- binding region.

>KOG0347|consensus

Probab=99.81  E-value=1.7e-20  Score=149.87  Aligned_cols=103  Identities=32%  Similarity=0.532  Sum_probs=86.1

Q ss_pred             ccccCCCCCCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcC-CCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCC
Q psy7268          31 EAVSRIDLGTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSG-KSAILVAETGCGKTLSFLAPLVQQILTWKSRPE  109 (134)
Q Consensus        31 ~~~~~~~~~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g-~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~  109 (134)
                      +.+....+..|.+++|+.+++++|..+||..||+||..++|++..| .||+..|.||||||++|-||+++.+.......+
T Consensus       173 ~~~~~~DvsAW~~l~lp~~iL~aL~~~gFs~Pt~IQsl~lp~ai~gk~DIlGaAeTGSGKTLAFGIPiv~~l~~~s~~s~  252 (731)
T KOG0347|consen  173 DDSSKVDVSAWKNLFLPMEILRALSNLGFSRPTEIQSLVLPAAIRGKVDILGAAETGSGKTLAFGIPIVERLLESSDDSQ  252 (731)
T ss_pred             ccccccChHHHhcCCCCHHHHHHHHhcCCCCCccchhhcccHhhccchhcccccccCCCceeeecchhhhhhhhccchHh
Confidence            4555678889999999999999999999999999999999999999 799999999999999999999997765433111


Q ss_pred             --CCCCCCCcE--EEEEcCcHHHHHHhc
Q psy7268         110 --YKPELNAPL--ALIITPGRELVFQIG  133 (134)
Q Consensus       110 --~~~~~~~~~--~lil~Pt~~La~Qi~  133 (134)
                        .+....+++  +||++||||||.||-
T Consensus       253 e~~~~~~k~~k~~~LV~tPTRELa~QV~  280 (731)
T KOG0347|consen  253 ELSNTSAKYVKPIALVVTPTRELAHQVK  280 (731)
T ss_pred             hhhhHHhccCcceeEEecChHHHHHHHH
Confidence              011113445  999999999999984

>KOG0344|consensus

Probab=99.77  E-value=1.1e-18  Score=139.91  Aligned_cols=100  Identities=31%  Similarity=0.447  Sum_probs=87.6

Q ss_pred             ccccCCCCCCccc----CCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcC
Q psy7268          31 EAVSRIDLGTFED----TGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKS  106 (134)
Q Consensus        31 ~~~~~~~~~~f~~----~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~  106 (134)
                      ......++.+|.+    ...++.+++++.+.||..|+++|++++|.++.++|++.|+|||+|||++|++|+++++.....
T Consensus       124 G~~~~~~l~~f~~lt~~~~~~~~ll~nl~~~~F~~Pt~iq~~aipvfl~~r~~lAcapTGsgKtlaf~~Pil~~L~~~~~  203 (593)
T KOG0344|consen  124 GFHLPPPLLSFSDLTYDYSMNKRLLENLQELGFDEPTPIQKQAIPVFLEKRDVLACAPTGSGKTLAFNLPILQHLKDLSQ  203 (593)
T ss_pred             CCCCCCccccccccchhhhhcHHHHHhHhhCCCCCCCcccchhhhhhhcccceEEeccCCCcchhhhhhHHHHHHHHhhc
Confidence            3344577888886    668999999999999999999999999999999999999999999999999999999986542


Q ss_pred             CCCCCCCCCCcEEEEEcCcHHHHHHhcC
Q psy7268         107 RPEYKPELNAPLALIITPGRELVFQIGQ  134 (134)
Q Consensus       107 ~~~~~~~~~~~~~lil~Pt~~La~Qi~~  134 (134)
                          .+...|.+++|+.|||+|+.|+++
T Consensus       204 ----~~~~~gl~a~Il~ptreLa~Qi~r  227 (593)
T KOG0344|consen  204 ----EKHKVGLRALILSPTRELAAQIYR  227 (593)
T ss_pred             ----ccCccceEEEEecchHHHHHHHHH
Confidence                223368899999999999999973

>KOG0336|consensus

Probab=99.77  E-value=1.2e-19  Score=141.33  Aligned_cols=97  Identities=40%  Similarity=0.558  Sum_probs=85.5

Q ss_pred             cCCCCCCccc-CCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCC
Q psy7268          34 SRIDLGTFED-TGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKP  112 (134)
Q Consensus        34 ~~~~~~~f~~-~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~  112 (134)
                      -++|.-+|++ +.-.+++++++++.||.+|||+|.++||.+++|.|++.+|.||+|||++||+|-+.++..+...   ..
T Consensus       214 IPnP~ctFddAFq~~pevmenIkK~GFqKPtPIqSQaWPI~LQG~DliGVAQTgtgKtL~~L~pg~ihi~aqp~~---~~  290 (629)
T KOG0336|consen  214 IPNPVCTFDDAFQCYPEVMENIKKTGFQKPTPIQSQAWPILLQGIDLIGVAQTGTGKTLAFLLPGFIHIDAQPKR---RE  290 (629)
T ss_pred             CCCCcCcHHHHHhhhHHHHHHHHhccCCCCCcchhcccceeecCcceEEEEecCCCcCHHHhccceeeeeccchh---hh
Confidence            4577788875 5677999999999999999999999999999999999999999999999999998888765443   33


Q ss_pred             CCCCcEEEEEcCcHHHHHHhc
Q psy7268         113 ELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus       113 ~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      +.+++.+|+++|||||+.|+.
T Consensus       291 qr~~p~~lvl~ptreLalqie  311 (629)
T KOG0336|consen  291 QRNGPGVLVLTPTRELALQIE  311 (629)
T ss_pred             ccCCCceEEEeccHHHHHHHH
Confidence            457899999999999999984

>KOG0326|consensus

Probab=99.76  E-value=7.5e-20  Score=138.68  Aligned_cols=89  Identities=33%  Similarity=0.513  Sum_probs=82.2

Q ss_pred             CCCCCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCC
Q psy7268          36 IDLGTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELN  115 (134)
Q Consensus        36 ~~~~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~  115 (134)
                      ..-..|++++|.++++..+.+.||++|+|+|.++||.++.|+|+++.|.+|+|||-+|++|+++.+..         ..+
T Consensus        82 TkG~efEd~~Lkr~LLmgIfe~G~ekPSPiQeesIPiaLtGrdiLaRaKNGTGKT~a~~IP~Lekid~---------~~~  152 (459)
T KOG0326|consen   82 TKGNEFEDYCLKRELLMGIFEKGFEKPSPIQEESIPIALTGRDILARAKNGTGKTAAYCIPVLEKIDP---------KKN  152 (459)
T ss_pred             ccCccHHHhhhhHHHHHHHHHhccCCCCCccccccceeecchhhhhhccCCCCCccceechhhhhcCc---------ccc
Confidence            44467999999999999999999999999999999999999999999999999999999999999954         337


Q ss_pred             CcEEEEEcCcHHHHHHhc
Q psy7268         116 APLALIITPGRELVFQIG  133 (134)
Q Consensus       116 ~~~~lil~Pt~~La~Qi~  133 (134)
                      .-+++|++||||||.|+.
T Consensus       153 ~IQ~~ilVPtrelALQtS  170 (459)
T KOG0326|consen  153 VIQAIILVPTRELALQTS  170 (459)
T ss_pred             ceeEEEEeecchhhHHHH
Confidence            789999999999999974

>PRK02362 ski2-like helicase; Provisional

Probab=99.76  E-value=2.4e-18  Score=144.67  Aligned_cols=82  Identities=24%  Similarity=0.305  Sum_probs=76.4

Q ss_pred             CcccCCCCHHHHHHHHHCCCCCChHHHHHHHHH-HHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcE
Q psy7268          40 TFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPT-LLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPL  118 (134)
Q Consensus        40 ~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~-~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~  118 (134)
                      .|++++|++.+++++.+.||+.|+|+|.++++. ++.|+|+++++|||+|||++|.+|++..+.            ++.+
T Consensus         2 ~~~~l~lp~~~~~~l~~~g~~~l~p~Q~~ai~~~~~~g~nvlv~APTGSGKTlia~lail~~l~------------~~~k   69 (737)
T PRK02362          2 KIAELPLPEGVIEFYEAEGIEELYPPQAEAVEAGLLDGKNLLAAIPTASGKTLIAELAMLKAIA------------RGGK   69 (737)
T ss_pred             ChhhcCCCHHHHHHHHhCCCCcCCHHHHHHHHHHHhCCCcEEEECCCcchHHHHHHHHHHHHHh------------cCCc
Confidence            588999999999999999999999999999998 778999999999999999999999999984            3568


Q ss_pred             EEEEcCcHHHHHHhc
Q psy7268         119 ALIITPGRELVFQIG  133 (134)
Q Consensus       119 ~lil~Pt~~La~Qi~  133 (134)
                      +||++|+++||.|.+
T Consensus        70 al~i~P~raLa~q~~   84 (737)
T PRK02362         70 ALYIVPLRALASEKF   84 (737)
T ss_pred             EEEEeChHHHHHHHH
Confidence            999999999999975

>KOG0341|consensus

Probab=99.75  E-value=4.3e-19  Score=137.50  Aligned_cols=102  Identities=30%  Similarity=0.423  Sum_probs=89.8

Q ss_pred             ccccCCCCCCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCC
Q psy7268          31 EAVSRIDLGTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEY  110 (134)
Q Consensus        31 ~~~~~~~~~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~  110 (134)
                      ......|+.+|.++.++..+++.|++.|+.+|||+|-+-+|.+++|+|+|-.|-||||||++|.+|++-.-+++... .+
T Consensus       162 Gd~ipPPIksF~eMKFP~~~L~~lk~KGI~~PTpIQvQGlPvvLsGRDmIGIAfTGSGKTlvFvLP~imf~LeqE~~-lP  240 (610)
T KOG0341|consen  162 GDDIPPPIKSFKEMKFPKPLLRGLKKKGIVHPTPIQVQGLPVVLSGRDMIGIAFTGSGKTLVFVLPVIMFALEQEMM-LP  240 (610)
T ss_pred             CCCCCCchhhhhhccCCHHHHHHHHhcCCCCCCceeecCcceEeecCceeeEEeecCCceEEEeHHHHHHHHHHHhc-Cc
Confidence            34456899999999999999999999999999999999999999999999999999999999999998887765432 12


Q ss_pred             CCCCCCcEEEEEcCcHHHHHHhc
Q psy7268         111 KPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus       111 ~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      .....||..|||||+||||.|.+
T Consensus       241 f~~~EGP~gLiicPSRELArQt~  263 (610)
T KOG0341|consen  241 FARGEGPYGLIICPSRELARQTH  263 (610)
T ss_pred             cccCCCCeeEEEcCcHHHHHHHH
Confidence            23347899999999999999986

>PRK00254 ski2-like helicase; Provisional

Probab=99.75  E-value=5.3e-18  Score=142.27  Aligned_cols=83  Identities=22%  Similarity=0.309  Sum_probs=77.1

Q ss_pred             CcccCCCCHHHHHHHHHCCCCCChHHHHHHHHH-HHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcE
Q psy7268          40 TFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPT-LLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPL  118 (134)
Q Consensus        40 ~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~-~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~  118 (134)
                      +|+++++++.+.+.+.+.||+.|+++|.++++. ++.|+|+++++|||+|||++|.+|++..+..           .+.+
T Consensus         2 ~~~~l~l~~~~~~~l~~~g~~~l~~~Q~~ai~~~~~~g~nvlv~apTGsGKT~~~~l~il~~l~~-----------~~~~   70 (720)
T PRK00254          2 KVDELRVDERIKRVLKERGIEELYPPQAEALKSGVLEGKNLVLAIPTASGKTLVAEIVMVNKLLR-----------EGGK   70 (720)
T ss_pred             cHHHcCCCHHHHHHHHhCCCCCCCHHHHHHHHHHHhCCCcEEEECCCCcHHHHHHHHHHHHHHHh-----------cCCe
Confidence            578999999999999999999999999999986 7899999999999999999999999998864           3568


Q ss_pred             EEEEcCcHHHHHHhc
Q psy7268         119 ALIITPGRELVFQIG  133 (134)
Q Consensus       119 ~lil~Pt~~La~Qi~  133 (134)
                      +||++|+++|+.|.+
T Consensus        71 ~l~l~P~~aLa~q~~   85 (720)
T PRK00254         71 AVYLVPLKALAEEKY   85 (720)
T ss_pred             EEEEeChHHHHHHHH
Confidence            999999999999976

>KOG0339|consensus

Probab=99.74  E-value=2.1e-18  Score=137.11  Aligned_cols=102  Identities=31%  Similarity=0.476  Sum_probs=91.3

Q ss_pred             CCcccccCCCCCCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCC
Q psy7268          28 RGYEAVSRIDLGTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSR  107 (134)
Q Consensus        28 ~~~~~~~~~~~~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~  107 (134)
                      +..+.....|+++|+++++.+.++.++++..|++||++|.+++|..++|+||+-.|.||||||-+|+.|++.++..+.. 
T Consensus       212 rv~g~s~~rpvtsfeh~gfDkqLm~airk~Ey~kptpiq~qalptalsgrdvigIAktgSgktaAfi~pm~~himdq~e-  290 (731)
T KOG0339|consen  212 RVSGSSPPRPVTSFEHFGFDKQLMTAIRKSEYEKPTPIQCQALPTALSGRDVIGIAKTGSGKTAAFIWPMIVHIMDQPE-  290 (731)
T ss_pred             eeccCCCCCCcchhhhcCchHHHHHHHhhhhcccCCcccccccccccccccchheeeccCcchhHHHHHHHHHhcchhh-
Confidence            3445556689999999999999999999999999999999999999999999999999999999999999999986543 


Q ss_pred             CCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268         108 PEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus       108 ~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                         -....+|..||++||||||.||+
T Consensus       291 ---L~~g~gPi~vilvPTrela~Qi~  313 (731)
T KOG0339|consen  291 ---LKPGEGPIGVILVPTRELASQIF  313 (731)
T ss_pred             ---hcCCCCCeEEEEeccHHHHHHHH
Confidence               22247899999999999999996

>KOG0327|consensus

Probab=99.73  E-value=9.6e-19  Score=134.56  Aligned_cols=90  Identities=32%  Similarity=0.463  Sum_probs=83.2

Q ss_pred             CCCCCCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCC
Q psy7268          35 RIDLGTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPEL  114 (134)
Q Consensus        35 ~~~~~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~  114 (134)
                      ..-+.+|++++|.+++++.+...||++|+.+|++||+++..|.|+++++.+|+|||.+|++++++.+....         
T Consensus        22 ~evvdsfddm~L~e~LLrgiy~yGFekPSaIQqraI~p~i~G~dv~~qaqsgTgKt~af~i~iLq~iD~~~---------   92 (397)
T KOG0327|consen   22 NEVVDSFDDMNLKESLLRGIYAYGFEKPSAIQQRAILPCIKGHDVIAQAQSGTGKTAAFLISILQQIDMSV---------   92 (397)
T ss_pred             HHHhhhhhhcCCCHHHHhHHHhhccCCchHHHhccccccccCCceeEeeeccccchhhhHHHHHhhcCcch---------
Confidence            34567999999999999999999999999999999999999999999999999999999999999985433         


Q ss_pred             CCcEEEEEcCcHHHHHHhc
Q psy7268         115 NAPLALIITPGRELVFQIG  133 (134)
Q Consensus       115 ~~~~~lil~Pt~~La~Qi~  133 (134)
                      ...++++++|+|+||.|++
T Consensus        93 ke~qalilaPtreLa~qi~  111 (397)
T KOG0327|consen   93 KETQALILAPTRELAQQIQ  111 (397)
T ss_pred             HHHHHHHhcchHHHHHHHH
Confidence            5788999999999999985

>KOG0337|consensus

Probab=99.71  E-value=7.3e-18  Score=131.37  Aligned_cols=88  Identities=36%  Similarity=0.645  Sum_probs=82.0

Q ss_pred             CCCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCc
Q psy7268          38 LGTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAP  117 (134)
Q Consensus        38 ~~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~  117 (134)
                      -..|..++|...++++|.+.||+.|||+|+.+||.++.|+|++..+.||||||.||++|+++++....        ..+.
T Consensus        20 ~g~fqsmgL~~~v~raI~kkg~~~ptpiqRKTipliLe~~dvv~martgsgktaaf~ipm~e~Lk~~s--------~~g~   91 (529)
T KOG0337|consen   20 SGGFQSMGLDYKVLRAIHKKGFNTPTPIQRKTIPLILEGRDVVGMARTGSGKTAAFLIPMIEKLKSHS--------QTGL   91 (529)
T ss_pred             CCCccccCCCHHHHHHHHHhhcCCCCchhcccccceeeccccceeeecCCcchhhHHHHHHHHHhhcc--------cccc
Confidence            36899999999999999999999999999999999999999999999999999999999999997533        2688


Q ss_pred             EEEEEcCcHHHHHHhc
Q psy7268         118 LALIITPGRELVFQIG  133 (134)
Q Consensus       118 ~~lil~Pt~~La~Qi~  133 (134)
                      +++|++|||+|+.|..
T Consensus        92 RalilsptreLa~qtl  107 (529)
T KOG0337|consen   92 RALILSPTRELALQTL  107 (529)
T ss_pred             ceeeccCcHHHHHHHH
Confidence            9999999999999974

>PRK13767 ATP-dependent helicase; Provisional

Probab=99.71  E-value=4.9e-17  Score=138.88  Aligned_cols=84  Identities=26%  Similarity=0.422  Sum_probs=72.3

Q ss_pred             CCHHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCc
Q psy7268          46 LAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPG  125 (134)
Q Consensus        46 l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt  125 (134)
                      |++.+.+++.+ +|..|+++|+++|+.+++|+|++++||||||||++|++|+++.+......   .....++++|||+|+
T Consensus        18 l~~~v~~~~~~-~~~~~tpiQ~~Ai~~il~g~nvli~APTGSGKTlaa~Lpil~~l~~~~~~---~~~~~~~~~LyIsPt   93 (876)
T PRK13767         18 LRPYVREWFKE-KFGTFTPPQRYAIPLIHEGKNVLISSPTGSGKTLAAFLAIIDELFRLGRE---GELEDKVYCLYVSPL   93 (876)
T ss_pred             cCHHHHHHHHH-ccCCCCHHHHHHHHHHHcCCCEEEECCCCCcHHHHHHHHHHHHHHhhccc---cCCCCCeEEEEEcCH
Confidence            77888888877 79999999999999999999999999999999999999999998753211   111257889999999


Q ss_pred             HHHHHHhc
Q psy7268         126 RELVFQIG  133 (134)
Q Consensus       126 ~~La~Qi~  133 (134)
                      |+|+.|++
T Consensus        94 raLa~di~  101 (876)
T PRK13767         94 RALNNDIH  101 (876)
T ss_pred             HHHHHHHH
Confidence            99999975

>COG1201 Lhr Lhr-like helicases [General function prediction only]

Probab=99.69  E-value=9.8e-17  Score=134.59  Aligned_cols=83  Identities=30%  Similarity=0.512  Sum_probs=74.8

Q ss_pred             CCHHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCc
Q psy7268          46 LAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPG  125 (134)
Q Consensus        46 l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt  125 (134)
                      |++.+.+++.+. |..||+.|.++||.+.+|+|+++.||||||||++.++|++..+.+..    ..+...+..+|||+|.
T Consensus         8 l~~~v~~~~~~~-~~~~t~~Q~~a~~~i~~G~nvLiiAPTGsGKTeAAfLpil~~l~~~~----~~~~~~~i~~lYIsPL   82 (814)
T COG1201           8 LDPRVREWFKRK-FTSLTPPQRYAIPEIHSGENVLIIAPTGSGKTEAAFLPVINELLSLG----KGKLEDGIYALYISPL   82 (814)
T ss_pred             cCHHHHHHHHHh-cCCCCHHHHHHHHHHhCCCceEEEcCCCCChHHHHHHHHHHHHHhcc----CCCCCCceEEEEeCcH
Confidence            789999999997 99999999999999999999999999999999999999999999863    1222257899999999


Q ss_pred             HHHHHHhc
Q psy7268         126 RELVFQIG  133 (134)
Q Consensus       126 ~~La~Qi~  133 (134)
                      |+|..++.
T Consensus        83 kALn~Di~   90 (814)
T COG1201          83 KALNNDIR   90 (814)
T ss_pred             HHHHHHHH
Confidence            99999875

>PRK01172 ski2-like helicase; Provisional

Probab=99.69  E-value=8.1e-17  Score=134.28  Aligned_cols=81  Identities=25%  Similarity=0.382  Sum_probs=74.8

Q ss_pred             CcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEE
Q psy7268          40 TFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLA  119 (134)
Q Consensus        40 ~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~  119 (134)
                      +|++++|++++++.+.+.||+ ++++|.++++.+..|+|+++++|||+|||+++.++++..+.            .+.++
T Consensus         2 ~~~~~~l~~~~~~~~~~~~~~-l~~~Q~~ai~~l~~~~nvlv~apTGSGKTl~a~lail~~l~------------~~~k~   68 (674)
T PRK01172          2 KISDLGYDDEFLNLFTGNDFE-LYDHQRMAIEQLRKGENVIVSVPTAAGKTLIAYSAIYETFL------------AGLKS   68 (674)
T ss_pred             cHhhcCCCHHHHHHHhhCCCC-CCHHHHHHHHHHhcCCcEEEECCCCchHHHHHHHHHHHHHH------------hCCcE
Confidence            578899999999999999995 99999999999999999999999999999999999998875            34579


Q ss_pred             EEEcCcHHHHHHhc
Q psy7268         120 LIITPGRELVFQIG  133 (134)
Q Consensus       120 lil~Pt~~La~Qi~  133 (134)
                      ||++|+++||.|++
T Consensus        69 v~i~P~raLa~q~~   82 (674)
T PRK01172         69 IYIVPLRSLAMEKY   82 (674)
T ss_pred             EEEechHHHHHHHH
Confidence            99999999999976

>KOG0350|consensus

Probab=99.68  E-value=5.9e-17  Score=128.48  Aligned_cols=92  Identities=27%  Similarity=0.351  Sum_probs=77.4

Q ss_pred             CCCCCCcccCCCCHHHHHH----------HHHCCCCCChHHHHHHHHHHH---------cCCCeEEEcCCCCchhHHhHH
Q psy7268          35 RIDLGTFEDTGLAPEIIDI----------FTKRGLTTPTEIQKYSIPTLL---------SGKSAILVAETGCGKTLSFLA   95 (134)
Q Consensus        35 ~~~~~~f~~~~l~~~i~~~----------l~~~g~~~~t~iQ~~~i~~~~---------~g~dvli~a~tGsGKT~~~~l   95 (134)
                      .....-|+.+++++.+...          +.++++....|+|..++|.++         .++|+.+.||||||||++|.+
T Consensus       123 ~nslq~~s~l~~se~k~~~d~lea~~~q~l~k~~is~~FPVQ~aVlp~ll~~~~~p~~~r~rDIcV~ApTGSGKTLaY~i  202 (620)
T KOG0350|consen  123 NNSLQIFSVLGKSEMKNLEDTLEATIDQLLVKMAISRLFPVQYAVLPSLLEEIRSPPPSRPRDICVNAPTGSGKTLAYVI  202 (620)
T ss_pred             CCceeeeeccchhHHHHHHHHHHHHHHHHHHHhhcccccchHHHHHHHHHHhhcCCCCCCCCceEEecCCCCCceeeehh
Confidence            3455567777776665544          889999999999999999885         378999999999999999999


Q ss_pred             HHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhcC
Q psy7268          96 PLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIGQ  134 (134)
Q Consensus        96 pil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~~  134 (134)
                      ||++.+.....        +..|||||+||++|+.||++
T Consensus       203 PIVQ~L~~R~v--------~~LRavVivPtr~L~~QV~~  233 (620)
T KOG0350|consen  203 PIVQLLSSRPV--------KRLRAVVIVPTRELALQVYD  233 (620)
T ss_pred             HHHHHHccCCc--------cceEEEEEeeHHHHHHHHHH
Confidence            99999976433        46899999999999999974

>KOG0332|consensus

Probab=99.65  E-value=2.3e-16  Score=121.66  Aligned_cols=94  Identities=26%  Similarity=0.444  Sum_probs=83.8

Q ss_pred             ccccCCCCCCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcC--CCeEEEcCCCCchhHHhHHHHHHHHHhhcCCC
Q psy7268          31 EAVSRIDLGTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSG--KSAILVAETGCGKTLSFLAPLVQQILTWKSRP  108 (134)
Q Consensus        31 ~~~~~~~~~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g--~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~  108 (134)
                      ...+.....+|++|.|.|++++.+..++|++|+.||..++|.++..  +++|.++.+|+|||.+|.+.+|.++...    
T Consensus        82 pnsPlyS~ksFeeL~LkPellkgly~M~F~kPskIQe~aLPlll~~Pp~nlIaQsqsGtGKTaaFvL~MLsrvd~~----  157 (477)
T KOG0332|consen   82 PNSPLYSAKSFEELRLKPELLKGLYAMKFQKPSKIQETALPLLLAEPPQNLIAQSQSGTGKTAAFVLTMLSRVDPD----  157 (477)
T ss_pred             CCCCccccccHHhhCCCHHHHhHHHHhccCCcchHHHhhcchhhcCCchhhhhhhcCCCchhHHHHHHHHHhcCcc----
Confidence            4444566789999999999999999999999999999999999975  6899999999999999999999999543    


Q ss_pred             CCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268         109 EYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus       109 ~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                           ...|+++-|+||||||.|+.
T Consensus       158 -----~~~PQ~iCLaPtrELA~Q~~  177 (477)
T KOG0332|consen  158 -----VVVPQCICLAPTRELAPQTG  177 (477)
T ss_pred             -----ccCCCceeeCchHHHHHHHH
Confidence                 36788999999999999974

>KOG0329|consensus

Probab=99.61  E-value=4.6e-16  Score=115.35  Aligned_cols=86  Identities=33%  Similarity=0.484  Sum_probs=79.3

Q ss_pred             CCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcE
Q psy7268          39 GTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPL  118 (134)
Q Consensus        39 ~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~  118 (134)
                      ..|.++-|.|++++++.+.||++|+++|+.|||....|-|++++|.+|.|||.+|+++.++.+..         ......
T Consensus        42 sgfrdfllkpellraivdcgfehpsevqhecipqailgmdvlcqaksgmgktavfvl~tlqqiep---------v~g~vs  112 (387)
T KOG0329|consen   42 SGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQIEP---------VDGQVS  112 (387)
T ss_pred             cchhhhhcCHHHHHHHHhccCCCchHhhhhhhhHHhhcchhheecccCCCceeeeehhhhhhcCC---------CCCeEE
Confidence            46889999999999999999999999999999999999999999999999999999999999843         235678


Q ss_pred             EEEEcCcHHHHHHhc
Q psy7268         119 ALIITPGRELVFQIG  133 (134)
Q Consensus       119 ~lil~Pt~~La~Qi~  133 (134)
                      ++++|.|||||-||.
T Consensus       113 vlvmchtrelafqi~  127 (387)
T KOG0329|consen  113 VLVMCHTRELAFQIS  127 (387)
T ss_pred             EEEEeccHHHHHHHH
Confidence            999999999999985

>KOG4284|consensus

Probab=99.60  E-value=1.5e-16  Score=129.47  Aligned_cols=89  Identities=30%  Similarity=0.401  Sum_probs=82.3

Q ss_pred             CCCCCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCC
Q psy7268          36 IDLGTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELN  115 (134)
Q Consensus        36 ~~~~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~  115 (134)
                      .....|+++.|..+++..|+..+|..||++|..|||.++.+-|+||++.+|+|||++|.+.+++.+..         ...
T Consensus        22 ~~~~~fe~l~l~r~vl~glrrn~f~~ptkiQaaAIP~~~~kmDliVQaKSGTGKTlVfsv~av~sl~~---------~~~   92 (980)
T KOG4284|consen   22 NCTPGFEQLALWREVLLGLRRNAFALPTKIQAAAIPAIFSKMDLIVQAKSGTGKTLVFSVLAVESLDS---------RSS   92 (980)
T ss_pred             CCCCCHHHHHHHHHHHHHHHhhcccCCCchhhhhhhhhhcccceEEEecCCCCceEEEEeeeehhcCc---------ccC
Confidence            44578999999999999999999999999999999999999999999999999999999999988854         337


Q ss_pred             CcEEEEEcCcHHHHHHhc
Q psy7268         116 APLALIITPGRELVFQIG  133 (134)
Q Consensus       116 ~~~~lil~Pt~~La~Qi~  133 (134)
                      .++++|++||||+|.||.
T Consensus        93 ~~q~~Iv~PTREiaVQI~  110 (980)
T KOG4284|consen   93 HIQKVIVTPTREIAVQIK  110 (980)
T ss_pred             cceeEEEecchhhhhHHH
Confidence            899999999999999986

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=99.59  E-value=3.4e-15  Score=120.08  Aligned_cols=62  Identities=27%  Similarity=0.392  Sum_probs=56.2

Q ss_pred             CCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          57 RGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        57 ~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      .||..|+|+|.++|+.+++|+|+++++|||+|||++|++|++.               .+..+||++|+++|+.|..
T Consensus         7 ~g~~~~r~~Q~~ai~~~l~g~dvlv~apTGsGKTl~y~lp~l~---------------~~~~~lVi~P~~~L~~dq~   68 (470)
T TIGR00614         7 FGLSSFRPVQLEVINAVLLGRDCFVVMPTGGGKSLCYQLPALC---------------SDGITLVISPLISLMEDQV   68 (470)
T ss_pred             cCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCcHhHHHHHHHHH---------------cCCcEEEEecHHHHHHHHH
Confidence            5999999999999999999999999999999999999999875               2346899999999998753

This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>PLN03137 ATP-dependent DNA helicase; Q4-like; Provisional

Probab=99.56  E-value=2.4e-14  Score=123.32  Aligned_cols=79  Identities=23%  Similarity=0.275  Sum_probs=67.4

Q ss_pred             CCcc--cCCCCHHHHHHHHH-CCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCC
Q psy7268          39 GTFE--DTGLAPEIIDIFTK-RGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELN  115 (134)
Q Consensus        39 ~~f~--~~~l~~~i~~~l~~-~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~  115 (134)
                      ..|.  +++....+...+++ .||..++|+|.++|+.++.|+|+++++|||+|||++|++|++..               
T Consensus       435 ~~W~~~~fpw~~~L~~~lk~~FG~~sFRp~Q~eaI~aiL~GrDVLVimPTGSGKSLcYQLPAL~~---------------  499 (1195)
T PLN03137        435 KKWSSRNFPWTKKLEVNNKKVFGNHSFRPNQREIINATMSGYDVFVLMPTGGGKSLTYQLPALIC---------------  499 (1195)
T ss_pred             ccccccCCCchHHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCccHHHHHHHHHHHc---------------
Confidence            3465  45566777777777 59999999999999999999999999999999999999999852               


Q ss_pred             CcEEEEEcCcHHHHH-Hh
Q psy7268         116 APLALIITPGRELVF-QI  132 (134)
Q Consensus       116 ~~~~lil~Pt~~La~-Qi  132 (134)
                      +..+|||+|+++|+. |+
T Consensus       500 ~GiTLVISPLiSLmqDQV  517 (1195)
T PLN03137        500 PGITLVISPLVSLIQDQI  517 (1195)
T ss_pred             CCcEEEEeCHHHHHHHHH
Confidence            246999999999997 54

>PF00270 DEAD: DEAD/DEAH box helicase; InterPro: IPR011545 Members of this family include the DEAD and DEAH box helicases

Probab=99.55  E-value=2.5e-14  Score=99.35  Aligned_cols=61  Identities=34%  Similarity=0.520  Sum_probs=54.7

Q ss_pred             hHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          63 TEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        63 t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      ||+|.++|+.+.+|+|+++.+|||+|||++|+++++..+.+.          ...+++|++|+++|+.|++
T Consensus         1 t~~Q~~~~~~i~~~~~~li~aptGsGKT~~~~~~~l~~~~~~----------~~~~~lii~P~~~l~~q~~   61 (169)
T PF00270_consen    1 TPLQQEAIEAIISGKNVLISAPTGSGKTLAYILPALNRLQEG----------KDARVLIIVPTRALAEQQF   61 (169)
T ss_dssp             -HHHHHHHHHHHTTSEEEEECSTTSSHHHHHHHHHHHHHHTT----------SSSEEEEEESSHHHHHHHH
T ss_pred             CHHHHHHHHHHHcCCCEEEECCCCCccHHHHHHHHHhhhccC----------CCceEEEEeeccccccccc
Confidence            789999999999999999999999999999999999998753          2248999999999999975

Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression. ; GO: 0003676 nucleic acid binding, 0005524 ATP binding, 0008026 ATP-dependent helicase activity; PDB: 3RRM_A 3RRN_A 3PEW_A 2KBE_A 3PEY_A 3FHO_A 2ZJA_A 2ZJ8_A 2ZJ5_A 2ZJ2_A ....

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=99.55  E-value=2e-14  Score=118.82  Aligned_cols=73  Identities=25%  Similarity=0.333  Sum_probs=61.5

Q ss_pred             CCHHHHHHHHH-CCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcC
Q psy7268          46 LAPEIIDIFTK-RGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITP  124 (134)
Q Consensus        46 l~~~i~~~l~~-~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~P  124 (134)
                      +.+...+.|++ .||..|+|+|.++|+.+++|+|+++.+|||+|||++|++|++..               ...+||++|
T Consensus         9 ~~~~~~~~l~~~fG~~~~r~~Q~~ai~~il~g~dvlv~apTGsGKTl~y~lpal~~---------------~g~tlVisP   73 (607)
T PRK11057          9 LESLAKQVLQETFGYQQFRPGQQEIIDAVLSGRDCLVVMPTGGGKSLCYQIPALVL---------------DGLTLVVSP   73 (607)
T ss_pred             chhHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCchHHHHHHHHHHHc---------------CCCEEEEec
Confidence            33444455555 59999999999999999999999999999999999999998852               235899999


Q ss_pred             cHHHHHHhc
Q psy7268         125 GRELVFQIG  133 (134)
Q Consensus       125 t~~La~Qi~  133 (134)
                      +++|+.|..
T Consensus        74 l~sL~~dqv   82 (607)
T PRK11057         74 LISLMKDQV   82 (607)
T ss_pred             HHHHHHHHH
Confidence            999998753

>COG1205 Distinct helicase family with a unique C-terminal domain including a metal-binding cysteine cluster [General function prediction only]

Probab=99.52  E-value=6.8e-14  Score=119.08  Aligned_cols=76  Identities=24%  Similarity=0.372  Sum_probs=68.8

Q ss_pred             CCHHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCc
Q psy7268          46 LAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPG  125 (134)
Q Consensus        46 l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt  125 (134)
                      ....+..++.+.|...++.+|.+|+..+.+|+|++|.++||||||.+|++||++.+.+..          ..++|+|.||
T Consensus        55 ~~~~l~~~l~~~g~~~lY~HQ~~A~~~~~~G~~vvVtTgTgSGKTe~FllPIld~~l~~~----------~a~AL~lYPt  124 (851)
T COG1205          55 RDESLKSALVKAGIERLYSHQVDALRLIREGRNVVVTTGTGSGKTESFLLPILDHLLRDP----------SARALLLYPT  124 (851)
T ss_pred             hhhHHHHHHHHhccccccHHHHHHHHHHHCCCCEEEECCCCCchhHHHHHHHHHHHhhCc----------CccEEEEech
Confidence            455668888888999999999999999999999999999999999999999999998753          3389999999


Q ss_pred             HHHHHH
Q psy7268         126 RELVFQ  131 (134)
Q Consensus       126 ~~La~Q  131 (134)
                      ++||++
T Consensus       125 nALa~D  130 (851)
T COG1205         125 NALAND  130 (851)
T ss_pred             hhhHhh
Confidence            999986

>PRK09401 reverse gyrase; Reviewed

Probab=99.52  E-value=5.6e-14  Score=122.81  Aligned_cols=73  Identities=33%  Similarity=0.396  Sum_probs=60.3

Q ss_pred             HHHHHHHHHC-CCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcH
Q psy7268          48 PEIIDIFTKR-GLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGR  126 (134)
Q Consensus        48 ~~i~~~l~~~-g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~  126 (134)
                      +++.+.+++. |+ .|+++|+.++|.++.|+|++++||||+|||. |.++++..+..           ++.+++||+||+
T Consensus        67 ~~~~~~f~~~~G~-~pt~iQ~~~i~~il~g~dv~i~ApTGsGKT~-f~l~~~~~l~~-----------~g~~alIL~PTr  133 (1176)
T PRK09401         67 KEFEKFFKKKTGS-KPWSLQRTWAKRLLLGESFAIIAPTGVGKTT-FGLVMSLYLAK-----------KGKKSYIIFPTR  133 (1176)
T ss_pred             HHHHHHHHHhcCC-CCcHHHHHHHHHHHCCCcEEEEcCCCCCHHH-HHHHHHHHHHh-----------cCCeEEEEeccH
Confidence            3445556554 88 8999999999999999999999999999996 55666655532           467899999999


Q ss_pred             HHHHHhc
Q psy7268         127 ELVFQIG  133 (134)
Q Consensus       127 ~La~Qi~  133 (134)
                      +|+.|++
T Consensus       134 eLa~Qi~  140 (1176)
T PRK09401        134 LLVEQVV  140 (1176)
T ss_pred             HHHHHHH
Confidence            9999986

>TIGR01054 rgy reverse gyrase

Probab=99.50  E-value=7.3e-14  Score=122.11  Aligned_cols=74  Identities=31%  Similarity=0.371  Sum_probs=61.9

Q ss_pred             HHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHH
Q psy7268          48 PEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRE  127 (134)
Q Consensus        48 ~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~  127 (134)
                      .++.+.+.+.....|+++|+.+++.++.|+|++++||||+|||. |.+|++..+..           .+++++|++||++
T Consensus        65 ~~f~~~f~~~~g~~p~~iQ~~~i~~il~G~d~vi~ApTGsGKT~-f~l~~~~~l~~-----------~g~~vLIL~PTre  132 (1171)
T TIGR01054        65 KEFEEFFKKAVGSEPWSIQKMWAKRVLRGDSFAIIAPTGVGKTT-FGLAMSLFLAK-----------KGKRCYIILPTTL  132 (1171)
T ss_pred             HHHHHHHHHhcCCCCcHHHHHHHHHHhCCCeEEEECCCCCCHHH-HHHHHHHHHHh-----------cCCeEEEEeCHHH
Confidence            55666666643348999999999999999999999999999997 66777766643           4678999999999


Q ss_pred             HHHHhc
Q psy7268         128 LVFQIG  133 (134)
Q Consensus       128 La~Qi~  133 (134)
                      ||.|++
T Consensus       133 La~Qi~  138 (1171)
T TIGR01054       133 LVIQVA  138 (1171)
T ss_pred             HHHHHH
Confidence            999986

Generally, these gyrases are encoded as a single polypeptide. An exception was found in Methanopyrus kandleri, where enzyme is split within the topoisomerase domain, yielding a heterodimer of gene products designated RgyB and RgyA.

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=99.49  E-value=1.2e-13  Score=118.35  Aligned_cols=75  Identities=17%  Similarity=0.153  Sum_probs=65.0

Q ss_pred             CCHHHHHHHHH-CCCCCChHHHHHHHHHHHcC------CCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcE
Q psy7268          46 LAPEIIDIFTK-RGLTTPTEIQKYSIPTLLSG------KSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPL  118 (134)
Q Consensus        46 l~~~i~~~l~~-~g~~~~t~iQ~~~i~~~~~g------~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~  118 (134)
                      ....+.+.+.+ .+| .||+.|.++|+.++++      .|++++|+||+|||.+|+++++..+.            ++.+
T Consensus       436 ~~~~~~~~~~~~~~f-~~T~~Q~~aI~~I~~d~~~~~~~d~Ll~adTGsGKT~val~a~l~al~------------~g~q  502 (926)
T TIGR00580       436 PDLEWQQEFEDSFPF-EETPDQLKAIEEIKADMESPRPMDRLVCGDVGFGKTEVAMRAAFKAVL------------DGKQ  502 (926)
T ss_pred             CCHHHHHHHHHhCCC-CCCHHHHHHHHHHHhhhcccCcCCEEEECCCCccHHHHHHHHHHHHHH------------hCCe
Confidence            44566666666 599 6999999999999874      69999999999999999999998875            4578


Q ss_pred             EEEEcCcHHHHHHhc
Q psy7268         119 ALIITPGRELVFQIG  133 (134)
Q Consensus       119 ~lil~Pt~~La~Qi~  133 (134)
                      ++|++||++||.|++
T Consensus       503 vlvLvPT~~LA~Q~~  517 (926)
T TIGR00580       503 VAVLVPTTLLAQQHF  517 (926)
T ss_pred             EEEEeCcHHHHHHHH
Confidence            999999999999986

All proteins in this family for which functions are known are DNA-dependent ATPases that function in the process of transcription-coupled DNA repair in which the repair of the transcribed strand of actively transacribed genes is repaired at a higher rate than the repair of non-transcribed regions of the genome and than the non-transcribed strand of the same gene. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). This family is closely related to the RecG and UvrB families.

>PRK14701 reverse gyrase; Provisional

Probab=99.49  E-value=1.1e-13  Score=123.75  Aligned_cols=73  Identities=33%  Similarity=0.266  Sum_probs=62.0

Q ss_pred             HHHHHHHHH-CCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcH
Q psy7268          48 PEIIDIFTK-RGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGR  126 (134)
Q Consensus        48 ~~i~~~l~~-~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~  126 (134)
                      +++.+.+++ .|| .|+++|+.++|.+++|+|+++++|||+|||++++++.+....            .+.+++||+||+
T Consensus        66 ~~~~~~f~~~~G~-~pt~iQ~~~i~~il~G~d~li~APTGsGKTl~~~~~al~~~~------------~g~~aLVl~PTr  132 (1638)
T PRK14701         66 EEFEEFFEKITGF-EFWSIQKTWAKRILRGKSFSIVAPTGMGKSTFGAFIALFLAL------------KGKKCYIILPTT  132 (1638)
T ss_pred             HHHHHHHHHhhCC-CCCHHHHHHHHHHHcCCCEEEEEcCCCCHHHHHHHHHHHHHh------------cCCeEEEEECHH
Confidence            566677777 799 699999999999999999999999999999976665554321            467899999999


Q ss_pred             HHHHHhc
Q psy7268         127 ELVFQIG  133 (134)
Q Consensus       127 ~La~Qi~  133 (134)
                      +|+.|++
T Consensus       133 eLa~Qi~  139 (1638)
T PRK14701        133 LLVKQTV  139 (1638)
T ss_pred             HHHHHHH
Confidence            9999985

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=99.48  E-value=1.3e-13  Score=115.31  Aligned_cols=73  Identities=22%  Similarity=0.241  Sum_probs=62.6

Q ss_pred             HHHHHHH-HHCCCCCChHHHHHHHHHHHcC------CCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEE
Q psy7268          48 PEIIDIF-TKRGLTTPTEIQKYSIPTLLSG------KSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLAL  120 (134)
Q Consensus        48 ~~i~~~l-~~~g~~~~t~iQ~~~i~~~~~g------~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~l  120 (134)
                      ..+++.+ ..++| .||++|.++++.+.++      .+++++|+||||||++|++|++..+.            ++.+++
T Consensus       248 ~~~~~~~~~~l~f-~lt~~Q~~ai~~I~~d~~~~~~~~~Ll~~~TGSGKT~va~~~il~~~~------------~g~q~l  314 (681)
T PRK10917        248 GELLKKFLASLPF-ELTGAQKRVVAEILADLASPKPMNRLLQGDVGSGKTVVAALAALAAIE------------AGYQAA  314 (681)
T ss_pred             hHHHHHHHHhCCC-CCCHHHHHHHHHHHHhhhccCCceEEEECCCCCcHHHHHHHHHHHHHH------------cCCeEE
Confidence            3444444 45699 7999999999999876      37999999999999999999998874            578999


Q ss_pred             EEcCcHHHHHHhc
Q psy7268         121 IITPGRELVFQIG  133 (134)
Q Consensus       121 il~Pt~~La~Qi~  133 (134)
                      |++||++||.|++
T Consensus       315 ilaPT~~LA~Q~~  327 (681)
T PRK10917        315 LMAPTEILAEQHY  327 (681)
T ss_pred             EEeccHHHHHHHH
Confidence            9999999999986

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=99.48  E-value=1.4e-13  Score=114.23  Aligned_cols=73  Identities=19%  Similarity=0.206  Sum_probs=63.1

Q ss_pred             HHHHHHHHHCCCCCChHHHHHHHHHHHcCC------CeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEE
Q psy7268          48 PEIIDIFTKRGLTTPTEIQKYSIPTLLSGK------SAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALI  121 (134)
Q Consensus        48 ~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~------dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~li  121 (134)
                      +.+.+.+..++| .||+.|+++|+.++++.      +.+++++||||||++|++|++..+.            ++.+++|
T Consensus       223 ~~~~~~~~~lpf-~lt~~Q~~ai~~I~~~~~~~~~~~~Ll~g~TGSGKT~va~l~il~~~~------------~g~qvli  289 (630)
T TIGR00643       223 ELLTKFLASLPF-KLTRAQKRVVKEILQDLKSDVPMNRLLQGDVGSGKTLVAALAMLAAIE------------AGYQVAL  289 (630)
T ss_pred             HHHHHHHHhCCC-CCCHHHHHHHHHHHHHhccCCCccEEEECCCCCcHHHHHHHHHHHHHH------------cCCcEEE
Confidence            344556677899 89999999999998752      5899999999999999999998874            5678999


Q ss_pred             EcCcHHHHHHhc
Q psy7268         122 ITPGRELVFQIG  133 (134)
Q Consensus       122 l~Pt~~La~Qi~  133 (134)
                      ++||++||.|++
T Consensus       290 laPT~~LA~Q~~  301 (630)
T TIGR00643       290 MAPTEILAEQHY  301 (630)
T ss_pred             ECCHHHHHHHHH
Confidence            999999999986

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=99.48  E-value=1.1e-13  Score=113.96  Aligned_cols=65  Identities=25%  Similarity=0.387  Sum_probs=57.3

Q ss_pred             HHHH-CCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHH
Q psy7268          53 IFTK-RGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQ  131 (134)
Q Consensus        53 ~l~~-~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Q  131 (134)
                      .|++ +||..++++|.++|+.+++|+|+++++|||+|||++|++|++..               +..++||+|+++|+.|
T Consensus         4 ~l~~~fg~~~fr~~Q~~~i~~il~g~dvlv~~PTG~GKTl~y~lpal~~---------------~g~~lVisPl~sL~~d   68 (591)
T TIGR01389         4 VLKRTFGYDDFRPGQEEIISHVLDGRDVLVVMPTGGGKSLCYQVPALLL---------------KGLTVVISPLISLMKD   68 (591)
T ss_pred             HHHHhcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCccHhHHHHHHHHHc---------------CCcEEEEcCCHHHHHH
Confidence            4555 69999999999999999999999999999999999999998742               2358999999999987


Q ss_pred             h
Q psy7268         132 I  132 (134)
Q Consensus       132 i  132 (134)
                      .
T Consensus        69 q   69 (591)
T TIGR01389        69 Q   69 (591)
T ss_pred             H
Confidence            5

The ATP-dependent DNA helicase RecQ of E. coli is about 600 residues long. This model represents bacterial proteins with a high degree of similarity in domain architecture and in primary sequence to E. coli RecQ. The model excludes eukaryotic and archaeal proteins with RecQ-like regions, as well as more distantly related bacterial helicases related to RecQ.

>PRK12899 secA preprotein translocase subunit SecA; Reviewed

Probab=99.47  E-value=1.5e-13  Score=116.46  Aligned_cols=80  Identities=21%  Similarity=0.208  Sum_probs=70.7

Q ss_pred             ccCCCCHHHHHHHH-----HCCCCCC---hHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCC
Q psy7268          42 EDTGLAPEIIDIFT-----KRGLTTP---TEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPE  113 (134)
Q Consensus        42 ~~~~l~~~i~~~l~-----~~g~~~~---t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~  113 (134)
                      +.+.+.+++.+.+.     ..||..|   +|+|.++++.+..++|++++++||+|||++|++|++..+..          
T Consensus        65 eafal~re~~~r~lg~~~~~~G~~~p~~~tp~qvQ~I~~i~l~~gvIAeaqTGeGKTLAf~LP~l~~aL~----------  134 (970)
T PRK12899         65 EAYGVVKNVCRRLAGTPVEVSGYHQQWDMVPYDVQILGAIAMHKGFITEMQTGEGKTLTAVMPLYLNALT----------  134 (970)
T ss_pred             HHhCCCHHHHHHHhccccccccccCCCCCChHHHHHhhhhhcCCCeEEEeCCCCChHHHHHHHHHHHHhh----------
Confidence            56778888888877     5799998   99999999999999999999999999999999999988863          


Q ss_pred             CCCcEEEEEcCcHHHHHHhc
Q psy7268         114 LNAPLALIITPGRELVFQIG  133 (134)
Q Consensus       114 ~~~~~~lil~Pt~~La~Qi~  133 (134)
                        +..++||+||++||.|++
T Consensus       135 --g~~v~IVTpTrELA~Qda  152 (970)
T PRK12899        135 --GKPVHLVTVNDYLAQRDC  152 (970)
T ss_pred             --cCCeEEEeCCHHHHHHHH
Confidence              123889999999999986

>PRK10689 transcription-repair coupling factor; Provisional

Probab=99.38  E-value=1.5e-12  Score=113.69  Aligned_cols=73  Identities=19%  Similarity=0.172  Sum_probs=62.0

Q ss_pred             HHHHHH-HHHCCCCCChHHHHHHHHHHHcC------CCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEE
Q psy7268          48 PEIIDI-FTKRGLTTPTEIQKYSIPTLLSG------KSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLAL  120 (134)
Q Consensus        48 ~~i~~~-l~~~g~~~~t~iQ~~~i~~~~~g------~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~l  120 (134)
                      ....+. ....+| .||+.|.++|+.++++      .|++++++||+|||.+|+.++...+.            .+.+++
T Consensus       587 ~~~~~~~~~~~~~-~~T~~Q~~aI~~il~d~~~~~~~d~Ll~a~TGsGKT~val~aa~~~~~------------~g~qvl  653 (1147)
T PRK10689        587 REQYQLFCDSFPF-ETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVE------------NHKQVA  653 (1147)
T ss_pred             HHHHHHHHHhCCC-CCCHHHHHHHHHHHHHhhcCCCCCEEEEcCCCcCHHHHHHHHHHHHHH------------cCCeEE
Confidence            344444 455689 7999999999999987      89999999999999999888776653            567899


Q ss_pred             EEcCcHHHHHHhc
Q psy7268         121 IITPGRELVFQIG  133 (134)
Q Consensus       121 il~Pt~~La~Qi~  133 (134)
                      |++||++||.|++
T Consensus       654 vLvPT~eLA~Q~~  666 (1147)
T PRK10689        654 VLVPTTLLAQQHY  666 (1147)
T ss_pred             EEeCcHHHHHHHH
Confidence            9999999999986

>TIGR02621 cas3_GSU0051 CRISPR-associated helicase Cas3, Anaes-subtype

Probab=99.37  E-value=1.2e-12  Score=110.77  Aligned_cols=73  Identities=22%  Similarity=0.252  Sum_probs=54.7

Q ss_pred             HHHHHH-CCCCCChHHHHHHHHHHHcCC-CeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEE-EcCcHH
Q psy7268          51 IDIFTK-RGLTTPTEIQKYSIPTLLSGK-SAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALI-ITPGRE  127 (134)
Q Consensus        51 ~~~l~~-~g~~~~t~iQ~~~i~~~~~g~-dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~li-l~Pt~~  127 (134)
                      -+.+.+ .||+ |+|+|.+++|.++.|+ ++++++|||||||.++.++.+.. ..         ....++.|| ++|+|+
T Consensus         5 ~~ff~~~~G~~-PtpiQ~~~i~~il~G~~~v~~~apTGSGKTaa~aafll~~-~~---------~~~~~~rLv~~vPtRe   73 (844)
T TIGR02621         5 DEWYQGLHGYS-PFPWQLSLAERFVAGQPPESCSTPTGLGKTSIIAAWLLAV-EI---------GAKVPRRLVYVVNRRT   73 (844)
T ss_pred             HHHHHHHhCCC-CCHHHHHHHHHHHcCCCcceEecCCCCcccHHHHHhhccc-cc---------cccccceEEEeCchHH
Confidence            344555 4996 9999999999999998 58888999999999765444422 11         114566666 669999


Q ss_pred             HHHHhcC
Q psy7268         128 LVFQIGQ  134 (134)
Q Consensus       128 La~Qi~~  134 (134)
                      |+.|+++
T Consensus        74 La~Qi~~   80 (844)
T TIGR02621        74 VVDQVTE   80 (844)
T ss_pred             HHHHHHH
Confidence            9999863

This model describes a CRISPR-associated putative DEAH-box helicase, or Cas3, of a subtype found in Actinomyces naeslundii MG1, Geobacter sulfurreducens PCA, Gemmata obscuriglobus UQM 2246, and Desulfotalea psychrophila. This protein includes both DEAH and HD motifs.

>KOG0952|consensus

Probab=99.33  E-value=2e-12  Score=109.81  Aligned_cols=75  Identities=19%  Similarity=0.183  Sum_probs=64.4

Q ss_pred             CCCCCChHHHHHHHHHHH-cCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          57 RGLTTPTEIQKYSIPTLL-SGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        57 ~g~~~~t~iQ~~~i~~~~-~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      .+|++++.+|+.++|.++ ...|++||||||+|||..+++.||+.+.+.  ..+..-..++.++|||+|+++||..+.
T Consensus       106 f~f~~fN~iQS~vFp~aY~SneNMLIcAPTGsGKT~la~L~ILr~ik~~--~~~~~i~k~~fKiVYIaPmKALa~Em~  181 (1230)
T KOG0952|consen  106 FSFEEFNRIQSEVFPVAYKSNENMLICAPTGSGKTVLAELCILRTIKEH--EEQGDIAKDDFKIVYIAPMKALAAEMV  181 (1230)
T ss_pred             ccHHHHHHHHHHhhhhhhcCCCCEEEECCCCCCchHHHHHHHHHHHHhh--ccccccccCCceEEEEechHHHHHHHH
Confidence            478999999999999887 567999999999999999999999999862  233444557899999999999998765

>PRK12898 secA preprotein translocase subunit SecA; Reviewed

Probab=99.31  E-value=4.7e-12  Score=104.93  Aligned_cols=62  Identities=27%  Similarity=0.230  Sum_probs=57.2

Q ss_pred             CCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          57 RGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        57 ~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      +|. .|+++|..+++.++.|+  ++.+.||+|||++|.+|++....            .+.+++|++||++||.|.+
T Consensus       100 lg~-~p~~VQ~~~~~~ll~G~--Iae~~TGeGKTla~~lp~~~~al------------~G~~v~VvTptreLA~qda  161 (656)
T PRK12898        100 LGQ-RHFDVQLMGGLALLSGR--LAEMQTGEGKTLTATLPAGTAAL------------AGLPVHVITVNDYLAERDA  161 (656)
T ss_pred             hCC-CCChHHHHHHHHHhCCC--eeeeeCCCCcHHHHHHHHHHHhh------------cCCeEEEEcCcHHHHHHHH
Confidence            477 89999999999999999  89999999999999999998764            5778999999999999976

>COG1204 Superfamily II helicase [General function prediction only]

Probab=99.24  E-value=1.9e-11  Score=103.32  Aligned_cols=78  Identities=24%  Similarity=0.356  Sum_probs=66.5

Q ss_pred             CCCHHHHHHHHHCCCCCChHHHHHHHHH-HHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEc
Q psy7268          45 GLAPEIIDIFTKRGLTTPTEIQKYSIPT-LLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIIT  123 (134)
Q Consensus        45 ~l~~~i~~~l~~~g~~~~t~iQ~~~i~~-~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~  123 (134)
                      .+.+.+.+.++..|+....+-|+.++.. +..|+|+++++|||+|||+.+++.++..+.+           .+.++||++
T Consensus        15 ~~~~~v~~i~~~~~~~el~~~qq~av~~~~~~~~N~li~aPTgsGKTlIA~lai~~~l~~-----------~~~k~vYiv   83 (766)
T COG1204          15 KLDDRVLEILKGDGIDELFNPQQEAVEKGLLSDENVLISAPTGSGKTLIALLAILSTLLE-----------GGGKVVYIV   83 (766)
T ss_pred             cccHHHHHHhccCChHHhhHHHHHHhhccccCCCcEEEEcCCCCchHHHHHHHHHHHHHh-----------cCCcEEEEe
Confidence            3677888888888997777777777765 5567999999999999999999999999975           367899999


Q ss_pred             CcHHHHHHhc
Q psy7268         124 PGRELVFQIG  133 (134)
Q Consensus       124 Pt~~La~Qi~  133 (134)
                      |+|+||.+.+
T Consensus        84 PlkALa~Ek~   93 (766)
T COG1204          84 PLKALAEEKY   93 (766)
T ss_pred             ChHHHHHHHH
Confidence            9999999875

>TIGR01407 dinG_rel DnaQ family exonuclease/DinG family helicase, putative

Probab=99.22  E-value=5.5e-11  Score=101.79  Aligned_cols=75  Identities=24%  Similarity=0.246  Sum_probs=62.0

Q ss_pred             CCHHHHHHHHHCCCCCChHHHHHHHH----HHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEE
Q psy7268          46 LAPEIIDIFTKRGLTTPTEIQKYSIP----TLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALI  121 (134)
Q Consensus        46 l~~~i~~~l~~~g~~~~t~iQ~~~i~----~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~li  121 (134)
                      +.+.+.+.+...|| .+++.|.+.+.    .+..|+++++.||||+|||++|++|++....            ++.+++|
T Consensus       231 ~~~~~~~~~~~~~~-~~r~~Q~~~~~~i~~~~~~~~~~~~eA~TG~GKT~ayLlp~~~~~~------------~~~~vvi  297 (850)
T TIGR01407       231 LSSLFSKNIDRLGL-EYRPEQLKLAELVLDQLTHSEKSLIEAPTGTGKTLGYLLPALYYAI------------TEKPVVI  297 (850)
T ss_pred             ccHHHHHhhhhcCC-ccCHHHHHHHHHHHHHhccCCcEEEECCCCCchhHHHHHHHHHHhc------------CCCeEEE
Confidence            33467777888899 47899998776    4457899999999999999999999988764            2347999


Q ss_pred             EcCcHHHHHHhc
Q psy7268         122 ITPGRELVFQIG  133 (134)
Q Consensus       122 l~Pt~~La~Qi~  133 (134)
                      .+||++|..|+.
T Consensus       298 ~t~t~~Lq~Ql~  309 (850)
T TIGR01407       298 STNTKVLQSQLL  309 (850)
T ss_pred             EeCcHHHHHHHH
Confidence            999999999974

This model represents a family of proteins in Gram-positive bacteria. The N-terminal region of about 200 amino acids resembles the epsilon subunit of E. coli DNA polymerase III and the homologous region of the Gram-positive type DNA polymerase III alpha subunit. The epsilon subunit contains an exonuclease domain. The remainder of this protein family resembles a predicted ATP-dependent helicase, the DNA damage-inducible protein DinG of E. coli.

>COG1202 Superfamily II helicase, archaea-specific [General function prediction only]

Probab=99.13  E-value=9.3e-11  Score=95.23  Aligned_cols=83  Identities=19%  Similarity=0.298  Sum_probs=76.2

Q ss_pred             CcccCCCCHHHHHHHHHCCCCCChHHHHHHHHH-HHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcE
Q psy7268          40 TFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPT-LLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPL  118 (134)
Q Consensus        40 ~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~-~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~  118 (134)
                      ..+++++++++.+-|+..|++.+.|+|..++.. ++.|+|.+++++|+||||++.-++=+.++..           .+.+
T Consensus       195 ~vdeLdipe~fk~~lk~~G~~eLlPVQ~laVe~GLLeG~nllVVSaTasGKTLIgElAGi~~~l~-----------~g~K  263 (830)
T COG1202         195 PVDELDIPEKFKRMLKREGIEELLPVQVLAVEAGLLEGENLLVVSATASGKTLIGELAGIPRLLS-----------GGKK  263 (830)
T ss_pred             cccccCCcHHHHHHHHhcCcceecchhhhhhhhccccCCceEEEeccCCCcchHHHhhCcHHHHh-----------CCCe
Confidence            457899999999999999999999999999987 7799999999999999999999999998875           5778


Q ss_pred             EEEEcCcHHHHHHhc
Q psy7268         119 ALIITPGRELVFQIG  133 (134)
Q Consensus       119 ~lil~Pt~~La~Qi~  133 (134)
                      -|+++|..+||+|=|
T Consensus       264 mlfLvPLVALANQKy  278 (830)
T COG1202         264 MLFLVPLVALANQKY  278 (830)
T ss_pred             EEEEehhHHhhcchH
Confidence            999999999999954

>PRK05580 primosome assembly protein PriA; Validated

Probab=99.13  E-value=3.1e-10  Score=95.17  Aligned_cols=61  Identities=23%  Similarity=0.292  Sum_probs=53.9

Q ss_pred             CChHHHHHHHHHHHcC---CCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          61 TPTEIQKYSIPTLLSG---KSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        61 ~~t~iQ~~~i~~~~~g---~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      .+++.|++++..+.++   +++++.++||+|||.+|+.++...+.            .+.++||++|+++|+.|++
T Consensus       144 ~Lt~~Q~~ai~~i~~~~~~~~~Ll~~~TGSGKT~v~l~~i~~~l~------------~g~~vLvLvPt~~L~~Q~~  207 (679)
T PRK05580        144 TLNPEQAAAVEAIRAAAGFSPFLLDGVTGSGKTEVYLQAIAEVLA------------QGKQALVLVPEIALTPQML  207 (679)
T ss_pred             CCCHHHHHHHHHHHhccCCCcEEEECCCCChHHHHHHHHHHHHHH------------cCCeEEEEeCcHHHHHHHH
Confidence            5899999999999874   78999999999999999888777664            3568999999999999986

>PHA02558 uvsW UvsW helicase; Provisional

Probab=99.12  E-value=2.4e-10  Score=92.84  Aligned_cols=63  Identities=25%  Similarity=0.171  Sum_probs=50.9

Q ss_pred             CCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          60 TTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        60 ~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      ..|++.|.++++.++.+++.++++|||+|||+++... .......          ...++||++||++|+.|+.
T Consensus       113 ~~~r~~Q~~av~~~l~~~~~il~apTGsGKT~i~~~l-~~~~~~~----------~~~~vLilvpt~eL~~Q~~  175 (501)
T PHA02558        113 IEPHWYQYDAVYEGLKNNRRLLNLPTSAGKSLIQYLL-SRYYLEN----------YEGKVLIIVPTTSLVTQMI  175 (501)
T ss_pred             CCCCHHHHHHHHHHHhcCceEEEeCCCCCHHHHHHHH-HHHHHhc----------CCCeEEEEECcHHHHHHHH
Confidence            4899999999999999999999999999999976442 2222221          2348999999999999985

>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type

Probab=99.09  E-value=1.9e-10  Score=89.84  Aligned_cols=54  Identities=28%  Similarity=0.372  Sum_probs=46.9

Q ss_pred             HHHHHHHHHHcCCC--eEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          65 IQKYSIPTLLSGKS--AILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        65 iQ~~~i~~~~~g~d--vli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      +|.++++.+.++++  +++++|||+|||++|++|++.               .+.++++++|+++|+.|.+
T Consensus         1 hQ~~~~~~~~~~~~~~~~i~apTGsGKT~~~~~~~l~---------------~~~~~~~~~P~~aL~~~~~   56 (357)
T TIGR03158         1 HQVATFEALQSKDADIIFNTAPTGAGKTLAWLTPLLH---------------GENDTIALYPTNALIEDQT   56 (357)
T ss_pred             CHHHHHHHHHcCCCCEEEEECCCCCCHHHHHHHHHHH---------------cCCCEEEEeChHHHHHHHH
Confidence            49999999999885  788999999999999999884               1235899999999999865

subtype of CRISPR/Cas locus, found in several species of Cyanobacteria and several archaeal species. It contains helicase motifs and appears to represent the Cas3 protein of the Cyano subtype of CRISPR/Cas system.

>smart00487 DEXDc DEAD-like helicases superfamily

Probab=99.08  E-value=4e-10  Score=78.68  Aligned_cols=67  Identities=37%  Similarity=0.490  Sum_probs=58.4

Q ss_pred             CCCCCChHHHHHHHHHHHcC-CCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          57 RGLTTPTEIQKYSIPTLLSG-KSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        57 ~g~~~~t~iQ~~~i~~~~~g-~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      .++..+++.|.+++..+..+ +.+++.+++|+|||.++..+++..+...          ...++++++|+++++.|+.
T Consensus         4 ~~~~~~~~~Q~~~~~~~~~~~~~~~i~~~~GsGKT~~~~~~~~~~~~~~----------~~~~~l~~~p~~~~~~~~~   71 (201)
T smart00487        4 FGFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKRG----------KGKRVLVLVPTRELAEQWA   71 (201)
T ss_pred             cCCCCCCHHHHHHHHHHHcCCCcEEEECCCCCchhHHHHHHHHHHhccc----------CCCcEEEEeCCHHHHHHHH
Confidence            46779999999999999998 9999999999999999999988887642          1357999999999999864

>PRK09200 preprotein translocase subunit SecA; Reviewed

Probab=99.06  E-value=6.1e-10  Score=94.21  Aligned_cols=62  Identities=29%  Similarity=0.314  Sum_probs=55.8

Q ss_pred             CCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          57 RGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        57 ~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      +|. +|+++|..+++.+..|+  ++.+.||+|||+++++|++....            .|.+++|++||++||.|.+
T Consensus        75 ~g~-~p~~vQl~~~~~l~~G~--Iaem~TGeGKTL~a~lp~~l~al------------~G~~v~VvTpt~~LA~qd~  136 (790)
T PRK09200         75 LGM-RPYDVQLIGALVLHEGN--IAEMQTGEGKTLTATMPLYLNAL------------EGKGVHLITVNDYLAKRDA  136 (790)
T ss_pred             hCC-CCchHHHHhHHHHcCCc--eeeecCCCcchHHHHHHHHHHHH------------cCCCeEEEeCCHHHHHHHH
Confidence            487 99999999999998887  89999999999999999986654            5778999999999999975

>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated

Probab=99.05  E-value=5.5e-10  Score=95.35  Aligned_cols=65  Identities=28%  Similarity=0.336  Sum_probs=53.5

Q ss_pred             HHCCCCCChHHHHHHHHHHH----cCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHH
Q psy7268          55 TKRGLTTPTEIQKYSIPTLL----SGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVF  130 (134)
Q Consensus        55 ~~~g~~~~t~iQ~~~i~~~~----~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~  130 (134)
                      .-.|| .+.+.|.+....+.    .+..+++.|+||+|||++|++|++...             .+.++||++||++|+.
T Consensus       240 ~~~~~-e~R~~Q~~ma~~V~~~l~~~~~~~~eA~tGtGKT~ayllp~l~~~-------------~~~~vvI~t~T~~Lq~  305 (820)
T PRK07246        240 ALLGL-EERPKQESFAKLVGEDFHDGPASFIEAQTGIGKTYGYLLPLLAQS-------------DQRQIIVSVPTKILQD  305 (820)
T ss_pred             ccCCC-ccCHHHHHHHHHHHHHHhCCCcEEEECCCCCcHHHHHHHHHHHhc-------------CCCcEEEEeCcHHHHH
Confidence            33478 67999999665443    678899999999999999999988753             3467999999999999


Q ss_pred             Hhc
Q psy7268         131 QIG  133 (134)
Q Consensus       131 Qi~  133 (134)
                      |+.
T Consensus       306 Ql~  308 (820)
T PRK07246        306 QIM  308 (820)
T ss_pred             HHH
Confidence            983

>TIGR03117 cas_csf4 CRISPR-associated DEAD/DEAH-box helicase Csf4

Probab=99.02  E-value=7.8e-10  Score=91.79  Aligned_cols=52  Identities=25%  Similarity=0.284  Sum_probs=44.6

Q ss_pred             HHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          72 TLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        72 ~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      .+..++.+++.|+||+|||++|++|++..+...          .+.++||++||++|+.|+.
T Consensus        12 al~~~~~lliEA~TGtGKTlAYLlpal~~~~~~----------~~~rvlIstpT~~Lq~Ql~   63 (636)
T TIGR03117        12 SLRQKRIGMLEASTGVGKTLAMIMAALTMLKER----------PDQKIAIAVPTLALMGQLW   63 (636)
T ss_pred             HHhcCCeEEEEcCCCCcHHHHHHHHHHHHHHhc----------cCceEEEECCcHHHHHHHH
Confidence            345678899999999999999999999987531          3568999999999999986

Members of this family show up near CRISPR repeats in Acidithiobacillus ferrooxidans ATCC 23270, Azoarcus sp. EbN1, and Rhodoferax ferrireducens DSM 15236. In the latter two species, the CRISPR/cas locus is found on a plasmid. This family is one of several characteristic of a type of CRISPR-associated (cas) gene cluster we designate Aferr after A. ferrooxidans, where it is both chromosomal and the only type of cas gene cluster found. The gene is designated csf4 (CRISPR/cas Subtype as in A. ferrooxidans protein 1), as it lies farthest (fourth closest) from the repeats in the A. ferrooxidans genome.

>KOG0349|consensus

Probab=99.02  E-value=7.4e-11  Score=93.31  Aligned_cols=67  Identities=34%  Similarity=0.547  Sum_probs=63.6

Q ss_pred             CCCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhh
Q psy7268          38 LGTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTW  104 (134)
Q Consensus        38 ~~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~  104 (134)
                      ++.|+++++-|++-.+..++.+.-||.+|.++||.++.|.|++..+.||||||-+|++|+++.+++.
T Consensus         1 m~af~e~gv~pel~~a~~e~dw~lptdvqaeaiplilgggdvlmaaetgsgktgaf~lpilqiv~et   67 (725)
T KOG0349|consen    1 MTAFEEFGVLPELGMATDELDWTLPTDVQAEAIPLILGGGDVLMAAETGSGKTGAFCLPILQIVWET   67 (725)
T ss_pred             CcchHhhCcchHhhhhhhhhccccccccccccccEEecCCcEEEEeccCCCCccceehhhHHHHHHH
Confidence            3579999999999999999999999999999999999999999999999999999999999998854

>PHA02653 RNA helicase NPH-II; Provisional

Probab=99.00  E-value=8.9e-10  Score=92.15  Aligned_cols=64  Identities=22%  Similarity=0.250  Sum_probs=50.3

Q ss_pred             HHHHHHHHHHHcCCCeEEEcCCCCchhHH---------hHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          64 EIQKYSIPTLLSGKSAILVAETGCGKTLS---------FLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        64 ~iQ~~~i~~~~~g~dvli~a~tGsGKT~~---------~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      .+|+++++.+++|+|++++|+||+|||.+         |++|.+..+..-.      +...+.++++++|+||||.|++
T Consensus       167 ~iQ~qil~~i~~gkdvIv~A~TGSGKTtqvPq~l~~~~flf~~l~~l~~~~------~~~~~~~ilvt~PrreLa~qi~  239 (675)
T PHA02653        167 DVQLKIFEAWISRKPVVLTGGTGVGKTSQVPKLLLWFNYLFGGFDNLDKID------PNFIERPIVLSLPRVALVRLHS  239 (675)
T ss_pred             HHHHHHHHHHHhCCCEEEECCCCCCchhHHHHHHHHhhhccchhhhhhhcc------cccCCcEEEEECcHHHHHHHHH
Confidence            48999999999999999999999999987         5555555543211      1114568999999999999975

>TIGR00963 secA preprotein translocase, SecA subunit

Probab=98.97  E-value=1.5e-09  Score=91.00  Aligned_cols=62  Identities=27%  Similarity=0.272  Sum_probs=53.6

Q ss_pred             CCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          57 RGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        57 ~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      +|. .|+++|..+.+.+..|+  ++.++||+|||+++.+|++....            .+.++.|++||++||.|.+
T Consensus        53 lg~-~p~~vQlig~~~l~~G~--Iaem~TGeGKTLva~lpa~l~aL------------~G~~V~VvTpt~~LA~qda  114 (745)
T TIGR00963        53 LGM-RPFDVQLIGGIALHKGK--IAEMKTGEGKTLTATLPAYLNAL------------TGKGVHVVTVNDYLAQRDA  114 (745)
T ss_pred             hCC-CccchHHhhhhhhcCCc--eeeecCCCccHHHHHHHHHHHHH------------hCCCEEEEcCCHHHHHHHH
Confidence            487 99999999999988887  89999999999999999964443            3456999999999999975

The proteins SecA-F and SecY, not all of which are necessary, comprise the standard prokaryotic protein translocation apparatus. Other, specialized translocation systems also exist but are not as broadly distributed. This model describes SecA, an essential member of the apparatus.

>TIGR01587 cas3_core CRISPR-associated helicase Cas3

Probab=98.93  E-value=1.5e-09  Score=84.22  Aligned_cols=46  Identities=26%  Similarity=0.243  Sum_probs=40.2

Q ss_pred             CeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          78 SAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        78 dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      |+++.+|||+|||++|+++++..+...          .+.+++|++|+++|+.|++
T Consensus         1 ~vvi~apTGsGKT~~~~~~~l~~~~~~----------~~~~ii~v~P~~~L~~q~~   46 (358)
T TIGR01587         1 LLVIEAPTGYGKTEAALLWALHSIKSQ----------KADRVIIALPTRATINAMY   46 (358)
T ss_pred             CEEEEeCCCCCHHHHHHHHHHHHHhhC----------CCCeEEEEeehHHHHHHHH
Confidence            689999999999999999999886432          4568999999999999986

This model represents the highly conserved core region of an alignment of Cas3, a protein found in association with CRISPR repeat elements in a broad range of bacteria and archaea. Cas3 appears to be a helicase, with regions found by pfam00270 (DEAD/DEAH box helicase) and pfam00271 (Helicase conserved C-terminal domain). Some but not all members have an N-terminal HD domain region (pfam01966) that is not included within this model.

>smart00489 DEXDc3 DEAD-like helicases superfamily

Probab=98.92  E-value=4.8e-09  Score=79.91  Aligned_cols=68  Identities=25%  Similarity=0.266  Sum_probs=52.8

Q ss_pred             CCCCChHHHHHHHHH----HHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHh
Q psy7268          58 GLTTPTEIQKYSIPT----LLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQI  132 (134)
Q Consensus        58 g~~~~t~iQ~~~i~~----~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi  132 (134)
                      .| .|++.|.+.+..    +..|.++++.+|||+|||++|++|++.++......      ..+.+++|.++|..+..|+
T Consensus         6 Py-~~r~~Q~~~m~~v~~~~~~~~~~~~eapTGtGKTl~~L~~al~~~~~~~~~------~~~~kvi~~t~T~~~~~q~   77 (289)
T smart00489        6 PY-EPYPIQYEFMEELKRVLDRGKIGILESPTGTGKTLSLLCLTLTWLRSFPER------IQKIKLIYLSRTVSEIEKR   77 (289)
T ss_pred             CC-CCCHHHHHHHHHHHHHHHcCCcEEEECCCCcchhHHHHHHHHHHHHhCccc------ccccceeEEeccHHHHHHH
Confidence            46 469999996554    45789999999999999999999999887642210      0234799999999987774

>smart00488 DEXDc2 DEAD-like helicases superfamily

Probab=98.92  E-value=4.8e-09  Score=79.91  Aligned_cols=68  Identities=25%  Similarity=0.266  Sum_probs=52.8

Q ss_pred             CCCCChHHHHHHHHH----HHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHh
Q psy7268          58 GLTTPTEIQKYSIPT----LLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQI  132 (134)
Q Consensus        58 g~~~~t~iQ~~~i~~----~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi  132 (134)
                      .| .|++.|.+.+..    +..|.++++.+|||+|||++|++|++.++......      ..+.+++|.++|..+..|+
T Consensus         6 Py-~~r~~Q~~~m~~v~~~~~~~~~~~~eapTGtGKTl~~L~~al~~~~~~~~~------~~~~kvi~~t~T~~~~~q~   77 (289)
T smart00488        6 PY-EPYPIQYEFMEELKRVLDRGKIGILESPTGTGKTLSLLCLTLTWLRSFPER------IQKIKLIYLSRTVSEIEKR   77 (289)
T ss_pred             CC-CCCHHHHHHHHHHHHHHHcCCcEEEECCCCcchhHHHHHHHHHHHHhCccc------ccccceeEEeccHHHHHHH
Confidence            46 469999996554    45789999999999999999999999887642210      0234799999999987774

>TIGR03714 secA2 accessory Sec system translocase SecA2

Probab=98.91  E-value=3.6e-09  Score=89.10  Aligned_cols=62  Identities=29%  Similarity=0.340  Sum_probs=50.8

Q ss_pred             CCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          57 RGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        57 ~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      +|. .|+++|......+..|  .++.++||+|||++|++|++....            .+..++|++|+++||.|.+
T Consensus        67 lgl-rpydVQlig~l~l~~G--~Iaem~TGeGKTLta~Lpa~l~aL------------~g~~V~VVTpn~yLA~Rda  128 (762)
T TIGR03714        67 LGM-FPYDVQVLGAIVLHQG--NIAEMKTGEGKTLTATMPLYLNAL------------TGKGAMLVTTNDYLAKRDA  128 (762)
T ss_pred             cCC-CccHHHHHHHHHhcCC--ceeEecCCcchHHHHHHHHHHHhh------------cCCceEEeCCCHHHHHHHH
Confidence            466 7788887777766666  689999999999999999876654            3456999999999999875

Members of this protein family are homologous to SecA and part of the accessory Sec system. This system, including both five core proteins for export and a variable number of proteins for glycosylation, operates in certain Gram-positive pathogens for the maturation and delivery of serine-rich glycoproteins such as the cell surface glycoprotein GspB in Streptococcus gordonii.

>PF04851 ResIII: Type III restriction enzyme, res subunit; InterPro: IPR006935 This entry represents a domain found in the N terminus of several proteins, including helicases, the R subunit (HsdR) of type I restriction endonucleases (3

Probab=98.87  E-value=5.4e-09  Score=72.93  Aligned_cols=58  Identities=28%  Similarity=0.350  Sum_probs=47.2

Q ss_pred             CChHHHHHHHHHHHc-------CCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          61 TPTEIQKYSIPTLLS-------GKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        61 ~~t~iQ~~~i~~~~~-------g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      .+++.|.+++..+..       .+.+++.+|||+|||.+++..+....             .  ++++++|+..|+.|..
T Consensus         3 ~lr~~Q~~ai~~i~~~~~~~~~~~~~ll~~~tGsGKT~~~~~~~~~l~-------------~--~~l~~~p~~~l~~Q~~   67 (184)
T PF04851_consen    3 KLRPYQQEAIARIINSLENKKEERRVLLNAPTGSGKTIIALALILELA-------------R--KVLIVAPNISLLEQWY   67 (184)
T ss_dssp             EE-HHHHHHHHHHHHHHHTTSGCSEEEEEESTTSSHHHHHHHHHHHHH-------------C--EEEEEESSHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHHhcCCCCCEEEEECCCCCcChhhhhhhhccc-------------c--ceeEecCHHHHHHHHH
Confidence            578999999998873       58899999999999999875444443             2  7999999999999974

1.21.3 from EC), the Res subunit of type III endonucleases (3.1.21.5 from EC), and the B subunit of excinuclease ABC (uvrB) [, , ].; GO: 0003677 DNA binding, 0005524 ATP binding, 0016787 hydrolase activity; PDB: 2Y3T_B 2W74_B 2FWR_A 2FZ4_A 3UWX_B 3H1T_A 3B6E_A 2FDC_A 1D9Z_A 1T5L_B ....

>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated

Probab=98.85  E-value=1.1e-08  Score=88.59  Aligned_cols=64  Identities=23%  Similarity=0.228  Sum_probs=54.4

Q ss_pred             CCCCChHHHHHHHHHHH----cCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          58 GLTTPTEIQKYSIPTLL----SGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        58 g~~~~t~iQ~~~i~~~~----~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      || .+.+-|.+.+..+.    .++.+++.|+||+|||++|++|.+.....           ++.+++|.++|+.|..|+.
T Consensus       255 ~~-e~R~~Q~~m~~~v~~~l~~~~~~~iEA~TGtGKTlaYLlpa~~~a~~-----------~~~~vvIsT~T~~LQ~Ql~  322 (928)
T PRK08074        255 KY-EKREGQQEMMKEVYTALRDSEHALIEAGTGTGKSLAYLLPAAYFAKK-----------KEEPVVISTYTIQLQQQLL  322 (928)
T ss_pred             CC-cCCHHHHHHHHHHHHHHhcCCCEEEECCCCCchhHHHHHHHHHHhhc-----------cCCeEEEEcCCHHHHHHHH
Confidence            77 78999999776544    67889999999999999999999876643           4567999999999999974

>COG4581 Superfamily II RNA helicase [DNA replication, recombination, and repair]

Probab=98.82  E-value=9.5e-09  Score=88.60  Aligned_cols=71  Identities=18%  Similarity=0.158  Sum_probs=61.4

Q ss_pred             HHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHH
Q psy7268          51 IDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVF  130 (134)
Q Consensus        51 ~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~  130 (134)
                      .......|| .+.++|++++-.+-+|.+|+++||||+|||++...++-..+.            .+-+++|.+|.++|.+
T Consensus       110 ~~~~~~~~F-~LD~fQ~~a~~~Ler~esVlV~ApTssGKTvVaeyAi~~al~------------~~qrviYTsPIKALsN  176 (1041)
T COG4581         110 APPAREYPF-ELDPFQQEAIAILERGESVLVCAPTSSGKTVVAEYAIALALR------------DGQRVIYTSPIKALSN  176 (1041)
T ss_pred             CcHHHhCCC-CcCHHHHHHHHHHhCCCcEEEEccCCCCcchHHHHHHHHHHH------------cCCceEeccchhhhhh
Confidence            344566789 899999999999999999999999999999998888777765            4556999999999999


Q ss_pred             HhcC
Q psy7268         131 QIGQ  134 (134)
Q Consensus       131 Qi~~  134 (134)
                      |.++
T Consensus       177 QKyr  180 (1041)
T COG4581         177 QKYR  180 (1041)
T ss_pred             hHHH
Confidence            9863

>PRK13766 Hef nuclease; Provisional

Probab=98.79  E-value=2.1e-08  Score=85.18  Aligned_cols=62  Identities=26%  Similarity=0.295  Sum_probs=53.5

Q ss_pred             CCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          60 TTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        60 ~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      -.+.+.|..++..++.+ |+++++|||+|||+++++++...+..           .+.++||++||++|+.|..
T Consensus        14 ~~~r~yQ~~~~~~~l~~-n~lv~~ptG~GKT~~a~~~i~~~l~~-----------~~~~vLvl~Pt~~L~~Q~~   75 (773)
T PRK13766         14 IEARLYQQLLAATALKK-NTLVVLPTGLGKTAIALLVIAERLHK-----------KGGKVLILAPTKPLVEQHA   75 (773)
T ss_pred             CCccHHHHHHHHHHhcC-CeEEEcCCCccHHHHHHHHHHHHHHh-----------CCCeEEEEeCcHHHHHHHH
Confidence            47788999999888877 89999999999999999998887732           4568999999999998864

>PRK09751 putative ATP-dependent helicase Lhr; Provisional

Probab=98.79  E-value=5e-09  Score=93.43  Aligned_cols=53  Identities=21%  Similarity=0.258  Sum_probs=40.5

Q ss_pred             EEcCCCCchhHHhHHHHHHHHHhhcCCCC-CCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          81 LVAETGCGKTLSFLAPLVQQILTWKSRPE-YKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        81 i~a~tGsGKT~~~~lpil~~~~~~~~~~~-~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      |++|||||||++|++|+++.+........ .....++.++|||+|+|+|+.|++
T Consensus         1 V~APTGSGKTLAA~LpaL~~Ll~~~~~~~~~~~~~~~~raLYISPLKALa~Dv~   54 (1490)
T PRK09751          1 VIAPTGSGKTLAAFLYALDRLFREGGEDTREAHKRKTSRILYISPIKALGTDVQ   54 (1490)
T ss_pred             CcCCCCcHHHHHHHHHHHHHHHhcccccccccccCCCCEEEEEeChHHHHHHHH
Confidence            57999999999999999999986431100 001124689999999999999986

>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional

Probab=98.77  E-value=4.8e-08  Score=82.36  Aligned_cols=64  Identities=28%  Similarity=0.325  Sum_probs=53.5

Q ss_pred             CCCCChHHHHHHHHHHH---c------CCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHH
Q psy7268          58 GLTTPTEIQKYSIPTLL---S------GKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGREL  128 (134)
Q Consensus        58 g~~~~t~iQ~~~i~~~~---~------g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~L  128 (134)
                      || .+.+-|.+.+..+.   .      ++.+++.|+||+|||++|++|.+.....           ++-++||-+.|+.|
T Consensus        23 ~~-e~R~~Q~~M~~~V~~al~~~~~~~~~~lviEAgTGtGKTlaYLlPai~~A~~-----------~~k~vVIST~T~~L   90 (697)
T PRK11747         23 GF-IPRAGQRQMIAEVAKTLAGEYLKDGRILVIEAGTGVGKTLSYLLAGIPIARA-----------EKKKLVISTATVAL   90 (697)
T ss_pred             CC-CcCHHHHHHHHHHHHHHhcccccccceEEEECCCCcchhHHHHHHHHHHHHH-----------cCCeEEEEcCCHHH
Confidence            78 77999999776654   3      3568899999999999999999877654           45679999999999


Q ss_pred             HHHhc
Q psy7268         129 VFQIG  133 (134)
Q Consensus       129 a~Qi~  133 (134)
                      -.|+.
T Consensus        91 QeQL~   95 (697)
T PRK11747         91 QEQLV   95 (697)
T ss_pred             HHHHH
Confidence            99984

>COG1110 Reverse gyrase [DNA replication, recombination, and repair]

Probab=98.77  E-value=4.1e-08  Score=84.12  Aligned_cols=74  Identities=31%  Similarity=0.339  Sum_probs=60.3

Q ss_pred             HHHHHHHHHC-CCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcH
Q psy7268          48 PEIIDIFTKR-GLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGR  126 (134)
Q Consensus        48 ~~i~~~l~~~-g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~  126 (134)
                      +++.+.+++. || .|+..|+.....+..|+++-+.||||.|||..-++..+..-.            .|.+++||+||+
T Consensus        69 e~~~~fF~k~~G~-~~ws~QR~WakR~~rg~SFaiiAPTGvGKTTfg~~~sl~~a~------------kgkr~yii~PT~  135 (1187)
T COG1110          69 EEFEEFFKKATGF-RPWSAQRVWAKRLVRGKSFAIIAPTGVGKTTFGLLMSLYLAK------------KGKRVYIIVPTT  135 (1187)
T ss_pred             HHHHHHHHHhhCC-CchHHHHHHHHHHHcCCceEEEcCCCCchhHHHHHHHHHHHh------------cCCeEEEEecCH
Confidence            4555566665 77 999999999999999999999999999999776555444332            567899999999


Q ss_pred             HHHHHhcC
Q psy7268         127 ELVFQIGQ  134 (134)
Q Consensus       127 ~La~Qi~~  134 (134)
                      .|+.|+++
T Consensus       136 ~Lv~Q~~~  143 (1187)
T COG1110         136 TLVRQVYE  143 (1187)
T ss_pred             HHHHHHHH
Confidence            99999863

>KOG0353|consensus

Probab=98.72  E-value=3.2e-08  Score=77.65  Aligned_cols=75  Identities=28%  Similarity=0.394  Sum_probs=65.0

Q ss_pred             ccCCCCHHHHHHHHHC-CCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEE
Q psy7268          42 EDTGLAPEIIDIFTKR-GLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLAL  120 (134)
Q Consensus        42 ~~~~l~~~i~~~l~~~-g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~l  120 (134)
                      ++++.+.+.-+.|++. ..+++.|.|..+|...+.|+|+++.-|||-||++||-+|.+.               ....+|
T Consensus        74 d~fpws~e~~~ilk~~f~lekfrplq~~ain~~ma~ed~~lil~tgggkslcyqlpal~---------------adg~al  138 (695)
T KOG0353|consen   74 DDFPWSDEAKDILKEQFHLEKFRPLQLAAINATMAGEDAFLILPTGGGKSLCYQLPALC---------------ADGFAL  138 (695)
T ss_pred             CCCCCchHHHHHHHHHhhHHhcChhHHHHhhhhhccCceEEEEeCCCccchhhhhhHHh---------------cCCceE
Confidence            4677888888887774 678899999999999999999999999999999999999886               344689


Q ss_pred             EEcCcHHHHHH
Q psy7268         121 IITPGRELVFQ  131 (134)
Q Consensus       121 il~Pt~~La~Q  131 (134)
                      +++|...|..+
T Consensus       139 vi~plislmed  149 (695)
T KOG0353|consen  139 VICPLISLMED  149 (695)
T ss_pred             eechhHHHHHH
Confidence            99999988754

>KOG0352|consensus

Probab=98.71  E-value=4.3e-08  Score=77.71  Aligned_cols=68  Identities=19%  Similarity=0.361  Sum_probs=56.4

Q ss_pred             HHHHHHHHC-CCCCC-hHHHHHHHHHHHcC-CCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCc
Q psy7268          49 EIIDIFTKR-GLTTP-TEIQKYSIPTLLSG-KSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPG  125 (134)
Q Consensus        49 ~i~~~l~~~-g~~~~-t~iQ~~~i~~~~~g-~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt  125 (134)
                      .+.++|++. |+.++ ++.|++++..+..+ .||.++.|||+||++||-+|.|-.               +...|+++|.
T Consensus         6 ~VreaLKK~FGh~kFKs~LQE~A~~c~VK~k~DVyVsMPTGaGKSLCyQLPaL~~---------------~gITIV~SPL   70 (641)
T KOG0352|consen    6 KVREALKKLFGHKKFKSRLQEQAINCIVKRKCDVYVSMPTGAGKSLCYQLPALVH---------------GGITIVISPL   70 (641)
T ss_pred             HHHHHHHHHhCchhhcChHHHHHHHHHHhccCcEEEeccCCCchhhhhhchHHHh---------------CCeEEEehHH
Confidence            455677774 77665 78999999998865 599999999999999999998864               2378999999


Q ss_pred             HHHHHH
Q psy7268         126 RELVFQ  131 (134)
Q Consensus       126 ~~La~Q  131 (134)
                      .+|+++
T Consensus        71 iALIkD   76 (641)
T KOG0352|consen   71 IALIKD   76 (641)
T ss_pred             HHHHHH
Confidence            999875

>KOG0354|consensus

Probab=98.71  E-value=3.7e-08  Score=82.39  Aligned_cols=62  Identities=24%  Similarity=0.252  Sum_probs=55.0

Q ss_pred             CCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHh
Q psy7268          60 TTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQI  132 (134)
Q Consensus        60 ~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi  132 (134)
                      -.+...|......++ |++++|++|||+|||+++..-+.+++...          ...++|+++|++-|+.|-
T Consensus        61 ~~lR~YQ~eivq~AL-gkNtii~lPTG~GKTfIAa~Vm~nh~rw~----------p~~KiVF~aP~~pLv~QQ  122 (746)
T KOG0354|consen   61 LELRNYQEELVQPAL-GKNTIIALPTGSGKTFIAAVIMKNHFEWR----------PKGKVVFLAPTRPLVNQQ  122 (746)
T ss_pred             ccccHHHHHHhHHhh-cCCeEEEeecCCCccchHHHHHHHHHhcC----------CcceEEEeeCCchHHHHH
Confidence            377889999999999 99999999999999999999999988653          347899999999999884

>PRK11664 ATP-dependent RNA helicase HrpB; Provisional

Probab=98.69  E-value=3.7e-08  Score=84.15  Aligned_cols=55  Identities=20%  Similarity=0.202  Sum_probs=45.2

Q ss_pred             HHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          67 KYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        67 ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      .+.+..+.++++++++|+||||||.+|.+++++...            .+.+++++.|+|++|.|++
T Consensus        11 ~~i~~~l~~~~~vvv~A~TGSGKTt~~pl~lL~~~~------------~~~~ilvlqPrR~aA~qia   65 (812)
T PRK11664         11 PELLTALKTAPQVLLKAPTGAGKSTWLPLQLLQHGG------------INGKIIMLEPRRLAARNVA   65 (812)
T ss_pred             HHHHHHHHhCCCEEEEcCCCCCHHHHHHHHHHHcCC------------cCCeEEEECChHHHHHHHH
Confidence            344555667899999999999999999999987532            2348999999999999986

>COG0514 RecQ Superfamily II DNA helicase [DNA replication, recombination, and repair]

Probab=98.68  E-value=5.5e-08  Score=79.99  Aligned_cols=66  Identities=29%  Similarity=0.434  Sum_probs=57.3

Q ss_pred             HHHHHH-CCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHH
Q psy7268          51 IDIFTK-RGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELV  129 (134)
Q Consensus        51 ~~~l~~-~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La  129 (134)
                      ...|++ .||..+.+-|.++|..+++|+|+++.-|||.||++||.+|.+-.              .| -.|||+|..+|-
T Consensus         6 ~~~L~~~fGy~~FR~gQ~evI~~~l~g~d~lvvmPTGgGKSlCyQiPAll~--------------~G-~TLVVSPLiSLM   70 (590)
T COG0514           6 QQVLKQVFGYASFRPGQQEIIDALLSGKDTLVVMPTGGGKSLCYQIPALLL--------------EG-LTLVVSPLISLM   70 (590)
T ss_pred             HHHHHHHhCccccCCCHHHHHHHHHcCCcEEEEccCCCCcchHhhhHHHhc--------------CC-CEEEECchHHHH
Confidence            345666 49999999999999999999999999999999999999998875              22 589999999987


Q ss_pred             HH
Q psy7268         130 FQ  131 (134)
Q Consensus       130 ~Q  131 (134)
                      .+
T Consensus        71 ~D   72 (590)
T COG0514          71 KD   72 (590)
T ss_pred             HH
Confidence            54

>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB

Probab=98.64  E-value=8.4e-08  Score=82.02  Aligned_cols=55  Identities=16%  Similarity=0.135  Sum_probs=46.3

Q ss_pred             HHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          67 KYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        67 ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      .+.+..+.++.+++++|+||||||..|.+++++...            .+.+++++.|+|++|.|++
T Consensus         8 ~~i~~~l~~~~~vIi~a~TGSGKTT~vpl~lL~~~~------------~~~~ilvlqPrR~aA~qiA   62 (819)
T TIGR01970         8 PALRDALAAHPQVVLEAPPGAGKSTAVPLALLDAPG------------IGGKIIMLEPRRLAARSAA   62 (819)
T ss_pred             HHHHHHHHcCCcEEEECCCCCCHHHHHHHHHHHhhc------------cCCeEEEEeCcHHHHHHHH
Confidence            345556667889999999999999999999998752            3458999999999999986

This model represents HrpB, one of two related but uncharacterized DEAH-box ATP-dependent helicases in many Proteobacteria, but also in a few species of other lineages. The member from Rhizobium meliloti has been designated HelO. HrpB is typically about 800 residues in length, while its paralog HrpA (TIGR01967), also uncharacterized, is about 1300 amino acids long. Related characterized eukarotic proteins are RNA helicases associated with pre-mRNA processing.

>COG1199 DinG Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]

Probab=98.63  E-value=1.9e-07  Score=78.06  Aligned_cols=64  Identities=25%  Similarity=0.291  Sum_probs=54.5

Q ss_pred             CCCChHHHHHHHHHHH----cCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          59 LTTPTEIQKYSIPTLL----SGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        59 ~~~~t~iQ~~~i~~~~----~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      ...+.+.|.+.+..+.    .|+.+++.||||+|||++|++|++.....           .+.+++|.++|+.|-.|+.
T Consensus        13 ~~~~r~~Q~~~~~~v~~a~~~~~~~~iEapTGtGKTl~yL~~al~~~~~-----------~~~~viist~t~~lq~q~~   80 (654)
T COG1199          13 GFEPRPEQREMAEAVAEALKGGEGLLIEAPTGTGKTLAYLLPALAYARE-----------EGKKVIISTRTKALQEQLL   80 (654)
T ss_pred             CCCCCHHHHHHHHHHHHHHcCCCcEEEECCCCccHHHHHHHHHHHHHHH-----------cCCcEEEECCCHHHHHHHH
Confidence            3489999999996543    45669999999999999999999998865           4467999999999999875

>PRK13104 secA preprotein translocase subunit SecA; Reviewed

Probab=98.62  E-value=7.7e-08  Score=82.18  Aligned_cols=62  Identities=26%  Similarity=0.194  Sum_probs=50.1

Q ss_pred             CCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          57 RGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        57 ~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      +|. .|+++|-..--.+..|+  +..++||+|||++|.+|++....            .+..++|++||++||.|.+
T Consensus        79 lg~-~~ydvQliGg~~Lh~G~--Iaem~TGeGKTL~a~Lpa~~~al------------~G~~V~VvTpn~yLA~qd~  140 (896)
T PRK13104         79 LGL-RHFDVQLIGGMVLHEGN--IAEMRTGEGKTLVATLPAYLNAI------------SGRGVHIVTVNDYLAKRDS  140 (896)
T ss_pred             cCC-CcchHHHhhhhhhccCc--cccccCCCCchHHHHHHHHHHHh------------cCCCEEEEcCCHHHHHHHH
Confidence            366 77888877665555555  68999999999999999998775            3446999999999999975

>COG1061 SSL2 DNA or RNA helicases of superfamily II [Transcription / DNA replication, recombination, and repair]

Probab=98.58  E-value=1.8e-07  Score=75.15  Aligned_cols=58  Identities=22%  Similarity=0.348  Sum_probs=48.5

Q ss_pred             CChHHHHHHHHHHHc----CCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          61 TPTEIQKYSIPTLLS----GKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        61 ~~t~iQ~~~i~~~~~----g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      .+.+.|++++..+.+    ++..+++.|||+|||+.++..+-...               ..+|||+|+++|+.|-+
T Consensus        36 ~lr~yQ~~al~a~~~~~~~~~~gvivlpTGaGKT~va~~~~~~~~---------------~~~Lvlv~~~~L~~Qw~   97 (442)
T COG1061          36 ELRPYQEEALDALVKNRRTERRGVIVLPTGAGKTVVAAEAIAELK---------------RSTLVLVPTKELLDQWA   97 (442)
T ss_pred             CCcHHHHHHHHHHHhhcccCCceEEEeCCCCCHHHHHHHHHHHhc---------------CCEEEEECcHHHHHHHH
Confidence            689999999999987    88999999999999998855443321               22999999999999963

>KOG0951|consensus

Probab=98.52  E-value=3e-07  Score=80.33  Aligned_cols=84  Identities=24%  Similarity=0.245  Sum_probs=65.7

Q ss_pred             CCHHHHHHHHHCCCCCChHHHHHHHHHHHcCC-CeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcC
Q psy7268          46 LAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGK-SAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITP  124 (134)
Q Consensus        46 l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~-dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~P  124 (134)
                      +++.-..++.  |...++++|.......+.+. ++++|||||+|||...++.+|+.+-.... .....++...+++|++|
T Consensus       296 lP~Wnq~aF~--g~~sLNrIQS~v~daAl~~~EnmLlCAPTGaGKTNVAvLtiLqel~~h~r-~dgs~nl~~fKIVYIAP  372 (1674)
T KOG0951|consen  296 LPKWNQPAFF--GKQSLNRIQSKVYDAALRGDENMLLCAPTGAGKTNVAVLTILQELGNHLR-EDGSVNLAPFKIVYIAP  372 (1674)
T ss_pred             Ccchhhhhcc--cchhhhHHHHHHHHHHhcCcCcEEEeccCCCCchHHHHHHHHHHHhcccc-cccceecccceEEEEee
Confidence            3333344443  67779999999999988765 79999999999999999999999976543 23344456779999999


Q ss_pred             cHHHHHHh
Q psy7268         125 GRELVFQI  132 (134)
Q Consensus       125 t~~La~Qi  132 (134)
                      +++|++-+
T Consensus       373 mKaLvqE~  380 (1674)
T KOG0951|consen  373 MKALVQEM  380 (1674)
T ss_pred             HHHHHHHH
Confidence            99999764

>PRK09694 helicase Cas3; Provisional

Probab=98.45  E-value=5.5e-07  Score=77.51  Aligned_cols=64  Identities=22%  Similarity=0.163  Sum_probs=48.8

Q ss_pred             CCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          60 TTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        60 ~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      ..|+|+|+.+......+.-+++.+|||+|||.+.+..+.. +....         ...++++..||+++++|++
T Consensus       285 ~~p~p~Q~~~~~~~~~pgl~ileApTGsGKTEAAL~~A~~-l~~~~---------~~~gi~~aLPT~Atan~m~  348 (878)
T PRK09694        285 YQPRQLQTLVDALPLQPGLTIIEAPTGSGKTEAALAYAWR-LIDQG---------LADSIIFALPTQATANAML  348 (878)
T ss_pred             CCChHHHHHHHhhccCCCeEEEEeCCCCCHHHHHHHHHHH-HHHhC---------CCCeEEEECcHHHHHHHHH
Confidence            3899999988654444566899999999999998766553 33211         3457999999999999886

>cd00046 DEXDc DEAD-like helicases superfamily

Probab=98.45  E-value=4.6e-07  Score=59.59  Aligned_cols=47  Identities=34%  Similarity=0.581  Sum_probs=38.7

Q ss_pred             CCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          77 KSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        77 ~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      +++++.++||+|||..++..+.......          ...+++|++|++.++.|..
T Consensus         1 ~~~~i~~~~G~GKT~~~~~~~~~~~~~~----------~~~~~lv~~p~~~l~~~~~   47 (144)
T cd00046           1 RDVLLAAPTGSGKTLAALLPILELLDSL----------KGGQVLVLAPTRELANQVA   47 (144)
T ss_pred             CCEEEECCCCCchhHHHHHHHHHHHhcc----------cCCCEEEEcCcHHHHHHHH
Confidence            4689999999999999988877766541          3467999999999999864

A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.

>COG1200 RecG RecG-like helicase [DNA replication, recombination, and repair / Transcription]

Probab=98.39  E-value=1.1e-06  Score=73.00  Aligned_cols=76  Identities=22%  Similarity=0.239  Sum_probs=63.5

Q ss_pred             CCCHHHHHH-HHHCCCCCChHHHHHHHHHHHcC------CCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCc
Q psy7268          45 GLAPEIIDI-FTKRGLTTPTEIQKYSIPTLLSG------KSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAP  117 (134)
Q Consensus        45 ~l~~~i~~~-l~~~g~~~~t~iQ~~~i~~~~~g------~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~  117 (134)
                      ....++++. +..+.| .+|..|++++..|...      -+-+++|--|||||++.+++++..+.            .|.
T Consensus       246 ~~~~~l~~~~~~~LPF-~LT~aQ~~vi~EI~~Dl~~~~~M~RLlQGDVGSGKTvVA~laml~ai~------------~G~  312 (677)
T COG1200         246 PANGELLAKFLAALPF-KLTNAQKRVIKEILADLASPVPMNRLLQGDVGSGKTVVALLAMLAAIE------------AGY  312 (677)
T ss_pred             CccHHHHHHHHHhCCC-CccHHHHHHHHHHHhhhcCchhhHHHhccCcCCCHHHHHHHHHHHHHH------------cCC
Confidence            344555544 466799 9999999999999843      25789999999999999999999885            788


Q ss_pred             EEEEEcCcHHHHHHhc
Q psy7268         118 LALIITPGRELVFQIG  133 (134)
Q Consensus       118 ~~lil~Pt~~La~Qi~  133 (134)
                      ++..++||.-||.|=+
T Consensus       313 Q~ALMAPTEILA~QH~  328 (677)
T COG1200         313 QAALMAPTEILAEQHY  328 (677)
T ss_pred             eeEEeccHHHHHHHHH
Confidence            9999999999999965

>PRK11448 hsdR type I restriction enzyme EcoKI subunit R; Provisional

Probab=98.36  E-value=2.1e-06  Score=75.74  Aligned_cols=63  Identities=24%  Similarity=0.218  Sum_probs=49.6

Q ss_pred             CChHHHHHHHHHHH----cC-CCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          61 TPTEIQKYSIPTLL----SG-KSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        61 ~~t~iQ~~~i~~~~----~g-~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      .+.+.|.+++..+.    +| +.++++.+||||||.+. +.++.++.+..         ...++|+++|+++|+.|..
T Consensus       413 ~lR~YQ~~AI~ai~~a~~~g~r~~Ll~maTGSGKT~ta-i~li~~L~~~~---------~~~rVLfLvDR~~L~~Qa~  480 (1123)
T PRK11448        413 GLRYYQEDAIQAVEKAIVEGQREILLAMATGTGKTRTA-IALMYRLLKAK---------RFRRILFLVDRSALGEQAE  480 (1123)
T ss_pred             CCCHHHHHHHHHHHHHHHhccCCeEEEeCCCCCHHHHH-HHHHHHHHhcC---------ccCeEEEEecHHHHHHHHH
Confidence            58999999998765    33 57999999999999885 44556555432         3468999999999999975

>KOG0351|consensus

Probab=98.33  E-value=4.9e-07  Score=78.03  Aligned_cols=69  Identities=25%  Similarity=0.317  Sum_probs=58.1

Q ss_pred             HHHHHHHH-CCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHH
Q psy7268          49 EIIDIFTK-RGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRE  127 (134)
Q Consensus        49 ~i~~~l~~-~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~  127 (134)
                      +.+..+.. .|...+.+-|.++|...+.|+|+++..|||.||.+||-+|.+-.               +.-.|+|+|..+
T Consensus       251 ~~~~~l~~~Fg~~~FR~~Q~eaI~~~l~Gkd~fvlmpTG~GKSLCYQlPA~l~---------------~gitvVISPL~S  315 (941)
T KOG0351|consen  251 ELELLLKEVFGHKGFRPNQLEAINATLSGKDCFVLMPTGGGKSLCYQLPALLL---------------GGVTVVISPLIS  315 (941)
T ss_pred             HHHHHHHHHhccccCChhHHHHHHHHHcCCceEEEeecCCceeeEeecccccc---------------CCceEEeccHHH
Confidence            34444444 59999999999999999999999999999999999998887652               336899999999


Q ss_pred             HHHHh
Q psy7268         128 LVFQI  132 (134)
Q Consensus       128 La~Qi  132 (134)
                      |.++.
T Consensus       316 Lm~DQ  320 (941)
T KOG0351|consen  316 LMQDQ  320 (941)
T ss_pred             HHHHH
Confidence            98753

>TIGR00604 rad3 DNA repair helicase (rad3)

Probab=98.32  E-value=2.3e-06  Score=72.39  Aligned_cols=66  Identities=20%  Similarity=0.163  Sum_probs=53.0

Q ss_pred             CCCCChHHHHHHHHHHH----cCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHh
Q psy7268          58 GLTTPTEIQKYSIPTLL----SGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQI  132 (134)
Q Consensus        58 g~~~~t~iQ~~~i~~~~----~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi  132 (134)
                      .|..++|.|.+.+..+.    .|.++++.+|||+|||++.+.|.+.......         ...+++|.+.|..-..|+
T Consensus         7 Py~~~y~~Q~~~m~~v~~~l~~~~~~llEsPTGtGKTlslL~~aL~~~~~~~---------~~~kIiy~sRThsQl~q~   76 (705)
T TIGR00604         7 PYEKIYPEQRSYMRDLKRSLDRGDEAILEMPSGTGKTISLLSLILAYQQEKP---------EVRKIIYASRTHSQLEQA   76 (705)
T ss_pred             CCCCCCHHHHHHHHHHHHHhccCCceEEeCCCCCCccHHHHHHHHHHHHhcc---------ccccEEEEcccchHHHHH
Confidence            57667999999887654    6889999999999999999999999875422         336788888887766665

All proteins in this family for which funcitons are known are DNA-DNA helicases that funciton in the initiation of transcription and nucleotide excision repair as part of the TFIIH complex. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>PRK12904 preprotein translocase subunit SecA; Reviewed

Probab=98.31  E-value=1.4e-06  Score=74.33  Aligned_cols=61  Identities=25%  Similarity=0.215  Sum_probs=50.4

Q ss_pred             CCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHH-HHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          57 RGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLV-QQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        57 ~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil-~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      +|. .|+++|-..--.+..|+  +..+.||+|||+++.+|++ +.+             .|..+-|++||.+||.|.+
T Consensus        78 lg~-~~~dvQlig~l~L~~G~--Iaem~TGeGKTLva~lpa~l~aL-------------~G~~V~IvTpn~yLA~rd~  139 (830)
T PRK12904         78 LGM-RHFDVQLIGGMVLHEGK--IAEMKTGEGKTLVATLPAYLNAL-------------TGKGVHVVTVNDYLAKRDA  139 (830)
T ss_pred             hCC-CCCccHHHhhHHhcCCc--hhhhhcCCCcHHHHHHHHHHHHH-------------cCCCEEEEecCHHHHHHHH
Confidence            477 88999998887776775  7899999999999999996 554             3445779999999999975

>PF13086 AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV_A 2XZP_A 2GK6_A 2GK7_A 2GJK_A

Probab=98.25  E-value=4e-06  Score=60.38  Aligned_cols=69  Identities=22%  Similarity=0.307  Sum_probs=44.5

Q ss_pred             CChHHHHHHHHHHHcCCC-eEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          61 TPTEIQKYSIPTLLSGKS-AILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        61 ~~t~iQ~~~i~~~~~g~d-vli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      ++++-|..++..+++..+ .+|.||+|||||.... .++..+.....   ......+.++|+++|+..-+.++.
T Consensus         1 ~ln~~Q~~Ai~~~~~~~~~~~i~GpPGTGKT~~l~-~~i~~~~~~~~---~~~~~~~~~il~~~~sN~avd~~~   70 (236)
T PF13086_consen    1 KLNESQREAIQSALSSNGITLIQGPPGTGKTTTLA-SIIAQLLQRFK---SRSADRGKKILVVSPSNAAVDNIL   70 (236)
T ss_dssp             ---HHHHHHHHHHCTSSE-EEEE-STTSSHHHHHH-HHHHHH----------HCCCSS-EEEEESSHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHcCCCCEEEECCCCCChHHHHH-HHHHHhccchh---hhhhhccccceeecCCchhHHHHH
Confidence            357899999999999998 9999999999995543 44444421000   001126778999999998877653

>COG1111 MPH1 ERCC4-like helicases [DNA replication, recombination, and repair]

Probab=98.23  E-value=4.6e-06  Score=67.29  Aligned_cols=60  Identities=23%  Similarity=0.298  Sum_probs=48.5

Q ss_pred             CChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHh
Q psy7268          61 TPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQI  132 (134)
Q Consensus        61 ~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi  132 (134)
                      .+...|....-..+.+ |.+++.|||-|||...++-+..++...          .+ ++|+++||+-|+.|=
T Consensus        15 e~R~YQ~~i~a~al~~-NtLvvlPTGLGKT~IA~~V~~~~l~~~----------~~-kvlfLAPTKPLV~Qh   74 (542)
T COG1111          15 EPRLYQLNIAAKALFK-NTLVVLPTGLGKTFIAAMVIANRLRWF----------GG-KVLFLAPTKPLVLQH   74 (542)
T ss_pred             cHHHHHHHHHHHHhhc-CeEEEecCCccHHHHHHHHHHHHHHhc----------CC-eEEEecCCchHHHHH
Confidence            4556677666556555 889999999999999988888888653          34 899999999999984

>PRK13107 preprotein translocase subunit SecA; Reviewed

Probab=98.15  E-value=4.1e-06  Score=71.82  Aligned_cols=62  Identities=24%  Similarity=0.143  Sum_probs=49.0

Q ss_pred             CCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          57 RGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        57 ~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      .|. .|+++|-..--.+..|+  +...+||.|||+++.+|++...+            .+..+.|++|+.+||.|..
T Consensus        79 lgm-~~ydVQliGgl~L~~G~--IaEm~TGEGKTL~a~lp~~l~al------------~g~~VhIvT~ndyLA~RD~  140 (908)
T PRK13107         79 FEM-RHFDVQLLGGMVLDSNR--IAEMRTGEGKTLTATLPAYLNAL------------TGKGVHVITVNDYLARRDA  140 (908)
T ss_pred             hCC-CcCchHHhcchHhcCCc--cccccCCCCchHHHHHHHHHHHh------------cCCCEEEEeCCHHHHHHHH
Confidence            366 77888876554444444  68999999999999999988775            3455999999999999864

>PF13245 AAA_19: Part of AAA domain

Probab=98.15  E-value=1.2e-05  Score=49.54  Aligned_cols=57  Identities=18%  Similarity=0.344  Sum_probs=37.4

Q ss_pred             HHHHHHcCCC-eEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          69 SIPTLLSGKS-AILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        69 ~i~~~~~g~d-vli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      ++...+++.+ +++.+|+|||||...+--+...+....       . .+.++++++|++..+..+.
T Consensus         2 av~~al~~~~~~vv~g~pGtGKT~~~~~~i~~l~~~~~-------~-~~~~vlv~a~t~~aa~~l~   59 (76)
T PF13245_consen    2 AVRRALAGSPLFVVQGPPGTGKTTTLAARIAELLAARA-------D-PGKRVLVLAPTRAAADELR   59 (76)
T ss_pred             HHHHHHhhCCeEEEECCCCCCHHHHHHHHHHHHHHHhc-------C-CCCeEEEECCCHHHHHHHH
Confidence            3443334455 555999999999776555444442111       0 2567999999999998774

>TIGR00603 rad25 DNA repair helicase rad25

Probab=98.09  E-value=9.2e-06  Score=68.74  Aligned_cols=57  Identities=23%  Similarity=0.297  Sum_probs=45.2

Q ss_pred             CChHHHHHHHHHHH-cC--CCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHh
Q psy7268          61 TPTEIQKYSIPTLL-SG--KSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQI  132 (134)
Q Consensus        61 ~~t~iQ~~~i~~~~-~g--~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi  132 (134)
                      .+.+.|.+++..++ +|  +..+++.|||+|||+..+..+ ..+              +.++|||||+.+|+.|-
T Consensus       255 ~LRpYQ~eAl~~~~~~gr~r~GIIvLPtGaGKTlvai~aa-~~l--------------~k~tLILvps~~Lv~QW  314 (732)
T TIGR00603       255 QIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKSLVGVTAA-CTV--------------KKSCLVLCTSAVSVEQW  314 (732)
T ss_pred             CcCHHHHHHHHHHHhcCCCCCcEEEeCCCCChHHHHHHHH-HHh--------------CCCEEEEeCcHHHHHHH
Confidence            57889999998877 44  368899999999999986443 333              13499999999999885

All proteins in this family for which functions are known are DNA-DNA helicases used for the initiation of nucleotide excision repair and transacription as part of the TFIIH complex.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>KOG0947|consensus

Probab=98.02  E-value=1.4e-05  Score=68.64  Aligned_cols=64  Identities=22%  Similarity=0.147  Sum_probs=54.3

Q ss_pred             CCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          57 RGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        57 ~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      .+| .+..+|++||-++.+|.+|++.|+|.+|||+++..++...-.            .+.+++|-+|-++|.+|=+
T Consensus       294 ~pF-elD~FQk~Ai~~lerg~SVFVAAHTSAGKTvVAEYAialaq~------------h~TR~iYTSPIKALSNQKf  357 (1248)
T KOG0947|consen  294 YPF-ELDTFQKEAIYHLERGDSVFVAAHTSAGKTVVAEYAIALAQK------------HMTRTIYTSPIKALSNQKF  357 (1248)
T ss_pred             CCC-CccHHHHHHHHHHHcCCeEEEEecCCCCcchHHHHHHHHHHh------------hccceEecchhhhhccchH
Confidence            477 889999999999999999999999999999996665543322            5678999999999999854

>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]

Probab=98.00  E-value=3.4e-05  Score=65.36  Aligned_cols=61  Identities=23%  Similarity=0.329  Sum_probs=50.8

Q ss_pred             CChHHHHHHHHHHHcC----CCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          61 TPTEIQKYSIPTLLSG----KSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        61 ~~t~iQ~~~i~~~~~g----~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      .+++-|+.+...+...    ...++.+.||||||.+|+-.+-..+.            .|.++|+++|-.+|..|+.
T Consensus       198 ~Ln~~Q~~a~~~i~~~~~~~~~~Ll~GvTGSGKTEvYl~~i~~~L~------------~GkqvLvLVPEI~Ltpq~~  262 (730)
T COG1198         198 ALNQEQQAAVEAILSSLGGFAPFLLDGVTGSGKTEVYLEAIAKVLA------------QGKQVLVLVPEIALTPQLL  262 (730)
T ss_pred             ccCHHHHHHHHHHHHhcccccceeEeCCCCCcHHHHHHHHHHHHHH------------cCCEEEEEeccccchHHHH
Confidence            6688999999988755    56899999999999999666555554            5778999999999999874

>PF00580 UvrD-helicase: UvrD/REP helicase N-terminal domain; InterPro: IPR000212 Members of this family are helicases that catalyse ATP dependent unwinding of double stranded DNA to single stranded DNA

Probab=97.87  E-value=4.5e-05  Score=57.41  Aligned_cols=61  Identities=18%  Similarity=0.207  Sum_probs=44.5

Q ss_pred             ChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHh
Q psy7268          62 PTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQI  132 (134)
Q Consensus        62 ~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi  132 (134)
                      +|+-|.+++..  ...+++|.|..|||||.+.+-=++..+....        ....+.++++.|+..+..+
T Consensus         1 l~~eQ~~~i~~--~~~~~lV~a~AGSGKT~~l~~ri~~ll~~~~--------~~~~~Il~lTft~~aa~e~   61 (315)
T PF00580_consen    1 LTDEQRRIIRS--TEGPLLVNAGAGSGKTTTLLERIAYLLYEGG--------VPPERILVLTFTNAAAQEM   61 (315)
T ss_dssp             S-HHHHHHHHS---SSEEEEEE-TTSSHHHHHHHHHHHHHHTSS--------STGGGEEEEESSHHHHHHH
T ss_pred             CCHHHHHHHhC--CCCCEEEEeCCCCCchHHHHHHHHHhhcccc--------CChHHheecccCHHHHHHH
Confidence            47789998877  6778999999999999988666666555431        1345699999999988765

THe family includes both Rep and UvrD helcases. The Rep family helicases are composed of four structural domains []. The Rep proteins function as dimers.; GO: 0003677 DNA binding, 0004003 ATP-dependent DNA helicase activity, 0005524 ATP binding; PDB: 1UAA_B 1W36_B 3K70_B 2IS6_B 3LFU_A 2IS2_B 2IS1_B 2IS4_A 1QHG_A 1PJR_A ....

>TIGR00348 hsdR type I site-specific deoxyribonuclease, HsdR family

Probab=97.87  E-value=3.2e-05  Score=65.18  Aligned_cols=63  Identities=19%  Similarity=0.332  Sum_probs=47.0

Q ss_pred             CChHHHHHHHHHHH----c------CCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHH
Q psy7268          61 TPTEIQKYSIPTLL----S------GKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVF  130 (134)
Q Consensus        61 ~~t~iQ~~~i~~~~----~------g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~  130 (134)
                      .+...|..++..+.    .      .+..++..+||||||++.+..+...+ ...         ..+++|+|+|.++|..
T Consensus       238 ~~r~~Q~~av~~~~~~~~~~~~~~~~~~gli~~~TGsGKT~t~~~la~~l~-~~~---------~~~~vl~lvdR~~L~~  307 (667)
T TIGR00348       238 YQRYMQYRAVKKIVESITRKTWGKDERGGLIWHTQGSGKTLTMLFAARKAL-ELL---------KNPKVFFVVDRRELDY  307 (667)
T ss_pred             ehHHHHHHHHHHHHHHHHhcccCCCCceeEEEEecCCCccHHHHHHHHHHH-hhc---------CCCeEEEEECcHHHHH
Confidence            36778999998754    2      24688999999999988755443333 211         5678999999999999


Q ss_pred             Hhc
Q psy7268         131 QIG  133 (134)
Q Consensus       131 Qi~  133 (134)
                      |..
T Consensus       308 Q~~  310 (667)
T TIGR00348       308 QLM  310 (667)
T ss_pred             HHH
Confidence            975

Members of this family are assumed to differ from each other in DNA site specificity.

>PF13604 AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL_A 3E1S_A 3GP8_A

Probab=97.82  E-value=0.0001  Score=53.12  Aligned_cols=61  Identities=18%  Similarity=0.283  Sum_probs=42.8

Q ss_pred             CChHHHHHHHHHHHcCC--CeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          61 TPTEIQKYSIPTLLSGK--SAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        61 ~~t~iQ~~~i~~~~~g~--dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      ++++-|..++..++.+.  -.++.|+.|+|||... -.+...+..           .+.++++++||...+..+.
T Consensus         1 ~L~~~Q~~a~~~~l~~~~~~~~l~G~aGtGKT~~l-~~~~~~~~~-----------~g~~v~~~apT~~Aa~~L~   63 (196)
T PF13604_consen    1 TLNEEQREAVRAILTSGDRVSVLQGPAGTGKTTLL-KALAEALEA-----------AGKRVIGLAPTNKAAKELR   63 (196)
T ss_dssp             -S-HHHHHHHHHHHHCTCSEEEEEESTTSTHHHHH-HHHHHHHHH-----------TT--EEEEESSHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHhcCCeEEEEEECCCCCHHHHH-HHHHHHHHh-----------CCCeEEEECCcHHHHHHHH
Confidence            36889999999997544  3677899999999653 344544443           4578999999998877653

>PRK12906 secA preprotein translocase subunit SecA; Reviewed

Probab=97.81  E-value=7.6e-05  Score=63.72  Aligned_cols=60  Identities=28%  Similarity=0.303  Sum_probs=52.2

Q ss_pred             CCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHH
Q psy7268          57 RGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQ  131 (134)
Q Consensus        57 ~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Q  131 (134)
                      .|. .|+++|-..--.+..|+  +..-.||+|||++..+|++....            .|.++-+++||..||.|
T Consensus        77 ~g~-~~~dvQlig~l~l~~G~--iaEm~TGEGKTLvA~l~a~l~al------------~G~~v~vvT~neyLA~R  136 (796)
T PRK12906         77 LGL-RPFDVQIIGGIVLHEGN--IAEMKTGEGKTLTATLPVYLNAL------------TGKGVHVVTVNEYLSSR  136 (796)
T ss_pred             hCC-CCchhHHHHHHHHhcCC--cccccCCCCCcHHHHHHHHHHHH------------cCCCeEEEeccHHHHHh
Confidence            477 89999998887777777  78999999999999999888776            67789999999999987

>KOG0948|consensus

Probab=97.76  E-value=3.4e-05  Score=65.08  Aligned_cols=64  Identities=20%  Similarity=0.179  Sum_probs=56.8

Q ss_pred             CCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          57 RGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        57 ~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      +-| .+.|+|+.+|-++-++.+|++.|-|..|||.++..+|...+..            .-|+||-+|-++|.+|=|
T Consensus       126 YPF-~LDpFQ~~aI~Cidr~eSVLVSAHTSAGKTVVAeYAIA~sLr~------------kQRVIYTSPIKALSNQKY  189 (1041)
T KOG0948|consen  126 YPF-TLDPFQSTAIKCIDRGESVLVSAHTSAGKTVVAEYAIAMSLRE------------KQRVIYTSPIKALSNQKY  189 (1041)
T ss_pred             CCc-ccCchHhhhhhhhcCCceEEEEeecCCCcchHHHHHHHHHHHh------------cCeEEeeChhhhhcchhH
Confidence            345 6789999999999999999999999999999999998888864            457999999999999865

>COG1197 Mfd Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]

Probab=97.69  E-value=0.00033  Score=61.59  Aligned_cols=76  Identities=20%  Similarity=0.203  Sum_probs=62.1

Q ss_pred             CCCHHHHHHHHH-CCCCCChHHHHHHHHHHH----cCC--CeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCc
Q psy7268          45 GLAPEIIDIFTK-RGLTTPTEIQKYSIPTLL----SGK--SAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAP  117 (134)
Q Consensus        45 ~l~~~i~~~l~~-~g~~~~t~iQ~~~i~~~~----~g~--dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~  117 (134)
                      +.+.+..+.+.+ .+| ..|+=|..||..+.    +++  |-++||--|-|||.+++=++...+.            .|.
T Consensus       578 ~~d~~~q~~F~~~FPy-eET~DQl~AI~eVk~DM~~~kpMDRLiCGDVGFGKTEVAmRAAFkAV~------------~GK  644 (1139)
T COG1197         578 PPDTEWQEEFEASFPY-EETPDQLKAIEEVKRDMESGKPMDRLICGDVGFGKTEVAMRAAFKAVM------------DGK  644 (1139)
T ss_pred             CCChHHHHHHHhcCCC-cCCHHHHHHHHHHHHHhccCCcchheeecCcCCcHHHHHHHHHHHHhc------------CCC
Confidence            344566666666 477 66999999999987    454  8899999999999999877777764            678


Q ss_pred             EEEEEcCcHHHHHHhc
Q psy7268         118 LALIITPGRELVFQIG  133 (134)
Q Consensus       118 ~~lil~Pt~~La~Qi~  133 (134)
                      |+.+++||.-||+|=+
T Consensus       645 QVAvLVPTTlLA~QHy  660 (1139)
T COG1197         645 QVAVLVPTTLLAQQHY  660 (1139)
T ss_pred             eEEEEcccHHhHHHHH
Confidence            9999999999999944

>PRK12326 preprotein translocase subunit SecA; Reviewed

Probab=97.68  E-value=0.00023  Score=60.26  Aligned_cols=61  Identities=28%  Similarity=0.290  Sum_probs=52.5

Q ss_pred             CCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHh
Q psy7268          57 RGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQI  132 (134)
Q Consensus        57 ~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi  132 (134)
                      +|. .|+++|-...-.++.|+  ++.-.||.|||++..+|+.....            .|.++.+++|+..||.|=
T Consensus        75 lg~-r~ydvQlig~l~Ll~G~--VaEM~TGEGKTLvA~l~a~l~AL------------~G~~VhvvT~NdyLA~RD  135 (764)
T PRK12326         75 LGL-RPFDVQLLGALRLLAGD--VIEMATGEGKTLAGAIAAAGYAL------------QGRRVHVITVNDYLARRD  135 (764)
T ss_pred             cCC-CcchHHHHHHHHHhCCC--cccccCCCCHHHHHHHHHHHHHH------------cCCCeEEEcCCHHHHHHH
Confidence            477 89999999998888874  56999999999999998887765            577899999999999873

>TIGR00376 DNA helicase, putative

Probab=97.68  E-value=0.0002  Score=60.11  Aligned_cols=60  Identities=23%  Similarity=0.327  Sum_probs=46.0

Q ss_pred             CChHHHHHHHHHHHcC-CCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHh
Q psy7268          61 TPTEIQKYSIPTLLSG-KSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQI  132 (134)
Q Consensus        61 ~~t~iQ~~~i~~~~~g-~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi  132 (134)
                      .+++.|..++..++.. ..+++.||+|+|||.... .++..+..           .+.++++++||..-+.++
T Consensus       157 ~ln~~Q~~Av~~~l~~~~~~lI~GpPGTGKT~t~~-~ii~~~~~-----------~g~~VLv~a~sn~Avd~l  217 (637)
T TIGR00376       157 NLNESQKEAVSFALSSKDLFLIHGPPGTGKTRTLV-ELIRQLVK-----------RGLRVLVTAPSNIAVDNL  217 (637)
T ss_pred             CCCHHHHHHHHHHhcCCCeEEEEcCCCCCHHHHHH-HHHHHHHH-----------cCCCEEEEcCcHHHHHHH
Confidence            5689999999998876 568899999999996653 34444433           455899999999777665

The gene product may represent a DNA helicase. Eukaryotic members of this family have been characterized as binding certain single-stranded G-rich DNA sequences (GGGGT and GGGCT). A number of related proteins are characterized as helicases.

>COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms]

Probab=97.62  E-value=0.0002  Score=61.09  Aligned_cols=66  Identities=20%  Similarity=0.150  Sum_probs=53.0

Q ss_pred             CChHHHHHHHHHHHcC---C-CeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhcC
Q psy7268          61 TPTEIQKYSIPTLLSG---K-SAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIGQ  134 (134)
Q Consensus        61 ~~t~iQ~~~i~~~~~g---~-dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~~  134 (134)
                      ...+.|..++..+..+   . .+++.+|||.|||.+.+.+........        .....+.+++.|++.++.++++
T Consensus       195 ~~~~~~~~~~~~~~~~~~~~~~~vl~aPTG~GKT~asl~~a~~~~~~~--------~~~~~r~i~vlP~~t~ie~~~~  264 (733)
T COG1203         195 EGYELQEKALELILRLEKRSLLVVLEAPTGYGKTEASLILALALLDEK--------IKLKSRVIYVLPFRTIIEDMYR  264 (733)
T ss_pred             hhhHHHHHHHHHHHhcccccccEEEEeCCCCChHHHHHHHHHHHhhcc--------ccccceEEEEccHHHHHHHHHH
Confidence            3478899999887742   3 788999999999999999888877642        1156789999999999999863

>PF02562 PhoH: PhoH-like protein; InterPro: IPR003714 PhoH is a cytoplasmic protein and predicted ATPase that is induced by phosphate starvation and belongings to the phosphate regulon (pho) in Escherichia coli []

Probab=97.59  E-value=0.00017  Score=52.48  Aligned_cols=59  Identities=25%  Similarity=0.316  Sum_probs=41.2

Q ss_pred             CCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHH
Q psy7268          60 TTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGREL  128 (134)
Q Consensus        60 ~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~L  128 (134)
                      +..|.-|+.++..+++..-+++.||.|||||+..+...++.+...          ..-+.+|+-|..+.
T Consensus         3 ~p~~~~Q~~~~~al~~~~~v~~~G~AGTGKT~LA~a~Al~~v~~g----------~~~kiii~Rp~v~~   61 (205)
T PF02562_consen    3 KPKNEEQKFALDALLNNDLVIVNGPAGTGKTFLALAAALELVKEG----------EYDKIIITRPPVEA   61 (205)
T ss_dssp             ---SHHHHHHHHHHHH-SEEEEE--TTSSTTHHHHHHHHHHHHTT----------S-SEEEEEE-S--T
T ss_pred             cCCCHHHHHHHHHHHhCCeEEEECCCCCcHHHHHHHHHHHHHHhC----------CCcEEEEEecCCCC
Confidence            456889999999999777799999999999999998888888652          34567777777654

; GO: 0005524 ATP binding; PDB: 3B85_A.

>KOG1803|consensus

Probab=97.55  E-value=0.00027  Score=58.38  Aligned_cols=60  Identities=22%  Similarity=0.275  Sum_probs=47.0

Q ss_pred             CChHHHHHHHHHHHcCCC-eEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHh
Q psy7268          61 TPTEIQKYSIPTLLSGKS-AILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQI  132 (134)
Q Consensus        61 ~~t~iQ~~~i~~~~~g~d-vli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi  132 (134)
                      .+.+-|..|+....+.++ .+++||+|+|||.....-+.+.+.            .+-++|+.+||.+-+.-|
T Consensus       185 ~ln~SQk~Av~~~~~~k~l~~I~GPPGTGKT~TlvEiI~qlvk------------~~k~VLVcaPSn~AVdNi  245 (649)
T KOG1803|consen  185 NLNSSQKAAVSFAINNKDLLIIHGPPGTGKTRTLVEIISQLVK------------QKKRVLVCAPSNVAVDNI  245 (649)
T ss_pred             cccHHHHHHHHHHhccCCceEeeCCCCCCceeeHHHHHHHHHH------------cCCeEEEEcCchHHHHHH
Confidence            567789999998888766 688999999999887555555553            457899999998766544

>KOG0949|consensus

Probab=97.42  E-value=0.00037  Score=60.49  Aligned_cols=65  Identities=25%  Similarity=0.411  Sum_probs=52.7

Q ss_pred             CCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          58 GLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        58 g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      +| .|...|.+.+..+=.+++++|+|||.+|||.+-- -.++.+++..         ..-.+|+++|+++|+.|+.
T Consensus       509 dF-~Pd~WQ~elLDsvDr~eSavIVAPTSaGKTfisf-Y~iEKVLRes---------D~~VVIyvaPtKaLVnQvs  573 (1330)
T KOG0949|consen  509 DF-CPDEWQRELLDSVDRNESAVIVAPTSAGKTFISF-YAIEKVLRES---------DSDVVIYVAPTKALVNQVS  573 (1330)
T ss_pred             cc-CCcHHHHHHhhhhhcccceEEEeeccCCceeccH-HHHHHHHhhc---------CCCEEEEecchHHHhhhhh
Confidence            56 7899999999999999999999999999998743 3345555543         3446899999999999984

>KOG1802|consensus

Probab=97.41  E-value=0.00044  Score=57.97  Aligned_cols=70  Identities=19%  Similarity=0.218  Sum_probs=55.7

Q ss_pred             HHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHh
Q psy7268          53 IFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQI  132 (134)
Q Consensus        53 ~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi  132 (134)
                      .+...|+.+++.-|..|..+++...=-+|++|+|+|||.+-.-.+.+.+..           .+..+|+.+|+.--+.|+
T Consensus       402 ~~s~~~lpkLN~SQ~~AV~~VL~rplsLIQGPPGTGKTvtsa~IVyhl~~~-----------~~~~VLvcApSNiAVDqL  470 (935)
T KOG1802|consen  402 RFSVPNLPKLNASQSNAVKHVLQRPLSLIQGPPGTGKTVTSATIVYHLARQ-----------HAGPVLVCAPSNIAVDQL  470 (935)
T ss_pred             hhcCCCchhhchHHHHHHHHHHcCCceeeecCCCCCceehhHHHHHHHHHh-----------cCCceEEEcccchhHHHH
Confidence            455568889999999999999999989999999999998875555554433           345689999998777766


Q ss_pred             c
Q psy7268         133 G  133 (134)
Q Consensus       133 ~  133 (134)
                      +
T Consensus       471 a  471 (935)
T KOG1802|consen  471 A  471 (935)
T ss_pred             H
Confidence            4

>COG0556 UvrB Helicase subunit of the DNA excision repair complex [DNA replication, recombination, and repair]

Probab=97.38  E-value=0.00023  Score=58.22  Aligned_cols=61  Identities=26%  Similarity=0.437  Sum_probs=44.6

Q ss_pred             CCCCChHHHHHHHHHHHcC-----CCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHh
Q psy7268          58 GLTTPTEIQKYSIPTLLSG-----KSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQI  132 (134)
Q Consensus        58 g~~~~t~iQ~~~i~~~~~g-----~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi  132 (134)
                      .| .|+.=|-+||..+..|     +.-.+.|.||||||+.. .-++..+             +. -+||++|++.||.|+
T Consensus        10 ~f-~PaGDQP~AI~~Lv~gi~~g~~~QtLLGvTGSGKTfT~-AnVI~~~-------------~r-PtLV~AhNKTLAaQL   73 (663)
T COG0556          10 PF-KPAGDQPEAIAELVEGIENGLKHQTLLGVTGSGKTFTM-ANVIAKV-------------QR-PTLVLAHNKTLAAQL   73 (663)
T ss_pred             CC-CCCCCcHHHHHHHHHHHhcCceeeEEeeeccCCchhHH-HHHHHHh-------------CC-CeEEEecchhHHHHH
Confidence            46 7777888888776643     35678899999999765 2333333             22 389999999999998


Q ss_pred             cC
Q psy7268         133 GQ  134 (134)
Q Consensus       133 ~~  134 (134)
                      |+
T Consensus        74 y~   75 (663)
T COG0556          74 YS   75 (663)
T ss_pred             HH
Confidence            73

>KOG0951|consensus

Probab=97.29  E-value=5.7e-05  Score=66.64  Aligned_cols=61  Identities=21%  Similarity=0.181  Sum_probs=50.4

Q ss_pred             CCChHHHHHHHHHHHcCC-CeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          60 TTPTEIQKYSIPTLLSGK-SAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        60 ~~~t~iQ~~~i~~~~~g~-dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      ...+++|.++++.+.+.+ ++++++|+|||||.+..++++..-             ...+++++.|..+.+.-.+
T Consensus      1142 ~~~n~iqtqVf~~~y~~nd~v~vga~~gsgkt~~ae~a~l~~~-------------~~~~~vyi~p~~~i~~~~~ 1203 (1674)
T KOG0951|consen 1142 QDFNPIQTQVFTSLYNTNDNVLVGAPNGSGKTACAELALLRPD-------------TIGRAVYIAPLEEIADEQY 1203 (1674)
T ss_pred             cccCCceEEEEeeeecccceEEEecCCCCchhHHHHHHhcCCc-------------cceEEEEecchHHHHHHHH
Confidence            344899999999988654 699999999999999999988721             5678999999998887554

>PRK15483 type III restriction-modification system StyLTI enzyme res; Provisional

Probab=97.26  E-value=0.0012  Score=57.55  Aligned_cols=46  Identities=17%  Similarity=0.183  Sum_probs=35.1

Q ss_pred             CCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHh
Q psy7268          77 KSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQI  132 (134)
Q Consensus        77 ~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi  132 (134)
                      .++.+..+||+|||.+|+-.++......          ...+.||+||+.+.-..+
T Consensus        60 ~n~~~~M~TGtGKT~~~~~~i~~l~~~~----------~~~~fii~vp~~aI~egv  105 (986)
T PRK15483         60 ANIDIKMETGTGKTYVYTRLMYELHQKY----------GLFKFIIVVPTPAIKEGT  105 (986)
T ss_pred             ceEEEEeCCCCCHHHHHHHHHHHHHHHc----------CCcEEEEEeCCHHHHHHH
Confidence            3789999999999999977776554331          346799999998876554

>PRK13103 secA preprotein translocase subunit SecA; Reviewed

Probab=97.25  E-value=0.00085  Score=58.04  Aligned_cols=60  Identities=25%  Similarity=0.187  Sum_probs=48.1

Q ss_pred             CCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHH
Q psy7268          57 RGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQ  131 (134)
Q Consensus        57 ~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Q  131 (134)
                      +|. .|+++|-..--.+..|  -+....||.|||++..+|++....            .|.++.+++|+..||.|
T Consensus        79 lGm-~~ydVQliGg~~Lh~G--~iaEM~TGEGKTLvA~l~a~l~al------------~G~~VhvvT~ndyLA~R  138 (913)
T PRK13103         79 MGM-RHFDVQLIGGMTLHEG--KIAEMRTGEGKTLVGTLAVYLNAL------------SGKGVHVVTVNDYLARR  138 (913)
T ss_pred             hCC-CcchhHHHhhhHhccC--ccccccCCCCChHHHHHHHHHHHH------------cCCCEEEEeCCHHHHHH
Confidence            475 7888887665445444  457899999999999999887665            67789999999999987

>PF07517 SecA_DEAD: SecA DEAD-like domain; InterPro: IPR011115 SecA protein binds to the plasma membrane where it interacts with proOmpA to support translocation of proOmpA through the membrane

Probab=97.22  E-value=0.0024  Score=48.35  Aligned_cols=60  Identities=27%  Similarity=0.323  Sum_probs=46.0

Q ss_pred             CCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHH
Q psy7268          57 RGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQ  131 (134)
Q Consensus        57 ~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Q  131 (134)
                      .|+ .|.++|-.++-.+..|+  ++.-.||-|||++..+|.....+            .|..+-|++.+..||.+
T Consensus        74 ~g~-~p~~vQll~~l~L~~G~--laEm~TGEGKTli~~l~a~~~AL------------~G~~V~vvT~NdyLA~R  133 (266)
T PF07517_consen   74 LGL-RPYDVQLLGALALHKGR--LAEMKTGEGKTLIAALPAALNAL------------QGKGVHVVTSNDYLAKR  133 (266)
T ss_dssp             TS-----HHHHHHHHHHHTTS--EEEESTTSHHHHHHHHHHHHHHT------------TSS-EEEEESSHHHHHH
T ss_pred             cCC-cccHHHHhhhhhcccce--eEEecCCCCcHHHHHHHHHHHHH------------hcCCcEEEeccHHHhhc
Confidence            477 89999999997776776  88999999999998887766655            56678999999999874

SecA protein achieves this translocation, in association with SecY protein, in an ATP-dependent manner [,]. This domain represents the N-terminal ATP-dependent helicase domain, which is related to the IPR0011545 from INTERPRO.; GO: 0005524 ATP binding, 0017038 protein import, 0016020 membrane; PDB: 1NL3_B 1NKT_B 3DIN_B 3JUX_A 2FSG_B 2VDA_A 2FSH_A 2FSF_A 2FSI_A 3BXZ_A ....

>PRK10536 hypothetical protein; Provisional

Probab=97.15  E-value=0.0011  Score=49.95  Aligned_cols=46  Identities=22%  Similarity=0.289  Sum_probs=38.4

Q ss_pred             CCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHH
Q psy7268          57 RGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQIL  102 (134)
Q Consensus        57 ~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~  102 (134)
                      .++..-+..|...+..+.++.-+++.|+.|+|||+..+...++.+.
T Consensus        55 ~~i~p~n~~Q~~~l~al~~~~lV~i~G~aGTGKT~La~a~a~~~l~  100 (262)
T PRK10536         55 SPILARNEAQAHYLKAIESKQLIFATGEAGCGKTWISAAKAAEALI  100 (262)
T ss_pred             ccccCCCHHHHHHHHHHhcCCeEEEECCCCCCHHHHHHHHHHHHHh
Confidence            3666678899999998888888999999999999988777776664

>COG4096 HsdR Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]

Probab=97.10  E-value=0.0013  Score=56.25  Aligned_cols=63  Identities=25%  Similarity=0.324  Sum_probs=51.2

Q ss_pred             CChHHHHHHHHHHH----cCCC-eEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          61 TPTEIQKYSIPTLL----SGKS-AILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        61 ~~t~iQ~~~i~~~~----~g~d-vli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      .+...|..||..+.    .|++ ++++..||+|||-.. +.++.++.+..         .--++|+++-.++|+.|-+
T Consensus       165 ~~RyyQ~~AI~rv~Eaf~~g~~raLlvMATGTGKTrTA-iaii~rL~r~~---------~~KRVLFLaDR~~Lv~QA~  232 (875)
T COG4096         165 GPRYYQIIAIRRVIEAFSKGQNRALLVMATGTGKTRTA-IAIIDRLIKSG---------WVKRVLFLADRNALVDQAY  232 (875)
T ss_pred             cchHHHHHHHHHHHHHHhcCCceEEEEEecCCCcceeH-HHHHHHHHhcc---------hhheeeEEechHHHHHHHH
Confidence            56778999997654    4543 999999999999887 77888887644         5568999999999999965

>CHL00122 secA preprotein translocase subunit SecA; Validated

Probab=97.03  E-value=0.0021  Score=55.48  Aligned_cols=61  Identities=26%  Similarity=0.162  Sum_probs=47.8

Q ss_pred             CCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHh
Q psy7268          57 RGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQI  132 (134)
Q Consensus        57 ~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi  132 (134)
                      .|. .|+++|-...-.+.  ..-++...||.|||+++.+|+.-..+            .|..+.|++++..||.+-
T Consensus        73 lG~-r~ydvQlig~l~L~--~G~IaEm~TGEGKTL~a~l~ayl~aL------------~G~~VhVvT~NdyLA~RD  133 (870)
T CHL00122         73 LGL-RHFDVQLIGGLVLN--DGKIAEMKTGEGKTLVATLPAYLNAL------------TGKGVHIVTVNDYLAKRD  133 (870)
T ss_pred             hCC-CCCchHhhhhHhhc--CCccccccCCCCchHHHHHHHHHHHh------------cCCceEEEeCCHHHHHHH
Confidence            477 78899887764443  45678999999999999999864443            466799999999999864

>PRK13889 conjugal transfer relaxase TraA; Provisional

Probab=97.00  E-value=0.0071  Score=53.26  Aligned_cols=63  Identities=16%  Similarity=0.132  Sum_probs=47.7

Q ss_pred             CCCCCChHHHHHHHHHHHcCCC-eEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHh
Q psy7268          57 RGLTTPTEIQKYSIPTLLSGKS-AILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQI  132 (134)
Q Consensus        57 ~g~~~~t~iQ~~~i~~~~~g~d-vli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi  132 (134)
                      .|+ .+++-|..++..++.+++ +++.|..|+|||.. +-.+...+..           .+.+++.++||---|..+
T Consensus       343 ~g~-~Ls~eQr~Av~~il~s~~v~vv~G~AGTGKTT~-l~~~~~~~e~-----------~G~~V~~~ApTGkAA~~L  406 (988)
T PRK13889        343 RGL-VLSGEQADALAHVTDGRDLGVVVGYAGTGKSAM-LGVAREAWEA-----------AGYEVRGAALSGIAAENL  406 (988)
T ss_pred             cCC-CCCHHHHHHHHHHhcCCCeEEEEeCCCCCHHHH-HHHHHHHHHH-----------cCCeEEEecCcHHHHHHH
Confidence            466 789999999999998766 67889999999975 3344444332           467899999997766554

>PRK13894 conjugal transfer ATPase TrbB; Provisional

Probab=96.98  E-value=0.005  Score=47.75  Aligned_cols=48  Identities=23%  Similarity=0.544  Sum_probs=33.8

Q ss_pred             HHHHHHCCCCCChHHHHHHHHH-HHcCCCeEEEcCCCCchhHHhHHHHHHHH
Q psy7268          51 IDIFTKRGLTTPTEIQKYSIPT-LLSGKSAILVAETGCGKTLSFLAPLVQQI  101 (134)
Q Consensus        51 ~~~l~~~g~~~~t~iQ~~~i~~-~~~g~dvli~a~tGsGKT~~~~lpil~~~  101 (134)
                      ++.+.+.|+  +++.|...+.. +..++++++.|+|||||| .++-.++..+
T Consensus       124 l~~l~~~g~--~~~~~~~~L~~~v~~~~~ilI~G~tGSGKT-Tll~aL~~~~  172 (319)
T PRK13894        124 LDQYVERGI--MTAAQREAIIAAVRAHRNILVIGGTGSGKT-TLVNAIINEM  172 (319)
T ss_pred             HHHHHhcCC--CCHHHHHHHHHHHHcCCeEEEECCCCCCHH-HHHHHHHHhh
Confidence            445555555  45667777764 557889999999999999 5556666654

>PF07652 Flavi_DEAD: Flavivirus DEAD domain ; InterPro: IPR011492 This is the Flavivirus DEAD domain

Probab=96.95  E-value=0.00098  Score=46.02  Aligned_cols=47  Identities=23%  Similarity=0.395  Sum_probs=33.5

Q ss_pred             CCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          76 GKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      |+--++--.+|+|||--.+.-++..-..           .+.++||+.|||.++..++
T Consensus         4 g~~~~~d~hpGaGKTr~vlp~~~~~~i~-----------~~~rvLvL~PTRvva~em~   50 (148)
T PF07652_consen    4 GELTVLDLHPGAGKTRRVLPEIVREAIK-----------RRLRVLVLAPTRVVAEEMY   50 (148)
T ss_dssp             TEEEEEE--TTSSTTTTHHHHHHHHHHH-----------TT--EEEEESSHHHHHHHH
T ss_pred             CceeEEecCCCCCCcccccHHHHHHHHH-----------ccCeEEEecccHHHHHHHH
Confidence            4446778899999998886666665544           5778999999999998765

The domain is related to the DEAD/DEAH box helicase domain which is found in a large family of ATPases.; GO: 0005524 ATP binding, 0008026 ATP-dependent helicase activity, 0019079 viral genome replication; PDB: 2QEQ_A 2V6J_A 2V6I_A 8OHM_A 4A92_B 1JR6_A 1HEI_A 1ONB_A 1A1V_A 1YMF_A ....

>TIGR02782 TrbB_P P-type conjugative transfer ATPase TrbB

Probab=96.94  E-value=0.008  Score=46.15  Aligned_cols=50  Identities=28%  Similarity=0.426  Sum_probs=32.6

Q ss_pred             HHHHHHHCCCCCChHHHHHHHHH-HHcCCCeEEEcCCCCchhHHhHHHHHHHHH
Q psy7268          50 IIDIFTKRGLTTPTEIQKYSIPT-LLSGKSAILVAETGCGKTLSFLAPLVQQIL  102 (134)
Q Consensus        50 i~~~l~~~g~~~~t~iQ~~~i~~-~~~g~dvli~a~tGsGKT~~~~lpil~~~~  102 (134)
                      -++.+.+.|.  +++-|...+.. +..+++++++|+||||||... -.++..+.
T Consensus       107 tl~~l~~~g~--~~~~~~~~L~~~v~~~~~ilI~G~tGSGKTTll-~al~~~i~  157 (299)
T TIGR02782       107 TLDDYVEAGI--MTAAQRDVLREAVLARKNILVVGGTGSGKTTLA-NALLAEIA  157 (299)
T ss_pred             CHHHHHhcCC--CCHHHHHHHHHHHHcCCeEEEECCCCCCHHHHH-HHHHHHhh
Confidence            3445555554  45555555544 556779999999999999553 55565553

The TrbB protein is found in the trb locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for plasmid conjugative transfer. TrbB is a homolog of the vir system VirB11 ATPase, and the Flp pilus sytem ATPase TadA.

>PRK13833 conjugal transfer protein TrbB; Provisional

Probab=96.92  E-value=0.0066  Score=47.18  Aligned_cols=47  Identities=23%  Similarity=0.296  Sum_probs=32.3

Q ss_pred             HHHHCCCCCChHHHHHHHHH-HHcCCCeEEEcCCCCchhHHhHHHHHHHHH
Q psy7268          53 IFTKRGLTTPTEIQKYSIPT-LLSGKSAILVAETGCGKTLSFLAPLVQQIL  102 (134)
Q Consensus        53 ~l~~~g~~~~t~iQ~~~i~~-~~~g~dvli~a~tGsGKT~~~~lpil~~~~  102 (134)
                      .+.+.|.  +++.|...+.. +..+.+++++|+||||||.. +-.++..+.
T Consensus       122 ~lv~~g~--~~~~~~~~L~~~v~~~~nilI~G~tGSGKTTl-l~aL~~~i~  169 (323)
T PRK13833        122 DYVTSKI--MTEAQASVIRSAIDSRLNIVISGGTGSGKTTL-ANAVIAEIV  169 (323)
T ss_pred             HHHHcCC--CCHHHHHHHHHHHHcCCeEEEECCCCCCHHHH-HHHHHHHHh
Confidence            3445444  56667766655 44677999999999999955 355666553

>KOG1133|consensus

Probab=96.91  E-value=0.0021  Score=54.06  Aligned_cols=46  Identities=30%  Similarity=0.472  Sum_probs=39.6

Q ss_pred             CCCCChHHHHHHHHHHH----cCCCeEEEcCCCCchhHHhHHHHHHHHHhh
Q psy7268          58 GLTTPTEIQKYSIPTLL----SGKSAILVAETGCGKTLSFLAPLVQQILTW  104 (134)
Q Consensus        58 g~~~~t~iQ~~~i~~~~----~g~dvli~a~tGsGKT~~~~lpil~~~~~~  104 (134)
                      .| +|+.||.+.+..++    .|+=-|..+|||+|||++.+-..+.++...
T Consensus        13 Py-~PYdIQ~~lM~elyrvLe~GkIgIfESPTGTGKSLSLiCaaltWL~~~   62 (821)
T KOG1133|consen   13 PY-TPYDIQEDLMRELYRVLEEGKIGIFESPTGTGKSLSLICAALTWLRDF   62 (821)
T ss_pred             CC-CchhHHHHHHHHHHHHHhcCCeeeeeCCCCCCchHHHHHHHHHHHHHh
Confidence            45 78999999987765    688788999999999999999999988754

>TIGR01448 recD_rel helicase, putative, RecD/TraA family

Probab=96.89  E-value=0.0086  Score=51.17  Aligned_cols=65  Identities=18%  Similarity=0.136  Sum_probs=47.5

Q ss_pred             CCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHh
Q psy7268          57 RGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQI  132 (134)
Q Consensus        57 ~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi  132 (134)
                      .++ .+++-|+.++..+..++-+++.|+.|+|||... -.++..+....         ....+++++||-.-|..+
T Consensus       320 ~~~-~l~~~Q~~Ai~~~~~~~~~iitGgpGTGKTt~l-~~i~~~~~~~~---------~~~~v~l~ApTg~AA~~L  384 (720)
T TIGR01448       320 LRK-GLSEEQKQALDTAIQHKVVILTGGPGTGKTTIT-RAIIELAEELG---------GLLPVGLAAPTGRAAKRL  384 (720)
T ss_pred             cCC-CCCHHHHHHHHHHHhCCeEEEECCCCCCHHHHH-HHHHHHHHHcC---------CCceEEEEeCchHHHHHH
Confidence            465 789999999999988888999999999999654 34444443210         115678889997766655

This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD.

>TIGR02768 TraA_Ti Ti-type conjugative transfer relaxase TraA

Probab=96.82  E-value=0.014  Score=50.18  Aligned_cols=74  Identities=14%  Similarity=0.141  Sum_probs=50.6

Q ss_pred             CCHHHHHHHHHCCCCCChHHHHHHHHHHHcC-CCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcC
Q psy7268          46 LAPEIIDIFTKRGLTTPTEIQKYSIPTLLSG-KSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITP  124 (134)
Q Consensus        46 l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g-~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~P  124 (134)
                      +++..++..-..++ .+++-|+.++..++.+ +-+++.|+.|+|||... -.++..+..           .+.+++.++|
T Consensus       338 ~~~~~~~~~l~~~~-~Ls~~Q~~Av~~i~~s~~~~il~G~aGTGKTtll-~~i~~~~~~-----------~g~~V~~~Ap  404 (744)
T TIGR02768       338 VSPPIVDAAIDQHY-RLSEEQYEAVRHVTGSGDIAVVVGRAGTGKSTML-KAAREAWEA-----------AGYRVIGAAL  404 (744)
T ss_pred             CCHHHHHHHHhccC-CCCHHHHHHHHHHhcCCCEEEEEecCCCCHHHHH-HHHHHHHHh-----------CCCeEEEEeC
Confidence            34444443333455 6899999999998875 45789999999998553 333333322           4667899999


Q ss_pred             cHHHHHHh
Q psy7268         125 GRELVFQI  132 (134)
Q Consensus       125 t~~La~Qi  132 (134)
                      |---+..+
T Consensus       405 Tg~Aa~~L  412 (744)
T TIGR02768       405 SGKAAEGL  412 (744)
T ss_pred             cHHHHHHH
Confidence            98766654

This protein contains domains distinctive of a single strand exonuclease (N-terminus, MobA/MobL, pfam03389) as well as a helicase domain (central region, homologous to the corresponding region of the F-type relaxase TraI, TIGR02760). This protein likely fills the same role as TraI(F), nicking (at the oriT site) and unwinding the coiled plasmid prior to conjugative transfer.

>PRK11131 ATP-dependent RNA helicase HrpA; Provisional

Probab=96.74  E-value=0.0032  Score=56.53  Aligned_cols=34  Identities=24%  Similarity=0.310  Sum_probs=23.3

Q ss_pred             HHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHH
Q psy7268          65 IQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQ  100 (134)
Q Consensus        65 iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~  100 (134)
                      .-.+.+..+..+..++++|+||||||.  .+|.+..
T Consensus        78 ~r~~Il~ai~~~~VviI~GeTGSGKTT--qlPq~ll  111 (1294)
T PRK11131         78 KKQDILEAIRDHQVVIVAGETGSGKTT--QLPKICL  111 (1294)
T ss_pred             HHHHHHHHHHhCCeEEEECCCCCCHHH--HHHHHHH
Confidence            333444555566678888999999998  4774443

>COG2805 PilT Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=96.60  E-value=0.0055  Score=47.27  Aligned_cols=51  Identities=24%  Similarity=0.405  Sum_probs=34.6

Q ss_pred             CCCCCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhc
Q psy7268          36 IDLGTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWK  105 (134)
Q Consensus        36 ~~~~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~  105 (134)
                      ..+.+|+++++++.+.+.+..-                  .-=++|.+||||||+... .+++.++.+..
T Consensus       103 ~~i~~~e~LglP~i~~~~~~~~------------------~GLILVTGpTGSGKSTTl-AamId~iN~~~  153 (353)
T COG2805         103 SKIPTLEELGLPPIVRELAESP------------------RGLILVTGPTGSGKSTTL-AAMIDYINKHK  153 (353)
T ss_pred             ccCCCHHHcCCCHHHHHHHhCC------------------CceEEEeCCCCCcHHHHH-HHHHHHHhccC
Confidence            4556777777777666522211                  112788999999999765 78888887643

>TIGR00631 uvrb excinuclease ABC, B subunit

Probab=96.56  E-value=0.0069  Score=51.25  Aligned_cols=61  Identities=28%  Similarity=0.429  Sum_probs=45.6

Q ss_pred             CCCCChHHHHHHHHHHHc----C-CCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHh
Q psy7268          58 GLTTPTEIQKYSIPTLLS----G-KSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQI  132 (134)
Q Consensus        58 g~~~~t~iQ~~~i~~~~~----g-~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi  132 (134)
                      .| .|+.-|..+|..+.+    | ++.++.|.||||||+... .++..+              +...|||+|++.+|.|+
T Consensus         7 ~~-~~~~~Q~~ai~~l~~~~~~~~~~~~l~Gvtgs~kt~~~a-~~~~~~--------------~~p~Lvi~~n~~~A~ql   70 (655)
T TIGR00631         7 PF-QPAGDQPKAIAKLVEGLTDGEKHQTLLGVTGSGKTFTMA-NVIAQV--------------NRPTLVIAHNKTLAAQL   70 (655)
T ss_pred             CC-CCChHHHHHHHHHHHhhhcCCCcEEEECCCCcHHHHHHH-HHHHHh--------------CCCEEEEECCHHHHHHH
Confidence            46 789999999988763    3 256789999999997753 233322              22489999999999998


Q ss_pred             cC
Q psy7268         133 GQ  134 (134)
Q Consensus       133 ~~  134 (134)
                      ++
T Consensus        71 ~~   72 (655)
T TIGR00631        71 YN   72 (655)
T ss_pred             HH
Confidence            63

This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University)

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

Probab=96.55  E-value=0.0059  Score=43.37  Aligned_cols=46  Identities=22%  Similarity=0.349  Sum_probs=29.4

Q ss_pred             cCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          75 SGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      +++++++.|++|+|||... ..+...+..           .+..++++ ...+|...+.
T Consensus        46 ~~~~l~l~G~~G~GKThLa-~ai~~~~~~-----------~g~~v~f~-~~~~L~~~l~   91 (178)
T PF01695_consen   46 NGENLILYGPPGTGKTHLA-VAIANEAIR-----------KGYSVLFI-TASDLLDELK   91 (178)
T ss_dssp             C--EEEEEESTTSSHHHHH-HHHHHHHHH-----------TT--EEEE-EHHHHHHHHH
T ss_pred             cCeEEEEEhhHhHHHHHHH-HHHHHHhcc-----------CCcceeEe-ecCceecccc
Confidence            6788999999999999775 445555544           34445554 6667776654

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.

>PRK10919 ATP-dependent DNA helicase Rep; Provisional

Probab=96.43  E-value=0.0096  Score=50.49  Aligned_cols=62  Identities=15%  Similarity=0.092  Sum_probs=44.4

Q ss_pred             CChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHh
Q psy7268          61 TPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQI  132 (134)
Q Consensus        61 ~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi  132 (134)
                      .+++-|++++..  ....++|.|..|||||.+...=+...+.....        ...++++++-|+.-|..+
T Consensus         2 ~Ln~~Q~~av~~--~~g~~lV~AgpGSGKT~vL~~Ria~Li~~~~v--------~p~~IL~lTFT~kAA~em   63 (672)
T PRK10919          2 RLNPGQQQAVEF--VTGPCLVLAGAGSGKTRVITNKIAHLIRGCGY--------QARHIAAVTFTNKAAREM   63 (672)
T ss_pred             CCCHHHHHHHhC--CCCCEEEEecCCCCHHHHHHHHHHHHHHhcCC--------CHHHeeeEechHHHHHHH
Confidence            468899998854  34578899999999998875555555532111        234689999999888765

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

Probab=96.36  E-value=0.011  Score=44.33  Aligned_cols=63  Identities=19%  Similarity=0.303  Sum_probs=41.9

Q ss_pred             CCCCChHHHHHHHHHHH-------cCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHH
Q psy7268          58 GLTTPTEIQKYSIPTLL-------SGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVF  130 (134)
Q Consensus        58 g~~~~t~iQ~~~i~~~~-------~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~  130 (134)
                      .|......+..++..+.       +++++++.|++|+|||... .++...+..           .|..++ .+++.+|+.
T Consensus        80 d~~~~~~~~~~~l~~~~~~~~~~~~~~nl~l~G~~G~GKThLa-~Ai~~~l~~-----------~g~sv~-f~~~~el~~  146 (254)
T COG1484          80 DFEFQPGIDKKALEDLASLVEFFERGENLVLLGPPGVGKTHLA-IAIGNELLK-----------AGISVL-FITAPDLLS  146 (254)
T ss_pred             cccCCcchhHHHHHHHHHHHHHhccCCcEEEECCCCCcHHHHH-HHHHHHHHH-----------cCCeEE-EEEHHHHHH
Confidence            44455555666554433       6789999999999999766 455555553           344444 457888887


Q ss_pred             Hhc
Q psy7268         131 QIG  133 (134)
Q Consensus       131 Qi~  133 (134)
                      ++.
T Consensus       147 ~Lk  149 (254)
T COG1484         147 KLK  149 (254)
T ss_pred             HHH
Confidence            764

>TIGR02525 plasmid_TraJ plasmid transfer ATPase TraJ

Probab=96.34  E-value=0.018  Score=45.63  Aligned_cols=27  Identities=26%  Similarity=0.311  Sum_probs=20.3

Q ss_pred             CCCeEEEcCCCCchhHHhHHHHHHHHHh
Q psy7268          76 GKSAILVAETGCGKTLSFLAPLVQQILT  103 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~~lpil~~~~~  103 (134)
                      +..++++||||||||... -.++..+..
T Consensus       149 ~GlilI~G~TGSGKTT~l-~al~~~i~~  175 (372)
T TIGR02525       149 AGLGLICGETGSGKSTLA-ASIYQHCGE  175 (372)
T ss_pred             CCEEEEECCCCCCHHHHH-HHHHHHHHh
Confidence            446899999999999654 566676653

Members of this protein family are predicted ATPases associated with plasmid transfer loci in bacteria. This family is most similar to the DotB ATPase of a type-IV secretion-like system of obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii (TIGR02524).

>PRK12902 secA preprotein translocase subunit SecA; Reviewed

Probab=96.33  E-value=0.013  Score=50.92  Aligned_cols=60  Identities=25%  Similarity=0.208  Sum_probs=47.4

Q ss_pred             CCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHH
Q psy7268          57 RGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQ  131 (134)
Q Consensus        57 ~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Q  131 (134)
                      +|. .|+++|-..--.+..|  -+....||-|||+++.+|+.-..+            .|..+.||+++..||.+
T Consensus        82 lG~-r~ydVQliGgl~Lh~G--~IAEM~TGEGKTL~atlpaylnAL------------~GkgVhVVTvNdYLA~R  141 (939)
T PRK12902         82 LGM-RHFDVQLIGGMVLHEG--QIAEMKTGEGKTLVATLPSYLNAL------------TGKGVHVVTVNDYLARR  141 (939)
T ss_pred             hCC-CcchhHHHhhhhhcCC--ceeeecCCCChhHHHHHHHHHHhh------------cCCCeEEEeCCHHHHHh
Confidence            477 8888887766555444  467999999999999998877654            56679999999999975

>PRK11054 helD DNA helicase IV; Provisional

Probab=96.31  E-value=0.028  Score=47.89  Aligned_cols=63  Identities=17%  Similarity=0.212  Sum_probs=44.3

Q ss_pred             CCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHh
Q psy7268          60 TTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQI  132 (134)
Q Consensus        60 ~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi  132 (134)
                      ..+++-|++++-.  ...+++|.|..|||||.+.+--+...+.....        ...++++++.|+..|..+
T Consensus       195 ~~L~~~Q~~av~~--~~~~~lV~agaGSGKT~vl~~r~ayLl~~~~~--------~~~~IL~ltft~~AA~em  257 (684)
T PRK11054        195 SPLNPSQARAVVN--GEDSLLVLAGAGSGKTSVLVARAGWLLARGQA--------QPEQILLLAFGRQAAEEM  257 (684)
T ss_pred             CCCCHHHHHHHhC--CCCCeEEEEeCCCCHHHHHHHHHHHHHHhCCC--------CHHHeEEEeccHHHHHHH
Confidence            4789999998742  33468899999999998875444433332111        345799999999988765

>PRK10875 recD exonuclease V subunit alpha; Provisional

Probab=96.22  E-value=0.049  Score=45.89  Aligned_cols=62  Identities=16%  Similarity=0.244  Sum_probs=43.6

Q ss_pred             hHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHh
Q psy7268          63 TEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQI  132 (134)
Q Consensus        63 t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi  132 (134)
                      .+.|+.|+-..+.++-.++.|++|+|||... .-++..+.+...       ....++++.+||..-|..+
T Consensus       154 ~d~Qk~Av~~a~~~~~~vItGgpGTGKTt~v-~~ll~~l~~~~~-------~~~~~i~l~APTgkAA~rL  215 (615)
T PRK10875        154 VDWQKVAAAVALTRRISVISGGPGTGKTTTV-AKLLAALIQLAD-------GERCRIRLAAPTGKAAARL  215 (615)
T ss_pred             CHHHHHHHHHHhcCCeEEEEeCCCCCHHHHH-HHHHHHHHHhcC-------CCCcEEEEECCcHHHHHHH
Confidence            5799999999999889999999999999764 222322322110       0235688889998766654

>TIGR01074 rep ATP-dependent DNA helicase Rep

Probab=96.18  E-value=0.018  Score=48.57  Aligned_cols=61  Identities=15%  Similarity=0.096  Sum_probs=43.4

Q ss_pred             ChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHh
Q psy7268          62 PTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQI  132 (134)
Q Consensus        62 ~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi  132 (134)
                      +++-|++++..  ...+++|.|..|||||.+.+-=+...+.....        ...++++|+.|+.-|..+
T Consensus         2 Ln~~Q~~av~~--~~~~~~V~Ag~GSGKT~~L~~ri~~ll~~~~~--------~p~~IL~vTFt~~Aa~em   62 (664)
T TIGR01074         2 LNPQQQEAVEY--VTGPCLVLAGAGSGKTRVITNKIAYLIQNCGY--------KARNIAAVTFTNKAAREM   62 (664)
T ss_pred             CCHHHHHHHhC--CCCCEEEEecCCCCHHHHHHHHHHHHHHhcCC--------CHHHeEEEeccHHHHHHH
Confidence            67889888754  35689999999999998876555555532111        234588888888887765

Designed to identify rep members of the uvrD/rep subfamily.

>PF05970 PIF1: PIF1-like helicase; InterPro: IPR010285 This entry represents PIF1 helicase and related proteins

Probab=96.17  E-value=0.023  Score=44.71  Aligned_cols=59  Identities=19%  Similarity=0.292  Sum_probs=41.4

Q ss_pred             ChHHHHHHHHHH------HcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHh
Q psy7268          62 PTEIQKYSIPTL------LSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQI  132 (134)
Q Consensus        62 ~t~iQ~~~i~~~------~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi  132 (134)
                      +++-|+.++..+      ..+..+++.|+-|+|||..+ -.+.+.+ +.          .+..+++++||-.=|..|
T Consensus         2 Ln~eQ~~~~~~v~~~~~~~~~~~~fv~G~~GtGKs~l~-~~i~~~~-~~----------~~~~~~~~a~tg~AA~~i   66 (364)
T PF05970_consen    2 LNEEQRRVFDTVIEAIENEEGLNFFVTGPAGTGKSFLI-KAIIDYL-RS----------RGKKVLVTAPTGIAAFNI   66 (364)
T ss_pred             CCHHHHHHHHHHHHHHHccCCcEEEEEcCCCCChhHHH-HHHHHHh-cc----------ccceEEEecchHHHHHhc
Confidence            567799998877      57888999999999998554 2333333 21          345688888887665544

The PIF1 helicase inhibits telomerase activity and is cell cycle regulated [, ].

>PRK05973 replicative DNA helicase; Provisional

Probab=96.16  E-value=0.015  Score=43.36  Aligned_cols=59  Identities=24%  Similarity=0.265  Sum_probs=37.1

Q ss_pred             ccCCCCHHHHHHHHHCCCCCChHHHHHHH---------HHHHcCCCeEEEcCCCCchhHHhHHHHHHH
Q psy7268          42 EDTGLAPEIIDIFTKRGLTTPTEIQKYSI---------PTLLSGKSAILVAETGCGKTLSFLAPLVQQ  100 (134)
Q Consensus        42 ~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i---------~~~~~g~dvli~a~tGsGKT~~~~lpil~~  100 (134)
                      ..++|++.+-+.-.+-||...+-+...+-         .-+..|.-++|.|++|+|||...+--+.+.
T Consensus        21 ~~~~~~~~~~~~a~~~g~~~w~~~~~~~~~~~p~~~l~GGl~~Gsl~LIaG~PG~GKT~lalqfa~~~   88 (237)
T PRK05973         21 QNIPLHEALDRIAAEEGFSSWSLLAAKAAATTPAEELFSQLKPGDLVLLGARPGHGKTLLGLELAVEA   88 (237)
T ss_pred             cCCcHHHHHHHHHHHhccchHHHHHHhccCCCCHHHhcCCCCCCCEEEEEeCCCCCHHHHHHHHHHHH
Confidence            34567777776666678865444443332         223356678999999999997654444433

>KOG0950|consensus

Probab=96.16  E-value=0.012  Score=51.15  Aligned_cols=58  Identities=26%  Similarity=0.317  Sum_probs=47.0

Q ss_pred             CCHHHH-HHHHHCCCCCChHHHHHHH--HHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHh
Q psy7268          46 LAPEII-DIFTKRGLTTPTEIQKYSI--PTLLSGKSAILVAETGCGKTLSFLAPLVQQILT  103 (134)
Q Consensus        46 l~~~i~-~~l~~~g~~~~t~iQ~~~i--~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~  103 (134)
                      +++... -..+..|..+++..|.+++  |.++.+++.+...||+.|||++.-+-++..+..
T Consensus       207 ~~~k~~~~~~~~kgi~~~fewq~ecls~~~~~e~~nliys~Pts~gktlvaeilml~~~l~  267 (1008)
T KOG0950|consen  207 LPTKVSHLYAKDKGILKLFEWQAECLSLPRLLERKNLIYSLPTSAGKTLVAEILMLREVLC  267 (1008)
T ss_pred             CchHHHHHHHHhhhHHHHHHHHHHHhcchhhhcccceEEeCCCccchHHHHHHHHHHHHHH
Confidence            344444 3444469999999999998  678899999999999999999998888877765

>COG4889 Predicted helicase [General function prediction only]

Probab=96.14  E-value=0.0064  Score=52.91  Aligned_cols=78  Identities=19%  Similarity=0.245  Sum_probs=52.9

Q ss_pred             CcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcCC-----CeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCC
Q psy7268          40 TFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGK-----SAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPEL  114 (134)
Q Consensus        40 ~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~-----dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~  114 (134)
                      .|+.+.. .++..++.-..-++|.|+|+.++....+|-     .=+| ...|+|||+.. +-+.+.+.            
T Consensus       141 DW~~f~p-~e~~~nl~l~~~kk~R~hQq~Aid~a~~~F~~n~RGkLI-MAcGTGKTfTs-LkisEala------------  205 (1518)
T COG4889         141 DWDIFDP-TELQDNLPLKKPKKPRPHQQTAIDAAKEGFSDNDRGKLI-MACGTGKTFTS-LKISEALA------------  205 (1518)
T ss_pred             ChhhcCc-cccccccccCCCCCCChhHHHHHHHHHhhcccccCCcEE-EecCCCccchH-HHHHHHHh------------
Confidence            4544432 355555555556799999999999987542     2222 33489999887 44455552            


Q ss_pred             CCcEEEEEcCcHHHHHHhc
Q psy7268         115 NAPLALIITPGRELVFQIG  133 (134)
Q Consensus       115 ~~~~~lil~Pt~~La~Qi~  133 (134)
                       ..++|+++|+..|..|..
T Consensus       206 -~~~iL~LvPSIsLLsQTl  223 (1518)
T COG4889         206 -AARILFLVPSISLLSQTL  223 (1518)
T ss_pred             -hhheEeecchHHHHHHHH
Confidence             367999999999998853

>COG2804 PulE Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=96.14  E-value=0.019  Score=46.94  Aligned_cols=46  Identities=24%  Similarity=0.369  Sum_probs=33.7

Q ss_pred             HHHCCCCCChHHHHHHHHHHHcCCC--eEEEcCCCCchhHHhHHHHHHHHHh
Q psy7268          54 FTKRGLTTPTEIQKYSIPTLLSGKS--AILVAETGCGKTLSFLAPLVQQILT  103 (134)
Q Consensus        54 l~~~g~~~~t~iQ~~~i~~~~~g~d--vli~a~tGsGKT~~~~lpil~~~~~  103 (134)
                      +.++|+   ++.|...+..+++...  +++.||||||||... ..++..+..
T Consensus       237 l~~Lg~---~~~~~~~~~~~~~~p~GliLvTGPTGSGKTTTL-Y~~L~~ln~  284 (500)
T COG2804         237 LEKLGM---SPFQLARLLRLLNRPQGLILVTGPTGSGKTTTL-YAALSELNT  284 (500)
T ss_pred             HHHhCC---CHHHHHHHHHHHhCCCeEEEEeCCCCCCHHHHH-HHHHHHhcC
Confidence            455555   6778888877776554  778899999999764 677777754

>PRK13851 type IV secretion system protein VirB11; Provisional

Probab=96.11  E-value=0.012  Score=46.18  Aligned_cols=29  Identities=28%  Similarity=0.409  Sum_probs=21.9

Q ss_pred             HHHcCCCeEEEcCCCCchhHHhHHHHHHHH
Q psy7268          72 TLLSGKSAILVAETGCGKTLSFLAPLVQQI  101 (134)
Q Consensus        72 ~~~~g~dvli~a~tGsGKT~~~~lpil~~~  101 (134)
                      .+..+.+++++|+||||||.. +-.++..+
T Consensus       158 ~v~~~~nilI~G~tGSGKTTl-l~aLl~~i  186 (344)
T PRK13851        158 CVVGRLTMLLCGPTGSGKTTM-SKTLISAI  186 (344)
T ss_pred             HHHcCCeEEEECCCCccHHHH-HHHHHccc
Confidence            455788999999999999954 34555544

>cd01129 PulE-GspE PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP)

Probab=96.07  E-value=0.031  Score=42.14  Aligned_cols=46  Identities=22%  Similarity=0.239  Sum_probs=30.6

Q ss_pred             HHHHCCCCCChHHHHHHHHHHHc--CCCeEEEcCCCCchhHHhHHHHHHHHH
Q psy7268          53 IFTKRGLTTPTEIQKYSIPTLLS--GKSAILVAETGCGKTLSFLAPLVQQIL  102 (134)
Q Consensus        53 ~l~~~g~~~~t~iQ~~~i~~~~~--g~dvli~a~tGsGKT~~~~lpil~~~~  102 (134)
                      .+.++|+   .+-|.+.+..++.  +.-+++.++||||||... -.++..+.
T Consensus        58 ~l~~lg~---~~~~~~~l~~~~~~~~GlilisG~tGSGKTT~l-~all~~i~  105 (264)
T cd01129          58 DLEKLGL---KPENLEIFRKLLEKPHGIILVTGPTGSGKTTTL-YSALSELN  105 (264)
T ss_pred             CHHHcCC---CHHHHHHHHHHHhcCCCEEEEECCCCCcHHHHH-HHHHhhhC
Confidence            4566665   5556666665553  335899999999999654 45555553

It is responsible for the export the majority of Gram-negative bacterial exoenzymes and toxins. PulE is a cytoplasmic protein of the GSP, which contains an ATP binding site and a tetracysteine motif. This subgroup also includes PillB and HofB.

>PF00176 SNF2_N: SNF2 family N-terminal domain; InterPro: IPR000330 This domain is found in proteins involved in a variety of processes including transcription regulation (e

Probab=96.07  E-value=0.021  Score=42.59  Aligned_cols=48  Identities=27%  Similarity=0.408  Sum_probs=24.9

Q ss_pred             CCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHH
Q psy7268          76 GKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQ  131 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Q  131 (134)
                      .+..+++-..|.|||+..+. ++..+.....      ......+|||+|. .+..|
T Consensus        25 ~~g~lL~de~GlGKT~~~i~-~~~~l~~~~~------~~~~~~~LIv~P~-~l~~~   72 (299)
T PF00176_consen   25 PRGGLLADEMGLGKTITAIA-LISYLKNEFP------QRGEKKTLIVVPS-SLLSQ   72 (299)
T ss_dssp             T-EEEE---TTSSHHHHHHH-HHHHHHHCCT------TSS-S-EEEEE-T-TTHHH
T ss_pred             CCCEEEEECCCCCchhhhhh-hhhhhhhccc------cccccceeEeecc-chhhh
Confidence            45689999999999987744 4444433221      0011249999999 44433

g., SNF2, STH1, brahma, MOT1), DNA repair (e.g., ERCC6, RAD16, RAD5), DNA recombination (e.g., RAD54), and chromatin unwinding (e.g., ISWI) as well as a variety of other proteins with little functional information (e.g., lodestar, ETL1) [, ]. SNF2 functions as the ATPase component of the SNF2/SWI multisubunit complex, which utilises energy derived from ATP hydrolysis to disrupt histone-DNA interactions, resulting in the increased accessibility of DNA to transcription factors. Proteins that contain this domain appear to be distantly related to the DEAX box helicases IPR001410 from INTERPRO, however no helicase activity has ever been demonstrated for these proteins. ; GO: 0003677 DNA binding, 0005524 ATP binding; PDB: 1Z63_B 1Z3I_X 3DMQ_A 3MWY_W.

>COG4962 CpaF Flp pilus assembly protein, ATPase CpaF [Intracellular trafficking and secretion]

Probab=96.06  E-value=0.025  Score=44.31  Aligned_cols=35  Identities=17%  Similarity=0.115  Sum_probs=30.2

Q ss_pred             CCCCChHHHHHHHHHHHcCC-CeEEEcCCCCchhHH
Q psy7268          58 GLTTPTEIQKYSIPTLLSGK-SAILVAETGCGKTLS   92 (134)
Q Consensus        58 g~~~~t~iQ~~~i~~~~~g~-dvli~a~tGsGKT~~   92 (134)
                      .|..+++-|...+-.+..++ ++++++.||||||..
T Consensus       154 ~~gt~~~~~a~~L~~av~~r~NILisGGTGSGKTTl  189 (355)
T COG4962         154 IFGTMIRRAAKFLRRAVGIRCNILISGGTGSGKTTL  189 (355)
T ss_pred             HcCCcCHHHHHHHHHHHhhceeEEEeCCCCCCHHHH
Confidence            47889999999988877666 999999999999954

>TIGR01447 recD exodeoxyribonuclease V, alpha subunit

Probab=96.01  E-value=0.028  Score=47.06  Aligned_cols=61  Identities=16%  Similarity=0.232  Sum_probs=42.1

Q ss_pred             HHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHH
Q psy7268          64 EIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQ  131 (134)
Q Consensus        64 ~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Q  131 (134)
                      +.|+.++..++.++-.++.|++|||||... ..++..+.+...      .....++++.+||---|..
T Consensus       148 ~~Qk~A~~~al~~~~~vitGgpGTGKTt~v-~~ll~~l~~~~~------~~~~~~I~l~APTGkAA~r  208 (586)
T TIGR01447       148 NWQKVAVALALKSNFSLITGGPGTGKTTTV-ARLLLALVKQSP------KQGKLRIALAAPTGKAAAR  208 (586)
T ss_pred             HHHHHHHHHHhhCCeEEEEcCCCCCHHHHH-HHHHHHHHHhcc------ccCCCcEEEECCcHHHHHH
Confidence            689999999999999999999999999764 233333322111      0013578899999655544

This family describes the exodeoxyribonuclease V alpha subunit, RecD. RecD is part of a RecBCD complex. A related family in the Gram-positive bacteria separates in a phylogenetic tree, has an additional N-terminal extension of about 200 residues, and is not supported as a member of a RecBCD complex by neighboring genes. The related family is consequently described by a different model.

>cd01130 VirB11-like_ATPase Type IV secretory pathway component VirB11, and related ATPases

Probab=95.96  E-value=0.018  Score=40.91  Aligned_cols=39  Identities=23%  Similarity=0.252  Sum_probs=27.7

Q ss_pred             HHHHCCCCCChHHHHHHHHH-HHcCCCeEEEcCCCCchhHHh
Q psy7268          53 IFTKRGLTTPTEIQKYSIPT-LLSGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        53 ~l~~~g~~~~t~iQ~~~i~~-~~~g~dvli~a~tGsGKT~~~   93 (134)
                      .|.+.|  ..++-|...+.. +..|..+++.++||+|||...
T Consensus         3 ~l~~~g--~~~~~~~~~l~~~v~~g~~i~I~G~tGSGKTTll   42 (186)
T cd01130           3 DLIAQG--TFSPLQAAYLWLAVEARKNILISGGTGSGKTTLL   42 (186)
T ss_pred             HHHHcC--CCCHHHHHHHHHHHhCCCEEEEECCCCCCHHHHH
Confidence            344444  355666666655 447889999999999999654

The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to plant cells. The pilus is a fibrous cell surface organelle, which mediates adhesion between bacteria during conjugative transfer or between bacteria and host eukaryotic cells during infection. VirB11- related ATPases include the archaeal flagella biosynthesis protein and the pilus assembly proteins CpaF/TadA and TrbB. This alignment contains the C-terminal domain, which is the ATPase.

>PRK13900 type IV secretion system ATPase VirB11; Provisional

Probab=95.96  E-value=0.038  Score=43.08  Aligned_cols=30  Identities=27%  Similarity=0.334  Sum_probs=22.4

Q ss_pred             HHHcCCCeEEEcCCCCchhHHhHHHHHHHHH
Q psy7268          72 TLLSGKSAILVAETGCGKTLSFLAPLVQQIL  102 (134)
Q Consensus        72 ~~~~g~dvli~a~tGsGKT~~~~lpil~~~~  102 (134)
                      ++..+.+++++|+||||||.. +-.++..+-
T Consensus       156 ~v~~~~nili~G~tgSGKTTl-l~aL~~~ip  185 (332)
T PRK13900        156 AVISKKNIIISGGTSTGKTTF-TNAALREIP  185 (332)
T ss_pred             HHHcCCcEEEECCCCCCHHHH-HHHHHhhCC
Confidence            345788999999999999954 355555553

>KOG1132|consensus

Probab=95.89  E-value=0.012  Score=50.84  Aligned_cols=46  Identities=24%  Similarity=0.306  Sum_probs=36.8

Q ss_pred             CCCCChHHHHHHHHHHH----cCCCeEEEcCCCCchhHHhHHHHHHHHHhh
Q psy7268          58 GLTTPTEIQKYSIPTLL----SGKSAILVAETGCGKTLSFLAPLVQQILTW  104 (134)
Q Consensus        58 g~~~~t~iQ~~~i~~~~----~g~dvli~a~tGsGKT~~~~lpil~~~~~~  104 (134)
                      .| .|++.|...+..++    .+.+.++.+|||+|||++.+-..|......
T Consensus        19 P~-qpY~~Q~a~M~rvl~~L~~~q~~llESPTGTGKSLsLLCS~LAW~q~~   68 (945)
T KOG1132|consen   19 PF-QPYPTQLAFMTRVLSCLDRKQNGLLESPTGTGKSLSLLCSTLAWQQHL   68 (945)
T ss_pred             cC-CcchHHHHHHHHHHHHHHHhhhhhccCCCCCCccHHHHHHHHHHHHHh
Confidence            45 77999998887665    456789999999999999987777766543

>PRK10436 hypothetical protein; Provisional

Probab=95.87  E-value=0.032  Score=45.43  Aligned_cols=46  Identities=22%  Similarity=0.263  Sum_probs=30.3

Q ss_pred             HHHHCCCCCChHHHHHHHHHHHc--CCCeEEEcCCCCchhHHhHHHHHHHHH
Q psy7268          53 IFTKRGLTTPTEIQKYSIPTLLS--GKSAILVAETGCGKTLSFLAPLVQQIL  102 (134)
Q Consensus        53 ~l~~~g~~~~t~iQ~~~i~~~~~--g~dvli~a~tGsGKT~~~~lpil~~~~  102 (134)
                      .|.++|+   .+-|...+..++.  +.-+++.||||||||... ..++..+.
T Consensus       196 ~L~~LG~---~~~~~~~l~~~~~~~~GliLvtGpTGSGKTTtL-~a~l~~~~  243 (462)
T PRK10436        196 DLETLGM---TPAQLAQFRQALQQPQGLILVTGPTGSGKTVTL-YSALQTLN  243 (462)
T ss_pred             CHHHcCc---CHHHHHHHHHHHHhcCCeEEEECCCCCChHHHH-HHHHHhhC
Confidence            3455565   4556666655543  345889999999999765 45666654

>PRK13764 ATPase; Provisional

Probab=95.87  E-value=0.026  Score=47.33  Aligned_cols=27  Identities=15%  Similarity=0.272  Sum_probs=21.0

Q ss_pred             cCCCeEEEcCCCCchhHHhHHHHHHHHH
Q psy7268          75 SGKSAILVAETGCGKTLSFLAPLVQQIL  102 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~~lpil~~~~  102 (134)
                      .+++++++|+||||||.. +-.++..+.
T Consensus       256 ~~~~ILIsG~TGSGKTTl-l~AL~~~i~  282 (602)
T PRK13764        256 RAEGILIAGAPGAGKSTF-AQALAEFYA  282 (602)
T ss_pred             cCCEEEEECCCCCCHHHH-HHHHHHHHh
Confidence            467899999999999964 466666664

>COG4098 comFA Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [DNA replication, recombination, and repair]

Probab=95.86  E-value=0.031  Score=43.95  Aligned_cols=61  Identities=23%  Similarity=0.257  Sum_probs=46.2

Q ss_pred             CCChHHHHHHHHHHH----cCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHh
Q psy7268          60 TTPTEIQKYSIPTLL----SGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQI  132 (134)
Q Consensus        60 ~~~t~iQ~~~i~~~~----~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi  132 (134)
                      ..+|+.|+.+-..++    +.+|.++.|-||+|||.-. ...++...+           +|.++.|.+|-.+.+..+
T Consensus        96 G~Ls~~Q~~as~~l~q~i~~k~~~lv~AV~GaGKTEMi-f~~i~~al~-----------~G~~vciASPRvDVclEl  160 (441)
T COG4098          96 GTLSPGQKKASNQLVQYIKQKEDTLVWAVTGAGKTEMI-FQGIEQALN-----------QGGRVCIASPRVDVCLEL  160 (441)
T ss_pred             cccChhHHHHHHHHHHHHHhcCcEEEEEecCCCchhhh-HHHHHHHHh-----------cCCeEEEecCcccchHHH
Confidence            478999988876544    6789999999999999764 555666655           677888888876655444

>PRK05298 excinuclease ABC subunit B; Provisional

Probab=95.85  E-value=0.026  Score=47.79  Aligned_cols=60  Identities=25%  Similarity=0.404  Sum_probs=45.4

Q ss_pred             CCCCChHHHHHHHHHHHc----C-CCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHh
Q psy7268          58 GLTTPTEIQKYSIPTLLS----G-KSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQI  132 (134)
Q Consensus        58 g~~~~t~iQ~~~i~~~~~----g-~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi  132 (134)
                      +| .|++.|..++..+.+    | +..++.+.+|+||++... .++...              +..+|||+|+.+.|.|+
T Consensus        10 ~~-~~~~~Q~~ai~~l~~~~~~~~~~~ll~Gl~gs~ka~lia-~l~~~~--------------~r~vLIVt~~~~~A~~l   73 (652)
T PRK05298         10 PY-KPAGDQPQAIEELVEGIEAGEKHQTLLGVTGSGKTFTMA-NVIARL--------------QRPTLVLAHNKTLAAQL   73 (652)
T ss_pred             CC-CCChHHHHHHHHHHHhhhcCCCcEEEEcCCCcHHHHHHH-HHHHHh--------------CCCEEEEECCHHHHHHH
Confidence            56 899999999988763    3 256789999999997743 222221              23599999999999998


Q ss_pred             c
Q psy7268         133 G  133 (134)
Q Consensus       133 ~  133 (134)
                      +
T Consensus        74 ~   74 (652)
T PRK05298         74 Y   74 (652)
T ss_pred             H
Confidence            6

>COG3973 Superfamily I DNA and RNA helicases [General function prediction only]

Probab=95.79  E-value=0.086  Score=44.30  Aligned_cols=85  Identities=24%  Similarity=0.318  Sum_probs=54.3

Q ss_pred             cCCCCHHHH-HHHHHCCCCCChH----HHHHHHHHHHc--CCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCC
Q psy7268          43 DTGLAPEII-DIFTKRGLTTPTE----IQKYSIPTLLS--GKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELN  115 (134)
Q Consensus        43 ~~~l~~~i~-~~l~~~g~~~~t~----iQ~~~i~~~~~--g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~  115 (134)
                      +.++.++++ .+|.+.--.++..    +|.+==..+..  ++-++|+|..|||||.+.+-=+...++....      ...
T Consensus       186 d~~~~dEvL~~~Lek~ss~~mrdIV~TIQkEQneIIR~ek~~ilVVQGaAGSGKTtiALHRvAyLlY~~R~------~l~  259 (747)
T COG3973         186 DTGGRDEVLQRVLEKNSSAKMRDIVETIQKEQNEIIRFEKNKILVVQGAAGSGKTTIALHRVAYLLYGYRG------PLQ  259 (747)
T ss_pred             CCchHHHHHHHHHHhccchhHHHHHHHhhHhHHHHHhccCCCeEEEecCCCCCchhHHHHHHHHHHhcccc------ccc
Confidence            455665555 6677653334433    45554445553  4458899999999999987666555554321      112


Q ss_pred             CcEEEEEcCcHHHHHHhc
Q psy7268         116 APLALIITPGRELVFQIG  133 (134)
Q Consensus       116 ~~~~lil~Pt~~La~Qi~  133 (134)
                      +..++|+.|++-+..-|.
T Consensus       260 ~k~vlvl~PN~vFleYis  277 (747)
T COG3973         260 AKPVLVLGPNRVFLEYIS  277 (747)
T ss_pred             cCceEEEcCcHHHHHHHH
Confidence            334999999998876653

>TIGR01075 uvrD DNA helicase II

Probab=95.79  E-value=0.027  Score=48.04  Aligned_cols=63  Identities=11%  Similarity=0.137  Sum_probs=44.3

Q ss_pred             CCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHh
Q psy7268          60 TTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQI  132 (134)
Q Consensus        60 ~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi  132 (134)
                      ..+++-|++++..  ....++|.|..|||||.+..-=+...+.....        ...++|+++-|+.-|..+
T Consensus         3 ~~Ln~~Q~~av~~--~~g~~lV~AgaGSGKT~~L~~Ria~Li~~~~v--------~p~~IL~lTFTnkAA~em   65 (715)
T TIGR01075         3 DGLNDKQREAVAA--PPGNLLVLAGAGSGKTRVLTHRIAWLLSVENA--------SPHSIMAVTFTNKAAAEM   65 (715)
T ss_pred             cccCHHHHHHHcC--CCCCEEEEecCCCCHHHHHHHHHHHHHHcCCC--------CHHHeEeeeccHHHHHHH
Confidence            3578999998854  34579999999999998865444444422111        234689999999888765

Designed to identify uvrD members of the uvrD/rep subfamily.

>PRK04914 ATP-dependent helicase HepA; Validated

Probab=95.77  E-value=0.049  Score=48.00  Aligned_cols=60  Identities=30%  Similarity=0.284  Sum_probs=43.8

Q ss_pred             CChHHHHHHHHHHHcC--CCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHH
Q psy7268          61 TPTEIQKYSIPTLLSG--KSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQ  131 (134)
Q Consensus        61 ~~t~iQ~~~i~~~~~g--~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Q  131 (134)
                      .|.|+|..+.-.++..  ..+++.-..|.|||.-..+.+-..+...          ...++|||||. .|..|
T Consensus       152 ~l~pHQl~~~~~vl~~~~~R~LLADEvGLGKTIeAglil~~l~~~g----------~~~rvLIVvP~-sL~~Q  213 (956)
T PRK04914        152 SLIPHQLYIAHEVGRRHAPRVLLADEVGLGKTIEAGMIIHQQLLTG----------RAERVLILVPE-TLQHQ  213 (956)
T ss_pred             CCCHHHHHHHHHHhhccCCCEEEEeCCcCcHHHHHHHHHHHHHHcC----------CCCcEEEEcCH-HHHHH
Confidence            5899999988776543  3689999999999988855554444321          23479999997 67665

>TIGR02538 type_IV_pilB type IV-A pilus assembly ATPase PilB

Probab=95.76  E-value=0.035  Score=46.26  Aligned_cols=46  Identities=22%  Similarity=0.218  Sum_probs=31.7

Q ss_pred             HHHHCCCCCChHHHHHHHHHHHc--CCCeEEEcCCCCchhHHhHHHHHHHHH
Q psy7268          53 IFTKRGLTTPTEIQKYSIPTLLS--GKSAILVAETGCGKTLSFLAPLVQQIL  102 (134)
Q Consensus        53 ~l~~~g~~~~t~iQ~~~i~~~~~--g~dvli~a~tGsGKT~~~~lpil~~~~  102 (134)
                      .|.++||   .+-|...+..++.  ..-++++||||||||... ..++..+.
T Consensus       294 ~l~~lg~---~~~~~~~l~~~~~~~~Glilv~G~tGSGKTTtl-~a~l~~~~  341 (564)
T TIGR02538       294 DIDKLGF---EPDQKALFLEAIHKPQGMVLVTGPTGSGKTVSL-YTALNILN  341 (564)
T ss_pred             CHHHcCC---CHHHHHHHHHHHHhcCCeEEEECCCCCCHHHHH-HHHHHhhC
Confidence            4566676   5566666666554  334789999999999774 55666664

This model describes a protein of type IV pilus biogenesis designated PilB in Pseudomonas aeruginosa but PilF in Neisseria gonorrhoeae; the more common usage, reflected here, is PilB. This protein is an ATPase involved in protein export for pilin assembly and is closely related to GspE (TIGR02533) of type II secretion, also called the main terminal branch of the general secretion pathway. Note that type IV pilus systems are often divided into type IV-A and IV-B, with the latter group including bundle-forming pilus, mannose-sensitive hemagglutinin, etc. Members of this family are found in type IV-A systems.

>TIGR02524 dot_icm_DotB Dot/Icm secretion system ATPase DotB

Probab=95.68  E-value=0.044  Score=43.18  Aligned_cols=27  Identities=19%  Similarity=0.413  Sum_probs=20.5

Q ss_pred             cCCCeEEEcCCCCchhHHhHHHHHHHHH
Q psy7268          75 SGKSAILVAETGCGKTLSFLAPLVQQIL  102 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~~lpil~~~~  102 (134)
                      .+.-++++||||||||... -.++..+.
T Consensus       133 ~~glilI~GpTGSGKTTtL-~aLl~~i~  159 (358)
T TIGR02524       133 QEGIVFITGATGSGKSTLL-AAIIRELA  159 (358)
T ss_pred             cCCEEEEECCCCCCHHHHH-HHHHHHHh
Confidence            5667999999999999664 55666554

Members of this protein family are the DotB component of Dot/Icm secretion systems, as found in obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii. While this system resembles type IV secretion systems and has been called a form of type IV, the liturature now seems to favor calling this the Dot/Icm system. This family is most closely related to TraJ proteins of plasmid transfer, rather than to proteins of other type IV secretion systems.

>TIGR02785 addA_Gpos recombination helicase AddA, Firmicutes type

Probab=95.63  E-value=0.04  Score=49.84  Aligned_cols=60  Identities=22%  Similarity=0.260  Sum_probs=45.6

Q ss_pred             ChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHh
Q psy7268          62 PTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQI  132 (134)
Q Consensus        62 ~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi  132 (134)
                      .|+-|.++|.  ..|++++|.|.-|||||.+.+-=++..+....         .--+.++|+=|+.-|..+
T Consensus         2 ~t~~Q~~ai~--~~~~~~lv~A~AGsGKT~~lv~r~~~~~~~~~---------~~~~il~~tFt~~aa~e~   61 (1232)
T TIGR02785         2 WTDEQWQAIY--TRGQNILVSASAGSGKTAVLVERIIKKILRGV---------DIDRLLVVTFTNAAAREM   61 (1232)
T ss_pred             CCHHHHHHHh--CCCCCEEEEecCCCcHHHHHHHHHHHHHhcCC---------CHhhEEEEeccHHHHHHH
Confidence            5889999996  46889999999999999888666666664320         223589999888877543

AddAB, also called RexAB, substitutes for RecBCD in several bacterial lineages. These DNA recombination proteins act before synapse and are particularly important for DNA repair of double-stranded breaks by homologous recombination. The term AddAB is used broadly, with AddA homologous between the Firmicutes (as modeled here) and the alphaproteobacteria, while the partner AddB proteins show no strong homology across the two groups of species.

>PRK13826 Dtr system oriT relaxase; Provisional

Probab=95.61  E-value=0.14  Score=45.93  Aligned_cols=75  Identities=15%  Similarity=0.107  Sum_probs=52.6

Q ss_pred             CCCHHHHHHHHHCCCCCChHHHHHHHHHHHc-CCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEc
Q psy7268          45 GLAPEIIDIFTKRGLTTPTEIQKYSIPTLLS-GKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIIT  123 (134)
Q Consensus        45 ~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~-g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~  123 (134)
                      ++++..+++....++ .+++-|..++..+.. ++-+++.|+.|+|||... -.+...+..           .+.+++.++
T Consensus       366 ~v~~~~l~a~~~~~~-~Ls~eQ~~Av~~i~~~~r~~~v~G~AGTGKTt~l-~~~~~~~e~-----------~G~~V~g~A  432 (1102)
T PRK13826        366 GVREAVLAATFARHA-RLSDEQKTAIEHVAGPARIAAVVGRAGAGKTTMM-KAAREAWEA-----------AGYRVVGGA  432 (1102)
T ss_pred             CCCHHHHHHHHhcCC-CCCHHHHHHHHHHhccCCeEEEEeCCCCCHHHHH-HHHHHHHHH-----------cCCeEEEEc
Confidence            355666665555455 789999999998864 345788999999999654 334444332           467788899


Q ss_pred             CcHHHHHHh
Q psy7268         124 PGRELVFQI  132 (134)
Q Consensus       124 Pt~~La~Qi  132 (134)
                      ||---|..+
T Consensus       433 pTgkAA~~L  441 (1102)
T PRK13826        433 LAGKAAEGL  441 (1102)
T ss_pred             CcHHHHHHH
Confidence            997666554

>PF12340 DUF3638: Protein of unknown function (DUF3638); InterPro: IPR022099 This domain family is found in eukaryotes, and is approximately 230 amino acids in length

Probab=95.59  E-value=0.095  Score=38.85  Aligned_cols=80  Identities=19%  Similarity=0.262  Sum_probs=57.8

Q ss_pred             CCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHc---CCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCC
Q psy7268          39 GTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLS---GKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELN  115 (134)
Q Consensus        39 ~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~---g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~  115 (134)
                      ..|+...-++.++-.+.. ++ -..+.|.+....+.+   |.+.+.+.-.|.|||.+. +|++..+..+.          
T Consensus         3 ~~w~p~~~P~wLl~E~e~-~i-liR~~Q~~ia~~mi~~~~~~n~v~QlnMGeGKTsVI-~Pmla~~LAdg----------   69 (229)
T PF12340_consen    3 RNWDPMEYPDWLLFEIES-NI-LIRPVQVEIAREMISPPSGKNSVMQLNMGEGKTSVI-VPMLALALADG----------   69 (229)
T ss_pred             CCCCchhChHHHHHHHHc-Cc-eeeHHHHHHHHHHhCCCCCCCeEeeecccCCccchH-HHHHHHHHcCC----------
Confidence            356666667777766665 56 779999999988874   678999999999999665 78888877532          


Q ss_pred             CcEEEEEcCcHHHHHHh
Q psy7268         116 APLALIITPGRELVFQI  132 (134)
Q Consensus       116 ~~~~lil~Pt~~La~Qi  132 (134)
                      ..-+.+++|. +|..|.
T Consensus        70 ~~LvrviVpk-~Ll~q~   85 (229)
T PF12340_consen   70 SRLVRVIVPK-ALLEQM   85 (229)
T ss_pred             CcEEEEEcCH-HHHHHH
Confidence            2345556664 466654

There are two conserved sequence motifs: LLE and NMG.

>TIGR02533 type_II_gspE general secretory pathway protein E

Probab=95.53  E-value=0.041  Score=45.08  Aligned_cols=46  Identities=15%  Similarity=0.237  Sum_probs=30.5

Q ss_pred             HHHHCCCCCChHHHHHHHHHHHcC-CC-eEEEcCCCCchhHHhHHHHHHHHH
Q psy7268          53 IFTKRGLTTPTEIQKYSIPTLLSG-KS-AILVAETGCGKTLSFLAPLVQQIL  102 (134)
Q Consensus        53 ~l~~~g~~~~t~iQ~~~i~~~~~g-~d-vli~a~tGsGKT~~~~lpil~~~~  102 (134)
                      .|.++||   .+-|.+.+..+... +. +++.||||||||... ..++..+.
T Consensus       220 ~l~~Lg~---~~~~~~~l~~~~~~~~GlilitGptGSGKTTtL-~a~L~~l~  267 (486)
T TIGR02533       220 DLETLGM---SPELLSRFERLIRRPHGIILVTGPTGSGKTTTL-YAALSRLN  267 (486)
T ss_pred             CHHHcCC---CHHHHHHHHHHHhcCCCEEEEEcCCCCCHHHHH-HHHHhccC
Confidence            4556666   55566666665543 33 789999999999764 44555553

This family describes GspE, the E protein of the type II secretion system, also called the main terminal branch of the general secretion pathway. This model separates GspE from the PilB protein of type IV pilin biosynthesis.

>PRK08181 transposase; Validated

Probab=95.52  E-value=0.057  Score=40.94  Aligned_cols=46  Identities=22%  Similarity=0.281  Sum_probs=29.4

Q ss_pred             HcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHh
Q psy7268          74 LSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQI  132 (134)
Q Consensus        74 ~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi  132 (134)
                      -.++++++.||+|+|||... ..+...+..           .+..++++ +..+|..++
T Consensus       104 ~~~~nlll~Gp~GtGKTHLa-~Aia~~a~~-----------~g~~v~f~-~~~~L~~~l  149 (269)
T PRK08181        104 AKGANLLLFGPPGGGKSHLA-AAIGLALIE-----------NGWRVLFT-RTTDLVQKL  149 (269)
T ss_pred             hcCceEEEEecCCCcHHHHH-HHHHHHHHH-----------cCCceeee-eHHHHHHHH
Confidence            36789999999999999554 344444433           34445444 456666654

>PRK11773 uvrD DNA-dependent helicase II; Provisional

Probab=95.47  E-value=0.051  Score=46.44  Aligned_cols=62  Identities=11%  Similarity=0.147  Sum_probs=43.9

Q ss_pred             CChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHh
Q psy7268          61 TPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQI  132 (134)
Q Consensus        61 ~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi  132 (134)
                      .+++-|++++..  ....++|.|..|||||.+..-=+...+.....        ...++++|+-|+.-|..+
T Consensus         9 ~Ln~~Q~~av~~--~~g~~lV~AgaGSGKT~vl~~Ria~Li~~~~v--------~p~~IL~lTFT~kAA~Em   70 (721)
T PRK11773          9 SLNDKQREAVAA--PLGNMLVLAGAGSGKTRVLVHRIAWLMQVENA--------SPYSIMAVTFTNKAAAEM   70 (721)
T ss_pred             hcCHHHHHHHhC--CCCCEEEEecCCCCHHHHHHHHHHHHHHcCCC--------ChhHeEeeeccHHHHHHH
Confidence            579999998853  34578999999999998865444444422111        234689999999888765

>PF12846 AAA_10: AAA-like domain

Probab=95.45  E-value=0.036  Score=41.29  Aligned_cols=40  Identities=25%  Similarity=0.528  Sum_probs=27.0

Q ss_pred             CCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHH
Q psy7268          76 GKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRE  127 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~  127 (134)
                      +.++++.|+||+|||.... .++.....           .+..++++=|..+
T Consensus         1 n~h~~i~G~tGsGKT~~~~-~l~~~~~~-----------~g~~~~i~D~~g~   40 (304)
T PF12846_consen    1 NPHTLILGKTGSGKTTLLK-NLLEQLIR-----------RGPRVVIFDPKGD   40 (304)
T ss_pred             CCeEEEECCCCCcHHHHHH-HHHHHHHH-----------cCCCEEEEcCCch
Confidence            3578999999999997765 55555544           3455666555443

>PRK06835 DNA replication protein DnaC; Validated

Probab=95.31  E-value=0.12  Score=40.26  Aligned_cols=45  Identities=18%  Similarity=0.303  Sum_probs=29.7

Q ss_pred             cCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHh
Q psy7268          75 SGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQI  132 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi  132 (134)
                      .+.++++.|++|+|||... ..+...+..           .+..++++ +..+|..++
T Consensus       182 ~~~~Lll~G~~GtGKThLa-~aIa~~l~~-----------~g~~V~y~-t~~~l~~~l  226 (329)
T PRK06835        182 NNENLLFYGNTGTGKTFLS-NCIAKELLD-----------RGKSVIYR-TADELIEIL  226 (329)
T ss_pred             cCCcEEEECCCCCcHHHHH-HHHHHHHHH-----------CCCeEEEE-EHHHHHHHH
Confidence            4578999999999999643 455555553           34556655 445565543

>PRK06526 transposase; Provisional

Probab=95.28  E-value=0.04  Score=41.36  Aligned_cols=21  Identities=19%  Similarity=0.352  Sum_probs=17.7

Q ss_pred             HcCCCeEEEcCCCCchhHHhH
Q psy7268          74 LSGKSAILVAETGCGKTLSFL   94 (134)
Q Consensus        74 ~~g~dvli~a~tGsGKT~~~~   94 (134)
                      ..+.++++.||+|+|||....
T Consensus        96 ~~~~nlll~Gp~GtGKThLa~  116 (254)
T PRK06526         96 TGKENVVFLGPPGTGKTHLAI  116 (254)
T ss_pred             hcCceEEEEeCCCCchHHHHH
Confidence            367899999999999997653

>PRK14873 primosome assembly protein PriA; Provisional

Probab=95.28  E-value=0.019  Score=48.67  Aligned_cols=41  Identities=17%  Similarity=0.118  Sum_probs=31.9

Q ss_pred             EEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          81 LVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        81 i~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      ..+.+|||||..|+-.+-..+.            .|.++|+++|...|+.|+.
T Consensus       165 ~~~~~GSGKTevyl~~i~~~l~------------~Gk~vLvLvPEi~lt~q~~  205 (665)
T PRK14873        165 WQALPGEDWARRLAAAAAATLR------------AGRGALVVVPDQRDVDRLE  205 (665)
T ss_pred             hhcCCCCcHHHHHHHHHHHHHH------------cCCeEEEEecchhhHHHHH
Confidence            3444699999999666555553            4668999999999999975

>PF10412 TrwB_AAD_bind: Type IV secretion-system coupling protein DNA-binding domain; InterPro: IPR019476 The plasmid conjugative coupling protein TraD (also known as TrwB) is a basic integral inner-membrane nucleoside-triphosphate-binding protein

Probab=95.23  E-value=0.025  Score=44.87  Aligned_cols=48  Identities=25%  Similarity=0.362  Sum_probs=31.7

Q ss_pred             HHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHh
Q psy7268          73 LLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQI  132 (134)
Q Consensus        73 ~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi  132 (134)
                      -...+++++.|.||+|||. ++-.++..+..           .+-++||.=|.-+.....
T Consensus        12 ~~e~~~~li~G~~GsGKT~-~i~~ll~~~~~-----------~g~~~iI~D~kg~~~~~f   59 (386)
T PF10412_consen   12 DSENRHILIIGATGSGKTQ-AIRHLLDQIRA-----------RGDRAIIYDPKGEFTERF   59 (386)
T ss_dssp             GGGGG-EEEEE-TTSSHHH-HHHHHHHHHHH-----------TT-EEEEEEETTHHHHHH
T ss_pred             chhhCcEEEECCCCCCHHH-HHHHHHHHHHH-----------cCCEEEEEECCchHHHHh
Confidence            3456789999999999996 44677777765           345677666666655443

It is the structural prototype for the type IV secretion system coupling proteins, a family of proteins essential for macromolecular transport between cells []. This protein forms hexamers from six structurally very similar protomers []. This hexamer contains a central channel running from the cytosolic pole (formed by the all-alpha domains) to the membrane pole ending at the transmembrane pore shaped by 12 transmembrane helices, rendering an overall mushroom-like structure. The TrwB all-alpha domain appears to be the DNA-binding domain of the structure. ; PDB: 1E9S_D 1E9R_F 1GKI_B 1GL7_G 1GL6_A.

>PRK12903 secA preprotein translocase subunit SecA; Reviewed

Probab=95.20  E-value=0.095  Score=45.70  Aligned_cols=59  Identities=25%  Similarity=0.263  Sum_probs=46.5

Q ss_pred             CCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHH
Q psy7268          57 RGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVF  130 (134)
Q Consensus        57 ~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~  130 (134)
                      +|. +|+++|-..--.+..|+  +....||-|||++..+|+.-..+            .|..+-|++.+-.||.
T Consensus        75 lG~-r~ydVQliGglvLh~G~--IAEMkTGEGKTLvAtLpayLnAL------------~GkgVhVVTvNdYLA~  133 (925)
T PRK12903         75 LGK-RPYDVQIIGGIILDLGS--VAEMKTGEGKTITSIAPVYLNAL------------TGKGVIVSTVNEYLAE  133 (925)
T ss_pred             hCC-CcCchHHHHHHHHhcCC--eeeecCCCCccHHHHHHHHHHHh------------cCCceEEEecchhhhh
Confidence            477 88999988886666664  68999999999999998865443            4566788888888875

>COG0630 VirB11 Type IV secretory pathway, VirB11 components, and related ATPases involved in archaeal flagella biosynthesis [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=95.17  E-value=0.075  Score=41.10  Aligned_cols=58  Identities=28%  Similarity=0.287  Sum_probs=36.0

Q ss_pred             CCcccCCCCHHHHHHHHHCCCCCChHHHHH-HHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHH
Q psy7268          39 GTFEDTGLAPEIIDIFTKRGLTTPTEIQKY-SIPTLLSGKSAILVAETGCGKTLSFLAPLVQQIL  102 (134)
Q Consensus        39 ~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~-~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~  102 (134)
                      ..|..-++.+.-   +.+.  ..+++.|.. .|-.+-.+++++++++||||||. ++.+++..+-
T Consensus       110 Rk~~~~~~t~~~---l~~~--gt~~~~~~ayL~~~ie~~~siii~G~t~sGKTt-~lnall~~Ip  168 (312)
T COG0630         110 RKFSDEPITPED---LIEY--GTISPEQAAYLWLAIEARKSIIICGGTASGKTT-LLNALLDFIP  168 (312)
T ss_pred             EcCCCCCCCHHH---Hhhc--CCCCHHHHHHHHHHHHcCCcEEEECCCCCCHHH-HHHHHHHhCC
Confidence            344444444433   3333  345555544 44556689999999999999994 4466665553

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=95.15  E-value=0.026  Score=42.32  Aligned_cols=26  Identities=31%  Similarity=0.277  Sum_probs=21.2

Q ss_pred             HHHHHHHcCCCeEEEcCCCCchhHHh
Q psy7268          68 YSIPTLLSGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        68 ~~i~~~~~g~dvli~a~tGsGKT~~~   93 (134)
                      +++..+..|+++++.|++|+|||...
T Consensus        13 ~~l~~l~~g~~vLL~G~~GtGKT~lA   38 (262)
T TIGR02640        13 RALRYLKSGYPVHLRGPAGTGKTTLA   38 (262)
T ss_pred             HHHHHHhcCCeEEEEcCCCCCHHHHH
Confidence            34445668999999999999999875

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).

>COG1875 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]

Probab=95.15  E-value=0.064  Score=42.57  Aligned_cols=66  Identities=26%  Similarity=0.311  Sum_probs=49.5

Q ss_pred             CCCCChHHHHHHHHHHHcCC-C-eEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHh
Q psy7268          58 GLTTPTEIQKYSIPTLLSGK-S-AILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQI  132 (134)
Q Consensus        58 g~~~~t~iQ~~~i~~~~~g~-d-vli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi  132 (134)
                      |+..-+.-|..|+..++.-. + |.+.++-|||||+-.+.+-++.....+         ...+.|+--|+..+.++|
T Consensus       225 Gi~prn~eQ~~ALdlLld~dI~lV~L~G~AGtGKTlLALaAgleqv~e~~---------~y~KiiVtRp~vpvG~dI  292 (436)
T COG1875         225 GIRPRNAEQRVALDLLLDDDIDLVSLGGKAGTGKTLLALAAGLEQVLERK---------RYRKIIVTRPTVPVGEDI  292 (436)
T ss_pred             ccCcccHHHHHHHHHhcCCCCCeEEeeccCCccHhHHHHHHHHHHHHHHh---------hhceEEEecCCcCccccc
Confidence            77666778888887777543 3 778899999999999999898887654         345677777877665544

>PF09848 DUF2075: Uncharacterized conserved protein (DUF2075); InterPro: IPR018647 This domain, found in putative ATP/GTP binding proteins, has no known function

Probab=95.14  E-value=0.034  Score=43.45  Aligned_cols=45  Identities=16%  Similarity=0.203  Sum_probs=31.5

Q ss_pred             eEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          79 AILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        79 vli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      ++|.|..|||||+.. +-++..+...         ..+.++++++.+..|...++
T Consensus         4 ~~I~G~aGTGKTvla-~~l~~~l~~~---------~~~~~~~~l~~n~~l~~~l~   48 (352)
T PF09848_consen    4 ILITGGAGTGKTVLA-LNLAKELQNS---------EEGKKVLYLCGNHPLRNKLR   48 (352)
T ss_pred             EEEEecCCcCHHHHH-HHHHHHhhcc---------ccCCceEEEEecchHHHHHH
Confidence            688999999999876 3334444111         14667899999998887553

It is found in some proteins described as Schlafen family members, which may have a role in hematopoeitic cell differentiation [].

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=95.04  E-value=0.019  Score=37.12  Aligned_cols=18  Identities=33%  Similarity=0.527  Sum_probs=15.4

Q ss_pred             CCCeEEEcCCCCchhHHh
Q psy7268          76 GKSAILVAETGCGKTLSF   93 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~   93 (134)
                      +..+++.||+|+|||...
T Consensus         2 ~~~~~l~G~~G~GKTtl~   19 (148)
T smart00382        2 GEVILIVGPPGSGKTTLA   19 (148)
T ss_pred             CCEEEEECCCCCcHHHHH
Confidence            567899999999999665

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.

>PF00437 T2SE: Type II/IV secretion system protein; InterPro: IPR001482 A number of bacterial proteins, some of which are involved in a general secretion pathway (GSP) for the export of proteins (also called the type II pathway) belong to this group [, ]

Probab=94.98  E-value=0.031  Score=41.84  Aligned_cols=30  Identities=23%  Similarity=0.376  Sum_probs=22.5

Q ss_pred             HHcCCCeEEEcCCCCchhHHhHHHHHHHHHh
Q psy7268          73 LLSGKSAILVAETGCGKTLSFLAPLVQQILT  103 (134)
Q Consensus        73 ~~~g~dvli~a~tGsGKT~~~~lpil~~~~~  103 (134)
                      +..+.+++++|+||||||... -.++..+..
T Consensus       124 v~~~~~ili~G~tGSGKTT~l-~all~~i~~  153 (270)
T PF00437_consen  124 VRGRGNILISGPTGSGKTTLL-NALLEEIPP  153 (270)
T ss_dssp             HHTTEEEEEEESTTSSHHHHH-HHHHHHCHT
T ss_pred             cccceEEEEECCCccccchHH-HHHhhhccc
Confidence            345789999999999999654 555665543

These proteins are probably located in the cytoplasm and, on the basis of the presence of a conserved P-loop region IPR001687 from INTERPRO, bind ATP.; GO: 0005524 ATP binding, 0006810 transport, 0005622 intracellular; PDB: 1NLZ_C 2PT7_B 1OPX_A 1NLY_A 1G6O_B 2OAQ_2 2OAP_1 2JNQ_A 2JMZ_A 2GZA_B ....

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=94.98  E-value=0.2  Score=38.13  Aligned_cols=19  Identities=42%  Similarity=0.574  Sum_probs=15.3

Q ss_pred             CCCeEEEcCCCCchhHHhH
Q psy7268          76 GKSAILVAETGCGKTLSFL   94 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~~   94 (134)
                      ++.++++||||+|||....
T Consensus       194 ~~vi~~vGptGvGKTTt~~  212 (282)
T TIGR03499       194 GGVIALVGPTGVGKTTTLA  212 (282)
T ss_pred             CeEEEEECCCCCCHHHHHH
Confidence            3458899999999997753

>TIGR03819 heli_sec_ATPase helicase/secretion neighborhood ATPase

Probab=94.97  E-value=0.1  Score=40.85  Aligned_cols=42  Identities=17%  Similarity=0.174  Sum_probs=28.7

Q ss_pred             HHHHHHHCCCCCChHHHHHHHHHH-HcCCCeEEEcCCCCchhHHh
Q psy7268          50 IIDIFTKRGLTTPTEIQKYSIPTL-LSGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        50 i~~~l~~~g~~~~t~iQ~~~i~~~-~~g~dvli~a~tGsGKT~~~   93 (134)
                      -++.+.+.|+  +++.+...+..+ ..+.+++++++||+|||...
T Consensus       153 tl~~l~~~g~--~~~~~~~~L~~~v~~~~~ili~G~tGsGKTTll  195 (340)
T TIGR03819       153 TLDELVASGT--FPPGVARLLRAIVAARLAFLISGGTGSGKTTLL  195 (340)
T ss_pred             CHHHHHHcCC--CCHHHHHHHHHHHhCCCeEEEECCCCCCHHHHH
Confidence            3455566565  445566666554 46779999999999998543

Members of this protein family comprise a distinct clade of putative ATPase associated with an integral membrane complex likely to act in pilus formation, secretion, or conjugal transfer. The association of most members with a nearby gene for a DEAH-box helicase suggests a role in conjugal transfer.

>cd01127 TrwB Bacterial conjugation protein TrwB, ATP binding domain

Probab=94.93  E-value=0.037  Score=44.21  Aligned_cols=33  Identities=24%  Similarity=0.419  Sum_probs=23.3

Q ss_pred             HHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHh
Q psy7268          70 IPTLLSGKSAILVAETGCGKTLSFLAPLVQQILT  103 (134)
Q Consensus        70 i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~  103 (134)
                      +|.-...+++++.|+||+|||.. +..++..+..
T Consensus        36 ~~~~~~~~h~~i~g~tGsGKt~~-i~~l~~~~~~   68 (410)
T cd01127          36 FPKDAEEAHTMIIGTTGTGKTTQ-IRELLASIRA   68 (410)
T ss_pred             CCcchhhccEEEEcCCCCCHHHH-HHHHHHHHHh
Confidence            44444567999999999999975 4455555543

TrwB is a homohexamer encoded by conjugative plasmids in Gram-negative bacteria. TrwB also has an all alpha domain which has been hypothesized to be responsible for DNA binding. TrwB is a component of Type IV secretion and is responsible for the horizontal transfer of DNA between bacteria.

>PF06745 KaiC: KaiC; InterPro: IPR014774 This entry represents a domain within bacterial and archaeal proteins, most of which are hypothetical

Probab=94.78  E-value=0.073  Score=38.69  Aligned_cols=38  Identities=21%  Similarity=0.269  Sum_probs=25.2

Q ss_pred             cCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEc
Q psy7268          75 SGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIIT  123 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~  123 (134)
                      .|..+++.|++|+|||.-.+--+...+.+           .+-++++++
T Consensus        18 ~gs~~li~G~~GsGKT~l~~q~l~~~~~~-----------~ge~vlyvs   55 (226)
T PF06745_consen   18 KGSVVLISGPPGSGKTTLALQFLYNGLKN-----------FGEKVLYVS   55 (226)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHHHH-----------HT--EEEEE
T ss_pred             CCcEEEEEeCCCCCcHHHHHHHHHHhhhh-----------cCCcEEEEE
Confidence            45679999999999997664444444432           145678877

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 ....

>PF02534 T4SS-DNA_transf: Type IV secretory system Conjugative DNA transfer; InterPro: IPR003688 This entry represents TraG proteins and their homologues

Probab=94.75  E-value=0.02  Score=46.13  Aligned_cols=23  Identities=35%  Similarity=0.622  Sum_probs=20.6

Q ss_pred             CCeEEEcCCCCchhHHhHHHHHH
Q psy7268          77 KSAILVAETGCGKTLSFLAPLVQ   99 (134)
Q Consensus        77 ~dvli~a~tGsGKT~~~~lpil~   99 (134)
                      .++++.||||||||..+++|.+.
T Consensus        45 ~h~lvig~tgSGKt~~~viP~ll   67 (469)
T PF02534_consen   45 THVLVIGPTGSGKTTSFVIPNLL   67 (469)
T ss_pred             eEEEEEeCCCCCccceeeHhHHH
Confidence            46999999999999999999774

These proteins contain a P-loop and walker-B site for nucleotide binding. TraG is essential for DNA transfer in bacterial conjugation. These proteins are thought to mediate interactions between the DNA-processing (Dtr) and the mating pair formation (Mpf) systems [, ].; GO: 0009291 unidirectional conjugation, 0016020 membrane

>PRK06921 hypothetical protein; Provisional

Probab=94.74  E-value=0.31  Score=36.82  Aligned_cols=45  Identities=18%  Similarity=0.141  Sum_probs=28.4

Q ss_pred             cCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHH
Q psy7268          75 SGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQ  131 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Q  131 (134)
                      .+..+++.|++|+|||... ..+...+...          .+..++++. ..++..+
T Consensus       116 ~~~~l~l~G~~G~GKThLa-~aia~~l~~~----------~g~~v~y~~-~~~l~~~  160 (266)
T PRK06921        116 RKNSIALLGQPGSGKTHLL-TAAANELMRK----------KGVPVLYFP-FVEGFGD  160 (266)
T ss_pred             CCCeEEEECCCCCcHHHHH-HHHHHHHhhh----------cCceEEEEE-HHHHHHH
Confidence            3567999999999999544 4555555431          145566654 4454443

>TIGR01073 pcrA ATP-dependent DNA helicase PcrA

Probab=94.69  E-value=0.1  Score=44.63  Aligned_cols=63  Identities=17%  Similarity=0.140  Sum_probs=43.0

Q ss_pred             CCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHh
Q psy7268          60 TTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQI  132 (134)
Q Consensus        60 ~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi  132 (134)
                      ..+++-|.+++..  ...+++|.|..|||||.+..-=+...+.....        ..-++|.++-|+.-|..+
T Consensus         3 ~~Ln~~Q~~av~~--~~g~~lV~AgaGSGKT~~l~~ria~Li~~~~i--------~P~~IL~lTFT~kAA~em   65 (726)
T TIGR01073         3 AHLNPEQREAVKT--TEGPLLIMAGAGSGKTRVLTHRIAHLIAEKNV--------APWNILAITFTNKAAREM   65 (726)
T ss_pred             cccCHHHHHHHhC--CCCCEEEEeCCCCCHHHHHHHHHHHHHHcCCC--------CHHHeeeeeccHHHHHHH
Confidence            3578999998864  34679999999999998875555554432111        123588888887766544

Designed to identify pcrA members of the uvrD/rep subfamily.

>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA

Probab=94.69  E-value=0.09  Score=47.68  Aligned_cols=42  Identities=19%  Similarity=0.219  Sum_probs=28.0

Q ss_pred             CCCCCChHHHH---HHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHH
Q psy7268          57 RGLTTPTEIQK---YSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQ  100 (134)
Q Consensus        57 ~g~~~~t~iQ~---~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~  100 (134)
                      ..|....|+.+   +.+..+..+..++++|+||||||.  .+|.+..
T Consensus        60 ~~~~~~LPi~~~~~~Il~~l~~~~vvii~g~TGSGKTT--qlPq~ll  104 (1283)
T TIGR01967        60 IRYPDNLPVSAKREDIAEAIAENQVVIIAGETGSGKTT--QLPKICL  104 (1283)
T ss_pred             ccCCCCCCHHHHHHHHHHHHHhCceEEEeCCCCCCcHH--HHHHHHH
Confidence            45665566654   344445456678999999999998  3565543

This model represents HrpA, one of two related but uncharacterized DEAH-box ATP-dependent helicases in many Proteobacteria and a few high-GC Gram-positive bacteria. HrpA is about 1300 amino acids long, while its paralog HrpB, also uncharacterized, is about 800 amino acids long. Related characterized eukarotic proteins are RNA helicases associated with pre-mRNA processing.

>KOG0952|consensus

Probab=94.66  E-value=0.0088  Score=52.52  Aligned_cols=61  Identities=23%  Similarity=0.245  Sum_probs=47.5

Q ss_pred             CCChHHHHHHHHHHHc-CCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHH
Q psy7268          60 TTPTEIQKYSIPTLLS-GKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVF  130 (134)
Q Consensus        60 ~~~t~iQ~~~i~~~~~-g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~  130 (134)
                      +...|+|.+.+-.+.. ..++++.+|||+|||++|.+.+.......          .+.+++|++|.++|..
T Consensus       926 ~~fn~~q~~if~~~y~td~~~~~g~ptgsgkt~~ae~a~~~~~~~~----------p~~kvvyIap~kalvk  987 (1230)
T KOG0952|consen  926 KYFNPIQTQIFHCLYHTDLNFLLGAPTGSGKTVVAELAIFRALSYY----------PGSKVVYIAPDKALVK  987 (1230)
T ss_pred             cccCCccceEEEEEeecchhhhhcCCccCcchhHHHHHHHHHhccC----------CCccEEEEcCCchhhc
Confidence            3556677776655543 45789999999999999999988776543          4578999999999875

>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=94.63  E-value=0.072  Score=37.19  Aligned_cols=34  Identities=26%  Similarity=0.280  Sum_probs=22.3

Q ss_pred             eEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcC
Q psy7268          79 AILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITP  124 (134)
Q Consensus        79 vli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~P  124 (134)
                      +++.|++|+|||...+--+.... +           ++.+++|++.
T Consensus         2 ~li~G~~G~GKT~l~~~~~~~~~-~-----------~g~~v~~~s~   35 (187)
T cd01124           2 TLLSGGPGTGKTTFALQFLYAGL-A-----------RGEPGLYVTL   35 (187)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHH-H-----------CCCcEEEEEC
Confidence            68899999999976533333333 2           4556777764

A related protein is found in archaea.

>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI

Probab=94.58  E-value=0.18  Score=47.73  Aligned_cols=61  Identities=25%  Similarity=0.258  Sum_probs=44.4

Q ss_pred             CChHHHHHHHHHHHcCC--CeEEEcCCCCchhHHhH---HHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHh
Q psy7268          61 TPTEIQKYSIPTLLSGK--SAILVAETGCGKTLSFL---APLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQI  132 (134)
Q Consensus        61 ~~t~iQ~~~i~~~~~g~--dvli~a~tGsGKT~~~~---lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi  132 (134)
                      .+++.|+.++..++.+.  -+++.|..|+|||...-   -++.+.+..           .+.+++.++||-.-+..+
T Consensus      1019 ~Lt~~Q~~Ai~~il~~~~~~~~i~G~AGtGKTt~l~~~~~~i~~~~~~-----------~g~~v~glApT~~Aa~~L 1084 (1960)
T TIGR02760      1019 RLTHGQKQAIHLIISTKDRFVAVQGLAGVGKTTMLESRYKPVLQAFES-----------EQLQVIGLAPTHEAVGEL 1084 (1960)
T ss_pred             CCCHHHHHHHHHHHhCCCcEEEEEeCCCCCHHHhHHHHHHHHHHHHHh-----------cCCeEEEEeChHHHHHHH
Confidence            78999999999998764  47788999999996651   122232211           466788899998776655

This protein is a component of the relaxosome complex. In the process of conjugative plasmid transfer the realaxosome binds to the plasmid at the oriT (origin of transfer) site. The relaxase protein TraI mediates the single-strand nicking and ATP-dependent unwinding (relaxation, helicase activity) of the plasmid molecule. These two activities reside in separate domains of the protein.

>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=94.52  E-value=0.067  Score=34.85  Aligned_cols=25  Identities=24%  Similarity=0.369  Sum_probs=18.2

Q ss_pred             CCCeEEEcCCCCchhHHhHHHHHHHH
Q psy7268          76 GKSAILVAETGCGKTLSFLAPLVQQI  101 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~~lpil~~~  101 (134)
                      ++.+++.|++|+|||... --+...+
T Consensus        19 ~~~v~i~G~~G~GKT~l~-~~i~~~~   43 (151)
T cd00009          19 PKNLLLYGPPGTGKTTLA-RAIANEL   43 (151)
T ss_pred             CCeEEEECCCCCCHHHHH-HHHHHHh
Confidence            678999999999999543 3444443

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.

>COG5008 PilU Tfp pilus assembly protein, ATPase PilU [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=94.51  E-value=0.041  Score=42.12  Aligned_cols=23  Identities=30%  Similarity=0.488  Sum_probs=16.9

Q ss_pred             eEEEcCCCCchhHHhHHHHHHHHH
Q psy7268          79 AILVAETGCGKTLSFLAPLVQQIL  102 (134)
Q Consensus        79 vli~a~tGsGKT~~~~lpil~~~~  102 (134)
                      ++++++|||||+... ..++.+..
T Consensus       130 viiVGaTGSGKSTtm-AaMi~yRN  152 (375)
T COG5008         130 VIIVGATGSGKSTTM-AAMIGYRN  152 (375)
T ss_pred             EEEECCCCCCchhhH-HHHhcccc
Confidence            788999999998664 45555443

>PRK07952 DNA replication protein DnaC; Validated

Probab=94.47  E-value=0.23  Score=37.09  Aligned_cols=26  Identities=27%  Similarity=0.383  Sum_probs=19.2

Q ss_pred             CCeEEEcCCCCchhHHhHHHHHHHHHh
Q psy7268          77 KSAILVAETGCGKTLSFLAPLVQQILT  103 (134)
Q Consensus        77 ~dvli~a~tGsGKT~~~~lpil~~~~~  103 (134)
                      ..+++.|++|+|||... ..+...+..
T Consensus       100 ~~~~l~G~~GtGKThLa-~aia~~l~~  125 (244)
T PRK07952        100 ASFIFSGKPGTGKNHLA-AAICNELLL  125 (244)
T ss_pred             ceEEEECCCCCCHHHHH-HHHHHHHHh
Confidence            47999999999999655 455555543

>PRK12377 putative replication protein; Provisional

Probab=94.43  E-value=0.2  Score=37.59  Aligned_cols=44  Identities=11%  Similarity=0.270  Sum_probs=27.7

Q ss_pred             CCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHh
Q psy7268          76 GKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQI  132 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi  132 (134)
                      ..++++.|++|+|||-.. ..+...+..           .+..++++ +..+|..++
T Consensus       101 ~~~l~l~G~~GtGKThLa-~AIa~~l~~-----------~g~~v~~i-~~~~l~~~l  144 (248)
T PRK12377        101 CTNFVFSGKPGTGKNHLA-AAIGNRLLA-----------KGRSVIVV-TVPDVMSRL  144 (248)
T ss_pred             CCeEEEECCCCCCHHHHH-HHHHHHHHH-----------cCCCeEEE-EHHHHHHHH
Confidence            357999999999999544 455555543           33344443 455666544

>PF12775 AAA_7: P-loop containing dynein motor region D3; PDB: 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A

Probab=94.40  E-value=0.031  Score=42.32  Aligned_cols=21  Identities=38%  Similarity=0.627  Sum_probs=17.8

Q ss_pred             HHcCCCeEEEcCCCCchhHHh
Q psy7268          73 LLSGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        73 ~~~g~dvli~a~tGsGKT~~~   93 (134)
                      +.+++.++++||+|+|||...
T Consensus        30 ~~~~~pvLl~G~~GtGKT~li   50 (272)
T PF12775_consen   30 LSNGRPVLLVGPSGTGKTSLI   50 (272)
T ss_dssp             HHCTEEEEEESSTTSSHHHHH
T ss_pred             HHcCCcEEEECCCCCchhHHH
Confidence            447889999999999999653

>COG1219 ClpX ATP-dependent protease Clp, ATPase subunit [Posttranslational modification, protein turnover, chaperones]

Probab=94.27  E-value=0.029  Score=43.84  Aligned_cols=56  Identities=21%  Similarity=0.247  Sum_probs=31.6

Q ss_pred             CCCcccCCCCHHHHHHHHHC--CCCCChHHHHH-HHHHH-------------HcCCCeEEEcCCCCchhHHh
Q psy7268          38 LGTFEDTGLAPEIIDIFTKR--GLTTPTEIQKY-SIPTL-------------LSGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        38 ~~~f~~~~l~~~i~~~l~~~--g~~~~t~iQ~~-~i~~~-------------~~g~dvli~a~tGsGKT~~~   93 (134)
                      ..+.++++-+.+|.+.|.++  |=..--.+=+. +..+.             +...|+++.+|||||||+..
T Consensus        43 ~~~~~~lPtP~eik~~Ld~YVIGQe~AKKvLsVAVYNHYKRl~~~~~~~dvEL~KSNILLiGPTGsGKTlLA  114 (408)
T COG1219          43 EKELSELPTPKEIKAHLDEYVIGQEQAKKVLSVAVYNHYKRLNNKEDNDDVELSKSNILLIGPTGSGKTLLA  114 (408)
T ss_pred             chhhccCCChHHHHHHhhhheecchhhhceeeeeehhHHHHHhccCCCCceeeeeccEEEECCCCCcHHHHH
Confidence            34566777888888888764  21110000000 00111             12347999999999999754

>PRK13700 conjugal transfer protein TraD; Provisional

Probab=94.18  E-value=0.073  Score=45.52  Aligned_cols=72  Identities=17%  Similarity=0.185  Sum_probs=45.6

Q ss_pred             HHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHH
Q psy7268          48 PEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRE  127 (134)
Q Consensus        48 ~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~  127 (134)
                      .++-+.+++.|-..+..+--.-+|.-...+++++.|.||+|||.+. --++..+..           ++-++||.=|+-+
T Consensus       157 ~~l~k~lk~~~~~s~i~I~gvPip~~~E~~H~li~GttGSGKS~~i-~~LL~~ir~-----------RGdrAIIyD~~Ge  224 (732)
T PRK13700        157 KDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVI-RRLANYARQ-----------RGDMVVIYDRSGE  224 (732)
T ss_pred             HHHHHHHHhcCCCCCeeEccccCCcchhhcceEEeCCCCCCHHHHH-HHHHHHHHH-----------cCCeEEEEeCCCc
Confidence            5566677765543333332222333446789999999999999854 666666654           4556777766666


Q ss_pred             HHHH
Q psy7268         128 LVFQ  131 (134)
Q Consensus       128 La~Q  131 (134)
                      ....
T Consensus       225 Fv~~  228 (732)
T PRK13700        225 FVKS  228 (732)
T ss_pred             hHHH
Confidence            5543

>PRK09183 transposase/IS protein; Provisional

Probab=94.16  E-value=0.17  Score=37.98  Aligned_cols=22  Identities=23%  Similarity=0.415  Sum_probs=18.1

Q ss_pred             HHcCCCeEEEcCCCCchhHHhH
Q psy7268          73 LLSGKSAILVAETGCGKTLSFL   94 (134)
Q Consensus        73 ~~~g~dvli~a~tGsGKT~~~~   94 (134)
                      +..|.++++.||+|+|||....
T Consensus        99 i~~~~~v~l~Gp~GtGKThLa~  120 (259)
T PRK09183         99 IERNENIVLLGPSGVGKTHLAI  120 (259)
T ss_pred             hhcCCeEEEEeCCCCCHHHHHH
Confidence            4468899999999999996653

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family

Probab=94.14  E-value=0.11  Score=38.38  Aligned_cols=37  Identities=14%  Similarity=0.162  Sum_probs=26.1

Q ss_pred             cCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEc
Q psy7268          75 SGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIIT  123 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~  123 (134)
                      .|..+++.|++|+|||...+--+...+.            ++-++++++
T Consensus        20 ~gs~~lI~G~pGsGKT~la~~~l~~~~~------------~ge~~lyvs   56 (237)
T TIGR03877        20 ERNVVLLSGGPGTGKSIFSQQFLWNGLQ------------MGEPGIYVA   56 (237)
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHHHH------------cCCcEEEEE
Confidence            4667999999999999766444444442            455677776

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.

>PRK13709 conjugal transfer nickase/helicase TraI; Provisional

Probab=94.12  E-value=0.26  Score=46.15  Aligned_cols=64  Identities=20%  Similarity=0.253  Sum_probs=44.6

Q ss_pred             CChHHHHHHHHHHHcCC--CeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHh
Q psy7268          61 TPTEIQKYSIPTLLSGK--SAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQI  132 (134)
Q Consensus        61 ~~t~iQ~~~i~~~~~g~--dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi  132 (134)
                      .+++-|+.++..++.+.  -+++.|..|+|||... -.++..+....       ...+.+++.++||-.-+..+
T Consensus       967 ~Lt~~Q~~Av~~il~s~dr~~~I~G~AGTGKTT~l-~~v~~~~~~l~-------~~~~~~V~glAPTgrAAk~L 1032 (1747)
T PRK13709        967 GLTSGQRAATRMILESTDRFTVVQGYAGVGKTTQF-RAVMSAVNTLP-------ESERPRVVGLGPTHRAVGEM 1032 (1747)
T ss_pred             CCCHHHHHHHHHHHhCCCcEEEEEeCCCCCHHHHH-HHHHHHHHHhh-------cccCceEEEECCcHHHHHHH
Confidence            68999999999999764  5889999999999663 23333332110       01356788899998666554

>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional

Probab=94.06  E-value=0.25  Score=44.07  Aligned_cols=59  Identities=24%  Similarity=0.363  Sum_probs=41.8

Q ss_pred             CChHHHHHHHHHHH----cCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHH
Q psy7268          61 TPTEIQKYSIPTLL----SGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGREL  128 (134)
Q Consensus        61 ~~t~iQ~~~i~~~~----~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~L  128 (134)
                      .+.++|.+.+..+.    +|.+.|+.-..|.|||+-. +.++..+.....        .....|||||..-+
T Consensus       169 ~Lr~YQleGlnWLi~l~~~g~gGILADEMGLGKTlQa-IalL~~L~~~~~--------~~gp~LIVvP~SlL  231 (1033)
T PLN03142        169 KMRDYQLAGLNWLIRLYENGINGILADEMGLGKTLQT-ISLLGYLHEYRG--------ITGPHMVVAPKSTL  231 (1033)
T ss_pred             chHHHHHHHHHHHHHHHhcCCCEEEEeCCCccHHHHH-HHHHHHHHHhcC--------CCCCEEEEeChHHH
Confidence            67889999998764    6788999999999999875 444444433211        22347999997554

>cd01131 PilT Pilus retraction ATPase PilT

Probab=94.04  E-value=0.094  Score=37.65  Aligned_cols=23  Identities=26%  Similarity=0.525  Sum_probs=17.3

Q ss_pred             eEEEcCCCCchhHHhHHHHHHHHH
Q psy7268          79 AILVAETGCGKTLSFLAPLVQQIL  102 (134)
Q Consensus        79 vli~a~tGsGKT~~~~lpil~~~~  102 (134)
                      ++++||||||||... ..++..+.
T Consensus         4 ilI~GptGSGKTTll-~~ll~~~~   26 (198)
T cd01131           4 VLVTGPTGSGKSTTL-AAMIDYIN   26 (198)
T ss_pred             EEEECCCCCCHHHHH-HHHHHHhh
Confidence            688999999999774 44555554

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.

>KOG1805|consensus

Probab=94.02  E-value=0.11  Score=45.64  Aligned_cols=67  Identities=19%  Similarity=0.273  Sum_probs=45.5

Q ss_pred             CCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcCCC-eEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEE
Q psy7268          44 TGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKS-AILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALII  122 (134)
Q Consensus        44 ~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~d-vli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil  122 (134)
                      ..+.|.+...+    +..++.-|++|+-.++..+| .+|.|=+|+|||...+.-+ ..+..           .+.++|+.
T Consensus       656 ~~~~p~~~~~~----~~~LN~dQr~A~~k~L~aedy~LI~GMPGTGKTTtI~~LI-kiL~~-----------~gkkVLLt  719 (1100)
T KOG1805|consen  656 KVLIPKIKKII----LLRLNNDQRQALLKALAAEDYALILGMPGTGKTTTISLLI-KILVA-----------LGKKVLLT  719 (1100)
T ss_pred             cccCchhhHHH----HhhcCHHHHHHHHHHHhccchheeecCCCCCchhhHHHHH-HHHHH-----------cCCeEEEE
Confidence            44556665542    35778899999999998877 7889999999998764333 22222           45566666


Q ss_pred             cCcH
Q psy7268         123 TPGR  126 (134)
Q Consensus       123 ~Pt~  126 (134)
                      +-|-
T Consensus       720 syTh  723 (1100)
T KOG1805|consen  720 SYTH  723 (1100)
T ss_pred             ehhh
Confidence            5543

>TIGR00595 priA primosomal protein N'

Probab=93.98  E-value=0.038  Score=45.45  Aligned_cols=22  Identities=32%  Similarity=0.548  Sum_probs=17.0

Q ss_pred             EEEcCCCCchhHHhHHHHHHHH
Q psy7268          80 ILVAETGCGKTLSFLAPLVQQI  101 (134)
Q Consensus        80 li~a~tGsGKT~~~~lpil~~~  101 (134)
                      ++.|+||+|||.+|+..+...+
T Consensus         1 LL~g~TGsGKT~v~l~~i~~~l   22 (505)
T TIGR00595         1 LLFGVTGSGKTEVYLQAIEKVL   22 (505)
T ss_pred             CccCCCCCCHHHHHHHHHHHHH
Confidence            4689999999999976554443

All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=93.98  E-value=0.51  Score=37.51  Aligned_cols=58  Identities=19%  Similarity=0.292  Sum_probs=33.6

Q ss_pred             CCcccCCCCHHHHHHHHHC---C--CCCChHHHHHHHHHH--------------HcCCCeEEEcCCCCchhHHhHHH
Q psy7268          39 GTFEDTGLAPEIIDIFTKR---G--LTTPTEIQKYSIPTL--------------LSGKSAILVAETGCGKTLSFLAP   96 (134)
Q Consensus        39 ~~f~~~~l~~~i~~~l~~~---g--~~~~t~iQ~~~i~~~--------------~~g~dvli~a~tGsGKT~~~~lp   96 (134)
                      ..+.+.++++.+.+.|-+.   +  ...+...+...-..+              -.|..+++.||||+|||....--
T Consensus        81 ~~L~~~g~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~g~ii~lvGptGvGKTTtiakL  157 (374)
T PRK14722         81 KYLFAAGFSAQLVRMIVDNLPEGEGYDTLDAAADWAQSVLAANLPVLDSEDALMERGGVFALMGPTGVGKTTTTAKL  157 (374)
T ss_pred             HHHHHCCCCHHHHHHHHHhhhhhcccCCHHHHHHHHHHHHHhcchhhcCCCccccCCcEEEEECCCCCCHHHHHHHH
Confidence            4456778888887777552   1  112222222111111              13567899999999999886433

>PRK14712 conjugal transfer nickase/helicase TraI; Provisional

Probab=93.91  E-value=0.28  Score=45.57  Aligned_cols=62  Identities=19%  Similarity=0.245  Sum_probs=44.8

Q ss_pred             CChHHHHHHHHHHHcC--CCeEEEcCCCCchhHHh--HHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHh
Q psy7268          61 TPTEIQKYSIPTLLSG--KSAILVAETGCGKTLSF--LAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQI  132 (134)
Q Consensus        61 ~~t~iQ~~~i~~~~~g--~dvli~a~tGsGKT~~~--~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi  132 (134)
                      .+++-|+.++..++.+  +-+++.|..|+|||...  ++.++..+.+.          .+.+++.++||-.-+..+
T Consensus       835 ~Lt~~Qr~Av~~iLts~dr~~~IqG~AGTGKTT~l~~i~~~~~~l~e~----------~g~~V~glAPTgkAa~~L  900 (1623)
T PRK14712        835 KLTSGQRAATRMILETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPES----------ERPRVVGLGPTHRAVGEM  900 (1623)
T ss_pred             ccCHHHHHHHHHHHhCCCceEEEEeCCCCCHHHHHHHHHHHHHHHhhc----------cCceEEEEechHHHHHHH
Confidence            7899999999999965  55899999999999763  23333332211          456788899997766554

>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=93.81  E-value=0.12  Score=38.67  Aligned_cols=23  Identities=22%  Similarity=0.606  Sum_probs=17.4

Q ss_pred             CeEEEcCCCCchhHHhHHHHHHHH
Q psy7268          78 SAILVAETGCGKTLSFLAPLVQQI  101 (134)
Q Consensus        78 dvli~a~tGsGKT~~~~lpil~~~  101 (134)
                      .+++.|++||||| .+++-++..+
T Consensus        15 r~viIG~sGSGKT-~li~~lL~~~   37 (241)
T PF04665_consen   15 RMVIIGKSGSGKT-TLIKSLLYYL   37 (241)
T ss_pred             eEEEECCCCCCHH-HHHHHHHHhh
Confidence            6889999999999 4555555554

This is thought to be an ATPase involved in viral DNA packaging [].

>PF01580 FtsK_SpoIIIE: FtsK/SpoIIIE family; InterPro: IPR002543 The FtsK/SpoIIIE domain is found extensively in a wide variety of proteins from prokaryotes and plasmids [] some of which contain up to three copies

Probab=93.69  E-value=0.17  Score=36.17  Aligned_cols=27  Identities=22%  Similarity=0.340  Sum_probs=17.2

Q ss_pred             CCCeEEEcCCCCchhHHhHHHHHHHHH
Q psy7268          76 GKSAILVAETGCGKTLSFLAPLVQQIL  102 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~~lpil~~~~  102 (134)
                      ..++++.|.||+|||.....-+...+.
T Consensus        38 ~~h~li~G~tgsGKS~~l~~ll~~l~~   64 (205)
T PF01580_consen   38 NPHLLIAGATGSGKSTLLRTLLLSLAL   64 (205)
T ss_dssp             S-SEEEE--TTSSHHHHHHHHHHHHHT
T ss_pred             CceEEEEcCCCCCccHHHHHHHHHHHH
Confidence            348999999999999776544444443

The domain contains a putative ATP binding P-loop motif. A mutation in FtsK causes a temperature sensitive block in cell division and it is involved in peptidoglycan synthesis or modification []. The SpoIIIE protein is implicated in intercellular chromosomal DNA transfer []. ; GO: 0000166 nucleotide binding, 0003677 DNA binding, 0005524 ATP binding, 0007049 cell cycle, 0007059 chromosome segregation, 0051301 cell division, 0016021 integral to membrane; PDB: 2IUS_E 2IUU_A 2IUT_A.

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

Probab=93.62  E-value=0.037  Score=41.26  Aligned_cols=25  Identities=40%  Similarity=0.392  Sum_probs=19.0

Q ss_pred             HHHcCCCeEEEcCCCCchhHHhHHH
Q psy7268          72 TLLSGKSAILVAETGCGKTLSFLAP   96 (134)
Q Consensus        72 ~~~~g~dvli~a~tGsGKT~~~~lp   96 (134)
                      -+..|.-+++.|++|+|||...+--
T Consensus        26 G~~~g~~~~i~g~~G~GKT~l~~~~   50 (271)
T cd01122          26 GLRKGELIILTAGTGVGKTTFLREY   50 (271)
T ss_pred             EEcCCcEEEEEcCCCCCHHHHHHHH
Confidence            3456778999999999999655433

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

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=93.59  E-value=0.37  Score=38.86  Aligned_cols=19  Identities=42%  Similarity=0.590  Sum_probs=15.8

Q ss_pred             CCCeEEEcCCCCchhHHhH
Q psy7268          76 GKSAILVAETGCGKTLSFL   94 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~~   94 (134)
                      |+.+++.+|||+|||....
T Consensus       221 ~~~i~~vGptGvGKTTt~~  239 (424)
T PRK05703        221 GGVVALVGPTGVGKTTTLA  239 (424)
T ss_pred             CcEEEEECCCCCCHHHHHH
Confidence            5568899999999997754

>PF02399 Herpes_ori_bp: Origin of replication binding protein; InterPro: IPR003450 This entry represents replication origin binding protein

Probab=93.50  E-value=0.12  Score=44.75  Aligned_cols=44  Identities=18%  Similarity=0.291  Sum_probs=32.2

Q ss_pred             eEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          79 AILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        79 vli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      .++.+|.|||||.+..-.+-+.+..           ...++++|+.-+.|+.++.
T Consensus        52 ~vVRSpMGTGKTtaLi~wLk~~l~~-----------~~~~VLvVShRrSL~~sL~   95 (824)
T PF02399_consen   52 LVVRSPMGTGKTTALIRWLKDALKN-----------PDKSVLVVSHRRSLTKSLA   95 (824)
T ss_pred             EEEECCCCCCcHHHHHHHHHHhccC-----------CCCeEEEEEhHHHHHHHHH
Confidence            6788999999997763333222211           5678999999999998874

It functions as a docking protein to recruit essential components of the viral replication machinery to viral DNA origins. In the presence of the major DNA-binding protein, it opens dsDNA which leads to a conformational change in the origin that facilitates DNA unwinding and subsequent replication [].; GO: 0003688 DNA replication origin binding, 0005524 ATP binding, 0006260 DNA replication

>COG3587 Restriction endonuclease [Defense mechanisms]

Probab=93.48  E-value=0.095  Score=45.46  Aligned_cols=41  Identities=22%  Similarity=0.352  Sum_probs=29.6

Q ss_pred             CeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHH
Q psy7268          78 SAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGREL  128 (134)
Q Consensus        78 dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~L  128 (134)
                      ++=|...||+|||.+|+=-+...-..          ..-.+.||+||+.+.
T Consensus        76 NiDI~METGTGKTy~YlrtmfeLhk~----------YG~~KFIivVPs~AI  116 (985)
T COG3587          76 NIDILMETGTGKTYTYLRTMFELHKK----------YGLFKFIIVVPSLAI  116 (985)
T ss_pred             eeeEEEecCCCceeeHHHHHHHHHHH----------hCceeEEEEeccHHH
Confidence            56678999999999997555443221          144678999999764

>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=93.44  E-value=0.062  Score=35.04  Aligned_cols=15  Identities=33%  Similarity=0.375  Sum_probs=12.9

Q ss_pred             eEEEcCCCCchhHHh
Q psy7268          79 AILVAETGCGKTLSF   93 (134)
Q Consensus        79 vli~a~tGsGKT~~~   93 (134)
                      +++.||+|+|||...
T Consensus         1 ill~G~~G~GKT~l~   15 (132)
T PF00004_consen    1 ILLHGPPGTGKTTLA   15 (132)
T ss_dssp             EEEESSTTSSHHHHH
T ss_pred             CEEECcCCCCeeHHH
Confidence            589999999999664

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 ....

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

Probab=93.42  E-value=0.056  Score=35.46  Aligned_cols=19  Identities=26%  Similarity=0.396  Sum_probs=12.6

Q ss_pred             cCCCeEEEcCCCCchhHHh
Q psy7268          75 SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~   93 (134)
                      .++.+++.|++|+|||...
T Consensus         3 ~~~~~~i~G~~G~GKT~~~   21 (131)
T PF13401_consen    3 SQRILVISGPPGSGKTTLI   21 (131)
T ss_dssp             ----EEEEE-TTSSHHHHH
T ss_pred             CCcccEEEcCCCCCHHHHH
Confidence            3567899999999999764

>PRK08116 hypothetical protein; Validated

Probab=93.39  E-value=0.55  Score=35.47  Aligned_cols=26  Identities=23%  Similarity=0.341  Sum_probs=19.7

Q ss_pred             CCeEEEcCCCCchhHHhHHHHHHHHHh
Q psy7268          77 KSAILVAETGCGKTLSFLAPLVQQILT  103 (134)
Q Consensus        77 ~dvli~a~tGsGKT~~~~lpil~~~~~  103 (134)
                      ..+++.|++|+|||... ..+.+.+..
T Consensus       115 ~gl~l~G~~GtGKThLa-~aia~~l~~  140 (268)
T PRK08116        115 VGLLLWGSVGTGKTYLA-ACIANELIE  140 (268)
T ss_pred             ceEEEECCCCCCHHHHH-HHHHHHHHH
Confidence            34999999999999655 456666654

>PF01078 Mg_chelatase: Magnesium chelatase, subunit ChlI; InterPro: IPR000523 Magnesium-chelatase is a three-component enzyme that catalyses the insertion of Mg2+ into protoporphyrin IX

Probab=93.39  E-value=0.1  Score=38.15  Aligned_cols=27  Identities=26%  Similarity=0.431  Sum_probs=17.2

Q ss_pred             HHHHHHH-HcCCCeEEEcCCCCchhHHh
Q psy7268          67 KYSIPTL-LSGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        67 ~~~i~~~-~~g~dvli~a~tGsGKT~~~   93 (134)
                      ++++... ..+.++++.+|+|+|||+..
T Consensus        12 KrAL~iAAaG~h~lLl~GppGtGKTmlA   39 (206)
T PF01078_consen   12 KRALEIAAAGGHHLLLIGPPGTGKTMLA   39 (206)
T ss_dssp             HHHHHHHHHCC--EEEES-CCCTHHHHH
T ss_pred             HHHHHHHHcCCCCeEEECCCCCCHHHHH
Confidence            3444433 35678999999999999774

This is the first unique step in the synthesis of (bacterio)chlorophyll. As a result, it is thought that Mg-chelatase has an important role in channeling intermediates into the (bacterio)chlorophyll branch in response to conditions suitable for photosynthetic growth. ChlI and BchD have molecular weights between 38-42 kDa.; GO: 0016851 magnesium chelatase activity, 0015979 photosynthesis, 0015995 chlorophyll biosynthetic process; PDB: 2X31_J 1G8P_A 3K1J_B.

>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional

Probab=93.31  E-value=0.071  Score=42.60  Aligned_cols=55  Identities=20%  Similarity=0.182  Sum_probs=35.1

Q ss_pred             CCCCCcccCCCCHHHHHHHHHC---CCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHh
Q psy7268          36 IDLGTFEDTGLAPEIIDIFTKR---GLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        36 ~~~~~f~~~~l~~~i~~~l~~~---g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~   93 (134)
                      .|-.+|++++-.+...+.+.+.   .+..|.-.+..-   +...+.+++.||+|+|||+..
T Consensus       139 ~p~v~~~digGl~~~k~~l~~~v~~pl~~~~~~~~~G---l~~pkgvLL~GppGTGKT~LA  196 (398)
T PTZ00454        139 KPDVTYSDIGGLDIQKQEIREAVELPLTCPELYEQIG---IDPPRGVLLYGPPGTGKTMLA  196 (398)
T ss_pred             CCCCCHHHcCCHHHHHHHHHHHHHHHhcCHHHHHhcC---CCCCceEEEECCCCCCHHHHH
Confidence            3445788888777777777663   233322222111   124678999999999999864

>PRK13531 regulatory ATPase RavA; Provisional

Probab=93.28  E-value=0.18  Score=41.49  Aligned_cols=27  Identities=30%  Similarity=0.452  Sum_probs=22.0

Q ss_pred             HHHHHHHHcCCCeEEEcCCCCchhHHh
Q psy7268          67 KYSIPTLLSGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        67 ~~~i~~~~~g~dvli~a~tGsGKT~~~   93 (134)
                      ..++-.++.|.++++.||+|+|||...
T Consensus        30 ~lll~aalag~hVLL~GpPGTGKT~LA   56 (498)
T PRK13531         30 RLCLLAALSGESVFLLGPPGIAKSLIA   56 (498)
T ss_pred             HHHHHHHccCCCEEEECCCChhHHHHH
Confidence            344445678999999999999999775

>cd00984 DnaB_C DnaB helicase C terminal domain

Probab=93.23  E-value=0.16  Score=37.09  Aligned_cols=39  Identities=21%  Similarity=0.158  Sum_probs=25.4

Q ss_pred             HcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEc
Q psy7268          74 LSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIIT  123 (134)
Q Consensus        74 ~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~  123 (134)
                      ..|.-+++.|++|+|||...+--+.+....           .+..+++++
T Consensus        11 ~~G~l~lI~G~~G~GKT~~~~~~~~~~~~~-----------~g~~vly~s   49 (242)
T cd00984          11 QPGDLIIIAARPSMGKTAFALNIAENIAKK-----------QGKPVLFFS   49 (242)
T ss_pred             CCCeEEEEEeCCCCCHHHHHHHHHHHHHHh-----------CCCceEEEe
Confidence            356678999999999996554333443322           145677776

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.

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

Probab=93.18  E-value=0.15  Score=41.45  Aligned_cols=31  Identities=26%  Similarity=0.261  Sum_probs=24.6

Q ss_pred             hHHHHHHHHHHHcCCCeEEEcCCCCchhHHh
Q psy7268          63 TEIQKYSIPTLLSGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        63 t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~   93 (134)
                      -......+..+..++++++.+++|+|||...
T Consensus       181 e~~le~l~~~L~~~~~iil~GppGtGKT~lA  211 (459)
T PRK11331        181 ETTIETILKRLTIKKNIILQGPPGVGKTFVA  211 (459)
T ss_pred             HHHHHHHHHHHhcCCCEEEECCCCCCHHHHH
Confidence            3444556666778999999999999999765

>PF01935 DUF87: Domain of unknown function DUF87; InterPro: IPR002789 The function of this domain is unknown

Probab=93.18  E-value=0.18  Score=36.62  Aligned_cols=27  Identities=22%  Similarity=0.429  Sum_probs=20.4

Q ss_pred             cCCCeEEEcCCCCchhHHhHHHHHHHHH
Q psy7268          75 SGKSAILVAETGCGKTLSFLAPLVQQIL  102 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~~lpil~~~~  102 (134)
                      -++++.|.|.||||||... --+++.+.
T Consensus        22 ~~~H~~I~G~TGsGKS~~~-~~ll~~l~   48 (229)
T PF01935_consen   22 FNRHIAIFGTTGSGKSNTV-KVLLEELL   48 (229)
T ss_pred             ccceEEEECCCCCCHHHHH-HHHHHHHH
Confidence            3578999999999999765 44555554

It contains several conserved aspartates and histidines that could be metal ligands.

>cd01126 TraG_VirD4 The TraG/TraD/VirD4 family are bacterial conjugation proteins involved in type IV secretion

Probab=93.17  E-value=0.02  Score=45.15  Aligned_cols=23  Identities=26%  Similarity=0.462  Sum_probs=19.9

Q ss_pred             CeEEEcCCCCchhHHhHHHHHHH
Q psy7268          78 SAILVAETGCGKTLSFLAPLVQQ  100 (134)
Q Consensus        78 dvli~a~tGsGKT~~~~lpil~~  100 (134)
                      ++++.|+||+|||.++++|-+..
T Consensus         1 H~lv~g~tGsGKt~~~viP~ll~   23 (384)
T cd01126           1 HVLVFAPTRSGKGVGFVIPNLLT   23 (384)
T ss_pred             CeeEecCCCCCCccEEEccchhc
Confidence            47899999999999999887654

These proteins aid the transfer of DNA from the plasmid into the host bacterial chromosome. They contain an ATP binding domain. VirD4 is involved in DNA transfer to plant cells and is required for virulence.

>TIGR01420 pilT_fam pilus retraction protein PilT

Probab=93.16  E-value=0.2  Score=39.12  Aligned_cols=27  Identities=22%  Similarity=0.391  Sum_probs=20.0

Q ss_pred             cCCCeEEEcCCCCchhHHhHHHHHHHHH
Q psy7268          75 SGKSAILVAETGCGKTLSFLAPLVQQIL  102 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~~lpil~~~~  102 (134)
                      .+..++++||||||||... -.++..+.
T Consensus       121 ~~g~ili~G~tGSGKTT~l-~al~~~i~  147 (343)
T TIGR01420       121 PRGLILVTGPTGSGKSTTL-ASMIDYIN  147 (343)
T ss_pred             cCcEEEEECCCCCCHHHHH-HHHHHhhC
Confidence            4567999999999999664 45555553

This model represents the PilT subfamily of proteins related to GspE, a protein involved in type II secretion (also called the General Secretion Pathway). PilT is an apparent cytosolic ATPase associated with type IV pilus systems. It is not required for pilin biogenesis, but is required for twitching motility and social gliding behaviors, shown in some species, powered by pilus retraction. Members of this family may be found in some species that type IV pili but have related structures for DNA uptake and natural transformation.

>TIGR02759 TraD_Ftype type IV conjugative transfer system coupling protein TraD

Probab=93.14  E-value=0.16  Score=42.46  Aligned_cols=29  Identities=21%  Similarity=0.340  Sum_probs=21.2

Q ss_pred             HcCCCeEEEcCCCCchhHHhHHHHHHHHHh
Q psy7268          74 LSGKSAILVAETGCGKTLSFLAPLVQQILT  103 (134)
Q Consensus        74 ~~g~dvli~a~tGsGKT~~~~lpil~~~~~  103 (134)
                      ...+++++.|+||||||. ++-.++..+..
T Consensus       174 ~e~~h~li~G~tGsGKs~-~i~~ll~~~~~  202 (566)
T TIGR02759       174 SETQHILIHGTTGSGKSV-AIRKLLRWIRQ  202 (566)
T ss_pred             ccccceEEEcCCCCCHHH-HHHHHHHHHHh
Confidence            346689999999999995 34555666543

The TraD protein performs an essential coupling function in conjugative type IV secretion systems. This protein sits at the inner membrane in contact with the assembled pilus and its scaffold as well as the relaxosome-plasmid DNA complex (through TraM).

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

Probab=93.12  E-value=0.19  Score=37.40  Aligned_cols=37  Identities=22%  Similarity=0.313  Sum_probs=25.1

Q ss_pred             cCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEc
Q psy7268          75 SGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIIT  123 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~  123 (134)
                      .|+.+++.+++|+|||....--+...+.            .+-.+++++
T Consensus        22 ~g~~~lI~G~pGsGKT~f~~qfl~~~~~------------~ge~vlyvs   58 (260)
T COG0467          22 RGSVVLITGPPGTGKTIFALQFLYEGAR------------EGEPVLYVS   58 (260)
T ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHHHHh------------cCCcEEEEE
Confidence            5678999999999999655333333332            355677775

>PF13555 AAA_29: P-loop containing region of AAA domain

Probab=93.08  E-value=0.093  Score=30.97  Aligned_cols=19  Identities=21%  Similarity=0.513  Sum_probs=15.6

Q ss_pred             cCCCeEEEcCCCCchhHHh
Q psy7268          75 SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~   93 (134)
                      .|...++.+++|+|||..+
T Consensus        22 ~g~~tli~G~nGsGKSTll   40 (62)
T PF13555_consen   22 RGDVTLITGPNGSGKSTLL   40 (62)
T ss_pred             CCcEEEEECCCCCCHHHHH
Confidence            3556899999999999764

>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family

Probab=93.07  E-value=0.2  Score=37.56  Aligned_cols=25  Identities=16%  Similarity=0.062  Sum_probs=18.4

Q ss_pred             cCCCeEEEcCCCCchhHHhHHHHHH
Q psy7268          75 SGKSAILVAETGCGKTLSFLAPLVQ   99 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~~lpil~   99 (134)
                      .|.-+++.|++|+|||...+--+.+
T Consensus        35 ~gs~~lI~G~pGtGKT~l~~qf~~~   59 (259)
T TIGR03878        35 AYSVINITGVSDTGKSLMVEQFAVT   59 (259)
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHH
Confidence            4567899999999999765443333

This KaiC domain-containing protein family occurs sporadically across a broad taxonomic range (Euryarchaeota, Aquificae, Dictyoglomi, Epsilonproteobacteria, and Firmicutes), but exclusively in thermophiles.

>TIGR02788 VirB11 P-type DNA transfer ATPase VirB11

Probab=92.85  E-value=0.16  Score=39.05  Aligned_cols=21  Identities=38%  Similarity=0.493  Sum_probs=17.8

Q ss_pred             HHcCCCeEEEcCCCCchhHHh
Q psy7268          73 LLSGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        73 ~~~g~dvli~a~tGsGKT~~~   93 (134)
                      +..|.++++.|+||+|||...
T Consensus       141 v~~~~~ili~G~tGsGKTTll  161 (308)
T TIGR02788       141 IASRKNIIISGGTGSGKTTFL  161 (308)
T ss_pred             hhCCCEEEEECCCCCCHHHHH
Confidence            447889999999999999653

The VirB11 protein is found in the vir locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for DNA transfer. VirB11 is believed to be an ATPase. VirB11 is a homolog of the P-like conjugation system TrbB protein and the Flp pilus sytem protein TadA.

>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=92.81  E-value=0.073  Score=35.55  Aligned_cols=16  Identities=38%  Similarity=0.490  Sum_probs=13.8

Q ss_pred             CeEEEcCCCCchhHHh
Q psy7268          78 SAILVAETGCGKTLSF   93 (134)
Q Consensus        78 dvli~a~tGsGKT~~~   93 (134)
                      +|++.||+|+|||...
T Consensus         1 ~vlL~G~~G~GKt~l~   16 (139)
T PF07728_consen    1 PVLLVGPPGTGKTTLA   16 (139)
T ss_dssp             EEEEEESSSSSHHHHH
T ss_pred             CEEEECCCCCCHHHHH
Confidence            4899999999999764

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.

>PRK13897 type IV secretion system component VirD4; Provisional

Probab=92.76  E-value=0.089  Score=44.29  Aligned_cols=25  Identities=36%  Similarity=0.547  Sum_probs=22.2

Q ss_pred             CCeEEEcCCCCchhHHhHHHHHHHH
Q psy7268          77 KSAILVAETGCGKTLSFLAPLVQQI  101 (134)
Q Consensus        77 ~dvli~a~tGsGKT~~~~lpil~~~  101 (134)
                      .++++.||||||||..+++|-+...
T Consensus       159 ~hvLviapTgSGKg~g~VIPnLL~~  183 (606)
T PRK13897        159 QHALLFAPTGSGKGVGFVIPNLLFW  183 (606)
T ss_pred             ceEEEEcCCCCCcceEEehhhHHhC
Confidence            3689999999999999999988764

>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI

Probab=92.72  E-value=0.56  Score=44.62  Aligned_cols=60  Identities=20%  Similarity=0.145  Sum_probs=44.7

Q ss_pred             CChHHHHHHHHHHHcCC--CeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHh
Q psy7268          61 TPTEIQKYSIPTLLSGK--SAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQI  132 (134)
Q Consensus        61 ~~t~iQ~~~i~~~~~g~--dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi  132 (134)
                      .+++-|+.++..++...  -.++.++.|+|||... -.++..+..           .|.+++.++||..-+.++
T Consensus       429 ~Ls~~Q~~Av~~il~s~~~v~ii~G~aGTGKTt~l-~~l~~~~~~-----------~G~~V~~lAPTgrAA~~L  490 (1960)
T TIGR02760       429 ALSPSNKDAVSTLFTSTKRFIIINGFGGTGSTEIA-QLLLHLASE-----------QGYEIQIITAGSLSAQEL  490 (1960)
T ss_pred             CCCHHHHHHHHHHHhCCCCeEEEEECCCCCHHHHH-HHHHHHHHh-----------cCCeEEEEeCCHHHHHHH
Confidence            67899999999988754  4788999999999553 333443322           467899999998766654

This protein is a component of the relaxosome complex. In the process of conjugative plasmid transfer the realaxosome binds to the plasmid at the oriT (origin of transfer) site. The relaxase protein TraI mediates the single-strand nicking and ATP-dependent unwinding (relaxation, helicase activity) of the plasmid molecule. These two activities reside in separate domains of the protein.

>KOG1533|consensus

Probab=92.70  E-value=0.12  Score=38.71  Aligned_cols=24  Identities=17%  Similarity=0.450  Sum_probs=19.3

Q ss_pred             eEEEcCCCCchhHHhHHHHHHHHHh
Q psy7268          79 AILVAETGCGKTLSFLAPLVQQILT  103 (134)
Q Consensus        79 vli~a~tGsGKT~~~~lpil~~~~~  103 (134)
                      -++.||+||||| +|+....+.+..
T Consensus         5 qvVIGPPgSGKs-TYc~g~~~fls~   28 (290)
T KOG1533|consen    5 QVVIGPPGSGKS-TYCNGMSQFLSA   28 (290)
T ss_pred             eEEEcCCCCCcc-chhhhHHHHHHH
Confidence            468899999998 788877777654

>TIGR03881 KaiC_arch_4 KaiC domain protein, PAE1156 family

Probab=92.66  E-value=0.28  Score=35.63  Aligned_cols=25  Identities=28%  Similarity=0.292  Sum_probs=18.4

Q ss_pred             cCCCeEEEcCCCCchhHHhHHHHHH
Q psy7268          75 SGKSAILVAETGCGKTLSFLAPLVQ   99 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~~lpil~   99 (134)
                      .|..+++.+++|+|||...+.-+.+
T Consensus        19 ~G~~~~i~G~~G~GKT~l~~~~~~~   43 (229)
T TIGR03881        19 RGFFVAVTGEPGTGKTIFCLHFAYK   43 (229)
T ss_pred             CCeEEEEECCCCCChHHHHHHHHHH
Confidence            4678999999999998665433333

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.

>PTZ00361 26 proteosome regulatory subunit 4-like protein; Provisional

Probab=92.63  E-value=0.071  Score=43.16  Aligned_cols=55  Identities=24%  Similarity=0.280  Sum_probs=31.0

Q ss_pred             CCCCCCcccCCCCHHHHHHHHHC-CCCCChHHHHH-HHH--HHHcCCCeEEEcCCCCchhHHh
Q psy7268          35 RIDLGTFEDTGLAPEIIDIFTKR-GLTTPTEIQKY-SIP--TLLSGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        35 ~~~~~~f~~~~l~~~i~~~l~~~-g~~~~t~iQ~~-~i~--~~~~g~dvli~a~tGsGKT~~~   93 (134)
                      ..|-.+|++++--+..++.+.+. .+    ++... .+.  .+...+.+++.||+|+|||+..
T Consensus       176 ~~p~~~~~DIgGl~~qi~~l~e~v~l----pl~~p~~~~~~gi~~p~gVLL~GPPGTGKT~LA  234 (438)
T PTZ00361        176 KAPLESYADIGGLEQQIQEIKEAVEL----PLTHPELYDDIGIKPPKGVILYGPPGTGKTLLA  234 (438)
T ss_pred             cCCCCCHHHhcCHHHHHHHHHHHHHh----hhhCHHHHHhcCCCCCcEEEEECCCCCCHHHHH
Confidence            34556777776555555555542 11    11111 111  1224567999999999999775

>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=92.61  E-value=0.092  Score=34.04  Aligned_cols=15  Identities=27%  Similarity=0.388  Sum_probs=12.8

Q ss_pred             eEEEcCCCCchhHHh
Q psy7268          79 AILVAETGCGKTLSF   93 (134)
Q Consensus        79 vli~a~tGsGKT~~~   93 (134)
                      +++.|++|||||...
T Consensus         2 I~I~G~~gsGKST~a   16 (121)
T PF13207_consen    2 IIISGPPGSGKSTLA   16 (121)
T ss_dssp             EEEEESTTSSHHHHH
T ss_pred             EEEECCCCCCHHHHH
Confidence            678999999999654

...

>KOG0925|consensus

Probab=92.59  E-value=0.29  Score=40.39  Aligned_cols=56  Identities=29%  Similarity=0.363  Sum_probs=41.5

Q ss_pred             CCCCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHH
Q psy7268          37 DLGTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLS   92 (134)
Q Consensus        37 ~~~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~   92 (134)
                      .+.-|.+.+.++.-.+.+++..=-.-+..+.+.+..+.++.-+++.|.||||||.-
T Consensus        23 ~~Npf~~~p~s~rY~~ilk~R~~LPvw~~k~~F~~~l~~nQ~~v~vGetgsGKttQ   78 (699)
T KOG0925|consen   23 AINPFNGKPYSQRYYDILKKRRELPVWEQKEEFLKLLLNNQIIVLVGETGSGKTTQ   78 (699)
T ss_pred             hcCCCCCCcCcHHHHHHHHHHhcCchHHhHHHHHHHHhcCceEEEEecCCCCcccc
Confidence            37788999999998888887532233444555555666777899999999999954

>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=92.58  E-value=0.28  Score=35.32  Aligned_cols=16  Identities=44%  Similarity=0.567  Sum_probs=13.7

Q ss_pred             eEEEcCCCCchhHHhH
Q psy7268          79 AILVAETGCGKTLSFL   94 (134)
Q Consensus        79 vli~a~tGsGKT~~~~   94 (134)
                      ++++||||+|||....
T Consensus         4 i~lvGptGvGKTTt~a   19 (196)
T PF00448_consen    4 IALVGPTGVGKTTTIA   19 (196)
T ss_dssp             EEEEESTTSSHHHHHH
T ss_pred             EEEECCCCCchHhHHH
Confidence            6789999999998753

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 ....

>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=92.46  E-value=0.097  Score=34.88  Aligned_cols=15  Identities=33%  Similarity=0.437  Sum_probs=12.9

Q ss_pred             eEEEcCCCCchhHHh
Q psy7268          79 AILVAETGCGKTLSF   93 (134)
Q Consensus        79 vli~a~tGsGKT~~~   93 (134)
                      ++++|++|+|||...
T Consensus         2 ii~~G~pgsGKSt~a   16 (143)
T PF13671_consen    2 IILCGPPGSGKSTLA   16 (143)
T ss_dssp             EEEEESTTSSHHHHH
T ss_pred             EEEECCCCCCHHHHH
Confidence            688999999999663

...

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=92.42  E-value=0.31  Score=34.83  Aligned_cols=25  Identities=24%  Similarity=0.284  Sum_probs=18.2

Q ss_pred             cCCCeEEEcCCCCchhHHhHHHHHH
Q psy7268          75 SGKSAILVAETGCGKTLSFLAPLVQ   99 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~~lpil~   99 (134)
                      .|.-+.+.+++|+|||...+.-+.+
T Consensus        11 ~g~i~~i~G~~GsGKT~l~~~~~~~   35 (209)
T TIGR02237        11 RGTITQIYGPPGSGKTNICMILAVN   35 (209)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            3456889999999999776544333

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

>KOG4150|consensus

Probab=92.32  E-value=0.13  Score=43.26  Aligned_cols=65  Identities=11%  Similarity=-0.099  Sum_probs=51.3

Q ss_pred             CCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHH
Q psy7268          57 RGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQ  131 (134)
Q Consensus        57 ~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Q  131 (134)
                      +.-+....+|..++..+..|+++++...+.+||.++|-+.........          .....+++.|+++++..
T Consensus       282 ~~~E~~~~~~~~~~~~~~~G~~~~~~~~~~~GK~~~~~~~s~~~~~~~----------~~s~~~~~~~~~~~~~~  346 (1034)
T KOG4150|consen  282 NTGESGIAISLELLKFASEGRADGGNEARQAGKGTCPTSGSRKFQTLC----------HATNSLLPSEMVEHLRN  346 (1034)
T ss_pred             ccccchhhhhHHHHhhhhhcccccccchhhcCCccCcccchhhhhhcC----------cccceecchhHHHHhhc
Confidence            344567889999999999999999999999999999988887766542          22346777788887754

>PRK04328 hypothetical protein; Provisional

Probab=92.32  E-value=0.3  Score=36.36  Aligned_cols=27  Identities=19%  Similarity=0.219  Sum_probs=19.3

Q ss_pred             cCCCeEEEcCCCCchhHHhHHHHHHHH
Q psy7268          75 SGKSAILVAETGCGKTLSFLAPLVQQI  101 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~~lpil~~~  101 (134)
                      .|..+++.+++|+|||.-.+--+.+.+
T Consensus        22 ~gs~ili~G~pGsGKT~l~~~fl~~~~   48 (249)
T PRK04328         22 ERNVVLLSGGPGTGKSIFSQQFLWNGL   48 (249)
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHHHH
Confidence            466789999999999966544444443

>PRK13880 conjugal transfer coupling protein TraG; Provisional

Probab=92.29  E-value=0.075  Score=44.94  Aligned_cols=24  Identities=21%  Similarity=0.369  Sum_probs=21.5

Q ss_pred             CCeEEEcCCCCchhHHhHHHHHHH
Q psy7268          77 KSAILVAETGCGKTLSFLAPLVQQ  100 (134)
Q Consensus        77 ~dvli~a~tGsGKT~~~~lpil~~  100 (134)
                      .++++.||||||||..+++|-+..
T Consensus       176 ~HvlviapTgSGKgvg~ViPnLL~  199 (636)
T PRK13880        176 EHVLTYAPTRSGKGVGLVVPTLLS  199 (636)
T ss_pred             ceEEEEecCCCCCceEEEccchhh
Confidence            469999999999999999998764

>PRK08727 hypothetical protein; Validated

Probab=92.25  E-value=0.29  Score=36.07  Aligned_cols=25  Identities=24%  Similarity=0.137  Sum_probs=17.3

Q ss_pred             CCeEEEcCCCCchhHHhHHHHHHHHH
Q psy7268          77 KSAILVAETGCGKTLSFLAPLVQQIL  102 (134)
Q Consensus        77 ~dvli~a~tGsGKT~~~~lpil~~~~  102 (134)
                      ..+++.|++|+|||-.. -.+...+.
T Consensus        42 ~~l~l~G~~G~GKThL~-~a~~~~~~   66 (233)
T PRK08727         42 DWLYLSGPAGTGKTHLA-LALCAAAE   66 (233)
T ss_pred             CeEEEECCCCCCHHHHH-HHHHHHHH
Confidence            34999999999999443 34444443

>PRK13850 type IV secretion system protein VirD4; Provisional

Probab=92.23  E-value=0.11  Score=44.18  Aligned_cols=25  Identities=24%  Similarity=0.424  Sum_probs=21.9

Q ss_pred             CCeEEEcCCCCchhHHhHHHHHHHH
Q psy7268          77 KSAILVAETGCGKTLSFLAPLVQQI  101 (134)
Q Consensus        77 ~dvli~a~tGsGKT~~~~lpil~~~  101 (134)
                      .++++.||||||||..+++|-+-.+
T Consensus       140 ~hvlviApTgSGKgvg~VIPnLL~~  164 (670)
T PRK13850        140 PHSLVVAPTRAGKGVGVVIPTLLTF  164 (670)
T ss_pred             ceEEEEecCCCCceeeehHhHHhcC
Confidence            3799999999999999999987653

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=92.22  E-value=0.27  Score=40.23  Aligned_cols=28  Identities=32%  Similarity=0.487  Sum_probs=21.1

Q ss_pred             cCCCeEEEcCCCCchhHHhHHHHHHHHH
Q psy7268          75 SGKSAILVAETGCGKTLSFLAPLVQQIL  102 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~~lpil~~~~  102 (134)
                      .|+.+++.+++|+|||...+--+.+.+.
T Consensus        20 ~g~~~Li~G~pGsGKT~la~qfl~~g~~   47 (484)
T TIGR02655        20 IGRSTLVSGTSGTGKTLFSIQFLYNGII   47 (484)
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHHHH
Confidence            4678999999999999776555555443

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.

>PRK08084 DNA replication initiation factor; Provisional

Probab=92.15  E-value=0.37  Score=35.54  Aligned_cols=25  Identities=12%  Similarity=0.231  Sum_probs=17.6

Q ss_pred             CCCeEEEcCCCCchhHHhHHHHHHHH
Q psy7268          76 GKSAILVAETGCGKTLSFLAPLVQQI  101 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~~lpil~~~  101 (134)
                      +..+++.||+|+|||-.. ..+.+.+
T Consensus        45 ~~~l~l~Gp~G~GKThLl-~a~~~~~   69 (235)
T PRK08084         45 SGYIYLWSREGAGRSHLL-HAACAEL   69 (235)
T ss_pred             CCeEEEECCCCCCHHHHH-HHHHHHH
Confidence            457999999999999543 2334443

>PRK06893 DNA replication initiation factor; Validated

Probab=92.02  E-value=0.29  Score=35.88  Aligned_cols=25  Identities=12%  Similarity=0.126  Sum_probs=17.0

Q ss_pred             CCeEEEcCCCCchhHHhHHHHHHHHH
Q psy7268          77 KSAILVAETGCGKTLSFLAPLVQQIL  102 (134)
Q Consensus        77 ~dvli~a~tGsGKT~~~~lpil~~~~  102 (134)
                      ..+++.||+|+|||-.. ..+.+.+.
T Consensus        40 ~~l~l~G~~G~GKThL~-~ai~~~~~   64 (229)
T PRK06893         40 PFFYIWGGKSSGKSHLL-KAVSNHYL   64 (229)
T ss_pred             CeEEEECCCCCCHHHHH-HHHHHHHH
Confidence            34799999999999443 34444443

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional

Probab=91.98  E-value=1.2  Score=37.29  Aligned_cols=56  Identities=21%  Similarity=0.220  Sum_probs=31.6

Q ss_pred             CCcccCCCCHHHHHHHHHC-CC-CCChHHHHHHHHHH------------HcCCCeEEEcCCCCchhHHhH
Q psy7268          39 GTFEDTGLAPEIIDIFTKR-GL-TTPTEIQKYSIPTL------------LSGKSAILVAETGCGKTLSFL   94 (134)
Q Consensus        39 ~~f~~~~l~~~i~~~l~~~-g~-~~~t~iQ~~~i~~~------------~~g~dvli~a~tGsGKT~~~~   94 (134)
                      ..+.+.|+++.+.+.|.+. .- .............+            ..|+.+.+.||+|+|||....
T Consensus       299 ~~L~~~Gvs~~la~~L~~~l~~~~~~~~~~~~l~~~L~~~l~v~~~~~l~~G~vIaLVGPtGvGKTTtaa  368 (559)
T PRK12727        299 ELMDDYGFDAGLTRDVAMQIPADTELHRGRGLMLGLLSKRLPVAPVDPLERGGVIALVGPTGAGKTTTIA  368 (559)
T ss_pred             HHHHHCCCCHHHHHHHHHhhhcccchhhHHHHHHHHHHHhcCcCccccccCCCEEEEECCCCCCHHHHHH
Confidence            3445667777777776542 11 11122222222221            246678899999999997763

>PF09439 SRPRB: Signal recognition particle receptor beta subunit; InterPro: IPR019009 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=91.94  E-value=0.13  Score=36.79  Aligned_cols=20  Identities=35%  Similarity=0.536  Sum_probs=14.5

Q ss_pred             CCCeEEEcCCCCchhHHhHH
Q psy7268          76 GKSAILVAETGCGKTLSFLA   95 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~~l   95 (134)
                      .+.+++.||.|+|||.-|..
T Consensus         3 ~~~vlL~Gps~SGKTaLf~~   22 (181)
T PF09439_consen    3 RPTVLLVGPSGSGKTALFSQ   22 (181)
T ss_dssp             --EEEEE-STTSSHHHHHHH
T ss_pred             CceEEEEcCCCCCHHHHHHH
Confidence            45799999999999977643

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 []. The SR receptor is a monomer consisting of the loosely membrane-associated SR-alpha homologue FtsY, while the eukaryotic SR receptor is a heterodimer of SR-alpha (70 kDa) and SR-beta (25 kDa), both of which contain a GTP-binding domain []. SR-alpha regulates the targeting of SRP-ribosome-nascent polypeptide complexes to the translocon []. SR-alpha binds to the SRP54 subunit of the SRP complex. The SR-beta subunit is a transmembrane GTPase that anchors the SR-alpha subunit (a peripheral membrane GTPase) to the ER membrane []. SR-beta interacts with the N-terminal SRX-domain of SR-alpha, which is not present in the bacterial FtsY homologue. SR-beta also functions in recruiting the SRP-nascent polypeptide to the protein-conducting channel. The beta subunit of the signal recognition particle receptor (SRP) is a transmembrane GTPase, which anchors the alpha subunit to the endoplasmic reticulum membrane []. ; PDB: 2GED_B 1NRJ_B 2GO5_2 2FH5_B.

>TIGR03743 SXT_TraD conjugative coupling factor TraD, SXT/TOL subfamily

Probab=91.91  E-value=0.33  Score=41.14  Aligned_cols=26  Identities=27%  Similarity=0.280  Sum_probs=19.5

Q ss_pred             CCCeEEEcCCCCchhHHhHHHHHHHH
Q psy7268          76 GKSAILVAETGCGKTLSFLAPLVQQI  101 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~~lpil~~~  101 (134)
                      ..++++.|+||+|||..+.+-+.+.+
T Consensus       176 ~~H~lv~G~TGsGKT~l~~~l~~q~i  201 (634)
T TIGR03743       176 VGHTLVLGTTGVGKTRLAELLITQDI  201 (634)
T ss_pred             CCcEEEECCCCCCHHHHHHHHHHHHH
Confidence            35799999999999977744444444

Members of this protein family are the putative conjugative coupling factor, TraD (or TraG), rather distantly related to the well-characterized TraD of the F plasmid. Members are associated with conjugative-transposon-like mobile genetic elements of the class that includes SXT, an antibiotic resistance transfer element in some Vibrio cholerae strains.

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

Probab=91.91  E-value=0.3  Score=36.14  Aligned_cols=33  Identities=24%  Similarity=0.337  Sum_probs=24.2

Q ss_pred             CChHHHHHHHHHHH----cCC-CeEEEcCCCCchhHHh
Q psy7268          61 TPTEIQKYSIPTLL----SGK-SAILVAETGCGKTLSF   93 (134)
Q Consensus        61 ~~t~iQ~~~i~~~~----~g~-dvli~a~tGsGKT~~~   93 (134)
                      .+++.+.+++..+.    .+. .+++.|++|+|||...
T Consensus        23 ~~~~~~~~~~~~l~~~~~~~~~~~~l~G~~G~GKTtl~   60 (269)
T TIGR03015        23 YPSKGHKRAMAYLEYGLSQREGFILITGEVGAGKTTLI   60 (269)
T ss_pred             CCCHHHHHHHHHHHHHHhcCCCEEEEEcCCCCCHHHHH
Confidence            66777777776543    333 5889999999999664

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.

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=91.86  E-value=0.39  Score=34.87  Aligned_cols=19  Identities=21%  Similarity=0.347  Sum_probs=15.3

Q ss_pred             cCCCeEEEcCCCCchhHHh
Q psy7268          75 SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~   93 (134)
                      .++.+++.|++|+|||-..
T Consensus        41 ~~~~~~l~G~~G~GKT~La   59 (227)
T PRK08903         41 ADRFFYLWGEAGSGRSHLL   59 (227)
T ss_pred             CCCeEEEECCCCCCHHHHH
Confidence            3457999999999999543

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=91.84  E-value=0.5  Score=31.56  Aligned_cols=16  Identities=38%  Similarity=0.495  Sum_probs=13.3

Q ss_pred             eEEEcCCCCchhHHhH
Q psy7268          79 AILVAETGCGKTLSFL   94 (134)
Q Consensus        79 vli~a~tGsGKT~~~~   94 (134)
                      +++.|++|+|||....
T Consensus         2 ~~i~G~~G~GKT~l~~   17 (165)
T cd01120           2 ILVFGPTGSGKTTLAL   17 (165)
T ss_pred             eeEeCCCCCCHHHHHH
Confidence            5789999999997653

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.

>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=91.73  E-value=0.14  Score=33.25  Aligned_cols=15  Identities=27%  Similarity=0.180  Sum_probs=13.0

Q ss_pred             eEEEcCCCCchhHHh
Q psy7268          79 AILVAETGCGKTLSF   93 (134)
Q Consensus        79 vli~a~tGsGKT~~~   93 (134)
                      |++.|++|||||...
T Consensus         1 I~i~G~~GsGKtTia   15 (129)
T PF13238_consen    1 IGISGIPGSGKTTIA   15 (129)
T ss_dssp             EEEEESTTSSHHHHH
T ss_pred             CEEECCCCCCHHHHH
Confidence            578999999999774

...

>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=91.72  E-value=0.4  Score=35.04  Aligned_cols=36  Identities=17%  Similarity=0.274  Sum_probs=25.5

Q ss_pred             CeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEc
Q psy7268          78 SAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIIT  123 (134)
Q Consensus        78 dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~  123 (134)
                      .+++.|++|+|||= .+-++.+.+.+..         .+.+++++.
T Consensus        36 ~l~l~G~~G~GKTH-LL~Ai~~~~~~~~---------~~~~v~y~~   71 (219)
T PF00308_consen   36 PLFLYGPSGLGKTH-LLQAIANEAQKQH---------PGKRVVYLS   71 (219)
T ss_dssp             EEEEEESTTSSHHH-HHHHHHHHHHHHC---------TTS-EEEEE
T ss_pred             ceEEECCCCCCHHH-HHHHHHHHHHhcc---------ccccceeec
Confidence            48999999999995 5567766665432         456777775

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.

>PRK04296 thymidine kinase; Provisional

Probab=91.71  E-value=0.44  Score=33.95  Aligned_cols=36  Identities=14%  Similarity=0.192  Sum_probs=22.9

Q ss_pred             CCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcC
Q psy7268          77 KSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITP  124 (134)
Q Consensus        77 ~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~P  124 (134)
                      .=.++.|++|+|||... +-.+.+...           .+.+++++-|
T Consensus         3 ~i~litG~~GsGKTT~~-l~~~~~~~~-----------~g~~v~i~k~   38 (190)
T PRK04296          3 KLEFIYGAMNSGKSTEL-LQRAYNYEE-----------RGMKVLVFKP   38 (190)
T ss_pred             EEEEEECCCCCHHHHHH-HHHHHHHHH-----------cCCeEEEEec
Confidence            34678899999999655 344444432           3455666655

>TIGR03744 traC_PFL_4706 conjugative transfer ATPase, PFL_4706 family

Probab=91.69  E-value=0.38  Score=42.33  Aligned_cols=26  Identities=23%  Similarity=0.445  Sum_probs=19.3

Q ss_pred             CCCeEEEcCCCCchhHHhHHHHHHHH
Q psy7268          76 GKSAILVAETGCGKTLSFLAPLVQQI  101 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~~lpil~~~  101 (134)
                      ..+.+|.|+||+|||...-.-+.+.+
T Consensus       475 n~n~~I~G~TGSGKS~l~~~li~q~~  500 (893)
T TIGR03744       475 NAHLLILGPTGAGKSATLTNLLMQVM  500 (893)
T ss_pred             cccEEEECCCCCCHHHHHHHHHHHHH
Confidence            45789999999999977654444444

Members of this protein family are predicted ATP-binding proteins apparently associated with DNA conjugal transfer. Members are found both in plasmids and in bacterial chromosomal regions that appear to derive from integrative elements such as conjugative transposons. More distant homologs, outside the scope of this family, include type IV secretion/conjugal transfer proteins such as TraC, VirB4 and TrsE. The granularity of this protein family definition is chosen so as to represent one distinctive clade and act as a marker through which to define and recognize the class of mobile element it serves.

>COG0606 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]

Probab=91.68  E-value=0.2  Score=40.91  Aligned_cols=26  Identities=27%  Similarity=0.424  Sum_probs=19.6

Q ss_pred             HHHHHHH-cCCCeEEEcCCCCchhHHh
Q psy7268          68 YSIPTLL-SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        68 ~~i~~~~-~g~dvli~a~tGsGKT~~~   93 (134)
                      +++.... -|+++++.+|+|||||+..
T Consensus       189 rAleiAAAGgHnLl~~GpPGtGKTmla  215 (490)
T COG0606         189 RALEIAAAGGHNLLLVGPPGTGKTMLA  215 (490)
T ss_pred             HHHHHHHhcCCcEEEecCCCCchHHhh
Confidence            3443333 5789999999999999874

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=91.63  E-value=0.14  Score=39.04  Aligned_cols=18  Identities=22%  Similarity=0.213  Sum_probs=15.5

Q ss_pred             CCCeEEEcCCCCchhHHh
Q psy7268          76 GKSAILVAETGCGKTLSF   93 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~   93 (134)
                      +.++++.||+|+|||...
T Consensus        58 ~~~vll~G~pGTGKT~lA   75 (284)
T TIGR02880        58 TLHMSFTGNPGTGKTTVA   75 (284)
T ss_pred             CceEEEEcCCCCCHHHHH
Confidence            447999999999999775

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.

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

Probab=91.63  E-value=0.23  Score=34.28  Aligned_cols=27  Identities=30%  Similarity=0.512  Sum_probs=15.9

Q ss_pred             CCCeEEEcCCCCchhHHhHHHHHHHHHh
Q psy7268          76 GKSAILVAETGCGKTLSFLAPLVQQILT  103 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~~lpil~~~~~  103 (134)
                      ++.+++.|+.|+|||.. +-.++..+..
T Consensus        24 ~~~~ll~G~~G~GKT~l-l~~~~~~~~~   50 (185)
T PF13191_consen   24 PRNLLLTGESGSGKTSL-LRALLDRLAE   50 (185)
T ss_dssp             ---EEE-B-TTSSHHHH-HHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHH-HHHHHHHHHh
Confidence            46799999999999955 3445555554

>KOG0744|consensus

Probab=91.46  E-value=0.24  Score=38.93  Aligned_cols=26  Identities=31%  Similarity=0.438  Sum_probs=19.7

Q ss_pred             CCeEEEcCCCCchhHHhHHHHHHHHHh
Q psy7268          77 KSAILVAETGCGKTLSFLAPLVQQILT  103 (134)
Q Consensus        77 ~dvli~a~tGsGKT~~~~lpil~~~~~  103 (134)
                      |=++++||+|+||| ..+=++.+++.-
T Consensus       178 RliLlhGPPGTGKT-SLCKaLaQkLSI  203 (423)
T KOG0744|consen  178 RLILLHGPPGTGKT-SLCKALAQKLSI  203 (423)
T ss_pred             eEEEEeCCCCCChh-HHHHHHHHhhee
Confidence            34889999999999 455677777653

>TIGR03880 KaiC_arch_3 KaiC domain protein, AF_0351 family

Probab=91.44  E-value=0.47  Score=34.41  Aligned_cols=20  Identities=35%  Similarity=0.523  Sum_probs=15.8

Q ss_pred             cCCCeEEEcCCCCchhHHhH
Q psy7268          75 SGKSAILVAETGCGKTLSFL   94 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~~   94 (134)
                      .|.-+++.+++|+|||...+
T Consensus        15 ~g~~~li~G~~G~GKt~~~~   34 (224)
T TIGR03880        15 EGHVIVVIGEYGTGKTTFSL   34 (224)
T ss_pred             CCeEEEEECCCCCCHHHHHH
Confidence            35668999999999986543

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.

>PRK13876 conjugal transfer coupling protein TraG; Provisional

Probab=91.42  E-value=0.16  Score=43.15  Aligned_cols=25  Identities=20%  Similarity=0.341  Sum_probs=22.3

Q ss_pred             CCeEEEcCCCCchhHHhHHHHHHHH
Q psy7268          77 KSAILVAETGCGKTLSFLAPLVQQI  101 (134)
Q Consensus        77 ~dvli~a~tGsGKT~~~~lpil~~~  101 (134)
                      .++++.||||||||..+++|-|..+
T Consensus       145 ~hvLviApTrSGKgvg~VIPnLL~~  169 (663)
T PRK13876        145 EHVLCFAPTRSGKGVGLVVPTLLTW  169 (663)
T ss_pred             ceEEEEecCCCCcceeEehhhHHhC
Confidence            4799999999999999999987754

>TIGR02767 TraG-Ti Ti-type conjugative transfer system protien TraG

Probab=91.41  E-value=0.17  Score=42.82  Aligned_cols=24  Identities=29%  Similarity=0.317  Sum_probs=21.0

Q ss_pred             CCeEEEcCCCCchhHHhHHHHHHH
Q psy7268          77 KSAILVAETGCGKTLSFLAPLVQQ  100 (134)
Q Consensus        77 ~dvli~a~tGsGKT~~~~lpil~~  100 (134)
                      .++++.||||+|||..+++|-+-.
T Consensus       212 ~H~lv~ApTgsGKgvg~VIPnLL~  235 (623)
T TIGR02767       212 THMIFFAGSGGFKTTSVVVPTALK  235 (623)
T ss_pred             ceEEEEeCCCCCccceeehhhhhc
Confidence            479999999999999999996543

This protein is found in the Agrobacterium tumefaciens Ti plasmid tra region responsible for conjugative transfer of the entire plasmid among Agrobacterium strains. The protein is distantly related to the F-type conjugation system TraG protein. Both of these systems are examples of type IV secretion systems.

>KOG1807|consensus

Probab=91.39  E-value=0.43  Score=41.31  Aligned_cols=66  Identities=18%  Similarity=0.174  Sum_probs=46.0

Q ss_pred             CChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHh
Q psy7268          61 TPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQI  132 (134)
Q Consensus        61 ~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi  132 (134)
                      .+..-|..|....+.-+=-++++|+|+|||++-+..+=..+.....      .......+++|-|..-+.|+
T Consensus       378 ildsSq~~A~qs~ltyelsliqgppGTgkt~vtlkav~tLL~n~s~------~~~~epIlvvC~Tnhavdq~  443 (1025)
T KOG1807|consen  378 ILDSSQQFAKQSKLTYELSLIQGPPGTGKTLVTLKAVDTLLLNSSG------YTEPEPILVVCLTNHAVDQY  443 (1025)
T ss_pred             eecHHHHHHHHHHhhhhhheeecCCCCCceeehHHHHHHHHhcccc------cccccceeeeehhhHHHHHH
Confidence            3344689999888888888999999999999987665444443211      11233478888887777664

>COG0714 MoxR-like ATPases [General function prediction only]

Probab=91.35  E-value=0.28  Score=37.95  Aligned_cols=23  Identities=39%  Similarity=0.527  Sum_probs=19.8

Q ss_pred             HHHHcCCCeEEEcCCCCchhHHh
Q psy7268          71 PTLLSGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        71 ~~~~~g~dvli~a~tGsGKT~~~   93 (134)
                      -.++.|+.+++.+++|+|||...
T Consensus        38 ~a~~~~~~vll~G~PG~gKT~la   60 (329)
T COG0714          38 LALLAGGHVLLEGPPGVGKTLLA   60 (329)
T ss_pred             HHHHcCCCEEEECCCCccHHHHH
Confidence            35668999999999999999764

>KOG0390|consensus

Probab=91.29  E-value=0.52  Score=40.75  Aligned_cols=62  Identities=24%  Similarity=0.332  Sum_probs=41.6

Q ss_pred             CCChHHHHHHHHHHHc---CC-------CeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcH
Q psy7268          60 TTPTEIQKYSIPTLLS---GK-------SAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGR  126 (134)
Q Consensus        60 ~~~t~iQ~~~i~~~~~---g~-------dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~  126 (134)
                      ..+.|+|++.+..+..   |.       ..|+.-..|+|||+-. ++.+..++++.+.  ..+  .-.++|||+|..
T Consensus       237 ~~LrPHQ~EG~~FL~knl~g~~~~~~~~GCImAd~~GlGKTlq~-IsflwtlLrq~P~--~~~--~~~k~lVV~P~s  308 (776)
T KOG0390|consen  237 KILRPHQREGFEFLYKNLAGLIRPKNSGGCIMADEPGLGKTLQC-ISFIWTLLRQFPQ--AKP--LINKPLVVAPSS  308 (776)
T ss_pred             hhcCchHHHHHHHHHhhhhcccccCCCCceEeeCCCCcchHHHH-HHHHHHHHHhCcC--ccc--cccccEEEccHH
Confidence            3778999999987652   22       3566677899999765 6777777665421  000  125789999964

>PRK06067 flagellar accessory protein FlaH; Validated

Probab=91.24  E-value=0.54  Score=34.36  Aligned_cols=26  Identities=12%  Similarity=0.100  Sum_probs=18.4

Q ss_pred             cCCCeEEEcCCCCchhHHhHHHHHHH
Q psy7268          75 SGKSAILVAETGCGKTLSFLAPLVQQ  100 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~~lpil~~  100 (134)
                      .|.-+++.+++|+|||.....-+...
T Consensus        24 ~g~~~~i~G~~GsGKt~l~~~~~~~~   49 (234)
T PRK06067         24 FPSLILIEGDHGTGKSVLSQQFVYGA   49 (234)
T ss_pred             CCcEEEEECCCCCChHHHHHHHHHHH
Confidence            35568899999999996654443333

>TIGR03689 pup_AAA proteasome ATPase

Probab=91.17  E-value=0.16  Score=41.95  Aligned_cols=54  Identities=28%  Similarity=0.385  Sum_probs=29.5

Q ss_pred             CCCCcccCCCCHHHHHHHHHC---CCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHh
Q psy7268          37 DLGTFEDTGLAPEIIDIFTKR---GLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        37 ~~~~f~~~~l~~~i~~~l~~~---g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~   93 (134)
                      |-.+|++++--+..++.+.+.   .+.+|......-   +...+.+++.||+|+|||+..
T Consensus       177 p~v~~~dIgGl~~~i~~i~~~v~lp~~~~~l~~~~g---l~~p~GILLyGPPGTGKT~LA  233 (512)
T TIGR03689       177 PDVTYADIGGLDSQIEQIRDAVELPFLHPELYREYD---LKPPKGVLLYGPPGCGKTLIA  233 (512)
T ss_pred             CCCCHHHcCChHHHHHHHHHHHHHHhhCHHHHHhcc---CCCCcceEEECCCCCcHHHHH
Confidence            345788877333444444431   232222222111   113467999999999999753

In the Actinobacteria, as shown for Mycobacterium tuberculosis, some proteins are modified by ligation between an epsilon-amino group of a lysine side chain and the C-terminal carboxylate of the ubiquitin-like protein Pup. This modification leads to protein degradation by the archaeal-like proteasome found in the Actinobacteria. Members of this protein family belong to the AAA family of ATPases and tend to be clustered with the genes for Pup, the Pup ligase PafA, and structural components of the proteasome. This protein forms hexameric rings with ATPase activity.

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=91.15  E-value=0.16  Score=37.88  Aligned_cols=17  Identities=29%  Similarity=0.327  Sum_probs=14.9

Q ss_pred             CCeEEEcCCCCchhHHh
Q psy7268          77 KSAILVAETGCGKTLSF   93 (134)
Q Consensus        77 ~dvli~a~tGsGKT~~~   93 (134)
                      .++++.||+|+|||...
T Consensus        43 ~~vll~GppGtGKTtlA   59 (261)
T TIGR02881        43 LHMIFKGNPGTGKTTVA   59 (261)
T ss_pred             ceEEEEcCCCCCHHHHH
Confidence            46899999999999775

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.

>PHA02244 ATPase-like protein

Probab=91.09  E-value=0.37  Score=38.36  Aligned_cols=22  Identities=18%  Similarity=0.194  Sum_probs=18.3

Q ss_pred             HHHcCCCeEEEcCCCCchhHHh
Q psy7268          72 TLLSGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        72 ~~~~g~dvli~a~tGsGKT~~~   93 (134)
                      .+..+.++++.||+|+|||...
T Consensus       115 ~l~~~~PVLL~GppGtGKTtLA  136 (383)
T PHA02244        115 IVNANIPVFLKGGAGSGKNHIA  136 (383)
T ss_pred             HHhcCCCEEEECCCCCCHHHHH
Confidence            3457889999999999999654

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=91.04  E-value=0.36  Score=36.86  Aligned_cols=19  Identities=26%  Similarity=0.391  Sum_probs=15.7

Q ss_pred             cCC--CeEEEcCCCCchhHHh
Q psy7268          75 SGK--SAILVAETGCGKTLSF   93 (134)
Q Consensus        75 ~g~--dvli~a~tGsGKT~~~   93 (134)
                      +++  .+++.||+|+|||...
T Consensus        33 ~~~~~~lll~Gp~GtGKT~la   53 (337)
T PRK12402         33 SPNLPHLLVQGPPGSGKTAAV   53 (337)
T ss_pred             CCCCceEEEECCCCCCHHHHH
Confidence            444  7999999999999665

>KOG0738|consensus

Probab=90.96  E-value=0.19  Score=40.34  Aligned_cols=56  Identities=20%  Similarity=0.494  Sum_probs=34.0

Q ss_pred             CCCCcccCCCCHHHHHHHHHC------CCCCChH----------HHHHH-----HHHHHcC-----CCeEEEcCCCCchh
Q psy7268          37 DLGTFEDTGLAPEIIDIFTKR------GLTTPTE----------IQKYS-----IPTLLSG-----KSAILVAETGCGKT   90 (134)
Q Consensus        37 ~~~~f~~~~l~~~i~~~l~~~------g~~~~t~----------iQ~~~-----i~~~~~g-----~dvli~a~tGsGKT   90 (134)
                      ....|+..+....+.+.+++-      ++ +.+.          +++.+     +|.+++|     +.++..+|+|+|||
T Consensus       181 ~~~~f~~~~~d~~Lve~lerdIl~~np~i-kW~DIagl~~AK~lL~EAVvlPi~mPe~F~GirrPWkgvLm~GPPGTGKT  259 (491)
T KOG0738|consen  181 EDKKFDSLGYDADLVEALERDILQRNPNI-KWDDIAGLHEAKKLLKEAVVLPIWMPEFFKGIRRPWKGVLMVGPPGTGKT  259 (491)
T ss_pred             ccCCCCcccchHHHHHHHHHHHhccCCCc-ChHhhcchHHHHHHHHHHHhhhhhhHHHHhhcccccceeeeeCCCCCcHH
Confidence            445677777777777777651      11 1111          12221     1344555     47999999999999


Q ss_pred             HHh
Q psy7268          91 LSF   93 (134)
Q Consensus        91 ~~~   93 (134)
                      +..
T Consensus       260 lLA  262 (491)
T KOG0738|consen  260 LLA  262 (491)
T ss_pred             HHH
Confidence            764

>CHL00181 cbbX CbbX; Provisional

Probab=90.95  E-value=0.18  Score=38.53  Aligned_cols=19  Identities=32%  Similarity=0.394  Sum_probs=15.9

Q ss_pred             CCCeEEEcCCCCchhHHhH
Q psy7268          76 GKSAILVAETGCGKTLSFL   94 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~~   94 (134)
                      |.++++.||+|+|||...-
T Consensus        59 ~~~ill~G~pGtGKT~lAr   77 (287)
T CHL00181         59 GLHMSFTGSPGTGKTTVAL   77 (287)
T ss_pred             CceEEEECCCCCCHHHHHH
Confidence            4568999999999998753

>TIGR01242 26Sp45 26S proteasome subunit P45 family

Probab=90.93  E-value=0.16  Score=39.85  Aligned_cols=55  Identities=25%  Similarity=0.296  Sum_probs=31.2

Q ss_pred             CCCCCcccCCCCHHHHHHHHHC---CCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHh
Q psy7268          36 IDLGTFEDTGLAPEIIDIFTKR---GLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        36 ~~~~~f~~~~l~~~i~~~l~~~---g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~   93 (134)
                      .|-.+|++++-.++..+.+.+.   .+.++.-...  + -+...+.+++.||+|+|||...
T Consensus       116 ~p~~~~~di~Gl~~~~~~l~~~i~~~~~~~~~~~~--~-g~~~p~gvLL~GppGtGKT~la  173 (364)
T TIGR01242       116 RPNVSYEDIGGLEEQIREIREAVELPLKHPELFEE--V-GIEPPKGVLLYGPPGTGKTLLA  173 (364)
T ss_pred             CCCCCHHHhCChHHHHHHHHHHHHHHhcCHHHHHh--c-CCCCCceEEEECCCCCCHHHHH
Confidence            3444677777666666666552   1222111110  0 0122456999999999999764

Many proteins may score above the trusted cutoff because an internal

>PRK08533 flagellar accessory protein FlaH; Reviewed

Probab=90.89  E-value=0.59  Score=34.40  Aligned_cols=21  Identities=14%  Similarity=0.270  Sum_probs=17.2

Q ss_pred             HcCCCeEEEcCCCCchhHHhH
Q psy7268          74 LSGKSAILVAETGCGKTLSFL   94 (134)
Q Consensus        74 ~~g~dvli~a~tGsGKT~~~~   94 (134)
                      -.|.-+++.+++|+|||...+
T Consensus        22 ~~g~~~~i~G~~G~GKTtl~~   42 (230)
T PRK08533         22 PAGSLILIEGDESTGKSILSQ   42 (230)
T ss_pred             CCCcEEEEECCCCCCHHHHHH
Confidence            357789999999999997643

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=90.87  E-value=0.17  Score=40.20  Aligned_cols=54  Identities=28%  Similarity=0.294  Sum_probs=30.0

Q ss_pred             CCCCcccCCCCHHHHHHHHHC---CCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHh
Q psy7268          37 DLGTFEDTGLAPEIIDIFTKR---GLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        37 ~~~~f~~~~l~~~i~~~l~~~---g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~   93 (134)
                      |-.+|++++-.++..+.+.+.   .+.++-..+..   -+..-+.+++.||+|+|||+..
T Consensus       126 p~~~~~di~Gl~~~~~~l~~~i~~pl~~~~~~~~~---g~~~p~gvLL~GppGtGKT~lA  182 (389)
T PRK03992        126 PNVTYEDIGGLEEQIREVREAVELPLKKPELFEEV---GIEPPKGVLLYGPPGTGKTLLA  182 (389)
T ss_pred             CCCCHHHhCCcHHHHHHHHHHHHHHhhCHHHHHhc---CCCCCCceEEECCCCCChHHHH
Confidence            334677777666666666552   12221111110   0112357999999999999764

>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH

Probab=90.75  E-value=0.26  Score=40.36  Aligned_cols=55  Identities=27%  Similarity=0.258  Sum_probs=33.2

Q ss_pred             CCCCCcccCCCCHHHHHHHHHC--CCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHh
Q psy7268          36 IDLGTFEDTGLAPEIIDIFTKR--GLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        36 ~~~~~f~~~~l~~~i~~~l~~~--g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~   93 (134)
                      .+-.+|+++.-.++..+.+.+.  -+..+...+..-   ....+.+++.||+|+|||...
T Consensus        49 ~~~~~~~di~g~~~~k~~l~~~~~~l~~~~~~~~~g---~~~~~giLL~GppGtGKT~la  105 (495)
T TIGR01241        49 KPKVTFKDVAGIDEAKEELMEIVDFLKNPSKFTKLG---AKIPKGVLLVGPPGTGKTLLA  105 (495)
T ss_pred             CCCCCHHHhCCHHHHHHHHHHHHHHHHCHHHHHhcC---CCCCCcEEEECCCCCCHHHHH
Confidence            4556888888777776666542  122222221110   112357999999999999763

HflB(FtsH) is a pleiotropic protein required for correct cell division in bacteria. It has ATP-dependent zinc metalloprotease activity. It was formerly designated cell division protein FtsH.

>PRK13822 conjugal transfer coupling protein TraG; Provisional

Probab=90.75  E-value=0.2  Score=42.53  Aligned_cols=23  Identities=26%  Similarity=0.306  Sum_probs=20.7

Q ss_pred             CCeEEEcCCCCchhHHhHHHHHH
Q psy7268          77 KSAILVAETGCGKTLSFLAPLVQ   99 (134)
Q Consensus        77 ~dvli~a~tGsGKT~~~~lpil~   99 (134)
                      .++++.||||+|||..+++|-+-
T Consensus       225 ~H~Lv~ApTgsGKt~g~VIPnLL  247 (641)
T PRK13822        225 THGLVFAGSGGFKTTSVVVPTAL  247 (641)
T ss_pred             ceEEEEeCCCCCccceEehhhhh
Confidence            47899999999999999999764

>cd01394 radB RadB

Probab=90.73  E-value=0.52  Score=33.95  Aligned_cols=22  Identities=23%  Similarity=0.238  Sum_probs=16.6

Q ss_pred             CCCeEEEcCCCCchhHHhHHHH
Q psy7268          76 GKSAILVAETGCGKTLSFLAPL   97 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~~lpi   97 (134)
                      |.-+.+.+++|+|||...+--+
T Consensus        19 g~i~~i~G~~GsGKT~l~~~~a   40 (218)
T cd01394          19 GTVTQVYGPPGTGKTNIAIQLA   40 (218)
T ss_pred             CeEEEEECCCCCCHHHHHHHHH
Confidence            4558899999999997654433

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

>PRK10078 ribose 1,5-bisphosphokinase; Provisional

Probab=90.71  E-value=0.2  Score=35.37  Aligned_cols=18  Identities=33%  Similarity=0.492  Sum_probs=15.4

Q ss_pred             CCCeEEEcCCCCchhHHh
Q psy7268          76 GKSAILVAETGCGKTLSF   93 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~   93 (134)
                      |..+++.||+|+|||...
T Consensus         2 g~~i~l~G~sGsGKsTl~   19 (186)
T PRK10078          2 GKLIWLMGPSGSGKDSLL   19 (186)
T ss_pred             CcEEEEECCCCCCHHHHH
Confidence            567899999999999764

>PF14532 Sigma54_activ_2: Sigma-54 interaction domain; PDB: 3CO5_B 3N70_H

Probab=90.66  E-value=0.47  Score=31.83  Aligned_cols=22  Identities=27%  Similarity=0.386  Sum_probs=17.0

Q ss_pred             HHHcCCCeEEEcCCCCchhHHh
Q psy7268          72 TLLSGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        72 ~~~~g~dvli~a~tGsGKT~~~   93 (134)
                      ....+..|++.|+.|+||+.+.
T Consensus        17 ~a~~~~pvli~GE~GtGK~~~A   38 (138)
T PF14532_consen   17 LAKSSSPVLITGEPGTGKSLLA   38 (138)
T ss_dssp             HHCSSS-EEEECCTTSSHHHHH
T ss_pred             HhCCCCcEEEEcCCCCCHHHHH
Confidence            3446778999999999999753

>PRK05642 DNA replication initiation factor; Validated

Probab=90.59  E-value=0.57  Score=34.54  Aligned_cols=25  Identities=16%  Similarity=0.189  Sum_probs=17.7

Q ss_pred             CCeEEEcCCCCchhHHhHHHHHHHHH
Q psy7268          77 KSAILVAETGCGKTLSFLAPLVQQIL  102 (134)
Q Consensus        77 ~dvli~a~tGsGKT~~~~lpil~~~~  102 (134)
                      +.+++.|++|+|||-- +-.+.+.+.
T Consensus        46 ~~l~l~G~~G~GKTHL-l~a~~~~~~   70 (234)
T PRK05642         46 SLIYLWGKDGVGRSHL-LQAACLRFE   70 (234)
T ss_pred             CeEEEECCCCCCHHHH-HHHHHHHHH
Confidence            4688999999999954 344444443

>TIGR02746 TraC-F-type type-IV secretion system protein TraC

Probab=90.57  E-value=0.56  Score=40.45  Aligned_cols=39  Identities=23%  Similarity=0.377  Sum_probs=25.2

Q ss_pred             CCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcH
Q psy7268          76 GKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGR  126 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~  126 (134)
                      +.+++|.|+||+|||...-. ++.....           .+.+++|+=|..
T Consensus       430 n~n~~I~G~tGsGKS~~~~~-l~~~~~~-----------~g~~v~iiD~~~  468 (797)
T TIGR02746       430 NYNIAVVGGSGAGKSFFMQE-LIVDNLS-----------RGGKVWVIDVGR  468 (797)
T ss_pred             ccceEEEcCCCCCHHHHHHH-HHHHHHh-----------CCCEEEEEeCCC
Confidence            34799999999999977544 3333332           345566665543

The protein family described here is common among the F, P and I-like type IV secretion systems. Gene symbols include TraC (F-type), TrbE/VirB4 (P-type) and TraU (I-type). The protein conyains the Walker A and B motifs and so is a putative nucleotide triphosphatase.

>COG1643 HrpA HrpA-like helicases [DNA replication, recombination, and repair]

Probab=90.52  E-value=0.99  Score=39.55  Aligned_cols=38  Identities=26%  Similarity=0.411  Sum_probs=26.1

Q ss_pred             hHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHH
Q psy7268          63 TEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQ  100 (134)
Q Consensus        63 t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~  100 (134)
                      +....+.+..+.+..-++++|+||+|||...=.-+++.
T Consensus        52 ~~~~~~i~~ai~~~~vvii~getGsGKTTqlP~~lle~   89 (845)
T COG1643          52 TAVRDEILKAIEQNQVVIIVGETGSGKTTQLPQFLLEE   89 (845)
T ss_pred             HHHHHHHHHHHHhCCEEEEeCCCCCChHHHHHHHHHhh
Confidence            34455555566677779999999999997653333443

>TIGR03754 conj_TOL_TraD conjugative coupling factor TraD, TOL family

Probab=90.51  E-value=0.55  Score=39.87  Aligned_cols=27  Identities=22%  Similarity=0.149  Sum_probs=21.5

Q ss_pred             CCCeEEEcCCCCchhHHhHHHHHHHHH
Q psy7268          76 GKSAILVAETGCGKTLSFLAPLVQQIL  102 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~~lpil~~~~  102 (134)
                      ..+.+|.|+||+|||..+.+-+.+.+.
T Consensus       180 ~gHtlV~GtTGsGKT~l~~~li~q~i~  206 (643)
T TIGR03754       180 VGHTLVLGTTRVGKTRLAELLITQDIR  206 (643)
T ss_pred             cCceEEECCCCCCHHHHHHHHHHHHHH
Confidence            457899999999999988776666654

Members of this protein are assigned by homology to the TraD family of conjugative coupling factor. This particular clade serves as a marker for an extended gene region that occurs occasionally on plasmids, including the toluene catabolism TOL plasmid. More commonly, the gene region is chromosomal, flanked by various markers of conjugative transfer and insertion.

>KOG1131|consensus

Probab=90.43  E-value=2  Score=35.98  Aligned_cols=46  Identities=22%  Similarity=0.187  Sum_probs=32.9

Q ss_pred             CCCCChHHHHHHHHHHH----cCCCeEEEcCCCCchhHHhHHHHHHHHHh
Q psy7268          58 GLTTPTEIQKYSIPTLL----SGKSAILVAETGCGKTLSFLAPLVQQILT  103 (134)
Q Consensus        58 g~~~~t~iQ~~~i~~~~----~g~dvli~a~tGsGKT~~~~lpil~~~~~  103 (134)
                      .|.+-+|-|..-+-.+.    .+.+.++..|+|+|||.+.+--++.+-..
T Consensus        13 PY~~iYPEQ~~YM~elKrsLDakGh~llEMPSGTGKTvsLLSli~aYq~~   62 (755)
T KOG1131|consen   13 PYDYIYPEQYEYMRELKRSLDAKGHCLLEMPSGTGKTVSLLSLIIAYQLH   62 (755)
T ss_pred             CCcccCHHHHHHHHHHHHhhccCCcEEEECCCCCCcchHHHHHHHHHHHh
Confidence            45666788877665554    45678899999999998876555555443

>PRK08939 primosomal protein DnaI; Reviewed

Probab=90.42  E-value=0.6  Score=36.03  Aligned_cols=26  Identities=23%  Similarity=0.382  Sum_probs=19.2

Q ss_pred             CCCeEEEcCCCCchhHHhHHHHHHHHH
Q psy7268          76 GKSAILVAETGCGKTLSFLAPLVQQIL  102 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~~lpil~~~~  102 (134)
                      ++.+++.|++|+|||... .++...+.
T Consensus       156 ~~gl~L~G~~G~GKThLa-~Aia~~l~  181 (306)
T PRK08939        156 VKGLYLYGDFGVGKSYLL-AAIANELA  181 (306)
T ss_pred             CCeEEEECCCCCCHHHHH-HHHHHHHH
Confidence            457999999999999654 34455554

>TIGR01650 PD_CobS cobaltochelatase, CobS subunit

Probab=90.35  E-value=0.37  Score=37.62  Aligned_cols=23  Identities=13%  Similarity=0.263  Sum_probs=19.0

Q ss_pred             HHHHcCCCeEEEcCCCCchhHHh
Q psy7268          71 PTLLSGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        71 ~~~~~g~dvli~a~tGsGKT~~~   93 (134)
                      -.+..++++++.+++|+|||...
T Consensus        59 ~~l~~~~~ilL~G~pGtGKTtla   81 (327)
T TIGR01650        59 AGFAYDRRVMVQGYHGTGKSTHI   81 (327)
T ss_pred             HHHhcCCcEEEEeCCCChHHHHH
Confidence            34556889999999999999764

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.

>PF03193 DUF258: Protein of unknown function, DUF258; InterPro: IPR004881 This entry contains Escherichia coli (strain K12) RsgA, which may play a role in 30S ribosomal subunit biogenesis

Probab=90.34  E-value=0.51  Score=33.12  Aligned_cols=44  Identities=27%  Similarity=0.501  Sum_probs=32.2

Q ss_pred             HHHHHHHHHCCCCC-----ChHHHHHHHHHHHcCCCeEEEcCCCCchhH
Q psy7268          48 PEIIDIFTKRGLTT-----PTEIQKYSIPTLLSGKSAILVAETGCGKTL   91 (134)
Q Consensus        48 ~~i~~~l~~~g~~~-----~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~   91 (134)
                      +++++..+++||+-     -+......+...+.++-+++.+++|.||+.
T Consensus         2 ~~~~~~y~~~gy~v~~~S~~~~~g~~~l~~~l~~k~~vl~G~SGvGKSS   50 (161)
T PF03193_consen    2 EELLEQYEKLGYPVFFISAKTGEGIEELKELLKGKTSVLLGQSGVGKSS   50 (161)
T ss_dssp             HHHHHHHHHTTSEEEE-BTTTTTTHHHHHHHHTTSEEEEECSTTSSHHH
T ss_pred             HHHHHHHHHcCCcEEEEeCCCCcCHHHHHHHhcCCEEEEECCCCCCHHH
Confidence            45667777777751     133445666677888999999999999983

RsgA is an unusual circulary permuted GTPase that catalyzes rapid hydrolysis of GTP with a slow catalytic turnover. It is dispensible for viability, but important for overall fitness. The intrinsic GTPase activity is stimulated by the presence of 30S (160-fold increase in kcat) or 70S (96 fold increase in kcat) ribosomes []. The GTPase is inhibited by aminoglycoside antibiotics such as neomycin and paromycin [] streptomycin and spectinomycin []. This inhibition is not due to competition for binding sites on the 30S or 70S ribosome []. ; GO: 0003924 GTPase activity, 0005525 GTP binding; PDB: 2YKR_W 2YV5_A 1T9H_A 2RCN_A 4A2I_V 1U0L_B.

>PRK12726 flagellar biosynthesis regulator FlhF; Provisional

Probab=90.32  E-value=1.4  Score=35.47  Aligned_cols=19  Identities=32%  Similarity=0.555  Sum_probs=15.7

Q ss_pred             CCCeEEEcCCCCchhHHhH
Q psy7268          76 GKSAILVAETGCGKTLSFL   94 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~~   94 (134)
                      ++-+++.||+|+|||....
T Consensus       206 ~~ii~lvGptGvGKTTt~a  224 (407)
T PRK12726        206 HRIISLIGQTGVGKTTTLV  224 (407)
T ss_pred             CeEEEEECCCCCCHHHHHH
Confidence            4568899999999997754

>cd01363 Motor_domain Myosin and Kinesin motor domain

Probab=90.32  E-value=0.25  Score=35.12  Aligned_cols=26  Identities=27%  Similarity=0.415  Sum_probs=20.8

Q ss_pred             HHHHHHHcCCC--eEEEcCCCCchhHHh
Q psy7268          68 YSIPTLLSGKS--AILVAETGCGKTLSF   93 (134)
Q Consensus        68 ~~i~~~~~g~d--vli~a~tGsGKT~~~   93 (134)
                      .++..++.|.|  +++-+.||+|||...
T Consensus        14 ~~v~~~~~G~n~~i~~yG~tGsGKT~Tm   41 (186)
T cd01363          14 PLLQSALDGYNVCIFAYGQTGSGKTYTM   41 (186)
T ss_pred             HHHHHHhCCcceeEEEECCCCCcceEec
Confidence            56677788876  778899999999553

These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes.

>KOG0745|consensus

Probab=90.31  E-value=0.17  Score=41.22  Aligned_cols=17  Identities=41%  Similarity=0.604  Sum_probs=14.5

Q ss_pred             CCeEEEcCCCCchhHHh
Q psy7268          77 KSAILVAETGCGKTLSF   93 (134)
Q Consensus        77 ~dvli~a~tGsGKT~~~   93 (134)
                      .|+++.+|||||||+..
T Consensus       227 SNvLllGPtGsGKTlla  243 (564)
T KOG0745|consen  227 SNVLLLGPTGSGKTLLA  243 (564)
T ss_pred             ccEEEECCCCCchhHHH
Confidence            36999999999999754

>KOG0733|consensus

Probab=90.24  E-value=0.29  Score=41.44  Aligned_cols=51  Identities=20%  Similarity=0.347  Sum_probs=30.7

Q ss_pred             CcccCCCCHHHHHHHHHC--CCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHh
Q psy7268          40 TFEDTGLAPEIIDIFTKR--GLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        40 ~f~~~~l~~~i~~~l~~~--g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~   93 (134)
                      +|+++|=-+..+..|.++  ...+|-.+++.-   +.--+.+++++|+|+|||...
T Consensus       188 ~f~diGG~d~~~~el~~li~~i~~Pe~~~~lG---v~PprGvLlHGPPGCGKT~lA  240 (802)
T KOG0733|consen  188 SFSDIGGLDKTLAELCELIIHIKHPEVFSSLG---VRPPRGVLLHGPPGCGKTSLA  240 (802)
T ss_pred             chhhccChHHHHHHHHHHHHHhcCchhHhhcC---CCCCCceeeeCCCCccHHHHH
Confidence            677777556666555553  233333332221   112467999999999999654

>KOG2340|consensus

Probab=90.11  E-value=0.83  Score=38.11  Aligned_cols=74  Identities=18%  Similarity=0.231  Sum_probs=52.8

Q ss_pred             CCChHHHHHHHHHHHcCCCeEEEcC-CCCch--hHHhHHHHHHHHHhhcC-------------------CCCCCCCCCCc
Q psy7268          60 TTPTEIQKYSIPTLLSGKSAILVAE-TGCGK--TLSFLAPLVQQILTWKS-------------------RPEYKPELNAP  117 (134)
Q Consensus        60 ~~~t~iQ~~~i~~~~~g~dvli~a~-tGsGK--T~~~~lpil~~~~~~~~-------------------~~~~~~~~~~~  117 (134)
                      ..+|+.|.+.+..+.+-+|++.... -+.|+  +-.|++=+|+++++...                   ....+.....|
T Consensus       215 ~pltalQ~~L~~~m~~YrDl~y~~~s~kn~~e~R~lYclH~lNHi~K~r~~IL~Nn~r~~Sqk~g~~~~~~frDQG~tRp  294 (698)
T KOG2340|consen  215 EPLTALQKELFKIMFNYRDLLYPTRSQKNGEEYRSLYCLHALNHILKTRDLILGNNRRLASQKEGENPDESFRDQGFTRP  294 (698)
T ss_pred             CcchHHHHHHHHHHHhhhhhccccccccccchhhhhHHHHHHHHHHHHHHHHhcchHhhhhhhcCCCCchhhhhcCCCCc
Confidence            4679999999999999999764322 23455  45688888998885422                   11123344679


Q ss_pred             EEEEEcCcHHHHHHhc
Q psy7268         118 LALIITPGRELVFQIG  133 (134)
Q Consensus       118 ~~lil~Pt~~La~Qi~  133 (134)
                      ++||++|+|+-|..|.
T Consensus       295 kVLivvpfRe~A~riV  310 (698)
T KOG2340|consen  295 KVLIVVPFRESAYRIV  310 (698)
T ss_pred             eEEEEecchHHHHHHH
Confidence            9999999999988764

>PRK09361 radB DNA repair and recombination protein RadB; Provisional

Probab=90.10  E-value=0.73  Score=33.36  Aligned_cols=24  Identities=29%  Similarity=0.337  Sum_probs=17.8

Q ss_pred             CCCeEEEcCCCCchhHHhHHHHHH
Q psy7268          76 GKSAILVAETGCGKTLSFLAPLVQ   99 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~~lpil~   99 (134)
                      |.-+.+.+++|+|||...+--+.+
T Consensus        23 g~i~~i~G~~GsGKT~l~~~la~~   46 (225)
T PRK09361         23 GTITQIYGPPGSGKTNICLQLAVE   46 (225)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH
Confidence            556899999999999766444333

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=89.90  E-value=0.6  Score=38.18  Aligned_cols=22  Identities=27%  Similarity=0.250  Sum_probs=17.0

Q ss_pred             cCCCeEEEcCCCCchhHHhHHH
Q psy7268          75 SGKSAILVAETGCGKTLSFLAP   96 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~~lp   96 (134)
                      .|.-+++.+++|+|||...+--
T Consensus       262 ~gs~~li~G~~G~GKt~l~~~f  283 (484)
T TIGR02655       262 KDSIILATGATGTGKTLLVSKF  283 (484)
T ss_pred             CCcEEEEECCCCCCHHHHHHHH
Confidence            4557999999999999765433

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.

>PF03205 MobB: Molybdopterin guanine dinucleotide synthesis protein B; PDB: 2F1R_B 1P9N_A 1NP6_B 2NPI_A 1XJC_A

Probab=89.87  E-value=0.84  Score=31.06  Aligned_cols=24  Identities=21%  Similarity=0.342  Sum_probs=16.9

Q ss_pred             eEEEcCCCCchhHHhHHHHHHHHHh
Q psy7268          79 AILVAETGCGKTLSFLAPLVQQILT  103 (134)
Q Consensus        79 vli~a~tGsGKT~~~~lpil~~~~~  103 (134)
                      +.++|+.++|||.. +--++..+.+
T Consensus         3 v~VvG~~~sGKTTl-~~~Li~~l~~   26 (140)
T PF03205_consen    3 VQVVGPKNSGKTTL-IRKLINELKR   26 (140)
T ss_dssp             EEEEESTTSSHHHH-HHHHHHHHHH
T ss_pred             EEEECCCCCCHHHH-HHHHHHHHhH
Confidence            67899999999955 3445555543

>TIGR00176 mobB molybdopterin-guanine dinucleotide biosynthesis protein MobB

Probab=89.79  E-value=0.87  Score=31.49  Aligned_cols=14  Identities=29%  Similarity=0.302  Sum_probs=11.6

Q ss_pred             eEEEcCCCCchhHH
Q psy7268          79 AILVAETGCGKTLS   92 (134)
Q Consensus        79 vli~a~tGsGKT~~   92 (134)
                      +.+.|++|+|||..
T Consensus         2 i~i~G~~gsGKTtl   15 (155)
T TIGR00176         2 LQIVGPKNSGKTTL   15 (155)
T ss_pred             EEEECCCCCCHHHH
Confidence            45789999999964

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.

>PF00625 Guanylate_kin: Guanylate kinase; InterPro: IPR008144 Guanylate kinase (2

Probab=89.74  E-value=0.62  Score=32.75  Aligned_cols=17  Identities=29%  Similarity=0.548  Sum_probs=14.5

Q ss_pred             CCCeEEEcCCCCchhHH
Q psy7268          76 GKSAILVAETGCGKTLS   92 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~   92 (134)
                      ++-++++||+|+||+..
T Consensus         2 ~r~ivl~Gpsg~GK~~l   18 (183)
T PF00625_consen    2 RRPIVLVGPSGSGKSTL   18 (183)
T ss_dssp             SSEEEEESSTTSSHHHH
T ss_pred             CCEEEEECCCCCCHHHH
Confidence            56789999999999854

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 ....

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=89.59  E-value=0.29  Score=35.25  Aligned_cols=19  Identities=26%  Similarity=0.378  Sum_probs=16.0

Q ss_pred             cCCCeEEEcCCCCchhHHh
Q psy7268          75 SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~   93 (134)
                      .+..+++.|++|+|||...
T Consensus        37 ~~~~lll~G~~G~GKT~la   55 (226)
T TIGR03420        37 GDRFLYLWGESGSGKSHLL   55 (226)
T ss_pred             CCCeEEEECCCCCCHHHHH
Confidence            4567999999999999665

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.

>KOG0926|consensus

Probab=89.57  E-value=0.58  Score=40.85  Aligned_cols=33  Identities=33%  Similarity=0.526  Sum_probs=22.3

Q ss_pred             CCChHHHHHHH------------HHHHcCCCeEEEcCCCCchhHH
Q psy7268          60 TTPTEIQKYSI------------PTLLSGKSAILVAETGCGKTLS   92 (134)
Q Consensus        60 ~~~t~iQ~~~i------------~~~~~g~dvli~a~tGsGKT~~   92 (134)
                      .++.++|..-+            ..|..+--+||||.||||||.-
T Consensus       243 ~R~~EIQ~sR~~LPI~aeEq~IMEaIn~n~vvIIcGeTGsGKTTQ  287 (1172)
T KOG0926|consen  243 SRPAEIQESRLDLPIVAEEQRIMEAINENPVVIICGETGSGKTTQ  287 (1172)
T ss_pred             cCcHHHHHHHhcCchhHHHHHHHHHhhcCCeEEEecCCCCCcccc
Confidence            35666765433            3333445589999999999964

>TIGR02688 conserved hypothetical protein TIGR02688

Probab=89.56  E-value=0.48  Score=38.44  Aligned_cols=24  Identities=21%  Similarity=0.342  Sum_probs=19.8

Q ss_pred             HHHHcCCCeEEEcCCCCchhHHhH
Q psy7268          71 PTLLSGKSAILVAETGCGKTLSFL   94 (134)
Q Consensus        71 ~~~~~g~dvli~a~tGsGKT~~~~   94 (134)
                      +.+-++.|++..||+|+|||-.|.
T Consensus       204 ~fve~~~Nli~lGp~GTGKThla~  227 (449)
T TIGR02688       204 PLVEPNYNLIELGPKGTGKSYIYN  227 (449)
T ss_pred             HHHhcCCcEEEECCCCCCHHHHHH
Confidence            445578899999999999996654

Members of this family are uncharacterized proteins sporadically distributed in bacteria and archaea, about 470 amino acids in length. Several members of this family appear in public databases with annotation as ATP-dependent protease La, despite the lack of similarity to families TIGR00763 (ATP-dependent protease La) or pfam02190 (ATP-dependent protease La (LON) domain). This protein is repeatedly found downstream of another uncharacterized protein of about 880 amino acids in length, described by model TIGR02687.

>TIGR03238 dnd_assoc_3 dnd system-associated protein 3

Probab=89.52  E-value=0.47  Score=39.00  Aligned_cols=31  Identities=26%  Similarity=0.251  Sum_probs=24.3

Q ss_pred             hHHHHHHHHHHH-------cCCCeEEEcCCCCchhHHh
Q psy7268          63 TEIQKYSIPTLL-------SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        63 t~iQ~~~i~~~~-------~g~dvli~a~tGsGKT~~~   93 (134)
                      ++||......+.       .|.-+.++||+|+|||...
T Consensus        12 r~Ie~~l~~vL~~Vsl~i~~GEiv~L~G~SGsGKSTLL   49 (504)
T TIGR03238        12 RKIQTDLERILVKFNKELPSSSLLFLCGSSGDGKSEIL   49 (504)
T ss_pred             hHHHHHHHHHHhCCceeecCCCEEEEECCCCCCHHHHH
Confidence            678887766553       5778999999999999654

cereus E33L, Hahella chejuensis KCTC 2396, Pseudoalteromonas haloplanktis TAC12, and Escherichia coli B7A.

>cd00227 CPT Chloramphenicol (Cm) phosphotransferase (CPT)

Probab=89.42  E-value=0.31  Score=34.07  Aligned_cols=18  Identities=28%  Similarity=0.366  Sum_probs=15.6

Q ss_pred             CCCeEEEcCCCCchhHHh
Q psy7268          76 GKSAILVAETGCGKTLSF   93 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~   93 (134)
                      |+-+++.|++|+|||...
T Consensus         2 ~~~i~l~G~~gsGKst~a   19 (175)
T cd00227           2 GRIIILNGGSSAGKSSIA   19 (175)
T ss_pred             CCEEEEECCCCCCHHHHH
Confidence            667899999999999774

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

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=89.37  E-value=0.88  Score=36.36  Aligned_cols=18  Identities=44%  Similarity=0.597  Sum_probs=15.2

Q ss_pred             CCeEEEcCCCCchhHHhH
Q psy7268          77 KSAILVAETGCGKTLSFL   94 (134)
Q Consensus        77 ~dvli~a~tGsGKT~~~~   94 (134)
                      +.+++.||||+|||.+..
T Consensus       175 ~vi~lvGptGvGKTTT~a  192 (388)
T PRK12723        175 RVFILVGPTGVGKTTTIA  192 (388)
T ss_pred             eEEEEECCCCCCHHHHHH
Confidence            458899999999998864

>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]

Probab=89.28  E-value=0.29  Score=38.95  Aligned_cols=26  Identities=23%  Similarity=0.494  Sum_probs=19.8

Q ss_pred             cCCCeEEEcCCCCchhHHhHHHHHHHH
Q psy7268          75 SGKSAILVAETGCGKTLSFLAPLVQQI  101 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~~lpil~~~  101 (134)
                      .|+-+++.+|+|||||..+ +.+.+-+
T Consensus        64 aGrgiLi~GppgTGKTAlA-~gIa~eL   89 (450)
T COG1224          64 AGRGILIVGPPGTGKTALA-MGIAREL   89 (450)
T ss_pred             cccEEEEECCCCCcHHHHH-HHHHHHh
Confidence            5788999999999999544 5554444

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=89.25  E-value=0.49  Score=36.72  Aligned_cols=24  Identities=21%  Similarity=0.389  Sum_probs=17.8

Q ss_pred             CCeEEEcCCCCchhHHhHHHHHHHH
Q psy7268          77 KSAILVAETGCGKTLSFLAPLVQQI  101 (134)
Q Consensus        77 ~dvli~a~tGsGKT~~~~lpil~~~  101 (134)
                      .++++.||+|+|||... -.++..+
T Consensus        41 ~~i~I~G~~GtGKT~l~-~~~~~~l   64 (365)
T TIGR02928        41 SNVFIYGKTGTGKTAVT-KYVMKEL   64 (365)
T ss_pred             CcEEEECCCCCCHHHHH-HHHHHHH
Confidence            57999999999999654 3444444

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.

>COG1419 FlhF Flagellar GTP-binding protein [Cell motility and secretion]

Probab=89.22  E-value=0.92  Score=36.42  Aligned_cols=19  Identities=37%  Similarity=0.506  Sum_probs=16.6

Q ss_pred             CCCeEEEcCCCCchhHHhH
Q psy7268          76 GKSAILVAETGCGKTLSFL   94 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~~   94 (134)
                      ++-+.+.||||.|||....
T Consensus       203 ~~vi~LVGPTGVGKTTTlA  221 (407)
T COG1419         203 KRVIALVGPTGVGKTTTLA  221 (407)
T ss_pred             CcEEEEECCCCCcHHHHHH
Confidence            6779999999999998854

>PRK14530 adenylate kinase; Provisional

Probab=89.11  E-value=0.3  Score=35.31  Aligned_cols=19  Identities=26%  Similarity=0.364  Sum_probs=15.9

Q ss_pred             cCCCeEEEcCCCCchhHHh
Q psy7268          75 SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~   93 (134)
                      .+..+++.|++|||||...
T Consensus         2 ~~~~I~i~G~pGsGKsT~~   20 (215)
T PRK14530          2 SQPRILLLGAPGAGKGTQS   20 (215)
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            4667999999999999664

>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=89.04  E-value=0.3  Score=34.42  Aligned_cols=15  Identities=33%  Similarity=0.468  Sum_probs=13.1

Q ss_pred             CeEEEcCCCCchhHH
Q psy7268          78 SAILVAETGCGKTLS   92 (134)
Q Consensus        78 dvli~a~tGsGKT~~   92 (134)
                      ++++.+|||+|||..
T Consensus         5 ~~ll~GpsGvGKT~l   19 (171)
T PF07724_consen    5 NFLLAGPSGVGKTEL   19 (171)
T ss_dssp             EEEEESSTTSSHHHH
T ss_pred             EEEEECCCCCCHHHH
Confidence            578999999999964

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 ....

>COG1136 SalX ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]

Probab=89.02  E-value=0.24  Score=36.67  Aligned_cols=27  Identities=22%  Similarity=0.315  Sum_probs=19.6

Q ss_pred             HcCCCeEEEcCCCCchhHHhHHHHHHHHH
Q psy7268          74 LSGKSAILVAETGCGKTLSFLAPLVQQIL  102 (134)
Q Consensus        74 ~~g~dvli~a~tGsGKT~~~~lpil~~~~  102 (134)
                      ..|.-+.|.+|+|||||.-  +-++..+.
T Consensus        29 ~~Ge~vaI~GpSGSGKSTL--Lniig~ld   55 (226)
T COG1136          29 EAGEFVAIVGPSGSGKSTL--LNLLGGLD   55 (226)
T ss_pred             cCCCEEEEECCCCCCHHHH--HHHHhccc
Confidence            4688899999999999853  34444443

>PF06068 TIP49: TIP49 C-terminus; InterPro: IPR010339 This family consists of the C-terminal region of several eukaryotic and archaeal RuvB-like 1 (Pontin or TIP49a) and RuvB-like 2 (Reptin or TIP49b) proteins

Probab=88.97  E-value=0.3  Score=38.89  Aligned_cols=26  Identities=19%  Similarity=0.486  Sum_probs=18.0

Q ss_pred             cCCCeEEEcCCCCchhHHhHHHHHHHH
Q psy7268          75 SGKSAILVAETGCGKTLSFLAPLVQQI  101 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~~lpil~~~  101 (134)
                      .|+-+++.+|+|+|||... +.+.+.+
T Consensus        49 aGr~iLiaGppGtGKTAlA-~~ia~eL   74 (398)
T PF06068_consen   49 AGRAILIAGPPGTGKTALA-MAIAKEL   74 (398)
T ss_dssp             TT-EEEEEE-TTSSHHHHH-HHHHHHC
T ss_pred             cCcEEEEeCCCCCCchHHH-HHHHHHh
Confidence            5788999999999999544 5555544

The N-terminal domain contains the AAA ATPase, central region IPR003959 from INTERPRO domain. In zebrafish, the liebeskummer (lik) mutation, causes development of hyperplastic embryonic hearts. lik encodes Reptin, a component of a DNA-stimulated ATPase complex. Beta-catenin and Pontin, a DNA-stimulated ATPase that is often part of complexes with Reptin, are in the same genetic pathways. The Reptin/Pontin ratio serves to regulate heart growth during development, at least in part via the beta-catenin pathway []. TBP-interacting protein 49 (TIP49) was originally identified as a TBP-binding protein, and two related proteins are encoded by individual genes, tip49a and b. Although the function of this gene family has not been elucidated, they are supposed to play a critical role in nuclear events because they interact with various kinds of nuclear factors and have DNA helicase activities. TIP49a has been suggested to act as an autoantigen in some patients with autoimmune diseases [].; GO: 0003678 DNA helicase activity, 0005524 ATP binding; PDB: 2XSZ_E 2CQA_A 2C9O_C.

>COG1222 RPT1 ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones]

Probab=88.95  E-value=0.3  Score=38.76  Aligned_cols=55  Identities=29%  Similarity=0.289  Sum_probs=31.8

Q ss_pred             CCCCCcccCCCCHHHHHHHHH---CCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHh
Q psy7268          36 IDLGTFEDTGLAPEIIDIFTK---RGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        36 ~~~~~f~~~~l~~~i~~~l~~---~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~   93 (134)
                      .|=.+|++.|=-++=++.+++   +-.++|--+++.-|   ---+.|++.+|+|+|||+..
T Consensus       145 ~PdvtY~dIGGL~~Qi~EirE~VELPL~~PElF~~~GI---~PPKGVLLYGPPGTGKTLLA  202 (406)
T COG1222         145 KPDVTYEDIGGLDEQIQEIREVVELPLKNPELFEELGI---DPPKGVLLYGPPGTGKTLLA  202 (406)
T ss_pred             CCCCChhhccCHHHHHHHHHHHhcccccCHHHHHHcCC---CCCCceEeeCCCCCcHHHHH
Confidence            344578887744444444554   23333333322211   12357999999999999865

>KOG0989|consensus

Probab=88.95  E-value=0.91  Score=35.38  Aligned_cols=34  Identities=24%  Similarity=0.135  Sum_probs=22.8

Q ss_pred             HHHHHHHHHH---cC---CCeEEEcCCCCchhHHhHHHHH
Q psy7268          65 IQKYSIPTLL---SG---KSAILVAETGCGKTLSFLAPLV   98 (134)
Q Consensus        65 iQ~~~i~~~~---~g---~dvli~a~tGsGKT~~~~lpil   98 (134)
                      .|..+...+.   .+   -+.+..||+|+|||-+.++..-
T Consensus        40 gQe~vV~~L~~a~~~~~lp~~LFyGPpGTGKTStalafar   79 (346)
T KOG0989|consen   40 GQEHVVQVLKNALLRRILPHYLFYGPPGTGKTSTALAFAR   79 (346)
T ss_pred             chHHHHHHHHHHHhhcCCceEEeeCCCCCcHhHHHHHHHH
Confidence            3555554443   22   3689999999999988755443

>COG1855 ATPase (PilT family) [General function prediction only]

Probab=88.89  E-value=1.1  Score=36.91  Aligned_cols=46  Identities=20%  Similarity=0.420  Sum_probs=34.3

Q ss_pred             CCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHh
Q psy7268          39 GTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILT  103 (134)
Q Consensus        39 ~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~  103 (134)
                      .+.++++|++.+.+.|.+                  +.+.+++.+++|+||| .|.-++.+.+..
T Consensus       244 ~~ledY~L~dkl~eRL~e------------------raeGILIAG~PGaGKs-TFaqAlAefy~~  289 (604)
T COG1855         244 LSLEDYGLSDKLKERLEE------------------RAEGILIAGAPGAGKS-TFAQALAEFYAS  289 (604)
T ss_pred             echhhcCCCHHHHHHHHh------------------hhcceEEecCCCCChh-HHHHHHHHHHHh
Confidence            356677888888877765                  2356899999999998 566777777664

>PRK00131 aroK shikimate kinase; Reviewed

Probab=88.89  E-value=0.3  Score=33.49  Aligned_cols=19  Identities=26%  Similarity=0.396  Sum_probs=16.3

Q ss_pred             cCCCeEEEcCCCCchhHHh
Q psy7268          75 SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~   93 (134)
                      .+..+++.|++|||||...
T Consensus         3 ~~~~i~l~G~~GsGKstla   21 (175)
T PRK00131          3 KGPNIVLIGFMGAGKSTIG   21 (175)
T ss_pred             CCCeEEEEcCCCCCHHHHH
Confidence            4667999999999999774

>PRK14729 miaA tRNA delta(2)-isopentenylpyrophosphate transferase; Provisional

Probab=88.84  E-value=0.32  Score=37.54  Aligned_cols=17  Identities=24%  Similarity=0.333  Sum_probs=13.8

Q ss_pred             CCeEEEcCCCCchhHHh
Q psy7268          77 KSAILVAETGCGKTLSF   93 (134)
Q Consensus        77 ~dvli~a~tGsGKT~~~   93 (134)
                      +=++|.||||||||-..
T Consensus         5 ~ii~I~GpTasGKS~LA   21 (300)
T PRK14729          5 KIVFIFGPTAVGKSNIL   21 (300)
T ss_pred             cEEEEECCCccCHHHHH
Confidence            34788999999999654

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

Probab=88.78  E-value=0.54  Score=37.22  Aligned_cols=24  Identities=25%  Similarity=0.414  Sum_probs=17.3

Q ss_pred             CeEEEcCCCCchhHHhHHHHHHHHH
Q psy7268          78 SAILVAETGCGKTLSFLAPLVQQIL  102 (134)
Q Consensus        78 dvli~a~tGsGKT~~~~lpil~~~~  102 (134)
                      ++++-|+||+|||... --++..+.
T Consensus        44 n~~iyG~~GTGKT~~~-~~v~~~l~   67 (366)
T COG1474          44 NIIIYGPTGTGKTATV-KFVMEELE   67 (366)
T ss_pred             cEEEECCCCCCHhHHH-HHHHHHHH
Confidence            6999999999999774 23344443

>KOG1806|consensus

Probab=88.73  E-value=0.69  Score=41.24  Aligned_cols=64  Identities=19%  Similarity=0.150  Sum_probs=45.6

Q ss_pred             CCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHH
Q psy7268          58 GLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQ  131 (134)
Q Consensus        58 g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Q  131 (134)
                      ++-..|+-|-++|-.-..-.++++.+|+|+|||-..+ =++..++...         ...+++|++.+..--+|
T Consensus       735 n~v~ft~~qveai~sg~qpgltmvvgppgtgktd~av-qil~~lyhn~---------p~qrTlivthsnqaln~  798 (1320)
T KOG1806|consen  735 NQVKFTPTQVEAILSGMQPGLTMVVGPPGTGKTDVAV-QILSVLYHNS---------PNQRTLIVTHSNQALNQ  798 (1320)
T ss_pred             chhccCHHHHHHHHhcCCCCceeeecCCCCCCcchhh-hhhhhhhhcC---------CCcceEEEEecccchhH
Confidence            4446688999988777777899999999999997763 3444443322         56788888876544444

>PRK07261 topology modulation protein; Provisional

Probab=88.62  E-value=0.34  Score=33.95  Aligned_cols=16  Identities=19%  Similarity=0.335  Sum_probs=13.6

Q ss_pred             CeEEEcCCCCchhHHh
Q psy7268          78 SAILVAETGCGKTLSF   93 (134)
Q Consensus        78 dvli~a~tGsGKT~~~   93 (134)
                      -+++.|++|+|||...
T Consensus         2 ri~i~G~~GsGKSTla   17 (171)
T PRK07261          2 KIAIIGYSGSGKSTLA   17 (171)
T ss_pred             EEEEEcCCCCCHHHHH
Confidence            3789999999999765

>PRK08118 topology modulation protein; Reviewed

Probab=88.61  E-value=0.34  Score=33.85  Aligned_cols=15  Identities=33%  Similarity=0.547  Sum_probs=13.0

Q ss_pred             CeEEEcCCCCchhHH
Q psy7268          78 SAILVAETGCGKTLS   92 (134)
Q Consensus        78 dvli~a~tGsGKT~~   92 (134)
                      .++|.|++|+|||..
T Consensus         3 rI~I~G~~GsGKSTl   17 (167)
T PRK08118          3 KIILIGSGGSGKSTL   17 (167)
T ss_pred             EEEEECCCCCCHHHH
Confidence            478999999999964

>PF00225 Kinesin: Kinesin motor domain; InterPro: IPR001752 Kinesin [, , ] is a microtubule-associated force-producing protein that may play a role in organelle transport

Probab=88.60  E-value=0.53  Score=36.34  Aligned_cols=25  Identities=28%  Similarity=0.510  Sum_probs=18.5

Q ss_pred             HHHHHHcCCC--eEEEcCCCCchhHHh
Q psy7268          69 SIPTLLSGKS--AILVAETGCGKTLSF   93 (134)
Q Consensus        69 ~i~~~~~g~d--vli~a~tGsGKT~~~   93 (134)
                      .+..++.|.|  ++..|+||||||.+.
T Consensus        66 ~v~~~l~G~n~~i~ayG~tgSGKT~Tm   92 (335)
T PF00225_consen   66 LVDSVLDGYNATIFAYGQTGSGKTYTM   92 (335)
T ss_dssp             HHHHHHTT-EEEEEEEESTTSSHHHHH
T ss_pred             HHHHhhcCCceEEEeeccccccccccc
Confidence            3445678987  777899999999764

The kinesin motor activity is directed toward the microtubule's plus end. Kinesin is an oligomeric complex composed of two heavy chains and two light chains. The maintenance of the quaternary structure does not require interchain disulphide bonds. The heavy chain is composed of three structural domains: a large globular N-terminal domain which is responsible for the motor activity of kinesin (it is known to hydrolyse ATP, to bind and move on microtubules), a central alpha-helical coiled coil domain that mediates the heavy chain dimerisation; and a small globular C-terminal domain which interacts with other proteins (such as the kinesin light chains), vesicles and membranous organelles. A number of proteins have been recently found that contain a domain similar to that of the kinesin 'motor' domain [, ]: Drosophila melanogaster claret segregational protein (ncd). Ncd is required for normal chromosomal segregation in meiosis, in females, and in early mitotic divisions of the embryo. The ncd motor activity is directed toward the microtubule's minus end. Homo sapiens CENP-E []. CENP-E is a protein that associates with kinetochores during chromosome congression, relocates to the spindle midzone at anaphase, and is quantitatively discarded at the end of the cell division. CENP-E is probably an important motor molecule in chromosome movement and/or spindle elongation. H. sapiens mitotic kinesin-like protein-1 (MKLP-1), a motor protein whose activity is directed toward the microtubule's plus end. Saccharomyces cerevisiae KAR3 protein, which is essential for nuclear fusion during mating. KAR3 may mediate microtubule sliding during nuclear fusion and possibly mitosis. S. cerevisiae CIN8 and KIP1 proteins which are required for the assembly of the mitotic spindle. Both proteins seem to interact with spindle microtubules to produce an outwardly directed force acting upon the poles. Emericella nidulans (Aspergillus nidulans) bimC, which plays an important role in nuclear division. A. nidulans klpA. Caenorhabditis elegans unc-104, which may be required for the transport of substances needed for neuronal cell differentiation. C. elegans osm-3. Xenopus laevis Eg5, which may be involved in mitosis. Arabidopsis thaliana KatA, KatB and katC. Chlamydomonas reinhardtii FLA10/KHP1 and KLP1. Both proteins seem to play a role in the rotation or twisting of the microtubules of the flagella. C. elegans hypothetical protein T09A5.2. The kinesin motor domain is located in the N-terminal part of most of the above proteins, with the exception of KAR3, klpA, and ncd where it is located in the C-terminal section. The kinesin motor domain contains about 330 amino acids. An ATP-binding motif of type A is found near position 80 to 90, the C-terminal half of the domain is involved in microtubule-binding.; GO: 0003777 microtubule motor activity, 0005524 ATP binding, 0007018 microtubule-based movement; PDB: 3NWN_A 2Y5W_A 2Y65_C 3BFN_A 2WBE_C 2ZFL_A 2ZFI_A 1I6I_A 2ZFM_A 1IA0_K ....

>KOG0920|consensus

Probab=88.53  E-value=3.1  Score=36.88  Aligned_cols=41  Identities=17%  Similarity=0.389  Sum_probs=32.9

Q ss_pred             hHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHh
Q psy7268          63 TEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILT  103 (134)
Q Consensus        63 t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~  103 (134)
                      +..+...+..+.+..-++|.|.||+|||.=.---+++....
T Consensus       175 ~~~r~~Il~~i~~~qVvvIsGeTGcGKTTQvpQfiLd~~~~  215 (924)
T KOG0920|consen  175 YKMRDTILDAIEENQVVVISGETGCGKTTQVPQFILDEAIE  215 (924)
T ss_pred             HHHHHHHHHHHHhCceEEEeCCCCCCchhhhhHHHHHHHHh
Confidence            56778888888889999999999999998765556665544

>TIGR00390 hslU ATP-dependent protease HslVU, ATPase subunit

Probab=88.52  E-value=0.93  Score=36.77  Aligned_cols=17  Identities=35%  Similarity=0.520  Sum_probs=15.1

Q ss_pred             CCeEEEcCCCCchhHHh
Q psy7268          77 KSAILVAETGCGKTLSF   93 (134)
Q Consensus        77 ~dvli~a~tGsGKT~~~   93 (134)
                      +++++.+|+|+|||...
T Consensus        48 ~~ILLiGppG~GKT~lA   64 (441)
T TIGR00390        48 KNILMIGPTGVGKTEIA   64 (441)
T ss_pred             ceEEEECCCCCCHHHHH
Confidence            68999999999999764

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.

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

Probab=88.52  E-value=1.1  Score=31.45  Aligned_cols=27  Identities=22%  Similarity=0.286  Sum_probs=19.0

Q ss_pred             cCCCeEEEcCCCCchhHHhHHHHHHHH
Q psy7268          75 SGKSAILVAETGCGKTLSFLAPLVQQI  101 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~~lpil~~~  101 (134)
                      .|.=+++.|++|+|||...+--+....
T Consensus        31 ~g~l~~i~g~~g~GKT~~~~~l~~~~~   57 (193)
T PF13481_consen   31 RGELTLIAGPPGSGKTTLALQLAAALA   57 (193)
T ss_dssp             TTSEEEEEECSTSSHHHHHHHHHHHHH
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHH
Confidence            466689999999999966543333333

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=88.51  E-value=1.4  Score=35.75  Aligned_cols=43  Identities=19%  Similarity=0.159  Sum_probs=27.1

Q ss_pred             CCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHH
Q psy7268          77 KSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVF  130 (134)
Q Consensus        77 ~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~  130 (134)
                      +.+++.|++|+|||- .+-.+.+.+....         .+.+++++.. .++..
T Consensus       142 npl~i~G~~G~GKTH-Ll~Ai~~~l~~~~---------~~~~v~yv~~-~~f~~  184 (450)
T PRK14087        142 NPLFIYGESGMGKTH-LLKAAKNYIESNF---------SDLKVSYMSG-DEFAR  184 (450)
T ss_pred             CceEEECCCCCcHHH-HHHHHHHHHHHhC---------CCCeEEEEEH-HHHHH
Confidence            358999999999993 3355566554321         3556777654 34433

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=88.50  E-value=1  Score=35.81  Aligned_cols=38  Identities=16%  Similarity=0.243  Sum_probs=24.9

Q ss_pred             CCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcC
Q psy7268          77 KSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITP  124 (134)
Q Consensus        77 ~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~P  124 (134)
                      +.+++.|++|+|||... ..+...+....         .+.+++++..
T Consensus       137 n~l~l~G~~G~GKThL~-~ai~~~l~~~~---------~~~~v~yi~~  174 (405)
T TIGR00362       137 NPLFIYGGVGLGKTHLL-HAIGNEILENN---------PNAKVVYVSS  174 (405)
T ss_pred             CeEEEECCCCCcHHHHH-HHHHHHHHHhC---------CCCcEEEEEH
Confidence            35889999999999654 55555554421         2456677643

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).

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=88.49  E-value=0.41  Score=41.09  Aligned_cols=53  Identities=25%  Similarity=0.296  Sum_probs=31.0

Q ss_pred             CCCcccCCCCHHHHHHHHHC---CCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHh
Q psy7268          38 LGTFEDTGLAPEIIDIFTKR---GLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        38 ~~~f~~~~l~~~i~~~l~~~---g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~   93 (134)
                      -.+|++++..+.+.+.|.+.   .+.++.-.+..   .+...+.+++.||+|+|||+..
T Consensus       449 ~~~~~di~g~~~~k~~l~~~v~~~~~~~~~~~~~---g~~~~~giLL~GppGtGKT~la  504 (733)
T TIGR01243       449 NVRWSDIGGLEEVKQELREAVEWPLKHPEIFEKM---GIRPPKGVLLFGPPGTGKTLLA  504 (733)
T ss_pred             ccchhhcccHHHHHHHHHHHHHhhhhCHHHHHhc---CCCCCceEEEECCCCCCHHHHH
Confidence            34677777777777666652   22222111111   0112356999999999999764

This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=88.47  E-value=1  Score=36.44  Aligned_cols=38  Identities=16%  Similarity=0.198  Sum_probs=25.1

Q ss_pred             CCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcC
Q psy7268          77 KSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITP  124 (134)
Q Consensus        77 ~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~P  124 (134)
                      +.+++.|++|+|||-.. ..+.+.+.+..         .+.+++++..
T Consensus       131 n~l~lyG~~G~GKTHLl-~ai~~~l~~~~---------~~~~v~yi~~  168 (440)
T PRK14088        131 NPLFIYGGVGLGKTHLL-QSIGNYVVQNE---------PDLRVMYITS  168 (440)
T ss_pred             CeEEEEcCCCCcHHHHH-HHHHHHHHHhC---------CCCeEEEEEH
Confidence            35999999999999544 55566554421         2446777653

>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=88.45  E-value=1.1  Score=30.93  Aligned_cols=15  Identities=40%  Similarity=0.532  Sum_probs=12.9

Q ss_pred             eEEEcCCCCchhHHh
Q psy7268          79 AILVAETGCGKTLSF   93 (134)
Q Consensus        79 vli~a~tGsGKT~~~   93 (134)
                      +++.+++|+|||...
T Consensus         3 ~~~~G~~G~GKTt~~   17 (173)
T cd03115           3 ILLVGLQGVGKTTTA   17 (173)
T ss_pred             EEEECCCCCCHHHHH
Confidence            578899999999775

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.

>COG3451 VirB4 Type IV secretory pathway, VirB4 components [Intracellular trafficking and secretion]

Probab=88.39  E-value=0.87  Score=39.68  Aligned_cols=17  Identities=29%  Similarity=0.600  Sum_probs=14.5

Q ss_pred             CeEEEcCCCCchhHHhH
Q psy7268          78 SAILVAETGCGKTLSFL   94 (134)
Q Consensus        78 dvli~a~tGsGKT~~~~   94 (134)
                      +.+|+||||+|||.-.-
T Consensus       438 hT~I~G~tGaGKTvLl~  454 (796)
T COG3451         438 HTLIIGPTGAGKTVLLS  454 (796)
T ss_pred             CeEEECCCCCCHHHHHH
Confidence            78999999999996543

>KOG0060|consensus

Probab=88.37  E-value=0.31  Score=40.83  Aligned_cols=20  Identities=35%  Similarity=0.713  Sum_probs=17.5

Q ss_pred             HHcCCCeEEEcCCCCchhHH
Q psy7268          73 LLSGKSAILVAETGCGKTLS   92 (134)
Q Consensus        73 ~~~g~dvli~a~tGsGKT~~   92 (134)
                      +.+|.+++|++|+|+|||--
T Consensus       458 V~~g~~LLItG~sG~GKtSL  477 (659)
T KOG0060|consen  458 VPSGQNLLITGPSGCGKTSL  477 (659)
T ss_pred             ecCCCeEEEECCCCCchhHH
Confidence            45899999999999999954

>TIGR01313 therm_gnt_kin carbohydrate kinase, thermoresistant glucokinase family

Probab=88.36  E-value=0.32  Score=33.32  Aligned_cols=15  Identities=27%  Similarity=0.406  Sum_probs=12.3

Q ss_pred             eEEEcCCCCchhHHh
Q psy7268          79 AILVAETGCGKTLSF   93 (134)
Q Consensus        79 vli~a~tGsGKT~~~   93 (134)
                      ++++|++|+|||...
T Consensus         1 i~l~G~~GsGKSTla   15 (163)
T TIGR01313         1 FVLMGVAGSGKSTIA   15 (163)
T ss_pred             CEEECCCCCCHHHHH
Confidence            468899999999653

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.

>PRK09302 circadian clock protein KaiC; Reviewed

Probab=88.35  E-value=0.91  Score=37.23  Aligned_cols=27  Identities=37%  Similarity=0.537  Sum_probs=19.5

Q ss_pred             cCCCeEEEcCCCCchhHHhHHHHHHHH
Q psy7268          75 SGKSAILVAETGCGKTLSFLAPLVQQI  101 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~~lpil~~~  101 (134)
                      .|.-+++.|++|+|||...+--+.+.+
T Consensus        30 ~Gs~~li~G~pGsGKT~l~~qf~~~~~   56 (509)
T PRK09302         30 KGRPTLVSGTAGTGKTLFALQFLVNGI   56 (509)
T ss_pred             CCcEEEEEeCCCCCHHHHHHHHHHHHH
Confidence            466799999999999976544444444

>TIGR00382 clpX endopeptidase Clp ATP-binding regulatory subunit (clpX)

Probab=88.19  E-value=0.37  Score=38.80  Aligned_cols=17  Identities=41%  Similarity=0.612  Sum_probs=14.9

Q ss_pred             CCeEEEcCCCCchhHHh
Q psy7268          77 KSAILVAETGCGKTLSF   93 (134)
Q Consensus        77 ~dvli~a~tGsGKT~~~   93 (134)
                      .++++.+|||+|||...
T Consensus       117 ~~iLL~GP~GsGKT~lA  133 (413)
T TIGR00382       117 SNILLIGPTGSGKTLLA  133 (413)
T ss_pred             ceEEEECCCCcCHHHHH
Confidence            36999999999999775

A member of the ATP-dependent proteases, ClpX has ATP-dependent chaperone activity and is required for specific ATP-dependent proteolytic activities expressed by ClpPX. The gene is also found to be involved in stress tolerance in Bacillus subtilis and is essential for the efficient acquisition of genes specifying type IA and IB restriction.

>PLN03025 replication factor C subunit; Provisional

Probab=88.18  E-value=0.86  Score=35.04  Aligned_cols=17  Identities=41%  Similarity=0.520  Sum_probs=14.4

Q ss_pred             CCeEEEcCCCCchhHHh
Q psy7268          77 KSAILVAETGCGKTLSF   93 (134)
Q Consensus        77 ~dvli~a~tGsGKT~~~   93 (134)
                      .++++.||+|+|||...
T Consensus        35 ~~lll~Gp~G~GKTtla   51 (319)
T PLN03025         35 PNLILSGPPGTGKTTSI   51 (319)
T ss_pred             ceEEEECCCCCCHHHHH
Confidence            36899999999999654

>PRK05342 clpX ATP-dependent protease ATP-binding subunit ClpX; Provisional

Probab=88.18  E-value=0.38  Score=38.71  Aligned_cols=17  Identities=41%  Similarity=0.612  Sum_probs=15.0

Q ss_pred             CCeEEEcCCCCchhHHh
Q psy7268          77 KSAILVAETGCGKTLSF   93 (134)
Q Consensus        77 ~dvli~a~tGsGKT~~~   93 (134)
                      .++++.||||+|||...
T Consensus       109 ~~iLl~Gp~GtGKT~lA  125 (412)
T PRK05342        109 SNILLIGPTGSGKTLLA  125 (412)
T ss_pred             ceEEEEcCCCCCHHHHH
Confidence            56999999999999775

>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=88.18  E-value=1.4  Score=33.87  Aligned_cols=41  Identities=20%  Similarity=0.195  Sum_probs=27.4

Q ss_pred             CeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEc--CcHHHHH
Q psy7268          78 SAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIIT--PGRELVF  130 (134)
Q Consensus        78 dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~--Pt~~La~  130 (134)
                      =+++.|+-|.|||.+...-.+....            .|.++++++  |...|+.
T Consensus         3 ~~~~~GKGGVGKTT~aaA~A~~~A~------------~G~rtLlvS~Dpa~~L~d   45 (305)
T PF02374_consen    3 ILFFGGKGGVGKTTVAAALALALAR------------RGKRTLLVSTDPAHSLSD   45 (305)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHHH------------TTS-EEEEESSTTTHHHH
T ss_pred             EEEEecCCCCCcHHHHHHHHHHHhh------------CCCCeeEeecCCCccHHH
Confidence            3678999999999988665555443            455677665  5555543

...

>TIGR03600 phage_DnaB phage replicative helicase, DnaB family, HK022 subfamily

Probab=88.12  E-value=3.1  Score=33.26  Aligned_cols=26  Identities=19%  Similarity=0.286  Sum_probs=18.1

Q ss_pred             cCCCeEEEcCCCCchhHHhHHHHHHHH
Q psy7268          75 SGKSAILVAETGCGKTLSFLAPLVQQI  101 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~~lpil~~~  101 (134)
                      .|.=+++.|++|+|||... +-+...+
T Consensus       193 ~g~liviag~pg~GKT~~a-l~ia~~~  218 (421)
T TIGR03600       193 KGDLIVIGARPSMGKTTLA-LNIAENV  218 (421)
T ss_pred             CCceEEEEeCCCCCHHHHH-HHHHHHH
Confidence            4556888999999999554 4444333

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.

>PF14516 AAA_35: AAA-like domain

Probab=88.11  E-value=2.3  Score=33.07  Aligned_cols=39  Identities=18%  Similarity=0.222  Sum_probs=31.2

Q ss_pred             HHHHHHHHHHHc-CCCeEEEcCCCCchhHHhHHHHHHHHHh
Q psy7268          64 EIQKYSIPTLLS-GKSAILVAETGCGKTLSFLAPLVQQILT  103 (134)
Q Consensus        64 ~iQ~~~i~~~~~-g~dvli~a~tGsGKT~~~~lpil~~~~~  103 (134)
                      ++.+.++..+.+ |.-+.|.||-.+|||.. +.-+++++..
T Consensus        18 ~~e~~~~~~i~~~G~~~~I~apRq~GKTSl-l~~l~~~l~~   57 (331)
T PF14516_consen   18 PAEQECYQEIVQPGSYIRIKAPRQMGKTSL-LLRLLERLQQ   57 (331)
T ss_pred             HHHHHHHHHHhcCCCEEEEECcccCCHHHH-HHHHHHHHHH
Confidence            588899999887 99999999999999944 4556666643

>PF07088 GvpD: GvpD gas vesicle protein; InterPro: IPR009788 This family consists of several archaeal GvpD gas vesicle proteins

Probab=88.09  E-value=0.38  Score=38.72  Aligned_cols=28  Identities=29%  Similarity=0.542  Sum_probs=22.3

Q ss_pred             cCCCeEEEcCCCCchhHHhHHHHHHHHHh
Q psy7268          75 SGKSAILVAETGCGKTLSFLAPLVQQILT  103 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~~lpil~~~~~  103 (134)
                      .|+.++|.+.+|+|||+ |.+-++..+..
T Consensus         9 ~G~TLLIKG~PGTGKTt-faLelL~~l~~   36 (484)
T PF07088_consen    9 PGQTLLIKGEPGTGKTT-FALELLNSLKD   36 (484)
T ss_pred             CCcEEEEecCCCCCcee-eehhhHHHHhc
Confidence            47889999999999995 44677777754

GvpD is thought to be involved in the regulation of gas vesicle formation [,].; GO: 0005524 ATP binding

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

Probab=88.05  E-value=0.39  Score=33.43  Aligned_cols=17  Identities=24%  Similarity=0.419  Sum_probs=14.3

Q ss_pred             CCeEEEcCCCCchhHHh
Q psy7268          77 KSAILVAETGCGKTLSF   93 (134)
Q Consensus        77 ~dvli~a~tGsGKT~~~   93 (134)
                      +-+++.|++|+|||...
T Consensus         2 ~~~~i~G~sGsGKttl~   18 (179)
T TIGR02322         2 RLIYVVGPSGAGKDTLL   18 (179)
T ss_pred             cEEEEECCCCCCHHHHH
Confidence            44789999999999775

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.

>PRK00300 gmk guanylate kinase; Provisional

Probab=87.96  E-value=0.43  Score=33.93  Aligned_cols=18  Identities=28%  Similarity=0.446  Sum_probs=15.2

Q ss_pred             cCCCeEEEcCCCCchhHH
Q psy7268          75 SGKSAILVAETGCGKTLS   92 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~   92 (134)
                      .|+-+++.||+|+|||..
T Consensus         4 ~g~~i~i~G~sGsGKstl   21 (205)
T PRK00300          4 RGLLIVLSGPSGAGKSTL   21 (205)
T ss_pred             CCCEEEEECCCCCCHHHH
Confidence            467789999999999954

>PRK06620 hypothetical protein; Validated

Probab=87.86  E-value=0.35  Score=35.28  Aligned_cols=17  Identities=18%  Similarity=0.215  Sum_probs=14.4

Q ss_pred             CCeEEEcCCCCchhHHh
Q psy7268          77 KSAILVAETGCGKTLSF   93 (134)
Q Consensus        77 ~dvli~a~tGsGKT~~~   93 (134)
                      +.+++.||+|+|||-..
T Consensus        45 ~~l~l~Gp~G~GKThLl   61 (214)
T PRK06620         45 FTLLIKGPSSSGKTYLT   61 (214)
T ss_pred             ceEEEECCCCCCHHHHH
Confidence            45899999999999654

>PF00005 ABC_tran: ABC transporter This structure is on hold until Dec 1999; InterPro: IPR003439 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energise diverse biological systems

Probab=87.86  E-value=0.45  Score=31.44  Aligned_cols=19  Identities=26%  Similarity=0.510  Sum_probs=15.9

Q ss_pred             cCCCeEEEcCCCCchhHHh
Q psy7268          75 SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~   93 (134)
                      .|.-+.+.|++|+|||...
T Consensus        10 ~g~~~~i~G~nGsGKStLl   28 (137)
T PF00005_consen   10 PGEIVAIVGPNGSGKSTLL   28 (137)
T ss_dssp             TTSEEEEEESTTSSHHHHH
T ss_pred             CCCEEEEEccCCCccccce
Confidence            5777899999999999543

ABC transporters minimally consist of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain []. The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyse ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarise the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site [, , ]. The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis [, , , , , ]. The ATP-Binding Cassette (ABC) superfamily forms one of the largest of all protein families with a diversity of physiological functions []. Several studies have shown that there is a correlation between the functional characterisation and the phylogenetic classification of the ABC cassette [, ]. More than 50 subfamilies have been described based on a phylogenetic and functional classification [, , ]; (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). On the basis of sequence similarities a family of related ATP-binding proteins has been characterised [, , , , ]. The proteins belonging to this family also contain one or two copies of the 'A' consensus sequence [] or the 'P-loop' [] (see IPR001687 from INTERPRO).; GO: 0005524 ATP binding, 0016887 ATPase activity; PDB: 3NHB_A 3NH9_A 3NHA_A 3NH6_A 1VCI_A 1V43_A 2YZ2_B 2PMK_A 2FFA_A 1XEF_D ....

>PLN02165 adenylate isopentenyltransferase

Probab=87.82  E-value=0.46  Score=37.22  Aligned_cols=20  Identities=25%  Similarity=0.429  Sum_probs=16.1

Q ss_pred             cCCCeEEEcCCCCchhHHhH
Q psy7268          75 SGKSAILVAETGCGKTLSFL   94 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~~   94 (134)
                      .|.-+++.||||+|||....
T Consensus        42 ~g~iivIiGPTGSGKStLA~   61 (334)
T PLN02165         42 KDKVVVIMGATGSGKSRLSV   61 (334)
T ss_pred             CCCEEEEECCCCCcHHHHHH
Confidence            35568899999999997663

>cd01370 KISc_KIP3_like Kinesin motor domain, KIP3-like subgroup

Probab=87.80  E-value=0.64  Score=36.22  Aligned_cols=25  Identities=28%  Similarity=0.450  Sum_probs=19.4

Q ss_pred             HHHHHHcCCC--eEEEcCCCCchhHHh
Q psy7268          69 SIPTLLSGKS--AILVAETGCGKTLSF   93 (134)
Q Consensus        69 ~i~~~~~g~d--vli~a~tGsGKT~~~   93 (134)
                      .+..++.|.+  ++.-|+||||||...
T Consensus        79 lv~~~~~G~n~~i~ayGqtGSGKTyTm  105 (338)
T cd01370          79 LVDGVLNGYNATVFAYGATGAGKTHTM  105 (338)
T ss_pred             HHHHHHCCCCceEEeeCCCCCCCeEEE
Confidence            3445568886  788899999999875

The yeast kinesin KIP3 plays a role in positioning the mitotic spindle. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus (N-type). N-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also, the neck linker binds to the motor domain, which repositions the other head domain through the coiled-coil domain close to a sec

>PRK12724 flagellar biosynthesis regulator FlhF; Provisional

Probab=87.79  E-value=1.2  Score=36.03  Aligned_cols=20  Identities=35%  Similarity=0.398  Sum_probs=15.5

Q ss_pred             CeEEEcCCCCchhHHhHHHH
Q psy7268          78 SAILVAETGCGKTLSFLAPL   97 (134)
Q Consensus        78 dvli~a~tGsGKT~~~~lpi   97 (134)
                      -+++.+|+|+|||....--+
T Consensus       225 vi~lvGptGvGKTTtaaKLA  244 (432)
T PRK12724        225 VVFFVGPTGSGKTTSIAKLA  244 (432)
T ss_pred             EEEEECCCCCCHHHHHHHHH
Confidence            37789999999998764433

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=87.79  E-value=1.3  Score=35.85  Aligned_cols=26  Identities=23%  Similarity=0.305  Sum_probs=18.9

Q ss_pred             CCeEEEcCCCCchhHHhHHHHHHHHHh
Q psy7268          77 KSAILVAETGCGKTLSFLAPLVQQILT  103 (134)
Q Consensus        77 ~dvli~a~tGsGKT~~~~lpil~~~~~  103 (134)
                      +.+++.||+|+|||... -.+...+.+
T Consensus       149 ~~l~l~G~~G~GKThL~-~ai~~~~~~  174 (450)
T PRK00149        149 NPLFIYGGVGLGKTHLL-HAIGNYILE  174 (450)
T ss_pred             CeEEEECCCCCCHHHHH-HHHHHHHHH
Confidence            45899999999999554 455555543

>PF05729 NACHT: NACHT domain

Probab=87.78  E-value=0.41  Score=32.24  Aligned_cols=24  Identities=29%  Similarity=0.410  Sum_probs=17.6

Q ss_pred             eEEEcCCCCchhHHhHHHHHHHHHh
Q psy7268          79 AILVAETGCGKTLSFLAPLVQQILT  103 (134)
Q Consensus        79 vli~a~tGsGKT~~~~lpil~~~~~  103 (134)
                      ++|.|+.|+|||... --++..+..
T Consensus         3 l~I~G~~G~GKStll-~~~~~~~~~   26 (166)
T PF05729_consen    3 LWISGEPGSGKSTLL-RKLAQQLAE   26 (166)
T ss_pred             EEEECCCCCChHHHH-HHHHHHHHh
Confidence            689999999999654 455555544

>cd03114 ArgK-like The function of this protein family is unkown

Probab=87.75  E-value=1.5  Score=30.01  Aligned_cols=15  Identities=20%  Similarity=0.273  Sum_probs=12.2

Q ss_pred             eEEEcCCCCchhHHh
Q psy7268          79 AILVAETGCGKTLSF   93 (134)
Q Consensus        79 vli~a~tGsGKT~~~   93 (134)
                      +.+.|+.|+|||...
T Consensus         2 i~~~G~~GsGKTt~~   16 (148)
T cd03114           2 IGITGVPGAGKSTLI   16 (148)
T ss_pred             EEEECCCCCcHHHHH
Confidence            467899999999654

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.

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=87.74  E-value=0.33  Score=41.66  Aligned_cols=53  Identities=25%  Similarity=0.291  Sum_probs=31.4

Q ss_pred             CCCcccCCCCHHHHHHHHHC---CCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHh
Q psy7268          38 LGTFEDTGLAPEIIDIFTKR---GLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        38 ~~~f~~~~l~~~i~~~l~~~---g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~   93 (134)
                      -.+|++++-.+...+.+.+.   .+.+|.-.+..   .+..++.+++.||+|+|||...
T Consensus       174 ~~~~~di~G~~~~~~~l~~~i~~~~~~~~~~~~~---gi~~~~giLL~GppGtGKT~la  229 (733)
T TIGR01243       174 KVTYEDIGGLKEAKEKIREMVELPMKHPELFEHL---GIEPPKGVLLYGPPGTGKTLLA  229 (733)
T ss_pred             CCCHHHhcCHHHHHHHHHHHHHHHhhCHHHHHhc---CCCCCceEEEECCCCCChHHHH
Confidence            35677777666666666553   12121111111   1224678999999999999653

This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.

>PRK12900 secA preprotein translocase subunit SecA; Reviewed

Probab=87.64  E-value=0.95  Score=40.24  Aligned_cols=56  Identities=30%  Similarity=0.255  Sum_probs=40.5

Q ss_pred             CChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHH
Q psy7268          61 TPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVF  130 (134)
Q Consensus        61 ~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~  130 (134)
                      .|+++|-..=-.+..|+  |....||-|||++..+|+.-..+            .|..+-||+-+-.||.
T Consensus       138 ~~ydVQLiGgivLh~G~--IAEM~TGEGKTLvatlp~yLnAL------------~G~gVHvVTvNDYLA~  193 (1025)
T PRK12900        138 VPYDVQLIGGIVLHSGK--ISEMATGEGKTLVSTLPTFLNAL------------TGRGVHVVTVNDYLAQ  193 (1025)
T ss_pred             cccchHHhhhHHhhcCC--ccccCCCCCcchHhHHHHHHHHH------------cCCCcEEEeechHhhh
Confidence            57778766655555554  57899999999999999866665            3445677777767764

>cd00071 GMPK Guanosine monophosphate kinase (GMPK, EC 2

Probab=87.54  E-value=0.46  Score=32.08  Aligned_cols=14  Identities=29%  Similarity=0.508  Sum_probs=11.9

Q ss_pred             eEEEcCCCCchhHH
Q psy7268          79 AILVAETGCGKTLS   92 (134)
Q Consensus        79 vli~a~tGsGKT~~   92 (134)
                      +++.||+|+|||..
T Consensus         2 i~i~GpsGsGKstl   15 (137)
T cd00071           2 IVLSGPSGVGKSTL   15 (137)
T ss_pred             EEEECCCCCCHHHH
Confidence            57899999999963

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.

>cd01369 KISc_KHC_KIF5 Kinesin motor domain, kinesin heavy chain (KHC) or KIF5-like subgroup

Probab=87.46  E-value=0.55  Score=36.27  Aligned_cols=25  Identities=28%  Similarity=0.437  Sum_probs=19.4

Q ss_pred             HHHHHHHcCCC--eEEEcCCCCchhHH
Q psy7268          68 YSIPTLLSGKS--AILVAETGCGKTLS   92 (134)
Q Consensus        68 ~~i~~~~~g~d--vli~a~tGsGKT~~   92 (134)
                      ..++.++.|.+  ++..|+||||||..
T Consensus        67 ~~v~~~~~G~n~~i~ayG~tgSGKT~T   93 (325)
T cd01369          67 PIVDDVLNGYNGTIFAYGQTGSGKTYT   93 (325)
T ss_pred             HHHHHHHcCccceEEEeCCCCCCceEE
Confidence            34455678886  78889999999977

Members of this group have been associated with organelle transport. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus (N-type). N-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also, the neck linker binds to the motor domain, which repositions the other head domain through the coiled-c

>PRK13873 conjugal transfer ATPase TrbE; Provisional

Probab=87.42  E-value=1  Score=39.16  Aligned_cols=18  Identities=28%  Similarity=0.530  Sum_probs=15.3

Q ss_pred             CeEEEcCCCCchhHHhHH
Q psy7268          78 SAILVAETGCGKTLSFLA   95 (134)
Q Consensus        78 dvli~a~tGsGKT~~~~l   95 (134)
                      +.+|.|+||+|||...-.
T Consensus       443 n~~I~G~tGsGKS~l~~~  460 (811)
T PRK13873        443 HTLVVGPTGAGKSVLLAL  460 (811)
T ss_pred             eEEEECCCCCCHHHHHHH
Confidence            789999999999977544

>TIGR00764 lon_rel lon-related putative ATP-dependent protease

Probab=87.40  E-value=1.2  Score=37.65  Aligned_cols=46  Identities=24%  Similarity=0.412  Sum_probs=28.8

Q ss_pred             CCcccCCCCHHHHHHHHHCCCCCChHHHHHHHH----HHHcCCCeEEEcCCCCchhHHh
Q psy7268          39 GTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIP----TLLSGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        39 ~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~----~~~~g~dvli~a~tGsGKT~~~   93 (134)
                      .+=+++.+++.+++.+.  |       |..+..    .+..++++++.+++|+|||...
T Consensus         5 ~~~~~~~~~~~~~~~vi--G-------~~~a~~~l~~a~~~~~~~ll~G~pG~GKT~la   54 (608)
T TIGR00764         5 ETTEEIPVPERLIDQVI--G-------QEEAVEIIKKAAKQKRNVLLIGEPGVGKSMLA   54 (608)
T ss_pred             ccccccCcchhhHhhcc--C-------HHHHHHHHHHHHHcCCCEEEECCCCCCHHHHH
Confidence            34456666665554432  1       223222    3446789999999999999664

Members of this family from Pyrococcus horikoshii and Pyrococcus abyssi each contain a predicted intein.

>PHA02533 17 large terminase protein; Provisional

Probab=87.36  E-value=3.3  Score=34.49  Aligned_cols=63  Identities=11%  Similarity=-0.001  Sum_probs=46.6

Q ss_pred             CChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          61 TPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        61 ~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      .+.|.|...+..+..++-.++..+=..|||.....-.+......          .+.++++++|+++-|..+.
T Consensus        59 ~L~p~Q~~i~~~~~~~R~~ii~~aRq~GKStl~a~~al~~a~~~----------~~~~v~i~A~~~~QA~~vF  121 (534)
T PHA02533         59 QMRDYQKDMLKIMHKNRFNACNLSRQLGKTTVVAIFLLHYVCFN----------KDKNVGILAHKASMAAEVL  121 (534)
T ss_pred             CCcHHHHHHHHHHhcCeEEEEEEcCcCChHHHHHHHHHHHHHhC----------CCCEEEEEeCCHHHHHHHH
Confidence            57889999998776666667888889999988765444444321          3558999999998877654

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=87.35  E-value=1.3  Score=35.79  Aligned_cols=19  Identities=32%  Similarity=0.536  Sum_probs=15.5

Q ss_pred             CCeEEEcCCCCchhHHhHH
Q psy7268          77 KSAILVAETGCGKTLSFLA   95 (134)
Q Consensus        77 ~dvli~a~tGsGKT~~~~l   95 (134)
                      +.+.+.||+|+|||.....
T Consensus       242 ~vI~LVGptGvGKTTTiaK  260 (436)
T PRK11889        242 QTIALIGPTGVGKTTTLAK  260 (436)
T ss_pred             cEEEEECCCCCcHHHHHHH
Confidence            4678999999999977543

>cd01368 KISc_KIF23_like Kinesin motor domain, KIF23-like subgroup

Probab=87.34  E-value=0.55  Score=36.74  Aligned_cols=25  Identities=32%  Similarity=0.454  Sum_probs=19.2

Q ss_pred             HHHHHHcCCC--eEEEcCCCCchhHHh
Q psy7268          69 SIPTLLSGKS--AILVAETGCGKTLSF   93 (134)
Q Consensus        69 ~i~~~~~g~d--vli~a~tGsGKT~~~   93 (134)
                      .+..++.|.+  ++.-|.||||||.+.
T Consensus        80 ~v~~~l~G~n~ti~aYGqtGSGKTyTm  106 (345)
T cd01368          80 LVQDLLKGKNSLLFTYGVTNSGKTYTM  106 (345)
T ss_pred             HHHHHhCCCceEEEEeCCCCCCCeEEe
Confidence            3445668886  777899999999774

Members of this group may play a role in mitosis. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus (N-type). N-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also, the neck linker binds to the motor domain, which repositions the other head domain through the coiled-coil domain close to a second tubulin dimer, a

>cd01365 KISc_KIF1A_KIF1B Kinesin motor domain, KIF1_like proteins

Probab=87.33  E-value=0.55  Score=36.80  Aligned_cols=24  Identities=21%  Similarity=0.439  Sum_probs=18.8

Q ss_pred             HHHHHcCCC--eEEEcCCCCchhHHh
Q psy7268          70 IPTLLSGKS--AILVAETGCGKTLSF   93 (134)
Q Consensus        70 i~~~~~g~d--vli~a~tGsGKT~~~   93 (134)
                      +..++.|.+  ++..|+||||||...
T Consensus        81 v~~~l~G~n~~i~ayGqtGSGKT~Tm  106 (356)
T cd01365          81 LDHAFEGYNVCLFAYGQTGSGKSYTM  106 (356)
T ss_pred             HHHHhCCCceEEEEecCCCCCCeEEe
Confidence            445678886  777899999999854

KIF1A (Unc104) transports synaptic vesicles to the nerve terminal, KIF1B has been implicated in transport of mitochondria. Both proteins are expressed in neurons. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus (N-type). N-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. In contrast to the majority of dimeric kinesins, most KIF1A/Unc104 kinesins are monomeric motors. A lysine-rich loop in KIF1A binds to the negatively charged C-terminus of tubulin and compensates for the lack of a second motor domain, allowing KIF1A to move processively.

>cd01376 KISc_KID_like Kinesin motor domain, KIF22/Kid-like subgroup

Probab=87.31  E-value=0.61  Score=35.98  Aligned_cols=25  Identities=40%  Similarity=0.672  Sum_probs=19.6

Q ss_pred             HHHHHHcCCC--eEEEcCCCCchhHHh
Q psy7268          69 SIPTLLSGKS--AILVAETGCGKTLSF   93 (134)
Q Consensus        69 ~i~~~~~g~d--vli~a~tGsGKT~~~   93 (134)
                      .++.++.|.|  ++..|.||||||...
T Consensus        72 lv~~~~~G~n~~i~ayG~tgSGKTyTm   98 (319)
T cd01376          72 IVPHLLSGQNATVFAYGSTGAGKTHTM   98 (319)
T ss_pred             HHHHHhCCCceEEEEECCCCCCCcEEE
Confidence            4455678887  677799999999864

Members of this group might play a role in regulating chromosomal movement along microtubules in mitosis. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus (N-type). N-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also, the neck linker binds to the motor domain, which repositions the other head domain through

>PRK14723 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=87.29  E-value=3.4  Score=35.96  Aligned_cols=19  Identities=37%  Similarity=0.371  Sum_probs=15.2

Q ss_pred             CCeEEEcCCCCchhHHhHH
Q psy7268          77 KSAILVAETGCGKTLSFLA   95 (134)
Q Consensus        77 ~dvli~a~tGsGKT~~~~l   95 (134)
                      +-+.+.||||+|||.+...
T Consensus       186 ~Vi~lVGpnGvGKTTTiaK  204 (767)
T PRK14723        186 GVLALVGPTGVGKTTTTAK  204 (767)
T ss_pred             eEEEEECCCCCcHHHHHHH
Confidence            3478999999999987643

>KOG0733|consensus

Probab=87.26  E-value=0.51  Score=40.04  Aligned_cols=54  Identities=24%  Similarity=0.323  Sum_probs=29.5

Q ss_pred             CCCCcccCCCCHHHHHHHHHC---CCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHh
Q psy7268          37 DLGTFEDTGLAPEIIDIFTKR---GLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        37 ~~~~f~~~~l~~~i~~~l~~~---g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~   93 (134)
                      |=.+|++.|=-+++...|...   -.++|.-+++.-+   -.-..+++++|+|+|||+..
T Consensus       506 PdVtW~dIGaL~~vR~eL~~aI~~PiK~pd~~k~lGi---~~PsGvLL~GPPGCGKTLlA  562 (802)
T KOG0733|consen  506 PDVTWDDIGALEEVRLELNMAILAPIKRPDLFKALGI---DAPSGVLLCGPPGCGKTLLA  562 (802)
T ss_pred             CCCChhhcccHHHHHHHHHHHHhhhccCHHHHHHhCC---CCCCceEEeCCCCccHHHHH
Confidence            334666666555555444432   2333322222111   11335999999999999865

>TIGR00064 ftsY signal recognition particle-docking protein FtsY

Probab=87.25  E-value=1.4  Score=33.35  Aligned_cols=18  Identities=28%  Similarity=0.468  Sum_probs=14.4

Q ss_pred             CCeEEEcCCCCchhHHhH
Q psy7268          77 KSAILVAETGCGKTLSFL   94 (134)
Q Consensus        77 ~dvli~a~tGsGKT~~~~   94 (134)
                      +-+++.+++|+|||....
T Consensus        73 ~vi~l~G~~G~GKTTt~a   90 (272)
T TIGR00064        73 NVILFVGVNGVGKTTTIA   90 (272)
T ss_pred             eEEEEECCCCCcHHHHHH
Confidence            347788999999998754

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.

>cd01367 KISc_KIF2_like Kinesin motor domain, KIF2-like group

Probab=87.15  E-value=0.55  Score=36.33  Aligned_cols=26  Identities=35%  Similarity=0.612  Sum_probs=19.6

Q ss_pred             HHHHHHcCCC--eEEEcCCCCchhHHhH
Q psy7268          69 SIPTLLSGKS--AILVAETGCGKTLSFL   94 (134)
Q Consensus        69 ~i~~~~~g~d--vli~a~tGsGKT~~~~   94 (134)
                      .+..++.|.|  ++.-|+||||||.+..
T Consensus        76 lv~~~~~G~n~~i~ayGqtGSGKTyTm~  103 (322)
T cd01367          76 LIPHVFEGGVATCFAYGQTGSGKTYTML  103 (322)
T ss_pred             HHHHHhCCCceEEEeccCCCCCCceEec
Confidence            3445667876  7777999999998753

KIF2 is a protein expressed in neurons, which has been associated with axonal transport and neuron development; alternative splice forms have been implicated in lysosomal translocation. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In this subgroup the motor domain is found in the middle (M-type) of the protein chain. M-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second (KIF2 may be slower). To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and lo

>KOG1942|consensus

Probab=87.15  E-value=0.68  Score=36.13  Aligned_cols=26  Identities=27%  Similarity=0.507  Sum_probs=20.3

Q ss_pred             cCCCeEEEcCCCCchhHHhHHHHHHHH
Q psy7268          75 SGKSAILVAETGCGKTLSFLAPLVQQI  101 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~~lpil~~~  101 (134)
                      +|+-+++.+|+|+|||... +.+-+-+
T Consensus        63 aGravLlaGppgtGKTAlA-laisqEL   88 (456)
T KOG1942|consen   63 AGRAVLLAGPPGTGKTALA-LAISQEL   88 (456)
T ss_pred             cCcEEEEecCCCCchhHHH-HHHHHHh
Confidence            7899999999999999554 5554444

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=87.08  E-value=0.48  Score=37.16  Aligned_cols=24  Identities=17%  Similarity=0.408  Sum_probs=17.6

Q ss_pred             CCeEEEcCCCCchhHHhHHHHHHHH
Q psy7268          77 KSAILVAETGCGKTLSFLAPLVQQI  101 (134)
Q Consensus        77 ~dvli~a~tGsGKT~~~~lpil~~~  101 (134)
                      .++++.||+|+|||... --++..+
T Consensus        56 ~~~lI~G~~GtGKT~l~-~~v~~~l   79 (394)
T PRK00411         56 LNVLIYGPPGTGKTTTV-KKVFEEL   79 (394)
T ss_pred             CeEEEECCCCCCHHHHH-HHHHHHH
Confidence            57999999999999764 3334443

>PRK04220 2-phosphoglycerate kinase; Provisional

Probab=86.98  E-value=1.2  Score=34.48  Aligned_cols=46  Identities=11%  Similarity=0.122  Sum_probs=28.9

Q ss_pred             CCHHHHHHHHHCCCCCChHHHHHHHHHHHcCC---CeEEEcCCCCchhHH
Q psy7268          46 LAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGK---SAILVAETGCGKTLS   92 (134)
Q Consensus        46 l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~---dvli~a~tGsGKT~~   92 (134)
                      |.+.+.+.|.+.++..+.+- ...|..+...+   -+++.|++|+|||..
T Consensus        60 l~~~V~~~L~~~~~~~~~~~-y~~~~~i~~~~~p~iIlI~G~sgsGKStl  108 (301)
T PRK04220         60 LRRRVYYKLIEKDYEEVAEK-YLLWRRIRKSKEPIIILIGGASGVGTSTI  108 (301)
T ss_pred             HHHHHHHHHHHhCcHhHHHH-HHHHHHHhcCCCCEEEEEECCCCCCHHHH
Confidence            44566677777777654332 33333344322   388899999999974

>TIGR02012 tigrfam_recA protein RecA

Probab=86.76  E-value=1.9  Score=33.61  Aligned_cols=26  Identities=19%  Similarity=0.263  Sum_probs=18.8

Q ss_pred             cCCCeEEEcCCCCchhHHhHHHHHHH
Q psy7268          75 SGKSAILVAETGCGKTLSFLAPLVQQ  100 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~~lpil~~  100 (134)
                      .|+-+.+.+|+|+|||...+..+.+.
T Consensus        54 ~G~iteI~G~~GsGKTtLaL~~~~~~   79 (321)
T TIGR02012        54 RGRIIEIYGPESSGKTTLALHAIAEA   79 (321)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            34568899999999997765444443

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.

>TIGR03263 guanyl_kin guanylate kinase

Probab=86.72  E-value=0.55  Score=32.64  Aligned_cols=17  Identities=24%  Similarity=0.442  Sum_probs=13.9

Q ss_pred             CCCeEEEcCCCCchhHH
Q psy7268          76 GKSAILVAETGCGKTLS   92 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~   92 (134)
                      |+=+++.||+|+|||..
T Consensus         1 g~ii~l~G~~GsGKsTl   17 (180)
T TIGR03263         1 GLLIVISGPSGVGKSTL   17 (180)
T ss_pred             CcEEEEECCCCCCHHHH
Confidence            44578999999999964

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.

>PF00158 Sigma54_activat: Sigma-54 interaction domain; InterPro: IPR002078 Some bacterial regulatory proteins activate the expression of genes from promoters recognised by core RNA polymerase associated with the alternative sigma-54 factor

Probab=86.69  E-value=0.91  Score=31.86  Aligned_cols=19  Identities=37%  Similarity=0.497  Sum_probs=15.4

Q ss_pred             cCCCeEEEcCCCCchhHHh
Q psy7268          75 SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~   93 (134)
                      ....|++.+++|+||++..
T Consensus        21 ~~~pVlI~GE~GtGK~~lA   39 (168)
T PF00158_consen   21 SDLPVLITGETGTGKELLA   39 (168)
T ss_dssp             STS-EEEECSTTSSHHHHH
T ss_pred             CCCCEEEEcCCCCcHHHHH
Confidence            4567999999999999764

These have a conserved domain of about 230 residues involved in the ATP-dependent [, ] interaction with sigma-54. About half of the proteins in which this domain is found (algB, dcdT, flbD, hoxA, hupR1, hydG, ntrC, pgtA and pilR) belong to signal transduction two-component systems [] and possess a domain that can be phosphorylated by a sensor-kinase protein in their N-terminal section. Almost all of these proteins possess a helix-turn-helix DNA-binding domain in their C-terminal section. The domain which interacts with the sigma-54 factor has an ATPase activity. This may be required to promote a conformational change necessary for the interaction []. The domain contains an atypical ATP-binding motif A (P-loop) as well as a form of motif B. The two ATP-binding motifs are located in the N-terminal section of the domain.; GO: 0005524 ATP binding, 0008134 transcription factor binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1NY6_K 3M0E_G 1NY5_A 1OJL_A 3DZD_B 2C9C_A 2C98_A 2C96_A 2BJV_A 2C99_A ....

>KOG0731|consensus

Probab=86.62  E-value=0.48  Score=40.91  Aligned_cols=51  Identities=25%  Similarity=0.307  Sum_probs=30.5

Q ss_pred             CcccCCCCHHHHHHHHHC-CC-CCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHh
Q psy7268          40 TFEDTGLAPEIIDIFTKR-GL-TTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        40 ~f~~~~l~~~i~~~l~~~-g~-~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~   93 (134)
                      +|.+.---++..+.|.+. .| ++|-..|..   -+.-=+-+++++|+|+|||+.+
T Consensus       309 ~FkDVAG~deAK~El~E~V~fLKNP~~Y~~l---GAKiPkGvLL~GPPGTGKTLLA  361 (774)
T KOG0731|consen  309 KFKDVAGVDEAKEELMEFVKFLKNPEQYQEL---GAKIPKGVLLVGPPGTGKTLLA  361 (774)
T ss_pred             ccccccCcHHHHHHHHHHHHHhcCHHHHHHc---CCcCcCceEEECCCCCcHHHHH
Confidence            566655555666555553 23 333333332   1122357999999999999875

>PRK09354 recA recombinase A; Provisional

Probab=86.59  E-value=1.4  Score=34.67  Aligned_cols=26  Identities=19%  Similarity=0.253  Sum_probs=19.2

Q ss_pred             CCCeEEEcCCCCchhHHhHHHHHHHH
Q psy7268          76 GKSAILVAETGCGKTLSFLAPLVQQI  101 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~~lpil~~~  101 (134)
                      |+-+.+.+|+|+|||...+..+.+..
T Consensus        60 G~IteI~G~~GsGKTtLal~~~~~~~   85 (349)
T PRK09354         60 GRIVEIYGPESSGKTTLALHAIAEAQ   85 (349)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHH
Confidence            45688999999999977755544443

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

Probab=86.56  E-value=1.2  Score=32.02  Aligned_cols=24  Identities=33%  Similarity=0.419  Sum_probs=17.8

Q ss_pred             CCCeEEEcCCCCchhHHhHHHHHH
Q psy7268          76 GKSAILVAETGCGKTLSFLAPLVQ   99 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~~lpil~   99 (134)
                      |.=+.+.+++|+|||...+.-+..
T Consensus        19 g~v~~I~G~~GsGKT~l~~~ia~~   42 (226)
T cd01393          19 GRITEIFGEFGSGKTQLCLQLAVE   42 (226)
T ss_pred             CcEEEEeCCCCCChhHHHHHHHHH
Confidence            556889999999999776544333

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.

>PRK00091 miaA tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed

Probab=86.52  E-value=0.54  Score=36.36  Aligned_cols=16  Identities=31%  Similarity=0.362  Sum_probs=13.6

Q ss_pred             CeEEEcCCCCchhHHh
Q psy7268          78 SAILVAETGCGKTLSF   93 (134)
Q Consensus        78 dvli~a~tGsGKT~~~   93 (134)
                      =++++||||+|||...
T Consensus         6 ~i~i~GptgsGKt~la   21 (307)
T PRK00091          6 VIVIVGPTASGKTALA   21 (307)
T ss_pred             EEEEECCCCcCHHHHH
Confidence            4788999999999665

>COG1126 GlnQ ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]

Probab=86.50  E-value=0.51  Score=35.01  Aligned_cols=19  Identities=21%  Similarity=0.515  Sum_probs=15.6

Q ss_pred             HcCCCeEEEcCCCCchhHH
Q psy7268          74 LSGKSAILVAETGCGKTLS   92 (134)
Q Consensus        74 ~~g~dvli~a~tGsGKT~~   92 (134)
                      ..|.-+.+++|+|||||..
T Consensus        26 ~~Gevv~iiGpSGSGKSTl   44 (240)
T COG1126          26 EKGEVVVIIGPSGSGKSTL   44 (240)
T ss_pred             cCCCEEEEECCCCCCHHHH
Confidence            3567789999999999853

>PRK10416 signal recognition particle-docking protein FtsY; Provisional

Probab=86.42  E-value=1.6  Score=33.93  Aligned_cols=16  Identities=31%  Similarity=0.530  Sum_probs=13.6

Q ss_pred             CeEEEcCCCCchhHHh
Q psy7268          78 SAILVAETGCGKTLSF   93 (134)
Q Consensus        78 dvli~a~tGsGKT~~~   93 (134)
                      -+.+.||+|+|||...
T Consensus       116 vi~lvGpnGsGKTTt~  131 (318)
T PRK10416        116 VILVVGVNGVGKTTTI  131 (318)
T ss_pred             EEEEECCCCCcHHHHH
Confidence            4778899999999775

>PF13476 AAA_23: AAA domain; PDB: 3AV0_B 3AUY_B 3AUX_A 2O5V_A 3QG5_B 3QF7_A 3THO_A

Probab=86.42  E-value=0.54  Score=32.73  Aligned_cols=15  Identities=20%  Similarity=0.488  Sum_probs=12.8

Q ss_pred             eEEEcCCCCchhHHh
Q psy7268          79 AILVAETGCGKTLSF   93 (134)
Q Consensus        79 vli~a~tGsGKT~~~   93 (134)
                      .++.|++|+|||..+
T Consensus        22 ~vi~G~Ng~GKStil   36 (202)
T PF13476_consen   22 NVIYGPNGSGKSTIL   36 (202)
T ss_dssp             EEEEESTTSSHHHHH
T ss_pred             EEEECCCCCCHHHHH
Confidence            567899999999775

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=86.38  E-value=1.3  Score=35.95  Aligned_cols=26  Identities=23%  Similarity=0.310  Sum_probs=18.9

Q ss_pred             CCeEEEcCCCCchhHHhHHHHHHHHHh
Q psy7268          77 KSAILVAETGCGKTLSFLAPLVQQILT  103 (134)
Q Consensus        77 ~dvli~a~tGsGKT~~~~lpil~~~~~  103 (134)
                      +.+++.|++|+|||-.. -.+...+..
T Consensus       142 npl~L~G~~G~GKTHLl-~Ai~~~l~~  167 (445)
T PRK12422        142 NPIYLFGPEGSGKTHLM-QAAVHALRE  167 (445)
T ss_pred             ceEEEEcCCCCCHHHHH-HHHHHHHHH
Confidence            45899999999999543 466666543

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

Probab=86.34  E-value=1.6  Score=34.05  Aligned_cols=24  Identities=21%  Similarity=0.290  Sum_probs=17.6

Q ss_pred             CCCeEEEcCCCCchhHHhHHHHHH
Q psy7268          76 GKSAILVAETGCGKTLSFLAPLVQ   99 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~~lpil~   99 (134)
                      |+-+.+.+|+|+|||...+..+.+
T Consensus        55 G~iteI~Gp~GsGKTtLal~~~~~   78 (325)
T cd00983          55 GRIIEIYGPESSGKTTLALHAIAE   78 (325)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH
Confidence            456889999999999665444433

RecA couples ATP hydrolysis to DNA strand exchange.

>cd01373 KISc_KLP2_like Kinesin motor domain, KLP2-like subgroup

Probab=86.34  E-value=0.62  Score=36.30  Aligned_cols=24  Identities=33%  Similarity=0.520  Sum_probs=18.2

Q ss_pred             HHHHHcCCC--eEEEcCCCCchhHHh
Q psy7268          70 IPTLLSGKS--AILVAETGCGKTLSF   93 (134)
Q Consensus        70 i~~~~~g~d--vli~a~tGsGKT~~~   93 (134)
                      +..++.|.+  ++.-|.||||||...
T Consensus        67 v~~~~~G~n~ti~aYGqTGSGKTyTm   92 (337)
T cd01373          67 VEDCLSGYNGSIFAYGQTGSGKTYTM   92 (337)
T ss_pred             HHHHhCCCceeEEEeCCCCCCceEEe
Confidence            345568887  778899999999553

Members of this subgroup seem to play a role in mitosis and meiosis. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus (N-type). N-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also, the neck linker binds to the motor domain, which repositions the other head domain through the coiled-coil domain close to a second

>PRK12901 secA preprotein translocase subunit SecA; Reviewed

Probab=86.30  E-value=1.3  Score=39.71  Aligned_cols=56  Identities=25%  Similarity=0.191  Sum_probs=39.4

Q ss_pred             CChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHH
Q psy7268          61 TPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVF  130 (134)
Q Consensus        61 ~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~  130 (134)
                      .|+++|-..=-.+..|  -|....||-|||++..+|+.-..+            .|..+-||+.+-.||.
T Consensus       169 ~~yDVQliGgivLh~G--~IAEM~TGEGKTLvAtlp~yLnAL------------~GkgVHvVTVNDYLA~  224 (1112)
T PRK12901        169 VHYDVQLIGGVVLHQG--KIAEMATGEGKTLVATLPVYLNAL------------TGNGVHVVTVNDYLAK  224 (1112)
T ss_pred             cccchHHhhhhhhcCC--ceeeecCCCCchhHHHHHHHHHHH------------cCCCcEEEEechhhhh
Confidence            5667776554444444  467899999999999999877665            3445667777777764

>PRK04195 replication factor C large subunit; Provisional

Probab=86.28  E-value=0.53  Score=38.41  Aligned_cols=43  Identities=21%  Similarity=0.217  Sum_probs=28.0

Q ss_pred             CCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHc---CCCeEEEcCCCCchhHHh
Q psy7268          39 GTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLS---GKSAILVAETGCGKTLSF   93 (134)
Q Consensus        39 ~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~---g~dvli~a~tGsGKT~~~   93 (134)
                      .+|+++-.++...+.|.+. +           .....   .+.+++.||+|+|||...
T Consensus        11 ~~l~dlvg~~~~~~~l~~~-l-----------~~~~~g~~~~~lLL~GppG~GKTtla   56 (482)
T PRK04195         11 KTLSDVVGNEKAKEQLREW-I-----------ESWLKGKPKKALLLYGPPGVGKTSLA   56 (482)
T ss_pred             CCHHHhcCCHHHHHHHHHH-H-----------HHHhcCCCCCeEEEECCCCCCHHHHH
Confidence            3567777777766666542 0           01112   457999999999999664

>cd01375 KISc_KIF9_like Kinesin motor domain, KIF9-like subgroup; might play a role in cell shape remodeling

Probab=86.16  E-value=0.68  Score=35.99  Aligned_cols=24  Identities=29%  Similarity=0.552  Sum_probs=18.5

Q ss_pred             HHHHHcCCC--eEEEcCCCCchhHHh
Q psy7268          70 IPTLLSGKS--AILVAETGCGKTLSF   93 (134)
Q Consensus        70 i~~~~~g~d--vli~a~tGsGKT~~~   93 (134)
                      +..++.|.|  ++.-|+||||||...
T Consensus        73 v~~~~~G~n~~i~ayG~tgSGKTyTm   98 (334)
T cd01375          73 VDSALDGYNGTIFAYGQTGAGKTFTM   98 (334)
T ss_pred             HHHHhCCCccceeeecCCCCCCeEEc
Confidence            345667876  788899999999663

This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus (N-type). N-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also, the neck linker binds to the motor domain, which repositions the other head domain through the coiled-coil domain close to a second tubulin dimer, about 80

>cd01374 KISc_CENP_E Kinesin motor domain, CENP-E/KIP2-like subgroup, involved in chromosome movement and/or spindle elongation during mitosis

Probab=86.14  E-value=0.71  Score=35.60  Aligned_cols=26  Identities=23%  Similarity=0.379  Sum_probs=19.9

Q ss_pred             HHHHHHcCCC--eEEEcCCCCchhHHhH
Q psy7268          69 SIPTLLSGKS--AILVAETGCGKTLSFL   94 (134)
Q Consensus        69 ~i~~~~~g~d--vli~a~tGsGKT~~~~   94 (134)
                      .+..++.|.+  ++..|+||||||....
T Consensus        65 ~v~~~l~G~n~~i~ayG~tgSGKT~T~~   92 (321)
T cd01374          65 VVRSALEGYNGTIFAYGQTSSGKTFTMS   92 (321)
T ss_pred             HHHHHHCCCceeEEeecCCCCCCceecc
Confidence            3445678876  7788999999997753

This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus (N-type). N-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also, the neck linker binds to the motor domain, which repositions the other head domain through the coiled-coil domain close to

>COG1223 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=86.07  E-value=0.56  Score=36.00  Aligned_cols=18  Identities=28%  Similarity=0.444  Sum_probs=15.6

Q ss_pred             CCCeEEEcCCCCchhHHh
Q psy7268          76 GKSAILVAETGCGKTLSF   93 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~   93 (134)
                      -++|+..+|+|+|||+..
T Consensus       151 PknVLFyGppGTGKTm~A  168 (368)
T COG1223         151 PKNVLFYGPPGTGKTMMA  168 (368)
T ss_pred             cceeEEECCCCccHHHHH
Confidence            368999999999999754

>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional

Probab=86.07  E-value=1  Score=34.91  Aligned_cols=27  Identities=22%  Similarity=0.261  Sum_probs=20.2

Q ss_pred             HHHHHHHHcCCCeEEEcCCCCchhHHh
Q psy7268          67 KYSIPTLLSGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        67 ~~~i~~~~~g~dvli~a~tGsGKT~~~   93 (134)
                      +++-.....+..|++.|.+|+||+...
T Consensus        20 ~~i~~~a~~~~pVlI~GE~GtGK~~lA   46 (326)
T PRK11608         20 EQVSRLAPLDKPVLIIGERGTGKELIA   46 (326)
T ss_pred             HHHHHHhCCCCCEEEECCCCCcHHHHH
Confidence            333334456778999999999999765

>KOG0736|consensus

Probab=86.05  E-value=0.88  Score=39.54  Aligned_cols=56  Identities=21%  Similarity=0.229  Sum_probs=30.2

Q ss_pred             CCCCCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHc-CCCeEEEcCCCCchhHHh
Q psy7268          36 IDLGTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLS-GKSAILVAETGCGKTLSF   93 (134)
Q Consensus        36 ~~~~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~-g~dvli~a~tGsGKT~~~   93 (134)
                      .|--+|++.|=-+++-..+.+. +.-|-.+ -..+-.-+. .-.+++-||+|+|||+.+
T Consensus       666 IPnV~WdDVGGLeevK~eIldT-IqlPL~h-peLfssglrkRSGILLYGPPGTGKTLlA  722 (953)
T KOG0736|consen  666 IPNVSWDDVGGLEEVKTEILDT-IQLPLKH-PELFSSGLRKRSGILLYGPPGTGKTLLA  722 (953)
T ss_pred             CCccchhcccCHHHHHHHHHHH-hcCcccC-hhhhhccccccceeEEECCCCCchHHHH
Confidence            4445788877555555444441 1111111 011111122 335999999999999875

>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=85.83  E-value=2  Score=31.86  Aligned_cols=38  Identities=24%  Similarity=0.290  Sum_probs=24.8

Q ss_pred             CCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcC
Q psy7268          76 GKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITP  124 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~P  124 (134)
                      |.=+++.|.+|.|||...+--+.+....           .+..+++++.
T Consensus        19 g~L~vi~a~pg~GKT~~~l~ia~~~a~~-----------~~~~vly~Sl   56 (259)
T PF03796_consen   19 GELTVIAARPGVGKTAFALQIALNAALN-----------GGYPVLYFSL   56 (259)
T ss_dssp             T-EEEEEESTTSSHHHHHHHHHHHHHHT-----------TSSEEEEEES
T ss_pred             CcEEEEEecccCCchHHHHHHHHHHHHh-----------cCCeEEEEcC
Confidence            3447889999999996665444444432           2456787763

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 ....

>smart00129 KISc Kinesin motor, catalytic domain

Probab=85.63  E-value=0.98  Score=34.92  Aligned_cols=26  Identities=27%  Similarity=0.447  Sum_probs=19.7

Q ss_pred             HHHHHHHcCCC--eEEEcCCCCchhHHh
Q psy7268          68 YSIPTLLSGKS--AILVAETGCGKTLSF   93 (134)
Q Consensus        68 ~~i~~~~~g~d--vli~a~tGsGKT~~~   93 (134)
                      ..+..++.|.+  ++..|+||||||...
T Consensus        70 p~v~~~~~G~~~~i~~yG~tgSGKT~tl   97 (335)
T smart00129       70 PLVDSVLEGYNATIFAYGQTGSGKTYTM   97 (335)
T ss_pred             HHHHHHhcCCceeEEEeCCCCCCCceEe
Confidence            44455678886  677899999999664

ATPase. Microtubule-dependent molecular motors that play important roles in intracellular transport of organelles and in cell division.

>KOG0991|consensus

Probab=85.58  E-value=0.65  Score=35.11  Aligned_cols=17  Identities=41%  Similarity=0.587  Sum_probs=15.3

Q ss_pred             CeEEEcCCCCchhHHhH
Q psy7268          78 SAILVAETGCGKTLSFL   94 (134)
Q Consensus        78 dvli~a~tGsGKT~~~~   94 (134)
                      ++++.+|+|+|||.+.+
T Consensus        50 ~liisGpPG~GKTTsi~   66 (333)
T KOG0991|consen   50 NLIISGPPGTGKTTSIL   66 (333)
T ss_pred             ceEeeCCCCCchhhHHH
Confidence            79999999999998864

>PRK06762 hypothetical protein; Provisional

Probab=85.58  E-value=0.65  Score=31.88  Aligned_cols=16  Identities=31%  Similarity=0.385  Sum_probs=13.2

Q ss_pred             CeEEEcCCCCchhHHh
Q psy7268          78 SAILVAETGCGKTLSF   93 (134)
Q Consensus        78 dvli~a~tGsGKT~~~   93 (134)
                      =++++|++|||||...
T Consensus         4 li~i~G~~GsGKST~A   19 (166)
T PRK06762          4 LIIIRGNSGSGKTTIA   19 (166)
T ss_pred             EEEEECCCCCCHHHHH
Confidence            3678999999999754

>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=85.56  E-value=0.73  Score=30.15  Aligned_cols=21  Identities=24%  Similarity=0.366  Sum_probs=16.8

Q ss_pred             cCCCeEEEcCCCCchhHHhHH
Q psy7268          75 SGKSAILVAETGCGKTLSFLA   95 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~~l   95 (134)
                      .|+-+.+.+|+|+|||....+
T Consensus        14 ~ge~v~I~GpSGsGKSTLl~~   34 (107)
T cd00820          14 GKVGVLITGDSGIGKTELALE   34 (107)
T ss_pred             CCEEEEEEcCCCCCHHHHHHH
Confidence            356689999999999986544

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

>PRK11823 DNA repair protein RadA; Provisional

Probab=85.55  E-value=1.5  Score=35.68  Aligned_cols=38  Identities=16%  Similarity=0.315  Sum_probs=24.3

Q ss_pred             cCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcC
Q psy7268          75 SGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITP  124 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~P  124 (134)
                      .|.-+++.+++|+|||...+-- +....+           .+.+++|++-
T Consensus        79 ~Gs~~lI~G~pG~GKTtL~lq~-a~~~a~-----------~g~~vlYvs~  116 (446)
T PRK11823         79 PGSVVLIGGDPGIGKSTLLLQV-AARLAA-----------AGGKVLYVSG  116 (446)
T ss_pred             CCEEEEEECCCCCCHHHHHHHH-HHHHHh-----------cCCeEEEEEc
Confidence            3456889999999999655333 333322           3456777763

>cd00106 KISc Kinesin motor domain

Probab=85.54  E-value=0.95  Score=34.82  Aligned_cols=25  Identities=28%  Similarity=0.446  Sum_probs=19.1

Q ss_pred             HHHHHHHcCCC--eEEEcCCCCchhHH
Q psy7268          68 YSIPTLLSGKS--AILVAETGCGKTLS   92 (134)
Q Consensus        68 ~~i~~~~~g~d--vli~a~tGsGKT~~   92 (134)
                      ..+..++.|.|  ++..|+||||||..
T Consensus        69 ~~v~~~~~G~~~~i~~yG~tgSGKT~t   95 (328)
T cd00106          69 PLVESVLEGYNGTIFAYGQTGSGKTYT   95 (328)
T ss_pred             HHHHHHhCCCceeEEEecCCCCCCeEE
Confidence            44455677886  77789999999964

This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus (N-type), in some its is found in the middle (M-type), or C-terminal (C-type). N-type and M-type kinesins are (+) end-directed motors, while C-type kinesins are (-) end-directed motors, i.e. they transport cargo towards the (-) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also, the neck linker binds to the motor domain, which repositions the other head domain through the coil

>TIGR02974 phageshock_pspF psp operon transcriptional activator PspF

Probab=85.50  E-value=1.1  Score=34.82  Aligned_cols=27  Identities=19%  Similarity=0.255  Sum_probs=20.0

Q ss_pred             HHHHHHHHcCCCeEEEcCCCCchhHHh
Q psy7268          67 KYSIPTLLSGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        67 ~~~i~~~~~g~dvli~a~tGsGKT~~~   93 (134)
                      +++-.....+..|++.|++|+||+...
T Consensus        13 ~~~~~~a~~~~pVLI~GE~GtGK~~lA   39 (329)
T TIGR02974        13 EQVSRLAPLDRPVLIIGERGTGKELIA   39 (329)
T ss_pred             HHHHHHhCCCCCEEEECCCCChHHHHH
Confidence            333334456778999999999999764

Members of this protein family are PspF, the sigma-54-dependent transcriptional activator of the phage shock protein (psp) operon, in Escherichia coli and numerous other species. The psp operon is induced by a number of stress conditions, including heat shock, ethanol, and filamentous phage infection. Changed com_name to adhere to TIGR role notes conventions. 09/15/06 - DMH

>CHL00195 ycf46 Ycf46; Provisional

Probab=85.48  E-value=0.61  Score=38.38  Aligned_cols=18  Identities=33%  Similarity=0.536  Sum_probs=15.5

Q ss_pred             CCCeEEEcCCCCchhHHh
Q psy7268          76 GKSAILVAETGCGKTLSF   93 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~   93 (134)
                      .+.+++.||+|+|||+..
T Consensus       259 pkGILL~GPpGTGKTllA  276 (489)
T CHL00195        259 PRGLLLVGIQGTGKSLTA  276 (489)
T ss_pred             CceEEEECCCCCcHHHHH
Confidence            456999999999999764

>TIGR01359 UMP_CMP_kin_fam UMP-CMP kinase family

Probab=85.44  E-value=0.66  Score=32.32  Aligned_cols=15  Identities=20%  Similarity=0.401  Sum_probs=12.8

Q ss_pred             eEEEcCCCCchhHHh
Q psy7268          79 AILVAETGCGKTLSF   93 (134)
Q Consensus        79 vli~a~tGsGKT~~~   93 (134)
                      +++.|++|||||...
T Consensus         2 i~i~G~pGsGKst~a   16 (183)
T TIGR01359         2 VFVLGGPGSGKGTQC   16 (183)
T ss_pred             EEEECCCCCCHHHHH
Confidence            578999999999763

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.

>cd01123 Rad51_DMC1_radA Rad51_DMC1_radA,B

Probab=85.31  E-value=1.1  Score=32.58  Aligned_cols=25  Identities=28%  Similarity=0.287  Sum_probs=18.3

Q ss_pred             cCCCeEEEcCCCCchhHHhHHHHHH
Q psy7268          75 SGKSAILVAETGCGKTLSFLAPLVQ   99 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~~lpil~   99 (134)
                      .|.-+.+.+++|+|||...+.-++.
T Consensus        18 ~g~i~~i~G~~GsGKT~l~~~l~~~   42 (235)
T cd01123          18 TGSITEIFGEFGSGKTQLCHQLAVT   42 (235)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            3556899999999999776544333

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 .

>PRK13891 conjugal transfer protein TrbE; Provisional

Probab=85.28  E-value=1.6  Score=38.26  Aligned_cols=17  Identities=24%  Similarity=0.419  Sum_probs=14.5

Q ss_pred             CeEEEcCCCCchhHHhH
Q psy7268          78 SAILVAETGCGKTLSFL   94 (134)
Q Consensus        78 dvli~a~tGsGKT~~~~   94 (134)
                      +.+|.|+||+|||+..-
T Consensus       490 h~~I~G~tGsGKS~l~~  506 (852)
T PRK13891        490 HTFMFGPTGAGKSTHLG  506 (852)
T ss_pred             eEEEECCCCCCHHHHHH
Confidence            48999999999997654

>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=85.20  E-value=0.76  Score=34.18  Aligned_cols=16  Identities=25%  Similarity=0.306  Sum_probs=14.1

Q ss_pred             CeEEEcCCCCchhHHh
Q psy7268          78 SAILVAETGCGKTLSF   93 (134)
Q Consensus        78 dvli~a~tGsGKT~~~   93 (134)
                      ++++.||+|+|||...
T Consensus        52 h~lf~GPPG~GKTTLA   67 (233)
T PF05496_consen   52 HMLFYGPPGLGKTTLA   67 (233)
T ss_dssp             EEEEESSTTSSHHHHH
T ss_pred             eEEEECCCccchhHHH
Confidence            5899999999999655

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.

>KOG0924|consensus

Probab=85.19  E-value=1  Score=38.86  Aligned_cols=33  Identities=21%  Similarity=0.345  Sum_probs=25.0

Q ss_pred             CChHHHHHHHHHHHcCCCeEEEcCCCCchhHHh
Q psy7268          61 TPTEIQKYSIPTLLSGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        61 ~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~   93 (134)
                      .-...+.+.+..+..+.-+++.+.||||||.-.
T Consensus       356 Pvf~~R~~ll~~ir~n~vvvivgETGSGKTTQl  388 (1042)
T KOG0924|consen  356 PVFACRDQLLSVIRENQVVVIVGETGSGKTTQL  388 (1042)
T ss_pred             chHHHHHHHHHHHhhCcEEEEEecCCCCchhhh
Confidence            345566666666677788999999999999653

>PRK09825 idnK D-gluconate kinase; Provisional

Probab=85.19  E-value=0.7  Score=32.60  Aligned_cols=19  Identities=42%  Similarity=0.590  Sum_probs=16.0

Q ss_pred             cCCCeEEEcCCCCchhHHh
Q psy7268          75 SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~   93 (134)
                      .|+-+.+.|++|+|||...
T Consensus         2 ~ge~i~l~G~sGsGKSTl~   20 (176)
T PRK09825          2 AGESYILMGVSGSGKSLIG   20 (176)
T ss_pred             CCcEEEEECCCCCCHHHHH
Confidence            4677899999999999754

>TIGR00750 lao LAO/AO transport system ATPase

Probab=85.17  E-value=2  Score=32.80  Aligned_cols=18  Identities=17%  Similarity=0.292  Sum_probs=14.7

Q ss_pred             cCCCeEEEcCCCCchhHH
Q psy7268          75 SGKSAILVAETGCGKTLS   92 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~   92 (134)
                      .+.-+.+.+++|+|||..
T Consensus        33 ~~~~i~i~G~~G~GKttl   50 (300)
T TIGR00750        33 NAHRVGITGTPGAGKSTL   50 (300)
T ss_pred             CceEEEEECCCCCCHHHH
Confidence            356688899999999954

Mutations have also been found that do not phosphorylate the periplasmic binding proteins, yet still allow transport. The ATPase activity of this protein seems to be necessary, however.

>TIGR01360 aden_kin_iso1 adenylate kinase, isozyme 1 subfamily

Probab=85.16  E-value=0.69  Score=32.18  Aligned_cols=16  Identities=25%  Similarity=0.374  Sum_probs=13.5

Q ss_pred             CeEEEcCCCCchhHHh
Q psy7268          78 SAILVAETGCGKTLSF   93 (134)
Q Consensus        78 dvli~a~tGsGKT~~~   93 (134)
                      -+++.|++|||||...
T Consensus         5 ii~i~G~~GsGKsTl~   20 (188)
T TIGR01360         5 IIFIVGGPGSGKGTQC   20 (188)
T ss_pred             EEEEECCCCCCHHHHH
Confidence            4678999999999865

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.

>PRK13765 ATP-dependent protease Lon; Provisional

Probab=84.98  E-value=1.4  Score=37.40  Aligned_cols=49  Identities=18%  Similarity=0.355  Sum_probs=31.4

Q ss_pred             CCCCCcccCCCCHHHHHHHHHCCCCCChHHHHHHHH----HHHcCCCeEEEcCCCCchhHHh
Q psy7268          36 IDLGTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIP----TLLSGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        36 ~~~~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~----~~~~g~dvli~a~tGsGKT~~~   93 (134)
                      ..+.+-++..+++.+++.+..         |..++.    .+..++.+++.+++|+|||...
T Consensus        15 ~~~~~~~~~~~~~~~~~~vig---------q~~a~~~L~~~~~~~~~~l~~G~~G~GKttla   67 (637)
T PRK13765         15 LDFETTSDIEVPERLIDQVIG---------QEHAVEVIKKAAKQRRHVMMIGSPGTGKSMLA   67 (637)
T ss_pred             cCcccceecccCcccHHHcCC---------hHHHHHHHHHHHHhCCeEEEECCCCCcHHHHH
Confidence            344555566677765554432         233322    3446788999999999999764

>TIGR00959 ffh signal recognition particle protein

Probab=84.93  E-value=2.1  Score=34.72  Aligned_cols=16  Identities=31%  Similarity=0.416  Sum_probs=13.9

Q ss_pred             eEEEcCCCCchhHHhH
Q psy7268          79 AILVAETGCGKTLSFL   94 (134)
Q Consensus        79 vli~a~tGsGKT~~~~   94 (134)
                      +++++++|+|||....
T Consensus       102 i~~vG~~GsGKTTtaa  117 (428)
T TIGR00959       102 ILMVGLQGSGKTTTCG  117 (428)
T ss_pred             EEEECCCCCcHHHHHH
Confidence            7889999999998753

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.

>TIGR00416 sms DNA repair protein RadA

Probab=84.92  E-value=1.5  Score=35.78  Aligned_cols=38  Identities=21%  Similarity=0.338  Sum_probs=24.8

Q ss_pred             cCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcC
Q psy7268          75 SGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITP  124 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~P  124 (134)
                      .|.-+++.+++|+|||...+. ++..+..           ++.+++|++.
T Consensus        93 ~GsvilI~G~pGsGKTTL~lq-~a~~~a~-----------~g~kvlYvs~  130 (454)
T TIGR00416        93 PGSLILIGGDPGIGKSTLLLQ-VACQLAK-----------NQMKVLYVSG  130 (454)
T ss_pred             CCeEEEEEcCCCCCHHHHHHH-HHHHHHh-----------cCCcEEEEEC
Confidence            355689999999999976543 3333332           3345777764

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)).

>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=84.89  E-value=0.8  Score=27.05  Aligned_cols=15  Identities=20%  Similarity=0.352  Sum_probs=12.2

Q ss_pred             eEEEcCCCCchhHHh
Q psy7268          79 AILVAETGCGKTLSF   93 (134)
Q Consensus        79 vli~a~tGsGKT~~~   93 (134)
                      +.+.++.|+|||...
T Consensus         2 i~i~G~~gsGKst~~   16 (69)
T cd02019           2 IAITGGSGSGKSTVA   16 (69)
T ss_pred             EEEECCCCCCHHHHH
Confidence            567899999998653

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.

>PRK06995 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=84.85  E-value=1.8  Score=35.58  Aligned_cols=20  Identities=35%  Similarity=0.414  Sum_probs=15.9

Q ss_pred             CCCeEEEcCCCCchhHHhHH
Q psy7268          76 GKSAILVAETGCGKTLSFLA   95 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~~l   95 (134)
                      |+-+.+.||||+|||.+...
T Consensus       256 g~Vi~LvGpnGvGKTTTiaK  275 (484)
T PRK06995        256 GGVFALMGPTGVGKTTTTAK  275 (484)
T ss_pred             CcEEEEECCCCccHHHHHHH
Confidence            44578999999999988643

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=84.85  E-value=2.9  Score=35.48  Aligned_cols=41  Identities=15%  Similarity=0.173  Sum_probs=25.5

Q ss_pred             CeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHH
Q psy7268          78 SAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELV  129 (134)
Q Consensus        78 dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La  129 (134)
                      .+++.|++|+|||-.. ..+.+.+....         .+.+++++. ..++.
T Consensus       316 pL~LyG~sGsGKTHLL-~AIa~~a~~~~---------~g~~V~Yit-aeef~  356 (617)
T PRK14086        316 PLFIYGESGLGKTHLL-HAIGHYARRLY---------PGTRVRYVS-SEEFT  356 (617)
T ss_pred             cEEEECCCCCCHHHHH-HHHHHHHHHhC---------CCCeEEEee-HHHHH
Confidence            4899999999999443 45555554311         345666664 44444

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=84.78  E-value=2  Score=34.93  Aligned_cols=17  Identities=35%  Similarity=0.471  Sum_probs=14.3

Q ss_pred             CeEEEcCCCCchhHHhH
Q psy7268          78 SAILVAETGCGKTLSFL   94 (134)
Q Consensus        78 dvli~a~tGsGKT~~~~   94 (134)
                      .++++|++|+|||....
T Consensus        97 vI~lvG~~GsGKTTtaa  113 (437)
T PRK00771         97 TIMLVGLQGSGKTTTAA  113 (437)
T ss_pred             EEEEECCCCCcHHHHHH
Confidence            47889999999997753

>COG0419 SbcC ATPase involved in DNA repair [DNA replication, recombination, and repair]

Probab=84.76  E-value=0.62  Score=41.00  Aligned_cols=24  Identities=17%  Similarity=0.344  Sum_probs=16.5

Q ss_pred             CeEEEcCCCCchhHHhHHHHHHHHH
Q psy7268          78 SAILVAETGCGKTLSFLAPLVQQIL  102 (134)
Q Consensus        78 dvli~a~tGsGKT~~~~lpil~~~~  102 (134)
                      =.+|+|+||+|||..+ =+|...++
T Consensus        27 i~lI~G~nGsGKSSIl-dAI~~ALy   50 (908)
T COG0419          27 IFLIVGPNGAGKSSIL-DAITFALY   50 (908)
T ss_pred             eEEEECCCCCcHHHHH-HHHHHHHc
Confidence            3678999999999765 33333343

>smart00072 GuKc Guanylate kinase homologues

Probab=84.73  E-value=1.8  Score=30.44  Aligned_cols=17  Identities=24%  Similarity=0.409  Sum_probs=14.3

Q ss_pred             CCCeEEEcCCCCchhHH
Q psy7268          76 GKSAILVAETGCGKTLS   92 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~   92 (134)
                      ++-+++.||+|+||+..
T Consensus         2 ~r~ivl~Gpsg~GK~tl   18 (184)
T smart00072        2 RRPIVLSGPSGVGKGTL   18 (184)
T ss_pred             CcEEEEECCCCCCHHHH
Confidence            56689999999999953

Active enzymes catalyze ATP-dependent phosphorylation of GMP to GDP. Structure resembles that of adenylate kinase. So-called membrane-associated guanylate kinase homologues (MAGUKs) do not possess guanylate kinase activities; instead at least some possess protein-binding functions.

>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=84.66  E-value=0.78  Score=30.45  Aligned_cols=15  Identities=20%  Similarity=0.275  Sum_probs=12.7

Q ss_pred             eEEEcCCCCchhHHh
Q psy7268          79 AILVAETGCGKTLSF   93 (134)
Q Consensus        79 vli~a~tGsGKT~~~   93 (134)
                      +++.+++|||||...
T Consensus         2 I~i~G~~GsGKst~a   16 (147)
T cd02020           2 IAIDGPAGSGKSTVA   16 (147)
T ss_pred             EEEECCCCCCHHHHH
Confidence            578899999999854

>PRK08233 hypothetical protein; Provisional

Probab=84.62  E-value=0.67  Score=32.06  Aligned_cols=15  Identities=33%  Similarity=0.330  Sum_probs=12.1

Q ss_pred             eEEEcCCCCchhHHh
Q psy7268          79 AILVAETGCGKTLSF   93 (134)
Q Consensus        79 vli~a~tGsGKT~~~   93 (134)
                      +.+.|++|||||...
T Consensus         6 I~I~G~~GsGKtTla   20 (182)
T PRK08233          6 ITIAAVSGGGKTTLT   20 (182)
T ss_pred             EEEECCCCCCHHHHH
Confidence            567899999999643

>PRK09302 circadian clock protein KaiC; Reviewed

Probab=84.57  E-value=2  Score=35.30  Aligned_cols=26  Identities=27%  Similarity=0.242  Sum_probs=18.5

Q ss_pred             cCCCeEEEcCCCCchhHHhHHHHHHH
Q psy7268          75 SGKSAILVAETGCGKTLSFLAPLVQQ  100 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~~lpil~~  100 (134)
                      .|.-+++.+++|+|||...+--+.+.
T Consensus       272 ~g~~~li~G~~G~GKT~l~~~~~~~~  297 (509)
T PRK09302        272 RGSIILVSGATGTGKTLLASKFAEAA  297 (509)
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHHH
Confidence            35668889999999997654444333

>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=84.53  E-value=0.82  Score=30.69  Aligned_cols=16  Identities=31%  Similarity=0.420  Sum_probs=13.8

Q ss_pred             CeEEEcCCCCchhHHh
Q psy7268          78 SAILVAETGCGKTLSF   93 (134)
Q Consensus        78 dvli~a~tGsGKT~~~   93 (134)
                      +++++|++|+|||...
T Consensus         1 ~i~l~G~~GsGKstla   16 (154)
T cd00464           1 NIVLIGMMGAGKTTVG   16 (154)
T ss_pred             CEEEEcCCCCCHHHHH
Confidence            4789999999999764

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.

>PRK06547 hypothetical protein; Provisional

Probab=84.48  E-value=0.78  Score=32.33  Aligned_cols=15  Identities=27%  Similarity=0.412  Sum_probs=12.3

Q ss_pred             eEEEcCCCCchhHHh
Q psy7268          79 AILVAETGCGKTLSF   93 (134)
Q Consensus        79 vli~a~tGsGKT~~~   93 (134)
                      +++.|++|||||...
T Consensus        18 i~i~G~~GsGKTt~a   32 (172)
T PRK06547         18 VLIDGRSGSGKTTLA   32 (172)
T ss_pred             EEEECCCCCCHHHHH
Confidence            666699999999764

>PRK14531 adenylate kinase; Provisional

Probab=84.46  E-value=0.66  Score=32.68  Aligned_cols=17  Identities=18%  Similarity=0.378  Sum_probs=14.4

Q ss_pred             CCeEEEcCCCCchhHHh
Q psy7268          77 KSAILVAETGCGKTLSF   93 (134)
Q Consensus        77 ~dvli~a~tGsGKT~~~   93 (134)
                      +.+++.|++|||||...
T Consensus         3 ~~i~i~G~pGsGKsT~~   19 (183)
T PRK14531          3 QRLLFLGPPGAGKGTQA   19 (183)
T ss_pred             cEEEEECCCCCCHHHHH
Confidence            35899999999999764

>PRK13768 GTPase; Provisional

Probab=84.46  E-value=2  Score=32.05  Aligned_cols=16  Identities=25%  Similarity=0.366  Sum_probs=12.9

Q ss_pred             CeEEEcCCCCchhHHh
Q psy7268          78 SAILVAETGCGKTLSF   93 (134)
Q Consensus        78 dvli~a~tGsGKT~~~   93 (134)
                      -+++.++.|+|||...
T Consensus         4 ~i~v~G~~G~GKTt~~   19 (253)
T PRK13768          4 IVFFLGTAGSGKTTLT   19 (253)
T ss_pred             EEEEECCCCccHHHHH
Confidence            3678899999999753

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=84.36  E-value=0.76  Score=35.45  Aligned_cols=18  Identities=28%  Similarity=0.277  Sum_probs=15.2

Q ss_pred             CCeEEEcCCCCchhHHhH
Q psy7268          77 KSAILVAETGCGKTLSFL   94 (134)
Q Consensus        77 ~dvli~a~tGsGKT~~~~   94 (134)
                      ..+++.||+|+|||....
T Consensus        52 ~~~ll~GppG~GKT~la~   69 (328)
T PRK00080         52 DHVLLYGPPGLGKTTLAN   69 (328)
T ss_pred             CcEEEECCCCccHHHHHH
Confidence            469999999999997653

>PF02456 Adeno_IVa2: Adenovirus IVa2 protein; InterPro: IPR003389 Va2 protein can interact with the adenoviral packaging signal and this interaction involves DNA sequences that have previously been demonstrated to be required for packaging []

Probab=84.32  E-value=1.1  Score=35.07  Aligned_cols=13  Identities=31%  Similarity=0.595  Sum_probs=10.7

Q ss_pred             eEEEcCCCCchhH
Q psy7268          79 AILVAETGCGKTL   91 (134)
Q Consensus        79 vli~a~tGsGKT~   91 (134)
                      .+|-||||+||+-
T Consensus        90 ~~VYGPTG~GKSq  102 (369)
T PF02456_consen   90 GVVYGPTGSGKSQ  102 (369)
T ss_pred             EEEECCCCCCHHH
Confidence            4677999999973

During the course of lytic infection, the adenovirus major late promoter (MLP) is induced to high levels after replication of viral DNA has started. IVa2 is a transcriptional activator of the major late promoter [].; GO: 0019083 viral transcription

>PLN02796 D-glycerate 3-kinase

Probab=84.32  E-value=3.4  Score=32.62  Aligned_cols=15  Identities=40%  Similarity=0.567  Sum_probs=12.9

Q ss_pred             eEEEcCCCCchhHHh
Q psy7268          79 AILVAETGCGKTLSF   93 (134)
Q Consensus        79 vli~a~tGsGKT~~~   93 (134)
                      +-|.|++|||||...
T Consensus       103 IGI~G~sGSGKSTLa  117 (347)
T PLN02796        103 IGISAPQGCGKTTLV  117 (347)
T ss_pred             EEEECCCCCcHHHHH
Confidence            778899999999764

>TIGR02784 addA_alphas double-strand break repair helicase AddA, alphaproteobacterial type

Probab=84.30  E-value=3  Score=37.78  Aligned_cols=48  Identities=21%  Similarity=0.231  Sum_probs=34.9

Q ss_pred             CCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHh
Q psy7268          76 GKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQI  132 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi  132 (134)
                      .++++|.|+-|||||....--++..+....         ..-++++|+-|+.=|..+
T Consensus        10 ~~~~~~~a~agsgkt~~l~~~~~~~~~~~~---------~~~~i~~~t~t~~aa~em   57 (1141)
T TIGR02784        10 KTSAWVSANAGSGKTHVLTQRVIRLLLNGV---------PPSKILCLTYTKAAAAEM   57 (1141)
T ss_pred             CCCEEEEEECCCCHHHHHHHHHHHHHHcCC---------CCCeEEEEecCHHHHHHH
Confidence            467999999999999888766666664321         223688889888766554

AddAB, also called RexAB, substitutes for RecBCD in several bacterial lineages. These DNA recombination proteins act before synapse and are particularly important for DNA repair of double-stranded breaks by homologous recombination. The term AddAB is used broadly, with AddA homologous between the alphaproteobacteria (as modeled here) and the Firmicutes, while the partner AddB proteins show no strong homology across the two groups of species.

>PRK08356 hypothetical protein; Provisional

Probab=84.29  E-value=0.79  Score=32.61  Aligned_cols=15  Identities=27%  Similarity=0.237  Sum_probs=13.0

Q ss_pred             eEEEcCCCCchhHHh
Q psy7268          79 AILVAETGCGKTLSF   93 (134)
Q Consensus        79 vli~a~tGsGKT~~~   93 (134)
                      ++++||+|||||...
T Consensus         8 i~~~G~~gsGK~t~a   22 (195)
T PRK08356          8 VGVVGKIAAGKTTVA   22 (195)
T ss_pred             EEEECCCCCCHHHHH
Confidence            678999999999764

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=84.20  E-value=0.8  Score=34.68  Aligned_cols=17  Identities=29%  Similarity=0.327  Sum_probs=14.4

Q ss_pred             CCeEEEcCCCCchhHHh
Q psy7268          77 KSAILVAETGCGKTLSF   93 (134)
Q Consensus        77 ~dvli~a~tGsGKT~~~   93 (134)
                      .++++.||+|+|||...
T Consensus        31 ~~~ll~Gp~G~GKT~la   47 (305)
T TIGR00635        31 DHLLLYGPPGLGKTTLA   47 (305)
T ss_pred             CeEEEECCCCCCHHHHH
Confidence            35999999999999654

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.

>PF10662 PduV-EutP: Ethanolamine utilisation - propanediol utilisation; InterPro: IPR012381 Members of this family function in ethanolamine [] and propanediol [] degradation pathways

Probab=84.19  E-value=1.7  Score=29.91  Aligned_cols=15  Identities=40%  Similarity=0.689  Sum_probs=12.8

Q ss_pred             CCeEEEcCCCCchhH
Q psy7268          77 KSAILVAETGCGKTL   91 (134)
Q Consensus        77 ~dvli~a~tGsGKT~   91 (134)
                      +-+++.|++|+|||.
T Consensus         2 krimliG~~g~GKTT   16 (143)
T PF10662_consen    2 KRIMLIGPSGSGKTT   16 (143)
T ss_pred             ceEEEECCCCCCHHH
Confidence            357899999999994

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

>PF08283 Gemini_AL1_M: Geminivirus rep protein central domain; InterPro: IPR022692 Geminiviruses are characterised by a genome of circular single-stranded DNA encapsidated in twinned (geminate) quasi-isometric particles, from which the group derives its name []

Probab=84.18  E-value=0.71  Score=30.20  Aligned_cols=55  Identities=13%  Similarity=0.021  Sum_probs=35.5

Q ss_pred             cccccCCCCCCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhH
Q psy7268          30 YEAVSRIDLGTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTL   91 (134)
Q Consensus        30 ~~~~~~~~~~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~   91 (134)
                      .......|+..-+.+..+++|.+++.+.=+ ...+      ..-++-.++++++++.+|||+
T Consensus        51 ~~e~y~~Pf~~ssf~~~pe~i~~W~~~nv~-~~aa------~rp~rp~SivieG~sRTGKT~  105 (106)
T PF08283_consen   51 PPEPYVSPFPLSSFLQVPEEIEEWADENVY-SVAA------ARPLRPISIVIEGDSRTGKTM  105 (106)
T ss_pred             CCccccCCCCChhhccCChHHHHHHHhccC-cccc------cCCCCCCceeEecCCccCcCC
Confidence            334445566644566688999999987422 1110      012345689999999999995

Most geminiviruses can be divided into two subgroups on the basis of host range and/or insect vector: i.e. those that infect dicotyledenous plants and are transmitted by the same whitefly species, and those that infect monocotyledenous plants and are transmitted by different leafhopper vectors. The genomes of the whitefly-transmitted African cassava mosaic virus, Tomato golden mosaic virus (TGMV) and Bean golden mosaic virus (BGMV) possess a bipartite genome. By contrast, only a single DNA component has been identified for the leafhopper-transmitted Maize streak virus (MSV) and Wheat dwarf virus (WDV) [, ]. Beet curly top virus (BCTV), and Tobacco yellow dwarf virus belong to a third possible subgroup. Like MSV and WDV, BCTV is transmitted by a specific leafhopper species, yet like the whitefly-transmitted geminiviruses it has a host range confined to dicotyledenous plants. Sequence comparison of the whitefly-transmitted Squash leaf curl virus (SqLCV) and Tomato yellow leaf curl virus (TYLCV) with the genomic components of TGMV and BGMV reveals a close evolutionary relationship [, , ]. Amino acid sequence alignments of Potato yellow mosaic virus (PYMV) proteins with those encoded by other geminiviruses show that PYMV is closely related to geminiviruses isolated from the New World, especially in the putative coat protein gene regions []. Comparison of MSV DNA-encoded proteins with those of other geminiviruses infecting monocotyledonous plants, including Panicum streak virus [] and Miscanthus streak virus (MiSV) [], reveal high levels of similarity. This is the central region of the geminivirus rep proteins []. It is found C-terminal to PF00799 from PFAM and is thought to be responsible for oligomerisation.; GO: 0016888 endodeoxyribonuclease activity, producing 5'-phosphomonoesters

>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=84.14  E-value=0.81  Score=32.03  Aligned_cols=15  Identities=27%  Similarity=0.443  Sum_probs=13.0

Q ss_pred             eEEEcCCCCchhHHh
Q psy7268          79 AILVAETGCGKTLSF   93 (134)
Q Consensus        79 vli~a~tGsGKT~~~   93 (134)
                      +++.|++|||||...
T Consensus         2 I~i~G~pGsGKst~a   16 (194)
T cd01428           2 ILLLGPPGSGKGTQA   16 (194)
T ss_pred             EEEECCCCCCHHHHH
Confidence            789999999999654

This enzyme is required for the biosynthesis of ADP and is essential for homeostasis of adenosine phosphates.

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

Probab=84.13  E-value=0.83  Score=30.75  Aligned_cols=15  Identities=20%  Similarity=0.364  Sum_probs=12.8

Q ss_pred             eEEEcCCCCchhHHh
Q psy7268          79 AILVAETGCGKTLSF   93 (134)
Q Consensus        79 vli~a~tGsGKT~~~   93 (134)
                      +++.|++|+|||...
T Consensus         2 i~l~G~~GsGKST~a   16 (150)
T cd02021           2 IVVMGVSGSGKSTVG   16 (150)
T ss_pred             EEEEcCCCCCHHHHH
Confidence            578999999999764

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

>KOG0953|consensus

Probab=84.12  E-value=1.2  Score=37.39  Aligned_cols=41  Identities=22%  Similarity=0.216  Sum_probs=31.2

Q ss_pred             CeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhcC
Q psy7268          78 SAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIGQ  134 (134)
Q Consensus        78 dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~~  134 (134)
                      =++-+|||-||||..+    |+++...            -.+++--|.|-||..|++
T Consensus       193 Ii~H~GPTNSGKTy~A----Lqrl~~a------------ksGvycGPLrLLA~EV~~  233 (700)
T KOG0953|consen  193 IIMHVGPTNSGKTYRA----LQRLKSA------------KSGVYCGPLRLLAHEVYD  233 (700)
T ss_pred             EEEEeCCCCCchhHHH----HHHHhhh------------ccceecchHHHHHHHHHH
Confidence            3566799999999655    6776532            347888899999998874

>PRK10867 signal recognition particle protein; Provisional

Probab=84.05  E-value=2.1  Score=34.69  Aligned_cols=16  Identities=31%  Similarity=0.387  Sum_probs=13.7

Q ss_pred             eEEEcCCCCchhHHhH
Q psy7268          79 AILVAETGCGKTLSFL   94 (134)
Q Consensus        79 vli~a~tGsGKT~~~~   94 (134)
                      +++++++|+|||.+..
T Consensus       103 I~~vG~~GsGKTTtaa  118 (433)
T PRK10867        103 IMMVGLQGAGKTTTAG  118 (433)
T ss_pred             EEEECCCCCcHHHHHH
Confidence            7889999999997753

>cd01371 KISc_KIF3 Kinesin motor domain, kinesins II or KIF3_like proteins

Probab=84.00  E-value=0.93  Score=35.19  Aligned_cols=23  Identities=30%  Similarity=0.577  Sum_probs=17.7

Q ss_pred             HHHHHcCCC--eEEEcCCCCchhHH
Q psy7268          70 IPTLLSGKS--AILVAETGCGKTLS   92 (134)
Q Consensus        70 i~~~~~g~d--vli~a~tGsGKT~~   92 (134)
                      ++.++.|.+  ++..|.||||||..
T Consensus        74 v~~~~~G~n~~i~ayG~tgSGKTyT   98 (333)
T cd01371          74 VDSVLEGYNGTIFAYGQTGTGKTFT   98 (333)
T ss_pred             HHHHhCCCceeEEecCCCCCCCcEe
Confidence            345667876  78889999999944

Subgroup of kinesins, which form heterotrimers composed of 2 kinesins and one non-motor accessory subunit. Kinesins II play important roles in ciliary transport, and have been implicated in neuronal transport, melanosome transport, the secretory pathway, and mitosis. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In this group the motor domain is found at the N-terminus (N-type). N-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain

>PRK05541 adenylylsulfate kinase; Provisional

Probab=83.98  E-value=0.91  Score=31.55  Aligned_cols=19  Identities=26%  Similarity=0.291  Sum_probs=15.9

Q ss_pred             cCCCeEEEcCCCCchhHHh
Q psy7268          75 SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~   93 (134)
                      .|.-+++.|++|+|||...
T Consensus         6 ~~~~I~i~G~~GsGKst~a   24 (176)
T PRK05541          6 NGYVIWITGLAGSGKTTIA   24 (176)
T ss_pred             CCCEEEEEcCCCCCHHHHH
Confidence            4667899999999999665

>COG0210 UvrD Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]

Probab=83.97  E-value=3.3  Score=34.99  Aligned_cols=61  Identities=16%  Similarity=0.115  Sum_probs=40.2

Q ss_pred             CChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHH
Q psy7268          61 TPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQ  131 (134)
Q Consensus        61 ~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Q  131 (134)
                      .+++-|++++...  ...++|.|..|||||-+..-=+.+.+.....        .-.+++.++=|+--|..
T Consensus         2 ~Ln~~Q~~av~~~--~gp~lV~AGaGsGKT~vlt~Ria~li~~~~v--------~p~~Il~vTFTnkAA~e   62 (655)
T COG0210           2 KLNPEQREAVLHP--DGPLLVLAGAGSGKTRVLTERIAYLIAAGGV--------DPEQILAITFTNKAAAE   62 (655)
T ss_pred             CCCHHHHHHHhcC--CCCeEEEECCCCCchhhHHHHHHHHHHcCCc--------ChHHeeeeechHHHHHH
Confidence            5688899988665  5668888999999998876666666643221        11235666656555543

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

Probab=83.90  E-value=0.83  Score=32.44  Aligned_cols=15  Identities=27%  Similarity=0.277  Sum_probs=12.3

Q ss_pred             eEEEcCCCCchhHHh
Q psy7268          79 AILVAETGCGKTLSF   93 (134)
Q Consensus        79 vli~a~tGsGKT~~~   93 (134)
                      |-|.|++|||||...
T Consensus         2 IgI~G~sgSGKTTla   16 (194)
T PF00485_consen    2 IGIAGPSGSGKTTLA   16 (194)
T ss_dssp             EEEEESTTSSHHHHH
T ss_pred             EEEECCCCCCHHHHH
Confidence            458899999999654

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 ....

>cd01372 KISc_KIF4 Kinesin motor domain, KIF4-like subfamily

Probab=83.85  E-value=0.98  Score=35.06  Aligned_cols=24  Identities=29%  Similarity=0.560  Sum_probs=19.0

Q ss_pred             HHHHHcCCC--eEEEcCCCCchhHHh
Q psy7268          70 IPTLLSGKS--AILVAETGCGKTLSF   93 (134)
Q Consensus        70 i~~~~~g~d--vli~a~tGsGKT~~~   93 (134)
                      +..++.|.|  ++..|.||||||...
T Consensus        66 v~~~~~G~n~~i~ayG~tgSGKT~Tm   91 (341)
T cd01372          66 VDGLFEGYNATVLAYGQTGSGKTYTM   91 (341)
T ss_pred             HHHHhCCCccceeeecCCCCCCcEEe
Confidence            344567876  788899999999875

Members of this group seem to perform a variety of functions, and have been implicated in neuronal organelle transport and chromosome segregation during mitosis. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus (N-type). N-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also, the neck linker binds to the motor domain,

>PF03215 Rad17: Rad17 cell cycle checkpoint protein

Probab=83.81  E-value=1.4  Score=36.63  Aligned_cols=16  Identities=38%  Similarity=0.750  Sum_probs=13.4

Q ss_pred             CeEEEcCCCCchhHHh
Q psy7268          78 SAILVAETGCGKTLSF   93 (134)
Q Consensus        78 dvli~a~tGsGKT~~~   93 (134)
                      =+++.||+|+|||.+.
T Consensus        47 iLlLtGP~G~GKtttv   62 (519)
T PF03215_consen   47 ILLLTGPSGCGKTTTV   62 (519)
T ss_pred             eEEEECCCCCCHHHHH
Confidence            3788999999999764

>cd03292 ABC_FtsE_transporter FtsE is a hydrophilic nucleotide-binding protein that binds FtsX to form a heterodimeric ATP-binding cassette (ABC)-type transporter that associates with the bacterial inner membrane

Probab=83.81  E-value=0.67  Score=33.18  Aligned_cols=18  Identities=33%  Similarity=0.577  Sum_probs=15.5

Q ss_pred             cCCCeEEEcCCCCchhHH
Q psy7268          75 SGKSAILVAETGCGKTLS   92 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~   92 (134)
                      .|.-+.+.|++|+|||..
T Consensus        26 ~G~~~~i~G~nGsGKSTL   43 (214)
T cd03292          26 AGEFVFLVGPSGAGKSTL   43 (214)
T ss_pred             CCCEEEEECCCCCCHHHH
Confidence            677889999999999953

The FtsE/X transporter is thought to be involved in cell division and is important for assembly or stability of the septal ring.

>cd03258 ABC_MetN_methionine_transporter MetN (also known as YusC) is an ABC-type transporter encoded by metN of the metNPQ operon in Bacillus subtilis that is involved in methionine transport

Probab=83.80  E-value=0.75  Score=33.46  Aligned_cols=20  Identities=20%  Similarity=0.370  Sum_probs=16.7

Q ss_pred             HHcCCCeEEEcCCCCchhHH
Q psy7268          73 LLSGKSAILVAETGCGKTLS   92 (134)
Q Consensus        73 ~~~g~dvli~a~tGsGKT~~   92 (134)
                      +..|.-+.+.|++|+|||..
T Consensus        28 i~~Ge~~~l~G~nGsGKSTL   47 (233)
T cd03258          28 VPKGEIFGIIGRSGAGKSTL   47 (233)
T ss_pred             EcCCCEEEEECCCCCCHHHH
Confidence            34688899999999999953

Other members of this system include the MetP permease and the MetQ substrate binding protein. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>KOG0732|consensus

Probab=83.75  E-value=1.1  Score=40.02  Aligned_cols=61  Identities=16%  Similarity=0.140  Sum_probs=39.0

Q ss_pred             ccccCCCCCCcccCCCCHHHHHHHHHCCC-CCChHHHHHHHHHHHcCCCeEEEcCCCCchhHH
Q psy7268          31 EAVSRIDLGTFEDTGLAPEIIDIFTKRGL-TTPTEIQKYSIPTLLSGKSAILVAETGCGKTLS   92 (134)
Q Consensus        31 ~~~~~~~~~~f~~~~l~~~i~~~l~~~g~-~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~   92 (134)
                      +....+..-.|++.|.-+..++.|+++-. ..++|-+..-+ .+.--+.++.++|+|+|||+.
T Consensus       254 dp~~~~~~v~fd~vggl~~~i~~LKEmVl~PLlyPE~f~~~-~itpPrgvL~~GppGTGkTl~  315 (1080)
T KOG0732|consen  254 DPLSVDSSVGFDSVGGLENYINQLKEMVLLPLLYPEFFDNF-NITPPRGVLFHGPPGTGKTLM  315 (1080)
T ss_pred             CchhhhcccCccccccHHHHHHHHHHHHHhHhhhhhHhhhc-ccCCCcceeecCCCCCchhHH
Confidence            33334555679999988999999988622 12222111111 123356799999999999976

>PRK14974 cell division protein FtsY; Provisional

Probab=83.70  E-value=3.8  Score=32.10  Aligned_cols=16  Identities=31%  Similarity=0.530  Sum_probs=13.6

Q ss_pred             CeEEEcCCCCchhHHh
Q psy7268          78 SAILVAETGCGKTLSF   93 (134)
Q Consensus        78 dvli~a~tGsGKT~~~   93 (134)
                      -+++.|++|+|||...
T Consensus       142 vi~~~G~~GvGKTTti  157 (336)
T PRK14974        142 VIVFVGVNGTGKTTTI  157 (336)
T ss_pred             EEEEEcCCCCCHHHHH
Confidence            3778999999999765

>PRK08506 replicative DNA helicase; Provisional

Probab=83.70  E-value=2.2  Score=34.93  Aligned_cols=26  Identities=27%  Similarity=0.345  Sum_probs=17.7

Q ss_pred             cCCCeEEEcCCCCchhHHhHHHHHHHH
Q psy7268          75 SGKSAILVAETGCGKTLSFLAPLVQQI  101 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~~lpil~~~  101 (134)
                      .|.=+++.|.+|.|||...+ -++..+
T Consensus       191 ~G~LivIaarpg~GKT~fal-~ia~~~  216 (472)
T PRK08506        191 KGDLIIIAARPSMGKTTLCL-NMALKA  216 (472)
T ss_pred             CCceEEEEcCCCCChHHHHH-HHHHHH
Confidence            34457889999999996554 444444

>PRK14737 gmk guanylate kinase; Provisional

Probab=83.67  E-value=0.83  Score=32.55  Aligned_cols=17  Identities=29%  Similarity=0.307  Sum_probs=14.1

Q ss_pred             CCCeEEEcCCCCchhHH
Q psy7268          76 GKSAILVAETGCGKTLS   92 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~   92 (134)
                      ++=++++||+|+||+..
T Consensus         4 ~~~ivl~GpsG~GK~tl   20 (186)
T PRK14737          4 PKLFIISSVAGGGKSTI   20 (186)
T ss_pred             CeEEEEECCCCCCHHHH
Confidence            45588999999999954

>KOG0737|consensus

Probab=83.65  E-value=1  Score=35.74  Aligned_cols=52  Identities=23%  Similarity=0.292  Sum_probs=31.2

Q ss_pred             CCcccCCCCHHHHHHHHHCCCCCChHHHHHHH----HHHHcCCCeEEEcCCCCchhHHh
Q psy7268          39 GTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSI----PTLLSGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        39 ~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i----~~~~~g~dvli~a~tGsGKT~~~   93 (134)
                      -+|.+.+=-+.+.+.+.+.=   .-|.|..=+    ..+..-+.+++.+|+|+|||+..
T Consensus        89 v~f~DIggLe~v~~~L~e~V---ilPlr~pelF~~g~Ll~p~kGiLL~GPpG~GKTmlA  144 (386)
T KOG0737|consen   89 VSFDDIGGLEEVKDALQELV---ILPLRRPELFAKGKLLRPPKGILLYGPPGTGKTMLA  144 (386)
T ss_pred             eehhhccchHHHHHHHHHHH---hhcccchhhhcccccccCCccceecCCCCchHHHHH
Confidence            36777776677777776631   111111111    11113457999999999999876

>TIGR03783 Bac_Flav_CT_G Bacteroides conjugation system ATPase, TraG family

Probab=83.62  E-value=2.4  Score=37.21  Aligned_cols=21  Identities=14%  Similarity=0.313  Sum_probs=16.4

Q ss_pred             CCCeEEEcCCCCchhHHhHHH
Q psy7268          76 GKSAILVAETGCGKTLSFLAP   96 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~~lp   96 (134)
                      ..+++|.|+||+|||...-.-
T Consensus       438 n~N~~I~G~sGsGKS~l~~~l  458 (829)
T TIGR03783       438 NRNKFILGPSGSGKSFFTNHL  458 (829)
T ss_pred             cCceEEECCCCCCHHHHHHHH
Confidence            457899999999999664333

Members of this family include the predicted ATPase, TraG, encoded by transfer region genes of conjugative transposons of Bacteroides, such as CTnDOT, found on the main chromosome. Members also include TraG homologs borne on plasmids in Bacteroides. The protein family is related to the conjugative transfer system ATPase VirB4.

>KOG0729|consensus

Probab=83.49  E-value=0.83  Score=35.23  Aligned_cols=53  Identities=25%  Similarity=0.268  Sum_probs=30.0

Q ss_pred             CCcccCCCCHHHHHHHHHC-CCCCChHHHHHHHHH-HHcCCCeEEEcCCCCchhHHh
Q psy7268          39 GTFEDTGLAPEIIDIFTKR-GLTTPTEIQKYSIPT-LLSGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        39 ~~f~~~~l~~~i~~~l~~~-g~~~~t~iQ~~~i~~-~~~g~dvli~a~tGsGKT~~~   93 (134)
                      .++++.+=..+-++.|++- ...-+.|  .+.... +---+.+++-+|+|+|||++.
T Consensus       174 vty~dvggckeqieklrevve~pll~p--erfv~lgidppkgvllygppgtgktl~a  228 (435)
T KOG0729|consen  174 VTYSDVGGCKEQIEKLREVVELPLLHP--ERFVNLGIDPPKGVLLYGPPGTGKTLCA  228 (435)
T ss_pred             cccccccchHHHHHHHHHHHhccccCH--HHHhhcCCCCCCceEEeCCCCCchhHHH
Confidence            4666777666666666552 1111122  111111 112356999999999999986

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=83.43  E-value=2.1  Score=33.98  Aligned_cols=20  Identities=25%  Similarity=0.506  Sum_probs=16.0

Q ss_pred             cCCCeEEEcCCCCchhHHhH
Q psy7268          75 SGKSAILVAETGCGKTLSFL   94 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~~   94 (134)
                      .|.-+++.+++|+|||...+
T Consensus        81 ~GslvLI~G~pG~GKStLll  100 (372)
T cd01121          81 PGSVILIGGDPGIGKSTLLL  100 (372)
T ss_pred             CCeEEEEEeCCCCCHHHHHH
Confidence            35568999999999996654

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.

>KOG0240|consensus

Probab=83.35  E-value=1.3  Score=36.98  Aligned_cols=32  Identities=28%  Similarity=0.405  Sum_probs=23.9

Q ss_pred             CChHHHHHHHHH--------HHcCCC--eEEEcCCCCchhHH
Q psy7268          61 TPTEIQKYSIPT--------LLSGKS--AILVAETGCGKTLS   92 (134)
Q Consensus        61 ~~t~iQ~~~i~~--------~~~g~d--vli~a~tGsGKT~~   92 (134)
                      .|+..|.++...        ++.|.+  |+..|+||+|||-.
T Consensus        58 ~pnatQe~Vy~~~a~~Iv~dVL~GYNGTvfaYGqT~sGKTyt   99 (607)
T KOG0240|consen   58 SPNATQEDVYEFAAKPIVDDVLLGYNGTVFAYGQTGSGKTYT   99 (607)
T ss_pred             CCCccHHHHHHHHHHHHHHHHhcccceeEEEecCCCCCccee
Confidence            777777766643        346776  88889999999965

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

Probab=83.34  E-value=1.5  Score=29.33  Aligned_cols=28  Identities=32%  Similarity=0.574  Sum_probs=18.1

Q ss_pred             HHcCCCeEEEcCCCCchhHHhHHHHHHHH
Q psy7268          73 LLSGKSAILVAETGCGKTLSFLAPLVQQI  101 (134)
Q Consensus        73 ~~~g~dvli~a~tGsGKT~~~~lpil~~~  101 (134)
                      +..|.=+++.|+-|+|||. |.=.++..+
T Consensus        12 l~~g~vi~L~GdLGaGKTt-f~r~l~~~l   39 (123)
T PF02367_consen   12 LKPGDVILLSGDLGAGKTT-FVRGLARAL   39 (123)
T ss_dssp             HSS-EEEEEEESTTSSHHH-HHHHHHHHT
T ss_pred             CCCCCEEEEECCCCCCHHH-HHHHHHHHc
Confidence            3345557889999999994 434444443

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.

>TIGR00174 miaA tRNA isopentenyltransferase (miaA)

Probab=83.24  E-value=0.95  Score=34.70  Aligned_cols=15  Identities=20%  Similarity=0.288  Sum_probs=12.8

Q ss_pred             eEEEcCCCCchhHHh
Q psy7268          79 AILVAETGCGKTLSF   93 (134)
Q Consensus        79 vli~a~tGsGKT~~~   93 (134)
                      +++.||||+|||...
T Consensus         2 i~i~G~t~~GKs~la   16 (287)
T TIGR00174         2 IFIMGPTAVGKSQLA   16 (287)
T ss_pred             EEEECCCCCCHHHHH
Confidence            578999999999654

Catalyzes the first step in the modification of an adenosine near the anticodon to 2-methylthio-N6-isopentyladenosine.

>PRK01184 hypothetical protein; Provisional

Probab=83.23  E-value=0.89  Score=31.81  Aligned_cols=16  Identities=25%  Similarity=0.073  Sum_probs=13.4

Q ss_pred             eEEEcCCCCchhHHhH
Q psy7268          79 AILVAETGCGKTLSFL   94 (134)
Q Consensus        79 vli~a~tGsGKT~~~~   94 (134)
                      +++.|++|||||...-
T Consensus         4 i~l~G~~GsGKsT~a~   19 (184)
T PRK01184          4 IGVVGMPGSGKGEFSK   19 (184)
T ss_pred             EEEECCCCCCHHHHHH
Confidence            6789999999998643

>PRK14721 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=83.16  E-value=3.3  Score=33.52  Aligned_cols=19  Identities=37%  Similarity=0.471  Sum_probs=15.6

Q ss_pred             CCCeEEEcCCCCchhHHhH
Q psy7268          76 GKSAILVAETGCGKTLSFL   94 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~~   94 (134)
                      |.-+.+.||||+|||....
T Consensus       191 g~vi~lvGpnG~GKTTtla  209 (420)
T PRK14721        191 GGVYALIGPTGVGKTTTTA  209 (420)
T ss_pred             CcEEEEECCCCCCHHHHHH
Confidence            4458899999999998764

>PF06414 Zeta_toxin: Zeta toxin; InterPro: IPR010488 This entry represents a domain originally identified in bacterial zeta toxin proteins, where it comprises the whole protein []

Probab=83.13  E-value=0.88  Score=32.47  Aligned_cols=16  Identities=25%  Similarity=0.387  Sum_probs=12.4

Q ss_pred             eEEEcCCCCchhHHhH
Q psy7268          79 AILVAETGCGKTLSFL   94 (134)
Q Consensus        79 vli~a~tGsGKT~~~~   94 (134)
                      +++.|++|+|||...-
T Consensus        18 ~i~aG~~GsGKSt~~~   33 (199)
T PF06414_consen   18 IIIAGQPGSGKSTLAR   33 (199)
T ss_dssp             EEEES-TTSTTHHHHH
T ss_pred             EEEeCCCCCCHHHHHH
Confidence            7888999999986653

It has subsequently been found in a number of other proteins, such as polynucleotide kinase and 2',3'-cyclic-nucleotide 3'-phosphodiesterase. It appears to function as a kinase domain [, ].; GO: 0005524 ATP binding, 0016301 kinase activity; PDB: 2P5T_H 1GVN_B 3Q8X_D.

>PHA00729 NTP-binding motif containing protein

Probab=83.13  E-value=0.94  Score=33.56  Aligned_cols=22  Identities=27%  Similarity=0.430  Sum_probs=16.3

Q ss_pred             CeEEEcCCCCchhHHhHHHHHHH
Q psy7268          78 SAILVAETGCGKTLSFLAPLVQQ  100 (134)
Q Consensus        78 dvli~a~tGsGKT~~~~lpil~~  100 (134)
                      ++++.|++|+|||... ..+...
T Consensus        19 nIlItG~pGvGKT~LA-~aLa~~   40 (226)
T PHA00729         19 SAVIFGKQGSGKTTYA-LKVARD   40 (226)
T ss_pred             EEEEECCCCCCHHHHH-HHHHHH
Confidence            7999999999999554 333333

>TIGR01166 cbiO cobalt transport protein ATP-binding subunit

Probab=83.06  E-value=0.85  Score=32.12  Aligned_cols=19  Identities=26%  Similarity=0.415  Sum_probs=16.1

Q ss_pred             HcCCCeEEEcCCCCchhHH
Q psy7268          74 LSGKSAILVAETGCGKTLS   92 (134)
Q Consensus        74 ~~g~dvli~a~tGsGKT~~   92 (134)
                      ..|.-+.+.|++|+|||..
T Consensus        16 ~~Ge~~~i~G~nGsGKSTL   34 (190)
T TIGR01166        16 ERGEVLALLGANGAGKSTL   34 (190)
T ss_pred             cCCCEEEEECCCCCCHHHH
Confidence            3677899999999999964

This model describes the ATP binding subunit of the multisubunit cobalt transporter in bacteria and its equivalents in archaea. The model is restricted to ATP subunit that is a part of the cobalt transporter, which belongs to the ABC transporter superfamily (ATP Binding Cassette). The model excludes ATP binding subunit that are associated with other transporters belonging to ABC transporter superfamily. This superfamily includes two groups, one which catalyze the uptake of small molecules, including ions from the external milieu and the other group which is engaged in the efflux of small molecular weight compounds and ions from within the cell. Energy derived from the hydrolysis of ATP drive the both the process of uptake and efflux.

>PRK05480 uridine/cytidine kinase; Provisional

Probab=83.04  E-value=0.95  Score=32.41  Aligned_cols=16  Identities=25%  Similarity=0.239  Sum_probs=13.2

Q ss_pred             CeEEEcCCCCchhHHh
Q psy7268          78 SAILVAETGCGKTLSF   93 (134)
Q Consensus        78 dvli~a~tGsGKT~~~   93 (134)
                      -+.+.|++|||||...
T Consensus         8 iI~I~G~sGsGKTTl~   23 (209)
T PRK05480          8 IIGIAGGSGSGKTTVA   23 (209)
T ss_pred             EEEEECCCCCCHHHHH
Confidence            4778999999999553

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

Probab=83.02  E-value=4.2  Score=24.33  Aligned_cols=15  Identities=27%  Similarity=0.399  Sum_probs=11.7

Q ss_pred             eEEEcCCCCchhHHh
Q psy7268          79 AILVAETGCGKTLSF   93 (134)
Q Consensus        79 vli~a~tGsGKT~~~   93 (134)
                      +++.+..|+|||...
T Consensus         2 ~~~~g~~G~Gktt~~   16 (99)
T cd01983           2 IVVTGKGGVGKTTLA   16 (99)
T ss_pred             EEEECCCCCCHHHHH
Confidence            456778899999764

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

>PF03237 Terminase_6: Terminase-like family; InterPro: IPR004921 The terminase is a component of the molecular motor that translocates genomic DNA into empty capsids during DNA packaging []

Probab=83.02  E-value=3.5  Score=31.29  Aligned_cols=24  Identities=25%  Similarity=0.232  Sum_probs=17.4

Q ss_pred             EEEcCCCCchhHHhHHHHHHHHHh
Q psy7268          80 ILVAETGCGKTLSFLAPLVQQILT  103 (134)
Q Consensus        80 li~a~tGsGKT~~~~lpil~~~~~  103 (134)
                      ++.++.|+|||....+-++.....
T Consensus         1 ~i~~~r~~GKT~~~~~~~~~~~~~   24 (384)
T PF03237_consen    1 LINGGRGSGKTTLIAIWFLWWALT   24 (384)
T ss_dssp             -EEE-SSS-HHHHHHHHHHHHHHS
T ss_pred             CCcCCccccHHHHHHHHHHHHHhh
Confidence            467899999999988877777765

The large subunit heterodimerises with the small terminase protein, which is docked on the capsid portal protein. The latter forms a ring through which genomic DNA is translocated into the capsid. The terminase protein may have or induce an endonuclease activity to cleave DNA after encapsidation. This entry represents a family of terminase large subunits found in a variety of the Caudovirales and prophage regions of bacterial genomes. Homologues are also found in Gene Transfer Agents (GTA) [], including ORFg2 (RCAP_rcc01683) of the GTA of Rhodobacter capsulatus (Rhodopseudomonas capsulata) [see Fig.1, in ].; PDB: 2O0K_A 3CPE_A 2O0J_A 2O0H_A 3C6H_A 3C6A_A.

>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=83.01  E-value=0.93  Score=31.41  Aligned_cols=19  Identities=21%  Similarity=0.389  Sum_probs=16.2

Q ss_pred             cCCCeEEEcCCCCchhHHh
Q psy7268          75 SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~   93 (134)
                      .|+-+++.+++|+|||...
T Consensus        13 ~g~gvLi~G~sG~GKStla   31 (149)
T cd01918          13 GGIGVLITGPSGIGKSELA   31 (149)
T ss_pred             CCEEEEEEcCCCCCHHHHH
Confidence            4678999999999999655

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.

>cd01125 repA Hexameric Replicative Helicase RepA

Probab=82.82  E-value=4.1  Score=29.84  Aligned_cols=22  Identities=32%  Similarity=0.379  Sum_probs=16.0

Q ss_pred             CeEEEcCCCCchhHHhHHHHHH
Q psy7268          78 SAILVAETGCGKTLSFLAPLVQ   99 (134)
Q Consensus        78 dvli~a~tGsGKT~~~~lpil~   99 (134)
                      -.++.||.|+|||...+--.+.
T Consensus         3 ~~ll~g~~G~GKS~lal~la~~   24 (239)
T cd01125           3 VSALVAPGGTGKSSLLLVLALA   24 (239)
T ss_pred             eeEEEcCCCCCHHHHHHHHHHH
Confidence            3578999999999776444333

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.

>cd01366 KISc_C_terminal Kinesin motor domain, KIFC2/KIFC3/ncd-like carboxy-terminal kinesins

Probab=82.81  E-value=1.3  Score=34.28  Aligned_cols=26  Identities=27%  Similarity=0.419  Sum_probs=20.3

Q ss_pred             HHHHHHHcCCC--eEEEcCCCCchhHHh
Q psy7268          68 YSIPTLLSGKS--AILVAETGCGKTLSF   93 (134)
Q Consensus        68 ~~i~~~~~g~d--vli~a~tGsGKT~~~   93 (134)
                      ..+..++.|.+  ++..|+||||||...
T Consensus        68 p~v~~~~~G~~~~i~ayG~tgSGKT~tl   95 (329)
T cd01366          68 PLVQSALDGYNVCIFAYGQTGSGKTYTM   95 (329)
T ss_pred             HHHHHHhCCCceEEEEeCCCCCCCcEEe
Confidence            34556678887  778899999999765

Ncd is a spindle motor protein necessary for chromosome segregation in meiosis. KIFC2/KIFC3-like kinesins have been implicated in motility of the Golgi apparatus as well as dentritic and axonal transport in neurons. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In this subgroup the motor domain is found at the C-terminus (C-type). C-type kinesins are (-) end-directed motors, i.e. they transport cargo towards the (-) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for mi

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=82.78  E-value=2.4  Score=35.14  Aligned_cols=18  Identities=33%  Similarity=0.318  Sum_probs=15.3

Q ss_pred             CeEEEcCCCCchhHHhHH
Q psy7268          78 SAILVAETGCGKTLSFLA   95 (134)
Q Consensus        78 dvli~a~tGsGKT~~~~l   95 (134)
                      .++++||.|+|||....+
T Consensus        45 a~Lf~Gp~G~GKTT~Ari   62 (507)
T PRK06645         45 GYLLTGIRGVGKTTSARI   62 (507)
T ss_pred             eEEEECCCCCCHHHHHHH
Confidence            589999999999987643

>TIGR00665 DnaB replicative DNA helicase

Probab=82.77  E-value=2.7  Score=33.65  Aligned_cols=26  Identities=23%  Similarity=0.224  Sum_probs=17.8

Q ss_pred             cCCCeEEEcCCCCchhHHhHHHHHHHH
Q psy7268          75 SGKSAILVAETGCGKTLSFLAPLVQQI  101 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~~lpil~~~  101 (134)
                      .|.=+++.|++|+|||... +-++..+
T Consensus       194 ~G~l~vi~g~pg~GKT~~~-l~~a~~~  219 (434)
T TIGR00665       194 PSDLIILAARPSMGKTAFA-LNIAENA  219 (434)
T ss_pred             CCeEEEEEeCCCCChHHHH-HHHHHHH
Confidence            3445788999999999554 4444443

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.

>COG1074 RecB ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains) [DNA replication, recombination, and repair]

Probab=82.77  E-value=2.4  Score=38.40  Aligned_cols=50  Identities=22%  Similarity=0.344  Sum_probs=36.9

Q ss_pred             cCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHH
Q psy7268          75 SGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQ  131 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Q  131 (134)
                      .+.+++|.|.-|||||.+..-=++..+....       ...-.+.|+|+-|+.=+.-
T Consensus        15 ~~~~~lveASAGSGKT~vL~~r~lrlLl~~~-------~~~v~~ILvvTFT~aAa~E   64 (1139)
T COG1074          15 PGQSVLVEASAGTGKTFVLAERVLRLLLEGG-------PLDVDEILVVTFTKAAAAE   64 (1139)
T ss_pred             CCCcEEEEEcCCCCchhHHHHHHHHHHhhcC-------CCChhHeeeeeccHHHHHH
Confidence            5679999999999999998777777776531       0123468899988865543

>COG0324 MiaA tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]

Probab=82.77  E-value=0.99  Score=34.99  Aligned_cols=22  Identities=23%  Similarity=0.371  Sum_probs=15.7

Q ss_pred             eEEEcCCCCchhHHhHHHHHHHH
Q psy7268          79 AILVAETGCGKTLSFLAPLVQQI  101 (134)
Q Consensus        79 vli~a~tGsGKT~~~~lpil~~~  101 (134)
                      +++.|||++|||-.. +-+.+.+
T Consensus         6 i~I~GPTAsGKT~la-i~LAk~~   27 (308)
T COG0324           6 IVIAGPTASGKTALA-IALAKRL   27 (308)
T ss_pred             EEEECCCCcCHHHHH-HHHHHHc
Confidence            688999999999543 4444443

>KOG0742|consensus

Probab=82.74  E-value=0.74  Score=37.48  Aligned_cols=49  Identities=16%  Similarity=0.236  Sum_probs=29.1

Q ss_pred             CCcccCCCCHHHHHHHHHCCCC-CChHHHHHHHHHHHcCCCeEEEcCCCCchhHHh
Q psy7268          39 GTFEDTGLAPEIIDIFTKRGLT-TPTEIQKYSIPTLLSGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        39 ~~f~~~~l~~~i~~~l~~~g~~-~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~   93 (134)
                      .-|++.-|++.+-+.+.++-.. .-|.-.+      ---+|++..+|+|+|||+..
T Consensus       352 ~pl~~ViL~psLe~Rie~lA~aTaNTK~h~------apfRNilfyGPPGTGKTm~A  401 (630)
T KOG0742|consen  352 DPLEGVILHPSLEKRIEDLAIATANTKKHQ------APFRNILFYGPPGTGKTMFA  401 (630)
T ss_pred             CCcCCeecCHHHHHHHHHHHHHhccccccc------chhhheeeeCCCCCCchHHH
Confidence            3466666777777666653211 1011000      01268999999999999875

>PF02463 SMC_N: RecF/RecN/SMC N terminal domain; InterPro: IPR003395 This domain is found at the N terminus of structural maintenance of chromosomes (SMC) proteins, which function together with other proteins in a range of chromosomal transactions, including chromosome condensation, sister-chromatid cohesion, recombination, DNA repair and epigenetic silencing of gene expression []

Probab=82.62  E-value=0.99  Score=32.47  Aligned_cols=17  Identities=24%  Similarity=0.423  Sum_probs=13.7

Q ss_pred             CCeEEEcCCCCchhHHh
Q psy7268          77 KSAILVAETGCGKTLSF   93 (134)
Q Consensus        77 ~dvli~a~tGsGKT~~~   93 (134)
                      .-.++.||+|+|||..+
T Consensus        25 ~~~~i~G~NGsGKS~il   41 (220)
T PF02463_consen   25 GLNVIVGPNGSGKSNIL   41 (220)
T ss_dssp             SEEEEEESTTSSHHHHH
T ss_pred             CCEEEEcCCCCCHHHHH
Confidence            34788999999999654

The domain is also found in RecF and RecN proteins, which are involved in DNA metabolism and recombination.; PDB: 3HTK_A 1W1W_C 2WD5_A 3L51_A 1XEW_Y 3KTA_B 3NWC_B 1XEX_A 1GXL_C 1GXK_A ....

>cd03269 ABC_putative_ATPase This subfamily is involved in drug resistance, nodulation, lipid transport, and bacteriocin and lantibiotic immunity

Probab=82.59  E-value=0.79  Score=32.77  Aligned_cols=19  Identities=32%  Similarity=0.394  Sum_probs=15.9

Q ss_pred             HcCCCeEEEcCCCCchhHH
Q psy7268          74 LSGKSAILVAETGCGKTLS   92 (134)
Q Consensus        74 ~~g~dvli~a~tGsGKT~~   92 (134)
                      ..|.-+.+.|++|+|||.-
T Consensus        24 ~~G~~~~i~G~nGsGKSTL   42 (210)
T cd03269          24 EKGEIFGLLGPNGAGKTTT   42 (210)
T ss_pred             cCCcEEEEECCCCCCHHHH
Confidence            3677789999999999954

In eubacteria and archaea, the typical organization consists of one ABC and one or two IMs. Eukaryote systems of the ABCA subfamily display ABC domains strongly similar to this family. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region in addition to the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>TIGR01425 SRP54_euk signal recognition particle protein SRP54

Probab=82.57  E-value=2.6  Score=34.21  Aligned_cols=15  Identities=33%  Similarity=0.516  Sum_probs=13.1

Q ss_pred             eEEEcCCCCchhHHh
Q psy7268          79 AILVAETGCGKTLSF   93 (134)
Q Consensus        79 vli~a~tGsGKT~~~   93 (134)
                      ++++|++|+|||...
T Consensus       103 i~lvG~~GvGKTTta  117 (429)
T TIGR01425       103 IMFVGLQGSGKTTTC  117 (429)
T ss_pred             EEEECCCCCCHHHHH
Confidence            788999999998764

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.

>cd03238 ABC_UvrA The excision repair protein UvrA; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion

Probab=82.56  E-value=1.1  Score=31.62  Aligned_cols=20  Identities=15%  Similarity=0.190  Sum_probs=16.5

Q ss_pred             cCCCeEEEcCCCCchhHHhH
Q psy7268          75 SGKSAILVAETGCGKTLSFL   94 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~~   94 (134)
                      .|.-+.+.+|+|+|||..+-
T Consensus        20 ~G~~~~l~G~nG~GKSTLl~   39 (176)
T cd03238          20 LNVLVVVTGVSGSGKSTLVN   39 (176)
T ss_pred             CCCEEEEECCCCCCHHHHHH
Confidence            56678899999999997653

Recognition and cleavage of the damaged DNA is a multistep ATP-dependent reaction that requires the UvrA, UvrB, and UvrC proteins. Both UvrA and UvrB are ATPases, with UvrA having two ATP binding sites, which have the characteristic signature of the family of ABC proteins, and UvrB having one ATP binding site that is structurally related to that of helicases.

>PRK14532 adenylate kinase; Provisional

Probab=82.49  E-value=0.98  Score=31.71  Aligned_cols=16  Identities=25%  Similarity=0.297  Sum_probs=13.6

Q ss_pred             CeEEEcCCCCchhHHh
Q psy7268          78 SAILVAETGCGKTLSF   93 (134)
Q Consensus        78 dvli~a~tGsGKT~~~   93 (134)
                      ++++.|++|||||...
T Consensus         2 ~i~~~G~pGsGKsT~a   17 (188)
T PRK14532          2 NLILFGPPAAGKGTQA   17 (188)
T ss_pred             EEEEECCCCCCHHHHH
Confidence            4789999999999664

>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=82.46  E-value=1.3  Score=32.95  Aligned_cols=22  Identities=27%  Similarity=0.501  Sum_probs=16.0

Q ss_pred             EEcCCCCchhHHhHHHHHHHHHh
Q psy7268          81 LVAETGCGKTLSFLAPLVQQILT  103 (134)
Q Consensus        81 i~a~tGsGKT~~~~lpil~~~~~  103 (134)
                      |.||.||||| .|+-.+-+++..
T Consensus         1 ViGpaGSGKT-T~~~~~~~~~~~   22 (238)
T PF03029_consen    1 VIGPAGSGKT-TFCKGLSEWLES   22 (238)
T ss_dssp             -EESTTSSHH-HHHHHHHHHHTT
T ss_pred             CCCCCCCCHH-HHHHHHHHHHHh
Confidence            5799999998 676776666643

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

>cd01364 KISc_BimC_Eg5 Kinesin motor domain, BimC/Eg5 spindle pole proteins, participate in spindle assembly and chromosome segregation during cell division

Probab=82.44  E-value=1.1  Score=34.90  Aligned_cols=24  Identities=29%  Similarity=0.500  Sum_probs=18.0

Q ss_pred             HHHHHcCCC--eEEEcCCCCchhHHh
Q psy7268          70 IPTLLSGKS--AILVAETGCGKTLSF   93 (134)
Q Consensus        70 i~~~~~g~d--vli~a~tGsGKT~~~   93 (134)
                      +..++.|.|  ++.-|.||||||.+.
T Consensus        74 v~~~~~G~n~~i~ayG~tgSGKTyTl   99 (352)
T cd01364          74 LDEVLMGYNCTIFAYGQTGTGKTYTM   99 (352)
T ss_pred             HHHHhCCCeEEEEECCCCCCCCcEEe
Confidence            334567887  677799999999653

This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus (N-type), N-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also, the neck linker binds to the motor domain, which repositions the other head domain through the coiled-coil d

>PRK06217 hypothetical protein; Validated

Probab=82.42  E-value=1  Score=31.61  Aligned_cols=16  Identities=19%  Similarity=0.187  Sum_probs=13.3

Q ss_pred             CeEEEcCCCCchhHHh
Q psy7268          78 SAILVAETGCGKTLSF   93 (134)
Q Consensus        78 dvli~a~tGsGKT~~~   93 (134)
                      .|++.|.+|||||...
T Consensus         3 ~I~i~G~~GsGKSTla   18 (183)
T PRK06217          3 RIHITGASGSGTTTLG   18 (183)
T ss_pred             EEEEECCCCCCHHHHH
Confidence            3789999999999653

>cd02023 UMPK Uridine monophosphate kinase (UMPK, EC 2

Probab=82.41  E-value=0.99  Score=31.99  Aligned_cols=15  Identities=27%  Similarity=0.295  Sum_probs=12.3

Q ss_pred             eEEEcCCCCchhHHh
Q psy7268          79 AILVAETGCGKTLSF   93 (134)
Q Consensus        79 vli~a~tGsGKT~~~   93 (134)
                      +.+.|++|||||...
T Consensus         2 igi~G~~GsGKSTl~   16 (198)
T cd02023           2 IGIAGGSGSGKTTVA   16 (198)
T ss_pred             EEEECCCCCCHHHHH
Confidence            467899999999663

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.

>TIGR02673 FtsE cell division ATP-binding protein FtsE

Probab=82.40  E-value=0.94  Score=32.44  Aligned_cols=20  Identities=30%  Similarity=0.438  Sum_probs=16.7

Q ss_pred             HcCCCeEEEcCCCCchhHHh
Q psy7268          74 LSGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        74 ~~g~dvli~a~tGsGKT~~~   93 (134)
                      ..|.-+.+.|++|+|||..+
T Consensus        26 ~~G~~~~l~G~nGsGKSTLl   45 (214)
T TIGR02673        26 RKGEFLFLTGPSGAGKTTLL   45 (214)
T ss_pred             cCCCEEEEECCCCCCHHHHH
Confidence            46778899999999999654

This model describes FtsE, a member of the ABC transporter ATP-binding protein family. This protein, and its permease partner FtsX, localize to the division site. In a number of species, the ftsEX gene pair is located next to FtsY, the signal recognition particle-docking protein.

>COG3839 MalK ABC-type sugar transport systems, ATPase components [Carbohydrate transport and metabolism]

Probab=82.40  E-value=1  Score=35.39  Aligned_cols=19  Identities=32%  Similarity=0.688  Sum_probs=16.1

Q ss_pred             HcCCCeEEEcCCCCchhHH
Q psy7268          74 LSGKSAILVAETGCGKTLS   92 (134)
Q Consensus        74 ~~g~dvli~a~tGsGKT~~   92 (134)
                      ..|.-+.+.||+|+|||..
T Consensus        27 ~~Gef~vllGPSGcGKSTl   45 (338)
T COG3839          27 EDGEFVVLLGPSGCGKSTL   45 (338)
T ss_pred             cCCCEEEEECCCCCCHHHH
Confidence            3677799999999999965

>cd03259 ABC_Carb_Solutes_like ABC Carbohydrate and Solute Transporters-like subgroup

Probab=82.26  E-value=0.93  Score=32.48  Aligned_cols=20  Identities=35%  Similarity=0.615  Sum_probs=16.4

Q ss_pred             HcCCCeEEEcCCCCchhHHh
Q psy7268          74 LSGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        74 ~~g~dvli~a~tGsGKT~~~   93 (134)
                      ..|.-+.+.|++|+|||...
T Consensus        24 ~~Ge~~~i~G~nGsGKSTLl   43 (213)
T cd03259          24 EPGEFLALLGPSGCGKTTLL   43 (213)
T ss_pred             cCCcEEEEECCCCCCHHHHH
Confidence            36778899999999999543

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

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

Probab=82.26  E-value=1  Score=28.96  Aligned_cols=23  Identities=22%  Similarity=0.306  Sum_probs=15.7

Q ss_pred             eEEEcCCCCchhHHhHHHHHHHHH
Q psy7268          79 AILVAETGCGKTLSFLAPLVQQIL  102 (134)
Q Consensus        79 vli~a~tGsGKT~~~~lpil~~~~  102 (134)
                      |.+.|++|.|||...- .++..+.
T Consensus         1 I~i~G~~G~GKS~l~~-~l~~~l~   23 (107)
T PF00910_consen    1 IWIYGPPGIGKSTLAK-ELAKDLL   23 (107)
T ss_pred             CEEECCCCCCHHHHHH-HHHHHHH
Confidence            4678999999997753 3344443

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

>TIGR01547 phage_term_2 phage terminase, large subunit, PBSX family

Probab=82.23  E-value=4.1  Score=32.15  Aligned_cols=40  Identities=20%  Similarity=0.175  Sum_probs=31.1

Q ss_pred             eEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHH
Q psy7268          79 AILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRE  127 (134)
Q Consensus        79 vli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~  127 (134)
                      .++.|..|||||.+..+-++..+....         .+.+++++.++..
T Consensus         4 ~i~~GgrgSGKS~~~~~~~~~~~~~~~---------~~~~~~~~r~~~~   43 (396)
T TIGR01547         4 IIAKGGRRSGKTFAIALKLVEKLAINK---------KQQNILAARKVQN   43 (396)
T ss_pred             EEEeCCCCcccHHHHHHHHHHHHHhcC---------CCcEEEEEehhhh
Confidence            578899999999999888888877631         3456888877765

This model detects members of a highly divergent family of the large subunit of phage terminase. All members are encoded by phage genomes or within prophage regions of bacterial genomes. This is a distinct family from pfam03354.

>PLN02199 shikimate kinase

Probab=82.22  E-value=1.7  Score=33.66  Aligned_cols=23  Identities=39%  Similarity=0.455  Sum_probs=19.2

Q ss_pred             HHHHcCCCeEEEcCCCCchhHHh
Q psy7268          71 PTLLSGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        71 ~~~~~g~dvli~a~tGsGKT~~~   93 (134)
                      -..+.|+++++.|.+|+|||...
T Consensus        97 ~~~l~~~~I~LIG~~GSGKSTVg  119 (303)
T PLN02199         97 KPYLNGRSMYLVGMMGSGKTTVG  119 (303)
T ss_pred             HHHcCCCEEEEECCCCCCHHHHH
Confidence            34557899999999999999774

>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=82.13  E-value=0.98  Score=28.83  Aligned_cols=13  Identities=31%  Similarity=0.703  Sum_probs=11.6

Q ss_pred             eEEEcCCCCchhH
Q psy7268          79 AILVAETGCGKTL   91 (134)
Q Consensus        79 vli~a~tGsGKT~   91 (134)
                      +++.|+.|+|||.
T Consensus         2 I~V~G~~g~GKTs   14 (119)
T PF08477_consen    2 IVVLGDSGVGKTS   14 (119)
T ss_dssp             EEEECSTTSSHHH
T ss_pred             EEEECcCCCCHHH
Confidence            6889999999993

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.

>TIGR01817 nifA Nif-specific regulatory protein

Probab=82.10  E-value=1.7  Score=35.90  Aligned_cols=19  Identities=37%  Similarity=0.534  Sum_probs=16.4

Q ss_pred             cCCCeEEEcCCCCchhHHh
Q psy7268          75 SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~   93 (134)
                      .+..|++.|++|+||+...
T Consensus       218 ~~~pvli~Ge~GtGK~~lA  236 (534)
T TIGR01817       218 SNSTVLLRGESGTGKELIA  236 (534)
T ss_pred             cCCCEEEECCCCccHHHHH
Confidence            5668999999999999764

This model represents NifA, a DNA-binding regulatory protein for nitrogen fixation. The model produces scores between the trusted and noise cutoffs for a well-described NifA homolog in Aquifex aeolicus (which lacks nitrogenase), for transcriptional activators of alternative nitrogenases (VFe or FeFe instead of MoFe), and truncated forms.

>PRK13721 conjugal transfer ATP-binding protein TraC; Provisional

Probab=81.99  E-value=2.6  Score=36.94  Aligned_cols=24  Identities=25%  Similarity=0.457  Sum_probs=17.8

Q ss_pred             CCeEEEcCCCCchhHHhHHHHHHHH
Q psy7268          77 KSAILVAETGCGKTLSFLAPLVQQI  101 (134)
Q Consensus        77 ~dvli~a~tGsGKT~~~~lpil~~~  101 (134)
                      .+++|.|+||+|||...- .++...
T Consensus       450 ~N~~I~G~sGsGKS~l~k-~l~~~~  473 (844)
T PRK13721        450 YNMAVCGTSGAGKTGLIQ-PLIRSV  473 (844)
T ss_pred             ccEEEEcCCCCCHHHHHH-HHHHhh
Confidence            479999999999997653 444444

>PRK10247 putative ABC transporter ATP-binding protein YbbL; Provisional

Probab=81.96  E-value=0.98  Score=32.80  Aligned_cols=20  Identities=25%  Similarity=0.644  Sum_probs=16.6

Q ss_pred             HcCCCeEEEcCCCCchhHHh
Q psy7268          74 LSGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        74 ~~g~dvli~a~tGsGKT~~~   93 (134)
                      ..|.-+.+.||+|+|||.-+
T Consensus        31 ~~Ge~~~i~G~nGsGKSTLl   50 (225)
T PRK10247         31 RAGEFKLITGPSGCGKSTLL   50 (225)
T ss_pred             cCCCEEEEECCCCCCHHHHH
Confidence            36788999999999999643

>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional

Probab=81.92  E-value=2  Score=36.68  Aligned_cols=19  Identities=37%  Similarity=0.592  Sum_probs=16.0

Q ss_pred             cCCCeEEEcCCCCchhHHh
Q psy7268          75 SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~   93 (134)
                      .+..|+|.|++|+|||...
T Consensus       398 ~~~pVLI~GE~GTGK~~lA  416 (686)
T PRK15429        398 SDSTVLILGETGTGKELIA  416 (686)
T ss_pred             CCCCEEEECCCCcCHHHHH
Confidence            4568999999999999754

>TIGR02562 cas3_yersinia CRISPR-associated helicase Cas3

Probab=81.84  E-value=3.2  Score=37.39  Aligned_cols=61  Identities=26%  Similarity=0.235  Sum_probs=38.7

Q ss_pred             hHHHHHHHHHHHc--------CCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          63 TEIQKYSIPTLLS--------GKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        63 t~iQ~~~i~~~~~--------g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      ...|-.|+..+..        |--++-.|.||+|||++= .=|+..+...         ..++|..|-.-.|.|..|.+
T Consensus       410 F~WQdkA~d~a~~~r~~~~~~GfF~vNMASTGcGKT~aN-ARImyaLsd~---------~~g~RfsiALGLRTLTLQTG  478 (1110)
T TIGR02562       410 FRWQNKAFNLAQKLRQKSPEQGAFGVNMASTGCGKTLAN-ARAMYALRDD---------KQGARFAIALGLRSLTLQTG  478 (1110)
T ss_pred             cchHHHHHHHHHHHHhhcccCCeEEEEecCCCcchHHHH-HHHHHHhCCC---------CCCceEEEEccccceeccch
Confidence            4589999987663        333566699999999874 2233333221         25667777667777766643

The helicase in many CRISPR-associated (cas) gene clusters is designated Cas3, and most Cas3 proteins are described by model TIGR01587. Members of this family are considerably larger, show a number of motifs in common with TIGR01587 sequences, and replace Cas3 in some CRISPR/cas loci in a number of Proteobacteria, including Yersinia pestis, Chromobacterium violaceum, Erwinia carotovora subsp. atroseptica SCRI1043, Photorhabdus luminescens subsp. laumondii TTO1, Legionella pneumophila, etc.

---

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	134
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	3e-26
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	7e-26
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	1e-25
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	1e-24
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	3e-24
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	3e-23
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	4e-23
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	6e-23
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	2e-21
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	3e-21
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	5e-21
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	1e-20
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	2e-20
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	2e-20
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	9e-20
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	2e-19
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	5e-19
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	7e-19
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	1e-18
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	2e-18
3bor_A	237	Human initiation factor 4A-II; translation initiat	4e-18
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	7e-18
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	1e-17
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	2e-17
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	2e-17
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	2e-15
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	2e-15
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	4e-15
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	4e-15
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	6e-15
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	9e-12
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	1e-04
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	2e-04
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	4e-04
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	5e-04

>1wrb_A DJVLGB; RNA helicase, DEAD BOX, VASA, structural genomics, NPPSFA, N project on protein structural and functional analyses; 2.40A {Dugesia japonica} SCOP: c.37.1.19 Length = 253

 Score = 97.6 bits (244), Expect = 3e-26
 Identities = 30/95 (31%), Positives = 46/95 (48%)

Query: 40  TFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQ 99
            F++  L P I +         PT IQK +IP +L  +  +  A+TG GKT +FL P++ 
Sbjct: 24  NFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIIN 83

Query: 100 QILTWKSRPEYKPELNAPLALIITPGRELVFQIGQ 134
            ++      +   +   P  LI+ P REL  QI  
Sbjct: 84  HLVCQDLNQQRYSKTAYPKCLILAPTRELAIQILS 118

>3iuy_A Probable ATP-dependent RNA helicase DDX53; REC-A-like, DEAD-BOX, structural genomics, structural genomi consortium, SGC, ATP-binding, hydrolase; HET: AMP; 2.40A {Homo sapiens} Length = 228

 Score = 96.1 bits (240), Expect = 7e-26
 Identities = 33/96 (34%), Positives = 51/96 (53%), Gaps = 4/96 (4%)

Query: 40  TFEDT-GLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLV 98
            F+D     P+++    + G+  PT IQ  + P +L G   I+VA+TG GKTLS+L P  
Sbjct: 20  RFKDAFQQYPDLLKSIIRVGILKPTPIQSQAWPIILQGIDLIVVAQTGTGKTLSYLMPGF 79

Query: 99  QQILTWKSRPEYKPELNAPLALIITPGRELVFQIGQ 134
             +    S+P  + + N P  L++TP REL   +  
Sbjct: 80  IHLD---SQPISREQRNGPGMLVLTPTRELALHVEA 112

>3fe2_A Probable ATP-dependent RNA helicase DDX5; DEAD, ADP, ATP-binding, hydrolase, nucleotide- RNA-binding, methylation, mRNA processing, mRNA S nucleus; HET: ADP; 2.60A {Homo sapiens} Length = 242

 Score = 95.7 bits (239), Expect = 1e-25
 Identities = 32/95 (33%), Positives = 49/95 (51%), Gaps = 4/95 (4%)

Query: 40  TFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQ 99
            F +      ++D+  ++  T PT IQ    P  LSG   + VA+TG GKTLS+L P + 
Sbjct: 30  NFYEANFPANVMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLLPAIV 89

Query: 100 QILTWKSRPEYKPELNAPLALIITPGRELVFQIGQ 134
            I     +P  +   + P+ L++ P REL  Q+ Q
Sbjct: 90  HIN---HQPFLERG-DGPICLVLAPTRELAQQVQQ 120

>2db3_A ATP-dependent RNA helicase VASA; DEAD-BOX, protein-RNA complex, ATPase, riken structural genomics/proteomics initiative, RSGI; HET: ANP; 2.20A {Drosophila melanogaster} Length = 434

 Score = 96.1 bits (240), Expect = 1e-24
 Identities = 35/93 (37%), Positives = 47/93 (50%), Gaps = 4/93 (4%)

Query: 40  TFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQ 99
            F    L   IID   K G   PT IQK SIP + SG+  +  A+TG GKT +FL P++ 
Sbjct: 57  HFTSADLRDIIIDNVNKSGYKIPTPIQKCSIPVISSGRDLMACAQTGSGKTAAFLLPILS 116

Query: 100 QILTWKSRPEYKPELNAPLALIITPGRELVFQI 132
           ++L              P  +I++P REL  QI
Sbjct: 117 KLLE-DPHELELGR---PQVVIVSPTRELAIQI 145

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens} Length = 417

 Score = 94.9 bits (237), Expect = 3e-24
 Identities = 31/102 (30%), Positives = 48/102 (47%), Gaps = 9/102 (8%)

Query: 40  TFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQ 99
           +F D  +   I+        T PT +QK++IP +   +  +  A+TG GKT +FL P++ 
Sbjct: 16  SFSDVEMGEIIMGNIELTRYTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLLPILS 75

Query: 100 QIL---------TWKSRPEYKPELNAPLALIITPGRELVFQI 132
           QI            K    Y      P++L++ P REL  QI
Sbjct: 76  QIYSDGPGEALRAMKENGRYGRRKQYPISLVLAPTRELAVQI 117

>3dkp_A Probable ATP-dependent RNA helicase DDX52; DEAD, ADP, structural genomics, structural GEN consortium, SGC, rRNA, ATP-binding, hydrolase; HET: ADP; 2.10A {Homo sapiens} Length = 245

 Score = 89.6 bits (223), Expect = 3e-23
 Identities = 32/101 (31%), Positives = 48/101 (47%), Gaps = 12/101 (11%)

Query: 38  LGTFEDT----GLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSF 93
           + TF+       +   ++      G   PT IQ  +IP +L G+  +  A TG GKTL+F
Sbjct: 24  IATFQQLDQEYKINSRLLQNILDAGFQMPTPIQMQAIPVMLHGRELLASAPTGSGKTLAF 83

Query: 94  LAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIGQ 134
             P++ Q+         +P      ALII+P REL  QI +
Sbjct: 84  SIPILMQLK--------QPANKGFRALIISPTRELASQIHR 116

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens} Length = 236

 Score = 89.2 bits (222), Expect = 4e-23
 Identities = 32/105 (30%), Positives = 53/105 (50%), Gaps = 5/105 (4%)

Query: 30  YEAVSRIDLGTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGK 89
           YE ++  ++  F D  L+ + +    +      TEIQK +I   L GK  +  A+TG GK
Sbjct: 16  YEKINVNEITRFSDFPLSKKTLKGLQEAQYRLVTEIQKQTIGLALQGKDVLGAAKTGSGK 75

Query: 90  TLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIGQ 134
           TL+FL P+++ +   +         +    LII+P REL +Q  +
Sbjct: 76  TLAFLVPVLEALYRLQWTST-----DGLGVLIISPTRELAYQTFE 115

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19 Length = 219

 Score = 88.4 bits (220), Expect = 6e-23
 Identities = 33/95 (34%), Positives = 46/95 (48%), Gaps = 9/95 (9%)

Query: 40  TFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQ 99
            F      P II+         PTEIQ+  IP  L G+S +  ++TG GKT ++L P+++
Sbjct: 5   QFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIME 64

Query: 100 QILTWKSRPEYKPELNAPLALIITPGRELVFQIGQ 134
           +I         KPE     A+I  P REL  QI  
Sbjct: 65  KI---------KPERAEVQAVITAPTRELATQIYH 90

>3ber_A Probable ATP-dependent RNA helicase DDX47; DEAD, AMP, structural genomics, structural GEN consortium, SGC, ATP-binding, hydrolase; HET: AMP PGE; 1.40A {Homo sapiens} Length = 249

 Score = 85.0 bits (211), Expect = 2e-21
 Identities = 36/95 (37%), Positives = 52/95 (54%), Gaps = 9/95 (9%)

Query: 40  TFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQ 99
           TF+D G+   + +   + G T PT+IQ  +IP  L G+  I +AETG GKT +F  P++ 
Sbjct: 44  TFKDLGVTDVLCEACDQLGWTKPTKIQIEAIPLALQGRDIIGLAETGSGKTGAFALPILN 103

Query: 100 QILTWKSRPEYKPELNAPLALIITPGRELVFQIGQ 134
            +L    R           AL++TP REL FQI +
Sbjct: 104 ALLETPQRLF---------ALVLTPTRELAFQISE 129

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C} Length = 579

 Score = 86.8 bits (215), Expect = 3e-21
 Identities = 29/95 (30%), Positives = 45/95 (47%), Gaps = 7/95 (7%)

Query: 40  TFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSA--ILVAETGCGKTLSFLAPL 97
             E+  L  EI    T+      T +Q+ +I  +LS +    I  A+TG GKT +FL P+
Sbjct: 22  LLEEGVLDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPI 81

Query: 98  VQQILTWKSRPEYKPELNAPLALIITPGRELVFQI 132
            Q ++  K   +         A+I+ P R+L  QI
Sbjct: 82  FQHLINTKFDSQ-----YMVKAVIVAPTRDLALQI 111

>3i5x_A ATP-dependent RNA helicase MSS116; protein-RNA complex, RNA helicase, DEAD-BOX, ATP-binding, HE hydrolase, mitochondrion; HET: ANP; 1.90A {Saccharomyces cerevisiae} PDB: 3i5y_A* 3i61_A* 3i62_A* 3sqx_A* Length = 563

 Score = 86.4 bits (214), Expect = 5e-21
 Identities = 28/95 (29%), Positives = 46/95 (48%), Gaps = 7/95 (7%)

Query: 40  TFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILV--AETGCGKTLSFLAPL 97
             E+  L  EI    T+      T +Q+ +I  +LS +   ++  A+TG GKT +FL P+
Sbjct: 73  LLEEGVLDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPI 132

Query: 98  VQQILTWKSRPEYKPELNAPLALIITPGRELVFQI 132
            Q ++  K   +         A+I+ P R+L  QI
Sbjct: 133 FQHLINTKFDSQ-----YMVKAVIVAPTRDLALQI 162

>3ly5_A ATP-dependent RNA helicase DDX18; alpha-beta, structural genomics, structural genomics consort ATP-binding, hydrolase, nucleotide-binding, RNA-B; 2.80A {Homo sapiens} Length = 262

 Score = 83.1 bits (206), Expect = 1e-20
 Identities = 33/97 (34%), Positives = 46/97 (47%), Gaps = 7/97 (7%)

Query: 40  TFED--TGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPL 97
           +F      +    +    + G T  TEIQ  SI  LL G+  +  A+TG GKTL+FL P 
Sbjct: 53  SFASLCNLVNENTLKAIKEMGFTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPA 112

Query: 98  VQQILTWKSRPEYKPELNAPLALIITPGRELVFQIGQ 134
           V+ I+  +  P      N    LI++P REL  Q   
Sbjct: 113 VELIVKLRFMPR-----NGTGVLILSPTRELAMQTFG 144

>2gxq_A Heat resistant RNA dependent ATPase; RNA helicase, atomic resolution, AMP complex, ribosome biogenesis, thermophilic, hydrolase; HET: AMP; 1.20A {Thermus thermophilus HB27} PDB: 2gxs_A* 2gxu_A 3mwj_A 3mwk_A* 3mwl_A* 3nbf_A* 3nej_A Length = 207

 Score = 81.4 bits (202), Expect = 2e-20
 Identities = 39/95 (41%), Positives = 53/95 (55%), Gaps = 6/95 (6%)

Query: 40  TFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQ 99
            F+D  L PEI++    RGLTTPT IQ  ++P  L GK  I  A TG GKTL+F  P+ +
Sbjct: 2   EFKDFPLKPEILEALHGRGLTTPTPIQAAALPLALEGKDLIGQARTGTGKTLAFALPIAE 61

Query: 100 QILTWKSRPEYKPELNAPLALIITPGRELVFQIGQ 134
           ++   + R         P AL++TP REL  Q+  
Sbjct: 62  RLAPSQERG------RKPRALVLTPTRELALQVAS 90

>1vec_A ATP-dependent RNA helicase P54; DEAD-box protein, RNA binding protein; HET: TLA; 2.01A {Homo sapiens} SCOP: c.37.1.19 Length = 206

 Score = 81.4 bits (202), Expect = 2e-20
 Identities = 30/95 (31%), Positives = 50/95 (52%), Gaps = 9/95 (9%)

Query: 40  TFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQ 99
            FED  L  E++    + G   P+ IQ+ SIP  LSG+  +  A+ G GK+ ++L PL++
Sbjct: 4   EFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLE 63

Query: 100 QILTWKSRPEYKPELNAPLALIITPGRELVFQIGQ 134
           ++           + +   A++I P REL  Q+ Q
Sbjct: 64  RL---------DLKKDNIQAMVIVPTRELALQVSQ 89

>1t6n_A Probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA processing protein; HET: FLC; 1.94A {Homo sapiens} SCOP: c.37.1.19 Length = 220

 Score = 80.0 bits (198), Expect = 9e-20
 Identities = 28/93 (30%), Positives = 42/93 (45%), Gaps = 9/93 (9%)

Query: 40  TFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQ 99
            F D  L PE++      G   P+E+Q   IP  + G   +  A++G GKT  F+   +Q
Sbjct: 15  GFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQ 74

Query: 100 QILTWKSRPEYKPELNAPLALIITPGRELVFQI 132
           Q+         +P       L++   REL FQI
Sbjct: 75  QL---------EPVTGQVSVLVMCHTRELAFQI 98

>1hv8_A Putative ATP-dependent RNA helicase MJ0669; RNA-binding protein, ATPase, RNA binding protein; 3.00A {Methanocaldococcus jannaschii} SCOP: c.37.1.19 c.37.1.19 Length = 367

 Score = 81.4 bits (202), Expect = 2e-19
 Identities = 31/94 (32%), Positives = 46/94 (48%), Gaps = 11/94 (11%)

Query: 40  TFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAIL-VAETGCGKTLSFLAPLV 98
            F +  L+  I++    +G   PT+IQ   IP  L+ +  I+  A TG GKT SF  PL+
Sbjct: 7   NFNELNLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLI 66

Query: 99  QQILTWKSRPEYKPELNAPLALIITPGRELVFQI 132
           + +             N   A+I+TP REL  Q+
Sbjct: 67  ELV---------NEN-NGIEAIILTPTRELAIQV 90

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A* Length = 414

 Score = 80.5 bits (199), Expect = 5e-19
 Identities = 18/89 (20%), Positives = 30/89 (33%), Gaps = 12/89 (13%)

Query: 46  LAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWK 105
              +    F K+     T  Q+     ++ GKS  +VA TG GKT   +   +       
Sbjct: 6   EYEDFRSFFKKKFGKDLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLA---- 61

Query: 106 SRPEYKPELNAPLALIITPGRELVFQIGQ 134
                        + ++ P   LV Q  +
Sbjct: 62  --------RKGKKSALVFPTVTLVKQTLE 82

>1s2m_A Putative ATP-dependent RNA helicase DHH1; ATP-binding, RNA-binding, RNA binding protein; 2.10A {Saccharomyces cerevisiae} SCOP: c.37.1.19 c.37.1.19 PDB: 2wax_A* 2way_A Length = 400

 Score = 79.9 bits (198), Expect = 7e-19
 Identities = 34/104 (32%), Positives = 54/104 (51%), Gaps = 9/104 (8%)

Query: 31  EAVSRIDLGTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKT 90
           + V      TFED  L  E++    + G   P+ IQ+ +IP  ++G+  +  A+ G GKT
Sbjct: 13  DDVLNTKGNTFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKT 72

Query: 91  LSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIGQ 134
            +F+ P ++++         KP+LN   ALI+ P REL  Q  Q
Sbjct: 73  AAFVIPTLEKV---------KPKLNKIQALIMVPTRELALQTSQ 107

>2oxc_A Probable ATP-dependent RNA helicase DDX20; DEAD, structural genomics, structural genomics consortium, SGC, hydrolase; HET: ADP; 1.30A {Homo sapiens} PDB: 3b7g_A* Length = 230

 Score = 77.3 bits (191), Expect = 1e-18
 Identities = 25/104 (24%), Positives = 41/104 (39%), Gaps = 9/104 (8%)

Query: 31  EAVSRIDLGTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKT 90
             V   +   FE   L+  +++     G   P+ +Q  +IP    G   I+ A++G GKT
Sbjct: 16  GDVLLAEPADFESLLLSRPVLEGLRAAGFERPSPVQLKAIPLGRCGLDLIVQAKSGTGKT 75

Query: 91  LSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIGQ 134
             F    +  +           E  +   LI+ P RE+  QI  
Sbjct: 76  CVFSTIALDSL---------VLENLSTQILILAPTREIAVQIHS 110

>1xti_A Probable ATP-dependent RNA helicase P47; alpha-beta fold, gene regulation; 1.95A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 1xtj_A* 1xtk_A Length = 391

 Score = 78.8 bits (195), Expect = 2e-18
 Identities = 28/95 (29%), Positives = 43/95 (45%), Gaps = 9/95 (9%)

Query: 40  TFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQ 99
            F D  L PE++      G   P+E+Q   IP  + G   +  A++G GKT  F+   +Q
Sbjct: 9   GFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQ 68

Query: 100 QILTWKSRPEYKPELNAPLALIITPGRELVFQIGQ 134
           Q+         +P       L++   REL FQI +
Sbjct: 69  QL---------EPVTGQVSVLVMCHTRELAFQISK 94

>3bor_A Human initiation factor 4A-II; translation initiation, DEAD BOX, structural genomics, helic binding, HOST-virus interaction, hydrolase; 1.85A {Homo sapiens} PDB: 2g9n_A* Length = 237

 Score = 76.1 bits (188), Expect = 4e-18
 Identities = 27/93 (29%), Positives = 43/93 (46%), Gaps = 9/93 (9%)

Query: 40  TFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQ 99
            F+D  L   ++      G   P+ IQ+ +I   + G   I  A++G GKT +F   ++Q
Sbjct: 31  NFDDMNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGYDVIAQAQSGTGKTATFAISILQ 90

Query: 100 QILTWKSRPEYKPELNAPLALIITPGRELVFQI 132
           Q+         + E     AL++ P REL  QI
Sbjct: 91  QL---------EIEFKETQALVLAPTRELAQQI 114

>1qde_A EIF4A, translation initiation factor 4A; DEAD box protein family, gene regulation; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 1qva_A Length = 224

 Score = 75.3 bits (186), Expect = 7e-18
 Identities = 27/93 (29%), Positives = 44/93 (47%), Gaps = 9/93 (9%)

Query: 40  TFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQ 99
            F+D  L   ++      G   P+ IQ+ +I  ++ G   +  A++G GKT +F    +Q
Sbjct: 15  KFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQ 74

Query: 100 QILTWKSRPEYKPELNAPLALIITPGRELVFQI 132
           +I            + AP AL++ P REL  QI
Sbjct: 75  RI---------DTSVKAPQALMLAPTRELALQI 98

>1fuu_A Yeast initiation factor 4A; IF4A, helicase, DEAD-box protein, translation; 2.50A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 2vso_A* 2vsx_A* Length = 394

 Score = 76.4 bits (189), Expect = 1e-17
 Identities = 27/95 (28%), Positives = 45/95 (47%), Gaps = 9/95 (9%)

Query: 40  TFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQ 99
            F+D  L   ++      G   P+ IQ+ +I  ++ G   +  A++G GKT +F    +Q
Sbjct: 22  KFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQ 81

Query: 100 QILTWKSRPEYKPELNAPLALIITPGRELVFQIGQ 134
           +I            + AP AL++ P REL  QI +
Sbjct: 82  RI---------DTSVKAPQALMLAPTRELALQIQK 107

>2j0s_A ATP-dependent RNA helicase DDX48; mRNA processing, phosphorylation, rRNA processing, mRNA splicing, mRNA transport; HET: ANP; 2.21A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 2j0q_A* 2hyi_C* 3ex7_C* 2xb2_A* 2hxy_A 2j0u_A 2j0u_B 2zu6_A Length = 410

 Score = 76.1 bits (188), Expect = 2e-17
 Identities = 26/95 (27%), Positives = 47/95 (49%), Gaps = 9/95 (9%)

Query: 40  TFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQ 99
           TF+  GL  +++      G   P+ IQ+ +I  ++ G+  I  +++G GKT +F   ++Q
Sbjct: 38  TFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQ 97

Query: 100 QILTWKSRPEYKPELNAPLALIITPGRELVFQIGQ 134
            +           ++    ALI+ P REL  QI +
Sbjct: 98  CL---------DIQVRETQALILAPTRELAVQIQK 123

>3eiq_A Eukaryotic initiation factor 4A-I; PDCD4, anti-oncogene, apoptosis, cell cycle, nucleus, phosph RNA-binding, ATP-binding, helicase, hydrolase; 3.50A {Homo sapiens} Length = 414

 Score = 76.1 bits (188), Expect = 2e-17
 Identities = 29/95 (30%), Positives = 48/95 (50%), Gaps = 9/95 (9%)

Query: 40  TFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQ 99
           +F+D  L+  ++      G   P+ IQ+ +I   + G   I  A++G GKT +F   ++Q
Sbjct: 41  SFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQ 100

Query: 100 QILTWKSRPEYKPELNAPLALIITPGRELVFQIGQ 134
           QI         + +L A  AL++ P REL  QI +
Sbjct: 101 QI---------ELDLKATQALVLAPTRELAQQIQK 126

>3pey_A ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, ATPase, helicase, mRNA-export, nuclear pore, hydrolase-RNA complex; HET: ADP; 1.40A {Saccharomyces cerevisiae} PDB: 3pew_A* 3pex_A* 3pez_A* 3rrm_A* 3rrn_A* 2kbe_A 3gfp_A 2kbf_A 3pev_A* 3peu_A* Length = 395

 Score = 70.3 bits (173), Expect = 2e-15
 Identities = 26/97 (26%), Positives = 50/97 (51%), Gaps = 11/97 (11%)

Query: 40  TFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILV--AETGCGKTLSFLAPL 97
           +F++ GLAPE++          P++IQ+ ++P LL      ++  +++G GKT +F   +
Sbjct: 6   SFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLTM 65

Query: 98  VQQILTWKSRPEYKPELNAPLALIITPGRELVFQIGQ 134
           + ++          PE  +P A+ + P REL  Q  +
Sbjct: 66  LTRV---------NPEDASPQAICLAPSRELARQTLE 93

>3fmo_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 2.51A {Homo sapiens} Length = 300

 Score = 69.7 bits (171), Expect = 2e-15
 Identities = 25/97 (25%), Positives = 50/97 (51%), Gaps = 11/97 (11%)

Query: 40  TFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILV--AETGCGKTLSFLAPL 97
           +FE+  L P+++      G   P++IQ+ ++P +L+     L+  +++G GKT +F+  +
Sbjct: 93  SFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAM 152

Query: 98  VQQILTWKSRPEYKPELNAPLALIITPGRELVFQIGQ 134
           + Q+         +P    P  L ++P  EL  Q G+
Sbjct: 153 LSQV---------EPANKYPQCLCLSPTYELALQTGK 180

>3fht_A ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box helicase, RNA dependent ATPase, mRNA export, nucleocytoplasmic transport, NUP214, CAN; HET: ANP; 2.20A {Homo sapiens} PDB: 3ews_A* 3g0h_A* 3fhc_B Length = 412

 Score = 69.5 bits (171), Expect = 4e-15
 Identities = 25/97 (25%), Positives = 50/97 (51%), Gaps = 11/97 (11%)

Query: 40  TFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILV--AETGCGKTLSFLAPL 97
           +FE+  L P+++      G   P++IQ+ ++P +L+     L+  +++G GKT +F+  +
Sbjct: 26  SFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAM 85

Query: 98  VQQILTWKSRPEYKPELNAPLALIITPGRELVFQIGQ 134
           + Q+         +P    P  L ++P  EL  Q G+
Sbjct: 86  LSQV---------EPANKYPQCLCLSPTYELALQTGK 113

>2z0m_A 337AA long hypothetical ATP-dependent RNA helicase DEAD; ATP-binding, hydrolase, nucleotide-binding, RNA binding protein, structural genomics; 1.90A {Sulfolobus tokodaii} Length = 337

 Score = 69.1 bits (170), Expect = 4e-15
 Identities = 24/89 (26%), Positives = 43/89 (48%), Gaps = 15/89 (16%)

Query: 46  LAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWK 105
           +  +I     + G    TE+Q  +IP +L GK+ ++ A+TG GKT ++  P+++      
Sbjct: 1   MNEKIEQAIREMGFKNFTEVQSKTIPLMLQGKNVVVRAKTGSGKTAAYAIPILE------ 54

Query: 106 SRPEYKPELNAPLALIITPGRELVFQIGQ 134
                        +L++TP REL  Q+  
Sbjct: 55  ---------LGMKSLVVTPTRELTRQVAS 74

>3fmp_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 3.19A {Homo sapiens} Length = 479

 Score = 68.9 bits (169), Expect = 6e-15
 Identities = 25/97 (25%), Positives = 50/97 (51%), Gaps = 11/97 (11%)

Query: 40  TFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILV--AETGCGKTLSFLAPL 97
           +FE+  L P+++      G   P++IQ+ ++P +L+     L+  +++G GKT +F+  +
Sbjct: 93  SFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAM 152

Query: 98  VQQILTWKSRPEYKPELNAPLALIITPGRELVFQIGQ 134
           + Q+         +P    P  L ++P  EL  Q G+
Sbjct: 153 LSQV---------EPANKYPQCLCLSPTYELALQTGK 180

>1wp9_A ATP-dependent RNA helicase, putative; ATPase, DNA replication, DNA repair, DNA recombina hydrolase; 2.90A {Pyrococcus furiosus} SCOP: c.37.1.19 c.37.1.19 Length = 494

 Score = 39.4 bits (91), Expect = 1e-04
 Identities = 16/76 (21%), Positives = 29/76 (38%), Gaps = 12/76 (15%)

Query: 56  KRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELN 115
           +R L  P   Q+          + ++V  TG GKTL  +     ++  +  +        
Sbjct: 4   RRDLIQPRIYQEVIYAKCK-ETNCLIVLPTGLGKTLIAMMIAEYRLTKYGGK-------- 54

Query: 116 APLALIITPGRELVFQ 131
               L++ P + LV Q
Sbjct: 55  ---VLMLAPTKPLVLQ 67

>2p6r_A Afuhel308 helicase; protein-DNA complex, SF2 helicase, archaeal helicase, DNA repair,, DNA binding protein/DNA complex; 3.00A {Archaeoglobus fulgidus} SCOP: a.4.5.43 a.289.1.2 c.37.1.19 c.37.1.19 PDB: 2p6u_A Length = 702

 Score = 39.0 bits (91), Expect = 2e-04
 Identities = 13/60 (21%), Positives = 27/60 (45%)

Query: 43  DTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQIL 102
              ++   + I  + G+      Q  ++  + SGK+ +L   T  GKTL     +V++ +
Sbjct: 7   AESISSYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAI 66

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus} Length = 715

 Score = 37.8 bits (88), Expect = 4e-04
 Identities = 19/51 (37%), Positives = 26/51 (50%), Gaps = 1/51 (1%)

Query: 42 EDTGLAPEIIDIFTKRGLTTPTEIQKYSIPT-LLSGKSAILVAETGCGKTL 91
          ED  L   +I+I  KRG+      Q  ++   LL G   +L + TG GKTL
Sbjct: 11 EDLKLPSNVIEIIKKRGIKKLNPPQTEAVKKGLLEGNRLLLTSPTGSGKTL 61

>1gku_B Reverse gyrase, TOP-RG; topoisomerase, DNA supercoiling, archaea, helicase; 2.7A {Archaeoglobus fulgidus} SCOP: c.37.1.16 c.37.1.16 e.10.1.1 PDB: 1gl9_B* Length = 1054

 Score = 37.7 bits (88), Expect = 5e-04
 Identities = 21/84 (25%), Positives = 33/84 (39%), Gaps = 13/84 (15%)

Query: 49  EIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRP 108
           E ++ F ++ +  P  IQK     +L  +S    A TG GKT SF   +      + +  
Sbjct: 45  EFVEFF-RKCVGEPRAIQKMWAKRILRKESFAATAPTGVGKT-SFGLAMS----LFLALK 98

Query: 109 EYKPELNAPLALIITPGRELVFQI 132
             +         +I P   LV Q 
Sbjct: 99  GKR-------CYVIFPTSLLVIQA 115

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	134
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	99.9
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	99.9
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	99.89
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	99.89
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	99.89
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	99.88
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	99.88
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	99.88
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	99.88
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	99.88
3bor_A	237	Human initiation factor 4A-II; translation initiat	99.88
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	99.88
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	99.88
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	99.87
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	99.86
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	99.86
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	99.85
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	99.85
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	99.84
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	99.83
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	99.83
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	99.82
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	99.81
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	99.81
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	99.81
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	99.79
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	99.79
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	99.78
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	99.72
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	99.71
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	99.71
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	99.7
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	99.67
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	99.66
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	99.64
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	99.64
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	99.56
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	99.56
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	99.53
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	99.53
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	99.53
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	99.52
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.52
1tf5_A	844	Preprotein translocase SECA subunit; ATPase, helic	99.51
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	99.49
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.48
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	99.47
3b6e_A	216	Interferon-induced helicase C domain-containing P;	99.47
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	99.47
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	99.47
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	99.42
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	99.41
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	99.4
2fsf_A	853	Preprotein translocase SECA subunit; ATPase, DNA-R	99.39
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	99.38
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	99.35
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	99.34
1nkt_A	922	Preprotein translocase SECA 1 subunit; preprotein	99.33
1rif_A	282	DAR protein, DNA helicase UVSW; bacteriophage, REC	99.33
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	99.33
4gl2_A	699	Interferon-induced helicase C domain-containing P;	99.32
2ipc_A	997	Preprotein translocase SECA subunit; nucleotide bi	99.32
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	99.27
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	99.27
3crv_A	551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	99.26
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	99.25
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	99.24
1yks_A	440	Genome polyprotein [contains: flavivirin protease	99.24
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	99.22
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	99.22
2vl7_A	540	XPD; helicase, unknown function; 2.25A {Sulfolobus	99.19
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	99.15
3h1t_A	590	Type I site-specific restriction-modification syst	98.99
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	98.93
2w00_A	1038	HSDR, R.ECOR124I; ATP-binding, DNA-binding, restri	98.79
3rc3_A	677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	98.66
1w36_D	608	RECD, exodeoxyribonuclease V alpha chain; recombin	98.46
1z63_A	500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	98.35
3jux_A	822	Protein translocase subunit SECA; protein transloc	98.33
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	98.25
4b3f_X	646	DNA-binding protein smubp-2; hydrolase, helicase;	98.03
3mwy_W	800	Chromo domain-containing protein 1; SWI2/SNF2 ATPa	97.81
2gk6_A	624	Regulator of nonsense transcripts 1; UPF1, helicas	97.76
2xzl_A	802	ATP-dependent helicase NAM7; hydrolase-RNA complex	97.65
1z3i_X	644	Similar to RAD54-like; recombination ATPase helica	97.63
3e1s_A	574	Exodeoxyribonuclease V, subunit RECD; alpha and be	97.56
2wjy_A	800	Regulator of nonsense transcripts 1; nonsense medi	97.56
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	97.51
3lfu_A	647	DNA helicase II; SF1 helicase, ATP-binding, DNA da	97.4
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	97.21
1uaa_A	673	REP helicase, protein (ATP-dependent DNA helicase	96.93
1pjr_A	724	PCRA; DNA repair, DNA replication, SOS response, h	96.77
3u4q_A	1232	ATP-dependent helicase/nuclease subunit A; helicas	96.58
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	95.6
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	95.45
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	95.43
3cpe_A	592	Terminase, DNA packaging protein GP17; large termi	95.41
3co5_A	143	Putative two-component system transcriptional RES	95.21
2o0j_A	385	Terminase, DNA packaging protein GP17; nucleotide-	95.19
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	95.07
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	95.01
1e9r_A	437	Conjugal transfer protein TRWB; coupling protein,	94.69
1u0j_A	267	DNA replication protein; AAA+ protein, P-loop atpa	94.27
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	94.06
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	94.05
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	94.05
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	93.99
1tue_A	212	Replication protein E1; helicase, replication, E1E	93.98
2oap_1	511	GSPE-2, type II secretion system protein; hexameri	93.96
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	93.95
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	93.94
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	93.9
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	93.8
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	93.66
3vkw_A	446	Replicase large subunit; alpha/beta domain, helica	93.3
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	93.29
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	93.2
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	93.09
3b85_A	208	Phosphate starvation-inducible protein; PHOH2, ATP	93.08
2qgz_A	308	Helicase loader, putative primosome component; str	93.03
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	92.84
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	92.8
2r44_A	331	Uncharacterized protein; putative ATPase, structur	92.79
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	92.69
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	92.63
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	92.59
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	92.48
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	92.26
3bos_A	242	Putative DNA replication factor; P-loop containing	92.19
2zts_A	251	Putative uncharacterized protein PH0186; KAIC like	91.89
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	91.89
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	91.84
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	91.82
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	91.68
1kgd_A	180	CASK, peripheral plasma membrane CASK; maguk, guan	91.54
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	91.49
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	91.46
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	91.43
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	91.41
2gza_A	361	Type IV secretion system protein VIRB11; ATPase, h	91.39
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	91.16
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	91.1
1p9r_A	418	General secretion pathway protein E; bacterial typ	91.06
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	91.02
1lvg_A	198	Guanylate kinase, GMP kinase; transferase; HET: AD	91.0
4ag6_A	392	VIRB4 ATPase, type IV secretory pathway VIRB4 comp	90.99
3vaa_A	199	Shikimate kinase, SK; structural genomics, center	90.99
1xx6_A	191	Thymidine kinase; NESG, northeast structural genom	90.98
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	90.85
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	90.81
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	90.66
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	90.49
2pt7_A	330	CAG-ALFA; ATPase, protein-protein complex, type IV	90.38
3tau_A	208	Guanylate kinase, GMP kinase; structural genomics,	90.31
2eyu_A	261	Twitching motility protein PILT; pilus retraction	90.2
2qor_A	204	Guanylate kinase; phosphotransferase, purine metab	90.18
1zp6_A	191	Hypothetical protein ATU3015; alpha-beta protein.,	90.11
4gp7_A	171	Metallophosphoesterase; polynucleotide kinase phos	90.11
3bgw_A	444	DNAB-like replicative helicase; ATPase, replicatio	90.1
2chg_A	226	Replication factor C small subunit; DNA-binding pr	90.03
2j41_A	207	Guanylate kinase; GMP, GMK, transferase, ATP-bindi	90.0
1qhx_A	178	CPT, protein (chloramphenicol phosphotransferase);	90.0
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	89.98
3lw7_A	179	Adenylate kinase related protein (ADKA-like); AMP,	89.97
3trf_A	185	Shikimate kinase, SK; amino acid biosynthesis, tra	89.9
3tr0_A	205	Guanylate kinase, GMP kinase; purines, pyrimidines	89.83
3iij_A	180	Coilin-interacting nuclear ATPase protein; alpha a	89.79
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	89.74
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	89.7
1kag_A	173	SKI, shikimate kinase I; transferase, structural g	89.7
2ius_A	512	DNA translocase FTSK; nucleotide-binding, chromoso	89.61
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	89.58
1z6g_A	218	Guanylate kinase; structural genomics, SGC, struct	89.54
3nwn_A	359	Kinesin-like protein KIF9; motor domain, ADP, stru	89.52
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	89.42
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	89.4
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	89.39
1bg2_A	325	Kinesin; motor protein, ATPase, microtubule associ	89.36
1znw_A	207	Guanylate kinase, GMP kinase; ATP:GMP-phosphotrans	89.32
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	89.09
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	89.07
3a00_A	186	Guanylate kinase, GMP kinase; domain movement, dim	88.99
1s96_A	219	Guanylate kinase, GMP kinase; E.coli, dimer, SAD,	88.99
3dc4_A	344	Kinesin-like protein NOD; catalytic domain, ATPase	88.93
1ly1_A	181	Polynucleotide kinase; PNK, phosphatase, transfera	88.89
4eun_A	200	Thermoresistant glucokinase; putative sugar kinase	88.85
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	88.85
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	88.76
4a14_A	344	Kinesin, kinesin-like protein KIF7; motor protein,	88.76
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	88.73
1ex7_A	186	Guanylate kinase; substrate-induced FIT, domain mo	88.7
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	88.7
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	88.6
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	88.54
1kht_A	192	Adenylate kinase; phosphotransferase, signaling pr	88.53
2ehv_A	251	Hypothetical protein PH0186; KAIC, RECA ATPase, un	88.49
3b6u_A	372	Kinesin-like protein KIF3B; structural genomics co	88.48
2y65_A	365	Kinesin, kinesin heavy chain; motor protein; HET:	88.47
2vvg_A	350	Kinesin-2; motor protein, nucleotide-binding, micr	88.43
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	88.41
2ze6_A	253	Isopentenyl transferase; crown GALL tumor, cytokin	88.39
2h58_A	330	Kinesin-like protein KIFC3 variant; motor domain,	88.39
2zfi_A	366	Kinesin-like protein KIF1A, kinesin heavy chain is	88.35
1knq_A	175	Gluconate kinase; ALFA/beta structure, transferase	88.33
1y63_A	184	LMAJ004144AAA protein; structural genomics, protei	88.28
1goj_A	355	Kinesin, kinesin heavy chain; motor protein, ATPas	88.28
3gbj_A	354	KIF13B protein; kinesin, motor domain, ADP, struct	88.19
2iut_A	574	DNA translocase FTSK; nucleotide-binding, chromoso	88.18
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	88.18
3kb2_A	173	SPBC2 prophage-derived uncharacterized protein YOR	88.18
2nr8_A	358	Kinesin-like protein KIF9; motor domain, ADP, stru	88.09
1t5c_A	349	CENP-E protein, centromeric protein E; kinesin mot	88.08
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	88.05
3lre_A	355	Kinesin-like protein KIF18A; motor protein, nucleo	88.05
3ney_A	197	55 kDa erythrocyte membrane protein; structural ge	88.02
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	87.99
2ewv_A	372	Twitching motility protein PILT; pilus retraction	87.95
4etp_A	403	Kinesin-like protein KAR3; kinesin motor protein,	87.95
1xp8_A	366	RECA protein, recombinase A; recombination, radior	87.9
1g8p_A	350	Magnesium-chelatase 38 kDa subunit; parallel beta	87.83
1x88_A	359	Kinesin-like protein KIF11; switch II, motor domai	87.62
3u06_A	412	Protein claret segregational; motor domain, stalk	87.61
2wbe_C	373	Bipolar kinesin KRP-130; EG5, KLP61F, tubulin, mit	87.47
3hr8_A	356	Protein RECA; alpha and beta proteins (A/B, A+B),	87.44
2px0_A	296	Flagellar biosynthesis protein FLHF; SRP GTPase, f	87.43
3jvv_A	356	Twitching mobility protein; hexameric P-loop ATPas	87.37
3cob_A	369	Kinesin heavy chain-like protein; motor, switch II	87.19
1v8k_A	410	Kinesin-like protein KIF2C; microtubule destabiliz	87.09
3cm0_A	186	Adenylate kinase; ATP-binding, cytoplasm, nucleoti	87.05
1cr0_A	296	DNA primase/helicase; RECA-type protein fold, tran	86.99
2zr9_A	349	Protein RECA, recombinase A; recombination, RECA m	86.91
3nwj_A	250	ATSK2; P loop, shikimate, nucleoside monophosphate	86.85
3exa_A	322	TRNA delta(2)-isopentenylpyrophosphate transferase	86.84
3t0q_A	349	AGR253WP; kinesin, alpha and beta proteins, P-loop	86.83
3foz_A	316	TRNA delta(2)-isopentenylpyrophosphate transferas;	86.82
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	86.81
3a8t_A	339	Adenylate isopentenyltransferase; rossmann fold pr	86.78
2heh_A	387	KIF2C protein; kinesin, motor domain, ADP, structu	86.74
3u4q_B	1166	ATP-dependent helicase/deoxyribonuclease subunit;	86.67
3uie_A	200	Adenylyl-sulfate kinase 1, chloroplastic; rossmann	86.63
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	86.61
2j9r_A	214	Thymidine kinase; TK1, DNK, lasso, transferase, AT	86.53
2owm_A	443	Nckin3-434, related to kinesin-like protein KIF1C;	86.47
2bdt_A	189	BH3686; alpha-beta protein, structural genomics, P	86.37
1u94_A	356	RECA protein, recombinase A; homologous recombinat	86.28
2q6t_A	444	DNAB replication FORK helicase; hydrolase; 2.90A {	86.13
3t61_A	202	Gluconokinase; PSI-biology, structural genomics, p	86.12
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	86.09
3pxg_A	468	Negative regulator of genetic competence CLPC/MEC;	86.08
2r6a_A	454	DNAB helicase, replicative helicase; replication,	86.0
3bfn_A	388	Kinesin-like protein KIF22; limited proteolysis, s	85.99
1f9v_A	347	Kinesin-like protein KAR3; kinesin-related protein	85.95
1gvn_B	287	Zeta; postsegregational killing system, plasmid; 1	85.94
2chq_A	319	Replication factor C small subunit; DNA-binding pr	85.94
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	85.88
1xjc_A	169	MOBB protein homolog; structural genomics, midwest	85.8
2cvh_A	220	DNA repair and recombination protein RADB; filamen	85.75
3k1j_A	604	LON protease, ATP-dependent protease LON; ATP-bind	85.72
3c8u_A	208	Fructokinase; YP_612366.1, putative fructose trans	85.66
2rhm_A	193	Putative kinase; P-loop containing nucleoside trip	85.64
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	85.56
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	85.49
2qmh_A	205	HPR kinase/phosphorylase; V267F mutation, ATP-bind	85.47
1m7g_A	211	Adenylylsulfate kinase; APS kinase, transferase, s	85.42
3tif_A	235	Uncharacterized ABC transporter ATP-binding prote;	85.33
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	85.18
1tev_A	196	UMP-CMP kinase; ploop, NMP binding region, LID reg	85.0
2rep_A	376	Kinesin-like protein KIFC1; structural genomics co	84.96
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	84.92
1ye8_A	178	Protein THEP1, hypothetical UPF0334 kinase-like pr	84.92
3kta_A	182	Chromosome segregation protein SMC; structural mai	84.86
3f9v_A	595	Minichromosome maintenance protein MCM; replicativ	84.86
2c95_A	196	Adenylate kinase 1; transferase, AP4A, nucleotide	84.75
1w4r_A	195	Thymidine kinase; type II, human, cytosolic, phosp	84.72
1f2t_A	149	RAD50 ABC-ATPase; DNA double-strand break repair,	84.6
3crm_A	323	TRNA delta(2)-isopentenylpyrophosphate transferase	84.51
2v54_A	204	DTMP kinase, thymidylate kinase; nucleotide biosyn	84.47
4a74_A	231	DNA repair and recombination protein RADA; hydrola	84.45
2i3b_A	189	HCR-ntpase, human cancer-related ntpase; AAA, ross	84.38
3lnc_A	231	Guanylate kinase, GMP kinase; ALS collaborative cr	84.33
3asz_A	211	Uridine kinase; cytidine phosphorylation, transfer	84.22
2r2a_A	199	Uncharacterized protein; zonular occludens toxin,	84.22
3qf7_A	365	RAD50; ABC-ATPase, ATPase, hydrolase; HET: ANP; 1.	84.2
2r8r_A	228	Sensor protein; KDPD, PFAM02702, MCSG, structural	84.15
1nks_A	194	Adenylate kinase; thermophilic, transferase; HET:	84.04
3m6a_A	543	ATP-dependent protease LA 1; alpha, beta, ATP-bind	83.98
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	83.97
2z43_A	324	DNA repair and recombination protein RADA; archaea	83.95
1via_A	175	Shikimate kinase; structural genomics, transferase	83.95
3pvs_A	447	Replication-associated recombination protein A; ma	83.87
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	83.86
3d3q_A	340	TRNA delta(2)-isopentenylpyrophosphate transferase	83.79
3fb4_A	216	Adenylate kinase; psychrophIle, phosphotransferase	83.77
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	83.74
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	83.72
2cbz_A	237	Multidrug resistance-associated protein 1; ABC pro	83.57
1g41_A	444	Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dep	83.35
2pez_A	179	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	83.26
2iyv_A	184	Shikimate kinase, SK; transferase, aromatic amino	83.2
2bwj_A	199	Adenylate kinase 5; phosphoryl transfer reaction,	83.06
3dl0_A	216	Adenylate kinase; phosphotransferase, zinc coordin	83.04
1sgw_A	214	Putative ABC transporter; structural genomics, P p	83.0
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	82.96
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	82.92
1cke_A	227	CK, MSSA, protein (cytidine monophosphate kinase);	82.92
1nlf_A	279	Regulatory protein REPA; replicative DNA helicase	82.86
1aky_A	220	Adenylate kinase; ATP:AMP phosphotransferase, myok	82.82
2yvu_A	186	Probable adenylyl-sulfate kinase; transferase, str	82.81
2bbw_A	246	Adenylate kinase 4, AK4; nucleotide kinase, nucleo	82.75
1zd8_A	227	GTP:AMP phosphotransferase mitochondrial; ATP:AMP	82.7
1zak_A	222	Adenylate kinase; ATP:AMP-phosphotransferase, tran	82.65
1qf9_A	194	UMP/CMP kinase, protein (uridylmonophosphate/cytid	82.62
1e6c_A	173	Shikimate kinase; phosphoryl transfer, ADP, shikim	82.6
2pze_A	229	Cystic fibrosis transmembrane conductance regulat;	82.58
2v9p_A	305	Replication protein E1; AAA+ molecular motor, DNA	82.46
2pcj_A	224	ABC transporter, lipoprotein-releasing system ATP-	82.33
2plr_A	213	DTMP kinase, probable thymidylate kinase; TMP-bind	82.3
1g6h_A	257	High-affinity branched-chain amino acid transport	82.26
2wwf_A	212	Thymidilate kinase, putative; transferase, malaria	82.15
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	82.15
2ff7_A	247	Alpha-hemolysin translocation ATP-binding protein	82.12
2if2_A	204	Dephospho-COA kinase; alpha-beta protein, structur	82.11
2cdn_A	201	Adenylate kinase; phosphoryl transfer, associative	82.0
2ghi_A	260	Transport protein; multidrug resistance protein, M	81.99
3gfo_A	275	Cobalt import ATP-binding protein CBIO 1; structur	81.97
1ji0_A	240	ABC transporter; ATP binding protein, structural g	81.95
3a4m_A	260	L-seryl-tRNA(SEC) kinase; P-loop motif, walker A m	81.92
3eph_A	409	TRNA isopentenyltransferase; transferase, alternat	81.91
1rj9_A	304	FTSY, signal recognition protein; SRP-GTPase domai	81.84
4g1u_C	266	Hemin import ATP-binding protein HMUV; membrane tr	81.82
1nn5_A	215	Similar to deoxythymidylate kinase (thymidylate K;	81.73
1jjv_A	206	Dephospho-COA kinase; P-loop nucleotide-binding fo	81.69
1ukz_A	203	Uridylate kinase; transferase; HET: ADP AMP; 1.90A	81.64
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	81.54
4h1g_A	715	Maltose binding protein-cakar3 motor domain fusio;	81.5
1np6_A	174	Molybdopterin-guanine dinucleotide biosynthesis pr	81.43
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	81.41
1b0u_A	262	Histidine permease; ABC transporter, transport pro	81.27
4e22_A	252	Cytidylate kinase; P-loop, CMP/ATP binding, transf	81.15
2vli_A	183	Antibiotic resistance protein; transferase, tunica	81.02
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	81.01
2jaq_A	205	Deoxyguanosine kinase; transferase, deoxyribonucle	80.95
2d2e_A	250	SUFC protein; ABC-ATPase, SUF protein, 310-helix,	80.93
1mv5_A	243	LMRA, multidrug resistance ABC transporter ATP-bin	80.89
3b9q_A	302	Chloroplast SRP receptor homolog, alpha subunit CP	80.88
2qi9_C	249	Vitamin B12 import ATP-binding protein BTUD; inner	80.86
3auy_A	371	DNA double-strand break repair RAD50 ATPase; DNA r	80.85
2yz2_A	266	Putative ABC transporter ATP-binding protein TM_0;	80.79
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	80.73
2zu0_C	267	Probable ATP-dependent transporter SUFC; iron-sulf	80.64
2pt5_A	168	Shikimate kinase, SK; aromatic amino acid biosynth	80.58
2qt1_A	207	Nicotinamide riboside kinase 1; non-protein kinase	80.57
2ixe_A	271	Antigen peptide transporter 1; ABC ATPase, hydrola	80.54
1g5t_A	196	COB(I)alamin adenosyltransferase; P-loop protein,	80.52
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	80.44
2pbr_A	195	DTMP kinase, thymidylate kinase; transferase, nucl	80.32
1ry6_A	360	Internal kinesin; kinesin motor domain, nucleotide	80.25
3qks_A	203	DNA double-strand break repair RAD50 ATPase; RECA-	80.25
2olj_A	263	Amino acid ABC transporter; ABC domain, ATPase, hy	80.19
2nq2_C	253	Hypothetical ABC transporter ATP-binding protein H	80.16
1vpl_A	256	ABC transporter, ATP-binding protein; TM0544, stru	80.1
3hjh_A	483	Transcription-repair-coupling factor; MFD, mutatio	80.08

>3fmo_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 2.51A {Homo sapiens}

Probab=99.90  E-value=7.6e-24  Score=159.98  Aligned_cols=89  Identities=27%  Similarity=0.527  Sum_probs=81.9

Q ss_pred             CCCCCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcC--CCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCC
Q psy7268          36 IDLGTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSG--KSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPE  113 (134)
Q Consensus        36 ~~~~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g--~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~  113 (134)
                      ..+.+|++++|++.++++|.++||..|+++|.++||.++.|  +|+++++|||||||++|++|+++++....        
T Consensus        89 ~~~~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~ai~~il~~~~~~~l~~a~TGsGKT~a~~lp~l~~l~~~~--------  160 (300)
T 3fmo_B           89 YSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPAN--------  160 (300)
T ss_dssp             CCCCCSGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHTSSSCCCEEEECCTTSSHHHHHHHHHHHHCCTTS--------
T ss_pred             CCcCCHhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCCeEEEECCCCCCccHHHHHHHHHhhhccC--------
Confidence            45689999999999999999999999999999999999987  99999999999999999999999885432        


Q ss_pred             CCCcEEEEEcCcHHHHHHhc
Q psy7268         114 LNAPLALIITPGRELVFQIG  133 (134)
Q Consensus       114 ~~~~~~lil~Pt~~La~Qi~  133 (134)
                       .++++||++|||+||.|++
T Consensus       161 -~~~~~lil~PtreLa~Q~~  179 (300)
T 3fmo_B          161 -KYPQCLCLSPTYELALQTG  179 (300)
T ss_dssp             -CSCCEEEECSSHHHHHHHH
T ss_pred             -CCceEEEEcCcHHHHHHHH
Confidence             5778999999999999985

>3fe2_A Probable ATP-dependent RNA helicase DDX5; DEAD, ADP, ATP-binding, hydrolase, nucleotide- RNA-binding, methylation, mRNA processing, mRNA S nucleus; HET: ADP; 2.60A {Homo sapiens} PDB: 4a4d_A

Probab=99.90  E-value=2.6e-23  Score=151.86  Aligned_cols=96  Identities=31%  Similarity=0.502  Sum_probs=85.7

Q ss_pred             cCCCCCCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCC
Q psy7268          34 SRIDLGTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPE  113 (134)
Q Consensus        34 ~~~~~~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~  113 (134)
                      ...++.+|+++++++.+++++.+.||..|+++|.++|+.+++|+|+++++|||+|||++|++|++..+.....    ...
T Consensus        24 ~p~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~g~~~l~~apTGsGKT~~~~l~~l~~l~~~~~----~~~   99 (242)
T 3fe2_A           24 CPKPVLNFYEANFPANVMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLLPAIVHINHQPF----LER   99 (242)
T ss_dssp             CCCCCSSTTTTTCCHHHHHHHHTTTCCSCCHHHHHHHHHHHHTCCEEEEECTTSCHHHHHHHHHHHHHHTSCC----CCT
T ss_pred             CCCccCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCcCHHHHHHHHHHHHHHHhccc----ccc
Confidence            4567889999999999999999999999999999999999999999999999999999999999999875321    112


Q ss_pred             CCCcEEEEEcCcHHHHHHhc
Q psy7268         114 LNAPLALIITPGRELVFQIG  133 (134)
Q Consensus       114 ~~~~~~lil~Pt~~La~Qi~  133 (134)
                      ..++++||++||++|+.|++
T Consensus       100 ~~~~~~lil~Pt~~L~~Q~~  119 (242)
T 3fe2_A          100 GDGPICLVLAPTRELAQQVQ  119 (242)
T ss_dssp             TCCCSEEEECSSHHHHHHHH
T ss_pred             CCCCEEEEEeCcHHHHHHHH
Confidence            25778999999999999985

>2db3_A ATP-dependent RNA helicase VASA; DEAD-BOX, protein-RNA complex, ATPase, riken structural genomics/proteomics initiative, RSGI; HET: ANP; 2.20A {Drosophila melanogaster}

Probab=99.89  E-value=5.4e-23  Score=161.79  Aligned_cols=95  Identities=39%  Similarity=0.578  Sum_probs=85.8

Q ss_pred             CCCCCCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCC
Q psy7268          35 RIDLGTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPEL  114 (134)
Q Consensus        35 ~~~~~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~  114 (134)
                      ..++.+|++++|++.++++|.+.||+.|+++|+++||.+++|+|++++++||||||++|++|+++++......    ...
T Consensus        52 p~~~~~f~~~~l~~~l~~~l~~~g~~~pt~iQ~~ai~~i~~g~d~i~~a~TGsGKT~a~~lpil~~l~~~~~~----~~~  127 (434)
T 2db3_A           52 PQPIQHFTSADLRDIIIDNVNKSGYKIPTPIQKCSIPVISSGRDLMACAQTGSGKTAAFLLPILSKLLEDPHE----LEL  127 (434)
T ss_dssp             CCCCCCGGGSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHHSCCC----CCT
T ss_pred             CCCcCChhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCEEEECCCCCCchHHHHHHHHHHHHhcccc----ccc
Confidence            4678899999999999999999999999999999999999999999999999999999999999999864321    123


Q ss_pred             CCcEEEEEcCcHHHHHHhc
Q psy7268         115 NAPLALIITPGRELVFQIG  133 (134)
Q Consensus       115 ~~~~~lil~Pt~~La~Qi~  133 (134)
                      .++++||++|||+|+.|++
T Consensus       128 ~~~~~lil~PtreLa~Q~~  146 (434)
T 2db3_A          128 GRPQVVIVSPTRELAIQIF  146 (434)
T ss_dssp             TCCSEEEECSSHHHHHHHH
T ss_pred             CCccEEEEecCHHHHHHHH
Confidence            5789999999999999986

>3iuy_A Probable ATP-dependent RNA helicase DDX53; REC-A-like, DEAD-BOX, structural genomics, structural genomi consortium, SGC, ATP-binding, hydrolase; HET: AMP; 2.40A {Homo sapiens}

Probab=99.89  E-value=3.9e-23  Score=149.36  Aligned_cols=102  Identities=31%  Similarity=0.493  Sum_probs=85.5

Q ss_pred             CcccccCCCCCCccc-CCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCC
Q psy7268          29 GYEAVSRIDLGTFED-TGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSR  107 (134)
Q Consensus        29 ~~~~~~~~~~~~f~~-~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~  107 (134)
                      +.......+..+|++ +++++.+++++.+.||..|+++|.++++.+++|+|+++++|||+|||++|++|++..+......
T Consensus         9 ~~~~~~p~p~~~f~~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~l~~apTGsGKT~~~~l~~~~~l~~~~~~   88 (228)
T 3iuy_A            9 GEKRLIPKPTCRFKDAFQQYPDLLKSIIRVGILKPTPIQSQAWPIILQGIDLIVVAQTGTGKTLSYLMPGFIHLDSQPIS   88 (228)
T ss_dssp             SSCCCCCCCCCSHHHHHTTCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHC-----
T ss_pred             CccCcCCCChhhHhhhhccCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhccch
Confidence            334555678889999 8999999999999999999999999999999999999999999999999999999988643211


Q ss_pred             CCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268         108 PEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus       108 ~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                         .....++++||++||++|+.|++
T Consensus        89 ---~~~~~~~~~lil~Pt~~L~~q~~  111 (228)
T 3iuy_A           89 ---REQRNGPGMLVLTPTRELALHVE  111 (228)
T ss_dssp             -------CCCSEEEECSSHHHHHHHH
T ss_pred             ---hhccCCCcEEEEeCCHHHHHHHH
Confidence               11225788999999999999986

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens}

Probab=99.89  E-value=1.2e-22  Score=147.55  Aligned_cols=96  Identities=31%  Similarity=0.439  Sum_probs=84.8

Q ss_pred             ccCCCCCCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCC
Q psy7268          33 VSRIDLGTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKP  112 (134)
Q Consensus        33 ~~~~~~~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~  112 (134)
                      .+..++.+|+++++++.+++.|.+.||..|+++|.++++.+++|+|+++++|||+|||++|++|+++.+.....     .
T Consensus        19 ~~~~~~~~f~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~li~a~TGsGKT~~~~~~~l~~l~~~~~-----~   93 (236)
T 2pl3_A           19 INVNEITRFSDFPLSKKTLKGLQEAQYRLVTEIQKQTIGLALQGKDVLGAAKTGSGKTLAFLVPVLEALYRLQW-----T   93 (236)
T ss_dssp             CCGGGCSBGGGSCCCHHHHHHHHHTTCCBCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHHTTC-----C
T ss_pred             CCCcccCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEEeCCCCcHHHHHHHHHHHHHHhhcc-----c
Confidence            33456778999999999999999999999999999999999999999999999999999999999999875321     1


Q ss_pred             CCCCcEEEEEcCcHHHHHHhc
Q psy7268         113 ELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus       113 ~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      ...++++||++||++|+.|++
T Consensus        94 ~~~~~~~lil~Pt~~L~~q~~  114 (236)
T 2pl3_A           94 STDGLGVLIISPTRELAYQTF  114 (236)
T ss_dssp             GGGCCCEEEECSSHHHHHHHH
T ss_pred             ccCCceEEEEeCCHHHHHHHH
Confidence            124678999999999999985

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19

Probab=99.88  E-value=5.5e-23  Score=147.89  Aligned_cols=88  Identities=34%  Similarity=0.456  Sum_probs=80.0

Q ss_pred             CCCCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCC
Q psy7268          37 DLGTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNA  116 (134)
Q Consensus        37 ~~~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~  116 (134)
                      +..+|++++|++.+++++.+.||..|+++|.++++.+++|+|+++++|||+|||++|++|+++.+....         .+
T Consensus         2 ~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~~~~l~~l~~~~---------~~   72 (219)
T 1q0u_A            2 AETQFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIMEKIKPER---------AE   72 (219)
T ss_dssp             --CCGGGSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCSSHHHHHHHHHHHHHHCCTTS---------CS
T ss_pred             CCCCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhCc---------CC
Confidence            456899999999999999999999999999999999999999999999999999999999999875422         46


Q ss_pred             cEEEEEcCcHHHHHHhc
Q psy7268         117 PLALIITPGRELVFQIG  133 (134)
Q Consensus       117 ~~~lil~Pt~~La~Qi~  133 (134)
                      .++||++||++|+.|++
T Consensus        73 ~~~lil~Pt~~L~~q~~   89 (219)
T 1q0u_A           73 VQAVITAPTRELATQIY   89 (219)
T ss_dssp             CCEEEECSSHHHHHHHH
T ss_pred             ceEEEEcCcHHHHHHHH
Confidence            78999999999999985

>3dkp_A Probable ATP-dependent RNA helicase DDX52; DEAD, ADP, structural genomics, structural GEN consortium, SGC, rRNA, ATP-binding, hydrolase; HET: ADP; 2.10A {Homo sapiens}

Probab=99.88  E-value=1e-22  Score=148.59  Aligned_cols=93  Identities=33%  Similarity=0.467  Sum_probs=83.8

Q ss_pred             ccCCCCCCcccC----CCCHHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCC
Q psy7268          33 VSRIDLGTFEDT----GLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRP  108 (134)
Q Consensus        33 ~~~~~~~~f~~~----~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~  108 (134)
                      ....++.+|+++    ++++.+++++.+.||..|+++|.++++.+++|+|+++++|||+|||++|++|++..+....   
T Consensus        19 ~~p~~~~~f~~l~~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~l~~a~TGsGKT~~~~l~~l~~l~~~~---   95 (245)
T 3dkp_A           19 DLPDPIATFQQLDQEYKINSRLLQNILDAGFQMPTPIQMQAIPVMLHGRELLASAPTGSGKTLAFSIPILMQLKQPA---   95 (245)
T ss_dssp             SCCCCCSSHHHHHHHHCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHCSCC---
T ss_pred             CCCCcccCHHHhhhccCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHHhhcc---
Confidence            345678899887    8999999999999999999999999999999999999999999999999999999985422   


Q ss_pred             CCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268         109 EYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus       109 ~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                           ..++++||++||++|+.|++
T Consensus        96 -----~~~~~~lil~Pt~~L~~q~~  115 (245)
T 3dkp_A           96 -----NKGFRALIISPTRELASQIH  115 (245)
T ss_dssp             -----SSSCCEEEECSSHHHHHHHH
T ss_pred             -----cCCceEEEEeCCHHHHHHHH
Confidence                 25678999999999999986

>3ber_A Probable ATP-dependent RNA helicase DDX47; DEAD, AMP, structural genomics, structural GEN consortium, SGC, ATP-binding, hydrolase; HET: AMP PGE; 1.40A {Homo sapiens}

Probab=99.88  E-value=8.1e-23  Score=150.37  Aligned_cols=90  Identities=39%  Similarity=0.589  Sum_probs=83.0

Q ss_pred             CCCCCCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCC
Q psy7268          35 RIDLGTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPEL  114 (134)
Q Consensus        35 ~~~~~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~  114 (134)
                      ..+..+|+++++++.+++++.++||..|+++|.++++.+++|+|+++++|||+|||++|++|+++.+....         
T Consensus        39 ~~~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~lv~a~TGsGKT~~~~~~il~~l~~~~---------  109 (249)
T 3ber_A           39 EEETKTFKDLGVTDVLCEACDQLGWTKPTKIQIEAIPLALQGRDIIGLAETGSGKTGAFALPILNALLETP---------  109 (249)
T ss_dssp             HHHHCCTGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHHSC---------
T ss_pred             ccccCCHHHcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEEcCCCCCchhHhHHHHHHHHhcCC---------
Confidence            34567899999999999999999999999999999999999999999999999999999999999987642         


Q ss_pred             CCcEEEEEcCcHHHHHHhc
Q psy7268         115 NAPLALIITPGRELVFQIG  133 (134)
Q Consensus       115 ~~~~~lil~Pt~~La~Qi~  133 (134)
                      .++++||++||++|+.|++
T Consensus       110 ~~~~~lil~Ptr~L~~q~~  128 (249)
T 3ber_A          110 QRLFALVLTPTRELAFQIS  128 (249)
T ss_dssp             CSSCEEEECSSHHHHHHHH
T ss_pred             CCceEEEEeCCHHHHHHHH
Confidence            4678999999999999986

>2oxc_A Probable ATP-dependent RNA helicase DDX20; DEAD, structural genomics, structural genomics consortium, SGC, hydrolase; HET: ADP; 1.30A {Homo sapiens} PDB: 3b7g_A*

Probab=99.88  E-value=1.1e-22  Score=147.64  Aligned_cols=93  Identities=26%  Similarity=0.360  Sum_probs=80.1

Q ss_pred             cccCCCCCCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCC
Q psy7268          32 AVSRIDLGTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYK  111 (134)
Q Consensus        32 ~~~~~~~~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~  111 (134)
                      +....+..+|+++++++.+++++.+.||..|+++|.++++.+++|+|+++++|||+|||++|++|++..+....      
T Consensus        17 ~~~~~~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~l~~a~TGsGKT~~~~l~~l~~l~~~~------   90 (230)
T 2oxc_A           17 DVLLAEPADFESLLLSRPVLEGLRAAGFERPSPVQLKAIPLGRCGLDLIVQAKSGTGKTCVFSTIALDSLVLEN------   90 (230)
T ss_dssp             -------CCGGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCTTS------
T ss_pred             CCCCCCCCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHHHhcC------
Confidence            33445667899999999999999999999999999999999999999999999999999999999999875422      


Q ss_pred             CCCCCcEEEEEcCcHHHHHHhc
Q psy7268         112 PELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus       112 ~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                         .+.++||++||++|+.|++
T Consensus        91 ---~~~~~lil~Pt~~L~~q~~  109 (230)
T 2oxc_A           91 ---LSTQILILAPTREIAVQIH  109 (230)
T ss_dssp             ---CSCCEEEECSSHHHHHHHH
T ss_pred             ---CCceEEEEeCCHHHHHHHH
Confidence               4678999999999999985

>1wrb_A DJVLGB; RNA helicase, DEAD BOX, VASA, structural genomics, NPPSFA, N project on protein structural and functional analyses; 2.40A {Dugesia japonica} SCOP: c.37.1.19

Probab=99.88  E-value=3.8e-23  Score=151.64  Aligned_cols=98  Identities=31%  Similarity=0.488  Sum_probs=83.9

Q ss_pred             CCCCCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCC
Q psy7268          36 IDLGTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELN  115 (134)
Q Consensus        36 ~~~~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~  115 (134)
                      .++.+|++++|++.++++|.+.||..|+++|.++++.+++|+|+++++|||+|||++|++|+++.+..............
T Consensus        20 ~~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~l~~a~TGsGKT~~~~~~~l~~l~~~~~~~~~~~~~~   99 (253)
T 1wrb_A           20 NVIENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIINHLVCQDLNQQRYSKTA   99 (253)
T ss_dssp             SCCCSSGGGSCCCSTTTTTTTTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHTTCC------CCB
T ss_pred             CccCCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhhccccccccccC
Confidence            47789999999999999999999999999999999999999999999999999999999999999876432211112234


Q ss_pred             CcEEEEEcCcHHHHHHhc
Q psy7268         116 APLALIITPGRELVFQIG  133 (134)
Q Consensus       116 ~~~~lil~Pt~~La~Qi~  133 (134)
                      ++++||++||++|+.|++
T Consensus       100 ~~~~lil~Pt~~L~~q~~  117 (253)
T 1wrb_A          100 YPKCLILAPTRELAIQIL  117 (253)
T ss_dssp             CCSEEEECSSHHHHHHHH
T ss_pred             CceEEEEECCHHHHHHHH
Confidence            678999999999999975

>3bor_A Human initiation factor 4A-II; translation initiation, DEAD BOX, structural genomics, helic binding, HOST-virus interaction, hydrolase; 1.85A {Homo sapiens} PDB: 2g9n_A*

Probab=99.88  E-value=7.7e-23  Score=149.10  Aligned_cols=93  Identities=28%  Similarity=0.385  Sum_probs=82.0

Q ss_pred             cccCCCCCCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCC
Q psy7268          32 AVSRIDLGTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYK  111 (134)
Q Consensus        32 ~~~~~~~~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~  111 (134)
                      .....+..+|++++|++.+++++.+.||..|+++|.++++.+++|+|+++++|||+|||++|++|+++.+....      
T Consensus        23 ~~~~~~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~ai~~i~~~~~~li~apTGsGKT~~~~l~~l~~l~~~~------   96 (237)
T 3bor_A           23 SNWNEIVDNFDDMNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGYDVIAQAQSGTGKTATFAISILQQLEIEF------   96 (237)
T ss_dssp             ----CCCCSGGGSCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEECCCSSHHHHHHHHHHHHHHCCTTS------
T ss_pred             CCCCCccCChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHHHhcC------
Confidence            33445678999999999999999999999999999999999999999999999999999999999999875321      


Q ss_pred             CCCCCcEEEEEcCcHHHHHHhc
Q psy7268         112 PELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus       112 ~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                         .+.++||++||++|+.|++
T Consensus        97 ---~~~~~lil~Pt~~L~~q~~  115 (237)
T 3bor_A           97 ---KETQALVLAPTRELAQQIQ  115 (237)
T ss_dssp             ---CSCCEEEECSSHHHHHHHH
T ss_pred             ---CCceEEEEECcHHHHHHHH
Confidence               4678999999999999985

>1vec_A ATP-dependent RNA helicase P54; DEAD-box protein, RNA binding protein; HET: TLA; 2.01A {Homo sapiens} SCOP: c.37.1.19

Probab=99.88  E-value=1.4e-22  Score=144.01  Aligned_cols=86  Identities=35%  Similarity=0.537  Sum_probs=79.4

Q ss_pred             CCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcE
Q psy7268          39 GTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPL  118 (134)
Q Consensus        39 ~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~  118 (134)
                      .+|++++|++++++++.+.||..|+++|.++++.+++|+|+++++|||+|||++|++|++..+....         .+++
T Consensus         3 ~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~apTGsGKT~~~~~~~~~~~~~~~---------~~~~   73 (206)
T 1vec_A            3 NEFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLERLDLKK---------DNIQ   73 (206)
T ss_dssp             SSGGGSCCCHHHHHHHHTTTCCSCCHHHHHHHHHHHTTCCEEEECCSSSTTHHHHHHHHHHHCCTTS---------CSCC
T ss_pred             CChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHccCCCEEEECCCCCchHHHHHHHHHHHhcccC---------CCee
Confidence            4799999999999999999999999999999999999999999999999999999999999875322         5678


Q ss_pred             EEEEcCcHHHHHHhc
Q psy7268         119 ALIITPGRELVFQIG  133 (134)
Q Consensus       119 ~lil~Pt~~La~Qi~  133 (134)
                      +||++|+++|+.|++
T Consensus        74 ~lil~Pt~~L~~q~~   88 (206)
T 1vec_A           74 AMVIVPTRELALQVS   88 (206)
T ss_dssp             EEEECSCHHHHHHHH
T ss_pred             EEEEeCcHHHHHHHH
Confidence            999999999999975

>1qde_A EIF4A, translation initiation factor 4A; DEAD box protein family, gene regulation; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 1qva_A

Probab=99.88  E-value=2.3e-22  Score=144.64  Aligned_cols=91  Identities=31%  Similarity=0.440  Sum_probs=82.9

Q ss_pred             cCCCCCCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCC
Q psy7268          34 SRIDLGTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPE  113 (134)
Q Consensus        34 ~~~~~~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~  113 (134)
                      ...++.+|+++++++.+++.+.+.||..|+++|.++++.+++|+|+++++|||+|||++|++|+++.+....        
T Consensus         9 ~~~~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~~pTGsGKT~~~~~~~l~~l~~~~--------   80 (224)
T 1qde_A            9 YDKVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSV--------   80 (224)
T ss_dssp             CCCCCCCGGGGTCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCTTC--------
T ss_pred             cCcccCChhhcCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHHhccC--------
Confidence            345677899999999999999999999999999999999999999999999999999999999999885422        


Q ss_pred             CCCcEEEEEcCcHHHHHHhc
Q psy7268         114 LNAPLALIITPGRELVFQIG  133 (134)
Q Consensus       114 ~~~~~~lil~Pt~~La~Qi~  133 (134)
                       .+.++||++|+++|+.|++
T Consensus        81 -~~~~~lil~Pt~~L~~q~~   99 (224)
T 1qde_A           81 -KAPQALMLAPTRELALQIQ   99 (224)
T ss_dssp             -CSCCEEEECSSHHHHHHHH
T ss_pred             -CCceEEEEECCHHHHHHHH
Confidence             5678999999999999975

>1t6n_A Probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA processing protein; HET: FLC; 1.94A {Homo sapiens} SCOP: c.37.1.19

Probab=99.87  E-value=6.3e-22  Score=142.16  Aligned_cols=89  Identities=31%  Similarity=0.480  Sum_probs=79.0

Q ss_pred             CCCCCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCC
Q psy7268          36 IDLGTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELN  115 (134)
Q Consensus        36 ~~~~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~  115 (134)
                      ....+|++++|++.++++|.+.||+.|+++|.++++.+++|+|+++++|||+|||++|++|++..+...         ..
T Consensus        11 ~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~li~~~TGsGKT~~~~~~~~~~~~~~---------~~   81 (220)
T 1t6n_A           11 IHSSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPV---------TG   81 (220)
T ss_dssp             ---CCSTTSCCCHHHHHHHHHTTCCCCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCCC---------TT
T ss_pred             ccCCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCchhhhhhHHHHHhhhcc---------CC
Confidence            344679999999999999999999999999999999999999999999999999999999999887432         14


Q ss_pred             CcEEEEEcCcHHHHHHhc
Q psy7268         116 APLALIITPGRELVFQIG  133 (134)
Q Consensus       116 ~~~~lil~Pt~~La~Qi~  133 (134)
                      ++++||++|+++|+.|++
T Consensus        82 ~~~~lil~Pt~~L~~q~~   99 (220)
T 1t6n_A           82 QVSVLVMCHTRELAFQIS   99 (220)
T ss_dssp             CCCEEEECSCHHHHHHHH
T ss_pred             CEEEEEEeCCHHHHHHHH
Confidence            568999999999999975

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens}

Probab=99.86  E-value=1.3e-21  Score=151.28  Aligned_cols=99  Identities=30%  Similarity=0.476  Sum_probs=84.6

Q ss_pred             CCCCCCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCC-------
Q psy7268          35 RIDLGTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSR-------  107 (134)
Q Consensus        35 ~~~~~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~-------  107 (134)
                      ..++.+|++++|++.++++|.+.||..|+++|.++|+.++.|+|+++++|||+|||++|++|+++.+......       
T Consensus        11 p~~~~~f~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~~lv~a~TGsGKT~~~~~~~l~~~~~~~~~~~~~~~~   90 (417)
T 2i4i_A           11 PPHIESFSDVEMGEIIMGNIELTRYTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLLPILSQIYSDGPGEALRAMK   90 (417)
T ss_dssp             CCCCSSGGGSCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHHHCCCHHHHHHH
T ss_pred             CcccCCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHccCCCEEEEcCCCCHHHHHHHHHHHHHHHhccccchhhccc
Confidence            4667899999999999999999999999999999999999999999999999999999999999998754311       


Q ss_pred             --CCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268         108 --PEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus       108 --~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                        ........++++||++||++|+.|++
T Consensus        91 ~~~~~~~~~~~~~~lil~Pt~~L~~q~~  118 (417)
T 2i4i_A           91 ENGRYGRRKQYPISLVLAPTRELAVQIY  118 (417)
T ss_dssp             HCBTTBSCSBCCSEEEECSSHHHHHHHH
T ss_pred             cccccccccCCccEEEECCcHHHHHHHH
Confidence              00011123578999999999999986

>2gxq_A Heat resistant RNA dependent ATPase; RNA helicase, atomic resolution, AMP complex, ribosome biogenesis, thermophilic, hydrolase; HET: AMP; 1.20A {Thermus thermophilus HB27} PDB: 2gxs_A* 2gxu_A 3mwj_A 3mwk_A* 3mwl_A* 3nbf_A* 3nej_A

Probab=99.86  E-value=1.6e-21  Score=138.41  Aligned_cols=88  Identities=43%  Similarity=0.672  Sum_probs=79.7

Q ss_pred             CcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEE
Q psy7268          40 TFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLA  119 (134)
Q Consensus        40 ~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~  119 (134)
                      +|++++|++.+++++.+.||..|+++|.++++.+++|+|+++++|||+|||++|++|+++.+....      ....++++
T Consensus         2 ~f~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~li~~~TGsGKT~~~~~~~~~~l~~~~------~~~~~~~~   75 (207)
T 2gxq_A            2 EFKDFPLKPEILEALHGRGLTTPTPIQAAALPLALEGKDLIGQARTGTGKTLAFALPIAERLAPSQ------ERGRKPRA   75 (207)
T ss_dssp             CGGGSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCCCC------CTTCCCSE
T ss_pred             ChhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHcCCCCEEEECCCCChHHHHHHHHHHHHHhhcc------ccCCCCcE
Confidence            699999999999999999999999999999999999999999999999999999999999886421      11256789


Q ss_pred             EEEcCcHHHHHHhc
Q psy7268         120 LIITPGRELVFQIG  133 (134)
Q Consensus       120 lil~Pt~~La~Qi~  133 (134)
                      +|++|+++|+.|++
T Consensus        76 lil~P~~~L~~q~~   89 (207)
T 2gxq_A           76 LVLTPTRELALQVA   89 (207)
T ss_dssp             EEECSSHHHHHHHH
T ss_pred             EEEECCHHHHHHHH
Confidence            99999999999985

>3ly5_A ATP-dependent RNA helicase DDX18; alpha-beta, structural genomics, structural genomics consort ATP-binding, hydrolase, nucleotide-binding, RNA-B; 2.80A {Homo sapiens}

Probab=99.85  E-value=1.8e-21  Score=144.07  Aligned_cols=89  Identities=36%  Similarity=0.505  Sum_probs=76.0

Q ss_pred             CcccCC--CCHHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCc
Q psy7268          40 TFEDTG--LAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAP  117 (134)
Q Consensus        40 ~f~~~~--l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~  117 (134)
                      +|++++  +++.+++.+.+.||+.|+++|.++++.++.|+|+++++|||+|||++|++|+++.+.....     ....+.
T Consensus        53 ~f~~l~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~l~~l~~l~~~~~-----~~~~~~  127 (262)
T 3ly5_A           53 SFASLCNLVNENTLKAIKEMGFTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPAVELIVKLRF-----MPRNGT  127 (262)
T ss_dssp             CC-----CCCHHHHHHHHHTTCCBCCHHHHHHHHHHHHTCCCEECCCTTSCHHHHHHHHHHHHHHHTTC-----CGGGCC
T ss_pred             ChhHhccccCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCcEEEEccCCCCchHHHHHHHHHHHHhccc-----cccCCc
Confidence            466666  9999999999999999999999999999999999999999999999999999999876321     112467


Q ss_pred             EEEEEcCcHHHHHHhc
Q psy7268         118 LALIITPGRELVFQIG  133 (134)
Q Consensus       118 ~~lil~Pt~~La~Qi~  133 (134)
                      ++||++||++|+.|++
T Consensus       128 ~~lil~Pt~~La~q~~  143 (262)
T 3ly5_A          128 GVLILSPTRELAMQTF  143 (262)
T ss_dssp             CEEEECSSHHHHHHHH
T ss_pred             eEEEEeCCHHHHHHHH
Confidence            8999999999999985

>2j0s_A ATP-dependent RNA helicase DDX48; mRNA processing, phosphorylation, rRNA processing, mRNA splicing, mRNA transport; HET: ANP; 2.21A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 2j0q_A* 2hyi_C* 3ex7_C* 2xb2_A* 2hxy_A 2j0u_A 2j0u_B 2zu6_A

Probab=99.85  E-value=3.2e-21  Score=149.18  Aligned_cols=90  Identities=29%  Similarity=0.451  Sum_probs=81.7

Q ss_pred             CCCCCCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCC
Q psy7268          35 RIDLGTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPEL  114 (134)
Q Consensus        35 ~~~~~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~  114 (134)
                      ..+..+|++++|++.++++|.+.||..|+++|.++++.+++|+|+++++|||+|||++|++|+++.+...         .
T Consensus        33 ~~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~ai~~i~~~~~~lv~a~TGsGKT~~~~~~~~~~l~~~---------~  103 (410)
T 2j0s_A           33 VDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQ---------V  103 (410)
T ss_dssp             CCCCCSGGGGCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHTCCTT---------S
T ss_pred             ccCCCCHhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCCCchHHHHHHHHHHHhhc---------c
Confidence            3556789999999999999999999999999999999999999999999999999999999999877432         1


Q ss_pred             CCcEEEEEcCcHHHHHHhc
Q psy7268         115 NAPLALIITPGRELVFQIG  133 (134)
Q Consensus       115 ~~~~~lil~Pt~~La~Qi~  133 (134)
                      .+.++||++|+++|+.|++
T Consensus       104 ~~~~~lil~Pt~~L~~q~~  122 (410)
T 2j0s_A          104 RETQALILAPTRELAVQIQ  122 (410)
T ss_dssp             CSCCEEEECSSHHHHHHHH
T ss_pred             CCceEEEEcCcHHHHHHHH
Confidence            5678999999999999985

>3fht_A ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box helicase, RNA dependent ATPase, mRNA export, nucleocytoplasmic transport, NUP214, CAN; HET: ANP; 2.20A {Homo sapiens} PDB: 3ews_A* 3g0h_A* 3fhc_B

Probab=99.84  E-value=1.1e-20  Score=145.56  Aligned_cols=90  Identities=27%  Similarity=0.513  Sum_probs=81.9

Q ss_pred             CCCCCCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcC--CCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCC
Q psy7268          35 RIDLGTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSG--KSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKP  112 (134)
Q Consensus        35 ~~~~~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g--~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~  112 (134)
                      ..++.+|+++++++.++++|.+.||..|+++|.++++.+++|  +|+++++|||+|||++|++|+++.+....       
T Consensus        21 ~~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~~~lv~apTGsGKT~~~~~~~~~~~~~~~-------   93 (412)
T 3fht_A           21 LYSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPAN-------   93 (412)
T ss_dssp             TCCSSCTGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHHSSSCCCEEEECCTTSCHHHHHHHHHHHHCCTTS-------
T ss_pred             ccccCCHhhCCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCCeEEEECCCCchHHHHHHHHHHHHhhhcC-------
Confidence            456789999999999999999999999999999999999987  89999999999999999999999875422       


Q ss_pred             CCCCcEEEEEcCcHHHHHHhc
Q psy7268         113 ELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus       113 ~~~~~~~lil~Pt~~La~Qi~  133 (134)
                        .++++||++|+++|+.|++
T Consensus        94 --~~~~~lil~P~~~L~~q~~  112 (412)
T 3fht_A           94 --KYPQCLCLSPTYELALQTG  112 (412)
T ss_dssp             --CSCCEEEECSSHHHHHHHH
T ss_pred             --CCCCEEEECCCHHHHHHHH
Confidence              5668999999999999974

>3fmp_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 3.19A {Homo sapiens}

Probab=99.83  E-value=8.2e-21  Score=150.31  Aligned_cols=89  Identities=27%  Similarity=0.527  Sum_probs=80.7

Q ss_pred             CCCCCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcC--CCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCC
Q psy7268          36 IDLGTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSG--KSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPE  113 (134)
Q Consensus        36 ~~~~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g--~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~  113 (134)
                      .++.+|++++|++.++++|.++||..|+++|.++|+.+++|  +|+++++|||+|||++|++|++..+....        
T Consensus        89 ~~~~~f~~~~l~~~l~~~l~~~g~~~p~~~Q~~ai~~il~~~~~~~l~~a~TGsGKT~~~~l~il~~l~~~~--------  160 (479)
T 3fmp_B           89 YSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPAN--------  160 (479)
T ss_dssp             CCCCCSGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHTSBSCCEEEEECCSSSSHHHHHHHHHHTTCCTTS--------
T ss_pred             cCcCCHHHcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCCcEEEEcCCCCchhHHHHHHHHHHHhhcC--------
Confidence            34678999999999999999999999999999999999987  89999999999999999999998875322        


Q ss_pred             CCCcEEEEEcCcHHHHHHhc
Q psy7268         114 LNAPLALIITPGRELVFQIG  133 (134)
Q Consensus       114 ~~~~~~lil~Pt~~La~Qi~  133 (134)
                       .++++||++|+++|+.|++
T Consensus       161 -~~~~~lil~Pt~~La~Q~~  179 (479)
T 3fmp_B          161 -KYPQCLCLSPTYELALQTG  179 (479)
T ss_dssp             -CSCCEEEECSSHHHHHHHH
T ss_pred             -CCCcEEEEeChHHHHHHHH
Confidence             4668999999999999984

>3pey_A ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, ATPase, helicase, mRNA-export, nuclear pore, hydrolase-RNA complex; HET: ADP; 1.40A {Saccharomyces cerevisiae} PDB: 3pew_A* 3pex_A* 3pez_A* 3rrm_A* 3rrn_A* 2kbe_A 3gfp_A 2kbf_A 3pev_A* 3peu_A*

Probab=99.83  E-value=2.8e-20  Score=142.25  Aligned_cols=87  Identities=29%  Similarity=0.504  Sum_probs=80.0

Q ss_pred             CCCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcC--CCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCC
Q psy7268          38 LGTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSG--KSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELN  115 (134)
Q Consensus        38 ~~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g--~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~  115 (134)
                      ..+|++++|++.++++|.+.||..|+++|.++++.++.|  +++++++|||+|||++|++|++..+....         .
T Consensus         4 ~~~f~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~~~~~~---------~   74 (395)
T 3pey_A            4 AKSFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLTMLTRVNPED---------A   74 (395)
T ss_dssp             CCSSTTSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHCSSCCCEEEECCTTSCHHHHHHHHHHHHCCTTC---------C
T ss_pred             ccCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCCeEEEECCCCCcHHHHHHHHHHHHhccCC---------C
Confidence            478999999999999999999999999999999999988  89999999999999999999999875422         5


Q ss_pred             CcEEEEEcCcHHHHHHhc
Q psy7268         116 APLALIITPGRELVFQIG  133 (134)
Q Consensus       116 ~~~~lil~Pt~~La~Qi~  133 (134)
                      +.++||++|+++|+.|++
T Consensus        75 ~~~~lil~P~~~L~~q~~   92 (395)
T 3pey_A           75 SPQAICLAPSRELARQTL   92 (395)
T ss_dssp             SCCEEEECSSHHHHHHHH
T ss_pred             CccEEEECCCHHHHHHHH
Confidence            678999999999999975

>1s2m_A Putative ATP-dependent RNA helicase DHH1; ATP-binding, RNA-binding, RNA binding protein; 2.10A {Saccharomyces cerevisiae} SCOP: c.37.1.19 c.37.1.19 PDB: 2wax_A* 2way_A

Probab=99.82  E-value=4.1e-20  Score=142.40  Aligned_cols=89  Identities=33%  Similarity=0.491  Sum_probs=79.4

Q ss_pred             CCCCCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCC
Q psy7268          36 IDLGTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELN  115 (134)
Q Consensus        36 ~~~~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~  115 (134)
                      ....+|++++|++.++++|.+.||+.|+++|.++++.+++|+|+++++|||+|||++|++|++..+....         .
T Consensus        18 ~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~li~a~TGsGKT~~~~~~~~~~~~~~~---------~   88 (400)
T 1s2m_A           18 TKGNTFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEKVKPKL---------N   88 (400)
T ss_dssp             ---CCGGGGCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCTTSCHHHHHHHHHHHHCCTTS---------C
T ss_pred             cccCChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCEEEECCCCcHHHHHHHHHHHHHHhhcc---------C
Confidence            3456899999999999999999999999999999999999999999999999999999999998874321         4


Q ss_pred             CcEEEEEcCcHHHHHHhc
Q psy7268         116 APLALIITPGRELVFQIG  133 (134)
Q Consensus       116 ~~~~lil~Pt~~La~Qi~  133 (134)
                      +.++||++|+++|+.|++
T Consensus        89 ~~~~lil~P~~~L~~q~~  106 (400)
T 1s2m_A           89 KIQALIMVPTRELALQTS  106 (400)
T ss_dssp             SCCEEEECSSHHHHHHHH
T ss_pred             CccEEEEcCCHHHHHHHH
Confidence            668999999999999975

>1fuu_A Yeast initiation factor 4A; IF4A, helicase, DEAD-box protein, translation; 2.50A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 2vso_A* 2vsx_A*

Probab=99.81  E-value=3.5e-20  Score=142.02  Aligned_cols=90  Identities=31%  Similarity=0.452  Sum_probs=82.0

Q ss_pred             CCCCCCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCC
Q psy7268          35 RIDLGTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPEL  114 (134)
Q Consensus        35 ~~~~~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~  114 (134)
                      ..+..+|++++|++.+++++.+.||..|+++|.++++.+++|+|+++++|||+|||++|++|++..+....         
T Consensus        17 ~~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~lv~~~TGsGKT~~~~~~~~~~l~~~~---------   87 (394)
T 1fuu_A           17 DKVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSV---------   87 (394)
T ss_dssp             CCCCCSSGGGCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCCEEECCCSSHHHHHHHHHHHHHHCCTTC---------
T ss_pred             ccccCChhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHhhccC---------
Confidence            35567899999999999999999999999999999999999999999999999999999999999875422         


Q ss_pred             CCcEEEEEcCcHHHHHHhc
Q psy7268         115 NAPLALIITPGRELVFQIG  133 (134)
Q Consensus       115 ~~~~~lil~Pt~~La~Qi~  133 (134)
                      .++++||++|+++|+.|++
T Consensus        88 ~~~~~lil~P~~~L~~q~~  106 (394)
T 1fuu_A           88 KAPQALMLAPTRELALQIQ  106 (394)
T ss_dssp             CSCCEEEECSSHHHHHHHH
T ss_pred             CCCCEEEEcCCHHHHHHHH
Confidence            5678999999999999975

>3eiq_A Eukaryotic initiation factor 4A-I; PDCD4, anti-oncogene, apoptosis, cell cycle, nucleus, phosph RNA-binding, ATP-binding, helicase, hydrolase; 3.50A {Homo sapiens}

Probab=99.81  E-value=1.1e-19  Score=140.31  Aligned_cols=90  Identities=31%  Similarity=0.437  Sum_probs=82.2

Q ss_pred             CCCCCCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCC
Q psy7268          35 RIDLGTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPEL  114 (134)
Q Consensus        35 ~~~~~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~  114 (134)
                      .....+|+++++++.+++.+.+.||..|+++|.++++.+++|+|+++++|||+|||++|++|+++.+....         
T Consensus        36 ~~~~~~f~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~~~~~~---------  106 (414)
T 3eiq_A           36 NEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIELDL---------  106 (414)
T ss_dssp             CCCCCCGGGGCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEECCCSCSSSHHHHHHHHHHHCCTTS---------
T ss_pred             cchhcCHhhCCCCHHHHHHHHHcCCCCCCHHHHHHhHHHhCCCCEEEECCCCCcccHHHHHHHHHHHhhcC---------
Confidence            45667899999999999999999999999999999999999999999999999999999999999875422         


Q ss_pred             CCcEEEEEcCcHHHHHHhc
Q psy7268         115 NAPLALIITPGRELVFQIG  133 (134)
Q Consensus       115 ~~~~~lil~Pt~~La~Qi~  133 (134)
                      .+.++||++|+++|+.|++
T Consensus       107 ~~~~~lil~P~~~L~~q~~  125 (414)
T 3eiq_A          107 KATQALVLAPTRELAQQIQ  125 (414)
T ss_dssp             CSCCEEEECSSHHHHHHHH
T ss_pred             CceeEEEEeChHHHHHHHH
Confidence            4678999999999999975

>1xti_A Probable ATP-dependent RNA helicase P47; alpha-beta fold, gene regulation; 1.95A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 1xtj_A* 1xtk_A

Probab=99.81  E-value=6e-20  Score=140.74  Aligned_cols=86  Identities=31%  Similarity=0.487  Sum_probs=78.2

Q ss_pred             CCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcE
Q psy7268          39 GTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPL  118 (134)
Q Consensus        39 ~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~  118 (134)
                      .+|++++|++.++++|.+.||..|+++|.++++.++.|+|+++.+|||+|||++|++|++..+...         ..+.+
T Consensus         8 ~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~l~~~---------~~~~~   78 (391)
T 1xti_A            8 SGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPV---------TGQVS   78 (391)
T ss_dssp             -CGGGGCCCHHHHHHHHHHSCCSCCHHHHHHHHHHTTTCCEEEECSSCSSHHHHHHHHHHHHCCCC---------TTCCC
T ss_pred             CChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCcEEEECCCCCcHHHHHHHHHHHhhccc---------CCCee
Confidence            479999999999999999999999999999999999999999999999999999999999887432         14678


Q ss_pred             EEEEcCcHHHHHHhc
Q psy7268         119 ALIITPGRELVFQIG  133 (134)
Q Consensus       119 ~lil~Pt~~La~Qi~  133 (134)
                      +||++|+++|+.|++
T Consensus        79 ~lil~P~~~L~~q~~   93 (391)
T 1xti_A           79 VLVMCHTRELAFQIS   93 (391)
T ss_dssp             EEEECSCHHHHHHHH
T ss_pred             EEEECCCHHHHHHHH
Confidence            999999999999975

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C}

Probab=99.79  E-value=1.8e-19  Score=146.06  Aligned_cols=83  Identities=33%  Similarity=0.470  Sum_probs=74.8

Q ss_pred             CCHHHHHHHHHCCCCCChHHHHHHHHHHH--cCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEc
Q psy7268          46 LAPEIIDIFTKRGLTTPTEIQKYSIPTLL--SGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIIT  123 (134)
Q Consensus        46 l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~--~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~  123 (134)
                      |++++++++.++||..|+++|.++|+.++  .|+|+++++|||+|||++|++|+++.+.....     ....++++||++
T Consensus        28 l~~~l~~~l~~~g~~~~~~~Q~~~i~~il~~~~~dvlv~apTGsGKTl~~~lpil~~l~~~~~-----~~~~~~~~lvl~  102 (579)
T 3sqw_A           28 LDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKF-----DSQYMVKAVIVA  102 (579)
T ss_dssp             SCHHHHHHHHTTTCSSCCHHHHHHHHHHHCSSSEEEEEECCTTSCHHHHHHHHHHHHHHHTTT-----SSTTSCCEEEEC
T ss_pred             CCHHHHHHHHHCCCCCCCHHHHHHHHHHHccCCCeEEEEcCCCcHHHHHHHHHHHHHHHhccc-----cccCCCeEEEEc
Confidence            99999999999999999999999999999  78899999999999999999999999986432     112467899999


Q ss_pred             CcHHHHHHhc
Q psy7268         124 PGRELVFQIG  133 (134)
Q Consensus       124 Pt~~La~Qi~  133 (134)
                      ||++|+.|++
T Consensus       103 Ptr~La~Q~~  112 (579)
T 3sqw_A          103 PTRDLALQIE  112 (579)
T ss_dssp             SSHHHHHHHH
T ss_pred             chHHHHHHHH
Confidence            9999999985

>3i5x_A ATP-dependent RNA helicase MSS116; protein-RNA complex, RNA helicase, DEAD-BOX, ATP-binding, HE hydrolase, mitochondrion; HET: ANP; 1.90A {Saccharomyces cerevisiae} PDB: 3i5y_A* 3i61_A* 3i62_A* 3sqx_A* 4db2_A 4db4_A

Probab=99.79  E-value=2.1e-19  Score=144.62  Aligned_cols=83  Identities=33%  Similarity=0.470  Sum_probs=74.6

Q ss_pred             CCHHHHHHHHHCCCCCChHHHHHHHHHHH--cCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEc
Q psy7268          46 LAPEIIDIFTKRGLTTPTEIQKYSIPTLL--SGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIIT  123 (134)
Q Consensus        46 l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~--~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~  123 (134)
                      |++.+++++.+.||..|+++|.++|+.++  .|+|+++++|||+|||++|++|+++.+.....     ....++++||++
T Consensus        79 l~~~l~~~l~~~g~~~~~~~Q~~~i~~~l~~~~~~~lv~apTGsGKTl~~~lpil~~l~~~~~-----~~~~~~~~lil~  153 (563)
T 3i5x_A           79 LDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKF-----DSQYMVKAVIVA  153 (563)
T ss_dssp             SCHHHHHHHHTTCCSSCCHHHHHHHHHHHSSSSEEEEEECCTTSCHHHHHHHHHHHHHHHTTT-----SSTTSCCEEEEC
T ss_pred             CCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCCeEEEECCCCCCccHHHHHHHHHHHHhccc-----cccCCeeEEEEc
Confidence            99999999999999999999999999999  67899999999999999999999999986432     112457899999


Q ss_pred             CcHHHHHHhc
Q psy7268         124 PGRELVFQIG  133 (134)
Q Consensus       124 Pt~~La~Qi~  133 (134)
                      ||++|+.|++
T Consensus       154 Ptr~La~Q~~  163 (563)
T 3i5x_A          154 PTRDLALQIE  163 (563)
T ss_dssp             SSHHHHHHHH
T ss_pred             CcHHHHHHHH
Confidence            9999999985

>1hv8_A Putative ATP-dependent RNA helicase MJ0669; RNA-binding protein, ATPase, RNA binding protein; 3.00A {Methanocaldococcus jannaschii} SCOP: c.37.1.19 c.37.1.19

Probab=99.78  E-value=4e-19  Score=134.61  Aligned_cols=86  Identities=35%  Similarity=0.562  Sum_probs=78.3

Q ss_pred             CCCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcC-CCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCC
Q psy7268          38 LGTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSG-KSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNA  116 (134)
Q Consensus        38 ~~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g-~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~  116 (134)
                      ..+|++++|++.++++|.+.||..|+++|.++++.+++| +++++.+|||+|||++|++|++..+...          .+
T Consensus         5 ~~~f~~~~l~~~~~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~~l~~~~TGsGKT~~~~~~~~~~~~~~----------~~   74 (367)
T 1hv8_A            5 YMNFNELNLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIELVNEN----------NG   74 (367)
T ss_dssp             CCCGGGSSCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCSEEEEECCSSSSHHHHHHHHHHHHSCSS----------SS
T ss_pred             cCchhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCEEEECCCCChHHHHHHHHHHHHhccc----------CC
Confidence            457999999999999999999999999999999999988 6999999999999999999998876431          46


Q ss_pred             cEEEEEcCcHHHHHHhc
Q psy7268         117 PLALIITPGRELVFQIG  133 (134)
Q Consensus       117 ~~~lil~Pt~~La~Qi~  133 (134)
                      .++||++|+++|+.|++
T Consensus        75 ~~~lil~P~~~L~~q~~   91 (367)
T 1hv8_A           75 IEAIILTPTRELAIQVA   91 (367)
T ss_dssp             CCEEEECSCHHHHHHHH
T ss_pred             CcEEEEcCCHHHHHHHH
Confidence            78999999999999975

>2z0m_A 337AA long hypothetical ATP-dependent RNA helicase DEAD; ATP-binding, hydrolase, nucleotide-binding, RNA binding protein, structural genomics; 1.90A {Sulfolobus tokodaii}

Probab=99.72  E-value=1.7e-17  Score=124.45  Aligned_cols=73  Identities=33%  Similarity=0.570  Sum_probs=67.8

Q ss_pred             CCHHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCc
Q psy7268          46 LAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPG  125 (134)
Q Consensus        46 l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt  125 (134)
                      |++++.++|.++||..|+++|.++++.+++|+++++.+|||+|||++|++|++..               +.++||++|+
T Consensus         1 l~~~i~~~l~~~g~~~l~~~Q~~~i~~i~~~~~~lv~~~TGsGKT~~~~~~~~~~---------------~~~~liv~P~   65 (337)
T 2z0m_A            1 MNEKIEQAIREMGFKNFTEVQSKTIPLMLQGKNVVVRAKTGSGKTAAYAIPILEL---------------GMKSLVVTPT   65 (337)
T ss_dssp             CCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHH---------------TCCEEEECSS
T ss_pred             CCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCEEEEcCCCCcHHHHHHHHHHhh---------------cCCEEEEeCC
Confidence            5789999999999999999999999999999999999999999999999998763               3569999999


Q ss_pred             HHHHHHhc
Q psy7268         126 RELVFQIG  133 (134)
Q Consensus       126 ~~La~Qi~  133 (134)
                      ++|+.|++
T Consensus        66 ~~L~~q~~   73 (337)
T 2z0m_A           66 RELTRQVA   73 (337)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            99999975

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus}

Probab=99.71  E-value=2.7e-17  Score=136.00  Aligned_cols=84  Identities=31%  Similarity=0.413  Sum_probs=78.1

Q ss_pred             CCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHH-HHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCc
Q psy7268          39 GTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPT-LLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAP  117 (134)
Q Consensus        39 ~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~-~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~  117 (134)
                      -+|++++|++.+.+++.+.||..|+++|.++++. +..|+++++++|||+|||++|.+++++.+..           .+.
T Consensus         8 ~~~~~l~l~~~~~~~l~~~g~~~l~~~Q~~~i~~~~~~~~~~lv~apTGsGKT~~~~l~il~~~~~-----------~~~   76 (715)
T 2va8_A            8 MPIEDLKLPSNVIEIIKKRGIKKLNPPQTEAVKKGLLEGNRLLLTSPTGSGKTLIAEMGIISFLLK-----------NGG   76 (715)
T ss_dssp             CBGGGSSSCHHHHHHHHTTSCCBCCHHHHHHHHTTTTTTCCEEEECCTTSCHHHHHHHHHHHHHHH-----------SCS
T ss_pred             CcHHHcCCCHHHHHHHHhCCCCCCCHHHHHHHHHHhcCCCcEEEEcCCCCcHHHHHHHHHHHHHHH-----------CCC
Confidence            4799999999999999999999999999999999 7889999999999999999999999998864           356


Q ss_pred             EEEEEcCcHHHHHHhc
Q psy7268         118 LALIITPGRELVFQIG  133 (134)
Q Consensus       118 ~~lil~Pt~~La~Qi~  133 (134)
                      +++|++|+++|+.|++
T Consensus        77 ~il~i~P~r~La~q~~   92 (715)
T 2va8_A           77 KAIYVTPLRALTNEKY   92 (715)
T ss_dssp             EEEEECSCHHHHHHHH
T ss_pred             eEEEEeCcHHHHHHHH
Confidence            8999999999999975

>2zj8_A DNA helicase, putative SKI2-type helicase; RECA fold, ATP-binding, hydrolase, nucleotide- binding; 2.00A {Pyrococcus furiosus} PDB: 2zj5_A* 2zj2_A 2zja_A*

Probab=99.71  E-value=1.4e-17  Score=137.96  Aligned_cols=83  Identities=25%  Similarity=0.326  Sum_probs=77.6

Q ss_pred             CcccCCCCHHHHHHHHHCCCCCChHHHHHHHHH-HHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcE
Q psy7268          40 TFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPT-LLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPL  118 (134)
Q Consensus        40 ~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~-~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~  118 (134)
                      +|++++|++.+.+.+.+.||..|+++|.++++. +..|+++++++|||+|||++|.+++++.+..           .+.+
T Consensus         2 ~f~~l~l~~~~~~~l~~~g~~~l~~~Q~~~i~~~~~~~~~~lv~apTGsGKT~~~~l~il~~~~~-----------~~~~   70 (720)
T 2zj8_A            2 RVDELRVDERIKSTLKERGIESFYPPQAEALKSGILEGKNALISIPTASGKTLIAEIAMVHRILT-----------QGGK   70 (720)
T ss_dssp             BGGGCCSCHHHHHHHHHTTCCBCCHHHHHHHTTTGGGTCEEEEECCGGGCHHHHHHHHHHHHHHH-----------HCSE
T ss_pred             cHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCcEEEEcCCccHHHHHHHHHHHHHHHh-----------CCCE
Confidence            589999999999999999999999999999998 8899999999999999999999999998874           3568


Q ss_pred             EEEEcCcHHHHHHhc
Q psy7268         119 ALIITPGRELVFQIG  133 (134)
Q Consensus       119 ~lil~Pt~~La~Qi~  133 (134)
                      ++|++|+++|+.|++
T Consensus        71 ~l~i~P~raLa~q~~   85 (720)
T 2zj8_A           71 AVYIVPLKALAEEKF   85 (720)
T ss_dssp             EEEECSSGGGHHHHH
T ss_pred             EEEEcCcHHHHHHHH
Confidence            999999999999985

>1oyw_A RECQ helicase, ATP-dependent DNA helicase; winged helix, helix-turn-helix, ATP binding, Zn(2+) binding, hydrolase; 1.80A {Escherichia coli} SCOP: a.4.5.43 c.37.1.19 c.37.1.19 PDB: 1oyy_A*

Probab=99.70  E-value=1.9e-17  Score=133.24  Aligned_cols=81  Identities=23%  Similarity=0.309  Sum_probs=74.2

Q ss_pred             CCCcccCCCCHHHHHHHHH-CCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCC
Q psy7268          38 LGTFEDTGLAPEIIDIFTK-RGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNA  116 (134)
Q Consensus        38 ~~~f~~~~l~~~i~~~l~~-~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~  116 (134)
                      +.+|++++|++.+.+.|++ .||..|+++|.++|+.+++|+|+++.+|||+|||++|++|++..               .
T Consensus         1 ~~~fe~l~L~~~~~~~l~~~~g~~~~r~~Q~~~i~~il~g~d~lv~apTGsGKTl~~~lp~l~~---------------~   65 (523)
T 1oyw_A            1 MAQAEVLNLESGAKQVLQETFGYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPALLL---------------N   65 (523)
T ss_dssp             CCCCCCSSHHHHHHHHHHHTTCCSSCCTTHHHHHHHHHTTCCEEEECSCHHHHHHHHHHHHHHS---------------S
T ss_pred             CCChhhCCCCHHHHHHHHHHhCCCCCCHHHHHHHHHHHcCCCEEEECCCCcHHHHHHHHHHHHh---------------C
Confidence            4689999999999999999 79999999999999999999999999999999999999998742               2


Q ss_pred             cEEEEEcCcHHHHHHhc
Q psy7268         117 PLALIITPGRELVFQIG  133 (134)
Q Consensus       117 ~~~lil~Pt~~La~Qi~  133 (134)
                      .++||++|+++|+.|..
T Consensus        66 g~~lvi~P~~aL~~q~~   82 (523)
T 1oyw_A           66 GLTVVVSPLISLMKDQV   82 (523)
T ss_dssp             SEEEEECSCHHHHHHHH
T ss_pred             CCEEEECChHHHHHHHH
Confidence            46899999999999864

>2v1x_A ATP-dependent DNA helicase Q1; DNA strand annealing, mismatch repair, nucleotide-binding, DNA-binding, polymorphism, nuclear protein, ATPase; HET: ADP; 2.00A {Homo sapiens} PDB: 2wwy_A*

Probab=99.67  E-value=1e-16  Score=130.84  Aligned_cols=78  Identities=27%  Similarity=0.319  Sum_probs=71.0

Q ss_pred             cccCCCCHHHHHHHHH-CCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEE
Q psy7268          41 FEDTGLAPEIIDIFTK-RGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLA  119 (134)
Q Consensus        41 f~~~~l~~~i~~~l~~-~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~  119 (134)
                      ++++++++.+.+.|++ .||..|+|+|.++|+.+++|+|+++.+|||+|||++|++|++.               ...++
T Consensus        23 ~~~~~l~~~l~~~L~~~fg~~~~rp~Q~~~i~~il~g~d~lv~~pTGsGKTl~~~lpal~---------------~~g~~   87 (591)
T 2v1x_A           23 KEDFPWSGKVKDILQNVFKLEKFRPLQLETINVTMAGKEVFLVMPTGGGKSLCYQLPALC---------------SDGFT   87 (591)
T ss_dssp             CSCSTTHHHHHHHHHHTSCCCSCCTTHHHHHHHHHTTCCEEEECCTTSCTTHHHHHHHHT---------------SSSEE
T ss_pred             cccCCCCHHHHHHHHHHhCCCCCCHHHHHHHHHHHcCCCEEEEECCCChHHHHHHHHHHH---------------cCCcE
Confidence            3468899999999999 5999999999999999999999999999999999999999975               23479


Q ss_pred             EEEcCcHHHHHHhc
Q psy7268         120 LIITPGRELVFQIG  133 (134)
Q Consensus       120 lil~Pt~~La~Qi~  133 (134)
                      |||+|+++|+.|..
T Consensus        88 lVisP~~~L~~q~~  101 (591)
T 2v1x_A           88 LVICPLISLMEDQL  101 (591)
T ss_dssp             EEECSCHHHHHHHH
T ss_pred             EEEeCHHHHHHHHH
Confidence            99999999999864

>2p6r_A Afuhel308 helicase; protein-DNA complex, SF2 helicase, archaeal helicase, DNA repair,, DNA binding protein/DNA complex; 3.00A {Archaeoglobus fulgidus} SCOP: a.4.5.43 a.289.1.2 c.37.1.19 c.37.1.19 PDB: 2p6u_A

Probab=99.66  E-value=1.4e-17  Score=137.66  Aligned_cols=82  Identities=22%  Similarity=0.305  Sum_probs=73.4

Q ss_pred             CcccCC--CCHHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCc
Q psy7268          40 TFEDTG--LAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAP  117 (134)
Q Consensus        40 ~f~~~~--l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~  117 (134)
                      +|++++  |++.+.+++.+.||+.|+++|.++++.++.|+++++++|||+|||++|.++++..+.            ++.
T Consensus         2 ~f~~l~~~l~~~~~~~l~~~g~~~l~~~Q~~~i~~i~~~~~~lv~apTGsGKT~~~~l~il~~~~------------~~~   69 (702)
T 2p6r_A            2 KVEELAESISSYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAI------------KGG   69 (702)
T ss_dssp             CSHHHHHHHHHHHHHHHHCC---CCCCCCHHHHHHHTTCSCEEEECSSHHHHHHHHHHHHHHHHH------------TTC
T ss_pred             chhhhhhccCHHHHHHHHhCCCCCCCHHHHHHHHHHhCCCcEEEEcCCccHHHHHHHHHHHHHHH------------hCC
Confidence            588888  999999999999999999999999999999999999999999999999999999875            246


Q ss_pred             EEEEEcCcHHHHHHhc
Q psy7268         118 LALIITPGRELVFQIG  133 (134)
Q Consensus       118 ~~lil~Pt~~La~Qi~  133 (134)
                      +++|++|+++|+.|++
T Consensus        70 ~~l~i~P~r~La~q~~   85 (702)
T 2p6r_A           70 KSLYVVPLRALAGEKY   85 (702)
T ss_dssp             CEEEEESSHHHHHHHH
T ss_pred             cEEEEeCcHHHHHHHH
Confidence            8999999999999975

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A*

Probab=99.64  E-value=2.4e-16  Score=122.34  Aligned_cols=73  Identities=26%  Similarity=0.235  Sum_probs=64.3

Q ss_pred             HHHHHHHHH-CCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcH
Q psy7268          48 PEIIDIFTK-RGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGR  126 (134)
Q Consensus        48 ~~i~~~l~~-~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~  126 (134)
                      +++.+.+++ .|| .|+++|.++++.+++|+|+++++|||+|||++|+++++....            .++++||++||+
T Consensus         8 ~~~~~~l~~~~~~-~~~~~Q~~~i~~i~~~~~~lv~apTGsGKT~~~l~~~~~~~~------------~~~~~lil~Pt~   74 (414)
T 3oiy_A            8 EDFRSFFKKKFGK-DLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLAR------------KGKKSALVFPTV   74 (414)
T ss_dssp             HHHHHHHHHHHSS-CCCHHHHHHHHHHTTTCCEECCSCSSSSHHHHHHHHHHHHHT------------TTCCEEEEESSH
T ss_pred             HHHHHHHHHhcCC-CCCHHHHHHHHHHhcCCCEEEEeCCCCCHHHHHHHHHHHHhc------------CCCEEEEEECCH
Confidence            456666766 477 899999999999999999999999999999999999888762            567899999999


Q ss_pred             HHHHHhc
Q psy7268         127 ELVFQIG  133 (134)
Q Consensus       127 ~La~Qi~  133 (134)
                      +|+.|++
T Consensus        75 ~L~~q~~   81 (414)
T 3oiy_A           75 TLVKQTL   81 (414)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            9999986

>3l9o_A ATP-dependent RNA helicase DOB1; REC-A fold, winged-helix-turn-helix, antiparallel-coiled-COI domain, ATP-binding, helicase, hydrolase; 3.39A {Saccharomyces cerevisiae}

Probab=99.56  E-value=1.7e-15  Score=130.97  Aligned_cols=83  Identities=20%  Similarity=0.142  Sum_probs=74.2

Q ss_pred             CCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcE
Q psy7268          39 GTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPL  118 (134)
Q Consensus        39 ~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~  118 (134)
                      ..|+.+++++.+...+.+.++-.|+++|.++|+.+.+|+|+++++|||+|||++|.+|++..+.            .+.+
T Consensus       162 ~~~~~~~l~~~~~~~~~~~~~f~ltp~Q~~AI~~i~~g~dvLV~ApTGSGKTlva~l~i~~~l~------------~g~r  229 (1108)
T 3l9o_A          162 PNYDYTPIAEHKRVNEARTYPFTLDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLK------------NKQR  229 (1108)
T ss_dssp             SCCCSSTTTTTCCCSCSSCCSSCCCHHHHHHHHHHTTTCCEEEECCSSSHHHHHHHHHHHHHHH------------TTCE
T ss_pred             CCcccCCCChhhhHHHHHhCCCCCCHHHHHHHHHHHcCCCEEEECCCCCChHHHHHHHHHHHHh------------cCCe
Confidence            4677788888887777776666899999999999999999999999999999999999999884            4678


Q ss_pred             EEEEcCcHHHHHHhc
Q psy7268         119 ALIITPGRELVFQIG  133 (134)
Q Consensus       119 ~lil~Pt~~La~Qi~  133 (134)
                      ++|++|+++|+.|++
T Consensus       230 vlvl~PtraLa~Q~~  244 (1108)
T 3l9o_A          230 VIYTSPIKALSNQKY  244 (1108)
T ss_dssp             EEEEESSHHHHHHHH
T ss_pred             EEEEcCcHHHHHHHH
Confidence            999999999999986

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*

Probab=99.56  E-value=6e-15  Score=121.12  Aligned_cols=76  Identities=18%  Similarity=0.152  Sum_probs=62.1

Q ss_pred             HHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHH
Q psy7268          51 IDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVF  130 (134)
Q Consensus        51 ~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~  130 (134)
                      ..++..+||..|+++|.++++.++.|+|+++++|||+|||++|++|+++.+.....       ..+.++||++||++|+.
T Consensus         3 ~~~l~~~g~~~lr~~Q~~~i~~~l~g~~~iv~~~TGsGKTl~~~~~i~~~l~~~~~-------~~~~~~lvl~Pt~~L~~   75 (696)
T 2ykg_A            3 VSDTNLYSPFKPRNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFPQ-------GQKGKVVFFANQIPVYE   75 (696)
T ss_dssp             ----CTTC--CCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHHSCT-------TCCCCEEEECSSHHHHH
T ss_pred             CCcccccCCCCccHHHHHHHHHHHcCCCEEEEcCCCchHHHHHHHHHHHHHHhCcc-------CCCCeEEEEECCHHHHH
Confidence            34667789999999999999999999999999999999999999999998875321       13468999999999999


Q ss_pred             Hhc
Q psy7268         131 QIG  133 (134)
Q Consensus       131 Qi~  133 (134)
                      |..
T Consensus        76 Q~~   78 (696)
T 2ykg_A           76 QNK   78 (696)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            975

>1gku_B Reverse gyrase, TOP-RG; topoisomerase, DNA supercoiling, archaea, helicase; 2.7A {Archaeoglobus fulgidus} SCOP: c.37.1.16 c.37.1.16 e.10.1.1 PDB: 1gl9_B*

Probab=99.53  E-value=6.1e-15  Score=126.95  Aligned_cols=70  Identities=29%  Similarity=0.321  Sum_probs=62.0

Q ss_pred             HHHHHHH-CCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHH
Q psy7268          50 IIDIFTK-RGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGREL  128 (134)
Q Consensus        50 i~~~l~~-~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~L  128 (134)
                      +.+.+.+ +||. | ++|.++|+.+++|+|+++++|||||||+ |.+|++..+..           .++++||++||++|
T Consensus        46 ~~~~~~~~~g~~-p-~iQ~~ai~~il~g~dvlv~apTGSGKTl-~~lp~l~~~~~-----------~~~~~lil~PtreL  111 (1054)
T 1gku_B           46 FVEFFRKCVGEP-R-AIQKMWAKRILRKESFAATAPTGVGKTS-FGLAMSLFLAL-----------KGKRCYVIFPTSLL  111 (1054)
T ss_dssp             HHHHHHTTTCSC-C-HHHHHHHHHHHTTCCEECCCCBTSCSHH-HHHHHHHHHHT-----------TSCCEEEEESCHHH
T ss_pred             HHHHHHHhcCCC-H-HHHHHHHHHHHhCCCEEEEcCCCCCHHH-HHHHHHHHHhh-----------cCCeEEEEeccHHH
Confidence            3455555 6998 9 9999999999999999999999999998 99999988864           46789999999999


Q ss_pred             HHHhc
Q psy7268         129 VFQIG  133 (134)
Q Consensus       129 a~Qi~  133 (134)
                      +.|++
T Consensus       112 a~Q~~  116 (1054)
T 1gku_B          112 VIQAA  116 (1054)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            99986

>4ddu_A Reverse gyrase; topoisomerase, DNA supercoiling, archaea, helicase, hydrolas; 3.00A {Thermotoga maritima} PDB: 4ddt_A 4ddv_A 4ddw_A 4ddx_A

Probab=99.53  E-value=1.4e-14  Score=125.19  Aligned_cols=71  Identities=27%  Similarity=0.231  Sum_probs=61.8

Q ss_pred             HHHHHHH-CCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHH
Q psy7268          50 IIDIFTK-RGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGREL  128 (134)
Q Consensus        50 i~~~l~~-~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~L  128 (134)
                      +.+.+.+ .|| .|+++|+++++.+++|+|+++++|||+|||++|+++++..+.            .+.++||++||++|
T Consensus        67 ~~~~~~~~~gf-~pt~iQ~~ai~~il~g~dvlv~ApTGSGKTl~~l~~il~~~~------------~~~~~Lil~PtreL  133 (1104)
T 4ddu_A           67 FRSFFKKKFGK-DLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLAR------------KGKKSALVFPTVTL  133 (1104)
T ss_dssp             HHHHHHHHSSS-CCCHHHHHHHHHHTTTCCEEECCSTTCCHHHHHHHHHHHHHT------------TTCCEEEEESSHHH
T ss_pred             HHHHHHHhcCC-CCCHHHHHHHHHHHcCCCEEEEeCCCCcHHHHHHHHHHHHHh------------cCCeEEEEechHHH
Confidence            3344443 689 799999999999999999999999999999999888888772            57789999999999


Q ss_pred             HHHhc
Q psy7268         129 VFQIG  133 (134)
Q Consensus       129 a~Qi~  133 (134)
                      |.|++
T Consensus       134 a~Q~~  138 (1104)
T 4ddu_A          134 VKQTL  138 (1104)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            99986

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus}

Probab=99.53  E-value=2.1e-14  Score=114.01  Aligned_cols=66  Identities=21%  Similarity=0.211  Sum_probs=59.2

Q ss_pred             CChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          61 TPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        61 ~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      .|+++|.++++.++.|+|+++++|||+|||++|++|+++.+.....       ..+.++||++||++|+.|++
T Consensus         4 ~~~~~Q~~~i~~~~~~~~~l~~~~tGsGKT~~~~~~~~~~~~~~~~-------~~~~~~lil~P~~~L~~q~~   69 (555)
T 3tbk_A            4 KPRNYQLELALPAKKGKNTIICAPTGCGKTFVSLLICEHHLKKFPC-------GQKGKVVFFANQIPVYEQQA   69 (555)
T ss_dssp             CCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHTCCS-------SCCCCEEEECSSHHHHHHHH
T ss_pred             CCcHHHHHHHHHHhCCCCEEEEeCCCChHHHHHHHHHHHHHHhccc-------CCCCEEEEEeCCHHHHHHHH
Confidence            7999999999999999999999999999999999999999876321       13678999999999999975

>4a2p_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.00A {Anas platyrhynchos} PDB: 4a36_A*

Probab=99.52  E-value=2.4e-14  Score=114.05  Aligned_cols=68  Identities=16%  Similarity=0.132  Sum_probs=58.3

Q ss_pred             CCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          59 LTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        59 ~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      .-.|+++|.++++.+++|+|+++++|||+|||++|++|+++.+.....       ..+.++||++|+++|+.|++
T Consensus         5 ~~~~~~~Q~~~i~~~~~~~~~l~~~~tGsGKT~~~~~~~~~~~~~~~~-------~~~~~~lil~P~~~L~~q~~   72 (556)
T 4a2p_A            5 TKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPA-------GRKAKVVFLATKVPVYEQQK   72 (556)
T ss_dssp             ---CCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHTCCS-------SCCCCEEEECSSHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHcCCCEEEEcCCCChHHHHHHHHHHHHHHhCcc-------cCCCeEEEEeCCHHHHHHHH
Confidence            348999999999999999999999999999999999999999875321       13678999999999999975

>4f92_B U5 small nuclear ribonucleoprotein 200 kDa helica; RNP remodeling, PRE-mRNA splicing, spliceosome catalytic ACT DEXD/H-box RNA helicase; HET: SAN; 2.66A {Homo sapiens} PDB: 4f93_B* 4f91_B

Probab=99.52  E-value=2.5e-14  Score=127.80  Aligned_cols=78  Identities=21%  Similarity=0.216  Sum_probs=69.3

Q ss_pred             CCHHHHHHHHHCCCCCChHHHHHHHHHHHc-CCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcC
Q psy7268          46 LAPEIIDIFTKRGLTTPTEIQKYSIPTLLS-GKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITP  124 (134)
Q Consensus        46 l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~-g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~P  124 (134)
                      |++...+++...+|+.++|+|.++++.++. ++|++++||||||||++|.+|++..+.+.          .+.++||++|
T Consensus       911 L~~~~~e~l~~~~f~~fnpiQ~q~~~~l~~~~~nvlv~APTGSGKTliaelail~~l~~~----------~~~kavyi~P  980 (1724)
T 4f92_B          911 LRNSAFESLYQDKFPFFNPIQTQVFNTVYNSDDNVFVGAPTGSGKTICAEFAILRMLLQS----------SEGRCVYITP  980 (1724)
T ss_dssp             SCCHHHHTTTTTTCSBCCHHHHHHHHHHHSCCSCEEEECCTTSCCHHHHHHHHHHHHHHC----------TTCCEEEECS
T ss_pred             ccCHHHHHHHHhcCCCCCHHHHHHHHHHhcCCCcEEEEeCCCCCchHHHHHHHHHHHHhC----------CCCEEEEEcC
Confidence            567788888888999999999999999986 56799999999999999999999999753          3567999999


Q ss_pred             cHHHHHHhc
Q psy7268         125 GRELVFQIG  133 (134)
Q Consensus       125 t~~La~Qi~  133 (134)
                      +|+||.|++
T Consensus       981 ~raLa~q~~  989 (1724)
T 4f92_B          981 MEALAEQVY  989 (1724)
T ss_dssp             CHHHHHHHH
T ss_pred             hHHHHHHHH
Confidence            999999975

>1tf5_A Preprotein translocase SECA subunit; ATPase, helicase, translocation, secretion, protein transport; 2.18A {Bacillus subtilis} SCOP: a.162.1.1 a.172.1.1 c.37.1.19 c.37.1.19 PDB: 1tf2_A 3iqy_A 1m6n_A 1m74_A* 3iqm_A 3jv2_A* 2ibm_A* 3dl8_A 1sx0_A 1sx1_A 1tm6_A

Probab=99.51  E-value=3e-14  Score=119.44  Aligned_cols=63  Identities=25%  Similarity=0.263  Sum_probs=56.8

Q ss_pred             HCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          56 KRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        56 ~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      .+|| .|+++|..++|.++.|+  +..++||+|||++|.+|++....            .+.+++||+||++||.|++
T Consensus        79 ~lG~-~pt~VQ~~~ip~ll~G~--Iaea~TGeGKTlaf~LP~~l~aL------------~g~~vlVltptreLA~qd~  141 (844)
T 1tf5_A           79 VTGM-FPFKVQLMGGVALHDGN--IAEMKTGEGKTLTSTLPVYLNAL------------TGKGVHVVTVNEYLASRDA  141 (844)
T ss_dssp             HHSC-CCCHHHHHHHHHHHTTS--EEECCTTSCHHHHHHHHHHHHHT------------TSSCEEEEESSHHHHHHHH
T ss_pred             HcCC-CCcHHHHHhhHHHhCCC--EEEccCCcHHHHHHHHHHHHHHH------------cCCCEEEEeCCHHHHHHHH
Confidence            4799 99999999999999999  89999999999999999985543            3567999999999999985

>4a2q_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.40A {Anas platyrhynchos}

Probab=99.49  E-value=6e-14  Score=117.53  Aligned_cols=70  Identities=16%  Similarity=0.116  Sum_probs=59.4

Q ss_pred             CCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          57 RGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        57 ~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      .|+..|+++|.++++.++.|+|+++++|||+|||++|++|++..+.....       ..+.++||++|+++|+.|++
T Consensus       244 ~g~~~l~~~Q~~~i~~~l~~~~~ll~~~TGsGKTl~~~~~i~~~l~~~~~-------~~~~~~Lvl~Pt~~L~~Q~~  313 (797)
T 4a2q_A          244 YETKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPA-------GRKAKVVFLATKVPVYEQQK  313 (797)
T ss_dssp             ----CCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHTCCS-------SCCCCEEEECSSHHHHHHHH
T ss_pred             cCCCCCCHHHHHHHHHHHhCCCEEEEeCCCChHHHHHHHHHHHHHHhccc-------cCCCeEEEEeCCHHHHHHHH
Confidence            47889999999999999999999999999999999999999999875321       13678999999999999975

>4f92_B U5 small nuclear ribonucleoprotein 200 kDa helica; RNP remodeling, PRE-mRNA splicing, spliceosome catalytic ACT DEXD/H-box RNA helicase; HET: SAN; 2.66A {Homo sapiens} PDB: 4f93_B* 4f91_B

Probab=99.48  E-value=7.4e-14  Score=124.77  Aligned_cols=75  Identities=25%  Similarity=0.255  Sum_probs=63.5

Q ss_pred             CCCCChHHHHHHHHHHH-cCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          58 GLTTPTEIQKYSIPTLL-SGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        58 g~~~~t~iQ~~~i~~~~-~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      ||++++++|++++|.++ .++|++++||||+|||+++.++++..+.+..... ......+.++||++|+|+||.|++
T Consensus        76 g~~~ln~iQs~~~~~al~~~~N~lv~APTGsGKTlva~l~il~~l~~~~~~~-~~~~~~~~k~lyiaP~kALa~e~~  151 (1724)
T 4f92_B           76 GFKTLNRIQSKLYRAALETDENLLLCAPTGAGKTNVALMCMLREIGKHINMD-GTINVDDFKIIYIAPMRSLVQEMV  151 (1724)
T ss_dssp             TCSBCCHHHHHTHHHHHTCCCCEEEECCTTSCCHHHHHHHHHHHHGGGCCTT-SSCCTTSCEEEEECSSHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHcCCCcEEEEeCCcchHHHHHHHHHHHHHHhhcccc-ccccCCCCEEEEECCHHHHHHHHH
Confidence            89999999999999987 5789999999999999999999999998643321 122235789999999999999985

>1gm5_A RECG; helicase, replication restart; HET: DNA ADP; 3.24A {Thermotoga maritima} SCOP: a.24.21.1 b.40.4.9 c.37.1.19 c.37.1.19

Probab=99.47  E-value=8.3e-14  Score=116.80  Aligned_cols=73  Identities=15%  Similarity=0.134  Sum_probs=63.7

Q ss_pred             HHHHHHHHHCCCCCChHHHHHHHHHHHcC------CCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEE
Q psy7268          48 PEIIDIFTKRGLTTPTEIQKYSIPTLLSG------KSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALI  121 (134)
Q Consensus        48 ~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g------~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~li  121 (134)
                      +.+.+.+..++| .||++|.++++.++++      .|++++++||||||++|++|++..+.            .+.+++|
T Consensus       356 ~~~~~~~~~lpf-~lt~~Q~~ai~~I~~~l~~~~~~~~Ll~a~TGSGKTlvall~il~~l~------------~g~qvlv  422 (780)
T 1gm5_A          356 KLAEEFIKSLPF-KLTNAQKRAHQEIRNDMISEKPMNRLLQGDVGSGKTVVAQLAILDNYE------------AGFQTAF  422 (780)
T ss_dssp             HHHHHHHHHSSS-CCCHHHHHHHHHHHHHHHSSSCCCCEEECCSSSSHHHHHHHHHHHHHH------------HTSCEEE
T ss_pred             HHHHHHHHhCCC-CCCHHHHHHHHHHHhhccccCCCcEEEEcCCCCCHHHHHHHHHHHHHH------------cCCeEEE
Confidence            444555677899 9999999999998865      58999999999999999999999885            3578999


Q ss_pred             EcCcHHHHHHhc
Q psy7268         122 ITPGRELVFQIG  133 (134)
Q Consensus       122 l~Pt~~La~Qi~  133 (134)
                      ++||++||.|++
T Consensus       423 laPtr~La~Q~~  434 (780)
T 1gm5_A          423 MVPTSILAIQHY  434 (780)
T ss_dssp             ECSCHHHHHHHH
T ss_pred             EeCcHHHHHHHH
Confidence            999999999986

>3b6e_A Interferon-induced helicase C domain-containing P; DECH, DEXD/H RNA-binding helicase, innate immunity, IFIH1, S genomics; 1.60A {Homo sapiens}

Probab=99.47  E-value=6.7e-14  Score=99.11  Aligned_cols=68  Identities=21%  Similarity=0.099  Sum_probs=58.4

Q ss_pred             CCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHH
Q psy7268          58 GLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQ  131 (134)
Q Consensus        58 g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Q  131 (134)
                      +...|+++|.++++.+++|+++++.+|||+|||++++++++..+.....      ...+.++||++|+++|+.|
T Consensus        30 ~~~~l~~~Q~~~i~~~~~~~~~li~~~tGsGKT~~~~~~~~~~~~~~~~------~~~~~~~lil~p~~~L~~q   97 (216)
T 3b6e_A           30 PELQLRPYQMEVAQPALEGKNIIICLPTGSGKTRVAVYIAKDHLDKKKK------ASEPGKVIVLVNKVLLVEQ   97 (216)
T ss_dssp             CCCCCCHHHHHHHHHHHTTCCEEEECSCHHHHHHHHHHHHHHHHHHHHH------TTCCCCEEEEESSHHHHHH
T ss_pred             CCCCchHHHHHHHHHHhcCCCEEEEcCCCCCHHHHHHHHHHHHHhhccc------ccCCCcEEEEECHHHHHHH
Confidence            4458999999999999999999999999999999999999988765321      1135689999999999998

>2jlq_A Serine protease subunit NS3; ribonucleoprotein, nucleotide-binding, viral nucleoprotein, endoplasmic reticulum, helicase, hydrolase; 1.67A {Dengue virus 4} PDB: 2jly_A* 2jls_A* 2jlu_A 2jlv_A* 2jlw_A 2jlx_A* 2jlz_A* 2jlr_A* 2bmf_A 2bhr_A

Probab=99.47  E-value=5.1e-15  Score=117.04  Aligned_cols=64  Identities=22%  Similarity=0.287  Sum_probs=57.7

Q ss_pred             CCCCChHHHHHHHHHHHcCCCe-EEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          58 GLTTPTEIQKYSIPTLLSGKSA-ILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        58 g~~~~t~iQ~~~i~~~~~g~dv-li~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      |+..|+++|+ +||.+++|+|+ ++++|||||||++|++|++..+..           .+.++||++||++|+.|++
T Consensus         1 G~~q~~~iq~-~i~~~l~~~~~~lv~a~TGsGKT~~~~~~~l~~~~~-----------~~~~~lvl~Ptr~La~Q~~   65 (451)
T 2jlq_A            1 GSAMGEPDYE-VDEDIFRKKRLTIMDLHPGAGKTKRILPSIVREALL-----------RRLRTLILAPTRVVAAEME   65 (451)
T ss_dssp             CCCCCSCCCC-CCGGGGSTTCEEEECCCTTSSCCTTHHHHHHHHHHH-----------TTCCEEEEESSHHHHHHHH
T ss_pred             CCCCCCCcHH-HHHHHHhcCCeEEEECCCCCCHhhHHHHHHHHHHHh-----------cCCcEEEECCCHHHHHHHH
Confidence            7889999986 79999999987 899999999999999999988765           4678999999999999986

>2whx_A Serine protease/ntpase/helicase NS3; transcription, hydrolase, ATP-binding, reticulum, nucleotidyltransferase, multifunctional enzyme; HET: ADP; 2.20A {Dengue virus 4} PDB: 2vbc_A 2wzq_A

Probab=99.47  E-value=1.3e-15  Score=124.88  Aligned_cols=78  Identities=17%  Similarity=0.211  Sum_probs=62.8

Q ss_pred             CCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEc
Q psy7268          44 TGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIIT  123 (134)
Q Consensus        44 ~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~  123 (134)
                      +++++.+++.+.+. .+.++|+|+.+++.+++|+|+++++|||||||++|++|+++.+..           .+.++||++
T Consensus       155 l~~~~~~~~~l~~~-~~~~lpiq~~~i~~l~~g~dvlv~a~TGSGKT~~~~lpil~~l~~-----------~~~~vLvl~  222 (618)
T 2whx_A          155 VTKSGDYVSAITQA-ERIGEPDYEVDEDIFRKKRLTIMDLHPGAGKTKRILPSIVREALK-----------RRLRTLILA  222 (618)
T ss_dssp             -------CEECBCC-CCCCCCCCCCCGGGGSTTCEEEECCCTTSSTTTTHHHHHHHHHHH-----------TTCCEEEEE
T ss_pred             ccchHHHHHHHhhc-cccCCCccccCHHHHhcCCeEEEEcCCCCCHHHHHHHHHHHHHHh-----------CCCeEEEEc
Confidence            55666666655543 588999998899999999999999999999999999999999875           457899999


Q ss_pred             CcHHHHHHhc
Q psy7268         124 PGRELVFQIG  133 (134)
Q Consensus       124 Pt~~La~Qi~  133 (134)
                      |||+||.|++
T Consensus       223 PtreLa~Qi~  232 (618)
T 2whx_A          223 PTRVVAAEME  232 (618)
T ss_dssp             SSHHHHHHHH
T ss_pred             ChHHHHHHHH
Confidence            9999999986

>2xgj_A ATP-dependent RNA helicase DOB1; hydrolase-RNA complex, hydrolase, tramp, exosome, DEAD, nucleotide-binding; HET: ADP; 2.90A {Saccharomyces cerevisiae}

Probab=99.42  E-value=2.8e-13  Score=116.26  Aligned_cols=67  Identities=22%  Similarity=0.204  Sum_probs=60.4

Q ss_pred             HHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          54 FTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        54 l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      ....+| .|+++|.++++.+.+|+++++++|||+|||++|.++++..+.            .+.++||++|+++|+.|++
T Consensus        80 ~~~~~f-~L~~~Q~eai~~l~~g~~vLV~apTGSGKTlva~lai~~~l~------------~g~rvL~l~PtkaLa~Q~~  146 (1010)
T 2xgj_A           80 ARTYPF-TLDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLK------------NKQRVIYTSPIKALSNQKY  146 (1010)
T ss_dssp             SCCCSS-CCCHHHHHHHHHHHHTCEEEEECCTTSCHHHHHHHHHHHHHH------------TTCEEEEEESSHHHHHHHH
T ss_pred             HHhCCC-CCCHHHHHHHHHHHcCCCEEEECCCCCChHHHHHHHHHHHhc------------cCCeEEEECChHHHHHHHH
Confidence            344588 599999999999999999999999999999999999998874            4678999999999999986

>2wv9_A Flavivirin protease NS2B regulatory subunit, FLAV protease NS3 catalytic subunit; nucleotide-binding, capsid protein; 2.75A {Murray valley encephalitis virus}

Probab=99.41  E-value=6.3e-15  Score=121.89  Aligned_cols=70  Identities=16%  Similarity=0.295  Sum_probs=59.6

Q ss_pred             HHHHCCCC-----CChHHHH-----HHHHHHH------cCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCC
Q psy7268          53 IFTKRGLT-----TPTEIQK-----YSIPTLL------SGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNA  116 (134)
Q Consensus        53 ~l~~~g~~-----~~t~iQ~-----~~i~~~~------~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~  116 (134)
                      .+...||.     +||++|+     ++||.++      +|+|+++++|||||||++|++|+++.+..           .+
T Consensus       202 ~l~~~Gf~~~~~~~pt~IQ~~~r~~~aIp~~l~~~~l~~g~dvlv~apTGSGKTl~~ll~il~~l~~-----------~~  270 (673)
T 2wv9_A          202 GLYGNGVILGNGAYVSAIVQGERVEEPVPEAYNPEMLKKRQLTVLDLHPGAGKTRRILPQIIKDAIQ-----------KR  270 (673)
T ss_dssp             EEEEEEEECSSSCEEEEEECC-------CCCCCGGGGSTTCEEEECCCTTTTTTTTHHHHHHHHHHH-----------TT
T ss_pred             EeeeccccccCCCccCceeeccccccchHHHhhHHHHhcCCeEEEEeCCCCCHHHHHHHHHHHHHHh-----------CC
Confidence            45556777     8999999     9999888      89999999999999999999999998765           46


Q ss_pred             cEEEEEcCcHHHHHHhc
Q psy7268         117 PLALIITPGRELVFQIG  133 (134)
Q Consensus       117 ~~~lil~Pt~~La~Qi~  133 (134)
                      .+++|++||++||.|++
T Consensus       271 ~~~lilaPTr~La~Q~~  287 (673)
T 2wv9_A          271 LRTAVLAPTRVVAAEMA  287 (673)
T ss_dssp             CCEEEEESSHHHHHHHH
T ss_pred             CcEEEEccHHHHHHHHH
Confidence            78999999999999986

>4a2w_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.70A {Anas platyrhynchos}

Probab=99.40  E-value=2.6e-13  Score=115.59  Aligned_cols=70  Identities=16%  Similarity=0.111  Sum_probs=58.5

Q ss_pred             CCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          57 RGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        57 ~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      .|+..|+++|.++++.++.|+|+++++|||+|||++|++|+++.+....       ...+.++||++|+++|+.|++
T Consensus       244 ~~~~~~r~~Q~~ai~~il~g~~~ll~a~TGsGKTl~~~~~i~~~l~~~~-------~~~~~~vLvl~Pt~~L~~Q~~  313 (936)
T 4a2w_A          244 YETKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMP-------AGRKAKVVFLATKVPVYEQQK  313 (936)
T ss_dssp             ----CCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHTTTTTCC-------SSCCCCEEEECSSHHHHHHHH
T ss_pred             cCCCCCCHHHHHHHHHHHcCCCEEEEeCCCchHHHHHHHHHHHHHHhcc-------ccCCCeEEEEeCCHHHHHHHH
Confidence            3678999999999999999999999999999999999999998876432       113678999999999999975

>2fsf_A Preprotein translocase SECA subunit; ATPase, DNA-RNA helicase, protein translocation, protein transport; 2.00A {Escherichia coli} PDB: 2fsg_A* 2fsh_A* 2fsi_A* 2vda_A 3bxz_A*

Probab=99.39  E-value=3.4e-13  Score=113.07  Aligned_cols=62  Identities=23%  Similarity=0.139  Sum_probs=55.8

Q ss_pred             CCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          57 RGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        57 ~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      +|. .|+++|..++|.++.|+  ++.++||+|||++|++|++....            .+.+++|++||++||.|++
T Consensus        71 lg~-~p~~VQ~~~i~~ll~G~--Iaem~TGsGKTlaf~LP~l~~~l------------~g~~vlVltPTreLA~Q~~  132 (853)
T 2fsf_A           71 FGM-RHFDVQLLGGMVLNERC--IAEMRTGEGKTLTATLPAYLNAL------------TGKGVHVVTVNDYLAQRDA  132 (853)
T ss_dssp             HSC-CCCHHHHHHHHHHHSSE--EEECCTTSCHHHHHHHHHHHHHT------------TSSCCEEEESSHHHHHHHH
T ss_pred             cCC-CCChHHHhhcccccCCe--eeeecCCchHHHHHHHHHHHHHH------------cCCcEEEEcCCHHHHHHHH
Confidence            476 99999999999999998  89999999999999999987653            4567999999999999985

>4a4z_A Antiviral helicase SKI2; hydrolase, ATPase, mRNA degradation, exosome; HET: ANP; 2.40A {Saccharomyces cerevisiae} PDB: 4a4k_A

Probab=99.38  E-value=5.9e-13  Score=114.17  Aligned_cols=65  Identities=22%  Similarity=0.158  Sum_probs=58.7

Q ss_pred             HCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          56 KRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        56 ~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      ..+| .|+++|.++|+.+++|+|+++++|||+|||++|++++...+.            .+.++||++|+++|+.|++
T Consensus        35 ~~~f-~l~~~Q~~aI~~il~g~~vlv~apTGsGKTlv~~~~i~~~~~------------~g~~vlvl~PtraLa~Q~~   99 (997)
T 4a4z_A           35 SWPF-ELDTFQKEAVYHLEQGDSVFVAAHTSAGKTVVAEYAIAMAHR------------NMTKTIYTSPIKALSNQKF   99 (997)
T ss_dssp             CCSS-CCCHHHHHHHHHHHTTCEEEEECCTTSCSHHHHHHHHHHHHH------------TTCEEEEEESCGGGHHHHH
T ss_pred             hCCC-CCCHHHHHHHHHHHcCCCEEEEECCCCcHHHHHHHHHHHHHh------------cCCeEEEEeCCHHHHHHHH
Confidence            3578 689999999999999999999999999999999999888764            4678999999999999986

>3llm_A ATP-dependent RNA helicase A; alpha-beta-alpha, structural genomics, structural genomics consortium, SGC, activator, ATP-binding, DNA-binding; HET: ADP; 2.80A {Homo sapiens}

Probab=99.35  E-value=1.3e-12  Score=94.72  Aligned_cols=67  Identities=13%  Similarity=0.222  Sum_probs=57.7

Q ss_pred             CCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          60 TTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        60 ~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      ..++++|.++++.+..|++++++|+||||||..+.++++........       ..+.+++++.|+++|+.|++
T Consensus        60 ~p~~~~q~~~i~~i~~g~~~~i~g~TGsGKTt~~~~~~~~~~~~~~~-------~~~~~~l~~~p~~~la~q~~  126 (235)
T 3llm_A           60 LPVKKFESEILEAISQNSVVIIRGATGCGKTTQVPQFILDDFIQNDR-------AAECNIVVTQPRRISAVSVA  126 (235)
T ss_dssp             SGGGGGHHHHHHHHHHCSEEEEECCTTSSHHHHHHHHHHHHHHHTTC-------GGGCEEEEEESSHHHHHHHH
T ss_pred             CChHHHHHHHHHHHhcCCEEEEEeCCCCCcHHhHHHHHhcchhhcCC-------CCceEEEEeccchHHHHHHH
Confidence            36789999999999999999999999999999999999887765321       13568999999999999985

>2eyq_A TRCF, transcription-repair coupling factor; MFD, SF2 ATPase, hydrolase; HET: EPE; 3.20A {Escherichia coli} SCOP: b.34.18.1 c.37.1.19 c.37.1.19 c.37.1.19 c.37.1.19 d.315.1.1

Probab=99.34  E-value=3.5e-12  Score=110.72  Aligned_cols=77  Identities=19%  Similarity=0.157  Sum_probs=65.2

Q ss_pred             CCCCHHHHHHHHH-CCCCCChHHHHHHHHHHHc----CC--CeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCC
Q psy7268          44 TGLAPEIIDIFTK-RGLTTPTEIQKYSIPTLLS----GK--SAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNA  116 (134)
Q Consensus        44 ~~l~~~i~~~l~~-~g~~~~t~iQ~~~i~~~~~----g~--dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~  116 (134)
                      ++.++...+.+.+ .+| .+|++|.++++.++.    |+  |++++++||+|||++++++++..+.            .+
T Consensus       586 ~~~~~~~~~~~~~~f~~-~~t~~Q~~ai~~il~~~~~g~p~d~ll~~~TGsGKT~val~aa~~~~~------------~g  652 (1151)
T 2eyq_A          586 FKHDREQYQLFCDSFPF-ETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVD------------NH  652 (1151)
T ss_dssp             CCCCHHHHHHHHHTCCS-CCCHHHHHHHHHHHHHHHSSSCCEEEEECCCCTTTHHHHHHHHHHHHT------------TT
T ss_pred             CCCCHHHHHHHHHhCCC-CCCHHHHHHHHHHHHHHhcCCcCcEEEECCCCCCHHHHHHHHHHHHHH------------hC
Confidence            4566777777755 588 579999999999886    66  9999999999999999999887653            45


Q ss_pred             cEEEEEcCcHHHHHHhc
Q psy7268         117 PLALIITPGRELVFQIG  133 (134)
Q Consensus       117 ~~~lil~Pt~~La~Qi~  133 (134)
                      .+++|++||++|+.|.+
T Consensus       653 ~~vlvlvPt~~La~Q~~  669 (1151)
T 2eyq_A          653 KQVAVLVPTTLLAQQHY  669 (1151)
T ss_dssp             CEEEEECSSHHHHHHHH
T ss_pred             CeEEEEechHHHHHHHH
Confidence            69999999999999975

>1nkt_A Preprotein translocase SECA 1 subunit; preprotein translocation, ATPase, transmembrane transport, helicase-like motor domain; HET: ADP; 2.60A {Mycobacterium tuberculosis} SCOP: a.162.1.1 a.172.1.1 c.37.1.19 c.37.1.19 PDB: 1nl3_A

Probab=99.33  E-value=2.1e-12  Score=108.78  Aligned_cols=62  Identities=24%  Similarity=0.244  Sum_probs=56.0

Q ss_pred             CCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          57 RGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        57 ~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      +|+ +|+++|..++|.++.|+  ++.++||+|||++|.+|++....            .+.+++||+||++||.|++
T Consensus       108 lG~-rP~~VQ~~~ip~Ll~G~--Iaem~TGeGKTLa~~LP~~l~aL------------~g~~v~VvTpTreLA~Qda  169 (922)
T 1nkt_A          108 LDQ-RPFDVQVMGAAALHLGN--VAEMKTGEGKTLTCVLPAYLNAL------------AGNGVHIVTVNDYLAKRDS  169 (922)
T ss_dssp             HSC-CCCHHHHHHHHHHHTTE--EEECCTTSCHHHHTHHHHHHHHT------------TTSCEEEEESSHHHHHHHH
T ss_pred             cCC-CCCHHHHHHHHhHhcCC--EEEecCCCccHHHHHHHHHHHHH------------hCCCeEEEeCCHHHHHHHH
Confidence            699 99999999999999998  89999999999999999976554            3457999999999999975

>1rif_A DAR protein, DNA helicase UVSW; bacteriophage, RECG, SF2, DNA binding protein; HET: DNA; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.23

Probab=99.33  E-value=1.9e-12  Score=96.11  Aligned_cols=62  Identities=24%  Similarity=0.182  Sum_probs=54.6

Q ss_pred             CChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          61 TPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        61 ~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      .|+++|.++++.++++++.++++|||+|||++++.++...+..           ...++||++|+++|+.|.+
T Consensus       113 ~l~~~Q~~ai~~~l~~~~~ll~~~tGsGKT~~~~~~~~~~~~~-----------~~~~~lil~Pt~~L~~q~~  174 (282)
T 1rif_A          113 EPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALLARYYLEN-----------YEGKILIIVPTTALTTQMA  174 (282)
T ss_dssp             CCCHHHHHHHHHHHHHSEEEECCCTTSCHHHHHHHHHHHHHHH-----------CSSEEEEECSSHHHHHHHH
T ss_pred             CccHHHHHHHHHHHhcCCeEEEcCCCCCcHHHHHHHHHHHHHc-----------CCCeEEEEECCHHHHHHHH
Confidence            8999999999999988888999999999999998887776643           3347999999999999975

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4}

Probab=99.33  E-value=1.8e-12  Score=103.03  Aligned_cols=62  Identities=24%  Similarity=0.182  Sum_probs=56.3

Q ss_pred             CChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          61 TPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        61 ~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      .|++.|.++++.++++++++++++||+|||++|+.++...+..           .+.++||++|+++|+.|.+
T Consensus       113 ~l~~~Q~~ai~~~~~~~~~ll~~~tGsGKT~~~~~~~~~~~~~-----------~~~~vlvl~P~~~L~~Q~~  174 (510)
T 2oca_A          113 EPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALLARYYLEN-----------YEGKILIIVPTTALTTQMA  174 (510)
T ss_dssp             CCCHHHHHHHHHHHHHSEEEEECCSTTTHHHHHHHHHHHHHHH-----------CSSEEEEEESSHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHhcCCcEEEeCCCCCHHHHHHHHHHHHHhC-----------CCCeEEEEECcHHHHHHHH
Confidence            8999999999999999999999999999999999998887753           3348999999999999975

>4gl2_A Interferon-induced helicase C domain-containing P; MDA5, dsRNA, anti-viral signaling, RIG-I, MAVS, oligomerizat helicase, ATPase; HET: ANP; 3.56A {Homo sapiens}

Probab=99.32  E-value=6.8e-13  Score=108.96  Aligned_cols=68  Identities=24%  Similarity=0.199  Sum_probs=57.9

Q ss_pred             CCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHh
Q psy7268          58 GLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQI  132 (134)
Q Consensus        58 g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi  132 (134)
                      +| .|+++|.++++.+++|+|+++.+|||+|||++|++|++..+.....      ...+.++||++|+++|+.|.
T Consensus         5 ~~-~l~~~Q~~~i~~il~g~~~ll~~~TGsGKTl~~~~~i~~~l~~~~~------~~~~~~vlvl~P~~~L~~Q~   72 (699)
T 4gl2_A            5 ML-QLRPYQMEVAQPALEGKNIIICLPTGCGKTRVAVYIAKDHLDKKKK------ASEPGKVIVLVNKVLLVEQL   72 (699)
T ss_dssp             ---CCCHHHHHHHHHHHSSCCEEECCCTTSCHHHHHHHHHHHHHHHHHH------HTCCCCBCCEESCSHHHHHH
T ss_pred             CC-CccHHHHHHHHHHHhCCCEEEEcCCCCcHHHHHHHHHHHHHHhccc------cCCCCeEEEEECCHHHHHHH
Confidence            34 7999999999999999999999999999999999999998875421      01236799999999999997

>2ipc_A Preprotein translocase SECA subunit; nucleotide binding fold, ATPase, parallel dimer; 2.80A {Thermus thermophilus}

Probab=99.32  E-value=2.5e-12  Score=108.47  Aligned_cols=62  Identities=24%  Similarity=0.205  Sum_probs=55.9

Q ss_pred             CCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          57 RGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        57 ~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      +|+ +|+++|..++|.++.|+  ++.+.||+|||++|.+|++....            .+.+++|++||++||.|++
T Consensus        76 lG~-~Pt~VQ~~~ip~LlqG~--IaeakTGeGKTLvf~Lp~~L~aL------------~G~qv~VvTPTreLA~Qda  137 (997)
T 2ipc_A           76 LGM-RHFDVQLIGGAVLHEGK--IAEMKTGEGKTLVATLAVALNAL------------TGKGVHVVTVNDYLARRDA  137 (997)
T ss_dssp             TCC-CCCHHHHHHHHHHHTTS--EEECCSTHHHHHHHHHHHHHHHT------------TCSCCEEEESSHHHHHHHH
T ss_pred             hCC-CCcHHHHhhcccccCCc--eeeccCCCchHHHHHHHHHHHHH------------hCCCEEEEeCCHHHHHHHH
Confidence            699 99999999999999998  89999999999999999975543            3557999999999999975

>2xau_A PRE-mRNA-splicing factor ATP-dependent RNA helica; hydrolase, ribosome biogenesis, ATPase, ATP-binding, OB-fold; HET: ADP; 1.90A {Saccharomyces cerevisiae} PDB: 3kx2_B*

Probab=99.27  E-value=9.9e-12  Score=104.20  Aligned_cols=88  Identities=22%  Similarity=0.326  Sum_probs=70.8

Q ss_pred             CCCCCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHc-CCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCC
Q psy7268          36 IDLGTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLS-GKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPEL  114 (134)
Q Consensus        36 ~~~~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~-g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~  114 (134)
                      .++..|+++++++.+.+.+.+.+ ..|+++|+++|+.++. |++++++||||+|||+  ++|++.......       ..
T Consensus        69 ~~~~~f~~~~l~~~~~~~l~~r~-~lP~~~q~~~i~~~l~~~~~vii~gpTGSGKTt--llp~ll~~~~~~-------~~  138 (773)
T 2xau_A           69 GKINPFTGREFTPKYVDILKIRR-ELPVHAQRDEFLKLYQNNQIMVFVGETGSGKTT--QIPQFVLFDEMP-------HL  138 (773)
T ss_dssp             SSBCTTTCSBCCHHHHHHHHHHT-TSGGGGGHHHHHHHHHHCSEEEEECCTTSSHHH--HHHHHHHHHHCG-------GG
T ss_pred             CCCCCccccCCCHHHHHHHHHhh-cCChHHHHHHHHHHHhCCCeEEEECCCCCCHHH--HHHHHHHHhccc-------cC
Confidence            56778999999999999999988 6999999999998775 5679999999999999  566663222111       01


Q ss_pred             CCcEEEEEcCcHHHHHHhc
Q psy7268         115 NAPLALIITPGRELVFQIG  133 (134)
Q Consensus       115 ~~~~~lil~Pt~~La~Qi~  133 (134)
                      .+.++++++|+++|+.|++
T Consensus       139 ~g~~ilvl~P~r~La~q~~  157 (773)
T 2xau_A          139 ENTQVACTQPRRVAAMSVA  157 (773)
T ss_dssp             GTCEEEEEESCHHHHHHHH
T ss_pred             CCceEEecCchHHHHHHHH
Confidence            2567999999999999875

>2fwr_A DNA repair protein RAD25; DNA unwinding, XPB, DNA binding protein; HET: DNA; 2.60A {Archaeoglobus fulgidus} SCOP: c.37.1.19 c.37.1.19 PDB: 2fzl_A*

Probab=99.27  E-value=1.4e-11  Score=97.03  Aligned_cols=58  Identities=26%  Similarity=0.304  Sum_probs=52.5

Q ss_pred             CChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          61 TPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        61 ~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      .|+++|.++++.++.+++++++++||+|||++|+.++...               +.++||++|+++|+.|.+
T Consensus        93 ~l~~~Q~~ai~~i~~~~~~ll~~~TGsGKT~~~l~~i~~~---------------~~~~Lvl~P~~~L~~Q~~  150 (472)
T 2fwr_A           93 SLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAAINEL---------------STPTLIVVPTLALAEQWK  150 (472)
T ss_dssp             CBCHHHHHHHHHHTTTTEEEEECCTTSCHHHHHHHHHHHH---------------CSCEEEEESSHHHHHHHH
T ss_pred             CcCHHHHHHHHHHHhcCCEEEEeCCCCCHHHHHHHHHHHc---------------CCCEEEEECCHHHHHHHH
Confidence            6899999999999999999999999999999999887753               346999999999999975

>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer aging, hydrolase; HET: FLC; 2.00A {Sulfolobus acidocaldarius} PDB: 3crw_1*

Probab=99.26  E-value=6.4e-12  Score=101.55  Aligned_cols=60  Identities=23%  Similarity=0.166  Sum_probs=52.7

Q ss_pred             CCCCChHHHHHHHHH----HHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          58 GLTTPTEIQKYSIPT----LLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        58 g~~~~t~iQ~~~i~~----~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      || .+++.|.+.+..    +..|+|+++.+|||+|||++|++|++.               .+.+++|++||++|+.|+.
T Consensus         1 ~~-~~r~~Q~~~~~~v~~~l~~~~~~~~~a~TGtGKT~~~l~p~l~---------------~~~~v~i~~pt~~l~~q~~   64 (551)
T 3crv_A            1 MV-KLRDWQEKLKDKVIEGLRNNFLVALNAPTGSGKTLFSLLVSLE---------------VKPKVLFVVRTHNEFYPIY   64 (551)
T ss_dssp             CC-SCCHHHHHHHHHHHHHHHTTCEEEEECCTTSSHHHHHHHHHHH---------------HCSEEEEEESSGGGHHHHH
T ss_pred             CC-CCCHHHHHHHHHHHHHHHcCCcEEEECCCCccHHHHHHHHHHh---------------CCCeEEEEcCCHHHHHHHH
Confidence            56 789999998765    457999999999999999999999998               1468999999999999985

>2z83_A Helicase/nucleoside triphosphatase; hydrolase, membrane, nucleotide-binding, RNA replication, transmembrane, viral protein; 1.80A {Japanese encephalitis virus} PDB: 2v8o_A 2qeq_A

Probab=99.25  E-value=1.7e-12  Score=102.79  Aligned_cols=51  Identities=18%  Similarity=0.341  Sum_probs=45.6

Q ss_pred             HHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          72 TLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        72 ~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      .+..|+++++++|||||||++|++|+++.+..           .+.++||++|||+|+.|++
T Consensus        17 ~l~~~~~vlv~a~TGsGKT~~~~l~il~~~~~-----------~~~~~lvl~Ptr~La~Q~~   67 (459)
T 2z83_A           17 MLRKRQMTVLDLHPGSGKTRKILPQIIKDAIQ-----------QRLRTAVLAPTRVVAAEMA   67 (459)
T ss_dssp             GGSTTCEEEECCCTTSCTTTTHHHHHHHHHHH-----------TTCCEEEEECSHHHHHHHH
T ss_pred             HHhcCCcEEEECCCCCCHHHHHHHHHHHHHHh-----------CCCcEEEECchHHHHHHHH
Confidence            45678899999999999999999999998865           4578999999999999986

>1wp9_A ATP-dependent RNA helicase, putative; ATPase, DNA replication, DNA repair, DNA recombina hydrolase; 2.90A {Pyrococcus furiosus} SCOP: c.37.1.19 c.37.1.19

Probab=99.24  E-value=1.6e-11  Score=95.03  Aligned_cols=61  Identities=23%  Similarity=0.280  Sum_probs=55.6

Q ss_pred             CChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          61 TPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        61 ~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      .|+++|.++++.++.+ ++++.+|||+|||++++++++..+..           .+.++||++|+++|+.|.+
T Consensus         9 ~l~~~Q~~~i~~~~~~-~~ll~~~tG~GKT~~~~~~~~~~~~~-----------~~~~~liv~P~~~L~~q~~   69 (494)
T 1wp9_A            9 QPRIYQEVIYAKCKET-NCLIVLPTGLGKTLIAMMIAEYRLTK-----------YGGKVLMLAPTKPLVLQHA   69 (494)
T ss_dssp             CCCHHHHHHHHHGGGS-CEEEECCTTSCHHHHHHHHHHHHHHH-----------SCSCEEEECSSHHHHHHHH
T ss_pred             CccHHHHHHHHHHhhC-CEEEEcCCCCCHHHHHHHHHHHHHhc-----------CCCeEEEEECCHHHHHHHH
Confidence            7899999999999999 99999999999999999999988762           4568999999999999875

>1yks_A Genome polyprotein [contains: flavivirin protease NS3 catalytic subunit]; helicase, flavivirus, DEAD-BOX, ATPase, rtpase, hydrolase; 1.80A {Yellow fever virus} SCOP: c.37.1.14 c.37.1.14 PDB: 1ymf_A*

Probab=99.24  E-value=2.8e-12  Score=101.12  Aligned_cols=50  Identities=24%  Similarity=0.420  Sum_probs=45.6

Q ss_pred             HHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          73 LLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        73 ~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      +++|+|+++++|||||||++|++|+++.+..           ++.+++|++||++||.|++
T Consensus         5 l~~g~~vlv~a~TGSGKT~~~l~~~l~~~~~-----------~~~~~lil~Ptr~La~Q~~   54 (440)
T 1yks_A            5 LKKGMTTVLDFHPGAGKTRRFLPQILAECAR-----------RRLRTLVLAPTRVVLSEMK   54 (440)
T ss_dssp             TSTTCEEEECCCTTSSTTTTHHHHHHHHHHH-----------TTCCEEEEESSHHHHHHHH
T ss_pred             hhCCCCEEEEcCCCCCHHHHHHHHHHHHHHh-----------cCCeEEEEcchHHHHHHHH
Confidence            5689999999999999999999999998865           4678999999999999986

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A*

Probab=99.22  E-value=1.2e-11  Score=101.46  Aligned_cols=62  Identities=21%  Similarity=0.109  Sum_probs=53.4

Q ss_pred             CChHHHHHHHHH----HHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          61 TPTEIQKYSIPT----LLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        61 ~~t~iQ~~~i~~----~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      .|.+.|.+.+..    +.+|+++++.+|||+|||++|++|++..+..           .+.+++|++||++|+.|+.
T Consensus         3 ~~R~~Q~~~~~~v~~~l~~~~~~~~~apTGtGKT~a~l~p~l~~~~~-----------~~~kvli~t~T~~l~~Qi~   68 (620)
T 4a15_A            3 ENRQYQVEAIDFLRSSLQKSYGVALESPTGSGKTIMALKSALQYSSE-----------RKLKVLYLVRTNSQEEQVI   68 (620)
T ss_dssp             --CHHHHHHHHHHHHHHHHSSEEEEECCTTSCHHHHHHHHHHHHHHH-----------HTCEEEEEESSHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHHcCCCEEEECCCCCCHHHHHHHHHHHhhhh-----------cCCeEEEECCCHHHHHHHH
Confidence            578999998864    4589999999999999999999999999865           3568999999999999985

>2fz4_A DNA repair protein RAD25; RECA-like domain, DNA damage recognition domain, DNA binding; HET: DNA; 2.40A {Archaeoglobus fulgidus} SCOP: c.37.1.19

Probab=99.22  E-value=4.8e-11  Score=86.98  Aligned_cols=58  Identities=26%  Similarity=0.304  Sum_probs=51.0

Q ss_pred             CChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          61 TPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        61 ~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      .++++|.+++..++.++++++++|||+|||.+++.++...               +.+++|++|+++|+.|.+
T Consensus        93 ~l~~~Q~~ai~~~~~~~~~ll~~~tG~GKT~~a~~~~~~~---------------~~~~liv~P~~~L~~q~~  150 (237)
T 2fz4_A           93 SLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAAINEL---------------STPTLIVVPTLALAEQWK  150 (237)
T ss_dssp             CCCHHHHHHHHHHTTTSEEEEEESSSTTHHHHHHHHHHHS---------------CSCEEEEESSHHHHHHHH
T ss_pred             CcCHHHHHHHHHHHhCCCEEEEeCCCCCHHHHHHHHHHHc---------------CCCEEEEeCCHHHHHHHH
Confidence            7899999999999999999999999999999987776542               346999999999999875

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}

Probab=99.19  E-value=1.9e-11  Score=98.63  Aligned_cols=61  Identities=26%  Similarity=0.177  Sum_probs=49.3

Q ss_pred             CCCCCChHHHHHHHHH----HHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHh
Q psy7268          57 RGLTTPTEIQKYSIPT----LLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQI  132 (134)
Q Consensus        57 ~g~~~~t~iQ~~~i~~----~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi  132 (134)
                      .|| .|+++|.+++..    +..|+++++.+|||+|||++|++|++..               +.+++|++||++|+.|+
T Consensus         4 ~~~-~~r~~Q~~~~~~v~~~~~~~~~~~~~a~TGtGKT~~~l~~~~~~---------------~~~~~~~~~t~~l~~q~   67 (540)
T 2vl7_A            4 LKL-QLRQWQAEKLGEAINALKHGKTLLLNAKPGLGKTVFVEVLGMQL---------------KKKVLIFTRTHSQLDSI   67 (540)
T ss_dssp             ------CCHHHHHHHHHHHHHHTTCEEEEECCTTSCHHHHHHHHHHHH---------------TCEEEEEESCHHHHHHH
T ss_pred             CCC-CCCHHHHHHHHHHHHHHHcCCCEEEEcCCCCcHHHHHHHHHHhC---------------CCcEEEEcCCHHHHHHH
Confidence            478 899999998754    4589999999999999999999998652               46899999999999998


Q ss_pred             c
Q psy7268         133 G  133 (134)
Q Consensus       133 ~  133 (134)
                      .
T Consensus        68 ~   68 (540)
T 2vl7_A           68 Y   68 (540)
T ss_dssp             H
T ss_pred             H
Confidence            5

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A

Probab=99.15  E-value=2.3e-11  Score=95.62  Aligned_cols=48  Identities=23%  Similarity=0.344  Sum_probs=42.7

Q ss_pred             cCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          75 SGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      +|+|+++++|||||||++|++|+++.+..           .+.+++|++||++|+.|++
T Consensus         1 kg~~~lv~a~TGsGKT~~~l~~~l~~~~~-----------~g~~~lvl~Pt~~La~Q~~   48 (431)
T 2v6i_A            1 KRELTVLDLHPGAGKTRRVLPQLVREAVK-----------KRLRTVILAPTRVVASEMY   48 (431)
T ss_dssp             -CCEEEEECCTTSCTTTTHHHHHHHHHHH-----------TTCCEEEEESSHHHHHHHH
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHHHHHh-----------CCCCEEEECcHHHHHHHHH
Confidence            47899999999999999999999977764           5678999999999999986

>3h1t_A Type I site-specific restriction-modification system, R (restriction) subunit; hydrolase, restriction enzyme HSDR, ATP-binding; 2.30A {Vibrio vulnificus}

Probab=98.99  E-value=8.5e-10  Score=89.32  Aligned_cols=70  Identities=20%  Similarity=0.271  Sum_probs=43.5

Q ss_pred             CChHHHHHHHHHHHc----C-CCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          61 TPTEIQKYSIPTLLS----G-KSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        61 ~~t~iQ~~~i~~~~~----g-~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      .|+++|.++++.++.    | ++++++++||+|||+++ ++++..+.......  .....+.++||++|+++|+.|.+
T Consensus       178 ~lr~~Q~~ai~~~~~~~~~~~~~~ll~~~TGsGKT~~~-~~~~~~l~~~~~~~--~~~~~~~~vlil~P~~~L~~Q~~  252 (590)
T 3h1t_A          178 SPRYYQQIAINRAVQSVLQGKKRSLITMATGTGKTVVA-FQISWKLWSARWNR--TGDYRKPRILFLADRNVLVDDPK  252 (590)
T ss_dssp             -CCHHHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHH-HHHHHHHHHTTCCS--SCSSSCCCEEEEEC---------
T ss_pred             CchHHHHHHHHHHHHHHhcCCCceEEEecCCCChHHHH-HHHHHHHHhccccc--ccccCCCeEEEEeCCHHHHHHHH
Confidence            699999999998875    5 56899999999999996 45555554432100  01124678999999999999976

>3o8b_A HCV NS3 protease/helicase; ntpase, RNA, translocation, protein-RNA compl protease/ntpase/helicase, hydrolase; 1.95A {Hepatitis c virus} PDB: 3o8c_A* 3o8d_A* 3o8r_A* 4b71_A* 4b73_A* 4b74_A* 4b76_A* 4b75_A* 4a92_A* 1cu1_A 4b6e_A* 4b6f_A* 2zjo_A* 1a1v_A* 1hei_A 3kqn_A* 3kql_A* 3kqu_A* 3kqh_A 3kqk_A ...

Probab=98.93  E-value=4e-11  Score=99.01  Aligned_cols=57  Identities=21%  Similarity=0.156  Sum_probs=46.6

Q ss_pred             ChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          62 PTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        62 ~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      +.+.|+.+++.+..++|++++||||||||.+|.+++++               ++.+++|++|||+||.|++
T Consensus       218 ~~~~q~~i~~~L~~~~~vlv~ApTGSGKT~a~~l~ll~---------------~g~~vLVl~PTReLA~Qia  274 (666)
T 3o8b_A          218 VFTDNSSPPAVPQSFQVAHLHAPTGSGKSTKVPAAYAA---------------QGYKVLVLNPSVAATLGFG  274 (666)
T ss_dssp             SCCCCCSCCCCCSSCEEEEEECCTTSCTTTHHHHHHHH---------------TTCCEEEEESCHHHHHHHH
T ss_pred             cHHHHHHHHHHHHcCCeEEEEeCCchhHHHHHHHHHHH---------------CCCeEEEEcchHHHHHHHH
Confidence            34455555555668889999999999999999998875               2457999999999999986

>2w00_A HSDR, R.ECOR124I; ATP-binding, DNA-binding, restriction system, helicase, HYDR R.ECOR124I, nucleotide-binding; HET: ATP; 2.6A {Escherichia coli} PDB: 2y3t_A* 2w74_B*

Probab=98.79  E-value=4.3e-09  Score=90.68  Aligned_cols=76  Identities=14%  Similarity=0.141  Sum_probs=57.1

Q ss_pred             HHHHHHHHHCC-------CCCChHHHHHHHHHHHc--------------CCCeEEEcCCCCchhHHhHHHHHHHHHhhcC
Q psy7268          48 PEIIDIFTKRG-------LTTPTEIQKYSIPTLLS--------------GKSAILVAETGCGKTLSFLAPLVQQILTWKS  106 (134)
Q Consensus        48 ~~i~~~l~~~g-------~~~~t~iQ~~~i~~~~~--------------g~dvli~a~tGsGKT~~~~lpil~~~~~~~~  106 (134)
                      +.+++.+.+.-       -..|+++|..+++.++.              +++.++.++||||||+++ ++++..+...  
T Consensus       251 ~~ll~~l~~f~~~~~~~~~~~~R~~Q~~AI~~il~~i~~~~~~~~~~~~~~~gli~~~TGSGKT~t~-~~l~~ll~~~--  327 (1038)
T 2w00_A          251 HTLLNVLVNYSVFDSSQTLLVMRPYQIAATERILWKIKSSFTAKNWSKPESGGYIWHTTGSGKTLTS-FKAARLATEL--  327 (1038)
T ss_dssp             HHHHHHHHHSEEECTTCCEEECCHHHHHHHHHHHHHHHHHHHHTCCSSGGGSEEEEECTTSSHHHHH-HHHHHHHTTC--
T ss_pred             HHHHHHHHhheeeccccccccCCHHHHHHHHHHHHHHHhcccccccccCCCCEEEEecCCCCHHHHH-HHHHHHHHhc--
Confidence            45555565531       12599999999998875              368999999999999997 6666554321  


Q ss_pred             CCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268         107 RPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus       107 ~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                             ....++|||+|+++|+.|+.
T Consensus       328 -------~~~~rvLvlvpr~eL~~Q~~  347 (1038)
T 2w00_A          328 -------DFIDKVFFVVDRKDLDYQTM  347 (1038)
T ss_dssp             -------TTCCEEEEEECGGGCCHHHH
T ss_pred             -------CCCceEEEEeCcHHHHHHHH
Confidence                   13468999999999999974

>3rc3_A ATP-dependent RNA helicase SUPV3L1, mitochondrial; SUV3, nucleus, hydrolase; HET: ANP; 2.08A {Homo sapiens} PDB: 3rc8_A

Probab=98.66  E-value=9.5e-09  Score=85.11  Aligned_cols=46  Identities=20%  Similarity=0.169  Sum_probs=36.8

Q ss_pred             HHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          72 TLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        72 ~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      ..++|++++++||||||||+    +++..+...            .+++|++|||+||.|++
T Consensus       151 r~l~rk~vlv~apTGSGKT~----~al~~l~~~------------~~gl~l~PtR~LA~Qi~  196 (677)
T 3rc3_A          151 RAMQRKIIFHSGPTNSGKTY----HAIQKYFSA------------KSGVYCGPLKLLAHEIF  196 (677)
T ss_dssp             HTSCCEEEEEECCTTSSHHH----HHHHHHHHS------------SSEEEEESSHHHHHHHH
T ss_pred             HhcCCCEEEEEcCCCCCHHH----HHHHHHHhc------------CCeEEEeCHHHHHHHHH
Confidence            45689999999999999997    555555542            23599999999999986

>1w36_D RECD, exodeoxyribonuclease V alpha chain; recombination, helicase, hydrolase, DNA repair; HET: DNA; 3.1A {Escherichia coli} SCOP: c.37.1.19 c.37.1.19 PDB: 3k70_D*

Probab=98.46  E-value=6.2e-07  Score=73.36  Aligned_cols=61  Identities=16%  Similarity=0.190  Sum_probs=51.1

Q ss_pred             hHHHHHHHHHHHcCCCeEEEcCCCCchh--HHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          63 TEIQKYSIPTLLSGKSAILVAETGCGKT--LSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        63 t~iQ~~~i~~~~~g~dvli~a~tGsGKT--~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      ++.|+.+++.++.++++++.|++|||||  ++++++.+..+..          ..+.++++++||.++|.++.
T Consensus       151 ~~~Q~~Ai~~~l~~~~~vi~G~pGTGKTt~l~~ll~~l~~~~~----------~~~~~vll~APTg~AA~~L~  213 (608)
T 1w36_D          151 INWQKVAAAVALTRRISVISGGPGTGKTTTVAKLLAALIQMAD----------GERCRIRLAAPTGKAAARLT  213 (608)
T ss_dssp             CCHHHHHHHHHHTBSEEEEECCTTSTHHHHHHHHHHHHHHTCS----------SCCCCEEEEBSSHHHHHHHH
T ss_pred             CHHHHHHHHHHhcCCCEEEEeCCCCCHHHHHHHHHHHHHHhhh----------cCCCeEEEEeCChhHHHHHH
Confidence            7899999999999999999999999999  6677777765421          14568999999999999863

>1z63_A Helicase of the SNF2/RAD54 hamily; protein-DNA complex, hydrolase/DNA complex complex; 3.00A {Sulfolobus solfataricus} SCOP: c.37.1.19 c.37.1.19 PDB: 1z6a_A

Probab=98.35  E-value=8.8e-07  Score=70.02  Aligned_cols=61  Identities=18%  Similarity=0.170  Sum_probs=46.1

Q ss_pred             CChHHHHHHHHHHH----cCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHh
Q psy7268          61 TPTEIQKYSIPTLL----SGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQI  132 (134)
Q Consensus        61 ~~t~iQ~~~i~~~~----~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi  132 (134)
                      .++|+|.+++..+.    .|+++++..+||+|||+..+ +++..+....         ...++|||+|+ +|+.|.
T Consensus        37 ~L~~~Q~~~v~~l~~~~~~~~~~ilad~~GlGKT~~ai-~~i~~~~~~~---------~~~~~LIv~P~-~l~~qw  101 (500)
T 1z63_A           37 NLRPYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQTI-AVFSDAKKEN---------ELTPSLVICPL-SVLKNW  101 (500)
T ss_dssp             CCCHHHHHHHHHHHHHHHTTCCEEECCCTTSCHHHHHH-HHHHHHHHTT---------CCSSEEEEECS-TTHHHH
T ss_pred             cchHHHHHHHHHHHHHhhCCCCEEEEeCCCCcHHHHHH-HHHHHHHhcC---------CCCCEEEEccH-HHHHHH
Confidence            78999999998763    68899999999999999974 4444443321         34579999995 577764

>3jux_A Protein translocase subunit SECA; protein translocation, ATPase, conformational change, peptide binding, ATP-binding, cell inner membrane; HET: ADP; 3.10A {Thermotoga maritima} PDB: 3din_A*

Probab=98.33  E-value=1.7e-06  Score=72.34  Aligned_cols=61  Identities=26%  Similarity=0.274  Sum_probs=53.7

Q ss_pred             CCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHh
Q psy7268          57 RGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQI  132 (134)
Q Consensus        57 ~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi  132 (134)
                      +|. +|+++|-.....+..|+  |....||+|||+++.+|++-..+            .|..+.|++|+++||.|-
T Consensus        72 lg~-r~~dvQligg~~L~~G~--iaEM~TGEGKTLva~lp~~lnAL------------~G~~vhVvT~ndyLA~rd  132 (822)
T 3jux_A           72 LGM-RPFDVQVMGGIALHEGK--VAEMKTGEGKTLAATMPIYLNAL------------IGKGVHLVTVNDYLARRD  132 (822)
T ss_dssp             TSC-CCCHHHHHHHHHHHTTC--EEECCTTSCHHHHTHHHHHHHHT------------TSSCEEEEESSHHHHHHH
T ss_pred             hCC-CCcHHHHHHHHHHhCCC--hhhccCCCCccHHHHHHHHHHHh------------cCCceEEEeccHHHHHhH
Confidence            588 89999999998888888  88999999999999999986654            466799999999999884

>3dmq_A RNA polymerase-associated protein RAPA; SWF2/SNF2, transcription factor, RNA polymerase recycling, activator, ATP-binding, DNA-binding; 3.20A {Escherichia coli K12}

Probab=98.25  E-value=1.5e-06  Score=74.50  Aligned_cols=61  Identities=30%  Similarity=0.232  Sum_probs=49.0

Q ss_pred             CChHHHHHHHHHHHc--CCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHh
Q psy7268          61 TPTEIQKYSIPTLLS--GKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQI  132 (134)
Q Consensus        61 ~~t~iQ~~~i~~~~~--g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi  132 (134)
                      .|+|+|..++..++.  +.+++++.+||+|||+.++..+...+...          ...++|||+|+ .|+.|-
T Consensus       153 ~LrpyQ~eav~~~l~~~~~~~LLad~tGlGKTi~Ai~~i~~l~~~g----------~~~rvLIVvP~-sLl~Qw  215 (968)
T 3dmq_A          153 SLIPHQLNIAHDVGRRHAPRVLLADEVGLGKTIEAGMILHQQLLSG----------AAERVLIIVPE-TLQHQW  215 (968)
T ss_dssp             CCCHHHHHHHHHHHHSSSCEEEECCCTTSCHHHHHHHHHHHHHHTS----------SCCCEEEECCT-TTHHHH
T ss_pred             CCcHHHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHHHhC----------CCCeEEEEeCH-HHHHHH
Confidence            789999999998875  45789999999999999977766655421          23479999999 888774

>4b3f_X DNA-binding protein smubp-2; hydrolase, helicase; 2.50A {Homo sapiens} PDB: 4b3g_A

Probab=98.03  E-value=1.6e-05  Score=65.24  Aligned_cols=60  Identities=25%  Similarity=0.253  Sum_probs=46.7

Q ss_pred             CChHHHHHHHHHHHcCCC-eEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHh
Q psy7268          61 TPTEIQKYSIPTLLSGKS-AILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQI  132 (134)
Q Consensus        61 ~~t~iQ~~~i~~~~~g~d-vli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi  132 (134)
                      .+++-|.+|+..++..++ .+|+||+|||||.+..--+.+ +..           ++.++|+.+||..-+..+
T Consensus       189 ~LN~~Q~~AV~~al~~~~~~lI~GPPGTGKT~ti~~~I~~-l~~-----------~~~~ILv~a~TN~AvD~i  249 (646)
T 4b3f_X          189 CLDTSQKEAVLFALSQKELAIIHGPPGTGKTTTVVEIILQ-AVK-----------QGLKVLCCAPSNIAVDNL  249 (646)
T ss_dssp             TCCHHHHHHHHHHHHCSSEEEEECCTTSCHHHHHHHHHHH-HHH-----------TTCCEEEEESSHHHHHHH
T ss_pred             CCCHHHHHHHHHHhcCCCceEEECCCCCCHHHHHHHHHHH-HHh-----------CCCeEEEEcCchHHHHHH
Confidence            568899999999987776 688999999999876444443 433           456799999998777655

>3mwy_W Chromo domain-containing protein 1; SWI2/SNF2 ATPase, double chromodomains, hydrolase; HET: ATG; 3.70A {Saccharomyces cerevisiae}

Probab=97.81  E-value=3.3e-05  Score=64.84  Aligned_cols=61  Identities=23%  Similarity=0.281  Sum_probs=45.3

Q ss_pred             CChHHHHHHHHHHH----cCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHH
Q psy7268          61 TPTEIQKYSIPTLL----SGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQ  131 (134)
Q Consensus        61 ~~t~iQ~~~i~~~~----~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Q  131 (134)
                      .+.+.|.+++..++    .|++.++..++|.|||+..+..+...+....         ....+|||+| .+|+.|
T Consensus       236 ~Lr~yQ~egv~~l~~~~~~~~~~ILademGlGKT~~ai~~i~~l~~~~~---------~~~~~LIV~P-~sll~q  300 (800)
T 3mwy_W          236 ELRDFQLTGINWMAFLWSKGDNGILADEMGLGKTVQTVAFISWLIFARR---------QNGPHIIVVP-LSTMPA  300 (800)
T ss_dssp             CCCTHHHHHHHHHHHHHTTTCCEEECCCTTSSTTHHHHHHHHHHHHHHS---------CCSCEEEECC-TTTHHH
T ss_pred             CcCHHHHHHHHHHHHHhhcCCCEEEEeCCCcchHHHHHHHHHHHHHhcC---------CCCCEEEEEC-chHHHH
Confidence            67899999998665    7889999999999999987555544433322         3345899999 455554

>2gk6_A Regulator of nonsense transcripts 1; UPF1, helicase, NMD, hydrolase; HET: ADP; 2.40A {Homo sapiens} PDB: 2gjk_A* 2gk7_A 2xzo_A* 2xzp_A

Probab=97.76  E-value=8.8e-05  Score=60.72  Aligned_cols=64  Identities=22%  Similarity=0.294  Sum_probs=49.2

Q ss_pred             CCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          59 LTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        59 ~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      +..+++-|..++..++.+.-.+|.||+|||||.... .++..+...          .+.++++++||..-+.++.
T Consensus       178 ~~~ln~~Q~~av~~~l~~~~~li~GppGTGKT~~~~-~~i~~l~~~----------~~~~ilv~a~tn~A~~~l~  241 (624)
T 2gk6_A          178 LPDLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSA-TIVYHLARQ----------GNGPVLVCAPSNIAVDQLT  241 (624)
T ss_dssp             SCCCCHHHHHHHHHHHTCSEEEEECCTTSCHHHHHH-HHHHHHHTS----------SSCCEEEEESSHHHHHHHH
T ss_pred             cCCCCHHHHHHHHHHhcCCCeEEECCCCCCHHHHHH-HHHHHHHHc----------CCCeEEEEeCcHHHHHHHH
Confidence            346789999999998887778999999999998753 344444321          3457999999998887763

>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA degradation, allosteric REGU; HET: ADP 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=97.65  E-value=0.00013  Score=61.56  Aligned_cols=63  Identities=16%  Similarity=0.249  Sum_probs=48.2

Q ss_pred             CCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHh
Q psy7268          59 LTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQI  132 (134)
Q Consensus        59 ~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi  132 (134)
                      +..+++-|..++..++.+.-++|.||+|||||.... .++..+...          .+.++++++||..-+.++
T Consensus       358 ~~~Ln~~Q~~Av~~~l~~~~~lI~GppGTGKT~~i~-~~i~~l~~~----------~~~~ILv~a~tn~A~d~l  420 (802)
T 2xzl_A          358 FAQLNSSQSNAVSHVLQRPLSLIQGPPGTGKTVTSA-TIVYHLSKI----------HKDRILVCAPSNVAVDHL  420 (802)
T ss_dssp             SCCCCHHHHHHHHHHTTCSEEEEECSTTSSHHHHHH-HHHHHHHHH----------HCCCEEEEESSHHHHHHH
T ss_pred             cccCCHHHHHHHHHHhcCCCEEEECCCCCCHHHHHH-HHHHHHHhC----------CCCeEEEEcCcHHHHHHH
Confidence            346789999999999887778999999999997753 334444331          245799999999888765

>1z3i_X Similar to RAD54-like; recombination ATPase helicase, recombination-DNA binding COM; 3.00A {Danio rerio} SCOP: c.37.1.19 c.37.1.19

Probab=97.63  E-value=0.00015  Score=59.57  Aligned_cols=65  Identities=18%  Similarity=0.237  Sum_probs=45.0

Q ss_pred             CChHHHHHHHHHHH---------cCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHH
Q psy7268          61 TPTEIQKYSIPTLL---------SGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQ  131 (134)
Q Consensus        61 ~~t~iQ~~~i~~~~---------~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Q  131 (134)
                      .+.|+|.+++..+.         .++..|+..++|.|||+..+..+...+.....     ......++|||+|+ +|+.|
T Consensus        55 ~LrpyQ~~gv~~l~~~~~~~~~~~~~g~ILad~mGlGKT~~~i~~i~~l~~~~~~-----~~p~~~~~LiV~P~-sll~q  128 (644)
T 1z3i_X           55 VLRPHQREGVKFLWDCVTGRRIENSYGCIMADEMGLGKTLQCITLIWTLLKQSPD-----CKPEIDKVIVVSPS-SLVRN  128 (644)
T ss_dssp             TCCHHHHHHHHHHHHHHTTSSSTTCCEEEECCCTTSCHHHHHHHHHHHHHHCCTT-----SSCSCSCEEEEECH-HHHHH
T ss_pred             cccHHHHHHHHHHHHhhhcccccCCCCeEeeeCCCchHHHHHHHHHHHHHHhCcc-----ccCCCCcEEEEecH-HHHHH
Confidence            68899999998764         35678999999999999886555554432110     00123458999997 56555

>3e1s_A Exodeoxyribonuclease V, subunit RECD; alpha and beta protein, ATP-binding, nucleotide-binding, HYD; 2.20A {Deinococcus radiodurans} PDB: 3gp8_A 3gpl_A*

Probab=97.56  E-value=0.00024  Score=57.83  Aligned_cols=60  Identities=13%  Similarity=0.121  Sum_probs=48.4

Q ss_pred             CChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHh
Q psy7268          61 TPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQI  132 (134)
Q Consensus        61 ~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi  132 (134)
                      .+++-|+.++..++.++.+++.|++|+|||... ..++..+..           .+.++++++||...+..+
T Consensus       189 ~L~~~Q~~Av~~~~~~~~~~I~G~pGTGKTt~i-~~l~~~l~~-----------~g~~Vl~~ApT~~Aa~~L  248 (574)
T 3e1s_A          189 GLSEEQASVLDQLAGHRLVVLTGGPGTGKSTTT-KAVADLAES-----------LGLEVGLCAPTGKAARRL  248 (574)
T ss_dssp             TCCHHHHHHHHHHTTCSEEEEECCTTSCHHHHH-HHHHHHHHH-----------TTCCEEEEESSHHHHHHH
T ss_pred             CCCHHHHHHHHHHHhCCEEEEEcCCCCCHHHHH-HHHHHHHHh-----------cCCeEEEecCcHHHHHHh
Confidence            679999999999999999999999999999663 344444433           456799999999888765

>2wjy_A Regulator of nonsense transcripts 1; nonsense mediated decay, zinc-finger, ATP-binding, metal-BIN UPF2, UPF1, helicase, hydrolase; 2.50A {Homo sapiens} PDB: 2wjv_A 2iyk_A

Probab=97.56  E-value=0.00026  Score=59.70  Aligned_cols=62  Identities=23%  Similarity=0.307  Sum_probs=48.4

Q ss_pred             CCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHh
Q psy7268          60 TTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQI  132 (134)
Q Consensus        60 ~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi  132 (134)
                      ..+++-|..++..++.+.-.++.||+|||||... ..++..+...          .+.++++++||..-+.++
T Consensus       355 ~~Ln~~Q~~Av~~~l~~~~~lI~GppGTGKT~ti-~~~i~~l~~~----------~~~~ilv~a~tn~A~~~l  416 (800)
T 2wjy_A          355 PDLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTS-ATIVYHLARQ----------GNGPVLVCAPSNIAVDQL  416 (800)
T ss_dssp             CCCCHHHHHHHHHHHTSSEEEEECCTTSCHHHHH-HHHHHHHHTT----------CSSCEEEEESSHHHHHHH
T ss_pred             cCCCHHHHHHHHHhccCCeEEEEcCCCCCHHHHH-HHHHHHHHHc----------CCCcEEEEcCcHHHHHHH
Confidence            4578999999999888777899999999999875 3444444431          345799999999887765

>3upu_A ATP-dependent DNA helicase DDA; RECA-like domain, SH3 domain, PIN-tower interface, coupling hydrolysis to DNA unwinding, ssDNA; 3.30A {Enterobacteria phage T4}

Probab=97.51  E-value=0.00027  Score=55.65  Aligned_cols=65  Identities=14%  Similarity=0.153  Sum_probs=47.9

Q ss_pred             CCCCCChHHHHHHHHHHHc----CC-CeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHH
Q psy7268          57 RGLTTPTEIQKYSIPTLLS----GK-SAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQ  131 (134)
Q Consensus        57 ~g~~~~t~iQ~~~i~~~~~----g~-dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Q  131 (134)
                      ..|..+++-|+.++..++.    ++ .+++.|+.|||||... ..++..+...          ....+++++||...+..
T Consensus        21 ~~~~~Ln~~Q~~av~~~~~~i~~~~~~~li~G~aGTGKT~ll-~~~~~~l~~~----------~~~~il~~a~T~~Aa~~   89 (459)
T 3upu_A           21 MTFDDLTEGQKNAFNIVMKAIKEKKHHVTINGPAGTGATTLT-KFIIEALIST----------GETGIILAAPTHAAKKI   89 (459)
T ss_dssp             CCSSCCCHHHHHHHHHHHHHHHSSSCEEEEECCTTSCHHHHH-HHHHHHHHHT----------TCCCEEEEESSHHHHHH
T ss_pred             CccccCCHHHHHHHHHHHHHHhcCCCEEEEEeCCCCCHHHHH-HHHHHHHHhc----------CCceEEEecCcHHHHHH
Confidence            4788999999999987653    24 8999999999999544 4555555442          12368889999887764


Q ss_pred             h
Q psy7268         132 I  132 (134)
Q Consensus       132 i  132 (134)
                      +
T Consensus        90 l   90 (459)
T 3upu_A           90 L   90 (459)
T ss_dssp             H
T ss_pred             H
Confidence            4

>3lfu_A DNA helicase II; SF1 helicase, ATP-binding, DNA damage, DNA REP replication, DNA-binding, hydrolase, nucleotide-B SOS response; HET: DNA; 1.80A {Escherichia coli} PDB: 2is6_A* 2is2_A* 2is1_A* 2is4_A*

Probab=97.40  E-value=0.00035  Score=56.70  Aligned_cols=64  Identities=11%  Similarity=0.142  Sum_probs=46.6

Q ss_pred             CCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          60 TTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        60 ~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      ..+++-|.+++.  ..+..++|.|+.|||||.+.+--+...+.....        ...+++++++|+..+..+.
T Consensus         8 ~~Ln~~Q~~av~--~~~~~~lV~a~aGsGKT~~l~~ri~~l~~~~~~--------~~~~iL~ltft~~aa~e~~   71 (647)
T 3lfu_A            8 DSLNDKQREAVA--APRSNLLVLAGAGSGKTRVLVHRIAWLMSVENC--------SPYSIMAVTFTNKAAAEMR   71 (647)
T ss_dssp             TTCCHHHHHHHT--CCSSCEEEEECTTSCHHHHHHHHHHHHHHTSCC--------CGGGEEEEESSHHHHHHHH
T ss_pred             hcCCHHHHHHHh--CCCCCEEEEECCCCCHHHHHHHHHHHHHHhCCC--------ChhhEEEEeccHHHHHHHH
Confidence            467999999996  235679999999999998775555554432110        2347999999999887763

>1c4o_A DNA nucleotide excision repair enzyme UVRB; uvrabc, helicase, hypertherm protein, replication; HET: DNA BOG; 1.50A {Thermus thermophilus} SCOP: c.37.1.19 c.37.1.19 PDB: 1d2m_A*

Probab=97.21  E-value=0.0005  Score=56.75  Aligned_cols=60  Identities=28%  Similarity=0.500  Sum_probs=45.4

Q ss_pred             CCCCChHHHHHHHHHHH----cCC-CeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHh
Q psy7268          58 GLTTPTEIQKYSIPTLL----SGK-SAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQI  132 (134)
Q Consensus        58 g~~~~t~iQ~~~i~~~~----~g~-dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi  132 (134)
                      +| .|++.|..++..+.    .|. ..++.+.||||||+.+.- ++...             +. .+|||+|++.+|.|+
T Consensus         6 ~~-~~~~~q~~ai~~l~~~~~~~~~~~~l~g~tgs~kt~~~a~-~~~~~-------------~~-~~lvv~~~~~~A~ql   69 (664)
T 1c4o_A            6 GP-SPKGDQPKAIAGLVEALRDGERFVTLLGATGTGKTVTMAK-VIEAL-------------GR-PALVLAPNKILAAQL   69 (664)
T ss_dssp             SC-CCCTTHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHHH-HHHHH-------------TC-CEEEEESSHHHHHHH
T ss_pred             CC-CCCCCChHHHHHHHHHHhcCCCcEEEEcCCCcHHHHHHHH-HHHHh-------------CC-CEEEEecCHHHHHHH
Confidence            67 89999999988655    343 467889999999987632 33333             11 389999999999998


Q ss_pred             c
Q psy7268         133 G  133 (134)
Q Consensus       133 ~  133 (134)
                      +
T Consensus        70 ~   70 (664)
T 1c4o_A           70 A   70 (664)
T ss_dssp             H
T ss_pred             H
Confidence            6

>1uaa_A REP helicase, protein (ATP-dependent DNA helicase REP.); complex (helicase/DNA), DNA unwinding, hydrolase/DNA complex; HET: DNA; 3.00A {Escherichia coli} SCOP: c.37.1.19 c.37.1.19

Probab=96.93  E-value=0.0014  Score=53.73  Aligned_cols=63  Identities=14%  Similarity=0.085  Sum_probs=46.1

Q ss_pred             CChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          61 TPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        61 ~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      .+++-|++++..  .+..++|.|+.|||||.+..-=+...+.....        ...++++++.|+..|..+.
T Consensus         2 ~L~~~Q~~av~~--~~~~~lV~AgaGSGKT~~l~~ri~~ll~~~~~--------~~~~IL~lTfT~~Aa~em~   64 (673)
T 1uaa_A            2 RLNPGQQQAVEF--VTGPCLVLAGAGSGKTRVITNKIAHLIRGCGY--------QARHIAAVTFTNKAAREMK   64 (673)
T ss_dssp             CCCHHHHHHHHC--CSSEEEECCCTTSCHHHHHHHHHHHHHHHHCC--------CGGGEEEEESSHHHHHHHH
T ss_pred             CCCHHHHHHHhC--CCCCEEEEeCCCCChHHHHHHHHHHHHHhcCC--------CHHHeEEEeccHHHHHHHH
Confidence            468999999864  36679999999999998875555555543211        2346999999999887653

>1pjr_A PCRA; DNA repair, DNA replication, SOS response, helicase, ATP- binding, DNA-binding; 2.50A {Geobacillus stearothermophilus} SCOP: c.37.1.19 c.37.1.19 PDB: 1qhg_A* 3pjr_A* 2pjr_A* 1qhh_B* 1qhh_D* 1qhh_A* 1qhh_C* 2pjr_B*

Probab=96.77  E-value=0.0034  Score=52.14  Aligned_cols=63  Identities=16%  Similarity=0.116  Sum_probs=46.0

Q ss_pred             CCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHh
Q psy7268          60 TTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQI  132 (134)
Q Consensus        60 ~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi  132 (134)
                      ..+++-|++++..  .+..++|.|..|||||.+..-=+...+.....        ...++++++.|+..|..+
T Consensus        10 ~~Ln~~Q~~av~~--~~g~~lV~AgAGSGKT~vL~~ri~~ll~~~~~--------~p~~IL~vTFTnkAA~Em   72 (724)
T 1pjr_A           10 AHLNKEQQEAVRT--TEGPLLIMAGAGSGKTRVLTHRIAYLMAEKHV--------APWNILAITFTNKAAREM   72 (724)
T ss_dssp             TTSCHHHHHHHHC--CSSCEEEEECTTSCHHHHHHHHHHHHHHTTCC--------CGGGEEEEESSHHHHHHH
T ss_pred             hhCCHHHHHHHhC--CCCCEEEEEcCCCCHHHHHHHHHHHHHHhcCC--------CHHHeEEEeccHHHHHHH
Confidence            4689999998864  35679999999999998876555555543211        234699999999777654

>3u4q_A ATP-dependent helicase/nuclease subunit A; helicase, nuclease, double strand DNA repair, protein-DNA CO hydrolase-DNA complex; HET: DNA; 2.80A {Bacillus subtilis} PDB: 3u44_A*

Probab=96.58  E-value=0.0036  Score=54.98  Aligned_cols=65  Identities=20%  Similarity=0.263  Sum_probs=48.3

Q ss_pred             CChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          61 TPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        61 ~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      .+|+-|.++|..-  +.+++|.|..|||||.+.+-=++..+....      .....-+++++++|+..|..+.
T Consensus        10 ~~t~eQ~~~i~~~--~~~~~v~a~AGSGKT~vl~~ri~~ll~~~~------~~~~~~~il~~Tft~~aa~e~~   74 (1232)
T 3u4q_A           10 TWTDDQWNAIVST--GQDILVAAAAGSGKTAVLVERMIRKITAEE------NPIDVDRLLVVTFTNASAAEMK   74 (1232)
T ss_dssp             CCCHHHHHHHHCC--SSCEEEEECTTCCHHHHHHHHHHHHHSCSS------SCCCGGGEEEECSSHHHHHHHH
T ss_pred             CCCHHHHHHHhCC--CCCEEEEecCCCcHHHHHHHHHHHHHhcCC------CCCCccceEEEeccHHHHHHHH
Confidence            6799999998643  889999999999999887666666664321      0113347999999988887653

>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=95.60  E-value=0.015  Score=39.45  Aligned_cols=19  Identities=37%  Similarity=0.482  Sum_probs=16.4

Q ss_pred             cCCCeEEEcCCCCchhHHh
Q psy7268          75 SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~   93 (134)
                      .|+.+++.||+|+|||...
T Consensus        37 ~g~~~~l~G~~G~GKTtL~   55 (180)
T 3ec2_A           37 EGKGLTFVGSPGVGKTHLA   55 (180)
T ss_dssp             GCCEEEECCSSSSSHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            4788999999999999664

>2d7d_A Uvrabc system protein B; helicase, protein-DNA-ADP ternary complex, hydrolase/DNA complex; HET: ADP; 2.10A {Bacillus subtilis} PDB: 2nmv_A* 2fdc_A* 1t5l_A 3uwx_B 1d9z_A* 1d9x_A 2d7d_B* 2nmv_B*

Probab=95.45  E-value=0.037  Score=45.57  Aligned_cols=58  Identities=31%  Similarity=0.461  Sum_probs=42.4

Q ss_pred             CChHHHHHHHHHHH----cCC-CeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          61 TPTEIQKYSIPTLL----SGK-SAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        61 ~~t~iQ~~~i~~~~----~g~-dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      .|+.-|..++..+.    .|. ...+.+.||+|||+...- ++...             +. ..|||+|++.+|.|++
T Consensus        12 ~p~~~Q~~~i~~l~~~~~~~~~~~~l~g~~gs~k~~~~a~-~~~~~-------------~~-~~lvv~~~~~~A~~l~   74 (661)
T 2d7d_A           12 QPQGDQPKAIEKLVKGIQEGKKHQTLLGATGTGKTFTVSN-LIKEV-------------NK-PTLVIAHNKTLAGQLY   74 (661)
T ss_dssp             CCCTTHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHHH-HHHHH-------------CC-CEEEECSSHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHhcCCCcEEEECcCCcHHHHHHHH-HHHHh-------------CC-CEEEEECCHHHHHHHH
Confidence            78888988887554    343 467889999999976532 33332             12 3899999999999986

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=95.43  E-value=0.0099  Score=46.82  Aligned_cols=57  Identities=19%  Similarity=0.289  Sum_probs=38.0

Q ss_pred             cCCCCCCcccCCCCHHHHHHHHHC---CCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHh
Q psy7268          34 SRIDLGTFEDTGLAPEIIDIFTKR---GLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        34 ~~~~~~~f~~~~l~~~i~~~l~~~---g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~   93 (134)
                      ...|-.+|++.+-.++..+.|.+.   -+.+|.-++..-   +.-.+.+++.||+|+|||+..
T Consensus       173 ~~~p~~t~~digGl~~~k~~l~e~v~~pl~~pe~f~~~g---~~~prGvLLyGPPGTGKTllA  232 (434)
T 4b4t_M          173 DEKPTETYSDVGGLDKQIEELVEAIVLPMKRADKFKDMG---IRAPKGALMYGPPGTGKTLLA  232 (434)
T ss_dssp             ESSCSCCGGGSCSCHHHHHHHHHHTHHHHHCSHHHHHHC---CCCCCEEEEESCTTSSHHHHH
T ss_pred             CCCCCCChHhcCcHHHHHHHHHHHHHHHHhCHHHHHhCC---CCCCCeeEEECcCCCCHHHHH
Confidence            345667999999999888888763   122232222211   112467999999999999764

>3cpe_A Terminase, DNA packaging protein GP17; large terminase, alternative initiation, ATP-binding, DNA- binding, hydrolase, nuclease; HET: DNA; 2.80A {Bacteriophage T4} PDB: 3ezk_A*

Probab=95.41  E-value=0.058  Score=43.77  Aligned_cols=63  Identities=11%  Similarity=0.019  Sum_probs=48.6

Q ss_pred             CChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          61 TPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        61 ~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      .+++.|...+..+-..+.+++..+-|+|||.....-++..+...          .+..+++++|+++.|..+.
T Consensus       163 ~l~p~Q~~i~~~l~~~r~~~i~~~Rq~GKS~~~a~~~l~~~~~~----------~~~~i~~va~t~~qA~~~~  225 (592)
T 3cpe_A          163 QLRDYQRDMLKIMSSKRMTVCNLSRQLGKTTVVAIFLAHFVCFN----------KDKAVGILAHKGSMSAEVL  225 (592)
T ss_dssp             CCCHHHHHHHHHHHHCSEEEEEECSSSCHHHHHHHHHHHHHHTS----------SSCEEEEEESSHHHHHHHH
T ss_pred             cCCHHHHHHHHhhccccEEEEEEcCccChHHHHHHHHHHHHHhC----------CCCeEEEEECCHHHHHHHH
Confidence            57999999998775567789999999999998765555444331          3457999999999987753

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=95.21  E-value=0.019  Score=37.74  Aligned_cols=21  Identities=14%  Similarity=0.047  Sum_probs=17.4

Q ss_pred             HHcCCCeEEEcCCCCchhHHh
Q psy7268          73 LLSGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        73 ~~~g~dvli~a~tGsGKT~~~   93 (134)
                      ...+.++++.|++|+|||...
T Consensus        24 ~~~~~~vll~G~~GtGKt~lA   44 (143)
T 3co5_A           24 AKRTSPVFLTGEAGSPFETVA   44 (143)
T ss_dssp             HTCSSCEEEEEETTCCHHHHH
T ss_pred             hCCCCcEEEECCCCccHHHHH
Confidence            346778999999999999654

>2o0j_A Terminase, DNA packaging protein GP17; nucleotide-binding fold, hydrolase; HET: DNA ADP; 1.80A {Enterobacteria phage T4} PDB: 2o0h_A* 2o0k_A*

Probab=95.19  E-value=0.08  Score=40.99  Aligned_cols=62  Identities=11%  Similarity=0.043  Sum_probs=48.1

Q ss_pred             CChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHh
Q psy7268          61 TPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQI  132 (134)
Q Consensus        61 ~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi  132 (134)
                      .++|.|...+..+...+-+++..+-+.|||.....-++......          .+..+++++|+++.|..+
T Consensus       163 ~L~p~Qk~il~~l~~~R~~vi~~sRq~GKT~l~a~~~l~~a~~~----------~g~~v~~vA~t~~qA~~v  224 (385)
T 2o0j_A          163 QLRDYQRDMLKIMSSKRMTVCNLSRQLGKTTVVAIFLAHFVCFN----------KDKAVGILAHKGSMSAEV  224 (385)
T ss_dssp             CCCHHHHHHHHHHHHSSEEEEEECSSSCHHHHHHHHHHHHHHSS----------SSCEEEEEESSHHHHHHH
T ss_pred             CCCHHHHHHHHhhccCcEEEEEEcCcCChhHHHHHHHHHHHHhC----------CCCeEEEEeCCHHHHHHH
Confidence            78999999998765556688999999999998766555544321          456799999999988755

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=95.07  E-value=0.024  Score=37.27  Aligned_cols=20  Identities=15%  Similarity=0.189  Sum_probs=17.2

Q ss_pred             HcCCCeEEEcCCCCchhHHh
Q psy7268          74 LSGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        74 ~~g~dvli~a~tGsGKT~~~   93 (134)
                      ..+.++++.|++|+|||...
T Consensus        22 ~~~~~vll~G~~GtGKt~lA   41 (145)
T 3n70_A           22 ETDIAVWLYGAPGTGRMTGA   41 (145)
T ss_dssp             TCCSCEEEESSTTSSHHHHH
T ss_pred             CCCCCEEEECCCCCCHHHHH
Confidence            46778999999999999765

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=95.01  E-value=0.015  Score=45.36  Aligned_cols=57  Identities=21%  Similarity=0.284  Sum_probs=36.7

Q ss_pred             cCCCCCCcccCCCCHHHHHHHHHC---CCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHh
Q psy7268          34 SRIDLGTFEDTGLAPEIIDIFTKR---GLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        34 ~~~~~~~f~~~~l~~~i~~~l~~~---g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~   93 (134)
                      ...|-.+|++.+=-++..+.|++.   -+++|--.+..-   +.--+.+++.||+|+|||+..
T Consensus       140 ~~~p~v~~~dIgGl~~~k~~l~e~v~~Pl~~pe~f~~~g---i~~prGvLL~GPPGTGKTllA  199 (405)
T 4b4t_J          140 EKVPDSTYDMVGGLTKQIKEIKEVIELPVKHPELFESLG---IAQPKGVILYGPPGTGKTLLA  199 (405)
T ss_dssp             ECSCSCCGGGSCSCHHHHHHHHHHTHHHHHCHHHHHHHT---CCCCCCEEEESCSSSSHHHHH
T ss_pred             cCCCCCCHHHhCCHHHHHHHHHHHHHHHHhCHHHHHhCC---CCCCCceEEeCCCCCCHHHHH
Confidence            334556899999888888888773   111221111110   112468999999999999764

>1e9r_A Conjugal transfer protein TRWB; coupling protein, bacterial conjugation, F1-ATPase-like quaternary structure, ring helicases; 2.4A {Escherichia coli} SCOP: c.37.1.11 PDB: 1e9s_A 1gki_A* 1gl7_A* 1gl6_A*

Probab=94.69  E-value=0.053  Score=41.94  Aligned_cols=44  Identities=18%  Similarity=0.316  Sum_probs=30.4

Q ss_pred             cCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHH
Q psy7268          75 SGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVF  130 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~  130 (134)
                      ...++++.|+||+|||... -.++..+..           .+..++|+=|..++..
T Consensus        52 ~~~h~~i~G~tGsGKs~~~-~~li~~~~~-----------~g~~viv~Dpkge~~~   95 (437)
T 1e9r_A           52 EPRHLLVNGATGTGKSVLL-RELAYTGLL-----------RGDRMVIVDPNGDMLS   95 (437)
T ss_dssp             GGGCEEEEECTTSSHHHHH-HHHHHHHHH-----------TTCEEEEEEETTHHHH
T ss_pred             CcceEEEECCCCCCHHHHH-HHHHHHHHH-----------CCCcEEEEeCCCchhH
Confidence            4568999999999999874 445555543           3455677667666643

>1u0j_A DNA replication protein; AAA+ protein, P-loop atpases, helicase; HET: DNA ADP; 2.10A {Adeno-associated virus - 2} SCOP: c.37.1.20 PDB: 1s9h_A

Probab=94.27  E-value=0.081  Score=39.03  Aligned_cols=44  Identities=20%  Similarity=0.102  Sum_probs=31.7

Q ss_pred             HHHHHHHHHCCCCCChHHHHHH-HHHHHcCC-----CeEEEcCCCCchhHHhH
Q psy7268          48 PEIIDIFTKRGLTTPTEIQKYS-IPTLLSGK-----SAILVAETGCGKTLSFL   94 (134)
Q Consensus        48 ~~i~~~l~~~g~~~~t~iQ~~~-i~~~~~g~-----dvli~a~tGsGKT~~~~   94 (134)
                      ..+.+.|+..||   .+++... +...+.|+     .+++.||+|+|||+.+.
T Consensus        73 n~i~~~l~~qg~---~~~~~~~~l~~~l~~~~~~~n~~~l~GppgtGKt~~a~  122 (267)
T 1u0j_A           73 NRIYKILELNGY---DPQYAASVFLGWATKKFGKRNTIWLFGPATTGKTNIAE  122 (267)
T ss_dssp             CHHHHHHHHTTC---CHHHHHHHHHHHHTTCSTTCCEEEEECSTTSSHHHHHH
T ss_pred             HHHHHHHHHcCC---CHHHHHHHHHHHHhCCCCCCcEEEEECCCCCCHHHHHH
Confidence            478888888888   3554333 34555544     49999999999998774

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=94.06  E-value=0.021  Score=41.38  Aligned_cols=56  Identities=20%  Similarity=0.135  Sum_probs=34.9

Q ss_pred             CCCCCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHH--HHcCCCeEEEcCCCCchhHHh
Q psy7268          36 IDLGTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPT--LLSGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        36 ~~~~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~--~~~g~dvli~a~tGsGKT~~~   93 (134)
                      .+-.+|+++.-.+...+.|.+.=- .+. .....+..  +..++.+++.||+|+|||...
T Consensus        11 ~~~~~~~~i~G~~~~~~~l~~~~~-~~~-~~~~~~~~~~~~~~~~~ll~G~~GtGKT~la   68 (285)
T 3h4m_A           11 RPNVRYEDIGGLEKQMQEIREVVE-LPL-KHPELFEKVGIEPPKGILLYGPPGTGKTLLA   68 (285)
T ss_dssp             SCCCCGGGSCSCHHHHHHHHHHTH-HHH-HCHHHHHHHCCCCCSEEEEESSSSSSHHHHH
T ss_pred             CCCCCHHHhcCHHHHHHHHHHHHH-HHh-hCHHHHHhcCCCCCCeEEEECCCCCcHHHHH
Confidence            344578998888888888876310 100 01112222  134667999999999999664

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=94.05  E-value=0.024  Score=44.71  Aligned_cols=55  Identities=27%  Similarity=0.283  Sum_probs=34.8

Q ss_pred             CCCCCcccCCCCHHHHHHHHHC---CCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHh
Q psy7268          36 IDLGTFEDTGLAPEIIDIFTKR---GLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        36 ~~~~~f~~~~l~~~i~~~l~~~---g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~   93 (134)
                      .|-.+|++.+--++..+.|.+.   -+++|--.+..   .+.--+.+++.||+|+|||+..
T Consensus       175 ~p~v~~~digGl~~~k~~l~e~v~~pl~~p~~f~~~---g~~~prGvLL~GPPGtGKTllA  232 (437)
T 4b4t_L          175 QGEITFDGIGGLTEQIRELREVIELPLKNPEIFQRV---GIKPPKGVLLYGPPGTGKTLLA  232 (437)
T ss_dssp             SCSSCSGGGCSCHHHHHHHHHHHHHHHHCHHHHHHH---CCCCCCEEEEESCTTSSHHHHH
T ss_pred             CCCCChhHhCChHHHHHHHHHHHHHHHhCHHHHHhC---CCCCCCeEEEECCCCCcHHHHH
Confidence            4556899999888888877763   11111111111   0112467999999999999775

>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=94.05  E-value=0.11  Score=39.17  Aligned_cols=19  Identities=37%  Similarity=0.536  Sum_probs=16.1

Q ss_pred             cCCCeEEEcCCCCchhHHh
Q psy7268          75 SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~   93 (134)
                      .+..+++.||+|+|||...
T Consensus        50 ~~~~vll~GppGtGKT~la   68 (363)
T 3hws_A           50 GKSNILLIGPTGSGKTLLA   68 (363)
T ss_dssp             CCCCEEEECCTTSSHHHHH
T ss_pred             CCCeEEEECCCCCCHHHHH
Confidence            3567999999999999764

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=93.99  E-value=0.21  Score=34.08  Aligned_cols=24  Identities=29%  Similarity=0.443  Sum_probs=18.0

Q ss_pred             CCeEEEcCCCCchhHHhHHHHHHHH
Q psy7268          77 KSAILVAETGCGKTLSFLAPLVQQI  101 (134)
Q Consensus        77 ~dvli~a~tGsGKT~~~~lpil~~~  101 (134)
                      +.+++.||+|+|||... -.+...+
T Consensus        55 ~~~~l~G~~GtGKT~la-~~i~~~~   78 (202)
T 2w58_A           55 KGLYLHGSFGVGKTYLL-AAIANEL   78 (202)
T ss_dssp             CEEEEECSTTSSHHHHH-HHHHHHH
T ss_pred             CeEEEECCCCCCHHHHH-HHHHHHH
Confidence            68999999999999754 3444444

>1tue_A Replication protein E1; helicase, replication, E1E2 complex, AAA+ protein; 2.10A {Human papillomavirus type 18} SCOP: c.37.1.20

Probab=93.98  E-value=0.14  Score=36.58  Aligned_cols=52  Identities=12%  Similarity=0.212  Sum_probs=35.1

Q ss_pred             HHHHHHHHHCCCCCChHHHHHHHHHHHcC----CCeEEEcCCCCchhHHhHHHHHHHHH
Q psy7268          48 PEIIDIFTKRGLTTPTEIQKYSIPTLLSG----KSAILVAETGCGKTLSFLAPLVQQIL  102 (134)
Q Consensus        48 ~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g----~dvli~a~tGsGKT~~~~lpil~~~~  102 (134)
                      ..|.+.|+-.|+ .+... -..+..++.+    +.+++.||+|+|||..+ ..++..+.
T Consensus        28 ~~I~~~l~yq~~-~~~~f-~~~l~~~~~~iPkkn~ili~GPPGtGKTt~a-~ala~~l~   83 (212)
T 1tue_A           28 RPIVQFLRYQQI-EFITF-LGALKSFLKGTPKKNCLVFCGPANTGKSYFG-MSFIHFIQ   83 (212)
T ss_dssp             HHHHHHHHHTTC-CHHHH-HHHHHHHHHTCTTCSEEEEESCGGGCHHHHH-HHHHHHHT
T ss_pred             HHHHHHHHHcCc-CHHHH-HHHHHHHHhcCCcccEEEEECCCCCCHHHHH-HHHHHHhC
Confidence            577777877666 44454 4445555544    35999999999999655 55666553

>2oap_1 GSPE-2, type II secretion system protein; hexameric ATPase, hydrolase; HET: ANP; 2.95A {Archaeoglobus fulgidus} PDB: 2oaq_1

Probab=93.96  E-value=0.11  Score=41.63  Aligned_cols=41  Identities=24%  Similarity=0.154  Sum_probs=26.3

Q ss_pred             HHHHHHCCCCCChHHHHHHH-HHHHcCCCeEEEcCCCCchhHHh
Q psy7268          51 IDIFTKRGLTTPTEIQKYSI-PTLLSGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        51 ~~~l~~~g~~~~t~iQ~~~i-~~~~~g~dvli~a~tGsGKT~~~   93 (134)
                      +..+.+.|.  +++.+..-+ -.+..|..+++.||||||||...
T Consensus       236 ~~~l~~~G~--~~~~~l~~l~~~v~~g~~i~I~GptGSGKTTlL  277 (511)
T 2oap_1          236 PIDLIEKGT--VPSGVLAYLWLAIEHKFSAIVVGETASGKTTTL  277 (511)
T ss_dssp             HHHHHHTTS--SCHHHHHHHHHHHHTTCCEEEEESTTSSHHHHH
T ss_pred             hhhHHhcCC--CCHHHHHHHHHHHhCCCEEEEECCCCCCHHHHH
Confidence            445566663  233333333 24567889999999999999653

>4b4t_I 26S protease regulatory subunit 4 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=93.95  E-value=0.043  Score=43.23  Aligned_cols=57  Identities=25%  Similarity=0.311  Sum_probs=36.7

Q ss_pred             cCCCCCCcccCCCCHHHHHHHHHC---CCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHh
Q psy7268          34 SRIDLGTFEDTGLAPEIIDIFTKR---GLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        34 ~~~~~~~f~~~~l~~~i~~~l~~~---g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~   93 (134)
                      ...|-.+|++.+=-++..+.|.+.   -+++|--.+..-   +--.+.+++.||+|+|||+..
T Consensus       174 ~~~p~v~~~DIgGld~~k~~L~e~v~~Pl~~pe~f~~~G---i~~prGvLLyGPPGTGKTlLA  233 (437)
T 4b4t_I          174 DKSPTESYSDIGGLESQIQEIKESVELPLTHPELYEEMG---IKPPKGVILYGAPGTGKTLLA  233 (437)
T ss_dssp             ESSCCCCGGGTCSCHHHHHHHHHHHHHHHHCCHHHHHHT---CCCCSEEEEESSTTTTHHHHH
T ss_pred             ccCCCCcceecCcHHHHHHHHHHHHHHHHhCHHHHHhCC---CCCCCCCceECCCCchHHHHH
Confidence            345556999999778888888763   122222222111   112467999999999999764

>4b4t_H 26S protease regulatory subunit 7 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=93.94  E-value=0.031  Score=44.46  Aligned_cols=55  Identities=24%  Similarity=0.290  Sum_probs=35.7

Q ss_pred             CCCCCcccCCCCHHHHHHHHHC---CCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHh
Q psy7268          36 IDLGTFEDTGLAPEIIDIFTKR---GLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        36 ~~~~~f~~~~l~~~i~~~l~~~---g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~   93 (134)
                      .|--+|++.+--++..+.|++.   -+.+|-..+..   -+.--+.+++.||+|+|||+..
T Consensus       203 ~P~vt~~DIgGl~~~k~~L~e~V~~pl~~pe~f~~~---Gi~pprGILLyGPPGTGKTlLA  260 (467)
T 4b4t_H          203 KPDVTYSDVGGCKDQIEKLREVVELPLLSPERFATL---GIDPPKGILLYGPPGTGKTLCA  260 (467)
T ss_dssp             SCSCCCSSCTTCHHHHHHHHHHTHHHHHCHHHHHHH---TCCCCSEEEECSCTTSSHHHHH
T ss_pred             CCCCCHHHhccHHHHHHHHHHHHHHHhcCHHHHHHC---CCCCCCceEeeCCCCCcHHHHH
Confidence            4446899999888888888773   11111111111   0123467999999999999764

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli}

Probab=93.90  E-value=0.099  Score=41.79  Aligned_cols=44  Identities=25%  Similarity=0.369  Sum_probs=29.2

Q ss_pred             HHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHh
Q psy7268          49 EIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        49 ~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~   93 (134)
                      .+.+.+.+ ++-.-..+=..+.-.+..|.++++.||+|+|||...
T Consensus        15 ~l~~~l~~-~ivGq~~~i~~l~~al~~~~~VLL~GpPGtGKT~LA   58 (500)
T 3nbx_X           15 RLSSSLEK-GLYERSHAIRLCLLAALSGESVFLLGPPGIAKSLIA   58 (500)
T ss_dssp             HHHHHHHT-TCSSCHHHHHHHHHHHHHTCEEEEECCSSSSHHHHH
T ss_pred             HHHHHHHh-hhHHHHHHHHHHHHHHhcCCeeEeecCchHHHHHHH
Confidence            34444443 343334444555556778999999999999999754

>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=93.80  E-value=0.034  Score=39.56  Aligned_cols=52  Identities=27%  Similarity=0.293  Sum_probs=29.7

Q ss_pred             CCcccCCCCHHHHHHHHHC--CCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHh
Q psy7268          39 GTFEDTGLAPEIIDIFTKR--GLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        39 ~~f~~~~l~~~i~~~l~~~--g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~   93 (134)
                      .+|+++.-.+...+.+.+.  .+..+......   .+...+.+++.||+|+|||...
T Consensus         3 ~~~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~---g~~~~~~vll~G~~GtGKT~la   56 (262)
T 2qz4_A            3 VSFKDVAGMHEAKLEVREFVDYLKSPERFLQL---GAKVPKGALLLGPPGCGKTLLA   56 (262)
T ss_dssp             CCTTSSCSCHHHHHHHHHHHHHHHCCC---------CCCCCEEEEESCTTSSHHHHH
T ss_pred             CCHHHhCCHHHHHHHHHHHHHHHHCHHHHHHc---CCCCCceEEEECCCCCCHHHHH
Confidence            3677777777777777652  01111111110   1123467999999999999764

>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=93.66  E-value=0.02  Score=42.32  Aligned_cols=56  Identities=23%  Similarity=0.326  Sum_probs=33.6

Q ss_pred             CCCCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHH-HHcCCCeEEEcCCCCchhHHh
Q psy7268          37 DLGTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPT-LLSGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        37 ~~~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~-~~~g~dvli~a~tGsGKT~~~   93 (134)
                      +-.+|+++.-.+...+.|.+. ...|.......... +..++.+++.||+|+|||...
T Consensus        10 ~~~~~~di~G~~~~~~~l~~~-v~~~~~~~~~~~~~~~~~~~~vLL~Gp~GtGKT~la   66 (301)
T 3cf0_A           10 PQVTWEDIGGLEDVKRELQEL-VQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLA   66 (301)
T ss_dssp             CCCCGGGSCSCHHHHHHHHHH-HHHHHHCHHHHHHHCCCCCSEEEEECSSSSSHHHHH
T ss_pred             CCCCHHHhCCHHHHHHHHHHH-HHHHhhCHHHHHHcCCCCCceEEEECCCCcCHHHHH
Confidence            445788988888888777763 10000000000011 124667999999999999764

>3vkw_A Replicase large subunit; alpha/beta domain, helicase, transferase; 1.90A {Tomato mosaic virus}

Probab=93.30  E-value=0.061  Score=42.50  Aligned_cols=38  Identities=29%  Similarity=0.524  Sum_probs=27.3

Q ss_pred             eEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          79 AILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        79 vli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      .++.|+.|+|||...    .+.+ .            ....+|++||++++..+.
T Consensus       164 ~~I~G~aGsGKTt~I----~~~~-~------------~~~~lVlTpT~~aa~~l~  201 (446)
T 3vkw_A          164 VLVDGVPGCGKTKEI----LSRV-N------------FEEDLILVPGRQAAEMIR  201 (446)
T ss_dssp             EEEEECTTSCHHHHH----HHHC-C------------TTTCEEEESCHHHHHHHH
T ss_pred             EEEEcCCCCCHHHHH----HHHh-c------------cCCeEEEeCCHHHHHHHH
Confidence            678999999999654    2222 1            123699999999998763

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=93.29  E-value=0.053  Score=42.57  Aligned_cols=55  Identities=16%  Similarity=0.138  Sum_probs=34.3

Q ss_pred             CCCCCcccCCCCHHHHHHHHHC---CCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHh
Q psy7268          36 IDLGTFEDTGLAPEIIDIFTKR---GLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        36 ~~~~~f~~~~l~~~i~~~l~~~---g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~   93 (134)
                      .|-.+|++.+--++..+.|.+.   -+.+|--.+..   -+.-.+.+++.||+|+|||+..
T Consensus       166 ~p~v~~~digGl~~~k~~l~e~v~~pl~~p~~~~~~---g~~~prGiLL~GPPGtGKT~la  223 (428)
T 4b4t_K          166 KPDVTYADVGGLDMQKQEIREAVELPLVQADLYEQI---GIDPPRGVLLYGPPGTGKTMLV  223 (428)
T ss_dssp             SCSCCGGGSCSCHHHHHHHHHHHHHHHHCHHHHHHH---CCCCCCEEEEESCTTTTHHHHH
T ss_pred             CCCCCHHHhccHHHHHHHHHHHHHHHHhCHHHHHhC---CCCCCceEEEECCCCCCHHHHH
Confidence            4456899998888888877762   11111111110   0112456999999999999765

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=93.20  E-value=0.12  Score=38.52  Aligned_cols=50  Identities=16%  Similarity=0.234  Sum_probs=32.0

Q ss_pred             CCCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHc-----CCCeEEEcCCCCchhHHh
Q psy7268          38 LGTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLS-----GKSAILVAETGCGKTLSF   93 (134)
Q Consensus        38 ~~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~-----g~dvli~a~tGsGKT~~~   93 (134)
                      -.+|++++-.+...+.|.+.=.   .|..   .|.++.     .+.+++.||+|+|||...
T Consensus         8 ~~~~~di~G~~~~k~~l~~~v~---~p~~---~~~~~~~~~~~~~~iLL~GppGtGKT~la   62 (322)
T 1xwi_A            8 NVKWSDVAGLEGAKEALKEAVI---LPIK---FPHLFTGKRTPWRGILLFGPPGTGKSYLA   62 (322)
T ss_dssp             CCCGGGSCSCHHHHHHHHHHHH---HHHH---CGGGSCTTCCCCSEEEEESSSSSCHHHHH
T ss_pred             CCCHHHhcCHHHHHHHHHHHHH---HHHh---CHHHHhCCCCCCceEEEECCCCccHHHHH
Confidence            3589998888888887765200   0100   012222     357999999999999764

>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=93.09  E-value=0.022  Score=40.76  Aligned_cols=53  Identities=25%  Similarity=0.179  Sum_probs=32.8

Q ss_pred             CCCCCcccCCCCHHHHHHHHHCC--CCCChHHHHHHHHHHH--cCCCeEEEcCCCCchhHHh
Q psy7268          36 IDLGTFEDTGLAPEIIDIFTKRG--LTTPTEIQKYSIPTLL--SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        36 ~~~~~f~~~~l~~~i~~~l~~~g--~~~~t~iQ~~~i~~~~--~g~dvli~a~tGsGKT~~~   93 (134)
                      .+-.+|+++.-.+.....+++.-  |..     ...+..+-  -.+.+++.||+|+|||...
T Consensus        10 ~~~~~~~~i~g~~~~~~~l~~l~~~~~~-----~~~~~~~~~~~~~g~ll~G~~G~GKTtl~   66 (254)
T 1ixz_A           10 APKVTFKDVAGAEEAKEELKEIVEFLKN-----PSRFHEMGARIPKGVLLVGPPGVGKTHLA   66 (254)
T ss_dssp             CCSCCGGGCCSCHHHHHHHHHHHHHHHC-----HHHHHHTTCCCCSEEEEECCTTSSHHHHH
T ss_pred             CCCCCHHHhCCcHHHHHHHHHHHHHHHC-----HHHHHHcCCCCCCeEEEECCCCCCHHHHH
Confidence            34468888887787777776531  111     12222221  1234999999999999654

>3b85_A Phosphate starvation-inducible protein; PHOH2, ATPase, PFAM: PF02562, ST genomics, PSI-2, protein structure initiative; 2.35A {Corynebacterium glutamicum atcc 13032}

Probab=93.08  E-value=0.11  Score=36.54  Aligned_cols=35  Identities=20%  Similarity=0.143  Sum_probs=27.6

Q ss_pred             CCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHh
Q psy7268          59 LTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        59 ~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~   93 (134)
                      ++.-+--|..++..+..|.-+.+.+|+|+|||..+
T Consensus         5 i~pk~~g~~~~l~~i~~Ge~~~liG~nGsGKSTLl   39 (208)
T 3b85_A            5 IRPKTLGQKHYVDAIDTNTIVFGLGPAGSGKTYLA   39 (208)
T ss_dssp             CCCCSHHHHHHHHHHHHCSEEEEECCTTSSTTHHH
T ss_pred             cccCCHhHHHHHHhccCCCEEEEECCCCCCHHHHH
Confidence            33345567778888888999999999999999764

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=93.03  E-value=0.26  Score=36.66  Aligned_cols=26  Identities=23%  Similarity=0.413  Sum_probs=19.1

Q ss_pred             CCCeEEEcCCCCchhHHhHHHHHHHHH
Q psy7268          76 GKSAILVAETGCGKTLSFLAPLVQQIL  102 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~~lpil~~~~  102 (134)
                      ++++++.||+|+|||... ..+...+.
T Consensus       152 ~~~lll~G~~GtGKT~La-~aia~~~~  177 (308)
T 2qgz_A          152 QKGLYLYGDMGIGKSYLL-AAMAHELS  177 (308)
T ss_dssp             CCEEEEECSTTSSHHHHH-HHHHHHHH
T ss_pred             CceEEEECCCCCCHHHHH-HHHHHHHH
Confidence            578999999999999664 34444443

>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=92.84  E-value=0.2  Score=37.18  Aligned_cols=52  Identities=15%  Similarity=0.202  Sum_probs=33.8

Q ss_pred             CCCCCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHH-----cCCCeEEEcCCCCchhHHh
Q psy7268          36 IDLGTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLL-----SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        36 ~~~~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~-----~g~dvli~a~tGsGKT~~~   93 (134)
                      .+-.+|+++.-.+...+.|.+.=.   .+.   ..|.+.     ..+.+++.||+|+|||...
T Consensus        12 ~~~~~~~di~G~~~~~~~l~~~i~---~~~---~~~~~~~~~~~~~~~vLl~GppGtGKT~la   68 (322)
T 3eie_A           12 KPNVKWEDVAGLEGAKEALKEAVI---LPV---KFPHLFKGNRKPTSGILLYGPPGTGKSYLA   68 (322)
T ss_dssp             CCCCCGGGSCSCHHHHHHHHHHTH---HHH---HCGGGCCTTCCCCCEEEEECSSSSCHHHHH
T ss_pred             CCCCCHHHhcChHHHHHHHHHHHH---HHH---hCHHHHhcCCCCCCeEEEECCCCCcHHHHH
Confidence            344579999888888888876310   111   111221     2346999999999999764

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20

Probab=92.80  E-value=0.039  Score=39.49  Aligned_cols=54  Identities=28%  Similarity=0.245  Sum_probs=31.3

Q ss_pred             CCCCcccCCCCHHHHHHHHHC--CCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHh
Q psy7268          37 DLGTFEDTGLAPEIIDIFTKR--GLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        37 ~~~~f~~~~l~~~i~~~l~~~--g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~   93 (134)
                      +-.+|+++.-.+...+.+.+.  .+..+...+..   .....+.+++.||+|+|||...
T Consensus         7 ~~~~~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~---~~~~~~~vll~G~~GtGKT~la   62 (257)
T 1lv7_A            7 IKTTFADVAGCDEAKEEVAELVEYLREPSRFQKL---GGKIPKGVLMVGPPGTGKTLLA   62 (257)
T ss_dssp             SCCCGGGSCSCHHHHHHTHHHHHHHHCGGGC--------CCCCEEEEECCTTSCHHHHH
T ss_pred             CCCCHHHhcCcHHHHHHHHHHHHHHhCHHHHHHc---CCCCCCeEEEECcCCCCHHHHH
Confidence            345788888888877777652  01111100000   0112356999999999999664

>2r44_A Uncharacterized protein; putative ATPase, structural genomics, joint center for struc genomics, JCSG; HET: MSE PG4; 2.00A {Cytophaga hutchinsonii atcc 33406}

Probab=92.79  E-value=0.071  Score=39.56  Aligned_cols=26  Identities=27%  Similarity=0.305  Sum_probs=20.2

Q ss_pred             HHHHHHHcCCCeEEEcCCCCchhHHh
Q psy7268          68 YSIPTLLSGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        68 ~~i~~~~~g~dvli~a~tGsGKT~~~   93 (134)
                      .+.-.+..|.++++.||+|+|||...
T Consensus        38 ~l~~~l~~~~~vll~G~pGtGKT~la   63 (331)
T 2r44_A           38 RLLIGICTGGHILLEGVPGLAKTLSV   63 (331)
T ss_dssp             HHHHHHHHTCCEEEESCCCHHHHHHH
T ss_pred             HHHHHHHcCCeEEEECCCCCcHHHHH
Confidence            33344557899999999999999654

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=92.69  E-value=0.16  Score=33.72  Aligned_cols=19  Identities=26%  Similarity=0.408  Sum_probs=16.7

Q ss_pred             cCCCeEEEcCCCCchhHHh
Q psy7268          75 SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~   93 (134)
                      .|+.+++.+|+|+|||...
T Consensus        35 ~g~~~~l~G~~G~GKTtL~   53 (149)
T 2kjq_A           35 HGQFIYVWGEEGAGKSHLL   53 (149)
T ss_dssp             CCSEEEEESSSTTTTCHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            6888999999999999654

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=92.63  E-value=0.063  Score=35.64  Aligned_cols=25  Identities=36%  Similarity=0.561  Sum_probs=18.0

Q ss_pred             CCCeEEEcCCCCchhHHhHHHHHHHH
Q psy7268          76 GKSAILVAETGCGKTLSFLAPLVQQI  101 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~~lpil~~~  101 (134)
                      +..+++.|++|+|||... -.+...+
T Consensus        43 ~~~~ll~G~~G~GKT~l~-~~~~~~~   67 (195)
T 1jbk_A           43 KNNPVLIGEPGVGKTAIV-EGLAQRI   67 (195)
T ss_dssp             SCEEEEECCTTSCHHHHH-HHHHHHH
T ss_pred             CCceEEECCCCCCHHHHH-HHHHHHH
Confidence            457999999999999764 3334443

>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=92.59  E-value=0.42  Score=34.51  Aligned_cols=18  Identities=33%  Similarity=0.462  Sum_probs=15.7

Q ss_pred             CCCeEEEcCCCCchhHHh
Q psy7268          76 GKSAILVAETGCGKTLSF   93 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~   93 (134)
                      +..+++.||+|+|||...
T Consensus        50 ~~~vll~G~~GtGKT~la   67 (310)
T 1ofh_A           50 PKNILMIGPTGVGKTEIA   67 (310)
T ss_dssp             CCCEEEECCTTSSHHHHH
T ss_pred             CceEEEECCCCCCHHHHH
Confidence            568999999999999664

>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=92.48  E-value=0.13  Score=36.90  Aligned_cols=19  Identities=32%  Similarity=0.527  Sum_probs=16.3

Q ss_pred             cCCCeEEEcCCCCchhHHh
Q psy7268          75 SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~   93 (134)
                      .+..+++.|++|+|||...
T Consensus        28 ~~~~vll~G~~GtGKt~la   46 (265)
T 2bjv_A           28 LDKPVLIIGERGTGKELIA   46 (265)
T ss_dssp             SCSCEEEECCTTSCHHHHH
T ss_pred             CCCCEEEECCCCCcHHHHH
Confidence            5678999999999999654

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=92.26  E-value=0.21  Score=34.95  Aligned_cols=20  Identities=25%  Similarity=0.313  Sum_probs=16.7

Q ss_pred             cCCCeEEEcCCCCchhHHhH
Q psy7268          75 SGKSAILVAETGCGKTLSFL   94 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~~   94 (134)
                      .|.-+++.|++|+|||...+
T Consensus        22 ~G~~~~i~G~~GsGKTtl~~   41 (247)
T 2dr3_A           22 ERNVVLLSGGPGTGKTIFSQ   41 (247)
T ss_dssp             TTCEEEEEECTTSSHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHH
Confidence            56778999999999997653

>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=92.19  E-value=0.075  Score=36.89  Aligned_cols=19  Identities=16%  Similarity=0.132  Sum_probs=16.3

Q ss_pred             cCCCeEEEcCCCCchhHHh
Q psy7268          75 SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~   93 (134)
                      .+..+++.||+|+|||...
T Consensus        51 ~~~~~ll~G~~G~GKT~la   69 (242)
T 3bos_A           51 GVQAIYLWGPVKSGRTHLI   69 (242)
T ss_dssp             SCSEEEEECSTTSSHHHHH
T ss_pred             CCCeEEEECCCCCCHHHHH
Confidence            4678999999999999754

>2zts_A Putative uncharacterized protein PH0186; KAIC like protein, ATP-binding, nucleotide-binding, ATP- binding protein; HET: ADP; 2.07A {Pyrococcus horikoshii}

Probab=91.89  E-value=0.2  Score=35.10  Aligned_cols=25  Identities=28%  Similarity=0.368  Sum_probs=17.9

Q ss_pred             cCCCeEEEcCCCCchhHHhHHHHHH
Q psy7268          75 SGKSAILVAETGCGKTLSFLAPLVQ   99 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~~lpil~   99 (134)
                      .|.-+++.|++|+|||...+--+.+
T Consensus        29 ~G~l~~i~G~pG~GKT~l~l~~~~~   53 (251)
T 2zts_A           29 EGTTVLLTGGTGTGKTTFAAQFIYK   53 (251)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHH
Confidence            3566899999999999655433333

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*

Probab=91.89  E-value=0.27  Score=33.73  Aligned_cols=19  Identities=32%  Similarity=0.473  Sum_probs=15.2

Q ss_pred             CCCeEEEcCCCCchhHHhH
Q psy7268          76 GKSAILVAETGCGKTLSFL   94 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~~   94 (134)
                      |.=.++.|+.|+|||...+
T Consensus         3 g~i~vi~G~~gsGKTT~ll   21 (184)
T 2orw_A            3 GKLTVITGPMYSGKTTELL   21 (184)
T ss_dssp             CCEEEEEESTTSSHHHHHH
T ss_pred             cEEEEEECCCCCCHHHHHH
Confidence            4557789999999997763

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=91.84  E-value=0.064  Score=40.46  Aligned_cols=27  Identities=7%  Similarity=0.105  Sum_probs=19.7

Q ss_pred             cCCCeEEEcCCCCchhHHhHHHHHHHHH
Q psy7268          75 SGKSAILVAETGCGKTLSFLAPLVQQIL  102 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~~lpil~~~~  102 (134)
                      .+.++++.||+|+|||... -.++..+.
T Consensus        44 ~~~~lli~GpPGTGKT~~v-~~v~~~L~   70 (318)
T 3te6_A           44 QNKLFYITNADDSTKFQLV-NDVMDELI   70 (318)
T ss_dssp             CCCEEEEECCCSHHHHHHH-HHHHHHHH
T ss_pred             CCCeEEEECCCCCCHHHHH-HHHHHHHH
Confidence            3567999999999999764 34445554

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=91.82  E-value=0.077  Score=38.73  Aligned_cols=17  Identities=24%  Similarity=0.247  Sum_probs=14.8

Q ss_pred             CCeEEEcCCCCchhHHh
Q psy7268          77 KSAILVAETGCGKTLSF   93 (134)
Q Consensus        77 ~dvli~a~tGsGKT~~~   93 (134)
                      .++++.||+|+|||...
T Consensus        68 ~~vll~G~~GtGKT~la   84 (309)
T 3syl_A           68 LHMSFTGNPGTGKTTVA   84 (309)
T ss_dssp             CEEEEEECTTSSHHHHH
T ss_pred             ceEEEECCCCCCHHHHH
Confidence            46999999999999765

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=91.68  E-value=0.068  Score=35.52  Aligned_cols=18  Identities=33%  Similarity=0.556  Sum_probs=15.2

Q ss_pred             CCCeEEEcCCCCchhHHh
Q psy7268          76 GKSAILVAETGCGKTLSF   93 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~   93 (134)
                      ...+++.||+|+|||...
T Consensus        43 ~~~vll~G~~G~GKT~la   60 (187)
T 2p65_A           43 KNNPILLGDPGVGKTAIV   60 (187)
T ss_dssp             SCEEEEESCGGGCHHHHH
T ss_pred             CCceEEECCCCCCHHHHH
Confidence            457999999999999654

>1kgd_A CASK, peripheral plasma membrane CASK; maguk, guanylate kinase like domain, protein binding; 1.31A {Homo sapiens} SCOP: c.37.1.1

Probab=91.54  E-value=0.1  Score=35.41  Aligned_cols=19  Identities=21%  Similarity=0.333  Sum_probs=15.9

Q ss_pred             cCCCeEEEcCCCCchhHHh
Q psy7268          75 SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~   93 (134)
                      .|+-+.+.||+|+|||...
T Consensus         4 ~g~~i~i~GpsGsGKSTL~   22 (180)
T 1kgd_A            4 MRKTLVLLGAHGVGRRHIK   22 (180)
T ss_dssp             CCCEEEEECCTTSSHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            5677899999999999654

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens}

Probab=91.49  E-value=0.03  Score=41.08  Aligned_cols=53  Identities=25%  Similarity=0.295  Sum_probs=28.4

Q ss_pred             CCCcccCCCCHHHHHHHHHCCCCCChHHH-HHHHHHHH--cCCCeEEEcCCCCchhHHh
Q psy7268          38 LGTFEDTGLAPEIIDIFTKRGLTTPTEIQ-KYSIPTLL--SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        38 ~~~f~~~~l~~~i~~~l~~~g~~~~t~iQ-~~~i~~~~--~g~dvli~a~tGsGKT~~~   93 (134)
                      -.+|++++-.+++.+.|.+.=   ..|.. ..++..+-  -.+.+++.||+|+|||...
T Consensus         6 ~~~~~di~g~~~~~~~l~~~i---~~~~~~~~~l~~~~l~~~~GvlL~Gp~GtGKTtLa   61 (274)
T 2x8a_A            6 NVTWADIGALEDIREELTMAI---LAPVRNPDQFKALGLVTPAGVLLAGPPGCGKTLLA   61 (274)
T ss_dssp             ------CCHHHHHHHHHHHHH---THHHHSHHHHHHTTCCCCSEEEEESSTTSCHHHHH
T ss_pred             CCCHHHhCCHHHHHHHHHHHH---HHHhhCHHHHHHcCCCCCCeEEEECCCCCcHHHHH
Confidence            357889888888888887621   11211 12222221  1234999999999999764

>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=91.46  E-value=0.24  Score=35.35  Aligned_cols=39  Identities=15%  Similarity=0.156  Sum_probs=24.7

Q ss_pred             cCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCc
Q psy7268          75 SGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPG  125 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt  125 (134)
                      .|.=+++.|++|+|||... +-++.+...           .+.+++++.|.
T Consensus        11 ~G~i~litG~mGsGKTT~l-l~~~~r~~~-----------~g~kVli~~~~   49 (223)
T 2b8t_A           11 IGWIEFITGPMFAGKTAEL-IRRLHRLEY-----------ADVKYLVFKPK   49 (223)
T ss_dssp             CCEEEEEECSTTSCHHHHH-HHHHHHHHH-----------TTCCEEEEEEC
T ss_pred             CcEEEEEECCCCCcHHHHH-HHHHHHHHh-----------cCCEEEEEEec
Confidence            3455788899999999766 444444433           34456666544

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20

Probab=91.43  E-value=0.05  Score=39.53  Aligned_cols=52  Identities=25%  Similarity=0.187  Sum_probs=33.1

Q ss_pred             CCCCcccCCCCHHHHHHHHHCC--CCCChHHHHHHHHHHH--cCCCeEEEcCCCCchhHHh
Q psy7268          37 DLGTFEDTGLAPEIIDIFTKRG--LTTPTEIQKYSIPTLL--SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        37 ~~~~f~~~~l~~~i~~~l~~~g--~~~~t~iQ~~~i~~~~--~g~dvli~a~tGsGKT~~~   93 (134)
                      +-.+|+++...++..+.+.+.-  |..     ...+..+-  -.+.+++.+|+|+|||...
T Consensus        35 ~~~~~~~i~g~~~~~~~l~~l~~~~~~-----~~~l~~~~~~~~~gvll~Gp~GtGKTtl~   90 (278)
T 1iy2_A           35 PKVTFKDVAGAEEAKEELKEIVEFLKN-----PSRFHEMGARIPKGVLLVGPPGVGKTHLA   90 (278)
T ss_dssp             CCCCGGGSSSCHHHHHHHHHHHHHHHC-----HHHHHHTTCCCCCEEEEECCTTSSHHHHH
T ss_pred             CCCCHHHhCChHHHHHHHHHHHHHHHC-----HHHHHHcCCCCCCeEEEECCCcChHHHHH
Confidence            5568999988888887777641  111     12222221  1234999999999999654

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=91.41  E-value=0.093  Score=38.17  Aligned_cols=54  Identities=17%  Similarity=0.100  Sum_probs=32.2

Q ss_pred             CCCCcccCCCCHHHHHHHHHCCCCCChHHHH-HHHHHH-HcCCCeEEEcCCCCchhHHh
Q psy7268          37 DLGTFEDTGLAPEIIDIFTKRGLTTPTEIQK-YSIPTL-LSGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        37 ~~~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~-~~i~~~-~~g~dvli~a~tGsGKT~~~   93 (134)
                      +-.+|+++.-.+...+.+.+.=.   .+... ..+..+ ..++.+++.||+|+|||...
T Consensus        16 ~~~~~~~i~G~~~~~~~l~~~i~---~~~~~~~~~~~~~~~~~~vll~Gp~GtGKT~la   71 (297)
T 3b9p_A           16 AKVEWTDIAGQDVAKQALQEMVI---LPSVRPELFTGLRAPAKGLLLFGPPGNGKTLLA   71 (297)
T ss_dssp             SCCCGGGSCCCHHHHHHHHHHTH---HHHHCGGGSCGGGCCCSEEEEESSSSSCHHHHH
T ss_pred             CCCCHHHhCChHHHHHHHHHHHH---hhhhCHHHHhcCCCCCCeEEEECcCCCCHHHHH
Confidence            33578888878888877765310   00000 000001 13568999999999999764

>2gza_A Type IV secretion system protein VIRB11; ATPase, hydrolase; 2.60A {Brucella suis}

Probab=91.39  E-value=0.12  Score=39.28  Aligned_cols=21  Identities=29%  Similarity=0.430  Sum_probs=17.9

Q ss_pred             HHcCCCeEEEcCCCCchhHHh
Q psy7268          73 LLSGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        73 ~~~g~dvli~a~tGsGKT~~~   93 (134)
                      +..|..+.+.||||+|||...
T Consensus       172 i~~G~~i~ivG~sGsGKSTll  192 (361)
T 2gza_A          172 VQLERVIVVAGETGSGKTTLM  192 (361)
T ss_dssp             HHTTCCEEEEESSSSCHHHHH
T ss_pred             HhcCCEEEEECCCCCCHHHHH
Confidence            457999999999999999653

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=91.16  E-value=0.25  Score=34.04  Aligned_cols=19  Identities=37%  Similarity=0.403  Sum_probs=15.8

Q ss_pred             cCCCeEEEcCCCCchhHHh
Q psy7268          75 SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~   93 (134)
                      .|.-+++.||+|+|||...
T Consensus        22 ~G~~~~i~G~~GsGKTtl~   40 (235)
T 2w0m_A           22 QGFFIALTGEPGTGKTIFS   40 (235)
T ss_dssp             TTCEEEEECSTTSSHHHHH
T ss_pred             CCCEEEEEcCCCCCHHHHH
Confidence            4667899999999999654

>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=91.10  E-value=0.36  Score=36.42  Aligned_cols=18  Identities=39%  Similarity=0.438  Sum_probs=15.5

Q ss_pred             CCCeEEEcCCCCchhHHh
Q psy7268          76 GKSAILVAETGCGKTLSF   93 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~   93 (134)
                      .+.+++.||+|+|||...
T Consensus       117 ~~~vLl~GppGtGKT~la  134 (357)
T 3d8b_A          117 PKGILLFGPPGTGKTLIG  134 (357)
T ss_dssp             CSEEEEESSTTSSHHHHH
T ss_pred             CceEEEECCCCCCHHHHH
Confidence            457999999999999765

>1p9r_A General secretion pathway protein E; bacterial type II secretion system cytoplasmic protein - GSPE, putative ATPase/ ATP binding protein; 2.50A {Vibrio cholerae} SCOP: c.37.1.11 PDB: 1p9w_A*

Probab=91.06  E-value=0.18  Score=39.35  Aligned_cols=35  Identities=17%  Similarity=0.301  Sum_probs=22.3

Q ss_pred             HHHHHHHHH--cCCCeEEEcCCCCchhHHhHHHHHHHH
Q psy7268          66 QKYSIPTLL--SGKSAILVAETGCGKTLSFLAPLVQQI  101 (134)
Q Consensus        66 Q~~~i~~~~--~g~dvli~a~tGsGKT~~~~lpil~~~  101 (134)
                      +..++..++  .|.-+++.||||||||... -.++..+
T Consensus       155 ~~~~L~~l~~~~ggii~I~GpnGSGKTTlL-~allg~l  191 (418)
T 1p9r_A          155 NHDNFRRLIKRPHGIILVTGPTGSGKSTTL-YAGLQEL  191 (418)
T ss_dssp             HHHHHHHHHTSSSEEEEEECSTTSCHHHHH-HHHHHHH
T ss_pred             HHHHHHHHHHhcCCeEEEECCCCCCHHHHH-HHHHhhc
Confidence            444554444  3445889999999999653 3444444

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=91.02  E-value=0.47  Score=35.02  Aligned_cols=42  Identities=17%  Similarity=0.078  Sum_probs=27.7

Q ss_pred             CcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHH----cCCCeEEEcCCCCchhHHh
Q psy7268          40 TFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLL----SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        40 ~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~----~g~dvli~a~tGsGKT~~~   93 (134)
                      +|+++--.+..++.+..            .+....    ...++++.||+|+|||...
T Consensus        27 ~~~~iiG~~~~~~~l~~------------~l~~~~~~~~~~~~vll~G~~GtGKT~la   72 (338)
T 3pfi_A           27 NFDGYIGQESIKKNLNV------------FIAAAKKRNECLDHILFSGPAGLGKTTLA   72 (338)
T ss_dssp             SGGGCCSCHHHHHHHHH------------HHHHHHHTTSCCCCEEEECSTTSSHHHHH
T ss_pred             CHHHhCChHHHHHHHHH------------HHHHHHhcCCCCCeEEEECcCCCCHHHHH
Confidence            67777666766666543            111111    2247999999999999764

>1lvg_A Guanylate kinase, GMP kinase; transferase; HET: ADP 5GP; 2.10A {Mus musculus} SCOP: c.37.1.1

Probab=91.00  E-value=0.12  Score=35.66  Aligned_cols=19  Identities=21%  Similarity=0.468  Sum_probs=15.0

Q ss_pred             cCCCeEEEcCCCCchhHHh
Q psy7268          75 SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~   93 (134)
                      .|+-+.+.||+|+|||...
T Consensus         3 ~g~~i~lvGpsGaGKSTLl   21 (198)
T 1lvg_A            3 GPRPVVLSGPSGAGKSTLL   21 (198)
T ss_dssp             --CCEEEECCTTSSHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            4778899999999999764

>4ag6_A VIRB4 ATPase, type IV secretory pathway VIRB4 components-like P; hydrolase, type IV secretion, conjugation; 2.35A {Thermoanaerobacter pseudethanolicus} PDB: 4ag5_A

Probab=90.99  E-value=0.26  Score=37.52  Aligned_cols=21  Identities=19%  Similarity=0.379  Sum_probs=17.0

Q ss_pred             cCCCeEEEcCCCCchhHHhHH
Q psy7268          75 SGKSAILVAETGCGKTLSFLA   95 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~~l   95 (134)
                      .+.++++.|+||+|||...-.
T Consensus        34 ~~~~~~i~G~~G~GKs~~~~~   54 (392)
T 4ag6_A           34 TNSNWTILAKPGAGKSFTAKM   54 (392)
T ss_dssp             CCCCEEEECCTTSSHHHHHHH
T ss_pred             ccCceEEEcCCCCCHHHHHHH
Confidence            567899999999999966433

>3vaa_A Shikimate kinase, SK; structural genomics, center for structural genomics of infec diseases, csgid, metal binding, transferase; 1.70A {Bacteroides thetaiotaomicron}

Probab=90.99  E-value=0.12  Score=35.47  Aligned_cols=20  Identities=25%  Similarity=0.084  Sum_probs=16.7

Q ss_pred             HcCCCeEEEcCCCCchhHHh
Q psy7268          74 LSGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        74 ~~g~dvli~a~tGsGKT~~~   93 (134)
                      ..++.+++.|++|+|||...
T Consensus        23 ~~~~~i~l~G~~GsGKsTl~   42 (199)
T 3vaa_A           23 NAMVRIFLTGYMGAGKTTLG   42 (199)
T ss_dssp             -CCCEEEEECCTTSCHHHHH
T ss_pred             CCCCEEEEEcCCCCCHHHHH
Confidence            35778999999999999774

>1xx6_A Thymidine kinase; NESG, northeast structural genomics consortium, protein STRU initiative, PSI, structural genomics, DNA synthesis; HET: ADP; 2.00A {Clostridium acetobutylicum} SCOP: c.37.1.24 g.39.1.14

Probab=90.98  E-value=0.31  Score=33.87  Aligned_cols=39  Identities=13%  Similarity=0.199  Sum_probs=24.7

Q ss_pred             CCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcH
Q psy7268          76 GKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGR  126 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~  126 (134)
                      |+=.++.|+.|+|||...+ -++.+...           .+.+++++.|..
T Consensus         8 g~i~v~~G~mgsGKTT~ll-~~a~r~~~-----------~g~kV~v~k~~~   46 (191)
T 1xx6_A            8 GWVEVIVGPMYSGKSEELI-RRIRRAKI-----------AKQKIQVFKPEI   46 (191)
T ss_dssp             CEEEEEECSTTSSHHHHHH-HHHHHHHH-----------TTCCEEEEEEC-
T ss_pred             CEEEEEECCCCCcHHHHHH-HHHHHHHH-----------CCCEEEEEEecc
Confidence            4446788999999997654 44444433           455677776553

>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor, microtubles, motor protein; HET: ADP SPM; 2.81A {Dictyostelium discoideum} PDB: 3vkh_A*

Probab=90.85  E-value=0.28  Score=47.17  Aligned_cols=49  Identities=29%  Similarity=0.340  Sum_probs=32.5

Q ss_pred             CCHHHHHHHHHCCCCCChHHHHHHHHH---HHcCCCeEEEcCCCCchhHHhH
Q psy7268          46 LAPEIIDIFTKRGLTTPTEIQKYSIPT---LLSGKSAILVAETGCGKTLSFL   94 (134)
Q Consensus        46 l~~~i~~~l~~~g~~~~t~iQ~~~i~~---~~~g~dvli~a~tGsGKT~~~~   94 (134)
                      |.+.+.+.+.+.|+..--..-.+++..   +.....++++||+|+|||.++-
T Consensus       873 l~~ai~~~~~~~~L~~~~~~v~KviQLye~~~vRhGvmlVGp~gsGKTt~~~  924 (3245)
T 3vkg_A          873 LRKKIQEIAKQRHLVTKQEWVEKILQLHQILNINHGVMMVGPSGGGKTTSWE  924 (3245)
T ss_dssp             HHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHTTCSEEEEECSSSSSHHHHHH
T ss_pred             HHHHHHHHHHHcCCccCHHHHHHHHHHHHHHHheeeEEEECCCCCCHHHHHH
Confidence            445666777778884433344444433   2245569999999999999873

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=90.81  E-value=0.11  Score=38.86  Aligned_cols=18  Identities=28%  Similarity=0.586  Sum_probs=15.4

Q ss_pred             CCCeEEEcCCCCchhHHh
Q psy7268          76 GKSAILVAETGCGKTLSF   93 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~   93 (134)
                      ++.+++.||+|+|||...
T Consensus        70 ~~~vLl~GppGtGKT~la   87 (368)
T 3uk6_A           70 GRAVLIAGQPGTGKTAIA   87 (368)
T ss_dssp             TCEEEEEESTTSSHHHHH
T ss_pred             CCEEEEECCCCCCHHHHH
Confidence            457999999999999764

>4akg_A Glutathione S-transferase class-MU 26 kDa isozyme heavy chain cytoplasmic; motor protein, AAA+ protein, ASCE protein, P-loop ntpase; HET: ATP ADP; 3.30A {Schistosoma japonicum} PDB: 4ai6_A* 4akh_A* 4aki_A* 3qmz_A

Probab=90.66  E-value=0.72  Score=43.86  Aligned_cols=48  Identities=25%  Similarity=0.391  Sum_probs=32.6

Q ss_pred             CCHHHHHHHHHCCCCCChHHH-HHHHH---HHHcCCCeEEEcCCCCchhHHhH
Q psy7268          46 LAPEIIDIFTKRGLTTPTEIQ-KYSIP---TLLSGKSAILVAETGCGKTLSFL   94 (134)
Q Consensus        46 l~~~i~~~l~~~g~~~~t~iQ-~~~i~---~~~~g~dvli~a~tGsGKT~~~~   94 (134)
                      +.+.+.+.+.+.|+ .+++.+ ..++.   .+.....+++.||||+|||.++-
T Consensus       890 l~~~i~~~~~~~~l-~~~~~~~~K~~ql~e~~~~r~gvmlvGptgsGKTt~~~  941 (2695)
T 4akg_A          890 IVQCLKDAGQRSGF-SMSEEFLKKCMQFYYMQKTQQALILVGKAGCGKTATWK  941 (2695)
T ss_dssp             HHHHHHHHHHHHTC-CCCHHHHHHHHHHHHHHHHCSEEEEECSTTSSHHHHHH
T ss_pred             HHHHHHHHHHHcCC-cccHHHHHHHHHHHHHHHhcceEEEECCCCCCHHHHHH
Confidence            34556677777788 455543 33333   23456779999999999999853

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=90.49  E-value=0.22  Score=36.85  Aligned_cols=19  Identities=26%  Similarity=0.497  Sum_probs=16.2

Q ss_pred             cCCCeEEEcCCCCchhHHh
Q psy7268          75 SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~   93 (134)
                      .+..+++.|++|+|||...
T Consensus        24 ~~~~vLi~Ge~GtGKt~lA   42 (304)
T 1ojl_A           24 SDATVLIHGDSGTGKELVA   42 (304)
T ss_dssp             TTSCEEEESCTTSCHHHHH
T ss_pred             CCCcEEEECCCCchHHHHH
Confidence            4668999999999999764

>2pt7_A CAG-ALFA; ATPase, protein-protein complex, type IV secretion, hydrolas binding complex; 2.40A {Helicobacter pylori} SCOP: c.37.1.11 PDB: 1nly_A* 1nlz_A 1opx_A* 1g6o_A

Probab=90.38  E-value=0.16  Score=38.30  Aligned_cols=20  Identities=40%  Similarity=0.574  Sum_probs=17.3

Q ss_pred             HHcCCCeEEEcCCCCchhHH
Q psy7268          73 LLSGKSAILVAETGCGKTLS   92 (134)
Q Consensus        73 ~~~g~dvli~a~tGsGKT~~   92 (134)
                      +..|..+.+.||||+|||..
T Consensus       168 i~~g~~v~i~G~~GsGKTTl  187 (330)
T 2pt7_A          168 IAIGKNVIVCGGTGSGKTTY  187 (330)
T ss_dssp             HHHTCCEEEEESTTSCHHHH
T ss_pred             ccCCCEEEEECCCCCCHHHH
Confidence            44789999999999999964

>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=90.31  E-value=0.15  Score=35.37  Aligned_cols=19  Identities=26%  Similarity=0.331  Sum_probs=15.6

Q ss_pred             cCCCeEEEcCCCCchhHHh
Q psy7268          75 SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~   93 (134)
                      .|+-+++.||+|+|||...
T Consensus         7 ~g~~i~l~GpsGsGKsTl~   25 (208)
T 3tau_A            7 RGLLIVLSGPSGVGKGTVR   25 (208)
T ss_dssp             CCCEEEEECCTTSCHHHHH
T ss_pred             CCcEEEEECcCCCCHHHHH
Confidence            4666889999999999654

>2eyu_A Twitching motility protein PILT; pilus retraction motor, C-terminal domain PILT, protein transport; 1.87A {Aquifex aeolicus}

Probab=90.20  E-value=0.12  Score=37.62  Aligned_cols=21  Identities=19%  Similarity=0.237  Sum_probs=17.2

Q ss_pred             HHcCCCeEEEcCCCCchhHHh
Q psy7268          73 LLSGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        73 ~~~g~dvli~a~tGsGKT~~~   93 (134)
                      +..|.-+.+.||||+|||...
T Consensus        22 i~~g~~v~i~Gp~GsGKSTll   42 (261)
T 2eyu_A           22 HRKMGLILVTGPTGSGKSTTI   42 (261)
T ss_dssp             GCSSEEEEEECSTTCSHHHHH
T ss_pred             hCCCCEEEEECCCCccHHHHH
Confidence            346777999999999999764

>2qor_A Guanylate kinase; phosphotransferase, purine metabolism, structural genomics, structural genomics of pathogenic protozoa consortium; HET: 5GP POP; 1.80A {Plasmodium vivax}

Probab=90.18  E-value=0.14  Score=35.37  Aligned_cols=21  Identities=14%  Similarity=0.237  Sum_probs=17.2

Q ss_pred             HHcCCCeEEEcCCCCchhHHh
Q psy7268          73 LLSGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        73 ~~~g~dvli~a~tGsGKT~~~   93 (134)
                      +..|+-++++||+|+|||...
T Consensus         9 ~~~~~~i~l~G~sGsGKsTl~   29 (204)
T 2qor_A            9 MARIPPLVVCGPSGVGKGTLI   29 (204)
T ss_dssp             CCCCCCEEEECCTTSCHHHHH
T ss_pred             cccCCEEEEECCCCCCHHHHH
Confidence            346778999999999999653

>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=90.11  E-value=0.12  Score=34.89  Aligned_cols=20  Identities=30%  Similarity=0.471  Sum_probs=16.3

Q ss_pred             HcCCCeEEEcCCCCchhHHh
Q psy7268          74 LSGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        74 ~~g~dvli~a~tGsGKT~~~   93 (134)
                      ..|.-+.+.|++|+|||...
T Consensus         7 ~~g~~i~l~G~~GsGKSTl~   26 (191)
T 1zp6_A            7 LGGNILLLSGHPGSGKSTIA   26 (191)
T ss_dssp             CTTEEEEEEECTTSCHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHH
Confidence            35677899999999999653

>4gp7_A Metallophosphoesterase; polynucleotide kinase phosphatase, RNA repair, transferase; HET: ATP CIT; 2.00A {Clostridium thermocellum} PDB: 4gp6_A*

Probab=90.11  E-value=0.13  Score=34.65  Aligned_cols=20  Identities=20%  Similarity=0.265  Sum_probs=16.4

Q ss_pred             cCCCeEEEcCCCCchhHHhH
Q psy7268          75 SGKSAILVAETGCGKTLSFL   94 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~~   94 (134)
                      .|.-+.+.||+|+|||..+-
T Consensus         8 ~gei~~l~G~nGsGKSTl~~   27 (171)
T 4gp7_A            8 ELSLVVLIGSSGSGKSTFAK   27 (171)
T ss_dssp             SSEEEEEECCTTSCHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHH
Confidence            45668899999999997764

>3bgw_A DNAB-like replicative helicase; ATPase, replication; 3.91A {Bacillus phage SPP1}

Probab=90.10  E-value=0.44  Score=37.34  Aligned_cols=37  Identities=14%  Similarity=0.129  Sum_probs=24.3

Q ss_pred             cCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEc
Q psy7268          75 SGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIIT  123 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~  123 (134)
                      .|.-+++.|++|+|||... +-++..+..           ++..+++++
T Consensus       196 ~G~liiIaG~pG~GKTtla-l~ia~~~a~-----------~g~~vl~fS  232 (444)
T 3bgw_A          196 RRNFVLIAARPSMGKTAFA-LKQAKNMSD-----------NDDVVNLHS  232 (444)
T ss_dssp             SSCEEEEEECSSSSHHHHH-HHHHHHHHH-----------TTCEEEEEC
T ss_pred             CCcEEEEEeCCCCChHHHH-HHHHHHHHH-----------cCCEEEEEE
Confidence            4556899999999999655 444444433           244577775

>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=90.03  E-value=0.19  Score=34.02  Aligned_cols=17  Identities=24%  Similarity=0.360  Sum_probs=14.5

Q ss_pred             CCeEEEcCCCCchhHHh
Q psy7268          77 KSAILVAETGCGKTLSF   93 (134)
Q Consensus        77 ~dvli~a~tGsGKT~~~   93 (134)
                      ..+++.||+|+|||...
T Consensus        39 ~~~ll~G~~G~GKT~l~   55 (226)
T 2chg_A           39 PHLLFSGPPGTGKTATA   55 (226)
T ss_dssp             CCEEEECSTTSSHHHHH
T ss_pred             CeEEEECCCCCCHHHHH
Confidence            46999999999999654

>2j41_A Guanylate kinase; GMP, GMK, transferase, ATP-binding, nucleotide- binding; HET: 5GP; 1.9A {Staphylococcus aureus}

Probab=90.00  E-value=0.15  Score=34.74  Aligned_cols=20  Identities=25%  Similarity=0.273  Sum_probs=16.5

Q ss_pred             HcCCCeEEEcCCCCchhHHh
Q psy7268          74 LSGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        74 ~~g~dvli~a~tGsGKT~~~   93 (134)
                      ..|.-+.+.|++|+|||...
T Consensus         4 ~~g~~i~l~G~~GsGKSTl~   23 (207)
T 2j41_A            4 EKGLLIVLSGPSGVGKGTVR   23 (207)
T ss_dssp             CCCCEEEEECSTTSCHHHHH
T ss_pred             CCCCEEEEECCCCCCHHHHH
Confidence            35777899999999999654

>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=90.00  E-value=0.15  Score=33.97  Aligned_cols=18  Identities=22%  Similarity=0.233  Sum_probs=15.2

Q ss_pred             CCCeEEEcCCCCchhHHh
Q psy7268          76 GKSAILVAETGCGKTLSF   93 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~   93 (134)
                      +.-+++.|++|+|||...
T Consensus         3 ~~~i~l~G~~GsGKST~a   20 (178)
T 1qhx_A            3 TRMIILNGGSSAGKSGIV   20 (178)
T ss_dssp             CCEEEEECCTTSSHHHHH
T ss_pred             ceEEEEECCCCCCHHHHH
Confidence            456899999999999764

>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=89.98  E-value=0.18  Score=37.29  Aligned_cols=25  Identities=16%  Similarity=0.181  Sum_probs=18.2

Q ss_pred             CCCeEEEcCCCCchhHHhHHHHHHHH
Q psy7268          76 GKSAILVAETGCGKTLSFLAPLVQQI  101 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~~lpil~~~  101 (134)
                      +..+++.||+|+|||... -.+...+
T Consensus        37 ~~~lll~G~~GtGKT~la-~~i~~~~   61 (324)
T 1l8q_A           37 YNPIFIYGSVGTGKTHLL-QAAGNEA   61 (324)
T ss_dssp             CSSEEEECSSSSSHHHHH-HHHHHHH
T ss_pred             CCeEEEECCCCCcHHHHH-HHHHHHH
Confidence            468999999999999664 3344444

>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=89.97  E-value=0.16  Score=33.31  Aligned_cols=16  Identities=19%  Similarity=0.262  Sum_probs=13.4

Q ss_pred             CeEEEcCCCCchhHHh
Q psy7268          78 SAILVAETGCGKTLSF   93 (134)
Q Consensus        78 dvli~a~tGsGKT~~~   93 (134)
                      -+++.|++|||||...
T Consensus         3 ~I~l~G~~GsGKsT~a   18 (179)
T 3lw7_A            3 VILITGMPGSGKSEFA   18 (179)
T ss_dssp             EEEEECCTTSCHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            3678999999999764

>3trf_A Shikimate kinase, SK; amino acid biosynthesis, transferase; 2.60A {Coxiella burnetii}

Probab=89.90  E-value=0.17  Score=34.02  Aligned_cols=18  Identities=28%  Similarity=0.194  Sum_probs=15.5

Q ss_pred             CCCeEEEcCCCCchhHHh
Q psy7268          76 GKSAILVAETGCGKTLSF   93 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~   93 (134)
                      ++.+++.|++|+|||...
T Consensus         5 ~~~i~l~G~~GsGKst~a   22 (185)
T 3trf_A            5 LTNIYLIGLMGAGKTSVG   22 (185)
T ss_dssp             CCEEEEECSTTSSHHHHH
T ss_pred             CCEEEEECCCCCCHHHHH
Confidence            567899999999999764

>3tr0_A Guanylate kinase, GMP kinase; purines, pyrimidines, nucleosides, nucleotides, transferase; HET: 5GP; 1.85A {Coxiella burnetii}

Probab=89.83  E-value=0.18  Score=34.39  Aligned_cols=19  Identities=32%  Similarity=0.378  Sum_probs=15.9

Q ss_pred             cCCCeEEEcCCCCchhHHh
Q psy7268          75 SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~   93 (134)
                      .|.-+.+.||+|+|||...
T Consensus         6 ~g~ii~l~Gp~GsGKSTl~   24 (205)
T 3tr0_A            6 KANLFIISAPSGAGKTSLV   24 (205)
T ss_dssp             CCCEEEEECCTTSCHHHHH
T ss_pred             CCcEEEEECcCCCCHHHHH
Confidence            5677889999999999754

>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=89.79  E-value=0.21  Score=33.50  Aligned_cols=20  Identities=25%  Similarity=0.225  Sum_probs=16.8

Q ss_pred             HcCCCeEEEcCCCCchhHHh
Q psy7268          74 LSGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        74 ~~g~dvli~a~tGsGKT~~~   93 (134)
                      ..++.+++.|++|+|||...
T Consensus         9 ~~~~~i~i~G~~GsGKst~~   28 (180)
T 3iij_A            9 MLLPNILLTGTPGVGKTTLG   28 (180)
T ss_dssp             CCCCCEEEECSTTSSHHHHH
T ss_pred             ccCCeEEEEeCCCCCHHHHH
Confidence            35678999999999999764

>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=89.74  E-value=0.15  Score=36.73  Aligned_cols=17  Identities=29%  Similarity=0.217  Sum_probs=14.8

Q ss_pred             CCeEEEcCCCCchhHHh
Q psy7268          77 KSAILVAETGCGKTLSF   93 (134)
Q Consensus        77 ~dvli~a~tGsGKT~~~   93 (134)
                      ..+++.||+|+|||...
T Consensus        65 ~~vLl~G~~GtGKT~la   81 (272)
T 1d2n_A           65 VSVLLEGPPHSGKTALA   81 (272)
T ss_dssp             EEEEEECSTTSSHHHHH
T ss_pred             eEEEEECCCCCcHHHHH
Confidence            36999999999999765

>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=89.70  E-value=0.66  Score=36.83  Aligned_cols=17  Identities=35%  Similarity=0.530  Sum_probs=15.0

Q ss_pred             CCeEEEcCCCCchhHHh
Q psy7268          77 KSAILVAETGCGKTLSF   93 (134)
Q Consensus        77 ~dvli~a~tGsGKT~~~   93 (134)
                      +.+++.||+|+|||...
T Consensus        78 ~~lLL~GppGtGKTtla   94 (516)
T 1sxj_A           78 RAAMLYGPPGIGKTTAA   94 (516)
T ss_dssp             SEEEEECSTTSSHHHHH
T ss_pred             cEEEEECCCCCCHHHHH
Confidence            57999999999999765

>1kag_A SKI, shikimate kinase I; transferase, structural genomics, PSI, protein structure initiative; 2.05A {Escherichia coli} SCOP: c.37.1.2

Probab=89.70  E-value=0.21  Score=33.15  Aligned_cols=18  Identities=28%  Similarity=0.364  Sum_probs=15.3

Q ss_pred             CCCeEEEcCCCCchhHHh
Q psy7268          76 GKSAILVAETGCGKTLSF   93 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~   93 (134)
                      +..+.+.|++|+|||...
T Consensus         4 ~~~i~l~G~~GsGKSTl~   21 (173)
T 1kag_A            4 KRNIFLVGPMGAGKSTIG   21 (173)
T ss_dssp             CCCEEEECCTTSCHHHHH
T ss_pred             CCeEEEECCCCCCHHHHH
Confidence            567899999999999763

>2ius_A DNA translocase FTSK; nucleotide-binding, chromosome partition, ATP-binding, DNA- binding, cell division, transmembrane, inner membrane; HET: DNA; 2.7A {Escherichia coli} PDB: 2j5p_A*

Probab=89.61  E-value=0.6  Score=37.46  Aligned_cols=27  Identities=15%  Similarity=0.279  Sum_probs=19.4

Q ss_pred             cCCCeEEEcCCCCchhHHhHHHHHHHH
Q psy7268          75 SGKSAILVAETGCGKTLSFLAPLVQQI  101 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~~lpil~~~  101 (134)
                      .+.++++.|.||||||.+.-.-++..+
T Consensus       166 ~~pHlLIaG~TGSGKSt~L~~li~sLl  192 (512)
T 2ius_A          166 KMPHLLVAGTTGSGASVGVNAMILSML  192 (512)
T ss_dssp             GSCSEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             cCceEEEECCCCCCHHHHHHHHHHHHH
Confidence            356899999999999976543333333

>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=89.58  E-value=0.36  Score=32.94  Aligned_cols=16  Identities=25%  Similarity=0.326  Sum_probs=13.9

Q ss_pred             CeEEEcCCCCchhHHh
Q psy7268          78 SAILVAETGCGKTLSF   93 (134)
Q Consensus        78 dvli~a~tGsGKT~~~   93 (134)
                      .+++.||+|+|||...
T Consensus        47 ~~ll~G~~G~GKT~l~   62 (250)
T 1njg_A           47 AYLFSGTRGVGKTSIA   62 (250)
T ss_dssp             EEEEECSTTSCHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            5899999999999654

>1z6g_A Guanylate kinase; structural genomics, SGC, structural genom consortium, transferase; HET: EPE; 2.18A {Plasmodium falciparum}

Probab=89.54  E-value=0.22  Score=34.96  Aligned_cols=21  Identities=14%  Similarity=0.218  Sum_probs=16.6

Q ss_pred             HHcCCCeEEEcCCCCchhHHh
Q psy7268          73 LLSGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        73 ~~~g~dvli~a~tGsGKT~~~   93 (134)
                      +..|+-+.+.||+|+|||...
T Consensus        20 i~~G~~~~lvGpsGsGKSTLl   40 (218)
T 1z6g_A           20 MNNIYPLVICGPSGVGKGTLI   40 (218)
T ss_dssp             --CCCCEEEECSTTSSHHHHH
T ss_pred             cCCCCEEEEECCCCCCHHHHH
Confidence            346888999999999999654

>3nwn_A Kinesin-like protein KIF9; motor domain, ADP, structural genomics, structural consortium, SGC, contractIle protein; HET: ADP; 2.00A {Homo sapiens}

Probab=89.52  E-value=0.31  Score=37.32  Aligned_cols=24  Identities=29%  Similarity=0.535  Sum_probs=18.9

Q ss_pred             HHHHHcCCC--eEEEcCCCCchhHHh
Q psy7268          70 IPTLLSGKS--AILVAETGCGKTLSF   93 (134)
Q Consensus        70 i~~~~~g~d--vli~a~tGsGKT~~~   93 (134)
                      +..++.|.|  ++.-|.||||||...
T Consensus        97 v~~~l~G~N~tifAYGQTGSGKTyTM  122 (359)
T 3nwn_A           97 VSQALDGYNGTIMCYGQTGAGKTYTM  122 (359)
T ss_dssp             HHHHHTTCCEEEEEEESTTSSHHHHH
T ss_pred             HHHHhCCCCEEEEEeCCCCCCccEEe
Confidence            344568887  777899999999874

>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=89.42  E-value=0.2  Score=37.87  Aligned_cols=51  Identities=16%  Similarity=0.203  Sum_probs=29.8

Q ss_pred             CCCCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHH-----cCCCeEEEcCCCCchhHHh
Q psy7268          37 DLGTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLL-----SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        37 ~~~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~-----~g~dvli~a~tGsGKT~~~   93 (134)
                      +-.+|+++.-.+...+.|.+. ..  .+   .-.|.++     ..+.+++.||+|+|||...
T Consensus        46 ~~~~~~di~G~~~~~~~l~~~-v~--~~---~~~~~~~~~~~~~~~~iLL~GppGtGKT~la  101 (355)
T 2qp9_X           46 PNVKWEDVAGLEGAKEALKEA-VI--LP---VKFPHLFKGNRKPTSGILLYGPPGTGKSYLA  101 (355)
T ss_dssp             -CCCGGGSCCGGGHHHHHHHH-TH--HH---HHCGGGGCSSCCCCCCEEEECSTTSCHHHHH
T ss_pred             CCCCHHHhCCHHHHHHHHHHH-HH--HH---HhCHHHHhcCCCCCceEEEECCCCCcHHHHH
Confidence            345677777666666666552 10  00   0011122     2357999999999999765

>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=89.40  E-value=0.17  Score=39.54  Aligned_cols=45  Identities=13%  Similarity=0.095  Sum_probs=29.6

Q ss_pred             CCCCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHH----cCCCeEEEcCCCCchhHHh
Q psy7268          37 DLGTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLL----SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        37 ~~~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~----~g~dvli~a~tGsGKT~~~   93 (134)
                      +-..|+++.-.++..+.+...            +..+.    .++.+++.||+|+|||...
T Consensus        32 ~~~~~~~iiG~~~~~~~l~~~------------~~~~~~~~~~~~~iLl~GppGtGKT~la   80 (456)
T 2c9o_A           32 AKQAASGLVGQENAREACGVI------------VELIKSKKMAGRAVLLAGPPGTGKTALA   80 (456)
T ss_dssp             BCSEETTEESCHHHHHHHHHH------------HHHHHTTCCTTCEEEEECCTTSSHHHHH
T ss_pred             hhhchhhccCHHHHHHHHHHH------------HHHHHhCCCCCCeEEEECCCcCCHHHHH
Confidence            334577776677776655431            11222    3467999999999999775

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A

Probab=89.39  E-value=0.16  Score=37.29  Aligned_cols=17  Identities=18%  Similarity=0.145  Sum_probs=14.3

Q ss_pred             CCeEEEcCCCCchhHHh
Q psy7268          77 KSAILVAETGCGKTLSF   93 (134)
Q Consensus        77 ~dvli~a~tGsGKT~~~   93 (134)
                      +.+++.||+|+|||...
T Consensus        37 ~~lLl~GppGtGKT~la   53 (293)
T 3t15_A           37 LILGIWGGKGQGKSFQC   53 (293)
T ss_dssp             SEEEEEECTTSCHHHHH
T ss_pred             eEEEEECCCCCCHHHHH
Confidence            45889999999999764

>1bg2_A Kinesin; motor protein, ATPase, microtubule associated; HET: ADP; 1.80A {Homo sapiens} SCOP: c.37.1.9 PDB: 2p4n_K* 1mkj_A* 2kin_A* 3kin_A*

Probab=89.36  E-value=0.35  Score=36.51  Aligned_cols=24  Identities=25%  Similarity=0.425  Sum_probs=19.2

Q ss_pred             HHHHHcCCC--eEEEcCCCCchhHHh
Q psy7268          70 IPTLLSGKS--AILVAETGCGKTLSF   93 (134)
Q Consensus        70 i~~~~~g~d--vli~a~tGsGKT~~~   93 (134)
                      +..++.|.|  ++.-|.||||||...
T Consensus        70 v~~~l~G~n~tifAYGqTGSGKTyTm   95 (325)
T 1bg2_A           70 VKDVLEGYNGTIFAYGQTSSGKTHTM   95 (325)
T ss_dssp             HHHHHTTCCEEEEEECSTTSSHHHHH
T ss_pred             HHHHhCCCeEEEEEECCCCCCCceEe
Confidence            344568887  777899999999885

>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=89.32  E-value=0.21  Score=34.59  Aligned_cols=22  Identities=18%  Similarity=0.339  Sum_probs=16.8

Q ss_pred             HHHcCCCeEEEcCCCCchhHHh
Q psy7268          72 TLLSGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        72 ~~~~g~dvli~a~tGsGKT~~~   93 (134)
                      .+..|+-+.+.||+|+|||...
T Consensus        16 ~i~~Gei~~l~GpnGsGKSTLl   37 (207)
T 1znw_A           16 PAAVGRVVVLSGPSAVGKSTVV   37 (207)
T ss_dssp             ---CCCEEEEECSTTSSHHHHH
T ss_pred             CCCCCCEEEEECCCCCCHHHHH
Confidence            5667888999999999999754

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=89.09  E-value=0.19  Score=37.37  Aligned_cols=19  Identities=37%  Similarity=0.382  Sum_probs=15.9

Q ss_pred             cCCCeEEEcCCCCchhHHh
Q psy7268          75 SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~   93 (134)
                      .+..+++.||+|+|||...
T Consensus        43 ~~~~vll~G~~G~GKT~l~   61 (387)
T 2v1u_A           43 KPSNALLYGLTGTGKTAVA   61 (387)
T ss_dssp             CCCCEEECBCTTSSHHHHH
T ss_pred             CCCcEEEECCCCCCHHHHH
Confidence            3567999999999999764

>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=89.07  E-value=0.11  Score=37.12  Aligned_cols=18  Identities=44%  Similarity=0.564  Sum_probs=15.4

Q ss_pred             CCCeEEEcCCCCchhHHh
Q psy7268          76 GKSAILVAETGCGKTLSF   93 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~   93 (134)
                      .+.+++.||+|+|||...
T Consensus        44 ~~~vll~G~~GtGKT~la   61 (268)
T 2r62_A           44 PKGVLLVGPPGTGKTLLA   61 (268)
T ss_dssp             CSCCCCBCSSCSSHHHHH
T ss_pred             CceEEEECCCCCcHHHHH
Confidence            456999999999999765

>1s96_A Guanylate kinase, GMP kinase; E.coli, dimer, SAD, transferase; 2.00A {Escherichia coli} SCOP: c.37.1.1 PDB: 2an9_A* 2anb_A* 2anc_A 2f3r_A* 2f3t_A*

Probab=88.99  E-value=0.22  Score=35.25  Aligned_cols=21  Identities=29%  Similarity=0.439  Sum_probs=16.6

Q ss_pred             HHcCCCeEEEcCCCCchhHHh
Q psy7268          73 LLSGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        73 ~~~g~dvli~a~tGsGKT~~~   93 (134)
                      +-.|+-+.+.||+|+|||...
T Consensus        13 ~~~G~ii~l~GpsGsGKSTLl   33 (219)
T 1s96_A           13 MAQGTLYIVSAPSGAGKSSLI   33 (219)
T ss_dssp             --CCCEEEEECCTTSCHHHHH
T ss_pred             CCCCcEEEEECCCCCCHHHHH
Confidence            456888999999999999754

>3dc4_A Kinesin-like protein NOD; catalytic domain, ATPase, microtubule, ADP, nucleotide-binding protein, ATP-binding, coiled coil, motor protein; HET: ADP; 1.90A {Drosophila melanogaster} PDB: 3dcb_A* 3dco_N* 3pxn_A*

Probab=88.93  E-value=0.33  Score=36.95  Aligned_cols=23  Identities=39%  Similarity=0.579  Sum_probs=18.3

Q ss_pred             HHHHcCCC--eEEEcCCCCchhHHh
Q psy7268          71 PTLLSGKS--AILVAETGCGKTLSF   93 (134)
Q Consensus        71 ~~~~~g~d--vli~a~tGsGKT~~~   93 (134)
                      ..++.|.+  ++.-|.||||||...
T Consensus        88 ~~~l~G~N~tifAYGQTGSGKTyTM  112 (344)
T 3dc4_A           88 DKLLEGFQCTALAYGQTGTGKSYSM  112 (344)
T ss_dssp             HHHHHTCCEEEEEESSTTSSHHHHH
T ss_pred             hHhhCCCceEEEEecCCCCCCCeEE
Confidence            34567887  677899999999874

>1ly1_A Polynucleotide kinase; PNK, phosphatase, transferase; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.1

Probab=88.89  E-value=0.21  Score=33.12  Aligned_cols=16  Identities=19%  Similarity=0.225  Sum_probs=13.4

Q ss_pred             CeEEEcCCCCchhHHh
Q psy7268          78 SAILVAETGCGKTLSF   93 (134)
Q Consensus        78 dvli~a~tGsGKT~~~   93 (134)
                      -+++.|++|||||...
T Consensus         4 ~I~i~G~~GsGKST~a   19 (181)
T 1ly1_A            4 IILTIGCPGSGKSTWA   19 (181)
T ss_dssp             EEEEECCTTSSHHHHH
T ss_pred             EEEEecCCCCCHHHHH
Confidence            3788999999999764

>4eun_A Thermoresistant glucokinase; putative sugar kinase, enzyme function initiative, EFI, STRU genomics, transferase; 1.60A {Janibacter SP}

Probab=88.85  E-value=0.23  Score=34.07  Aligned_cols=19  Identities=21%  Similarity=0.389  Sum_probs=16.1

Q ss_pred             cCCCeEEEcCCCCchhHHh
Q psy7268          75 SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~   93 (134)
                      .|.-+.+.|++|+|||...
T Consensus        28 ~g~~i~l~G~~GsGKSTl~   46 (200)
T 4eun_A           28 PTRHVVVMGVSGSGKTTIA   46 (200)
T ss_dssp             CCCEEEEECCTTSCHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHH
Confidence            4677999999999999764

>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=88.85  E-value=0.23  Score=37.52  Aligned_cols=18  Identities=39%  Similarity=0.571  Sum_probs=15.5

Q ss_pred             CCCeEEEcCCCCchhHHh
Q psy7268          76 GKSAILVAETGCGKTLSF   93 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~   93 (134)
                      ..++++.||+|+|||...
T Consensus        72 ~~~ill~Gp~GtGKT~la   89 (376)
T 1um8_A           72 KSNILLIGPTGSGKTLMA   89 (376)
T ss_dssp             CCCEEEECCTTSSHHHHH
T ss_pred             CCCEEEECCCCCCHHHHH
Confidence            457999999999999764

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=88.76  E-value=0.67  Score=34.39  Aligned_cols=26  Identities=15%  Similarity=0.161  Sum_probs=18.2

Q ss_pred             cCCCeEEEcCCCCchhHHhHHHHHHHH
Q psy7268          75 SGKSAILVAETGCGKTLSFLAPLVQQI  101 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~~lpil~~~  101 (134)
                      .|.-+++.|++|+|||... +-++...
T Consensus        67 ~G~l~li~G~pG~GKTtl~-l~ia~~~   92 (315)
T 3bh0_A           67 RRNFVLIAARPSMGKTAFA-LKQAKNM   92 (315)
T ss_dssp             TTCEEEEECCTTSSHHHHH-HHHHHHH
T ss_pred             CCcEEEEEeCCCCCHHHHH-HHHHHHH
Confidence            4556899999999999554 4344333

>4a14_A Kinesin, kinesin-like protein KIF7; motor protein, motor domain; HET: ADP; 1.60A {Homo sapiens} SCOP: c.37.1.0 PDB: 2xt3_A*

Probab=88.76  E-value=0.41  Score=36.42  Aligned_cols=24  Identities=25%  Similarity=0.513  Sum_probs=18.8

Q ss_pred             HHHHHcCCC--eEEEcCCCCchhHHh
Q psy7268          70 IPTLLSGKS--AILVAETGCGKTLSF   93 (134)
Q Consensus        70 i~~~~~g~d--vli~a~tGsGKT~~~   93 (134)
                      +..++.|.|  ++.-|.||||||...
T Consensus        76 v~~~l~G~n~tifAYGqTGSGKTyTm  101 (344)
T 4a14_A           76 LEAFFEGFNATVFAYGQTGSGKTYTM  101 (344)
T ss_dssp             HHHHHTTCCEEEEEESSTTSSHHHHH
T ss_pred             HHHHHhhcCeeEEEecccCCCceEee
Confidence            344568887  677799999999874

>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=88.73  E-value=0.67  Score=33.62  Aligned_cols=16  Identities=25%  Similarity=0.418  Sum_probs=14.2

Q ss_pred             CeEEEcCCCCchhHHh
Q psy7268          78 SAILVAETGCGKTLSF   93 (134)
Q Consensus        78 dvli~a~tGsGKT~~~   93 (134)
                      ++++.||+|+|||...
T Consensus        48 ~~ll~G~~G~GKT~la   63 (327)
T 1iqp_A           48 HLLFAGPPGVGKTTAA   63 (327)
T ss_dssp             EEEEESCTTSSHHHHH
T ss_pred             eEEEECcCCCCHHHHH
Confidence            6999999999999764

>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=88.70  E-value=0.26  Score=34.14  Aligned_cols=16  Identities=19%  Similarity=0.474  Sum_probs=13.7

Q ss_pred             CCeEEEcCCCCchhHH
Q psy7268          77 KSAILVAETGCGKTLS   92 (134)
Q Consensus        77 ~dvli~a~tGsGKT~~   92 (134)
                      +-+++.||+|+|||..
T Consensus         2 RpIVi~GPSG~GK~Tl   17 (186)
T 1ex7_A            2 RPIVISGPSGTGKSTL   17 (186)
T ss_dssp             CCEEEECCTTSSHHHH
T ss_pred             CEEEEECCCCCCHHHH
Confidence            5589999999999964

>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=88.70  E-value=0.35  Score=35.66  Aligned_cols=17  Identities=24%  Similarity=0.415  Sum_probs=14.6

Q ss_pred             CCeEEEcCCCCchhHHh
Q psy7268          77 KSAILVAETGCGKTLSF   93 (134)
Q Consensus        77 ~dvli~a~tGsGKT~~~   93 (134)
                      .++++.||+|+|||...
T Consensus        59 ~~~ll~G~~G~GKT~la   75 (353)
T 1sxj_D           59 PHMLFYGPPGTGKTSTI   75 (353)
T ss_dssp             CCEEEECSTTSSHHHHH
T ss_pred             CEEEEECCCCCCHHHHH
Confidence            46999999999999664

>4fcw_A Chaperone protein CLPB; AAA domain; HET: ADP; 2.35A {Thermus thermophilus} PDB: 4fcv_A* 4fd2_A* 4fct_A*

Probab=88.60  E-value=0.27  Score=35.73  Aligned_cols=17  Identities=35%  Similarity=0.386  Sum_probs=14.7

Q ss_pred             CCeEEEcCCCCchhHHh
Q psy7268          77 KSAILVAETGCGKTLSF   93 (134)
Q Consensus        77 ~dvli~a~tGsGKT~~~   93 (134)
                      ..+++.||+|+|||...
T Consensus        48 ~~~ll~G~~GtGKt~la   64 (311)
T 4fcw_A           48 GSFLFLGPTGVGKTELA   64 (311)
T ss_dssp             EEEEEESCSSSSHHHHH
T ss_pred             eEEEEECCCCcCHHHHH
Confidence            36999999999999765

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=88.54  E-value=0.22  Score=37.97  Aligned_cols=18  Identities=28%  Similarity=0.462  Sum_probs=15.7

Q ss_pred             CCCeEEEcCCCCchhHHh
Q psy7268          76 GKSAILVAETGCGKTLSF   93 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~   93 (134)
                      .+.+++.||+|+|||...
T Consensus       148 ~~~vLL~GppGtGKT~la  165 (389)
T 3vfd_A          148 ARGLLLFGPPGNGKTMLA  165 (389)
T ss_dssp             CSEEEEESSTTSCHHHHH
T ss_pred             CceEEEECCCCCCHHHHH
Confidence            468999999999999764

>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=88.53  E-value=0.24  Score=33.15  Aligned_cols=18  Identities=28%  Similarity=0.375  Sum_probs=15.2

Q ss_pred             CCCeEEEcCCCCchhHHh
Q psy7268          76 GKSAILVAETGCGKTLSF   93 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~   93 (134)
                      |.-+++.|++|+|||...
T Consensus         3 ~~~I~i~G~~GsGKsT~~   20 (192)
T 1kht_A            3 NKVVVVTGVPGVGSTTSS   20 (192)
T ss_dssp             CCEEEEECCTTSCHHHHH
T ss_pred             CeEEEEECCCCCCHHHHH
Confidence            566899999999999753

>3b6u_A Kinesin-like protein KIF3B; structural genomics consortium, motor domain, ADP, SGC, ATP-binding, coiled coil, microtubule, motor protein; HET: ADP; 1.80A {Homo sapiens} PDB: 3b6v_A*

Probab=88.48  E-value=0.41  Score=36.88  Aligned_cols=24  Identities=29%  Similarity=0.531  Sum_probs=18.9

Q ss_pred             HHHHHcCCC--eEEEcCCCCchhHHh
Q psy7268          70 IPTLLSGKS--AILVAETGCGKTLSF   93 (134)
Q Consensus        70 i~~~~~g~d--vli~a~tGsGKT~~~   93 (134)
                      +..++.|.+  ++.-|.||||||...
T Consensus        94 v~~~l~G~n~tifAYGqTGSGKTyTM  119 (372)
T 3b6u_A           94 VDSVLQGFNGTIFAYGQTGTGKTYTM  119 (372)
T ss_dssp             HHHHHTTCCEEEEEEESTTSSHHHHH
T ss_pred             HHHHhCCCeeeEEeecCCCCCCCEeE
Confidence            344668887  677899999999874

>2y65_A Kinesin, kinesin heavy chain; motor protein; HET: ADP; 2.20A {Drosophila melanogaster} PDB: 2y5w_A*

Probab=88.47  E-value=0.43  Score=36.62  Aligned_cols=23  Identities=26%  Similarity=0.421  Sum_probs=18.6

Q ss_pred             HHHHcCCC--eEEEcCCCCchhHHh
Q psy7268          71 PTLLSGKS--AILVAETGCGKTLSF   93 (134)
Q Consensus        71 ~~~~~g~d--vli~a~tGsGKT~~~   93 (134)
                      ..++.|.+  ++.-|.||||||...
T Consensus        78 ~~~l~G~n~tifAYGqTGSGKTyTm  102 (365)
T 2y65_A           78 TDVLAGYNGTIFAYGQTSSGKTHTM  102 (365)
T ss_dssp             HHHHTTCCEEEEEECSTTSSHHHHH
T ss_pred             HHHhCCCceEEEeecCCCCCCceEE
Confidence            34568887  677899999999885

>2vvg_A Kinesin-2; motor protein, nucleotide-binding, microtubule, ATP-binding; HET: ADP; 1.60A {Giardia intestinalis}

Probab=88.43  E-value=0.44  Score=36.37  Aligned_cols=23  Identities=30%  Similarity=0.501  Sum_probs=18.5

Q ss_pred             HHHHcCCC--eEEEcCCCCchhHHh
Q psy7268          71 PTLLSGKS--AILVAETGCGKTLSF   93 (134)
Q Consensus        71 ~~~~~g~d--vli~a~tGsGKT~~~   93 (134)
                      ..++.|.+  ++.-|.||||||...
T Consensus        83 ~~~l~G~n~tifAYGqTGSGKTyTm  107 (350)
T 2vvg_A           83 DAVLEGFNSTIFAYGQTGAGKTWTM  107 (350)
T ss_dssp             HHHHTTCCEEEEEECSTTSSHHHHH
T ss_pred             HHHhCCCceeEEeecCCCCCCCEEe
Confidence            34568887  777899999999885

>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=88.41  E-value=0.21  Score=36.56  Aligned_cols=42  Identities=14%  Similarity=0.082  Sum_probs=26.8

Q ss_pred             CcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHH----HcCCCeEEEcCCCCchhHHh
Q psy7268          40 TFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTL----LSGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        40 ~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~----~~g~dvli~a~tGsGKT~~~   93 (134)
                      +|+++--.+..++.+.+.            +..+    .....+++.||+|+|||...
T Consensus        10 ~~~~~ig~~~~~~~l~~~------------l~~~~~~~~~~~~vll~G~~GtGKT~la   55 (324)
T 1hqc_A           10 TLDEYIGQERLKQKLRVY------------LEAAKARKEPLEHLLLFGPPGLGKTTLA   55 (324)
T ss_dssp             STTTCCSCHHHHHHHHHH------------HHHHHHHCSCCCCCEEECCTTCCCHHHH
T ss_pred             cHHHhhCHHHHHHHHHHH------------HHHHHccCCCCCcEEEECCCCCCHHHHH
Confidence            666665566666555431            1111    13367999999999999764

>2ze6_A Isopentenyl transferase; crown GALL tumor, cytokinin biosynthesis; HET: DST AMP; 2.10A {Agrobacterium tumefaciens} PDB: 2ze5_A* 2ze7_A* 2ze8_A

Probab=88.39  E-value=0.23  Score=35.77  Aligned_cols=15  Identities=27%  Similarity=0.200  Sum_probs=12.9

Q ss_pred             eEEEcCCCCchhHHh
Q psy7268          79 AILVAETGCGKTLSF   93 (134)
Q Consensus        79 vli~a~tGsGKT~~~   93 (134)
                      +++.||+|||||...
T Consensus         4 i~I~G~~GSGKSTla   18 (253)
T 2ze6_A            4 HLIYGPTCSGKTDMA   18 (253)
T ss_dssp             EEEECCTTSSHHHHH
T ss_pred             EEEECCCCcCHHHHH
Confidence            678999999999764

>2h58_A Kinesin-like protein KIFC3 variant; motor domain, ADP, structural genomics, structur Al genomics consortium, SGC; HET: ADP; 1.85A {Homo sapiens}

Probab=88.39  E-value=0.45  Score=36.00  Aligned_cols=26  Identities=23%  Similarity=0.405  Sum_probs=21.0

Q ss_pred             HHHHHHHcCCC--eEEEcCCCCchhHHh
Q psy7268          68 YSIPTLLSGKS--AILVAETGCGKTLSF   93 (134)
Q Consensus        68 ~~i~~~~~g~d--vli~a~tGsGKT~~~   93 (134)
                      ..+..++.|.|  ++.-|.||||||...
T Consensus        71 ~lv~~~l~G~n~tifAYGqTGSGKTyTm   98 (330)
T 2h58_A           71 ALVTSCIDGFNVCIFAYGQTGAGKTYTM   98 (330)
T ss_dssp             HHHHHHHTTCCEEEEEESSTTSSHHHHH
T ss_pred             HHHHHHhCCCEEEEEeECCCCCCCcEEE
Confidence            35566789987  777899999999875

>2zfi_A Kinesin-like protein KIF1A, kinesin heavy chain isoform 5C; alpha and beta protein, enzyme, ATPase, P-loop, motor protein, ATP-binding, coiled coil; HET: ADP; 1.55A {Mus musculus} SCOP: c.37.1.9 PDB: 1vfw_A* 1vfx_A* 1vfz_A* 1vfv_A* 2zfj_A* 2zfk_A* 2zfl_A* 2zfm_A* 1i5s_A* 1i6i_A* 2hxf_C* 1ia0_K* 2hxh_C*

Probab=88.35  E-value=0.45  Score=36.54  Aligned_cols=24  Identities=21%  Similarity=0.457  Sum_probs=19.1

Q ss_pred             HHHHHcCCC--eEEEcCCCCchhHHh
Q psy7268          70 IPTLLSGKS--AILVAETGCGKTLSF   93 (134)
Q Consensus        70 i~~~~~g~d--vli~a~tGsGKT~~~   93 (134)
                      +..++.|.+  ++.-|.||||||...
T Consensus        82 v~~~l~G~N~tifAYGqTGSGKTyTm  107 (366)
T 2zfi_A           82 LQHAFEGYNVCIFAYGQTGAGKSYTM  107 (366)
T ss_dssp             HHHHHTTCCEEEEEECSTTSSHHHHH
T ss_pred             HHHHhcCCeeEEEEeCCCCCCCceEe
Confidence            345668887  777899999999875

>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=88.33  E-value=0.21  Score=33.29  Aligned_cols=18  Identities=22%  Similarity=0.325  Sum_probs=15.1

Q ss_pred             CCCeEEEcCCCCchhHHh
Q psy7268          76 GKSAILVAETGCGKTLSF   93 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~   93 (134)
                      |.-+.+.|++|+|||...
T Consensus         8 g~~i~l~G~~GsGKSTl~   25 (175)
T 1knq_A            8 HHIYVLMGVSGSGKSAVA   25 (175)
T ss_dssp             SEEEEEECSTTSCHHHHH
T ss_pred             CcEEEEEcCCCCCHHHHH
Confidence            556889999999999764

>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=88.28  E-value=0.25  Score=33.47  Aligned_cols=19  Identities=26%  Similarity=0.412  Sum_probs=16.1

Q ss_pred             cCCCeEEEcCCCCchhHHh
Q psy7268          75 SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~   93 (134)
                      .+..+++.|++|+|||...
T Consensus         9 ~~~~I~l~G~~GsGKSTv~   27 (184)
T 1y63_A            9 KGINILITGTPGTGKTSMA   27 (184)
T ss_dssp             SSCEEEEECSTTSSHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            4667999999999999764

>1goj_A Kinesin, kinesin heavy chain; motor protein, ATPase; HET: ADP; 2.3A {Neurospora crassa} SCOP: c.37.1.9

Probab=88.28  E-value=0.42  Score=36.56  Aligned_cols=23  Identities=26%  Similarity=0.543  Sum_probs=18.5

Q ss_pred             HHHHcCCC--eEEEcCCCCchhHHh
Q psy7268          71 PTLLSGKS--AILVAETGCGKTLSF   93 (134)
Q Consensus        71 ~~~~~g~d--vli~a~tGsGKT~~~   93 (134)
                      ..++.|.+  ++.-|.||||||...
T Consensus        74 ~~~l~G~n~tifAYGqTGSGKTyTm   98 (355)
T 1goj_A           74 DDILNGYNGTVFAYGQTGAGKSYTM   98 (355)
T ss_dssp             HHHTTTCCEEEEEECSTTSSHHHHH
T ss_pred             HHHhCCCcceEEEECCCCCCcceEe
Confidence            34568887  777899999999885

>3gbj_A KIF13B protein; kinesin, motor domain, ADP, structural genomics, structural genomics consortium, SGC, ATP-binding, microtubule, motor protein; HET: ADP; 2.10A {Homo sapiens} SCOP: c.37.1.9

Probab=88.19  E-value=0.44  Score=36.42  Aligned_cols=25  Identities=20%  Similarity=0.424  Sum_probs=19.7

Q ss_pred             HHHHHHcCCC--eEEEcCCCCchhHHh
Q psy7268          69 SIPTLLSGKS--AILVAETGCGKTLSF   93 (134)
Q Consensus        69 ~i~~~~~g~d--vli~a~tGsGKT~~~   93 (134)
                      .+..++.|.|  ++.-|.||||||...
T Consensus        84 lv~~~l~G~n~tifAYGqTGSGKTyTm  110 (354)
T 3gbj_A           84 ILQNAFDGYNACIFAYGQTGSGKSYTM  110 (354)
T ss_dssp             HHHHHHTTCCEEEEEEECTTSSHHHHH
T ss_pred             HHHHHhCCceeEEEeeCCCCCCCceEE
Confidence            3445668987  677799999999886

>2iut_A DNA translocase FTSK; nucleotide-binding, chromosome partition, ATP-binding, DNA- cell division, DNA translocation, KOPS, membrane; HET: DNA SAP; 2.25A {Pseudomonas aeruginosa} PDB: 2iuu_A*

Probab=88.18  E-value=0.84  Score=37.15  Aligned_cols=27  Identities=22%  Similarity=0.351  Sum_probs=19.5

Q ss_pred             CCCeEEEcCCCCchhHHhHHHHHHHHH
Q psy7268          76 GKSAILVAETGCGKTLSFLAPLVQQIL  102 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~~lpil~~~~  102 (134)
                      ..+++|.|.||||||.+.-.-++..+.
T Consensus       214 ~pHlLIaG~TGSGKS~~L~tlI~sLl~  240 (574)
T 2iut_A          214 MPHLLVAGTTGSGKSVGVNAMLLSILF  240 (574)
T ss_dssp             SCCEEEECCTTSSHHHHHHHHHHHHHT
T ss_pred             CCeeEEECCCCCCHHHHHHHHHHHHHH
Confidence            357999999999999775444444443

>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=88.18  E-value=0.22  Score=39.51  Aligned_cols=51  Identities=33%  Similarity=0.393  Sum_probs=31.7

Q ss_pred             CCCcccCCCCHHHHHHHHHC--CCCCChHHHHHHHHHH--HcCCCeEEEcCCCCchhHHh
Q psy7268          38 LGTFEDTGLAPEIIDIFTKR--GLTTPTEIQKYSIPTL--LSGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        38 ~~~f~~~~l~~~i~~~l~~~--g~~~~t~iQ~~~i~~~--~~g~dvli~a~tGsGKT~~~   93 (134)
                      -.+|+++.-.++..+.+.+.  .+..+..     +..+  .-.+.+++.||+|+|||+..
T Consensus        12 ~~~f~di~G~~~~~~~l~e~v~~l~~~~~-----~~~~g~~~p~gvLL~GppGtGKT~La   66 (476)
T 2ce7_A           12 RVTFKDVGGAEEAIEELKEVVEFLKDPSK-----FNRIGARMPKGILLVGPPGTGKTLLA   66 (476)
T ss_dssp             CCCGGGCCSCHHHHHHHHHHHHHHHCTHH-----HHTTTCCCCSEEEEECCTTSSHHHHH
T ss_pred             CCCHHHhCCcHHHHHHHHHHHHHhhChHH-----HhhcCCCCCCeEEEECCCCCCHHHHH
Confidence            34788888778877777663  1111111     1111  11346999999999999764

>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=88.18  E-value=0.25  Score=32.51  Aligned_cols=16  Identities=25%  Similarity=0.160  Sum_probs=13.4

Q ss_pred             CeEEEcCCCCchhHHh
Q psy7268          78 SAILVAETGCGKTLSF   93 (134)
Q Consensus        78 dvli~a~tGsGKT~~~   93 (134)
                      -+++.|++|+|||...
T Consensus         3 ~i~l~G~~GsGKsT~~   18 (173)
T 3kb2_A            3 LIILEGPDCCFKSTVA   18 (173)
T ss_dssp             EEEEECSSSSSHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            3788999999999764

>1t5c_A CENP-E protein, centromeric protein E; kinesin motor-domain-ADP complex, stranded beta-sheet core with solvent exposed alpha-helices; HET: ADP PIN; 2.50A {Homo sapiens}

Probab=88.08  E-value=0.45  Score=36.28  Aligned_cols=24  Identities=25%  Similarity=0.426  Sum_probs=19.3

Q ss_pred             HHHHHcCCC--eEEEcCCCCchhHHh
Q psy7268          70 IPTLLSGKS--AILVAETGCGKTLSF   93 (134)
Q Consensus        70 i~~~~~g~d--vli~a~tGsGKT~~~   93 (134)
                      +..++.|.+  ++.-|.||||||...
T Consensus        70 v~~~l~G~n~tifAYGqTGSGKTyTM   95 (349)
T 1t5c_A           70 IDSAIQGYNGTIFAYGQTASGKTYTM   95 (349)
T ss_dssp             HHHHHTTCCEEEEEEESTTSSHHHHH
T ss_pred             HHHHHcCCccceeeecCCCCCCCeEE
Confidence            345668887  777899999999886

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori}

Probab=88.05  E-value=0.75  Score=34.86  Aligned_cols=27  Identities=30%  Similarity=0.332  Sum_probs=18.7

Q ss_pred             cCCCeEEEcCCCCchhHHhHHHHHHHHH
Q psy7268          75 SGKSAILVAETGCGKTLSFLAPLVQQIL  102 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~~lpil~~~~  102 (134)
                      .|.=+++.|++|+|||... +-++..+.
T Consensus        45 ~G~LiiIaG~pG~GKTt~a-l~ia~~~a   71 (338)
T 4a1f_A           45 KGSLVIIGARPSMGKTSLM-MNMVLSAL   71 (338)
T ss_dssp             TTCEEEEEECTTSCHHHHH-HHHHHHHH
T ss_pred             CCcEEEEEeCCCCCHHHHH-HHHHHHHH
Confidence            4555889999999999654 44444443

>3lre_A Kinesin-like protein KIF18A; motor protein, nucleotide binding, microtubule binding, ATP- cell projection, cytoskeleton, glycoprotein, microtubule; HET: ADP; 2.20A {Homo sapiens} SCOP: c.37.1.0

Probab=88.05  E-value=0.44  Score=36.44  Aligned_cols=23  Identities=30%  Similarity=0.538  Sum_probs=18.5

Q ss_pred             HHHHcCCC--eEEEcCCCCchhHHh
Q psy7268          71 PTLLSGKS--AILVAETGCGKTLSF   93 (134)
Q Consensus        71 ~~~~~g~d--vli~a~tGsGKT~~~   93 (134)
                      ..++.|.+  ++.-|.||||||...
T Consensus        99 ~~~l~G~n~tifAYGqTGSGKTyTm  123 (355)
T 3lre_A           99 RSFLNGYNCTVLAYGATGAGKTHTM  123 (355)
T ss_dssp             HHHTTTCCEEEEEECCTTSSHHHHH
T ss_pred             HHHhCCCceEEEEeCCCCCCceeee
Confidence            34568887  677899999999885

>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=88.02  E-value=0.28  Score=34.35  Aligned_cols=20  Identities=20%  Similarity=0.400  Sum_probs=16.5

Q ss_pred             HcCCCeEEEcCCCCchhHHh
Q psy7268          74 LSGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        74 ~~g~dvli~a~tGsGKT~~~   93 (134)
                      ..|+-+++.||+|+|||...
T Consensus        17 ~~g~~ivl~GPSGaGKsTL~   36 (197)
T 3ney_A           17 QGRKTLVLIGASGVGRSHIK   36 (197)
T ss_dssp             CSCCEEEEECCTTSSHHHHH
T ss_pred             CCCCEEEEECcCCCCHHHHH
Confidence            36778999999999999653

>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=87.99  E-value=1  Score=33.24  Aligned_cols=43  Identities=12%  Similarity=0.132  Sum_probs=29.1

Q ss_pred             CCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHh
Q psy7268          39 GTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        39 ~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~   93 (134)
                      .+|+++--++.+.+.+.+.=+..            -...++++.||+|+|||...
T Consensus        11 ~~~~~~vg~~~~~~~l~~~~~~~------------~~~~~~ll~Gp~G~GKTtl~   53 (354)
T 1sxj_E           11 KSLNALSHNEELTNFLKSLSDQP------------RDLPHLLLYGPNGTGKKTRC   53 (354)
T ss_dssp             CSGGGCCSCHHHHHHHHTTTTCT------------TCCCCEEEECSTTSSHHHHH
T ss_pred             CCHHHhcCCHHHHHHHHHHHhhC------------CCCCeEEEECCCCCCHHHHH
Confidence            46777777788887777631111            12234999999999999764

>2ewv_A Twitching motility protein PILT; pilus retraction motor, ATPase, hexameric PILT, protein TRAN; HET: ADP; 2.80A {Aquifex aeolicus} PDB: 2eww_A* 2gsz_A*

Probab=87.95  E-value=0.21  Score=38.23  Aligned_cols=20  Identities=20%  Similarity=0.280  Sum_probs=16.6

Q ss_pred             HcCCCeEEEcCCCCchhHHh
Q psy7268          74 LSGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        74 ~~g~dvli~a~tGsGKT~~~   93 (134)
                      ..|.-+++.||||+|||...
T Consensus       134 ~~g~~i~ivG~~GsGKTTll  153 (372)
T 2ewv_A          134 RKMGLILVTGPTGSGKSTTI  153 (372)
T ss_dssp             SSSEEEEEECSSSSSHHHHH
T ss_pred             cCCCEEEEECCCCCCHHHHH
Confidence            35677999999999999664

>4etp_A Kinesin-like protein KAR3; kinesin motor protein, kinesin motor homology domain, karyog mitosis, microtubules; HET: ADP EBC; 2.30A {Saccharomyces cerevisiae}

Probab=87.95  E-value=0.54  Score=36.55  Aligned_cols=25  Identities=28%  Similarity=0.492  Sum_probs=20.5

Q ss_pred             HHHHHHcCCC--eEEEcCCCCchhHHh
Q psy7268          69 SIPTLLSGKS--AILVAETGCGKTLSF   93 (134)
Q Consensus        69 ~i~~~~~g~d--vli~a~tGsGKT~~~   93 (134)
                      .+..++.|.|  ++.-|.||||||...
T Consensus       132 lv~~~l~G~N~tifAYGqTGSGKTyTM  158 (403)
T 4etp_A          132 LVQSSLDGYNVAIFAYGQTGSGKTFTM  158 (403)
T ss_dssp             HHHHHHTTCCEEEEEESCTTSSHHHHH
T ss_pred             HHHHHhCCcceEEEEECCCCCCCceEe
Confidence            5566778987  677799999999886

>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=87.90  E-value=0.67  Score=35.43  Aligned_cols=26  Identities=23%  Similarity=0.225  Sum_probs=18.3

Q ss_pred             CCCeEEEcCCCCchhHHhHHHHHHHHH
Q psy7268          76 GKSAILVAETGCGKTLSFLAPLVQQIL  102 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~~lpil~~~~  102 (134)
                      |.-+++.+++|+|||... +.++....
T Consensus        74 G~li~I~G~pGsGKTtla-l~la~~~~   99 (366)
T 1xp8_A           74 GRITEIYGPESGGKTTLA-LAIVAQAQ   99 (366)
T ss_dssp             TSEEEEEESTTSSHHHHH-HHHHHHHH
T ss_pred             CcEEEEEcCCCCChHHHH-HHHHHHHH
Confidence            456888999999999654 44444443

>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=87.83  E-value=0.17  Score=37.41  Aligned_cols=19  Identities=16%  Similarity=0.358  Sum_probs=15.8

Q ss_pred             cCCCeEEEcCCCCchhHHh
Q psy7268          75 SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~   93 (134)
                      ...++++.||+|+|||...
T Consensus        44 ~~~~vLl~G~~GtGKT~la   62 (350)
T 1g8p_A           44 GIGGVLVFGDRGTGKSTAV   62 (350)
T ss_dssp             GGCCEEEECCGGGCTTHHH
T ss_pred             CCceEEEECCCCccHHHHH
Confidence            3457999999999999764

>1x88_A Kinesin-like protein KIF11; switch II, motor domain, NECK linker, cell cycle; HET: ADP NAT; 1.80A {Homo sapiens} SCOP: c.37.1.9 PDB: 3hqd_A* 3ken_A* 2pg2_A* 1yrs_A* 2fme_A* 2g1q_A* 2gm1_A* 1ii6_A* 2uyi_A* 2uym_A* 2wog_A* 2x2r_A* 2x7c_A* 2x7d_A* 2x7e_A* 2xae_A* 3k3b_A* 3k5e_A* 3l9h_A* 1q0b_A* ...

Probab=87.62  E-value=0.44  Score=36.47  Aligned_cols=25  Identities=24%  Similarity=0.466  Sum_probs=19.3

Q ss_pred             HHHHHHcCCC--eEEEcCCCCchhHHh
Q psy7268          69 SIPTLLSGKS--AILVAETGCGKTLSF   93 (134)
Q Consensus        69 ~i~~~~~g~d--vli~a~tGsGKT~~~   93 (134)
                      .+..++.|.+  ++.-|.||||||...
T Consensus        80 lv~~~l~G~n~tifAYGqTGSGKTyTM  106 (359)
T 1x88_A           80 ILDEVIMGYNCTIFAYGQTGTGKTFTM  106 (359)
T ss_dssp             HHHHHHTTCEEEEEEEECTTSSHHHHH
T ss_pred             hHHHHhCCCceEEEEeCCCCCCCceEE
Confidence            3445668887  677899999999864

>3u06_A Protein claret segregational; motor domain, stalk rotation, power stroke, kinesin-14, MICR binding, NCD, transport, molecular motor; HET: ADP GOL; 2.35A {Drosophila melanogaster} PDB: 2ncd_A* 1n6m_A* 1cz7_A* 3l1c_A*

Probab=87.61  E-value=0.45  Score=37.14  Aligned_cols=26  Identities=31%  Similarity=0.431  Sum_probs=21.0

Q ss_pred             HHHHHHHcCCC--eEEEcCCCCchhHHh
Q psy7268          68 YSIPTLLSGKS--AILVAETGCGKTLSF   93 (134)
Q Consensus        68 ~~i~~~~~g~d--vli~a~tGsGKT~~~   93 (134)
                      ..+..++.|.+  ++.-|.||||||...
T Consensus       129 plv~~~l~G~n~tifAYGqTGSGKTyTM  156 (412)
T 3u06_A          129 PLIQSALDGYNICIFAYGQTGSGKTYTM  156 (412)
T ss_dssp             HHHHHHHTTCCEEEEEESSTTSSHHHHH
T ss_pred             HHHHHHHCCCceEEEEecCCCCCCeeEe
Confidence            35667789987  677799999999885

>2wbe_C Bipolar kinesin KRP-130; EG5, KLP61F, tubulin, mitosis, GTP-binding, motor protein, cell division, cell cycle, microtubule, ATP-binding; HET: GTP ANP GDP TA1; 9.40A {Drosophila melanogaster}

Probab=87.47  E-value=0.47  Score=36.54  Aligned_cols=23  Identities=30%  Similarity=0.502  Sum_probs=18.3

Q ss_pred             HHHHcCCC--eEEEcCCCCchhHHh
Q psy7268          71 PTLLSGKS--AILVAETGCGKTLSF   93 (134)
Q Consensus        71 ~~~~~g~d--vli~a~tGsGKT~~~   93 (134)
                      ..++.|.+  ++.-|.||||||...
T Consensus        94 ~~~l~G~n~tifAYGqTGSGKTyTm  118 (373)
T 2wbe_C           94 EEVLNGYNCTVFAYGQTGTGKTHTM  118 (373)
T ss_dssp             HHHHHTCCEEEEEECSTTSSHHHHH
T ss_pred             HHHhCCceEEEEeecCCCCCcceec
Confidence            34567887  777899999999874

>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=87.44  E-value=0.65  Score=35.47  Aligned_cols=26  Identities=15%  Similarity=0.203  Sum_probs=18.4

Q ss_pred             CCCeEEEcCCCCchhHHhHHHHHHHHH
Q psy7268          76 GKSAILVAETGCGKTLSFLAPLVQQIL  102 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~~lpil~~~~  102 (134)
                      |.-+++.+|+|+|||... +.++..+.
T Consensus        61 G~i~~I~GppGsGKSTLa-l~la~~~~   86 (356)
T 3hr8_A           61 GRIVEIFGQESSGKTTLA-LHAIAEAQ   86 (356)
T ss_dssp             TEEEEEEESTTSSHHHHH-HHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHH-HHHHHHHH
Confidence            556889999999999654 44444443

>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=87.43  E-value=0.85  Score=33.69  Aligned_cols=18  Identities=39%  Similarity=0.610  Sum_probs=14.8

Q ss_pred             CCCeEEEcCCCCchhHHh
Q psy7268          76 GKSAILVAETGCGKTLSF   93 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~   93 (134)
                      |+-+++.|++|+|||...
T Consensus       105 g~vi~lvG~~GsGKTTl~  122 (296)
T 2px0_A          105 SKYIVLFGSTGAGKTTTL  122 (296)
T ss_dssp             SSEEEEEESTTSSHHHHH
T ss_pred             CcEEEEECCCCCCHHHHH
Confidence            445888999999999765

>3jvv_A Twitching mobility protein; hexameric P-loop ATPase, secretion ATPase, ATP-binding, FIMB nucleotide-binding, transport; HET: ACP CIT; 2.60A {Pseudomonas aeruginosa} PDB: 3jvu_A*

Probab=87.37  E-value=0.24  Score=37.75  Aligned_cols=27  Identities=19%  Similarity=0.370  Sum_probs=18.9

Q ss_pred             cCCCeEEEcCCCCchhHHhHHHHHHHHH
Q psy7268          75 SGKSAILVAETGCGKTLSFLAPLVQQIL  102 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~~lpil~~~~  102 (134)
                      .|.-+++.||||||||... -.++..+.
T Consensus       122 ~~g~i~I~GptGSGKTTlL-~~l~g~~~  148 (356)
T 3jvv_A          122 PRGLVLVTGPTGSGKSTTL-AAMLDYLN  148 (356)
T ss_dssp             SSEEEEEECSTTSCHHHHH-HHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH-HHHHhccc
Confidence            4557899999999999654 33444443

>3cob_A Kinesin heavy chain-like protein; motor, switch II, loop L11, conformation, nucleotide, ATP-binding, microtubule, motor protein; HET: ADP; 2.20A {Solanum tuberosum} SCOP: c.37.1.9 PDB: 3cnz_A* 1sdm_A* 3h4s_A*

Probab=87.19  E-value=0.42  Score=36.78  Aligned_cols=25  Identities=24%  Similarity=0.466  Sum_probs=20.4

Q ss_pred             HHHHHHcCCC--eEEEcCCCCchhHHh
Q psy7268          69 SIPTLLSGKS--AILVAETGCGKTLSF   93 (134)
Q Consensus        69 ~i~~~~~g~d--vli~a~tGsGKT~~~   93 (134)
                      .+..++.|.+  ++.-|.||||||...
T Consensus        71 lv~~~l~G~n~tifAYGqTGSGKTyTM   97 (369)
T 3cob_A           71 LVQSAVDGYNVCIFAYGQTGSGKTFTI   97 (369)
T ss_dssp             HHHHHHTTCEEEEEEEECTTSSHHHHH
T ss_pred             hhHhhhcCCceEEEEECCCCCCCeEee
Confidence            4556778987  677899999999885

>1v8k_A Kinesin-like protein KIF2C; microtubule destabilizer, structural P; HET: ANP; 2.25A {Mus musculus} SCOP: c.37.1.9 PDB: 1v8j_A* 2gry_A*

Probab=87.09  E-value=0.55  Score=36.65  Aligned_cols=24  Identities=29%  Similarity=0.558  Sum_probs=18.9

Q ss_pred             HHHHHcCCC--eEEEcCCCCchhHHh
Q psy7268          70 IPTLLSGKS--AILVAETGCGKTLSF   93 (134)
Q Consensus        70 i~~~~~g~d--vli~a~tGsGKT~~~   93 (134)
                      +..++.|.+  ++.-|.||||||...
T Consensus       147 V~~~l~G~N~tifAYGQTGSGKTyTM  172 (410)
T 1v8k_A          147 VQTIFEGGKATCFAYGQTGSGKTHTM  172 (410)
T ss_dssp             HHHHHTTCEEEEEEEESTTSSHHHHH
T ss_pred             HHHHhcCCceeEEeecCCCCCCCeEe
Confidence            344668886  777899999999875

>3cm0_A Adenylate kinase; ATP-binding, cytoplasm, nucleotide biosynthesis, nucleotide-binding, transferase, structural genomics; 1.80A {Thermus thermophilus}

Probab=87.05  E-value=0.22  Score=33.39  Aligned_cols=19  Identities=26%  Similarity=0.503  Sum_probs=15.6

Q ss_pred             cCCCeEEEcCCCCchhHHh
Q psy7268          75 SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~   93 (134)
                      .|..+++.|++|||||...
T Consensus         3 ~g~~I~l~G~~GsGKST~~   21 (186)
T 3cm0_A            3 VGQAVIFLGPPGAGKGTQA   21 (186)
T ss_dssp             CEEEEEEECCTTSCHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHH
Confidence            4556899999999999764

>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=86.99  E-value=0.96  Score=32.82  Aligned_cols=21  Identities=19%  Similarity=0.336  Sum_probs=17.0

Q ss_pred             HcCCCeEEEcCCCCchhHHhH
Q psy7268          74 LSGKSAILVAETGCGKTLSFL   94 (134)
Q Consensus        74 ~~g~dvli~a~tGsGKT~~~~   94 (134)
                      ..|.-+++.|++|+|||....
T Consensus        33 ~~G~~~~i~G~~G~GKTTl~~   53 (296)
T 1cr0_A           33 RGGEVIMVTSGSGMGKSTFVR   53 (296)
T ss_dssp             CTTCEEEEEESTTSSHHHHHH
T ss_pred             CCCeEEEEEeCCCCCHHHHHH
Confidence            357778999999999996653

>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=86.91  E-value=0.88  Score=34.46  Aligned_cols=23  Identities=22%  Similarity=0.287  Sum_probs=17.4

Q ss_pred             cCCCeEEEcCCCCchhHHhHHHH
Q psy7268          75 SGKSAILVAETGCGKTLSFLAPL   97 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~~lpi   97 (134)
                      .|+-+++.+++|+|||...+.-+
T Consensus        60 ~G~iv~I~G~pGsGKTtLal~la   82 (349)
T 2zr9_A           60 RGRVIEIYGPESSGKTTVALHAV   82 (349)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHH
Confidence            35668999999999997654433

>3nwj_A ATSK2; P loop, shikimate, nucleoside monophosphate kinase, shikimat ATP binding, chloroplast, transferase; 2.35A {Arabidopsis thaliana}

Probab=86.85  E-value=0.45  Score=34.43  Aligned_cols=20  Identities=45%  Similarity=0.531  Sum_probs=17.5

Q ss_pred             HcCCCeEEEcCCCCchhHHh
Q psy7268          74 LSGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        74 ~~g~dvli~a~tGsGKT~~~   93 (134)
                      +.|+.+++.|++|+|||...
T Consensus        46 l~g~~i~l~G~~GsGKSTl~   65 (250)
T 3nwj_A           46 LNGRSMYLVGMMGSGKTTVG   65 (250)
T ss_dssp             HTTCCEEEECSTTSCHHHHH
T ss_pred             cCCCEEEEECCCCCCHHHHH
Confidence            35999999999999999774

>3exa_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2, protein structure initiative; 2.30A {Bacillus halodurans} PDB: 2qgn_A

Probab=86.84  E-value=0.34  Score=36.67  Aligned_cols=16  Identities=31%  Similarity=0.320  Sum_probs=13.2

Q ss_pred             CeEEEcCCCCchhHHh
Q psy7268          78 SAILVAETGCGKTLSF   93 (134)
Q Consensus        78 dvli~a~tGsGKT~~~   93 (134)
                      -+++.||||+|||...
T Consensus         5 ~i~i~GptgsGKt~la   20 (322)
T 3exa_A            5 LVAIVGPTAVGKTKTS   20 (322)
T ss_dssp             EEEEECCTTSCHHHHH
T ss_pred             EEEEECCCcCCHHHHH
Confidence            4678999999999654

>3t0q_A AGR253WP; kinesin, alpha and beta proteins, P-loop containing nucleosi triphosphate hydrolases, microtubule motor protein; HET: ADP; 2.35A {Ashbya gossypii}

Probab=86.83  E-value=0.48  Score=36.08  Aligned_cols=25  Identities=28%  Similarity=0.465  Sum_probs=20.2

Q ss_pred             HHHHHHcCCC--eEEEcCCCCchhHHh
Q psy7268          69 SIPTLLSGKS--AILVAETGCGKTLSF   93 (134)
Q Consensus        69 ~i~~~~~g~d--vli~a~tGsGKT~~~   93 (134)
                      .+..++.|.|  ++.-|.||||||...
T Consensus        77 lv~~~l~G~n~tifAYGqTGSGKTyTm  103 (349)
T 3t0q_A           77 LVQSSLDGYNVCIFAYGQTGSGKTYTM  103 (349)
T ss_dssp             HHHGGGTTCEEEEEEECSTTSSHHHHH
T ss_pred             HHHHHHCCcceeEEEeCCCCCCCceEe
Confidence            4556678987  677899999999876

>3foz_A TRNA delta(2)-isopentenylpyrophosphate transferas; nucleoside modification, isopentenyl-tRNA transferase, transferase-RNA complex; 2.50A {Escherichia coli k-12} PDB: 2zxu_A* 2zm5_A

Probab=86.82  E-value=0.34  Score=36.56  Aligned_cols=15  Identities=33%  Similarity=0.348  Sum_probs=12.8

Q ss_pred             eEEEcCCCCchhHHh
Q psy7268          79 AILVAETGCGKTLSF   93 (134)
Q Consensus        79 vli~a~tGsGKT~~~   93 (134)
                      +++.||||+|||...
T Consensus        13 i~i~GptgsGKt~la   27 (316)
T 3foz_A           13 IFLMGPTASGKTALA   27 (316)
T ss_dssp             EEEECCTTSCHHHHH
T ss_pred             EEEECCCccCHHHHH
Confidence            678999999999654

>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=86.81  E-value=0.31  Score=38.00  Aligned_cols=54  Identities=11%  Similarity=0.052  Sum_probs=31.0

Q ss_pred             CCCCcccCCCCHHHHHHHHHCCCCCChHHHHH-HHH-HHHcCCCeEEEcCCCCchhHHh
Q psy7268          37 DLGTFEDTGLAPEIIDIFTKRGLTTPTEIQKY-SIP-TLLSGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        37 ~~~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~-~i~-~~~~g~dvli~a~tGsGKT~~~   93 (134)
                      +-.+|+++.-.+...+.|.+.-.   .|+... .+. .....+.+++.||+|+|||...
T Consensus       129 ~~~~~~di~G~~~~k~~l~~~v~---~p~~~~~~~~~~~~~~~~vLL~GppGtGKT~lA  184 (444)
T 2zan_A          129 PNVKWSDVAGLEGAKEALKEAVI---LPIKFPHLFTGKRTPWRGILLFGPPGTGKSYLA  184 (444)
T ss_dssp             CCCCGGGSCSCHHHHHHHHHHHT---HHHHCTTTTSGGGCCCSEEEEECSTTSSHHHHH
T ss_pred             CCCCHHHhcCHHHHHHHHHHHHH---HHhhCHHHhhccCCCCceEEEECCCCCCHHHHH
Confidence            34568887777777777765210   010000 000 0112367999999999999764

>3a8t_A Adenylate isopentenyltransferase; rossmann fold protein; HET: ATP; 2.37A {Humulus lupulus}

Probab=86.78  E-value=0.34  Score=36.89  Aligned_cols=17  Identities=35%  Similarity=0.431  Sum_probs=14.2

Q ss_pred             CCeEEEcCCCCchhHHh
Q psy7268          77 KSAILVAETGCGKTLSF   93 (134)
Q Consensus        77 ~dvli~a~tGsGKT~~~   93 (134)
                      +-+++.||||+|||...
T Consensus        41 ~lIvI~GPTgsGKTtLa   57 (339)
T 3a8t_A           41 KLLVLMGATGTGKSRLS   57 (339)
T ss_dssp             EEEEEECSTTSSHHHHH
T ss_pred             ceEEEECCCCCCHHHHH
Confidence            45889999999999654

>2heh_A KIF2C protein; kinesin, motor domain, ADP, structural genomics, structural genomics consortium, SGC, structural protein; HET: ADP; 2.15A {Homo sapiens} PDB: 3edl_D*

Probab=86.74  E-value=0.55  Score=36.36  Aligned_cols=24  Identities=29%  Similarity=0.558  Sum_probs=18.9

Q ss_pred             HHHHHcCCC--eEEEcCCCCchhHHh
Q psy7268          70 IPTLLSGKS--AILVAETGCGKTLSF   93 (134)
Q Consensus        70 i~~~~~g~d--vli~a~tGsGKT~~~   93 (134)
                      +..++.|.+  ++.-|.||||||...
T Consensus       127 v~~~l~G~N~tifAYGQTGSGKTyTM  152 (387)
T 2heh_A          127 VQTIFEGGKATCFAYGQTGSGKTHTM  152 (387)
T ss_dssp             HHHHHTTCEEEEEEESCTTSSHHHHH
T ss_pred             HHHHhcCCceEEEEecCCCCCCCeEe
Confidence            344668886  777899999999874

>3u4q_B ATP-dependent helicase/deoxyribonuclease subunit; helicase, nuclease, double strand DNA repair, protein-DNA CO hydrolase-DNA complex; HET: DNA; 2.80A {Bacillus subtilis} PDB: 3u44_B*

Probab=86.67  E-value=0.77  Score=40.04  Aligned_cols=39  Identities=18%  Similarity=0.354  Sum_probs=27.2

Q ss_pred             EEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHH
Q psy7268          80 ILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRE  127 (134)
Q Consensus        80 li~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~  127 (134)
                      +|.|..|||||.+.+-=+...+.. ..        .+.++++++|...
T Consensus         5 lV~agAGSGKT~~l~~ri~~ll~~-~~--------~~~~il~lVP~q~   43 (1166)
T 3u4q_B            5 FLVGRSGSGKTKLIINSIQDELRR-AP--------FGKPIIFLVPDQM   43 (1166)
T ss_dssp             EEEECTTSSHHHHHHHHHHHHHHH-CT--------TSSCEEEECCGGG
T ss_pred             EEEeCCCCChHHHHHHHHHHHHHh-CC--------CCCcEEEEecCcc
Confidence            678999999998876665555543 11        3457899988653

>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=86.63  E-value=0.31  Score=33.46  Aligned_cols=19  Identities=21%  Similarity=0.240  Sum_probs=16.0

Q ss_pred             cCCCeEEEcCCCCchhHHh
Q psy7268          75 SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~   93 (134)
                      .|.-+.+.|++|+|||...
T Consensus        24 ~g~~i~l~G~sGsGKSTl~   42 (200)
T 3uie_A           24 KGCVIWVTGLSGSGKSTLA   42 (200)
T ss_dssp             CCEEEEEECSTTSSHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHH
Confidence            5667889999999999764

>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=86.61  E-value=1.6  Score=32.38  Aligned_cols=15  Identities=27%  Similarity=0.476  Sum_probs=13.5

Q ss_pred             eEEEcCCCCchhHHh
Q psy7268          79 AILVAETGCGKTLSF   93 (134)
Q Consensus        79 vli~a~tGsGKT~~~   93 (134)
                      +++.||+|+|||...
T Consensus        49 ~ll~Gp~G~GKTtla   63 (340)
T 1sxj_C           49 LLFYGPPGTGKTSTI   63 (340)
T ss_dssp             EEEECSSSSSHHHHH
T ss_pred             EEEECCCCCCHHHHH
Confidence            899999999999664

>2j9r_A Thymidine kinase; TK1, DNK, lasso, transferase, ATP-binding, deoxyribonucleoside kinase, DNA synthesis, phosphate accept nucleotide-binding; HET: THM; 2.7A {Bacillus anthracis} PDB: 2ja1_A*

Probab=86.53  E-value=1.2  Score=31.65  Aligned_cols=37  Identities=14%  Similarity=0.202  Sum_probs=23.6

Q ss_pred             eEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHH
Q psy7268          79 AILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRE  127 (134)
Q Consensus        79 vli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~  127 (134)
                      .++.++-|+|||... +-.+.+...           .+.+++++.|.+.
T Consensus        31 ~vitG~MgsGKTT~l-L~~a~r~~~-----------~g~kVli~k~~~d   67 (214)
T 2j9r_A           31 EVICGSMFSGKSEEL-IRRVRRTQF-----------AKQHAIVFKPCID   67 (214)
T ss_dssp             EEEECSTTSCHHHHH-HHHHHHHHH-----------TTCCEEEEECC--
T ss_pred             EEEECCCCCcHHHHH-HHHHHHHHH-----------CCCEEEEEEeccC
Confidence            457899999999765 344444433           4567888877643

>2owm_A Nckin3-434, related to kinesin-like protein KIF1C; motor domain, ADP, NECK linker, motor PR; HET: ADP; 3.25A {Neurospora crassa}

Probab=86.47  E-value=0.79  Score=36.07  Aligned_cols=23  Identities=22%  Similarity=0.381  Sum_probs=18.6

Q ss_pred             HHHHcCCC--eEEEcCCCCchhHHh
Q psy7268          71 PTLLSGKS--AILVAETGCGKTLSF   93 (134)
Q Consensus        71 ~~~~~g~d--vli~a~tGsGKT~~~   93 (134)
                      ..++.|.|  ++.-|.||||||...
T Consensus       130 ~~~l~GyN~tIfAYGQTGSGKTyTM  154 (443)
T 2owm_A          130 DHNFEGYHTCIFAYGQTGSGKSYTM  154 (443)
T ss_dssp             HHHHTTCCEEEEEESSTTSSHHHHH
T ss_pred             HHhhcCCceEEEEeCCCCCCCCEEe
Confidence            34568887  777899999999886

>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=86.37  E-value=0.37  Score=32.53  Aligned_cols=17  Identities=29%  Similarity=0.464  Sum_probs=13.8

Q ss_pred             CCeEEEcCCCCchhHHh
Q psy7268          77 KSAILVAETGCGKTLSF   93 (134)
Q Consensus        77 ~dvli~a~tGsGKT~~~   93 (134)
                      .-+++.||+|+|||...
T Consensus         3 ~ii~l~G~~GaGKSTl~   19 (189)
T 2bdt_A            3 KLYIITGPAGVGKSTTC   19 (189)
T ss_dssp             EEEEEECSTTSSHHHHH
T ss_pred             eEEEEECCCCCcHHHHH
Confidence            34678999999999764

>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=86.28  E-value=1  Score=34.21  Aligned_cols=22  Identities=23%  Similarity=0.219  Sum_probs=17.1

Q ss_pred             cCCCeEEEcCCCCchhHHhHHH
Q psy7268          75 SGKSAILVAETGCGKTLSFLAP   96 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~~lp   96 (134)
                      .|+-+++.+++|+|||...+--
T Consensus        62 ~G~ii~I~G~pGsGKTtLal~l   83 (356)
T 1u94_A           62 MGRIVEIYGPESSGKTTLTLQV   83 (356)
T ss_dssp             TTSEEEEECSTTSSHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHH
Confidence            3566899999999999766433

>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus}

Probab=86.13  E-value=1  Score=35.02  Aligned_cols=27  Identities=26%  Similarity=0.289  Sum_probs=18.4

Q ss_pred             cCCCeEEEcCCCCchhHHhHHHHHHHHH
Q psy7268          75 SGKSAILVAETGCGKTLSFLAPLVQQIL  102 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~~lpil~~~~  102 (134)
                      .|.-+++.|++|+|||... +-+...+.
T Consensus       199 ~G~l~ii~G~pg~GKT~la-l~ia~~~a  225 (444)
T 2q6t_A          199 PGSLNIIAARPAMGKTAFA-LTIAQNAA  225 (444)
T ss_dssp             TTCEEEEEECTTSCHHHHH-HHHHHHHH
T ss_pred             CCcEEEEEeCCCCCHHHHH-HHHHHHHH
Confidence            3455889999999999554 44444443

>3t61_A Gluconokinase; PSI-biology, structural genomics, protein structure initiati YORK structural genomics research consortium, nysgrc; 2.20A {Sinorhizobium meliloti}

Probab=86.12  E-value=0.38  Score=32.85  Aligned_cols=17  Identities=24%  Similarity=0.327  Sum_probs=14.5

Q ss_pred             CCeEEEcCCCCchhHHh
Q psy7268          77 KSAILVAETGCGKTLSF   93 (134)
Q Consensus        77 ~dvli~a~tGsGKT~~~   93 (134)
                      .-+++.|++|+|||...
T Consensus        19 ~~I~l~G~~GsGKSTla   35 (202)
T 3t61_A           19 GSIVVMGVSGSGKSSVG   35 (202)
T ss_dssp             SCEEEECSTTSCHHHHH
T ss_pred             eEEEEECCCCCCHHHHH
Confidence            46899999999999764

>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=86.09  E-value=0.42  Score=35.43  Aligned_cols=18  Identities=28%  Similarity=0.344  Sum_probs=15.5

Q ss_pred             CCCeEEEcCCCCchhHHh
Q psy7268          76 GKSAILVAETGCGKTLSF   93 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~   93 (134)
                      +..+++.||+|+|||...
T Consensus        45 ~~~vli~G~~G~GKTtl~   62 (386)
T 2qby_A           45 PNNIFIYGLTGTGKTAVV   62 (386)
T ss_dssp             CCCEEEEECTTSSHHHHH
T ss_pred             CCeEEEECCCCCCHHHHH
Confidence            567999999999999664

>3pxg_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 3.65A {Bacillus subtilis}

Probab=86.08  E-value=0.52  Score=37.03  Aligned_cols=26  Identities=38%  Similarity=0.543  Sum_probs=18.6

Q ss_pred             cCCCeEEEcCCCCchhHHhHHHHHHHH
Q psy7268          75 SGKSAILVAETGCGKTLSFLAPLVQQI  101 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~~lpil~~~  101 (134)
                      ...++++.||+|+|||... -.+...+
T Consensus       200 ~~~~~LL~G~pG~GKT~la-~~la~~l  225 (468)
T 3pxg_A          200 TKNNPVLIGEPGVGKTAIA-EGLAQQI  225 (468)
T ss_dssp             SSCEEEEESCTTTTTHHHH-HHHHHHH
T ss_pred             CCCCeEEECCCCCCHHHHH-HHHHHHH
Confidence            3457999999999999765 3334444

>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A 2r6e_A 2vyf_A 2vye_A

Probab=86.00  E-value=1.1  Score=35.00  Aligned_cols=26  Identities=23%  Similarity=0.262  Sum_probs=18.4

Q ss_pred             cCCCeEEEcCCCCchhHHhHHHHHHHH
Q psy7268          75 SGKSAILVAETGCGKTLSFLAPLVQQI  101 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~~lpil~~~  101 (134)
                      .|.-+++.|++|+|||... +-++..+
T Consensus       202 ~G~liiI~G~pG~GKTtl~-l~ia~~~  227 (454)
T 2r6a_A          202 RSDLIIVAARPSVGKTAFA-LNIAQNV  227 (454)
T ss_dssp             TTCEEEEECCTTSCHHHHH-HHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH-HHHHHHH
Confidence            4556899999999999655 4444444

>3bfn_A Kinesin-like protein KIF22; limited proteolysis, structural genomics consortium domain, ADP, SGC, ATP-binding, DNA-binding, microtubule, MO protein; HET: ADP; 2.30A {Homo sapiens}

Probab=85.99  E-value=0.48  Score=36.71  Aligned_cols=32  Identities=28%  Similarity=0.404  Sum_probs=23.2

Q ss_pred             ChHHHHHHHH--------HHHcCCC--eEEEcCCCCchhHHh
Q psy7268          62 PTEIQKYSIP--------TLLSGKS--AILVAETGCGKTLSF   93 (134)
Q Consensus        62 ~t~iQ~~~i~--------~~~~g~d--vli~a~tGsGKT~~~   93 (134)
                      +..-|.+++.        .++.|.+  ++.-|.||||||...
T Consensus        75 ~~~tQ~~Vy~~~~~plv~~~l~G~N~tifAYGqTGSGKTyTM  116 (388)
T 3bfn_A           75 ERSTQQDIYAGSVQPILRHLLEGQNASVLAYGPTGAGKTHTM  116 (388)
T ss_dssp             TTCCHHHHHHHHTGGGHHHHTTTCCEEEEEESCTTSSHHHHH
T ss_pred             CCCCHhHHHHHHHHHHHHHhhcCceeeEeeecCCCCCCCeEe
Confidence            3445666664        3557887  677899999999875

>1f9v_A Kinesin-like protein KAR3; kinesin-related protein, motor protein, microtubinding proteinbule, contractIle protein; HET: ADP; 1.30A {Saccharomyces cerevisiae} SCOP: c.37.1.9 PDB: 1f9t_A* 1f9w_A* 1f9u_A* 3kar_A*

Probab=85.95  E-value=0.53  Score=35.87  Aligned_cols=25  Identities=28%  Similarity=0.492  Sum_probs=19.7

Q ss_pred             HHHHHHcCCC--eEEEcCCCCchhHHh
Q psy7268          69 SIPTLLSGKS--AILVAETGCGKTLSF   93 (134)
Q Consensus        69 ~i~~~~~g~d--vli~a~tGsGKT~~~   93 (134)
                      .+..++.|.|  ++.-|.||||||...
T Consensus        76 lv~~~l~G~n~tifAYGqTGSGKTyTM  102 (347)
T 1f9v_A           76 LVQSSLDGYNVCIFAYGQTGSGKTFTM  102 (347)
T ss_dssp             HHGGGGGTCCEEEEEECCTTSSHHHHH
T ss_pred             HHHHhcCCceeEEEEECCCCCCCcEec
Confidence            4445668887  677899999999875

>1gvn_B Zeta; postsegregational killing system, plasmid; 1.95A {Streptococcus pyogenes} SCOP: c.37.1.21 PDB: 3q8x_B*

Probab=85.94  E-value=0.36  Score=35.47  Aligned_cols=17  Identities=29%  Similarity=0.321  Sum_probs=14.0

Q ss_pred             CCeEEEcCCCCchhHHh
Q psy7268          77 KSAILVAETGCGKTLSF   93 (134)
Q Consensus        77 ~dvli~a~tGsGKT~~~   93 (134)
                      .-+++.|++|+|||...
T Consensus        34 ~livl~G~sGsGKSTla   50 (287)
T 1gvn_B           34 TAFLLGGQPGSGKTSLR   50 (287)
T ss_dssp             EEEEEECCTTSCTHHHH
T ss_pred             eEEEEECCCCCCHHHHH
Confidence            34889999999999654

>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=85.94  E-value=1.4  Score=31.75  Aligned_cols=42  Identities=17%  Similarity=0.183  Sum_probs=28.3

Q ss_pred             CCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHh
Q psy7268          39 GTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        39 ~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~   93 (134)
                      .+|+++.-++..++.+.+. +..            -...++++.||+|+|||...
T Consensus        14 ~~~~~~~g~~~~~~~l~~~-l~~------------~~~~~~ll~G~~G~GKt~la   55 (319)
T 2chq_A           14 RTLDEVVGQDEVIQRLKGY-VER------------KNIPHLLFSGPPGTGKTATA   55 (319)
T ss_dssp             SSGGGSCSCHHHHHHHHTT-TTT------------TCCCCEEEESSSSSSHHHHH
T ss_pred             CCHHHHhCCHHHHHHHHHH-HhC------------CCCCeEEEECcCCcCHHHHH
Confidence            3677776677777777653 111            11225999999999999664

>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=85.88  E-value=0.58  Score=34.87  Aligned_cols=16  Identities=38%  Similarity=0.669  Sum_probs=14.3

Q ss_pred             CeEEEcCCCCchhHHh
Q psy7268          78 SAILVAETGCGKTLSF   93 (134)
Q Consensus        78 dvli~a~tGsGKT~~~   93 (134)
                      .+++.||+|+|||...
T Consensus        46 ~~li~G~~G~GKTtl~   61 (389)
T 1fnn_A           46 RATLLGRPGTGKTVTL   61 (389)
T ss_dssp             EEEEECCTTSSHHHHH
T ss_pred             eEEEECCCCCCHHHHH
Confidence            7999999999999664

>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=85.80  E-value=1.3  Score=30.22  Aligned_cols=22  Identities=23%  Similarity=0.119  Sum_probs=15.1

Q ss_pred             eEEEcCCCCchhHHhHHHHHHHH
Q psy7268          79 AILVAETGCGKTLSFLAPLVQQI  101 (134)
Q Consensus        79 vli~a~tGsGKT~~~~lpil~~~  101 (134)
                      +.+.+++|+|||... .-++..+
T Consensus         7 i~i~G~sGsGKTTl~-~~L~~~l   28 (169)
T 1xjc_A            7 WQVVGYKHSGKTTLM-EKWVAAA   28 (169)
T ss_dssp             EEEECCTTSSHHHHH-HHHHHHH
T ss_pred             EEEECCCCCCHHHHH-HHHHHhh
Confidence            678899999999643 3344443

>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=85.75  E-value=0.5  Score=32.33  Aligned_cols=21  Identities=24%  Similarity=0.188  Sum_probs=16.6

Q ss_pred             cCCCeEEEcCCCCchhHHhHH
Q psy7268          75 SGKSAILVAETGCGKTLSFLA   95 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~~l   95 (134)
                      .|.-+++.+++|+|||.....
T Consensus        19 ~G~~~~i~G~~GsGKTtl~~~   39 (220)
T 2cvh_A           19 PGVLTQVYGPYASGKTTLALQ   39 (220)
T ss_dssp             TTSEEEEECSTTSSHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHH
Confidence            456689999999999976543

>3k1j_A LON protease, ATP-dependent protease LON; ATP-binding, nucleotide-binding, Pro hydrolase; HET: ADP PE8; 2.00A {Thermococcus onnurineus}

Probab=85.72  E-value=0.74  Score=37.31  Aligned_cols=23  Identities=22%  Similarity=0.366  Sum_probs=19.4

Q ss_pred             HHHHcCCCeEEEcCCCCchhHHh
Q psy7268          71 PTLLSGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        71 ~~~~~g~dvli~a~tGsGKT~~~   93 (134)
                      ..+..|..+++.||+|+|||...
T Consensus        55 ~~i~~g~~vll~Gp~GtGKTtla   77 (604)
T 3k1j_A           55 TAANQKRHVLLIGEPGTGKSMLG   77 (604)
T ss_dssp             HHHHTTCCEEEECCTTSSHHHHH
T ss_pred             ccccCCCEEEEEeCCCCCHHHHH
Confidence            34568899999999999999665

>3c8u_A Fructokinase; YP_612366.1, putative fructose transport system kinase, STRU genomics, joint center for structural genomics, JCSG; 1.95A {Silicibacter SP}

Probab=85.66  E-value=0.35  Score=33.43  Aligned_cols=19  Identities=21%  Similarity=0.239  Sum_probs=15.0

Q ss_pred             cCCCeEEEcCCCCchhHHh
Q psy7268          75 SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~   93 (134)
                      .|.-+.+.||+|+|||...
T Consensus        21 ~g~~v~I~G~sGsGKSTl~   39 (208)
T 3c8u_A           21 GRQLVALSGAPGSGKSTLS   39 (208)
T ss_dssp             SCEEEEEECCTTSCTHHHH
T ss_pred             CCeEEEEECCCCCCHHHHH
Confidence            3556888999999999653

>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=85.64  E-value=0.35  Score=32.49  Aligned_cols=18  Identities=22%  Similarity=0.150  Sum_probs=14.7

Q ss_pred             CCCeEEEcCCCCchhHHh
Q psy7268          76 GKSAILVAETGCGKTLSF   93 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~   93 (134)
                      +.-+++.|++|+|||...
T Consensus         5 ~~~I~l~G~~GsGKST~~   22 (193)
T 2rhm_A            5 PALIIVTGHPATGKTTLS   22 (193)
T ss_dssp             CEEEEEEESTTSSHHHHH
T ss_pred             CeEEEEECCCCCCHHHHH
Confidence            445889999999999763

>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=85.56  E-value=0.44  Score=35.54  Aligned_cols=17  Identities=29%  Similarity=0.376  Sum_probs=14.8

Q ss_pred             CCeEEEcCCCCchhHHh
Q psy7268          77 KSAILVAETGCGKTLSF   93 (134)
Q Consensus        77 ~dvli~a~tGsGKT~~~   93 (134)
                      ..+++.||+|+|||...
T Consensus        52 ~~~ll~Gp~G~GKTTLa   68 (334)
T 1in4_A           52 DHVLLAGPPGLGKTTLA   68 (334)
T ss_dssp             CCEEEESSTTSSHHHHH
T ss_pred             CeEEEECCCCCcHHHHH
Confidence            57999999999999764

>3hu3_A Transitional endoplasmic reticulum ATPase; VCP, transport protein; HET: AGS; 2.20A {Homo sapiens} PDB: 3hu2_A* 3hu1_A* 1e32_A* 1s3s_A*

Probab=85.49  E-value=0.41  Score=38.04  Aligned_cols=52  Identities=17%  Similarity=0.280  Sum_probs=28.3

Q ss_pred             CcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHH--HcCCCeEEEcCCCCchhHHh
Q psy7268          40 TFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTL--LSGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        40 ~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~--~~g~dvli~a~tGsGKT~~~   93 (134)
                      +|+++.-....++.+.+. +..+.. ....+..+  ...+.+++.||+|+|||+..
T Consensus       202 ~~~~i~G~~~~~~~l~~~-i~~~l~-~~~~~~~~g~~~~~~vLL~GppGtGKT~lA  255 (489)
T 3hu3_A          202 GYDDIGGCRKQLAQIKEM-VELPLR-HPALFKAIGVKPPRGILLYGPPGTGKTLIA  255 (489)
T ss_dssp             CGGGCCSCHHHHHHHHHH-THHHHH-CHHHHHHHTCCCCCEEEEECSTTSSHHHHH
T ss_pred             CHHHcCCHHHHHHHHHHH-HHHHhh-CHHHHHhcCCCCCCcEEEECcCCCCHHHHH
Confidence            566666556666666552 100000 01111111  23457999999999999764

>2qmh_A HPR kinase/phosphorylase; V267F mutation, ATP-binding, carbohydrate metabolism, magnesium, metal-binding, multifunctional enzyme; 2.60A {Lactobacillus casei} PDB: 1jb1_A 1kkl_A 1kkm_A*

Probab=85.47  E-value=0.38  Score=34.09  Aligned_cols=19  Identities=21%  Similarity=0.487  Sum_probs=15.0

Q ss_pred             cCCCeEEEcCCCCchhHHh
Q psy7268          75 SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~   93 (134)
                      .|+-+++.+|||+|||...
T Consensus        33 ~g~~ilI~GpsGsGKStLA   51 (205)
T 2qmh_A           33 YGLGVLITGDSGVGKSETA   51 (205)
T ss_dssp             TTEEEEEECCCTTTTHHHH
T ss_pred             CCEEEEEECCCCCCHHHHH
Confidence            3566899999999998443

>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=85.42  E-value=0.5  Score=32.62  Aligned_cols=30  Identities=17%  Similarity=0.106  Sum_probs=21.5

Q ss_pred             hHHHHHHHHHHHcCCCeEEEcCCCCchhHHh
Q psy7268          63 TEIQKYSIPTLLSGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        63 t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~   93 (134)
                      ++.++.. ..+..|.-+++.|++|+|||...
T Consensus        13 ~~~~r~~-~~~~~~~~i~~~G~~GsGKsT~~   42 (211)
T 1m7g_A           13 TRSERTE-LRNQRGLTIWLTGLSASGKSTLA   42 (211)
T ss_dssp             CHHHHHH-HHTSSCEEEEEECSTTSSHHHHH
T ss_pred             CHHHhhc-ccCCCCCEEEEECCCCCCHHHHH
Confidence            4454444 34556778999999999999754

>3tif_A Uncharacterized ABC transporter ATP-binding prote; nucleotide-binding domain, ABC transporter ATPase; HET: ADP; 1.80A {Methanocaldococcus jannaschii dsm 2661ORGANISM_TAXID} PDB: 1l2t_A* 1f3o_A*

Probab=85.33  E-value=0.47  Score=33.83  Aligned_cols=18  Identities=22%  Similarity=0.459  Sum_probs=15.3

Q ss_pred             cCCCeEEEcCCCCchhHH
Q psy7268          75 SGKSAILVAETGCGKTLS   92 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~   92 (134)
                      .|.-+.+.||+|+|||..
T Consensus        30 ~Ge~~~iiG~nGsGKSTL   47 (235)
T 3tif_A           30 EGEFVSIMGPSGSGKSTM   47 (235)
T ss_dssp             TTCEEEEECSTTSSHHHH
T ss_pred             CCCEEEEECCCCCcHHHH
Confidence            577788999999999954

>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=85.18  E-value=0.44  Score=35.59  Aligned_cols=18  Identities=33%  Similarity=0.388  Sum_probs=15.1

Q ss_pred             CCCeEEEcCCCCchhHHh
Q psy7268          76 GKSAILVAETGCGKTLSF   93 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~   93 (134)
                      ++.+++.||+|+|||...
T Consensus        45 ~~~vll~G~~G~GKT~la   62 (384)
T 2qby_B           45 KFSNLFLGLTGTGKTFVS   62 (384)
T ss_dssp             CCEEEEEECTTSSHHHHH
T ss_pred             CCcEEEECCCCCCHHHHH
Confidence            346999999999999664

>1tev_A UMP-CMP kinase; ploop, NMP binding region, LID region, conformational changes, transferase; 2.10A {Homo sapiens} SCOP: c.37.1.1

Probab=85.00  E-value=0.39  Score=32.15  Aligned_cols=18  Identities=17%  Similarity=0.255  Sum_probs=14.8

Q ss_pred             CCCeEEEcCCCCchhHHh
Q psy7268          76 GKSAILVAETGCGKTLSF   93 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~   93 (134)
                      +.-+++.|++|||||...
T Consensus         3 ~~~I~l~G~~GsGKsT~a   20 (196)
T 1tev_A            3 PLVVFVLGGPGAGKGTQC   20 (196)
T ss_dssp             CEEEEEECCTTSSHHHHH
T ss_pred             ceEEEEECCCCCCHHHHH
Confidence            445889999999999764

>2rep_A Kinesin-like protein KIFC1; structural genomics consortium, motor domain, ADP, binding, cell cycle, cell division, endosome, microtubule; HET: ADP; 2.60A {Homo sapiens}

Probab=84.96  E-value=0.57  Score=36.11  Aligned_cols=24  Identities=29%  Similarity=0.547  Sum_probs=18.9

Q ss_pred             HHHHHcCCC--eEEEcCCCCchhHHh
Q psy7268          70 IPTLLSGKS--AILVAETGCGKTLSF   93 (134)
Q Consensus        70 i~~~~~g~d--vli~a~tGsGKT~~~   93 (134)
                      +..++.|.+  ++.-|.||||||...
T Consensus       108 v~~~l~G~N~tifAYGqTGSGKTyTM  133 (376)
T 2rep_A          108 VQSALDGYPVCIFAYGQTGSGKTFTM  133 (376)
T ss_dssp             HHGGGGTCCEEEEEECSTTSSHHHHH
T ss_pred             HHHhcCCCceEEEEeCCCCCCCceEe
Confidence            344568887  677799999999875

>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=84.92  E-value=0.57  Score=32.58  Aligned_cols=21  Identities=24%  Similarity=0.230  Sum_probs=17.0

Q ss_pred             cCCCeEEEcCCCCchhHHhHH
Q psy7268          75 SGKSAILVAETGCGKTLSFLA   95 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~~l   95 (134)
                      .|.-+.+.+|+|+|||.....
T Consensus        23 ~G~~~~i~G~~GsGKTtl~~~   43 (243)
T 1n0w_A           23 TGSITEMFGEFRTGKTQICHT   43 (243)
T ss_dssp             TTSEEEEECCTTSSHHHHHHH
T ss_pred             CCeEEEEECCCCCcHHHHHHH
Confidence            466789999999999976543

>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=84.92  E-value=0.47  Score=32.32  Aligned_cols=16  Identities=38%  Similarity=0.540  Sum_probs=13.2

Q ss_pred             CeEEEcCCCCchhHHh
Q psy7268          78 SAILVAETGCGKTLSF   93 (134)
Q Consensus        78 dvli~a~tGsGKT~~~   93 (134)
                      .+.+.||+|+|||...
T Consensus         2 ~i~l~G~nGsGKTTLl   17 (178)
T 1ye8_A            2 KIIITGEPGVGKTTLV   17 (178)
T ss_dssp             EEEEECCTTSSHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            3678999999999764

>3kta_A Chromosome segregation protein SMC; structural maintenance of chromosomes, ABC ATPase, CFTR adenylate kinase, AP5A, transferase; HET: AP5; 1.63A {Pyrococcus furiosus} PDB: 1xex_A* 1xew_X*

Probab=84.86  E-value=0.45  Score=31.81  Aligned_cols=16  Identities=25%  Similarity=0.256  Sum_probs=13.3

Q ss_pred             CeEEEcCCCCchhHHh
Q psy7268          78 SAILVAETGCGKTLSF   93 (134)
Q Consensus        78 dvli~a~tGsGKT~~~   93 (134)
                      -.++.+++|+|||..+
T Consensus        28 ~~~i~G~NGsGKStll   43 (182)
T 3kta_A           28 FTAIVGANGSGKSNIG   43 (182)
T ss_dssp             EEEEEECTTSSHHHHH
T ss_pred             cEEEECCCCCCHHHHH
Confidence            4578999999999764

>3f9v_A Minichromosome maintenance protein MCM; replicative helicase, DNA replication, MCM complex, AAA+ Pro ATP-binding, DNA-binding, helicase; 4.35A {Sulfolobus solfataricus}

Probab=84.86  E-value=0.44  Score=38.73  Aligned_cols=16  Identities=13%  Similarity=0.445  Sum_probs=14.4

Q ss_pred             CeEEEcCCCCchhHHh
Q psy7268          78 SAILVAETGCGKTLSF   93 (134)
Q Consensus        78 dvli~a~tGsGKT~~~   93 (134)
                      ++++.||+|+|||...
T Consensus       329 ~vLL~GppGtGKT~LA  344 (595)
T 3f9v_A          329 HILIIGDPGTAKSQML  344 (595)
T ss_dssp             CEEEEESSCCTHHHHH
T ss_pred             ceEEECCCchHHHHHH
Confidence            8999999999999653

>2c95_A Adenylate kinase 1; transferase, AP4A, nucleotide kinase, transferase ATP-bindi; HET: B4P; 1.71A {Homo sapiens} PDB: 1z83_A* 3adk_A

Probab=84.75  E-value=0.51  Score=31.74  Aligned_cols=19  Identities=21%  Similarity=0.295  Sum_probs=16.0

Q ss_pred             cCCCeEEEcCCCCchhHHh
Q psy7268          75 SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~   93 (134)
                      .+.-+++.|++|||||...
T Consensus         8 ~~~~I~l~G~~GsGKsT~~   26 (196)
T 2c95_A            8 KTNIIFVVGGPGSGKGTQC   26 (196)
T ss_dssp             TSCEEEEEECTTSSHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            5667899999999999763

>1w4r_A Thymidine kinase; type II, human, cytosolic, phosphorylation, transferase; HET: TTP; 1.83A {Homo sapiens} PDB: 1xbt_A* 2wvj_A* 2j87_A*

Probab=84.72  E-value=1.2  Score=31.16  Aligned_cols=39  Identities=13%  Similarity=0.210  Sum_probs=26.0

Q ss_pred             cCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCc
Q psy7268          75 SGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPG  125 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt  125 (134)
                      .|+=.++.|+.|+|||.-.+-.+-....            .+.+++++.|.
T Consensus        19 ~g~l~fiyG~MgsGKTt~Ll~~i~n~~~------------~~~kvl~~kp~   57 (195)
T 1w4r_A           19 RGQIQVILGPMFSGKSTELMRRVRRFQI------------AQYKCLVIKYA   57 (195)
T ss_dssp             CCEEEEEEECTTSCHHHHHHHHHHHHHH------------TTCCEEEEEET
T ss_pred             ceEEEEEECCCCCcHHHHHHHHHHHHHH------------cCCeEEEEccc
Confidence            3555788999999999655444333332            34568888765

>1f2t_A RAD50 ABC-ATPase; DNA double-strand break repair, replication; 1.60A {Pyrococcus furiosus} SCOP: c.37.1.12 PDB: 1f2u_A* 1us8_A*

Probab=84.60  E-value=0.51  Score=31.14  Aligned_cols=15  Identities=20%  Similarity=0.598  Sum_probs=12.8

Q ss_pred             eEEEcCCCCchhHHh
Q psy7268          79 AILVAETGCGKTLSF   93 (134)
Q Consensus        79 vli~a~tGsGKT~~~   93 (134)
                      .++.+|+|+|||...
T Consensus        26 ~~I~G~NGsGKStil   40 (149)
T 1f2t_A           26 NLIIGQNGSGKSSLL   40 (149)
T ss_dssp             EEEECCTTSSHHHHH
T ss_pred             EEEECCCCCCHHHHH
Confidence            578899999999764

>3crm_A TRNA delta(2)-isopentenylpyrophosphate transferase; ATP-binding, nucleotide-binding, nucleotidyltransferase, tRNA processing; 1.90A {Pseudomonas aeruginosa} PDB: 3crq_A 3crr_A

Probab=84.51  E-value=0.48  Score=35.80  Aligned_cols=16  Identities=31%  Similarity=0.299  Sum_probs=13.6

Q ss_pred             CeEEEcCCCCchhHHh
Q psy7268          78 SAILVAETGCGKTLSF   93 (134)
Q Consensus        78 dvli~a~tGsGKT~~~   93 (134)
                      -+++.||||+|||...
T Consensus         7 ~i~i~GptGsGKTtla   22 (323)
T 3crm_A            7 AIFLMGPTAAGKTDLA   22 (323)
T ss_dssp             EEEEECCTTSCHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            5789999999999654

>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=84.47  E-value=0.53  Score=31.92  Aligned_cols=19  Identities=21%  Similarity=0.237  Sum_probs=15.8

Q ss_pred             cCCCeEEEcCCCCchhHHh
Q psy7268          75 SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~   93 (134)
                      .|.-+++.|+.|||||...
T Consensus         3 ~~~~I~l~G~~GsGKsT~~   21 (204)
T 2v54_A            3 RGALIVFEGLDKSGKTTQC   21 (204)
T ss_dssp             CCCEEEEECCTTSSHHHHH
T ss_pred             CCcEEEEEcCCCCCHHHHH
Confidence            4667899999999999764

>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=84.45  E-value=0.48  Score=32.64  Aligned_cols=19  Identities=26%  Similarity=0.230  Sum_probs=15.8

Q ss_pred             cCCCeEEEcCCCCchhHHh
Q psy7268          75 SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~   93 (134)
                      .|.-+.+.+|+|+|||...
T Consensus        24 ~G~~~~l~G~nGsGKSTll   42 (231)
T 4a74_A           24 TQAITEVFGEFGSGKTQLA   42 (231)
T ss_dssp             SSEEEEEEESTTSSHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHH
Confidence            4666899999999999654

>2i3b_A HCR-ntpase, human cancer-related ntpase; AAA, rossmann, hydrolase; NMR {Homo sapiens} SCOP: c.37.1.11

Probab=84.38  E-value=0.62  Score=32.14  Aligned_cols=18  Identities=28%  Similarity=0.458  Sum_probs=14.8

Q ss_pred             CCCeEEEcCCCCchhHHh
Q psy7268          76 GKSAILVAETGCGKTLSF   93 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~   93 (134)
                      |.-+.+.+++|+|||...
T Consensus         1 G~~i~i~G~nG~GKTTll   18 (189)
T 2i3b_A            1 ARHVFLTGPPGVGKTTLI   18 (189)
T ss_dssp             CCCEEEESCCSSCHHHHH
T ss_pred             CCEEEEECCCCChHHHHH
Confidence            456789999999999764

>3lnc_A Guanylate kinase, GMP kinase; ALS collaborative crystallography, emerald biostructures, ATP-binding, cytoplasm, nucleotide-binding; HET: 5GP; 1.95A {Anaplasma phagocytophilum}

Probab=84.33  E-value=0.4  Score=33.60  Aligned_cols=19  Identities=37%  Similarity=0.613  Sum_probs=12.1

Q ss_pred             cCCCeEEEcCCCCchhHHh
Q psy7268          75 SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~   93 (134)
                      .|+-+.+.||+|+|||...
T Consensus        26 ~G~ii~l~Gp~GsGKSTl~   44 (231)
T 3lnc_A           26 VGVILVLSSPSGCGKTTVA   44 (231)
T ss_dssp             CCCEEEEECSCC----CHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            5777889999999999664

>3asz_A Uridine kinase; cytidine phosphorylation, transferase; HET: C5P; 2.25A {Thermus thermophilus} PDB: 3asy_A*

Probab=84.22  E-value=0.44  Score=32.68  Aligned_cols=19  Identities=21%  Similarity=0.024  Sum_probs=14.8

Q ss_pred             cCCCeEEEcCCCCchhHHh
Q psy7268          75 SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~   93 (134)
                      .|.-+.+.|++|||||...
T Consensus         5 ~~~~i~i~G~~GsGKSTl~   23 (211)
T 3asz_A            5 KPFVIGIAGGTASGKTTLA   23 (211)
T ss_dssp             CCEEEEEEESTTSSHHHHH
T ss_pred             CcEEEEEECCCCCCHHHHH
Confidence            3445778999999999764

>2r2a_A Uncharacterized protein; zonular occludens toxin, structural genomics, APC84050.2, PS protein structure initiative; HET: MSE; 1.82A {Neisseria meningitidis MC58}

Probab=84.22  E-value=0.83  Score=31.84  Aligned_cols=15  Identities=33%  Similarity=0.696  Sum_probs=13.0

Q ss_pred             eEEEcCCCCchhHHh
Q psy7268          79 AILVAETGCGKTLSF   93 (134)
Q Consensus        79 vli~a~tGsGKT~~~   93 (134)
                      .++.|++|||||...
T Consensus         8 ~l~tG~pGsGKT~~a   22 (199)
T 2r2a_A            8 CLITGTPGSGKTLKM   22 (199)
T ss_dssp             EEEECCTTSSHHHHH
T ss_pred             EEEEeCCCCCHHHHH
Confidence            578999999999865

>3qf7_A RAD50; ABC-ATPase, ATPase, hydrolase; HET: ANP; 1.90A {Thermotoga maritima} PDB: 3qg5_A 3tho_A*

Probab=84.20  E-value=0.49  Score=35.99  Aligned_cols=16  Identities=25%  Similarity=0.490  Sum_probs=13.6

Q ss_pred             CeEEEcCCCCchhHHh
Q psy7268          78 SAILVAETGCGKTLSF   93 (134)
Q Consensus        78 dvli~a~tGsGKT~~~   93 (134)
                      -.++.||||+|||..+
T Consensus        25 ~~~i~G~NGaGKTTll   40 (365)
T 3qf7_A           25 ITVVEGPNGAGKSSLF   40 (365)
T ss_dssp             EEEEECCTTSSHHHHH
T ss_pred             eEEEECCCCCCHHHHH
Confidence            4678999999999766

>2r8r_A Sensor protein; KDPD, PFAM02702, MCSG, structural genomics, protein structure initiative, midwest center for structural genomics, kinase; 2.30A {Pseudomonas syringae PV}

Probab=84.15  E-value=1.5  Score=31.43  Aligned_cols=19  Identities=42%  Similarity=0.690  Sum_probs=15.6

Q ss_pred             CC-CeEEEcCCCCchhHHhH
Q psy7268          76 GK-SAILVAETGCGKTLSFL   94 (134)
Q Consensus        76 g~-dvli~a~tGsGKT~~~~   94 (134)
                      |+ ++++.++.|+|||...+
T Consensus         5 g~l~I~~~~kgGvGKTt~a~   24 (228)
T 2r8r_A            5 GRLKVFLGAAPGVGKTYAML   24 (228)
T ss_dssp             CCEEEEEESSTTSSHHHHHH
T ss_pred             ceEEEEEECCCCCcHHHHHH
Confidence            44 58899999999998764

>1nks_A Adenylate kinase; thermophilic, transferase; HET: AMP ADP; 2.57A {Sulfolobus acidocaldarius} SCOP: c.37.1.1

Probab=84.04  E-value=0.52  Score=31.47  Aligned_cols=16  Identities=25%  Similarity=0.418  Sum_probs=13.2

Q ss_pred             CeEEEcCCCCchhHHh
Q psy7268          78 SAILVAETGCGKTLSF   93 (134)
Q Consensus        78 dvli~a~tGsGKT~~~   93 (134)
                      -+++.|++|+|||...
T Consensus         3 ~I~i~G~~GsGKsT~~   18 (194)
T 1nks_A            3 IGIVTGIPGVGKSTVL   18 (194)
T ss_dssp             EEEEEECTTSCHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            3788999999999654

>3m6a_A ATP-dependent protease LA 1; alpha, beta, ATP-binding, hydrolase, nucleotide-binding, Pro serine protease, stress response; HET: ADP; 3.40A {Bacillus subtilis} PDB: 1x37_A

Probab=83.98  E-value=0.52  Score=37.83  Aligned_cols=19  Identities=32%  Similarity=0.328  Sum_probs=16.3

Q ss_pred             cCCCeEEEcCCCCchhHHh
Q psy7268          75 SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~   93 (134)
                      .|..+++.||+|+|||...
T Consensus       107 ~g~~vll~Gp~GtGKTtla  125 (543)
T 3m6a_A          107 KGPILCLAGPPGVGKTSLA  125 (543)
T ss_dssp             CSCEEEEESSSSSSHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            4778999999999999764

>4akg_A Glutathione S-transferase class-MU 26 kDa isozyme heavy chain cytoplasmic; motor protein, AAA+ protein, ASCE protein, P-loop ntpase; HET: ATP ADP; 3.30A {Schistosoma japonicum} PDB: 4ai6_A* 4akh_A* 4aki_A* 3qmz_A

Probab=83.97  E-value=0.5  Score=44.86  Aligned_cols=21  Identities=38%  Similarity=0.542  Sum_probs=18.1

Q ss_pred             HHcCCCeEEEcCCCCchhHHh
Q psy7268          73 LLSGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        73 ~~~g~dvli~a~tGsGKT~~~   93 (134)
                      +..|+.++++||+|+|||+..
T Consensus      1264 l~~~~~vLL~GPpGtGKT~la 1284 (2695)
T 4akg_A         1264 LNSKRGIILCGPPGSGKTMIM 1284 (2695)
T ss_dssp             HHHTCEEEEECSTTSSHHHHH
T ss_pred             HHCCCeEEEECCCCCCHHHHH
Confidence            447899999999999999764

>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=83.95  E-value=0.97  Score=33.58  Aligned_cols=20  Identities=25%  Similarity=0.202  Sum_probs=15.9

Q ss_pred             CCCeEEEcCCCCchhHHhHH
Q psy7268          76 GKSAILVAETGCGKTLSFLA   95 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~~l   95 (134)
                      |.-+++.|++|+|||...+-
T Consensus       107 G~i~~i~G~~GsGKT~la~~  126 (324)
T 2z43_A          107 RTMTEFFGEFGSGKTQLCHQ  126 (324)
T ss_dssp             TSEEEEEESTTSSHHHHHHH
T ss_pred             CcEEEEECCCCCCHhHHHHH
Confidence            45689999999999966543

>1via_A Shikimate kinase; structural genomics, transferase; HET: MSE; 1.57A {Campylobacter jejuni} SCOP: c.37.1.2

Probab=83.95  E-value=0.63  Score=30.96  Aligned_cols=16  Identities=19%  Similarity=0.347  Sum_probs=13.9

Q ss_pred             CeEEEcCCCCchhHHh
Q psy7268          78 SAILVAETGCGKTLSF   93 (134)
Q Consensus        78 dvli~a~tGsGKT~~~   93 (134)
                      .+++.+++|||||...
T Consensus         6 ~i~i~G~~GsGKsTla   21 (175)
T 1via_A            6 NIVFIGFMGSGKSTLA   21 (175)
T ss_dssp             CEEEECCTTSCHHHHH
T ss_pred             EEEEEcCCCCCHHHHH
Confidence            5889999999999763

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=83.87  E-value=0.51  Score=37.02  Aligned_cols=17  Identities=41%  Similarity=0.399  Sum_probs=14.7

Q ss_pred             CCeEEEcCCCCchhHHh
Q psy7268          77 KSAILVAETGCGKTLSF   93 (134)
Q Consensus        77 ~dvli~a~tGsGKT~~~   93 (134)
                      .++++.||+|+|||...
T Consensus        51 ~~vLL~GppGtGKTtlA   67 (447)
T 3pvs_A           51 HSMILWGPPGTGKTTLA   67 (447)
T ss_dssp             CEEEEECSTTSSHHHHH
T ss_pred             cEEEEECCCCCcHHHHH
Confidence            36999999999999765

>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=83.86  E-value=0.58  Score=36.47  Aligned_cols=26  Identities=15%  Similarity=0.225  Sum_probs=18.6

Q ss_pred             CCCeEEEcCCCCchhHHhHHHHHHHHH
Q psy7268          76 GKSAILVAETGCGKTLSFLAPLVQQIL  102 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~~lpil~~~~  102 (134)
                      +..+++.||+|+|||... -.+...+.
T Consensus       130 ~~~lll~Gp~G~GKTtLa-~aia~~l~  155 (440)
T 2z4s_A          130 YNPLFIYGGVGLGKTHLL-QSIGNYVV  155 (440)
T ss_dssp             SCCEEEECSSSSSHHHHH-HHHHHHHH
T ss_pred             CCeEEEECCCCCCHHHHH-HHHHHHHH
Confidence            457999999999999654 34444443

>3d3q_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2; 2.70A {Staphylococcus epidermidis atcc 12228}

Probab=83.79  E-value=0.53  Score=35.79  Aligned_cols=16  Identities=31%  Similarity=0.295  Sum_probs=13.5

Q ss_pred             CeEEEcCCCCchhHHh
Q psy7268          78 SAILVAETGCGKTLSF   93 (134)
Q Consensus        78 dvli~a~tGsGKT~~~   93 (134)
                      -++|.||||||||...
T Consensus         9 lI~I~GptgSGKTtla   24 (340)
T 3d3q_A            9 LIVIVGPTASGKTELS   24 (340)
T ss_dssp             EEEEECSTTSSHHHHH
T ss_pred             eEEEECCCcCcHHHHH
Confidence            4789999999999654

>3fb4_A Adenylate kinase; psychrophIle, phosphotransferase, ATP-binding, nucleotide-binding, transferase; HET: AP5; 2.00A {Marinibacillus marinus}

Probab=83.77  E-value=0.57  Score=32.24  Aligned_cols=15  Identities=27%  Similarity=0.403  Sum_probs=13.1

Q ss_pred             eEEEcCCCCchhHHh
Q psy7268          79 AILVAETGCGKTLSF   93 (134)
Q Consensus        79 vli~a~tGsGKT~~~   93 (134)
                      +++.|++|||||...
T Consensus         3 I~l~G~~GsGKsT~a   17 (216)
T 3fb4_A            3 IVLMGLPGAGKGTQA   17 (216)
T ss_dssp             EEEECSTTSSHHHHH
T ss_pred             EEEECCCCCCHHHHH
Confidence            688999999999764

>3cf2_A TER ATPase, transitional endoplasmic reticulum ATPase, valosi; AAA, CDC48, ERAD, transport protein; HET: ADP ANP; 3.50A {Mus musculus} PDB: 3cf1_A* 3cf3_A* 1r7r_A*

Probab=83.74  E-value=0.54  Score=39.80  Aligned_cols=54  Identities=24%  Similarity=0.397  Sum_probs=34.5

Q ss_pred             CCCCcccCCCCHHHHHHHHHC-CC--CCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHh
Q psy7268          37 DLGTFEDTGLAPEIIDIFTKR-GL--TTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        37 ~~~~f~~~~l~~~i~~~l~~~-g~--~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~   93 (134)
                      |-.+|++++.-++..+.|.+. -+  ++|...+..   .+...+.+++.||+|+|||+..
T Consensus       472 p~v~w~diggl~~~k~~l~e~v~~p~~~p~~f~~~---g~~~~~gvLl~GPPGtGKT~lA  528 (806)
T 3cf2_A          472 PQVTWEDIGGLEDVKRELQELVQYPVEHPDKFLKF---GMTPSKGVLFYGPPGCGKTLLA  528 (806)
T ss_dssp             CCCCSTTCCSCHHHHHHHTTTTTTTTTCSGGGSSS---CCCCCSCCEEESSTTSSHHHHH
T ss_pred             CCCCHHHhCCHHHHHHHHHHHHHhhhhCHHHHHhc---CCCCCceEEEecCCCCCchHHH
Confidence            445799999889998888874 21  222111100   0112357999999999999764

>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=83.72  E-value=1.8  Score=31.97  Aligned_cols=16  Identities=25%  Similarity=0.326  Sum_probs=13.7

Q ss_pred             CeEEEcCCCCchhHHh
Q psy7268          78 SAILVAETGCGKTLSF   93 (134)
Q Consensus        78 dvli~a~tGsGKT~~~   93 (134)
                      .+++.||+|+|||...
T Consensus        40 ~~ll~G~~G~GKT~la   55 (373)
T 1jr3_A           40 AYLFSGTRGVGKTSIA   55 (373)
T ss_dssp             EEEEESCTTSSHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            3789999999999664

>2cbz_A Multidrug resistance-associated protein 1; ABC proteins, MRP1/ABCC1, nucleotide-binding domain, ATP- binding, hydrolysis, transport; HET: ATP; 1.5A {Homo sapiens}

Probab=83.57  E-value=0.62  Score=33.22  Aligned_cols=19  Identities=32%  Similarity=0.670  Sum_probs=15.8

Q ss_pred             cCCCeEEEcCCCCchhHHh
Q psy7268          75 SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~   93 (134)
                      .|.-+.+.||+|+|||...
T Consensus        30 ~Ge~~~i~G~nGsGKSTLl   48 (237)
T 2cbz_A           30 EGALVAVVGQVGCGKSSLL   48 (237)
T ss_dssp             TTCEEEEECSTTSSHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            5777889999999999543

>1g41_A Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dependent proteolysis, chaperone; HET: ADP; 2.30A {Haemophilus influenzae} SCOP: c.37.1.20 PDB: 1g3i_A* 1im2_A* 1kyi_A* 1g4a_E* 1g4b_E 1yyf_A* 1do0_A* 1do2_A* 1e94_E* 1hqy_E* 1ht1_E* 1ht2_E*

Probab=83.35  E-value=0.68  Score=36.48  Aligned_cols=18  Identities=33%  Similarity=0.462  Sum_probs=15.5

Q ss_pred             CCCeEEEcCCCCchhHHh
Q psy7268          76 GKSAILVAETGCGKTLSF   93 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~   93 (134)
                      .+++++.+|+|+|||...
T Consensus        50 ~~~iLl~GppGtGKT~la   67 (444)
T 1g41_A           50 PKNILMIGPTGVGKTEIA   67 (444)
T ss_dssp             CCCEEEECCTTSSHHHHH
T ss_pred             CceEEEEcCCCCCHHHHH
Confidence            467999999999999764

>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=83.26  E-value=0.54  Score=31.42  Aligned_cols=19  Identities=32%  Similarity=0.368  Sum_probs=15.4

Q ss_pred             cCCCeEEEcCCCCchhHHh
Q psy7268          75 SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~   93 (134)
                      .|.-+.+.|+.|+|||...
T Consensus         4 ~g~~i~l~G~~GsGKST~~   22 (179)
T 2pez_A            4 RGCTVWLTGLSGAGKTTVS   22 (179)
T ss_dssp             CCEEEEEECCTTSSHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHH
Confidence            4566889999999999753

>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=83.20  E-value=0.76  Score=30.71  Aligned_cols=17  Identities=35%  Similarity=0.391  Sum_probs=14.3

Q ss_pred             CCeEEEcCCCCchhHHh
Q psy7268          77 KSAILVAETGCGKTLSF   93 (134)
Q Consensus        77 ~dvli~a~tGsGKT~~~   93 (134)
                      .-+++.|++|||||...
T Consensus         3 ~~I~l~G~~GsGKsT~a   19 (184)
T 2iyv_A            3 PKAVLVGLPGSGKSTIG   19 (184)
T ss_dssp             CSEEEECSTTSSHHHHH
T ss_pred             CeEEEECCCCCCHHHHH
Confidence            45889999999999764

>2bwj_A Adenylate kinase 5; phosphoryl transfer reaction, transferase; HET: AMP; 2.3A {Homo sapiens}

Probab=83.06  E-value=0.64  Score=31.30  Aligned_cols=19  Identities=21%  Similarity=0.333  Sum_probs=15.8

Q ss_pred             cCCCeEEEcCCCCchhHHh
Q psy7268          75 SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~   93 (134)
                      .+.-+++.|++|||||...
T Consensus        11 ~~~~I~l~G~~GsGKsT~a   29 (199)
T 2bwj_A           11 KCKIIFIIGGPGSGKGTQC   29 (199)
T ss_dssp             HSCEEEEEECTTSSHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            4667899999999999763

>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=83.04  E-value=0.63  Score=32.04  Aligned_cols=15  Identities=27%  Similarity=0.330  Sum_probs=13.1

Q ss_pred             eEEEcCCCCchhHHh
Q psy7268          79 AILVAETGCGKTLSF   93 (134)
Q Consensus        79 vli~a~tGsGKT~~~   93 (134)
                      +++.|++|||||...
T Consensus         3 I~l~G~~GsGKsT~a   17 (216)
T 3dl0_A            3 LVLMGLPGAGKGTQG   17 (216)
T ss_dssp             EEEECSTTSSHHHHH
T ss_pred             EEEECCCCCCHHHHH
Confidence            788999999999764

>1sgw_A Putative ABC transporter; structural genomics, P protein structure initiative, southeast collaboratory for S genomics, secsg; 1.70A {Pyrococcus furiosus} SCOP: c.37.1.12

Probab=83.00  E-value=0.77  Score=32.35  Aligned_cols=19  Identities=26%  Similarity=0.365  Sum_probs=16.0

Q ss_pred             cCCCeEEEcCCCCchhHHh
Q psy7268          75 SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~   93 (134)
                      .|.-+.+.||+|+|||...
T Consensus        34 ~Ge~~~iiG~NGsGKSTLl   52 (214)
T 1sgw_A           34 KGNVVNFHGPNGIGKTTLL   52 (214)
T ss_dssp             TTCCEEEECCTTSSHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            5777889999999999653

>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=82.96  E-value=1.5  Score=34.44  Aligned_cols=16  Identities=31%  Similarity=0.482  Sum_probs=13.8

Q ss_pred             CeEEEcCCCCchhHHh
Q psy7268          78 SAILVAETGCGKTLSF   93 (134)
Q Consensus        78 dvli~a~tGsGKT~~~   93 (134)
                      -+++.+++|+|||...
T Consensus       102 vIlivG~~G~GKTTt~  117 (443)
T 3dm5_A          102 ILLMVGIQGSGKTTTV  117 (443)
T ss_dssp             EEEEECCTTSSHHHHH
T ss_pred             EEEEECcCCCCHHHHH
Confidence            4788999999999775

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=82.92  E-value=0.57  Score=38.91  Aligned_cols=26  Identities=38%  Similarity=0.543  Sum_probs=18.6

Q ss_pred             cCCCeEEEcCCCCchhHHhHHHHHHHH
Q psy7268          75 SGKSAILVAETGCGKTLSFLAPLVQQI  101 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~~lpil~~~  101 (134)
                      ...++++.||+|+|||... -.+...+
T Consensus       200 ~~~~vLL~G~pGtGKT~la-~~la~~l  225 (758)
T 3pxi_A          200 TKNNPVLIGEPGVGKTAIA-EGLAQQI  225 (758)
T ss_dssp             SSCEEEEESCTTTTTHHHH-HHHHHHH
T ss_pred             CCCCeEEECCCCCCHHHHH-HHHHHHH
Confidence            3458999999999999765 3334443

>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=82.92  E-value=0.63  Score=32.14  Aligned_cols=17  Identities=18%  Similarity=0.198  Sum_probs=14.1

Q ss_pred             CCeEEEcCCCCchhHHh
Q psy7268          77 KSAILVAETGCGKTLSF   93 (134)
Q Consensus        77 ~dvli~a~tGsGKT~~~   93 (134)
                      .-+.+.|++|||||...
T Consensus         6 ~~i~i~G~~GsGKSTl~   22 (227)
T 1cke_A            6 PVITIDGPSGAGKGTLC   22 (227)
T ss_dssp             CEEEEECCTTSSHHHHH
T ss_pred             eEEEEECCCCCCHHHHH
Confidence            45788999999998764

>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=82.86  E-value=0.84  Score=32.94  Aligned_cols=24  Identities=29%  Similarity=0.505  Sum_probs=19.1

Q ss_pred             HHcCCCeEEEcCCCCchhHHhHHH
Q psy7268          73 LLSGKSAILVAETGCGKTLSFLAP   96 (134)
Q Consensus        73 ~~~g~dvli~a~tGsGKT~~~~lp   96 (134)
                      +..|.-+++.|++|+|||.....-
T Consensus        27 l~~G~i~~i~G~~GsGKTtl~~~l   50 (279)
T 1nlf_A           27 MVAGTVGALVSPGGAGKSMLALQL   50 (279)
T ss_dssp             EETTSEEEEEESTTSSHHHHHHHH
T ss_pred             ccCCCEEEEEcCCCCCHHHHHHHH
Confidence            457788999999999999765443

>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=82.82  E-value=0.71  Score=31.97  Aligned_cols=18  Identities=22%  Similarity=0.373  Sum_probs=15.0

Q ss_pred             CCCeEEEcCCCCchhHHh
Q psy7268          76 GKSAILVAETGCGKTLSF   93 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~   93 (134)
                      +..+++.|++|||||...
T Consensus         4 ~~~I~l~G~~GsGKsT~a   21 (220)
T 1aky_A            4 SIRMVLIGPPGAGKGTQA   21 (220)
T ss_dssp             CCEEEEECCTTSSHHHHH
T ss_pred             CcEEEEECCCCCCHHHHH
Confidence            456899999999999763

>2yvu_A Probable adenylyl-sulfate kinase; transferase, structural genomics, NPPSFA, national P protein structural and functional analyses; 2.10A {Aeropyrum pernix}

Probab=82.81  E-value=0.58  Score=31.49  Aligned_cols=19  Identities=32%  Similarity=0.305  Sum_probs=15.5

Q ss_pred             cCCCeEEEcCCCCchhHHh
Q psy7268          75 SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~   93 (134)
                      .|.-+++.|++|+|||...
T Consensus        12 ~~~~i~l~G~~GsGKsT~~   30 (186)
T 2yvu_A           12 KGIVVWLTGLPGSGKTTIA   30 (186)
T ss_dssp             CCEEEEEECCTTSSHHHHH
T ss_pred             CCcEEEEEcCCCCCHHHHH
Confidence            3556889999999999764

>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=82.75  E-value=0.67  Score=32.76  Aligned_cols=18  Identities=22%  Similarity=0.294  Sum_probs=15.1

Q ss_pred             CCCeEEEcCCCCchhHHh
Q psy7268          76 GKSAILVAETGCGKTLSF   93 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~   93 (134)
                      +.-+.+.|++|+|||...
T Consensus        27 ~~~i~l~G~~GsGKSTl~   44 (246)
T 2bbw_A           27 LLRAVILGPPGSGKGTVC   44 (246)
T ss_dssp             CCEEEEECCTTSSHHHHH
T ss_pred             CcEEEEECCCCCCHHHHH
Confidence            456899999999999754

>1zd8_A GTP:AMP phosphotransferase mitochondrial; ATP:AMP phosphotransferase, myokinase, structural genomics, structural genomics consortium, SGC; 1.48A {Homo sapiens} PDB: 2ak3_A*

Probab=82.70  E-value=0.65  Score=32.39  Aligned_cols=18  Identities=22%  Similarity=0.263  Sum_probs=15.1

Q ss_pred             CCCeEEEcCCCCchhHHh
Q psy7268          76 GKSAILVAETGCGKTLSF   93 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~   93 (134)
                      +.-+++.|++|||||...
T Consensus         7 ~~~I~l~G~~GsGKsT~a   24 (227)
T 1zd8_A            7 LLRAVIMGAPGSGKGTVS   24 (227)
T ss_dssp             CCEEEEEECTTSSHHHHH
T ss_pred             CcEEEEECCCCCCHHHHH
Confidence            456899999999999764

>1zak_A Adenylate kinase; ATP:AMP-phosphotransferase, transferase; HET: AP5; 3.50A {Zea mays} SCOP: c.37.1.1 g.41.2.1

Probab=82.65  E-value=0.77  Score=31.84  Aligned_cols=18  Identities=11%  Similarity=0.165  Sum_probs=15.0

Q ss_pred             CCCeEEEcCCCCchhHHh
Q psy7268          76 GKSAILVAETGCGKTLSF   93 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~   93 (134)
                      +..+++.|++|+|||...
T Consensus         5 ~~~I~l~G~~GsGKsT~~   22 (222)
T 1zak_A            5 PLKVMISGAPASGKGTQC   22 (222)
T ss_dssp             SCCEEEEESTTSSHHHHH
T ss_pred             CeEEEEECCCCCCHHHHH
Confidence            456899999999999764

>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=82.62  E-value=0.64  Score=30.99  Aligned_cols=16  Identities=19%  Similarity=0.355  Sum_probs=13.6

Q ss_pred             CeEEEcCCCCchhHHh
Q psy7268          78 SAILVAETGCGKTLSF   93 (134)
Q Consensus        78 dvli~a~tGsGKT~~~   93 (134)
                      -+++.|++|||||...
T Consensus         8 ~I~l~G~~GsGKsT~~   23 (194)
T 1qf9_A            8 VVFVLGGPGSGKGTQC   23 (194)
T ss_dssp             EEEEEESTTSSHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            4788999999999763

>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=82.60  E-value=0.69  Score=30.46  Aligned_cols=17  Identities=29%  Similarity=0.522  Sum_probs=14.2

Q ss_pred             CCeEEEcCCCCchhHHh
Q psy7268          77 KSAILVAETGCGKTLSF   93 (134)
Q Consensus        77 ~dvli~a~tGsGKT~~~   93 (134)
                      +-+++.|++|||||...
T Consensus         3 ~~I~l~G~~GsGKsT~a   19 (173)
T 1e6c_A            3 EPIFMVGARGCGMTTVG   19 (173)
T ss_dssp             CCEEEESCTTSSHHHHH
T ss_pred             ceEEEECCCCCCHHHHH
Confidence            45889999999999763

>2pze_A Cystic fibrosis transmembrane conductance regulat; NBD, ABC transporter, CFTR, hydrolase; HET: ATP; 1.70A {Homo sapiens} PDB: 2pzg_A* 2pzf_A* 1ckx_A 1cky_A 1ckw_A 1ckz_A

Probab=82.58  E-value=0.71  Score=32.69  Aligned_cols=19  Identities=32%  Similarity=0.459  Sum_probs=15.9

Q ss_pred             cCCCeEEEcCCCCchhHHh
Q psy7268          75 SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~   93 (134)
                      .|.-+.+.||+|+|||...
T Consensus        33 ~Ge~~~i~G~nGsGKSTLl   51 (229)
T 2pze_A           33 RGQLLAVAGSTGAGKTSLL   51 (229)
T ss_dssp             TTCEEEEECCTTSSHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            5777889999999999643

>2v9p_A Replication protein E1; AAA+ molecular motor, DNA replication, DNA translocation, nucleotide-binding, DNA-binding; 3.00A {Bovine papillomavirus type 1} PDB: 2gxa_A*

Probab=82.46  E-value=0.79  Score=34.24  Aligned_cols=19  Identities=11%  Similarity=0.251  Sum_probs=16.4

Q ss_pred             cCCCeEEEcCCCCchhHHh
Q psy7268          75 SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~   93 (134)
                      .|+-+.+.||+|+|||...
T Consensus       125 ~Ge~vaIvGpsGsGKSTLl  143 (305)
T 2v9p_A          125 KKNCLAFIGPPNTGKSMLC  143 (305)
T ss_dssp             TCSEEEEECSSSSSHHHHH
T ss_pred             CCCEEEEECCCCCcHHHHH
Confidence            6888999999999998654

>2pcj_A ABC transporter, lipoprotein-releasing system ATP-binding protein; structural genomics; 1.70A {Aquifex aeolicus} PDB: 2pcl_A

Probab=82.33  E-value=0.7  Score=32.61  Aligned_cols=18  Identities=22%  Similarity=0.481  Sum_probs=15.2

Q ss_pred             cCCCeEEEcCCCCchhHH
Q psy7268          75 SGKSAILVAETGCGKTLS   92 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~   92 (134)
                      .|.-+.+.||+|+|||..
T Consensus        29 ~Ge~~~iiG~nGsGKSTL   46 (224)
T 2pcj_A           29 KGEFVSIIGASGSGKSTL   46 (224)
T ss_dssp             TTCEEEEEECTTSCHHHH
T ss_pred             CCCEEEEECCCCCCHHHH
Confidence            567788999999999954

>2plr_A DTMP kinase, probable thymidylate kinase; TMP-binding, ATP-binding, structural GEN NPPSFA; HET: 1PE PGE EPE PG4; 1.60A {Sulfolobus tokodaii}

Probab=82.30  E-value=0.61  Score=31.65  Aligned_cols=19  Identities=21%  Similarity=0.230  Sum_probs=15.4

Q ss_pred             cCCCeEEEcCCCCchhHHh
Q psy7268          75 SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~   93 (134)
                      .|.-+++.|+.|||||...
T Consensus         3 ~~~~I~i~G~~GsGKsT~~   21 (213)
T 2plr_A            3 KGVLIAFEGIDGSGKSSQA   21 (213)
T ss_dssp             CCEEEEEECCTTSSHHHHH
T ss_pred             CCeEEEEEcCCCCCHHHHH
Confidence            3556889999999999764

>1g6h_A High-affinity branched-chain amino acid transport ATP-binding protein; beta-core domain; HET: ADP; 1.60A {Methanocaldococcus jannaschii} SCOP: c.37.1.12 PDB: 1gaj_A 1g9x_A*

Probab=82.26  E-value=0.74  Score=33.19  Aligned_cols=19  Identities=21%  Similarity=0.555  Sum_probs=15.8

Q ss_pred             cCCCeEEEcCCCCchhHHh
Q psy7268          75 SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~   93 (134)
                      .|.-+.+.||+|+|||...
T Consensus        32 ~Ge~~~liG~nGsGKSTLl   50 (257)
T 1g6h_A           32 KGDVTLIIGPNGSGKSTLI   50 (257)
T ss_dssp             TTCEEEEECSTTSSHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            5777889999999999653

>2wwf_A Thymidilate kinase, putative; transferase, malaria; HET: TMP ADP; 1.89A {Plasmodium falciparum} PDB: 2wwg_A* 2wwh_A* 2wwi_A*

Probab=82.15  E-value=0.69  Score=31.52  Aligned_cols=19  Identities=21%  Similarity=0.242  Sum_probs=15.8

Q ss_pred             cCCCeEEEcCCCCchhHHh
Q psy7268          75 SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~   93 (134)
                      .|.-+++.|+.|||||...
T Consensus         9 ~~~~I~l~G~~GsGKST~~   27 (212)
T 2wwf_A            9 KGKFIVFEGLDRSGKSTQS   27 (212)
T ss_dssp             CSCEEEEEESTTSSHHHHH
T ss_pred             cCCEEEEEcCCCCCHHHHH
Confidence            4567899999999999764

>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=82.15  E-value=1.6  Score=31.85  Aligned_cols=40  Identities=23%  Similarity=0.232  Sum_probs=25.2

Q ss_pred             CCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcCC--C-eEEEcCCCCchhHHh
Q psy7268          39 GTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGK--S-AILVAETGCGKTLSF   93 (134)
Q Consensus        39 ~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~--d-vli~a~tGsGKT~~~   93 (134)
                      .+|+++-.++...+.+.+               .+..|+  + +++.+|+|+|||...
T Consensus        23 ~~~~~ivg~~~~~~~l~~---------------~l~~~~~~~~~L~~G~~G~GKT~la   65 (324)
T 3u61_B           23 STIDECILPAFDKETFKS---------------ITSKGKIPHIILHSPSPGTGKTTVA   65 (324)
T ss_dssp             CSTTTSCCCHHHHHHHHH---------------HHHTTCCCSEEEECSSTTSSHHHHH
T ss_pred             CCHHHHhCcHHHHHHHHH---------------HHHcCCCCeEEEeeCcCCCCHHHHH
Confidence            467777666666655543               112333  3 566778999999764

>2ff7_A Alpha-hemolysin translocation ATP-binding protein HLYB; ABC-transporter, transport protein; HET: ADP; 1.60A {Escherichia coli} SCOP: c.37.1.12 PDB: 2ffb_A* 2fgk_A* 2ffa_A* 2fgj_A* 2pmk_A* 3b5j_A* 1mt0_A 1xef_A*

Probab=82.12  E-value=0.76  Score=33.00  Aligned_cols=19  Identities=26%  Similarity=0.399  Sum_probs=16.0

Q ss_pred             cCCCeEEEcCCCCchhHHh
Q psy7268          75 SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~   93 (134)
                      .|.-+.+.||+|+|||...
T Consensus        34 ~Ge~~~i~G~nGsGKSTLl   52 (247)
T 2ff7_A           34 QGEVIGIVGRSGSGKSTLT   52 (247)
T ss_dssp             TTCEEEEECSTTSSHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            5777889999999999654

>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=82.11  E-value=0.68  Score=31.53  Aligned_cols=16  Identities=31%  Similarity=0.503  Sum_probs=13.5

Q ss_pred             CeEEEcCCCCchhHHh
Q psy7268          78 SAILVAETGCGKTLSF   93 (134)
Q Consensus        78 dvli~a~tGsGKT~~~   93 (134)
                      -+.+.|++|+|||...
T Consensus         3 ~i~i~G~~GsGKSTl~   18 (204)
T 2if2_A            3 RIGLTGNIGCGKSTVA   18 (204)
T ss_dssp             EEEEEECTTSSHHHHH
T ss_pred             EEEEECCCCcCHHHHH
Confidence            3678999999999874

>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=82.00  E-value=0.81  Score=31.15  Aligned_cols=18  Identities=22%  Similarity=0.338  Sum_probs=14.6

Q ss_pred             CCCeEEEcCCCCchhHHh
Q psy7268          76 GKSAILVAETGCGKTLSF   93 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~   93 (134)
                      +.-+++.|++|||||...
T Consensus        20 ~~~I~l~G~~GsGKST~a   37 (201)
T 2cdn_A           20 HMRVLLLGPPGAGKGTQA   37 (201)
T ss_dssp             CCEEEEECCTTSSHHHHH
T ss_pred             CeEEEEECCCCCCHHHHH
Confidence            345889999999999763

>2ghi_A Transport protein; multidrug resistance protein, MDR, structural genomics, structural genomics consortium, SGC; 2.20A {Plasmodium yoelii yoelii str}

Probab=81.99  E-value=0.77  Score=33.23  Aligned_cols=19  Identities=42%  Similarity=0.588  Sum_probs=16.2

Q ss_pred             cCCCeEEEcCCCCchhHHh
Q psy7268          75 SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~   93 (134)
                      .|.-+.+.||+|+|||...
T Consensus        45 ~Ge~~~i~G~nGsGKSTLl   63 (260)
T 2ghi_A           45 SGTTCALVGHTGSGKSTIA   63 (260)
T ss_dssp             TTCEEEEECSTTSSHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            5777899999999999654

>3gfo_A Cobalt import ATP-binding protein CBIO 1; structural genomics, cell membrane, cobalt transport, hydrolase, ION transport; 2.30A {Clostridium perfringens atcc 13124}

Probab=81.97  E-value=0.74  Score=33.74  Aligned_cols=19  Identities=26%  Similarity=0.574  Sum_probs=15.7

Q ss_pred             cCCCeEEEcCCCCchhHHh
Q psy7268          75 SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~   93 (134)
                      .|.-+.+.||+|+|||...
T Consensus        33 ~Ge~~~iiGpnGsGKSTLl   51 (275)
T 3gfo_A           33 RGEVTAILGGNGVGKSTLF   51 (275)
T ss_dssp             TTSEEEEECCTTSSHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            5777889999999999653

>1ji0_A ABC transporter; ATP binding protein, structural genomics, PSI, protein structure initiative, midwest center for structural genomics, MCSG; HET: ATP; 2.00A {Thermotoga maritima} SCOP: c.37.1.12

Probab=81.95  E-value=0.78  Score=32.72  Aligned_cols=19  Identities=32%  Similarity=0.620  Sum_probs=15.8

Q ss_pred             cCCCeEEEcCCCCchhHHh
Q psy7268          75 SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~   93 (134)
                      .|.-+.+.||+|+|||...
T Consensus        31 ~Ge~~~l~G~nGsGKSTLl   49 (240)
T 1ji0_A           31 RGQIVTLIGANGAGKTTTL   49 (240)
T ss_dssp             TTCEEEEECSTTSSHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            5677889999999999653

>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=81.92  E-value=0.71  Score=33.13  Aligned_cols=17  Identities=29%  Similarity=0.247  Sum_probs=14.2

Q ss_pred             CCeEEEcCCCCchhHHh
Q psy7268          77 KSAILVAETGCGKTLSF   93 (134)
Q Consensus        77 ~dvli~a~tGsGKT~~~   93 (134)
                      .-++++|++|||||...
T Consensus         5 ~lIvl~G~pGSGKSTla   21 (260)
T 3a4m_A            5 MLIILTGLPGVGKSTFS   21 (260)
T ss_dssp             EEEEEECCTTSSHHHHH
T ss_pred             EEEEEEcCCCCCHHHHH
Confidence            45889999999999764

>3eph_A TRNA isopentenyltransferase; transferase, alternative initiation, ATP-binding, cytoplasm, mitochondrion, nucleotide-binding, nucleus; 2.95A {Saccharomyces cerevisiae} PDB: 3epj_A 3epk_A* 3epl_A*

Probab=81.91  E-value=0.68  Score=36.15  Aligned_cols=22  Identities=27%  Similarity=0.422  Sum_probs=15.7

Q ss_pred             eEEEcCCCCchhHHhHHHHHHHH
Q psy7268          79 AILVAETGCGKTLSFLAPLVQQI  101 (134)
Q Consensus        79 vli~a~tGsGKT~~~~lpil~~~  101 (134)
                      ++|.||||+|||... .-+...+
T Consensus         5 i~i~GptgsGKttla-~~La~~~   26 (409)
T 3eph_A            5 IVIAGTTGVGKSQLS-IQLAQKF   26 (409)
T ss_dssp             EEEEECSSSSHHHHH-HHHHHHH
T ss_pred             EEEECcchhhHHHHH-HHHHHHC
Confidence            678999999999554 4444443

>1rj9_A FTSY, signal recognition protein; SRP-GTPase domain, heterodimer, nucleotide twinning, protein complex, protein transport; HET: GCP; 1.90A {Thermus aquaticus} SCOP: a.24.13.1 c.37.1.10 PDB: 2q9c_A* 2q9b_A* 2q9a_A* 1okk_D* 2xkv_D 2iyl_D* 2cnw_D* 2j7p_D*

Probab=81.84  E-value=0.75  Score=34.19  Aligned_cols=18  Identities=33%  Similarity=0.660  Sum_probs=14.6

Q ss_pred             CCCeEEEcCCCCchhHHh
Q psy7268          76 GKSAILVAETGCGKTLSF   93 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~   93 (134)
                      |.-+.+.||+|+|||...
T Consensus       102 g~vi~lvG~nGsGKTTll  119 (304)
T 1rj9_A          102 GRVVLVVGVNGVGKTTTI  119 (304)
T ss_dssp             SSEEEEECSTTSSHHHHH
T ss_pred             CeEEEEECCCCCcHHHHH
Confidence            445788999999999764

>4g1u_C Hemin import ATP-binding protein HMUV; membrane transporter, type II ABC importer, HMUT, plasma MEM transport protein-hydrolase complex; 3.01A {Yersinia pestis}

Probab=81.82  E-value=0.78  Score=33.37  Aligned_cols=19  Identities=26%  Similarity=0.550  Sum_probs=15.8

Q ss_pred             cCCCeEEEcCCCCchhHHh
Q psy7268          75 SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~   93 (134)
                      .|.-+.+.||+|+|||...
T Consensus        36 ~Ge~~~liG~nGsGKSTLl   54 (266)
T 4g1u_C           36 SGEMVAIIGPNGAGKSTLL   54 (266)
T ss_dssp             TTCEEEEECCTTSCHHHHH
T ss_pred             CCCEEEEECCCCCcHHHHH
Confidence            5777889999999999653

>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=81.73  E-value=0.75  Score=31.36  Aligned_cols=19  Identities=21%  Similarity=0.244  Sum_probs=16.0

Q ss_pred             cCCCeEEEcCCCCchhHHh
Q psy7268          75 SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~   93 (134)
                      .|.-+++.|+.|||||...
T Consensus         8 ~~~~I~l~G~~GsGKsT~~   26 (215)
T 1nn5_A            8 RGALIVLEGVDRAGKSTQS   26 (215)
T ss_dssp             CCCEEEEEESTTSSHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHH
Confidence            4667899999999999764

>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=81.69  E-value=0.77  Score=31.35  Aligned_cols=15  Identities=33%  Similarity=0.275  Sum_probs=12.8

Q ss_pred             eEEEcCCCCchhHHh
Q psy7268          79 AILVAETGCGKTLSF   93 (134)
Q Consensus        79 vli~a~tGsGKT~~~   93 (134)
                      +.+.|+.|||||...
T Consensus         5 i~l~G~~GsGKST~~   19 (206)
T 1jjv_A            5 VGLTGGIGSGKTTIA   19 (206)
T ss_dssp             EEEECSTTSCHHHHH
T ss_pred             EEEECCCCCCHHHHH
Confidence            678899999999764

>1ukz_A Uridylate kinase; transferase; HET: ADP AMP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1uky_A*

Probab=81.64  E-value=0.77  Score=31.21  Aligned_cols=16  Identities=19%  Similarity=0.345  Sum_probs=13.6

Q ss_pred             CeEEEcCCCCchhHHh
Q psy7268          78 SAILVAETGCGKTLSF   93 (134)
Q Consensus        78 dvli~a~tGsGKT~~~   93 (134)
                      -+++.|+.|||||...
T Consensus        17 ~I~l~G~~GsGKsT~~   32 (203)
T 1ukz_A           17 VIFVLGGPGAGKGTQC   32 (203)
T ss_dssp             EEEEECSTTSSHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            4788999999999764

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=81.54  E-value=1.7  Score=40.35  Aligned_cols=44  Identities=16%  Similarity=0.185  Sum_probs=29.2

Q ss_pred             HHHHHc------CCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCc
Q psy7268          70 IPTLLS------GKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPG  125 (134)
Q Consensus        70 i~~~~~------g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt  125 (134)
                      +..++.      |+.+++.+|+|+|||.....-+.+.. .           ++.+++++...
T Consensus      1415 LD~lLG~GGi~~g~~vll~GppGtGKT~LA~ala~ea~-~-----------~G~~v~Fi~~e 1464 (2050)
T 3cmu_A         1415 LDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIAAAQ-R-----------EGKTCAFIDAE 1464 (2050)
T ss_dssp             HHHHHSSSSEETTSEEEEECCTTSSHHHHHHHHHHHHH-T-----------TTCCEEEECTT
T ss_pred             HHHhcCCCCccCCeEEEEECCCCCCHHHHHHHHHHHHH-H-----------cCCcEEEEEcc
Confidence            555554      77899999999999987644433322 2           45567766543

>4h1g_A Maltose binding protein-cakar3 motor domain fusio; kinesin motor domain, motor protein, chimera; HET: MTT ADP EDO; 2.15A {Escherichia coli}

Probab=81.50  E-value=1.3  Score=36.66  Aligned_cols=26  Identities=31%  Similarity=0.477  Sum_probs=21.0

Q ss_pred             HHHHHHHcCCC--eEEEcCCCCchhHHh
Q psy7268          68 YSIPTLLSGKS--AILVAETGCGKTLSF   93 (134)
Q Consensus        68 ~~i~~~~~g~d--vli~a~tGsGKT~~~   93 (134)
                      ..+..+++|.|  ++.-|.||||||...
T Consensus       453 ~~v~~~~~G~n~~i~ayGqtgsGKT~Tm  480 (715)
T 4h1g_A          453 QLIQCSLDGTNVCVFAYGQTGSGKTFTM  480 (715)
T ss_dssp             HHHHHHHTTCCEEEEEESSTTSSHHHHH
T ss_pred             HHHHHHhCCceEEEEccCCCCCchhhcc
Confidence            35677889987  677799999999874

>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=81.43  E-value=2.5  Score=28.72  Aligned_cols=23  Identities=26%  Similarity=0.336  Sum_probs=15.5

Q ss_pred             CeEEEcCCCCchhHHhHHHHHHHH
Q psy7268          78 SAILVAETGCGKTLSFLAPLVQQI  101 (134)
Q Consensus        78 dvli~a~tGsGKT~~~~lpil~~~  101 (134)
                      -+.+.+++|+|||... -.++..+
T Consensus         8 ~i~i~G~sGsGKTTl~-~~l~~~l   30 (174)
T 1np6_A            8 LLAFAAWSGTGKTTLL-KKLIPAL   30 (174)
T ss_dssp             EEEEECCTTSCHHHHH-HHHHHHH
T ss_pred             EEEEEeCCCCCHHHHH-HHHHHhc
Confidence            3678899999998542 3334433

>1b0u_A Histidine permease; ABC transporter, transport protein; HET: ATP; 1.50A {Salmonella typhimurium} SCOP: c.37.1.12

Probab=81.27  E-value=0.84  Score=33.07  Aligned_cols=19  Identities=21%  Similarity=0.503  Sum_probs=15.6

Q ss_pred             cCCCeEEEcCCCCchhHHh
Q psy7268          75 SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~   93 (134)
                      .|.-+.+.||+|+|||...
T Consensus        31 ~Ge~~~liG~nGsGKSTLl   49 (262)
T 1b0u_A           31 AGDVISIIGSSGSGKSTFL   49 (262)
T ss_dssp             TTCEEEEECCTTSSHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            5667889999999999653

>4e22_A Cytidylate kinase; P-loop, CMP/ATP binding, transferase; 2.32A {Yersinia pseudotuberculosis}

Probab=81.15  E-value=0.84  Score=32.61  Aligned_cols=19  Identities=16%  Similarity=0.137  Sum_probs=15.8

Q ss_pred             cCCCeEEEcCCCCchhHHh
Q psy7268          75 SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~   93 (134)
                      .|.-+.+.||+|||||...
T Consensus        26 ~g~~I~I~G~~GsGKSTl~   44 (252)
T 4e22_A           26 IAPVITVDGPSGAGKGTLC   44 (252)
T ss_dssp             TSCEEEEECCTTSSHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHH
Confidence            4567889999999999764

>2vli_A Antibiotic resistance protein; transferase, tunicamycin, phosphotransferase; 1.95A {Deinococcus radiodurans}

Probab=81.02  E-value=0.65  Score=30.89  Aligned_cols=19  Identities=21%  Similarity=0.174  Sum_probs=11.1

Q ss_pred             cCCCeEEEcCCCCchhHHh
Q psy7268          75 SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~   93 (134)
                      .+.-+++.|+.|||||...
T Consensus         4 ~~~~I~l~G~~GsGKST~a   22 (183)
T 2vli_A            4 RSPIIWINGPFGVGKTHTA   22 (183)
T ss_dssp             -CCEEEEECCC----CHHH
T ss_pred             CCeEEEEECCCCCCHHHHH
Confidence            3556889999999999764

>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=81.01  E-value=1.7  Score=34.03  Aligned_cols=16  Identities=38%  Similarity=0.476  Sum_probs=13.5

Q ss_pred             CeEEEcCCCCchhHHh
Q psy7268          78 SAILVAETGCGKTLSF   93 (134)
Q Consensus        78 dvli~a~tGsGKT~~~   93 (134)
                      -+++.|++|+|||...
T Consensus        99 vI~lvG~~GsGKTTt~  114 (433)
T 3kl4_A           99 IIMLVGVQGSGKTTTA  114 (433)
T ss_dssp             EEEECCCTTSCHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            3788899999999765

>2jaq_A Deoxyguanosine kinase; transferase, deoxyribonucleoside kinase; HET: DCP; 2.3A {Mycoplasma mycoides subsp} PDB: 2jat_A* 2jas_A*

Probab=80.95  E-value=0.84  Score=30.74  Aligned_cols=15  Identities=20%  Similarity=0.317  Sum_probs=12.8

Q ss_pred             eEEEcCCCCchhHHh
Q psy7268          79 AILVAETGCGKTLSF   93 (134)
Q Consensus        79 vli~a~tGsGKT~~~   93 (134)
                      +++.|++|+|||...
T Consensus         3 I~i~G~~GsGKsT~~   17 (205)
T 2jaq_A            3 IAIFGTVGAGKSTIS   17 (205)
T ss_dssp             EEEECCTTSCHHHHH
T ss_pred             EEEECCCccCHHHHH
Confidence            678999999999753

>2d2e_A SUFC protein; ABC-ATPase, SUF protein, 310-helix, riken structural genomics/proteomics initiative, RSGI, structural genomics, binding; 1.70A {Thermus thermophilus} PDB: 2d2f_A*

Probab=80.93  E-value=0.89  Score=32.63  Aligned_cols=19  Identities=26%  Similarity=0.373  Sum_probs=15.9

Q ss_pred             cCCCeEEEcCCCCchhHHh
Q psy7268          75 SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~   93 (134)
                      .|.-+.+.||+|+|||...
T Consensus        28 ~Ge~~~l~G~nGsGKSTLl   46 (250)
T 2d2e_A           28 KGEVHALMGPNGAGKSTLG   46 (250)
T ss_dssp             TTCEEEEECSTTSSHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            5777889999999999654

>1mv5_A LMRA, multidrug resistance ABC transporter ATP-binding and permease protein; asymmetric dimer, tetramer, P-glycoprotein; HET: ATP ADP; 3.10A {Lactococcus lactis} SCOP: c.37.1.12

Probab=80.89  E-value=0.71  Score=32.97  Aligned_cols=19  Identities=21%  Similarity=0.368  Sum_probs=15.7

Q ss_pred             cCCCeEEEcCCCCchhHHh
Q psy7268          75 SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~   93 (134)
                      .|.-+.+.||+|+|||...
T Consensus        27 ~Ge~~~i~G~nGsGKSTLl   45 (243)
T 1mv5_A           27 PNSIIAFAGPSGGGKSTIF   45 (243)
T ss_dssp             TTEEEEEECCTTSSHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            5667889999999999653

>3b9q_A Chloroplast SRP receptor homolog, alpha subunit CPFTSY; protein translocation, GTP-binding, nucleotide-binding, protein transport; 1.75A {Arabidopsis thaliana}

Probab=80.88  E-value=0.71  Score=34.25  Aligned_cols=16  Identities=38%  Similarity=0.538  Sum_probs=13.6

Q ss_pred             CeEEEcCCCCchhHHh
Q psy7268          78 SAILVAETGCGKTLSF   93 (134)
Q Consensus        78 dvli~a~tGsGKT~~~   93 (134)
                      -+.+.||+|+|||...
T Consensus       102 vi~lvG~nGsGKTTll  117 (302)
T 3b9q_A          102 VIMIVGVNGGGKTTSL  117 (302)
T ss_dssp             EEEEECCTTSCHHHHH
T ss_pred             EEEEEcCCCCCHHHHH
Confidence            4778999999999764

>2qi9_C Vitamin B12 import ATP-binding protein BTUD; inner membrane, membrane, transmembrane, transport, ATP- binding, hydrolase, nucleotide-binding, periplasm; HET: 1PE; 2.60A {Escherichia coli} PDB: 1l7v_C* 4dbl_C

Probab=80.86  E-value=0.89  Score=32.77  Aligned_cols=19  Identities=32%  Similarity=0.503  Sum_probs=15.8

Q ss_pred             cCCCeEEEcCCCCchhHHh
Q psy7268          75 SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~   93 (134)
                      .|.-+.+.||+|+|||...
T Consensus        25 ~Ge~~~liG~NGsGKSTLl   43 (249)
T 2qi9_C           25 AGEILHLVGPNGAGKSTLL   43 (249)
T ss_dssp             TTCEEEEECCTTSSHHHHH
T ss_pred             CCCEEEEECCCCCcHHHHH
Confidence            5777889999999999653

>3auy_A DNA double-strand break repair RAD50 ATPase; DNA repair, ABC transporter ATPase domain-like; HET: DNA ADP; 2.70A {Methanocaldococcus jannaschii} PDB: 3aux_A* 3av0_B*

Probab=80.85  E-value=0.74  Score=34.89  Aligned_cols=15  Identities=33%  Similarity=0.687  Sum_probs=12.9

Q ss_pred             eEEEcCCCCchhHHh
Q psy7268          79 AILVAETGCGKTLSF   93 (134)
Q Consensus        79 vli~a~tGsGKT~~~   93 (134)
                      .++.|+||+|||..+
T Consensus        28 ~vi~G~NGaGKT~il   42 (371)
T 3auy_A           28 VAIIGENGSGKSSIF   42 (371)
T ss_dssp             EEEEECTTSSHHHHH
T ss_pred             EEEECCCCCCHHHHH
Confidence            578999999999774

>2yz2_A Putative ABC transporter ATP-binding protein TM_0; cobalt transport, TM02 hydrolase, inner membrane, membrane, nucleotide-binding; 2.30A {Thermotoga maritima}

Probab=80.79  E-value=0.89  Score=32.96  Aligned_cols=19  Identities=26%  Similarity=0.564  Sum_probs=15.7

Q ss_pred             cCCCeEEEcCCCCchhHHh
Q psy7268          75 SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~   93 (134)
                      .|.-+.+.||+|+|||...
T Consensus        32 ~Ge~~~liG~nGsGKSTLl   50 (266)
T 2yz2_A           32 EGECLLVAGNTGSGKSTLL   50 (266)
T ss_dssp             TTCEEEEECSTTSSHHHHH
T ss_pred             CCCEEEEECCCCCcHHHHH
Confidence            5677889999999999653

>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor, microtubles, motor protein; HET: ADP SPM; 2.81A {Dictyostelium discoideum} PDB: 3vkh_A*

Probab=80.73  E-value=1.4  Score=42.59  Aligned_cols=20  Identities=35%  Similarity=0.567  Sum_probs=17.3

Q ss_pred             HHcCCCeEEEcCCCCchhHH
Q psy7268          73 LLSGKSAILVAETGCGKTLS   92 (134)
Q Consensus        73 ~~~g~dvli~a~tGsGKT~~   92 (134)
                      +..|+.++++||||+|||..
T Consensus      1301 l~~~~pvLL~GptGtGKT~l 1320 (3245)
T 3vkg_A         1301 LSEHRPLILCGPPGSGKTMT 1320 (3245)
T ss_dssp             HHTTCCCEEESSTTSSHHHH
T ss_pred             HHCCCcEEEECCCCCCHHHH
Confidence            44789999999999999953

>2zu0_C Probable ATP-dependent transporter SUFC; iron-sulfur cluster, ABC-ATPase, ATP-binding, cytoplasm, nucleotide-binding; HET: MES; 2.20A {Escherichia coli} PDB: 2d3w_A

Probab=80.64  E-value=0.9  Score=32.98  Aligned_cols=19  Identities=21%  Similarity=0.392  Sum_probs=15.9

Q ss_pred             cCCCeEEEcCCCCchhHHh
Q psy7268          75 SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~   93 (134)
                      .|.-+.+.||+|+|||...
T Consensus        45 ~Ge~~~l~G~NGsGKSTLl   63 (267)
T 2zu0_C           45 PGEVHAIMGPNGSGKSTLS   63 (267)
T ss_dssp             TTCEEEEECCTTSSHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            5777889999999999654

>2pt5_A Shikimate kinase, SK; aromatic amino acid biosynthesis, P-loop kinase, SHI kinase, shikimate pathway; 2.10A {Aquifex aeolicus}

Probab=80.58  E-value=0.9  Score=29.76  Aligned_cols=16  Identities=19%  Similarity=0.071  Sum_probs=13.3

Q ss_pred             CeEEEcCCCCchhHHh
Q psy7268          78 SAILVAETGCGKTLSF   93 (134)
Q Consensus        78 dvli~a~tGsGKT~~~   93 (134)
                      .+++.|+.|||||...
T Consensus         2 ~I~l~G~~GsGKsT~a   17 (168)
T 2pt5_A            2 RIYLIGFMCSGKSTVG   17 (168)
T ss_dssp             EEEEESCTTSCHHHHH
T ss_pred             eEEEECCCCCCHHHHH
Confidence            3788999999999763

>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=80.57  E-value=0.73  Score=31.53  Aligned_cols=19  Identities=21%  Similarity=-0.022  Sum_probs=15.1

Q ss_pred             cCCCeEEEcCCCCchhHHh
Q psy7268          75 SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~   93 (134)
                      .+.-+.+.|++|+|||...
T Consensus        20 ~~~~i~i~G~~GsGKSTl~   38 (207)
T 2qt1_A           20 KTFIIGISGVTNSGKTTLA   38 (207)
T ss_dssp             CCEEEEEEESTTSSHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHH
Confidence            4556789999999999654

>2ixe_A Antigen peptide transporter 1; ABC ATPase, hydrolase; HET: ATP; 2.0A {Rattus norvegicus} PDB: 2ixg_A* 2ixf_A* 1jj7_A*

Probab=80.54  E-value=0.92  Score=33.04  Aligned_cols=19  Identities=37%  Similarity=0.532  Sum_probs=15.9

Q ss_pred             cCCCeEEEcCCCCchhHHh
Q psy7268          75 SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~   93 (134)
                      .|.-+.+.||+|+|||...
T Consensus        44 ~Ge~~~i~G~nGsGKSTLl   62 (271)
T 2ixe_A           44 PGKVTALVGPNGSGKSTVA   62 (271)
T ss_dssp             TTCEEEEECSTTSSHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            5777889999999999643

>1g5t_A COB(I)alamin adenosyltransferase; P-loop protein, cobalamin biosynthesis, RECA fold; HET: ATP; 1.80A {Salmonella typhimurium} SCOP: c.37.1.11 PDB: 1g5r_A* 1g64_A*

Probab=80.52  E-value=2.7  Score=29.34  Aligned_cols=35  Identities=14%  Similarity=0.160  Sum_probs=25.4

Q ss_pred             CCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEE
Q psy7268          76 GKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALII  122 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil  122 (134)
                      ...+++...+|.|||.+.+--.+..+-            .|.+++++
T Consensus        28 ~g~i~v~tG~GkGKTTaA~GlalRA~g------------~G~rV~~v   62 (196)
T 1g5t_A           28 RGIIIVFTGNGKGKTTAAFGTAARAVG------------HGKNVGVV   62 (196)
T ss_dssp             CCCEEEEESSSSCHHHHHHHHHHHHHH------------TTCCEEEE
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHHHH------------CCCeEEEE
Confidence            347899999999999888555555443            46667776

>1a5t_A Delta prime, HOLB; zinc finger, DNA replication; 2.20A {Escherichia coli K12} SCOP: a.80.1.1 c.37.1.20 PDB: 1jr3_E* 1xxh_E* 1xxi_E* 3glf_E* 3glg_E* 3glh_E* 3gli_E*

Probab=80.44  E-value=1.4  Score=32.82  Aligned_cols=39  Identities=18%  Similarity=0.255  Sum_probs=24.6

Q ss_pred             hHHHHHHHHHH----HcCC---CeEEEcCCCCchhHHhHHHHHHHHH
Q psy7268          63 TEIQKYSIPTL----LSGK---SAILVAETGCGKTLSFLAPLVQQIL  102 (134)
Q Consensus        63 t~iQ~~~i~~~----~~g~---dvli~a~tGsGKT~~~~lpil~~~~  102 (134)
                      .|.|..++..+    .+|+   -+++.||.|+|||... ..+...+.
T Consensus         4 ~pw~~~~~~~l~~~i~~~~~~~a~L~~G~~G~GKt~~a-~~la~~l~   49 (334)
T 1a5t_A            4 YPWLRPDFEKLVASYQAGRGHHALLIQALPGMGDDALI-YALSRYLL   49 (334)
T ss_dssp             CGGGHHHHHHHHHHHHTTCCCSEEEEECCTTSCHHHHH-HHHHHHHT
T ss_pred             CCchHHHHHHHHHHHHcCCcceeEEEECCCCchHHHHH-HHHHHHHh
Confidence            45566665443    3454   3899999999999665 33444443

>2pbr_A DTMP kinase, thymidylate kinase; transferase, nucleotide biosynthesis, TMP-binding, A binding, structural genomics, NPPSFA; 1.96A {Aquifex aeolicus}

Probab=80.32  E-value=0.87  Score=30.39  Aligned_cols=15  Identities=27%  Similarity=0.266  Sum_probs=12.7

Q ss_pred             eEEEcCCCCchhHHh
Q psy7268          79 AILVAETGCGKTLSF   93 (134)
Q Consensus        79 vli~a~tGsGKT~~~   93 (134)
                      +.+.|+.|||||...
T Consensus         3 I~l~G~~GsGKsT~~   17 (195)
T 2pbr_A            3 IAFEGIDGSGKTTQA   17 (195)
T ss_dssp             EEEECSTTSCHHHHH
T ss_pred             EEEECCCCCCHHHHH
Confidence            678999999999753

>1ry6_A Internal kinesin; kinesin motor domain, nucleotide-free, transport protein; 1.60A {Plasmodium falciparum} SCOP: c.37.1.9

Probab=80.25  E-value=1.5  Score=33.57  Aligned_cols=19  Identities=32%  Similarity=0.522  Sum_probs=16.0

Q ss_pred             cCCC--eEEEcCCCCchhHHh
Q psy7268          75 SGKS--AILVAETGCGKTLSF   93 (134)
Q Consensus        75 ~g~d--vli~a~tGsGKT~~~   93 (134)
                      .|.+  ++.-|.||||||...
T Consensus        82 ~G~n~tifAYGqTGSGKTyTM  102 (360)
T 1ry6_A           82 NGCVCSCFAYGQTGSGKTYTM  102 (360)
T ss_dssp             HCCEEEEEEECCTTSSHHHHH
T ss_pred             CCceeEEEeeCCCCCCCCEEE
Confidence            4776  688899999999875

>3qks_A DNA double-strand break repair RAD50 ATPase; RECA-like fold, coiled-coils, ATPase, exonuclease, endonucle binding, DNA binding; HET: DNA; 2.10A {Pyrococcus furiosus} PDB: 3qkr_A*

Probab=80.25  E-value=0.9  Score=31.45  Aligned_cols=15  Identities=20%  Similarity=0.598  Sum_probs=12.8

Q ss_pred             eEEEcCCCCchhHHh
Q psy7268          79 AILVAETGCGKTLSF   93 (134)
Q Consensus        79 vli~a~tGsGKT~~~   93 (134)
                      .++.||+|+|||..+
T Consensus        26 ~~I~G~NgsGKStil   40 (203)
T 3qks_A           26 NLIIGQNGSGKSSLL   40 (203)
T ss_dssp             EEEECCTTSSHHHHH
T ss_pred             EEEEcCCCCCHHHHH
Confidence            578899999999774

>2olj_A Amino acid ABC transporter; ABC domain, ATPase, hydrolase; HET: ADP; 2.05A {Geobacillus stearothermophilus} PDB: 2olk_A* 2ouk_A 2q0h_A* 3c4j_A* 3c41_J*

Probab=80.19  E-value=0.96  Score=32.89  Aligned_cols=19  Identities=21%  Similarity=0.571  Sum_probs=15.8

Q ss_pred             cCCCeEEEcCCCCchhHHh
Q psy7268          75 SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~   93 (134)
                      .|.-+.+.||+|+|||...
T Consensus        49 ~Gei~~liG~NGsGKSTLl   67 (263)
T 2olj_A           49 EGEVVVVIGPSGSGKSTFL   67 (263)
T ss_dssp             TTCEEEEECCTTSSHHHHH
T ss_pred             CCCEEEEEcCCCCcHHHHH
Confidence            5677889999999999654

>2nq2_C Hypothetical ABC transporter ATP-binding protein HI1470; putative iron chelatin ABC transporter, nucleotide binding domain; 2.40A {Haemophilus influenzae}

Probab=80.16  E-value=0.94  Score=32.65  Aligned_cols=19  Identities=26%  Similarity=0.662  Sum_probs=15.7

Q ss_pred             cCCCeEEEcCCCCchhHHh
Q psy7268          75 SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~   93 (134)
                      .|.-+.+.||+|+|||...
T Consensus        30 ~Ge~~~l~G~nGsGKSTLl   48 (253)
T 2nq2_C           30 KGDILAVLGQNGCGKSTLL   48 (253)
T ss_dssp             TTCEEEEECCSSSSHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            5677889999999999653

>1vpl_A ABC transporter, ATP-binding protein; TM0544, structural GENO joint center for structural genomics, JCSG, protein structu initiative, PSI; 2.10A {Thermotoga maritima} SCOP: c.37.1.12

Probab=80.10  E-value=0.97  Score=32.70  Aligned_cols=19  Identities=32%  Similarity=0.503  Sum_probs=15.8

Q ss_pred             cCCCeEEEcCCCCchhHHh
Q psy7268          75 SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~   93 (134)
                      .|.-+.+.||+|+|||...
T Consensus        40 ~Gei~~l~G~NGsGKSTLl   58 (256)
T 1vpl_A           40 EGEIFGLIGPNGAGKTTTL   58 (256)
T ss_dssp             TTCEEEEECCTTSSHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHH
Confidence            5677889999999999653

>3hjh_A Transcription-repair-coupling factor; MFD, mutation frequency decline, ATP-binding, DNA DAMA repair, DNA-binding, helicase, hydrolase; 1.95A {Escherichia coli} PDB: 2b2n_A* 4dfc_A

Probab=80.08  E-value=3  Score=33.08  Aligned_cols=44  Identities=16%  Similarity=0.281  Sum_probs=31.1

Q ss_pred             cCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          75 SGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      .|....+.+-+|+||++... .++..              .+...|||+|+...|.|++
T Consensus        13 ~~~~~~l~g~~gs~ka~~~a-~l~~~--------------~~~p~lvv~~~~~~A~~l~   56 (483)
T 3hjh_A           13 AGEQRLLGELTGAACATLVA-EIAER--------------HAGPVVLIAPDMQNALRLH   56 (483)
T ss_dssp             TTCEEEEECCCTTHHHHHHH-HHHHH--------------SSSCEEEEESSHHHHHHHH
T ss_pred             CCCeEEEeCCCchHHHHHHH-HHHHH--------------hCCCEEEEeCCHHHHHHHH
Confidence            45668899999999986542 11211              1223889999999999876

---

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	134
d1wrba1	238	c.37.1.19 (A:164-401) putative ATP-dependent RNA h	7e-16
d2g9na1	218	c.37.1.19 (A:21-238) Initiation factor 4a {Human (	3e-13
d2j0sa1	222	c.37.1.19 (A:22-243) Probable ATP-dependent RNA he	6e-13
d1gkub1	237	c.37.1.16 (B:1-250) Helicase-like "domain" of reve	1e-12
d2p6ra3	202	c.37.1.19 (A:1-202) Hel308 helicase {Archaeoglobus	8e-12
d1t6na_	207	c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP5	1e-11
d1veca_	206	c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Huma	2e-11
d1s2ma1	206	c.37.1.19 (A:46-251) Putative ATP-dependent RNA he	4e-11
d1qdea_	212	c.37.1.19 (A:) Initiation factor 4a {Baker's yeast	4e-11
d1q0ua_	209	c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR	1e-10
d2bmfa2	305	c.37.1.14 (A:178-482) Dengue virus helicase {Dengu	7e-10
d1hv8a1	208	c.37.1.19 (A:3-210) Putative DEAD box RNA helicase	2e-09
d1oywa2	206	c.37.1.19 (A:1-206) RecQ helicase domain {Escheric	6e-09
d1wp9a1	200	c.37.1.19 (A:1-200) putative ATP-dependent RNA hel	4e-05
d1yksa1	140	c.37.1.14 (A:185-324) YFV helicase domain {Yellow	0.004

>d1wrba1 c.37.1.19 (A:164-401) putative ATP-dependent RNA helicase VlgB {Flatworm (Dugesia japonica) [TaxId: 6161]} Length = 238

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase VlgB
species: Flatworm (Dugesia japonica) [TaxId: 6161]

 Score = 69.2 bits (168), Expect = 7e-16
 Identities = 29/92 (31%), Positives = 45/92 (48%)

Query: 40  TFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQ 99
            F++  L P I +         PT IQK +IP +L  +  +  A+TG GKT +FL P++ 
Sbjct: 22  NFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIIN 81

Query: 100 QILTWKSRPEYKPELNAPLALIITPGRELVFQ 131
            ++      +   +   P  LI+ P REL  Q
Sbjct: 82  HLVCQDLNQQRYSKTAYPKCLILAPTRELAIQ 113

>d2g9na1 c.37.1.19 (A:21-238) Initiation factor 4a {Human (Homo sapiens) [TaxId: 9606]} Length = 218

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 61.8 bits (149), Expect = 3e-13
 Identities = 26/93 (27%), Positives = 43/93 (46%), Gaps = 9/93 (9%)

Query: 40  TFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQ 99
           +F+D  L+  ++      G   P+ IQ+ +I   + G   I  A++G GKT +F      
Sbjct: 13  SFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFA----- 67

Query: 100 QILTWKSRPEYKPELNAPLALIITPGRELVFQI 132
                    + + +L A  AL++ P REL  QI
Sbjct: 68  ----ISILQQIELDLKATQALVLAPTRELAQQI 96

>d2j0sa1 c.37.1.19 (A:22-243) Probable ATP-dependent RNA helicase DDX48 {Human (Homo sapiens) [TaxId: 9606]} Length = 222

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable ATP-dependent RNA helicase DDX48
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 61.0 bits (147), Expect = 6e-13
 Identities = 17/69 (24%), Positives = 34/69 (49%)

Query: 40  TFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQ 99
           TF+  GL  +++      G   P+ IQ+ +I  ++ G+  I  +++G GKT +F   ++Q
Sbjct: 18  TFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQ 77

Query: 100 QILTWKSRP 108
            +       
Sbjct: 78  CLDIQVRET 86

>d1gkub1 c.37.1.16 (B:1-250) Helicase-like "domain" of reverse gyrase {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} Length = 237

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Helicase-like "domain" of reverse gyrase
domain: Helicase-like "domain" of reverse gyrase
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

 Score = 60.3 bits (145), Expect = 1e-12
 Identities = 21/68 (30%), Positives = 30/68 (44%), Gaps = 1/68 (1%)

Query: 38  LGTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPL 97
           L  F +  L  E ++ F ++ +  P  IQK     +L  +S    A TG GKT   LA  
Sbjct: 21  LCLFPEDFLLKEFVEFF-RKCVGEPRAIQKMWAKRILRKESFAATAPTGVGKTSFGLAMS 79

Query: 98  VQQILTWK 105
           +   L  K
Sbjct: 80  LFLALKGK 87

>d2p6ra3 c.37.1.19 (A:1-202) Hel308 helicase {Archaeoglobus fulgidus [TaxId: 2234]} Length = 202

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Hel308 helicase
species: Archaeoglobus fulgidus [TaxId: 2234]

 Score = 57.7 bits (138), Expect = 8e-12
 Identities = 18/95 (18%), Positives = 36/95 (37%), Gaps = 14/95 (14%)

Query: 40  TFED--TGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPL 97
             E+    ++   + I  + G+      Q  ++  + SGK+ +L   T  GKTL     +
Sbjct: 2   KVEELAESISSYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAM 61

Query: 98  VQQILTWKSRPEYKPELNAPLALIITPGRELVFQI 132
           V++ +                +L + P R L  + 
Sbjct: 62  VREAIKG------------GKSLYVVPLRALAGEK 84

>d1t6na_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]} Length = 207

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Spliceosome RNA helicase BAT1 (UAP56)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.2 bits (137), Expect = 1e-11
 Identities = 20/69 (28%), Positives = 32/69 (46%)

Query: 40  TFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQ 99
            F D  L PE++      G   P+E+Q   IP  + G   +  A++G GKT  F+   +Q
Sbjct: 2   GFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQ 61

Query: 100 QILTWKSRP 108
           Q+     + 
Sbjct: 62  QLEPVTGQV 70

>d1veca_ c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Human (Homo sapiens) [TaxId: 9606]} Length = 206

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEAD box RNA helicase rck/p54
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.9 bits (136), Expect = 2e-11
 Identities = 23/71 (32%), Positives = 39/71 (54%)

Query: 40  TFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQ 99
            FED  L  E++    + G   P+ IQ+ SIP  LSG+  +  A+ G GK+ ++L PL++
Sbjct: 4   EFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLE 63

Query: 100 QILTWKSRPEY 110
           ++   K   + 
Sbjct: 64  RLDLKKDNIQA 74

>d1s2ma1 c.37.1.19 (A:46-251) Putative ATP-dependent RNA helicase DHH1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 206

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative ATP-dependent RNA helicase DHH1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 56.1 bits (134), Expect = 4e-11
 Identities = 20/61 (32%), Positives = 36/61 (59%)

Query: 40  TFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQ 99
           TFED  L  E++    + G   P+ IQ+ +IP  ++G+  +  A+ G GKT +F+ P ++
Sbjct: 2   TFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLE 61

Query: 100 Q 100
           +
Sbjct: 62  K 62

>d1qdea_ c.37.1.19 (A:) Initiation factor 4a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 212

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 56.0 bits (134), Expect = 4e-11
 Identities = 19/69 (27%), Positives = 33/69 (47%)

Query: 40  TFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQ 99
            F+D  L   ++      G   P+ IQ+ +I  ++ G   +  A++G GKT +F    +Q
Sbjct: 11  KFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQ 70

Query: 100 QILTWKSRP 108
           +I T    P
Sbjct: 71  RIDTSVKAP 79

>d1q0ua_ c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR {Bacillus stearothermophilus [TaxId: 1422]} Length = 209

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable DEAD box RNA helicase YqfR
species: Bacillus stearothermophilus [TaxId: 1422]

 Score = 54.7 bits (130), Expect = 1e-10
 Identities = 19/54 (35%), Positives = 27/54 (50%)

Query: 40 TFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSF 93
           F      P II+         PTEIQ+  IP  L G+S +  ++TG GKT ++
Sbjct: 2  QFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAY 55

>d2bmfa2 c.37.1.14 (A:178-482) Dengue virus helicase {Dengue virus type 2 [TaxId: 11060]} Length = 305

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: Dengue virus helicase
species: Dengue virus type 2 [TaxId: 11060]

 Score = 53.0 bits (126), Expect = 7e-10
 Identities = 12/62 (19%), Positives = 24/62 (38%), Gaps = 11/62 (17%)

Query: 73  LLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQI 132
               +  I+    G GKT  +L  +V++ +    R            LI+ P R +  ++
Sbjct: 6   FRKKRLTIMDLHPGAGKTKRYLPAIVREAIKRGLR-----------TLILAPTRVVAAEM 54

Query: 133 GQ 134
            +
Sbjct: 55  EE 56

>d1hv8a1 c.37.1.19 (A:3-210) Putative DEAD box RNA helicase {Archaeon Methanococcus jannaschii [TaxId: 2190]} Length = 208

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative DEAD box RNA helicase
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

 Score = 51.2 bits (122), Expect = 2e-09
 Identities = 22/66 (33%), Positives = 34/66 (51%), Gaps = 1/66 (1%)

Query: 40  TFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILV-AETGCGKTLSFLAPLV 98
            F +  L+  I++    +G   PT+IQ   IP  L+ +  I+  A TG GKT SF  PL+
Sbjct: 5   NFNELNLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLI 64

Query: 99  QQILTW 104
           + +   
Sbjct: 65  ELVNEN 70

>d1oywa2 c.37.1.19 (A:1-206) RecQ helicase domain {Escherichia coli [TaxId: 562]} Length = 206

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecQ helicase domain
species: Escherichia coli [TaxId: 562]

 Score = 50.0 bits (118), Expect = 6e-09
 Identities = 16/63 (25%), Positives = 26/63 (41%), Gaps = 1/63 (1%)

Query: 40  TFEDTGLAPEIIDIFTKR-GLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLV 98
             E   L      +  +  G       Q+  I T+LSG+  ++V  TG GK+L +  P +
Sbjct: 3   QAEVLNLESGAKQVLQETFGYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPAL 62

Query: 99  QQI 101
              
Sbjct: 63  LLN 65

>d1wp9a1 c.37.1.19 (A:1-200) putative ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]} Length = 200

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase PF2015
species: Pyrococcus furiosus [TaxId: 2261]

 Score = 39.4 bits (90), Expect = 4e-05
 Identities = 11/50 (22%), Positives = 20/50 (40%), Gaps = 1/50 (2%)

Query: 56  KRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWK 105
           +R L  P   Q+          + ++V  TG GKTL  +     ++  + 
Sbjct: 4   RRDLIQPRIYQEVIYAKCK-ETNCLIVLPTGLGKTLIAMMIAEYRLTKYG 52

>d1yksa1 c.37.1.14 (A:185-324) YFV helicase domain {Yellow fever virus [TaxId: 11089]} Length = 140

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: YFV helicase domain
species: Yellow fever virus [TaxId: 11089]

 Score = 33.1 bits (74), Expect = 0.004
 Identities = 9/33 (27%), Positives = 15/33 (45%)

Query: 73  LLSGKSAILVAETGCGKTLSFLAPLVQQILTWK 105
           L  G + +L    G GKT  FL  ++ +    +
Sbjct: 4   LKKGMTTVLDFHPGAGKTRRFLPQILAECARRR 36

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	134
d1wrba1	238	putative ATP-dependent RNA helicase VlgB {Flatworm	99.95
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	99.95
d2g9na1	218	Initiation factor 4a {Human (Homo sapiens) [TaxId:	99.95
d1t6na_	207	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	99.95
d1veca_	206	DEAD box RNA helicase rck/p54 {Human (Homo sapiens	99.95
d1qdea_	212	Initiation factor 4a {Baker's yeast (Saccharomyces	99.94
d1hv8a1	208	Putative DEAD box RNA helicase {Archaeon Methanoco	99.9
d1s2ma1	206	Putative ATP-dependent RNA helicase DHH1 {Baker's	99.9
d1q0ua_	209	Probable DEAD box RNA helicase YqfR {Bacillus stea	99.9
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	99.77
d1oywa2	206	RecQ helicase domain {Escherichia coli [TaxId: 562	99.76
d2p6ra3	202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	99.74
d1wp9a1	200	putative ATP-dependent RNA helicase PF2015 {Pyroco	99.42
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	99.25
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	99.06
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	99.05
d1rifa_	282	DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]	99.04
d2fz4a1	206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	98.99
d1yksa1	140	YFV helicase domain {Yellow fever virus [TaxId: 11	98.92
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	98.55
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	98.11
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	97.88
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	97.59
g1qhh.1	623	DEXX box DNA helicase {Bacillus stearothermophilus	97.27
d1z63a1	230	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	97.05
d1z3ix2	298	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	96.67
d1t5la1	413	Nucleotide excision repair enzyme UvrB {Bacillus c	96.55
d1tf5a3	273	Translocation ATPase SecA, nucleotide-binding doma	96.36
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	96.05
d1p9ra_	401	Extracellular secretion NTPase EpsE {Vibrio choler	95.94
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	95.6
d1e9ra_	433	Bacterial conjugative coupling protein TrwB {Esche	95.51
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	95.41
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	95.17
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	95.06
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	94.94
d1nkta3	288	Translocation ATPase SecA, nucleotide-binding doma	94.89
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	94.78
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	94.67
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	94.6
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	94.55
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	94.46
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	94.44
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	94.28
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	94.25
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	94.11
d1okkd2	207	GTPase domain of the signal recognition particle r	93.98
d1np6a_	170	Molybdopterin-guanine dinucleotide biosynthesis pr	93.95
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	93.63
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	93.61
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	93.53
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	93.39
d1vmaa2	213	GTPase domain of the signal recognition particle r	93.35
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	93.34
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	93.33
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	93.09
d2qy9a2	211	GTPase domain of the signal recognition particle r	93.05
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	93.02
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	92.74
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	92.6
d1ls1a2	207	GTPase domain of the signal sequence recognition p	92.58
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	92.55
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	92.47
d1svma_	362	Papillomavirus large T antigen helicase domain {Si	92.27
d1j8yf2	211	GTPase domain of the signal sequence recognition p	92.23
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	92.12
d1c4oa1	408	Nucleotide excision repair enzyme UvrB {Thermus th	92.09
d1gkya_	186	Guanylate kinase {Baker's yeast (Saccharomyces cer	91.8
d1viaa_	161	Shikimate kinase (AroK) {Campylobacter jejuni [Tax	91.74
d1tf7a1	242	Circadian clock protein KaiC {Synechococcus sp. st	91.69
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	91.55
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	91.38
d1g8pa_	333	ATPase subunit of magnesium chelatase, BchI {Rhodo	91.33
d1yj5a2	172	5' polynucleotide kinase-3' phosphatase, C-termina	91.31
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	91.17
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	91.15
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	91.12
d1bg2a_	323	Kinesin {Human (Homo sapiens) [TaxId: 9606]}	91.12
d1qhxa_	178	Chloramphenicol phosphotransferase {Streptomyces v	90.95
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	90.75
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	90.55
d1xjca_	165	Molybdopterin-guanine dinucleotide biosynthesis pr	90.54
d1x6va3	195	Adenosine-5'phosphosulfate kinase (APS kinase) {Hu	90.2
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	89.81
d1goja_	354	Kinesin {Neurospora crassa [TaxId: 5141]}	89.36
d1w36b1	485	Exodeoxyribonuclease V beta chain (RecB), N-termin	89.33
d1n0wa_	242	DNA repair protein Rad51, catalytic domain {Human	89.12
d1ak2a1	190	Adenylate kinase {Cow (Bos taurus), mitochondrial	89.08
d2zfia1	349	Kinesin {Mouse (Mus musculus), kif1a [TaxId: 10090	88.87
d1lvga_	190	Guanylate kinase {Mouse (Mus musculus) [TaxId: 100	88.85
d1v8ka_	362	Kinesin {Mouse (Mus musculus), kif2c [TaxId: 10090	88.8
d1e6ca_	170	Shikimate kinase (AroK) {Erwinia chrysanthemi [Tax	88.74
d1znwa1	182	Guanylate kinase {Mycobacterium tuberculosis [TaxI	88.72
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	88.68
d1sdma_	364	Kinesin heavy chain-like protein {Potato (Solanum	88.32
d2ncda_	368	Kinesin motor Ncd (non-claret disjunctional) {Frui	88.29
d1zaka1	189	Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}	88.28
d1x88a1	345	Kinesin {Human (Homo sapiens), mitotic kinesin eg5	88.26
d1s96a_	205	Guanylate kinase {Escherichia coli [TaxId: 562]}	88.12
d1qf9a_	194	UMP/CMP kinase {Dictyostelium discoideum [TaxId: 4	88.1
d1zina1	182	Adenylate kinase {Bacillus stearothermophilus [Tax	88.05
d2cdna1	181	Adenylate kinase {Mycobacterium tuberculosis [TaxI	87.47
d1khta_	190	Adenylate kinase {Archaeon Methanococcus voltae [T	87.43
d1ukza_	196	Uridylate kinase {Baker's yeast (Saccharomyces cer	87.33
d1pzna2	254	DNA repair protein Rad51, catalytic domain {Archae	87.3
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	87.29
d1s3ga1	182	Adenylate kinase {Bacillus globisporus [TaxId: 145	87.12
d1e4va1	179	Adenylate kinase {Escherichia coli [TaxId: 562]}	87.12
d1ny5a2	247	Transcriptional activator sigm54 (NtrC1), C-termin	86.75
d1bifa1	213	6-phosphofructo-2-kinase/fructose-2,6-bisphosphata	86.66
d1kgda_	178	Guanylate kinase-like domain of Cask {Human (Homo	86.46
d1byia_	224	Dethiobiotin synthetase {Escherichia coli [TaxId:	86.46
d3adka_	194	Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}	86.23
d1akya1	180	Adenylate kinase {Baker's yeast (Saccharomyces cer	86.19
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	86.17
d1sgwa_	200	Putative ABC transporter PF0895 {Pyrococcus furios	85.93
d1rz3a_	198	Hypothetical protein rbstp0775 {Bacillus stearothe	85.68
d1f9va_	342	Kinesin motor Ncd (non-claret disjunctional) {Bake	85.68
d1nksa_	194	Adenylate kinase {Archaeon Sulfolobus acidocaldari	85.68
d1teva_	194	UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]	85.66
d2ak3a1	189	Adenylate kinase {Cow (Bos taurus), mitochondrial	85.66
d2iyva1	165	Shikimate kinase (AroK) {Mycobacterium tuberculosi	85.42
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	85.41
d1nlfa_	274	Hexameric replicative helicase repA {Escherichia c	84.59
d1r6bx3	315	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	84.55
d2fnaa2	283	Archaeal ATPase SSO1545 {Sulfolobus solfataricus [	84.47
d1v5wa_	258	Meiotic recombination protein DMC1/LIM15 homolog {	84.42
d2i1qa2	258	DNA repair protein Rad51, catalytic domain {Archae	83.79
d2pmka1	241	Haemolysin B ATP-binding protein {Escherichia coli	83.57
d1jj7a_	251	Peptide transporter Tap1, C-terminal ABC domain {H	82.9
d1w44a_	321	NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}	82.82
d2hyda1	255	Putative multidrug export ATP-binding/permease pro	82.03
d3b60a1	253	Multidrug resistance ABC transporter MsbA, C-termi	81.98
d1yrba1	244	ATP(GTP)-binding protein PAB0955 {Pyrococcus abyss	81.9
d1uj2a_	213	Uridine-cytidine kinase 2 {Human (Homo sapiens) [T	81.76
d1l2ta_	230	MJ0796 {Archaeon Methanococcus jannaschii [TaxId:	81.73
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	81.27
d1ckea_	225	CMP kinase {Escherichia coli [TaxId: 562]}	81.24
g1ii8.1	369	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	81.01
d1tuea_	205	Replication protein E1 helicase domain {Human papi	80.99
d1qvra3	315	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	80.69
d1xx6a1	141	Thymidine kinase, TK1, N-terminal domain {Clostrid	80.65
d1ry6a_	330	Kinesin {Malaria parasite (Plasmodium falciparum)	80.49
d2awna2	232	Maltose transport protein MalK, N-terminal domain	80.28
d3dhwc1	240	Methionine import ATP-binding protein MetN {Escher	80.23
g1xew.1	329	Smc head domain {Pyrococcus furiosus [TaxId: 2261]	80.08

>d1wrba1 c.37.1.19 (A:164-401) putative ATP-dependent RNA helicase VlgB {Flatworm (Dugesia japonica) [TaxId: 6161]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase VlgB
species: Flatworm (Dugesia japonica) [TaxId: 6161]

Probab=99.95  E-value=7.3e-29  Score=180.66  Aligned_cols=106  Identities=29%  Similarity=0.463  Sum_probs=91.3

Q ss_pred             CCcccccCCCCCCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCC
Q psy7268          28 RGYEAVSRIDLGTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSR  107 (134)
Q Consensus        28 ~~~~~~~~~~~~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~  107 (134)
                      .+.+.....++.+|++++|+++++++|.++||+.||++|+++||.+++|+|++++||||||||++|++|+++++......
T Consensus        10 ~~~~~~~~~~~~~F~~l~l~~~l~~~L~~~g~~~pt~iQ~~~ip~il~g~dvvi~a~TGsGKTlayllp~l~~l~~~~~~   89 (238)
T d1wrba1          10 TGPDYSATNVIENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIINHLVCQDLN   89 (238)
T ss_dssp             ECCSSSCCSCCCSSGGGSCCCSTTTTTTTTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHTTCC-
T ss_pred             eCCCCCCCCccCCHHHCCCCHHHHHHHHHCCCCCCCHHHHHHhhhhhCCCCEEEECCCCCCcceeeHHHHHHHHHhcccc
Confidence            34455556788999999999999999999999999999999999999999999999999999999999999999876544


Q ss_pred             CCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268         108 PEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus       108 ~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      ........+++++|++||+||+.|++
T Consensus        90 ~~~~~~~~~~~alil~pt~el~~q~~  115 (238)
T d1wrba1          90 QQRYSKTAYPKCLILAPTRELAIQIL  115 (238)
T ss_dssp             -----CCBCCSEEEECSSHHHHHHHH
T ss_pred             cccccCCCCceEEEeccchhhhcchh
Confidence            44444557899999999999999986

>d2j0sa1 c.37.1.19 (A:22-243) Probable ATP-dependent RNA helicase DDX48 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable ATP-dependent RNA helicase DDX48
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.95  E-value=2.2e-28  Score=176.65  Aligned_cols=89  Identities=29%  Similarity=0.450  Sum_probs=82.8

Q ss_pred             CCCCCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCC
Q psy7268          36 IDLGTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELN  115 (134)
Q Consensus        36 ~~~~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~  115 (134)
                      ....+|++++|+++++++|.++||+.||++|+++||.+++|+|++++|+||||||++|++|+++++....         .
T Consensus        14 ~~~~sF~~l~L~~~l~~~L~~~g~~~pt~IQ~~aIp~il~g~dvi~~a~TGSGKTlayllPil~~l~~~~---------~   84 (222)
T d2j0sa1          14 DVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQV---------R   84 (222)
T ss_dssp             CCCCSGGGGCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHTCCTTS---------C
T ss_pred             CCCCCHHHCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCeEEEcCcchhhhhhhcccccccccccc---------c
Confidence            4456999999999999999999999999999999999999999999999999999999999999886433         6


Q ss_pred             CcEEEEEcCcHHHHHHhc
Q psy7268         116 APLALIITPGRELVFQIG  133 (134)
Q Consensus       116 ~~~~lil~Pt~~La~Qi~  133 (134)
                      +++++|++||||||.|++
T Consensus        85 ~~~~lil~PtreLa~Qi~  102 (222)
T d2j0sa1          85 ETQALILAPTRELAVQIQ  102 (222)
T ss_dssp             SCCEEEECSSHHHHHHHH
T ss_pred             CceeEEecchHHHHHHHH
Confidence            789999999999999986

>d2g9na1 c.37.1.19 (A:21-238) Initiation factor 4a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.95  E-value=3.2e-28  Score=175.24  Aligned_cols=90  Identities=31%  Similarity=0.437  Sum_probs=84.4

Q ss_pred             CCCCCCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCC
Q psy7268          35 RIDLGTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPEL  114 (134)
Q Consensus        35 ~~~~~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~  114 (134)
                      ..++.+|++++|++.++++|.++||++||++|+++||.++.|+|++++|+||||||++|++|+++++....         
T Consensus         8 ~e~i~sF~~l~L~~~l~~~L~~~g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKTlayllp~l~~i~~~~---------   78 (218)
T d2g9na1           8 NEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIELDL---------   78 (218)
T ss_dssp             CCCCCCGGGSCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCCEEEECCTTSSHHHHHHHHHHHHCCTTC---------
T ss_pred             CCccCCHHHCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEEEcccchhhhhhhhhhhhheecccc---------
Confidence            45788999999999999999999999999999999999999999999999999999999999999985432         


Q ss_pred             CCcEEEEEcCcHHHHHHhc
Q psy7268         115 NAPLALIITPGRELVFQIG  133 (134)
Q Consensus       115 ~~~~~lil~Pt~~La~Qi~  133 (134)
                      +++++||++||+|||.|++
T Consensus        79 ~~~~alil~Pt~eL~~Q~~   97 (218)
T d2g9na1          79 KATQALVLAPTRELAQQIQ   97 (218)
T ss_dssp             CSCCEEEECSSHHHHHHHH
T ss_pred             cCccEEEEcccchhhhhHH
Confidence            7889999999999999986

>d1t6na_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Spliceosome RNA helicase BAT1 (UAP56)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.95  E-value=4.7e-28  Score=172.96  Aligned_cols=86  Identities=31%  Similarity=0.487  Sum_probs=80.4

Q ss_pred             CCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcE
Q psy7268          39 GTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPL  118 (134)
Q Consensus        39 ~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~  118 (134)
                      .+|++++|+++++++|.++||++|||+|+++||.+++|+|++++||||||||++|++|+++++...         ..+++
T Consensus         1 s~F~dl~L~~~l~~~l~~~g~~~pt~iQ~~aip~il~g~dvl~~A~TGsGKTla~~lp~l~~~~~~---------~~~~~   71 (207)
T d1t6na_           1 SGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPV---------TGQVS   71 (207)
T ss_dssp             CCSTTSCCCHHHHHHHHHTTCCCCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCCC---------TTCCC
T ss_pred             CCccccCcCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCeEEEeccccccccccccceeeeeccc---------CCCce
Confidence            379999999999999999999999999999999999999999999999999999999999987543         26789


Q ss_pred             EEEEcCcHHHHHHhc
Q psy7268         119 ALIITPGRELVFQIG  133 (134)
Q Consensus       119 ~lil~Pt~~La~Qi~  133 (134)
                      ++|++|||||+.|++
T Consensus        72 ~lil~PtreL~~qi~   86 (207)
T d1t6na_          72 VLVMCHTRELAFQIS   86 (207)
T ss_dssp             EEEECSCHHHHHHHH
T ss_pred             EEEEeccchhhHHHH
Confidence            999999999999986

>d1veca_ c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEAD box RNA helicase rck/p54
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.95  E-value=4.7e-28  Score=172.84  Aligned_cols=86  Identities=35%  Similarity=0.537  Sum_probs=81.3

Q ss_pred             CCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcE
Q psy7268          39 GTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPL  118 (134)
Q Consensus        39 ~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~  118 (134)
                      ++|++++|+++++++|.++||+.||++|+++||.+++|+|++++||||||||++|++|+++++....         ++++
T Consensus         3 ~~F~~l~L~~~l~~~l~~~g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKTlayllP~l~~~~~~~---------~~~~   73 (206)
T d1veca_           3 NEFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLERLDLKK---------DNIQ   73 (206)
T ss_dssp             SSGGGSCCCHHHHHHHHTTTCCSCCHHHHHHHHHHHTTCCEEEECCSSSTTHHHHHHHHHHHCCTTS---------CSCC
T ss_pred             CChhccCcCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEeeccCccccccccccchhhcccccc---------cCcc
Confidence            6899999999999999999999999999999999999999999999999999999999999875433         6789


Q ss_pred             EEEEcCcHHHHHHhc
Q psy7268         119 ALIITPGRELVFQIG  133 (134)
Q Consensus       119 ~lil~Pt~~La~Qi~  133 (134)
                      ++|++||++|+.|++
T Consensus        74 ~lil~pt~el~~q~~   88 (206)
T d1veca_          74 AMVIVPTRELALQVS   88 (206)
T ss_dssp             EEEECSCHHHHHHHH
T ss_pred             eEEEeecchhhHHHH
Confidence            999999999999986

>d1qdea_ c.37.1.19 (A:) Initiation factor 4a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.94  E-value=5e-27  Score=168.22  Aligned_cols=90  Identities=31%  Similarity=0.465  Sum_probs=84.1

Q ss_pred             CCCCCCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCC
Q psy7268          35 RIDLGTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPEL  114 (134)
Q Consensus        35 ~~~~~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~  114 (134)
                      ..++.+|++++|+++++++|.++||++||++|+++||.++.|+|+++++|||||||++|++|+++++...         .
T Consensus         6 ~~~~~sF~~l~l~~~l~~~L~~~g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKT~a~~lp~i~~l~~~---------~   76 (212)
T d1qdea_           6 DKVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTS---------V   76 (212)
T ss_dssp             CCCCCCGGGGTCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCTT---------C
T ss_pred             cccccChhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEeecccccchhhhhHhhhHhhhhcc---------C
Confidence            4568899999999999999999999999999999999999999999999999999999999999998543         2


Q ss_pred             CCcEEEEEcCcHHHHHHhc
Q psy7268         115 NAPLALIITPGRELVFQIG  133 (134)
Q Consensus       115 ~~~~~lil~Pt~~La~Qi~  133 (134)
                      ++++++|++||++|+.|++
T Consensus        77 ~~~~~lil~pt~el~~q~~   95 (212)
T d1qdea_          77 KAPQALMLAPTRELALQIQ   95 (212)
T ss_dssp             CSCCEEEECSSHHHHHHHH
T ss_pred             CCcceEEEcccHHHhhhhh
Confidence            7899999999999999986

>d1hv8a1 c.37.1.19 (A:3-210) Putative DEAD box RNA helicase {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative DEAD box RNA helicase
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=99.90  E-value=1.9e-24  Score=153.96  Aligned_cols=86  Identities=35%  Similarity=0.577  Sum_probs=79.0

Q ss_pred             CCCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcCC-CeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCC
Q psy7268          38 LGTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGK-SAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNA  116 (134)
Q Consensus        38 ~~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~-dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~  116 (134)
                      +-+|++++|+++++++|.+.||+.|||+|+++||.+++|+ |+++++|||+|||++|++|+++....          ..+
T Consensus         3 ~msf~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~g~~d~iv~a~TGsGKT~~~~l~~~~~~~~----------~~~   72 (208)
T d1hv8a1           3 YMNFNELNLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIELVNE----------NNG   72 (208)
T ss_dssp             CCCGGGSSCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCSEEEEECCSSSSHHHHHHHHHHHHSCS----------SSS
T ss_pred             ccCHHHcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCCeeeechhcccccceeeccccccccc----------ccC
Confidence            4589999999999999999999999999999999999885 99999999999999999999987543          267


Q ss_pred             cEEEEEcCcHHHHHHhc
Q psy7268         117 PLALIITPGRELVFQIG  133 (134)
Q Consensus       117 ~~~lil~Pt~~La~Qi~  133 (134)
                      ++++|++||++||.|++
T Consensus        73 ~~~lil~pt~~l~~q~~   89 (208)
T d1hv8a1          73 IEAIILTPTRELAIQVA   89 (208)
T ss_dssp             CCEEEECSCHHHHHHHH
T ss_pred             cceEEEeeccccchhhh
Confidence            89999999999999985

>d1s2ma1 c.37.1.19 (A:46-251) Putative ATP-dependent RNA helicase DHH1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative ATP-dependent RNA helicase DHH1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.90  E-value=5.9e-24  Score=151.09  Aligned_cols=86  Identities=34%  Similarity=0.525  Sum_probs=80.1

Q ss_pred             CCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcE
Q psy7268          39 GTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPL  118 (134)
Q Consensus        39 ~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~  118 (134)
                      .+|++++|++.++++|.++||++||++|+++||.+++|+|+++.||||||||++|++|+++.+....         .+.+
T Consensus         1 ~sF~~l~L~~~l~~~L~~~g~~~pt~iQ~~aip~il~g~dvi~~a~tGsGKTlay~lp~i~~~~~~~---------~~~~   71 (206)
T d1s2ma1           1 NTFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEKVKPKL---------NKIQ   71 (206)
T ss_dssp             CCGGGGCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCTTSCHHHHHHHHHHHHCCTTS---------CSCC
T ss_pred             CChHHcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEEecCCcchhhhhhcccccccccccc---------cccc
Confidence            4899999999999999999999999999999999999999999999999999999999999875533         6788


Q ss_pred             EEEEcCcHHHHHHhc
Q psy7268         119 ALIITPGRELVFQIG  133 (134)
Q Consensus       119 ~lil~Pt~~La~Qi~  133 (134)
                      +++++|+++++.|.+
T Consensus        72 ~~~~~~~~~~~~~~~   86 (206)
T d1s2ma1          72 ALIMVPTRELALQTS   86 (206)
T ss_dssp             EEEECSSHHHHHHHH
T ss_pred             ceeeccchhhhhhhh
Confidence            999999999998864

>d1q0ua_ c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable DEAD box RNA helicase YqfR
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=99.90  E-value=6.5e-24  Score=150.55  Aligned_cols=86  Identities=35%  Similarity=0.478  Sum_probs=79.1

Q ss_pred             CCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcE
Q psy7268          39 GTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPL  118 (134)
Q Consensus        39 ~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~  118 (134)
                      ++|++++|++.++++|++.||++||++|+++||.+++|+|++++||||||||++|++|+++.+....         ....
T Consensus         1 t~F~~l~L~~~l~~~l~~~g~~~pt~iQ~~aip~~l~G~dvii~a~TGSGKTlayllp~l~~~~~~~---------~~~~   71 (209)
T d1q0ua_           1 TQFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIMEKIKPER---------AEVQ   71 (209)
T ss_dssp             CCGGGSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCSSHHHHHHHHHHHHHHCCTTS---------CSCC
T ss_pred             CccccCCcCHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCeEeecccccccceeeeeeecccccccc---------cccc
Confidence            4799999999999999999999999999999999999999999999999999999999999886533         5677


Q ss_pred             EEEEcCcHHHHHHhc
Q psy7268         119 ALIITPGRELVFQIG  133 (134)
Q Consensus       119 ~lil~Pt~~La~Qi~  133 (134)
                      .++++|+++++.+.+
T Consensus        72 ~~~~~~~~~~~~~~~   86 (209)
T d1q0ua_          72 AVITAPTRELATQIY   86 (209)
T ss_dssp             EEEECSSHHHHHHHH
T ss_pred             ccccccccchhHHHH
Confidence            899999999988764

>d1gkub1 c.37.1.16 (B:1-250) Helicase-like "domain" of reverse gyrase {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Helicase-like "domain" of reverse gyrase
domain: Helicase-like "domain" of reverse gyrase
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.77  E-value=1.9e-19  Score=129.54  Aligned_cols=85  Identities=29%  Similarity=0.302  Sum_probs=70.4

Q ss_pred             CCCCCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCC
Q psy7268          36 IDLGTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELN  115 (134)
Q Consensus        36 ~~~~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~  115 (134)
                      ..+..|.+..+.+.+.+ +.+.++.+|+++|+.+++.++.|+|+++++|||+|||++++++++....            +
T Consensus        19 ~~~~~~~~~~~~~~~~~-~~~~~~~~p~~~Q~~~i~~~l~g~~~~i~apTGsGKT~~~~~~~~~~~~------------~   85 (237)
T d1gkub1          19 ASLCLFPEDFLLKEFVE-FFRKCVGEPRAIQKMWAKRILRKESFAATAPTGVGKTSFGLAMSLFLAL------------K   85 (237)
T ss_dssp             CCCSCCTTHHHHHHHHH-HHHTTTCSCCHHHHHHHHHHHTTCCEECCCCBTSCSHHHHHHHHHHHHT------------T
T ss_pred             cccccCccchhHHHHHH-HHHhccCCCCHHHHHHHHHHHCCCCEEEEecCCChHHHHHHHHHHHHHH------------h
Confidence            34455655555556544 4555888999999999999999999999999999999999999887664            4


Q ss_pred             CcEEEEEcCcHHHHHHhc
Q psy7268         116 APLALIITPGRELVFQIG  133 (134)
Q Consensus       116 ~~~~lil~Pt~~La~Qi~  133 (134)
                      +.+++|++||++|+.|++
T Consensus        86 ~~rvliv~Pt~~La~Q~~  103 (237)
T d1gkub1          86 GKRCYVIFPTSLLVIQAA  103 (237)
T ss_dssp             SCCEEEEESCHHHHHHHH
T ss_pred             cCeEEEEeccHHHHHHHH
Confidence            568999999999999985

>d1oywa2 c.37.1.19 (A:1-206) RecQ helicase domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecQ helicase domain
species: Escherichia coli [TaxId: 562]

Probab=99.76  E-value=4.4e-19  Score=124.93  Aligned_cols=80  Identities=24%  Similarity=0.308  Sum_probs=72.8

Q ss_pred             CCcccCCCCHHHHHHHHHC-CCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCc
Q psy7268          39 GTFEDTGLAPEIIDIFTKR-GLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAP  117 (134)
Q Consensus        39 ~~f~~~~l~~~i~~~l~~~-g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~  117 (134)
                      ...+.++|++.+.+.|++. ||+.++|+|.++|+.+++|+|+++++|||+|||++|.+|++.               ...
T Consensus         2 ~~~e~~~l~~~~~~~l~~~fg~~~~rp~Q~~ai~~~l~g~~vlv~apTGsGKT~~~~~~~~~---------------~~~   66 (206)
T d1oywa2           2 AQAEVLNLESGAKQVLQETFGYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPALL---------------LNG   66 (206)
T ss_dssp             CCCCCSSHHHHHHHHHHHTTCCSSCCTTHHHHHHHHHTTCCEEEECSCHHHHHHHHHHHHHH---------------SSS
T ss_pred             CchhhCCCCHHHHHHHHHhcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCCCcchhhhhhhh---------------ccC
Confidence            3578899999999999997 999999999999999999999999999999999999999875               345


Q ss_pred             EEEEEcCcHHHHHHhc
Q psy7268         118 LALIITPGRELVFQIG  133 (134)
Q Consensus       118 ~~lil~Pt~~La~Qi~  133 (134)
                      ++++++|+++|+.|..
T Consensus        67 ~~~~v~P~~~L~~q~~   82 (206)
T d1oywa2          67 LTVVVSPLISLMKDQV   82 (206)
T ss_dssp             EEEEECSCHHHHHHHH
T ss_pred             ceEEeccchhhhhhHH
Confidence            7999999999999975

>d2p6ra3 c.37.1.19 (A:1-202) Hel308 helicase {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Hel308 helicase
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.74  E-value=3.2e-19  Score=125.56  Aligned_cols=76  Identities=22%  Similarity=0.304  Sum_probs=67.1

Q ss_pred             CCHHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCc
Q psy7268          46 LAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPG  125 (134)
Q Consensus        46 l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt  125 (134)
                      +++.+++.|++.||+.|+|+|+++++.+++|+|+++++|||+|||+++.++++..+.            ++.++|+++|+
T Consensus        10 ~~~~~~~~l~~~g~~~l~~~Q~~ai~~l~~~~~~il~apTGsGKT~~a~l~i~~~~~------------~~~~vl~l~P~   77 (202)
T d2p6ra3          10 ISSYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAI------------KGGKSLYVVPL   77 (202)
T ss_dssp             HHHHHHHHHHCC---CCCCCCHHHHHHHTTCSCEEEECSSHHHHHHHHHHHHHHHHH------------TTCCEEEEESS
T ss_pred             hhHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCchhHHHHHHHHHHhh------------ccCcceeeccc
Confidence            678899999999999999999999999999999999999999999999999988875            34579999999


Q ss_pred             HHHHHHhc
Q psy7268         126 RELVFQIG  133 (134)
Q Consensus       126 ~~La~Qi~  133 (134)
                      ++|+.|.+
T Consensus        78 ~~L~~q~~   85 (202)
T d2p6ra3          78 RALAGEKY   85 (202)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            99999975

>d1wp9a1 c.37.1.19 (A:1-200) putative ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase PF2015
species: Pyrococcus furiosus [TaxId: 2261]

Probab=99.42  E-value=1.6e-13  Score=95.18  Aligned_cols=62  Identities=23%  Similarity=0.274  Sum_probs=52.6

Q ss_pred             CCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          60 TTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        60 ~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      -.|.++|.+++..+. ++|+++++|||+|||+++++++...+.+           .+.+++|++|+++|+.|.+
T Consensus         8 ~~pr~~Q~~~~~~~~-~~n~lv~~pTGsGKT~i~~~~~~~~~~~-----------~~~~il~i~P~~~L~~q~~   69 (200)
T d1wp9a1           8 IQPRIYQEVIYAKCK-ETNCLIVLPTGLGKTLIAMMIAEYRLTK-----------YGGKVLMLAPTKPLVLQHA   69 (200)
T ss_dssp             HCCCHHHHHHHHHGG-GSCEEEECCTTSCHHHHHHHHHHHHHHH-----------SCSCEEEECSSHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHh-cCCeEEEeCCCCcHHHHHHHHHHHHHHh-----------cCCcEEEEcCchHHHHHHH
Confidence            378999999998875 5678999999999999999888777654           3457999999999999965

>d2bmfa2 c.37.1.14 (A:178-482) Dengue virus helicase {Dengue virus type 2 [TaxId: 11060]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: Dengue virus helicase
species: Dengue virus type 2 [TaxId: 11060]

Probab=99.25  E-value=7.6e-13  Score=96.57  Aligned_cols=50  Identities=22%  Similarity=0.415  Sum_probs=43.6

Q ss_pred             HHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          73 LLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        73 ~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      +.+|+++++.+|||+|||++|+++++.....           ++.++||++||++||.|++
T Consensus         6 ~~~~~~~lv~~~TGsGKT~~~l~~~~~~~~~-----------~~~~~lvi~Ptr~La~q~~   55 (305)
T d2bmfa2           6 FRKKRLTIMDLHPGAGKTKRYLPAIVREAIK-----------RGLRTLILAPTRVVAAEME   55 (305)
T ss_dssp             SSTTCEEEECCCTTSSTTTTHHHHHHHHHHH-----------HTCCEEEEESSHHHHHHHH
T ss_pred             hhcCCcEEEEECCCCCHHHHHHHHHHHHHHh-----------cCCEEEEEccHHHHHHHHH
Confidence            3578999999999999999998898887665           4568999999999999986

>d1gm5a3 c.37.1.19 (A:286-549) RecG helicase domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecG helicase domain
species: Thermotoga maritima [TaxId: 2336]

Probab=99.06  E-value=4.6e-10  Score=81.63  Aligned_cols=71  Identities=17%  Similarity=0.171  Sum_probs=59.6

Q ss_pred             HHHHHHHCCCCCChHHHHHHHHHHHc----CC--CeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEc
Q psy7268          50 IIDIFTKRGLTTPTEIQKYSIPTLLS----GK--SAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIIT  123 (134)
Q Consensus        50 i~~~l~~~g~~~~t~iQ~~~i~~~~~----g~--dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~  123 (134)
                      .-+.+..+.| .+|+-|.+++..+..    ++  +.+++|.+|||||.+|+..++..+.            +|.++++++
T Consensus        73 ~~~f~~~LPF-eLT~~Q~~ai~ei~~d~~~~~~m~rLL~GdvGSGKT~Va~~a~~~~~~------------~g~q~~~m~  139 (264)
T d1gm5a3          73 AEEFIKSLPF-KLTNAQKRAHQEIRNDMISEKPMNRLLQGDVGSGKTVVAQLAILDNYE------------AGFQTAFMV  139 (264)
T ss_dssp             HHHHHHHSSS-CCCHHHHHHHHHHHHHHHSSSCCCCEEECCSSSSHHHHHHHHHHHHHH------------HTSCEEEEC
T ss_pred             HHHHHhhccc-cCCchHHHHHHHHHHHhhccCcceeeeeccccccccHHHHHHHHHHHh------------cccceeEEe
Confidence            3344455788 899999999998862    33  6799999999999999999988886            567899999


Q ss_pred             CcHHHHHHhc
Q psy7268         124 PGRELVFQIG  133 (134)
Q Consensus       124 Pt~~La~Qi~  133 (134)
                      ||..||.|.+
T Consensus       140 Pt~~La~Qh~  149 (264)
T d1gm5a3         140 PTSILAIQHY  149 (264)
T ss_dssp             SCHHHHHHHH
T ss_pred             ehHhhhHHHH
Confidence            9999999975

>d2eyqa3 c.37.1.19 (A:546-778) Transcription-repair coupling factor, TRCF {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Transcription-repair coupling factor, TRCF
species: Escherichia coli [TaxId: 562]

Probab=99.05  E-value=9.3e-10  Score=78.66  Aligned_cols=75  Identities=19%  Similarity=0.167  Sum_probs=62.4

Q ss_pred             CCHHHHHHHHH-CCCCCChHHHHHHHHHHH----cCC--CeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcE
Q psy7268          46 LAPEIIDIFTK-RGLTTPTEIQKYSIPTLL----SGK--SAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPL  118 (134)
Q Consensus        46 l~~~i~~~l~~-~g~~~~t~iQ~~~i~~~~----~g~--dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~  118 (134)
                      .+++..+.+.+ ..| .+|+-|..++..+.    +++  +.+++|.||||||.+|+..+...+.            +|.+
T Consensus        40 ~~~~~~~~~~~~lP~-~lt~~Q~~~~~~i~~~~~~~~~~~~LL~GdvGsGKT~V~~~a~~~~~~------------~g~q  106 (233)
T d2eyqa3          40 HDREQYQLFCDSFPF-ETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVD------------NHKQ  106 (233)
T ss_dssp             CCHHHHHHHHHTCCS-CCCHHHHHHHHHHHHHHHSSSCCEEEEECCCCTTTHHHHHHHHHHHHT------------TTCE
T ss_pred             CCHHHHHhhhhcccc-ccchhHHHHHHHHHHHHhccCccCeEEEcCCCCCcHHHHHHHHHHHHH------------cCCc
Confidence            34666666665 467 88999999998875    333  6899999999999999999888884            6789


Q ss_pred             EEEEcCcHHHHHHhc
Q psy7268         119 ALIITPGRELVFQIG  133 (134)
Q Consensus       119 ~lil~Pt~~La~Qi~  133 (134)
                      +++++||..|+.|.+
T Consensus       107 v~~l~Pt~~La~Q~~  121 (233)
T d2eyqa3         107 VAVLVPTTLLAQQHY  121 (233)
T ss_dssp             EEEECSSHHHHHHHH
T ss_pred             eEEEccHHHhHHHHH
Confidence            999999999999975

>d1rifa_ c.37.1.23 (A:) DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: DNA helicase UvsW
domain: DNA helicase UvsW
species: Bacteriophage T4 [TaxId: 10665]

Probab=99.04  E-value=1.7e-10  Score=84.49  Aligned_cols=62  Identities=26%  Similarity=0.205  Sum_probs=50.4

Q ss_pred             CChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          61 TPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        61 ~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      .|.+.|.+++..++..+..++.+|||+|||+.....+ ..+...          ...++|||+|+++|+.|.+
T Consensus       113 ~~rdyQ~~av~~~l~~~~~il~~pTGsGKT~i~~~i~-~~~~~~----------~~~k~Liivp~~~Lv~Q~~  174 (282)
T d1rifa_         113 EPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALLA-RYYLEN----------YEGKILIIVPTTALTTQMA  174 (282)
T ss_dssp             CCCHHHHHHHHHHHHHSEEEECCCTTSCHHHHHHHHH-HHHHHH----------CSSEEEEECSSHHHHHHHH
T ss_pred             ccchHHHHHHHHHHhcCCceeEEEcccCccHHHHHHH-HHhhhc----------ccceEEEEEcCchhHHHHH
Confidence            6899999999999988889999999999998865433 333222          3457999999999999975

>d2fz4a1 c.37.1.19 (A:24-229) DNA repair protein RAD25 {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DNA repair protein RAD25
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=98.99  E-value=3.9e-10  Score=78.81  Aligned_cols=58  Identities=26%  Similarity=0.315  Sum_probs=47.7

Q ss_pred             CChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          61 TPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        61 ~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      .+.+.|++++..+++++..++.+|||+|||+..+.. +..              .+.++||++|+++|+.|..
T Consensus        70 ~Lr~yQ~eav~~~~~~~~~ll~~~tG~GKT~~a~~~-~~~--------------~~~~~Liv~p~~~L~~q~~  127 (206)
T d2fz4a1          70 SLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAA-INE--------------LSTPTLIVVPTLALAEQWK  127 (206)
T ss_dssp             CCCHHHHHHHHHHTTTSEEEEEESSSTTHHHHHHHH-HHH--------------SCSCEEEEESSHHHHHHHH
T ss_pred             CcCHHHHHHHHHHHhCCCcEEEeCCCCCceehHHhH-HHH--------------hcCceeEEEcccchHHHHH
Confidence            688999999999999888899999999999876433 322              2346899999999999864

>d1yksa1 c.37.1.14 (A:185-324) YFV helicase domain {Yellow fever virus [TaxId: 11089]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: YFV helicase domain
species: Yellow fever virus [TaxId: 11089]

Probab=98.92  E-value=2.9e-10  Score=73.33  Aligned_cols=49  Identities=22%  Similarity=0.402  Sum_probs=41.5

Q ss_pred             HcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          74 LSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        74 ~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      .+|+++++++|||+|||..++..++.....           .+.++++++|+++++.|.+
T Consensus         5 ~~~~~~il~~~tGsGKT~~~~~~~~~~~~~-----------~~~~vli~~p~~~l~~q~~   53 (140)
T d1yksa1           5 KKGMTTVLDFHPGAGKTRRFLPQILAECAR-----------RRLRTLVLAPTRVVLSEMK   53 (140)
T ss_dssp             STTCEEEECCCTTSSTTTTHHHHHHHHHHH-----------TTCCEEEEESSHHHHHHHH
T ss_pred             HcCCcEEEEcCCCCChhHHHHHHHHHHhhh-----------cCceeeeeecchhHHHHHH
Confidence            468999999999999999887777776654           4568999999999999875

>d1a1va1 c.37.1.14 (A:190-325) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: HCV helicase domain
species: Human hepatitis C virus (HCV), different isolates [TaxId: 11103]

Probab=98.55  E-value=1.8e-08  Score=65.33  Aligned_cols=42  Identities=26%  Similarity=0.343  Sum_probs=32.1

Q ss_pred             CCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          77 KSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        77 ~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      +..++.+|||+|||+.+...    +..           .+.+++|++|+++|+.|.+
T Consensus         9 ~~~ll~apTGsGKT~~~~~~----~~~-----------~~~~vli~~P~~~l~~q~~   50 (136)
T d1a1va1           9 QVAHLHAPTGSGKSTKVPAA----YAA-----------QGYKVLVLNPSVAATLGFG   50 (136)
T ss_dssp             EEEEEECCTTSCTTTHHHHH----HHT-----------TTCCEEEEESCHHHHHHHH
T ss_pred             CEEEEEeCCCCCHHHHHHHH----HHH-----------cCCcEEEEcChHHHHHHHH
Confidence            45789999999999654222    222           4567999999999999975

>d1uaaa1 c.37.1.19 (A:2-307) DEXX box DNA helicase {Escherichia coli, RepD [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEXX box DNA helicase
species: Escherichia coli, RepD [TaxId: 562]

Probab=98.11  E-value=2.8e-06  Score=60.83  Aligned_cols=62  Identities=15%  Similarity=0.092  Sum_probs=44.1

Q ss_pred             CChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHh
Q psy7268          61 TPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQI  132 (134)
Q Consensus        61 ~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi  132 (134)
                      +++|-|.+++..  ....++|.|+.|||||.+.+--+...+.....        ...+++++++|+.++..+
T Consensus         1 ~L~~eQ~~av~~--~~~~~lI~g~aGTGKTt~l~~rv~~ll~~~~~--------~~~~ILvlt~tn~a~~~i   62 (306)
T d1uaaa1           1 RLNPGQQQAVEF--VTGPCLVLAGAGSGKTRVITNKIAHLIRGCGY--------QARHIAAVTFTNKAAREM   62 (306)
T ss_dssp             CCCHHHHHHHHC--CSSEEEECCCTTSCHHHHHHHHHHHHHHHHCC--------CGGGEEEEESSHHHHHHH
T ss_pred             CcCHHHHHHHhC--CCCCEEEEeeCCccHHHHHHHHHHHHHHhcCC--------ChhHEEEEeCcHHHHHHH
Confidence            468899999953  34568999999999998865444443332211        234699999999998765

>d1pjra1 c.37.1.19 (A:1-318) DEXX box DNA helicase {Bacillus stearothermophilus, PcrA [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEXX box DNA helicase
species: Bacillus stearothermophilus, PcrA [TaxId: 1422]

Probab=97.88  E-value=1.9e-05  Score=56.94  Aligned_cols=63  Identities=16%  Similarity=0.108  Sum_probs=46.2

Q ss_pred             CChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          61 TPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        61 ~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      .+++-|++++..  .+..++|.|+.|||||.+.+--+...+.....        ..-+++++++|+..+..+.
T Consensus        11 ~L~~eQ~~~v~~--~~g~~lV~g~aGSGKTt~l~~ri~~ll~~~~~--------~p~~il~lt~t~~aa~~~~   73 (318)
T d1pjra1          11 HLNKEQQEAVRT--TEGPLLIMAGAGSGKTRVLTHRIAYLMAEKHV--------APWNILAITFTNKAAREMR   73 (318)
T ss_dssp             TSCHHHHHHHHC--CSSCEEEEECTTSCHHHHHHHHHHHHHHTTCC--------CGGGEEEEESSHHHHHHHH
T ss_pred             hCCHHHHHHHhC--CCCCEEEEecCCccHHHHHHHHHHHHHHcCCC--------CHHHeEeEeccHHHHHHHH
Confidence            478999999964  34569999999999998876555555443211        2246999999999888763

>d1w36d1 c.37.1.19 (D:2-360) Exodeoxyribonuclease V alpha chain (RecD) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Exodeoxyribonuclease V alpha chain (RecD)
species: Escherichia coli [TaxId: 562]

Probab=97.59  E-value=0.00021  Score=53.15  Aligned_cols=64  Identities=16%  Similarity=0.220  Sum_probs=46.8

Q ss_pred             CChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHh
Q psy7268          61 TPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQI  132 (134)
Q Consensus        61 ~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi  132 (134)
                      ..++.|++|+..++.++-++|.|++|||||... .-++..+.+...       ..+.++++.+||-.-|..+
T Consensus       148 ~~~~~Q~~A~~~al~~~~~vI~G~pGTGKTt~i-~~~l~~l~~~~~-------~~~~~I~l~ApTgkAA~~L  211 (359)
T d1w36d1         148 DEINWQKVAAAVALTRRISVISGGPGTGKTTTV-AKLLAALIQMAD-------GERCRIRLAAPTGKAAARL  211 (359)
T ss_dssp             TSCCHHHHHHHHHHTBSEEEEECCTTSTHHHHH-HHHHHHHHHTCS-------SCCCCEEEEBSSHHHHHHH
T ss_pred             ccccHHHHHHHHHHcCCeEEEEcCCCCCceehH-HHHHHHHHHHHh-------ccCCeEEEecCcHHHHHHH
Confidence            456789999999999888999999999999774 333333333211       1567799999998766554

>d1z63a1 c.37.1.19 (A:432-661) Helicase of the SNF2/Rad54 hamily {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Helicase of the SNF2/Rad54 hamily
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=97.05  E-value=0.00095  Score=45.86  Aligned_cols=56  Identities=20%  Similarity=0.188  Sum_probs=40.0

Q ss_pred             CChHHHHHHHHHHH----cCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcH
Q psy7268          61 TPTEIQKYSIPTLL----SGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGR  126 (134)
Q Consensus        61 ~~t~iQ~~~i~~~~----~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~  126 (134)
                      .+.++|.+++..+.    .+..+++.-..|.|||+..+ .++..+....         ...+++|++|..
T Consensus        12 ~L~~yQ~~~v~~~~~~~~~~~g~iLaDe~GlGKT~~~i-~~~~~~~~~~---------~~~~~LIv~p~~   71 (230)
T d1z63a1          12 NLRPYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQTI-AVFSDAKKEN---------ELTPSLVICPLS   71 (230)
T ss_dssp             CCCHHHHHHHHHHHHHHHTTCCEEECCCTTSCHHHHHH-HHHHHHHHTT---------CCSSEEEEECST
T ss_pred             chhHHHHHHHHHHHHhhhcCCCEEEEeCCCCChHHHHH-Hhhhhhhhcc---------cccccceecchh
Confidence            57899999997543    45678999999999999874 4444444321         334689999854

>d1z3ix2 c.37.1.19 (X:92-389) Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxId: 7955]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Rad54-like, Rad54L
species: Zebra fish (Danio rerio) [TaxId: 7955]

Probab=96.67  E-value=0.0034  Score=44.71  Aligned_cols=65  Identities=22%  Similarity=0.291  Sum_probs=41.8

Q ss_pred             CChHHHHHHHHHHH---------cCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHH
Q psy7268          61 TPTEIQKYSIPTLL---------SGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQ  131 (134)
Q Consensus        61 ~~t~iQ~~~i~~~~---------~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Q  131 (134)
                      .+.|+|.+++..+.         .+...|+.-..|.|||+.. +.++..+......    .......+|||+|.. |..|
T Consensus        55 ~Lr~hQ~~gv~~l~~~~~~~~~~~~~g~iLaDemGlGKT~qa-ia~l~~l~~~~~~----~~~~~~~~LIV~P~s-l~~q  128 (298)
T d1z3ix2          55 VLRPHQREGVKFLWDCVTGRRIENSYGCIMADEMGLGKTLQC-ITLIWTLLKQSPD----CKPEIDKVIVVSPSS-LVRN  128 (298)
T ss_dssp             TCCHHHHHHHHHHHHHHTTSSSTTCCEEEECCCTTSCHHHHH-HHHHHHHHHCCTT----SSCSCSCEEEEECHH-HHHH
T ss_pred             cccHHHHHHHHHHHHHHHhhhhccCCceEEEeCCCCCHHHHH-HHHHHHHHHhccc----ccCCCCcEEEEccch-hhHH
Confidence            67899999997653         3456889999999999865 3444444432211    011234589999975 4443

>d1t5la1 c.37.1.19 (A:2-414) Nucleotide excision repair enzyme UvrB {Bacillus caldotenax [TaxId: 1395]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Nucleotide excision repair enzyme UvrB
species: Bacillus caldotenax [TaxId: 1395]

Probab=96.55  E-value=0.0016  Score=49.12  Aligned_cols=59  Identities=29%  Similarity=0.437  Sum_probs=41.4

Q ss_pred             CChHHHHHHHHHHH----cC-CCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhcC
Q psy7268          61 TPTEIQKYSIPTLL----SG-KSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIGQ  134 (134)
Q Consensus        61 ~~t~iQ~~~i~~~~----~g-~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~~  134 (134)
                      .|+.=|=++|..+.    .| ++.++.|-||||||+.. ..++...              +...|||+|+..+|.|+++
T Consensus        11 ~p~gDQP~aI~~l~~~l~~g~~~q~l~GltGS~ka~~i-A~l~~~~--------------~rp~LVVt~n~~~A~qL~~   74 (413)
T d1t5la1          11 EPQGDQPQAIAKLVDGLRRGVKHQTLLGATGTGKTFTI-SNVIAQV--------------NKPTLVIAHNKTLAGQLYS   74 (413)
T ss_dssp             CCCTTHHHHHHHHHHHHHHTCSEEEEEECTTSCHHHHH-HHHHHHH--------------TCCEEEECSSHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHhcCCCcEEEeCCCCcHHHHHH-HHHHHHh--------------CCCEEEEeCCHHHHHHHHH
Confidence            56666766666554    44 56889999999999554 2333332              1238999999999999863

>d1tf5a3 c.37.1.19 (A:1-226,A:349-395) Translocation ATPase SecA, nucleotide-binding domains {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Translocation ATPase SecA, nucleotide-binding domains
species: Bacillus subtilis [TaxId: 1423]

Probab=96.36  E-value=0.0096  Score=42.32  Aligned_cols=60  Identities=27%  Similarity=0.304  Sum_probs=48.3

Q ss_pred             CCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHH
Q psy7268          57 RGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQ  131 (134)
Q Consensus        57 ~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Q  131 (134)
                      +|. +|+++|-..--.+..|+  +..-.||-|||++..+|+.-..+            .|..+-|++.+-.||..
T Consensus        77 lG~-RhyDVQLiGgi~L~~G~--iaem~TGEGKTL~a~l~a~l~al------------~g~~vhvvTvNdyLA~R  136 (273)
T d1tf5a3          77 TGM-FPFKVQLMGGVALHDGN--IAEMKTGEGKTLTSTLPVYLNAL------------TGKGVHVVTVNEYLASR  136 (273)
T ss_dssp             HSC-CCCHHHHHHHHHHHTTS--EEECCTTSCHHHHHHHHHHHHHT------------TSSCEEEEESSHHHHHH
T ss_pred             hce-EEehhHHHHHHHHHhhh--heeecCCCcchhHHHHHHHHHHh------------cCCCceEEecCccccch
Confidence            376 88999988887777774  78999999999999888776665            45568888888888863

>d1g6oa_ c.37.1.11 (A:) Hexameric traffic ATPase, HP0525 {Helicobacter pylori [TaxId: 210]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hexameric traffic ATPase, HP0525
species: Helicobacter pylori [TaxId: 210]

Probab=96.05  E-value=0.0038  Score=45.48  Aligned_cols=49  Identities=27%  Similarity=0.430  Sum_probs=30.2

Q ss_pred             HHHHHCCCCC---ChHHHHHHHH-HHHcCCCeEEEcCCCCchhHHhHHHHHHHH
Q psy7268          52 DIFTKRGLTT---PTEIQKYSIP-TLLSGKSAILVAETGCGKTLSFLAPLVQQI  101 (134)
Q Consensus        52 ~~l~~~g~~~---~t~iQ~~~i~-~~~~g~dvli~a~tGsGKT~~~~lpil~~~  101 (134)
                      ..+.+.|+-.   ..+-+...+. .+..+++++++|+||||||.. +-.++..+
T Consensus       138 ~~l~~~g~~~~~~~~~~~~~~l~~~v~~~~nili~G~tgSGKTT~-l~al~~~i  190 (323)
T d1g6oa_         138 SFFEEQGFYNLLDNKEQAISAIKDGIAIGKNVIVCGGTGSGKTTY-IKSIMEFI  190 (323)
T ss_dssp             HHHHHTTTTTTCSSHHHHHHHHHHHHHHTCCEEEEESTTSSHHHH-HHHHGGGS
T ss_pred             HHHHHHhhhcccccHHHHHHHHHHHHHhCCCEEEEeeccccchHH-HHHHhhhc
Confidence            3455555432   2344444444 355788999999999999965 34444443

>d1p9ra_ c.37.1.11 (A:) Extracellular secretion NTPase EpsE {Vibrio cholerae [TaxId: 666]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Extracellular secretion NTPase EpsE
species: Vibrio cholerae [TaxId: 666]

Probab=95.94  E-value=0.0056  Score=45.68  Aligned_cols=39  Identities=18%  Similarity=0.266  Sum_probs=27.1

Q ss_pred             hHHHHHHHHHHHcCCC--eEEEcCCCCchhHHhHHHHHHHHH
Q psy7268          63 TEIQKYSIPTLLSGKS--AILVAETGCGKTLSFLAPLVQQIL  102 (134)
Q Consensus        63 t~iQ~~~i~~~~~g~d--vli~a~tGsGKT~~~~lpil~~~~  102 (134)
                      .+-|.+.+..++....  +++.||||||||... ..++..+.
T Consensus       143 ~~~~~~~l~~l~~~~~GliLvtGpTGSGKSTTl-~~~l~~~~  183 (401)
T d1p9ra_         143 TAHNHDNFRRLIKRPHGIILVTGPTGSGKSTTL-YAGLQELN  183 (401)
T ss_dssp             CHHHHHHHHHHHTSSSEEEEEECSTTSCHHHHH-HHHHHHHC
T ss_pred             cHHHHHHHHHHHhhhhceEEEEcCCCCCccHHH-HHHhhhhc
Confidence            4555556666665444  888999999999775 55666664

>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=95.60  E-value=0.007  Score=38.71  Aligned_cols=26  Identities=19%  Similarity=0.372  Sum_probs=19.9

Q ss_pred             CCeEEEcCCCCchhHHhHHHHHHHHHh
Q psy7268          77 KSAILVAETGCGKTLSFLAPLVQQILT  103 (134)
Q Consensus        77 ~dvli~a~tGsGKT~~~~lpil~~~~~  103 (134)
                      |++++.||+|+|||. .+-.++..+..
T Consensus         2 k~v~ItG~~GtGKTt-l~~~i~~~l~~   27 (189)
T d2i3ba1           2 RHVFLTGPPGVGKTT-LIHKASEVLKS   27 (189)
T ss_dssp             CCEEEESCCSSCHHH-HHHHHHHHHHH
T ss_pred             cEEEEECCCCCcHHH-HHHHHHHHHHH
Confidence            689999999999997 44555666654

>d1e9ra_ c.37.1.11 (A:) Bacterial conjugative coupling protein TrwB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Bacterial conjugative coupling protein TrwB
species: Escherichia coli [TaxId: 562]

Probab=95.51  E-value=0.01  Score=43.87  Aligned_cols=46  Identities=17%  Similarity=0.304  Sum_probs=32.1

Q ss_pred             HcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHH
Q psy7268          74 LSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQ  131 (134)
Q Consensus        74 ~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Q  131 (134)
                      ...+++++.|+||+|||... ..++..+..           .+..++|+=|.-++...
T Consensus        48 ~~~~H~~I~G~tGsGKT~~l-~~li~~~~~-----------~g~~~iiiD~kge~~~~   93 (433)
T d1e9ra_          48 AEPRHLLVNGATGTGKSVLL-RELAYTGLL-----------RGDRMVIVDPNGDMLSK   93 (433)
T ss_dssp             GGGGCEEEEECTTSSHHHHH-HHHHHHHHH-----------TTCEEEEEEETTHHHHH
T ss_pred             cccceEEEEeCCCCcHHHHH-HHHHHHHHh-----------CCCCEEEEeCChhHHHH
Confidence            45678999999999999764 444555443           34567777777776554

>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=95.41  E-value=0.014  Score=39.68  Aligned_cols=44  Identities=14%  Similarity=0.066  Sum_probs=29.5

Q ss_pred             CCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHc----CCCeEEEcCCCCchhHHhH
Q psy7268          39 GTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLS----GKSAILVAETGCGKTLSFL   94 (134)
Q Consensus        39 ~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~----g~dvli~a~tGsGKT~~~~   94 (134)
                      ++|+++--.+++.+.|+..            +.....    -.++++.||+|+|||...-
T Consensus         6 ~~~ddivGq~~~~~~L~~~------------i~~~~~~~~~~~~~Ll~GPpG~GKTtla~   53 (239)
T d1ixsb2           6 KTLDEYIGQERLKQKLRVY------------LEAAKARKEPLEHLLLFGPPGLGKTTLAH   53 (239)
T ss_dssp             CSGGGSCSCHHHHHHHHHH------------HHHHTTSSSCCCCEEEECCTTSCHHHHHH
T ss_pred             CCHHHhCCHHHHHHHHHHH------------HHHHHhcCCCCCeEEEECCCCCCHHHHHH
Confidence            3788877677777666542            112222    2479999999999997653

>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=95.17  E-value=0.0098  Score=40.26  Aligned_cols=42  Identities=17%  Similarity=0.193  Sum_probs=29.2

Q ss_pred             CCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHh
Q psy7268          39 GTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        39 ~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~   93 (134)
                      .+|+++-.++++.+.|.+.       ++.      -.-.++++.||+|+|||...
T Consensus        21 ~~~~diig~~~~~~~l~~~-------i~~------~~~~~lll~Gp~G~GKTtla   62 (231)
T d1iqpa2          21 QRLDDIVGQEHIVKRLKHY-------VKT------GSMPHLLFAGPPGVGKTTAA   62 (231)
T ss_dssp             CSTTTCCSCHHHHHHHHHH-------HHH------TCCCEEEEESCTTSSHHHHH
T ss_pred             CCHHHccCcHHHHHHHHHH-------HHc------CCCCeEEEECCCCCcHHHHH
Confidence            3788888888877777652       000      01236999999999999765

>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=95.06  E-value=0.0049  Score=46.76  Aligned_cols=18  Identities=33%  Similarity=0.462  Sum_probs=15.7

Q ss_pred             CCCeEEEcCCCCchhHHh
Q psy7268          76 GKSAILVAETGCGKTLSF   93 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~   93 (134)
                      .+|+++.||||+|||+..
T Consensus        49 ksNILliGPTGvGKTlLA   66 (443)
T d1g41a_          49 PKNILMIGPTGVGKTEIA   66 (443)
T ss_dssp             CCCEEEECCTTSSHHHHH
T ss_pred             cccEEEECCCCCCHHHHH
Confidence            458999999999999765

>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=94.94  E-value=0.02  Score=38.93  Aligned_cols=50  Identities=16%  Similarity=0.248  Sum_probs=33.9

Q ss_pred             CCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHhHHHHHHHH
Q psy7268          39 GTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSFLAPLVQQI  101 (134)
Q Consensus        39 ~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~  101 (134)
                      .+|+++..++++.+.|.+. +...           ....++++.||+|+|||... ..++..+
T Consensus         8 ~~~~diig~~~~~~~L~~~-~~~~-----------~~~~~lll~Gp~G~GKTt~~-~~la~~l   57 (252)
T d1sxje2           8 KSLNALSHNEELTNFLKSL-SDQP-----------RDLPHLLLYGPNGTGKKTRC-MALLESI   57 (252)
T ss_dssp             CSGGGCCSCHHHHHHHHTT-TTCT-----------TCCCCEEEECSTTSSHHHHH-HTHHHHH
T ss_pred             CCHHHccCcHHHHHHHHHH-HHcC-----------CCCCeEEEECCCCCCHHHHH-HHHHHhh
Confidence            4788998899999988763 1100           01225899999999999765 3444444

>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=94.78  E-value=0.0072  Score=43.41  Aligned_cols=18  Identities=33%  Similarity=0.462  Sum_probs=16.2

Q ss_pred             CCCeEEEcCCCCchhHHh
Q psy7268          76 GKSAILVAETGCGKTLSF   93 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~   93 (134)
                      .+.+++.||||+|||+..
T Consensus        49 ~~~iLl~GPpG~GKT~lA   66 (309)
T d1ofha_          49 PKNILMIGPTGVGKTEIA   66 (309)
T ss_dssp             CCCEEEECCTTSSHHHHH
T ss_pred             CceEEEECCCCCCHHHHH
Confidence            578999999999999876

>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=94.67  E-value=0.029  Score=38.12  Aligned_cols=53  Identities=19%  Similarity=0.104  Sum_probs=31.4

Q ss_pred             CCcccCCCCHHHHHHHHHCCCCCChHHHH-HHHHHH-H----cCCCeEEEcCCCCchhHHh
Q psy7268          39 GTFEDTGLAPEIIDIFTKRGLTTPTEIQK-YSIPTL-L----SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        39 ~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~-~~i~~~-~----~g~dvli~a~tGsGKT~~~   93 (134)
                      .+|+++..++...+.|.+. + .-..... ..++.. .    ..+.+++.||+|+|||...
T Consensus        11 ~~~~dlig~~~~~~~L~~~-l-~~~~~~~~~~~~~~~~~~~~~~~~lll~GPpG~GKTt~a   69 (253)
T d1sxja2          11 TNLQQVCGNKGSVMKLKNW-L-ANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAA   69 (253)
T ss_dssp             SSGGGCCSCHHHHHHHHHH-H-HTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHH
T ss_pred             CCHHHhcCCHHHHHHHHHH-H-HhhhhcchhhhhhhcccCCCCCceEEEECCCCCCHHHHH
Confidence            4799999999888877762 0 0011000 000000 0    1246999999999999764

>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=94.60  E-value=0.024  Score=38.10  Aligned_cols=41  Identities=27%  Similarity=0.263  Sum_probs=28.2

Q ss_pred             CCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcCC--CeEEEcCCCCchhHHhH
Q psy7268          39 GTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGK--SAILVAETGCGKTLSFL   94 (134)
Q Consensus        39 ~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~--dvli~a~tGsGKT~~~~   94 (134)
                      ++|+++-.++++.+.|.+.               +.+++  ++++.||+|+|||...-
T Consensus        12 ~~~~d~ig~~~~~~~L~~~---------------~~~~~~~~~ll~Gp~G~GKTt~a~   54 (224)
T d1sxjb2          12 QVLSDIVGNKETIDRLQQI---------------AKDGNMPHMIISGMPGIGKTTSVH   54 (224)
T ss_dssp             SSGGGCCSCTHHHHHHHHH---------------HHSCCCCCEEEECSTTSSHHHHHH
T ss_pred             CCHHHhcCCHHHHHHHHHH---------------HHcCCCCeEEEECCCCCCchhhHH
Confidence            4677776677776666542               12332  58999999999997753

>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=94.55  E-value=0.03  Score=37.51  Aligned_cols=40  Identities=25%  Similarity=0.323  Sum_probs=28.8

Q ss_pred             CCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcCC--CeEEEcCCCCchhHHh
Q psy7268          39 GTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGK--SAILVAETGCGKTLSF   93 (134)
Q Consensus        39 ~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~--dvli~a~tGsGKT~~~   93 (134)
                      ++|+++-.++++.+.|.+.               +.+++  ++++.||+|+|||...
T Consensus        11 ~~~~divg~~~~~~~L~~~---------------i~~~~~~~lLl~Gp~G~GKttl~   52 (227)
T d1sxjc2          11 ETLDEVYGQNEVITTVRKF---------------VDEGKLPHLLFYGPPGTGKTSTI   52 (227)
T ss_dssp             SSGGGCCSCHHHHHHHHHH---------------HHTTCCCCEEEECSSSSSHHHHH
T ss_pred             CCHHHccCcHHHHHHHHHH---------------HHcCCCCeEEEECCCCCChhHHH
Confidence            4788887788877777552               12222  5899999999999654

>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=94.46  E-value=0.0094  Score=40.51  Aligned_cols=44  Identities=14%  Similarity=0.140  Sum_probs=29.9

Q ss_pred             CCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHc---CCCeEEEcCCCCchhHHh
Q psy7268          39 GTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLS---GKSAILVAETGCGKTLSF   93 (134)
Q Consensus        39 ~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~---g~dvli~a~tGsGKT~~~   93 (134)
                      .+|+++--.+.+.+.|... .      +.    ....   ..++++.||+|+|||...
T Consensus         6 ~~~~divGqe~~~~~l~~~-i------~~----~~~~~~~~~~~L~~GPpGtGKT~lA   52 (238)
T d1in4a2           6 KSLDEFIGQENVKKKLSLA-L------EA----AKMRGEVLDHVLLAGPPGLGKTTLA   52 (238)
T ss_dssp             SSGGGCCSCHHHHHHHHHH-H------HH----HHHHTCCCCCEEEESSTTSSHHHHH
T ss_pred             CcHHHcCChHHHHHHHHHH-H------HH----HHhcCCCCCeEEEECCCCCcHHHHH
Confidence            4788888788877766541 0      00    1112   247999999999999875

>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=94.44  E-value=0.0045  Score=43.58  Aligned_cols=53  Identities=28%  Similarity=0.273  Sum_probs=31.6

Q ss_pred             CCCcccCCCCHHHHHHHHHC--CCCCChHHHHHHHHHHHcCCCeEEEcCCCCchhHHh
Q psy7268          38 LGTFEDTGLAPEIIDIFTKR--GLTTPTEIQKYSIPTLLSGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        38 ~~~f~~~~l~~~i~~~l~~~--g~~~~t~iQ~~~i~~~~~g~dvli~a~tGsGKT~~~   93 (134)
                      --+|++.+-.+...+.|.+.  -++.+...|..   .+...+.+++.||+|+|||...
T Consensus         8 ~~t~~Di~Gl~~~k~~l~e~v~~~~~~~~~~~~---g~~~~~~iLL~GppGtGKT~la   62 (256)
T d1lv7a_           8 KTTFADVAGCDEAKEEVAELVEYLREPSRFQKL---GGKIPKGVLMVGPPGTGKTLLA   62 (256)
T ss_dssp             CCCGGGSCSCHHHHHHTHHHHHHHHCGGGC--------CCCCEEEEECCTTSCHHHHH
T ss_pred             CCCHHHHhchHHHHHHHHHHHHHHHCHHHHHHc---CCCCCCeEEeeCCCCCCccHHH
Confidence            34899998888877777542  01111111111   0112357999999999999774

>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=94.28  E-value=0.013  Score=36.57  Aligned_cols=18  Identities=28%  Similarity=0.364  Sum_probs=15.5

Q ss_pred             CCCeEEEcCCCCchhHHh
Q psy7268          76 GKSAILVAETGCGKTLSF   93 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~   93 (134)
                      .+++++.|++|+|||...
T Consensus         2 ~k~I~l~G~~GsGKSTva   19 (169)
T d1kaga_           2 KRNIFLVGPMGAGKSTIG   19 (169)
T ss_dssp             CCCEEEECCTTSCHHHHH
T ss_pred             CCeEEEECCCCCCHHHHH
Confidence            468999999999999764

>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=94.25  E-value=0.016  Score=39.39  Aligned_cols=24  Identities=29%  Similarity=0.433  Sum_probs=17.5

Q ss_pred             CCeEEEcCCCCchhHHhHHHHHHHH
Q psy7268          77 KSAILVAETGCGKTLSFLAPLVQQI  101 (134)
Q Consensus        77 ~dvli~a~tGsGKT~~~~lpil~~~  101 (134)
                      .++++.||+|+|||... -.+...+
T Consensus        44 ~~lll~GppGtGKT~l~-~~l~~~l   67 (276)
T d1fnna2          44 PRATLLGRPGTGKTVTL-RKLWELY   67 (276)
T ss_dssp             CEEEEECCTTSSHHHHH-HHHHHHH
T ss_pred             CceEEECCCCCCHHHHH-HHHHHHH
Confidence            57999999999999664 2344444

>d1um8a_ c.37.1.20 (A:) ClpX {Helicobacter pylori [TaxId: 210]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpX
species: Helicobacter pylori [TaxId: 210]

Probab=94.11  E-value=0.028  Score=41.32  Aligned_cols=17  Identities=41%  Similarity=0.626  Sum_probs=14.9

Q ss_pred             CCeEEEcCCCCchhHHh
Q psy7268          77 KSAILVAETGCGKTLSF   93 (134)
Q Consensus        77 ~dvli~a~tGsGKT~~~   93 (134)
                      .+++..||||+|||...
T Consensus        69 ~niLfiGPTGvGKTElA   85 (364)
T d1um8a_          69 SNILLIGPTGSGKTLMA   85 (364)
T ss_dssp             CCEEEECCTTSSHHHHH
T ss_pred             cceeeeCCCCccHHHHH
Confidence            47999999999999765

>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=93.98  E-value=0.039  Score=37.43  Aligned_cols=19  Identities=32%  Similarity=0.604  Sum_probs=15.2

Q ss_pred             CCCeEEEcCCCCchhHHhH
Q psy7268          76 GKSAILVAETGCGKTLSFL   94 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~~   94 (134)
                      ++-++++||||+|||.+..
T Consensus         6 ~~vi~lvGptGvGKTTTia   24 (207)
T d1okkd2           6 GRVVLVVGVNGVGKTTTIA   24 (207)
T ss_dssp             SSEEEEECSTTSSHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHH
Confidence            3447789999999998854

>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=93.95  E-value=0.04  Score=34.69  Aligned_cols=24  Identities=29%  Similarity=0.423  Sum_probs=16.7

Q ss_pred             eEEEcCCCCchhHHhHHHHHHHHHh
Q psy7268          79 AILVAETGCGKTLSFLAPLVQQILT  103 (134)
Q Consensus        79 vli~a~tGsGKT~~~~lpil~~~~~  103 (134)
                      +.+.|+.|||||. ++--++..+..
T Consensus         5 i~itG~~GSGKTT-L~~~L~~~l~~   28 (170)
T d1np6a_           5 LAFAAWSGTGKTT-LLKKLIPALCA   28 (170)
T ss_dssp             EEEECCTTSCHHH-HHHHHHHHHHH
T ss_pred             EEEEcCCCCCHHH-HHHHHHHHHHH
Confidence            5688999999994 33455555543

>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=93.63  E-value=0.015  Score=40.49  Aligned_cols=54  Identities=22%  Similarity=0.143  Sum_probs=31.9

Q ss_pred             CCCCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHH--cCCCeEEEcCCCCchhHHh
Q psy7268          37 DLGTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLL--SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        37 ~~~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~--~g~dvli~a~tGsGKT~~~   93 (134)
                      |-.+|++++-.++..+.|.+. . .+- .+...+...-  .-+.+++.||+|+|||...
T Consensus         4 p~~~~~di~G~~~~k~~l~~~-i-~~l-~~~~~~~~~g~~~~~giLl~GppGtGKT~la   59 (247)
T d1ixza_           4 PKVTFKDVAGAEEAKEELKEI-V-EFL-KNPSRFHEMGARIPKGVLLVGPPGVGKTHLA   59 (247)
T ss_dssp             CSCCGGGCCSCHHHHHHHHHH-H-HHH-HCHHHHHHTTCCCCSEEEEECCTTSSHHHHH
T ss_pred             CCCcHHHHccHHHHHHHHHHH-H-HHH-HCHHHHHHcCCCCCceEEEecCCCCChhHHH
Confidence            335899998777777777542 0 000 0111121111  1246999999999999764

>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=93.61  E-value=0.022  Score=38.29  Aligned_cols=16  Identities=25%  Similarity=0.453  Sum_probs=13.9

Q ss_pred             CeEEEcCCCCchhHHh
Q psy7268          78 SAILVAETGCGKTLSF   93 (134)
Q Consensus        78 dvli~a~tGsGKT~~~   93 (134)
                      ++++.||+|+|||...
T Consensus        35 ~lll~Gp~G~GKTtl~   50 (237)
T d1sxjd2          35 HMLFYGPPGTGKTSTI   50 (237)
T ss_dssp             CEEEECSTTSSHHHHH
T ss_pred             eEEEECCCCCChHHHH
Confidence            5899999999999654

>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=93.53  E-value=0.017  Score=36.12  Aligned_cols=15  Identities=20%  Similarity=0.279  Sum_probs=12.8

Q ss_pred             eEEEcCCCCchhHHh
Q psy7268          79 AILVAETGCGKTLSF   93 (134)
Q Consensus        79 vli~a~tGsGKT~~~   93 (134)
                      ++++|++|||||...
T Consensus         5 Iii~G~pGsGKTTla   19 (152)
T d1ly1a_           5 ILTIGCPGSGKSTWA   19 (152)
T ss_dssp             EEEECCTTSSHHHHH
T ss_pred             EEEECCCCCCHHHHH
Confidence            678999999998753

>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=93.39  E-value=0.019  Score=36.26  Aligned_cols=15  Identities=27%  Similarity=0.501  Sum_probs=13.2

Q ss_pred             eEEEcCCCCchhHHh
Q psy7268          79 AILVAETGCGKTLSF   93 (134)
Q Consensus        79 vli~a~tGsGKT~~~   93 (134)
                      +++.|++|+|||...
T Consensus         5 I~i~G~~GsGKTTva   19 (176)
T d2bdta1           5 YIITGPAGVGKSTTC   19 (176)
T ss_dssp             EEEECSTTSSHHHHH
T ss_pred             EEEECCCCCCHHHHH
Confidence            788999999999764

>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=93.35  E-value=0.053  Score=36.95  Aligned_cols=16  Identities=38%  Similarity=0.420  Sum_probs=13.6

Q ss_pred             eEEEcCCCCchhHHhH
Q psy7268          79 AILVAETGCGKTLSFL   94 (134)
Q Consensus        79 vli~a~tGsGKT~~~~   94 (134)
                      ++++||||+|||....
T Consensus        14 i~lvGptGvGKTTTiA   29 (213)
T d1vmaa2          14 IMVVGVNGTGKTTSCG   29 (213)
T ss_dssp             EEEECCTTSSHHHHHH
T ss_pred             EEEECCCCCCHHHHHH
Confidence            6779999999998854

>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=93.34  E-value=0.021  Score=36.37  Aligned_cols=18  Identities=28%  Similarity=0.433  Sum_probs=15.3

Q ss_pred             CCCeEEEcCCCCchhHHh
Q psy7268          76 GKSAILVAETGCGKTLSF   93 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~   93 (134)
                      +.++++.|++|+|||...
T Consensus         5 ~~~I~i~G~~GsGKTT~~   22 (174)
T d1y63a_           5 GINILITGTPGTGKTSMA   22 (174)
T ss_dssp             SCEEEEECSTTSSHHHHH
T ss_pred             CCEEEEEeCCCCCHHHHH
Confidence            456999999999999764

>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=93.33  E-value=0.014  Score=37.27  Aligned_cols=19  Identities=26%  Similarity=0.426  Sum_probs=15.8

Q ss_pred             cCCCeEEEcCCCCchhHHh
Q psy7268          75 SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~   93 (134)
                      .|+=+++.|++|||||...
T Consensus         3 ~g~iI~l~G~~GsGKSTia   21 (176)
T d1zp6a1           3 GGNILLLSGHPGSGKSTIA   21 (176)
T ss_dssp             TTEEEEEEECTTSCHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHH
Confidence            4666889999999999754

>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=93.09  E-value=0.023  Score=35.95  Aligned_cols=17  Identities=29%  Similarity=0.337  Sum_probs=14.1

Q ss_pred             CCeEEEcCCCCchhHHh
Q psy7268          77 KSAILVAETGCGKTLSF   93 (134)
Q Consensus        77 ~dvli~a~tGsGKT~~~   93 (134)
                      -.+++.|++|||||...
T Consensus         5 ~~I~i~G~pGsGKTTia   21 (173)
T d1rkba_           5 PNILLTGTPGVGKTTLG   21 (173)
T ss_dssp             CCEEEECSTTSSHHHHH
T ss_pred             CEEEEECCCCCCHHHHH
Confidence            35889999999999754

>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=93.05  E-value=0.066  Score=36.42  Aligned_cols=16  Identities=31%  Similarity=0.480  Sum_probs=13.6

Q ss_pred             eEEEcCCCCchhHHhH
Q psy7268          79 AILVAETGCGKTLSFL   94 (134)
Q Consensus        79 vli~a~tGsGKT~~~~   94 (134)
                      ++++||||+|||.+..
T Consensus        12 i~lvGptGvGKTTTiA   27 (211)
T d2qy9a2          12 ILMVGVNGVGKTTTIG   27 (211)
T ss_dssp             EEEECCTTSCHHHHHH
T ss_pred             EEEECCCCCCHHHHHH
Confidence            5679999999998864

>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=93.02  E-value=0.02  Score=39.08  Aligned_cols=16  Identities=31%  Similarity=0.339  Sum_probs=13.9

Q ss_pred             CeEEEcCCCCchhHHh
Q psy7268          78 SAILVAETGCGKTLSF   93 (134)
Q Consensus        78 dvli~a~tGsGKT~~~   93 (134)
                      .+++.||+|+|||...
T Consensus        34 ~ilL~GpPGtGKT~la   49 (273)
T d1gvnb_          34 AFLLGGQPGSGKTSLR   49 (273)
T ss_dssp             EEEEECCTTSCTHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            4899999999999754

>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=92.74  E-value=0.019  Score=36.54  Aligned_cols=17  Identities=18%  Similarity=0.389  Sum_probs=14.5

Q ss_pred             CCeEEEcCCCCchhHHh
Q psy7268          77 KSAILVAETGCGKTLSF   93 (134)
Q Consensus        77 ~dvli~a~tGsGKT~~~   93 (134)
                      +.+++.|++|+|||...
T Consensus         8 K~I~i~G~~GsGKTTla   24 (192)
T d1lw7a2           8 KTVAILGGESSGKSVLV   24 (192)
T ss_dssp             EEEEEECCTTSHHHHHH
T ss_pred             eEEEEECCCCCCHHHHH
Confidence            56899999999999654

>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=92.60  E-value=0.11  Score=35.30  Aligned_cols=48  Identities=21%  Similarity=0.261  Sum_probs=33.2

Q ss_pred             CCcccCCCCHHHHHHHHHCCCCCChHHHHHHHHHHHcCC---CeEEEcCCCCchhHHhHHHHHHHHH
Q psy7268          39 GTFEDTGLAPEIIDIFTKRGLTTPTEIQKYSIPTLLSGK---SAILVAETGCGKTLSFLAPLVQQIL  102 (134)
Q Consensus        39 ~~f~~~~l~~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g~---dvli~a~tGsGKT~~~~lpil~~~~  102 (134)
                      ++|+++-.++++.+.|...               +.+++   .+++.||+|+|||.... .++..+.
T Consensus         9 ~~~~dlig~~~~~~~L~~~---------------i~~~~~~~~~Ll~Gp~G~GKtt~a~-~~~~~l~   59 (239)
T d1njfa_           9 QTFADVVGQEHVLTALANG---------------LSLGRIHHAYLFSGTRGVGKTSIAR-LLAKGLN   59 (239)
T ss_dssp             SSGGGSCSCHHHHHHHHHH---------------HHTTCCCSEEEEECSTTSSHHHHHH-HHHHHHH
T ss_pred             CCHHHccChHHHHHHHHHH---------------HHcCCCCeeEEEECCCCCcHHHHHH-HHHHHhc
Confidence            5888888888888877652               22222   38999999999997654 3444443

>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=92.58  E-value=0.078  Score=35.83  Aligned_cols=16  Identities=38%  Similarity=0.380  Sum_probs=13.1

Q ss_pred             eEEEcCCCCchhHHhH
Q psy7268          79 AILVAETGCGKTLSFL   94 (134)
Q Consensus        79 vli~a~tGsGKT~~~~   94 (134)
                      +++.+|||+|||.+..
T Consensus        13 i~lvGp~GvGKTTTia   28 (207)
T d1ls1a2          13 WFLVGLQGSGKTTTAA   28 (207)
T ss_dssp             EEEECCTTTTHHHHHH
T ss_pred             EEEECCCCCCHHHHHH
Confidence            5668999999997753

>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=92.55  E-value=0.022  Score=39.55  Aligned_cols=16  Identities=31%  Similarity=0.266  Sum_probs=14.3

Q ss_pred             CeEEEcCCCCchhHHh
Q psy7268          78 SAILVAETGCGKTLSF   93 (134)
Q Consensus        78 dvli~a~tGsGKT~~~   93 (134)
                      .+++.||+|+|||...
T Consensus        42 ~vLL~GppGtGKT~la   57 (246)
T d1d2na_          42 SVLLEGPPHSGKTALA   57 (246)
T ss_dssp             EEEEECSTTSSHHHHH
T ss_pred             EEEEECcCCCCHHHHH
Confidence            5999999999999765

>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=92.47  E-value=0.073  Score=36.63  Aligned_cols=39  Identities=13%  Similarity=0.078  Sum_probs=24.9

Q ss_pred             HcCCCeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEc
Q psy7268          74 LSGKSAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIIT  123 (134)
Q Consensus        74 ~~g~dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~  123 (134)
                      ..|.=+++.|++|+|||...+--+.+....           .+.++++++
T Consensus        33 ~~G~l~vi~G~~G~GKT~~~~~la~~~a~~-----------~g~~v~~~s   71 (277)
T d1cr2a_          33 RGGEVIMVTSGSGMGKSTFVRQQALQWGTA-----------MGKKVGLAM   71 (277)
T ss_dssp             CTTCEEEEECSTTSSHHHHHHHHHHHHHHT-----------SCCCEEEEE
T ss_pred             CCCeEEEEEeCCCCCHHHHHHHHHHhhhhh-----------cccceeEee
Confidence            456678899999999995543333333222           345677776

>d1svma_ c.37.1.20 (A:) Papillomavirus large T antigen helicase domain {Simian virus 40 [TaxId: 10633]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Papillomavirus large T antigen helicase domain
species: Simian virus 40 [TaxId: 10633]

Probab=92.27  E-value=0.089  Score=38.48  Aligned_cols=43  Identities=14%  Similarity=0.070  Sum_probs=26.1

Q ss_pred             CCCCChHHHHHHHHHHHc----CCCeEEEcCCCCchhHHhHHHHHHHH
Q psy7268          58 GLTTPTEIQKYSIPTLLS----GKSAILVAETGCGKTLSFLAPLVQQI  101 (134)
Q Consensus        58 g~~~~t~iQ~~~i~~~~~----g~dvli~a~tGsGKT~~~~lpil~~~  101 (134)
                      ++......-..++..++.    ++.+++.||+|+|||... ..++..+
T Consensus       132 ~~~~~~~~i~~~l~~~~~~~~~~~~~~~~g~~~~gk~~~~-~~~~~~~  178 (362)
T d1svma_         132 LLPKMDSVVYDFLKCMVYNIPKKRYWLFKGPIDSGKTTLA-AALLELC  178 (362)
T ss_dssp             TSTTHHHHHHHHHHHHHHCCTTCCEEEEECSTTSSHHHHH-HHHHHHH
T ss_pred             cccchHHHHHHHHHHHHhCCCCcCeEEEECCCCCCHHHHH-HHHHHHc
Confidence            454444333344444444    457999999999999664 4444444

>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=92.23  E-value=0.079  Score=35.98  Aligned_cols=16  Identities=31%  Similarity=0.370  Sum_probs=9.5

Q ss_pred             eEEEcCCCCchhHHhH
Q psy7268          79 AILVAETGCGKTLSFL   94 (134)
Q Consensus        79 vli~a~tGsGKT~~~~   94 (134)
                      ++++||||+|||.+..
T Consensus        15 i~lvGptGvGKTTTiA   30 (211)
T d1j8yf2          15 IMLVGVQGTGKATTAG   30 (211)
T ss_dssp             EEEECSCCC----HHH
T ss_pred             EEEECCCCCCHHHHHH
Confidence            5678999999998753

>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=92.12  E-value=0.093  Score=35.15  Aligned_cols=24  Identities=25%  Similarity=0.234  Sum_probs=17.7

Q ss_pred             CCCeEEEcCCCCchhHHhHHHHHH
Q psy7268          76 GKSAILVAETGCGKTLSFLAPLVQ   99 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~~lpil~   99 (134)
                      |.-+++.|++|+|||...+--+.+
T Consensus        26 gsl~li~G~pGsGKT~l~~qia~~   49 (242)
T d1tf7a2          26 DSIILATGATGTGKTLLVSRFVEN   49 (242)
T ss_dssp             SCEEEEEECTTSSHHHHHHHHHHH
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHH
Confidence            456899999999999766433333

>d1c4oa1 c.37.1.19 (A:2-409) Nucleotide excision repair enzyme UvrB {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: Tandem AAA-ATPase domain
domain: Nucleotide excision repair enzyme UvrB
species: Thermus thermophilus [TaxId: 274]

Probab=92.09  E-value=0.094  Score=39.02  Aligned_cols=57  Identities=30%  Similarity=0.489  Sum_probs=36.7

Q ss_pred             ChHHHHHHHHHH----HcCC-CeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHHHHhc
Q psy7268          62 PTEIQKYSIPTL----LSGK-SAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELVFQIG  133 (134)
Q Consensus        62 ~t~iQ~~~i~~~----~~g~-dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~Qi~  133 (134)
                      |+.=|-++|..+    ..|. .+.+.|.+||+|++.. ..++...             +. ..|||+|+.+.|.+++
T Consensus         9 p~~dqp~aI~~l~~~L~~g~~~~~L~GlsgS~ka~~~-A~l~~~~-------------~r-p~LvVt~~~~~A~~l~   70 (408)
T d1c4oa1           9 PKGDQPKAIAGLVEALRDGERFVTLLGATGTGKTVTM-AKVIEAL-------------GR-PALVLAPNKILAAQLA   70 (408)
T ss_dssp             CCTTHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHH-HHHHHHH-------------TC-CEEEEESSHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHhcCCCcEEEecCCCCHHHHHH-HHHHHHh-------------CC-CEEEEeCCHHHHHHHH
Confidence            333454566554    3555 4788999999998543 1222222             12 3788999999999875

>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=91.80  E-value=0.061  Score=35.19  Aligned_cols=15  Identities=20%  Similarity=0.552  Sum_probs=13.4

Q ss_pred             CCeEEEcCCCCchhH
Q psy7268          77 KSAILVAETGCGKTL   91 (134)
Q Consensus        77 ~dvli~a~tGsGKT~   91 (134)
                      +-+++.||+|+|||.
T Consensus         2 rpIvl~GpsG~GK~t   16 (186)
T d1gkya_           2 RPIVISGPSGTGKST   16 (186)
T ss_dssp             CCEEEECCTTSSHHH
T ss_pred             CeEEEECCCCCCHHH
Confidence            568999999999995

>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=91.74  E-value=0.043  Score=35.10  Aligned_cols=17  Identities=24%  Similarity=0.389  Sum_probs=14.6

Q ss_pred             CCeEEEcCCCCchhHHh
Q psy7268          77 KSAILVAETGCGKTLSF   93 (134)
Q Consensus        77 ~dvli~a~tGsGKT~~~   93 (134)
                      +++++.|++|+|||...
T Consensus         1 k~I~liG~~GsGKsTi~   17 (161)
T d1viaa_           1 KNIVFIGFMGSGKSTLA   17 (161)
T ss_dssp             CCEEEECCTTSCHHHHH
T ss_pred             CcEEEECCCCCCHHHHH
Confidence            57899999999999763

>d1tf7a1 c.37.1.11 (A:14-255) Circadian clock protein KaiC {Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Circadian clock protein KaiC
species: Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]

Probab=91.69  E-value=0.098  Score=34.42  Aligned_cols=20  Identities=35%  Similarity=0.591  Sum_probs=16.2

Q ss_pred             cCCCeEEEcCCCCchhHHhH
Q psy7268          75 SGKSAILVAETGCGKTLSFL   94 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~~   94 (134)
                      .|.-+++.|++|+|||...+
T Consensus        25 ~G~~~~I~G~~G~GKT~la~   44 (242)
T d1tf7a1          25 IGRSTLVSGTSGTGKTLFSI   44 (242)
T ss_dssp             TTSEEEEEESTTSSHHHHHH
T ss_pred             CCeEEEEEeCCCCCHHHHHH
Confidence            45678999999999996653

>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=91.55  E-value=0.022  Score=38.83  Aligned_cols=15  Identities=27%  Similarity=0.164  Sum_probs=12.2

Q ss_pred             eEEEcCCCCchhHHh
Q psy7268          79 AILVAETGCGKTLSF   93 (134)
Q Consensus        79 vli~a~tGsGKT~~~   93 (134)
                      +++.||+|+|||...
T Consensus        49 l~l~GppGtGKT~l~   63 (287)
T d1w5sa2          49 YGSIGRVGIGKTTLA   63 (287)
T ss_dssp             EECTTCCSSSHHHHH
T ss_pred             EEeECCCCCCHHHHH
Confidence            456799999999774

>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=91.38  E-value=0.047  Score=34.49  Aligned_cols=15  Identities=27%  Similarity=0.448  Sum_probs=13.1

Q ss_pred             eEEEcCCCCchhHHh
Q psy7268          79 AILVAETGCGKTLSF   93 (134)
Q Consensus        79 vli~a~tGsGKT~~~   93 (134)
                      +++.|++|||||...
T Consensus         9 ivl~G~~GsGKsT~a   23 (171)
T d1knqa_           9 YVLMGVSGSGKSAVA   23 (171)
T ss_dssp             EEEECSTTSCHHHHH
T ss_pred             EEEECCCCCCHHHHH
Confidence            678999999999775

>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=91.33  E-value=0.04  Score=39.36  Aligned_cols=19  Identities=16%  Similarity=0.358  Sum_probs=16.3

Q ss_pred             cCCCeEEEcCCCCchhHHh
Q psy7268          75 SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~   93 (134)
                      .+.++++.|++|+|||+..
T Consensus        27 ~~h~vLl~G~pG~GKT~la   45 (333)
T d1g8pa_          27 GIGGVLVFGDRGTGKSTAV   45 (333)
T ss_dssp             GGCCEEEECCGGGCTTHHH
T ss_pred             CCCeEEEECCCCccHHHHH
Confidence            4568999999999999764

>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=91.31  E-value=0.047  Score=35.53  Aligned_cols=15  Identities=27%  Similarity=0.388  Sum_probs=12.8

Q ss_pred             eEEEcCCCCchhHHh
Q psy7268          79 AILVAETGCGKTLSF   93 (134)
Q Consensus        79 vli~a~tGsGKT~~~   93 (134)
                      ++++|++|||||...
T Consensus        17 iil~G~pGsGKST~a   31 (172)
T d1yj5a2          17 VVAVGFPGAGKSTFI   31 (172)
T ss_dssp             EEEECCTTSSHHHHH
T ss_pred             EEEECCCCCCHHHHH
Confidence            788999999999643

>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=91.17  E-value=0.047  Score=37.87  Aligned_cols=16  Identities=38%  Similarity=0.598  Sum_probs=14.3

Q ss_pred             CCeEEEcCCCCchhHH
Q psy7268          77 KSAILVAETGCGKTLS   92 (134)
Q Consensus        77 ~dvli~a~tGsGKT~~   92 (134)
                      +.+++.||+|+|||+.
T Consensus        39 ~giLL~GppGtGKT~l   54 (258)
T d1e32a2          39 RGILLYGPPGTGKTLI   54 (258)
T ss_dssp             CEEEEECCTTSSHHHH
T ss_pred             ceeEEecCCCCCchHH
Confidence            5799999999999975

>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=91.15  E-value=0.026  Score=35.75  Aligned_cols=19  Identities=21%  Similarity=0.202  Sum_probs=16.1

Q ss_pred             cCCCeEEEcCCCCchhHHh
Q psy7268          75 SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~   93 (134)
                      +|.-|++.|++|+|||...
T Consensus         5 ~g~~I~l~G~~GsGKTTia   23 (183)
T d1m8pa3           5 QGFTIFLTGYMNSGKDAIA   23 (183)
T ss_dssp             CCEEEEEECSTTSSHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHH
Confidence            5667889999999999775

>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=91.12  E-value=0.091  Score=35.10  Aligned_cols=38  Identities=16%  Similarity=0.256  Sum_probs=25.1

Q ss_pred             hHHHHHHHHHHH----cCC---CeEEEcCCCCchhHHhHHHHHHHH
Q psy7268          63 TEIQKYSIPTLL----SGK---SAILVAETGCGKTLSFLAPLVQQI  101 (134)
Q Consensus        63 t~iQ~~~i~~~~----~g~---dvli~a~tGsGKT~~~~lpil~~~  101 (134)
                      +|+|..++..+.    +++   .+++.||.|+|||... ..++..+
T Consensus         4 yPw~~~~~~~l~~~~~~~~l~h~lLl~Gp~G~GKtt~a-~~~a~~l   48 (207)
T d1a5ta2           4 YPWLRPDFEKLVASYQAGRGHHALLIQALPGMGDDALI-YALSRYL   48 (207)
T ss_dssp             CGGGHHHHHHHHHHHHTTCCCSEEEEECCTTSCHHHHH-HHHHHHH
T ss_pred             CcccHHHHHHHHHHHHcCCcCeEEEEECCCCCcHHHHH-HHHHHhc
Confidence            466666666543    444   3899999999999765 3334444

>d1bg2a_ c.37.1.9 (A:) Kinesin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.12  E-value=0.096  Score=37.45  Aligned_cols=24  Identities=25%  Similarity=0.425  Sum_probs=19.7

Q ss_pred             HHHHHcCCC--eEEEcCCCCchhHHh
Q psy7268          70 IPTLLSGKS--AILVAETGCGKTLSF   93 (134)
Q Consensus        70 i~~~~~g~d--vli~a~tGsGKT~~~   93 (134)
                      ++.+++|.+  ++.-|+||||||...
T Consensus        68 v~~~l~G~n~~i~aYGqtgSGKTyT~   93 (323)
T d1bg2a_          68 VKDVLEGYNGTIFAYGQTSSGKTHTM   93 (323)
T ss_dssp             HHHHHTTCCEEEEEECSTTSSHHHHH
T ss_pred             HHHHHcCCCcceeeecccCCCCceec
Confidence            455678987  788899999999885

>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=90.95  E-value=0.054  Score=34.14  Aligned_cols=18  Identities=22%  Similarity=0.233  Sum_probs=14.6

Q ss_pred             CCCeEEEcCCCCchhHHh
Q psy7268          76 GKSAILVAETGCGKTLSF   93 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~   93 (134)
                      .+=|++.|++|||||...
T Consensus         3 ~kiI~l~G~~GsGKsTva   20 (178)
T d1qhxa_           3 TRMIILNGGSSAGKSGIV   20 (178)
T ss_dssp             CCEEEEECCTTSSHHHHH
T ss_pred             CeEEEEECCCCCCHHHHH
Confidence            455788899999999664

>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=90.75  E-value=0.18  Score=33.86  Aligned_cols=25  Identities=20%  Similarity=0.278  Sum_probs=17.9

Q ss_pred             CeEEEcCCCCchhHHhHHHHHHHHHh
Q psy7268          78 SAILVAETGCGKTLSFLAPLVQQILT  103 (134)
Q Consensus        78 dvli~a~tGsGKT~~~~lpil~~~~~  103 (134)
                      .+++.||+|+|||- .+.++.+....
T Consensus        38 ~l~l~G~~G~GKTH-Ll~A~~~~~~~   62 (213)
T d1l8qa2          38 PIFIYGSVGTGKTH-LLQAAGNEAKK   62 (213)
T ss_dssp             SEEEECSSSSSHHH-HHHHHHHHHHH
T ss_pred             cEEEECCCCCcHHH-HHHHHHHHhcc
Confidence            48999999999993 33455555543

>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=90.55  E-value=0.062  Score=34.20  Aligned_cols=22  Identities=32%  Similarity=0.587  Sum_probs=16.0

Q ss_pred             eEEEcCCCCchhHHhHHHHHHHH
Q psy7268          79 AILVAETGCGKTLSFLAPLVQQI  101 (134)
Q Consensus        79 vli~a~tGsGKT~~~~lpil~~~  101 (134)
                      +++.||+|+|||.. +-.++..+
T Consensus         3 i~I~G~~G~GKSTL-l~~i~~~l   24 (178)
T d1ye8a1           3 IIITGEPGVGKTTL-VKKIVERL   24 (178)
T ss_dssp             EEEECCTTSSHHHH-HHHHHHHH
T ss_pred             EEEECCCCcHHHHH-HHHHHhcC
Confidence            78999999999974 33444444

>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=90.54  E-value=0.19  Score=31.72  Aligned_cols=23  Identities=22%  Similarity=0.206  Sum_probs=15.5

Q ss_pred             EEEcCCCCchhHHhHHHHHHHHHh
Q psy7268          80 ILVAETGCGKTLSFLAPLVQQILT  103 (134)
Q Consensus        80 li~a~tGsGKT~~~~lpil~~~~~  103 (134)
                      -|.|+.|||||.. +--++..+..
T Consensus         5 ~I~G~~gSGKTTl-i~~l~~~L~~   27 (165)
T d1xjca_           5 QVVGYKHSGKTTL-MEKWVAAAVR   27 (165)
T ss_dssp             EEECCTTSSHHHH-HHHHHHHHHH
T ss_pred             EEEeCCCCCHHHH-HHHHHHHHHh
Confidence            4889999999954 3444555443

>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=90.20  E-value=0.034  Score=35.97  Aligned_cols=18  Identities=33%  Similarity=0.392  Sum_probs=14.7

Q ss_pred             CCCeEEEcCCCCchhHHh
Q psy7268          76 GKSAILVAETGCGKTLSF   93 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~   93 (134)
                      |.-+++.|++|||||...
T Consensus        19 g~vI~L~G~pGSGKTTiA   36 (195)
T d1x6va3          19 GCTVWLTGLSGAGKTTVS   36 (195)
T ss_dssp             CEEEEEESSCHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHH
Confidence            446778999999999765

>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=89.81  E-value=0.067  Score=37.26  Aligned_cols=18  Identities=39%  Similarity=0.702  Sum_probs=15.3

Q ss_pred             CCCeEEEcCCCCchhHHh
Q psy7268          76 GKSAILVAETGCGKTLSF   93 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~   93 (134)
                      .+.+++.||+|+|||...
T Consensus        41 ~~giLL~Gp~GtGKT~l~   58 (265)
T d1r7ra3          41 SKGVLFYGPPGCGKTLLA   58 (265)
T ss_dssp             CCEEEEBCCTTSSHHHHH
T ss_pred             CCeEEEECCCCCcchhHH
Confidence            467999999999999763

>d1goja_ c.37.1.9 (A:) Kinesin {Neurospora crassa [TaxId: 5141]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Neurospora crassa [TaxId: 5141]

Probab=89.36  E-value=0.15  Score=36.90  Aligned_cols=24  Identities=25%  Similarity=0.563  Sum_probs=18.9

Q ss_pred             HHHHHcCCC--eEEEcCCCCchhHHh
Q psy7268          70 IPTLLSGKS--AILVAETGCGKTLSF   93 (134)
Q Consensus        70 i~~~~~g~d--vli~a~tGsGKT~~~   93 (134)
                      +..++.|.+  ++.-|+||||||...
T Consensus        72 v~~~l~G~n~ti~aYG~tgSGKT~Tm   97 (354)
T d1goja_          72 VDDILNGYNGTVFAYGQTGAGKSYTM   97 (354)
T ss_dssp             HHHHTTTCCEEEEEECSTTSSHHHHH
T ss_pred             HHHhhccCceeEEecccCCCCcceee
Confidence            345568887  777899999999774

>d1w36b1 c.37.1.19 (B:1-485) Exodeoxyribonuclease V beta chain (RecB), N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Exodeoxyribonuclease V beta chain (RecB), N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=89.33  E-value=0.5  Score=34.23  Aligned_cols=52  Identities=19%  Similarity=0.287  Sum_probs=29.7

Q ss_pred             CeEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcHHHH
Q psy7268          78 SAILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGRELV  129 (134)
Q Consensus        78 dvli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La  129 (134)
                      .++|.|.-|||||.+..-=++..+............-.--++|+|+=|+.=|
T Consensus        18 ~~lv~A~AGsGKT~~l~~r~~~ll~~~~~~~~~~~~~~~~~IL~lTFT~kAA   69 (485)
T d1w36b1          18 ERLIEASAGTGKTFTIAALYLRLLLGLGGSAAFPRPLTVEELLVVTFTEAAT   69 (485)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHHHTTCSSSSSCSSCCCGGGEEEEESCHHHH
T ss_pred             CeEEEEcCchHHHHHHHHHHHHHHhhCcccccccCCCCcccEeEeccHHHHH
Confidence            5789999999999887666666554322110000000112477777776433

>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=89.12  E-value=0.16  Score=32.52  Aligned_cols=19  Identities=26%  Similarity=0.277  Sum_probs=15.5

Q ss_pred             cCCCeEEEcCCCCchhHHh
Q psy7268          75 SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~   93 (134)
                      .|+-+++.|++|+|||...
T Consensus        22 ~G~v~~i~G~~GsGKT~l~   40 (242)
T d1n0wa_          22 TGSITEMFGEFRTGKTQIC   40 (242)
T ss_dssp             TTSEEEEECCTTSSHHHHH
T ss_pred             CCEEEEEEeCCCCCHHHHH
Confidence            3566899999999999654

>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=89.08  E-value=0.1  Score=33.81  Aligned_cols=18  Identities=33%  Similarity=0.528  Sum_probs=15.0

Q ss_pred             CCCeEEEcCCCCchhHHh
Q psy7268          76 GKSAILVAETGCGKTLSF   93 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~   93 (134)
                      |-.+++.||+|||||...
T Consensus         3 ~~riil~G~pGSGKsT~a   20 (190)
T d1ak2a1           3 GVRAVLLGPPGAGKGTQA   20 (190)
T ss_dssp             CCEEEEECCTTSSHHHHH
T ss_pred             ccEEEEECCCCCCHHHHH
Confidence            556888999999999764

>d2zfia1 c.37.1.9 (A:4-352) Kinesin {Mouse (Mus musculus), kif1a [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Mouse (Mus musculus), kif1a [TaxId: 10090]

Probab=88.87  E-value=0.19  Score=36.29  Aligned_cols=24  Identities=21%  Similarity=0.457  Sum_probs=19.5

Q ss_pred             HHHHHcCCC--eEEEcCCCCchhHHh
Q psy7268          70 IPTLLSGKS--AILVAETGCGKTLSF   93 (134)
Q Consensus        70 i~~~~~g~d--vli~a~tGsGKT~~~   93 (134)
                      +..+++|.+  ++.-|.||||||...
T Consensus        79 v~~~l~G~n~ti~aYGqTgSGKT~Tm  104 (349)
T d2zfia1          79 LQHAFEGYNVCIFAYGQTGAGKSYTM  104 (349)
T ss_dssp             HHHHHTTCCEEEEEECSTTSSHHHHH
T ss_pred             HHHHHhccCceeeeeccCCCCCceee
Confidence            445678987  777899999999885

>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=88.85  E-value=0.11  Score=34.05  Aligned_cols=16  Identities=25%  Similarity=0.538  Sum_probs=13.6

Q ss_pred             CCeEEEcCCCCchhHH
Q psy7268          77 KSAILVAETGCGKTLS   92 (134)
Q Consensus        77 ~dvli~a~tGsGKT~~   92 (134)
                      +-+++.||+|+|||..
T Consensus         1 rpIvl~GPsGsGK~tl   16 (190)
T d1lvga_           1 RPVVLSGPSGAGKSTL   16 (190)
T ss_dssp             CCEEEECCTTSSHHHH
T ss_pred             CeEEEECCCCCCHHHH
Confidence            3588999999999964

>d1v8ka_ c.37.1.9 (A:) Kinesin {Mouse (Mus musculus), kif2c [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Mouse (Mus musculus), kif2c [TaxId: 10090]

Probab=88.80  E-value=0.18  Score=36.69  Aligned_cols=24  Identities=29%  Similarity=0.558  Sum_probs=18.7

Q ss_pred             HHHHHcCCC--eEEEcCCCCchhHHh
Q psy7268          70 IPTLLSGKS--AILVAETGCGKTLSF   93 (134)
Q Consensus        70 i~~~~~g~d--vli~a~tGsGKT~~~   93 (134)
                      +..+++|.+  ++.-|.||||||...
T Consensus       106 v~~~l~G~n~tifaYGqTGSGKTyTm  131 (362)
T d1v8ka_         106 VQTIFEGGKATCFAYGQTGSGKTHTM  131 (362)
T ss_dssp             HHHHHTTCEEEEEEEESTTSSHHHHH
T ss_pred             HHHHHhccCceEEeeccCCCCCceee
Confidence            345678887  667799999999775

>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=88.74  E-value=0.12  Score=33.07  Aligned_cols=18  Identities=28%  Similarity=0.473  Sum_probs=14.9

Q ss_pred             CCCeEEEcCCCCchhHHh
Q psy7268          76 GKSAILVAETGCGKTLSF   93 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~   93 (134)
                      .+.+++.|++|+|||...
T Consensus         2 ~~~Iil~G~~GsGKSTia   19 (170)
T d1e6ca_           2 TEPIFMVGARGCGMTTVG   19 (170)
T ss_dssp             CCCEEEESCTTSSHHHHH
T ss_pred             CCCEEEECCCCCCHHHHH
Confidence            356889999999998764

>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=88.72  E-value=0.11  Score=33.57  Aligned_cols=17  Identities=24%  Similarity=0.501  Sum_probs=14.7

Q ss_pred             CCCeEEEcCCCCchhHH
Q psy7268          76 GKSAILVAETGCGKTLS   92 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~   92 (134)
                      |+=+++.||+|+||+..
T Consensus         2 G~iivl~GpsG~GK~tl   18 (182)
T d1znwa1           2 GRVVVLSGPSAVGKSTV   18 (182)
T ss_dssp             CCEEEEECSTTSSHHHH
T ss_pred             CeEEEEECCCCCCHHHH
Confidence            56688999999999965

>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=88.68  E-value=0.11  Score=34.37  Aligned_cols=19  Identities=26%  Similarity=0.275  Sum_probs=15.6

Q ss_pred             cCCCeEEEcCCCCchhHHh
Q psy7268          75 SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~   93 (134)
                      .|+-+++.|++|+|||...
T Consensus        33 ~G~~~li~G~pGsGKT~l~   51 (251)
T d1szpa2          33 TGSITELFGEFRTGKSQLC   51 (251)
T ss_dssp             SSSEEEEEESTTSSHHHHH
T ss_pred             CCeEEEEEcCCCCCHHHHH
Confidence            4567999999999999654

>d1sdma_ c.37.1.9 (A:) Kinesin heavy chain-like protein {Potato (Solanum tuberosum) [TaxId: 4113]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin heavy chain-like protein
species: Potato (Solanum tuberosum) [TaxId: 4113]

Probab=88.32  E-value=0.16  Score=36.92  Aligned_cols=25  Identities=24%  Similarity=0.466  Sum_probs=20.6

Q ss_pred             HHHHHHcCCC--eEEEcCCCCchhHHh
Q psy7268          69 SIPTLLSGKS--AILVAETGCGKTLSF   93 (134)
Q Consensus        69 ~i~~~~~g~d--vli~a~tGsGKT~~~   93 (134)
                      .+..++.|.|  ++.-|.||||||...
T Consensus        66 lv~~~l~G~n~~i~aYGqTGSGKTyTm   92 (364)
T d1sdma_          66 LVQSAVDGYNVCIFAYGQTGSGKTFTI   92 (364)
T ss_dssp             HHHHHHTTCEEEEEEECSTTSSHHHHH
T ss_pred             HHHHHhcCCceeeeccccCCCCccccc
Confidence            4667788987  677799999999885

>d2ncda_ c.37.1.9 (A:) Kinesin motor Ncd (non-claret disjunctional) {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin motor Ncd (non-claret disjunctional)
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=88.29  E-value=0.16  Score=36.96  Aligned_cols=25  Identities=32%  Similarity=0.489  Sum_probs=20.6

Q ss_pred             HHHHHHcCCC--eEEEcCCCCchhHHh
Q psy7268          69 SIPTLLSGKS--AILVAETGCGKTLSF   93 (134)
Q Consensus        69 ~i~~~~~g~d--vli~a~tGsGKT~~~   93 (134)
                      .+..++.|.+  ++.-|+||||||...
T Consensus       116 lv~~vl~G~n~ti~aYGqtGSGKT~Tm  142 (368)
T d2ncda_         116 LIQSALDGYNICIFAYGQTGSGKTYTM  142 (368)
T ss_dssp             HHHHHHTTCEEEEEEECSTTSSHHHHH
T ss_pred             HHHHHhcccceeEEeeccCCCccceEe
Confidence            5567788987  777899999999874

>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=88.28  E-value=0.11  Score=33.72  Aligned_cols=16  Identities=13%  Similarity=0.262  Sum_probs=13.4

Q ss_pred             CeEEEcCCCCchhHHh
Q psy7268          78 SAILVAETGCGKTLSF   93 (134)
Q Consensus        78 dvli~a~tGsGKT~~~   93 (134)
                      .+++.||+|||||...
T Consensus         5 ~I~i~GppGsGKsT~a   20 (189)
T d1zaka1           5 KVMISGAPASGKGTQC   20 (189)
T ss_dssp             CEEEEESTTSSHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            4789999999998754

>d1x88a1 c.37.1.9 (A:18-362) Kinesin {Human (Homo sapiens), mitotic kinesin eg5 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Human (Homo sapiens), mitotic kinesin eg5 [TaxId: 9606]

Probab=88.26  E-value=0.18  Score=36.28  Aligned_cols=25  Identities=24%  Similarity=0.466  Sum_probs=19.7

Q ss_pred             HHHHHHcCCC--eEEEcCCCCchhHHh
Q psy7268          69 SIPTLLSGKS--AILVAETGCGKTLSF   93 (134)
Q Consensus        69 ~i~~~~~g~d--vli~a~tGsGKT~~~   93 (134)
                      .+..+++|.+  ++.-|.||||||...
T Consensus        72 lv~~~l~G~n~~i~aYGqtgSGKTyTm   98 (345)
T d1x88a1          72 ILDEVIMGYNCTIFAYGQTGTGKTFTM   98 (345)
T ss_dssp             HHHHHHTTCEEEEEEEECTTSSHHHHH
T ss_pred             hHHHHhccCCceEEeeeeccccceEEe
Confidence            3455678987  678899999999773

>d1s96a_ c.37.1.1 (A:) Guanylate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Escherichia coli [TaxId: 562]

Probab=88.12  E-value=0.13  Score=34.41  Aligned_cols=19  Identities=32%  Similarity=0.457  Sum_probs=15.4

Q ss_pred             cCCCeEEEcCCCCchhHHh
Q psy7268          75 SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~   93 (134)
                      +|+=++++||+|+||+...
T Consensus         1 ~G~livi~GPSG~GK~tl~   19 (205)
T d1s96a_           1 QGTLYIVSAPSGAGKSSLI   19 (205)
T ss_dssp             CCCEEEEECCTTSCHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHH
Confidence            3666889999999999553

>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=88.10  E-value=0.11  Score=33.68  Aligned_cols=15  Identities=20%  Similarity=0.401  Sum_probs=12.9

Q ss_pred             eEEEcCCCCchhHHh
Q psy7268          79 AILVAETGCGKTLSF   93 (134)
Q Consensus        79 vli~a~tGsGKT~~~   93 (134)
                      +++.||+|||||...
T Consensus         9 I~i~G~pGSGKsT~a   23 (194)
T d1qf9a_           9 VFVLGGPGSGKGTQC   23 (194)
T ss_dssp             EEEEESTTSSHHHHH
T ss_pred             EEEECCCCCCHHHHH
Confidence            688999999999753

>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=88.05  E-value=0.12  Score=32.92  Aligned_cols=15  Identities=27%  Similarity=0.394  Sum_probs=13.3

Q ss_pred             eEEEcCCCCchhHHh
Q psy7268          79 AILVAETGCGKTLSF   93 (134)
Q Consensus        79 vli~a~tGsGKT~~~   93 (134)
                      +++.||+|||||...
T Consensus         3 I~i~G~pGSGKsT~a   17 (182)
T d1zina1           3 LVLMGLPGAGKGTQA   17 (182)
T ss_dssp             EEEECSTTSSHHHHH
T ss_pred             EEEECCCCCCHHHHH
Confidence            789999999999765

>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=87.47  E-value=0.13  Score=33.08  Aligned_cols=16  Identities=25%  Similarity=0.438  Sum_probs=13.6

Q ss_pred             CeEEEcCCCCchhHHh
Q psy7268          78 SAILVAETGCGKTLSF   93 (134)
Q Consensus        78 dvli~a~tGsGKT~~~   93 (134)
                      .+++.||+|||||...
T Consensus         2 ~I~i~G~pGsGKsT~a   17 (181)
T d2cdna1           2 RVLLLGPPGAGKGTQA   17 (181)
T ss_dssp             EEEEECCTTSSHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            4788999999999764

>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=87.43  E-value=0.14  Score=32.27  Aligned_cols=17  Identities=29%  Similarity=0.390  Sum_probs=13.6

Q ss_pred             CCeEEEcCCCCchhHHh
Q psy7268          77 KSAILVAETGCGKTLSF   93 (134)
Q Consensus        77 ~dvli~a~tGsGKT~~~   93 (134)
                      +=+++.|++|+|||...
T Consensus         2 kiI~i~G~~GsGKsT~~   18 (190)
T d1khta_           2 KVVVVTGVPGVGSTTSS   18 (190)
T ss_dssp             CEEEEECCTTSCHHHHH
T ss_pred             CEEEEECCCCCCHHHHH
Confidence            34788999999999653

>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=87.33  E-value=0.14  Score=33.27  Aligned_cols=15  Identities=20%  Similarity=0.390  Sum_probs=12.6

Q ss_pred             eEEEcCCCCchhHHh
Q psy7268          79 AILVAETGCGKTLSF   93 (134)
Q Consensus        79 vli~a~tGsGKT~~~   93 (134)
                      +++.||+|||||...
T Consensus        11 I~i~GppGSGKsT~a   25 (196)
T d1ukza_          11 IFVLGGPGAGKGTQC   25 (196)
T ss_dssp             EEEECSTTSSHHHHH
T ss_pred             EEEECCCCCCHHHHH
Confidence            778899999998654

>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=87.30  E-value=0.18  Score=33.63  Aligned_cols=20  Identities=25%  Similarity=0.187  Sum_probs=16.1

Q ss_pred             cCCCeEEEcCCCCchhHHhH
Q psy7268          75 SGKSAILVAETGCGKTLSFL   94 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~~   94 (134)
                      .|+-+++.|++|+|||...+
T Consensus        35 ~G~~~li~G~pGsGKT~~~l   54 (254)
T d1pzna2          35 TQAITEVFGEFGSGKTQLAH   54 (254)
T ss_dssp             SSEEEEEEESTTSSHHHHHH
T ss_pred             CCEEEEEEcCCCCCHHHHHH
Confidence            34568999999999996653

>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=87.29  E-value=0.56  Score=32.70  Aligned_cols=27  Identities=33%  Similarity=0.463  Sum_probs=19.5

Q ss_pred             CCCeEEEcCCCCchhHHhHHHHHHHHHh
Q psy7268          76 GKSAILVAETGCGKTLSFLAPLVQQILT  103 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~~lpil~~~~~  103 (134)
                      ..+++++|++|.|||... -.+..++..
T Consensus        39 k~n~lLVG~~GvGKTalv-~~la~ri~~   65 (268)
T d1r6bx2          39 KNNPLLVGESGVGKTAIA-EGLAWRIVQ   65 (268)
T ss_dssp             SCEEEEECCTTSSHHHHH-HHHHHHHHH
T ss_pred             cCCcEEECCCCCcHHHHH-HHHHHHHHh
Confidence            357999999999999543 445555554

>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=87.12  E-value=0.15  Score=32.79  Aligned_cols=15  Identities=27%  Similarity=0.403  Sum_probs=13.1

Q ss_pred             eEEEcCCCCchhHHh
Q psy7268          79 AILVAETGCGKTLSF   93 (134)
Q Consensus        79 vli~a~tGsGKT~~~   93 (134)
                      +++.||+|||||...
T Consensus         3 I~i~G~pGSGKsT~a   17 (182)
T d1s3ga1           3 IVLMGLPGAGKGTQA   17 (182)
T ss_dssp             EEEECSTTSSHHHHH
T ss_pred             EEEECCCCCCHHHHH
Confidence            688999999999764

>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=87.12  E-value=0.14  Score=32.78  Aligned_cols=16  Identities=25%  Similarity=0.250  Sum_probs=13.4

Q ss_pred             CeEEEcCCCCchhHHh
Q psy7268          78 SAILVAETGCGKTLSF   93 (134)
Q Consensus        78 dvli~a~tGsGKT~~~   93 (134)
                      .+++.||+|||||...
T Consensus         2 ~I~i~G~pGSGKsT~~   17 (179)
T d1e4va1           2 RIILLGAPVAGKGTQA   17 (179)
T ss_dssp             EEEEEESTTSSHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            3678999999999864

>d1ny5a2 c.37.1.20 (A:138-384) Transcriptional activator sigm54 (NtrC1), C-terminal domain {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Transcriptional activator sigm54 (NtrC1), C-terminal domain
species: Aquifex aeolicus [TaxId: 63363]

Probab=86.75  E-value=0.33  Score=33.24  Aligned_cols=20  Identities=20%  Similarity=0.376  Sum_probs=16.5

Q ss_pred             HcCCCeEEEcCCCCchhHHh
Q psy7268          74 LSGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        74 ~~g~dvli~a~tGsGKT~~~   93 (134)
                      ..+..|++.|++|+||+...
T Consensus        21 ~~~~pvlI~Ge~GtGK~~~A   40 (247)
T d1ny5a2          21 CAECPVLITGESGVGKEVVA   40 (247)
T ss_dssp             TCCSCEEEECSTTSSHHHHH
T ss_pred             CCCCCEEEECCCCcCHHHHH
Confidence            35678999999999998653

>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=86.66  E-value=0.16  Score=32.91  Aligned_cols=15  Identities=27%  Similarity=0.275  Sum_probs=13.1

Q ss_pred             eEEEcCCCCchhHHh
Q psy7268          79 AILVAETGCGKTLSF   93 (134)
Q Consensus        79 vli~a~tGsGKT~~~   93 (134)
                      ++++|.+|||||..+
T Consensus         5 i~l~GlpgsGKSTla   19 (213)
T d1bifa1           5 IVMVGLPARGKTYIS   19 (213)
T ss_dssp             EEEECCTTSSHHHHH
T ss_pred             EEEECCCCCCHHHHH
Confidence            578899999999775

>d1kgda_ c.37.1.1 (A:) Guanylate kinase-like domain of Cask {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase-like domain of Cask
species: Human (Homo sapiens) [TaxId: 9606]

Probab=86.46  E-value=0.18  Score=32.81  Aligned_cols=18  Identities=22%  Similarity=0.377  Sum_probs=14.6

Q ss_pred             CCCeEEEcCCCCchhHHh
Q psy7268          76 GKSAILVAETGCGKTLSF   93 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~   93 (134)
                      .+-+++.||+|+||+...
T Consensus         3 ~k~ivl~Gpsg~GK~tl~   20 (178)
T d1kgda_           3 RKTLVLLGAHGVGRRHIK   20 (178)
T ss_dssp             CCEEEEECCTTSSHHHHH
T ss_pred             CCcEEEECCCCCCHHHHH
Confidence            356889999999999653

>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=86.46  E-value=0.38  Score=31.14  Aligned_cols=25  Identities=24%  Similarity=0.291  Sum_probs=15.5

Q ss_pred             CeEEEcC-CCCchhHHhHHHHHHHHHh
Q psy7268          78 SAILVAE-TGCGKTLSFLAPLVQQILT  103 (134)
Q Consensus        78 dvli~a~-tGsGKT~~~~lpil~~~~~  103 (134)
                      .++|++- ||.|||..- .-+...+.+
T Consensus         3 ~~~i~gt~~GVGKTtvs-~~La~aLa~   28 (224)
T d1byia_           3 RYFVTGTDTEVGKTVAS-CALLQAAKA   28 (224)
T ss_dssp             EEEEEESSTTSCHHHHH-HHHHHHHHH
T ss_pred             eEEEEECCCCccHHHHH-HHHHHHHHH
Confidence            4566666 699999775 333444433

>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=86.23  E-value=0.2  Score=32.52  Aligned_cols=21  Identities=29%  Similarity=0.358  Sum_probs=16.6

Q ss_pred             HHcCCCeEEEcCCCCchhHHh
Q psy7268          73 LLSGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        73 ~~~g~dvli~a~tGsGKT~~~   93 (134)
                      +..++-+++.||+||||+...
T Consensus         5 ~~~~~iI~l~G~pGSGKsT~a   25 (194)
T d3adka_           5 LKKSKIIFVVGGPGSGKGTQC   25 (194)
T ss_dssp             HHTSCEEEEEECTTSSHHHHH
T ss_pred             ccCCcEEEEECCCCCCHHHHH
Confidence            345667889999999999754

>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=86.19  E-value=0.16  Score=32.73  Aligned_cols=16  Identities=25%  Similarity=0.455  Sum_probs=13.4

Q ss_pred             CeEEEcCCCCchhHHh
Q psy7268          78 SAILVAETGCGKTLSF   93 (134)
Q Consensus        78 dvli~a~tGsGKT~~~   93 (134)
                      -+++.||+|||||...
T Consensus         4 rIvl~G~pGSGKtT~a   19 (180)
T d1akya1           4 RMVLIGPPGAGKGTQA   19 (180)
T ss_dssp             EEEEECCTTSSHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            3778899999999764

>d1qvra2 c.37.1.20 (A:149-535) ClpB, AAA+ modules {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Thermus thermophilus [TaxId: 274]

Probab=86.17  E-value=1.4  Score=32.14  Aligned_cols=36  Identities=33%  Similarity=0.524  Sum_probs=23.2

Q ss_pred             HHHHHHHH--cCCCeEEEcCCCCchhHHhHHHHHHHHHh
Q psy7268          67 KYSIPTLL--SGKSAILVAETGCGKTLSFLAPLVQQILT  103 (134)
Q Consensus        67 ~~~i~~~~--~g~dvli~a~tGsGKT~~~~lpil~~~~~  103 (134)
                      .+.+..+.  ...|+++.|++|.|||... -.+.+++..
T Consensus        32 ~~~~~~L~r~~k~n~llvG~~GvGKtaiv-~~la~~i~~   69 (387)
T d1qvra2          32 RRVIQILLRRTKNNPVLIGEPGVGKTAIV-EGLAQRIVK   69 (387)
T ss_dssp             HHHHHHHHCSSCCCCEEEECTTSCHHHHH-HHHHHHHHH
T ss_pred             HHHHHHHhcCCCCCCeEECCCCCCHHHHH-HHHHHHHHh
Confidence            34444444  3447999999999999553 344555554

>d1sgwa_ c.37.1.12 (A:) Putative ABC transporter PF0895 {Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Putative ABC transporter PF0895
species: Pyrococcus furiosus [TaxId: 2261]

Probab=85.93  E-value=0.23  Score=33.09  Aligned_cols=19  Identities=26%  Similarity=0.365  Sum_probs=15.9

Q ss_pred             cCCCeEEEcCCCCchhHHh
Q psy7268          75 SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~   93 (134)
                      .|.-+.+.||+|+|||..+
T Consensus        26 ~Gei~~l~G~NGsGKSTLl   44 (200)
T d1sgwa_          26 KGNVVNFHGPNGIGKTTLL   44 (200)
T ss_dssp             TTCCEEEECCTTSSHHHHH
T ss_pred             CCCEEEEECCCCChHHHHH
Confidence            5777889999999999654

>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=85.68  E-value=0.18  Score=32.15  Aligned_cols=15  Identities=20%  Similarity=-0.017  Sum_probs=11.9

Q ss_pred             eEEEcCCCCchhHHh
Q psy7268          79 AILVAETGCGKTLSF   93 (134)
Q Consensus        79 vli~a~tGsGKT~~~   93 (134)
                      |-|.|++|||||...
T Consensus        25 IgI~G~~GSGKSTla   39 (198)
T d1rz3a_          25 LGIDGLSRSGKTTLA   39 (198)
T ss_dssp             EEEEECTTSSHHHHH
T ss_pred             EEEECCCCCCHHHHH
Confidence            338899999999653

>d1f9va_ c.37.1.9 (A:) Kinesin motor Ncd (non-claret disjunctional) {Baker's yeast (Saccharomyces cerevisiae), Kar [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin motor Ncd (non-claret disjunctional)
species: Baker's yeast (Saccharomyces cerevisiae), Kar [TaxId: 4932]

Probab=85.68  E-value=0.26  Score=35.37  Aligned_cols=26  Identities=31%  Similarity=0.524  Sum_probs=20.2

Q ss_pred             HHHHHHcCCC--eEEEcCCCCchhHHhH
Q psy7268          69 SIPTLLSGKS--AILVAETGCGKTLSFL   94 (134)
Q Consensus        69 ~i~~~~~g~d--vli~a~tGsGKT~~~~   94 (134)
                      .+..++.|.+  ++.-|.||||||....
T Consensus        74 ~v~~~l~G~n~~i~aYGqtgSGKT~T~~  101 (342)
T d1f9va_          74 LVQSSLDGYNVCIFAYGQTGSGKTFTML  101 (342)
T ss_dssp             HHGGGGGTCCEEEEEECCTTSSHHHHHH
T ss_pred             hhcchhcccccceeeeeccCCccccccc
Confidence            4455678887  6778999999998763

>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=85.68  E-value=0.18  Score=31.95  Aligned_cols=15  Identities=27%  Similarity=0.485  Sum_probs=12.3

Q ss_pred             eEEEcCCCCchhHHh
Q psy7268          79 AILVAETGCGKTLSF   93 (134)
Q Consensus        79 vli~a~tGsGKT~~~   93 (134)
                      +++.|++|+|||...
T Consensus         4 ivi~G~~GsGKTT~~   18 (194)
T d1nksa_           4 GIVTGIPGVGKSTVL   18 (194)
T ss_dssp             EEEEECTTSCHHHHH
T ss_pred             EEEECCCCCCHHHHH
Confidence            467899999999654

>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=85.66  E-value=0.19  Score=32.41  Aligned_cols=15  Identities=20%  Similarity=0.410  Sum_probs=12.9

Q ss_pred             eEEEcCCCCchhHHh
Q psy7268          79 AILVAETGCGKTLSF   93 (134)
Q Consensus        79 vli~a~tGsGKT~~~   93 (134)
                      +++.||+|||||...
T Consensus         4 I~i~GppGSGKsT~a   18 (194)
T d1teva_           4 VFVLGGPGAGKGTQC   18 (194)
T ss_dssp             EEEECCTTSSHHHHH
T ss_pred             EEEECCCCCCHHHHH
Confidence            678899999998764

>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=85.66  E-value=0.19  Score=32.80  Aligned_cols=16  Identities=25%  Similarity=0.349  Sum_probs=13.7

Q ss_pred             CeEEEcCCCCchhHHh
Q psy7268          78 SAILVAETGCGKTLSF   93 (134)
Q Consensus        78 dvli~a~tGsGKT~~~   93 (134)
                      .+++.||+|||||...
T Consensus         8 rIiliG~PGSGKtT~a   23 (189)
T d2ak3a1           8 RAAIMGAPGSGKGTVS   23 (189)
T ss_dssp             EEEEECCTTSSHHHHH
T ss_pred             eEEEECCCCCCHHHHH
Confidence            5788999999999764

>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=85.42  E-value=0.22  Score=31.47  Aligned_cols=16  Identities=38%  Similarity=0.428  Sum_probs=13.5

Q ss_pred             CeEEEcCCCCchhHHh
Q psy7268          78 SAILVAETGCGKTLSF   93 (134)
Q Consensus        78 dvli~a~tGsGKT~~~   93 (134)
                      .+++.|++|+|||...
T Consensus         3 ~IvliG~~G~GKSTig   18 (165)
T d2iyva1           3 KAVLVGLPGSGKSTIG   18 (165)
T ss_dssp             SEEEECSTTSSHHHHH
T ss_pred             cEEEECCCCCCHHHHH
Confidence            4778899999999764

>d2gnoa2 c.37.1.20 (A:11-208) gamma subunit of DNA polymerase III, N-domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: gamma subunit of DNA polymerase III, N-domain
species: Thermotoga maritima [TaxId: 2336]

Probab=85.41  E-value=0.99  Score=29.64  Aligned_cols=35  Identities=17%  Similarity=0.133  Sum_probs=23.6

Q ss_pred             HHHHHHHHHc---CCCeEEEcCCCCchhHHhHHHHHHHH
Q psy7268          66 QKYSIPTLLS---GKSAILVAETGCGKTLSFLAPLVQQI  101 (134)
Q Consensus        66 Q~~~i~~~~~---g~dvli~a~tGsGKT~~~~lpil~~~  101 (134)
                      |.+.+..+..   +.++++.||.|+|||.... .+...+
T Consensus         2 ~~~~l~~~i~~~~~~~~l~~G~~g~gk~~~a~-~l~~~i   39 (198)
T d2gnoa2           2 QLETLKRIIEKSEGISILINGEDLSYPREVSL-ELPEYV   39 (198)
T ss_dssp             HHHHHHHHHHTCSSEEEEEECSSSSHHHHHHH-HHHHHH
T ss_pred             HHHHHHHHHhcCCCceEEEECCCCCCHHHHHH-HHHHHH
Confidence            5556665553   3469999999999997753 333444

>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=84.59  E-value=0.87  Score=30.65  Aligned_cols=32  Identities=34%  Similarity=0.614  Sum_probs=21.9

Q ss_pred             HHHHHcCCCeEEEcCCCCchhHHhHHHHHHHHH
Q psy7268          70 IPTLLSGKSAILVAETGCGKTLSFLAPLVQQIL  102 (134)
Q Consensus        70 i~~~~~g~dvli~a~tGsGKT~~~~lpil~~~~  102 (134)
                      ++-++.|.-.++.|++|+|||...+- +...+.
T Consensus        23 i~G~~pg~~~~i~G~~G~GKS~l~l~-la~~ia   54 (274)
T d1nlfa_          23 LPNMVAGTVGALVSPGGAGKSMLALQ-LAAQIA   54 (274)
T ss_dssp             ETTEETTSEEEEEESTTSSHHHHHHH-HHHHHH
T ss_pred             hCCccCCcEEEEEeCCCCCHHHHHHH-HHHHHH
Confidence            34455677788999999999966543 444443

>d1r6bx3 c.37.1.20 (X:437-751) ClpA, an Hsp100 chaperone, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpA, an Hsp100 chaperone, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=84.55  E-value=0.22  Score=35.38  Aligned_cols=17  Identities=35%  Similarity=0.432  Sum_probs=14.3

Q ss_pred             CeEEEcCCCCchhHHhH
Q psy7268          78 SAILVAETGCGKTLSFL   94 (134)
Q Consensus        78 dvli~a~tGsGKT~~~~   94 (134)
                      .++.+||||+|||...-
T Consensus        54 ~~lf~Gp~GvGKT~lak   70 (315)
T d1r6bx3          54 SFLFAGPTGVGKTEVTV   70 (315)
T ss_dssp             EEEEECSTTSSHHHHHH
T ss_pred             EEEEECCCcchhHHHHH
Confidence            48899999999997653

>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=84.47  E-value=0.19  Score=33.64  Aligned_cols=18  Identities=11%  Similarity=0.178  Sum_probs=14.9

Q ss_pred             CCCeEEEcCCCCchhHHh
Q psy7268          76 GKSAILVAETGCGKTLSF   93 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~   93 (134)
                      ++.+++.||.|+|||...
T Consensus        29 ~~~i~i~G~~G~GKTsLl   46 (283)
T d2fnaa2          29 APITLVLGLRRTGKSSII   46 (283)
T ss_dssp             SSEEEEEESTTSSHHHHH
T ss_pred             CCEEEEEcCCCCcHHHHH
Confidence            467899999999999543

>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=84.42  E-value=0.32  Score=32.23  Aligned_cols=22  Identities=23%  Similarity=-0.059  Sum_probs=17.1

Q ss_pred             cCCCeEEEcCCCCchhHHhHHH
Q psy7268          75 SGKSAILVAETGCGKTLSFLAP   96 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~~lp   96 (134)
                      .|+-+++.|++|+|||...+--
T Consensus        36 ~G~~~~i~G~~GsGKT~lalq~   57 (258)
T d1v5wa_          36 SMAITEAFGEFRTGKTQLSHTL   57 (258)
T ss_dssp             SSEEEEEECCTTCTHHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHH
Confidence            4567899999999999765433

>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=83.79  E-value=0.34  Score=31.75  Aligned_cols=26  Identities=23%  Similarity=0.171  Sum_probs=18.7

Q ss_pred             cCCCeEEEcCCCCchhHHhHHHHHHH
Q psy7268          75 SGKSAILVAETGCGKTLSFLAPLVQQ  100 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~~lpil~~  100 (134)
                      .|.-+++.|++|+|||...+--+.+.
T Consensus        33 ~G~l~~i~G~~G~GKT~~~l~~a~~~   58 (258)
T d2i1qa2          33 SQSVTEFAGVFGSGKTQIMHQSCVNL   58 (258)
T ss_dssp             TTEEEEEEESTTSSHHHHHHHHHHHT
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHH
Confidence            35568999999999997664444443

>d2pmka1 c.37.1.12 (A:467-707) Haemolysin B ATP-binding protein {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Haemolysin B ATP-binding protein
species: Escherichia coli [TaxId: 562]

Probab=83.57  E-value=0.34  Score=33.28  Aligned_cols=17  Identities=29%  Similarity=0.530  Sum_probs=15.3

Q ss_pred             cCCCeEEEcCCCCchhH
Q psy7268          75 SGKSAILVAETGCGKTL   91 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~   91 (134)
                      .|.-+.++|++|+|||.
T Consensus        28 ~Ge~vaIvG~sGsGKST   44 (241)
T d2pmka1          28 QGEVIGIVGRSGSGKST   44 (241)
T ss_dssp             TTCEEEEECSTTSSHHH
T ss_pred             CCCEEEEECCCCCCHHH
Confidence            57889999999999995

>d1jj7a_ c.37.1.12 (A:) Peptide transporter Tap1, C-terminal ABC domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Peptide transporter Tap1, C-terminal ABC domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=82.90  E-value=0.37  Score=33.23  Aligned_cols=19  Identities=32%  Similarity=0.497  Sum_probs=16.3

Q ss_pred             cCCCeEEEcCCCCchhHHh
Q psy7268          75 SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~   93 (134)
                      .|.-+.+.||+|+|||...
T Consensus        39 ~Ge~vaivG~sGsGKSTLl   57 (251)
T d1jj7a_          39 PGEVTALVGPNGSGKSTVA   57 (251)
T ss_dssp             TTCEEEEECSTTSSHHHHH
T ss_pred             CCCEEEEECCCCCcHHHHH
Confidence            5788999999999998654

>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=82.82  E-value=0.29  Score=35.21  Aligned_cols=15  Identities=27%  Similarity=0.335  Sum_probs=12.4

Q ss_pred             eEEEcCCCCchhHHh
Q psy7268          79 AILVAETGCGKTLSF   93 (134)
Q Consensus        79 vli~a~tGsGKT~~~   93 (134)
                      +++.||+|+|||+..
T Consensus       126 ~l~~G~pG~GKT~la  140 (321)
T d1w44a_         126 VIVTGKGNSGKTPLV  140 (321)
T ss_dssp             EEEECSSSSCHHHHH
T ss_pred             EEEECCCCccHHHHH
Confidence            555899999999775

>d2hyda1 c.37.1.12 (A:324-578) Putative multidrug export ATP-binding/permease protein SAV1866 {Staphylococcus aureus [TaxId: 1280]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Putative multidrug export ATP-binding/permease protein SAV1866
species: Staphylococcus aureus [TaxId: 1280]

Probab=82.03  E-value=0.36  Score=33.44  Aligned_cols=18  Identities=28%  Similarity=0.494  Sum_probs=15.8

Q ss_pred             cCCCeEEEcCCCCchhHH
Q psy7268          75 SGKSAILVAETGCGKTLS   92 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~   92 (134)
                      .|.-+.+++++|+|||..
T Consensus        43 ~Ge~vaivG~sGsGKSTL   60 (255)
T d2hyda1          43 KGETVAFVGMSGGGKSTL   60 (255)
T ss_dssp             TTCEEEEECSTTSSHHHH
T ss_pred             CCCEEEEECCCCCcHHHH
Confidence            678899999999999854

>d3b60a1 c.37.1.12 (A:329-581) Multidrug resistance ABC transporter MsbA, C-terminal domain {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Multidrug resistance ABC transporter MsbA, C-terminal domain
species: Salmonella typhimurium [TaxId: 90371]

Probab=81.98  E-value=0.39  Score=33.13  Aligned_cols=19  Identities=37%  Similarity=0.599  Sum_probs=16.2

Q ss_pred             cCCCeEEEcCCCCchhHHh
Q psy7268          75 SGKSAILVAETGCGKTLSF   93 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~~   93 (134)
                      .|.-+.+.+|+|+|||...
T Consensus        40 ~Ge~iaivG~sGsGKSTLl   58 (253)
T d3b60a1          40 AGKTVALVGRSGSGKSTIA   58 (253)
T ss_dssp             TTCEEEEEECTTSSHHHHH
T ss_pred             CCCEEEEECCCCChHHHHH
Confidence            6788999999999999543

>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=81.90  E-value=0.9  Score=29.76  Aligned_cols=21  Identities=24%  Similarity=0.422  Sum_probs=14.4

Q ss_pred             eEEEcCCCCchhHHhHHHHHHH
Q psy7268          79 AILVAETGCGKTLSFLAPLVQQ  100 (134)
Q Consensus        79 vli~a~tGsGKT~~~~lpil~~  100 (134)
                      +++.|+.|+|||. ++--++++
T Consensus         3 i~v~G~~GsGKTT-Ll~~ll~~   23 (244)
T d1yrba1           3 VVFVGTAGSGKTT-LTGEFGRY   23 (244)
T ss_dssp             EEEECSTTSSHHH-HHHHHHHH
T ss_pred             EEEEcCCCCcHHH-HHHHHHHH
Confidence            5788999999984 33344443

>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=81.76  E-value=0.35  Score=31.66  Aligned_cols=14  Identities=21%  Similarity=0.157  Sum_probs=11.3

Q ss_pred             EEEcCCCCchhHHh
Q psy7268          80 ILVAETGCGKTLSF   93 (134)
Q Consensus        80 li~a~tGsGKT~~~   93 (134)
                      -|.|++|||||...
T Consensus         6 gI~G~~gSGKSTla   19 (213)
T d1uj2a_           6 GVSGGTASGKSSVC   19 (213)
T ss_dssp             EEECSTTSSHHHHH
T ss_pred             EEECCCCCCHHHHH
Confidence            46799999999654

>d1l2ta_ c.37.1.12 (A:) MJ0796 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: MJ0796
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=81.73  E-value=0.38  Score=32.84  Aligned_cols=18  Identities=22%  Similarity=0.459  Sum_probs=15.6

Q ss_pred             cCCCeEEEcCCCCchhHH
Q psy7268          75 SGKSAILVAETGCGKTLS   92 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~   92 (134)
                      .|.-+-+.||+|+|||..
T Consensus        30 ~Ge~~~iiG~sGsGKSTL   47 (230)
T d1l2ta_          30 EGEFVSIMGPSGSGKSTM   47 (230)
T ss_dssp             TTCEEEEECSTTSSHHHH
T ss_pred             CCCEEEEECCCCCCcchh
Confidence            577889999999999954

>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=81.27  E-value=0.64  Score=30.92  Aligned_cols=27  Identities=33%  Similarity=0.560  Sum_probs=19.5

Q ss_pred             CCCeEEEcCCCCchhHHhHHHHHHHHHh
Q psy7268          76 GKSAILVAETGCGKTLSFLAPLVQQILT  103 (134)
Q Consensus        76 g~dvli~a~tGsGKT~~~~lpil~~~~~  103 (134)
                      ..++++.|++|.|||... --+..++..
T Consensus        43 k~n~lLvG~pGVGKTalv-~~LA~ri~~   69 (195)
T d1jbka_          43 KNNPVLIGEPGVGKTAIV-EGLAQRIIN   69 (195)
T ss_dssp             SCEEEEECCTTSCHHHHH-HHHHHHHHH
T ss_pred             CCCeEEEecCCcccHHHH-HHHHHHHHh
Confidence            347999999999999553 445555544

>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=81.24  E-value=0.33  Score=31.58  Aligned_cols=15  Identities=20%  Similarity=0.259  Sum_probs=11.9

Q ss_pred             eEEEcCCCCchhHHh
Q psy7268          79 AILVAETGCGKTLSF   93 (134)
Q Consensus        79 vli~a~tGsGKT~~~   93 (134)
                      +.|-||+||||+...
T Consensus         6 I~I~GppGSGKgT~a   20 (225)
T d1ckea_           6 ITIDGPSGAGKGTLC   20 (225)
T ss_dssp             EEEECCTTSSHHHHH
T ss_pred             EEEECCCCCCHHHHH
Confidence            445599999999765

>d1tuea_ c.37.1.20 (A:) Replication protein E1 helicase domain {Human papillomavirus type 18 [TaxId: 333761]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication protein E1 helicase domain
species: Human papillomavirus type 18 [TaxId: 333761]

Probab=80.99  E-value=1.8  Score=28.84  Aligned_cols=51  Identities=12%  Similarity=0.227  Sum_probs=33.8

Q ss_pred             HHHHHHHHHCCCCCChHHHHHHHHHHHcC----CCeEEEcCCCCchhHHhHHHHHHHH
Q psy7268          48 PEIIDIFTKRGLTTPTEIQKYSIPTLLSG----KSAILVAETGCGKTLSFLAPLVQQI  101 (134)
Q Consensus        48 ~~i~~~l~~~g~~~~t~iQ~~~i~~~~~g----~dvli~a~tGsGKT~~~~lpil~~~  101 (134)
                      ..|++.|+..|++ +-+. ..++..++.|    +.+++.||+++|||+-. ..++..+
T Consensus        23 ~~I~~~l~~q~i~-~~~F-l~~l~~~l~~~PKkn~i~~~GP~~TGKS~f~-~sl~~~l   77 (205)
T d1tuea_          23 RPIVQFLRYQQIE-FITF-LGALKSFLKGTPKKNCLVFCGPANTGKSYFG-MSFIHFI   77 (205)
T ss_dssp             HHHHHHHHHTTCC-HHHH-HHHHHHHHHTCTTCSEEEEESCGGGCHHHHH-HHHHHHH
T ss_pred             HHHHHHHHhcCcc-HHHH-HHHHHHHHcCCCCceEEEEECCCCccHHHHH-HHHHHHh
Confidence            7888889888773 3333 2333444544    45889999999999664 4455555

>d1qvra3 c.37.1.20 (A:536-850) ClpB, AAA+ modules {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Thermus thermophilus [TaxId: 274]

Probab=80.69  E-value=0.32  Score=34.56  Aligned_cols=16  Identities=38%  Similarity=0.432  Sum_probs=13.7

Q ss_pred             CeEEEcCCCCchhHHh
Q psy7268          78 SAILVAETGCGKTLSF   93 (134)
Q Consensus        78 dvli~a~tGsGKT~~~   93 (134)
                      .++.+||||+|||...
T Consensus        55 ~~lf~Gp~G~GKt~la   70 (315)
T d1qvra3          55 SFLFLGPTGVGKTELA   70 (315)
T ss_dssp             EEEEBSCSSSSHHHHH
T ss_pred             EEEEECCCcchHHHHH
Confidence            4688899999999775

>d1xx6a1 c.37.1.24 (A:2-142) Thymidine kinase, TK1, N-terminal domain {Clostridium acetobutylicum [TaxId: 1488]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Type II thymidine kinase
domain: Thymidine kinase, TK1, N-terminal domain
species: Clostridium acetobutylicum [TaxId: 1488]

Probab=80.65  E-value=1.1  Score=28.07  Aligned_cols=36  Identities=11%  Similarity=0.163  Sum_probs=22.8

Q ss_pred             eEEEcCCCCchhHHhHHHHHHHHHhhcCCCCCCCCCCCcEEEEEcCcH
Q psy7268          79 AILVAETGCGKTLSFLAPLVQQILTWKSRPEYKPELNAPLALIITPGR  126 (134)
Q Consensus        79 vli~a~tGsGKT~~~~lpil~~~~~~~~~~~~~~~~~~~~~lil~Pt~  126 (134)
                      -++.||-.||||.-. +-.+.+...           .+.+++++-|..
T Consensus        10 ~lI~GpMfSGKTteL-i~~~~~~~~-----------~g~~vl~i~~~~   45 (141)
T d1xx6a1          10 EVIVGPMYSGKSEEL-IRRIRRAKI-----------AKQKIQVFKPEI   45 (141)
T ss_dssp             EEEECSTTSSHHHHH-HHHHHHHHH-----------TTCCEEEEEEC-
T ss_pred             EEEEeccccHHHHHH-HHHHHHhhh-----------cCCcEEEEEecc
Confidence            467899999999544 555554433           344577777643

>d1ry6a_ c.37.1.9 (A:) Kinesin {Malaria parasite (Plasmodium falciparum) [TaxId: 5833]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Malaria parasite (Plasmodium falciparum) [TaxId: 5833]

Probab=80.49  E-value=0.63  Score=33.04  Aligned_cols=19  Identities=32%  Similarity=0.522  Sum_probs=15.9

Q ss_pred             cCCC--eEEEcCCCCchhHHh
Q psy7268          75 SGKS--AILVAETGCGKTLSF   93 (134)
Q Consensus        75 ~g~d--vli~a~tGsGKT~~~   93 (134)
                      +|.+  ++.-|.||||||...
T Consensus        82 ~G~n~~i~aYGqTGSGKTyTm  102 (330)
T d1ry6a_          82 NGCVCSCFAYGQTGSGKTYTM  102 (330)
T ss_dssp             HCCEEEEEEECCTTSSHHHHH
T ss_pred             cCCCeEEEeeeccccccceee
Confidence            5887  677799999999884

>d2awna2 c.37.1.12 (A:4-235) Maltose transport protein MalK, N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Maltose transport protein MalK, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=80.28  E-value=0.45  Score=32.50  Aligned_cols=18  Identities=33%  Similarity=0.765  Sum_probs=15.3

Q ss_pred             cCCCeEEEcCCCCchhHH
Q psy7268          75 SGKSAILVAETGCGKTLS   92 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~   92 (134)
                      .|.-+.+.+|+|+|||..
T Consensus        25 ~Gei~~liGpsGsGKSTL   42 (232)
T d2awna2          25 EGEFVVFVGPSGCGKSTL   42 (232)
T ss_dssp             TTCEEEEECCTTSSHHHH
T ss_pred             CCCEEEEECCCCChHHHH
Confidence            577788999999999854

>d3dhwc1 c.37.1.12 (C:1-240) Methionine import ATP-binding protein MetN {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Methionine import ATP-binding protein MetN
species: Escherichia coli [TaxId: 562]

Probab=80.23  E-value=0.43  Score=32.78  Aligned_cols=18  Identities=22%  Similarity=0.420  Sum_probs=15.5

Q ss_pred             cCCCeEEEcCCCCchhHH
Q psy7268          75 SGKSAILVAETGCGKTLS   92 (134)
Q Consensus        75 ~g~dvli~a~tGsGKT~~   92 (134)
                      .|.-+-+.||+|+|||..
T Consensus        30 ~Ge~~~iiG~sGsGKSTL   47 (240)
T d3dhwc1          30 AGQIYGVIGASGAGKSTL   47 (240)
T ss_dssp             SSCEEEEEESTTSSHHHH
T ss_pred             CCCEEEEECCCCCCHHHH
Confidence            577789999999999954