Citrus Sinensis ID: 037567

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370----
Protein Sequence
MVSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVTGKTALVVSPLISLMQDQVMSLKQRGINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEKVRIDIINSLKLKNPYVTIASFDRKNLFYGVKVINRGQSFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFYCGESQTENQRTAIMESLLAAQRYCLLTTCRR
Secondary Structure (PSIPRED)
cHHHHHHccccccccccHHHHHHHHHHcccEEEEEccccccccccccccccccccEEEEccHHHHHHHHHHHHHHccccEEEEcccccHHHHHHHHHcccccEEEEcccccccccHHHHHHHHcccccEEEEEcccccccccccccHHcccHHHHHHHcccccEEEEEccccHHHHHHHHHHcccccccEEEccccccccEEEEEEccccHHHHHHHHHHHHHccccccccEEEEcccHHHHHHHHHHHHcccccccccccccHHHHHHHHHHHHcccccEEEEEccccccccccccEEEEEccccccHHHHHHHcccccccccccEEEEEccccHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHcccccc
Secondary Structure Prediction (SSPRO)
cHHHHHHHcccccccHHHHHHHHHHHccccEEEEEcccccccHHHHcHHHHcccEEEEEcHHHHHHHHHHHHHHHccccEEEEcccccHHHHHHHHHccccEEEEEccHHHHHccHHHHHHHHHcccEEEEEEcHHHHHHccccccHHHHHHHHHHHHcccccEEEEEEcccHHHHHHHHHHHcccccEEEEEcccccccEEEEEEccccHHHHHHHHHHHHHHccccccEEEEEccHHHHHHHHHHHHHcccccHHHcccccHHHHHHHHHHHHcccccEEEEEHHHHcccccccEEEEEEEcccccHHHHHHHHccccccccccEEEEEEcHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHcccccc
Coil and Loop (DISEMBL)
mvstlkkyfgysvfrpyQKDVIQRIIEKRDCLVVMAtgsgkslcyqlpplvtgktaLVVSPLISLMQDQVMSLKQRGinaeflgsaqtdssvqtkAETGYFQLlfmtpekaciiPISFWSKLLKAGVCLfavdeahcisewgHDFRLEYKQLDKLRTFLLGVPFVALTATATEKVRIDIINslklknpyvtiasfdrknlfygVKVINRGQSFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVkagtyhgqmgsKAREEAHRLFIRDEIRVMVATMAFgmgidkpdvrhvihygcpktlesyyqesgrcgrdgIASVCWLYYARsnfakgdfycgesqteNQRTAIMESLLAAQRYCLLTTCRR
Flexible Loop (DISEMBL)
mvstlkkyfgysvfrpyqKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVTGKTALVVSPLISLMQDQVMSLKQRGINAEFLgsaqtdssvqTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEKVRIDiinslklknpyVTIASFDRKNLFYGVKVINRGQSFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAgtyhgqmgskAREEAHRLFIRDEIRVMVATMAFgmgidkpdvRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFYCGESQTENQRTAIMESLLAAQRYCLLTTCRR
Low Complexity Region (SEG)
MVSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVTGKTALVVSPLISLMQDQVMSLKQRGINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEKVRIDIINSLKLKNPYVTIASFDRKNLFYGVKVINRGQSFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFYCGESQTENQRTAIMESLLAAQRYCLLTTCRR
Disordered region (IsUnstruct)
****LKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVTGKTALVVSPLISLMQDQVMSLKQRGINAEFLG*********TKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEKVRIDIINSLKLKNPYVTIASFDRKNLFYGVKVINRGQSFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMG***REEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFYCGESQTENQRTAIMESLLAAQRYCLLTTC**
Disordered Region (DISOPRED)
MVSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVTGKTALVVSPLISLMQDQVMSLKQRGINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEKVRIDIINSLKLKNPYVTIASFDRKNLFYGVKVINRGQSFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDF*****************LLAAQRYCLLTTCRR
Disordered Region (DISEMBL)
MVSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVTGKTALVVSPLISLMQDQVMSLKQRGINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEKVRIDIINSLKLKNPYVTIASFDRKNLFYGVKVINRGQSFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFYCGESQTENQRTAIMESLLAAQRYCLLTTCRR
Disordered Region (DISPRO)
MVSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVTGKTALVVSPLISLMQDQVMSLKQRGINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEKVRIDIINSLKLKNPYVTIASFDRKNLFYGVKVINRGQSFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFYCGESQTENQRTAIMESLLAAQRYCLLTTC**
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MVSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVTGKTALVVSPLISLMQDQVMSLKQRGINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEKVRIDIINSLKLKNPYVTIASFDRKNLFYGVKVINRGQSFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFYCGESQTENQRTAIMESLLAAQRYCLLTTCRR
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	374	2.2.26 [Sep-21-2011]
O93530	1436	Werner syndrome ATP-depen	N/A	no	0.986	0.256	0.471	1e-91
Q14191	1432	Werner syndrome ATP-depen	yes	no	0.986	0.257	0.439	2e-86
O09053	1401	Werner syndrome ATP-depen	yes	no	0.991	0.264	0.440	1e-84
Q19546	1056	Probable Werner syndrome	yes	no	0.973	0.344	0.410	3e-79
P71359	619	ATP-dependent DNA helicas	yes	no	0.978	0.591	0.428	5e-78
P15043	609	ATP-dependent DNA helicas	N/A	no	0.967	0.594	0.417	9e-78
Q9CL21	632	ATP-dependent DNA helicas	yes	no	0.978	0.579	0.417	1e-77
Q9FT73	705	Mediator of RNA polymeras	yes	no	0.951	0.504	0.436	3e-77
Q9FT72	713	ATP-dependent DNA helicas	no	no	0.975	0.511	0.405	2e-75
P40724	609	ATP-dependent DNA helicas	yes	no	0.970	0.596	0.413	6e-75

>sp|O93530|WRN_XENLA Werner syndrome ATP-dependent helicase homolog OS=Xenopus laevis GN=wrn PE=2 SV=1

 Score =  336 bits (862), Expect = 1e-91,   Method: Compositional matrix adjust.
 Identities = 179/380 (47%), Positives = 240/380 (63%), Gaps = 11/380 (2%)

Query: 2   VSTLKKYFGYSVFRPYQKDVIQRII-EKRDCLVVMATGSGKSLCYQLPPLVTGKTALVVS 60
           +S LK YFG+S F+P Q  V+  ++ E+RD LVVMATG GKSLCYQ  P+ T    +V+ 
Sbjct: 478 ISCLKTYFGHSSFKPVQWKVVHSVLRERRDNLVVMATGYGKSLCYQFAPVYTSGIGIVIC 537

Query: 61  PLISLMQDQVMSLKQRGINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWS 120
           PLISLM+DQV+ L+   I++ FLGSAQ+ + +Q   + G  ++++MTPE  C   IS   
Sbjct: 538 PLISLMEDQVLQLEMSNISSCFLGSAQSKNVLQD-VKDGKMRVIYMTPE-FCSRGISLLQ 595

Query: 121 KL-LKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEKVRIDI 179
            L  + G+ L A+DEAHCISEWGHDFR  Y+ L  L+  L  VP VALTATA+  +R DI
Sbjct: 596 DLDNRYGITLIAIDEAHCISEWGHDFRSAYRSLGSLKRMLPNVPIVALTATASPSIREDI 655

Query: 180 INSLKLKNPYVTIASFDRKNLFYGVKVINRGQSFVDELVQEILKSVAGAG-----SIIVY 234
             SL L NP VT  SFDR NL+  + V  +  +   +L Q ++K   G+G     + IVY
Sbjct: 656 TKSLNLHNPQVTCTSFDRPNLY--LDVARKTTNISIDLRQFLIKKQQGSGWEFEGATIVY 713

Query: 235 CMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDK 294
           C T K  E+++  L +LG+  GTYH  MG K R E H  F+RDEI  +VAT+AFGMGI+K
Sbjct: 714 CPTRKTSEQVTAELIKLGIACGTYHAGMGIKQRREVHHRFMRDEIHCVVATVAFGMGINK 773

Query: 295 PDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFYCGESQTENQRT 354
           PD+R VIHYG PK +ESYYQE GR GRDG+ S C   +A+++        GE   +  R 
Sbjct: 774 PDIRKVIHYGAPKEMESYYQEIGRAGRDGLPSCCHALWAQADMNFNRHMLGEIPNKGFRE 833

Query: 355 AIMESLLAAQRYCLLTTCRR 374
             ++ L   ++Y   +TCRR
Sbjct: 834 YKLKMLTKMEKYLNSSTCRR 853

Multifunctional enzyme that has both magnesium and ATP-dependent DNA-helicase activity and 3'->5' exonuclease activity towards double-stranded DNA with a 5'-overhang. Has no nuclease activity towards single-stranded DNA or blunt-ended double-stranded DNA. Binds preferentially to DNA substrates containing alternate secondary structures, such as replication forks and Holliday junctions. May play an important role in the dissociation of joint DNA molecules that can arise as products of homologous recombination, at stalled replication forks or during DNA repair. Alleviates stalling of DNA polymerases at the site of DNA lesions. Important for genomic integrity. Plays a role in the formation of DNA replication focal centers; stably associates with foci elements generating binding sites for RP-A.
Xenopus laevis (taxid: 8355)
EC: 3EC: .EC: 1EC: .EC: -EC: .EC: -

>sp|Q14191|WRN_HUMAN Werner syndrome ATP-dependent helicase OS=Homo sapiens GN=WRN PE=1 SV=2

 Score =  319 bits (818), Expect = 2e-86,   Method: Compositional matrix adjust.
 Identities = 166/378 (43%), Positives = 241/378 (63%), Gaps = 9/378 (2%)

Query: 2   VSTLKKYFGYSVFRPYQKDVIQRIIE-KRDCLVVMATGSGKSLCYQLPPLVTGKTALVVS 60
           V+ LK YFG+S F+P Q  VI  ++E +RD + VMATG GKSLC+Q PP+  GK  LV+S
Sbjct: 537 VTCLKMYFGHSSFKPVQWKVIHSVLEERRDNVAVMATGYGKSLCFQYPPVYVGKIGLVIS 596

Query: 61  PLISLMQDQVMSLKQRGINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWS 120
           PLISLM+DQV+ LK   I A FLGSAQ+++ V T  + G ++++++TPE  C   +    
Sbjct: 597 PLISLMEDQVLQLKMSNIPACFLGSAQSEN-VLTDIKLGKYRIVYVTPE-YCSGNMGLLQ 654

Query: 121 KL-LKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEKVRIDI 179
           +L    G+ L AVDEAHCISEWGHDFR  +++L  L+T L  VP VALTATA+  +R DI
Sbjct: 655 QLEADIGITLIAVDEAHCISEWGHDFRDSFRKLGSLKTALPMVPIVALTATASSSIREDI 714

Query: 180 INSLKLKNPYVTIASFDRKNLFYGVKVINRGQSFVDELVQEILKSVAG---AGSIIVYCM 236
           +  L L+NP +T   FDR NL+  V+   +  + + +L   ++K+ +     G  I+YC 
Sbjct: 715 VRCLNLRNPQITCTGFDRPNLYLEVR--RKTGNILQDLQPFLVKTSSHWEFEGPTIIYCP 772

Query: 237 TIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPD 296
           + K  ++++  L++L +  GTYH  M    R++ H  F+RDEI+ ++AT+AFGMGI+K D
Sbjct: 773 SRKMTQQVTGELRKLNLSCGTYHAGMSFSTRKDIHHRFVRDEIQCVIATIAFGMGINKAD 832

Query: 297 VRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFYCGESQTENQRTAI 356
           +R VIHYG PK +ESYYQE GR GRDG+ S C + +A ++         E + E  R   
Sbjct: 833 IRQVIHYGAPKDMESYYQEIGRAGRDGLQSSCHVLWAPADINLNRHLLTEIRNEKFRLYK 892

Query: 357 MESLLAAQRYCLLTTCRR 374
           ++ +   ++Y   + CRR
Sbjct: 893 LKMMAKMEKYLHSSRCRR 910

Multifunctional enzyme that has both magnesium and ATP-dependent DNA-helicase activity and 3'->5' exonuclease activity towards double-stranded DNA with a 5'-overhang. Has no nuclease activity towards single-stranded DNA or blunt-ended double-stranded DNA. Binds preferentially to DNA substrates containing alternate secondary structures, such as replication forks and Holliday junctions. May play an important role in the dissociation of joint DNA molecules that can arise as products of homologous recombination, at stalled replication forks or during DNA repair. Alleviates stalling of DNA polymerases at the site of DNA lesions. Important for genomic integrity. Plays a role in the formation of DNA replication focal centers; stably associates with foci elements generating binding sites for RP-A.

Homo sapiens (taxid: 9606)

EC: 3

EC: .

EC: 1

EC: .

EC: -

EC: .

EC: -

>sp|O09053|WRN_MOUSE Werner syndrome ATP-dependent helicase homolog OS=Mus musculus GN=Wrn PE=1 SV=3

 Score =  313 bits (802), Expect = 1e-84,   Method: Compositional matrix adjust.
 Identities = 166/377 (44%), Positives = 237/377 (62%), Gaps = 6/377 (1%)

Query: 2   VSTLKKYFGYSVFRPYQKDVIQRIIE-KRDCLVVMATGSGKSLCYQLPPLVTGKTALVVS 60
           ++ LK YFG+S F+P Q  VI  ++E +RD +VVMATG GKSLC+Q PP+ TGK  +V+S
Sbjct: 501 INCLKTYFGHSSFKPVQWKVIHSVLEERRDNVVVMATGYGKSLCFQYPPVYTGKIGIVIS 560

Query: 61  PLISLMQDQVMSLKQRGINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWS 120
           PLISLM+DQV+ L+   + A  LGSAQ+  ++    + G ++++++TPE  C   +    
Sbjct: 561 PLISLMEDQVLQLELSNVPACLLGSAQS-KNILGDVKLGKYRVIYITPE-FCSGNLDLLQ 618

Query: 121 KLLKA-GVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEKVRIDI 179
           +L  + G+ L AVDEAHCISEWGHDFR  ++ L  L+T L  VP +AL+ATA+  +R DI
Sbjct: 619 QLDSSIGITLIAVDEAHCISEWGHDFRSSFRMLGSLKTALPLVPVIALSATASSSIREDI 678

Query: 180 INSLKLKNPYVTIASFDRKNLFY--GVKVINRGQSFVDELVQEILKSVAGAGSIIVYCMT 237
           I+ L LK+P +T   FDR NL+   G K  N  Q     LV++   +    G  I+YC +
Sbjct: 679 ISCLNLKDPQITCTGFDRPNLYLEVGRKTGNILQDLKPFLVRKASSAWEFEGPTIIYCPS 738

Query: 238 IKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDV 297
            K  E+++  L +L +   TYH  M    R++ H  F+RDEI+ +VAT+AFGMGI+K D+
Sbjct: 739 RKMTEQVTAELGKLNLACRTYHAGMKISERKDVHHRFLRDEIQCVVATVAFGMGINKADI 798

Query: 298 RHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFYCGESQTENQRTAIM 357
           R VIHYG PK +ESYYQE GR GRDG+ S C L +A ++F        E   E  R   +
Sbjct: 799 RKVIHYGAPKEMESYYQEIGRAGRDGLQSSCHLLWAPADFNTSRNLLIEIHDEKFRLYKL 858

Query: 358 ESLLAAQRYCLLTTCRR 374
           + ++  ++Y   + CRR
Sbjct: 859 KMMVKMEKYLHSSQCRR 875

Multifunctional enzyme that has both magnesium and ATP-dependent DNA-helicase activity and 3'->5' exonuclease activity towards double-stranded DNA with a 5'-overhang. Has no nuclease activity towards single-stranded DNA or blunt-ended double-stranded DNA. Binds preferentially to DNA substrates containing alternate secondary structures, such as replication forks and Holliday junctions. May play an important role in the dissociation of joint DNA molecules that can arise as products of homologous recombination, at stalled replication forks or during DNA repair. Alleviates stalling of DNA polymerases at the site of DNA lesions. Important for genomic integrity. Plays a role in the formation of DNA replication focal centers; stably associates with foci elements generating binding sites for RP-A.

Mus musculus (taxid: 10090)

EC: 3

EC: .

EC: 1

EC: .

EC: -

EC: .

EC: -

>sp|Q19546|WRN_CAEEL Probable Werner syndrome ATP-dependent helicase homolog 1 OS=Caenorhabditis elegans GN=wrn-1 PE=3 SV=2

 Score =  295 bits (756), Expect = 3e-79,   Method: Compositional matrix adjust.
 Identities = 159/387 (41%), Positives = 239/387 (61%), Gaps = 23/387 (5%)

Query: 2   VSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVTGKTALVVSP 61
           ++ L ++FG+  FR  Q DV++ ++  +D  V+M+TG GKS+CYQLP L+     +VVSP
Sbjct: 216 LNALNEFFGHKGFREKQWDVVRNVLGGKDQFVLMSTGYGKSVCYQLPSLLLNSMTVVVSP 275

Query: 62  LISLMQDQVMSLKQRGINAEFLGSAQTDSSVQTKAETGY-FQLLFMTPEKACIIPISFWS 120
           LISLM DQV +L  +GI+A  L    T       A   +  + ++M+PE   ++      
Sbjct: 276 LISLMNDQVTTLVSKGIDAVKLDGHSTQIEWDQVANNMHRIRFIYMSPE---MVTSQKGL 332

Query: 121 KLL---KAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLR--TFLLGVPFVALTATATEKV 175
           +LL   +  + L A+DEAHC+S+WGHDFR  Y+ L ++R  + L  +P +ALTATAT +V
Sbjct: 333 ELLTSCRKHISLLAIDEAHCVSQWGHDFRNSYRHLAEIRNRSDLCNIPMIALTATATVRV 392

Query: 176 RIDIINSLKLKNPYVTIASFDRKNLFYGVKVINRGQSFVDEL----VQEILKSVAGAGSI 231
           R D+I +L+L+ P +T  SFDRKNL+  V   +  +   ++L      + +K     G  
Sbjct: 393 RDDVIANLRLRKPLITTTSFDRKNLYISV---HSSKDMAEDLGLFMKTDEVKGRHFGGPT 449

Query: 232 IVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMG 291
           I+YC T + V++++  L+++GV++  YH  +    RE+AH  F+RD+I  +VAT+AFGMG
Sbjct: 450 IIYCQTKQMVDDVNCVLRRIGVRSAHYHAGLTKNQREKAHTDFMRDKITTIVATVAFGMG 509

Query: 292 IDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFYCGESQTEN 351
           IDKPDVR+VIHYGCP  +ESYYQE GR GRDG  S+C +++A  +     F    SQ   
Sbjct: 510 IDKPDVRNVIHYGCPNNIESYYQEIGRAGRDGSPSICRVFWAPKDLNTIKFKLRNSQ--- 566

Query: 352 QRTAIMESL--LAAQRYCLLTT--CRR 374
           Q+  ++E+L  +  Q   +LTT  CRR
Sbjct: 567 QKEEVVENLTMMLRQLELVLTTVGCRR 593

Essential for the formation of DNA replication focal centers; stably associates with foci elements generating binding sites for RP-A. Exhibits a magnesium-dependent ATP-dependent DNA-helicase activity. May be involved in the control of genomic stability.

Caenorhabditis elegans (taxid: 6239)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

>sp|P71359|RECQ_HAEIN ATP-dependent DNA helicase RecQ OS=Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) GN=recQ PE=3 SV=1

 Score =  291 bits (745), Expect = 5e-78,   Method: Compositional matrix adjust.
 Identities = 161/376 (42%), Positives = 224/376 (59%), Gaps = 10/376 (2%)

Query: 2   VSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVTGKTALVVSP 61
           +S LK  FGY  FR  Q++VI   +  +D LVVMATG+GKSLCYQ+P L      LV+SP
Sbjct: 17  LSVLKSVFGYQSFRKGQEEVINAALNGQDALVVMATGNGKSLCYQIPALCFDGLTLVISP 76

Query: 62  LISLMQDQVMSLKQRGINAEFLGSAQT---DSSVQTKAETGYFQLLFMTPEKACIIPISF 118
           LISLM+DQV  L+  GI A+FL S+QT      VQ K  +G  +LL+++PEK  ++  SF
Sbjct: 77  LISLMKDQVDQLQANGIEADFLNSSQTLEQQQQVQNKLISGQLKLLYVSPEK--VMTNSF 134

Query: 119 WSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEKVRID 178
           +  +  + VC  A+DEAHCIS+WGHDFR EY QL  L+      P +ALTATA    + D
Sbjct: 135 FQLISYSKVCFIAIDEAHCISQWGHDFRPEYTQLGGLKASFPDAPIMALTATADYATQQD 194

Query: 179 IINSLKLKNPYVTIASFDRKNLFYGVKVINRGQSFVDELVQEILKSVAGAGSIIVYCMTI 238
           I+  L LKN +  I SFDR N+ Y    +      +++L + +L     +G  I+YC + 
Sbjct: 195 ILRHLNLKNLHKYIGSFDRPNIRY---TLEEKYKPMEQLTRFVLAQKGKSG--IIYCNSR 249

Query: 239 KDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVR 298
             VE I+++L+  GV A  YH  M +  RE   + F RD ++V+VAT+AFGMGI+K +VR
Sbjct: 250 NKVERIAESLRNKGVSAAAYHAGMETAIRERVQQDFQRDNVQVVVATIAFGMGINKSNVR 309

Query: 299 HVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFYCGESQTENQRTAIME 358
            V H+  P+++ESYYQE+GR GRD + +   L+Y  +++A       E     QR     
Sbjct: 310 FVAHFDLPRSIESYYQETGRAGRDDLPAEAVLFYEPADYAWLQKILLEKPETPQRQIEQH 369

Query: 359 SLLAAQRYCLLTTCRR 374
            L A   +    TCRR
Sbjct: 370 KLEAIGEFAESQTCRR 385

DNA helicase.

Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) (taxid: 71421)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

>sp|P15043|RECQ_ECOLI ATP-dependent DNA helicase RecQ OS=Escherichia coli (strain K12) GN=recQ PE=1 SV=5

 Score =  290 bits (743), Expect = 9e-78,   Method: Compositional matrix adjust.
 Identities = 156/374 (41%), Positives = 225/374 (60%), Gaps = 12/374 (3%)

Query: 5   LKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVTGKTALVVSPLIS 64
           L++ FGY  FRP Q+++I  ++  RDCLVVM TG GKSLCYQ+P L+     +VVSPLIS
Sbjct: 17  LQETFGYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPALLLNGLTVVVSPLIS 76

Query: 65  LMQDQVMSLKQRGINAEFLGSAQTDS---SVQTKAETGYFQLLFMTPEKACIIPISFWSK 121
           LM+DQV  L+  G+ A  L S QT      V T   TG  +LL++ PE+  ++  +F   
Sbjct: 77  LMKDQVDQLQANGVAAACLNSTQTREQQLEVMTGCRTGQIRLLYIAPER--LMLDNFLEH 134

Query: 122 LLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEKVRIDIIN 181
           L      L AVDEAHCIS+WGHDFR EY  L +LR     +PF+ALTATA +  R DI+ 
Sbjct: 135 LAHWNPVLLAVDEAHCISQWGHDFRPEYAALGQLRQRFPTLPFMALTATADDTTRQDIVR 194

Query: 182 SLKLKNPYVTIASFDRKNLFYGVKVINRGQSFVDELVQEILKSVAGAGSIIVYCMTIKDV 241
            L L +P + I+SFDR N+ Y   ++      +D+L++ + +    +G  I+YC +   V
Sbjct: 195 LLGLNDPLIQISSFDRPNIRY---MLMEKFKPLDQLMRYVQEQRGKSG--IIYCNSRAKV 249

Query: 242 EEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVI 301
           E+ +  L+  G+ A  YH  + +  R +    F RD+++++VAT+AFGMGI+KP+VR V+
Sbjct: 250 EDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGMGINKPNVRFVV 309

Query: 302 HYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFYCGESQTENQRTAIMESLL 361
           H+  P+ +ESYYQE+GR GRDG+ +   L+Y  ++ A     C E + + Q   I    L
Sbjct: 310 HFDIPRNIESYYQETGRAGRDGLPAEAMLFYDPADMAWLR-RCLEEKPQGQLQDIERHKL 368

Query: 362 AAQ-RYCLLTTCRR 374
            A   +    TCRR
Sbjct: 369 NAMGAFAEAQTCRR 382

Involved in the recF recombination pathway; its gene expression is under the regulation of the SOS system. It is a DNA helicase.

Escherichia coli (strain K12) (taxid: 83333)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

>sp|Q9CL21|RECQ_PASMU ATP-dependent DNA helicase RecQ OS=Pasteurella multocida (strain Pm70) GN=recQ PE=3 SV=1

 Score =  290 bits (742), Expect = 1e-77,   Method: Compositional matrix adjust.
 Identities = 157/376 (41%), Positives = 227/376 (60%), Gaps = 10/376 (2%)

Query: 2   VSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVTGKTALVVSP 61
           +  L   FGY  FR  Q++VI   +  +D LV+MATG+GKSLCYQ+P L      LV+SP
Sbjct: 27  LDVLHAVFGYQSFRKGQEEVIDATLMGKDSLVIMATGNGKSLCYQIPALCFEGLTLVISP 86

Query: 62  LISLMQDQVMSLKQRGINAEFLGSAQT---DSSVQTKAETGYFQLLFMTPEKACIIPISF 118
           LISLM+DQV  L   GI A++L S+QT      VQ K  +G  +LL+++PEK  ++  SF
Sbjct: 87  LISLMKDQVDQLLANGIEADYLNSSQTFTEQQQVQNKLMSGTLKLLYVSPEK--VMTTSF 144

Query: 119 WSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEKVRID 178
           +  +    V   A+DEAHCIS+WGHDFR EY QL  L++     P +ALTATA    R D
Sbjct: 145 FHLISHCKVSFVAIDEAHCISQWGHDFRPEYTQLGGLKSCFPHAPIMALTATADHATRQD 204

Query: 179 IINSLKLKNPYVTIASFDRKNLFYGVKVINRGQSFVDELVQEILKSVAGAGSIIVYCMTI 238
           I+  L L++P+V I SFDR N+ Y   ++ + +  +++L + +L     +G  I+YC + 
Sbjct: 205 ILRHLNLQSPHVYIGSFDRPNIRY--TLVEKFKP-MEQLCRFVLGQKGKSG--IIYCNSR 259

Query: 239 KDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVR 298
             VE I+++L+  GV A  YH  + +  RE+  R F RD ++V+VAT+AFGMGI+K +VR
Sbjct: 260 SKVERIAESLRNKGVSAQAYHAGLETSQREQVQRAFQRDNVQVVVATIAFGMGINKSNVR 319

Query: 299 HVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFYCGESQTENQRTAIME 358
            V+H+  P+++ESYYQE+GR GRD + +   L+Y  +++A       E     QR     
Sbjct: 320 FVVHFDLPRSIESYYQETGRAGRDDLPAEAVLFYEPADYAWLHKILLEKPESPQRQIEAL 379

Query: 359 SLLAAQRYCLLTTCRR 374
            L A   +    TCRR
Sbjct: 380 KLQAIGEFAESQTCRR 395

DNA helicase.

Pasteurella multocida (strain Pm70) (taxid: 272843)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

>sp|Q9FT73|MED34_ARATH Mediator of RNA polymerase II transcription subunit 34 OS=Arabidopsis thaliana GN=MED34 PE=1 SV=1

 Score =  289 bits (739), Expect = 3e-77,   Method: Compositional matrix adjust.
 Identities = 166/380 (43%), Positives = 234/380 (61%), Gaps = 24/380 (6%)

Query: 9   FGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVTGKTALVVSPLISLMQD 68
           FG S +R  QK++I  I+  RD LV+MA G GKSLCYQLP ++ G T LVVSPL+SL+QD
Sbjct: 85  FGISKYRANQKEIINAIMTGRDVLVIMAAGGGKSLCYQLPAMLRGGTTLVVSPLLSLIQD 144

Query: 69  QVMSLKQRGINAEFLGSA---QTDSSVQTKAETGY--FQLLFMTPEKACIIPISFWSKLL 123
           QVM L   GI+A  L S    + +  V    E G    ++L++TPEK       F SKL 
Sbjct: 145 QVMGLAALGISAYMLTSTSGKENEKFVYKALEKGEDDLKILYVTPEKVSKSK-RFMSKLE 203

Query: 124 K---AG-VCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEKVRIDI 179
           K   AG + L ++DEAHC S+WGHDFR +YK L  L+T    VP VALTATAT+KV+ D+
Sbjct: 204 KCHNAGRLSLISIDEAHCCSQWGHDFRPDYKNLSILKTQFPKVPMVALTATATQKVQNDL 263

Query: 180 INSLKLKNPYVTIASFDRKNLFYGVKVINR-GQSFVDELVQEILKSVAGAGSIIVYCMTI 238
           I  L +      ++S +R NLFY V+  +  G+  VDE+ + I +S +   S IVYC + 
Sbjct: 264 IEMLHIPKCVKFVSSVNRPNLFYSVREKSAVGKLVVDEIAEFIRESYSNNESGIVYCFSR 323

Query: 239 KDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVR 298
           K+ E+I+  L++ G+ A  YH  M +  RE+ H  + +++++V+V T+AFGMGI+KPDVR
Sbjct: 324 KECEQIAGDLRERGISADYYHADMDANMREKVHMRWSKNKLQVIVGTVAFGMGINKPDVR 383

Query: 299 HVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGD---FYCGESQTENQRTA 355
            VIH+   K++E+YYQESGR GRDG+ S C L++  ++  +     FY           +
Sbjct: 384 FVIHHSLSKSMETYYQESGRAGRDGLPSECILFFRSADVPRQSSMVFY---------EYS 434

Query: 356 IMESLLAAQRYCL-LTTCRR 374
            +++L    RYC   T CRR
Sbjct: 435 GLQNLYDIVRYCQSKTKCRR 454

3'-5' DNA helicase that may play a role in the repair of DNA. Exhibits a magnesium-dependent ATP or dATP-dependent DNA-helicase activity. Can use GTP/dGTP, CTP/dCTP or UTP/dUTP as nucleotide cofactors. Catalyzes Holliday junction branch migration and replication fork regression. Disrupts D-loop structures.

Arabidopsis thaliana (taxid: 3702)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

>sp|Q9FT72|RQL3_ARATH ATP-dependent DNA helicase Q-like 3 OS=Arabidopsis thaliana GN=RECQL3 PE=1 SV=1

 Score =  283 bits (723), Expect = 2e-75,   Method: Compositional matrix adjust.
 Identities = 158/390 (40%), Positives = 230/390 (58%), Gaps = 25/390 (6%)

Query: 1   MVSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVTGKTALVVS 60
           +V  L+ +FG++ FR  Q + IQ ++  RDC  +M TG GKS+CYQ+P L      LVVS
Sbjct: 24  LVKLLRWHFGHADFRGKQLEAIQAVVSGRDCFCLMPTGGGKSICYQIPALAKPGIVLVVS 83

Query: 61  PLISLMQDQVMSLKQRGINAEFLGSAQT---DSSVQTKAETG--YFQLLFMTPEKACIIP 115
           PLI+LM++QVM+LK++GI AE+L S Q     + +    ++G    +LL++TPE   I  
Sbjct: 84  PLIALMENQVMALKEKGIAAEYLSSTQATHVKNKIHEDLDSGKPSVRLLYVTPE--LIAT 141

Query: 116 ISFWSKLLKAG----VCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATA 171
             F  KL K      + L A+DEAHCIS WGHDFR  Y+QL  LR  L  VP +ALTATA
Sbjct: 142 KGFMLKLRKLHSRGLLNLIAIDEAHCISSWGHDFRPSYRQLSTLRDSLADVPVLALTATA 201

Query: 172 TEKVRIDIINSLKLKNPYVTIASFDRKNLFYGVKVINRGQSFVDELVQEILKSVAGAGSI 231
             KV+ D+I+SL L+NP V  +SF+R N+FY V    R +  +D    ++   +   G+I
Sbjct: 202 APKVQKDVIDSLNLRNPLVLKSSFNRPNIFYEV----RYKDLLDNAYTDLGNLLKSCGNI 257

Query: 232 --IVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFG 289
             I+YC+     +++S  L  +G+ +  YH  + SK R      ++  + +++VAT+AFG
Sbjct: 258 CAIIYCLERTTCDDLSVHLSSIGISSAAYHAGLNSKMRSTVLDDWLSSKKQIIVATVAFG 317

Query: 290 MGIDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFYCGESQT 349
           MGIDK DVR V H+  PK++ES+YQESGR GRD + S   LYY   +  K ++    S+ 
Sbjct: 318 MGIDKKDVRMVCHFNIPKSMESFYQESGRAGRDQLPSRSVLYYGVDDRKKMEYLLRNSEN 377

Query: 350 ENQR-----TAIMESLLAAQRYCLLTTCRR 374
           +        T+  E ++    YC  + CRR
Sbjct: 378 KKSSSSKKPTSDFEQIVT---YCEGSGCRR 404

3'-5' DNA helicase that may play a role in the repair of DNA. Exhibits an ATP or dATP-dependent DNA-helicase activity. Can not use GTP/dGTP, CTP/dCTP or UTP/dUTP as nucleotide cofactors. Catalyzes DNA strand annealing. On nicked Holliday junctions, unwinds the lagging strand. Can not act on intact Holliday junctions.

Arabidopsis thaliana (taxid: 3702)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

>sp|P40724|RECQ_SALTY ATP-dependent DNA helicase RecQ OS=Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) GN=recQ PE=3 SV=3

 Score =  281 bits (719), Expect = 6e-75,   Method: Compositional matrix adjust.
 Identities = 155/375 (41%), Positives = 220/375 (58%), Gaps = 12/375 (3%)

Query: 4   TLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVTGKTALVVSPLI 63
            L++ FGY  FRP Q+ +I   +  RDCLVVM TG GKSLCYQ+P L+     +VVSPLI
Sbjct: 16  VLQETFGYQQFRPGQEAIIDTALSGRDCLVVMPTGGGKSLCYQIPALLLDGLTVVVSPLI 75

Query: 64  SLMQDQVMSLKQRGINAEFLGSAQTDS---SVQTKAETGYFQLLFMTPEKACIIPISFWS 120
           SLM+DQV  L   G+ A  L S Q+      V     TG  +LL++ PE+  ++  +F  
Sbjct: 76  SLMKDQVDQLLANGVAAACLNSTQSREQQLEVMAGCRTGQIRLLYIAPER--LMLDNFLD 133

Query: 121 KLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEKVRIDII 180
            L      L AVDEAHCIS+WGHDFR EY  L +LR     +PF+ALTATA +  R DII
Sbjct: 134 HLAHWNPVLLAVDEAHCISQWGHDFRPEYAALGQLRQRFPALPFMALTATADDTTRQDII 193

Query: 181 NSLKLKNPYVTIASFDRKNLFYGVKVINRGQSFVDELVQEILKSVAGAGSIIVYCMTIKD 240
             L L +P + I+SFDR N+ Y   ++      +D+L++ + +    +G  I+YC +   
Sbjct: 194 RLLGLNDPLIQISSFDRPNIRY---MLMEKFKPLDQLMRYVQEQRGKSG--IIYCNSRAK 248

Query: 241 VEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHV 300
           VE+ +  L+  G+ A  YH  + +  R +    F RD+++++VAT+AFGMGI+KP+VR V
Sbjct: 249 VEDTAARLQSRGISAAAYHAGLENAIRVDVQEKFQRDDLQIVVATVAFGMGINKPNVRFV 308

Query: 301 IHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFYCGESQTENQRTAIMESL 360
           +H+  P+ +ESYYQE+GR GRDG+ +   L+Y  ++ A     C E +   Q   I    
Sbjct: 309 VHFDIPRNIESYYQETGRAGRDGLPAEAMLFYDPADMAWLR-RCLEEKPAGQLQDIERHK 367

Query: 361 LAAQ-RYCLLTTCRR 374
           L A   +    TCRR
Sbjct: 368 LNAMGAFAEAQTCRR 382

Involved in the recF recombination pathway; its gene expression is under the regulation of the SOS system. It is a DNA helicase.

Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (taxid: 99287)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	374
356569961	920	PREDICTED: Werner syndrome ATP-dependent	1.0	0.406	0.772	1e-178
356537724	920	PREDICTED: LOW QUALITY PROTEIN: Werner s	1.0	0.406	0.759	1e-174
359478480	913	PREDICTED: Werner syndrome ATP-dependent	0.997	0.408	0.756	1e-172
449517403	919	PREDICTED: Werner syndrome ATP-dependent	1.0	0.406	0.745	1e-170
297745728	969	unnamed protein product [Vitis vinifera]	0.986	0.380	0.751	1e-170
449462782	906	PREDICTED: ATP-dependent DNA helicase Re	1.0	0.412	0.740	1e-169
147845197	447	hypothetical protein VITISV_016935 [Viti	0.997	0.834	0.745	1e-169
449462784	822	PREDICTED: ATP-dependent DNA helicase Re	1.0	0.454	0.703	1e-162
224124876	854	predicted protein [Populus trichocarpa]	0.909	0.398	0.782	1e-161
255570869	795	conserved hypothetical protein [Ricinus	0.922	0.433	0.742	1e-160

>gi|356569961|ref|XP_003553162.1| PREDICTED: Werner syndrome ATP-dependent helicase homolog [Glycine max]

 Score =  632 bits (1629), Expect = e-178,   Method: Compositional matrix adjust.
 Identities = 289/374 (77%), Positives = 329/374 (87%)

Query: 1   MVSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVTGKTALVVS 60
           M S LKKYFG+S FRPYQ++VI++IIEKRDCLVVMATGSGKSLCYQ+PPLV  KT +VVS
Sbjct: 6   MCSVLKKYFGFSDFRPYQREVIEKIIEKRDCLVVMATGSGKSLCYQVPPLVAKKTGIVVS 65

Query: 61  PLISLMQDQVMSLKQRGINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWS 120
           PLISLMQDQVM+LKQRGI AE+LGSAQ D +V +KAE G F +LFMTPEKAC +P SFWS
Sbjct: 66  PLISLMQDQVMALKQRGIKAEYLGSAQKDFTVHSKAEHGQFDILFMTPEKACTVPSSFWS 125

Query: 121 KLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEKVRIDII 180
            LLKAG+ LFAVDEAHCISEWGHDFR+EYK LDKLR  LL VPFV LTATATEKVR DII
Sbjct: 126 NLLKAGISLFAVDEAHCISEWGHDFRVEYKHLDKLREVLLDVPFVGLTATATEKVRYDII 185

Query: 181 NSLKLKNPYVTIASFDRKNLFYGVKVINRGQSFVDELVQEILKSVAGAGSIIVYCMTIKD 240
           +SLKL NPYVTI SFDR NLFYGVK++NRGQSF+DELV+EI K V   GS I+YC TIKD
Sbjct: 186 SSLKLNNPYVTIGSFDRTNLFYGVKLLNRGQSFIDELVREISKEVTNGGSTIIYCTTIKD 245

Query: 241 VEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHV 300
           VE+I K+  + G++AG YHGQM  KAREE+HRLF+RDE++VMVAT+AFGMGIDKP++R V
Sbjct: 246 VEQIFKSFAEAGIEAGMYHGQMNGKAREESHRLFVRDELQVMVATIAFGMGIDKPNIRQV 305

Query: 301 IHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFYCGESQTENQRTAIMESL 360
           IHYGCPK+LESYYQESGRCGRDGIASVCWLYY RS+FAKGDFYCG+ ++E QR AIMESL
Sbjct: 306 IHYGCPKSLESYYQESGRCGRDGIASVCWLYYTRSDFAKGDFYCGDVKSEKQRKAIMESL 365

Query: 361 LAAQRYCLLTTCRR 374
           LAA+RYC+LTTCRR
Sbjct: 366 LAAERYCVLTTCRR 379

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356537724|ref|XP_003537375.1| PREDICTED: LOW QUALITY PROTEIN: Werner syndrome ATP-dependent helicase homolog [Glycine max]

 Score =  617 bits (1591), Expect = e-174,   Method: Compositional matrix adjust.
 Identities = 284/374 (75%), Positives = 325/374 (86%)

Query: 1   MVSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVTGKTALVVS 60
           M S LKKYF +S FRPYQ++VI++IIEKRDCLVVMATGSGKSLCYQ+PPLV  KT +VVS
Sbjct: 6   MRSVLKKYFRFSDFRPYQREVIEKIIEKRDCLVVMATGSGKSLCYQVPPLVVKKTGIVVS 65

Query: 61  PLISLMQDQVMSLKQRGINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWS 120
           PLISLM+DQVM+LKQRGI AE+LGSAQ D +V +KAE G F +LFMTPEKAC +P SFWS
Sbjct: 66  PLISLMRDQVMALKQRGIKAEYLGSAQKDFTVHSKAEHGQFDILFMTPEKACTVPSSFWS 125

Query: 121 KLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEKVRIDII 180
            LLKAG+ LFAVDEAHCISEWGHDFR+EYK LDKLR  LL VPFV LTATATEKV+ DII
Sbjct: 126 NLLKAGISLFAVDEAHCISEWGHDFRVEYKHLDKLREVLLDVPFVGLTATATEKVQYDII 185

Query: 181 NSLKLKNPYVTIASFDRKNLFYGVKVINRGQSFVDELVQEILKSVAGAGSIIVYCMTIKD 240
            SLKL  P+VTI S DR NLFYGVK++NRGQSF+DELV+EI K V   GS I+YC TIKD
Sbjct: 186 GSLKLNYPFVTIGSVDRTNLFYGVKLLNRGQSFIDELVREISKEVTNGGSTIIYCTTIKD 245

Query: 241 VEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHV 300
           VE+I K+  + G++AG YHGQM  KAREE+HRLF+RDE++VMVAT+AFGMGIDKP++R V
Sbjct: 246 VEQIFKSFAEAGIEAGMYHGQMNGKAREESHRLFVRDELQVMVATIAFGMGIDKPNIRQV 305

Query: 301 IHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFYCGESQTENQRTAIMESL 360
           IHYGCPK+LESYYQESGRCGRDGIASVCWLYY RS+FAKGDFYCGE ++E QR AIMESL
Sbjct: 306 IHYGCPKSLESYYQESGRCGRDGIASVCWLYYTRSDFAKGDFYCGEVKSEKQRKAIMESL 365

Query: 361 LAAQRYCLLTTCRR 374
           LAA+RYC+LTTCRR
Sbjct: 366 LAAERYCVLTTCRR 379

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359478480|ref|XP_002275696.2| PREDICTED: Werner syndrome ATP-dependent helicase-like [Vitis vinifera]

 Score =  612 bits (1577), Expect = e-172,   Method: Compositional matrix adjust.
 Identities = 283/374 (75%), Positives = 323/374 (86%), Gaps = 1/374 (0%)

Query: 1   MVSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVTGKTALVVS 60
           M STLK+YFGYS FRPYQKD+IQ+I+E+RD LV+MATGSGKSLCYQLPPL+ GKTA+V+S
Sbjct: 1   MESTLKRYFGYSGFRPYQKDIIQKILERRDSLVIMATGSGKSLCYQLPPLILGKTAIVIS 60

Query: 61  PLISLMQDQVMSLKQRGINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWS 120
           PLISLMQDQVM+LKQRGI AEFL SAQTD +V   AE+G F +LFMTPEKAC IP SFWS
Sbjct: 61  PLISLMQDQVMALKQRGIRAEFLASAQTDPTVHKNAESGTFHVLFMTPEKACSIPGSFWS 120

Query: 121 KLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEKVRIDII 180
           KLLK G+CLFAVDEAHCISEWGHDFR+EYKQLDKLR  LL VPFV LTATAT+KVR+DII
Sbjct: 121 KLLKVGICLFAVDEAHCISEWGHDFRMEYKQLDKLRAILLDVPFVGLTATATKKVRMDII 180

Query: 181 NSLKLKNPYVTIASFDRKNLFYGVKVINRGQSFVDELVQEILKSVAGAGSIIVYCMTIKD 240
           NSLK+++P V I SFDRKNLFYGVK   R   F+DE V EI K VA + S I+YC TIKD
Sbjct: 181 NSLKMRDPNVFIGSFDRKNLFYGVKSFIRNSQFMDEFVGEISKFVASSDSTIIYCTTIKD 240

Query: 241 VEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHV 300
           VE+I K+L++ G+KAG YHGQM + AREE+HR+FIRDE+ VMVAT+AFGMGIDKP++RHV
Sbjct: 241 VEQIYKSLQEAGIKAGIYHGQMANSAREESHRIFIRDEVHVMVATIAFGMGIDKPNIRHV 300

Query: 301 IHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFYCGESQTENQRTAIMESL 360
           IHYGCPK+LESYYQESGRCGRDGIASVCWLYY R +F K DFYCGE+ T NQR AIM+SL
Sbjct: 301 IHYGCPKSLESYYQESGRCGRDGIASVCWLYYNRGDFMKADFYCGEA-TGNQRRAIMDSL 359

Query: 361 LAAQRYCLLTTCRR 374
           +AAQ YCL TTCRR
Sbjct: 360 VAAQNYCLQTTCRR 373

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449517403|ref|XP_004165735.1| PREDICTED: Werner syndrome ATP-dependent helicase homolog [Cucumis sativus]

 Score =  605 bits (1559), Expect = e-170,   Method: Compositional matrix adjust.
 Identities = 279/374 (74%), Positives = 323/374 (86%)

Query: 1   MVSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVTGKTALVVS 60
           M + LK YFG+S FR YQK++I+ I+  +DCLVVM+TGSGKSLCYQ+PPLV GKT +VVS
Sbjct: 1   MEAILKSYFGFSAFRLYQKEIIRDILLGKDCLVVMSTGSGKSLCYQVPPLVVGKTGIVVS 60

Query: 61  PLISLMQDQVMSLKQRGINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWS 120
           PLISLMQDQVM+LKQRGI +E+LGS QTDS+VQ KAE+G + +LFMTPEKAC +P+SFWS
Sbjct: 61  PLISLMQDQVMALKQRGIKSEYLGSTQTDSTVQAKAESGQYNVLFMTPEKACSVPMSFWS 120

Query: 121 KLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEKVRIDII 180
           KL KAG+CLFAVDEAHCISEWGHDFR+EYKQLDKLR  L  +PFVALTATATEKVR DII
Sbjct: 121 KLKKAGICLFAVDEAHCISEWGHDFRVEYKQLDKLRDVLPDLPFVALTATATEKVRSDII 180

Query: 181 NSLKLKNPYVTIASFDRKNLFYGVKVINRGQSFVDELVQEILKSVAGAGSIIVYCMTIKD 240
           NSLK+K+P VTI SFDR NLFYGVK  NRG  F++E V +I K VA  GS I+YC TIKD
Sbjct: 181 NSLKMKDPQVTIGSFDRTNLFYGVKSFNRGPLFMNEFVLDISKYVASGGSTIIYCTTIKD 240

Query: 241 VEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHV 300
           VE+I KAL++ G+ AG YHGQM  K+R E+HRLFIRDE++VMVAT+AFGMGIDKP++R V
Sbjct: 241 VEQIFKALEEAGISAGIYHGQMDKKSRAESHRLFIRDELQVMVATIAFGMGIDKPNIRQV 300

Query: 301 IHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFYCGESQTENQRTAIMESL 360
           IHYGCPK+LESYYQESGRCGRDGIASVCWLYY RS+FAK DFYCGESQTENQR AI ESL
Sbjct: 301 IHYGCPKSLESYYQESGRCGRDGIASVCWLYYTRSDFAKADFYCGESQTENQRRAIRESL 360

Query: 361 LAAQRYCLLTTCRR 374
           +AAQ+YC + TCRR
Sbjct: 361 MAAQQYCSIATCRR 374

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297745728|emb|CBI15784.3| unnamed protein product [Vitis vinifera]

 Score =  603 bits (1555), Expect = e-170,   Method: Compositional matrix adjust.
 Identities = 278/370 (75%), Positives = 320/370 (86%), Gaps = 1/370 (0%)

Query: 5   LKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVTGKTALVVSPLIS 64
           +++YFGYS FRPYQKD+IQ+I+E+RD LV+MATGSGKSLCYQLPPL+ GKTA+V+SPLIS
Sbjct: 5   VQRYFGYSGFRPYQKDIIQKILERRDSLVIMATGSGKSLCYQLPPLILGKTAIVISPLIS 64

Query: 65  LMQDQVMSLKQRGINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLK 124
           LMQDQVM+LKQRGI AEFL SAQTD +V   AE+G F +LFMTPEKAC IP SFWSKLLK
Sbjct: 65  LMQDQVMALKQRGIRAEFLASAQTDPTVHKNAESGTFHVLFMTPEKACSIPGSFWSKLLK 124

Query: 125 AGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEKVRIDIINSLK 184
            G+CLFAVDEAHCISEWGHDFR+EYKQLDKLR  LL VPFV LTATAT+KVR+DIINSLK
Sbjct: 125 VGICLFAVDEAHCISEWGHDFRMEYKQLDKLRAILLDVPFVGLTATATKKVRMDIINSLK 184

Query: 185 LKNPYVTIASFDRKNLFYGVKVINRGQSFVDELVQEILKSVAGAGSIIVYCMTIKDVEEI 244
           +++P V I SFDRKNLFYGVK   R   F+DE V EI K VA + S I+YC TIKDVE+I
Sbjct: 185 MRDPNVFIGSFDRKNLFYGVKSFIRNSQFMDEFVGEISKFVASSDSTIIYCTTIKDVEQI 244

Query: 245 SKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYG 304
            K+L++ G+KAG YHGQM + AREE+HR+FIRDE+ VMVAT+AFGMGIDKP++RHVIHYG
Sbjct: 245 YKSLQEAGIKAGIYHGQMANSAREESHRIFIRDEVHVMVATIAFGMGIDKPNIRHVIHYG 304

Query: 305 CPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFYCGESQTENQRTAIMESLLAAQ 364
           CPK+LESYYQESGRCGRDGIASVCWLYY R +F K DFYCGE+ T NQR AIM+SL+AAQ
Sbjct: 305 CPKSLESYYQESGRCGRDGIASVCWLYYNRGDFMKADFYCGEA-TGNQRRAIMDSLVAAQ 363

Query: 365 RYCLLTTCRR 374
            YCL TTCRR
Sbjct: 364 NYCLQTTCRR 373

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449462782|ref|XP_004149119.1| PREDICTED: ATP-dependent DNA helicase RecQ-like [Cucumis sativus]

 Score =  600 bits (1547), Expect = e-169,   Method: Compositional matrix adjust.
 Identities = 277/374 (74%), Positives = 321/374 (85%)

Query: 1   MVSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVTGKTALVVS 60
           M + LK YFG+S FR YQK++I+ I+  +DCLVVM+TGSGKSLCYQ+PPLV GKT +VVS
Sbjct: 1   MEAILKSYFGFSAFRLYQKEIIRDILLGKDCLVVMSTGSGKSLCYQVPPLVVGKTGIVVS 60

Query: 61  PLISLMQDQVMSLKQRGINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWS 120
           PLISLMQDQVM+LKQRGI +E+LGS Q DS+VQ  AE+G + +LFMTPEKAC +P+SFWS
Sbjct: 61  PLISLMQDQVMALKQRGIKSEYLGSTQADSTVQANAESGQYSILFMTPEKACSVPMSFWS 120

Query: 121 KLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEKVRIDII 180
           KL KAG+CLFAVDEAHCISEWGHDFR+EYKQLDKLR  L  +PFVALTATATEKVR DII
Sbjct: 121 KLKKAGICLFAVDEAHCISEWGHDFRVEYKQLDKLRDVLPDLPFVALTATATEKVRSDII 180

Query: 181 NSLKLKNPYVTIASFDRKNLFYGVKVINRGQSFVDELVQEILKSVAGAGSIIVYCMTIKD 240
           NSLK+K+P VTI SFDR NLFYGVK  NRG  F++E V +I K VA  GS I+YC TIKD
Sbjct: 181 NSLKMKDPQVTIGSFDRTNLFYGVKSFNRGPLFMNEFVLDISKYVASGGSTIIYCTTIKD 240

Query: 241 VEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHV 300
           VE+I KAL++ G+ AG YHGQM  K+R E+HRLFIRDE++VMVAT+AFGMGIDKP++R V
Sbjct: 241 VEQIFKALEEAGISAGIYHGQMDKKSRAESHRLFIRDEVQVMVATVAFGMGIDKPNIRLV 300

Query: 301 IHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFYCGESQTENQRTAIMESL 360
           IHYGCPK+LESYYQESGRCGRDGIASVCWLYY RS+FAK DFYCGESQTENQR AI ESL
Sbjct: 301 IHYGCPKSLESYYQESGRCGRDGIASVCWLYYTRSDFAKADFYCGESQTENQRRAIRESL 360

Query: 361 LAAQRYCLLTTCRR 374
           +AAQ+YC + TCRR
Sbjct: 361 MAAQQYCSIATCRR 374

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147845197|emb|CAN79469.1| hypothetical protein VITISV_016935 [Vitis vinifera]

 Score =  600 bits (1547), Expect = e-169,   Method: Compositional matrix adjust.
 Identities = 279/374 (74%), Positives = 321/374 (85%), Gaps = 1/374 (0%)

Query: 1   MVSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVTGKTALVVS 60
           M   +++YFGYS FRPYQKD+IQ+I+E+RD LV+MATGSGKSLCYQLPPL+ GKTA+V+S
Sbjct: 1   MWVLVQRYFGYSGFRPYQKDIIQKILERRDSLVIMATGSGKSLCYQLPPLILGKTAIVIS 60

Query: 61  PLISLMQDQVMSLKQRGINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWS 120
           PLISLMQDQVM+LKQRGI AEFL SAQTD +V   AE+G F +LFMTPEKAC IP SFWS
Sbjct: 61  PLISLMQDQVMALKQRGIRAEFLASAQTDPTVHKNAESGTFHVLFMTPEKACSIPGSFWS 120

Query: 121 KLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEKVRIDII 180
           KLLK G+CLFAVDEAHCISEWGHDFR+EYKQLDKLR  LL VPFV LTATAT+KVR+DII
Sbjct: 121 KLLKVGICLFAVDEAHCISEWGHDFRMEYKQLDKLRAILLDVPFVGLTATATKKVRMDII 180

Query: 181 NSLKLKNPYVTIASFDRKNLFYGVKVINRGQSFVDELVQEILKSVAGAGSIIVYCMTIKD 240
           NSLK+++P V I SFDRKNLFYGVK   R   F+DE V EI K VA + S I+YC TIKD
Sbjct: 181 NSLKMRDPNVFIGSFDRKNLFYGVKSFIRNSQFMDEFVGEISKFVASSDSTIIYCTTIKD 240

Query: 241 VEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHV 300
           VE+I K+L++ G+KAG YHGQM + AREE+HR+FIRDE+ VMVAT+AFGMGIDKP++RHV
Sbjct: 241 VEQIYKSLQEAGIKAGIYHGQMANSAREESHRIFIRDEVHVMVATIAFGMGIDKPNIRHV 300

Query: 301 IHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFYCGESQTENQRTAIMESL 360
           IHYGCPK+LESYYQESGRCGRDGIASVCWLYY R +F K DFYCGE+ T NQR AIM+SL
Sbjct: 301 IHYGCPKSLESYYQESGRCGRDGIASVCWLYYNRGDFMKADFYCGEA-TGNQRRAIMDSL 359

Query: 361 LAAQRYCLLTTCRR 374
           +AAQ YCL TTCRR
Sbjct: 360 VAAQNYCLQTTCRR 373

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449462784|ref|XP_004149120.1| PREDICTED: ATP-dependent DNA helicase RecQ-like [Cucumis sativus]

 Score =  578 bits (1490), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 263/374 (70%), Positives = 315/374 (84%)

Query: 1   MVSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVTGKTALVVS 60
           M + LK+YFG+S  RPYQK+VIQ I+  +DCLVV  TGSGKSLCYQ+PPLV GKT +VVS
Sbjct: 1   MEAILKRYFGFSALRPYQKEVIQSILRGKDCLVVTGTGSGKSLCYQVPPLVVGKTGIVVS 60

Query: 61  PLISLMQDQVMSLKQRGINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWS 120
           PL+SLMQDQVM+LKQRGI +E+LGS Q DS+VQ  AE+G + +LFMTPEKAC +P+SFWS
Sbjct: 61  PLVSLMQDQVMALKQRGIKSEYLGSTQADSTVQANAESGQYSILFMTPEKACSLPMSFWS 120

Query: 121 KLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEKVRIDII 180
           KL KAG+CLFAVDEAHCIS+WGH+FR EY+ LD  R  L G+PFVALTATA+EKVR DII
Sbjct: 121 KLKKAGICLFAVDEAHCISDWGHNFRAEYELLDNFRDILPGLPFVALTATASEKVRNDII 180

Query: 181 NSLKLKNPYVTIASFDRKNLFYGVKVINRGQSFVDELVQEILKSVAGAGSIIVYCMTIKD 240
           NSLK+K+P VTI SFDR NLFYGVK  N  +  ++ELV +I K V   GS I+YC TIKD
Sbjct: 181 NSLKMKDPQVTIGSFDRTNLFYGVKFFNHRRLLMNELVLDISKYVGSGGSTIIYCRTIKD 240

Query: 241 VEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHV 300
           VE+ISK+LK+ G+ AG YH QM  ++R E+HRLF+RDE++VMVAT+AFGMGIDKP++R V
Sbjct: 241 VEQISKSLKEAGISAGIYHAQMVKESRAESHRLFVRDELQVMVATVAFGMGIDKPNIRLV 300

Query: 301 IHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFYCGESQTENQRTAIMESL 360
           IHYGCPK+LESYYQESGRCGRDGIASVCWLYY RS+FAK + YCG+S TEN+RTAIMESL
Sbjct: 301 IHYGCPKSLESYYQESGRCGRDGIASVCWLYYTRSDFAKAELYCGDSPTENERTAIMESL 360

Query: 361 LAAQRYCLLTTCRR 374
           +AAQ+YC + TCRR
Sbjct: 361 MAAQQYCSIATCRR 374

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224124876|ref|XP_002319444.1| predicted protein [Populus trichocarpa] gi|222857820|gb|EEE95367.1| predicted protein [Populus trichocarpa]

 Score =  572 bits (1475), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 266/340 (78%), Positives = 296/340 (87%)

Query: 35  MATGSGKSLCYQLPPLVTGKTALVVSPLISLMQDQVMSLKQRGINAEFLGSAQTDSSVQT 94
           MATGSGKSLCYQ+PPL+  KTA+V+SPLISLMQDQVMSLKQRGI AEFLGSAQTD SV T
Sbjct: 1   MATGSGKSLCYQVPPLLLEKTAVVISPLISLMQDQVMSLKQRGIRAEFLGSAQTDGSVHT 60

Query: 95  KAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDK 154
           KA+TG+F LLFMTPEKAC  P+SFW KLL+AG+CLFAVDEAHCISEWGHDFR+EYKQL K
Sbjct: 61  KAQTGHFHLLFMTPEKACSTPLSFWLKLLEAGICLFAVDEAHCISEWGHDFRVEYKQLYK 120

Query: 155 LRTFLLGVPFVALTATATEKVRIDIINSLKLKNPYVTIASFDRKNLFYGVKVINRGQSFV 214
           LR  LL VPFVALTATATEKVRIDIINSLK+ NPYV + SFDRKNLFYGVK  NR   FV
Sbjct: 121 LRDVLLEVPFVALTATATEKVRIDIINSLKMNNPYVAVGSFDRKNLFYGVKHFNRSLQFV 180

Query: 215 DELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLF 274
           DELVQEI K    AGS I+YC TIKDVE+I K+LK+ G+K G YHGQM SKAREE+HR F
Sbjct: 181 DELVQEISKYARKAGSTIIYCTTIKDVEQIHKSLKEAGIKTGIYHGQMSSKAREESHRSF 240

Query: 275 IRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYAR 334
           +RDE+ VMVAT+AFGMGIDKP++R VIHYGCPK++ESYYQESGRCGRDGI SVCWLYY R
Sbjct: 241 VRDELLVMVATIAFGMGIDKPNIRQVIHYGCPKSIESYYQESGRCGRDGIPSVCWLYYTR 300

Query: 335 SNFAKGDFYCGESQTENQRTAIMESLLAAQRYCLLTTCRR 374
           ++FAK DFYCG  +TENQR A+MESL+AAQ YC LTTCRR
Sbjct: 301 ADFAKADFYCGGLRTENQRRAVMESLMAAQHYCSLTTCRR 340

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255570869|ref|XP_002526386.1| conserved hypothetical protein [Ricinus communis] gi|223534248|gb|EEF35962.1| conserved hypothetical protein [Ricinus communis]

 Score =  570 bits (1468), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 256/345 (74%), Positives = 298/345 (86%)

Query: 1   MVSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVTGKTALVVS 60
           M S LKKYFG+S FRPYQK+VI++I+E++DCLVVMATGSGKSLCYQ+PPLV GKTA+V+S
Sbjct: 1   MESALKKYFGFSGFRPYQKEVIEKILERKDCLVVMATGSGKSLCYQVPPLVAGKTAVVIS 60

Query: 61  PLISLMQDQVMSLKQRGINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWS 120
           PLISLMQDQVM+LKQRGI AE+LG+ QTD SV   A+ G+F LLF+TPEKAC +P+SFWS
Sbjct: 61  PLISLMQDQVMALKQRGIRAEYLGTGQTDHSVHNSAQNGHFNLLFVTPEKACSLPVSFWS 120

Query: 121 KLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEKVRIDII 180
            LLK GVCL AVDEAHCISEWGHDFR+EYKQL KLR  LL VPFV LTATAT KVR DII
Sbjct: 121 SLLKVGVCLLAVDEAHCISEWGHDFRVEYKQLYKLRNILLDVPFVGLTATATAKVRFDII 180

Query: 181 NSLKLKNPYVTIASFDRKNLFYGVKVINRGQSFVDELVQEILKSVAGAGSIIVYCMTIKD 240
           NSLK+ +PY+++ SFDRKNLFYGVK  NRG  F+DELVQEI K V    S I+YC T+KD
Sbjct: 181 NSLKMNDPYISVGSFDRKNLFYGVKHFNRGSQFMDELVQEISKFVGNGDSTIIYCTTVKD 240

Query: 241 VEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHV 300
           VE++ + L+Q G++AG YHGQMG+KAREE+H+ FIRDE+ VMVAT+AFGMGIDKP++R V
Sbjct: 241 VEQVFQLLQQAGIRAGIYHGQMGNKAREESHKSFIRDELHVMVATIAFGMGIDKPNIRQV 300

Query: 301 IHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFYCG 345
           IHYGCPK+LESYYQESGRCGRDGI SVCWLYY  S+FAKGDFYCG
Sbjct: 301 IHYGCPKSLESYYQESGRCGRDGIPSVCWLYYTGSDFAKGDFYCG 345

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	374
UNIPROTKB|O93530	1436	wrn "Werner syndrome ATP-depen	0.986	0.256	0.471	6.4e-83
UNIPROTKB|F1NAR0	1367	F1NAR0 "Uncharacterized protei	0.983	0.269	0.448	1.5e-80
UNIPROTKB|F1PZR2	1336	WRN "Uncharacterized protein"	0.989	0.276	0.456	2.7e-79
UNIPROTKB|F1PZR3	1499	WRN "Uncharacterized protein"	0.983	0.245	0.447	3.5e-79
UNIPROTKB|F1PUF8	1574	WRN "Uncharacterized protein"	0.983	0.233	0.447	4.1e-79
UNIPROTKB|Q14191	1432	WRN "Werner syndrome ATP-depen	0.986	0.257	0.439	7.9e-79
ZFIN|ZDB-GENE-070702-2	1436	wrn "Werner syndrome" [Danio r	0.775	0.201	0.448	3.6e-78
MGI|MGI:109635	1401	Wrn "Werner syndrome homolog (	0.991	0.264	0.440	1.3e-76
UNIPROTKB|F1RX70	1409	WRN "Uncharacterized protein"	0.991	0.263	0.442	1.3e-76
UNIPROTKB|I3LC91	1507	WRN "Uncharacterized protein"	0.991	0.246	0.442	1.7e-76

UNIPROTKB|O93530 wrn "Werner syndrome ATP-dependent helicase homolog" [Xenopus laevis (taxid:8355)]

 Score = 840 (300.8 bits), Expect = 6.4e-83, P = 6.4e-83
 Identities = 179/380 (47%), Positives = 240/380 (63%)

Query:     2 VSTLKKYFGYSVFRPYQKDVIQRII-EKRDCLVVMATGSGKSLCYQLPPLVTGKTALVVS 60
             +S LK YFG+S F+P Q  V+  ++ E+RD LVVMATG GKSLCYQ  P+ T    +V+ 
Sbjct:   478 ISCLKTYFGHSSFKPVQWKVVHSVLRERRDNLVVMATGYGKSLCYQFAPVYTSGIGIVIC 537

Query:    61 PLISLMQDQVMSLKQRGINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWS 120
             PLISLM+DQV+ L+   I++ FLGSAQ+ + +Q   + G  ++++MTPE  C   IS   
Sbjct:   538 PLISLMEDQVLQLEMSNISSCFLGSAQSKNVLQD-VKDGKMRVIYMTPE-FCSRGISLLQ 595

Query:   121 KL-LKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEKVRIDI 179
              L  + G+ L A+DEAHCISEWGHDFR  Y+ L  L+  L  VP VALTATA+  +R DI
Sbjct:   596 DLDNRYGITLIAIDEAHCISEWGHDFRSAYRSLGSLKRMLPNVPIVALTATASPSIREDI 655

Query:   180 INSLKLKNPYVTIASFDRKNLFYGVKVINRGQSFVDELVQEILKSVAGAG-----SIIVY 234
               SL L NP VT  SFDR NL+  + V  +  +   +L Q ++K   G+G     + IVY
Sbjct:   656 TKSLNLHNPQVTCTSFDRPNLY--LDVARKTTNISIDLRQFLIKKQQGSGWEFEGATIVY 713

Query:   235 CMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDK 294
             C T K  E+++  L +LG+  GTYH  MG K R E H  F+RDEI  +VAT+AFGMGI+K
Sbjct:   714 CPTRKTSEQVTAELIKLGIACGTYHAGMGIKQRREVHHRFMRDEIHCVVATVAFGMGINK 773

Query:   295 PDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFYCGESQTENQRT 354
             PD+R VIHYG PK +ESYYQE GR GRDG+ S C   +A+++        GE   +  R 
Sbjct:   774 PDIRKVIHYGAPKEMESYYQEIGRAGRDGLPSCCHALWAQADMNFNRHMLGEIPNKGFRE 833

Query:   355 AIMESLLAAQRYCLLTTCRR 374
               ++ L   ++Y   +TCRR
Sbjct:   834 YKLKMLTKMEKYLNSSTCRR 853

GO:0000287 "magnesium ion binding" evidence=ISS

GO:0006259 "DNA metabolic process" evidence=ISS

GO:0008408 "3'-5' exonuclease activity" evidence=ISS

GO:0030145 "manganese ion binding" evidence=ISS

UNIPROTKB|F1NAR0 F1NAR0 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 817 (292.7 bits), Expect = 1.5e-80, P = 1.5e-80
 Identities = 170/379 (44%), Positives = 240/379 (63%)

Query:     2 VSTLKKYFGYSVFRPYQKDVIQRIIE-KRDCLVVMATGSGKSLCYQLPPLVTGKTALVVS 60
             ++ LK YFG+S F+P Q  VI  ++E KRD LVVMATG GKSLCYQ PP+ TG T +V+ 
Sbjct:   448 IACLKTYFGHSSFKPVQWKVIHSVLEDKRDNLVVMATGYGKSLCYQFPPVYTGGTGIVIC 507

Query:    61 PLISLMQDQVMSLKQRGINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWS 120
             PLISLM+DQV+ L   GI++  LGSAQ+   V+   + G +++++MTPE  C   +    
Sbjct:   508 PLISLMEDQVLQLTMSGISSCLLGSAQS-KDVKDNIKAGLYRVIYMTPE-FCSGNLELLQ 565

Query:   121 KLLKA-GVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEKVRIDI 179
              + +  G+ L AVDEAHCISEWGHDFR+ +++L+ L+  L  VP VALTATA+  +R DI
Sbjct:   566 DIDRTTGIALIAVDEAHCISEWGHDFRISFRKLNSLKKALPSVPIVALTATASPSIREDI 625

Query:   180 INSLKLKNPYVTIASFDRKNLFYGVKVINRGQSFVDELVQEILKSVAGA-----GSIIVY 234
             +N L LKNP VT  SFDR NL+  ++V  +  + + +L Q + +  + +     G  I+Y
Sbjct:   626 VNCLNLKNPQVTCTSFDRPNLY--LEVGRQSGNTLRDLKQFLTRKGSSSTYEFEGPTIIY 683

Query:   235 CMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDK 294
             C + K  E++   L +LGV  G YH  MG + R + H  F+RDEI+ +VAT+AFGMGI+K
Sbjct:   684 CPSRKATEQVMFELNKLGVTCGAYHAGMGIQKRRDTHHQFMRDEIQCVVATVAFGMGINK 743

Query:   295 PDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFYCGESQTENQRT 354
              D+R VIHYG PK +ESYYQE GR GRDG+ + C + +  ++         E   E  R 
Sbjct:   744 ADIRMVIHYGAPKEMESYYQEIGRAGRDGLPASCHVLWTAADLVLNRRLLNEIHNEKFRL 803

Query:   355 AIMESLLAAQRYCLLTTCR 373
               ++ L   ++Y    +CR
Sbjct:   804 YKLKMLEKMEKYLSSNSCR 822

GO:0006310 "DNA recombination" evidence=IEA

GO:0043140 "ATP-dependent 3'-5' DNA helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0000287 "magnesium ion binding" evidence=IEA

GO:0000403 "Y-form DNA binding" evidence=IEA

GO:0000405 "bubble DNA binding" evidence=IEA

GO:0000723 "telomere maintenance" evidence=IEA

GO:0000731 "DNA synthesis involved in DNA repair" evidence=IEA

GO:0001302 "replicative cell aging" evidence=IEA

GO:0005654 "nucleoplasm" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

GO:0005813 "centrosome" evidence=IEA

GO:0006284 "base-excision repair" evidence=IEA

GO:0006979 "response to oxidative stress" evidence=IEA

GO:0008408 "3'-5' exonuclease activity" evidence=IEA

GO:0009267 "cellular response to starvation" evidence=IEA

GO:0009378 "four-way junction helicase activity" evidence=IEA

GO:0010225 "response to UV-C" evidence=IEA

GO:0010259 "multicellular organismal aging" evidence=IEA

GO:0030145 "manganese ion binding" evidence=IEA

GO:0031297 "replication fork processing" evidence=IEA

GO:0032066 "nucleolus to nucleoplasm transport" evidence=IEA

GO:0032389 "MutLalpha complex" evidence=IEA

GO:0032403 "protein complex binding" evidence=IEA

GO:0040009 "regulation of growth rate" evidence=IEA

GO:0042803 "protein homodimerization activity" evidence=IEA

GO:0042981 "regulation of apoptotic process" evidence=IEA

GO:0051345 "positive regulation of hydrolase activity" evidence=IEA

GO:0051880 "G-quadruplex DNA binding" evidence=IEA

UNIPROTKB|F1PZR2 WRN "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 805 (288.4 bits), Expect = 2.7e-79, P = 2.7e-79
 Identities = 173/379 (45%), Positives = 240/379 (63%)

Query:     2 VSTLKKYFGYSVFRPYQKDVIQRIIE-KRDCLVVMATGSGKSLCYQLPPLVTGKTALVVS 60
             ++ LK YFG+S F+P Q  VI  ++E +RD +VVMATG GKSLC+Q PP+ +G+  LV+S
Sbjct:   514 INFLKIYFGHSSFKPVQWKVIHSVLEERRDNVVVMATGYGKSLCFQYPPVYSGRIGLVIS 573

Query:    61 PLISLMQDQVMSLKQRGINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWS 120
             PLISLM+DQV+ LK   I A FLGSAQ+  +V    + G ++++++TPE  C   + F  
Sbjct:   574 PLISLMEDQVLQLKMSNIPACFLGSAQS-KNVLEDIKLGKYRIVYITPE-FCSGNL-FLL 630

Query:   121 KLLKA--GVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEKVRID 178
             + L+A  G+ L AVDEAHCISEWGHDFR  ++ L  L+  L  VP VALTATA+  +R D
Sbjct:   631 QQLQADIGITLIAVDEAHCISEWGHDFRSSFRTLGSLKAILPSVPIVALTATASSSIRED 690

Query:   179 IINSLKLKNPYVTIASFDRKNLFYGV--KVINRGQSFVDELVQEILKSV-AGAGSIIVYC 235
             I+  L LKNP +T   FDR NL+  V  K  +  Q     LVQ+   S+    G  I+YC
Sbjct:   691 IVRCLNLKNPQITCTGFDRPNLYLEVRRKTGSILQDLDQFLVQKTRNSIWEFEGPTIIYC 750

Query:   236 MTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKP 295
              + K  E+++  L++L +  G YH  +  K+R E H  F+RDEI+ +VAT+AFGMGI+K 
Sbjct:   751 PSRKTTEQVTAELRKLKLACGAYHAGLDIKSRREIHHRFMRDEIQCVVATIAFGMGINKA 810

Query:   296 DVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFYCGESQTENQRTA 355
             D+R VIHYG PK +ESYYQE GR GRDG+ S C + +A ++         E  +E  R  
Sbjct:   811 DIRKVIHYGAPKEMESYYQEIGRAGRDGLQSSCHVLWAPADICLNRHRLSEITSEKFRLY 870

Query:   356 IMESLLAAQRYCLLTTCRR 374
              ++ +   ++Y   T CRR
Sbjct:   871 KLKMMAKMEKYLHSTRCRR 889

GO:0005524 "ATP binding" evidence=IEA

GO:0043140 "ATP-dependent 3'-5' DNA helicase activity" evidence=IEA

GO:0008408 "3'-5' exonuclease activity" evidence=IEA

GO:0006310 "DNA recombination" evidence=IEA

GO:0006281 "DNA repair" evidence=IEA

GO:0006260 "DNA replication" evidence=IEA

GO:0005622 "intracellular" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|F1PZR3 WRN "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 806 (288.8 bits), Expect = 3.5e-79, P = 3.5e-79
 Identities = 170/380 (44%), Positives = 242/380 (63%)

Query:     2 VSTLKKYFGYSVFRPYQKDVIQRIIE-KRDCLVVMATGSGKSLCYQLPPLVTGKTALVVS 60
             ++ LK YFG+S F+P Q  VI  ++E +RD +VVMATG GKSLC+Q PP+ +G+  LV+S
Sbjct:   595 INFLKIYFGHSSFKPVQWKVIHSVLEERRDNVVVMATGYGKSLCFQYPPVYSGRIGLVIS 654

Query:    61 PLISLMQDQVMSLKQRGINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWS 120
             PLISLM+DQV+ LK   I A FLGSAQ+  +V    + G ++++++TPE  C   + F  
Sbjct:   655 PLISLMEDQVLQLKMSNIPACFLGSAQS-KNVLEDIKLGKYRIVYITPE-FCSGNL-FLL 711

Query:   121 KLLKA--GVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEKVRID 178
             + L+A  G+ L AVDEAHCISEWGHDFR  ++ L  L+  L  VP VALTATA+  +R D
Sbjct:   712 QQLQADIGITLIAVDEAHCISEWGHDFRSSFRTLGSLKAILPSVPIVALTATASSSIRED 771

Query:   179 IINSLKLKNPYVTIASFDRKNLFYGVKVINRGQSFVDELVQEILKSVAGA----GSIIVY 234
             I+  L LKNP +T   FDR NL+  V+   +  S + +L Q +++  +      G  I+Y
Sbjct:   772 IVRCLNLKNPQITCTGFDRPNLYLEVR--RKTGSILQDLDQFLVQKTSSIWEFEGPTIIY 829

Query:   235 CMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDK 294
             C + K  E+++  L++L +  G YH  +  K+R E H  F+RDEI+ +VAT+AFGMGI+K
Sbjct:   830 CPSRKTTEQVTAELRKLKLACGAYHAGLDIKSRREIHHRFMRDEIQCVVATIAFGMGINK 889

Query:   295 PDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFYCGESQTENQRT 354
              D+R VIHYG PK +ESYYQE GR GRDG+ S C + +A ++         E  +E  R 
Sbjct:   890 ADIRKVIHYGAPKEMESYYQEIGRAGRDGLQSSCHVLWAPADICLNRHRLSEITSEKFRL 949

Query:   355 AIMESLLAAQRYCLLTTCRR 374
               ++ +   ++Y   T CRR
Sbjct:   950 YKLKMMAKMEKYLHSTRCRR 969

GO:0005524 "ATP binding" evidence=IEA

GO:0043140 "ATP-dependent 3'-5' DNA helicase activity" evidence=IEA

GO:0008408 "3'-5' exonuclease activity" evidence=IEA

GO:0006310 "DNA recombination" evidence=IEA

GO:0006281 "DNA repair" evidence=IEA

GO:0006260 "DNA replication" evidence=IEA

GO:0005622 "intracellular" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|F1PUF8 WRN "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 806 (288.8 bits), Expect = 4.1e-79, P = 4.1e-79
 Identities = 170/380 (44%), Positives = 242/380 (63%)

Query:     2 VSTLKKYFGYSVFRPYQKDVIQRIIE-KRDCLVVMATGSGKSLCYQLPPLVTGKTALVVS 60
             ++ LK YFG+S F+P Q  VI  ++E +RD +VVMATG GKSLC+Q PP+ +G+  LV+S
Sbjct:   627 INFLKIYFGHSSFKPVQWKVIHSVLEERRDNVVVMATGYGKSLCFQYPPVYSGRIGLVIS 686

Query:    61 PLISLMQDQVMSLKQRGINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWS 120
             PLISLM+DQV+ LK   I A FLGSAQ+  +V    + G ++++++TPE  C   + F  
Sbjct:   687 PLISLMEDQVLQLKMSNIPACFLGSAQS-KNVLEDIKLGKYRIVYITPE-FCSGNL-FLL 743

Query:   121 KLLKA--GVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEKVRID 178
             + L+A  G+ L AVDEAHCISEWGHDFR  ++ L  L+  L  VP VALTATA+  +R D
Sbjct:   744 QQLQADIGITLIAVDEAHCISEWGHDFRSSFRTLGSLKAILPSVPIVALTATASSSIRED 803

Query:   179 IINSLKLKNPYVTIASFDRKNLFYGVKVINRGQSFVDELVQEILKSVAGA----GSIIVY 234
             I+  L LKNP +T   FDR NL+  V+   +  S + +L Q +++  +      G  I+Y
Sbjct:   804 IVRCLNLKNPQITCTGFDRPNLYLEVR--RKTGSILQDLDQFLVQKTSSIWEFEGPTIIY 861

Query:   235 CMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDK 294
             C + K  E+++  L++L +  G YH  +  K+R E H  F+RDEI+ +VAT+AFGMGI+K
Sbjct:   862 CPSRKTTEQVTAELRKLKLACGAYHAGLDIKSRREIHHRFMRDEIQCVVATIAFGMGINK 921

Query:   295 PDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFYCGESQTENQRT 354
              D+R VIHYG PK +ESYYQE GR GRDG+ S C + +A ++         E  +E  R 
Sbjct:   922 ADIRKVIHYGAPKEMESYYQEIGRAGRDGLQSSCHVLWAPADICLNRHRLSEITSEKFRL 981

Query:   355 AIMESLLAAQRYCLLTTCRR 374
               ++ +   ++Y   T CRR
Sbjct:   982 YKLKMMAKMEKYLHSTRCRR 1001

GO:0005524 "ATP binding" evidence=IEA

GO:0043140 "ATP-dependent 3'-5' DNA helicase activity" evidence=IEA

GO:0008408 "3'-5' exonuclease activity" evidence=IEA

GO:0006310 "DNA recombination" evidence=IEA

GO:0006281 "DNA repair" evidence=IEA

GO:0006260 "DNA replication" evidence=IEA

GO:0005622 "intracellular" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|Q14191 WRN "Werner syndrome ATP-dependent helicase" [Homo sapiens (taxid:9606)]

 Score = 802 (287.4 bits), Expect = 7.9e-79, P = 7.9e-79
 Identities = 166/378 (43%), Positives = 241/378 (63%)

Query:     2 VSTLKKYFGYSVFRPYQKDVIQRIIE-KRDCLVVMATGSGKSLCYQLPPLVTGKTALVVS 60
             V+ LK YFG+S F+P Q  VI  ++E +RD + VMATG GKSLC+Q PP+  GK  LV+S
Sbjct:   537 VTCLKMYFGHSSFKPVQWKVIHSVLEERRDNVAVMATGYGKSLCFQYPPVYVGKIGLVIS 596

Query:    61 PLISLMQDQVMSLKQRGINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWS 120
             PLISLM+DQV+ LK   I A FLGSAQ+++ V T  + G ++++++TPE  C   +    
Sbjct:   597 PLISLMEDQVLQLKMSNIPACFLGSAQSEN-VLTDIKLGKYRIVYVTPEY-CSGNMGLLQ 654

Query:   121 KL-LKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEKVRIDI 179
             +L    G+ L AVDEAHCISEWGHDFR  +++L  L+T L  VP VALTATA+  +R DI
Sbjct:   655 QLEADIGITLIAVDEAHCISEWGHDFRDSFRKLGSLKTALPMVPIVALTATASSSIREDI 714

Query:   180 INSLKLKNPYVTIASFDRKNLFYGVKVINRGQSFVDELVQEILKSVAG---AGSIIVYCM 236
             +  L L+NP +T   FDR NL+  V+   +  + + +L   ++K+ +     G  I+YC 
Sbjct:   715 VRCLNLRNPQITCTGFDRPNLYLEVR--RKTGNILQDLQPFLVKTSSHWEFEGPTIIYCP 772

Query:   237 TIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPD 296
             + K  ++++  L++L +  GTYH  M    R++ H  F+RDEI+ ++AT+AFGMGI+K D
Sbjct:   773 SRKMTQQVTGELRKLNLSCGTYHAGMSFSTRKDIHHRFVRDEIQCVIATIAFGMGINKAD 832

Query:   297 VRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFYCGESQTENQRTAI 356
             +R VIHYG PK +ESYYQE GR GRDG+ S C + +A ++         E + E  R   
Sbjct:   833 IRQVIHYGAPKDMESYYQEIGRAGRDGLQSSCHVLWAPADINLNRHLLTEIRNEKFRLYK 892

Query:   357 MESLLAAQRYCLLTTCRR 374
             ++ +   ++Y   + CRR
Sbjct:   893 LKMMAKMEKYLHSSRCRR 910

GO:0006310 "DNA recombination" evidence=IEA

GO:0043140 "ATP-dependent 3'-5' DNA helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0001302 "replicative cell aging" evidence=IEA

GO:0040009 "regulation of growth rate" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0016887 "ATPase activity" evidence=IDA

GO:0031297 "replication fork processing" evidence=IMP;IDA

GO:0005730 "nucleolus" evidence=IDA

GO:0000723 "telomere maintenance" evidence=IMP

GO:0007569 "cell aging" evidence=IMP

GO:0010259 "multicellular organismal aging" evidence=IMP

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

GO:0007568 "aging" evidence=NAS

GO:0003677 "DNA binding" evidence=IDA

GO:0003678 "DNA helicase activity" evidence=IDA;IMP

GO:0004386 "helicase activity" evidence=IDA

GO:0008408 "3'-5' exonuclease activity" evidence=IDA

GO:0042803 "protein homodimerization activity" evidence=IDA

GO:0032403 "protein complex binding" evidence=IDA

GO:0000731 "DNA synthesis involved in DNA repair" evidence=IDA

GO:0010225 "response to UV-C" evidence=IDA

GO:0006974 "response to DNA damage stimulus" evidence=IDA

GO:0006260 "DNA replication" evidence=IMP

GO:0032389 "MutLalpha complex" evidence=IDA

GO:0000403 "Y-form DNA binding" evidence=IDA

GO:0043138 "3'-5' DNA helicase activity" evidence=IDA

GO:0000405 "bubble DNA binding" evidence=IDA

GO:0009378 "four-way junction helicase activity" evidence=IDA

GO:0051880 "G-quadruplex DNA binding" evidence=IDA

GO:0006284 "base-excision repair" evidence=IDA

GO:0051345 "positive regulation of hydrolase activity" evidence=IDA

GO:0006979 "response to oxidative stress" evidence=IDA

GO:0005813 "centrosome" evidence=IDA

GO:0000287 "magnesium ion binding" evidence=IDA

GO:0030145 "manganese ion binding" evidence=IDA

GO:0006259 "DNA metabolic process" evidence=IDA

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

GO:0005654 "nucleoplasm" evidence=IDA

GO:0071480 "cellular response to gamma radiation" evidence=IDA

GO:0004527 "exonuclease activity" evidence=IDA

GO:0009267 "cellular response to starvation" evidence=IDA

GO:0032066 "nucleolus to nucleoplasm transport" evidence=IDA

GO:0042981 "regulation of apoptotic process" evidence=IGI

GO:0005634 "nucleus" evidence=IDA

GO:0006200 "ATP catabolic process" evidence=IDA

GO:0032508 "DNA duplex unwinding" evidence=IMP;IDA

ZFIN|ZDB-GENE-070702-2 wrn "Werner syndrome" [Danio rerio (taxid:7955)]

 Score = 601 (216.6 bits), Expect = 3.6e-78, Sum P(2) = 3.6e-78
 Identities = 136/303 (44%), Positives = 188/303 (62%)

Query:     2 VSTLKKYFGYSVFRPYQKDVIQRII-EKRDCLVVMATGSGKSLCYQLPPLVTGKTALVVS 60
             +  LK +FG+  F+P Q  VIQ I+ E+RD LVVMATG GKSLC+Q PP+     ++V+S
Sbjct:   432 IKCLKMFFGHHSFKPVQWKVIQSILTERRDNLVVMATGYGKSLCFQFPPVYCQTISVVIS 491

Query:    61 PLISLMQDQVMSLKQRGINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWS 120
             PLI+LM+DQV+ L    I A FLGSAQT  ++  + + G F++++MTPE  C   I    
Sbjct:   492 PLIALMEDQVLQLTMSNIPACFLGSAQT-KNLNEQVKRGDFRVVYMTPE-FCSGNIPLLV 549

Query:   121 KLLKA-GVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEKVRIDI 179
             +L +  G+ L AVDEAHCIS+WGHDFR  Y++L KL+  L  VPF+ALTATA+  +R DI
Sbjct:   550 QLDRTVGLSLIAVDEAHCISQWGHDFRSAYRELGKLKKNLPTVPFLALTATASPSIRDDI 609

Query:   180 INSLKLKNPYVTIASFDRKNLFYGVKVINRGQSFVDELVQEILKSVAGA----GSIIVYC 235
             I SL L NP +T  SFDR NL+  V    +    + +L + ++K   G     GS IVYC
Sbjct:   610 IKSLHLINPMITCTSFDRPNLYLDVN--RKSGDVIQDLKRFLVKKKGGGYEFEGSAIVYC 667

Query:   236 MTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVM---VATMAFGMGI 292
              + K+ E ++ AL +L +  G YH  +  K R E    F+RDEI+V    VA +    G+
Sbjct:   668 PSKKEAERVTTALFKLDIPCGVYHAGLSIKQRRETQHQFMRDEIQVHAYDVAAVVSVPGV 727

Query:   293 DKP 295
             + P
Sbjct:   728 NPP 730

GO:0043140 "ATP-dependent 3'-5' DNA helicase activity" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005622 "intracellular" evidence=IEA

GO:0006281 "DNA repair" evidence=IEA

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

GO:0044237 "cellular metabolic process" evidence=IEA

GO:0003824 "catalytic activity" evidence=IEA

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

GO:0006310 "DNA recombination" evidence=IEA

GO:0008408 "3'-5' exonuclease activity" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0006260 "DNA replication" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

MGI|MGI:109635 Wrn "Werner syndrome homolog (human)" [Mus musculus (taxid:10090)]

 Score = 781 (280.0 bits), Expect = 1.3e-76, P = 1.3e-76
 Identities = 166/377 (44%), Positives = 237/377 (62%)

Query:     2 VSTLKKYFGYSVFRPYQKDVIQRIIE-KRDCLVVMATGSGKSLCYQLPPLVTGKTALVVS 60
             ++ LK YFG+S F+P Q  VI  ++E +RD +VVMATG GKSLC+Q PP+ TGK  +V+S
Sbjct:   501 INCLKTYFGHSSFKPVQWKVIHSVLEERRDNVVVMATGYGKSLCFQYPPVYTGKIGIVIS 560

Query:    61 PLISLMQDQVMSLKQRGINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWS 120
             PLISLM+DQV+ L+   + A  LGSAQ+  ++    + G ++++++TPE  C   +    
Sbjct:   561 PLISLMEDQVLQLELSNVPACLLGSAQS-KNILGDVKLGKYRVIYITPE-FCSGNLDLLQ 618

Query:   121 KLLKA-GVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEKVRIDI 179
             +L  + G+ L AVDEAHCISEWGHDFR  ++ L  L+T L  VP +AL+ATA+  +R DI
Sbjct:   619 QLDSSIGITLIAVDEAHCISEWGHDFRSSFRMLGSLKTALPLVPVIALSATASSSIREDI 678

Query:   180 INSLKLKNPYVTIASFDRKNLFY--GVKVINRGQSFVDELVQEILKSVAGAGSIIVYCMT 237
             I+ L LK+P +T   FDR NL+   G K  N  Q     LV++   +    G  I+YC +
Sbjct:   679 ISCLNLKDPQITCTGFDRPNLYLEVGRKTGNILQDLKPFLVRKASSAWEFEGPTIIYCPS 738

Query:   238 IKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDV 297
              K  E+++  L +L +   TYH  M    R++ H  F+RDEI+ +VAT+AFGMGI+K D+
Sbjct:   739 RKMTEQVTAELGKLNLACRTYHAGMKISERKDVHHRFLRDEIQCVVATVAFGMGINKADI 798

Query:   298 RHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFYCGESQTENQRTAIM 357
             R VIHYG PK +ESYYQE GR GRDG+ S C L +A ++F        E   E  R   +
Sbjct:   799 RKVIHYGAPKEMESYYQEIGRAGRDGLQSSCHLLWAPADFNTSRNLLIEIHDEKFRLYKL 858

Query:   358 ESLLAAQRYCLLTTCRR 374
             + ++  ++Y   + CRR
Sbjct:   859 KMMVKMEKYLHSSQCRR 875

GO:0000166 "nucleotide binding" evidence=IEA

GO:0000287 "magnesium ion binding" evidence=ISO

GO:0000403 "Y-form DNA binding" evidence=ISO

GO:0000405 "bubble DNA binding" evidence=ISO

GO:0000723 "telomere maintenance" evidence=ISO;IGI;IMP

GO:0000731 "DNA synthesis involved in DNA repair" evidence=ISO

GO:0001302 "replicative cell aging" evidence=IMP

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003677 "DNA binding" evidence=ISO

GO:0003678 "DNA helicase activity" evidence=ISO

GO:0003824 "catalytic activity" evidence=IEA

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

GO:0004386 "helicase activity" evidence=ISO

GO:0004518 "nuclease activity" evidence=IEA

GO:0004527 "exonuclease activity" evidence=ISO

GO:0005515 "protein binding" evidence=IPI

GO:0005524 "ATP binding" evidence=IEA

GO:0005622 "intracellular" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

GO:0005654 "nucleoplasm" evidence=ISO;IDA

GO:0005730 "nucleolus" evidence=ISO;IDA

GO:0005813 "centrosome" evidence=ISO

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

GO:0006200 "ATP catabolic process" evidence=ISO

GO:0006259 "DNA metabolic process" evidence=ISO;IMP

GO:0006260 "DNA replication" evidence=ISO;IMP

GO:0006281 "DNA repair" evidence=IEA

GO:0006284 "base-excision repair" evidence=ISO

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

GO:0006310 "DNA recombination" evidence=IEA

GO:0006974 "response to DNA damage stimulus" evidence=ISO

GO:0006979 "response to oxidative stress" evidence=ISO

GO:0007569 "cell aging" evidence=ISO

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

GO:0008152 "metabolic process" evidence=IEA

GO:0008408 "3'-5' exonuclease activity" evidence=ISO;IDA

GO:0009267 "cellular response to starvation" evidence=ISO

GO:0009378 "four-way junction helicase activity" evidence=ISO

GO:0010225 "response to UV-C" evidence=ISO

GO:0010259 "multicellular organismal aging" evidence=ISO;IGI

GO:0016787 "hydrolase activity" evidence=IEA

GO:0016887 "ATPase activity" evidence=ISO

GO:0030145 "manganese ion binding" evidence=ISO

GO:0031297 "replication fork processing" evidence=ISO

GO:0032066 "nucleolus to nucleoplasm transport" evidence=ISO

GO:0032403 "protein complex binding" evidence=ISO

GO:0032508 "DNA duplex unwinding" evidence=ISO

GO:0040009 "regulation of growth rate" evidence=IMP

GO:0042803 "protein homodimerization activity" evidence=ISO

GO:0042981 "regulation of apoptotic process" evidence=ISO

GO:0043138 "3'-5' DNA helicase activity" evidence=ISO

GO:0043140 "ATP-dependent 3'-5' DNA helicase activity" evidence=IEA

GO:0044237 "cellular metabolic process" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

GO:0051345 "positive regulation of hydrolase activity" evidence=ISO

GO:0051880 "G-quadruplex DNA binding" evidence=ISO

GO:0071480 "cellular response to gamma radiation" evidence=ISO

UNIPROTKB|F1RX70 WRN "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 781 (280.0 bits), Expect = 1.3e-76, P = 1.3e-76
 Identities = 167/377 (44%), Positives = 233/377 (61%)

Query:     2 VSTLKKYFGYSVFRPYQKDVIQRIIE-KRDCLVVMATGSGKSLCYQLPPLVTGKTALVVS 60
             ++ LK YFG+S F+P Q  VI  I+E +RD +VVMATG GKSLC+Q PP+  G   LV+S
Sbjct:   505 INCLKTYFGHSSFKPVQWKVIHSILEERRDNVVVMATGYGKSLCFQYPPVSVGGIGLVIS 564

Query:    61 PLISLMQDQVMSLKQRGINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWS 120
             PLISLM+DQV+ L+   I A FLGSAQ+  +V    + G ++++++TPE  C   +    
Sbjct:   565 PLISLMEDQVLQLEMSNIPACFLGSAQS-KNVLEDIKLGKYRIVYLTPE-FCSGNLDLLQ 622

Query:   121 KL-LKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEKVRIDI 179
              L    G+ + AVDEAHCISEWGHDFR  ++ L  L++ L  VP VALTAT T  +R DI
Sbjct:   623 HLEANIGITVIAVDEAHCISEWGHDFRNSFRTLGSLKSALPLVPIVALTATGTSSIREDI 682

Query:   180 INSLKLKNPYVTIASFDRKNLFY--GVKVINRGQSFVDELVQEILKSVAGAGSIIVYCMT 237
             +  LKLK+P +T   FDR NL+   G K  +  Q     LVQ+   +    G  I+YC +
Sbjct:   683 VRCLKLKDPQITCTGFDRPNLYLEVGRKTGDILQDLKQFLVQKTSSAWEFEGPTIIYCPS 742

Query:   238 IKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDV 297
              K  E+++  LK+L +   TYH  +    R++ H  F+RDEI+ ++AT+AFGMGI+K D+
Sbjct:   743 RKMTEQVTAELKKLKLACETYHAGLSIHLRKQVHHKFMRDEIQCVIATIAFGMGINKADI 802

Query:   298 RHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFYCGESQTENQRTAIM 357
             R VIHYG PK +ESYYQE GR GRDG+ S C + +A ++         E   EN R   +
Sbjct:   803 RKVIHYGAPKEIESYYQEIGRAGRDGLQSSCHILWAPADINLNRHLLSEICNENFRLYKL 862

Query:   358 ESLLAAQRYCLLTTCRR 374
             + +   ++Y   + CRR
Sbjct:   863 KMMAKMEKYLHSSRCRR 879

GO:0005524 "ATP binding" evidence=IEA

GO:0043140 "ATP-dependent 3'-5' DNA helicase activity" evidence=IEA

GO:0008408 "3'-5' exonuclease activity" evidence=IEA

GO:0006310 "DNA recombination" evidence=IEA

GO:0006281 "DNA repair" evidence=IEA

GO:0006260 "DNA replication" evidence=IEA

GO:0005622 "intracellular" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|I3LC91 WRN "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 781 (280.0 bits), Expect = 1.7e-76, P = 1.7e-76
 Identities = 167/377 (44%), Positives = 233/377 (61%)

Query:     2 VSTLKKYFGYSVFRPYQKDVIQRIIE-KRDCLVVMATGSGKSLCYQLPPLVTGKTALVVS 60
             ++ LK YFG+S F+P Q  VI  I+E +RD +VVMATG GKSLC+Q PP+  G   LV+S
Sbjct:   604 INCLKTYFGHSSFKPVQWKVIHSILEERRDNVVVMATGYGKSLCFQYPPVSVGGIGLVIS 663

Query:    61 PLISLMQDQVMSLKQRGINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWS 120
             PLISLM+DQV+ L+   I A FLGSAQ+  +V    + G ++++++TPE  C   +    
Sbjct:   664 PLISLMEDQVLQLEMSNIPACFLGSAQS-KNVLEDIKLGKYRIVYLTPE-FCSGNLDLLQ 721

Query:   121 KL-LKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEKVRIDI 179
              L    G+ + AVDEAHCISEWGHDFR  ++ L  L++ L  VP VALTAT T  +R DI
Sbjct:   722 HLEANIGITVIAVDEAHCISEWGHDFRNSFRTLGSLKSALPLVPIVALTATGTSSIREDI 781

Query:   180 INSLKLKNPYVTIASFDRKNLFY--GVKVINRGQSFVDELVQEILKSVAGAGSIIVYCMT 237
             +  LKLK+P +T   FDR NL+   G K  +  Q     LVQ+   +    G  I+YC +
Sbjct:   782 VRCLKLKDPQITCTGFDRPNLYLEVGRKTGDILQDLKQFLVQKTSSAWEFEGPTIIYCPS 841

Query:   238 IKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDV 297
              K  E+++  LK+L +   TYH  +    R++ H  F+RDEI+ ++AT+AFGMGI+K D+
Sbjct:   842 RKMTEQVTAELKKLKLACETYHAGLSIHLRKQVHHKFMRDEIQCVIATIAFGMGINKADI 901

Query:   298 RHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFYCGESQTENQRTAIM 357
             R VIHYG PK +ESYYQE GR GRDG+ S C + +A ++         E   EN R   +
Sbjct:   902 RKVIHYGAPKEIESYYQEIGRAGRDGLQSSCHILWAPADINLNRHLLSEICNENFRLYKL 961

Query:   358 ESLLAAQRYCLLTTCRR 374
             + +   ++Y   + CRR
Sbjct:   962 KMMAKMEKYLHSSRCRR 978

GO:0051880 "G-quadruplex DNA binding" evidence=IEA

GO:0051345 "positive regulation of hydrolase activity" evidence=IEA

GO:0042981 "regulation of apoptotic process" evidence=IEA

GO:0042803 "protein homodimerization activity" evidence=IEA

GO:0040009 "regulation of growth rate" evidence=IEA

GO:0032403 "protein complex binding" evidence=IEA

GO:0032389 "MutLalpha complex" evidence=IEA

GO:0032066 "nucleolus to nucleoplasm transport" evidence=IEA

GO:0031297 "replication fork processing" evidence=IEA

GO:0030145 "manganese ion binding" evidence=IEA

GO:0010259 "multicellular organismal aging" evidence=IEA

GO:0010225 "response to UV-C" evidence=IEA

GO:0009378 "four-way junction helicase activity" evidence=IEA

GO:0009267 "cellular response to starvation" evidence=IEA

GO:0008408 "3'-5' exonuclease activity" evidence=IEA

GO:0006979 "response to oxidative stress" evidence=IEA

GO:0006284 "base-excision repair" evidence=IEA

GO:0005813 "centrosome" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

GO:0005654 "nucleoplasm" evidence=IEA

GO:0001302 "replicative cell aging" evidence=IEA

GO:0000731 "DNA synthesis involved in DNA repair" evidence=IEA

GO:0000723 "telomere maintenance" evidence=IEA

GO:0000405 "bubble DNA binding" evidence=IEA

GO:0000403 "Y-form DNA binding" evidence=IEA

GO:0000287 "magnesium ion binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0043140 "ATP-dependent 3'-5' DNA helicase activity" evidence=IEA

GO:0006310 "DNA recombination" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	3.6.4.12	0.737
3rd Layer	3.6.4	0.691

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	374
TIGR00614	470	TIGR00614, recQ_fam, ATP-dependent DNA helicase, R	1e-147
COG0514	590	COG0514, RecQ, Superfamily II DNA helicase [DNA re	1e-135
TIGR01389	591	TIGR01389, recQ, ATP-dependent DNA helicase RecQ	1e-129
PRK11057	607	PRK11057, PRK11057, ATP-dependent DNA helicase Rec	1e-109
PLN03137	1195	PLN03137, PLN03137, ATP-dependent DNA helicase; Q4	7e-84
cd00079	131	cd00079, HELICc, Helicase superfamily c-terminal d	8e-34
pfam00270	169	pfam00270, DEAD, DEAD/DEAH box helicase	2e-32
smart00490	82	smart00490, HELICc, helicase superfamily c-termina	5e-27
pfam00271	78	pfam00271, Helicase_C, Helicase conserved C-termin	7e-26
smart00487	201	smart00487, DEXDc, DEAD-like helicases superfamily	3e-23
COG0513	513	COG0513, SrmB, Superfamily II DNA and RNA helicase	1e-20
cd00046	144	cd00046, DEXDc, DEAD-like helicases superfamily	2e-19
COG1205	851	COG1205, COG1205, Distinct helicase family with a	8e-16
COG1201	814	COG1201, Lhr, Lhr-like helicases [General function	3e-13
COG1202	830	COG1202, COG1202, Superfamily II helicase, archaea	3e-12
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	6e-11
PTZ00110	545	PTZ00110, PTZ00110, helicase; Provisional	4e-10
PLN00206	518	PLN00206, PLN00206, DEAD-box ATP-dependent RNA hel	7e-10
PTZ00424	401	PTZ00424, PTZ00424, helicase 45; Provisional	2e-09
PRK10590	456	PRK10590, PRK10590, ATP-dependent RNA helicase Rhl	3e-09
cd09639	353	cd09639, Cas3_I, CRISPR/Cas system-associated prot	7e-08
TIGR01587	358	TIGR01587, cas3_core, CRISPR-associated helicase C	1e-07
COG1203	733	COG1203, COG1203, CRISPR-associated helicase Cas3	3e-07
pfam04851	100	pfam04851, ResIII, Type III restriction enzyme, re	4e-07
TIGR00580	926	TIGR00580, mfd, transcription-repair coupling fact	5e-07
PRK01297	475	PRK01297, PRK01297, ATP-dependent RNA helicase Rhl	7e-07
TIGR01054	1171	TIGR01054, rgy, reverse gyrase	3e-06
COG1200	677	COG1200, RecG, RecG-like helicase [DNA replication	3e-06
COG1204	766	COG1204, COG1204, Superfamily II helicase [General	3e-06
TIGR03817	742	TIGR03817, DECH_helic, helicase/secretion neighbor	5e-06
PRK11634	629	PRK11634, PRK11634, ATP-dependent RNA helicase Dea	7e-06
COG1110	1187	COG1110, COG1110, Reverse gyrase [DNA replication,	8e-06
PRK11776	460	PRK11776, PRK11776, ATP-dependent RNA helicase Dbp	2e-05
COG1061	442	COG1061, SSL2, DNA or RNA helicases of superfamily	3e-05
PRK04537	572	PRK04537, PRK04537, ATP-dependent RNA helicase Rhl	6e-05
TIGR00643	630	TIGR00643, recG, ATP-dependent DNA helicase RecG	1e-04
COG4096	875	COG4096, HsdR, Type I site-specific restriction-mo	3e-04
TIGR04121	803	TIGR04121, DEXH_lig_assoc, DEXH box helicase, DNA	7e-04
PRK09751	1490	PRK09751, PRK09751, putative ATP-dependent helicas	8e-04
COG1197	1139	COG1197, Mfd, Transcription-repair coupling factor	0.001
PRK11448	1123	PRK11448, hsdR, type I restriction enzyme EcoKI su	0.001
COG0513	513	COG0513, SrmB, Superfamily II DNA and RNA helicase	0.002
PRK04837	423	PRK04837, PRK04837, ATP-dependent RNA helicase Rhl	0.002
PRK13766	773	PRK13766, PRK13766, Hef nuclease; Provisional	0.002
TIGR03817	742	TIGR03817, DECH_helic, helicase/secretion neighbor	0.003
PRK10689	1147	PRK10689, PRK10689, transcription-repair coupling	0.003
COG1199	654	COG1199, DinG, Rad3-related DNA helicases [Transcr	0.004

>gnl|CDD|129701 TIGR00614, recQ_fam, ATP-dependent DNA helicase, RecQ family

 Score =  425 bits (1095), Expect = e-147
 Identities = 184/377 (48%), Positives = 237/377 (62%), Gaps = 10/377 (2%)

Query: 3   STLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVTGKTALVVSPL 62
           S LK  FG S FRP Q +VI  ++  RDC VVM TG GKSLCYQLP L +    LV+SPL
Sbjct: 1   SILKTVFGLSSFRPVQLEVINAVLLGRDCFVVMPTGGGKSLCYQLPALCSDGITLVISPL 60

Query: 63  ISLMQDQVMSLKQRGINAEFLGSAQTDSS---VQTKAETGYFQLLFMTPEKACIIPISFW 119
           ISLM+DQV+ LK  GI A FL S+Q+      V T  + G  +LL++TPEK C       
Sbjct: 61  ISLMEDQVLQLKASGIPATFLNSSQSKEQQKNVLTDLKDGKIKLLYVTPEK-CSASNRLL 119

Query: 120 SKLLKA-GVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEKVRID 178
             L +  G+ L AVDEAHCIS+WGHDFR +YK L  L+     VP +ALTATA+  VR D
Sbjct: 120 QTLEERKGITLIAVDEAHCISQWGHDFRPDYKALGSLKQKFPNVPIMALTATASPSVRED 179

Query: 179 IINSLKLKNPYVTIASFDRKNLFYGVKVINRGQSFVDELVQEILKSVAGAGSIIVYCMTI 238
           I+  L LKNP +   SFDR NL+Y  +V  +    +++L++ I K   G  S I+YC + 
Sbjct: 180 ILRQLNLKNPQIFCTSFDRPNLYY--EVRRKTPKILEDLLRFIRKEFKGK-SGIIYCPSR 236

Query: 239 KDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVR 298
           K  E+++ +L+ LG+ AG YH  +   AR++ H  F RDEI+V+VAT+AFGMGI+KPDVR
Sbjct: 237 KKSEQVTASLQNLGIAAGAYHAGLEISARDDVHHKFQRDEIQVVVATVAFGMGINKPDVR 296

Query: 299 HVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFYCGESQTENQRTAIME 358
            VIHY  PK++ESYYQESGR GRDG+ S C L+YA ++  +      E     QRT    
Sbjct: 297 FVIHYSLPKSMESYYQESGRAGRDGLPSECHLFYAPADINRLRRLLMEEPDGQQRT-YKL 355

Query: 359 SLLAAQRYCL-LTTCRR 374
            L     YCL  +TCRR
Sbjct: 356 KLYEMMEYCLNSSTCRR 372

All proteins in this family for which functions are known are 3'-5' DNA-DNA helicases. These proteins are used for recombination, recombinational repair, and possibly maintenance of chromosome stability. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) [DNA metabolism, DNA replication, recombination, and repair]. Length = 470

>gnl|CDD|223588 COG0514, RecQ, Superfamily II DNA helicase [DNA replication, recombination, and repair]

 Score =  397 bits (1021), Expect = e-135
 Identities = 163/379 (43%), Positives = 234/379 (61%), Gaps = 11/379 (2%)

Query: 1   MVSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVTGKTALVVS 60
               LK+ FGY+ FRP Q+++I  ++  +D LVVM TG GKSLCYQ+P L+     LVVS
Sbjct: 5   AQQVLKQVFGYASFRPGQQEIIDALLSGKDTLVVMPTGGGKSLCYQIPALLLEGLTLVVS 64

Query: 61  PLISLMQDQVMSLKQRGINAEFLGSAQTD---SSVQTKAETGYFQLLFMTPEKACIIPIS 117
           PLISLM+DQV  L+  GI A +L S  +      V  + ++G  +LL+++PE+       
Sbjct: 65  PLISLMKDQVDQLEAAGIRAAYLNSTLSREERQQVLNQLKSGQLKLLYISPERLMSPR-- 122

Query: 118 FWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEKVRI 177
           F   L +  + L A+DEAHCIS+WGHDFR +Y++L +LR  L   P +ALTATAT +VR 
Sbjct: 123 FLELLKRLPISLVAIDEAHCISQWGHDFRPDYRRLGRLRAGLPNPPVLALTATATPRVRD 182

Query: 178 DIINSLKLKNPYVTIASFDRKNLFYGVKVINRGQSFVD-ELVQEILKSVAGAGSIIVYCM 236
           DI   L L++  +   SFDR NL    KV+ +G+       +  +L  ++ +G  I+YC+
Sbjct: 183 DIREQLGLQDANIFRGSFDRPNLAL--KVVEKGEPSDQLAFLATVLPQLSKSG--IIYCL 238

Query: 237 TIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPD 296
           T K VEE+++ L++ G+ AG YH  + ++ RE   + F+ DEI+VMVAT AFGMGIDKPD
Sbjct: 239 TRKKVEELAEWLRKNGISAGAYHAGLSNEERERVQQAFLNDEIKVMVATNAFGMGIDKPD 298

Query: 297 VRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFYCGESQTENQRTAI 356
           VR VIHY  P ++ESYYQE+GR GRDG+ +   L Y+  +     +   +S+ + ++  I
Sbjct: 299 VRFVIHYDLPGSIESYYQETGRAGRDGLPAEAILLYSPEDIRWQRYLIEQSKPDEEQKQI 358

Query: 357 MESLLAAQR-YCLLTTCRR 374
             + L     YC   TCRR
Sbjct: 359 ELAKLRQMIAYCETQTCRR 377

Length = 590

>gnl|CDD|130456 TIGR01389, recQ, ATP-dependent DNA helicase RecQ

 Score =  381 bits (981), Expect = e-129
 Identities = 159/376 (42%), Positives = 224/376 (59%), Gaps = 13/376 (3%)

Query: 4   TLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVTGKTALVVSPLI 63
            LK+ FGY  FRP Q+++I  +++ RD LVVM TG GKSLCYQ+P L+     +V+SPLI
Sbjct: 4   VLKRTFGYDDFRPGQEEIISHVLDGRDVLVVMPTGGGKSLCYQVPALLLKGLTVVISPLI 63

Query: 64  SLMQDQVMSLKQRGINAEFLGSAQT---DSSVQTKAETGYFQLLFMTPEKACIIPISFWS 120
           SLM+DQV  L+  G+ A +L S  +      ++     G  +LL++ PE+  +    F +
Sbjct: 64  SLMKDQVDQLRAAGVAAAYLNSTLSAKEQQDIEKALVNGELKLLYVAPER--LEQDYFLN 121

Query: 121 KLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEKVRIDII 180
            L +  + L AVDEAHC+S+WGHDFR EY++L  L      VP +ALTATA  + R DI 
Sbjct: 122 MLQRIPIALVAVDEAHCVSQWGHDFRPEYQRLGSLAERFPQVPRIALTATADAETRQDIR 181

Query: 181 NSLKLKNPYVTIASFDRKNLFYGV-KVINRGQSFVDELVQEILKSVAGAGSIIVYCMTIK 239
             L+L +    I SFDR NL + V K  N+ +  +D L +   +  +G    I+Y  + K
Sbjct: 182 ELLRLADANEFITSFDRPNLRFSVVKKNNKQKFLLDYLKKH--RGQSG----IIYASSRK 235

Query: 240 DVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRH 299
            VEE+++ L+  G+ A  YH  + +K R E    F+ D+++VMVAT AFGMGIDKP+VR 
Sbjct: 236 KVEELAERLESQGISALAYHAGLSNKVRAENQEDFLYDDVKVMVATNAFGMGIDKPNVRF 295

Query: 300 VIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFYCGESQTENQRTAIM-E 358
           VIHY  P  LESYYQE+GR GRDG+ +   L Y+ ++ A       +S+ ++    I  E
Sbjct: 296 VIHYDMPGNLESYYQEAGRAGRDGLPAEAILLYSPADIALLKRRIEQSEADDDYKQIERE 355

Query: 359 SLLAAQRYCLLTTCRR 374
            L A   YC   TCRR
Sbjct: 356 KLRAMIAYCETQTCRR 371

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 [DNA metabolism, DNA replication, recombination, and repair]. Length = 591

>gnl|CDD|182933 PRK11057, PRK11057, ATP-dependent DNA helicase RecQ; Provisional

 Score =  331 bits (851), Expect = e-109
 Identities = 148/333 (44%), Positives = 207/333 (62%), Gaps = 14/333 (4%)

Query: 5   LKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVTGKTALVVSPLIS 64
           L++ FGY  FRP Q+++I  ++  RDCLVVM TG GKSLCYQ+P LV     LVVSPLIS
Sbjct: 17  LQETFGYQQFRPGQQEIIDAVLSGRDCLVVMPTGGGKSLCYQIPALVLDGLTLVVSPLIS 76

Query: 65  LMQDQVMSLKQRGINAEFLGSAQTDS---SVQTKAETGYFQLLFMTPEKACIIPISFWSK 121
           LM+DQV  L   G+ A  L S QT      V     TG  +LL++ PE+  ++  +F   
Sbjct: 77  LMKDQVDQLLANGVAAACLNSTQTREQQLEVMAGCRTGQIKLLYIAPER--LMMDNFLEH 134

Query: 122 LLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEKVRIDIIN 181
           L      L AVDEAHCIS+WGHDFR EY  L +LR     +PF+ALTATA +  R DI+ 
Sbjct: 135 LAHWNPALLAVDEAHCISQWGHDFRPEYAALGQLRQRFPTLPFMALTATADDTTRQDIVR 194

Query: 182 SLKLKNPYVTIASFDRKNLFYGVKVINRGQSF--VDELVQEILKSVAGAGSIIVYCMTIK 239
            L L +P + I+SFDR N+ Y +      + F  +D+L++  ++   G   II YC +  
Sbjct: 195 LLGLNDPLIQISSFDRPNIRYTLV-----EKFKPLDQLMR-YVQEQRGKSGII-YCNSRA 247

Query: 240 DVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRH 299
            VE+ +  L+  G+ A  YH  + +  R +    F RD+++++VAT+AFGMGI+KP+VR 
Sbjct: 248 KVEDTAARLQSRGISAAAYHAGLDNDVRADVQEAFQRDDLQIVVATVAFGMGINKPNVRF 307

Query: 300 VIHYGCPKTLESYYQESGRCGRDGIASVCWLYY 332
           V+H+  P+ +ESYYQE+GR GRDG+ +   L+Y
Sbjct: 308 VVHFDIPRNIESYYQETGRAGRDGLPAEAMLFY 340

Length = 607

>gnl|CDD|215597 PLN03137, PLN03137, ATP-dependent DNA helicase; Q4-like; Provisional

 Score =  276 bits (707), Expect = 7e-84
 Identities = 143/345 (41%), Positives = 206/345 (59%), Gaps = 21/345 (6%)

Query: 6   KKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVTGKTALVVSPLISL 65
           KK FG   FRP Q+++I   +   D  V+M TG GKSL YQLP L+     LV+SPL+SL
Sbjct: 453 KKVFGNHSFRPNQREIINATMSGYDVFVLMPTGGGKSLTYQLPALICPGITLVISPLVSL 512

Query: 66  MQDQVMSLKQRGINAEFLGSAQTDSSVQTK------AETGYFQLLFMTPEKACIIPI--- 116
           +QDQ+M+L Q  I A  L SA  + + Q +      +E   ++LL++TPEK         
Sbjct: 513 IQDQIMNLLQANIPAASL-SAGMEWAEQLEILQELSSEYSKYKLLYVTPEKVAKSDSLLR 571

Query: 117 ---SFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATE 173
              +  S+ L A    F +DEAHC+S+WGHDFR +Y+ L  L+     +P +ALTATAT 
Sbjct: 572 HLENLNSRGLLA---RFVIDEAHCVSQWGHDFRPDYQGLGILKQKFPNIPVLALTATATA 628

Query: 174 KVRIDIINSLKLKNPYVTIASFDRKNLFYGV-KVINRGQSFVDELVQEILKSVAGAGSII 232
            V+ D++ +L L N  V   SF+R NL+Y V     +    +D+ ++E      G    I
Sbjct: 629 SVKEDVVQALGLVNCVVFRQSFNRPNLWYSVVPKTKKCLEDIDKFIKENHFDECG----I 684

Query: 233 VYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGI 292
           +YC++  D E++++ L++ G KA  YHG M    R    + + +DEI ++ AT+AFGMGI
Sbjct: 685 IYCLSRMDCEKVAERLQEFGHKAAFYHGSMDPAQRAFVQKQWSKDEINIICATVAFGMGI 744

Query: 293 DKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNF 337
           +KPDVR VIH+  PK++E Y+QE GR GRDG  S C LYY+ S++
Sbjct: 745 NKPDVRFVIHHSLPKSIEGYHQECGRAGRDGQRSSCVLYYSYSDY 789

Length = 1195

>gnl|CDD|238034 cd00079, HELICc, Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process

 Score =  121 bits (306), Expect = 8e-34
 Identities = 39/127 (30%), Positives = 66/127 (51%)

Query: 205 KVINRGQSFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGS 264
            V+      ++ L++ + + +   G ++++C + K ++E+++ L++ G+K    HG    
Sbjct: 5   YVLPVEDEKLEALLELLKEHLKKGGKVLIFCPSKKMLDELAELLRKPGIKVAALHGDGSQ 64

Query: 265 KAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRDGI 324
           + REE  + F   EI V+VAT     GID P+V  VI+Y  P +  SY Q  GR GR G 
Sbjct: 65  EEREEVLKDFREGEIVVLVATDVIARGIDLPNVSVVINYDLPWSPSSYLQRIGRAGRAGQ 124

Query: 325 ASVCWLY 331
                L 
Sbjct: 125 KGTAILL 131

Length = 131

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

 Score =  119 bits (301), Expect = 2e-32
 Identities = 42/172 (24%), Positives = 68/172 (39%), Gaps = 15/172 (8%)

Query: 15  RPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLP------PLVTGKTALVVSPLISLMQD 68
            P Q   I  I+  +D LV   TGSGK+L + LP      P   G  ALV++P   L + 
Sbjct: 1   TPIQAQAIPAILSGKDVLVQAPTGSGKTLAFLLPILQALLPKKGGPQALVLAPTRELAEQ 60

Query: 69  QVMSLKQRG----INAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLK 124
               LK+      +    L    +      K + G   +L  TP +  +  +      L 
Sbjct: 61  IYEELKKLFKILGLRVALLTGGTSLKEQARKLKKGKADILVGTPGR-LLDLLRRGKLKLL 119

Query: 125 AGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEKVR 176
             + L  +DEAH + + G  F  + +++  L         + L+AT    + 
Sbjct: 120 KNLKLLVLDEAHRLLDMG--FGDDLEEI--LSRLPPDRQILLLSATLPRNLE 167

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|197757 smart00490, HELICc, helicase superfamily c-terminal domain

 Score =  101 bits (255), Expect = 5e-27
 Identities = 34/82 (41%), Positives = 46/82 (56%)

Query: 242 EEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVI 301
           EE+++ LK+LG+K    HG +  + REE    F   +I+V+VAT     G+D P V  VI
Sbjct: 1   EELAELLKELGIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVI 60

Query: 302 HYGCPKTLESYYQESGRCGRDG 323
            Y  P +  SY Q  GR GR G
Sbjct: 61  IYDLPWSPASYIQRIGRAGRAG 82

Length = 82

>gnl|CDD|201125 pfam00271, Helicase_C, Helicase conserved C-terminal domain

 Score = 98.7 bits (247), Expect = 7e-26
 Identities = 33/78 (42%), Positives = 42/78 (53%)

Query: 246 KALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGC 305
           K L++ G+K    HG +  + REE    F   + +V+VAT   G GID PDV  VI+Y  
Sbjct: 1   KLLRKPGIKVARLHGGLSQEEREEILEDFRNGKSKVLVATDVAGRGIDLPDVNLVINYDL 60

Query: 306 PKTLESYYQESGRCGRDG 323
           P    SY Q  GR GR G
Sbjct: 61  PWNPASYIQRIGRAGRAG 78

The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase. Length = 78

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

 Score = 95.6 bits (238), Expect = 3e-23
 Identities = 53/182 (29%), Positives = 81/182 (44%), Gaps = 20/182 (10%)

Query: 7   KYFGYSVFRPYQKDVIQRIIE-KRDCLVVMATGSGKSLCYQLPPL-----VTGKTALVVS 60
           + FG+   RPYQK+ I+ ++   RD ++   TGSGK+L   LP L       G   LV+ 
Sbjct: 2   EKFGFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKRGKGGRVLVLV 61

Query: 61  PLISLMQDQVMSLKQRG-----INAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIP 115
           P   L +     LK+ G           G       ++ K E+G   +L  TP +   + 
Sbjct: 62  PTRELAEQWAEELKKLGPSLGLKVVGLYGGDSKREQLR-KLESGKTDILVTTPGRLLDLL 120

Query: 116 ISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLG-VPFVALTATATEK 174
            +   KL  + V L  +DEAH + + G        QL+KL   L   V  + L+AT  E+
Sbjct: 121 EN--DKLSLSNVDLVILDEAHRLLDGGF-----GDQLEKLLKLLPKNVQLLLLSATPPEE 173

Query: 175 VR 176
           + 
Sbjct: 174 IE 175

Length = 201

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

 Score = 92.9 bits (231), Expect = 1e-20
 Identities = 42/108 (38%), Positives = 61/108 (56%), Gaps = 1/108 (0%)

Query: 216 ELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFI 275
           EL+ ++LK     G +IV+  T + VEE++++L++ G K    HG +  + R+ A   F 
Sbjct: 262 ELLLKLLKD-EDEGRVIVFVRTKRLVEELAESLRKRGFKVAALHGDLPQEERDRALEKFK 320

Query: 276 RDEIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRDG 323
             E+RV+VAT     G+D PDV HVI+Y  P   E Y    GR GR G
Sbjct: 321 DGELRVLVATDVAARGLDIPDVSHVINYDLPLDPEDYVHRIGRTGRAG 368

Length = 513

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

 Score = 83.2 bits (206), Expect = 2e-19
 Identities = 41/150 (27%), Positives = 59/150 (39%), Gaps = 15/150 (10%)

Query: 29  RDCLVVMATGSGKSLCYQLPPL-----VTGKTALVVSPLISLMQDQVMSLKQR---GINA 80
           RD L+   TGSGK+L   LP L     + G   LV++P   L       LK+    GI  
Sbjct: 1   RDVLLAAPTGSGKTLAALLPILELLDSLKGGQVLVLAPTRELANQVAERLKELFGEGIKV 60

Query: 81  EFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISE 140
            +L    T    Q K  +G   ++  TP +  ++      KL    + L  +DEAH +  
Sbjct: 61  GYLIGG-TSIKQQEKLLSGKTDIVVGTPGR--LLDELERLKLSLKKLDLLILDEAHRLLN 117

Query: 141 WGHDFRLEYKQLDKLRTFLLGVPFVALTAT 170
            G         L  L         + L+AT
Sbjct: 118 QGFGLL----GLKILLKLPKDRQVLLLSAT 143

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

>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 = 78.6 bits (194), Expect = 8e-16
 Identities = 74/380 (19%), Positives = 129/380 (33%), Gaps = 60/380 (15%)

Query: 8   YFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVT-----GKTALVVSPL 62
             G      +Q D ++ I E R+ +V   TGSGK+  + LP L          AL++ P 
Sbjct: 65  KAGIERLYSHQVDALRLIREGRNVVVTTGTGSGKTESFLLPILDHLLRDPSARALLLYPT 124

Query: 63  ISLMQDQVMSLKQRGINAEFLGSAQ----TDSSVQTKAETGYFQ---LLFMTPEK--ACI 113
            +L  DQ   L++  + ++  G       T  +   +          +L   P+     +
Sbjct: 125 NALANDQAERLRE--LISDLPGKVTFGRYTGDTPPEERRAIIRNPPDILLTNPDMLHYLL 182

Query: 114 IPISFWSKLLKAGVCLFAVDEAHC-ISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATAT 172
           +        L   +    VDE H      G +  L  ++L   R    G P   +  +AT
Sbjct: 183 LRNHDAWLWLLRNLKYLVVDELHTYRGVQGSEVALLLRRL-LRRLRRYGSPLQIICTSAT 241

Query: 173 EKVRIDIINSLKLKNPYVTIASFD-----------RKNLFYGVKVINRGQ------SFVD 215
                +    L     +      D           R+     +    R        +   
Sbjct: 242 LANPGEFAEEL-FGRDFEVPVDEDGSPRGLRYFVRREPPIRELAESIRRSALAELATLAA 300

Query: 216 ELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQ--------LGVKAGTYHGQMGSKAR 267
            LV+  ++        +V+  + K VE +  + ++        L     TY   +  + R
Sbjct: 301 LLVRNGIQ-------TLVFFRSRKQVELLYLSPRRRLVREGGKLLDAVSTYRAGLHREER 353

Query: 268 EEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYG-CPKTLESYYQESGRCGRDGIAS 326
                 F   E+  ++AT A  +GID   +  VI YG    ++ S+ Q +GR GR G  S
Sbjct: 354 RRIEAEFKEGELLGVIATNALELGIDIGSLDAVIAYGYPGVSVLSFRQRAGRAGRRGQES 413

Query: 327 V--------CWLYYARSNFA 338
           +            Y   +  
Sbjct: 414 LVLVVLRSDPLDSYYLRHPE 433

Length = 851

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

 Score = 70.8 bits (174), Expect = 3e-13
 Identities = 82/355 (23%), Positives = 139/355 (39%), Gaps = 57/355 (16%)

Query: 5   LKKYF--GYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLP-----------PLV 51
           ++++F   ++   P Q+  I  I    + L++  TGSGK+    LP            L 
Sbjct: 12  VREWFKRKFTSLTPPQRYAIPEIHSGENVLIIAPTGSGKTEAAFLPVINELLSLGKGKLE 71

Query: 52  TGKTALVVSPLISLMQDQVMSLKQRGINAEFLG---------SAQTDSSVQTKAETGYFQ 102
            G  AL +SPL +L  D    L++       LG         + Q++     K       
Sbjct: 72  DGIYALYISPLKALNNDIRRRLEEPL---RELGIEVAVRHGDTPQSEKQKMLKNPPH--- 125

Query: 103 LLFMTPEKACIIPISFWSKLLK--AGVCLFAVDEAHCI--SEWGHDFRLEYKQLDKLRTF 158
           +L  TPE   I+      K  +    V    VDE H +  S+ G    L    L++LR  
Sbjct: 126 ILITTPESLAILLN--SPKFRELLRDVRYVIVDEIHALAESKRGVQLAL---SLERLREL 180

Query: 159 LLGVPFVALTAT--ATEKVR---------IDIINSLKLKNPYVTIASFDRKNLFYGVKVI 207
                 + L+AT    E+V           +I++    K   + + S     ++      
Sbjct: 181 AGDFQRIGLSATVGPPEEVAKFLVGFGDPCEIVDVSAAKKLEIKVISPVEDLIYDEELWA 240

Query: 208 NRGQSFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLG-VKAGTYHGQMGSKA 266
                   E + E++K      + +++  T    E ++  LK+LG      +HG +  + 
Sbjct: 241 ALY-----ERIAELVKK---HRTTLIFTNTRSGAERLAFRLKKLGPDIIEVHHGSLSREL 292

Query: 267 REEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGR 321
           R E        E++ +VAT +  +GID  D+  VI  G PK++  + Q  GR G 
Sbjct: 293 RLEVEERLKEGELKAVVATSSLELGIDIGDIDLVIQLGSPKSVNRFLQRIGRAGH 347

Length = 814

>gnl|CDD|224123 COG1202, COG1202, Superfamily II helicase, archaea-specific [General function prediction only]

 Score = 67.9 bits (166), Expect = 3e-12
 Identities = 86/354 (24%), Positives = 137/354 (38%), Gaps = 67/354 (18%)

Query: 10  GYSVFRPYQKDVIQR-IIEKRDCLVVMATGSGKSLCYQLP----PLVTGKTALVVSPLIS 64
           G     P Q   ++  ++E  + LVV AT SGK+L  +L      L  GK  L + PL++
Sbjct: 213 GIEELLPVQVLAVEAGLLEGENLLVVSATASGKTLIGELAGIPRLLSGGKKMLFLVPLVA 272

Query: 65  LMQDQVMSLKQRGINAEFLGSAQTDSS-VQTKAETGYFQLLFMTPEKACIIPISF--WSK 121
           L   +    K+R        + +   S ++T+ E     ++  T   A II  ++     
Sbjct: 273 LANQKYEDFKERYSKLGLKVAIRVGMSRIKTREEP----VVVDTSPDADIIVGTYEGIDY 328

Query: 122 LLKAGVCL-----FAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEKVR 176
           LL+ G  L       +DE H + +     RL+   + +LR    G  F+ L+AT      
Sbjct: 329 LLRTGKDLGDIGTVVIDEIHTLEDEERGPRLD-GLIGRLRYLFPGAQFIYLSAT------ 381

Query: 177 IDIINSLKLKNPYVTIASFDRKNLFYGVK--------VINRGQSFVDELVQEILK----- 223
                   + NP         K + Y  +        V  R +S   +++  ++K     
Sbjct: 382 --------VGNPEELAKKLGAKLVLYDERPVPLERHLVFARNESEKWDIIARLVKREFST 433

Query: 224 --SVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRV 281
             S    G  IV+  + +   E++ AL   G+KA  YH  +  K R+   R F   E+  
Sbjct: 434 ESSKGYRGQTIVFTYSRRRCHELADALTGKGLKAAPYHAGLPYKERKSVERAFAAQELAA 493

Query: 282 MVATMAFGMGIDKPDVRHVIHYGCPKTLES------------YYQESGRCGRDG 323
           +V T A   G+D P    VI        ES            + Q  GR GR  
Sbjct: 494 VVTTAALAAGVDFP-ASQVI-------FESLAMGIEWLSVREFQQMLGRAGRPD 539

Length = 830

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

 Score = 63.0 bits (154), Expect = 6e-11
 Identities = 31/92 (33%), Positives = 48/92 (52%)

Query: 232 IVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMG 291
           IV+  T + V E++  L++ G+      G+M    R EA +      + V+VAT     G
Sbjct: 249 IVFVRTRERVHELAGWLRKAGINCCYLEGEMVQAKRNEAIKRLTDGRVNVLVATDVAARG 308

Query: 292 IDKPDVRHVIHYGCPKTLESYYQESGRCGRDG 323
           ID  DV HVI++  P++ ++Y    GR GR G
Sbjct: 309 IDIDDVSHVINFDMPRSADTYLHRIGRTGRAG 340

Length = 434

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

 Score = 60.6 bits (147), Expect = 4e-10
 Identities = 34/113 (30%), Positives = 57/113 (50%), Gaps = 13/113 (11%)

Query: 216 ELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFI 275
            L+Q I++       I+++  T K  + ++K L+  G  A   HG    K +EE  R ++
Sbjct: 368 MLLQRIMRD---GDKILIFVETKKGADFLTKELRLDGWPALCIHG---DKKQEE--RTWV 419

Query: 276 RDEIR-----VMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRDG 323
            +E +     +M+AT     G+D  DV++VI++  P  +E Y    GR GR G
Sbjct: 420 LNEFKTGKSPIMIATDVASRGLDVKDVKYVINFDFPNQIEDYVHRIGRTGRAG 472

Length = 545

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

 Score = 59.8 bits (145), Expect = 7e-10
 Identities = 97/359 (27%), Positives = 149/359 (41%), Gaps = 69/359 (19%)

Query: 10  GYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLP------------------PLV 51
           GY    P Q   I   +  R  LV   TGSGK+  + +P                  PL 
Sbjct: 140 GYEFPTPIQMQAIPAALSGRSLLVSADTGSGKTASFLVPIISRCCTIRSGHPSEQRNPL- 198

Query: 52  TGKTALVVSP---LISLMQDQVMSLKQRGI---NAEFLGS---AQTDSSVQTKAETGYFQ 102
               A+V++P   L   ++DQ   L  +G+    A  +G     Q    +Q   E     
Sbjct: 199 ----AMVLTPTRELCVQVEDQAKVLG-KGLPFKTALVVGGDAMPQQLYRIQQGVE----- 248

Query: 103 LLFMTPEKACIIPISFWSK--LLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLL 160
           L+  TP +     I   SK  +    V +  +DE  C+ E G  FR +  Q+ +     L
Sbjct: 249 LIVGTPGRL----IDLLSKHDIELDNVSVLVLDEVDCMLERG--FRDQVMQIFQA----L 298

Query: 161 GVPFVAL-TATATEKVRIDIINSLKLKNP-YVTIASFDR-----KNLFYGVKVINRGQSF 213
             P V L +AT + +V     +SL  K+   ++I + +R     K L   V+   + Q  
Sbjct: 299 SQPQVLLFSATVSPEVE-KFASSL-AKDIILISIGNPNRPNKAVKQLAIWVETKQKKQKL 356

Query: 214 VDELVQEILKS-VAGAGSIIVYCMTIKDVEEISKAL-KQLGVKAGTYHGQMGSKAREEAH 271
            D     ILKS        +V+  +    + ++ A+    G+KA + HG+   K R E  
Sbjct: 357 FD-----ILKSKQHFKPPAVVFVSSRLGADLLANAITVVTGLKALSIHGEKSMKERREVM 411

Query: 272 RLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGR---DGIASV 327
           + F+  E+ V+VAT   G G+D   VR VI +  P T++ Y  + GR  R    G A V
Sbjct: 412 KSFLVGEVPVIVATGVLGRGVDLLRVRQVIIFDMPNTIKEYIHQIGRASRMGEKGTAIV 470

Length = 518

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

 Score = 58.7 bits (142), Expect = 2e-09
 Identities = 33/97 (34%), Positives = 47/97 (48%), Gaps = 3/97 (3%)

Query: 232 IVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMG 291
           I+YC T + V+ ++K + +        HG M  K R+   R F     RV++ T     G
Sbjct: 271 IIYCNTRRKVDYLTKKMHERDFTVSCMHGDMDQKDRDLIMREFRSGSTRVLITTDLLARG 330

Query: 292 IDKPDVRHVIHYGCPKTLESYYQ---ESGRCGRDGIA 325
           ID   V  VI+Y  P + E+Y      SGR GR G+A
Sbjct: 331 IDVQQVSLVINYDLPASPENYIHRIGRSGRFGRKGVA 367

Length = 401

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

 Score = 57.9 bits (140), Expect = 3e-09
 Identities = 84/347 (24%), Positives = 144/347 (41%), Gaps = 63/347 (18%)

Query: 10  GYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVTGKTALVVSPLISLM-QD 68
           GY    P Q+  I  ++E RD +    TG             TGKTA    PL+  +   
Sbjct: 20  GYREPTPIQQQAIPAVLEGRDLMASAQTG-------------TGKTAGFTLPLLQHLITR 66

Query: 69  QVMSLKQRGINAEFLG-----SAQTDSSVQTKAE----------------------TGYF 101
           Q  +  +R + A  L      +AQ   +V+  ++                       G  
Sbjct: 67  QPHAKGRRPVRALILTPTRELAAQIGENVRDYSKYLNIRSLVVFGGVSINPQMMKLRGGV 126

Query: 102 QLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWG--HDFRLEYKQLDKLRTFL 159
            +L  TP +  ++ +   + +    V +  +DEA  + + G  HD R    +L   R  L
Sbjct: 127 DVLVATPGR--LLDLEHQNAVKLDQVEILVLDEADRMLDMGFIHDIRRVLAKLPAKRQNL 184

Query: 160 LGVPFVALTATATEKVRIDIINSLKLKNPY-VTIASFDRKNLFYGVKVINRGQSFVDE-L 217
           L       +AT ++ ++  +   L L NP  + +A   R+N     + + +   FVD+  
Sbjct: 185 L------FSATFSDDIK-ALAEKL-LHNPLEIEVA---RRNT--ASEQVTQHVHFVDKKR 231

Query: 218 VQEILKSVAGAGS---IIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLF 274
            +E+L  + G G+   ++V+  T      +++ L + G+++   HG     AR  A   F
Sbjct: 232 KRELLSQMIGKGNWQQVLVFTRTKHGANHLAEQLNKDGIRSAAIHGNKSQGARTRALADF 291

Query: 275 IRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGR 321
              +IRV+VAT     G+D  ++ HV++Y  P   E Y    GR GR
Sbjct: 292 KSGDIRVLVATDIAARGLDIEELPHVVNYELPNVPEDYVHRIGRTGR 338

Length = 456

>gnl|CDD|187770 cd09639, Cas3_I, CRISPR/Cas system-associated protein Cas3

 Score = 53.2 bits (128), Expect = 7e-08
 Identities = 41/200 (20%), Positives = 74/200 (37%), Gaps = 18/200 (9%)

Query: 132 VDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEKVRIDIINSLKLKNPYVT 191
            DE H   E+     L    L+ L+     VP + ++AT  + ++        ++     
Sbjct: 129 FDEVHFYDEYTLALIL--AVLEVLKDN--DVPILLMSATLPKFLKEYAEKIGYVEENEPL 184

Query: 192 IASFDRKNLFYG-VKVINRGQSFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQ 250
               + +  F           S ++ L++ I K     GS+ +   T+   +E  + LK+
Sbjct: 185 DLKPNERAPFIKIESDKVGEISSLERLLEFIKK----GGSVAIIVNTVDRAQEFYQQLKE 240

Query: 251 LG--VKAGTYHGQMGSKAREEAHRLFI----RDEIRVMVATMAFGMGIDKPDVRHVIHYG 304
            G   +    H +   K R +     +    + E  V+VAT      +D   V  +I   
Sbjct: 241 KGPEEEIMLIHSRFTEKDRAKKEAELLLEFKKSEKFVIVATQVIEASLDI-SVDVMITEL 299

Query: 305 CPKTLESYYQESGRCGRDGI 324
            P  ++S  Q  GR  R G 
Sbjct: 300 AP--IDSLIQRLGRLHRYGE 317

CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; DEAD/DEAH box helicase DNA helicase cas3'; Often but not always is fused to HD nuclease domain; signature gene for Type I. Length = 353

>gnl|CDD|233483 TIGR01587, cas3_core, CRISPR-associated helicase Cas3

 Score = 52.5 bits (126), Expect = 1e-07
 Identities = 67/334 (20%), Positives = 119/334 (35%), Gaps = 53/334 (15%)

Query: 31  CLVVMA-TGSGK---SLCYQLPPLVTGKT--ALVVSPLISLMQDQVMSLKQRGINAEFLG 84
            LV+ A TG GK   +L + L  + + K    ++  P  + +    M  + + +    LG
Sbjct: 1   LLVIEAPTGYGKTEAALLWALHSIKSQKADRVIIALPTRATINA--MYRRAKELFGSNLG 58

Query: 85  SAQTDSSVQ---TKAETGYFQL-----------LFMTPEKACIIPISFWSKLLKAGVCLF 130
              + SS +      ++  F+            LF+ P   C I     S   + G   F
Sbjct: 59  LLHSSSSFKRIKEMGDSEEFEHLFPLYIHSNDKLFLDPITVCTIDQVLKSVFGEFGHYEF 118

Query: 131 A----------VDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEKVRIDII 180
                       DE H   E+     L    L+ L+     VP + ++AT  + ++    
Sbjct: 119 TLASIANSLLIFDEVHFYDEYTLALIL--AVLEVLKDN--DVPILLMSATLPKFLKEYAE 174

Query: 181 NSLKLKN----PYVTIASFDRKNLFYGVKVINRGQSFVDELVQEILKSVAGAGSIIVYCM 236
               ++            F+R              S ++ L++ I K     G I +   
Sbjct: 175 KIGYVEFNEPLDLKEERRFERHRFIKIESDKVGEISSLERLLEFIKK----GGKIAIIVN 230

Query: 237 TIKDVEEISKALKQLG--VKAGTYHGQM--GSKAREEAHRL--FIRDEIRVMVATMAFGM 290
           T+   +E  + LK+     +    H +     +A++EA  L    ++E  V+VAT     
Sbjct: 231 TVDRAQEFYQQLKENAPEEEIMLLHSRFTEKDRAKKEAELLEEMKKNEKFVIVATQVIEA 290

Query: 291 GIDKPDVRHVIHYGCPKTLESYYQESGRCGRDGI 324
            +D      +I    P  ++S  Q  GR  R G 
Sbjct: 291 SLDI-SADVMITELAP--IDSLIQRLGRLHRYGR 321

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 [Mobile and extrachromosomal element functions, Other]. Length = 358

>gnl|CDD|224124 COG1203, COG1203, CRISPR-associated helicase Cas3 [Defense mechanisms]

 Score = 51.7 bits (124), Expect = 3e-07
 Identities = 45/178 (25%), Positives = 71/178 (39%), Gaps = 22/178 (12%)

Query: 160 LGVPFVALTATATEKVRIDIINSLKLKNPYVTI-ASFDRKNLFYGVKVINRGQSFVDELV 218
            GVP + ++AT    ++ + +     K   V   A F  K    G+K   R     D   
Sbjct: 369 AGVPVLLMSATLPPFLK-EKLKKALGKGREVVENAKFCPKEDEPGLKRKER-VDVEDGPQ 426

Query: 219 QE----ILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHR-- 272
           +E    I + V     ++V   T+    E+ + LK+ G K    H +   K REE  R  
Sbjct: 427 EELIELISEEVKEGKKVLVIVNTVDRAIELYEKLKEKGPKVLLLHSRFTLKDREEKEREL 486

Query: 273 --LFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGC----PKTLESYYQESGRCGRDGI 324
             LF ++E  ++VAT     G+D       I +         ++S  Q +GR  R G 
Sbjct: 487 KKLFKQNEGFIVVATQVIEAGVD-------IDFDVLITELAPIDSLIQRAGRVNRHGK 537

Length = 733

>gnl|CDD|218292 pfam04851, ResIII, Type III restriction enzyme, res subunit

 Score = 47.2 bits (113), Expect = 4e-07
 Identities = 18/33 (54%), Positives = 26/33 (78%)

Query: 13 VFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCY 45
            RPYQ++ I+R++EK+  L+VMATGSGK+L  
Sbjct: 3  ELRPYQEEAIERLLEKKRGLIVMATGSGKTLTA 35

Length = 100

>gnl|CDD|233032 TIGR00580, mfd, transcription-repair coupling factor (mfd)

 Score = 51.6 bits (124), Expect = 5e-07
 Identities = 36/133 (27%), Positives = 57/133 (42%), Gaps = 12/133 (9%)

Query: 211 QSFVDELVQE-ILKSVAGAGSIIVYCMTIKDVEEISKALKQL--GVKAGTYHGQMGSKAR 267
             +  ELV+E I + +   G +      I+ +E+++  L++L    +    HGQM     
Sbjct: 642 MEYDPELVREAIRRELLRGGQVFYVHNRIESIEKLATQLRELVPEARIAIAHGQMTENEL 701

Query: 268 EEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVI-----HYGCPKTLESYYQESGRCGRD 322
           EE    F + E +V+V T     GID P+   +I      +G    L   YQ  GR GR 
Sbjct: 702 EEVMLEFYKGEFQVLVCTTIIETGIDIPNANTIIIERADKFG----LAQLYQLRGRVGRS 757

Query: 323 GIASVCWLYYARS 335
              +  +L Y   
Sbjct: 758 KKKAYAYLLYPHQ 770

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 transcribed 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 [DNA metabolism, DNA replication, recombination, and repair]. Length = 926

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

 Score = 50.7 bits (121), Expect = 7e-07
 Identities = 29/97 (29%), Positives = 46/97 (47%)

Query: 231 IIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGM 290
           ++V+     +V  I + L + G+ A    G +    R +    F   +IRV+VAT   G 
Sbjct: 338 VMVFANRKDEVRRIEERLVKDGINAAQLSGDVPQHKRIKTLEGFREGKIRVLVATDVAGR 397

Query: 291 GIDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASV 327
           GI    + HVI++  P+  + Y    GR GR G + V
Sbjct: 398 GIHIDGISHVINFTLPEDPDDYVHRIGRTGRAGASGV 434

Length = 475

>gnl|CDD|233251 TIGR01054, rgy, reverse gyrase

 Score = 49.1 bits (117), Expect = 3e-06
 Identities = 31/100 (31%), Positives = 49/100 (49%), Gaps = 14/100 (14%)

Query: 216 ELVQEILKSVAGAGSIIVYC---MTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHR 272
           E + EI+K +   G  IVY       +  EEI++ L+  GVKA  YH    +   +E + 
Sbjct: 316 ETLLEIVKKLGTGG--IVYVSIDYGKEKAEEIAEFLENHGVKAVAYH----ATKPKEDYE 369

Query: 273 LFIRDEIRVMVATMAF----GMGIDKPD-VRHVIHYGCPK 307
            F   EI V++   ++      G+D P+ VR+ +  G PK
Sbjct: 370 KFAEGEIDVLIGVASYYGTLVRGLDLPERVRYAVFLGVPK 409

This model describes reverse gyrase, found in both archaeal and bacterial thermophiles. This enzyme, a fusion of a type I topoisomerase domain and a helicase domain, introduces positive supercoiling to increase the melting temperature of DNA double strands. 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 [DNA metabolism, DNA replication, recombination, and repair]. Length = 1171

>gnl|CDD|224121 COG1200, RecG, RecG-like helicase [DNA replication, recombination, and repair / Transcription]

 Score = 48.7 bits (117), Expect = 3e-06
 Identities = 39/160 (24%), Positives = 63/160 (39%), Gaps = 29/160 (18%)

Query: 215 DELVQEILKSVAGAGSIIVYC--------MTIKDVEEISKALKQL--GVKAGTYHGQMGS 264
            E+ + I + +A      V C        + ++  EE+ + LK     +K G  HG+M  
Sbjct: 460 PEVYERIREEIAKGRQAYVVCPLIEESEKLELQAAEELYEELKSFLPELKVGLVHGRMKP 519

Query: 265 KAREEAHRLFIRDEIRVMVATMAFGMGIDKPD-----VRHVIHYGCPKTLESYYQESGRC 319
             ++     F   EI ++VAT    +G+D P+     + +   +G    L   +Q  GR 
Sbjct: 520 AEKDAVMEAFKEGEIDILVATTVIEVGVDVPNATVMVIENAERFG----LAQLHQLRGRV 575

Query: 320 GRDGIASVCWLYYARSNFAKGDFYCGESQTENQRTAIMES 359
           GR  + S C L Y              S+   QR  IM  
Sbjct: 576 GRGDLQSYCVLLYKPP----------LSEVAKQRLKIMRE 605

Length = 677

>gnl|CDD|224125 COG1204, COG1204, Superfamily II helicase [General function prediction only]

 Score = 48.9 bits (117), Expect = 3e-06
 Identities = 69/378 (18%), Positives = 127/378 (33%), Gaps = 85/378 (22%)

Query: 16  PYQKDVIQRIIEK-RDCLVVMATGSGKSLCYQLPPLVT----GKTALVVSPLISLMQDQV 70
             Q++ +++ +    + L+   TGSGK+L   L  L T    G   + + PL +L +++ 
Sbjct: 34  NPQQEAVEKGLLSDENVLISAPTGSGKTLIALLAILSTLLEGGGKVVYIVPLKALAEEKY 93

Query: 71  MSLKQRGINAEFLG---SAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGV 127
               +     E LG      T            + ++  TPEK   +     S + +   
Sbjct: 94  EEFSRL----EELGIRVGISTGDYDLDDERLARYDVIVTTPEKLDSLTRKRPSWIEEVD- 148

Query: 128 CLFAVDEAHCISEWGHDFR---LEYKQLDKLRTFLLGVPFVALTAT---ATEKVRIDIIN 181
            L  +DE H + +     R   LE   + ++R     +  V L+AT   A E    D +N
Sbjct: 149 -LVVIDEIHLLGD---RTRGPVLE-SIVARMRRLNELIRIVGLSATLPNAEEVA--DWLN 201

Query: 182 SLKLKNPYVTIASFD--RKNLFYGVKVINRGQSFV------DELVQE-ILKSVAGAGSII 232
           +        +       R+ + Y    +             D L  E +L+S+A  G ++
Sbjct: 202 A----KLVESDWRPVPLRRGVPYVGAFLGADGKKKTWPLLIDNLALELVLESLAEGGQVL 257

Query: 233 VYC----MTIKDVEEISKALKQ---------LGVKAGTYHGQMGSKAREE---------- 269
           V+        K  +++   +           L   A          + +E          
Sbjct: 258 VFVHSRKEAEKTAKKLRIKMSATLSDDEKIVLDEGASPILIPETPTSEDEELAELVLRGV 317

Query: 270 ---------AHRLFIRDE-----IRVMVATMAFGMGIDKPD----VRHVIHYGCPKTLES 311
                      R  + D      I+V+V+T     G++ P     ++    Y     +  
Sbjct: 318 AFHHAGLPREDRQLVEDAFRKGKIKVLVSTPTLAAGVNLPARTVIIKDTRRYDPKGGIVD 377

Query: 312 -----YYQESGRCGRDGI 324
                  Q +GR GR G 
Sbjct: 378 IPVLDVLQMAGRAGRPGY 395

Length = 766

>gnl|CDD|234365 TIGR03817, DECH_helic, helicase/secretion neighborhood putative DEAH-box helicase

 Score = 48.2 bits (115), Expect = 5e-06
 Identities = 26/59 (44%), Positives = 31/59 (52%), Gaps = 10/59 (16%)

Query: 33  VVMATG--SGKSLCYQLPPLVT-----GKTALVVSPLISLMQDQ---VMSLKQRGINAE 81
           VV+ATG  SGKSL YQLP L         TAL ++P  +L  DQ   V  L  RG+   
Sbjct: 54  VVVATGTASGKSLAYQLPVLSALADDPRATALYLAPTKALAADQLRAVRELTLRGVRPA 112

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. Length = 742

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

 Score = 47.5 bits (113), Expect = 7e-06
 Identities = 88/348 (25%), Positives = 138/348 (39%), Gaps = 50/348 (14%)

Query: 10  GYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLP------PLVTGKTALVVSPLI 63
           GY    P Q + I  ++  RD L +  TGSGK+  + LP      P +     LV++P  
Sbjct: 25  GYEKPSPIQAECIPHLLNGRDVLGMAQTGSGKTAAFSLPLLHNLDPELKAPQILVLAPTR 84

Query: 64  SLMQDQV------MSLKQRGINAEFLGSAQTDSSVQTKAETGYFQLLFMTPE------KA 111
            L   QV       S   RG+N   L   Q    VQ +A     Q++  TP       K 
Sbjct: 85  ELAV-QVAEAMTDFSKHMRGVNVVALYGGQR-YDVQLRALRQGPQIVVGTPGRLLDHLKR 142

Query: 112 CIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTA-- 169
             + +S  S L+        +DEA        D  L    ++ + T +  +P    TA  
Sbjct: 143 GTLDLSKLSGLV--------LDEA--------DEMLRMGFIEDVETIMAQIPEGHQTALF 186

Query: 170 TATEKVRIDIINSLKLKNPY-VTIASF-----DRKNLFYGVKVINRGQSFVDELVQEILK 223
           +AT    I  I    +K P  V I S      D    ++ V  + + ++ V  L  E   
Sbjct: 187 SATMPEAIRRITRRFMKEPQEVRIQSSVTTRPDISQSYWTVWGMRKNEALVRFLEAEDFD 246

Query: 224 SVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMV 283
           +       I++  T     E+++AL++ G  +   +G M    RE+         + +++
Sbjct: 247 AA------IIFVRTKNATLEVAEALERNGYNSAALNGDMNQALREQTLERLKDGRLDILI 300

Query: 284 ATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLY 331
           AT     G+D   +  V++Y  P   ESY    GR GR G A    L+
Sbjct: 301 ATDVAARGLDVERISLVVNYDIPMDSESYVHRIGRTGRAGRAGRALLF 348

Length = 629

>gnl|CDD|224035 COG1110, COG1110, Reverse gyrase [DNA replication, recombination, and repair]

 Score = 47.8 bits (114), Expect = 8e-06
 Identities = 30/103 (29%), Positives = 50/103 (48%), Gaps = 13/103 (12%)

Query: 212 SFVDELVQEILKSVAGAGSIIVY--CMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREE 269
           S   E V E++K   G G +I        +  EE+++ L+  G+ A   H +     +EE
Sbjct: 321 SESLEKVVELVKK-LGDGGLIFVPIDYGREKAEELAEYLRSHGINAELIHAE-----KEE 374

Query: 270 AHRLFIRDEIRVMVATMAF-GM---GIDKPD-VRHVIHYGCPK 307
           A   F   E+ V+V   ++ G+   G+D P  +R+ + YG PK
Sbjct: 375 ALEDFEEGEVDVLVGVASYYGVLVRGLDLPHRIRYAVFYGVPK 417

Length = 1187

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

 Score = 45.9 bits (110), Expect = 2e-05
 Identities = 30/96 (31%), Positives = 46/96 (47%), Gaps = 4/96 (4%)

Query: 230 SIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVAT--MA 287
           S +V+C T K+ +E++ AL   G  A   HG +  + R++    F      V+VAT   A
Sbjct: 244 SCVVFCNTKKECQEVADALNAQGFSALALHGDLEQRDRDQVLVRFANRSCSVLVATDVAA 303

Query: 288 FGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRDG 323
            G+ I   +   VI+Y   +  E +    GR GR G
Sbjct: 304 RGLDIKALEA--VINYELARDPEVHVHRIGRTGRAG 337

Length = 460

>gnl|CDD|223989 COG1061, SSL2, DNA or RNA helicases of superfamily II [Transcription / DNA replication, recombination, and repair]

 Score = 45.5 bits (108), Expect = 3e-05
 Identities = 68/370 (18%), Positives = 117/370 (31%), Gaps = 101/370 (27%)

Query: 15  RPYQKDVIQRII----EKRDCLVVMATGSGKSL-----CYQLPPLVTGKTALVVSP-LIS 64
           RPYQ++ +  ++     +R  ++V+ TG+GK++       +L      ++ LV+ P    
Sbjct: 38  RPYQEEALDALVKNRRTERRGVIVLPTGAGKTVVAAEAIAEL-----KRSTLVLVPTKEL 92

Query: 65  LMQ------DQVMSLKQRGINA----EFLGSAQTDSSVQTKAETGYFQLLFMTPEKACII 114
           L Q        ++   + GI      E   +  T ++VQT          F+  E   II
Sbjct: 93  LDQWAEALKKFLLLNDEIGIYGGGEKELEPAKVTVATVQT-LARRQLLDEFLGNEFGLII 151

Query: 115 PISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKL---RTFLLGVPFVALTATA 171
                             DE H      H     Y+++ +L       LG     LTAT 
Sbjct: 152 -----------------FDEVH------HLPAPSYRRILELLSAAYPRLG-----LTATP 183

Query: 172 --TEKVRIDIINSL----------------KLKNPYVTIASF-----DRKNLFYGVKVIN 208
              +  RI  +  L                    PY  +        D +  +       
Sbjct: 184 EREDGGRIGDLFDLIGPIVYEVSLKELIDEGYLAPYKYVEIKVTLTEDEEREYAKESARF 243

Query: 209 RGQSFVD--------------------ELVQEILKSVAGAGSIIVYCMTIKDVEEISKAL 248
           R                            V+ +L   A     +++   ++   EI+K  
Sbjct: 244 RELLRARGTLRAENEARRIAIASERKIAAVRGLLLKHARGDKTLIFASDVEHAYEIAKLF 303

Query: 249 KQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPKT 308
              G+      G+   + RE     F    I+V+V       G+D PD   +I      +
Sbjct: 304 LAPGIVEAIT-GETPKEEREAILERFRTGGIKVLVTVKVLDEGVDIPDADVLIILRPTGS 362

Query: 309 LESYYQESGR 318
              + Q  GR
Sbjct: 363 RRLFIQRLGR 372

Length = 442

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

 Score = 44.6 bits (105), Expect = 6e-05
 Identities = 32/107 (29%), Positives = 51/107 (47%), Gaps = 9/107 (8%)

Query: 232 IVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVAT--MAFG 289
           +V+  T   VE +++ L++ G + G   G +  K RE     F + ++ ++VAT   A G
Sbjct: 261 MVFVNTKAFVERVARTLERHGYRVGVLSGDVPQKKRESLLNRFQKGQLEILVATDVAARG 320

Query: 290 MGIDKPDVRHVIHYGCPKTLESYYQESGRCGR-----DGIASVCWLY 331
           + ID   V++V +Y  P   E Y    GR  R     D I+  C  Y
Sbjct: 321 LHID--GVKYVYNYDLPFDAEDYVHRIGRTARLGEEGDAISFACERY 365

Length = 572

>gnl|CDD|233069 TIGR00643, recG, ATP-dependent DNA helicase RecG

 Score = 43.9 bits (104), Expect = 1e-04
 Identities = 33/129 (25%), Positives = 53/129 (41%), Gaps = 21/129 (16%)

Query: 238 IKDVEEISKALKQLGVKA--GTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKP 295
           +K  E + + LK+   K   G  HG+M S  +E     F   E+ ++VAT    +G+D P
Sbjct: 466 LKAAEALYERLKKAFPKYNVGLLHGRMKSDEKEAVMEEFREGEVDILVATTVIEVGVDVP 525

Query: 296 D-----VRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFYCGESQTE 350
           +     +     +G    L   +Q  GR GR    S C L Y             +S++ 
Sbjct: 526 NATVMVIEDAERFG----LSQLHQLRGRVGRGDHQSYCLLVYKNP----------KSESA 571

Query: 351 NQRTAIMES 359
            +R  +M  
Sbjct: 572 KKRLRVMAD 580

[DNA metabolism, DNA replication, recombination, and repair]. Length = 630

>gnl|CDD|226581 COG4096, HsdR, Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]

 Score = 42.8 bits (101), Expect = 3e-04
 Identities = 16/43 (37%), Positives = 24/43 (55%), Gaps = 10/43 (23%)

Query: 15  RPYQKDVIQRIIE-----KRDCLVVMATGSGK-----SLCYQL 47
           R YQ   I+R+IE     +   L+VMATG+GK     ++  +L
Sbjct: 167 RYYQIIAIRRVIEAFSKGQNRALLVMATGTGKTRTAIAIIDRL 209

Length = 875

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

 Score = 41.4 bits (98), Expect = 7e-04
 Identities = 29/109 (26%), Positives = 47/109 (43%), Gaps = 14/109 (12%)

Query: 15  RPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV---------TGKTALVVSPLISL 65
           RP+Q ++    +E R  L++  TGSGK+L   LP L+          G   L ++PL +L
Sbjct: 15  RPFQLEMWAAALEGRSGLLIAPTGSGKTLAGFLPSLIDLAGPEKPKKGLHTLYITPLRAL 74

Query: 66  MQDQVMSLKQ--RGINAEF---LGSAQTDSSVQTKAETGYFQLLFMTPE 109
             D   +L+     +         +  T SS + +       +L  TPE
Sbjct: 75  AVDIARNLQAPIEELGLPIRVETRTGDTSSSERARQRKKPPDILLTTPE 123

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|137505 PRK09751, PRK09751, putative ATP-dependent helicase Lhr; Provisional

 Score = 41.4 bits (97), Expect = 8e-04
 Identities = 24/83 (28%), Positives = 40/83 (48%), Gaps = 4/83 (4%)

Query: 255 AGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQ 314
           A ++HG +  + R    +     E+R +VAT +  +GID   V  VI    P ++ S  Q
Sbjct: 304 ARSHHGSVSKEQRAITEQALKSGELRCVVATSSLELGIDMGAVDLVIQVATPLSVASGLQ 363

Query: 315 ESGRCGRD--GIASVCWLYYARS 335
             GR G    G++    L++ R+
Sbjct: 364 RIGRAGHQVGGVSK--GLFFPRT 384

Length = 1490

>gnl|CDD|224118 COG1197, Mfd, Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]

 Score = 40.7 bits (96), Expect = 0.001
 Identities = 36/134 (26%), Positives = 59/134 (44%), Gaps = 16/134 (11%)

Query: 211 QSFV----DELVQE-ILKSVAGAGSIIVYCMTIKDVEEISKALKQL--GVKAGTYHGQMG 263
           ++FV    D L++E IL+ +   G +      ++ +E+ ++ L++L    +    HGQM 
Sbjct: 781 KTFVSEYDDLLIREAILRELLRGGQVFYVHNRVESIEKKAERLRELVPEARIAVAHGQMR 840

Query: 264 SKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVI-----HYGCPKTLESYYQESGR 318
            +  EE    F   E  V+V T     GID P+   +I      +G    L   YQ  GR
Sbjct: 841 ERELEEVMLDFYNGEYDVLVCTTIIETGIDIPNANTIIIERADKFG----LAQLYQLRGR 896

Query: 319 CGRDGIASVCWLYY 332
            GR    +  +  Y
Sbjct: 897 VGRSNKQAYAYFLY 910

Length = 1139

>gnl|CDD|236912 PRK11448, hsdR, type I restriction enzyme EcoKI subunit R; Provisional

 Score = 40.7 bits (96), Expect = 0.001
 Identities = 19/43 (44%), Positives = 27/43 (62%), Gaps = 10/43 (23%)

Query: 15  RPYQKDVIQ----RIIE-KRDCLVVMATGSGK-----SLCYQL 47
           R YQ+D IQ     I+E +R+ L+ MATG+GK     +L Y+L
Sbjct: 415 RYYQEDAIQAVEKAIVEGQREILLAMATGTGKTRTAIALMYRL 457

Length = 1123

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

 Score = 39.8 bits (93), Expect = 0.002
 Identities = 17/60 (28%), Positives = 26/60 (43%), Gaps = 8/60 (13%)

Query: 10  GYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLP--------PLVTGKTALVVSP 61
           G+    P Q   I  I+  RD L    TG+GK+  + LP              +AL+++P
Sbjct: 48  GFEEPTPIQLAAIPLILAGRDVLGQAQTGTGKTAAFLLPLLQKILKSVERKYVSALILAP 107

Length = 513

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

 Score = 39.6 bits (93), Expect = 0.002
 Identities = 30/92 (32%), Positives = 40/92 (43%)

Query: 232 IVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMG 291
           I++  T    EEI   L   G + G   G +  K R      F R ++ ++VAT     G
Sbjct: 259 IIFANTKHRCEEIWGHLAADGHRVGLLTGDVAQKKRLRILEEFTRGDLDILVATDVAARG 318

Query: 292 IDKPDVRHVIHYGCPKTLESYYQESGRCGRDG 323
           +  P V HV +Y  P   E Y    GR GR G
Sbjct: 319 LHIPAVTHVFNYDLPDDCEDYVHRIGRTGRAG 350

Length = 423

>gnl|CDD|237496 PRK13766, PRK13766, Hef nuclease; Provisional

 Score = 39.9 bits (94), Expect = 0.002
 Identities = 39/122 (31%), Positives = 53/122 (43%), Gaps = 13/122 (10%)

Query: 216 ELVQEILKSVAGAGSIIVYCMTIKD-VEEISKALKQLGVKAGTYHGQ--------MGSKA 266
           E+V+E L        IIV+    +D  E+I   L++ G+KA  + GQ        M  K 
Sbjct: 354 EIVKEQLGK-NPDSRIIVFT-QYRDTAEKIVDLLEKEGIKAVRFVGQASKDGDKGMSQKE 411

Query: 267 REEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHY-GCPKTLESYYQESGRCGRDGIA 325
           + E    F   E  V+V+T     G+D P V  VI Y   P  + S  Q  GR GR    
Sbjct: 412 QIEILDKFRAGEFNVLVSTSVAEEGLDIPSVDLVIFYEPVPSEIRS-IQRKGRTGRQEEG 470

Query: 326 SV 327
            V
Sbjct: 471 RV 472

Length = 773

>gnl|CDD|234365 TIGR03817, DECH_helic, helicase/secretion neighborhood putative DEAH-box helicase

 Score = 39.3 bits (92), Expect = 0.003
 Identities = 21/82 (25%), Positives = 34/82 (41%)

Query: 242 EEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVI 301
             + +    L  +   Y      + R E  R     E+  +  T A  +G+D   +  V+
Sbjct: 293 RLLGEVDPDLAERVAAYRAGYLPEDRRELERALRDGELLGVATTNALELGVDISGLDAVV 352

Query: 302 HYGCPKTLESYYQESGRCGRDG 323
             G P T  S +Q++GR GR G
Sbjct: 353 IAGFPGTRASLWQQAGRAGRRG 374

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. Length = 742

>gnl|CDD|182649 PRK10689, PRK10689, transcription-repair coupling factor; Provisional

 Score = 39.3 bits (92), Expect = 0.003
 Identities = 41/135 (30%), Positives = 56/135 (41%), Gaps = 22/135 (16%)

Query: 211 QSFV---DELV--QEILKSVAGAGSIIVYCMTIKDVEEISKALKQLG-----VKAGTYHG 260
           ++FV   D LV  + IL+ +   G   VY +   DVE I KA ++L       +    HG
Sbjct: 787 KTFVREYDSLVVREAILREILRGGQ--VYYL-YNDVENIQKAAERLAELVPEARIAIGHG 843

Query: 261 QMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVI-----HYGCPKTLESYYQE 315
           QM  +  E     F      V+V T     GID P    +I     H+G    L   +Q 
Sbjct: 844 QMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIERADHFG----LAQLHQL 899

Query: 316 SGRCGRDGIASVCWL 330
            GR GR    +  WL
Sbjct: 900 RGRVGRSHHQAYAWL 914

Length = 1147

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

 Score = 39.0 bits (91), Expect = 0.004
 Identities = 25/96 (26%), Positives = 41/96 (42%), Gaps = 17/96 (17%)

Query: 4   TLKKYFGYSVFRPYQKDVIQRIIE----KRDCLVVMATGSGKSLCYQLPPL----VTGKT 55
            L   F     RP Q+++ + + E        L+   TG+GK+L Y LP L      GK 
Sbjct: 6   YLAVAFPGFEPRPEQREMAEAVAEALKGGEGLLIEAPTGTGKTLAYLLPALAYAREEGKK 65

Query: 56  ALVVSPLISLMQDQVMS--------LKQRGINAEFL 83
            ++ +   +L Q+Q++         LK+ G     L
Sbjct: 66  VIISTRTKAL-QEQLLEEDLPIHKLLKKLGGKFALL 100

Length = 654

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	374
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	100.0
PLN03137	1195	ATP-dependent DNA helicase; Q4-like; Provisional	100.0
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	100.0
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	100.0
COG0514	590	RecQ Superfamily II DNA helicase [DNA replication,	100.0
KOG0331	519	consensus ATP-dependent RNA helicase [RNA processi	100.0
PTZ00110	545	helicase; Provisional	100.0
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	100.0
PLN00206	518	DEAD-box ATP-dependent RNA helicase; Provisional	100.0
KOG0330	476	consensus ATP-dependent RNA helicase [RNA processi	100.0
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	100.0
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	100.0
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	100.0
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	100.0
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	100.0
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	100.0
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	100.0
KOG0328	400	consensus Predicted ATP-dependent RNA helicase FAL	100.0
KOG0345	567	consensus ATP-dependent RNA helicase [RNA processi	100.0
PTZ00424	401	helicase 45; Provisional	100.0
KOG0336	629	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0333	673	consensus U5 snRNP-like RNA helicase subunit [RNA	100.0
KOG0351	941	consensus ATP-dependent DNA helicase [Replication,	100.0
TIGR03817	742	DECH_helic helicase/secretion neighborhood putativ	100.0
KOG0342	543	consensus ATP-dependent RNA helicase pitchoune [RN	100.0
KOG0338	691	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0352	641	consensus ATP-dependent DNA helicase [Replication,	100.0
KOG0340	442	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0335	482	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0326	459	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0348	708	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0353	695	consensus ATP-dependent DNA helicase [General func	100.0
PRK13767	876	ATP-dependent helicase; Provisional	100.0
KOG0343	758	consensus RNA Helicase [RNA processing and modific	100.0
PRK02362	737	ski2-like helicase; Provisional	100.0
KOG0346	569	consensus RNA helicase [RNA processing and modific	100.0
KOG0339	731	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0341	610	consensus DEAD-box protein abstrakt [RNA processin	100.0
KOG0332	477	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0350	620	consensus DEAD-box ATP-dependent RNA helicase [RNA	100.0
COG1201	814	Lhr Lhr-like helicases [General function predictio	100.0
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	100.0
KOG0347	731	consensus RNA helicase [RNA processing and modific	100.0
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	100.0
PRK00254	720	ski2-like helicase; Provisional	100.0
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	100.0
KOG0334	997	consensus RNA helicase [RNA processing and modific	100.0
PRK01172	674	ski2-like helicase; Provisional	100.0
PRK10689	1147	transcription-repair coupling factor; Provisional	100.0
KOG0344	593	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG4284	980	consensus DEAD box protein [Transcription]	100.0
PHA02558	501	uvsW UvsW helicase; Provisional	100.0
KOG0327	397	consensus Translation initiation factor 4F, helica	100.0
TIGR02621	844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	100.0
KOG0337	529	consensus ATP-dependent RNA helicase [RNA processi	100.0
PRK09751	1490	putative ATP-dependent helicase Lhr; Provisional	100.0
COG1204	766	Superfamily II helicase [General function predicti	100.0
COG1202	830	Superfamily II helicase, archaea-specific [General	100.0
TIGR01587	358	cas3_core CRISPR-associated helicase Cas3. This mo	100.0
TIGR00603	732	rad25 DNA repair helicase rad25. All proteins in t	100.0
PHA02653	675	RNA helicase NPH-II; Provisional	100.0
COG1111	542	MPH1 ERCC4-like helicases [DNA replication, recomb	100.0
TIGR03158	357	cas3_cyano CRISPR-associated helicase, Cyano-type.	100.0
PRK11664	812	ATP-dependent RNA helicase HrpB; Provisional	100.0
COG1205	851	Distinct helicase family with a unique C-terminal	100.0
TIGR01970	819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	100.0
KOG0952	1230	consensus DNA/RNA helicase MER3/SLH1, DEAD-box sup	100.0
PRK14701	1638	reverse gyrase; Provisional	100.0
PRK09401	1176	reverse gyrase; Reviewed	100.0
COG1061	442	SSL2 DNA or RNA helicases of superfamily II [Trans	100.0
PRK12898	656	secA preprotein translocase subunit SecA; Reviewed	100.0
TIGR03714	762	secA2 accessory Sec system translocase SecA2. Memb	100.0
PRK09200	790	preprotein translocase subunit SecA; Reviewed	100.0
PRK13766	773	Hef nuclease; Provisional	100.0
TIGR00963	745	secA preprotein translocase, SecA subunit. The pro	100.0
PRK04914	956	ATP-dependent helicase HepA; Validated	100.0
PRK05580	679	primosome assembly protein PriA; Validated	100.0
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	100.0
KOG0354	746	consensus DEAD-box like helicase [General function	100.0
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	100.0
TIGR00595	505	priA primosomal protein N'. All proteins in this f	100.0
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	100.0
PRK11131	1294	ATP-dependent RNA helicase HrpA; Provisional	100.0
KOG0329	387	consensus ATP-dependent RNA helicase [RNA processi	99.98
KOG0951	1674	consensus RNA helicase BRR2, DEAD-box superfamily	99.98
PRK09694	878	helicase Cas3; Provisional	99.97
TIGR01967	1283	DEAH_box_HrpA ATP-dependent helicase HrpA. This mo	99.97
PRK11448	1123	hsdR type I restriction enzyme EcoKI subunit R; Pr	99.97
COG4098	441	comFA Superfamily II DNA/RNA helicase required for	99.97
PLN03142	1033	Probable chromatin-remodeling complex ATPase chain	99.97
KOG0947	1248	consensus Cytoplasmic exosomal RNA helicase SKI2,	99.97
PRK13104	896	secA preprotein translocase subunit SecA; Reviewed	99.96
PRK12904	830	preprotein translocase subunit SecA; Reviewed	99.96
KOG0349	725	consensus Putative DEAD-box RNA helicase DDX1 [RNA	99.96
KOG0948	1041	consensus Nuclear exosomal RNA helicase MTR4, DEAD	99.96
PRK12906	796	secA preprotein translocase subunit SecA; Reviewed	99.96
KOG0950	1008	consensus DNA polymerase theta/eta, DEAD-box super	99.95
COG4581	1041	Superfamily II RNA helicase [DNA replication, reco	99.95
KOG0922	674	consensus DEAH-box RNA helicase [RNA processing an	99.95
TIGR00348	667	hsdR type I site-specific deoxyribonuclease, HsdR	99.95
COG1643	845	HrpA HrpA-like helicases [DNA replication, recombi	99.94
COG1203	733	CRISPR-associated helicase Cas3 [Defense mechanism	99.94
PRK13107	908	preprotein translocase subunit SecA; Reviewed	99.94
PRK12899	970	secA preprotein translocase subunit SecA; Reviewed	99.94
COG0556	663	UvrB Helicase subunit of the DNA excision repair c	99.94
COG1198	730	PriA Primosomal protein N' (replication factor Y)	99.94
KOG0385	971	consensus Chromatin remodeling complex WSTF-ISWI,	99.93
COG4096	875	HsdR Type I site-specific restriction-modification	99.93
KOG0387	923	consensus Transcription-coupled repair protein CSB	99.92
KOG1123	776	consensus RNA polymerase II transcription initiati	99.92
cd00268	203	DEADc DEAD-box helicases. A diverse family of prot	99.92
TIGR00631	655	uvrb excinuclease ABC, B subunit. This family is b	99.92
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	99.91
KOG0923	902	consensus mRNA splicing factor ATP-dependent RNA h	99.91
PF00270	169	DEAD: DEAD/DEAH box helicase; InterPro: IPR011545	99.9
KOG0390	776	consensus DNA repair protein, SNF2 family [Replica	99.9
KOG0924	1042	consensus mRNA splicing factor ATP-dependent RNA h	99.9
PRK12326	764	preprotein translocase subunit SecA; Reviewed	99.9
PRK05298	652	excinuclease ABC subunit B; Provisional	99.89
TIGR01407	850	dinG_rel DnaQ family exonuclease/DinG family helic	99.89
KOG0949	1330	consensus Predicted helicase, DEAD-box superfamily	99.88
KOG0920	924	consensus ATP-dependent RNA helicase A [RNA proces	99.87
PRK13103	913	secA preprotein translocase subunit SecA; Reviewed	99.87
PRK12900	1025	secA preprotein translocase subunit SecA; Reviewed	99.87
KOG0926	1172	consensus DEAH-box RNA helicase [RNA processing an	99.86
PRK07246	820	bifunctional ATP-dependent DNA helicase/DNA polyme	99.86
KOG0384	1373	consensus Chromodomain-helicase DNA-binding protei	99.86
KOG0389	941	consensus SNF2 family DNA-dependent ATPase [Chroma	99.86
KOG0953	700	consensus Mitochondrial RNA helicase SUV3, DEAD-bo	99.86
KOG1000	689	consensus Chromatin remodeling protein HARP/SMARCA	99.85
COG4889	1518	Predicted helicase [General function prediction on	99.84
PRK12903	925	secA preprotein translocase subunit SecA; Reviewed	99.83
CHL00122	870	secA preprotein translocase subunit SecA; Validate	99.82
cd00079	131	HELICc Helicase superfamily c-terminal domain; ass	99.81
PRK08074	928	bifunctional ATP-dependent DNA helicase/DNA polyme	99.81
KOG0392	1549	consensus SNF2 family DNA-dependent ATPase domain-	99.81
PF04851	184	ResIII: Type III restriction enzyme, res subunit;	99.8
KOG0925	699	consensus mRNA splicing factor ATP-dependent RNA h	99.8
KOG4150	1034	consensus Predicted ATP-dependent RNA helicase [RN	99.8
smart00487	201	DEXDc DEAD-like helicases superfamily.	99.78
TIGR03117	636	cas_csf4 CRISPR-associated DEAD/DEAH-box helicase	99.78
PF00271	78	Helicase_C: Helicase conserved C-terminal domain;	99.77
PRK12902	939	secA preprotein translocase subunit SecA; Reviewed	99.76
COG1199	654	DinG Rad3-related DNA helicases [Transcription / D	99.75
PRK11747	697	dinG ATP-dependent DNA helicase DinG; Provisional	99.75
TIGR00604	705	rad3 DNA repair helicase (rad3). All proteins in t	99.75
KOG0951	1674	consensus RNA helicase BRR2, DEAD-box superfamily	99.73
KOG0391	1958	consensus SNF2 family DNA-dependent ATPase [Genera	99.72
KOG0386	1157	consensus Chromatin remodeling complex SWI/SNF, co	99.72
KOG4439	901	consensus RNA polymerase II transcription terminat	99.71
PRK14873	665	primosome assembly protein PriA; Provisional	99.7
PF02399	824	Herpes_ori_bp: Origin of replication binding prote	99.67
COG0610	962	Type I site-specific restriction-modification syst	99.67
cd00046	144	DEXDc DEAD-like helicases superfamily. A diverse f	99.66
smart00490	82	HELICc helicase superfamily c-terminal domain.	99.65
KOG0388	1185	consensus SNF2 family DNA-dependent ATPase [Replic	99.62
PRK12901	1112	secA preprotein translocase subunit SecA; Reviewed	99.62
KOG1015	1567	consensus Transcription regulator XNP/ATRX, DEAD-b	99.6
KOG1002	791	consensus Nucleotide excision repair protein RAD16	99.59
TIGR02562	1110	cas3_yersinia CRISPR-associated helicase Cas3. The	99.57
COG0553	866	HepA Superfamily II DNA/RNA helicases, SNF2 family	99.48
PF00176	299	SNF2_N: SNF2 family N-terminal domain; InterPro: I	99.47
PF07652	148	Flavi_DEAD: Flavivirus DEAD domain ; InterPro: IPR	99.45
PF06862	442	DUF1253: Protein of unknown function (DUF1253); In	99.36
COG0653	822	SecA Preprotein translocase subunit SecA (ATPase,	99.33
KOG1016	1387	consensus Predicted DNA helicase, DEAD-box superfa	99.12
KOG2340	698	consensus Uncharacterized conserved protein [Funct	99.09
KOG1132	945	consensus Helicase of the DEAD superfamily [Replic	98.95
KOG0952	1230	consensus DNA/RNA helicase MER3/SLH1, DEAD-box sup	98.92
PRK15483	986	type III restriction-modification system StyLTI en	98.9
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	98.83
PF13307	167	Helicase_C_2: Helicase C-terminal domain; PDB: 4A1	98.82
PF07517	266	SecA_DEAD: SecA DEAD-like domain; InterPro: IPR011	98.72
KOG0921	1282	consensus Dosage compensation complex, subunit MLE	98.72
KOG1802	935	consensus RNA helicase nonsense mRNA reducing fact	98.7
PF13872	303	AAA_34: P-loop containing NTP hydrolase pore-1	98.7
COG3587	985	Restriction endonuclease [Defense mechanisms]	98.69
smart00488	289	DEXDc2 DEAD-like helicases superfamily.	98.62
smart00489	289	DEXDc3 DEAD-like helicases superfamily.	98.62
KOG1001	674	consensus Helicase-like transcription factor HLTF/	98.51
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	98.47
KOG1803	649	consensus DNA helicase [Replication, recombination	98.37
TIGR00376	637	DNA helicase, putative. The gene product may repre	98.28
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	98.26
KOG1513	1300	consensus Nuclear helicase MOP-3/SNO (DEAD-box sup	98.2
smart00492	141	HELICc3 helicase superfamily c-terminal domain.	98.2
smart00491	142	HELICc2 helicase superfamily c-terminal domain.	98.2
COG3421	812	Uncharacterized protein conserved in bacteria [Fun	98.18
PF13245	76	AAA_19: Part of AAA domain	98.08
TIGR01447	586	recD exodeoxyribonuclease V, alpha subunit. This f	98.05
PF09848	352	DUF2075: Uncharacterized conserved protein (DUF207	97.99
KOG1131	755	consensus RNA polymerase II transcription initiati	97.96
COG2256	436	MGS1 ATPase related to the helicase subunit of the	97.93
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	97.89
PRK10875	615	recD exonuclease V subunit alpha; Provisional	97.89
KOG1805	1100	consensus DNA replication helicase [Replication, r	97.88
TIGR01448	720	recD_rel helicase, putative, RecD/TraA family. Thi	97.85
PRK10536	262	hypothetical protein; Provisional	97.72
COG1875	436	NYN ribonuclease and ATPase of PhoH family domains	97.6
KOG0298	1394	consensus DEAD box-containing helicase-like transc	97.53
KOG0383	696	consensus Predicted helicase [General function pre	97.52
PRK08181	269	transposase; Validated	97.49
PRK06526	254	transposase; Provisional	97.48
PF13871	278	Helicase_C_4: Helicase_C-like	97.47
PRK04296	190	thymidine kinase; Provisional	97.46
PF12340	229	DUF3638: Protein of unknown function (DUF3638); In	97.46
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	97.45
PRK08727	233	hypothetical protein; Validated	97.45
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	97.43
KOG0739	439	consensus AAA+-type ATPase [Posttranslational modi	97.42
PF00580	315	UvrD-helicase: UvrD/REP helicase N-terminal domain	97.39
KOG2028	554	consensus ATPase related to the helicase subunit o	97.36
TIGR02768	744	TraA_Ti Ti-type conjugative transfer relaxase TraA	97.35
PHA03368	738	DNA packaging terminase subunit 1; Provisional	97.31
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	97.28
PRK13826	1102	Dtr system oriT relaxase; Provisional	97.26
KOG1133	821	consensus Helicase of the DEAD superfamily [Replic	97.25
TIGR02760	1960	TraI_TIGR conjugative transfer relaxase protein Tr	97.2
PRK07952	244	DNA replication protein DnaC; Validated	97.18
PF00004	132	AAA: ATPase family associated with various cellula	97.17
PRK12377	248	putative replication protein; Provisional	97.16
PF05970	364	PIF1: PIF1-like helicase; InterPro: IPR010285 This	97.13
PF05127	177	Helicase_RecD: Helicase; InterPro: IPR007807 This	97.12
PRK13342	413	recombination factor protein RarA; Reviewed	97.09
PRK13889	988	conjugal transfer relaxase TraA; Provisional	97.08
PRK06835	329	DNA replication protein DnaC; Validated	97.08
KOG0729	435	consensus 26S proteasome regulatory complex, ATPas	97.04
smart00382	148	AAA ATPases associated with a variety of cellular	97.03
KOG0738	491	consensus AAA+-type ATPase [Posttranslational modi	97.03
KOG0989	346	consensus Replication factor C, subunit RFC4 [Repl	97.02
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	97.0
PRK05642	234	DNA replication initiation factor; Validated	97.0
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	96.98
PRK06893	229	DNA replication initiation factor; Validated	96.97
PRK05707	328	DNA polymerase III subunit delta'; Validated	96.96
PF05621	302	TniB: Bacterial TniB protein; InterPro: IPR008868	96.95
COG1484	254	DnaC DNA replication protein [DNA replication, rec	96.94
COG1419	407	FlhF Flagellar GTP-binding protein [Cell motility	96.92
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	96.91
PRK14974	336	cell division protein FtsY; Provisional	96.91
PRK13341	725	recombination factor protein RarA/unknown domain f	96.9
PHA03333	752	putative ATPase subunit of terminase; Provisional	96.88
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	96.87
PRK08084	235	DNA replication initiation factor; Provisional	96.86
PRK08116	268	hypothetical protein; Validated	96.86
PRK12422	445	chromosomal replication initiation protein; Provis	96.79
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	96.78
PRK00149	450	dnaA chromosomal replication initiation protein; R	96.76
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	96.76
PHA02533	534	17 large terminase protein; Provisional	96.75
TIGR01075	715	uvrD DNA helicase II. Designed to identify uvrD me	96.74
PF06745	226	KaiC: KaiC; InterPro: IPR014774 This entry represe	96.73
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	96.7
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	96.68
PRK06921	266	hypothetical protein; Provisional	96.67
TIGR00596	814	rad1 DNA repair protein (rad1). This family is bas	96.65
PF03354	477	Terminase_1: Phage Terminase ; InterPro: IPR005021	96.63
PRK11773	721	uvrD DNA-dependent helicase II; Provisional	96.61
PF13173	128	AAA_14: AAA domain	96.56
COG1222	406	RPT1 ATP-dependent 26S proteasome regulatory subun	96.54
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	96.5
COG4626	546	Phage terminase-like protein, large subunit [Gener	96.5
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	96.48
PRK14088	440	dnaA chromosomal replication initiation protein; P	96.48
PRK13709	1747	conjugal transfer nickase/helicase TraI; Provision	96.47
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	96.47
PF05876	557	Terminase_GpA: Phage terminase large subunit (GpA)	96.47
PRK14087	450	dnaA chromosomal replication initiation protein; P	96.43
PRK06871	325	DNA polymerase III subunit delta'; Validated	96.43
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	96.42
PRK08533	230	flagellar accessory protein FlaH; Reviewed	96.41
PLN03025	319	replication factor C subunit; Provisional	96.4
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	96.4
TIGR01074	664	rep ATP-dependent DNA helicase Rep. Designed to id	96.38
PRK04195	482	replication factor C large subunit; Provisional	96.37
CHL00176	638	ftsH cell division protein; Validated	96.37
PRK09183	259	transposase/IS protein; Provisional	96.33
KOG0734	752	consensus AAA+-type ATPase containing the peptidas	96.32
PRK08769	319	DNA polymerase III subunit delta'; Validated	96.3
PF01443	234	Viral_helicase1: Viral (Superfamily 1) RNA helicas	96.28
TIGR02760	1960	TraI_TIGR conjugative transfer relaxase protein Tr	96.28
PRK06067	234	flagellar accessory protein FlaH; Validated	96.27
PRK05580	679	primosome assembly protein PriA; Validated	96.26
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	96.26
KOG1133	821	consensus Helicase of the DEAD superfamily [Replic	96.25
PF02456	369	Adeno_IVa2: Adenovirus IVa2 protein; InterPro: IPR	96.25
PRK10919	672	ATP-dependent DNA helicase Rep; Provisional	96.24
PRK14964	491	DNA polymerase III subunits gamma and tau; Provisi	96.23
PRK07993	334	DNA polymerase III subunit delta'; Validated	96.22
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	96.22
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	96.21
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	96.21
COG1223	368	Predicted ATPase (AAA+ superfamily) [General funct	96.21
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	96.21
TIGR00595	505	priA primosomal protein N'. All proteins in this f	96.19
PRK06620	214	hypothetical protein; Validated	96.18
PRK04328	249	hypothetical protein; Provisional	96.18
PHA02544	316	44 clamp loader, small subunit; Provisional	96.18
PRK14712	1623	conjugal transfer nickase/helicase TraI; Provision	96.16
PRK07764	824	DNA polymerase III subunits gamma and tau; Validat	96.15
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	96.15
PHA03372	668	DNA packaging terminase subunit 1; Provisional	96.15
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	96.15
PRK14958	509	DNA polymerase III subunits gamma and tau; Provisi	96.14
PRK06964	342	DNA polymerase III subunit delta'; Validated	96.12
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	96.12
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	96.11
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	96.1
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	96.09
PF13177	162	DNA_pol3_delta2: DNA polymerase III, delta subunit	96.07
COG0464	494	SpoVK ATPases of the AAA+ class [Posttranslational	96.06
PRK14086	617	dnaA chromosomal replication initiation protein; P	96.01
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	95.99
PRK05973	237	replicative DNA helicase; Provisional	95.98
PRK08903	227	DnaA regulatory inactivator Hda; Validated	95.95
TIGR03878	259	thermo_KaiC_2 KaiC domain protein, AF_0795 family.	95.93
PRK07940	394	DNA polymerase III subunit delta'; Validated	95.89
PRK14873	665	primosome assembly protein PriA; Provisional	95.89
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	95.86
COG0593	408	DnaA ATPase involved in DNA replication initiation	95.84
PRK03992	389	proteasome-activating nucleotidase; Provisional	95.83
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	95.75
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	95.74
TIGR01241	495	FtsH_fam ATP-dependent metalloprotease FtsH. HflB(	95.73
PRK11823	446	DNA repair protein RadA; Provisional	95.73
cd01126	384	TraG_VirD4 The TraG/TraD/VirD4 family are bacteria	95.73
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	95.72
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	95.68
PRK11054	684	helD DNA helicase IV; Provisional	95.65
CHL00181	287	cbbX CbbX; Provisional	95.63
KOG0991	333	consensus Replication factor C, subunit RFC2 [Repl	95.6
PF10593	239	Z1: Z1 domain; InterPro: IPR018310 This entry repr	95.59
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	95.58
TIGR02012	321	tigrfam_recA protein RecA. This model describes or	95.54
COG4962	355	CpaF Flp pilus assembly protein, ATPase CpaF [Intr	95.52
TIGR00064	272	ftsY signal recognition particle-docking protein F	95.52
PRK12402	337	replication factor C small subunit 2; Reviewed	95.52
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	95.51
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	95.5
PRK06090	319	DNA polymerase III subunit delta'; Validated	95.48
PRK10416	318	signal recognition particle-docking protein FtsY;	95.46
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	95.26
cd00984	242	DnaB_C DnaB helicase C terminal domain. The hexame	95.26
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	95.25
PRK09354	349	recA recombinase A; Provisional	95.24
cd00983	325	recA RecA is a bacterial enzyme which has roles in	95.18
COG0467	260	RAD55 RecA-superfamily ATPases implicated in signa	95.17
PRK12727	559	flagellar biosynthesis regulator FlhF; Provisional	95.16
cd01122	271	GP4d_helicase GP4d_helicase is a homohexameric 5'-	95.16
PRK09111	598	DNA polymerase III subunits gamma and tau; Validat	95.16
PRK14957	546	DNA polymerase III subunits gamma and tau; Provisi	95.14
PTZ00361	438	26 proteosome regulatory subunit 4-like protein; P	95.14
COG1435	201	Tdk Thymidine kinase [Nucleotide transport and met	95.13
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	95.12
PRK10689	1147	transcription-repair coupling factor; Provisional	95.11
PRK14951	618	DNA polymerase III subunits gamma and tau; Provisi	95.09
PRK07133	725	DNA polymerase III subunits gamma and tau; Validat	95.08
PRK14955	397	DNA polymerase III subunits gamma and tau; Provisi	95.06
TIGR01242	364	26Sp45 26S proteasome subunit P45 family. Many pro	95.04
PRK00771	437	signal recognition particle protein Srp54; Provisi	95.04
PRK12724	432	flagellar biosynthesis regulator FlhF; Provisional	95.03
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	95.02
CHL00206	2281	ycf2 Ycf2; Provisional	95.0
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	94.95
COG1198	730	PriA Primosomal protein N' (replication factor Y)	94.91
CHL00195	489	ycf46 Ycf46; Provisional	94.91
PRK06731	270	flhF flagellar biosynthesis regulator FlhF; Valida	94.9
COG1219	408	ClpX ATP-dependent protease Clp, ATPase subunit [P	94.89
KOG0737	386	consensus AAA+-type ATPase [Posttranslational modi	94.89
TIGR01073	726	pcrA ATP-dependent DNA helicase PcrA. Designed to	94.87
PRK13833	323	conjugal transfer protein TrbB; Provisional	94.87
PF02534	469	T4SS-DNA_transf: Type IV secretory system Conjugat	94.83
PRK13897	606	type IV secretion system component VirD4; Provisio	94.82
PRK09112	351	DNA polymerase III subunit delta'; Validated	94.81
KOG0740	428	consensus AAA+-type ATPase [Posttranslational modi	94.79
COG0470	325	HolB ATPase involved in DNA replication [DNA repli	94.79
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	94.74
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	94.74
PRK10865	857	protein disaggregation chaperone; Provisional	94.74
PRK14959	624	DNA polymerase III subunits gamma and tau; Provisi	94.7
TIGR03689	512	pup_AAA proteasome ATPase. In the Actinobacteria,	94.67
PRK09087	226	hypothetical protein; Validated	94.66
PRK08699	325	DNA polymerase III subunit delta'; Validated	94.66
TIGR01547	396	phage_term_2 phage terminase, large subunit, PBSX	94.56
PRK05563	559	DNA polymerase III subunits gamma and tau; Validat	94.55
KOG0736	953	consensus Peroxisome assembly factor 2 containing	94.54
CHL00095	821	clpC Clp protease ATP binding subunit	94.49
PF00265	176	TK: Thymidine kinase; InterPro: IPR001267 Thymidin	94.49
PRK10867	433	signal recognition particle protein; Provisional	94.46
PRK14965	576	DNA polymerase III subunits gamma and tau; Provisi	94.45
PRK13851	344	type IV secretion system protein VirB11; Provision	94.45
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	94.42
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	94.41
KOG0298	1394	consensus DEAD box-containing helicase-like transc	94.38
PRK07471	365	DNA polymerase III subunit delta'; Validated	94.38
PF14617	252	CMS1: U3-containing 90S pre-ribosomal complex subu	94.37
COG2804	500	PulE Type II secretory pathway, ATPase PulE/Tfp pi	94.34
KOG1807	1025	consensus Helicases [Replication, recombination an	94.24
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	94.21
PRK13894	319	conjugal transfer ATPase TrbB; Provisional	94.19
cd03115	173	SRP The signal recognition particle (SRP) mediates	94.18
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	94.14
TIGR02785	1232	addA_Gpos recombination helicase AddA, Firmicutes	94.11
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	94.11
COG3973	747	Superfamily I DNA and RNA helicases [General funct	94.07
COG1444	758	Predicted P-loop ATPase fused to an acetyltransfer	94.01
PRK06995	484	flhF flagellar biosynthesis regulator FlhF; Valida	94.01
KOG2543	438	consensus Origin recognition complex, subunit 5 [R	94.0
PRK08058	329	DNA polymerase III subunit delta'; Validated	93.99
TIGR02782	299	TrbB_P P-type conjugative transfer ATPase TrbB. Th	93.93
PRK12726	407	flagellar biosynthesis regulator FlhF; Provisional	93.92
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	93.91
TIGR03880	224	KaiC_arch_3 KaiC domain protein, AF_0351 family. T	93.87
PRK14954	620	DNA polymerase III subunits gamma and tau; Provisi	93.86
PRK14950	585	DNA polymerase III subunits gamma and tau; Provisi	93.86
PF08423	256	Rad51: Rad51; InterPro: IPR013632 This domain is f	93.82
PRK13900	332	type IV secretion system ATPase VirB11; Provisiona	93.79
PRK10733	644	hflB ATP-dependent metalloprotease; Reviewed	93.78
PTZ00112	1164	origin recognition complex 1 protein; Provisional	93.73
KOG0730	693	consensus AAA+-type ATPase [Posttranslational modi	93.71
KOG0742	630	consensus AAA+-type ATPase [Posttranslational modi	93.69
PHA00350	399	putative assembly protein	93.67
PRK13850	670	type IV secretion system protein VirD4; Provisiona	93.61
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	93.61
TIGR00708	173	cobA cob(I)alamin adenosyltransferase. Alternate n	93.6
TIGR00678	188	holB DNA polymerase III, delta' subunit. At positi	93.6
PRK14721	420	flhF flagellar biosynthesis regulator FlhF; Provis	93.58
PRK14948	620	DNA polymerase III subunits gamma and tau; Provisi	93.57
TIGR02237	209	recomb_radB DNA repair and recombination protein R	93.54
cd01130	186	VirB11-like_ATPase Type IV secretory pathway compo	93.53
TIGR03600	421	phage_DnaB phage replicative helicase, DnaB family	93.44
TIGR01425	429	SRP54_euk signal recognition particle protein SRP5	93.36
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	93.26
KOG0741	744	consensus AAA+-type ATPase [Posttranslational modi	93.26
PF03796	259	DnaB_C: DnaB-like helicase C terminal domain; Inte	93.26
PRK00411	394	cdc6 cell division control protein 6; Reviewed	93.23
KOG0701	1606	consensus dsRNA-specific nuclease Dicer and relate	93.15
PRK07399	314	DNA polymerase III subunit delta'; Validated	93.11
PRK13822	641	conjugal transfer coupling protein TraG; Provision	93.09
PRK05986	191	cob(I)alamin adenolsyltransferase/cobinamide ATP-d	92.88
PRK00440	319	rfc replication factor C small subunit; Reviewed	92.87
PF06733	174	DEAD_2: DEAD_2; InterPro: IPR010614 This represent	92.85
PF03237	384	Terminase_6: Terminase-like family; InterPro: IPR0	92.8
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	92.75
PRK05595	444	replicative DNA helicase; Provisional	92.71
PRK14971	614	DNA polymerase III subunits gamma and tau; Provisi	92.68
TIGR00959	428	ffh signal recognition particle protein. This mode	92.66
KOG0652	424	consensus 26S proteasome regulatory complex, ATPas	92.65
PRK08451	535	DNA polymerase III subunits gamma and tau; Validat	92.64
PRK14723	767	flhF flagellar biosynthesis regulator FlhF; Provis	92.61
cd01393	226	recA_like RecA is a bacterial enzyme which has rol	92.58
TIGR00416	454	sms DNA repair protein RadA. The gene protuct code	92.58
PRK08840	464	replicative DNA helicase; Provisional	92.54
cd01123	235	Rad51_DMC1_radA Rad51_DMC1_radA,B. This group of r	92.49
PRK09302	509	circadian clock protein KaiC; Reviewed	92.48
cd00561	159	CobA_CobO_BtuR ATP:corrinoid adenosyltransferase B	92.39
TIGR02767	623	TraG-Ti Ti-type conjugative transfer system protie	92.37
PF05729	166	NACHT: NACHT domain	92.3
KOG2228	408	consensus Origin recognition complex, subunit 4 [R	92.28
TIGR02397	355	dnaX_nterm DNA polymerase III, subunit gamma and t	92.28
PRK14953	486	DNA polymerase III subunits gamma and tau; Provisi	92.2
PRK06904	472	replicative DNA helicase; Validated	92.19
TIGR00665	434	DnaB replicative DNA helicase. This model describe	92.15
TIGR00767	415	rho transcription termination factor Rho. Members	92.06
KOG0745	564	consensus Putative ATP-dependent Clp-type protease	91.95
PRK08506	472	replicative DNA helicase; Provisional	91.89
PRK06647	563	DNA polymerase III subunits gamma and tau; Validat	91.84
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	91.79
PF01745	233	IPT: Isopentenyl transferase; InterPro: IPR002648	91.71
cd01125	239	repA Hexameric Replicative Helicase RepA. RepA is	91.65
cd01129	264	PulE-GspE PulE/GspE The type II secretory pathway	91.6
TIGR03819	340	heli_sec_ATPase helicase/secretion neighborhood AT	91.58
PRK10436	462	hypothetical protein; Provisional	91.51
PRK04841	903	transcriptional regulator MalT; Provisional	91.49
PRK09519	790	recA DNA recombination protein RecA; Reviewed	91.45
TIGR02238	313	recomb_DMC1 meiotic recombinase Dmc1. This model d	91.35
PRK14701	1638	reverse gyrase; Provisional	91.31
PRK13880	636	conjugal transfer coupling protein TraG; Provision	91.31
PF00437	270	T2SE: Type II/IV secretion system protein; InterPr	91.25
PRK09361	225	radB DNA repair and recombination protein RadB; Pr	91.25
TIGR02788	308	VirB11 P-type DNA transfer ATPase VirB11. The VirB	91.24
PRK13876	663	conjugal transfer coupling protein TraG; Provision	91.18
TIGR02533	486	type_II_gspE general secretory pathway protein E.	91.11
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	91.09
KOG0727	408	consensus 26S proteasome regulatory complex, ATPas	91.09
PF01078	206	Mg_chelatase: Magnesium chelatase, subunit ChlI; I	91.09
cd00544	169	CobU Adenosylcobinamide kinase / adenosylcobinamid	91.09
PRK15483	986	type III restriction-modification system StyLTI en	91.08
KOG1806	1320	consensus DEAD box containing helicases [Replicati	91.02
PF07728	139	AAA_5: AAA domain (dynein-related subfamily); Inte	90.99
PF13207	121	AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6	90.96
COG4185	187	Uncharacterized protein conserved in bacteria [Fun	90.9
PRK08760	476	replicative DNA helicase; Provisional	90.87
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	90.87
PF01637	234	Arch_ATPase: Archaeal ATPase; InterPro: IPR011579	90.87
cd01128	249	rho_factor Transcription termination factor rho is	90.81
smart00488	289	DEXDc2 DEAD-like helicases superfamily.	90.78
smart00489	289	DEXDc3 DEAD-like helicases superfamily.	90.78
PF13555	62	AAA_29: P-loop containing region of AAA domain	90.72
PRK13531	498	regulatory ATPase RavA; Provisional	90.71

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=100.00  E-value=3.3e-60  Score=435.52  Aligned_cols=367  Identities=48%  Similarity=0.782  Sum_probs=316.6

Q ss_pred             HHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccccCCcEEEEcchHHHHHHHHHHHHHcCCceEEc
Q 037567            4 TLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVTGKTALVVSPLISLMQDQVMSLKQRGINAEFL   83 (374)
Q Consensus         4 ~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~   83 (374)
                      .|++.|||++|+|+|.++++.+++++++++.+|||+|||++|++|++.....++|++|+++|+.|+.+.+...|+....+
T Consensus         2 ~l~~~~g~~~~r~~Q~~ai~~~l~g~dvlv~apTGsGKTl~y~lp~l~~~~~~lVi~P~~~L~~dq~~~l~~~gi~~~~l   81 (470)
T TIGR00614         2 ILKTVFGLSSFRPVQLEVINAVLLGRDCFVVMPTGGGKSLCYQLPALCSDGITLVISPLISLMEDQVLQLKASGIPATFL   81 (470)
T ss_pred             hhHhhcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCcHhHHHHHHHHHcCCcEEEEecHHHHHHHHHHHHHHcCCcEEEE
Confidence            58899999999999999999999999999999999999999999999888999999999999999999999999988887


Q ss_pred             CCCCCchhh---hhhhhcCCeeEEEEcCcccccCchhhHHHH-HhcCccEEEEeccchhhcccCcchHHHHHHHHHHHhc
Q 037567           84 GSAQTDSSV---QTKAETGYFQLLFMTPEKACIIPISFWSKL-LKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFL  159 (374)
Q Consensus        84 ~~~~~~~~~---~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~-~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~  159 (374)
                      .+.....+.   ......+.++|+++||+++..... ....+ ...+++++||||||.+.+||.+++..+..+..+...+
T Consensus        82 ~~~~~~~~~~~i~~~~~~~~~~il~~TPe~l~~~~~-~~~~l~~~~~i~~iViDEaH~i~~~g~~fr~~~~~l~~l~~~~  160 (470)
T TIGR00614        82 NSSQSKEQQKNVLTDLKDGKIKLLYVTPEKCSASNR-LLQTLEERKGITLIAVDEAHCISQWGHDFRPDYKALGSLKQKF  160 (470)
T ss_pred             eCCCCHHHHHHHHHHHhcCCCCEEEECHHHHcCchh-HHHHHHhcCCcCEEEEeCCcccCccccccHHHHHHHHHHHHHc
Confidence            776544322   223345678999999999865432 22333 5678999999999999999999999999998888888


Q ss_pred             CCCCeeEEEeecCcccHHHHHHhcCCCCCeEEEeccCCCceeEEEEeecCCcchHHHHHHHHHHhhcCCCcEEEEecchh
Q 037567          160 LGVPFVALTATATEKVRIDIINSLKLKNPYVTIASFDRKNLFYGVKVINRGQSFVDELVQEILKSVAGAGSIIVYCMTIK  239 (374)
Q Consensus       160 ~~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lVf~~~~~  239 (374)
                      ++.+++++|||+++....++...+++..+.+...+.+++++.+.+.....  ....+++..+ .....+..+||||++++
T Consensus       161 ~~~~~l~lTAT~~~~~~~di~~~l~l~~~~~~~~s~~r~nl~~~v~~~~~--~~~~~l~~~l-~~~~~~~~~IIF~~s~~  237 (470)
T TIGR00614       161 PNVPIMALTATASPSVREDILRQLNLKNPQIFCTSFDRPNLYYEVRRKTP--KILEDLLRFI-RKEFKGKSGIIYCPSRK  237 (470)
T ss_pred             CCCceEEEecCCCHHHHHHHHHHcCCCCCcEEeCCCCCCCcEEEEEeCCc--cHHHHHHHHH-HHhcCCCceEEEECcHH
Confidence            99999999999999988888999998888888888888887665544322  2233333333 32335667799999999


Q ss_pred             HHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEEEEECCCCChhHHHHhhccC
Q 037567          240 DVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRC  319 (374)
Q Consensus       240 ~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~~~~p~s~~~~~Q~~GR~  319 (374)
                      .++.+++.|++.|+.+..+||+++.++|..+++.|.+|+.+|||||+++++|+|+|++++||++++|.|+..|+||+||+
T Consensus       238 ~~e~la~~L~~~g~~~~~~H~~l~~~eR~~i~~~F~~g~~~vLVaT~~~~~GID~p~V~~VI~~~~P~s~~~y~Qr~GRa  317 (470)
T TIGR00614       238 KSEQVTASLQNLGIAAGAYHAGLEISARDDVHHKFQRDEIQVVVATVAFGMGINKPDVRFVIHYSLPKSMESYYQESGRA  317 (470)
T ss_pred             HHHHHHHHHHhcCCCeeEeeCCCCHHHHHHHHHHHHcCCCcEEEEechhhccCCcccceEEEEeCCCCCHHHHHhhhcCc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCceEEEEEeeccCCCcccceeccccchHHHHHHHHHHHHHHHHhhhcccCC
Q 037567          320 GRDGIASVCWLYYARSNFAKGDFYCGESQTENQRTAIMESLLAAQRYCLLTTCRR  374 (374)
Q Consensus       320 ~R~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~  374 (374)
                      ||.|.+|.|++++.+.|...++.++.......++......+..|..+++.+.|||
T Consensus       318 GR~G~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~crr  372 (470)
T TIGR00614       318 GRDGLPSECHLFYAPADINRLRRLLMEEPDGQQRTYKLKLYEMMEYCLNSSTCRR  372 (470)
T ss_pred             CCCCCCceEEEEechhHHHHHHHHHhcCCchhHHHHHHHHHHHHHHHhccccCHH
Confidence            9999999999999999999999888777666666666777888889999999997

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=100.00  E-value=9.1e-60  Score=446.89  Aligned_cols=369  Identities=39%  Similarity=0.645  Sum_probs=309.7

Q ss_pred             hHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccccCCcEEEEcchHHHHHHHHHHHHHcCCceEE
Q 037567            3 STLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVTGKTALVVSPLISLMQDQVMSLKQRGINAEF   82 (374)
Q Consensus         3 ~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~   82 (374)
                      ..++++||+..|+|+|.++++.+++|+++++.+|||+|||++|++|++.....+||++|+++|+.++...+...|+....
T Consensus       450 ~~lk~~FG~~sFRp~Q~eaI~aiL~GrDVLVimPTGSGKSLcYQLPAL~~~GiTLVISPLiSLmqDQV~~L~~~GI~Aa~  529 (1195)
T PLN03137        450 VNNKKVFGNHSFRPNQREIINATMSGYDVFVLMPTGGGKSLTYQLPALICPGITLVISPLVSLIQDQIMNLLQANIPAAS  529 (1195)
T ss_pred             HHHHHHcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCccHHHHHHHHHHHcCCcEEEEeCHHHHHHHHHHHHHhCCCeEEE
Confidence            46788999999999999999999999999999999999999999999998899999999999999888888888988887


Q ss_pred             cCCCCCchhhhhhh---h--cCCeeEEEEcCcccccC--chhhHHHH-HhcCccEEEEeccchhhcccCcchHHHHHHHH
Q 037567           83 LGSAQTDSSVQTKA---E--TGYFQLLFMTPEKACII--PISFWSKL-LKAGVCLFAVDEAHCISEWGHDFRLEYKQLDK  154 (374)
Q Consensus        83 ~~~~~~~~~~~~~~---~--~~~~~i~i~T~~~l~~~--~~~~~~~~-~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~  154 (374)
                      +.++..........   .  .+.++|+++||+++...  +......+ ....+.+|||||||.+.+||.++++.+..+..
T Consensus       530 L~s~~s~~eq~~ilr~l~s~~g~~~ILyvTPERL~~~d~ll~~L~~L~~~~~LslIVIDEAHcVSqWGhDFRpdYr~L~~  609 (1195)
T PLN03137        530 LSAGMEWAEQLEILQELSSEYSKYKLLYVTPEKVAKSDSLLRHLENLNSRGLLARFVIDEAHCVSQWGHDFRPDYQGLGI  609 (1195)
T ss_pred             EECCCCHHHHHHHHHHHHhcCCCCCEEEEChHHhhcchHHHHHHHhhhhccccceeccCcchhhhhcccchHHHHHHHHH
Confidence            76655443332211   1  26789999999998642  11212222 22457899999999999999999999998888


Q ss_pred             HHHhcCCCCeeEEEeecCcccHHHHHHhcCCCCCeEEEeccCCCceeEEEEeecCCcchHHHHHHHHHHhhcCCCcEEEE
Q 037567          155 LRTFLLGVPFVALTATATEKVRIDIINSLKLKNPYVTIASFDRKNLFYGVKVINRGQSFVDELVQEILKSVAGAGSIIVY  234 (374)
Q Consensus       155 ~~~~~~~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lVf  234 (374)
                      +...+++.++++||||++.....++...+++.++.+...+.+++++.+.+....  ..... .+..++.....+..+|||
T Consensus       610 Lr~~fp~vPilALTATAT~~V~eDI~~~L~l~~~~vfr~Sf~RpNL~y~Vv~k~--kk~le-~L~~~I~~~~~~esgIIY  686 (1195)
T PLN03137        610 LKQKFPNIPVLALTATATASVKEDVVQALGLVNCVVFRQSFNRPNLWYSVVPKT--KKCLE-DIDKFIKENHFDECGIIY  686 (1195)
T ss_pred             HHHhCCCCCeEEEEecCCHHHHHHHHHHcCCCCcEEeecccCccceEEEEeccc--hhHHH-HHHHHHHhcccCCCceeE
Confidence            888888999999999999999888999999988888888888888776654322  11122 333333333346789999


Q ss_pred             ecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEEEEECCCCChhHHHH
Q 037567          235 CMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQ  314 (374)
Q Consensus       235 ~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~~~~p~s~~~~~Q  314 (374)
                      |.+++.++.+++.|.+.|+.+..+||+++.++|..++++|..|+++|||||.++++|||+|++++||++++|.|+..|+|
T Consensus       687 C~SRke~E~LAe~L~~~Gika~~YHAGLs~eeR~~vqe~F~~Gei~VLVATdAFGMGIDkPDVR~VIHydlPkSiEsYyQ  766 (1195)
T PLN03137        687 CLSRMDCEKVAERLQEFGHKAAFYHGSMDPAQRAFVQKQWSKDEINIICATVAFGMGINKPDVRFVIHHSLPKSIEGYHQ  766 (1195)
T ss_pred             eCchhHHHHHHHHHHHCCCCeeeeeCCCCHHHHHHHHHHHhcCCCcEEEEechhhcCCCccCCcEEEEcCCCCCHHHHHh
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhccCCCCCCceEEEEEeeccCCCcccceeccccchH---------------HHHHHHHHHHHHHHHhhhc-ccCC
Q 037567          315 ESGRCGRDGIASVCWLYYARSNFAKGDFYCGESQTEN---------------QRTAIMESLLAAQRYCLLT-TCRR  374 (374)
Q Consensus       315 ~~GR~~R~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~---------------~~~~~~~~l~~~~~~~~~~-~~~~  374 (374)
                      ++|||||.|.++.|+++|...|+...+.++.....+.               ..+..++.|..|.+||+.+ .|||
T Consensus       767 riGRAGRDG~~g~cILlys~~D~~~~~~lI~~~~~~~s~~~~~~~r~~~s~~~~e~~~~~L~~m~~yce~~~~CRR  842 (1195)
T PLN03137        767 ECGRAGRDGQRSSCVLYYSYSDYIRVKHMISQGGVEQSPMAMGYNRMASSGRILETNTENLLRMVSYCENEVDCRR  842 (1195)
T ss_pred             hhcccCCCCCCceEEEEecHHHHHHHHHHHhccccccchhhhhhcccchhHHHHHHHHHHHHHHHHHHhChHhhHH
Confidence            9999999999999999999999888887775432211               2344678999999999996 8997

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=100.00  E-value=1.6e-58  Score=434.75  Aligned_cols=365  Identities=42%  Similarity=0.720  Sum_probs=314.7

Q ss_pred             hHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccccCCcEEEEcchHHHHHHHHHHHHHcCCceEE
Q 037567            3 STLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVTGKTALVVSPLISLMQDQVMSLKQRGINAEF   82 (374)
Q Consensus         3 ~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~   82 (374)
                      +.|++.|||++|+|+|.++++.+++++++++.+|||+|||++|+++++.....++|++|+++|+.|+.+.+...|+....
T Consensus        15 ~~l~~~fG~~~~r~~Q~~ai~~il~g~dvlv~apTGsGKTl~y~lpal~~~g~tlVisPl~sL~~dqv~~l~~~gi~~~~   94 (607)
T PRK11057         15 QVLQETFGYQQFRPGQQEIIDAVLSGRDCLVVMPTGGGKSLCYQIPALVLDGLTLVVSPLISLMKDQVDQLLANGVAAAC   94 (607)
T ss_pred             HHHHHHcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCchHHHHHHHHHHHcCCCEEEEecHHHHHHHHHHHHHHcCCcEEE
Confidence            57889999999999999999999999999999999999999999999988889999999999999999999999988877


Q ss_pred             cCCCCCchhh---hhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHHhc
Q 037567           83 LGSAQTDSSV---QTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFL  159 (374)
Q Consensus        83 ~~~~~~~~~~---~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~  159 (374)
                      ..+.......   ......+..+++++||+++...  .....+...+++++||||||.+.+||.++++.+..+..+...+
T Consensus        95 ~~s~~~~~~~~~~~~~~~~g~~~il~~tPe~l~~~--~~~~~l~~~~l~~iVIDEaH~i~~~G~~fr~~y~~L~~l~~~~  172 (607)
T PRK11057         95 LNSTQTREQQLEVMAGCRTGQIKLLYIAPERLMMD--NFLEHLAHWNPALLAVDEAHCISQWGHDFRPEYAALGQLRQRF  172 (607)
T ss_pred             EcCCCCHHHHHHHHHHHhCCCCcEEEEChHHhcCh--HHHHHHhhCCCCEEEEeCccccccccCcccHHHHHHHHHHHhC
Confidence            7665544332   2223456689999999998642  3334455567899999999999999999999999999888888


Q ss_pred             CCCCeeEEEeecCcccHHHHHHhcCCCCCeEEEeccCCCceeEEEEeecCCcchHHHHHHHHHHhhcCCCcEEEEecchh
Q 037567          160 LGVPFVALTATATEKVRIDIINSLKLKNPYVTIASFDRKNLFYGVKVINRGQSFVDELVQEILKSVAGAGSIIVYCMTIK  239 (374)
Q Consensus       160 ~~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lVf~~~~~  239 (374)
                      ++.+++++|||++.....++...+++.++.+...+.+++++.+.+...   ......++.. +.. ..++++||||++++
T Consensus       173 p~~~~v~lTAT~~~~~~~di~~~l~l~~~~~~~~~~~r~nl~~~v~~~---~~~~~~l~~~-l~~-~~~~~~IIFc~tr~  247 (607)
T PRK11057        173 PTLPFMALTATADDTTRQDIVRLLGLNDPLIQISSFDRPNIRYTLVEK---FKPLDQLMRY-VQE-QRGKSGIIYCNSRA  247 (607)
T ss_pred             CCCcEEEEecCCChhHHHHHHHHhCCCCeEEEECCCCCCcceeeeeec---cchHHHHHHH-HHh-cCCCCEEEEECcHH
Confidence            899999999999998887888888888888877777777765443221   1222333333 222 36789999999999


Q ss_pred             HHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEEEEECCCCChhHHHHhhccC
Q 037567          240 DVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRC  319 (374)
Q Consensus       240 ~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~~~~p~s~~~~~Q~~GR~  319 (374)
                      .++.+++.|++.|+.+..+||+++.++|..+++.|..|+.+|||||+++++|+|+|++++||++++|.|...|+|++||+
T Consensus       248 ~~e~la~~L~~~g~~v~~~Ha~l~~~~R~~i~~~F~~g~~~VLVaT~a~~~GIDip~V~~VI~~d~P~s~~~y~Qr~GRa  327 (607)
T PRK11057        248 KVEDTAARLQSRGISAAAYHAGLDNDVRADVQEAFQRDDLQIVVATVAFGMGINKPNVRFVVHFDIPRNIESYYQETGRA  327 (607)
T ss_pred             HHHHHHHHHHhCCCCEEEecCCCCHHHHHHHHHHHHCCCCCEEEEechhhccCCCCCcCEEEEeCCCCCHHHHHHHhhhc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCceEEEEEeeccCCCcccceeccccchHHHHHHHHHHHHHHHHhhhcccCC
Q 037567          320 GRDGIASVCWLYYARSNFAKGDFYCGESQTENQRTAIMESLLAAQRYCLLTTCRR  374 (374)
Q Consensus       320 ~R~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~  374 (374)
                      ||.|.+|.+++++++.|...++.++.+.............|..|.+||+++.|||
T Consensus       328 GR~G~~~~~ill~~~~d~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~Crr  382 (607)
T PRK11057        328 GRDGLPAEAMLFYDPADMAWLRRCLEEKPAGQQQDIERHKLNAMGAFAEAQTCRR  382 (607)
T ss_pred             cCCCCCceEEEEeCHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHHHhcccCHH
Confidence            9999999999999999998888888777666666667789999999999999997

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=100.00  E-value=2.9e-57  Score=427.89  Aligned_cols=366  Identities=43%  Similarity=0.693  Sum_probs=316.5

Q ss_pred             hhHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccccCCcEEEEcchHHHHHHHHHHHHHcCCceE
Q 037567            2 VSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVTGKTALVVSPLISLMQDQVMSLKQRGINAE   81 (374)
Q Consensus         2 ~~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~   81 (374)
                      .+.|++.|||++|+|+|.++++.+++|+++++.+|||+|||++|+++++.....++|++|+++|+.|+.+.++..|+.+.
T Consensus         2 ~~~l~~~fg~~~fr~~Q~~~i~~il~g~dvlv~~PTG~GKTl~y~lpal~~~g~~lVisPl~sL~~dq~~~l~~~gi~~~   81 (591)
T TIGR01389         2 QQVLKRTFGYDDFRPGQEEIISHVLDGRDVLVVMPTGGGKSLCYQVPALLLKGLTVVISPLISLMKDQVDQLRAAGVAAA   81 (591)
T ss_pred             hHHHHHhcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCccHhHHHHHHHHHcCCcEEEEcCCHHHHHHHHHHHHHcCCcEE
Confidence            46799999999999999999999999999999999999999999999998888999999999999999999999999888


Q ss_pred             EcCCCCCchhh---hhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHHh
Q 037567           82 FLGSAQTDSSV---QTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTF  158 (374)
Q Consensus        82 ~~~~~~~~~~~---~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~  158 (374)
                      .+.+.......   ......+.++|+++||+++...  .+.......++++|||||||.+.+||.++++.+..+..+...
T Consensus        82 ~~~s~~~~~~~~~~~~~l~~~~~~il~~tpe~l~~~--~~~~~l~~~~l~~iViDEaH~i~~~g~~frp~y~~l~~l~~~  159 (591)
T TIGR01389        82 YLNSTLSAKEQQDIEKALVNGELKLLYVAPERLEQD--YFLNMLQRIPIALVAVDEAHCVSQWGHDFRPEYQRLGSLAER  159 (591)
T ss_pred             EEeCCCCHHHHHHHHHHHhCCCCCEEEEChhHhcCh--HHHHHHhcCCCCEEEEeCCcccccccCccHHHHHHHHHHHHh
Confidence            77766544432   2233456789999999998653  333455567899999999999999999999999999999888


Q ss_pred             cCCCCeeEEEeecCcccHHHHHHhcCCCCCeEEEeccCCCceeEEEEeecCCcchHHHHHHHHHHhhcCCCcEEEEecch
Q 037567          159 LLGVPFVALTATATEKVRIDIINSLKLKNPYVTIASFDRKNLFYGVKVINRGQSFVDELVQEILKSVAGAGSIIVYCMTI  238 (374)
Q Consensus       159 ~~~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lVf~~~~  238 (374)
                      +++.+++++|||+++....++...+++..+.....+.+++++.+.+.....    ..+.+.+++... .+.++||||+++
T Consensus       160 ~~~~~vi~lTAT~~~~~~~~i~~~l~~~~~~~~~~~~~r~nl~~~v~~~~~----~~~~l~~~l~~~-~~~~~IIf~~sr  234 (591)
T TIGR01389       160 FPQVPRIALTATADAETRQDIRELLRLADANEFITSFDRPNLRFSVVKKNN----KQKFLLDYLKKH-RGQSGIIYASSR  234 (591)
T ss_pred             CCCCCEEEEEeCCCHHHHHHHHHHcCCCCCCeEecCCCCCCcEEEEEeCCC----HHHHHHHHHHhc-CCCCEEEEECcH
Confidence            888899999999999988889999998888777777778777665543222    223333343332 368899999999


Q ss_pred             hHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEEEEECCCCChhHHHHhhcc
Q 037567          239 KDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGR  318 (374)
Q Consensus       239 ~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~~~~p~s~~~~~Q~~GR  318 (374)
                      +.++.+++.|...|+++..+||+++.++|..+++.|..|+++|||||+++++|+|+|++++||++++|.|...|.|++||
T Consensus       235 ~~~e~la~~L~~~g~~~~~~H~~l~~~~R~~i~~~F~~g~~~vlVaT~a~~~GID~p~v~~VI~~~~p~s~~~y~Q~~GR  314 (591)
T TIGR01389       235 KKVEELAERLESQGISALAYHAGLSNKVRAENQEDFLYDDVKVMVATNAFGMGIDKPNVRFVIHYDMPGNLESYYQEAGR  314 (591)
T ss_pred             HHHHHHHHHHHhCCCCEEEEECCCCHHHHHHHHHHHHcCCCcEEEEechhhccCcCCCCCEEEEcCCCCCHHHHhhhhcc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCceEEEEEeeccCCCcccceeccccchHH-HHHHHHHHHHHHHHhhhcccCC
Q 037567          319 CGRDGIASVCWLYYARSNFAKGDFYCGESQTENQ-RTAIMESLLAAQRYCLLTTCRR  374 (374)
Q Consensus       319 ~~R~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~~~  374 (374)
                      +||.|.++.++++|.+.|....+.++.+...... .......+.+|..||+...|||
T Consensus       315 aGR~G~~~~~il~~~~~d~~~~~~~i~~~~~~~~~~~~~~~~l~~~~~~~~~~~c~r  371 (591)
T TIGR01389       315 AGRDGLPAEAILLYSPADIALLKRRIEQSEADDDYKQIEREKLRAMIAYCETQTCRR  371 (591)
T ss_pred             ccCCCCCceEEEecCHHHHHHHHHHHhccCCcHHHHHHHHHHHHHHHHHHcccccHh
Confidence            9999999999999999999888888877554443 3446788999999999999997

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.

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

Probab=100.00  E-value=1e-56  Score=403.61  Aligned_cols=367  Identities=44%  Similarity=0.723  Sum_probs=328.7

Q ss_pred             hHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccccCCcEEEEcchHHHHHHHHHHHHHcCCceEE
Q 037567            3 STLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVTGKTALVVSPLISLMQDQVMSLKQRGINAEF   82 (374)
Q Consensus         3 ~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~   82 (374)
                      ..|+++||+..++|-|.+++..+++++++++.+|||.|||++|.+|++.....+|||+|..+|..+..+.+...|+.+..
T Consensus         7 ~~L~~~fGy~~FR~gQ~evI~~~l~g~d~lvvmPTGgGKSlCyQiPAll~~G~TLVVSPLiSLM~DQV~~l~~~Gi~A~~   86 (590)
T COG0514           7 QVLKQVFGYASFRPGQQEIIDALLSGKDTLVVMPTGGGKSLCYQIPALLLEGLTLVVSPLISLMKDQVDQLEAAGIRAAY   86 (590)
T ss_pred             HHHHHHhCccccCCCHHHHHHHHHcCCcEEEEccCCCCcchHhhhHHHhcCCCEEEECchHHHHHHHHHHHHHcCceeeh
Confidence            46899999999999999999999999999999999999999999999988889999999999999999999999999988


Q ss_pred             cCCCCCchhh---hhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHHhc
Q 037567           83 LGSAQTDSSV---QTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFL  159 (374)
Q Consensus        83 ~~~~~~~~~~---~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~  159 (374)
                      ..+.....+.   ......+..++++.+||++..-  .....+....+.+++|||||.+.+||.++++.+..+..+...+
T Consensus        87 lnS~l~~~e~~~v~~~l~~g~~klLyisPErl~~~--~f~~~L~~~~i~l~vIDEAHCiSqWGhdFRP~Y~~lg~l~~~~  164 (590)
T COG0514          87 LNSTLSREERQQVLNQLKSGQLKLLYISPERLMSP--RFLELLKRLPISLVAIDEAHCISQWGHDFRPDYRRLGRLRAGL  164 (590)
T ss_pred             hhcccCHHHHHHHHHHHhcCceeEEEECchhhcCh--HHHHHHHhCCCceEEechHHHHhhcCCccCHhHHHHHHHHhhC
Confidence            8877555443   3445567789999999998765  4446666678899999999999999999999999999999999


Q ss_pred             CCCCeeEEEeecCcccHHHHHHhcCCCCCeEEEeccCCCceeEEEEeecCCcchHHHHHHHHHHhhcCCCcEEEEecchh
Q 037567          160 LGVPFVALTATATEKVRIDIINSLKLKNPYVTIASFDRKNLFYGVKVINRGQSFVDELVQEILKSVAGAGSIIVYCMTIK  239 (374)
Q Consensus       160 ~~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lVf~~~~~  239 (374)
                      ++.+++++|||.++....++...+++..+.+...+++++++.+.+........... .+.+  ......+..||||.|++
T Consensus       165 ~~~p~~AlTATA~~~v~~DI~~~L~l~~~~~~~~sfdRpNi~~~v~~~~~~~~q~~-fi~~--~~~~~~~~GIIYc~sRk  241 (590)
T COG0514         165 PNPPVLALTATATPRVRDDIREQLGLQDANIFRGSFDRPNLALKVVEKGEPSDQLA-FLAT--VLPQLSKSGIIYCLTRK  241 (590)
T ss_pred             CCCCEEEEeCCCChHHHHHHHHHhcCCCcceEEecCCCchhhhhhhhcccHHHHHH-HHHh--hccccCCCeEEEEeeHH
Confidence            99999999999999999999999999999999999999999988876653222222 2222  12235677899999999


Q ss_pred             HHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEEEEECCCCChhHHHHhhccC
Q 037567          240 DVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRC  319 (374)
Q Consensus       240 ~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~~~~p~s~~~~~Q~~GR~  319 (374)
                      .++.+++.|...|+.+..+|++++.++|+.+-+.|..++.+|+|||.+.++|||-|++++|||+++|.|++.|.|-+|||
T Consensus       242 ~~E~ia~~L~~~g~~a~~YHaGl~~~eR~~~q~~f~~~~~~iiVAT~AFGMGIdKpdVRfViH~~lP~s~EsYyQE~GRA  321 (590)
T COG0514         242 KVEELAEWLRKNGISAGAYHAGLSNEERERVQQAFLNDEIKVMVATNAFGMGIDKPDVRFVIHYDLPGSIESYYQETGRA  321 (590)
T ss_pred             hHHHHHHHHHHCCCceEEecCCCCHHHHHHHHHHHhcCCCcEEEEeccccCccCCCCceEEEEecCCCCHHHHHHHHhhc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCceEEEEEeeccCCCcccceecccc-chHHHHHHHHHHHHHHHHhhhcccCC
Q 037567          320 GRDGIASVCWLYYARSNFAKGDFYCGESQ-TENQRTAIMESLLAAQRYCLLTTCRR  374 (374)
Q Consensus       320 ~R~~~~g~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~l~~~~~~~~~~~~~~  374 (374)
                      ||.|.+..|+++|.+.|....+.++.... .....+....+|.+|.++|+.+.|||
T Consensus       322 GRDG~~a~aill~~~~D~~~~~~~i~~~~~~~~~~~~~~~kl~~~~~~~e~~~crr  377 (590)
T COG0514         322 GRDGLPAEAILLYSPEDIRWQRYLIEQSKPDEEQKQIELAKLRQMIAYCETQTCRR  377 (590)
T ss_pred             cCCCCcceEEEeeccccHHHHHHHHHhhcchHHHHHHHHHHHHHHHHhcccccchH
Confidence            99999999999999999999999888766 44455557899999999999999996

>KOG0331 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=100.00  E-value=1.1e-55  Score=389.72  Aligned_cols=333  Identities=23%  Similarity=0.330  Sum_probs=269.4

Q ss_pred             hHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc------------cCCcEEEEcchHHHHHHHH
Q 037567            3 STLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV------------TGKTALVVSPLISLMQDQV   70 (374)
Q Consensus         3 ~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~------------~~~~~lil~P~~~l~~q~~   70 (374)
                      .+++. .||+.|+|+|.+.|+.++.|+|++..|.||||||++|++|++.            .++.+||++|||+|+.|+.
T Consensus       104 ~~lk~-~g~~~PtpIQaq~wp~~l~GrD~v~iA~TGSGKTLay~lP~i~~l~~~~~~~~~~~~P~vLVL~PTRELA~QV~  182 (519)
T KOG0331|consen  104 KALKE-QGFEKPTPIQAQGWPIALSGRDLVGIARTGSGKTLAYLLPAIVHLNNEQGKLSRGDGPIVLVLAPTRELAVQVQ  182 (519)
T ss_pred             HHHHh-cCCCCCchhhhcccceeccCCceEEEeccCCcchhhhhhHHHHHHHhccccccCCCCCeEEEEcCcHHHHHHHH
Confidence            45556 7999999999999999999999999999999999999999764            2678999999999999999


Q ss_pred             HHHHHcCCc----eEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcch
Q 037567           71 MSLKQRGIN----AEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFR  146 (374)
Q Consensus        71 ~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~  146 (374)
                      +.+..++..    ..+++++..... +......+.+|+|+||+++.++++.  ....+..+.++|+||||+|.+.|++  
T Consensus       183 ~~~~~~~~~~~~~~~cvyGG~~~~~-Q~~~l~~gvdiviaTPGRl~d~le~--g~~~l~~v~ylVLDEADrMldmGFe--  257 (519)
T KOG0331|consen  183 AEAREFGKSLRLRSTCVYGGAPKGP-QLRDLERGVDVVIATPGRLIDLLEE--GSLNLSRVTYLVLDEADRMLDMGFE--  257 (519)
T ss_pred             HHHHHHcCCCCccEEEEeCCCCccH-HHHHHhcCCcEEEeCChHHHHHHHc--CCccccceeEEEeccHHhhhccccH--
Confidence            999887433    334444444433 3344556689999999999988776  6777889999999999999998876  


Q ss_pred             HHHHHHHHHHHhc-C-CCCeeEEEeecCcccHHHHHHhcCCCCCeEEEeccC----CCceeEEEEeecCCcchHHHHHHH
Q 037567          147 LEYKQLDKLRTFL-L-GVPFVALTATATEKVRIDIINSLKLKNPYVTIASFD----RKNLFYGVKVINRGQSFVDELVQE  220 (374)
Q Consensus       147 ~~~~~~~~~~~~~-~-~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~  220 (374)
                         ..+..+.... + ..+.+++|||++.....-....+. .+..+.....+    ..++...+...+  .......+..
T Consensus       258 ---~qI~~Il~~i~~~~rQtlm~saTwp~~v~~lA~~fl~-~~~~i~ig~~~~~~a~~~i~qive~~~--~~~K~~~l~~  331 (519)
T KOG0331|consen  258 ---PQIRKILSQIPRPDRQTLMFSATWPKEVRQLAEDFLN-NPIQINVGNKKELKANHNIRQIVEVCD--ETAKLRKLGK  331 (519)
T ss_pred             ---HHHHHHHHhcCCCcccEEEEeeeccHHHHHHHHHHhc-CceEEEecchhhhhhhcchhhhhhhcC--HHHHHHHHHH
Confidence               6666666666 3 347999999999988754444444 43334443332    122222222222  3333444444


Q ss_pred             HHHhh--cCCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCcc
Q 037567          221 ILKSV--AGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVR  298 (374)
Q Consensus       221 ~~~~~--~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~  298 (374)
                      ++...  ...+|+||||+++..|++++..++..++++..+||+.+..+|..+++.|++|+..|||||+.+++|+|+|+++
T Consensus       332 lL~~~~~~~~~KvIIFc~tkr~~~~l~~~l~~~~~~a~~iHGd~sQ~eR~~~L~~FreG~~~vLVATdVAaRGLDi~dV~  411 (519)
T KOG0331|consen  332 LLEDISSDSEGKVIIFCETKRTCDELARNLRRKGWPAVAIHGDKSQSERDWVLKGFREGKSPVLVATDVAARGLDVPDVD  411 (519)
T ss_pred             HHHHHhccCCCcEEEEecchhhHHHHHHHHHhcCcceeeecccccHHHHHHHHHhcccCCcceEEEcccccccCCCcccc
Confidence            54444  3678999999999999999999999899999999999999999999999999999999999999999999999


Q ss_pred             EEEEECCCCChhHHHHhhccCCCCCCceEEEEEeeccCCCcccceeccc
Q 037567          299 HVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFYCGES  347 (374)
Q Consensus       299 ~vi~~~~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~~~~~~~~~~~~  347 (374)
                      +||+|++|.+.++|+||+||+||.|+.|.+++|++..+......+.+..
T Consensus       412 lVInydfP~~vEdYVHRiGRTGRa~~~G~A~tfft~~~~~~a~~l~~~l  460 (519)
T KOG0331|consen  412 LVINYDFPNNVEDYVHRIGRTGRAGKKGTAITFFTSDNAKLARELIKVL  460 (519)
T ss_pred             EEEeCCCCCCHHHHHhhcCccccCCCCceEEEEEeHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999988877776544

>PTZ00110 helicase; Provisional

Probab=100.00  E-value=4.6e-55  Score=405.90  Aligned_cols=358  Identities=22%  Similarity=0.277  Sum_probs=269.7

Q ss_pred             hhHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc-----------cCCcEEEEcchHHHHHHHH
Q 037567            2 VSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV-----------TGKTALVVSPLISLMQDQV   70 (374)
Q Consensus         2 ~~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~-----------~~~~~lil~P~~~l~~q~~   70 (374)
                      .++|++ +||.+|+|+|.+++|.+++++++++.||||||||++|++|++.           .++.+||++||++|+.|+.
T Consensus       142 ~~~l~~-~g~~~pt~iQ~~aip~~l~G~dvI~~ApTGSGKTlaylLP~l~~i~~~~~~~~~~gp~~LIL~PTreLa~Qi~  220 (545)
T PTZ00110        142 LKSLKN-AGFTEPTPIQVQGWPIALSGRDMIGIAETGSGKTLAFLLPAIVHINAQPLLRYGDGPIVLVLAPTRELAEQIR  220 (545)
T ss_pred             HHHHHH-CCCCCCCHHHHHHHHHHhcCCCEEEEeCCCChHHHHHHHHHHHHHHhcccccCCCCcEEEEECChHHHHHHHH
Confidence            466777 8999999999999999999999999999999999999988753           1467999999999999999


Q ss_pred             HHHHHcC----CceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcch
Q 037567           71 MSLKQRG----INAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFR  146 (374)
Q Consensus        71 ~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~  146 (374)
                      +.+..++    +......++....... ......++|+|+||++|.+++..  ....+..+++||+||||++.++++.  
T Consensus       221 ~~~~~~~~~~~i~~~~~~gg~~~~~q~-~~l~~~~~IlVaTPgrL~d~l~~--~~~~l~~v~~lViDEAd~mld~gf~--  295 (545)
T PTZ00110        221 EQCNKFGASSKIRNTVAYGGVPKRGQI-YALRRGVEILIACPGRLIDFLES--NVTNLRRVTYLVLDEADRMLDMGFE--  295 (545)
T ss_pred             HHHHHHhcccCccEEEEeCCCCHHHHH-HHHHcCCCEEEECHHHHHHHHHc--CCCChhhCcEEEeehHHhhhhcchH--
Confidence            9998874    3344444444333332 23345689999999998776654  2344677899999999999987754  


Q ss_pred             HHHHHHHHHHHhc-CCCCeeEEEeecCcccHHHHHHhcCCCCCe-EEEeccC---CCceeEEEEeecCCcchHHHHHHHH
Q 037567          147 LEYKQLDKLRTFL-LGVPFVALTATATEKVRIDIINSLKLKNPY-VTIASFD---RKNLFYGVKVINRGQSFVDELVQEI  221 (374)
Q Consensus       147 ~~~~~~~~~~~~~-~~~~~i~~SaT~~~~~~~~~~~~~~~~~~~-~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~  221 (374)
                         ..+..+.... ++.+++++|||++..... +...+....+. +......   ..++...+.....  ......+..+
T Consensus       296 ---~~i~~il~~~~~~~q~l~~SAT~p~~v~~-l~~~l~~~~~v~i~vg~~~l~~~~~i~q~~~~~~~--~~k~~~L~~l  369 (545)
T PTZ00110        296 ---PQIRKIVSQIRPDRQTLMWSATWPKEVQS-LARDLCKEEPVHVNVGSLDLTACHNIKQEVFVVEE--HEKRGKLKML  369 (545)
T ss_pred             ---HHHHHHHHhCCCCCeEEEEEeCCCHHHHH-HHHHHhccCCEEEEECCCccccCCCeeEEEEEEec--hhHHHHHHHH
Confidence               3344444433 468899999999876543 34433333332 2222211   1222222222222  2223334444


Q ss_pred             HHhhc-CCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEE
Q 037567          222 LKSVA-GAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHV  300 (374)
Q Consensus       222 ~~~~~-~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~v  300 (374)
                      +.... .+.++||||++++.++.+++.|...++.+..+||+++..+|..+++.|++|+.+|||||+++++|+|+|++++|
T Consensus       370 l~~~~~~~~k~LIF~~t~~~a~~l~~~L~~~g~~~~~ihg~~~~~eR~~il~~F~~G~~~ILVaTdv~~rGIDi~~v~~V  449 (545)
T PTZ00110        370 LQRIMRDGDKILIFVETKKGADFLTKELRLDGWPALCIHGDKKQEERTWVLNEFKTGKSPIMIATDVASRGLDVKDVKYV  449 (545)
T ss_pred             HHHhcccCCeEEEEecChHHHHHHHHHHHHcCCcEEEEECCCcHHHHHHHHHHHhcCCCcEEEEcchhhcCCCcccCCEE
Confidence            44433 67899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEECCCCChhHHHHhhccCCCCCCceEEEEEeeccCCCcccceeccccchHHHHHHHHHHHHHHHHhhh-cccC
Q 037567          301 IHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFYCGESQTENQRTAIMESLLAAQRYCLL-TTCR  373 (374)
Q Consensus       301 i~~~~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~-~~~~  373 (374)
                      |++++|.+..+|+||+||+||.|..|.+++|+++++...+..+.+-.....  +.+..+|.+|....+. ..||
T Consensus       450 I~~d~P~s~~~yvqRiGRtGR~G~~G~ai~~~~~~~~~~~~~l~~~l~~~~--q~vp~~l~~~~~~~~~~~~~~  521 (545)
T PTZ00110        450 INFDFPNQIEDYVHRIGRTGRAGAKGASYTFLTPDKYRLARDLVKVLREAK--QPVPPELEKLSNERSNGTERR  521 (545)
T ss_pred             EEeCCCCCHHHHHHHhcccccCCCCceEEEEECcchHHHHHHHHHHHHHcc--CCCCHHHHHHHHHhcCCcccc
Confidence            999999999999999999999999999999999998777666654433322  2355677777666653 3444

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=100.00  E-value=1.6e-53  Score=387.97  Aligned_cols=332  Identities=19%  Similarity=0.232  Sum_probs=252.4

Q ss_pred             ChhHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc-------------cCCcEEEEcchHHHHH
Q 037567            1 MVSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV-------------TGKTALVVSPLISLMQ   67 (374)
Q Consensus         1 l~~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~-------------~~~~~lil~P~~~l~~   67 (374)
                      |+++|.. +||..|+|+|.++++.+++|+|+++.||||||||++|+++++.             .+.++||++|+++|+.
T Consensus        19 l~~~l~~-~g~~~pt~iQ~~aip~il~g~dvi~~ApTGsGKTla~llp~l~~l~~~~~~~~~~~~~~~~lil~PtreLa~   97 (423)
T PRK04837         19 VVEALEK-KGFHNCTPIQALALPLTLAGRDVAGQAQTGTGKTMAFLTATFHYLLSHPAPEDRKVNQPRALIMAPTRELAV   97 (423)
T ss_pred             HHHHHHH-CCCCCCCHHHHHHHHHHhCCCcEEEECCCCchHHHHHHHHHHHHHHhcccccccccCCceEEEECCcHHHHH
Confidence            3567777 8999999999999999999999999999999999999988763             1367999999999999


Q ss_pred             HHHHHHHHc----CCceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccC
Q 037567           68 DQVMSLKQR----GINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGH  143 (374)
Q Consensus        68 q~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~  143 (374)
                      |+.+.+..+    ++.+..+.++...... ......+++|+|+||+++..++..  ....+.+++++|+||||++.++++
T Consensus        98 Qi~~~~~~l~~~~~~~v~~~~gg~~~~~~-~~~l~~~~~IlV~TP~~l~~~l~~--~~~~l~~v~~lViDEad~l~~~~f  174 (423)
T PRK04837         98 QIHADAEPLAQATGLKLGLAYGGDGYDKQ-LKVLESGVDILIGTTGRLIDYAKQ--NHINLGAIQVVVLDEADRMFDLGF  174 (423)
T ss_pred             HHHHHHHHHhccCCceEEEEECCCCHHHH-HHHhcCCCCEEEECHHHHHHHHHc--CCcccccccEEEEecHHHHhhccc
Confidence            998887654    5566655554433322 223345689999999998766543  334567899999999999988765


Q ss_pred             cchHHHHHHHHHHHhcC---CCCeeEEEeecCcccHHHHHHhcCCCCCeEEEeccCCCceeEEEEeecCCcchHHHHHHH
Q 037567          144 DFRLEYKQLDKLRTFLL---GVPFVALTATATEKVRIDIINSLKLKNPYVTIASFDRKNLFYGVKVINRGQSFVDELVQE  220 (374)
Q Consensus       144 ~~~~~~~~~~~~~~~~~---~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  220 (374)
                      .     ..+..+....+   ..+.+++|||++..........+. .+..+...........................+..
T Consensus       175 ~-----~~i~~i~~~~~~~~~~~~~l~SAT~~~~~~~~~~~~~~-~p~~i~v~~~~~~~~~i~~~~~~~~~~~k~~~l~~  248 (423)
T PRK04837        175 I-----KDIRWLFRRMPPANQRLNMLFSATLSYRVRELAFEHMN-NPEYVEVEPEQKTGHRIKEELFYPSNEEKMRLLQT  248 (423)
T ss_pred             H-----HHHHHHHHhCCCccceeEEEEeccCCHHHHHHHHHHCC-CCEEEEEcCCCcCCCceeEEEEeCCHHHHHHHHHH
Confidence            3     33344444443   345789999998776543333332 22222222111111111111222222333445555


Q ss_pred             HHHhhcCCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEE
Q 037567          221 ILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHV  300 (374)
Q Consensus       221 ~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~v  300 (374)
                      ++.. ....++||||+++..++.+++.|.+.|+.+..+||+++.++|..+++.|++|+.+|||||+++++|+|+|++++|
T Consensus       249 ll~~-~~~~~~lVF~~t~~~~~~l~~~L~~~g~~v~~lhg~~~~~~R~~~l~~F~~g~~~vLVaTdv~~rGiDip~v~~V  327 (423)
T PRK04837        249 LIEE-EWPDRAIIFANTKHRCEEIWGHLAADGHRVGLLTGDVAQKKRLRILEEFTRGDLDILVATDVAARGLHIPAVTHV  327 (423)
T ss_pred             HHHh-cCCCeEEEEECCHHHHHHHHHHHHhCCCcEEEecCCCChhHHHHHHHHHHcCCCcEEEEechhhcCCCccccCEE
Confidence            5544 256889999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEECCCCChhHHHHhhccCCCCCCceEEEEEeeccCCCcccce
Q 037567          301 IHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFY  343 (374)
Q Consensus       301 i~~~~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~~~~~~~~  343 (374)
                      |++++|.+..+|+||+||+||.|+.|.+++|+.+.+...+..+
T Consensus       328 I~~d~P~s~~~yiqR~GR~gR~G~~G~ai~~~~~~~~~~~~~i  370 (423)
T PRK04837        328 FNYDLPDDCEDYVHRIGRTGRAGASGHSISLACEEYALNLPAI  370 (423)
T ss_pred             EEeCCCCchhheEeccccccCCCCCeeEEEEeCHHHHHHHHHH
Confidence            9999999999999999999999999999999998865444443

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

Probab=100.00  E-value=4.1e-53  Score=391.92  Aligned_cols=333  Identities=23%  Similarity=0.284  Sum_probs=251.8

Q ss_pred             hhHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc-------------cCCcEEEEcchHHHHHH
Q 037567            2 VSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV-------------TGKTALVVSPLISLMQD   68 (374)
Q Consensus         2 ~~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~-------------~~~~~lil~P~~~l~~q   68 (374)
                      .++|.+ .||..|+|+|.++++.+++|+++++.||||||||++|++|++.             .++++||++||++|+.|
T Consensus       133 ~~~L~~-~g~~~ptpiQ~~aip~il~g~dviv~ApTGSGKTlayllPil~~l~~~~~~~~~~~~~~~aLIL~PTreLa~Q  211 (518)
T PLN00206        133 LLNLET-AGYEFPTPIQMQAIPAALSGRSLLVSADTGSGKTASFLVPIISRCCTIRSGHPSEQRNPLAMVLTPTRELCVQ  211 (518)
T ss_pred             HHHHHH-cCCCCCCHHHHHHHHHHhcCCCEEEEecCCCCccHHHHHHHHHHHHhhccccccccCCceEEEEeCCHHHHHH
Confidence            456766 7999999999999999999999999999999999999998763             24679999999999999


Q ss_pred             HHHHHHHcC----CceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCc
Q 037567           69 QVMSLKQRG----INAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHD  144 (374)
Q Consensus        69 ~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~  144 (374)
                      +.+.++.++    .....+.++....... .....+++|+|+||++|..++..  ....+.++.+||+||||++.++|+.
T Consensus       212 i~~~~~~l~~~~~~~~~~~~gG~~~~~q~-~~l~~~~~IiV~TPgrL~~~l~~--~~~~l~~v~~lViDEad~ml~~gf~  288 (518)
T PLN00206        212 VEDQAKVLGKGLPFKTALVVGGDAMPQQL-YRIQQGVELIVGTPGRLIDLLSK--HDIELDNVSVLVLDEVDCMLERGFR  288 (518)
T ss_pred             HHHHHHHHhCCCCceEEEEECCcchHHHH-HHhcCCCCEEEECHHHHHHHHHc--CCccchheeEEEeecHHHHhhcchH
Confidence            988887653    3333333333222222 22345689999999998777654  3455678899999999999887753


Q ss_pred             chHHHHHHHHHHHhcCCCCeeEEEeecCcccHHHHHHhcCCCCCeEEEeccCCCceeEEEEeecCCcchHHHHHHHHHHh
Q 037567          145 FRLEYKQLDKLRTFLLGVPFVALTATATEKVRIDIINSLKLKNPYVTIASFDRKNLFYGVKVINRGQSFVDELVQEILKS  224 (374)
Q Consensus       145 ~~~~~~~~~~~~~~~~~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  224 (374)
                           ..+..+....++.+++++|||++.... .+...+......+...........................+.+++..
T Consensus       289 -----~~i~~i~~~l~~~q~l~~SATl~~~v~-~l~~~~~~~~~~i~~~~~~~~~~~v~q~~~~~~~~~k~~~l~~~l~~  362 (518)
T PLN00206        289 -----DQVMQIFQALSQPQVLLFSATVSPEVE-KFASSLAKDIILISIGNPNRPNKAVKQLAIWVETKQKKQKLFDILKS  362 (518)
T ss_pred             -----HHHHHHHHhCCCCcEEEEEeeCCHHHH-HHHHHhCCCCEEEEeCCCCCCCcceeEEEEeccchhHHHHHHHHHHh
Confidence                 344555556678899999999988764 34444433322233322222221111111111111222333344433


Q ss_pred             h-cCCCcEEEEecchhHHHHHHHHHHH-cCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEEEE
Q 037567          225 V-AGAGSIIVYCMTIKDVEEISKALKQ-LGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIH  302 (374)
Q Consensus       225 ~-~~~~~~lVf~~~~~~~~~l~~~l~~-~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~  302 (374)
                      . ....++||||+++..++.+++.|.. .++.+..+||+++.++|..+++.|++|+.+|||||+.+++|+|+|++++||+
T Consensus       363 ~~~~~~~~iVFv~s~~~a~~l~~~L~~~~g~~~~~~Hg~~~~~eR~~il~~Fr~G~~~ILVaTdvl~rGiDip~v~~VI~  442 (518)
T PLN00206        363 KQHFKPPAVVFVSSRLGADLLANAITVVTGLKALSIHGEKSMKERREVMKSFLVGEVPVIVATGVLGRGVDLLRVRQVII  442 (518)
T ss_pred             hcccCCCEEEEcCCchhHHHHHHHHhhccCcceEEeeCCCCHHHHHHHHHHHHCCCCCEEEEecHhhccCCcccCCEEEE
Confidence            2 2346899999999999999999975 5889999999999999999999999999999999999999999999999999


Q ss_pred             ECCCCChhHHHHhhccCCCCCCceEEEEEeeccCCCccccee
Q 037567          303 YGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFYC  344 (374)
Q Consensus       303 ~~~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~~~~~~~~~  344 (374)
                      +++|.+..+|+||+||+||.|..|.+++|++.++...+..+.
T Consensus       443 ~d~P~s~~~yihRiGRaGR~g~~G~ai~f~~~~~~~~~~~l~  484 (518)
T PLN00206        443 FDMPNTIKEYIHQIGRASRMGEKGTAIVFVNEEDRNLFPELV  484 (518)
T ss_pred             eCCCCCHHHHHHhccccccCCCCeEEEEEEchhHHHHHHHHH
Confidence            999999999999999999999999999999988765555544

>KOG0330 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=100.00  E-value=2e-53  Score=353.10  Aligned_cols=331  Identities=22%  Similarity=0.278  Sum_probs=264.8

Q ss_pred             hhHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc------cCCcEEEEcchHHHHHHHHHHHHH
Q 037567            2 VSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV------TGKTALVVSPLISLMQDQVMSLKQ   75 (374)
Q Consensus         2 ~~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~------~~~~~lil~P~~~l~~q~~~~~~~   75 (374)
                      .++.++ .|+..|+++|.+++|.+++|++++..|.||||||.+|++|+++      +...++|++|+|+|+.|..+.+..
T Consensus        73 ~~ac~~-l~~~~PT~IQ~~aiP~~L~g~dvIglAeTGSGKT~afaLPIl~~LL~~p~~~~~lVLtPtRELA~QI~e~fe~  151 (476)
T KOG0330|consen   73 LEACQE-LGWKKPTKIQSEAIPVALGGRDVIGLAETGSGKTGAFALPILQRLLQEPKLFFALVLTPTRELAQQIAEQFEA  151 (476)
T ss_pred             HHHHHH-hCcCCCchhhhhhcchhhCCCcEEEEeccCCCchhhhHHHHHHHHHcCCCCceEEEecCcHHHHHHHHHHHHH
Confidence            456666 7899999999999999999999999999999999999999886      357799999999999999999988


Q ss_pred             cC----CceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHH
Q 037567           76 RG----INAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQ  151 (374)
Q Consensus        76 ~~----~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~  151 (374)
                      +|    +.+.++.++. +...+.......|+|+|+||++|.+++... +.+.+..++++|+|||+++.+..+.     ..
T Consensus       152 Lg~~iglr~~~lvGG~-~m~~q~~~L~kkPhilVaTPGrL~dhl~~T-kgf~le~lk~LVlDEADrlLd~dF~-----~~  224 (476)
T KOG0330|consen  152 LGSGIGLRVAVLVGGM-DMMLQANQLSKKPHILVATPGRLWDHLENT-KGFSLEQLKFLVLDEADRLLDMDFE-----EE  224 (476)
T ss_pred             hccccCeEEEEEecCc-hHHHHHHHhhcCCCEEEeCcHHHHHHHHhc-cCccHHHhHHHhhchHHhhhhhhhH-----HH
Confidence            74    4444554443 333444555677999999999998776532 4556678899999999999986554     34


Q ss_pred             HHHHHHhcC-CCCeeEEEeecCcccHHHHHHhcCCCCCeEEEeccCCC---ceeEEEEeecCCcchHHHHHHHHHHhhcC
Q 037567          152 LDKLRTFLL-GVPFVALTATATEKVRIDIINSLKLKNPYVTIASFDRK---NLFYGVKVINRGQSFVDELVQEILKSVAG  227 (374)
Q Consensus       152 ~~~~~~~~~-~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  227 (374)
                      +..++..++ ..+.+++|||++....+  +....+..+.....+....   .+...+-...  ..+....+-++++.. .
T Consensus       225 ld~ILk~ip~erqt~LfsATMt~kv~k--L~rasl~~p~~v~~s~ky~tv~~lkQ~ylfv~--~k~K~~yLV~ll~e~-~  299 (476)
T KOG0330|consen  225 LDYILKVIPRERQTFLFSATMTKKVRK--LQRASLDNPVKVAVSSKYQTVDHLKQTYLFVP--GKDKDTYLVYLLNEL-A  299 (476)
T ss_pred             HHHHHHhcCccceEEEEEeecchhhHH--HHhhccCCCeEEeccchhcchHHhhhheEecc--ccccchhHHHHHHhh-c
Confidence            444444444 68899999999998875  3344555554443332211   1111222222  222333444455543 6


Q ss_pred             CCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEEEEECCCC
Q 037567          228 AGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPK  307 (374)
Q Consensus       228 ~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~~~~p~  307 (374)
                      ++.+||||++......++-.|...|+.+..+||.|+.+.|...++.|++|..+||+||+.+++|+|+|.+++||+||.|.
T Consensus       300 g~s~iVF~~t~~tt~~la~~L~~lg~~a~~LhGqmsq~~Rlg~l~~Fk~~~r~iLv~TDVaSRGLDip~Vd~VVNyDiP~  379 (476)
T KOG0330|consen  300 GNSVIVFCNTCNTTRFLALLLRNLGFQAIPLHGQMSQSKRLGALNKFKAGARSILVCTDVASRGLDIPHVDVVVNYDIPT  379 (476)
T ss_pred             CCcEEEEEeccchHHHHHHHHHhcCcceecccchhhHHHHHHHHHHHhccCCcEEEecchhcccCCCCCceEEEecCCCC
Confidence            79999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ChhHHHHhhccCCCCCCceEEEEEeeccCCCcccceec
Q 037567          308 TLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFYCG  345 (374)
Q Consensus       308 s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~~~~~~~~~~  345 (374)
                      +..+|+||+||++|.|..|.++.+++..|++.+.++..
T Consensus       380 ~skDYIHRvGRtaRaGrsG~~ItlVtqyDve~~qrIE~  417 (476)
T KOG0330|consen  380 HSKDYIHRVGRTARAGRSGKAITLVTQYDVELVQRIEH  417 (476)
T ss_pred             cHHHHHHHcccccccCCCcceEEEEehhhhHHHHHHHH
Confidence            99999999999999999999999999999888777654

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=100.00  E-value=9.3e-53  Score=387.10  Aligned_cols=329  Identities=21%  Similarity=0.260  Sum_probs=254.7

Q ss_pred             hhHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhcccccc------CCcEEEEcchHHHHHHHHHHHHH
Q 037567            2 VSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVT------GKTALVVSPLISLMQDQVMSLKQ   75 (374)
Q Consensus         2 ~~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~~------~~~~lil~P~~~l~~q~~~~~~~   75 (374)
                      .++|.. +||..|+|+|.++++.+++++++++.||||||||++|+++++..      ..+++|++||++|+.|+.++++.
T Consensus        16 ~~~l~~-~g~~~~t~iQ~~ai~~~l~g~dvi~~a~TGsGKT~a~~lpil~~l~~~~~~~~~lil~PtreLa~Q~~~~~~~   94 (460)
T PRK11776         16 LANLNE-LGYTEMTPIQAQSLPAILAGKDVIAQAKTGSGKTAAFGLGLLQKLDVKRFRVQALVLCPTRELADQVAKEIRR   94 (460)
T ss_pred             HHHHHH-CCCCCCCHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHhhhccCCceEEEEeCCHHHHHHHHHHHHH
Confidence            456666 89999999999999999999999999999999999999888752      34799999999999999998886


Q ss_pred             c-----CCceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHH
Q 037567           76 R-----GINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYK  150 (374)
Q Consensus        76 ~-----~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~  150 (374)
                      +     +..+..+.++....... ......++|+|+||+++..++..  ....+.+++++|+||||++.+.++.     .
T Consensus        95 ~~~~~~~~~v~~~~Gg~~~~~~~-~~l~~~~~IvV~Tp~rl~~~l~~--~~~~l~~l~~lViDEad~~l~~g~~-----~  166 (460)
T PRK11776         95 LARFIPNIKVLTLCGGVPMGPQI-DSLEHGAHIIVGTPGRILDHLRK--GTLDLDALNTLVLDEADRMLDMGFQ-----D  166 (460)
T ss_pred             HHhhCCCcEEEEEECCCChHHHH-HHhcCCCCEEEEChHHHHHHHHc--CCccHHHCCEEEEECHHHHhCcCcH-----H
Confidence            5     34444555544433322 33346789999999999776554  3345678899999999999887653     3


Q ss_pred             HHHHHHHhcC-CCCeeEEEeecCcccHHHHHHhcCCCCCeEEEecc-CCCceeEEEEeecCCcchHHHHHHHHHHhhcCC
Q 037567          151 QLDKLRTFLL-GVPFVALTATATEKVRIDIINSLKLKNPYVTIASF-DRKNLFYGVKVINRGQSFVDELVQEILKSVAGA  228 (374)
Q Consensus       151 ~~~~~~~~~~-~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  228 (374)
                      .+..+....+ ..++++||||+++.... +...+...+..+..... ....+...+  +........+.+..++... ..
T Consensus       167 ~l~~i~~~~~~~~q~ll~SAT~~~~~~~-l~~~~~~~~~~i~~~~~~~~~~i~~~~--~~~~~~~k~~~l~~ll~~~-~~  242 (460)
T PRK11776        167 AIDAIIRQAPARRQTLLFSATYPEGIAA-ISQRFQRDPVEVKVESTHDLPAIEQRF--YEVSPDERLPALQRLLLHH-QP  242 (460)
T ss_pred             HHHHHHHhCCcccEEEEEEecCcHHHHH-HHHHhcCCCEEEEECcCCCCCCeeEEE--EEeCcHHHHHHHHHHHHhc-CC
Confidence            4444444444 57899999999876543 33333222222322222 222222222  2222222445555555543 56


Q ss_pred             CcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEEEEECCCCC
Q 037567          229 GSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPKT  308 (374)
Q Consensus       229 ~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~~~~p~s  308 (374)
                      +++||||+++..++.+++.|.+.++.+..+||+++..+|+.+++.|++|+.+|||||+.+++|+|+|++++||+++.|.+
T Consensus       243 ~~~lVF~~t~~~~~~l~~~L~~~~~~v~~~hg~~~~~eR~~~l~~F~~g~~~vLVaTdv~~rGiDi~~v~~VI~~d~p~~  322 (460)
T PRK11776        243 ESCVVFCNTKKECQEVADALNAQGFSALALHGDLEQRDRDQVLVRFANRSCSVLVATDVAARGLDIKALEAVINYELARD  322 (460)
T ss_pred             CceEEEECCHHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHHcCCCcEEEEecccccccchhcCCeEEEecCCCC
Confidence            78999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhHHHHhhccCCCCCCceEEEEEeeccCCCcccce
Q 037567          309 LESYYQESGRCGRDGIASVCWLYYARSNFAKGDFY  343 (374)
Q Consensus       309 ~~~~~Q~~GR~~R~~~~g~~~~~~~~~~~~~~~~~  343 (374)
                      +..|+||+||+||.|..|.+++++.+.|...++.+
T Consensus       323 ~~~yiqR~GRtGR~g~~G~ai~l~~~~e~~~~~~i  357 (460)
T PRK11776        323 PEVHVHRIGRTGRAGSKGLALSLVAPEEMQRANAI  357 (460)
T ss_pred             HhHhhhhcccccCCCCcceEEEEEchhHHHHHHHH
Confidence            99999999999999999999999999876554443

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=100.00  E-value=1.3e-52  Score=384.28  Aligned_cols=331  Identities=20%  Similarity=0.285  Sum_probs=253.4

Q ss_pred             ChhHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhcccccc------------CCcEEEEcchHHHHHH
Q 037567            1 MVSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVT------------GKTALVVSPLISLMQD   68 (374)
Q Consensus         1 l~~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~~------------~~~~lil~P~~~l~~q   68 (374)
                      |.++|.+ +||.+|+|+|.++++.+++++++++.||||||||++|+++++..            ..++||++||++|+.|
T Consensus        12 l~~~l~~-~g~~~pt~iQ~~ai~~il~g~dvlv~apTGsGKTla~~lpil~~l~~~~~~~~~~~~~~aLil~PtreLa~Q   90 (456)
T PRK10590         12 ILRAVAE-QGYREPTPIQQQAIPAVLEGRDLMASAQTGTGKTAGFTLPLLQHLITRQPHAKGRRPVRALILTPTRELAAQ   90 (456)
T ss_pred             HHHHHHH-CCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHhhhcccccccCCCceEEEEeCcHHHHHH
Confidence            3567777 89999999999999999999999999999999999999987642            2369999999999999


Q ss_pred             HHHHHHHc----CCceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCc
Q 037567           69 QVMSLKQR----GINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHD  144 (374)
Q Consensus        69 ~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~  144 (374)
                      +.+.+..+    ++....+.++..... ......+.++|+|+||++|..+...  ....+.++++||+||||++.++++.
T Consensus        91 i~~~~~~~~~~~~~~~~~~~gg~~~~~-~~~~l~~~~~IiV~TP~rL~~~~~~--~~~~l~~v~~lViDEah~ll~~~~~  167 (456)
T PRK10590         91 IGENVRDYSKYLNIRSLVVFGGVSINP-QMMKLRGGVDVLVATPGRLLDLEHQ--NAVKLDQVEILVLDEADRMLDMGFI  167 (456)
T ss_pred             HHHHHHHHhccCCCEEEEEECCcCHHH-HHHHHcCCCcEEEEChHHHHHHHHc--CCcccccceEEEeecHHHHhccccH
Confidence            99998865    344444444433322 2223446789999999998766443  3345678999999999999887643


Q ss_pred             chHHHHHHHHHHHhcC-CCCeeEEEeecCcccHHHHHHhcCCCCCeEEEecc--CCCceeEEEEeecCCcchHHHHHHHH
Q 037567          145 FRLEYKQLDKLRTFLL-GVPFVALTATATEKVRIDIINSLKLKNPYVTIASF--DRKNLFYGVKVINRGQSFVDELVQEI  221 (374)
Q Consensus       145 ~~~~~~~~~~~~~~~~-~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~  221 (374)
                           ..+..+...++ ..+.+++|||++..... +...+...+..+.....  ....+...+...  ......+++..+
T Consensus       168 -----~~i~~il~~l~~~~q~l~~SAT~~~~~~~-l~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~--~~~~k~~~l~~l  239 (456)
T PRK10590        168 -----HDIRRVLAKLPAKRQNLLFSATFSDDIKA-LAEKLLHNPLEIEVARRNTASEQVTQHVHFV--DKKRKRELLSQM  239 (456)
T ss_pred             -----HHHHHHHHhCCccCeEEEEeCCCcHHHHH-HHHHHcCCCeEEEEecccccccceeEEEEEc--CHHHHHHHHHHH
Confidence                 33333444443 56799999999876543 33333333322322211  122222222222  222334555555


Q ss_pred             HHhhcCCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEEE
Q 037567          222 LKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVI  301 (374)
Q Consensus       222 ~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi  301 (374)
                      +.. ....++||||+++..++.+++.|...++.+..+||+++..+|..+++.|++|+++|||||+++++|+|+|++++||
T Consensus       240 ~~~-~~~~~~lVF~~t~~~~~~l~~~L~~~g~~~~~lhg~~~~~~R~~~l~~F~~g~~~iLVaTdv~~rGiDip~v~~VI  318 (456)
T PRK10590        240 IGK-GNWQQVLVFTRTKHGANHLAEQLNKDGIRSAAIHGNKSQGARTRALADFKSGDIRVLVATDIAARGLDIEELPHVV  318 (456)
T ss_pred             HHc-CCCCcEEEEcCcHHHHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHHHHHcCCCcEEEEccHHhcCCCcccCCEEE
Confidence            544 3567899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EECCCCChhHHHHhhccCCCCCCceEEEEEeeccCCCccccee
Q 037567          302 HYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFYC  344 (374)
Q Consensus       302 ~~~~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~~~~~~~~~  344 (374)
                      ++++|.++.+|+||+||+||.|..|.+++++...|...+..+.
T Consensus       319 ~~~~P~~~~~yvqR~GRaGR~g~~G~ai~l~~~~d~~~~~~ie  361 (456)
T PRK10590        319 NYELPNVPEDYVHRIGRTGRAAATGEALSLVCVDEHKLLRDIE  361 (456)
T ss_pred             EeCCCCCHHHhhhhccccccCCCCeeEEEEecHHHHHHHHHHH
Confidence            9999999999999999999999999999999988765554443

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=100.00  E-value=1.6e-52  Score=386.29  Aligned_cols=326  Identities=19%  Similarity=0.272  Sum_probs=251.1

Q ss_pred             ChhHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhcccccc-------------CCcEEEEcchHHHHH
Q 037567            1 MVSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVT-------------GKTALVVSPLISLMQ   67 (374)
Q Consensus         1 l~~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~~-------------~~~~lil~P~~~l~~   67 (374)
                      |+++|.+ +||..|+++|.++++.+++|+|+++.+|||||||++|+++++..             ..++||++||++|+.
T Consensus        98 l~~~l~~-~g~~~~~~iQ~~ai~~~~~G~dvi~~apTGSGKTlay~lpil~~l~~~~~~~~~~~~~~~aLil~PtreLa~  176 (475)
T PRK01297         98 LMHAIHD-LGFPYCTPIQAQVLGYTLAGHDAIGRAQTGTGKTAAFLISIINQLLQTPPPKERYMGEPRALIIAPTRELVV  176 (475)
T ss_pred             HHHHHHH-CCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhcCcccccccCCceEEEEeCcHHHHH
Confidence            3567777 89999999999999999999999999999999999999987742             468999999999999


Q ss_pred             HHHHHHHHc----CCceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccC
Q 037567           68 DQVMSLKQR----GINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGH  143 (374)
Q Consensus        68 q~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~  143 (374)
                      |+.+.++.+    +..+..+.++..............++|+|+||++|..+...  ....+.++++|||||+|++.+.++
T Consensus       177 Q~~~~~~~l~~~~~~~v~~~~gg~~~~~~~~~~~~~~~~Iiv~TP~~Ll~~~~~--~~~~l~~l~~lViDEah~l~~~~~  254 (475)
T PRK01297        177 QIAKDAAALTKYTGLNVMTFVGGMDFDKQLKQLEARFCDILVATPGRLLDFNQR--GEVHLDMVEVMVLDEADRMLDMGF  254 (475)
T ss_pred             HHHHHHHHhhccCCCEEEEEEccCChHHHHHHHhCCCCCEEEECHHHHHHHHHc--CCcccccCceEEechHHHHHhccc
Confidence            999988765    45555555544433333444456789999999998765443  344567899999999999987654


Q ss_pred             cchHHHHHHHHHHHhcC---CCCeeEEEeecCcccHHHHHHhcCCCCCeEEEeccCC--CceeEEEEeecCCcchHHHHH
Q 037567          144 DFRLEYKQLDKLRTFLL---GVPFVALTATATEKVRIDIINSLKLKNPYVTIASFDR--KNLFYGVKVINRGQSFVDELV  218 (374)
Q Consensus       144 ~~~~~~~~~~~~~~~~~---~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~  218 (374)
                      .     ..+..+....+   +.+++++|||.+..... +...+...+..+.......  ......+....  .......+
T Consensus       255 ~-----~~l~~i~~~~~~~~~~q~i~~SAT~~~~~~~-~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~--~~~k~~~l  326 (475)
T PRK01297        255 I-----PQVRQIIRQTPRKEERQTLLFSATFTDDVMN-LAKQWTTDPAIVEIEPENVASDTVEQHVYAVA--GSDKYKLL  326 (475)
T ss_pred             H-----HHHHHHHHhCCCCCCceEEEEEeecCHHHHH-HHHHhccCCEEEEeccCcCCCCcccEEEEEec--chhHHHHH
Confidence            2     33344444332   46899999998876553 3333333332222221111  12222222211  22234455


Q ss_pred             HHHHHhhcCCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCcc
Q 037567          219 QEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVR  298 (374)
Q Consensus       219 ~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~  298 (374)
                      ..++.. ....++||||+++..++.+++.|.+.++.+..+||+++.++|.++++.|++|++++||||+++++|+|+|+++
T Consensus       327 ~~ll~~-~~~~~~IVF~~s~~~~~~l~~~L~~~~~~~~~~~g~~~~~~R~~~~~~Fr~G~~~vLvaT~~l~~GIDi~~v~  405 (475)
T PRK01297        327 YNLVTQ-NPWERVMVFANRKDEVRRIEERLVKDGINAAQLSGDVPQHKRIKTLEGFREGKIRVLVATDVAGRGIHIDGIS  405 (475)
T ss_pred             HHHHHh-cCCCeEEEEeCCHHHHHHHHHHHHHcCCCEEEEECCCCHHHHHHHHHHHhCCCCcEEEEccccccCCcccCCC
Confidence            555544 2457999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEECCCCChhHHHHhhccCCCCCCceEEEEEeeccCCC
Q 037567          299 HVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFA  338 (374)
Q Consensus       299 ~vi~~~~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~~~  338 (374)
                      +||++++|.|..+|+||+||+||.|..|.+++++..+|..
T Consensus       406 ~VI~~~~P~s~~~y~Qr~GRaGR~g~~g~~i~~~~~~d~~  445 (475)
T PRK01297        406 HVINFTLPEDPDDYVHRIGRTGRAGASGVSISFAGEDDAF  445 (475)
T ss_pred             EEEEeCCCCCHHHHHHhhCccCCCCCCceEEEEecHHHHH
Confidence            9999999999999999999999999999999999887643

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=100.00  E-value=5e-52  Score=386.76  Aligned_cols=331  Identities=17%  Similarity=0.190  Sum_probs=251.5

Q ss_pred             ChhHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhcccccc-------------CCcEEEEcchHHHHH
Q 037567            1 MVSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVT-------------GKTALVVSPLISLMQ   67 (374)
Q Consensus         1 l~~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~~-------------~~~~lil~P~~~l~~   67 (374)
                      |+++|.+ +||..|+|+|.++++.+++++|+++.||||||||++|+++++..             ..++||++|+++|+.
T Consensus        20 l~~~L~~-~g~~~ptpiQ~~~ip~~l~G~Dvi~~ApTGSGKTlafllpil~~l~~~~~~~~~~~~~~raLIl~PTreLa~   98 (572)
T PRK04537         20 LLAGLES-AGFTRCTPIQALTLPVALPGGDVAGQAQTGTGKTLAFLVAVMNRLLSRPALADRKPEDPRALILAPTRELAI   98 (572)
T ss_pred             HHHHHHH-CCCCCCCHHHHHHHHHHhCCCCEEEEcCCCCcHHHHHHHHHHHHHHhcccccccccCCceEEEEeCcHHHHH
Confidence            3567777 89999999999999999999999999999999999999887641             368999999999999


Q ss_pred             HHHHHHHHcC----CceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccC
Q 037567           68 DQVMSLKQRG----INAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGH  143 (374)
Q Consensus        68 q~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~  143 (374)
                      |+.+.+..++    +.+..+.++..... ........++|+|+||++|..++... ..+.+..+++|||||+|++.++++
T Consensus        99 Qi~~~~~~l~~~~~i~v~~l~Gg~~~~~-q~~~l~~~~dIiV~TP~rL~~~l~~~-~~~~l~~v~~lViDEAh~lld~gf  176 (572)
T PRK04537         99 QIHKDAVKFGADLGLRFALVYGGVDYDK-QRELLQQGVDVIIATPGRLIDYVKQH-KVVSLHACEICVLDEADRMFDLGF  176 (572)
T ss_pred             HHHHHHHHHhccCCceEEEEECCCCHHH-HHHHHhCCCCEEEECHHHHHHHHHhc-cccchhheeeeEecCHHHHhhcch
Confidence            9999988763    44555555443332 23334456899999999987665431 123456788999999999987664


Q ss_pred             cchHHHHHHHHHHHhcC---CCCeeEEEeecCcccHHHHHHhcCCCCCeEEEeccC--CCceeEEEEeecCCcchHHHHH
Q 037567          144 DFRLEYKQLDKLRTFLL---GVPFVALTATATEKVRIDIINSLKLKNPYVTIASFD--RKNLFYGVKVINRGQSFVDELV  218 (374)
Q Consensus       144 ~~~~~~~~~~~~~~~~~---~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~  218 (374)
                      .     ..+..+...++   ..++++||||++..........+.. +..+......  ...+...  ............+
T Consensus       177 ~-----~~i~~il~~lp~~~~~q~ll~SATl~~~v~~l~~~~l~~-p~~i~v~~~~~~~~~i~q~--~~~~~~~~k~~~L  248 (572)
T PRK04537        177 I-----KDIRFLLRRMPERGTRQTLLFSATLSHRVLELAYEHMNE-PEKLVVETETITAARVRQR--IYFPADEEKQTLL  248 (572)
T ss_pred             H-----HHHHHHHHhcccccCceEEEEeCCccHHHHHHHHHHhcC-CcEEEeccccccccceeEE--EEecCHHHHHHHH
Confidence            3     33344444444   5789999999988765433333322 2222221111  1122221  1122222233444


Q ss_pred             HHHHHhhcCCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCcc
Q 037567          219 QEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVR  298 (374)
Q Consensus       219 ~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~  298 (374)
                      ..++.. ..+.++||||+++..++.+++.|.+.++.+..+||+++..+|..+++.|++|+.+|||||+++++|+|+|+++
T Consensus       249 ~~ll~~-~~~~k~LVF~nt~~~ae~l~~~L~~~g~~v~~lhg~l~~~eR~~il~~Fr~G~~~VLVaTdv~arGIDip~V~  327 (572)
T PRK04537        249 LGLLSR-SEGARTMVFVNTKAFVERVARTLERHGYRVGVLSGDVPQKKRESLLNRFQKGQLEILVATDVAARGLHIDGVK  327 (572)
T ss_pred             HHHHhc-ccCCcEEEEeCCHHHHHHHHHHHHHcCCCEEEEeCCCCHHHHHHHHHHHHcCCCeEEEEehhhhcCCCccCCC
Confidence            444443 3578999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEECCCCChhHHHHhhccCCCCCCceEEEEEeeccCCCcccce
Q 037567          299 HVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFY  343 (374)
Q Consensus       299 ~vi~~~~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~~~~~~~~  343 (374)
                      +||+++.|.+..+|+||+||+||.|..|.+++|+...+...+..+
T Consensus       328 ~VInyd~P~s~~~yvqRiGRaGR~G~~G~ai~~~~~~~~~~l~~i  372 (572)
T PRK04537        328 YVYNYDLPFDAEDYVHRIGRTARLGEEGDAISFACERYAMSLPDI  372 (572)
T ss_pred             EEEEcCCCCCHHHHhhhhcccccCCCCceEEEEecHHHHHHHHHH
Confidence            999999999999999999999999999999999988765443333

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=100.00  E-value=6.9e-52  Score=379.15  Aligned_cols=331  Identities=20%  Similarity=0.250  Sum_probs=256.7

Q ss_pred             hhHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhcccccc----------CCcEEEEcchHHHHHHHHH
Q 037567            2 VSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVT----------GKTALVVSPLISLMQDQVM   71 (374)
Q Consensus         2 ~~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~~----------~~~~lil~P~~~l~~q~~~   71 (374)
                      .++|.+ +||.+|+++|.++++.+++++++++.||||+|||++|+++++..          ..++||++|+++|+.|+.+
T Consensus        13 ~~~l~~-~g~~~p~~iQ~~ai~~~~~g~d~l~~apTGsGKT~~~~lp~l~~l~~~~~~~~~~~~~lil~Pt~eLa~Q~~~   91 (434)
T PRK11192         13 LEALQD-KGYTRPTAIQAEAIPPALDGRDVLGSAPTGTGKTAAFLLPALQHLLDFPRRKSGPPRILILTPTRELAMQVAD   91 (434)
T ss_pred             HHHHHH-CCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHhhccccCCCCceEEEECCcHHHHHHHHH
Confidence            466777 89999999999999999999999999999999999999887641          3689999999999999988


Q ss_pred             HHHHc----CCceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchH
Q 037567           72 SLKQR----GINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRL  147 (374)
Q Consensus        72 ~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~  147 (374)
                      .+..+    +..+..+.++...... .....++++|+|+||++|..++..  ..+...++++||+||||++.++++.   
T Consensus        92 ~~~~l~~~~~~~v~~~~gg~~~~~~-~~~l~~~~~IlV~Tp~rl~~~~~~--~~~~~~~v~~lViDEah~~l~~~~~---  165 (434)
T PRK11192         92 QARELAKHTHLDIATITGGVAYMNH-AEVFSENQDIVVATPGRLLQYIKE--ENFDCRAVETLILDEADRMLDMGFA---  165 (434)
T ss_pred             HHHHHHccCCcEEEEEECCCCHHHH-HHHhcCCCCEEEEChHHHHHHHHc--CCcCcccCCEEEEECHHHHhCCCcH---
Confidence            87764    4555555554443332 233445689999999998766443  3344677899999999999887643   


Q ss_pred             HHHHHHHHHHhc-CCCCeeEEEeecCcccHHHHHHhcCCCCCeEEEeccCC--CceeEEEEeecCCcchHHHHHHHHHHh
Q 037567          148 EYKQLDKLRTFL-LGVPFVALTATATEKVRIDIINSLKLKNPYVTIASFDR--KNLFYGVKVINRGQSFVDELVQEILKS  224 (374)
Q Consensus       148 ~~~~~~~~~~~~-~~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~  224 (374)
                        ..+..+.... ...+.++||||+.......+...+...+..+.......  ..+... ...........+++..+++.
T Consensus       166 --~~~~~i~~~~~~~~q~~~~SAT~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~-~~~~~~~~~k~~~l~~l~~~  242 (434)
T PRK11192        166 --QDIETIAAETRWRKQTLLFSATLEGDAVQDFAERLLNDPVEVEAEPSRRERKKIHQW-YYRADDLEHKTALLCHLLKQ  242 (434)
T ss_pred             --HHHHHHHHhCccccEEEEEEeecCHHHHHHHHHHHccCCEEEEecCCcccccCceEE-EEEeCCHHHHHHHHHHHHhc
Confidence              2223332222 35689999999987655566665543333332222211  122211 11222234455666666654


Q ss_pred             hcCCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEEEEEC
Q 037567          225 VAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYG  304 (374)
Q Consensus       225 ~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~~~  304 (374)
                       ...+++||||+++..++.+++.|.+.++.+..+||+++..+|..+++.|++|+++|||||+++++|+|+|++++||+++
T Consensus       243 -~~~~~~lVF~~s~~~~~~l~~~L~~~~~~~~~l~g~~~~~~R~~~l~~f~~G~~~vLVaTd~~~~GiDip~v~~VI~~d  321 (434)
T PRK11192        243 -PEVTRSIVFVRTRERVHELAGWLRKAGINCCYLEGEMVQAKRNEAIKRLTDGRVNVLVATDVAARGIDIDDVSHVINFD  321 (434)
T ss_pred             -CCCCeEEEEeCChHHHHHHHHHHHhCCCCEEEecCCCCHHHHHHHHHHHhCCCCcEEEEccccccCccCCCCCEEEEEC
Confidence             3568999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCChhHHHHhhccCCCCCCceEEEEEeeccCCCcccce
Q 037567          305 CPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFY  343 (374)
Q Consensus       305 ~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~~~~~~~~  343 (374)
                      +|.+...|+||+||+||.|..|.++++++..|...+..+
T Consensus       322 ~p~s~~~yiqr~GR~gR~g~~g~ai~l~~~~d~~~~~~i  360 (434)
T PRK11192        322 MPRSADTYLHRIGRTGRAGRKGTAISLVEAHDHLLLGKI  360 (434)
T ss_pred             CCCCHHHHhhcccccccCCCCceEEEEecHHHHHHHHHH
Confidence            999999999999999999999999999988876555443

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

Probab=100.00  E-value=4.3e-52  Score=382.39  Aligned_cols=330  Identities=25%  Similarity=0.347  Sum_probs=263.2

Q ss_pred             hhHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhcccccc-------CCc-EEEEcchHHHHHHHHHHH
Q 037567            2 VSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVT-------GKT-ALVVSPLISLMQDQVMSL   73 (374)
Q Consensus         2 ~~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~~-------~~~-~lil~P~~~l~~q~~~~~   73 (374)
                      .+++.+ .||..|+|+|.+++|.++.|+|++..|+||||||.+|.+|++..       ... +||++|||+|+.|+.+.+
T Consensus        41 l~~l~~-~gf~~pt~IQ~~~IP~~l~g~Dvi~~A~TGsGKT~Af~lP~l~~l~~~~~~~~~~aLil~PTRELA~Qi~~~~  119 (513)
T COG0513          41 LQALKD-LGFEEPTPIQLAAIPLILAGRDVLGQAQTGTGKTAAFLLPLLQKILKSVERKYVSALILAPTRELAVQIAEEL  119 (513)
T ss_pred             HHHHHH-cCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHhcccccCCCceEEECCCHHHHHHHHHHH
Confidence            567788 89999999999999999999999999999999999999998763       112 899999999999999998


Q ss_pred             HHcC-----CceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHH
Q 037567           74 KQRG-----INAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLE  148 (374)
Q Consensus        74 ~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~  148 (374)
                      ..++     +.+..+.++............ +++|+|+||+++.+++..  ..+.+.++.++|+|||+.+.+.|+.    
T Consensus       120 ~~~~~~~~~~~~~~i~GG~~~~~q~~~l~~-~~~ivVaTPGRllD~i~~--~~l~l~~v~~lVlDEADrmLd~Gf~----  192 (513)
T COG0513         120 RKLGKNLGGLRVAVVYGGVSIRKQIEALKR-GVDIVVATPGRLLDLIKR--GKLDLSGVETLVLDEADRMLDMGFI----  192 (513)
T ss_pred             HHHHhhcCCccEEEEECCCCHHHHHHHHhc-CCCEEEECccHHHHHHHc--CCcchhhcCEEEeccHhhhhcCCCH----
Confidence            8653     444556666555555544444 599999999999988776  3677889999999999999998764    


Q ss_pred             HHHHHHHHHhcC-CCCeeEEEeecCcccHHHHHHhcCCCCCeEEEeccC----CCceeEEEEeecCCcchHHHHHHHHHH
Q 037567          149 YKQLDKLRTFLL-GVPFVALTATATEKVRIDIINSLKLKNPYVTIASFD----RKNLFYGVKVINRGQSFVDELVQEILK  223 (374)
Q Consensus       149 ~~~~~~~~~~~~-~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~  223 (374)
                       ..+..+....+ +.+.++||||++.... .+...+-..+..+......    ...+...+..... .....+++..+++
T Consensus       193 -~~i~~I~~~~p~~~qtllfSAT~~~~i~-~l~~~~l~~p~~i~v~~~~~~~~~~~i~q~~~~v~~-~~~k~~~L~~ll~  269 (513)
T COG0513         193 -DDIEKILKALPPDRQTLLFSATMPDDIR-ELARRYLNDPVEIEVSVEKLERTLKKIKQFYLEVES-EEEKLELLLKLLK  269 (513)
T ss_pred             -HHHHHHHHhCCcccEEEEEecCCCHHHH-HHHHHHccCCcEEEEccccccccccCceEEEEEeCC-HHHHHHHHHHHHh
Confidence             45555555554 6899999999999644 3444333333333333122    2222222222222 2236667777777


Q ss_pred             hhcCCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEEEEE
Q 037567          224 SVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHY  303 (374)
Q Consensus       224 ~~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~~  303 (374)
                      .. ...++||||+++..++.++..|...|+.+..+||+++..+|.+.++.|++|+.+|||||+.+++|+|+|++++||+|
T Consensus       270 ~~-~~~~~IVF~~tk~~~~~l~~~l~~~g~~~~~lhG~l~q~~R~~~l~~F~~g~~~vLVaTDvaaRGiDi~~v~~Viny  348 (513)
T COG0513         270 DE-DEGRVIVFVRTKRLVEELAESLRKRGFKVAALHGDLPQEERDRALEKFKDGELRVLVATDVAARGLDIPDVSHVINY  348 (513)
T ss_pred             cC-CCCeEEEEeCcHHHHHHHHHHHHHCCCeEEEecCCCCHHHHHHHHHHHHcCCCCEEEEechhhccCCccccceeEEc
Confidence            64 45579999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCChhHHHHhhccCCCCCCceEEEEEeecc-CCCcccce
Q 037567          304 GCPKTLESYYQESGRCGRDGIASVCWLYYARS-NFAKGDFY  343 (374)
Q Consensus       304 ~~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~-~~~~~~~~  343 (374)
                      +.|.+++.|+||+||+||.|..|.++.|+.+. |...+..+
T Consensus       349 D~p~~~e~yvHRiGRTgRaG~~G~ai~fv~~~~e~~~l~~i  389 (513)
T COG0513         349 DLPLDPEDYVHRIGRTGRAGRKGVAISFVTEEEEVKKLKRI  389 (513)
T ss_pred             cCCCCHHHheeccCccccCCCCCeEEEEeCcHHHHHHHHHH
Confidence            99999999999999999999999999999875 54444433

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=100.00  E-value=3.2e-51  Score=383.31  Aligned_cols=329  Identities=23%  Similarity=0.284  Sum_probs=253.5

Q ss_pred             hhHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc------cCCcEEEEcchHHHHHHHHHHHHH
Q 037567            2 VSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV------TGKTALVVSPLISLMQDQVMSLKQ   75 (374)
Q Consensus         2 ~~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~------~~~~~lil~P~~~l~~q~~~~~~~   75 (374)
                      .++|.+ +||.+|+|+|.++++.+++++++++.||||||||++|.++++.      ..+++||++||++|+.|+.+.+..
T Consensus        18 l~al~~-~G~~~ptpiQ~~ai~~ll~g~dvl~~ApTGsGKT~af~lpll~~l~~~~~~~~~LIL~PTreLa~Qv~~~l~~   96 (629)
T PRK11634         18 LEALND-LGYEKPSPIQAECIPHLLNGRDVLGMAQTGSGKTAAFSLPLLHNLDPELKAPQILVLAPTRELAVQVAEAMTD   96 (629)
T ss_pred             HHHHHH-CCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCcHHHHHHHHHHHHhhhccCCCeEEEEeCcHHHHHHHHHHHHH
Confidence            467777 8999999999999999999999999999999999999888764      356899999999999999988876


Q ss_pred             c-----CCceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHH
Q 037567           76 R-----GINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYK  150 (374)
Q Consensus        76 ~-----~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~  150 (374)
                      +     +..+..++++.... .+.......++|+|+||+++.+++..  ..+.+.++.+||+||||.+.++++.     .
T Consensus        97 ~~~~~~~i~v~~~~gG~~~~-~q~~~l~~~~~IVVgTPgrl~d~l~r--~~l~l~~l~~lVlDEAd~ml~~gf~-----~  168 (629)
T PRK11634         97 FSKHMRGVNVVALYGGQRYD-VQLRALRQGPQIVVGTPGRLLDHLKR--GTLDLSKLSGLVLDEADEMLRMGFI-----E  168 (629)
T ss_pred             HHhhcCCceEEEEECCcCHH-HHHHHhcCCCCEEEECHHHHHHHHHc--CCcchhhceEEEeccHHHHhhcccH-----H
Confidence            5     45554454443322 22333445689999999998766544  3445678899999999999887653     3


Q ss_pred             HHHHHHHhcC-CCCeeEEEeecCcccHHHHHHhcCCCCCeEEEeccC--CCceeEEEEeecCCcchHHHHHHHHHHhhcC
Q 037567          151 QLDKLRTFLL-GVPFVALTATATEKVRIDIINSLKLKNPYVTIASFD--RKNLFYGVKVINRGQSFVDELVQEILKSVAG  227 (374)
Q Consensus       151 ~~~~~~~~~~-~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  227 (374)
                      .+..+...++ ..+.++||||++..... +...+...+..+......  ...+...+  +........+.+..++.. ..
T Consensus       169 di~~Il~~lp~~~q~llfSAT~p~~i~~-i~~~~l~~~~~i~i~~~~~~~~~i~q~~--~~v~~~~k~~~L~~~L~~-~~  244 (629)
T PRK11634        169 DVETIMAQIPEGHQTALFSATMPEAIRR-ITRRFMKEPQEVRIQSSVTTRPDISQSY--WTVWGMRKNEALVRFLEA-ED  244 (629)
T ss_pred             HHHHHHHhCCCCCeEEEEEccCChhHHH-HHHHHcCCCeEEEccCccccCCceEEEE--EEechhhHHHHHHHHHHh-cC
Confidence            3444444444 67899999999887653 333333333333222221  12222111  111122233444444444 24


Q ss_pred             CCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEEEEECCCC
Q 037567          228 AGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPK  307 (374)
Q Consensus       228 ~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~~~~p~  307 (374)
                      ..++||||+++..++.+++.|.+.++.+..+||+++..+|..+++.|++|+.+|||||+++++|+|+|++++||+++.|.
T Consensus       245 ~~~~IVF~~tk~~a~~l~~~L~~~g~~~~~lhgd~~q~~R~~il~~Fr~G~~~ILVATdv~arGIDip~V~~VI~~d~P~  324 (629)
T PRK11634        245 FDAAIIFVRTKNATLEVAEALERNGYNSAALNGDMNQALREQTLERLKDGRLDILIATDVAARGLDVERISLVVNYDIPM  324 (629)
T ss_pred             CCCEEEEeccHHHHHHHHHHHHhCCCCEEEeeCCCCHHHHHHHHHHHhCCCCCEEEEcchHhcCCCcccCCEEEEeCCCC
Confidence            57899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ChhHHHHhhccCCCCCCceEEEEEeeccCCCcccce
Q 037567          308 TLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFY  343 (374)
Q Consensus       308 s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~~~~~~~~  343 (374)
                      +...|+||+||+||.|+.|.+++++.+.+...++.+
T Consensus       325 ~~e~yvqRiGRtGRaGr~G~ai~~v~~~e~~~l~~i  360 (629)
T PRK11634        325 DSESYVHRIGRTGRAGRAGRALLFVENRERRLLRNI  360 (629)
T ss_pred             CHHHHHHHhccccCCCCcceEEEEechHHHHHHHHH
Confidence            999999999999999999999999998775555544

>KOG0328 consensus Predicted ATP-dependent RNA helicase FAL1, involved in rRNA maturation, DEAD-box superfamily [Translation, ribosomal structure and biogenesis]

Probab=100.00  E-value=3.7e-51  Score=325.85  Aligned_cols=328  Identities=19%  Similarity=0.260  Sum_probs=265.1

Q ss_pred             cCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhcccccc------CCcEEEEcchHHHHHHHHHHHHHcC----C
Q 037567            9 FGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVT------GKTALVVSPLISLMQDQVMSLKQRG----I   78 (374)
Q Consensus         9 ~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~~------~~~~lil~P~~~l~~q~~~~~~~~~----~   78 (374)
                      +||++|..+|..|++++++|++++..|..|+|||.+|.+.+++.      .-++++++|||+|+.|..+.+...|    +
T Consensus        45 yGfekPS~IQqrAi~~IlkGrdViaQaqSGTGKTa~~si~vlq~~d~~~r~tQ~lilsPTRELa~Qi~~vi~alg~~mnv  124 (400)
T KOG0328|consen   45 YGFEKPSAIQQRAIPQILKGRDVIAQAQSGTGKTATFSISVLQSLDISVRETQALILSPTRELAVQIQKVILALGDYMNV  124 (400)
T ss_pred             hccCCchHHHhhhhhhhhcccceEEEecCCCCceEEEEeeeeeecccccceeeEEEecChHHHHHHHHHHHHHhcccccc
Confidence            79999999999999999999999999999999999988877762      5679999999999999999998775    4


Q ss_pred             ceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHHh
Q 037567           79 NAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTF  158 (374)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~  158 (374)
                      +...+.++..-.+...... .+.+++.+||++..++..+  ..+.-.++.++|+||++.+.+.|+.     .++-.+...
T Consensus       125 q~hacigg~n~gedikkld-~G~hvVsGtPGrv~dmikr--~~L~tr~vkmlVLDEaDemL~kgfk-----~Qiydiyr~  196 (400)
T KOG0328|consen  125 QCHACIGGKNLGEDIKKLD-YGQHVVSGTPGRVLDMIKR--RSLRTRAVKMLVLDEADEMLNKGFK-----EQIYDIYRY  196 (400)
T ss_pred             eEEEEecCCccchhhhhhc-ccceEeeCCCchHHHHHHh--ccccccceeEEEeccHHHHHHhhHH-----HHHHHHHHh
Confidence            4444444444444444433 6789999999999888776  6666788999999999999987654     555566666


Q ss_pred             cC-CCCeeEEEeecCcccHHHHHHhcCCCCCeEEE-eccCCCce-eEEEEeecCCcchHHHHHHHHHHhhcCCCcEEEEe
Q 037567          159 LL-GVPFVALTATATEKVRIDIINSLKLKNPYVTI-ASFDRKNL-FYGVKVINRGQSFVDELVQEILKSVAGAGSIIVYC  235 (374)
Q Consensus       159 ~~-~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lVf~  235 (374)
                      +| +.|++++|||.+.........+  ..++.... .......- ...+..-.....+.-+.+.++...+ .-.+++|||
T Consensus       197 lp~~~Qvv~~SATlp~eilemt~kf--mtdpvrilvkrdeltlEgIKqf~v~ve~EewKfdtLcdLYd~L-tItQavIFc  273 (400)
T KOG0328|consen  197 LPPGAQVVLVSATLPHEILEMTEKF--MTDPVRILVKRDELTLEGIKQFFVAVEKEEWKFDTLCDLYDTL-TITQAVIFC  273 (400)
T ss_pred             CCCCceEEEEeccCcHHHHHHHHHh--cCCceeEEEecCCCchhhhhhheeeechhhhhHhHHHHHhhhh-ehheEEEEe
Confidence            65 8999999999999887543333  34443332 22222111 1112222333455556666666665 567899999


Q ss_pred             cchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEEEEECCCCChhHHHHh
Q 037567          236 MTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQE  315 (374)
Q Consensus       236 ~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~~~~p~s~~~~~Q~  315 (374)
                      +++..+..+.+.+++..+.+..+||++..++|..++++|+.|+.+||++|+..++|+|+|.+++||+|++|.+...|+||
T Consensus       274 nTk~kVdwLtekm~~~nftVssmHGDm~qkERd~im~dFRsg~SrvLitTDVwaRGiDv~qVslviNYDLP~nre~YIHR  353 (400)
T KOG0328|consen  274 NTKRKVDWLTEKMREANFTVSSMHGDMEQKERDKIMNDFRSGKSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHR  353 (400)
T ss_pred             cccchhhHHHHHHHhhCceeeeccCCcchhHHHHHHHHhhcCCceEEEEechhhccCCcceeEEEEecCCCccHHHHhhh
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hccCCCCCCceEEEEEeeccCCCcccceeccc
Q 037567          316 SGRCGRDGIASVCWLYYARSNFAKGDFYCGES  347 (374)
Q Consensus       316 ~GR~~R~~~~g~~~~~~~~~~~~~~~~~~~~~  347 (374)
                      +||.||+|..|.++.|+..+|++.++.+.+..
T Consensus       354 IGRSGRFGRkGvainFVk~~d~~~lrdieq~y  385 (400)
T KOG0328|consen  354 IGRSGRFGRKGVAINFVKSDDLRILRDIEQYY  385 (400)
T ss_pred             hccccccCCcceEEEEecHHHHHHHHHHHHHH
Confidence            99999999999999999999987777665443

>KOG0345 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=100.00  E-value=2e-50  Score=342.82  Aligned_cols=331  Identities=23%  Similarity=0.275  Sum_probs=270.8

Q ss_pred             hhHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhcccccc---------C--CcEEEEcchHHHHHHHH
Q 037567            2 VSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVT---------G--KTALVVSPLISLMQDQV   70 (374)
Q Consensus         2 ~~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~~---------~--~~~lil~P~~~l~~q~~   70 (374)
                      .+++.. .||..++|.|..++|.++.++|+++.++||||||++|++|++..         .  --++|++|||+|+.|..
T Consensus        18 ~~~l~~-~GF~~mTpVQa~tIPlll~~KDVvveavTGSGKTlAFllP~le~i~rr~~~~~~~~vgalIIsPTRELa~QI~   96 (567)
T KOG0345|consen   18 LEALDE-SGFEKMTPVQAATIPLLLKNKDVVVEAVTGSGKTLAFLLPMLEIIYRREAKTPPGQVGALIISPTRELARQIR   96 (567)
T ss_pred             HHHHHh-cCCcccCHHHHhhhHHHhcCCceEEEcCCCCCchhhHHHHHHHHHHhhccCCCccceeEEEecCcHHHHHHHH
Confidence            456777 89999999999999999999999999999999999999998751         2  25899999999999988


Q ss_pred             HHHHHc-----CCceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcc
Q 037567           71 MSLKQR-----GINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDF  145 (374)
Q Consensus        71 ~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~  145 (374)
                      +-...|     .++...+.++.+..+........+++|+|+||++|.+++++....+.+.+++++|+|||+++.+.|++ 
T Consensus        97 ~V~~~F~~~l~~l~~~l~vGG~~v~~Di~~fkee~~nIlVgTPGRL~di~~~~~~~l~~rsLe~LVLDEADrLldmgFe-  175 (567)
T KOG0345|consen   97 EVAQPFLEHLPNLNCELLVGGRSVEEDIKTFKEEGPNILVGTPGRLLDILQREAEKLSFRSLEILVLDEADRLLDMGFE-  175 (567)
T ss_pred             HHHHHHHHhhhccceEEEecCccHHHHHHHHHHhCCcEEEeCchhHHHHHhchhhhccccccceEEecchHhHhcccHH-
Confidence            887765     45566777776666666777778899999999999999888667777789999999999999999987 


Q ss_pred             hHHHHHHHHHHHhcC-CCCeeEEEeecCcccHHHHHHhcCCCCCeEEEeccCC-----CceeEEEEeecCCcchHHHHHH
Q 037567          146 RLEYKQLDKLRTFLL-GVPFVALTATATEKVRIDIINSLKLKNPYVTIASFDR-----KNLFYGVKVINRGQSFVDELVQ  219 (374)
Q Consensus       146 ~~~~~~~~~~~~~~~-~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~  219 (374)
                          ..++.++..+| +++.=+||||...+...  +...++.++..+......     +.+...+...  ........+-
T Consensus       176 ----~~~n~ILs~LPKQRRTGLFSATq~~~v~d--L~raGLRNpv~V~V~~k~~~~tPS~L~~~Y~v~--~a~eK~~~lv  247 (567)
T KOG0345|consen  176 ----ASVNTILSFLPKQRRTGLFSATQTQEVED--LARAGLRNPVRVSVKEKSKSATPSSLALEYLVC--EADEKLSQLV  247 (567)
T ss_pred             ----HHHHHHHHhcccccccccccchhhHHHHH--HHHhhccCceeeeecccccccCchhhcceeeEe--cHHHHHHHHH
Confidence                67777877777 57788999999988765  666777777644332222     1122222222  2222334444


Q ss_pred             HHHHhhcCCCcEEEEecchhHHHHHHHHHHHc--CCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCc
Q 037567          220 EILKSVAGAGSIIVYCMTIKDVEEISKALKQL--GVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDV  297 (374)
Q Consensus       220 ~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~--~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~  297 (374)
                      +++.. ...+++|||+++...++..+..+...  +..+..+||.++.+.|..+++.|.+..-.+++||+.+.+|+|+|++
T Consensus       248 ~~L~~-~~~kK~iVFF~TCasVeYf~~~~~~~l~~~~i~~iHGK~~q~~R~k~~~~F~~~~~~vl~~TDVaARGlDip~i  326 (567)
T KOG0345|consen  248 HLLNN-NKDKKCIVFFPTCASVEYFGKLFSRLLKKREIFSIHGKMSQKARAKVLEAFRKLSNGVLFCTDVAARGLDIPGI  326 (567)
T ss_pred             HHHhc-cccccEEEEecCcchHHHHHHHHHHHhCCCcEEEecchhcchhHHHHHHHHHhccCceEEeehhhhccCCCCCc
Confidence            44444 46789999999999999999998874  5678999999999999999999999888899999999999999999


Q ss_pred             cEEEEECCCCChhHHHHhhccCCCCCCceEEEEEeeccCCCcccce
Q 037567          298 RHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFY  343 (374)
Q Consensus       298 ~~vi~~~~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~~~~~~~~  343 (374)
                      ++||++|+|.++..|+||+||++|.|..|.+++|+.+.+..+..++
T Consensus       327 D~VvQ~DpP~~~~~FvHR~GRTaR~gr~G~Aivfl~p~E~aYveFl  372 (567)
T KOG0345|consen  327 DLVVQFDPPKDPSSFVHRCGRTARAGREGNAIVFLNPREEAYVEFL  372 (567)
T ss_pred             eEEEecCCCCChhHHHhhcchhhhccCccceEEEecccHHHHHHHH
Confidence            9999999999999999999999999999999999999776555444

>PTZ00424 helicase 45; Provisional

Probab=100.00  E-value=3e-50  Score=366.11  Aligned_cols=330  Identities=18%  Similarity=0.242  Sum_probs=246.3

Q ss_pred             hhHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc------cCCcEEEEcchHHHHHHHHHHHHH
Q 037567            2 VSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV------TGKTALVVSPLISLMQDQVMSLKQ   75 (374)
Q Consensus         2 ~~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~------~~~~~lil~P~~~l~~q~~~~~~~   75 (374)
                      ++++.. +||.+|+|+|.++++.+++++++++.||||||||++|+++++.      ...++||++|+++|+.|+.+.+..
T Consensus        40 ~~~l~~-~~~~~~~~~Q~~ai~~i~~~~d~ii~apTGsGKT~~~~l~~l~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~  118 (401)
T PTZ00424         40 LRGIYS-YGFEKPSAIQQRGIKPILDGYDTIGQAQSGTGKTATFVIAALQLIDYDLNACQALILAPTRELAQQIQKVVLA  118 (401)
T ss_pred             HHHHHH-cCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHhcCCCCCceEEEECCCHHHHHHHHHHHHH
Confidence            456766 8999999999999999999999999999999999999888664      356799999999999999988877


Q ss_pred             cCC----ceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHH
Q 037567           76 RGI----NAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQ  151 (374)
Q Consensus        76 ~~~----~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~  151 (374)
                      ++.    ......++..... ........++|+|+||+++..++..  ....+.+++++|+||+|++.+.+..     ..
T Consensus       119 ~~~~~~~~~~~~~g~~~~~~-~~~~~~~~~~Ivv~Tp~~l~~~l~~--~~~~l~~i~lvViDEah~~~~~~~~-----~~  190 (401)
T PTZ00424        119 LGDYLKVRCHACVGGTVVRD-DINKLKAGVHMVVGTPGRVYDMIDK--RHLRVDDLKLFILDEADEMLSRGFK-----GQ  190 (401)
T ss_pred             HhhhcCceEEEEECCcCHHH-HHHHHcCCCCEEEECcHHHHHHHHh--CCcccccccEEEEecHHHHHhcchH-----HH
Confidence            642    2222233222222 2223334579999999998765543  2345678999999999999876543     22


Q ss_pred             HHHHHHh-cCCCCeeEEEeecCcccHHHHHHhcCCCCCeEEEecc--CCCceeEEEEeecCCcchHHHHHHHHHHhhcCC
Q 037567          152 LDKLRTF-LLGVPFVALTATATEKVRIDIINSLKLKNPYVTIASF--DRKNLFYGVKVINRGQSFVDELVQEILKSVAGA  228 (374)
Q Consensus       152 ~~~~~~~-~~~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  228 (374)
                      +..+... .++.+++++|||++..... +...+...+..+.....  ....+...... ..........+..+.+.. ..
T Consensus       191 ~~~i~~~~~~~~~~i~~SAT~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~-~~  267 (401)
T PTZ00424        191 IYDVFKKLPPDVQVALFSATMPNEILE-LTTKFMRDPKRILVKKDELTLEGIRQFYVA-VEKEEWKFDTLCDLYETL-TI  267 (401)
T ss_pred             HHHHHhhCCCCcEEEEEEecCCHHHHH-HHHHHcCCCEEEEeCCCCcccCCceEEEEe-cChHHHHHHHHHHHHHhc-CC
Confidence            3333333 3468899999999876543 22222222222221111  11121111111 122222334444444432 46


Q ss_pred             CcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEEEEECCCCC
Q 037567          229 GSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPKT  308 (374)
Q Consensus       229 ~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~~~~p~s  308 (374)
                      .++||||+++..++.+++.|.+.++.+..+||+++.++|..+++.|++|+++|||||+++++|+|+|++++||++++|.+
T Consensus       268 ~~~ivF~~t~~~~~~l~~~l~~~~~~~~~~h~~~~~~~R~~i~~~f~~g~~~vLvaT~~l~~GiDip~v~~VI~~~~p~s  347 (401)
T PTZ00424        268 TQAIIYCNTRRKVDYLTKKMHERDFTVSCMHGDMDQKDRDLIMREFRSGSTRVLITTDLLARGIDVQQVSLVINYDLPAS  347 (401)
T ss_pred             CeEEEEecCcHHHHHHHHHHHHCCCcEEEEeCCCCHHHHHHHHHHHHcCCCCEEEEcccccCCcCcccCCEEEEECCCCC
Confidence            78999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhHHHHhhccCCCCCCceEEEEEeeccCCCcccce
Q 037567          309 LESYYQESGRCGRDGIASVCWLYYARSNFAKGDFY  343 (374)
Q Consensus       309 ~~~~~Q~~GR~~R~~~~g~~~~~~~~~~~~~~~~~  343 (374)
                      ..+|+||+||+||.|..|.|++++++.+...+..+
T Consensus       348 ~~~y~qr~GRagR~g~~G~~i~l~~~~~~~~~~~~  382 (401)
T PTZ00424        348 PENYIHRIGRSGRFGRKGVAINFVTPDDIEQLKEI  382 (401)
T ss_pred             HHHEeecccccccCCCCceEEEEEcHHHHHHHHHH
Confidence            99999999999999999999999998876655544

>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=100.00  E-value=1.2e-50  Score=338.71  Aligned_cols=340  Identities=23%  Similarity=0.337  Sum_probs=278.3

Q ss_pred             hhHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc------------cCCcEEEEcchHHHHHHH
Q 037567            2 VSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV------------TGKTALVVSPLISLMQDQ   69 (374)
Q Consensus         2 ~~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~------------~~~~~lil~P~~~l~~q~   69 (374)
                      .+++++ .||.+|+|+|+++||-+++|.+++-+|.||+|||++|+++.+.            .++.+|+++||++|+.|+
T Consensus       232 menIkK-~GFqKPtPIqSQaWPI~LQG~DliGVAQTgtgKtL~~L~pg~ihi~aqp~~~~qr~~p~~lvl~ptreLalqi  310 (629)
T KOG0336|consen  232 MENIKK-TGFQKPTPIQSQAWPILLQGIDLIGVAQTGTGKTLAFLLPGFIHIDAQPKRREQRNGPGVLVLTPTRELALQI  310 (629)
T ss_pred             HHHHHh-ccCCCCCcchhcccceeecCcceEEEEecCCCcCHHHhccceeeeeccchhhhccCCCceEEEeccHHHHHHH
Confidence            356777 8999999999999999999999999999999999999988653            267899999999999999


Q ss_pred             HHHHHHc---CCceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcch
Q 037567           70 VMSLKQR---GINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFR  146 (374)
Q Consensus        70 ~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~  146 (374)
                      .-+..++   |.....+.++... ..+.....++.+|+++||++|.++...  ..+.+.++.++|+|||+.+.+.|++  
T Consensus       311 e~e~~kysyng~ksvc~ygggnR-~eqie~lkrgveiiiatPgrlndL~~~--n~i~l~siTYlVlDEADrMLDMgFE--  385 (629)
T KOG0336|consen  311 EGEVKKYSYNGLKSVCVYGGGNR-NEQIEDLKRGVEIIIATPGRLNDLQMD--NVINLASITYLVLDEADRMLDMGFE--  385 (629)
T ss_pred             HhHHhHhhhcCcceEEEecCCCc-hhHHHHHhcCceEEeeCCchHhhhhhc--CeeeeeeeEEEEecchhhhhccccc--
Confidence            8887764   5554444444333 333445567789999999999988655  6677889999999999999998876  


Q ss_pred             HHHHHHH-HHHHhcCCCCeeEEEeecCcccHHHHHHhcCCCCCeEEE-eccCCCceeEE-EEeecCCcchHHHHHHHHHH
Q 037567          147 LEYKQLD-KLRTFLLGVPFVALTATATEKVRIDIINSLKLKNPYVTI-ASFDRKNLFYG-VKVINRGQSFVDELVQEILK  223 (374)
Q Consensus       147 ~~~~~~~-~~~~~~~~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~  223 (374)
                         -++. -++...|+.+.++.|||+++....  +....++++.+.. .+.+....... ...+...+....+.+..+.+
T Consensus       386 ---pqIrkilldiRPDRqtvmTSATWP~~Vrr--La~sY~Kep~~v~vGsLdL~a~~sVkQ~i~v~~d~~k~~~~~~f~~  460 (629)
T KOG0336|consen  386 ---PQIRKILLDIRPDRQTVMTSATWPEGVRR--LAQSYLKEPMIVYVGSLDLVAVKSVKQNIIVTTDSEKLEIVQFFVA  460 (629)
T ss_pred             ---HHHHHHhhhcCCcceeeeecccCchHHHH--HHHHhhhCceEEEecccceeeeeeeeeeEEecccHHHHHHHHHHHH
Confidence               3333 344566789999999999998865  4444455555443 33333222111 11233445555678888888


Q ss_pred             hhcCCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEEEEE
Q 037567          224 SVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHY  303 (374)
Q Consensus       224 ~~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~~  303 (374)
                      ...+..++||||.++..++.|...|.-.|+.+..+||+....+|+..+++|++|+++|||+|+.+++|+|+|+++||++|
T Consensus       461 ~ms~ndKvIiFv~~K~~AD~LSSd~~l~gi~~q~lHG~r~Q~DrE~al~~~ksG~vrILvaTDlaSRGlDv~DiTHV~Ny  540 (629)
T KOG0336|consen  461 NMSSNDKVIIFVSRKVMADHLSSDFCLKGISSQSLHGNREQSDREMALEDFKSGEVRILVATDLASRGLDVPDITHVYNY  540 (629)
T ss_pred             hcCCCceEEEEEechhhhhhccchhhhcccchhhccCChhhhhHHHHHHhhhcCceEEEEEechhhcCCCchhcceeecc
Confidence            88899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCChhHHHHhhccCCCCCCceEEEEEeeccCCCcccceeccccchHH
Q 037567          304 GCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFYCGESQTENQ  352 (374)
Q Consensus       304 ~~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~  352 (374)
                      +.|.+.++|+||+||+||.|..|..+.++...|-...+.+++-++..++
T Consensus       541 DFP~nIeeYVHRvGrtGRaGr~G~sis~lt~~D~~~a~eLI~ILe~aeQ  589 (629)
T KOG0336|consen  541 DFPRNIEEYVHRVGRTGRAGRTGTSISFLTRNDWSMAEELIQILERAEQ  589 (629)
T ss_pred             CCCccHHHHHHHhcccccCCCCcceEEEEehhhHHHHHHHHHHHHHhhh
Confidence            9999999999999999999999999999999999888888876555444

>KOG0333 consensus U5 snRNP-like RNA helicase subunit [RNA processing and modification]

Probab=100.00  E-value=1.5e-49  Score=341.67  Aligned_cols=325  Identities=26%  Similarity=0.301  Sum_probs=260.1

Q ss_pred             hHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc---------------cCCcEEEEcchHHHHH
Q 037567            3 STLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV---------------TGKTALVVSPLISLMQ   67 (374)
Q Consensus         3 ~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~---------------~~~~~lil~P~~~l~~   67 (374)
                      +.+.+ .||.+|+|+|..++|-.++.+|+|..|.||||||.+|+++++.               .++.+++++||++|++
T Consensus       258 ~~I~~-~~y~eptpIqR~aipl~lQ~rD~igvaETgsGktaaf~ipLl~~IsslP~~~~~en~~~gpyaiilaptReLaq  336 (673)
T KOG0333|consen  258 SVIKK-PGYKEPTPIQRQAIPLGLQNRDPIGVAETGSGKTAAFLIPLLIWISSLPPMARLENNIEGPYAIILAPTRELAQ  336 (673)
T ss_pred             HHHHh-cCCCCCchHHHhhccchhccCCeeeEEeccCCccccchhhHHHHHHcCCCcchhhhcccCceeeeechHHHHHH
Confidence            44555 8999999999999999999999999999999999999887662               3788999999999999


Q ss_pred             HHHHHHHHc----CCceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccC
Q 037567           68 DQVMSLKQR----GINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGH  143 (374)
Q Consensus        68 q~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~  143 (374)
                      |+.++-.++    |+++..+.++....+.. .....+|+|+|+||+.|.+.+.+  ..+.++.+.++|+|||+.+.+.|+
T Consensus       337 qIeeEt~kf~~~lg~r~vsvigg~s~EEq~-fqls~gceiviatPgrLid~Len--r~lvl~qctyvvldeadrmiDmgf  413 (673)
T KOG0333|consen  337 QIEEETNKFGKPLGIRTVSVIGGLSFEEQG-FQLSMGCEIVIATPGRLIDSLEN--RYLVLNQCTYVVLDEADRMIDMGF  413 (673)
T ss_pred             HHHHHHHHhcccccceEEEEecccchhhhh-hhhhccceeeecCchHHHHHHHH--HHHHhccCceEeccchhhhhcccc
Confidence            999998876    44555555554444432 23455699999999999988777  566778899999999999998877


Q ss_pred             cchHHHHHHHHHHHhcC------------------------C--CCeeEEEeecCcccHHHHHHhcCCCCCeEEEeccCC
Q 037567          144 DFRLEYKQLDKLRTFLL------------------------G--VPFVALTATATEKVRIDIINSLKLKNPYVTIASFDR  197 (374)
Q Consensus       144 ~~~~~~~~~~~~~~~~~------------------------~--~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~~~  197 (374)
                      +.     ....++..++                        .  .+.++||||+++... .+...+...+..+.......
T Consensus       414 E~-----dv~~iL~~mPssn~k~~tde~~~~~~~~~~~~~~k~yrqT~mftatm~p~ve-rlar~ylr~pv~vtig~~gk  487 (673)
T KOG0333|consen  414 EP-----DVQKILEQMPSSNAKPDTDEKEGEERVRKNFSSSKKYRQTVMFTATMPPAVE-RLARSYLRRPVVVTIGSAGK  487 (673)
T ss_pred             cH-----HHHHHHHhCCccccCCCccchhhHHHHHhhcccccceeEEEEEecCCChHHH-HHHHHHhhCCeEEEeccCCC
Confidence            53     2222222221                        1  468999999999876 45555554555555554444


Q ss_pred             CceeEEEEeecCCcchHHHHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcC
Q 037567          198 KNLFYGVKVINRGQSFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRD  277 (374)
Q Consensus       198 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g  277 (374)
                      +.......+..-........+.++++.. ...++|||+|+++.++.+++.|.+.|+++..+||+.+.++|+..++.|++|
T Consensus       488 ~~~rveQ~v~m~~ed~k~kkL~eil~~~-~~ppiIIFvN~kk~~d~lAk~LeK~g~~~~tlHg~k~qeQRe~aL~~fr~~  566 (673)
T KOG0333|consen  488 PTPRVEQKVEMVSEDEKRKKLIEILESN-FDPPIIIFVNTKKGADALAKILEKAGYKVTTLHGGKSQEQRENALADFREG  566 (673)
T ss_pred             CccchheEEEEecchHHHHHHHHHHHhC-CCCCEEEEEechhhHHHHHHHHhhccceEEEeeCCccHHHHHHHHHHHHhc
Confidence            3333333333222233355555666653 578899999999999999999999999999999999999999999999999


Q ss_pred             CeeEEEEeccccccccccCccEEEEECCCCChhHHHHhhccCCCCCCceEEEEEeeccCCC
Q 037567          278 EIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFA  338 (374)
Q Consensus       278 ~~~ilv~t~~~~~G~d~~~~~~vi~~~~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~~~  338 (374)
                      ..+|+|||+++++|+|+|++.+||+|+++.+..+|.|||||+||.|+.|++++|+++.|-.
T Consensus       567 t~dIlVaTDvAgRGIDIpnVSlVinydmaksieDYtHRIGRTgRAGk~GtaiSflt~~dt~  627 (673)
T KOG0333|consen  567 TGDILVATDVAGRGIDIPNVSLVINYDMAKSIEDYTHRIGRTGRAGKSGTAISFLTPADTA  627 (673)
T ss_pred             CCCEEEEecccccCCCCCccceeeecchhhhHHHHHHHhccccccccCceeEEEeccchhH
Confidence            9999999999999999999999999999999999999999999999999999999998743

>KOG0351 consensus ATP-dependent DNA helicase [Replication, recombination and repair]

Probab=100.00  E-value=2.7e-49  Score=375.53  Aligned_cols=371  Identities=45%  Similarity=0.711  Sum_probs=328.4

Q ss_pred             hhHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccccCCcEEEEcchHHHHHHHHHHHHHcCCceE
Q 037567            2 VSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVTGKTALVVSPLISLMQDQVMSLKQRGINAE   81 (374)
Q Consensus         2 ~~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~   81 (374)
                      ..++..+||...++|-|.+++.+++.|+++++.+|||.||+++|.+|++...+.++||.|..+|.++....+...++...
T Consensus       253 ~~~l~~~Fg~~~FR~~Q~eaI~~~l~Gkd~fvlmpTG~GKSLCYQlPA~l~~gitvVISPL~SLm~DQv~~L~~~~I~a~  332 (941)
T KOG0351|consen  253 ELLLKEVFGHKGFRPNQLEAINATLSGKDCFVLMPTGGGKSLCYQLPALLLGGVTVVISPLISLMQDQVTHLSKKGIPAC  332 (941)
T ss_pred             HHHHHHHhccccCChhHHHHHHHHHcCCceEEEeecCCceeeEeeccccccCCceEEeccHHHHHHHHHHhhhhcCccee
Confidence            45788999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EcCCCCCchh---hhhhhhcC--CeeEEEEcCcccccCchhhHHHHHhcC---ccEEEEeccchhhcccCcchHHHHHHH
Q 037567           82 FLGSAQTDSS---VQTKAETG--YFQLLFMTPEKACIIPISFWSKLLKAG---VCLFAVDEAHCISEWGHDFRLEYKQLD  153 (374)
Q Consensus        82 ~~~~~~~~~~---~~~~~~~~--~~~i~i~T~~~l~~~~~~~~~~~~~~~---~~~vviDE~h~~~~~~~~~~~~~~~~~  153 (374)
                      .+.+.....+   .......+  .++|+..|||++............+..   +.++||||||.+.+||.+|++.+..+.
T Consensus       333 ~L~s~q~~~~~~~i~q~l~~~~~~ikilYvtPE~v~~~~~l~~~~~~L~~~~~lal~vIDEAHCVSqWgHdFRp~Yk~l~  412 (941)
T KOG0351|consen  333 FLSSIQTAAERLAILQKLANGNPIIKILYVTPEKVVASEGLLESLADLYARGLLALFVIDEAHCVSQWGHDFRPSYKRLG  412 (941)
T ss_pred             eccccccHHHHHHHHHHHhCCCCeEEEEEeCHHHhhcccchhhHHHhccCCCeeEEEEecHHHHhhhhcccccHHHHHHH
Confidence            8888776642   33333444  789999999998766444333334444   789999999999999999999999999


Q ss_pred             HHHHhcCCCCeeEEEeecCcccHHHHHHhcCCCCCeEEEeccCCCceeEEEEeecCCcchHHHHHHHHHHhhcCCCcEEE
Q 037567          154 KLRTFLLGVPFVALTATATEKVRIDIINSLKLKNPYVTIASFDRKNLFYGVKVINRGQSFVDELVQEILKSVAGAGSIIV  233 (374)
Q Consensus       154 ~~~~~~~~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lV  233 (374)
                      .++..+++.+++++|||.......+++..+++.++.+...+++++++.+.+.......  ....+....+.....+.+||
T Consensus       413 ~l~~~~~~vP~iALTATAT~~v~~DIi~~L~l~~~~~~~~sfnR~NL~yeV~~k~~~~--~~~~~~~~~~~~~~~~s~II  490 (941)
T KOG0351|consen  413 LLRIRFPGVPFIALTATATERVREDVIRSLGLRNPELFKSSFNRPNLKYEVSPKTDKD--ALLDILEESKLRHPDQSGII  490 (941)
T ss_pred             HHHhhCCCCCeEEeehhccHHHHHHHHHHhCCCCcceecccCCCCCceEEEEeccCcc--chHHHHHHhhhcCCCCCeEE
Confidence            9999999999999999999999999999999999999999999999999988766422  22233334445568899999


Q ss_pred             EecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEEEEECCCCChhHHH
Q 037567          234 YCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYY  313 (374)
Q Consensus       234 f~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~~~~p~s~~~~~  313 (374)
                      ||.++.+++.++..|.+.+..+..+|+++++.+|..+-..|..++++|+++|-+.++|+|-|+++.||+++.|.|.+.|.
T Consensus       491 YC~sr~~ce~vs~~L~~~~~~a~~YHAGl~~~~R~~Vq~~w~~~~~~VivATVAFGMGIdK~DVR~ViH~~lPks~E~YY  570 (941)
T KOG0351|consen  491 YCLSRKECEQVSAVLRSLGKSAAFYHAGLPPKERETVQKAWMSDKIRVIVATVAFGMGIDKPDVRFVIHYSLPKSFEGYY  570 (941)
T ss_pred             EeCCcchHHHHHHHHHHhchhhHhhhcCCCHHHHHHHHHHHhcCCCeEEEEEeeccCCCCCCceeEEEECCCchhHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HhhccCCCCCCceEEEEEeeccCCCcccceeccccchHHHHH--HHHHHHHHHHHhhh-cccCC
Q 037567          314 QESGRCGRDGIASVCWLYYARSNFAKGDFYCGESQTENQRTA--IMESLLAAQRYCLL-TTCRR  374 (374)
Q Consensus       314 Q~~GR~~R~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~l~~~~~~~~~-~~~~~  374 (374)
                      |-+|||||.|....|++||...|+..++.++...........  -..++.++.+||++ +.|||
T Consensus       571 QE~GRAGRDG~~s~C~l~y~~~D~~~l~~ll~s~~~~~~~~~~~~~~~l~~~~~yCen~t~crr  634 (941)
T KOG0351|consen  571 QEAGRAGRDGLPSSCVLLYGYADISELRRLLTSGNRLSGVKKFTRLLELVQVVTYCENETDCRR  634 (941)
T ss_pred             HhccccCcCCCcceeEEecchhHHHHHHHHHHccccccchhhccchhhHHHHHHhhcCccchhH
Confidence            999999999999999999999999999998877744333333  68899999999995 79997

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

Probab=100.00  E-value=1.1e-48  Score=373.07  Aligned_cols=324  Identities=19%  Similarity=0.243  Sum_probs=241.2

Q ss_pred             hhHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc-----cCCcEEEEcchHHHHHHHHHHHHHc
Q 037567            2 VSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV-----TGKTALVVSPLISLMQDQVMSLKQR   76 (374)
Q Consensus         2 ~~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~-----~~~~~lil~P~~~l~~q~~~~~~~~   76 (374)
                      .++|++ +||.+|+++|.++++.+.+|+|+++.+|||||||++|++|++.     ...++||++|+++|+.|..+.++.+
T Consensus        26 ~~~L~~-~g~~~p~~~Q~~ai~~il~G~nvvv~apTGSGKTla~~LPiL~~l~~~~~~~aL~l~PtraLa~q~~~~l~~l  104 (742)
T TIGR03817        26 VAALEA-AGIHRPWQHQARAAELAHAGRHVVVATGTASGKSLAYQLPVLSALADDPRATALYLAPTKALAADQLRAVREL  104 (742)
T ss_pred             HHHHHH-cCCCcCCHHHHHHHHHHHCCCCEEEECCCCCcHHHHHHHHHHHHHhhCCCcEEEEEcChHHHHHHHHHHHHHh
Confidence            467777 8999999999999999999999999999999999999999875     2568999999999999999999887


Q ss_pred             C---CceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccC-c-hhhHHHHHhcCccEEEEeccchhhc-ccCcchHHHH
Q 037567           77 G---INAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACII-P-ISFWSKLLKAGVCLFAVDEAHCISE-WGHDFRLEYK  150 (374)
Q Consensus        77 ~---~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~-~-~~~~~~~~~~~~~~vviDE~h~~~~-~~~~~~~~~~  150 (374)
                      +   +.+..+.++..... . ......++|+++||+++... + ........+.++++||+||+|.+.+ .|......+.
T Consensus       105 ~~~~i~v~~~~Gdt~~~~-r-~~i~~~~~IivtTPd~L~~~~L~~~~~~~~~l~~l~~vViDEah~~~g~fg~~~~~il~  182 (742)
T TIGR03817       105 TLRGVRPATYDGDTPTEE-R-RWAREHARYVLTNPDMLHRGILPSHARWARFLRRLRYVVIDECHSYRGVFGSHVALVLR  182 (742)
T ss_pred             ccCCeEEEEEeCCCCHHH-H-HHHhcCCCEEEEChHHHHHhhccchhHHHHHHhcCCEEEEeChhhccCccHHHHHHHHH
Confidence            4   44555555443322 2 22334579999999988532 1 1111233478999999999999864 3444444455


Q ss_pred             HHHHHHHhc-CCCCeeEEEeecCcccHHHHHHhcCCCCCeEEEeccCCCceeEEEEeecCC----------------cch
Q 037567          151 QLDKLRTFL-LGVPFVALTATATEKVRIDIINSLKLKNPYVTIASFDRKNLFYGVKVINRG----------------QSF  213 (374)
Q Consensus       151 ~~~~~~~~~-~~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----------------~~~  213 (374)
                      ++.++.... .+.+++++|||.+++..  ....+...+..+ ......+.....+......                ...
T Consensus       183 rL~ri~~~~g~~~q~i~~SATi~n~~~--~~~~l~g~~~~~-i~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~r~~~~~~  259 (742)
T TIGR03817       183 RLRRLCARYGASPVFVLASATTADPAA--AASRLIGAPVVA-VTEDGSPRGARTVALWEPPLTELTGENGAPVRRSASAE  259 (742)
T ss_pred             HHHHHHHhcCCCCEEEEEecCCCCHHH--HHHHHcCCCeEE-ECCCCCCcCceEEEEecCCccccccccccccccchHHH
Confidence            555555443 35789999999998753  344433233222 2221111111111111110                011


Q ss_pred             HHHHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHHc--------CCceeeeecCCChHHHHHHHHhhhcCCeeEEEEe
Q 037567          214 VDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQL--------GVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVAT  285 (374)
Q Consensus       214 ~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~--------~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t  285 (374)
                      ..+++..++   ..+.++||||++++.++.+++.+++.        +..+..+||+++.++|..++++|++|++++||||
T Consensus       260 ~~~~l~~l~---~~~~~~IVF~~sr~~ae~l~~~l~~~l~~~~~~l~~~v~~~hgg~~~~eR~~ie~~f~~G~i~vLVaT  336 (742)
T TIGR03817       260 AADLLADLV---AEGARTLTFVRSRRGAELVAAIARRLLGEVDPDLAERVAAYRAGYLPEDRRELERALRDGELLGVATT  336 (742)
T ss_pred             HHHHHHHHH---HCCCCEEEEcCCHHHHHHHHHHHHHHHHhhccccccchhheecCCCHHHHHHHHHHHHcCCceEEEEC
Confidence            223333333   35789999999999999999998764        5678899999999999999999999999999999


Q ss_pred             ccccccccccCccEEEEECCCCChhHHHHhhccCCCCCCceEEEEEeec
Q 037567          286 MAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYAR  334 (374)
Q Consensus       286 ~~~~~G~d~~~~~~vi~~~~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~  334 (374)
                      +++++|+|+|++++||+++.|.+...|+||+||+||.|+.|.++++...
T Consensus       337 d~lerGIDI~~vd~VI~~~~P~s~~~y~qRiGRaGR~G~~g~ai~v~~~  385 (742)
T TIGR03817       337 NALELGVDISGLDAVVIAGFPGTRASLWQQAGRAGRRGQGALVVLVARD  385 (742)
T ss_pred             chHhccCCcccccEEEEeCCCCCHHHHHHhccccCCCCCCcEEEEEeCC
Confidence            9999999999999999999999999999999999999999999988763

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.

>KOG0342 consensus ATP-dependent RNA helicase pitchoune [RNA processing and modification]

Probab=100.00  E-value=3.7e-49  Score=337.16  Aligned_cols=332  Identities=22%  Similarity=0.293  Sum_probs=265.8

Q ss_pred             hHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc----------cCCcEEEEcchHHHHHHHHHH
Q 037567            3 STLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV----------TGKTALVVSPLISLMQDQVMS   72 (374)
Q Consensus         3 ~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~----------~~~~~lil~P~~~l~~q~~~~   72 (374)
                      +++++ +||..+++.|...++.++.|++++..|.||+|||++|++|+.+          ..-.++|++|||+|+.|.+.+
T Consensus        95 kAi~~-~GF~~MT~VQ~~ti~pll~gkDvl~~AKTGtGKTlAFLiPaie~l~k~~~~~r~~~~vlIi~PTRELA~Q~~~e  173 (543)
T KOG0342|consen   95 KAIKE-MGFETMTPVQQKTIPPLLEGKDVLAAAKTGTGKTLAFLLPAIELLRKLKFKPRNGTGVLIICPTRELAMQIFAE  173 (543)
T ss_pred             HHHHh-cCccchhHHHHhhcCccCCCccceeeeccCCCceeeehhHHHHHHHhcccCCCCCeeEEEecccHHHHHHHHHH
Confidence            57778 9999999999999999999999999999999999999999875          244699999999999999888


Q ss_pred             HHHc-----CCceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchH
Q 037567           73 LKQR-----GINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRL  147 (374)
Q Consensus        73 ~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~  147 (374)
                      ++..     ++.+.++.++............ +++|+|+||++|.+.+++... +...+.+++|+|||+++.+.|+.   
T Consensus       174 ak~Ll~~h~~~~v~~viGG~~~~~e~~kl~k-~~niliATPGRLlDHlqNt~~-f~~r~~k~lvlDEADrlLd~GF~---  248 (543)
T KOG0342|consen  174 AKELLKYHESITVGIVIGGNNFSVEADKLVK-GCNILIATPGRLLDHLQNTSG-FLFRNLKCLVLDEADRLLDIGFE---  248 (543)
T ss_pred             HHHHHhhCCCcceEEEeCCccchHHHHHhhc-cccEEEeCCchHHhHhhcCCc-chhhccceeEeecchhhhhcccH---
Confidence            7653     5666777776666666665555 799999999999998887533 45566789999999999998865   


Q ss_pred             HHHHHHHHHHhc-CCCCeeEEEeecCcccHHHHHHhcCCCCCeEEEeccCC----CceeEEEEeecCCcchHHHHHHHHH
Q 037567          148 EYKQLDKLRTFL-LGVPFVALTATATEKVRIDIINSLKLKNPYVTIASFDR----KNLFYGVKVINRGQSFVDELVQEIL  222 (374)
Q Consensus       148 ~~~~~~~~~~~~-~~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~  222 (374)
                        .-+..+...+ ...+.++||||.++....-..-.+.-....+.......    ..+...+...+... . -.++..++
T Consensus       249 --~di~~Ii~~lpk~rqt~LFSAT~~~kV~~l~~~~L~~d~~~v~~~d~~~~~The~l~Qgyvv~~~~~-~-f~ll~~~L  324 (543)
T KOG0342|consen  249 --EDVEQIIKILPKQRQTLLFSATQPSKVKDLARGALKRDPVFVNVDDGGERETHERLEQGYVVAPSDS-R-FSLLYTFL  324 (543)
T ss_pred             --HHHHHHHHhccccceeeEeeCCCcHHHHHHHHHhhcCCceEeecCCCCCcchhhcccceEEeccccc-h-HHHHHHHH
Confidence              3344444433 37889999999999887533334443222233222221    12222222223322 2 33445555


Q ss_pred             HhhcCCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEEEE
Q 037567          223 KSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIH  302 (374)
Q Consensus       223 ~~~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~  302 (374)
                      +......++||||++......+++.|....++|..+||+.+...|..+...|.+.+.-||+||+...+|+|+|++++|+.
T Consensus       325 Kk~~~~~KiiVF~sT~~~vk~~~~lL~~~dlpv~eiHgk~~Q~kRT~~~~~F~kaesgIL~cTDVaARGlD~P~V~~VvQ  404 (543)
T KOG0342|consen  325 KKNIKRYKIIVFFSTCMSVKFHAELLNYIDLPVLEIHGKQKQNKRTSTFFEFCKAESGILVCTDVAARGLDIPDVDWVVQ  404 (543)
T ss_pred             HHhcCCceEEEEechhhHHHHHHHHHhhcCCchhhhhcCCcccccchHHHHHhhcccceEEecchhhccCCCCCceEEEE
Confidence            55445589999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ECCCCChhHHHHhhccCCCCCCceEEEEEeeccCCCccccee
Q 037567          303 YGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFYC  344 (374)
Q Consensus       303 ~~~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~~~~~~~~~  344 (374)
                      +++|.++.+|+||+||++|.|..|.+++++.+.+...++.+-
T Consensus       405 ~~~P~d~~~YIHRvGRTaR~gk~G~alL~l~p~El~Flr~LK  446 (543)
T KOG0342|consen  405 YDPPSDPEQYIHRVGRTAREGKEGKALLLLAPWELGFLRYLK  446 (543)
T ss_pred             eCCCCCHHHHHHHhccccccCCCceEEEEeChhHHHHHHHHh
Confidence            999999999999999999999999999999999987766653

>KOG0338 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=100.00  E-value=1.7e-49  Score=340.21  Aligned_cols=335  Identities=23%  Similarity=0.279  Sum_probs=272.0

Q ss_pred             hhHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhcccccc---------CCcEEEEcchHHHHHHHHHH
Q 037567            2 VSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVT---------GKTALVVSPLISLMQDQVMS   72 (374)
Q Consensus         2 ~~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~~---------~~~~lil~P~~~l~~q~~~~   72 (374)
                      .+++.. +||..|+|+|..+||..+-|++++-+|.||||||.+|++|++.+         .-+|||++|||+|+-|+..-
T Consensus       193 Lka~~~-lGy~~PTpIQ~a~IPvallgkDIca~A~TGsGKTAAF~lPiLERLlYrPk~~~~TRVLVL~PTRELaiQv~sV  271 (691)
T KOG0338|consen  193 LKACST-LGYKKPTPIQVATIPVALLGKDICACAATGSGKTAAFALPILERLLYRPKKVAATRVLVLVPTRELAIQVHSV  271 (691)
T ss_pred             HHHHHh-cCCCCCCchhhhcccHHhhcchhhheecccCCchhhhHHHHHHHHhcCcccCcceeEEEEeccHHHHHHHHHH
Confidence            345555 89999999999999999999999999999999999999998862         45799999999999987776


Q ss_pred             HHHc----CCceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHH
Q 037567           73 LKQR----GINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLE  148 (374)
Q Consensus        73 ~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~  148 (374)
                      .++.    .+.+++..++..-.. +.......|||+|+||++|.+++.+. ..+.+.++.++|+|||++|.+.|+.    
T Consensus       272 ~~qlaqFt~I~~~L~vGGL~lk~-QE~~LRs~PDIVIATPGRlIDHlrNs-~sf~ldsiEVLvlDEADRMLeegFa----  345 (691)
T KOG0338|consen  272 TKQLAQFTDITVGLAVGGLDLKA-QEAVLRSRPDIVIATPGRLIDHLRNS-PSFNLDSIEVLVLDEADRMLEEGFA----  345 (691)
T ss_pred             HHHHHhhccceeeeeecCccHHH-HHHHHhhCCCEEEecchhHHHHhccC-CCccccceeEEEechHHHHHHHHHH----
Confidence            6543    466666666554443 33445567999999999998877653 3566788999999999999997765    


Q ss_pred             HHHHHHHHHhcC-CCCeeEEEeecCcccHHHHHHhcCCCCCeEEEeccCC-CceeEEEE---eecCCcchHHHHHHHHHH
Q 037567          149 YKQLDKLRTFLL-GVPFVALTATATEKVRIDIINSLKLKNPYVTIASFDR-KNLFYGVK---VINRGQSFVDELVQEILK  223 (374)
Q Consensus       149 ~~~~~~~~~~~~-~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~---~~~~~~~~~~~~~~~~~~  223 (374)
                       ..++++....+ +.|.++||||+......  +..+.+..|.......+. ........   ..+.........+..++.
T Consensus       346 -demnEii~lcpk~RQTmLFSATMteeVkd--L~slSL~kPvrifvd~~~~~a~~LtQEFiRIR~~re~dRea~l~~l~~  422 (691)
T KOG0338|consen  346 -DEMNEIIRLCPKNRQTMLFSATMTEEVKD--LASLSLNKPVRIFVDPNKDTAPKLTQEFIRIRPKREGDREAMLASLIT  422 (691)
T ss_pred             -HHHHHHHHhccccccceeehhhhHHHHHH--HHHhhcCCCeEEEeCCccccchhhhHHHheeccccccccHHHHHHHHH
Confidence             67777777665 68999999999998764  555666666644443322 21111111   112333334555666666


Q ss_pred             hhcCCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEEEEE
Q 037567          224 SVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHY  303 (374)
Q Consensus       224 ~~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~~  303 (374)
                      .. -...++||+.++..|.++.-.|--.|++++-+||.++..+|-..++.|+++++++||||+.+++|+|++++.+||+|
T Consensus       423 rt-f~~~~ivFv~tKk~AHRl~IllGLlgl~agElHGsLtQ~QRlesL~kFk~~eidvLiaTDvAsRGLDI~gV~tVINy  501 (691)
T KOG0338|consen  423 RT-FQDRTIVFVRTKKQAHRLRILLGLLGLKAGELHGSLTQEQRLESLEKFKKEEIDVLIATDVASRGLDIEGVQTVINY  501 (691)
T ss_pred             Hh-cccceEEEEehHHHHHHHHHHHHHhhchhhhhcccccHHHHHHHHHHHHhccCCEEEEechhhccCCccceeEEEec
Confidence            54 36789999999999999999988889999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCChhHHHHhhccCCCCCCceEEEEEeeccCCCcccceeccc
Q 037567          304 GCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFYCGES  347 (374)
Q Consensus       304 ~~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~~~~~~~~~~~~  347 (374)
                      .+|.+...|+||+||+.|.|..|..++++..+|...++.++.+.
T Consensus       502 ~mP~t~e~Y~HRVGRTARAGRaGrsVtlvgE~dRkllK~iik~~  545 (691)
T KOG0338|consen  502 AMPKTIEHYLHRVGRTARAGRAGRSVTLVGESDRKLLKEIIKSS  545 (691)
T ss_pred             cCchhHHHHHHHhhhhhhcccCcceEEEeccccHHHHHHHHhhh
Confidence            99999999999999999999999999999999988888887763

>KOG0352 consensus ATP-dependent DNA helicase [Replication, recombination and repair]

Probab=100.00  E-value=5.5e-48  Score=324.47  Aligned_cols=372  Identities=39%  Similarity=0.631  Sum_probs=302.0

Q ss_pred             hhHHHhHcCCCCC-chhHHHHHHHHHc-CCCEEEEccCCCCchhhhhccccccCCcEEEEcchHHHHHHHHHHHHHcCCc
Q 037567            2 VSTLKKYFGYSVF-RPYQKDVIQRIIE-KRDCLVVMATGSGKSLCYQLPPLVTGKTALVVSPLISLMQDQVMSLKQRGIN   79 (374)
Q Consensus         2 ~~~l~~~~~~~~~-~~~Q~~~~~~~~~-~~~~l~~a~tGsGKT~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~   79 (374)
                      .++|++.||++++ ++.|++|+..+.. ++++.+++|||+||+++|.||++..+...+|+.|..+|+.+..+.+.++...
T Consensus         8 reaLKK~FGh~kFKs~LQE~A~~c~VK~k~DVyVsMPTGaGKSLCyQLPaL~~~gITIV~SPLiALIkDQiDHL~~LKVp   87 (641)
T KOG0352|consen    8 REALKKLFGHKKFKSRLQEQAINCIVKRKCDVYVSMPTGAGKSLCYQLPALVHGGITIVISPLIALIKDQIDHLKRLKVP   87 (641)
T ss_pred             HHHHHHHhCchhhcChHHHHHHHHHHhccCcEEEeccCCCchhhhhhchHHHhCCeEEEehHHHHHHHHHHHHHHhcCCc
Confidence            4789999999986 5699999998876 5699999999999999999999998889999999999999999999988777


Q ss_pred             eEEcCCCCCchhhh-----hhhhcCCeeEEEEcCcccccCchh-hHHH-HHhcCccEEEEeccchhhcccCcchHHHHHH
Q 037567           80 AEFLGSAQTDSSVQ-----TKAETGYFQLLFMTPEKACIIPIS-FWSK-LLKAGVCLFAVDEAHCISEWGHDFRLEYKQL  152 (374)
Q Consensus        80 ~~~~~~~~~~~~~~-----~~~~~~~~~i~i~T~~~l~~~~~~-~~~~-~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~  152 (374)
                      ...+.+..+..+..     ......+..+++.|||........ .... .....+.++|+||||.+.+||.++++.+..+
T Consensus        88 ~~SLNSKlSt~ER~ri~~DL~~ekp~~K~LYITPE~AAt~~FQ~lLn~L~~r~~L~Y~vVDEAHCVSQWGHDFRPDYL~L  167 (641)
T KOG0352|consen   88 CESLNSKLSTVERSRIMGDLAKEKPTIKMLYITPEGAATDGFQKLLNGLANRDVLRYIVVDEAHCVSQWGHDFRPDYLTL  167 (641)
T ss_pred             hhHhcchhhHHHHHHHHHHHHhcCCceeEEEEchhhhhhhhHHHHHHHHhhhceeeeEEechhhhHhhhccccCcchhhh
Confidence            66665544433321     112234568999999976443221 1111 1234478999999999999999999999999


Q ss_pred             HHHHHhcCCCCeeEEEeecCcccHHHHHHhcCCCCCeEEE-eccCCCceeEEEEeecC---CcchHHHHHHHHHHh----
Q 037567          153 DKLRTFLLGVPFVALTATATEKVRIDIINSLKLKNPYVTI-ASFDRKNLFYGVKVINR---GQSFVDELVQEILKS----  224 (374)
Q Consensus       153 ~~~~~~~~~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~----  224 (374)
                      .+++...++.+++++|||.++...+++...+.+..|.-.. ...=+.++.+.+...+.   ....+.+.....+..    
T Consensus       168 G~LRS~~~~vpwvALTATA~~~VqEDi~~qL~L~~PVAiFkTP~FR~NLFYD~~~K~~I~D~~~~LaDF~~~~LG~~~~~  247 (641)
T KOG0352|consen  168 GSLRSVCPGVPWVALTATANAKVQEDIAFQLKLRNPVAIFKTPTFRDNLFYDNHMKSFITDCLTVLADFSSSNLGKHEKA  247 (641)
T ss_pred             hhHHhhCCCCceEEeecccChhHHHHHHHHHhhcCcHHhccCcchhhhhhHHHHHHHHhhhHhHhHHHHHHHhcCChhhh
Confidence            9999999999999999999999999999999998886433 33334555544433222   111222222222221    


Q ss_pred             ----hcCCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEE
Q 037567          225 ----VAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHV  300 (374)
Q Consensus       225 ----~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~v  300 (374)
                          ....+-.||||.+++.++.++-.|...|+++..+|.++...+|..+-++|.+++..|+++|...++|+|-|++++|
T Consensus       248 ~~~~K~~~GCGIVYCRTR~~cEq~AI~l~~~Gi~A~AYHAGLK~~ERTeVQe~WM~~~~PvI~AT~SFGMGVDKp~VRFV  327 (641)
T KOG0352|consen  248 SQNKKTFTGCGIVYCRTRNECEQVAIMLEIAGIPAMAYHAGLKKKERTEVQEKWMNNEIPVIAATVSFGMGVDKPDVRFV  327 (641)
T ss_pred             hcCCCCcCcceEEEeccHHHHHHHHHHhhhcCcchHHHhcccccchhHHHHHHHhcCCCCEEEEEeccccccCCcceeEE
Confidence                0123569999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEECCCCChhHHHHhhccCCCCCCceEEEEEeeccCCCcccceeccccchH--------HHHHHHHHHHHHHHHhhhccc
Q 037567          301 IHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFYCGESQTEN--------QRTAIMESLLAAQRYCLLTTC  372 (374)
Q Consensus       301 i~~~~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~--------~~~~~~~~l~~~~~~~~~~~~  372 (374)
                      |++++|.|+.-|.|-.||+||.|.+..|-++|.+.|.+.+.++++......        ..+....-+..|-.|||.+.|
T Consensus       328 iHW~~~qn~AgYYQESGRAGRDGk~SyCRLYYsR~D~~~i~FLi~~e~aklrek~~ke~~~k~~I~~F~k~~eFCE~~~C  407 (641)
T KOG0352|consen  328 IHWSPSQNLAGYYQESGRAGRDGKRSYCRLYYSRQDKNALNFLVSGELAKLREKAKKEMQIKSIITGFAKMLEFCESARC  407 (641)
T ss_pred             EecCchhhhHHHHHhccccccCCCccceeeeecccchHHHHHHHhhHHHHHHHhcchhhhHHHHHHHHHHHHHHHHHccc
Confidence            999999999999999999999999999999999999999999987554333        334456778999999999999


Q ss_pred             C
Q 037567          373 R  373 (374)
Q Consensus       373 ~  373 (374)
                      |
T Consensus       408 R  408 (641)
T KOG0352|consen  408 R  408 (641)
T ss_pred             c
Confidence            9

>KOG0340 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=100.00  E-value=3e-48  Score=318.63  Aligned_cols=334  Identities=23%  Similarity=0.309  Sum_probs=260.5

Q ss_pred             ChhHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhcccccc------CCcEEEEcchHHHHHHHHHHHH
Q 037567            1 MVSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVT------GKTALVVSPLISLMQDQVMSLK   74 (374)
Q Consensus         1 l~~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~~------~~~~lil~P~~~l~~q~~~~~~   74 (374)
                      |++.++. +|+.+|+|+|..++|.+++|+|++=+|.||||||.+|.+|++.+      +.-++|++||++|+.|..+.|.
T Consensus        18 lve~l~~-l~i~~pTpiQ~~cIpkILeGrdcig~AkTGsGKT~AFaLPil~rLsedP~giFalvlTPTrELA~QiaEQF~   96 (442)
T KOG0340|consen   18 LVEQLKA-LGIKKPTPIQQACIPKILEGRDCIGCAKTGSGKTAAFALPILNRLSEDPYGIFALVLTPTRELALQIAEQFI   96 (442)
T ss_pred             HHHHHHH-hcCCCCCchHhhhhHHHhcccccccccccCCCcchhhhHHHHHhhccCCCcceEEEecchHHHHHHHHHHHH
Confidence            4667777 89999999999999999999999999999999999999999974      4558999999999999999998


Q ss_pred             HcC----CceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHH--HHHhcCccEEEEeccchhhcccCcchHH
Q 037567           75 QRG----INAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWS--KLLKAGVCLFAVDEAHCISEWGHDFRLE  148 (374)
Q Consensus        75 ~~~----~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~--~~~~~~~~~vviDE~h~~~~~~~~~~~~  148 (374)
                      ..|    .+..++.++ .+.-.+.......++++++||+++..++.+...  ...++++.++|+|||+.+.+..+.    
T Consensus        97 alGk~l~lK~~vivGG-~d~i~qa~~L~~rPHvVvatPGRlad~l~sn~~~~~~~~~rlkflVlDEADrvL~~~f~----  171 (442)
T KOG0340|consen   97 ALGKLLNLKVSVIVGG-TDMIMQAAILSDRPHVVVATPGRLADHLSSNLGVCSWIFQRLKFLVLDEADRVLAGCFP----  171 (442)
T ss_pred             HhcccccceEEEEEcc-HHHhhhhhhcccCCCeEecCccccccccccCCccchhhhhceeeEEecchhhhhccchh----
Confidence            764    444444443 333344555667799999999999988776422  345678999999999999875443    


Q ss_pred             HHHHHHHHHhcC-CCCeeEEEeecCcccHHHHHHhcCCCC--CeEEEeccCC---CceeEEEEeecCCcchHHHHHHHHH
Q 037567          149 YKQLDKLRTFLL-GVPFVALTATATEKVRIDIINSLKLKN--PYVTIASFDR---KNLFYGVKVINRGQSFVDELVQEIL  222 (374)
Q Consensus       149 ~~~~~~~~~~~~-~~~~i~~SaT~~~~~~~~~~~~~~~~~--~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~  222 (374)
                       ..+.-+.+..| ..+.++||||.......  +.......  ........+.   ..+...  ............+.+++
T Consensus       172 -d~L~~i~e~lP~~RQtLlfSATitd~i~q--l~~~~i~k~~a~~~e~~~~vstvetL~q~--yI~~~~~vkdaYLv~~L  246 (442)
T KOG0340|consen  172 -DILEGIEECLPKPRQTLLFSATITDTIKQ--LFGCPITKSIAFELEVIDGVSTVETLYQG--YILVSIDVKDAYLVHLL  246 (442)
T ss_pred             -hHHhhhhccCCCccceEEEEeehhhHHHH--hhcCCcccccceEEeccCCCCchhhhhhh--eeecchhhhHHHHHHHH
Confidence             33444444444 45899999999876643  22222222  1111111111   111111  11222233445555555


Q ss_pred             HhhcC--CCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEE
Q 037567          223 KSVAG--AGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHV  300 (374)
Q Consensus       223 ~~~~~--~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~v  300 (374)
                      ....+  .+.++||+++..+++.++..|+..++.++.+||.++.++|-..+.+|+.+..+|||||+.+++|+|+|.++.|
T Consensus       247 r~~~~~~~~simIFvnttr~cQ~l~~~l~~le~r~~~lHs~m~Q~eR~~aLsrFrs~~~~iliaTDVAsRGLDIP~V~LV  326 (442)
T KOG0340|consen  247 RDFENKENGSIMIFVNTTRECQLLSMTLKNLEVRVVSLHSQMPQKERLAALSRFRSNAARILIATDVASRGLDIPTVELV  326 (442)
T ss_pred             hhhhhccCceEEEEeehhHHHHHHHHHHhhhceeeeehhhcchHHHHHHHHHHHhhcCccEEEEechhhcCCCCCceeEE
Confidence            55544  7899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEECCCCChhHHHHhhccCCCCCCceEEEEEeeccCCCcccceec
Q 037567          301 IHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFYCG  345 (374)
Q Consensus       301 i~~~~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~~~~~~~~~~  345 (374)
                      ++++.|.++.+|+||+||+.|.|..|.++.+++..|.+.+..+.+
T Consensus       327 vN~diPr~P~~yiHRvGRtARAGR~G~aiSivt~rDv~l~~aiE~  371 (442)
T KOG0340|consen  327 VNHDIPRDPKDYIHRVGRTARAGRKGMAISIVTQRDVELLQAIEE  371 (442)
T ss_pred             EecCCCCCHHHHHHhhcchhcccCCcceEEEechhhHHHHHHHHH
Confidence            999999999999999999999999999999999999877665544

>KOG0335 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=100.00  E-value=1e-48  Score=339.67  Aligned_cols=326  Identities=23%  Similarity=0.305  Sum_probs=258.1

Q ss_pred             cCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhcccccc----------------CCcEEEEcchHHHHHHHHHH
Q 037567            9 FGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVT----------------GKTALVVSPLISLMQDQVMS   72 (374)
Q Consensus         9 ~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~~----------------~~~~lil~P~~~l~~q~~~~   72 (374)
                      .++..|+|+|..++|.+..|++.+.+|+||||||.+|++|++..                .+.++|++||++|+.|.+.+
T Consensus        92 ~~~~~ptpvQk~sip~i~~Grdl~acAqTGsGKT~aFLiPii~~~~~~~~~~~~~~~~~~~P~~lIlapTReL~~Qi~ne  171 (482)
T KOG0335|consen   92 SGYTKPTPVQKYSIPIISGGRDLMACAQTGSGKTAAFLIPIISYLLDEGPEDRGESGGGVYPRALILAPTRELVDQIYNE  171 (482)
T ss_pred             ccccCCCcceeeccceeecCCceEEEccCCCcchHHHHHHHHHHHHhcCcccCcccCCCCCCceEEEeCcHHHhhHHHHH
Confidence            68999999999999999999999999999999999999998741                47899999999999999999


Q ss_pred             HHHc----CCceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhc-ccCcchH
Q 037567           73 LKQR----GINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISE-WGHDFRL  147 (374)
Q Consensus        73 ~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~-~~~~~~~  147 (374)
                      .+++    +.....+.++ .....+......+|+|+|+||++|.++...  ..+.+.++.++|+|||+.+.+ .++.   
T Consensus       172 a~k~~~~s~~~~~~~ygg-~~~~~q~~~~~~gcdIlvaTpGrL~d~~e~--g~i~l~~~k~~vLDEADrMlD~mgF~---  245 (482)
T KOG0335|consen  172 ARKFSYLSGMKSVVVYGG-TDLGAQLRFIKRGCDILVATPGRLKDLIER--GKISLDNCKFLVLDEADRMLDEMGFE---  245 (482)
T ss_pred             HHhhcccccceeeeeeCC-cchhhhhhhhccCccEEEecCchhhhhhhc--ceeehhhCcEEEecchHHhhhhcccc---
Confidence            9876    3333444444 333344555667899999999999999777  777888999999999999988 6655   


Q ss_pred             HHHHHHHHHHhc-----CCCCeeEEEeecCcccHHHHHHhcCCCCCe---EEEeccCCCceeEEEEeecCCcchHHHHHH
Q 037567          148 EYKQLDKLRTFL-----LGVPFVALTATATEKVRIDIINSLKLKNPY---VTIASFDRKNLFYGVKVINRGQSFVDELVQ  219 (374)
Q Consensus       148 ~~~~~~~~~~~~-----~~~~~i~~SaT~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  219 (374)
                        ..+.++....     .+.+.++||||.+..... ....+....+.   +........++...+..... .....+++.
T Consensus       246 --p~Ir~iv~~~~~~~~~~~qt~mFSAtfp~~iq~-l~~~fl~~~yi~laV~rvg~~~~ni~q~i~~V~~-~~kr~~Lld  321 (482)
T KOG0335|consen  246 --PQIRKIVEQLGMPPKNNRQTLLFSATFPKEIQR-LAADFLKDNYIFLAVGRVGSTSENITQKILFVNE-MEKRSKLLD  321 (482)
T ss_pred             --ccHHHHhcccCCCCccceeEEEEeccCChhhhh-hHHHHhhccceEEEEeeeccccccceeEeeeecc-hhhHHHHHH
Confidence              3344443333     257899999999998775 33333333232   22233345555555544443 233344444


Q ss_pred             HHHHhhc--CCC-----cEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccc
Q 037567          220 EILKSVA--GAG-----SIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGI  292 (374)
Q Consensus       220 ~~~~~~~--~~~-----~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~  292 (374)
                      .+.....  ..+     +++|||.+++.+..++..|...++++..+||+.+..+|.+.++.|+.|+..++|||+++.+|+
T Consensus       322 ll~~~~~~~~~~~~~~e~tlvFvEt~~~~d~l~~~l~~~~~~~~sIhg~~tq~er~~al~~Fr~g~~pvlVaT~VaaRGl  401 (482)
T KOG0335|consen  322 LLNKDDGPPSDGEPKWEKTLVFVETKRGADELAAFLSSNGYPAKSIHGDRTQIEREQALNDFRNGKAPVLVATNVAARGL  401 (482)
T ss_pred             HhhcccCCcccCCcccceEEEEeeccchhhHHHHHHhcCCCCceeecchhhhhHHHHHHHHhhcCCcceEEEehhhhcCC
Confidence            4433221  233     899999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccCccEEEEECCCCChhHHHHhhccCCCCCCceEEEEEeeccCCCccccee
Q 037567          293 DKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFYC  344 (374)
Q Consensus       293 d~~~~~~vi~~~~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~~~~~~~~~  344 (374)
                      |+|++++||+|++|.+..+|+|||||+||.|+.|.+..|++..+....+.+.
T Consensus       402 Di~~V~hVInyDmP~d~d~YvHRIGRTGR~Gn~G~atsf~n~~~~~i~~~L~  453 (482)
T KOG0335|consen  402 DIPNVKHVINYDMPADIDDYVHRIGRTGRVGNGGRATSFFNEKNQNIAKALV  453 (482)
T ss_pred             CCCCCceeEEeecCcchhhHHHhccccccCCCCceeEEEeccccchhHHHHH
Confidence            9999999999999999999999999999999999999999965554444443

>KOG0326 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=100.00  E-value=1.2e-47  Score=310.92  Aligned_cols=331  Identities=21%  Similarity=0.229  Sum_probs=262.5

Q ss_pred             cCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhcccccc------CCcEEEEcchHHHHHHHHHHHHHc----CC
Q 037567            9 FGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVT------GKTALVVSPLISLMQDQVMSLKQR----GI   78 (374)
Q Consensus         9 ~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~~------~~~~lil~P~~~l~~q~~~~~~~~----~~   78 (374)
                      .||+.|.|+|++++|..+.|++++..|..|+|||-+|.+|.+.+      .-+.+|++|+++|+.|..+-....    ++
T Consensus       103 ~G~ekPSPiQeesIPiaLtGrdiLaRaKNGTGKT~a~~IP~Lekid~~~~~IQ~~ilVPtrelALQtSqvc~~lskh~~i  182 (459)
T KOG0326|consen  103 KGFEKPSPIQEESIPIALTGRDILARAKNGTGKTAAYCIPVLEKIDPKKNVIQAIILVPTRELALQTSQVCKELSKHLGI  182 (459)
T ss_pred             hccCCCCCccccccceeecchhhhhhccCCCCCccceechhhhhcCccccceeEEEEeecchhhHHHHHHHHHHhcccCe
Confidence            69999999999999999999999999999999999999998874      446899999999999877666543    55


Q ss_pred             ceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHHh
Q 037567           79 NAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTF  158 (374)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~  158 (374)
                      .+-+.+++..-.... .......+++|+||+++.++...  .-..++...++|+|||+.+.+..+.     ..+..+..+
T Consensus       183 ~vmvttGGT~lrDDI-~Rl~~~VH~~vgTPGRIlDL~~K--gVa~ls~c~~lV~DEADKlLs~~F~-----~~~e~li~~  254 (459)
T KOG0326|consen  183 KVMVTTGGTSLRDDI-MRLNQTVHLVVGTPGRILDLAKK--GVADLSDCVILVMDEADKLLSVDFQ-----PIVEKLISF  254 (459)
T ss_pred             EEEEecCCcccccce-eeecCceEEEEcCChhHHHHHhc--ccccchhceEEEechhhhhhchhhh-----hHHHHHHHh
Confidence            555555554443332 33456689999999999888665  4455678889999999999875544     455666666


Q ss_pred             cC-CCCeeEEEeecCcccHHHHHHhcCCCCCeEEEeccCCCceeEEEEeecCCcchHHHHHHHHHHhhcCCCcEEEEecc
Q 037567          159 LL-GVPFVALTATATEKVRIDIINSLKLKNPYVTIASFDRKNLFYGVKVINRGQSFVDELVQEILKSVAGAGSIIVYCMT  237 (374)
Q Consensus       159 ~~-~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lVf~~~  237 (374)
                      +| +.+++++|||.+......+...+..+..+....+.....+...+.+.  ........++.+..++ +-.+.||||++
T Consensus       255 lP~~rQillySATFP~tVk~Fm~~~l~kPy~INLM~eLtl~GvtQyYafV--~e~qKvhCLntLfskL-qINQsIIFCNS  331 (459)
T KOG0326|consen  255 LPKERQILLYSATFPLTVKGFMDRHLKKPYEINLMEELTLKGVTQYYAFV--EERQKVHCLNTLFSKL-QINQSIIFCNS  331 (459)
T ss_pred             CCccceeeEEecccchhHHHHHHHhccCcceeehhhhhhhcchhhheeee--chhhhhhhHHHHHHHh-cccceEEEecc
Confidence            65 68999999999988775445444433222222222222222111111  1233456677777766 67788999999


Q ss_pred             hhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEEEEECCCCChhHHHHhhc
Q 037567          238 IKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESG  317 (374)
Q Consensus       238 ~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~~~~p~s~~~~~Q~~G  317 (374)
                      .+.++.+++++.+.|+.+..+|+.|..+.|+.+..+|++|..+.||||+.+.+|+|++++++||+++.|.+++.|.||+|
T Consensus       332 ~~rVELLAkKITelGyscyyiHakM~Q~hRNrVFHdFr~G~crnLVctDL~TRGIDiqavNvVINFDfpk~aEtYLHRIG  411 (459)
T KOG0326|consen  332 TNRVELLAKKITELGYSCYYIHAKMAQEHRNRVFHDFRNGKCRNLVCTDLFTRGIDIQAVNVVINFDFPKNAETYLHRIG  411 (459)
T ss_pred             chHhHHHHHHHHhccchhhHHHHHHHHhhhhhhhhhhhccccceeeehhhhhcccccceeeEEEecCCCCCHHHHHHHcc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCCCceEEEEEeeccCCCcccceeccccch
Q 037567          318 RCGRDGIASVCWLYYARSNFAKGDFYCGESQTE  350 (374)
Q Consensus       318 R~~R~~~~g~~~~~~~~~~~~~~~~~~~~~~~~  350 (374)
                      |.||+|..|.++.+++.+|...+..+..++..+
T Consensus       412 RsGRFGhlGlAInLityedrf~L~~IE~eLGtE  444 (459)
T KOG0326|consen  412 RSGRFGHLGLAINLITYEDRFNLYRIEQELGTE  444 (459)
T ss_pred             CCccCCCcceEEEEEehhhhhhHHHHHHHhccc
Confidence            999999999999999999887777776655544

>KOG0348 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=100.00  E-value=1.4e-46  Score=323.99  Aligned_cols=336  Identities=23%  Similarity=0.264  Sum_probs=251.3

Q ss_pred             ChhHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc------------cCCcEEEEcchHHHHHH
Q 037567            1 MVSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV------------TGKTALVVSPLISLMQD   68 (374)
Q Consensus         1 l~~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~------------~~~~~lil~P~~~l~~q   68 (374)
                      |++.|...+++..|+.+|.+++|.+++|+|++|.++||||||++|++|+.+            .+.-+||++|||+|+.|
T Consensus       147 lv~~L~~~m~i~~pTsVQkq~IP~lL~grD~lV~aQTGSGKTLAYllPiVq~Lq~m~~ki~Rs~G~~ALVivPTREL~~Q  226 (708)
T KOG0348|consen  147 LVSHLNTKMKISAPTSVQKQAIPVLLEGRDALVRAQTGSGKTLAYLLPIVQSLQAMEPKIQRSDGPYALVIVPTRELALQ  226 (708)
T ss_pred             HHHHHHHHhccCccchHhhcchhhhhcCcceEEEcCCCCcccHHHHHHHHHHHHhcCccccccCCceEEEEechHHHHHH
Confidence            467899999999999999999999999999999999999999999999875            26779999999999999


Q ss_pred             HHHHHHHcCCce-----EEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccC
Q 037567           69 QVMSLKQRGINA-----EFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGH  143 (374)
Q Consensus        69 ~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~  143 (374)
                      .++.+++.-...     +++.++.... ........+++|+|+||++|.+.+.+- ..+.++.++.+|+||++.+.+-|+
T Consensus       227 ~y~~~qKLl~~~hWIVPg~lmGGEkkK-SEKARLRKGiNILIgTPGRLvDHLknT-~~i~~s~LRwlVlDEaDrlleLGf  304 (708)
T KOG0348|consen  227 IYETVQKLLKPFHWIVPGVLMGGEKKK-SEKARLRKGINILIGTPGRLVDHLKNT-KSIKFSRLRWLVLDEADRLLELGF  304 (708)
T ss_pred             HHHHHHHHhcCceEEeeceeecccccc-cHHHHHhcCceEEEcCchHHHHHHhcc-chheeeeeeEEEecchhHHHhccc
Confidence            999998763222     2333333332 233445567999999999998887653 455667899999999999998776


Q ss_pred             cchHHHHHHHHHHHhc-----------CCCCeeEEEeecCcccHHHHHHhcCCCCCeEEEeccCCC--------------
Q 037567          144 DFRLEYKQLDKLRTFL-----------LGVPFVALTATATEKVRIDIINSLKLKNPYVTIASFDRK--------------  198 (374)
Q Consensus       144 ~~~~~~~~~~~~~~~~-----------~~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~~~~--------------  198 (374)
                      +.  .+..+-......           +..+.+++|||+......  +..+.+.++..+..+....              
T Consensus       305 ek--dit~Il~~v~~~~~~e~~~~~lp~q~q~mLlSATLtd~V~r--La~~sLkDpv~I~ld~s~~~~~p~~~a~~ev~~  380 (708)
T KOG0348|consen  305 EK--DITQILKAVHSIQNAECKDPKLPHQLQNMLLSATLTDGVNR--LADLSLKDPVYISLDKSHSQLNPKDKAVQEVDD  380 (708)
T ss_pred             hh--hHHHHHHHHhhccchhcccccccHHHHhHhhhhhhHHHHHH--HhhccccCceeeeccchhhhcCcchhhhhhcCC
Confidence            52  222222222111           125679999999887754  6666666665444111000              


Q ss_pred             --------------ceeEEEEeecCCcc--hHHHHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHHc-----------
Q 037567          199 --------------NLFYGVKVINRGQS--FVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQL-----------  251 (374)
Q Consensus       199 --------------~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~-----------  251 (374)
                                    .+..++.+.+..-.  .+..++....+. ....++|||+.+.+.++-=+..|...           
T Consensus       381 ~~~~~~l~~~~iPeqL~qry~vVPpKLRLV~Laa~L~~~~k~-~~~qk~iVF~S~~d~VeFHy~lf~~~l~~~~e~~s~~  459 (708)
T KOG0348|consen  381 GPAGDKLDSFAIPEQLLQRYTVVPPKLRLVALAALLLNKVKF-EEKQKMIVFFSCSDSVEFHYSLFSEALLSHLEGSSGA  459 (708)
T ss_pred             cccccccccccCcHHhhhceEecCCchhHHHHHHHHHHHhhh-hhhceeEEEEechhHHHHHHHHHHhhhhcccccccCC
Confidence                          01111111111111  112333333333 24568999999999888777776542           


Q ss_pred             -----------CCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEEEEECCCCChhHHHHhhccCC
Q 037567          252 -----------GVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCG  320 (374)
Q Consensus       252 -----------~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~~~~p~s~~~~~Q~~GR~~  320 (374)
                                 +.++..+||+|+.++|..+++.|...+-.||+||+.+++|+|+|.+++||.|++|.+..+|+||+||+.
T Consensus       460 ~~s~g~~~l~~~~k~~rLHGsm~QeeRts~f~~Fs~~~~~VLLcTDVAaRGLDlP~V~~vVQYd~P~s~adylHRvGRTA  539 (708)
T KOG0348|consen  460 PDSEGLPPLFMDLKFYRLHGSMEQEERTSVFQEFSHSRRAVLLCTDVAARGLDLPHVGLVVQYDPPFSTADYLHRVGRTA  539 (708)
T ss_pred             cccCCChhhhhcceEEEecCchhHHHHHHHHHhhccccceEEEehhhhhccCCCCCcCeEEEeCCCCCHHHHHHHhhhhh
Confidence                       334778999999999999999999998889999999999999999999999999999999999999999


Q ss_pred             CCCCceEEEEEeeccCCCcccce
Q 037567          321 RDGIASVCWLYYARSNFAKGDFY  343 (374)
Q Consensus       321 R~~~~g~~~~~~~~~~~~~~~~~  343 (374)
                      |.|..|.+++|+.+.+.++++.+
T Consensus       540 RaG~kG~alLfL~P~Eaey~~~l  562 (708)
T KOG0348|consen  540 RAGEKGEALLFLLPSEAEYVNYL  562 (708)
T ss_pred             hccCCCceEEEecccHHHHHHHH
Confidence            99999999999999987754443

>KOG0353 consensus ATP-dependent DNA helicase [General function prediction only]

Probab=100.00  E-value=2e-45  Score=305.42  Aligned_cols=366  Identities=40%  Similarity=0.659  Sum_probs=316.1

Q ss_pred             hHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccccCCcEEEEcchHHHHHHHHHHHHHcCCceEE
Q 037567            3 STLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVTGKTALVVSPLISLMQDQVMSLKQRGINAEF   82 (374)
Q Consensus         3 ~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~   82 (374)
                      .-|++.|..++++|.|..++++...++++++..|||.||+++|.+|++....-+|+++|..+|.++..-.+++.|+....
T Consensus        84 ~ilk~~f~lekfrplq~~ain~~ma~ed~~lil~tgggkslcyqlpal~adg~alvi~plislmedqil~lkqlgi~as~  163 (695)
T KOG0353|consen   84 DILKEQFHLEKFRPLQLAAINATMAGEDAFLILPTGGGKSLCYQLPALCADGFALVICPLISLMEDQILQLKQLGIDASM  163 (695)
T ss_pred             HHHHHHhhHHhcChhHHHHhhhhhccCceEEEEeCCCccchhhhhhHHhcCCceEeechhHHHHHHHHHHHHHhCcchhh
Confidence            45788899999999999999999999999999999999999999999999999999999999999999999999999887


Q ss_pred             cCCCCCchhhhh-----hhhcCCeeEEEEcCcccccC---chhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHH
Q 037567           83 LGSAQTDSSVQT-----KAETGYFQLLFMTPEKACII---PISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDK  154 (374)
Q Consensus        83 ~~~~~~~~~~~~-----~~~~~~~~i~i~T~~~l~~~---~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~  154 (374)
                      +......++...     -..+..+.+++.||+++...   ++..........+.++-+||+|...+||.++++.+..+..
T Consensus       164 lnansske~~k~v~~~i~nkdse~kliyvtpekiaksk~~mnkleka~~~~~~~~iaidevhccsqwghdfr~dy~~l~i  243 (695)
T KOG0353|consen  164 LNANSSKEEAKRVEAAITNKDSEFKLIYVTPEKIAKSKKFMNKLEKALEAGFFKLIAIDEVHCCSQWGHDFRPDYKALGI  243 (695)
T ss_pred             ccCcccHHHHHHHHHHHcCCCceeEEEEecHHHHHHHHHHHHHHHHHhhcceeEEEeecceeehhhhCcccCcchHHHHH
Confidence            766555443211     12235678999999988543   2333334445668899999999999999999999999999


Q ss_pred             HHHhcCCCCeeEEEeecCcccHHHHHHhcCCCCCeEEEeccCCCceeEEEEeecCCcchHHHHHHHHHHhhcCCCcEEEE
Q 037567          155 LRTFLLGVPFVALTATATEKVRIDIINSLKLKNPYVTIASFDRKNLFYGVKVINRGQSFVDELVQEILKSVAGAGSIIVY  234 (374)
Q Consensus       155 ~~~~~~~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lVf  234 (374)
                      +...+++.+++++|||.......+....+++.........++++++.+.+...+.......+-+..+++.-..+...|||
T Consensus       244 lkrqf~~~~iigltatatn~vl~d~k~il~ie~~~tf~a~fnr~nl~yev~qkp~n~dd~~edi~k~i~~~f~gqsgiiy  323 (695)
T KOG0353|consen  244 LKRQFKGAPIIGLTATATNHVLDDAKDILCIEAAFTFRAGFNRPNLKYEVRQKPGNEDDCIEDIAKLIKGDFAGQSGIIY  323 (695)
T ss_pred             HHHhCCCCceeeeehhhhcchhhHHHHHHhHHhhheeecccCCCCceeEeeeCCCChHHHHHHHHHHhccccCCCcceEE
Confidence            99999999999999999999988888889998888899999999999999887766554443333343333467889999


Q ss_pred             ecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEEEEECCCCChhHHHH
Q 037567          235 CMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQ  314 (374)
Q Consensus       235 ~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~~~~p~s~~~~~Q  314 (374)
                      |-+.+++++++..|+.+|+.+..+|..+.+.++....+.|..|++.|+|+|-+.++|+|-|++++||++++|.|..+|.|
T Consensus       324 c~sq~d~ekva~alkn~gi~a~~yha~lep~dks~~hq~w~a~eiqvivatvafgmgidkpdvrfvihhsl~ksienyyq  403 (695)
T KOG0353|consen  324 CFSQKDCEKVAKALKNHGIHAGAYHANLEPEDKSGAHQGWIAGEIQVIVATVAFGMGIDKPDVRFVIHHSLPKSIENYYQ  403 (695)
T ss_pred             EeccccHHHHHHHHHhcCccccccccccCccccccccccccccceEEEEEEeeecccCCCCCeeEEEecccchhHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             -------------------------------------------hhccCCCCCCceEEEEEeeccCCCcccceeccccchH
Q 037567          315 -------------------------------------------ESGRCGRDGIASVCWLYYARSNFAKGDFYCGESQTEN  351 (374)
Q Consensus       315 -------------------------------------------~~GR~~R~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~  351 (374)
                                                                 -.||+||.+.+..|+++|.-.|+-+.      +....
T Consensus       404 asarillrmtkqknksdtggstqinilevctnfkiffavfsekesgragrd~~~a~cilyy~~~difk~------ssmv~  477 (695)
T KOG0353|consen  404 ASARILLRMTKQKNKSDTGGSTQINILEVCTNFKIFFAVFSEKESGRAGRDDMKADCILYYGFADIFKI------SSMVQ  477 (695)
T ss_pred             HHHHHHHHHhhhcccccCCCcceeehhhhhccceeeeeeecchhccccccCCCcccEEEEechHHHHhH------HHHHH
Confidence                                                       57999999999999999988765443      34445


Q ss_pred             HHHHHHHHHHHHHHHhhh-cccCC
Q 037567          352 QRTAIMESLLAAQRYCLL-TTCRR  374 (374)
Q Consensus       352 ~~~~~~~~l~~~~~~~~~-~~~~~  374 (374)
                      ....-.++|-+|.+||.. +.|||
T Consensus       478 ~e~~g~q~ly~mv~y~~d~s~crr  501 (695)
T KOG0353|consen  478 MENTGIQKLYEMVRYAADISKCRR  501 (695)
T ss_pred             HHhhhHHHHHHHHHHHhhhHHHHH
Confidence            556678899999999998 69997

>PRK13767 ATP-dependent helicase; Provisional

Probab=100.00  E-value=2.5e-44  Score=350.01  Aligned_cols=309  Identities=23%  Similarity=0.266  Sum_probs=223.1

Q ss_pred             CCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc------------cCCcEEEEcchHHHHHHHHHHHHH--
Q 037567           10 GYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV------------TGKTALVVSPLISLMQDQVMSLKQ--   75 (374)
Q Consensus        10 ~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~------------~~~~~lil~P~~~l~~q~~~~~~~--   75 (374)
                      +|..|+|+|.++++.+.+++++++.||||||||++|.++++.            .+.+++|++|+++|++|+.+.+..  
T Consensus        29 ~~~~~tpiQ~~Ai~~il~g~nvli~APTGSGKTlaa~Lpil~~l~~~~~~~~~~~~~~~LyIsPtraLa~di~~~L~~~l  108 (876)
T PRK13767         29 KFGTFTPPQRYAIPLIHEGKNVLISSPTGSGKTLAAFLAIIDELFRLGREGELEDKVYCLYVSPLRALNNDIHRNLEEPL  108 (876)
T ss_pred             ccCCCCHHHHHHHHHHHcCCCEEEECCCCCcHHHHHHHHHHHHHHhhccccCCCCCeEEEEEcCHHHHHHHHHHHHHHHH
Confidence            688999999999999999999999999999999999888763            134699999999999998875541  


Q ss_pred             ---------c-----CCceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcc
Q 037567           76 ---------R-----GINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEW  141 (374)
Q Consensus        76 ---------~-----~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~  141 (374)
                               .     ++.+.+.+++..... ........++|+|+||+++..++........+.++++||+||+|.+.+.
T Consensus       109 ~~i~~~~~~~g~~~~~i~v~v~~Gdt~~~~-r~~~l~~~p~IlVtTPE~L~~ll~~~~~~~~l~~l~~VVIDE~H~l~~~  187 (876)
T PRK13767        109 TEIREIAKERGEELPEIRVAIRTGDTSSYE-KQKMLKKPPHILITTPESLAILLNSPKFREKLRTVKWVIVDEIHSLAEN  187 (876)
T ss_pred             HHHHHHHHhcCCCcCCeeEEEEcCCCCHHH-HHHHHhCCCCEEEecHHHHHHHhcChhHHHHHhcCCEEEEechhhhccC
Confidence                     1     334455555544333 2334445689999999999777655433345788999999999999753


Q ss_pred             --cCcchHHHHHHHHHHHhcCCCCeeEEEeecCcccHHHHHHhcCCC------CCeEEEeccCCCceeEEEEe-----ec
Q 037567          142 --GHDFRLEYKQLDKLRTFLLGVPFVALTATATEKVRIDIINSLKLK------NPYVTIASFDRKNLFYGVKV-----IN  208 (374)
Q Consensus       142 --~~~~~~~~~~~~~~~~~~~~~~~i~~SaT~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~-----~~  208 (374)
                        |......+.++..+.  ..+.+++++|||+.+..  .+..++...      .+..................     ..
T Consensus       188 ~RG~~l~~~L~rL~~l~--~~~~q~IglSATl~~~~--~va~~L~~~~~~~~~r~~~iv~~~~~k~~~i~v~~p~~~l~~  263 (876)
T PRK13767        188 KRGVHLSLSLERLEELA--GGEFVRIGLSATIEPLE--EVAKFLVGYEDDGEPRDCEIVDARFVKPFDIKVISPVDDLIH  263 (876)
T ss_pred             ccHHHHHHHHHHHHHhc--CCCCeEEEEecccCCHH--HHHHHhcCccccCCCCceEEEccCCCccceEEEeccCccccc
Confidence              333333333333322  14678999999998743  345554432      11111111111111111100     00


Q ss_pred             CC-cchHHHHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHHc------CCceeeeecCCChHHHHHHHHhhhcCCeeE
Q 037567          209 RG-QSFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQL------GVKAGTYHGQMGSKAREEAHRLFIRDEIRV  281 (374)
Q Consensus       209 ~~-~~~~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~------~~~~~~~~~~~~~~~r~~~~~~f~~g~~~i  281 (374)
                      .. ......+...+.+....++++||||++++.++.++..|++.      +..+..+||+++.++|..+++.|++|+.++
T Consensus       264 ~~~~~~~~~l~~~L~~~i~~~~~~LVF~nTr~~ae~la~~L~~~~~~~~~~~~i~~hHg~ls~~~R~~ve~~fk~G~i~v  343 (876)
T PRK13767        264 TPAEEISEALYETLHELIKEHRTTLIFTNTRSGAERVLYNLRKRFPEEYDEDNIGAHHSSLSREVRLEVEEKLKRGELKV  343 (876)
T ss_pred             cccchhHHHHHHHHHHHHhcCCCEEEEeCCHHHHHHHHHHHHHhchhhccccceeeeeCCCCHHHHHHHHHHHHcCCCeE
Confidence            11 11122333334444446789999999999999999999873      357899999999999999999999999999


Q ss_pred             EEEeccccccccccCccEEEEECCCCChhHHHHhhccCCCCC
Q 037567          282 MVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRDG  323 (374)
Q Consensus       282 lv~t~~~~~G~d~~~~~~vi~~~~p~s~~~~~Q~~GR~~R~~  323 (374)
                      ||||+.+++|+|+|++++||+++.|.+...|+||+||+||.+
T Consensus       344 LVaTs~Le~GIDip~Vd~VI~~~~P~sv~~ylQRiGRaGR~~  385 (876)
T PRK13767        344 VVSSTSLELGIDIGYIDLVVLLGSPKSVSRLLQRIGRAGHRL  385 (876)
T ss_pred             EEECChHHhcCCCCCCcEEEEeCCCCCHHHHHHhcccCCCCC
Confidence            999999999999999999999999999999999999999863

>KOG0343 consensus RNA Helicase [RNA processing and modification]

Probab=100.00  E-value=2.3e-45  Score=317.64  Aligned_cols=320  Identities=24%  Similarity=0.316  Sum_probs=254.8

Q ss_pred             hHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhcccccc----------CCcEEEEcchHHHHHHHHHH
Q 037567            3 STLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVT----------GKTALVVSPLISLMQDQVMS   72 (374)
Q Consensus         3 ~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~~----------~~~~lil~P~~~l~~q~~~~   72 (374)
                      +.|++ .+|..++.+|.++|+..++|++++-.|.||||||++|+.|++..          +-=+||+.|||+|+.|.++.
T Consensus        82 kgLke-~~fv~~teiQ~~~Ip~aL~G~DvlGAAkTGSGKTLAFlvPvlE~L~r~kWs~~DGlGalIISPTRELA~QtFev  160 (758)
T KOG0343|consen   82 KGLKE-AKFVKMTEIQRDTIPMALQGHDVLGAAKTGSGKTLAFLVPVLEALYRLKWSPTDGLGALIISPTRELALQTFEV  160 (758)
T ss_pred             HhHhh-cCCccHHHHHHhhcchhccCcccccccccCCCceeeehHHHHHHHHHcCCCCCCCceeEEecchHHHHHHHHHH
Confidence            46777 78999999999999999999999999999999999999998852          55699999999999999999


Q ss_pred             HHHcCCc----eEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHH
Q 037567           73 LKQRGIN----AEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLE  148 (374)
Q Consensus        73 ~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~  148 (374)
                      +.+.|..    ..++.++..-.....  .-...+|+||||++|+.++... -.+...++.++|+|||+++.+.|+.    
T Consensus       161 L~kvgk~h~fSaGLiiGG~~~k~E~e--Ri~~mNILVCTPGRLLQHmde~-~~f~t~~lQmLvLDEADR~LDMGFk----  233 (758)
T KOG0343|consen  161 LNKVGKHHDFSAGLIIGGKDVKFELE--RISQMNILVCTPGRLLQHMDEN-PNFSTSNLQMLVLDEADRMLDMGFK----  233 (758)
T ss_pred             HHHHhhccccccceeecCchhHHHHH--hhhcCCeEEechHHHHHHhhhc-CCCCCCcceEEEeccHHHHHHHhHH----
Confidence            9987543    344444443333222  2345799999999987655431 2234467899999999999998876    


Q ss_pred             HHHHHHHHHhcC-CCCeeEEEeecCcccHHHHHHhcCCCCCeEEEeccC-----CCceeEEEEeecCCcchHHHHHHHHH
Q 037567          149 YKQLDKLRTFLL-GVPFVALTATATEKVRIDIINSLKLKNPYVTIASFD-----RKNLFYGVKVINRGQSFVDELVQEIL  222 (374)
Q Consensus       149 ~~~~~~~~~~~~-~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~  222 (374)
                       ..++.+...+| ..|.++||||...+...  +..+.+.+|..+....+     +.++...+...+.  ......+-.++
T Consensus       234 -~tL~~Ii~~lP~~RQTLLFSATqt~svkd--LaRLsL~dP~~vsvhe~a~~atP~~L~Q~y~~v~l--~~Ki~~L~sFI  308 (758)
T KOG0343|consen  234 -KTLNAIIENLPKKRQTLLFSATQTKSVKD--LARLSLKDPVYVSVHENAVAATPSNLQQSYVIVPL--EDKIDMLWSFI  308 (758)
T ss_pred             -HHHHHHHHhCChhheeeeeecccchhHHH--HHHhhcCCCcEEEEeccccccChhhhhheEEEEeh--hhHHHHHHHHH
Confidence             67777777776 58899999999998764  55566666654433321     1222222222111  22334444444


Q ss_pred             HhhcCCCcEEEEecchhHHHHHHHHHHHc--CCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEE
Q 037567          223 KSVAGAGSIIVYCMTIKDVEEISKALKQL--GVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHV  300 (374)
Q Consensus       223 ~~~~~~~~~lVf~~~~~~~~~l~~~l~~~--~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~v  300 (374)
                      +. +...+.|||+.+.+++..+++.+.+.  |+++..+||.++...|..+...|...+..||+||+.+++|+|+|.+++|
T Consensus       309 ~s-hlk~K~iVF~SscKqvkf~~e~F~rlrpg~~l~~L~G~~~Q~~R~ev~~~F~~~~~~vLF~TDv~aRGLDFpaVdwV  387 (758)
T KOG0343|consen  309 KS-HLKKKSIVFLSSCKQVKFLYEAFCRLRPGIPLLALHGTMSQKKRIEVYKKFVRKRAVVLFCTDVAARGLDFPAVDWV  387 (758)
T ss_pred             Hh-ccccceEEEEehhhHHHHHHHHHHhcCCCCceeeeccchhHHHHHHHHHHHHHhcceEEEeehhhhccCCCcccceE
Confidence            44 36789999999999999999999874  7888999999999999999999999999999999999999999999999


Q ss_pred             EEECCCCChhHHHHhhccCCCCCCceEEEEEeeccC
Q 037567          301 IHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSN  336 (374)
Q Consensus       301 i~~~~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~  336 (374)
                      |.+++|.++.+|+||+||+.|.+..|.+++++.+.+
T Consensus       388 iQ~DCPedv~tYIHRvGRtAR~~~~G~sll~L~psE  423 (758)
T KOG0343|consen  388 IQVDCPEDVDTYIHRVGRTARYKERGESLLMLTPSE  423 (758)
T ss_pred             EEecCchhHHHHHHHhhhhhcccCCCceEEEEcchh
Confidence            999999999999999999999999999999999988

>PRK02362 ski2-like helicase; Provisional

Probab=100.00  E-value=6.9e-45  Score=350.96  Aligned_cols=324  Identities=21%  Similarity=0.275  Sum_probs=235.1

Q ss_pred             hhHHHhHcCCCCCchhHHHHHHH-HHcCCCEEEEccCCCCchhhhhccccc---cCCcEEEEcchHHHHHHHHHHHHHc-
Q 037567            2 VSTLKKYFGYSVFRPYQKDVIQR-IIEKRDCLVVMATGSGKSLCYQLPPLV---TGKTALVVSPLISLMQDQVMSLKQR-   76 (374)
Q Consensus         2 ~~~l~~~~~~~~~~~~Q~~~~~~-~~~~~~~l~~a~tGsGKT~~~~l~~~~---~~~~~lil~P~~~l~~q~~~~~~~~-   76 (374)
                      .+++++ .||.+|+|+|.++++. +.++++++++||||||||++|.++++.   ++.+++|++|+++|+.|+.++++.+ 
T Consensus        13 ~~~l~~-~g~~~l~p~Q~~ai~~~~~~g~nvlv~APTGSGKTlia~lail~~l~~~~kal~i~P~raLa~q~~~~~~~~~   91 (737)
T PRK02362         13 IEFYEA-EGIEELYPPQAEAVEAGLLDGKNLLAAIPTASGKTLIAELAMLKAIARGGKALYIVPLRALASEKFEEFERFE   91 (737)
T ss_pred             HHHHHh-CCCCcCCHHHHHHHHHHHhCCCcEEEECCCcchHHHHHHHHHHHHHhcCCcEEEEeChHHHHHHHHHHHHHhh
Confidence            456766 7999999999999998 678999999999999999999888765   5789999999999999999999876 


Q ss_pred             --CCceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHH
Q 037567           77 --GINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDK  154 (374)
Q Consensus        77 --~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~  154 (374)
                        |.++...+++......    ..+.++|+|+||+++..+.+.  ....+.+++++|+||+|.+.+.+...... ..+.+
T Consensus        92 ~~g~~v~~~tGd~~~~~~----~l~~~~IiV~Tpek~~~llr~--~~~~l~~v~lvViDE~H~l~d~~rg~~le-~il~r  164 (737)
T PRK02362         92 ELGVRVGISTGDYDSRDE----WLGDNDIIVATSEKVDSLLRN--GAPWLDDITCVVVDEVHLIDSANRGPTLE-VTLAK  164 (737)
T ss_pred             cCCCEEEEEeCCcCcccc----ccCCCCEEEECHHHHHHHHhc--ChhhhhhcCEEEEECccccCCCcchHHHH-HHHHH
Confidence              6777766665433221    124579999999998776554  22346789999999999997644322111 12344


Q ss_pred             HHHhcCCCCeeEEEeecCcccHHHHHHhcCCCCCeEEEeccC-------CCceeEEEEeecCCcchHHHHHHHHHHhhcC
Q 037567          155 LRTFLLGVPFVALTATATEKVRIDIINSLKLKNPYVTIASFD-------RKNLFYGVKVINRGQSFVDELVQEILKSVAG  227 (374)
Q Consensus       155 ~~~~~~~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  227 (374)
                      +....++.+++++|||+++..  ++..|++............       .....................+..+.+....
T Consensus       165 l~~~~~~~qii~lSATl~n~~--~la~wl~~~~~~~~~rpv~l~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  242 (737)
T PRK02362        165 LRRLNPDLQVVALSATIGNAD--ELADWLDAELVDSEWRPIDLREGVFYGGAIHFDDSQREVEVPSKDDTLNLVLDTLEE  242 (737)
T ss_pred             HHhcCCCCcEEEEcccCCCHH--HHHHHhCCCcccCCCCCCCCeeeEecCCeeccccccccCCCccchHHHHHHHHHHHc
Confidence            444446789999999998643  5567665432100000000       0000000000000000112333444444457


Q ss_pred             CCcEEEEecchhHHHHHHHHHHHcC------------------------------------CceeeeecCCChHHHHHHH
Q 037567          228 AGSIIVYCMTIKDVEEISKALKQLG------------------------------------VKAGTYHGQMGSKAREEAH  271 (374)
Q Consensus       228 ~~~~lVf~~~~~~~~~l~~~l~~~~------------------------------------~~~~~~~~~~~~~~r~~~~  271 (374)
                      ++++||||+++..++.+++.|....                                    ..+..+|++++..+|..++
T Consensus       243 ~~~~LVF~~sr~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~L~~~l~~gva~hHagl~~~eR~~ve  322 (737)
T PRK02362        243 GGQCLVFVSSRRNAEGFAKRAASALKKTLTAAERAELAELAEEIREVSDTETSKDLADCVAKGAAFHHAGLSREHRELVE  322 (737)
T ss_pred             CCCeEEEEeCHHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHhccCccccHHHHHHHHhCEEeecCCCCHHHHHHHH
Confidence            8899999999999999888876431                                    2578899999999999999


Q ss_pred             HhhhcCCeeEEEEeccccccccccCccEEEE----EC-----CCCChhHHHHhhccCCCCCCc--eEEEEEeecc
Q 037567          272 RLFIRDEIRVMVATMAFGMGIDKPDVRHVIH----YG-----CPKTLESYYQESGRCGRDGIA--SVCWLYYARS  335 (374)
Q Consensus       272 ~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~----~~-----~p~s~~~~~Q~~GR~~R~~~~--g~~~~~~~~~  335 (374)
                      +.|++|.++|||||+.+++|+|+|..++||.    |+     .|.+..+|.||+|||||.|.+  |.+++++...
T Consensus       323 ~~Fr~G~i~VLvaT~tla~GvnlPa~~VVI~~~~~yd~~~g~~~~s~~~y~Qm~GRAGR~g~d~~G~~ii~~~~~  397 (737)
T PRK02362        323 DAFRDRLIKVISSTPTLAAGLNLPARRVIIRDYRRYDGGAGMQPIPVLEYHQMAGRAGRPGLDPYGEAVLLAKSY  397 (737)
T ss_pred             HHHHcCCCeEEEechhhhhhcCCCceEEEEecceeecCCCCceeCCHHHHHHHhhcCCCCCCCCCceEEEEecCc
Confidence            9999999999999999999999999999886    44     578999999999999999865  8888888664

>KOG0346 consensus RNA helicase [RNA processing and modification]

Probab=100.00  E-value=4.4e-45  Score=307.87  Aligned_cols=326  Identities=22%  Similarity=0.286  Sum_probs=256.7

Q ss_pred             hhHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc------------cCCcEEEEcchHHHHHHH
Q 037567            2 VSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV------------TGKTALVVSPLISLMQDQ   69 (374)
Q Consensus         2 ~~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~------------~~~~~lil~P~~~l~~q~   69 (374)
                      .+++.+ .|+.+|+-+|+.+||-+++|+|++..|.||||||.+|++|+++            .+..++|++||++|+.|+
T Consensus        31 lkAi~~-lG~ekpTlIQs~aIplaLEgKDvvarArTGSGKT~AYliPllqkll~~k~t~~~e~~~sa~iLvPTkEL~qQv  109 (569)
T KOG0346|consen   31 LKAITK-LGWEKPTLIQSSAIPLALEGKDVVARARTGSGKTAAYLIPLLQKLLAEKKTNDGEQGPSAVILVPTKELAQQV  109 (569)
T ss_pred             HHHHHH-hCcCCcchhhhcccchhhcCcceeeeeccCCCchHHHHHHHHHHHHHhhhcccccccceeEEEechHHHHHHH
Confidence            466777 8999999999999999999999999999999999999999885            266799999999999999


Q ss_pred             HHHHHHc------CCceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccC
Q 037567           70 VMSLKQR------GINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGH  143 (374)
Q Consensus        70 ~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~  143 (374)
                      +..+.+.      .+++.-+.....+.. ......+.++|+|+||..+..+..... ......+.++|+|||+.+..+|.
T Consensus       110 y~viekL~~~c~k~lr~~nl~s~~sdsv-~~~~L~d~pdIvV~TP~~ll~~~~~~~-~~~~~~l~~LVvDEADLllsfGY  187 (569)
T KOG0346|consen  110 YKVIEKLVEYCSKDLRAINLASSMSDSV-NSVALMDLPDIVVATPAKLLRHLAAGV-LEYLDSLSFLVVDEADLLLSFGY  187 (569)
T ss_pred             HHHHHHHHHHHHHhhhhhhhhcccchHH-HHHHHccCCCeEEeChHHHHHHHhhcc-chhhhheeeEEechhhhhhhccc
Confidence            9888764      122222222222222 224456779999999999987766521 15667889999999999998887


Q ss_pred             cchHHHHHHHHHHHhcC-CCCeeEEEeecCcccHHHHHHhcCCCCCeEEEe-ccCCC--ceeEEEEeecCCcchHHHHHH
Q 037567          144 DFRLEYKQLDKLRTFLL-GVPFVALTATATEKVRIDIINSLKLKNPYVTIA-SFDRK--NLFYGVKVINRGQSFVDELVQ  219 (374)
Q Consensus       144 ~~~~~~~~~~~~~~~~~-~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~-~~~~~--~~~~~~~~~~~~~~~~~~~~~  219 (374)
                      +     ..+..+...+| ..|.++||||.+.+...  +..+.+.+|.+... +.+.+  +-...+.+... ....-.++.
T Consensus       188 e-----edlk~l~~~LPr~~Q~~LmSATl~dDv~~--LKkL~l~nPviLkl~e~el~~~dqL~Qy~v~cs-e~DKfllly  259 (569)
T KOG0346|consen  188 E-----EDLKKLRSHLPRIYQCFLMSATLSDDVQA--LKKLFLHNPVILKLTEGELPNPDQLTQYQVKCS-EEDKFLLLY  259 (569)
T ss_pred             H-----HHHHHHHHhCCchhhheeehhhhhhHHHH--HHHHhccCCeEEEeccccCCCcccceEEEEEec-cchhHHHHH
Confidence            6     55666666665 57889999999988754  67777777765433 22222  22222222222 222333444


Q ss_pred             HHHHhhcCCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEec-------------
Q 037567          220 EILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATM-------------  286 (374)
Q Consensus       220 ~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~-------------  286 (374)
                      .+++.---.++.|||+|+.+.+.++.=.|...|++...++|+++...|.-++++|+.|-++++|+|+             
T Consensus       260 allKL~LI~gKsliFVNtIdr~YrLkLfLeqFGiksciLNseLP~NSR~Hii~QFNkG~YdivIAtD~s~~~~~~eee~k  339 (569)
T KOG0346|consen  260 ALLKLRLIRGKSLIFVNTIDRCYRLKLFLEQFGIKSCILNSELPANSRCHIIEQFNKGLYDIVIATDDSADGDKLEEEVK  339 (569)
T ss_pred             HHHHHHHhcCceEEEEechhhhHHHHHHHHHhCcHhhhhcccccccchhhHHHHhhCcceeEEEEccCccchhhhhcccc
Confidence            4444333578999999999999999999999999999999999999999999999999999999998             


Q ss_pred             ----------------------cccccccccCccEEEEECCCCChhHHHHhhccCCCCCCceEEEEEeeccCCC
Q 037567          287 ----------------------AFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFA  338 (374)
Q Consensus       287 ----------------------~~~~G~d~~~~~~vi~~~~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~~~  338 (374)
                                            -.++|+|+..+..|+++|+|.+...|+||+||++|.+++|.+..|+.+.+..
T Consensus       340 gk~~e~~~kndkkskkK~D~E~GVsRGIDF~~V~~VlNFD~P~t~~sYIHRvGRTaRg~n~GtalSfv~P~e~~  413 (569)
T KOG0346|consen  340 GKSDEKNPKNDKKSKKKLDKESGVSRGIDFHHVSNVLNFDFPETVTSYIHRVGRTARGNNKGTALSFVSPKEEF  413 (569)
T ss_pred             ccccccCCCCccccccccCchhchhccccchheeeeeecCCCCchHHHHHhccccccCCCCCceEEEecchHHh
Confidence                                  1458999999999999999999999999999999999999999999998755

>KOG0339 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=100.00  E-value=1.3e-44  Score=310.14  Aligned_cols=339  Identities=18%  Similarity=0.290  Sum_probs=285.5

Q ss_pred             hHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc-----------cCCcEEEEcchHHHHHHHHH
Q 037567            3 STLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV-----------TGKTALVVSPLISLMQDQVM   71 (374)
Q Consensus         3 ~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~-----------~~~~~lil~P~~~l~~q~~~   71 (374)
                      .++++ --|++|+|+|.+++|..+.+++++=.|.||||||-+|+++++.           .++..+|++||++|+.|++.
T Consensus       236 ~airk-~Ey~kptpiq~qalptalsgrdvigIAktgSgktaAfi~pm~~himdq~eL~~g~gPi~vilvPTrela~Qi~~  314 (731)
T KOG0339|consen  236 TAIRK-SEYEKPTPIQCQALPTALSGRDVIGIAKTGSGKTAAFIWPMIVHIMDQPELKPGEGPIGVILVPTRELASQIFS  314 (731)
T ss_pred             HHHhh-hhcccCCcccccccccccccccchheeeccCcchhHHHHHHHHHhcchhhhcCCCCCeEEEEeccHHHHHHHHH
Confidence            45555 4688999999999999999999999999999999999988763           26779999999999999999


Q ss_pred             HHHHc----CCceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchH
Q 037567           72 SLKQR----GINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRL  147 (374)
Q Consensus        72 ~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~  147 (374)
                      +.++|    |+++..++++....+....+. .++.|+|+||++|.+++.-  +..++.+..++|+||+++|.+.|++   
T Consensus       315 eaKkf~K~ygl~~v~~ygGgsk~eQ~k~Lk-~g~EivVaTPgRlid~Vkm--Katn~~rvS~LV~DEadrmfdmGfe---  388 (731)
T KOG0339|consen  315 EAKKFGKAYGLRVVAVYGGGSKWEQSKELK-EGAEIVVATPGRLIDMVKM--KATNLSRVSYLVLDEADRMFDMGFE---  388 (731)
T ss_pred             HHHHhhhhccceEEEeecCCcHHHHHHhhh-cCCeEEEechHHHHHHHHh--hcccceeeeEEEEechhhhhccccH---
Confidence            98876    677777777777766665555 7799999999999888554  7778899999999999999998876   


Q ss_pred             HHHHHHHHHHhc-CCCCeeEEEeecCcccHHHHHHhcCCCCCeEEEecc--CCCceeEEEEeecCCcchHHHHHHHHHHh
Q 037567          148 EYKQLDKLRTFL-LGVPFVALTATATEKVRIDIINSLKLKNPYVTIASF--DRKNLFYGVKVINRGQSFVDELVQEILKS  224 (374)
Q Consensus       148 ~~~~~~~~~~~~-~~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  224 (374)
                        .++..+.... ++.|.++||||......+ +.+.+...+..++..+.  ....+...+.++.+....+.-++.++...
T Consensus       389 --~qVrSI~~hirpdrQtllFsaTf~~kIe~-lard~L~dpVrvVqg~vgean~dITQ~V~V~~s~~~Kl~wl~~~L~~f  465 (731)
T KOG0339|consen  389 --PQVRSIKQHIRPDRQTLLFSATFKKKIEK-LARDILSDPVRVVQGEVGEANEDITQTVSVCPSEEKKLNWLLRHLVEF  465 (731)
T ss_pred             --HHHHHHHhhcCCcceEEEeeccchHHHHH-HHHHHhcCCeeEEEeehhccccchhheeeeccCcHHHHHHHHHHhhhh
Confidence              4555555544 478999999999988775 34444444444444443  33456666777777777777777777665


Q ss_pred             hcCCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEEEEEC
Q 037567          225 VAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYG  304 (374)
Q Consensus       225 ~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~~~  304 (374)
                      . ..+++|||+..+..+++++..|+-.++++..+||++...+|++++..|+.+...|+++|+...+|+|+|.+..|++++
T Consensus       466 ~-S~gkvlifVTKk~~~e~i~a~Lklk~~~v~llhgdkdqa~rn~~ls~fKkk~~~VlvatDvaargldI~~ikTVvnyD  544 (731)
T KOG0339|consen  466 S-SEGKVLIFVTKKADAEEIAANLKLKGFNVSLLHGDKDQAERNEVLSKFKKKRKPVLVATDVAARGLDIPSIKTVVNYD  544 (731)
T ss_pred             c-cCCcEEEEEeccCCHHHHHHHhccccceeeeecCchhhHHHHHHHHHHhhcCCceEEEeeHhhcCCCccccceeeccc
Confidence            4 778999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCChhHHHHhhccCCCCCCceEEEEEeeccCCCcccceeccccchHH
Q 037567          305 CPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFYCGESQTENQ  352 (374)
Q Consensus       305 ~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~  352 (374)
                      .-.+++.+.||+||+||.|..|..|+++++.|.+....+.+.++...+
T Consensus       545 ~ardIdththrigrtgRag~kGvayTlvTeKDa~fAG~LVnnLe~agQ  592 (731)
T KOG0339|consen  545 FARDIDTHTHRIGRTGRAGEKGVAYTLVTEKDAEFAGHLVNNLEGAGQ  592 (731)
T ss_pred             ccchhHHHHHHhhhcccccccceeeEEechhhHHHhhHHHHHHhhccc
Confidence            999999999999999999999999999999999888877776665554

>KOG0341 consensus DEAD-box protein abstrakt [RNA processing and modification]

Probab=100.00  E-value=1.1e-45  Score=307.19  Aligned_cols=321  Identities=23%  Similarity=0.307  Sum_probs=247.4

Q ss_pred             hHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc--------------cCCcEEEEcchHHHHHH
Q 037567            3 STLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV--------------TGKTALVVSPLISLMQD   68 (374)
Q Consensus         3 ~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~--------------~~~~~lil~P~~~l~~q   68 (374)
                      +-+++ -|+..|+|+|.+.+|.+++|++.+=.|-||||||+.|.+|++.              .++-.||+||+++|+.|
T Consensus       183 ~~lk~-KGI~~PTpIQvQGlPvvLsGRDmIGIAfTGSGKTlvFvLP~imf~LeqE~~lPf~~~EGP~gLiicPSRELArQ  261 (610)
T KOG0341|consen  183 RGLKK-KGIVHPTPIQVQGLPVVLSGRDMIGIAFTGSGKTLVFVLPVIMFALEQEMMLPFARGEGPYGLIICPSRELARQ  261 (610)
T ss_pred             HHHHh-cCCCCCCceeecCcceEeecCceeeEEeecCCceEEEeHHHHHHHHHHHhcCccccCCCCeeEEEcCcHHHHHH
Confidence            34555 6999999999999999999999999999999999999887552              37789999999999999


Q ss_pred             HHHHHHHc-------CC---ceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchh
Q 037567           69 QVMSLKQR-------GI---NAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCI  138 (374)
Q Consensus        69 ~~~~~~~~-------~~---~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~  138 (374)
                      ..+-+..+       |.   +..++.++. ....+..-...+.+|+|+||++|.+++..  +...+.-++++.+|||+++
T Consensus       262 t~~iie~~~~~L~e~g~P~lRs~LciGG~-~v~eql~~v~~GvHivVATPGRL~DmL~K--K~~sLd~CRyL~lDEADRm  338 (610)
T KOG0341|consen  262 THDIIEQYVAALQEAGYPELRSLLCIGGV-PVREQLDVVRRGVHIVVATPGRLMDMLAK--KIMSLDACRYLTLDEADRM  338 (610)
T ss_pred             HHHHHHHHHHHHHhcCChhhhhhhhhcCc-cHHHHHHHHhcCeeEEEcCcchHHHHHHH--hhccHHHHHHhhhhhHHHH
Confidence            88777654       21   222333333 33334445567789999999999988776  5556667789999999999


Q ss_pred             hcccCcchHHHHHHHHHHHhcC-CCCeeEEEeecCcccHHHHHHhcCCCCCeEEEeccCCCceeEEEEeecCCcchHHHH
Q 037567          139 SEWGHDFRLEYKQLDKLRTFLL-GVPFVALTATATEKVRIDIINSLKLKNPYVTIASFDRKNLFYGVKVINRGQSFVDEL  217 (374)
Q Consensus       139 ~~~~~~~~~~~~~~~~~~~~~~-~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  217 (374)
                      .+.|++     .-+..+..++. .++.++||||++..... +....-+.+..+........++....++-.-........
T Consensus       339 iDmGFE-----ddir~iF~~FK~QRQTLLFSATMP~KIQ~-FAkSALVKPvtvNVGRAGAAsldViQevEyVkqEaKiVy  412 (610)
T KOG0341|consen  339 IDMGFE-----DDIRTIFSFFKGQRQTLLFSATMPKKIQN-FAKSALVKPVTVNVGRAGAASLDVIQEVEYVKQEAKIVY  412 (610)
T ss_pred             hhccch-----hhHHHHHHHHhhhhheeeeeccccHHHHH-HHHhhcccceEEecccccccchhHHHHHHHHHhhhhhhh
Confidence            998876     55555555554 68899999999988763 444433344333333322222211111100011111122


Q ss_pred             HHHHHHhhcCCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCc
Q 037567          218 VQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDV  297 (374)
Q Consensus       218 ~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~  297 (374)
                      +-+.+++  ..-++||||..+.+++.+.++|--.|..++.+||+-..++|..-++.|+.|+.+|||+|+.++.|+|+|++
T Consensus       413 lLeCLQK--T~PpVLIFaEkK~DVD~IhEYLLlKGVEavaIHGGKDQedR~~ai~afr~gkKDVLVATDVASKGLDFp~i  490 (610)
T KOG0341|consen  413 LLECLQK--TSPPVLIFAEKKADVDDIHEYLLLKGVEAVAIHGGKDQEDRHYAIEAFRAGKKDVLVATDVASKGLDFPDI  490 (610)
T ss_pred             HHHHhcc--CCCceEEEeccccChHHHHHHHHHccceeEEeecCcchhHHHHHHHHHhcCCCceEEEecchhccCCCccc
Confidence            2233333  46789999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cEEEEECCCCChhHHHHhhccCCCCCCceEEEEEeecc
Q 037567          298 RHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARS  335 (374)
Q Consensus       298 ~~vi~~~~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~  335 (374)
                      .+||+|++|....+|+|||||+||.|+.|.+.+|+.+.
T Consensus       491 qHVINyDMP~eIENYVHRIGRTGRsg~~GiATTfINK~  528 (610)
T KOG0341|consen  491 QHVINYDMPEEIENYVHRIGRTGRSGKTGIATTFINKN  528 (610)
T ss_pred             hhhccCCChHHHHHHHHHhcccCCCCCcceeeeeeccc
Confidence            99999999999999999999999999999999998764

>KOG0332 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=100.00  E-value=9.4e-45  Score=299.90  Aligned_cols=321  Identities=17%  Similarity=0.217  Sum_probs=248.1

Q ss_pred             cCCCCCchhHHHHHHHHHcC--CCEEEEccCCCCchhhhhcccccc------CCcEEEEcchHHHHHHHHHHHHHcCCce
Q 037567            9 FGYSVFRPYQKDVIQRIIEK--RDCLVVMATGSGKSLCYQLPPLVT------GKTALVVSPLISLMQDQVMSLKQRGINA   80 (374)
Q Consensus         9 ~~~~~~~~~Q~~~~~~~~~~--~~~l~~a~tGsGKT~~~~l~~~~~------~~~~lil~P~~~l~~q~~~~~~~~~~~~   80 (374)
                      |+|..|+.+|+.++|-++..  ++.|..+..|+|||.+|.+.++.+      .+.+++++|+++|+.|..+-+.+.|...
T Consensus       108 M~F~kPskIQe~aLPlll~~Pp~nlIaQsqsGtGKTaaFvL~MLsrvd~~~~~PQ~iCLaPtrELA~Q~~eVv~eMGKf~  187 (477)
T KOG0332|consen  108 MKFQKPSKIQETALPLLLAEPPQNLIAQSQSGTGKTAAFVLTMLSRVDPDVVVPQCICLAPTRELAPQTGEVVEEMGKFT  187 (477)
T ss_pred             hccCCcchHHHhhcchhhcCCchhhhhhhcCCCchhHHHHHHHHHhcCccccCCCceeeCchHHHHHHHHHHHHHhcCce
Confidence            89999999999999999874  688999999999999999998864      6789999999999999999999887665


Q ss_pred             EEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhc-ccCcchHHHHHHHHHHHhc
Q 037567           81 EFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISE-WGHDFRLEYKQLDKLRTFL  159 (374)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~-~~~~~~~~~~~~~~~~~~~  159 (374)
                      .+................-.-.|+|+||+.+.++.... ..+....+.++|+|||+.+.+ .|++     ..-.++....
T Consensus       188 ~ita~yair~sk~~rG~~i~eqIviGTPGtv~Dlm~kl-k~id~~kikvfVlDEAD~Mi~tqG~~-----D~S~rI~~~l  261 (477)
T KOG0332|consen  188 ELTASYAIRGSKAKRGNKLTEQIVIGTPGTVLDLMLKL-KCIDLEKIKVFVLDEADVMIDTQGFQ-----DQSIRIMRSL  261 (477)
T ss_pred             eeeEEEEecCcccccCCcchhheeeCCCccHHHHHHHH-HhhChhhceEEEecchhhhhhccccc-----ccchhhhhhc
Confidence            33222222222111111122379999999988765542 455667889999999999976 3433     2222333333


Q ss_pred             -CCCCeeEEEeecCcccHHHHHHhcCCCCCeEEEeccCCCceeEEEEeecCCcchHHHHHHHHHHhhcCCCcEEEEecch
Q 037567          160 -LGVPFVALTATATEKVRIDIINSLKLKNPYVTIASFDRKNLFYGVKVINRGQSFVDELVQEILKSVAGAGSIIVYCMTI  238 (374)
Q Consensus       160 -~~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lVf~~~~  238 (374)
                       ++.+.+.||||..............-.++.+...........+.............+++.++.... .-++.||||.++
T Consensus       262 P~~~QllLFSATf~e~V~~Fa~kivpn~n~i~Lk~eel~L~~IkQlyv~C~~~~~K~~~l~~lyg~~-tigqsiIFc~tk  340 (477)
T KOG0332|consen  262 PRNQQLLLFSATFVEKVAAFALKIVPNANVIILKREELALDNIKQLYVLCACRDDKYQALVNLYGLL-TIGQSIIFCHTK  340 (477)
T ss_pred             CCcceEEeeechhHHHHHHHHHHhcCCCceeeeehhhccccchhhheeeccchhhHHHHHHHHHhhh-hhhheEEEEeeh
Confidence             489999999999988776555555444444444333322222233333333344455555565554 568899999999


Q ss_pred             hHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEEEEECCCC------ChhHH
Q 037567          239 KDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPK------TLESY  312 (374)
Q Consensus       239 ~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~~~~p~------s~~~~  312 (374)
                      ..+..++..+.+.|..+..+||++...+|..++..|+.|+.+|||+|+.+.+|+|++.++.||+|++|.      +...|
T Consensus       341 ~ta~~l~~~m~~~Gh~V~~l~G~l~~~~R~~ii~~Fr~g~~kVLitTnV~ARGiDv~qVs~VvNydlP~~~~~~pD~etY  420 (477)
T KOG0332|consen  341 ATAMWLYEEMRAEGHQVSLLHGDLTVEQRAAIIDRFREGKEKVLITTNVCARGIDVAQVSVVVNYDLPVKYTGEPDYETY  420 (477)
T ss_pred             hhHHHHHHHHHhcCceeEEeeccchhHHHHHHHHHHhcCcceEEEEechhhcccccceEEEEEecCCccccCCCCCHHHH
Confidence            999999999999999999999999999999999999999999999999999999999999999999995      78999


Q ss_pred             HHhhccCCCCCCceEEEEEeeccC
Q 037567          313 YQESGRCGRDGIASVCWLYYARSN  336 (374)
Q Consensus       313 ~Q~~GR~~R~~~~g~~~~~~~~~~  336 (374)
                      +||+||+||+|+.|.++.+++..+
T Consensus       421 lHRiGRtGRFGkkG~a~n~v~~~~  444 (477)
T KOG0332|consen  421 LHRIGRTGRFGKKGLAINLVDDKD  444 (477)
T ss_pred             HHHhcccccccccceEEEeecccC
Confidence            999999999999999999988755

>KOG0350 consensus DEAD-box ATP-dependent RNA helicase [RNA processing and modification]

Probab=100.00  E-value=1.2e-44  Score=309.69  Aligned_cols=335  Identities=21%  Similarity=0.253  Sum_probs=247.1

Q ss_pred             HHhHcCCCCCchhHHHHHHHHHc---------CCCEEEEccCCCCchhhhhccccc-------cCCcEEEEcchHHHHHH
Q 037567            5 LKKYFGYSVFRPYQKDVIQRIIE---------KRDCLVVMATGSGKSLCYQLPPLV-------TGKTALVVSPLISLMQD   68 (374)
Q Consensus         5 l~~~~~~~~~~~~Q~~~~~~~~~---------~~~~l~~a~tGsGKT~~~~l~~~~-------~~~~~lil~P~~~l~~q   68 (374)
                      +.+ +++....|.|...++.++.         .+|+++.||||||||++|.+|+.+       +.-+++|++|+++|+.|
T Consensus       152 l~k-~~is~~FPVQ~aVlp~ll~~~~~p~~~r~rDIcV~ApTGSGKTLaY~iPIVQ~L~~R~v~~LRavVivPtr~L~~Q  230 (620)
T KOG0350|consen  152 LVK-MAISRLFPVQYAVLPSLLEEIRSPPPSRPRDICVNAPTGSGKTLAYVIPIVQLLSSRPVKRLRAVVIVPTRELALQ  230 (620)
T ss_pred             HHH-hhcccccchHHHHHHHHHHhhcCCCCCCCCceEEecCCCCCceeeehhHHHHHHccCCccceEEEEEeeHHHHHHH
Confidence            444 7899999999999999864         478999999999999999999875       25689999999999999


Q ss_pred             HHHHHHHc----CCceEEcCCCCCchhhhhhhhcCCe----eEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhc
Q 037567           69 QVMSLKQR----GINAEFLGSAQTDSSVQTKAETGYF----QLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISE  140 (374)
Q Consensus        69 ~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~----~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~  140 (374)
                      +++.|..+    |+.++.+.+...-..+...+....+    ||+|+||++|.+++++ ...+.+.+++++|||||+++.+
T Consensus       231 V~~~f~~~~~~tgL~V~~~sgq~sl~~E~~qL~~~~~~~~~DIlVaTPGRLVDHl~~-~k~f~Lk~LrfLVIDEADRll~  309 (620)
T KOG0350|consen  231 VYDTFKRLNSGTGLAVCSLSGQNSLEDEARQLASDPPECRIDILVATPGRLVDHLNN-TKSFDLKHLRFLVIDEADRLLD  309 (620)
T ss_pred             HHHHHHHhccCCceEEEecccccchHHHHHHHhcCCCccccceEEcCchHHHHhccC-CCCcchhhceEEEechHHHHHH
Confidence            99999987    4445555555455555555555555    9999999999988876 3677889999999999999986


Q ss_pred             ccCcchHHH--------------------------HHHHHHHHh----cCCCCeeEEEeecCcccHHHHHHhcCCCCCeE
Q 037567          141 WGHDFRLEY--------------------------KQLDKLRTF----LLGVPFVALTATATEKVRIDIINSLKLKNPYV  190 (374)
Q Consensus       141 ~~~~~~~~~--------------------------~~~~~~~~~----~~~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~  190 (374)
                      ..++-+...                          ..+.++...    .++...+++|||.+....+  +..+.+..|..
T Consensus       310 qsfQ~Wl~~v~~~~~~~k~~~~~~nii~~~~~~~pt~~~e~~t~~~~~~~~l~kL~~satLsqdP~K--l~~l~l~~Prl  387 (620)
T KOG0350|consen  310 QSFQEWLDTVMSLCKTMKRVACLDNIIRQRQAPQPTVLSELLTKLGKLYPPLWKLVFSATLSQDPSK--LKDLTLHIPRL  387 (620)
T ss_pred             HHHHHHHHHHHHHhCCchhhcChhhhhhhcccCCchhhHHHHhhcCCcCchhHhhhcchhhhcChHH--HhhhhcCCCce
Confidence            433211110                          011111111    1223367888887776544  55555555532


Q ss_pred             EEeccC------CCceeEEEEeecCCcchHHHHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHH-H---cCCceeeeec
Q 037567          191 TIASFD------RKNLFYGVKVINRGQSFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALK-Q---LGVKAGTYHG  260 (374)
Q Consensus       191 ~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~-~---~~~~~~~~~~  260 (374)
                      ......      .+....+...... ....--.+..++.. ....++|+|+++.+.+.+++..|+ .   ...++-.+.|
T Consensus       388 ~~v~~~~~~ryslp~~l~~~~vv~~-~~~kpl~~~~lI~~-~k~~r~lcf~~S~~sa~Rl~~~L~v~~~~~~~~~s~~t~  465 (620)
T KOG0350|consen  388 FHVSKPLIGRYSLPSSLSHRLVVTE-PKFKPLAVYALITS-NKLNRTLCFVNSVSSANRLAHVLKVEFCSDNFKVSEFTG  465 (620)
T ss_pred             EEeecccceeeecChhhhhceeecc-cccchHhHHHHHHH-hhcceEEEEecchHHHHHHHHHHHHHhccccchhhhhhh
Confidence            222211      1111111111111 11112223333333 478899999999999999999988 3   2445566889


Q ss_pred             CCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEEEEECCCCChhHHHHhhccCCCCCCceEEEEEeeccCCCcc
Q 037567          261 QMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKG  340 (374)
Q Consensus       261 ~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~~~~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~~~~~  340 (374)
                      .++.+.|...++.|..|++.+|||++++.+|+|+.+++.||+|++|.+...|+||+||++|.|+.|.+|.+....+.+.+
T Consensus       466 ~l~~k~r~k~l~~f~~g~i~vLIcSD~laRGiDv~~v~~VINYd~P~~~ktyVHR~GRTARAgq~G~a~tll~~~~~r~F  545 (620)
T KOG0350|consen  466 QLNGKRRYKMLEKFAKGDINVLICSDALARGIDVNDVDNVINYDPPASDKTYVHRAGRTARAGQDGYAITLLDKHEKRLF  545 (620)
T ss_pred             hhhHHHHHHHHHHHhcCCceEEEehhhhhcCCcccccceEeecCCCchhhHHHHhhcccccccCCceEEEeeccccchHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999998887


Q ss_pred             cceec
Q 037567          341 DFYCG  345 (374)
Q Consensus       341 ~~~~~  345 (374)
                      .++.+
T Consensus       546 ~klL~  550 (620)
T KOG0350|consen  546 SKLLK  550 (620)
T ss_pred             HHHHH
Confidence            77755

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

Probab=100.00  E-value=7.4e-43  Score=325.45  Aligned_cols=321  Identities=26%  Similarity=0.331  Sum_probs=249.9

Q ss_pred             hhHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc----c-------CCcEEEEcchHHHHHHHH
Q 037567            2 VSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV----T-------GKTALVVSPLISLMQDQV   70 (374)
Q Consensus         2 ~~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~----~-------~~~~lil~P~~~l~~q~~   70 (374)
                      .+.|++.  |.+|||.|.+|++.+.+|+++++.||||||||.++.+|++.    .       +-.+|+++|.++|.+++.
T Consensus        13 ~~~~~~~--~~~~t~~Q~~a~~~i~~G~nvLiiAPTGsGKTeAAfLpil~~l~~~~~~~~~~~i~~lYIsPLkALn~Di~   90 (814)
T COG1201          13 REWFKRK--FTSLTPPQRYAIPEIHSGENVLIIAPTGSGKTEAAFLPVINELLSLGKGKLEDGIYALYISPLKALNNDIR   90 (814)
T ss_pred             HHHHHHh--cCCCCHHHHHHHHHHhCCCceEEEcCCCCChHHHHHHHHHHHHHhccCCCCCCceEEEEeCcHHHHHHHHH
Confidence            4567774  99999999999999999999999999999999999888764    1       246999999999999988


Q ss_pred             HHHH----HcCCceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhc--ccCc
Q 037567           71 MSLK----QRGINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISE--WGHD  144 (374)
Q Consensus        71 ~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~--~~~~  144 (374)
                      +.+.    ..|+.+.+.+++.+... .......+|+|+++|||+|..++....-.-.+.++.++||||.|.+.+  .|.+
T Consensus        91 ~rL~~~~~~~G~~v~vRhGDT~~~e-r~r~~~~PPdILiTTPEsL~lll~~~~~r~~l~~vr~VIVDEiHel~~sKRG~~  169 (814)
T COG1201          91 RRLEEPLRELGIEVAVRHGDTPQSE-KQKMLKNPPHILITTPESLAILLNSPKFRELLRDVRYVIVDEIHALAESKRGVQ  169 (814)
T ss_pred             HHHHHHHHHcCCccceecCCCChHH-hhhccCCCCcEEEeChhHHHHHhcCHHHHHHhcCCcEEEeehhhhhhccccchh
Confidence            8876    45888877777655544 345566789999999999988887766667789999999999999965  5555


Q ss_pred             chHHHHHHHHHHHhcCCCCeeEEEeecCcccHHHHHHhcCCCC-C-eEEEeccCCCceeEEEEeecCC----cchHHHHH
Q 037567          145 FRLEYKQLDKLRTFLLGVPFVALTATATEKVRIDIINSLKLKN-P-YVTIASFDRKNLFYGVKVINRG----QSFVDELV  218 (374)
Q Consensus       145 ~~~~~~~~~~~~~~~~~~~~i~~SaT~~~~~~~~~~~~~~~~~-~-~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~  218 (374)
                      ....   +.++....++.+.|++|||..+..  ...+++.... + .+...... .+....+......    .......+
T Consensus       170 Lsl~---LeRL~~l~~~~qRIGLSATV~~~~--~varfL~g~~~~~~Iv~~~~~-k~~~i~v~~p~~~~~~~~~~~~~~~  243 (814)
T COG1201         170 LALS---LERLRELAGDFQRIGLSATVGPPE--EVAKFLVGFGDPCEIVDVSAA-KKLEIKVISPVEDLIYDEELWAALY  243 (814)
T ss_pred             hhhh---HHHHHhhCcccEEEeehhccCCHH--HHHHHhcCCCCceEEEEcccC-CcceEEEEecCCccccccchhHHHH
Confidence            4433   344444444789999999999655  5677777665 2 23333222 2222222211111    22334445


Q ss_pred             HHHHHhhcCCCcEEEEecchhHHHHHHHHHHHcC-CceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCc
Q 037567          219 QEILKSVAGAGSIIVYCMTIKDVEEISKALKQLG-VKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDV  297 (374)
Q Consensus       219 ~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~~-~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~  297 (374)
                      ..+.+.....+.+|||+||+..++.++..|++.+ ..+..+||.++.+.|....++|++|+.+++|||+.++-|||+.++
T Consensus       244 ~~i~~~v~~~~ttLIF~NTR~~aE~l~~~L~~~~~~~i~~HHgSlSre~R~~vE~~lk~G~lravV~TSSLELGIDiG~v  323 (814)
T COG1201         244 ERIAELVKKHRTTLIFTNTRSGAERLAFRLKKLGPDIIEVHHGSLSRELRLEVEERLKEGELKAVVATSSLELGIDIGDI  323 (814)
T ss_pred             HHHHHHHhhcCcEEEEEeChHHHHHHHHHHHHhcCCceeeecccccHHHHHHHHHHHhcCCceEEEEccchhhccccCCc
Confidence            5555555566799999999999999999999976 788999999999999999999999999999999999999999999


Q ss_pred             cEEEEECCCCChhHHHHhhccCCCC-CCceEEEEE
Q 037567          298 RHVIHYGCPKTLESYYQESGRCGRD-GIASVCWLY  331 (374)
Q Consensus       298 ~~vi~~~~p~s~~~~~Q~~GR~~R~-~~~g~~~~~  331 (374)
                      +.||+++.|.++..+.||+||+|.. +.....+++
T Consensus       324 dlVIq~~SP~sV~r~lQRiGRsgHr~~~~Skg~ii  358 (814)
T COG1201         324 DLVIQLGSPKSVNRFLQRIGRAGHRLGEVSKGIII  358 (814)
T ss_pred             eEEEEeCCcHHHHHHhHhccccccccCCcccEEEE
Confidence            9999999999999999999999964 443444444

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=100.00  E-value=1.4e-42  Score=334.26  Aligned_cols=311  Identities=23%  Similarity=0.318  Sum_probs=232.8

Q ss_pred             hhHHHhHcCCCCCchhHHHHHHHHHcC------CCEEEEccCCCCchhhhhcccc---ccCCcEEEEcchHHHHHHHHHH
Q 037567            2 VSTLKKYFGYSVFRPYQKDVIQRIIEK------RDCLVVMATGSGKSLCYQLPPL---VTGKTALVVSPLISLMQDQVMS   72 (374)
Q Consensus         2 ~~~l~~~~~~~~~~~~Q~~~~~~~~~~------~~~l~~a~tGsGKT~~~~l~~~---~~~~~~lil~P~~~l~~q~~~~   72 (374)
                      ...|.+.++|. |+|.|.++++.+.++      .+.+++||||||||.+++++++   ..+.+++|++||++|+.|+++.
T Consensus       441 ~~~~~~~~~f~-~T~~Q~~aI~~I~~d~~~~~~~d~Ll~adTGsGKT~val~a~l~al~~g~qvlvLvPT~~LA~Q~~~~  519 (926)
T TIGR00580       441 QQEFEDSFPFE-ETPDQLKAIEEIKADMESPRPMDRLVCGDVGFGKTEVAMRAAFKAVLDGKQVAVLVPTTLLAQQHFET  519 (926)
T ss_pred             HHHHHHhCCCC-CCHHHHHHHHHHHhhhcccCcCCEEEECCCCccHHHHHHHHHHHHHHhCCeEEEEeCcHHHHHHHHHH
Confidence            45677889995 999999999999874      6899999999999999887765   3578999999999999999998


Q ss_pred             HHHc----CCceEEcCCCCCchh---hhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcc
Q 037567           73 LKQR----GINAEFLGSAQTDSS---VQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDF  145 (374)
Q Consensus        73 ~~~~----~~~~~~~~~~~~~~~---~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~  145 (374)
                      +++.    +.++..+.+.....+   .......+.++|+|+||..+.       ....+.+++++||||+|++..     
T Consensus       520 f~~~~~~~~i~v~~Lsg~~~~~e~~~~~~~l~~g~~dIVIGTp~ll~-------~~v~f~~L~llVIDEahrfgv-----  587 (926)
T TIGR00580       520 FKERFANFPVTIELLSRFRSAKEQNEILKELASGKIDILIGTHKLLQ-------KDVKFKDLGLLIIDEEQRFGV-----  587 (926)
T ss_pred             HHHHhccCCcEEEEEeccccHHHHHHHHHHHHcCCceEEEchHHHhh-------CCCCcccCCEEEeecccccch-----
Confidence            8764    455555554433322   222334567899999995432       223457889999999998532     


Q ss_pred             hHHHHHHHHHHHhcCCCCeeEEEeecCcccHHHHHHhcCCCCCeEEEe-ccCCCceeEEEEeecCCcchHHHHHHHHHHh
Q 037567          146 RLEYKQLDKLRTFLLGVPFVALTATATEKVRIDIINSLKLKNPYVTIA-SFDRKNLFYGVKVINRGQSFVDELVQEILKS  224 (374)
Q Consensus       146 ~~~~~~~~~~~~~~~~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  224 (374)
                          .....+.....+.++++|||||.+....  ....+..+...... ...+..+...+.  ....   ..+...+.+.
T Consensus       588 ----~~~~~L~~~~~~~~vL~~SATpiprtl~--~~l~g~~d~s~I~~~p~~R~~V~t~v~--~~~~---~~i~~~i~~e  656 (926)
T TIGR00580       588 ----KQKEKLKELRTSVDVLTLSATPIPRTLH--MSMSGIRDLSIIATPPEDRLPVRTFVM--EYDP---ELVREAIRRE  656 (926)
T ss_pred             ----hHHHHHHhcCCCCCEEEEecCCCHHHHH--HHHhcCCCcEEEecCCCCccceEEEEE--ecCH---HHHHHHHHHH
Confidence                1122333334578999999998775443  22334444433322 222222222111  1111   2222334444


Q ss_pred             hcCCCcEEEEecchhHHHHHHHHHHHc--CCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEEEE
Q 037567          225 VAGAGSIIVYCMTIKDVEEISKALKQL--GVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIH  302 (374)
Q Consensus       225 ~~~~~~~lVf~~~~~~~~~l~~~l~~~--~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~  302 (374)
                      ...+++++|||++++.++.+++.|++.  +.++..+||+++..+|..++++|.+|+.+|||||+++++|+|+|++++||+
T Consensus       657 l~~g~qv~if~n~i~~~e~l~~~L~~~~p~~~v~~lHG~m~~~eRe~im~~F~~Gk~~ILVaT~iie~GIDIp~v~~VIi  736 (926)
T TIGR00580       657 LLRGGQVFYVHNRIESIEKLATQLRELVPEARIAIAHGQMTENELEEVMLEFYKGEFQVLVCTTIIETGIDIPNANTIII  736 (926)
T ss_pred             HHcCCeEEEEECCcHHHHHHHHHHHHhCCCCeEEEecCCCCHHHHHHHHHHHHcCCCCEEEECChhhcccccccCCEEEE
Confidence            557899999999999999999999984  678999999999999999999999999999999999999999999999999


Q ss_pred             ECCCC-ChhHHHHhhccCCCCCCceEEEEEeeccC
Q 037567          303 YGCPK-TLESYYQESGRCGRDGIASVCWLYYARSN  336 (374)
Q Consensus       303 ~~~p~-s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~  336 (374)
                      +++|. +..+|.||+||+||.|..|.|++++++.+
T Consensus       737 ~~a~~~gls~l~Qr~GRvGR~g~~g~aill~~~~~  771 (926)
T TIGR00580       737 ERADKFGLAQLYQLRGRVGRSKKKAYAYLLYPHQK  771 (926)
T ss_pred             ecCCCCCHHHHHHHhcCCCCCCCCeEEEEEECCcc
Confidence            98865 67899999999999999999999987643

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.

>KOG0347 consensus RNA helicase [RNA processing and modification]

Probab=100.00  E-value=4.5e-45  Score=315.73  Aligned_cols=332  Identities=23%  Similarity=0.271  Sum_probs=251.5

Q ss_pred             hhHHHhHcCCCCCchhHHHHHHHHHcC-CCEEEEccCCCCchhhhhccccc-----------------cCCc--EEEEcc
Q 037567            2 VSTLKKYFGYSVFRPYQKDVIQRIIEK-RDCLVVMATGSGKSLCYQLPPLV-----------------TGKT--ALVVSP   61 (374)
Q Consensus         2 ~~~l~~~~~~~~~~~~Q~~~~~~~~~~-~~~l~~a~tGsGKT~~~~l~~~~-----------------~~~~--~lil~P   61 (374)
                      ..+|.+ +||..|+++|...+|++..+ .|++=.|.||||||++|-+|++.                 ++.+  .||++|
T Consensus       193 L~aL~~-~gFs~Pt~IQsl~lp~ai~gk~DIlGaAeTGSGKTLAFGIPiv~~l~~~s~~s~e~~~~~~k~~k~~~LV~tP  271 (731)
T KOG0347|consen  193 LRALSN-LGFSRPTEIQSLVLPAAIRGKVDILGAAETGSGKTLAFGIPIVERLLESSDDSQELSNTSAKYVKPIALVVTP  271 (731)
T ss_pred             HHHHHh-cCCCCCccchhhcccHhhccchhcccccccCCCceeeecchhhhhhhhccchHhhhhhHHhccCcceeEEecC
Confidence            356777 89999999999999999998 68888999999999999999886                 1444  999999


Q ss_pred             hHHHHHHHHHHHHHc----CCceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHH-HHHhcCccEEEEeccc
Q 037567           62 LISLMQDQVMSLKQR----GINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWS-KLLKAGVCLFAVDEAH  136 (374)
Q Consensus        62 ~~~l~~q~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~-~~~~~~~~~vviDE~h  136 (374)
                      ||+|+-|+...+...    ++.+..++++......+ ......++|+|+||++|..+++.... ...+..+.++|+||++
T Consensus       272 TRELa~QV~~Hl~ai~~~t~i~v~si~GGLavqKQq-RlL~~~p~IVVATPGRlweli~e~n~~l~~~k~vkcLVlDEaD  350 (731)
T KOG0347|consen  272 TRELAHQVKQHLKAIAEKTQIRVASITGGLAVQKQQ-RLLNQRPDIVVATPGRLWELIEEDNTHLGNFKKVKCLVLDEAD  350 (731)
T ss_pred             hHHHHHHHHHHHHHhccccCeEEEEeechhHHHHHH-HHHhcCCCEEEecchHHHHHHHhhhhhhhhhhhceEEEEccHH
Confidence            999999999888754    56666666655444333 34445799999999999887664322 3345678899999999


Q ss_pred             hhhcccCcchHHHHHHHHHHHhc--CCCCeeEEEeecCcccHH--------------------HHHHhcCCCCC-eEEEe
Q 037567          137 CISEWGHDFRLEYKQLDKLRTFL--LGVPFVALTATATEKVRI--------------------DIINSLKLKNP-YVTIA  193 (374)
Q Consensus       137 ~~~~~~~~~~~~~~~~~~~~~~~--~~~~~i~~SaT~~~~~~~--------------------~~~~~~~~~~~-~~~~~  193 (374)
                      +|.+.|...... ..+..+.+..  +..|.+.||||..-....                    .+....++... .+...
T Consensus       351 RmvekghF~Els-~lL~~L~e~~~~~qrQTlVFSATlt~~~~~~~~~~~k~~~k~~~~~~kiq~Lmk~ig~~~kpkiiD~  429 (731)
T KOG0347|consen  351 RMVEKGHFEELS-KLLKHLNEEQKNRQRQTLVFSATLTLVLQQPLSSSRKKKDKEDELNAKIQHLMKKIGFRGKPKIIDL  429 (731)
T ss_pred             HHhhhccHHHHH-HHHHHhhhhhcccccceEEEEEEeehhhcChhHHhhhccchhhhhhHHHHHHHHHhCccCCCeeEec
Confidence            999988642211 2222222111  257899999996644322                    12222222222 11111


Q ss_pred             ccCCCceeEEEEeecCCcchHHHHHHHHHHh-------------hcCCCcEEEEecchhHHHHHHHHHHHcCCceeeeec
Q 037567          194 SFDRKNLFYGVKVINRGQSFVDELVQEILKS-------------VAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHG  260 (374)
Q Consensus       194 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------------~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~  260 (374)
                      ..+              ......+....+.-             ....|++|||||+.+.+.+++-.|...+++...+|+
T Consensus       430 t~q--------------~~ta~~l~Es~I~C~~~eKD~ylyYfl~ryPGrTlVF~NsId~vKRLt~~L~~L~i~p~~LHA  495 (731)
T KOG0347|consen  430 TPQ--------------SATASTLTESLIECPPLEKDLYLYYFLTRYPGRTLVFCNSIDCVKRLTVLLNNLDIPPLPLHA  495 (731)
T ss_pred             Ccc--------------hhHHHHHHHHhhcCCccccceeEEEEEeecCCceEEEechHHHHHHHHHHHhhcCCCCchhhH
Confidence            110              00011111111110             124588999999999999999999999999999999


Q ss_pred             CCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEEEEECCCCChhHHHHhhccCCCCCCceEEEEEeeccCCCcc
Q 037567          261 QMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKG  340 (374)
Q Consensus       261 ~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~~~~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~~~~~  340 (374)
                      .|..++|-+.++.|.+...-||+||+.+.+|+|+|++.|||+|-.|.+.+-|+||.||+.|.+..|..+.++.+.+...+
T Consensus       496 ~M~QKqRLknLEkF~~~~~~VLiaTDVAARGLDIp~V~HVIHYqVPrtseiYVHRSGRTARA~~~Gvsvml~~P~e~~~~  575 (731)
T KOG0347|consen  496 SMIQKQRLKNLEKFKQSPSGVLIATDVAARGLDIPGVQHVIHYQVPRTSEIYVHRSGRTARANSEGVSVMLCGPQEVGPL  575 (731)
T ss_pred             HHHHHHHHHhHHHHhcCCCeEEEeehhhhccCCCCCcceEEEeecCCccceeEecccccccccCCCeEEEEeChHHhHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cceeccccch
Q 037567          341 DFYCGESQTE  350 (374)
Q Consensus       341 ~~~~~~~~~~  350 (374)
                      .++|..++..
T Consensus       576 ~KL~ktL~k~  585 (731)
T KOG0347|consen  576 KKLCKTLKKK  585 (731)
T ss_pred             HHHHHHHhhc
Confidence            9888765543

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=100.00  E-value=9.5e-42  Score=324.54  Aligned_cols=309  Identities=23%  Similarity=0.289  Sum_probs=230.8

Q ss_pred             hhHHHhHcCCCCCchhHHHHHHHHHcC------CCEEEEccCCCCchhhhhccccc---cCCcEEEEcchHHHHHHHHHH
Q 037567            2 VSTLKKYFGYSVFRPYQKDVIQRIIEK------RDCLVVMATGSGKSLCYQLPPLV---TGKTALVVSPLISLMQDQVMS   72 (374)
Q Consensus         2 ~~~l~~~~~~~~~~~~Q~~~~~~~~~~------~~~l~~a~tGsGKT~~~~l~~~~---~~~~~lil~P~~~l~~q~~~~   72 (374)
                      ++++...++|. |+++|.++++.+.++      .+.+++||||||||++|+++++.   .+.+++|++||++|+.|+++.
T Consensus       251 ~~~~~~~l~f~-lt~~Q~~ai~~I~~d~~~~~~~~~Ll~~~TGSGKT~va~~~il~~~~~g~q~lilaPT~~LA~Q~~~~  329 (681)
T PRK10917        251 LKKFLASLPFE-LTGAQKRVVAEILADLASPKPMNRLLQGDVGSGKTVVAALAALAAIEAGYQAALMAPTEILAEQHYEN  329 (681)
T ss_pred             HHHHHHhCCCC-CCHHHHHHHHHHHHhhhccCCceEEEECCCCCcHHHHHHHHHHHHHHcCCeEEEEeccHHHHHHHHHH
Confidence            45677789995 999999999999875      37899999999999999887754   578999999999999999999


Q ss_pred             HHHc----CCceEEcCCCCCchh---hhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcc
Q 037567           73 LKQR----GINAEFLGSAQTDSS---VQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDF  145 (374)
Q Consensus        73 ~~~~----~~~~~~~~~~~~~~~---~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~  145 (374)
                      ++++    ++++..++++.....   .......+.++|+|+||+.+..       ...+.+++++|+||+|++...    
T Consensus       330 l~~l~~~~~i~v~ll~G~~~~~~r~~~~~~l~~g~~~IvVgT~~ll~~-------~v~~~~l~lvVIDE~Hrfg~~----  398 (681)
T PRK10917        330 LKKLLEPLGIRVALLTGSLKGKERREILEAIASGEADIVIGTHALIQD-------DVEFHNLGLVIIDEQHRFGVE----  398 (681)
T ss_pred             HHHHHhhcCcEEEEEcCCCCHHHHHHHHHHHhCCCCCEEEchHHHhcc-------cchhcccceEEEechhhhhHH----
Confidence            8764    577777777665432   2334455679999999987643       234578899999999986421    


Q ss_pred             hHHHHHHHHHHHhcCCCCeeEEEeecCcccHHHHHHhcCCCCCeEEEe-ccCCCceeEEEEeecCCcchHHHHHHHHHHh
Q 037567          146 RLEYKQLDKLRTFLLGVPFVALTATATEKVRIDIINSLKLKNPYVTIA-SFDRKNLFYGVKVINRGQSFVDELVQEILKS  224 (374)
Q Consensus       146 ~~~~~~~~~~~~~~~~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  224 (374)
                           ....+.....+.++++|||||.+....  ...++..+...... ...+..+...  ...  ......++..+.+.
T Consensus       399 -----qr~~l~~~~~~~~iL~~SATp~prtl~--~~~~g~~~~s~i~~~p~~r~~i~~~--~~~--~~~~~~~~~~i~~~  467 (681)
T PRK10917        399 -----QRLALREKGENPHVLVMTATPIPRTLA--MTAYGDLDVSVIDELPPGRKPITTV--VIP--DSRRDEVYERIREE  467 (681)
T ss_pred             -----HHHHHHhcCCCCCEEEEeCCCCHHHHH--HHHcCCCceEEEecCCCCCCCcEEE--EeC--cccHHHHHHHHHHH
Confidence                 112222333357899999999775432  22223222222211 1112222111  111  22234444555555


Q ss_pred             hcCCCcEEEEecchh--------HHHHHHHHHHHc--CCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccc
Q 037567          225 VAGAGSIIVYCMTIK--------DVEEISKALKQL--GVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDK  294 (374)
Q Consensus       225 ~~~~~~~lVf~~~~~--------~~~~l~~~l~~~--~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~  294 (374)
                      ...+++++|||+..+        .++.+++.|.+.  +.++..+||+++..+|..++++|.+|+.+|||||+++++|+|+
T Consensus       468 ~~~g~q~~v~~~~ie~s~~l~~~~~~~~~~~L~~~~~~~~v~~lHG~m~~~eR~~i~~~F~~g~~~ILVaT~vie~GiDi  547 (681)
T PRK10917        468 IAKGRQAYVVCPLIEESEKLDLQSAEETYEELQEAFPELRVGLLHGRMKPAEKDAVMAAFKAGEIDILVATTVIEVGVDV  547 (681)
T ss_pred             HHcCCcEEEEEcccccccchhHHHHHHHHHHHHHHCCCCcEEEEeCCCCHHHHHHHHHHHHcCCCCEEEECcceeeCccc
Confidence            567889999999543        456677777765  4689999999999999999999999999999999999999999


Q ss_pred             cCccEEEEECCCC-ChhHHHHhhccCCCCCCceEEEEEee
Q 037567          295 PDVRHVIHYGCPK-TLESYYQESGRCGRDGIASVCWLYYA  333 (374)
Q Consensus       295 ~~~~~vi~~~~p~-s~~~~~Q~~GR~~R~~~~g~~~~~~~  333 (374)
                      |++++||++++|. ....+.|++||+||.|..|.|++++.
T Consensus       548 p~v~~VIi~~~~r~gls~lhQ~~GRvGR~g~~g~~ill~~  587 (681)
T PRK10917        548 PNATVMVIENAERFGLAQLHQLRGRVGRGAAQSYCVLLYK  587 (681)
T ss_pred             CCCcEEEEeCCCCCCHHHHHHHhhcccCCCCceEEEEEEC
Confidence            9999999999986 57889999999999999999999985

>PRK00254 ski2-like helicase; Provisional

Probab=100.00  E-value=2.5e-42  Score=332.46  Aligned_cols=321  Identities=20%  Similarity=0.283  Sum_probs=227.3

Q ss_pred             hhHHHhHcCCCCCchhHHHHHHH-HHcCCCEEEEccCCCCchhhhhccccc----cCCcEEEEcchHHHHHHHHHHHHHc
Q 037567            2 VSTLKKYFGYSVFRPYQKDVIQR-IIEKRDCLVVMATGSGKSLCYQLPPLV----TGKTALVVSPLISLMQDQVMSLKQR   76 (374)
Q Consensus         2 ~~~l~~~~~~~~~~~~Q~~~~~~-~~~~~~~l~~a~tGsGKT~~~~l~~~~----~~~~~lil~P~~~l~~q~~~~~~~~   76 (374)
                      .+.|++ .||.+|+|+|.++++. +.+++++++++|||||||+++.++++.    .+.++++++|+++|+.|+++.+..+
T Consensus        13 ~~~l~~-~g~~~l~~~Q~~ai~~~~~~g~nvlv~apTGsGKT~~~~l~il~~l~~~~~~~l~l~P~~aLa~q~~~~~~~~   91 (720)
T PRK00254         13 KRVLKE-RGIEELYPPQAEALKSGVLEGKNLVLAIPTASGKTLVAEIVMVNKLLREGGKAVYLVPLKALAEEKYREFKDW   91 (720)
T ss_pred             HHHHHh-CCCCCCCHHHHHHHHHHHhCCCcEEEECCCCcHHHHHHHHHHHHHHHhcCCeEEEEeChHHHHHHHHHHHHHH
Confidence            456677 8999999999999986 788999999999999999999887654    4779999999999999999888753


Q ss_pred             ---CCceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHH
Q 037567           77 ---GINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLD  153 (374)
Q Consensus        77 ---~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~  153 (374)
                         |..+...+++......    ..+.++|+|+||+++..+...  ....++++++||+||+|.+.+.+..     ..+.
T Consensus        92 ~~~g~~v~~~~Gd~~~~~~----~~~~~~IiV~Tpe~~~~ll~~--~~~~l~~l~lvViDE~H~l~~~~rg-----~~le  160 (720)
T PRK00254         92 EKLGLRVAMTTGDYDSTDE----WLGKYDIIIATAEKFDSLLRH--GSSWIKDVKLVVADEIHLIGSYDRG-----ATLE  160 (720)
T ss_pred             hhcCCEEEEEeCCCCCchh----hhccCCEEEEcHHHHHHHHhC--CchhhhcCCEEEEcCcCccCCccch-----HHHH
Confidence               6666666665443221    224579999999998766543  2234678999999999999765443     2222


Q ss_pred             HHHHh-cCCCCeeEEEeecCcccHHHHHHhcCCCCCeEEEeccCCC-ceeE-EEEeecCC-c-chHHHHHHHHHHhhcCC
Q 037567          154 KLRTF-LLGVPFVALTATATEKVRIDIINSLKLKNPYVTIASFDRK-NLFY-GVKVINRG-Q-SFVDELVQEILKSVAGA  228 (374)
Q Consensus       154 ~~~~~-~~~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~-~~~~~~~~-~-~~~~~~~~~~~~~~~~~  228 (374)
                      .+... ..+.+++++|||+++.  .++..|++.............. .+.. ........ . .........+.+....+
T Consensus       161 ~il~~l~~~~qiI~lSATl~n~--~~la~wl~~~~~~~~~rpv~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~  238 (720)
T PRK00254        161 MILTHMLGRAQILGLSATVGNA--EELAEWLNAELVVSDWRPVKLRKGVFYQGFLFWEDGKIERFPNSWESLVYDAVKKG  238 (720)
T ss_pred             HHHHhcCcCCcEEEEEccCCCH--HHHHHHhCCccccCCCCCCcceeeEecCCeeeccCcchhcchHHHHHHHHHHHHhC
Confidence            22222 2368999999999764  3567777643211100000000 0000 00001110 0 00111222233333467


Q ss_pred             CcEEEEecchhHHHHHHHHHHHc---------------------------------CCceeeeecCCChHHHHHHHHhhh
Q 037567          229 GSIIVYCMTIKDVEEISKALKQL---------------------------------GVKAGTYHGQMGSKAREEAHRLFI  275 (374)
Q Consensus       229 ~~~lVf~~~~~~~~~l~~~l~~~---------------------------------~~~~~~~~~~~~~~~r~~~~~~f~  275 (374)
                      +++||||+++..++.++..+.+.                                 ...+.++|++++.++|..+.+.|+
T Consensus       239 ~~vLVF~~sr~~~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~gv~~hHagl~~~eR~~ve~~F~  318 (720)
T PRK00254        239 KGALVFVNTRRSAEKEALELAKKIKRFLTKPELRALKELADSLEENPTNEKLKKALRGGVAFHHAGLGRTERVLIEDAFR  318 (720)
T ss_pred             CCEEEEEcChHHHHHHHHHHHHHHHHhcCchhHHHHHHHHHHHhcCCCcHHHHHHHhhCEEEeCCCCCHHHHHHHHHHHH
Confidence            89999999999998877666321                                 224889999999999999999999


Q ss_pred             cCCeeEEEEeccccccccccCccEEEE-------ECCCC-ChhHHHHhhccCCCCC--CceEEEEEeeccC
Q 037567          276 RDEIRVMVATMAFGMGIDKPDVRHVIH-------YGCPK-TLESYYQESGRCGRDG--IASVCWLYYARSN  336 (374)
Q Consensus       276 ~g~~~ilv~t~~~~~G~d~~~~~~vi~-------~~~p~-s~~~~~Q~~GR~~R~~--~~g~~~~~~~~~~  336 (374)
                      +|.++|||||+.+++|+|+|..++||.       ++.|. +..+|.||+|||||.|  ..|.++++....+
T Consensus       319 ~G~i~VLvaT~tLa~Gvnipa~~vVI~~~~~~~~~~~~~~~~~~~~Qm~GRAGR~~~d~~G~~ii~~~~~~  389 (720)
T PRK00254        319 EGLIKVITATPTLSAGINLPAFRVIIRDTKRYSNFGWEDIPVLEIQQMMGRAGRPKYDEVGEAIIVATTEE  389 (720)
T ss_pred             CCCCeEEEeCcHHhhhcCCCceEEEECCceEcCCCCceeCCHHHHHHhhhccCCCCcCCCceEEEEecCcc
Confidence            999999999999999999999999883       33332 5679999999999975  5688888887654

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=100.00  E-value=9.9e-42  Score=322.52  Aligned_cols=308  Identities=23%  Similarity=0.278  Sum_probs=226.8

Q ss_pred             hHHHhHcCCCCCchhHHHHHHHHHcC------CCEEEEccCCCCchhhhhccccc---cCCcEEEEcchHHHHHHHHHHH
Q 037567            3 STLKKYFGYSVFRPYQKDVIQRIIEK------RDCLVVMATGSGKSLCYQLPPLV---TGKTALVVSPLISLMQDQVMSL   73 (374)
Q Consensus         3 ~~l~~~~~~~~~~~~Q~~~~~~~~~~------~~~l~~a~tGsGKT~~~~l~~~~---~~~~~lil~P~~~l~~q~~~~~   73 (374)
                      .++.+.++| +|++.|.++++.+.++      .+.+++||||||||.+|+++++.   .+.++++++||++|+.|+++.+
T Consensus       226 ~~~~~~lpf-~lt~~Q~~ai~~I~~~~~~~~~~~~Ll~g~TGSGKT~va~l~il~~~~~g~qvlilaPT~~LA~Q~~~~~  304 (630)
T TIGR00643       226 TKFLASLPF-KLTRAQKRVVKEILQDLKSDVPMNRLLQGDVGSGKTLVAALAMLAAIEAGYQVALMAPTEILAEQHYNSL  304 (630)
T ss_pred             HHHHHhCCC-CCCHHHHHHHHHHHHHhccCCCccEEEECCCCCcHHHHHHHHHHHHHHcCCcEEEECCHHHHHHHHHHHH
Confidence            455566999 6999999999999875      25799999999999998877654   5789999999999999999988


Q ss_pred             HHc----CCceEEcCCCCCchh---hhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcch
Q 037567           74 KQR----GINAEFLGSAQTDSS---VQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFR  146 (374)
Q Consensus        74 ~~~----~~~~~~~~~~~~~~~---~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~  146 (374)
                      +++    |+++..++++.....   .......+.++|+|+||..+..       ...+.+++++|+||+|++...     
T Consensus       305 ~~l~~~~gi~v~lltg~~~~~~r~~~~~~i~~g~~~IiVgT~~ll~~-------~~~~~~l~lvVIDEaH~fg~~-----  372 (630)
T TIGR00643       305 RNLLAPLGIEVALLTGSLKGKRRKELLETIASGQIHLVVGTHALIQE-------KVEFKRLALVIIDEQHRFGVE-----  372 (630)
T ss_pred             HHHhcccCcEEEEEecCCCHHHHHHHHHHHhCCCCCEEEecHHHHhc-------cccccccceEEEechhhccHH-----
Confidence            764    577777777655443   2334455778999999987642       234578899999999986421     


Q ss_pred             HHHHHHHHHHHhcC---CCCeeEEEeecCcccHHHHHHhcCCCCCe-EEEeccCCCceeEEEEeecCCcchHHHHHHHHH
Q 037567          147 LEYKQLDKLRTFLL---GVPFVALTATATEKVRIDIINSLKLKNPY-VTIASFDRKNLFYGVKVINRGQSFVDELVQEIL  222 (374)
Q Consensus       147 ~~~~~~~~~~~~~~---~~~~i~~SaT~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  222 (374)
                          ....+.....   +.++++|||||.+....  ....+..+.. +......+..+...  ....  .....++..+.
T Consensus       373 ----qr~~l~~~~~~~~~~~~l~~SATp~prtl~--l~~~~~l~~~~i~~~p~~r~~i~~~--~~~~--~~~~~~~~~i~  442 (630)
T TIGR00643       373 ----QRKKLREKGQGGFTPHVLVMSATPIPRTLA--LTVYGDLDTSIIDELPPGRKPITTV--LIKH--DEKDIVYEFIE  442 (630)
T ss_pred             ----HHHHHHHhcccCCCCCEEEEeCCCCcHHHH--HHhcCCcceeeeccCCCCCCceEEE--EeCc--chHHHHHHHHH
Confidence                1112222222   57899999998775432  1222211111 11111111111111  1111  22245555555


Q ss_pred             HhhcCCCcEEEEecch--------hHHHHHHHHHHHc--CCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccc
Q 037567          223 KSVAGAGSIIVYCMTI--------KDVEEISKALKQL--GVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGI  292 (374)
Q Consensus       223 ~~~~~~~~~lVf~~~~--------~~~~~l~~~l~~~--~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~  292 (374)
                      +....+.+++|||+..        ..++.+++.|.+.  +..+..+||+++.++|..+++.|++|+.+|||||+++++|+
T Consensus       443 ~~l~~g~q~~v~~~~i~~s~~~~~~~a~~~~~~L~~~~~~~~v~~lHG~m~~~eR~~i~~~F~~g~~~ILVaT~vie~Gv  522 (630)
T TIGR00643       443 EEIAKGRQAYVVYPLIEESEKLDLKAAEALYERLKKAFPKYNVGLLHGRMKSDEKEAVMEEFREGEVDILVATTVIEVGV  522 (630)
T ss_pred             HHHHhCCcEEEEEccccccccchHHHHHHHHHHHHhhCCCCcEEEEeCCCCHHHHHHHHHHHHcCCCCEEEECceeecCc
Confidence            5556788999999876        4466777777763  67899999999999999999999999999999999999999


Q ss_pred             cccCccEEEEECCCC-ChhHHHHhhccCCCCCCceEEEEEee
Q 037567          293 DKPDVRHVIHYGCPK-TLESYYQESGRCGRDGIASVCWLYYA  333 (374)
Q Consensus       293 d~~~~~~vi~~~~p~-s~~~~~Q~~GR~~R~~~~g~~~~~~~  333 (374)
                      |+|++++||+++.|. +...+.|++||+||.|..|.|++++.
T Consensus       523 DiP~v~~VIi~~~~r~gls~lhQ~~GRvGR~g~~g~~il~~~  564 (630)
T TIGR00643       523 DVPNATVMVIEDAERFGLSQLHQLRGRVGRGDHQSYCLLVYK  564 (630)
T ss_pred             ccCCCcEEEEeCCCcCCHHHHHHHhhhcccCCCCcEEEEEEC
Confidence            999999999999886 67899999999999999999999984

>KOG0334 consensus RNA helicase [RNA processing and modification]

Probab=100.00  E-value=9.4e-43  Score=323.48  Aligned_cols=337  Identities=22%  Similarity=0.309  Sum_probs=264.0

Q ss_pred             hHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc-----------cCCcEEEEcchHHHHHHHHH
Q 037567            3 STLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV-----------TGKTALVVSPLISLMQDQVM   71 (374)
Q Consensus         3 ~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~-----------~~~~~lil~P~~~l~~q~~~   71 (374)
                      ..+ +.+||.+++|+|.+|||++..|+++|.+|.||||||++|++|++.           .++.++|++||++|+.|..+
T Consensus       378 ~tl-kkl~y~k~~~IQ~qAiP~ImsGrdvIgvakTgSGKT~af~LPmirhi~dQr~~~~gdGPi~li~aPtrela~QI~r  456 (997)
T KOG0334|consen  378 ETL-KKLGYEKPTPIQAQAIPAIMSGRDVIGVAKTGSGKTLAFLLPMIRHIKDQRPLEEGDGPIALILAPTRELAMQIHR  456 (997)
T ss_pred             HHH-HHhcCCCCcchhhhhcchhccCcceEEeeccCCccchhhhcchhhhhhcCCChhhCCCceEEEEcCCHHHHHHHHH
Confidence            345 449999999999999999999999999999999999999999875           27889999999999999999


Q ss_pred             HHHHc----CCceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHH-HhcCccEEEEeccchhhcccCcch
Q 037567           72 SLKQR----GINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKL-LKAGVCLFAVDEAHCISEWGHDFR  146 (374)
Q Consensus        72 ~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~-~~~~~~~vviDE~h~~~~~~~~~~  146 (374)
                      ++..|    ++.+..+.+.............+ .+|+|+||+++.+++-.....+ .+....++|+||++++.+.+++..
T Consensus       457 ~~~kf~k~l~ir~v~vygg~~~~~qiaelkRg-~eIvV~tpGRmiD~l~~n~grvtnlrR~t~lv~deaDrmfdmgfePq  535 (997)
T KOG0334|consen  457 EVRKFLKLLGIRVVCVYGGSGISQQIAELKRG-AEIVVCTPGRMIDILCANSGRVTNLRRVTYLVLDEADRMFDMGFEPQ  535 (997)
T ss_pred             HHHHHHhhcCceEEEecCCccHHHHHHHHhcC-CceEEeccchhhhhHhhcCCccccccccceeeechhhhhheeccCcc
Confidence            98876    66666666655555555555445 9999999999988765522222 223445999999999998776642


Q ss_pred             HHHHHHHHHHHhcCCCCeeEEEeecCcccHHHHHHhcCCCCCeEEEe--ccCCCceeEEEEeecCCcchHHHHHHHHHHh
Q 037567          147 LEYKQLDKLRTFLLGVPFVALTATATEKVRIDIINSLKLKNPYVTIA--SFDRKNLFYGVKVINRGQSFVDELVQEILKS  224 (374)
Q Consensus       147 ~~~~~~~~~~~~~~~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  224 (374)
                      ...    -+....+..|.+++|||.+.... .+.......+..+...  +.....+...+.+.......+..++ +++..
T Consensus       536 ~~~----Ii~nlrpdrQtvlfSatfpr~m~-~la~~vl~~Pveiiv~~~svV~k~V~q~v~V~~~e~eKf~kL~-eLl~e  609 (997)
T KOG0334|consen  536 ITR----ILQNLRPDRQTVLFSATFPRSME-ALARKVLKKPVEIIVGGRSVVCKEVTQVVRVCAIENEKFLKLL-ELLGE  609 (997)
T ss_pred             cch----HHhhcchhhhhhhhhhhhhHHHH-HHHHHhhcCCeeEEEccceeEeccceEEEEEecCchHHHHHHH-HHHHH
Confidence            221    22223457899999999998844 3333332232222222  2223344444555554444444433 33444


Q ss_pred             hcCCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEEEEEC
Q 037567          225 VAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYG  304 (374)
Q Consensus       225 ~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~~~  304 (374)
                      ....+++||||.+...|..+.+.|.+.|+.+..+||+.+..+|..++++|+++...+|++|+.+.+|+|++.+..||+|+
T Consensus       610 ~~e~~~tiiFv~~qe~~d~l~~~L~~ag~~~~slHGgv~q~dR~sti~dfK~~~~~LLvaTsvvarGLdv~~l~Lvvnyd  689 (997)
T KOG0334|consen  610 RYEDGKTIIFVDKQEKADALLRDLQKAGYNCDSLHGGVDQHDRSSTIEDFKNGVVNLLVATSVVARGLDVKELILVVNYD  689 (997)
T ss_pred             HhhcCCEEEEEcCchHHHHHHHHHHhcCcchhhhcCCCchHHHHhHHHHHhccCceEEEehhhhhcccccccceEEEEcc
Confidence            45689999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCChhHHHHhhccCCCCCCceEEEEEeeccCCCcccceeccc
Q 037567          305 CPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFYCGES  347 (374)
Q Consensus       305 ~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~~~~~~~~~~~~  347 (374)
                      +|....+|+||.||+||.|..|.+++|..+++......++...
T Consensus       690 ~pnh~edyvhR~gRTgragrkg~AvtFi~p~q~~~a~dl~~al  732 (997)
T KOG0334|consen  690 FPNHYEDYVHRVGRTGRAGRKGAAVTFITPDQLKYAGDLCKAL  732 (997)
T ss_pred             cchhHHHHHHHhcccccCCccceeEEEeChHHhhhHHHHHHHH
Confidence            9999999999999999999999999999998888877776644

>PRK01172 ski2-like helicase; Provisional

Probab=100.00  E-value=8.7e-42  Score=327.45  Aligned_cols=326  Identities=20%  Similarity=0.255  Sum_probs=225.0

Q ss_pred             HHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc---cCCcEEEEcchHHHHHHHHHHHHHc---C
Q 037567            4 TLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV---TGKTALVVSPLISLMQDQVMSLKQR---G   77 (374)
Q Consensus         4 ~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~---~~~~~lil~P~~~l~~q~~~~~~~~---~   77 (374)
                      .+.+ .+|. ++|+|.++++.+.+++++++++|||||||+++.++++.   .+.++++++|+++|+.|++++++++   |
T Consensus        15 ~~~~-~~~~-l~~~Q~~ai~~l~~~~nvlv~apTGSGKTl~a~lail~~l~~~~k~v~i~P~raLa~q~~~~~~~l~~~g   92 (674)
T PRK01172         15 LFTG-NDFE-LYDHQRMAIEQLRKGENVIVSVPTAAGKTLIAYSAIYETFLAGLKSIYIVPLRSLAMEKYEELSRLRSLG   92 (674)
T ss_pred             HHhh-CCCC-CCHHHHHHHHHHhcCCcEEEECCCCchHHHHHHHHHHHHHHhCCcEEEEechHHHHHHHHHHHHHHhhcC
Confidence            3444 5776 99999999999999999999999999999998877654   4788999999999999999988754   5


Q ss_pred             CceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHH
Q 037567           78 INAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRT  157 (374)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~  157 (374)
                      ..+....++......    ....++|+|+||+++..+..+  ....+.+++++|+||+|.+.+.+...... ..+..+..
T Consensus        93 ~~v~~~~G~~~~~~~----~~~~~dIiv~Tpek~~~l~~~--~~~~l~~v~lvViDEaH~l~d~~rg~~le-~ll~~~~~  165 (674)
T PRK01172         93 MRVKISIGDYDDPPD----FIKRYDVVILTSEKADSLIHH--DPYIINDVGLIVADEIHIIGDEDRGPTLE-TVLSSARY  165 (674)
T ss_pred             CeEEEEeCCCCCChh----hhccCCEEEECHHHHHHHHhC--ChhHHhhcCEEEEecchhccCCCccHHHH-HHHHHHHh
Confidence            555555544332211    123469999999998776554  23456789999999999997644332111 12223333


Q ss_pred             hcCCCCeeEEEeecCcccHHHHHHhcCCCCCeEEEeccCCCceeEEE----Ee-ecCCcchHHHHHHHHHHhhcCCCcEE
Q 037567          158 FLLGVPFVALTATATEKVRIDIINSLKLKNPYVTIASFDRKNLFYGV----KV-INRGQSFVDELVQEILKSVAGAGSII  232 (374)
Q Consensus       158 ~~~~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~-~~~~~~~~~~~~~~~~~~~~~~~~~l  232 (374)
                      ..++.+++++|||+++..  ++..|++.....   .......+....    .. ..............+.+...+++++|
T Consensus       166 ~~~~~riI~lSATl~n~~--~la~wl~~~~~~---~~~r~vpl~~~i~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~vL  240 (674)
T PRK01172        166 VNPDARILALSATVSNAN--ELAQWLNASLIK---SNFRPVPLKLGILYRKRLILDGYERSQVDINSLIKETVNDGGQVL  240 (674)
T ss_pred             cCcCCcEEEEeCccCCHH--HHHHHhCCCccC---CCCCCCCeEEEEEecCeeeecccccccccHHHHHHHHHhCCCcEE
Confidence            335789999999997643  566776543211   000000011000    00 11111111111222222244688999


Q ss_pred             EEecchhHHHHHHHHHHHcC-------------------------CceeeeecCCChHHHHHHHHhhhcCCeeEEEEecc
Q 037567          233 VYCMTIKDVEEISKALKQLG-------------------------VKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMA  287 (374)
Q Consensus       233 Vf~~~~~~~~~l~~~l~~~~-------------------------~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~  287 (374)
                      |||++++.++.+++.|.+..                         ..+..+||+++.++|..+.+.|++|.++|||||+.
T Consensus       241 VF~~sr~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~gv~~~hagl~~~eR~~ve~~f~~g~i~VLvaT~~  320 (674)
T PRK01172        241 VFVSSRKNAEDYAEMLIQHFPEFNDFKVSSENNNVYDDSLNEMLPHGVAFHHAGLSNEQRRFIEEMFRNRYIKVIVATPT  320 (674)
T ss_pred             EEeccHHHHHHHHHHHHHhhhhcccccccccccccccHHHHHHHhcCEEEecCCCCHHHHHHHHHHHHcCCCeEEEecch
Confidence            99999999999998886531                         24678999999999999999999999999999999


Q ss_pred             ccccccccCccEEEEECC---------CCChhHHHHhhccCCCCCC--ceEEEEEeeccC-CCccccee
Q 037567          288 FGMGIDKPDVRHVIHYGC---------PKTLESYYQESGRCGRDGI--ASVCWLYYARSN-FAKGDFYC  344 (374)
Q Consensus       288 ~~~G~d~~~~~~vi~~~~---------p~s~~~~~Q~~GR~~R~~~--~g~~~~~~~~~~-~~~~~~~~  344 (374)
                      +++|+|+|+..+|| .+.         |.+..+|.||+|||||.|.  .|.+++++...+ ++.+++++
T Consensus       321 la~Gvnipa~~VII-~~~~~~~~~~~~~~s~~~~~Qm~GRAGR~g~d~~g~~~i~~~~~~~~~~~~~~l  388 (674)
T PRK01172        321 LAAGVNLPARLVIV-RDITRYGNGGIRYLSNMEIKQMIGRAGRPGYDQYGIGYIYAASPASYDAAKKYL  388 (674)
T ss_pred             hhccCCCcceEEEE-cCceEeCCCCceeCCHHHHHHHhhcCCCCCCCCcceEEEEecCcccHHHHHHHH
Confidence            99999999865555 332         4578899999999999984  555666654433 44454554

>PRK10689 transcription-repair coupling factor; Provisional

Probab=100.00  E-value=1.2e-40  Score=327.78  Aligned_cols=310  Identities=20%  Similarity=0.253  Sum_probs=227.7

Q ss_pred             hhHHHhHcCCCCCchhHHHHHHHHHcC------CCEEEEccCCCCchhhhhcccc---ccCCcEEEEcchHHHHHHHHHH
Q 037567            2 VSTLKKYFGYSVFRPYQKDVIQRIIEK------RDCLVVMATGSGKSLCYQLPPL---VTGKTALVVSPLISLMQDQVMS   72 (374)
Q Consensus         2 ~~~l~~~~~~~~~~~~Q~~~~~~~~~~------~~~l~~a~tGsGKT~~~~l~~~---~~~~~~lil~P~~~l~~q~~~~   72 (374)
                      ..++...|+| +|++.|.++++.+.++      .+.+++|+||+|||.+++.++.   ..+.+++|++||++|+.|+++.
T Consensus       590 ~~~~~~~~~~-~~T~~Q~~aI~~il~d~~~~~~~d~Ll~a~TGsGKT~val~aa~~~~~~g~qvlvLvPT~eLA~Q~~~~  668 (1147)
T PRK10689        590 YQLFCDSFPF-ETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVENHKQVAVLVPTTLLAQQHYDN  668 (1147)
T ss_pred             HHHHHHhCCC-CCCHHHHHHHHHHHHHhhcCCCCCEEEEcCCCcCHHHHHHHHHHHHHHcCCeEEEEeCcHHHHHHHHHH
Confidence            3567777999 5999999999999886      7899999999999987665543   4688999999999999999998


Q ss_pred             HHHc----CCceEEcCCCCCchhhh---hhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcc
Q 037567           73 LKQR----GINAEFLGSAQTDSSVQ---TKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDF  145 (374)
Q Consensus        73 ~~~~----~~~~~~~~~~~~~~~~~---~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~  145 (374)
                      +++.    ++.+..+.+..+..+..   .....+.++|+|+||+.+..       ...+.+++++||||+|++.   .. 
T Consensus       669 f~~~~~~~~v~i~~l~g~~s~~e~~~il~~l~~g~~dIVVgTp~lL~~-------~v~~~~L~lLVIDEahrfG---~~-  737 (1147)
T PRK10689        669 FRDRFANWPVRIEMLSRFRSAKEQTQILAEAAEGKIDILIGTHKLLQS-------DVKWKDLGLLIVDEEHRFG---VR-  737 (1147)
T ss_pred             HHHhhccCCceEEEEECCCCHHHHHHHHHHHHhCCCCEEEECHHHHhC-------CCCHhhCCEEEEechhhcc---hh-
Confidence            8753    34444444433333222   22234678999999975421       2234678999999999973   21 


Q ss_pred             hHHHHHHHHHHHhcCCCCeeEEEeecCcccHHHHHHhcCCCCCeEEEecc-CCCceeEEEEeecCCcchHHHHHHHHHHh
Q 037567          146 RLEYKQLDKLRTFLLGVPFVALTATATEKVRIDIINSLKLKNPYVTIASF-DRKNLFYGVKVINRGQSFVDELVQEILKS  224 (374)
Q Consensus       146 ~~~~~~~~~~~~~~~~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  224 (374)
                           ....+.....+.++++|||||.+.....  ...+..++.+..... .+..+....... . .   ......++..
T Consensus       738 -----~~e~lk~l~~~~qvLl~SATpiprtl~l--~~~gl~d~~~I~~~p~~r~~v~~~~~~~-~-~---~~~k~~il~e  805 (1147)
T PRK10689        738 -----HKERIKAMRADVDILTLTATPIPRTLNM--AMSGMRDLSIIATPPARRLAVKTFVREY-D-S---LVVREAILRE  805 (1147)
T ss_pred             -----HHHHHHhcCCCCcEEEEcCCCCHHHHHH--HHhhCCCcEEEecCCCCCCCceEEEEec-C-c---HHHHHHHHHH
Confidence                 1223333445789999999998765432  223344444333222 222221111111 1 1   1122334444


Q ss_pred             hcCCCcEEEEecchhHHHHHHHHHHHc--CCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEEEE
Q 037567          225 VAGAGSIIVYCMTIKDVEEISKALKQL--GVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIH  302 (374)
Q Consensus       225 ~~~~~~~lVf~~~~~~~~~l~~~l~~~--~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~  302 (374)
                      ...+++++|||++++.++.+++.|++.  +..+..+||+|+.++|..++.+|.+|+.+|||||+++++|+|+|++++||.
T Consensus       806 l~r~gqv~vf~n~i~~ie~la~~L~~~~p~~~v~~lHG~m~q~eRe~im~~Fr~Gk~~VLVaTdIierGIDIP~v~~VIi  885 (1147)
T PRK10689        806 ILRGGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIII  885 (1147)
T ss_pred             HhcCCeEEEEECCHHHHHHHHHHHHHhCCCCcEEEEeCCCCHHHHHHHHHHHHhcCCCEEEECchhhcccccccCCEEEE
Confidence            456789999999999999999999986  678999999999999999999999999999999999999999999999996


Q ss_pred             ECCC-CChhHHHHhhccCCCCCCceEEEEEeecc
Q 037567          303 YGCP-KTLESYYQESGRCGRDGIASVCWLYYARS  335 (374)
Q Consensus       303 ~~~p-~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~  335 (374)
                      .... .+..+|.|++||+||.|+.|.|++++...
T Consensus       886 ~~ad~fglaq~~Qr~GRvGR~g~~g~a~ll~~~~  919 (1147)
T PRK10689        886 ERADHFGLAQLHQLRGRVGRSHHQAYAWLLTPHP  919 (1147)
T ss_pred             ecCCCCCHHHHHHHhhccCCCCCceEEEEEeCCC
Confidence            5543 46788999999999999999999888653

>KOG0344 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=100.00  E-value=6.9e-42  Score=299.33  Aligned_cols=336  Identities=21%  Similarity=0.252  Sum_probs=251.3

Q ss_pred             hHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhcccccc-----------CCcEEEEcchHHHHHHHHH
Q 037567            3 STLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVT-----------GKTALVVSPLISLMQDQVM   71 (374)
Q Consensus         3 ~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~~-----------~~~~lil~P~~~l~~q~~~   71 (374)
                      +++.. .+|++|+|.|.+++|.++++++++.+||||||||++|.+|++.+           +.+++|+.|+++|+.|.++
T Consensus       149 ~nl~~-~~F~~Pt~iq~~aipvfl~~r~~lAcapTGsgKtlaf~~Pil~~L~~~~~~~~~~gl~a~Il~ptreLa~Qi~r  227 (593)
T KOG0344|consen  149 ENLQE-LGFDEPTPIQKQAIPVFLEKRDVLACAPTGSGKTLAFNLPILQHLKDLSQEKHKVGLRALILSPTRELAAQIYR  227 (593)
T ss_pred             HhHhh-CCCCCCCcccchhhhhhhcccceEEeccCCCcchhhhhhHHHHHHHHhhcccCccceEEEEecchHHHHHHHHH
Confidence            45556 79999999999999999999999999999999999999998752           4689999999999999999


Q ss_pred             HHHHcCCce--E----EcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcc
Q 037567           72 SLKQRGINA--E----FLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDF  145 (374)
Q Consensus        72 ~~~~~~~~~--~----~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~  145 (374)
                      ++..+..+.  .    ...................++++++||-++...+......+.+.++..+|+||++.+.+. ..+
T Consensus       228 e~~k~~~~~~t~~~a~~~~~~~~~~qk~a~~~~~k~dili~TP~ri~~~~~~~~~~idl~~V~~lV~dEaD~lfe~-~~f  306 (593)
T KOG0344|consen  228 EMRKYSIDEGTSLRAAQFSKPAYPSQKPAFLSDEKYDILISTPMRIVGLLGLGKLNIDLSKVEWLVVDEADLLFEP-EFF  306 (593)
T ss_pred             HHHhcCCCCCCchhhhhcccccchhhccchhHHHHHHHHhcCHHHHHHHhcCCCccchhheeeeEeechHHhhhCh-hhH
Confidence            999875331  1    111111122222333445679999999987766554333457788999999999999875 223


Q ss_pred             hHHHHHHHHHHHhcCCCCeeEEEeecCcccHHHHHHhcCCCCCe-EEEeccCCCceeEEE-EeecCCcchHHHHHHHHHH
Q 037567          146 RLEYKQLDKLRTFLLGVPFVALTATATEKVRIDIINSLKLKNPY-VTIASFDRKNLFYGV-KVINRGQSFVDELVQEILK  223 (374)
Q Consensus       146 ~~~~~~~~~~~~~~~~~~~i~~SaT~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~  223 (374)
                      ...+..+-..+.. ++..+-+||||.+....+  +..+...+.. +.+...+..+..... ..+........-.+..++.
T Consensus       307 ~~Qla~I~sac~s-~~i~~a~FSat~~~~VEE--~~~~i~~~~~~vivg~~~sa~~~V~QelvF~gse~~K~lA~rq~v~  383 (593)
T KOG0344|consen  307 VEQLADIYSACQS-PDIRVALFSATISVYVEE--WAELIKSDLKRVIVGLRNSANETVDQELVFCGSEKGKLLALRQLVA  383 (593)
T ss_pred             HHHHHHHHHHhcC-cchhhhhhhccccHHHHH--HHHHhhccceeEEEecchhHhhhhhhhheeeecchhHHHHHHHHHh
Confidence            3223333333332 567788999999887753  3333333333 333322222111111 1122222222333444444


Q ss_pred             hhcCCCcEEEEecchhHHHHHHHHH-HHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEEEE
Q 037567          224 SVAGAGSIIVYCMTIKDVEEISKAL-KQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIH  302 (374)
Q Consensus       224 ~~~~~~~~lVf~~~~~~~~~l~~~l-~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~  302 (374)
                      .. -.-+++||+.+.+.+..|...| .-.++++..+||+.+..+|...++.|+.|++.+|+||+.+++|+|+.+++.||+
T Consensus       384 ~g-~~PP~lIfVQs~eRak~L~~~L~~~~~i~v~vIh~e~~~~qrde~~~~FR~g~IwvLicTdll~RGiDf~gvn~VIn  462 (593)
T KOG0344|consen  384 SG-FKPPVLIFVQSKERAKQLFEELEIYDNINVDVIHGERSQKQRDETMERFRIGKIWVLICTDLLARGIDFKGVNLVIN  462 (593)
T ss_pred             cc-CCCCeEEEEecHHHHHHHHHHhhhccCcceeeEecccchhHHHHHHHHHhccCeeEEEehhhhhccccccCcceEEe
Confidence            42 4578999999999999999999 567889999999999999999999999999999999999999999999999999


Q ss_pred             ECCCCChhHHHHhhccCCCCCCceEEEEEeeccCCCccccee
Q 037567          303 YGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFYC  344 (374)
Q Consensus       303 ~~~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~~~~~~~~~  344 (374)
                      +|.|.+...|+||+||+||.|+.|.+++||+..|+..++-+.
T Consensus       463 yD~p~s~~syihrIGRtgRag~~g~Aitfytd~d~~~ir~ia  504 (593)
T KOG0344|consen  463 YDFPQSDLSYIHRIGRTGRAGRSGKAITFYTDQDMPRIRSIA  504 (593)
T ss_pred             cCCCchhHHHHHHhhccCCCCCCcceEEEeccccchhhhhHH
Confidence            999999999999999999999999999999999988776653

>KOG4284 consensus DEAD box protein [Transcription]

Probab=100.00  E-value=3.8e-41  Score=296.47  Aligned_cols=320  Identities=18%  Similarity=0.219  Sum_probs=251.3

Q ss_pred             HHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc------cCCcEEEEcchHHHHHHHHHHHHHcCC
Q 037567            5 LKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV------TGKTALVVSPLISLMQDQVMSLKQRGI   78 (374)
Q Consensus         5 l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~------~~~~~lil~P~~~l~~q~~~~~~~~~~   78 (374)
                      |++ .+|..|+++|..|+|.++.+-|.|+.+..|+|||++|...++.      .....+||+|||+++-|+.+.+...++
T Consensus        40 lrr-n~f~~ptkiQaaAIP~~~~kmDliVQaKSGTGKTlVfsv~av~sl~~~~~~~q~~Iv~PTREiaVQI~~tv~~v~~  118 (980)
T KOG4284|consen   40 LRR-NAFALPTKIQAAAIPAIFSKMDLIVQAKSGTGKTLVFSVLAVESLDSRSSHIQKVIVTPTREIAVQIKETVRKVAP  118 (980)
T ss_pred             HHh-hcccCCCchhhhhhhhhhcccceEEEecCCCCceEEEEeeeehhcCcccCcceeEEEecchhhhhHHHHHHHHhcc
Confidence            444 6999999999999999999999999999999999999877775      367899999999999999999887643


Q ss_pred             -----ceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHH
Q 037567           79 -----NAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLD  153 (374)
Q Consensus        79 -----~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~  153 (374)
                           ...++.++......  ......++|+|+||+++..+...  +..+..+++++|+|||+.+.+.+..    -..++
T Consensus       119 sf~g~~csvfIGGT~~~~d--~~rlk~~rIvIGtPGRi~qL~el--~~~n~s~vrlfVLDEADkL~~t~sf----q~~In  190 (980)
T KOG4284|consen  119 SFTGARCSVFIGGTAHKLD--LIRLKQTRIVIGTPGRIAQLVEL--GAMNMSHVRLFVLDEADKLMDTESF----QDDIN  190 (980)
T ss_pred             cccCcceEEEecCchhhhh--hhhhhhceEEecCchHHHHHHHh--cCCCccceeEEEeccHHhhhchhhH----HHHHH
Confidence                 44445444333332  23335578999999999877554  5667789999999999999874322    15667


Q ss_pred             HHHHhcC-CCCeeEEEeecCcccHHHHHHhcCCCCCeEEEeccCCCceeEE--EEeecC---C---cchHHHHHHHHHHh
Q 037567          154 KLRTFLL-GVPFVALTATATEKVRIDIINSLKLKNPYVTIASFDRKNLFYG--VKVINR---G---QSFVDELVQEILKS  224 (374)
Q Consensus       154 ~~~~~~~-~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~---~---~~~~~~~~~~~~~~  224 (374)
                      .+...+| ..+++++|||.+......+...+ -++..+.....+..-+...  +.....   .   .....+.+.++.+.
T Consensus       191 ~ii~slP~~rQv~a~SATYp~nLdn~Lsk~m-rdp~lVr~n~~d~~L~GikQyv~~~~s~nnsveemrlklq~L~~vf~~  269 (980)
T KOG4284|consen  191 IIINSLPQIRQVAAFSATYPRNLDNLLSKFM-RDPALVRFNADDVQLFGIKQYVVAKCSPNNSVEEMRLKLQKLTHVFKS  269 (980)
T ss_pred             HHHHhcchhheeeEEeccCchhHHHHHHHHh-cccceeecccCCceeechhheeeeccCCcchHHHHHHHHHHHHHHHhh
Confidence            6777666 68899999999998775444433 2333333333222221111  111111   1   12244556666666


Q ss_pred             hcCCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEEEEEC
Q 037567          225 VAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYG  304 (374)
Q Consensus       225 ~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~~~  304 (374)
                      + +..+.||||+....|+-++..|+..|+++-++.|.|+.++|...+..++.-..+|||+|+..++|+|-++++.||+.|
T Consensus       270 i-py~QAlVF~~~~sra~~~a~~L~ssG~d~~~ISgaM~Q~~Rl~a~~~lr~f~~rILVsTDLtaRGIDa~~vNLVVNiD  348 (980)
T KOG4284|consen  270 I-PYVQALVFCDQISRAEPIATHLKSSGLDVTFISGAMSQKDRLLAVDQLRAFRVRILVSTDLTARGIDADNVNLVVNID  348 (980)
T ss_pred             C-chHHHHhhhhhhhhhhHHHHHhhccCCCeEEeccccchhHHHHHHHHhhhceEEEEEecchhhccCCccccceEEecC
Confidence            5 678899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCChhHHHHhhccCCCCCCceEEEEEeecc
Q 037567          305 CPKTLESYYQESGRCGRDGIASVCWLYYARS  335 (374)
Q Consensus       305 ~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~  335 (374)
                      +|.+..+|.||||||||+|..|.+++++...
T Consensus       349 ~p~d~eTY~HRIGRAgRFG~~G~aVT~~~~~  379 (980)
T KOG4284|consen  349 APADEETYFHRIGRAGRFGAHGAAVTLLEDE  379 (980)
T ss_pred             CCcchHHHHHHhhhcccccccceeEEEeccc
Confidence            9999999999999999999999999988764

>PHA02558 uvsW UvsW helicase; Provisional

Probab=100.00  E-value=1.3e-39  Score=300.69  Aligned_cols=297  Identities=17%  Similarity=0.130  Sum_probs=207.4

Q ss_pred             CCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccc---ccc-CCcEEEEcchHHHHHHHHHHHHHcCCc----eEEc
Q 037567           12 SVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPP---LVT-GKTALVVSPLISLMQDQVMSLKQRGIN----AEFL   83 (374)
Q Consensus        12 ~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~---~~~-~~~~lil~P~~~l~~q~~~~~~~~~~~----~~~~   83 (374)
                      ..|+++|.++++.+++++++++++|||+|||.++...+   +.+ ..++||++|+++|+.||.+.+.+++..    ...+
T Consensus       113 ~~~r~~Q~~av~~~l~~~~~il~apTGsGKT~i~~~l~~~~~~~~~~~vLilvpt~eL~~Q~~~~l~~~~~~~~~~~~~i  192 (501)
T PHA02558        113 IEPHWYQYDAVYEGLKNNRRLLNLPTSAGKSLIQYLLSRYYLENYEGKVLIIVPTTSLVTQMIDDFVDYRLFPREAMHKI  192 (501)
T ss_pred             CCCCHHHHHHHHHHHhcCceEEEeCCCCCHHHHHHHHHHHHHhcCCCeEEEEECcHHHHHHHHHHHHHhccccccceeEE
Confidence            47999999999999999999999999999998764332   223 348999999999999999999987532    1112


Q ss_pred             CCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHHhcC-CC
Q 037567           84 GSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLL-GV  162 (374)
Q Consensus        84 ~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~~-~~  162 (374)
                      .++...        ....+|+|+||+++....     ...+.++++||+||||++....         +..+....+ ..
T Consensus       193 ~~g~~~--------~~~~~I~VaT~qsl~~~~-----~~~~~~~~~iIvDEaH~~~~~~---------~~~il~~~~~~~  250 (501)
T PHA02558        193 YSGTAK--------DTDAPIVVSTWQSAVKQP-----KEWFDQFGMVIVDECHLFTGKS---------LTSIITKLDNCK  250 (501)
T ss_pred             ecCccc--------CCCCCEEEeeHHHHhhch-----hhhccccCEEEEEchhcccchh---------HHHHHHhhhccc
Confidence            121111        123689999999886542     2235788999999999986522         233333333 46


Q ss_pred             CeeEEEeecCcccHHH--HHHhcCCCCCeEEEecc----CC---CceeEE-EEe--------------ec------CCcc
Q 037567          163 PFVALTATATEKVRID--IINSLKLKNPYVTIASF----DR---KNLFYG-VKV--------------IN------RGQS  212 (374)
Q Consensus       163 ~~i~~SaT~~~~~~~~--~~~~~~~~~~~~~~~~~----~~---~~~~~~-~~~--------------~~------~~~~  212 (374)
                      ++++|||||.......  +...++   +.......    ..   ...... +..              +.      ....
T Consensus       251 ~~lGLTATp~~~~~~~~~~~~~fG---~i~~~v~~~~li~~g~l~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~l~~~~  327 (501)
T PHA02558        251 FKFGLTGSLRDGKANILQYVGLFG---DIFKPVTTSQLMEEGQVTDLKINSIFLRYPDEDRVKLKGEDYQEEIKYITSHT  327 (501)
T ss_pred             eEEEEeccCCCccccHHHHHHhhC---CceEEecHHHHHhCCCcCCceEEEEeccCCHHHhhhhcccchHHHHHHHhccH
Confidence            7999999997643211  111121   11100000    00   000000 000              00      0001


Q ss_pred             hHHHHHHHHHH-hhcCCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEe-ccccc
Q 037567          213 FVDELVQEILK-SVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVAT-MAFGM  290 (374)
Q Consensus       213 ~~~~~~~~~~~-~~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t-~~~~~  290 (374)
                      ....++..+.. ....+.+++||+.+.++++.+++.|.+.+.++..+||+++.++|..+++.|++|+..+||+| +.+++
T Consensus       328 ~Rn~~I~~~~~~~~~~~~~~lV~~~~~~h~~~L~~~L~~~g~~v~~i~G~~~~~eR~~i~~~~~~~~~~vLvaT~~~l~e  407 (501)
T PHA02558        328 KRNKWIANLALKLAKKGENTFVMFKYVEHGKPLYEMLKKVYDKVYYVSGEVDTEDRNEMKKIAEGGKGIIIVASYGVFST  407 (501)
T ss_pred             HHHHHHHHHHHHHHhcCCCEEEEEEEHHHHHHHHHHHHHcCCCEEEEeCCCCHHHHHHHHHHHhCCCCeEEEEEcceecc
Confidence            11122222222 22356889999999999999999999999999999999999999999999999998899988 79999


Q ss_pred             cccccCccEEEEECCCCChhHHHHhhccCCCCCCceEEEEEee
Q 037567          291 GIDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYA  333 (374)
Q Consensus       291 G~d~~~~~~vi~~~~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~  333 (374)
                      |+|+|++++||+..++.|...|+||+||++|.+.++....+++
T Consensus       408 G~Dip~ld~vIl~~p~~s~~~~~QriGR~~R~~~~K~~~~i~D  450 (501)
T PHA02558        408 GISIKNLHHVIFAHPSKSKIIVLQSIGRVLRKHGSKSIATVWD  450 (501)
T ss_pred             ccccccccEEEEecCCcchhhhhhhhhccccCCCCCceEEEEE
Confidence            9999999999999999999999999999999987654444443

>KOG0327 consensus Translation initiation factor 4F, helicase subunit (eIF-4A) and related helicases [Translation, ribosomal structure and biogenesis]

Probab=100.00  E-value=5.8e-41  Score=279.37  Aligned_cols=324  Identities=20%  Similarity=0.287  Sum_probs=254.5

Q ss_pred             cCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhcccccc------CCcEEEEcchHHHHHHHHHHHHHcCCce--
Q 037567            9 FGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVT------GKTALVVSPLISLMQDQVMSLKQRGINA--   80 (374)
Q Consensus         9 ~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~~------~~~~lil~P~~~l~~q~~~~~~~~~~~~--   80 (374)
                      +||++|+.+|..|+.....|.++...+.+|+|||.+|..++++.      ...+++++|+++|+.|........|...  
T Consensus        44 yGFekPSaIQqraI~p~i~G~dv~~qaqsgTgKt~af~i~iLq~iD~~~ke~qalilaPtreLa~qi~~v~~~lg~~~~~  123 (397)
T KOG0327|consen   44 YGFEKPSAIQQRAILPCIKGHDVIAQAQSGTGKTAAFLISILQQIDMSVKETQALILAPTRELAQQIQKVVRALGDHMDV  123 (397)
T ss_pred             hccCCchHHHhccccccccCCceeEeeeccccchhhhHHHHHhhcCcchHHHHHHHhcchHHHHHHHHHHHHhhhcccce
Confidence            78999999999999999999999999999999999998888863      6679999999999999997777664333  


Q ss_pred             --EEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHHh
Q 037567           81 --EFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTF  158 (374)
Q Consensus        81 --~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~  158 (374)
                        ..+.++..............++|+++||++...+++.  ..+....+.++|+||++.+...|+.     ..+..+...
T Consensus       124 ~v~~~igg~~~~~~~~~i~~~~~hivvGTpgrV~dml~~--~~l~~~~iKmfvlDEaDEmLs~gfk-----dqI~~if~~  196 (397)
T KOG0327|consen  124 SVHACIGGTNVRREDQALLKDKPHIVVGTPGRVFDMLNR--GSLSTDGIKMFVLDEADEMLSRGFK-----DQIYDIFQE  196 (397)
T ss_pred             eeeeecCcccchhhhhhhhccCceeecCCchhHHHhhcc--ccccccceeEEeecchHhhhccchH-----HHHHHHHHH
Confidence              2233333333333444556689999999999888776  3566677999999999999887765     666666666


Q ss_pred             cC-CCCeeEEEeecCcccHHHHHHhcCCCCCeEEEeccCCCcee-EEEEeecCCcchHHHHHHHHHHhhcCCCcEEEEec
Q 037567          159 LL-GVPFVALTATATEKVRIDIINSLKLKNPYVTIASFDRKNLF-YGVKVINRGQSFVDELVQEILKSVAGAGSIIVYCM  236 (374)
Q Consensus       159 ~~-~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lVf~~  236 (374)
                      .+ +.|++++|||.+..... +...+ ..++..+....+..... ....+.......+.+.+.++.+   .-.+.+|||+
T Consensus       197 lp~~vQv~l~SAT~p~~vl~-vt~~f-~~~pv~i~vkk~~ltl~gikq~~i~v~k~~k~~~l~dl~~---~~~q~~if~n  271 (397)
T KOG0327|consen  197 LPSDVQVVLLSATMPSDVLE-VTKKF-MREPVRILVKKDELTLEGIKQFYINVEKEEKLDTLCDLYR---RVTQAVIFCN  271 (397)
T ss_pred             cCcchhheeecccCcHHHHH-HHHHh-ccCceEEEecchhhhhhheeeeeeeccccccccHHHHHHH---hhhcceEEec
Confidence            65 68999999999988764 33333 33444333322221111 1111111111113444444544   5578899999


Q ss_pred             chhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEEEEECCCCChhHHHHhh
Q 037567          237 TIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQES  316 (374)
Q Consensus       237 ~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~~~~p~s~~~~~Q~~  316 (374)
                      +...+..+...|.+++..+..+|+++...+|..++..|+.|..+|||+|+.+++|+|+..+..|++++.|....+|.||+
T Consensus       272 t~r~v~~l~~~L~~~~~~~s~~~~d~~q~~R~~~~~ef~~gssrvlIttdl~argidv~~~slvinydlP~~~~~yihR~  351 (397)
T KOG0327|consen  272 TRRKVDNLTDKLRAHGFTVSAIHGDMEQNERDTLMREFRSGSSRVLITTDLLARGIDVQQVSLVVNYDLPARKENYIHRI  351 (397)
T ss_pred             chhhHHHHHHHHhhCCceEEEeecccchhhhhHHHHHhhcCCceEEeeccccccccchhhcceeeeeccccchhhhhhhc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCCCCCCceEEEEEeeccCCCccccee
Q 037567          317 GRCGRDGIASVCWLYYARSNFAKGDFYC  344 (374)
Q Consensus       317 GR~~R~~~~g~~~~~~~~~~~~~~~~~~  344 (374)
                      ||+||.|.+|.++.++...+.+.++.+.
T Consensus       352 gr~gr~grkg~~in~v~~~d~~~lk~ie  379 (397)
T KOG0327|consen  352 GRAGRFGRKGVAINFVTEEDVRDLKDIE  379 (397)
T ss_pred             ccccccCCCceeeeeehHhhHHHHHhHH
Confidence            9999999999999999998876655544

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

Probab=100.00  E-value=1.2e-38  Score=299.07  Aligned_cols=318  Identities=19%  Similarity=0.174  Sum_probs=208.8

Q ss_pred             hHHHhHcCCCCCchhHHHHHHHHHcCC-CEEEEccCCCCchhhh---hccccc--cCC-cEEEEcchHHHHHHHHHHHHH
Q 037567            3 STLKKYFGYSVFRPYQKDVIQRIIEKR-DCLVVMATGSGKSLCY---QLPPLV--TGK-TALVVSPLISLMQDQVMSLKQ   75 (374)
Q Consensus         3 ~~l~~~~~~~~~~~~Q~~~~~~~~~~~-~~l~~a~tGsGKT~~~---~l~~~~--~~~-~~lil~P~~~l~~q~~~~~~~   75 (374)
                      ..|....||. |+|+|.++++.++.|+ ++++.+|||||||.++   ++++..  ... ++++++|+++|++|..+.+.+
T Consensus         6 ~ff~~~~G~~-PtpiQ~~~i~~il~G~~~v~~~apTGSGKTaa~aafll~~~~~~~~~~rLv~~vPtReLa~Qi~~~~~~   84 (844)
T TIGR02621         6 EWYQGLHGYS-PFPWQLSLAERFVAGQPPESCSTPTGLGKTSIIAAWLLAVEIGAKVPRRLVYVVNRRTVVDQVTEEAEK   84 (844)
T ss_pred             HHHHHHhCCC-CCHHHHHHHHHHHcCCCcceEecCCCCcccHHHHHhhccccccccccceEEEeCchHHHHHHHHHHHHH
Confidence            4577888998 9999999999999998 5777899999999844   343322  123 445577999999999998876


Q ss_pred             cC---------------------------CceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCch----------hh
Q 037567           76 RG---------------------------INAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPI----------SF  118 (374)
Q Consensus        76 ~~---------------------------~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~----------~~  118 (374)
                      ++                           +++..+.++....... ......++|+|+|++.+.+-.-          ..
T Consensus        85 ~~k~l~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~GG~~~~~q~-~~l~~~p~IIVgT~D~i~sr~L~~gYg~~~~~~p  163 (844)
T TIGR02621        85 IGERLPDVPEVEAALWALCSTRPEKKDRPLAISTLRGQFADNDEW-MLDPHRPAVIVGTVDMIGSRLLFSGYGCGFKSRP  163 (844)
T ss_pred             HHHHhcccchhhhhhhhhhccccccccCCeEEEEEECCCChHHHH-HhcCCCCcEEEECHHHHcCCcccccccccccccc
Confidence            54                           2233445554443333 3445678999999876643210          00


Q ss_pred             HHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHHhcC---CCCeeEEEeecCcccHHHHHHhcCCCCCeEEEecc
Q 037567          119 WSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLL---GVPFVALTATATEKVRIDIINSLKLKNPYVTIASF  195 (374)
Q Consensus       119 ~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~~---~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~  195 (374)
                      .....+.++.++|+|||| + +.+  +...+..+.......+   +.++++||||++..... ....+...+..+.....
T Consensus       164 i~ag~L~~v~~LVLDEAD-L-d~g--F~~~l~~Il~~l~rp~~~rprQtLLFSAT~p~ei~~-l~~~~~~~p~~i~V~~~  238 (844)
T TIGR02621       164 LHAGFLGQDALIVHDEAH-L-EPA--FQELLKQIMNEQQRPPDFLPLRVVELTATSRTDGPD-RTTLLSAEDYKHPVLKK  238 (844)
T ss_pred             chhhhhccceEEEEehhh-h-ccc--cHHHHHHHHHhcccCcccccceEEEEecCCCccHHH-HHHHHccCCceeecccc
Confidence            111235778999999999 3 334  3333333333211111   26899999999876543 33333222222222111


Q ss_pred             --CCCceeEEEEeecCCcchHHHHHHHHHHh-hcCCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHH----
Q 037567          196 --DRKNLFYGVKVINRGQSFVDELVQEILKS-VAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKARE----  268 (374)
Q Consensus       196 --~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~----  268 (374)
                        ....+...  ............+..+... ...++++||||++++.++.+++.|++.++  ..+||+++..+|.    
T Consensus       239 ~l~a~ki~q~--v~v~~e~Kl~~lv~~L~~ll~e~g~~vLVF~NTv~~Aq~L~~~L~~~g~--~lLHG~m~q~dR~~~~~  314 (844)
T TIGR02621       239 RLAAKKIVKL--VPPSDEKFLSTMVKELNLLMKDSGGAILVFCRTVKHVRKVFAKLPKEKF--ELLTGTLRGAERDDLVK  314 (844)
T ss_pred             cccccceEEE--EecChHHHHHHHHHHHHHHHhhCCCcEEEEECCHHHHHHHHHHHHhcCC--eEeeCCCCHHHHhhHHH
Confidence              11111111  1111112222223222211 13568899999999999999999998776  8999999999999    


Q ss_pred             -HHHHhhhc----CC-------eeEEEEeccccccccccCccEEEEECCCCChhHHHHhhccCCCCCCc-eEEEEEeec
Q 037567          269 -EAHRLFIR----DE-------IRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIA-SVCWLYYAR  334 (374)
Q Consensus       269 -~~~~~f~~----g~-------~~ilv~t~~~~~G~d~~~~~~vi~~~~p~s~~~~~Q~~GR~~R~~~~-g~~~~~~~~  334 (374)
                       .+++.|.+    |+       ..|||+|+++++|+|++. ++||+...|  ...|+||+||+||.|.. +..++++..
T Consensus       315 ~~il~~Fk~~~~~g~~~~~~~g~~ILVATdVaerGLDId~-d~VI~d~aP--~esyIQRiGRtgR~G~~~~~~i~vv~~  390 (844)
T TIGR02621       315 KEIFNRFLPQMLSGSRARPQQGTVYLVCTSAGEVGVNISA-DHLVCDLAP--FESMQQRFGRVNRFGELQACQIAVVHL  390 (844)
T ss_pred             HHHHHHHhccccccccccccccceEEeccchhhhcccCCc-ceEEECCCC--HHHHHHHhcccCCCCCCCCceEEEEee
Confidence             77899987    43       689999999999999986 788876655  78999999999999885 333455444

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.

>KOG0337 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=100.00  E-value=2.3e-40  Score=277.96  Aligned_cols=327  Identities=21%  Similarity=0.277  Sum_probs=260.0

Q ss_pred             hHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhcccccc-------CCcEEEEcchHHHHHHHHHHHHH
Q 037567            3 STLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVT-------GKTALVVSPLISLMQDQVMSLKQ   75 (374)
Q Consensus         3 ~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~~-------~~~~lil~P~~~l~~q~~~~~~~   75 (374)
                      +++.+ -||..|+|+|.+.+|.++++++++-.+-||||||.+|+++++++       +.+++++.|+++|+.|+.+-++.
T Consensus        34 raI~k-kg~~~ptpiqRKTipliLe~~dvv~martgsgktaaf~ipm~e~Lk~~s~~g~RalilsptreLa~qtlkvvkd  112 (529)
T KOG0337|consen   34 RAIHK-KGFNTPTPIQRKTIPLILEGRDVVGMARTGSGKTAAFLIPMIEKLKSHSQTGLRALILSPTRELALQTLKVVKD  112 (529)
T ss_pred             HHHHH-hhcCCCCchhcccccceeeccccceeeecCCcchhhHHHHHHHHHhhccccccceeeccCcHHHHHHHHHHHHH
Confidence            45555 69999999999999999999999999999999999999998862       56999999999999999999988


Q ss_pred             cCCceE----EcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHH
Q 037567           76 RGINAE----FLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQ  151 (374)
Q Consensus        76 ~~~~~~----~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~  151 (374)
                      +|-...    +..++. ..+.+......++||+++||+++..+...  -.+.++.+.+||+||++.+.+.|++     .+
T Consensus       113 lgrgt~lr~s~~~ggD-~~eeqf~~l~~npDii~ATpgr~~h~~ve--m~l~l~sveyVVfdEadrlfemgfq-----eq  184 (529)
T KOG0337|consen  113 LGRGTKLRQSLLVGGD-SIEEQFILLNENPDIIIATPGRLLHLGVE--MTLTLSSVEYVVFDEADRLFEMGFQ-----EQ  184 (529)
T ss_pred             hccccchhhhhhcccc-hHHHHHHHhccCCCEEEecCceeeeeehh--eeccccceeeeeehhhhHHHhhhhH-----HH
Confidence            754333    222332 23344455566789999999999877554  3366789999999999999998876     67


Q ss_pred             HHHHHHhcC-CCCeeEEEeecCcccHHHHHHhcCCCCCeEEEeccC-CCceeEEEEeecCCcchHHHHHHHHHHhhcCCC
Q 037567          152 LDKLRTFLL-GVPFVALTATATEKVRIDIINSLKLKNPYVTIASFD-RKNLFYGVKVINRGQSFVDELVQEILKSVAGAG  229 (374)
Q Consensus       152 ~~~~~~~~~-~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  229 (374)
                      +.++...++ +.+.++||||.+..... +. ..++.++..+..+.+ .-+-...+.............+..++......+
T Consensus       185 l~e~l~rl~~~~QTllfSatlp~~lv~-fa-kaGl~~p~lVRldvetkise~lk~~f~~~~~a~K~aaLl~il~~~~~~~  262 (529)
T KOG0337|consen  185 LHEILSRLPESRQTLLFSATLPRDLVD-FA-KAGLVPPVLVRLDVETKISELLKVRFFRVRKAEKEAALLSILGGRIKDK  262 (529)
T ss_pred             HHHHHHhCCCcceEEEEeccCchhhHH-HH-HccCCCCceEEeehhhhcchhhhhheeeeccHHHHHHHHHHHhcccccc
Confidence            777777766 67999999999987653 33 345555543332211 111111111122223334555555555554567


Q ss_pred             cEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEEEEECCCCCh
Q 037567          230 SIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPKTL  309 (374)
Q Consensus       230 ~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~~~~p~s~  309 (374)
                      +++||+++...++.+...|...|+.+..++|.+....|...+.+|..++..++|.|+.+.+|+|+|..+.||+++.|.+.
T Consensus       263 ~t~vf~~tk~hve~~~~ll~~~g~~~s~iysslD~~aRk~~~~~F~~~k~~~lvvTdvaaRG~diplldnvinyd~p~~~  342 (529)
T KOG0337|consen  263 QTIVFVATKHHVEYVRGLLRDFGGEGSDIYSSLDQEARKINGRDFRGRKTSILVVTDVAARGLDIPLLDNVINYDFPPDD  342 (529)
T ss_pred             ceeEEecccchHHHHHHHHHhcCCCccccccccChHhhhhccccccCCccceEEEehhhhccCCCccccccccccCCCCC
Confidence            89999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hHHHHhhccCCCCCCceEEEEEeeccCCCcc
Q 037567          310 ESYYQESGRCGRDGIASVCWLYYARSNFAKG  340 (374)
Q Consensus       310 ~~~~Q~~GR~~R~~~~g~~~~~~~~~~~~~~  340 (374)
                      .-|+||+||+.|.|..|..|.++.+.+..++
T Consensus       343 klFvhRVgr~aragrtg~aYs~V~~~~~~yl  373 (529)
T KOG0337|consen  343 KLFVHRVGRVARAGRTGRAYSLVASTDDPYL  373 (529)
T ss_pred             ceEEEEecchhhccccceEEEEEecccchhh
Confidence            9999999999999999999999998886554

>PRK09751 putative ATP-dependent helicase Lhr; Provisional

Probab=100.00  E-value=2.1e-39  Score=320.72  Aligned_cols=284  Identities=25%  Similarity=0.299  Sum_probs=206.4

Q ss_pred             EEccCCCCchhhhhccccc----------------cCCcEEEEcchHHHHHHHHHHHHH----------------cCCce
Q 037567           33 VVMATGSGKSLCYQLPPLV----------------TGKTALVVSPLISLMQDQVMSLKQ----------------RGINA   80 (374)
Q Consensus        33 ~~a~tGsGKT~~~~l~~~~----------------~~~~~lil~P~~~l~~q~~~~~~~----------------~~~~~   80 (374)
                      |+||||||||++|.++++.                ++.++||++|+++|++|+.+.++.                .++.+
T Consensus         1 V~APTGSGKTLAA~LpaL~~Ll~~~~~~~~~~~~~~~~raLYISPLKALa~Dv~~~L~~pl~~i~~~~~~~g~~~~~i~V   80 (1490)
T PRK09751          1 VIAPTGSGKTLAAFLYALDRLFREGGEDTREAHKRKTSRILYISPIKALGTDVQRNLQIPLKGIADERRRRGETEVNLRV   80 (1490)
T ss_pred             CcCCCCcHHHHHHHHHHHHHHHhcccccccccccCCCCEEEEEeChHHHHHHHHHHHHHHHHhhhhhhhhcccccCceEE
Confidence            5799999999999987653                135799999999999999988753                24555


Q ss_pred             EEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhc--ccCcchHHHHHHHHHHHh
Q 037567           81 EFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISE--WGHDFRLEYKQLDKLRTF  158 (374)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~--~~~~~~~~~~~~~~~~~~  158 (374)
                      ...+++....+. .......++|+|+||+++..++.+. ....++++++|||||+|.+.+  .|..+...+.++..+.. 
T Consensus        81 ~vrtGDt~~~eR-~rll~~ppdILVTTPEsL~~LLtsk-~r~~L~~Vr~VIVDE~H~L~g~kRG~~Lel~LeRL~~l~~-  157 (1490)
T PRK09751         81 GIRTGDTPAQER-SKLTRNPPDILITTPESLYLMLTSR-ARETLRGVETVIIDEVHAVAGSKRGAHLALSLERLDALLH-  157 (1490)
T ss_pred             EEEECCCCHHHH-HHHhcCCCCEEEecHHHHHHHHhhh-hhhhhccCCEEEEecHHHhcccccccHHHHHHHHHHHhCC-
Confidence            556665544433 2344457899999999998765542 234678999999999999975  35555555555554432 


Q ss_pred             cCCCCeeEEEeecCcccHHHHHHhcCCCCCeEEEeccCCCc--eeEEEEeecCC-----------------cchH-HHHH
Q 037567          159 LLGVPFVALTATATEKVRIDIINSLKLKNPYVTIASFDRKN--LFYGVKVINRG-----------------QSFV-DELV  218 (374)
Q Consensus       159 ~~~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~-----------------~~~~-~~~~  218 (374)
                       .+.|+|++|||..+.  .++..+++...+...........  +...+......                 .... ..+.
T Consensus       158 -~~~QrIgLSATI~n~--eevA~~L~g~~pv~Iv~~~~~r~~~l~v~vp~~d~~~~~~~~~~~~~~~~~~r~~~i~~~v~  234 (1490)
T PRK09751        158 -TSAQRIGLSATVRSA--SDVAAFLGGDRPVTVVNPPAMRHPQIRIVVPVANMDDVSSVASGTGEDSHAGREGSIWPYIE  234 (1490)
T ss_pred             -CCCeEEEEEeeCCCH--HHHHHHhcCCCCEEEECCCCCcccceEEEEecCchhhccccccccccccchhhhhhhhHHHH
Confidence             367999999999874  36677777554433322222111  11111111000                 0001 1122


Q ss_pred             HHHHHhhcCCCcEEEEecchhHHHHHHHHHHHcC---------------------------------CceeeeecCCChH
Q 037567          219 QEILKSVAGAGSIIVYCMTIKDVEEISKALKQLG---------------------------------VKAGTYHGQMGSK  265 (374)
Q Consensus       219 ~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~~---------------------------------~~~~~~~~~~~~~  265 (374)
                      ..++.....++++|||||++..++.++..|++..                                 ..+..+||+++.+
T Consensus       235 ~~il~~i~~~~stLVFvNSR~~AE~La~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ia~~HHGsLSke  314 (1490)
T PRK09751        235 TGILDEVLRHRSTIVFTNSRGLAEKLTARLNELYAARLQRSPSIAVDAAHFESTSGATSNRVQSSDVFIARSHHGSVSKE  314 (1490)
T ss_pred             HHHHHHHhcCCCEEEECCCHHHHHHHHHHHHHhhhhhccccccccchhhhhhhccccchhccccccceeeeeccccCCHH
Confidence            3344444567899999999999999999987631                                 1146789999999


Q ss_pred             HHHHHHHhhhcCCeeEEEEeccccccccccCccEEEEECCCCChhHHHHhhccCCCC
Q 037567          266 AREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRD  322 (374)
Q Consensus       266 ~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~~~~p~s~~~~~Q~~GR~~R~  322 (374)
                      +|..+++.|++|++++||||++++.|||++++++||+++.|.+..+|+||+||+||.
T Consensus       315 eR~~IE~~fK~G~LrvLVATssLELGIDIg~VDlVIq~gsP~sVas~LQRiGRAGR~  371 (1490)
T PRK09751        315 QRAITEQALKSGELRCVVATSSLELGIDMGAVDLVIQVATPLSVASGLQRIGRAGHQ  371 (1490)
T ss_pred             HHHHHHHHHHhCCceEEEeCcHHHccCCcccCCEEEEeCCCCCHHHHHHHhCCCCCC
Confidence            999999999999999999999999999999999999999999999999999999997

>COG1204 Superfamily II helicase [General function prediction only]

Probab=100.00  E-value=3.4e-39  Score=304.91  Aligned_cols=339  Identities=20%  Similarity=0.240  Sum_probs=243.7

Q ss_pred             hHcCCCCCchhHHHHHHHHHc-CCCEEEEccCCCCchhhhhcccccc----CCcEEEEcchHHHHHHHHHHHH---HcCC
Q 037567            7 KYFGYSVFRPYQKDVIQRIIE-KRDCLVVMATGSGKSLCYQLPPLVT----GKTALVVSPLISLMQDQVMSLK---QRGI   78 (374)
Q Consensus         7 ~~~~~~~~~~~Q~~~~~~~~~-~~~~l~~a~tGsGKT~~~~l~~~~~----~~~~lil~P~~~l~~q~~~~~~---~~~~   78 (374)
                      +-.++.++.+.|..++..... ++|+++++|||||||++++++++..    +.+++++||+++|++|.+++++   .+|+
T Consensus        25 ~~~~~~el~~~qq~av~~~~~~~~N~li~aPTgsGKTlIA~lai~~~l~~~~~k~vYivPlkALa~Ek~~~~~~~~~~Gi  104 (766)
T COG1204          25 KGDGIDELFNPQQEAVEKGLLSDENVLISAPTGSGKTLIALLAILSTLLEGGGKVVYIVPLKALAEEKYEEFSRLEELGI  104 (766)
T ss_pred             ccCChHHhhHHHHHHhhccccCCCcEEEEcCCCCchHHHHHHHHHHHHHhcCCcEEEEeChHHHHHHHHHHhhhHHhcCC
Confidence            336776778877777776554 5999999999999999988887752    5799999999999999999988   7899


Q ss_pred             ceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcc--cCcchHHHHHHHHHH
Q 037567           79 NAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEW--GHDFRLEYKQLDKLR  156 (374)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~--~~~~~~~~~~~~~~~  156 (374)
                      ++...+++.......    ...++|+|+|||++..+.++...  ....+++||+||+|.+.+.  |.....   -+.+.+
T Consensus       105 rV~~~TgD~~~~~~~----l~~~~ViVtT~EK~Dsl~R~~~~--~~~~V~lvViDEiH~l~d~~RG~~lE~---iv~r~~  175 (766)
T COG1204         105 RVGISTGDYDLDDER----LARYDVIVTTPEKLDSLTRKRPS--WIEEVDLVVIDEIHLLGDRTRGPVLES---IVARMR  175 (766)
T ss_pred             EEEEecCCcccchhh----hccCCEEEEchHHhhHhhhcCcc--hhhcccEEEEeeeeecCCcccCceehh---HHHHHH
Confidence            999998876654422    23479999999999887776433  6678999999999999763  433332   233333


Q ss_pred             HhcCCCCeeEEEeecCcccHHHHHHhcCCCCCeE-EEeccCCCceeEEEEeecCC-------cchHHHHHHHHHHhhcCC
Q 037567          157 TFLLGVPFVALTATATEKVRIDIINSLKLKNPYV-TIASFDRKNLFYGVKVINRG-------QSFVDELVQEILKSVAGA  228 (374)
Q Consensus       157 ~~~~~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~~~~~~~~~  228 (374)
                      ......+++++|||.++..  ++..|++...... ..+................+       ...-...+..+......+
T Consensus       176 ~~~~~~rivgLSATlpN~~--evA~wL~a~~~~~~~rp~~l~~~v~~~~~~~~~~~~~k~~~~~~~~~~~~~v~~~~~~~  253 (766)
T COG1204         176 RLNELIRIVGLSATLPNAE--EVADWLNAKLVESDWRPVPLRRGVPYVGAFLGADGKKKTWPLLIDNLALELVLESLAEG  253 (766)
T ss_pred             hhCcceEEEEEeeecCCHH--HHHHHhCCcccccCCCCcccccCCccceEEEEecCccccccccchHHHHHHHHHHHhcC
Confidence            4334579999999999876  5788888765521 11111112222222222111       122355666677778889


Q ss_pred             CcEEEEecchhHHHHHHHHHHHc-------------------------------------CCceeeeecCCChHHHHHHH
Q 037567          229 GSIIVYCMTIKDVEEISKALKQL-------------------------------------GVKAGTYHGQMGSKAREEAH  271 (374)
Q Consensus       229 ~~~lVf~~~~~~~~~l~~~l~~~-------------------------------------~~~~~~~~~~~~~~~r~~~~  271 (374)
                      +++||||++++.+...++.+...                                     ...+.++|++++.++|+.+.
T Consensus       254 ~qvLvFv~sR~~a~~~A~~l~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~l~e~v~~GvafHhAGL~~~~R~~vE  333 (766)
T COG1204         254 GQVLVFVHSRKEAEKTAKKLRIKMSATLSDDEKIVLDEGASPILIPETPTSEDEELAELVLRGVAFHHAGLPREDRQLVE  333 (766)
T ss_pred             CeEEEEEecCchHHHHHHHHHHHHhhcCChhhhhhccccccccccccccccchHHHHHHHHhCccccccCCCHHHHHHHH
Confidence            99999999999999999888731                                     11256899999999999999


Q ss_pred             HhhhcCCeeEEEEeccccccccccCccEEE----EEC-----CCCChhHHHHhhccCCCCCC--ceEEEEEe-eccCCCc
Q 037567          272 RLFIRDEIRVMVATMAFGMGIDKPDVRHVI----HYG-----CPKTLESYYQESGRCGRDGI--ASVCWLYY-ARSNFAK  339 (374)
Q Consensus       272 ~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi----~~~-----~p~s~~~~~Q~~GR~~R~~~--~g~~~~~~-~~~~~~~  339 (374)
                      ..|+.|.++||+||+.+..|+|+|.-.+||    .++     -+.+..++.|++|||||.|-  .|..+++. +..+...
T Consensus       334 ~~Fr~g~ikVlv~TpTLA~GVNLPA~~VIIk~~~~y~~~~g~~~i~~~dv~QM~GRAGRPg~d~~G~~~i~~~~~~~~~~  413 (766)
T COG1204         334 DAFRKGKIKVLVSTPTLAAGVNLPARTVIIKDTRRYDPKGGIVDIPVLDVLQMAGRAGRPGYDDYGEAIILATSHDELEY  413 (766)
T ss_pred             HHHhcCCceEEEechHHhhhcCCcceEEEEeeeEEEcCCCCeEECchhhHhhccCcCCCCCcCCCCcEEEEecCccchhH
Confidence            999999999999999999999999877766    344     34478999999999999874  34444444 4444444


Q ss_pred             ccceeccccchHHHHHH
Q 037567          340 GDFYCGESQTENQRTAI  356 (374)
Q Consensus       340 ~~~~~~~~~~~~~~~~~  356 (374)
                      ....+....++.....+
T Consensus       414 ~~~~~~~~~~e~~~s~l  430 (766)
T COG1204         414 LAELYIQSEPEPIESKL  430 (766)
T ss_pred             HHHHhhccCcchHHHhh
Confidence            44444444443333333

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

Probab=100.00  E-value=2e-38  Score=276.32  Aligned_cols=318  Identities=23%  Similarity=0.299  Sum_probs=239.6

Q ss_pred             HcCCCCCchhHHHHHHH-HHcCCCEEEEccCCCCchhhhhccccc----cCCcEEEEcchHHHHHHHHHHHHH----cCC
Q 037567            8 YFGYSVFRPYQKDVIQR-IIEKRDCLVVMATGSGKSLCYQLPPLV----TGKTALVVSPLISLMQDQVMSLKQ----RGI   78 (374)
Q Consensus         8 ~~~~~~~~~~Q~~~~~~-~~~~~~~l~~a~tGsGKT~~~~l~~~~----~~~~~lil~P~~~l~~q~~~~~~~----~~~   78 (374)
                      ..|+.++.|.|.-++.+ +++|.|.+++++|+||||++..++-+.    .+++.|+++|..+|++|.+++|+.    .|+
T Consensus       211 ~~G~~eLlPVQ~laVe~GLLeG~nllVVSaTasGKTLIgElAGi~~~l~~g~KmlfLvPLVALANQKy~dF~~rYs~Lgl  290 (830)
T COG1202         211 REGIEELLPVQVLAVEAGLLEGENLLVVSATASGKTLIGELAGIPRLLSGGKKMLFLVPLVALANQKYEDFKERYSKLGL  290 (830)
T ss_pred             hcCcceecchhhhhhhhccccCCceEEEeccCCCcchHHHhhCcHHHHhCCCeEEEEehhHHhhcchHHHHHHHhhcccc
Confidence            37999999999999975 678999999999999999988777554    489999999999999999999874    455


Q ss_pred             ceEEcCCCCCchhh---hhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHH
Q 037567           79 NAEFLGSAQTDSSV---QTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKL  155 (374)
Q Consensus        79 ~~~~~~~~~~~~~~---~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~  155 (374)
                      .+.+-.+-......   .........||+|+|++-+..+++.  . ..+.++..|||||+|.+.+.....+.. ..+.++
T Consensus       291 kvairVG~srIk~~~~pv~~~t~~dADIIVGTYEGiD~lLRt--g-~~lgdiGtVVIDEiHtL~deERG~RLd-GLI~RL  366 (830)
T COG1202         291 KVAIRVGMSRIKTREEPVVVDTSPDADIIVGTYEGIDYLLRT--G-KDLGDIGTVVIDEIHTLEDEERGPRLD-GLIGRL  366 (830)
T ss_pred             eEEEEechhhhcccCCccccCCCCCCcEEEeechhHHHHHHc--C-CcccccceEEeeeeeeccchhcccchh-hHHHHH
Confidence            55443332111111   1122234569999999987666554  2 456788999999999997644433333 678888


Q ss_pred             HHhcCCCCeeEEEeecCcccHHHHHHhcCCCCCeEEEeccCCCceeEEEEeecCCcchHHHHHHHHHHhh-------cCC
Q 037567          156 RTFLLGVPFVALTATATEKVRIDIINSLKLKNPYVTIASFDRKNLFYGVKVINRGQSFVDELVQEILKSV-------AGA  228 (374)
Q Consensus       156 ~~~~~~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~  228 (374)
                      +...+..|+|++|||..++.  .+...++...........   .+. ..-.+..+.....+++..+.+..       ...
T Consensus       367 r~l~~~AQ~i~LSATVgNp~--elA~~l~a~lV~y~~RPV---plE-rHlvf~~~e~eK~~ii~~L~k~E~~~~sskg~r  440 (830)
T COG1202         367 RYLFPGAQFIYLSATVGNPE--ELAKKLGAKLVLYDERPV---PLE-RHLVFARNESEKWDIIARLVKREFSTESSKGYR  440 (830)
T ss_pred             HHhCCCCeEEEEEeecCChH--HHHHHhCCeeEeecCCCC---Chh-HeeeeecCchHHHHHHHHHHHHHHhhhhccCcC
Confidence            88888999999999998875  456666644321111111   111 11223333444555665555432       234


Q ss_pred             CcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEEE---EECC
Q 037567          229 GSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVI---HYGC  305 (374)
Q Consensus       229 ~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi---~~~~  305 (374)
                      +++|||++|+..|..++..|..+|+++.++|++++..+|..+...|.++++.++|+|.+++.|+|+|...+|+   -.+.
T Consensus       441 GQtIVFT~SRrr~h~lA~~L~~kG~~a~pYHaGL~y~eRk~vE~~F~~q~l~~VVTTAAL~AGVDFPASQVIFEsLaMG~  520 (830)
T COG1202         441 GQTIVFTYSRRRCHELADALTGKGLKAAPYHAGLPYKERKSVERAFAAQELAAVVTTAALAAGVDFPASQVIFESLAMGI  520 (830)
T ss_pred             CceEEEecchhhHHHHHHHhhcCCcccccccCCCcHHHHHHHHHHHhcCCcceEeehhhhhcCCCCchHHHHHHHHHccc
Confidence            7899999999999999999999999999999999999999999999999999999999999999999765544   1233


Q ss_pred             CC-ChhHHHHhhccCCCCC--CceEEEEEeecc
Q 037567          306 PK-TLESYYQESGRCGRDG--IASVCWLYYARS  335 (374)
Q Consensus       306 p~-s~~~~~Q~~GR~~R~~--~~g~~~~~~~~~  335 (374)
                      .| |+.+|.||.|||||.+  ..|.+|+++++.
T Consensus       521 ~WLs~~EF~QM~GRAGRp~yHdrGkVyllvepg  553 (830)
T COG1202         521 EWLSVREFQQMLGRAGRPDYHDRGKVYLLVEPG  553 (830)
T ss_pred             ccCCHHHHHHHhcccCCCCcccCceEEEEecCC
Confidence            33 7999999999999974  689999998886

>TIGR01587 cas3_core CRISPR-associated helicase Cas3

Probab=100.00  E-value=1.3e-37  Score=278.69  Aligned_cols=300  Identities=17%  Similarity=0.141  Sum_probs=196.2

Q ss_pred             CEEEEccCCCCchhhhhccccc-----cCCcEEEEcchHHHHHHHHHHHHHc-CCceEEcCCCCCch------------h
Q 037567           30 DCLVVMATGSGKSLCYQLPPLV-----TGKTALVVSPLISLMQDQVMSLKQR-GINAEFLGSAQTDS------------S   91 (374)
Q Consensus        30 ~~l~~a~tGsGKT~~~~l~~~~-----~~~~~lil~P~~~l~~q~~~~~~~~-~~~~~~~~~~~~~~------------~   91 (374)
                      ++++.||||||||.+++++++.     ...++++++|+++|+.|+.+.+... +......++.....            .
T Consensus         1 ~vvi~apTGsGKT~~~~~~~l~~~~~~~~~~ii~v~P~~~L~~q~~~~l~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~   80 (358)
T TIGR01587         1 LLVIEAPTGYGKTEAALLWALHSIKSQKADRVIIALPTRATINAMYRRAKELFGSNLGLLHSSSSFKRIKEMGDSEEFEH   80 (358)
T ss_pred             CEEEEeCCCCCHHHHHHHHHHHHHhhCCCCeEEEEeehHHHHHHHHHHHHHHhCcccEEeeccHHHHHHhccCCchhHHH
Confidence            4789999999999998888773     4678999999999999999999875 65444333321100            0


Q ss_pred             hhhhh-----hcCCeeEEEEcCcccccCchh----hHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHHhcCCC
Q 037567           92 VQTKA-----ETGYFQLLFMTPEKACIIPIS----FWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGV  162 (374)
Q Consensus        92 ~~~~~-----~~~~~~i~i~T~~~l~~~~~~----~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~~~~  162 (374)
                      .....     .....+|+++||+++......    ..........+++|+||+|.+.+.+...  ....+..+.  ..+.
T Consensus        81 ~~~~~~~~~~~~~~~~I~v~T~~~l~~~~~~~~~~~~~~~~~~~~~~iViDE~h~~~~~~~~~--l~~~l~~l~--~~~~  156 (358)
T TIGR01587        81 LFPLYIHSNDKLFLDPITVCTIDQVLKSVFGEFGHYEFTLASIANSLLIFDEVHFYDEYTLAL--ILAVLEVLK--DNDV  156 (358)
T ss_pred             HHHHHhhchhhhhhCCeeeCCHHHHHHHHhcccchHHHHHHHhcCCEEEEeCCCCCCHHHHHH--HHHHHHHHH--HcCC
Confidence            00000     012357999999987654333    1111122234789999999997644322  112222222  2368


Q ss_pred             CeeEEEeecCcccHHHHHHhcCCCCCeEEEeccCCC-ceeEEEEeecCCcchHHHHHHHHHHhhcCCCcEEEEecchhHH
Q 037567          163 PFVALTATATEKVRIDIINSLKLKNPYVTIASFDRK-NLFYGVKVINRGQSFVDELVQEILKSVAGAGSIIVYCMTIKDV  241 (374)
Q Consensus       163 ~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lVf~~~~~~~  241 (374)
                      ++++||||++.... .+................... .....+.............+..+++....++++||||++++.+
T Consensus       157 ~~i~~SATlp~~l~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~lVf~~t~~~~  235 (358)
T TIGR01587       157 PILLMSATLPKFLK-EYAEKIGYVEFNEPLDLKEERRFERHRFIKIESDKVGEISSLERLLEFIKKGGKIAIIVNTVDRA  235 (358)
T ss_pred             CEEEEecCchHHHH-HHHhcCCCcccccCCCCccccccccccceeeccccccCHHHHHHHHHHhhCCCeEEEEECCHHHH
Confidence            89999999985432 333322221111000000000 0011111111111122334455555555788999999999999


Q ss_pred             HHHHHHHHHcCC--ceeeeecCCChHHHHH----HHHhhhcCCeeEEEEeccccccccccCccEEEEECCCCChhHHHHh
Q 037567          242 EEISKALKQLGV--KAGTYHGQMGSKAREE----AHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQE  315 (374)
Q Consensus       242 ~~l~~~l~~~~~--~~~~~~~~~~~~~r~~----~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~~~~p~s~~~~~Q~  315 (374)
                      +.+++.|++.+.  .+..+||+++..+|..    +++.|.+|+..+||||+++++|+|++ ++.+|.+..|  +..|+||
T Consensus       236 ~~~~~~L~~~~~~~~~~~~h~~~~~~~r~~~~~~~~~~f~~~~~~ilvaT~~~~~GiDi~-~~~vi~~~~~--~~~~iqr  312 (358)
T TIGR01587       236 QEFYQQLKENAPEEEIMLLHSRFTEKDRAKKEAELLEEMKKNEKFVIVATQVIEASLDIS-ADVMITELAP--IDSLIQR  312 (358)
T ss_pred             HHHHHHHHhhcCCCeEEEEECCCCHHHHHHHHHHHHHHhcCCCCeEEEECcchhceeccC-CCEEEEcCCC--HHHHHHH
Confidence            999999988766  4899999999999876    48899999999999999999999996 7888877665  7899999


Q ss_pred             hccCCCCCCc----eEEEEEeeccCC
Q 037567          316 SGRCGRDGIA----SVCWLYYARSNF  337 (374)
Q Consensus       316 ~GR~~R~~~~----g~~~~~~~~~~~  337 (374)
                      +||+||.|+.    |.++++....+.
T Consensus       313 ~GR~gR~g~~~~~~~~~~v~~~~~~~  338 (358)
T TIGR01587       313 LGRLHRYGRKNGENFEVYIITIAPEG  338 (358)
T ss_pred             hccccCCCCCCCCCCeEEEEeecCCC
Confidence            9999998753    367777666553

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.

>TIGR00603 rad25 DNA repair helicase rad25

Probab=100.00  E-value=1.5e-37  Score=288.75  Aligned_cols=302  Identities=17%  Similarity=0.159  Sum_probs=207.4

Q ss_pred             CCchhHHHHHHHHHcC---CCEEEEccCCCCchhhhhccccccCCcEEEEcchHHHHHHHHHHHHHcC-C---ceEEcCC
Q 037567           13 VFRPYQKDVIQRIIEK---RDCLVVMATGSGKSLCYQLPPLVTGKTALVVSPLISLMQDQVMSLKQRG-I---NAEFLGS   85 (374)
Q Consensus        13 ~~~~~Q~~~~~~~~~~---~~~l~~a~tGsGKT~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~-~---~~~~~~~   85 (374)
                      ++||||.+++..++.+   +..++++|||+|||++.+..+.....++||+||+..|++||.+++.++. +   .+..+.+
T Consensus       255 ~LRpYQ~eAl~~~~~~gr~r~GIIvLPtGaGKTlvai~aa~~l~k~tLILvps~~Lv~QW~~ef~~~~~l~~~~I~~~tg  334 (732)
T TIGR00603       255 QIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKSLVGVTAACTVKKSCLVLCTSAVSVEQWKQQFKMWSTIDDSQICRFTS  334 (732)
T ss_pred             CcCHHHHHHHHHHHhcCCCCCcEEEeCCCCChHHHHHHHHHHhCCCEEEEeCcHHHHHHHHHHHHHhcCCCCceEEEEec
Confidence            6999999999998853   4789999999999998877666667889999999999999999999873 2   2222222


Q ss_pred             CCCchhhhhhhhcCCeeEEEEcCcccccCchh------hHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHHhc
Q 037567           86 AQTDSSVQTKAETGYFQLLFMTPEKACIIPIS------FWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFL  159 (374)
Q Consensus        86 ~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~------~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~  159 (374)
                      ....      .......|+|+|++++.....+      ....+....++++|+||||++..         .....+...+
T Consensus       335 ~~k~------~~~~~~~VvVtTYq~l~~~~~r~~~~~~~l~~l~~~~~gLII~DEvH~lpA---------~~fr~il~~l  399 (732)
T TIGR00603       335 DAKE------RFHGEAGVVVSTYSMVAHTGKRSYESEKVMEWLTNREWGLILLDEVHVVPA---------AMFRRVLTIV  399 (732)
T ss_pred             Cccc------ccccCCcEEEEEHHHhhcccccchhhhHHHHHhccccCCEEEEEccccccH---------HHHHHHHHhc
Confidence            2111      1112358999999987543221      11223335789999999999854         2334444445


Q ss_pred             CCCCeeEEEeecCcccHHH-HHHhcCCCCCeEEEecc---C-C---CceeEEEEeecC---------------------C
Q 037567          160 LGVPFVALTATATEKVRID-IINSLKLKNPYVTIASF---D-R---KNLFYGVKVINR---------------------G  210 (374)
Q Consensus       160 ~~~~~i~~SaT~~~~~~~~-~~~~~~~~~~~~~~~~~---~-~---~~~~~~~~~~~~---------------------~  210 (374)
                      ....+++|||||...+... .+..+  -.+.+...+.   . .   ..........+.                     .
T Consensus       400 ~a~~RLGLTATP~ReD~~~~~L~~L--iGP~vye~~~~eLi~~G~LA~~~~~ev~v~~t~~~~~~yl~~~~~~k~~l~~~  477 (732)
T TIGR00603       400 QAHCKLGLTATLVREDDKITDLNFL--IGPKLYEANWMELQKKGFIANVQCAEVWCPMTPEFYREYLRENSRKRMLLYVM  477 (732)
T ss_pred             CcCcEEEEeecCcccCCchhhhhhh--cCCeeeecCHHHHHhCCccccceEEEEEecCCHHHHHHHHHhcchhhhHHhhh
Confidence            5678999999998765421 11111  1122211110   0 0   000000000000                     0


Q ss_pred             cchHHHHHHHHHHhh-cCCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcC-CeeEEEEeccc
Q 037567          211 QSFVDELVQEILKSV-AGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRD-EIRVMVATMAF  288 (374)
Q Consensus       211 ~~~~~~~~~~~~~~~-~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g-~~~ilv~t~~~  288 (374)
                      ...+...+..+++.. ..+.++||||.+...++.+++.|.     +..+||+++..+|..+++.|+.| .+++||+|.++
T Consensus       478 np~K~~~~~~Li~~he~~g~kiLVF~~~~~~l~~~a~~L~-----~~~I~G~ts~~ER~~il~~Fr~~~~i~vLv~SkVg  552 (732)
T TIGR00603       478 NPNKFRACQFLIRFHEQRGDKIIVFSDNVFALKEYAIKLG-----KPFIYGPTSQQERMQILQNFQHNPKVNTIFLSKVG  552 (732)
T ss_pred             ChHHHHHHHHHHHHHhhcCCeEEEEeCCHHHHHHHHHHcC-----CceEECCCCHHHHHHHHHHHHhCCCccEEEEeccc
Confidence            111223333344332 367899999999999999988872     45689999999999999999875 78999999999


Q ss_pred             cccccccCccEEEEECCCC-ChhHHHHhhccCCCCCCceEE-------EEEeeccC
Q 037567          289 GMGIDKPDVRHVIHYGCPK-TLESYYQESGRCGRDGIASVC-------WLYYARSN  336 (374)
Q Consensus       289 ~~G~d~~~~~~vi~~~~p~-s~~~~~Q~~GR~~R~~~~g~~-------~~~~~~~~  336 (374)
                      .+|+|+|+++++|++++|. |..+|+||+||++|.+.+|.+       |.+++++.
T Consensus       553 deGIDlP~a~vvI~~s~~~gS~~q~iQRlGRilR~~~~~~~~~~~A~fY~lVs~dT  608 (732)
T TIGR00603       553 DTSIDLPEANVLIQISSHYGSRRQEAQRLGRILRAKKGSDAEEYNAFFYSLVSKDT  608 (732)
T ss_pred             ccccCCCCCCEEEEeCCCCCCHHHHHHHhcccccCCCCCccccccceEEEEecCCc
Confidence            9999999999999999874 999999999999999876654       66666554

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).

>PHA02653 RNA helicase NPH-II; Provisional

Probab=100.00  E-value=1.5e-36  Score=283.30  Aligned_cols=300  Identities=16%  Similarity=0.158  Sum_probs=203.2

Q ss_pred             hHHHHHHHHHcCCCEEEEccCCCCchhh---------hhccccc---------cCCcEEEEcchHHHHHHHHHHHHHc--
Q 037567           17 YQKDVIQRIIEKRDCLVVMATGSGKSLC---------YQLPPLV---------TGKTALVVSPLISLMQDQVMSLKQR--   76 (374)
Q Consensus        17 ~Q~~~~~~~~~~~~~l~~a~tGsGKT~~---------~~l~~~~---------~~~~~lil~P~~~l~~q~~~~~~~~--   76 (374)
                      .|.++++.+.+++++++.|+||||||..         |+++.+.         ...++++++||++|+.|+...+.+.  
T Consensus       168 iQ~qil~~i~~gkdvIv~A~TGSGKTtqvPq~l~~~~flf~~l~~l~~~~~~~~~~~ilvt~PrreLa~qi~~~i~~~vg  247 (675)
T PHA02653        168 VQLKIFEAWISRKPVVLTGGTGVGKTSQVPKLLLWFNYLFGGFDNLDKIDPNFIERPIVLSLPRVALVRLHSITLLKSLG  247 (675)
T ss_pred             HHHHHHHHHHhCCCEEEECCCCCCchhHHHHHHHHhhhccchhhhhhhcccccCCcEEEEECcHHHHHHHHHHHHHHHhC
Confidence            7899999999999999999999999976         3322221         2458999999999999998888652  


Q ss_pred             -----CCceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHH
Q 037567           77 -----GINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQ  151 (374)
Q Consensus        77 -----~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~  151 (374)
                           +..+.+..++.....  ........+++++|+....         ..+.++++||+||||.....+..   ....
T Consensus       248 ~~~~~g~~v~v~~Gg~~~~~--~~t~~k~~~Ilv~T~~L~l---------~~L~~v~~VVIDEaHEr~~~~Dl---lL~l  313 (675)
T PHA02653        248 FDEIDGSPISLKYGSIPDEL--INTNPKPYGLVFSTHKLTL---------NKLFDYGTVIIDEVHEHDQIGDI---IIAV  313 (675)
T ss_pred             ccccCCceEEEEECCcchHH--hhcccCCCCEEEEeCcccc---------cccccCCEEEccccccCccchhH---HHHH
Confidence                 233344444443211  1112224689999976311         13567899999999998664421   1111


Q ss_pred             HHHHHHhcCCCCeeEEEeecCcccHHHHHHhcCCCCCeEEEeccCCCceeEEEEeec-C---C----cchHHHHHHHHHH
Q 037567          152 LDKLRTFLLGVPFVALTATATEKVRIDIINSLKLKNPYVTIASFDRKNLFYGVKVIN-R---G----QSFVDELVQEILK  223 (374)
Q Consensus       152 ~~~~~~~~~~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~---~----~~~~~~~~~~~~~  223 (374)
                      +.....  ...++++||||++.... .+...++ ....+.........+........ .   .    ......++..+.+
T Consensus       314 lk~~~~--~~rq~ILmSATl~~dv~-~l~~~~~-~p~~I~I~grt~~pV~~~yi~~~~~~~~~~~y~~~~k~~~l~~L~~  389 (675)
T PHA02653        314 ARKHID--KIRSLFLMTATLEDDRD-RIKEFFP-NPAFVHIPGGTLFPISEVYVKNKYNPKNKRAYIEEEKKNIVTALKK  389 (675)
T ss_pred             HHHhhh--hcCEEEEEccCCcHhHH-HHHHHhc-CCcEEEeCCCcCCCeEEEEeecCcccccchhhhHHHHHHHHHHHHH
Confidence            211111  12479999999986643 3444333 33333332211111111110000 0   0    0111222333322


Q ss_pred             hh-cCCCcEEEEecchhHHHHHHHHHHHc--CCceeeeecCCChHHHHHHHHhh-hcCCeeEEEEeccccccccccCccE
Q 037567          224 SV-AGAGSIIVYCMTIKDVEEISKALKQL--GVKAGTYHGQMGSKAREEAHRLF-IRDEIRVMVATMAFGMGIDKPDVRH  299 (374)
Q Consensus       224 ~~-~~~~~~lVf~~~~~~~~~l~~~l~~~--~~~~~~~~~~~~~~~r~~~~~~f-~~g~~~ilv~t~~~~~G~d~~~~~~  299 (374)
                      .. ..++++|||++++.+++.+++.|.+.  ++.+..+||+++..  ++.++.| .+|+.+|||||+.+++|+|+|++++
T Consensus       390 ~~~~~~g~iLVFlpg~~ei~~l~~~L~~~~~~~~v~~LHG~Lsq~--eq~l~~ff~~gk~kILVATdIAERGIDIp~V~~  467 (675)
T PHA02653        390 YTPPKGSSGIVFVASVSQCEEYKKYLEKRLPIYDFYIIHGKVPNI--DEILEKVYSSKNPSIIISTPYLESSVTIRNATH  467 (675)
T ss_pred             hhcccCCcEEEEECcHHHHHHHHHHHHhhcCCceEEeccCCcCHH--HHHHHHHhccCceeEEeccChhhccccccCeeE
Confidence            22 24578999999999999999999987  68899999999864  4666777 6899999999999999999999999


Q ss_pred             EEEEC---CCC---------ChhHHHHhhccCCCCCCceEEEEEeeccCC
Q 037567          300 VIHYG---CPK---------TLESYYQESGRCGRDGIASVCWLYYARSNF  337 (374)
Q Consensus       300 vi~~~---~p~---------s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~~  337 (374)
                      ||+++   .|.         |..++.||.||+||. ++|.|+.++++++.
T Consensus       468 VID~G~~k~p~~~~g~~~~iSkasa~QRaGRAGR~-~~G~c~rLyt~~~~  516 (675)
T PHA02653        468 VYDTGRVYVPEPFGGKEMFISKSMRTQRKGRVGRV-SPGTYVYFYDLDLL  516 (675)
T ss_pred             EEECCCccCCCcccCcccccCHHHHHHhccCcCCC-CCCeEEEEECHHHh
Confidence            99998   454         788999999999999 79999999999874

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

Probab=100.00  E-value=1.2e-36  Score=262.65  Aligned_cols=316  Identities=21%  Similarity=0.232  Sum_probs=221.8

Q ss_pred             CCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc----cCCcEEEEcchHHHHHHHHHHHHHc-CCc---eE
Q 037567           10 GYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV----TGKTALVVSPLISLMQDQVMSLKQR-GIN---AE   81 (374)
Q Consensus        10 ~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~----~~~~~lil~P~~~l~~q~~~~~~~~-~~~---~~   81 (374)
                      +.-++|.||.......+.+ +.+++.|||.|||+++++.+..    .++++|+++||+-|+.|..+.+.+. |++   +.
T Consensus        12 ~~ie~R~YQ~~i~a~al~~-NtLvvlPTGLGKT~IA~~V~~~~l~~~~~kvlfLAPTKPLV~Qh~~~~~~v~~ip~~~i~   90 (542)
T COG1111          12 NTIEPRLYQLNIAAKALFK-NTLVVLPTGLGKTFIAAMVIANRLRWFGGKVLFLAPTKPLVLQHAEFCRKVTGIPEDEIA   90 (542)
T ss_pred             ccccHHHHHHHHHHHHhhc-CeEEEecCCccHHHHHHHHHHHHHHhcCCeEEEecCCchHHHHHHHHHHHHhCCChhhee
Confidence            3447899999999887766 8899999999999887766652    3448999999999999999999875 442   33


Q ss_pred             EcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHH-HHHHHhcC
Q 037567           82 FLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQL-DKLRTFLL  160 (374)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~-~~~~~~~~  160 (374)
                      .+++......  .......-.|+|+||+.+.+-+..  +.+....+.++|+||||+-..  ...   +-.+ .+....-.
T Consensus        91 ~ltGev~p~~--R~~~w~~~kVfvaTPQvveNDl~~--Grid~~dv~~lifDEAHRAvG--nyA---Yv~Va~~y~~~~k  161 (542)
T COG1111          91 ALTGEVRPEE--REELWAKKKVFVATPQVVENDLKA--GRIDLDDVSLLIFDEAHRAVG--NYA---YVFVAKEYLRSAK  161 (542)
T ss_pred             eecCCCChHH--HHHHHhhCCEEEeccHHHHhHHhc--CccChHHceEEEechhhhccC--cch---HHHHHHHHHHhcc
Confidence            4555443332  222333458999999988665444  566777889999999998643  211   1222 22334444


Q ss_pred             CCCeeEEEeecCcccH--HHHHHhcCCCCCeEEEeccC-CCc--------------------------------------
Q 037567          161 GVPFVALTATATEKVR--IDIINSLKLKNPYVTIASFD-RKN--------------------------------------  199 (374)
Q Consensus       161 ~~~~i~~SaT~~~~~~--~~~~~~~~~~~~~~~~~~~~-~~~--------------------------------------  199 (374)
                      +..+++|||||-.+..  .++...+++....+...... ...                                      
T Consensus       162 ~~~ilgLTASPGs~~ekI~eV~~nLgIe~vevrTE~d~DV~~Yv~~~kve~ikV~lp~e~~~ir~~l~~~l~~~Lk~L~~  241 (542)
T COG1111         162 NPLILGLTASPGSDLEKIQEVVENLGIEKVEVRTEEDPDVRPYVKKIKVEWIKVDLPEEIKEIRDLLRDALKPRLKPLKE  241 (542)
T ss_pred             CceEEEEecCCCCCHHHHHHHHHhCCcceEEEecCCCccHHHhhccceeEEEeccCcHHHHHHHHHHHHHHHHHHHHHHH
Confidence            6679999999987643  34566666543222111000 000                                      


Q ss_pred             --eeEEEE------------------e-----------------------------------------------------
Q 037567          200 --LFYGVK------------------V-----------------------------------------------------  206 (374)
Q Consensus       200 --~~~~~~------------------~-----------------------------------------------------  206 (374)
                        +.....                  .                                                     
T Consensus       242 ~g~~~~~~~~~~kdl~~~~~~~~~~a~~~~~~~~~~l~~~a~~~kl~~a~elletqGi~~~~~Yl~~l~e~~~~~~sk~a  321 (542)
T COG1111         242 LGVIESSSPVSKKDLLELRQIRLIMAKNEDSDKFRLLSVLAEAIKLAHALELLETQGIRPFYQYLEKLEEEATKGGSKAA  321 (542)
T ss_pred             cCceeccCcccHhHHHHHHHHHHHhccCccHHHHHHHHHHHHHHHHHHHHHHHHhhChHHHHHHHHHHHHHhcccchHHH
Confidence              000000                  0                                                     


Q ss_pred             ------------------------ecCCcchHHHHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHHcCCcee-eee--
Q 037567          207 ------------------------INRGQSFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAG-TYH--  259 (374)
Q Consensus       207 ------------------------~~~~~~~~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~-~~~--  259 (374)
                                              -+.+...+.+++.+.+++ ..+.++|||++.+++++.+.+.|.+.+..+. .+-  
T Consensus       322 ~~l~~d~~~~~al~~~~~~~~~~v~HPKl~~l~eilke~~~k-~~~~RvIVFT~yRdTae~i~~~L~~~~~~~~~rFiGQ  400 (542)
T COG1111         322 KSLLADPYFKRALRLLIRADESGVEHPKLEKLREILKEQLEK-NGDSRVIVFTEYRDTAEEIVNFLKKIGIKARVRFIGQ  400 (542)
T ss_pred             HHHhcChhhHHHHHHHHHhccccCCCccHHHHHHHHHHHHhc-CCCceEEEEehhHhHHHHHHHHHHhcCCcceeEEeec
Confidence                                    000001111222222222 2446899999999999999999999888774 222  


Q ss_pred             ------cCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEEEEECCCCChhHHHHhhccCCCCCCceEEEEEee
Q 037567          260 ------GQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYA  333 (374)
Q Consensus       260 ------~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~~~~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~  333 (374)
                            .||+.++..+++++|+.|+++|||||++.++|+|+|.++.||+|++..|...++||.||+||. ..|.+++++.
T Consensus       401 a~r~~~~GMsQkeQ~eiI~~Fr~Ge~nVLVaTSVgEEGLDIp~vDlVifYEpvpSeIR~IQR~GRTGR~-r~Grv~vLvt  479 (542)
T COG1111         401 ASREGDKGMSQKEQKEIIDQFRKGEYNVLVATSVGEEGLDIPEVDLVIFYEPVPSEIRSIQRKGRTGRK-RKGRVVVLVT  479 (542)
T ss_pred             cccccccccCHHHHHHHHHHHhcCCceEEEEcccccccCCCCcccEEEEecCCcHHHHHHHhhCccccC-CCCeEEEEEe
Confidence                  469999999999999999999999999999999999999999999999999999999999997 6888888888


Q ss_pred             ccCC
Q 037567          334 RSNF  337 (374)
Q Consensus       334 ~~~~  337 (374)
                      ..+.
T Consensus       480 ~gtr  483 (542)
T COG1111         480 EGTR  483 (542)
T ss_pred             cCch
Confidence            8743

>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type

Probab=100.00  E-value=1.6e-36  Score=268.34  Aligned_cols=295  Identities=19%  Similarity=0.217  Sum_probs=194.0

Q ss_pred             hHHHHHHHHHcCCC--EEEEccCCCCchhhhhccccccCCcEEEEcchHHHHHHHHHHHHHcC--------CceEEcCCC
Q 037567           17 YQKDVIQRIIEKRD--CLVVMATGSGKSLCYQLPPLVTGKTALVVSPLISLMQDQVMSLKQRG--------INAEFLGSA   86 (374)
Q Consensus        17 ~Q~~~~~~~~~~~~--~l~~a~tGsGKT~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~--------~~~~~~~~~   86 (374)
                      +|.++++++.++++  +++.+|||||||.+++++++....++++++|+++|++|+.+.+..+-        ..+..+.+.
T Consensus         1 hQ~~~~~~~~~~~~~~~~i~apTGsGKT~~~~~~~l~~~~~~~~~~P~~aL~~~~~~~~~~~~~~~~~~~~~~v~~~~g~   80 (357)
T TIGR03158         1 HQVATFEALQSKDADIIFNTAPTGAGKTLAWLTPLLHGENDTIALYPTNALIEDQTEAIKEFVDVFKPERDVNLLHVSKA   80 (357)
T ss_pred             CHHHHHHHHHcCCCCEEEEECCCCCCHHHHHHHHHHHcCCCEEEEeChHHHHHHHHHHHHHHHHhcCCCCCceEEEecCC
Confidence            69999999999874  68899999999999999988888889999999999999988877651        222222222


Q ss_pred             CCch-hh------------------hhhhhcCCeeEEEEcCcccccCchhhHH------HHHhcCccEEEEeccchhhcc
Q 037567           87 QTDS-SV------------------QTKAETGYFQLLFMTPEKACIIPISFWS------KLLKAGVCLFAVDEAHCISEW  141 (374)
Q Consensus        87 ~~~~-~~------------------~~~~~~~~~~i~i~T~~~l~~~~~~~~~------~~~~~~~~~vviDE~h~~~~~  141 (374)
                      .... ..                  ........+.|+++||+.+..++..+..      .....+++++|+||+|.+..+
T Consensus        81 ~~~d~~~~~~~~~~~~~g~~~~~~~r~~~~~~~p~illT~p~~l~~llr~~~~~~~~~~~~~~~~~~~iV~DE~H~~~~~  160 (357)
T TIGR03158        81 TLKDIKEYANDKVGSSKGEKLYNLLRNPIGTSTPIILLTNPDIFVYLTRFAYIDRGDIAAGFYTKFSTVIFDEFHLYDAK  160 (357)
T ss_pred             chHHHHHhhhhhcccCccchhhhhHHHHHhcCCCCEEEecHHHHHHHHhhhccCcccchhhhhcCCCEEEEecccccCcc
Confidence            1110 00                  0111134688999999988765433211      123578999999999998764


Q ss_pred             cCcchHHH-HHHHHHHHhcCCCCeeEEEeecCcccHHHHHHhcCCCCCeEEEecc------------CC---------Cc
Q 037567          142 GHDFRLEY-KQLDKLRTFLLGVPFVALTATATEKVRIDIINSLKLKNPYVTIASF------------DR---------KN  199 (374)
Q Consensus       142 ~~~~~~~~-~~~~~~~~~~~~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~------------~~---------~~  199 (374)
                      +....... ..+..+.......+++++|||+++.....+........+.......            ..         +.
T Consensus       161 ~~~~~~~~l~~~~~~~~~~~~~~~i~lSAT~~~~~~~~l~~~~~~~~~~~~v~g~~~~~~~~~~~~~~~~~~~~~~~~~~  240 (357)
T TIGR03158       161 QLVGMLFLLAYMQLIRFFECRRKFVFLSATPDPALILRLQNAKQAGVKIAPIDGEKYQFPDNPELEADNKTQSFRPVLPP  240 (357)
T ss_pred             cchhhhhhhHHHHHHHhhhcCCcEEEEecCCCHHHHHHHHhccccCceeeeecCcccccCCChhhhccccccccceeccc
Confidence            43322211 2222222222357999999999887655444432222222221111            00         11


Q ss_pred             eeEEEEeec-CCcchHHHHHHHHHHhh--cCCCcEEEEecchhHHHHHHHHHHHcC--CceeeeecCCChHHHHHHHHhh
Q 037567          200 LFYGVKVIN-RGQSFVDELVQEILKSV--AGAGSIIVYCMTIKDVEEISKALKQLG--VKAGTYHGQMGSKAREEAHRLF  274 (374)
Q Consensus       200 ~~~~~~~~~-~~~~~~~~~~~~~~~~~--~~~~~~lVf~~~~~~~~~l~~~l~~~~--~~~~~~~~~~~~~~r~~~~~~f  274 (374)
                      +...+.... ........++..+.+..  .+++++||||+++..++.+++.|++.+  ..+..+||.++..+|.+.    
T Consensus       241 i~~~~~~~~~~~~~~l~~l~~~i~~~~~~~~~~k~LIf~nt~~~~~~l~~~L~~~~~~~~~~~l~g~~~~~~R~~~----  316 (357)
T TIGR03158       241 VELELIPAPDFKEEELSELAEEVIERFRQLPGERGAIILDSLDEVNRLSDLLQQQGLGDDIGRITGFAPKKDRERA----  316 (357)
T ss_pred             eEEEEEeCCchhHHHHHHHHHHHHHHHhccCCCeEEEEECCHHHHHHHHHHHhhhCCCceEEeeecCCCHHHHHHh----
Confidence            222121101 11111222223333322  256799999999999999999999864  567889999999888754    


Q ss_pred             hcCCeeEEEEeccccccccccCccEEEEECCCCChhHHHHhhccCC
Q 037567          275 IRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCG  320 (374)
Q Consensus       275 ~~g~~~ilv~t~~~~~G~d~~~~~~vi~~~~p~s~~~~~Q~~GR~~  320 (374)
                        ++.+|||||+++++|+|+|.. .|| ++ |.+...|+||+||+|
T Consensus       317 --~~~~iLVaTdv~~rGiDi~~~-~vi-~~-p~~~~~yiqR~GR~g  357 (357)
T TIGR03158       317 --MQFDILLGTSTVDVGVDFKRD-WLI-FS-ARDAAAFWQRLGRLG  357 (357)
T ss_pred             --ccCCEEEEecHHhcccCCCCc-eEE-EC-CCCHHHHhhhcccCC
Confidence              367899999999999999976 555 44 889999999999986

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.

>PRK11664 ATP-dependent RNA helicase HrpB; Provisional

Probab=100.00  E-value=9.2e-37  Score=292.04  Aligned_cols=327  Identities=17%  Similarity=0.192  Sum_probs=225.4

Q ss_pred             chhHHHHHHHHHcCCCEEEEccCCCCchhhhhcccccc---CCcEEEEcchHHHHHHHHHHHHH-cCCc----eEEcCCC
Q 037567           15 RPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVT---GKTALVVSPLISLMQDQVMSLKQ-RGIN----AEFLGSA   86 (374)
Q Consensus        15 ~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~~---~~~~lil~P~~~l~~q~~~~~~~-~~~~----~~~~~~~   86 (374)
                      +.+-.+.+.++.+++++++.|+||||||..+.++++..   ..+++++.|++.++.|+.+.+.. ++..    +......
T Consensus         7 ~~~~~~i~~~l~~~~~vvv~A~TGSGKTt~~pl~lL~~~~~~~~ilvlqPrR~aA~qia~rva~~l~~~~g~~VGy~vr~   86 (812)
T PRK11664          7 AAVLPELLTALKTAPQVLLKAPTGAGKSTWLPLQLLQHGGINGKIIMLEPRRLAARNVAQRLAEQLGEKPGETVGYRMRA   86 (812)
T ss_pred             HHHHHHHHHHHHhCCCEEEEcCCCCCHHHHHHHHHHHcCCcCCeEEEECChHHHHHHHHHHHHHHhCcccCceEEEEecC
Confidence            34445677777788999999999999999988777753   45899999999999999998853 3332    2222211


Q ss_pred             CCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHHh-cCCCCee
Q 037567           87 QTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTF-LLGVPFV  165 (374)
Q Consensus        87 ~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~-~~~~~~i  165 (374)
                      ..       .......|+|+||+.+.+.+..   ...+.++++||+||+|...   .+....+..+..+... .++.+++
T Consensus        87 ~~-------~~~~~t~I~v~T~G~Llr~l~~---d~~L~~v~~IIlDEaHER~---l~~Dl~L~ll~~i~~~lr~~lqli  153 (812)
T PRK11664         87 ES-------KVGPNTRLEVVTEGILTRMIQR---DPELSGVGLVILDEFHERS---LQADLALALLLDVQQGLRDDLKLL  153 (812)
T ss_pred             cc-------ccCCCCcEEEEChhHHHHHHhh---CCCcCcCcEEEEcCCCccc---cccchHHHHHHHHHHhCCccceEE
Confidence            11       1122347999999998765443   3457889999999999631   1111111222333332 3478899


Q ss_pred             EEEeecCcccHHHHHHhcCCCCCeEEEeccCCCceeEEEEeecCCcchHH----HHHHHHHHhhcCCCcEEEEecchhHH
Q 037567          166 ALTATATEKVRIDIINSLKLKNPYVTIASFDRKNLFYGVKVINRGQSFVD----ELVQEILKSVAGAGSIIVYCMTIKDV  241 (374)
Q Consensus       166 ~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~lVf~~~~~~~  241 (374)
                      +||||++...   +...+. ..+.+...... ..+...+.... ......    ..+..++..  ..+++|||+++..++
T Consensus       154 lmSATl~~~~---l~~~~~-~~~~I~~~gr~-~pV~~~y~~~~-~~~~~~~~v~~~l~~~l~~--~~g~iLVFlpg~~ei  225 (812)
T PRK11664        154 IMSATLDNDR---LQQLLP-DAPVIVSEGRS-FPVERRYQPLP-AHQRFDEAVARATAELLRQ--ESGSLLLFLPGVGEI  225 (812)
T ss_pred             EEecCCCHHH---HHHhcC-CCCEEEecCcc-ccceEEeccCc-hhhhHHHHHHHHHHHHHHh--CCCCEEEEcCCHHHH
Confidence            9999998653   233332 22333222111 11111111111 111222    223333332  468999999999999


Q ss_pred             HHHHHHHHH---cCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEEEEECCCC-----------
Q 037567          242 EEISKALKQ---LGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPK-----------  307 (374)
Q Consensus       242 ~~l~~~l~~---~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~~~~p~-----------  307 (374)
                      +.+++.|++   .++.+..+||+++.+++...+..|.+|+.+|+|||+++++|+|+|++++||+++.+.           
T Consensus       226 ~~l~~~L~~~~~~~~~v~~Lhg~l~~~eq~~~~~~~~~G~rkVlvATnIAErsLtIp~V~~VID~Gl~r~~~yd~~~g~~  305 (812)
T PRK11664        226 QRVQEQLASRVASDVLLCPLYGALSLAEQQKAILPAPAGRRKVVLATNIAETSLTIEGIRLVVDSGLERVARFDPKTGLT  305 (812)
T ss_pred             HHHHHHHHHhccCCceEEEeeCCCCHHHHHHHhccccCCCeEEEEecchHHhcccccCceEEEECCCcccccccccCCcc
Confidence            999999987   467889999999999999999999999999999999999999999999999988764           


Q ss_pred             -------ChhHHHHhhccCCCCCCceEEEEEeeccCCCcccceeccccchHHHHHHHHHHHHHHHH
Q 037567          308 -------TLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFYCGESQTENQRTAIMESLLAAQRY  366 (374)
Q Consensus       308 -------s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  366 (374)
                             |..++.||.||+||. .+|.||.+|++.++..   +.....++..+..+..-..++..+
T Consensus       306 ~L~~~~iSkasa~QR~GRaGR~-~~G~cyrL~t~~~~~~---l~~~~~PEI~r~dL~~~~L~l~~~  367 (812)
T PRK11664        306 RLVTQRISQASMTQRAGRAGRL-EPGICLHLYSKEQAER---AAAQSEPEILHSDLSGLLLELLQW  367 (812)
T ss_pred             eeEEEeechhhhhhhccccCCC-CCcEEEEecCHHHHhh---CccCCCCceeccchHHHHHHHHHc
Confidence                   346899999999998 6999999999987754   344455555555555555555444

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

Probab=100.00  E-value=3.3e-36  Score=288.64  Aligned_cols=328  Identities=23%  Similarity=0.251  Sum_probs=245.0

Q ss_pred             hHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc-----cCCcEEEEcchHHHHHHHHHHHHHc-
Q 037567            3 STLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV-----TGKTALVVSPLISLMQDQVMSLKQR-   76 (374)
Q Consensus         3 ~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~-----~~~~~lil~P~~~l~~q~~~~~~~~-   76 (374)
                      .+|.. .|+..|++||.+|+..+.+|++++|..|||||||.+|++|++.     ...++|++.|+++|+++..+.+.++ 
T Consensus        61 ~~l~~-~g~~~lY~HQ~~A~~~~~~G~~vvVtTgTgSGKTe~FllPIld~~l~~~~a~AL~lYPtnALa~DQ~~rl~~~~  139 (851)
T COG1205          61 SALVK-AGIERLYSHQVDALRLIREGRNVVVTTGTGSGKTESFLLPILDHLLRDPSARALLLYPTNALANDQAERLRELI  139 (851)
T ss_pred             HHHHH-hccccccHHHHHHHHHHHCCCCEEEECCCCCchhHHHHHHHHHHHhhCcCccEEEEechhhhHhhHHHHHHHHH
Confidence            45666 6777899999999999999999999999999999999999886     3567899999999999999998865 


Q ss_pred             ---C--CceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchh--hHHHHHhcCccEEEEeccchhhc-ccCcchHH
Q 037567           77 ---G--INAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPIS--FWSKLLKAGVCLFAVDEAHCISE-WGHDFRLE  148 (374)
Q Consensus        77 ---~--~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~--~~~~~~~~~~~~vviDE~h~~~~-~~~~~~~~  148 (374)
                         +  +....+.+...... .......+++|++|||++|..++-.  ......+.++++||+||+|.+.. .|.+....
T Consensus       140 ~~~~~~v~~~~y~Gdt~~~~-r~~~~~~pp~IllTNpdMLh~~llr~~~~~~~~~~~Lk~lVvDElHtYrGv~GS~vA~l  218 (851)
T COG1205         140 SDLPGKVTFGRYTGDTPPEE-RRAIIRNPPDILLTNPDMLHYLLLRNHDAWLWLLRNLKYLVVDELHTYRGVQGSEVALL  218 (851)
T ss_pred             HhCCCcceeeeecCCCChHH-HHHHHhCCCCEEEeCHHHHHHHhccCcchHHHHHhcCcEEEEecceeccccchhHHHHH
Confidence               3  33444444433333 3355667899999999999773322  22344567799999999999954 78888878


Q ss_pred             HHHHHHHHHhcC-CCCeeEEEeecCcccHHHHHHhcCCCCCeE-EEeccCCCceeEEEEeec------C--CcchHHHHH
Q 037567          149 YKQLDKLRTFLL-GVPFVALTATATEKVRIDIINSLKLKNPYV-TIASFDRKNLFYGVKVIN------R--GQSFVDELV  218 (374)
Q Consensus       149 ~~~~~~~~~~~~-~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~------~--~~~~~~~~~  218 (374)
                      ++++........ +.++|+.|||...+..  +...+....... +..+.........+....      .  ........-
T Consensus       219 lRRL~~~~~~~~~~~q~i~~SAT~~np~e--~~~~l~~~~f~~~v~~~g~~~~~~~~~~~~p~~~~~~~~~r~s~~~~~~  296 (851)
T COG1205         219 LRRLLRRLRRYGSPLQIICTSATLANPGE--FAEELFGRDFEVPVDEDGSPRGLRYFVRREPPIRELAESIRRSALAELA  296 (851)
T ss_pred             HHHHHHHHhccCCCceEEEEeccccChHH--HHHHhcCCcceeeccCCCCCCCceEEEEeCCcchhhhhhcccchHHHHH
Confidence            788877776554 6789999999988763  344444333333 222222222221111111      0  111112222


Q ss_pred             HHHHHhhcCCCcEEEEecchhHHHHHH----HHHHHcC----CceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccc
Q 037567          219 QEILKSVAGAGSIIVYCMTIKDVEEIS----KALKQLG----VKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGM  290 (374)
Q Consensus       219 ~~~~~~~~~~~~~lVf~~~~~~~~~l~----~~l~~~~----~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~  290 (374)
                      .-+-....++-++|+|+.+...++.+.    +.+...+    ..+..+++++...+|..+...|+.|+..++++|++++-
T Consensus       297 ~~~~~~~~~~~~tL~F~~sr~~~e~~~~~~~~~~~~~~~~l~~~v~~~~~~~~~~er~~ie~~~~~g~~~~~~st~Alel  376 (851)
T COG1205         297 TLAALLVRNGIQTLVFFRSRKQVELLYLSPRRRLVREGGKLLDAVSTYRAGLHREERRRIEAEFKEGELLGVIATNALEL  376 (851)
T ss_pred             HHHHHHHHcCceEEEEEehhhhhhhhhhchhHHHhhcchhhhhheeeccccCCHHHHHHHHHHHhcCCccEEecchhhhh
Confidence            222223347889999999999999997    4444445    45778899999999999999999999999999999999


Q ss_pred             cccccCccEEEEECCCC-ChhHHHHhhccCCCCCCceEEEEEeec
Q 037567          291 GIDKPDVRHVIHYGCPK-TLESYYQESGRCGRDGIASVCWLYYAR  334 (374)
Q Consensus       291 G~d~~~~~~vi~~~~p~-s~~~~~Q~~GR~~R~~~~g~~~~~~~~  334 (374)
                      |+|+.+++.+|..+.|. +..+++|+.||+||.++.+..++.+..
T Consensus       377 gidiG~ldavi~~g~P~~s~~~~~Q~~GRaGR~~~~~l~~~v~~~  421 (851)
T COG1205         377 GIDIGSLDAVIAYGYPGVSVLSFRQRAGRAGRRGQESLVLVVLRS  421 (851)
T ss_pred             ceeehhhhhHhhcCCCCchHHHHHHhhhhccCCCCCceEEEEeCC
Confidence            99999999999999999 899999999999999987777777663

>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB

Probab=100.00  E-value=2e-36  Score=289.07  Aligned_cols=328  Identities=16%  Similarity=0.174  Sum_probs=224.5

Q ss_pred             hhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc---cCCcEEEEcchHHHHHHHHHHHH-HcCCceEEcCCCCCchh
Q 037567           16 PYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV---TGKTALVVSPLISLMQDQVMSLK-QRGINAEFLGSAQTDSS   91 (374)
Q Consensus        16 ~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~---~~~~~lil~P~~~l~~q~~~~~~-~~~~~~~~~~~~~~~~~   91 (374)
                      .+-.+++..+.++.++++.|+||||||..+.++++.   .+.+++++.|++.++.|.++.+. .++.......+..... 
T Consensus         5 ~~~~~i~~~l~~~~~vIi~a~TGSGKTT~vpl~lL~~~~~~~~ilvlqPrR~aA~qiA~rva~~~~~~~g~~VGy~vr~-   83 (819)
T TIGR01970         5 AVLPALRDALAAHPQVVLEAPPGAGKSTAVPLALLDAPGIGGKIIMLEPRRLAARSAAQRLASQLGEAVGQTVGYRVRG-   83 (819)
T ss_pred             HHHHHHHHHHHcCCcEEEECCCCCCHHHHHHHHHHHhhccCCeEEEEeCcHHHHHHHHHHHHHHhCCCcCcEEEEEEcc-
Confidence            344567777778899999999999999998877764   35689999999999999999885 3433221111110000 


Q ss_pred             hhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccch-hhcccCcchHHHHHHHHHHH-hcCCCCeeEEEe
Q 037567           92 VQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHC-ISEWGHDFRLEYKQLDKLRT-FLLGVPFVALTA  169 (374)
Q Consensus        92 ~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~-~~~~~~~~~~~~~~~~~~~~-~~~~~~~i~~Sa  169 (374)
                        ........+|.|+|++.|...+..   ...+.++++|||||+|. ..+....    ...+..+.. ..++.++++|||
T Consensus        84 --~~~~s~~t~I~v~T~G~Llr~l~~---d~~L~~v~~VIiDEaHER~L~~Dl~----L~ll~~i~~~lr~dlqlIlmSA  154 (819)
T TIGR01970        84 --ENKVSRRTRLEVVTEGILTRMIQD---DPELDGVGALIFDEFHERSLDADLG----LALALDVQSSLREDLKILAMSA  154 (819)
T ss_pred             --ccccCCCCcEEEECCcHHHHHHhh---CcccccCCEEEEeccchhhhccchH----HHHHHHHHHhcCCCceEEEEeC
Confidence              011223468999999988765443   34578899999999995 4432211    122223333 234789999999


Q ss_pred             ecCcccHHHHHHhcCCCCCeEEEeccCCCceeEEEEeecC-CcchH----HHHHHHHHHhhcCCCcEEEEecchhHHHHH
Q 037567          170 TATEKVRIDIINSLKLKNPYVTIASFDRKNLFYGVKVINR-GQSFV----DELVQEILKSVAGAGSIIVYCMTIKDVEEI  244 (374)
Q Consensus       170 T~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~----~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l  244 (374)
                      |++....   ...++ ..+.+......   ......+... .....    ...+..+++.  ..+++|||+++..+++.+
T Consensus       155 Tl~~~~l---~~~l~-~~~vI~~~gr~---~pVe~~y~~~~~~~~~~~~v~~~l~~~l~~--~~g~iLVFlpg~~eI~~l  225 (819)
T TIGR01970       155 TLDGERL---SSLLP-DAPVVESEGRS---FPVEIRYLPLRGDQRLEDAVSRAVEHALAS--ETGSILVFLPGQAEIRRV  225 (819)
T ss_pred             CCCHHHH---HHHcC-CCcEEEecCcc---eeeeeEEeecchhhhHHHHHHHHHHHHHHh--cCCcEEEEECCHHHHHHH
Confidence            9987542   33332 22333222111   1111111111 11112    1223333332  468899999999999999


Q ss_pred             HHHHHH---cCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEEEEECCCC--------------
Q 037567          245 SKALKQ---LGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPK--------------  307 (374)
Q Consensus       245 ~~~l~~---~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~~~~p~--------------  307 (374)
                      ++.|++   .++.+..+||+++.++|..+++.|.+|+.+|||||+++++|+|+|++++||+++.+.              
T Consensus       226 ~~~L~~~~~~~~~v~pLHg~L~~~eq~~~~~~~~~G~rkVlVATnIAErgItIp~V~~VID~Gl~r~~~yd~~~g~~~L~  305 (819)
T TIGR01970       226 QEQLAERLDSDVLICPLYGELSLAAQDRAIKPDPQGRRKVVLATNIAETSLTIEGIRVVIDSGLARVARFDPKTGITRLE  305 (819)
T ss_pred             HHHHHhhcCCCcEEEEecCCCCHHHHHHHHhhcccCCeEEEEecchHhhcccccCceEEEEcCcccccccccccCCceee
Confidence            999987   378899999999999999999999999999999999999999999999999999875              


Q ss_pred             ----ChhHHHHhhccCCCCCCceEEEEEeeccCCCcccceeccccchHHHHHHHHHHHHHHHH
Q 037567          308 ----TLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFYCGESQTENQRTAIMESLLAAQRY  366 (374)
Q Consensus       308 ----s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  366 (374)
                          |..++.||.||+||. .+|.||.+|+++++..+..   ...++..+..+..-..++..+
T Consensus       306 ~~~iSkasa~QR~GRAGR~-~~G~cyrL~t~~~~~~l~~---~~~PEI~r~~L~~~~L~l~~~  364 (819)
T TIGR01970       306 TVRISQASATQRAGRAGRL-EPGVCYRLWSEEQHQRLPA---QDEPEILQADLSGLALELAQW  364 (819)
T ss_pred             EEEECHHHHHhhhhhcCCC-CCCEEEEeCCHHHHHhhhc---CCCcceeccCcHHHHHHHHHc
Confidence                345689999999998 7999999999987755433   335555554554445555444

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.

>KOG0952 consensus DNA/RNA helicase MER3/SLH1, DEAD-box superfamily [RNA processing and modification]

Probab=100.00  E-value=2.6e-36  Score=279.10  Aligned_cols=342  Identities=17%  Similarity=0.217  Sum_probs=253.8

Q ss_pred             hHcCCCCCchhHHHHHHHHHc-CCCEEEEccCCCCchhhhhccccc-------------cCCcEEEEcchHHHHHHHHHH
Q 037567            7 KYFGYSVFRPYQKDVIQRIIE-KRDCLVVMATGSGKSLCYQLPPLV-------------TGKTALVVSPLISLMQDQVMS   72 (374)
Q Consensus         7 ~~~~~~~~~~~Q~~~~~~~~~-~~~~l~~a~tGsGKT~~~~l~~~~-------------~~~~~lil~P~~~l~~q~~~~   72 (374)
                      ..|+|..+..+|+.++|..+. +.|.+++||||||||..++|.+++             ...++++++|+++||.++.+.
T Consensus       104 ~~f~f~~fN~iQS~vFp~aY~SneNMLIcAPTGsGKT~la~L~ILr~ik~~~~~~~i~k~~fKiVYIaPmKALa~Em~~~  183 (1230)
T KOG0952|consen  104 GFFSFEEFNRIQSEVFPVAYKSNENMLICAPTGSGKTVLAELCILRTIKEHEEQGDIAKDDFKIVYIAPMKALAAEMVDK  183 (1230)
T ss_pred             hcccHHHHHHHHHHhhhhhhcCCCCEEEECCCCCCchHHHHHHHHHHHHhhccccccccCCceEEEEechHHHHHHHHHH
Confidence            678999999999999999887 579999999999999999888875             267899999999999998877


Q ss_pred             HHH----cCCceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHH-HHHhcCccEEEEeccchhhc-ccCcch
Q 037567           73 LKQ----RGINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWS-KLLKAGVCLFAVDEAHCISE-WGHDFR  146 (374)
Q Consensus        73 ~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~-~~~~~~~~~vviDE~h~~~~-~~~~~~  146 (374)
                      +.+    +|+.+..++++.......    -..++|+|+|||++.-..++... ...++.+.+||+||+|.+-+ .|...+
T Consensus       184 ~~kkl~~~gi~v~ELTGD~ql~~te----i~~tqiiVTTPEKwDvvTRk~~~d~~l~~~V~LviIDEVHlLhd~RGpvlE  259 (1230)
T KOG0952|consen  184 FSKKLAPLGISVRELTGDTQLTKTE----IADTQIIVTTPEKWDVVTRKSVGDSALFSLVRLVIIDEVHLLHDDRGPVLE  259 (1230)
T ss_pred             HhhhcccccceEEEecCcchhhHHH----HHhcCEEEecccceeeeeeeeccchhhhhheeeEEeeeehhhcCcccchHH
Confidence            764    477777777765443332    23479999999999666555433 33456789999999999954 676666


Q ss_pred             HHHHHHHHHHHhc-CCCCeeEEEeecCcccHHHHHHhcCCCCCe-EEEeccCCCceeEEEEee--cCC------cchHHH
Q 037567          147 LEYKQLDKLRTFL-LGVPFVALTATATEKVRIDIINSLKLKNPY-VTIASFDRKNLFYGVKVI--NRG------QSFVDE  216 (374)
Q Consensus       147 ~~~~~~~~~~~~~-~~~~~i~~SaT~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~--~~~------~~~~~~  216 (374)
                      ....+..+..+.. ...++|++|||.++..  ++..+++...+. +...+.............  ...      ...-.-
T Consensus       260 tiVaRtlr~vessqs~IRivgLSATlPN~e--DvA~fL~vn~~~glfsFd~~yRPvpL~~~~iG~k~~~~~~~~~~~d~~  337 (1230)
T KOG0952|consen  260 TIVARTLRLVESSQSMIRIVGLSATLPNYE--DVARFLRVNPYAGLFSFDQRYRPVPLTQGFIGIKGKKNRQQKKNIDEV  337 (1230)
T ss_pred             HHHHHHHHHHHhhhhheEEEEeeccCCCHH--HHHHHhcCCCccceeeecccccccceeeeEEeeecccchhhhhhHHHH
Confidence            5555555544432 3688999999999865  678888887432 222222222222222111  111      111123


Q ss_pred             HHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHHcC-----------------------CceeeeecCCChHHHHHHHHh
Q 037567          217 LVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLG-----------------------VKAGTYHGQMGSKAREEAHRL  273 (374)
Q Consensus       217 ~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~~-----------------------~~~~~~~~~~~~~~r~~~~~~  273 (374)
                      ...++.+.+..+.+++|||.+++...+.++.|.+..                       ...+++|.++..++|+.....
T Consensus       338 ~~~kv~e~~~~g~qVlvFvhsR~~Ti~tA~~l~~~a~~~g~~~~f~~~~~~k~l~elf~~g~~iHhAGm~r~DR~l~E~~  417 (1230)
T KOG0952|consen  338 CYDKVVEFLQEGHQVLVFVHSRNETIRTAKKLRERAETNGEKDLFLPSPRNKQLKELFQQGMGIHHAGMLRSDRQLVEKE  417 (1230)
T ss_pred             HHHHHHHHHHcCCeEEEEEecChHHHHHHHHHHHHHHhcCcccccCCChhhHHHHHHHHhhhhhcccccchhhHHHHHHH
Confidence            345566667789999999999999999998887641                       225678999999999999999


Q ss_pred             hhcCCeeEEEEeccccccccccCccEEEE----ECCC------CChhHHHHhhccCCCC--CCceEEEEEeeccCCCccc
Q 037567          274 FIRDEIRVMVATMAFGMGIDKPDVRHVIH----YGCP------KTLESYYQESGRCGRD--GIASVCWLYYARSNFAKGD  341 (374)
Q Consensus       274 f~~g~~~ilv~t~~~~~G~d~~~~~~vi~----~~~p------~s~~~~~Q~~GR~~R~--~~~g~~~~~~~~~~~~~~~  341 (374)
                      |..|.++||+||+.+..|+|+|+-.++|-    ++..      ....+.+|++|||||.  ...|.+++..+.+-+.++.
T Consensus       418 F~~G~i~vL~cTaTLAwGVNLPA~aViIKGT~~ydsskg~f~dlgilDVlQifGRAGRPqFd~~G~giIiTt~dkl~~Y~  497 (1230)
T KOG0952|consen  418 FKEGHIKVLCCTATLAWGVNLPAYAVIIKGTQVYDSSKGSFVDLGILDVLQIFGRAGRPQFDSSGEGIIITTRDKLDHYE  497 (1230)
T ss_pred             HhcCCceEEEecceeeeccCCcceEEEecCCcccccccCceeeehHHHHHHHHhccCCCCCCCCceEEEEecccHHHHHH
Confidence            99999999999999999999996555551    2221      1567889999999997  4678899998888888888


Q ss_pred             ceeccccchHHHH
Q 037567          342 FYCGESQTENQRT  354 (374)
Q Consensus       342 ~~~~~~~~~~~~~  354 (374)
                      .++....+-+.+.
T Consensus       498 sLl~~~~piES~~  510 (1230)
T KOG0952|consen  498 SLLTGQNPIESQL  510 (1230)
T ss_pred             HHHcCCChhHHHH
Confidence            8888877766553

>PRK14701 reverse gyrase; Provisional

Probab=100.00  E-value=2.6e-36  Score=303.78  Aligned_cols=327  Identities=20%  Similarity=0.220  Sum_probs=226.0

Q ss_pred             hHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc---cCCcEEEEcchHHHHHHHHHHHHHcC--
Q 037567            3 STLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV---TGKTALVVSPLISLMQDQVMSLKQRG--   77 (374)
Q Consensus         3 ~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~---~~~~~lil~P~~~l~~q~~~~~~~~~--   77 (374)
                      +.|++.+|| +|+++|.++++.+++|+++++.||||+|||+.++++++.   ++.+++|++||++|+.|+.+.++.++  
T Consensus        70 ~~f~~~~G~-~pt~iQ~~~i~~il~G~d~li~APTGsGKTl~~~~~al~~~~~g~~aLVl~PTreLa~Qi~~~l~~l~~~  148 (1638)
T PRK14701         70 EFFEKITGF-EFWSIQKTWAKRILRGKSFSIVAPTGMGKSTFGAFIALFLALKGKKCYIILPTTLLVKQTVEKIESFCEK  148 (1638)
T ss_pred             HHHHHhhCC-CCCHHHHHHHHHHHcCCCEEEEEcCCCCHHHHHHHHHHHHHhcCCeEEEEECHHHHHHHHHHHHHHHHhh
Confidence            457788999 699999999999999999999999999999855444332   46789999999999999999998753  


Q ss_pred             ----CceEEcCCCCCchhh---hhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccC-------
Q 037567           78 ----INAEFLGSAQTDSSV---QTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGH-------  143 (374)
Q Consensus        78 ----~~~~~~~~~~~~~~~---~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~-------  143 (374)
                          ..+..++++......   ......+.++|+|+||+.+......    ....+++++|+||||.+.++|.       
T Consensus       149 ~~~~v~v~~~~g~~s~~e~~~~~~~l~~g~~dILV~TPgrL~~~~~~----l~~~~i~~iVVDEAD~ml~~~knid~~L~  224 (1638)
T PRK14701        149 ANLDVRLVYYHSNLRKKEKEEFLERIENGDFDILVTTAQFLARNFPE----MKHLKFDFIFVDDVDAFLKASKNIDRSLQ  224 (1638)
T ss_pred             cCCceeEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECCchhHHhHHH----HhhCCCCEEEEECceeccccccccchhhh
Confidence                333445555444332   1223456689999999987654332    2236789999999999987554       


Q ss_pred             --cchHHHHH-----------------------HHHHHHhcCC-CC-eeEEEeecCcccHHHHHHhcCCCCCeEEEeccC
Q 037567          144 --DFRLEYKQ-----------------------LDKLRTFLLG-VP-FVALTATATEKVRIDIINSLKLKNPYVTIASFD  196 (374)
Q Consensus       144 --~~~~~~~~-----------------------~~~~~~~~~~-~~-~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~~  196 (374)
                        +++..+..                       +......++. .+ .+.+|||.++...  ....+  ..+........
T Consensus       225 llGF~~e~~~~~~~il~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~ll~~SAT~~~r~~--~~~l~--~~~l~f~v~~~  300 (1638)
T PRK14701        225 LLGFYEEIIEKAWKIIYLKKQGNIEDAMEKREILNKEIEKIGNKIGCLIVASATGKAKGD--RVKLY--RELLGFEVGSG  300 (1638)
T ss_pred             cCCChHHHHHHHHHhhhcccccccchhhhhhhhhhhhhhhcCCCccEEEEEecCCCchhH--HHHHh--hcCeEEEecCC
Confidence              34333321                       1111112222 33 5678999986321  12222  22222223333


Q ss_pred             CCceeEEEEeec-CCcchHHHHHHHHHHhhcCCCcEEEEecchhH---HHHHHHHHHHcCCceeeeecCCChHHHHHHHH
Q 037567          197 RKNLFYGVKVIN-RGQSFVDELVQEILKSVAGAGSIIVYCMTIKD---VEEISKALKQLGVKAGTYHGQMGSKAREEAHR  272 (374)
Q Consensus       197 ~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~lVf~~~~~~---~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~  272 (374)
                      ........+.+. ...... ..+.++++..  +..+||||+++..   ++.+++.|.+.|+++..+||+     |...++
T Consensus       301 ~~~lr~i~~~yi~~~~~~k-~~L~~ll~~~--g~~gIVF~~t~~~~e~ae~la~~L~~~Gi~a~~~h~~-----R~~~l~  372 (1638)
T PRK14701        301 RSALRNIVDVYLNPEKIIK-EHVRELLKKL--GKGGLIFVPIDEGAEKAEEIEKYLLEDGFKIELVSAK-----NKKGFD  372 (1638)
T ss_pred             CCCCCCcEEEEEECCHHHH-HHHHHHHHhC--CCCeEEEEeccccchHHHHHHHHHHHCCCeEEEecch-----HHHHHH
Confidence            333222222211 111212 3455555554  5689999999775   589999999999999999985     888999


Q ss_pred             hhhcCCeeEEEEec----cccccccccC-ccEEEEECCCC---ChhHHHHhh-------------ccCCCCCCceEEEEE
Q 037567          273 LFIRDEIRVMVATM----AFGMGIDKPD-VRHVIHYGCPK---TLESYYQES-------------GRCGRDGIASVCWLY  331 (374)
Q Consensus       273 ~f~~g~~~ilv~t~----~~~~G~d~~~-~~~vi~~~~p~---s~~~~~Q~~-------------GR~~R~~~~g~~~~~  331 (374)
                      +|.+|+.+|||+|+    .+.+|+|+|+ +++||+++.|.   +...+.|-.             ||++|.|.+..++..
T Consensus       373 ~F~~G~~~VLVaT~s~~gvaaRGIDiP~~Vryvi~~~~Pk~~~~~e~~~~~~~~~~~~~~~~~~~~~a~~~g~~~~~~~~  452 (1638)
T PRK14701        373 LFEEGEIDYLIGVATYYGTLVRGLDLPERIRFAVFYGVPKFRFRVDLEDPTIYRILGLLSEILKIEEELKEGIPIEGVLD  452 (1638)
T ss_pred             HHHcCCCCEEEEecCCCCeeEecCccCCccCEEEEeCCCCCCcchhhcccchhhhhcchHHHHHhhhhcccCCcchhHHH
Confidence            99999999999994    8899999999 99999999998   777665554             999999988777655


Q ss_pred             eeccCCCcccceecc
Q 037567          332 YARSNFAKGDFYCGE  346 (374)
Q Consensus       332 ~~~~~~~~~~~~~~~  346 (374)
                      +...+...++.++++
T Consensus       453 ~~~~~~~~~~~~l~~  467 (1638)
T PRK14701        453 VFPEDVEFLRSILKD  467 (1638)
T ss_pred             hHHHHHHHHHHHhcc
Confidence            555555555555543

>PRK09401 reverse gyrase; Reviewed

Probab=100.00  E-value=9.6e-36  Score=293.78  Aligned_cols=300  Identities=21%  Similarity=0.244  Sum_probs=205.9

Q ss_pred             hHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhcccc---ccCCcEEEEcchHHHHHHHHHHHHHcCC-
Q 037567            3 STLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPL---VTGKTALVVSPLISLMQDQVMSLKQRGI-   78 (374)
Q Consensus         3 ~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~---~~~~~~lil~P~~~l~~q~~~~~~~~~~-   78 (374)
                      +.|++.+|+ +|+++|..+++.+++|+++++.||||+|||..++..+.   .++.+++|++||++|+.|+.+.++.++. 
T Consensus        71 ~~f~~~~G~-~pt~iQ~~~i~~il~g~dv~i~ApTGsGKT~f~l~~~~~l~~~g~~alIL~PTreLa~Qi~~~l~~l~~~  149 (1176)
T PRK09401         71 KFFKKKTGS-KPWSLQRTWAKRLLLGESFAIIAPTGVGKTTFGLVMSLYLAKKGKKSYIIFPTRLLVEQVVEKLEKFGEK  149 (1176)
T ss_pred             HHHHHhcCC-CCcHHHHHHHHHHHCCCcEEEEcCCCCCHHHHHHHHHHHHHhcCCeEEEEeccHHHHHHHHHHHHHHhhh
Confidence            346777898 79999999999999999999999999999964333222   2478899999999999999999998754 


Q ss_pred             ---ceEEcCCCCC--c---hhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCc------
Q 037567           79 ---NAEFLGSAQT--D---SSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHD------  144 (374)
Q Consensus        79 ---~~~~~~~~~~--~---~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~------  144 (374)
                         ......+...  .   .........+.++|+|+||+++....    ..+....++++|+||||++.+++..      
T Consensus       150 ~~~~~~~~~g~~~~~~~ek~~~~~~l~~~~~~IlV~Tp~rL~~~~----~~l~~~~~~~lVvDEaD~~L~~~k~id~~l~  225 (1176)
T PRK09401        150 VGCGVKILYYHSSLKKKEKEEFLERLKEGDFDILVTTSQFLSKNF----DELPKKKFDFVFVDDVDAVLKSSKNIDKLLY  225 (1176)
T ss_pred             cCceEEEEEccCCcchhHHHHHHHHHhcCCCCEEEECHHHHHHHH----HhccccccCEEEEEChHHhhhcccchhhHHH
Confidence               3233322221  1   11122233467899999999886532    2334456999999999999864322      


Q ss_pred             ---ch-HHHH-----------------HHHHHHHhc-----CCCCeeEEEeecCcc-cHHHHHHh-cCCCCCeEEEeccC
Q 037567          145 ---FR-LEYK-----------------QLDKLRTFL-----LGVPFVALTATATEK-VRIDIINS-LKLKNPYVTIASFD  196 (374)
Q Consensus       145 ---~~-~~~~-----------------~~~~~~~~~-----~~~~~i~~SaT~~~~-~~~~~~~~-~~~~~~~~~~~~~~  196 (374)
                         +. ..+.                 .+.++...+     ...+++++|||.++. ....+... +++.   +......
T Consensus       226 ~lGF~~~~i~~i~~~i~~~~~~~~~~~~i~~l~~~i~~~~~~~~q~ilfSAT~~~~~~~~~l~~~ll~~~---v~~~~~~  302 (1176)
T PRK09401        226 LLGFSEEDIEKAMELIRLKRKYEEIYEKIRELEEKIAELKDKKGVLVVSSATGRPRGNRVKLFRELLGFE---VGSPVFY  302 (1176)
T ss_pred             hCCCCHHHHHHHHHhcccccccchhhhHHHHHHHhhhhcccCCceEEEEeCCCCccchHHHHhhccceEE---ecCcccc
Confidence               21 1111                 111111111     156899999999874 32211111 1111   1111111


Q ss_pred             CCceeEEEEeecCCcchHHHHHHHHHHhhcCCCcEEEEecchhH---HHHHHHHHHHcCCceeeeecCCChHHHHHHHHh
Q 037567          197 RKNLFYGVKVINRGQSFVDELVQEILKSVAGAGSIIVYCMTIKD---VEEISKALKQLGVKAGTYHGQMGSKAREEAHRL  273 (374)
Q Consensus       197 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lVf~~~~~~---~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~  273 (374)
                      ..++...+....    ...+.+.++++..  +.++||||++...   ++.+++.|...|+++..+||++    + ..+++
T Consensus       303 ~rnI~~~yi~~~----~k~~~L~~ll~~l--~~~~LIFv~t~~~~~~ae~l~~~L~~~gi~v~~~hg~l----~-~~l~~  371 (1176)
T PRK09401        303 LRNIVDSYIVDE----DSVEKLVELVKRL--GDGGLIFVPSDKGKEYAEELAEYLEDLGINAELAISGF----E-RKFEK  371 (1176)
T ss_pred             cCCceEEEEEcc----cHHHHHHHHHHhc--CCCEEEEEecccChHHHHHHHHHHHHCCCcEEEEeCcH----H-HHHHH
Confidence            222222221111    2334455555554  4689999999777   9999999999999999999998    2 23599


Q ss_pred             hhcCCeeEEEE----eccccccccccC-ccEEEEECCCC------ChhHHHHhhccCCC
Q 037567          274 FIRDEIRVMVA----TMAFGMGIDKPD-VRHVIHYGCPK------TLESYYQESGRCGR  321 (374)
Q Consensus       274 f~~g~~~ilv~----t~~~~~G~d~~~-~~~vi~~~~p~------s~~~~~Q~~GR~~R  321 (374)
                      |++|+.+|||+    |+.+++|+|+|+ +++||+++.|.      ....+.+++||+..
T Consensus       372 F~~G~~~VLVatas~tdv~aRGIDiP~~IryVI~y~vP~~~~~~~~~~~~~~~~~r~~~  430 (1176)
T PRK09401        372 FEEGEVDVLVGVASYYGVLVRGIDLPERIRYAIFYGVPKFKFSLEEELAPPFLLLRLLS  430 (1176)
T ss_pred             HHCCCCCEEEEecCCCCceeecCCCCcceeEEEEeCCCCEEEeccccccCHHHHHHHHh
Confidence            99999999999    589999999999 89999999998      56889999999863

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

Probab=100.00  E-value=5.8e-35  Score=264.54  Aligned_cols=290  Identities=20%  Similarity=0.269  Sum_probs=204.8

Q ss_pred             CCchhHHHHHHHHHc----CCCEEEEccCCCCchhhhhccccccCCcEEEEcchHHHHHHHHHHHHHcCCce---EEcCC
Q 037567           13 VFRPYQKDVIQRIIE----KRDCLVVMATGSGKSLCYQLPPLVTGKTALVVSPLISLMQDQVMSLKQRGINA---EFLGS   85 (374)
Q Consensus        13 ~~~~~Q~~~~~~~~~----~~~~l~~a~tGsGKT~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~---~~~~~   85 (374)
                      .+++||.+++.++..    ++..++++|||+|||.+++..+..-..++|||||+.+|+.||.+.+..+....   ...++
T Consensus        36 ~lr~yQ~~al~a~~~~~~~~~~gvivlpTGaGKT~va~~~~~~~~~~~Lvlv~~~~L~~Qw~~~~~~~~~~~~~~g~~~~  115 (442)
T COG1061          36 ELRPYQEEALDALVKNRRTERRGVIVLPTGAGKTVVAAEAIAELKRSTLVLVPTKELLDQWAEALKKFLLLNDEIGIYGG  115 (442)
T ss_pred             CCcHHHHHHHHHHHhhcccCCceEEEeCCCCCHHHHHHHHHHHhcCCEEEEECcHHHHHHHHHHHHHhcCCccccceecC
Confidence            599999999999998    88999999999999999887777766779999999999999998877664332   22322


Q ss_pred             CCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHHhcCCCC-e
Q 037567           86 AQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVP-F  164 (374)
Q Consensus        86 ~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~~~~~-~  164 (374)
                      +......        ..|.|+|.+++....  .......+.+++||+|||||+....         ...+...+.+.. +
T Consensus       116 ~~~~~~~--------~~i~vat~qtl~~~~--~l~~~~~~~~~liI~DE~Hh~~a~~---------~~~~~~~~~~~~~~  176 (442)
T COG1061         116 GEKELEP--------AKVTVATVQTLARRQ--LLDEFLGNEFGLIIFDEVHHLPAPS---------YRRILELLSAAYPR  176 (442)
T ss_pred             ceeccCC--------CcEEEEEhHHHhhhh--hhhhhcccccCEEEEEccccCCcHH---------HHHHHHhhhcccce
Confidence            2111110        269999999886542  2234444579999999999987522         233333333444 9


Q ss_pred             eEEEeecCcccHHHHHHhcCCCCCeEEEecc--------CCCceeEEEEe-ecC--------------------------
Q 037567          165 VALTATATEKVRIDIINSLKLKNPYVTIASF--------DRKNLFYGVKV-INR--------------------------  209 (374)
Q Consensus       165 i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~--------~~~~~~~~~~~-~~~--------------------------  209 (374)
                      ++|||||...+............+.+.....        -.+........ ...                          
T Consensus       177 LGLTATp~R~D~~~~~~l~~~~g~~vy~~~~~~li~~g~Lap~~~~~i~~~~t~~~~~~~~~~~~~~~~~~~~~~~~~~~  256 (442)
T COG1061         177 LGLTATPEREDGGRIGDLFDLIGPIVYEVSLKELIDEGYLAPYKYVEIKVTLTEDEEREYAKESARFRELLRARGTLRAE  256 (442)
T ss_pred             eeeccCceeecCCchhHHHHhcCCeEeecCHHHHHhCCCccceEEEEEEeccchHHHHHhhhhhhhhhhhhhhhhhhhHH
Confidence            9999998876522222211111122221110        01111111111 000                          


Q ss_pred             --------CcchHHHHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeE
Q 037567          210 --------GQSFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRV  281 (374)
Q Consensus       210 --------~~~~~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~i  281 (374)
                              ........+..++.....+.+++||+.+..++..++..+...+. +..+.++.+..+|.++++.|+.|.+++
T Consensus       257 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lif~~~~~~a~~i~~~~~~~~~-~~~it~~t~~~eR~~il~~fr~g~~~~  335 (442)
T COG1061         257 NEARRIAIASERKIAAVRGLLLKHARGDKTLIFASDVEHAYEIAKLFLAPGI-VEAITGETPKEEREAILERFRTGGIKV  335 (442)
T ss_pred             HHHHHHhhccHHHHHHHHHHHHHhcCCCcEEEEeccHHHHHHHHHHhcCCCc-eEEEECCCCHHHHHHHHHHHHcCCCCE
Confidence                    00001111222222211577999999999999999999988777 889999999999999999999999999


Q ss_pred             EEEeccccccccccCccEEEEECCCCChhHHHHhhccCCCC
Q 037567          282 MVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRD  322 (374)
Q Consensus       282 lv~t~~~~~G~d~~~~~~vi~~~~p~s~~~~~Q~~GR~~R~  322 (374)
                      |+++.++.+|+|+|+++++|..++..|...|.||+||..|.
T Consensus       336 lv~~~vl~EGvDiP~~~~~i~~~~t~S~~~~~Q~lGR~LR~  376 (442)
T COG1061         336 LVTVKVLDEGVDIPDADVLIILRPTGSRRLFIQRLGRGLRP  376 (442)
T ss_pred             EEEeeeccceecCCCCcEEEEeCCCCcHHHHHHHhhhhccC
Confidence            99999999999999999999999999999999999999993

>PRK12898 secA preprotein translocase subunit SecA; Reviewed

Probab=100.00  E-value=8.2e-35  Score=267.51  Aligned_cols=325  Identities=18%  Similarity=0.160  Sum_probs=227.3

Q ss_pred             hhHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc---cCCcEEEEcchHHHHHHHHHHHHH---
Q 037567            2 VSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV---TGKTALVVSPLISLMQDQVMSLKQ---   75 (374)
Q Consensus         2 ~~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~---~~~~~lil~P~~~l~~q~~~~~~~---   75 (374)
                      .++.++.+|+. |+|.|..+++.+++|+  +..+.||+|||+++.+|++.   .++.++|++|++.|+.|.++++..   
T Consensus        93 rEa~~R~lg~~-p~~VQ~~~~~~ll~G~--Iae~~TGeGKTla~~lp~~~~al~G~~v~VvTptreLA~qdae~~~~l~~  169 (656)
T PRK12898         93 REASGRVLGQR-HFDVQLMGGLALLSGR--LAEMQTGEGKTLTATLPAGTAALAGLPVHVITVNDYLAERDAELMRPLYE  169 (656)
T ss_pred             HHHHHHHhCCC-CChHHHHHHHHHhCCC--eeeeeCCCCcHHHHHHHHHHHhhcCCeEEEEcCcHHHHHHHHHHHHHHHh
Confidence            45677888995 8999999999999998  99999999999999988875   478999999999999998888775   


Q ss_pred             -cCCceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccc-cCchhhH-----------------------HHHHhcCccEE
Q 037567           76 -RGINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKAC-IIPISFW-----------------------SKLLKAGVCLF  130 (374)
Q Consensus        76 -~~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~-~~~~~~~-----------------------~~~~~~~~~~v  130 (374)
                       +|+.+..+.++....   .......++|+++|...+. ++++...                       .......+.+.
T Consensus       170 ~lGlsv~~i~gg~~~~---~r~~~y~~dIvygT~~e~~FDyLrd~~~~~~~~~~~~~~~~~l~~~~~~~~~~v~r~~~~a  246 (656)
T PRK12898        170 ALGLTVGCVVEDQSPD---ERRAAYGADITYCTNKELVFDYLRDRLALGQRASDARLALESLHGRSSRSTQLLLRGLHFA  246 (656)
T ss_pred             hcCCEEEEEeCCCCHH---HHHHHcCCCEEEECCCchhhhhccccccccccccchhhhhhhhccccCchhhhccccccee
Confidence             377877776654322   2223456899999998762 2332211                       11223567899


Q ss_pred             EEeccchhh-cc--------c---Cc-chHHH--------------------------------HHHHHH----------
Q 037567          131 AVDEAHCIS-EW--------G---HD-FRLEY--------------------------------KQLDKL----------  155 (374)
Q Consensus       131 viDE~h~~~-~~--------~---~~-~~~~~--------------------------------~~~~~~----------  155 (374)
                      ||||++.+. +.        |   .. ....+                                ..+...          
T Consensus       247 IvDEvDSiLiDeartpliis~~~~~~~~~~~y~~~~~~~~~l~~~~~y~~d~~~~~v~lt~~g~~~~e~~~~~l~~~~~~  326 (656)
T PRK12898        247 IVDEADSVLIDEARTPLIISAPAKEADEAEVYRQALELAAQLKEGEDYTIDAAEKRIELTEAGRARIAELAESLPPAWRG  326 (656)
T ss_pred             EeecccceeeccCCCceEEECCCCCCchhHHHHHHHHHHHhcCCCCceEEECCCCeEEEcHHHHHHHHHHhCcchhhccc
Confidence            999999974 10        0   00 00000                                000000          


Q ss_pred             -----------H---Hhc-------------------------------------------C------------------
Q 037567          156 -----------R---TFL-------------------------------------------L------------------  160 (374)
Q Consensus       156 -----------~---~~~-------------------------------------------~------------------  160 (374)
                                 +   ..+                                           +                  
T Consensus       327 ~~~~~~~i~~Al~A~~l~~~d~dYiV~d~~V~ivD~~TGR~~~gr~w~~GLhQaieaKE~v~i~~e~~t~a~It~q~~Fr  406 (656)
T PRK12898        327 AVRREELVRQALSALHLFRRDEHYIVRDGKVVIVDEFTGRVMPDRSWEDGLHQMIEAKEGCELTDPRETLARITYQRFFR  406 (656)
T ss_pred             chHHHHHHHHHHHHHHHHhcCCceEEECCeEEEEECCCCeECCCCCcChHHHHHHHHhcCCCCCcCceeeeeehHHHHHH
Confidence                       0   000                                           0                  


Q ss_pred             -CCCeeEEEeecCcccHHHHHHhcCCCCCeEEEeccCCCceeEEEEeecCCcchHHHHHHHHHHhhcCCCcEEEEecchh
Q 037567          161 -GVPFVALTATATEKVRIDIINSLKLKNPYVTIASFDRKNLFYGVKVINRGQSFVDELVQEILKSVAGAGSIIVYCMTIK  239 (374)
Q Consensus       161 -~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lVf~~~~~  239 (374)
                       -.++.+||||.... ..++...+++....+...... ........++.........++..+......+.++||||++++
T Consensus       407 ~Y~kl~GmTGTa~~~-~~El~~~y~l~vv~IPt~kp~-~r~~~~~~v~~t~~~K~~aL~~~i~~~~~~~~pvLIft~t~~  484 (656)
T PRK12898        407 RYLRLAGMTGTAREV-AGELWSVYGLPVVRIPTNRPS-QRRHLPDEVFLTAAAKWAAVAARVRELHAQGRPVLVGTRSVA  484 (656)
T ss_pred             hhHHHhcccCcChHH-HHHHHHHHCCCeEEeCCCCCc-cceecCCEEEeCHHHHHHHHHHHHHHHHhcCCCEEEEeCcHH
Confidence             01367888888754 346777776653222222222 212222223333333444444444443335688999999999


Q ss_pred             HHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEecccccccccc---Ccc-----EEEEECCCCChhH
Q 037567          240 DVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKP---DVR-----HVIHYGCPKTLES  311 (374)
Q Consensus       240 ~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~---~~~-----~vi~~~~p~s~~~  311 (374)
                      .++.+++.|.+.|+++..+||+++.  ++..+..+..++..|+|||+++++|+|++   ++.     +||+++.|.|...
T Consensus       485 ~se~L~~~L~~~gi~~~~Lhg~~~~--rE~~ii~~ag~~g~VlVATdmAgRGtDI~l~~~V~~~GGLhVI~~d~P~s~r~  562 (656)
T PRK12898        485 ASERLSALLREAGLPHQVLNAKQDA--EEAAIVARAGQRGRITVATNMAGRGTDIKLEPGVAARGGLHVILTERHDSARI  562 (656)
T ss_pred             HHHHHHHHHHHCCCCEEEeeCCcHH--HHHHHHHHcCCCCcEEEEccchhcccCcCCccchhhcCCCEEEEcCCCCCHHH
Confidence            9999999999999999999998654  44445555555567999999999999999   565     8999999999999


Q ss_pred             HHHhhccCCCCCCceEEEEEeeccC
Q 037567          312 YYQESGRCGRDGIASVCWLYYARSN  336 (374)
Q Consensus       312 ~~Q~~GR~~R~~~~g~~~~~~~~~~  336 (374)
                      |.||+||+||.|.+|.++.+++.+|
T Consensus       563 y~hr~GRTGRqG~~G~s~~~is~eD  587 (656)
T PRK12898        563 DRQLAGRCGRQGDPGSYEAILSLED  587 (656)
T ss_pred             HHHhcccccCCCCCeEEEEEechhH
Confidence            9999999999999999999999876

>TIGR03714 secA2 accessory Sec system translocase SecA2

Probab=100.00  E-value=2.7e-35  Score=273.78  Aligned_cols=324  Identities=17%  Similarity=0.158  Sum_probs=222.6

Q ss_pred             hHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc---cCCcEEEEcchHHHHHHHHHHHH----H
Q 037567            3 STLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV---TGKTALVVSPLISLMQDQVMSLK----Q   75 (374)
Q Consensus         3 ~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~---~~~~~lil~P~~~l~~q~~~~~~----~   75 (374)
                      ++-++.+|.   +|+|.+++..+..+++.++.++||+|||++|.+|++.   .+..++|++|++.|+.|+.+++.    .
T Consensus        61 Ea~~R~lgl---rpydVQlig~l~l~~G~Iaem~TGeGKTLta~Lpa~l~aL~g~~V~VVTpn~yLA~Rdae~m~~l~~~  137 (762)
T TIGR03714        61 EADKRVLGM---FPYDVQVLGAIVLHQGNIAEMKTGEGKTLTATMPLYLNALTGKGAMLVTTNDYLAKRDAEEMGPVYEW  137 (762)
T ss_pred             HHHHhhcCC---CccHHHHHHHHHhcCCceeEecCCcchHHHHHHHHHHHhhcCCceEEeCCCHHHHHHHHHHHHHHHhh
Confidence            455666665   5666666666555555799999999999999988654   46779999999999999999885    4


Q ss_pred             cCCceEEcCCCCC--chhhhhhhhcCCeeEEEEcCccc-ccCchhh----HHHHHhcCccEEEEeccchhhc-c------
Q 037567           76 RGINAEFLGSAQT--DSSVQTKAETGYFQLLFMTPEKA-CIIPISF----WSKLLKAGVCLFAVDEAHCISE-W------  141 (374)
Q Consensus        76 ~~~~~~~~~~~~~--~~~~~~~~~~~~~~i~i~T~~~l-~~~~~~~----~~~~~~~~~~~vviDE~h~~~~-~------  141 (374)
                      +|+.+.+..++..  ............++|+++||+.+ .+++...    .......++.++|+||||.+.- .      
T Consensus       138 LGLsv~~~~~~s~~~~~~~~~rr~~y~~dIvygTp~~LgfDyLrD~l~~~~~~~~~r~l~~~IVDEaDsILiDeartpli  217 (762)
T TIGR03714       138 LGLTVSLGVVDDPDEEYDANEKRKIYNSDIVYTTNSALGFDYLIDNLASNKEGKFLRPFNYVIVDEVDSVLLDSAQTPLV  217 (762)
T ss_pred             cCCcEEEEECCCCccccCHHHHHHhCCCCEEEECchhhhhhHHHHHhhcchhhcccccCcEEEEecHhhHhhccCcCCee
Confidence            5777766544311  11111222335689999999998 3333221    1223456788999999999841 0      


Q ss_pred             --cC--cchHHHHHHHHHHHhcC---------------------------------------------------------
Q 037567          142 --GH--DFRLEYKQLDKLRTFLL---------------------------------------------------------  160 (374)
Q Consensus       142 --~~--~~~~~~~~~~~~~~~~~---------------------------------------------------------  160 (374)
                        |.  .....+.....+...+.                                                         
T Consensus       218 isg~~~~~~~~y~~~~~~v~~l~~~~dy~~d~~~~~v~lt~~G~~~~e~~~~~~~l~~~~~~~~~~~i~~al~A~~~~~~  297 (762)
T TIGR03714       218 ISGAPRVQSNLYHIADTFVRTLKEDVDYIFKKDKKEVWLTDKGIEKAEQYFKIDNLYSEEYFELVRHINLALRAHYLFKR  297 (762)
T ss_pred             eeCCCccchHHHHHHHHHHHhcCCCCCeEEEcCCCeeeecHhHHHHHHHHcCCCccCChhhHHHHHHHHHHHHHHHHHhc
Confidence              00  00000000000000000                                                         


Q ss_pred             -------------------------------------------------------------CCCeeEEEeecCcccHHHH
Q 037567          161 -------------------------------------------------------------GVPFVALTATATEKVRIDI  179 (374)
Q Consensus       161 -------------------------------------------------------------~~~~i~~SaT~~~~~~~~~  179 (374)
                                                                                   -.++.+||+|.... ..++
T Consensus       298 d~dYiV~~~~v~ivD~~TGr~~~gr~~~~GLhQaieaKE~v~i~~e~~t~a~It~qn~Fr~Y~kl~GmTGTa~~~-~~Ef  376 (762)
T TIGR03714       298 NKDYVVTNGEVVLLDRITGRLLEGTKLQSGIHQAIEAKEHVELSKETRAMASITYQNLFKMFNKLSGMTGTGKVA-EKEF  376 (762)
T ss_pred             CCceEEECCEEEEEECCCCcCCCCCCcchHHHHHHHhhcCCCCCCCceeeeeeeHHHHHhhCchhcccCCCChhH-HHHH
Confidence                                                                         01366777775432 2344


Q ss_pred             HHhcCCCCCeEEEeccCCCceeEEE--EeecCCcchHHHHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHHcCCceee
Q 037567          180 INSLKLKNPYVTIASFDRKNLFYGV--KVINRGQSFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGT  257 (374)
Q Consensus       180 ~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~  257 (374)
                      ...+++.   +...+.+.+......  ..+.........++..+.+....+.++||||+++..++.+++.|.+.|+++..
T Consensus       377 ~~iY~l~---v~~IPt~kp~~r~d~~d~i~~~~~~K~~ai~~~i~~~~~~~~pvLIft~s~~~se~ls~~L~~~gi~~~~  453 (762)
T TIGR03714       377 IETYSLS---VVKIPTNKPIIRIDYPDKIYATLPEKLMATLEDVKEYHETGQPVLLITGSVEMSEIYSELLLREGIPHNL  453 (762)
T ss_pred             HHHhCCC---EEEcCCCCCeeeeeCCCeEEECHHHHHHHHHHHHHHHhhCCCCEEEEECcHHHHHHHHHHHHHCCCCEEE
Confidence            4444332   222222333222222  23344445566666666665567899999999999999999999999999999


Q ss_pred             eecCCChHHHHHHHHhhhcCCeeEEEEecccccccccc---------CccEEEEECCCCChhHHHHhhccCCCCCCceEE
Q 037567          258 YHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKP---------DVRHVIHYGCPKTLESYYQESGRCGRDGIASVC  328 (374)
Q Consensus       258 ~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~---------~~~~vi~~~~p~s~~~~~Q~~GR~~R~~~~g~~  328 (374)
                      +|+++...++..+...++.|  .|+|||+++++|+|+|         ++.+|+++++|....+ .||+||+||.|.+|.+
T Consensus       454 L~a~~~~~E~~ii~~ag~~g--~VlIATdmAgRGtDI~l~~~v~~~GGL~vIit~~~ps~rid-~qr~GRtGRqG~~G~s  530 (762)
T TIGR03714       454 LNAQNAAKEAQIIAEAGQKG--AVTVATSMAGRGTDIKLGKGVAELGGLAVIGTERMENSRVD-LQLRGRSGRQGDPGSS  530 (762)
T ss_pred             ecCCChHHHHHHHHHcCCCC--eEEEEccccccccCCCCCccccccCCeEEEEecCCCCcHHH-HHhhhcccCCCCceeE
Confidence            99999988888887777776  7999999999999999         8999999999988766 9999999999999999


Q ss_pred             EEEeeccC
Q 037567          329 WLYYARSN  336 (374)
Q Consensus       329 ~~~~~~~~  336 (374)
                      +.+++.+|
T Consensus       531 ~~~is~eD  538 (762)
T TIGR03714       531 QFFVSLED  538 (762)
T ss_pred             EEEEccch
Confidence            99998876

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.

>PRK09200 preprotein translocase subunit SecA; Reviewed

Probab=100.00  E-value=7.3e-35  Score=273.51  Aligned_cols=324  Identities=18%  Similarity=0.142  Sum_probs=230.2

Q ss_pred             hhHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc---cCCcEEEEcchHHHHHHHHHHHHH---
Q 037567            2 VSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV---TGKTALVVSPLISLMQDQVMSLKQ---   75 (374)
Q Consensus         2 ~~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~---~~~~~lil~P~~~l~~q~~~~~~~---   75 (374)
                      +++.++.+|+ .|++.|..+...+.+|+  +..+.||+|||+++++|++.   .+..++|++|++.||.|.++++..   
T Consensus        68 rea~~R~~g~-~p~~vQl~~~~~l~~G~--Iaem~TGeGKTL~a~lp~~l~al~G~~v~VvTpt~~LA~qd~e~~~~l~~  144 (790)
T PRK09200         68 REAAKRVLGM-RPYDVQLIGALVLHEGN--IAEMQTGEGKTLTATMPLYLNALEGKGVHLITVNDYLAKRDAEEMGQVYE  144 (790)
T ss_pred             HHHHHHHhCC-CCchHHHHhHHHHcCCc--eeeecCCCcchHHHHHHHHHHHHcCCCeEEEeCCHHHHHHHHHHHHHHHh
Confidence            4667788898 59999999999888776  99999999999999988763   588999999999999998888765   


Q ss_pred             -cCCceEEcCCCCCchhhhhhhhcCCeeEEEEcCccc-ccCchhh----HHHHHhcCccEEEEeccchhh-cc-------
Q 037567           76 -RGINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKA-CIIPISF----WSKLLKAGVCLFAVDEAHCIS-EW-------  141 (374)
Q Consensus        76 -~~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l-~~~~~~~----~~~~~~~~~~~vviDE~h~~~-~~-------  141 (374)
                       +|+.+.+..++........  ....++|+++||..+ .+++...    .......++.++|+||+|.+. +.       
T Consensus       145 ~lGl~v~~i~g~~~~~~~r~--~~y~~dIvygT~~~l~fDyLrd~~~~~~~~~~~r~~~~~IvDEaDsiLiDea~tplii  222 (790)
T PRK09200        145 FLGLTVGLNFSDIDDASEKK--AIYEADIIYTTNSELGFDYLRDNLADSKEDKVQRPLNYAIIDEIDSILLDEAQTPLII  222 (790)
T ss_pred             hcCCeEEEEeCCCCcHHHHH--HhcCCCEEEECCccccchhHHhccccchhhhcccccceEEEeccccceeccCCCceee
Confidence             4788887776655222222  234589999999988 2222221    123445778999999999985 10       


Q ss_pred             -cC--cchHHHHHHHHHHHhcC----------------------------------------------------------
Q 037567          142 -GH--DFRLEYKQLDKLRTFLL----------------------------------------------------------  160 (374)
Q Consensus       142 -~~--~~~~~~~~~~~~~~~~~----------------------------------------------------------  160 (374)
                       |.  .....+.....+...+.                                                          
T Consensus       223 sg~~~~~~~~y~~~~~~~~~l~~~~dy~~d~~~~~~~lt~~g~~~~e~~~~i~~l~~~~~~~~~~~i~~Al~A~~~~~~d  302 (790)
T PRK09200        223 SGKPRVQSNLYHIAAKFVKTLEEDVDYEFDEEKKEVWLTDQGIEKAESYFGIDNLYSLEHQVLYRHIILALRAHVLFKRD  302 (790)
T ss_pred             eCCCccccHHHHHHHHHHHhcccCCCeEEecCCCeEEecHhHHHHHHHhcCCccccChhhhHHHHHHHHHHHHHHHhhcC
Confidence             00  00000000000000000                                                          


Q ss_pred             ------------------------------------------------------------CCCeeEEEeecCcccHHHHH
Q 037567          161 ------------------------------------------------------------GVPFVALTATATEKVRIDII  180 (374)
Q Consensus       161 ------------------------------------------------------------~~~~i~~SaT~~~~~~~~~~  180 (374)
                                                                                  =.++.+||+|..... .++.
T Consensus       303 ~dYiV~~~~v~ivD~~TGr~~~gr~~s~GlhQaieaKe~v~i~~e~~t~a~It~q~~fr~Y~kl~GmTGTa~t~~-~e~~  381 (790)
T PRK09200        303 VDYIVYDGEIVLVDRFTGRVLPGRKLQDGLHQAIEAKEGVEITEENRTMASITIQNLFRMFPKLSGMTGTAKTEE-KEFF  381 (790)
T ss_pred             CcEEEECCEEEEEECCCCcCCCCCccChHHHHHHHHhcCCCcCCCceehhhhhHHHHHHHhHHHhccCCCChHHH-HHHH
Confidence                                                                        012667777764432 2444


Q ss_pred             HhcCCCCCeEEEeccCCCceeEEE--EeecCCcchHHHHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHHcCCceeee
Q 037567          181 NSLKLKNPYVTIASFDRKNLFYGV--KVINRGQSFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTY  258 (374)
Q Consensus       181 ~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~  258 (374)
                      ..+++.-   ...+.+.+......  ..+.........++..+.+....+.++||||+++..++.+++.|.+.|+++..+
T Consensus       382 ~~Y~l~v---~~IPt~kp~~r~d~~~~i~~~~~~K~~al~~~i~~~~~~~~pvLIf~~t~~~se~l~~~L~~~gi~~~~L  458 (790)
T PRK09200        382 EVYNMEV---VQIPTNRPIIRIDYPDKVFVTLDEKYKAVIEEVKERHETGRPVLIGTGSIEQSETFSKLLDEAGIPHNLL  458 (790)
T ss_pred             HHhCCcE---EECCCCCCcccccCCCeEEcCHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHCCCCEEEe
Confidence            4444322   22222233222221  223333444555556555544578999999999999999999999999999999


Q ss_pred             ecCCChHHHHHHHHhhhcCCeeEEEEeccccccccc---cCcc-----EEEEECCCCChhHHHHhhccCCCCCCceEEEE
Q 037567          259 HGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDK---PDVR-----HVIHYGCPKTLESYYQESGRCGRDGIASVCWL  330 (374)
Q Consensus       259 ~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~---~~~~-----~vi~~~~p~s~~~~~Q~~GR~~R~~~~g~~~~  330 (374)
                      ||++...++..+...+..|  .|+|||+++++|+|+   |++.     +||+++.|.|...|.||+||+||.|.+|.++.
T Consensus       459 ~~~~~~~e~~~i~~ag~~g--~VlIATdmAgRG~DI~l~~~V~~~GGL~VI~~d~p~s~r~y~qr~GRtGR~G~~G~s~~  536 (790)
T PRK09200        459 NAKNAAKEAQIIAEAGQKG--AVTVATNMAGRGTDIKLGEGVHELGGLAVIGTERMESRRVDLQLRGRSGRQGDPGSSQF  536 (790)
T ss_pred             cCCccHHHHHHHHHcCCCC--eEEEEccchhcCcCCCcccccccccCcEEEeccCCCCHHHHHHhhccccCCCCCeeEEE
Confidence            9999888888887777766  799999999999999   6898     99999999999999999999999999999999


Q ss_pred             EeeccC
Q 037567          331 YYARSN  336 (374)
Q Consensus       331 ~~~~~~  336 (374)
                      +++.+|
T Consensus       537 ~is~eD  542 (790)
T PRK09200        537 FISLED  542 (790)
T ss_pred             EEcchH
Confidence            998765

>PRK13766 Hef nuclease; Provisional

Probab=100.00  E-value=2.9e-34  Score=280.63  Aligned_cols=317  Identities=21%  Similarity=0.224  Sum_probs=215.4

Q ss_pred             CCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc----cCCcEEEEcchHHHHHHHHHHHHHc-CC---ceEE
Q 037567           11 YSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV----TGKTALVVSPLISLMQDQVMSLKQR-GI---NAEF   82 (374)
Q Consensus        11 ~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~----~~~~~lil~P~~~l~~q~~~~~~~~-~~---~~~~   82 (374)
                      .-++++||.+++..++.+ ++++++|||+|||+++++++..    .+.++||++|+++|++||.+.++.+ +.   .+..
T Consensus        13 ~~~~r~yQ~~~~~~~l~~-n~lv~~ptG~GKT~~a~~~i~~~l~~~~~~vLvl~Pt~~L~~Q~~~~~~~~~~~~~~~v~~   91 (773)
T PRK13766         13 TIEARLYQQLLAATALKK-NTLVVLPTGLGKTAIALLVIAERLHKKGGKVLILAPTKPLVEQHAEFFRKFLNIPEEKIVV   91 (773)
T ss_pred             cCCccHHHHHHHHHHhcC-CeEEEcCCCccHHHHHHHHHHHHHHhCCCeEEEEeCcHHHHHHHHHHHHHHhCCCCceEEE
Confidence            347999999999988777 8999999999999887665543    3689999999999999999999875 33   4444


Q ss_pred             cCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHH-HHHHHhcCC
Q 037567           83 LGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQL-DKLRTFLLG  161 (374)
Q Consensus        83 ~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~-~~~~~~~~~  161 (374)
                      +.+...... . .......+|+|+||+.+...+..  .......++++|+||||++......     ..+ .......+.
T Consensus        92 ~~g~~~~~~-r-~~~~~~~~iiv~T~~~l~~~l~~--~~~~~~~~~liVvDEaH~~~~~~~~-----~~i~~~~~~~~~~  162 (773)
T PRK13766         92 FTGEVSPEK-R-AELWEKAKVIVATPQVIENDLIA--GRISLEDVSLLIFDEAHRAVGNYAY-----VYIAERYHEDAKN  162 (773)
T ss_pred             EeCCCCHHH-H-HHHHhCCCEEEECHHHHHHHHHc--CCCChhhCcEEEEECCccccccccH-----HHHHHHHHhcCCC
Confidence            444433322 1 12223468999999877543221  2334567899999999998642211     112 222222334


Q ss_pred             CCeeEEEeecCcccH--HHHHHhcCCCCCeEE-----------------EeccCC------------------------C
Q 037567          162 VPFVALTATATEKVR--IDIINSLKLKNPYVT-----------------IASFDR------------------------K  198 (374)
Q Consensus       162 ~~~i~~SaT~~~~~~--~~~~~~~~~~~~~~~-----------------~~~~~~------------------------~  198 (374)
                      ..+++|||||.....  ..+...+++....+.                 ......                        .
T Consensus       163 ~~il~lTaTP~~~~~~i~~~~~~L~i~~v~~~~~~~~~v~~~~~~~~v~~~~v~l~~~~~~i~~~l~~~~~~~l~~l~~~  242 (773)
T PRK13766        163 PLVLGLTASPGSDEEKIKEVCENLGIEHVEVRTEDDPDVKPYVHKVKIEWVRVELPEELKEIRDLLNEALKDRLKKLKEL  242 (773)
T ss_pred             CEEEEEEcCCCCCHHHHHHHHHhCCceEEEEcCCCChhHHhhhccceeEEEEeCCcHHHHHHHHHHHHHHHHHHHHHHHC
Confidence            569999999854321  122222221110000                 000000                        0


Q ss_pred             ceeEEEE-------------------------------------------------------------------------
Q 037567          199 NLFYGVK-------------------------------------------------------------------------  205 (374)
Q Consensus       199 ~~~~~~~-------------------------------------------------------------------------  205 (374)
                      .......                                                                         
T Consensus       243 ~~~~~~~~~~~~~~l~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~~~~~y~~~l~~~~~~~~~~~~  322 (773)
T PRK13766        243 GVIVSISPDVSKKELLGLQKKLQQEIANDDSEGYEAISILAEAMKLRHAVELLETQGVEALRRYLERLREEARSSGGSKA  322 (773)
T ss_pred             CCcccCCCCcCHHHHHHHHHHHHHHhhcCchHHHHHHHHHHHHHHHHHHHHHHHHhCHHHHHHHHHHHHhhccccCCcHH
Confidence            0000000                                                                         


Q ss_pred             ------------------eecCCcchHHHHHHHHHHhh---cCCCcEEEEecchhHHHHHHHHHHHcCCceeeeecC---
Q 037567          206 ------------------VINRGQSFVDELVQEILKSV---AGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQ---  261 (374)
Q Consensus       206 ------------------~~~~~~~~~~~~~~~~~~~~---~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~---  261 (374)
                                        ..... ..+.+.+.++++..   .+++++||||++...++.+++.|...++.+..+||.   
T Consensus       323 ~~~l~~~~~~~~~~~~~~~~~~~-~pK~~~L~~il~~~~~~~~~~kvlIF~~~~~t~~~L~~~L~~~~~~~~~~~g~~~~  401 (773)
T PRK13766        323 SKRLVEDPRFRKAVRKAKELDIE-HPKLEKLREIVKEQLGKNPDSRIIVFTQYRDTAEKIVDLLEKEGIKAVRFVGQASK  401 (773)
T ss_pred             HHHHHhCHHHHHHHHHHHhcccC-ChHHHHHHHHHHHHHhcCCCCeEEEEeCcHHHHHHHHHHHHhCCCceEEEEccccc
Confidence                              00000 00111122222221   467899999999999999999999999999999886   


Q ss_pred             -----CChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEEEEECCCCChhHHHHhhccCCCCCCceEEEEEeeccC
Q 037567          262 -----MGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSN  336 (374)
Q Consensus       262 -----~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~~~~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~  336 (374)
                           ++..+|..++++|++|+.++||+|+++++|+|+|.+++||++++|++...++||+||+||.+. |.+++++..+.
T Consensus       402 ~~~~~~~~~~r~~~~~~F~~g~~~vLvaT~~~~eGldi~~~~~VI~yd~~~s~~r~iQR~GR~gR~~~-~~v~~l~~~~t  480 (773)
T PRK13766        402 DGDKGMSQKEQIEILDKFRAGEFNVLVSTSVAEEGLDIPSVDLVIFYEPVPSEIRSIQRKGRTGRQEE-GRVVVLIAKGT  480 (773)
T ss_pred             cccCCCCHHHHHHHHHHHHcCCCCEEEECChhhcCCCcccCCEEEEeCCCCCHHHHHHHhcccCcCCC-CEEEEEEeCCC
Confidence                 788899999999999999999999999999999999999999999999999999999999875 77777777765


Q ss_pred             CCc
Q 037567          337 FAK  339 (374)
Q Consensus       337 ~~~  339 (374)
                      .+.
T Consensus       481 ~ee  483 (773)
T PRK13766        481 RDE  483 (773)
T ss_pred             hHH
Confidence            543

>TIGR00963 secA preprotein translocase, SecA subunit

Probab=100.00  E-value=2.3e-34  Score=266.01  Aligned_cols=323  Identities=20%  Similarity=0.159  Sum_probs=234.0

Q ss_pred             hhHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc---cCCcEEEEcchHHHHHHHHHHHHHc--
Q 037567            2 VSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV---TGKTALVVSPLISLMQDQVMSLKQR--   76 (374)
Q Consensus         2 ~~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~---~~~~~lil~P~~~l~~q~~~~~~~~--   76 (374)
                      +++.++.+|+. |++.|..+...+.+|+  +..++||+|||+++.++++.   .+..+.|++|+..||.|.++++..+  
T Consensus        46 rEa~~R~lg~~-p~~vQlig~~~l~~G~--Iaem~TGeGKTLva~lpa~l~aL~G~~V~VvTpt~~LA~qdae~~~~l~~  122 (745)
T TIGR00963        46 REASKRVLGMR-PFDVQLIGGIALHKGK--IAEMKTGEGKTLTATLPAYLNALTGKGVHVVTVNDYLAQRDAEWMGQVYR  122 (745)
T ss_pred             HHHHHHHhCCC-ccchHHhhhhhhcCCc--eeeecCCCccHHHHHHHHHHHHHhCCCEEEEcCCHHHHHHHHHHHHHHhc
Confidence            46677888885 8999999888887776  99999999999999888742   4778999999999999999888764  


Q ss_pred             --CCceEEcCCCCCchhhhhhhhcCCeeEEEEcCccc-ccCchhh----HHHHHhcCccEEEEeccchhhc-c-------
Q 037567           77 --GINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKA-CIIPISF----WSKLLKAGVCLFAVDEAHCISE-W-------  141 (374)
Q Consensus        77 --~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l-~~~~~~~----~~~~~~~~~~~vviDE~h~~~~-~-------  141 (374)
                        |+.+.+..++......   .....++|+++||..+ .++++..    .......++.++|+||+|.+.- .       
T Consensus       123 ~LGLsv~~i~g~~~~~~r---~~~y~~dIvyGT~~rlgfDyLrd~~~~~~~~~~~r~l~~aIIDEaDs~LIDeaRtpLii  199 (745)
T TIGR00963       123 FLGLSVGLILSGMSPEER---REAYACDITYGTNNELGFDYLRDNMAHSKEEKVQRPFHFAIIDEVDSILIDEARTPLII  199 (745)
T ss_pred             cCCCeEEEEeCCCCHHHH---HHhcCCCEEEECCCchhhHHHhcccccchhhhhccccceeEeecHHHHhHHhhhhHHhh
Confidence              6777777665443322   2223479999999988 5554432    1245667899999999999852 0       


Q ss_pred             -cC--cchHHHH--------------------------------HHHH----------------------HHH--hc---
Q 037567          142 -GH--DFRLEYK--------------------------------QLDK----------------------LRT--FL---  159 (374)
Q Consensus       142 -~~--~~~~~~~--------------------------------~~~~----------------------~~~--~~---  159 (374)
                       |.  .....+.                                .+..                      +..  .+   
T Consensus       200 sg~~~~~~~ly~~a~~i~r~L~~~~dy~~de~~k~v~Lt~~G~~~~e~~~~~~~ly~~~~~~~~~~i~~Al~A~~l~~~d  279 (745)
T TIGR00963       200 SGPAEKSTELYLQANRFAKALEKEVHYEVDEKNRAVLLTEKGIKKAEDLLGVDNLYDLENSPLIHYINNALKAKELFEKD  279 (745)
T ss_pred             cCCCCCchHHHHHHHHHHHhhccCCCeEEecCCCceeECHHHHHHHHHHcCCccccChhhhHHHHHHHHHHHHHHHHhcC
Confidence             10  0000000                                0000                      000  00   


Q ss_pred             -----------------------------------------------------------CCCCeeEEEeecCcccHHHHH
Q 037567          160 -----------------------------------------------------------LGVPFVALTATATEKVRIDII  180 (374)
Q Consensus       160 -----------------------------------------------------------~~~~~i~~SaT~~~~~~~~~~  180 (374)
                                                                                 .-.++.+||+|..... ..+.
T Consensus       280 ~dYiV~d~~V~ivD~~TGR~~~gr~ws~GLhQaiEaKE~v~i~~e~~t~a~It~qn~Fr~Y~kl~GmTGTa~te~-~E~~  358 (745)
T TIGR00963       280 VDYIVRDGEVVIVDEFTGRIMEGRRWSDGLHQAIEAKEGVEIQNENQTLATITYQNFFRLYEKLSGMTGTAKTEE-EEFE  358 (745)
T ss_pred             CcEEEECCEEEEEECCCCcCCCCCccchHHHHHHHHhcCCCcCCCceeeeeeeHHHHHhhCchhhccCCCcHHHH-HHHH
Confidence                                                                       0012566666664332 2344


Q ss_pred             HhcCCCCCeEEEeccCCCce--eEEEEeecCCcchHHHHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHHcCCceeee
Q 037567          181 NSLKLKNPYVTIASFDRKNL--FYGVKVINRGQSFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTY  258 (374)
Q Consensus       181 ~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~  258 (374)
                      ..+++.   +...+.+.+..  .....++.........++.++.+....+.++||||+++..++.+++.|.+.|++...+
T Consensus       359 ~iY~l~---vv~IPtnkp~~R~d~~d~i~~t~~~k~~ai~~~i~~~~~~grpvLV~t~si~~se~ls~~L~~~gi~~~~L  435 (745)
T TIGR00963       359 KIYNLE---VVVVPTNRPVIRKDLSDLVYKTEEEKWKAVVDEIKERHAKGQPVLVGTTSVEKSELLSNLLKERGIPHNVL  435 (745)
T ss_pred             HHhCCC---EEEeCCCCCeeeeeCCCeEEcCHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHcCCCeEEe
Confidence            444433   22222222222  2222233444455667778887777789999999999999999999999999999999


Q ss_pred             ecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccC-------ccEEEEECCCCChhHHHHhhccCCCCCCceEEEEE
Q 037567          259 HGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPD-------VRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLY  331 (374)
Q Consensus       259 ~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~-------~~~vi~~~~p~s~~~~~Q~~GR~~R~~~~g~~~~~  331 (374)
                      |++  ..+|+..+..|..+...|+|||+++++|+|++.       ..+||+++.|.|...+.|++||+||.|.+|.+..+
T Consensus       436 na~--q~~rEa~ii~~ag~~g~VtIATnmAgRGtDI~l~~V~~~GGl~VI~t~~p~s~ri~~q~~GRtGRqG~~G~s~~~  513 (745)
T TIGR00963       436 NAK--NHEREAEIIAQAGRKGAVTIATNMAGRGTDIKLEEVKELGGLYVIGTERHESRRIDNQLRGRSGRQGDPGSSRFF  513 (745)
T ss_pred             eCC--hHHHHHHHHHhcCCCceEEEEeccccCCcCCCccchhhcCCcEEEecCCCCcHHHHHHHhccccCCCCCcceEEE
Confidence            998  778899999999999999999999999999998       45999999999999999999999999999999999


Q ss_pred             eeccC
Q 037567          332 YARSN  336 (374)
Q Consensus       332 ~~~~~  336 (374)
                      ++.+|
T Consensus       514 ls~eD  518 (745)
T TIGR00963       514 LSLED  518 (745)
T ss_pred             EeccH
Confidence            98876

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.

>PRK04914 ATP-dependent helicase HepA; Validated

Probab=100.00  E-value=1.4e-32  Score=264.34  Aligned_cols=318  Identities=17%  Similarity=0.159  Sum_probs=213.4

Q ss_pred             CCchhHHHHHHHHHcC--CCEEEEccCCCCchhhhhccccc-----cCCcEEEEcchHHHHHHHHHHHH-HcCCceEEcC
Q 037567           13 VFRPYQKDVIQRIIEK--RDCLVVMATGSGKSLCYQLPPLV-----TGKTALVVSPLISLMQDQVMSLK-QRGINAEFLG   84 (374)
Q Consensus        13 ~~~~~Q~~~~~~~~~~--~~~l~~a~tGsGKT~~~~l~~~~-----~~~~~lil~P~~~l~~q~~~~~~-~~~~~~~~~~   84 (374)
                      .|.|||..+...+.+.  ..+++...+|.|||+.+.+.+..     ...++||+||. .|..||..++. ++++...++.
T Consensus       152 ~l~pHQl~~~~~vl~~~~~R~LLADEvGLGKTIeAglil~~l~~~g~~~rvLIVvP~-sL~~QW~~El~~kF~l~~~i~~  230 (956)
T PRK04914        152 SLIPHQLYIAHEVGRRHAPRVLLADEVGLGKTIEAGMIIHQQLLTGRAERVLILVPE-TLQHQWLVEMLRRFNLRFSLFD  230 (956)
T ss_pred             CCCHHHHHHHHHHhhccCCCEEEEeCCcCcHHHHHHHHHHHHHHcCCCCcEEEEcCH-HHHHHHHHHHHHHhCCCeEEEc
Confidence            5999999999887653  47899999999999776544322     34689999998 89999999985 5777766654


Q ss_pred             CCCCchhh-hhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHHhcCCCC
Q 037567           85 SAQTDSSV-QTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVP  163 (374)
Q Consensus        85 ~~~~~~~~-~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~~~~~  163 (374)
                      ........ .........+++|++++.+..... ....+....++++|+||||++..........+..+..+...  ...
T Consensus       231 ~~~~~~~~~~~~~pf~~~~~vI~S~~~l~~~~~-~~~~l~~~~wdlvIvDEAH~lk~~~~~~s~~y~~v~~La~~--~~~  307 (956)
T PRK04914        231 EERYAEAQHDADNPFETEQLVICSLDFLRRNKQ-RLEQALAAEWDLLVVDEAHHLVWSEEAPSREYQVVEQLAEV--IPG  307 (956)
T ss_pred             CcchhhhcccccCccccCcEEEEEHHHhhhCHH-HHHHHhhcCCCEEEEechhhhccCCCCcCHHHHHHHHHhhc--cCC
Confidence            43211100 000111245799999988754321 22344456899999999999974221222223444444332  347


Q ss_pred             eeEEEeecCcccHHHHHHhcCCCCCeEEE---------------------------------------------------
Q 037567          164 FVALTATATEKVRIDIINSLKLKNPYVTI---------------------------------------------------  192 (374)
Q Consensus       164 ~i~~SaT~~~~~~~~~~~~~~~~~~~~~~---------------------------------------------------  192 (374)
                      ++++||||......++...+.+-+|....                                                   
T Consensus       308 ~LLLTATP~q~~~~e~falL~lLdP~~f~~~~~F~~e~~~~~~~a~~v~~l~~~~~~~~~~~~~l~~ll~~~~~~~l~~~  387 (956)
T PRK04914        308 VLLLTATPEQLGQESHFARLRLLDPDRFHDYEAFVEEQQQYRPVADAVQALLAGEKLSDDALNALGELLGEQDIEPLLQA  387 (956)
T ss_pred             EEEEEcCcccCCcHHHHHhhhhhCCCcCCCHHHHHHHHHhhHHHHHHHHHHhcCCcCCHHHHHHHHHHhcccchhHHHhh
Confidence            89999998764333222221111110000                                                   


Q ss_pred             -----------------------------eccC------C-CceeEEEEeecCC--------------------------
Q 037567          193 -----------------------------ASFD------R-KNLFYGVKVINRG--------------------------  210 (374)
Q Consensus       193 -----------------------------~~~~------~-~~~~~~~~~~~~~--------------------------  210 (374)
                                                   ....      . ......+. ....                          
T Consensus       388 ~~~~~~~~~~~~~~~i~~L~d~hg~~rvm~RntR~~v~~fp~R~~~~~~-l~~~~~y~~~~~~~~~~~~~~~l~pe~~~~  466 (956)
T PRK04914        388 ANSDSEEAQAARQELISELLDRHGTGRVLFRNTRAAVKGFPKRELHPIP-LPLPEQYQTAIKVSLEARARDMLYPEQIYQ  466 (956)
T ss_pred             hcccccccHHHHHHHHHHHHhhcCcceEEEeccHHhhcCCCcCceeEee-cCCCHHHHHHHHHhHHHHHHhhcCHHHHHH
Confidence                                         0000      0 00000000 0000                          


Q ss_pred             ----------cchHHHHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHH-HcCCceeeeecCCChHHHHHHHHhhhcC--
Q 037567          211 ----------QSFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALK-QLGVKAGTYHGQMGSKAREEAHRLFIRD--  277 (374)
Q Consensus       211 ----------~~~~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~-~~~~~~~~~~~~~~~~~r~~~~~~f~~g--  277 (374)
                                .....+.+.++++.. .+.|+||||+++..+..+.+.|+ ..|+++..+||+++..+|.+.++.|+++  
T Consensus       467 ~~~~~~~~~~~d~Ki~~L~~~L~~~-~~~KvLVF~~~~~t~~~L~~~L~~~~Gi~~~~ihG~~s~~eR~~~~~~F~~~~~  545 (956)
T PRK04914        467 EFEDNATWWNFDPRVEWLIDFLKSH-RSEKVLVICAKAATALQLEQALREREGIRAAVFHEGMSIIERDRAAAYFADEED  545 (956)
T ss_pred             HHhhhhhccccCHHHHHHHHHHHhc-CCCeEEEEeCcHHHHHHHHHHHhhccCeeEEEEECCCCHHHHHHHHHHHhcCCC
Confidence                      001112233333332 36799999999999999999995 5699999999999999999999999984  


Q ss_pred             CeeEEEEeccccccccccCccEEEEECCCCChhHHHHhhccCCCCCCceEEEEEeeccC
Q 037567          278 EIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSN  336 (374)
Q Consensus       278 ~~~ilv~t~~~~~G~d~~~~~~vi~~~~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~  336 (374)
                      ...|||||.++++|+|++.+++||++++|+++..|.||+||++|.|+.+.+.+++....
T Consensus       546 ~~~VLIsTdvgseGlNlq~a~~VInfDlP~nP~~~eQRIGR~~RiGQ~~~V~i~~~~~~  604 (956)
T PRK04914        546 GAQVLLCSEIGSEGRNFQFASHLVLFDLPFNPDLLEQRIGRLDRIGQKHDIQIHVPYLE  604 (956)
T ss_pred             CccEEEechhhccCCCcccccEEEEecCCCCHHHHHHHhcccccCCCCceEEEEEccCC
Confidence            58999999999999999999999999999999999999999999999988766665443

>PRK05580 primosome assembly protein PriA; Validated

Probab=100.00  E-value=1.3e-32  Score=261.16  Aligned_cols=322  Identities=20%  Similarity=0.228  Sum_probs=224.7

Q ss_pred             CCchhHHHHHHHHHcC---CCEEEEccCCCCchhhhhccc---cccCCcEEEEcchHHHHHHHHHHHHH-cCCceEEcCC
Q 037567           13 VFRPYQKDVIQRIIEK---RDCLVVMATGSGKSLCYQLPP---LVTGKTALVVSPLISLMQDQVMSLKQ-RGINAEFLGS   85 (374)
Q Consensus        13 ~~~~~Q~~~~~~~~~~---~~~l~~a~tGsGKT~~~~l~~---~~~~~~~lil~P~~~l~~q~~~~~~~-~~~~~~~~~~   85 (374)
                      .+++.|.++++.+.++   +++++.|+||||||.+|+.++   +..+.++||++|+++|+.|+.+.+++ ++..+..+++
T Consensus       144 ~Lt~~Q~~ai~~i~~~~~~~~~Ll~~~TGSGKT~v~l~~i~~~l~~g~~vLvLvPt~~L~~Q~~~~l~~~fg~~v~~~~s  223 (679)
T PRK05580        144 TLNPEQAAAVEAIRAAAGFSPFLLDGVTGSGKTEVYLQAIAEVLAQGKQALVLVPEIALTPQMLARFRARFGAPVAVLHS  223 (679)
T ss_pred             CCCHHHHHHHHHHHhccCCCcEEEECCCCChHHHHHHHHHHHHHHcCCeEEEEeCcHHHHHHHHHHHHHHhCCCEEEEEC
Confidence            5899999999999874   789999999999999887654   34578999999999999999999986 5777777777


Q ss_pred             CCCchhh---hhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCc-chHHHHHHHHHHHhcCC
Q 037567           86 AQTDSSV---QTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHD-FRLEYKQLDKLRTFLLG  161 (374)
Q Consensus        86 ~~~~~~~---~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~-~~~~~~~~~~~~~~~~~  161 (374)
                      +.+..+.   +.....+.++|+|+|+..+.         ..+.++++||+||+|....++.. .......+...+....+
T Consensus       224 ~~s~~~r~~~~~~~~~g~~~IVVgTrsal~---------~p~~~l~liVvDEeh~~s~~~~~~p~y~~r~va~~ra~~~~  294 (679)
T PRK05580        224 GLSDGERLDEWRKAKRGEAKVVIGARSALF---------LPFKNLGLIIVDEEHDSSYKQQEGPRYHARDLAVVRAKLEN  294 (679)
T ss_pred             CCCHHHHHHHHHHHHcCCCCEEEeccHHhc---------ccccCCCEEEEECCCccccccCcCCCCcHHHHHHHHhhccC
Confidence            6555432   33344567899999987542         23578899999999987543321 11112344445555668


Q ss_pred             CCeeEEEeecCcccHHHHHHhcCCCCCeEEEe-ccCCCceeEEEEeecC--------CcchHHHHHHHHHHhhcCCCcEE
Q 037567          162 VPFVALTATATEKVRIDIINSLKLKNPYVTIA-SFDRKNLFYGVKVINR--------GQSFVDELVQEILKSVAGAGSII  232 (374)
Q Consensus       162 ~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~--------~~~~~~~~~~~~~~~~~~~~~~l  232 (374)
                      .+++++||||+.........  + ........ ...... ...+.....        .......++..+.+.+..++++|
T Consensus       295 ~~~il~SATps~~s~~~~~~--g-~~~~~~l~~r~~~~~-~p~v~~id~~~~~~~~~~~~ls~~l~~~i~~~l~~g~qvl  370 (679)
T PRK05580        295 IPVVLGSATPSLESLANAQQ--G-RYRLLRLTKRAGGAR-LPEVEIIDMRELLRGENGSFLSPPLLEAIKQRLERGEQVL  370 (679)
T ss_pred             CCEEEEcCCCCHHHHHHHhc--c-ceeEEEeccccccCC-CCeEEEEechhhhhhcccCCCCHHHHHHHHHHHHcCCeEE
Confidence            99999999998765432211  1 11111111 100000 001111110        01123556666777777788999


Q ss_pred             EEecchh------------------------------------------------------------HHHHHHHHHHHc-
Q 037567          233 VYCMTIK------------------------------------------------------------DVEEISKALKQL-  251 (374)
Q Consensus       233 Vf~~~~~------------------------------------------------------------~~~~l~~~l~~~-  251 (374)
                      ||+|++.                                                            ..+++++.|++. 
T Consensus       371 l~~nrrGy~~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~l~~~g~G~e~~~e~l~~~f  450 (679)
T PRK05580        371 LFLNRRGYAPFLLCRDCGWVAECPHCDASLTLHRFQRRLRCHHCGYQEPIPKACPECGSTDLVPVGPGTERLEEELAELF  450 (679)
T ss_pred             EEEcCCCCCCceEhhhCcCccCCCCCCCceeEECCCCeEECCCCcCCCCCCCCCCCCcCCeeEEeeccHHHHHHHHHHhC
Confidence            9987532                                                            456777778775 


Q ss_pred             -CCceeeeecCCC--hHHHHHHHHhhhcCCeeEEEEeccccccccccCccEEEEECCC--CC----------hhHHHHhh
Q 037567          252 -GVKAGTYHGQMG--SKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCP--KT----------LESYYQES  316 (374)
Q Consensus       252 -~~~~~~~~~~~~--~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~~~~p--~s----------~~~~~Q~~  316 (374)
                       +.++..+|+++.  ..+++.++++|.+|+.+|||+|++++.|+|+|+++.|+.++..  .+          ...+.|++
T Consensus       451 p~~~v~~~~~d~~~~~~~~~~~l~~f~~g~~~ILVgT~~iakG~d~p~v~lV~il~aD~~l~~pdfra~Er~~~~l~q~~  530 (679)
T PRK05580        451 PEARILRIDRDTTRRKGALEQLLAQFARGEADILIGTQMLAKGHDFPNVTLVGVLDADLGLFSPDFRASERTFQLLTQVA  530 (679)
T ss_pred             CCCcEEEEeccccccchhHHHHHHHHhcCCCCEEEEChhhccCCCCCCcCEEEEEcCchhccCCccchHHHHHHHHHHHH
Confidence             678899999985  4678999999999999999999999999999999998765543  22          35689999


Q ss_pred             ccCCCCCCceEEEEEeeccCCCcccceeccc
Q 037567          317 GRCGRDGIASVCWLYYARSNFAKGDFYCGES  347 (374)
Q Consensus       317 GR~~R~~~~g~~~~~~~~~~~~~~~~~~~~~  347 (374)
                      ||+||.+.+|.+++.....+-..++.+...+
T Consensus       531 GRagR~~~~g~viiqT~~p~~~~~~~~~~~d  561 (679)
T PRK05580        531 GRAGRAEKPGEVLIQTYHPEHPVIQALLAQD  561 (679)
T ss_pred             hhccCCCCCCEEEEEeCCCCCHHHHHHHhCC
Confidence            9999999999999776555544444444333

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

Probab=100.00  E-value=5.4e-32  Score=243.66  Aligned_cols=312  Identities=22%  Similarity=0.290  Sum_probs=236.3

Q ss_pred             hhHHHhHcCCCCCchhHHHHHHHHHcC------CCEEEEccCCCCchhhhhcccc---ccCCcEEEEcchHHHHHHHHHH
Q 037567            2 VSTLKKYFGYSVFRPYQKDVIQRIIEK------RDCLVVMATGSGKSLCYQLPPL---VTGKTALVVSPLISLMQDQVMS   72 (374)
Q Consensus         2 ~~~l~~~~~~~~~~~~Q~~~~~~~~~~------~~~l~~a~tGsGKT~~~~l~~~---~~~~~~lil~P~~~l~~q~~~~   72 (374)
                      .+.|...++|. ||..|.+++..+...      -+-++.|+.|||||+.++++++   ..+.++.+++||.-||+|.+..
T Consensus       252 ~~~~~~~LPF~-LT~aQ~~vi~EI~~Dl~~~~~M~RLlQGDVGSGKTvVA~laml~ai~~G~Q~ALMAPTEILA~QH~~~  330 (677)
T COG1200         252 LAKFLAALPFK-LTNAQKRVIKEILADLASPVPMNRLLQGDVGSGKTVVALLAMLAAIEAGYQAALMAPTEILAEQHYES  330 (677)
T ss_pred             HHHHHHhCCCC-ccHHHHHHHHHHHhhhcCchhhHHHhccCcCCCHHHHHHHHHHHHHHcCCeeEEeccHHHHHHHHHHH
Confidence            45666678995 999999999998863      2449999999999988777655   4799999999999999999988


Q ss_pred             HHH----cCCceEEcCCCCCchh---hhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcc
Q 037567           73 LKQ----RGINAEFLGSAQTDSS---VQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDF  145 (374)
Q Consensus        73 ~~~----~~~~~~~~~~~~~~~~---~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~  145 (374)
                      +.+    +|+.+..+++......   .......+..+++|+|..-+.       +...+.++.++|+||=|++.-.+   
T Consensus       331 ~~~~l~~~~i~V~lLtG~~kgk~r~~~l~~l~~G~~~ivVGTHALiQ-------d~V~F~~LgLVIiDEQHRFGV~Q---  400 (677)
T COG1200         331 LRKWLEPLGIRVALLTGSLKGKARKEILEQLASGEIDIVVGTHALIQ-------DKVEFHNLGLVIIDEQHRFGVHQ---  400 (677)
T ss_pred             HHHHhhhcCCeEEEeecccchhHHHHHHHHHhCCCCCEEEEcchhhh-------cceeecceeEEEEeccccccHHH---
Confidence            775    4788888887665544   344556788999999987553       44556788999999999875422   


Q ss_pred             hHHHHHHHHHHHhcC-CCCeeEEEeecCcccHHHHHHhcCCCCCe-EEEeccCCCceeEEEEeecCCcchHHHHHHHHHH
Q 037567          146 RLEYKQLDKLRTFLL-GVPFVALTATATEKVRIDIINSLKLKNPY-VTIASFDRKNLFYGVKVINRGQSFVDELVQEILK  223 (374)
Q Consensus       146 ~~~~~~~~~~~~~~~-~~~~i~~SaT~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  223 (374)
                            -..+.+.-. ...++.|||||-|...-  +..++--+.. +..-...+..+.-...    ......+++..+.+
T Consensus       401 ------R~~L~~KG~~~Ph~LvMTATPIPRTLA--lt~fgDldvS~IdElP~GRkpI~T~~i----~~~~~~~v~e~i~~  468 (677)
T COG1200         401 ------RLALREKGEQNPHVLVMTATPIPRTLA--LTAFGDLDVSIIDELPPGRKPITTVVI----PHERRPEVYERIRE  468 (677)
T ss_pred             ------HHHHHHhCCCCCcEEEEeCCCchHHHH--HHHhccccchhhccCCCCCCceEEEEe----ccccHHHHHHHHHH
Confidence                  122333333 45799999999986543  4444433332 2222333333322222    22445666777777


Q ss_pred             hhcCCCcEEEEecchhH--------HHHHHHHHHHc--CCceeeeecCCChHHHHHHHHhhhcCCeeEEEEecccccccc
Q 037567          224 SVAGAGSIIVYCMTIKD--------VEEISKALKQL--GVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGID  293 (374)
Q Consensus       224 ~~~~~~~~lVf~~~~~~--------~~~l~~~l~~~--~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d  293 (374)
                      .+..+.++.|.||-.++        ++.+++.|+..  +..++.+||.|+.++++++++.|++|+++|||+|..++.|+|
T Consensus       469 ei~~GrQaY~VcPLIeESE~l~l~~a~~~~~~L~~~~~~~~vgL~HGrm~~~eKd~vM~~Fk~~e~~ILVaTTVIEVGVd  548 (677)
T COG1200         469 EIAKGRQAYVVCPLIEESEKLELQAAEELYEELKSFLPELKVGLVHGRMKPAEKDAVMEAFKEGEIDILVATTVIEVGVD  548 (677)
T ss_pred             HHHcCCEEEEEeccccccccchhhhHHHHHHHHHHHcccceeEEEecCCChHHHHHHHHHHHcCCCcEEEEeeEEEeccc
Confidence            77889999999997664        44555666643  566999999999999999999999999999999999999999


Q ss_pred             ccCccEEEEECCC-CChhHHHHhhccCCCCCCceEEEEEeeccC
Q 037567          294 KPDVRHVIHYGCP-KTLESYYQESGRCGRDGIASVCWLYYARSN  336 (374)
Q Consensus       294 ~~~~~~vi~~~~p-~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~  336 (374)
                      +|+.+++++.++- .-..+.-|..||+||.+..+.|++++.+..
T Consensus       549 VPnATvMVIe~AERFGLaQLHQLRGRVGRG~~qSyC~Ll~~~~~  592 (677)
T COG1200         549 VPNATVMVIENAERFGLAQLHQLRGRVGRGDLQSYCVLLYKPPL  592 (677)
T ss_pred             CCCCeEEEEechhhhhHHHHHHhccccCCCCcceEEEEEeCCCC
Confidence            9999998877754 467899999999999999999999988754

>KOG0354 consensus DEAD-box like helicase [General function prediction only]

Probab=100.00  E-value=9.3e-33  Score=252.16  Aligned_cols=316  Identities=22%  Similarity=0.245  Sum_probs=207.0

Q ss_pred             CCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc-----cCCcEEEEcchHHHHHHHHHHHHHcCCceEEcC
Q 037567           10 GYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV-----TGKTALVVSPLISLMQDQVMSLKQRGINAEFLG   84 (374)
Q Consensus        10 ~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~-----~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~   84 (374)
                      +.-++|.||.+..+..+ +++.++++|||+|||++++..+..     +..++++++|++-|+.|....+..++......+
T Consensus        59 ~~~~lR~YQ~eivq~AL-gkNtii~lPTG~GKTfIAa~Vm~nh~rw~p~~KiVF~aP~~pLv~QQ~a~~~~~~~~~~~T~  137 (746)
T KOG0354|consen   59 TNLELRNYQEELVQPAL-GKNTIIALPTGSGKTFIAAVIMKNHFEWRPKGKVVFLAPTRPLVNQQIACFSIYLIPYSVTG  137 (746)
T ss_pred             CcccccHHHHHHhHHhh-cCCeEEEeecCCCccchHHHHHHHHHhcCCcceEEEeeCCchHHHHHHHHHhhccCccccee
Confidence            34479999999999999 999999999999999988776653     478999999999999999988888776533211


Q ss_pred             CC-CCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHHhcC-CC
Q 037567           85 SA-QTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLL-GV  162 (374)
Q Consensus        85 ~~-~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~~-~~  162 (374)
                      .. ...............+|+|+||+.+.+.+.+....- ++.+.++||||||+-..... +.   .-+.......- ..
T Consensus       138 ~l~~~~~~~~r~~i~~s~~vff~TpQil~ndL~~~~~~~-ls~fs~iv~DE~Hra~kn~~-Y~---~Vmr~~l~~k~~~~  212 (746)
T KOG0354|consen  138 QLGDTVPRSNRGEIVASKRVFFRTPQILENDLKSGLHDE-LSDFSLIVFDECHRTSKNHP-YN---NIMREYLDLKNQGN  212 (746)
T ss_pred             eccCccCCCchhhhhcccceEEeChHhhhhhcccccccc-cceEEEEEEccccccccccc-HH---HHHHHHHHhhhccc
Confidence            11 111111122344567999999998877665532222 57799999999998654221 11   22222222222 34


Q ss_pred             CeeEEEeecCcccHHHHHH---hcC------------------------------------------------------C
Q 037567          163 PFVALTATATEKVRIDIIN---SLK------------------------------------------------------L  185 (374)
Q Consensus       163 ~~i~~SaT~~~~~~~~~~~---~~~------------------------------------------------------~  185 (374)
                      +++++||||...... +..   .+.                                                      +
T Consensus       213 qILgLTASpG~~~~~-v~~~I~~L~asldvr~~ssi~~~y~~lr~~~~i~v~~~~~~~~~~~~f~~~i~p~l~~l~~~~l  291 (746)
T KOG0354|consen  213 QILGLTASPGSKLEQ-VQNVIDNLCASLDVRTESSIKSNYEELREHVQIPVDLSLCERDIEDPFGMIIEPLLQQLQEEGL  291 (746)
T ss_pred             cEEEEecCCCccHHH-HHHHHHhhheecccchhhhhhhhHHHHhccCcccCcHHHhhhhhhhhHHHHHHHHHHHHHhcCc
Confidence            999999996643211 100   000                                                      0


Q ss_pred             CC---Ce-------EEEeccCCCceeEEE----------------------E----------------------------
Q 037567          186 KN---PY-------VTIASFDRKNLFYGV----------------------K----------------------------  205 (374)
Q Consensus       186 ~~---~~-------~~~~~~~~~~~~~~~----------------------~----------------------------  205 (374)
                      ..   ..       ........++.....                      .                            
T Consensus       292 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~~f~~~~~~~~~~~ll~~~gir~~~~l~~~~~f~~e~~~~k~~~~~~e~~  371 (746)
T KOG0354|consen  292 IEISDKSTSYEQWVVQAEKAAAPNGPENQRNCFYALHLRKYNLALLISDGIRFVDALDYLEDFYEEVALKKYLKLELEAR  371 (746)
T ss_pred             cccccccccccchhhhhhhhhccCCCccchhhHHHHHHHHHHHHHHhhcchhhHHHHhhhhhhccccchhHHHHHHhcch
Confidence            00   00       000000000000000                      0                            


Q ss_pred             -------------eec----CCcchHHHHHHHHHHh--hcCCCcEEEEecchhHHHHHHHHHHH---cCCceeeee----
Q 037567          206 -------------VIN----RGQSFVDELVQEILKS--VAGAGSIIVYCMTIKDVEEISKALKQ---LGVKAGTYH----  259 (374)
Q Consensus       206 -------------~~~----~~~~~~~~~~~~~~~~--~~~~~~~lVf~~~~~~~~~l~~~l~~---~~~~~~~~~----  259 (374)
                                   ...    ...+.+..+...+.+.  ..+..++|||+.+++.+..+.+.|..   .++....+.    
T Consensus       372 ~~~~~~~~m~~~~~l~~~~~~~npkle~l~~~l~e~f~~~~dsR~IIFve~R~sa~~l~~~l~~~~~~~ir~~~fiGq~~  451 (746)
T KOG0354|consen  372 LIRNFTENMNELEHLSLDPPKENPKLEKLVEILVEQFEQNPDSRTIIFVETRESALALKKWLLQLHELGIKAEIFIGQGK  451 (746)
T ss_pred             hhHHHHHHHHhhhhhhcCCCccChhHHHHHHHHHHHhhcCCCccEEEEEehHHHHHHHHHHHHhhhhcccccceeeeccc
Confidence                         000    0012222222222222  24567899999999999999999873   233433333    


Q ss_pred             ----cCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEEEEECCCCChhHHHHhhccCCCCCCceEEEEEeec
Q 037567          260 ----GQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYAR  334 (374)
Q Consensus       260 ----~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~~~~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~  334 (374)
                          .+|+..+..+++..|++|++.|||||+++++|+|++.++.||-|+...|+..++||.|| ||.. +|.+++++..
T Consensus       452 s~~~~gmtqk~Q~evl~~Fr~G~~NvLVATSV~EEGLDI~ec~lVIcYd~~snpIrmIQrrGR-gRa~-ns~~vll~t~  528 (746)
T KOG0354|consen  452 STQSTGMTQKEQKEVLDKFRDGEINVLVATSVAEEGLDIGECNLVICYDYSSNPIRMVQRRGR-GRAR-NSKCVLLTTG  528 (746)
T ss_pred             cccccccCHHHHHHHHHHHhCCCccEEEEecchhccCCcccccEEEEecCCccHHHHHHHhcc-cccc-CCeEEEEEcc
Confidence                36889999999999999999999999999999999999999999999999999999999 9975 5666666663

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

Probab=100.00  E-value=3.1e-31  Score=251.71  Aligned_cols=310  Identities=21%  Similarity=0.298  Sum_probs=237.6

Q ss_pred             hhHHHhHcCCCCCchhHHHHHHHHHc----CC--CEEEEccCCCCchhhhhcc---ccccCCcEEEEcchHHHHHHHHHH
Q 037567            2 VSTLKKYFGYSVFRPYQKDVIQRIIE----KR--DCLVVMATGSGKSLCYQLP---PLVTGKTALVVSPLISLMQDQVMS   72 (374)
Q Consensus         2 ~~~l~~~~~~~~~~~~Q~~~~~~~~~----~~--~~l~~a~tGsGKT~~~~l~---~~~~~~~~lil~P~~~l~~q~~~~   72 (374)
                      ..+|...|+|. -||-|..|+..+.+    ++  |-++||+.|.|||-.++-+   +...+++|.++|||.-|++|.++.
T Consensus       584 q~~F~~~FPye-ET~DQl~AI~eVk~DM~~~kpMDRLiCGDVGFGKTEVAmRAAFkAV~~GKQVAvLVPTTlLA~QHy~t  662 (1139)
T COG1197         584 QEEFEASFPYE-ETPDQLKAIEEVKRDMESGKPMDRLICGDVGFGKTEVAMRAAFKAVMDGKQVAVLVPTTLLAQQHYET  662 (1139)
T ss_pred             HHHHHhcCCCc-CCHHHHHHHHHHHHHhccCCcchheeecCcCCcHHHHHHHHHHHHhcCCCeEEEEcccHHhHHHHHHH
Confidence            45788889996 89999999999875    33  6699999999999776544   446799999999999999999999


Q ss_pred             HHH----cCCceEEcCC---CCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcc
Q 037567           73 LKQ----RGINAEFLGS---AQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDF  145 (374)
Q Consensus        73 ~~~----~~~~~~~~~~---~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~  145 (374)
                      |+.    +++++..+..   .............+..||+|+|..-|.       +.+.+.++.++||||=|++.-     
T Consensus       663 FkeRF~~fPV~I~~LSRF~s~kE~~~il~~la~G~vDIvIGTHrLL~-------kdv~FkdLGLlIIDEEqRFGV-----  730 (1139)
T COG1197         663 FKERFAGFPVRIEVLSRFRSAKEQKEILKGLAEGKVDIVIGTHRLLS-------KDVKFKDLGLLIIDEEQRFGV-----  730 (1139)
T ss_pred             HHHHhcCCCeeEEEecccCCHHHHHHHHHHHhcCCccEEEechHhhC-------CCcEEecCCeEEEechhhcCc-----
Confidence            874    3455554433   222333455667899999999986553       344567889999999999754     


Q ss_pred             hHHHHHHHHHHHhcCCCCeeEEEeecCcccHHHHHHhcCCCCCeEEEecc-CCCceeEEEEeecCCcchHHHHHHHHHHh
Q 037567          146 RLEYKQLDKLRTFLLGVPFVALTATATEKVRIDIINSLKLKNPYVTIASF-DRKNLFYGVKVINRGQSFVDELVQEILKS  224 (374)
Q Consensus       146 ~~~~~~~~~~~~~~~~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  224 (374)
                          ..-.+++....+.-++-|||||-|....  ....|+.+-.+....+ ++..+.-.+.  +.+...+   -..+++.
T Consensus       731 ----k~KEkLK~Lr~~VDvLTLSATPIPRTL~--Msm~GiRdlSvI~TPP~~R~pV~T~V~--~~d~~~i---reAI~RE  799 (1139)
T COG1197         731 ----KHKEKLKELRANVDVLTLSATPIPRTLN--MSLSGIRDLSVIATPPEDRLPVKTFVS--EYDDLLI---REAILRE  799 (1139)
T ss_pred             ----cHHHHHHHHhccCcEEEeeCCCCcchHH--HHHhcchhhhhccCCCCCCcceEEEEe--cCChHHH---HHHHHHH
Confidence                2234455555688899999999997654  4445666655444433 3333332222  2222222   2233445


Q ss_pred             hcCCCcEEEEecchhHHHHHHHHHHHc--CCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEEEE
Q 037567          225 VAGAGSIIVYCMTIKDVEEISKALKQL--GVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIH  302 (374)
Q Consensus       225 ~~~~~~~lVf~~~~~~~~~l~~~l~~~--~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~  302 (374)
                      +..+|++....|.++..+.+++.|++.  ...+...||-|++.+-+.++.+|.+|+++|||||.+++.|+|+|+++++|.
T Consensus       800 l~RgGQvfYv~NrV~~Ie~~~~~L~~LVPEarI~vaHGQM~e~eLE~vM~~F~~g~~dVLv~TTIIEtGIDIPnANTiII  879 (1139)
T COG1197         800 LLRGGQVFYVHNRVESIEKKAERLRELVPEARIAVAHGQMRERELEEVMLDFYNGEYDVLVCTTIIETGIDIPNANTIII  879 (1139)
T ss_pred             HhcCCEEEEEecchhhHHHHHHHHHHhCCceEEEEeecCCCHHHHHHHHHHHHcCCCCEEEEeeeeecCcCCCCCceEEE
Confidence            567999999999999999999999985  567889999999999999999999999999999999999999999999886


Q ss_pred             ECCC-CChhHHHHhhccCCCCCCceEEEEEeecc
Q 037567          303 YGCP-KTLESYYQESGRCGRDGIASVCWLYYARS  335 (374)
Q Consensus       303 ~~~p-~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~  335 (374)
                      .+.. .-..+..|.-||+||.+..+.||.+|++.
T Consensus       880 e~AD~fGLsQLyQLRGRVGRS~~~AYAYfl~p~~  913 (1139)
T COG1197         880 ERADKFGLAQLYQLRGRVGRSNKQAYAYFLYPPQ  913 (1139)
T ss_pred             eccccccHHHHHHhccccCCccceEEEEEeecCc
Confidence            6543 46899999999999999999999999875

>TIGR00595 priA primosomal protein N'

Probab=100.00  E-value=7.6e-32  Score=247.09  Aligned_cols=292  Identities=22%  Similarity=0.229  Sum_probs=201.3

Q ss_pred             EEEccCCCCchhhhhccc---cccCCcEEEEcchHHHHHHHHHHHHH-cCCceEEcCCCCCchhh---hhhhhcCCeeEE
Q 037567           32 LVVMATGSGKSLCYQLPP---LVTGKTALVVSPLISLMQDQVMSLKQ-RGINAEFLGSAQTDSSV---QTKAETGYFQLL  104 (374)
Q Consensus        32 l~~a~tGsGKT~~~~l~~---~~~~~~~lil~P~~~l~~q~~~~~~~-~~~~~~~~~~~~~~~~~---~~~~~~~~~~i~  104 (374)
                      ++.||||||||.+|+..+   +..+.++||++|+.+|+.|+.+.+++ ++..+.++++..+..+.   +.....+..+|+
T Consensus         1 LL~g~TGsGKT~v~l~~i~~~l~~g~~vLvlvP~i~L~~Q~~~~l~~~f~~~v~vlhs~~~~~er~~~~~~~~~g~~~IV   80 (505)
T TIGR00595         1 LLFGVTGSGKTEVYLQAIEKVLALGKSVLVLVPEIALTPQMIQRFKYRFGSQVAVLHSGLSDSEKLQAWRKVKNGEILVV   80 (505)
T ss_pred             CccCCCCCCHHHHHHHHHHHHHHcCCeEEEEeCcHHHHHHHHHHHHHHhCCcEEEEECCCCHHHHHHHHHHHHcCCCCEE
Confidence            478999999998876443   45688999999999999999999985 57777777776554432   334445678999


Q ss_pred             EEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcc-hHHHHHHHHHHHhcCCCCeeEEEeecCcccHHHHHHhc
Q 037567          105 FMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDF-RLEYKQLDKLRTFLLGVPFVALTATATEKVRIDIINSL  183 (374)
Q Consensus       105 i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~-~~~~~~~~~~~~~~~~~~~i~~SaT~~~~~~~~~~~~~  183 (374)
                      |+|+..+.         ..+.++++|||||.|....++... +.....+...+....+.+++++||||+.+.......  
T Consensus        81 VGTrsalf---------~p~~~l~lIIVDEeh~~sykq~~~p~y~ar~~a~~ra~~~~~~vil~SATPsles~~~~~~--  149 (505)
T TIGR00595        81 IGTRSALF---------LPFKNLGLIIVDEEHDSSYKQEEGPRYHARDVAVYRAKKFNCPVVLGSATPSLESYHNAKQ--  149 (505)
T ss_pred             ECChHHHc---------CcccCCCEEEEECCCccccccccCCCCcHHHHHHHHHHhcCCCEEEEeCCCCHHHHHHHhc--
Confidence            99987542         235788999999999876433322 111233455556667899999999988765432211  


Q ss_pred             CCCCCeE-EEec-c-CCCceeEEEEeecC---CcchHHHHHHHHHHhhcCCCcEEEEecchhH-----------------
Q 037567          184 KLKNPYV-TIAS-F-DRKNLFYGVKVINR---GQSFVDELVQEILKSVAGAGSIIVYCMTIKD-----------------  240 (374)
Q Consensus       184 ~~~~~~~-~~~~-~-~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~lVf~~~~~~-----------------  240 (374)
                      +  .... .... . ........+.....   .......++..+.+.+..++++|||+|++..                 
T Consensus       150 g--~~~~~~l~~r~~~~~~p~v~vid~~~~~~~~~ls~~l~~~i~~~l~~g~qvLvflnrrGya~~~~C~~Cg~~~~C~~  227 (505)
T TIGR00595       150 K--AYRLLVLTRRVSGRKPPEVKLIDMRKEPRQSFLSPELITAIEQTLAAGEQSILFLNRRGYSKNLLCRSCGYILCCPN  227 (505)
T ss_pred             C--CeEEeechhhhcCCCCCeEEEEecccccccCCccHHHHHHHHHHHHcCCcEEEEEeCCcCCCeeEhhhCcCccCCCC
Confidence            1  1111 1100 0 00111111100111   0122345667777777788999999876542                 


Q ss_pred             -------------------------------------------HHHHHHHHHHc--CCceeeeecCCChHHH--HHHHHh
Q 037567          241 -------------------------------------------VEEISKALKQL--GVKAGTYHGQMGSKAR--EEAHRL  273 (374)
Q Consensus       241 -------------------------------------------~~~l~~~l~~~--~~~~~~~~~~~~~~~r--~~~~~~  273 (374)
                                                                 .+++.+.|++.  +.++..+|++++...+  +.+++.
T Consensus       228 C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~C~s~~l~~~g~Gte~~~e~l~~~fp~~~v~~~d~d~~~~~~~~~~~l~~  307 (505)
T TIGR00595       228 CDVSLTYHKKEGKLRCHYCGYQEPIPKTCPQCGSEDLVYKGYGTEQVEEELAKLFPGARIARIDSDTTSRKGAHEALLNQ  307 (505)
T ss_pred             CCCceEEecCCCeEEcCCCcCcCCCCCCCCCCCCCeeEeecccHHHHHHHHHhhCCCCcEEEEecccccCccHHHHHHHH
Confidence                                                       57788888875  6788999999876655  889999


Q ss_pred             hhcCCeeEEEEeccccccccccCccEEEEECCC--C----------ChhHHHHhhccCCCCCCceEEEEEeeccC
Q 037567          274 FIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCP--K----------TLESYYQESGRCGRDGIASVCWLYYARSN  336 (374)
Q Consensus       274 f~~g~~~ilv~t~~~~~G~d~~~~~~vi~~~~p--~----------s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~  336 (374)
                      |.+|+.+|||+|++++.|+|+|+++.|+..+..  .          ....+.|++||+||.+.+|.+++.....+
T Consensus       308 f~~g~~~ILVgT~~i~kG~d~~~v~lV~vl~aD~~l~~pd~ra~E~~~~ll~q~~GRagR~~~~g~viiqt~~p~  382 (505)
T TIGR00595       308 FANGKADILIGTQMIAKGHHFPNVTLVGVLDADSGLHSPDFRAAERGFQLLTQVAGRAGRAEDPGQVIIQTYNPN  382 (505)
T ss_pred             HhcCCCCEEEeCcccccCCCCCcccEEEEEcCcccccCcccchHHHHHHHHHHHHhccCCCCCCCEEEEEeCCCC
Confidence            999999999999999999999999988654432  1          24678999999999999998886544433

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).

>TIGR01054 rgy reverse gyrase

Probab=100.00  E-value=1.9e-31  Score=263.87  Aligned_cols=285  Identities=22%  Similarity=0.245  Sum_probs=188.9

Q ss_pred             HHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhcccc----ccCCcEEEEcchHHHHHHHHHHHHHcC--
Q 037567            4 TLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPL----VTGKTALVVSPLISLMQDQVMSLKQRG--   77 (374)
Q Consensus         4 ~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~----~~~~~~lil~P~~~l~~q~~~~~~~~~--   77 (374)
                      .|.+..|+ +|+++|..+++.++.|+++++.||||+|||.. .+++.    .++.+++|++||++|+.|+.+.+..+.  
T Consensus        70 ~f~~~~g~-~p~~iQ~~~i~~il~G~d~vi~ApTGsGKT~f-~l~~~~~l~~~g~~vLIL~PTreLa~Qi~~~l~~l~~~  147 (1171)
T TIGR01054        70 FFKKAVGS-EPWSIQKMWAKRVLRGDSFAIIAPTGVGKTTF-GLAMSLFLAKKGKRCYIILPTTLLVIQVAEKISSLAEK  147 (1171)
T ss_pred             HHHHhcCC-CCcHHHHHHHHHHhCCCeEEEECCCCCCHHHH-HHHHHHHHHhcCCeEEEEeCHHHHHHHHHHHHHHHHHh
Confidence            35555555 69999999999999999999999999999973 33332    247889999999999999999988763  


Q ss_pred             --CceE---EcCCCCCchhh---hhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccC------
Q 037567           78 --INAE---FLGSAQTDSSV---QTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGH------  143 (374)
Q Consensus        78 --~~~~---~~~~~~~~~~~---~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~------  143 (374)
                        +...   .++++......   ......+.++|+|+||+++....    ..+. .+++++|+||||.+.+++.      
T Consensus       148 ~~i~~~~i~~~~Gg~~~~e~~~~~~~l~~~~~dIlV~Tp~rL~~~~----~~l~-~~~~~iVvDEaD~~L~~~k~vd~il  222 (1171)
T TIGR01054       148 AGVGTVNIGAYHSRLPTKEKKEFMERIENGDFDILITTTMFLSKNY----DELG-PKFDFIFVDDVDALLKASKNVDKLL  222 (1171)
T ss_pred             cCCceeeeeeecCCCCHHHHHHHHHHHhcCCCCEEEECHHHHHHHH----HHhc-CCCCEEEEeChHhhhhccccHHHHH
Confidence              2322   23344333222   22233456899999999875432    2222 2789999999999987431      


Q ss_pred             ---cchHH-HHH-------------------HHHHHHhc-CCCC--eeEEEeecCc-ccHHHHHHhcCCCCCeEEEeccC
Q 037567          144 ---DFRLE-YKQ-------------------LDKLRTFL-LGVP--FVALTATATE-KVRIDIINSLKLKNPYVTIASFD  196 (374)
Q Consensus       144 ---~~~~~-~~~-------------------~~~~~~~~-~~~~--~i~~SaT~~~-~~~~~~~~~~~~~~~~~~~~~~~  196 (374)
                         ++... +..                   +....... ...+  ++++|||..+ .....+...+  ....+......
T Consensus       223 ~llGF~~e~i~~il~~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~li~~SAT~~p~~~~~~l~r~l--l~~~v~~~~~~  300 (1171)
T TIGR01054       223 KLLGFSEELIEKAWKLIRLRLKLYRALHAKKRLELLEAIPGKKRGCLIVSSATGRPRGKRAKLFREL--LGFEVGGGSDT  300 (1171)
T ss_pred             HHcCCCHHHHHHHHHHhhhccccchHHHHHHHHHHHHhhhhccCcEEEEEeCCCCccccHHHHcccc--cceEecCcccc
Confidence               12111 111                   11111122 2233  5678999544 3322121111  01111111111


Q ss_pred             CCceeEEEEeecCCcchHHHHHHHHHHhhcCCCcEEEEecch---hHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHh
Q 037567          197 RKNLFYGVKVINRGQSFVDELVQEILKSVAGAGSIIVYCMTI---KDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRL  273 (374)
Q Consensus       197 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lVf~~~~---~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~  273 (374)
                      ..++.....  .. ... ...+.++++..  +.++||||+++   +.++.+++.|++.|+++..+||+++    +..++.
T Consensus       301 ~r~I~~~~~--~~-~~~-~~~L~~ll~~l--~~~~IVFv~t~~~~~~a~~l~~~L~~~g~~a~~lhg~~~----~~~l~~  370 (1171)
T TIGR01054       301 LRNVVDVYV--ED-EDL-KETLLEIVKKL--GTGGIVYVSIDYGKEKAEEIAEFLENHGVKAVAYHATKP----KEDYEK  370 (1171)
T ss_pred             ccceEEEEE--ec-ccH-HHHHHHHHHHc--CCCEEEEEeccccHHHHHHHHHHHHhCCceEEEEeCCCC----HHHHHH
Confidence            222222211  11 111 23345555554  46899999999   9999999999999999999999986    368899


Q ss_pred             hhcCCeeEEEEe----ccccccccccC-ccEEEEECCCC
Q 037567          274 FIRDEIRVMVAT----MAFGMGIDKPD-VRHVIHYGCPK  307 (374)
Q Consensus       274 f~~g~~~ilv~t----~~~~~G~d~~~-~~~vi~~~~p~  307 (374)
                      |++|+++|||+|    +.+.+|+|+|+ +++||+++.|.
T Consensus       371 Fr~G~~~vLVata~~tdv~aRGIDip~~V~~vI~~~~P~  409 (1171)
T TIGR01054       371 FAEGEIDVLIGVASYYGTLVRGLDLPERVRYAVFLGVPK  409 (1171)
T ss_pred             HHcCCCCEEEEeccccCcccccCCCCccccEEEEECCCC
Confidence            999999999995    89999999999 89999999996

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.

>PRK11131 ATP-dependent RNA helicase HrpA; Provisional

Probab=100.00  E-value=1.6e-31  Score=260.70  Aligned_cols=325  Identities=17%  Similarity=0.215  Sum_probs=215.1

Q ss_pred             chhHHHHHHHHHcCCCEEEEccCCCCchhhhhcc-c-cc--c--CCcEEEEcch----HHHHHHHHHHHHH-cCCceEEc
Q 037567           15 RPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLP-P-LV--T--GKTALVVSPL----ISLMQDQVMSLKQ-RGINAEFL   83 (374)
Q Consensus        15 ~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~-~-~~--~--~~~~lil~P~----~~l~~q~~~~~~~-~~~~~~~~   83 (374)
                      +.+-.+++..+.+++.++++|+||||||..  +| + +.  .  ...+++.-|+    ++++.++.+++.. .|..+++.
T Consensus        76 ~~~r~~Il~ai~~~~VviI~GeTGSGKTTq--lPq~lle~g~g~~g~I~~TQPRRlAArsLA~RVA~El~~~lG~~VGY~  153 (1294)
T PRK11131         76 SQKKQDILEAIRDHQVVIVAGETGSGKTTQ--LPKICLELGRGVKGLIGHTQPRRLAARTVANRIAEELETELGGCVGYK  153 (1294)
T ss_pred             HHHHHHHHHHHHhCCeEEEECCCCCCHHHH--HHHHHHHcCCCCCCceeeCCCcHHHHHHHHHHHHHHHhhhhcceecee
Confidence            335556666776777788999999999973  33 1 11  1  2345555675    4777777777763 34333221


Q ss_pred             CCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccch-hhcccCcchHHHHHHHHHHHhcCCC
Q 037567           84 GSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHC-ISEWGHDFRLEYKQLDKLRTFLLGV  162 (374)
Q Consensus        84 ~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~-~~~~~~~~~~~~~~~~~~~~~~~~~  162 (374)
                      .    ...   ......+.|+++||+.|...+..   ...+.++++|||||||. ..+.++.    ...+..+....++.
T Consensus       154 v----rf~---~~~s~~t~I~v~TpG~LL~~l~~---d~~Ls~~~~IIIDEAHERsLn~DfL----Lg~Lk~lL~~rpdl  219 (1294)
T PRK11131        154 V----RFN---DQVSDNTMVKLMTDGILLAEIQQ---DRLLMQYDTIIIDEAHERSLNIDFI----LGYLKELLPRRPDL  219 (1294)
T ss_pred             e----cCc---cccCCCCCEEEEChHHHHHHHhc---CCccccCcEEEecCccccccccchH----HHHHHHhhhcCCCc
Confidence            1    111   11124579999999998876543   23478899999999994 4443322    23445555545678


Q ss_pred             CeeEEEeecCcccHHHHHHhcCCCCCeEEEeccCCCceeEEEEeecCC-----cchHHHHHHHHHHh-hcCCCcEEEEec
Q 037567          163 PFVALTATATEKVRIDIINSLKLKNPYVTIASFDRKNLFYGVKVINRG-----QSFVDELVQEILKS-VAGAGSIIVYCM  236 (374)
Q Consensus       163 ~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~-~~~~~~~lVf~~  236 (374)
                      ++|+||||++..   .+...++ ..+.+....... .+...+......     ......++..+... ....+++|||++
T Consensus       220 KvILmSATid~e---~fs~~F~-~apvI~V~Gr~~-pVei~y~p~~~~~~~~~~d~l~~ll~~V~~l~~~~~GdILVFLp  294 (1294)
T PRK11131        220 KVIITSATIDPE---RFSRHFN-NAPIIEVSGRTY-PVEVRYRPIVEEADDTERDQLQAIFDAVDELGREGPGDILIFMS  294 (1294)
T ss_pred             eEEEeeCCCCHH---HHHHHcC-CCCEEEEcCccc-cceEEEeecccccchhhHHHHHHHHHHHHHHhcCCCCCEEEEcC
Confidence            999999999753   3444443 233333322111 111111111111     11222222222111 135688999999


Q ss_pred             chhHHHHHHHHHHHcCCc---eeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEEEEECC--------
Q 037567          237 TIKDVEEISKALKQLGVK---AGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGC--------  305 (374)
Q Consensus       237 ~~~~~~~l~~~l~~~~~~---~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~~~~--------  305 (374)
                      +..+++.+++.|.+.+.+   +..+||+++.+++..+++.  .|..+|+|||+++++|+|+|++++||+++.        
T Consensus       295 g~~EIe~lae~L~~~~~~~~~VlpLhg~Ls~~eQ~~Vf~~--~g~rkIIVATNIAEtSITIpgI~yVID~Gl~k~~~Yd~  372 (1294)
T PRK11131        295 GEREIRDTADALNKLNLRHTEILPLYARLSNSEQNRVFQS--HSGRRIVLATNVAETSLTVPGIKYVIDPGTARISRYSY  372 (1294)
T ss_pred             CHHHHHHHHHHHHhcCCCcceEeecccCCCHHHHHHHhcc--cCCeeEEEeccHHhhccccCcceEEEECCCcccccccc
Confidence            999999999999987664   6789999999999999876  477899999999999999999999999863        


Q ss_pred             -------C---CChhHHHHhhccCCCCCCceEEEEEeeccCCCcccceeccccchHHHHHHHHHHHHHHHH
Q 037567          306 -------P---KTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFYCGESQTENQRTAIMESLLAAQRY  366 (374)
Q Consensus       306 -------p---~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  366 (374)
                             |   .|..++.||.||+||. .+|.||.+|+++++....   ....++..+..+...+.+|..+
T Consensus       373 ~~~~~~Lp~~~iSkasa~QRaGRAGR~-~~G~c~rLyte~d~~~~~---~~~~PEIlR~~L~~viL~lk~l  439 (1294)
T PRK11131        373 RTKVQRLPIEPISQASANQRKGRCGRV-SEGICIRLYSEDDFLSRP---EFTDPEILRTNLASVILQMTAL  439 (1294)
T ss_pred             ccCcccCCeeecCHhhHhhhccccCCC-CCcEEEEeCCHHHHHhhh---cccCCccccCCHHHHHHHHHHc
Confidence                   2   3568999999999999 699999999998876543   3355666666666666666554

>KOG0329 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.98  E-value=3.8e-33  Score=219.96  Aligned_cols=288  Identities=17%  Similarity=0.261  Sum_probs=206.8

Q ss_pred             hHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhcccccc------CCcEEEEcchHHHHHHHHHHHHHc
Q 037567            3 STLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVT------GKTALVVSPLISLMQDQVMSLKQR   76 (374)
Q Consensus         3 ~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~~------~~~~lil~P~~~l~~q~~~~~~~~   76 (374)
                      +++-. -||++|.+.|-+++|+..-|-++++.|..|.|||..|.++.+++      .-.++++|.+|+|+-|...++.++
T Consensus        55 raivd-cgfehpsevqhecipqailgmdvlcqaksgmgktavfvl~tlqqiepv~g~vsvlvmchtrelafqi~~ey~rf  133 (387)
T KOG0329|consen   55 RAIVD-CGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQIEPVDGQVSVLVMCHTRELAFQISKEYERF  133 (387)
T ss_pred             HHHHh-ccCCCchHhhhhhhhHHhhcchhheecccCCCceeeeehhhhhhcCCCCCeEEEEEEeccHHHHHHHHHHHHHH
Confidence            44445 69999999999999999999999999999999999998888764      446899999999999999888765


Q ss_pred             -----CCceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHH
Q 037567           77 -----GINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQ  151 (374)
Q Consensus        77 -----~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~  151 (374)
                           +.++.++.++......... ....|+|+|+||+++..+.+.  ..+.+.++..+|+|||+.+.+ ..+++.   -
T Consensus       134 skymP~vkvaVFfGG~~Ikkdee~-lk~~PhivVgTPGrilALvr~--k~l~lk~vkhFvlDEcdkmle-~lDMrR---D  206 (387)
T KOG0329|consen  134 SKYMPSVKVSVFFGGLFIKKDEEL-LKNCPHIVVGTPGRILALVRN--RSLNLKNVKHFVLDECDKMLE-QLDMRR---D  206 (387)
T ss_pred             HhhCCCceEEEEEcceeccccHHH-HhCCCeEEEcCcHHHHHHHHh--ccCchhhcceeehhhHHHHHH-HHHHHH---H
Confidence                 4555666666554443333 333899999999999888666  667788999999999998876 233332   2


Q ss_pred             HHHHHH-hcCCCCeeEEEeecCcccHHHHHHhcCCCCCe-EEEeccCCCceeE-EEEeecCCcchHHHHHHHHHHhhcCC
Q 037567          152 LDKLRT-FLLGVPFVALTATATEKVRIDIINSLKLKNPY-VTIASFDRKNLFY-GVKVINRGQSFVDELVQEILKSVAGA  228 (374)
Q Consensus       152 ~~~~~~-~~~~~~~i~~SaT~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~  228 (374)
                      +.++.. ..+..+++.||||.+.+..+ ++..+ +.+|. +.........+.- ......-.......-+.+++..+ ..
T Consensus       207 vQEifr~tp~~KQvmmfsatlskeiRp-vC~kF-mQdPmEi~vDdE~KLtLHGLqQ~YvkLke~eKNrkl~dLLd~L-eF  283 (387)
T KOG0329|consen  207 VQEIFRMTPHEKQVMMFSATLSKEIRP-VCHKF-MQDPMEIFVDDEAKLTLHGLQQYYVKLKENEKNRKLNDLLDVL-EF  283 (387)
T ss_pred             HHHHhhcCcccceeeeeeeecchhhHH-HHHhh-hcCchhhhccchhhhhhhhHHHHHHhhhhhhhhhhhhhhhhhh-hh
Confidence            333332 33468899999999998764 33333 23332 2222211111100 00011111222233344444444 56


Q ss_pred             CcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEEEEECCCCC
Q 037567          229 GSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPKT  308 (374)
Q Consensus       229 ~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~~~~p~s  308 (374)
                      ++++||+.+.....                               |   ..+ +|+|+..++|+|+..++.+++|+.|.+
T Consensus       284 NQVvIFvKsv~Rl~-------------------------------f---~kr-~vat~lfgrgmdiervNi~~NYdmp~~  328 (387)
T KOG0329|consen  284 NQVVIFVKSVQRLS-------------------------------F---QKR-LVATDLFGRGMDIERVNIVFNYDMPED  328 (387)
T ss_pred             cceeEeeehhhhhh-------------------------------h---hhh-hHHhhhhccccCcccceeeeccCCCCC
Confidence            78999998876510                               2   123 899999999999999999999999999


Q ss_pred             hhHHHHhhccCCCCCCceEEEEEeeccC
Q 037567          309 LESYYQESGRCGRDGIASVCWLYYARSN  336 (374)
Q Consensus       309 ~~~~~Q~~GR~~R~~~~g~~~~~~~~~~  336 (374)
                      .++|.||.|||||.|..|.++.+++..+
T Consensus       329 ~DtYlHrv~rAgrfGtkglaitfvs~e~  356 (387)
T KOG0329|consen  329 SDTYLHRVARAGRFGTKGLAITFVSDEN  356 (387)
T ss_pred             chHHHHHhhhhhccccccceeehhcchh
Confidence            9999999999999999999999988754

>KOG0951 consensus RNA helicase BRR2, DEAD-box superfamily [RNA processing and modification]

Probab=99.98  E-value=3.9e-31  Score=248.25  Aligned_cols=337  Identities=20%  Similarity=0.228  Sum_probs=242.5

Q ss_pred             HcCCCCCchhHHHHHHHHHcC-CCEEEEccCCCCchhhhhcccccc--------------CCcEEEEcchHHHHHHHHHH
Q 037567            8 YFGYSVFRPYQKDVIQRIIEK-RDCLVVMATGSGKSLCYQLPPLVT--------------GKTALVVSPLISLMQDQVMS   72 (374)
Q Consensus         8 ~~~~~~~~~~Q~~~~~~~~~~-~~~l~~a~tGsGKT~~~~l~~~~~--------------~~~~lil~P~~~l~~q~~~~   72 (374)
                      .+|..++.++|+...++.+.+ .+++++||||+|||..+++.++++              ..++.+++|.++|++.|...
T Consensus       304 F~g~~sLNrIQS~v~daAl~~~EnmLlCAPTGaGKTNVAvLtiLqel~~h~r~dgs~nl~~fKIVYIAPmKaLvqE~Vgs  383 (1674)
T KOG0951|consen  304 FFGKQSLNRIQSKVYDAALRGDENMLLCAPTGAGKTNVAVLTILQELGNHLREDGSVNLAPFKIVYIAPMKALVQEMVGS  383 (1674)
T ss_pred             cccchhhhHHHHHHHHHHhcCcCcEEEeccCCCCchHHHHHHHHHHHhcccccccceecccceEEEEeeHHHHHHHHHHH
Confidence            467788999999999988875 588999999999999999888852              45899999999999999987


Q ss_pred             HHH----cCCceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchh-hcccCcchH
Q 037567           73 LKQ----RGINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCI-SEWGHDFRL  147 (374)
Q Consensus        73 ~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~-~~~~~~~~~  147 (374)
                      +.+    +|+.+.-.++.........    ....++|+|||+...+.+...+....+-++++|+||.|.+ .+.|.-...
T Consensus       384 fSkRla~~GI~V~ElTgD~~l~~~qi----eeTqVIV~TPEK~DiITRk~gdraY~qlvrLlIIDEIHLLhDdRGpvLES  459 (1674)
T KOG0951|consen  384 FSKRLAPLGITVLELTGDSQLGKEQI----EETQVIVTTPEKWDIITRKSGDRAYEQLVRLLIIDEIHLLHDDRGPVLES  459 (1674)
T ss_pred             HHhhccccCcEEEEecccccchhhhh----hcceeEEeccchhhhhhcccCchhHHHHHHHHhhhhhhhcccccchHHHH
Confidence            764    5777776666544333222    2358999999998666555444555567789999999998 445654433


Q ss_pred             HHHHHHHHH-HhcCCCCeeEEEeecCcccHHHHHHhcCCCCCeEEEeccCCCceeEEEEee--cCCcchH------HHHH
Q 037567          148 EYKQLDKLR-TFLLGVPFVALTATATEKVRIDIINSLKLKNPYVTIASFDRKNLFYGVKVI--NRGQSFV------DELV  218 (374)
Q Consensus       148 ~~~~~~~~~-~~~~~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~------~~~~  218 (374)
                      ...+..+-. ..-...+.+++|||+++..  +...++...++................+++  ..+....      +...
T Consensus       460 IVaRt~r~ses~~e~~RlVGLSATLPNy~--DV~~Fl~v~~~glf~fd~syRpvPL~qq~Igi~ek~~~~~~qamNe~~y  537 (1674)
T KOG0951|consen  460 IVARTFRRSESTEEGSRLVGLSATLPNYE--DVASFLRVDPEGLFYFDSSYRPVPLKQQYIGITEKKPLKRFQAMNEACY  537 (1674)
T ss_pred             HHHHHHHHhhhcccCceeeeecccCCchh--hhHHHhccCcccccccCcccCcCCccceEeccccCCchHHHHHHHHHHH
Confidence            333333222 2223688999999999876  557777777665555533333333333322  2211111      2334


Q ss_pred             HHHHHhhcCCCcEEEEecchhHHHHHHHHHHHc-------------------------------------CCceeeeecC
Q 037567          219 QEILKSVAGAGSIIVYCMTIKDVEEISKALKQL-------------------------------------GVKAGTYHGQ  261 (374)
Q Consensus       219 ~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~-------------------------------------~~~~~~~~~~  261 (374)
                      ..++++. .++++|||+.++++..+.++.++..                                     .+..+++|.+
T Consensus       538 eKVm~~a-gk~qVLVFVHsRkET~ktA~aIRd~~le~dtls~fmre~s~s~eilrtea~~~kn~dLkdLLpygfaIHhAG  616 (1674)
T KOG0951|consen  538 EKVLEHA-GKNQVLVFVHSRKETAKTARAIRDKALEEDTLSRFMREDSASREILRTEAGQAKNPDLKDLLPYGFAIHHAG  616 (1674)
T ss_pred             HHHHHhC-CCCcEEEEEEechHHHHHHHHHHHHHhhhhHHHHHHhcccchhhhhhhhhhcccChhHHHHhhccceeeccC
Confidence            4455554 4589999999999888888777621                                     3446789999


Q ss_pred             CChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEEE----EECC------CCChhHHHHhhccCCCCCC--ceEEE
Q 037567          262 MGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVI----HYGC------PKTLESYYQESGRCGRDGI--ASVCW  329 (374)
Q Consensus       262 ~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi----~~~~------p~s~~~~~Q~~GR~~R~~~--~g~~~  329 (374)
                      ++..+|......|.+|.++++++|..+..|+|+|.-+++|    .+++      +.++.+.+||.||+||.+-  .|-.+
T Consensus       617 l~R~dR~~~EdLf~~g~iqvlvstatlawgvnlpahtViikgtqvy~pekg~w~elsp~dv~qmlgragrp~~D~~gegi  696 (1674)
T KOG0951|consen  617 LNRKDRELVEDLFADGHIQVLVSTATLAWGVNLPAHTVIIKGTQVYDPEKGRWTELSPLDVMQMLGRAGRPQYDTCGEGI  696 (1674)
T ss_pred             CCcchHHHHHHHHhcCceeEEEeehhhhhhcCCCcceEEecCccccCcccCccccCCHHHHHHHHhhcCCCccCcCCcee
Confidence            9999999999999999999999999999999999777666    2222      3489999999999999753  45667


Q ss_pred             EEeeccCCCcccceeccccchH
Q 037567          330 LYYARSNFAKGDFYCGESQTEN  351 (374)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~  351 (374)
                      +.....++...-.++++..+.+
T Consensus       697 iit~~se~qyyls~mn~qLpie  718 (1674)
T KOG0951|consen  697 IITDHSELQYYLSLMNQQLPIE  718 (1674)
T ss_pred             eccCchHhhhhHHhhhhcCCCh
Confidence            7777777777666666555543

>PRK09694 helicase Cas3; Provisional

Probab=99.97  E-value=6.2e-30  Score=244.65  Aligned_cols=309  Identities=17%  Similarity=0.181  Sum_probs=197.9

Q ss_pred             cCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc-----cCCcEEEEcchHHHHHHHHHHHHH-----cC-
Q 037567            9 FGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV-----TGKTALVVSPLISLMQDQVMSLKQ-----RG-   77 (374)
Q Consensus         9 ~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~-----~~~~~lil~P~~~l~~q~~~~~~~-----~~-   77 (374)
                      ++..+|+|+|..+.........+++.||||+|||.+++..+..     ...++++..||+++++++++.+.+     ++ 
T Consensus       282 ~~~~~p~p~Q~~~~~~~~~pgl~ileApTGsGKTEAAL~~A~~l~~~~~~~gi~~aLPT~Atan~m~~Rl~~~~~~~f~~  361 (878)
T PRK09694        282 DNGYQPRQLQTLVDALPLQPGLTIIEAPTGSGKTEAALAYAWRLIDQGLADSIIFALPTQATANAMLSRLEALASKLFPS  361 (878)
T ss_pred             cCCCCChHHHHHHHhhccCCCeEEEEeCCCCCHHHHHHHHHHHHHHhCCCCeEEEECcHHHHHHHHHHHHHHHHHHhcCC
Confidence            4445799999988654334566899999999999887655432     246899999999999999998864     22 


Q ss_pred             CceEEcCCCCCchh-----------------------hhhh-hhc--CCeeEEEEcCcccccCchhh-HH--HHHhcCcc
Q 037567           78 INAEFLGSAQTDSS-----------------------VQTK-AET--GYFQLLFMTPEKACIIPISF-WS--KLLKAGVC  128 (374)
Q Consensus        78 ~~~~~~~~~~~~~~-----------------------~~~~-~~~--~~~~i~i~T~~~l~~~~~~~-~~--~~~~~~~~  128 (374)
                      ..+.+.++......                       .+.. ..+  --..|+|+|.+++....-.. ..  +...-.-+
T Consensus       362 ~~v~L~Hg~a~l~~~~~~~~~~~~~~~~~~~~~~~~~~w~~~~~kr~llapi~V~TiDQlL~a~l~~kh~~lR~~~La~s  441 (878)
T PRK09694        362 PNLILAHGNSRFNHLFQSLKSRAATEQGQEEAWVQCCEWLSQSNKRVFLGQIGVCTIDQVLISVLPVKHRFIRGFGLGRS  441 (878)
T ss_pred             CceEeecCcchhhhhhhhhhcccccccccchhhhHHHHHHhhhhhhhhcCCEEEcCHHHHHHHHHccchHHHHHHhhccC
Confidence            23444443221100                       0000 000  01489999999876322111 01  11112235


Q ss_pred             EEEEeccchhhcccCcchHHHHHHHHHHHhcCCCCeeEEEeecCcccHHHHHHhcCCCC--------CeEEEec------
Q 037567          129 LFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEKVRIDIINSLKLKN--------PYVTIAS------  194 (374)
Q Consensus       129 ~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~SaT~~~~~~~~~~~~~~~~~--------~~~~~~~------  194 (374)
                      +|||||+|.+...   +...+..+-+.... ...++|+||||++......+...++...        +.+....      
T Consensus       442 vvIiDEVHAyD~y---m~~lL~~~L~~l~~-~g~~vIllSATLP~~~r~~L~~a~~~~~~~~~~~~YPlvt~~~~~~~~~  517 (878)
T PRK09694        442 VLIVDEVHAYDAY---MYGLLEAVLKAQAQ-AGGSVILLSATLPATLKQKLLDTYGGHDPVELSSAYPLITWRGVNGAQR  517 (878)
T ss_pred             eEEEechhhCCHH---HHHHHHHHHHHHHh-cCCcEEEEeCCCCHHHHHHHHHHhcccccccccccccccccccccccee
Confidence            8999999987432   11111222222111 2578999999999887766665443210        1110000      


Q ss_pred             c--C------CCceeEEEEeec-CCcchHHHHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHHcC---CceeeeecCC
Q 037567          195 F--D------RKNLFYGVKVIN-RGQSFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLG---VKAGTYHGQM  262 (374)
Q Consensus       195 ~--~------~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~~---~~~~~~~~~~  262 (374)
                      .  .      .......+.... ........++..+.+....+++++||||+++.++.+++.|++.+   .++..+||++
T Consensus       518 ~~~~~~~~~~~~~~~v~v~~~~~~~~~~~~~~l~~i~~~~~~g~~vLVf~NTV~~Aq~ly~~L~~~~~~~~~v~llHsrf  597 (878)
T PRK09694        518 FDLSAHPEQLPARFTIQLEPICLADMLPDLTLLQRMIAAANAGAQVCLICNLVDDAQKLYQRLKELNNTQVDIDLFHARF  597 (878)
T ss_pred             eeccccccccCcceEEEEEeeccccccCHHHHHHHHHHHHhcCCEEEEEECCHHHHHHHHHHHHhhCCCCceEEEEeCCC
Confidence            0  0      000111111111 11112245666666666678999999999999999999999764   5789999999


Q ss_pred             ChHHHH----HHHHhh-hcCC---eeEEEEeccccccccccCccEEEEECCCCChhHHHHhhccCCCCCC
Q 037567          263 GSKARE----EAHRLF-IRDE---IRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRDGI  324 (374)
Q Consensus       263 ~~~~r~----~~~~~f-~~g~---~~ilv~t~~~~~G~d~~~~~~vi~~~~p~s~~~~~Q~~GR~~R~~~  324 (374)
                      +..+|.    ++++.| ++|+   ..|||+|++++.|+|+ +++++|....|  .+.++||+||++|.+.
T Consensus       598 ~~~dR~~~E~~vl~~fgk~g~r~~~~ILVaTQViE~GLDI-d~DvlItdlaP--idsLiQRaGR~~R~~~  664 (878)
T PRK09694        598 TLNDRREKEQRVIENFGKNGKRNQGRILVATQVVEQSLDL-DFDWLITQLCP--VDLLFQRLGRLHRHHR  664 (878)
T ss_pred             CHHHHHHHHHHHHHHHHhcCCcCCCeEEEECcchhheeec-CCCeEEECCCC--HHHHHHHHhccCCCCC
Confidence            999984    567778 5555   4799999999999999 58988887777  7899999999999875

>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA

Probab=99.97  E-value=2.7e-30  Score=253.02  Aligned_cols=326  Identities=15%  Similarity=0.178  Sum_probs=215.3

Q ss_pred             HHHHHHHHcCCCEEEEccCCCCchhhhhccccc----cCCcEEEEcchHHHHHHHHHHHHH-cCCceEEcCCCCCchhhh
Q 037567           19 KDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV----TGKTALVVSPLISLMQDQVMSLKQ-RGINAEFLGSAQTDSSVQ   93 (374)
Q Consensus        19 ~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~----~~~~~lil~P~~~l~~q~~~~~~~-~~~~~~~~~~~~~~~~~~   93 (374)
                      .+++..+.++..++++|+||||||...-..++.    ...++++.-|++-.+..+...+.. +|..+....+.....+. 
T Consensus        73 ~~Il~~l~~~~vvii~g~TGSGKTTqlPq~lle~~~~~~~~I~~tQPRRlAA~svA~RvA~elg~~lG~~VGY~vR~~~-  151 (1283)
T TIGR01967        73 EDIAEAIAENQVVIIAGETGSGKTTQLPKICLELGRGSHGLIGHTQPRRLAARTVAQRIAEELGTPLGEKVGYKVRFHD-  151 (1283)
T ss_pred             HHHHHHHHhCceEEEeCCCCCCcHHHHHHHHHHcCCCCCceEecCCccHHHHHHHHHHHHHHhCCCcceEEeeEEcCCc-
Confidence            456666667778899999999999642111221    234677788988777777766543 45544332222111111 


Q ss_pred             hhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccch-hhcccCcchHHHHHHHHHHHhcCCCCeeEEEeecC
Q 037567           94 TKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHC-ISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATAT  172 (374)
Q Consensus        94 ~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~-~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~SaT~~  172 (374)
                        .......|.++|++.|...+..   ...+.++++|||||+|. ..+.+    .....+..+....++.++|+||||+.
T Consensus       152 --~~s~~T~I~~~TdGiLLr~l~~---d~~L~~~~~IIIDEaHERsL~~D----~LL~lLk~il~~rpdLKlIlmSATld  222 (1283)
T TIGR01967       152 --QVSSNTLVKLMTDGILLAETQQ---DRFLSRYDTIIIDEAHERSLNID----FLLGYLKQLLPRRPDLKIIITSATID  222 (1283)
T ss_pred             --ccCCCceeeeccccHHHHHhhh---CcccccCcEEEEcCcchhhccch----hHHHHHHHHHhhCCCCeEEEEeCCcC
Confidence              1123468999999998765443   23468899999999994 44322    22234555555567889999999997


Q ss_pred             cccHHHHHHhcCCCCCeEEEeccCCCceeEEEEeecC-C----cchHH---HHHHHHHHhhcCCCcEEEEecchhHHHHH
Q 037567          173 EKVRIDIINSLKLKNPYVTIASFDRKNLFYGVKVINR-G----QSFVD---ELVQEILKSVAGAGSIIVYCMTIKDVEEI  244 (374)
Q Consensus       173 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~----~~~~~---~~~~~~~~~~~~~~~~lVf~~~~~~~~~l  244 (374)
                      ..   .+...++. .+.+....... .+...+..... .    .....   +.+..+...  ..+++|||+++..+++.+
T Consensus       223 ~~---~fa~~F~~-apvI~V~Gr~~-PVev~Y~~~~~~~~~~~~~~~~~i~~~I~~l~~~--~~GdILVFLpg~~EI~~l  295 (1283)
T TIGR01967       223 PE---RFSRHFNN-APIIEVSGRTY-PVEVRYRPLVEEQEDDDLDQLEAILDAVDELFAE--GPGDILIFLPGEREIRDA  295 (1283)
T ss_pred             HH---HHHHHhcC-CCEEEECCCcc-cceeEEecccccccchhhhHHHHHHHHHHHHHhh--CCCCEEEeCCCHHHHHHH
Confidence            53   34554432 33333322111 11111111111 0    01112   222332222  468999999999999999


Q ss_pred             HHHHHHcC---CceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEEEEECCC---------------
Q 037567          245 SKALKQLG---VKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCP---------------  306 (374)
Q Consensus       245 ~~~l~~~~---~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~~~~p---------------  306 (374)
                      ++.|.+.+   ..+..+||+++.+++..++..+  +..+|+++|+++++|+|+|++++||+++.+               
T Consensus       296 ~~~L~~~~~~~~~VlpLhg~Ls~~eQ~~vf~~~--~~rkIVLATNIAEtSLTIpgV~yVIDsGl~r~~~yd~~~~~~~L~  373 (1283)
T TIGR01967       296 AEILRKRNLRHTEILPLYARLSNKEQQRVFQPH--SGRRIVLATNVAETSLTVPGIHYVIDTGTARISRYSYRTKVQRLP  373 (1283)
T ss_pred             HHHHHhcCCCCcEEEeccCCCCHHHHHHHhCCC--CCceEEEeccHHHhccccCCeeEEEeCCCccccccccccCccccC
Confidence            99998864   3478899999999999986654  246899999999999999999999998853               


Q ss_pred             ---CChhHHHHhhccCCCCCCceEEEEEeeccCCCcccceeccccchHHHHHHHHHHHHHHHHh
Q 037567          307 ---KTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFYCGESQTENQRTAIMESLLAAQRYC  367 (374)
Q Consensus       307 ---~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  367 (374)
                         .|..++.||.||+||.+ +|.||.+|+.+++....   ....++..+..+..-+.+|..+.
T Consensus       374 ~~~ISkasa~QRaGRAGR~~-~G~cyRLyte~~~~~~~---~~~~PEIlR~~L~~viL~l~~lg  433 (1283)
T TIGR01967       374 IEPISQASANQRKGRCGRVA-PGICIRLYSEEDFNSRP---EFTDPEILRTNLASVILQMLALR  433 (1283)
T ss_pred             CccCCHHHHHHHhhhhCCCC-CceEEEecCHHHHHhhh---hccCcccccccHHHHHHHHHhcC
Confidence               36689999999999997 99999999998876543   33466666666666666666553

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.

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

Probab=99.97  E-value=1e-29  Score=249.88  Aligned_cols=305  Identities=18%  Similarity=0.203  Sum_probs=191.5

Q ss_pred             CCchhHHHHHHHHHc-----CCCEEEEccCCCCchhhhhcccc---c--cCCcEEEEcchHHHHHHHHHHHHHcCCceEE
Q 037567           13 VFRPYQKDVIQRIIE-----KRDCLVVMATGSGKSLCYQLPPL---V--TGKTALVVSPLISLMQDQVMSLKQRGINAEF   82 (374)
Q Consensus        13 ~~~~~Q~~~~~~~~~-----~~~~l~~a~tGsGKT~~~~l~~~---~--~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~   82 (374)
                      .+|+||.+|+.++.+     .+++++++|||||||.+++..+.   .  ..+++|+++|+.+|+.|+...|..++.....
T Consensus       413 ~lR~YQ~~AI~ai~~a~~~g~r~~Ll~maTGSGKT~tai~li~~L~~~~~~~rVLfLvDR~~L~~Qa~~~F~~~~~~~~~  492 (1123)
T PRK11448        413 GLRYYQEDAIQAVEKAIVEGQREILLAMATGTGKTRTAIALMYRLLKAKRFRRILFLVDRSALGEQAEDAFKDTKIEGDQ  492 (1123)
T ss_pred             CCCHHHHHHHHHHHHHHHhccCCeEEEeCCCCCHHHHHHHHHHHHHhcCccCeEEEEecHHHHHHHHHHHHHhccccccc
Confidence            589999999988763     35789999999999977543221   1  3478999999999999999999987653321


Q ss_pred             -cCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhH---HHHHhcCccEEEEeccchhhccc-------Ccc---hHH
Q 037567           83 -LGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFW---SKLLKAGVCLFAVDEAHCISEWG-------HDF---RLE  148 (374)
Q Consensus        83 -~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~---~~~~~~~~~~vviDE~h~~~~~~-------~~~---~~~  148 (374)
                       +...................|+|+|++++........   .......+++||+||||+.....       ..+   ...
T Consensus       493 ~~~~i~~i~~L~~~~~~~~~~I~iaTiQtl~~~~~~~~~~~~~~~~~~fdlIIiDEaHRs~~~d~~~~~~~~~~~~~~~~  572 (1123)
T PRK11448        493 TFASIYDIKGLEDKFPEDETKVHVATVQGMVKRILYSDDPMDKPPVDQYDCIIVDEAHRGYTLDKEMSEGELQFRDQLDY  572 (1123)
T ss_pred             chhhhhchhhhhhhcccCCCCEEEEEHHHHHHhhhccccccccCCCCcccEEEEECCCCCCccccccccchhccchhhhH
Confidence             1110000100111122345899999998754321110   11234678899999999853100       000   111


Q ss_pred             HHHHHHHHHhcCCCCeeEEEeecCcccHHHHHHhcCC----------------C---CCeEEEeccCCCceeEE------
Q 037567          149 YKQLDKLRTFLLGVPFVALTATATEKVRIDIINSLKL----------------K---NPYVTIASFDRKNLFYG------  203 (374)
Q Consensus       149 ~~~~~~~~~~~~~~~~i~~SaT~~~~~~~~~~~~~~~----------------~---~~~~~~~~~~~~~~~~~------  203 (374)
                      +..+..+...+ +...|+|||||.....    ..++.                .   ++..+........+...      
T Consensus       573 ~~~yr~iL~yF-dA~~IGLTATP~r~t~----~~FG~pv~~Ysl~eAI~DG~Lv~~~~p~~i~t~~~~~gi~~~~~e~~~  647 (1123)
T PRK11448        573 VSKYRRVLDYF-DAVKIGLTATPALHTT----EIFGEPVYTYSYREAVIDGYLIDHEPPIRIETRLSQEGIHFEKGEEVE  647 (1123)
T ss_pred             HHHHHHHHhhc-CccEEEEecCCccchh----HHhCCeeEEeeHHHHHhcCCcccCcCCEEEEEEeccccccccccchhh
Confidence            34455555544 5689999999985432    11221                0   11111111000000000      


Q ss_pred             --------E--EeecCC--------------cchHHHHHHHHHHhh--cCCCcEEEEecchhHHHHHHHHHHHc------
Q 037567          204 --------V--KVINRG--------------QSFVDELVQEILKSV--AGAGSIIVYCMTIKDVEEISKALKQL------  251 (374)
Q Consensus       204 --------~--~~~~~~--------------~~~~~~~~~~~~~~~--~~~~~~lVf~~~~~~~~~l~~~l~~~------  251 (374)
                              .  ......              ......++.++.+..  ...+|+||||.+..+|+.+++.|.+.      
T Consensus       648 ~~~~~~~~i~~~~l~d~~~~~~~~~~~~vi~~~~~~~i~~~l~~~l~~~~~~KtiIF~~s~~HA~~i~~~L~~~f~~~~~  727 (1123)
T PRK11448        648 VINTQTGEIDLATLEDEVDFEVEDFNRRVITESFNRVVCEELAKYLDPTGEGKTLIFAATDAHADMVVRLLKEAFKKKYG  727 (1123)
T ss_pred             hcchhhhhhhhccCcHHHhhhHHHHHHHHhhHHHHHHHHHHHHHHHhccCCCcEEEEEcCHHHHHHHHHHHHHHHHhhcC
Confidence                    0  000000              000011122232222  13479999999999999999887763      


Q ss_pred             CC---ceeeeecCCChHHHHHHHHhhhcCCe-eEEEEeccccccccccCccEEEEECCCCChhHHHHhhccCCCCCC
Q 037567          252 GV---KAGTYHGQMGSKAREEAHRLFIRDEI-RVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRDGI  324 (374)
Q Consensus       252 ~~---~~~~~~~~~~~~~r~~~~~~f~~g~~-~ilv~t~~~~~G~d~~~~~~vi~~~~p~s~~~~~Q~~GR~~R~~~  324 (374)
                      +.   .+..++|+.+  ++..++++|++++. .|+|+++++.+|+|+|.+.+|+++.++.|...|+||+||+.|...
T Consensus       728 ~~~~~~v~~itg~~~--~~~~li~~Fk~~~~p~IlVsvdmL~TG~DvP~v~~vVf~rpvkS~~lf~QmIGRgtR~~~  802 (1123)
T PRK11448        728 QVEDDAVIKITGSID--KPDQLIRRFKNERLPNIVVTVDLLTTGIDVPSICNLVFLRRVRSRILYEQMLGRATRLCP  802 (1123)
T ss_pred             CcCccceEEEeCCcc--chHHHHHHHhCCCCCeEEEEecccccCCCcccccEEEEecCCCCHHHHHHHHhhhccCCc
Confidence            12   3456888764  56789999999876 689999999999999999999999999999999999999999754

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

Probab=99.97  E-value=6.5e-29  Score=204.34  Aligned_cols=321  Identities=18%  Similarity=0.184  Sum_probs=217.4

Q ss_pred             CCchhHHHHHHHHHc----CCCEEEEccCCCCchhhh---hccccccCCcEEEEcchHHHHHHHHHHHHHc--CCceEEc
Q 037567           13 VFRPYQKDVIQRIIE----KRDCLVVMATGSGKSLCY---QLPPLVTGKTALVVSPLISLMQDQVMSLKQR--GINAEFL   83 (374)
Q Consensus        13 ~~~~~Q~~~~~~~~~----~~~~l~~a~tGsGKT~~~---~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~--~~~~~~~   83 (374)
                      +++|.|+.+.+++.+    .++.+++|-||+|||-..   +-.++.++.++.+.+|+.+.+.+.+..+++.  +..+..+
T Consensus        97 ~Ls~~Q~~as~~l~q~i~~k~~~lv~AV~GaGKTEMif~~i~~al~~G~~vciASPRvDVclEl~~Rlk~aF~~~~I~~L  176 (441)
T COG4098          97 TLSPGQKKASNQLVQYIKQKEDTLVWAVTGAGKTEMIFQGIEQALNQGGRVCIASPRVDVCLELYPRLKQAFSNCDIDLL  176 (441)
T ss_pred             ccChhHHHHHHHHHHHHHhcCcEEEEEecCCCchhhhHHHHHHHHhcCCeEEEecCcccchHHHHHHHHHhhccCCeeeE
Confidence            689999999887764    689999999999999543   2345668999999999999999999999864  3566666


Q ss_pred             CCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHHhcCCCC
Q 037567           84 GSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVP  163 (374)
Q Consensus        84 ~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~~~~~  163 (374)
                      +++......        ..++|+|..+|.++         ...++++||||+|.+.- ..+..   .....-........
T Consensus       177 yg~S~~~fr--------~plvVaTtHQLlrF---------k~aFD~liIDEVDAFP~-~~d~~---L~~Av~~ark~~g~  235 (441)
T COG4098         177 YGDSDSYFR--------APLVVATTHQLLRF---------KQAFDLLIIDEVDAFPF-SDDQS---LQYAVKKARKKEGA  235 (441)
T ss_pred             ecCCchhcc--------ccEEEEehHHHHHH---------HhhccEEEEeccccccc-cCCHH---HHHHHHHhhcccCc
Confidence            665444332        26888888877543         24568999999997642 11111   11222222334678


Q ss_pred             eeEEEeecCcccHHHHHHhcCCCCCeEEEecc-CCCceeEEEEeecCCcch-----H-HHHHHHHHHhhcCCCcEEEEec
Q 037567          164 FVALTATATEKVRIDIINSLKLKNPYVTIASF-DRKNLFYGVKVINRGQSF-----V-DELVQEILKSVAGAGSIIVYCM  236 (374)
Q Consensus       164 ~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~-----~-~~~~~~~~~~~~~~~~~lVf~~  236 (374)
                      .|++|||++.....++...-.  ......... ..+-....+.....-...     + ..+...+.+....+.+++||++
T Consensus       236 ~IylTATp~k~l~r~~~~g~~--~~~klp~RfH~~pLpvPkf~w~~~~~k~l~r~kl~~kl~~~lekq~~~~~P~liF~p  313 (441)
T COG4098         236 TIYLTATPTKKLERKILKGNL--RILKLPARFHGKPLPVPKFVWIGNWNKKLQRNKLPLKLKRWLEKQRKTGRPVLIFFP  313 (441)
T ss_pred             eEEEecCChHHHHHHhhhCCe--eEeecchhhcCCCCCCCceEEeccHHHHhhhccCCHHHHHHHHHHHhcCCcEEEEec
Confidence            999999999876544333110  000000111 111111111111111111     1 2334444444556789999999


Q ss_pred             chhHHHHHHHHHHHc--CCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEEEEECC--CCChhHH
Q 037567          237 TIKDVEEISKALKQL--GVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGC--PKTLESY  312 (374)
Q Consensus       237 ~~~~~~~l~~~l~~~--~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~~~~--p~s~~~~  312 (374)
                      +.+..++++..|++.  ...+..+|+.  +..|.+..+.|++|++++|++|.++++|+.+|++++.+.-.-  ..+...+
T Consensus       314 ~I~~~eq~a~~lk~~~~~~~i~~Vhs~--d~~R~EkV~~fR~G~~~lLiTTTILERGVTfp~vdV~Vlgaeh~vfTesaL  391 (441)
T COG4098         314 EIETMEQVAAALKKKLPKETIASVHSE--DQHRKEKVEAFRDGKITLLITTTILERGVTFPNVDVFVLGAEHRVFTESAL  391 (441)
T ss_pred             chHHHHHHHHHHHhhCCccceeeeecc--CccHHHHHHHHHcCceEEEEEeehhhcccccccceEEEecCCcccccHHHH
Confidence            999999999999653  2345778876  667888999999999999999999999999999999775432  3578999


Q ss_pred             HHhhccCCCCCC--ceEEEEEeeccCCCcccceeccccchHHHHHHHHHHHHHHHHhhhccc
Q 037567          313 YQESGRCGRDGI--ASVCWLYYARSNFAKGDFYCGESQTENQRTAIMESLLAAQRYCLLTTC  372 (374)
Q Consensus       313 ~Q~~GR~~R~~~--~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  372 (374)
                      +|..||+||.-.  .|.+.. +..             .....+....+++++|++..-+..|
T Consensus       392 VQIaGRvGRs~~~PtGdv~F-FH~-------------G~skaM~~A~keIk~MN~lg~k~~~  439 (441)
T COG4098         392 VQIAGRVGRSLERPTGDVLF-FHY-------------GKSKAMKQARKEIKEMNKLGFKRGL  439 (441)
T ss_pred             HHHhhhccCCCcCCCCcEEE-Eec-------------cchHHHHHHHHHHHHHHHHhhhccc
Confidence            999999999743  444433 332             3455677788899999988766554

>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional

Probab=99.97  E-value=7.7e-29  Score=239.45  Aligned_cols=307  Identities=17%  Similarity=0.145  Sum_probs=210.9

Q ss_pred             CCchhHHHHHHHHH----cCCCEEEEccCCCCchhhhhccc--cc----cCCcEEEEcchHHHHHHHHHHHHHcCCce--
Q 037567           13 VFRPYQKDVIQRII----EKRDCLVVMATGSGKSLCYQLPP--LV----TGKTALVVSPLISLMQDQVMSLKQRGINA--   80 (374)
Q Consensus        13 ~~~~~Q~~~~~~~~----~~~~~l~~a~tGsGKT~~~~l~~--~~----~~~~~lil~P~~~l~~q~~~~~~~~~~~~--   80 (374)
                      .++|||.+++..+.    .+.++|+...+|.|||+..+..+  +.    ...++|||||. ++..||.+++.++....  
T Consensus       169 ~Lr~YQleGlnWLi~l~~~g~gGILADEMGLGKTlQaIalL~~L~~~~~~~gp~LIVvP~-SlL~nW~~Ei~kw~p~l~v  247 (1033)
T PLN03142        169 KMRDYQLAGLNWLIRLYENGINGILADEMGLGKTLQTISLLGYLHEYRGITGPHMVVAPK-STLGNWMNEIRRFCPVLRA  247 (1033)
T ss_pred             chHHHHHHHHHHHHHHHhcCCCEEEEeCCCccHHHHHHHHHHHHHHhcCCCCCEEEEeCh-HHHHHHHHHHHHHCCCCce
Confidence            68999999998875    46788999999999997543322  21    24679999998 67888999999885433  


Q ss_pred             EEcCCCCCchhh--hhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHHh
Q 037567           81 EFLGSAQTDSSV--QTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTF  158 (374)
Q Consensus        81 ~~~~~~~~~~~~--~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~  158 (374)
                      ..+.+.......  ......+.++|+|+|++.+...    ...+...++++||+||+|.+.+..       .........
T Consensus       248 ~~~~G~~~eR~~~~~~~~~~~~~dVvITSYe~l~~e----~~~L~k~~W~~VIvDEAHrIKN~~-------Sklskalr~  316 (1033)
T PLN03142        248 VKFHGNPEERAHQREELLVAGKFDVCVTSFEMAIKE----KTALKRFSWRYIIIDEAHRIKNEN-------SLLSKTMRL  316 (1033)
T ss_pred             EEEeCCHHHHHHHHHHHhcccCCCcceecHHHHHHH----HHHhccCCCCEEEEcCccccCCHH-------HHHHHHHHH
Confidence            333332222111  1112345689999999986432    233344578999999999997644       223334444


Q ss_pred             cCCCCeeEEEeecCcccHHHHHHhcCCCCCeEEEec---------------------------------------cCCC-
Q 037567          159 LLGVPFVALTATATEKVRIDIINSLKLKNPYVTIAS---------------------------------------FDRK-  198 (374)
Q Consensus       159 ~~~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~---------------------------------------~~~~-  198 (374)
                      +.....+++||||..+...++...+.+..+......                                       ...+ 
T Consensus       317 L~a~~RLLLTGTPlqNnl~ELwsLL~FL~P~~f~s~~~F~~~f~~~~~~~~~e~i~~L~~~L~pf~LRR~KsdV~~~LPp  396 (1033)
T PLN03142        317 FSTNYRLLITGTPLQNNLHELWALLNFLLPEIFSSAETFDEWFQISGENDQQEVVQQLHKVLRPFLLRRLKSDVEKGLPP  396 (1033)
T ss_pred             hhcCcEEEEecCCCCCCHHHHHHHHhcCCCCcCCCHHHHHHHHccccccchHHHHHHHHHHhhHHHhhhhHHHHhhhCCC
Confidence            456678999999988766655554433222111000                                       0000 


Q ss_pred             ceeEEEEeecC------------------------------------------------------------CcchHHHHH
Q 037567          199 NLFYGVKVINR------------------------------------------------------------GQSFVDELV  218 (374)
Q Consensus       199 ~~~~~~~~~~~------------------------------------------------------------~~~~~~~~~  218 (374)
                      .....+.+...                                                            .......++
T Consensus       397 K~e~iv~v~LS~~Qk~lY~~ll~k~~~~l~~g~~~~~LlnilmqLRk~cnHP~L~~~~ep~~~~~~~e~lie~SgKl~lL  476 (1033)
T PLN03142        397 KKETILKVGMSQMQKQYYKALLQKDLDVVNAGGERKRLLNIAMQLRKCCNHPYLFQGAEPGPPYTTGEHLVENSGKMVLL  476 (1033)
T ss_pred             ceeEEEeeCCCHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHHHHHHhCCHHhhhcccccCcccchhHHhhhhhHHHHH
Confidence            00000000000                                                            000111222


Q ss_pred             HHHHHhh-cCCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcC---CeeEEEEeccccccccc
Q 037567          219 QEILKSV-AGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRD---EIRVMVATMAFGMGIDK  294 (374)
Q Consensus       219 ~~~~~~~-~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g---~~~ilv~t~~~~~G~d~  294 (374)
                      ..++..+ ..+.++|||+.....+..+.+.|...++....++|+++..+|+..++.|+..   ...+|++|.+.+.|+|+
T Consensus       477 dkLL~~Lk~~g~KVLIFSQft~~LdiLed~L~~~g~~y~rIdGsts~~eRq~~Id~Fn~~~s~~~VfLLSTrAGGlGINL  556 (1033)
T PLN03142        477 DKLLPKLKERDSRVLIFSQMTRLLDILEDYLMYRGYQYCRIDGNTGGEDRDASIDAFNKPGSEKFVFLLSTRAGGLGINL  556 (1033)
T ss_pred             HHHHHHHHhcCCeEEeehhHHHHHHHHHHHHHHcCCcEEEECCCCCHHHHHHHHHHhccccCCceEEEEeccccccCCch
Confidence            3333322 3467999999999999999999999999999999999999999999999863   34578899999999999


Q ss_pred             cCccEEEEECCCCChhHHHHhhccCCCCCCceEEEEE
Q 037567          295 PDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLY  331 (374)
Q Consensus       295 ~~~~~vi~~~~p~s~~~~~Q~~GR~~R~~~~g~~~~~  331 (374)
                      ..+++||+++++||+....|++||+.|.||...|.++
T Consensus       557 t~Ad~VIiyD~dWNP~~d~QAidRaHRIGQkk~V~Vy  593 (1033)
T PLN03142        557 ATADIVILYDSDWNPQVDLQAQDRAHRIGQKKEVQVF  593 (1033)
T ss_pred             hhCCEEEEeCCCCChHHHHHHHHHhhhcCCCceEEEE
Confidence            9999999999999999999999999999998766544

>KOG0947 consensus Cytoplasmic exosomal RNA helicase SKI2, DEAD-box superfamily [RNA processing and modification]

Probab=99.97  E-value=4.5e-29  Score=229.12  Aligned_cols=314  Identities=19%  Similarity=0.261  Sum_probs=222.2

Q ss_pred             ChhHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhcccc---ccCCcEEEEcchHHHHHHHHHHHHHcC
Q 037567            1 MVSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPL---VTGKTALVVSPLISLMQDQVMSLKQRG   77 (374)
Q Consensus         1 l~~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~---~~~~~~lil~P~~~l~~q~~~~~~~~~   77 (374)
                      +|......++|. +..+|.+|+-++.+|.++++.|+|.+|||+.+.-++.   .+.-++++.+|-++|-+|.+++|+..-
T Consensus       286 lVpe~a~~~pFe-lD~FQk~Ai~~lerg~SVFVAAHTSAGKTvVAEYAialaq~h~TR~iYTSPIKALSNQKfRDFk~tF  364 (1248)
T KOG0947|consen  286 LVPEMALIYPFE-LDTFQKEAIYHLERGDSVFVAAHTSAGKTVVAEYAIALAQKHMTRTIYTSPIKALSNQKFRDFKETF  364 (1248)
T ss_pred             hchhHHhhCCCC-ccHHHHHHHHHHHcCCeEEEEecCCCCcchHHHHHHHHHHhhccceEecchhhhhccchHHHHHHhc
Confidence            355666678995 9999999999999999999999999999987644332   257789999999999999999999764


Q ss_pred             CceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHH-
Q 037567           78 INAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLR-  156 (374)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~-  156 (374)
                      -.+.+++++.....        ....+|+|.|-|.+++++  +.-....++.||+||+|.+.+....     -.|.++. 
T Consensus       365 ~DvgLlTGDvqinP--------eAsCLIMTTEILRsMLYr--gadliRDvE~VIFDEVHYiND~eRG-----vVWEEViI  429 (1248)
T KOG0947|consen  365 GDVGLLTGDVQINP--------EASCLIMTTEILRSMLYR--GADLIRDVEFVIFDEVHYINDVERG-----VVWEEVII  429 (1248)
T ss_pred             cccceeecceeeCC--------CcceEeehHHHHHHHHhc--ccchhhccceEEEeeeeeccccccc-----ccceeeee
Confidence            55556666543322        236899999988887776  4445567899999999999764333     2233322 


Q ss_pred             HhcCCCCeeEEEeecCcccHHHHHHhcCCCCCe-EEEeccCCCceeEEEEeecC--------------------------
Q 037567          157 TFLLGVPFVALTATATEKVRIDIINSLKLKNPY-VTIASFDRKNLFYGVKVINR--------------------------  209 (374)
Q Consensus       157 ~~~~~~~~i~~SaT~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~--------------------------  209 (374)
                      -..++.++|++|||.++..  ++..|.|..... +.+.+.....+......+..                          
T Consensus       430 MlP~HV~~IlLSATVPN~~--EFA~WIGRtK~K~IyViST~kRPVPLEh~l~t~~~l~kiidq~g~fl~~~~~~a~~~~~  507 (1248)
T KOG0947|consen  430 MLPRHVNFILLSATVPNTL--EFADWIGRTKQKTIYVISTSKRPVPLEHYLYTKKSLFKIIDQNGIFLLKGIKDAKDSLK  507 (1248)
T ss_pred             eccccceEEEEeccCCChH--HHHHHhhhccCceEEEEecCCCccceEEEEEeccceehhhcccchhhhhcchhhhhhhc
Confidence            2334789999999999877  568887754322 22222211111111100000                          


Q ss_pred             ------------------------------C----------c---chHHHHHHHHHHhhcCCCcEEEEecchhHHHHHHH
Q 037567          210 ------------------------------G----------Q---SFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISK  246 (374)
Q Consensus       210 ------------------------------~----------~---~~~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~  246 (374)
                                                    .          .   ....+++..+.++  +--+++|||-+++.|+..++
T Consensus       508 ~~ak~~~~~~~~~~~~rgs~~~ggk~~~~~g~~r~~~~~~nrr~~~~~l~lin~L~k~--~lLP~VvFvFSkkrCde~a~  585 (1248)
T KOG0947|consen  508 KEAKFVDVEKSDARGGRGSQKRGGKTNYHNGGSRGSGIGKNRRKQPTWLDLINHLRKK--NLLPVVVFVFSKKRCDEYAD  585 (1248)
T ss_pred             ccccccccccccccccccccccCCcCCCCCCCcccccccccccccchHHHHHHHHhhc--ccCceEEEEEccccHHHHHH
Confidence                                          0          0   0123333333322  34579999999999999998


Q ss_pred             HHHHcC---------------------------------------CceeeeecCCChHHHHHHHHhhhcCCeeEEEEecc
Q 037567          247 ALKQLG---------------------------------------VKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMA  287 (374)
Q Consensus       247 ~l~~~~---------------------------------------~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~  287 (374)
                      .|....                                       -.++.+||++-+--++-+.-.|+.|-++||++|..
T Consensus       586 ~L~~~nL~~~~EKseV~lfl~k~~~rLk~~DR~LPQvl~m~~ll~RGiaVHH~GlLPivKE~VE~LFqrGlVKVLFATET  665 (1248)
T KOG0947|consen  586 YLTNLNLTDSKEKSEVHLFLSKAVARLKGEDRNLPQVLSMRSLLLRGIAVHHGGLLPIVKEVVELLFQRGLVKVLFATET  665 (1248)
T ss_pred             HHhccCcccchhHHHHHHHHHHHHHhcChhhccchHHHHHHHHHhhcchhhcccchHHHHHHHHHHHhcCceEEEeehhh
Confidence            885431                                       12467899999989999999999999999999999


Q ss_pred             ccccccccCccEEEEECCC---------CChhHHHHhhccCCCCCC--ceEEEEEeecc
Q 037567          288 FGMGIDKPDVRHVIHYGCP---------KTLESYYQESGRCGRDGI--ASVCWLYYARS  335 (374)
Q Consensus       288 ~~~G~d~~~~~~vi~~~~p---------~s~~~~~Q~~GR~~R~~~--~g~~~~~~~~~  335 (374)
                      ..+|+|.|.-.+|+ .+..         -.+.+|.||.|||||.|-  .|+++++....
T Consensus       666 FAMGVNMPARtvVF-~Sl~KhDG~efR~L~PGEytQMAGRAGRRGlD~tGTVii~~~~~  723 (1248)
T KOG0947|consen  666 FAMGVNMPARTVVF-SSLRKHDGNEFRELLPGEYTQMAGRAGRRGLDETGTVIIMCKDS  723 (1248)
T ss_pred             hhhhcCCCceeEEe-eehhhccCcceeecCChhHHhhhccccccccCcCceEEEEecCC
Confidence            99999999655554 4333         268999999999999885  57777766554

>PRK13104 secA preprotein translocase subunit SecA; Reviewed

Probab=99.96  E-value=2.1e-27  Score=223.07  Aligned_cols=322  Identities=17%  Similarity=0.142  Sum_probs=217.1

Q ss_pred             hHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc---cCCcEEEEcchHHHHHHHHHHHHHc---
Q 037567            3 STLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV---TGKTALVVSPLISLMQDQVMSLKQR---   76 (374)
Q Consensus         3 ~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~---~~~~~lil~P~~~l~~q~~~~~~~~---   76 (374)
                      ++-++.+|.. +++.|.-+--.+.+|+  +..++||+|||+++.+|++.   .+..++|++|++.||.|.++++..+   
T Consensus        73 Ea~~R~lg~~-~ydvQliGg~~Lh~G~--Iaem~TGeGKTL~a~Lpa~~~al~G~~V~VvTpn~yLA~qd~e~m~~l~~~  149 (896)
T PRK13104         73 EVSLRTLGLR-HFDVQLIGGMVLHEGN--IAEMRTGEGKTLVATLPAYLNAISGRGVHIVTVNDYLAKRDSQWMKPIYEF  149 (896)
T ss_pred             HHHHHHcCCC-cchHHHhhhhhhccCc--cccccCCCCchHHHHHHHHHHHhcCCCEEEEcCCHHHHHHHHHHHHHHhcc
Confidence            4556667764 6676666655555554  99999999999999988774   4678999999999999998888764   


Q ss_pred             -CCceEEcCCCCCchhhhhhhhcCCeeEEEEcCccc-ccCchhhH----HHHHhcCccEEEEeccchhh-cc--------
Q 037567           77 -GINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKA-CIIPISFW----SKLLKAGVCLFAVDEAHCIS-EW--------  141 (374)
Q Consensus        77 -~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l-~~~~~~~~----~~~~~~~~~~vviDE~h~~~-~~--------  141 (374)
                       |+.+.++.++.......   ....++|+++||+.| .++++...    .......+.++|+||+|.+. +.        
T Consensus       150 lGLtv~~i~gg~~~~~r~---~~y~~dIvygT~grlgfDyLrd~~~~~~~~~v~r~l~~~IvDEaDsiLIDeArtPLIIS  226 (896)
T PRK13104        150 LGLTVGVIYPDMSHKEKQ---EAYKADIVYGTNNEYGFDYLRDNMAFSLTDKVQRELNFAIVDEVDSILIDEARTPLIIS  226 (896)
T ss_pred             cCceEEEEeCCCCHHHHH---HHhCCCEEEECChhhhHHHHhcCCccchHhhhccccceEEeccHhhhhhhccCCceeee
Confidence             67777776654433322   223579999999998 55544321    11223578999999999985 11        


Q ss_pred             c--CcchHHHHHHHHHHHhcC---------------CCCeeEEEee----------------------------------
Q 037567          142 G--HDFRLEYKQLDKLRTFLL---------------GVPFVALTAT----------------------------------  170 (374)
Q Consensus       142 ~--~~~~~~~~~~~~~~~~~~---------------~~~~i~~SaT----------------------------------  170 (374)
                      |  ......+.....+...+.               ..+.+.+|..                                  
T Consensus       227 g~~~~~~~~y~~~~~~v~~l~~~~~~~~~~dy~idek~~~v~Lte~G~~~~e~~~~~~~il~~~~~l~~~~~~~~~~~i~  306 (896)
T PRK13104        227 GAAEDSSELYIKINSLIPQLKKQEEEGDEGDYTIDEKQKQAHLTDAGHLHIEELLTKAKLLDPGESLYHASNIMLMHHVN  306 (896)
T ss_pred             CCCccchHHHHHHHHHHHHHHhccccCCCCCEEEEcCCCceEEchHHHHHHHHHHHhCCccCCcccccCchhhhHHHHHH
Confidence            0  011111111111111110               1223434332                                  


Q ss_pred             --------------------------------------------------------------------------------
Q 037567          171 --------------------------------------------------------------------------------  170 (374)
Q Consensus       171 --------------------------------------------------------------------------------  170 (374)
                                                                                                      
T Consensus       307 ~aL~A~~lf~~d~dYiV~dg~V~iVDe~TGR~m~grr~s~GLHQaiEaKE~v~i~~e~~t~AsIT~Qn~Fr~Y~kLsGMT  386 (896)
T PRK13104        307 AALKAHAMFHRDIDYIVKDNQVVIVDEHTGRTMPGRRWSEGLHQAVEAKEGVPIQNENQTLASITFQNFFRMYNKLSGMT  386 (896)
T ss_pred             HHHHHHHHhcCCCceEEECCEEEEEECCCCCcCCCCCcChHHHHHHHHHcCCCCCCCceeeeeehHHHHHHhcchhccCC
Confidence                                                                                            


Q ss_pred             --cCcccHHHHHHhcCCCCCeEEEeccCCCcee--EEEEeecCCcchHHHHHHHHHHhhcCCCcEEEEecchhHHHHHHH
Q 037567          171 --ATEKVRIDIINSLKLKNPYVTIASFDRKNLF--YGVKVINRGQSFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISK  246 (374)
Q Consensus       171 --~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~  246 (374)
                        ..... .++...++   ..+...+.+.+...  ....++.........++.++.+....+.++||||+++..++.+++
T Consensus       387 GTa~te~-~Ef~~iY~---l~Vv~IPtnkp~~R~d~~d~v~~t~~~k~~av~~~i~~~~~~g~PVLVgt~Sie~sE~ls~  462 (896)
T PRK13104        387 GTADTEA-YEFQQIYN---LEVVVIPTNRSMIRKDEADLVYLTQADKFQAIIEDVRECGVRKQPVLVGTVSIEASEFLSQ  462 (896)
T ss_pred             CCChhHH-HHHHHHhC---CCEEECCCCCCcceecCCCeEEcCHHHHHHHHHHHHHHHHhCCCCEEEEeCcHHHHHHHHH
Confidence              11100 00111111   00111111111111  111123333455667788887777789999999999999999999


Q ss_pred             HHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCc-----------------------------
Q 037567          247 ALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDV-----------------------------  297 (374)
Q Consensus       247 ~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~-----------------------------  297 (374)
                      .|.+.|++...+|+++...+++.+.+.|+.|.  |+|||+++++|+|+.--                             
T Consensus       463 ~L~~~gi~h~vLnak~~q~Ea~iia~Ag~~G~--VtIATNmAGRGtDI~Lggn~~~~~~~~~~~~~~~~~~~~~~~~~~~  540 (896)
T PRK13104        463 LLKKENIKHQVLNAKFHEKEAQIIAEAGRPGA--VTIATNMAGRGTDIVLGGSLAADLANLPADASEQEKEAVKKEWQKR  540 (896)
T ss_pred             HHHHcCCCeEeecCCCChHHHHHHHhCCCCCc--EEEeccCccCCcceecCCchhhhhhccccchhhHHHHHHHHHhhhh
Confidence            99999999999999999999999999999994  99999999999998621                             


Q ss_pred             ---------cEEEEECCCCChhHHHHhhccCCCCCCceEEEEEeeccC
Q 037567          298 ---------RHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSN  336 (374)
Q Consensus       298 ---------~~vi~~~~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~  336 (374)
                               -+||....+.|..--.|..||+||.|.+|.+-.|++-+|
T Consensus       541 ~~~V~~~GGL~VIgTerhesrRID~QLrGRaGRQGDPGss~f~lSleD  588 (896)
T PRK13104        541 HDEVIAAGGLRIIGSERHESRRIDNQLRGRAGRQGDPGSSRFYLSLED  588 (896)
T ss_pred             hhHHHHcCCCEEEeeccCchHHHHHHhccccccCCCCCceEEEEEcCc
Confidence                     257778888888888999999999999999988888766

>PRK12904 preprotein translocase subunit SecA; Reviewed

Probab=99.96  E-value=2.1e-27  Score=222.81  Aligned_cols=323  Identities=21%  Similarity=0.195  Sum_probs=227.3

Q ss_pred             hhHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc---cCCcEEEEcchHHHHHHHHHHHHH---
Q 037567            2 VSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV---TGKTALVVSPLISLMQDQVMSLKQ---   75 (374)
Q Consensus         2 ~~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~---~~~~~lil~P~~~l~~q~~~~~~~---   75 (374)
                      .++.++.+|+. |++.|.-+.-.+.+|+  +..+.||+|||+++.+++..   .+..+-|++|+..||.|.++++..   
T Consensus        71 rEa~~R~lg~~-~~dvQlig~l~L~~G~--Iaem~TGeGKTLva~lpa~l~aL~G~~V~IvTpn~yLA~rd~e~~~~l~~  147 (830)
T PRK12904         71 REASKRVLGMR-HFDVQLIGGMVLHEGK--IAEMKTGEGKTLVATLPAYLNALTGKGVHVVTVNDYLAKRDAEWMGPLYE  147 (830)
T ss_pred             HHHHHHHhCCC-CCccHHHhhHHhcCCc--hhhhhcCCCcHHHHHHHHHHHHHcCCCEEEEecCHHHHHHHHHHHHHHHh
Confidence            45667778884 8888887777776664  99999999999999888752   467789999999999998888765   


Q ss_pred             -cCCceEEcCCCCCchhhhhhhhcCCeeEEEEcCccc-ccCchhhH----HHHHhcCccEEEEeccchhh-cc-------
Q 037567           76 -RGINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKA-CIIPISFW----SKLLKAGVCLFAVDEAHCIS-EW-------  141 (374)
Q Consensus        76 -~~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l-~~~~~~~~----~~~~~~~~~~vviDE~h~~~-~~-------  141 (374)
                       +|+.+.+..++.........   ..++|+++||..+ .++++...    .......+.++||||++.+. +.       
T Consensus       148 ~LGlsv~~i~~~~~~~er~~~---y~~dI~ygT~~elgfDyLrd~~~~~~~~~~~r~~~~aIvDEaDsiLIDeArtpLii  224 (830)
T PRK12904        148 FLGLSVGVILSGMSPEERREA---YAADITYGTNNEFGFDYLRDNMVFSLEERVQRGLNYAIVDEVDSILIDEARTPLII  224 (830)
T ss_pred             hcCCeEEEEcCCCCHHHHHHh---cCCCeEEECCcchhhhhhhcccccchhhhcccccceEEEechhhheeccCCCceee
Confidence             47888777765544433222   3479999999998 55554422    22345678899999999985 10       


Q ss_pred             -c--CcchHHHHHHHHHHHhc-----------------------------------------------------------
Q 037567          142 -G--HDFRLEYKQLDKLRTFL-----------------------------------------------------------  159 (374)
Q Consensus       142 -~--~~~~~~~~~~~~~~~~~-----------------------------------------------------------  159 (374)
                       |  ......+..+..+...+                                                           
T Consensus       225 Sg~~~~~~~~y~~~~~~v~~l~~~~dy~vde~~~~v~lte~G~~~~e~~~~~~~ly~~~~~~~~~~i~~AL~A~~l~~~d  304 (830)
T PRK12904        225 SGPAEDSSELYKRANKIVPTLEKEGDYTVDEKSRTVGLTEEGIEKAEKLLGIENLYDPENIALVHHLNQALRAHELFKRD  304 (830)
T ss_pred             ECCCCcccHHHHHHHHHHHhcCCCCCeEEEcCCCeeeECHHHHHHHHHHhCCccccChhhhHHHHHHHHHHHHHHHHhcC
Confidence             0  00000000000000000                                                           


Q ss_pred             -----------------------------------------------------------CCCCeeEEEeecCcccHHHHH
Q 037567          160 -----------------------------------------------------------LGVPFVALTATATEKVRIDII  180 (374)
Q Consensus       160 -----------------------------------------------------------~~~~~i~~SaT~~~~~~~~~~  180 (374)
                                                                                 .-.++.+||+|..... ..+.
T Consensus       305 ~dYiV~dg~V~ivDe~TGR~~~gr~ws~GLHQaiEaKE~v~i~~e~~t~a~It~qn~Fr~Y~kl~GmTGTa~te~-~E~~  383 (830)
T PRK12904        305 VDYIVKDGEVVIVDEFTGRLMPGRRYSDGLHQAIEAKEGVKIQNENQTLASITFQNYFRMYEKLAGMTGTADTEA-EEFR  383 (830)
T ss_pred             CcEEEECCEEEEEECCCCccCCCCccchHHHHHHHHhcCCCCCCCceeeeeeeHHHHHHhcchhcccCCCcHHHH-HHHH
Confidence                                                                       0013567777765432 2344


Q ss_pred             HhcCCCCCeEEEeccCCCceeEE--EEeecCCcchHHHHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHHcCCceeee
Q 037567          181 NSLKLKNPYVTIASFDRKNLFYG--VKVINRGQSFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTY  258 (374)
Q Consensus       181 ~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~  258 (374)
                      ..+++.   +...+.+.+.....  ..++.........++..+.+....+.++||||+++..++.+++.|.+.|++...+
T Consensus       384 ~iY~l~---vv~IPtnkp~~r~d~~d~i~~t~~~K~~aI~~~I~~~~~~grpVLIft~Si~~se~Ls~~L~~~gi~~~vL  460 (830)
T PRK12904        384 EIYNLD---VVVIPTNRPMIRIDHPDLIYKTEKEKFDAVVEDIKERHKKGQPVLVGTVSIEKSELLSKLLKKAGIPHNVL  460 (830)
T ss_pred             HHhCCC---EEEcCCCCCeeeeeCCCeEEECHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHCCCceEec
Confidence            444432   22222233332222  2233344445566666666655678899999999999999999999999999999


Q ss_pred             ecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCc--------------------------------------cEE
Q 037567          259 HGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDV--------------------------------------RHV  300 (374)
Q Consensus       259 ~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~--------------------------------------~~v  300 (374)
                      |+.  ..+|+..+..|..++..|+|||+++++|+|++--                                      -+|
T Consensus       461 nak--q~eREa~Iia~Ag~~g~VtIATNmAGRGtDI~LgGn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~GGLhV  538 (830)
T PRK12904        461 NAK--NHEREAEIIAQAGRPGAVTIATNMAGRGTDIKLGGNPEMLAAALLEEETEEQIAKIKAEWQEEHEEVLEAGGLHV  538 (830)
T ss_pred             cCc--hHHHHHHHHHhcCCCceEEEecccccCCcCccCCCchhhhhhhhhhhhhhHHHHHHHHHHhhhhhhHHHcCCCEE
Confidence            996  6789999999999999999999999999999643                                      257


Q ss_pred             EEECCCCChhHHHHhhccCCCCCCceEEEEEeeccC
Q 037567          301 IHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSN  336 (374)
Q Consensus       301 i~~~~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~  336 (374)
                      |....+.|..--.|..||+||.|.+|.+-.+++-+|
T Consensus       539 igTerhesrRid~QlrGRagRQGdpGss~f~lSleD  574 (830)
T PRK12904        539 IGTERHESRRIDNQLRGRSGRQGDPGSSRFYLSLED  574 (830)
T ss_pred             EecccCchHHHHHHhhcccccCCCCCceeEEEEcCc
Confidence            888888899999999999999999999988888776

>KOG0349 consensus Putative DEAD-box RNA helicase DDX1 [RNA processing and modification]

Probab=99.96  E-value=1.2e-28  Score=208.68  Aligned_cols=275  Identities=16%  Similarity=0.201  Sum_probs=186.9

Q ss_pred             CCcEEEEcchHHHHHHHHHHHHHcCCce-----E-EcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcC
Q 037567           53 GKTALVVSPLISLMQDQVMSLKQRGINA-----E-FLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAG  126 (374)
Q Consensus        53 ~~~~lil~P~~~l~~q~~~~~~~~~~~~-----~-~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~  126 (374)
                      .+.++|+-|+++|++|+...+++|....     . ++..+......+......+.+|+|+||+++......  ....+.+
T Consensus       286 ap~avivepsrelaEqt~N~i~~Fk~h~~np~~r~lLmiggv~~r~Q~~ql~~g~~ivvGtpgRl~~~is~--g~~~lt~  363 (725)
T KOG0349|consen  286 APEAVIVEPSRELAEQTHNQIEEFKMHTSNPEVRSLLMIGGVLKRTQCKQLKDGTHIVVGTPGRLLQPISK--GLVTLTH  363 (725)
T ss_pred             CcceeEecCcHHHHHHHHhhHHHHHhhcCChhhhhhhhhhhHHhHHHHHHhhcCceeeecCchhhhhhhhc--cceeeee
Confidence            3468999999999999998776653221     2 122222233334445566789999999999877655  5556678


Q ss_pred             ccEEEEeccchhhcccCcchHHHHHHHHHHHhcC-------CCCeeEEEeecCcccHHHHHHh-------cCCCCCe---
Q 037567          127 VCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLL-------GVPFVALTATATEKVRIDIINS-------LKLKNPY---  189 (374)
Q Consensus       127 ~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~i~~SaT~~~~~~~~~~~~-------~~~~~~~---  189 (374)
                      ++++|+||++.+...+..     ..+.++...++       ..+.+.+|||...-..+.+.+.       ..+....   
T Consensus       364 crFlvlDead~lL~qgy~-----d~I~r~h~qip~~tsdg~rlq~~vCsatlh~feVkk~~ervmhfptwVdLkgeD~vp  438 (725)
T KOG0349|consen  364 CRFLVLDEADLLLGQGYD-----DKIYRFHGQIPHMTSDGFRLQSPVCSATLHIFEVKKVGERVMHFPTWVDLKGEDLVP  438 (725)
T ss_pred             eEEEEecchhhhhhcccH-----HHHHHHhccchhhhcCCcccccceeeeEEeEEEeeehhhhhccCceeEecccccccc
Confidence            899999999999876654     34444433333       3578999999765332222211       1111100   


Q ss_pred             ---EEE-----eccCCCc--e--------------eEEEEeecCCcchHHHHHH-----HHHHhhcCCCcEEEEecchhH
Q 037567          190 ---VTI-----ASFDRKN--L--------------FYGVKVINRGQSFVDELVQ-----EILKSVAGAGSIIVYCMTIKD  240 (374)
Q Consensus       190 ---~~~-----~~~~~~~--~--------------~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~lVf~~~~~~  240 (374)
                         ...     ++.+...  +              ...-...+...+....++.     ..+++ ....++||||.++.+
T Consensus       439 etvHhvv~lv~p~~d~sw~~lr~~i~td~vh~kdn~~pg~~Spe~~s~a~kilkgEy~v~ai~~-h~mdkaiifcrtk~d  517 (725)
T KOG0349|consen  439 ETVHHVVKLVCPSVDGSWCDLRQFIETDKVHTKDNLLPGQVSPENPSSATKILKGEYGVVAIRR-HAMDKAIIFCRTKQD  517 (725)
T ss_pred             hhhccceeecCCccCccHHHHhhhhccCCcccccccccccCCCCChhhhhHHhcCchhhhhhhh-hccCceEEEEecccc
Confidence               000     0000000  0              0000000111111111111     11111 356789999999999


Q ss_pred             HHHHHHHHHHcC---CceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEEEEECCCCChhHHHHhhc
Q 037567          241 VEEISKALKQLG---VKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESG  317 (374)
Q Consensus       241 ~~~l~~~l~~~~---~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~~~~p~s~~~~~Q~~G  317 (374)
                      |+.+.+.+.++|   +.++.+||+..+.+|.+.++.|..++.+.||||+.+.+|+|+.++.++|++.+|....+|+||||
T Consensus       518 cDnLer~~~qkgg~~~scvclhgDrkP~Erk~nle~Fkk~dvkflictdvaargldi~g~p~~invtlpd~k~nyvhrig  597 (725)
T KOG0349|consen  518 CDNLERMMNQKGGKHYSCVCLHGDRKPDERKANLESFKKFDVKFLICTDVAARGLDITGLPFMINVTLPDDKTNYVHRIG  597 (725)
T ss_pred             chHHHHHHHHcCCccceeEEEecCCChhHHHHHHHhhhhcCeEEEEEehhhhccccccCCceEEEEecCcccchhhhhhh
Confidence            999999998864   57999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCCCceEEEEEeecc
Q 037567          318 RCGRDGIASVCWLYYARS  335 (374)
Q Consensus       318 R~~R~~~~g~~~~~~~~~  335 (374)
                      |+||.-..|.++.++...
T Consensus       598 rvgraermglaislvat~  615 (725)
T KOG0349|consen  598 RVGRAERMGLAISLVATV  615 (725)
T ss_pred             ccchhhhcceeEEEeecc
Confidence            999998888888877654

>KOG0948 consensus Nuclear exosomal RNA helicase MTR4, DEAD-box superfamily [RNA processing and modification]

Probab=99.96  E-value=5.7e-29  Score=223.21  Aligned_cols=320  Identities=20%  Similarity=0.244  Sum_probs=225.4

Q ss_pred             HcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccc---cccCCcEEEEcchHHHHHHHHHHHHHcCCceEEcC
Q 037567            8 YFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPP---LVTGKTALVVSPLISLMQDQVMSLKQRGINAEFLG   84 (374)
Q Consensus         8 ~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~---~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~   84 (374)
                      .|.|. +.|+|..++..+-++.++++.|.|.+|||.++.-++   +..+.+|++..|-++|-+|.++++..--..+++.+
T Consensus       125 ~YPF~-LDpFQ~~aI~Cidr~eSVLVSAHTSAGKTVVAeYAIA~sLr~kQRVIYTSPIKALSNQKYREl~~EF~DVGLMT  203 (1041)
T KOG0948|consen  125 TYPFT-LDPFQSTAIKCIDRGESVLVSAHTSAGKTVVAEYAIAMSLREKQRVIYTSPIKALSNQKYRELLEEFKDVGLMT  203 (1041)
T ss_pred             CCCcc-cCchHhhhhhhhcCCceEEEEeecCCCcchHHHHHHHHHHHhcCeEEeeChhhhhcchhHHHHHHHhcccceee
Confidence            36674 999999999999999999999999999997754433   44688999999999999999999886556666666


Q ss_pred             CCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHH-HHHhcCCCC
Q 037567           85 SAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDK-LRTFLLGVP  163 (374)
Q Consensus        85 ~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~-~~~~~~~~~  163 (374)
                      ++.+....        ..-+|+|.+-|..++.+  +.-....+..||+||+|.+.+.....     .|.+ +.-...+.+
T Consensus       204 GDVTInP~--------ASCLVMTTEILRsMLYR--GSEvmrEVaWVIFDEIHYMRDkERGV-----VWEETIIllP~~vr  268 (1041)
T KOG0948|consen  204 GDVTINPD--------ASCLVMTTEILRSMLYR--GSEVMREVAWVIFDEIHYMRDKERGV-----VWEETIILLPDNVR  268 (1041)
T ss_pred             cceeeCCC--------CceeeeHHHHHHHHHhc--cchHhheeeeEEeeeehhccccccce-----eeeeeEEeccccce
Confidence            65544322        24688999988777665  55556778899999999997643321     1222 222334789


Q ss_pred             eeEEEeecCcccHHHHHHh---cCCCCCeEEEeccCCCceeEEEE---------eecCC---------------------
Q 037567          164 FVALTATATEKVRIDIINS---LKLKNPYVTIASFDRKNLFYGVK---------VINRG---------------------  210 (374)
Q Consensus       164 ~i~~SaT~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~---------~~~~~---------------------  210 (374)
                      .+++|||.++...  +..|   +...+..+++.+.....+.....         +.+.+                     
T Consensus       269 ~VFLSATiPNA~q--FAeWI~~ihkQPcHVVYTdyRPTPLQHyifP~ggdGlylvVDek~~FrednF~~am~~l~~~~~~  346 (1041)
T KOG0948|consen  269 FVFLSATIPNARQ--FAEWICHIHKQPCHVVYTDYRPTPLQHYIFPAGGDGLYLVVDEKGKFREDNFQKAMSVLRKAGES  346 (1041)
T ss_pred             EEEEeccCCCHHH--HHHHHHHHhcCCceEEeecCCCCcceeeeecCCCCeeEEEEecccccchHHHHHHHHHhhccCCC
Confidence            9999999999764  3544   33445555554443222111110         00000                     


Q ss_pred             ---------------------cchHHHHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHHc------------------
Q 037567          211 ---------------------QSFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQL------------------  251 (374)
Q Consensus       211 ---------------------~~~~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~------------------  251 (374)
                                           ...+..++..+..+  +..++|||+-++++|+.++-.+.+.                  
T Consensus       347 ~~~~~~~~k~~kG~~~~~~~~~s~i~kiVkmi~~~--~~~PVIvFSFSkkeCE~~Alqm~kldfN~deEk~~V~~iF~nA  424 (1041)
T KOG0948|consen  347 DGKKKANKKGRKGGTGGKGPGDSDIYKIVKMIMER--NYLPVIVFSFSKKECEAYALQMSKLDFNTDEEKELVETIFNNA  424 (1041)
T ss_pred             ccccccccccccCCcCCCCCCcccHHHHHHHHHhh--cCCceEEEEecHhHHHHHHHhhccCcCCChhHHHHHHHHHHHH
Confidence                                 01223444444443  4578999999999999999766443                  


Q ss_pred             ---------------------CCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEEEEECCCC---
Q 037567          252 ---------------------GVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPK---  307 (374)
Q Consensus       252 ---------------------~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~~~~p~---  307 (374)
                                           .-.++.+||++-+--++.+.-.|++|-+++|+||...+.|+|.|.-++|+ .....   
T Consensus       425 i~~LseeDr~LPqie~iLPLL~RGIGIHHsGLLPIlKE~IEILFqEGLvKvLFATETFsiGLNMPAkTVvF-T~~rKfDG  503 (1041)
T KOG0948|consen  425 IDQLSEEDRELPQIENILPLLRRGIGIHHSGLLPILKEVIEILFQEGLVKVLFATETFSIGLNMPAKTVVF-TAVRKFDG  503 (1041)
T ss_pred             HHhcChhhccchHHHHHHHHHHhccccccccchHHHHHHHHHHHhccHHHHHHhhhhhhhccCCcceeEEE-eeccccCC
Confidence                                 11257899999988889999999999999999999999999999655554 33221   


Q ss_pred             ------ChhHHHHhhccCCCCCC--ceEEEEEeecc-CCCcccceecccc
Q 037567          308 ------TLESYYQESGRCGRDGI--ASVCWLYYARS-NFAKGDFYCGESQ  348 (374)
Q Consensus       308 ------s~~~~~Q~~GR~~R~~~--~g~~~~~~~~~-~~~~~~~~~~~~~  348 (374)
                            |.-+|+|+.|||||.|.  .|.|+++++.. +....+.+++...
T Consensus       504 ~~fRwissGEYIQMSGRAGRRG~DdrGivIlmiDekm~~~~ak~m~kG~a  553 (1041)
T KOG0948|consen  504 KKFRWISSGEYIQMSGRAGRRGIDDRGIVILMIDEKMEPQVAKDMLKGSA  553 (1041)
T ss_pred             cceeeecccceEEecccccccCCCCCceEEEEecCcCCHHHHHHHhcCCC
Confidence                  67899999999999985  68888887763 3444455554433

>PRK12906 secA preprotein translocase subunit SecA; Reviewed

Probab=99.96  E-value=1.2e-27  Score=223.45  Aligned_cols=323  Identities=19%  Similarity=0.180  Sum_probs=224.2

Q ss_pred             hhHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc---cCCcEEEEcchHHHHHHHHHHHHH---
Q 037567            2 VSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV---TGKTALVVSPLISLMQDQVMSLKQ---   75 (374)
Q Consensus         2 ~~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~---~~~~~lil~P~~~l~~q~~~~~~~---   75 (374)
                      .++.++.+|+. |++.|.-+.-.+.+|+  +..+.||+|||+++.+++..   .+..+-+++|+.-||.+.++++..   
T Consensus        70 rEa~~R~~g~~-~~dvQlig~l~l~~G~--iaEm~TGEGKTLvA~l~a~l~al~G~~v~vvT~neyLA~Rd~e~~~~~~~  146 (796)
T PRK12906         70 REGAKRVLGLR-PFDVQIIGGIVLHEGN--IAEMKTGEGKTLTATLPVYLNALTGKGVHVVTVNEYLSSRDATEMGELYR  146 (796)
T ss_pred             HHHHHHHhCCC-CchhHHHHHHHHhcCC--cccccCCCCCcHHHHHHHHHHHHcCCCeEEEeccHHHHHhhHHHHHHHHH
Confidence            46677888884 8888888777776666  99999999999988877654   688999999999999998877764   


Q ss_pred             -cCCceEEcCCCCCchhhhhhhhcCCeeEEEEcCccccc-Cchh----hHHHHHhcCccEEEEeccchhh-cc-------
Q 037567           76 -RGINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACI-IPIS----FWSKLLKAGVCLFAVDEAHCIS-EW-------  141 (374)
Q Consensus        76 -~~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~-~~~~----~~~~~~~~~~~~vviDE~h~~~-~~-------  141 (374)
                       +|+.+.+..+.......   .....++|+++|...+.. +++.    .........+.+.||||++.+. +.       
T Consensus       147 ~LGl~vg~i~~~~~~~~r---~~~y~~dI~Y~t~~e~gfDyLRD~m~~~~~~~v~r~~~~aIvDEvDSiLiDeartPLii  223 (796)
T PRK12906        147 WLGLTVGLNLNSMSPDEK---RAAYNCDITYSTNSELGFDYLRDNMVVYKEQMVQRPLNYAIVDEVDSILIDEARTPLII  223 (796)
T ss_pred             hcCCeEEEeCCCCCHHHH---HHHhcCCCeecCCccccccchhhccccchhhhhccCcceeeeccchheeeccCCCceec
Confidence             58888877665444332   223457999999987642 2221    1123334568899999999974 10       


Q ss_pred             ---cCcchHHHHHHHHHHHhcC--------------------C-------------------------------------
Q 037567          142 ---GHDFRLEYKQLDKLRTFLL--------------------G-------------------------------------  161 (374)
Q Consensus       142 ---~~~~~~~~~~~~~~~~~~~--------------------~-------------------------------------  161 (374)
                         .......+..+..+...+.                    .                                     
T Consensus       224 sg~~~~~~~~y~~~~~~v~~l~~~~~~~~~~~~~~~dy~id~~~k~v~lte~G~~~~e~~~~i~~l~~~~~~~~~~~i~~  303 (796)
T PRK12906        224 SGQAEKATDLYIRADRFVKTLIKDEAEDGDDDEDTGDYKIDEKTKTISLTEQGIRKAEKLFGLDNLYDSENTALAHHIDQ  303 (796)
T ss_pred             CCCCCcchHHHHHHHHHHHHHHhhhhccccccCCCCceEEEcccCceeecHHHHHHHHHHcCCccccCchhhhHHHHHHH
Confidence               0000001111100000000                    0                                     


Q ss_pred             ------------------------------------------------------------------------CCeeEEEe
Q 037567          162 ------------------------------------------------------------------------VPFVALTA  169 (374)
Q Consensus       162 ------------------------------------------------------------------------~~~i~~Sa  169 (374)
                                                                                              .++.+||+
T Consensus       304 Al~A~~l~~~d~dYiV~d~~V~ivD~~TGR~~~gr~ws~GLHQaieaKe~v~i~~e~~t~a~It~qnfFr~Y~kl~GmTG  383 (796)
T PRK12906        304 ALRANYIMLKDIDYVVQDGEVLIVDEFTGRVMEGRRYSDGLHQAIEAKEGVKIQEENQTLATITYQNFFRMYKKLSGMTG  383 (796)
T ss_pred             HHHHHHHHhcCCcEEEECCEEEEEeCCCCCcCCCCccChHHHHHHHHhcCCCcCCCceeeeeehHHHHHHhcchhhccCC
Confidence                                                                                    12445555


Q ss_pred             ecCcccHHHHHHhcCCCCCeEEEeccCCCceeEEE--EeecCCcchHHHHHHHHHHhhcCCCcEEEEecchhHHHHHHHH
Q 037567          170 TATEKVRIDIINSLKLKNPYVTIASFDRKNLFYGV--KVINRGQSFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKA  247 (374)
Q Consensus       170 T~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~  247 (374)
                      |..... ..+...+++.   +...+.+.+......  ..+.........++..+......+.++||||+++..++.+++.
T Consensus       384 Ta~~e~-~Ef~~iY~l~---vv~IPtnkp~~r~d~~d~i~~t~~~K~~al~~~i~~~~~~g~pvLI~t~si~~se~ls~~  459 (796)
T PRK12906        384 TAKTEE-EEFREIYNME---VITIPTNRPVIRKDSPDLLYPTLDSKFNAVVKEIKERHAKGQPVLVGTVAIESSERLSHL  459 (796)
T ss_pred             CCHHHH-HHHHHHhCCC---EEEcCCCCCeeeeeCCCeEEcCHHHHHHHHHHHHHHHHhCCCCEEEEeCcHHHHHHHHHH
Confidence            543221 2233333322   222222333322222  2233334455566666666666889999999999999999999


Q ss_pred             HHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEecccccccccc---Ccc-----EEEEECCCCChhHHHHhhccC
Q 037567          248 LKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKP---DVR-----HVIHYGCPKTLESYYQESGRC  319 (374)
Q Consensus       248 l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~---~~~-----~vi~~~~p~s~~~~~Q~~GR~  319 (374)
                      |.+.+++...+|+++...++..+...++.|.  |+|||+++++|+|++   ++.     +||++..|.|...+.|+.||+
T Consensus       460 L~~~gi~~~~Lna~~~~~Ea~ii~~ag~~g~--VtIATnmAGRGtDI~l~~~V~~~GGLhVI~te~pes~ri~~Ql~GRt  537 (796)
T PRK12906        460 LDEAGIPHAVLNAKNHAKEAEIIMNAGQRGA--VTIATNMAGRGTDIKLGPGVKELGGLAVIGTERHESRRIDNQLRGRS  537 (796)
T ss_pred             HHHCCCCeeEecCCcHHHHHHHHHhcCCCce--EEEEeccccCCCCCCCCcchhhhCCcEEEeeecCCcHHHHHHHhhhh
Confidence            9999999999999988888888877777775  999999999999995   788     999999999999999999999


Q ss_pred             CCCCCceEEEEEeeccC
Q 037567          320 GRDGIASVCWLYYARSN  336 (374)
Q Consensus       320 ~R~~~~g~~~~~~~~~~  336 (374)
                      ||.|.+|.+..+++.+|
T Consensus       538 GRqG~~G~s~~~~sleD  554 (796)
T PRK12906        538 GRQGDPGSSRFYLSLED  554 (796)
T ss_pred             ccCCCCcceEEEEeccc
Confidence            99999999999988875

>KOG0950 consensus DNA polymerase theta/eta, DEAD-box superfamily [General function prediction only]

Probab=99.95  E-value=4e-27  Score=217.47  Aligned_cols=334  Identities=22%  Similarity=0.257  Sum_probs=230.2

Q ss_pred             HhHcCCCCCchhHHHHH--HHHHcCCCEEEEccCCCCchhhhhccccc----cCCcEEEEcchHHHHHHHHHHHHHc---
Q 037567            6 KKYFGYSVFRPYQKDVI--QRIIEKRDCLVVMATGSGKSLCYQLPPLV----TGKTALVVSPLISLMQDQVMSLKQR---   76 (374)
Q Consensus         6 ~~~~~~~~~~~~Q~~~~--~~~~~~~~~l~~a~tGsGKT~~~~l~~~~----~~~~~lil~P~~~l~~q~~~~~~~~---   76 (374)
                      .+..|...++.||.+++  +++.++++.+..+||+.|||+++.+.++.    ..+.++.+.|..+.+.+....+..+   
T Consensus       216 ~~~kgi~~~fewq~ecls~~~~~e~~nliys~Pts~gktlvaeilml~~~l~~rr~~llilp~vsiv~Ek~~~l~~~~~~  295 (1008)
T KOG0950|consen  216 AKDKGILKLFEWQAECLSLPRLLERKNLIYSLPTSAGKTLVAEILMLREVLCRRRNVLLILPYVSIVQEKISALSPFSID  295 (1008)
T ss_pred             HHhhhHHHHHHHHHHHhcchhhhcccceEEeCCCccchHHHHHHHHHHHHHHHhhceeEecceeehhHHHHhhhhhhccc
Confidence            34468889999999998  57888999999999999999988776665    4788999999999988888888765   


Q ss_pred             -CCceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHH
Q 037567           77 -GINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKL  155 (374)
Q Consensus        77 -~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~  155 (374)
                       |+.+...++..+.....     ..-.+.|+|.|+-..+.++....-....+.+|||||.|.+.+.+.+.... ..+.++
T Consensus       296 ~G~~ve~y~g~~~p~~~~-----k~~sv~i~tiEkanslin~lie~g~~~~~g~vvVdElhmi~d~~rg~~lE-~~l~k~  369 (1008)
T KOG0950|consen  296 LGFPVEEYAGRFPPEKRR-----KRESVAIATIEKANSLINSLIEQGRLDFLGMVVVDELHMIGDKGRGAILE-LLLAKI  369 (1008)
T ss_pred             cCCcchhhcccCCCCCcc-----cceeeeeeehHhhHhHHHHHHhcCCccccCcEEEeeeeeeeccccchHHH-HHHHHH
Confidence             55555454433333322     22489999999998888887777777788999999999998876654333 222333


Q ss_pred             HHhcCC--CCeeEEEeecCcccHHHHHHhcCCCCCeEEEecc------CCCceeEEE-E---------eecC--CcchHH
Q 037567          156 RTFLLG--VPFVALTATATEKVRIDIINSLKLKNPYVTIASF------DRKNLFYGV-K---------VINR--GQSFVD  215 (374)
Q Consensus       156 ~~~~~~--~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~-~---------~~~~--~~~~~~  215 (374)
                      .-....  .++|+||||.++...  +..++...-+.....+.      ......+.. .         ....  ....-+
T Consensus       370 ~y~~~~~~~~iIGMSATi~N~~l--L~~~L~A~~y~t~fRPv~L~E~ik~G~~i~~~~r~~~lr~ia~l~~~~~g~~dpD  447 (1008)
T KOG0950|consen  370 LYENLETSVQIIGMSATIPNNSL--LQDWLDAFVYTTRFRPVPLKEYIKPGSLIYESSRNKVLREIANLYSSNLGDEDPD  447 (1008)
T ss_pred             HHhccccceeEeeeecccCChHH--HHHHhhhhheecccCcccchhccCCCcccccchhhHHHHHhhhhhhhhcccCCCc
Confidence            222222  569999999988653  23333311110000000      000000000 0         0000  000012


Q ss_pred             HHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHHc--------------------------------------CCceee
Q 037567          216 ELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQL--------------------------------------GVKAGT  257 (374)
Q Consensus       216 ~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~--------------------------------------~~~~~~  257 (374)
                      .++....+...++.++||||++++.|+.++..+...                                      ...+.+
T Consensus       448 ~~v~L~tet~~e~~~~lvfc~sk~~ce~~a~~~~~~vpk~~~~e~~~~~~~~~s~s~~lr~~~~~ld~Vl~~ti~~GvAy  527 (1008)
T KOG0950|consen  448 HLVGLCTETAPEGSSVLVFCPSKKNCENVASLIAKKVPKHIKSEKRLGLWELLSISNLLRRIPGILDPVLAKTIPYGVAY  527 (1008)
T ss_pred             ceeeehhhhhhcCCeEEEEcCcccchHHHHHHHHHHhhHhhhhhhhhhHHHHHHHHhHhhcCCcccchHHheecccccee
Confidence            223333344445667999999999999888554321                                      234678


Q ss_pred             eecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEEEEECC----CCChhHHHHhhccCCCCCC--ceEEEEE
Q 037567          258 YHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGC----PKTLESYYQESGRCGRDGI--ASVCWLY  331 (374)
Q Consensus       258 ~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~~~~----p~s~~~~~Q~~GR~~R~~~--~g~~~~~  331 (374)
                      +|++++.++|+.+...|++|...|+++|+.+..|+|+|..++++-...    ..+..+|.||+|||||.|-  .|.+++.
T Consensus       528 HhaGLT~eER~~iE~afr~g~i~vl~aTSTlaaGVNLPArRVIiraP~~g~~~l~~~~YkQM~GRAGR~gidT~GdsiLI  607 (1008)
T KOG0950|consen  528 HHAGLTSEEREIIEAAFREGNIFVLVATSTLAAGVNLPARRVIIRAPYVGREFLTRLEYKQMVGRAGRTGIDTLGDSILI  607 (1008)
T ss_pred             cccccccchHHHHHHHHHhcCeEEEEecchhhccCcCCcceeEEeCCccccchhhhhhHHhhhhhhhhcccccCcceEEE
Confidence            899999999999999999999999999999999999999888875432    3477999999999999975  5778999


Q ss_pred             eeccCCCcccceeccc
Q 037567          332 YARSNFAKGDFYCGES  347 (374)
Q Consensus       332 ~~~~~~~~~~~~~~~~  347 (374)
                      +...+......+....
T Consensus       608 ~k~~e~~~~~~lv~~~  623 (1008)
T KOG0950|consen  608 IKSSEKKRVRELVNSP  623 (1008)
T ss_pred             eeccchhHHHHHHhcc
Confidence            8888876555554433

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

Probab=99.95  E-value=1.9e-26  Score=219.12  Aligned_cols=309  Identities=20%  Similarity=0.251  Sum_probs=212.0

Q ss_pred             HHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhcc---ccccCCcEEEEcchHHHHHHHHHHHHHcCCce-
Q 037567            5 LKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLP---PLVTGKTALVVSPLISLMQDQVMSLKQRGINA-   80 (374)
Q Consensus         5 l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~---~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~-   80 (374)
                      +...+||+ |.++|.+++..+.++.+++++||||+|||.....+   ++..+.++++.+|.++|.+|.++++...-..+ 
T Consensus       112 ~~~~~~F~-LD~fQ~~a~~~Ler~esVlV~ApTssGKTvVaeyAi~~al~~~qrviYTsPIKALsNQKyrdl~~~fgdv~  190 (1041)
T COG4581         112 PAREYPFE-LDPFQQEAIAILERGESVLVCAPTSSGKTVVAEYAIALALRDGQRVIYTSPIKALSNQKYRDLLAKFGDVA  190 (1041)
T ss_pred             HHHhCCCC-cCHHHHHHHHHHhCCCcEEEEccCCCCcchHHHHHHHHHHHcCCceEeccchhhhhhhHHHHHHHHhhhhh
Confidence            44458895 99999999999999999999999999999775433   33467789999999999999999987543322 


Q ss_pred             ---EEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHH
Q 037567           81 ---EFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRT  157 (374)
Q Consensus        81 ---~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~  157 (374)
                         .+.+++..        ...+..++|+|.|-|..++..  .......+..||+||+|.+.+....     -.+.+..-
T Consensus       191 ~~vGL~TGDv~--------IN~~A~clvMTTEILRnMlyr--g~~~~~~i~~ViFDEvHyi~D~eRG-----~VWEE~Ii  255 (1041)
T COG4581         191 DMVGLMTGDVS--------INPDAPCLVMTTEILRNMLYR--GSESLRDIEWVVFDEVHYIGDRERG-----VVWEEVII  255 (1041)
T ss_pred             hhccceeccee--------eCCCCceEEeeHHHHHHHhcc--CcccccccceEEEEeeeeccccccc-----hhHHHHHH
Confidence               33333222        223347888888888777665  4455677899999999999875544     44555555


Q ss_pred             hcC-CCCeeEEEeecCcccHHHHHHhcCC---CCCeEEEeccCCCceeEEEE-------eecCCcch-------------
Q 037567          158 FLL-GVPFVALTATATEKVRIDIINSLKL---KNPYVTIASFDRKNLFYGVK-------VINRGQSF-------------  213 (374)
Q Consensus       158 ~~~-~~~~i~~SaT~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~-------------  213 (374)
                      .++ ..++|+||||.+++..  +..|+..   .+..++..+.....+...+.       ..+.....             
T Consensus       256 ~lP~~v~~v~LSATv~N~~E--F~~Wi~~~~~~~~~vv~t~~RpvPL~~~~~~~~~l~~lvde~~~~~~~~~~~a~~~l~  333 (1041)
T COG4581         256 LLPDHVRFVFLSATVPNAEE--FAEWIQRVHSQPIHVVSTEHRPVPLEHFVYVGKGLFDLVDEKKKFNAENFPSANRSLS  333 (1041)
T ss_pred             hcCCCCcEEEEeCCCCCHHH--HHHHHHhccCCCeEEEeecCCCCCeEEEEecCCceeeeecccccchhhcchhhhhhhh
Confidence            555 5699999999998774  4555542   22222222222111111110       00100000             


Q ss_pred             ---------------------------------HHHHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHHc---------
Q 037567          214 ---------------------------------VDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQL---------  251 (374)
Q Consensus       214 ---------------------------------~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~---------  251 (374)
                                                       ..++++.+..  .+.-++++|+-++..|+..+..+...         
T Consensus       334 ~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~iv~~l~~--~~~lP~I~F~FSr~~Ce~~a~~~~~ldl~~~~~~e  411 (1041)
T COG4581         334 CFSEKVRETDDGDVGRYARRTKALRGSAKGPAGRPEIVNKLDK--DNLLPAIVFSFSRRGCEEAAQILSTLDLVLTEEKE  411 (1041)
T ss_pred             ccchhccccCccccccccccccccCCcccccccchHHHhhhhh--hcCCceEEEEEchhhHHHHHHHhcccccccCCcHH
Confidence                                             0112222211  24457999999999998888666421         


Q ss_pred             -------------------CCc-------------eeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccE
Q 037567          252 -------------------GVK-------------AGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRH  299 (374)
Q Consensus       252 -------------------~~~-------------~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~  299 (374)
                                         +++             ++.+|+++=+..+..+...|+.|-++|+++|..++.|+|.|.-++
T Consensus       412 ~~i~~ii~~~i~~L~~ed~~lp~~~~~~~~~L~RGiavHH~GlLP~~K~~vE~Lfq~GLvkvvFaTeT~s~GiNmPartv  491 (1041)
T COG4581         412 RAIREIIDHAIGDLAEEDRELPLQILEISALLLRGIAVHHAGLLPAIKELVEELFQEGLVKVVFATETFAIGINMPARTV  491 (1041)
T ss_pred             HHHHHHHHHHHhhcChhhhcCcccHHHHHHHHhhhhhhhccccchHHHHHHHHHHhccceeEEeehhhhhhhcCCcccce
Confidence                               111             346899999999999999999999999999999999999996655


Q ss_pred             EEEECC---------CCChhHHHHhhccCCCCCCc--eEEEEEeec
Q 037567          300 VIHYGC---------PKTLESYYQESGRCGRDGIA--SVCWLYYAR  334 (374)
Q Consensus       300 vi~~~~---------p~s~~~~~Q~~GR~~R~~~~--g~~~~~~~~  334 (374)
                      |+ .+.         .-++.+|.|+.|||||.|.+  |.+++...+
T Consensus       492 v~-~~l~K~dG~~~r~L~~gEy~QmsGRAGRRGlD~~G~vI~~~~~  536 (1041)
T COG4581         492 VF-TSLSKFDGNGHRWLSPGEYTQMSGRAGRRGLDVLGTVIVIEPP  536 (1041)
T ss_pred             ee-eeeEEecCCceeecChhHHHHhhhhhccccccccceEEEecCC
Confidence            55 322         23789999999999999864  666665333

>KOG0922 consensus DEAH-box RNA helicase [RNA processing and modification]

Probab=99.95  E-value=3.6e-26  Score=204.27  Aligned_cols=327  Identities=17%  Similarity=0.216  Sum_probs=227.4

Q ss_pred             chhHHHHHHHHHcCCCEEEEccCCCCchhh---hhccc-cccCCcEEEEcchHHHHHHHHHHHHH-c----CCceEEcCC
Q 037567           15 RPYQKDVIQRIIEKRDCLVVMATGSGKSLC---YQLPP-LVTGKTALVVSPLISLMQDQVMSLKQ-R----GINAEFLGS   85 (374)
Q Consensus        15 ~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~---~~l~~-~~~~~~~lil~P~~~l~~q~~~~~~~-~----~~~~~~~~~   85 (374)
                      +.+-.+++..+.+++-+++.|+||||||.-   |+..+ .....++.+.-|+|-.+-.+++.+.. .    |..+.+.. 
T Consensus        53 ~~~r~~il~~ve~nqvlIviGeTGsGKSTQipQyL~eaG~~~~g~I~~TQPRRVAavslA~RVAeE~~~~lG~~VGY~I-  131 (674)
T KOG0922|consen   53 YKYRDQILYAVEDNQVLIVIGETGSGKSTQIPQYLAEAGFASSGKIACTQPRRVAAVSLAKRVAEEMGCQLGEEVGYTI-  131 (674)
T ss_pred             HHHHHHHHHHHHHCCEEEEEcCCCCCccccHhHHHHhcccccCCcEEeecCchHHHHHHHHHHHHHhCCCcCceeeeEE-
Confidence            345556777777788899999999999942   22211 23455588999999777766666542 2    33332211 


Q ss_pred             CCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHHhcCCCCee
Q 037567           86 AQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFV  165 (374)
Q Consensus        86 ~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~~~~~~i  165 (374)
                         .   ..........|.++|.+.|++   .....-.+..+++||+||||.   ........+..+.++....++.++|
T Consensus       132 ---R---Fed~ts~~TrikymTDG~LLR---E~l~Dp~LskYsvIIlDEAHE---Rsl~TDiLlGlLKki~~~R~~LklI  199 (674)
T KOG0922|consen  132 ---R---FEDSTSKDTRIKYMTDGMLLR---EILKDPLLSKYSVIILDEAHE---RSLHTDILLGLLKKILKKRPDLKLI  199 (674)
T ss_pred             ---E---ecccCCCceeEEEecchHHHH---HHhcCCccccccEEEEechhh---hhhHHHHHHHHHHHHHhcCCCceEE
Confidence               1   111112235799999997754   333444578899999999994   4455556667888888888889999


Q ss_pred             EEEeecCcccHHHHHHhcCCCCCeEEEeccCCCceeEEEEee-cCCcchHHHHHHH---HHHhhcCCCcEEEEecchhHH
Q 037567          166 ALTATATEKVRIDIINSLKLKNPYVTIASFDRKNLFYGVKVI-NRGQSFVDELVQE---ILKSVAGAGSIIVYCMTIKDV  241 (374)
Q Consensus       166 ~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~---~~~~~~~~~~~lVf~~~~~~~  241 (374)
                      .||||...+..   ...++. -+.+..+.-.   ....+.+. ....+.+.+.+..   +... .+.+.+|||....++.
T Consensus       200 imSATlda~kf---S~yF~~-a~i~~i~GR~---fPVei~y~~~p~~dYv~a~~~tv~~Ih~~-E~~GDILvFLtGqeEI  271 (674)
T KOG0922|consen  200 IMSATLDAEKF---SEYFNN-APILTIPGRT---FPVEILYLKEPTADYVDAALITVIQIHLT-EPPGDILVFLTGQEEI  271 (674)
T ss_pred             EEeeeecHHHH---HHHhcC-CceEeecCCC---CceeEEeccCCchhhHHHHHHHHHHHHcc-CCCCCEEEEeCCHHHH
Confidence            99999986543   333322 2222222211   11111111 2223333333333   3333 5778999999999999


Q ss_pred             HHHHHHHHHc----CC----ceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEEEEECC--------
Q 037567          242 EEISKALKQL----GV----KAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGC--------  305 (374)
Q Consensus       242 ~~l~~~l~~~----~~----~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~~~~--------  305 (374)
                      +.+++.|.+.    +.    -+.++||.++.++..++...--.|..+|+++|+++++++.+|++..||+.+.        
T Consensus       272 e~~~~~l~e~~~~~~~~~~~~~lply~aL~~e~Q~rvF~p~p~g~RKvIlsTNIAETSlTI~GI~YVVDsG~vK~~~y~p  351 (674)
T KOG0922|consen  272 EAACELLRERAKSLPEDCPELILPLYGALPSEEQSRVFDPAPPGKRKVILSTNIAETSLTIDGIRYVVDSGFVKQKKYNP  351 (674)
T ss_pred             HHHHHHHHHHhhhccccCcceeeeecccCCHHHhhccccCCCCCcceEEEEcceeeeeEEecceEEEEcCCceEEEeecc
Confidence            9999999875    11    2468999999999999988888899999999999999999999999996654        


Q ss_pred             ----------CCChhHHHHhhccCCCCCCceEEEEEeeccCCCcccceeccccchHHHHHHHHHHHHHHHH
Q 037567          306 ----------PKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFYCGESQTENQRTAIMESLLAAQRY  366 (374)
Q Consensus       306 ----------p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  366 (374)
                                |-|...-.||.|||||.+ +|.||-+|+++++   +++-....++.++-.+-.-+.+|.+.
T Consensus       352 ~~g~~~L~v~~ISkasA~QRaGRAGRt~-pGkcyRLYte~~~---~~~~~~~~PEI~R~~Ls~~vL~Lkal  418 (674)
T KOG0922|consen  352 RTGLDSLIVVPISKASANQRAGRAGRTG-PGKCYRLYTESAY---DKMPLQTVPEIQRVNLSSAVLQLKAL  418 (674)
T ss_pred             ccCccceeEEechHHHHhhhcccCCCCC-CceEEEeeeHHHH---hhcccCCCCceeeechHHHHHHHHhc
Confidence                      337888999999999986 8999999999888   66667778888877776666666554

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

Probab=99.95  E-value=3.2e-26  Score=217.48  Aligned_cols=298  Identities=16%  Similarity=0.125  Sum_probs=181.0

Q ss_pred             CchhHHHHHHHHHc----------CCCEEEEccCCCCchhhhhcccc-----ccCCcEEEEcchHHHHHHHHHHHHHcCC
Q 037567           14 FRPYQKDVIQRIIE----------KRDCLVVMATGSGKSLCYQLPPL-----VTGKTALVVSPLISLMQDQVMSLKQRGI   78 (374)
Q Consensus        14 ~~~~Q~~~~~~~~~----------~~~~l~~a~tGsGKT~~~~l~~~-----~~~~~~lil~P~~~l~~q~~~~~~~~~~   78 (374)
                      ++++|..|+..+..          .+..++++|||||||++++..+.     ...+++|+++|+.+|..|+.+.+..++.
T Consensus       239 ~r~~Q~~av~~~~~~~~~~~~~~~~~~gli~~~TGsGKT~t~~~la~~l~~~~~~~~vl~lvdR~~L~~Q~~~~f~~~~~  318 (667)
T TIGR00348       239 QRYMQYRAVKKIVESITRKTWGKDERGGLIWHTQGSGKTLTMLFAARKALELLKNPKVFFVVDRRELDYQLMKEFQSLQK  318 (667)
T ss_pred             hHHHHHHHHHHHHHHHHhcccCCCCceeEEEEecCCCccHHHHHHHHHHHhhcCCCeEEEEECcHHHHHHHHHHHHhhCC
Confidence            78899999987643          24789999999999987654432     2467899999999999999999999865


Q ss_pred             ceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCc-cEEEEeccchhhcccCcchHHHHHHHHHHH
Q 037567           79 NAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGV-CLFAVDEAHCISEWGHDFRLEYKQLDKLRT  157 (374)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~-~~vviDE~h~~~~~~~~~~~~~~~~~~~~~  157 (374)
                      ....  ...+..............|+|+|.+++................ .+||+||||+... +       .....+..
T Consensus       319 ~~~~--~~~s~~~L~~~l~~~~~~iivtTiQk~~~~~~~~~~~~~~~~~~~lvIvDEaHrs~~-~-------~~~~~l~~  388 (667)
T TIGR00348       319 DCAE--RIESIAELKRLLEKDDGGIIITTIQKFDKKLKEEEEKFPVDRKEVVVIFDEAHRSQY-G-------ELAKNLKK  388 (667)
T ss_pred             CCCc--ccCCHHHHHHHHhCCCCCEEEEEhHHhhhhHhhhhhccCCCCCCEEEEEEcCccccc-h-------HHHHHHHh
Confidence            3111  1111111112222334689999999986532221111111111 2899999998532 1       12233445


Q ss_pred             hcCCCCeeEEEeecCcccHHHHHHhcCCC-CCeEEEecc---CCCceeEEEEeec--------C----------------
Q 037567          158 FLLGVPFVALTATATEKVRIDIINSLKLK-NPYVTIASF---DRKNLFYGVKVIN--------R----------------  209 (374)
Q Consensus       158 ~~~~~~~i~~SaT~~~~~~~~~~~~~~~~-~~~~~~~~~---~~~~~~~~~~~~~--------~----------------  209 (374)
                      .+++..+++|||||...........++.. ...+...+.   ........+....        .                
T Consensus       389 ~~p~a~~lGfTaTP~~~~d~~t~~~f~~~fg~~i~~Y~~~~AI~dG~~~~i~Y~~~~~~~~~~~~~l~~~~~~~~~~~~~  468 (667)
T TIGR00348       389 ALKNASFFGFTGTPIFKKDRDTSLTFAYVFGRYLHRYFITDAIRDGLTVKIDYEDRLPEDHLDRKKLDAFFDEIFELLPE  468 (667)
T ss_pred             hCCCCcEEEEeCCCcccccccccccccCCCCCeEEEeeHHHHhhcCCeeeEEEEecchhhccChHHHHHHHHHHHHhhhc
Confidence            67789999999999754221112222210 011111000   0000000000000        0                


Q ss_pred             ----------------------CcchHHHHHHHHHHhh----c-CCCcEEEEecchhHHHHHHHHHHHc-----CCceee
Q 037567          210 ----------------------GQSFVDELVQEILKSV----A-GAGSIIVYCMTIKDVEEISKALKQL-----GVKAGT  257 (374)
Q Consensus       210 ----------------------~~~~~~~~~~~~~~~~----~-~~~~~lVf~~~~~~~~~l~~~l~~~-----~~~~~~  257 (374)
                                            ..........++.++.    . .+++++|+|.++..|..+++.|.+.     +.....
T Consensus       469 ~~~~~~~~~l~~~~~~~~~~~~~~~~~~~ia~~i~~h~~~~~~~~~~kamvv~~sr~~a~~~~~~l~~~~~~~~~~~~vv  548 (667)
T TIGR00348       469 RIREITKESLKEKLQKTKKILFNEDRLESIAKDIAEHYAKFKELFKFKAMVVAISRYACVEEKNALDEELNEKFEASAIV  548 (667)
T ss_pred             cccHHHHHHHHHHHHHHHhhhcChHHHHHHHHHHHHHHHHhhhcccCceeEEEecHHHHHHHHHHHHhhcccccCCeeEE
Confidence                                  0001112222222221    1 2589999999999999999998764     233444


Q ss_pred             eecCCChH---------------------HHHHHHHhhhc-CCeeEEEEeccccccccccCccEEEEECCCCChhHHHHh
Q 037567          258 YHGQMGSK---------------------AREEAHRLFIR-DEIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQE  315 (374)
Q Consensus       258 ~~~~~~~~---------------------~r~~~~~~f~~-g~~~ilv~t~~~~~G~d~~~~~~vi~~~~p~s~~~~~Q~  315 (374)
                      +++..+.+                     ....++++|.+ +..+|+|+++++.+|+|.|.+.+++...+..+ ..++|+
T Consensus       549 ~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Fk~~~~~~ilIVvdmllTGFDaP~l~tLyldKplk~-h~LlQa  627 (667)
T TIGR00348       549 MTGKESDDAEIRDYNKHIRTKFDKSDGFEIYYKDLERFKKEENPKLLIVVDMLLTGFDAPILNTLYLDKPLKY-HGLLQA  627 (667)
T ss_pred             ecCCccchhHHHHHHHHhccccccchhhhHHHHHHHHhcCCCCceEEEEEcccccccCCCccceEEEeccccc-cHHHHH
Confidence            55443322                     12467888876 57899999999999999999999997776665 458999


Q ss_pred             hccCCCC
Q 037567          316 SGRCGRD  322 (374)
Q Consensus       316 ~GR~~R~  322 (374)
                      +||+.|.
T Consensus       628 i~R~nR~  634 (667)
T TIGR00348       628 IARTNRI  634 (667)
T ss_pred             HHHhccc
Confidence            9999994

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

>COG1643 HrpA HrpA-like helicases [DNA replication, recombination, and repair]

Probab=99.94  E-value=9.4e-26  Score=213.00  Aligned_cols=336  Identities=16%  Similarity=0.155  Sum_probs=231.9

Q ss_pred             CchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc----cCCcEEEEcchHHHHHHHHHHHHH-cCCceEEcCCCCC
Q 037567           14 FRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV----TGKTALVVSPLISLMQDQVMSLKQ-RGINAEFLGSAQT   88 (374)
Q Consensus        14 ~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~----~~~~~lil~P~~~l~~q~~~~~~~-~~~~~~~~~~~~~   88 (374)
                      .+....+.+.++.++..+++.|+||||||.-.-..++.    ...++.+.-|+|--+..+...+.. +|.+..-..+...
T Consensus        51 v~~~~~~i~~ai~~~~vvii~getGsGKTTqlP~~lle~g~~~~g~I~~tQPRRlAArsvA~RvAeel~~~~G~~VGY~i  130 (845)
T COG1643          51 VTAVRDEILKAIEQNQVVIIVGETGSGKTTQLPQFLLEEGLGIAGKIGCTQPRRLAARSVAERVAEELGEKLGETVGYSI  130 (845)
T ss_pred             cHHHHHHHHHHHHhCCEEEEeCCCCCChHHHHHHHHHhhhcccCCeEEecCchHHHHHHHHHHHHHHhCCCcCceeeEEE
Confidence            34456677777878889999999999999642222222    356889999999777777776653 3333221111111


Q ss_pred             chhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHHhcC-CCCeeEE
Q 037567           89 DSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLL-GVPFVAL  167 (374)
Q Consensus        89 ~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~~-~~~~i~~  167 (374)
                      .   ..........|-++|.+.|...+.   ....++.+++||+||+|+   .+.+....+..+..+....+ +.++|.|
T Consensus       131 R---fe~~~s~~Trik~mTdGiLlrei~---~D~~Ls~ys~vIiDEaHE---RSl~tDilLgllk~~~~~rr~DLKiIim  201 (845)
T COG1643         131 R---FESKVSPRTRIKVMTDGILLREIQ---NDPLLSGYSVVIIDEAHE---RSLNTDILLGLLKDLLARRRDDLKLIIM  201 (845)
T ss_pred             E---eeccCCCCceeEEeccHHHHHHHh---hCcccccCCEEEEcchhh---hhHHHHHHHHHHHHHHhhcCCCceEEEE
Confidence            1   112223345799999998865443   344578999999999995   44555566677777666666 6999999


Q ss_pred             EeecCcccHHHHHHhcCCCCCeEEEeccCCCceeEEEEeecCCcchHHHHHHHHHHh--hcCCCcEEEEecchhHHHHHH
Q 037567          168 TATATEKVRIDIINSLKLKNPYVTIASFDRKNLFYGVKVINRGQSFVDELVQEILKS--VAGAGSIIVYCMTIKDVEEIS  245 (374)
Q Consensus       168 SaT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~lVf~~~~~~~~~l~  245 (374)
                      |||......   ...++. -+.+...... -.+...+......+..+.+.+...+..  ....|.+|||.+...+.+..+
T Consensus       202 SATld~~rf---s~~f~~-apvi~i~GR~-fPVei~Y~~~~~~d~~l~~ai~~~v~~~~~~~~GdILvFLpG~~EI~~~~  276 (845)
T COG1643         202 SATLDAERF---SAYFGN-APVIEIEGRT-YPVEIRYLPEAEADYILLDAIVAAVDIHLREGSGSILVFLPGQREIERTA  276 (845)
T ss_pred             ecccCHHHH---HHHcCC-CCEEEecCCc-cceEEEecCCCCcchhHHHHHHHHHHHhccCCCCCEEEECCcHHHHHHHH
Confidence            999987643   444432 2222222111 111111101111111133333333222  135789999999999999999


Q ss_pred             HHHHH----cCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEEEEECCC---------------
Q 037567          246 KALKQ----LGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCP---------------  306 (374)
Q Consensus       246 ~~l~~----~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~~~~p---------------  306 (374)
                      +.|.+    ....+.++||.++.++..++++.-..|+.+|+++|+++++++.+|+++.||+.+.-               
T Consensus       277 ~~L~~~~l~~~~~i~PLy~~L~~~eQ~rvF~p~~~~~RKVVlATNIAETSLTI~gIr~VIDsG~ak~~~y~~~~g~~~L~  356 (845)
T COG1643         277 EWLEKAELGDDLEILPLYGALSAEEQVRVFEPAPGGKRKVVLATNIAETSLTIPGIRYVIDSGLAKEKRYDPRTGLTRLE  356 (845)
T ss_pred             HHHHhccccCCcEEeeccccCCHHHHHhhcCCCCCCcceEEEEccccccceeeCCeEEEecCCcccccccccccCceeee
Confidence            99998    34678899999999999998888878877899999999999999999999976643               


Q ss_pred             ---CChhHHHHhhccCCCCCCceEEEEEeeccCCCcccceeccccchHHHHHHHHHHHHHHHHh
Q 037567          307 ---KTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFYCGESQTENQRTAIMESLLAAQRYC  367 (374)
Q Consensus       307 ---~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  367 (374)
                         -|-.+..||.|||||.+ +|.||-+|+.+++.   .+.....++..+..+..-..+|..+.
T Consensus       357 ~~~ISqAsA~QRaGRAGR~~-pGicyRLyse~~~~---~~~~~t~PEIlrtdLs~~vL~l~~~G  416 (845)
T COG1643         357 TEPISKASADQRAGRAGRTG-PGICYRLYSEEDFL---AFPEFTLPEILRTDLSGLVLQLKSLG  416 (845)
T ss_pred             EEEechhhhhhhccccccCC-CceEEEecCHHHHH---hcccCCChhhhhcchHHHHHHHHhcC
Confidence               37788999999999985 89999999997765   66777788888877777777776654

>COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms]

Probab=99.94  E-value=1.1e-25  Score=216.01  Aligned_cols=325  Identities=21%  Similarity=0.217  Sum_probs=206.5

Q ss_pred             CchhHHHHHHHHHc---CC-CEEEEccCCCCchhhhhccccc-------cCCcEEEEcchHHHHHHHHHHHHHcCCceEE
Q 037567           14 FRPYQKDVIQRIIE---KR-DCLVVMATGSGKSLCYQLPPLV-------TGKTALVVSPLISLMQDQVMSLKQRGINAEF   82 (374)
Q Consensus        14 ~~~~Q~~~~~~~~~---~~-~~l~~a~tGsGKT~~~~l~~~~-------~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~   82 (374)
                      .++.|..++..+.+   .. .+++.||||+|||.+.+..+..       ...+++++.|+++++++..+.+..+......
T Consensus       196 ~~~~~~~~~~~~~~~~~~~~~~vl~aPTG~GKT~asl~~a~~~~~~~~~~~~r~i~vlP~~t~ie~~~~r~~~~~~~~~~  275 (733)
T COG1203         196 GYELQEKALELILRLEKRSLLVVLEAPTGYGKTEASLILALALLDEKIKLKSRVIYVLPFRTIIEDMYRRAKEIFGLFSV  275 (733)
T ss_pred             hhHHHHHHHHHHHhcccccccEEEEeCCCCChHHHHHHHHHHHhhccccccceEEEEccHHHHHHHHHHHHHhhhccccc
Confidence            47889999988775   34 6789999999999876655432       3678999999999999999999875322222


Q ss_pred             cC----CCCCchhhhhh-------------hhcCCeeEEEEcCcccccCch--hhHHHHHhcCccEEEEeccchhhcccC
Q 037567           83 LG----SAQTDSSVQTK-------------AETGYFQLLFMTPEKACIIPI--SFWSKLLKAGVCLFAVDEAHCISEWGH  143 (374)
Q Consensus        83 ~~----~~~~~~~~~~~-------------~~~~~~~i~i~T~~~l~~~~~--~~~~~~~~~~~~~vviDE~h~~~~~~~  143 (374)
                      ..    +..........             .......+.++||.+......  ..+.....-..+.+|+||+|.+.+.. 
T Consensus       276 ~~~~~h~~~~~~~~~~~~~~~~~~~~~~ds~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~S~vIlDE~h~~~~~~-  354 (733)
T COG1203         276 IGKSLHSSSKEPLLLEPDQDILLTLTTNDSYKKLLLALIVVTPIQILIFSVKGFKFEFLALLLTSLVILDEVHLYADET-  354 (733)
T ss_pred             ccccccccccchhhhccccccceeEEecccccceeccccccCHhHhhhhhccccchHHHHHHHhhchhhccHHhhcccc-
Confidence            11    11111100000             001112334444444333100  00011222345689999999987643 


Q ss_pred             cchHHHHHHHHHHHhcCCCCeeEEEeecCcccHHHHHHhcCCCCCeEEEec----cCCCceeEEEEeecCCcchHHHHHH
Q 037567          144 DFRLEYKQLDKLRTFLLGVPFVALTATATEKVRIDIINSLKLKNPYVTIAS----FDRKNLFYGVKVINRGQSFVDELVQ  219 (374)
Q Consensus       144 ~~~~~~~~~~~~~~~~~~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~  219 (374)
                       ....+..+...... .+.++++||||+++.....+....+..........    .+................ ......
T Consensus       355 -~~~~l~~~i~~l~~-~g~~ill~SATlP~~~~~~l~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~-~~~~~~  431 (733)
T COG1203         355 -MLAALLALLEALAE-AGVPVLLMSATLPPFLKEKLKKALGKGREVVENAKFCPKEDEPGLKRKERVDVEDGP-QEELIE  431 (733)
T ss_pred             -hHHHHHHHHHHHHh-CCCCEEEEecCCCHHHHHHHHHHHhcccceeccccccccccccccccccchhhhhhh-hHhhhh
Confidence             22222222222222 27899999999999887655555543333222211    011111111000000000 013344


Q ss_pred             HHHHhhcCCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhh----cCCeeEEEEecccccccccc
Q 037567          220 EILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFI----RDEIRVMVATMAFGMGIDKP  295 (374)
Q Consensus       220 ~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~----~g~~~ilv~t~~~~~G~d~~  295 (374)
                      ........+++++|.|||+..|.++++.|+..+.++..+||.+...+|.+.++.+.    .+...|+|+|+.++.|+|+ 
T Consensus       432 ~~~~~~~~~~kvlvI~NTV~~Aie~Y~~Lk~~~~~v~LlHSRf~~~dR~~ke~~l~~~~~~~~~~IvVaTQVIEagvDi-  510 (733)
T COG1203         432 LISEEVKEGKKVLVIVNTVDRAIELYEKLKEKGPKVLLLHSRFTLKDREEKERELKKLFKQNEGFIVVATQVIEAGVDI-  510 (733)
T ss_pred             cchhhhccCCcEEEEEecHHHHHHHHHHHHhcCCCEEEEecccchhhHHHHHHHHHHHHhccCCeEEEEeeEEEEEecc-
Confidence            45556678899999999999999999999998778999999999999998877544    4677899999999999999 


Q ss_pred             CccEEEEECCCCChhHHHHhhccCCCCC--CceEEEEEeeccCCCcccceec
Q 037567          296 DVRHVIHYGCPKTLESYYQESGRCGRDG--IASVCWLYYARSNFAKGDFYCG  345 (374)
Q Consensus       296 ~~~~vi~~~~p~s~~~~~Q~~GR~~R~~--~~g~~~~~~~~~~~~~~~~~~~  345 (374)
                      +.+.+|-=-.|  ++..+||+||++|.|  .+|.++++..............
T Consensus       511 dfd~mITe~aP--idSLIQR~GRv~R~g~~~~~~~~v~~~~~~~~~~~~~~~  560 (733)
T COG1203         511 DFDVLITELAP--IDSLIQRAGRVNRHGKKENGKIYVYNDEERGPYLKYSYE  560 (733)
T ss_pred             ccCeeeecCCC--HHHHHHHHHHHhhcccccCCceeEeecccCCCchhhhhh
Confidence            47777644444  899999999999999  6777777776666555554443

>PRK13107 preprotein translocase subunit SecA; Reviewed

Probab=99.94  E-value=8e-25  Score=205.24  Aligned_cols=322  Identities=17%  Similarity=0.146  Sum_probs=217.6

Q ss_pred             hHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc---cCCcEEEEcchHHHHHHHHHHHHH----
Q 037567            3 STLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV---TGKTALVVSPLISLMQDQVMSLKQ----   75 (374)
Q Consensus         3 ~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~---~~~~~lil~P~~~l~~q~~~~~~~----   75 (374)
                      ++-++.+|+. +++.|.-+--.+.+|+  +..++||.|||+++.+|++.   .+..|.|++|+..|+.+..+++..    
T Consensus        73 Eaa~R~lgm~-~ydVQliGgl~L~~G~--IaEm~TGEGKTL~a~lp~~l~al~g~~VhIvT~ndyLA~RD~e~m~~l~~~  149 (908)
T PRK13107         73 EASKRVFEMR-HFDVQLLGGMVLDSNR--IAEMRTGEGKTLTATLPAYLNALTGKGVHVITVNDYLARRDAENNRPLFEF  149 (908)
T ss_pred             HHHHHHhCCC-cCchHHhcchHhcCCc--cccccCCCCchHHHHHHHHHHHhcCCCEEEEeCCHHHHHHHHHHHHHHHHh
Confidence            4556667774 7777765555554444  99999999999999888764   467799999999999987777664    


Q ss_pred             cCCceEEcCCCCCchhhhhhhhcCCeeEEEEcCccc-ccCchhhH----HHHHhcCccEEEEeccchhhcc---------
Q 037567           76 RGINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKA-CIIPISFW----SKLLKAGVCLFAVDEAHCISEW---------  141 (374)
Q Consensus        76 ~~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l-~~~~~~~~----~~~~~~~~~~vviDE~h~~~~~---------  141 (374)
                      +|+.+....++...   ........++|+++||..+ .++++..+    .......+.++||||++.+.-.         
T Consensus       150 lGlsv~~i~~~~~~---~~r~~~Y~~dI~YgT~~e~gfDyLrdnm~~~~~~~vqr~~~~aIvDEvDsiLiDEArtPLIIS  226 (908)
T PRK13107        150 LGLTVGINVAGLGQ---QEKKAAYNADITYGTNNEFGFDYLRDNMAFSPQERVQRPLHYALIDEVDSILIDEARTPLIIS  226 (908)
T ss_pred             cCCeEEEecCCCCH---HHHHhcCCCCeEEeCCCcccchhhhccCccchhhhhccccceeeecchhhhccccCCCceeec
Confidence            47887776654443   2233345689999999998 55555421    1223367889999999998521         


Q ss_pred             cC--cchHHHHHHHHHHHhcC--------------------CCCeeEEE-------------------------------
Q 037567          142 GH--DFRLEYKQLDKLRTFLL--------------------GVPFVALT-------------------------------  168 (374)
Q Consensus       142 ~~--~~~~~~~~~~~~~~~~~--------------------~~~~i~~S-------------------------------  168 (374)
                      |.  .....+..+..+...+.                    ..+.+.+|                               
T Consensus       227 g~~~~~~~~y~~~~~~v~~L~~~~~~~~~~~~~~~dy~idek~~~v~LTe~G~~~~e~~l~~~~~~~~~~~l~~~~~~~~  306 (908)
T PRK13107        227 GAAEDSSELYIKINTLIPNLIRQDKEDTEEYVGEGDYSIDEKAKQVHFTERGQEKVENLLIERGMLAEGDSLYSAANISL  306 (908)
T ss_pred             CCCccchHHHHHHHHHHHHHHhhhhccccccCCCCCEEEecCCCeeeechHHHHHHHHHHHhCCcccCcccccCchhhHH
Confidence            00  00111111111111100                    11222222                               


Q ss_pred             --------------------------------------------------------------------------------
Q 037567          169 --------------------------------------------------------------------------------  168 (374)
Q Consensus       169 --------------------------------------------------------------------------------  168 (374)
                                                                                                      
T Consensus       307 ~~~i~~aL~A~~lf~~d~dYiV~dg~V~IVDe~TGRim~grrwsdGLHQaIEaKE~v~I~~e~~t~AsIT~QnfFr~Y~k  386 (908)
T PRK13107        307 LHHVNAALRAHTLFEKDVDYIVQDNEVIIVDEHTGRTMPGRRWSEGLHQAVEAKEGVHIQNENQTLASITFQNYFRQYEK  386 (908)
T ss_pred             HHHHHHHHHHHHHHhcCCceEEECCEEEEEECCCCCCCCCCccchHHHHHHHHhcCCCCCCCceeeeeehHHHHHHhhhH
Confidence                                                                                            


Q ss_pred             -----eecCcccHHHHHHhcCCCCCeEEEeccCCCceeEEE--EeecCCcchHHHHHHHHHHhhcCCCcEEEEecchhHH
Q 037567          169 -----ATATEKVRIDIINSLKLKNPYVTIASFDRKNLFYGV--KVINRGQSFVDELVQEILKSVAGAGSIIVYCMTIKDV  241 (374)
Q Consensus       169 -----aT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~lVf~~~~~~~  241 (374)
                           +|...... ++...+++   .+...+.+.+......  .++.........++.++.+....+.++||||.++..+
T Consensus       387 L~GMTGTa~te~~-Ef~~iY~l---~Vv~IPTnkp~~R~d~~d~iy~t~~~K~~Aii~ei~~~~~~GrpVLV~t~sv~~s  462 (908)
T PRK13107        387 LAGMTGTADTEAF-EFQHIYGL---DTVVVPTNRPMVRKDMADLVYLTADEKYQAIIKDIKDCRERGQPVLVGTVSIEQS  462 (908)
T ss_pred             hhcccCCChHHHH-HHHHHhCC---CEEECCCCCCccceeCCCcEEeCHHHHHHHHHHHHHHHHHcCCCEEEEeCcHHHH
Confidence                 22211110 11111111   1111111111111111  1233334556778888877777899999999999999


Q ss_pred             HHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCc------------------------
Q 037567          242 EEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDV------------------------  297 (374)
Q Consensus       242 ~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~------------------------  297 (374)
                      +.++..|.+.+++...+|++.+..++..+.+.|+.|.  |+|||+++++|+|+.--                        
T Consensus       463 e~ls~~L~~~gi~~~vLnak~~~~Ea~ii~~Ag~~G~--VtIATnmAGRGTDIkLggn~~~~~~~~~~~~~~~~~~~~~~  540 (908)
T PRK13107        463 ELLARLMVKEKIPHEVLNAKFHEREAEIVAQAGRTGA--VTIATNMAGRGTDIVLGGNWNMEIEALENPTAEQKAKIKAD  540 (908)
T ss_pred             HHHHHHHHHCCCCeEeccCcccHHHHHHHHhCCCCCc--EEEecCCcCCCcceecCCchHHhhhhhcchhhHHHHHHHHH
Confidence            9999999999999999999999999999999999998  99999999999999621                        


Q ss_pred             -------------cEEEEECCCCChhHHHHhhccCCCCCCceEEEEEeeccC
Q 037567          298 -------------RHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSN  336 (374)
Q Consensus       298 -------------~~vi~~~~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~  336 (374)
                                   -+||....+.|..-=.|..||+||.|.+|..-.|++-+|
T Consensus       541 ~~~~~~~V~~~GGL~VIgTerheSrRID~QLrGRaGRQGDPGss~f~lSlED  592 (908)
T PRK13107        541 WQIRHDEVVAAGGLHILGTERHESRRIDNQLRGRAGRQGDAGSSRFYLSMED  592 (908)
T ss_pred             HHhhHHHHHHcCCCEEEecccCchHHHHhhhhcccccCCCCCceeEEEEeCc
Confidence                         268888888898888999999999999999988888776

>PRK12899 secA preprotein translocase subunit SecA; Reviewed

Probab=99.94  E-value=4.1e-25  Score=207.52  Aligned_cols=126  Identities=19%  Similarity=0.132  Sum_probs=102.6

Q ss_pred             CCcchHHHHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccc
Q 037567          209 RGQSFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAF  288 (374)
Q Consensus       209 ~~~~~~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~  288 (374)
                      ........++.++.+....+.++||-|.+....+.++..|.+.|++...++......+-..+.+.-+.  -.|.|+|+++
T Consensus       549 t~~~k~~ai~~ei~~~~~~grPvLigt~si~~se~ls~~L~~~gi~h~vLNak~~~~Ea~iia~AG~~--g~VTIATNmA  626 (970)
T PRK12899        549 TEREKYHAIVAEIASIHRKGNPILIGTESVEVSEKLSRILRQNRIEHTVLNAKNHAQEAEIIAGAGKL--GAVTVATNMA  626 (970)
T ss_pred             CHHHHHHHHHHHHHHHHhCCCCEEEEeCcHHHHHHHHHHHHHcCCcceecccchhhhHHHHHHhcCCC--CcEEEeeccc
Confidence            33456677888888888889999999999999999999999999998888877544444444333222  4699999999


Q ss_pred             cccccccCc--------cEEEEECCCCChhHHHHhhccCCCCCCceEEEEEeeccC
Q 037567          289 GMGIDKPDV--------RHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSN  336 (374)
Q Consensus       289 ~~G~d~~~~--------~~vi~~~~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~  336 (374)
                      ++|.|+.--        -+||....+.|..--.|..||+||.|.+|.+..+++-+|
T Consensus       627 GRGTDIkl~~~v~~~GGLhVIgTer~es~Rid~Ql~GRagRQGdpGss~f~lSlED  682 (970)
T PRK12899        627 GRGTDIKLDEEAVAVGGLYVIGTSRHQSRRIDRQLRGRCARLGDPGAAKFFLSFED  682 (970)
T ss_pred             cCCcccccCchHHhcCCcEEEeeccCchHHHHHHHhcccccCCCCCceeEEEEcch
Confidence            999998532        258888889999999999999999999999988888776

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

Probab=99.94  E-value=1.5e-24  Score=188.75  Aligned_cols=165  Identities=24%  Similarity=0.258  Sum_probs=130.6

Q ss_pred             CCeeEEEeecCcccHHHHHHhcCCCCCeEEEeccCCCceeEEEEeecCCcchHHHHHHHHHHhhcCCCcEEEEecchhHH
Q 037567          162 VPFVALTATATEKVRIDIINSLKLKNPYVTIASFDRKNLFYGVKVINRGQSFVDELVQEILKSVAGAGSIIVYCMTIKDV  241 (374)
Q Consensus       162 ~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lVf~~~~~~~  241 (374)
                      .++|++||||.+....   . .+..-...........+....+   ......+.+++.++......+.+++|-+=+++.+
T Consensus       387 ~q~i~VSATPg~~E~e---~-s~~~vveQiIRPTGLlDP~iev---Rp~~~QvdDL~~EI~~r~~~~eRvLVTtLTKkmA  459 (663)
T COG0556         387 PQTIYVSATPGDYELE---Q-SGGNVVEQIIRPTGLLDPEIEV---RPTKGQVDDLLSEIRKRVAKNERVLVTTLTKKMA  459 (663)
T ss_pred             CCEEEEECCCChHHHH---h-ccCceeEEeecCCCCCCCceee---ecCCCcHHHHHHHHHHHHhcCCeEEEEeehHHHH
Confidence            5799999999875432   1 1101111111111111111122   2345578899999999888999999999999999


Q ss_pred             HHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEEEEECCC-----CChhHHHHhh
Q 037567          242 EEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCP-----KTLESYYQES  316 (374)
Q Consensus       242 ~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~~~~p-----~s~~~~~Q~~  316 (374)
                      +.+.+.|.+.|+++..+|++...-+|.+++.+++.|.++|||+.+.+-+|+|+|.+..|.+++..     .|-..++|-+
T Consensus       460 EdLT~Yl~e~gikv~YlHSdidTlER~eIirdLR~G~~DvLVGINLLREGLDiPEVsLVAIlDADKeGFLRse~SLIQtI  539 (663)
T COG0556         460 EDLTEYLKELGIKVRYLHSDIDTLERVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSERSLIQTI  539 (663)
T ss_pred             HHHHHHHHhcCceEEeeeccchHHHHHHHHHHHhcCCccEEEeehhhhccCCCcceeEEEEeecCccccccccchHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999988754     5889999999


Q ss_pred             ccCCCCCCceEEEEEeec
Q 037567          317 GRCGRDGIASVCWLYYAR  334 (374)
Q Consensus       317 GR~~R~~~~g~~~~~~~~  334 (374)
                      |||.|. ..|.++.+.+.
T Consensus       540 GRAARN-~~GkvIlYAD~  556 (663)
T COG0556         540 GRAARN-VNGKVILYADK  556 (663)
T ss_pred             HHHhhc-cCCeEEEEchh
Confidence            999994 57888877654

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

Probab=99.94  E-value=4.5e-25  Score=205.41  Aligned_cols=333  Identities=20%  Similarity=0.199  Sum_probs=239.5

Q ss_pred             CCchhHHHHHHHHHcC----CCEEEEccCCCCchhhhhcc---ccccCCcEEEEcchHHHHHHHHHHHH-HcCCceEEcC
Q 037567           13 VFRPYQKDVIQRIIEK----RDCLVVMATGSGKSLCYQLP---PLVTGKTALVVSPLISLMQDQVMSLK-QRGINAEFLG   84 (374)
Q Consensus        13 ~~~~~Q~~~~~~~~~~----~~~l~~a~tGsGKT~~~~l~---~~~~~~~~lil~P~~~l~~q~~~~~~-~~~~~~~~~~   84 (374)
                      .+.+-|..++..+.+.    +..++.+.||||||-+|+-.   ++.+++.+|+++|-.+|..|+...|+ .||.++.+++
T Consensus       198 ~Ln~~Q~~a~~~i~~~~~~~~~~Ll~GvTGSGKTEvYl~~i~~~L~~GkqvLvLVPEI~Ltpq~~~rf~~rFg~~v~vlH  277 (730)
T COG1198         198 ALNQEQQAAVEAILSSLGGFAPFLLDGVTGSGKTEVYLEAIAKVLAQGKQVLVLVPEIALTPQLLARFKARFGAKVAVLH  277 (730)
T ss_pred             ccCHHHHHHHHHHHHhcccccceeEeCCCCCcHHHHHHHHHHHHHHcCCEEEEEeccccchHHHHHHHHHHhCCChhhhc
Confidence            5778999999998765    67899999999999887644   44579999999999999999999997 5788888888


Q ss_pred             CCCCchh---hhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhccc-CcchHHHHHHHHHHHhcC
Q 037567           85 SAQTDSS---VQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWG-HDFRLEYKQLDKLRTFLL  160 (374)
Q Consensus        85 ~~~~~~~---~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~-~~~~~~~~~~~~~~~~~~  160 (374)
                      ++.++.+   .+.....+...|+|+|--.         -...+.++.+|||||=|.-.-.+ ...+.-.+-+...+....
T Consensus       278 S~Ls~~er~~~W~~~~~G~~~vVIGtRSA---------lF~Pf~~LGLIIvDEEHD~sYKq~~~prYhARdvA~~Ra~~~  348 (730)
T COG1198         278 SGLSPGERYRVWRRARRGEARVVIGTRSA---------LFLPFKNLGLIIVDEEHDSSYKQEDGPRYHARDVAVLRAKKE  348 (730)
T ss_pred             ccCChHHHHHHHHHHhcCCceEEEEechh---------hcCchhhccEEEEeccccccccCCcCCCcCHHHHHHHHHHHh
Confidence            8776654   4556667889999999322         23456788999999999764221 122333355666666677


Q ss_pred             CCCeeEEEeecCcccHHHHHHhcCCCCCeEEEeccC---CCceeEEE-E--eecCCcchHHHHHHHHHHhhcCCCcEEEE
Q 037567          161 GVPFVALTATATEKVRIDIINSLKLKNPYVTIASFD---RKNLFYGV-K--VINRGQSFVDELVQEILKSVAGAGSIIVY  234 (374)
Q Consensus       161 ~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~-~--~~~~~~~~~~~~~~~~~~~~~~~~~~lVf  234 (374)
                      +.++|+-||||+-+.......  +............   .+.+.... .  ...........++..+.+.+..++++|+|
T Consensus       349 ~~pvvLgSATPSLES~~~~~~--g~y~~~~L~~R~~~a~~p~v~iiDmr~e~~~~~~~lS~~Ll~~i~~~l~~geQ~llf  426 (730)
T COG1198         349 NAPVVLGSATPSLESYANAES--GKYKLLRLTNRAGRARLPRVEIIDMRKEPLETGRSLSPALLEAIRKTLERGEQVLLF  426 (730)
T ss_pred             CCCEEEecCCCCHHHHHhhhc--CceEEEEccccccccCCCcceEEeccccccccCccCCHHHHHHHHHHHhcCCeEEEE
Confidence            999999999999876543311  1011111111111   11111111 1  11111114577888888888899999999


Q ss_pred             ecchh------------------------------------------------------------HHHHHHHHHHHc--C
Q 037567          235 CMTIK------------------------------------------------------------DVEEISKALKQL--G  252 (374)
Q Consensus       235 ~~~~~------------------------------------------------------------~~~~l~~~l~~~--~  252 (374)
                      .|.+.                                                            -.+++.+.|++.  +
T Consensus       427 lnRRGys~~l~C~~Cg~v~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~~~~p~~Cp~Cgs~~L~~~G~GterieeeL~~~FP~  506 (730)
T COG1198         427 LNRRGYAPLLLCRDCGYIAECPNCDSPLTLHKATGQLRCHYCGYQEPIPQSCPECGSEHLRAVGPGTERIEEELKRLFPG  506 (730)
T ss_pred             EccCCccceeecccCCCcccCCCCCcceEEecCCCeeEeCCCCCCCCCCCCCCCCCCCeeEEecccHHHHHHHHHHHCCC
Confidence            99877                                                            466666777664  5


Q ss_pred             CceeeeecCCCh--HHHHHHHHhhhcCCeeEEEEeccccccccccCccEEEEECCCC------------ChhHHHHhhcc
Q 037567          253 VKAGTYHGQMGS--KAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPK------------TLESYYQESGR  318 (374)
Q Consensus       253 ~~~~~~~~~~~~--~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~~~~p~------------s~~~~~Q~~GR  318 (374)
                      .++..+.++.+.  ..-+..+..|..|+.+|||.|+++..|.|+|+++.|...+...            ...-+.|-.||
T Consensus       507 ~rv~r~d~Dtt~~k~~~~~~l~~~~~ge~dILiGTQmiaKG~~fp~vtLVgvl~aD~~L~~~DfRA~Er~fqll~QvaGR  586 (730)
T COG1198         507 ARIIRIDSDTTRRKGALEDLLDQFANGEADILIGTQMIAKGHDFPNVTLVGVLDADTGLGSPDFRASERTFQLLMQVAGR  586 (730)
T ss_pred             CcEEEEccccccchhhHHHHHHHHhCCCCCeeecchhhhcCCCcccceEEEEEechhhhcCCCcchHHHHHHHHHHHHhh
Confidence            677788887654  3456789999999999999999999999999999876554321            34566899999


Q ss_pred             CCCCCCceEEEEEeeccCCCcccceeccccchHHHHHH
Q 037567          319 CGRDGIASVCWLYYARSNFAKGDFYCGESQTENQRTAI  356 (374)
Q Consensus       319 ~~R~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  356 (374)
                      +||.+.+|.+++-....|...++.+..++...+..+.+
T Consensus       587 AgR~~~~G~VvIQT~~P~hp~i~~~~~~dy~~F~~~El  624 (730)
T COG1198         587 AGRAGKPGEVVIQTYNPDHPAIQALKRGDYEAFYEQEL  624 (730)
T ss_pred             hccCCCCCeEEEEeCCCCcHHHHHHHhcCHHHHHHHHH
Confidence            99998888888888777777777777777666665544

>KOG0385 consensus Chromatin remodeling complex WSTF-ISWI, small subunit [Transcription]

Probab=99.93  E-value=2.4e-24  Score=194.34  Aligned_cols=307  Identities=19%  Similarity=0.186  Sum_probs=214.4

Q ss_pred             CCchhHHHHHHHHHc----CCCEEEEccCCCCchhhh--hcccc----ccCCcEEEEcchHHHHHHHHHHHHHcCCceE-
Q 037567           13 VFRPYQKDVIQRIIE----KRDCLVVMATGSGKSLCY--QLPPL----VTGKTALVVSPLISLMQDQVMSLKQRGINAE-   81 (374)
Q Consensus        13 ~~~~~Q~~~~~~~~~----~~~~l~~a~tGsGKT~~~--~l~~~----~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~-   81 (374)
                      ++++||.+.++.+.+    |-++|+...+|.|||+-.  ++.-+    ...++.||++|...|. +|..++.+|-..+. 
T Consensus       167 ~lr~YQveGlnWLi~l~engingILaDEMGLGKTlQtIs~l~yl~~~~~~~GPfLVi~P~StL~-NW~~Ef~rf~P~l~~  245 (971)
T KOG0385|consen  167 ELRDYQLEGLNWLISLYENGINGILADEMGLGKTLQTISLLGYLKGRKGIPGPFLVIAPKSTLD-NWMNEFKRFTPSLNV  245 (971)
T ss_pred             ccchhhhccHHHHHHHHhcCcccEeehhcccchHHHHHHHHHHHHHhcCCCCCeEEEeeHhhHH-HHHHHHHHhCCCcce
Confidence            699999999987764    668899999999999432  22222    2367899999996555 59999999965544 


Q ss_pred             -EcCCCCCchhh--hhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHHh
Q 037567           82 -FLGSAQTDSSV--QTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTF  158 (374)
Q Consensus        82 -~~~~~~~~~~~--~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~  158 (374)
                       .+.++......  ......+.++|+|+|++....-    ...+...+|+++||||+|++.+..       ..+.+....
T Consensus       246 ~~~~Gdk~eR~~~~r~~~~~~~fdV~iTsYEi~i~d----k~~lk~~~W~ylvIDEaHRiKN~~-------s~L~~~lr~  314 (971)
T KOG0385|consen  246 VVYHGDKEERAALRRDIMLPGRFDVCITSYEIAIKD----KSFLKKFNWRYLVIDEAHRIKNEK-------SKLSKILRE  314 (971)
T ss_pred             EEEeCCHHHHHHHHHHhhccCCCceEeehHHHHHhh----HHHHhcCCceEEEechhhhhcchh-------hHHHHHHHH
Confidence             44443322211  2223346889999999976532    244555789999999999998755       445566666


Q ss_pred             cCCCCeeEEEeecCcccHHHHHHhcCCCCCeEEEec--------------------------------------------
Q 037567          159 LLGVPFVALTATATEKVRIDIINSLKLKNPYVTIAS--------------------------------------------  194 (374)
Q Consensus       159 ~~~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~--------------------------------------------  194 (374)
                      +.....+++|+||-.+..-+++..+..--|.+....                                            
T Consensus       315 f~~~nrLLlTGTPLQNNL~ELWaLLnFllPdiF~~~e~F~swF~~~~~~~~~e~v~~Lh~vL~pFlLRR~K~dVe~sLpp  394 (971)
T KOG0385|consen  315 FKTDNRLLLTGTPLQNNLHELWALLNFLLPDIFNSAEDFDSWFDFTNCEGDQELVSRLHKVLRPFLLRRIKSDVEKSLPP  394 (971)
T ss_pred             hcccceeEeeCCcccccHHHHHHHHHhhchhhccCHHHHHHHHcccccccCHHHHHHHHhhhhHHHHHHHHHhHhhcCCC
Confidence            667788999999877655443332221111111000                                            


Q ss_pred             ---------c-----------------------------------------CCCceeEEEEe---ecCC-----cchHHH
Q 037567          195 ---------F-----------------------------------------DRKNLFYGVKV---INRG-----QSFVDE  216 (374)
Q Consensus       195 ---------~-----------------------------------------~~~~~~~~~~~---~~~~-----~~~~~~  216 (374)
                               .                                         +.+.+.....+   +...     ..-...
T Consensus       395 KkE~~iyvgms~mQkk~Y~~iL~kdl~~~n~~~~~~k~kL~NI~mQLRKccnHPYLF~g~ePg~pyttdehLv~nSGKm~  474 (971)
T KOG0385|consen  395 KKELIIYVGMSSMQKKWYKAILMKDLDALNGEGKGEKTKLQNIMMQLRKCCNHPYLFDGAEPGPPYTTDEHLVTNSGKML  474 (971)
T ss_pred             cceeeEeccchHHHHHHHHHHHHhcchhhcccccchhhHHHHHHHHHHHhcCCccccCCCCCCCCCCcchHHHhcCccee
Confidence                     0                                         00000000000   0000     011112


Q ss_pred             HHHHHHHhh-cCCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCC---eeEEEEeccccccc
Q 037567          217 LVQEILKSV-AGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDE---IRVMVATMAFGMGI  292 (374)
Q Consensus       217 ~~~~~~~~~-~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~---~~ilv~t~~~~~G~  292 (374)
                      ++..++..+ ..+.++|||..-.....-+...+.-+++....+.|.++.++|...++.|+...   .-.+++|.+.+.|+
T Consensus       475 vLDkLL~~Lk~~GhRVLIFSQmt~mLDILeDyc~~R~y~ycRiDGSt~~eeR~~aI~~fn~~~s~~FiFlLSTRAGGLGI  554 (971)
T KOG0385|consen  475 VLDKLLPKLKEQGHRVLIFSQMTRMLDILEDYCMLRGYEYCRLDGSTSHEEREDAIEAFNAPPSEKFIFLLSTRAGGLGI  554 (971)
T ss_pred             hHHHHHHHHHhCCCeEEEeHHHHHHHHHHHHHHHhcCceeEeecCCCCcHHHHHHHHhcCCCCcceEEEEEecccccccc
Confidence            333343333 35779999999999999999998889999999999999999999999999864   44678999999999


Q ss_pred             cccCccEEEEECCCCChhHHHHhhccCCCCCCceEEEEE
Q 037567          293 DKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLY  331 (374)
Q Consensus       293 d~~~~~~vi~~~~p~s~~~~~Q~~GR~~R~~~~g~~~~~  331 (374)
                      |+..+++||+|+..|++..-.|...||.|.||...|.++
T Consensus       555 NL~aADtVIlyDSDWNPQ~DLQAmDRaHRIGQ~K~V~V~  593 (971)
T KOG0385|consen  555 NLTAADTVILYDSDWNPQVDLQAMDRAHRIGQKKPVVVY  593 (971)
T ss_pred             ccccccEEEEecCCCCchhhhHHHHHHHhhCCcCceEEE
Confidence            999999999999999999999999999999998776655

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

Probab=99.93  E-value=5.4e-25  Score=201.44  Aligned_cols=294  Identities=20%  Similarity=0.154  Sum_probs=187.8

Q ss_pred             CCCCchhHHHHHHHHHc----C-CCEEEEccCCCCchhhhhcccc--c---cCCcEEEEcchHHHHHHHHHHHHHcCCce
Q 037567           11 YSVFRPYQKDVIQRIIE----K-RDCLVVMATGSGKSLCYQLPPL--V---TGKTALVVSPLISLMQDQVMSLKQRGINA   80 (374)
Q Consensus        11 ~~~~~~~Q~~~~~~~~~----~-~~~l~~a~tGsGKT~~~~l~~~--~---~~~~~lil~P~~~l~~q~~~~~~~~~~~~   80 (374)
                      -..+|+||..|+..+.+    | +.++++++||+|||.++...+-  .   ..+++|+++.+++|++|....+..+-+..
T Consensus       163 ~i~~RyyQ~~AI~rv~Eaf~~g~~raLlvMATGTGKTrTAiaii~rL~r~~~~KRVLFLaDR~~Lv~QA~~af~~~~P~~  242 (875)
T COG4096         163 AIGPRYYQIIAIRRVIEAFSKGQNRALLVMATGTGKTRTAIAIIDRLIKSGWVKRVLFLADRNALVDQAYGAFEDFLPFG  242 (875)
T ss_pred             cccchHHHHHHHHHHHHHHhcCCceEEEEEecCCCcceeHHHHHHHHHhcchhheeeEEechHHHHHHHHHHHHHhCCCc
Confidence            34689999999988764    2 4689999999999976543222  1   36889999999999999998888774433


Q ss_pred             EEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhh---HHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHH
Q 037567           81 EFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISF---WSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRT  157 (374)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~---~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~  157 (374)
                      ........      ......++|.++|++++..-....   ...+....+++||+||||+-.-         +....+..
T Consensus       243 ~~~n~i~~------~~~~~s~~i~lsTyqt~~~~~~~~~~~~~~f~~g~FDlIvIDEaHRgi~---------~~~~~I~d  307 (875)
T COG4096         243 TKMNKIED------KKGDTSSEIYLSTYQTMTGRIEQKEDEYRRFGPGFFDLIVIDEAHRGIY---------SEWSSILD  307 (875)
T ss_pred             cceeeeec------ccCCcceeEEEeehHHHHhhhhccccccccCCCCceeEEEechhhhhHH---------hhhHHHHH
Confidence            22211111      111125799999999886544332   1233445689999999997432         33445555


Q ss_pred             hcCCCCeeEEEeecCcccHHHHHHhc-CCC-----------------CCeEEEe-ccCCCceeE----------------
Q 037567          158 FLLGVPFVALTATATEKVRIDIINSL-KLK-----------------NPYVTIA-SFDRKNLFY----------------  202 (374)
Q Consensus       158 ~~~~~~~i~~SaT~~~~~~~~~~~~~-~~~-----------------~~~~~~~-~~~~~~~~~----------------  202 (374)
                      .+. ...+++||||......+....+ +.+                 +..+... ......+.+                
T Consensus       308 YFd-A~~~gLTATP~~~~d~~T~~~F~g~Pt~~YsleeAV~DGfLvpy~vi~i~~~~~~~G~~~~~~serek~~g~~i~~  386 (875)
T COG4096         308 YFD-AATQGLTATPKETIDRSTYGFFNGEPTYAYSLEEAVEDGFLVPYKVIRIDTDFDLDGWKPDAGSEREKLQGEAIDE  386 (875)
T ss_pred             HHH-HHHHhhccCcccccccccccccCCCcceeecHHHHhhccccCCCCceEEeeeccccCcCcCccchhhhhhccccCc
Confidence            543 3345569999885543333333 211                 1111110 000000000                


Q ss_pred             EEEe-----------ecCCcchHHHHHHHHHHhhcC---CCcEEEEecchhHHHHHHHHHHHc-----CCceeeeecCCC
Q 037567          203 GVKV-----------INRGQSFVDELVQEILKSVAG---AGSIIVYCMTIKDVEEISKALKQL-----GVKAGTYHGQMG  263 (374)
Q Consensus       203 ~~~~-----------~~~~~~~~~~~~~~~~~~~~~---~~~~lVf~~~~~~~~~l~~~l~~~-----~~~~~~~~~~~~  263 (374)
                      ....           .......+...+.+.+.....   .+|+||||.+..+|+.+.+.|.+.     +--+..+.|+  
T Consensus       387 dd~~~~~~d~dr~~v~~~~~~~V~r~~~~~l~~~~~g~~~~KTIvFa~n~dHAe~i~~~~~~~ype~~~~~a~~IT~d--  464 (875)
T COG4096         387 DDQNFEARDFDRTLVIPFRTETVARELTEYLKRGATGDEIGKTIVFAKNHDHAERIREALVNEYPEYNGRYAMKITGD--  464 (875)
T ss_pred             ccccccccccchhccccchHHHHHHHHHHHhccccCCCccCceEEEeeCcHHHHHHHHHHHHhCccccCceEEEEecc--
Confidence            0000           001112223334444443111   468999999999999999999874     2235566665  


Q ss_pred             hHHHHHHHHhhhcC--CeeEEEEeccccccccccCccEEEEECCCCChhHHHHhhccCCCC
Q 037567          264 SKAREEAHRLFIRD--EIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRD  322 (374)
Q Consensus       264 ~~~r~~~~~~f~~g--~~~ilv~t~~~~~G~d~~~~~~vi~~~~p~s~~~~~Q~~GR~~R~  322 (374)
                      .++-++.+..|...  --.|.++++++.+|+|+|.+-.+++.....|...|.||+||+-|.
T Consensus       465 ~~~~q~~Id~f~~ke~~P~IaitvdlL~TGiDvpev~nlVF~r~VrSktkF~QMvGRGTRl  525 (875)
T COG4096         465 AEQAQALIDNFIDKEKYPRIAITVDLLTTGVDVPEVVNLVFDRKVRSKTKFKQMVGRGTRL  525 (875)
T ss_pred             chhhHHHHHHHHhcCCCCceEEehhhhhcCCCchheeeeeehhhhhhHHHHHHHhcCcccc
Confidence            44455566667663  246888999999999999999999999999999999999999995

>KOG0387 consensus Transcription-coupled repair protein CSB/RAD26 (contains SNF2 family DNA-dependent ATPase domain) [Transcription; Replication, recombination and repair]

Probab=99.92  E-value=8.1e-24  Score=191.75  Aligned_cols=307  Identities=15%  Similarity=0.149  Sum_probs=212.9

Q ss_pred             CCchhHHHHHHHHHc----CCCEEEEccCCCCch---hhhhcccccc---CCcEEEEcchHHHHHHHHHHHHHcCCceE-
Q 037567           13 VFRPYQKDVIQRIIE----KRDCLVVMATGSGKS---LCYQLPPLVT---GKTALVVSPLISLMQDQVMSLKQRGINAE-   81 (374)
Q Consensus        13 ~~~~~Q~~~~~~~~~----~~~~l~~a~tGsGKT---~~~~l~~~~~---~~~~lil~P~~~l~~q~~~~~~~~~~~~~-   81 (374)
                      .+.+||.++++.+++    +...|+...+|.|||   ++|+.++.++   .+++|||||. .+..||..++..+..... 
T Consensus       205 ~Lf~yQreGV~WL~~L~~q~~GGILgDeMGLGKTIQiisFLaaL~~S~k~~~paLIVCP~-Tii~qW~~E~~~w~p~~rv  283 (923)
T KOG0387|consen  205 KLFPYQREGVQWLWELYCQRAGGILGDEMGLGKTIQIISFLAALHHSGKLTKPALIVCPA-TIIHQWMKEFQTWWPPFRV  283 (923)
T ss_pred             HhhHHHHHHHHHHHHHHhccCCCeecccccCccchhHHHHHHHHhhcccccCceEEEccH-HHHHHHHHHHHHhCcceEE
Confidence            689999999998875    567899999999999   4454444444   4789999999 799999999999976554 


Q ss_pred             -EcCCCCCchh--------h----hhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHH
Q 037567           82 -FLGSAQTDSS--------V----QTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLE  148 (374)
Q Consensus        82 -~~~~~~~~~~--------~----~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~  148 (374)
                       ++++......        .    ..........|+++|++.+...-    ..+....|+++|+||.|.+.+.+.     
T Consensus       284 ~ilh~t~s~~r~~~~~~~~~~~~~L~r~~~~~~~ilitty~~~r~~~----d~l~~~~W~y~ILDEGH~IrNpns-----  354 (923)
T KOG0387|consen  284 FILHGTGSGARYDASHSSHKKDKLLIRKVATDGGILITTYDGFRIQG----DDLLGILWDYVILDEGHRIRNPNS-----  354 (923)
T ss_pred             EEEecCCcccccccchhhhhhhhhheeeecccCcEEEEehhhhcccC----cccccccccEEEecCcccccCCcc-----
Confidence             4444333210        0    11111233479999998874431    234446789999999999987663     


Q ss_pred             HHHHHHHHHhcCCCCeeEEEeecCcccHHHHHHhcCCCCC----------------eEEEec------------------
Q 037567          149 YKQLDKLRTFLLGVPFVALTATATEKVRIDIINSLKLKNP----------------YVTIAS------------------  194 (374)
Q Consensus       149 ~~~~~~~~~~~~~~~~i~~SaT~~~~~~~~~~~~~~~~~~----------------~~~~~~------------------  194 (374)
                        .+...+..++..++|.+|+||-.+...+++..+....|                +..-..                  
T Consensus       355 --~islackki~T~~RiILSGTPiQNnL~ELwsLfDFv~PG~Lgt~~~F~~~f~~pI~~GgyaNAs~~qv~~aykca~~L  432 (923)
T KOG0387|consen  355 --KISLACKKIRTVHRIILSGTPIQNNLTELWSLFDFVFPGKLGTLPVFQQNFEHPINRGGYANASPRQVQTAYKCAVAL  432 (923)
T ss_pred             --HHHHHHHhccccceEEeeCccccchHHHHHHHhhhccCCcccchHHHHhhhhhheeccccCCCCHHHHHHHHHHHHHH
Confidence              45555555667889999999877765554432221100                000000                  


Q ss_pred             ----------------------------------------------------------------------cCCCceeEEE
Q 037567          195 ----------------------------------------------------------------------FDRKNLFYGV  204 (374)
Q Consensus       195 ----------------------------------------------------------------------~~~~~~~~~~  204 (374)
                                                                                            .+.+.+....
T Consensus       433 r~lI~PylLRR~K~dv~~~~Lp~K~E~VlfC~LT~~QR~~Y~~fl~s~~v~~i~ng~~~~l~Gi~iLrkICnHPdll~~~  512 (923)
T KOG0387|consen  433 RDLISPYLLRRMKSDVKGLKLPKKEEIVLFCRLTKLQRRLYQRFLNSSEVNKILNGKRNCLSGIDILRKICNHPDLLDRR  512 (923)
T ss_pred             HHHhHHHHHHHHHHHhhhccCCCccceEEEEeccHHHHHHHHHHhhhHHHHHHHcCCccceechHHHHhhcCCcccccCc
Confidence                                                                                  0000000000


Q ss_pred             ---EeecCC------cchHHHHHHH-HHHhhcCCCcEEEEecchhHHHHHHHHHH-HcCCceeeeecCCChHHHHHHHHh
Q 037567          205 ---KVINRG------QSFVDELVQE-ILKSVAGAGSIIVYCMTIKDVEEISKALK-QLGVKAGTYHGQMGSKAREEAHRL  273 (374)
Q Consensus       205 ---~~~~~~------~~~~~~~~~~-~~~~~~~~~~~lVf~~~~~~~~~l~~~l~-~~~~~~~~~~~~~~~~~r~~~~~~  273 (374)
                         .....+      ..-...++.. +.....++.++++|..++....-+...|. ..++....+.|.++...|+.++.+
T Consensus       513 ~~~~~~~~D~~g~~k~sGKm~vl~~ll~~W~kqg~rvllFsqs~~mLdilE~fL~~~~~ysylRmDGtT~~~~R~~lVd~  592 (923)
T KOG0387|consen  513 DEDEKQGPDYEGDPKRSGKMKVLAKLLKDWKKQGDRVLLFSQSRQMLDILESFLRRAKGYSYLRMDGTTPAALRQKLVDR  592 (923)
T ss_pred             ccccccCCCcCCChhhcchHHHHHHHHHHHhhCCCEEEEehhHHHHHHHHHHHHHhcCCceEEEecCCCccchhhHHHHh
Confidence               000000      0111222222 23334567899999999999999999998 589999999999999999999999


Q ss_pred             hhcCC-ee-EEEEeccccccccccCccEEEEECCCCChhHHHHhhccCCCCCCceEEEEE
Q 037567          274 FIRDE-IR-VMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLY  331 (374)
Q Consensus       274 f~~g~-~~-ilv~t~~~~~G~d~~~~~~vi~~~~p~s~~~~~Q~~GR~~R~~~~g~~~~~  331 (374)
                      |+++. +. .|++|.+.+-|+|+..++-||+|||.|++..-.|..-||.|.||..-|.+|
T Consensus       593 Fne~~s~~VFLLTTrvGGLGlNLTgAnRVIIfDPdWNPStD~QAreRawRiGQkkdV~VY  652 (923)
T KOG0387|consen  593 FNEDESIFVFLLTTRVGGLGLNLTGANRVIIFDPDWNPSTDNQARERAWRIGQKKDVVVY  652 (923)
T ss_pred             hcCCCceEEEEEEecccccccccccCceEEEECCCCCCccchHHHHHHHhhcCccceEEE
Confidence            99875 34 466888999999999999999999999999999999999999997665554

>KOG1123 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, 3'-5' helicase subunit SSL2 [Transcription; Replication, recombination and repair]

Probab=99.92  E-value=3.6e-24  Score=184.76  Aligned_cols=288  Identities=18%  Similarity=0.158  Sum_probs=195.6

Q ss_pred             CCchhHHHHHHHHHcC---CCEEEEccCCCCchhhhhccccccCCcEEEEcchHHHHHHHHHHHHHc----CCceEEcCC
Q 037567           13 VFRPYQKDVIQRIIEK---RDCLVVMATGSGKSLCYQLPPLVTGKTALVVSPLISLMQDQVMSLKQR----GINAEFLGS   85 (374)
Q Consensus        13 ~~~~~Q~~~~~~~~~~---~~~l~~a~tGsGKT~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~----~~~~~~~~~   85 (374)
                      .+||||++++..++-+   ++.+++.|||+|||+...-++..-.+++|++|.+...+.||..+++.|    ...++.+++
T Consensus       302 ~iRpYQEksL~KMFGNgRARSGiIVLPCGAGKtLVGvTAa~tikK~clvLcts~VSVeQWkqQfk~wsti~d~~i~rFTs  381 (776)
T KOG1123|consen  302 QIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKTLVGVTAACTIKKSCLVLCTSAVSVEQWKQQFKQWSTIQDDQICRFTS  381 (776)
T ss_pred             ccCchHHHHHHHHhCCCcccCceEEEecCCCCceeeeeeeeeecccEEEEecCccCHHHHHHHHHhhcccCccceEEeec
Confidence            6899999999999853   578999999999999888777778899999999999999999999887    233444444


Q ss_pred             CCCchhhhhhhhcCCeeEEEEcCcccccCchhhHH------HHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHHhc
Q 037567           86 AQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWS------KLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFL  159 (374)
Q Consensus        86 ~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~------~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~  159 (374)
                      ....      ....++.|+|+|+.++...-.+.+.      .+....|.++++||+|.+..         ....+.....
T Consensus       382 d~Ke------~~~~~~gvvvsTYsMva~t~kRS~eaek~m~~l~~~EWGllllDEVHvvPA---------~MFRRVlsiv  446 (776)
T KOG1123|consen  382 DAKE------RFPSGAGVVVTTYSMVAYTGKRSHEAEKIMDFLRGREWGLLLLDEVHVVPA---------KMFRRVLSIV  446 (776)
T ss_pred             cccc------cCCCCCcEEEEeeehhhhcccccHHHHHHHHHHhcCeeeeEEeehhccchH---------HHHHHHHHHH
Confidence            3222      1234568999999988766544332      33456799999999998865         2223333333


Q ss_pred             CCCCeeEEEeecCcccHHHHHHhcC-CCCCeEEEecc-----------------C------------CCceeEEEEeecC
Q 037567          160 LGVPFVALTATATEKVRIDIINSLK-LKNPYVTIASF-----------------D------------RKNLFYGVKVINR  209 (374)
Q Consensus       160 ~~~~~i~~SaT~~~~~~~~~~~~~~-~~~~~~~~~~~-----------------~------------~~~~~~~~~~~~~  209 (374)
                      .....+++|||+-.++.+  ...+. +-.|.......                 .            ..+.....-...-
T Consensus       447 ~aHcKLGLTATLvREDdK--I~DLNFLIGPKlYEAnWmdL~~kGhIA~VqCaEVWCpMt~eFy~eYL~~~t~kr~lLyvM  524 (776)
T KOG1123|consen  447 QAHCKLGLTATLVREDDK--ITDLNFLIGPKLYEANWMDLQKKGHIAKVQCAEVWCPMTPEFYREYLRENTRKRMLLYVM  524 (776)
T ss_pred             HHHhhccceeEEeecccc--ccccceeecchhhhccHHHHHhCCceeEEeeeeeecCCCHHHHHHHHhhhhhhhheeeec
Confidence            344568999998877654  11111 11111111100                 0            0000000001111


Q ss_pred             CcchHHHHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcC-CeeEEEEeccc
Q 037567          210 GQSFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRD-EIRVMVATMAF  288 (374)
Q Consensus       210 ~~~~~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g-~~~ilv~t~~~  288 (374)
                      +.......-..+..+...+.++|||..++-.....+-.|.+     -+++|.++..+|.++++.|+.+ .+..++.+...
T Consensus       525 NP~KFraCqfLI~~HE~RgDKiIVFsDnvfALk~YAikl~K-----pfIYG~Tsq~ERm~ILqnFq~n~~vNTIFlSKVg  599 (776)
T KOG1123|consen  525 NPNKFRACQFLIKFHERRGDKIIVFSDNVFALKEYAIKLGK-----PFIYGPTSQNERMKILQNFQTNPKVNTIFLSKVG  599 (776)
T ss_pred             CcchhHHHHHHHHHHHhcCCeEEEEeccHHHHHHHHHHcCC-----ceEECCCchhHHHHHHHhcccCCccceEEEeecc
Confidence            11222222222333344789999999987777666665533     3789999999999999999976 57889999999


Q ss_pred             cccccccCccEEEEECCC-CChhHHHHhhccCCCC
Q 037567          289 GMGIDKPDVRHVIHYGCP-KTLESYYQESGRCGRD  322 (374)
Q Consensus       289 ~~G~d~~~~~~vi~~~~p-~s~~~~~Q~~GR~~R~  322 (374)
                      .+++|+|..+++|..+.- -|..+-.||.||..|.
T Consensus       600 DtSiDLPEAnvLIQISSH~GSRRQEAQRLGRILRA  634 (776)
T KOG1123|consen  600 DTSIDLPEANVLIQISSHGGSRRQEAQRLGRILRA  634 (776)
T ss_pred             CccccCCcccEEEEEcccccchHHHHHHHHHHHHH
Confidence            999999999999976543 4678889999998885

>cd00268 DEADc DEAD-box helicases

Probab=99.92  E-value=1.2e-24  Score=179.17  Aligned_cols=166  Identities=20%  Similarity=0.260  Sum_probs=123.2

Q ss_pred             hhHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc--------cCCcEEEEcchHHHHHHHHHHH
Q 037567            2 VSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV--------TGKTALVVSPLISLMQDQVMSL   73 (374)
Q Consensus         2 ~~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~--------~~~~~lil~P~~~l~~q~~~~~   73 (374)
                      .+.+.+ +|+..|+++|.++++.+.+++++++.+|||+|||++|+++++.        .+.+++|++|+++|+.|+...+
T Consensus        11 ~~~l~~-~~~~~~~~~Q~~~~~~~~~~~~~li~~~TG~GKT~~~~~~~l~~~~~~~~~~~~~viii~p~~~L~~q~~~~~   89 (203)
T cd00268          11 LRGIYA-LGFEKPTPIQARAIPPLLSGRDVIGQAQTGSGKTAAFLIPILEKLDPSPKKDGPQALILAPTRELALQIAEVA   89 (203)
T ss_pred             HHHHHH-cCCCCCCHHHHHHHHHHhcCCcEEEECCCCCcHHHHHHHHHHHHHHhhcccCCceEEEEcCCHHHHHHHHHHH
Confidence            456677 7999999999999999999999999999999999998877653        2458999999999999999888


Q ss_pred             HHc----CCceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHH
Q 037567           74 KQR----GINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEY  149 (374)
Q Consensus        74 ~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~  149 (374)
                      ..+    +.......++....... ....++++|+|+||+++...+...  ...+.+++++|+||+|.+.+.+.  .   
T Consensus        90 ~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~iiv~T~~~l~~~l~~~--~~~~~~l~~lIvDE~h~~~~~~~--~---  161 (203)
T cd00268          90 RKLGKHTNLKVVVIYGGTSIDKQI-RKLKRGPHIVVATPGRLLDLLERG--KLDLSKVKYLVLDEADRMLDMGF--E---  161 (203)
T ss_pred             HHHhccCCceEEEEECCCCHHHHH-HHhcCCCCEEEEChHHHHHHHHcC--CCChhhCCEEEEeChHHhhccCh--H---
Confidence            776    44444454444332222 223356899999999887765542  24556789999999999875432  2   


Q ss_pred             HHHHHHHHhc-CCCCeeEEEeecCcccH
Q 037567          150 KQLDKLRTFL-LGVPFVALTATATEKVR  176 (374)
Q Consensus       150 ~~~~~~~~~~-~~~~~i~~SaT~~~~~~  176 (374)
                      ..+..+...+ .+.+++++|||+++...
T Consensus       162 ~~~~~~~~~l~~~~~~~~~SAT~~~~~~  189 (203)
T cd00268         162 DQIREILKLLPKDRQTLLFSATMPKEVR  189 (203)
T ss_pred             HHHHHHHHhCCcccEEEEEeccCCHHHH
Confidence            2222222222 36889999999997654

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.

>TIGR00631 uvrb excinuclease ABC, B subunit

Probab=99.92  E-value=2.4e-22  Score=188.92  Aligned_cols=124  Identities=27%  Similarity=0.383  Sum_probs=113.4

Q ss_pred             cchHHHHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccc
Q 037567          211 QSFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGM  290 (374)
Q Consensus       211 ~~~~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~  290 (374)
                      ......++.++.+....+.+++|||+++..++.+++.|.+.|+++..+||+++..+|.+++..|+.|+++|+|||+.+++
T Consensus       425 ~~qi~~Ll~eI~~~~~~g~~vLIf~~tk~~ae~L~~~L~~~gi~~~~lh~~~~~~eR~~~l~~fr~G~i~VLV~t~~L~r  504 (655)
T TIGR00631       425 DGQVDDLLSEIRQRVARNERVLVTTLTKKMAEDLTDYLKELGIKVRYLHSEIDTLERVEIIRDLRLGEFDVLVGINLLRE  504 (655)
T ss_pred             cchHHHHHHHHHHHHcCCCEEEEEECCHHHHHHHHHHHhhhccceeeeeCCCCHHHHHHHHHHHhcCCceEEEEcChhcC
Confidence            34556777777777778899999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccccCccEEEEEC-----CCCChhHHHHhhccCCCCCCceEEEEEeecc
Q 037567          291 GIDKPDVRHVIHYG-----CPKTLESYYQESGRCGRDGIASVCWLYYARS  335 (374)
Q Consensus       291 G~d~~~~~~vi~~~-----~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~  335 (374)
                      |+|+|++++|++++     .|.+...|+||+||+||. ..|.++++.+..
T Consensus       505 GfDiP~v~lVvi~DadifG~p~~~~~~iqriGRagR~-~~G~vi~~~~~~  553 (655)
T TIGR00631       505 GLDLPEVSLVAILDADKEGFLRSERSLIQTIGRAARN-VNGKVIMYADKI  553 (655)
T ss_pred             CeeeCCCcEEEEeCcccccCCCCHHHHHHHhcCCCCC-CCCEEEEEEcCC
Confidence            99999999999887     788999999999999997 578888888764

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

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

Probab=99.91  E-value=9.2e-23  Score=189.97  Aligned_cols=285  Identities=20%  Similarity=0.246  Sum_probs=195.3

Q ss_pred             hHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhcc---ccccCCcEEEEcchHHHHHHHHHHHHHcC--
Q 037567            3 STLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLP---PLVTGKTALVVSPLISLMQDQVMSLKQRG--   77 (374)
Q Consensus         3 ~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~---~~~~~~~~lil~P~~~l~~q~~~~~~~~~--   77 (374)
                      +.|++..|+ +|+..|.-....+..|+++-+.||||.|||...++.   ...+++++++++||..|+.|+.+.++++.  
T Consensus        73 ~fF~k~~G~-~~ws~QR~WakR~~rg~SFaiiAPTGvGKTTfg~~~sl~~a~kgkr~yii~PT~~Lv~Q~~~kl~~~~e~  151 (1187)
T COG1110          73 EFFKKATGF-RPWSAQRVWAKRLVRGKSFAIIAPTGVGKTTFGLLMSLYLAKKGKRVYIIVPTTTLVRQVYERLKKFAED  151 (1187)
T ss_pred             HHHHHhhCC-CchHHHHHHHHHHHcCCceEEEcCCCCchhHHHHHHHHHHHhcCCeEEEEecCHHHHHHHHHHHHHHHhh
Confidence            457777888 699999999999999999999999999999543332   33468999999999999999999999874  


Q ss_pred             ---CceEE-cCCCCCc---hhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHH--
Q 037567           78 ---INAEF-LGSAQTD---SSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLE--  148 (374)
Q Consensus        78 ---~~~~~-~~~~~~~---~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~--  148 (374)
                         ..+.+ .++..+.   .+.......++++|+|+|..-|.    .....+...+++++++|+++.+...+......  
T Consensus       152 ~~~~~~~~~yh~~l~~~ekee~le~i~~gdfdIlitTs~FL~----k~~e~L~~~kFdfifVDDVDA~LkaskNvDriL~  227 (1187)
T COG1110         152 AGSLDVLVVYHSALPTKEKEEALERIESGDFDILITTSQFLS----KRFEELSKLKFDFIFVDDVDAILKASKNVDRLLR  227 (1187)
T ss_pred             cCCcceeeeeccccchHHHHHHHHHHhcCCccEEEEeHHHHH----hhHHHhcccCCCEEEEccHHHHHhccccHHHHHH
Confidence               33333 2222222   23345566789999999976442    33445555679999999999986422111000  


Q ss_pred             ---------------------------HHHHHHHH---------HhcCCCCeeEEEeecCcccH--HHHHHhcCCCCCeE
Q 037567          149 ---------------------------YKQLDKLR---------TFLLGVPFVALTATATEKVR--IDIINSLKLKNPYV  190 (374)
Q Consensus       149 ---------------------------~~~~~~~~---------~~~~~~~~i~~SaT~~~~~~--~~~~~~~~~~~~~~  190 (374)
                                                 ...+.+..         ........++.|||..+...  .-+...++......
T Consensus       228 LlGf~eE~i~~a~~~~~lr~~~~~~~~~~~~~e~~~~~e~~~~~~r~k~g~LvvsSATg~~rg~R~~LfReLlgFevG~~  307 (1187)
T COG1110         228 LLGFSEEVIESAYELIKLRRKLYGEKRAERVREELREVEREREKKRRKLGILVVSSATGKPRGSRLKLFRELLGFEVGSG  307 (1187)
T ss_pred             HcCCCHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHhccCCceEEEeeccCCCCCchHHHHHHHhCCccCcc
Confidence                                       01111111         12234678999999877542  22344444443321


Q ss_pred             EEeccCCCceeEEEEeecCCcchHHHHHHHHHHhhcCCCcEEEEecc---hhHHHHHHHHHHHcCCceeeeecCCChHHH
Q 037567          191 TIASFDRKNLFYGVKVINRGQSFVDELVQEILKSVAGAGSIIVYCMT---IKDVEEISKALKQLGVKAGTYHGQMGSKAR  267 (374)
Q Consensus       191 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lVf~~~---~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r  267 (374)
                      ...   ..|+.   +.....  ....-+.++++.+  +..+|||++.   .+.++.+++.|+.+|+++..+|++     +
T Consensus       308 ~~~---LRNIv---D~y~~~--~~~e~~~elvk~l--G~GgLIfV~~d~G~e~aeel~e~Lr~~Gi~a~~~~a~-----~  372 (1187)
T COG1110         308 GEG---LRNIV---DIYVES--ESLEKVVELVKKL--GDGGLIFVPIDYGREKAEELAEYLRSHGINAELIHAE-----K  372 (1187)
T ss_pred             chh---hhhee---eeeccC--ccHHHHHHHHHHh--CCCeEEEEEcHHhHHHHHHHHHHHHhcCceEEEeecc-----c
Confidence            111   11211   111111  2233344455554  4467999999   999999999999999999999984     2


Q ss_pred             HHHHHhhhcCCeeEEEEec----cccccccccC-ccEEEEECCCC
Q 037567          268 EEAHRLFIRDEIRVMVATM----AFGMGIDKPD-VRHVIHYGCPK  307 (374)
Q Consensus       268 ~~~~~~f~~g~~~ilv~t~----~~~~G~d~~~-~~~vi~~~~p~  307 (374)
                      ...++.|..|++++||++.    .+-+|+|+|. ++.+|+++.|.
T Consensus       373 ~~~le~F~~GeidvLVGvAsyYG~lVRGlDLP~rirYaIF~GvPk  417 (1187)
T COG1110         373 EEALEDFEEGEVDVLVGVASYYGVLVRGLDLPHRIRYAVFYGVPK  417 (1187)
T ss_pred             hhhhhhhccCceeEEEEecccccceeecCCchhheeEEEEecCCc
Confidence            6778999999999999775    7789999998 88999999994

>KOG0923 consensus mRNA splicing factor ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.91  E-value=3.6e-23  Score=184.01  Aligned_cols=315  Identities=17%  Similarity=0.198  Sum_probs=218.1

Q ss_pred             HhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhh---hc--cccccCCcEEEEcchHHHHHHHHHHHH-HcCCc
Q 037567            6 KKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCY---QL--PPLVTGKTALVVSPLISLMQDQVMSLK-QRGIN   79 (374)
Q Consensus         6 ~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~---~l--~~~~~~~~~lil~P~~~l~~q~~~~~~-~~~~~   79 (374)
                      .+....-+.+++-.+.+.++..+..++|.|.||||||.-.   +.  .....++++=+.-|+|..+-.++..+. ..|.+
T Consensus       258 ee~RksLPVy~ykdell~av~e~QVLiI~GeTGSGKTTQiPQyL~EaGytk~gk~IgcTQPRRVAAmSVAaRVA~EMgvk  337 (902)
T KOG0923|consen  258 EEVRKSLPVYPYKDELLKAVKEHQVLIIVGETGSGKTTQIPQYLYEAGYTKGGKKIGCTQPRRVAAMSVAARVAEEMGVK  337 (902)
T ss_pred             HHHHhcCCchhhHHHHHHHHHhCcEEEEEcCCCCCccccccHHHHhcccccCCceEeecCcchHHHHHHHHHHHHHhCcc
Confidence            3334455677888899999999999999999999999531   11  111234558888899988877766654 34444


Q ss_pred             eEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHHhc
Q 037567           80 AEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFL  159 (374)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~  159 (374)
                      ..--.+.....+..   .....-+-++|.++|++   .+.....+.+++++||||||.   ........+..+..+..+.
T Consensus       338 LG~eVGYsIRFEdc---TSekTvlKYMTDGmLlR---EfL~epdLasYSViiiDEAHE---RTL~TDILfgLvKDIar~R  408 (902)
T KOG0923|consen  338 LGHEVGYSIRFEDC---TSEKTVLKYMTDGMLLR---EFLSEPDLASYSVIIVDEAHE---RTLHTDILFGLVKDIARFR  408 (902)
T ss_pred             cccccceEEEeccc---cCcceeeeeecchhHHH---HHhccccccceeEEEeehhhh---hhhhhhHHHHHHHHHHhhC
Confidence            33222221111111   11234577899997754   445566778899999999994   4455667778888898888


Q ss_pred             CCCCeeEEEeecCcccHHHHHHhcCCCCCeEEEeccCCCceeEEEEee-cCCcchHHHHHHHHHH--hhcCCCcEEEEec
Q 037567          160 LGVPFVALTATATEKVRIDIINSLKLKNPYVTIASFDRKNLFYGVKVI-NRGQSFVDELVQEILK--SVAGAGSIIVYCM  236 (374)
Q Consensus       160 ~~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~--~~~~~~~~lVf~~  236 (374)
                      ++.+.+.+|||+.....   ..++. .-++...+. .+  ......+. .....++...+..+++  ...+.+.+|||..
T Consensus       409 pdLKllIsSAT~DAekF---S~fFD-dapIF~iPG-RR--yPVdi~Yt~~PEAdYldAai~tVlqIH~tqp~GDILVFlt  481 (902)
T KOG0923|consen  409 PDLKLLISSATMDAEKF---SAFFD-DAPIFRIPG-RR--YPVDIFYTKAPEADYLDAAIVTVLQIHLTQPLGDILVFLT  481 (902)
T ss_pred             CcceEEeeccccCHHHH---HHhcc-CCcEEeccC-cc--cceeeecccCCchhHHHHHHhhheeeEeccCCccEEEEec
Confidence            99999999999987543   33332 222222221 11  11111111 1223345555555533  2346789999999


Q ss_pred             chhHHHHHHHHHHHc---------CCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEEEEECC--
Q 037567          237 TIKDVEEISKALKQL---------GVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGC--  305 (374)
Q Consensus       237 ~~~~~~~l~~~l~~~---------~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~~~~--  305 (374)
                      ..++.+...+.|++.         .+-+.++|+.++.+....+.+.--.|-.+|+++|+++++++.++++..||+.+.  
T Consensus       482 GQeEIEt~~e~l~~~~~~LGski~eliv~PiYaNLPselQakIFePtP~gaRKVVLATNIAETSlTIdgI~yViDpGf~K  561 (902)
T KOG0923|consen  482 GQEEIETVKENLKERCRRLGSKIRELIVLPIYANLPSELQAKIFEPTPPGARKVVLATNIAETSLTIDGIKYVIDPGFVK  561 (902)
T ss_pred             cHHHHHHHHHHHHHHHHHhccccceEEEeeccccCChHHHHhhcCCCCCCceeEEEeecchhhceeecCeEEEecCcccc
Confidence            999998888887763         234778999999999999988888888999999999999999999999996553  


Q ss_pred             ----------------CCChhHHHHhhccCCCCCCceEEEEEeeccCC
Q 037567          306 ----------------PKTLESYYQESGRCGRDGIASVCWLYYARSNF  337 (374)
Q Consensus       306 ----------------p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~~  337 (374)
                                      |.|...-.||.|||||.| +|.|+-+|+.-.+
T Consensus       562 ~nsynprtGmesL~v~piSKAsA~QRaGRAGRtg-PGKCfRLYt~~aY  608 (902)
T KOG0923|consen  562 QNSYNPRTGMESLLVTPISKASANQRAGRAGRTG-PGKCFRLYTAWAY  608 (902)
T ss_pred             ccCcCCCcCceeEEEeeechhhhhhhccccCCCC-CCceEEeechhhh
Confidence                            347788899999999987 8899999985443

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

Probab=99.90  E-value=5.5e-24  Score=170.18  Aligned_cols=155  Identities=27%  Similarity=0.357  Sum_probs=115.0

Q ss_pred             chhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc---c--CCcEEEEcchHHHHHHHHHHHHHcCC----ceEEcCC
Q 037567           15 RPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV---T--GKTALVVSPLISLMQDQVMSLKQRGI----NAEFLGS   85 (374)
Q Consensus        15 ~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~---~--~~~~lil~P~~~l~~q~~~~~~~~~~----~~~~~~~   85 (374)
                      +|+|.++++.+.+++++++.||||+|||++++++++.   +  ..++++++|+++|++|..+.+..+..    ....+.+
T Consensus         1 t~~Q~~~~~~i~~~~~~li~aptGsGKT~~~~~~~l~~~~~~~~~~~lii~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~   80 (169)
T PF00270_consen    1 TPLQQEAIEAIISGKNVLISAPTGSGKTLAYILPALNRLQEGKDARVLIIVPTRALAEQQFERLRKFFSNTNVRVVLLHG   80 (169)
T ss_dssp             -HHHHHHHHHHHTTSEEEEECSTTSSHHHHHHHHHHHHHHTTSSSEEEEEESSHHHHHHHHHHHHHHTTTTTSSEEEEST
T ss_pred             CHHHHHHHHHHHcCCCEEEECCCCCccHHHHHHHHHhhhccCCCceEEEEeecccccccccccccccccccccccccccc
Confidence            6899999999999999999999999999998877654   2  34899999999999999999987744    4455555


Q ss_pred             CCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHHhcCCCCee
Q 037567           86 AQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFV  165 (374)
Q Consensus        86 ~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~~~~~~i  165 (374)
                      +............++++|+|+||+++.......  .....++++||+||+|.+..++  +...+..+.......++.+++
T Consensus        81 ~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~--~~~~~~~~~iViDE~h~l~~~~--~~~~~~~i~~~~~~~~~~~~i  156 (169)
T PF00270_consen   81 GQSISEDQREVLSNQADILVTTPEQLLDLISNG--KINISRLSLIVIDEAHHLSDET--FRAMLKSILRRLKRFKNIQII  156 (169)
T ss_dssp             TSCHHHHHHHHHHTTSSEEEEEHHHHHHHHHTT--SSTGTTESEEEEETHHHHHHTT--HHHHHHHHHHHSHTTTTSEEE
T ss_pred             cccccccccccccccccccccCcchhhcccccc--ccccccceeeccCccccccccc--HHHHHHHHHHHhcCCCCCcEE
Confidence            444332333333556899999999987765551  1234558999999999998753  233334444444444568899


Q ss_pred             EEEeecCc
Q 037567          166 ALTATATE  173 (374)
Q Consensus       166 ~~SaT~~~  173 (374)
                      ++|||++.
T Consensus       157 ~~SAT~~~  164 (169)
T PF00270_consen  157 LLSATLPS  164 (169)
T ss_dssp             EEESSSTH
T ss_pred             EEeeCCCh
Confidence            99999983

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 ....

>KOG0390 consensus DNA repair protein, SNF2 family [Replication, recombination and repair]

Probab=99.90  E-value=4.9e-22  Score=184.26  Aligned_cols=306  Identities=19%  Similarity=0.169  Sum_probs=195.1

Q ss_pred             CCchhHHHHHHHHHcC----------CCEEEEccCCCCchhhh---hccccc--cC-----CcEEEEcchHHHHHHHHHH
Q 037567           13 VFRPYQKDVIQRIIEK----------RDCLVVMATGSGKSLCY---QLPPLV--TG-----KTALVVSPLISLMQDQVMS   72 (374)
Q Consensus        13 ~~~~~Q~~~~~~~~~~----------~~~l~~a~tGsGKT~~~---~l~~~~--~~-----~~~lil~P~~~l~~q~~~~   72 (374)
                      .++|||.+++..+++.          ..+|+...+|+|||+..   +...+.  .+     .+.|||+|. .|+..|.++
T Consensus       238 ~LrPHQ~EG~~FL~knl~g~~~~~~~~GCImAd~~GlGKTlq~IsflwtlLrq~P~~~~~~~k~lVV~P~-sLv~nWkkE  316 (776)
T KOG0390|consen  238 ILRPHQREGFEFLYKNLAGLIRPKNSGGCIMADEPGLGKTLQCISFIWTLLRQFPQAKPLINKPLVVAPS-SLVNNWKKE  316 (776)
T ss_pred             hcCchHHHHHHHHHhhhhcccccCCCCceEeeCCCCcchHHHHHHHHHHHHHhCcCccccccccEEEccH-HHHHHHHHH
Confidence            5899999999998751          24677777999999542   233333  34     789999999 799999999


Q ss_pred             HHHcCCc--eE--EcCCCCCc-hh-----hhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhccc
Q 037567           73 LKQRGIN--AE--FLGSAQTD-SS-----VQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWG  142 (374)
Q Consensus        73 ~~~~~~~--~~--~~~~~~~~-~~-----~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~  142 (374)
                      |.++...  ..  .+.+.... ..     .......-..-+++.+++.+.    .....+....++++|+||.|.+.+..
T Consensus       317 F~KWl~~~~i~~l~~~~~~~~~w~~~~sil~~~~~~~~~~vli~sye~~~----~~~~~il~~~~glLVcDEGHrlkN~~  392 (776)
T KOG0390|consen  317 FGKWLGNHRINPLDFYSTKKSSWIKLKSILFLGYKQFTTPVLIISYETAS----DYCRKILLIRPGLLVCDEGHRLKNSD  392 (776)
T ss_pred             HHHhccccccceeeeecccchhhhhhHHHHHhhhhheeEEEEeccHHHHH----HHHHHHhcCCCCeEEECCCCCccchh
Confidence            9998543  22  12221111 00     000111122356677777664    33355667789999999999987633


Q ss_pred             CcchHHHHHHHHHHHhcCCCCeeEEEeecCcccHHHHHHhcCCCCCeEEEecc---------------------C-----
Q 037567          143 HDFRLEYKQLDKLRTFLLGVPFVALTATATEKVRIDIINSLKLKNPYVTIASF---------------------D-----  196 (374)
Q Consensus       143 ~~~~~~~~~~~~~~~~~~~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~---------------------~-----  196 (374)
                             ..+...+..+.-.+.|++|+||-.+...++.+.+.+..|.......                     +     
T Consensus       393 -------s~~~kaL~~l~t~rRVLLSGTp~QNdl~EyFnlL~fvrP~~Lgs~~sf~k~~~~~i~~~~~~~~s~e~~~~~~  465 (776)
T KOG0390|consen  393 -------SLTLKALSSLKTPRRVLLTGTPIQNDLKEYFNLLDFVRPGFLGSISSFKKKFEIPILRGRDADASEEDREREE  465 (776)
T ss_pred             -------hHHHHHHHhcCCCceEEeeCCcccccHHHHHHHHhhcChhhccchHHHHHHhhcccccccCCCcchhhhhhHH
Confidence                   3444455555677899999999999887766665544332111000                     0     


Q ss_pred             ------------------------CCceeEEEEeecCCcchHHHHHHHHHH-------------------hh--------
Q 037567          197 ------------------------RKNLFYGVKVINRGQSFVDELVQEILK-------------------SV--------  225 (374)
Q Consensus       197 ------------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~-------------------~~--------  225 (374)
                                              .+.....+.+..... .-..+...++.                   ..        
T Consensus       466 rl~eL~~~t~~fi~rrt~~il~k~LP~k~e~vv~~n~t~-~Q~~~~~~l~~~~~~~~~~~~~l~~~~~L~k~cnhP~L~~  544 (776)
T KOG0390|consen  466 RLQELRELTNKFILRRTGDILLKYLPGKYEYVVFCNPTP-IQKELYKKLLDSMKMRTLKGYALELITKLKKLCNHPSLLL  544 (776)
T ss_pred             HHHHHHHHHHhheeecccchhhhhCCCceeEEEEeCCcH-HHHHHHHHHHHHHHhhhhhcchhhHHHHHHHHhcCHHhhc
Confidence                                    000000000111000 00000000000                   00        


Q ss_pred             ------------------------------------------------cCCCcEEEEecchhHHHHHHHHHHHcCCceee
Q 037567          226 ------------------------------------------------AGAGSIIVYCMTIKDVEEISKALKQLGVKAGT  257 (374)
Q Consensus       226 ------------------------------------------------~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~  257 (374)
                                                                      ....++.+..|-....+.+.+.++-+|..+..
T Consensus       545 ~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~ks~kl~~L~~ll~~~~ek~~~~~v~Isny~~tldl~e~~~~~~g~~~~r  624 (776)
T KOG0390|consen  545 LCEKTEKEKAFKNPALLLDPGKLKLDAGDGSKSGKLLVLVFLLEVIREKLLVKSVLISNYTQTLDLFEQLCRWRGYEVLR  624 (776)
T ss_pred             ccccccccccccChHhhhcccccccccccchhhhHHHHHHHHHHHHhhhcceEEEEeccHHHHHHHHHHHHhhcCceEEE
Confidence                                                            00012333334444555555555557999999


Q ss_pred             eecCCChHHHHHHHHhhhcCC--eeE-EEEeccccccccccCccEEEEECCCCChhHHHHhhccCCCCCCceEEEEE
Q 037567          258 YHGQMGSKAREEAHRLFIRDE--IRV-MVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLY  331 (374)
Q Consensus       258 ~~~~~~~~~r~~~~~~f~~g~--~~i-lv~t~~~~~G~d~~~~~~vi~~~~p~s~~~~~Q~~GR~~R~~~~g~~~~~  331 (374)
                      ++|.++..+|+.+++.|++..  ..| |.++.+.++|+|+-+.+-+|.+|+.||+..-.|+++|+.|.||...|++|
T Consensus       625 LdG~~~~~qRq~~vd~FN~p~~~~~vfLlSsKAgg~GinLiGAsRlil~D~dWNPa~d~QAmaR~~RdGQKk~v~iY  701 (776)
T KOG0390|consen  625 LDGKTSIKQRQKLVDTFNDPESPSFVFLLSSKAGGEGLNLIGASRLILFDPDWNPAVDQQAMARAWRDGQKKPVYIY  701 (776)
T ss_pred             EcCCCchHHHHHHHHhccCCCCCceEEEEecccccCceeecccceEEEeCCCCCchhHHHHHHHhccCCCcceEEEE
Confidence            999999999999999999853  234 45777999999999999999999999999999999999999999888765

>KOG0924 consensus mRNA splicing factor ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.90  E-value=1.9e-22  Score=179.97  Aligned_cols=333  Identities=16%  Similarity=0.159  Sum_probs=223.5

Q ss_pred             cCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccc----cccCCcEEEEcchHHHHHHHHHHHHH-cCCceEEc
Q 037567            9 FGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPP----LVTGKTALVVSPLISLMQDQVMSLKQ-RGINAEFL   83 (374)
Q Consensus         9 ~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~----~~~~~~~lil~P~~~l~~q~~~~~~~-~~~~~~~~   83 (374)
                      -.+-+....+.+.+..+-.++-+++.+.||||||.-..--+    ...+.-+-+.-|++..+-.+++.+.. .|....-.
T Consensus       352 rq~LPvf~~R~~ll~~ir~n~vvvivgETGSGKTTQl~QyL~edGY~~~GmIGcTQPRRvAAiSVAkrVa~EM~~~lG~~  431 (1042)
T KOG0924|consen  352 RQYLPVFACRDQLLSVIRENQVVVIVGETGSGKTTQLAQYLYEDGYADNGMIGCTQPRRVAAISVAKRVAEEMGVTLGDT  431 (1042)
T ss_pred             HhhcchHHHHHHHHHHHhhCcEEEEEecCCCCchhhhHHHHHhcccccCCeeeecCchHHHHHHHHHHHHHHhCCccccc
Confidence            34445556677777777778889999999999995322111    22355667778999888887777653 33332221


Q ss_pred             CCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHHhcCCCC
Q 037567           84 GSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVP  163 (374)
Q Consensus        84 ~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~~~~~  163 (374)
                      .+....-+.   -......|-++|.+-|+.   .......+..+++||+||||.   ........+..+........+.+
T Consensus       432 VGYsIRFEd---vT~~~T~IkymTDGiLLr---EsL~d~~L~kYSviImDEAHE---RslNtDilfGllk~~larRrdlK  502 (1042)
T KOG0924|consen  432 VGYSIRFED---VTSEDTKIKYMTDGILLR---ESLKDRDLDKYSVIIMDEAHE---RSLNTDILFGLLKKVLARRRDLK  502 (1042)
T ss_pred             cceEEEeee---cCCCceeEEEeccchHHH---HHhhhhhhhheeEEEechhhh---cccchHHHHHHHHHHHHhhccce
Confidence            111111111   111234677889886543   444556678889999999995   44555666777888888888999


Q ss_pred             eeEEEeecCcccHHHHHHhcCCCCCeEEEeccCCCceeEEEE-eecCCcchHHHHHHHHHHh--hcCCCcEEEEecchhH
Q 037567          164 FVALTATATEKVRIDIINSLKLKNPYVTIASFDRKNLFYGVK-VINRGQSFVDELVQEILKS--VAGAGSIIVYCMTIKD  240 (374)
Q Consensus       164 ~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~--~~~~~~~lVf~~~~~~  240 (374)
                      +|.+|||+...   .+.++++.-+. ...+.   ........ .......++...+...+.-  ....+.+|||....+.
T Consensus       503 liVtSATm~a~---kf~nfFgn~p~-f~IpG---RTyPV~~~~~k~p~eDYVeaavkq~v~Ihl~~~~GdilIfmtGqed  575 (1042)
T KOG0924|consen  503 LIVTSATMDAQ---KFSNFFGNCPQ-FTIPG---RTYPVEIMYTKTPVEDYVEAAVKQAVQIHLSGPPGDILIFMTGQED  575 (1042)
T ss_pred             EEEeeccccHH---HHHHHhCCCce-eeecC---CccceEEEeccCchHHHHHHHHhhheEeeccCCCCCEEEecCCCcc
Confidence            99999999754   45666662222 11111   11111111 1122233344444443221  1245889999998887


Q ss_pred             HHHHHHHHHHc----------CCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEEEEECC-----
Q 037567          241 VEEISKALKQL----------GVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGC-----  305 (374)
Q Consensus       241 ~~~l~~~l~~~----------~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~~~~-----  305 (374)
                      .+-.+..+++.          ++.+..+++-++..-..++.+.-..|-.+++|+|+++++++.+|++.+||..++     
T Consensus       576 iE~t~~~i~~~l~ql~~~~~~~L~vlpiYSQLp~dlQ~kiFq~a~~~vRK~IvATNIAETSLTi~gI~yVID~Gy~K~kv  655 (1042)
T KOG0924|consen  576 IECTCDIIKEKLEQLDSAPTTDLAVLPIYSQLPADLQAKIFQKAEGGVRKCIVATNIAETSLTIPGIRYVIDTGYCKLKV  655 (1042)
T ss_pred             hhHHHHHHHHHHHhhhcCCCCceEEEeehhhCchhhhhhhcccCCCCceeEEEeccchhhceeecceEEEEecCceeeee
Confidence            76666555442          567889999999988888888777888999999999999999999999997664     


Q ss_pred             -------------CCChhHHHHhhccCCCCCCceEEEEEeeccCCCcccceeccccchHHHHHHHHHH
Q 037567          306 -------------PKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFYCGESQTENQRTAIMESL  360 (374)
Q Consensus       306 -------------p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l  360 (374)
                                   |.|-.+-.||.|||||.| +|.||-+|+.+  .....++....++.++-++--..
T Consensus       656 yn~~~G~D~L~~~pIS~AnA~QRaGRAGRt~-pG~cYRlYTe~--ay~~eml~stvPEIqRTNl~nvV  720 (1042)
T KOG0924|consen  656 YNPRIGMDALQIVPISQANADQRAGRAGRTG-PGTCYRLYTED--AYKNEMLPSTVPEIQRTNLSNVV  720 (1042)
T ss_pred             cccccccceeEEEechhccchhhccccCCCC-Ccceeeehhhh--HHHhhcccCCCchhhhcchhhHH
Confidence                         347788899999999987 89999999886  34667788888888876654333

>PRK12326 preprotein translocase subunit SecA; Reviewed

Probab=99.90  E-value=1.2e-21  Score=179.97  Aligned_cols=323  Identities=17%  Similarity=0.161  Sum_probs=220.5

Q ss_pred             hhHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc---cCCcEEEEcchHHHHHHHHHHHHH---
Q 037567            2 VSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV---TGKTALVVSPLISLMQDQVMSLKQ---   75 (374)
Q Consensus         2 ~~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~---~~~~~lil~P~~~l~~q~~~~~~~---   75 (374)
                      .++.++.+|+. |++.|.-+.-.+++|+  +..+.||+|||+++.+++..   .+..|.+++|+.-|+.+-++++..   
T Consensus        68 REa~~R~lg~r-~ydvQlig~l~Ll~G~--VaEM~TGEGKTLvA~l~a~l~AL~G~~VhvvT~NdyLA~RDae~m~~ly~  144 (764)
T PRK12326         68 REAAERTLGLR-PFDVQLLGALRLLAGD--VIEMATGEGKTLAGAIAAAGYALQGRRVHVITVNDYLARRDAEWMGPLYE  144 (764)
T ss_pred             HHHHHHHcCCC-cchHHHHHHHHHhCCC--cccccCCCCHHHHHHHHHHHHHHcCCCeEEEcCCHHHHHHHHHHHHHHHH
Confidence            45677788885 8999999998888775  88999999999988877654   588999999999999998888764   


Q ss_pred             -cCCceEEcCCCCCchhhhhhhhcCCeeEEEEcCccccc-Cchhh----HHHHHhcCccEEEEeccchhh-cc-------
Q 037567           76 -RGINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACI-IPISF----WSKLLKAGVCLFAVDEAHCIS-EW-------  141 (374)
Q Consensus        76 -~~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~-~~~~~----~~~~~~~~~~~vviDE~h~~~-~~-------  141 (374)
                       +|+.+....+..+...   ......++|+++|...+.. +++..    ........+.+.||||++.+. +.       
T Consensus       145 ~LGLsvg~i~~~~~~~e---rr~aY~~DItYgTn~e~gFDyLRDnm~~~~~~~v~R~~~faIVDEvDSiLIDeArtPLiI  221 (764)
T PRK12326        145 ALGLTVGWITEESTPEE---RRAAYACDVTYASVNEIGFDVLRDQLVTDVADLVSPNPDVAIIDEADSVLVDEALVPLVL  221 (764)
T ss_pred             hcCCEEEEECCCCCHHH---HHHHHcCCCEEcCCcccccccchhhhccChHhhcCCccceeeecchhhheeccccCceee
Confidence             4888887766544332   2223457999999986532 22221    122334568899999999874 10       


Q ss_pred             -cCcc-hHHHHHHHHHHHhcC-----------------------------------------------------------
Q 037567          142 -GHDF-RLEYKQLDKLRTFLL-----------------------------------------------------------  160 (374)
Q Consensus       142 -~~~~-~~~~~~~~~~~~~~~-----------------------------------------------------------  160 (374)
                       |... ...+..+..+...+.                                                           
T Consensus       222 Sg~~~~~~~y~~~~~~v~~L~~~~dy~ide~~k~v~LTe~G~~~~e~~l~~~~ly~~~~~~~~~~~i~~AL~A~~l~~~d  301 (764)
T PRK12326        222 AGSTPGEAPRGEIAELVRRLREGKDYEIDDDGRNVHLTDKGARKVEKALGGIDLYSEEHVGTTLTQVNVALHAHALLQRD  301 (764)
T ss_pred             eCCCcchhHHHHHHHHHHhcCcCCcEEEEcCCCeeEecHHHHHHHHHHcCCccccCcchhHHHHHHHHHHHHHHHHHhcC
Confidence             0000 000000000000000                                                           


Q ss_pred             ------------------------------------------------------------CCCeeEEEeecCcccHHHHH
Q 037567          161 ------------------------------------------------------------GVPFVALTATATEKVRIDII  180 (374)
Q Consensus       161 ------------------------------------------------------------~~~~i~~SaT~~~~~~~~~~  180 (374)
                                                                                  -.++.+||+|...... .+.
T Consensus       302 ~dYiV~dgeV~iVDe~TGRvm~grrwsdGLHQaIEaKE~v~i~~e~~t~AsIT~QnfFr~Y~kLsGMTGTa~t~~~-Ef~  380 (764)
T PRK12326        302 VHYIVRDGKVHLINASRGRIAQLQRWPDGLQAAVEAKEGLETTETGEVLDTITVQALIGRYPTVCGMTGTAVAAGE-QLR  380 (764)
T ss_pred             CcEEEECCEEEEEECCCCCcCCCCccChHHHHHHHHHcCCCCCCCceeeehhhHHHHHHhcchheeecCCChhHHH-HHH
Confidence                                                                        0125677777654332 445


Q ss_pred             HhcCCCCCeEEEeccCCCcee--EEEEeecCCcchHHHHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHHcCCceeee
Q 037567          181 NSLKLKNPYVTIASFDRKNLF--YGVKVINRGQSFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTY  258 (374)
Q Consensus       181 ~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~  258 (374)
                      ..+++.   +...+.+.+...  .....+.....+...++.++.+....+.++||.+.+.+..+.+++.|.+.|++...+
T Consensus       381 ~iY~l~---Vv~IPtnkp~~R~d~~d~iy~t~~~k~~Aii~ei~~~~~~GrPVLVgt~sI~~SE~ls~~L~~~gI~h~vL  457 (764)
T PRK12326        381 QFYDLG---VSVIPPNKPNIREDEADRVYATAAEKNDAIVEHIAEVHETGQPVLVGTHDVAESEELAERLRAAGVPAVVL  457 (764)
T ss_pred             HHhCCc---EEECCCCCCceeecCCCceEeCHHHHHHHHHHHHHHHHHcCCCEEEEeCCHHHHHHHHHHHHhCCCcceee
Confidence            545443   222222222222  222344455566778888888887899999999999999999999999999999999


Q ss_pred             ecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCc---------------cEEEEECCCCChhHHHHhhccCCCCC
Q 037567          259 HGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDV---------------RHVIHYGCPKTLESYYQESGRCGRDG  323 (374)
Q Consensus       259 ~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~---------------~~vi~~~~p~s~~~~~Q~~GR~~R~~  323 (374)
                      +......+-..+.+.=+  .-.|.|+|+++++|.|+.--               -+||....+.|..--.|..||+||.|
T Consensus       458 NAk~~~~EA~IIa~AG~--~gaVTIATNMAGRGTDIkLg~~~~~~~~~V~~~GGLhVIgTerheSrRID~QLrGRaGRQG  535 (764)
T PRK12326        458 NAKNDAEEARIIAEAGK--YGAVTVSTQMAGRGTDIRLGGSDEADRDRVAELGGLHVIGTGRHRSERLDNQLRGRAGRQG  535 (764)
T ss_pred             ccCchHhHHHHHHhcCC--CCcEEEEecCCCCccCeecCCCcccchHHHHHcCCcEEEeccCCchHHHHHHHhcccccCC
Confidence            88755444333333222  23689999999999998621               26888888999999999999999999


Q ss_pred             CceEEEEEeeccC
Q 037567          324 IASVCWLYYARSN  336 (374)
Q Consensus       324 ~~g~~~~~~~~~~  336 (374)
                      .+|.+-.|++-+|
T Consensus       536 DpGss~f~lSleD  548 (764)
T PRK12326        536 DPGSSVFFVSLED  548 (764)
T ss_pred             CCCceeEEEEcch
Confidence            9999988888766

>PRK05298 excinuclease ABC subunit B; Provisional

Probab=99.89  E-value=3.2e-21  Score=182.81  Aligned_cols=122  Identities=29%  Similarity=0.402  Sum_probs=110.8

Q ss_pred             chHHHHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEecccccc
Q 037567          212 SFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMG  291 (374)
Q Consensus       212 ~~~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G  291 (374)
                      .....++.++.+....+.+++|||++...++.+++.|.+.|+++..+||+++..+|..++..|+.|++.|+|+|+.+++|
T Consensus       430 ~q~~~L~~~L~~~~~~g~~viIf~~t~~~ae~L~~~L~~~gi~~~~~h~~~~~~~R~~~l~~f~~g~i~vlV~t~~L~rG  509 (652)
T PRK05298        430 GQVDDLLSEIRKRVAKGERVLVTTLTKRMAEDLTDYLKELGIKVRYLHSDIDTLERVEIIRDLRLGEFDVLVGINLLREG  509 (652)
T ss_pred             ccHHHHHHHHHHHHhCCCEEEEEeCCHHHHHHHHHHHhhcceeEEEEECCCCHHHHHHHHHHHHcCCceEEEEeCHHhCC
Confidence            33566777776666678899999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccCccEEEEECC-----CCChhHHHHhhccCCCCCCceEEEEEeec
Q 037567          292 IDKPDVRHVIHYGC-----PKTLESYYQESGRCGRDGIASVCWLYYAR  334 (374)
Q Consensus       292 ~d~~~~~~vi~~~~-----p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~  334 (374)
                      +|+|++++|++++.     |.+...|+||+||+||. ..|.++.+++.
T Consensus       510 fdlp~v~lVii~d~eifG~~~~~~~yiqr~GR~gR~-~~G~~i~~~~~  556 (652)
T PRK05298        510 LDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARN-VNGKVILYADK  556 (652)
T ss_pred             ccccCCcEEEEeCCcccccCCCHHHHHHHhccccCC-CCCEEEEEecC
Confidence            99999999998875     77999999999999996 68999988883

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

Probab=99.89  E-value=3.2e-21  Score=189.13  Aligned_cols=172  Identities=15%  Similarity=0.131  Sum_probs=107.5

Q ss_pred             CeeEEEeecCcc-cHHHHHHhcCCCCCeEEEe--c-cC-CCceeEEE--Eeec----CCcchHHHHHHHHHHhh-cCCCc
Q 037567          163 PFVALTATATEK-VRIDIINSLKLKNPYVTIA--S-FD-RKNLFYGV--KVIN----RGQSFVDELVQEILKSV-AGAGS  230 (374)
Q Consensus       163 ~~i~~SaT~~~~-~~~~~~~~~~~~~~~~~~~--~-~~-~~~~~~~~--~~~~----~~~~~~~~~~~~~~~~~-~~~~~  230 (374)
                      .+|++|||+... ....+...+|+.+......  + ++ ..+....+  ....    +.......+...+.+-. ...++
T Consensus       597 ~~il~SATL~~~~~~~~~~~~lGl~~~~~~~~~~spf~~~~~~~l~v~~d~~~~~~~~~~~~~~~ia~~i~~l~~~~~g~  676 (850)
T TIGR01407       597 SLIFTSATLKFSHSFESFPQLLGLTDVHFNTIEPTPLNYAENQRVLIPTDAPAIQNKSLEEYAQEIASYIIEITAITSPK  676 (850)
T ss_pred             eEEEEecccccCCChHHHHHhcCCCccccceecCCCCCHHHcCEEEecCCCCCCCCCChHHHHHHHHHHHHHHHHhcCCC
Confidence            479999999854 2335667788765432211  1 11 11111111  1110    11122223333332221 24679


Q ss_pred             EEEEecchhHHHHHHHHHHHcC--CceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCcc--EEEEECCC
Q 037567          231 IIVYCMTIKDVEEISKALKQLG--VKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVR--HVIHYGCP  306 (374)
Q Consensus       231 ~lVf~~~~~~~~~l~~~l~~~~--~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~--~vi~~~~p  306 (374)
                      +|||+++.+.++.+++.|....  .....+..+.. .+|.++++.|++++..||++|+..++|+|+|+..  .||..+.|
T Consensus       677 ~LVlftS~~~l~~v~~~L~~~~~~~~~~~l~q~~~-~~r~~ll~~F~~~~~~iLlgt~sf~EGVD~~g~~l~~viI~~LP  755 (850)
T TIGR01407       677 ILVLFTSYEMLHMVYDMLNELPEFEGYEVLAQGIN-GSRAKIKKRFNNGEKAILLGTSSFWEGVDFPGNGLVCLVIPRLP  755 (850)
T ss_pred             EEEEeCCHHHHHHHHHHHhhhccccCceEEecCCC-ccHHHHHHHHHhCCCeEEEEcceeecccccCCCceEEEEEeCCC
Confidence            9999999999999999997621  11222333333 5788999999999999999999999999999954  57777776


Q ss_pred             C------------------------------ChhHHHHhhccCCCCCCceEEEEEeecc
Q 037567          307 K------------------------------TLESYYQESGRCGRDGIASVCWLYYARS  335 (374)
Q Consensus       307 ~------------------------------s~~~~~Q~~GR~~R~~~~g~~~~~~~~~  335 (374)
                      .                              ....+.|.+||.-|..++..+++++++.
T Consensus       756 f~~p~dp~~~a~~~~~~~~g~~~f~~~~lP~A~~~l~Qa~GRlIRs~~D~G~v~ilD~R  814 (850)
T TIGR01407       756 FANPKHPLTKKYWQKLEQEGKNPFYDYVLPMAIIRLRQALGRLIRRENDRGSIVILDRR  814 (850)
T ss_pred             CCCCCCHHHHHHHHHHHHhcCCchHHhhHHHHHHHHHHhhccccccCCceEEEEEEccc
Confidence            4                              1245689999999987655556665554

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.

>KOG0949 consensus Predicted helicase, DEAD-box superfamily [General function prediction only]

Probab=99.88  E-value=3.9e-22  Score=184.30  Aligned_cols=155  Identities=18%  Similarity=0.199  Sum_probs=107.2

Q ss_pred             CCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhc---cccc--cCCcEEEEcchHHHHHHHHHHHHHcC-CceE--
Q 037567           10 GYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQL---PPLV--TGKTALVVSPLISLMQDQVMSLKQRG-INAE--   81 (374)
Q Consensus        10 ~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l---~~~~--~~~~~lil~P~~~l~~q~~~~~~~~~-~~~~--   81 (374)
                      +| .|..||.+.+..+-+++..+++|||.+|||++-.-   ..++  ....+++++|+++|++|+...+...- ....  
T Consensus       509 dF-~Pd~WQ~elLDsvDr~eSavIVAPTSaGKTfisfY~iEKVLResD~~VVIyvaPtKaLVnQvsa~VyaRF~~~t~~r  587 (1330)
T KOG0949|consen  509 DF-CPDEWQRELLDSVDRNESAVIVAPTSAGKTFISFYAIEKVLRESDSDVVIYVAPTKALVNQVSANVYARFDTKTFLR  587 (1330)
T ss_pred             cc-CCcHHHHHHhhhhhcccceEEEeeccCCceeccHHHHHHHHhhcCCCEEEEecchHHHhhhhhHHHHHhhccCcccc
Confidence            34 37889999999999999999999999999965221   2232  36678999999999999988876431 2111  


Q ss_pred             --EcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchh-hHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHHh
Q 037567           82 --FLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPIS-FWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTF  158 (374)
Q Consensus        82 --~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~-~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~  158 (374)
                        ...+..+.+..   ...-+|.|+|+-|+-+..++.+ .........++++|+||+|.+.+...      ..+.+..-.
T Consensus       588 g~sl~g~ltqEYs---inp~nCQVLITvPecleslLlspp~~q~~cerIRyiIfDEVH~iG~~ed------~l~~Eqll~  658 (1330)
T KOG0949|consen  588 GVSLLGDLTQEYS---INPWNCQVLITVPECLESLLLSPPHHQKFCERIRYIIFDEVHLIGNEED------GLLWEQLLL  658 (1330)
T ss_pred             chhhHhhhhHHhc---CCchhceEEEEchHHHHHHhcCchhhhhhhhcceEEEechhhhcccccc------chHHHHHHH
Confidence              11111122111   1234689999999988777665 34455667899999999999876332      223333334


Q ss_pred             cCCCCeeEEEeecCcc
Q 037567          159 LLGVPFVALTATATEK  174 (374)
Q Consensus       159 ~~~~~~i~~SaT~~~~  174 (374)
                      +..++++++|||..+.
T Consensus       659 li~CP~L~LSATigN~  674 (1330)
T KOG0949|consen  659 LIPCPFLVLSATIGNP  674 (1330)
T ss_pred             hcCCCeeEEecccCCH
Confidence            4578999999996654

>KOG0920 consensus ATP-dependent RNA helicase A [RNA processing and modification]

Probab=99.87  E-value=1.7e-21  Score=183.74  Aligned_cols=315  Identities=17%  Similarity=0.154  Sum_probs=211.4

Q ss_pred             CCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc------cCCcEEEEcchHHHHHHHHHHHHHc-CCceEEcCC
Q 037567           13 VFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV------TGKTALVVSPLISLMQDQVMSLKQR-GINAEFLGS   85 (374)
Q Consensus        13 ~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~------~~~~~lil~P~~~l~~q~~~~~~~~-~~~~~~~~~   85 (374)
                      ..++.+.++++++.++..+++.|.||+|||.-.-.-++.      ...++++--|+|--|-.+++++..- +...+...+
T Consensus       173 Pa~~~r~~Il~~i~~~qVvvIsGeTGcGKTTQvpQfiLd~~~~~~~~~~IicTQPRRIsAIsvAeRVa~ER~~~~g~~VG  252 (924)
T KOG0920|consen  173 PAYKMRDTILDAIEENQVVVISGETGCGKTTQVPQFILDEAIESGAACNIICTQPRRISAISVAERVAKERGESLGEEVG  252 (924)
T ss_pred             ccHHHHHHHHHHHHhCceEEEeCCCCCCchhhhhHHHHHHHHhcCCCCeEEecCCchHHHHHHHHHHHHHhccccCCeee
Confidence            456788899999999999999999999999532111221      2456888899987776666666532 222111111


Q ss_pred             CCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHHhcCCCCee
Q 037567           86 AQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFV  165 (374)
Q Consensus        86 ~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~~~~~~i  165 (374)
                      .   .............+++||.+-|++.+..   ...+.++..+|+||+|.=   +.+....+..+..+....++.++|
T Consensus       253 Y---qvrl~~~~s~~t~L~fcTtGvLLr~L~~---~~~l~~vthiivDEVHER---~i~~DflLi~lk~lL~~~p~LkvI  323 (924)
T KOG0920|consen  253 Y---QVRLESKRSRETRLLFCTTGVLLRRLQS---DPTLSGVTHIIVDEVHER---SINTDFLLILLKDLLPRNPDLKVI  323 (924)
T ss_pred             E---EEeeecccCCceeEEEecHHHHHHHhcc---CcccccCceeeeeeEEEc---cCCcccHHHHHHHHhhhCCCceEE
Confidence            1   1111112222358999999988766554   445678899999999953   333334445566666777899999


Q ss_pred             EEEeecCcccHHHHHHhcCCCCCeEEEeccCCC------------------ceeEE------------EEe--ecCCcch
Q 037567          166 ALTATATEKVRIDIINSLKLKNPYVTIASFDRK------------------NLFYG------------VKV--INRGQSF  213 (374)
Q Consensus       166 ~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~~~~------------------~~~~~------------~~~--~~~~~~~  213 (374)
                      +||||...+.   +...++ .-+.+..+....+                  .....            ...  .+.+...
T Consensus       324 LMSAT~dae~---fs~YF~-~~pvi~i~grtfpV~~~fLEDil~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~id~~L  399 (924)
T KOG0920|consen  324 LMSATLDAEL---FSDYFG-GCPVITIPGRTFPVKEYFLEDILSKTGYVSEDDSARSGPERSQLRLARLKLWEPEIDYDL  399 (924)
T ss_pred             EeeeecchHH---HHHHhC-CCceEeecCCCcchHHHHHHHHHHHhcccccccccccccccCccccccchhccccccHHH
Confidence            9999988443   334333 2222222111100                  00000            000  0011222


Q ss_pred             HHHHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHHc-------CCceeeeecCCChHHHHHHHHhhhcCCeeEEEEec
Q 037567          214 VDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQL-------GVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATM  286 (374)
Q Consensus       214 ~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~-------~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~  286 (374)
                      ..+++..+.+. ...+.+|||.+..+++..+.+.|...       ..-+.++|+.++..+.+.+....-.|..+|+++|+
T Consensus       400 i~~li~~I~~~-~~~GaILVFLPG~~eI~~~~~~L~~~~~f~~~~~~~ilplHs~~~s~eQ~~VF~~pp~g~RKIIlaTN  478 (924)
T KOG0920|consen  400 IEDLIEYIDER-EFEGAILVFLPGWEEILQLKELLEVNLPFADSLKFAILPLHSSIPSEEQQAVFKRPPKGTRKIILATN  478 (924)
T ss_pred             HHHHHHhcccC-CCCceEEEEcCCHHHHHHHHHHhhhccccccccceEEEeccccCChHHHHHhcCCCCCCcchhhhhhh
Confidence            33444444443 45788999999999999999999753       24467899999999999999988899999999999


Q ss_pred             cccccccccCccEEEEECCCC------------------ChhHHHHhhccCCCCCCceEEEEEeeccCCCcccc
Q 037567          287 AFGMGIDKPDVRHVIHYGCPK------------------TLESYYQESGRCGRDGIASVCWLYYARSNFAKGDF  342 (374)
Q Consensus       287 ~~~~G~d~~~~~~vi~~~~p~------------------s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~~~~~~~  342 (374)
                      +++.++.++++-+||+.+.-.                  |..+-.||.|||||. ++|.||.+|+...++..-.
T Consensus       479 IAETSITIdDVvyVIDsG~~Ke~~yD~~~~~s~l~~~wvSkAna~QR~GRAGRv-~~G~cy~L~~~~~~~~~~~  551 (924)
T KOG0920|consen  479 IAETSITIDDVVYVIDSGLVKEKSYDPERKVSCLLLSWVSKANAKQRRGRAGRV-RPGICYHLYTRSRYEKLML  551 (924)
T ss_pred             hHhhcccccCeEEEEecCeeeeeeecccCCcchhheeeccccchHHhcccccCc-cCCeeEEeechhhhhhccc
Confidence            999999999999999665321                  667789999999997 5899999999977655443

>PRK13103 secA preprotein translocase subunit SecA; Reviewed

Probab=99.87  E-value=5.7e-20  Score=173.02  Aligned_cols=322  Identities=19%  Similarity=0.150  Sum_probs=205.3

Q ss_pred             hHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc---cCCcEEEEcchHHHHHHHHHHHHH----
Q 037567            3 STLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV---TGKTALVVSPLISLMQDQVMSLKQ----   75 (374)
Q Consensus         3 ~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~---~~~~~lil~P~~~l~~q~~~~~~~----   75 (374)
                      ++-++.+|. .+++.|.-+--.+.+|  -+..+.||+|||+++.+++..   .+..|.+++|+..||.+.++++..    
T Consensus        73 Ea~~R~lGm-~~ydVQliGg~~Lh~G--~iaEM~TGEGKTLvA~l~a~l~al~G~~VhvvT~ndyLA~RD~e~m~~l~~~  149 (913)
T PRK13103         73 EAGKRVMGM-RHFDVQLIGGMTLHEG--KIAEMRTGEGKTLVGTLAVYLNALSGKGVHVVTVNDYLARRDANWMRPLYEF  149 (913)
T ss_pred             HHHHHHhCC-CcchhHHHhhhHhccC--ccccccCCCCChHHHHHHHHHHHHcCCCEEEEeCCHHHHHHHHHHHHHHhcc
Confidence            455677786 3777776665555444  499999999999998877653   688999999999999998888765    


Q ss_pred             cCCceEEcCCCCCchhhhhhhhcCCeeEEEEcCccc-----ccCchhhHHHHHhcCccEEEEeccchhh-cc--------
Q 037567           76 RGINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKA-----CIIPISFWSKLLKAGVCLFAVDEAHCIS-EW--------  141 (374)
Q Consensus        76 ~~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l-----~~~~~~~~~~~~~~~~~~vviDE~h~~~-~~--------  141 (374)
                      +|+.+.+..+........   ....++|+++|...+     .+-+..........++.++||||+|.+. +.        
T Consensus       150 lGl~v~~i~~~~~~~err---~~Y~~dI~YGT~~e~gFDYLrD~~~~~~~~~vqr~l~~aIVDEvDsiLIDEArtPLIIS  226 (913)
T PRK13103        150 LGLSVGIVTPFQPPEEKR---AAYAADITYGTNNEFGFDYLRDNMAFSLDDKFQRELNFAVIDEVDSILIDEARTPLIIS  226 (913)
T ss_pred             cCCEEEEECCCCCHHHHH---HHhcCCEEEEcccccccchhhccceechhhhcccccceeEechhhheeccccCCceeec
Confidence            478888776654433322   223379999999875     2211111233344778999999999974 11        


Q ss_pred             cC--cchHHHHHHHHHHHhc--------------------CCCC------------------------------------
Q 037567          142 GH--DFRLEYKQLDKLRTFL--------------------LGVP------------------------------------  163 (374)
Q Consensus       142 ~~--~~~~~~~~~~~~~~~~--------------------~~~~------------------------------------  163 (374)
                      |.  .....+..+..+...+                    ...+                                    
T Consensus       227 g~~~~~~~~y~~~~~~v~~L~~~~~~~~~~~~~~~~y~idek~~~v~LTe~G~~~~e~~~~~~~i~~~~~~ly~~~~~~~  306 (913)
T PRK13103        227 GQAEDSSKLYIEINRLIPRLKQHIEEVEGQVTQEGHFTIDEKTRQVELNEAGHQFIEEMLTQAGLLAEGESLYSAHNLGL  306 (913)
T ss_pred             CCCccchHHHHHHHHHHHHHHhhhhccccccCCCCCeEEEcCCCeeeechHHHHHHHHHhhhCCCcccchhccChhhhHH
Confidence            00  0011111111111111                    0011                                    


Q ss_pred             --------------------------------------------------------------------------------
Q 037567          164 --------------------------------------------------------------------------------  163 (374)
Q Consensus       164 --------------------------------------------------------------------------------  163 (374)
                                                                                                      
T Consensus       307 ~~~i~~AL~A~~lf~~d~dYiV~dg~V~IVDe~TGR~m~grrwsdGLHQaIEaKE~v~I~~e~~t~AsIT~QnfFr~Y~k  386 (913)
T PRK13103        307 LTHVYAGLRAHKLFHRNVEYIVQDGQVLLIDEHTGRTMPGRRLSEGLHQAIEAKENLNIQAESQTLASTTFQNYFRLYNK  386 (913)
T ss_pred             HHHHHHHHHHHHHHhcCCcEEEECCEEEEEECCCCCcCCCCccchHHHHHHHHHcCCCcCCCceeEEeehHHHHHHhcch
Confidence                                                                                            


Q ss_pred             eeEEEeecCcccHHHHHHhcCCCCCeEEEeccCCCce--eEEEEeecCCcchHHHHHHHHHHhhcCCCcEEEEecchhHH
Q 037567          164 FVALTATATEKVRIDIINSLKLKNPYVTIASFDRKNL--FYGVKVINRGQSFVDELVQEILKSVAGAGSIIVYCMTIKDV  241 (374)
Q Consensus       164 ~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lVf~~~~~~~  241 (374)
                      +.+||+|...... .+...+++.   +...+.+.+..  .....++.........++.++......+.++||-+.|+...
T Consensus       387 LsGMTGTa~te~~-Ef~~iY~l~---Vv~IPTnkP~~R~D~~d~vy~t~~eK~~Ai~~ei~~~~~~GrPVLVGT~SVe~S  462 (913)
T PRK13103        387 LSGMTGTADTEAF-EFRQIYGLD---VVVIPPNKPLARKDFNDLVYLTAEEKYAAIITDIKECMALGRPVLVGTATIETS  462 (913)
T ss_pred             hccCCCCCHHHHH-HHHHHhCCC---EEECCCCCCcccccCCCeEEcCHHHHHHHHHHHHHHHHhCCCCEEEEeCCHHHH
Confidence            2222222221111 111111111   11111111111  11112333444566788888888778899999999999999


Q ss_pred             HHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEecccccccccc--------------------------
Q 037567          242 EEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKP--------------------------  295 (374)
Q Consensus       242 ~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~--------------------------  295 (374)
                      +.+++.|++.+++...++......+-..+.+.=+  .-.|.|+|+|+++|.|+.                          
T Consensus       463 E~ls~~L~~~gi~h~VLNAk~~~~EA~IIa~AG~--~GaVTIATNMAGRGTDIkLg~n~~~~~~~~~~~~~~~~~~~~~~  540 (913)
T PRK13103        463 EHMSNLLKKEGIEHKVLNAKYHEKEAEIIAQAGR--PGALTIATNMAGRGTDILLGGNWEVEVAALENPTPEQIAQIKAD  540 (913)
T ss_pred             HHHHHHHHHcCCcHHHhccccchhHHHHHHcCCC--CCcEEEeccCCCCCCCEecCCchHHHHHhhhhhhHHHHHHHHHH
Confidence            9999999999998877777655444444443222  346999999999999994                          


Q ss_pred             -----------CccEEEEECCCCChhHHHHhhccCCCCCCceEEEEEeeccC
Q 037567          296 -----------DVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSN  336 (374)
Q Consensus       296 -----------~~~~vi~~~~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~  336 (374)
                                 +=-+||....+.|..-=.|..||+||.|.+|.+-.|++-+|
T Consensus       541 ~~~~~e~V~e~GGLhVIgTerheSrRID~QLrGRaGRQGDPGsS~f~lSlED  592 (913)
T PRK13103        541 WQKRHQQVIEAGGLHVIASERHESRRIDNQLRGRAGRQGDPGSSRFYLSLED  592 (913)
T ss_pred             HHhHHHHHHHcCCCEEEeeccCchHHHHHHhccccccCCCCCceEEEEEcCc
Confidence                       11257888888899999999999999999999988888766

>PRK12900 secA preprotein translocase subunit SecA; Reviewed

Probab=99.87  E-value=2.1e-20  Score=176.62  Aligned_cols=123  Identities=18%  Similarity=0.192  Sum_probs=107.9

Q ss_pred             chHHHHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEecccccc
Q 037567          212 SFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMG  291 (374)
Q Consensus       212 ~~~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G  291 (374)
                      .....++..+......+.++||||+++..++.+++.|++.+++...+|+  ...+|+..+..|..+...|+|||+++++|
T Consensus       582 eK~~Ali~~I~~~~~~grpVLIft~Sve~sE~Ls~~L~~~gI~h~vLna--kq~~REa~Iia~AG~~g~VtIATNMAGRG  659 (1025)
T PRK12900        582 EKYNAIVLKVEELQKKGQPVLVGTASVEVSETLSRMLRAKRIAHNVLNA--KQHDREAEIVAEAGQKGAVTIATNMAGRG  659 (1025)
T ss_pred             HHHHHHHHHHHHHhhCCCCEEEEeCcHHHHHHHHHHHHHcCCCceeecC--CHHHhHHHHHHhcCCCCeEEEeccCcCCC
Confidence            3445566666555567899999999999999999999999999999997  47789999999999999999999999999


Q ss_pred             cccc---Ccc-----EEEEECCCCChhHHHHhhccCCCCCCceEEEEEeeccC
Q 037567          292 IDKP---DVR-----HVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSN  336 (374)
Q Consensus       292 ~d~~---~~~-----~vi~~~~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~  336 (374)
                      +|++   .+.     +||.+..|.|...+.|++||+||.|.+|.+..+++.+|
T Consensus       660 tDIkl~~~V~~vGGL~VIgterhes~Rid~Ql~GRtGRqGdpGsS~ffvSleD  712 (1025)
T PRK12900        660 TDIKLGEGVRELGGLFILGSERHESRRIDRQLRGRAGRQGDPGESVFYVSLED  712 (1025)
T ss_pred             CCcCCccchhhhCCceeeCCCCCchHHHHHHHhhhhhcCCCCcceEEEechhH
Confidence            9999   443     34888889999999999999999999999999998876

>KOG0926 consensus DEAH-box RNA helicase [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.86  E-value=4.9e-20  Score=167.46  Aligned_cols=302  Identities=16%  Similarity=0.212  Sum_probs=192.6

Q ss_pred             HHHHHHHHcCCCEEEEccCCCCchhh-----hhccccc----cCCcEEEEcchHHHHHHHHHHHH----HcCCceEEcCC
Q 037567           19 KDVIQRIIEKRDCLVVMATGSGKSLC-----YQLPPLV----TGKTALVVSPLISLMQDQVMSLK----QRGINAEFLGS   85 (374)
Q Consensus        19 ~~~~~~~~~~~~~l~~a~tGsGKT~~-----~~l~~~~----~~~~~lil~P~~~l~~q~~~~~~----~~~~~~~~~~~   85 (374)
                      .++..++..+.-+|++|.||||||.-     |...-..    ...-+=|.-|+|..+--+++...    .++..+.+...
T Consensus       262 q~IMEaIn~n~vvIIcGeTGsGKTTQvPQFLYEAGf~s~~~~~~gmIGITqPRRVAaiamAkRVa~EL~~~~~eVsYqIR  341 (1172)
T KOG0926|consen  262 QRIMEAINENPVVIICGETGSGKTTQVPQFLYEAGFASEQSSSPGMIGITQPRRVAAIAMAKRVAFELGVLGSEVSYQIR  341 (1172)
T ss_pred             HHHHHHhhcCCeEEEecCCCCCccccchHHHHHcccCCccCCCCCeeeecCchHHHHHHHHHHHHHHhccCccceeEEEE
Confidence            35666777778889999999999942     2222111    13456778899877665555443    33333332211


Q ss_pred             CCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHHhc------
Q 037567           86 AQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFL------  159 (374)
Q Consensus        86 ~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~------  159 (374)
                             ..........|.++|.+-|++   .....+.+..++.||+||||.=   +......+..+.++....      
T Consensus       342 -------fd~ti~e~T~IkFMTDGVLLr---Ei~~DflL~kYSvIIlDEAHER---SvnTDILiGmLSRiV~LR~k~~ke  408 (1172)
T KOG0926|consen  342 -------FDGTIGEDTSIKFMTDGVLLR---EIENDFLLTKYSVIILDEAHER---SVNTDILIGMLSRIVPLRQKYYKE  408 (1172)
T ss_pred             -------eccccCCCceeEEecchHHHH---HHHHhHhhhhceeEEechhhhc---cchHHHHHHHHHHHHHHHHHHhhh
Confidence                   111122335799999997654   4446777889999999999953   333334444444433322      


Q ss_pred             ----CCCCeeEEEeecCcccHHHHHHhcCCCCCeEEEeccCCCceeEEEEeecC-CcchHHHHHHHH---HHhhcCCCcE
Q 037567          160 ----LGVPFVALTATATEKVRIDIINSLKLKNPYVTIASFDRKNLFYGVKVINR-GQSFVDELVQEI---LKSVAGAGSI  231 (374)
Q Consensus       160 ----~~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~---~~~~~~~~~~  231 (374)
                          .+.+.|.||||+.-.+...--..+.+.++.+.+..   ..+...+++... ...++.+..+..   .+++ +.|.+
T Consensus       409 ~~~~kpLKLIIMSATLRVsDFtenk~LFpi~pPlikVdA---RQfPVsIHF~krT~~DYi~eAfrKtc~IH~kL-P~G~I  484 (1172)
T KOG0926|consen  409 QCQIKPLKLIIMSATLRVSDFTENKRLFPIPPPLIKVDA---RQFPVSIHFNKRTPDDYIAEAFRKTCKIHKKL-PPGGI  484 (1172)
T ss_pred             hcccCceeEEEEeeeEEecccccCceecCCCCceeeeec---ccCceEEEeccCCCchHHHHHHHHHHHHhhcC-CCCcE
Confidence                24678999999988765444445556666443333   223333333222 224444444443   3333 67889


Q ss_pred             EEEecchhHHHHHHHHHHHcC-----------------------------------------------------------
Q 037567          232 IVYCMTIKDVEEISKALKQLG-----------------------------------------------------------  252 (374)
Q Consensus       232 lVf~~~~~~~~~l~~~l~~~~-----------------------------------------------------------  252 (374)
                      |||+....++..+++.|++.-                                                           
T Consensus       485 LVFvTGQqEV~qL~~kLRK~~p~~f~~~k~~k~~k~~~e~k~~~s~~~~~~k~~dfe~Ed~~~~~ed~d~~~~~~~~~~~  564 (1172)
T KOG0926|consen  485 LVFVTGQQEVDQLCEKLRKRFPESFGGVKMKKNVKAFKELKENPSDIGDSNKTDDFEEEDMYESDEDIDQELVDSGFASL  564 (1172)
T ss_pred             EEEEeChHHHHHHHHHHHhhCccccccchhhhhhhhccccccchhhhccCcccccchhcccccchhhhhhhhhcccchhh
Confidence            999999999999999987640                                                           


Q ss_pred             ----------------------------------------CceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccc
Q 037567          253 ----------------------------------------VKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGI  292 (374)
Q Consensus       253 ----------------------------------------~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~  292 (374)
                                                              .-|.++++=++......+...--+|..-++|+|+.+++++
T Consensus       565 raa~~~~~De~~~~nge~e~d~~e~~~E~~~~~~~~~~~pLyvLPLYSLLs~~~Q~RVF~~~p~g~RLcVVaTNVAETSL  644 (1172)
T KOG0926|consen  565 RAAFNALADENGSVNGEPEKDESEEGQEAEQGKGKFSPGPLYVLPLYSLLSTEKQMRVFDEVPKGERLCVVATNVAETSL  644 (1172)
T ss_pred             hhhhhccccccccccCCcccchhhhchhhhhccCCCCCCceEEeehhhhcCHHHhhhhccCCCCCceEEEEeccchhccc
Confidence                                                    0022334444444455555555567777999999999999


Q ss_pred             cccCccEEEEECCCC------------------ChhHHHHhhccCCCCCCceEEEEEeeccCCC
Q 037567          293 DKPDVRHVIHYGCPK------------------TLESYYQESGRCGRDGIASVCWLYYARSNFA  338 (374)
Q Consensus       293 d~~~~~~vi~~~~p~------------------s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~~~  338 (374)
                      .+|++++||+.+...                  |-..--||.|||||.| +|.||-+|+..-+.
T Consensus       645 TIPgIkYVVD~Gr~K~R~Yd~~TGV~~FeV~wiSkASadQRAGRAGRtg-pGHcYRLYSSAVf~  707 (1172)
T KOG0926|consen  645 TIPGIKYVVDCGRVKERLYDSKTGVSSFEVDWISKASADQRAGRAGRTG-PGHCYRLYSSAVFS  707 (1172)
T ss_pred             ccCCeeEEEeccchhhhccccccCceeEEEEeeeccccchhccccCCCC-CCceeehhhhHHhh
Confidence            999999999776432                  4556679999999987 88999998876554

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

Probab=99.86  E-value=8.7e-20  Score=176.67  Aligned_cols=184  Identities=16%  Similarity=0.119  Sum_probs=111.0

Q ss_pred             CeeEEEeecCcccHHHHHHhcCCCCCeEEEeccCC--CceeEEE-Eeec----CCcchHHHHHHHHHHhhcCCCcEEEEe
Q 037567          163 PFVALTATATEKVRIDIINSLKLKNPYVTIASFDR--KNLFYGV-KVIN----RGQSFVDELVQEILKSVAGAGSIIVYC  235 (374)
Q Consensus       163 ~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~-~~~~----~~~~~~~~~~~~~~~~~~~~~~~lVf~  235 (374)
                      .+|++|||+.-.....+...+|+............  ....... ....    +...+...+...+..-...+++++|++
T Consensus       575 ~~i~tSATL~v~~~f~~~~~lGl~~~~~~~~~~~~~~~~~~~i~~~~p~~~~~~~~~~~~~~~~~i~~~~~~~g~~LVLF  654 (820)
T PRK07246        575 KTYFVSATLQISPRVSLADLLGFEEYLFHKIEKDKKQDQLVVVDQDMPLVTETSDEVYAEEIAKRLEELKQLQQPILVLF  654 (820)
T ss_pred             eEEEEecccccCCCCcHHHHcCCCccceecCCCChHHccEEEeCCCCCCCCCCChHHHHHHHHHHHHHHHhcCCCEEEEE
Confidence            47999999973222246777887543322111111  1111100 0110    112233333333333334678999999


Q ss_pred             cchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccC--ccEEEEECCCC------
Q 037567          236 MTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPD--VRHVIHYGCPK------  307 (374)
Q Consensus       236 ~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~--~~~vi~~~~p~------  307 (374)
                      +|.+..+.+++.|......+ ...|...  .+..+++.|+.++..||++|...++|+|+|+  ...+|...+|.      
T Consensus       655 tS~~~l~~v~~~l~~~~~~~-l~Qg~~~--~~~~l~~~F~~~~~~vLlG~~sFwEGVD~p~~~~~~viI~kLPF~~P~dP  731 (820)
T PRK07246        655 NSKKHLLAVSDLLDQWQVSH-LAQEKNG--TAYNIKKRFDRGEQQILLGLGSFWEGVDFVQADRMIEVITRLPFDNPEDP  731 (820)
T ss_pred             CcHHHHHHHHHHHhhcCCcE-EEeCCCc--cHHHHHHHHHcCCCeEEEecchhhCCCCCCCCCeEEEEEecCCCCCCCCH
Confidence            99999999999997654443 4444322  3566899999988889999999999999974  45566677663      


Q ss_pred             ------------------------ChhHHHHhhccCCCCCCceEEEEEeeccC--CCcccceeccccc
Q 037567          308 ------------------------TLESYYQESGRCGRDGIASVCWLYYARSN--FAKGDFYCGESQT  349 (374)
Q Consensus       308 ------------------------s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~--~~~~~~~~~~~~~  349 (374)
                                              ....+.|.+||.-|...+.-+++++++.-  ..+-+.|.+...+
T Consensus       732 ~~~a~~~~~~~~g~~~F~~~~lP~A~iklkQg~GRLIRs~~D~Gvv~ilD~R~~~k~Yg~~~l~sLP~  799 (820)
T PRK07246        732 FVKKMNQYLLQEGKNPFYDYFLPMTILRLKQAIGRTMRREDQKSAVLILDRRILTKSYGKQILASLAE  799 (820)
T ss_pred             HHHHHHHHHHHhCCCchhheeHHHHHHHHHHHhcccccCCCCcEEEEEECCcccccHHHHHHHHhCCC
Confidence                                    23456899999999876444555555542  2233445554443

>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]

Probab=99.86  E-value=1.5e-20  Score=177.90  Aligned_cols=312  Identities=17%  Similarity=0.218  Sum_probs=212.7

Q ss_pred             CCCchhHHHHHHHHH----cCCCEEEEccCCCCchh---hh---hccccccCCcEEEEcchHHHHHHHHHHHHHc-CCce
Q 037567           12 SVFRPYQKDVIQRII----EKRDCLVVMATGSGKSL---CY---QLPPLVTGKTALVVSPLISLMQDQVMSLKQR-GINA   80 (374)
Q Consensus        12 ~~~~~~Q~~~~~~~~----~~~~~l~~a~tGsGKT~---~~---~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~-~~~~   80 (374)
                      .++|.||.+.++.++    .++++|+...+|.|||+   +|   +....+..++.|||+|...+ ..|.+++..+ ..++
T Consensus       369 ~~LRdyQLeGlNWl~~~W~~~~n~ILADEmgLgktvqti~fl~~l~~~~~~~gpflvvvplst~-~~W~~ef~~w~~mn~  447 (1373)
T KOG0384|consen  369 NELRDYQLEGLNWLLYSWYKRNNCILADEMGLGKTVQTITFLSYLFHSLQIHGPFLVVVPLSTI-TAWEREFETWTDMNV  447 (1373)
T ss_pred             chhhhhhcccchhHHHHHHhcccceehhhcCCCcchHHHHHHHHHHHhhhccCCeEEEeehhhh-HHHHHHHHHHhhhce
Confidence            579999999998764    57899999999999993   33   33334457889999999655 4588888766 4555


Q ss_pred             EEcCCCCCchhhhhhh---hc-----CCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHH
Q 037567           81 EFLGSAQTDSSVQTKA---ET-----GYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQL  152 (374)
Q Consensus        81 ~~~~~~~~~~~~~~~~---~~-----~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~  152 (374)
                      .++++...........   ..     -.++++++|++.++.-.    ..+....+.+++|||||++.+...       .+
T Consensus       448 i~y~g~~~sr~~i~~ye~~~~~~~~~lkf~~lltTye~~LkDk----~~L~~i~w~~~~vDeahrLkN~~~-------~l  516 (1373)
T KOG0384|consen  448 IVYHGNLESRQLIRQYEFYHSSNTKKLKFNALLTTYEIVLKDK----AELSKIPWRYLLVDEAHRLKNDES-------KL  516 (1373)
T ss_pred             eeeecchhHHHHHHHHHheecCCccccccceeehhhHHHhccH----hhhccCCcceeeecHHhhcCchHH-------HH
Confidence            5555554443322111   11     25899999999875431    233345688999999999986442       22


Q ss_pred             HHHHHhcCCCCeeEEEeecCcccHHHHHHhcCCCCCeEEE--------------------------------------ec
Q 037567          153 DKLRTFLLGVPFVALTATATEKVRIDIINSLKLKNPYVTI--------------------------------------AS  194 (374)
Q Consensus       153 ~~~~~~~~~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~--------------------------------------~~  194 (374)
                      -..+..+.-...+++|+||-.+..+++...+.+..|....                                      ..
T Consensus       517 ~~~l~~f~~~~rllitgTPlQNsikEL~sLl~Fl~P~kf~~~~~f~~~~~~~~e~~~~~L~~~L~P~~lRr~kkdveksl  596 (1373)
T KOG0384|consen  517 YESLNQFKMNHRLLITGTPLQNSLKELWSLLHFLMPGKFDSWDEFLEEFDEETEEQVRKLQQILKPFLLRRLKKDVEKSL  596 (1373)
T ss_pred             HHHHHHhcccceeeecCCCccccHHHHHHHhcccCCCCCCcHHHHHHhhcchhHHHHHHHHHHhhHHHHHHHHhhhccCC
Confidence            2223444456789999999887776655444322111000                                      00


Q ss_pred             cCCCceeEEEEe----------------------------------------------ecCCcc-------------hHH
Q 037567          195 FDRKNLFYGVKV----------------------------------------------INRGQS-------------FVD  215 (374)
Q Consensus       195 ~~~~~~~~~~~~----------------------------------------------~~~~~~-------------~~~  215 (374)
                      .....-...+..                                              +.....             .+.
T Consensus       597 p~k~E~IlrVels~lQk~yYk~ILtkN~~~LtKG~~g~~~~lLNimmELkKccNHpyLi~gaee~~~~~~~~~~~d~~L~  676 (1373)
T KOG0384|consen  597 PPKEETILRVELSDLQKQYYKAILTKNFSALTKGAKGSTPSLLNIMMELKKCCNHPYLIKGAEEKILGDFRDKMRDEALQ  676 (1373)
T ss_pred             CCCcceEEEeehhHHHHHHHHHHHHhhHHHHhccCCCCCchHHHHHHHHHHhcCCccccCcHHHHHHHhhhhcchHHHHH
Confidence            000000111110                                              000000             000


Q ss_pred             ---------HHHHHHHHhhc-CCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcC---CeeEE
Q 037567          216 ---------ELVQEILKSVA-GAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRD---EIRVM  282 (374)
Q Consensus       216 ---------~~~~~~~~~~~-~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g---~~~il  282 (374)
                               -++..++.++. .+.+||||..-+....-|+++|.-++++...+.|....+-|++.+..|+..   .+..|
T Consensus       677 ~lI~sSGKlVLLDKLL~rLk~~GHrVLIFSQMVRmLDIL~eYL~~r~ypfQRLDGsvrgelRq~AIDhFnap~SddFvFL  756 (1373)
T KOG0384|consen  677 ALIQSSGKLVLLDKLLPRLKEGGHRVLIFSQMVRMLDILAEYLSLRGYPFQRLDGSVRGELRQQAIDHFNAPDSDDFVFL  756 (1373)
T ss_pred             HHHHhcCcEEeHHHHHHHHhcCCceEEEhHHHHHHHHHHHHHHHHcCCcceeccCCcchHHHHHHHHhccCCCCCceEEE
Confidence                     11222333332 346899999999999999999999999999999999999999999999974   46688


Q ss_pred             EEeccccccccccCccEEEEECCCCChhHHHHhhccCCCCCCceEE--EEEeecc
Q 037567          283 VATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVC--WLYYARS  335 (374)
Q Consensus       283 v~t~~~~~G~d~~~~~~vi~~~~p~s~~~~~Q~~GR~~R~~~~g~~--~~~~~~~  335 (374)
                      ++|.+.+-|||+-.+++||+||..|++.+=+|...||.|.||...|  |-+++..
T Consensus       757 LSTRAGGLGINLatADTVIIFDSDWNPQNDLQAqARaHRIGQkk~VnVYRLVTk~  811 (1373)
T KOG0384|consen  757 LSTRAGGLGINLATADTVIIFDSDWNPQNDLQAQARAHRIGQKKHVNVYRLVTKN  811 (1373)
T ss_pred             EecccCcccccccccceEEEeCCCCCcchHHHHHHHHHhhcccceEEEEEEecCC
Confidence            9999999999999999999999999999999999999999997654  4455554

>KOG0389 consensus SNF2 family DNA-dependent ATPase [Chromatin structure and dynamics]

Probab=99.86  E-value=3.4e-20  Score=168.32  Aligned_cols=315  Identities=16%  Similarity=0.180  Sum_probs=207.7

Q ss_pred             CCchhHHHHHHHHH----cCCCEEEEccCCCCchh---hhhccccc--cCCcEEEEcchHHHHHHHHHHHHHcCCceEE-
Q 037567           13 VFRPYQKDVIQRII----EKRDCLVVMATGSGKSL---CYQLPPLV--TGKTALVVSPLISLMQDQVMSLKQRGINAEF-   82 (374)
Q Consensus        13 ~~~~~Q~~~~~~~~----~~~~~l~~a~tGsGKT~---~~~l~~~~--~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~-   82 (374)
                      ++.+||.-.++.+.    ++-++|+...+|.|||.   +|+..+.+  ..++-|||||+. ..+.|.+++.+|-....+ 
T Consensus       399 ~LkdYQlvGvNWL~Llyk~~l~gILADEMGLGKTiQvIaFlayLkq~g~~gpHLVVvPsS-TleNWlrEf~kwCPsl~Ve  477 (941)
T KOG0389|consen  399 QLKDYQLVGVNWLLLLYKKKLNGILADEMGLGKTIQVIAFLAYLKQIGNPGPHLVVVPSS-TLENWLREFAKWCPSLKVE  477 (941)
T ss_pred             cccchhhhhHHHHHHHHHccccceehhhccCcchhHHHHHHHHHHHcCCCCCcEEEecch-hHHHHHHHHHHhCCceEEE
Confidence            48899999988764    34577999999999993   33222222  367799999995 456699999999766554 


Q ss_pred             -cCCCCCchhh-hhhh--hcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHHh
Q 037567           83 -LGSAQTDSSV-QTKA--ETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTF  158 (374)
Q Consensus        83 -~~~~~~~~~~-~~~~--~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~  158 (374)
                       +++....... ....  ....++|+++||.....-... ...+...+++++|+||.|.+.+...+      +...+.. 
T Consensus       478 ~YyGSq~ER~~lR~~i~~~~~~ydVllTTY~la~~~kdD-Rsflk~~~~n~viyDEgHmLKN~~Se------Ry~~LM~-  549 (941)
T KOG0389|consen  478 PYYGSQDERRELRERIKKNKDDYDVLLTTYNLAASSKDD-RSFLKNQKFNYVIYDEGHMLKNRTSE------RYKHLMS-  549 (941)
T ss_pred             eccCcHHHHHHHHHHHhccCCCccEEEEEeecccCChHH-HHHHHhccccEEEecchhhhhccchH------HHHHhcc-
Confidence             3333322222 1111  234789999999876543221 12334567899999999999876542      2232222 


Q ss_pred             cCCCCeeEEEeecCcccHHHHHHhcCCC----------------------------------------------------
Q 037567          159 LLGVPFVALTATATEKVRIDIINSLKLK----------------------------------------------------  186 (374)
Q Consensus       159 ~~~~~~i~~SaT~~~~~~~~~~~~~~~~----------------------------------------------------  186 (374)
                      .+....+++|+||-.+...++...+.+.                                                    
T Consensus       550 I~An~RlLLTGTPLQNNL~ELiSLL~FvlP~vF~~~~~dl~~if~~k~~~d~d~e~~~l~qerIsrAK~im~PFILRR~K  629 (941)
T KOG0389|consen  550 INANFRLLLTGTPLQNNLKELISLLAFVLPKVFDSSMEDLDVIFKAKKTSDGDIENALLSQERISRAKTIMKPFILRRLK  629 (941)
T ss_pred             ccccceEEeeCCcccccHHHHHHHHHHHhhHhhhccchHHHHHHhccCCccchhhHHHHHHHHHHHHHHhhhHHHHHHHH
Confidence            2355689999998877655433322210                                                    


Q ss_pred             -------CCe---EEEeccC-----------------CCceeEEEEeec---------------------C---------
Q 037567          187 -------NPY---VTIASFD-----------------RKNLFYGVKVIN---------------------R---------  209 (374)
Q Consensus       187 -------~~~---~~~~~~~-----------------~~~~~~~~~~~~---------------------~---------  209 (374)
                             ++.   +..-...                 .......-....                     .         
T Consensus       630 ~qVL~~LPpK~~~Ie~c~mse~Q~~~Y~~~~~~~~~~~~~~~~ns~~~~~~vlmqlRK~AnHPLL~R~~Y~de~L~~mak  709 (941)
T KOG0389|consen  630 SQVLKQLPPKIQRIEYCEMSEKQKQLYDELIELYDVKLNEVSKNSELKSGNVLMQLRKAANHPLLFRSIYTDEKLRKMAK  709 (941)
T ss_pred             HHHHHhcCCccceeEeeecchHHHHHHHHHHHHHhhhccccccccccccchHHHHHHHHhcChhHHHHhccHHHHHHHHH
Confidence                   000   0000000                 000000000000                     0         


Q ss_pred             --------------------------------------------C----cchHHHHHHHHHHhh-cCCCcEEEEecchhH
Q 037567          210 --------------------------------------------G----QSFVDELVQEILKSV-AGAGSIIVYCMTIKD  240 (374)
Q Consensus       210 --------------------------------------------~----~~~~~~~~~~~~~~~-~~~~~~lVf~~~~~~  240 (374)
                                                                  +    .+..-..+..++... ..+.++|||......
T Consensus       710 ~il~e~ay~~~n~qyIfEDm~~msDfelHqLc~~f~~~~~f~L~d~~~mdSgK~r~L~~LLp~~k~~G~RVLiFSQFTqm  789 (941)
T KOG0389|consen  710 RILNEPAYKKANEQYIFEDMEVMSDFELHQLCCQFRHLSKFQLKDDLWMDSGKCRKLKELLPKIKKKGDRVLIFSQFTQM  789 (941)
T ss_pred             HHhCchhhhhcCHHHHHHHHHhhhHHHHHHHHHhcCCCcccccCCchhhhhhhHhHHHHHHHHHhhcCCEEEEeeHHHHH
Confidence                                                        0    011112233333332 245789999999999


Q ss_pred             HHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCC--eeEEEEeccccccccccCccEEEEECCCCChhHHHHhhcc
Q 037567          241 VEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDE--IRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGR  318 (374)
Q Consensus       241 ~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~--~~ilv~t~~~~~G~d~~~~~~vi~~~~p~s~~~~~Q~~GR  318 (374)
                      ..-+...|...++....+.|.+.-.+|+.++..|...+  ...|++|.+.+.|||+..+++||.++...++-+-.|.-.|
T Consensus       790 LDILE~~L~~l~~~ylRLDGsTqV~~RQ~lId~Fn~d~difVFLLSTKAGG~GINLt~An~VIihD~dFNP~dD~QAEDR  869 (941)
T KOG0389|consen  790 LDILEVVLDTLGYKYLRLDGSTQVNDRQDLIDEFNTDKDIFVFLLSTKAGGFGINLTCANTVIIHDIDFNPYDDKQAEDR  869 (941)
T ss_pred             HHHHHHHHHhcCceEEeecCCccchHHHHHHHhhccCCceEEEEEeeccCcceecccccceEEEeecCCCCcccchhHHH
Confidence            99999999999999999999999999999999999864  3467799999999999999999999999999999999999


Q ss_pred             CCCCCCceEE--EEEeeccC
Q 037567          319 CGRDGIASVC--WLYYARSN  336 (374)
Q Consensus       319 ~~R~~~~g~~--~~~~~~~~  336 (374)
                      |.|.||..-|  +-+++++.
T Consensus       870 cHRvGQtkpVtV~rLItk~T  889 (941)
T KOG0389|consen  870 CHRVGQTKPVTVYRLITKST  889 (941)
T ss_pred             HHhhCCcceeEEEEEEecCc
Confidence            9999986644  44555543

>KOG0953 consensus Mitochondrial RNA helicase SUV3, DEAD-box superfamily [RNA processing and modification]

Probab=99.86  E-value=2.2e-20  Score=163.54  Aligned_cols=289  Identities=19%  Similarity=0.218  Sum_probs=192.1

Q ss_pred             CCEEEEccCCCCchhhhhccccccCCcEEEEcchHHHHHHHHHHHHHcCCceEEcCCCCCchhhhhhhhcCCeeEEEEcC
Q 037567           29 RDCLVVMATGSGKSLCYQLPPLVTGKTALVVSPLISLMQDQVMSLKQRGINAEFLGSAQTDSSVQTKAETGYFQLLFMTP  108 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~  108 (374)
                      +-++-+|||+||||.-+ +.-+.+.+..++.-|.+-|+.++++.+...|+...++++........+   ......+-+|.
T Consensus       192 kIi~H~GPTNSGKTy~A-Lqrl~~aksGvycGPLrLLA~EV~~r~na~gipCdL~TGeE~~~~~~~---~~~a~hvScTV  267 (700)
T KOG0953|consen  192 KIIMHVGPTNSGKTYRA-LQRLKSAKSGVYCGPLRLLAHEVYDRLNALGIPCDLLTGEERRFVLDN---GNPAQHVSCTV  267 (700)
T ss_pred             eEEEEeCCCCCchhHHH-HHHHhhhccceecchHHHHHHHHHHHhhhcCCCccccccceeeecCCC---CCcccceEEEE
Confidence            44566899999999874 444556788999999999999999999999999888876433322221   22346777888


Q ss_pred             cccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHHhcCCCCeeEEEeecCcccHHHHHHhcCCCCC
Q 037567          109 EKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEKVRIDIINSLKLKNP  188 (374)
Q Consensus       109 ~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~SaT~~~~~~~~~~~~~~~~~~  188 (374)
                      |+..--          ..+++.|+||++.+.+.....     .+.+.+--+...- |=+.+-|.-  ..-+.........
T Consensus       268 EM~sv~----------~~yeVAViDEIQmm~Dp~RGw-----AWTrALLGl~AdE-iHLCGepsv--ldlV~~i~k~TGd  329 (700)
T KOG0953|consen  268 EMVSVN----------TPYEVAVIDEIQMMRDPSRGW-----AWTRALLGLAADE-IHLCGEPSV--LDLVRKILKMTGD  329 (700)
T ss_pred             EEeecC----------CceEEEEehhHHhhcCcccch-----HHHHHHHhhhhhh-hhccCCchH--HHHHHHHHhhcCC
Confidence            876321          456899999999998755542     2222211111111 112222222  2122223333333


Q ss_pred             eEEEeccCCCceeEEEEeecCCcchHHHHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHHcCCc-eeeeecCCChHHH
Q 037567          189 YVTIASFDRKNLFYGVKVINRGQSFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVK-AGTYHGQMGSKAR  267 (374)
Q Consensus       189 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~-~~~~~~~~~~~~r  267 (374)
                      .+.....++.....           +.+.+..-+..+.+++ ++| |-+++..-.+...+.+.+.. +..++|+++++.|
T Consensus       330 ~vev~~YeRl~pL~-----------v~~~~~~sl~nlk~GD-CvV-~FSkk~I~~~k~kIE~~g~~k~aVIYGsLPPeTr  396 (700)
T KOG0953|consen  330 DVEVREYERLSPLV-----------VEETALGSLSNLKPGD-CVV-AFSKKDIFTVKKKIEKAGNHKCAVIYGSLPPETR  396 (700)
T ss_pred             eeEEEeecccCcce-----------ehhhhhhhhccCCCCC-eEE-EeehhhHHHHHHHHHHhcCcceEEEecCCCCchh
Confidence            34443333322211           1112222333443444 433 33677888999999888766 9999999999999


Q ss_pred             HHHHHhhhc--CCeeEEEEeccccccccccCccEEEEECCC---------CChhHHHHhhccCCCCCC--ceEEEEEeec
Q 037567          268 EEAHRLFIR--DEIRVMVATMAFGMGIDKPDVRHVIHYGCP---------KTLESYYQESGRCGRDGI--ASVCWLYYAR  334 (374)
Q Consensus       268 ~~~~~~f~~--g~~~ilv~t~~~~~G~d~~~~~~vi~~~~p---------~s~~~~~Q~~GR~~R~~~--~g~~~~~~~~  334 (374)
                      .+....|++  ++.+|+|+|+++++|+|+ +++-||++++.         .+..+..|..|||||.|.  +.-.++.+..
T Consensus       397 ~aQA~~FNd~~~e~dvlVAsDAIGMGLNL-~IrRiiF~sl~Kysg~e~~~it~sqikQIAGRAGRf~s~~~~G~vTtl~~  475 (700)
T KOG0953|consen  397 LAQAALFNDPSNECDVLVASDAIGMGLNL-NIRRIIFYSLIKYSGRETEDITVSQIKQIAGRAGRFGSKYPQGEVTTLHS  475 (700)
T ss_pred             HHHHHHhCCCCCccceEEeeccccccccc-ceeEEEEeecccCCcccceeccHHHHHHHhhcccccccCCcCceEEEeeH
Confidence            999999998  789999999999999999 68888888765         367889999999999864  2334555667


Q ss_pred             cCCCcccceeccccchHHH
Q 037567          335 SNFAKGDFYCGESQTENQR  353 (374)
Q Consensus       335 ~~~~~~~~~~~~~~~~~~~  353 (374)
                      +|+..+...++........
T Consensus       476 eDL~~L~~~l~~p~epi~~  494 (700)
T KOG0953|consen  476 EDLKLLKRILKRPVEPIKN  494 (700)
T ss_pred             hhHHHHHHHHhCCchHHHh
Confidence            7888888887765555444

>KOG1000 consensus Chromatin remodeling protein HARP/SMARCAL1, DEAD-box superfamily [Chromatin structure and dynamics]

Probab=99.85  E-value=1.3e-19  Score=156.66  Aligned_cols=306  Identities=15%  Similarity=0.137  Sum_probs=196.7

Q ss_pred             CCCchhHHHHHHHHHc-CCCEEEEccCCCCchhhhhcccc--ccCCcEEEEcchHHHHHHHHHHHHHcCCc---eEEcCC
Q 037567           12 SVFRPYQKDVIQRIIE-KRDCLVVMATGSGKSLCYQLPPL--VTGKTALVVSPLISLMQDQVMSLKQRGIN---AEFLGS   85 (374)
Q Consensus        12 ~~~~~~Q~~~~~~~~~-~~~~l~~a~tGsGKT~~~~l~~~--~~~~~~lil~P~~~l~~q~~~~~~~~~~~---~~~~~~   85 (374)
                      +.+-|+|.+.+...++ |..+++...+|.|||+-++..+.  ......||+||. .+-..|.+++.+|-..   +.++..
T Consensus       197 s~LlPFQreGv~faL~RgGR~llADeMGLGKTiQAlaIA~yyraEwplliVcPA-svrftWa~al~r~lps~~pi~vv~~  275 (689)
T KOG1000|consen  197 SRLLPFQREGVIFALERGGRILLADEMGLGKTIQALAIARYYRAEWPLLIVCPA-SVRFTWAKALNRFLPSIHPIFVVDK  275 (689)
T ss_pred             HhhCchhhhhHHHHHhcCCeEEEecccccchHHHHHHHHHHHhhcCcEEEEecH-HHhHHHHHHHHHhcccccceEEEec
Confidence            3578999999986665 77888888899999976543332  367889999998 5777799999887322   122221


Q ss_pred             CCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHHhcC-CCCe
Q 037567           86 AQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLL-GVPF  164 (374)
Q Consensus        86 ~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~~-~~~~  164 (374)
                      ......    ..-....|.|.+++.+..+    ........+.++|+||+|++.+...      .+...+..... ..++
T Consensus       276 ~~D~~~----~~~t~~~v~ivSye~ls~l----~~~l~~~~~~vvI~DEsH~Lk~skt------kr~Ka~~dllk~akhv  341 (689)
T KOG1000|consen  276 SSDPLP----DVCTSNTVAIVSYEQLSLL----HDILKKEKYRVVIFDESHMLKDSKT------KRTKAATDLLKVAKHV  341 (689)
T ss_pred             ccCCcc----ccccCCeEEEEEHHHHHHH----HHHHhcccceEEEEechhhhhccch------hhhhhhhhHHHHhhhe
Confidence            111100    0011246888999877433    1223334489999999999976221      11222222211 4579


Q ss_pred             eEEEeecCcccHHHHHHhcCCCCCeE-------------------EEec---------------------------cCCC
Q 037567          165 VALTATATEKVRIDIINSLKLKNPYV-------------------TIAS---------------------------FDRK  198 (374)
Q Consensus       165 i~~SaT~~~~~~~~~~~~~~~~~~~~-------------------~~~~---------------------------~~~~  198 (374)
                      |++|+||.-+..-++.......+...                   -...                           ...+
T Consensus       342 ILLSGTPavSRP~elytqi~avd~tlfp~f~efa~rYCd~k~vr~~~Dykg~tnl~EL~~lL~k~lMIRRlK~dvL~qLP  421 (689)
T KOG1000|consen  342 ILLSGTPAVSRPSELYTQIRAVDHTLFPNFHEFAIRYCDGKQVRFCFDYKGCTNLEELAALLFKRLMIRRLKADVLKQLP  421 (689)
T ss_pred             EEecCCcccCCchhhhhhhhhhcccccccHHHHHHHhcCccccceeeecCCCCCHHHHHHHHHHHHHHHHHHHHHHhhCC
Confidence            99999987554322111111000000                   0000                           0000


Q ss_pred             ceeEEEEeecC------------------------------------Cc-chHHHHHHHHHH----hhcCCCcEEEEecc
Q 037567          199 NLFYGVKVINR------------------------------------GQ-SFVDELVQEILK----SVAGAGSIIVYCMT  237 (374)
Q Consensus       199 ~~~~~~~~~~~------------------------------------~~-~~~~~~~~~~~~----~~~~~~~~lVf~~~  237 (374)
                      .....+.....                                    .. .....+...++.    -..++.|.+||+..
T Consensus       422 pKrr~Vv~~~~gr~da~~~~lv~~a~~~t~~~~~e~~~~~l~l~y~~tgiaK~~av~eyi~~~~~l~d~~~~KflVFaHH  501 (689)
T KOG1000|consen  422 PKRREVVYVSGGRIDARMDDLVKAAADYTKVNSMERKHESLLLFYSLTGIAKAAAVCEYILENYFLPDAPPRKFLVFAHH  501 (689)
T ss_pred             ccceEEEEEcCCccchHHHHHHHHhhhcchhhhhhhhhHHHHHHHHHhcccccHHHHHHHHhCcccccCCCceEEEEehh
Confidence            00000000000                                    00 011122222222    12356799999999


Q ss_pred             hhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCC-eeE-EEEeccccccccccCccEEEEECCCCChhHHHHh
Q 037567          238 IKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDE-IRV-MVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQE  315 (374)
Q Consensus       238 ~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~-~~i-lv~t~~~~~G~d~~~~~~vi~~~~p~s~~~~~Q~  315 (374)
                      ....+.+...+.++++....|.|..+..+|+...+.|+..+ ..| +++..++++|+++...+.|++..+++++.-++|.
T Consensus       502 ~~vLd~Iq~~~~~r~vg~IRIDGst~s~~R~ll~qsFQ~seev~VAvlsItA~gvGLt~tAa~~VVFaEL~wnPgvLlQA  581 (689)
T KOG1000|consen  502 QIVLDTIQVEVNKRKVGSIRIDGSTPSHRRTLLCQSFQTSEEVRVAVLSITAAGVGLTLTAASVVVFAELHWNPGVLLQA  581 (689)
T ss_pred             HHHHHHHHHHHHHcCCCeEEecCCCCchhHHHHHHHhccccceEEEEEEEeecccceeeeccceEEEEEecCCCceEEec
Confidence            99999999999999999999999999999999999999764 454 4577789999999999999999999999999999


Q ss_pred             hccCCCCCCceEEEEEe
Q 037567          316 SGRCGRDGIASVCWLYY  332 (374)
Q Consensus       316 ~GR~~R~~~~g~~~~~~  332 (374)
                      -.|+.|.||...+.+.|
T Consensus       582 EDRaHRiGQkssV~v~y  598 (689)
T KOG1000|consen  582 EDRAHRIGQKSSVFVQY  598 (689)
T ss_pred             hhhhhhccccceeeEEE
Confidence            99999999987665443

>COG4889 Predicted helicase [General function prediction only]

Probab=99.84  E-value=7.5e-21  Score=174.24  Aligned_cols=309  Identities=19%  Similarity=0.214  Sum_probs=181.6

Q ss_pred             CCchhHHHHHHHHHcC----CCEEEEccCCCCchhhhhccccc-cCCcEEEEcchHHHHHHHHHHHHHc---CCceEEcC
Q 037567           13 VFRPYQKDVIQRIIEK----RDCLVVMATGSGKSLCYQLPPLV-TGKTALVVSPLISLMQDQVMSLKQR---GINAEFLG   84 (374)
Q Consensus        13 ~~~~~Q~~~~~~~~~~----~~~l~~a~tGsGKT~~~~l~~~~-~~~~~lil~P~~~l~~q~~~~~~~~---~~~~~~~~   84 (374)
                      +|||||..|+.+..++    ...=+.++||+|||++.+-..-. ...++|+++|+.+|..|..+++...   .+....++
T Consensus       161 k~R~hQq~Aid~a~~~F~~n~RGkLIMAcGTGKTfTsLkisEala~~~iL~LvPSIsLLsQTlrew~~~~~l~~~a~aVc  240 (1518)
T COG4889         161 KPRPHQQTAIDAAKEGFSDNDRGKLIMACGTGKTFTSLKISEALAAARILFLVPSISLLSQTLREWTAQKELDFRASAVC  240 (1518)
T ss_pred             CCChhHHHHHHHHHhhcccccCCcEEEecCCCccchHHHHHHHHhhhheEeecchHHHHHHHHHHHhhccCccceeEEEe
Confidence            6999999999998874    34567789999999886533221 2489999999999999999998753   33333333


Q ss_pred             CCCCchhhh------------------------hhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhc
Q 037567           85 SAQTDSSVQ------------------------TKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISE  140 (374)
Q Consensus        85 ~~~~~~~~~------------------------~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~  140 (374)
                      ++.......                        ......+--|+++|++++......  ...-+..+++||.||||+-..
T Consensus       241 SD~kvsrs~eDik~sdl~~p~sT~~~~il~~~~~~~k~~~~~vvFsTYQSl~~i~eA--Qe~G~~~fDliicDEAHRTtG  318 (1518)
T COG4889         241 SDDKVSRSAEDIKASDLPIPVSTDLEDILSEMEHRQKANGLTVVFSTYQSLPRIKEA--QEAGLDEFDLIICDEAHRTTG  318 (1518)
T ss_pred             cCccccccccccccccCCCCCcccHHHHHHHHHHhhccCCcEEEEEcccchHHHHHH--HHcCCCCccEEEecchhcccc
Confidence            321111000                        011123446899999998776444  455567899999999999753


Q ss_pred             ccC--cchHHHHHHHHHHHhcCCCCeeEEEeecCcccHH--HHHHh-------------cC----------------CCC
Q 037567          141 WGH--DFRLEYKQLDKLRTFLLGVPFVALTATATEKVRI--DIINS-------------LK----------------LKN  187 (374)
Q Consensus       141 ~~~--~~~~~~~~~~~~~~~~~~~~~i~~SaT~~~~~~~--~~~~~-------------~~----------------~~~  187 (374)
                      ...  .-...+.++.. -......++++|||||.-....  .-...             +|                +.+
T Consensus       319 a~~a~dd~saFt~vHs-~~niKa~kRlYmTATPkiy~eS~K~kAkd~s~~l~SMDDe~~fGeef~rl~FgeAv~rdlLTD  397 (1518)
T COG4889         319 ATLAGDDKSAFTRVHS-DQNIKAAKRLYMTATPKIYSESSKAKAKDHSAELSSMDDELTFGEEFHRLGFGEAVERDLLTD  397 (1518)
T ss_pred             ceecccCcccceeecC-cchhHHHHhhhcccCchhhchhhhhhhhhccceeeccchhhhhchhhhcccHHHHHHhhhhcc
Confidence            110  00101111110 0111235678999997643211  00000             00                111


Q ss_pred             CeEEEeccCCCceeEEEEeecCC------cchHHHHHHHH---HHh-------------hcCCCcEEEEecchhHHHHHH
Q 037567          188 PYVTIASFDRKNLFYGVKVINRG------QSFVDELVQEI---LKS-------------VAGAGSIIVYCMTIKDVEEIS  245 (374)
Q Consensus       188 ~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~---~~~-------------~~~~~~~lVf~~~~~~~~~l~  245 (374)
                      +.+..-..+...+..........      ......++...   .+.             ..+..+.+-||.+.++...++
T Consensus       398 YKVmvlaVd~~~i~~~~~~~~~~~~~~L~~dd~~kIvG~wnGlakr~g~~n~~~~~~~d~ap~~RAIaF~k~I~tSK~i~  477 (1518)
T COG4889         398 YKVMVLAVDKEVIAGVLQSVLSGPSKGLALDDVSKIVGCWNGLAKRNGEDNDLKNIKADTAPMQRAIAFAKDIKTSKQIA  477 (1518)
T ss_pred             ceEEEEEechhhhhhhhhhhccCcccccchhhhhhhhhhhhhhhhhccccccccCCcCCchHHHHHHHHHHhhHHHHHHH
Confidence            22221111111111111000000      01111111111   110             011235788888888877777


Q ss_pred             HHHHHc-------------CCc--eeeeecCCChHHHHHHHHh---hhcCCeeEEEEeccccccccccCccEEEEECCCC
Q 037567          246 KALKQL-------------GVK--AGTYHGQMGSKAREEAHRL---FIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPK  307 (374)
Q Consensus       246 ~~l~~~-------------~~~--~~~~~~~~~~~~r~~~~~~---f~~g~~~ilv~t~~~~~G~d~~~~~~vi~~~~p~  307 (374)
                      +.+.+-             ++.  +.-+.|.|+..+|...+..   |...+.+||--...+++|+|+|.++.||++++..
T Consensus       478 ~sFe~Vve~Y~~Elk~d~~nL~iSi~HvDGtmNal~R~~l~~l~~~~~~neckIlSNaRcLSEGVDVPaLDsViFf~pr~  557 (1518)
T COG4889         478 ESFETVVEAYDEELKKDFKNLKISIDHVDGTMNALERLDLLELKNTFEPNECKILSNARCLSEGVDVPALDSVIFFDPRS  557 (1518)
T ss_pred             HHHHHHHHHHHHHHHhcCCCceEEeecccccccHHHHHHHHhccCCCCcchheeeccchhhhcCCCccccceEEEecCch
Confidence            665431             233  3445678888888665443   4556788888888999999999999999999999


Q ss_pred             ChhHHHHhhccCCCCCC
Q 037567          308 TLESYYQESGRCGRDGI  324 (374)
Q Consensus       308 s~~~~~Q~~GR~~R~~~  324 (374)
                      +..+.+|.+||+.|...
T Consensus       558 smVDIVQaVGRVMRKa~  574 (1518)
T COG4889         558 SMVDIVQAVGRVMRKAK  574 (1518)
T ss_pred             hHHHHHHHHHHHHHhCc
Confidence            99999999999999743

>PRK12903 secA preprotein translocase subunit SecA; Reviewed

Probab=99.83  E-value=4.9e-18  Score=158.57  Aligned_cols=322  Identities=15%  Similarity=0.138  Sum_probs=208.1

Q ss_pred             hhHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc---cCCcEEEEcchHHHHHHHHHHHH----
Q 037567            2 VSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV---TGKTALVVSPLISLMQDQVMSLK----   74 (374)
Q Consensus         2 ~~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~---~~~~~lil~P~~~l~~q~~~~~~----   74 (374)
                      .++.++.+|.. |++.|.-+--.+.+|+  +..+.||-|||+++.+|+..   .++.|-|++...-|+.--.+++.    
T Consensus        68 REA~~R~lG~r-~ydVQliGglvLh~G~--IAEMkTGEGKTLvAtLpayLnAL~GkgVhVVTvNdYLA~RDae~mg~vy~  144 (925)
T PRK12903         68 REATKRVLGKR-PYDVQIIGGIILDLGS--VAEMKTGEGKTITSIAPVYLNALTGKGVIVSTVNEYLAERDAEEMGKVFN  144 (925)
T ss_pred             HHHHHHHhCCC-cCchHHHHHHHHhcCC--eeeecCCCCccHHHHHHHHHHHhcCCceEEEecchhhhhhhHHHHHHHHH
Confidence            45677788884 8888877776666554  89999999999998887653   58889999999999875444443    


Q ss_pred             HcCCceEEcCCCCCchhhhhhhhcCCeeEEEEcCccccc-Cchh----hHHHHHhcCccEEEEeccchhh-ccc------
Q 037567           75 QRGINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACI-IPIS----FWSKLLKAGVCLFAVDEAHCIS-EWG------  142 (374)
Q Consensus        75 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~-~~~~----~~~~~~~~~~~~vviDE~h~~~-~~~------  142 (374)
                      -+|+.+.+.........   ......+||+++|...|.. +++.    .........+.+.||||++.+. +..      
T Consensus       145 fLGLsvG~i~~~~~~~~---rr~aY~~DItYgTn~E~gFDYLRDnm~~~~~~~vqR~~~faIVDEVDSILIDEArTPLII  221 (925)
T PRK12903        145 FLGLSVGINKANMDPNL---KREAYACDITYSVHSELGFDYLRDNMVSSKEEKVQRGLNFCLIDEVDSILIDEAKTPLII  221 (925)
T ss_pred             HhCCceeeeCCCCChHH---HHHhccCCCeeecCcccchhhhhhcccccHHHhcCcccceeeeccchheeecccCCcccc
Confidence            45888887765433332   2233458999999986633 1211    1223344678899999999974 110      


Q ss_pred             ----CcchHHHHHHHHHHHhcC--------CCC-----------------------------------------------
Q 037567          143 ----HDFRLEYKQLDKLRTFLL--------GVP-----------------------------------------------  163 (374)
Q Consensus       143 ----~~~~~~~~~~~~~~~~~~--------~~~-----------------------------------------------  163 (374)
                          ......+.....+...+.        ..+                                               
T Consensus       222 Sg~~~~~~~~Y~~~~~~v~~L~~~dy~iDek~k~v~LTe~G~~~~E~~l~i~nLy~~~n~~l~h~i~~AL~A~~lf~rd~  301 (925)
T PRK12903        222 SGGQSNDSNLYLAADQFVRTLKEDDYKIDEETKAISLTEKGIKKANKFFKLKNLYDIENSELVHRIQNALRAHKVMKEDV  301 (925)
T ss_pred             cCCCccchHHHHHHHHHHHhccccceEEecccceEEECHhHHHHHHHHcCCCcccChhhHHHHHHHHHHHHHHHHHhcCC
Confidence                000111222222222111        011                                               


Q ss_pred             --------------------------------------------------------------eeEEEeecCcccHHHHHH
Q 037567          164 --------------------------------------------------------------FVALTATATEKVRIDIIN  181 (374)
Q Consensus       164 --------------------------------------------------------------~i~~SaT~~~~~~~~~~~  181 (374)
                                                                                    +.+||+|..... .++..
T Consensus       302 dYiV~dg~V~IVDefTGR~m~gRrwsdGLHQaIEAKEgv~I~~e~~TlAsIT~QnfFr~Y~kLsGMTGTA~te~-~Ef~~  380 (925)
T PRK12903        302 EYIVRDGKIELVDQFTGRIMEGRSYSEGLQQAIQAKEMVEIEPETKTLATITYQNFFRLFKKLSGMTGTAKTEE-QEFID  380 (925)
T ss_pred             ceEEECCEEEEEECCCCCCCCCCccchHHHHHHHHHcCCCCCCCceeeeeehHHHHHHhcchhhccCCCCHHHH-HHHHH
Confidence                                                                          333333332211 12222


Q ss_pred             hcCCCCCeEEEeccCCCceeEEE--EeecCCcchHHHHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHHcCCceeeee
Q 037567          182 SLKLKNPYVTIASFDRKNLFYGV--KVINRGQSFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYH  259 (374)
Q Consensus       182 ~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~  259 (374)
                      .+++   .+...+.+.+......  ..+.........++.++.+....+.++||.|.+.+..+.+++.|.+.|++...++
T Consensus       381 iY~l---~Vv~IPTnkP~~R~D~~d~iy~t~~~K~~Aii~ei~~~~~~gqPVLVgT~SIe~SE~ls~~L~~~gi~h~vLN  457 (925)
T PRK12903        381 IYNM---RVNVVPTNKPVIRKDEPDSIFGTKHAKWKAVVKEVKRVHKKGQPILIGTAQVEDSETLHELLLEANIPHTVLN  457 (925)
T ss_pred             HhCC---CEEECCCCCCeeeeeCCCcEEEcHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHCCCCceeec
Confidence            2221   1222222222222221  1233344556677888877777899999999999999999999999999988888


Q ss_pred             cCCChHHHHHHHHhhhcC-CeeEEEEeccccccccccCcc--------EEEEECCCCChhHHHHhhccCCCCCCceEEEE
Q 037567          260 GQMGSKAREEAHRLFIRD-EIRVMVATMAFGMGIDKPDVR--------HVIHYGCPKTLESYYQESGRCGRDGIASVCWL  330 (374)
Q Consensus       260 ~~~~~~~r~~~~~~f~~g-~~~ilv~t~~~~~G~d~~~~~--------~vi~~~~p~s~~~~~Q~~GR~~R~~~~g~~~~  330 (374)
                      ......+-..+.   ..| .-.|.|+|+++++|.|+.--.        +||....+.|..--.|..||+||.|.+|.+-.
T Consensus       458 Ak~~e~EA~IIa---~AG~~GaVTIATNMAGRGTDI~Lg~~V~~~GGLhVIgTerheSrRIDnQLrGRaGRQGDpGss~f  534 (925)
T PRK12903        458 AKQNAREAEIIA---KAGQKGAITIATNMAGRGTDIKLSKEVLELGGLYVLGTDKAESRRIDNQLRGRSGRQGDVGESRF  534 (925)
T ss_pred             ccchhhHHHHHH---hCCCCCeEEEecccccCCcCccCchhHHHcCCcEEEecccCchHHHHHHHhcccccCCCCCcceE
Confidence            875444433332   234 347999999999999996322        78888888898888999999999999999888


Q ss_pred             EeeccC
Q 037567          331 YYARSN  336 (374)
Q Consensus       331 ~~~~~~  336 (374)
                      |++-+|
T Consensus       535 ~lSLeD  540 (925)
T PRK12903        535 FISLDD  540 (925)
T ss_pred             EEecch
Confidence            887765

>CHL00122 secA preprotein translocase subunit SecA; Validated

Probab=99.82  E-value=3e-18  Score=160.85  Aligned_cols=282  Identities=17%  Similarity=0.132  Sum_probs=178.9

Q ss_pred             hhHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc---cCCcEEEEcchHHHHHHHHHHHH----
Q 037567            2 VSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV---TGKTALVVSPLISLMQDQVMSLK----   74 (374)
Q Consensus         2 ~~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~---~~~~~lil~P~~~l~~q~~~~~~----   74 (374)
                      +++.++.+|+. |++.|.-+.-.+.  +.-+..+.||.|||+++.+|+..   .+..|-|++++..|+..-++++.    
T Consensus        66 rEa~~R~lG~r-~ydvQlig~l~L~--~G~IaEm~TGEGKTL~a~l~ayl~aL~G~~VhVvT~NdyLA~RD~e~m~pvy~  142 (870)
T CHL00122         66 REASFRTLGLR-HFDVQLIGGLVLN--DGKIAEMKTGEGKTLVATLPAYLNALTGKGVHIVTVNDYLAKRDQEWMGQIYR  142 (870)
T ss_pred             HHHHHHHhCCC-CCchHhhhhHhhc--CCccccccCCCCchHHHHHHHHHHHhcCCceEEEeCCHHHHHHHHHHHHHHHH
Confidence            45677788885 7787776655544  45699999999999998877643   58889999999999987666655    


Q ss_pred             HcCCceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccc-cCchh----hHHHHHhcCccEEEEeccchhh-cc-------
Q 037567           75 QRGINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKAC-IIPIS----FWSKLLKAGVCLFAVDEAHCIS-EW-------  141 (374)
Q Consensus        75 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~-~~~~~----~~~~~~~~~~~~vviDE~h~~~-~~-------  141 (374)
                      .+|+.+.+..+.....   .......++|+++|...+. ++++.    .........+.+.||||++.+. +.       
T Consensus       143 ~LGLsvg~i~~~~~~~---err~aY~~DItYgTn~e~gFDyLRDnm~~~~~~~v~r~~~faIVDEvDSiLIDeArTPLiI  219 (870)
T CHL00122        143 FLGLTVGLIQEGMSSE---ERKKNYLKDITYVTNSELGFDYLRDNMALSLSDVVQRPFNYCIIDEVDSILIDEARTPLII  219 (870)
T ss_pred             HcCCceeeeCCCCChH---HHHHhcCCCCEecCCccccccchhhccCcChHHhhccccceeeeecchhheeccCCCceec
Confidence            3588887765543332   2233455799999997553 12221    1223344678899999999974 10       


Q ss_pred             -cC----------------------cc------------hHHHHHHHH---------------------HHHh--c-C--
Q 037567          142 -GH----------------------DF------------RLEYKQLDK---------------------LRTF--L-L--  160 (374)
Q Consensus       142 -~~----------------------~~------------~~~~~~~~~---------------------~~~~--~-~--  160 (374)
                       |.                      ++            ......+..                     +...  + .  
T Consensus       220 Sg~~~~~~~~y~~~~~~v~~L~~~~dy~vdek~k~v~LTe~G~~~~e~~l~i~~ly~~~~~~~~~i~~AL~A~~lf~~d~  299 (870)
T CHL00122        220 SGQSKTNIDKYIVADELAKYLEKNVHYEVDEKNKNVILTEQGILFIEKILKIEDLYSANDPWIPYILNALKAKELFFKNV  299 (870)
T ss_pred             cCCCccchHHHHHHHHHHHhcCcCCCeEEEcCCCceEecHHHHHHHHHHcCCccccccccHHHHHHHHHHHHHHHHhcCC
Confidence             00                      00            000000100                     0000  0 0  


Q ss_pred             -----------------------------------------------------------CCCeeEEEeecCcccHHHHHH
Q 037567          161 -----------------------------------------------------------GVPFVALTATATEKVRIDIIN  181 (374)
Q Consensus       161 -----------------------------------------------------------~~~~i~~SaT~~~~~~~~~~~  181 (374)
                                                                                 =.++.+||+|..... ..+..
T Consensus       300 dYiV~dgeV~iVDe~TGR~m~grrws~GLHQaiEaKEgv~It~e~~tlAsIT~QnfFr~Y~kL~GMTGTa~te~-~Ef~~  378 (870)
T CHL00122        300 HYIVRNNEIIIVDEFTGRIMPGRRWSDGLHQAIEAKENLPIRQETETLASITYQNFFLLYPKLSGMTGTAKTEE-LEFEK  378 (870)
T ss_pred             cEEEECCEEEEEECCCCcCCCCCccchHHHHHHHhhcCCCCCCCceeeeeeeHHHHHHhCchhcccCCCCHHHH-HHHHH
Confidence                                                                       013677777775432 23444


Q ss_pred             hcCCCCCeEEEeccCCCcee--EEEEeecCCcchHHHHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHHcCCceeeee
Q 037567          182 SLKLKNPYVTIASFDRKNLF--YGVKVINRGQSFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYH  259 (374)
Q Consensus       182 ~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~  259 (374)
                      .+++.   +...+.+.+...  ....++.........++.++.+....+.++||-|.+....+.+++.|.+.|++...++
T Consensus       379 iY~l~---vv~IPtnkp~~R~d~~d~v~~t~~~K~~AI~~ei~~~~~~grPVLIgT~SIe~SE~ls~~L~~~gi~h~vLN  455 (870)
T CHL00122        379 IYNLE---VVCIPTHRPMLRKDLPDLIYKDELSKWRAIADECLQMHQTGRPILIGTTTIEKSELLSQLLKEYRLPHQLLN  455 (870)
T ss_pred             HhCCC---EEECCCCCCccceeCCCeEEeCHHHHHHHHHHHHHHHHhcCCCEEEeeCCHHHHHHHHHHHHHcCCccceee
Confidence            44432   222222222222  2223344555566778888888888999999999999999999999999999988888


Q ss_pred             cCCC--hHHHHHHHHhhhcCCeeEEEEecccccccccc
Q 037567          260 GQMG--SKAREEAHRLFIRDEIRVMVATMAFGMGIDKP  295 (374)
Q Consensus       260 ~~~~--~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~  295 (374)
                      ....  ..+-..+.+.=+  .-.|.|+|+|+++|.|+.
T Consensus       456 Ak~~~~~~EA~IIA~AG~--~G~VTIATNMAGRGTDI~  491 (870)
T CHL00122        456 AKPENVRRESEIVAQAGR--KGSITIATNMAGRGTDII  491 (870)
T ss_pred             CCCccchhHHHHHHhcCC--CCcEEEeccccCCCcCee
Confidence            8632  333333333222  346999999999999883

>cd00079 HELICc Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process

Probab=99.81  E-value=6.6e-19  Score=134.46  Aligned_cols=118  Identities=32%  Similarity=0.566  Sum_probs=105.2

Q ss_pred             HHHHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEecccccccc
Q 037567          214 VDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGID  293 (374)
Q Consensus       214 ~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d  293 (374)
                      ...+...+.+....++++||||++...++.+++.|++.+.++..+||+++..++..+.+.|.++...++++|.++++|+|
T Consensus        14 ~~~i~~~i~~~~~~~~~~lvf~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~ili~t~~~~~G~d   93 (131)
T cd00079          14 LEALLELLKEHLKKGGKVLIFCPSKKMLDELAELLRKPGIKVAALHGDGSQEEREEVLKDFREGEIVVLVATDVIARGID   93 (131)
T ss_pred             HHHHHHHHHhcccCCCcEEEEeCcHHHHHHHHHHHHhcCCcEEEEECCCCHHHHHHHHHHHHcCCCcEEEEcChhhcCcC
Confidence            33333333333336889999999999999999999988889999999999999999999999999999999999999999


Q ss_pred             ccCccEEEEECCCCChhHHHHhhccCCCCCCceEEEEE
Q 037567          294 KPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLY  331 (374)
Q Consensus       294 ~~~~~~vi~~~~p~s~~~~~Q~~GR~~R~~~~g~~~~~  331 (374)
                      +|.+++++++++|++...+.|++||++|.|+.|.++++
T Consensus        94 ~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~~  131 (131)
T cd00079          94 LPNVSVVINYDLPWSPSSYLQRIGRAGRAGQKGTAILL  131 (131)
T ss_pred             hhhCCEEEEeCCCCCHHHheecccccccCCCCceEEeC
Confidence            99999999999999999999999999999998887653

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

Probab=99.81  E-value=1.8e-17  Score=163.56  Aligned_cols=186  Identities=19%  Similarity=0.220  Sum_probs=114.0

Q ss_pred             CeeEEEeecCcccHH-HHHHhcCCCCCe---EEEec-cCC---CceeEEEEeec----CCcchHHHHHHHHHHhh-cCCC
Q 037567          163 PFVALTATATEKVRI-DIINSLKLKNPY---VTIAS-FDR---KNLFYGVKVIN----RGQSFVDELVQEILKSV-AGAG  229 (374)
Q Consensus       163 ~~i~~SaT~~~~~~~-~~~~~~~~~~~~---~~~~~-~~~---~~~~~~~~~~~----~~~~~~~~~~~~~~~~~-~~~~  229 (374)
                      .+|++|||+...... .+...+|+.+..   ....+ ++.   ..+........    ....+...+...+.+-. ..++
T Consensus       674 ~~iltSATL~~~~~f~~~~~~lGl~~~~~~~~~~~SpF~~~~q~~l~vp~d~p~~~~~~~~~~~~~la~~i~~l~~~~~g  753 (928)
T PRK08074        674 SVILTSATLTVNGSFDYIIERLGLEDFYPRTLQIPSPFSYEEQAKLMIPTDMPPIKDVPIEEYIEEVAAYIAKIAKATKG  753 (928)
T ss_pred             cEEEEeeecccCCCcHHHHHhcCCCCCCccEEEeCCCCCHHHhcEEEeecCCCCCCCCChHHHHHHHHHHHHHHHHhCCC
Confidence            378999998864332 345677775421   22222 121   11111111111    11222333333333322 2567


Q ss_pred             cEEEEecchhHHHHHHHHHHHcCCc--eeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccC--ccEEEEECC
Q 037567          230 SIIVYCMTIKDVEEISKALKQLGVK--AGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPD--VRHVIHYGC  305 (374)
Q Consensus       230 ~~lVf~~~~~~~~~l~~~l~~~~~~--~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~--~~~vi~~~~  305 (374)
                      +++|+++|.+..+.+++.|+.....  ...+.-+++...|.++++.|+.++-.||++|...++|+|+|+  +..||..+.
T Consensus       754 ~~LVLFtSy~~l~~v~~~l~~~~~~~~~~ll~Qg~~~~~r~~l~~~F~~~~~~iLlG~~sFwEGVD~pg~~l~~viI~kL  833 (928)
T PRK08074        754 RMLVLFTSYEMLKKTYYNLKNEEELEGYVLLAQGVSSGSRARLTKQFQQFDKAILLGTSSFWEGIDIPGDELSCLVIVRL  833 (928)
T ss_pred             CEEEEECCHHHHHHHHHHHhhcccccCceEEecCCCCCCHHHHHHHHHhcCCeEEEecCcccCccccCCCceEEEEEecC
Confidence            9999999999999999999764321  222332344456789999999988889999999999999998  577888886


Q ss_pred             CC------------------------------ChhHHHHhhccCCCCCCceEEEEEeeccC--CCcccceecccc
Q 037567          306 PK------------------------------TLESYYQESGRCGRDGIASVCWLYYARSN--FAKGDFYCGESQ  348 (374)
Q Consensus       306 p~------------------------------s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~--~~~~~~~~~~~~  348 (374)
                      |.                              ....+.|.+||.-|..++..+++++++.-  ..+-+.|.+...
T Consensus       834 PF~~p~dp~~~a~~~~~~~~g~~~F~~~~lP~A~~~lkQg~GRlIRs~~D~G~v~ilD~R~~~k~Yg~~~l~sLP  908 (928)
T PRK08074        834 PFAPPDQPVMEAKSEWAKEQGENPFQELSLPQAVLRFKQGFGRLIRTETDRGTVFVLDRRLTTTSYGKYFLESLP  908 (928)
T ss_pred             CCCCCCCHHHHHHHHHHHHhCCCchhhhhhHHHHHHHHhhhhhhcccCCceEEEEEecCccccchHHHHHHHhCC
Confidence            64                              13445899999999876554555555542  223344555544

>KOG0392 consensus SNF2 family DNA-dependent ATPase domain-containing protein [Transcription]

Probab=99.81  E-value=1.1e-18  Score=165.04  Aligned_cols=306  Identities=16%  Similarity=0.147  Sum_probs=198.0

Q ss_pred             CCchhHHHHHHHH--Hc--CCCEEEEccCCCCchhhhhccccc------------cCCcEEEEcchHHHHHHHHHHHHHc
Q 037567           13 VFRPYQKDVIQRI--IE--KRDCLVVMATGSGKSLCYQLPPLV------------TGKTALVVSPLISLMQDQVMSLKQR   76 (374)
Q Consensus        13 ~~~~~Q~~~~~~~--~~--~~~~l~~a~tGsGKT~~~~l~~~~------------~~~~~lil~P~~~l~~q~~~~~~~~   76 (374)
                      .+|.||.+.++.+  ++  +-+.|++.++|-|||+-.+..+..            ...+.||+||+ .|+.+|..++.+|
T Consensus       975 ~LRkYQqEGVnWLaFLnky~LHGILcDDMGLGKTLQticilAsd~y~r~s~~~e~~~~PSLIVCPs-TLtGHW~~E~~kf 1053 (1549)
T KOG0392|consen  975 KLRKYQQEGVNWLAFLNKYKLHGILCDDMGLGKTLQTICILASDHYKRRSESSEFNRLPSLIVCPS-TLTGHWKSEVKKF 1053 (1549)
T ss_pred             HHHHHHHhccHHHHHHHHhcccceeeccccccHHHHHHHHHHHHHHhhcccchhhccCCeEEECCc-hhhhHHHHHHHHh
Confidence            5788999998754  23  457899999999999653322221            14459999999 7999999999998


Q ss_pred             CCceEEcCCCCCchhh-hhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHH
Q 037567           77 GINAEFLGSAQTDSSV-QTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKL  155 (374)
Q Consensus        77 ~~~~~~~~~~~~~~~~-~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~  155 (374)
                      -....+.......... .....-.+.+|+|++|+-+.    +-...+....|.+.|+||-|.+.+..       ..+.+.
T Consensus      1054 ~pfL~v~~yvg~p~~r~~lR~q~~~~~iiVtSYDv~R----nD~d~l~~~~wNYcVLDEGHVikN~k-------tkl~ka 1122 (1549)
T KOG0392|consen 1054 FPFLKVLQYVGPPAERRELRDQYKNANIIVTSYDVVR----NDVDYLIKIDWNYCVLDEGHVIKNSK-------TKLTKA 1122 (1549)
T ss_pred             cchhhhhhhcCChHHHHHHHhhccccceEEeeHHHHH----HHHHHHHhcccceEEecCcceecchH-------HHHHHH
Confidence            5553332222112111 11111234589999998653    22234445678899999999987633       333444


Q ss_pred             HHhcCCCCeeEEEeecCcccHHHHHHhcCCC-------------------------------------------------
Q 037567          156 RTFLLGVPFVALTATATEKVRIDIINSLKLK-------------------------------------------------  186 (374)
Q Consensus       156 ~~~~~~~~~i~~SaT~~~~~~~~~~~~~~~~-------------------------------------------------  186 (374)
                      ...+...+++.+|+||-.+...+++..+..-                                                 
T Consensus      1123 vkqL~a~hRLILSGTPIQNnvleLWSLFdFLMPGfLGtEKqFqsrf~kpI~asRd~K~Sske~EaG~lAleaLHKqVLPF 1202 (1549)
T KOG0392|consen 1123 VKQLRANHRLILSGTPIQNNVLELWSLFDFLMPGFLGTEKQFQSRFGKPILASRDPKSSSKEQEAGVLALEALHKQVLPF 1202 (1549)
T ss_pred             HHHHhhcceEEeeCCCcccCHHHHHHHHHHhcccccCcHHHHHHHhcchhhhhcCcccchhHHHhhHHHHHHHHHHHHHH
Confidence            4444566789999998877655444422100                                                 


Q ss_pred             -------------CCeEEEe-ccC-----------------------------CCce----------------eEEEEee
Q 037567          187 -------------NPYVTIA-SFD-----------------------------RKNL----------------FYGVKVI  207 (374)
Q Consensus       187 -------------~~~~~~~-~~~-----------------------------~~~~----------------~~~~~~~  207 (374)
                                   ++.++.. ..+                             ....                ...--+.
T Consensus      1203 ~LRRlKedVL~DLPpKIIQDyyCeLs~lQ~kLY~df~~~~k~~~~~~~d~~~~S~gt~~~HvFqaLqYlrKLcnHpaLvl 1282 (1549)
T KOG0392|consen 1203 LLRRLKEDVLKDLPPKIIQDYYCELSPLQKKLYRDFVKKAKQCVSSQIDGGEESLGTDKTHVFQALQYLRKLCNHPALVL 1282 (1549)
T ss_pred             HHHHHHHHHHhhCChhhhhheeeccCHHHHHHHHHHHHHhccccccccccchhccCcchHHHHHHHHHHHHhcCCcceee
Confidence                         0000000 000                             0000                0000000


Q ss_pred             cCCc----------------------chHHHHHHHHHHhhc---------------CCCcEEEEecchhHHHHHHHHHHH
Q 037567          208 NRGQ----------------------SFVDELVQEILKSVA---------------GAGSIIVYCMTIKDVEEISKALKQ  250 (374)
Q Consensus       208 ~~~~----------------------~~~~~~~~~~~~~~~---------------~~~~~lVf~~~~~~~~~l~~~l~~  250 (374)
                      ....                      .-+...+..++....               .+.++||||.-++.+..+.+.|.+
T Consensus      1283 t~~hp~la~i~~~l~~~~~~LHdi~hspKl~AL~qLL~eCGig~~~~~~~g~~s~vsqHRiLIFcQlK~mlDlVekDL~k 1362 (1549)
T KOG0392|consen 1283 TPVHPDLAAIVSHLAHFNSSLHDIQHSPKLSALKQLLSECGIGNNSDSEVGTPSDVSQHRILIFCQLKSMLDLVEKDLFK 1362 (1549)
T ss_pred             CCCcchHHHHHHHHHHhhhhHHHhhhchhHHHHHHHHHHhCCCCCCcccccCcchhccceeEEeeeHHHHHHHHHHHHhh
Confidence            0000                      001122222322211               124799999999999999988876


Q ss_pred             cCC-ce--eeeecCCChHHHHHHHHhhhcC-CeeEEE-EeccccccccccCccEEEEECCCCChhHHHHhhccCCCCCCc
Q 037567          251 LGV-KA--GTYHGQMGSKAREEAHRLFIRD-EIRVMV-ATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIA  325 (374)
Q Consensus       251 ~~~-~~--~~~~~~~~~~~r~~~~~~f~~g-~~~ilv-~t~~~~~G~d~~~~~~vi~~~~p~s~~~~~Q~~GR~~R~~~~  325 (374)
                      .-. .+  ..+.|..++.+|+++.++|+++ .++||+ +|...+-|+|+.+.+.||++.-.|++..-+|.+.||.|.||.
T Consensus      1363 ~~mpsVtymRLDGSVpp~~R~kiV~~FN~DptIDvLlLTThVGGLGLNLTGADTVVFvEHDWNPMrDLQAMDRAHRIGQK 1442 (1549)
T KOG0392|consen 1363 KYMPSVTYMRLDGSVPPGDRQKIVERFNEDPTIDVLLLTTHVGGLGLNLTGADTVVFVEHDWNPMRDLQAMDRAHRIGQK 1442 (1549)
T ss_pred             hhcCceeEEEecCCCCcHHHHHHHHHhcCCCceeEEEEeeeccccccccCCCceEEEEecCCCchhhHHHHHHHHhhcCc
Confidence            432 23  3788999999999999999998 688875 778999999999999999999999999999999999999998


Q ss_pred             eEEEE
Q 037567          326 SVCWL  330 (374)
Q Consensus       326 g~~~~  330 (374)
                      ..+=+
T Consensus      1443 rvVNV 1447 (1549)
T KOG0392|consen 1443 RVVNV 1447 (1549)
T ss_pred             eeeee
Confidence            75533

>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=99.80  E-value=8e-20  Score=148.23  Aligned_cols=152  Identities=26%  Similarity=0.276  Sum_probs=100.7

Q ss_pred             CCchhHHHHHHHHHc-------CCCEEEEccCCCCchhhhhccccccCCcEEEEcchHHHHHHHHHHHHHcCCceEEcCC
Q 037567           13 VFRPYQKDVIQRIIE-------KRDCLVVMATGSGKSLCYQLPPLVTGKTALVVSPLISLMQDQVMSLKQRGINAEFLGS   85 (374)
Q Consensus        13 ~~~~~Q~~~~~~~~~-------~~~~l~~a~tGsGKT~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~   85 (374)
                      +|+++|.+++..+.+       .+.+++.+|||||||.+++..+..-..++++++|+..|++|+...+..++........
T Consensus         3 ~lr~~Q~~ai~~i~~~~~~~~~~~~~ll~~~tGsGKT~~~~~~~~~l~~~~l~~~p~~~l~~Q~~~~~~~~~~~~~~~~~   82 (184)
T PF04851_consen    3 KLRPYQQEAIARIINSLENKKEERRVLLNAPTGSGKTIIALALILELARKVLIVAPNISLLEQWYDEFDDFGSEKYNFFE   82 (184)
T ss_dssp             EE-HHHHHHHHHHHHHHHTTSGCSEEEEEESTTSSHHHHHHHHHHHHHCEEEEEESSHHHHHHHHHHHHHHSTTSEEEEE
T ss_pred             CCCHHHHHHHHHHHHHHHhcCCCCCEEEEECCCCCcChhhhhhhhccccceeEecCHHHHHHHHHHHHHHhhhhhhhhcc
Confidence            589999999999884       5789999999999998877544443339999999999999999999665433221110


Q ss_pred             --------------CCCchhhhhhhhcCCeeEEEEcCcccccCchhh---------HHHHHhcCccEEEEeccchhhccc
Q 037567           86 --------------AQTDSSVQTKAETGYFQLLFMTPEKACIIPISF---------WSKLLKAGVCLFAVDEAHCISEWG  142 (374)
Q Consensus        86 --------------~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~---------~~~~~~~~~~~vviDE~h~~~~~~  142 (374)
                                    ................+++++|.+++.......         ........+++||+||||++....
T Consensus        83 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~vI~DEaH~~~~~~  162 (184)
T PF04851_consen   83 KSIKPAYDSKEFISIQDDISDKSESDNNDKDIILTTYQSLQSDIKEEKKIDESARRSYKLLKNKFDLVIIDEAHHYPSDS  162 (184)
T ss_dssp             --GGGCCE-SEEETTTTEEEHHHHHCBSS-SEEEEEHHHHHHHHHH---------GCHHGGGGSESEEEEETGGCTHHHH
T ss_pred             cccccccccccccccccccccccccccccccchhhHHHHHHhhcccccccccchhhhhhhccccCCEEEEehhhhcCCHH
Confidence                          001111112233456789999999886553321         122334567899999999986522


Q ss_pred             CcchHHHHHHHHHHHhcCCCCeeEEEeecCc
Q 037567          143 HDFRLEYKQLDKLRTFLLGVPFVALTATATE  173 (374)
Q Consensus       143 ~~~~~~~~~~~~~~~~~~~~~~i~~SaT~~~  173 (374)
                      .        +..+.. .++..+++|||||.+
T Consensus       163 ~--------~~~i~~-~~~~~~l~lTATp~r  184 (184)
T PF04851_consen  163 S--------YREIIE-FKAAFILGLTATPFR  184 (184)
T ss_dssp             H--------HHHHHH-SSCCEEEEEESS-S-
T ss_pred             H--------HHHHHc-CCCCeEEEEEeCccC
Confidence            1        233333 567789999999963

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 ....

>KOG0925 consensus mRNA splicing factor ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.80  E-value=5.2e-18  Score=146.51  Aligned_cols=303  Identities=15%  Similarity=0.153  Sum_probs=190.7

Q ss_pred             CchhHHHHHHHHHcCCCEEEEccCCCCchhhhhc----cccccCCcEEEEcchHHHHHHHHHHHH-HcCCceEEcCCCCC
Q 037567           14 FRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQL----PPLVTGKTALVVSPLISLMQDQVMSLK-QRGINAEFLGSAQT   88 (374)
Q Consensus        14 ~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l----~~~~~~~~~lil~P~~~l~~q~~~~~~-~~~~~~~~~~~~~~   88 (374)
                      .+.++.+-+..+.+++-++++|.||||||.-.--    ..+....-+...-|++..+-+++.... ..+...+--.+...
T Consensus        48 vw~~k~~F~~~l~~nQ~~v~vGetgsGKttQiPq~~~~~~~~~~~~v~CTQprrvaamsva~RVadEMDv~lG~EVGysI  127 (699)
T KOG0925|consen   48 VWEQKEEFLKLLLNNQIIVLVGETGSGKTTQIPQFVLEYELSHLTGVACTQPRRVAAMSVAQRVADEMDVTLGEEVGYSI  127 (699)
T ss_pred             hHHhHHHHHHHHhcCceEEEEecCCCCccccCcHHHHHHHHhhccceeecCchHHHHHHHHHHHHHHhccccchhccccc
Confidence            4555566666666788889999999999953110    011223667888899988888776654 23333221111111


Q ss_pred             chhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHHhcCCCCeeEEE
Q 037567           89 DSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALT  168 (374)
Q Consensus        89 ~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~S  168 (374)
                      .-+...   ....-+-++|.++|.+   .....-.+..+.++|+||||.=   ..........+.++....++.++|.||
T Consensus       128 rfEdC~---~~~T~Lky~tDgmLlr---Eams~p~l~~y~viiLDeahER---tlATDiLmGllk~v~~~rpdLk~vvmS  198 (699)
T KOG0925|consen  128 RFEDCT---SPNTLLKYCTDGMLLR---EAMSDPLLGRYGVIILDEAHER---TLATDILMGLLKEVVRNRPDLKLVVMS  198 (699)
T ss_pred             cccccC---ChhHHHHHhcchHHHH---HHhhCcccccccEEEechhhhh---hHHHHHHHHHHHHHHhhCCCceEEEee
Confidence            111000   0001122456665533   2334445678899999999953   333444556777777777899999999


Q ss_pred             eecCcccHHHHHHhcCCCCCeEEEeccCCCceeEEEEeecCCcchHHHHHHHHHH--hhcCCCcEEEEecchhHHHHHHH
Q 037567          169 ATATEKVRIDIINSLKLKNPYVTIASFDRKNLFYGVKVINRGQSFVDELVQEILK--SVAGAGSIIVYCMTIKDVEEISK  246 (374)
Q Consensus       169 aT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~lVf~~~~~~~~~l~~  246 (374)
                      ||.....   +...+ ...+.+..+....-.+   +-..+...+.++..++.+++  .....|.++||....++.+..++
T Consensus       199 atl~a~K---fq~yf-~n~Pll~vpg~~PvEi---~Yt~e~erDylEaairtV~qih~~ee~GDilvFLtgeeeIe~aC~  271 (699)
T KOG0925|consen  199 ATLDAEK---FQRYF-GNAPLLAVPGTHPVEI---FYTPEPERDYLEAAIRTVLQIHMCEEPGDILVFLTGEEEIEDACR  271 (699)
T ss_pred             cccchHH---HHHHh-CCCCeeecCCCCceEE---EecCCCChhHHHHHHHHHHHHHhccCCCCEEEEecCHHHHHHHHH
Confidence            9987654   23333 3444444443111111   11222334456666666544  23457899999999999999999


Q ss_pred             HHHHc---------CCceeeeecCCChHHHHHHHHhhhc---C--CeeEEEEeccccccccccCccEEEEEC--------
Q 037567          247 ALKQL---------GVKAGTYHGQMGSKAREEAHRLFIR---D--EIRVMVATMAFGMGIDKPDVRHVIHYG--------  304 (374)
Q Consensus       247 ~l~~~---------~~~~~~~~~~~~~~~r~~~~~~f~~---g--~~~ilv~t~~~~~G~d~~~~~~vi~~~--------  304 (374)
                      .+.+.         .+.+..+|    +++.+.+.+.-..   |  ..+|+|+|.+++..+.++++.+||+.+        
T Consensus       272 ~i~re~~~L~~~~g~l~v~PLy----P~~qq~iFep~p~~~~~~~~RkvVvstniaetsltidgiv~VIDpGf~kqkVYN  347 (699)
T KOG0925|consen  272 KISREVDNLGPQVGPLKVVPLY----PAQQQRIFEPAPEKRNGAYGRKVVVSTNIAETSLTIDGIVFVIDPGFSKQKVYN  347 (699)
T ss_pred             HHHHHHHhhccccCCceEEecC----chhhccccCCCCcccCCCccceEEEEecchheeeeeccEEEEecCchhhhcccC
Confidence            98753         23566776    4444444333221   1  357999999999999999999999655        


Q ss_pred             ----------CCCChhHHHHhhccCCCCCCceEEEEEeeccCC
Q 037567          305 ----------CPKTLESYYQESGRCGRDGIASVCWLYYARSNF  337 (374)
Q Consensus       305 ----------~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~~  337 (374)
                                .|.|..+-.||.||+||. .+|.|+-+|++.-+
T Consensus       348 PRIRvesllv~PISkasA~qR~gragrt-~pGkcfrLYte~~~  389 (699)
T KOG0925|consen  348 PRIRVESLLVSPISKASAQQRAGRAGRT-RPGKCFRLYTEEAF  389 (699)
T ss_pred             cceeeeeeeeccchHhHHHHHhhhccCC-CCCceEEeecHHhh
Confidence                      345788889999999996 58999999998644

>KOG4150 consensus Predicted ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.80  E-value=2e-18  Score=151.85  Aligned_cols=325  Identities=14%  Similarity=0.082  Sum_probs=209.5

Q ss_pred             CCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc-----cCCcEEEEcchHHHHHHHHHHHHHc------CC
Q 037567           10 GYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV-----TGKTALVVSPLISLMQDQVMSLKQR------GI   78 (374)
Q Consensus        10 ~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~-----~~~~~lil~P~~~l~~q~~~~~~~~------~~   78 (374)
                      --+....+|.+++..+.+|++.++.-.+.+||++++.+....     .....++..|+.+++++..+.+.-.      ..
T Consensus       283 ~~E~~~~~~~~~~~~~~~G~~~~~~~~~~~GK~~~~~~~s~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~V~~~~I~~~K  362 (1034)
T KOG4150|consen  283 TGESGIAISLELLKFASEGRADGGNEARQAGKGTCPTSGSRKFQTLCHATNSLLPSEMVEHLRNGSKGQVVHVEVIKARK  362 (1034)
T ss_pred             cccchhhhhHHHHhhhhhcccccccchhhcCCccCcccchhhhhhcCcccceecchhHHHHhhccCCceEEEEEehhhhh
Confidence            334688899999999999999999999999999998776543     4677899999999988654443211      01


Q ss_pred             ceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccC--chhhHHHHHhcCccEEEEeccchhhc-ccCcchHHHHHHHHH
Q 037567           79 NAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACII--PISFWSKLLKAGVCLFAVDEAHCISE-WGHDFRLEYKQLDKL  155 (374)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~--~~~~~~~~~~~~~~~vviDE~h~~~~-~~~~~~~~~~~~~~~  155 (374)
                      +..+-..+...+.........+..++++.|+.....  .++.-.........++++||+|.+.. .+......++++.++
T Consensus       363 ~A~V~~~D~~sE~~~~A~~R~~~~~~~s~~~~~~s~~L~~~~~~~~~~~~~~~~~~~~~~~Y~~~~~~~~~~~~R~L~~L  442 (1034)
T KOG4150|consen  363 SAYVEMSDKLSETTKSALKRIGLNTLYSHQAEAISAALAKSLCYNVPVFEELCKDTNSCALYLFPTKALAQDQLRALSDL  442 (1034)
T ss_pred             cceeecccCCCchhHHHHHhcCcceeecCHHHHHHHHhhhccccccHHHHHHHhcccceeeeecchhhHHHHHHHHHHHH
Confidence            111222222222222333445568888888754321  11111112223345789999998753 333333333444333


Q ss_pred             HHhc---CCCCeeEEEeecCcccHHHHHHhcCCCCCeEEEeccCC--CceeEEEEee------cCCcchHHHHHHHHHHh
Q 037567          156 RTFL---LGVPFVALTATATEKVRIDIINSLKLKNPYVTIASFDR--KNLFYGVKVI------NRGQSFVDELVQEILKS  224 (374)
Q Consensus       156 ~~~~---~~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~------~~~~~~~~~~~~~~~~~  224 (374)
                      ..-+   .+.+++-.|+|...... .....+++.+...+......  ......+.+.      .....++.+.-.-+.+.
T Consensus       443 ~~~F~~~~~~~~~~~~~~~K~~~~-~~~~~~~~~E~~Li~~DGSPs~~K~~V~WNP~~~P~~~~~~~~~i~E~s~~~~~~  521 (1034)
T KOG4150|consen  443 IKGFEASINMGVYDGDTPYKDRTR-LRSELANLSELELVTIDGSPSSEKLFVLWNPSAPPTSKSEKSSKVVEVSHLFAEM  521 (1034)
T ss_pred             HHHHHhhcCcceEeCCCCcCCHHH-HHHHhcCCcceEEEEecCCCCccceEEEeCCCCCCcchhhhhhHHHHHHHHHHHH
Confidence            3322   25677777777666543 23344454444333322221  1111111110      11122333333344555


Q ss_pred             hcCCCcEEEEecchhHHHHHHHHHHH----cCC----ceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccC
Q 037567          225 VAGAGSIIVYCMTIKDVEEISKALKQ----LGV----KAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPD  296 (374)
Q Consensus       225 ~~~~~~~lVf~~~~~~~~~l~~~l~~----~~~----~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~  296 (374)
                      ..++-++|-||+.+..|+.+-...++    .+.    .+..+.|+.+.++|.++..+.-.|+..-+|+|++++-|+|+..
T Consensus       522 i~~~~R~IAFC~~R~~CEL~~~~~R~I~~ET~~~LV~~i~SYRGGY~A~DRRKIE~~~F~G~L~giIaTNALELGIDIG~  601 (1034)
T KOG4150|consen  522 VQHGLRCIAFCPSRKLCELVLCLTREILAETAPHLVEAITSYRGGYIAEDRRKIESDLFGGKLCGIIATNALELGIDIGH  601 (1034)
T ss_pred             HHcCCcEEEeccHHHHHHHHHHHHHHHHHHhhHHHHHHHHhhcCccchhhHHHHHHHhhCCeeeEEEecchhhhcccccc
Confidence            56788999999999998877655443    222    1345778999999999999999999999999999999999999


Q ss_pred             ccEEEEECCCCChhHHHHhhccCCCCCCceEEEEEeecc
Q 037567          297 VRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARS  335 (374)
Q Consensus       297 ~~~vi~~~~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~  335 (374)
                      ++.|+..+.|.|..++.|..|||||.+++...+++....
T Consensus       602 LDAVl~~GFP~S~aNl~QQ~GRAGRRNk~SLavyva~~~  640 (1034)
T KOG4150|consen  602 LDAVLHLGFPGSIANLWQQAGRAGRRNKPSLAVYVAFLG  640 (1034)
T ss_pred             ceeEEEccCchhHHHHHHHhccccccCCCceEEEEEecc
Confidence            999999999999999999999999999988776665443

>smart00487 DEXDc DEAD-like helicases superfamily

Probab=99.78  E-value=1.3e-18  Score=142.95  Aligned_cols=161  Identities=33%  Similarity=0.479  Sum_probs=113.4

Q ss_pred             cCCCCCchhHHHHHHHHHcC-CCEEEEccCCCCchhhhhccccc---c--CCcEEEEcchHHHHHHHHHHHHHcCCc---
Q 037567            9 FGYSVFRPYQKDVIQRIIEK-RDCLVVMATGSGKSLCYQLPPLV---T--GKTALVVSPLISLMQDQVMSLKQRGIN---   79 (374)
Q Consensus         9 ~~~~~~~~~Q~~~~~~~~~~-~~~l~~a~tGsGKT~~~~l~~~~---~--~~~~lil~P~~~l~~q~~~~~~~~~~~---   79 (374)
                      +++..++++|.++++.+... +.+++.+|||+|||.++...++.   .  ..++++++|+..++.|+...+......   
T Consensus         4 ~~~~~~~~~Q~~~~~~~~~~~~~~~i~~~~GsGKT~~~~~~~~~~~~~~~~~~~l~~~p~~~~~~~~~~~~~~~~~~~~~   83 (201)
T smart00487        4 FGFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKRGKGKRVLVLVPTRELAEQWAEELKKLGPSLGL   83 (201)
T ss_pred             cCCCCCCHHHHHHHHHHHcCCCcEEEECCCCCchhHHHHHHHHHHhcccCCCcEEEEeCCHHHHHHHHHHHHHHhccCCe
Confidence            57788999999999999998 99999999999999876655543   2  378999999999999999999876522   


Q ss_pred             --eEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHH
Q 037567           80 --AEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRT  157 (374)
Q Consensus        80 --~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~  157 (374)
                        .....+. ...........+..+++++|++.+.......  ......++++|+||+|.+.....  .   ..+..+..
T Consensus        84 ~~~~~~~~~-~~~~~~~~~~~~~~~v~~~t~~~l~~~~~~~--~~~~~~~~~iIiDE~h~~~~~~~--~---~~~~~~~~  155 (201)
T smart00487       84 KVVGLYGGD-SKREQLRKLESGKTDILVTTPGRLLDLLEND--LLELSNVDLVILDEAHRLLDGGF--G---DQLEKLLK  155 (201)
T ss_pred             EEEEEeCCc-chHHHHHHHhcCCCCEEEeChHHHHHHHHcC--CcCHhHCCEEEEECHHHHhcCCc--H---HHHHHHHH
Confidence              2223222 2222222333343499999999876554331  13445678999999999975321  1   33333333


Q ss_pred             hc-CCCCeeEEEeecCcccHH
Q 037567          158 FL-LGVPFVALTATATEKVRI  177 (374)
Q Consensus       158 ~~-~~~~~i~~SaT~~~~~~~  177 (374)
                      .. ++.+++++|||++.....
T Consensus       156 ~~~~~~~~v~~saT~~~~~~~  176 (201)
T smart00487      156 LLPKNVQLLLLSATPPEEIEN  176 (201)
T ss_pred             hCCccceEEEEecCCchhHHH
Confidence            33 478899999999876554

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

Probab=99.78  E-value=9.7e-17  Score=149.03  Aligned_cols=107  Identities=17%  Similarity=0.115  Sum_probs=80.1

Q ss_pred             CCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhc----CCeeEEEEeccccccccc--------
Q 037567          227 GAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIR----DEIRVMVATMAFGMGIDK--------  294 (374)
Q Consensus       227 ~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~----g~~~ilv~t~~~~~G~d~--------  294 (374)
                      .+|.++|.+.+...++.+++.+...-.-...+.|+.+  .+..+++.|+.    |...||++|..+++|+|+        
T Consensus       469 ~~G~~lvLfTS~~~~~~~~~~l~~~l~~~~l~qg~~~--~~~~l~~~f~~~~~~~~~~vL~gt~sfweGvDv~~~~~~p~  546 (636)
T TIGR03117       469 AQGGTLVLTTAFSHISAIGQLVELGIPAEIVIQSEKN--RLASAEQQFLALYANGIQPVLIAAGGAWTGIDLTHKPVSPD  546 (636)
T ss_pred             cCCCEEEEechHHHHHHHHHHHHhhcCCCEEEeCCCc--cHHHHHHHHHHhhcCCCCcEEEeCCccccccccCCccCCCC
Confidence            5779999999999999999999764223455556432  45667888887    467899999999999999        


Q ss_pred             cC--ccEEEEECCCC-------------------------ChhHHHHhhccCCCCCCc--eEEEEEeecc
Q 037567          295 PD--VRHVIHYGCPK-------------------------TLESYYQESGRCGRDGIA--SVCWLYYARS  335 (374)
Q Consensus       295 ~~--~~~vi~~~~p~-------------------------s~~~~~Q~~GR~~R~~~~--g~~~~~~~~~  335 (374)
                      |+  ++.||+..+|.                         ....+.|.+||.-|...+  .-++.++++.
T Consensus       547 ~G~~Ls~ViI~kLPF~~~dp~a~~~~~~~~g~~~f~~~p~a~i~lkQg~GRLIR~~~D~~~G~i~ilD~R  616 (636)
T TIGR03117       547 KDNLLTDLIITCAPFGLNRSLSMLKRIRKTSVRPWEIINESLMMLRQGLGRLVRHPDMPQNRRIHMLDGR  616 (636)
T ss_pred             CCCcccEEEEEeCCCCcCChHHHHHHHHhcCCChHhhhHHHHHHHHHhcCceeecCCCcCceEEEEEeCC
Confidence            34  78898887773                         134568999999998665  4455555554

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.

>PF00271 Helicase_C: Helicase conserved C-terminal domain; InterPro: IPR001650 The domain, which defines this group of proteins is found in a wide variety of helicases and helicase related proteins

Probab=99.77  E-value=1.3e-18  Score=119.52  Aligned_cols=78  Identities=46%  Similarity=0.707  Sum_probs=75.2

Q ss_pred             HHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEEEEECCCCChhHHHHhhccCCCCC
Q 037567          246 KALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRDG  323 (374)
Q Consensus       246 ~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~~~~p~s~~~~~Q~~GR~~R~~  323 (374)
                      +.|++.++.+..+||+++..+|+.+++.|+.++..|||+|+++++|+|+|.+++|+++++|+|+.+|.|++||++|.|
T Consensus         1 ~~L~~~~~~~~~i~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~Gid~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~g   78 (78)
T PF00271_consen    1 KFLEKKGIKVAIIHGDMSQKERQEILKKFNSGEIRVLIATDILGEGIDLPDASHVIFYDPPWSPEEYIQRIGRAGRIG   78 (78)
T ss_dssp             HHHHHTTSSEEEESTTSHHHHHHHHHHHHHTTSSSEEEESCGGTTSSTSTTESEEEESSSESSHHHHHHHHTTSSTTT
T ss_pred             CChHHCCCcEEEEECCCCHHHHHHHHHHhhccCceEEEeeccccccccccccccccccccCCCHHHHHHHhhcCCCCC
Confidence            467888999999999999999999999999999999999999999999999999999999999999999999999986

It may be that this is not an autonomously folding unit, but an integral part of the helicase. The eukaryotic translation initiation factor 4A (eIF4A) is a member of the DEA(D/H)-box RNA helicase family This is a diverse group of proteins that couples an ATPase activity to RNA binding and unwinding. The structure of the carboxyl-terminal domain of eIF4A has been determined to 1.75 A resolution; it has a parallel alpha-beta topology that superimposes, with minor variations, on the structures and conserved motifs of the equivalent domain in other, distantly related helicases [].; GO: 0003676 nucleic acid binding, 0004386 helicase activity, 0005524 ATP binding; PDB: 2Z83_A 2JGN_C 2I4I_A 2BMF_A 2BHR_B 1WP9_E 2WAX_C 2WAY_C 3JUX_A 3DIN_B ....

>PRK12902 secA preprotein translocase subunit SecA; Reviewed

Probab=99.76  E-value=3.5e-16  Score=146.91  Aligned_cols=132  Identities=18%  Similarity=0.172  Sum_probs=92.6

Q ss_pred             hhHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc---cCCcEEEEcchHHHHHHHHHHHH----
Q 037567            2 VSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV---TGKTALVVSPLISLMQDQVMSLK----   74 (374)
Q Consensus         2 ~~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~---~~~~~lil~P~~~l~~q~~~~~~----   74 (374)
                      .++-++..|.. |++.|.-+--.+.+|+  +..+.||.|||+++.+|+..   .++.|-|++++.-||..-++++.    
T Consensus        75 REa~~R~lG~r-~ydVQliGgl~Lh~G~--IAEM~TGEGKTL~atlpaylnAL~GkgVhVVTvNdYLA~RDae~m~~vy~  151 (939)
T PRK12902         75 REASKRVLGMR-HFDVQLIGGMVLHEGQ--IAEMKTGEGKTLVATLPSYLNALTGKGVHVVTVNDYLARRDAEWMGQVHR  151 (939)
T ss_pred             HHHHHHHhCCC-cchhHHHhhhhhcCCc--eeeecCCCChhHHHHHHHHHHhhcCCCeEEEeCCHHHHHhHHHHHHHHHH
Confidence            35666777774 7777766665554444  99999999999998888664   58889999999999987666654    


Q ss_pred             HcCCceEEcCCCCCchhhhhhhhcCCeeEEEEcCccccc-CchhhH----HHHHhcCccEEEEeccchhh
Q 037567           75 QRGINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACI-IPISFW----SKLLKAGVCLFAVDEAHCIS  139 (374)
Q Consensus        75 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~-~~~~~~----~~~~~~~~~~vviDE~h~~~  139 (374)
                      -+|+.+.+..+.....   .......+||+++|+..+.. +++..+    .......+.+.||||++.+.
T Consensus       152 ~LGLtvg~i~~~~~~~---err~aY~~DItYgTn~e~gFDYLRDnm~~~~~~~vqR~~~faIVDEvDSIL  218 (939)
T PRK12902        152 FLGLSVGLIQQDMSPE---ERKKNYACDITYATNSELGFDYLRDNMATDISEVVQRPFNYCVIDEVDSIL  218 (939)
T ss_pred             HhCCeEEEECCCCChH---HHHHhcCCCeEEecCCcccccchhhhhcccccccccCccceEEEeccccee
Confidence            3588888775543332   23344668999999987722 222211    12234668899999999974

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

Probab=99.75  E-value=2.4e-16  Score=152.12  Aligned_cols=169  Identities=20%  Similarity=0.248  Sum_probs=106.9

Q ss_pred             CeeEEEeecCcccHHH-HHHhcCCCCCe--EEEecc-CCCc-eeEEE--EeecCCc-chHHHH---HHHHHHhhcCCCcE
Q 037567          163 PFVALTATATEKVRID-IINSLKLKNPY--VTIASF-DRKN-LFYGV--KVINRGQ-SFVDEL---VQEILKSVAGAGSI  231 (374)
Q Consensus       163 ~~i~~SaT~~~~~~~~-~~~~~~~~~~~--~~~~~~-~~~~-~~~~~--~~~~~~~-~~~~~~---~~~~~~~~~~~~~~  231 (374)
                      .+|++|||+.+..... +....+.....  ....+. +... ....+  ....... ....++   +.++...  .++++
T Consensus       405 ~~vl~SaTL~~~~~f~~~~~~~~~~~~~~~~~~~spf~~~~~~~~~v~~~~~~~~~~~~~~~~~~~i~~~~~~--~~~~~  482 (654)
T COG1199         405 SVVLTSATLSPLDSFSSLLGLLGLEEKLRFLSLPSPFNYEEQGQLYVPTDLPEPREPELLAKLAAYLREILKA--SPGGV  482 (654)
T ss_pred             cEEEeeeeccCCCcHHHHHHHcCCccccceeccCCCCChhhcceEeccccCCCCCChHHHHHHHHHHHHHHhh--cCCCE
Confidence            3899999998865443 55555554444  122221 1111 11111  1111111 233333   3333333  45699


Q ss_pred             EEEecchhHHHHHHHHHHHcCCc-eeeeecCCChHHHHHHHHhhhcCCe-eEEEEeccccccccccC--ccEEEEECCCC
Q 037567          232 IVYCMTIKDVEEISKALKQLGVK-AGTYHGQMGSKAREEAHRLFIRDEI-RVMVATMAFGMGIDKPD--VRHVIHYGCPK  307 (374)
Q Consensus       232 lVf~~~~~~~~~l~~~l~~~~~~-~~~~~~~~~~~~r~~~~~~f~~g~~-~ilv~t~~~~~G~d~~~--~~~vi~~~~p~  307 (374)
                      +||++|...++.+.+.+...... ....+|.   ..+..+++.|..+.- .++|++..+++|+|+|+  +..||..+.|.
T Consensus       483 lvlF~Sy~~l~~~~~~~~~~~~~~~v~~q~~---~~~~~~l~~f~~~~~~~~lv~~gsf~EGVD~~g~~l~~vvI~~lPf  559 (654)
T COG1199         483 LVLFPSYEYLKRVAERLKDERSTLPVLTQGE---DEREELLEKFKASGEGLILVGGGSFWEGVDFPGDALRLVVIVGLPF  559 (654)
T ss_pred             EEEeccHHHHHHHHHHHhhcCccceeeecCC---CcHHHHHHHHHHhcCCeEEEeeccccCcccCCCCCeeEEEEEecCC
Confidence            99999999999999999876542 3344444   344478888887654 89999999999999998  56788777764


Q ss_pred             ------------------------------ChhHHHHhhccCCCCCCceEEEEEeeccC
Q 037567          308 ------------------------------TLESYYQESGRCGRDGIASVCWLYYARSN  336 (374)
Q Consensus       308 ------------------------------s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~  336 (374)
                                                    .+..+.|.+||+-|...+.-++++++..-
T Consensus       560 p~p~dp~~~~r~~~~~~~g~~~f~~~~l~~A~~~l~QavGRlIR~~~D~G~ivllD~R~  618 (654)
T COG1199         560 PNPDDPLLKARLEFLKRLGGDPFEEFYLPPAVIKLRQAVGRLIRSEDDRGVIVLLDKRY  618 (654)
T ss_pred             CCCCCHHHHHHHHHHHHhcCCCceEeehHHHHHHHHHhhccccccCCCceEEEEecccc
Confidence                                          45677999999999766555555555543

>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional

Probab=99.75  E-value=1.6e-15  Score=145.27  Aligned_cols=169  Identities=16%  Similarity=0.098  Sum_probs=105.7

Q ss_pred             eeEEEeecCcc-cHHHHHHhcCCCC---Ce-EEEec-cCCCc-eeEEEEe---ec-CCcchHHHHHHHHHHhhcCCCcEE
Q 037567          164 FVALTATATEK-VRIDIINSLKLKN---PY-VTIAS-FDRKN-LFYGVKV---IN-RGQSFVDELVQEILKSVAGAGSII  232 (374)
Q Consensus       164 ~i~~SaT~~~~-~~~~~~~~~~~~~---~~-~~~~~-~~~~~-~~~~~~~---~~-~~~~~~~~~~~~~~~~~~~~~~~l  232 (374)
                      +|++|||+... ....+...+|+.+   .. ...++ ++..+ ....+..   .. ....+...+...+.+.....+.++
T Consensus       459 vIltSATL~~~~~f~~~~~~lGL~~~~~~~~~~~~SpF~~~~q~~l~vp~~~~~p~~~~~~~~~~~~~i~~l~~~~gg~L  538 (697)
T PRK11747        459 AVLTSATLRSLNSFDRFQEQSGLPEKDGDRFLALPSPFDYPNQGKLVIPKMRAEPDNEEAHTAEMAEFLPELLEKHKGSL  538 (697)
T ss_pred             EEEEeeeCCCCCchHHHHHHcCCCCCCCceEEEcCCCCCHHHccEEEeCCCCCCCCCcHHHHHHHHHHHHHHHhcCCCEE
Confidence            68999998874 3334667778763   22 11111 21111 1111111   11 222334444444444444556689


Q ss_pred             EEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhh----cCCeeEEEEeccccccccccC--ccEEEEECCC
Q 037567          233 VYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFI----RDEIRVMVATMAFGMGIDKPD--VRHVIHYGCP  306 (374)
Q Consensus       233 Vf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~----~g~~~ilv~t~~~~~G~d~~~--~~~vi~~~~p  306 (374)
                      |+++|....+.+++.|..........+|.   ..+..+++.|+    .++-.||++|...++|+|+|+  ++.||..+.|
T Consensus       539 VlFtSy~~l~~v~~~l~~~~~~~ll~Q~~---~~~~~ll~~f~~~~~~~~~~VL~g~~sf~EGVD~pGd~l~~vII~kLP  615 (697)
T PRK11747        539 VLFASRRQMQKVADLLPRDLRLMLLVQGD---QPRQRLLEKHKKRVDEGEGSVLFGLQSFAEGLDLPGDYLTQVIITKIP  615 (697)
T ss_pred             EEeCcHHHHHHHHHHHHHhcCCcEEEeCC---chHHHHHHHHHHHhccCCCeEEEEeccccccccCCCCceEEEEEEcCC
Confidence            99999999999999987532223445553   35667776666    466789999999999999998  6889888877


Q ss_pred             C------------------------------ChhHHHHhhccCCCCCCceEEEEEeecc
Q 037567          307 K------------------------------TLESYYQESGRCGRDGIASVCWLYYARS  335 (374)
Q Consensus       307 ~------------------------------s~~~~~Q~~GR~~R~~~~g~~~~~~~~~  335 (374)
                      .                              ....+.|.+||.-|...+.-+++++++.
T Consensus       616 F~~p~dp~~~ar~~~~~~~g~~~F~~~~lP~A~~kl~Qg~GRlIRs~~D~G~i~ilD~R  674 (697)
T PRK11747        616 FAVPDSPVEATLAEWLKSRGGNPFMEISVPDASFKLIQAVGRLIRSEQDRGRVTILDRR  674 (697)
T ss_pred             CCCCCCHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhccccccCCceEEEEEEccc
Confidence            4                              1234578999999986655456665554

>TIGR00604 rad3 DNA repair helicase (rad3)

Probab=99.75  E-value=1.1e-15  Score=147.72  Aligned_cols=108  Identities=20%  Similarity=0.215  Sum_probs=80.3

Q ss_pred             CCCcEEEEecchhHHHHHHHHHHHcCC-------ceeeeecCCChHHHHHHHHhhhc----CCeeEEEEe--cccccccc
Q 037567          227 GAGSIIVYCMTIKDVEEISKALKQLGV-------KAGTYHGQMGSKAREEAHRLFIR----DEIRVMVAT--MAFGMGID  293 (374)
Q Consensus       227 ~~~~~lVf~~~~~~~~~l~~~l~~~~~-------~~~~~~~~~~~~~r~~~~~~f~~----g~~~ilv~t--~~~~~G~d  293 (374)
                      ..+.++||++|....+.+.+.+.+.+.       ...++- .....++..+++.|..    |+-.||+++  ..+++|+|
T Consensus       521 ~pgg~lvfFpSy~~l~~v~~~~~~~~~~~~i~~~k~i~~E-~~~~~~~~~~l~~f~~~~~~~~gavL~av~gGk~sEGID  599 (705)
T TIGR00604       521 IPDGIVVFFPSYSYLENIVSTWKEMGILENIEKKKLIFVE-TKDAQETSDALERYKQAVSEGRGAVLLSVAGGKVSEGID  599 (705)
T ss_pred             CCCcEEEEccCHHHHHHHHHHHHhcCHHHHHhcCCCEEEe-CCCcchHHHHHHHHHHHHhcCCceEEEEecCCcccCccc
Confidence            358899999999999999998876432       122222 2223578889999964    455699998  79999999


Q ss_pred             ccC--ccEEEEECCCC-C------------------------------hhHHHHhhccCCCCCCceEEEEEeecc
Q 037567          294 KPD--VRHVIHYGCPK-T------------------------------LESYYQESGRCGRDGIASVCWLYYARS  335 (374)
Q Consensus       294 ~~~--~~~vi~~~~p~-s------------------------------~~~~~Q~~GR~~R~~~~g~~~~~~~~~  335 (374)
                      +++  ++.||..+.|. +                              .....|.+||+-|..++-.++++++..
T Consensus       600 f~~~~~r~ViivGlPf~~~~~~~~~~~~~~~~~~~~~~~~~~~y~~~a~~~v~QaiGR~IR~~~D~G~iillD~R  674 (705)
T TIGR00604       600 FCDDLGRAVIMVGIPYEYTESRILLARLEFLRDQYPIRENQDFYEFDAMRAVNQAIGRVIRHKDDYGSIVLLDKR  674 (705)
T ss_pred             cCCCCCcEEEEEccCCCCCCCHHHHHHHHHHHhhcCCCccHHHHHHHHHHHHHHHhCccccCcCceEEEEEEehh
Confidence            998  68899899885 1                              133479999999987766666666664

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).

>KOG0951 consensus RNA helicase BRR2, DEAD-box superfamily [RNA processing and modification]

Probab=99.73  E-value=5.3e-17  Score=154.30  Aligned_cols=318  Identities=19%  Similarity=0.217  Sum_probs=215.7

Q ss_pred             CchhHHHHHHHHHcC-CCEEEEccCCCCchhhhhcccccc--CCcEEEEcchHHHHHHHHHHHHH-c----CCceEEcCC
Q 037567           14 FRPYQKDVIQRIIEK-RDCLVVMATGSGKSLCYQLPPLVT--GKTALVVSPLISLMQDQVMSLKQ-R----GINAEFLGS   85 (374)
Q Consensus        14 ~~~~Q~~~~~~~~~~-~~~l~~a~tGsGKT~~~~l~~~~~--~~~~lil~P~~~l~~q~~~~~~~-~----~~~~~~~~~   85 (374)
                      ..|+|.+.++.+++. .++++.+|+|||||.++.++++.+  ..++++++|..+.+...++.+.+ +    |..+...++
T Consensus      1144 ~n~iqtqVf~~~y~~nd~v~vga~~gsgkt~~ae~a~l~~~~~~~~vyi~p~~~i~~~~~~~w~~~f~~~~G~~~~~l~g 1223 (1674)
T KOG0951|consen 1144 FNPIQTQVFTSLYNTNDNVLVGAPNGSGKTACAELALLRPDTIGRAVYIAPLEEIADEQYRDWEKKFSKLLGLRIVKLTG 1223 (1674)
T ss_pred             cCCceEEEEeeeecccceEEEecCCCCchhHHHHHHhcCCccceEEEEecchHHHHHHHHHHHHHhhccccCceEEecCC
Confidence            478899999988874 578899999999999998888874  56899999999998877766654 2    333344433


Q ss_pred             CCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhc-ccCcchHHH--HHHHHHHHhcCCC
Q 037567           86 AQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISE-WGHDFRLEY--KQLDKLRTFLLGV  162 (374)
Q Consensus        86 ~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~-~~~~~~~~~--~~~~~~~~~~~~~  162 (374)
                      ...-    .......-+++|+||+++..+ +      ..+.+++.|.||.|.+.. .|.-....+  +.+.....  .+.
T Consensus      1224 e~s~----~lkl~~~~~vii~tpe~~d~l-q------~iQ~v~l~i~d~lh~igg~~g~v~evi~S~r~ia~q~~--k~i 1290 (1674)
T KOG0951|consen 1224 ETSL----DLKLLQKGQVIISTPEQWDLL-Q------SIQQVDLFIVDELHLIGGVYGAVYEVICSMRYIASQLE--KKI 1290 (1674)
T ss_pred             cccc----chHHhhhcceEEechhHHHHH-h------hhhhcceEeeehhhhhcccCCceEEEEeeHHHHHHHHH--hhe
Confidence            2222    222233458999999988554 1      557889999999999864 333222222  33333322  367


Q ss_pred             CeeEEEeecCcccHHHHHHhcCCCCCeEEEeccCCCce--eEEEEeecC------CcchHHHHHHHHHHhhcCCCcEEEE
Q 037567          163 PFVALTATATEKVRIDIINSLKLKNPYVTIASFDRKNL--FYGVKVINR------GQSFVDELVQEILKSVAGAGSIIVY  234 (374)
Q Consensus       163 ~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~lVf  234 (374)
                      +++++|....+...  +   ++.....+.-..++....  ..+++....      ...+.......+.+...++++.+||
T Consensus      1291 r~v~ls~~lana~d--~---ig~s~~~v~Nf~p~~R~~Pl~i~i~~~~~~~~~~~~~am~~~~~~ai~~~a~~~k~~~vf 1365 (1674)
T KOG0951|consen 1291 RVVALSSSLANARD--L---IGASSSGVFNFSPSVRPVPLEIHIQSVDISHFESRMLAMTKPTYTAIVRHAGNRKPAIVF 1365 (1674)
T ss_pred             eEEEeehhhccchh--h---ccccccceeecCcccCCCceeEEEEEeccchhHHHHHHhhhhHHHHHHHHhcCCCCeEEE
Confidence            89999987766543  2   454444444333332222  222222221      1123344555666666788999999


Q ss_pred             ecchhHHHHHHHHHHHc----------------------CCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccc
Q 037567          235 CMTIKDVEEISKALKQL----------------------GVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGI  292 (374)
Q Consensus       235 ~~~~~~~~~l~~~l~~~----------------------~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~  292 (374)
                      +++++.+..++..+-..                      ..+.+.-|.+++..+.+.+-..|..|.+.|+|...- ..|+
T Consensus      1366 ~p~rk~~~~~a~~~~~~s~~~~~~~l~~~~e~~~~~l~e~l~~gvg~e~~s~~d~~iv~~l~e~g~i~v~v~s~~-~~~~ 1444 (1674)
T KOG0951|consen 1366 LPTRKHARLVAVDLVTFSHADEPDYLLSELEECDETLRESLKHGVGHEGLSSNDQEIVQQLFEAGAIQVCVMSRD-CYGT 1444 (1674)
T ss_pred             eccchhhhhhhhccchhhccCcHHHHHHHHhcchHhhhhcccccccccccCcchHHHHHHHHhcCcEEEEEEEcc-cccc
Confidence            99999988877544221                      222233388999999999999999999999998777 7777


Q ss_pred             cccCccEEEEEC-----------CCCChhHHHHhhccCCCCCCceEEEEEeeccCCCcccceeccccchHHHH
Q 037567          293 DKPDVRHVIHYG-----------CPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFYCGESQTENQRT  354 (374)
Q Consensus       293 d~~~~~~vi~~~-----------~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~  354 (374)
                      -.. .+.|+..+           .+.+..+..|+.|+|.|   .|.|+++........+++|..+..+-+...
T Consensus      1445 ~~~-~~lVvvmgt~~ydg~e~~~~~y~i~~ll~m~G~a~~---~~k~vi~~~~~~k~yykkfl~e~lPves~l 1513 (1674)
T KOG0951|consen 1445 KLK-AHLVVVMGTQYYDGKEHSYEDYPIAELLQMVGLASG---AGKCVIMCHTPKKEYYKKFLYEPLPVESHL 1513 (1674)
T ss_pred             ccc-ceEEEEecceeecccccccccCchhHHHHHhhhhcC---CccEEEEecCchHHHHHHhccCcCchHHHH
Confidence            654 33444222           23468999999999988   578999999999999999988877766553

>KOG0391 consensus SNF2 family DNA-dependent ATPase [General function prediction only]

Probab=99.72  E-value=3.4e-16  Score=147.58  Aligned_cols=133  Identities=17%  Similarity=0.191  Sum_probs=107.4

Q ss_pred             chHHHHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCC-e-eEEEEecccc
Q 037567          212 SFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDE-I-RVMVATMAFG  289 (374)
Q Consensus       212 ~~~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~-~-~ilv~t~~~~  289 (374)
                      ..+..+.-.+.+....+.++|||+.-....+.|...|.-+|+..+.+.|..+-++|+.++++|+... + -.|++|...+
T Consensus      1260 GKLQtLAiLLqQLk~eghRvLIfTQMtkmLDVLeqFLnyHgylY~RLDg~t~vEqRQaLmerFNaD~RIfcfILSTrSgg 1339 (1958)
T KOG0391|consen 1260 GKLQTLAILLQQLKSEGHRVLIFTQMTKMLDVLEQFLNYHGYLYVRLDGNTSVEQRQALMERFNADRRIFCFILSTRSGG 1339 (1958)
T ss_pred             chHHHHHHHHHHHHhcCceEEehhHHHHHHHHHHHHHhhcceEEEEecCCccHHHHHHHHHHhcCCCceEEEEEeccCCc
Confidence            3444443334444457889999999999999999999999999999999999999999999999875 3 3456899999


Q ss_pred             ccccccCccEEEEECCCCChhHHHHhhccCCCCCCceEEEEEeeccCCCccccee
Q 037567          290 MGIDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFYC  344 (374)
Q Consensus       290 ~G~d~~~~~~vi~~~~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~~~~~~~~~  344 (374)
                      .|+|+.+.+.||+||..|++.--.|.-.||.|.|+...+.+|---++...-.+++
T Consensus      1340 vGiNLtgADTVvFYDsDwNPtMDaQAQDrChRIGqtRDVHIYRLISe~TIEeniL 1394 (1958)
T KOG0391|consen 1340 VGINLTGADTVVFYDSDWNPTMDAQAQDRCHRIGQTRDVHIYRLISERTIEENIL 1394 (1958)
T ss_pred             cccccccCceEEEecCCCCchhhhHHHHHHHhhcCccceEEEEeeccchHHHHHH
Confidence            9999999999999999999988889999999999877666655444444333333

>KOG0386 consensus Chromatin remodeling complex SWI/SNF, component SWI2 and related ATPases (DNA/RNA helicase superfamily) [Chromatin structure and dynamics; Transcription]

Probab=99.72  E-value=2.2e-17  Score=153.92  Aligned_cols=311  Identities=17%  Similarity=0.155  Sum_probs=212.4

Q ss_pred             CCCchhHHHHHHHHHc----CCCEEEEccCCCCchhh------hhccccccCCcEEEEcchHHHHHHHHHHHHHcCCceE
Q 037567           12 SVFRPYQKDVIQRIIE----KRDCLVVMATGSGKSLC------YQLPPLVTGKTALVVSPLISLMQDQVMSLKQRGINAE   81 (374)
Q Consensus        12 ~~~~~~Q~~~~~~~~~----~~~~l~~a~tGsGKT~~------~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~   81 (374)
                      ..+.+||...++.+..    +-+.++...+|.|||+.      |++-.....++.||+||+..|.+ |..++..+...+.
T Consensus       393 G~Lk~YQl~GLqWmVSLyNNnLNGILADEMGLGKTIQtIsLitYLmE~K~~~GP~LvivPlstL~N-W~~Ef~kWaPSv~  471 (1157)
T KOG0386|consen  393 GELKEYQLHGLQWMVSLYNNNLNGILADEMGLGKTIQTISLITYLMEHKQMQGPFLIIVPLSTLVN-WSSEFPKWAPSVQ  471 (1157)
T ss_pred             CCCchhhhhhhHHHhhccCCCcccccchhcccchHHHHHHHHHHHHHHcccCCCeEEeccccccCC-chhhcccccccee
Confidence            4799999999988754    34779999999999943      22333335778999999987777 8999988877665


Q ss_pred             EcCCCCCch---hhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHH-
Q 037567           82 FLGSAQTDS---SVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRT-  157 (374)
Q Consensus        82 ~~~~~~~~~---~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~-  157 (374)
                      ......+..   ........+.++|+++|++.+..    ....+..-.|.++||||-|++.+..       ..+...+. 
T Consensus       472 ~i~YkGtp~~R~~l~~qir~gKFnVLlTtyEyiik----dk~lLsKI~W~yMIIDEGHRmKNa~-------~KLt~~L~t  540 (1157)
T KOG0386|consen  472 KIQYKGTPQQRSGLTKQQRHGKFNVLLTTYEYIIK----DKALLSKISWKYMIIDEGHRMKNAI-------CKLTDTLNT  540 (1157)
T ss_pred             eeeeeCCHHHHhhHHHHHhcccceeeeeeHHHhcC----CHHHHhccCCcceeecccccccchh-------hHHHHHhhc
Confidence            443333222   22334455889999999998765    1133444578899999999998744       22332222 


Q ss_pred             hcCCCCeeEEEeecCcccHHHHHHhcCCCCCeEEEeccC-----------------------------------------
Q 037567          158 FLLGVPFVALTATATEKVRIDIINSLKLKNPYVTIASFD-----------------------------------------  196 (374)
Q Consensus       158 ~~~~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~~-----------------------------------------  196 (374)
                      .....+.+++|+||..+..++++..+...-+.+......                                         
T Consensus       541 ~y~~q~RLLLTGTPLQN~LpELWaLLNFlLP~IFnS~~~FeqWFN~PFantGek~eLteEEtlLIIrRLHkVLRPFlLRR  620 (1157)
T KOG0386|consen  541 HYRAQRRLLLTGTPLQNNLPELWALLNFLLPNIFNSCKAFEQWFNQPFANTGEKVELTEEETLLIIRRLHKVLRPFLLRR  620 (1157)
T ss_pred             cccchhhhhhcCChhhhccHHHHHHHHHhccchhhhHhHHHHHhhhhhhhcCCcccccchHHHHHHHHHHHhhhHHHHHh
Confidence            444667899999988776554444332111111100000                                         


Q ss_pred             ----------------------------------------------------------------CCcee----EEEEeec
Q 037567          197 ----------------------------------------------------------------RKNLF----YGVKVIN  208 (374)
Q Consensus       197 ----------------------------------------------------------------~~~~~----~~~~~~~  208 (374)
                                                                                      .+...    ..+....
T Consensus       621 lKkeVE~~LPdKve~viKC~mSalQq~lY~~m~~~g~l~~d~~~g~~g~k~L~N~imqLRKiCNHP~lf~~ve~~~~~~~  700 (1157)
T KOG0386|consen  621 LKKEVEQELPDKVEDVIKCDMSALQQSLYKQMQNKGQLLKDTAKGKKGYKPLFNTIMQLRKLCNHPYLFANVENSYTLHY  700 (1157)
T ss_pred             hhHHHhhhCchhhhHhhheehhhhhHhhhHHHHhCCCCCcCchhccccchhhhhHhHHHHHhcCCchhhhhhcccccccc
Confidence                                                                            00000    0000000


Q ss_pred             CC-----cchHHHHHHHHHHhh-cCCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCe---
Q 037567          209 RG-----QSFVDELVQEILKSV-AGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEI---  279 (374)
Q Consensus       209 ~~-----~~~~~~~~~~~~~~~-~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~---  279 (374)
                      ..     ..-..+++..++.++ ..+.+++.|+........+...|.-.++....+.|.+..++|...+..|+....   
T Consensus       701 ~~~dL~R~sGKfELLDRiLPKLkatgHRVLlF~qMTrlmdimEdyL~~~~~kYlRLDG~TK~~eRg~ll~~FN~Pds~yf  780 (1157)
T KOG0386|consen  701 DIKDLVRVSGKFELLDRILPKLKATGHRVLLFSQMTRLMDILEDYLQIREYKYLRLDGQTKVEERGDLLEIFNAPDSPYF  780 (1157)
T ss_pred             ChhHHHHhccHHHHHHhhhHHHHhcCcchhhHHHHHHHHHHHHHHHhhhhhheeeecCCcchhhHHHHHHHhcCCCCcee
Confidence            00     011123344443333 246789999999888888999998888889999999999999999999998643   


Q ss_pred             eEEEEeccccccccccCccEEEEECCCCChhHHHHhhccCCCCCCceEEEEEeec
Q 037567          280 RVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYAR  334 (374)
Q Consensus       280 ~ilv~t~~~~~G~d~~~~~~vi~~~~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~  334 (374)
                      ..|.+|.+.+.|+|+..++.||.++..|++....|+-.||.|.|+..-+-++...
T Consensus       781 ~FllstragglglNlQtadtviifdsdwnp~~d~qaqdrahrigq~~evRv~rl~  835 (1157)
T KOG0386|consen  781 IFLLSTRAGGLGLNLQTADTVIIFDSDWNPHQDLQAQDRAHRIGQKKEVRVLRLI  835 (1157)
T ss_pred             eeeeeecccccccchhhcceEEEecCCCCchhHHHHHHHHHHhhchhheeeeeee
Confidence            3567999999999999999999999999999999999999999987766555443

>KOG4439 consensus RNA polymerase II transcription termination factor TTF2/lodestar, DEAD-box superfamily [Transcription; Replication, recombination and repair]

Probab=99.71  E-value=4.9e-16  Score=139.95  Aligned_cols=119  Identities=17%  Similarity=0.190  Sum_probs=97.6

Q ss_pred             cCCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhc--CCeeE-EEEeccccccccccCccEEEE
Q 037567          226 AGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIR--DEIRV-MVATMAFGMGIDKPDVRHVIH  302 (374)
Q Consensus       226 ~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~--g~~~i-lv~t~~~~~G~d~~~~~~vi~  302 (374)
                      ..+.+++|...=.+...-+...+++.|.....+||....++|+.+++.|+.  |..+| |++-.+.+.|+|+-+.+|+|.
T Consensus       744 ~skeK~viVSQwtsvLniv~~hi~~~g~~y~si~Gqv~vK~Rq~iv~~FN~~k~~~rVmLlSLtAGGVGLNL~GaNHlil  823 (901)
T KOG4439|consen  744 SSKEKVVIVSQWTSVLNIVRKHIQKGGHIYTSITGQVLVKDRQEIVDEFNQEKGGARVMLLSLTAGGVGLNLIGANHLIL  823 (901)
T ss_pred             cccceeeehhHHHHHHHHHHHHHhhCCeeeeeecCccchhHHHHHHHHHHhccCCceEEEEEEccCcceeeecccceEEE
Confidence            356677776666666778888899999999999999999999999999996  33444 456668899999999999999


Q ss_pred             ECCCCChhHHHHhhccCCCCCCceEEEEEeeccCCCcccceeccccchHHH
Q 037567          303 YGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFYCGESQTENQR  353 (374)
Q Consensus       303 ~~~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~  353 (374)
                      +++-|++.--.|.+.|..|.||...+++.         +.++.+..+....
T Consensus       824 vDlHWNPaLEqQAcDRIYR~GQkK~V~Ih---------R~~~~gTvEqrV~  865 (901)
T KOG4439|consen  824 VDLHWNPALEQQACDRIYRMGQKKDVFIH---------RLMCKGTVEQRVK  865 (901)
T ss_pred             EecccCHHHHHHHHHHHHHhcccCceEEE---------EEEecCcHHHHHH
Confidence            99999999999999999999998877765         5666666555443

>PRK14873 primosome assembly protein PriA; Provisional

Probab=99.70  E-value=1.2e-15  Score=143.77  Aligned_cols=295  Identities=11%  Similarity=-0.006  Sum_probs=180.7

Q ss_pred             EEEccCCCCchhhhhccc---cccCCcEEEEcchHHHHHHHHHHHHH-cC-CceEEcCCCCCchh---hhhhhhcCCeeE
Q 037567           32 LVVMATGSGKSLCYQLPP---LVTGKTALVVSPLISLMQDQVMSLKQ-RG-INAEFLGSAQTDSS---VQTKAETGYFQL  103 (374)
Q Consensus        32 l~~a~tGsGKT~~~~l~~---~~~~~~~lil~P~~~l~~q~~~~~~~-~~-~~~~~~~~~~~~~~---~~~~~~~~~~~i  103 (374)
                      +..+.+|||||-.|+-.+   +..++.+|+++|...|..|+.+.++. +| ..+.++++..+..+   .+.....+...|
T Consensus       164 i~~~~~GSGKTevyl~~i~~~l~~Gk~vLvLvPEi~lt~q~~~rl~~~f~~~~v~~lhS~l~~~~R~~~w~~~~~G~~~I  243 (665)
T PRK14873        164 VWQALPGEDWARRLAAAAAATLRAGRGALVVVPDQRDVDRLEAALRALLGAGDVAVLSAGLGPADRYRRWLAVLRGQARV  243 (665)
T ss_pred             HhhcCCCCcHHHHHHHHHHHHHHcCCeEEEEecchhhHHHHHHHHHHHcCCCcEEEECCCCCHHHHHHHHHHHhCCCCcE
Confidence            444446999998887554   45788999999999999999999985 45 56777877666554   344555777899


Q ss_pred             EEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcc-cCcchHHHHHHHHHHHhcCCCCeeEEEeecCcccHHHHHHh
Q 037567          104 LFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEW-GHDFRLEYKQLDKLRTFLLGVPFVALTATATEKVRIDIINS  182 (374)
Q Consensus       104 ~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~-~~~~~~~~~~~~~~~~~~~~~~~i~~SaT~~~~~~~~~~~~  182 (374)
                      +|+|-..+         ...+.++.+||+||=|.-.-. ....+...+.+...+....+.++|+.||||+-+....... 
T Consensus       244 ViGtRSAv---------FaP~~~LgLIIvdEEhd~sykq~~~p~yhaRdvA~~Ra~~~~~~lvLgSaTPSles~~~~~~-  313 (665)
T PRK14873        244 VVGTRSAV---------FAPVEDLGLVAIWDDGDDLLAEPRAPYPHAREVALLRAHQHGCALLIGGHARTAEAQALVES-  313 (665)
T ss_pred             EEEcceeE---------EeccCCCCEEEEEcCCchhhcCCCCCCccHHHHHHHHHHHcCCcEEEECCCCCHHHHHHHhc-
Confidence            99996543         234578899999999975332 2122223355666667777999999999999876532221 


Q ss_pred             cCCCCCeEEE---eccCCCceeEEEEe---e-----cCCcchHHHHHHHHHHhhcCCCcEEEEecchh------------
Q 037567          183 LKLKNPYVTI---ASFDRKNLFYGVKV---I-----NRGQSFVDELVQEILKSVAGAGSIIVYCMTIK------------  239 (374)
Q Consensus       183 ~~~~~~~~~~---~~~~~~~~~~~~~~---~-----~~~~~~~~~~~~~~~~~~~~~~~~lVf~~~~~------------  239 (374)
                       +........   .....+.+......   .     .........++..+.+.+..+ ++|||.|.+.            
T Consensus       314 -g~~~~~~~~~~~~~~~~P~v~~vd~~~~~~~~~~~~~g~~ls~~l~~~i~~~L~~g-qvll~lnRrGyap~l~C~~Cg~  391 (665)
T PRK14873        314 -GWAHDLVAPRPVVRARAPRVRALGDSGLALERDPAARAARLPSLAFRAARDALEHG-PVLVQVPRRGYVPSLACARCRT  391 (665)
T ss_pred             -CcceeeccccccccCCCCeEEEEeCchhhhccccccccCccCHHHHHHHHHHHhcC-cEEEEecCCCCCCeeEhhhCcC
Confidence             110000000   00111111111100   0     000113356677777777777 9999999876            


Q ss_pred             -----------------------------------------------HHHHHHHHHHHc--CCceeeeecCCChHHHHHH
Q 037567          240 -----------------------------------------------DVEEISKALKQL--GVKAGTYHGQMGSKAREEA  270 (374)
Q Consensus       240 -----------------------------------------------~~~~l~~~l~~~--~~~~~~~~~~~~~~~r~~~  270 (374)
                                                                     -.+++.+.|++.  +.++..+.       +..+
T Consensus       392 ~~~C~~C~~~L~~h~~~~~l~Ch~CG~~~~p~~Cp~Cgs~~l~~~g~Gter~eeeL~~~FP~~~V~r~d-------~d~~  464 (665)
T PRK14873        392 PARCRHCTGPLGLPSAGGTPRCRWCGRAAPDWRCPRCGSDRLRAVVVGARRTAEELGRAFPGVPVVTSG-------GDQV  464 (665)
T ss_pred             eeECCCCCCceeEecCCCeeECCCCcCCCcCccCCCCcCCcceeeeccHHHHHHHHHHHCCCCCEEEEC-------hHHH
Confidence                                                           233444444432  22222222       2346


Q ss_pred             HHhhhcCCeeEEEEec----cccccccccCccEEEEECCCC------------ChhHHHHhhccCCCCCCceEEEEEeec
Q 037567          271 HRLFIRDEIRVMVATM----AFGMGIDKPDVRHVIHYGCPK------------TLESYYQESGRCGRDGIASVCWLYYAR  334 (374)
Q Consensus       271 ~~~f~~g~~~ilv~t~----~~~~G~d~~~~~~vi~~~~p~------------s~~~~~Q~~GR~~R~~~~g~~~~~~~~  334 (374)
                      ++.|. ++.+|||+|+    ++.     ++++.|+..+...            ....+.|..||+||...+|.+++...+
T Consensus       465 l~~~~-~~~~IlVGTqgaepm~~-----g~~~lV~ildaD~~L~~pDfRA~Er~~qll~qvagragr~~~~G~V~iq~~p  538 (665)
T PRK14873        465 VDTVD-AGPALVVATPGAEPRVE-----GGYGAALLLDAWALLGRQDLRAAEDTLRRWMAAAALVRPRADGGQVVVVAES  538 (665)
T ss_pred             HHhhc-cCCCEEEECCCCccccc-----CCceEEEEEcchhhhcCCCcChHHHHHHHHHHHHHhhcCCCCCCEEEEEeCC
Confidence            77786 5899999999    555     3556665444321            345568999999999999999888644


Q ss_pred             cCCCcccceeccccchHH
Q 037567          335 SNFAKGDFYCGESQTENQ  352 (374)
Q Consensus       335 ~~~~~~~~~~~~~~~~~~  352 (374)
                      +. ..++.+..++...+-
T Consensus       539 ~~-~~~~~l~~~d~~~F~  555 (665)
T PRK14873        539 SL-PTVQALIRWDPVGHA  555 (665)
T ss_pred             CC-HHHHHHHhCCHHHHH
Confidence            43 344555444444333

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

Probab=99.67  E-value=9.4e-15  Score=136.05  Aligned_cols=291  Identities=15%  Similarity=0.125  Sum_probs=182.8

Q ss_pred             CEEEEccCCCCchhhhhcccc----ccCCcEEEEcchHHHHHHHHHHHHHcCCceEEcCCCCCchhhhhhhhcCCeeEEE
Q 037567           30 DCLVVMATGSGKSLCYQLPPL----VTGKTALVVSPLISLMQDQVMSLKQRGINAEFLGSAQTDSSVQTKAETGYFQLLF  105 (374)
Q Consensus        30 ~~l~~a~tGsGKT~~~~l~~~----~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~i  105 (374)
                      -.++.+|+|||||......+.    .+..++|+++.+++|+.+....++..+..-.....+.....    .....++-++
T Consensus        51 V~vVRSpMGTGKTtaLi~wLk~~l~~~~~~VLvVShRrSL~~sL~~rf~~~~l~gFv~Y~d~~~~~----i~~~~~~rLi  126 (824)
T PF02399_consen   51 VLVVRSPMGTGKTTALIRWLKDALKNPDKSVLVVSHRRSLTKSLAERFKKAGLSGFVNYLDSDDYI----IDGRPYDRLI  126 (824)
T ss_pred             eEEEECCCCCCcHHHHHHHHHHhccCCCCeEEEEEhHHHHHHHHHHHHhhcCCCcceeeecccccc----ccccccCeEE
Confidence            348899999999976443322    35789999999999999999999987664332222222211    1112457888


Q ss_pred             EcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHH----HHHHHHHhcC-CCCeeEEEeecCcccHHHHH
Q 037567          106 MTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYK----QLDKLRTFLL-GVPFVALTATATEKVRIDII  180 (374)
Q Consensus       106 ~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~----~~~~~~~~~~-~~~~i~~SaT~~~~~~~~~~  180 (374)
                      ++.++|.++..     ....++++||+||+-.+..+ . +...+.    .++.+...+. ...+|++-|+....... ++
T Consensus       127 vqIdSL~R~~~-----~~l~~yDvVIIDEv~svL~q-L-~S~Tm~~~~~v~~~L~~lI~~ak~VI~~DA~ln~~tvd-Fl  198 (824)
T PF02399_consen  127 VQIDSLHRLDG-----SLLDRYDVVIIDEVMSVLNQ-L-FSPTMRQREEVDNLLKELIRNAKTVIVMDADLNDQTVD-FL  198 (824)
T ss_pred             EEehhhhhccc-----ccccccCEEEEehHHHHHHH-H-hHHHHhhHHHHHHHHHHHHHhCCeEEEecCCCCHHHHH-HH
Confidence            88888865522     23456899999999887653 1 111111    1222222222 46789999999987764 44


Q ss_pred             HhcCCCCCe-EEEeccCCCceeEEEEee-------------c----------------------CCcchHHHHHHHHHHh
Q 037567          181 NSLKLKNPY-VTIASFDRKNLFYGVKVI-------------N----------------------RGQSFVDELVQEILKS  224 (374)
Q Consensus       181 ~~~~~~~~~-~~~~~~~~~~~~~~~~~~-------------~----------------------~~~~~~~~~~~~~~~~  224 (374)
                      ..+.-.... ++...............+             .                      ............+...
T Consensus       199 ~~~Rp~~~i~vI~n~y~~~~fs~R~~~~~~~l~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~tF~~~L~~~  278 (824)
T PF02399_consen  199 ASCRPDENIHVIVNTYASPGFSNRRCTFLRSLGTDTLAAALNPEDENADTSPTPKHSPDPTATAAISNDETTFFSELLAR  278 (824)
T ss_pred             HHhCCCCcEEEEEeeeecCCcccceEEEecccCcHHHHHHhCCcccccccCCCcCCCCccccccccccchhhHHHHHHHH
Confidence            444333322 332222221111111000             0                      0001224566777777


Q ss_pred             hcCCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCc--cEEEE
Q 037567          225 VAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDV--RHVIH  302 (374)
Q Consensus       225 ~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~--~~vi~  302 (374)
                      +..++++.||+.+.+.++.+++..+.....+..++|..+..+-    +.|  ++.+|++.|+.+..|+++...  +.++-
T Consensus       279 L~~gknIcvfsSt~~~~~~v~~~~~~~~~~Vl~l~s~~~~~dv----~~W--~~~~VviYT~~itvG~Sf~~~HF~~~f~  352 (824)
T PF02399_consen  279 LNAGKNICVFSSTVSFAEIVARFCARFTKKVLVLNSTDKLEDV----ESW--KKYDVVIYTPVITVGLSFEEKHFDSMFA  352 (824)
T ss_pred             HhCCCcEEEEeChHHHHHHHHHHHHhcCCeEEEEcCCCCcccc----ccc--cceeEEEEeceEEEEeccchhhceEEEE
Confidence            8889999999999999999999999888888888876554422    222  568999999999999998653  33444


Q ss_pred             ECCC----CChhHHHHhhccCCCCCCceEEEEEeeccCCCc
Q 037567          303 YGCP----KTLESYYQESGRCGRDGIASVCWLYYARSNFAK  339 (374)
Q Consensus       303 ~~~p----~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~~~~  339 (374)
                      |-.|    .++....|++||+-....+ ..+++++....+.
T Consensus       353 yvk~~~~gpd~~s~~Q~lgRvR~l~~~-ei~v~~d~~~~~~  392 (824)
T PF02399_consen  353 YVKPMSYGPDMVSVYQMLGRVRSLLDN-EIYVYIDASGARS  392 (824)
T ss_pred             EecCCCCCCcHHHHHHHHHHHHhhccC-eEEEEEecccccC
Confidence            4223    3566789999999776544 4556666554433

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

>COG0610 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]

Probab=99.67  E-value=3.6e-15  Score=146.54  Aligned_cols=295  Identities=18%  Similarity=0.126  Sum_probs=164.6

Q ss_pred             CCEEEEccCCCCchhhhhcccc-----ccCCcEEEEcchHHHHHHHHHHHHHcCCceEEcCCCCCchhhhhhhhcCCeeE
Q 037567           29 RDCLVVMATGSGKSLCYQLPPL-----VTGKTALVVSPLISLMQDQVMSLKQRGINAEFLGSAQTDSSVQTKAETGYFQL  103 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~~l~~~-----~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i  103 (374)
                      +.++|+..+|||||+++...+.     ...+++++|+.+++|-.|..+.++.++..........+..+.........-.|
T Consensus       274 ~~G~IWHtqGSGKTlTm~~~A~~l~~~~~~~~v~fvvDR~dLd~Q~~~~f~~~~~~~~~~~~~~s~~~Lk~~l~~~~~~i  353 (962)
T COG0610         274 KGGYIWHTQGSGKTLTMFKLARLLLELPKNPKVLFVVDRKDLDDQTSDEFQSFGKVAFNDPKAESTSELKELLEDGKGKI  353 (962)
T ss_pred             CceEEEeecCCchHHHHHHHHHHHHhccCCCeEEEEechHHHHHHHHHHHHHHHHhhhhcccccCHHHHHHHHhcCCCcE
Confidence            4689999999999987653322     35789999999999999999999998665544332222222223333344589


Q ss_pred             EEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHHhcCCCCeeEEEeecCcccHHHH-HHh
Q 037567          104 LFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEKVRIDI-INS  182 (374)
Q Consensus       104 ~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~SaT~~~~~~~~~-~~~  182 (374)
                      +|||.+++...............--+||+||||+- +.|       ..-..+...+++...++||+||-....... ...
T Consensus       354 i~TTIQKf~~~~~~~~~~~~~~~~ivvI~DEaHRS-Q~G-------~~~~~~~~~~~~a~~~gFTGTPi~~~d~~tt~~~  425 (962)
T COG0610         354 IVTTIQKFNKAVKEDELELLKRKNVVVIIDEAHRS-QYG-------ELAKLLKKALKKAIFIGFTGTPIFKEDKDTTKDV  425 (962)
T ss_pred             EEEEecccchhhhcccccccCCCcEEEEEechhhc-ccc-------HHHHHHHHHhccceEEEeeCCccccccccchhhh
Confidence            99999999776544211111122237889999973 222       122333555667899999999987654431 111


Q ss_pred             cCCCCCeEEEecc--CCC--ceeEEEE----eecC------------------------------------CcchHH---
Q 037567          183 LKLKNPYVTIASF--DRK--NLFYGVK----VINR------------------------------------GQSFVD---  215 (374)
Q Consensus       183 ~~~~~~~~~~~~~--~~~--~~~~~~~----~~~~------------------------------------~~~~~~---  215 (374)
                      ++..-........  +..  .+.+...    ....                                    ......   
T Consensus       426 fg~ylh~Y~i~daI~Dg~vl~i~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~~~r~~~~a  505 (962)
T COG0610         426 FGDYLHTYTITDAIRDGAVLPVYYENRVELELIEESIKEEAEELDERIEEITEDILEKIKKKTKNLEFLAMLAVRLIRAA  505 (962)
T ss_pred             hcceeEEEecchhhccCceeeEEEeecccccccccchhhhhhhhHHHHhhhHHHHHHHHHHHHhhhhHHhcchHHHHHHH
Confidence            2211000000000  000  0000000    0000                                    000111   


Q ss_pred             -HHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHHcCC---------c-eeee-------------ecCCChHHHHHHH
Q 037567          216 -ELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGV---------K-AGTY-------------HGQMGSKAREEAH  271 (374)
Q Consensus       216 -~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~~~---------~-~~~~-------------~~~~~~~~r~~~~  271 (374)
                       ++..+..+......++++.++++..+..+.+.......         . +..+             |.. .........
T Consensus       506 ~~i~~~f~~~~~~~~kam~V~~sr~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~-~~~~~~~~~  584 (962)
T COG0610         506 KDIYDHFKKEEVFDLKAMVVASSRKVAVELYEAEIAARLDWHSKESLEGAIKDYNTEFETDFDKKQSHAK-LKDEKKDLI  584 (962)
T ss_pred             HHHHHHHHhhcccCceEEEEEechHHHHHhHHHHhhhhhhhhhhhhhhhHHHHHHhhcccchhhhhhhHH-HHHHHhhhh
Confidence             12222222123456788888887755555544333200         0 0000             111 112222333


Q ss_pred             Hhh--hcCCeeEEEEeccccccccccCccEEEEECCCCChhHHHHhhccCCCCCC----ceEEEEEee
Q 037567          272 RLF--IRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRDGI----ASVCWLYYA  333 (374)
Q Consensus       272 ~~f--~~g~~~ilv~t~~~~~G~d~~~~~~vi~~~~p~s~~~~~Q~~GR~~R~~~----~g~~~~~~~  333 (374)
                      ..|  ...+.++||.++|+-+|+|.|.+.++. ++-|.-.-..+|.+.|++|.-.    .|.++-|..
T Consensus       585 ~r~~~~~d~~kilIV~dmlLTGFDaP~L~TmY-vDK~Lk~H~L~QAisRtNR~~~~~K~~G~IVDf~g  651 (962)
T COG0610         585 KRFKLKDDPLDLLIVVDMLLTGFDAPCLNTLY-VDKPLKYHNLIQAISRTNRVFPGKKKFGLIVDFRG  651 (962)
T ss_pred             hhhcCcCCCCCEEEEEccccccCCccccceEE-eccccccchHHHHHHHhccCCCCCCCCcEEEECcc
Confidence            332  235689999999999999999887776 5666777889999999999632    355554444

>cd00046 DEXDc DEAD-like helicases superfamily

Probab=99.66  E-value=1.8e-16  Score=122.75  Aligned_cols=136  Identities=28%  Similarity=0.296  Sum_probs=91.0

Q ss_pred             CCEEEEccCCCCchhhhhccccc-----cCCcEEEEcchHHHHHHHHHHHHHcC---CceEEcCCCCCchhhhhhhhcCC
Q 037567           29 RDCLVVMATGSGKSLCYQLPPLV-----TGKTALVVSPLISLMQDQVMSLKQRG---INAEFLGSAQTDSSVQTKAETGY  100 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~~l~~~~-----~~~~~lil~P~~~l~~q~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~  100 (374)
                      +++++.+|||+|||..++..+..     ..+++++++|++.++.|+.+.+....   ............... .......
T Consensus         1 ~~~~i~~~~G~GKT~~~~~~~~~~~~~~~~~~~lv~~p~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~   79 (144)
T cd00046           1 RDVLLAAPTGSGKTLAALLPILELLDSLKGGQVLVLAPTRELANQVAERLKELFGEGIKVGYLIGGTSIKQQ-EKLLSGK   79 (144)
T ss_pred             CCEEEECCCCCchhHHHHHHHHHHHhcccCCCEEEEcCcHHHHHHHHHHHHHHhhCCcEEEEEecCcchhHH-HHHhcCC
Confidence            46799999999999776655443     45899999999999999999888765   444444443322222 2233456


Q ss_pred             eeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHHhcCCCCeeEEEeec
Q 037567          101 FQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATA  171 (374)
Q Consensus       101 ~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~SaT~  171 (374)
                      .+++++|++.+.......  ......++++|+||+|.+.......    ...........+.+++++||||
T Consensus        80 ~~i~i~t~~~~~~~~~~~--~~~~~~~~~iiiDE~h~~~~~~~~~----~~~~~~~~~~~~~~~i~~saTp  144 (144)
T cd00046          80 TDIVVGTPGRLLDELERL--KLSLKKLDLLILDEAHRLLNQGFGL----LGLKILLKLPKDRQVLLLSATP  144 (144)
T ss_pred             CCEEEECcHHHHHHHHcC--CcchhcCCEEEEeCHHHHhhcchHH----HHHHHHhhCCccceEEEEeccC
Confidence            799999999775432221  1223468899999999987633221    1012333344578899999997

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

>smart00490 HELICc helicase superfamily c-terminal domain

Probab=99.65  E-value=6.4e-16  Score=107.41  Aligned_cols=81  Identities=41%  Similarity=0.628  Sum_probs=76.8

Q ss_pred             HHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEEEEECCCCChhHHHHhhccCCCC
Q 037567          243 EISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRD  322 (374)
Q Consensus       243 ~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~~~~p~s~~~~~Q~~GR~~R~  322 (374)
                      .+++.|+..++.+..+||+++.++|..++..|.++...++++|+++++|+|+|.+++|+.+++|++...+.|++||++|.
T Consensus         2 ~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~Gi~~~~~~~vi~~~~~~~~~~~~Q~~gR~~R~   81 (82)
T smart00490        2 ELAELLKELGIKVARLHGGLSQEEREEILEKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGRAGRA   81 (82)
T ss_pred             HHHHHHHHCCCeEEEEECCCCHHHHHHHHHHHHcCCCeEEEECChhhCCcChhcCCEEEEeCCCCCHHHHHHhhcccccC
Confidence            46777888899999999999999999999999999999999999999999999999999999999999999999999997


Q ss_pred             C
Q 037567          323 G  323 (374)
Q Consensus       323 ~  323 (374)
                      |
T Consensus        82 g   82 (82)
T smart00490       82 G   82 (82)
T ss_pred             C
Confidence            5

>KOG0388 consensus SNF2 family DNA-dependent ATPase [Replication, recombination and repair]

Probab=99.62  E-value=2.4e-14  Score=129.42  Aligned_cols=114  Identities=21%  Similarity=0.242  Sum_probs=99.2

Q ss_pred             HHHHHHHHhh-cCCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCe-eEEEEecccccccc
Q 037567          216 ELVQEILKSV-AGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEI-RVMVATMAFGMGID  293 (374)
Q Consensus       216 ~~~~~~~~~~-~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~-~ilv~t~~~~~G~d  293 (374)
                      ..+.+++.++ ..+.++|+|+.-.+....+.+.|..+++....+.|.....+|..+..+|+..++ -.|++|.+.+-|||
T Consensus      1031 ~~LDeLL~kLkaegHRvL~yfQMTkM~dl~EdYl~yr~Y~ylRLDGSsk~~dRrd~vrDwQ~sdiFvFLLSTRAGGLGIN 1110 (1185)
T KOG0388|consen 1031 VVLDELLPKLKAEGHRVLMYFQMTKMIDLIEDYLVYRGYTYLRLDGSSKASDRRDVVRDWQASDIFVFLLSTRAGGLGIN 1110 (1185)
T ss_pred             eeHHHHHHHhhcCCceEEehhHHHHHHHHHHHHHHhhccceEEecCcchhhHHHHHHhhccCCceEEEEEecccCccccc
Confidence            3445554444 356789999999999999999999999999999999999999999999999764 45679999999999


Q ss_pred             ccCccEEEEECCCCChhHHHHhhccCCCCCCceEEE
Q 037567          294 KPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCW  329 (374)
Q Consensus       294 ~~~~~~vi~~~~p~s~~~~~Q~~GR~~R~~~~g~~~  329 (374)
                      +...+.||+|+..|++.--.|.+.||.|.|+..-+.
T Consensus      1111 LTAADTViFYdSDWNPT~D~QAMDRAHRLGQTrdvt 1146 (1185)
T KOG0388|consen 1111 LTAADTVIFYDSDWNPTADQQAMDRAHRLGQTRDVT 1146 (1185)
T ss_pred             ccccceEEEecCCCCcchhhHHHHHHHhccCcccee
Confidence            999999999999999999999999999999866443

>PRK12901 secA preprotein translocase subunit SecA; Reviewed

Probab=99.62  E-value=1.7e-13  Score=130.53  Aligned_cols=124  Identities=19%  Similarity=0.186  Sum_probs=102.0

Q ss_pred             cchHHHHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccc
Q 037567          211 QSFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGM  290 (374)
Q Consensus       211 ~~~~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~  290 (374)
                      ......++.++.+....+.++||-+.|++..+.+++.|+..|++...++......+-+.+.+.=+.|  .|.|+|+|+++
T Consensus       611 ~eK~~Aii~ei~~~~~~GrPVLVGT~SVe~SE~lS~~L~~~gI~H~VLNAK~h~~EAeIVA~AG~~G--aVTIATNMAGR  688 (1112)
T PRK12901        611 REKYNAVIEEITELSEAGRPVLVGTTSVEISELLSRMLKMRKIPHNVLNAKLHQKEAEIVAEAGQPG--TVTIATNMAGR  688 (1112)
T ss_pred             HHHHHHHHHHHHHHHHCCCCEEEEeCcHHHHHHHHHHHHHcCCcHHHhhccchhhHHHHHHhcCCCC--cEEEeccCcCC
Confidence            3456788888888888999999999999999999999999999887787775555555444433333  68999999999


Q ss_pred             ccccc--------CccEEEEECCCCChhHHHHhhccCCCCCCceEEEEEeeccC
Q 037567          291 GIDKP--------DVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSN  336 (374)
Q Consensus       291 G~d~~--------~~~~vi~~~~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~  336 (374)
                      |.|+.        +=-+||....+.|..--.|..||+||.|.+|..-.|++-+|
T Consensus       689 GTDIkLg~~V~e~GGL~VIgTerheSrRID~QLrGRaGRQGDPGsS~f~lSLED  742 (1112)
T PRK12901        689 GTDIKLSPEVKAAGGLAIIGTERHESRRVDRQLRGRAGRQGDPGSSQFYVSLED  742 (1112)
T ss_pred             CcCcccchhhHHcCCCEEEEccCCCcHHHHHHHhcccccCCCCCcceEEEEccc
Confidence            99996        22468888889999999999999999999999888887765

>KOG1015 consensus Transcription regulator XNP/ATRX, DEAD-box superfamily [Transcription]

Probab=99.60  E-value=1.7e-14  Score=133.94  Aligned_cols=141  Identities=16%  Similarity=0.128  Sum_probs=109.6

Q ss_pred             CCCcEEEEecchhHHHHHHHHHHHc----------------------CCceeeeecCCChHHHHHHHHhhhcCC----ee
Q 037567          227 GAGSIIVYCMTIKDVEEISKALKQL----------------------GVKAGTYHGQMGSKAREEAHRLFIRDE----IR  280 (374)
Q Consensus       227 ~~~~~lVf~~~~~~~~~l~~~l~~~----------------------~~~~~~~~~~~~~~~r~~~~~~f~~g~----~~  280 (374)
                      -+.+.|||..+......+...|...                      |.....+.|.....+|......|++..    .-
T Consensus      1141 IGDKlLVFSQSL~SLdLIe~fLe~v~r~gk~~~d~~~~~~~eGkW~~GkDyyriDGst~s~~R~k~~~~FNdp~NlRaRl 1220 (1567)
T KOG1015|consen 1141 IGDKLLVFSQSLISLDLIEDFLELVSREGKEDKDKPLIYKGEGKWLRGKDYYRLDGSTTSQSRKKWAEEFNDPTNLRARL 1220 (1567)
T ss_pred             hcceeEEeecccchhHHHHHHHHhhcccCccccccccccccccceecCCceEEecCcccHHHHHHHHHHhcCcccceeEE
Confidence            4789999999998888888777532                      445677899999999999999999853    23


Q ss_pred             EEEEeccccccccccCccEEEEECCCCChhHHHHhhccCCCCCCceEEEEEeeccCCCcccceeccccchHHH-------
Q 037567          281 VMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFYCGESQTENQR-------  353 (374)
Q Consensus       281 ilv~t~~~~~G~d~~~~~~vi~~~~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~-------  353 (374)
                      .||+|.+.+-|+|+-..+-||+++..|++.--.|.|=|+.|+||...||+|---.....-+++|+-.......       
T Consensus      1221 ~LISTRAGsLGiNLvAANRVIIfDasWNPSyDtQSIFRvyRfGQtKPvyiYRfiAqGTmEeKIYkRQVTKqsls~RVVDe 1300 (1567)
T KOG1015|consen 1221 FLISTRAGSLGINLVAANRVIIFDASWNPSYDTQSIFRVYRFGQTKPVYIYRFIAQGTMEEKIYKRQVTKQSLSFRVVDE 1300 (1567)
T ss_pred             EEEeeccCccccceeecceEEEEecccCCccchHHHHHHHhhcCcCceeehhhhhcccHHHHHHHHHHhHhhhhhhhhhH
Confidence            6899999999999999999999999999999999999999999998888775555444455555544333221       


Q ss_pred             -----HHHHHHHHHHHHHh
Q 037567          354 -----TAIMESLLAAQRYC  367 (374)
Q Consensus       354 -----~~~~~~l~~~~~~~  367 (374)
                           .-.+.+|.+++.|.
T Consensus      1301 qQv~Rhy~~neLteLy~fe 1319 (1567)
T KOG1015|consen 1301 QQVERHYTMNELTELYTFE 1319 (1567)
T ss_pred             HHHHHHhhHhhhHHHhhcC
Confidence                 22366677777765

>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]

Probab=99.59  E-value=2.9e-14  Score=123.92  Aligned_cols=102  Identities=21%  Similarity=0.222  Sum_probs=90.1

Q ss_pred             CCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcC-CeeE-EEEeccccccccccCccEEEEEC
Q 037567          227 GAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRD-EIRV-MVATMAFGMGIDKPDVRHVIHYG  304 (374)
Q Consensus       227 ~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g-~~~i-lv~t~~~~~G~d~~~~~~vi~~~  304 (374)
                      ..-+.|||....+....+.-.|.+.|++++.+.|+|++..|...++.|.+. +..| |++-.+.+.-+|+....+|+..+
T Consensus       637 ~t~KsIVFSQFTSmLDLi~~rL~kaGfscVkL~GsMs~~ardatik~F~nd~~c~vfLvSLkAGGVALNLteASqVFmmD  716 (791)
T KOG1002|consen  637 RTAKSIVFSQFTSMLDLIEWRLGKAGFSCVKLVGSMSPAARDATIKYFKNDIDCRVFLVSLKAGGVALNLTEASQVFMMD  716 (791)
T ss_pred             cchhhhhHHHHHHHHHHHHHHhhccCceEEEeccCCChHHHHHHHHHhccCCCeEEEEEEeccCceEeeechhceeEeec
Confidence            345789999999999999999999999999999999999999999999986 4555 45666888999999999999999


Q ss_pred             CCCChhHHHHhhccCCCCCCceEE
Q 037567          305 CPKTLESYYQESGRCGRDGIASVC  328 (374)
Q Consensus       305 ~p~s~~~~~Q~~GR~~R~~~~g~~  328 (374)
                      +=|++.--+|...|..|.||...+
T Consensus       717 PWWNpaVe~Qa~DRiHRIGQ~rPv  740 (791)
T KOG1002|consen  717 PWWNPAVEWQAQDRIHRIGQYRPV  740 (791)
T ss_pred             ccccHHHHhhhhhhHHhhcCccce
Confidence            999999999999999999986533

>TIGR02562 cas3_yersinia CRISPR-associated helicase Cas3

Probab=99.57  E-value=2.4e-13  Score=130.11  Aligned_cols=91  Identities=22%  Similarity=0.277  Sum_probs=68.7

Q ss_pred             EEEEecchhHHHHHHHHHHHc----C--CceeeeecCCChHHHHHHHHhh----------------------hc----CC
Q 037567          231 IIVYCMTIKDVEEISKALKQL----G--VKAGTYHGQMGSKAREEAHRLF----------------------IR----DE  278 (374)
Q Consensus       231 ~lVf~~~~~~~~~l~~~l~~~----~--~~~~~~~~~~~~~~r~~~~~~f----------------------~~----g~  278 (374)
                      .+|-.++++.+..+++.|.+.    +  +.+..+|+......|..+.+..                      .+    +.
T Consensus       759 GliR~anI~p~V~~A~~L~~~~~~~~~~i~~~~yHSr~~l~~Rs~~E~~Ld~~L~R~~~~~~~~~~~i~~~l~~~~~~~~  838 (1110)
T TIGR02562       759 GLIRVANIDPLIRLAQFLYALLAEEKYQIHLCCYHAQDPLLLRSYIERRLDQLLTRHKPEQLFQDDEIIDLMQNSPALNH  838 (1110)
T ss_pred             EEEEEcCchHHHHHHHHHHhhccccCCceeEEEecccChHHHHHHHHHHHHHHhcccChhhhhchHHHHHHHhcccccCC
Confidence            678888899888888888764    2  3367789998777776655442                      11    34


Q ss_pred             eeEEEEeccccccccccCccEEEEECCCCChhHHHHhhccCCCCCC
Q 037567          279 IRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRDGI  324 (374)
Q Consensus       279 ~~ilv~t~~~~~G~d~~~~~~vi~~~~p~s~~~~~Q~~GR~~R~~~  324 (374)
                      ..|+|+|+.++.|+|+ +.+.+|.  -|.++...+|+.||+.|.+.
T Consensus       839 ~~i~v~Tqv~E~g~D~-dfd~~~~--~~~~~~sliQ~aGR~~R~~~  881 (1110)
T TIGR02562       839 LFIVLATPVEEVGRDH-DYDWAIA--DPSSMRSIIQLAGRVNRHRL  881 (1110)
T ss_pred             CeEEEEeeeEEEEecc-cCCeeee--ccCcHHHHHHHhhccccccc
Confidence            5799999999999998 5666553  34568999999999999875

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.

>COG0553 HepA Superfamily II DNA/RNA helicases, SNF2 family [Transcription / DNA replication, recombination, and repair]

Probab=99.48  E-value=9.4e-13  Score=132.27  Aligned_cols=312  Identities=20%  Similarity=0.188  Sum_probs=200.5

Q ss_pred             CCCchhHHHHHHHHHc-----CCCEEEEccCCCCchhhhhccc---ccc----CCcEEEEcchHHHHHHHHHHHHHcCCc
Q 037567           12 SVFRPYQKDVIQRIIE-----KRDCLVVMATGSGKSLCYQLPP---LVT----GKTALVVSPLISLMQDQVMSLKQRGIN   79 (374)
Q Consensus        12 ~~~~~~Q~~~~~~~~~-----~~~~l~~a~tGsGKT~~~~l~~---~~~----~~~~lil~P~~~l~~q~~~~~~~~~~~   79 (374)
                      ..+++||.+.+..+..     +.+.++...+|.|||+-.+..+   ...    .+++++++|+ +++.+|.+++.++-..
T Consensus       337 ~~lr~yq~~g~~wl~~~l~~~~~~~ilaD~mglGKTiq~i~~l~~~~~~~~~~~~~~liv~p~-s~~~nw~~e~~k~~~~  415 (866)
T COG0553         337 AELRPYQLEGVNWLSELLRSNLLGGILADDMGLGKTVQTIALLLSLLESIKVYLGPALIVVPA-SLLSNWKREFEKFAPD  415 (866)
T ss_pred             hhhHHHHHHHHHHHHHHHHhccCCCcccccccchhHHHHHHHHHhhhhcccCCCCCeEEEecH-HHHHHHHHHHhhhCcc
Confidence            4689999999977552     5677889999999995433222   221    4589999999 6888899999887443


Q ss_pred             eE---EcCCCCCc----hhhhhhhhcC----CeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHH
Q 037567           80 AE---FLGSAQTD----SSVQTKAETG----YFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLE  148 (374)
Q Consensus        80 ~~---~~~~~~~~----~~~~~~~~~~----~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~  148 (374)
                      ..   ...+....    ..........    .++++++|++.+.... ..........++.+|+||+|.+.+....    
T Consensus       416 ~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~v~itty~~l~~~~-~~~~~l~~~~~~~~v~DEa~~ikn~~s~----  490 (866)
T COG0553         416 LRLVLVYHGEKSELDKKREALRDLLKLHLVIIFDVVITTYELLRRFL-VDHGGLKKIEWDRVVLDEAHRIKNDQSS----  490 (866)
T ss_pred             ccceeeeeCCcccccHHHHHHHHHhhhcccceeeEEechHHHHHHhh-hhHHHHhhceeeeeehhhHHHHhhhhhH----
Confidence            33   33332221    1122222221    2799999999876522 1223445567889999999998663321    


Q ss_pred             HHHHHHHHHhcCCCCeeEEEeecCcccHHHHHHhcC-CCCCeEEE-----------------ec----------------
Q 037567          149 YKQLDKLRTFLLGVPFVALTATATEKVRIDIINSLK-LKNPYVTI-----------------AS----------------  194 (374)
Q Consensus       149 ~~~~~~~~~~~~~~~~i~~SaT~~~~~~~~~~~~~~-~~~~~~~~-----------------~~----------------  194 (374)
                        ....+. .+.....+.+|+||-.+...++...+. ...+....                 ..                
T Consensus       491 --~~~~l~-~~~~~~~~~LtgTPlen~l~eL~sl~~~f~~p~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  567 (866)
T COG0553         491 --EGKALQ-FLKALNRLDLTGTPLENRLGELWSLLQEFLNPGLLGTSFAIFTRLFEKPIQAEEDIGPLEARELGIELLRK  567 (866)
T ss_pred             --HHHHHH-HHhhcceeeCCCChHhhhHHHHHHHHHHHhCCccccchHHHHHHHHhhhhhhcccccchhhHHHHHHHHHH
Confidence              112222 333445588888874333222222111 10000000                 00                


Q ss_pred             -----------cC------CC----------------------------------ce-eE----------EEE-------
Q 037567          195 -----------FD------RK----------------------------------NL-FY----------GVK-------  205 (374)
Q Consensus       195 -----------~~------~~----------------------------------~~-~~----------~~~-------  205 (374)
                                 .+      .+                                  .. ..          ...       
T Consensus       568 ~i~~f~lrr~k~~~~v~~~Lp~k~e~~~~~~l~~~q~~~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~  647 (866)
T COG0553         568 LLSPFILRRTKEDVEVLKELPPKIEKVLECELSEEQRELYEALLEGAEKNQQLLEDLEKADSDENRIGDSELNILALLTR  647 (866)
T ss_pred             HHHHHhhcccccchhHHHhCChhhhhhhhhcccHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccccchhhHHHHHHHH
Confidence                       00      00                                  00 00          000       


Q ss_pred             ---e------ecCC----cc------------------------hHHHHHHHHH--HhhcCCC--cEEEEecchhHHHHH
Q 037567          206 ---V------INRG----QS------------------------FVDELVQEIL--KSVAGAG--SIIVYCMTIKDVEEI  244 (374)
Q Consensus       206 ---~------~~~~----~~------------------------~~~~~~~~~~--~~~~~~~--~~lVf~~~~~~~~~l  244 (374)
                         .      ....    ..                        .....+.+++  .....+.  +++||++.......+
T Consensus       648 lr~~~~~p~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~k~~~l~~ll~~~~~~~~~~~kvlifsq~t~~l~il  727 (866)
T COG0553         648 LRQICNHPALVDEGLEATFDRIVLLLREDKDFDYLKKPLIQLSKGKLQALDELLLDKLLEEGHYHKVLIFSQFTPVLDLL  727 (866)
T ss_pred             HHHhccCccccccccccccchhhhhhhcccccccccchhhhccchHHHHHHHHHHHHHHhhcccccEEEEeCcHHHHHHH
Confidence               0      0000    00                        2233333444  2334555  899999999999999


Q ss_pred             HHHHHHcCCceeeeecCCChHHHHHHHHhhhcC--CeeEEEEeccccccccccCccEEEEECCCCChhHHHHhhccCCCC
Q 037567          245 SKALKQLGVKAGTYHGQMGSKAREEAHRLFIRD--EIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRD  322 (374)
Q Consensus       245 ~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g--~~~ilv~t~~~~~G~d~~~~~~vi~~~~p~s~~~~~Q~~GR~~R~  322 (374)
                      ...+...++....++|.++.++|+..++.|.++  ....++++.+.+.|+|+...++||++++.+++....|...|+.|.
T Consensus       728 ~~~l~~~~~~~~~ldG~~~~~~r~~~i~~f~~~~~~~v~lls~kagg~glnLt~a~~vi~~d~~wnp~~~~Qa~dRa~Ri  807 (866)
T COG0553         728 EDYLKALGIKYVRLDGSTPAKRRQELIDRFNADEEEKVFLLSLKAGGLGLNLTGADTVILFDPWWNPAVELQAIDRAHRI  807 (866)
T ss_pred             HHHHHhcCCcEEEEeCCCChhhHHHHHHHhhcCCCCceEEEEecccccceeecccceEEEeccccChHHHHHHHHHHHHh
Confidence            999999888899999999999999999999996  344566778999999999999999999999999999999999999


Q ss_pred             CCceEEEEEe
Q 037567          323 GIASVCWLYY  332 (374)
Q Consensus       323 ~~~g~~~~~~  332 (374)
                      |+...+.++-
T Consensus       808 gQ~~~v~v~r  817 (866)
T COG0553         808 GQKRPVKVYR  817 (866)
T ss_pred             cCcceeEEEE
Confidence            9887665553

>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=99.47  E-value=1.4e-13  Score=120.58  Aligned_cols=158  Identities=18%  Similarity=0.136  Sum_probs=94.6

Q ss_pred             hHHHHHHHHHc-------------CCCEEEEccCCCCchhhhhccccc-----c---CCcEEEEcchHHHHHHHHHHHHH
Q 037567           17 YQKDVIQRIIE-------------KRDCLVVMATGSGKSLCYQLPPLV-----T---GKTALVVSPLISLMQDQVMSLKQ   75 (374)
Q Consensus        17 ~Q~~~~~~~~~-------------~~~~l~~a~tGsGKT~~~~l~~~~-----~---~~~~lil~P~~~l~~q~~~~~~~   75 (374)
                      ||.+++..++.             .+.+++...+|+|||+..+..+..     +   ..++||++|. .+..||..++.+
T Consensus         1 ~Q~~~v~~m~~~~~~~~~~~~~~~~~g~lL~de~GlGKT~~~i~~~~~l~~~~~~~~~~~~LIv~P~-~l~~~W~~E~~~   79 (299)
T PF00176_consen    1 HQLEAVRWMLDRELVEEYPNSESPPRGGLLADEMGLGKTITAIALISYLKNEFPQRGEKKTLIVVPS-SLLSQWKEEIEK   79 (299)
T ss_dssp             HHHHHHHHHHHHH----TTSSSTTT-EEEE---TTSSHHHHHHHHHHHHHHCCTTSS-S-EEEEE-T-TTHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHhhhhcccccccCCCCEEEEECCCCCchhhhhhhhhhhhhccccccccceeEeecc-chhhhhhhhhcc
Confidence            68888877642             356788889999999776544331     1   1259999999 888999999998


Q ss_pred             cCC----ceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccC-chhhHHHHHhcCccEEEEeccchhhcccCcchHHHH
Q 037567           76 RGI----NAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACII-PISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYK  150 (374)
Q Consensus        76 ~~~----~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~-~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~  150 (374)
                      +..    ++....+.. .............+++|+|++.+... .......+...++++||+||+|.+.+...      .
T Consensus        80 ~~~~~~~~v~~~~~~~-~~~~~~~~~~~~~~vvi~ty~~~~~~~~~~~~~~l~~~~~~~vIvDEaH~~k~~~s------~  152 (299)
T PF00176_consen   80 WFDPDSLRVIIYDGDS-ERRRLSKNQLPKYDVVITTYETLRKARKKKDKEDLKQIKWDRVIVDEAHRLKNKDS------K  152 (299)
T ss_dssp             HSGT-TS-EEEESSSC-HHHHTTSSSCCCSSEEEEEHHHHH--TSTHTTHHHHTSEEEEEEETTGGGGTTTTS------H
T ss_pred             cccccccccccccccc-ccccccccccccceeeeccccccccccccccccccccccceeEEEecccccccccc------c
Confidence            752    233333322 12222223345678999999988711 11222334445699999999999965442      2


Q ss_pred             HHHHHHHhcCCCCeeEEEeecCcccHHHHHHhc
Q 037567          151 QLDKLRTFLLGVPFVALTATATEKVRIDIINSL  183 (374)
Q Consensus       151 ~~~~~~~~~~~~~~i~~SaT~~~~~~~~~~~~~  183 (374)
                      ....+.. +....++++||||..+...++...+
T Consensus       153 ~~~~l~~-l~~~~~~lLSgTP~~n~~~dl~~~l  184 (299)
T PF00176_consen  153 RYKALRK-LRARYRWLLSGTPIQNSLEDLYSLL  184 (299)
T ss_dssp             HHHHHHC-CCECEEEEE-SS-SSSGSHHHHHHH
T ss_pred             ccccccc-cccceEEeeccccccccccccccch
Confidence            2233333 4577889999999988765555543

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.

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

Probab=99.45  E-value=4.2e-14  Score=104.45  Aligned_cols=133  Identities=15%  Similarity=0.079  Sum_probs=76.5

Q ss_pred             CCCEEEEccCCCCchhhhhcc----ccccCCcEEEEcchHHHHHHHHHHHHHcCCceEEcCCCCCchhhhhhhhcCCeeE
Q 037567           28 KRDCLVVMATGSGKSLCYQLP----PLVTGKTALVVSPLISLMQDQVMSLKQRGINAEFLGSAQTDSSVQTKAETGYFQL  103 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~l~----~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i  103 (374)
                      |+--++-.+||+|||.-.+..    .+.++.++||+.|||.+++++.+.++.......  ......      ...+..-|
T Consensus         4 g~~~~~d~hpGaGKTr~vlp~~~~~~i~~~~rvLvL~PTRvva~em~~aL~~~~~~~~--t~~~~~------~~~g~~~i   75 (148)
T PF07652_consen    4 GELTVLDLHPGAGKTRRVLPEIVREAIKRRLRVLVLAPTRVVAEEMYEALKGLPVRFH--TNARMR------THFGSSII   75 (148)
T ss_dssp             TEEEEEE--TTSSTTTTHHHHHHHHHHHTT--EEEEESSHHHHHHHHHHTTTSSEEEE--STTSS----------SSSSE
T ss_pred             CceeEEecCCCCCCcccccHHHHHHHHHccCeEEEecccHHHHHHHHHHHhcCCcccC--ceeeec------cccCCCcc
Confidence            444578899999999754433    344799999999999999999999986643332  211111      11233467


Q ss_pred             EEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHHhcCCCCeeEEEeecCccc
Q 037567          104 LFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEKV  175 (374)
Q Consensus       104 ~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~SaT~~~~~  175 (374)
                      -++|+..+...+..   .....++++||+||||.....+...+   ..+... .......+|+|||||+...
T Consensus        76 ~vMc~at~~~~~~~---p~~~~~yd~II~DEcH~~Dp~sIA~r---g~l~~~-~~~g~~~~i~mTATPPG~~  140 (148)
T PF07652_consen   76 DVMCHATYGHFLLN---PCRLKNYDVIIMDECHFTDPTSIAAR---GYLREL-AESGEAKVIFMTATPPGSE  140 (148)
T ss_dssp             EEEEHHHHHHHHHT---SSCTTS-SEEEECTTT--SHHHHHHH---HHHHHH-HHTTS-EEEEEESS-TT--
T ss_pred             cccccHHHHHHhcC---cccccCccEEEEeccccCCHHHHhhh---eeHHHh-hhccCeeEEEEeCCCCCCC
Confidence            78888765543322   23346899999999998654332211   122222 2223467999999999764

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 ....

>PF06862 DUF1253: Protein of unknown function (DUF1253); InterPro: IPR010678 This family is defined by a C-terminal region of approximately 500 residues, Digestive organ expansion factor (DEF) is thought to Regulate the p53 pathway to control the expansion growth of digestive organs and is required for the expansion growth of intestine, liver and exocrine pancreas, but not endocrine pancreas [, ]

Probab=99.36  E-value=1.5e-10  Score=102.86  Aligned_cols=243  Identities=9%  Similarity=0.093  Sum_probs=153.5

Q ss_pred             CeeEEEEcCcccccCchh----hHHHHHhcCccEEEEeccchhhcccCcc----------------hHHHHHHHHHHHhc
Q 037567          100 YFQLLFMTPEKACIIPIS----FWSKLLKAGVCLFAVDEAHCISEWGHDF----------------RLEYKQLDKLRTFL  159 (374)
Q Consensus       100 ~~~i~i~T~~~l~~~~~~----~~~~~~~~~~~~vviDE~h~~~~~~~~~----------------~~~~~~~~~~~~~~  159 (374)
                      ..||+|++|=-|...+..    ....-.++++.++|+|.+|.+.-.+.+.                ...++++....-.-
T Consensus       131 ~SDIIiASPLGLr~~i~~~~~~~~d~DFLSSIEv~iiD~ad~l~MQNW~Hv~~v~~~lN~~P~~~~~~DfsRVR~w~Ldg  210 (442)
T PF06862_consen  131 SSDIIIASPLGLRMIIGEEGEKKRDYDFLSSIEVLIIDQADVLLMQNWEHVLHVFEHLNLQPKKSHDTDFSRVRPWYLDG  210 (442)
T ss_pred             cCCEEEEChHHHHHHhccccccccccchhheeeeEeechhhHHHHhhHHHHHHHHHHhccCCCCCCCCCHHHHHHHHHcC
Confidence            559999999766443331    2233457889999999999986321100                01112221111100


Q ss_pred             ---CCCCeeEEEeecCcccHHHHHHhcC-CCCCeEEEec-----------cCCCceeEEEEeec---CCcchH----HHH
Q 037567          160 ---LGVPFVALTATATEKVRIDIINSLK-LKNPYVTIAS-----------FDRKNLFYGVKVIN---RGQSFV----DEL  217 (374)
Q Consensus       160 ---~~~~~i~~SaT~~~~~~~~~~~~~~-~~~~~~~~~~-----------~~~~~~~~~~~~~~---~~~~~~----~~~  217 (374)
                         .-.|.|++|+...+....-+..... ..........           .........+....   ..+...    ..+
T Consensus       211 ~a~~~RQtii~S~~~~pe~~slf~~~~~N~~G~v~~~~~~~~~g~i~~v~~~v~Q~F~r~~~~s~~~~~d~Rf~yF~~~i  290 (442)
T PF06862_consen  211 QAKYYRQTIIFSSFQTPEINSLFNRHCQNYAGKVRLKPPYEASGVISQVVVQVRQVFQRFDCSSPADDPDARFKYFTKKI  290 (442)
T ss_pred             cchheeEeEEecCCCCHHHHHHHHhhCcCccceEEEeeccccceeeeccccCCceEEEEecCCCcchhhhHHHHHHHHHH
Confidence               0257899999988876533333111 1111111111           11122222222111   111122    233


Q ss_pred             HHHHHHhhcCCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEecccc--cccccc
Q 037567          218 VQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFG--MGIDKP  295 (374)
Q Consensus       218 ~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~--~G~d~~  295 (374)
                      +..+.+ -...+.+|||+++.-+--.+.+.|++.++..+.+|...+..+-...-..|..|+..+|+.|.-+.  +=..+.
T Consensus       291 LP~l~~-~~~~~~~LIfIPSYfDfVRlRN~lk~~~~sF~~i~EYts~~~isRAR~~F~~G~~~iLL~TER~HFfrRy~ir  369 (442)
T PF06862_consen  291 LPQLKR-DSKMSGTLIFIPSYFDFVRLRNYLKKENISFVQISEYTSNSDISRARSQFFHGRKPILLYTERFHFFRRYRIR  369 (442)
T ss_pred             HHHhhh-ccCCCcEEEEecchhhhHHHHHHHHhcCCeEEEecccCCHHHHHHHHHHHHcCCceEEEEEhHHhhhhhceec
Confidence            333332 23668899999999999999999999999999999999999999999999999999999998443  566788


Q ss_pred             CccEEEEECCCCChhHHHHhhccCCCCCC------ceEEEEEeeccCCCcccce
Q 037567          296 DVRHVIHYGCPKTLESYYQESGRCGRDGI------ASVCWLYYARSNFAKGDFY  343 (374)
Q Consensus       296 ~~~~vi~~~~p~s~~~~~Q~~GR~~R~~~------~g~~~~~~~~~~~~~~~~~  343 (374)
                      ++++||+|++|..+.-|...++-.+....      ...|.++|++-|.-.++.+
T Consensus       370 Gi~~viFY~~P~~p~fY~El~n~~~~~~~~~~~~~~~~~~~lysk~D~~~LErI  423 (442)
T PF06862_consen  370 GIRHVIFYGPPENPQFYSELLNMLDESSGGEVDAADATVTVLYSKYDALRLERI  423 (442)
T ss_pred             CCcEEEEECCCCChhHHHHHHhhhcccccccccccCceEEEEecHhHHHHHHHH
Confidence            89999999999999888777755444332      5788999988765444444

; GO: 0005634 nucleus

>COG0653 SecA Preprotein translocase subunit SecA (ATPase, RNA helicase) [Intracellular trafficking and secretion]

Probab=99.33  E-value=2.3e-11  Score=114.53  Aligned_cols=322  Identities=20%  Similarity=0.194  Sum_probs=193.3

Q ss_pred             hHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc---cCCcEEEEcchHHHHHHHHHHH----HH
Q 037567            3 STLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV---TGKTALVVSPLISLMQDQVMSL----KQ   75 (374)
Q Consensus         3 ~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~---~~~~~lil~P~~~l~~q~~~~~----~~   75 (374)
                      ++-++++|+. ++.  .+.+..+.-...-+..+-||-|||+++.+|+.-   .++.+.+++...-|+.--..++    .-
T Consensus        71 Ea~~Rvlg~~-~~d--VQliG~i~lh~g~iaEM~TGEGKTL~atlp~ylnaL~gkgVhvVTvNdYLA~RDae~m~~l~~~  147 (822)
T COG0653          71 EASKRVLGMR-HFD--VQLLGGIVLHLGDIAEMRTGEGKTLVATLPAYLNALAGKGVHVVTVNDYLARRDAEWMGPLYEF  147 (822)
T ss_pred             HHHHHhcCCC-hhh--HHHhhhhhhcCCceeeeecCCchHHHHHHHHHHHhcCCCCcEEeeehHHhhhhCHHHHHHHHHH
Confidence            3445666664 333  455555555666699999999999998877653   4777889998888886434333    44


Q ss_pred             cCCceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccC-c----hhhHHHHHhcCccEEEEeccchhh-c--------c
Q 037567           76 RGINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACII-P----ISFWSKLLKAGVCLFAVDEAHCIS-E--------W  141 (374)
Q Consensus        76 ~~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~-~----~~~~~~~~~~~~~~vviDE~h~~~-~--------~  141 (374)
                      .|+.+.+..........   .....+||..+|..-+..- +    ..........+..+.|+||++.+. +        .
T Consensus       148 LGlsvG~~~~~m~~~ek---~~aY~~DItY~TnnElGFDYLRDNm~~~~ee~vqr~~~faIvDEvDSILIDEARtPLiIS  224 (822)
T COG0653         148 LGLSVGVILAGMSPEEK---RAAYACDITYGTNNELGFDYLRDNMVTSQEEKVQRGLNFAIVDEVDSILIDEARTPLIIS  224 (822)
T ss_pred             cCCceeeccCCCChHHH---HHHHhcCceeccccccCcchhhhhhhccHHHhhhccCCeEEEcchhheeeeccccceeee
Confidence            58888877766544332   2334579999998755321 1    111123334567889999999874 1        0


Q ss_pred             c-Ccc-hHHHHHHHHHHHhcC---------CCCee---------------------------------------------
Q 037567          142 G-HDF-RLEYKQLDKLRTFLL---------GVPFV---------------------------------------------  165 (374)
Q Consensus       142 ~-~~~-~~~~~~~~~~~~~~~---------~~~~i---------------------------------------------  165 (374)
                      | ... ...+..+..+...+.         ..+.+                                             
T Consensus       225 G~~~~~~~~Y~~~~~~v~~l~~~~d~~iDek~k~v~lte~G~~kae~~f~~~~Ly~~en~~~~h~~~~alrA~~l~~~D~  304 (822)
T COG0653         225 GPAEDSSELYKKVDDLVRLLSEDEDFTIDEKSKNVSLTESGLEKAEELLGIENLYDLENVNLVHHLNQALRAHILFFRDV  304 (822)
T ss_pred             cccccCchHHHHHHHHHHHhccccceeecchhcccccchhhHHHHHHHhCcccccchhhHHHHhhHHHHHHHHHHhhcCC
Confidence            1 000 011111111111110         01112                                             


Q ss_pred             ----------------------------------------------------------------EEEeecCcccHHHHHH
Q 037567          166 ----------------------------------------------------------------ALTATATEKVRIDIIN  181 (374)
Q Consensus       166 ----------------------------------------------------------------~~SaT~~~~~~~~~~~  181 (374)
                                                                                      +||+|...... ++..
T Consensus       305 dYIVrd~ev~IvD~ftGR~m~gRr~s~GLhQAiEAKEgv~i~~e~~tlatITfQn~fR~y~kl~gmTGTa~te~~-EF~~  383 (822)
T COG0653         305 DYIVRDGEVVIVDEFTGRMMEGRRWSDGLHQAIEAKEGVEIQEENQTLATITFQNLFRLYPKLAGMTGTADTEEE-EFDV  383 (822)
T ss_pred             eeEEecCeEEEEecccCCcccCcCCCchhHHHHHHhcCCcccccceeehhhhHHHHHhhhhhhcCCCCcchhhhh-hhhh
Confidence                                                                            22222211111 1122


Q ss_pred             hcCCCCCeEEEeccCCCc--eeEEEEeecCCcchHHHHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHHcCCceeeee
Q 037567          182 SLKLKNPYVTIASFDRKN--LFYGVKVINRGQSFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYH  259 (374)
Q Consensus       182 ~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~  259 (374)
                      .+++   .+.....+++.  .......+........+++.++......++++||-+.+.+..+.+.+.|.+.|++-..++
T Consensus       384 iY~l---~vv~iPTnrp~~R~D~~D~vy~t~~~K~~Aiv~~I~~~~~~gqPvLvgT~sie~SE~ls~~L~~~~i~h~VLN  460 (822)
T COG0653         384 IYGL---DVVVIPTNRPIIRLDEPDLVYKTEEEKFKAIVEDIKERHEKGQPVLVGTVSIEKSELLSKLLRKAGIPHNVLN  460 (822)
T ss_pred             ccCC---ceeeccCCCcccCCCCccccccchHHHHHHHHHHHHHHHhcCCCEEEcCcceecchhHHHHHHhcCCCceeec
Confidence            2211   11222222222  222223344555677888999988888999999999999999999999999999887787


Q ss_pred             cCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCcc-----------EEEEECCCCChhHHHHhhccCCCCCCceEE
Q 037567          260 GQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVR-----------HVIHYGCPKTLESYYQESGRCGRDGIASVC  328 (374)
Q Consensus       260 ~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~-----------~vi~~~~p~s~~~~~Q~~GR~~R~~~~g~~  328 (374)
                      ......+-+.+.+.-..  -.|-|+|+|+++|.|+.--.           +||-..--.|..--.|.-||+||.|.+|..
T Consensus       461 Ak~h~~EA~Iia~AG~~--gaVTiATNMAGRGTDIkLg~~~~~V~~lGGL~VIgTERhESRRIDnQLRGRsGRQGDpG~S  538 (822)
T COG0653         461 AKNHAREAEIIAQAGQP--GAVTIATNMAGRGTDIKLGGNPEFVMELGGLHVIGTERHESRRIDNQLRGRAGRQGDPGSS  538 (822)
T ss_pred             cccHHHHHHHHhhcCCC--CccccccccccCCcccccCCCHHHHHHhCCcEEEecccchhhHHHHHhhcccccCCCcchh
Confidence            77554444444433333  35889999999999984322           244444444555557999999999999877


Q ss_pred             EEEeeccC
Q 037567          329 WLYYARSN  336 (374)
Q Consensus       329 ~~~~~~~~  336 (374)
                      -.+++-+|
T Consensus       539 ~F~lSleD  546 (822)
T COG0653         539 RFYLSLED  546 (822)
T ss_pred             hhhhhhHH
Confidence            66665544

>KOG1016 consensus Predicted DNA helicase, DEAD-box superfamily [General function prediction only]

Probab=99.12  E-value=2.7e-09  Score=98.22  Aligned_cols=118  Identities=16%  Similarity=0.169  Sum_probs=96.3

Q ss_pred             CCCcEEEEecchhHHHHHHHHHHHcCCc------------------eeeeecCCChHHHHHHHHhhhcCC---eeEEEEe
Q 037567          227 GAGSIIVYCMTIKDVEEISKALKQLGVK------------------AGTYHGQMGSKAREEAHRLFIRDE---IRVMVAT  285 (374)
Q Consensus       227 ~~~~~lVf~~~~~~~~~l~~~l~~~~~~------------------~~~~~~~~~~~~r~~~~~~f~~g~---~~ilv~t  285 (374)
                      .+.++|||..+......+.+.|.+..++                  -..+.|..+..+|++++++|++..   .-++++|
T Consensus       718 ~g~kil~fSq~l~~Ld~ieeil~krq~pc~~gdnG~~aqkW~~n~sy~rldG~t~a~~rekLinqfN~e~~lsWlfllst  797 (1387)
T KOG1016|consen  718 IGEKILIFSQNLTALDMIEEILKKRQIPCKDGDNGCPAQKWEKNRSYLRLDGTTSAADREKLINQFNSEPGLSWLFLLST  797 (1387)
T ss_pred             cCceEEEeecchhHHHHHHHHHhcccccCCCCCCCCchhhhhhccceecccCCcccchHHHHHHhccCCCCceeeeeehh
Confidence            3568999999999999999988775222                  235677888999999999999752   4567789


Q ss_pred             ccccccccccCccEEEEECCCCChhHHHHhhccCCCCCCceEEEEEeeccCCCccccee
Q 037567          286 MAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFYC  344 (374)
Q Consensus       286 ~~~~~G~d~~~~~~vi~~~~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~~~~~~~~~  344 (374)
                      .+.+.|+|+-..+-++.++..|++..-.|.+-|+.|.|+...|+++----|...-++++
T Consensus       798 rag~lGinLIsanr~~ifda~wnpchdaqavcRvyrYGQ~KpcfvYRlVmD~~lEkkIy  856 (1387)
T KOG1016|consen  798 RAGSLGINLISANRCIIFDACWNPCHDAQAVCRVYRYGQQKPCFVYRLVMDNSLEKKIY  856 (1387)
T ss_pred             ccccccceeeccceEEEEEeecCccccchhhhhhhhhcCcCceeEEeehhhhhhHHHHH
Confidence            99999999988888888999999999999999999999999998887666655555554

>KOG2340 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.09  E-value=3.1e-09  Score=93.88  Aligned_cols=116  Identities=15%  Similarity=0.179  Sum_probs=92.1

Q ss_pred             CCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEecccc--ccccccCccEEEEECC
Q 037567          228 AGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFG--MGIDKPDVRHVIHYGC  305 (374)
Q Consensus       228 ~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~--~G~d~~~~~~vi~~~~  305 (374)
                      ...+|||.|+.-+--++.+.+++.++..+.+|...+...-...-+.|..|...+++.|.-+.  +-.++.+++.||+|.+
T Consensus       552 ~s~~LiyIPSYfDFVRvRNy~K~e~i~F~~i~EYssk~~vsRAR~lF~qgr~~vlLyTER~hffrR~~ikGVk~vVfYqp  631 (698)
T KOG2340|consen  552 ESGILIYIPSYFDFVRVRNYMKKEEISFVMINEYSSKSKVSRARELFFQGRKSVLLYTERAHFFRRYHIKGVKNVVFYQP  631 (698)
T ss_pred             cCceEEEecchhhHHHHHHHhhhhhcchHHHhhhhhHhhhhHHHHHHHhcCceEEEEehhhhhhhhheecceeeEEEecC
Confidence            34689999999999999999999998888888888888777888889999999999998554  5778999999999999


Q ss_pred             CCChhHH---HHhhccCCCCC----CceEEEEEeeccCCCcccce
Q 037567          306 PKTLESY---YQESGRCGRDG----IASVCWLYYARSNFAKGDFY  343 (374)
Q Consensus       306 p~s~~~~---~Q~~GR~~R~~----~~g~~~~~~~~~~~~~~~~~  343 (374)
                      |.++.-|   +-+++|+.-.|    ..-.|.++|++.|.-.+..+
T Consensus       632 P~~P~FYsEiinm~~k~~~~gn~d~d~~t~~ilytKyD~i~Le~i  676 (698)
T KOG2340|consen  632 PNNPHFYSEIINMSDKTTSQGNTDLDIFTVRILYTKYDRIRLENI  676 (698)
T ss_pred             CCCcHHHHHHHhhhhhhhccCCccccceEEEEEeechhhHHHHHh
Confidence            9988655   55555554333    23477888888765444443

>KOG1132 consensus Helicase of the DEAD superfamily [Replication, recombination and repair]

Probab=98.95  E-value=3.4e-07  Score=86.18  Aligned_cols=68  Identities=26%  Similarity=0.340  Sum_probs=51.7

Q ss_pred             cCCCCCchhHHHHHHHHHc----CCCEEEEccCCCCchhhhhccccc---------------------------------
Q 037567            9 FGYSVFRPYQKDVIQRIIE----KRDCLVVMATGSGKSLCYQLPPLV---------------------------------   51 (374)
Q Consensus         9 ~~~~~~~~~Q~~~~~~~~~----~~~~l~~a~tGsGKT~~~~l~~~~---------------------------------   51 (374)
                      |.| +|+|-|...+..++.    +.++++..|||+|||++.+...+.                                 
T Consensus        18 fP~-qpY~~Q~a~M~rvl~~L~~~q~~llESPTGTGKSLsLLCS~LAW~q~~k~~~~~~~~s~~~~~~~p~~~s~~~g~~   96 (945)
T KOG1132|consen   18 FPF-QPYPTQLAFMTRVLSCLDRKQNGLLESPTGTGKSLSLLCSTLAWQQHLKSRKPKGKISERKAGFIPTQPSDSGGEK   96 (945)
T ss_pred             ccC-CcchHHHHHHHHHHHHHHHhhhhhccCCCCCCccHHHHHHHHHHHHHhhccccccchhhhhccccCCCCccCCCCc
Confidence            556 489999888877764    678999999999999775433220                                 


Q ss_pred             ------c------CCcEEEEcchHHHHHHHHHHHHHcC
Q 037567           52 ------T------GKTALVVSPLISLMQDQVMSLKQRG   77 (374)
Q Consensus        52 ------~------~~~~lil~P~~~l~~q~~~~~~~~~   77 (374)
                            .      .+++++-.-|..-..|+.+++++.+
T Consensus        97 s~e~~e~~~~~~~ipkIyyaSRTHsQltQvvrElrrT~  134 (945)
T KOG1132|consen   97 SEEAGEPIACYTGIPKIYYASRTHSQLTQVVRELRRTG  134 (945)
T ss_pred             hhhhcCccccccCCceEEEecchHHHHHHHHHHHhhcC
Confidence                  0      3467888888888999999998753

>KOG0952 consensus DNA/RNA helicase MER3/SLH1, DEAD-box superfamily [RNA processing and modification]

Probab=98.92  E-value=5.5e-11  Score=112.57  Aligned_cols=243  Identities=17%  Similarity=0.177  Sum_probs=142.9

Q ss_pred             CCCEEEEccCCCCchhhhhccccc-----cCCcEEEEcchHHHHHHHHHHHHHc----CCceEEcCCCCCchhhhhhhhc
Q 037567           28 KRDCLVVMATGSGKSLCYQLPPLV-----TGKTALVVSPLISLMQDQVMSLKQR----GINAEFLGSAQTDSSVQTKAET   98 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~l~~~~-----~~~~~lil~P~~~l~~q~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~   98 (374)
                      ..++++-+|||+|||+.+.+++..     ...++++++|-++|+.....++...    |++..-..+......    ..-
T Consensus       943 d~~~~~g~ptgsgkt~~ae~a~~~~~~~~p~~kvvyIap~kalvker~~Dw~~r~~~~g~k~ie~tgd~~pd~----~~v 1018 (1230)
T KOG0952|consen  943 DLNFLLGAPTGSGKTVVAELAIFRALSYYPGSKVVYIAPDKALVKERSDDWSKRDELPGIKVIELTGDVTPDV----KAV 1018 (1230)
T ss_pred             chhhhhcCCccCcchhHHHHHHHHHhccCCCccEEEEcCCchhhcccccchhhhcccCCceeEeccCccCCCh----hhe
Confidence            356789999999999999887764     3789999999999988766665543    555555555443331    112


Q ss_pred             CCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcc-cCcchHHHHHHHHHHH-hcCCCCeeEEEeecCcccH
Q 037567           99 GYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEW-GHDFRLEYKQLDKLRT-FLLGVPFVALTATATEKVR  176 (374)
Q Consensus        99 ~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~-~~~~~~~~~~~~~~~~-~~~~~~~i~~SaT~~~~~~  176 (374)
                      ...+++|+||++.....++|.....+.++..+|+||.|.+.+. |.-........+.+.. .-+..+.+++|--+...  
T Consensus      1019 ~~~~~~ittpek~dgi~Rsw~~r~~v~~v~~iv~de~hllg~~rgPVle~ivsr~n~~s~~t~~~vr~~glsta~~na-- 1096 (1230)
T KOG0952|consen 1019 READIVITTPEKWDGISRSWQTRKYVQSVSLIVLDEIHLLGEDRGPVLEVIVSRMNYISSQTEEPVRYLGLSTALANA-- 1096 (1230)
T ss_pred             ecCceEEcccccccCccccccchhhhccccceeecccccccCCCcceEEEEeeccccCccccCcchhhhhHhhhhhcc--
Confidence            3358999999999999999889999999999999999998652 3221111111111111 11234556665333332  


Q ss_pred             HHHHHhcCCCCCeEEEeccCCCceeEEEEee------cCCcchHHHHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHH-
Q 037567          177 IDIINSLKLKNPYVTIASFDRKNLFYGVKVI------NRGQSFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALK-  249 (374)
Q Consensus       177 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~-  249 (374)
                      .++..|++..+..-..++.........+.-+      ......-.. ....++...+..+++||+.+......-+..|- 
T Consensus      1097 ~dla~wl~~~~~~nf~~svrpvp~~~~i~gfp~~~~cprm~smnkp-a~qaik~~sp~~p~lifv~srrqtrlta~~li~ 1175 (1230)
T KOG0952|consen 1097 NDLADWLNIKDMYNFRPSVRPVPLEVHIDGFPGQHYCPRMMSMNKP-AFQAIKTHSPIKPVLIFVSSRRQTRLTALDLIA 1175 (1230)
T ss_pred             HHHHHHhCCCCcCCCCcccccCCceEeecCCCchhcchhhhhcccH-HHHHHhcCCCCCceEEEeecccccccchHhHHh
Confidence            2678888877662222222222222222211      121222222 33344555688999999998775443333332 


Q ss_pred             ---HcCCceeeeecCCChHHHHHHHHhhhcCCe
Q 037567          250 ---QLGVKAGTYHGQMGSKAREEAHRLFIRDEI  279 (374)
Q Consensus       250 ---~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~  279 (374)
                         ...-+..+++.+  ..+-+.++....+...
T Consensus      1176 ~~~~~~~p~~fl~~d--e~e~e~~~~~~~d~~L 1206 (1230)
T KOG0952|consen 1176 SCATEDNPKQFLNMD--ELELEIIMSKVRDTNL 1206 (1230)
T ss_pred             hccCCCCchhccCCC--HHHHHHHHHHhcccch
Confidence               222223344433  5566666666655443

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

Probab=98.90  E-value=1.9e-08  Score=97.43  Aligned_cols=45  Identities=24%  Similarity=0.279  Sum_probs=42.3

Q ss_pred             CeeEEEEeccccccccccCccEEEEECCCCChhHHHHhhccCCCC
Q 037567          278 EIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRD  322 (374)
Q Consensus       278 ~~~ilv~t~~~~~G~d~~~~~~vi~~~~p~s~~~~~Q~~GR~~R~  322 (374)
                      ..+.+++-+++.+|+|.|++-.++.+....|...-.|.+||..|.
T Consensus       501 ~~~fifs~~al~egwd~~~~~~~~~l~~~~s~~~~~q~~gr~lr~  545 (986)
T PRK15483        501 TRRFLFSKWTLREGWDNPNVFQIAKLRSSGSETSKLQEVGRGLRL  545 (986)
T ss_pred             CeEEEEEhHHhhhcCCCCCeEEEEEeccCCchHHHHHHhccceec
Confidence            678999999999999999999999999888999999999999996

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

Probab=98.83  E-value=1.8e-08  Score=84.90  Aligned_cols=63  Identities=25%  Similarity=0.348  Sum_probs=48.6

Q ss_pred             CCchhHHHHHHHHHcCCC-EEEEccCCCCchhhh--hcc-c--------cccCCcEEEEcchHHHHHHHHHHHHH
Q 037567           13 VFRPYQKDVIQRIIEKRD-CLVVMATGSGKSLCY--QLP-P--------LVTGKTALVVSPLISLMQDQVMSLKQ   75 (374)
Q Consensus        13 ~~~~~Q~~~~~~~~~~~~-~l~~a~tGsGKT~~~--~l~-~--------~~~~~~~lil~P~~~l~~q~~~~~~~   75 (374)
                      ++.+.|.+|+..++.... .++.||+|+|||.+.  ++. +        ...+.++|+++|+...+++..+.+.+
T Consensus         1 ~ln~~Q~~Ai~~~~~~~~~~~i~GpPGTGKT~~l~~~i~~~~~~~~~~~~~~~~~il~~~~sN~avd~~~~~l~~   75 (236)
T PF13086_consen    1 KLNESQREAIQSALSSNGITLIQGPPGTGKTTTLASIIAQLLQRFKSRSADRGKKILVVSPSNAAVDNILERLKK   75 (236)
T ss_dssp             ---HHHHHHHHHHCTSSE-EEEE-STTSSHHHHHHHHHHHH-------HCCCSS-EEEEESSHHHHHHHHHHHHC
T ss_pred             CCCHHHHHHHHHHHcCCCCEEEECCCCCChHHHHHHHHHHhccchhhhhhhccccceeecCCchhHHHHHHHHHh
Confidence            467899999999999888 899999999999432  222 2        34688999999999999999988877

>PF13307 Helicase_C_2: Helicase C-terminal domain; PDB: 4A15_A 2VSF_A 3CRV_A 3CRW_1 2VL7_A

Probab=98.82  E-value=3.1e-08  Score=78.22  Aligned_cols=107  Identities=26%  Similarity=0.345  Sum_probs=75.6

Q ss_pred             CCCcEEEEecchhHHHHHHHHHHHcCC--ceeeeecCCChHHHHHHHHhhhcCCeeEEEEec--cccccccccC--ccEE
Q 037567          227 GAGSIIVYCMTIKDVEEISKALKQLGV--KAGTYHGQMGSKAREEAHRLFIRDEIRVMVATM--AFGMGIDKPD--VRHV  300 (374)
Q Consensus       227 ~~~~~lVf~~~~~~~~~l~~~l~~~~~--~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~--~~~~G~d~~~--~~~v  300 (374)
                      ..++++||+++....+.+.+.++....  ....+..  +..+...+++.|..++-.||+++.  .+++|+|+|+  ++.|
T Consensus         8 ~~g~~lv~f~Sy~~l~~~~~~~~~~~~~~~~~v~~q--~~~~~~~~l~~~~~~~~~il~~v~~g~~~EGiD~~~~~~r~v   85 (167)
T PF13307_consen    8 VPGGVLVFFPSYRRLEKVYERLKERLEEKGIPVFVQ--GSKSRDELLEEFKRGEGAILLAVAGGSFSEGIDFPGDLLRAV   85 (167)
T ss_dssp             CSSEEEEEESSHHHHHHHHTT-TSS-E-ETSCEEES--TCCHHHHHHHHHCCSSSEEEEEETTSCCGSSS--ECESEEEE
T ss_pred             CCCCEEEEeCCHHHHHHHHHHHHhhcccccceeeec--CcchHHHHHHHHHhccCeEEEEEecccEEEeecCCCchhhee
Confidence            459999999999999999999986532  1223332  366888999999999989999999  9999999998  7789


Q ss_pred             EEECCCCC------------------------------hhHHHHhhccCCCCCCceEEEEEeecc
Q 037567          301 IHYGCPKT------------------------------LESYYQESGRCGRDGIASVCWLYYARS  335 (374)
Q Consensus       301 i~~~~p~s------------------------------~~~~~Q~~GR~~R~~~~g~~~~~~~~~  335 (374)
                      |..+.|..                              .....|.+||+-|..++-.+++++++.
T Consensus        86 ii~glPfp~~~d~~~~~~~~~~~~~~~~~~~~~~~~~a~~~l~Qa~GR~iR~~~D~g~i~llD~R  150 (167)
T PF13307_consen   86 IIVGLPFPPPSDPLVQAKREYLDKQGKNPFRDWYLPPAIRKLKQAIGRLIRSEDDYGVIILLDSR  150 (167)
T ss_dssp             EEES-----TTCHHHHHHHHHHHHCCTTCHHHHTHHHHHHHHHHHHHCC--STT-EEEEEEESGG
T ss_pred             eecCCCCCCCCCHHHHHHHHHHHHHhccchhhHhhHHHHHHHhhhcCcceeccCCcEEEEEEcCc
Confidence            98888841                              233478899999987766566666553

>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=98.72  E-value=2.7e-08  Score=83.39  Aligned_cols=132  Identities=20%  Similarity=0.198  Sum_probs=86.7

Q ss_pred             hhHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc---cCCcEEEEcchHHHHHHHHHHHH----
Q 037567            2 VSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV---TGKTALVVSPLISLMQDQVMSLK----   74 (374)
Q Consensus         2 ~~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~---~~~~~lil~P~~~l~~q~~~~~~----   74 (374)
                      .++.++..|+. |++.|.-+.-.+.+|+  ++...||-|||++..+++..   .+..|-|++.+..|+..-++++.    
T Consensus        67 rea~~r~~g~~-p~~vQll~~l~L~~G~--laEm~TGEGKTli~~l~a~~~AL~G~~V~vvT~NdyLA~RD~~~~~~~y~  143 (266)
T PF07517_consen   67 REAARRTLGLR-PYDVQLLGALALHKGR--LAEMKTGEGKTLIAALPAALNALQGKGVHVVTSNDYLAKRDAEEMRPFYE  143 (266)
T ss_dssp             HHHHHHHTS-----HHHHHHHHHHHTTS--EEEESTTSHHHHHHHHHHHHHHTTSS-EEEEESSHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCc-ccHHHHhhhhhcccce--eEEecCCCCcHHHHHHHHHHHHHhcCCcEEEeccHHHhhccHHHHHHHHH
Confidence            35566777874 8899988888876666  99999999999887666543   58889999999999986666554    


Q ss_pred             HcCCceEEcCCCCCchhhhhhhhcCCeeEEEEcCccccc-CchhhH----HHHHhcCccEEEEeccchhh
Q 037567           75 QRGINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACI-IPISFW----SKLLKAGVCLFAVDEAHCIS  139 (374)
Q Consensus        75 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~-~~~~~~----~~~~~~~~~~vviDE~h~~~  139 (374)
                      .+|+.+.............   ....++|+++|...+.. +++...    ......+++++||||++.+.
T Consensus       144 ~LGlsv~~~~~~~~~~~r~---~~Y~~dI~Y~t~~~~~fD~Lrd~~~~~~~~~~~r~~~~~ivDEvDs~L  210 (266)
T PF07517_consen  144 FLGLSVGIITSDMSSEERR---EAYAADIVYGTNSEFGFDYLRDNLALSKNEQVQRGFDFAIVDEVDSIL  210 (266)
T ss_dssp             HTT--EEEEETTTEHHHHH---HHHHSSEEEEEHHHHHHHHHHHTT-SSGGG--SSSSSEEEECTHHHHT
T ss_pred             HhhhccccCccccCHHHHH---HHHhCcccccccchhhHHHHHHHHhhccchhccCCCCEEEEeccceEE
Confidence            4688888877655433221   22346899999986643 111100    11123678899999999874

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 ....

>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]

Probab=98.72  E-value=5.5e-08  Score=91.29  Aligned_cols=307  Identities=16%  Similarity=0.167  Sum_probs=176.7

Q ss_pred             hHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc----c----CCcEEEEcchHHHHHHHHHHHHHc-CCceEEcCCCC
Q 037567           17 YQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV----T----GKTALVVSPLISLMQDQVMSLKQR-GINAEFLGSAQ   87 (374)
Q Consensus        17 ~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~----~----~~~~lil~P~~~l~~q~~~~~~~~-~~~~~~~~~~~   87 (374)
                      +-+.+++.+..+.-+++.+.||+|||.-+.--++.    +    ...+.+.-|++-.+.-+.+++.+- +-..+-..+..
T Consensus       382 ~~~~i~q~v~dn~v~~I~getgcgk~tq~aq~iLe~~~~ns~g~~~na~v~qprrisaisiaerva~er~e~~g~tvgy~  461 (1282)
T KOG0921|consen  382 YRSEILQAVAENRVVIIKGETGCGKSTQVAQFLLESFLENSNGASFNAVVSQPRRISAISLAERVANERGEEVGETCGYN  461 (1282)
T ss_pred             HHHHHHHHHhcCceeeEeecccccchhHHHHHHHHHHhhccccccccceeccccccchHHHHHHHHHhhHHhhccccccc
Confidence            44566667777788899999999999554333332    1    345677778887777777666532 11111111111


Q ss_pred             CchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHHhcCCCCeeEE
Q 037567           88 TDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVAL  167 (374)
Q Consensus        88 ~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~  167 (374)
                      ........  ...-.|+.+|.+-+.+...+     -+..+.++++||.|...-.+.   .....+..+....+....++|
T Consensus       462 vRf~Sa~p--rpyg~i~fctvgvllr~~e~-----glrg~sh~i~deiherdv~~d---fll~~lr~m~~ty~dl~v~lm  531 (1282)
T KOG0921|consen  462 VRFDSATP--RPYGSIMFCTVGVLLRMMEN-----GLRGISHVIIDEIHERDVDTD---FVLIVLREMISTYRDLRVVLM  531 (1282)
T ss_pred             cccccccc--ccccceeeeccchhhhhhhh-----cccccccccchhhhhhccchH---HHHHHHHhhhccchhhhhhhh
Confidence            11111110  01125888999887766443     345677999999998643332   122333444555556778888


Q ss_pred             EeecCcccHHHHHHhc-------------------CCCCCeEEEeccCCCc----------eeE-----EEEeec-----
Q 037567          168 TATATEKVRIDIINSL-------------------KLKNPYVTIASFDRKN----------LFY-----GVKVIN-----  208 (374)
Q Consensus       168 SaT~~~~~~~~~~~~~-------------------~~~~~~~~~~~~~~~~----------~~~-----~~~~~~-----  208 (374)
                      |||........+....                   ..... ...++.....          ...     ......     
T Consensus       532 satIdTd~f~~~f~~~p~~~~~grt~pvq~F~led~~~~~-~~vp~~~~~~k~k~~~~~~~~~~ddK~~n~n~~~dd~~~  610 (1282)
T KOG0921|consen  532 SATIDTDLFTNFFSSIPDVTVHGRTFPVQSFFLEDIIQMT-QFVPSEPSQKKRKKDDDEEDEEVDDKGRNMNILCDPSYN  610 (1282)
T ss_pred             hcccchhhhhhhhccccceeeccccccHHHHHHHHhhhhh-hccCCCcCccchhhcccccCchhhhcccccccccChhhc
Confidence            8886654322111100                   00000 0000000000          000     000000     


Q ss_pred             ----------CCcchHHHHHHHHHHhh---cCCCcEEEEecchhHHHHHHHHHHHc-------CCceeeeecCCChHHHH
Q 037567          209 ----------RGQSFVDELVQEILKSV---AGAGSIIVYCMTIKDVEEISKALKQL-------GVKAGTYHGQMGSKARE  268 (374)
Q Consensus       209 ----------~~~~~~~~~~~~~~~~~---~~~~~~lVf~~~~~~~~~l~~~l~~~-------~~~~~~~~~~~~~~~r~  268 (374)
                                ........++..++...   .-.+-++||.+.....-.|...+...       .+.....|+.....+..
T Consensus       611 ~~~~~am~~~se~d~~f~l~Eal~~~i~s~~i~gailvflpgwa~i~~L~~~ll~~~~fg~~~~y~ilp~Hsq~~~~eqr  690 (1282)
T KOG0921|consen  611 ESTRTAMSRLSEKDIPFGLIEALLNDIASRNIDGAVLVFLPGWAEIMTLCNRLLEHQEFGQANKYEILPLHSQLTSQEQR  690 (1282)
T ss_pred             chhhhhhhcchhhcchhHHHHHHHhhhcccCCccceeeecCchHHhhhhhhhhhhhhhhccchhcccccchhhcccHhhh
Confidence                      00011112222222222   23467999999999999988888664       34577889988888888


Q ss_pred             HHHHhhhcCCeeEEEEeccccccccccCccEEEEECCC------------------CChhHHHHhhccCCCCCCceEEEE
Q 037567          269 EAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCP------------------KTLESYYQESGRCGRDGIASVCWL  330 (374)
Q Consensus       269 ~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~~~~p------------------~s~~~~~Q~~GR~~R~~~~g~~~~  330 (374)
                      ++.+....|..+++++|.+....+.+.++..|++...-                  .|....+||.||+||.. +|.|+.
T Consensus       691 kvf~~~p~gv~kii~stniaetsiTidd~v~vid~cka~~~~~~s~nn~~~~Atvw~sktn~eqr~gr~grvR-~G~~f~  769 (1282)
T KOG0921|consen  691 KVFEPVPEGVTKIILSTNIAETSITIDDVVYVIDSCKAKEKLFTSHNNMTHYATVWASKTNLEQRKGRAGRVR-PGFCFH  769 (1282)
T ss_pred             hccCcccccccccccccceeeEeeeecceeEEEeeeeeeeeeeccccceeeeeeecccccchHhhcccCceec-cccccc
Confidence            88888888999999999999998888776666533211                  25677899999999974 666776


Q ss_pred             Eeecc
Q 037567          331 YYARS  335 (374)
Q Consensus       331 ~~~~~  335 (374)
                      +...-
T Consensus       770 lcs~a  774 (1282)
T KOG0921|consen  770 LCSRA  774 (1282)
T ss_pred             ccHHH
Confidence            66553

>KOG1802 consensus RNA helicase nonsense mRNA reducing factor (pNORF1) [RNA processing and modification]

Probab=98.70  E-value=5.8e-08  Score=88.33  Aligned_cols=81  Identities=12%  Similarity=0.188  Sum_probs=67.6

Q ss_pred             hHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhcccc----ccCCcEEEEcchHHHHHHHHHHHHHcCC
Q 037567            3 STLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPL----VTGKTALVVSPLISLMQDQVMSLKQRGI   78 (374)
Q Consensus         3 ~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~----~~~~~~lil~P~~~l~~q~~~~~~~~~~   78 (374)
                      +.|.. +++.++..-|..|..++++..-.++.||+|+|||.+....+.    +...++|+++|+...++|..+.+.+-|+
T Consensus       401 ~~~s~-~~lpkLN~SQ~~AV~~VL~rplsLIQGPPGTGKTvtsa~IVyhl~~~~~~~VLvcApSNiAVDqLaeKIh~tgL  479 (935)
T KOG1802|consen  401 RRFSV-PNLPKLNASQSNAVKHVLQRPLSLIQGPPGTGKTVTSATIVYHLARQHAGPVLVCAPSNIAVDQLAEKIHKTGL  479 (935)
T ss_pred             hhhcC-CCchhhchHHHHHHHHHHcCCceeeecCCCCCceehhHHHHHHHHHhcCCceEEEcccchhHHHHHHHHHhcCc
Confidence            44444 889999999999999999999999999999999966433322    3588999999999999999999998887


Q ss_pred             ceEEcC
Q 037567           79 NAEFLG   84 (374)
Q Consensus        79 ~~~~~~   84 (374)
                      ++..+.
T Consensus       480 KVvRl~  485 (935)
T KOG1802|consen  480 KVVRLC  485 (935)
T ss_pred             eEeeee
Confidence            775443

>PF13872 AAA_34: P-loop containing NTP hydrolase pore-1

Probab=98.70  E-value=8.7e-08  Score=80.55  Aligned_cols=161  Identities=17%  Similarity=0.031  Sum_probs=100.2

Q ss_pred             CCchhHHHHHHHHHc----------CCCEEEEccCCCCchhhhhccccc----cCCcEEEEcchHHHHHHHHHHHHHcCC
Q 037567           13 VFRPYQKDVIQRIIE----------KRDCLVVMATGSGKSLCYQLPPLV----TGKTALVVSPLISLMQDQVMSLKQRGI   78 (374)
Q Consensus        13 ~~~~~Q~~~~~~~~~----------~~~~l~~a~tGsGKT~~~~l~~~~----~~~~~lil~P~~~l~~q~~~~~~~~~~   78 (374)
                      .+...|.+++-...+          ...+++-..||.||-....-.++.    -.++.++++.+.+|..+..++++..|.
T Consensus        37 ~LS~~QLEaV~yA~q~h~~~Lp~~~R~Gf~lGDGtGvGKGR~iAgiI~~n~l~Gr~r~vwvS~s~dL~~Da~RDl~DIG~  116 (303)
T PF13872_consen   37 LLSALQLEAVIYACQRHEQILPGGSRAGFFLGDGTGVGKGRQIAGIILENWLRGRKRAVWVSVSNDLKYDAERDLRDIGA  116 (303)
T ss_pred             cccHHHHHHHHHHHHHHHhhcccccCcEEEeccCCCcCccchhHHHHHHHHHcCCCceEEEECChhhhhHHHHHHHHhCC
Confidence            478889888866543          234566666999999654444433    356799999999999999999998765


Q ss_pred             ceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCch------hhHHHH---HhcCc-cEEEEeccchhhcccCc---c
Q 037567           79 NAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPI------SFWSKL---LKAGV-CLFAVDEAHCISEWGHD---F  145 (374)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~------~~~~~~---~~~~~-~~vviDE~h~~~~~~~~---~  145 (374)
                      ....+..-........  ..-...|+++|+..|..-..      .....+   ....+ .+||+||||...+....   .
T Consensus       117 ~~i~v~~l~~~~~~~~--~~~~~GvlF~TYs~L~~~~~~~~~~~sRl~ql~~W~g~dfdgvivfDEcH~akn~~~~~~~~  194 (303)
T PF13872_consen  117 DNIPVHPLNKFKYGDI--IRLKEGVLFSTYSTLISESQSGGKYRSRLDQLVDWCGEDFDGVIVFDECHKAKNLSSGSKKP  194 (303)
T ss_pred             CcccceechhhccCcC--CCCCCCccchhHHHHHhHHhccCCccchHHHHHHHHhcCCCceEEeccchhcCCCCccCccc
Confidence            4322211111110000  11133699999988765421      111211   11222 48999999998663221   1


Q ss_pred             hHHHHHHHHHHHhcCCCCeeEEEeecCccc
Q 037567          146 RLEYKQLDKLRTFLLGVPFVALTATATEKV  175 (374)
Q Consensus       146 ~~~~~~~~~~~~~~~~~~~i~~SaT~~~~~  175 (374)
                      ...-....++.+.+|+.+++++|||...+.
T Consensus       195 sk~g~avl~LQ~~LP~ARvvY~SATgasep  224 (303)
T PF13872_consen  195 SKTGIAVLELQNRLPNARVVYASATGASEP  224 (303)
T ss_pred             cHHHHHHHHHHHhCCCCcEEEecccccCCC
Confidence            122245566778889999999999977654

>COG3587 Restriction endonuclease [Defense mechanisms]

Probab=98.69  E-value=3.6e-07  Score=85.71  Aligned_cols=46  Identities=26%  Similarity=0.306  Sum_probs=42.7

Q ss_pred             CCeeEEEEeccccccccccCccEEEEECCCCChhHHHHhhccCCCC
Q 037567          277 DEIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRD  322 (374)
Q Consensus       277 g~~~ilv~t~~~~~G~d~~~~~~vi~~~~p~s~~~~~Q~~GR~~R~  322 (374)
                      ...+.+++-.++-+|+|-|++-.++-+....|...-.|-+||..|.
T Consensus       482 ~plRFIFS~waLrEGWDNPNVFtIckL~~S~SeiSK~QeVGRGLRL  527 (985)
T COG3587         482 EPLRFIFSKWALREGWDNPNVFTICKLRSSGSEISKLQEVGRGLRL  527 (985)
T ss_pred             CcceeeeehhHHhhcCCCCCeeEEEEecCCCcchHHHHHhccceee
Confidence            3478999999999999999999999999999999999999999995

>smart00488 DEXDc2 DEAD-like helicases superfamily

Probab=98.62  E-value=6.9e-08  Score=83.20  Aligned_cols=68  Identities=21%  Similarity=0.327  Sum_probs=55.5

Q ss_pred             HcCCCCCchhHHHHHHH----HHcCCCEEEEccCCCCchhhhhccccc----cCC-----cEEEEcchHHHHHHHHHHHH
Q 037567            8 YFGYSVFRPYQKDVIQR----IIEKRDCLVVMATGSGKSLCYQLPPLV----TGK-----TALVVSPLISLMQDQVMSLK   74 (374)
Q Consensus         8 ~~~~~~~~~~Q~~~~~~----~~~~~~~l~~a~tGsGKT~~~~l~~~~----~~~-----~~lil~P~~~l~~q~~~~~~   74 (374)
                      .|+|. ++|.|.+.+..    +.+++++++.||||+|||++++.+++.    ...     +++|+++|..+..|...+++
T Consensus         4 ~FPy~-~r~~Q~~~m~~v~~~~~~~~~~~~eapTGtGKTl~~L~~al~~~~~~~~~~~~~kvi~~t~T~~~~~q~i~~l~   82 (289)
T smart00488        4 YFPYE-PYPIQYEFMEELKRVLDRGKIGILESPTGTGKTLSLLCLTLTWLRSFPERIQKIKLIYLSRTVSEIEKRLEELR   82 (289)
T ss_pred             cCCCC-CCHHHHHHHHHHHHHHHcCCcEEEECCCCcchhHHHHHHHHHHHHhCcccccccceeEEeccHHHHHHHHHHHH
Confidence            37886 69999995554    446889999999999999999988752    222     89999999999999888887


Q ss_pred             Hc
Q 037567           75 QR   76 (374)
Q Consensus        75 ~~   76 (374)
                      +.
T Consensus        83 ~~   84 (289)
T smart00488       83 KL   84 (289)
T ss_pred             hc
Confidence            65

>smart00489 DEXDc3 DEAD-like helicases superfamily

Probab=98.62  E-value=6.9e-08  Score=83.20  Aligned_cols=68  Identities=21%  Similarity=0.327  Sum_probs=55.5

Q ss_pred             HcCCCCCchhHHHHHHH----HHcCCCEEEEccCCCCchhhhhccccc----cCC-----cEEEEcchHHHHHHHHHHHH
Q 037567            8 YFGYSVFRPYQKDVIQR----IIEKRDCLVVMATGSGKSLCYQLPPLV----TGK-----TALVVSPLISLMQDQVMSLK   74 (374)
Q Consensus         8 ~~~~~~~~~~Q~~~~~~----~~~~~~~l~~a~tGsGKT~~~~l~~~~----~~~-----~~lil~P~~~l~~q~~~~~~   74 (374)
                      .|+|. ++|.|.+.+..    +.+++++++.||||+|||++++.+++.    ...     +++|+++|..+..|...+++
T Consensus         4 ~FPy~-~r~~Q~~~m~~v~~~~~~~~~~~~eapTGtGKTl~~L~~al~~~~~~~~~~~~~kvi~~t~T~~~~~q~i~~l~   82 (289)
T smart00489        4 YFPYE-PYPIQYEFMEELKRVLDRGKIGILESPTGTGKTLSLLCLTLTWLRSFPERIQKIKLIYLSRTVSEIEKRLEELR   82 (289)
T ss_pred             cCCCC-CCHHHHHHHHHHHHHHHcCCcEEEECCCCcchhHHHHHHHHHHHHhCcccccccceeEEeccHHHHHHHHHHHH
Confidence            37886 69999995554    446889999999999999999988752    222     89999999999999888887


Q ss_pred             Hc
Q 037567           75 QR   76 (374)
Q Consensus        75 ~~   76 (374)
                      +.
T Consensus        83 ~~   84 (289)
T smart00489       83 KL   84 (289)
T ss_pred             hc
Confidence            65

>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]

Probab=98.51  E-value=1.5e-07  Score=89.15  Aligned_cols=103  Identities=18%  Similarity=0.140  Sum_probs=90.7

Q ss_pred             CcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCC-ee-EEEEeccccccccccCccEEEEECCC
Q 037567          229 GSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDE-IR-VMVATMAFGMGIDKPDVRHVIHYGCP  306 (374)
Q Consensus       229 ~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~-~~-ilv~t~~~~~G~d~~~~~~vi~~~~p  306 (374)
                      .+++||+.-...+..+.-.+...++....+.|.++...|.+.+..|..+. .. .+++..+.+.|+|+..+.+|+..++=
T Consensus       540 ~kiiifsq~~~~l~l~~~~l~~~~~~~~~~~g~~~~~~r~~s~~~~~~~~~~~vll~Slkag~~glnlt~a~~v~~~d~~  619 (674)
T KOG1001|consen  540 PKIVIFSQLIWGLALVCLRLFFKGFVFLRYDGEMLMKIRTKSFTDFPCDPLVTALLMSLKAGKVGLNLTAASHVLLMDPW  619 (674)
T ss_pred             CceeeehhHHHHHHHhhhhhhhcccccchhhhhhHHHHHHhhhcccccCccHHHHHHHHHHhhhhhchhhhhHHHhhchh
Confidence            48999999999999999888888888889999999999999999999654 23 44577789999999999999999999


Q ss_pred             CChhHHHHhhccCCCCCCceEEEEE
Q 037567          307 KTLESYYQESGRCGRDGIASVCWLY  331 (374)
Q Consensus       307 ~s~~~~~Q~~GR~~R~~~~g~~~~~  331 (374)
                      +++....|.+-|+.|.|+...+.+.
T Consensus       620 wnp~~eeQaidR~hrigq~k~v~v~  644 (674)
T KOG1001|consen  620 WNPAVEEQAIDRAHRIGQTKPVKVS  644 (674)
T ss_pred             cChHHHHHHHHHHHHhcccceeeee
Confidence            9999999999999999998776653

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

Probab=98.47  E-value=6.3e-07  Score=72.75  Aligned_cols=59  Identities=14%  Similarity=0.208  Sum_probs=43.0

Q ss_pred             CchhHHHHHHHHHcCC--CEEEEccCCCCchhhhhcc---ccccCCcEEEEcchHHHHHHHHHH
Q 037567           14 FRPYQKDVIQRIIEKR--DCLVVMATGSGKSLCYQLP---PLVTGKTALVVSPLISLMQDQVMS   72 (374)
Q Consensus        14 ~~~~Q~~~~~~~~~~~--~~l~~a~tGsGKT~~~~l~---~~~~~~~~lil~P~~~l~~q~~~~   72 (374)
                      |++-|.+++..++.++  -.++.|++|+|||.+....   +...+.++++++||...+....+.
T Consensus         2 L~~~Q~~a~~~~l~~~~~~~~l~G~aGtGKT~~l~~~~~~~~~~g~~v~~~apT~~Aa~~L~~~   65 (196)
T PF13604_consen    2 LNEEQREAVRAILTSGDRVSVLQGPAGTGKTTLLKALAEALEAAGKRVIGLAPTNKAAKELREK   65 (196)
T ss_dssp             S-HHHHHHHHHHHHCTCSEEEEEESTTSTHHHHHHHHHHHHHHTT--EEEEESSHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHhcCCeEEEEEECCCCCHHHHHHHHHHHHHhCCCeEEEECCcHHHHHHHHHh
Confidence            6789999999997644  4678899999999753221   123578999999999998886666

>KOG1803 consensus DNA helicase [Replication, recombination and repair]

Probab=98.37  E-value=1.2e-06  Score=79.56  Aligned_cols=62  Identities=19%  Similarity=0.185  Sum_probs=50.2

Q ss_pred             CCchhHHHHHHHHHcCC-CEEEEccCCCCchhhhhcc---ccccCCcEEEEcchHHHHHHHHHHHH
Q 037567           13 VFRPYQKDVIQRIIEKR-DCLVVMATGSGKSLCYQLP---PLVTGKTALVVSPLISLMQDQVMSLK   74 (374)
Q Consensus        13 ~~~~~Q~~~~~~~~~~~-~~l~~a~tGsGKT~~~~l~---~~~~~~~~lil~P~~~l~~q~~~~~~   74 (374)
                      .+.+-|.+|+......+ -.+++||||+|||.+....   ++.++.++|+++||...++...+.+.
T Consensus       185 ~ln~SQk~Av~~~~~~k~l~~I~GPPGTGKT~TlvEiI~qlvk~~k~VLVcaPSn~AVdNiverl~  250 (649)
T KOG1803|consen  185 NLNSSQKAAVSFAINNKDLLIIHGPPGTGKTRTLVEIISQLVKQKKRVLVCAPSNVAVDNIVERLT  250 (649)
T ss_pred             cccHHHHHHHHHHhccCCceEeeCCCCCCceeeHHHHHHHHHHcCCeEEEEcCchHHHHHHHHHhc
Confidence            57788999998888774 5688999999999764333   33478999999999999999888754

>TIGR00376 DNA helicase, putative

Probab=98.28  E-value=5.1e-06  Score=79.48  Aligned_cols=72  Identities=18%  Similarity=0.161  Sum_probs=56.7

Q ss_pred             CCchhHHHHHHHHHcC-CCEEEEccCCCCchhhhhc---cccccCCcEEEEcchHHHHHHHHHHHHHcCCceEEcC
Q 037567           13 VFRPYQKDVIQRIIEK-RDCLVVMATGSGKSLCYQL---PPLVTGKTALVVSPLISLMQDQVMSLKQRGINAEFLG   84 (374)
Q Consensus        13 ~~~~~Q~~~~~~~~~~-~~~l~~a~tGsGKT~~~~l---~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~   84 (374)
                      .+.+.|.+|+..++.. ...++.||+|+|||.+...   .++..+.++++++||...++++.+.+...+..+..++
T Consensus       157 ~ln~~Q~~Av~~~l~~~~~~lI~GpPGTGKT~t~~~ii~~~~~~g~~VLv~a~sn~Avd~l~e~l~~~~~~vvRlg  232 (637)
T TIGR00376       157 NLNESQKEAVSFALSSKDLFLIHGPPGTGKTRTLVELIRQLVKRGLRVLVTAPSNIAVDNLLERLALCDQKIVRLG  232 (637)
T ss_pred             CCCHHHHHHHHHHhcCCCeEEEEcCCCCCHHHHHHHHHHHHHHcCCCEEEEcCcHHHHHHHHHHHHhCCCcEEEeC
Confidence            5788999999998876 6678999999999965432   2334678999999999999999999987655544443

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.

>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=98.26  E-value=2.4e-06  Score=68.86  Aligned_cols=55  Identities=15%  Similarity=0.164  Sum_probs=36.2

Q ss_pred             CCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc-----cCCcEEEEcchHHH
Q 037567           11 YSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV-----TGKTALVVSPLISL   65 (374)
Q Consensus        11 ~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~-----~~~~~lil~P~~~l   65 (374)
                      +...++.|..++.++...+-+++.||.|||||+.++..+++     ...+++++-|..+.
T Consensus         2 I~p~~~~Q~~~~~al~~~~~v~~~G~AGTGKT~LA~a~Al~~v~~g~~~kiii~Rp~v~~   61 (205)
T PF02562_consen    2 IKPKNEEQKFALDALLNNDLVIVNGPAGTGKTFLALAAALELVKEGEYDKIIITRPPVEA   61 (205)
T ss_dssp             ----SHHHHHHHHHHHH-SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEEEE-S--T
T ss_pred             ccCCCHHHHHHHHHHHhCCeEEEECCCCCcHHHHHHHHHHHHHHhCCCcEEEEEecCCCC
Confidence            45678899999999998888899999999999876655543     34678888887643

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

>KOG1513 consensus Nuclear helicase MOP-3/SNO (DEAD-box superfamily) [Transcription; Signal transduction mechanisms]

Probab=98.20  E-value=1.8e-05  Score=74.08  Aligned_cols=159  Identities=16%  Similarity=0.080  Sum_probs=94.5

Q ss_pred             CCCchhHHHHHHHHHcCC----------CEEEEccCCCCchhhhhccccc----cCCcEEEEcchHHHHHHHHHHHHHcC
Q 037567           12 SVFRPYQKDVIQRIIEKR----------DCLVVMATGSGKSLCYQLPPLV----TGKTALVVSPLISLMQDQVMSLKQRG   77 (374)
Q Consensus        12 ~~~~~~Q~~~~~~~~~~~----------~~l~~a~tGsGKT~~~~l~~~~----~~~~~lil~P~~~l~~q~~~~~~~~~   77 (374)
                      ..+...|.+++-...+.+          .+++-...|.||-.+..-.++.    -.+++|++.-+.+|--+..+++...|
T Consensus       263 g~lSALQLEav~YAcQ~He~llPsG~RaGfLiGDGAGVGKGRTvAgiIfeNyLkGRKrAlW~SVSsDLKfDAERDL~Dig  342 (1300)
T KOG1513|consen  263 GHLSALQLEAVTYACQAHEVLLPSGQRAGFLIGDGAGVGKGRTVAGIIFENYLKGRKRALWFSVSSDLKFDAERDLRDIG  342 (1300)
T ss_pred             cchhHHHHHHHHHHHhhhhhcCCCCccceeeeccCcccCCCceeEEEEehhhhcccceeEEEEeccccccchhhchhhcC
Confidence            357889999987766532          3456555777777554444443    37889999999999999889998775


Q ss_pred             CceEEcCC-CCCchhhhhh--hhcCCeeEEEEcCcccccCchh----h---HH---HHHhcCc-cEEEEeccchhhcc--
Q 037567           78 INAEFLGS-AQTDSSVQTK--AETGYFQLLFMTPEKACIIPIS----F---WS---KLLKAGV-CLFAVDEAHCISEW--  141 (374)
Q Consensus        78 ~~~~~~~~-~~~~~~~~~~--~~~~~~~i~i~T~~~l~~~~~~----~---~~---~~~~~~~-~~vviDE~h~~~~~--  141 (374)
                      ..--.++. .+.+......  ...-.-.++++|+-.|..-.+.    +   ..   .+....+ .+||+||||.-.+-  
T Consensus       343 A~~I~V~alnK~KYakIss~en~n~krGViFaTYtaLIGEs~~~~~kyrtR~rQllqW~Ge~feGvIvfDECHkAKNL~p  422 (1300)
T KOG1513|consen  343 ATGIAVHALNKFKYAKISSKENTNTKRGVIFATYTALIGESQGKGGKYRTRFRQLLQWCGEDFEGVIVFDECHKAKNLVP  422 (1300)
T ss_pred             CCCccceehhhcccccccccccCCccceeEEEeeHhhhhhccccCchHHHHHHHHHHHhhhccceeEEehhhhhhccccc
Confidence            43322211 1111110000  1111236999999876443221    0   11   1112223 48999999986541  


Q ss_pred             --cCcchHHHHHHHHHHHhcCCCCeeEEEee
Q 037567          142 --GHDFRLEYKQLDKLRTFLLGVPFVALTAT  170 (374)
Q Consensus       142 --~~~~~~~~~~~~~~~~~~~~~~~i~~SaT  170 (374)
                        +......-..+..+...+|+.++|+-|||
T Consensus       423 ~~~~k~TKtG~tVLdLQk~LP~ARVVYASAT  453 (1300)
T KOG1513|consen  423 TAGAKSTKTGKTVLDLQKKLPNARVVYASAT  453 (1300)
T ss_pred             ccCCCcCcccHhHHHHHHhCCCceEEEeecc
Confidence              11111111456777888899999999999

>smart00492 HELICc3 helicase superfamily c-terminal domain

Probab=98.20  E-value=2.6e-05  Score=59.35  Aligned_cols=94  Identities=20%  Similarity=0.216  Sum_probs=63.2

Q ss_pred             HHHHHHHHHHcCC------ceeeeecCCChHHHHHHHHhhhcCC-eeEEEEeccccccccccC--ccEEEEECCCC----
Q 037567          241 VEEISKALKQLGV------KAGTYHGQMGSKAREEAHRLFIRDE-IRVMVATMAFGMGIDKPD--VRHVIHYGCPK----  307 (374)
Q Consensus       241 ~~~l~~~l~~~~~------~~~~~~~~~~~~~r~~~~~~f~~g~-~~ilv~t~~~~~G~d~~~--~~~vi~~~~p~----  307 (374)
                      .+.+.+.+++.+.      .-.++..+.+..+...+++.|.... ..||+++..+++|+|+|+  ++.||..+.|.    
T Consensus         4 m~~v~~~~~~~~~~~~l~~~~~i~~e~~~~~~~~~~l~~f~~~~~~~iL~~~~~~~EGiD~~g~~~r~vii~glPfp~~~   83 (141)
T smart00492        4 MESFVQYWKENGILENINKNLLLLVQGEDGKETGKLLEKYVEACENAILLATARFSEGVDFPGDYLRAVIIDGLPFPYPD   83 (141)
T ss_pred             HHHHHHHHHHcCchhhHhcCCeEEEeCCChhHHHHHHHHHHHcCCCEEEEEccceecceecCCCCeeEEEEEecCCCCCC
Confidence            4455555555432      1223333445556788888898754 379999988999999998  56788887663    


Q ss_pred             ---------------------------ChhHHHHhhccCCCCCCceEEEEEeec
Q 037567          308 ---------------------------TLESYYQESGRCGRDGIASVCWLYYAR  334 (374)
Q Consensus       308 ---------------------------s~~~~~Q~~GR~~R~~~~g~~~~~~~~  334 (374)
                                                 ....+.|.+||+-|..++-.+++++++
T Consensus        84 d~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~l~Qa~GR~iR~~~D~g~i~l~D~  137 (141)
T smart00492       84 SPILKARLELLRDKGQIRPFDFVSLPDAMRTLAQCVGRLIRGANDYGVVVIADK  137 (141)
T ss_pred             CHHHHHHHHHHHHhCCCCchhHHHHHHHHHHHHHHhCccccCcCceEEEEEEec
Confidence                                       124558889999998765555555554

>smart00491 HELICc2 helicase superfamily c-terminal domain

Probab=98.20  E-value=2.3e-05  Score=59.69  Aligned_cols=95  Identities=22%  Similarity=0.238  Sum_probs=62.7

Q ss_pred             HHHHHHHHHHHcCC---ceeeeecCCChHHHHHHHHhhhcCCe---eEEEEecc--ccccccccC--ccEEEEECCCC--
Q 037567          240 DVEEISKALKQLGV---KAGTYHGQMGSKAREEAHRLFIRDEI---RVMVATMA--FGMGIDKPD--VRHVIHYGCPK--  307 (374)
Q Consensus       240 ~~~~l~~~l~~~~~---~~~~~~~~~~~~~r~~~~~~f~~g~~---~ilv~t~~--~~~G~d~~~--~~~vi~~~~p~--  307 (374)
                      ..+.+++.+++.+.   ..-.+..+....+...+++.|.+..-   .||+++..  .++|+|+|+  ++.||..+.|.  
T Consensus         3 ~m~~v~~~~~~~~~~~~~~~i~~e~~~~~~~~~~l~~f~~~~~~~g~iL~~v~~G~~~EGiD~~g~~~r~vii~glPfp~   82 (142)
T smart00491        3 YLEQVVEYWKENGILEINKPVFIEGKDSGETEELLEKYSAACEARGALLLAVARGKVSEGIDFPDDLGRAVIIVGIPFPN   82 (142)
T ss_pred             HHHHHHHHHHhcCccccCceEEEECCCCchHHHHHHHHHHhcCCCCEEEEEEeCCeeecceecCCCccEEEEEEecCCCC
Confidence            34556666665432   12223323333455778888887543   68888876  999999999  67888888773  


Q ss_pred             -----------------------------ChhHHHHhhccCCCCCCceEEEEEeec
Q 037567          308 -----------------------------TLESYYQESGRCGRDGIASVCWLYYAR  334 (374)
Q Consensus       308 -----------------------------s~~~~~Q~~GR~~R~~~~g~~~~~~~~  334 (374)
                                                   ......|.+||+-|..++-.++++++.
T Consensus        83 ~~d~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~Qa~GR~iR~~~D~g~i~l~D~  138 (142)
T smart00491       83 PDSPILRARLEYLDEKGGIRPFDEVYLFDAMRALAQAIGRAIRHKNDYGVVVLLDK  138 (142)
T ss_pred             CCCHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHHHHhCccccCccceEEEEEEec
Confidence                                         123457899999998776656666654

>COG3421 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=98.18  E-value=7.3e-06  Score=74.32  Aligned_cols=142  Identities=16%  Similarity=0.112  Sum_probs=71.6

Q ss_pred             EEccCCCCchhhhhccccc---cC-CcEEEEcchHHHHHHHHHHHHH-----cCCceEEc-CCCCCc-hhhh-hhhhcCC
Q 037567           33 VVMATGSGKSLCYQLPPLV---TG-KTALVVSPLISLMQDQVMSLKQ-----RGINAEFL-GSAQTD-SSVQ-TKAETGY  100 (374)
Q Consensus        33 ~~a~tGsGKT~~~~l~~~~---~~-~~~lil~P~~~l~~q~~~~~~~-----~~~~~~~~-~~~~~~-~~~~-~~~~~~~  100 (374)
                      ..++||||||++++..+++   ++ ...|+.|.....++.....+..     +-..-.+. .+.... .... ...-...
T Consensus         2 f~matgsgkt~~ma~lil~~y~kgyr~flffvnq~nilekt~~nftd~~s~kylf~e~i~~~d~~i~ikkvn~fsehnd~   81 (812)
T COG3421           2 FEMATGSGKTLVMAGLILECYKKGYRNFLFFVNQANILEKTKLNFTDSVSSKYLFSENININDENIEIKKVNNFSEHNDA   81 (812)
T ss_pred             cccccCCChhhHHHHHHHHHHHhchhhEEEEecchhHHHHHHhhcccchhhhHhhhhhhhcCCceeeeeeecccCccCCc
Confidence            5689999999887666664   33 4578888887777765554432     10000000 000000 0000 0112345


Q ss_pred             eeEEEEcCcccccCchhhHH-HH---HhcCccE-EEEeccchhhccc----C----cchHHHHHHHHHHHhcCCCCeeEE
Q 037567          101 FQLLFMTPEKACIIPISFWS-KL---LKAGVCL-FAVDEAHCISEWG----H----DFRLEYKQLDKLRTFLLGVPFVAL  167 (374)
Q Consensus       101 ~~i~i~T~~~l~~~~~~~~~-~~---~~~~~~~-vviDE~h~~~~~~----~----~~~~~~~~~~~~~~~~~~~~~i~~  167 (374)
                      ..|.++|.+.|....-+-.. .+   .+....+ ++-||+||+....    .    ..+.+-+.+.-..+.-++.-++.+
T Consensus        82 iei~fttiq~l~~d~~~~ken~itledl~~~klvfl~deahhln~~tkkk~~de~~~~~~we~~v~la~~~nkd~~~lef  161 (812)
T COG3421          82 IEIYFTTIQGLFSDFTRAKENAITLEDLKDQKLVFLADEAHHLNTETKKKLNDEASEKRNWESVVKLALEQNKDNLLLEF  161 (812)
T ss_pred             eEEEEeehHHHHHHHHhhccccccHhhHhhCceEEEechhhhhhhhhhhhcccHHHHHhhHHHHHHHHHhcCCCceeehh
Confidence            68999999877544322111 11   2223333 4559999996311    0    111111222222233345567889


Q ss_pred             EeecCcc
Q 037567          168 TATATEK  174 (374)
Q Consensus       168 SaT~~~~  174 (374)
                      |||.+.+
T Consensus       162 ~at~~k~  168 (812)
T COG3421         162 SATIPKE  168 (812)
T ss_pred             hhcCCcc
Confidence            9998843

>PF13245 AAA_19: Part of AAA domain

Probab=98.08  E-value=5.5e-06  Score=55.54  Aligned_cols=46  Identities=24%  Similarity=0.274  Sum_probs=34.3

Q ss_pred             CCCEEEEccCCCCchhhhhcc---cccc----CCcEEEEcchHHHHHHHHHHH
Q 037567           28 KRDCLVVMATGSGKSLCYQLP---PLVT----GKTALVVSPLISLMQDQVMSL   73 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~l~---~~~~----~~~~lil~P~~~l~~q~~~~~   73 (374)
                      +.-+++.||+|||||.+.+-.   ....    +.++++++|++..+++..+.+
T Consensus        10 ~~~~vv~g~pGtGKT~~~~~~i~~l~~~~~~~~~~vlv~a~t~~aa~~l~~rl   62 (76)
T PF13245_consen   10 SPLFVVQGPPGTGKTTTLAARIAELLAARADPGKRVLVLAPTRAAADELRERL   62 (76)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHHHhcCCCCeEEEECCCHHHHHHHHHHH
Confidence            444566999999999543322   1112    678999999999999988887

>TIGR01447 recD exodeoxyribonuclease V, alpha subunit

Probab=98.05  E-value=2.5e-05  Score=73.81  Aligned_cols=61  Identities=20%  Similarity=0.222  Sum_probs=47.1

Q ss_pred             chhHHHHHHHHHcCCCEEEEccCCCCchhhh--hccccc---c---CCcEEEEcchHHHHHHHHHHHHH
Q 037567           15 RPYQKDVIQRIIEKRDCLVVMATGSGKSLCY--QLPPLV---T---GKTALVVSPLISLMQDQVMSLKQ   75 (374)
Q Consensus        15 ~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~--~l~~~~---~---~~~~lil~P~~~l~~q~~~~~~~   75 (374)
                      .++|..++..++.++-+++.|++|+|||.+.  ++..+.   +   ..++++++||..-+..+.+.+..
T Consensus       147 ~~~Qk~A~~~al~~~~~vitGgpGTGKTt~v~~ll~~l~~~~~~~~~~~I~l~APTGkAA~rL~e~~~~  215 (586)
T TIGR01447       147 QNWQKVAVALALKSNFSLITGGPGTGKTTTVARLLLALVKQSPKQGKLRIALAAPTGKAAARLAESLRK  215 (586)
T ss_pred             cHHHHHHHHHHhhCCeEEEEcCCCCCHHHHHHHHHHHHHHhccccCCCcEEEECCcHHHHHHHHHHHHh
Confidence            3789999999999999999999999999653  222221   1   25799999999888877776654

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.

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

Probab=97.99  E-value=7.6e-06  Score=73.10  Aligned_cols=47  Identities=19%  Similarity=0.157  Sum_probs=36.5

Q ss_pred             CEEEEccCCCCchhhhhccc-----cccCCcEEEEcchHHHHHHHHHHHHHc
Q 037567           30 DCLVVMATGSGKSLCYQLPP-----LVTGKTALVVSPLISLMQDQVMSLKQR   76 (374)
Q Consensus        30 ~~l~~a~tGsGKT~~~~l~~-----~~~~~~~lil~P~~~l~~q~~~~~~~~   76 (374)
                      -++|.|.+|||||+.++-.+     ...+.+++++++...|.......+...
T Consensus         3 v~~I~G~aGTGKTvla~~l~~~l~~~~~~~~~~~l~~n~~l~~~l~~~l~~~   54 (352)
T PF09848_consen    3 VILITGGAGTGKTVLALNLAKELQNSEEGKKVLYLCGNHPLRNKLREQLAKK   54 (352)
T ss_pred             EEEEEecCCcCHHHHHHHHHHHhhccccCCceEEEEecchHHHHHHHHHhhh
Confidence            46889999999997654222     235788999999999999888887654

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

>KOG1131 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, 5'-3' helicase subunit RAD3 [Transcription; Replication, recombination and repair]

Probab=97.96  E-value=5.2e-05  Score=67.82  Aligned_cols=68  Identities=21%  Similarity=0.387  Sum_probs=43.6

Q ss_pred             HhHcCCCCCchhHHHHHHHHH----cCCCEEEEccCCCCchhhhhccccc-------cCCcEEEEcchHHHHHHHHHHH
Q 037567            6 KKYFGYSVFRPYQKDVIQRII----EKRDCLVVMATGSGKSLCYQLPPLV-------TGKTALVVSPLISLMQDQVMSL   73 (374)
Q Consensus         6 ~~~~~~~~~~~~Q~~~~~~~~----~~~~~l~~a~tGsGKT~~~~l~~~~-------~~~~~lil~P~~~l~~q~~~~~   73 (374)
                      .-.|+|+..+|-|-+-.-.+.    .+.++++.+|+|+|||.+.+-.+..       ...+.++...|..-++....++
T Consensus         9 ~v~FPY~~iYPEQ~~YM~elKrsLDakGh~llEMPSGTGKTvsLLSli~aYq~~~p~~~~KliYCSRTvpEieK~l~El   87 (755)
T KOG1131|consen    9 LVYFPYDYIYPEQYEYMRELKRSLDAKGHCLLEMPSGTGKTVSLLSLIIAYQLHYPDEHRKLIYCSRTVPEIEKALEEL   87 (755)
T ss_pred             eEecCCcccCHHHHHHHHHHHHhhccCCcEEEECCCCCCcchHHHHHHHHHHHhCCcccceEEEecCcchHHHHHHHHH
Confidence            345889999998877665544    3678999999999999764322221       2345666655554444444444

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

Probab=97.93  E-value=3.8e-05  Score=66.89  Aligned_cols=104  Identities=18%  Similarity=0.195  Sum_probs=64.0

Q ss_pred             HHHHHHcC---CCEEEEccCCCCchhhhhccccccCCcEEEEcchHHHHHHHHHHHHHcCCceEEcCCCCCchhhhhhhh
Q 037567           21 VIQRIIEK---RDCLVVMATGSGKSLCYQLPPLVTGKTALVVSPLISLMQDQVMSLKQRGINAEFLGSAQTDSSVQTKAE   97 (374)
Q Consensus        21 ~~~~~~~~---~~~l~~a~tGsGKT~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   97 (374)
                      .+..+.++   .+.|++||+|+|||..+.+.+-..+..+.-+..+.+-+.++..-+.+.                     
T Consensus        38 ~lrr~v~~~~l~SmIl~GPPG~GKTTlA~liA~~~~~~f~~~sAv~~gvkdlr~i~e~a---------------------   96 (436)
T COG2256          38 PLRRAVEAGHLHSMILWGPPGTGKTTLARLIAGTTNAAFEALSAVTSGVKDLREIIEEA---------------------   96 (436)
T ss_pred             hHHHHHhcCCCceeEEECCCCCCHHHHHHHHHHhhCCceEEeccccccHHHHHHHHHHH---------------------
Confidence            33444443   367999999999998766655555666666666655555444443321                     


Q ss_pred             cCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHHhcCCCCeeEEEeecCccc
Q 037567           98 TGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEKV  175 (374)
Q Consensus        98 ~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~SaT~~~~~  175 (374)
                                         .  .......=.++++||+|++..         .+...++....+..+++.-||-.++.
T Consensus        97 -------------------~--~~~~~gr~tiLflDEIHRfnK---------~QQD~lLp~vE~G~iilIGATTENPs  144 (436)
T COG2256          97 -------------------R--KNRLLGRRTILFLDEIHRFNK---------AQQDALLPHVENGTIILIGATTENPS  144 (436)
T ss_pred             -------------------H--HHHhcCCceEEEEehhhhcCh---------hhhhhhhhhhcCCeEEEEeccCCCCC
Confidence                               0  000001114799999999865         33345555666788999999865553

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

Probab=97.89  E-value=4.3e-05  Score=57.78  Aligned_cols=18  Identities=28%  Similarity=0.340  Sum_probs=12.3

Q ss_pred             CCCEEEEccCCCCchhhh
Q 037567           28 KRDCLVVMATGSGKSLCY   45 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~   45 (374)
                      ++.+++.|++|+|||...
T Consensus         4 ~~~~~i~G~~G~GKT~~~   21 (131)
T PF13401_consen    4 QRILVISGPPGSGKTTLI   21 (131)
T ss_dssp             ---EEEEE-TTSSHHHHH
T ss_pred             CcccEEEcCCCCCHHHHH
Confidence            456789999999999664

>PRK10875 recD exonuclease V subunit alpha; Provisional

Probab=97.89  E-value=4.1e-05  Score=72.55  Aligned_cols=72  Identities=21%  Similarity=0.212  Sum_probs=52.1

Q ss_pred             HHHhHcCCCC-CchhHHHHHHHHHcCCCEEEEccCCCCchhhh--hccccc-----cCCcEEEEcchHHHHHHHHHHHHH
Q 037567            4 TLKKYFGYSV-FRPYQKDVIQRIIEKRDCLVVMATGSGKSLCY--QLPPLV-----TGKTALVVSPLISLMQDQVMSLKQ   75 (374)
Q Consensus         4 ~l~~~~~~~~-~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~--~l~~~~-----~~~~~lil~P~~~l~~q~~~~~~~   75 (374)
                      .|...|+... ..++|..|+...+.++-.++.|++|+|||.+.  ++..+.     ...++++++||..-+..+.+.+..
T Consensus       142 ~l~~lf~~~~~~~d~Qk~Av~~a~~~~~~vItGgpGTGKTt~v~~ll~~l~~~~~~~~~~i~l~APTgkAA~rL~e~~~~  221 (615)
T PRK10875        142 TLDALFGPVTDEVDWQKVAAAVALTRRISVISGGPGTGKTTTVAKLLAALIQLADGERCRIRLAAPTGKAAARLTESLGK  221 (615)
T ss_pred             HHHHhcCcCCCCCHHHHHHHHHHhcCCeEEEEeCCCCCHHHHHHHHHHHHHHhcCCCCcEEEEECCcHHHHHHHHHHHHh
Confidence            3445554432 35799999999989889999999999999653  222221     134789999999988887776653

>KOG1805 consensus DNA replication helicase [Replication, recombination and repair]

Probab=97.88  E-value=6.3e-05  Score=72.16  Aligned_cols=123  Identities=20%  Similarity=0.165  Sum_probs=86.3

Q ss_pred             CCCCchhHHHHHHHHHcCCCE-EEEccCCCCchhhhhcc---ccccCCcEEEEcchHHHHHHHHHHHHHcCCceEEcCCC
Q 037567           11 YSVFRPYQKDVIQRIIEKRDC-LVVMATGSGKSLCYQLP---PLVTGKTALVVSPLISLMQDQVMSLKQRGINAEFLGSA   86 (374)
Q Consensus        11 ~~~~~~~Q~~~~~~~~~~~~~-l~~a~tGsGKT~~~~l~---~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~   86 (374)
                      +..+..-|.+|+..++..++. ++.|=||+|||.+....   ++..+++||+.+-|...++.....++.+++..-.++..
T Consensus       667 ~~~LN~dQr~A~~k~L~aedy~LI~GMPGTGKTTtI~~LIkiL~~~gkkVLLtsyThsAVDNILiKL~~~~i~~lRLG~~  746 (1100)
T KOG1805|consen  667 LLRLNNDQRQALLKALAAEDYALILGMPGTGKTTTISLLIKILVALGKKVLLTSYTHSAVDNILIKLKGFGIYILRLGSE  746 (1100)
T ss_pred             HhhcCHHHHHHHHHHHhccchheeecCCCCCchhhHHHHHHHHHHcCCeEEEEehhhHHHHHHHHHHhccCcceeecCCc
Confidence            446888999999988887665 77888999999664332   23468999999999999999999999988876555543


Q ss_pred             CCchhhhh----------------hhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhh
Q 037567           87 QTDSSVQT----------------KAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCIS  139 (374)
Q Consensus        87 ~~~~~~~~----------------~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~  139 (374)
                      ........                ....+.+.|+.+|---+..      .-+....|++.|||||-.+.
T Consensus       747 ~kih~~v~e~~~~~~~s~ks~~~l~~~~~~~~IVa~TClgi~~------plf~~R~FD~cIiDEASQI~  809 (1100)
T KOG1805|consen  747 EKIHPDVEEFTLTNETSEKSYADLKKFLDQTSIVACTCLGINH------PLFVNRQFDYCIIDEASQIL  809 (1100)
T ss_pred             cccchHHHHHhcccccchhhHHHHHHHhCCCcEEEEEccCCCc------hhhhccccCEEEEccccccc
Confidence            32222111                1123456788777544432      23334669999999998875

>TIGR01448 recD_rel helicase, putative, RecD/TraA family

Probab=97.85  E-value=8.8e-05  Score=72.27  Aligned_cols=62  Identities=13%  Similarity=0.097  Sum_probs=47.3

Q ss_pred             cCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhh--hccccc-cC--CcEEEEcchHHHHHHHHH
Q 037567            9 FGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCY--QLPPLV-TG--KTALVVSPLISLMQDQVM   71 (374)
Q Consensus         9 ~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~--~l~~~~-~~--~~~lil~P~~~l~~q~~~   71 (374)
                      .++ .+++-|.+|+..+..++-+++.|++|+|||.+.  ++.++. .+  ..+++++||...+..+.+
T Consensus       320 ~~~-~l~~~Q~~Ai~~~~~~~~~iitGgpGTGKTt~l~~i~~~~~~~~~~~~v~l~ApTg~AA~~L~e  386 (720)
T TIGR01448       320 LRK-GLSEEQKQALDTAIQHKVVILTGGPGTGKTTITRAIIELAEELGGLLPVGLAAPTGRAAKRLGE  386 (720)
T ss_pred             cCC-CCCHHHHHHHHHHHhCCeEEEECCCCCCHHHHHHHHHHHHHHcCCCceEEEEeCchHHHHHHHH
Confidence            454 589999999999998888999999999999653  222232 23  678999999887775544

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.

>PRK10536 hypothetical protein; Provisional

Probab=97.72  E-value=0.00015  Score=60.25  Aligned_cols=54  Identities=15%  Similarity=0.123  Sum_probs=38.6

Q ss_pred             CCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhcccc----cc-CCcEEEEcchH
Q 037567           10 GYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPL----VT-GKTALVVSPLI   63 (374)
Q Consensus        10 ~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~----~~-~~~~lil~P~~   63 (374)
                      ++...+..|...+..+.++..+++.||+|+|||+.+...++    .. ..++++.-|..
T Consensus        56 ~i~p~n~~Q~~~l~al~~~~lV~i~G~aGTGKT~La~a~a~~~l~~~~~~kIiI~RP~v  114 (262)
T PRK10536         56 PILARNEAQAHYLKAIESKQLIFATGEAGCGKTWISAAKAAEALIHKDVDRIIVTRPVL  114 (262)
T ss_pred             cccCCCHHHHHHHHHHhcCCeEEEECCCCCCHHHHHHHHHHHHHhcCCeeEEEEeCCCC
Confidence            44566779999999998888889999999999976543332    22 34456665554

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

Probab=97.60  E-value=0.00014  Score=62.64  Aligned_cols=61  Identities=15%  Similarity=0.194  Sum_probs=46.8

Q ss_pred             HhHcCCCCCchhHHHHHHHHHcCC--CEEEEccCCCCchhhhhccccc------cCCcEEEEcchHHHH
Q 037567            6 KKYFGYSVFRPYQKDVIQRIIEKR--DCLVVMATGSGKSLCYQLPPLV------TGKTALVVSPLISLM   66 (374)
Q Consensus         6 ~~~~~~~~~~~~Q~~~~~~~~~~~--~~l~~a~tGsGKT~~~~l~~~~------~~~~~lil~P~~~l~   66 (374)
                      ++++|+......|.-|+..++...  =+.+.++.|||||+.++.+.+.      ...++++.=|+..+.
T Consensus       221 ~~vwGi~prn~eQ~~ALdlLld~dI~lV~L~G~AGtGKTlLALaAgleqv~e~~~y~KiiVtRp~vpvG  289 (436)
T COG1875         221 QEVWGIRPRNAEQRVALDLLLDDDIDLVSLGGKAGTGKTLLALAAGLEQVLERKRYRKIIVTRPTVPVG  289 (436)
T ss_pred             hhhhccCcccHHHHHHHHHhcCCCCCeEEeeccCCccHhHHHHHHHHHHHHHHhhhceEEEecCCcCcc
Confidence            477899888889999998888643  4567899999999887777665      256777777765544

>KOG0298 consensus DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]

Probab=97.53  E-value=6.8e-05  Score=73.87  Aligned_cols=138  Identities=11%  Similarity=0.046  Sum_probs=84.7

Q ss_pred             CCCEEEEccCCCCchhhhhccccc---------------------cCCcEEEEcchHHHHHHHHHHHHHc---CCceEEc
Q 037567           28 KRDCLVVMATGSGKSLCYQLPPLV---------------------TGKTALVVSPLISLMQDQVMSLKQR---GINAEFL   83 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~l~~~~---------------------~~~~~lil~P~~~l~~q~~~~~~~~---~~~~~~~   83 (374)
                      |+++++.-..|.|||...+...+.                     ..+.+||++|. ++..||..++...   ++.+..+
T Consensus       374 g~~~~~ade~~~qk~~~~l~~~l~~~~k~~~~~cS~~~~e~~n~~~tgaTLII~P~-aIl~QW~~EI~kH~~~~lKv~~Y  452 (1394)
T KOG0298|consen  374 GKRVQCADEMGWQKTSEKLILELSDLPKLCPSCCSELVKEGENLVETGATLIICPN-AILMQWFEEIHKHISSLLKVLLY  452 (1394)
T ss_pred             CcceeehhhhhccchHHHHHHHHhcccccchhhhhHHHhcccceeecCceEEECcH-HHHHHHHHHHHHhccccceEEEE
Confidence            456677777999999664433221                     14568999999 7999999999864   3344433


Q ss_pred             CCCCCchhhhhhhhcCCeeEEEEcCcccccCchhh-----HHHHHh-------------cCccEEEEeccchhhcccCcc
Q 037567           84 GSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISF-----WSKLLK-------------AGVCLFAVDEAHCISEWGHDF  145 (374)
Q Consensus        84 ~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~-----~~~~~~-------------~~~~~vviDE~h~~~~~~~~~  145 (374)
                      .|.-..... ......++||++|||+.|..-+...     .....+             -.|=-|++|||+.+...+   
T Consensus       453 ~Girk~~~~-~~~el~~yDIVlTtYdiLr~El~hte~~~~~R~lR~qsr~~~~~SPL~~v~wWRIclDEaQMvesss---  528 (1394)
T KOG0298|consen  453 FGIRKTFWL-SPFELLQYDIVLTTYDILRNELYHTEDFGSDRQLRHQSRYMRPNSPLLMVNWWRICLDEAQMVESSS---  528 (1394)
T ss_pred             echhhhccc-CchhhhccCEEEeehHHHHhHhhcccccCChhhhhcccCCCCCCCchHHHHHHHHhhhHHHhhcchH---
Confidence            332111111 1123356899999998764322111     001111             011138999999886522   


Q ss_pred             hHHHHHHHHHHHhcCCCCeeEEEeecCcc
Q 037567          146 RLEYKQLDKLRTFLLGVPFVALTATATEK  174 (374)
Q Consensus       146 ~~~~~~~~~~~~~~~~~~~i~~SaT~~~~  174 (374)
                          ++..+....++....=++||||-..
T Consensus       529 ----S~~a~M~~rL~~in~W~VTGTPiq~  553 (1394)
T KOG0298|consen  529 ----SAAAEMVRRLHAINRWCVTGTPIQK  553 (1394)
T ss_pred             ----HHHHHHHHHhhhhceeeecCCchhh
Confidence                4556666667778889999998776

>KOG0383 consensus Predicted helicase [General function prediction only]

Probab=97.52  E-value=7.4e-05  Score=70.54  Aligned_cols=65  Identities=18%  Similarity=0.305  Sum_probs=52.9

Q ss_pred             cCCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhc-C--CeeEEEEecccccc
Q 037567          226 AGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIR-D--EIRVMVATMAFGMG  291 (374)
Q Consensus       226 ~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~-g--~~~ilv~t~~~~~G  291 (374)
                      ..+.+++||..-....+-+...+...+ ....+.|..+..+|+..+..|+. |  ..-.|.+|.+.+.|
T Consensus       629 ~~ghrvl~~~q~~~~ldlled~~~~~~-~~~r~dG~~~~~~rq~ai~~~n~~~~~~~cfllstra~g~g  696 (696)
T KOG0383|consen  629 SSGHRVLIFSQMIHMLDLLEDYLTYEG-KYERIDGPITGPERQAAIDRFNAPGSNQFCFLLSTRAGGLG  696 (696)
T ss_pred             hcchhhHHHHHHHHHHHHhHHHHhccC-cceeccCCccchhhhhhccccCCCCccceEEEeecccccCC
Confidence            456789999988888888888887777 77889999999999999999994 2  35567788877655

>PRK08181 transposase; Validated

Probab=97.49  E-value=0.00097  Score=56.70  Aligned_cols=56  Identities=20%  Similarity=0.135  Sum_probs=34.2

Q ss_pred             CchhHHHHHHH----HHcCCCEEEEccCCCCchhhhhcc---ccccCCcEEEEcchHHHHHHHH
Q 037567           14 FRPYQKDVIQR----IIEKRDCLVVMATGSGKSLCYQLP---PLVTGKTALVVSPLISLMQDQV   70 (374)
Q Consensus        14 ~~~~Q~~~~~~----~~~~~~~l~~a~tGsGKT~~~~l~---~~~~~~~~lil~P~~~l~~q~~   70 (374)
                      +.+.|..++..    +-++.++++.||+|+|||..+...   +..++.+++++ +..+|..+..
T Consensus        88 ~~~~~~~~L~~~~~~~~~~~nlll~Gp~GtGKTHLa~Aia~~a~~~g~~v~f~-~~~~L~~~l~  150 (269)
T PRK08181         88 VSKAQVMAIAAGDSWLAKGANLLLFGPPGGGKSHLAAAIGLALIENGWRVLFT-RTTDLVQKLQ  150 (269)
T ss_pred             CCHHHHHHHHHHHHHHhcCceEEEEecCCCcHHHHHHHHHHHHHHcCCceeee-eHHHHHHHHH
Confidence            34556655532    335788999999999999443221   23456666554 4456666554

>PRK06526 transposase; Provisional

Probab=97.48  E-value=0.00048  Score=58.17  Aligned_cols=41  Identities=15%  Similarity=0.186  Sum_probs=26.1

Q ss_pred             cCCCEEEEccCCCCchhhhhc---cccccCCcEEEEcchHHHHHH
Q 037567           27 EKRDCLVVMATGSGKSLCYQL---PPLVTGKTALVVSPLISLMQD   68 (374)
Q Consensus        27 ~~~~~l~~a~tGsGKT~~~~l---~~~~~~~~~lil~P~~~l~~q   68 (374)
                      .+.++++.||+|+|||..+..   .+...+.++++.... ++.++
T Consensus        97 ~~~nlll~Gp~GtGKThLa~al~~~a~~~g~~v~f~t~~-~l~~~  140 (254)
T PRK06526         97 GKENVVFLGPPGTGKTHLAIGLGIRACQAGHRVLFATAA-QWVAR  140 (254)
T ss_pred             cCceEEEEeCCCCchHHHHHHHHHHHHHCCCchhhhhHH-HHHHH
Confidence            467899999999999955432   223456666664333 44444

>PF13871 Helicase_C_4: Helicase_C-like

Probab=97.47  E-value=0.00039  Score=58.68  Aligned_cols=60  Identities=23%  Similarity=0.212  Sum_probs=51.2

Q ss_pred             HHHHhhhcCCeeEEEEeccccccccccC--------ccEEEEECCCCChhHHHHhhccCCCCCCceEE
Q 037567          269 EAHRLFIRDEIRVMVATMAFGMGIDKPD--------VRHVIHYGCPKTLESYYQESGRCGRDGIASVC  328 (374)
Q Consensus       269 ~~~~~f~~g~~~ilv~t~~~~~G~d~~~--------~~~vi~~~~p~s~~~~~Q~~GR~~R~~~~g~~  328 (374)
                      ...+.|.+|+.+|+|.+.+.++|+.+..        -++-|.+.+|||+...+|..||+.|.||....
T Consensus        52 ~e~~~F~~g~k~v~iis~AgstGiSlHAd~~~~nqr~Rv~i~le~pwsad~aiQ~~GR~hRsnQ~~~P  119 (278)
T PF13871_consen   52 AEKQAFMDGEKDVAIISDAGSTGISLHADRRVKNQRRRVHITLELPWSADKAIQQFGRTHRSNQVSAP  119 (278)
T ss_pred             HHHHHHhCCCceEEEEecccccccchhccccCCCCCceEEEEeeCCCCHHHHHHHhccccccccccCC
Confidence            4566799999999999999999998863        34677899999999999999999999985433

>PRK04296 thymidine kinase; Provisional

Probab=97.46  E-value=7.5e-05  Score=60.37  Aligned_cols=32  Identities=28%  Similarity=0.213  Sum_probs=22.0

Q ss_pred             CEEEEccCCCCchhhhhcccc---ccCCcEEEEcc
Q 037567           30 DCLVVMATGSGKSLCYQLPPL---VTGKTALVVSP   61 (374)
Q Consensus        30 ~~l~~a~tGsGKT~~~~l~~~---~~~~~~lil~P   61 (374)
                      -.++.||+|+|||...+-.+.   ..+.+++++-|
T Consensus         4 i~litG~~GsGKTT~~l~~~~~~~~~g~~v~i~k~   38 (190)
T PRK04296          4 LEFIYGAMNSGKSTELLQRAYNYEERGMKVLVFKP   38 (190)
T ss_pred             EEEEECCCCCHHHHHHHHHHHHHHHcCCeEEEEec
Confidence            357899999999965432222   34778888866

>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=97.46  E-value=0.00028  Score=57.56  Aligned_cols=62  Identities=21%  Similarity=0.431  Sum_probs=47.2

Q ss_pred             CCchhHHHHHHHHHc---CCCEEEEccCCCCchhhhh---ccccccC-CcEEEEcchHHHHHHHHHHHHH
Q 037567           13 VFRPYQKDVIQRIIE---KRDCLVVMATGSGKSLCYQ---LPPLVTG-KTALVVSPLISLMQDQVMSLKQ   75 (374)
Q Consensus        13 ~~~~~Q~~~~~~~~~---~~~~l~~a~tGsGKT~~~~---l~~~~~~-~~~lil~P~~~l~~q~~~~~~~   75 (374)
                      -+|+-|.+....+.+   +++.+...-+|.|||.+.+   ..++..+ .-+-+++|. +|..|....+..
T Consensus        23 liR~~Q~~ia~~mi~~~~~~n~v~QlnMGeGKTsVI~Pmla~~LAdg~~LvrviVpk-~Ll~q~~~~L~~   91 (229)
T PF12340_consen   23 LIRPVQVEIAREMISPPSGKNSVMQLNMGEGKTSVIVPMLALALADGSRLVRVIVPK-ALLEQMRQMLRS   91 (229)
T ss_pred             eeeHHHHHHHHHHhCCCCCCCeEeeecccCCccchHHHHHHHHHcCCCcEEEEEcCH-HHHHHHHHHHHH
Confidence            489999999999986   4788999999999996532   2223343 446677777 799998888875

There are two conserved sequence motifs: LLE and NMG.

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

Probab=97.45  E-value=0.0019  Score=52.28  Aligned_cols=126  Identities=19%  Similarity=0.126  Sum_probs=66.0

Q ss_pred             EEEEccCCCCchhhhhcccc---ccCCcEEEEc-c--hHHHHHHHHHHHHHcCCceEEcCCCCCchhhhhhhhcCCeeEE
Q 037567           31 CLVVMATGSGKSLCYQLPPL---VTGKTALVVS-P--LISLMQDQVMSLKQRGINAEFLGSAQTDSSVQTKAETGYFQLL  104 (374)
Q Consensus        31 ~l~~a~tGsGKT~~~~l~~~---~~~~~~lil~-P--~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~  104 (374)
                      ++++||||+|||.+..-.+.   .++.++.+++ .  +..-.+|.....+..+..............             
T Consensus         4 i~lvGptGvGKTTt~aKLAa~~~~~~~~v~lis~D~~R~ga~eQL~~~a~~l~vp~~~~~~~~~~~~-------------   70 (196)
T PF00448_consen    4 IALVGPTGVGKTTTIAKLAARLKLKGKKVALISADTYRIGAVEQLKTYAEILGVPFYVARTESDPAE-------------   70 (196)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHHHHTT--EEEEEESTSSTHHHHHHHHHHHHHTEEEEESSTTSCHHH-------------
T ss_pred             EEEECCCCCchHhHHHHHHHHHhhccccceeecCCCCCccHHHHHHHHHHHhccccchhhcchhhHH-------------
Confidence            57899999999976442221   1255554444 3  224556666666666655443221111111             


Q ss_pred             EEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHHhc-CCCCeeEEEeecCcccHHHHHHh
Q 037567          105 FMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFL-LGVPFVALTATATEKVRIDIINS  182 (374)
Q Consensus       105 i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~-~~~~~i~~SaT~~~~~~~~~~~~  182 (374)
                               ............++++|+||-+.+...    .......+..+.... +....+.+|||........+...
T Consensus        71 ---------~~~~~l~~~~~~~~D~vlIDT~Gr~~~----d~~~~~el~~~~~~~~~~~~~LVlsa~~~~~~~~~~~~~  136 (196)
T PF00448_consen   71 ---------IAREALEKFRKKGYDLVLIDTAGRSPR----DEELLEELKKLLEALNPDEVHLVLSATMGQEDLEQALAF  136 (196)
T ss_dssp             ---------HHHHHHHHHHHTTSSEEEEEE-SSSST----HHHHHHHHHHHHHHHSSSEEEEEEEGGGGGHHHHHHHHH
T ss_pred             ---------HHHHHHHHHhhcCCCEEEEecCCcchh----hHHHHHHHHHHhhhcCCccceEEEecccChHHHHHHHHH
Confidence                     111222334446788999999875421    122224444444444 34567889999887765544443

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 ....

>PRK08727 hypothetical protein; Validated

Probab=97.45  E-value=0.00054  Score=57.39  Aligned_cols=32  Identities=13%  Similarity=0.116  Sum_probs=20.1

Q ss_pred             CCEEEEccCCCCchhhhhc---cccccCCcEEEEc
Q 037567           29 RDCLVVMATGSGKSLCYQL---PPLVTGKTALVVS   60 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~~l---~~~~~~~~~lil~   60 (374)
                      ..+++.||+|+|||-....   .+..++.+++++.
T Consensus        42 ~~l~l~G~~G~GKThL~~a~~~~~~~~~~~~~y~~   76 (233)
T PRK08727         42 DWLYLSGPAGTGKTHLALALCAAAEQAGRSSAYLP   76 (233)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEEe
Confidence            3479999999999943221   1233455666654

>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=97.43  E-value=0.0011  Score=50.94  Aligned_cols=35  Identities=17%  Similarity=0.189  Sum_probs=22.5

Q ss_pred             CCCEEEEccCCCCchhhhhcccc---ccCCcEEEEcch
Q 037567           28 KRDCLVVMATGSGKSLCYQLPPL---VTGKTALVVSPL   62 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~l~~~---~~~~~~lil~P~   62 (374)
                      ++.+++.||+|+|||......+.   ..+..++++...
T Consensus        19 ~~~v~i~G~~G~GKT~l~~~i~~~~~~~~~~v~~~~~~   56 (151)
T cd00009          19 PKNLLLYGPPGTGKTTLARAIANELFRPGAPFLYLNAS   56 (151)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHhhcCCCCeEEEehh
Confidence            56789999999999965432222   224556555544

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.

>KOG0739 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=97.42  E-value=0.0022  Score=53.85  Aligned_cols=117  Identities=11%  Similarity=0.093  Sum_probs=70.7

Q ss_pred             HHHHcCC-----CEEEEccCCCCchhhhhccccccCCcEEEEcchHHHHHHHHHHHHHcCCceEEcCCCCCchhhhhhhh
Q 037567           23 QRIIEKR-----DCLVVMATGSGKSLCYQLPPLVTGKTALVVSPLISLMQDQVMSLKQRGINAEFLGSAQTDSSVQTKAE   97 (374)
Q Consensus        23 ~~~~~~~-----~~l~~a~tGsGKT~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   97 (374)
                      |+++.|+     .+++.+|+|+||++.+-..+-. ....++-+.+..|+..|.-+-.++                     
T Consensus       156 PqlFtGkR~PwrgiLLyGPPGTGKSYLAKAVATE-AnSTFFSvSSSDLvSKWmGESEkL---------------------  213 (439)
T KOG0739|consen  156 PQLFTGKRKPWRGILLYGPPGTGKSYLAKAVATE-ANSTFFSVSSSDLVSKWMGESEKL---------------------  213 (439)
T ss_pred             hhhhcCCCCcceeEEEeCCCCCcHHHHHHHHHhh-cCCceEEeehHHHHHHHhccHHHH---------------------
Confidence            5556654     4799999999999764333333 346788888889999887664433                     


Q ss_pred             cCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHH-HHHHH-HHHHhcC-----CCCeeEEEee
Q 037567           98 TGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLE-YKQLD-KLRTFLL-----GVPFVALTAT  170 (374)
Q Consensus        98 ~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~-~~~~~-~~~~~~~-----~~~~i~~SaT  170 (374)
                                       ....+....-...++|+|||++.+.....+.... .+++. +++-.+.     +..++.+.||
T Consensus       214 -----------------VknLFemARe~kPSIIFiDEiDslcg~r~enEseasRRIKTEfLVQMqGVG~d~~gvLVLgAT  276 (439)
T KOG0739|consen  214 -----------------VKNLFEMARENKPSIIFIDEIDSLCGSRSENESEASRRIKTEFLVQMQGVGNDNDGVLVLGAT  276 (439)
T ss_pred             -----------------HHHHHHHHHhcCCcEEEeehhhhhccCCCCCchHHHHHHHHHHHHhhhccccCCCceEEEecC
Confidence                             0122233334566789999999886533322222 12332 2222222     3568889999


Q ss_pred             cCcccHHH
Q 037567          171 ATEKVRID  178 (374)
Q Consensus       171 ~~~~~~~~  178 (374)
                      -.+.....
T Consensus       277 NiPw~LDs  284 (439)
T KOG0739|consen  277 NIPWVLDS  284 (439)
T ss_pred             CCchhHHH
Confidence            77765543

>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=97.39  E-value=0.00018  Score=63.41  Aligned_cols=61  Identities=21%  Similarity=0.215  Sum_probs=45.7

Q ss_pred             CchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccc---c----ccCCcEEEEcchHHHHHHHHHHHHHc
Q 037567           14 FRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPP---L----VTGKTALVVSPLISLMQDQVMSLKQR   76 (374)
Q Consensus        14 ~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~---~----~~~~~~lil~P~~~l~~q~~~~~~~~   76 (374)
                      +++-|.+++..  ..++++|.|++|||||.+.+.-+   +    ....+++++++|+..+.++...+...
T Consensus         1 l~~eQ~~~i~~--~~~~~lV~a~AGSGKT~~l~~ri~~ll~~~~~~~~~Il~lTft~~aa~e~~~ri~~~   68 (315)
T PF00580_consen    1 LTDEQRRIIRS--TEGPLLVNAGAGSGKTTTLLERIAYLLYEGGVPPERILVLTFTNAAAQEMRERIREL   68 (315)
T ss_dssp             S-HHHHHHHHS---SSEEEEEE-TTSSHHHHHHHHHHHHHHTSSSTGGGEEEEESSHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHhC--CCCCEEEEeCCCCCchHHHHHHHHHhhccccCChHHheecccCHHHHHHHHHHHHHh
Confidence            46778888877  67889999999999997654222   1    13567999999999999998888763

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 ....

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

Probab=97.36  E-value=0.00089  Score=57.78  Aligned_cols=47  Identities=15%  Similarity=0.087  Sum_probs=29.4

Q ss_pred             CCEEEEccCCCCchhhhhcccccc---CCcEEEEcchHHHHHHHHHHHHH
Q 037567           29 RDCLVVMATGSGKSLCYQLPPLVT---GKTALVVSPLISLMQDQVMSLKQ   75 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~~l~~~~~---~~~~lil~P~~~l~~q~~~~~~~   75 (374)
                      ...++++|+|+|||..+-+.+-..   ..+.+=+..+.+-.+++..-+++
T Consensus       163 pSmIlWGppG~GKTtlArlia~tsk~~SyrfvelSAt~a~t~dvR~ife~  212 (554)
T KOG2028|consen  163 PSMILWGPPGTGKTTLARLIASTSKKHSYRFVELSATNAKTNDVRDIFEQ  212 (554)
T ss_pred             CceEEecCCCCchHHHHHHHHhhcCCCceEEEEEeccccchHHHHHHHHH
Confidence            367999999999997654444332   23355555565556655555443

>TIGR02768 TraA_Ti Ti-type conjugative transfer relaxase TraA

Probab=97.35  E-value=0.00053  Score=67.21  Aligned_cols=58  Identities=14%  Similarity=0.115  Sum_probs=44.4

Q ss_pred             CCchhHHHHHHHHHcC-CCEEEEccCCCCchhhhhc--ccc-ccCCcEEEEcchHHHHHHHH
Q 037567           13 VFRPYQKDVIQRIIEK-RDCLVVMATGSGKSLCYQL--PPL-VTGKTALVVSPLISLMQDQV   70 (374)
Q Consensus        13 ~~~~~Q~~~~~~~~~~-~~~l~~a~tGsGKT~~~~l--~~~-~~~~~~lil~P~~~l~~q~~   70 (374)
                      .+++-|.+|+..++.+ +-+++.|++|+|||.+.-.  .++ ..+.++++++||...+..+.
T Consensus       352 ~Ls~~Q~~Av~~i~~s~~~~il~G~aGTGKTtll~~i~~~~~~~g~~V~~~ApTg~Aa~~L~  413 (744)
T TIGR02768       352 RLSEEQYEAVRHVTGSGDIAVVVGRAGTGKSTMLKAAREAWEAAGYRVIGAALSGKAAEGLQ  413 (744)
T ss_pred             CCCHHHHHHHHHHhcCCCEEEEEecCCCCHHHHHHHHHHHHHhCCCeEEEEeCcHHHHHHHH
Confidence            5899999999999874 5668999999999965322  122 24788999999987776554

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.

>PHA03368 DNA packaging terminase subunit 1; Provisional

Probab=97.31  E-value=0.0024  Score=60.01  Aligned_cols=157  Identities=16%  Similarity=0.226  Sum_probs=93.2

Q ss_pred             hHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhh--cc-cc--ccCCcEEEEcchHHHHHHHHHHHHHcC
Q 037567            3 STLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQ--LP-PL--VTGKTALVVSPLISLMQDQVMSLKQRG   77 (374)
Q Consensus         3 ~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~--l~-~~--~~~~~~lil~P~~~l~~q~~~~~~~~~   77 (374)
                      ..|+..|+...+..   .+ -..++.+-.++..|=-.|||-...  +. ++  ..+.++++.+|.+..++.+++++...-
T Consensus       233 ~~lk~~Fdi~~~s~---~~-~~~fkqk~tVflVPRR~GKTwivv~iI~~ll~s~~Gi~IgytAH~~~ts~~vF~eI~~~l  308 (738)
T PHA03368        233 RFLRTVFNTPLFSD---AA-VRHFRQRATVFLVPRRHGKTWFLVPLIALALATFRGIKIGYTAHIRKATEPVFEEIGARL  308 (738)
T ss_pred             HHHHHHcCCccccH---HH-HHHhhccceEEEecccCCchhhHHHHHHHHHHhCCCCEEEEEcCcHHHHHHHHHHHHHHH
Confidence            56777777765544   23 344566777888899999995322  22 11  358899999999999999998887641


Q ss_pred             C----c--eEEcCCCCCchhhhhhhhcCC-eeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHH
Q 037567           78 I----N--AEFLGSAQTDSSVQTKAETGY-FQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYK  150 (374)
Q Consensus        78 ~----~--~~~~~~~~~~~~~~~~~~~~~-~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~  150 (374)
                      .    .  +....+    .........+. ..|.+.+.        +..+....+.++++|+|||+.+..         .
T Consensus       309 e~~f~~~~v~~vkG----e~I~i~f~nG~kstI~FaSa--------rntNsiRGqtfDLLIVDEAqFIk~---------~  367 (738)
T PHA03368        309 RQWFGASRVDHVKG----ETISFSFPDGSRSTIVFASS--------HNTNGIRGQDFNLLFVDEANFIRP---------D  367 (738)
T ss_pred             hhhcchhheeeecC----cEEEEEecCCCccEEEEEec--------cCCCCccCCcccEEEEechhhCCH---------H
Confidence            1    1  111110    00000001111 13333321        111234456789999999999876         2


Q ss_pred             HHHHHHHhc--CCCCeeEEEeecCcccHHHHHHhcC
Q 037567          151 QLDKLRTFL--LGVPFVALTATATEKVRIDIINSLK  184 (374)
Q Consensus       151 ~~~~~~~~~--~~~~~i~~SaT~~~~~~~~~~~~~~  184 (374)
                      .+..+...+  .+.++|++|.|-+......++..++
T Consensus       368 al~~ilp~l~~~n~k~I~ISS~Ns~~~sTSFL~nLk  403 (738)
T PHA03368        368 AVQTIMGFLNQTNCKIIFVSSTNTGKASTSFLYNLK  403 (738)
T ss_pred             HHHHHHHHHhccCccEEEEecCCCCccchHHHHhhc
Confidence            223332222  2789999999988877766666664

>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=97.28  E-value=0.00017  Score=58.41  Aligned_cols=21  Identities=19%  Similarity=0.148  Sum_probs=16.2

Q ss_pred             CEEEEccCCCCchhhhhcccc
Q 037567           30 DCLVVMATGSGKSLCYQLPPL   50 (374)
Q Consensus        30 ~~l~~a~tGsGKT~~~~l~~~   50 (374)
                      +++++||+|+|||..+.+.+-
T Consensus        52 h~lf~GPPG~GKTTLA~IIA~   72 (233)
T PF05496_consen   52 HMLFYGPPGLGKTTLARIIAN   72 (233)
T ss_dssp             EEEEESSTTSSHHHHHHHHHH
T ss_pred             eEEEECCCccchhHHHHHHHh
Confidence            579999999999976544433

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.

>PRK13826 Dtr system oriT relaxase; Provisional

Probab=97.26  E-value=0.0032  Score=63.45  Aligned_cols=59  Identities=17%  Similarity=0.107  Sum_probs=44.8

Q ss_pred             CCchhHHHHHHHHHc-CCCEEEEccCCCCchhhhhcc--cc-ccCCcEEEEcchHHHHHHHHH
Q 037567           13 VFRPYQKDVIQRIIE-KRDCLVVMATGSGKSLCYQLP--PL-VTGKTALVVSPLISLMQDQVM   71 (374)
Q Consensus        13 ~~~~~Q~~~~~~~~~-~~~~l~~a~tGsGKT~~~~l~--~~-~~~~~~lil~P~~~l~~q~~~   71 (374)
                      .|++-|.+++..+.. ++-+++.|+.|+|||.+.-..  ++ ..+.+++.++||..-+..+.+
T Consensus       381 ~Ls~eQ~~Av~~i~~~~r~~~v~G~AGTGKTt~l~~~~~~~e~~G~~V~g~ApTgkAA~~L~e  443 (1102)
T PRK13826        381 RLSDEQKTAIEHVAGPARIAAVVGRAGAGKTTMMKAAREAWEAAGYRVVGGALAGKAAEGLEK  443 (1102)
T ss_pred             CCCHHHHHHHHHHhccCCeEEEEeCCCCCHHHHHHHHHHHHHHcCCeEEEEcCcHHHHHHHHH
Confidence            599999999998865 445689999999999653221  12 257889999999877776543

>KOG1133 consensus Helicase of the DEAD superfamily [Replication, recombination and repair]

Probab=97.25  E-value=0.011  Score=55.47  Aligned_cols=116  Identities=16%  Similarity=0.224  Sum_probs=79.0

Q ss_pred             HHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHHcCCc-------eeeeecCCChHHHHHHHHhhhc----CCeeEEEEe
Q 037567          217 LVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVK-------AGTYHGQMGSKAREEAHRLFIR----DEIRVMVAT  285 (374)
Q Consensus       217 ~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~-------~~~~~~~~~~~~r~~~~~~f~~----g~~~ilv~t  285 (374)
                      .+..+...+  .+.+++|+|+......+.+.++..|+-       .+++-...+   -..+++.|..    |.-.+|++.
T Consensus       620 ~~~nL~~~V--PgGvV~FfPSy~yL~~v~k~w~~~gil~ri~~kK~vF~E~k~~---~~dvl~~Ya~a~~~g~GaiLlaV  694 (821)
T KOG1133|consen  620 SISNLSNAV--PGGVVCFFPSYAYLGQVRKRWEQNGILARIVGKKKVFYEPKDT---VEDVLEGYAEAAERGRGAILLAV  694 (821)
T ss_pred             HHHHHHhhC--CCcEEEEeccHHHHHHHHHHHHhcchHHHhhccchhhccCccc---HHHHHHHHHHHhhcCCCeEEEEE
Confidence            344444444  378999999999999999998876542       223322222   3455555553    443455544


Q ss_pred             --ccccccccccC--ccEEEEECCCCC--------------------------------hhHHHHhhccCCCCCCceEEE
Q 037567          286 --MAFGMGIDKPD--VRHVIHYGCPKT--------------------------------LESYYQESGRCGRDGIASVCW  329 (374)
Q Consensus       286 --~~~~~G~d~~~--~~~vi~~~~p~s--------------------------------~~~~~Q~~GR~~R~~~~g~~~  329 (374)
                        ..+++|||+.+  .+.|+-+++|..                                +....|.||||-|..++-.++
T Consensus       695 VGGKlSEGINF~D~LgRaVvvVGlPyPN~~s~EL~er~k~l~~k~~~~gagke~yEnlCMkAVNQsIGRAIRH~~DYA~i  774 (821)
T KOG1133|consen  695 VGGKLSEGINFSDDLGRAVVVVGLPYPNIQSVELQERMKHLDGKLPTPGAGKELYENLCMKAVNQSIGRAIRHRKDYASI  774 (821)
T ss_pred             eccccccccccccccccEEEEeecCCCCCCCHHHHHHHHHhhhccCCCCchHHHHHHHHHHHHHHHHHHHHhhhccceeE
Confidence              59999999988  677888887741                                233479999999998888888


Q ss_pred             EEeeccCC
Q 037567          330 LYYARSNF  337 (374)
Q Consensus       330 ~~~~~~~~  337 (374)
                      ++++...-
T Consensus       775 ~LlD~RY~  782 (821)
T KOG1133|consen  775 YLLDKRYA  782 (821)
T ss_pred             EEehhhhc
Confidence            88877543

>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI

Probab=97.20  E-value=0.019  Score=62.29  Aligned_cols=207  Identities=15%  Similarity=0.109  Sum_probs=108.8

Q ss_pred             CCchhHHHHHHHHHcC--CCEEEEccCCCCchhhhh--cccc-ccCCcEEEEcchHHHHHHHHHHHHHcCCceEEcCCCC
Q 037567           13 VFRPYQKDVIQRIIEK--RDCLVVMATGSGKSLCYQ--LPPL-VTGKTALVVSPLISLMQDQVMSLKQRGINAEFLGSAQ   87 (374)
Q Consensus        13 ~~~~~Q~~~~~~~~~~--~~~l~~a~tGsGKT~~~~--l~~~-~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~   87 (374)
                      .+.+-|.+++..++..  +-.++.++.|+|||.+.-  ..++ ..+.++++++|+..-+..+.+....   ....+.   
T Consensus       429 ~Ls~~Q~~Av~~il~s~~~v~ii~G~aGTGKTt~l~~l~~~~~~~G~~V~~lAPTgrAA~~L~e~~g~---~A~Ti~---  502 (1960)
T TIGR02760       429 ALSPSNKDAVSTLFTSTKRFIIINGFGGTGSTEIAQLLLHLASEQGYEIQIITAGSLSAQELRQKIPR---LASTFI---  502 (1960)
T ss_pred             CCCHHHHHHHHHHHhCCCCeEEEEECCCCCHHHHHHHHHHHHHhcCCeEEEEeCCHHHHHHHHHHhcc---hhhhHH---
Confidence            4889999999998875  456889999999996532  2222 2578999999998877766654221   110000   


Q ss_pred             CchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHHhc--CCCCee
Q 037567           88 TDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFL--LGVPFV  165 (374)
Q Consensus        88 ~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~--~~~~~i  165 (374)
                          .+......  .....|...+.   .   ....+..-++|||||+.++..         ..+..+....  .+.++|
T Consensus       503 ----~~l~~l~~--~~~~~tv~~fl---~---~~~~l~~~~vlIVDEAsMl~~---------~~~~~Ll~~a~~~garvV  561 (1960)
T TIGR02760       503 ----TWVKNLFN--DDQDHTVQGLL---D---KSSPFSNKDIFVVDEANKLSN---------NELLKLIDKAEQHNSKLI  561 (1960)
T ss_pred             ----HHHHhhcc--cccchhHHHhh---c---ccCCCCCCCEEEEECCCCCCH---------HHHHHHHHHHhhcCCEEE
Confidence                00000000  00011111111   0   111123457999999998764         2233333322  367788


Q ss_pred             EEEeecCcc-----cHHHHHHhcCCCCCeEEEeccCCCceeEEEEeecC-CcchHHHHHHHHHHhhcCCCcEEEEecchh
Q 037567          166 ALTATATEK-----VRIDIINSLKLKNPYVTIASFDRKNLFYGVKVINR-GQSFVDELVQEILKSVAGAGSIIVYCMTIK  239 (374)
Q Consensus       166 ~~SaT~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~lVf~~~~~  239 (374)
                      ++--+-...     .....+...++......  ...+..-..  ..... +......+...++.......+++|+..+..
T Consensus       562 lvGD~~QL~sV~aG~~f~~L~~~gv~t~~l~--~i~rq~~~v--~i~~~~~~~r~~~ia~~y~~L~~~r~~tliv~~t~~  637 (1960)
T TIGR02760       562 LLNDSAQRQGMSAGSAIDLLKEGGVTTYAWV--DTKQQKASV--EISEAVDKLRVDYIASAWLDLTPDRQNSQVLATTHR  637 (1960)
T ss_pred             EEcChhhcCccccchHHHHHHHCCCcEEEee--cccccCcce--eeeccCchHHHHHHHHHHHhcccccCceEEEcCCcH
Confidence            776652211     11123333333222221  111111111  12222 223344566677665555556999999988


Q ss_pred             HHHHHHHHHHH
Q 037567          240 DVEEISKALKQ  250 (374)
Q Consensus       240 ~~~~l~~~l~~  250 (374)
                      +...|....+.
T Consensus       638 dr~~Ln~~iR~  648 (1960)
T TIGR02760       638 EQQDLTQIIRN  648 (1960)
T ss_pred             HHHHHHHHHHH
Confidence            88887777654

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.

>PRK07952 DNA replication protein DnaC; Validated

Probab=97.18  E-value=0.0054  Score=51.38  Aligned_cols=55  Identities=16%  Similarity=0.216  Sum_probs=31.3

Q ss_pred             hhHHHHHHHHHc--------CCCEEEEccCCCCchhhhhcc---ccccCCcEEEEcchHHHHHHHHH
Q 037567           16 PYQKDVIQRIIE--------KRDCLVVMATGSGKSLCYQLP---PLVTGKTALVVSPLISLMQDQVM   71 (374)
Q Consensus        16 ~~Q~~~~~~~~~--------~~~~l~~a~tGsGKT~~~~l~---~~~~~~~~lil~P~~~l~~q~~~   71 (374)
                      +.|..++..+.+        ...+++.|++|+|||..+...   +...+..++++ +..++......
T Consensus        79 ~~q~~al~~a~~~~~~~~~~~~~~~l~G~~GtGKThLa~aia~~l~~~g~~v~~i-t~~~l~~~l~~  144 (244)
T PRK07952         79 EGQMNALSKARQYVEEFDGNIASFIFSGKPGTGKNHLAAAICNELLLRGKSVLII-TVADIMSAMKD  144 (244)
T ss_pred             chHHHHHHHHHHHHHhhccCCceEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEE-EHHHHHHHHHH
Confidence            456656654432        146899999999999543322   22345556555 44455544333

>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=97.17  E-value=0.0015  Score=49.28  Aligned_cols=32  Identities=16%  Similarity=0.108  Sum_probs=20.2

Q ss_pred             EEEEccCCCCchhhhhccccccCCcEEEEcch
Q 037567           31 CLVVMATGSGKSLCYQLPPLVTGKTALVVSPL   62 (374)
Q Consensus        31 ~l~~a~tGsGKT~~~~l~~~~~~~~~lil~P~   62 (374)
                      +++.||+|+|||...-..+..-+..++.+...
T Consensus         1 ill~G~~G~GKT~l~~~la~~l~~~~~~i~~~   32 (132)
T PF00004_consen    1 ILLHGPPGTGKTTLARALAQYLGFPFIEIDGS   32 (132)
T ss_dssp             EEEESSTTSSHHHHHHHHHHHTTSEEEEEETT
T ss_pred             CEEECcCCCCeeHHHHHHHhhccccccccccc
Confidence            57999999999976543333334444444444

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 ....

>PRK12377 putative replication protein; Provisional

Probab=97.16  E-value=0.0042  Score=52.19  Aligned_cols=43  Identities=19%  Similarity=0.220  Sum_probs=26.7

Q ss_pred             CCEEEEccCCCCchhhhhcc---ccccCCcEEEEcchHHHHHHHHHH
Q 037567           29 RDCLVVMATGSGKSLCYQLP---PLVTGKTALVVSPLISLMQDQVMS   72 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~~l~---~~~~~~~~lil~P~~~l~~q~~~~   72 (374)
                      .++++.||+|+|||..+...   +..++..+ +.++..++..+....
T Consensus       102 ~~l~l~G~~GtGKThLa~AIa~~l~~~g~~v-~~i~~~~l~~~l~~~  147 (248)
T PRK12377        102 TNFVFSGKPGTGKNHLAAAIGNRLLAKGRSV-IVVTVPDVMSRLHES  147 (248)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHcCCCe-EEEEHHHHHHHHHHH
Confidence            57899999999999543221   22344555 444555677765544

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

Probab=97.13  E-value=0.0012  Score=59.18  Aligned_cols=57  Identities=23%  Similarity=0.228  Sum_probs=42.3

Q ss_pred             CCchhHHHHHHHH------HcCCCEEEEccCCCCchhhhhcc---ccccCCcEEEEcchHHHHHHH
Q 037567           13 VFRPYQKDVIQRI------IEKRDCLVVMATGSGKSLCYQLP---PLVTGKTALVVSPLISLMQDQ   69 (374)
Q Consensus        13 ~~~~~Q~~~~~~~------~~~~~~l~~a~tGsGKT~~~~l~---~~~~~~~~lil~P~~~l~~q~   69 (374)
                      +|.+-|.+++..+      .++..+++.|+.|+|||+.+-..   +...+..+++++||...|...
T Consensus         1 ~Ln~eQ~~~~~~v~~~~~~~~~~~~fv~G~~GtGKs~l~~~i~~~~~~~~~~~~~~a~tg~AA~~i   66 (364)
T PF05970_consen    1 KLNEEQRRVFDTVIEAIENEEGLNFFVTGPAGTGKSFLIKAIIDYLRSRGKKVLVTAPTGIAAFNI   66 (364)
T ss_pred             CCCHHHHHHHHHHHHHHHccCCcEEEEEcCCCCChhHHHHHHHHHhccccceEEEecchHHHHHhc
Confidence            3677899998888      55788899999999999764221   122467899999997666543

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

>PF05127 Helicase_RecD: Helicase; InterPro: IPR007807 This domain is about 350 amino acid residues long and appears to have a P-loop motif, suggesting this is an ATPase

Probab=97.12  E-value=0.00071  Score=53.24  Aligned_cols=118  Identities=22%  Similarity=0.229  Sum_probs=51.3

Q ss_pred             EEEccCCCCchhhhhcccc--cc--CCcEEEEcchHHHHHHHHHHHHH----cCCceEEcCCCCCchhhhhhhhcCCeeE
Q 037567           32 LVVMATGSGKSLCYQLPPL--VT--GKTALVVSPLISLMQDQVMSLKQ----RGINAEFLGSAQTDSSVQTKAETGYFQL  103 (374)
Q Consensus        32 l~~a~tGsGKT~~~~l~~~--~~--~~~~lil~P~~~l~~q~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~i  103 (374)
                      ++.|+-|-|||.+.-+.+.  ..  ..+++|.+|+.+-++..++.+..    .+.+..    .................|
T Consensus         1 VltA~RGRGKSa~lGl~~a~l~~~~~~~I~vtAP~~~~~~~lf~~~~~~l~~~~~~~~----~~~~~~~~~~~~~~~~~i   76 (177)
T PF05127_consen    1 VLTADRGRGKSAALGLAAAALIQKGKIRILVTAPSPENVQTLFEFAEKGLKALGYKEE----KKKRIGQIIKLRFNKQRI   76 (177)
T ss_dssp             -EEE-TTSSHHHHHHHCCCCSSS-----EEEE-SS--S-HHHHHCC------------------------------CCC-
T ss_pred             CccCCCCCCHHHHHHHHHHHHHHhcCceEEEecCCHHHHHHHHHHHHhhccccccccc----cccccccccccccccceE
Confidence            5789999999965433322  22  34799999998877766655432    121110    000000000111112345


Q ss_pred             EEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHHhcCCCCeeEEEeecCcc
Q 037567          104 LFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEK  174 (374)
Q Consensus       104 ~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~SaT~~~~  174 (374)
                      -+..|+.+....         ...+++|||||-.+.-         ..+..+   ....+.++||.|....
T Consensus        77 ~f~~Pd~l~~~~---------~~~DlliVDEAAaIp~---------p~L~~l---l~~~~~vv~stTi~GY  126 (177)
T PF05127_consen   77 EFVAPDELLAEK---------PQADLLIVDEAAAIPL---------PLLKQL---LRRFPRVVFSTTIHGY  126 (177)
T ss_dssp             -B--HHHHCCT-------------SCEEECTGGGS-H---------HHHHHH---HCCSSEEEEEEEBSST
T ss_pred             EEECCHHHHhCc---------CCCCEEEEechhcCCH---------HHHHHH---HhhCCEEEEEeecccc
Confidence            555555443321         2348999999987643         233333   4467788999997653

This domain is often N-terminal to a GCN5-related N-acetyltransferase domain IPR000182 from INTERPRO and C-terminal to IPR013562 from INTERPRO.; PDB: 2ZPA_B.

>PRK13342 recombination factor protein RarA; Reviewed

Probab=97.09  E-value=0.002  Score=59.03  Aligned_cols=19  Identities=16%  Similarity=0.300  Sum_probs=15.3

Q ss_pred             CCEEEEccCCCCchhhhhc
Q 037567           29 RDCLVVMATGSGKSLCYQL   47 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~~l   47 (374)
                      ..+++.||+|+|||..+..
T Consensus        37 ~~ilL~GppGtGKTtLA~~   55 (413)
T PRK13342         37 SSMILWGPPGTGKTTLARI   55 (413)
T ss_pred             ceEEEECCCCCCHHHHHHH
Confidence            3689999999999976543

>PRK13889 conjugal transfer relaxase TraA; Provisional

Probab=97.08  E-value=0.0011  Score=66.17  Aligned_cols=58  Identities=19%  Similarity=0.129  Sum_probs=44.2

Q ss_pred             CCchhHHHHHHHHHcCC-CEEEEccCCCCchhhhhc--cccc-cCCcEEEEcchHHHHHHHH
Q 037567           13 VFRPYQKDVIQRIIEKR-DCLVVMATGSGKSLCYQL--PPLV-TGKTALVVSPLISLMQDQV   70 (374)
Q Consensus        13 ~~~~~Q~~~~~~~~~~~-~~l~~a~tGsGKT~~~~l--~~~~-~~~~~lil~P~~~l~~q~~   70 (374)
                      .+++-|.+++..++.++ -+++.|++|+|||.+.-.  .++. .+.+++.++||...+....
T Consensus       346 ~Ls~eQr~Av~~il~s~~v~vv~G~AGTGKTT~l~~~~~~~e~~G~~V~~~ApTGkAA~~L~  407 (988)
T PRK13889        346 VLSGEQADALAHVTDGRDLGVVVGYAGTGKSAMLGVAREAWEAAGYEVRGAALSGIAAENLE  407 (988)
T ss_pred             CCCHHHHHHHHHHhcCCCeEEEEeCCCCCHHHHHHHHHHHHHHcCCeEEEecCcHHHHHHHh
Confidence            49999999999999865 468899999999975321  1122 4788999999987776543

>PRK06835 DNA replication protein DnaC; Validated

Probab=97.08  E-value=0.0067  Score=53.30  Aligned_cols=42  Identities=21%  Similarity=0.192  Sum_probs=26.7

Q ss_pred             CCCEEEEccCCCCchhhhhcc---ccccCCcEEEEcchHHHHHHHH
Q 037567           28 KRDCLVVMATGSGKSLCYQLP---PLVTGKTALVVSPLISLMQDQV   70 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~l~---~~~~~~~~lil~P~~~l~~q~~   70 (374)
                      +.++++.||||+|||..+...   ++.++..|+++ +..++..+..
T Consensus       183 ~~~Lll~G~~GtGKThLa~aIa~~l~~~g~~V~y~-t~~~l~~~l~  227 (329)
T PRK06835        183 NENLLFYGNTGTGKTFLSNCIAKELLDRGKSVIYR-TADELIEILR  227 (329)
T ss_pred             CCcEEEECCCCCcHHHHHHHHHHHHHHCCCeEEEE-EHHHHHHHHH
Confidence            578999999999999543221   23345556554 4456666544

>KOG0729 consensus 26S proteasome regulatory complex, ATPase RPT1 [Posttranslational modification, protein turnover, chaperones]

Probab=97.04  E-value=0.017  Score=47.82  Aligned_cols=43  Identities=21%  Similarity=0.244  Sum_probs=29.1

Q ss_pred             CCCEEEEccCCCCchhhhhccccccCCcEEEEcchHHHHHHHHH
Q 037567           28 KRDCLVVMATGSGKSLCYQLPPLVTGKTALVVSPLISLMQDQVM   71 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~l~~~~~~~~~lil~P~~~l~~q~~~   71 (374)
                      -+.+++.+|+|+|||+++-..+-. ..-++|=+-..+|++...-
T Consensus       211 pkgvllygppgtgktl~aravanr-tdacfirvigselvqkyvg  253 (435)
T KOG0729|consen  211 PKGVLLYGPPGTGKTLCARAVANR-TDACFIRVIGSELVQKYVG  253 (435)
T ss_pred             CCceEEeCCCCCchhHHHHHHhcc-cCceEEeehhHHHHHHHhh
Confidence            478899999999999986444333 3445555555577765443

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=97.03  E-value=0.00059  Score=52.05  Aligned_cols=40  Identities=18%  Similarity=0.058  Sum_probs=25.9

Q ss_pred             CCCEEEEccCCCCchhhhhccccc-cCC--cEEEEcchHHHHH
Q 037567           28 KRDCLVVMATGSGKSLCYQLPPLV-TGK--TALVVSPLISLMQ   67 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~l~~~~-~~~--~~lil~P~~~l~~   67 (374)
                      +..+++.||+|+|||......+.. ...  .++++.+......
T Consensus         2 ~~~~~l~G~~G~GKTtl~~~l~~~~~~~~~~~~~~~~~~~~~~   44 (148)
T smart00382        2 GEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEE   44 (148)
T ss_pred             CCEEEEECCCCCcHHHHHHHHHhccCCCCCCEEEECCEEcccc
Confidence            456899999999999765433332 222  5777777654433

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.

>KOG0738 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=97.03  E-value=0.0037  Score=54.55  Aligned_cols=73  Identities=14%  Similarity=0.093  Sum_probs=46.9

Q ss_pred             CCEEEEccCCCCchhhhhccccccCCcEEEEcchHHHHHHHHHHHHHcCCceEEcCCCCCchhhhhhhhcCCeeEEEEcC
Q 037567           29 RDCLVVMATGSGKSLCYQLPPLVTGKTALVVSPLISLMQDQVMSLKQRGINAEFLGSAQTDSSVQTKAETGYFQLLFMTP  108 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~  108 (374)
                      +.+++++|+|+|||+.+- ++......+++=+-+..|+..|.-+-++.                                
T Consensus       246 kgvLm~GPPGTGKTlLAK-AvATEc~tTFFNVSsstltSKwRGeSEKl--------------------------------  292 (491)
T KOG0738|consen  246 KGVLMVGPPGTGKTLLAK-AVATECGTTFFNVSSSTLTSKWRGESEKL--------------------------------  292 (491)
T ss_pred             ceeeeeCCCCCcHHHHHH-HHHHhhcCeEEEechhhhhhhhccchHHH--------------------------------
Confidence            578999999999998642 23333446666666667777655443221                                


Q ss_pred             cccccCchhhHHHHHhcCccEEEEeccchhhc
Q 037567          109 EKACIIPISFWSKLLKAGVCLFAVDEAHCISE  140 (374)
Q Consensus       109 ~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~  140 (374)
                         .+   -.+....+.....|+|||++.+..
T Consensus       293 ---vR---lLFemARfyAPStIFiDEIDslcs  318 (491)
T KOG0738|consen  293 ---VR---LLFEMARFYAPSTIFIDEIDSLCS  318 (491)
T ss_pred             ---HH---HHHHHHHHhCCceeehhhHHHHHh
Confidence               11   222334455667899999999964

>KOG0989 consensus Replication factor C, subunit RFC4 [Replication, recombination and repair]

Probab=97.02  E-value=0.00046  Score=58.08  Aligned_cols=34  Identities=21%  Similarity=0.120  Sum_probs=25.2

Q ss_pred             hHHHHHHHHHc------CCCEEEEccCCCCchhhhhcccc
Q 037567           17 YQKDVIQRIIE------KRDCLVVMATGSGKSLCYQLPPL   50 (374)
Q Consensus        17 ~Q~~~~~~~~~------~~~~l~~a~tGsGKT~~~~l~~~   50 (374)
                      .|+...+.+.+      ..+.++.||+|+|||.++.+.+.
T Consensus        40 gQe~vV~~L~~a~~~~~lp~~LFyGPpGTGKTStalafar   79 (346)
T KOG0989|consen   40 GQEHVVQVLKNALLRRILPHYLFYGPPGTGKTSTALAFAR   79 (346)
T ss_pred             chHHHHHHHHHHHhhcCCceEEeeCCCCCcHhHHHHHHHH
Confidence            67777776654      24679999999999987655443

>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=97.00  E-value=0.0044  Score=51.32  Aligned_cols=103  Identities=15%  Similarity=0.201  Sum_probs=53.7

Q ss_pred             CEEEEccCCCCchhhhh-c-c-cc--ccCCcEEEEcchHHHHHHHHHHHHHcCCceEEcCCCCCchhhhhhhhcCCeeEE
Q 037567           30 DCLVVMATGSGKSLCYQ-L-P-PL--VTGKTALVVSPLISLMQDQVMSLKQRGINAEFLGSAQTDSSVQTKAETGYFQLL  104 (374)
Q Consensus        30 ~~l~~a~tGsGKT~~~~-l-~-~~--~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~  104 (374)
                      .+++.||+|+|||-... + . +.  .++.+++++... +........+.....                          
T Consensus        36 ~l~l~G~~G~GKTHLL~Ai~~~~~~~~~~~~v~y~~~~-~f~~~~~~~~~~~~~--------------------------   88 (219)
T PF00308_consen   36 PLFLYGPSGLGKTHLLQAIANEAQKQHPGKRVVYLSAE-EFIREFADALRDGEI--------------------------   88 (219)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHHHHCTTS-EEEEEHH-HHHHHHHHHHHTTSH--------------------------
T ss_pred             ceEEECCCCCCHHHHHHHHHHHHHhccccccceeecHH-HHHHHHHHHHHcccc--------------------------
Confidence            47999999999995311 1 1 11  135566666544 566655555443100                          


Q ss_pred             EEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHHhcCCCCeeEEEeecCcc
Q 037567          105 FMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEK  174 (374)
Q Consensus       105 i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~SaT~~~~  174 (374)
                                 ...  .....+.+++++|++|.+.....--...+..++.....  +.++|+.|..++..
T Consensus        89 -----------~~~--~~~~~~~DlL~iDDi~~l~~~~~~q~~lf~l~n~~~~~--~k~li~ts~~~P~~  143 (219)
T PF00308_consen   89 -----------EEF--KDRLRSADLLIIDDIQFLAGKQRTQEELFHLFNRLIES--GKQLILTSDRPPSE  143 (219)
T ss_dssp             -----------HHH--HHHHCTSSEEEEETGGGGTTHHHHHHHHHHHHHHHHHT--TSEEEEEESS-TTT
T ss_pred             -----------hhh--hhhhhcCCEEEEecchhhcCchHHHHHHHHHHHHHHhh--CCeEEEEeCCCCcc
Confidence                       011  11235789999999999865321112223344444332  44555555455443

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.

>PRK05642 DNA replication initiation factor; Validated

Probab=97.00  E-value=0.003  Score=52.96  Aligned_cols=33  Identities=18%  Similarity=0.084  Sum_probs=20.4

Q ss_pred             CCEEEEccCCCCchhhhhcc---ccccCCcEEEEcc
Q 037567           29 RDCLVVMATGSGKSLCYQLP---PLVTGKTALVVSP   61 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~~l~---~~~~~~~~lil~P   61 (374)
                      ..++++||+|+|||-.....   +..++.+++++..
T Consensus        46 ~~l~l~G~~G~GKTHLl~a~~~~~~~~~~~v~y~~~   81 (234)
T PRK05642         46 SLIYLWGKDGVGRSHLLQAACLRFEQRGEPAVYLPL   81 (234)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHhCCCcEEEeeH
Confidence            45789999999999542211   1223556666543

>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=96.98  E-value=0.0092  Score=48.11  Aligned_cols=48  Identities=19%  Similarity=0.239  Sum_probs=34.3

Q ss_pred             EEEEccCCCCchhhhh---ccccccCCcEEEEcchHHHHHHHHHHHHHcCCc
Q 037567           31 CLVVMATGSGKSLCYQ---LPPLVTGKTALVVSPLISLMQDQVMSLKQRGIN   79 (374)
Q Consensus        31 ~l~~a~tGsGKT~~~~---l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~   79 (374)
                      +++.||+|+|||...+   ...+..+.+++++... +...++.+.+..+|..
T Consensus         2 ~li~G~~G~GKT~l~~~~~~~~~~~g~~v~~~s~e-~~~~~~~~~~~~~g~~   52 (187)
T cd01124           2 TLLSGGPGTGKTTFALQFLYAGLARGEPGLYVTLE-ESPEELIENAESLGWD   52 (187)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHHCCCcEEEEECC-CCHHHHHHHHHHcCCC
Confidence            5899999999996533   3334567788888654 5677777777777654

A related protein is found in archaea.

>PRK06893 DNA replication initiation factor; Validated

Probab=96.97  E-value=0.0025  Score=53.27  Aligned_cols=49  Identities=8%  Similarity=0.146  Sum_probs=26.1

Q ss_pred             cCccEEEEeccchhhcccCcchHHHHHHHHHHHhcCCCCeeEEEeecCccc
Q 037567          125 AGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEKV  175 (374)
Q Consensus       125 ~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~SaT~~~~~  175 (374)
                      .+.+++++||+|.+..........+..++....  .+.+++.+|++..+..
T Consensus        90 ~~~dlLilDDi~~~~~~~~~~~~l~~l~n~~~~--~~~~illits~~~p~~  138 (229)
T PRK06893         90 EQQDLVCLDDLQAVIGNEEWELAIFDLFNRIKE--QGKTLLLISADCSPHA  138 (229)
T ss_pred             ccCCEEEEeChhhhcCChHHHHHHHHHHHHHHH--cCCcEEEEeCCCChHH
Confidence            356899999999875321111112233333322  1345667777765543

>PRK05707 DNA polymerase III subunit delta'; Validated

Probab=96.96  E-value=0.0034  Score=55.26  Aligned_cols=33  Identities=21%  Similarity=0.312  Sum_probs=27.1

Q ss_pred             CCchhHHHHHHHHHcCC----CEEEEccCCCCchhhh
Q 037567           13 VFRPYQKDVIQRIIEKR----DCLVVMATGSGKSLCY   45 (374)
Q Consensus        13 ~~~~~Q~~~~~~~~~~~----~~l~~a~tGsGKT~~~   45 (374)
                      .++|||...+..+.+.+    -.++.||.|.|||..+
T Consensus         3 ~~yPWl~~~~~~~~~~~r~~ha~Lf~G~~G~GK~~~A   39 (328)
T PRK05707          3 EIYPWQQSLWQQLAGRGRHPHAYLLHGPAGIGKRALA   39 (328)
T ss_pred             cCCCCcHHHHHHHHHCCCcceeeeeECCCCCCHHHHH
Confidence            35899999999998753    4689999999999553

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

Probab=96.95  E-value=0.0028  Score=54.03  Aligned_cols=49  Identities=27%  Similarity=0.272  Sum_probs=27.1

Q ss_pred             HHHhcCccEEEEeccchhhcc-cCcchHHHHHHHHHHHhcCCCCeeEEEeec
Q 037567          121 KLLKAGVCLFAVDEAHCISEW-GHDFRLEYKQLDKLRTFLLGVPFVALTATA  171 (374)
Q Consensus       121 ~~~~~~~~~vviDE~h~~~~~-~~~~~~~~~~~~~~~~~~~~~~~i~~SaT~  171 (374)
                      -+...+.+++||||+|++... ....+...+.++.+.+. -..++|++ +|.
T Consensus       140 llr~~~vrmLIIDE~H~lLaGs~~~qr~~Ln~LK~L~Ne-L~ipiV~v-Gt~  189 (302)
T PF05621_consen  140 LLRRLGVRMLIIDEFHNLLAGSYRKQREFLNALKFLGNE-LQIPIVGV-GTR  189 (302)
T ss_pred             HHHHcCCcEEEeechHHHhcccHHHHHHHHHHHHHHhhc-cCCCeEEe-ccH
Confidence            334467899999999998652 22223233333333222 24666655 564

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

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

Probab=96.94  E-value=0.0057  Score=51.80  Aligned_cols=65  Identities=11%  Similarity=0.184  Sum_probs=42.8

Q ss_pred             cCCCCCchhHHHHHHHHH-------cCCCEEEEccCCCCchhhhhc---cccccCCcEEEEcchHHHHHHHHHHHH
Q 037567            9 FGYSVFRPYQKDVIQRII-------EKRDCLVVMATGSGKSLCYQL---PPLVTGKTALVVSPLISLMQDQVMSLK   74 (374)
Q Consensus         9 ~~~~~~~~~Q~~~~~~~~-------~~~~~l~~a~tGsGKT~~~~l---~~~~~~~~~lil~P~~~l~~q~~~~~~   74 (374)
                      +.|+-....+.+++..+.       ++.++++.||+|+|||..+..   .+. +.+.-++++++.+++.++...+.
T Consensus        79 ~d~~~~~~~~~~~l~~~~~~~~~~~~~~nl~l~G~~G~GKThLa~Ai~~~l~-~~g~sv~f~~~~el~~~Lk~~~~  153 (254)
T COG1484          79 FDFEFQPGIDKKALEDLASLVEFFERGENLVLLGPPGVGKTHLAIAIGNELL-KAGISVLFITAPDLLSKLKAAFD  153 (254)
T ss_pred             ccccCCcchhHHHHHHHHHHHHHhccCCcEEEECCCCCcHHHHHHHHHHHHH-HcCCeEEEEEHHHHHHHHHHHHh
Confidence            455555556666665543       467999999999999954322   233 44455566677788887776654

>COG1419 FlhF Flagellar GTP-binding protein [Cell motility and secretion]

Probab=96.92  E-value=0.018  Score=51.18  Aligned_cols=130  Identities=19%  Similarity=0.132  Sum_probs=74.4

Q ss_pred             CCCEEEEccCCCCchhhhhc-c----ccccCCc-EEEEcch--HHHHHHHHHHHHHcCCceEEcCCCCCchhhhhhhhcC
Q 037567           28 KRDCLVVMATGSGKSLCYQL-P----PLVTGKT-ALVVSPL--ISLMQDQVMSLKQRGINAEFLGSAQTDSSVQTKAETG   99 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~l-~----~~~~~~~-~lil~P~--~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   99 (374)
                      ++.+.++||||.|||.+.+- +    .+...++ .||-+.+  ..-++|......-.+..+.++.               
T Consensus       203 ~~vi~LVGPTGVGKTTTlAKLAar~~~~~~~~kVaiITtDtYRIGA~EQLk~Ya~im~vp~~vv~---------------  267 (407)
T COG1419         203 KRVIALVGPTGVGKTTTLAKLAARYVMLKKKKKVAIITTDTYRIGAVEQLKTYADIMGVPLEVVY---------------  267 (407)
T ss_pred             CcEEEEECCCCCcHHHHHHHHHHHHHhhccCcceEEEEeccchhhHHHHHHHHHHHhCCceEEec---------------
Confidence            56678999999999966432 2    1233444 4555554  3445565555555555544433               


Q ss_pred             CeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHHhcC-CCCeeEEEeecCcccHHH
Q 037567          100 YFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLL-GVPFVALTATATEKVRID  178 (374)
Q Consensus       100 ~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~~-~~~~i~~SaT~~~~~~~~  178 (374)
                             +|.-|..      .-..+.+.++|.||=+-+-    ......+..+........ ....+.+|||....+.+.
T Consensus       268 -------~~~el~~------ai~~l~~~d~ILVDTaGrs----~~D~~~i~el~~~~~~~~~i~~~Lvlsat~K~~dlke  330 (407)
T COG1419         268 -------SPKELAE------AIEALRDCDVILVDTAGRS----QYDKEKIEELKELIDVSHSIEVYLVLSATTKYEDLKE  330 (407)
T ss_pred             -------CHHHHHH------HHHHhhcCCEEEEeCCCCC----ccCHHHHHHHHHHHhccccceEEEEEecCcchHHHHH
Confidence                   3322211      1223456688888877642    222222234444433332 234688999999999988


Q ss_pred             HHHhcCCCCCe
Q 037567          179 IINSLKLKNPY  189 (374)
Q Consensus       179 ~~~~~~~~~~~  189 (374)
                      +...+..-+..
T Consensus       331 i~~~f~~~~i~  341 (407)
T COG1419         331 IIKQFSLFPID  341 (407)
T ss_pred             HHHHhccCCcc
Confidence            88887765543

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

Probab=96.91  E-value=0.0013  Score=52.36  Aligned_cols=60  Identities=18%  Similarity=0.285  Sum_probs=27.8

Q ss_pred             cCCCCCchhHHHHHHHHH------cCCCEEEEccCCCCchhhhhcc---ccccCCcEEEEcchHHHHHHH
Q 037567            9 FGYSVFRPYQKDVIQRII------EKRDCLVVMATGSGKSLCYQLP---PLVTGKTALVVSPLISLMQDQ   69 (374)
Q Consensus         9 ~~~~~~~~~Q~~~~~~~~------~~~~~l~~a~tGsGKT~~~~l~---~~~~~~~~lil~P~~~l~~q~   69 (374)
                      +.|...++.+...+..+.      ++.++++.||+|+|||..+...   ++.++..++++ +..+|.+..
T Consensus        22 ~d~~~~~~~~~~~~~~l~~~~~~~~~~~l~l~G~~G~GKThLa~ai~~~~~~~g~~v~f~-~~~~L~~~l   90 (178)
T PF01695_consen   22 FDFSNERGIDKAQIAQLAALEFIENGENLILYGPPGTGKTHLAVAIANEAIRKGYSVLFI-TASDLLDEL   90 (178)
T ss_dssp             ------------HHHHHHHH-S-SC--EEEEEESTTSSHHHHHHHHHHHHHHTT--EEEE-EHHHHHHHH
T ss_pred             ccccchhhHHHHHHHHHhcCCCcccCeEEEEEhhHhHHHHHHHHHHHHHhccCCcceeEe-ecCceeccc
Confidence            444444455555555442      3578899999999999553322   33456666664 555666654

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.

>PRK14974 cell division protein FtsY; Provisional

Probab=96.91  E-value=0.021  Score=50.29  Aligned_cols=121  Identities=12%  Similarity=0.089  Sum_probs=62.2

Q ss_pred             CEEEEccCCCCchhhhhccc--c-ccCCcEEEEcc-h--HHHHHHHHHHHHHcCCceEEcCCCCCchhhhhhhhcCCeeE
Q 037567           30 DCLVVMATGSGKSLCYQLPP--L-VTGKTALVVSP-L--ISLMQDQVMSLKQRGINAEFLGSAQTDSSVQTKAETGYFQL  103 (374)
Q Consensus        30 ~~l~~a~tGsGKT~~~~l~~--~-~~~~~~lil~P-~--~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i  103 (374)
                      -+++.|++|+|||.+....+  + ..+.+++++.. +  .....|+.......|..+.....+..               
T Consensus       142 vi~~~G~~GvGKTTtiakLA~~l~~~g~~V~li~~Dt~R~~a~eqL~~~a~~lgv~v~~~~~g~d---------------  206 (336)
T PRK14974        142 VIVFVGVNGTGKTTTIAKLAYYLKKNGFSVVIAAGDTFRAGAIEQLEEHAERLGVKVIKHKYGAD---------------  206 (336)
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHHHcCCeEEEecCCcCcHHHHHHHHHHHHHcCCceecccCCCC---------------
Confidence            45789999999996543221  2 23556655543 2  45566776666666654331111000               


Q ss_pred             EEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHHh-cCCCCeeEEEeecCcccH
Q 037567          104 LFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTF-LLGVPFVALTATATEKVR  176 (374)
Q Consensus       104 ~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~-~~~~~~i~~SaT~~~~~~  176 (374)
                          |.   .............+.++|++|.++++....    ..+..+..+... .++..++.++||......
T Consensus       207 ----p~---~v~~~ai~~~~~~~~DvVLIDTaGr~~~~~----~lm~eL~~i~~~~~pd~~iLVl~a~~g~d~~  269 (336)
T PRK14974        207 ----PA---AVAYDAIEHAKARGIDVVLIDTAGRMHTDA----NLMDELKKIVRVTKPDLVIFVGDALAGNDAV  269 (336)
T ss_pred             ----HH---HHHHHHHHHHHhCCCCEEEEECCCccCCcH----HHHHHHHHHHHhhCCceEEEeeccccchhHH
Confidence                00   000111122233567899999999764211    111223333222 245567888887755433

>PRK13341 recombination factor protein RarA/unknown domain fusion protein; Reviewed

Probab=96.90  E-value=0.0058  Score=59.53  Aligned_cols=39  Identities=21%  Similarity=0.273  Sum_probs=24.7

Q ss_pred             CccEEEEeccchhhcccCcchHHHHHHHHHHHhcCCCCeeEEEeecCc
Q 037567          126 GVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATE  173 (374)
Q Consensus       126 ~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~SaT~~~  173 (374)
                      ...++++||+|.+..         .....+.....+..+++.++|..+
T Consensus       109 ~~~IL~IDEIh~Ln~---------~qQdaLL~~lE~g~IiLI~aTTen  147 (725)
T PRK13341        109 KRTILFIDEVHRFNK---------AQQDALLPWVENGTITLIGATTEN  147 (725)
T ss_pred             CceEEEEeChhhCCH---------HHHHHHHHHhcCceEEEEEecCCC
Confidence            346899999998754         122333344446677888777554

>PHA03333 putative ATPase subunit of terminase; Provisional

Probab=96.88  E-value=0.0085  Score=56.71  Aligned_cols=148  Identities=11%  Similarity=-0.003  Sum_probs=77.9

Q ss_pred             HHcCCCEEEEccCCCCchhhhh---ccccc-cCCcEEEEcchHHHHHHHHHHHHHcCCceE--EcCCCCCchhhhhhhhc
Q 037567           25 IIEKRDCLVVMATGSGKSLCYQ---LPPLV-TGKTALVVSPLISLMQDQVMSLKQRGINAE--FLGSAQTDSSVQTKAET   98 (374)
Q Consensus        25 ~~~~~~~l~~a~tGsGKT~~~~---l~~~~-~~~~~lil~P~~~l~~q~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~   98 (374)
                      .++.+-.++.+|=|.|||.+..   ..++. .+.+++|.+|...-+.+.++.++..-....  -+......   ......
T Consensus       184 ~fkq~~tV~taPRqrGKS~iVgi~l~~La~f~Gi~IlvTAH~~~ts~evF~rv~~~le~lg~~~~fp~~~~---iv~vkg  260 (752)
T PHA03333        184 EYGKCYTAATVPRRCGKTTIMAIILAAMISFLEIDIVVQAQRKTMCLTLYNRVETVVHAYQHKPWFPEEFK---IVTLKG  260 (752)
T ss_pred             HHhhcceEEEeccCCCcHHHHHHHHHHHHHhcCCeEEEECCChhhHHHHHHHHHHHHHHhccccccCCCce---EEEeeC
Confidence            3446667889999999994432   11222 478899999999888888877654311100  00000000   000111


Q ss_pred             CCeeEEEEcCcccc------cCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHHhc--CCCCeeEEEee
Q 037567           99 GYFQLLFMTPEKAC------IIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFL--LGVPFVALTAT  170 (374)
Q Consensus        99 ~~~~i~i~T~~~l~------~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~--~~~~~i~~SaT  170 (374)
                      +...|.+..|.-..      .+..+..+......++++|+|||+.+..         ..+..+...+  .+.+++++|.+
T Consensus       261 g~E~I~f~~p~gak~G~sti~F~Ars~~s~RG~~~DLLIVDEAAfI~~---------~~l~aIlP~l~~~~~k~IiISS~  331 (752)
T PHA03333        261 TDENLEYISDPAAKEGKTTAHFLASSPNAARGQNPDLVIVDEAAFVNP---------GALLSVLPLMAVKGTKQIHISSP  331 (752)
T ss_pred             CeeEEEEecCcccccCcceeEEecccCCCcCCCCCCEEEEECcccCCH---------HHHHHHHHHHccCCCceEEEeCC
Confidence            11123333322111      0000111222334578999999998865         2233333333  26788899888


Q ss_pred             cCcccHHHHHHhcC
Q 037567          171 ATEKVRIDIINSLK  184 (374)
Q Consensus       171 ~~~~~~~~~~~~~~  184 (374)
                      -.......++..+.
T Consensus       332 ~~~~s~tS~L~nLk  345 (752)
T PHA03333        332 VDADSWISRVGEVK  345 (752)
T ss_pred             CCcchHHHHhhhhc
Confidence            76666555555443

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.87  E-value=0.012  Score=52.84  Aligned_cols=124  Identities=13%  Similarity=0.016  Sum_probs=66.0

Q ss_pred             CCEEEEccCCCCchhhhhcccc--c-----cCCcEE-EEcch--HHHHHHHHHHHHHcCCceEEcCCCCCchhhhhhhhc
Q 037567           29 RDCLVVMATGSGKSLCYQLPPL--V-----TGKTAL-VVSPL--ISLMQDQVMSLKQRGINAEFLGSAQTDSSVQTKAET   98 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~~l~~~--~-----~~~~~l-il~P~--~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   98 (374)
                      +.+++.||||+|||.+..-.+.  .     .+.++. +-+.+  ..-..|+.......|..+....              
T Consensus       175 ~vi~lvGptGvGKTTT~aKLA~~~~~~~~~~g~~V~lit~Dt~R~aa~eQL~~~a~~lgvpv~~~~--------------  240 (388)
T PRK12723        175 RVFILVGPTGVGKTTTIAKLAAIYGINSDDKSLNIKIITIDNYRIGAKKQIQTYGDIMGIPVKAIE--------------  240 (388)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHhhhccCCCeEEEEeccCccHHHHHHHHHHhhcCCcceEeeC--------------
Confidence            4578899999999976542221  1     234444 44443  2334454444444554432111              


Q ss_pred             CCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHHhcC-C-CCeeEEEeecCcccH
Q 037567           99 GYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLL-G-VPFVALTATATEKVR  176 (374)
Q Consensus        99 ~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~~-~-~~~i~~SaT~~~~~~  176 (374)
                              +++.+.    ...  ....+.++|+||++.+...    ....+..+........ + ...+.+|||......
T Consensus       241 --------~~~~l~----~~L--~~~~~~DlVLIDTaGr~~~----~~~~l~el~~~l~~~~~~~e~~LVlsat~~~~~~  302 (388)
T PRK12723        241 --------SFKDLK----EEI--TQSKDFDLVLVDTIGKSPK----DFMKLAEMKELLNACGRDAEFHLAVSSTTKTSDV  302 (388)
T ss_pred             --------cHHHHH----HHH--HHhCCCCEEEEcCCCCCcc----CHHHHHHHHHHHHhcCCCCeEEEEEcCCCCHHHH
Confidence                    111110    111  1236789999999987642    1112234444433322 2 467999999988776


Q ss_pred             HHHHHhcC
Q 037567          177 IDIINSLK  184 (374)
Q Consensus       177 ~~~~~~~~  184 (374)
                      ..+...+.
T Consensus       303 ~~~~~~~~  310 (388)
T PRK12723        303 KEIFHQFS  310 (388)
T ss_pred             HHHHHHhc
Confidence            66655553

>PRK08084 DNA replication initiation factor; Provisional

Probab=96.86  E-value=0.0051  Score=51.58  Aligned_cols=16  Identities=19%  Similarity=0.169  Sum_probs=13.8

Q ss_pred             CCEEEEccCCCCchhh
Q 037567           29 RDCLVVMATGSGKSLC   44 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~   44 (374)
                      ..+++.||+|+|||..
T Consensus        46 ~~l~l~Gp~G~GKThL   61 (235)
T PRK08084         46 GYIYLWSREGAGRSHL   61 (235)
T ss_pred             CeEEEECCCCCCHHHH
Confidence            5689999999999954

>PRK08116 hypothetical protein; Validated

Probab=96.86  E-value=0.014  Score=49.93  Aligned_cols=43  Identities=14%  Similarity=0.148  Sum_probs=25.7

Q ss_pred             CEEEEccCCCCchhhhhcc---ccccCCcEEEEcchHHHHHHHHHHH
Q 037567           30 DCLVVMATGSGKSLCYQLP---PLVTGKTALVVSPLISLMQDQVMSL   73 (374)
Q Consensus        30 ~~l~~a~tGsGKT~~~~l~---~~~~~~~~lil~P~~~l~~q~~~~~   73 (374)
                      .+++.|++|+|||..+...   +..++..+++ .+..++..++...+
T Consensus       116 gl~l~G~~GtGKThLa~aia~~l~~~~~~v~~-~~~~~ll~~i~~~~  161 (268)
T PRK08116        116 GLLLWGSVGTGKTYLAACIANELIEKGVPVIF-VNFPQLLNRIKSTY  161 (268)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHHHcCCeEEE-EEHHHHHHHHHHHH
Confidence            4899999999999653322   1223445544 45556666554443

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=96.79  E-value=0.0082  Score=55.22  Aligned_cols=43  Identities=21%  Similarity=0.172  Sum_probs=26.1

Q ss_pred             CCEEEEccCCCCchhhhhcc---ccccCCcEEEEcchHHHHHHHHHH
Q 037567           29 RDCLVVMATGSGKSLCYQLP---PLVTGKTALVVSPLISLMQDQVMS   72 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~~l~---~~~~~~~~lil~P~~~l~~q~~~~   72 (374)
                      +.+++.||+|+|||......   +...+.+++++.. ..+..+....
T Consensus       142 npl~L~G~~G~GKTHLl~Ai~~~l~~~~~~v~yi~~-~~f~~~~~~~  187 (445)
T PRK12422        142 NPIYLFGPEGSGKTHLMQAAVHALRESGGKILYVRS-ELFTEHLVSA  187 (445)
T ss_pred             ceEEEEcCCCCCHHHHHHHHHHHHHHcCCCEEEeeH-HHHHHHHHHH
Confidence            45899999999999543221   2234667776654 3555544433

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.78  E-value=0.0065  Score=55.64  Aligned_cols=16  Identities=19%  Similarity=0.270  Sum_probs=13.8

Q ss_pred             EEEEccCCCCchhhhh
Q 037567           31 CLVVMATGSGKSLCYQ   46 (374)
Q Consensus        31 ~l~~a~tGsGKT~~~~   46 (374)
                      ++++||+|+|||.++.
T Consensus        43 ~Lf~GP~GtGKTTlAr   58 (484)
T PRK14956         43 YIFFGPRGVGKTTIAR   58 (484)
T ss_pred             EEEECCCCCCHHHHHH
Confidence            6999999999997654

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=96.76  E-value=0.0073  Score=56.07  Aligned_cols=44  Identities=18%  Similarity=0.144  Sum_probs=26.0

Q ss_pred             CCEEEEccCCCCchhhhhcc---cccc--CCcEEEEcchHHHHHHHHHHH
Q 037567           29 RDCLVVMATGSGKSLCYQLP---PLVT--GKTALVVSPLISLMQDQVMSL   73 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~~l~---~~~~--~~~~lil~P~~~l~~q~~~~~   73 (374)
                      +.+++.||+|+|||......   +...  +.+++++ +...+..+....+
T Consensus       149 ~~l~l~G~~G~GKThL~~ai~~~~~~~~~~~~v~yi-~~~~~~~~~~~~~  197 (450)
T PRK00149        149 NPLFIYGGVGLGKTHLLHAIGNYILEKNPNAKVVYV-TSEKFTNDFVNAL  197 (450)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEE-EHHHHHHHHHHHH
Confidence            35789999999999543221   1122  4455555 4445666554444

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=96.76  E-value=0.0075  Score=47.26  Aligned_cols=35  Identities=26%  Similarity=0.190  Sum_probs=22.4

Q ss_pred             EEEEccCCCCchhhhhccc---cccCCcEEEEcchHHH
Q 037567           31 CLVVMATGSGKSLCYQLPP---LVTGKTALVVSPLISL   65 (374)
Q Consensus        31 ~l~~a~tGsGKT~~~~l~~---~~~~~~~lil~P~~~l   65 (374)
                      +++.|++|+|||......+   ...+.+++++......
T Consensus         2 ~~i~G~~G~GKT~l~~~i~~~~~~~~~~v~~~~~e~~~   39 (165)
T cd01120           2 ILVFGPTGSGKTTLALQLALNIATKGGKVVYVDIEEEI   39 (165)
T ss_pred             eeEeCCCCCCHHHHHHHHHHHHHhcCCEEEEEECCcch
Confidence            5789999999996543221   2246667776665433

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.

>PHA02533 17 large terminase protein; Provisional

Probab=96.75  E-value=0.0071  Score=56.84  Aligned_cols=63  Identities=19%  Similarity=0.205  Sum_probs=49.6

Q ss_pred             CCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhcc-----ccccCCcEEEEcchHHHHHHHHHHHHH
Q 037567           13 VFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLP-----PLVTGKTALVVSPLISLMQDQVMSLKQ   75 (374)
Q Consensus        13 ~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~-----~~~~~~~~lil~P~~~l~~q~~~~~~~   75 (374)
                      .|.|+|.+.+..+..++-.++..+=..|||.+....     +...+..+++++|+...+...++.++.
T Consensus        59 ~L~p~Q~~i~~~~~~~R~~ii~~aRq~GKStl~a~~al~~a~~~~~~~v~i~A~~~~QA~~vF~~ik~  126 (534)
T PHA02533         59 QMRDYQKDMLKIMHKNRFNACNLSRQLGKTTVVAIFLLHYVCFNKDKNVGILAHKASMAAEVLDRTKQ  126 (534)
T ss_pred             CCcHHHHHHHHHHhcCeEEEEEEcCcCChHHHHHHHHHHHHHhCCCCEEEEEeCCHHHHHHHHHHHHH
Confidence            488999999988866666788899999999654321     224567999999999999988887764

>TIGR01075 uvrD DNA helicase II

Probab=96.74  E-value=0.0019  Score=63.64  Aligned_cols=63  Identities=14%  Similarity=0.148  Sum_probs=49.2

Q ss_pred             CCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccc---cc----cCCcEEEEcchHHHHHHHHHHHHHc
Q 037567           12 SVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPP---LV----TGKTALVVSPLISLMQDQVMSLKQR   76 (374)
Q Consensus        12 ~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~---~~----~~~~~lil~P~~~l~~q~~~~~~~~   76 (374)
                      ..|+|-|.+++..  ...+++|.|.+|||||.+..--+   +.    ...++|+++-|+..+.++.+.+.+.
T Consensus         3 ~~Ln~~Q~~av~~--~~g~~lV~AgaGSGKT~~L~~Ria~Li~~~~v~p~~IL~lTFTnkAA~em~~Rl~~~   72 (715)
T TIGR01075         3 DGLNDKQREAVAA--PPGNLLVLAGAGSGKTRVLTHRIAWLLSVENASPHSIMAVTFTNKAAAEMRHRIGAL   72 (715)
T ss_pred             cccCHHHHHHHcC--CCCCEEEEecCCCCHHHHHHHHHHHHHHcCCCCHHHeEeeeccHHHHHHHHHHHHHH
Confidence            4689999999864  45789999999999996532111   11    3467999999999999999998875

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

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

Probab=96.73  E-value=0.0018  Score=54.03  Aligned_cols=98  Identities=17%  Similarity=0.159  Sum_probs=54.5

Q ss_pred             CCCEEEEccCCCCchhhhh---cccccc-CCcEEEEcchHHHHHHHHHHHHHcCCceEEcCCCCCchhhhhhhhcCCeeE
Q 037567           28 KRDCLVVMATGSGKSLCYQ---LPPLVT-GKTALVVSPLISLMQDQVMSLKQRGINAEFLGSAQTDSSVQTKAETGYFQL  103 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~---l~~~~~-~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i  103 (374)
                      +..+++.|++|+|||...+   ...+.+ +.++++++-. +-..++.+.+..+|....-.            ...+...+
T Consensus        19 gs~~li~G~~GsGKT~l~~q~l~~~~~~~ge~vlyvs~e-e~~~~l~~~~~s~g~d~~~~------------~~~g~l~~   85 (226)
T PF06745_consen   19 GSVVLISGPPGSGKTTLALQFLYNGLKNFGEKVLYVSFE-EPPEELIENMKSFGWDLEEY------------EDSGKLKI   85 (226)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHHHHHHT--EEEEESS-S-HHHHHHHHHTTTS-HHHH------------HHTTSEEE
T ss_pred             CcEEEEEeCCCCCcHHHHHHHHHHhhhhcCCcEEEEEec-CCHHHHHHHHHHcCCcHHHH------------hhcCCEEE
Confidence            5678999999999995533   334456 7888888743 55677888888876542211            11111122


Q ss_pred             EEEcCc-------ccccCchhhHHHHHhcCccEEEEeccchh
Q 037567          104 LFMTPE-------KACIIPISFWSKLLKAGVCLFAVDEAHCI  138 (374)
Q Consensus       104 ~i~T~~-------~l~~~~~~~~~~~~~~~~~~vviDE~h~~  138 (374)
                      +=+.+.       .+..+...........+.+.+|||-...+
T Consensus        86 ~d~~~~~~~~~~~~~~~l~~~i~~~i~~~~~~~vVIDsls~l  127 (226)
T PF06745_consen   86 IDAFPERIGWSPNDLEELLSKIREAIEELKPDRVVIDSLSAL  127 (226)
T ss_dssp             EESSGGGST-TSCCHHHHHHHHHHHHHHHTSSEEEEETHHHH
T ss_pred             EecccccccccccCHHHHHHHHHHHHHhcCCCEEEEECHHHH
Confidence            222222       22222233333333445689999999888

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 ....

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=96.70  E-value=0.013  Score=57.28  Aligned_cols=90  Identities=18%  Similarity=0.190  Sum_probs=72.0

Q ss_pred             chHHHHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHH----cCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEecc
Q 037567          212 SFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQ----LGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMA  287 (374)
Q Consensus       212 ~~~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~----~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~  287 (374)
                      .+....+..++.....+.+++|.+|+..-+.+.++.+++    .++++..++|+++..++...+..+.+|+.+|+|+|+.
T Consensus       294 GKT~va~~~il~~~~~g~q~lilaPT~~LA~Q~~~~l~~l~~~~~i~v~ll~G~~~~~~r~~~~~~l~~g~~~IvVgT~~  373 (681)
T PRK10917        294 GKTVVAALAALAAIEAGYQAALMAPTEILAEQHYENLKKLLEPLGIRVALLTGSLKGKERREILEAIASGEADIVIGTHA  373 (681)
T ss_pred             cHHHHHHHHHHHHHHcCCeEEEEeccHHHHHHHHHHHHHHHhhcCcEEEEEcCCCCHHHHHHHHHHHhCCCCCEEEchHH
Confidence            333444445555556788999999999999988887765    3688999999999999999999999999999999984


Q ss_pred             -ccccccccCccEEE
Q 037567          288 -FGMGIDKPDVRHVI  301 (374)
Q Consensus       288 -~~~G~d~~~~~~vi  301 (374)
                       +...+.+.++.+||
T Consensus       374 ll~~~v~~~~l~lvV  388 (681)
T PRK10917        374 LIQDDVEFHNLGLVI  388 (681)
T ss_pred             HhcccchhcccceEE
Confidence             44566777787766

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.68  E-value=0.0084  Score=53.32  Aligned_cols=126  Identities=17%  Similarity=0.080  Sum_probs=64.8

Q ss_pred             CCEEEEccCCCCchhhhhcccc---ccCCcEEEEcc-h--HHHHHHHHHHHHHcCCceEEcCCCCCchhhhhhhhcCCee
Q 037567           29 RDCLVVMATGSGKSLCYQLPPL---VTGKTALVVSP-L--ISLMQDQVMSLKQRGINAEFLGSAQTDSSVQTKAETGYFQ  102 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~~l~~~---~~~~~~lil~P-~--~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  102 (374)
                      +.+.+.||+|+|||.+....+.   ..+.++.++.. +  ...++|+.......++.+..                    
T Consensus       242 ~vI~LVGptGvGKTTTiaKLA~~L~~~GkkVglI~aDt~RiaAvEQLk~yae~lgipv~v--------------------  301 (436)
T PRK11889        242 QTIALIGPTGVGKTTTLAKMAWQFHGKKKTVGFITTDHSRIGTVQQLQDYVKTIGFEVIA--------------------  301 (436)
T ss_pred             cEEEEECCCCCcHHHHHHHHHHHHHHcCCcEEEEecCCcchHHHHHHHHHhhhcCCcEEe--------------------
Confidence            4568999999999966443221   23555554443 2  24566666554444433221                    


Q ss_pred             EEEEcCcccccCchhhHHHHH-hcCccEEEEeccchhhcccCcchHHHHHHHHHHHhc-CCCCeeEEEeecCcccHHHHH
Q 037567          103 LLFMTPEKACIIPISFWSKLL-KAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFL-LGVPFVALTATATEKVRIDII  180 (374)
Q Consensus       103 i~i~T~~~l~~~~~~~~~~~~-~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~-~~~~~i~~SaT~~~~~~~~~~  180 (374)
                        ..+|+.+..    ...... ..++++|+||-+-+....    ...+..+.+..... +....+.+|||........+.
T Consensus       302 --~~d~~~L~~----aL~~lk~~~~~DvVLIDTaGRs~kd----~~lm~EL~~~lk~~~PdevlLVLsATtk~~d~~~i~  371 (436)
T PRK11889        302 --VRDEAAMTR----ALTYFKEEARVDYILIDTAGKNYRA----SETVEEMIETMGQVEPDYICLTLSASMKSKDMIEII  371 (436)
T ss_pred             --cCCHHHHHH----HHHHHHhccCCCEEEEeCccccCcC----HHHHHHHHHHHhhcCCCeEEEEECCccChHHHHHHH
Confidence              123332221    111111 125789999988764321    11223333333322 233456789987776655566


Q ss_pred             HhcC
Q 037567          181 NSLK  184 (374)
Q Consensus       181 ~~~~  184 (374)
                      ..+.
T Consensus       372 ~~F~  375 (436)
T PRK11889        372 TNFK  375 (436)
T ss_pred             HHhc
Confidence            5554

>PRK06921 hypothetical protein; Provisional

Probab=96.67  E-value=0.018  Score=49.14  Aligned_cols=41  Identities=20%  Similarity=0.233  Sum_probs=25.0

Q ss_pred             CCCEEEEccCCCCchhhhhc---ccccc-CCcEEEEcchHHHHHHH
Q 037567           28 KRDCLVVMATGSGKSLCYQL---PPLVT-GKTALVVSPLISLMQDQ   69 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~l---~~~~~-~~~~lil~P~~~l~~q~   69 (374)
                      +.++++.|++|+|||..+..   .+..+ +..++++. ..++..+.
T Consensus       117 ~~~l~l~G~~G~GKThLa~aia~~l~~~~g~~v~y~~-~~~l~~~l  161 (266)
T PRK06921        117 KNSIALLGQPGSGKTHLLTAAANELMRKKGVPVLYFP-FVEGFGDL  161 (266)
T ss_pred             CCeEEEECCCCCcHHHHHHHHHHHHhhhcCceEEEEE-HHHHHHHH
Confidence            56789999999999954322   12233 55565554 44555543

>TIGR00596 rad1 DNA repair protein (rad1)

Probab=96.65  E-value=0.0076  Score=59.26  Aligned_cols=41  Identities=15%  Similarity=0.409  Sum_probs=30.2

Q ss_pred             CcchHHHHHHHHHHhh------cCCCcEEEEecchhHHHHHHHHHHH
Q 037567          210 GQSFVDELVQEILKSV------AGAGSIIVYCMTIKDVEEISKALKQ  250 (374)
Q Consensus       210 ~~~~~~~~~~~~~~~~------~~~~~~lVf~~~~~~~~~l~~~l~~  250 (374)
                      +...+.+++.++....      .+.+++||||++..+|..+.+.|..
T Consensus       271 Kw~~L~eiL~eI~~~~~~~~~~~~~~~iLI~~~d~~T~~qL~~~L~~  317 (814)
T TIGR00596       271 KWEVLTDVLKEISHEMRMTNRLQGPGKVLIMCSDNRTCLQLRDYLTT  317 (814)
T ss_pred             CHHHHHHHHHHHHhHHhhhcccCCCCcEEEEEcchHHHHHHHHHHHh
Confidence            3445566666665542      3457899999999999999998865

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

>PF03354 Terminase_1: Phage Terminase ; InterPro: IPR005021 This entry is represented by Lactococcus phage bIL285, Orf41 (terminase)

Probab=96.63  E-value=0.0052  Score=57.41  Aligned_cols=61  Identities=18%  Similarity=0.183  Sum_probs=45.4

Q ss_pred             hhHHHHHHHHHc-----C----CCEEEEccCCCCchhhhhccc-----c--ccCCcEEEEcchHHHHHHHHHHHHHc
Q 037567           16 PYQKDVIQRIIE-----K----RDCLVVMATGSGKSLCYQLPP-----L--VTGKTALVVSPLISLMQDQVMSLKQR   76 (374)
Q Consensus        16 ~~Q~~~~~~~~~-----~----~~~l~~a~tGsGKT~~~~l~~-----~--~~~~~~lil~P~~~l~~q~~~~~~~~   76 (374)
                      |+|..++..++-     +    +.+++.-|=|.|||......+     +  ..+..+++++++++.+...++.+..+
T Consensus         1 PwQ~fi~~~i~G~~~~~g~rrf~~~~l~v~RkNGKS~l~a~i~ly~l~~~g~~~~~i~~~A~~~~QA~~~f~~~~~~   77 (477)
T PF03354_consen    1 PWQKFILRSIFGWRKDDGRRRFREVYLEVPRKNGKSTLAAAIALYMLFLDGEPGAEIYCAANTRDQAKIVFDEAKKM   77 (477)
T ss_pred             CcHHHHHHHHhceEcCCCCEEEEEEEEEEcCccCccHHHHHHHHHHHhcCCccCceEEEEeCCHHHHHHHHHHHHHH
Confidence            688888887762     1    356888899999995432221     1  24678999999999999999888765

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

>PRK11773 uvrD DNA-dependent helicase II; Provisional

Probab=96.61  E-value=0.0025  Score=62.73  Aligned_cols=63  Identities=14%  Similarity=0.160  Sum_probs=49.2

Q ss_pred             CCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccc---c----ccCCcEEEEcchHHHHHHHHHHHHHc
Q 037567           12 SVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPP---L----VTGKTALVVSPLISLMQDQVMSLKQR   76 (374)
Q Consensus        12 ~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~---~----~~~~~~lil~P~~~l~~q~~~~~~~~   76 (374)
                      ..|+|-|.+++..  ...+++|.|++|||||.+..--+   +    ....++|+++-|+..+.++.+.+.+.
T Consensus         8 ~~Ln~~Q~~av~~--~~g~~lV~AgaGSGKT~vl~~Ria~Li~~~~v~p~~IL~lTFT~kAA~Em~~Rl~~~   77 (721)
T PRK11773          8 DSLNDKQREAVAA--PLGNMLVLAGAGSGKTRVLVHRIAWLMQVENASPYSIMAVTFTNKAAAEMRHRIEQL   77 (721)
T ss_pred             HhcCHHHHHHHhC--CCCCEEEEecCCCCHHHHHHHHHHHHHHcCCCChhHeEeeeccHHHHHHHHHHHHHH
Confidence            4699999999874  45789999999999996532111   1    13567999999999999999998775

>PF13173 AAA_14: AAA domain

Probab=96.56  E-value=0.0096  Score=44.68  Aligned_cols=40  Identities=20%  Similarity=0.326  Sum_probs=24.2

Q ss_pred             CccEEEEeccchhhcccCcchHHHHHHHHHHHhcCCCCeeEEEeecCc
Q 037567          126 GVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATE  173 (374)
Q Consensus       126 ~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~SaT~~~  173 (374)
                      .-.++++||+|.+.++.       ..+..+....++. .+.+|++...
T Consensus        61 ~~~~i~iDEiq~~~~~~-------~~lk~l~d~~~~~-~ii~tgS~~~  100 (128)
T PF13173_consen   61 GKKYIFIDEIQYLPDWE-------DALKFLVDNGPNI-KIILTGSSSS  100 (128)
T ss_pred             CCcEEEEehhhhhccHH-------HHHHHHHHhccCc-eEEEEccchH
Confidence            44689999999987644       4455555543333 4555555443

>COG1222 RPT1 ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones]

Probab=96.54  E-value=0.02  Score=49.68  Aligned_cols=40  Identities=23%  Similarity=0.215  Sum_probs=27.0

Q ss_pred             CCCEEEEccCCCCchhhhhccccccCCcEEEEcchHHHHHH
Q 037567           28 KRDCLVVMATGSGKSLCYQLPPLVTGKTALVVSPLISLMQD   68 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~l~~~~~~~~~lil~P~~~l~~q   68 (374)
                      -+.+++.||+|+|||+.+-..+-+.+.. +|=+...+|++.
T Consensus       185 PKGVLLYGPPGTGKTLLAkAVA~~T~At-FIrvvgSElVqK  224 (406)
T COG1222         185 PKGVLLYGPPGTGKTLLAKAVANQTDAT-FIRVVGSELVQK  224 (406)
T ss_pred             CCceEeeCCCCCcHHHHHHHHHhccCce-EEEeccHHHHHH
Confidence            4789999999999998754444444444 444444477764

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

Probab=96.50  E-value=0.042  Score=55.13  Aligned_cols=142  Identities=15%  Similarity=0.134  Sum_probs=105.4

Q ss_pred             cchHHHHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHHc----CCceeeeecCCChHHHHHHHHhhhcCCeeEEEEec
Q 037567          211 QSFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQL----GVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATM  286 (374)
Q Consensus       211 ~~~~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~  286 (374)
                      ..+.+-.++.......+++++.|.+||.--|++=++.++++    ++++..+..-.+.++..++++...+|+++|+|.|.
T Consensus       626 FGKTEVAmRAAFkAV~~GKQVAvLVPTTlLA~QHy~tFkeRF~~fPV~I~~LSRF~s~kE~~~il~~la~G~vDIvIGTH  705 (1139)
T COG1197         626 FGKTEVAMRAAFKAVMDGKQVAVLVPTTLLAQQHYETFKERFAGFPVRIEVLSRFRSAKEQKEILKGLAEGKVDIVIGTH  705 (1139)
T ss_pred             CcHHHHHHHHHHHHhcCCCeEEEEcccHHhHHHHHHHHHHHhcCCCeeEEEecccCCHHHHHHHHHHHhcCCccEEEech
Confidence            45567778888888889999999999988777766666653    66777888888999999999999999999999998


Q ss_pred             -cccccccccCccEEEEECCCCChhHHHHhhc-------------------------cCCC---CCCceEEEEEeeccCC
Q 037567          287 -AFGMGIDKPDVRHVIHYGCPKTLESYYQESG-------------------------RCGR---DGIASVCWLYYARSNF  337 (374)
Q Consensus       287 -~~~~G~d~~~~~~vi~~~~p~s~~~~~Q~~G-------------------------R~~R---~~~~g~~~~~~~~~~~  337 (374)
                       .++.++-+.++-.+|.-.        .||.|                         |+.-   .|-....++-.+|.+.
T Consensus       706 rLL~kdv~FkdLGLlIIDE--------EqRFGVk~KEkLK~Lr~~VDvLTLSATPIPRTL~Msm~GiRdlSvI~TPP~~R  777 (1139)
T COG1197         706 RLLSKDVKFKDLGLLIIDE--------EQRFGVKHKEKLKELRANVDVLTLSATPIPRTLNMSLSGIRDLSVIATPPEDR  777 (1139)
T ss_pred             HhhCCCcEEecCCeEEEec--------hhhcCccHHHHHHHHhccCcEEEeeCCCCcchHHHHHhcchhhhhccCCCCCC
Confidence             777888888888777211        11111                         1111   1344566777777777


Q ss_pred             CcccceeccccchHHHHHHHHHH
Q 037567          338 AKGDFYCGESQTENQRTAIMESL  360 (374)
Q Consensus       338 ~~~~~~~~~~~~~~~~~~~~~~l  360 (374)
                      --++-+.....+...+..+++++
T Consensus       778 ~pV~T~V~~~d~~~ireAI~REl  800 (1139)
T COG1197         778 LPVKTFVSEYDDLLIREAILREL  800 (1139)
T ss_pred             cceEEEEecCChHHHHHHHHHHH
Confidence            77777777777777777776665

>COG4626 Phage terminase-like protein, large subunit [General function prediction only]

Probab=96.50  E-value=0.011  Score=54.33  Aligned_cols=146  Identities=12%  Similarity=0.074  Sum_probs=80.8

Q ss_pred             CCchhHHHHHHHHHc------C----CCEEEEccCCCCchhhhh-------ccccccCCcEEEEcchHHHHHHHHHHHHH
Q 037567           13 VFRPYQKDVIQRIIE------K----RDCLVVMATGSGKSLCYQ-------LPPLVTGKTALVVSPLISLMQDQVMSLKQ   75 (374)
Q Consensus        13 ~~~~~Q~~~~~~~~~------~----~~~l~~a~tGsGKT~~~~-------l~~~~~~~~~lil~P~~~l~~q~~~~~~~   75 (374)
                      ++-|||..++.+++-      +    +.+++..|-+-|||..+.       +....++..+.|++|+.+-+.+.+..++.
T Consensus        61 ~l~PwQkFiia~l~G~~~k~T~~rrf~e~fI~v~RkngKt~l~A~i~~~~~l~~~~~~~~~~i~A~s~~qa~~~F~~ar~  140 (546)
T COG4626          61 SLEPWQKFIVAALFGFYDKQTGIRRFKEAFIFIPRKNGKSTLAAGIMMTALLLNWRSGAGIYILAPSVEQAANSFNPARD  140 (546)
T ss_pred             ccchHHHHHHHHHhceeecCCCceEEEEEEEEEecCCchHHHHHHHHHHHHHhhhhcCCcEEEEeccHHHHHHhhHHHHH
Confidence            588999999999872      1    356899999999995432       11123688899999999999988887765


Q ss_pred             cCCceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHH
Q 037567           76 RGINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKL  155 (374)
Q Consensus        76 ~~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~  155 (374)
                      .-....       ..............|...--........+........+..+.|+||.|.....+    ..++.+..-
T Consensus       141 mv~~~~-------~l~~~~~~q~~s~~i~~~~~~s~ik~~aa~~~~~Dg~~~~~~I~DEih~f~~~~----~~~~~~~~g  209 (546)
T COG4626         141 MVKRDD-------DLRDLCNVQTHSRTITHRKTDSTIKAVAADPNTVDGLNSVGAIIDELHLFGKQE----DMYSEAKGG  209 (546)
T ss_pred             HHHhCc-------chhhhhccccceeEEEecccceeeeeeccCCCcccCCCcceEEEehhhhhcCHH----HHHHHHHhh
Confidence            411111       000000000000011111111111111222233344566799999999876532    222333333


Q ss_pred             HHhcCCCCeeEEEe
Q 037567          156 RTFLLGVPFVALTA  169 (374)
Q Consensus       156 ~~~~~~~~~i~~Sa  169 (374)
                      ....++..+++.|-
T Consensus       210 ~~ar~~~l~~~ITT  223 (546)
T COG4626         210 LGARPEGLVVYITT  223 (546)
T ss_pred             hccCcCceEEEEec
Confidence            34445666777764

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=96.48  E-value=0.012  Score=50.23  Aligned_cols=17  Identities=18%  Similarity=0.212  Sum_probs=14.4

Q ss_pred             CCEEEEccCCCCchhhh
Q 037567           29 RDCLVVMATGSGKSLCY   45 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~   45 (374)
                      .++++.||+|+|||..+
T Consensus        43 ~~vll~GppGtGKTtlA   59 (261)
T TIGR02881        43 LHMIFKGNPGTGKTTVA   59 (261)
T ss_pred             ceEEEEcCCCCCHHHHH
Confidence            36799999999999664

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.

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=96.48  E-value=0.022  Score=52.48  Aligned_cols=44  Identities=16%  Similarity=0.184  Sum_probs=25.6

Q ss_pred             CCEEEEccCCCCchhhhhcc---ccc--cCCcEEEEcchHHHHHHHHHHH
Q 037567           29 RDCLVVMATGSGKSLCYQLP---PLV--TGKTALVVSPLISLMQDQVMSL   73 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~~l~---~~~--~~~~~lil~P~~~l~~q~~~~~   73 (374)
                      +.+++.||+|+|||......   +..  .+.+++++.. ..+.++....+
T Consensus       131 n~l~lyG~~G~GKTHLl~ai~~~l~~~~~~~~v~yi~~-~~f~~~~~~~~  179 (440)
T PRK14088        131 NPLFIYGGVGLGKTHLLQSIGNYVVQNEPDLRVMYITS-EKFLNDLVDSM  179 (440)
T ss_pred             CeEEEEcCCCCcHHHHHHHHHHHHHHhCCCCeEEEEEH-HHHHHHHHHHH
Confidence            35899999999999543221   111  2446666654 34555444443

>PRK13709 conjugal transfer nickase/helicase TraI; Provisional

Probab=96.47  E-value=0.044  Score=58.32  Aligned_cols=58  Identities=16%  Similarity=0.191  Sum_probs=43.9

Q ss_pred             CCchhHHHHHHHHHcC--CCEEEEccCCCCchhhhh--ccccc-----cCCcEEEEcchHHHHHHHH
Q 037567           13 VFRPYQKDVIQRIIEK--RDCLVVMATGSGKSLCYQ--LPPLV-----TGKTALVVSPLISLMQDQV   70 (374)
Q Consensus        13 ~~~~~Q~~~~~~~~~~--~~~l~~a~tGsGKT~~~~--l~~~~-----~~~~~lil~P~~~l~~q~~   70 (374)
                      .+++.|.+++..++.+  +-++|.|.+|+|||.+.-  ..++.     .+.+++.++||..-+..+.
T Consensus       967 ~Lt~~Q~~Av~~il~s~dr~~~I~G~AGTGKTT~l~~v~~~~~~l~~~~~~~V~glAPTgrAAk~L~ 1033 (1747)
T PRK13709        967 GLTSGQRAATRMILESTDRFTVVQGYAGVGKTTQFRAVMSAVNTLPESERPRVVGLGPTHRAVGEMR 1033 (1747)
T ss_pred             CCCHHHHHHHHHHHhCCCcEEEEEeCCCCCHHHHHHHHHHHHHHhhcccCceEEEECCcHHHHHHHH
Confidence            5899999999999875  467899999999996532  22221     2467899999988877654

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=96.47  E-value=0.022  Score=55.28  Aligned_cols=88  Identities=17%  Similarity=0.210  Sum_probs=70.8

Q ss_pred             HHHHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHHc----CCceeeeecCCChHHHHHHHHhhhcCCeeEEEEec-cc
Q 037567          214 VDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQL----GVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATM-AF  288 (374)
Q Consensus       214 ~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~-~~  288 (374)
                      ....+..++.....+.++++.+|+..-+.+.++.+++.    ++++..++|+++..++...++...+|+.+|+|+|+ .+
T Consensus       270 T~va~l~il~~~~~g~qvlilaPT~~LA~Q~~~~~~~l~~~~gi~v~lltg~~~~~~r~~~~~~i~~g~~~IiVgT~~ll  349 (630)
T TIGR00643       270 TLVAALAMLAAIEAGYQVALMAPTEILAEQHYNSLRNLLAPLGIEVALLTGSLKGKRRKELLETIASGQIHLVVGTHALI  349 (630)
T ss_pred             HHHHHHHHHHHHHcCCcEEEECCHHHHHHHHHHHHHHHhcccCcEEEEEecCCCHHHHHHHHHHHhCCCCCEEEecHHHH
Confidence            33344445555567889999999999999888877653    68899999999999999999999999999999998 44


Q ss_pred             cccccccCccEEE
Q 037567          289 GMGIDKPDVRHVI  301 (374)
Q Consensus       289 ~~G~d~~~~~~vi  301 (374)
                      ...+++.++.+||
T Consensus       350 ~~~~~~~~l~lvV  362 (630)
T TIGR00643       350 QEKVEFKRLALVI  362 (630)
T ss_pred             hccccccccceEE
Confidence            4566777777766

>PF05876 Terminase_GpA: Phage terminase large subunit (GpA); InterPro: IPR008866 This entry is represented by Bacteriophage lambda, GpA

Probab=96.47  E-value=0.021  Score=54.16  Aligned_cols=160  Identities=16%  Similarity=0.084  Sum_probs=88.6

Q ss_pred             CCchhHHHHHHHHHcC--CCEEEEccCCCCchhhhhcccc----ccCCcEEEEcchHHHHHHHHHH-HHHc---CCceE-
Q 037567           13 VFRPYQKDVIQRIIEK--RDCLVVMATGSGKSLCYQLPPL----VTGKTALVVSPLISLMQDQVMS-LKQR---GINAE-   81 (374)
Q Consensus        13 ~~~~~Q~~~~~~~~~~--~~~l~~a~tGsGKT~~~~l~~~----~~~~~~lil~P~~~l~~q~~~~-~~~~---~~~~~-   81 (374)
                      ..+|||.+.+.++...  +.+.+..++-+|||.+.+..+.    .....++++.||...+.++.+. +...   ..... 
T Consensus        16 ~~~Py~~eimd~~~~~~v~~Vv~~k~aQ~GkT~~~~n~~g~~i~~~P~~~l~v~Pt~~~a~~~~~~rl~Pmi~~sp~l~~   95 (557)
T PF05876_consen   16 DRTPYLREIMDALSDPSVREVVVMKSAQVGKTELLLNWIGYSIDQDPGPMLYVQPTDDAAKDFSKERLDPMIRASPVLRR   95 (557)
T ss_pred             CCChhHHHHHHhcCCcCccEEEEEEcchhhHhHHHHhhceEEEEeCCCCEEEEEEcHHHHHHHHHHHHHHHHHhCHHHHH
Confidence            5789999999998765  5778999999999986544333    2467899999999999987643 4332   00000 


Q ss_pred             EcCC---CCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhc-ccCcchHHHHHHHHHHH
Q 037567           82 FLGS---AQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISE-WGHDFRLEYKQLDKLRT  157 (374)
Q Consensus        82 ~~~~---~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~-~~~~~~~~~~~~~~~~~  157 (374)
                      .+..   .........+.-.+ -.+.+....+-        ..+....++++++||++.+.. .+.+-.+.-....+...
T Consensus        96 ~~~~~~~~~~~~t~~~k~f~g-g~l~~~ga~S~--------~~l~s~~~r~~~~DEvD~~p~~~~~eGdp~~la~~R~~t  166 (557)
T PF05876_consen   96 KLSPSKSRDSGNTILYKRFPG-GFLYLVGANSP--------SNLRSRPARYLLLDEVDRYPDDVGGEGDPVELAEKRTKT  166 (557)
T ss_pred             HhCchhhcccCCchhheecCC-CEEEEEeCCCC--------cccccCCcCEEEEechhhccccCccCCCHHHHHHHHHhh
Confidence            1111   00111111111112 23444433322        223335678999999999853 12222222222233333


Q ss_pred             hcCCCCeeEEEeecCcccHHHHHHh
Q 037567          158 FLLGVPFVALTATATEKVRIDIINS  182 (374)
Q Consensus       158 ~~~~~~~i~~SaT~~~~~~~~~~~~  182 (374)
                      + .....+++.+||.......+...
T Consensus       167 f-~~~~K~~~~STPt~~~~~~I~~~  190 (557)
T PF05876_consen  167 F-GSNRKILRISTPTIEGTSRIERL  190 (557)
T ss_pred             h-ccCcEEEEeCCCCCCCCCHHHHH
Confidence            3 24456666678877643334443

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several phage terminase large subunit proteins as well as related sequences from several bacterial species. The DNA packaging enzyme of bacteriophage lambda, terminase, is a heteromultimer composed of a small subunit, gpNu1, and a large subunit, gpA, products of the Nu1 and A genes, respectively. Terminase is involved in the site-specific binding and cutting of the DNA in the initial stages of packaging. It is now known that gpA is actively involved in late stages of packaging, including DNA translocation, and that this enzyme contains separate functional domains for its early and late packaging activities [].

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=96.43  E-value=0.016  Score=53.60  Aligned_cols=45  Identities=13%  Similarity=0.097  Sum_probs=27.5

Q ss_pred             CCEEEEccCCCCchhhhhccc---c--ccCCcEEEEcchHHHHHHHHHHHH
Q 037567           29 RDCLVVMATGSGKSLCYQLPP---L--VTGKTALVVSPLISLMQDQVMSLK   74 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~~l~~---~--~~~~~~lil~P~~~l~~q~~~~~~   74 (374)
                      +.+++.|++|+|||.......   .  ..+.+++++.+ .++..+....+.
T Consensus       142 npl~i~G~~G~GKTHLl~Ai~~~l~~~~~~~~v~yv~~-~~f~~~~~~~l~  191 (450)
T PRK14087        142 NPLFIYGESGMGKTHLLKAAKNYIESNFSDLKVSYMSG-DEFARKAVDILQ  191 (450)
T ss_pred             CceEEECCCCCcHHHHHHHHHHHHHHhCCCCeEEEEEH-HHHHHHHHHHHH
Confidence            457899999999994422111   1  23456666555 466666665554

>PRK06871 DNA polymerase III subunit delta'; Validated

Probab=96.43  E-value=0.014  Score=51.11  Aligned_cols=32  Identities=19%  Similarity=0.292  Sum_probs=24.7

Q ss_pred             CchhHHHHHHHHHc----C---CCEEEEccCCCCchhhh
Q 037567           14 FRPYQKDVIQRIIE----K---RDCLVVMATGSGKSLCY   45 (374)
Q Consensus        14 ~~~~Q~~~~~~~~~----~---~~~l~~a~tGsGKT~~~   45 (374)
                      .+|+|...++.+.+    +   +-.++.||.|.||+..+
T Consensus         3 ~yPW~~~~~~~l~~~~~~~rl~HA~Lf~G~~G~GK~~lA   41 (325)
T PRK06871          3 LYPWLQPTYQQITQAFQQGLGHHALLFKADSGLGTEQLI   41 (325)
T ss_pred             CCcchHHHHHHHHHHHHcCCcceeEEeECCCCCCHHHHH
Confidence            57888888887764    2   34579999999999554

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=96.42  E-value=0.017  Score=52.93  Aligned_cols=42  Identities=19%  Similarity=0.156  Sum_probs=24.3

Q ss_pred             CEEEEccCCCCchhhhhcc---cccc--CCcEEEEcchHHHHHHHHHH
Q 037567           30 DCLVVMATGSGKSLCYQLP---PLVT--GKTALVVSPLISLMQDQVMS   72 (374)
Q Consensus        30 ~~l~~a~tGsGKT~~~~l~---~~~~--~~~~lil~P~~~l~~q~~~~   72 (374)
                      .+++.||+|+|||......   +...  +.+++++.. ..+..+....
T Consensus       138 ~l~l~G~~G~GKThL~~ai~~~l~~~~~~~~v~yi~~-~~~~~~~~~~  184 (405)
T TIGR00362       138 PLFIYGGVGLGKTHLLHAIGNEILENNPNAKVVYVSS-EKFTNDFVNA  184 (405)
T ss_pred             eEEEECCCCCcHHHHHHHHHHHHHHhCCCCcEEEEEH-HHHHHHHHHH
Confidence            5789999999999643221   1122  456666643 3454444333

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).

>PRK08533 flagellar accessory protein FlaH; Reviewed

Probab=96.41  E-value=0.042  Score=45.92  Aligned_cols=51  Identities=20%  Similarity=0.125  Sum_probs=34.5

Q ss_pred             cCCCEEEEccCCCCchhhhh---ccccccCCcEEEEcchHHHHHHHHHHHHHcCC
Q 037567           27 EKRDCLVVMATGSGKSLCYQ---LPPLVTGKTALVVSPLISLMQDQVMSLKQRGI   78 (374)
Q Consensus        27 ~~~~~l~~a~tGsGKT~~~~---l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~   78 (374)
                      .+.-+++.+++|+|||....   ...+.++.++++++.. +-..+..+.+.++|.
T Consensus        23 ~g~~~~i~G~~G~GKTtl~~~~~~~~~~~g~~~~yi~~e-~~~~~~~~~~~~~g~   76 (230)
T PRK08533         23 AGSLILIEGDESTGKSILSQRLAYGFLQNGYSVSYVSTQ-LTTTEFIKQMMSLGY   76 (230)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHhCCCcEEEEeCC-CCHHHHHHHHHHhCC
Confidence            46678999999999996632   2233467788888744 444566666666655

>PLN03025 replication factor C subunit; Provisional

Probab=96.40  E-value=0.011  Score=52.08  Aligned_cols=42  Identities=14%  Similarity=0.180  Sum_probs=24.3

Q ss_pred             CccEEEEeccchhhcccCcchHHHHHHHHHHHhcCCCCeeEEEeecCc
Q 037567          126 GVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATE  173 (374)
Q Consensus       126 ~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~SaT~~~  173 (374)
                      ...++++||+|.+.....      ..+.+..+..++...+.++++...
T Consensus        99 ~~kviiiDE~d~lt~~aq------~aL~~~lE~~~~~t~~il~~n~~~  140 (319)
T PLN03025         99 RHKIVILDEADSMTSGAQ------QALRRTMEIYSNTTRFALACNTSS  140 (319)
T ss_pred             CeEEEEEechhhcCHHHH------HHHHHHHhcccCCceEEEEeCCcc
Confidence            467999999999864221      334444444444444555555443

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=96.40  E-value=0.015  Score=48.54  Aligned_cols=18  Identities=33%  Similarity=0.257  Sum_probs=15.1

Q ss_pred             CCCEEEEccCCCCchhhh
Q 037567           28 KRDCLVVMATGSGKSLCY   45 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~   45 (374)
                      +..+++.||+|+|||..+
T Consensus        38 ~~~lll~G~~G~GKT~la   55 (226)
T TIGR03420        38 DRFLYLWGESGSGKSHLL   55 (226)
T ss_pred             CCeEEEECCCCCCHHHHH
Confidence            457899999999999654

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.

>TIGR01074 rep ATP-dependent DNA helicase Rep

Probab=96.38  E-value=0.0054  Score=60.06  Aligned_cols=61  Identities=16%  Similarity=0.256  Sum_probs=46.9

Q ss_pred             CchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccc---c-c---cCCcEEEEcchHHHHHHHHHHHHHc
Q 037567           14 FRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPP---L-V---TGKTALVVSPLISLMQDQVMSLKQR   76 (374)
Q Consensus        14 ~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~---~-~---~~~~~lil~P~~~l~~q~~~~~~~~   76 (374)
                      ++|-|.+++..  ...+++|.|++|||||.+...-+   + .   ...++++++.|+..+.++.+.+.+.
T Consensus         2 Ln~~Q~~av~~--~~~~~~V~Ag~GSGKT~~L~~ri~~ll~~~~~~p~~IL~vTFt~~Aa~em~~Rl~~~   69 (664)
T TIGR01074         2 LNPQQQEAVEY--VTGPCLVLAGAGSGKTRVITNKIAYLIQNCGYKARNIAAVTFTNKAAREMKERVAKT   69 (664)
T ss_pred             CCHHHHHHHhC--CCCCEEEEecCCCCHHHHHHHHHHHHHHhcCCCHHHeEEEeccHHHHHHHHHHHHHH
Confidence            78889998864  46789999999999996543221   1 1   2467999999999999999988754

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

>PRK04195 replication factor C large subunit; Provisional

Probab=96.37  E-value=0.012  Score=55.13  Aligned_cols=32  Identities=19%  Similarity=0.135  Sum_probs=20.6

Q ss_pred             CCCEEEEccCCCCchhhhhccccccCCcEEEE
Q 037567           28 KRDCLVVMATGSGKSLCYQLPPLVTGKTALVV   59 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~l~~~~~~~~~lil   59 (374)
                      .+.+++.||+|+|||..+...+-.-+..++.+
T Consensus        39 ~~~lLL~GppG~GKTtla~ala~el~~~~iel   70 (482)
T PRK04195         39 KKALLLYGPPGVGKTSLAHALANDYGWEVIEL   70 (482)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHcCCCEEEE
Confidence            45789999999999976543333333344444

>CHL00176 ftsH cell division protein; Validated

Probab=96.37  E-value=0.039  Score=53.14  Aligned_cols=31  Identities=19%  Similarity=0.220  Sum_probs=20.0

Q ss_pred             CCEEEEccCCCCchhhhhccccccCCcEEEE
Q 037567           29 RDCLVVMATGSGKSLCYQLPPLVTGKTALVV   59 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~~l~~~~~~~~~lil   59 (374)
                      +.+++.||+|+|||..+-..+-..+.+.+.+
T Consensus       217 ~gVLL~GPpGTGKT~LAralA~e~~~p~i~i  247 (638)
T CHL00176        217 KGVLLVGPPGTGKTLLAKAIAGEAEVPFFSI  247 (638)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHhCCCeeec
Confidence            4689999999999976533333333344433

>PRK09183 transposase/IS protein; Provisional

Probab=96.33  E-value=0.015  Score=49.51  Aligned_cols=44  Identities=14%  Similarity=0.164  Sum_probs=27.7

Q ss_pred             HHcCCCEEEEccCCCCchhhhhcc---ccccCCcEEEEcchHHHHHHH
Q 037567           25 IIEKRDCLVVMATGSGKSLCYQLP---PLVTGKTALVVSPLISLMQDQ   69 (374)
Q Consensus        25 ~~~~~~~l~~a~tGsGKT~~~~l~---~~~~~~~~lil~P~~~l~~q~   69 (374)
                      +.++.++++.||+|+|||..+...   +...+.+++++. ..++..+.
T Consensus        99 i~~~~~v~l~Gp~GtGKThLa~al~~~a~~~G~~v~~~~-~~~l~~~l  145 (259)
T PRK09183         99 IERNENIVLLGPSGVGKTHLAIALGYEAVRAGIKVRFTT-AADLLLQL  145 (259)
T ss_pred             hhcCCeEEEEeCCCCCHHHHHHHHHHHHHHcCCeEEEEe-HHHHHHHH
Confidence            345778999999999999544322   223566676654 33455443

>KOG0734 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]

Probab=96.32  E-value=0.032  Score=51.04  Aligned_cols=73  Identities=14%  Similarity=0.117  Sum_probs=40.3

Q ss_pred             HHHhcCccEEEEeccchhhccc--C---cchHHHHHH-HHHHHhcCCCCeeEEEeecCcccHHHHHHhcCCCCCeEEEe
Q 037567          121 KLLKAGVCLFAVDEAHCISEWG--H---DFRLEYKQL-DKLRTFLLGVPFVALTATATEKVRIDIINSLKLKNPYVTIA  193 (374)
Q Consensus       121 ~~~~~~~~~vviDE~h~~~~~~--~---~~~~~~~~~-~~~~~~~~~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~  193 (374)
                      ........+|+|||.+.+...-  .   ..+..+.++ .++-.+-++..+|.+-||-.++.....+..-+.-+..+.++
T Consensus       391 aAk~~APcIIFIDEiDavG~kR~~~~~~y~kqTlNQLLvEmDGF~qNeGiIvigATNfpe~LD~AL~RPGRFD~~v~Vp  469 (752)
T KOG0734|consen  391 AAKARAPCIIFIDEIDAVGGKRNPSDQHYAKQTLNQLLVEMDGFKQNEGIIVIGATNFPEALDKALTRPGRFDRHVTVP  469 (752)
T ss_pred             HHHhcCCeEEEEechhhhcccCCccHHHHHHHHHHHHHHHhcCcCcCCceEEEeccCChhhhhHHhcCCCccceeEecC
Confidence            3334566789999999986411  1   112222222 22333334788999999988876544444333333333333

>PRK08769 DNA polymerase III subunit delta'; Validated

Probab=96.30  E-value=0.013  Score=51.18  Aligned_cols=35  Identities=26%  Similarity=0.418  Sum_probs=27.7

Q ss_pred             CCCCchhHHHHHHHHHc----CC---CEEEEccCCCCchhhh
Q 037567           11 YSVFRPYQKDVIQRIIE----KR---DCLVVMATGSGKSLCY   45 (374)
Q Consensus        11 ~~~~~~~Q~~~~~~~~~----~~---~~l~~a~tGsGKT~~~   45 (374)
                      ++.++|+|..++..+.+    ++   -.++.||.|+||+..+
T Consensus         2 ~~~~yPW~~~~~~~l~~~~~~~rl~HA~Lf~Gp~G~GK~~lA   43 (319)
T PRK08769          2 TSAFSPWQQRAYDQTVAALDAGRLGHGLLICGPEGLGKRAVA   43 (319)
T ss_pred             CccccccHHHHHHHHHHHHHcCCcceeEeeECCCCCCHHHHH
Confidence            45789999999988764    22   4689999999999543

>PF01443 Viral_helicase1: Viral (Superfamily 1) RNA helicase; InterPro: IPR000606 This entry includes RNA and DNA helicases

Probab=96.28  E-value=0.0034  Score=52.73  Aligned_cols=15  Identities=40%  Similarity=0.359  Sum_probs=12.5

Q ss_pred             EEEEccCCCCchhhh
Q 037567           31 CLVVMATGSGKSLCY   45 (374)
Q Consensus        31 ~l~~a~tGsGKT~~~   45 (374)
                      +++.|++|||||...
T Consensus         1 ~vv~G~pGsGKSt~i   15 (234)
T PF01443_consen    1 IVVHGVPGSGKSTLI   15 (234)
T ss_pred             CEEEcCCCCCHHHHH
Confidence            378999999999753

Some of the members are found in positive-strand single stranded RNA viruses. The helicase has multiple roles at different stages of viral RNA replication, as dissected by mutational analysis [].; GO: 0004386 helicase activity

>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI

Probab=96.28  E-value=0.0091  Score=64.66  Aligned_cols=59  Identities=20%  Similarity=0.170  Sum_probs=44.4

Q ss_pred             CCCchhHHHHHHHHHcC--CCEEEEccCCCCchhhh------hccccc-cCCcEEEEcchHHHHHHHH
Q 037567           12 SVFRPYQKDVIQRIIEK--RDCLVVMATGSGKSLCY------QLPPLV-TGKTALVVSPLISLMQDQV   70 (374)
Q Consensus        12 ~~~~~~Q~~~~~~~~~~--~~~l~~a~tGsGKT~~~------~l~~~~-~~~~~lil~P~~~l~~q~~   70 (374)
                      ..+++.|.+|+..++.+  +-+++.|+.|+|||...      +..+.. .+.+++.++||..-+.++.
T Consensus      1018 ~~Lt~~Q~~Ai~~il~~~~~~~~i~G~AGtGKTt~l~~~~~~i~~~~~~~g~~v~glApT~~Aa~~L~ 1085 (1960)
T TIGR02760      1018 ERLTHGQKQAIHLIISTKDRFVAVQGLAGVGKTTMLESRYKPVLQAFESEQLQVIGLAPTHEAVGELK 1085 (1960)
T ss_pred             CCCCHHHHHHHHHHHhCCCcEEEEEeCCCCCHHHhHHHHHHHHHHHHHhcCCeEEEEeChHHHHHHHH
Confidence            36899999999998865  45578999999999764      111222 4678999999988777664

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.

>PRK06067 flagellar accessory protein FlaH; Validated

Probab=96.27  E-value=0.06  Score=45.16  Aligned_cols=59  Identities=20%  Similarity=0.233  Sum_probs=38.7

Q ss_pred             HHHHHHc-----CCCEEEEccCCCCchhhhhcc---ccccCCcEEEEcchHHHHHHHHHHHHHcCCce
Q 037567           21 VIQRIIE-----KRDCLVVMATGSGKSLCYQLP---PLVTGKTALVVSPLISLMQDQVMSLKQRGINA   80 (374)
Q Consensus        21 ~~~~~~~-----~~~~l~~a~tGsGKT~~~~l~---~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~   80 (374)
                      .++.++.     +.-+++.|++|+|||......   .+.++.+++++.-. +-..+..+.+.++|+..
T Consensus        13 ~LD~~l~gG~~~g~~~~i~G~~GsGKt~l~~~~~~~~~~~g~~~~y~~~e-~~~~~~~~~~~~~g~~~   79 (234)
T PRK06067         13 ELDRKLGGGIPFPSLILIEGDHGTGKSVLSQQFVYGALKQGKKVYVITTE-NTSKSYLKQMESVKIDI   79 (234)
T ss_pred             HHHHhhCCCCcCCcEEEEECCCCCChHHHHHHHHHHHHhCCCEEEEEEcC-CCHHHHHHHHHHCCCCh
Confidence            4445544     456788999999999543322   23457778777765 44567777788877553

>PRK05580 primosome assembly protein PriA; Validated

Probab=96.26  E-value=0.045  Score=53.46  Aligned_cols=85  Identities=15%  Similarity=0.179  Sum_probs=66.7

Q ss_pred             HHHHHHhhcCCCcEEEEecchhHHHHHHHHHHH-cCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccC
Q 037567          218 VQEILKSVAGAGSIIVYCMTIKDVEEISKALKQ-LGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPD  296 (374)
Q Consensus       218 ~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~-~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~  296 (374)
                      +..+......++++||.+|+...+.++.+.|++ .+..+..+||+++..++.........|+.+|+|+|...- -..+.+
T Consensus       180 l~~i~~~l~~g~~vLvLvPt~~L~~Q~~~~l~~~fg~~v~~~~s~~s~~~r~~~~~~~~~g~~~IVVgTrsal-~~p~~~  258 (679)
T PRK05580        180 LQAIAEVLAQGKQALVLVPEIALTPQMLARFRARFGAPVAVLHSGLSDGERLDEWRKAKRGEAKVVIGARSAL-FLPFKN  258 (679)
T ss_pred             HHHHHHHHHcCCeEEEEeCcHHHHHHHHHHHHHHhCCCEEEEECCCCHHHHHHHHHHHHcCCCCEEEeccHHh-cccccC
Confidence            333444445678999999999999999999987 477899999999999999888888899999999998432 134556


Q ss_pred             ccEEEEE
Q 037567          297 VRHVIHY  303 (374)
Q Consensus       297 ~~~vi~~  303 (374)
                      +..||.-
T Consensus       259 l~liVvD  265 (679)
T PRK05580        259 LGLIIVD  265 (679)
T ss_pred             CCEEEEE
Confidence            6766643

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family

Probab=96.26  E-value=0.0078  Score=50.62  Aligned_cols=59  Identities=20%  Similarity=0.228  Sum_probs=40.2

Q ss_pred             HHHHHHHc-----CCCEEEEccCCCCchhhhh---ccccccCCcEEEEcchHHHHHHHHHHHHHcCCc
Q 037567           20 DVIQRIIE-----KRDCLVVMATGSGKSLCYQ---LPPLVTGKTALVVSPLISLMQDQVMSLKQRGIN   79 (374)
Q Consensus        20 ~~~~~~~~-----~~~~l~~a~tGsGKT~~~~---l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~   79 (374)
                      ..++.++.     +..+++.||+|+|||..++   ...+..+.++++++- .+-..+..+.+..+|..
T Consensus         8 ~~LD~~l~GG~~~gs~~lI~G~pGsGKT~la~~~l~~~~~~ge~~lyvs~-ee~~~~i~~~~~~~g~~   74 (237)
T TIGR03877         8 PGMDEILHGGIPERNVVLLSGGPGTGKSIFSQQFLWNGLQMGEPGIYVAL-EEHPVQVRRNMAQFGWD   74 (237)
T ss_pred             HhHHHHhcCCCcCCeEEEEEcCCCCCHHHHHHHHHHHHHHcCCcEEEEEe-eCCHHHHHHHHHHhCCC
Confidence            34455544     5677999999999996543   223346778888874 45667777777777654

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.

>KOG1133 consensus Helicase of the DEAD superfamily [Replication, recombination and repair]

Probab=96.25  E-value=0.0034  Score=58.63  Aligned_cols=36  Identities=22%  Similarity=0.276  Sum_probs=29.8

Q ss_pred             CCchhHHHHHHHHHc----CCCEEEEccCCCCchhhhhcc
Q 037567           13 VFRPYQKDVIQRIIE----KRDCLVVMATGSGKSLCYQLP   48 (374)
Q Consensus        13 ~~~~~Q~~~~~~~~~----~~~~l~~a~tGsGKT~~~~l~   48 (374)
                      +|+.+|.+.+..+++    |+-.|+..|||+|||++.+.+
T Consensus        15 ~PYdIQ~~lM~elyrvLe~GkIgIfESPTGTGKSLSLiCa   54 (821)
T KOG1133|consen   15 TPYDIQEDLMRELYRVLEEGKIGIFESPTGTGKSLSLICA   54 (821)
T ss_pred             CchhHHHHHHHHHHHHHhcCCeeeeeCCCCCCchHHHHHH
Confidence            589999998887764    888899999999999775433

>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=96.25  E-value=0.0059  Score=51.62  Aligned_cols=36  Identities=25%  Similarity=0.357  Sum_probs=24.2

Q ss_pred             EEEEccCCCCchhhh--hcc--ccc-cCCcEEEEcchHHHH
Q 037567           31 CLVVMATGSGKSLCY--QLP--PLV-TGKTALVVSPLISLM   66 (374)
Q Consensus        31 ~l~~a~tGsGKT~~~--~l~--~~~-~~~~~lil~P~~~l~   66 (374)
                      .+|.||||+||+-..  ++.  ++. ..-.|++++|.+..+
T Consensus        90 ~~VYGPTG~GKSqLlRNLis~~lI~P~PETVfFItP~~~mI  130 (369)
T PF02456_consen   90 GVVYGPTGSGKSQLLRNLISCQLIQPPPETVFFITPQKDMI  130 (369)
T ss_pred             EEEECCCCCCHHHHHHHhhhcCcccCCCCceEEECCCCCCC
Confidence            378999999999421  111  122 245799999988665

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

>PRK10919 ATP-dependent DNA helicase Rep; Provisional

Probab=96.24  E-value=0.0058  Score=59.55  Aligned_cols=62  Identities=18%  Similarity=0.214  Sum_probs=47.2

Q ss_pred             CCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccc---cc----cCCcEEEEcchHHHHHHHHHHHHHc
Q 037567           13 VFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPP---LV----TGKTALVVSPLISLMQDQVMSLKQR   76 (374)
Q Consensus        13 ~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~---~~----~~~~~lil~P~~~l~~q~~~~~~~~   76 (374)
                      .+++-|.+++..  ....++|.|++|||||.+...-+   +.    ...++|+++.|+..+.++.+.+.+.
T Consensus         2 ~Ln~~Q~~av~~--~~g~~lV~AgpGSGKT~vL~~Ria~Li~~~~v~p~~IL~lTFT~kAA~em~~Rl~~~   70 (672)
T PRK10919          2 RLNPGQQQAVEF--VTGPCLVLAGAGSGKTRVITNKIAHLIRGCGYQARHIAAVTFTNKAAREMKERVAQT   70 (672)
T ss_pred             CCCHHHHHHHhC--CCCCEEEEecCCCCHHHHHHHHHHHHHHhcCCCHHHeeeEechHHHHHHHHHHHHHH
Confidence            478899999875  45788999999999996533211   11    2457999999999999998888653

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.23  E-value=0.018  Score=53.33  Aligned_cols=19  Identities=37%  Similarity=0.697  Sum_probs=15.3

Q ss_pred             CCEEEEccCCCCchhhhhc
Q 037567           29 RDCLVVMATGSGKSLCYQL   47 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~~l   47 (374)
                      +..++.||.|+|||.++.+
T Consensus        36 ha~Lf~Gp~G~GKTT~Ari   54 (491)
T PRK14964         36 QSILLVGASGVGKTTCARI   54 (491)
T ss_pred             ceEEEECCCCccHHHHHHH
Confidence            3579999999999976543

>PRK07993 DNA polymerase III subunit delta'; Validated

Probab=96.22  E-value=0.017  Score=50.96  Aligned_cols=33  Identities=12%  Similarity=0.282  Sum_probs=25.8

Q ss_pred             CCchhHHHHHHHHHc----C---CCEEEEccCCCCchhhh
Q 037567           13 VFRPYQKDVIQRIIE----K---RDCLVVMATGSGKSLCY   45 (374)
Q Consensus        13 ~~~~~Q~~~~~~~~~----~---~~~l~~a~tGsGKT~~~   45 (374)
                      .++|||...+..+.+    +   +-.++.||.|.||+..+
T Consensus         2 ~~yPWl~~~~~~l~~~~~~~rl~HA~Lf~G~~G~Gk~~lA   41 (334)
T PRK07993          2 KWYPWLRPDYEQLVGSYQAGRGHHALLIQALPGMGDDALI   41 (334)
T ss_pred             CCCCCChHHHHHHHHHHHcCCcceEEeeECCCCCCHHHHH
Confidence            368999999988764    2   24589999999999553

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=96.22  E-value=0.037  Score=55.67  Aligned_cols=90  Identities=13%  Similarity=0.139  Sum_probs=71.2

Q ss_pred             chHHHHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHHc----CCceeeeecCCChHHHHHHHHhhhcCCeeEEEEec-
Q 037567          212 SFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQL----GVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATM-  286 (374)
Q Consensus       212 ~~~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~-  286 (374)
                      .+....+..++.....+.+++|.+|+..-+.+.++.+++.    ++++..++|..+..++.++++.+..|+.+|+|+|+ 
T Consensus       484 GKT~val~a~l~al~~g~qvlvLvPT~~LA~Q~~~~f~~~~~~~~i~v~~Lsg~~~~~e~~~~~~~l~~g~~dIVIGTp~  563 (926)
T TIGR00580       484 GKTEVAMRAAFKAVLDGKQVAVLVPTTLLAQQHFETFKERFANFPVTIELLSRFRSAKEQNEILKELASGKIDILIGTHK  563 (926)
T ss_pred             cHHHHHHHHHHHHHHhCCeEEEEeCcHHHHHHHHHHHHHHhccCCcEEEEEeccccHHHHHHHHHHHHcCCceEEEchHH
Confidence            3344444445555567789999999999999999888763    56778899999999999999999999999999998 


Q ss_pred             cccccccccCccEEE
Q 037567          287 AFGMGIDKPDVRHVI  301 (374)
Q Consensus       287 ~~~~G~d~~~~~~vi  301 (374)
                      .+...+.+.++.++|
T Consensus       564 ll~~~v~f~~L~llV  578 (926)
T TIGR00580       564 LLQKDVKFKDLGLLI  578 (926)
T ss_pred             HhhCCCCcccCCEEE
Confidence            444566777777766

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.

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=96.21  E-value=0.011  Score=56.84  Aligned_cols=42  Identities=17%  Similarity=0.120  Sum_probs=23.7

Q ss_pred             cCccEEEEeccchhhcccCcchHHHHHHHHHHHhcCCCCeeEEEeecC
Q 037567          125 AGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATAT  172 (374)
Q Consensus       125 ~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~SaT~~  172 (374)
                      ..++++||||+|.+.....      ..+.+.++..+..-.+.|+.|-.
T Consensus       118 gr~KVIIIDEah~LT~~A~------NALLKtLEEPP~~v~FILaTtd~  159 (830)
T PRK07003        118 ARFKVYMIDEVHMLTNHAF------NAMLKTLEEPPPHVKFILATTDP  159 (830)
T ss_pred             CCceEEEEeChhhCCHHHH------HHHHHHHHhcCCCeEEEEEECCh
Confidence            3578999999999865321      33344444433333444444433

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

Probab=96.21  E-value=0.048  Score=49.47  Aligned_cols=33  Identities=24%  Similarity=0.240  Sum_probs=21.3

Q ss_pred             CCCEEEEccCCCCchhhhhccccccCCcEEEEc
Q 037567           28 KRDCLVVMATGSGKSLCYQLPPLVTGKTALVVS   60 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~l~~~~~~~~~lil~   60 (374)
                      .+.+++.||+|+|||..+-..+-......+-+.
T Consensus       179 pkgvLL~GppGTGKT~LAkalA~~l~~~fi~i~  211 (398)
T PTZ00454        179 PRGVLLYGPPGTGKTMLAKAVAHHTTATFIRVV  211 (398)
T ss_pred             CceEEEECCCCCCHHHHHHHHHHhcCCCEEEEe
Confidence            467899999999999765433333333344443

>COG1223 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=96.21  E-value=0.045  Score=45.39  Aligned_cols=42  Identities=19%  Similarity=0.323  Sum_probs=25.8

Q ss_pred             CCCEEEEccCCCCchhhhhccccccCCcEEEEcchHHHHHHHH
Q 037567           28 KRDCLVVMATGSGKSLCYQLPPLVTGKTALVVSPLISLMQDQV   70 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~l~~~~~~~~~lil~P~~~l~~q~~   70 (374)
                      -+++++.+|||+|||..+-..+ ...+.-++.+...+|+-+..
T Consensus       151 PknVLFyGppGTGKTm~Akala-ne~kvp~l~vkat~liGehV  192 (368)
T COG1223         151 PKNVLFYGPPGTGKTMMAKALA-NEAKVPLLLVKATELIGEHV  192 (368)
T ss_pred             cceeEEECCCCccHHHHHHHHh-cccCCceEEechHHHHHHHh
Confidence            4799999999999997542222 22333345555555655443

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=96.21  E-value=0.074  Score=48.71  Aligned_cols=126  Identities=17%  Similarity=0.119  Sum_probs=63.4

Q ss_pred             CCCEEEEccCCCCchhhhh-ccc-c---ccCCcEEEEc-ch-HH-HHHHHHHHHHHcCCceEEcCCCCCchhhhhhhhcC
Q 037567           28 KRDCLVVMATGSGKSLCYQ-LPP-L---VTGKTALVVS-PL-IS-LMQDQVMSLKQRGINAEFLGSAQTDSSVQTKAETG   99 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~-l~~-~---~~~~~~lil~-P~-~~-l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   99 (374)
                      ++.+++.+|||+|||.+.. ++. +   ..+.++.++. .+ +. ...|+..+....++.....                
T Consensus       221 ~~~i~~vGptGvGKTTt~~kLA~~~~~~~~g~~V~li~~D~~r~~a~eqL~~~a~~~~vp~~~~----------------  284 (424)
T PRK05703        221 GGVVALVGPTGVGKTTTLAKLAARYALLYGKKKVALITLDTYRIGAVEQLKTYAKIMGIPVEVV----------------  284 (424)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHhcCCCeEEEEECCccHHHHHHHHHHHHHHhCCceEcc----------------
Confidence            4567889999999996543 221 1   2344555443 22 22 3344444444444332211                


Q ss_pred             CeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHH-h-cCCCCeeEEEeecCcccHH
Q 037567          100 YFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRT-F-LLGVPFVALTATATEKVRI  177 (374)
Q Consensus       100 ~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~-~-~~~~~~i~~SaT~~~~~~~  177 (374)
                            .+++.+...    ..  ...+.++|+||.+-+...   + ......+..+.. . .+....+.+|||.......
T Consensus       285 ------~~~~~l~~~----l~--~~~~~DlVlIDt~G~~~~---d-~~~~~~L~~ll~~~~~~~~~~LVl~a~~~~~~l~  348 (424)
T PRK05703        285 ------YDPKELAKA----LE--QLRDCDVILIDTAGRSQR---D-KRLIEELKALIEFSGEPIDVYLVLSATTKYEDLK  348 (424)
T ss_pred             ------CCHHhHHHH----HH--HhCCCCEEEEeCCCCCCC---C-HHHHHHHHHHHhccCCCCeEEEEEECCCCHHHHH
Confidence                  122211111    11  234679999999865321   1 111123333333 1 1223478899998887776


Q ss_pred             HHHHhcCC
Q 037567          178 DIINSLKL  185 (374)
Q Consensus       178 ~~~~~~~~  185 (374)
                      .+...+..
T Consensus       349 ~~~~~f~~  356 (424)
T PRK05703        349 DIYKHFSR  356 (424)
T ss_pred             HHHHHhCC
Confidence            66666543

>TIGR00595 priA primosomal protein N'

Probab=96.19  E-value=0.046  Score=51.36  Aligned_cols=81  Identities=20%  Similarity=0.214  Sum_probs=64.6

Q ss_pred             HHHhhcCCCcEEEEecchhHHHHHHHHHHHc-CCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccE
Q 037567          221 ILKSVAGAGSIIVYCMTIKDVEEISKALKQL-GVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRH  299 (374)
Q Consensus       221 ~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~-~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~  299 (374)
                      +......+++++|.+|+...+.++++.|++. +..+..+||+++..+|.....+...|+.+|+|+|...-. ..++++..
T Consensus        18 i~~~l~~g~~vLvlvP~i~L~~Q~~~~l~~~f~~~v~vlhs~~~~~er~~~~~~~~~g~~~IVVGTrsalf-~p~~~l~l   96 (505)
T TIGR00595        18 IEKVLALGKSVLVLVPEIALTPQMIQRFKYRFGSQVAVLHSGLSDSEKLQAWRKVKNGEILVVIGTRSALF-LPFKNLGL   96 (505)
T ss_pred             HHHHHHcCCeEEEEeCcHHHHHHHHHHHHHHhCCcEEEEECCCCHHHHHHHHHHHHcCCCCEEECChHHHc-CcccCCCE
Confidence            3334456789999999999999999999864 677889999999999999888888999999999974322 34556676


Q ss_pred             EEE
Q 037567          300 VIH  302 (374)
Q Consensus       300 vi~  302 (374)
                      ||.
T Consensus        97 IIV   99 (505)
T TIGR00595        97 IIV   99 (505)
T ss_pred             EEE
Confidence            663

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).

>PRK06620 hypothetical protein; Validated

Probab=96.18  E-value=0.015  Score=47.88  Aligned_cols=17  Identities=24%  Similarity=0.188  Sum_probs=14.0

Q ss_pred             CCEEEEccCCCCchhhh
Q 037567           29 RDCLVVMATGSGKSLCY   45 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~   45 (374)
                      +.++++||+|+|||...
T Consensus        45 ~~l~l~Gp~G~GKThLl   61 (214)
T PRK06620         45 FTLLIKGPSSSGKTYLT   61 (214)
T ss_pred             ceEEEECCCCCCHHHHH
Confidence            34799999999999653

>PRK04328 hypothetical protein; Provisional

Probab=96.18  E-value=0.012  Score=49.82  Aligned_cols=58  Identities=22%  Similarity=0.267  Sum_probs=38.3

Q ss_pred             HHHHHHc-----CCCEEEEccCCCCchhhhh---ccccccCCcEEEEcchHHHHHHHHHHHHHcCCc
Q 037567           21 VIQRIIE-----KRDCLVVMATGSGKSLCYQ---LPPLVTGKTALVVSPLISLMQDQVMSLKQRGIN   79 (374)
Q Consensus        21 ~~~~~~~-----~~~~l~~a~tGsGKT~~~~---l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~   79 (374)
                      .++.++.     +..+++.|++|+|||...+   ...+.++.+++++. +.+-..+..+.++.+|..
T Consensus        11 ~LD~lL~GGip~gs~ili~G~pGsGKT~l~~~fl~~~~~~ge~~lyis-~ee~~~~i~~~~~~~g~d   76 (249)
T PRK04328         11 GMDEILYGGIPERNVVLLSGGPGTGKSIFSQQFLWNGLQMGEPGVYVA-LEEHPVQVRRNMRQFGWD   76 (249)
T ss_pred             hHHHHhcCCCcCCcEEEEEcCCCCCHHHHHHHHHHHHHhcCCcEEEEE-eeCCHHHHHHHHHHcCCC
Confidence            4455543     5667899999999995433   22344577787776 445566677777777654

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=96.18  E-value=0.016  Score=51.16  Aligned_cols=13  Identities=23%  Similarity=0.325  Sum_probs=11.1

Q ss_pred             CccEEEEeccchh
Q 037567          126 GVCLFAVDEAHCI  138 (374)
Q Consensus       126 ~~~~vviDE~h~~  138 (374)
                      ..+++|+||+|.+
T Consensus       100 ~~~vliiDe~d~l  112 (316)
T PHA02544        100 GGKVIIIDEFDRL  112 (316)
T ss_pred             CCeEEEEECcccc
Confidence            4579999999987

>PRK14712 conjugal transfer nickase/helicase TraI; Provisional

Probab=96.16  E-value=0.016  Score=60.75  Aligned_cols=58  Identities=16%  Similarity=0.190  Sum_probs=44.4

Q ss_pred             CCchhHHHHHHHHHcC--CCEEEEccCCCCchhhh--hcccc-----ccCCcEEEEcchHHHHHHHH
Q 037567           13 VFRPYQKDVIQRIIEK--RDCLVVMATGSGKSLCY--QLPPL-----VTGKTALVVSPLISLMQDQV   70 (374)
Q Consensus        13 ~~~~~Q~~~~~~~~~~--~~~l~~a~tGsGKT~~~--~l~~~-----~~~~~~lil~P~~~l~~q~~   70 (374)
                      .+++-|.+++..++..  +-+++.|..|+|||.+.  ++.++     ..+..++.++||..-+..+.
T Consensus       835 ~Lt~~Qr~Av~~iLts~dr~~~IqG~AGTGKTT~l~~i~~~~~~l~e~~g~~V~glAPTgkAa~~L~  901 (1623)
T PRK14712        835 KLTSGQRAATRMILETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMR  901 (1623)
T ss_pred             ccCHHHHHHHHHHHhCCCceEEEEeCCCCCHHHHHHHHHHHHHHHhhccCceEEEEechHHHHHHHH
Confidence            6899999999999864  66789999999999763  12221     13567889999988887664

>PRK07764 DNA polymerase III subunits gamma and tau; Validated

Probab=96.15  E-value=0.02  Score=56.72  Aligned_cols=16  Identities=31%  Similarity=0.588  Sum_probs=13.8

Q ss_pred             cCccEEEEeccchhhc
Q 037567          125 AGVCLFAVDEAHCISE  140 (374)
Q Consensus       125 ~~~~~vviDE~h~~~~  140 (374)
                      ..++++||||+|.|..
T Consensus       119 ~~~KV~IIDEad~lt~  134 (824)
T PRK07764        119 SRYKIFIIDEAHMVTP  134 (824)
T ss_pred             CCceEEEEechhhcCH
Confidence            5678999999999975

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.15  E-value=0.039  Score=49.21  Aligned_cols=124  Identities=11%  Similarity=0.007  Sum_probs=60.9

Q ss_pred             CCCEEEEccCCCCchhhhhcccc----ccC-CcEEEEcc-hH--HHHHHHHHHHHHcCCceEEcCCCCCchhhhhhhhcC
Q 037567           28 KRDCLVVMATGSGKSLCYQLPPL----VTG-KTALVVSP-LI--SLMQDQVMSLKQRGINAEFLGSAQTDSSVQTKAETG   99 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~l~~~----~~~-~~~lil~P-~~--~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   99 (374)
                      +..+++.||||+|||.+....+.    ..+ .++.++.. +-  .-.+|.....+.+|......                
T Consensus       137 g~ii~lvGptGvGKTTtiakLA~~~~~~~G~~~V~lit~D~~R~ga~EqL~~~a~~~gv~~~~~----------------  200 (374)
T PRK14722        137 GGVFALMGPTGVGKTTTTAKLAARCVMRFGASKVALLTTDSYRIGGHEQLRIFGKILGVPVHAV----------------  200 (374)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHhcCCCeEEEEecccccccHHHHHHHHHHHcCCceEec----------------
Confidence            45678999999999976543321    223 34444432 21  12344444444444433222                


Q ss_pred             CeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHHhc-CCCCeeEEEeecCcccHHH
Q 037567          100 YFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFL-LGVPFVALTATATEKVRID  178 (374)
Q Consensus       100 ~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~-~~~~~i~~SaT~~~~~~~~  178 (374)
                            -+++.+..      ......+.++|+||++-....    .......+..+.... +...++.+|||........
T Consensus       201 ------~~~~~l~~------~l~~l~~~DlVLIDTaG~~~~----d~~l~e~La~L~~~~~~~~~lLVLsAts~~~~l~e  264 (374)
T PRK14722        201 ------KDGGDLQL------ALAELRNKHMVLIDTIGMSQR----DRTVSDQIAMLHGADTPVQRLLLLNATSHGDTLNE  264 (374)
T ss_pred             ------CCcccHHH------HHHHhcCCCEEEEcCCCCCcc----cHHHHHHHHHHhccCCCCeEEEEecCccChHHHHH
Confidence                  22222211      112235668999999964321    111112233332211 1234788999988776554


Q ss_pred             HHHhc
Q 037567          179 IINSL  183 (374)
Q Consensus       179 ~~~~~  183 (374)
                      +...+
T Consensus       265 vi~~f  269 (374)
T PRK14722        265 VVQAY  269 (374)
T ss_pred             HHHHH
Confidence            44433

>PHA03372 DNA packaging terminase subunit 1; Provisional

Probab=96.15  E-value=0.057  Score=50.49  Aligned_cols=156  Identities=13%  Similarity=0.109  Sum_probs=91.5

Q ss_pred             hhHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCch--hhhhcccc---ccCCcEEEEcchHHHHHHHHHHHHH-
Q 037567            2 VSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKS--LCYQLPPL---VTGKTALVVSPLISLMQDQVMSLKQ-   75 (374)
Q Consensus         2 ~~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT--~~~~l~~~---~~~~~~lil~P~~~l~~q~~~~~~~-   75 (374)
                      .+.|+..||...+..   ..++. ++.+-.+..-|---|||  +..+++++   -.+-++-+++..+..++-+++++.. 
T Consensus       180 ~~~lk~~Fdi~~~s~---~~l~~-FKQkaTVFLVPRRHGKTWf~VpiIsllL~s~~gI~IGYvAHqKhvs~~Vf~EI~~~  255 (668)
T PHA03372        180 LEYLLHVFDIEFLSE---SSLNI-FKQKATVFLVPRRHGKTWFIIPIISFLLKNIIGISIGYVAHQKHVSQFVLKEVEFR  255 (668)
T ss_pred             HHHHHHHcCCcccCH---HHHHH-hhccceEEEecccCCceehHHHHHHHHHHhhcCceEEEEeeHHHHHHHHHHHHHHH
Confidence            356788888876665   44444 34455566669999999  22222222   2578899999999888877777652 


Q ss_pred             ---cCCceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCc---hhhHHHHHhcCccEEEEeccchhhcccCcchHHH
Q 037567           76 ---RGINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIP---ISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEY  149 (374)
Q Consensus        76 ---~~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~---~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~  149 (374)
                         +-....+...             .+-.|.+.-|+.=...+   -...+.+..+.+++++|||||.+..         
T Consensus       256 lrrwF~~~~vi~~-------------k~~tI~~s~pg~Kst~~fasc~n~NsiRGQ~fnll~VDEA~FI~~---------  313 (668)
T PHA03372        256 CRRMFPRKHTIEN-------------KDNVISIDHRGAKSTALFASCYNTNSIRGQNFHLLLVDEAHFIKK---------  313 (668)
T ss_pred             HhhhcCccceeee-------------cCcEEEEecCCCcceeeehhhccCccccCCCCCEEEEehhhccCH---------
Confidence               2111111100             00123333332110000   0112345567899999999998865         


Q ss_pred             HHHHHHHHhc--CCCCeeEEEeecCcccHHHHHHhc
Q 037567          150 KQLDKLRTFL--LGVPFVALTATATEKVRIDIINSL  183 (374)
Q Consensus       150 ~~~~~~~~~~--~~~~~i~~SaT~~~~~~~~~~~~~  183 (374)
                      ..+..+..++  .+.++|+.|.|-+......++..+
T Consensus       314 ~a~~tilgfm~q~~~KiIfISS~Nsg~~sTSfL~~L  349 (668)
T PHA03372        314 DAFNTILGFLAQNTTKIIFISSTNTTNDATCFLTKL  349 (668)
T ss_pred             HHHHHhhhhhcccCceEEEEeCCCCCCccchHHHhc
Confidence            3344444443  378999999997776665556555

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.15  E-value=0.015  Score=53.97  Aligned_cols=16  Identities=19%  Similarity=0.345  Sum_probs=13.6

Q ss_pred             EEEEccCCCCchhhhh
Q 037567           31 CLVVMATGSGKSLCYQ   46 (374)
Q Consensus        31 ~l~~a~tGsGKT~~~~   46 (374)
                      ++++||+|+|||..+.
T Consensus        39 ~Lf~GPpGtGKTTlA~   54 (472)
T PRK14962         39 YIFAGPRGTGKTTVAR   54 (472)
T ss_pred             EEEECCCCCCHHHHHH
Confidence            6899999999997654

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.14  E-value=0.026  Score=52.97  Aligned_cols=17  Identities=24%  Similarity=0.282  Sum_probs=14.0

Q ss_pred             CEEEEccCCCCchhhhh
Q 037567           30 DCLVVMATGSGKSLCYQ   46 (374)
Q Consensus        30 ~~l~~a~tGsGKT~~~~   46 (374)
                      -.++.||+|+|||.++.
T Consensus        40 a~Lf~Gp~G~GKTt~A~   56 (509)
T PRK14958         40 AYLFTGTRGVGKTTISR   56 (509)
T ss_pred             eEEEECCCCCCHHHHHH
Confidence            35899999999996653

>PRK06964 DNA polymerase III subunit delta'; Validated

Probab=96.12  E-value=0.019  Score=50.68  Aligned_cols=32  Identities=25%  Similarity=0.251  Sum_probs=25.7

Q ss_pred             CchhHHHHHHHHHcC-----CCEEEEccCCCCchhhh
Q 037567           14 FRPYQKDVIQRIIEK-----RDCLVVMATGSGKSLCY   45 (374)
Q Consensus        14 ~~~~Q~~~~~~~~~~-----~~~l~~a~tGsGKT~~~   45 (374)
                      ++|+|...+..+.+.     +..++.||.|.||+..+
T Consensus         2 ~yPW~~~~~~~l~~~~~rl~ha~Lf~Gp~G~GK~~lA   38 (342)
T PRK06964          2 LYPWQTDDWNRLQALRARLPHALLLHGQAGIGKLDFA   38 (342)
T ss_pred             CCcccHHHHHHHHHhcCCcceEEEEECCCCCCHHHHH
Confidence            579999999988752     35689999999999553

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.12  E-value=0.012  Score=55.83  Aligned_cols=16  Identities=19%  Similarity=0.517  Sum_probs=13.6

Q ss_pred             cCccEEEEeccchhhc
Q 037567          125 AGVCLFAVDEAHCISE  140 (374)
Q Consensus       125 ~~~~~vviDE~h~~~~  140 (374)
                      .+++++||||+|.+..
T Consensus       123 gr~KViIIDEah~Ls~  138 (700)
T PRK12323        123 GRFKVYMIDEVHMLTN  138 (700)
T ss_pred             CCceEEEEEChHhcCH
Confidence            4578999999999865

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.11  E-value=0.015  Score=57.14  Aligned_cols=16  Identities=25%  Similarity=0.274  Sum_probs=13.4

Q ss_pred             EEEEccCCCCchhhhh
Q 037567           31 CLVVMATGSGKSLCYQ   46 (374)
Q Consensus        31 ~l~~a~tGsGKT~~~~   46 (374)
                      +|+.||+|+|||.++.
T Consensus        41 yLFtGPpGtGKTTLAR   56 (944)
T PRK14949         41 YLFTGTRGVGKTSLAR   56 (944)
T ss_pred             EEEECCCCCCHHHHHH
Confidence            4899999999997653

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.10  E-value=0.015  Score=55.19  Aligned_cols=42  Identities=17%  Similarity=0.095  Sum_probs=24.1

Q ss_pred             cCccEEEEeccchhhcccCcchHHHHHHHHHHHhcCCCCeeEEEeecC
Q 037567          125 AGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATAT  172 (374)
Q Consensus       125 ~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~SaT~~  172 (374)
                      ...+++||||+|.+.....      ..+.+..+..++.-.+.+++|-.
T Consensus       117 gk~KV~IIDEVh~LS~~A~------NALLKtLEEPP~~v~FILaTtd~  158 (702)
T PRK14960        117 GRFKVYLIDEVHMLSTHSF------NALLKTLEEPPEHVKFLFATTDP  158 (702)
T ss_pred             CCcEEEEEechHhcCHHHH------HHHHHHHhcCCCCcEEEEEECCh
Confidence            4568999999999865321      34444444444333444444533

>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA

Probab=96.09  E-value=0.025  Score=55.92  Aligned_cols=18  Identities=33%  Similarity=0.386  Sum_probs=15.3

Q ss_pred             CCCEEEEccCCCCchhhh
Q 037567           28 KRDCLVVMATGSGKSLCY   45 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~   45 (374)
                      ..+.++.||+|+|||...
T Consensus       203 ~~n~lL~G~pG~GKT~l~  220 (731)
T TIGR02639       203 KNNPLLVGEPGVGKTAIA  220 (731)
T ss_pred             CCceEEECCCCCCHHHHH
Confidence            458899999999999654

>PF13177 DNA_pol3_delta2: DNA polymerase III, delta subunit; PDB: 1NJF_B 3GLG_G 1XXH_I 1NJG_A 3GLF_B 3GLI_G 1IQP_E 2GNO_A 1SXJ_E 1A5T_A

Probab=96.07  E-value=0.11  Score=40.83  Aligned_cols=50  Identities=18%  Similarity=0.102  Sum_probs=28.5

Q ss_pred             cCccEEEEeccchhhcccCcchHHHHHHHHHHHhcCCCCeeEEEeecCcccHHHHH
Q 037567          125 AGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEKVRIDII  180 (374)
Q Consensus       125 ~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~SaT~~~~~~~~~~  180 (374)
                      ...+++||||+|.+.....      ..+.+..+..+..-+++|+++-.....+.+.
T Consensus       101 ~~~KviiI~~ad~l~~~a~------NaLLK~LEepp~~~~fiL~t~~~~~il~TI~  150 (162)
T PF13177_consen  101 GKYKVIIIDEADKLTEEAQ------NALLKTLEEPPENTYFILITNNPSKILPTIR  150 (162)
T ss_dssp             SSSEEEEEETGGGS-HHHH------HHHHHHHHSTTTTEEEEEEES-GGGS-HHHH
T ss_pred             CCceEEEeehHhhhhHHHH------HHHHHHhcCCCCCEEEEEEECChHHChHHHH
Confidence            4578999999999865222      4555566655544455555554444444333

...

>COG0464 SpoVK ATPases of the AAA+ class [Posttranslational modification, protein turnover, chaperones]

Probab=96.06  E-value=0.033  Score=52.54  Aligned_cols=45  Identities=20%  Similarity=0.216  Sum_probs=31.2

Q ss_pred             CCEEEEccCCCCchhhhhccccccCCcEEEEcchHHHHHHHHHHHH
Q 037567           29 RDCLVVMATGSGKSLCYQLPPLVTGKTALVVSPLISLMQDQVMSLK   74 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~   74 (374)
                      +.+++.||+|+|||+.+-..+...+.+++-+-.. ++...|.-+..
T Consensus       277 ~giLl~GpPGtGKT~lAkava~~~~~~fi~v~~~-~l~sk~vGese  321 (494)
T COG0464         277 KGVLLYGPPGTGKTLLAKAVALESRSRFISVKGS-ELLSKWVGESE  321 (494)
T ss_pred             CeeEEECCCCCCHHHHHHHHHhhCCCeEEEeeCH-HHhccccchHH
Confidence            4689999999999987665555555665555555 67766555533

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=96.01  E-value=0.043  Score=52.02  Aligned_cols=43  Identities=16%  Similarity=0.151  Sum_probs=25.4

Q ss_pred             CEEEEccCCCCchhhhhc-c--ccc--cCCcEEEEcchHHHHHHHHHHH
Q 037567           30 DCLVVMATGSGKSLCYQL-P--PLV--TGKTALVVSPLISLMQDQVMSL   73 (374)
Q Consensus        30 ~~l~~a~tGsGKT~~~~l-~--~~~--~~~~~lil~P~~~l~~q~~~~~   73 (374)
                      .++++|++|+|||..... .  +..  .+.+++++. ..++.++....+
T Consensus       316 pL~LyG~sGsGKTHLL~AIa~~a~~~~~g~~V~Yit-aeef~~el~~al  363 (617)
T PRK14086        316 PLFIYGESGLGKTHLLHAIGHYARRLYPGTRVRYVS-SEEFTNEFINSI  363 (617)
T ss_pred             cEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEee-HHHHHHHHHHHH
Confidence            478999999999953221 1  111  245565554 456666655444

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=95.99  E-value=0.034  Score=52.63  Aligned_cols=17  Identities=18%  Similarity=0.196  Sum_probs=14.1

Q ss_pred             CEEEEccCCCCchhhhh
Q 037567           30 DCLVVMATGSGKSLCYQ   46 (374)
Q Consensus        30 ~~l~~a~tGsGKT~~~~   46 (374)
                      ..++.||.|+|||..+.
T Consensus        40 A~Lf~GP~GvGKTTlA~   56 (605)
T PRK05896         40 AYIFSGPRGIGKTSIAK   56 (605)
T ss_pred             eEEEECCCCCCHHHHHH
Confidence            46899999999996653

>PRK05973 replicative DNA helicase; Provisional

Probab=95.98  E-value=0.05  Score=45.34  Aligned_cols=55  Identities=20%  Similarity=0.213  Sum_probs=37.1

Q ss_pred             HHHcCCCEEEEccCCCCchhhhh---ccccccCCcEEEEcchHHHHHHHHHHHHHcCCc
Q 037567           24 RIIEKRDCLVVMATGSGKSLCYQ---LPPLVTGKTALVVSPLISLMQDQVMSLKQRGIN   79 (374)
Q Consensus        24 ~~~~~~~~l~~a~tGsGKT~~~~---l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~   79 (374)
                      .+..|.-++|.|+||+|||...+   ..+..++.++++++-- +-.+|..+.+..+|+.
T Consensus        60 Gl~~Gsl~LIaG~PG~GKT~lalqfa~~~a~~Ge~vlyfSlE-es~~~i~~R~~s~g~d  117 (237)
T PRK05973         60 QLKPGDLVLLGARPGHGKTLLGLELAVEAMKSGRTGVFFTLE-YTEQDVRDRLRALGAD  117 (237)
T ss_pred             CCCCCCEEEEEeCCCCCHHHHHHHHHHHHHhcCCeEEEEEEe-CCHHHHHHHHHHcCCC
Confidence            34445677899999999996543   2233457778888654 3467777788777643

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=95.95  E-value=0.025  Score=47.27  Aligned_cols=17  Identities=29%  Similarity=0.258  Sum_probs=14.3

Q ss_pred             CCCEEEEccCCCCchhh
Q 037567           28 KRDCLVVMATGSGKSLC   44 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~   44 (374)
                      +..+++.|++|+|||..
T Consensus        42 ~~~~~l~G~~G~GKT~L   58 (227)
T PRK08903         42 DRFFYLWGEAGSGRSHL   58 (227)
T ss_pred             CCeEEEECCCCCCHHHH
Confidence            35689999999999954

>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family

Probab=95.93  E-value=0.034  Score=47.42  Aligned_cols=52  Identities=17%  Similarity=0.131  Sum_probs=31.7

Q ss_pred             CCCEEEEccCCCCchhhhhc---cccccCCcEEEEcch---HHHHHHHHHHHHHcCCc
Q 037567           28 KRDCLVVMATGSGKSLCYQL---PPLVTGKTALVVSPL---ISLMQDQVMSLKQRGIN   79 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~l---~~~~~~~~~lil~P~---~~l~~q~~~~~~~~~~~   79 (374)
                      +.-+++.|++|+|||...+-   ..+.++.+++++.--   ..+..+..+....+|..
T Consensus        36 gs~~lI~G~pGtGKT~l~~qf~~~~a~~Ge~vlyis~Ee~~~~~~~~l~~~a~~~g~d   93 (259)
T TIGR03878        36 YSVINITGVSDTGKSLMVEQFAVTQASRGNPVLFVTVESPANFVYTSLKERAKAMGVD   93 (259)
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHHHHhCCCcEEEEEecCCchHHHHHHHHHHHHcCCC
Confidence            45678999999999954332   223456788887732   23344454445555443

This KaiC domain-containing protein family occurs sporadically across a broad taxonomic range (Euryarchaeota, Aquificae, Dictyoglomi, Epsilonproteobacteria, and Firmicutes), but exclusively in thermophiles.

>PRK07940 DNA polymerase III subunit delta'; Validated

Probab=95.89  E-value=0.087  Score=47.70  Aligned_cols=50  Identities=18%  Similarity=0.063  Sum_probs=28.6

Q ss_pred             cCccEEEEeccchhhcccCcchHHHHHHHHHHHhcCCCCeeEEEeecCcccHHHHH
Q 037567          125 AGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEKVRIDII  180 (374)
Q Consensus       125 ~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~SaT~~~~~~~~~~  180 (374)
                      .+..++||||+|.+.....      ..+.+..+..++..++.+++|-+....+.+.
T Consensus       116 ~~~kViiIDead~m~~~aa------naLLk~LEep~~~~~fIL~a~~~~~llpTIr  165 (394)
T PRK07940        116 GRWRIVVIEDADRLTERAA------NALLKAVEEPPPRTVWLLCAPSPEDVLPTIR  165 (394)
T ss_pred             CCcEEEEEechhhcCHHHH------HHHHHHhhcCCCCCeEEEEECChHHChHHHH
Confidence            3567999999999965221      3334444444445556666665444443333

>PRK14873 primosome assembly protein PriA; Provisional

Probab=95.89  E-value=0.085  Score=51.08  Aligned_cols=89  Identities=19%  Similarity=0.243  Sum_probs=69.2

Q ss_pred             chHHHHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHHc-C-CceeeeecCCChHHHHHHHHhhhcCCeeEEEEecccc
Q 037567          212 SFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQL-G-VKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFG  289 (374)
Q Consensus       212 ~~~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~-~-~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~  289 (374)
                      .+.+-++..+.+.+..++++||.+|.......+.+.|++. + ..+..+|+++++.+|.+......+|+.+|+|.|-++-
T Consensus       172 GKTevyl~~i~~~l~~Gk~vLvLvPEi~lt~q~~~rl~~~f~~~~v~~lhS~l~~~~R~~~w~~~~~G~~~IViGtRSAv  251 (665)
T PRK14873        172 DWARRLAAAAAATLRAGRGALVVVPDQRDVDRLEAALRALLGAGDVAVLSAGLGPADRYRRWLAVLRGQARVVVGTRSAV  251 (665)
T ss_pred             cHHHHHHHHHHHHHHcCCeEEEEecchhhHHHHHHHHHHHcCCCcEEEECCCCCHHHHHHHHHHHhCCCCcEEEEcceeE
Confidence            3344444445555567889999999999999999999875 3 5689999999999999999999999999999997532


Q ss_pred             ccccccCccEEE
Q 037567          290 MGIDKPDVRHVI  301 (374)
Q Consensus       290 ~G~d~~~~~~vi  301 (374)
                       -.-+++...||
T Consensus       252 -FaP~~~LgLII  262 (665)
T PRK14873        252 -FAPVEDLGLVA  262 (665)
T ss_pred             -EeccCCCCEEE
Confidence             22334555555

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=95.86  E-value=0.038  Score=54.73  Aligned_cols=33  Identities=21%  Similarity=0.318  Sum_probs=21.3

Q ss_pred             CCEEEEccCCCCchhhhhccccccCCcEEEEcc
Q 037567           29 RDCLVVMATGSGKSLCYQLPPLVTGKTALVVSP   61 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~~l~~~~~~~~~lil~P   61 (374)
                      +.+++.||+|+|||..+-..+-..+...+.+-+
T Consensus       488 ~giLL~GppGtGKT~lakalA~e~~~~fi~v~~  520 (733)
T TIGR01243       488 KGVLLFGPPGTGKTLLAKAVATESGANFIAVRG  520 (733)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHhcCCCEEEEeh
Confidence            468999999999997654433333444444433

This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.

>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]

Probab=95.84  E-value=0.062  Score=48.28  Aligned_cols=46  Identities=11%  Similarity=0.159  Sum_probs=26.2

Q ss_pred             CccEEEEeccchhhcccCcchHHHHHHHHHHHhcCCCCeeEEEeecCc
Q 037567          126 GVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATE  173 (374)
Q Consensus       126 ~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~SaT~~~  173 (374)
                      ++++++||+++.+..........+..++.+...  +.++++.|..++.
T Consensus       175 ~~dlllIDDiq~l~gk~~~qeefFh~FN~l~~~--~kqIvltsdr~P~  220 (408)
T COG0593         175 SLDLLLIDDIQFLAGKERTQEEFFHTFNALLEN--GKQIVLTSDRPPK  220 (408)
T ss_pred             ccCeeeechHhHhcCChhHHHHHHHHHHHHHhc--CCEEEEEcCCCch
Confidence            778999999999865432233334455555442  2344444444443

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=95.83  E-value=0.09  Score=47.75  Aligned_cols=19  Identities=26%  Similarity=0.429  Sum_probs=15.6

Q ss_pred             CCEEEEccCCCCchhhhhc
Q 037567           29 RDCLVVMATGSGKSLCYQL   47 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~~l   47 (374)
                      +.+++.||+|+|||..+-.
T Consensus       166 ~gvLL~GppGtGKT~lAka  184 (389)
T PRK03992        166 KGVLLYGPPGTGKTLLAKA  184 (389)
T ss_pred             CceEEECCCCCChHHHHHH
Confidence            5689999999999976433

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.75  E-value=0.011  Score=53.26  Aligned_cols=30  Identities=23%  Similarity=0.276  Sum_probs=19.7

Q ss_pred             hHHHHHHHHHc----C---CCEEEEccCCCCchhhhh
Q 037567           17 YQKDVIQRIIE----K---RDCLVVMATGSGKSLCYQ   46 (374)
Q Consensus        17 ~Q~~~~~~~~~----~---~~~l~~a~tGsGKT~~~~   46 (374)
                      .|..+...+.+    +   +.+++.||+|+|||..+.
T Consensus        20 Gq~~~~~~l~~~~~~~~~~h~~L~~Gp~G~GKTtla~   56 (363)
T PRK14961         20 GQKHIVTAISNGLSLGRIHHAWLLSGTRGVGKTTIAR   56 (363)
T ss_pred             ChHHHHHHHHHHHHcCCCCeEEEEecCCCCCHHHHHH
Confidence            45565554332    2   235899999999996643

>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional

Probab=95.74  E-value=0.054  Score=53.28  Aligned_cols=18  Identities=33%  Similarity=0.412  Sum_probs=15.3

Q ss_pred             CCCEEEEccCCCCchhhh
Q 037567           28 KRDCLVVMATGSGKSLCY   45 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~   45 (374)
                      ..+.++.||+|+|||...
T Consensus       207 ~~n~LLvGppGvGKT~la  224 (758)
T PRK11034        207 KNNPLLVGESGVGKTAIA  224 (758)
T ss_pred             CCCeEEECCCCCCHHHHH
Confidence            458899999999999763

>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH

Probab=95.73  E-value=0.062  Score=50.63  Aligned_cols=18  Identities=33%  Similarity=0.558  Sum_probs=15.2

Q ss_pred             CCEEEEccCCCCchhhhh
Q 037567           29 RDCLVVMATGSGKSLCYQ   46 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~~   46 (374)
                      +.+++.||+|+|||...-
T Consensus        89 ~giLL~GppGtGKT~la~  106 (495)
T TIGR01241        89 KGVLLVGPPGTGKTLLAK  106 (495)
T ss_pred             CcEEEECCCCCCHHHHHH
Confidence            478999999999997643

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.

>PRK11823 DNA repair protein RadA; Provisional

Probab=95.73  E-value=0.086  Score=48.72  Aligned_cols=88  Identities=15%  Similarity=0.155  Sum_probs=52.1

Q ss_pred             CCCEEEEccCCCCchhhhhccc---cccCCcEEEEcchHHHHHHHHHHHHHcCCceEEcCCCCCchhhhhhhhcCCeeEE
Q 037567           28 KRDCLVVMATGSGKSLCYQLPP---LVTGKTALVVSPLISLMQDQVMSLKQRGINAEFLGSAQTDSSVQTKAETGYFQLL  104 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~l~~---~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~  104 (374)
                      +.-+++.+++|+|||...+..+   ..++.+++++.-. +...|......+++....                    ++.
T Consensus        80 Gs~~lI~G~pG~GKTtL~lq~a~~~a~~g~~vlYvs~E-es~~qi~~ra~rlg~~~~--------------------~l~  138 (446)
T PRK11823         80 GSVVLIGGDPGIGKSTLLLQVAARLAAAGGKVLYVSGE-ESASQIKLRAERLGLPSD--------------------NLY  138 (446)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEEcc-ccHHHHHHHHHHcCCChh--------------------cEE
Confidence            3456899999999996433221   2346788888754 455677766666654311                    122


Q ss_pred             EEcCcccccCchhhHHHHHhcCccEEEEeccchhhc
Q 037567          105 FMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISE  140 (374)
Q Consensus       105 i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~  140 (374)
                      +.....+.    .....+...+.++||||+++.+..
T Consensus       139 ~~~e~~l~----~i~~~i~~~~~~lVVIDSIq~l~~  170 (446)
T PRK11823        139 LLAETNLE----AILATIEEEKPDLVVIDSIQTMYS  170 (446)
T ss_pred             EeCCCCHH----HHHHHHHhhCCCEEEEechhhhcc
Confidence            32222221    222333335788999999998754

>cd01126 TraG_VirD4 The TraG/TraD/VirD4 family are bacterial conjugation proteins involved in type IV secretion

Probab=95.73  E-value=0.018  Score=52.27  Aligned_cols=56  Identities=20%  Similarity=0.235  Sum_probs=43.6

Q ss_pred             CEEEEccCCCCchhhhhccccc-cCCcEEEEcchHHHHHHHHHHHHHcCCceEEcCC
Q 037567           30 DCLVVMATGSGKSLCYQLPPLV-TGKTALVVSPLISLMQDQVMSLKQRGINAEFLGS   85 (374)
Q Consensus        30 ~~l~~a~tGsGKT~~~~l~~~~-~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~   85 (374)
                      ++++.||||||||.++.+|.+. -...++|+=|.-++........+..|..+.++..
T Consensus         1 H~lv~g~tGsGKt~~~viP~ll~~~~s~vv~D~Kge~~~~t~~~r~~~G~~V~v~nP   57 (384)
T cd01126           1 HVLVFAPTRSGKGVGFVIPNLLTWPGSVVVLDPKGENFELTSEHRRALGRKVFVFDP   57 (384)
T ss_pred             CeeEecCCCCCCccEEEccchhcCCCCEEEEccchhHHHHHHHHHHHcCCeEEEEcC
Confidence            4689999999999988877554 3567888888889998887777777766665543

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.

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=95.72  E-value=0.021  Score=54.65  Aligned_cols=16  Identities=25%  Similarity=0.511  Sum_probs=13.7

Q ss_pred             cCccEEEEeccchhhc
Q 037567          125 AGVCLFAVDEAHCISE  140 (374)
Q Consensus       125 ~~~~~vviDE~h~~~~  140 (374)
                      ..+.++||||+|.+..
T Consensus       118 g~~KV~IIDEah~Ls~  133 (647)
T PRK07994        118 GRFKVYLIDEVHMLSR  133 (647)
T ss_pred             CCCEEEEEechHhCCH
Confidence            4678999999999875

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.68  E-value=0.053  Score=51.55  Aligned_cols=16  Identities=38%  Similarity=0.615  Sum_probs=13.6

Q ss_pred             cCccEEEEeccchhhc
Q 037567          125 AGVCLFAVDEAHCISE  140 (374)
Q Consensus       125 ~~~~~vviDE~h~~~~  140 (374)
                      ...+++||||+|.+..
T Consensus       117 ~~~KVvIIDEah~Lt~  132 (584)
T PRK14952        117 SRYRIFIVDEAHMVTT  132 (584)
T ss_pred             CCceEEEEECCCcCCH
Confidence            4678999999999865

>PRK11054 helD DNA helicase IV; Provisional

Probab=95.65  E-value=0.017  Score=56.15  Aligned_cols=62  Identities=18%  Similarity=0.220  Sum_probs=47.5

Q ss_pred             CCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccc---c----ccCCcEEEEcchHHHHHHHHHHHHH
Q 037567           12 SVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPP---L----VTGKTALVVSPLISLMQDQVMSLKQ   75 (374)
Q Consensus        12 ~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~---~----~~~~~~lil~P~~~l~~q~~~~~~~   75 (374)
                      ..+++-|.+++..  ...+++|.|.+|||||.+...-+   +    ....++|+++.++..++.+.+.+..
T Consensus       195 ~~L~~~Q~~av~~--~~~~~lV~agaGSGKT~vl~~r~ayLl~~~~~~~~~IL~ltft~~AA~em~eRL~~  263 (684)
T PRK11054        195 SPLNPSQARAVVN--GEDSLLVLAGAGSGKTSVLVARAGWLLARGQAQPEQILLLAFGRQAAEEMDERIRE  263 (684)
T ss_pred             CCCCHHHHHHHhC--CCCCeEEEEeCCCCHHHHHHHHHHHHHHhCCCCHHHeEEEeccHHHHHHHHHHHHH
Confidence            3699999998863  34678999999999996643222   1    1356899999999999998888764

>CHL00181 cbbX CbbX; Provisional

Probab=95.63  E-value=0.067  Score=46.29  Aligned_cols=18  Identities=17%  Similarity=0.137  Sum_probs=14.7

Q ss_pred             CCEEEEccCCCCchhhhh
Q 037567           29 RDCLVVMATGSGKSLCYQ   46 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~~   46 (374)
                      .++++.||||+|||..+-
T Consensus        60 ~~ill~G~pGtGKT~lAr   77 (287)
T CHL00181         60 LHMSFTGSPGTGKTTVAL   77 (287)
T ss_pred             ceEEEECCCCCCHHHHHH
Confidence            357999999999997653

>KOG0991 consensus Replication factor C, subunit RFC2 [Replication, recombination and repair]

Probab=95.60  E-value=0.003  Score=51.15  Aligned_cols=18  Identities=17%  Similarity=0.325  Sum_probs=15.4

Q ss_pred             CCEEEEccCCCCchhhhh
Q 037567           29 RDCLVVMATGSGKSLCYQ   46 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~~   46 (374)
                      .+.++.+|+|+|||.+..
T Consensus        49 P~liisGpPG~GKTTsi~   66 (333)
T KOG0991|consen   49 PNLIISGPPGTGKTTSIL   66 (333)
T ss_pred             CceEeeCCCCCchhhHHH
Confidence            478999999999998754

>PF10593 Z1: Z1 domain; InterPro: IPR018310 This entry represents the Z1 domain of unknown function that is found in a group of putative endonucleases

Probab=95.59  E-value=0.025  Score=47.29  Aligned_cols=104  Identities=12%  Similarity=0.156  Sum_probs=73.2

Q ss_pred             CCceeeeecCCChHHHHHHHHhhhcCC----eeEEEEeccccccccccCccEEEEECCCCChhHHHHhhccCC-CCCCce
Q 037567          252 GVKAGTYHGQMGSKAREEAHRLFIRDE----IRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCG-RDGIAS  326 (374)
Q Consensus       252 ~~~~~~~~~~~~~~~r~~~~~~f~~g~----~~ilv~t~~~~~G~d~~~~~~vi~~~~p~s~~~~~Q~~GR~~-R~~~~g  326 (374)
                      ++.+..++++.+...     -+|.++.    ..|+|+-+++++|+.++++.+......+.+.++++||.=..| |.|-.+
T Consensus       110 ~~~v~~vNS~~~~~~-----ldy~~~~~~~~~~I~VGGn~LsRGlTleGL~vsYf~R~s~~~DTL~QmgRwFGYR~gY~d  184 (239)
T PF10593_consen  110 GIEVVVVNSGSSDDS-----LDYDDGENLGLNVIAVGGNKLSRGLTLEGLTVSYFLRNSKQYDTLMQMGRWFGYRPGYED  184 (239)
T ss_pred             CceEEEEeCCCcccc-----ccccccccCCceEEEECCccccCceeECCcEEEEecCCCchHHHHHHHhhcccCCccccc
Confidence            577788887655433     3344443    778899999999999999999999988888899988854444 777788


Q ss_pred             EEEEEeeccCCCcccceeccccchHHHHHHHHHHHHHHHH
Q 037567          327 VCWLYYARSNFAKGDFYCGESQTENQRTAIMESLLAAQRY  366 (374)
Q Consensus       327 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  366 (374)
                      .|-+|.+++-...+..+..      ..+.+.+++..|...
T Consensus       185 l~Ri~~~~~l~~~f~~i~~------~~e~lr~~i~~~~~~  218 (239)
T PF10593_consen  185 LCRIYMPEELYDWFRHIAE------AEEELREEIKEMANN  218 (239)
T ss_pred             ceEEecCHHHHHHHHHHHH------HHHHHHHHHHHHHhc
Confidence            8999988865555554442      223345555555443

This domain is found associated with a helicase domain of superfamily type II [].

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=95.58  E-value=0.092  Score=47.14  Aligned_cols=87  Identities=17%  Similarity=0.149  Sum_probs=50.2

Q ss_pred             CCEEEEccCCCCchhhhhccc---cccCCcEEEEcchHHHHHHHHHHHHHcCCceEEcCCCCCchhhhhhhhcCCeeEEE
Q 037567           29 RDCLVVMATGSGKSLCYQLPP---LVTGKTALVVSPLISLMQDQVMSLKQRGINAEFLGSAQTDSSVQTKAETGYFQLLF  105 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~~l~~---~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~i  105 (374)
                      .-+++.+++|+|||...+..+   ...+.+++++.-. +...|......+++....                    ++.+
T Consensus        83 slvLI~G~pG~GKStLllq~a~~~a~~g~~VlYvs~E-Es~~qi~~Ra~rlg~~~~--------------------~l~l  141 (372)
T cd01121          83 SVILIGGDPGIGKSTLLLQVAARLAKRGGKVLYVSGE-ESPEQIKLRADRLGISTE--------------------NLYL  141 (372)
T ss_pred             eEEEEEeCCCCCHHHHHHHHHHHHHhcCCeEEEEECC-cCHHHHHHHHHHcCCCcc--------------------cEEE
Confidence            456899999999996543222   2245678887654 345566666665543210                    1222


Q ss_pred             EcCcccccCchhhHHHHHhcCccEEEEeccchhhc
Q 037567          106 MTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISE  140 (374)
Q Consensus       106 ~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~  140 (374)
                      .....+    ......+...+.++||||+++.+..
T Consensus       142 ~~e~~l----e~I~~~i~~~~~~lVVIDSIq~l~~  172 (372)
T cd01121         142 LAETNL----EDILASIEELKPDLVIIDSIQTVYS  172 (372)
T ss_pred             EccCcH----HHHHHHHHhcCCcEEEEcchHHhhc
Confidence            222111    1222333345789999999998853

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.

>TIGR02012 tigrfam_recA protein RecA

Probab=95.54  E-value=0.038  Score=48.26  Aligned_cols=97  Identities=15%  Similarity=0.101  Sum_probs=54.6

Q ss_pred             HHHHHHHc------CCCEEEEccCCCCchhhhhcc---ccccCCcEEEEcchHHHHHHHHHHHHHcCCceEEcCCCCCch
Q 037567           20 DVIQRIIE------KRDCLVVMATGSGKSLCYQLP---PLVTGKTALVVSPLISLMQDQVMSLKQRGINAEFLGSAQTDS   90 (374)
Q Consensus        20 ~~~~~~~~------~~~~l~~a~tGsGKT~~~~l~---~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~   90 (374)
                      ..++.++.      +.-+.+.+|+|+|||..++-.   ....+.+++++-.-..+-.+   .++++|....         
T Consensus        41 ~~LD~~Lg~GGlp~G~iteI~G~~GsGKTtLaL~~~~~~~~~g~~v~yId~E~~~~~~---~a~~lGvd~~---------  108 (321)
T TIGR02012        41 LSLDLALGVGGLPRGRIIEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHALDPV---YARKLGVDID---------  108 (321)
T ss_pred             HHHHHHhcCCCCcCCeEEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEEcccchhHHH---HHHHcCCCHH---------
Confidence            34555554      245679999999999654322   22356778877665444443   3444443211         


Q ss_pred             hhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhh
Q 037567           91 SVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCIS  139 (374)
Q Consensus        91 ~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~  139 (374)
                                 .+++..|+.....+...........+++||||-+-.+.
T Consensus       109 -----------~l~v~~p~~~eq~l~~~~~li~~~~~~lIVIDSv~al~  146 (321)
T TIGR02012       109 -----------NLLVSQPDTGEQALEIAETLVRSGAVDIIVVDSVAALV  146 (321)
T ss_pred             -----------HeEEecCCCHHHHHHHHHHHhhccCCcEEEEcchhhhc
Confidence                       34455555432222221122223568999999988775

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.

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

Probab=95.52  E-value=0.029  Score=48.58  Aligned_cols=61  Identities=15%  Similarity=0.190  Sum_probs=44.0

Q ss_pred             hHcCCCCCchhHHHHHHHHHcCC-CEEEEccCCCCchhhh--hccccccCCcEEEEcchHHHHH
Q 037567            7 KYFGYSVFRPYQKDVIQRIIEKR-DCLVVMATGSGKSLCY--QLPPLVTGKTALVVSPLISLMQ   67 (374)
Q Consensus         7 ~~~~~~~~~~~Q~~~~~~~~~~~-~~l~~a~tGsGKT~~~--~l~~~~~~~~~lil~P~~~l~~   67 (374)
                      ....|..+.+-|...+..+.... +++++|.||||||...  ++.-....-+++.+-.+.+|.-
T Consensus       151 dli~~gt~~~~~a~~L~~av~~r~NILisGGTGSGKTTlLNal~~~i~~~eRvItiEDtaELql  214 (355)
T COG4962         151 DLIIFGTMIRRAAKFLRRAVGIRCNILISGGTGSGKTTLLNALSGFIDSDERVITIEDTAELQL  214 (355)
T ss_pred             HHHHcCCcCHHHHHHHHHHHhhceeEEEeCCCCCCHHHHHHHHHhcCCCcccEEEEeehhhhcc
Confidence            44567778888888887777665 9999999999999542  2222334558999888877754

>TIGR00064 ftsY signal recognition particle-docking protein FtsY

Probab=95.52  E-value=0.42  Score=41.04  Aligned_cols=49  Identities=20%  Similarity=0.215  Sum_probs=27.5

Q ss_pred             CEEEEccCCCCchhhhhccc---cccCCcEEEEc-c-hHHH-HHHHHHHHHHcCC
Q 037567           30 DCLVVMATGSGKSLCYQLPP---LVTGKTALVVS-P-LISL-MQDQVMSLKQRGI   78 (374)
Q Consensus        30 ~~l~~a~tGsGKT~~~~l~~---~~~~~~~lil~-P-~~~l-~~q~~~~~~~~~~   78 (374)
                      -+++.+|+|+|||.+....+   ...+.+++++. . .+.- ..|...+....+.
T Consensus        74 vi~l~G~~G~GKTTt~akLA~~l~~~g~~V~li~~D~~r~~a~~ql~~~~~~~~i  128 (272)
T TIGR00064        74 VILFVGVNGVGKTTTIAKLANKLKKQGKSVLLAAGDTFRAAAIEQLEEWAKRLGV  128 (272)
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHhcCCEEEEEeCCCCCHHHHHHHHHHHHhCCe
Confidence            45678999999996643222   23455666654 3 2322 3444445555553

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.

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=95.52  E-value=0.038  Score=49.23  Aligned_cols=16  Identities=38%  Similarity=0.418  Sum_probs=14.1

Q ss_pred             CEEEEccCCCCchhhh
Q 037567           30 DCLVVMATGSGKSLCY   45 (374)
Q Consensus        30 ~~l~~a~tGsGKT~~~   45 (374)
                      .+++.||+|+|||..+
T Consensus        38 ~lll~Gp~GtGKT~la   53 (337)
T PRK12402         38 HLLVQGPPGSGKTAAV   53 (337)
T ss_pred             eEEEECCCCCCHHHHH
Confidence            6899999999999654

>KOG0733 consensus Nuclear AAA ATPase (VCP subfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=95.51  E-value=0.061  Score=50.12  Aligned_cols=30  Identities=23%  Similarity=0.151  Sum_probs=20.0

Q ss_pred             CCCEEEEccCCCCchhhhhccccccCCcEE
Q 037567           28 KRDCLVVMATGSGKSLCYQLPPLVTGKTAL   57 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~l~~~~~~~~~l   57 (374)
                      .+.++++||+|+|||..+-..+-+.+-..+
T Consensus       223 prGvLlHGPPGCGKT~lA~AiAgel~vPf~  252 (802)
T KOG0733|consen  223 PRGVLLHGPPGCGKTSLANAIAGELGVPFL  252 (802)
T ss_pred             CCceeeeCCCCccHHHHHHHHhhhcCCceE
Confidence            367899999999999765433333343333

>KOG0733 consensus Nuclear AAA ATPase (VCP subfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=95.50  E-value=0.089  Score=49.10  Aligned_cols=109  Identities=15%  Similarity=0.169  Sum_probs=57.8

Q ss_pred             CCCEEEEccCCCCchhhhhccccccCCcEEEEcchHHHHHHHHHHHHHcCCceEEcCCCCCchhhhhhhhcCCeeEEEEc
Q 037567           28 KRDCLVVMATGSGKSLCYQLPPLVTGKTALVVSPLISLMQDQVMSLKQRGINAEFLGSAQTDSSVQTKAETGYFQLLFMT  107 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T  107 (374)
                      -..++++||+|+|||+.+-..+-..+. =++-+--=+|.+-|.-+-.+-                               
T Consensus       545 PsGvLL~GPPGCGKTLlAKAVANEag~-NFisVKGPELlNkYVGESErA-------------------------------  592 (802)
T KOG0733|consen  545 PSGVLLCGPPGCGKTLLAKAVANEAGA-NFISVKGPELLNKYVGESERA-------------------------------  592 (802)
T ss_pred             CCceEEeCCCCccHHHHHHHHhhhccC-ceEeecCHHHHHHHhhhHHHH-------------------------------
Confidence            357899999999999864333322222 233344445666554442211                               


Q ss_pred             CcccccCchhhHHHHHhcCccEEEEeccchhhc-ccCc-chHHHHHHHHHHHhcC----CCCeeEEEeecCccc
Q 037567          108 PEKACIIPISFWSKLLKAGVCLFAVDEAHCISE-WGHD-FRLEYKQLDKLRTFLL----GVPFVALTATATEKV  175 (374)
Q Consensus       108 ~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~-~~~~-~~~~~~~~~~~~~~~~----~~~~i~~SaT~~~~~  175 (374)
                             .+..+.+...+...+|+|||++.+.. .+.. .....+.++.++-.+.    ...+..+-||-.+..
T Consensus       593 -------VR~vFqRAR~saPCVIFFDEiDaL~p~R~~~~s~~s~RvvNqLLtElDGl~~R~gV~viaATNRPDi  659 (802)
T KOG0733|consen  593 -------VRQVFQRARASAPCVIFFDEIDALVPRRSDEGSSVSSRVVNQLLTELDGLEERRGVYVIAATNRPDI  659 (802)
T ss_pred             -------HHHHHHHhhcCCCeEEEecchhhcCcccCCCCchhHHHHHHHHHHHhcccccccceEEEeecCCCcc
Confidence                   11222333445667899999999864 1111 1122233333333332    245667777866654

>PRK06090 DNA polymerase III subunit delta'; Validated

Probab=95.48  E-value=0.066  Score=46.83  Aligned_cols=33  Identities=18%  Similarity=0.037  Sum_probs=25.8

Q ss_pred             CCchhHHHHHHHHHc----C---CCEEEEccCCCCchhhh
Q 037567           13 VFRPYQKDVIQRIIE----K---RDCLVVMATGSGKSLCY   45 (374)
Q Consensus        13 ~~~~~Q~~~~~~~~~----~---~~~l~~a~tGsGKT~~~   45 (374)
                      .++|+|...+..+.+    +   +-.++.||.|.||+..+
T Consensus         3 ~~yPWl~~~~~~l~~~~~~~rl~hA~L~~G~~G~Gk~~lA   42 (319)
T PRK06090          3 NDYPWLVPVWQNWKAGLDAGRIPGALLLQSDEGLGVESLV   42 (319)
T ss_pred             cCcccHHHHHHHHHHHHHcCCcceeEeeECCCCCCHHHHH
Confidence            478999999988764    2   35689999999999543

>PRK10416 signal recognition particle-docking protein FtsY; Provisional

Probab=95.46  E-value=0.24  Score=43.56  Aligned_cols=125  Identities=15%  Similarity=0.119  Sum_probs=58.2

Q ss_pred             CEEEEccCCCCchhhhhcc-c-c-ccCCcEEEEc-ch-HH-HHHHHHHHHHHcCCceEEcCCCCCchhhhhhhhcCCeeE
Q 037567           30 DCLVVMATGSGKSLCYQLP-P-L-VTGKTALVVS-PL-IS-LMQDQVMSLKQRGINAEFLGSAQTDSSVQTKAETGYFQL  103 (374)
Q Consensus        30 ~~l~~a~tGsGKT~~~~l~-~-~-~~~~~~lil~-P~-~~-l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i  103 (374)
                      -+.+.||+|+|||.+.... . + ..+.+++++. ++ +. -.+|...+....++.........                
T Consensus       116 vi~lvGpnGsGKTTt~~kLA~~l~~~g~~V~Li~~D~~r~~a~eql~~~a~~~~i~~~~~~~~~----------------  179 (318)
T PRK10416        116 VILVVGVNGVGKTTTIGKLAHKYKAQGKKVLLAAGDTFRAAAIEQLQVWGERVGVPVIAQKEGA----------------  179 (318)
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHhcCCeEEEEecCccchhhHHHHHHHHHHcCceEEEeCCCC----------------
Confidence            4578999999999654322 1 1 2355666654 33 22 23454444444443322111000                


Q ss_pred             EEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHH----hcCCCCeeEEEeecCcccHH
Q 037567          104 LFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRT----FLLGVPFVALTATATEKVRI  177 (374)
Q Consensus       104 ~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~----~~~~~~~i~~SaT~~~~~~~  177 (374)
                         .|.   .............++++|+||=+.++...... ...+..+.+...    ..+...++.++||.......
T Consensus       180 ---dpa---~~v~~~l~~~~~~~~D~ViIDTaGr~~~~~~l-~~eL~~~~~v~~~~~~~~p~~~~LVl~a~~g~~~~~  250 (318)
T PRK10416        180 ---DPA---SVAFDAIQAAKARGIDVLIIDTAGRLHNKTNL-MEELKKIKRVIKKADPDAPHEVLLVLDATTGQNALS  250 (318)
T ss_pred             ---CHH---HHHHHHHHHHHhCCCCEEEEeCCCCCcCCHHH-HHHHHHHHHHHhhhcCCCCceEEEEEECCCChHHHH
Confidence               000   00001111223467889999988765321111 111222222221    12344578899996554443

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=95.26  E-value=0.032  Score=52.23  Aligned_cols=108  Identities=17%  Similarity=0.160  Sum_probs=63.6

Q ss_pred             HHHHHHHc-----CCCEEEEccCCCCchhhhh---ccccccCCcEEEEcchHHHHHHHHHHHHHcCCceEEcCCCCCchh
Q 037567           20 DVIQRIIE-----KRDCLVVMATGSGKSLCYQ---LPPLVTGKTALVVSPLISLMQDQVMSLKQRGINAEFLGSAQTDSS   91 (374)
Q Consensus        20 ~~~~~~~~-----~~~~l~~a~tGsGKT~~~~---l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~   91 (374)
                      ..++.++.     +.-+++.+|||+|||...+   ...+.++.++++++ ..+-..|..+.++.+|+...-+        
T Consensus       250 ~~lD~~lgGG~~~gs~~li~G~~G~GKt~l~~~f~~~~~~~ge~~~y~s-~eEs~~~i~~~~~~lg~~~~~~--------  320 (484)
T TIGR02655       250 VRLDEMCGGGFFKDSIILATGATGTGKTLLVSKFLENACANKERAILFA-YEESRAQLLRNAYSWGIDFEEM--------  320 (484)
T ss_pred             HhHHHHhcCCccCCcEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEE-eeCCHHHHHHHHHHcCCChHHH--------
Confidence            34555554     4567999999999996533   22334567888877 5577888888888887642111        


Q ss_pred             hhhhhhcCCeeEEEEcCccc--ccCchhhHHHHHhcCccEEEEeccchhhc
Q 037567           92 VQTKAETGYFQLLFMTPEKA--CIIPISFWSKLLKAGVCLFAVDEAHCISE  140 (374)
Q Consensus        92 ~~~~~~~~~~~i~i~T~~~l--~~~~~~~~~~~~~~~~~~vviDE~h~~~~  140 (374)
                          ...+...++-..|...  ..++......+...+.+.||||=...+..
T Consensus       321 ----~~~g~l~~~~~~p~~~~~~~~~~~i~~~i~~~~~~~vvIDsi~~~~~  367 (484)
T TIGR02655       321 ----EQQGLLKIICAYPESAGLEDHLQIIKSEIADFKPARIAIDSLSALAR  367 (484)
T ss_pred             ----hhCCcEEEEEcccccCChHHHHHHHHHHHHHcCCCEEEEcCHHHHHH
Confidence                1111122322222211  12223333444556788999999987743

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.

>cd00984 DnaB_C DnaB helicase C terminal domain

Probab=95.26  E-value=0.099  Score=44.10  Aligned_cols=35  Identities=17%  Similarity=0.054  Sum_probs=24.3

Q ss_pred             cCCCEEEEccCCCCchhhhhcc---cccc-CCcEEEEcc
Q 037567           27 EKRDCLVVMATGSGKSLCYQLP---PLVT-GKTALVVSP   61 (374)
Q Consensus        27 ~~~~~l~~a~tGsGKT~~~~l~---~~~~-~~~~lil~P   61 (374)
                      .|.-+++.|+||+|||...+-.   .... +.++++++.
T Consensus        12 ~G~l~lI~G~~G~GKT~~~~~~~~~~~~~~g~~vly~s~   50 (242)
T cd00984          12 PGDLIIIAARPSMGKTAFALNIAENIAKKQGKPVLFFSL   50 (242)
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHHHhCCCceEEEeC
Confidence            4566789999999999543322   2223 778888884

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.

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=95.25  E-value=0.04  Score=51.44  Aligned_cols=30  Identities=17%  Similarity=0.210  Sum_probs=20.3

Q ss_pred             hHHHHHHHHH----cC---CCEEEEccCCCCchhhhh
Q 037567           17 YQKDVIQRII----EK---RDCLVVMATGSGKSLCYQ   46 (374)
Q Consensus        17 ~Q~~~~~~~~----~~---~~~l~~a~tGsGKT~~~~   46 (374)
                      .|..+...+.    ++   +.+++.||+|+|||.++.
T Consensus        25 Gq~~vv~~L~~ai~~~ri~~a~Lf~Gp~G~GKTT~Ar   61 (507)
T PRK06645         25 GQEVLVKVLSYTILNDRLAGGYLLTGIRGVGKTTSAR   61 (507)
T ss_pred             CcHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHH
Confidence            4555554432    33   357999999999997654

>PRK09354 recA recombinase A; Provisional

Probab=95.24  E-value=0.026  Score=49.72  Aligned_cols=97  Identities=18%  Similarity=0.101  Sum_probs=55.7

Q ss_pred             HHHHHHHc-C-----CCEEEEccCCCCchhhhhccc---cccCCcEEEEcchHHHHHHHHHHHHHcCCceEEcCCCCCch
Q 037567           20 DVIQRIIE-K-----RDCLVVMATGSGKSLCYQLPP---LVTGKTALVVSPLISLMQDQVMSLKQRGINAEFLGSAQTDS   90 (374)
Q Consensus        20 ~~~~~~~~-~-----~~~l~~a~tGsGKT~~~~l~~---~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~   90 (374)
                      ..++.++. |     .-+.+.+|+|||||...+..+   ...+.+++++..-.++-..   .++++|....         
T Consensus        46 ~~LD~~LG~GGip~G~IteI~G~~GsGKTtLal~~~~~~~~~G~~~~yId~E~s~~~~---~a~~lGvdld---------  113 (349)
T PRK09354         46 LALDIALGIGGLPRGRIVEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHALDPV---YAKKLGVDID---------  113 (349)
T ss_pred             HHHHHHhcCCCCcCCeEEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEECCccchHHH---HHHHcCCCHH---------
Confidence            34555555 3     355799999999996544322   3457788887776555543   3445544311         


Q ss_pred             hhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhh
Q 037567           91 SVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCIS  139 (374)
Q Consensus        91 ~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~  139 (374)
                                 ++++..|+.....+...........+++||||=+-.+.
T Consensus       114 -----------~lli~qp~~~Eq~l~i~~~li~s~~~~lIVIDSvaaL~  151 (349)
T PRK09354        114 -----------NLLVSQPDTGEQALEIADTLVRSGAVDLIVVDSVAALV  151 (349)
T ss_pred             -----------HeEEecCCCHHHHHHHHHHHhhcCCCCEEEEeChhhhc
Confidence                       34555554432222221122223568899999887664

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

Probab=95.18  E-value=0.023  Score=49.59  Aligned_cols=97  Identities=18%  Similarity=0.058  Sum_probs=55.0

Q ss_pred             HHHHHHHc------CCCEEEEccCCCCchhhhhccc---cccCCcEEEEcchHHHHHHHHHHHHHcCCceEEcCCCCCch
Q 037567           20 DVIQRIIE------KRDCLVVMATGSGKSLCYQLPP---LVTGKTALVVSPLISLMQDQVMSLKQRGINAEFLGSAQTDS   90 (374)
Q Consensus        20 ~~~~~~~~------~~~~l~~a~tGsGKT~~~~l~~---~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~   90 (374)
                      ..++.++.      +.-+.+.+|+|+|||..++..+   ...+.+++++.+-..+-.+   .++.+|...          
T Consensus        41 ~~LD~~Lg~GGlp~G~iteI~Gp~GsGKTtLal~~~~~~~~~g~~~vyId~E~~~~~~---~a~~lGvd~----------  107 (325)
T cd00983          41 LSLDIALGIGGYPKGRIIEIYGPESSGKTTLALHAIAEAQKLGGTVAFIDAEHALDPV---YAKKLGVDL----------  107 (325)
T ss_pred             HHHHHHhcCCCccCCeEEEEECCCCCCHHHHHHHHHHHHHHcCCCEEEECccccHHHH---HHHHcCCCH----------
Confidence            44555555      3456799999999996544332   2357788888876655543   334444321          


Q ss_pred             hhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhh
Q 037567           91 SVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCIS  139 (374)
Q Consensus        91 ~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~  139 (374)
                                -++++..|......+...........+++||||=+-.+.
T Consensus       108 ----------~~l~v~~p~~~eq~l~i~~~li~s~~~~lIVIDSvaal~  146 (325)
T cd00983         108 ----------DNLLISQPDTGEQALEIADSLVRSGAVDLIVVDSVAALV  146 (325)
T ss_pred             ----------HHheecCCCCHHHHHHHHHHHHhccCCCEEEEcchHhhc
Confidence                      024455554332222221122233568999999987664

RecA couples ATP hydrolysis to DNA strand exchange.

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

Probab=95.17  E-value=0.025  Score=48.34  Aligned_cols=54  Identities=19%  Similarity=0.207  Sum_probs=38.3

Q ss_pred             cCCCEEEEccCCCCchhhhh---ccccccCCcEEEEcchHHHHHHHHHHHHHcCCceE
Q 037567           27 EKRDCLVVMATGSGKSLCYQ---LPPLVTGKTALVVSPLISLMQDQVMSLKQRGINAE   81 (374)
Q Consensus        27 ~~~~~l~~a~tGsGKT~~~~---l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~   81 (374)
                      .++.+++.|++|||||+..+   ...+..+.++++++-. +...+..+.+.++|....
T Consensus        22 ~g~~~lI~G~pGsGKT~f~~qfl~~~~~~ge~vlyvs~~-e~~~~l~~~~~~~g~d~~   78 (260)
T COG0467          22 RGSVVLITGPPGTGKTIFALQFLYEGAREGEPVLYVSTE-ESPEELLENARSFGWDLE   78 (260)
T ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHHHHhcCCcEEEEEec-CCHHHHHHHHHHcCCCHH
Confidence            46788999999999995432   3334457778887765 566777777777766553

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional

Probab=95.16  E-value=0.24  Score=46.25  Aligned_cols=55  Identities=18%  Similarity=0.042  Sum_probs=30.9

Q ss_pred             cCccEEEEeccchhhcccCcchHHHHHHHHHHHhcCCCCeeEEEeecCcccHHHHHHhc
Q 037567          125 AGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEKVRIDIINSL  183 (374)
Q Consensus       125 ~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~SaT~~~~~~~~~~~~~  183 (374)
                      .+.++|+||.+-......    .....+..+.........+.++++........+...+
T Consensus       427 ~~~DLVLIDTaG~s~~D~----~l~eeL~~L~aa~~~a~lLVLpAtss~~Dl~eii~~f  481 (559)
T PRK12727        427 RDYKLVLIDTAGMGQRDR----ALAAQLNWLRAARQVTSLLVLPANAHFSDLDEVVRRF  481 (559)
T ss_pred             ccCCEEEecCCCcchhhH----HHHHHHHHHHHhhcCCcEEEEECCCChhHHHHHHHHH
Confidence            467899999997542111    1112222232223345688888887766555555544

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

Probab=95.16  E-value=0.12  Score=44.36  Aligned_cols=37  Identities=16%  Similarity=0.177  Sum_probs=24.6

Q ss_pred             HHcCCCEEEEccCCCCchhhhhc---ccccc-CCcEEEEcc
Q 037567           25 IIEKRDCLVVMATGSGKSLCYQL---PPLVT-GKTALVVSP   61 (374)
Q Consensus        25 ~~~~~~~l~~a~tGsGKT~~~~l---~~~~~-~~~~lil~P   61 (374)
                      +..+.-+++.|++|+|||.....   .+... +.+++++.-
T Consensus        27 ~~~g~~~~i~g~~G~GKT~l~~~~~~~~~~~~g~~vl~iS~   67 (271)
T cd01122          27 LRKGELIILTAGTGVGKTTFLREYALDLITQHGVRVGTISL   67 (271)
T ss_pred             EcCCcEEEEEcCCCCCHHHHHHHHHHHHHHhcCceEEEEEc
Confidence            34466779999999999954332   22233 677888764

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

>PRK09111 DNA polymerase III subunits gamma and tau; Validated

Probab=95.16  E-value=0.074  Score=50.85  Aligned_cols=17  Identities=18%  Similarity=0.282  Sum_probs=14.4

Q ss_pred             CEEEEccCCCCchhhhh
Q 037567           30 DCLVVMATGSGKSLCYQ   46 (374)
Q Consensus        30 ~~l~~a~tGsGKT~~~~   46 (374)
                      .++++||.|+|||.++.
T Consensus        48 a~L~~Gp~GvGKTt~Ar   64 (598)
T PRK09111         48 AFMLTGVRGVGKTTTAR   64 (598)
T ss_pred             eEEEECCCCCCHHHHHH
Confidence            57999999999997654

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.14  E-value=0.1  Score=49.19  Aligned_cols=16  Identities=25%  Similarity=0.254  Sum_probs=13.5

Q ss_pred             EEEEccCCCCchhhhh
Q 037567           31 CLVVMATGSGKSLCYQ   46 (374)
Q Consensus        31 ~l~~a~tGsGKT~~~~   46 (374)
                      +++.||.|+|||..+.
T Consensus        41 ~Lf~Gp~GvGKTTlAr   56 (546)
T PRK14957         41 YLFTGTRGVGKTTLGR   56 (546)
T ss_pred             EEEECCCCCCHHHHHH
Confidence            6899999999996643

>PTZ00361 26 proteosome regulatory subunit 4-like protein; Provisional

Probab=95.14  E-value=0.11  Score=47.65  Aligned_cols=20  Identities=20%  Similarity=0.378  Sum_probs=16.2

Q ss_pred             CCCEEEEccCCCCchhhhhc
Q 037567           28 KRDCLVVMATGSGKSLCYQL   47 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~l   47 (374)
                      .+.+++.||+|+|||+.+-.
T Consensus       217 p~gVLL~GPPGTGKT~LAra  236 (438)
T PTZ00361        217 PKGVILYGPPGTGKTLLAKA  236 (438)
T ss_pred             CcEEEEECCCCCCHHHHHHH
Confidence            35789999999999976543

>COG1435 Tdk Thymidine kinase [Nucleotide transport and metabolism]

Probab=95.13  E-value=0.21  Score=39.73  Aligned_cols=34  Identities=24%  Similarity=0.112  Sum_probs=23.4

Q ss_pred             CEEEEccCCCCchhhhhcccc---ccCCcEEEEcchH
Q 037567           30 DCLVVMATGSGKSLCYQLPPL---VTGKTALVVSPLI   63 (374)
Q Consensus        30 ~~l~~a~tGsGKT~~~~l~~~---~~~~~~lil~P~~   63 (374)
                      =.++.+|++||||...+..+.   ..+.++++..|..
T Consensus         6 l~~i~gpM~SGKT~eLl~r~~~~~~~g~~v~vfkp~i   42 (201)
T COG1435           6 LEFIYGPMFSGKTEELLRRARRYKEAGMKVLVFKPAI   42 (201)
T ss_pred             EEEEEccCcCcchHHHHHHHHHHHHcCCeEEEEeccc
Confidence            357899999999975332222   1477788888864

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=95.12  E-value=0.11  Score=49.89  Aligned_cols=17  Identities=24%  Similarity=0.309  Sum_probs=14.3

Q ss_pred             CEEEEccCCCCchhhhh
Q 037567           30 DCLVVMATGSGKSLCYQ   46 (374)
Q Consensus        30 ~~l~~a~tGsGKT~~~~   46 (374)
                      .+|+.||+|+|||.++.
T Consensus        40 a~Lf~GP~GvGKTTlAr   56 (709)
T PRK08691         40 AYLLTGTRGVGKTTIAR   56 (709)
T ss_pred             EEEEECCCCCcHHHHHH
Confidence            46999999999997653

>PRK10689 transcription-repair coupling factor; Provisional

Probab=95.11  E-value=0.17  Score=52.35  Aligned_cols=79  Identities=11%  Similarity=0.099  Sum_probs=63.3

Q ss_pred             HhhcCCCcEEEEecchhHHHHHHHHHHHc----CCceeeeecCCChHHHHHHHHhhhcCCeeEEEEecc-ccccccccCc
Q 037567          223 KSVAGAGSIIVYCMTIKDVEEISKALKQL----GVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMA-FGMGIDKPDV  297 (374)
Q Consensus       223 ~~~~~~~~~lVf~~~~~~~~~l~~~l~~~----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~-~~~G~d~~~~  297 (374)
                      .....+.+++|.+|+..-+.+.++.+++.    ++.+..+++..+..++.++++....|..+|+|+|+. +...+++.++
T Consensus       644 ~~~~~g~qvlvLvPT~eLA~Q~~~~f~~~~~~~~v~i~~l~g~~s~~e~~~il~~l~~g~~dIVVgTp~lL~~~v~~~~L  723 (1147)
T PRK10689        644 LAVENHKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMLSRFRSAKEQTQILAEAAEGKIDILIGTHKLLQSDVKWKDL  723 (1147)
T ss_pred             HHHHcCCeEEEEeCcHHHHHHHHHHHHHhhccCCceEEEEECCCCHHHHHHHHHHHHhCCCCEEEECHHHHhCCCCHhhC
Confidence            33456889999999999999999888763    456778899999999999999999999999999984 4444566666


Q ss_pred             cEEE
Q 037567          298 RHVI  301 (374)
Q Consensus       298 ~~vi  301 (374)
                      ..+|
T Consensus       724 ~lLV  727 (1147)
T PRK10689        724 GLLI  727 (1147)
T ss_pred             CEEE
Confidence            6655

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.09  E-value=0.062  Score=51.37  Aligned_cols=16  Identities=25%  Similarity=0.328  Sum_probs=13.5

Q ss_pred             EEEEccCCCCchhhhh
Q 037567           31 CLVVMATGSGKSLCYQ   46 (374)
Q Consensus        31 ~l~~a~tGsGKT~~~~   46 (374)
                      ++++||.|+|||.++.
T Consensus        41 ~Lf~Gp~GvGKTtlAr   56 (618)
T PRK14951         41 YLFTGTRGVGKTTVSR   56 (618)
T ss_pred             EEEECCCCCCHHHHHH
Confidence            4899999999997654

>PRK07133 DNA polymerase III subunits gamma and tau; Validated

Probab=95.08  E-value=0.079  Score=51.36  Aligned_cols=17  Identities=24%  Similarity=0.305  Sum_probs=14.0

Q ss_pred             CEEEEccCCCCchhhhh
Q 037567           30 DCLVVMATGSGKSLCYQ   46 (374)
Q Consensus        30 ~~l~~a~tGsGKT~~~~   46 (374)
                      -+++.||.|+|||.++.
T Consensus        42 AYLF~GP~GtGKTt~Ar   58 (725)
T PRK07133         42 AYLFSGPRGTGKTSVAK   58 (725)
T ss_pred             EEEEECCCCCcHHHHHH
Confidence            35899999999997653

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.06  E-value=0.096  Score=47.76  Aligned_cols=17  Identities=18%  Similarity=0.237  Sum_probs=14.1

Q ss_pred             CEEEEccCCCCchhhhh
Q 037567           30 DCLVVMATGSGKSLCYQ   46 (374)
Q Consensus        30 ~~l~~a~tGsGKT~~~~   46 (374)
                      ..+++||+|+|||.++.
T Consensus        40 a~lf~Gp~G~GKtt~A~   56 (397)
T PRK14955         40 GYIFSGLRGVGKTTAAR   56 (397)
T ss_pred             eEEEECCCCCCHHHHHH
Confidence            37899999999996653

>TIGR01242 26Sp45 26S proteasome subunit P45 family

Probab=95.04  E-value=0.2  Score=45.13  Aligned_cols=19  Identities=26%  Similarity=0.429  Sum_probs=15.5

Q ss_pred             CCEEEEccCCCCchhhhhc
Q 037567           29 RDCLVVMATGSGKSLCYQL   47 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~~l   47 (374)
                      +.+++.||+|+|||..+-.
T Consensus       157 ~gvLL~GppGtGKT~laka  175 (364)
T TIGR01242       157 KGVLLYGPPGTGKTLLAKA  175 (364)
T ss_pred             ceEEEECCCCCCHHHHHHH
Confidence            4689999999999976543

Many proteins may score above the trusted cutoff because an internal

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=95.04  E-value=0.24  Score=45.47  Aligned_cols=50  Identities=16%  Similarity=0.110  Sum_probs=28.0

Q ss_pred             CEEEEccCCCCchhhhhcccc---ccCCcEEEEcc-h--HHHHHHHHHHHHHcCCc
Q 037567           30 DCLVVMATGSGKSLCYQLPPL---VTGKTALVVSP-L--ISLMQDQVMSLKQRGIN   79 (374)
Q Consensus        30 ~~l~~a~tGsGKT~~~~l~~~---~~~~~~lil~P-~--~~l~~q~~~~~~~~~~~   79 (374)
                      .++++|++|+|||.+....+.   ..+.+++++.. +  .+..+|+.......+..
T Consensus        97 vI~lvG~~GsGKTTtaakLA~~L~~~g~kV~lV~~D~~R~aa~eQL~~la~~~gvp  152 (437)
T PRK00771         97 TIMLVGLQGSGKTTTAAKLARYFKKKGLKVGLVAADTYRPAAYDQLKQLAEKIGVP  152 (437)
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHHcCCeEEEecCCCCCHHHHHHHHHHHHHcCCc
Confidence            467899999999966532221   23455555443 2  23345555554555443

>PRK12724 flagellar biosynthesis regulator FlhF; Provisional

Probab=95.03  E-value=0.21  Score=45.25  Aligned_cols=57  Identities=11%  Similarity=0.197  Sum_probs=33.0

Q ss_pred             hcCccEEEEeccchhhcccCcchHHHHHHHHHHHhc----CCCCeeEEEeecCcccHHHHHHhcC
Q 037567          124 KAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFL----LGVPFVALTATATEKVRIDIINSLK  184 (374)
Q Consensus       124 ~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~----~~~~~i~~SaT~~~~~~~~~~~~~~  184 (374)
                      ..+.++|+||=+.....    .......+..+....    +...++.+|||........+...+.
T Consensus       297 ~~~~D~VLIDTaGr~~r----d~~~l~eL~~~~~~~~~~~~~e~~LVLsAt~~~~~~~~~~~~f~  357 (432)
T PRK12724        297 RDGSELILIDTAGYSHR----NLEQLERMQSFYSCFGEKDSVENLLVLSSTSSYHHTLTVLKAYE  357 (432)
T ss_pred             hCCCCEEEEeCCCCCcc----CHHHHHHHHHHHHhhcCCCCCeEEEEEeCCCCHHHHHHHHHHhc
Confidence            35778999996654321    112223344333322    2346789999998876666666554

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

Probab=95.02  E-value=0.21  Score=47.42  Aligned_cols=87  Identities=22%  Similarity=0.266  Sum_probs=69.5

Q ss_pred             HHHHHHHHHhhcCCCcEEEEecchhHHHH----HHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccc-c
Q 037567          215 DELVQEILKSVAGAGSIIVYCMTIKDVEE----ISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAF-G  289 (374)
Q Consensus       215 ~~~~~~~~~~~~~~~~~lVf~~~~~~~~~----l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~-~  289 (374)
                      .-.+-..+.....+.++...+||.=-|++    +.+.|...|+.+.++.|.+....|.++++...+|+++++|.|.++ .
T Consensus       298 vVA~laml~ai~~G~Q~ALMAPTEILA~QH~~~~~~~l~~~~i~V~lLtG~~kgk~r~~~l~~l~~G~~~ivVGTHALiQ  377 (677)
T COG1200         298 VVALLAMLAAIEAGYQAALMAPTEILAEQHYESLRKWLEPLGIRVALLTGSLKGKARKEILEQLASGEIDIVVGTHALIQ  377 (677)
T ss_pred             HHHHHHHHHHHHcCCeeEEeccHHHHHHHHHHHHHHHhhhcCCeEEEeecccchhHHHHHHHHHhCCCCCEEEEcchhhh
Confidence            33444556667788899999999665554    445555568999999999999999999999999999999999954 5


Q ss_pred             ccccccCccEEE
Q 037567          290 MGIDKPDVRHVI  301 (374)
Q Consensus       290 ~G~d~~~~~~vi  301 (374)
                      ..+++.++-.||
T Consensus       378 d~V~F~~LgLVI  389 (677)
T COG1200         378 DKVEFHNLGLVI  389 (677)
T ss_pred             cceeecceeEEE
Confidence            688887777766

>CHL00206 ycf2 Ycf2; Provisional

Probab=95.00  E-value=0.11  Score=55.13  Aligned_cols=39  Identities=18%  Similarity=0.188  Sum_probs=26.1

Q ss_pred             CCCEEEEccCCCCchhhhhccccccCCcEEEEcchHHHHH
Q 037567           28 KRDCLVVMATGSGKSLCYQLPPLVTGKTALVVSPLISLMQ   67 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~l~~~~~~~~~lil~P~~~l~~   67 (374)
                      .+.+++.||+|+|||+.+-..+...+.+.+-+... +++.
T Consensus      1630 PKGILLiGPPGTGKTlLAKALA~es~VPFIsISgs-~fl~ 1668 (2281)
T CHL00206       1630 SRGILVIGSIGTGRSYLVKYLATNSYVPFITVFLN-KFLD 1668 (2281)
T ss_pred             CCceEEECCCCCCHHHHHHHHHHhcCCceEEEEHH-HHhh
Confidence            46789999999999987554444455555555444 4544

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

Probab=94.95  E-value=0.031  Score=48.01  Aligned_cols=31  Identities=16%  Similarity=0.217  Sum_probs=20.5

Q ss_pred             hhHHHHHHHHH----cCC-CEEEEccCCCCchhhhh
Q 037567           16 PYQKDVIQRII----EKR-DCLVVMATGSGKSLCYQ   46 (374)
Q Consensus        16 ~~Q~~~~~~~~----~~~-~~l~~a~tGsGKT~~~~   46 (374)
                      +.+.+++..+.    .+. .+++.||+|+|||....
T Consensus        26 ~~~~~~~~~l~~~~~~~~~~~~l~G~~G~GKTtl~~   61 (269)
T TIGR03015        26 KGHKRAMAYLEYGLSQREGFILITGEVGAGKTTLIR   61 (269)
T ss_pred             HHHHHHHHHHHHHHhcCCCEEEEEcCCCCCHHHHHH
Confidence            34455665543    223 47899999999997643

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.

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

Probab=94.91  E-value=0.11  Score=50.34  Aligned_cols=89  Identities=19%  Similarity=0.206  Sum_probs=70.5

Q ss_pred             chHHHHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHHc-CCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccc
Q 037567          212 SFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQL-GVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGM  290 (374)
Q Consensus       212 ~~~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~-~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~  290 (374)
                      .+.+-++..+.+.+..++++||.+|.......+.+.|+.+ |.++..+|+++++.+|...-.....|+.+|+|.|.++- 
T Consensus       229 GKTEvYl~~i~~~L~~GkqvLvLVPEI~Ltpq~~~rf~~rFg~~v~vlHS~Ls~~er~~~W~~~~~G~~~vVIGtRSAl-  307 (730)
T COG1198         229 GKTEVYLEAIAKVLAQGKQVLVLVPEIALTPQLLARFKARFGAKVAVLHSGLSPGERYRVWRRARRGEARVVIGTRSAL-  307 (730)
T ss_pred             cHHHHHHHHHHHHHHcCCEEEEEeccccchHHHHHHHHHHhCCChhhhcccCChHHHHHHHHHHhcCCceEEEEechhh-
Confidence            3344555556666678899999999999999999888874 78899999999999999999999999999999997532 


Q ss_pred             cccccCccEEE
Q 037567          291 GIDKPDVRHVI  301 (374)
Q Consensus       291 G~d~~~~~~vi  301 (374)
                      -.=++++..||
T Consensus       308 F~Pf~~LGLII  318 (730)
T COG1198         308 FLPFKNLGLII  318 (730)
T ss_pred             cCchhhccEEE
Confidence            22334555555

>CHL00195 ycf46 Ycf46; Provisional

Probab=94.91  E-value=0.17  Score=47.13  Aligned_cols=33  Identities=27%  Similarity=0.181  Sum_probs=20.9

Q ss_pred             CCCEEEEccCCCCchhhhhccccccCCcEEEEc
Q 037567           28 KRDCLVVMATGSGKSLCYQLPPLVTGKTALVVS   60 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~l~~~~~~~~~lil~   60 (374)
                      .+.+++.||+|+|||+.+-..+-.-+...+.+-
T Consensus       259 pkGILL~GPpGTGKTllAkaiA~e~~~~~~~l~  291 (489)
T CHL00195        259 PRGLLLVGIQGTGKSLTAKAIANDWQLPLLRLD  291 (489)
T ss_pred             CceEEEECCCCCcHHHHHHHHHHHhCCCEEEEE
Confidence            357899999999999765333323334444443

>PRK06731 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=94.90  E-value=0.14  Score=43.64  Aligned_cols=126  Identities=17%  Similarity=0.092  Sum_probs=64.9

Q ss_pred             CCEEEEccCCCCchhhhhcccc--c-cCCcEEEEcc-h--HHHHHHHHHHHHHcCCceEEcCCCCCchhhhhhhhcCCee
Q 037567           29 RDCLVVMATGSGKSLCYQLPPL--V-TGKTALVVSP-L--ISLMQDQVMSLKQRGINAEFLGSAQTDSSVQTKAETGYFQ  102 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~~l~~~--~-~~~~~lil~P-~--~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  102 (374)
                      ..+.+.+++|+|||..+...+.  . .+.++.++.. +  ...+.||.......+......                   
T Consensus        76 ~~i~~~G~~g~GKTtl~~~l~~~l~~~~~~v~~i~~D~~ri~~~~ql~~~~~~~~~~~~~~-------------------  136 (270)
T PRK06731         76 QTIALIGPTGVGKTTTLAKMAWQFHGKKKTVGFITTDHSRIGTVQQLQDYVKTIGFEVIAV-------------------  136 (270)
T ss_pred             CEEEEECCCCCcHHHHHHHHHHHHHHcCCeEEEEecCCCCHHHHHHHHHHhhhcCceEEec-------------------
Confidence            4668899999999976543222  1 2344544433 2  256667766555443322211                   


Q ss_pred             EEEEcCcccccCchhhHHHH-HhcCccEEEEeccchhhcccCcchHHHHHHHHHHHhc-CCCCeeEEEeecCcccHHHHH
Q 037567          103 LLFMTPEKACIIPISFWSKL-LKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFL-LGVPFVALTATATEKVRIDII  180 (374)
Q Consensus       103 i~i~T~~~l~~~~~~~~~~~-~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~-~~~~~i~~SaT~~~~~~~~~~  180 (374)
                         .+++.+.    ...... ...+++++++|-+-+....    ...+..+..+.... +....+.+|||........+.
T Consensus       137 ---~~~~~l~----~~l~~l~~~~~~D~ViIDt~Gr~~~~----~~~l~el~~~~~~~~~~~~~LVl~a~~~~~d~~~~~  205 (270)
T PRK06731        137 ---RDEAAMT----RALTYFKEEARVDYILIDTAGKNYRA----SETVEEMIETMGQVEPDYICLTLSASMKSKDMIEII  205 (270)
T ss_pred             ---CCHHHHH----HHHHHHHhcCCCCEEEEECCCCCcCC----HHHHHHHHHHHhhhCCCeEEEEEcCccCHHHHHHHH
Confidence               1222221    111111 1246799999998764321    11223333333322 233467799998776665666


Q ss_pred             HhcC
Q 037567          181 NSLK  184 (374)
Q Consensus       181 ~~~~  184 (374)
                      ..+.
T Consensus       206 ~~f~  209 (270)
T PRK06731        206 TNFK  209 (270)
T ss_pred             HHhC
Confidence            5544

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

Probab=94.89  E-value=0.013  Score=49.86  Aligned_cols=19  Identities=47%  Similarity=0.621  Sum_probs=16.1

Q ss_pred             CCCEEEEccCCCCchhhhh
Q 037567           28 KRDCLVVMATGSGKSLCYQ   46 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~   46 (374)
                      ..|+++.+|||||||+.+.
T Consensus        97 KSNILLiGPTGsGKTlLAq  115 (408)
T COG1219          97 KSNILLIGPTGSGKTLLAQ  115 (408)
T ss_pred             eccEEEECCCCCcHHHHHH
Confidence            4578999999999998654

>KOG0737 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=94.89  E-value=0.092  Score=45.87  Aligned_cols=27  Identities=19%  Similarity=0.287  Sum_probs=19.6

Q ss_pred             CCEEEEccCCCCchhhhhccccccCCc
Q 037567           29 RDCLVVMATGSGKSLCYQLPPLVTGKT   55 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~~l~~~~~~~~   55 (374)
                      +.+++.+|+|+|||..+-..+-..+..
T Consensus       128 kGiLL~GPpG~GKTmlAKA~Akeaga~  154 (386)
T KOG0737|consen  128 KGILLYGPPGTGKTMLAKAIAKEAGAN  154 (386)
T ss_pred             ccceecCCCCchHHHHHHHHHHHcCCC
Confidence            578999999999998765444444443

>TIGR01073 pcrA ATP-dependent DNA helicase PcrA

Probab=94.87  E-value=0.036  Score=54.90  Aligned_cols=63  Identities=13%  Similarity=0.198  Sum_probs=47.6

Q ss_pred             CCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccc---cc----cCCcEEEEcchHHHHHHHHHHHHHc
Q 037567           12 SVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPP---LV----TGKTALVVSPLISLMQDQVMSLKQR   76 (374)
Q Consensus        12 ~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~---~~----~~~~~lil~P~~~l~~q~~~~~~~~   76 (374)
                      ..|+|-|.+++..  ...+++|.|.+|||||.+..--+   +.    ...++|+++-|+..+.++.+.+.+.
T Consensus         3 ~~Ln~~Q~~av~~--~~g~~lV~AgaGSGKT~~l~~ria~Li~~~~i~P~~IL~lTFT~kAA~em~~Rl~~~   72 (726)
T TIGR01073         3 AHLNPEQREAVKT--TEGPLLIMAGAGSGKTRVLTHRIAHLIAEKNVAPWNILAITFTNKAAREMKERVEKL   72 (726)
T ss_pred             cccCHHHHHHHhC--CCCCEEEEeCCCCCHHHHHHHHHHHHHHcCCCCHHHeeeeeccHHHHHHHHHHHHHH
Confidence            4689999999974  45789999999999996533211   11    2357999999999999888887643

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

>PRK13833 conjugal transfer protein TrbB; Provisional

Probab=94.87  E-value=0.042  Score=48.10  Aligned_cols=53  Identities=17%  Similarity=0.293  Sum_probs=33.8

Q ss_pred             CCchhHHHHHHHHH-cCCCEEEEccCCCCchhhh--hcccc---ccCCcEEEEcchHHH
Q 037567           13 VFRPYQKDVIQRII-EKRDCLVVMATGSGKSLCY--QLPPL---VTGKTALVVSPLISL   65 (374)
Q Consensus        13 ~~~~~Q~~~~~~~~-~~~~~l~~a~tGsGKT~~~--~l~~~---~~~~~~lil~P~~~l   65 (374)
                      .+.+.|.+.+..+. .+.+++++|+||||||...  ++..+   ....+++.+-...+|
T Consensus       128 ~~~~~~~~~L~~~v~~~~nilI~G~tGSGKTTll~aL~~~i~~~~~~~rivtiEd~~El  186 (323)
T PRK13833        128 IMTEAQASVIRSAIDSRLNIVISGGTGSGKTTLANAVIAEIVASAPEDRLVILEDTAEI  186 (323)
T ss_pred             CCCHHHHHHHHHHHHcCCeEEEECCCCCCHHHHHHHHHHHHhcCCCCceEEEecCCccc
Confidence            35666776666544 4678899999999999543  22222   234566666666555

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

Probab=94.83  E-value=0.031  Score=52.37  Aligned_cols=54  Identities=30%  Similarity=0.437  Sum_probs=42.9

Q ss_pred             CEEEEccCCCCchhhhhcccccc-CCcEEEEcchHHHHHHHHHHHHHcCCceEEc
Q 037567           30 DCLVVMATGSGKSLCYQLPPLVT-GKTALVVSPLISLMQDQVMSLKQRGINAEFL   83 (374)
Q Consensus        30 ~~l~~a~tGsGKT~~~~l~~~~~-~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~   83 (374)
                      ++++.||||||||..+.+|.+.. ...++|.=|..++...+....++.|.++.++
T Consensus        46 h~lvig~tgSGKt~~~viP~ll~~~~s~iV~D~KgEl~~~t~~~r~~~G~~V~vl  100 (469)
T PF02534_consen   46 HVLVIGPTGSGKTTSFVIPNLLNYPGSMIVTDPKGELYEKTAGYRKKRGYKVYVL  100 (469)
T ss_pred             EEEEEeCCCCCccceeeHhHHHhccCCEEEEECCCcHHHHHHHHHHHCCCEEEEe
Confidence            58999999999998887775543 4578888888899988888888877665544

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

>PRK13897 type IV secretion system component VirD4; Provisional

Probab=94.82  E-value=0.043  Score=52.35  Aligned_cols=56  Identities=18%  Similarity=0.229  Sum_probs=46.2

Q ss_pred             CCEEEEccCCCCchhhhhcccccc-CCcEEEEcchHHHHHHHHHHHHHcCCceEEcC
Q 037567           29 RDCLVVMATGSGKSLCYQLPPLVT-GKTALVVSPLISLMQDQVMSLKQRGINAEFLG   84 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~~l~~~~~-~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~   84 (374)
                      .++++.||||||||..+.+|.+.. ...++|+=|.-++...+....++.|-.+.++.
T Consensus       159 ~hvLviapTgSGKg~g~VIPnLL~~~~S~VV~DpKGEl~~~Ta~~R~~~G~~V~vfd  215 (606)
T PRK13897        159 QHALLFAPTGSGKGVGFVIPNLLFWEDSVVVHDIKLENYELTSGWREKQGQKVFVWE  215 (606)
T ss_pred             ceEEEEcCCCCCcceEEehhhHHhCCCCEEEEeCcHHHHHHHHHHHHHCCCeEEEEe
Confidence            468999999999999998886654 56788888999999998888888887776554

>PRK09112 DNA polymerase III subunit delta'; Validated

Probab=94.81  E-value=0.18  Score=44.90  Aligned_cols=16  Identities=13%  Similarity=0.187  Sum_probs=13.5

Q ss_pred             cCccEEEEeccchhhc
Q 037567          125 AGVCLFAVDEAHCISE  140 (374)
Q Consensus       125 ~~~~~vviDE~h~~~~  140 (374)
                      .++.++||||+|.+..
T Consensus       140 g~~rVviIDeAd~l~~  155 (351)
T PRK09112        140 GNWRIVIIDPADDMNR  155 (351)
T ss_pred             CCceEEEEEchhhcCH
Confidence            4578999999999865

>KOG0740 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=94.79  E-value=0.059  Score=48.50  Aligned_cols=41  Identities=27%  Similarity=0.315  Sum_probs=29.6

Q ss_pred             CCEEEEccCCCCchhhhhccccccCCcEEEEcchHHHHHHHH
Q 037567           29 RDCLVVMATGSGKSLCYQLPPLVTGKTALVVSPLISLMQDQV   70 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~~l~~~~~~~~~lil~P~~~l~~q~~   70 (374)
                      +..++.+|+|+|||...-..+.+......-+.|+ .|+.-|.
T Consensus       187 rglLLfGPpgtGKtmL~~aiAsE~~atff~iSas-sLtsK~~  227 (428)
T KOG0740|consen  187 RGLLLFGPPGTGKTMLAKAIATESGATFFNISAS-SLTSKYV  227 (428)
T ss_pred             chhheecCCCCchHHHHHHHHhhhcceEeeccHH-Hhhhhcc
Confidence            4668999999999987655555666667777777 5665443

>COG0470 HolB ATPase involved in DNA replication [DNA replication, recombination, and repair]

Probab=94.79  E-value=0.051  Score=48.09  Aligned_cols=40  Identities=20%  Similarity=0.051  Sum_probs=24.3

Q ss_pred             cCccEEEEeccchhhcccCcchHHHHHHHHHHHhcCCCCeeEEEee
Q 037567          125 AGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTAT  170 (374)
Q Consensus       125 ~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~SaT  170 (374)
                      .+..++++|||+.+....      ...+.+..+..+....+.+++.
T Consensus       108 ~~~kviiidead~mt~~A------~nallk~lEep~~~~~~il~~n  147 (325)
T COG0470         108 GGYKVVIIDEADKLTEDA------ANALLKTLEEPPKNTRFILITN  147 (325)
T ss_pred             CCceEEEeCcHHHHhHHH------HHHHHHHhccCCCCeEEEEEcC
Confidence            457899999999986511      1444445554444445555544

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

Probab=94.74  E-value=0.091  Score=51.91  Aligned_cols=61  Identities=18%  Similarity=0.305  Sum_probs=52.6

Q ss_pred             CCCcEEEEecchhHHHHHHHHHHHcC-----Cceee-eecCCChHHHHHHHHhhhcCCeeEEEEecc
Q 037567          227 GAGSIIVYCMTIKDVEEISKALKQLG-----VKAGT-YHGQMGSKAREEAHRLFIRDEIRVMVATMA  287 (374)
Q Consensus       227 ~~~~~lVf~~~~~~~~~l~~~l~~~~-----~~~~~-~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~  287 (374)
                      .++++++.+||..-+.+.++.|+...     ..+.. +|+.++.++++..++++.+|+.+|+|+|+.
T Consensus       124 kgkr~yii~PT~~Lv~Q~~~kl~~~~e~~~~~~~~~~yh~~l~~~ekee~le~i~~gdfdIlitTs~  190 (1187)
T COG1110         124 KGKRVYIIVPTTTLVRQVYERLKKFAEDAGSLDVLVVYHSALPTKEKEEALERIESGDFDILITTSQ  190 (1187)
T ss_pred             cCCeEEEEecCHHHHHHHHHHHHHHHhhcCCcceeeeeccccchHHHHHHHHHHhcCCccEEEEeHH
Confidence            67899999999999999999988742     33322 899999999999999999999999999974

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.74  E-value=0.088  Score=49.36  Aligned_cols=16  Identities=25%  Similarity=0.285  Sum_probs=13.5

Q ss_pred             EEEEccCCCCchhhhh
Q 037567           31 CLVVMATGSGKSLCYQ   46 (374)
Q Consensus        31 ~l~~a~tGsGKT~~~~   46 (374)
                      .++.||+|+|||.++.
T Consensus        39 ~Lf~GppGtGKTTlA~   54 (504)
T PRK14963         39 YLFSGPRGVGKTTTAR   54 (504)
T ss_pred             EEEECCCCCCHHHHHH
Confidence            4999999999997653

>PRK10865 protein disaggregation chaperone; Provisional

Probab=94.74  E-value=0.17  Score=50.84  Aligned_cols=18  Identities=22%  Similarity=0.361  Sum_probs=15.2

Q ss_pred             CCCEEEEccCCCCchhhh
Q 037567           28 KRDCLVVMATGSGKSLCY   45 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~   45 (374)
                      ..+.++.||+|+|||...
T Consensus       199 ~~n~lL~G~pGvGKT~l~  216 (857)
T PRK10865        199 KNNPVLIGEPGVGKTAIV  216 (857)
T ss_pred             cCceEEECCCCCCHHHHH
Confidence            358899999999999654

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.70  E-value=0.087  Score=50.20  Aligned_cols=17  Identities=24%  Similarity=0.257  Sum_probs=14.1

Q ss_pred             CEEEEccCCCCchhhhh
Q 037567           30 DCLVVMATGSGKSLCYQ   46 (374)
Q Consensus        30 ~~l~~a~tGsGKT~~~~   46 (374)
                      .+|+.+|.|+|||.++.
T Consensus        40 a~Lf~GPpG~GKTtiAr   56 (624)
T PRK14959         40 AYLFSGTRGVGKTTIAR   56 (624)
T ss_pred             eEEEECCCCCCHHHHHH
Confidence            46889999999997654

>TIGR03689 pup_AAA proteasome ATPase

Probab=94.67  E-value=0.057  Score=50.35  Aligned_cols=18  Identities=28%  Similarity=0.418  Sum_probs=15.2

Q ss_pred             CCCEEEEccCCCCchhhh
Q 037567           28 KRDCLVVMATGSGKSLCY   45 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~   45 (374)
                      .+.+++.||+|+|||..+
T Consensus       216 p~GILLyGPPGTGKT~LA  233 (512)
T TIGR03689       216 PKGVLLYGPPGCGKTLIA  233 (512)
T ss_pred             CcceEEECCCCCcHHHHH
Confidence            367899999999999754

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.

>PRK09087 hypothetical protein; Validated

Probab=94.66  E-value=0.11  Score=43.25  Aligned_cols=16  Identities=25%  Similarity=0.254  Sum_probs=13.6

Q ss_pred             CEEEEccCCCCchhhh
Q 037567           30 DCLVVMATGSGKSLCY   45 (374)
Q Consensus        30 ~~l~~a~tGsGKT~~~   45 (374)
                      .++++||+|+|||...
T Consensus        46 ~l~l~G~~GsGKThLl   61 (226)
T PRK09087         46 VVVLAGPVGSGKTHLA   61 (226)
T ss_pred             eEEEECCCCCCHHHHH
Confidence            4899999999999643

>PRK08699 DNA polymerase III subunit delta'; Validated

Probab=94.66  E-value=0.33  Score=42.85  Aligned_cols=32  Identities=22%  Similarity=0.363  Sum_probs=25.7

Q ss_pred             CchhHHHHHHHHHcC-----CCEEEEccCCCCchhhh
Q 037567           14 FRPYQKDVIQRIIEK-----RDCLVVMATGSGKSLCY   45 (374)
Q Consensus        14 ~~~~Q~~~~~~~~~~-----~~~l~~a~tGsGKT~~~   45 (374)
                      ++|+|...+..+.+.     +..++.||.|.|||..+
T Consensus         2 ~yPW~~~~w~~l~~~~~r~~hA~Lf~G~~G~GK~~la   38 (325)
T PRK08699          2 IYPWHQEQWRQIAEHWERRPNAWLFAGKKGIGKTAFA   38 (325)
T ss_pred             CCCccHHHHHHHHHhcCCcceEEEeECCCCCCHHHHH
Confidence            479999999988742     34689999999999554

>TIGR01547 phage_term_2 phage terminase, large subunit, PBSX family

Probab=94.56  E-value=0.098  Score=47.81  Aligned_cols=129  Identities=17%  Similarity=0.211  Sum_probs=63.5

Q ss_pred             EEEEccCCCCchhhhhccc----cc--cCCcEEEEcchHH-HHHHHHHHHH----HcCCceEEcCCCCCchhhhhhhhcC
Q 037567           31 CLVVMATGSGKSLCYQLPP----LV--TGKTALVVSPLIS-LMQDQVMSLK----QRGINAEFLGSAQTDSSVQTKAETG   99 (374)
Q Consensus        31 ~l~~a~tGsGKT~~~~l~~----~~--~~~~~lil~P~~~-l~~q~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~   99 (374)
                      .++.|+.|||||....+.+    +.  .+.+++++-|+.. +...+..++.    .+|+....-......  ... ....
T Consensus         4 ~i~~GgrgSGKS~~~~~~~~~~~~~~~~~~~~~~~r~~~~sl~~sv~~~l~~~i~~~g~~~~~~~~~~~~--~i~-~~~~   80 (396)
T TIGR01547         4 IIAKGGRRSGKTFAIALKLVEKLAINKKQQNILAARKVQNSIRDSVFKDIENLLSIEGINYEFKKSKSSM--EIK-ILNT   80 (396)
T ss_pred             EEEeCCCCcccHHHHHHHHHHHHHhcCCCcEEEEEehhhhHHHHHHHHHHHHHHHHcCChhheeecCCcc--EEE-ecCC
Confidence            5789999999996654332    23  5677888888876 3444444443    445432111111000  000 0111


Q ss_pred             CeeEEEEcC-cccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHHhcCCCCeeEEEeecCccc
Q 037567          100 YFQLLFMTP-EKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEKV  175 (374)
Q Consensus       100 ~~~i~i~T~-~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~SaT~~~~~  175 (374)
                      +..|++..- +..       .+......+.++++||+..+...  .+.   ..+.+++. ......+++|.+|....
T Consensus        81 g~~i~f~g~~d~~-------~~ik~~~~~~~~~idEa~~~~~~--~~~---~l~~rlr~-~~~~~~i~~t~NP~~~~  144 (396)
T TIGR01547        81 GKKFIFKGLNDKP-------NKLKSGAGIAIIWFEEASQLTFE--DIK---ELIPRLRE-TGGKKFIIFSSNPESPL  144 (396)
T ss_pred             CeEEEeecccCCh-------hHhhCcceeeeehhhhhhhcCHH--HHH---HHHHHhhc-cCCccEEEEEcCcCCCc
Confidence            224444333 211       11112233689999999987531  111   11222221 11222588998987643

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.

>PRK05563 DNA polymerase III subunits gamma and tau; Validated

Probab=94.55  E-value=0.067  Score=50.95  Aligned_cols=17  Identities=24%  Similarity=0.315  Sum_probs=13.8

Q ss_pred             CEEEEccCCCCchhhhh
Q 037567           30 DCLVVMATGSGKSLCYQ   46 (374)
Q Consensus        30 ~~l~~a~tGsGKT~~~~   46 (374)
                      -++++||.|+|||.++-
T Consensus        40 ayLf~Gp~GtGKTt~Ak   56 (559)
T PRK05563         40 AYLFSGPRGTGKTSAAK   56 (559)
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            46889999999996643

>KOG0736 consensus Peroxisome assembly factor 2 containing the AAA+-type ATPase domain [Posttranslational modification, protein turnover, chaperones]

Probab=94.54  E-value=0.56  Score=45.31  Aligned_cols=56  Identities=18%  Similarity=0.113  Sum_probs=31.4

Q ss_pred             HHHhcCccEEEEeccchhhc-c------cCcchHHHHHHHHHHHhcC---CCCeeEEEeecCcccH
Q 037567          121 KLLKAGVCLFAVDEAHCISE-W------GHDFRLEYKQLDKLRTFLL---GVPFVALTATATEKVR  176 (374)
Q Consensus       121 ~~~~~~~~~vviDE~h~~~~-~------~~~~~~~~~~~~~~~~~~~---~~~~i~~SaT~~~~~~  176 (374)
                      +.......+|++||.+.+.. .      |--+....+++..-...++   ...+..+-||-.++..
T Consensus       759 rAR~A~PCVIFFDELDSlAP~RG~sGDSGGVMDRVVSQLLAELDgls~~~s~~VFViGATNRPDLL  824 (953)
T KOG0736|consen  759 RARSAAPCVIFFDELDSLAPNRGRSGDSGGVMDRVVSQLLAELDGLSDSSSQDVFVIGATNRPDLL  824 (953)
T ss_pred             HhhccCCeEEEeccccccCccCCCCCCccccHHHHHHHHHHHhhcccCCCCCceEEEecCCCcccc
Confidence            33345567899999999853 2      2222222233332233333   3567888888777654

>CHL00095 clpC Clp protease ATP binding subunit

Probab=94.49  E-value=0.22  Score=50.08  Aligned_cols=18  Identities=22%  Similarity=0.359  Sum_probs=15.4

Q ss_pred             CCCEEEEccCCCCchhhh
Q 037567           28 KRDCLVVMATGSGKSLCY   45 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~   45 (374)
                      .++.++.||+|+|||...
T Consensus       200 ~~n~lL~G~pGvGKTal~  217 (821)
T CHL00095        200 KNNPILIGEPGVGKTAIA  217 (821)
T ss_pred             cCCeEEECCCCCCHHHHH
Confidence            458899999999999764

>PF00265 TK: Thymidine kinase; InterPro: IPR001267 Thymidine kinase (TK) (2

Probab=94.49  E-value=0.21  Score=39.64  Aligned_cols=33  Identities=30%  Similarity=0.256  Sum_probs=22.1

Q ss_pred             EEEEccCCCCchhhhhcccc---ccCCcEEEEcchH
Q 037567           31 CLVVMATGSGKSLCYQLPPL---VTGKTALVVSPLI   63 (374)
Q Consensus        31 ~l~~a~tGsGKT~~~~l~~~---~~~~~~lil~P~~   63 (374)
                      .++.||++||||...+-.+.   ..+.+++++-|..
T Consensus         4 ~~i~GpM~sGKS~eLi~~~~~~~~~~~~v~~~kp~~   39 (176)
T PF00265_consen    4 EFITGPMFSGKSTELIRRIHRYEIAGKKVLVFKPAI   39 (176)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHHHHTT-EEEEEEEST
T ss_pred             EEEECCcCChhHHHHHHHHHHHHhCCCeEEEEEecc
Confidence            47889999999975332221   2477888888864

7.1.21 from EC) is an ubiquitous enzyme that catalyzes the ATP-dependent phosphorylation of thymidine. Two different families of Thymidine kinase have been identified [, ] and are represented in this entry; one groups together Thymidine kinase from herpesviruses, as well as cytosolic thymidylate kinases and the second family groups Thymidine kinase from various sources that include, vertebrates, bacteria, the Bacteriophage T4, poxviruses, African swine fever virus (ASFV) and Fish lymphocystis disease virus (FLDV). The major capsid protein of insect iridescent viruses also belongs to this family.; GO: 0004797 thymidine kinase activity, 0005524 ATP binding; PDB: 1XX6_B 2J9R_A 2J87_B 3E2I_A 2JA1_A 2UZ3_B 2B8T_B 2WVJ_A 1W4R_F 1XBT_F ....

>PRK10867 signal recognition particle protein; Provisional

Probab=94.46  E-value=0.18  Score=46.12  Aligned_cols=52  Identities=17%  Similarity=0.098  Sum_probs=30.9

Q ss_pred             EEEEccCCCCchhhhhcccc---cc-CCcEEEE-cc-hH-HHHHHHHHHHHHcCCceEE
Q 037567           31 CLVVMATGSGKSLCYQLPPL---VT-GKTALVV-SP-LI-SLMQDQVMSLKQRGINAEF   82 (374)
Q Consensus        31 ~l~~a~tGsGKT~~~~l~~~---~~-~~~~lil-~P-~~-~l~~q~~~~~~~~~~~~~~   82 (374)
                      +++++++|+|||.+..-.+.   .. +.+++++ +. .+ +..+|+.......++.+..
T Consensus       103 I~~vG~~GsGKTTtaakLA~~l~~~~G~kV~lV~~D~~R~aa~eQL~~~a~~~gv~v~~  161 (433)
T PRK10867        103 IMMVGLQGAGKTTTAGKLAKYLKKKKKKKVLLVAADVYRPAAIEQLKTLGEQIGVPVFP  161 (433)
T ss_pred             EEEECCCCCcHHHHHHHHHHHHHHhcCCcEEEEEccccchHHHHHHHHHHhhcCCeEEe
Confidence            57899999999976543222   23 4555544 33 23 3345776666666665443

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.45  E-value=0.14  Score=48.95  Aligned_cols=17  Identities=29%  Similarity=0.302  Sum_probs=13.8

Q ss_pred             CEEEEccCCCCchhhhh
Q 037567           30 DCLVVMATGSGKSLCYQ   46 (374)
Q Consensus        30 ~~l~~a~tGsGKT~~~~   46 (374)
                      .+++.||.|+|||.++.
T Consensus        40 ayLf~Gp~G~GKtt~A~   56 (576)
T PRK14965         40 AFLFTGARGVGKTSTAR   56 (576)
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            35899999999996653

>PRK13851 type IV secretion system protein VirB11; Provisional

Probab=94.45  E-value=0.057  Score=47.80  Aligned_cols=40  Identities=18%  Similarity=0.301  Sum_probs=27.2

Q ss_pred             HcCCCEEEEccCCCCchhhh--hccccccCCcEEEEcchHHH
Q 037567           26 IEKRDCLVVMATGSGKSLCY--QLPPLVTGKTALVVSPLISL   65 (374)
Q Consensus        26 ~~~~~~l~~a~tGsGKT~~~--~l~~~~~~~~~lil~P~~~l   65 (374)
                      ..++++++.||||||||...  ++..+....+++.+-++.++
T Consensus       160 ~~~~nilI~G~tGSGKTTll~aLl~~i~~~~rivtiEd~~El  201 (344)
T PRK13851        160 VGRLTMLLCGPTGSGKTTMSKTLISAIPPQERLITIEDTLEL  201 (344)
T ss_pred             HcCCeEEEECCCCccHHHHHHHHHcccCCCCCEEEECCCccc
Confidence            35789999999999999542  22333345567776666655

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=94.42  E-value=0.16  Score=50.39  Aligned_cols=18  Identities=28%  Similarity=0.436  Sum_probs=15.3

Q ss_pred             CCCEEEEccCCCCchhhh
Q 037567           28 KRDCLVVMATGSGKSLCY   45 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~   45 (374)
                      ++.+++.||+|+|||...
T Consensus       212 ~~giLL~GppGtGKT~la  229 (733)
T TIGR01243       212 PKGVLLYGPPGTGKTLLA  229 (733)
T ss_pred             CceEEEECCCCCChHHHH
Confidence            467899999999999754

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.

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=94.41  E-value=0.1  Score=45.77  Aligned_cols=17  Identities=24%  Similarity=0.217  Sum_probs=14.2

Q ss_pred             CCEEEEccCCCCchhhh
Q 037567           29 RDCLVVMATGSGKSLCY   45 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~   45 (374)
                      .++++.||+|+|||..+
T Consensus        31 ~~~ll~Gp~G~GKT~la   47 (305)
T TIGR00635        31 DHLLLYGPPGLGKTTLA   47 (305)
T ss_pred             CeEEEECCCCCCHHHHH
Confidence            35899999999999654

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.

>KOG0298 consensus DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]

Probab=94.38  E-value=0.062  Score=54.06  Aligned_cols=101  Identities=13%  Similarity=0.031  Sum_probs=76.0

Q ss_pred             cCCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEE-EEeccccccccccCccEEEEEC
Q 037567          226 AGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVM-VATMAFGMGIDKPDVRHVIHYG  304 (374)
Q Consensus       226 ~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~il-v~t~~~~~G~d~~~~~~vi~~~  304 (374)
                      ....++|||+.-......+...+...++....-.+   .++....+..|..  ++++ +-+...+.|+|+-+..+|+...
T Consensus      1219 ~~qekvIvfsqws~~ldV~e~~~~~N~I~~~~~~~---t~d~~dc~~~fk~--I~clll~~~~~~~GLNL~eA~Hvfl~e 1293 (1394)
T KOG0298|consen 1219 NEQEKVIVFSQWSVVLDVKELRYLMNLIKKQLDGE---TEDFDDCIICFKS--IDCLLLFVSKGSKGLNLIEATHVFLVE 1293 (1394)
T ss_pred             CcCceEEEEEehHHHHHHHHHHHHhhhhHhhhccC---Ccchhhhhhhccc--ceEEEEEeccCcccccHHhhhhhheec
Confidence            45578999988777777777777766655333222   3444555666655  5654 5777889999999999999999


Q ss_pred             CCCChhHHHHhhccCCCCCCceEEEEE
Q 037567          305 CPKTLESYYQESGRCGRDGIASVCWLY  331 (374)
Q Consensus       305 ~p~s~~~~~Q~~GR~~R~~~~g~~~~~  331 (374)
                      +-.++..-.|.+||+.|.||....++.
T Consensus      1294 PiLN~~~E~QAigRvhRiGQ~~pT~V~ 1320 (1394)
T KOG0298|consen 1294 PILNPGDEAQAIGRVHRIGQKRPTFVH 1320 (1394)
T ss_pred             cccCchHHHhhhhhhhhcccccchhhh
Confidence            999999999999999999987655443

>PRK07471 DNA polymerase III subunit delta'; Validated

Probab=94.38  E-value=0.11  Score=46.67  Aligned_cols=29  Identities=14%  Similarity=0.127  Sum_probs=19.8

Q ss_pred             hHHHHHHHHHc----C---CCEEEEccCCCCchhhh
Q 037567           17 YQKDVIQRIIE----K---RDCLVVMATGSGKSLCY   45 (374)
Q Consensus        17 ~Q~~~~~~~~~----~---~~~l~~a~tGsGKT~~~   45 (374)
                      .|.++...+.+    +   +-.++.||.|+||+..+
T Consensus        23 Gq~~~~~~L~~~~~~~rl~HA~Lf~Gp~G~GK~~lA   58 (365)
T PRK07471         23 GHAAAEAALLDAYRSGRLHHAWLIGGPQGIGKATLA   58 (365)
T ss_pred             ChHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHH
Confidence            46666555432    2   24789999999999553

>PF14617 CMS1: U3-containing 90S pre-ribosomal complex subunit

Probab=94.37  E-value=0.026  Score=47.24  Aligned_cols=83  Identities=13%  Similarity=0.037  Sum_probs=58.6

Q ss_pred             CCcEEEEcchHHHHHHHHHHHHHcC---CceEEcCCCCCc-hhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCcc
Q 037567           53 GKTALVVSPLISLMQDQVMSLKQRG---INAEFLGSAQTD-SSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVC  128 (374)
Q Consensus        53 ~~~~lil~P~~~l~~q~~~~~~~~~---~~~~~~~~~~~~-~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~  128 (374)
                      .+.+|||+.+--=+-++.+.++.+.   ..+.-+++.... .+...........|.||||+++..++..  +.+.+.++.
T Consensus       126 sP~~lvvs~SalRa~dl~R~l~~~~~k~~~v~KLFaKH~Kl~eqv~~L~~~~~~i~vGTP~Rl~kLle~--~~L~l~~l~  203 (252)
T PF14617_consen  126 SPHVLVVSSSALRAADLIRALRSFKGKDCKVAKLFAKHIKLEEQVKLLKKTRVHIAVGTPGRLSKLLEN--GALSLSNLK  203 (252)
T ss_pred             CCEEEEEcchHHHHHHHHHHHHhhccCCchHHHHHHhhccHHHHHHHHHhCCceEEEeChHHHHHHHHc--CCCCcccCe
Confidence            5678888888766889999999874   222233333322 2233333445789999999999988765  666778899


Q ss_pred             EEEEeccch
Q 037567          129 LFAVDEAHC  137 (374)
Q Consensus       129 ~vviDE~h~  137 (374)
                      +||+|--|.
T Consensus       204 ~ivlD~s~~  212 (252)
T PF14617_consen  204 RIVLDWSYL  212 (252)
T ss_pred             EEEEcCCcc
Confidence            999998764

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

Probab=94.34  E-value=0.044  Score=50.04  Aligned_cols=32  Identities=31%  Similarity=0.536  Sum_probs=25.6

Q ss_pred             CchhHHHHHHHHHcCCC--EEEEccCCCCchhhh
Q 037567           14 FRPYQKDVIQRIIEKRD--CLVVMATGSGKSLCY   45 (374)
Q Consensus        14 ~~~~Q~~~~~~~~~~~~--~l~~a~tGsGKT~~~   45 (374)
                      +.+.|.+.+..+.+...  +++.||||||||.+.
T Consensus       242 ~~~~~~~~~~~~~~~p~GliLvTGPTGSGKTTTL  275 (500)
T COG2804         242 MSPFQLARLLRLLNRPQGLILVTGPTGSGKTTTL  275 (500)
T ss_pred             CCHHHHHHHHHHHhCCCeEEEEeCCCCCCHHHHH
Confidence            47888888888887654  467999999999663

>KOG1807 consensus Helicases [Replication, recombination and repair]

Probab=94.24  E-value=0.098  Score=49.95  Aligned_cols=62  Identities=18%  Similarity=0.149  Sum_probs=49.7

Q ss_pred             CchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccc---cc------cCCcEEEEcchHHHHHHHHHHHHH
Q 037567           14 FRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPP---LV------TGKTALVVSPLISLMQDQVMSLKQ   75 (374)
Q Consensus        14 ~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~---~~------~~~~~lil~P~~~l~~q~~~~~~~   75 (374)
                      +..-|..|++..+..+-.++.+|+|+|||++.+.++   +.      ..-+++++|-|...++|....+..
T Consensus       379 ldsSq~~A~qs~ltyelsliqgppGTgkt~vtlkav~tLL~n~s~~~~~epIlvvC~Tnhavdq~ligiy~  449 (1025)
T KOG1807|consen  379 LDSSQQFAKQSKLTYELSLIQGPPGTGKTLVTLKAVDTLLLNSSGYTEPEPILVVCLTNHAVDQYLIGIYY  449 (1025)
T ss_pred             ecHHHHHHHHHHhhhhhheeecCCCCCceeehHHHHHHHHhcccccccccceeeeehhhHHHHHHHHHHHh
Confidence            445699999999999989999999999997754432   21      256799999999999998887764

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=94.21  E-value=0.059  Score=47.81  Aligned_cols=18  Identities=22%  Similarity=0.246  Sum_probs=15.1

Q ss_pred             CCEEEEccCCCCchhhhh
Q 037567           29 RDCLVVMATGSGKSLCYQ   46 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~~   46 (374)
                      ..+++.||+|+|||..+.
T Consensus        52 ~~~ll~GppG~GKT~la~   69 (328)
T PRK00080         52 DHVLLYGPPGLGKTTLAN   69 (328)
T ss_pred             CcEEEECCCCccHHHHHH
Confidence            468999999999997654

>PRK13894 conjugal transfer ATPase TrbB; Provisional

Probab=94.19  E-value=0.069  Score=46.87  Aligned_cols=52  Identities=19%  Similarity=0.216  Sum_probs=33.1

Q ss_pred             CchhHHHHHHHH-HcCCCEEEEccCCCCchhhhhccc-----cccCCcEEEEcchHHH
Q 037567           14 FRPYQKDVIQRI-IEKRDCLVVMATGSGKSLCYQLPP-----LVTGKTALVVSPLISL   65 (374)
Q Consensus        14 ~~~~Q~~~~~~~-~~~~~~l~~a~tGsGKT~~~~l~~-----~~~~~~~lil~P~~~l   65 (374)
                      +.+.|.+.+... ..++++++.|+||||||......+     .....+++++-.+.++
T Consensus       133 ~~~~~~~~L~~~v~~~~~ilI~G~tGSGKTTll~aL~~~~~~~~~~~rivtIEd~~El  190 (319)
T PRK13894        133 MTAAQREAIIAAVRAHRNILVIGGTGSGKTTLVNAIINEMVIQDPTERVFIIEDTGEI  190 (319)
T ss_pred             CCHHHHHHHHHHHHcCCeEEEECCCCCCHHHHHHHHHHhhhhcCCCceEEEEcCCCcc
Confidence            556677777654 457789999999999995432111     1234566666666554

>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=94.18  E-value=0.21  Score=39.60  Aligned_cols=30  Identities=30%  Similarity=0.319  Sum_probs=18.6

Q ss_pred             EEEEccCCCCchhhhhccc---cccCCcEEEEc
Q 037567           31 CLVVMATGSGKSLCYQLPP---LVTGKTALVVS   60 (374)
Q Consensus        31 ~l~~a~tGsGKT~~~~l~~---~~~~~~~lil~   60 (374)
                      +++.|++|+|||......+   ...+.+++++.
T Consensus         3 ~~~~G~~G~GKTt~~~~la~~~~~~g~~v~~i~   35 (173)
T cd03115           3 ILLVGLQGVGKTTTAAKLALYLKKKGKKVLLVA   35 (173)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEE
Confidence            5789999999996643222   22355555443

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.

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.14  E-value=0.12  Score=48.97  Aligned_cols=17  Identities=24%  Similarity=0.268  Sum_probs=13.8

Q ss_pred             CEEEEccCCCCchhhhh
Q 037567           30 DCLVVMATGSGKSLCYQ   46 (374)
Q Consensus        30 ~~l~~a~tGsGKT~~~~   46 (374)
                      -.++.||+|+|||.++.
T Consensus        40 a~Lf~Gp~G~GKTt~A~   56 (527)
T PRK14969         40 AYLFTGTRGVGKTTLAR   56 (527)
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            35899999999996643

>TIGR02785 addA_Gpos recombination helicase AddA, Firmicutes type

Probab=94.11  E-value=0.075  Score=55.68  Aligned_cols=61  Identities=18%  Similarity=0.161  Sum_probs=46.8

Q ss_pred             CCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccc---cc---cCCcEEEEcchHHHHHHHHHHHHH
Q 037567           13 VFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPP---LV---TGKTALVVSPLISLMQDQVMSLKQ   75 (374)
Q Consensus        13 ~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~---~~---~~~~~lil~P~~~l~~q~~~~~~~   75 (374)
                      ++++-|.+++..  .+++++|.|..|||||.+..--+   +.   ...++++++=|++.+.++...+..
T Consensus         1 ~~t~~Q~~ai~~--~~~~~lv~A~AGsGKT~~lv~r~~~~~~~~~~~~~il~~tFt~~aa~e~~~ri~~   67 (1232)
T TIGR02785         1 QWTDEQWQAIYT--RGQNILVSASAGSGKTAVLVERIIKKILRGVDIDRLLVVTFTNAAAREMKERIEE   67 (1232)
T ss_pred             CCCHHHHHHHhC--CCCCEEEEecCCCcHHHHHHHHHHHHHhcCCCHhhEEEEeccHHHHHHHHHHHHH
Confidence            368889999973  68899999999999996643221   21   234699999999999888877765

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.

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=94.11  E-value=0.057  Score=46.13  Aligned_cols=40  Identities=8%  Similarity=0.098  Sum_probs=26.3

Q ss_pred             HHHHHHHcCCCEEEEccCCCCchhhhhccccccCCcEEEE
Q 037567           20 DVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVTGKTALVV   59 (374)
Q Consensus        20 ~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~~~~~~lil   59 (374)
                      ++...+..+.++++.||+|+|||..+...+...+.+++.+
T Consensus        13 ~~l~~l~~g~~vLL~G~~GtGKT~lA~~la~~lg~~~~~i   52 (262)
T TIGR02640        13 RALRYLKSGYPVHLRGPAGTGKTTLAMHVARKRDRPVMLI   52 (262)
T ss_pred             HHHHHHhcCCeEEEEcCCCCCHHHHHHHHHHHhCCCEEEE
Confidence            3444455688999999999999966543332335555554

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).

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

Probab=94.07  E-value=0.12  Score=48.29  Aligned_cols=52  Identities=25%  Similarity=0.214  Sum_probs=36.3

Q ss_pred             CCCEEEEccCCCCchhhhh------ccccc---cCCcEEEEcchHHHHHHHHHHHHHcCCc
Q 037567           28 KRDCLVVMATGSGKSLCYQ------LPPLV---TGKTALVVSPLISLMQDQVMSLKQRGIN   79 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~------l~~~~---~~~~~lil~P~~~l~~q~~~~~~~~~~~   79 (374)
                      ++-.+|.|..|||||.+++      +--..   ..+.+||+.|.+....-..+-+=.+|..
T Consensus       226 ~~ilVVQGaAGSGKTtiALHRvAyLlY~~R~~l~~k~vlvl~PN~vFleYis~VLPeLGe~  286 (747)
T COG3973         226 NKILVVQGAAGSGKTTIALHRVAYLLYGYRGPLQAKPVLVLGPNRVFLEYISRVLPELGEE  286 (747)
T ss_pred             CCeEEEecCCCCCchhHHHHHHHHHHhccccccccCceEEEcCcHHHHHHHHHhchhhccC
Confidence            5667899999999996643      22111   3556999999998887666665555543

>COG1444 Predicted P-loop ATPase fused to an acetyltransferase [General function prediction only]

Probab=94.01  E-value=0.41  Score=46.49  Aligned_cols=133  Identities=20%  Similarity=0.237  Sum_probs=73.5

Q ss_pred             chhHHH---HHHHHHcCC--CEEEEccCCCCchhhhh---cccccc--CCcEEEEcchHHHHHHHHHHH----HHcCCce
Q 037567           15 RPYQKD---VIQRIIEKR--DCLVVMATGSGKSLCYQ---LPPLVT--GKTALVVSPLISLMQDQVMSL----KQRGINA   80 (374)
Q Consensus        15 ~~~Q~~---~~~~~~~~~--~~l~~a~tGsGKT~~~~---l~~~~~--~~~~lil~P~~~l~~q~~~~~----~~~~~~~   80 (374)
                      +.-|.+   .+..+++.+  -+++.|+=|=|||.+.=   ..+.+.  ..+++|.+|+.+-++..++-.    ...|.+.
T Consensus       213 T~dQ~~~l~~~~~l~~~~~~~~vlTAdRGRGKSA~lGi~~~~~~~~~~~~~iiVTAP~~~nv~~Lf~fa~~~l~~lg~~~  292 (758)
T COG1444         213 TEDQAEALEILERLLDAPKRALVLTADRGRGKSAALGIALAAAARLAGSVRIIVTAPTPANVQTLFEFAGKGLEFLGYKR  292 (758)
T ss_pred             ChhHHHHHHHHHHHHcCCCceEEEEcCCCCcHhHHHhHHHHHHHHhcCCceEEEeCCCHHHHHHHHHHHHHhHHHhCCcc
Confidence            344555   444555543  46789999999995432   122222  358999999988777655543    3344443


Q ss_pred             EEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHHhcC
Q 037567           81 EFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLL  160 (374)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~~  160 (374)
                      .+.......   ..........|=+.+|+...            ..-+++|||||-.+.-         ..+.++..   
T Consensus       293 ~v~~d~~g~---~~~~~~~~~~i~y~~P~~a~------------~~~DllvVDEAAaIpl---------plL~~l~~---  345 (758)
T COG1444         293 KVAPDALGE---IREVSGDGFRIEYVPPDDAQ------------EEADLLVVDEAAAIPL---------PLLHKLLR---  345 (758)
T ss_pred             ccccccccc---eeeecCCceeEEeeCcchhc------------ccCCEEEEehhhcCCh---------HHHHHHHh---
Confidence            222211111   01111122345566665432            1147999999986542         23333333   


Q ss_pred             CCCeeEEEeecCcc
Q 037567          161 GVPFVALTATATEK  174 (374)
Q Consensus       161 ~~~~i~~SaT~~~~  174 (374)
                      ..+.++||.|....
T Consensus       346 ~~~rv~~sTTIhGY  359 (758)
T COG1444         346 RFPRVLFSTTIHGY  359 (758)
T ss_pred             hcCceEEEeeeccc
Confidence            55789999996653

>PRK06995 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=94.01  E-value=0.29  Score=45.41  Aligned_cols=19  Identities=21%  Similarity=0.155  Sum_probs=14.9

Q ss_pred             CCCEEEEccCCCCchhhhh
Q 037567           28 KRDCLVVMATGSGKSLCYQ   46 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~   46 (374)
                      ++-+.+.||+|+|||.+..
T Consensus       256 g~Vi~LvGpnGvGKTTTia  274 (484)
T PRK06995        256 GGVFALMGPTGVGKTTTTA  274 (484)
T ss_pred             CcEEEEECCCCccHHHHHH
Confidence            3456789999999997654

>KOG2543 consensus Origin recognition complex, subunit 5 [Replication, recombination and repair]

Probab=94.00  E-value=0.23  Score=43.79  Aligned_cols=140  Identities=13%  Similarity=0.088  Sum_probs=71.5

Q ss_pred             CCchhHHHHHHHHHcCCCE------EEEccCCCCchhhhhccccccCCcEEEEcchH-----HHHHHHHHHHHHcCCceE
Q 037567           13 VFRPYQKDVIQRIIEKRDC------LVVMATGSGKSLCYQLPPLVTGKTALVVSPLI-----SLMQDQVMSLKQRGINAE   81 (374)
Q Consensus        13 ~~~~~Q~~~~~~~~~~~~~------l~~a~tGsGKT~~~~l~~~~~~~~~lil~P~~-----~l~~q~~~~~~~~~~~~~   81 (374)
                      ..+..|...+..++-.++.      ++.|.+|||||..-.-.....+...+++.+..     -+.++......       
T Consensus         9 ~~Re~qi~~L~~Llg~~~~~~PS~~~iyG~sgTGKT~~~r~~l~~~n~~~vw~n~~ecft~~~lle~IL~~~~-------   81 (438)
T KOG2543|consen    9 PCRESQIRRLKSLLGNNSCTIPSIVHIYGHSGTGKTYLVRQLLRKLNLENVWLNCVECFTYAILLEKILNKSQ-------   81 (438)
T ss_pred             cchHHHHHHHHHHhCCCCcccceeEEEeccCCCchhHHHHHHHhhcCCcceeeehHHhccHHHHHHHHHHHhc-------
Confidence            4678899999988876543      88999999999763322222345566666642     22222222221       


Q ss_pred             EcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHH--HH-HhcCccEEEEeccchhhcccCcchHHHHHHHHHHHh
Q 037567           82 FLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWS--KL-LKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTF  158 (374)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~--~~-~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~  158 (374)
                       ....  +..           -+=++.+.+.++++....  .. ....--++|+|.++.+-+.+...-..+-.+.++...
T Consensus        82 -~~d~--dg~-----------~~~~~~en~~d~i~~l~q~~~~t~~d~~~~liLDnad~lrD~~a~ll~~l~~L~el~~~  147 (438)
T KOG2543|consen   82 -LADK--DGD-----------KVEGDAENFSDFIYLLVQWPAATNRDQKVFLILDNADALRDMDAILLQCLFRLYELLNE  147 (438)
T ss_pred             -cCCC--chh-----------hhhhHHHHHHHHHHHHHhhHHhhccCceEEEEEcCHHhhhccchHHHHHHHHHHHHhCC
Confidence             0000  000           000111122222111111  11 111234799999999987665433333334333332


Q ss_pred             cCCCCeeEEEeecCccc
Q 037567          159 LLGVPFVALTATATEKV  175 (374)
Q Consensus       159 ~~~~~~i~~SaT~~~~~  175 (374)
                        +.-.+.+|+++.+..
T Consensus       148 --~~i~iils~~~~e~~  162 (438)
T KOG2543|consen  148 --PTIVIILSAPSCEKQ  162 (438)
T ss_pred             --CceEEEEeccccHHH
Confidence              455788888887754

>PRK08058 DNA polymerase III subunit delta'; Validated

Probab=93.99  E-value=0.5  Score=41.89  Aligned_cols=40  Identities=13%  Similarity=0.077  Sum_probs=23.9

Q ss_pred             cCccEEEEeccchhhcccCcchHHHHHHHHHHHhcCCCCeeEEEee
Q 037567          125 AGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTAT  170 (374)
Q Consensus       125 ~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~SaT  170 (374)
                      ...+++||||+|.+.....      ..+.+..+..++.-++.++++
T Consensus       109 ~~~kvviI~~a~~~~~~a~------NaLLK~LEEPp~~~~~Il~t~  148 (329)
T PRK08058        109 SNKKVYIIEHADKMTASAA------NSLLKFLEEPSGGTTAILLTE  148 (329)
T ss_pred             cCceEEEeehHhhhCHHHH------HHHHHHhcCCCCCceEEEEeC
Confidence            4568999999999865221      344445554444444445444

>TIGR02782 TrbB_P P-type conjugative transfer ATPase TrbB

Probab=93.93  E-value=0.12  Score=45.10  Aligned_cols=52  Identities=25%  Similarity=0.429  Sum_probs=32.5

Q ss_pred             CchhHHHHHHHHH-cCCCEEEEccCCCCchhhhh--ccccc---cCCcEEEEcchHHH
Q 037567           14 FRPYQKDVIQRII-EKRDCLVVMATGSGKSLCYQ--LPPLV---TGKTALVVSPLISL   65 (374)
Q Consensus        14 ~~~~Q~~~~~~~~-~~~~~l~~a~tGsGKT~~~~--l~~~~---~~~~~lil~P~~~l   65 (374)
                      +.+-|.+.+..+. .+++++++|+||||||...-  +..+.   ...+++.+-...++
T Consensus       117 ~~~~~~~~L~~~v~~~~~ilI~G~tGSGKTTll~al~~~i~~~~~~~ri~tiEd~~El  174 (299)
T TIGR02782       117 MTAAQRDVLREAVLARKNILVVGGTGSGKTTLANALLAEIAKNDPTDRVVIIEDTREL  174 (299)
T ss_pred             CCHHHHHHHHHHHHcCCeEEEECCCCCCHHHHHHHHHHHhhccCCCceEEEECCchhh
Confidence            4444555555444 46789999999999996532  22221   24667777776665

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.

>PRK12726 flagellar biosynthesis regulator FlhF; Provisional

Probab=93.92  E-value=0.27  Score=43.86  Aligned_cols=52  Identities=13%  Similarity=0.089  Sum_probs=30.1

Q ss_pred             CCCEEEEccCCCCchhhhhccc---cccCCcEEEE-cchH--HHHHHHHHHHHHcCCc
Q 037567           28 KRDCLVVMATGSGKSLCYQLPP---LVTGKTALVV-SPLI--SLMQDQVMSLKQRGIN   79 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~l~~---~~~~~~~lil-~P~~--~l~~q~~~~~~~~~~~   79 (374)
                      ++.+++.||+|+|||.+....+   ..++.++.++ +.+-  .-+.||.......+..
T Consensus       206 ~~ii~lvGptGvGKTTt~akLA~~l~~~g~~V~lItaDtyR~gAveQLk~yae~lgvp  263 (407)
T PRK12726        206 HRIISLIGQTGVGKTTTLVKLGWQLLKQNRTVGFITTDTFRSGAVEQFQGYADKLDVE  263 (407)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEeCCccCccHHHHHHHHhhcCCCC
Confidence            4456899999999996543222   2245555443 3332  2356766665555543

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

Probab=93.91  E-value=0.52  Score=42.29  Aligned_cols=18  Identities=22%  Similarity=0.429  Sum_probs=15.1

Q ss_pred             CCEEEEccCCCCchhhhh
Q 037567           29 RDCLVVMATGSGKSLCYQ   46 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~~   46 (374)
                      .++++.|+||+|||.+.-
T Consensus        43 ~n~~iyG~~GTGKT~~~~   60 (366)
T COG1474          43 SNIIIYGPTGTGKTATVK   60 (366)
T ss_pred             ccEEEECCCCCCHhHHHH
Confidence            468999999999997643

>TIGR03880 KaiC_arch_3 KaiC domain protein, AF_0351 family

Probab=93.87  E-value=0.5  Score=39.31  Aligned_cols=51  Identities=20%  Similarity=0.206  Sum_probs=35.7

Q ss_pred             CCCEEEEccCCCCchhhhh-c--cccccCCcEEEEcchHHHHHHHHHHHHHcCCc
Q 037567           28 KRDCLVVMATGSGKSLCYQ-L--PPLVTGKTALVVSPLISLMQDQVMSLKQRGIN   79 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~-l--~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~   79 (374)
                      +.-+++.|++|+|||...+ +  ..+.++.+++++.-. +-.++..+.+..++..
T Consensus        16 g~~~li~G~~G~GKt~~~~~~~~~~~~~g~~~~y~s~e-~~~~~l~~~~~~~~~~   69 (224)
T TIGR03880        16 GHVIVVIGEYGTGKTTFSLQFLYQGLKNGEKAMYISLE-EREERILGYAKSKGWD   69 (224)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEECC-CCHHHHHHHHHHcCCC
Confidence            4567899999999995432 2  233457778887665 4577788888877654

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.

>PRK14954 DNA polymerase III subunits gamma and tau; Provisional

Probab=93.86  E-value=0.28  Score=47.14  Aligned_cols=17  Identities=18%  Similarity=0.237  Sum_probs=14.2

Q ss_pred             CEEEEccCCCCchhhhh
Q 037567           30 DCLVVMATGSGKSLCYQ   46 (374)
Q Consensus        30 ~~l~~a~tGsGKT~~~~   46 (374)
                      ..+++||+|+|||.++.
T Consensus        40 a~Lf~Gp~GvGKttlA~   56 (620)
T PRK14954         40 GYIFSGLRGVGKTTAAR   56 (620)
T ss_pred             eEEEECCCCCCHHHHHH
Confidence            47899999999997653

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional

Probab=93.86  E-value=0.14  Score=49.30  Aligned_cols=17  Identities=24%  Similarity=0.266  Sum_probs=13.8

Q ss_pred             CEEEEccCCCCchhhhh
Q 037567           30 DCLVVMATGSGKSLCYQ   46 (374)
Q Consensus        30 ~~l~~a~tGsGKT~~~~   46 (374)
                      .+++.||+|+|||.++.
T Consensus        40 a~Lf~Gp~G~GKTtlA~   56 (585)
T PRK14950         40 AYLFTGPRGVGKTSTAR   56 (585)
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            35899999999996643

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

Probab=93.82  E-value=0.065  Score=45.53  Aligned_cols=107  Identities=14%  Similarity=0.200  Sum_probs=51.7

Q ss_pred             HHHHHHHcCC----C-EEEEccCCCCchhhh-hccc---cc-----cCCcEEEEcchHHHHHHHHHHH-HHcCCceEEcC
Q 037567           20 DVIQRIIEKR----D-CLVVMATGSGKSLCY-QLPP---LV-----TGKTALVVSPLISLMQDQVMSL-KQRGINAEFLG   84 (374)
Q Consensus        20 ~~~~~~~~~~----~-~l~~a~tGsGKT~~~-~l~~---~~-----~~~~~lil~P~~~l~~q~~~~~-~~~~~~~~~~~   84 (374)
                      ..++.++.|.    . .=++|++|+|||-.. .+++   +.     .+.+++|+.-....-.+-..++ ++++..     
T Consensus        25 ~~lD~~L~GGi~~g~itEi~G~~gsGKTql~l~l~~~~~l~~~~~g~~~~vvyidTe~~f~~~Rl~~i~~~~~~~-----   99 (256)
T PF08423_consen   25 KSLDELLGGGIPTGSITEIVGESGSGKTQLCLQLAVNVQLPEEIGGLGGKVVYIDTEGTFSPERLQQIAERFGLD-----   99 (256)
T ss_dssp             HHHHHHTTSSEETTSEEEEEESTTSSHHHHHHHHHHHTTSGGCTTSSSSEEEEEESSSSS-HHHHHHHHHHTTS------
T ss_pred             HHHHHhhCCCCCCCcEEEEEEecccccchHHHHHHHHhhcccccccCCCceEEEeCCCCCCHHHHHHHhhccccc-----
Confidence            4666776542    2 238999999999332 2221   11     2556888754332222211111 222211     


Q ss_pred             CCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhh
Q 037567           85 SAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCIS  139 (374)
Q Consensus        85 ~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~  139 (374)
                          ..+    ....-.-.-+.+.+.+..++..........++++||||-+-.+.
T Consensus       100 ----~~~----~l~~I~v~~~~~~~~l~~~L~~l~~~l~~~~ikLIVIDSIaalf  146 (256)
T PF08423_consen  100 ----PEE----ILDNIFVIRVFDLEELLELLEQLPKLLSESKIKLIVIDSIAALF  146 (256)
T ss_dssp             ----HHH----HHHTEEEEE-SSHHHHHHHHHHHHHHHHHSCEEEEEEETSSHHH
T ss_pred             ----cch----hhhceeeeecCCHHHHHHHHHHHHhhccccceEEEEecchHHHH
Confidence                111    11110112233444444444444344445689999999987764

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

>PRK13900 type IV secretion system ATPase VirB11; Provisional

Probab=93.79  E-value=0.068  Score=47.20  Aligned_cols=40  Identities=18%  Similarity=0.245  Sum_probs=25.8

Q ss_pred             HcCCCEEEEccCCCCchhhh--hccccccCCcEEEEcchHHH
Q 037567           26 IEKRDCLVVMATGSGKSLCY--QLPPLVTGKTALVVSPLISL   65 (374)
Q Consensus        26 ~~~~~~l~~a~tGsGKT~~~--~l~~~~~~~~~lil~P~~~l   65 (374)
                      ..+++++++|+||||||...  ++..+....+++.+-.+.++
T Consensus       158 ~~~~nili~G~tgSGKTTll~aL~~~ip~~~ri~tiEd~~El  199 (332)
T PRK13900        158 ISKKNIIISGGTSTGKTTFTNAALREIPAIERLITVEDAREI  199 (332)
T ss_pred             HcCCcEEEECCCCCCHHHHHHHHHhhCCCCCeEEEecCCCcc
Confidence            35789999999999999542  23333345566665444443

>PRK10733 hflB ATP-dependent metalloprotease; Reviewed

Probab=93.78  E-value=0.32  Score=47.36  Aligned_cols=33  Identities=21%  Similarity=0.218  Sum_probs=21.1

Q ss_pred             CCEEEEccCCCCchhhhhccccccCCcEEEEcc
Q 037567           29 RDCLVVMATGSGKSLCYQLPPLVTGKTALVVSP   61 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~~l~~~~~~~~~lil~P   61 (374)
                      +.+++.+|+|+|||...-..+-..+...+.+.+
T Consensus       186 ~gill~G~~G~GKt~~~~~~a~~~~~~f~~is~  218 (644)
T PRK10733        186 KGVLMVGPPGTGKTLLAKAIAGEAKVPFFTISG  218 (644)
T ss_pred             CcEEEECCCCCCHHHHHHHHHHHcCCCEEEEeh
Confidence            468999999999997654333333444444433

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=93.73  E-value=0.22  Score=49.14  Aligned_cols=14  Identities=21%  Similarity=0.349  Sum_probs=12.3

Q ss_pred             EEEccCCCCchhhh
Q 037567           32 LVVMATGSGKSLCY   45 (374)
Q Consensus        32 l~~a~tGsGKT~~~   45 (374)
                      +|.|+||+|||.+.
T Consensus       785 YIyG~PGTGKTATV  798 (1164)
T PTZ00112        785 YISGMPGTGKTATV  798 (1164)
T ss_pred             EEECCCCCCHHHHH
Confidence            59999999999764

>KOG0730 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=93.71  E-value=0.32  Score=45.91  Aligned_cols=110  Identities=15%  Similarity=0.139  Sum_probs=57.9

Q ss_pred             CCCEEEEccCCCCchhhhhccccccCCcEEEEcchHHHHHHHHHHHHHcCCceEEcCCCCCchhhhhhhhcCCeeEEEEc
Q 037567           28 KRDCLVVMATGSGKSLCYQLPPLVTGKTALVVSPLISLMQDQVMSLKQRGINAEFLGSAQTDSSVQTKAETGYFQLLFMT  107 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T  107 (374)
                      .+.+++.+|+|+|||+.+-..+-. ...-++-++--+|..-|+-+-++.                               
T Consensus       468 pkGVLlyGPPGC~KT~lAkalAne-~~~nFlsvkgpEL~sk~vGeSEr~-------------------------------  515 (693)
T KOG0730|consen  468 PKGVLLYGPPGCGKTLLAKALANE-AGMNFLSVKGPELFSKYVGESERA-------------------------------  515 (693)
T ss_pred             CceEEEECCCCcchHHHHHHHhhh-hcCCeeeccCHHHHHHhcCchHHH-------------------------------
Confidence            478999999999999865322222 233344445445554443322111                               


Q ss_pred             CcccccCchhhHHHHHhcCccEEEEeccchhhc-c-cCcchHHHHHHHHHHHhcC----CCCeeEEEeecCcccH
Q 037567          108 PEKACIIPISFWSKLLKAGVCLFAVDEAHCISE-W-GHDFRLEYKQLDKLRTFLL----GVPFVALTATATEKVR  176 (374)
Q Consensus       108 ~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~-~-~~~~~~~~~~~~~~~~~~~----~~~~i~~SaT~~~~~~  176 (374)
                             ++..+.........++++||++.+.. . |......-+.++.++..+.    ...++..-||-.+...
T Consensus       516 -------ir~iF~kAR~~aP~IiFfDEiDsi~~~R~g~~~~v~~RVlsqLLtEmDG~e~~k~V~ViAATNRpd~I  583 (693)
T KOG0730|consen  516 -------IREVFRKARQVAPCIIFFDEIDALAGSRGGSSSGVTDRVLSQLLTEMDGLEALKNVLVIAATNRPDMI  583 (693)
T ss_pred             -------HHHHHHHHhhcCCeEEehhhHHhHhhccCCCccchHHHHHHHHHHHcccccccCcEEEEeccCChhhc
Confidence                   11122233333447899999999853 2 1111112233333333332    3467888888776544

>KOG0742 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=93.69  E-value=0.3  Score=43.48  Aligned_cols=18  Identities=28%  Similarity=0.490  Sum_probs=15.5

Q ss_pred             CCEEEEccCCCCchhhhh
Q 037567           29 RDCLVVMATGSGKSLCYQ   46 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~~   46 (374)
                      +++++.+|+|+|||+.+-
T Consensus       385 RNilfyGPPGTGKTm~Ar  402 (630)
T KOG0742|consen  385 RNILFYGPPGTGKTMFAR  402 (630)
T ss_pred             hheeeeCCCCCCchHHHH
Confidence            588999999999998653

>PHA00350 putative assembly protein

Probab=93.67  E-value=0.66  Score=41.85  Aligned_cols=16  Identities=31%  Similarity=0.092  Sum_probs=13.1

Q ss_pred             EEEEccCCCCchhhhh
Q 037567           31 CLVVMATGSGKSLCYQ   46 (374)
Q Consensus        31 ~l~~a~tGsGKT~~~~   46 (374)
                      .++.|.+|||||+.+.
T Consensus         4 ~l~tG~pGSGKT~~aV   19 (399)
T PHA00350          4 YAIVGRPGSYKSYEAV   19 (399)
T ss_pred             EEEecCCCCchhHHHH
Confidence            4789999999997654

>PRK13850 type IV secretion system protein VirD4; Provisional

Probab=93.61  E-value=0.1  Score=50.48  Aligned_cols=56  Identities=21%  Similarity=0.213  Sum_probs=43.8

Q ss_pred             CCEEEEccCCCCchhhhhcccccc-CCcEEEEcchHHHHHHHHHHHHHcCCceEEcC
Q 037567           29 RDCLVVMATGSGKSLCYQLPPLVT-GKTALVVSPLISLMQDQVMSLKQRGINAEFLG   84 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~~l~~~~~-~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~   84 (374)
                      .++++.||||||||..+.+|.+.. ...++|+=|.-++........++.|-.+.++.
T Consensus       140 ~hvlviApTgSGKgvg~VIPnLL~~~gS~VV~DpKGE~~~~Ta~~R~~~G~~V~~Fn  196 (670)
T PRK13850        140 PHSLVVAPTRAGKGVGVVIPTLLTFKGSVIALDVKGELFELTSRARKASGDAVFKFA  196 (670)
T ss_pred             ceEEEEecCCCCceeeehHhHHhcCCCCEEEEeCCchHHHHHHHHHHhCCCEEEEec
Confidence            478999999999999998886654 46788888888888877777777776665443

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=93.61  E-value=0.43  Score=48.19  Aligned_cols=18  Identities=22%  Similarity=0.361  Sum_probs=15.2

Q ss_pred             CCCEEEEccCCCCchhhh
Q 037567           28 KRDCLVVMATGSGKSLCY   45 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~   45 (374)
                      .++.++.||+|+|||...
T Consensus       194 ~~n~lL~G~pGvGKT~l~  211 (852)
T TIGR03346       194 KNNPVLIGEPGVGKTAIV  211 (852)
T ss_pred             CCceEEEcCCCCCHHHHH
Confidence            358899999999999654

Members of this protein family are the bacterial ATP-dependent chaperone ClpB. This protein belongs to the AAA family, ATPases associated with various cellular activities (pfam00004). This molecular chaperone does not act as a protease, but rather serves to disaggregate misfolded and aggregated proteins.

>TIGR00708 cobA cob(I)alamin adenosyltransferase

Probab=93.60  E-value=0.3  Score=38.43  Aligned_cols=50  Identities=14%  Similarity=0.046  Sum_probs=32.9

Q ss_pred             HhcCccEEEEeccchhhcccCcchHHHHHHHHHHHhcCCCCeeEEEeecCccc
Q 037567          123 LKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEKV  175 (374)
Q Consensus       123 ~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~SaT~~~~~  175 (374)
                      ....+++||+||+=...+.|.-..   ..+..+....|...-+.+|+...+..
T Consensus        94 ~~~~~DlvVLDEi~~A~~~gli~~---~~v~~lL~~rp~~~evVlTGR~~p~~  143 (173)
T TIGR00708        94 ADPELDLVLLDELTYALKYGYLDV---EEVVEALQERPGHQHVIITGRGCPQD  143 (173)
T ss_pred             hcCCCCEEEehhhHHHHHCCCcCH---HHHHHHHHhCCCCCEEEEECCCCCHH
Confidence            346799999999988777665332   23444455555555788888766543

Alternate name: corrinoid adenosyltransferase.

>TIGR00678 holB DNA polymerase III, delta' subunit

Probab=93.60  E-value=0.16  Score=40.97  Aligned_cols=16  Identities=31%  Similarity=0.335  Sum_probs=13.4

Q ss_pred             CEEEEccCCCCchhhh
Q 037567           30 DCLVVMATGSGKSLCY   45 (374)
Q Consensus        30 ~~l~~a~tGsGKT~~~   45 (374)
                      ..++.||+|+|||..+
T Consensus        16 ~~L~~G~~G~gkt~~a   31 (188)
T TIGR00678        16 AYLFAGPEGVGKELLA   31 (188)
T ss_pred             EEEEECCCCCCHHHHH
Confidence            4789999999999554

At position 126-127 of the seed alignment, this family lacks the HM motif of gamma/tau; at 132 it has a near-invariant A vs. an invariant F in gamma/tau.

>PRK14721 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=93.58  E-value=0.94  Score=41.36  Aligned_cols=57  Identities=14%  Similarity=0.116  Sum_probs=31.3

Q ss_pred             hcCccEEEEeccchhhcccCcchHHHHHHHHHHHhc-CCCCeeEEEeecCcccHHHHHHhcC
Q 037567          124 KAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFL-LGVPFVALTATATEKVRIDIINSLK  184 (374)
Q Consensus       124 ~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~-~~~~~i~~SaT~~~~~~~~~~~~~~  184 (374)
                      +.+.+.+++|.+-+.    .........+..+.... +....+.+|||........+...+.
T Consensus       267 l~~~d~VLIDTaGrs----qrd~~~~~~l~~l~~~~~~~~~~LVl~at~~~~~~~~~~~~f~  324 (420)
T PRK14721        267 LRGKHMVLIDTVGMS----QRDQMLAEQIAMLSQCGTQVKHLLLLNATSSGDTLDEVISAYQ  324 (420)
T ss_pred             hcCCCEEEecCCCCC----cchHHHHHHHHHHhccCCCceEEEEEcCCCCHHHHHHHHHHhc
Confidence            456678888886321    11111223333332221 2345788999988877766666554

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional

Probab=93.57  E-value=0.44  Score=46.02  Aligned_cols=18  Identities=22%  Similarity=0.292  Sum_probs=14.5

Q ss_pred             CCEEEEccCCCCchhhhh
Q 037567           29 RDCLVVMATGSGKSLCYQ   46 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~~   46 (374)
                      ..+++.||.|+|||.++.
T Consensus        39 ~a~Lf~Gp~G~GKttlA~   56 (620)
T PRK14948         39 PAYLFTGPRGTGKTSSAR   56 (620)
T ss_pred             ceEEEECCCCCChHHHHH
Confidence            356899999999996643

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=93.54  E-value=0.093  Score=43.15  Aligned_cols=35  Identities=17%  Similarity=0.149  Sum_probs=23.1

Q ss_pred             CCCEEEEccCCCCchhhhhccc---cccCCcEEEEcch
Q 037567           28 KRDCLVVMATGSGKSLCYQLPP---LVTGKTALVVSPL   62 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~l~~---~~~~~~~lil~P~   62 (374)
                      +.-+.+.||+|+|||...+..+   ...+.+++++.-.
T Consensus        12 g~i~~i~G~~GsGKT~l~~~~~~~~~~~g~~v~yi~~e   49 (209)
T TIGR02237        12 GTITQIYGPPGSGKTNICMILAVNAARQGKKVVYIDTE   49 (209)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEECC
Confidence            4556899999999996543222   2345667776554

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

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

Probab=93.53  E-value=0.13  Score=41.42  Aligned_cols=33  Identities=30%  Similarity=0.495  Sum_probs=25.3

Q ss_pred             CCCchhHHHHHHHHHc-CCCEEEEccCCCCchhh
Q 037567           12 SVFRPYQKDVIQRIIE-KRDCLVVMATGSGKSLC   44 (374)
Q Consensus        12 ~~~~~~Q~~~~~~~~~-~~~~l~~a~tGsGKT~~   44 (374)
                      ..+.+-|.+.+....+ +..+++.+|||||||..
T Consensus         8 g~~~~~~~~~l~~~v~~g~~i~I~G~tGSGKTTl   41 (186)
T cd01130           8 GTFSPLQAAYLWLAVEARKNILISGGTGSGKTTL   41 (186)
T ss_pred             CCCCHHHHHHHHHHHhCCCEEEEECCCCCCHHHH
Confidence            3466777777776554 67889999999999964

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.

>TIGR03600 phage_DnaB phage replicative helicase, DnaB family, HK022 subfamily

Probab=93.44  E-value=0.59  Score=43.14  Aligned_cols=45  Identities=18%  Similarity=0.009  Sum_probs=26.7

Q ss_pred             CCCEEEEccCCCCchhhhhccc----cccCCcEEEEcchHHHHHHHHHHH
Q 037567           28 KRDCLVVMATGSGKSLCYQLPP----LVTGKTALVVSPLISLMQDQVMSL   73 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~l~~----~~~~~~~lil~P~~~l~~q~~~~~   73 (374)
                      |.-+++.|+||+|||...+-.+    ...+.++++++.- .-..|+...+
T Consensus       194 g~liviag~pg~GKT~~al~ia~~~a~~~g~~v~~fSlE-m~~~~l~~Rl  242 (421)
T TIGR03600       194 GDLIVIGARPSMGKTTLALNIAENVALREGKPVLFFSLE-MSAEQLGERL  242 (421)
T ss_pred             CceEEEEeCCCCCHHHHHHHHHHHHHHhCCCcEEEEECC-CCHHHHHHHH
Confidence            4456889999999995443222    2356778887632 2333444443

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.

>TIGR01425 SRP54_euk signal recognition particle protein SRP54

Probab=93.36  E-value=0.65  Score=42.43  Aligned_cols=31  Identities=26%  Similarity=0.275  Sum_probs=19.6

Q ss_pred             EEEEccCCCCchhhhh-ccc-c-ccCCcEEEEcc
Q 037567           31 CLVVMATGSGKSLCYQ-LPP-L-VTGKTALVVSP   61 (374)
Q Consensus        31 ~l~~a~tGsGKT~~~~-l~~-~-~~~~~~lil~P   61 (374)
                      ++++|++|+|||.+.. ++. + .++.++++++-
T Consensus       103 i~lvG~~GvGKTTtaaKLA~~l~~~G~kV~lV~~  136 (429)
T TIGR01425       103 IMFVGLQGSGKTTTCTKLAYYYQRKGFKPCLVCA  136 (429)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEcC
Confidence            5789999999996643 221 1 23556665543

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.

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=93.26  E-value=0.71  Score=46.51  Aligned_cols=28  Identities=21%  Similarity=0.456  Sum_probs=20.7

Q ss_pred             HHHHHHHHHc------CCCEEEEccCCCCchhhh
Q 037567           18 QKDVIQRIIE------KRDCLVVMATGSGKSLCY   45 (374)
Q Consensus        18 Q~~~~~~~~~------~~~~l~~a~tGsGKT~~~   45 (374)
                      |..-+..+.+      ..+.++.||+|+|||...
T Consensus       192 r~~ei~~~i~~l~r~~~~n~lLvG~pGvGKTal~  225 (852)
T TIGR03345       192 RDDEIRQMIDILLRRRQNNPILTGEAGVGKTAVV  225 (852)
T ss_pred             CHHHHHHHHHHHhcCCcCceeEECCCCCCHHHHH
Confidence            5555655543      358899999999999654

Members of this protein family are homologs of ClpB, an ATPase associated with chaperone-related functions. These ClpB homologs, designated ClpV1, are a key component of the bacterial pathogenicity-associated type VI secretion system.

>KOG0741 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=93.26  E-value=0.46  Score=43.85  Aligned_cols=116  Identities=15%  Similarity=0.148  Sum_probs=60.3

Q ss_pred             CEEEEccCCCCchhhhhccccccCCc-EEEEcchHHHHHHHHHHHHHcCCceEEcCCCCCchhhhhhhhcCCeeEEEEcC
Q 037567           30 DCLVVMATGSGKSLCYQLPPLVTGKT-ALVVSPLISLMQDQVMSLKQRGINAEFLGSAQTDSSVQTKAETGYFQLLFMTP  108 (374)
Q Consensus        30 ~~l~~a~tGsGKT~~~~l~~~~~~~~-~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~  108 (374)
                      .+++.+|+|||||..+.-.++.+..+ +=++.|..-....                    .....               
T Consensus       540 SvLl~Gp~~sGKTaLAA~iA~~S~FPFvKiiSpe~miG~s--------------------EsaKc---------------  584 (744)
T KOG0741|consen  540 SVLLEGPPGSGKTALAAKIALSSDFPFVKIISPEDMIGLS--------------------ESAKC---------------  584 (744)
T ss_pred             EEEEecCCCCChHHHHHHHHhhcCCCeEEEeChHHccCcc--------------------HHHHH---------------
Confidence            57999999999997665555555544 3444554211110                    00000               


Q ss_pred             cccccCchhhHHHHHhcCccEEEEeccchhhcc---cCcchHHHH-HHHHHHHhc-CCCCeeEEEeecCcccHHHHHHhc
Q 037567          109 EKACIIPISFWSKLLKAGVCLFAVDEAHCISEW---GHDFRLEYK-QLDKLRTFL-LGVPFVALTATATEKVRIDIINSL  183 (374)
Q Consensus       109 ~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~---~~~~~~~~~-~~~~~~~~~-~~~~~i~~SaT~~~~~~~~~~~~~  183 (374)
                          ..+.........+...++|+|+..++.+|   |..+..... .+.-++... |..+.++.-+|-+..   .+++.+
T Consensus       585 ----~~i~k~F~DAYkS~lsiivvDdiErLiD~vpIGPRfSN~vlQaL~VllK~~ppkg~kLli~~TTS~~---~vL~~m  657 (744)
T KOG0741|consen  585 ----AHIKKIFEDAYKSPLSIIVVDDIERLLDYVPIGPRFSNLVLQALLVLLKKQPPKGRKLLIFGTTSRR---EVLQEM  657 (744)
T ss_pred             ----HHHHHHHHHhhcCcceEEEEcchhhhhcccccCchhhHHHHHHHHHHhccCCCCCceEEEEecccHH---HHHHHc
Confidence                00112223444567789999999999885   333332222 222223322 334455555665543   446655


Q ss_pred             CCCC
Q 037567          184 KLKN  187 (374)
Q Consensus       184 ~~~~  187 (374)
                      ++.+
T Consensus       658 ~i~~  661 (744)
T KOG0741|consen  658 GILD  661 (744)
T ss_pred             CHHH
Confidence            5443

>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=93.26  E-value=0.5  Score=40.34  Aligned_cols=35  Identities=17%  Similarity=0.114  Sum_probs=23.1

Q ss_pred             CCCEEEEccCCCCchhhhhcc---cccc-CCcEEEEcch
Q 037567           28 KRDCLVVMATGSGKSLCYQLP---PLVT-GKTALVVSPL   62 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~l~---~~~~-~~~~lil~P~   62 (374)
                      +.-+++.|.||.|||..++-.   +... +.+|++++.-
T Consensus        19 g~L~vi~a~pg~GKT~~~l~ia~~~a~~~~~~vly~SlE   57 (259)
T PF03796_consen   19 GELTVIAARPGVGKTAFALQIALNAALNGGYPVLYFSLE   57 (259)
T ss_dssp             T-EEEEEESTTSSHHHHHHHHHHHHHHTTSSEEEEEESS
T ss_pred             CcEEEEEecccCCchHHHHHHHHHHHHhcCCeEEEEcCC
Confidence            345688999999999654322   2223 5788888874

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 ....

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=93.23  E-value=0.4  Score=43.76  Aligned_cols=17  Identities=24%  Similarity=0.382  Sum_probs=14.7

Q ss_pred             CCEEEEccCCCCchhhh
Q 037567           29 RDCLVVMATGSGKSLCY   45 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~   45 (374)
                      .++++.||+|+|||.+.
T Consensus        56 ~~~lI~G~~GtGKT~l~   72 (394)
T PRK00411         56 LNVLIYGPPGTGKTTTV   72 (394)
T ss_pred             CeEEEECCCCCCHHHHH
Confidence            56899999999999764

>KOG0701 consensus dsRNA-specific nuclease Dicer and related ribonucleases [RNA processing and modification]

Probab=93.15  E-value=0.077  Score=55.44  Aligned_cols=94  Identities=22%  Similarity=0.313  Sum_probs=75.8

Q ss_pred             cEEEEecchhHHHHHHHHHHHcC-CceeeeecCCC-----------hHHHHHHHHhhhcCCeeEEEEeccccccccccCc
Q 037567          230 SIIVYCMTIKDVEEISKALKQLG-VKAGTYHGQMG-----------SKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDV  297 (374)
Q Consensus       230 ~~lVf~~~~~~~~~l~~~l~~~~-~~~~~~~~~~~-----------~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~  297 (374)
                      ..++|++....+....+.+++.. ..+..+.|...           ...+.+++..|......+|++|.++.+|+|.+.+
T Consensus       294 ~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~k~~~~~~~~~~~~vl~~~~~~~ln~L~~~~~~~e~~d~~~~  373 (1606)
T KOG0701|consen  294 SGIIFVDQRYTAYVLLELLREIFSNDPLFVTGASGANLWKSFKNELELRQAEVLRRFHFHELNLLIATSVLEEGVDVPKC  373 (1606)
T ss_pred             hheeecccchHHHHHHHHHHHhhccCcceeeccccCccchhhHHHHHhhhHHHHHHHhhhhhhHHHHHHHHHhhcchhhh
Confidence            46899999999998888887642 23333444322           2235577888888999999999999999999999


Q ss_pred             cEEEEECCCCChhHHHHhhccCCCCC
Q 037567          298 RHVIHYGCPKTLESYYQESGRCGRDG  323 (374)
Q Consensus       298 ~~vi~~~~p~s~~~~~Q~~GR~~R~~  323 (374)
                      +.++.++.|.....|+|..||+.+..
T Consensus       374 ~~~~~~~~~~~~~~~vq~~~r~~~~~  399 (1606)
T KOG0701|consen  374 NLVVLFDAPTYYRSYVQKKGRARAAD  399 (1606)
T ss_pred             hhheeccCcchHHHHHHhhcccccch
Confidence            99999999999999999999997753

>PRK07399 DNA polymerase III subunit delta'; Validated

Probab=93.11  E-value=0.32  Score=42.70  Aligned_cols=38  Identities=13%  Similarity=0.055  Sum_probs=23.7

Q ss_pred             cCccEEEEeccchhhcccCcchHHHHHHHHHHHhcCCCCeeEEE
Q 037567          125 AGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALT  168 (374)
Q Consensus       125 ~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~S  168 (374)
                      ...+++|||++|.+...+.      ..+.+..+..++..++++|
T Consensus       123 ~~~kVvII~~ae~m~~~aa------NaLLK~LEEPp~~~fILi~  160 (314)
T PRK07399        123 APRKVVVIEDAETMNEAAA------NALLKTLEEPGNGTLILIA  160 (314)
T ss_pred             CCceEEEEEchhhcCHHHH------HHHHHHHhCCCCCeEEEEE
Confidence            4578999999999865222      4455555655544444443

>PRK13822 conjugal transfer coupling protein TraG; Provisional

Probab=93.09  E-value=0.17  Score=48.79  Aligned_cols=56  Identities=18%  Similarity=0.226  Sum_probs=43.8

Q ss_pred             CCEEEEccCCCCchhhhhcccccc-CCcEEEEcchHHHHHHHHHHHHHcCCceEEcC
Q 037567           29 RDCLVVMATGSGKSLCYQLPPLVT-GKTALVVSPLISLMQDQVMSLKQRGINAEFLG   84 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~~l~~~~~-~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~   84 (374)
                      .++++.||||+|||..+.+|.+.+ ...++|+=|..++...+....++.|.++.++.
T Consensus       225 ~H~Lv~ApTgsGKt~g~VIPnLL~~~gS~VV~DpKgEl~~~Ta~~R~~~G~~V~vfd  281 (641)
T PRK13822        225 THGLVFAGSGGFKTTSVVVPTALKWGGPLVVLDPSTEVAPMVSEHRRDAGREVIVLD  281 (641)
T ss_pred             ceEEEEeCCCCCccceEehhhhhcCCCCEEEEeCcHHHHHHHHHHHHHCCCeEEEEe
Confidence            478999999999999988887654 55677777888988877777777776665543

>PRK05986 cob(I)alamin adenolsyltransferase/cobinamide ATP-dependent adenolsyltransferase; Validated

Probab=92.88  E-value=0.4  Score=38.39  Aligned_cols=51  Identities=14%  Similarity=0.083  Sum_probs=33.7

Q ss_pred             HhcCccEEEEeccchhhcccCcchHHHHHHHHHHHhcCCCCeeEEEeecCcccH
Q 037567          123 LKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEKVR  176 (374)
Q Consensus       123 ~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~SaT~~~~~~  176 (374)
                      ....+++||+||+=...+.|.-..   ..+..+....|...-+.+|+...+...
T Consensus       112 ~~~~ydlvVLDEi~~Al~~gli~~---eevi~~L~~rp~~~evVlTGR~~p~~L  162 (191)
T PRK05986        112 ADESYDLVVLDELTYALKYGYLDV---EEVLEALNARPGMQHVVITGRGAPREL  162 (191)
T ss_pred             hCCCCCEEEEehhhHHHHCCCccH---HHHHHHHHcCCCCCEEEEECCCCCHHH
Confidence            346789999999988777665332   334444455555667888887666543

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=92.87  E-value=1.2  Score=39.35  Aligned_cols=16  Identities=25%  Similarity=0.343  Sum_probs=13.9

Q ss_pred             CEEEEccCCCCchhhh
Q 037567           30 DCLVVMATGSGKSLCY   45 (374)
Q Consensus        30 ~~l~~a~tGsGKT~~~   45 (374)
                      ++++.||+|+|||...
T Consensus        40 ~~ll~G~~G~GKt~~~   55 (319)
T PRK00440         40 HLLFAGPPGTGKTTAA   55 (319)
T ss_pred             eEEEECCCCCCHHHHH
Confidence            5899999999999654

>PF06733 DEAD_2: DEAD_2; InterPro: IPR010614 This represents a conserved region within a number of RAD3-like DNA-binding helicases that are seemingly ubiquitous - members include proteins of eukaryotic, bacterial and archaeal origin

Probab=92.85  E-value=0.049  Score=43.33  Aligned_cols=40  Identities=15%  Similarity=0.136  Sum_probs=25.7

Q ss_pred             CCeeEEEEcCcccccCchhhHHHH--HhcCccEEEEeccchhhc
Q 037567           99 GYFQLLFMTPEKACIIPISFWSKL--LKAGVCLFAVDEAHCISE  140 (374)
Q Consensus        99 ~~~~i~i~T~~~l~~~~~~~~~~~--~~~~~~~vviDE~h~~~~  140 (374)
                      ...+|+|+++..+..-...  ...  ....-.+|||||||.+.+
T Consensus       118 ~~adivi~~y~yl~~~~~~--~~~~~~~~~~~ivI~DEAHNL~~  159 (174)
T PF06733_consen  118 KNADIVICNYNYLFDPSIR--KSLFGIDLKDNIVIFDEAHNLED  159 (174)
T ss_dssp             GG-SEEEEETHHHHSHHHH--HHHCT--CCCEEEEETTGGGCGG
T ss_pred             ccCCEEEeCHHHHhhHHHH--hhhccccccCcEEEEecccchHH
Confidence            3469999999877653221  222  123446899999999876

RAD3 is involved in nucleotide excision repair, and forms part of the transcription factor TFIIH in yeast [].; GO: 0003677 DNA binding, 0004003 ATP-dependent DNA helicase activity, 0005524 ATP binding; PDB: 3CRV_A 3CRW_1 2VL7_A 4A15_A 2VSF_A.

>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=92.80  E-value=0.34  Score=43.75  Aligned_cols=37  Identities=19%  Similarity=0.219  Sum_probs=19.2

Q ss_pred             EEEccCCCCchhhhhcccc----ccCC-cEEEEcchHHHHHH
Q 037567           32 LVVMATGSGKSLCYQLPPL----VTGK-TALVVSPLISLMQD   68 (374)
Q Consensus        32 l~~a~tGsGKT~~~~l~~~----~~~~-~~lil~P~~~l~~q   68 (374)
                      ++.++.|+|||......++    .... +.++++|+..-+.+
T Consensus         1 ~i~~~r~~GKT~~~~~~~~~~~~~~~~~~~vi~~~~~~~~~~   42 (384)
T PF03237_consen    1 LINGGRGSGKTTLIAIWFLWWALTRPPGRRVIIASTYRQARD   42 (384)
T ss_dssp             -EEE-SSS-HHHHHHHHHHHHHHSSSS--EEEEEESSHHHHH
T ss_pred             CCcCCccccHHHHHHHHHHHHHhhCCCCcEEEEecCHHHHHH
Confidence            4788999999966443322    2332 44444476655554

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.

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=92.75  E-value=0.18  Score=47.30  Aligned_cols=52  Identities=21%  Similarity=0.229  Sum_probs=37.6

Q ss_pred             CCCEEEEccCCCCchhhhhccc---ccc-CCcEEEEcchHHHHHHHHHHHHHcCCce
Q 037567           28 KRDCLVVMATGSGKSLCYQLPP---LVT-GKTALVVSPLISLMQDQVMSLKQRGINA   80 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~l~~---~~~-~~~~lil~P~~~l~~q~~~~~~~~~~~~   80 (374)
                      +..+++.+++|+|||..++--+   +.+ +.++++++-- +-.+++.+.+.++|+..
T Consensus        21 g~~~Li~G~pGsGKT~la~qfl~~g~~~~ge~~lyvs~e-E~~~~l~~~~~~~G~~~   76 (484)
T TIGR02655        21 GRSTLVSGTSGTGKTLFSIQFLYNGIIHFDEPGVFVTFE-ESPQDIIKNARSFGWDL   76 (484)
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHHHHHHhCCCCEEEEEEe-cCHHHHHHHHHHcCCCH
Confidence            5678999999999996544222   233 6788888754 66778888888887653

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.

>PRK05595 replicative DNA helicase; Provisional

Probab=92.71  E-value=0.4  Score=44.51  Aligned_cols=44  Identities=18%  Similarity=0.102  Sum_probs=26.5

Q ss_pred             CCEEEEccCCCCchhhhhcc----ccccCCcEEEEcchHHHHHHHHHHH
Q 037567           29 RDCLVVMATGSGKSLCYQLP----PLVTGKTALVVSPLISLMQDQVMSL   73 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~~l~----~~~~~~~~lil~P~~~l~~q~~~~~   73 (374)
                      .-+++.|.||+|||...+-.    +..++.+++++..- .-..|+...+
T Consensus       202 ~liviaarpg~GKT~~al~ia~~~a~~~g~~vl~fSlE-ms~~~l~~R~  249 (444)
T PRK05595        202 DMILIAARPSMGKTTFALNIAEYAALREGKSVAIFSLE-MSKEQLAYKL  249 (444)
T ss_pred             cEEEEEecCCCChHHHHHHHHHHHHHHcCCcEEEEecC-CCHHHHHHHH
Confidence            34567888999999654322    22346778887664 2344444443

>PRK14971 DNA polymerase III subunits gamma and tau; Provisional

Probab=92.68  E-value=0.43  Score=46.04  Aligned_cols=41  Identities=17%  Similarity=0.207  Sum_probs=24.6

Q ss_pred             cCccEEEEeccchhhcccCcchHHHHHHHHHHHhcCCCCeeEEEeec
Q 037567          125 AGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATA  171 (374)
Q Consensus       125 ~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~SaT~  171 (374)
                      ...+++||||+|.+....      ...+.+..+..+..-++.+.+|-
T Consensus       120 ~~~KVvIIdea~~Ls~~a------~naLLK~LEepp~~tifIL~tt~  160 (614)
T PRK14971        120 GKYKIYIIDEVHMLSQAA------FNAFLKTLEEPPSYAIFILATTE  160 (614)
T ss_pred             CCcEEEEEECcccCCHHH------HHHHHHHHhCCCCCeEEEEEeCC
Confidence            457899999999986422      13444555544444445555553

>TIGR00959 ffh signal recognition particle protein

Probab=92.66  E-value=0.49  Score=43.35  Aligned_cols=52  Identities=27%  Similarity=0.259  Sum_probs=29.9

Q ss_pred             EEEEccCCCCchhhhhccc--c--ccCCcEEEE-cch-H-HHHHHHHHHHHHcCCceEE
Q 037567           31 CLVVMATGSGKSLCYQLPP--L--VTGKTALVV-SPL-I-SLMQDQVMSLKQRGINAEF   82 (374)
Q Consensus        31 ~l~~a~tGsGKT~~~~l~~--~--~~~~~~lil-~P~-~-~l~~q~~~~~~~~~~~~~~   82 (374)
                      +++++++|+|||.+..-.+  +  ..+.+++++ +.+ + ....|+.......+.....
T Consensus       102 i~~vG~~GsGKTTtaakLA~~l~~~~g~kV~lV~~D~~R~~a~~QL~~~a~~~gvp~~~  160 (428)
T TIGR00959       102 ILMVGLQGSGKTTTCGKLAYYLKKKQGKKVLLVACDLYRPAAIEQLKVLGQQVGVPVFA  160 (428)
T ss_pred             EEEECCCCCcHHHHHHHHHHHHHHhCCCeEEEEeccccchHHHHHHHHHHHhcCCceEe
Confidence            5789999999997643222  1  234555443 332 2 3345555555666665444

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.

>KOG0652 consensus 26S proteasome regulatory complex, ATPase RPT5 [Posttranslational modification, protein turnover, chaperones]

Probab=92.65  E-value=0.47  Score=39.52  Aligned_cols=18  Identities=28%  Similarity=0.482  Sum_probs=15.6

Q ss_pred             CCEEEEccCCCCchhhhh
Q 037567           29 RDCLVVMATGSGKSLCYQ   46 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~~   46 (374)
                      +.+++.+|+|+|||+.+-
T Consensus       206 KGvLmYGPPGTGKTlmAR  223 (424)
T KOG0652|consen  206 KGVLMYGPPGTGKTLMAR  223 (424)
T ss_pred             CceEeeCCCCCcHHHHHH
Confidence            678999999999998653

>PRK08451 DNA polymerase III subunits gamma and tau; Validated

Probab=92.64  E-value=0.44  Score=44.90  Aligned_cols=16  Identities=31%  Similarity=0.316  Sum_probs=13.3

Q ss_pred             EEEEccCCCCchhhhh
Q 037567           31 CLVVMATGSGKSLCYQ   46 (374)
Q Consensus        31 ~l~~a~tGsGKT~~~~   46 (374)
                      .+++||.|+|||.++.
T Consensus        39 yLf~Gp~G~GKTt~Ar   54 (535)
T PRK08451         39 YLFSGLRGSGKTSSAR   54 (535)
T ss_pred             EEEECCCCCcHHHHHH
Confidence            4899999999996643

>PRK14723 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=92.61  E-value=0.56  Score=45.96  Aligned_cols=52  Identities=13%  Similarity=0.104  Sum_probs=29.2

Q ss_pred             CCEEEEccCCCCchhhhhccc--c--ccC-CcEEEE-cchH--HHHHHHHHHHHHcCCce
Q 037567           29 RDCLVVMATGSGKSLCYQLPP--L--VTG-KTALVV-SPLI--SLMQDQVMSLKQRGINA   80 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~~l~~--~--~~~-~~~lil-~P~~--~l~~q~~~~~~~~~~~~   80 (374)
                      +-+.+.||+|+|||.+....+  +  ..+ +++.++ +.+-  ...+|+.......++..
T Consensus       186 ~Vi~lVGpnGvGKTTTiaKLA~~~~~~~G~kkV~lit~Dt~RigA~eQL~~~a~~~gvpv  245 (767)
T PRK14723        186 GVLALVGPTGVGKTTTTAKLAARCVAREGADQLALLTTDSFRIGALEQLRIYGRILGVPV  245 (767)
T ss_pred             eEEEEECCCCCcHHHHHHHHHhhHHHHcCCCeEEEecCcccchHHHHHHHHHHHhCCCCc
Confidence            346789999999996654322  1  233 344443 3322  24566666555555543

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

Probab=92.58  E-value=0.17  Score=42.16  Aligned_cols=36  Identities=17%  Similarity=0.080  Sum_probs=23.3

Q ss_pred             CCCEEEEccCCCCchhhhhccc---cccC------CcEEEEcchH
Q 037567           28 KRDCLVVMATGSGKSLCYQLPP---LVTG------KTALVVSPLI   63 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~l~~---~~~~------~~~lil~P~~   63 (374)
                      +.-..+.||+|+|||...+..+   ...+      .+++++....
T Consensus        19 g~v~~I~G~~GsGKT~l~~~ia~~~~~~~~~~g~~~~v~yi~~e~   63 (226)
T cd01393          19 GRITEIFGEFGSGKTQLCLQLAVEAQLPGELGGLEGKVVYIDTEG   63 (226)
T ss_pred             CcEEEEeCCCCCChhHHHHHHHHHhhcccccCCCcceEEEEecCC
Confidence            4567899999999996543222   2233      6677766543

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.

>TIGR00416 sms DNA repair protein RadA

Probab=92.58  E-value=0.3  Score=45.28  Aligned_cols=88  Identities=15%  Similarity=0.072  Sum_probs=50.9

Q ss_pred             CCCEEEEccCCCCchhhhhcc---ccccCCcEEEEcchHHHHHHHHHHHHHcCCceEEcCCCCCchhhhhhhhcCCeeEE
Q 037567           28 KRDCLVVMATGSGKSLCYQLP---PLVTGKTALVVSPLISLMQDQVMSLKQRGINAEFLGSAQTDSSVQTKAETGYFQLL  104 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~l~---~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~  104 (374)
                      +.-+++.+++|+|||...+..   +...+.+++++..- +...|+.....+++....                    ++.
T Consensus        94 GsvilI~G~pGsGKTTL~lq~a~~~a~~g~kvlYvs~E-Es~~qi~~ra~rlg~~~~--------------------~l~  152 (454)
T TIGR00416        94 GSLILIGGDPGIGKSTLLLQVACQLAKNQMKVLYVSGE-ESLQQIKMRAIRLGLPEP--------------------NLY  152 (454)
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHHHHHhcCCcEEEEECc-CCHHHHHHHHHHcCCChH--------------------HeE
Confidence            345688999999999654322   22345678888764 445677666666553211                    111


Q ss_pred             EEcCcccccCchhhHHHHHhcCccEEEEeccchhhc
Q 037567          105 FMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISE  140 (374)
Q Consensus       105 i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~  140 (374)
                      +.....+    ......+...+.+++|||....+..
T Consensus       153 ~~~e~~~----~~I~~~i~~~~~~~vVIDSIq~l~~  184 (454)
T TIGR00416       153 VLSETNW----EQICANIEEENPQACVIDSIQTLYS  184 (454)
T ss_pred             EcCCCCH----HHHHHHHHhcCCcEEEEecchhhcc
Confidence            2111111    1222333345788999999998753

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)).

>PRK08840 replicative DNA helicase; Provisional

Probab=92.54  E-value=0.99  Score=42.01  Aligned_cols=45  Identities=16%  Similarity=0.079  Sum_probs=26.7

Q ss_pred             CCEEEEccCCCCchhhhhcc----ccccCCcEEEEcchHHHHHHHHHHHH
Q 037567           29 RDCLVVMATGSGKSLCYQLP----PLVTGKTALVVSPLISLMQDQVMSLK   74 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~~l~----~~~~~~~~lil~P~~~l~~q~~~~~~   74 (374)
                      .-+++.|.||.|||..++-.    +..++.+++++..- --..|+...+-
T Consensus       218 ~LiviaarPg~GKTafalnia~~~a~~~~~~v~~fSlE-Ms~~ql~~Rll  266 (464)
T PRK08840        218 DLIIVAARPSMGKTTFAMNLCENAAMDQDKPVLIFSLE-MPAEQLMMRML  266 (464)
T ss_pred             ceEEEEeCCCCchHHHHHHHHHHHHHhCCCeEEEEecc-CCHHHHHHHHH
Confidence            44567888999999654211    22346678777654 33455554543

>cd01123 Rad51_DMC1_radA Rad51_DMC1_radA,B

Probab=92.49  E-value=0.2  Score=42.03  Aligned_cols=34  Identities=15%  Similarity=0.086  Sum_probs=21.9

Q ss_pred             CCCEEEEccCCCCchhhhhccc---ccc------CCcEEEEcc
Q 037567           28 KRDCLVVMATGSGKSLCYQLPP---LVT------GKTALVVSP   61 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~l~~---~~~------~~~~lil~P   61 (374)
                      +.-+.+.||+|+|||...+..+   ...      ...++++.-
T Consensus        19 g~i~~i~G~~GsGKT~l~~~l~~~~~~~~~~~g~~~~viyi~~   61 (235)
T cd01123          19 GSITEIFGEFGSGKTQLCHQLAVTVQLPIELGGLEGKAVYIDT   61 (235)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHeeCccccCCCCccEEEEeC
Confidence            4556899999999995543221   222      357777764

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 .

>PRK09302 circadian clock protein KaiC; Reviewed

Probab=92.48  E-value=0.23  Score=47.10  Aligned_cols=51  Identities=24%  Similarity=0.234  Sum_probs=35.4

Q ss_pred             CCCEEEEccCCCCchhhhhc---cccccCCcEEEEcchHHHHHHHHHHHHHcCCc
Q 037567           28 KRDCLVVMATGSGKSLCYQL---PPLVTGKTALVVSPLISLMQDQVMSLKQRGIN   79 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~l---~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~   79 (374)
                      +..+++.+++|+|||.....   ..+..+.++++++-. +..++..+.+..+|..
T Consensus       273 g~~~li~G~~G~GKT~l~~~~~~~~~~~g~~~~yis~e-~~~~~i~~~~~~~g~~  326 (509)
T PRK09302        273 GSIILVSGATGTGKTLLASKFAEAACRRGERCLLFAFE-ESRAQLIRNARSWGID  326 (509)
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHHHHhCCCcEEEEEec-CCHHHHHHHHHHcCCC
Confidence            45668899999999954322   233467788888654 4567777777777654

>cd00561 CobA_CobO_BtuR ATP:corrinoid adenosyltransferase BtuR/CobO/CobP

Probab=92.39  E-value=0.8  Score=35.58  Aligned_cols=49  Identities=16%  Similarity=0.013  Sum_probs=31.4

Q ss_pred             HhcCccEEEEeccchhhcccCcchHHHHHHHHHHHhcCCCCeeEEEeecCcc
Q 037567          123 LKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEK  174 (374)
Q Consensus       123 ~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~SaT~~~~  174 (374)
                      ....++++|+||+=...+.+.-..   ..+..+....+...-+.+|+.-.+.
T Consensus        92 ~~~~~dLlVLDEi~~a~~~gli~~---~~v~~ll~~rp~~~evIlTGr~~p~  140 (159)
T cd00561          92 ASGEYDLVILDEINYALGYGLLDV---EEVVDLLKAKPEDLELVLTGRNAPK  140 (159)
T ss_pred             hcCCCCEEEEechHhHhhCCCCCH---HHHHHHHHcCCCCCEEEEECCCCCH
Confidence            346789999999987766555322   3344455555555567777765554

This family consists of the BtuR, CobO, CobP proteins all of which are Cob(I)alamin (vitamin B12) adenosyltransferase, which is involved in cobalamin (vitamin B12) biosynthesis. This enzyme is a homodimer, which catalyzes the adenosylation reaction: ATP + cob(I)alamin + H2O <= phosphate + diphosphate + adenosylcobalamin.

>TIGR02767 TraG-Ti Ti-type conjugative transfer system protien TraG

Probab=92.37  E-value=0.26  Score=47.38  Aligned_cols=55  Identities=15%  Similarity=0.204  Sum_probs=42.9

Q ss_pred             CCEEEEccCCCCchhhhhcccccc-CCcEEEEcchHHHHHHHHHHHHHcC-CceEEc
Q 037567           29 RDCLVVMATGSGKSLCYQLPPLVT-GKTALVVSPLISLMQDQVMSLKQRG-INAEFL   83 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~~l~~~~~-~~~~lil~P~~~l~~q~~~~~~~~~-~~~~~~   83 (374)
                      .++++.||||||||..+.+|.+.. ...++|+=|..++...+...-++.| .++.++
T Consensus       212 ~H~lv~ApTgsGKgvg~VIPnLL~~~gS~VV~DpKgE~~~~Ta~~R~~~Gg~~V~vf  268 (623)
T TIGR02767       212 THMIFFAGSGGFKTTSVVVPTALKYGGPLVCLDPSTEVAPMVCEHRRQAGNRKVIVL  268 (623)
T ss_pred             ceEEEEeCCCCCccceeehhhhhcCCCCEEEEEChHHHHHHHHHHHHHcCCCcEEEE
Confidence            478999999999999988886654 6678888888898887776666666 445443

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.

>PF05729 NACHT: NACHT domain

Probab=92.30  E-value=0.5  Score=36.84  Aligned_cols=15  Identities=33%  Similarity=0.324  Sum_probs=12.7

Q ss_pred             EEEEccCCCCchhhh
Q 037567           31 CLVVMATGSGKSLCY   45 (374)
Q Consensus        31 ~l~~a~tGsGKT~~~   45 (374)
                      ++|.|++|+|||...
T Consensus         3 l~I~G~~G~GKStll   17 (166)
T PF05729_consen    3 LWISGEPGSGKSTLL   17 (166)
T ss_pred             EEEECCCCCChHHHH
Confidence            688999999999653

>KOG2228 consensus Origin recognition complex, subunit 4 [Replication, recombination and repair]

Probab=92.28  E-value=0.71  Score=40.15  Aligned_cols=17  Identities=24%  Similarity=0.548  Sum_probs=14.9

Q ss_pred             CCCEEEEccCCCCchhh
Q 037567           28 KRDCLVVMATGSGKSLC   44 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~   44 (374)
                      ++.+++.+|-|||||..
T Consensus        49 snsviiigprgsgkT~l   65 (408)
T KOG2228|consen   49 SNSVIIIGPRGSGKTIL   65 (408)
T ss_pred             CCceEEEccCCCCceEe
Confidence            57899999999999953

>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau

Probab=92.28  E-value=0.45  Score=42.72  Aligned_cols=16  Identities=25%  Similarity=0.270  Sum_probs=13.5

Q ss_pred             CEEEEccCCCCchhhh
Q 037567           30 DCLVVMATGSGKSLCY   45 (374)
Q Consensus        30 ~~l~~a~tGsGKT~~~   45 (374)
                      ..++.||+|+|||..+
T Consensus        38 ~~Ll~G~~G~GKt~~a   53 (355)
T TIGR02397        38 AYLFSGPRGTGKTSIA   53 (355)
T ss_pred             EEEEECCCCCCHHHHH
Confidence            4689999999999654

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

>PRK14953 DNA polymerase III subunits gamma and tau; Provisional

Probab=92.20  E-value=1.1  Score=42.04  Aligned_cols=17  Identities=18%  Similarity=0.358  Sum_probs=13.7

Q ss_pred             EEEEccCCCCchhhhhc
Q 037567           31 CLVVMATGSGKSLCYQL   47 (374)
Q Consensus        31 ~l~~a~tGsGKT~~~~l   47 (374)
                      +++.||+|+|||.++.+
T Consensus        41 yLf~Gp~G~GKTtlAr~   57 (486)
T PRK14953         41 YIFAGPRGTGKTTIARI   57 (486)
T ss_pred             EEEECCCCCCHHHHHHH
Confidence            57899999999976543

>PRK06904 replicative DNA helicase; Validated

Probab=92.19  E-value=1.6  Score=40.87  Aligned_cols=45  Identities=18%  Similarity=0.106  Sum_probs=26.9

Q ss_pred             CCEEEEccCCCCchhhhhcc----ccccCCcEEEEcchHHHHHHHHHHHH
Q 037567           29 RDCLVVMATGSGKSLCYQLP----PLVTGKTALVVSPLISLMQDQVMSLK   74 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~~l~----~~~~~~~~lil~P~~~l~~q~~~~~~   74 (374)
                      .=+++.|.||.|||..++-.    +...+.++++++.- --..|+...+-
T Consensus       222 ~LiiIaarPg~GKTafalnia~~~a~~~g~~Vl~fSlE-Ms~~ql~~Rll  270 (472)
T PRK06904        222 DLIIVAARPSMGKTTFAMNLCENAAMASEKPVLVFSLE-MPAEQIMMRML  270 (472)
T ss_pred             cEEEEEeCCCCChHHHHHHHHHHHHHhcCCeEEEEecc-CCHHHHHHHHH
Confidence            34567888999999643211    22346678777654 34555555544

>TIGR00665 DnaB replicative DNA helicase

Probab=92.15  E-value=0.57  Score=43.44  Aligned_cols=47  Identities=13%  Similarity=0.020  Sum_probs=27.4

Q ss_pred             CCCEEEEccCCCCchhhhhccc---c-ccCCcEEEEcchHHHHHHHHHHHHH
Q 037567           28 KRDCLVVMATGSGKSLCYQLPP---L-VTGKTALVVSPLISLMQDQVMSLKQ   75 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~l~~---~-~~~~~~lil~P~~~l~~q~~~~~~~   75 (374)
                      |.-+++.|+||+|||...+-.+   . ..+.++++++.- .-..|+.+.+..
T Consensus       195 G~l~vi~g~pg~GKT~~~l~~a~~~a~~~g~~vl~~SlE-m~~~~i~~R~~~  245 (434)
T TIGR00665       195 SDLIILAARPSMGKTAFALNIAENAAIKEGKPVAFFSLE-MSAEQLAMRMLS  245 (434)
T ss_pred             CeEEEEEeCCCCChHHHHHHHHHHHHHhCCCeEEEEeCc-CCHHHHHHHHHH
Confidence            3446889999999995443221   1 245677777654 334444444443

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.

>TIGR00767 rho transcription termination factor Rho

Probab=92.06  E-value=0.29  Score=44.02  Aligned_cols=20  Identities=25%  Similarity=0.398  Sum_probs=16.6

Q ss_pred             cCCCEEEEccCCCCchhhhh
Q 037567           27 EKRDCLVVMATGSGKSLCYQ   46 (374)
Q Consensus        27 ~~~~~l~~a~tGsGKT~~~~   46 (374)
                      .|+.+++.||+|+|||....
T Consensus       167 ~Gq~~~IvG~~g~GKTtL~~  186 (415)
T TIGR00767       167 KGQRGLIVAPPKAGKTVLLQ  186 (415)
T ss_pred             CCCEEEEECCCCCChhHHHH
Confidence            47789999999999996543

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

>KOG0745 consensus Putative ATP-dependent Clp-type protease (AAA+ ATPase superfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=91.95  E-value=0.1  Score=46.69  Aligned_cols=20  Identities=50%  Similarity=0.647  Sum_probs=16.8

Q ss_pred             cCCCEEEEccCCCCchhhhh
Q 037567           27 EKRDCLVVMATGSGKSLCYQ   46 (374)
Q Consensus        27 ~~~~~l~~a~tGsGKT~~~~   46 (374)
                      ++.|+++.+|||||||+.+.
T Consensus       225 eKSNvLllGPtGsGKTllaq  244 (564)
T KOG0745|consen  225 EKSNVLLLGPTGSGKTLLAQ  244 (564)
T ss_pred             ecccEEEECCCCCchhHHHH
Confidence            35689999999999998654

>PRK08506 replicative DNA helicase; Provisional

Probab=91.89  E-value=0.97  Score=42.27  Aligned_cols=45  Identities=11%  Similarity=0.013  Sum_probs=27.8

Q ss_pred             CCEEEEccCCCCchhhhhcc---ccccCCcEEEEcchHHHHHHHHHHHH
Q 037567           29 RDCLVVMATGSGKSLCYQLP---PLVTGKTALVVSPLISLMQDQVMSLK   74 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~~l~---~~~~~~~~lil~P~~~l~~q~~~~~~   74 (374)
                      .-+++.|.||.|||...+-.   +...+.++++++.- .-..|+...+.
T Consensus       193 ~LivIaarpg~GKT~fal~ia~~~~~~g~~V~~fSlE-Ms~~ql~~Rll  240 (472)
T PRK08506        193 DLIIIAARPSMGKTTLCLNMALKALNQDKGVAFFSLE-MPAEQLMLRML  240 (472)
T ss_pred             ceEEEEcCCCCChHHHHHHHHHHHHhcCCcEEEEeCc-CCHHHHHHHHH
Confidence            44577888999999543322   23356678777654 34555555553

>PRK06647 DNA polymerase III subunits gamma and tau; Validated

Probab=91.84  E-value=0.51  Score=44.99  Aligned_cols=17  Identities=18%  Similarity=0.235  Sum_probs=14.1

Q ss_pred             CEEEEccCCCCchhhhh
Q 037567           30 DCLVVMATGSGKSLCYQ   46 (374)
Q Consensus        30 ~~l~~a~tGsGKT~~~~   46 (374)
                      -+++.||.|+|||.++.
T Consensus        40 ayLf~Gp~G~GKTt~Ar   56 (563)
T PRK06647         40 AYIFSGPRGVGKTSSAR   56 (563)
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            36899999999997653

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=91.79  E-value=0.97  Score=42.39  Aligned_cols=60  Identities=17%  Similarity=0.187  Sum_probs=54.7

Q ss_pred             CCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEec
Q 037567          227 GAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATM  286 (374)
Q Consensus       227 ~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~  286 (374)
                      .++.+||.+|+++-+....+.|...|+.+..++++.+..++..++.....|..+++++|+
T Consensus        50 ~~~~~lVi~P~~~L~~dq~~~l~~~gi~~~~l~~~~~~~~~~~i~~~~~~~~~~il~~TP  109 (470)
T TIGR00614        50 SDGITLVISPLISLMEDQVLQLKASGIPATFLNSSQSKEQQKNVLTDLKDGKIKLLYVTP  109 (470)
T ss_pred             cCCcEEEEecHHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECH
Confidence            467899999999999999999999999999999999999888888888899999999998

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

>PF01745 IPT: Isopentenyl transferase; InterPro: IPR002648 Isopentenyl transferase / dimethylallyl transferase synthesizes isopentenyladensosine 5'-monophosphate, a cytokinin that induces shoot formation on host plants infected with the Ti plasmid []

Probab=91.71  E-value=0.094  Score=42.36  Aligned_cols=28  Identities=29%  Similarity=0.312  Sum_probs=17.0

Q ss_pred             EEEEccCCCCchhhhhccccccCCcEEE
Q 037567           31 CLVVMATGSGKSLCYQLPPLVTGKTALV   58 (374)
Q Consensus        31 ~l~~a~tGsGKT~~~~l~~~~~~~~~li   58 (374)
                      .++.||||+|||-.++..+...+..+++
T Consensus         4 ~~i~GpT~tGKt~~ai~lA~~~g~pvI~   31 (233)
T PF01745_consen    4 YLIVGPTGTGKTALAIALAQKTGAPVIS   31 (233)
T ss_dssp             EEEE-STTSSHHHHHHHHHHHH--EEEE
T ss_pred             EEEECCCCCChhHHHHHHHHHhCCCEEE
Confidence            5789999999997655444444444443

; GO: 0004161 dimethylallyltranstransferase activity, 0009058 biosynthetic process; PDB: 2ZE8_C 2ZE5_A 2ZE7_A 2ZE6_A.

>cd01125 repA Hexameric Replicative Helicase RepA

Probab=91.65  E-value=0.71  Score=38.82  Aligned_cols=17  Identities=29%  Similarity=0.288  Sum_probs=13.6

Q ss_pred             CEEEEccCCCCchhhhh
Q 037567           30 DCLVVMATGSGKSLCYQ   46 (374)
Q Consensus        30 ~~l~~a~tGsGKT~~~~   46 (374)
                      -.++.||+|+|||...+
T Consensus         3 ~~ll~g~~G~GKS~lal   19 (239)
T cd01125           3 VSALVAPGGTGKSSLLL   19 (239)
T ss_pred             eeEEEcCCCCCHHHHHH
Confidence            46899999999995543

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.

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

Probab=91.60  E-value=0.2  Score=42.76  Aligned_cols=32  Identities=28%  Similarity=0.489  Sum_probs=23.0

Q ss_pred             CchhHHHHHHHHHc-C-CCEEEEccCCCCchhhh
Q 037567           14 FRPYQKDVIQRIIE-K-RDCLVVMATGSGKSLCY   45 (374)
Q Consensus        14 ~~~~Q~~~~~~~~~-~-~~~l~~a~tGsGKT~~~   45 (374)
                      +.+.|.+.+..+.. . ..+++.++||||||.+.
T Consensus        64 ~~~~~~~~l~~~~~~~~GlilisG~tGSGKTT~l   97 (264)
T cd01129          64 LKPENLEIFRKLLEKPHGIILVTGPTGSGKTTTL   97 (264)
T ss_pred             CCHHHHHHHHHHHhcCCCEEEEECCCCCcHHHHH
Confidence            35567777766654 3 35789999999999653

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.

>TIGR03819 heli_sec_ATPase helicase/secretion neighborhood ATPase

Probab=91.58  E-value=0.33  Score=43.15  Aligned_cols=52  Identities=23%  Similarity=0.346  Sum_probs=33.7

Q ss_pred             CchhHHHHHHHHHc-CCCEEEEccCCCCchhhh--hccccccCCcEEEEcchHHH
Q 037567           14 FRPYQKDVIQRIIE-KRDCLVVMATGSGKSLCY--QLPPLVTGKTALVVSPLISL   65 (374)
Q Consensus        14 ~~~~Q~~~~~~~~~-~~~~l~~a~tGsGKT~~~--~l~~~~~~~~~lil~P~~~l   65 (374)
                      +.+.+.+.+..+.+ +.++++.++||||||...  ++..+....+++.+-.+.++
T Consensus       163 ~~~~~~~~L~~~v~~~~~ili~G~tGsGKTTll~al~~~i~~~~riv~iEd~~El  217 (340)
T TIGR03819       163 FPPGVARLLRAIVAARLAFLISGGTGSGKTTLLSALLALVAPDERIVLVEDAAEL  217 (340)
T ss_pred             CCHHHHHHHHHHHhCCCeEEEECCCCCCHHHHHHHHHccCCCCCcEEEECCccee
Confidence            44556666665544 678999999999999542  23333445566666666555

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.

>PRK10436 hypothetical protein; Provisional

Probab=91.51  E-value=0.19  Score=46.52  Aligned_cols=32  Identities=28%  Similarity=0.385  Sum_probs=23.3

Q ss_pred             CchhHHHHHHHHHc--CCCEEEEccCCCCchhhh
Q 037567           14 FRPYQKDVIQRIIE--KRDCLVVMATGSGKSLCY   45 (374)
Q Consensus        14 ~~~~Q~~~~~~~~~--~~~~l~~a~tGsGKT~~~   45 (374)
                      +.+.|.+.+..+..  +.-+++.||||||||.+.
T Consensus       202 ~~~~~~~~l~~~~~~~~GliLvtGpTGSGKTTtL  235 (462)
T PRK10436        202 MTPAQLAQFRQALQQPQGLILVTGPTGSGKTVTL  235 (462)
T ss_pred             cCHHHHHHHHHHHHhcCCeEEEECCCCCChHHHH
Confidence            45667777776654  345789999999999753

>PRK04841 transcriptional regulator MalT; Provisional

Probab=91.49  E-value=0.93  Score=46.47  Aligned_cols=33  Identities=21%  Similarity=-0.008  Sum_probs=21.4

Q ss_pred             CCCEEEEccCCCCchhhhhccccccCCcEEEEcc
Q 037567           28 KRDCLVVMATGSGKSLCYQLPPLVTGKTALVVSP   61 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~l~~~~~~~~~lil~P   61 (374)
                      .+-++|.||.|+|||....-.+.... .+.++.-
T Consensus        32 ~~~~~v~apaG~GKTtl~~~~~~~~~-~~~w~~l   64 (903)
T PRK04841         32 YRLVLVTSPAGYGKTTLISQWAAGKN-NLGWYSL   64 (903)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHhCC-CeEEEec
Confidence            34579999999999976443332233 5666543

>PRK09519 recA DNA recombination protein RecA; Reviewed

Probab=91.45  E-value=0.27  Score=48.22  Aligned_cols=96  Identities=15%  Similarity=0.134  Sum_probs=54.9

Q ss_pred             HHHHHHc------CCCEEEEccCCCCchhhhhc---cccccCCcEEEEcchHHHHHHHHHHHHHcCCceEEcCCCCCchh
Q 037567           21 VIQRIIE------KRDCLVVMATGSGKSLCYQL---PPLVTGKTALVVSPLISLMQDQVMSLKQRGINAEFLGSAQTDSS   91 (374)
Q Consensus        21 ~~~~~~~------~~~~l~~a~tGsGKT~~~~l---~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~   91 (374)
                      .++.++.      +.-+.+.+|+|+|||...+.   .+...+.+++++-.-..+...   .++++|+...          
T Consensus        47 ~LD~lLg~GGip~GsiteI~G~~GsGKTtLal~~~~~a~~~G~~v~yId~E~t~~~~---~A~~lGvDl~----------  113 (790)
T PRK09519         47 ALDVALGIGGLPRGRVIEIYGPESSGKTTVALHAVANAQAAGGVAAFIDAEHALDPD---YAKKLGVDTD----------  113 (790)
T ss_pred             HHHHhhcCCCccCCeEEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEECCccchhHH---HHHHcCCChh----------
Confidence            4555554      34567999999999965432   233457788888776655533   4455554321          


Q ss_pred             hhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhh
Q 037567           92 VQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCIS  139 (374)
Q Consensus        92 ~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~  139 (374)
                                .+++..|......+...........+++||||-+-.+.
T Consensus       114 ----------~llv~~~~~~E~~l~~i~~lv~~~~~~LVVIDSI~aL~  151 (790)
T PRK09519        114 ----------SLLVSQPDTGEQALEIADMLIRSGALDIVVIDSVAALV  151 (790)
T ss_pred             ----------HeEEecCCCHHHHHHHHHHHhhcCCCeEEEEcchhhhc
Confidence                      23344444332222221122223468999999988775

>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1

Probab=91.35  E-value=0.28  Score=42.99  Aligned_cols=49  Identities=10%  Similarity=-0.097  Sum_probs=27.8

Q ss_pred             CCEEEEccCCCCchhhhhccc----cc-----cCCcEEEEcchHHH-HHHHHHHHHHcC
Q 037567           29 RDCLVVMATGSGKSLCYQLPP----LV-----TGKTALVVSPLISL-MQDQVMSLKQRG   77 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~~l~~----~~-----~~~~~lil~P~~~l-~~q~~~~~~~~~   77 (374)
                      .-..+.|++|+|||...+..+    +.     .+.+++|+.--... .++..+...+++
T Consensus        97 ~iteI~G~~GsGKTql~lqla~~~~~~~~~gg~~~~vvYIdtE~~f~~eRi~~~a~~~g  155 (313)
T TIGR02238        97 SITEVFGEFRCGKTQLSHTLCVTAQLPREMGGGNGKVAYIDTEGTFRPDRIRAIAERFG  155 (313)
T ss_pred             eEEEEECCCCCCcCHHHHHHHHHHhcchhhcCCCCeEEEEEcCCCCCHHHHHHHHHHcC
Confidence            345799999999995433221    11     24578887644322 344444445554

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

>PRK14701 reverse gyrase; Provisional

Probab=91.31  E-value=0.63  Score=49.98  Aligned_cols=61  Identities=16%  Similarity=0.220  Sum_probs=53.3

Q ss_pred             CCCcEEEEecchhHHHHHHHHHHHc------CCceeeeecCCChHHHHHHHHhhhcCCeeEEEEecc
Q 037567          227 GAGSIIVYCMTIKDVEEISKALKQL------GVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMA  287 (374)
Q Consensus       227 ~~~~~lVf~~~~~~~~~l~~~l~~~------~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~  287 (374)
                      .+.+++|.+|++.-+.++++.++..      +..+..+||+++..++...++.+.+|+.+|+|+|+.
T Consensus       121 ~g~~aLVl~PTreLa~Qi~~~l~~l~~~~~~~v~v~~~~g~~s~~e~~~~~~~l~~g~~dILV~TPg  187 (1638)
T PRK14701        121 KGKKCYIILPTTLLVKQTVEKIESFCEKANLDVRLVYYHSNLRKKEKEEFLERIENGDFDILVTTAQ  187 (1638)
T ss_pred             cCCeEEEEECHHHHHHHHHHHHHHHHhhcCCceeEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECCc
Confidence            4668999999999999999998873      456788999999999988889999999999999983

>PRK13880 conjugal transfer coupling protein TraG; Provisional

Probab=91.31  E-value=0.34  Score=46.97  Aligned_cols=54  Identities=17%  Similarity=0.138  Sum_probs=39.4

Q ss_pred             CCEEEEccCCCCchhhhhcccccc-CCcEEEEcchHHHHHHHHHHHHH-cCCceEE
Q 037567           29 RDCLVVMATGSGKSLCYQLPPLVT-GKTALVVSPLISLMQDQVMSLKQ-RGINAEF   82 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~~l~~~~~-~~~~lil~P~~~l~~q~~~~~~~-~~~~~~~   82 (374)
                      .++++.||||||||..+.+|.+.. ...++|+=|..++...+....++ .|-.+.+
T Consensus       176 ~HvlviapTgSGKgvg~ViPnLL~~~~S~VV~D~KGE~~~~Tag~R~~~~G~~V~~  231 (636)
T PRK13880        176 EHVLTYAPTRSGKGVGLVVPTLLSWGHSSVITDLKGELWALTAGWRQKHAKNKVLR  231 (636)
T ss_pred             ceEEEEecCCCCCceEEEccchhhCCCCEEEEeCcHHHHHHHHHHHHHhCCCeEEE
Confidence            468999999999999988886654 56788888888887765555433 3444443

>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=91.25  E-value=0.14  Score=44.02  Aligned_cols=38  Identities=21%  Similarity=0.274  Sum_probs=24.0

Q ss_pred             CCCEEEEccCCCCchhhh--hccccccC-CcEEEEcchHHH
Q 037567           28 KRDCLVVMATGSGKSLCY--QLPPLVTG-KTALVVSPLISL   65 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~--~l~~~~~~-~~~lil~P~~~l   65 (374)
                      +.++++.|+||||||...  ++..+... .+++.+-...++
T Consensus       127 ~~~ili~G~tGSGKTT~l~all~~i~~~~~~iv~iEd~~E~  167 (270)
T PF00437_consen  127 RGNILISGPTGSGKTTLLNALLEEIPPEDERIVTIEDPPEL  167 (270)
T ss_dssp             TEEEEEEESTTSSHHHHHHHHHHHCHTTTSEEEEEESSS-S
T ss_pred             ceEEEEECCCccccchHHHHHhhhccccccceEEeccccce
Confidence            678899999999999653  22222234 566666555443

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 ....

>PRK09361 radB DNA repair and recombination protein RadB; Provisional

Probab=91.25  E-value=0.28  Score=40.81  Aligned_cols=42  Identities=14%  Similarity=0.208  Sum_probs=26.2

Q ss_pred             HHHHHHHc-----CCCEEEEccCCCCchhhhhccc---cccCCcEEEEcc
Q 037567           20 DVIQRIIE-----KRDCLVVMATGSGKSLCYQLPP---LVTGKTALVVSP   61 (374)
Q Consensus        20 ~~~~~~~~-----~~~~l~~a~tGsGKT~~~~l~~---~~~~~~~lil~P   61 (374)
                      ..++.++.     |.-+.+.|++|+|||...+..+   +..+.+++++.-
T Consensus        10 ~~lD~~l~GGi~~g~i~~i~G~~GsGKT~l~~~la~~~~~~~~~v~yi~~   59 (225)
T PRK09361         10 KMLDELLGGGFERGTITQIYGPPGSGKTNICLQLAVEAAKNGKKVIYIDT   59 (225)
T ss_pred             HHHHHHhcCCCCCCeEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEEC
Confidence            34556664     4456899999999995533222   234566766643

>TIGR02788 VirB11 P-type DNA transfer ATPase VirB11

Probab=91.24  E-value=0.3  Score=42.87  Aligned_cols=20  Identities=30%  Similarity=0.539  Sum_probs=16.7

Q ss_pred             HHcCCCEEEEccCCCCchhh
Q 037567           25 IIEKRDCLVVMATGSGKSLC   44 (374)
Q Consensus        25 ~~~~~~~l~~a~tGsGKT~~   44 (374)
                      +..+.++++.||||||||..
T Consensus       141 v~~~~~ili~G~tGsGKTTl  160 (308)
T TIGR02788       141 IASRKNIIISGGTGSGKTTF  160 (308)
T ss_pred             hhCCCEEEEECCCCCCHHHH
Confidence            33578999999999999964

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.

>PRK13876 conjugal transfer coupling protein TraG; Provisional

Probab=91.18  E-value=0.31  Score=47.28  Aligned_cols=49  Identities=24%  Similarity=0.153  Sum_probs=39.5

Q ss_pred             CCEEEEccCCCCchhhhhcccccc-CCcEEEEcchHHHHHHHHHHHHHcC
Q 037567           29 RDCLVVMATGSGKSLCYQLPPLVT-GKTALVVSPLISLMQDQVMSLKQRG   77 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~~l~~~~~-~~~~lil~P~~~l~~q~~~~~~~~~   77 (374)
                      .++++.||||||||..+.+|.+.. ...++|+=|..++...+....++.|
T Consensus       145 ~hvLviApTrSGKgvg~VIPnLL~~~~S~VV~D~KGEl~~~Ta~~R~~~G  194 (663)
T PRK13876        145 EHVLCFAPTRSGKGVGLVVPTLLTWPGSAIVHDIKGENWQLTAGFRARFG  194 (663)
T ss_pred             ceEEEEecCCCCcceeEehhhHHhCCCCEEEEeCcchHHHHHHHHHHhCC
Confidence            578999999999999988886654 5578888888888887777766665

>TIGR02533 type_II_gspE general secretory pathway protein E

Probab=91.11  E-value=0.24  Score=46.36  Aligned_cols=32  Identities=31%  Similarity=0.433  Sum_probs=23.6

Q ss_pred             CchhHHHHHHHHHcCC-C-EEEEccCCCCchhhh
Q 037567           14 FRPYQKDVIQRIIEKR-D-CLVVMATGSGKSLCY   45 (374)
Q Consensus        14 ~~~~Q~~~~~~~~~~~-~-~l~~a~tGsGKT~~~   45 (374)
                      +.+.|.+.+..+.... . +++.||||||||.+.
T Consensus       226 ~~~~~~~~l~~~~~~~~GlilitGptGSGKTTtL  259 (486)
T TIGR02533       226 MSPELLSRFERLIRRPHGIILVTGPTGSGKTTTL  259 (486)
T ss_pred             CCHHHHHHHHHHHhcCCCEEEEEcCCCCCHHHHH
Confidence            4566777777766543 3 579999999999654

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.

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

Probab=91.09  E-value=1.5  Score=41.51  Aligned_cols=67  Identities=22%  Similarity=0.385  Sum_probs=51.4

Q ss_pred             EEEEecchhHHHHHHHHHHHc-----CCceeeeecCCChHHHHHHHHhhhcCCeeEEEEec-----ccccc-ccccCccE
Q 037567          231 IIVYCMTIKDVEEISKALKQL-----GVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATM-----AFGMG-IDKPDVRH  299 (374)
Q Consensus       231 ~lVf~~~~~~~~~l~~~l~~~-----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~-----~~~~G-~d~~~~~~  299 (374)
                      +||.+||++-|.++++.+...     ++.+..++|+.+...+...++   .| .+|+|+|+     .+..| +|+..+.+
T Consensus       102 aLil~PTRELA~Qi~~~~~~~~~~~~~~~~~~i~GG~~~~~q~~~l~---~~-~~ivVaTPGRllD~i~~~~l~l~~v~~  177 (513)
T COG0513         102 ALILAPTRELAVQIAEELRKLGKNLGGLRVAVVYGGVSIRKQIEALK---RG-VDIVVATPGRLLDLIKRGKLDLSGVET  177 (513)
T ss_pred             eEEECCCHHHHHHHHHHHHHHHhhcCCccEEEEECCCCHHHHHHHHh---cC-CCEEEECccHHHHHHHcCCcchhhcCE
Confidence            899999999999999888763     466789999988766554444   46 89999997     34444 67777777


Q ss_pred             EE
Q 037567          300 VI  301 (374)
Q Consensus       300 vi  301 (374)
                      +|
T Consensus       178 lV  179 (513)
T COG0513         178 LV  179 (513)
T ss_pred             EE
Confidence            66

>KOG0727 consensus 26S proteasome regulatory complex, ATPase RPT3 [Posttranslational modification, protein turnover, chaperones]

Probab=91.09  E-value=1.5  Score=36.44  Aligned_cols=28  Identities=25%  Similarity=0.367  Sum_probs=19.1

Q ss_pred             HHHHHHHHHc--CCCEEEEccCCCCchhhh
Q 037567           18 QKDVIQRIIE--KRDCLVVMATGSGKSLCY   45 (374)
Q Consensus        18 Q~~~~~~~~~--~~~~l~~a~tGsGKT~~~   45 (374)
                      |.+.+.++--  .+.+++.+|+|+|||...
T Consensus       177 ~~~ly~qigidpprgvllygppg~gktml~  206 (408)
T KOG0727|consen  177 HADLYKQIGIDPPRGVLLYGPPGTGKTMLA  206 (408)
T ss_pred             HHHHHHHhCCCCCcceEEeCCCCCcHHHHH
Confidence            3444444322  467899999999999753

>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=91.09  E-value=0.2  Score=40.58  Aligned_cols=19  Identities=21%  Similarity=0.385  Sum_probs=13.7

Q ss_pred             cCCCEEEEccCCCCchhhh
Q 037567           27 EKRDCLVVMATGSGKSLCY   45 (374)
Q Consensus        27 ~~~~~l~~a~tGsGKT~~~   45 (374)
                      .++++++.+|+|+|||..+
T Consensus        21 G~h~lLl~GppGtGKTmlA   39 (206)
T PF01078_consen   21 GGHHLLLIGPPGTGKTMLA   39 (206)
T ss_dssp             CC--EEEES-CCCTHHHHH
T ss_pred             CCCCeEEECCCCCCHHHHH
Confidence            4689999999999999654

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.

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

Probab=91.09  E-value=0.18  Score=39.78  Aligned_cols=45  Identities=16%  Similarity=0.100  Sum_probs=31.1

Q ss_pred             EEEEccCCCCchhhhhccccccCCcEEEEcchHHHHHHHHHHHHH
Q 037567           31 CLVVMATGSGKSLCYQLPPLVTGKTALVVSPLISLMQDQVMSLKQ   75 (374)
Q Consensus        31 ~l~~a~tGsGKT~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~   75 (374)
                      +++.|++|||||..+.-.+...+.+++++.-...+-.++.+.+..
T Consensus         2 ~li~G~~~sGKS~~a~~~~~~~~~~~~y~at~~~~d~em~~rI~~   46 (169)
T cd00544           2 ILVTGGARSGKSRFAERLAAELGGPVTYIATAEAFDDEMAERIAR   46 (169)
T ss_pred             EEEECCCCCCHHHHHHHHHHhcCCCeEEEEccCcCCHHHHHHHHH
Confidence            478999999999655444444566888887776665555555443

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

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

Probab=91.08  E-value=0.39  Score=48.17  Aligned_cols=135  Identities=13%  Similarity=0.136  Sum_probs=79.2

Q ss_pred             CEEEEccCCCCchhhhhccccc-----cCCcEEEEcchHHHHHHHHHHHHH----------c-C--CceEEcCCCCC---
Q 037567           30 DCLVVMATGSGKSLCYQLPPLV-----TGKTALVVSPLISLMQDQVMSLKQ----------R-G--INAEFLGSAQT---   88 (374)
Q Consensus        30 ~~l~~a~tGsGKT~~~~l~~~~-----~~~~~lil~P~~~l~~q~~~~~~~----------~-~--~~~~~~~~~~~---   88 (374)
                      ++.+.++||+|||.+|+-.++.     ...++||+||+.++.+.+...+..          + +  +...++.+...   
T Consensus        61 n~~~~M~TGtGKT~~~~~~i~~l~~~~~~~~fii~vp~~aI~egv~~~l~s~~~k~hF~~~y~~~~~~~~~~~S~k~~k~  140 (986)
T PRK15483         61 NIDIKMETGTGKTYVYTRLMYELHQKYGLFKFIIVVPTPAIKEGTRNFIQSDYAKQHFSQFYENTRIELYVINAGDKKKS  140 (986)
T ss_pred             eEEEEeCCCCCHHHHHHHHHHHHHHHcCCcEEEEEeCCHHHHHHHHHHhhHHHHHHHHHHHcCCceeEEEEEecCccccc
Confidence            6789999999999988766654     356799999999988776655431          1 1  22223332210   


Q ss_pred             -----chhhhhh-----hhcCCeeEEEEcCcccccCch--h------------hHHHHHhcCccEEEEeccchhhcccCc
Q 037567           89 -----DSSVQTK-----AETGYFQLLFMTPEKACIIPI--S------------FWSKLLKAGVCLFAVDEAHCISEWGHD  144 (374)
Q Consensus        89 -----~~~~~~~-----~~~~~~~i~i~T~~~l~~~~~--~------------~~~~~~~~~~~~vviDE~h~~~~~~~~  144 (374)
                           ......-     .......|+++|.+.+..-..  .            .+..+... --+||+||.|++...+  
T Consensus       141 gr~~~~~~i~~Fa~~~~~~~~~I~Ilv~niqa~n~~~~~~~~~D~~l~~g~~~p~~~i~~~-~PivIiDEPh~~~~~~--  217 (986)
T PRK15483        141 GRKNFPAQLSNFVKASRQNSNTIHVLLINAGMLNSASMTRDDYDQTLLGGFTSPVDALAAT-RPVVIIDEPHRFPRDN--  217 (986)
T ss_pred             ccccChHHHHHHHhccccCCCceEEEEEehHHhcccccccchhhhhhccCCCChHHHHHhC-CCEEEEECCCCCCcch--
Confidence                 0110000     112257999999998865321  1            11111111 2379999999985422  


Q ss_pred             chHHHHHHHHHHHhcCCCCeeEEEeecCc
Q 037567          145 FRLEYKQLDKLRTFLLGVPFVALTATATE  173 (374)
Q Consensus       145 ~~~~~~~~~~~~~~~~~~~~i~~SaT~~~  173 (374)
                           ..+..+ ..+.+..++-+|||.+.
T Consensus       218 -----k~~~~i-~~lnpl~~lrysAT~~~  240 (986)
T PRK15483        218 -----KFYQAI-EALKPQMIIRFGATFPD  240 (986)
T ss_pred             -----HHHHHH-HhcCcccEEEEeeecCC
Confidence                 223333 33334557889999876

>KOG1806 consensus DEAD box containing helicases [Replication, recombination and repair]

Probab=91.02  E-value=0.34  Score=47.99  Aligned_cols=68  Identities=19%  Similarity=0.232  Sum_probs=53.1

Q ss_pred             CCchhHHHHHHHHHcCCCEEEEccCCCCchhhhh--cccc---ccCCcEEEEcchHHHHHHHHHHHHHcCCce
Q 037567           13 VFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQ--LPPL---VTGKTALVVSPLISLMQDQVMSLKQRGINA   80 (374)
Q Consensus        13 ~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~--l~~~---~~~~~~lil~P~~~l~~q~~~~~~~~~~~~   80 (374)
                      .++|-|-+++..-.+.....+.+|+|+|||-...  +..+   ....+++|++.+..-.+|.++...+.....
T Consensus       738 ~ft~~qveai~sg~qpgltmvvgppgtgktd~avqil~~lyhn~p~qrTlivthsnqaln~lfeKi~~~d~d~  810 (1320)
T KOG1806|consen  738 KFTPTQVEAILSGMQPGLTMVVGPPGTGKTDVAVQILSVLYHNSPNQRTLIVTHSNQALNQLFEKIMALDVDE  810 (1320)
T ss_pred             ccCHHHHHHHHhcCCCCceeeecCCCCCCcchhhhhhhhhhhcCCCcceEEEEecccchhHHHHHHHhcccch
Confidence            5688899998887788899999999999995432  2222   257899999999999999988887654433

>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=90.99  E-value=0.12  Score=39.24  Aligned_cols=16  Identities=31%  Similarity=0.414  Sum_probs=13.6

Q ss_pred             CEEEEccCCCCchhhh
Q 037567           30 DCLVVMATGSGKSLCY   45 (374)
Q Consensus        30 ~~l~~a~tGsGKT~~~   45 (374)
                      ++++.||+|+|||..+
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            4789999999999654

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.

>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=90.96  E-value=0.14  Score=37.82  Aligned_cols=15  Identities=33%  Similarity=0.368  Sum_probs=12.9

Q ss_pred             EEEEccCCCCchhhh
Q 037567           31 CLVVMATGSGKSLCY   45 (374)
Q Consensus        31 ~l~~a~tGsGKT~~~   45 (374)
                      ++|.|++|||||..+
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            578999999999754

...

>COG4185 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=90.90  E-value=0.2  Score=38.35  Aligned_cols=37  Identities=22%  Similarity=0.153  Sum_probs=25.8

Q ss_pred             EEEEccCCCCchhhhhccccccCCcEEEEcchHHHHHH
Q 037567           31 CLVVMATGSGKSLCYQLPPLVTGKTALVVSPLISLMQD   68 (374)
Q Consensus        31 ~l~~a~tGsGKT~~~~l~~~~~~~~~lil~P~~~l~~q   68 (374)
                      .++.+|.|||||..+......-.+ .++++...+++.|
T Consensus         5 ~IvaG~NGsGKstv~~~~~~~~~~-~~~~VN~D~iA~~   41 (187)
T COG4185           5 DIVAGPNGSGKSTVYASTLAPLLP-GIVFVNADEIAAQ   41 (187)
T ss_pred             EEEecCCCCCceeeeeccchhhcC-CeEEECHHHHhhh
Confidence            478899999999877655444333 6666677677654

>PRK08760 replicative DNA helicase; Provisional

Probab=90.87  E-value=1.2  Score=41.62  Aligned_cols=47  Identities=15%  Similarity=0.015  Sum_probs=28.4

Q ss_pred             CCEEEEccCCCCchhhhhcc---c-cccCCcEEEEcchHHHHHHHHHHHHHc
Q 037567           29 RDCLVVMATGSGKSLCYQLP---P-LVTGKTALVVSPLISLMQDQVMSLKQR   76 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~~l~---~-~~~~~~~lil~P~~~l~~q~~~~~~~~   76 (374)
                      .-++|.|.||+|||...+-.   + ...+.++++++.- .-..|+...+...
T Consensus       230 ~LivIaarPg~GKTafal~iA~~~a~~~g~~V~~fSlE-Ms~~ql~~Rl~a~  280 (476)
T PRK08760        230 DLIILAARPAMGKTTFALNIAEYAAIKSKKGVAVFSME-MSASQLAMRLISS  280 (476)
T ss_pred             ceEEEEeCCCCChhHHHHHHHHHHHHhcCCceEEEecc-CCHHHHHHHHHHh
Confidence            34577888999999654322   2 2346678777654 3345566665543

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

Probab=90.87  E-value=0.25  Score=45.10  Aligned_cols=30  Identities=17%  Similarity=0.381  Sum_probs=23.9

Q ss_pred             hHHHHHHHHHcCCCEEEEccCCCCchhhhh
Q 037567           17 YQKDVIQRIIEKRDCLVVMATGSGKSLCYQ   46 (374)
Q Consensus        17 ~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~   46 (374)
                      .....+..+..++++++.||+|+|||..+.
T Consensus       183 ~le~l~~~L~~~~~iil~GppGtGKT~lA~  212 (459)
T PRK11331        183 TIETILKRLTIKKNIILQGPPGVGKTFVAR  212 (459)
T ss_pred             HHHHHHHHHhcCCCEEEECCCCCCHHHHHH
Confidence            445666677779999999999999997653

>PF01637 Arch_ATPase: Archaeal ATPase; InterPro: IPR011579 This domain has been found in a number of bacterial and archaeal proteins, all of which contain a conserved P-loop motif that is involved in binding ATP

Probab=90.87  E-value=0.35  Score=40.23  Aligned_cols=17  Identities=29%  Similarity=0.368  Sum_probs=14.4

Q ss_pred             CCCEEEEccCCCCchhh
Q 037567           28 KRDCLVVMATGSGKSLC   44 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~   44 (374)
                      ++.+++.||.|+|||..
T Consensus        20 ~~~~~l~G~rg~GKTsL   36 (234)
T PF01637_consen   20 SQHILLYGPRGSGKTSL   36 (234)
T ss_dssp             SSEEEEEESTTSSHHHH
T ss_pred             CcEEEEEcCCcCCHHHH
Confidence            46788999999999964

; GO: 0005524 ATP binding; PDB: 2FNA_A 2QEN_A.

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

Probab=90.81  E-value=0.39  Score=40.55  Aligned_cols=20  Identities=25%  Similarity=0.293  Sum_probs=17.0

Q ss_pred             HHcCCCEEEEccCCCCchhh
Q 037567           25 IIEKRDCLVVMATGSGKSLC   44 (374)
Q Consensus        25 ~~~~~~~l~~a~tGsGKT~~   44 (374)
                      +..|+.+++.+|.|+|||..
T Consensus        13 i~~Gqr~~I~G~~G~GKTTL   32 (249)
T cd01128          13 IGKGQRGLIVAPPKAGKTTL   32 (249)
T ss_pred             cCCCCEEEEECCCCCCHHHH
Confidence            34688999999999999964

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

>smart00488 DEXDc2 DEAD-like helicases superfamily

Probab=90.78  E-value=0.11  Score=45.11  Aligned_cols=41  Identities=12%  Similarity=0.059  Sum_probs=26.5

Q ss_pred             CCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhc
Q 037567           99 GYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISE  140 (374)
Q Consensus        99 ~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~  140 (374)
                      ...+|+|+++..|..-..+......+ ...++||||||++.+
T Consensus       210 ~~Adivi~ny~yll~~~~r~~~~~~l-~~~~lIiDEAHnL~d  250 (289)
T smart00488      210 EFANVVVLPYQYLLDPKIRQALSIEL-KDSIVIFDEAHNLDN  250 (289)
T ss_pred             hcCCEEEECHHHHhcHHHHHHhcccc-cccEEEEeCccChHH
Confidence            35689999998776543221101112 356899999999975

>smart00489 DEXDc3 DEAD-like helicases superfamily

Probab=90.78  E-value=0.11  Score=45.11  Aligned_cols=41  Identities=12%  Similarity=0.059  Sum_probs=26.5

Q ss_pred             CCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhc
Q 037567           99 GYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISE  140 (374)
Q Consensus        99 ~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~  140 (374)
                      ...+|+|+++..|..-..+......+ ...++||||||++.+
T Consensus       210 ~~Adivi~ny~yll~~~~r~~~~~~l-~~~~lIiDEAHnL~d  250 (289)
T smart00489      210 EFANVVVLPYQYLLDPKIRQALSIEL-KDSIVIFDEAHNLDN  250 (289)
T ss_pred             hcCCEEEECHHHHhcHHHHHHhcccc-cccEEEEeCccChHH
Confidence            35689999998776543221101112 356899999999975

>PF13555 AAA_29: P-loop containing region of AAA domain

Probab=90.72  E-value=0.18  Score=32.04  Aligned_cols=18  Identities=33%  Similarity=0.327  Sum_probs=14.6

Q ss_pred             CCCEEEEccCCCCchhhh
Q 037567           28 KRDCLVVMATGSGKSLCY   45 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~   45 (374)
                      +...++.+|+|+|||..+
T Consensus        23 g~~tli~G~nGsGKSTll   40 (62)
T PF13555_consen   23 GDVTLITGPNGSGKSTLL   40 (62)
T ss_pred             CcEEEEECCCCCCHHHHH
Confidence            346899999999999653

>PRK13531 regulatory ATPase RavA; Provisional

Probab=90.71  E-value=0.25  Score=45.53  Aligned_cols=26  Identities=15%  Similarity=0.162  Sum_probs=20.7

Q ss_pred             HHHHHHHcCCCEEEEccCCCCchhhh
Q 037567           20 DVIQRIIEKRDCLVVMATGSGKSLCY   45 (374)
Q Consensus        20 ~~~~~~~~~~~~l~~a~tGsGKT~~~   45 (374)
                      .+...++.+.++++.||+|+|||..+
T Consensus        31 lll~aalag~hVLL~GpPGTGKT~LA   56 (498)
T PRK13531         31 LCLLAALSGESVFLLGPPGIAKSLIA   56 (498)
T ss_pred             HHHHHHccCCCEEEECCCChhHHHHH
Confidence            34445567899999999999999765

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	374
1oyy_A	523	Structure Of The Recq Catalytic Core Bound To Atp-G		7e-79
1oyw_A	523	Structure Of The Recq Catalytic Core Length = 523		5e-76
2v1x_A	591	Crystal Structure Of Human Recq-Like Dna Helicase L		1e-69
1hv8_A	367	Crystal Structure Of A Dead Box Protein From The Hy		2e-15
2j0u_B	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		7e-10
2j0u_A	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		8e-10
2hxy_A	391	Crystal Structure Of Human Apo-Eif4aiii Length = 39		9e-10
2xb2_A	411	Crystal Structure Of The Core Mago-Y14-Eif4aiii-Bar		9e-10
2hyi_C	413	Structure Of The Human Exon Junction Complex With A		9e-10
2j0q_A	410	The Crystal Structure Of The Exon Junction Complex		9e-10
2hjv_A	163	Structure Of The Second Domain (Residues 207-368) O		1e-09
1s2m_A	400	Crystal Structure Of The Dead Box Protein Dhh1p Len		3e-09
3i32_A	300	Dimeric Structure Of A Hera Helicase Fragment Inclu		3e-09
3eaq_A	212	Novel Dimerization Motif In The Dead Box Rna Helica		1e-08
2jgn_A	185	Ddx3 Helicase Domain Length = 185		3e-08
2z0m_A	337	Crystal Structure Of Hypothetical Atp-Dependent Rna		4e-08
2i4i_A	417	Crystal Structure Of Human Dead-Box Rna Helicase Dd		4e-08
2yjt_D	170	Crystal Structure Of E. Coli Dead-Box Protein Srmb		6e-08
2p6n_A	191	Human Dead-box Rna Helicase Ddx41, Helicase Domain		1e-07
2db3_A	434	Structural Basis For Rna Unwinding By The Dead-Box		2e-07
2wax_A	193	Structure Of The Human Ddx6 C-Terminal Domain In Co		6e-07
3pew_A	395	S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3		2e-05
2vso_A	395	Crystal Structure Of A Translation Initiation Compl		2e-05
3sqx_A	512	Structure Of Mss116p (Nte And C-Tail Double Deletio		4e-05
4db4_A	256	Mss116p Dead-Box Helicase Domain 2 Bound To A Chima		4e-05
4db2_C	257	Mss116p Dead-Box Helicase Domain 2 Bound To An Rna		4e-05
3i5x_A	563	Structure Of Mss116p Bound To Ssrna And Amp-Pnp Len		4e-05
3pey_A	395	S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3 Length		4e-05
4db2_A	257	Mss116p Dead-Box Helicase Domain 2 Bound To An Rna		4e-05
3sqw_A	579	Structure Of Mss116p (Nte Deletion) Bound To Ssrna		5e-05
1xti_A	391	Structure Of Wildtype Human Uap56 Length = 391		1e-04
1t5i_A	172	Crystal Structure Of The C-Terminal Domain Of Uap56		1e-04
1xtj_A	386	Structure Of Human Uap56 In Complex With Adp Length		1e-04
1xtk_A	390	Structure Of Decd To Dead Mutation Of Human Uap56 L		1e-04
3peu_A	188	S. Cerevisiae Dbp5 L327v C-Terminal Domain Bound To		1e-04
3gfp_A	189	Structure Of The C-Terminal Domain Of The Dead-Box		2e-04
2kbf_A	187	Solution Structure Of Carboxyl-Terminal Domain Of D		2e-04
2eyq_A	1151	Crystal Structure Of Escherichia Coli Transcription		6e-04
1fuk_A	165	Crystal Structure Of The Carboxy Terminal Domain Of		7e-04

>pdb|1OYY|A Chain A, Structure Of The Recq Catalytic Core Bound To Atp-Gamma-S Length = 523

Iteration: 1
 Score =  290 bits (743), Expect = 7e-79,   Method: Compositional matrix adjust.
 Identities = 156/374 (41%), Positives = 225/374 (60%), Gaps = 12/374 (3%)
Query: 5   LKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVTGKTALVVSPLIS 64
           L++ FGY  FRP Q+++I  ++  RDCLVVM TG GKSLCYQ+P L+     +VVSPLIS
Sbjct: 17  LQETFGYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPALLLNGLTVVVSPLIS 76
Query: 65  LMQDQVMSLKQRGINAEFLGSAQTDS---SVQTKAETGYFQLLFMTPEKACIIPISFWSK 121
           LM+DQV  L+  G+ A  L S QT      V T   TG  +LL++ PE+  ++  +F   
Sbjct: 77  LMKDQVDQLQANGVAAACLNSTQTREQQLEVMTGCRTGQIRLLYIAPER--LMLDNFLEH 134
Query: 122 LLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEKVRIDIIN 181
           L      L AVDEAHCIS+WGHDFR EY  L +LR     +PF+ALTATA +  R DI+ 
Sbjct: 135 LAHWNPVLLAVDEAHCISQWGHDFRPEYAALGQLRQRFPTLPFMALTATADDTTRQDIVR 194
Query: 182 SLKLKNPYVTIASFDRKNLFYGVKVINRGQSFVDELVQEILKSVAGAGSIIVYCMTIKDV 241
            L L +P + I+SFDR N+ Y   ++      +D+L++ + +    +G  I+YC +   V
Sbjct: 195 LLGLNDPLIQISSFDRPNIRY---MLMEKFKPLDQLMRYVQEQRGKSG--IIYCNSRAKV 249
Query: 242 EEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVI 301
           E+ +  L+  G+ A  YH  + +  R +    F RD+++++VAT+AFGMGI+KP+VR V+
Sbjct: 250 EDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGMGINKPNVRFVV 309
Query: 302 HYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFYCGESQTENQRTAIMESLL 361
           H+  P+ +ESYYQE+GR GRDG+ +   L+Y  ++ A     C E + + Q   I    L
Sbjct: 310 HFDIPRNIESYYQETGRAGRDGLPAEAMLFYDPADMAWLR-RCLEEKPQGQLQDIERHKL 368
Query: 362 AAQ-RYCLLTTCRR 374
            A   +    TCRR
Sbjct: 369 NAMGAFAEAQTCRR 382

>pdb|1OYW|A Chain A, Structure Of The Recq Catalytic Core Length = 523

Iteration: 1
 Score =  281 bits (718), Expect = 5e-76,   Method: Compositional matrix adjust.
 Identities = 154/376 (40%), Positives = 220/376 (58%), Gaps = 16/376 (4%)
Query: 5   LKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVTGKTALVVSPLIS 64
           L++ FGY  FRP Q+++I  ++  RDCLVV  TG GKSLCYQ+P L+     +VVSPLIS
Sbjct: 17  LQETFGYQQFRPGQEEIIDTVLSGRDCLVVXPTGGGKSLCYQIPALLLNGLTVVVSPLIS 76
Query: 65  LMQDQVMSLKQRGINAEFLGSAQTDS---SVQTKAETGYFQLLFMTPEKACIIPISFWSK 121
           L +DQV  L+  G+ A  L S QT      V T   TG  +LL++ PE+  +   +F   
Sbjct: 77  LXKDQVDQLQANGVAAACLNSTQTREQQLEVXTGCRTGQIRLLYIAPERLXLD--NFLEH 134
Query: 122 LLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEKVRIDIIN 181
           L      L AVDEAHCIS+WGHDFR EY  L +LR     +PF ALTATA +  R DI+ 
Sbjct: 135 LAHWNPVLLAVDEAHCISQWGHDFRPEYAALGQLRQRFPTLPFXALTATADDTTRQDIVR 194
Query: 182 SLKLKNPYVTIASFDRKNLFYGVKVINRGQSF--VDELVQEILKSVAGAGSIIVYCMTIK 239
            L L +P + I+SFDR N+ Y +      + F  +D+L + + +    +G  I+YC +  
Sbjct: 195 LLGLNDPLIQISSFDRPNIRYXLX-----EKFKPLDQLXRYVQEQRGKSG--IIYCNSRA 247
Query: 240 DVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRH 299
            VE+ +  L+  G+ A  YH  + +  R +    F RD+++++VAT+AFG GI+KP+VR 
Sbjct: 248 KVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGXGINKPNVRF 307
Query: 300 VIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFYCGESQTENQRTAI-ME 358
           V+H+  P+ +ESYYQE+GR GRDG+ +   L+Y  ++ A     C E + + Q   I   
Sbjct: 308 VVHFDIPRNIESYYQETGRAGRDGLPAEAXLFYDPADXAWLR-RCLEEKPQGQLQDIERH 366
Query: 359 SLLAAQRYCLLTTCRR 374
            L A   +    TCRR
Sbjct: 367 KLNAXGAFAEAQTCRR 382

>pdb|2V1X|A Chain A, Crystal Structure Of Human Recq-Like Dna Helicase Length = 591

Iteration: 1
 Score =  259 bits (663), Expect = 1e-69,   Method: Compositional matrix adjust.
 Identities = 143/341 (41%), Positives = 204/341 (59%), Gaps = 16/341 (4%)
Query: 5   LKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVTGKTALVVSPLIS 64
           L+  F    FRP Q + I   +  ++  +VM TG GKSLCYQLP L +    LV+ PLIS
Sbjct: 36  LQNVFKLEKFRPLQLETINVTMAGKEVFLVMPTGGGKSLCYQLPALCSDGFTLVICPLIS 95
Query: 65  LMQDQVMSLKQRGINAEFLGSAQTDSSVQ-TKAE----TGYFQLLFMTPEKACIIPISFW 119
           LM+DQ+M LKQ GI+A  L ++ +   V+   AE        +L+++TPEK     + F 
Sbjct: 96  LMEDQLMVLKQLGISATMLNASSSKEHVKWVHAEMVNKNSELKLIYVTPEKIAKSKM-FM 154
Query: 120 SKLLKA----GVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEKV 175
           S+L KA         AVDE HC S+WGHDFR +YK L  L+        + LTATAT  V
Sbjct: 155 SRLEKAYEARRFTRIAVDEVHCCSQWGHDFRPDYKALGILKRQFPNASLIGLTATATNHV 214
Query: 176 RIDIINSLKLKNPYVTIASFDRKNLFYGVKVINRGQSFVDELVQEILKSVAG---AGSII 232
             D    L ++  +   ASF+R NL+Y V+   +  S  ++ +++I+K + G     S I
Sbjct: 215 LTDAQKILCIEKCFTFTASFNRPNLYYEVR---QKPSNTEDFIEDIVKLINGRYKGQSGI 271
Query: 233 VYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGI 292
           +YC + KD E+++ +L+ LG+ AG YH  +  + +   HR +  +EI+V+VAT+AFGMGI
Sbjct: 272 IYCFSQKDSEQVTVSLQNLGIHAGAYHANLEPEDKTTVHRKWSANEIQVVVATVAFGMGI 331
Query: 293 DKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYA 333
           DKPDVR VIH+   K++E+YYQESGR GRD + + C LYY 
Sbjct: 332 DKPDVRFVIHHSMSKSMENYYQESGRAGRDDMKADCILYYG 372

>pdb|1HV8|A Chain A, Crystal Structure Of A Dead Box Protein From The Hyperthermophile Methanococcus Jannaschii Length = 367

Iteration: 1
 Score = 80.1 bits (196), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 37/92 (40%), Positives = 55/92 (59%)
Query: 232 IVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMG 291
           +V+C T +D +E++  L+ +G KAG  HG +    RE+  RLF + +IR+++AT     G
Sbjct: 242 LVFCKTKRDTKELASXLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATDVXSRG 301
Query: 292 IDKPDVRHVIHYGCPKTLESYYQESGRCGRDG 323
           ID  D+  VI+Y  P+  ESY    GR GR G
Sbjct: 302 IDVNDLNCVINYHLPQNPESYXHRIGRTGRAG 333

>pdb|2J0U|B Chain B, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0 A Resolution Length = 374

Iteration: 1
 Score = 61.6 bits (148), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 32/110 (29%), Positives = 52/110 (47%), Gaps = 6/110 (5%)
Query: 232 IVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMG 291
           +++C T + V+ +++ +++      + HG M  K RE   + F     RV+++T  +  G
Sbjct: 244 VIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARG 303
Query: 292 IDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGD 341
           +D P V  +I+Y  P   E Y    GR GR G   V        NF K D
Sbjct: 304 LDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVA------VNFVKND 347

>pdb|2J0U|A Chain A, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0 A Resolution Length = 374

Iteration: 1
 Score = 61.2 bits (147), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 32/110 (29%), Positives = 52/110 (47%), Gaps = 6/110 (5%)
Query: 232 IVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMG 291
           +++C T + V+ +++ +++      + HG M  K RE   + F     RV+++T  +  G
Sbjct: 244 VIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARG 303
Query: 292 IDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGD 341
           +D P V  +I+Y  P   E Y    GR GR G   V        NF K D
Sbjct: 304 LDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVA------VNFVKND 347

>pdb|2HXY|A Chain A, Crystal Structure Of Human Apo-Eif4aiii Length = 391

Iteration: 1
 Score = 61.2 bits (147), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 32/110 (29%), Positives = 52/110 (47%), Gaps = 6/110 (5%)
Query: 232 IVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMG 291
           +++C T + V+ +++ +++      + HG M  K RE   + F     RV+++T  +  G
Sbjct: 259 VIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARG 318
Query: 292 IDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGD 341
           +D P V  +I+Y  P   E Y    GR GR G   V        NF K D
Sbjct: 319 LDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAI------NFVKND 362

>pdb|2XB2|A Chain A, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz- Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd Machinery Length = 411

Iteration: 1
 Score = 61.2 bits (147), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 32/110 (29%), Positives = 52/110 (47%), Gaps = 6/110 (5%)
Query: 232 IVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMG 291
           +++C T + V+ +++ +++      + HG M  K RE   + F     RV+++T  +  G
Sbjct: 281 VIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARG 340
Query: 292 IDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGD 341
           +D P V  +I+Y  P   E Y    GR GR G   V        NF K D
Sbjct: 341 LDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAI------NFVKND 384

>pdb|2HYI|C Chain C, Structure Of The Human Exon Junction Complex With A Trapped Dead-Box Helicase Bound To Rna Length = 413

Iteration: 1
 Score = 61.2 bits (147), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 32/110 (29%), Positives = 52/110 (47%), Gaps = 6/110 (5%)
Query: 232 IVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMG 291
           +++C T + V+ +++ +++      + HG M  K RE   + F     RV+++T  +  G
Sbjct: 281 VIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARG 340
Query: 292 IDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGD 341
           +D P V  +I+Y  P   E Y    GR GR G   V        NF K D
Sbjct: 341 LDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAI------NFVKND 384

>pdb|2J0Q|A Chain A, The Crystal Structure Of The Exon Junction Complex At 3.2 A Resolution Length = 410

Iteration: 1
 Score = 61.2 bits (147), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 32/110 (29%), Positives = 52/110 (47%), Gaps = 6/110 (5%)
Query: 232 IVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMG 291
           +++C T + V+ +++ +++      + HG M  K RE   + F     RV+++T  +  G
Sbjct: 280 VIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARG 339
Query: 292 IDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGD 341
           +D P V  +I+Y  P   E Y    GR GR G   V        NF K D
Sbjct: 340 LDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAI------NFVKND 383

>pdb|2HJV|A Chain A, Structure Of The Second Domain (Residues 207-368) Of The Bacillus Subtilis Yxin Protein Length = 163

Iteration: 1
 Score = 60.5 bits (145), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 40/131 (30%), Positives = 62/131 (47%), Gaps = 3/131 (2%)
Query: 193 ASFDRKNLFYGVKVINRGQSFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLG 252
           A    +N+ + V  +     F   L++++L +     S I++C T + V +++  L  LG
Sbjct: 3   AGLTTRNIEHAVIQVREENKF--SLLKDVLMT-ENPDSCIIFCRTKEHVNQLTDELDDLG 59
Query: 253 VKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESY 312
                 HG M  + R +    F R E R +VAT     GID  ++  VI+Y  P   ESY
Sbjct: 60  YPCDKIHGGMIQEDRFDVMNEFKRGEYRYLVATDVAARGIDIENISLVINYDLPLEKESY 119
Query: 313 YQESGRCGRDG 323
              +GR GR G
Sbjct: 120 VHRTGRTGRAG 130

>pdb|1S2M|A Chain A, Crystal Structure Of The Dead Box Protein Dhh1p Length = 400

Iteration: 1
 Score = 59.7 bits (143), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 82/331 (24%), Positives = 133/331 (40%), Gaps = 34/331 (10%)
Query: 10  GYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLP------PLVTGKTALVVSPL- 62
           G+    P Q++ I   I  RD L     G+GK+  + +P      P +    AL++ P  
Sbjct: 40  GFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEKVKPKLNKIQALIMVPTR 99
Query: 63  -ISLMQDQVMSL--KQRGINAEFL-GSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISF 118
            ++L   QV+    K  GI+     G       +    ET    +L  TP +   +    
Sbjct: 100 ELALQTSQVVRTLGKHCGISCMVTTGGTNLRDDILRLNET--VHILVGTPGRVLDLASRK 157
Query: 119 WSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEKVRID 178
            + L  +   LF +DEA  +     DF+   +Q+       L     +L  +AT  + + 
Sbjct: 158 VADL--SDCSLFIMDEADKM--LSRDFKTIIEQI----LSFLPPTHQSLLFSATFPLTVK 209
Query: 179 IINSLKLKNPYVTIASFDRKNLF--YGVKVINRGQSFVDELVQ----EILKSVAGAGSII 232
                 L  PY         NL     +K I +  +FV+E  +      L S       I
Sbjct: 210 EFMVKHLHKPY-------EINLMEELTLKGITQYYAFVEERQKLHCLNTLFSKLQINQAI 262
Query: 233 VYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGI 292
           ++C +   VE ++K +  LG      H +M  + R +    F + ++R +V +     GI
Sbjct: 263 IFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSDLLTRGI 322
Query: 293 DKPDVRHVIHYGCPKTLESYYQESGRCGRDG 323
           D   V  VI++  PKT E+Y    GR GR G
Sbjct: 323 DIQAVNVVINFDFPKTAETYLHRIGRSGRFG 353

>pdb|3I32|A Chain A, Dimeric Structure Of A Hera Helicase Fragment Including The C-Terminal Reca Domain, The Dimerization Domain, And The Rna Binding Domain Length = 300

Iteration: 1
 Score = 59.3 bits (142), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 33/91 (36%), Positives = 45/91 (49%)
Query: 225 VAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVA 284
           VA     +V+  T  + EEI++ L +LG  A   HG M    RE     F + E+RV+VA
Sbjct: 25  VASPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDMSQGERERVMGAFRQGEVRVLVA 84
Query: 285 TMAFGMGIDKPDVRHVIHYGCPKTLESYYQE 315
           T     G+D P V  V+HY  P   E+Y   
Sbjct: 85  TDVAARGLDIPQVDLVVHYRMPDRAEAYQHR 115

>pdb|3EAQ|A Chain A, Novel Dimerization Motif In The Dead Box Rna Helicase Hera Form 2, Complete Dimer, Symmetric Length = 212

Iteration: 1
 Score = 57.8 bits (138), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 32/91 (35%), Positives = 45/91 (49%)
Query: 225 VAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVA 284
           VA     +V+  T  + EEI++ L +LG  A   HG +    RE     F + E+RV+VA
Sbjct: 28  VASPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDLSQGERERVLGAFRQGEVRVLVA 87
Query: 285 TMAFGMGIDKPDVRHVIHYGCPKTLESYYQE 315
           T     G+D P V  V+HY  P   E+Y   
Sbjct: 88  TDVAARGLDIPQVDLVVHYRLPDRAEAYQHR 118

>pdb|2JGN|A Chain A, Ddx3 Helicase Domain Length = 185

Iteration: 1
 Score = 56.2 bits (134), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 31/117 (26%), Positives = 52/117 (44%)
Query: 220 EILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEI 279
           ++L +       +V+  T K  + +   L   G    + HG    + REEA   F   + 
Sbjct: 38  DLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKS 97
Query: 280 RVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSN 336
            ++VAT     G+D  +V+HVI++  P  +E Y    GR GR G   +   ++   N
Sbjct: 98  PILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNERN 154

>pdb|2Z0M|A Chain A, Crystal Structure Of Hypothetical Atp-Dependent Rna Helicase From Sulfolobus Tokodaii Length = 337

Iteration: 1
 Score = 55.8 bits (133), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 76/326 (23%), Positives = 132/326 (40%), Gaps = 33/326 (10%)
Query: 7   KYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVTGKTALVVSPLISLM 66
           +  G+  F   Q   I  +++ ++ +V   TGSGK+  Y +P L  G  +LVV+P   L 
Sbjct: 10  REMGFKNFTEVQSKTIPLMLQGKNVVVRAKTGSGKTAAYAIPILELGMKSLVVTPTRELT 69
Query: 67  QDQVMSLKQRGINAEFLGS--AQTDSSVQTKAETGYFQ---LLFMTPEKACIIPISFWSK 121
           +     ++  G    ++ +  A+    +  KA+    +   ++  TP +     +  WSK
Sbjct: 70  RQVASHIRDIG---RYMDTKVAEVYGGMPYKAQINRVRNADIVVATPGRL----LDLWSK 122
Query: 122 --LLKAGVCLFAVDEAHCISEWG--HDFRLEYKQLDKLRTFLLGVPFVALTATATEKVRI 177
             +  +   +  +DEA  + E G   D ++   Q    +   L   F A       KV  
Sbjct: 123 GVIDLSSFEIVIIDEADLMFEMGFIDDIKIILAQTSNRKITGL---FSATIPEEIRKVVK 179
Query: 178 DIINSLKLKNPYVTIASFDRKNLFYGVKVINRGQSFVDELVQEILKSVAGAGSIIVYCMT 237
           D I + +     + +A+ + K  F  VK  +  +S V  L +   K V      IV+  T
Sbjct: 180 DFITNYEEIEACIGLANVEHK--FVHVK--DDWRSKVQALRENKDKGV------IVFVRT 229
Query: 238 IKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDV 297
              V ++ +        A    G +    R      F   E  +++ T     G+D P V
Sbjct: 230 RNRVAKLVRLFDN----AIELRGDLPQSVRNRNIDAFREGEYDMLITTDVASRGLDIPLV 285
Query: 298 RHVIHYGCPKTLESYYQESGRCGRDG 323
             VI++  P+ L +Y    GR GR G
Sbjct: 286 EKVINFDAPQDLRTYIHRIGRTGRMG 311

>pdb|2I4I|A Chain A, Crystal Structure Of Human Dead-Box Rna Helicase Ddx3x Length = 417

Iteration: 1
 Score = 55.8 bits (133), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 31/118 (26%), Positives = 52/118 (44%)
Query: 220 EILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEI 279
           ++L +       +V+  T K  + +   L   G    + HG    + REEA   F   + 
Sbjct: 268 DLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKS 327
Query: 280 RVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNF 337
            ++VAT     G+D  +V+HVI++  P  +E Y    GR GR G   +   ++   N 
Sbjct: 328 PILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNERNI 385

>pdb|2YJT|D Chain D, Crystal Structure Of E. Coli Dead-Box Protein Srmb Bound To Regulator Of Ribonuclease Activity A (Rraa) Length = 170

Iteration: 1
 Score = 55.1 bits (131), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 29/92 (31%), Positives = 46/92 (50%)
Query: 232 IVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMG 291
           IV+    + V E++  L++ G+      G+M    R EA +      + V+VAT     G
Sbjct: 34  IVFVRKRERVHELANWLREAGINNCYLEGEMVQGKRNEAIKRLTEGRVNVLVATDVAARG 93
Query: 292 IDKPDVRHVIHYGCPKTLESYYQESGRCGRDG 323
           ID PDV HV ++  P++ ++Y    GR  R G
Sbjct: 94  IDIPDVSHVFNFDMPRSGDTYLHRIGRTARAG 125

>pdb|2P6N|A Chain A, Human Dead-box Rna Helicase Ddx41, Helicase Domain Length = 191

Iteration: 1
 Score = 54.3 bits (129), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 34/129 (26%), Positives = 61/129 (47%), Gaps = 8/129 (6%)
Query: 231 IIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGM 290
           ++++     DV+ I + L   GV+A   HG    + R +A   F   +  V+VAT     
Sbjct: 57  VLIFAEKKADVDAIHEYLLLKGVEAVAIHGGKDQEERTKAIEAFREGKKDVLVATDVASK 116
Query: 291 GIDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFYCGESQTE 350
           G+D P ++HVI+Y  P+ +E+Y    GR G  G   +   +  ++        C ES   
Sbjct: 117 GLDFPAIQHVINYDMPEEIENYVHRIGRTGCSGNTGIATTFINKA--------CDESVLM 168
Query: 351 NQRTAIMES 359
           + +  ++E+
Sbjct: 169 DLKALLLEA 177

>pdb|2DB3|A Chain A, Structural Basis For Rna Unwinding By The Dead-Box Protein Drosophila Vasa Length = 434

Iteration: 1
 Score = 53.5 bits (127), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 28/96 (29%), Positives = 47/96 (48%)
Query: 228 AGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMA 287
           A   IV+  T +  + ++  L +      + HG      RE+A R F    ++V++AT  
Sbjct: 300 ADGTIVFVETKRGADFLASFLSEKEFPTTSIHGDRLQSQREQALRDFKNGSMKVLIATSV 359
Query: 288 FGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRDG 323
              G+D  +++HVI+Y  P  ++ Y    GR GR G
Sbjct: 360 ASRGLDIKNIKHVINYDMPSKIDDYVHRIGRTGRVG 395

>pdb|2WAX|A Chain A, Structure Of The Human Ddx6 C-Terminal Domain In Complex With An Edc3-Fdf Peptide Length = 193

Iteration: 1
 Score = 52.0 bits (123), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 31/92 (33%), Positives = 44/92 (47%)
Query: 232 IVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMG 291
           I++C + + VE ++K + QLG      H +M  + R      F     R +V T  F  G
Sbjct: 48  IIFCNSSQRVELLAKKISQLGYSCFYIHAKMRQEHRNRVFHDFRNGLCRNLVCTDLFTRG 107
Query: 292 IDKPDVRHVIHYGCPKTLESYYQESGRCGRDG 323
           ID   V  VI++  PK  E+Y    GR GR G
Sbjct: 108 IDIQAVNVVINFDFPKLAETYLHRIGRSGRFG 139

>pdb|3PEW|A Chain A, S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3 Length = 395

Iteration: 1
 Score = 47.0 bits (110), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 48/185 (25%), Positives = 73/185 (39%), Gaps = 19/185 (10%)
Query: 164 FVALTATATEKVR------IDIINSLKLKNPYVTIASFDRKNLFYGVKVINRGQSFVDEL 217
            V  +AT  + VR      +   N+L+L+   V + +   K L+   K  N    F D L
Sbjct: 180 LVLFSATFADAVRQYAKKIVPNANTLELQTNEVNVDAI--KQLYMDCK--NEADKF-DVL 234
Query: 218 VQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRD 277
            +  L  V   GS I++  T K    +   LK  G +    HG + ++ R+     F   
Sbjct: 235 TE--LYGVMTIGSSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREG 292
Query: 278 EIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLE------SYYQESGRCGRDGIASVCWLY 331
             +V++ T     GID P V  V++Y  P          +Y    GR GR G   V   +
Sbjct: 293 RSKVLITTNVLARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAISF 352
Query: 332 YARSN 336
               N
Sbjct: 353 VHDKN 357

>pdb|2VSO|A Chain A, Crystal Structure Of A Translation Initiation Complex Length = 395

Iteration: 1
 Score = 46.6 bits (109), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 78/327 (23%), Positives = 138/327 (42%), Gaps = 35/327 (10%)
Query: 5   LKKYFGYSVFRP--YQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPL------VTGKTA 56
           L+  FGY    P   Q+  I  IIE  D L    +G+GK+  + +  L      V    A
Sbjct: 34  LRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQA 93
Query: 57  LVVSPLISL---MQDQVMSLKQRGINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKA-- 111
           L+++P   L   +Q  VM+L    ++ +        S V+        Q++  TP +   
Sbjct: 94  LMLAPTRELALQIQKVVMALAFH-MDIKVHACIGGTSFVEDAEGLRDAQIVVGTPGRVFD 152
Query: 112 CIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVP---FVALT 168
            I    F +  +K    +F +DEA  +   G  F+ +  Q+     F L  P    V L+
Sbjct: 153 NIQRRRFRTDKIK----MFILDEADEMLSSG--FKEQIYQI-----FTLLPPTTQVVLLS 201
Query: 169 ATATEKVRIDIINSLKLKNPYVTIASFDRKNLFYGVK---VINRGQSFVDELVQEILKSV 225
           AT    V +++     ++NP   +   D   L  G+K   V    + +  E + ++  S+
Sbjct: 202 ATMPNDV-LEVTTKF-MRNPVRILVKKDELTL-EGIKQFYVNVEEEEYKYECLTDLYDSI 258
Query: 226 AGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVAT 285
           +   ++I +C T + VEE++  L+         +  +  + R+   + F     R++++T
Sbjct: 259 SVTQAVI-FCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILIST 317
Query: 286 MAFGMGIDKPDVRHVIHYGCPKTLESY 312
                GID   V  VI+Y  P   E+Y
Sbjct: 318 DLLARGIDVQQVSLVINYDLPANKENY 344

>pdb|3SQX|A Chain A, Structure Of Mss116p (Nte And C-Tail Double Deletion) Bound To Ssrna And Amp-Pnp Length = 512

Iteration: 1
 Score = 45.8 bits (107), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 22/74 (29%), Positives = 34/74 (45%)
Query: 258 YHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESG 317
           +HG++    R    + F +DE  ++V T     G+D P+V  V+  G P  L +Y    G
Sbjct: 321 FHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIG 380
Query: 318 RCGRDGIASVCWLY 331
           R  R G      L+
Sbjct: 381 RTARSGKEGSSVLF 394

>pdb|4DB4|A Chain A, Mss116p Dead-Box Helicase Domain 2 Bound To A Chimaeric Rna-Dna Duplex Length = 256

Iteration: 1
 Score = 45.8 bits (107), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 22/74 (29%), Positives = 34/74 (45%)
Query: 258 YHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESG 317
           +HG++    R    + F +DE  ++V T     G+D P+V  V+  G P  L +Y    G
Sbjct: 66  FHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIG 125
Query: 318 RCGRDGIASVCWLY 331
           R  R G      L+
Sbjct: 126 RTARSGKEGSSVLF 139

>pdb|4DB2|C Chain C, Mss116p Dead-Box Helicase Domain 2 Bound To An Rna Duplex Length = 257

Iteration: 1
 Score = 45.8 bits (107), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 22/74 (29%), Positives = 34/74 (45%)
Query: 258 YHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESG 317
           +HG++    R    + F +DE  ++V T     G+D P+V  V+  G P  L +Y    G
Sbjct: 66  FHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIG 125
Query: 318 RCGRDGIASVCWLY 331
           R  R G      L+
Sbjct: 126 RTARSGKEGSSVLF 139

>pdb|3I5X|A Chain A, Structure Of Mss116p Bound To Ssrna And Amp-Pnp Length = 563

Iteration: 1
 Score = 45.8 bits (107), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 22/74 (29%), Positives = 34/74 (45%)
Query: 258 YHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESG 317
           +HG++    R    + F +DE  ++V T     G+D P+V  V+  G P  L +Y    G
Sbjct: 372 FHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIG 431
Query: 318 RCGRDGIASVCWLY 331
           R  R G      L+
Sbjct: 432 RTARSGKEGSSVLF 445

>pdb|3PEY|A Chain A, S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3 Length = 395

Iteration: 1
 Score = 45.8 bits (107), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 47/185 (25%), Positives = 73/185 (39%), Gaps = 19/185 (10%)
Query: 164 FVALTATATEKVR------IDIINSLKLKNPYVTIASFDRKNLFYGVKVINRGQSFVDEL 217
            V  +AT  + VR      +   N+L+L+   V + +   K L+   K  N    F D L
Sbjct: 180 LVLFSATFADAVRQYAKKIVPNANTLELQTNEVNVDAI--KQLYMDCK--NEADKF-DVL 234
Query: 218 VQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRD 277
            +  L  +   GS I++  T K    +   LK  G +    HG + ++ R+     F   
Sbjct: 235 TE--LYGLMTIGSSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREG 292
Query: 278 EIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLE------SYYQESGRCGRDGIASVCWLY 331
             +V++ T     GID P V  V++Y  P          +Y    GR GR G   V   +
Sbjct: 293 RSKVLITTNVLARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAISF 352
Query: 332 YARSN 336
               N
Sbjct: 353 VHDKN 357

>pdb|4DB2|A Chain A, Mss116p Dead-Box Helicase Domain 2 Bound To An Rna Duplex Length = 257

Iteration: 1
 Score = 45.4 bits (106), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 22/74 (29%), Positives = 34/74 (45%)
Query: 258 YHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESG 317
           +HG++    R    + F +DE  ++V T     G+D P+V  V+  G P  L +Y    G
Sbjct: 66  FHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIG 125
Query: 318 RCGRDGIASVCWLY 331
           R  R G      L+
Sbjct: 126 RTARSGKEGSSVLF 139

>pdb|3SQW|A Chain A, Structure Of Mss116p (Nte Deletion) Bound To Ssrna And Amp-Pnp Length = 579

Iteration: 1
 Score = 45.4 bits (106), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 22/74 (29%), Positives = 34/74 (45%)
Query: 258 YHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESG 317
           +HG++    R    + F +DE  ++V T     G+D P+V  V+  G P  L +Y    G
Sbjct: 321 FHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIG 380
Query: 318 RCGRDGIASVCWLY 331
           R  R G      L+
Sbjct: 381 RTARSGKEGSSVLF 394

>pdb|1XTI|A Chain A, Structure Of Wildtype Human Uap56 Length = 391

Iteration: 1
 Score = 43.9 bits (102), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 27/118 (22%), Positives = 52/118 (44%)
Query: 222 LKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRV 281
           L  V     ++++  +++    +++ L +    A   H  M  + R   ++ F   + R+
Sbjct: 244 LLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRI 303
Query: 282 MVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAK 339
           +VAT  FG G+D   V    +Y  P+  ++Y     R GR G   +   + +  N AK
Sbjct: 304 LVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAK 361

>pdb|1T5I|A Chain A, Crystal Structure Of The C-Terminal Domain Of Uap56 Length = 172

Iteration: 1
 Score = 43.9 bits (102), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 27/118 (22%), Positives = 52/118 (44%)
Query: 222 LKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRV 281
           L  V     ++++  +++    +++ L +    A   H  M  + R   ++ F   + R+
Sbjct: 25  LLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRI 84
Query: 282 MVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAK 339
           +VAT  FG G+D   V    +Y  P+  ++Y     R GR G   +   + +  N AK
Sbjct: 85  LVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAK 142

>pdb|1XTJ|A Chain A, Structure Of Human Uap56 In Complex With Adp Length = 386

Iteration: 1
 Score = 43.9 bits (102), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 27/118 (22%), Positives = 52/118 (44%)
Query: 222 LKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRV 281
           L  V     ++++  +++    +++ L +    A   H  M  + R   ++ F   + R+
Sbjct: 244 LLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRI 303
Query: 282 MVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAK 339
           +VAT  FG G+D   V    +Y  P+  ++Y     R GR G   +   + +  N AK
Sbjct: 304 LVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAK 361

>pdb|1XTK|A Chain A, Structure Of Decd To Dead Mutation Of Human Uap56 Length = 390

Iteration: 1
 Score = 43.9 bits (102), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 27/118 (22%), Positives = 52/118 (44%)
Query: 222 LKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRV 281
           L  V     ++++  +++    +++ L +    A   H  M  + R   ++ F   + R+
Sbjct: 243 LLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRI 302
Query: 282 MVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAK 339
           +VAT  FG G+D   V    +Y  P+  ++Y     R GR G   +   + +  N AK
Sbjct: 303 LVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAK 360

>pdb|3PEU|A Chain A, S. Cerevisiae Dbp5 L327v C-Terminal Domain Bound To Gle1 H337r And Ip6 Length = 188

Iteration: 1
 Score = 43.9 bits (102), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 32/121 (26%), Positives = 47/121 (38%), Gaps = 6/121 (4%)
Query: 222 LKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRV 281
           L  V   GS I++  T K    +   LK  G +    HG + ++ R+     F     +V
Sbjct: 30  LYGVXTIGSSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKV 89
Query: 282 MVATMAFGMGIDKPDVRHVIHYGCPKTLE------SYYQESGRCGRDGIASVCWLYYARS 335
           ++ T     GID P V  V++Y  P          +Y    GR GR G   V   +    
Sbjct: 90  LITTNVLARGIDIPTVSXVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAISFVHDK 149
Query: 336 N 336
           N
Sbjct: 150 N 150

>pdb|3GFP|A Chain A, Structure Of The C-Terminal Domain Of The Dead-Box Protein Dbp5 Length = 189

Iteration: 1
 Score = 43.5 bits (101), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 30/114 (26%), Positives = 45/114 (39%), Gaps = 6/114 (5%)
Query: 229 GSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAF 288
           GS I++  T K    +   LK  G +    HG + ++ R+     F     +V++ T   
Sbjct: 38  GSSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVL 97
Query: 289 GMGIDKPDVRHVIHYGCPKTLE------SYYQESGRCGRDGIASVCWLYYARSN 336
             GID P V  V++Y  P          +Y    GR GR G   V   +    N
Sbjct: 98  ARGIDIPTVSXVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAISFVHDKN 151

>pdb|2KBF|A Chain A, Solution Structure Of Carboxyl-Terminal Domain Of Dbp5p Length = 187

Iteration: 1
 Score = 43.5 bits (101), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 30/114 (26%), Positives = 45/114 (39%), Gaps = 6/114 (5%)
Query: 229 GSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAF 288
           GS I++  T K    +   LK  G +    HG + ++ R+     F     +V++ T   
Sbjct: 36  GSSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVL 95
Query: 289 GMGIDKPDVRHVIHYGCPKTLE------SYYQESGRCGRDGIASVCWLYYARSN 336
             GID P V  V++Y  P          +Y    GR GR G   V   +    N
Sbjct: 96  ARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAISFVHDKN 149

>pdb|2EYQ|A Chain A, Crystal Structure Of Escherichia Coli Transcription-Repair Coupling Factor Length = 1151

Iteration: 1
 Score = 42.0 bits (97), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 36/122 (29%), Positives = 49/122 (40%), Gaps = 17/122 (13%)
Query: 219 QEILKSVAGAGSIIVYCMTIKDVEEISKALKQLG-----VKAGTYHGQMGSKAREEAHRL 273
           + IL+ +   G   VY +   DVE I KA ++L       +    HGQM  +  E     
Sbjct: 803 EAILREILRGGQ--VYYL-YNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMND 859
Query: 274 FIRDEIRVMVATMAFGMGIDKPDVRHVI-----HYGCPKTLESYYQESGRCGRDGIASVC 328
           F      V+V T     GID P    +I     H+G    L   +Q  GR GR    +  
Sbjct: 860 FHHQRFNVLVCTTIIETGIDIPTANTIIIERADHFG----LAQLHQLRGRVGRSHHQAYA 915
Query: 329 WL 330
           WL
Sbjct: 916 WL 917

>pdb|1FUK|A Chain A, Crystal Structure Of The Carboxy Terminal Domain Of Yeast Eif4a Length = 165

Iteration: 1
 Score = 41.6 bits (96), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 20/81 (24%), Positives = 38/81 (46%)
Query: 232 IVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMG 291
           +++C T + VEE++  L+         +  +  + R+   + F     R++++T     G
Sbjct: 34  VIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLARG 93
Query: 292 IDKPDVRHVIHYGCPKTLESY 312
           ID   V  VI+Y  P   E+Y
Sbjct: 94  IDVQQVSLVINYDLPANKENY 114

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	374
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	1e-167
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	1e-166
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	5e-19
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	2e-17
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	3e-17
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	6e-17
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	6e-16
3eaq_A	212	Heat resistant RNA dependent ATPase; DEAD box RNA	1e-15
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	1e-15
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	1e-15
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	3e-15
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	5e-15
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	5e-15
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	6e-15
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	9e-15
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	1e-14
3i32_A	300	Heat resistant RNA dependent ATPase; RNA helicase,	1e-14
2yjt_D	170	ATP-dependent RNA helicase SRMB, regulator of ribo	1e-14
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	2e-14
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	3e-14
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	3e-14
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	4e-14
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	5e-14
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	2e-13
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	1e-12
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	1e-12
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	8e-06
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	2e-12
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	7e-12
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	8e-12
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	1e-11
3b6e_A	216	Interferon-induced helicase C domain-containing P;	1e-10
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	4e-10
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	2e-08
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	4e-08
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	6e-08
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	2e-04
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	4e-07
3h1t_A	590	Type I site-specific restriction-modification syst	4e-07
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	6e-07
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	1e-04
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	1e-06
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	6e-04
1yks_A	440	Genome polyprotein [contains: flavivirin protease	2e-06
3rc3_A	677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	3e-06
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	1e-05
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	2e-04
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	2e-05
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	4e-05
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	2e-05
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	1e-04
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	5e-05
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	5e-05
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	9e-05
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	3e-04
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	3e-04
2vl7_A	540	XPD; helicase, unknown function; 2.25A {Sulfolobus	9e-04

>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* Length = 591

 Score =  479 bits (1234), Expect = e-167
 Identities = 146/385 (37%), Positives = 214/385 (55%), Gaps = 19/385 (4%)

Query: 1   MVSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVTGKTALVVS 60
           +   L+  F    FRP Q + I   +  ++  +VM TG GKSLCYQLP L +    LV+ 
Sbjct: 32  VKDILQNVFKLEKFRPLQLETINVTMAGKEVFLVMPTGGGKSLCYQLPALCSDGFTLVIC 91

Query: 61  PLISLMQDQVMSLKQRGINAEFLGSAQTDSSVQT-----KAETGYFQLLFMTPEKACIIP 115
           PLISLM+DQ+M LKQ GI+A  L ++ +   V+        +    +L+++TPEK     
Sbjct: 92  PLISLMEDQLMVLKQLGISATMLNASSSKEHVKWVHAEMVNKNSELKLIYVTPEKIAKSK 151

Query: 116 --ISFWSKLLKAG-VCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATAT 172
             +S   K  +A      AVDE HC S+WGHDFR +YK L  L+        + LTATAT
Sbjct: 152 MFMSRLEKAYEARRFTRIAVDEVHCCSQWGHDFRPDYKALGILKRQFPNASLIGLTATAT 211

Query: 173 EKVRIDIINSLKLKNPYVTIASFDRKNLFYGVKV-INRGQSFVDELVQEILKSVAG-AGS 230
             V  D    L ++  +   ASF+R NL+Y V+   +  + F++++V+ I     G +G 
Sbjct: 212 NHVLTDAQKILCIEKCFTFTASFNRPNLYYEVRQKPSNTEDFIEDIVKLINGRYKGQSG- 270

Query: 231 IIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGM 290
            I+YC + KD E+++ +L+ LG+ AG YH  +  + +   HR +  +EI+V+VAT+AFGM
Sbjct: 271 -IIYCFSQKDSEQVTVSLQNLGIHAGAYHANLEPEDKTTVHRKWSANEIQVVVATVAFGM 329

Query: 291 GIDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFYCGESQTE 350
           GIDKPDVR VIH+   K++E+YYQESGR GRD + + C LYY   +  +           
Sbjct: 330 GIDKPDVRFVIHHSMSKSMENYYQESGRAGRDDMKADCILYYGFGDIFRISSMVVMENVG 389

Query: 351 NQRTAIMESLLAAQRYCL-LTTCRR 374
            Q+      L     YC  ++ CRR
Sbjct: 390 QQK------LYEMVSYCQNISKCRR 408

>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* Length = 523

 Score =  475 bits (1224), Expect = e-166
 Identities = 153/375 (40%), Positives = 220/375 (58%), Gaps = 10/375 (2%)

Query: 3   STLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVTGKTALVVSPL 62
             L++ FGY  FRP Q+++I  ++  RDCLVVM TG GKSLCYQ+P L+     +VVSPL
Sbjct: 15  QVLQETFGYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPALLLNGLTVVVSPL 74

Query: 63  ISLMQDQVMSLKQRGINAEFLGSAQTDS---SVQTKAETGYFQLLFMTPEKACIIPISFW 119
           ISLM+DQV  L+  G+ A  L S QT      V T   TG  +LL++ PE+  ++  +F 
Sbjct: 75  ISLMKDQVDQLQANGVAAACLNSTQTREQQLEVMTGCRTGQIRLLYIAPER--LMLDNFL 132

Query: 120 SKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEKVRIDI 179
             L      L AVDEAHCIS+WGHDFR EY  L +LR     +PF+ALTATA +  R DI
Sbjct: 133 EHLAHWNPVLLAVDEAHCISQWGHDFRPEYAALGQLRQRFPTLPFMALTATADDTTRQDI 192

Query: 180 INSLKLKNPYVTIASFDRKNLFYGVKVINRGQSFVDELVQEILKSVAGAGSIIVYCMTIK 239
           +  L L +P + I+SFDR N+ Y +         +D+L++ + +    +G  I+YC +  
Sbjct: 193 VRLLGLNDPLIQISSFDRPNIRYMLM---EKFKPLDQLMRYVQEQRGKSG--IIYCNSRA 247

Query: 240 DVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRH 299
            VE+ +  L+  G+ A  YH  + +  R +    F RD+++++VAT+AFGMGI+KP+VR 
Sbjct: 248 KVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGMGINKPNVRF 307

Query: 300 VIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFYCGESQTENQRTAIMES 359
           V+H+  P+ +ESYYQE+GR GRDG+ +   L+Y  ++ A       E      +      
Sbjct: 308 VVHFDIPRNIESYYQETGRAGRDGLPAEAMLFYDPADMAWLRRCLEEKPQGQLQDIERHK 367

Query: 360 LLAAQRYCLLTTCRR 374
           L A   +    TCRR
Sbjct: 368 LNAMGAFAEAQTCRR 382

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A* Length = 414

 Score = 86.7 bits (215), Expect = 5e-19
 Identities = 63/356 (17%), Positives = 127/356 (35%), Gaps = 70/356 (19%)

Query: 10  GYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPL---VTGKTALVVSP---LI 63
                  YQ+   +RI++ +   +V  TG GK+    +  L     GK + +V P   L+
Sbjct: 18  FGKDLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLARKGKKSALVFPTVTLV 77

Query: 64  SLMQDQVMSLKQRGINAEFLGSAQTDSSVQTKA----ETGYFQLLFMTPEKACIIPISF- 118
               +++  L    +      S+      + K     E   + +L  +          F 
Sbjct: 78  KQTLERLQKLADEKVKIFGFYSSM-KKEEKEKFEKSFEEDDYHILVFST--------QFV 128

Query: 119 ---WSKLLKAGVCLFAVDEAHCISEWGHDFRLEY-KQLDKLRTFLLGVPF----VALTAT 170
                KL +       VD+         D  L+  + +D L   ++G+P      A +  
Sbjct: 129 SKNREKLSQKRFDFVFVDDV--------DAVLKASRNIDTLLM-MVGIPEEIIRKAFSTI 179

Query: 171 ATEKVRIDIINSLKLKNPYVTIASFDRKNL-------FYGVKVINRG-------QSFV-- 214
              K+  +   +LK     V+ A+   + +            V              +  
Sbjct: 180 KQGKIY-ERPKNLKPGILVVSSATAKPRGIRPLLFRDLLNFTVGRLVSVARNITHVRISS 238

Query: 215 --DELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHR 272
              E + E+L+        +++  T ++ +E+ + LK+     G    +      E+   
Sbjct: 239 RSKEKLVELLEIFRDGI--LIFAQTEEEGKELYEYLKRFKFNVGETWSE-----FEKNFE 291

Query: 273 LFIRDEIRVMVATMAFGM----GIDKPD-VRHVIHYGCPKTLE--SYYQESGRCGR 321
            F   +I +++   A+      G+D P+ +++VI +G P   +  +Y Q SGR  R
Sbjct: 292 DFKVGKINILIGVQAYYGKLTRGVDLPERIKYVIFWGTPSGPDVYTYIQASGRSSR 347

>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 = 83.3 bits (206), Expect = 2e-17
 Identities = 79/383 (20%), Positives = 136/383 (35%), Gaps = 91/383 (23%)

Query: 7   KYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQL---PPLVTGKTALVVSPLI 63
           K  G     P Q + ++++   ++ L+ M T +GK+L  ++      + G  +L V PL 
Sbjct: 19  KEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIKGGKSLYVVPLR 78

Query: 64  SLMQDQVMSLKQR---GINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWS 120
           +L  ++  S K+    G+         T          G   ++  T EKA  + I   +
Sbjct: 79  ALAGEKYESFKKWEKIGLRIGIS----TGDYESRDEHLGDCDIIVTTSEKADSL-IRNRA 133

Query: 121 KLLKAGVCLFAVDEAHCISEWGHDFR---LEYKQLDKLRTFLLGVPFVALTATATEKVRI 177
             +KA V    VDE H +     + R   LE   + K+R     +  + L+AT       
Sbjct: 134 SWIKA-VSCLVVDEIHLLDS---EKRGATLE-ILVTKMRRMNKALRVIGLSAT------- 181

Query: 178 DIINSLKLKNPYVTIASFDRKNLFY----------GVKVINRGQSF--------VDELVQ 219
                    N    IA +   + +           GV      + F          +  +
Sbjct: 182 -------APN-VTEIAEWLDADYYVSDWRPVPLVEGVLCEGTLELFDGAFSTSRRVKFEE 233

Query: 220 EILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVK------------------------- 254
            + + VA  G ++V+  T +  E+ +  L  +  K                         
Sbjct: 234 LVEECVAENGGVLVFESTRRGAEKTAVKLSAITAKYVENEGLEKAILEENEGEMSRKLAE 293

Query: 255 -----AGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVI------HY 303
                A  +H  + +  R      F R  I+V+VAT     G++ P  R VI        
Sbjct: 294 CVRKGAAFHHAGLLNGQRRVVEDAFRRGNIKVVVATPTLAAGVNLP-ARRVIVRSLYRFD 352

Query: 304 GCPKTLES--YYQESGRCGRDGI 324
           G  K ++   Y Q +GR GR G+
Sbjct: 353 GYSKRIKVSEYKQMAGRAGRPGM 375

>2jgn_A DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosphorylation, nucleotide-binding, hydrolase, RNA-binding, ATP-binding, DNA-binding, nuclear protein; 1.91A {Homo sapiens} Length = 185

 Score = 78.0 bits (193), Expect = 3e-17
 Identities = 30/104 (28%), Positives = 48/104 (46%)

Query: 220 EILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEI 279
           ++L +       +V+  T K  + +   L   G    + HG    + REEA   F   + 
Sbjct: 38  DLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKS 97

Query: 280 RVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRDG 323
            ++VAT     G+D  +V+HVI++  P  +E Y    GR GR G
Sbjct: 98  PILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVG 141

>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; 2.60A {Homo sapiens} Length = 191

 Score = 77.3 bits (191), Expect = 6e-17
 Identities = 32/105 (30%), Positives = 51/105 (48%), Gaps = 2/105 (1%)

Query: 219 QEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDE 278
            E L+       ++++     DV+ I + L   GV+A   HG    + R +A   F   +
Sbjct: 47  LECLQK--TPPPVLIFAEKKADVDAIHEYLLLKGVEAVAIHGGKDQEERTKAIEAFREGK 104

Query: 279 IRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRDG 323
             V+VAT     G+D P ++HVI+Y  P+ +E+Y    GR G  G
Sbjct: 105 KDVLVATDVASKGLDFPAIQHVINYDMPEEIENYVHRIGRTGCSG 149

>1t5i_A C_terminal domain of A probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA processing protein; 1.90A {Homo sapiens} SCOP: c.37.1.19 Length = 172

 Score = 73.8 bits (182), Expect = 6e-16
 Identities = 23/97 (23%), Positives = 46/97 (47%), Gaps = 3/97 (3%)

Query: 232 IVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMG 291
           +++  +++    +++ L +    A   H  M  + R   ++ F   + R++VAT  FG G
Sbjct: 35  VIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRG 94

Query: 292 IDKPDVRHVIHYGCPKTLESYYQ---ESGRCGRDGIA 325
           +D   V    +Y  P+  ++Y      +GR G  G+A
Sbjct: 95  MDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLA 131

>3eaq_A Heat resistant RNA dependent ATPase; DEAD box RNA helicase, dimer, ATP-binding, helicase, hydrolase, nucleotide-binding; 2.30A {Thermus thermophilus} PDB: 3ear_A 3eas_A Length = 212

 Score = 74.3 bits (183), Expect = 1e-15
 Identities = 36/92 (39%), Positives = 49/92 (53%)

Query: 232 IVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMG 291
           +V+  T  + EEI++ L +LG  A   HG +    RE     F + E+RV+VAT     G
Sbjct: 35  MVFTRTKAETEEIAQGLLRLGHPAQALHGDLSQGERERVLGAFRQGEVRVLVATDVAARG 94

Query: 292 IDKPDVRHVIHYGCPKTLESYYQESGRCGRDG 323
           +D P V  V+HY  P   E+Y   SGR GR G
Sbjct: 95  LDIPQVDLVVHYRLPDRAEAYQHRSGRTGRAG 126

>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 = 77.2 bits (190), Expect = 1e-15
 Identities = 37/168 (22%), Positives = 71/168 (42%), Gaps = 15/168 (8%)

Query: 169 ATATEKVRIDIINSLKLKNP-YVTIASFDRK------NLFYGVKVINRGQSFVDELVQEI 221
           AT  +KV+  + N++ +     + + + D+        +   V +  +  + +   V+ I
Sbjct: 221 ATLDDKVQ-KLANNI-MNKKECLFLDTVDKNEPEAHERIDQSVVISEKFANSIFAAVEHI 278

Query: 222 LKSVAGAGS---IIVYCMTIKDVEEISKALK---QLGVKAGTYHGQMGSKAREEAHRLFI 275
            K +    S    I++  T+K    +   LK   +  +    +HG++    R    + F 
Sbjct: 279 KKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFK 338

Query: 276 RDEIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRDG 323
           +DE  ++V T     G+D P+V  V+  G P  L +Y    GR  R G
Sbjct: 339 KDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSG 386

>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein, translation; 1.75A {Saccharomyces cerevisiae} SCOP: c.37.1.19 Length = 165

 Score = 72.6 bits (179), Expect = 1e-15
 Identities = 26/100 (26%), Positives = 45/100 (45%), Gaps = 3/100 (3%)

Query: 229 GSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAF 288
              +++C T + VEE++  L+         +  +  + R+   + F     R++++T   
Sbjct: 31  TQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLL 90

Query: 289 GMGIDKPDVRHVIHYGCPKTLESYYQ---ESGRCGRDGIA 325
             GID   V  VI+Y  P   E+Y       GR GR G+A
Sbjct: 91  ARGIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVA 130

>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 = 76.0 bits (187), Expect = 3e-15
 Identities = 37/168 (22%), Positives = 69/168 (41%), Gaps = 15/168 (8%)

Query: 169 ATATEKVRIDIINSLKLKNP-YVTIASFDRK------NLFYGVKVINRGQSFVDELVQEI 221
           AT  +KV+  + N   +     + + + D+        +   V +  +  + +   V+ I
Sbjct: 272 ATLDDKVQ-KLAN-NIMNKKECLFLDTVDKNEPEAHERIDQSVVISEKFANSIFAAVEHI 329

Query: 222 LKSVAGAGS---IIVYCMTIKDVEEISKALK---QLGVKAGTYHGQMGSKAREEAHRLFI 275
            K +    S    I++  T+K    +   LK   +  +    +HG++    R    + F 
Sbjct: 330 KKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFK 389

Query: 276 RDEIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRDG 323
           +DE  ++V T     G+D P+V  V+  G P  L +Y    GR  R G
Sbjct: 390 KDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSG 437

>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 = 74.9 bits (185), Expect = 5e-15
 Identities = 30/97 (30%), Positives = 48/97 (49%), Gaps = 3/97 (3%)

Query: 232 IVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMG 291
           I++C +   VE ++K +  LG      H +M  + R +    F + ++R +V +     G
Sbjct: 262 IIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSDLLTRG 321

Query: 292 IDKPDVRHVIHYGCPKTLESYYQ---ESGRCGRDGIA 325
           ID   V  VI++  PKT E+Y      SGR G  G+A
Sbjct: 322 IDIQAVNVVINFDFPKTAETYLHRIGRSGRFGHLGLA 358

>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 = 74.5 bits (184), Expect = 5e-15
 Identities = 26/97 (26%), Positives = 45/97 (46%), Gaps = 3/97 (3%)

Query: 232 IVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMG 291
           +++C T + VEE++  L+         +  +  + R+   + F     R++++T     G
Sbjct: 263 VIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLARG 322

Query: 292 IDKPDVRHVIHYGCPKTLESYYQ---ESGRCGRDGIA 325
           ID   V  VI+Y  P   E+Y       GR GR G+A
Sbjct: 323 IDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVA 359

>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 = 74.5 bits (184), Expect = 6e-15
 Identities = 28/97 (28%), Positives = 43/97 (44%), Gaps = 3/97 (3%)

Query: 232 IVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMG 291
           +++  T + V+ +++ +          HG M  K R+   R F     RV++ T     G
Sbjct: 284 VIFINTRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMREFRSGSSRVLITTDLLARG 343

Query: 292 IDKPDVRHVIHYGCPKTLESYYQ---ESGRCGRDGIA 325
           ID   V  VI+Y  P   E+Y       GR GR G+A
Sbjct: 344 IDVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGVA 380

>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* Length = 720

 Score = 74.9 bits (184), Expect = 9e-15
 Identities = 63/385 (16%), Positives = 112/385 (29%), Gaps = 94/385 (24%)

Query: 7   KYFGYSVFRPYQKDVIQRIIEKRDCLVVMA-TGSGKSLCYQL----PPLVTGKTALVVSP 61
           K  G   F P Q + ++  I +    ++   T SGK+L  ++      L  G  A+ + P
Sbjct: 17  KERGIESFYPPQAEALKSGILEGKNALISIPTASGKTLIAEIAMVHRILTQGGKAVYIVP 76

Query: 62  LISLMQDQVMSLKQR---GIN-AEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPIS 117
           L +L +++    +     G+  A   G   +      K       ++  T EK   + + 
Sbjct: 77  LKALAEEKFQEFQDWEKIGLRVAMATGDYDSKDEWLGKY-----DIIIATAEKFDSL-LR 130

Query: 118 FWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEKVRI 177
             S  +K  V +   DE H I        LE      L   L     + L+AT       
Sbjct: 131 HGSSWIKD-VKILVADEIHLIGSRDRGATLE----VILAHMLGKAQIIGLSAT------- 178

Query: 178 DIINSLKLKNPYVTIASFDRKNLF---------------YGVKVINRGQSF-VDELVQEI 221
                  + N    +A +    L                 G      G         + +
Sbjct: 179 -------IGN-PEELAEWLNAELIVSDWRPVKLRRGVFYQGFVTWEDGSIDRFSSWEELV 230

Query: 222 LKSVAGAGSIIVYCMTIKDVEEISKALKQ------------------------------- 250
             ++      +++    +  E ++  L +                               
Sbjct: 231 YDAIRKKKGALIFVNMRRKAERVALELSKKVKSLLTKPEIRALNELADSLEENPTNEKLA 290

Query: 251 --LGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVI------- 301
             +      +H  +G   R      F +  I+ +VAT     GI+ P    VI       
Sbjct: 291 KAIRGGVAFHHAGLGRDERVLVEENFRKGIIKAVVATPTLSAGINTP-AFRVIIRDIWRY 349

Query: 302 --HYGCPKTLESYYQESGRCGRDGI 324
                    +   +Q  GR GR   
Sbjct: 350 SDFGMERIPIIEVHQMLGRAGRPKY 374

>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 = 73.8 bits (182), Expect = 1e-14
 Identities = 29/97 (29%), Positives = 50/97 (51%), Gaps = 3/97 (3%)

Query: 232 IVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMG 291
           +++C T + V+ +++ +++      + HG M  K RE   + F     RV+++T  +  G
Sbjct: 280 VIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARG 339

Query: 292 IDKPDVRHVIHYGCPKTLESYYQ---ESGRCGRDGIA 325
           +D P V  +I+Y  P   E Y      SGR GR G+A
Sbjct: 340 LDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVA 376

>3i32_A Heat resistant RNA dependent ATPase; RNA helicase, dimer, RNA recognition motif, ATP-BIND helicase, nucleotide-binding; 2.80A {Thermus thermophilus} Length = 300

 Score = 72.5 bits (178), Expect = 1e-14
 Identities = 37/92 (40%), Positives = 49/92 (53%)

Query: 232 IVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMG 291
           +V+  T  + EEI++ L +LG  A   HG M    RE     F + E+RV+VAT     G
Sbjct: 32  MVFTRTKAETEEIAQGLLRLGHPAQALHGDMSQGERERVMGAFRQGEVRVLVATDVAARG 91

Query: 292 IDKPDVRHVIHYGCPKTLESYYQESGRCGRDG 323
           +D P V  V+HY  P   E+Y   SGR GR G
Sbjct: 92  LDIPQVDLVVHYRMPDRAEAYQHRSGRTGRAG 123

>2yjt_D ATP-dependent RNA helicase SRMB, regulator of ribonuclease activity A; hydrolase inhibitor-hydrolase complex, DEAD box RNA helicase; 2.90A {Escherichia coli} Length = 170

 Score = 69.9 bits (172), Expect = 1e-14
 Identities = 34/113 (30%), Positives = 53/113 (46%), Gaps = 4/113 (3%)

Query: 216 ELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFI 275
            L+  +LK    A   IV+    + V E++  L++ G+      G+M    R EA +   
Sbjct: 19  ALLVHLLKQ-PEATRSIVFVRKRERVHELANWLREAGINNCYLEGEMVQGKRNEAIKRLT 77

Query: 276 RDEIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGR---DGIA 325
              + V+VAT     GID PDV HV ++  P++ ++Y    GR  R    G A
Sbjct: 78  EGRVNVLVATDVAARGIDIPDVSHVFNFDMPRSGDTYLHRIGRTARAGRKGTA 130

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens} Length = 417

 Score = 73.0 bits (180), Expect = 2e-14
 Identities = 30/104 (28%), Positives = 48/104 (46%)

Query: 220 EILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEI 279
           ++L +       +V+  T K  + +   L   G    + HG    + REEA   F   + 
Sbjct: 268 DLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKS 327

Query: 280 RVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRDG 323
            ++VAT     G+D  +V+HVI++  P  +E Y    GR GR G
Sbjct: 328 PILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVG 371

>2rb4_A ATP-dependent RNA helicase DDX25; rossmann fold, structural genomics, structural consortium, SGC, alternative initiation, ATP-binding, devel protein; 2.80A {Homo sapiens} Length = 175

 Score = 69.5 bits (171), Expect = 3e-14
 Identities = 24/106 (22%), Positives = 48/106 (45%), Gaps = 9/106 (8%)

Query: 229 GSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAF 288
           G  I++C T ++ + ++  + Q G +     G++  + R    + F   + +V++ T   
Sbjct: 35  GQAIIFCQTRRNAKWLTVEMIQDGHQVSLLSGELTVEQRASIIQRFRDGKEKVLITTNVC 94

Query: 289 GMGIDKPDVRHVIHYGCPKT------LESYYQ---ESGRCGRDGIA 325
             GID   V  V+++  P         E+Y      +GR G+ G+A
Sbjct: 95  ARGIDVKQVTIVVNFDLPVKQGEEPDYETYLHRIGRTGRFGKKGLA 140

>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase; 1.95A {Bacillus subtilis} Length = 163

 Score = 68.7 bits (169), Expect = 3e-14
 Identities = 33/97 (34%), Positives = 46/97 (47%), Gaps = 3/97 (3%)

Query: 232 IVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMG 291
           I++C T + V +++  L  LG      HG M  + R +    F R E R +VAT     G
Sbjct: 39  IIFCRTKEHVNQLTDELDDLGYPCDKIHGGMIQEDRFDVMNEFKRGEYRYLVATDVAARG 98

Query: 292 IDKPDVRHVIHYGCPKTLESYYQ---ESGRCGRDGIA 325
           ID  ++  VI+Y  P   ESY      +GR G  G A
Sbjct: 99  IDIENISLVINYDLPLEKESYVHRTGRTGRAGNKGKA 135

>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 = 71.8 bits (177), Expect = 4e-14
 Identities = 23/97 (23%), Positives = 46/97 (47%), Gaps = 3/97 (3%)

Query: 232 IVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMG 291
           +++  +++    +++ L +    A   H  M  + R   ++ F   + R++VAT  FG G
Sbjct: 254 VIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRG 313

Query: 292 IDKPDVRHVIHYGCPKTLESYYQ---ESGRCGRDGIA 325
           +D   V    +Y  P+  ++Y      +GR G  G+A
Sbjct: 314 MDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLA 350

>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 = 71.8 bits (177), Expect = 5e-14
 Identities = 37/92 (40%), Positives = 55/92 (59%)

Query: 232 IVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMG 291
           +V+C T +D +E++  L+ +G KAG  HG +    RE+  RLF + +IR+++AT     G
Sbjct: 242 LVFCKTKRDTKELASMLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATDVMSRG 301

Query: 292 IDKPDVRHVIHYGCPKTLESYYQESGRCGRDG 323
           ID  D+  VI+Y  P+  ESY    GR GR G
Sbjct: 302 IDVNDLNCVINYHLPQNPESYMHRIGRTGRAG 333

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus} Length = 715

 Score = 70.5 bits (173), Expect = 2e-13
 Identities = 72/411 (17%), Positives = 137/411 (33%), Gaps = 92/411 (22%)

Query: 7   KYFGYSVFRPYQKDVIQRIIEKRDCLVVMA-TGSGKSLCYQL----PPLVTGKTALVVSP 61
           K  G     P Q + +++ + + + L++ + TGSGK+L  ++      L  G  A+ V+P
Sbjct: 24  KKRGIKKLNPPQTEAVKKGLLEGNRLLLTSPTGSGKTLIAEMGIISFLLKNGGKAIYVTP 83

Query: 62  LISLMQDQVMSLKQR---GIN-AEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPIS 117
           L +L  ++ ++ K     G   A   G   TD +           ++  T EK   +   
Sbjct: 84  LRALTNEKYLTFKDWELIGFKVAMTSGDYDTDDAWLKNY-----DIIITTYEKLDSL-WR 137

Query: 118 FWSKLLKAGVCLFAVDEAHCISEWGHDFR---LEYKQLDKLRTFLLGVPFVALTATA--T 172
              + L   V  F +DE H +++     R   +E      +         +AL+AT    
Sbjct: 138 HRPEWLNE-VNYFVLDELHYLNDPE---RGPVVE-----SVTIRAKRRNLLALSATISNY 188

Query: 173 EKV----RIDIINS----LKLKNPYVTIASFDRKNLFYGVKVINRGQSFVDELVQEILKS 224
           +++      + + +    + L    +      ++          +     D ++   L S
Sbjct: 189 KQIAKWLGAEPVATNWRPVPLIEGVIYPERKKKEYNVIFKDNTTKKVHGDDAIIAYTLDS 248

Query: 225 VAGAGSIIVYCMTIKDVEEISKALKQL--------------------------------- 251
           ++  G ++V+  + K  E  +  +                                    
Sbjct: 249 LSKNGQVLVFRNSRKMAESTALKIANYMNFVSLDENALSEILKQLDDIEEGGSDEKELLK 308

Query: 252 -----GVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVI----- 301
                GV    +H  +    R+     F + +I+V+VAT     G++ P  R VI     
Sbjct: 309 SLISKGV--AYHHAGLSKALRDLIEEGFRQRKIKVIVATPTLAAGVNLP-ARTVIIGDIY 365

Query: 302 -------HYGCPKTLESYYQESGRCGRDGIAS--VCWLYYARSNFAKGDFY 343
                   Y     +  Y Q SGR GR G        +           F 
Sbjct: 366 RFNKKIAGYYDEIPIMEYKQMSGRAGRPGFDQIGESIVVVRDKEDVDRVFK 416

>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 = 67.9 bits (165), Expect = 1e-12
 Identities = 31/114 (27%), Positives = 52/114 (45%), Gaps = 9/114 (7%)

Query: 216 ELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQ--------MGSKAR 267
           E+++E L+    +  IIV+    +  ++I   L + G+KA  + GQ        +  + +
Sbjct: 350 EIIREQLQRKQNSK-IIVFTNYRETAKKIVNELVKDGIKAKRFVGQASKENDRGLSQREQ 408

Query: 268 EEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGR 321
           +     F R E  V+VAT     G+D P+V  V+ Y    +     Q  GR GR
Sbjct: 409 KLILDEFARGEFNVLVATSVGEEGLDVPEVDLVVFYEPVPSAIRSIQRRGRTGR 462

>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 = 46.7 bits (110), Expect = 8e-06
 Identities = 25/129 (19%), Positives = 55/129 (42%), Gaps = 11/129 (8%)

Query: 15  RPYQKDVIQRIIEKRDCLVVMATGSGKS-----LCYQLPPLVTGKTALVVSPLISLMQDQ 69
           R YQ+ +  +   + +CL+V+ TG GK+     +         GK  ++  P   L+   
Sbjct: 11  RIYQEVIYAKCK-ETNCLIVLPTGLGKTLIAMMIAEYRLTKYGGKVLMLA-PTKPLVLQH 68

Query: 70  VMSLKQR-GINAEFLGSAQTDSSVQTKAET-GYFQLLFMTPEKACIIPISFWSKLLKAGV 127
             S ++   +  E + +   + S + +++     +++  TP+      ++   ++    V
Sbjct: 69  AESFRRLFNLPPEKIVALTGEKSPEERSKAWARAKVIVATPQTIENDLLA--GRISLEDV 126

Query: 128 CLFAVDEAH 136
            L   DEAH
Sbjct: 127 SLIVFDEAH 135

>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 = 66.8 bits (164), Expect = 2e-12
 Identities = 31/104 (29%), Positives = 50/104 (48%), Gaps = 2/104 (1%)

Query: 220 EILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEI 279
           EIL     A   IV+  T +  + ++  L +      + HG      RE+A R F    +
Sbjct: 294 EILS--EQADGTIVFVETKRGADFLASFLSEKEFPTTSIHGDRLQSQREQALRDFKNGSM 351

Query: 280 RVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRDG 323
           +V++AT     G+D  +++HVI+Y  P  ++ Y    GR GR G
Sbjct: 352 KVLIATSVASRGLDIKNIKHVINYDMPSKIDDYVHRIGRTGRVG 395

>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 = 65.3 bits (160), Expect = 7e-12
 Identities = 26/106 (24%), Positives = 44/106 (41%), Gaps = 9/106 (8%)

Query: 229 GSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAF 288
              +++C T K    ++  L + G +     G+M  + R      F   + +V+V T   
Sbjct: 267 AQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVC 326

Query: 289 GMGIDKPDVRHVIHYGCP------KTLESYYQ---ESGRCGRDGIA 325
             GID   V  VI++  P         E+Y      +GR G+ G+A
Sbjct: 327 ARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLA 372

>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 = 65.4 bits (160), Expect = 8e-12
 Identities = 26/106 (24%), Positives = 44/106 (41%), Gaps = 9/106 (8%)

Query: 229 GSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAF 288
              +++C T K    ++  L + G +     G+M  + R      F   + +V+V T   
Sbjct: 334 AQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVC 393

Query: 289 GMGIDKPDVRHVIHYGCP------KTLESYYQ---ESGRCGRDGIA 325
             GID   V  VI++  P         E+Y      +GR G+ G+A
Sbjct: 394 ARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLA 439

>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 = 64.1 bits (157), Expect = 1e-11
 Identities = 29/106 (27%), Positives = 45/106 (42%), Gaps = 9/106 (8%)

Query: 229 GSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAF 288
           GS I++  T K    +   LK  G +    HG + ++ R+     F     +V++ T   
Sbjct: 244 GSSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVL 303

Query: 289 GMGIDKPDVRHVIHYGCPKTL------ESYYQ---ESGRCGRDGIA 325
             GID P V  V++Y  P          +Y      +GR GR G+A
Sbjct: 304 ARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVA 349

>3b6e_A Interferon-induced helicase C domain-containing P; DECH, DEXD/H RNA-binding helicase, innate immunity, IFIH1, S genomics; 1.60A {Homo sapiens} Length = 216

 Score = 59.8 bits (145), Expect = 1e-10
 Identities = 29/182 (15%), Positives = 63/182 (34%), Gaps = 26/182 (14%)

Query: 15  RPYQKDVIQRIIEKRDCLVVMATGSGKSL---------CYQLPPLVTGKTALVVSPLISL 65
           RPYQ +V Q  +E ++ ++ + TGSGK+            +          +V+   + L
Sbjct: 35  RPYQMEVAQPALEGKNIIICLPTGSGKTRVAVYIAKDHLDKKKKASEPGKVIVLVNKVLL 94

Query: 66  -MQDQVMSLKQRGINAEFLGSAQTDSSVQTKAETGY--FQLLFMTPEK---ACIIPISFW 119
             Q      +        +     D+ ++           ++  T +    + +   +  
Sbjct: 95  VEQLFRKEFQPFLKKWYRVIGLSGDTQLKISFPEVVKSCDIIISTAQILENSLLNLENGE 154

Query: 120 SKLLKAG-VCLFAVDEAH---------CISEWGHDFRLEYKQLDKLRTFLLGVPFV-ALT 168
              ++     L  +DE H          I       +L+  +L K    ++ +P +  LT
Sbjct: 155 DAGVQLSDFSLIIIDECHHTNKEAVYNNIMRHYLMQKLKNNRLKKENKPVIPLPQILGLT 214

Query: 169 AT 170
           A+
Sbjct: 215 AS 216

>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 = 59.4 bits (145), Expect = 4e-10
 Identities = 24/94 (25%), Positives = 38/94 (40%), Gaps = 4/94 (4%)

Query: 230 SIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFG 289
            +IV+  T   V ++ +        A    G +    R      F   E  +++ T    
Sbjct: 222 GVIVFVRTRNRVAKLVRLFD----NAIELRGDLPQSVRNRNIDAFREGEYDMLITTDVAS 277

Query: 290 MGIDKPDVRHVIHYGCPKTLESYYQESGRCGRDG 323
            G+D P V  VI++  P+ L +Y    GR GR G
Sbjct: 278 RGLDIPLVEKVINFDAPQDLRTYIHRIGRTGRMG 311

>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* 4a92_A* 1cu1_A 2zjo_A* 1a1v_A* 1hei_A 3kqn_A* 3kql_A* 3kqu_A* 3kqh_A 3kqk_A 8ohm_A 2f55_A 1jr6_A 1onb_A Length = 666

 Score = 55.0 bits (132), Expect = 2e-08
 Identities = 55/357 (15%), Positives = 92/357 (25%), Gaps = 77/357 (21%)

Query: 2   VSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVT--GKTALVV 59
           V +++      VF              +   +   TGSGKS   ++P      G   LV+
Sbjct: 207 VESMETTMRSPVF-TDNSSPPAVPQSFQVAHLHAPTGSGKST--KVPAAYAAQGYKVLVL 263

Query: 60  SPLISLMQDQVMSLKQRGINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFW 119
           +P ++      +        ++  G          +  T    + + T  K         
Sbjct: 264 NPSVAA----TLGFGAY--MSKAHGIDPNIR-TGVRTITTGAPVTYSTYGKFLADGGCS- 315

Query: 120 SKLLKAGVCLFAVDEAHCIS-EWGHDFRLEYKQLDKLRTFLLGVPFVALTAT--ATEKVR 176
                    +   DE H               Q +     L+    V  TAT   +  V 
Sbjct: 316 ----GGAYDIIICDECHSTDSTTILGIGTVLDQAETAGARLV----VLATATPPGSVTVP 367

Query: 177 IDIINSLKLKNPYVTIASFDRKNLFYGVKVINRGQSFVDELVQEILKSVAGAGSIIVYCM 236
              I                         V       +    + I       G  +++C 
Sbjct: 368 HPNIEE-----------------------VALSNTGEIPFYGKAIPIEAIRGGRHLIFCH 404

Query: 237 TIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPD 296
           + K  +E++  L  LG+ A  Y+  +          + +       VAT A   G    D
Sbjct: 405 SKKKCDELAAKLSGLGINAVAYYRGLDVSVIPTIGDVVV-------VATDALMTGY-TGD 456

Query: 297 VRHVIHYG---------------------CPKTLESYYQESGRCGRDGIASVCWLYY 332
              VI                         P+   S  Q  GR GR     +     
Sbjct: 457 FDSVIDCNTCVTQTVDFSLDPTFTIETTTVPQDAVSRSQRRGRTGRGR-RGIYRFVT 512

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4} Length = 510

 Score = 53.8 bits (128), Expect = 4e-08
 Identities = 47/330 (14%), Positives = 98/330 (29%), Gaps = 20/330 (6%)

Query: 14  FRPYQKDVIQRIIEKRDCLVVMATGSGKS-----LCYQLPPLVTGKTALVVSPLISLMQD 68
              YQKD +   +  R  ++ + T +G+S     L         GK  ++V       Q 
Sbjct: 114 PHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALLARYYLENYEGKILIIVPTTALTTQM 173

Query: 69  QVMSLKQRGINAEFLGSAQTDSSVQTKAETG--YFQLLFMTPEKACIIPISFWSKLL--- 123
               +  R  +   +      +S   K +         + T  K      S +  ++   
Sbjct: 174 ADDFVDYRLFSHAMIKKIGGGASKDDKYKNDAPVVVGTWQTVVKQPKEWFSQFGMMMNDE 233

Query: 124 -------KAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEKVR 176
                       +  ++            R     + +       +     T+   E  +
Sbjct: 234 CHLATGKSISSIISGLNNCMFKFGLSGSLRDGKANIMQYVGMFGEIFKPVTTSKLMEDGQ 293

Query: 177 IDIINSLKLKNPYVTIASFDRKNLFYG--VKVINRGQSFVDELVQEILKSVAGAGSIIVY 234
           +  +    +   Y    +   K   Y   +K+I         + +  +K      +  V 
Sbjct: 294 VTELKINSIFLRYPDEFTTKLKGKTYQEEIKIITGLSKRNKWIAKLAIKLAQKDENAFVM 353

Query: 235 CMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMA-FGMGID 293
              +   + I   +K    K     G++ ++ R     L    +  ++VA+   F  GI 
Sbjct: 354 FKHVSHGKAIFDLIKNEYDKVYYVSGEVDTETRNIMKTLAENGKGIIIVASYGVFSTGIS 413

Query: 294 KPDVRHVIHYGCPKTLESYYQESGRCGRDG 323
             ++ HV+     K+     Q  GR  R  
Sbjct: 414 VKNLHHVVLAHGVKSKIIVLQTIGRVLRKH 443

>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* Length = 472

 Score = 53.3 bits (128), Expect = 6e-08
 Identities = 34/184 (18%), Positives = 62/184 (33%), Gaps = 15/184 (8%)

Query: 118 FWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEKVRI 177
            +   L     L              D R+EY++ +K+    L    + L   A +  +I
Sbjct: 249 LFPDSLAGKH-LAKYTIKRIFVPLAEDERVEYEKREKVYKQFLRARGITLR-RAEDFNKI 306

Query: 178 DIINSLKLKNPYVTIASFDRKNLFYGVKVINRGQSFVDELVQEILKSVAGAGSIIVYCMT 237
            + +    +      A  + + + +  K   R        ++EIL+       II++   
Sbjct: 307 VMASGYDERAYEALRAWEEARRIAFNSKNKIR-------KLREILERHRK-DKIIIFTRH 358

Query: 238 IKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDV 297
            + V  ISK              +   + REE    F     R +V++     GID PD 
Sbjct: 359 NELVYRISKVFL-----IPAITHRTSREEREEILEGFRTGRFRAIVSSQVLDEGIDVPDA 413

Query: 298 RHVI 301
              +
Sbjct: 414 NVGV 417

>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* Length = 472

 Score = 42.5 bits (100), Expect = 2e-04
 Identities = 14/52 (26%), Positives = 25/52 (48%)

Query: 15  RPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVTGKTALVVSPLISLM 66
           R YQ+  ++R +  +   +V+ TGSGK+              L+V P ++L 
Sbjct: 95  RDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAAINELSTPTLIVVPTLALA 146

>3dmq_A RNA polymerase-associated protein RAPA; SWF2/SNF2, transcription factor, RNA polymerase recycling, activator, ATP-binding, DNA-binding; 3.20A {Escherichia coli K12} Length = 968

 Score = 50.9 bits (121), Expect = 4e-07
 Identities = 22/114 (19%), Positives = 48/114 (42%), Gaps = 5/114 (4%)

Query: 215 DELVQEILKSVAGAGS--IIVYCMTIKDVEEISKAL-KQLGVKAGTYHGQMGSKAREEAH 271
           D  V+ ++  +    S  ++V C       ++ + L ++ G++A  +H  M    R+ A 
Sbjct: 488 DPRVEWLMGYLTSHRSQKVLVICAKAATALQLEQVLREREGIRAAVFHEGMSIIERDRAA 547

Query: 272 RLFIRDE--IRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRDG 323
             F  ++   +V++ +     G +     H++ +  P   +   Q  GR  R G
Sbjct: 548 AWFAEEDTGAQVLLCSEIGSEGRNFQFASHMVMFDLPFNPDLLEQRIGRLDRIG 601

>3h1t_A Type I site-specific restriction-modification system, R (restriction) subunit; hydrolase, restriction enzyme HSDR, ATP-binding; 2.30A {Vibrio vulnificus} Length = 590

 Score = 50.5 bits (121), Expect = 4e-07
 Identities = 56/374 (14%), Positives = 106/374 (28%), Gaps = 118/374 (31%)

Query: 15  RPYQKDVIQRIIE-----KRDCLVVMATGSGK-----SLCYQLPPLVTGKTALVVSPLIS 64
           R YQ+  I R ++     K+  L+ MATG+GK      + ++L      +T     P I 
Sbjct: 180 RYYQQIAINRAVQSVLQGKKRSLITMATGTGKTVVAFQISWKLWSARWNRTGDYRKPRIL 239

Query: 65  LMQDQVMSLKQ-RGINAEFLGSAQTD--------------SSVQTKAETGYFQLLFMTPE 109
            + D+ + +   +       G A+                +  Q+ A       L+    
Sbjct: 240 FLADRNVLVDDPKDKTFTPFGDARHKIEGGKVVKSREIYFAIYQSIASDERRPGLYKEFP 299

Query: 110 KA---CIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRT--------F 158
           +     II                 +DE H         R   +     R         F
Sbjct: 300 QDFFDLII-----------------IDECH---------RGSARDNSNWREILEYFEPAF 333

Query: 159 LLGVPFVALTATATEKVRIDIIN---------SLK--LKNPY------------------ 189
            +G     +TAT   +   D            SL+  + + +                  
Sbjct: 334 QIG-----MTATPLREDNRDTYRYFGNPIYTYSLRQGIDDGFLAPYRVHRVISEVDAAGW 388

Query: 190 ------VTIASFDRKNLFYGVKVINRG---QSFVDELVQEILKSVAGAGSI---IVYCMT 237
                 V     +  +  Y  K   R    ++  D   + +   +         IV+C+ 
Sbjct: 389 RPSKGDVDRFGREIPDGEYQTKDFERVIALKARTDAFAKHLTDFMKRTDRFAKTIVFCVD 448

Query: 238 IKDVEEISKALKQLGVKAGTYHGQM----------GSKAREEAHRLFIRDEIRVMVATMA 287
            +  +E+ +AL  L       H               K      +        ++  +  
Sbjct: 449 QEHADEMRRALNNLNSDLSRKHPDYVARVTSEEGKIGKGHLSRFQELETSTPVILTTSQL 508

Query: 288 FGMGIDKPDVRHVI 301
              G+D P  ++V+
Sbjct: 509 LTTGVDAPTCKNVV 522

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus} Length = 555

 Score = 50.3 bits (119), Expect = 6e-07
 Identities = 22/140 (15%), Positives = 42/140 (30%), Gaps = 26/140 (18%)

Query: 15  RPYQKDVIQRIIEKRDCLVVMATGSGKSLC--------YQLPPLVTGKTALVVSPLISLM 66
           R YQ ++     + ++ ++   TG GK+           +  P       +  +  I + 
Sbjct: 6   RNYQLELALPAKKGKNTIICAPTGCGKTFVSLLICEHHLKKFPCGQKGKVVFFANQIPVY 65

Query: 67  QDQVMSLKQR-GINAEFLG--SAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLL 123
           + Q     +        +   S  T  SV  +       ++ +TP+             L
Sbjct: 66  EQQATVFSRYFERLGYNIASISGATSDSVSVQHIIEDNDIIILTPQI--------LVNNL 117

Query: 124 KAG-------VCLFAVDEAH 136
             G         L   DE H
Sbjct: 118 NNGAIPSLSVFTLMIFDECH 137

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus} Length = 555

 Score = 43.0 bits (100), Expect = 1e-04
 Identities = 23/104 (22%), Positives = 40/104 (38%), Gaps = 14/104 (13%)

Query: 231 IIVYCMTIKDVEEISKALKQL----GVKAGTYHGQ--------MGSKAREEAHRLF-IRD 277
            I++  T   V+ + K +++      +K G   G+        M   A++     F    
Sbjct: 392 TILFVKTRALVDALKKWIEENPALSFLKPGILTGRGRTNRATGMTLPAQKCVLEAFRASG 451

Query: 278 EIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGR 321
           +  +++AT     GID  +   VI Y     +    Q  GR GR
Sbjct: 452 DNNILIATSVADEGIDIAECNLVILYEYVGNVIKMIQTRGR-GR 494

>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* Length = 556

 Score = 49.2 bits (116), Expect = 1e-06
 Identities = 24/133 (18%), Positives = 45/133 (33%), Gaps = 12/133 (9%)

Query: 15  RPYQKDVIQRIIEKRDCLVVMATGSGKSLC--------YQLPPLVTGKTALVVSPLISLM 66
           R YQ ++ Q  I  ++ L+   TGSGK+          +Q  P       + ++  + + 
Sbjct: 9   RSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVY 68

Query: 67  QDQVMSLKQR-GINAEFLGSAQTD--SSVQTKAETGYFQLLFMTPEKACIIPISFWSKLL 123
           + Q    K         +     +  S+V  +       ++ +TP+             L
Sbjct: 69  EQQKNVFKHHFERQGYSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFEDGTLTSL 128

Query: 124 KAGVCLFAVDEAH 136
                L   DE H
Sbjct: 129 SI-FTLMIFDECH 140

>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* Length = 556

 Score = 40.7 bits (94), Expect = 6e-04
 Identities = 21/104 (20%), Positives = 39/104 (37%), Gaps = 14/104 (13%)

Query: 231 IIVYCMTIKDVEEISKALKQL----GVKAGTYHGQ--------MGSKAREEAHRLFIRDE 278
            +++  T   V  + K +++      +K G   G+        M   +++     F   +
Sbjct: 393 TLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTSK 452

Query: 279 I-RVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGR 321
             R+++AT     GID      V+ Y     +    Q  GR GR
Sbjct: 453 DNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGR-GR 495

>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* Length = 440

 Score = 48.7 bits (116), Expect = 2e-06
 Identities = 41/353 (11%), Positives = 90/353 (25%), Gaps = 69/353 (19%)

Query: 25  IIEKRDCLVVMATGSGKSLCYQLPP------LVTGKTALVVSPLISLMQDQVMSLKQRGI 78
           + +    ++    G+GK+   +  P             LV++P   ++ +   +     +
Sbjct: 5   LKKGMTTVLDFHPGAGKTR--RFLPQILAECARRRLRTLVLAPTRVVLSEMKEAFHGLDV 62

Query: 79  NAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCI 138
                  +   S  +      +  L +   E   +               +  +DEAH +
Sbjct: 63  KFHTQAFSAHGSGREVIDAMCHATLTYRMLEPTRV-----------VNWEVIIMDEAHFL 111

Query: 139 SEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEKVRIDIINSLKLKNPYVTIASFDRK 198
                  R         R        + +TAT           S +  +    I      
Sbjct: 112 DPASIAARG----WAAHRARANESATILMTATPPGT-------SDEFPHSNGEIEDVQT- 159

Query: 199 NLFYGVKVINRGQSFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTY 258
                 +  N G  ++                   +  +I+    ++ +L++ G      
Sbjct: 160 --DIPSEPWNTGHDWILA----------DKRPTAWFLPSIRAANVMAASLRKAGKSVVVL 207

Query: 259 HGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYG-------------- 304
           + +   +          + +   ++AT    MG +   V  V+                 
Sbjct: 208 NRKTFEREYPTIK----QKKPDFILATDIAEMGANL-CVERVLDCRTAFKPVLVDEGRKV 262

Query: 305 -----CPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFYCGESQTENQ 352
                   +  S  Q  GR GR+         Y  S     +        E  
Sbjct: 263 AIKGPLRISASSAAQRRGRIGRNPNR--DGDSYYYSEPTSENNAHHVCWLEAS 313

>3rc3_A ATP-dependent RNA helicase SUPV3L1, mitochondrial; SUV3, nucleus, hydrolase; HET: ANP; 2.08A {Homo sapiens} PDB: 3rc8_A Length = 677

 Score = 48.0 bits (113), Expect = 3e-06
 Identities = 45/324 (13%), Positives = 97/324 (29%), Gaps = 54/324 (16%)

Query: 15  RPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVTGKTALVVSPLISLMQDQVMSLK 74
            P       R ++++       T SGK+  + +    + K+ +   PL  L  +      
Sbjct: 142 IPPNWYPDARAMQRKIIFHSGPTNSGKTY-HAIQKYFSAKSGVYCGPLKLLAHEIFEKSN 200

Query: 75  QRGINAEFL-GSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVD 133
             G+  + + G  +       K  +        T E   +             V +    
Sbjct: 201 AAGVPCDLVTGEERVTVQPNGKQASHVS----CTVEMCSVTT--------PYEVAVIDEI 248

Query: 134 EAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEKVRIDIINSLKLKNPYVTIA 193
           +       G  +             LLG+    +           ++  +      V + 
Sbjct: 249 QMIRDPARGWAWTRA----------LLGLCAEEVHLCGEPAAIDLVMELMYTTGEEVEVR 298

Query: 194 SFDRKNLFYGVKVINRGQSFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGV 253
            + R      +         +                  + C +  D+  +S+ ++  G+
Sbjct: 299 DYKRLTPISVLDHALESLDNLRPGDC-------------IVCFSKNDIYSVSRQIEIRGL 345

Query: 254 KAGTYHGQMGSKAREEAHRLFI--RDEIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLES 311
           ++   +G +    +    + F    D  +++VAT A GMG++   +R +I Y   K   +
Sbjct: 346 ESAVIYGSLPPGTKLAQAKKFNDPNDPCKILVATDAIGMGLNLS-IRRIIFYSLIKPSIN 404

Query: 312 YY--------------QESGRCGR 321
                           Q +GR GR
Sbjct: 405 EKGERELEPITTSQALQIAGRAGR 428

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A* Length = 696

 Score = 46.5 bits (109), Expect = 1e-05
 Identities = 21/142 (14%), Positives = 44/142 (30%), Gaps = 14/142 (9%)

Query: 11  YSVF--RPYQKDVIQRIIEKRDCLVVMATGSGKSLC--------YQLPPLVTGKTALVVS 60
           YS F  R YQ ++    ++ ++ ++   TG GK+           +  P       +  +
Sbjct: 9   YSPFKPRNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFPQGQKGKVVFFA 68

Query: 61  PLISLMQDQVMSLKQR-GINAEFLGSAQTDSSVQTKAETGY--FQLLFMTPEKACIIPIS 117
             I + +       +    +   +      ++     E       ++ +TP+        
Sbjct: 69  NQIPVYEQNKSVFSKYFERHGYRVTGISGATAENVPVEQIVENNDIIILTPQILVNNLKK 128

Query: 118 FWSKLLKAGVCLFAVDEAHCIS 139
                L     L   DE H  S
Sbjct: 129 GTIPSLSI-FTLMIFDECHNTS 149

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A* Length = 696

 Score = 42.3 bits (98), Expect = 2e-04
 Identities = 21/120 (17%), Positives = 42/120 (35%), Gaps = 15/120 (12%)

Query: 214 VDELVQEILK--SVAGAGSIIVYCMTIKDVEEISKALKQL----GVKAGTYHGQ------ 261
           +++L   + +   +      I++  T   V+ +   ++       +K G   G+      
Sbjct: 382 LEDLCFILQEEYHLNPETITILFVKTRALVDALKNWIEGNPKLSFLKPGILTGRGKTNQN 441

Query: 262 --MGSKAREEAHRLF-IRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGR 318
             M   A++     F    +  +++AT     GID      VI Y     +    Q  GR
Sbjct: 442 TGMTLPAQKCILDAFKASGDHNILIATSVADEGIDIAQCNLVILYEYVGNVIKMIQTRGR 501

>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} Length = 936

 Score = 45.7 bits (107), Expect = 2e-05
 Identities = 21/104 (20%), Positives = 39/104 (37%), Gaps = 14/104 (13%)

Query: 231 IIVYCMTIKDVEEISKALKQL----GVKAGTYHGQ--------MGSKAREEAHRLFIRDE 278
            +++  T   V  + K +++      +K G   G+        M   +++     F   +
Sbjct: 634 TLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTSK 693

Query: 279 I-RVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGR 321
             R+++AT     GID      V+ Y     +    Q  GR GR
Sbjct: 694 DNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGR-GR 736

>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} Length = 936

 Score = 44.6 bits (104), Expect = 4e-05
 Identities = 24/133 (18%), Positives = 45/133 (33%), Gaps = 12/133 (9%)

Query: 15  RPYQKDVIQRIIEKRDCLVVMATGSGKSLC--------YQLPPLVTGKTALVVSPLISLM 66
           R YQ ++ Q  I  ++ L+   TGSGK+          +Q  P       + ++  + + 
Sbjct: 250 RSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVY 309

Query: 67  QDQVMSLKQR-GINAEFLGSAQTD--SSVQTKAETGYFQLLFMTPEKACIIPISFWSKLL 123
           + Q    K         +     +  S+V  +       ++ +TP+             L
Sbjct: 310 EQQKNVFKHHFERQGYSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFEDGTLTSL 369

Query: 124 KAGVCLFAVDEAH 136
                L   DE H
Sbjct: 370 SI-FTLMIFDECH 381

>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} Length = 797

 Score = 45.7 bits (107), Expect = 2e-05
 Identities = 23/133 (17%), Positives = 46/133 (34%), Gaps = 12/133 (9%)

Query: 15  RPYQKDVIQRIIEKRDCLVVMATGSGKSLC--------YQLPPLVTGKTALVVSPLISLM 66
           R YQ ++ Q  I  ++ L+   TGSGK+          +Q  P       + ++  + + 
Sbjct: 250 RSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVY 309

Query: 67  QDQVMSLKQR-GINAEFLGSAQTD--SSVQTKAETGYFQLLFMTPEKACIIPISFWSKLL 123
           + Q    K         +     +  S+V  +       ++ +TP+          +   
Sbjct: 310 EQQKNVFKHHFERQGYSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNS-FEDGTLTS 368

Query: 124 KAGVCLFAVDEAH 136
            +   L   DE H
Sbjct: 369 LSIFTLMIFDECH 381

>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} Length = 797

 Score = 43.0 bits (100), Expect = 1e-04
 Identities = 21/104 (20%), Positives = 39/104 (37%), Gaps = 14/104 (13%)

Query: 231 IIVYCMTIKDVEEISKALKQL----GVKAGTYHGQ--------MGSKAREEAHRLFIRDE 278
            +++  T   V  + K +++      +K G   G+        M   +++     F   +
Sbjct: 634 TLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTSK 693

Query: 279 I-RVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGR 321
             R+++AT     GID      V+ Y     +    Q  GR GR
Sbjct: 694 DNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGR-GR 736

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 44.5 bits (104), Expect = 5e-05
 Identities = 52/402 (12%), Positives = 119/402 (29%), Gaps = 108/402 (26%)

Query: 2   VSTLKKYFGYSVFRPYQKDVIQRIIEK-RDC--LVV--MATGSGKSLCYQLPPLVTGKTA 56
                KY    V R      +++ + + R    +++  +  GSGK+              
Sbjct: 123 NQVFAKYN---VSRLQPYLKLRQALLELRPAKNVLIDGVL-GSGKT-------------W 165

Query: 57  LVVSPLISLMQDQVMSLKQRGINAEF---LGSAQTDSSVQTKAETGYFQL---LFMTPEK 110
           + +   +S      M      I   F   L +  +  +V    +   +Q+        + 
Sbjct: 166 VALDVCLSYKVQCKMD---FKI---FWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDH 219

Query: 111 ACIIPISFWS------KLLKAGV---CLFAVDEAHCISEWGHDFRLEYKQLDK--LRTFL 159
           +  I +   S      +LLK+     CL  +                    +      F 
Sbjct: 220 SSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNV-----Q-----------NAKAWNAFN 263

Query: 160 LGVPFVALT--ATATEKVRIDIINSLKLKNPYVTIASFDRKNLFYGVKVINRGQSFVDEL 217
           L    +  T     T+ +       + L +  +T+   + K+L   +K ++       +L
Sbjct: 264 LSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLL--LKYLDCR---PQDL 318

Query: 218 VQEILK------SVAGAGSIIVYCMTIK-----DVEEISKALKQLGVKAGTYHGQMGSKA 266
            +E+L       S+    SI     T       + ++++  ++       + +    ++ 
Sbjct: 319 PREVLTTNPRRLSIIAE-SIRDGLATWDNWKHVNCDKLTTIIES------SLNVLEPAEY 371

Query: 267 REEAHRLFI-RDEIRVMVATMA-FGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRDGI 324
           R+   RL +      +    ++     + K DV  V++     +L           +   
Sbjct: 372 RKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSL---------VEKQPK 422

Query: 325 ASVCWLYYARSNFAKGDFYCGESQTENQRTAIMESLLAAQRY 366
            S   +            Y           A+  S++    Y
Sbjct: 423 ESTISIP---------SIYLELKVKLENEYALHRSIV--DHY 453

>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 Length = 451

 Score = 44.1 bits (104), Expect = 5e-05
 Identities = 47/346 (13%), Positives = 93/346 (26%), Gaps = 79/346 (22%)

Query: 27  EKRDCLVVMATGSGKS----LCYQLPPLVTGKTALVVSP---LISLMQDQVMSL--KQRG 77
           +KR  ++ +  G+GK+           L+     L+++P   + + M++ +  L  + + 
Sbjct: 18  KKRLTIMDLHPGAGKTKRILPSIVREALLRRLRTLILAPTRVVAAEMEEALRGLPIRYQT 77

Query: 78  INAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHC 137
              +   + +    +        F    ++  +                  L  +DEAH 
Sbjct: 78  PAVKSDHTGREIVDLMC---HATFTTRLLSSTRV-------------PNYNLIVMDEAHF 121

Query: 138 ISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEKVRIDIINSLKLKNPYVTIASFDR 197
                   R       ++           +  TAT         +         I   +R
Sbjct: 122 TDPCSVAARGYISTRVEMGEAAA------IFMTATPPGS-----TDPFPQSNSPIEDIER 170

Query: 198 KNLFYGVKVINRGQSFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGT 257
           +                D +           G  + +  +IK   +I+  L++ G +   
Sbjct: 171 EIPERSWNTG------FDWITDY-------QGKTVWFVPSIKAGNDIANCLRKSGKRVIQ 217

Query: 258 YHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMG--IDKPDVRHVIHYG----------- 304
              +       +        +   +V T    MG          VI              
Sbjct: 218 LSRKTFDTEYPKTK----LTDWDFVVTTDISEMGANF---RAGRVIDPRRCLKPVILTDG 270

Query: 305 ---------CPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGD 341
                     P T  S  Q  GR GR+  A     Y    +  K D
Sbjct: 271 PERVILAGPIPVTPASAAQRRGRIGRNP-AQEDDQYVFSGDPLKND 315

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A Length = 431

 Score = 43.3 bits (102), Expect = 9e-05
 Identities = 45/349 (12%), Positives = 94/349 (26%), Gaps = 81/349 (23%)

Query: 28  KRDCLVVMA-TGSGKSLCYQLPP-------LVTGKTALVVSP---LISLMQDQVMSLKQR 76
           KR+  V+    G+GK+   ++ P           +T ++++P   + S M + +     R
Sbjct: 1   KRELTVLDLHPGAGKTR--RVLPQLVREAVKKRLRT-VILAPTRVVASEMYEALRGEPIR 57

Query: 77  GINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAH 136
            +      S +T + +        F +  +              ++    + +   DEAH
Sbjct: 58  YMTPAV-QSERTGNEIVDFMCHSTFTMKLLQG-----------VRVPNYNLYIM--DEAH 103

Query: 137 CISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEKVRIDIINSLKLKNPYVTIASFD 196
            +       R   +    +           +  TAT         +         I   +
Sbjct: 104 FLDPASVAARGYIETRVSMGDAGA------IFMTATPPGT-----TEAFPPSNSPIIDEE 152

Query: 197 RKNLFYGVKVINRGQSFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAG 256
            +                 E + E        G  + +  +IK   EI   L++ G K  
Sbjct: 153 TRIPDKAWNSGY-------EWITE------FDGRTVWFVHSIKQGAEIGTCLQKAGKKVL 199

Query: 257 TYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMG--IDKPDVRHVI-------HYGCPK 307
             + +       +       ++   ++ T    MG          VI             
Sbjct: 200 YLNRKTFESEYPKC----KSEKWDFVITTDISEMGANF---KADRVIDPRKTIKPILLDG 252

Query: 308 TLESYY----------QESGRCGR--DGIASVCWLYYARSNFAKGDFYC 344
            +              Q  GR GR  + +    + Y    +        
Sbjct: 253 RVSMQGPIAITPASAAQRRGRIGRNPEKLG-DIYAYSGNVSSDNEGHVS 300

>2z83_A Helicase/nucleoside triphosphatase; hydrolase, membrane, nucleotide-binding, RNA replication, transmembrane, viral protein; 1.80A {Japanese encephalitis virus} PDB: 2v8o_A 2qeq_A Length = 459

 Score = 41.4 bits (97), Expect = 3e-04
 Identities = 44/335 (13%), Positives = 86/335 (25%), Gaps = 77/335 (22%)

Query: 18  QKDVIQRIIEKRDCLVVMA-TGSGKSLCYQLPP------LVTGKTALVVSP---LISLMQ 67
                  ++ KR   V+    GSGK+   ++ P      +       V++P   + + M 
Sbjct: 10  MGRGSPNMLRKRQMTVLDLHPGSGKTR--KILPQIIKDAIQQRLRTAVLAPTRVVAAEMA 67

Query: 68  DQVMSLKQRGINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGV 127
           + +            +      + +             M+P +                 
Sbjct: 68  EALRG-LPVRYQTSAVQREHQGNEIVDVMCHATLTHRLMSPNRV-------------PNY 113

Query: 128 CLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEKVRIDIINSLKLKN 187
            LF +DEAH         R       +L         + +TAT                +
Sbjct: 114 NLFVMDEAHFTDPASIAARGYIATKVELGEAAA----IFMTATPPGTT-----------D 158

Query: 188 PYVTIASFDRKNLFYGVKVINRGQSFVDELVQEILKSVA-GAGSIIVYCMTIKDVEEISK 246
           P+                   + +   D       + +   AG  + +  ++K   EI+ 
Sbjct: 159 PFPDS---------NAPIHDLQDE-IPDRAWSSGYEWITEYAGKTVWFVASVKMGNEIAM 208

Query: 247 ALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCP 306
            L++ G K    + +       +        +   ++ T    MG +      VI     
Sbjct: 209 CLQRAGKKVIQLNRKSYDTEYPKCK----NGDWDFVITTDISEMGANF-GASRVIDCRKS 263

Query: 307 KTLESYY--------------------QESGRCGR 321
                                      Q  GR GR
Sbjct: 264 VKPTILEEGEGRVILGNPSPITSASAAQRRGRVGR 298

>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 Length = 237

 Score = 40.8 bits (96), Expect = 3e-04
 Identities = 14/59 (23%), Positives = 26/59 (44%), Gaps = 12/59 (20%)

Query: 15  RPYQKDVIQRIIEKRDCLVVMATGSGKSL------CYQLPPLVTGKTALVVSPLISLMQ 67
           R YQ+  ++R +  +   +V+ TGSGK+                    L+V P ++L +
Sbjct: 95  RDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAAINE------LSTPTLIVVPTLALAE 147

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii} Length = 540

 Score = 40.3 bits (94), Expect = 9e-04
 Identities = 14/85 (16%), Positives = 30/85 (35%), Gaps = 5/85 (5%)

Query: 7  KYFGYSVFRPYQKDVIQRIIE----KRDCLVVMATGSGKSLCYQLPPLVTGKTALVVSPL 62
          +       R +Q + +   I      +  L+    G GK++  ++  +   K  L+ +  
Sbjct: 2  EVLKLQ-LRQWQAEKLGEAINALKHGKTLLLNAKPGLGKTVFVEVLGMQLKKKVLIFTRT 60

Query: 63 ISLMQDQVMSLKQRGINAEFLGSAQ 87
           S +     + K  G+   FL    
Sbjct: 61 HSQLDSIYKNAKLLGLKTGFLIGKS 85

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	374
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	100.0
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	100.0
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	100.0
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	100.0
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	100.0
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	100.0
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	100.0
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	100.0
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	100.0
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	100.0
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	100.0
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	100.0
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	100.0
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	100.0
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	100.0
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	100.0
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	100.0
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	100.0
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	100.0
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	100.0
4gl2_A	699	Interferon-induced helicase C domain-containing P;	100.0
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	100.0
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	100.0
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	100.0
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	100.0
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	100.0
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	100.0
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	100.0
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	100.0
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	100.0
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	100.0
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	100.0
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	100.0
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	100.0
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	100.0
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	100.0
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	100.0
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	100.0
1tf5_A	844	Preprotein translocase SECA subunit; ATPase, helic	100.0
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	100.0
3h1t_A	590	Type I site-specific restriction-modification syst	100.0
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	100.0
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	100.0
1yks_A	440	Genome polyprotein [contains: flavivirin protease	100.0
2fsf_A	853	Preprotein translocase SECA subunit; ATPase, DNA-R	100.0
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	100.0
1nkt_A	922	Preprotein translocase SECA 1 subunit; preprotein	100.0
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	100.0
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	100.0
1z63_A	500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	100.0
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	100.0
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	100.0
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	100.0
3rc3_A	677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	100.0
3mwy_W	800	Chromo domain-containing protein 1; SWI2/SNF2 ATPa	100.0
1z3i_X	644	Similar to RAD54-like; recombination ATPase helica	100.0
2w00_A	1038	HSDR, R.ECOR124I; ATP-binding, DNA-binding, restri	100.0
3jux_A	822	Protein translocase subunit SECA; protein transloc	99.97
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	99.96
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	99.96
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	99.95
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	99.95
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	99.95
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	99.95
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	99.95
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	99.95
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	99.95
2ipc_A	997	Preprotein translocase SECA subunit; nucleotide bi	99.95
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	99.95
3bor_A	237	Human initiation factor 4A-II; translation initiat	99.95
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	99.95
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	99.95
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	99.95
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	99.94
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	99.94
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	99.94
2vl7_A	540	XPD; helicase, unknown function; 2.25A {Sulfolobus	99.93
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	99.93
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	99.93
3eaq_A	212	Heat resistant RNA dependent ATPase; DEAD box RNA	99.92
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	99.92
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	99.92
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	99.91
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	99.91
3i32_A	300	Heat resistant RNA dependent ATPase; RNA helicase,	99.9
2yjt_D	170	ATP-dependent RNA helicase SRMB, regulator of ribo	99.82
3crv_A	551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	99.88
3b6e_A	216	Interferon-induced helicase C domain-containing P;	99.88
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	99.87
1rif_A	282	DAR protein, DNA helicase UVSW; bacteriophage, REC	99.86
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	99.83
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	99.8
1z5z_A	271	Helicase of the SNF2/RAD54 family; hydrolase, reco	99.77
4b3f_X	646	DNA-binding protein smubp-2; hydrolase, helicase;	98.72
1w36_D	608	RECD, exodeoxyribonuclease V alpha chain; recombin	98.68
2gk6_A	624	Regulator of nonsense transcripts 1; UPF1, helicas	98.53
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	98.42
2xzl_A	802	ATP-dependent helicase NAM7; hydrolase-RNA complex	98.42
2wjy_A	800	Regulator of nonsense transcripts 1; nonsense medi	98.38
3e1s_A	574	Exodeoxyribonuclease V, subunit RECD; alpha and be	98.27
3lfu_A	647	DNA helicase II; SF1 helicase, ATP-binding, DNA da	98.11
3hgt_A	328	HDA1 complex subunit 3; RECA-like domain, SWI2/SNF	97.72
3vkw_A	446	Replicase large subunit; alpha/beta domain, helica	97.69
2o0j_A	385	Terminase, DNA packaging protein GP17; nucleotide-	97.63
3cpe_A	592	Terminase, DNA packaging protein GP17; large termi	97.49
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	97.45
2j9r_A	214	Thymidine kinase; TK1, DNK, lasso, transferase, AT	97.37
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	97.32
1xx6_A	191	Thymidine kinase; NESG, northeast structural genom	97.21
3e2i_A	219	Thymidine kinase; Zn-binding, ATP-binding, DNA syn	97.14
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	97.09
3co5_A	143	Putative two-component system transcriptional RES	97.05
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	96.93
2zpa_A	671	Uncharacterized protein YPFI; RNA modification enz	96.92
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	96.86
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	96.73
3pvs_A	447	Replication-associated recombination protein A; ma	96.7
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	96.69
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	96.63
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	96.54
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	96.53
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	96.5
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	96.46
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	96.45
3bos_A	242	Putative DNA replication factor; P-loop containing	96.44
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	96.43
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	96.43
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	96.39
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	96.36
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	96.34
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	96.3
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	96.3
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	96.29
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	96.27
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	96.24
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	96.21
1uaa_A	673	REP helicase, protein (ATP-dependent DNA helicase	96.2
1pjr_A	724	PCRA; DNA repair, DNA replication, SOS response, h	96.2
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	96.15
2orv_A	234	Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'- (2	96.14
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	96.1
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	96.09
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	96.05
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	96.04
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	95.97
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	95.85
1w4r_A	195	Thymidine kinase; type II, human, cytosolic, phosp	95.84
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	95.8
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	95.75
3u4q_A	1232	ATP-dependent helicase/nuclease subunit A; helicas	95.72
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	95.66
2chg_A	226	Replication factor C small subunit; DNA-binding pr	95.59
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	95.55
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	95.44
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	95.39
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	95.38
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	95.34
1g5t_A	196	COB(I)alamin adenosyltransferase; P-loop protein,	95.34
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	95.33
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	95.32
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	95.3
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	95.19
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	95.16
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	95.16
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	95.15
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	94.94
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	94.71
2cvh_A	220	DNA repair and recombination protein RADB; filamen	94.57
2r6a_A	454	DNAB helicase, replicative helicase; replication,	94.51
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	94.39
3hjh_A	483	Transcription-repair-coupling factor; MFD, mutatio	94.32
2q6t_A	444	DNAB replication FORK helicase; hydrolase; 2.90A {	94.28
1v5w_A	343	DMC1, meiotic recombination protein DMC1/LIM15 hom	94.24
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	94.22
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	94.21
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	94.19
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	94.04
2ehv_A	251	Hypothetical protein PH0186; KAIC, RECA ATPase, un	94.02
2vhj_A	331	Ntpase P4, P4; non- hydrolysable ATP analogue, hyd	93.94
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	93.92
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	93.9
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	93.84
2zts_A	251	Putative uncharacterized protein PH0186; KAIC like	93.74
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	93.73
1u94_A	356	RECA protein, recombinase A; homologous recombinat	93.57
2z43_A	324	DNA repair and recombination protein RADA; archaea	93.52
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	93.43
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	93.36
3hr8_A	356	Protein RECA; alpha and beta proteins (A/B, A+B),	93.3
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	93.1
1vma_A	306	Cell division protein FTSY; TM0570, structural gen	93.1
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	93.05
2zr9_A	349	Protein RECA, recombinase A; recombination, RECA m	93.01
1xp8_A	366	RECA protein, recombinase A; recombination, radior	92.93
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	92.73
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	92.66
3bgw_A	444	DNAB-like replicative helicase; ATPase, replicatio	91.93
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	91.91
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	91.89
3io5_A	333	Recombination and repair protein; storage dimer, i	91.59
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	91.49
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	91.46
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	91.43
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	91.3
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	91.24
3b85_A	208	Phosphate starvation-inducible protein; PHOH2, ATP	91.12
2l82_A	162	Designed protein OR32; structural genomics, northe	90.84
2i1q_A	322	DNA repair and recombination protein RADA; ATPase,	90.71
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	90.27
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	89.77
1tue_A	212	Replication protein E1; helicase, replication, E1E	89.73
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	89.1
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	89.04
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	88.96
2oap_1	511	GSPE-2, type II secretion system protein; hexameri	88.53
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	88.33
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	88.23
2r44_A	331	Uncharacterized protein; putative ATPase, structur	88.05
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	87.74
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	87.58
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	87.55
1ls1_A	295	Signal recognition particle protein; FFH, SRP54, S	87.41
2qgz_A	308	Helicase loader, putative primosome component; str	87.27
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	87.14
3nwn_A	359	Kinesin-like protein KIF9; motor domain, ADP, stru	87.09
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	86.98
3lda_A	400	DNA repair protein RAD51; DNA binding protein, ATP	86.8
1u0j_A	267	DNA replication protein; AAA+ protein, P-loop atpa	86.75
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	86.56
1q57_A	503	DNA primase/helicase; dntpase, DNA replication, tr	86.55
1lvg_A	198	Guanylate kinase, GMP kinase; transferase; HET: AD	86.43
3vaa_A	199	Shikimate kinase, SK; structural genomics, center	86.33
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	86.27
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	86.2
1kgd_A	180	CASK, peripheral plasma membrane CASK; maguk, guan	86.12
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	86.08
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	86.0
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	85.97
1bg2_A	325	Kinesin; motor protein, ATPase, microtubule associ	85.95
1xjc_A	169	MOBB protein homolog; structural genomics, midwest	85.69
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	85.66
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	85.42
3dr5_A	221	Putative O-methyltransferase; Q8NRD3, CGL1119, PF0	85.36
2yhs_A	503	FTSY, cell division protein FTSY; cell cycle, prot	85.32
2gza_A	361	Type IV secretion system protein VIRB11; ATPase, h	85.2
1p9r_A	418	General secretion pathway protein E; bacterial typ	85.16
1t5c_A	349	CENP-E protein, centromeric protein E; kinesin mot	85.11
3gbj_A	354	KIF13B protein; kinesin, motor domain, ADP, struct	85.1
1c9k_A	180	COBU, adenosylcobinamide kinase; alpha/beta struct	85.09
3b6u_A	372	Kinesin-like protein KIF3B; structural genomics co	85.08
2h58_A	330	Kinesin-like protein KIFC3 variant; motor domain,	85.07
2vvg_A	350	Kinesin-2; motor protein, nucleotide-binding, micr	85.0
3trf_A	185	Shikimate kinase, SK; amino acid biosynthesis, tra	84.93
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	84.93
2qor_A	204	Guanylate kinase; phosphotransferase, purine metab	84.91
2nr8_A	358	Kinesin-like protein KIF9; motor domain, ADP, stru	84.81
3lw7_A	179	Adenylate kinase related protein (ADKA-like); AMP,	84.78
1qhx_A	178	CPT, protein (chloramphenicol phosphotransferase);	84.69
2y65_A	365	Kinesin, kinesin heavy chain; motor protein; HET:	84.65
3dc4_A	344	Kinesin-like protein NOD; catalytic domain, ATPase	84.64
4etp_A	403	Kinesin-like protein KAR3; kinesin motor protein,	84.52
3lre_A	355	Kinesin-like protein KIF18A; motor protein, nucleo	84.5
1goj_A	355	Kinesin, kinesin heavy chain; motor protein, ATPas	84.47
2zfi_A	366	Kinesin-like protein KIF1A, kinesin heavy chain is	84.41
1j8m_F	297	SRP54, signal recognition 54 kDa protein; signalin	84.4
1kag_A	173	SKI, shikimate kinase I; transferase, structural g	84.34
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	84.27
2eyu_A	261	Twitching motility protein PILT; pilus retraction	84.27
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	84.21
1x88_A	359	Kinesin-like protein KIF11; switch II, motor domai	84.2
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	84.19
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	84.01
3a8t_A	339	Adenylate isopentenyltransferase; rossmann fold pr	84.0
3tau_A	208	Guanylate kinase, GMP kinase; structural genomics,	83.97
1zp6_A	191	Hypothetical protein ATU3015; alpha-beta protein.,	83.91
4a14_A	344	Kinesin, kinesin-like protein KIF7; motor protein,	83.87
3eaq_A	212	Heat resistant RNA dependent ATPase; DEAD box RNA	83.85
3cob_A	369	Kinesin heavy chain-like protein; motor, switch II	83.72
3iij_A	180	Coilin-interacting nuclear ATPase protein; alpha a	83.71
1v8k_A	410	Kinesin-like protein KIF2C; microtubule destabiliz	83.7
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	83.65
2j37_W	504	Signal recognition particle 54 kDa protein (SRP54)	83.64
3u06_A	412	Protein claret segregational; motor domain, stalk	83.6
2pt7_A	330	CAG-ALFA; ATPase, protein-protein complex, type IV	83.58
1yks_A	440	Genome polyprotein [contains: flavivirin protease	83.57
2wbe_C	373	Bipolar kinesin KRP-130; EG5, KLP61F, tubulin, mit	83.52
3tr0_A	205	Guanylate kinase, GMP kinase; purines, pyrimidines	83.47
1ex7_A	186	Guanylate kinase; substrate-induced FIT, domain mo	83.38
1e9r_A	437	Conjugal transfer protein TRWB; coupling protein,	83.21
1ly1_A	181	Polynucleotide kinase; PNK, phosphatase, transfera	83.07
2qmh_A	205	HPR kinase/phosphorylase; V267F mutation, ATP-bind	83.05
1y63_A	184	LMAJ004144AAA protein; structural genomics, protei	82.97
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	82.88
2owm_A	443	Nckin3-434, related to kinesin-like protein KIF1C;	82.84
3bfn_A	388	Kinesin-like protein KIF22; limited proteolysis, s	82.69
3kb2_A	173	SPBC2 prophage-derived uncharacterized protein YOR	82.66
2heh_A	387	KIF2C protein; kinesin, motor domain, ADP, structu	82.6
2j41_A	207	Guanylate kinase; GMP, GMK, transferase, ATP-bindi	82.53
2ze6_A	253	Isopentenyl transferase; crown GALL tumor, cytokin	82.51
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	82.49
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	82.42
1z6g_A	218	Guanylate kinase; structural genomics, SGC, struct	82.31
3a00_A	186	Guanylate kinase, GMP kinase; domain movement, dim	82.07
3t0q_A	349	AGR253WP; kinesin, alpha and beta proteins, P-loop	81.83
4gp7_A	171	Metallophosphoesterase; polynucleotide kinase phos	81.69
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	81.64
3cm0_A	186	Adenylate kinase; ATP-binding, cytoplasm, nucleoti	81.48
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	81.47
3ney_A	197	55 kDa erythrocyte membrane protein; structural ge	81.43
1f9v_A	347	Kinesin-like protein KAR3; kinesin-related protein	81.4
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	81.39
3exa_A	322	TRNA delta(2)-isopentenylpyrophosphate transferase	81.36
1znw_A	207	Guanylate kinase, GMP kinase; ATP:GMP-phosphotrans	81.29
1s96_A	219	Guanylate kinase, GMP kinase; E.coli, dimer, SAD,	81.06
3foz_A	316	TRNA delta(2)-isopentenylpyrophosphate transferas;	80.96
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	80.92
2rep_A	376	Kinesin-like protein KIFC1; structural genomics co	80.78
3bor_A	237	Human initiation factor 4A-II; translation initiat	80.64
2xxa_A	433	Signal recognition particle protein; protein trans	80.54
4eun_A	200	Thermoresistant glucokinase; putative sugar kinase	80.51
2ffh_A	425	Protein (FFH); SRP54, signal recognition particle,	80.38
1kht_A	192	Adenylate kinase; phosphotransferase, signaling pr	80.2

>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=100.00  E-value=1.5e-59  Score=437.24  Aligned_cols=366  Identities=41%  Similarity=0.705  Sum_probs=318.4

Q ss_pred             hhHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccccCCcEEEEcchHHHHHHHHHHHHHcCCceE
Q 037567            2 VSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVTGKTALVVSPLISLMQDQVMSLKQRGINAE   81 (374)
Q Consensus         2 ~~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~   81 (374)
                      .+.|++.|||.+|+|+|.++++.+++++++++.+|||+|||++|+++++....+++|++|+++|+.|+.+.+..+|+...
T Consensus        14 ~~~l~~~~g~~~~r~~Q~~~i~~il~g~d~lv~apTGsGKTl~~~lp~l~~~g~~lvi~P~~aL~~q~~~~l~~~gi~~~   93 (523)
T 1oyw_A           14 KQVLQETFGYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPALLLNGLTVVVSPLISLMKDQVDQLQANGVAAA   93 (523)
T ss_dssp             HHHHHHTTCCSSCCTTHHHHHHHHHTTCCEEEECSCHHHHHHHHHHHHHHSSSEEEEECSCHHHHHHHHHHHHHTTCCEE
T ss_pred             HHHHHHHhCCCCCCHHHHHHHHHHHcCCCEEEECCCCcHHHHHHHHHHHHhCCCEEEECChHHHHHHHHHHHHHcCCcEE
Confidence            46788889999999999999999999999999999999999999999988888999999999999999999999999988


Q ss_pred             EcCCCCCchhh---hhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHHh
Q 037567           82 FLGSAQTDSSV---QTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTF  158 (374)
Q Consensus        82 ~~~~~~~~~~~---~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~  158 (374)
                      .+.+.......   ......+.++|+++||+++...  .....+...++++|||||||.+.+||.++++.+..+..+...
T Consensus        94 ~l~~~~~~~~~~~~~~~~~~~~~~ilv~Tpe~l~~~--~~~~~l~~~~~~~vViDEaH~i~~~g~~fr~~~~~l~~l~~~  171 (523)
T 1oyw_A           94 CLNSTQTREQQLEVMTGCRTGQIRLLYIAPERLMLD--NFLEHLAHWNPVLLAVDEAHCISQWGHDFRPEYAALGQLRQR  171 (523)
T ss_dssp             EECTTSCHHHHHHHHHHHHHTCCSEEEECHHHHTST--THHHHHTTSCEEEEEESSGGGGCTTSSCCCHHHHGGGGHHHH
T ss_pred             EEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHhCh--HHHHHHhhCCCCEEEEeCccccCcCCCccHHHHHHHHHHHHh
Confidence            88776554332   2233456789999999998654  233445557899999999999999999999888888888888


Q ss_pred             cCCCCeeEEEeecCcccHHHHHHhcCCCCCeEEEeccCCCceeEEEEeecCCcchHHHHHHHHHHhhcCCCcEEEEecch
Q 037567          159 LLGVPFVALTATATEKVRIDIINSLKLKNPYVTIASFDRKNLFYGVKVINRGQSFVDELVQEILKSVAGAGSIIVYCMTI  238 (374)
Q Consensus       159 ~~~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lVf~~~~  238 (374)
                      +++.+++++|||+++....++...++..++.+...+.+++++.+.+....   ..... +.+++... .++++||||+++
T Consensus       172 ~~~~~~i~lSAT~~~~~~~~i~~~l~~~~~~~~~~~~~r~~l~~~v~~~~---~~~~~-l~~~l~~~-~~~~~IVf~~sr  246 (523)
T 1oyw_A          172 FPTLPFMALTATADDTTRQDIVRLLGLNDPLIQISSFDRPNIRYMLMEKF---KPLDQ-LMRYVQEQ-RGKSGIIYCNSR  246 (523)
T ss_dssp             CTTSCEEEEESCCCHHHHHHHHHHHTCCSCEEEECCCCCTTEEEEEEECS---SHHHH-HHHHHHHT-TTCCEEEECSSH
T ss_pred             CCCCCEEEEeCCCCHHHHHHHHHHhCCCCCeEEeCCCCCCceEEEEEeCC---CHHHH-HHHHHHhc-CCCcEEEEeCCH
Confidence            88999999999999988888899999888888888888888766654432   22233 33333332 678999999999


Q ss_pred             hHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEEEEECCCCChhHHHHhhcc
Q 037567          239 KDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGR  318 (374)
Q Consensus       239 ~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~~~~p~s~~~~~Q~~GR  318 (374)
                      +.++.+++.|++.++.+..+||+++.++|..+++.|.+|+.+|||||+++++|+|+|++++||++++|.|...|.||+||
T Consensus       247 ~~~e~l~~~L~~~g~~~~~~h~~l~~~~R~~~~~~f~~g~~~vlVaT~a~~~GiD~p~v~~VI~~~~p~s~~~y~Qr~GR  326 (523)
T 1oyw_A          247 AKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGMGINKPNVRFVVHFDIPRNIESYYQETGR  326 (523)
T ss_dssp             HHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECTTSCTTTCCTTCCEEEESSCCSSHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHCCCCEEEecCCCCHHHHHHHHHHHHcCCCeEEEEechhhCCCCccCccEEEEECCCCCHHHHHHHhcc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCceEEEEEeeccCCCcccceeccccchHHHHHHHHHHHHHHHHhhhcccCC
Q 037567          319 CGRDGIASVCWLYYARSNFAKGDFYCGESQTENQRTAIMESLLAAQRYCLLTTCRR  374 (374)
Q Consensus       319 ~~R~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~  374 (374)
                      +||.|++|.+++++++.|....+.++...............+.+|.+||+.+.|||
T Consensus       327 aGR~g~~~~~~l~~~~~d~~~~~~~~~~~~~~~~~~~~~~~l~~m~~~~~~~~crr  382 (523)
T 1oyw_A          327 AGRDGLPAEAMLFYDPADMAWLRRCLEEKPQGQLQDIERHKLNAMGAFAEAQTCRR  382 (523)
T ss_dssp             SCTTSSCEEEEEEECHHHHHHHHHHHHTSCCSHHHHHHHHHHHHHHHHHTCSSCHH
T ss_pred             ccCCCCCceEEEEeCHHHHHHHHHHHhccCcHHHHHHHHHHHHHHHHHHhccccHh
Confidence            99999999999999999999888888875555566778889999999999999996

>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=100.00  E-value=2.7e-59  Score=439.40  Aligned_cols=367  Identities=38%  Similarity=0.634  Sum_probs=314.6

Q ss_pred             hhHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccccCCcEEEEcchHHHHHHHHHHHHHcCCceE
Q 037567            2 VSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVTGKTALVVSPLISLMQDQVMSLKQRGINAE   81 (374)
Q Consensus         2 ~~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~   81 (374)
                      .+.|++.|||..|+|+|.++++.+++++++++.+|||+|||++|+++++....++||++|+++|+.|+.+.+..+|+.+.
T Consensus        33 ~~~L~~~fg~~~~rp~Q~~~i~~il~g~d~lv~~pTGsGKTl~~~lpal~~~g~~lVisP~~~L~~q~~~~l~~~gi~~~  112 (591)
T 2v1x_A           33 KDILQNVFKLEKFRPLQLETINVTMAGKEVFLVMPTGGGKSLCYQLPALCSDGFTLVICPLISLMEDQLMVLKQLGISAT  112 (591)
T ss_dssp             HHHHHHTSCCCSCCTTHHHHHHHHHTTCCEEEECCTTSCTTHHHHHHHHTSSSEEEEECSCHHHHHHHHHHHHHHTCCEE
T ss_pred             HHHHHHHhCCCCCCHHHHHHHHHHHcCCCEEEEECCCChHHHHHHHHHHHcCCcEEEEeCHHHHHHHHHHHHHhcCCcEE
Confidence            46788889999999999999999999999999999999999999999999889999999999999999999999999988


Q ss_pred             EcCCCCCchhhhhh---h--hcCCeeEEEEcCccccc---CchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHH
Q 037567           82 FLGSAQTDSSVQTK---A--ETGYFQLLFMTPEKACI---IPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLD  153 (374)
Q Consensus        82 ~~~~~~~~~~~~~~---~--~~~~~~i~i~T~~~l~~---~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~  153 (374)
                      .+.++.........   .  ..+.++|+++||+++..   +...........++++|||||||.+.+||.++++.+..+.
T Consensus       113 ~l~~~~~~~~~~~~~~~l~~~~~~~~Ilv~Tpe~L~~~~~~~~~l~~~~~~~~i~~iViDEAH~is~~g~dfr~~~~~l~  192 (591)
T 2v1x_A          113 MLNASSSKEHVKWVHAEMVNKNSELKLIYVTPEKIAKSKMFMSRLEKAYEARRFTRIAVDEVHCCSQWGHDFRPDYKALG  192 (591)
T ss_dssp             ECCSSCCHHHHHHHHHHHHCTTCCCCEEEECHHHHHSCHHHHHHHHHHHHTTCEEEEEEETGGGGSTTCTTCCGGGGGGG
T ss_pred             EEeCCCCHHHHHHHHHHhhcccCCCCEEEEChhHhhccHHHHHHHHhhhhccCCcEEEEECcccccccccccHHHHHHHH
Confidence            88876655433211   1  24678999999998853   2233333445678999999999999999988888887777


Q ss_pred             HHHHhcCCCCeeEEEeecCcccHHHHHHhcCCCCCeEEEeccCCCceeEEEEeecCCcchHHHHHHHHHHhhcCCCcEEE
Q 037567          154 KLRTFLLGVPFVALTATATEKVRIDIINSLKLKNPYVTIASFDRKNLFYGVKVINRGQSFVDELVQEILKSVAGAGSIIV  233 (374)
Q Consensus       154 ~~~~~~~~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lV  233 (374)
                      .+...+++.++++||||+++.....+...++...+.....+..++++.+.+.............+.+++.....++++||
T Consensus       193 ~l~~~~~~~~ii~lSAT~~~~v~~~i~~~l~~~~~~~~~~~~~r~nl~~~v~~~~~~~~~~~~~l~~~l~~~~~~~~~IV  272 (591)
T 2v1x_A          193 ILKRQFPNASLIGLTATATNHVLTDAQKILCIEKCFTFTASFNRPNLYYEVRQKPSNTEDFIEDIVKLINGRYKGQSGII  272 (591)
T ss_dssp             HHHHHCTTSEEEEEESSCCHHHHHHHHHHTTCCSCEEEECCCCCTTEEEEEEECCSSHHHHHHHHHHHHTTTTTTCEEEE
T ss_pred             HHHHhCCCCcEEEEecCCCHHHHHHHHHHhCCCCcEEEecCCCCcccEEEEEeCCCcHHHHHHHHHHHHHHhccCCCeEE
Confidence            77777888999999999999888888889998888888888888888777765544333333444444444446789999


Q ss_pred             EecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEEEEECCCCChhHHH
Q 037567          234 YCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYY  313 (374)
Q Consensus       234 f~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~~~~p~s~~~~~  313 (374)
                      ||++++.++.+++.|++.|+.+..+||+++..+|..+++.|..|+.+|||+|+++++|+|+|++++||++++|.|...|.
T Consensus       273 f~~sr~~~e~la~~L~~~g~~~~~~h~~l~~~~R~~~~~~F~~g~~~VlVAT~a~~~GID~p~V~~VI~~~~p~s~~~y~  352 (591)
T 2v1x_A          273 YCFSQKDSEQVTVSLQNLGIHAGAYHANLEPEDKTTVHRKWSANEIQVVVATVAFGMGIDKPDVRFVIHHSMSKSMENYY  352 (591)
T ss_dssp             ECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSSSEEEECTTSCTTCCCSCEEEEEESSCCSSHHHHH
T ss_pred             EeCcHHHHHHHHHHHHHCCCCEEEecCCCCHHHHHHHHHHHHcCCCeEEEEechhhcCCCcccccEEEEeCCCCCHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HhhccCCCCCCceEEEEEeeccCCCcccceeccccchHHHHHHHHHHHHHHHHhh-hcccCC
Q 037567          314 QESGRCGRDGIASVCWLYYARSNFAKGDFYCGESQTENQRTAIMESLLAAQRYCL-LTTCRR  374 (374)
Q Consensus       314 Q~~GR~~R~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-~~~~~~  374 (374)
                      |++||+||.|++|.|++++.+.|......++....      ...+.|.+|..||+ .+.|||
T Consensus       353 Qr~GRaGR~G~~g~~i~l~~~~D~~~~~~~~~~~~------~~~~~l~~~~~~~~~~~~Crr  408 (591)
T 2v1x_A          353 QESGRAGRDDMKADCILYYGFGDIFRISSMVVMEN------VGQQKLYEMVSYCQNISKCRR  408 (591)
T ss_dssp             HHHTTSCTTSSCEEEEEEECHHHHHHHHHHTTTST------THHHHHHHHHHHHTCSSSCHH
T ss_pred             HHhccCCcCCCCceEEEEEChHHHHHHHHHHhhhh------hhHHHHHHHHHHHhcccccHH
Confidence            99999999999999999999999888887775432      24568899999999 579986

>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=100.00  E-value=1.1e-52  Score=384.12  Aligned_cols=319  Identities=21%  Similarity=0.285  Sum_probs=247.0

Q ss_pred             hhHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhcccccc-----------CCcEEEEcchHHHHHHHH
Q 037567            2 VSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVT-----------GKTALVVSPLISLMQDQV   70 (374)
Q Consensus         2 ~~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~~-----------~~~~lil~P~~~l~~q~~   70 (374)
                      .++|.+ +||.+|+|+|.++++.+++++++++.||||||||++|+++++..           ++++||++|+++|+.|+.
T Consensus        68 ~~~l~~-~g~~~pt~iQ~~ai~~i~~g~d~i~~a~TGsGKT~a~~lpil~~l~~~~~~~~~~~~~~lil~PtreLa~Q~~  146 (434)
T 2db3_A           68 IDNVNK-SGYKIPTPIQKCSIPVISSGRDLMACAQTGSGKTAAFLLPILSKLLEDPHELELGRPQVVIVSPTRELAIQIF  146 (434)
T ss_dssp             HHHHHH-TTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHHSCCCCCTTCCSEEEECSSHHHHHHHH
T ss_pred             HHHHHH-cCCCCCCHHHHHHHHHHhcCCCEEEECCCCCCchHHHHHHHHHHHHhcccccccCCccEEEEecCHHHHHHHH
Confidence            456666 89999999999999999999999999999999999999887641           568999999999999999


Q ss_pred             HHHHHcC----CceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcch
Q 037567           71 MSLKQRG----INAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFR  146 (374)
Q Consensus        71 ~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~  146 (374)
                      +++++++    +.+..+.++...... ......+++|+|+||++|.+++..  ....+.+++++|+||||++.++++.  
T Consensus       147 ~~~~~~~~~~~~~~~~~~gg~~~~~~-~~~l~~~~~Ivv~Tp~~l~~~l~~--~~~~l~~~~~lVlDEah~~~~~gf~--  221 (434)
T 2db3_A          147 NEARKFAFESYLKIGIVYGGTSFRHQ-NECITRGCHVVIATPGRLLDFVDR--TFITFEDTRFVVLDEADRMLDMGFS--  221 (434)
T ss_dssp             HHHHHHTTTSSCCCCEECTTSCHHHH-HHHHTTCCSEEEECHHHHHHHHHT--TSCCCTTCCEEEEETHHHHTSTTTH--
T ss_pred             HHHHHHhccCCcEEEEEECCCCHHHH-HHHhhcCCCEEEEChHHHHHHHHh--CCcccccCCeEEEccHhhhhccCcH--
Confidence            9998864    444445544433322 233345689999999998766543  2234677899999999999887643  


Q ss_pred             HHHHHHHHHHHh---cCCCCeeEEEeecCcccHHHHHHhcCCCCCeEEEe-ccC--CCceeEEEEeecCCcchHHHHHHH
Q 037567          147 LEYKQLDKLRTF---LLGVPFVALTATATEKVRIDIINSLKLKNPYVTIA-SFD--RKNLFYGVKVINRGQSFVDELVQE  220 (374)
Q Consensus       147 ~~~~~~~~~~~~---~~~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~-~~~--~~~~~~~~~~~~~~~~~~~~~~~~  220 (374)
                         ..+..+...   .++.++++||||++..... +...+ +.++..... ...  ..++...+..  .........+.+
T Consensus       222 ---~~~~~i~~~~~~~~~~q~l~~SAT~~~~~~~-~~~~~-l~~~~~i~~~~~~~~~~~i~~~~~~--~~~~~k~~~l~~  294 (434)
T 2db3_A          222 ---EDMRRIMTHVTMRPEHQTLMFSATFPEEIQR-MAGEF-LKNYVFVAIGIVGGACSDVKQTIYE--VNKYAKRSKLIE  294 (434)
T ss_dssp             ---HHHHHHHHCTTSCSSCEEEEEESCCCHHHHH-HHHTT-CSSCEEEEESSTTCCCTTEEEEEEE--CCGGGHHHHHHH
T ss_pred             ---HHHHHHHHhcCCCCCceEEEEeccCCHHHHH-HHHHh-ccCCEEEEeccccccccccceEEEE--eCcHHHHHHHHH
Confidence               334444433   3568899999999887654 33322 233333222 221  1222222222  222233444445


Q ss_pred             HHHhhcCCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEE
Q 037567          221 ILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHV  300 (374)
Q Consensus       221 ~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~v  300 (374)
                      ++...  ..++||||+++..++.+++.|.+.++.+..+||+++..+|..+++.|++|+.+|||||+++++|+|+|++++|
T Consensus       295 ~l~~~--~~~~lVF~~t~~~a~~l~~~L~~~~~~~~~lhg~~~~~~R~~~l~~F~~g~~~vLvaT~v~~rGlDi~~v~~V  372 (434)
T 2db3_A          295 ILSEQ--ADGTIVFVETKRGADFLASFLSEKEFPTTSIHGDRLQSQREQALRDFKNGSMKVLIATSVASRGLDIKNIKHV  372 (434)
T ss_dssp             HHHHC--CTTEEEECSSHHHHHHHHHHHHHTTCCEEEESTTSCHHHHHHHHHHHHTSSCSEEEECGGGTSSCCCTTCCEE
T ss_pred             HHHhC--CCCEEEEEeCcHHHHHHHHHHHhCCCCEEEEeCCCCHHHHHHHHHHHHcCCCcEEEEchhhhCCCCcccCCEE
Confidence            55543  3459999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEECCCCChhHHHHhhccCCCCCCceEEEEEeecc
Q 037567          301 IHYGCPKTLESYYQESGRCGRDGIASVCWLYYARS  335 (374)
Q Consensus       301 i~~~~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~  335 (374)
                      |++++|.+..+|+||+||+||.|+.|.++++++++
T Consensus       373 I~~d~p~~~~~y~qriGR~gR~g~~G~a~~~~~~~  407 (434)
T 2db3_A          373 INYDMPSKIDDYVHRIGRTGRVGNNGRATSFFDPE  407 (434)
T ss_dssp             EESSCCSSHHHHHHHHTTSSCTTCCEEEEEEECTT
T ss_pred             EEECCCCCHHHHHHHhcccccCCCCCEEEEEEecc
Confidence            99999999999999999999999999999999864

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens}

Probab=100.00  E-value=1.3e-51  Score=377.13  Aligned_cols=332  Identities=21%  Similarity=0.269  Sum_probs=254.9

Q ss_pred             hhHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhcccccc------------------------CCcEE
Q 037567            2 VSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVT------------------------GKTAL   57 (374)
Q Consensus         2 ~~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~~------------------------~~~~l   57 (374)
                      .++|.. +||.+|+|+|.++++.+.+++++++.+|||+|||++|+++++..                        .++++
T Consensus        27 ~~~l~~-~~~~~~~~~Q~~~i~~i~~~~~~lv~a~TGsGKT~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l  105 (417)
T 2i4i_A           27 MGNIEL-TRYTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLLPILSQIYSDGPGEALRAMKENGRYGRRKQYPISL  105 (417)
T ss_dssp             HHHHHH-HTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHHHCCCHHHHHHHHCBTTBSCSBCCSEE
T ss_pred             HHHHHH-CCCCCCCHHHHHHHHHHccCCCEEEEcCCCCHHHHHHHHHHHHHHHhccccchhhccccccccccccCCccEE
Confidence            456666 79999999999999999999999999999999999998887641                        25799


Q ss_pred             EEcchHHHHHHHHHHHHHc----CCceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEe
Q 037567           58 VVSPLISLMQDQVMSLKQR----GINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVD  133 (374)
Q Consensus        58 il~P~~~l~~q~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviD  133 (374)
                      |++|+++|+.|+.+.+.++    +.....+.++....... .....+++|+|+||+++...+..  ....+..+++||+|
T Consensus       106 il~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~-~~~~~~~~I~v~Tp~~l~~~l~~--~~~~~~~~~~iViD  182 (417)
T 2i4i_A          106 VLAPTRELAVQIYEEARKFSYRSRVRPCVVYGGADIGQQI-RDLERGCHLLVATPGRLVDMMER--GKIGLDFCKYLVLD  182 (417)
T ss_dssp             EECSSHHHHHHHHHHHHHHHTTSSCCEEEECSSSCHHHHH-HHHTTCCSEEEECHHHHHHHHHT--TSBCCTTCCEEEES
T ss_pred             EECCcHHHHHHHHHHHHHHhCcCCceEEEEECCCCHHHHH-HHhhCCCCEEEEChHHHHHHHHc--CCcChhhCcEEEEE
Confidence            9999999999999999875    45555555544333322 22345689999999998765443  22345678999999


Q ss_pred             ccchhhcccCcchHHHHHHHHHHHh--cC---CCCeeEEEeecCcccHHHHHHhcCCCCCeEEEec--cCCCceeEEEEe
Q 037567          134 EAHCISEWGHDFRLEYKQLDKLRTF--LL---GVPFVALTATATEKVRIDIINSLKLKNPYVTIAS--FDRKNLFYGVKV  206 (374)
Q Consensus       134 E~h~~~~~~~~~~~~~~~~~~~~~~--~~---~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~  206 (374)
                      |+|++.++++.     ..+..+...  .+   ..+++++|||++..........+. ....+....  .....+...+..
T Consensus       183 Eah~~~~~~~~-----~~~~~i~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~i~~~~~~  256 (417)
T 2i4i_A          183 EADRMLDMGFE-----PQIRRIVEQDTMPPKGVRHTMMFSATFPKEIQMLARDFLD-EYIFLAVGRVGSTSENITQKVVW  256 (417)
T ss_dssp             SHHHHHHTTCH-----HHHHHHHTSSSCCCBTTBEEEEEESCCCHHHHHHHHHHCS-SCEEEEEC----CCSSEEEEEEE
T ss_pred             ChhHhhccCcH-----HHHHHHHHhccCCCcCCcEEEEEEEeCCHHHHHHHHHHcC-CCEEEEeCCCCCCccCceEEEEE
Confidence            99999876632     333333332  11   467999999998765543333332 222222211  122233322222


Q ss_pred             ecCCcchHHHHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEec
Q 037567          207 INRGQSFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATM  286 (374)
Q Consensus       207 ~~~~~~~~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~  286 (374)
                        .........+.++++....++++||||++++.++.+++.|++.++.+..+||+++.++|..+++.|++|+.+|||||+
T Consensus       257 --~~~~~~~~~l~~~l~~~~~~~~~lVf~~~~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlvaT~  334 (417)
T 2i4i_A          257 --VEESDKRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILVATA  334 (417)
T ss_dssp             --CCGGGHHHHHHHHHHTCCTTCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHHTSSCEEEECH
T ss_pred             --eccHhHHHHHHHHHHhcCCCCeEEEEECCHHHHHHHHHHHHHCCCCeeEecCCCCHHHHHHHHHHHHcCCCCEEEECC
Confidence              223445566677777766788999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccccccccCccEEEEECCCCChhHHHHhhccCCCCCCceEEEEEeeccCCCcccceec
Q 037567          287 AFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFYCG  345 (374)
Q Consensus       287 ~~~~G~d~~~~~~vi~~~~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~~~~~~~~~~  345 (374)
                      ++++|+|+|++++||++++|.+...|+||+||+||.|+.|.+++++++.+...+..+.+
T Consensus       335 ~~~~Gidip~v~~Vi~~~~p~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~~~~~~~~l~~  393 (417)
T 2i4i_A          335 VAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNERNINITKDLLD  393 (417)
T ss_dssp             HHHTTSCCCCEEEEEESSCCSSHHHHHHHHTTBCC--CCEEEEEEECGGGGGGHHHHHH
T ss_pred             hhhcCCCcccCCEEEEEcCCCCHHHHHHhcCccccCCCCceEEEEEccccHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999998877766654

>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=100.00  E-value=1e-50  Score=368.14  Aligned_cols=323  Identities=15%  Similarity=0.203  Sum_probs=250.3

Q ss_pred             hhHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhcccccc------CCcEEEEcchHHHHHHHHHHHHH
Q 037567            2 VSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVT------GKTALVVSPLISLMQDQVMSLKQ   75 (374)
Q Consensus         2 ~~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~~------~~~~lil~P~~~l~~q~~~~~~~   75 (374)
                      .++|.+ +||.+|+|+|.++++.+.+++++++.+|||+|||++|+++++..      ..+++|++|+++|+.||.+++.+
T Consensus        20 ~~~l~~-~g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~l~~~~~~~~~lil~P~~~L~~q~~~~~~~   98 (391)
T 1xti_A           20 LRAIVD-CGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRELAFQISKEYER   98 (391)
T ss_dssp             HHHHHH-HSCCSCCHHHHHHHHHHTTTCCEEEECSSCSSHHHHHHHHHHHHCCCCTTCCCEEEECSCHHHHHHHHHHHHH
T ss_pred             HHHHHH-CCCCCCCHHHHHHHHHHhcCCcEEEECCCCCcHHHHHHHHHHHhhcccCCCeeEEEECCCHHHHHHHHHHHHH
Confidence            456777 79999999999999999999999999999999999988776642      56899999999999999999987


Q ss_pred             c-----CCceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHH
Q 037567           76 R-----GINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYK  150 (374)
Q Consensus        76 ~-----~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~  150 (374)
                      +     +..+..+.++............+.++|+|+||+++......  ....+.+++++|+||||++.++. .+.   .
T Consensus        99 ~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~iiv~T~~~l~~~~~~--~~~~~~~~~~vViDEaH~~~~~~-~~~---~  172 (391)
T 1xti_A           99 FSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARN--KSLNLKHIKHFILDECDKMLEQL-DMR---R  172 (391)
T ss_dssp             HTTTCTTCCEEEECTTSCHHHHHHHHHHSCCSEEEECHHHHHHHHHT--TSSCCTTCSEEEECSHHHHTSSH-HHH---H
T ss_pred             HHhhCCCeEEEEEeCCCCHHHHHHHHhcCCCCEEEECHHHHHHHHHc--CCccccccCEEEEeCHHHHhhcc-chH---H
Confidence            6     56677776665544444444456679999999998765433  22345678999999999987531 111   3


Q ss_pred             HHHHHHHhc-CCCCeeEEEeecCcccHHHHHHhcCCCCCeEEEeccC---CCceeEEEEeecCCcchHHHHHHHHHHhhc
Q 037567          151 QLDKLRTFL-LGVPFVALTATATEKVRIDIINSLKLKNPYVTIASFD---RKNLFYGVKVINRGQSFVDELVQEILKSVA  226 (374)
Q Consensus       151 ~~~~~~~~~-~~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  226 (374)
                      .+..+.... ...+++++|||+++.........+. .+..+......   .........  ..........+.++++.. 
T Consensus       173 ~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~l~~~l~~~-  248 (391)
T 1xti_A          173 DVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQ-DPMEIFVDDETKLTLHGLQQYYV--KLKDNEKNRKLFDLLDVL-  248 (391)
T ss_dssp             HHHHHHHTSCSSSEEEEEESSCCSTHHHHHHHHCS-SCEEEECCCCCCCCCTTCEEEEE--ECCGGGHHHHHHHHHHHS-
T ss_pred             HHHHHHhhCCCCceEEEEEeeCCHHHHHHHHHHcC-CCeEEEecCccccCcccceEEEE--EcCchhHHHHHHHHHHhc-
Confidence            334444433 3678999999999876644444333 22222222111   112222211  122333445555555554 


Q ss_pred             CCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEEEEECCC
Q 037567          227 GAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCP  306 (374)
Q Consensus       227 ~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~~~~p  306 (374)
                      .++++||||++++.++.+++.|++.+..+..+||+++..+|..+++.|++|+.+|||+|+++++|+|+|++++||++++|
T Consensus       249 ~~~~~lvf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~~~~~Gidi~~~~~Vi~~~~p  328 (391)
T 1xti_A          249 EFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMP  328 (391)
T ss_dssp             CCSEEEEECSCHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTCCSEEEESCCCSSCBCCTTEEEEEESSCC
T ss_pred             CCCcEEEEeCcHHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcCCCcEEEECChhhcCCCcccCCEEEEeCCC
Confidence            67899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CChhHHHHhhccCCCCCCceEEEEEeecc
Q 037567          307 KTLESYYQESGRCGRDGIASVCWLYYARS  335 (374)
Q Consensus       307 ~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~  335 (374)
                      ++...|+||+||+||.|+.|.+++++.+.
T Consensus       329 ~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~  357 (391)
T 1xti_A          329 EDSDTYLHRVARAGRFGTKGLAITFVSDE  357 (391)
T ss_dssp             SSHHHHHHHHCBCSSSCCCCEEEEEECSH
T ss_pred             CCHHHHHHhcccccCCCCceEEEEEEccc
Confidence            99999999999999999999999999875

>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=100.00  E-value=3.8e-51  Score=373.16  Aligned_cols=328  Identities=18%  Similarity=0.304  Sum_probs=250.2

Q ss_pred             hhHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc------cCCcEEEEcchHHHHHHHHHHHHH
Q 037567            2 VSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV------TGKTALVVSPLISLMQDQVMSLKQ   75 (374)
Q Consensus         2 ~~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~------~~~~~lil~P~~~l~~q~~~~~~~   75 (374)
                      .+++.+ +||.+|+|+|.++++.+++++++++.+|||+|||++|+++++.      .+.++||++|+++|+.|+.+.+..
T Consensus        49 ~~~l~~-~g~~~~~~~Q~~ai~~i~~~~~~lv~a~TGsGKT~~~~~~~~~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~  127 (410)
T 2j0s_A           49 LRGIYA-YGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGLLA  127 (410)
T ss_dssp             HHHHHH-HTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHTCCTTSCSCCEEEECSSHHHHHHHHHHHHH
T ss_pred             HHHHHH-cCCCCCCHHHHHHHHHHhCCCCEEEECCCCCCchHHHHHHHHHHHhhccCCceEEEEcCcHHHHHHHHHHHHH
Confidence            356666 8999999999999999999999999999999999998877663      467899999999999999999987


Q ss_pred             cC----CceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHH
Q 037567           76 RG----INAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQ  151 (374)
Q Consensus        76 ~~----~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~  151 (374)
                      ++    .......++....... ......++|+|+||+++...+..  .......++++|+||+|++.+++..     ..
T Consensus       128 ~~~~~~~~~~~~~g~~~~~~~~-~~~~~~~~ivv~Tp~~l~~~l~~--~~~~~~~~~~vViDEah~~~~~~~~-----~~  199 (410)
T 2j0s_A          128 LGDYMNVQCHACIGGTNVGEDI-RKLDYGQHVVAGTPGRVFDMIRR--RSLRTRAIKMLVLDEADEMLNKGFK-----EQ  199 (410)
T ss_dssp             HTTTTTCCEEEECTTSCHHHHH-HHHHHCCSEEEECHHHHHHHHHT--TSSCCTTCCEEEEETHHHHTSTTTH-----HH
T ss_pred             HhccCCeEEEEEECCCCHHHHH-HHhhcCCCEEEcCHHHHHHHHHh--CCccHhheeEEEEccHHHHHhhhhH-----HH
Confidence            64    4444444443332222 22334579999999988765443  2234467899999999999876643     33


Q ss_pred             HHHHHHhc-CCCCeeEEEeecCcccHHHHHHhcCCCCCeEEE-ec--cCCCceeEEEEeecCCcchHHHHHHHHHHhhcC
Q 037567          152 LDKLRTFL-LGVPFVALTATATEKVRIDIINSLKLKNPYVTI-AS--FDRKNLFYGVKVINRGQSFVDELVQEILKSVAG  227 (374)
Q Consensus       152 ~~~~~~~~-~~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~-~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  227 (374)
                      +..+.... ++.+++++|||++..... +...+ ...+.... ..  .....+......... .....+.+.+++... .
T Consensus       200 ~~~i~~~~~~~~~~i~~SAT~~~~~~~-~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~k~~~l~~~~~~~-~  275 (410)
T 2j0s_A          200 IYDVYRYLPPATQVVLISATLPHEILE-MTNKF-MTDPIRILVKRDELTLEGIKQFFVAVER-EEWKFDTLCDLYDTL-T  275 (410)
T ss_dssp             HHHHHTTSCTTCEEEEEESCCCHHHHT-TGGGT-CSSCEEECCCGGGCSCTTEEEEEEEESS-TTHHHHHHHHHHHHH-T
T ss_pred             HHHHHHhCccCceEEEEEcCCCHHHHH-HHHHH-cCCCEEEEecCccccCCCceEEEEEeCc-HHhHHHHHHHHHHhc-C
Confidence            44444444 367899999999876432 22222 22232222 11  122233333332222 233444555555554 5


Q ss_pred             CCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEEEEECCCC
Q 037567          228 AGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPK  307 (374)
Q Consensus       228 ~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~~~~p~  307 (374)
                      .+++||||++++.++.+++.|.+.++.+..+||+++..+|..+++.|++|+.+|||+|+++++|+|+|++++||++++|.
T Consensus       276 ~~~~lVf~~~~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidi~~v~~Vi~~~~p~  355 (410)
T 2j0s_A          276 ITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPN  355 (410)
T ss_dssp             SSEEEEECSSHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHHTSSCEEEECGGGSSSCCCTTEEEEEESSCCS
T ss_pred             CCcEEEEEcCHHHHHHHHHHHHhCCCceEEeeCCCCHHHHHHHHHHHHCCCCCEEEECChhhCcCCcccCCEEEEECCCC
Confidence            67999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ChhHHHHhhccCCCCCCceEEEEEeeccCCCcccc
Q 037567          308 TLESYYQESGRCGRDGIASVCWLYYARSNFAKGDF  342 (374)
Q Consensus       308 s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~~~~~~~  342 (374)
                      +...|+||+||+||.|+.|.+++++.+.+...++.
T Consensus       356 s~~~~~Qr~GR~gR~g~~g~~~~~~~~~~~~~~~~  390 (410)
T 2j0s_A          356 NRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRD  390 (410)
T ss_dssp             SHHHHHHHHTTSSGGGCCEEEEEEEEGGGHHHHHH
T ss_pred             CHHHHHHhcccccCCCCceEEEEEecHHHHHHHHH
Confidence            99999999999999999999999999887554443

>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=100.00  E-value=2.4e-50  Score=381.95  Aligned_cols=338  Identities=20%  Similarity=0.262  Sum_probs=255.2

Q ss_pred             hhHHHhHcCCCCCchhHHHHHHHHH--cCCCEEEEccCCCCchhhhhcccccc----------CCcEEEEcchHHHHHHH
Q 037567            2 VSTLKKYFGYSVFRPYQKDVIQRII--EKRDCLVVMATGSGKSLCYQLPPLVT----------GKTALVVSPLISLMQDQ   69 (374)
Q Consensus         2 ~~~l~~~~~~~~~~~~Q~~~~~~~~--~~~~~l~~a~tGsGKT~~~~l~~~~~----------~~~~lil~P~~~l~~q~   69 (374)
                      .+++.+ +||.+|+|+|.++++.++  +++++++.||||||||++|+++++..          ..++||++|+++|+.|+
T Consensus        84 ~~~l~~-~g~~~~~~~Q~~~i~~~l~~~~~~~lv~apTGsGKTl~~~lpil~~l~~~~~~~~~~~~~lil~Ptr~La~Q~  162 (563)
T 3i5x_A           84 HKAITR-MEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFDSQYMVKAVIVAPTRDLALQI  162 (563)
T ss_dssp             HHHHHT-TCCSSCCHHHHHHHHHHHSSSSEEEEEECCTTSCHHHHHHHHHHHHHHHTTTSSTTSCCEEEECSSHHHHHHH
T ss_pred             HHHHHH-CCCCCCCHHHHHHHHHHhcCCCCeEEEECCCCCCccHHHHHHHHHHHHhccccccCCeeEEEEcCcHHHHHHH
Confidence            356666 799999999999999999  67899999999999999999887752          34899999999999999


Q ss_pred             HHHHHHc--------CCceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcc
Q 037567           70 VMSLKQR--------GINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEW  141 (374)
Q Consensus        70 ~~~~~~~--------~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~  141 (374)
                      .+.++++        +.......++..............++|+|+||+++...+... ....+..+++||+||||++.++
T Consensus       163 ~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~Iiv~Tp~~l~~~l~~~-~~~~~~~~~~lViDEah~l~~~  241 (563)
T 3i5x_A          163 EAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKY-SNKFFRFVDYKVLDEADRLLEI  241 (563)
T ss_dssp             HHHHHHHHHHCGGGTTSCEEEECTTSCHHHHHHHHHHHCCSEEEECHHHHHHHHHHH-HHHHCTTCCEEEEETHHHHTST
T ss_pred             HHHHHHHHhhccccCceeEEEEECCcCHHHHHHHHhcCCCCEEEECcHHHHHHHHhc-cccccccceEEEEeCHHHHhcc
Confidence            9999874        223444444444444444444556899999999997766543 2345678999999999999987


Q ss_pred             cCcchHHHHHHHHHHHhc-----CCCCeeEEEeecCcccHHHHHHhcCCCCCeEEEecc------CCCceeEEEEeecCC
Q 037567          142 GHDFRLEYKQLDKLRTFL-----LGVPFVALTATATEKVRIDIINSLKLKNPYVTIASF------DRKNLFYGVKVINRG  210 (374)
Q Consensus       142 ~~~~~~~~~~~~~~~~~~-----~~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~  210 (374)
                      +  +...+..+.......     ++.++++||||+++.... +...+...+..+.....      ....+..........
T Consensus       242 ~--f~~~~~~i~~~l~~~~~~~~~~~~~l~~SAT~~~~v~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  318 (563)
T 3i5x_A          242 G--FRDDLETISGILNEKNSKSADNIKTLLFSATLDDKVQK-LANNIMNKKECLFLDTVDKNEPEAHERIDQSVVISEKF  318 (563)
T ss_dssp             T--THHHHHHHHHHHHHHCSSCTTCCEEEEEESSCCTHHHH-HTTTTCCSSEEEEEESSCSSSCSSCTTEEEEEEEESST
T ss_pred             c--hHHHHHHHHHhhhhccccCccCceEEEEEccCCHHHHH-HHHHhcCCCceEEEeccCCCCccccccCceEEEECchh
Confidence            7  334444443333221     256899999999987653 23322222222222111      112233333333333


Q ss_pred             cchHHHHHHHHH---HhhcCCCcEEEEecchhHHHHHHHHHHHc---CCceeeeecCCChHHHHHHHHhhhcCCeeEEEE
Q 037567          211 QSFVDELVQEIL---KSVAGAGSIIVYCMTIKDVEEISKALKQL---GVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVA  284 (374)
Q Consensus       211 ~~~~~~~~~~~~---~~~~~~~~~lVf~~~~~~~~~l~~~l~~~---~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~  284 (374)
                      .......+..+.   .....+.++||||+++..++.+++.|++.   ++.+..+||+++..+|..+++.|++|+.+||||
T Consensus       319 ~~~~~~~~~~l~~~~~~~~~~~~~iVF~~s~~~~~~l~~~L~~~~~~~~~v~~~h~~~~~~~R~~~~~~f~~g~~~vLva  398 (563)
T 3i5x_A          319 ANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVC  398 (563)
T ss_dssp             THHHHHHHHHHHHHHHHTTTCCEEEEECSCHHHHHHHHHHHHHHHTTTSCEEEESTTSCHHHHHHHHHHHHHCSSEEEEE
T ss_pred             HhhHHHHHHHHHHHHhhcCCCCcEEEEcCcHHHHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhcCCCCEEEE
Confidence            333333333333   33346789999999999999999999986   889999999999999999999999999999999


Q ss_pred             eccccccccccCccEEEEECCCCChhHHHHhhccCCCCCCceEEEEEeeccCCCccccee
Q 037567          285 TMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFYC  344 (374)
Q Consensus       285 t~~~~~G~d~~~~~~vi~~~~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~~~~~~~~~  344 (374)
                      |+++++|+|+|++++||++++|.++..|+||+||+||.|+.|.+++++.+.+...++.+.
T Consensus       399 T~~~~~GiDip~v~~VI~~~~p~s~~~y~Qr~GRagR~g~~g~~i~~~~~~e~~~~~~l~  458 (563)
T 3i5x_A          399 TDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKDELPFVRELE  458 (563)
T ss_dssp             CGGGTSSCCCTTCCEEEEESCCSSTTHHHHHHTTSSCTTCCEEEEEEEEGGGHHHHHHHH
T ss_pred             cchhhcCCCcccCCEEEEECCCCchhhhhhhcCccccCCCCceEEEEEchhHHHHHHHHH
Confidence            999999999999999999999999999999999999999999999999999877666664

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C}

Probab=100.00  E-value=4.1e-50  Score=380.49  Aligned_cols=338  Identities=20%  Similarity=0.263  Sum_probs=255.1

Q ss_pred             hhHHHhHcCCCCCchhHHHHHHHHH--cCCCEEEEccCCCCchhhhhcccccc----------CCcEEEEcchHHHHHHH
Q 037567            2 VSTLKKYFGYSVFRPYQKDVIQRII--EKRDCLVVMATGSGKSLCYQLPPLVT----------GKTALVVSPLISLMQDQ   69 (374)
Q Consensus         2 ~~~l~~~~~~~~~~~~Q~~~~~~~~--~~~~~l~~a~tGsGKT~~~~l~~~~~----------~~~~lil~P~~~l~~q~   69 (374)
                      .+++.+ +||..|+|+|.++++.++  +++++++.||||+|||++|+++++..          ..++||++|+++|+.|+
T Consensus        33 ~~~l~~-~g~~~~~~~Q~~~i~~il~~~~~dvlv~apTGsGKTl~~~lpil~~l~~~~~~~~~~~~~lvl~Ptr~La~Q~  111 (579)
T 3sqw_A           33 HKAITR-MEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFDSQYMVKAVIVAPTRDLALQI  111 (579)
T ss_dssp             HHHHHT-TTCSSCCHHHHHHHHHHHCSSSEEEEEECCTTSCHHHHHHHHHHHHHHHTTTSSTTSCCEEEECSSHHHHHHH
T ss_pred             HHHHHH-CCCCCCCHHHHHHHHHHHccCCCeEEEEcCCCcHHHHHHHHHHHHHHHhccccccCCCeEEEEcchHHHHHHH
Confidence            456666 899999999999999999  67899999999999999999887741          35899999999999999


Q ss_pred             HHHHHHcC--------CceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcc
Q 037567           70 VMSLKQRG--------INAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEW  141 (374)
Q Consensus        70 ~~~~~~~~--------~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~  141 (374)
                      .+.+.++.        .......++..............++|+|+||+++..++... ....+..+++||+||||++.++
T Consensus       112 ~~~~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~-~~~~~~~~~~lViDEah~l~~~  190 (579)
T 3sqw_A          112 EAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKY-SNKFFRFVDYKVLDEADRLLEI  190 (579)
T ss_dssp             HHHHHHHHHHCGGGTTSCEEEECTTSCHHHHHHHHHHHCCSEEEECHHHHHHHHHHH-HHHHCTTCCEEEEETHHHHTST
T ss_pred             HHHHHHHHhhcccccceEEEEEECCccHHHHHHHHhcCCCCEEEECHHHHHHHHHhc-cccccccCCEEEEEChHHhhcC
Confidence            99998751        23344444444344444444456899999999997766542 2445678999999999999987


Q ss_pred             cCcchHHHHHHHHHHHhcC-----CCCeeEEEeecCcccHHHHHHhcCCCCCeEEEecc------CCCceeEEEEeecCC
Q 037567          142 GHDFRLEYKQLDKLRTFLL-----GVPFVALTATATEKVRIDIINSLKLKNPYVTIASF------DRKNLFYGVKVINRG  210 (374)
Q Consensus       142 ~~~~~~~~~~~~~~~~~~~-----~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~  210 (374)
                      +  +...+..+........     +.++++||||+++.... +...+...+..+.....      ....+..........
T Consensus       191 g--f~~~~~~i~~~l~~~~~~~~~~~~~l~~SAT~~~~v~~-~~~~~l~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~  267 (579)
T 3sqw_A          191 G--FRDDLETISGILNEKNSKSADNIKTLLFSATLDDKVQK-LANNIMNKKECLFLDTVDKNEPEAHERIDQSVVISEKF  267 (579)
T ss_dssp             T--THHHHHHHHHHHHHHCSSCTTCCEEEEEESSCCTHHHH-HTTTTCCSSEEEEEESSCSSSCSSCTTEEEEEEEESST
T ss_pred             C--CHHHHHHHHHHhhhhhcccccCceEEEEeccCChHHHH-HHHHHcCCCceEEEeecCccccccccccceEEEEecch
Confidence            7  3444444443333222     56899999999987653 22222222222222111      112233333333333


Q ss_pred             cchHHHHHHHHH---HhhcCCCcEEEEecchhHHHHHHHHHHHc---CCceeeeecCCChHHHHHHHHhhhcCCeeEEEE
Q 037567          211 QSFVDELVQEIL---KSVAGAGSIIVYCMTIKDVEEISKALKQL---GVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVA  284 (374)
Q Consensus       211 ~~~~~~~~~~~~---~~~~~~~~~lVf~~~~~~~~~l~~~l~~~---~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~  284 (374)
                      .......+..+.   .....+.++||||+++..++.+++.|++.   ++.+..+||+++..+|..+++.|++|+.+||||
T Consensus       268 ~~~~~~~~~~l~~~~~~~~~~~~~iVF~~t~~~~~~l~~~L~~~~~~~~~v~~~hg~~~~~~R~~~~~~F~~g~~~vLVa  347 (579)
T 3sqw_A          268 ANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVC  347 (579)
T ss_dssp             THHHHHHHHHHHHHHHHTTTCCEEEEECSSHHHHHHHHHHHHHHHTTTSCEEEESTTSCHHHHHHHHHHHHHCSSEEEEE
T ss_pred             hhhHHHHHHHHHHHHhhcCCCCcEEEECCcHHHHHHHHHHHHHhhcCCCcEEEecCCCCHHHHHHHHHHhhcCCCeEEEE
Confidence            333333333333   33346789999999999999999999987   889999999999999999999999999999999


Q ss_pred             eccccccccccCccEEEEECCCCChhHHHHhhccCCCCCCceEEEEEeeccCCCccccee
Q 037567          285 TMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFYC  344 (374)
Q Consensus       285 t~~~~~G~d~~~~~~vi~~~~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~~~~~~~~~  344 (374)
                      |+++++|+|+|++++||++++|.++..|+||+||+||.|+.|.+++++.+.+...++.+.
T Consensus       348 T~~~~~GiDip~v~~VI~~~~p~s~~~y~Qr~GRagR~g~~g~~i~~~~~~e~~~~~~l~  407 (579)
T 3sqw_A          348 TDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKDELPFVRELE  407 (579)
T ss_dssp             CGGGTSSCCCTTCCEEEEESCCSSTTHHHHHHTTSSCTTCCEEEEEEEEGGGHHHHHHHH
T ss_pred             cchhhcCCCcccCCEEEEcCCCCCHHHhhhhccccccCCCCceEEEEEcccHHHHHHHHH
Confidence            999999999999999999999999999999999999999999999999999876665553

>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=100.00  E-value=2.2e-51  Score=375.33  Aligned_cols=329  Identities=19%  Similarity=0.235  Sum_probs=238.5

Q ss_pred             hhHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc------cCCcEEEEcchHHHHHHHHHHHHH
Q 037567            2 VSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV------TGKTALVVSPLISLMQDQVMSLKQ   75 (374)
Q Consensus         2 ~~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~------~~~~~lil~P~~~l~~q~~~~~~~   75 (374)
                      .+.+.+ +||.+|+++|.++++.+++++++++.+|||+|||++|+++++.      ...+++|++|+++|+.|+.+.+..
T Consensus        52 ~~~l~~-~~~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~  130 (414)
T 3eiq_A           52 LRGIYA-YGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIELDLKATQALVLAPTRELAQQIQKVVMA  130 (414)
T ss_dssp             HHHHHH-TTCCSCCHHHHHHHHHHHTTCCEEECCCSCSSSHHHHHHHHHHHCCTTSCSCCEEEECSSHHHHHHHHHHHHH
T ss_pred             HHHHHH-cCCCCCCHHHHHHhHHHhCCCCEEEECCCCCcccHHHHHHHHHHHhhcCCceeEEEEeChHHHHHHHHHHHHH
Confidence            345666 8999999999999999999999999999999999998877664      467899999999999999999987


Q ss_pred             c----CCceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHH
Q 037567           76 R----GINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQ  151 (374)
Q Consensus        76 ~----~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~  151 (374)
                      +    +.......++..............++|+|+||+++...+..  .......+++||+||+|++.+++..     ..
T Consensus       131 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iiv~T~~~l~~~l~~--~~~~~~~~~~vViDEah~~~~~~~~-----~~  203 (414)
T 3eiq_A          131 LGDYMGASCHACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNR--RYLSPKYIKMFVLDEADEMLSRGFK-----DQ  203 (414)
T ss_dssp             HGGGSCCCEEECCCCTTHHHHHHHHTTTCCSEEEECHHHHHHHHHH--TSSCSTTCCEEEECSHHHHHHTTTH-----HH
T ss_pred             HhcccCceEEEEECCcchHHHHHHHhcCCCCEEEECHHHHHHHHHc--CCcccccCcEEEEECHHHhhccCcH-----HH
Confidence            6    34445555544444444444446789999999998665443  2234566899999999998876643     33


Q ss_pred             HHHHHHhc-CCCCeeEEEeecCcccHHHHHHhcCCCCCeEEEe-c--cCCCceeEEEEeecCCcchHHHHHHHHHHhhcC
Q 037567          152 LDKLRTFL-LGVPFVALTATATEKVRIDIINSLKLKNPYVTIA-S--FDRKNLFYGVKVINRGQSFVDELVQEILKSVAG  227 (374)
Q Consensus       152 ~~~~~~~~-~~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~-~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  227 (374)
                      +..+.... ++.++++||||++..... ....+. ..+..... .  .....+...... ..........+.++++.. .
T Consensus       204 ~~~~~~~~~~~~~~i~~SAT~~~~~~~-~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~-~  279 (414)
T 3eiq_A          204 IYDIFQKLNSNTQVVLLSATMPSDVLE-VTKKFM-RDPIRILVKKEELTLEGIRQFYIN-VEREEWKLDTLCDLYETL-T  279 (414)
T ss_dssp             HHHHHTTSCTTCEEEEECSCCCHHHHH-HHTTTC-SSCEEECCCCCCCCTTSCCEEEEE-CSSSTTHHHHHHHHHHSS-C
T ss_pred             HHHHHHhCCCCCeEEEEEEecCHHHHH-HHHHHc-CCCEEEEecCCccCCCCceEEEEE-eChHHhHHHHHHHHHHhC-C
Confidence            44444443 478899999999876653 223222 22222221 1  112222222222 222333455566666654 6


Q ss_pred             CCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEEEEECCCC
Q 037567          228 AGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPK  307 (374)
Q Consensus       228 ~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~~~~p~  307 (374)
                      .+++||||++++.++.+++.|.+.++.+..+||+++..+|..+++.|++|+.+|||+|+++++|+|+|++++||++++|.
T Consensus       280 ~~~~lvf~~~~~~~~~l~~~l~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidip~v~~Vi~~~~p~  359 (414)
T 3eiq_A          280 ITQAVIFINTRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPT  359 (414)
T ss_dssp             CSSCEEECSCHHHHHHHHHHHHTTTCCCEEC---CHHHHHHHHHHHHSCC---CEEECSSCC--CCGGGCSCEEESSCCS
T ss_pred             CCcEEEEeCCHHHHHHHHHHHHhcCCeEEEecCCCCHHHHHHHHHHHHcCCCcEEEECCccccCCCccCCCEEEEeCCCC
Confidence            67999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ChhHHHHhhccCCCCCCceEEEEEeeccCCCcccc
Q 037567          308 TLESYYQESGRCGRDGIASVCWLYYARSNFAKGDF  342 (374)
Q Consensus       308 s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~~~~~~~  342 (374)
                      +..+|+||+||+||.|+.|.+++++++.+...++.
T Consensus       360 s~~~~~Qr~GR~gR~g~~g~~~~~~~~~~~~~~~~  394 (414)
T 3eiq_A          360 NRENYIHRIGRGGRFGRKGVAINMVTEEDKRTLRD  394 (414)
T ss_dssp             STHHHHHHSCCC-------CEEEEECSTHHHHHHH
T ss_pred             CHHHhhhhcCcccCCCCCceEEEEEcHHHHHHHHH
Confidence            99999999999999999999999999876544433

>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=100.00  E-value=5.6e-50  Score=364.30  Aligned_cols=330  Identities=19%  Similarity=0.250  Sum_probs=250.8

Q ss_pred             hhHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc------cCCcEEEEcchHHHHHHHHHHHHH
Q 037567            2 VSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV------TGKTALVVSPLISLMQDQVMSLKQ   75 (374)
Q Consensus         2 ~~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~------~~~~~lil~P~~~l~~q~~~~~~~   75 (374)
                      .++|.+ +||.+|+|+|.++++.+++++++++.+|||+|||++|+++++.      .+.+++|++|+++|+.|+.+.+..
T Consensus        33 ~~~l~~-~g~~~~~~~Q~~~i~~i~~~~~~li~a~TGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~  111 (400)
T 1s2m_A           33 LMGIFE-AGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEKVKPKLNKIQALIMVPTRELALQTSQVVRT  111 (400)
T ss_dssp             HHHHHH-TTCCSCCHHHHHHHHHHHHTCCEEEECCTTSCHHHHHHHHHHHHCCTTSCSCCEEEECSSHHHHHHHHHHHHH
T ss_pred             HHHHHH-CCCCCCCHHHHHHHHHHhcCCCEEEECCCCcHHHHHHHHHHHHHHhhccCCccEEEEcCCHHHHHHHHHHHHH
Confidence            456666 7999999999999999999999999999999999998877664      356899999999999999999987


Q ss_pred             c----CCceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHH
Q 037567           76 R----GINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQ  151 (374)
Q Consensus        76 ~----~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~  151 (374)
                      +    +..+....++...... .......++|+|+||+++......  ....+.+++++|+||+|++.+.+..     ..
T Consensus       112 ~~~~~~~~~~~~~g~~~~~~~-~~~~~~~~~Ivv~T~~~l~~~~~~--~~~~~~~~~~vIiDEaH~~~~~~~~-----~~  183 (400)
T 1s2m_A          112 LGKHCGISCMVTTGGTNLRDD-ILRLNETVHILVGTPGRVLDLASR--KVADLSDCSLFIMDEADKMLSRDFK-----TI  183 (400)
T ss_dssp             HTTTTTCCEEEECSSSCHHHH-HHHTTSCCSEEEECHHHHHHHHHT--TCSCCTTCCEEEEESHHHHSSHHHH-----HH
T ss_pred             HhcccCceEEEEeCCcchHHH-HHHhcCCCCEEEEchHHHHHHHHh--CCcccccCCEEEEeCchHhhhhchH-----HH
Confidence            6    4455555544333222 222345689999999988654332  1233567899999999998763321     33


Q ss_pred             HHHHHHhcC-CCCeeEEEeecCcccHHHHHHhcCCCCCeEEEeccCCCceeEEEEeecCCcchHHHHHHHHHHhhcCCCc
Q 037567          152 LDKLRTFLL-GVPFVALTATATEKVRIDIINSLKLKNPYVTIASFDRKNLFYGVKVINRGQSFVDELVQEILKSVAGAGS  230 (374)
Q Consensus       152 ~~~~~~~~~-~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  230 (374)
                      +..+....+ ..++++||||++......+...+..+.............+.......  ........+..++... ..++
T Consensus       184 ~~~i~~~~~~~~~~i~lSAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~k~~~l~~~~~~~-~~~~  260 (400)
T 1s2m_A          184 IEQILSFLPPTHQSLLFSATFPLTVKEFMVKHLHKPYEINLMEELTLKGITQYYAFV--EERQKLHCLNTLFSKL-QINQ  260 (400)
T ss_dssp             HHHHHTTSCSSCEEEEEESCCCHHHHHHHHHHCSSCEEESCCSSCBCTTEEEEEEEC--CGGGHHHHHHHHHHHS-CCSE
T ss_pred             HHHHHHhCCcCceEEEEEecCCHHHHHHHHHHcCCCeEEEeccccccCCceeEEEEe--chhhHHHHHHHHHhhc-CCCc
Confidence            444444443 57899999999887665444444322111111112222232222222  2233445555665553 6789


Q ss_pred             EEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEEEEECCCCChh
Q 037567          231 IIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLE  310 (374)
Q Consensus       231 ~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~~~~p~s~~  310 (374)
                      +||||++++.++.+++.|++.+..+..+||+++..+|..+++.|++|+.+|||+|+++++|+|+|++++||++++|.+..
T Consensus       261 ~lVf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vLv~T~~~~~Gidip~~~~Vi~~~~p~s~~  340 (400)
T 1s2m_A          261 AIIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSDLLTRGIDIQAVNVVINFDFPKTAE  340 (400)
T ss_dssp             EEEECSSHHHHHHHHHHHHHHTCCEEEECTTSCHHHHHHHHHHHHTTSSSEEEESSCSSSSCCCTTEEEEEESSCCSSHH
T ss_pred             EEEEEecHHHHHHHHHHHHhcCCCeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCccccCCCccCCCEEEEeCCCCCHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhhccCCCCCCceEEEEEeeccCCCcccce
Q 037567          311 SYYQESGRCGRDGIASVCWLYYARSNFAKGDFY  343 (374)
Q Consensus       311 ~~~Q~~GR~~R~~~~g~~~~~~~~~~~~~~~~~  343 (374)
                      .|+||+||+||.|+.|.+++++++.|...++.+
T Consensus       341 ~~~Qr~GR~gR~g~~g~~~~l~~~~~~~~~~~i  373 (400)
T 1s2m_A          341 TYLHRIGRSGRFGHLGLAINLINWNDRFNLYKI  373 (400)
T ss_dssp             HHHHHHCBSSCTTCCEEEEEEECGGGHHHHHHH
T ss_pred             HHHHhcchhcCCCCCceEEEEeccchHHHHHHH
Confidence            999999999999999999999999876544443

>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=100.00  E-value=2e-49  Score=352.42  Aligned_cols=319  Identities=19%  Similarity=0.258  Sum_probs=243.4

Q ss_pred             hhHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccccCCcEEEEcchHHHHHHHHHHHHHcC----
Q 037567            2 VSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVTGKTALVVSPLISLMQDQVMSLKQRG----   77 (374)
Q Consensus         2 ~~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~----   77 (374)
                      .++|++ +||.+|+|+|.++++.+.+++++++.+|||+|||++++++++..+.+++|++|+++|+.|+.+.+++++    
T Consensus         6 ~~~l~~-~g~~~l~~~Q~~~i~~i~~~~~~lv~~~TGsGKT~~~~~~~~~~~~~~liv~P~~~L~~q~~~~~~~~~~~~~   84 (337)
T 2z0m_A            6 EQAIRE-MGFKNFTEVQSKTIPLMLQGKNVVVRAKTGSGKTAAYAIPILELGMKSLVVTPTRELTRQVASHIRDIGRYMD   84 (337)
T ss_dssp             HHHHHH-TTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHTCCEEEECSSHHHHHHHHHHHHHHTTTSC
T ss_pred             HHHHHH-cCCCCCCHHHHHHHHHHhcCCCEEEEcCCCCcHHHHHHHHHHhhcCCEEEEeCCHHHHHHHHHHHHHHhhhcC
Confidence            467776 899999999999999999999999999999999999999999889999999999999999999998753    


Q ss_pred             CceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHH
Q 037567           78 INAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRT  157 (374)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~  157 (374)
                      ..+....++.........  ...++|+|+||+++......  ......+++++|+||+|++.+++..     ..+..+..
T Consensus        85 ~~~~~~~~~~~~~~~~~~--~~~~~i~v~T~~~l~~~~~~--~~~~~~~~~~iViDEah~~~~~~~~-----~~~~~~~~  155 (337)
T 2z0m_A           85 TKVAEVYGGMPYKAQINR--VRNADIVVATPGRLLDLWSK--GVIDLSSFEIVIIDEADLMFEMGFI-----DDIKIILA  155 (337)
T ss_dssp             CCEEEECTTSCHHHHHHH--HTTCSEEEECHHHHHHHHHT--TSCCGGGCSEEEEESHHHHHHTTCH-----HHHHHHHH
T ss_pred             CcEEEEECCcchHHHHhh--cCCCCEEEECHHHHHHHHHc--CCcchhhCcEEEEEChHHhhccccH-----HHHHHHHh
Confidence            455555554433332222  23479999999998654332  2223567899999999999876643     33444444


Q ss_pred             hcC-CCCeeEEEeecCcccHHHHHHhcCCCCCeEEEeccCCCceeEEEEeecCCcchHHHHHHHHHHhhcCCCcEEEEec
Q 037567          158 FLL-GVPFVALTATATEKVRIDIINSLKLKNPYVTIASFDRKNLFYGVKVINRGQSFVDELVQEILKSVAGAGSIIVYCM  236 (374)
Q Consensus       158 ~~~-~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lVf~~  236 (374)
                      ..+ ..+++++|||+++.....+...+.  .+..........+............   ...+..+ .. ..++++||||+
T Consensus       156 ~~~~~~~~~~~SAT~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~-~~-~~~~~~lvf~~  228 (337)
T 2z0m_A          156 QTSNRKITGLFSATIPEEIRKVVKDFIT--NYEEIEACIGLANVEHKFVHVKDDW---RSKVQAL-RE-NKDKGVIVFVR  228 (337)
T ss_dssp             HCTTCSEEEEEESCCCHHHHHHHHHHSC--SCEEEECSGGGGGEEEEEEECSSSS---HHHHHHH-HT-CCCSSEEEECS
T ss_pred             hCCcccEEEEEeCcCCHHHHHHHHHhcC--CceeeecccccCCceEEEEEeChHH---HHHHHHH-Hh-CCCCcEEEEEc
Confidence            444 456778999999876654444433  2222222222333333333322222   2222222 22 46789999999


Q ss_pred             chhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEEEEECCCCChhHHHHhh
Q 037567          237 TIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQES  316 (374)
Q Consensus       237 ~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~~~~p~s~~~~~Q~~  316 (374)
                      +++.++.+++.|+    .+..+||+++..+|..+++.|++|+.+|||+|+++++|+|+|++++||++++|.|+..|.||+
T Consensus       229 ~~~~~~~l~~~l~----~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~~~~~Gid~~~~~~Vi~~~~~~s~~~~~Q~~  304 (337)
T 2z0m_A          229 TRNRVAKLVRLFD----NAIELRGDLPQSVRNRNIDAFREGEYDMLITTDVASRGLDIPLVEKVINFDAPQDLRTYIHRI  304 (337)
T ss_dssp             CHHHHHHHHTTCT----TEEEECTTSCHHHHHHHHHHHHTTSCSEEEECHHHHTTCCCCCBSEEEESSCCSSHHHHHHHH
T ss_pred             CHHHHHHHHHHhh----hhhhhcCCCCHHHHHHHHHHHHcCCCcEEEEcCccccCCCccCCCEEEEecCCCCHHHhhHhc
Confidence            9999999998886    578999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCCCCCCceEEEEEeeccCCCcccc
Q 037567          317 GRCGRDGIASVCWLYYARSNFAKGDF  342 (374)
Q Consensus       317 GR~~R~~~~g~~~~~~~~~~~~~~~~  342 (374)
                      ||+||.|+.|.+++++. .+....+.
T Consensus       305 GR~gR~g~~g~~~~~~~-~~~~~~~~  329 (337)
T 2z0m_A          305 GRTGRMGRKGEAITFIL-NEYWLEKE  329 (337)
T ss_dssp             TTBCGGGCCEEEEEEES-SCHHHHHH
T ss_pred             CccccCCCCceEEEEEe-CcHHHHHH
Confidence            99999999999999998 55443333

>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=100.00  E-value=6e-49  Score=357.02  Aligned_cols=319  Identities=18%  Similarity=0.287  Sum_probs=241.7

Q ss_pred             hhHHHhHcCCCCCchhHHHHHHHHHcC--CCEEEEccCCCCchhhhhccccc------cCCcEEEEcchHHHHHHHHHHH
Q 037567            2 VSTLKKYFGYSVFRPYQKDVIQRIIEK--RDCLVVMATGSGKSLCYQLPPLV------TGKTALVVSPLISLMQDQVMSL   73 (374)
Q Consensus         2 ~~~l~~~~~~~~~~~~Q~~~~~~~~~~--~~~l~~a~tGsGKT~~~~l~~~~------~~~~~lil~P~~~l~~q~~~~~   73 (374)
                      .+++.+ +||..|+|+|.++++.++++  +++++.+|||+|||++++++++.      .+.+++|++|+++|+.|+.+.+
T Consensus        17 ~~~l~~-~~~~~~~~~Q~~~i~~~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~   95 (395)
T 3pey_A           17 LKGIYA-MKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLTMLTRVNPEDASPQAICLAPSRELARQTLEVV   95 (395)
T ss_dssp             HHHHHH-TTCCSCCHHHHHHHHHHHCSSCCCEEEECCTTSCHHHHHHHHHHHHCCTTCCSCCEEEECSSHHHHHHHHHHH
T ss_pred             HHHHHH-CCCCCCCHHHHHHHHHHHcCCCCeEEEECCCCCcHHHHHHHHHHHHhccCCCCccEEEECCCHHHHHHHHHHH
Confidence            456766 89999999999999999998  89999999999999998877654      3668999999999999999999


Q ss_pred             HHcC----CceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhc-ccCcchHH
Q 037567           74 KQRG----INAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISE-WGHDFRLE  148 (374)
Q Consensus        74 ~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~-~~~~~~~~  148 (374)
                      ..++    .......+......     ....++|+|+||+++......  ....+.++++||+||+|++.+ .+.  .  
T Consensus        96 ~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~iiv~T~~~l~~~~~~--~~~~~~~~~~iIiDEah~~~~~~~~--~--  164 (395)
T 3pey_A           96 QEMGKFTKITSQLIVPDSFEKN-----KQINAQVIVGTPGTVLDLMRR--KLMQLQKIKIFVLDEADNMLDQQGL--G--  164 (395)
T ss_dssp             HHHTTTSCCCEEEESTTSSCTT-----SCBCCSEEEECHHHHHHHHHT--TCBCCTTCCEEEEETHHHHHHSTTH--H--
T ss_pred             HHHhcccCeeEEEEecCchhhh-----ccCCCCEEEEcHHHHHHHHHc--CCcccccCCEEEEEChhhhcCcccc--H--
Confidence            8864    33333333222111     123579999999988655433  223356789999999999876 232  1  


Q ss_pred             HHHHHHHHHhc-CCCCeeEEEeecCcccHHHHHHhcCCCCCeEEEec--cCCCceeEEEEeecCCcchHHHHHHHHHHhh
Q 037567          149 YKQLDKLRTFL-LGVPFVALTATATEKVRIDIINSLKLKNPYVTIAS--FDRKNLFYGVKVINRGQSFVDELVQEILKSV  225 (374)
Q Consensus       149 ~~~~~~~~~~~-~~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  225 (374)
                       ..+..+.... ++.+++++|||+++..... ..........+....  ........... ...........+..+....
T Consensus       165 -~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~l~~~~~~~  241 (395)
T 3pey_A          165 -DQCIRVKRFLPKDTQLVLFSATFADAVRQY-AKKIVPNANTLELQTNEVNVDAIKQLYM-DCKNEADKFDVLTELYGLM  241 (395)
T ss_dssp             -HHHHHHHHTSCTTCEEEEEESCCCHHHHHH-HHHHSCSCEEECCCGGGCSCTTEEEEEE-ECSSHHHHHHHHHHHHTTT
T ss_pred             -HHHHHHHHhCCCCcEEEEEEecCCHHHHHH-HHHhCCCCeEEEccccccccccccEEEE-EcCchHHHHHHHHHHHHhc
Confidence             2333333433 3678999999998765543 333322222222211  11222222222 2223334455556665554


Q ss_pred             cCCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEEEEECC
Q 037567          226 AGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGC  305 (374)
Q Consensus       226 ~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~~~~  305 (374)
                       .++++||||+++..++.+++.|++.+..+..+||+++..+|..+++.|++|+.+|||+|+++++|+|+|++++||++++
T Consensus       242 -~~~~~lvf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidip~~~~Vi~~~~  320 (395)
T 3pey_A          242 -TIGSSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSMVVNYDL  320 (395)
T ss_dssp             -TSSEEEEECSCHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHTTSCCEEEECGGGSSSCCCTTEEEEEESSC
T ss_pred             -cCCCEEEEeCCHHHHHHHHHHHHhcCCcEEEeCCCCCHHHHHHHHHHHHCCCCCEEEECChhhcCCCcccCCEEEEcCC
Confidence             6789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CC------ChhHHHHhhccCCCCCCceEEEEEeeccC
Q 037567          306 PK------TLESYYQESGRCGRDGIASVCWLYYARSN  336 (374)
Q Consensus       306 p~------s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~  336 (374)
                      |.      |...|+||+||+||.|+.|.+++++.+.+
T Consensus       321 p~~~~~~~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~~  357 (395)
T 3pey_A          321 PTLANGQADPATYIHRIGRTGRFGRKGVAISFVHDKN  357 (395)
T ss_dssp             CBCTTSSBCHHHHHHHHTTSSCTTCCEEEEEEECSHH
T ss_pred             CCCCcCCCCHHHhhHhccccccCCCCceEEEEEechH
Confidence            98      99999999999999999999999998643

>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=100.00  E-value=1.9e-49  Score=356.74  Aligned_cols=326  Identities=22%  Similarity=0.287  Sum_probs=247.3

Q ss_pred             hhHHHhHcCCCCCchhHHHHHHHHHcC-CCEEEEccCCCCchhhhhccccc-----cCCcEEEEcchHHHHHHHHHHHHH
Q 037567            2 VSTLKKYFGYSVFRPYQKDVIQRIIEK-RDCLVVMATGSGKSLCYQLPPLV-----TGKTALVVSPLISLMQDQVMSLKQ   75 (374)
Q Consensus         2 ~~~l~~~~~~~~~~~~Q~~~~~~~~~~-~~~l~~a~tGsGKT~~~~l~~~~-----~~~~~lil~P~~~l~~q~~~~~~~   75 (374)
                      .++|++ +||.+|+|+|.++++.++++ +++++.+|||+|||++++++++.     .+.+++|++|+++|+.|+.+++..
T Consensus        18 ~~~l~~-~g~~~~~~~Q~~~i~~~~~~~~~~l~~~~TGsGKT~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~   96 (367)
T 1hv8_A           18 LNAIRN-KGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIELVNENNGIEAIILTPTRELAIQVADEIES   96 (367)
T ss_dssp             HHHHHH-HTCCSCCHHHHHHHHHHHHTCSEEEEECCSSSSHHHHHHHHHHHHSCSSSSCCEEEECSCHHHHHHHHHHHHH
T ss_pred             HHHHHH-cCCCCCCHHHHHHHHHHhCCCCCEEEECCCCChHHHHHHHHHHHHhcccCCCcEEEEcCCHHHHHHHHHHHHH
Confidence            456777 89999999999999999988 68999999999999998777654     367899999999999999999987


Q ss_pred             c----CCceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHH
Q 037567           76 R----GINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQ  151 (374)
Q Consensus        76 ~----~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~  151 (374)
                      +    +..+....++..........  ..++|+|+||+++......  ....+.+++++|+||+|++.+++..     ..
T Consensus        97 ~~~~~~~~v~~~~~~~~~~~~~~~~--~~~~iiv~T~~~l~~~~~~--~~~~~~~~~~iIiDEah~~~~~~~~-----~~  167 (367)
T 1hv8_A           97 LKGNKNLKIAKIYGGKAIYPQIKAL--KNANIVVGTPGRILDHINR--GTLNLKNVKYFILDEADEMLNMGFI-----KD  167 (367)
T ss_dssp             HHCSSCCCEEEECTTSCHHHHHHHH--HTCSEEEECHHHHHHHHHT--TCSCTTSCCEEEEETHHHHHTTTTH-----HH
T ss_pred             HhCCCCceEEEEECCcchHHHHhhc--CCCCEEEecHHHHHHHHHc--CCcccccCCEEEEeCchHhhhhchH-----HH
Confidence            5    34444444443332222222  2579999999988654332  2233567899999999999876532     33


Q ss_pred             HHHHHHhc-CCCCeeEEEeecCcccHHHHHHhcCCCCCeEEEeccCCCceeEEEEeecCCcchHHHHHHHHHHhhcCCCc
Q 037567          152 LDKLRTFL-LGVPFVALTATATEKVRIDIINSLKLKNPYVTIASFDRKNLFYGVKVINRGQSFVDELVQEILKSVAGAGS  230 (374)
Q Consensus       152 ~~~~~~~~-~~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  230 (374)
                      +..+.... ++.+++++|||+++.........++  ........ ....+......  .......+.+..++.  ..+.+
T Consensus       168 ~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~--~~~~~~~~-~~~~~~~~~~~--~~~~~~~~~l~~~l~--~~~~~  240 (367)
T 1hv8_A          168 VEKILNACNKDKRILLFSATMPREILNLAKKYMG--DYSFIKAK-INANIEQSYVE--VNENERFEALCRLLK--NKEFY  240 (367)
T ss_dssp             HHHHHHTSCSSCEEEEECSSCCHHHHHHHHHHCC--SEEEEECC-SSSSSEEEEEE--CCGGGHHHHHHHHHC--STTCC
T ss_pred             HHHHHHhCCCCceEEEEeeccCHHHHHHHHHHcC--CCeEEEec-CCCCceEEEEE--eChHHHHHHHHHHHh--cCCCc
Confidence            44444433 4678999999999876544444333  22222111 11222222211  122223334444444  36789


Q ss_pred             EEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEEEEECCCCChh
Q 037567          231 IIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLE  310 (374)
Q Consensus       231 ~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~~~~p~s~~  310 (374)
                      +||||++++.++.+++.|++.+..+..+||+++..+|..+++.|++|+.+|||+|+++++|+|+|++++||++++|.|+.
T Consensus       241 ~lvf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~~~~~Gid~~~~~~Vi~~~~~~s~~  320 (367)
T 1hv8_A          241 GLVFCKTKRDTKELASMLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATDVMSRGIDVNDLNCVINYHLPQNPE  320 (367)
T ss_dssp             EEEECSSHHHHHHHHHHHHHTTCCEEEECSSSCHHHHHHHHHHHHTTSSSEEEECTTHHHHCCCSCCSEEEESSCCSCHH
T ss_pred             EEEEECCHHHHHHHHHHHHhcCCCeEEeeCCCCHHHHHHHHHHHHcCCCeEEEECChhhcCCCcccCCEEEEecCCCCHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhhccCCCCCCceEEEEEeeccCCCccccee
Q 037567          311 SYYQESGRCGRDGIASVCWLYYARSNFAKGDFYC  344 (374)
Q Consensus       311 ~~~Q~~GR~~R~~~~g~~~~~~~~~~~~~~~~~~  344 (374)
                      +|.||+||+||.|+.|.+++++++.+...+..+.
T Consensus       321 ~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~i~  354 (367)
T 1hv8_A          321 SYMHRIGRTGRAGKKGKAISIINRREYKKLRYIE  354 (367)
T ss_dssp             HHHHHSTTTCCSSSCCEEEEEECTTSHHHHHHHH
T ss_pred             HhhhcccccccCCCccEEEEEEcHHHHHHHHHHH
Confidence            9999999999999999999999987765554443

>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=100.00  E-value=1.9e-48  Score=355.76  Aligned_cols=321  Identities=17%  Similarity=0.219  Sum_probs=239.4

Q ss_pred             hhHHHhHcCCCCCchhHHHHHHHHHcC--CCEEEEccCCCCchhhhhccccc------cCCcEEEEcchHHHHHHHHHHH
Q 037567            2 VSTLKKYFGYSVFRPYQKDVIQRIIEK--RDCLVVMATGSGKSLCYQLPPLV------TGKTALVVSPLISLMQDQVMSL   73 (374)
Q Consensus         2 ~~~l~~~~~~~~~~~~Q~~~~~~~~~~--~~~l~~a~tGsGKT~~~~l~~~~------~~~~~lil~P~~~l~~q~~~~~   73 (374)
                      .++|.+ +||..|+|+|.++++.++++  +++++.+|||+|||++|+++++.      ...+++|++|+++|+.|+.+.+
T Consensus        37 ~~~l~~-~g~~~~~~~Q~~~i~~~~~~~~~~~lv~apTGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~  115 (412)
T 3fht_A           37 LQGVYA-MGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSPTYELALQTGKVI  115 (412)
T ss_dssp             HHHHHH-TTCCSCCHHHHHHHHHHHSSSCCCEEEECCTTSCHHHHHHHHHHHHCCTTSCSCCEEEECSSHHHHHHHHHHH
T ss_pred             HHHHHH-cCCCCCCHHHHHHHHHHhcCCCCeEEEECCCCchHHHHHHHHHHHHhhhcCCCCCEEEECCCHHHHHHHHHHH
Confidence            456776 89999999999999999987  89999999999999998877663      2458999999999999999888


Q ss_pred             HHcC-----CceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhc-ccCcchH
Q 037567           74 KQRG-----INAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISE-WGHDFRL  147 (374)
Q Consensus        74 ~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~-~~~~~~~  147 (374)
                      ..++     .......+......    .....++|+|+||+++...+... ....+.++++||+||+|++.+ .+..   
T Consensus       116 ~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~ivv~T~~~l~~~~~~~-~~~~~~~~~~iViDEah~~~~~~~~~---  187 (412)
T 3fht_A          116 EQMGKFYPELKLAYAVRGNKLER----GQKISEQIVIGTPGTVLDWCSKL-KFIDPKKIKVFVLDEADVMIATQGHQ---  187 (412)
T ss_dssp             HHHTTTSTTCCEEEECTTCCCCT----TCCCCCSEEEECHHHHHHHHTTS-CSSCGGGCCEEEEETHHHHHSTTTTH---
T ss_pred             HHHHhhcccceEEEeecCcchhh----hhcCCCCEEEECchHHHHHHHhc-CCcChhhCcEEEEeCHHHHhhcCCcH---
Confidence            8753     33343333322211    12345789999999886543221 122346789999999999875 3322   


Q ss_pred             HHHHHHHHHHhc-CCCCeeEEEeecCcccHHHHHHhcCCCCCeEEEec--cCCCceeEEEEeecCCcchHHHHHHHHHHh
Q 037567          148 EYKQLDKLRTFL-LGVPFVALTATATEKVRIDIINSLKLKNPYVTIAS--FDRKNLFYGVKVINRGQSFVDELVQEILKS  224 (374)
Q Consensus       148 ~~~~~~~~~~~~-~~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  224 (374)
                        ..+..+.... ++.+++++|||+++.........+. ....+....  .....+...... ..........+..++..
T Consensus       188 --~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~l~~~~~~  263 (412)
T 3fht_A          188 --DQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVP-DPNVIKLKREEETLDTIKQYYVL-CSSRDEKFQALCNLYGA  263 (412)
T ss_dssp             --HHHHHHHHTSCTTCEEEEEESCCCHHHHHHHHHHSS-SCEEECCCGGGSSCTTEEEEEEE-CSSHHHHHHHHHHHHHH
T ss_pred             --HHHHHHHhhCCCCceEEEEEeecCHHHHHHHHHhcC-CCeEEeeccccccccCceEEEEE-cCChHHHHHHHHHHHhh
Confidence              2223333333 3678999999999876543333332 222222111  112222222222 22233344455555554


Q ss_pred             hcCCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEEEEEC
Q 037567          225 VAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYG  304 (374)
Q Consensus       225 ~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~~~  304 (374)
                      . .++++||||+++..++.+++.|.+.+..+..+||+++..+|..+++.|++|+.+|||+|+++++|+|+|++++||+++
T Consensus       264 ~-~~~~~lvf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidip~~~~Vi~~~  342 (412)
T 3fht_A          264 I-TIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINFD  342 (412)
T ss_dssp             H-SSSEEEEECSSHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHTTSCSEEEECGGGTSSCCCTTEEEEEESS
T ss_pred             c-CCCCEEEEeCCHHHHHHHHHHHHhCCCeEEEecCCCCHHHHHHHHHHHHCCCCcEEEEcCccccCCCccCCCEEEEEC
Confidence            3 678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CC------CChhHHHHhhccCCCCCCceEEEEEeeccC
Q 037567          305 CP------KTLESYYQESGRCGRDGIASVCWLYYARSN  336 (374)
Q Consensus       305 ~p------~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~  336 (374)
                      +|      .+..+|+||+||+||.|+.|.+++++++.+
T Consensus       343 ~p~~~~~~~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~~  380 (412)
T 3fht_A          343 LPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSKH  380 (412)
T ss_dssp             CCBCSSSSBCHHHHHHHHTTSSCTTCCEEEEEEECSHH
T ss_pred             CCCCCCCCcchheeecccCcccCCCCCceEEEEEcChh
Confidence            99      467899999999999999999999998653

>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=100.00  E-value=1.6e-50  Score=367.21  Aligned_cols=335  Identities=19%  Similarity=0.232  Sum_probs=128.4

Q ss_pred             hhHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc------cCCcEEEEcchHHHHHHHHHHHHH
Q 037567            2 VSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV------TGKTALVVSPLISLMQDQVMSLKQ   75 (374)
Q Consensus         2 ~~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~------~~~~~lil~P~~~l~~q~~~~~~~   75 (374)
                      .+++.. +||.+|+|+|.++++.+++++++++.+|||+|||++|+++++.      .+.+++|++|+++|+.|+.+.+.+
T Consensus        33 ~~~l~~-~g~~~~~~~Q~~~i~~i~~~~~~lv~~~TGsGKT~~~~~~~~~~l~~~~~~~~~lil~P~~~L~~q~~~~~~~  111 (394)
T 1fuu_A           33 LRGVFG-YGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALMLAPTRELALQIQKVVMA  111 (394)
T ss_dssp             HHHHHH-HTCCSCCHHHHHHHHHHHHTCCEEECCCSSHHHHHHHHHHHHHHCCTTCCSCCEEEECSSHHHHHHHHHHHHH
T ss_pred             HHHHHH-cCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHhhccCCCCCEEEEcCCHHHHHHHHHHHHH
Confidence            456666 8999999999999999999999999999999999998877664      366899999999999999999887


Q ss_pred             c----CCceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHH
Q 037567           76 R----GINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQ  151 (374)
Q Consensus        76 ~----~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~  151 (374)
                      +    +..+....++..........  ..++|+|+||+++......  ......+++++|+||+|++.+++..     ..
T Consensus       112 ~~~~~~~~~~~~~g~~~~~~~~~~~--~~~~i~v~T~~~l~~~~~~--~~~~~~~~~~vIiDEah~~~~~~~~-----~~  182 (394)
T 1fuu_A          112 LAFHMDIKVHACIGGTSFVEDAEGL--RDAQIVVGTPGRVFDNIQR--RRFRTDKIKMFILDEADEMLSSGFK-----EQ  182 (394)
T ss_dssp             HTTTSCCCEEEECSSCCHHHHHHHH--HHCSEEEECHHHHHHHHHT--TSSCCTTCCEEEEETHHHHHHTTCH-----HH
T ss_pred             HhccCCeeEEEEeCCCchHHHHhhc--CCCCEEEECHHHHHHHHHh--CCcchhhCcEEEEEChHHhhCCCcH-----HH
Confidence            5    45555555544333222222  1478999999988654332  2233467899999999999776533     33


Q ss_pred             HHHHHHhc-CCCCeeEEEeecCcccHHHHHHhcCCCCCeEEEeccC--CCceeEEEEeecCCcchHHHHHHHHHHhhcCC
Q 037567          152 LDKLRTFL-LGVPFVALTATATEKVRIDIINSLKLKNPYVTIASFD--RKNLFYGVKVINRGQSFVDELVQEILKSVAGA  228 (374)
Q Consensus       152 ~~~~~~~~-~~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  228 (374)
                      +..+.... ++.+++++|||+++.........+. .+..+......  ...+....... .........+.++++.. ..
T Consensus       183 ~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~l~~~~~~~-~~  259 (394)
T 1fuu_A          183 IYQIFTLLPPTTQVVLLSATMPNDVLEVTTKFMR-NPVRILVKKDELTLEGIKQFYVNV-EEEEYKYECLTDLYDSI-SV  259 (394)
T ss_dssp             HHHHHHHSCTTCEEEEECSSCCHHHHHHHHHHCC-SCEEEEECC------------------------------------
T ss_pred             HHHHHHhCCCCceEEEEEEecCHHHHHHHHHhcC-CCeEEEecCccccCCCceEEEEEc-CchhhHHHHHHHHHhcC-CC
Confidence            33343333 4678999999999865543333332 22222221111  11111111111 11111233444444443 56


Q ss_pred             CcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEEEEECCCCC
Q 037567          229 GSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPKT  308 (374)
Q Consensus       229 ~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~~~~p~s  308 (374)
                      +++||||++++.++.+++.|++.+..+..+||+++..+|..+++.|++|+.+|||+|+++++|+|+|++++||++++|.+
T Consensus       260 ~~~lVf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~~~~~Gldi~~~~~Vi~~~~p~s  339 (394)
T 1fuu_A          260 TQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPAN  339 (394)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             CcEEEEECCHHHHHHHHHHHHHcCCeEEEeeCCCCHHHHHHHHHHHHCCCCcEEEECChhhcCCCcccCCEEEEeCCCCC
Confidence            79999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhHHHHhhccCCCCCCceEEEEEeeccCCCcccceeccccc
Q 037567          309 LESYYQESGRCGRDGIASVCWLYYARSNFAKGDFYCGESQT  349 (374)
Q Consensus       309 ~~~~~Q~~GR~~R~~~~g~~~~~~~~~~~~~~~~~~~~~~~  349 (374)
                      ...|+||+||+||.|+.|.+++++++.+...++.+......
T Consensus       340 ~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~l~~~~~~  380 (394)
T 1fuu_A          340 KENYIHRIGRGGRFGRKGVAINFVTNEDVGAMRELEKFYST  380 (394)
T ss_dssp             -----------------------------------------
T ss_pred             HHHHHHHcCcccCCCCCceEEEEEchhHHHHHHHHHHHhCC
Confidence            99999999999999999999999999998877777654333

>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=100.00  E-value=2.5e-49  Score=367.66  Aligned_cols=329  Identities=16%  Similarity=0.205  Sum_probs=122.5

Q ss_pred             hhHHHhHcCCCCCchhHHHHHHHHHcC--CCEEEEccCCCCchhhhhcccccc------CCcEEEEcchHHHHHHHHHHH
Q 037567            2 VSTLKKYFGYSVFRPYQKDVIQRIIEK--RDCLVVMATGSGKSLCYQLPPLVT------GKTALVVSPLISLMQDQVMSL   73 (374)
Q Consensus         2 ~~~l~~~~~~~~~~~~Q~~~~~~~~~~--~~~l~~a~tGsGKT~~~~l~~~~~------~~~~lil~P~~~l~~q~~~~~   73 (374)
                      .++|.+ +||..|+|+|.++++.++++  +++++.||||||||++|+++++..      .+++||++|+++|+.|+.+.+
T Consensus       104 ~~~l~~-~g~~~p~~~Q~~ai~~il~~~~~~~l~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~  182 (479)
T 3fmp_B          104 LQGVYA-MGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSPTYELALQTGKVI  182 (479)
T ss_dssp             HHHHHH-TTCCSCCHHHHHHHHHHTSBSCCEEEEECCSSSSHHHHHHHHHHTTCCTTSCSCCEEEECSSHHHHHHHHHHH
T ss_pred             HHHHHH-cCCCCCCHHHHHHHHHHHcCCCCcEEEEcCCCCchhHHHHHHHHHHHhhcCCCCcEEEEeChHHHHHHHHHHH
Confidence            456776 89999999999999999987  899999999999999998887642      348999999999999998887


Q ss_pred             HHc-----CCceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhc-ccCcchH
Q 037567           74 KQR-----GINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISE-WGHDFRL  147 (374)
Q Consensus        74 ~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~-~~~~~~~  147 (374)
                      ..+     +.......+......    .....++|+|+||+++..++... ....+.++++||+||+|.+.+ .+..   
T Consensus       183 ~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~Ivv~Tp~~l~~~l~~~-~~~~~~~~~~iViDEah~~~~~~~~~---  254 (479)
T 3fmp_B          183 EQMGKFYPELKLAYAVRGNKLER----GQKISEQIVIGTPGTVLDWCSKL-KFIDPKKIKVFVLDEADVMIATQGHQ---  254 (479)
T ss_dssp             HHHHTTSTTCCEEEESTTCCCCT----TCCCCCSEEEECHHHHHHHHTTS-CCCCGGGCCEEEECCHHHHHTSTTHH---
T ss_pred             HHHHhhCCCceEEEEeCCccccc----cccCCCCEEEECchHHHHHHHhc-CCcCcccCCEEEEECHHHHhhcCCcH---
Confidence            764     233333333222111    11234689999999986544321 123347789999999999875 2321   


Q ss_pred             HHHHHHHHHHhc-CCCCeeEEEeecCcccHHHHHHhcCCCCCeEEEeccC---CCceeEEEEeecCCcchHHHHHHHHHH
Q 037567          148 EYKQLDKLRTFL-LGVPFVALTATATEKVRIDIINSLKLKNPYVTIASFD---RKNLFYGVKVINRGQSFVDELVQEILK  223 (374)
Q Consensus       148 ~~~~~~~~~~~~-~~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~  223 (374)
                        ..+..+.... ++.+++++|||++..........+  ..+........   ...+......... .......+..++.
T Consensus       255 --~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~--~~~~~i~~~~~~~~~~~~~~~~~~~~~-~~~~~~~l~~~~~  329 (479)
T 3fmp_B          255 --DQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVV--PDPNVIKLKREEETLDTIKQYYVLCSS-RDEKFQALCNLYG  329 (479)
T ss_dssp             --HHHHHHHTTSCTTSEEEEEESCCCHHHHHHHHHHS--SSEEEEEEC--------------------------------
T ss_pred             --HHHHHHHhhCCccceEEEEeCCCCHHHHHHHHHHc--CCCeEEeccccccCcCCceEEEEEeCC-HHHHHHHHHHHHh
Confidence              2223333333 367899999999987654222222  22222221111   1111111111111 1122223333333


Q ss_pred             hhcCCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEEEEE
Q 037567          224 SVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHY  303 (374)
Q Consensus       224 ~~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~~  303 (374)
                      .. ..+++||||+++..++.+++.|...+..+..+||+++..+|..+++.|++|+.+|||||+++++|+|+|++++||++
T Consensus       330 ~~-~~~~~lvF~~s~~~~~~l~~~L~~~~~~v~~lh~~~~~~~R~~~~~~f~~g~~~iLv~T~~~~~GlDip~v~~VI~~  408 (479)
T 3fmp_B          330 AI-TIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINF  408 (479)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             hc-cCCceEEEeCcHHHHHHHHHHHHhCCccEEEecCCCCHHHHHHHHHHHHcCCCcEEEEccccccCCccccCCEEEEe
Confidence            32 56789999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCC------ChhHHHHhhccCCCCCCceEEEEEeeccC-CCcccceec
Q 037567          304 GCPK------TLESYYQESGRCGRDGIASVCWLYYARSN-FAKGDFYCG  345 (374)
Q Consensus       304 ~~p~------s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~-~~~~~~~~~  345 (374)
                      ++|.      +...|+||+||+||.|+.|.+++++++.+ ...++.+.+
T Consensus       409 d~p~~~~~~~s~~~~~Qr~GRagR~g~~G~~i~~~~~~~~~~~~~~i~~  457 (479)
T 3fmp_B          409 DLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSKHSMNILNRIQE  457 (479)
T ss_dssp             -------------------------------------------------
T ss_pred             cCCCCCccCCCHHHHHHHhcccccCCCCceEEEEEcCcchHHHHHHHHH
Confidence            9994      66899999999999999999999998765 444444443

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A*

Probab=100.00  E-value=3.3e-47  Score=347.21  Aligned_cols=308  Identities=21%  Similarity=0.261  Sum_probs=231.1

Q ss_pred             hhHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc---cCCcEEEEcchHHHHHHHHHHHHHc--
Q 037567            2 VSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV---TGKTALVVSPLISLMQDQVMSLKQR--   76 (374)
Q Consensus         2 ~~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~---~~~~~lil~P~~~l~~q~~~~~~~~--   76 (374)
                      .+.|++.+|| +|+|+|.++++.+++++++++.+|||||||++|+++++.   .+.+++|++|+++|+.|+.+.++.+  
T Consensus        11 ~~~l~~~~~~-~~~~~Q~~~i~~i~~~~~~lv~apTGsGKT~~~l~~~~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~   89 (414)
T 3oiy_A           11 RSFFKKKFGK-DLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLARKGKKSALVFPTVTLVKQTLERLQKLAD   89 (414)
T ss_dssp             HHHHHHHHSS-CCCHHHHHHHHHHTTTCCEECCSCSSSSHHHHHHHHHHHHHTTTCCEEEEESSHHHHHHHHHHHHHHCC
T ss_pred             HHHHHHhcCC-CCCHHHHHHHHHHhcCCCEEEEeCCCCCHHHHHHHHHHHHhcCCCEEEEEECCHHHHHHHHHHHHHHcc
Confidence            3567888899 699999999999999999999999999999988877665   6889999999999999999999985  


Q ss_pred             -CCceEEcCCCCCc---hhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhccc---------C
Q 037567           77 -GINAEFLGSAQTD---SSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWG---------H  143 (374)
Q Consensus        77 -~~~~~~~~~~~~~---~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~---------~  143 (374)
                       ++.+..+.++...   .........+.++|+|+||+++...+.    .....++++||+||+|++.+++         .
T Consensus        90 ~~~~v~~~~g~~~~~~~~~~~~~l~~~~~~Iiv~Tp~~l~~~l~----~~~~~~~~~iViDEaH~~~~~~~~~d~~l~~~  165 (414)
T 3oiy_A           90 EKVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNRE----KLSQKRFDFVFVDDVDAVLKASRNIDTLLMMV  165 (414)
T ss_dssp             SSCCEEECCTTSCHHHHHHHHHHHHHTCCSEEEEEHHHHHHCHH----HHTTCCCSEEEESCHHHHHHCHHHHHHHHHHT
T ss_pred             CCceEEEEECCCChhhHHHHHHHhhcCCCCEEEECHHHHHHHHH----HhccccccEEEEeChHhhhhccchhhhHHhhc
Confidence             5677777776655   223334445568999999999876543    3556789999999999987644         2


Q ss_pred             cchHHHHHHHHHHHhc------------CCCCeeEEEeecCc-ccHHHHHH-hcCCCCCeEEEeccCCCceeEEEEeecC
Q 037567          144 DFRLEYKQLDKLRTFL------------LGVPFVALTATATE-KVRIDIIN-SLKLKNPYVTIASFDRKNLFYGVKVINR  209 (374)
Q Consensus       144 ~~~~~~~~~~~~~~~~------------~~~~~i~~SaT~~~-~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~  209 (374)
                      .+...  .+..+...+            ++.+++++|||+.+ .....+.. .+......   ......++....... .
T Consensus       166 ~~~~~--~~~~i~~~~~~~~~~~~l~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~---~~~~~~~i~~~~~~~-~  239 (414)
T 3oiy_A          166 GIPEE--IIRKAFSTIKQGKIYERPKNLKPGILVVSSATAKPRGIRPLLFRDLLNFTVGR---LVSVARNITHVRISS-R  239 (414)
T ss_dssp             TCCHH--HHHHHHHHHHHTCCCCCCTTCCCCEEEESSCCSSCCSSTTHHHHHHHSCCSSC---CCCCCCSEEEEEESS-C
T ss_pred             CCcHH--HHHHHHHhcccchhhhhcccCCCceEEEEecCCCcchhHHHHHHHhhccCcCc---cccccccchheeecc-C
Confidence            22222  023333322            56789999999544 33322222 22211111   111112222222111 1


Q ss_pred             CcchHHHHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHHcCCcee-eeecCCChHHHHHHHHhhhcCCeeEEEE----
Q 037567          210 GQSFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAG-TYHGQMGSKAREEAHRLFIRDEIRVMVA----  284 (374)
Q Consensus       210 ~~~~~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~-~~~~~~~~~~r~~~~~~f~~g~~~ilv~----  284 (374)
                          ..+.+.++++.  .++++||||+++..++.+++.|++.++.+. .+||+    +|.  ++.|++|+.+||||    
T Consensus       240 ----~~~~l~~~l~~--~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~~h~~----~r~--~~~f~~g~~~vLvat~s~  307 (414)
T 3oiy_A          240 ----SKEKLVELLEI--FRDGILIFAQTEEEGKELYEYLKRFKFNVGETWSEF----EKN--FEDFKVGKINILIGVQAY  307 (414)
T ss_dssp             ----CHHHHHHHHHH--HCSSEEEEESSHHHHHHHHHHHHHTTCCEEESSSCH----HHH--HHHHHTTSCSEEEEECCT
T ss_pred             ----HHHHHHHHHHH--cCCCEEEEECCHHHHHHHHHHHHHcCCceehhhcCc----chH--HHHHhCCCCeEEEEecCc
Confidence                22334444444  358999999999999999999999999998 88885    444  99999999999999    


Q ss_pred             eccccccccccC-ccEEEEECCC--CChhHHHHhhccCCCCC----CceEEEEEe
Q 037567          285 TMAFGMGIDKPD-VRHVIHYGCP--KTLESYYQESGRCGRDG----IASVCWLYY  332 (374)
Q Consensus       285 t~~~~~G~d~~~-~~~vi~~~~p--~s~~~~~Q~~GR~~R~~----~~g~~~~~~  332 (374)
                      |+++++|+|+|+ +++||++++|  .+...|+||+||+||.|    ..|.+++++
T Consensus       308 T~~~~~GiDip~~v~~VI~~~~p~~~~~~~y~qr~GR~gR~g~~~~~~g~~i~~~  362 (414)
T 3oiy_A          308 YGKLTRGVDLPERIKYVIFWGTPSGPDVYTYIQASGRSSRILNGVLVKGVSVIFE  362 (414)
T ss_dssp             TCCCCCCCCCTTTCCEEEEESCCTTTCHHHHHHHHGGGCCEETTEECCEEEEEEC
T ss_pred             CchhhccCccccccCEEEEECCCCCCCHHHHHHHhCccccCCCCCCcceEEEEEE
Confidence            999999999999 9999999999  99999999999999987    478999988

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus}

Probab=100.00  E-value=2e-43  Score=342.79  Aligned_cols=317  Identities=20%  Similarity=0.279  Sum_probs=231.7

Q ss_pred             hHHHhHcCCCCCchhHHHHHHH-HHcCCCEEEEccCCCCchhhhhccccc----cCCcEEEEcchHHHHHHHHHHHHH--
Q 037567            3 STLKKYFGYSVFRPYQKDVIQR-IIEKRDCLVVMATGSGKSLCYQLPPLV----TGKTALVVSPLISLMQDQVMSLKQ--   75 (374)
Q Consensus         3 ~~l~~~~~~~~~~~~Q~~~~~~-~~~~~~~l~~a~tGsGKT~~~~l~~~~----~~~~~lil~P~~~l~~q~~~~~~~--   75 (374)
                      +.+++ +||.+|+|+|.++++. +.++++++++||||||||+++.++++.    .+.++++++|+++|+.|+.+.++.  
T Consensus        21 ~~l~~-~g~~~l~~~Q~~~i~~~~~~~~~~lv~apTGsGKT~~~~l~il~~~~~~~~~il~i~P~r~La~q~~~~~~~~~   99 (715)
T 2va8_A           21 EIIKK-RGIKKLNPPQTEAVKKGLLEGNRLLLTSPTGSGKTLIAEMGIISFLLKNGGKAIYVTPLRALTNEKYLTFKDWE   99 (715)
T ss_dssp             HHHHT-TSCCBCCHHHHHHHHTTTTTTCCEEEECCTTSCHHHHHHHHHHHHHHHSCSEEEEECSCHHHHHHHHHHHGGGG
T ss_pred             HHHHh-CCCCCCCHHHHHHHHHHhcCCCcEEEEcCCCCcHHHHHHHHHHHHHHHCCCeEEEEeCcHHHHHHHHHHHHHhh
Confidence            45555 7999999999999999 778999999999999999998877753    578999999999999999999854  


Q ss_pred             -cCCceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHH
Q 037567           76 -RGINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDK  154 (374)
Q Consensus        76 -~~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~  154 (374)
                       .|..+....++.......    ...++|+|+||+++..++..  ....+.++++||+||+|.+.+.+..     ..+..
T Consensus       100 ~~g~~v~~~~G~~~~~~~~----~~~~~Iiv~Tpe~l~~~~~~--~~~~l~~~~~vIiDE~H~l~~~~~~-----~~l~~  168 (715)
T 2va8_A          100 LIGFKVAMTSGDYDTDDAW----LKNYDIIITTYEKLDSLWRH--RPEWLNEVNYFVLDELHYLNDPERG-----PVVES  168 (715)
T ss_dssp             GGTCCEEECCSCSSSCCGG----GGGCSEEEECHHHHHHHHHH--CCGGGGGEEEEEECSGGGGGCTTTH-----HHHHH
T ss_pred             cCCCEEEEEeCCCCCchhh----cCCCCEEEEcHHHHHHHHhC--ChhHhhccCEEEEechhhcCCcccc-----hHHHH
Confidence             367777766654443321    13579999999998766544  2233678899999999998754332     22333


Q ss_pred             HHHhcCCCCeeEEEeecCcccHHHHHHhcCCCCCeEEEeccCCCcee------------EEEEeecCCcch---HHHHHH
Q 037567          155 LRTFLLGVPFVALTATATEKVRIDIINSLKLKNPYVTIASFDRKNLF------------YGVKVINRGQSF---VDELVQ  219 (374)
Q Consensus       155 ~~~~~~~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------------~~~~~~~~~~~~---~~~~~~  219 (374)
                      +....++.++++||||+++.  ..+..+++..   ..........+.            ............   ......
T Consensus       169 i~~~~~~~~ii~lSATl~n~--~~~~~~l~~~---~~~~~~r~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  243 (715)
T 2va8_A          169 VTIRAKRRNLLALSATISNY--KQIAKWLGAE---PVATNWRPVPLIEGVIYPERKKKEYNVIFKDNTTKKVHGDDAIIA  243 (715)
T ss_dssp             HHHHHHTSEEEEEESCCTTH--HHHHHHHTCE---EEECCCCSSCEEEEEEEECSSTTEEEEEETTSCEEEEESSSHHHH
T ss_pred             HHHhcccCcEEEEcCCCCCH--HHHHHHhCCC---ccCCCCCCCCceEEEEecCCcccceeeecCcchhhhcccchHHHH
Confidence            33333478999999999863  3566666532   111111000000            011111100000   122333


Q ss_pred             HHHHhhcCCCcEEEEecchhHHHHHHHHHHHcC------------------------------------CceeeeecCCC
Q 037567          220 EILKSVAGAGSIIVYCMTIKDVEEISKALKQLG------------------------------------VKAGTYHGQMG  263 (374)
Q Consensus       220 ~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~~------------------------------------~~~~~~~~~~~  263 (374)
                      .+.+....++++||||+++++++.+++.|.+..                                    ..+..+||+++
T Consensus       244 ~~~~~~~~~~~~LVF~~s~~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~l~~~~~~~v~~~h~~l~  323 (715)
T 2va8_A          244 YTLDSLSKNGQVLVFRNSRKMAESTALKIANYMNFVSLDENALSEILKQLDDIEEGGSDEKELLKSLISKGVAYHHAGLS  323 (715)
T ss_dssp             HHHHHHTTTCCEEEECSSHHHHHHHHHHHHHTTTSSCCCHHHHHHHHHHHHTCCSSCHHHHHHHHHHHTTTEEEECTTSC
T ss_pred             HHHHHHhcCCCEEEEECCHHHHHHHHHHHHHHHhhccCChHHHHHHHHHHHHhhhccccccHHHHHHHhcCEEEECCCCC
Confidence            333444578999999999999999999998642                                    24889999999


Q ss_pred             hHHHHHHHHhhhcCCeeEEEEeccccccccccCccEEEE----EC-------CCCChhHHHHhhccCCCCC--CceEEEE
Q 037567          264 SKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIH----YG-------CPKTLESYYQESGRCGRDG--IASVCWL  330 (374)
Q Consensus       264 ~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~----~~-------~p~s~~~~~Q~~GR~~R~~--~~g~~~~  330 (374)
                      .++|..+++.|.+|..+|||||+++++|+|+|++++||+    ++       .|.|..+|.||+|||||.|  ..|.|+.
T Consensus       324 ~~~r~~v~~~f~~g~~~vlvaT~~l~~Gidip~~~~VI~~~~~~d~~~~~~~~~~s~~~~~Qr~GRaGR~g~~~~G~~~~  403 (715)
T 2va8_A          324 KALRDLIEEGFRQRKIKVIVATPTLAAGVNLPARTVIIGDIYRFNKKIAGYYDEIPIMEYKQMSGRAGRPGFDQIGESIV  403 (715)
T ss_dssp             HHHHHHHHHHHHTTCSCEEEECGGGGGSSCCCBSEEEECCC--------------CHHHHHHHHTTBCCTTTCSCEEEEE
T ss_pred             HHHHHHHHHHHHcCCCeEEEEChHHhcccCCCceEEEEeCCeeccccCCCCCCcCCHHHHHHHhhhcCCCCCCCCceEEE
Confidence            999999999999999999999999999999999999998    87       7889999999999999988  4799999


Q ss_pred             EeeccC
Q 037567          331 YYARSN  336 (374)
Q Consensus       331 ~~~~~~  336 (374)
                      ++...+
T Consensus       404 l~~~~~  409 (715)
T 2va8_A          404 VVRDKE  409 (715)
T ss_dssp             ECSCGG
T ss_pred             EeCCch
Confidence            997765

>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=100.00  E-value=4.5e-44  Score=346.23  Aligned_cols=320  Identities=23%  Similarity=0.330  Sum_probs=233.9

Q ss_pred             hHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc---cCCcEEEEcchHHHHHHHHHHHHHc---
Q 037567            3 STLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV---TGKTALVVSPLISLMQDQVMSLKQR---   76 (374)
Q Consensus         3 ~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~---~~~~~lil~P~~~l~~q~~~~~~~~---   76 (374)
                      +.|++ +||.+|+|+|.++++.+.+++++++.||||||||+++.++++.   ++.+++|++|+++|+.|+.+.++.+   
T Consensus        16 ~~l~~-~g~~~l~~~Q~~~i~~i~~~~~~lv~apTGsGKT~~~~l~il~~~~~~~~~l~i~P~r~La~q~~~~~~~~~~~   94 (702)
T 2p6r_A           16 GILKE-EGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIKGGKSLYVVPLRALAGEKYESFKKWEKI   94 (702)
T ss_dssp             HHHHC-C---CCCCCCHHHHHHHTTCSCEEEECSSHHHHHHHHHHHHHHHHHTTCCEEEEESSHHHHHHHHHHHTTTTTT
T ss_pred             HHHHh-CCCCCCCHHHHHHHHHHhCCCcEEEEcCCccHHHHHHHHHHHHHHHhCCcEEEEeCcHHHHHHHHHHHHHHHhc
Confidence            45555 7999999999999999999999999999999999998877763   5789999999999999999998643   


Q ss_pred             CCceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHH
Q 037567           77 GINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLR  156 (374)
Q Consensus        77 ~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~  156 (374)
                      |..+....++......    ..+.++|+|+||+++..+...  ....+.++++||+||+|.+.+++...... ..+..+.
T Consensus        95 g~~v~~~~G~~~~~~~----~~~~~~Iiv~Tpe~l~~~l~~--~~~~l~~~~~vIiDE~H~l~~~~r~~~~~-~ll~~l~  167 (702)
T 2p6r_A           95 GLRIGISTGDYESRDE----HLGDCDIIVTTSEKADSLIRN--RASWIKAVSCLVVDEIHLLDSEKRGATLE-ILVTKMR  167 (702)
T ss_dssp             TCCEEEECSSCBCCSS----CSTTCSEEEEEHHHHHHHHHT--TCSGGGGCCEEEETTGGGGGCTTTHHHHH-HHHHHHH
T ss_pred             CCEEEEEeCCCCcchh----hccCCCEEEECHHHHHHHHHc--ChhHHhhcCEEEEeeeeecCCCCcccHHH-HHHHHHH
Confidence            6677766665433322    123679999999998766544  22335788999999999987644331111 1223333


Q ss_pred             HhcCCCCeeEEEeecCcccHHHHHHhcCCCCCeEEEeccCCCceeEEE------EeecCC-----cchHHHHHHHHHHhh
Q 037567          157 TFLLGVPFVALTATATEKVRIDIINSLKLKNPYVTIASFDRKNLFYGV------KVINRG-----QSFVDELVQEILKSV  225 (374)
Q Consensus       157 ~~~~~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~-----~~~~~~~~~~~~~~~  225 (374)
                      ...++.++++||||+++.  .++..+++..   ..........+...+      ......     .....+.+.+.   .
T Consensus       168 ~~~~~~~ii~lSATl~n~--~~~~~~l~~~---~~~~~~r~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~  239 (702)
T 2p6r_A          168 RMNKALRVIGLSATAPNV--TEIAEWLDAD---YYVSDWRPVPLVEGVLCEGTLELFDGAFSTSRRVKFEELVEEC---V  239 (702)
T ss_dssp             HHCTTCEEEEEECCCTTH--HHHHHHTTCE---EEECCCCSSCEEEEEECSSEEEEEETTEEEEEECCHHHHHHHH---H
T ss_pred             hcCcCceEEEECCCcCCH--HHHHHHhCCC---cccCCCCCccceEEEeeCCeeeccCcchhhhhhhhHHHHHHHH---H
Confidence            334578999999999863  3567776532   111111111111100      011100     00023333333   3


Q ss_pred             cCCCcEEEEecchhHHHHHHHHHHHc------------------------------CCceeeeecCCChHHHHHHHHhhh
Q 037567          226 AGAGSIIVYCMTIKDVEEISKALKQL------------------------------GVKAGTYHGQMGSKAREEAHRLFI  275 (374)
Q Consensus       226 ~~~~~~lVf~~~~~~~~~l~~~l~~~------------------------------~~~~~~~~~~~~~~~r~~~~~~f~  275 (374)
                      .+++++||||++++.++.+++.|.+.                              +..+..+||+++.++|..+++.|.
T Consensus       240 ~~~~~~LVF~~s~~~~~~~a~~L~~~~~~~~~~~~~~~~i~~~~~~~~~~~l~~~~~~~v~~~h~~l~~~~R~~v~~~f~  319 (702)
T 2p6r_A          240 AENGGVLVFESTRRGAEKTAVKLSAITAKYVENEGLEKAILEENEGEMSRKLAECVRKGAAFHHAGLLNGQRRVVEDAFR  319 (702)
T ss_dssp             HTTCCEEEECSSHHHHHHHHHHHHHHHHTTCCCSSHHHHHHTTCCSHHHHHHHHHHHTTCCEECTTSCHHHHHHHHHHHH
T ss_pred             hcCCCEEEEcCCHHHHHHHHHHHHHHHHhhcChHHHHHHHHhhccccccHHHHHHHhcCeEEecCCCCHHHHHHHHHHHH
Confidence            47899999999999999999988753                              135788999999999999999999


Q ss_pred             cCCeeEEEEeccccccccccCccEEEE----EC---CCCChhHHHHhhccCCCCC--CceEEEEEeeccCCC
Q 037567          276 RDEIRVMVATMAFGMGIDKPDVRHVIH----YG---CPKTLESYYQESGRCGRDG--IASVCWLYYARSNFA  338 (374)
Q Consensus       276 ~g~~~ilv~t~~~~~G~d~~~~~~vi~----~~---~p~s~~~~~Q~~GR~~R~~--~~g~~~~~~~~~~~~  338 (374)
                      +|..+|||||+++++|+|+|++++||+    |+   .|.|..+|.||+|||||.|  ..|.|+.++...+..
T Consensus       320 ~g~~~vlvaT~~l~~Gidip~~~~VI~~~~~yd~~~~~~s~~~~~Qr~GRaGR~g~~~~G~~~~l~~~~~~~  391 (702)
T 2p6r_A          320 RGNIKVVVATPTLAAGVNLPARRVIVRSLYRFDGYSKRIKVSEYKQMAGRAGRPGMDERGEAIIIVGKRDRE  391 (702)
T ss_dssp             TTSCCEEEECSTTTSSSCCCBSEEEECCSEEESSSEEECCHHHHHHHHTTBSCTTTCSCEEEEEECCGGGHH
T ss_pred             CCCCeEEEECcHHhccCCCCceEEEEcCceeeCCCCCcCCHHHHHHHhhhcCCCCCCCCceEEEEecCccHH
Confidence            999999999999999999999999998    55   6889999999999999988  479999999987743

>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=100.00  E-value=2e-44  Score=349.95  Aligned_cols=321  Identities=17%  Similarity=0.149  Sum_probs=212.1

Q ss_pred             CCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc-----cC----CcEEEEcchHHHHHHH-HHHHHHcC---Cc
Q 037567           13 VFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV-----TG----KTALVVSPLISLMQDQ-VMSLKQRG---IN   79 (374)
Q Consensus        13 ~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~-----~~----~~~lil~P~~~l~~q~-~~~~~~~~---~~   79 (374)
                      +|+|+|.++++.+++++++++.+|||+|||++|+++++.     ..    .++||++|+++|+.|| .+++++++   ..
T Consensus         7 ~l~~~Q~~~i~~il~g~~~ll~~~TGsGKTl~~~~~i~~~l~~~~~~~~~~~vlvl~P~~~L~~Q~~~~~l~~~~~~~~~   86 (699)
T 4gl2_A            7 QLRPYQMEVAQPALEGKNIIICLPTGCGKTRVAVYIAKDHLDKKKKASEPGKVIVLVNKVLLVEQLFRKEFQPFLKKWYR   86 (699)
T ss_dssp             CCCHHHHHHHHHHHSSCCEEECCCTTSCHHHHHHHHHHHHHHHHHHHTCCCCBCCEESCSHHHHHHHHHTHHHHHTTTSC
T ss_pred             CccHHHHHHHHHHHhCCCEEEEcCCCCcHHHHHHHHHHHHHHhccccCCCCeEEEEECCHHHHHHHHHHHHHHHcCcCce
Confidence            599999999999999999999999999999999888765     12    7899999999999999 99998875   56


Q ss_pred             eEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhh----HHHHHhcCccEEEEeccchhhcccCcchHHHHHHHH-
Q 037567           80 AEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISF----WSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDK-  154 (374)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~----~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~-  154 (374)
                      +..+.++........ ...+.++|+|+||+.|...+...    .....+..+++|||||||++...+.........+.. 
T Consensus        87 v~~~~g~~~~~~~~~-~~~~~~~Ilv~Tp~~L~~~l~~~~~~~~~~~~~~~~~lvViDEaH~~~~~~~~~~i~~~~l~~~  165 (699)
T 4gl2_A           87 VIGLSGDTQLKISFP-EVVKSCDIIISTAQILENSLLNLENGEDAGVQLSDFSLIIIDECHHTNKEAVYNNIMRHYLMQK  165 (699)
T ss_dssp             EEEEC----CCCCHH-HHHHSCSEEEEEHHHHHHHTC--------CCCGGGCSEEEEESGGGCBTTBSSCSHHHHHHHHH
T ss_pred             EEEEeCCcchhhHHH-hhhcCCCEEEECHHHHHHHHhccccccccceecccCcEEEEECccccCccchHHHHHHHHHHhh
Confidence            666666554433222 22255799999999987655321    122345778999999999985433222111111111 


Q ss_pred             HHHhc---------CCCCeeEEEeecCccc-------H---HHHHHhcCCCCCeEEEe-------ccCCCceeEEEEe--
Q 037567          155 LRTFL---------LGVPFVALTATATEKV-------R---IDIINSLKLKNPYVTIA-------SFDRKNLFYGVKV--  206 (374)
Q Consensus       155 ~~~~~---------~~~~~i~~SaT~~~~~-------~---~~~~~~~~~~~~~~~~~-------~~~~~~~~~~~~~--  206 (374)
                      .....         +..++++|||||....       .   ..+...+..........       ....+........  
T Consensus       166 ~~~~~~~~~~~~~~~~~~il~lTATp~~~~~~~~~~~~~~i~~l~~~l~~~~i~~~~~~~~~l~~~~~~p~~~~~~~~~~  245 (699)
T 4gl2_A          166 LKNNRLKKENKPVIPLPQILGLTASPGVGGATKQAKAEEHILKLCANLDAFTIKTVKENLDQLKNQIQEPCKKFAIADAT  245 (699)
T ss_dssp             HHHHHHHC----CCCCCEEEEECSCCCCCSCCSHHHHHHHHHHHHHHHTCSCCCCCCTTHHHHHHHSCCCEEEEEEEC--
T ss_pred             hcccccccccccCCCCCEEEEecccccccccccHHHHHHHHHHHHhhcCCCEEEeecCchHHHhhhcCCCceEEEEcccc
Confidence            11111         4568999999999741       1   11222222200000000       0000000000000  


Q ss_pred             --------------------------------------------------------------------------------
Q 037567          207 --------------------------------------------------------------------------------  206 (374)
Q Consensus       207 --------------------------------------------------------------------------------  206 (374)
                                                                                                      
T Consensus       246 ~~~~~~~~l~~l~~~i~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~  325 (699)
T 4gl2_A          246 REDPFKEKLLEIMTRIQTYCQMSPMSDFGTQPYEQWAIQMEKKAAKEGNRKERVCAEHLRKYNEALQINDTIRMIDAYTH  325 (699)
T ss_dssp             ---CHHHHHHHHHHHHHHHHTCCCCSCSSSHHHHHHHHHHHHHHHHHTCTTTHHHHHHHHHHHHHHHHHHHSCHHHHHHH
T ss_pred             cCChHHHHHHHHHHHHHHHhccCcchhccchHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence                                                                                            


Q ss_pred             -----------------------------------------------------ecCCcchHHHHHHHHHHhhcCCCcEEE
Q 037567          207 -----------------------------------------------------INRGQSFVDELVQEILKSVAGAGSIIV  233 (374)
Q Consensus       207 -----------------------------------------------------~~~~~~~~~~~~~~~~~~~~~~~~~lV  233 (374)
                                                                           .......+.+++.........++++||
T Consensus       326 l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~~~~~~~~~~~k~~~L~~~L~~~~~~~~~~~~~IV  405 (699)
T 4gl2_A          326 LETFYNEEKDKKFAVIEDDLKKPLKLDETDRFLMTLFFENNKMLKRLAENPEYENEKLTKLRNTIMEQYTRTEESARGII  405 (699)
T ss_dssp             HHHHHHHHHHHHC------------CCHHHHHHHHHHHHHHHHHHHHHTCCC----CSSCSHHHHHHHHHHSSSCCCEEE
T ss_pred             HHHHHHHHHhhhccccccccccccccchhHHHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHHhcCCCCCcEEE
Confidence                                                                 000011111222222222112789999


Q ss_pred             EecchhHHHHHHHHHHHc------CCceeeeecC--------CChHHHHHHHHhhhcCCeeEEEEeccccccccccCccE
Q 037567          234 YCMTIKDVEEISKALKQL------GVKAGTYHGQ--------MGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRH  299 (374)
Q Consensus       234 f~~~~~~~~~l~~~l~~~------~~~~~~~~~~--------~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~  299 (374)
                      ||+++..++.+++.|++.      |+.+..+||+        ++..+|..+++.|++|+.+|||||+++++|+|+|++++
T Consensus       406 F~~s~~~~~~l~~~L~~~~~l~~~g~~~~~lhg~~~~~~~~~~~~~eR~~~~~~F~~g~~~VLVaT~~~~~GIDip~v~~  485 (699)
T 4gl2_A          406 FTKTRQSAYALSQWITENEKFAEVGVKAHHLIGAGHSSEFKPMTQNEQKEVISKFRTGKINLLIATTVAEEGLDIKECNI  485 (699)
T ss_dssp             ECSCHHHHHHHHHHHHSSCSCC-----CEECCCSCCCTTCCCCCHHHHHHHHHHHCC---CCSEEECSCCTTSCCCSCCC
T ss_pred             EECcHHHHHHHHHHHHhCccccccCcceEEEECCCCccCCCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCccccCCE
Confidence            999999999999999987      8999999999        99999999999999999999999999999999999999


Q ss_pred             EEEECCCCChhHHHHhhccCCCCCCceEEEEEeeccC
Q 037567          300 VIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSN  336 (374)
Q Consensus       300 vi~~~~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~  336 (374)
                      ||++++|+|+..|+||+||+||.|  +.+++++..++
T Consensus       486 VI~~d~p~s~~~~~Qr~GRArr~g--~~~~l~~~~~~  520 (699)
T 4gl2_A          486 VIRYGLVTNEIAMVQARGRARADE--STYVLVAHSGS  520 (699)
T ss_dssp             CEEESCCCCHHHHHHHHTTSCSSS--CEEEEEEESSS
T ss_pred             EEEeCCCCCHHHHHHHcCCCCCCC--ceEEEEEeCCc
Confidence            999999999999999999987654  44444444444

>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=100.00  E-value=2e-43  Score=329.68  Aligned_cols=315  Identities=20%  Similarity=0.220  Sum_probs=226.9

Q ss_pred             CCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc----cCCcEEEEcchHHHHHHHHHHHHHc-CC---ceEEcC
Q 037567           13 VFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV----TGKTALVVSPLISLMQDQVMSLKQR-GI---NAEFLG   84 (374)
Q Consensus        13 ~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~----~~~~~lil~P~~~l~~q~~~~~~~~-~~---~~~~~~   84 (374)
                      +|+|+|.++++.++++ ++++.+|||+|||+++++++..    ...++||++|+++|+.||.+++.++ +.   .+..+.
T Consensus         9 ~l~~~Q~~~i~~~~~~-~~ll~~~tG~GKT~~~~~~~~~~~~~~~~~~liv~P~~~L~~q~~~~~~~~~~~~~~~v~~~~   87 (494)
T 1wp9_A            9 QPRIYQEVIYAKCKET-NCLIVLPTGLGKTLIAMMIAEYRLTKYGGKVLMLAPTKPLVLQHAESFRRLFNLPPEKIVALT   87 (494)
T ss_dssp             CCCHHHHHHHHHGGGS-CEEEECCTTSCHHHHHHHHHHHHHHHSCSCEEEECSSHHHHHHHHHHHHHHBCSCGGGEEEEC
T ss_pred             CccHHHHHHHHHHhhC-CEEEEcCCCCCHHHHHHHHHHHHHhcCCCeEEEEECCHHHHHHHHHHHHHHhCcchhheEEee
Confidence            6999999999999999 9999999999999998877665    4889999999999999999999987 44   566666


Q ss_pred             CCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHHhcCCCCe
Q 037567           85 SAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPF  164 (374)
Q Consensus        85 ~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~~~~~~  164 (374)
                      +.........  ....++|+|+||+.+......  ......++++||+||||++.+.... .   .....+....+..++
T Consensus        88 g~~~~~~~~~--~~~~~~ivv~T~~~l~~~~~~--~~~~~~~~~~vIiDEaH~~~~~~~~-~---~~~~~~~~~~~~~~~  159 (494)
T 1wp9_A           88 GEKSPEERSK--AWARAKVIVATPQTIENDLLA--GRISLEDVSLIVFDEAHRAVGNYAY-V---FIAREYKRQAKNPLV  159 (494)
T ss_dssp             SCSCHHHHHH--HHHHCSEEEECHHHHHHHHHT--TSCCTTSCSEEEEETGGGCSTTCHH-H---HHHHHHHHHCSSCCE
T ss_pred             CCcchhhhhh--hccCCCEEEecHHHHHHHHhc--CCcchhhceEEEEECCcccCCCCcH-H---HHHHHHHhcCCCCeE
Confidence            5544332211  123469999999988654332  2234567899999999998753211 1   222333344557889


Q ss_pred             eEEEeecCcc--cHHHHHHhcCCCCCeEEEeccC-------CCceeEEEEeec---------------------------
Q 037567          165 VALTATATEK--VRIDIINSLKLKNPYVTIASFD-------RKNLFYGVKVIN---------------------------  208 (374)
Q Consensus       165 i~~SaT~~~~--~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~~~---------------------------  208 (374)
                      ++|||||...  ....+...++............       ............                           
T Consensus       160 l~lTaTp~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  239 (494)
T 1wp9_A          160 IGLTASPGSTPEKIMEVINNLGIEHIEYRSENSPDVRPYVKGIRFEWVRVDLPEIYKEVRKLLREMLRDALKPLAETGLL  239 (494)
T ss_dssp             EEEESCSCSSHHHHHHHHHHTTCCEEEECCTTSTTTGGGCCCCCEEEEEECCCHHHHHHHHHHHHHHHHHHHHHHHHTSS
T ss_pred             EEEecCCCCCcHHHHHHHHhcChheeeccCCCcHHHHHhcCCCceeEEecCCcHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence            9999999843  2223444443221111000000       000000000000                           


Q ss_pred             --------------------------------------------------------------------------------
Q 037567          209 --------------------------------------------------------------------------------  208 (374)
Q Consensus       209 --------------------------------------------------------------------------------  208 (374)
                                                                                                      
T Consensus       240 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~  319 (494)
T 1wp9_A          240 ESSSPDIPKKEVLRAGQIINEEMAKGNHDLRGLLLYHAMALKLHHAIELLETQGLSALRAYIKKLYEEAKAGSTKASKEI  319 (494)
T ss_dssp             SCCCTTSCHHHHHHHHHHHHHHHTTTCCSTTTHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHTTCCHHHHHH
T ss_pred             cccCCCcchhHHHHHHHHHHHHhhccccchhhHHHHHHHHHHHHHHHHHHHhhcHHHHHHHHHHHHHhhccccchhhhhh
Confidence                                                                                            


Q ss_pred             -------------------CCcchHHHHHHHHHHhh---cCCCcEEEEecchhHHHHHHHHHHHcCCceeeeec------
Q 037567          209 -------------------RGQSFVDELVQEILKSV---AGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHG------  260 (374)
Q Consensus       209 -------------------~~~~~~~~~~~~~~~~~---~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~------  260 (374)
                                         .........+.+++...   ..+.++||||+++..++.+++.|++.++.+..+||      
T Consensus       320 ~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~l~~~~~~~~~~k~lVF~~~~~~~~~l~~~L~~~~~~~~~~~g~~~~~~  399 (494)
T 1wp9_A          320 FSDKRMKKAISLLVQAKEIGLDHPKMDKLKEIIREQLQRKQNSKIIVFTNYRETAKKIVNELVKDGIKAKRFVGQASKEN  399 (494)
T ss_dssp             HTSHHHHHHHHHHHHHHHHTCSCHHHHHHHHHHHHHHHHCTTCCEEEECSCHHHHHHHHHHHHHTTCCEEEECCSSCC--
T ss_pred             hhhHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHhccCCCCeEEEEEccHHHHHHHHHHHHHcCCCcEEEeccccccc
Confidence                               00111112223333332   46889999999999999999999999999999999      


Q ss_pred             --CCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEEEEECCCCChhHHHHhhccCCCCCCceEEEEEeeccCC
Q 037567          261 --QMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNF  337 (374)
Q Consensus       261 --~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~~~~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~~  337 (374)
                        +++..+|+.+++.|++|+.+|||+|+++++|+|+|++++||++++|+|+..|.||+||+||.|+ |.++.++.+.+.
T Consensus       400 ~~~~~~~~r~~~~~~F~~~~~~vLv~T~~~~~Gldl~~~~~Vi~~d~~~~~~~~~Qr~GR~~R~g~-g~~~~l~~~~t~  477 (494)
T 1wp9_A          400 DRGLSQREQKLILDEFARGEFNVLVATSVGEEGLDVPEVDLVVFYEPVPSAIRSIQRRGRTGRHMP-GRVIILMAKGTR  477 (494)
T ss_dssp             -----CCHHHHHHHHHHHTSCSEEEECGGGGGGGGSTTCCEEEESSCCHHHHHHHHHHTTSCSCCC-SEEEEEEETTSH
T ss_pred             cccCCHHHHHHHHHHHhcCCceEEEECCccccCCCchhCCEEEEeCCCCCHHHHHHHHhhccCCCC-ceEEEEEecCCH
Confidence              9999999999999999999999999999999999999999999999999999999999999998 999999988654

>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=100.00  E-value=6.3e-44  Score=338.15  Aligned_cols=321  Identities=16%  Similarity=0.173  Sum_probs=178.7

Q ss_pred             CCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhcccccc--------CCcEEEEcchHHHHHHHHHHHHHc----C
Q 037567           10 GYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVT--------GKTALVVSPLISLMQDQVMSLKQR----G   77 (374)
Q Consensus        10 ~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~~--------~~~~lil~P~~~l~~q~~~~~~~~----~   77 (374)
                      +.-+|+|+|.++++.+++++++++.+|||+|||++|+++++..        +.++||++|+++|+.||.+.+.++    +
T Consensus         4 ~~~~~~~~Q~~~i~~~~~~~~~l~~~~tGsGKT~~~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~   83 (556)
T 4a2p_A            4 ETKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYEQQKNVFKHHFERQG   83 (556)
T ss_dssp             ----CCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHTCCSSCCCCEEEECSSHHHHHHHHHHHHHHHGGGT
T ss_pred             CCCCCCHHHHHHHHHHHcCCCEEEEcCCCChHHHHHHHHHHHHHHhCcccCCCeEEEEeCCHHHHHHHHHHHHHHhcccC
Confidence            3447999999999999999999999999999999998887652        788999999999999999999876    7


Q ss_pred             CceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHH-HhcCccEEEEeccchhhcccCcchHHH-HHHHHH
Q 037567           78 INAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKL-LKAGVCLFAVDEAHCISEWGHDFRLEY-KQLDKL  155 (374)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~-~~~~~~~vviDE~h~~~~~~~~~~~~~-~~~~~~  155 (374)
                      ..+..+.++........ .....++|+|+||+++...+..  ... .+.++++||+||||++.+++. ..... ..+...
T Consensus        84 ~~~~~~~g~~~~~~~~~-~~~~~~~i~v~T~~~l~~~~~~--~~~~~~~~~~~vViDEah~~~~~~~-~~~~~~~~~~~~  159 (556)
T 4a2p_A           84 YSVQGISGENFSNVSVE-KVIEDSDIIVVTPQILVNSFED--GTLTSLSIFTLMIFDECHNTTGNHP-YNVLMTRYLEQK  159 (556)
T ss_dssp             CCEEECCCC-----CHH-HHHHHCSEEEECHHHHHHHHHS--SSCCCSTTCSEEEEETGGGCSTTSH-HHHHHHHHHHHH
T ss_pred             ceEEEEeCCCCcchhHH-HhhCCCCEEEECHHHHHHHHHh--CcccccccCCEEEEECCcccCCcch-HHHHHHHHHHhh
Confidence            77777776654333222 2223479999999998654432  122 456789999999999987653 11111 111111


Q ss_pred             HH-hcCCCCeeEEEeecCcccHH----------HHHHhcCCCCCeEEEecc---------CCCceeEEEEe---------
Q 037567          156 RT-FLLGVPFVALTATATEKVRI----------DIINSLKLKNPYVTIASF---------DRKNLFYGVKV---------  206 (374)
Q Consensus       156 ~~-~~~~~~~i~~SaT~~~~~~~----------~~~~~~~~~~~~~~~~~~---------~~~~~~~~~~~---------  206 (374)
                      .. ..+..++++||||+......          .+...+...  .+.....         ..+........         
T Consensus       160 ~~~~~~~~~~l~lSAT~~~~~~~~~~~~~~~i~~l~~~l~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  237 (556)
T 4a2p_A          160 FNSASQLPQILGLTASVGVGNAKNIEETIEHICSLCSYLDIQ--AISTVRENIQELQRFMNKPEIDVRLVKRRIHNPFAA  237 (556)
T ss_dssp             HCC---CCEEEEEESCCCCTTCSSHHHHHHHHHHHHHHHTCS--EEECCCTTHHHHHHHTCCCCEEEEECCCCSCCHHHH
T ss_pred             hcccCCCCeEEEEeCCcccCchhhHHHHHHHHHHHHHhcCCe--EecchhcchHHHHhcCCCCceEEEEcCCCcCChHHH
Confidence            10 12457899999999653211          111222211  0000000         00000000000         


Q ss_pred             -----------------------------ec-------------------------------------------------
Q 037567          207 -----------------------------IN-------------------------------------------------  208 (374)
Q Consensus       207 -----------------------------~~-------------------------------------------------  208 (374)
                                                   ..                                                 
T Consensus       238 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  317 (556)
T 4a2p_A          238 IISNLMSETEALMRTIYSVDTLSQNSKKDFGTQNYEHWIVVTQRKCRLLQLEDKEEESRICRALFICTEHLRKYNDALII  317 (556)
T ss_dssp             HHHHHHHHHHHHHHHHCC---------CCCSSHHHHHHHHHHHHHHHHC---CHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhhhhhhhcccccccchhhHHHHHHHHHHHHHhhcccccchhHHHHHHHHHHHHHHHHHHHHHHH
Confidence                                         00                                                 


Q ss_pred             --------------------------------------------------CCcchHHHHHHHHHH-hh--cCCCcEEEEe
Q 037567          209 --------------------------------------------------RGQSFVDELVQEILK-SV--AGAGSIIVYC  235 (374)
Q Consensus       209 --------------------------------------------------~~~~~~~~~~~~~~~-~~--~~~~~~lVf~  235 (374)
                                                                        .........+.+++. ..  ..+.++||||
T Consensus       318 ~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~K~~~L~~~l~~~~~~~~~~k~lVF~  397 (556)
T 4a2p_A          318 SEDARIIDALSYLTEFFTNVKNGPYTELEQHLTAKFQEKEPELIALSKDETNENPKLEELVCILDDAYRYNPQTRTLLFA  397 (556)
T ss_dssp             HHHSCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHTTHHHHHHHHHCSSSCCHHHHHHHHHHHHHHHHCTTCCEEEEE
T ss_pred             hhhhhHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHhhHHHHhhhhccCCCCCChHHHHHHHHHHHHhcCCCCceEEEEE
Confidence                                                              000011111222222 21  4678999999


Q ss_pred             cchhHHHHHHHHHHHc------------CCceeeeecCCChHHHHHHHHhhhc-CCeeEEEEeccccccccccCccEEEE
Q 037567          236 MTIKDVEEISKALKQL------------GVKAGTYHGQMGSKAREEAHRLFIR-DEIRVMVATMAFGMGIDKPDVRHVIH  302 (374)
Q Consensus       236 ~~~~~~~~l~~~l~~~------------~~~~~~~~~~~~~~~r~~~~~~f~~-g~~~ilv~t~~~~~G~d~~~~~~vi~  302 (374)
                      +++..++.+++.|.+.            |.....+||+++..+|..+++.|++ |+.+|||||+++++|+|+|++++||+
T Consensus       398 ~~~~~~~~l~~~L~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~R~~~~~~F~~~g~~~vLvaT~~~~~GiDip~v~~VI~  477 (556)
T 4a2p_A          398 KTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTSKDNRLLIATSVADEGIDIVQCNLVVL  477 (556)
T ss_dssp             SSHHHHHHHHHHHTTCSGGGSCCEEC------------------------------CCEEEEEC-----------CEEEE
T ss_pred             ccHHHHHHHHHHHHhCCCcceeeeeEEEccCCcccccccCHHHHHHHHHHhcccCceEEEEEcCchhcCCCchhCCEEEE
Confidence            9999999999999875            4445566788999999999999999 99999999999999999999999999


Q ss_pred             ECCCCChhHHHHhhccCCCCCCceEEEEEeeccCCC
Q 037567          303 YGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFA  338 (374)
Q Consensus       303 ~~~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~~~  338 (374)
                      +++|+|+..|+||+|| ||. .+|.+++++.+.+..
T Consensus       478 ~d~p~s~~~~~Qr~GR-gR~-~~g~~~~l~~~~~~~  511 (556)
T 4a2p_A          478 YEYSGNVTKMIQVRGR-GRA-AGSKCILVTSKTEVV  511 (556)
T ss_dssp             ETCCSCHHHHHHC----------CCEEEEESCHHHH
T ss_pred             eCCCCCHHHHHHhcCC-CCC-CCceEEEEEeCcchH
Confidence            9999999999999999 998 789999998887653

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*

Probab=100.00  E-value=3.8e-44  Score=347.90  Aligned_cols=330  Identities=16%  Similarity=0.139  Sum_probs=196.0

Q ss_pred             hHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhcccccc--------CCcEEEEcchHHHHHHHHHHHH
Q 037567            3 STLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVT--------GKTALVVSPLISLMQDQVMSLK   74 (374)
Q Consensus         3 ~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~~--------~~~~lil~P~~~l~~q~~~~~~   74 (374)
                      +++.. +||.+|+|+|.++++.+++++++++.+|||+|||++|+++++..        ..+++|++|+++|+.||.+.++
T Consensus         4 ~~l~~-~g~~~lr~~Q~~~i~~~l~g~~~iv~~~TGsGKTl~~~~~i~~~l~~~~~~~~~~~lvl~Pt~~L~~Q~~~~~~   82 (696)
T 2ykg_A            4 SDTNL-YSPFKPRNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFPQGQKGKVVFFANQIPVYEQNKSVFS   82 (696)
T ss_dssp             ---CT-TC--CCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHHSCTTCCCCEEEECSSHHHHHHHHHHHH
T ss_pred             Ccccc-cCCCCccHHHHHHHHHHHcCCCEEEEcCCCchHHHHHHHHHHHHHHhCccCCCCeEEEEECCHHHHHHHHHHHH
Confidence            44555 89999999999999999999999999999999999998887641        2789999999999999999998


Q ss_pred             Hc----CCceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHH-HhcCccEEEEeccchhhcccCcchHHH
Q 037567           75 QR----GINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKL-LKAGVCLFAVDEAHCISEWGHDFRLEY  149 (374)
Q Consensus        75 ~~----~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~-~~~~~~~vviDE~h~~~~~~~~~~~~~  149 (374)
                      ++    ++.+..+.++.......... ...++|+|+||++|...+..  ... .+.++++||+||||++.+... +....
T Consensus        83 ~~~~~~~~~v~~~~g~~~~~~~~~~~-~~~~~Iiv~Tp~~L~~~l~~--~~~~~l~~~~~vViDEaH~~~~~~~-~~~i~  158 (696)
T 2ykg_A           83 KYFERHGYRVTGISGATAENVPVEQI-VENNDIIILTPQILVNNLKK--GTIPSLSIFTLMIFDECHNTSKQHP-YNMIM  158 (696)
T ss_dssp             HHTTTTTCCEEEECSSSCSSSCHHHH-HHTCSEEEECHHHHHHHHHT--TSSCCGGGCSEEEEETGGGCSTTCH-HHHHH
T ss_pred             HHhccCCceEEEEeCCccccccHHHh-ccCCCEEEECHHHHHHHHhc--CcccccccccEEEEeCCCcccCccc-HHHHH
Confidence            87    66776666655433322222 23479999999998665433  112 356789999999999875432 11111


Q ss_pred             H-HHHHHHH--hcCCCCeeEEEeecCc-------ccHHHHHHhcCCC--------------------CCeEEEec-cCCC
Q 037567          150 K-QLDKLRT--FLLGVPFVALTATATE-------KVRIDIINSLKLK--------------------NPYVTIAS-FDRK  198 (374)
Q Consensus       150 ~-~~~~~~~--~~~~~~~i~~SaT~~~-------~~~~~~~~~~~~~--------------------~~~~~~~~-~~~~  198 (374)
                      . .+.....  ..+..++++||||+..       .....+.......                    .+...... ....
T Consensus       159 ~~~l~~~~~~~~~~~~~il~LTATp~~~~~~~~~~~~~~i~~~~~~l~~~~~~~~~~~~~~l~~~~~~p~~~~~~~~~~~  238 (696)
T 2ykg_A          159 FNYLDQKLGGSSGPLPQVIGLTASVGVGDAKTTDEALDYICKLCASLDASVIATVKHNLEELEQVVYKPQKFFRKVESRI  238 (696)
T ss_dssp             HHHHHHHHTTCCSCCCEEEEEESCCCCSSCCSHHHHHHHHHHHHHHTTCCEEECCCTTHHHHHHHSCCCEEEEEECCCCS
T ss_pred             HHHHHHhhcccCCCCCeEEEEeCccccCccccHHHHHHHHHHHHHhcCCceEeecccchHHHHhhcCCCceeEEecCccc
Confidence            1 1111111  0145789999999972       1122222211100                    01000000 0000


Q ss_pred             ceeEE----------------------------------------------------EE---------------------
Q 037567          199 NLFYG----------------------------------------------------VK---------------------  205 (374)
Q Consensus       199 ~~~~~----------------------------------------------------~~---------------------  205 (374)
                      .....                                                    ..                     
T Consensus       239 ~~~fs~~~~~l~~~i~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~  318 (696)
T 2ykg_A          239 SDKFKYIIAQLMRDTESLAKRICKDLENLSQIQNREFGTQKYEQWIVTVQKACMVFQMPDKDEESRICKALFLYTSHLRK  318 (696)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHHSTTGGGSSSCCSCCSSSHHHHHHHHHHHHTSCC------CCHHHHHHHHHHHHHHHHH
T ss_pred             CChHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccccchhHHHHHHHHHHHHHHhhcccchhhhHHHHHHHHHHHHHHH
Confidence            00000                                                    00                     


Q ss_pred             --------------------------------------ee----------------cCCcchHHHHHHHHHHhh---cCC
Q 037567          206 --------------------------------------VI----------------NRGQSFVDELVQEILKSV---AGA  228 (374)
Q Consensus       206 --------------------------------------~~----------------~~~~~~~~~~~~~~~~~~---~~~  228 (374)
                                                            ..                ..........+.+++...   .++
T Consensus       319 ~~~~~~i~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~k~~~L~~ll~~~~~~~~~  398 (696)
T 2ykg_A          319 YNDALIISEHARMKDALDYLKDFFSNVRAAGFDEIEQDLTQRFEEKLQELESVSRDPSNENPKLEDLCFILQEEYHLNPE  398 (696)
T ss_dssp             HHHHHHHHHHSCHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHTTHHHHHHHHHCGGGCCHHHHHHHHHHHHHHTTCTT
T ss_pred             HhHHHhccchhhHHHHHHHHHHHHHHHhhcccchHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhccCCC
Confidence                                                  00                000111223333344332   256


Q ss_pred             CcEEEEecchhHHHHHHHHHHHcC----Cceeee--------ecCCChHHHHHHHHhhhc-CCeeEEEEecccccccccc
Q 037567          229 GSIIVYCMTIKDVEEISKALKQLG----VKAGTY--------HGQMGSKAREEAHRLFIR-DEIRVMVATMAFGMGIDKP  295 (374)
Q Consensus       229 ~~~lVf~~~~~~~~~l~~~l~~~~----~~~~~~--------~~~~~~~~r~~~~~~f~~-g~~~ilv~t~~~~~G~d~~  295 (374)
                      +++||||+++..++.+++.|++.+    +.+..+        ||+++.++|.++++.|++ |+.+|||||+++++|+|+|
T Consensus       399 ~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~~~~l~G~~~~~~h~~~~~~eR~~v~~~F~~~g~~~vLVaT~v~~~GiDip  478 (696)
T 2ykg_A          399 TITILFVKTRALVDALKNWIEGNPKLSFLKPGILTGRGKTNQNTGMTLPAQKCILDAFKASGDHNILIATSVADEGIDIA  478 (696)
T ss_dssp             CCEEEECSCHHHHHHHHHHHHHCTTCCSCCEEC-----------------------------CCSCSEEEESSCCC---C
T ss_pred             CcEEEEeCcHHHHHHHHHHHHhCCCccccceeEEEccCCCccccCCCHHHHHHHHHHHHhcCCccEEEEechhhcCCcCc
Confidence            899999999999999999999987    788888        559999999999999998 9999999999999999999


Q ss_pred             CccEEEEECCCCChhHHHHhhccCCCCCCceEEEEEeeccCCCc
Q 037567          296 DVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAK  339 (374)
Q Consensus       296 ~~~~vi~~~~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~~~~  339 (374)
                      ++++||++++|+|+..|+||+|| ||. ++|.++.+++..+...
T Consensus       479 ~v~~VI~~d~p~s~~~~~Qr~GR-GR~-~~g~~~~l~~~~~~~~  520 (696)
T 2ykg_A          479 QCNLVILYEYVGNVIKMIQTRGR-GRA-RGSKCFLLTSNAGVIE  520 (696)
T ss_dssp             CCSEEEEESCC--CCCC-----------CCCEEEEEESCHHHHH
T ss_pred             cCCEEEEeCCCCCHHHHHHhhcc-CcC-CCceEEEEecCCCHHH
Confidence            99999999999999999999999 997 7889999998876643

>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=100.00  E-value=3.5e-43  Score=340.89  Aligned_cols=315  Identities=21%  Similarity=0.293  Sum_probs=233.5

Q ss_pred             hHHHhHcCCCCCchhHHHHHHH-HHcCCCEEEEccCCCCchhhhhccccc----cCCcEEEEcchHHHHHHHHHHHHH--
Q 037567            3 STLKKYFGYSVFRPYQKDVIQR-IIEKRDCLVVMATGSGKSLCYQLPPLV----TGKTALVVSPLISLMQDQVMSLKQ--   75 (374)
Q Consensus         3 ~~l~~~~~~~~~~~~Q~~~~~~-~~~~~~~l~~a~tGsGKT~~~~l~~~~----~~~~~lil~P~~~l~~q~~~~~~~--   75 (374)
                      +.+++ +||.+|+|+|.++++. +.+++++++++|||||||+++.++++.    .+.+++|++|+++|+.|+.+.++.  
T Consensus        14 ~~l~~-~g~~~l~~~Q~~~i~~~~~~~~~~lv~apTGsGKT~~~~l~il~~~~~~~~~~l~i~P~raLa~q~~~~~~~l~   92 (720)
T 2zj8_A           14 STLKE-RGIESFYPPQAEALKSGILEGKNALISIPTASGKTLIAEIAMVHRILTQGGKAVYIVPLKALAEEKFQEFQDWE   92 (720)
T ss_dssp             HHHHH-TTCCBCCHHHHHHHTTTGGGTCEEEEECCGGGCHHHHHHHHHHHHHHHHCSEEEEECSSGGGHHHHHHHTGGGG
T ss_pred             HHHHH-CCCCCCCHHHHHHHHHHhcCCCcEEEEcCCccHHHHHHHHHHHHHHHhCCCEEEEEcCcHHHHHHHHHHHHHHH
Confidence            45555 7999999999999998 788999999999999999998777763    478999999999999999999864  


Q ss_pred             -cCCceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHH
Q 037567           76 -RGINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDK  154 (374)
Q Consensus        76 -~~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~  154 (374)
                       +|..+...+++......    ..+.++|+|+||+++..+...  ....+.++++||+||+|.+.+++..     ..+..
T Consensus        93 ~~g~~v~~~~G~~~~~~~----~~~~~~Iiv~Tpe~l~~~~~~--~~~~l~~~~~vIiDE~H~l~~~~r~-----~~~~~  161 (720)
T 2zj8_A           93 KIGLRVAMATGDYDSKDE----WLGKYDIIIATAEKFDSLLRH--GSSWIKDVKILVADEIHLIGSRDRG-----ATLEV  161 (720)
T ss_dssp             GGTCCEEEECSCSSCCCG----GGGGCSEEEECHHHHHHHHHH--TCTTGGGEEEEEEETGGGGGCTTTH-----HHHHH
T ss_pred             hcCCEEEEecCCCCcccc----ccCCCCEEEECHHHHHHHHHc--ChhhhhcCCEEEEECCcccCCCccc-----HHHHH
Confidence             46777777765443322    123579999999998765443  2233578899999999998764432     22222


Q ss_pred             HHHhcC-CCCeeEEEeecCcccHHHHHHhcCCCCCeEEEeccCCCceeEEE------EeecCC---cchHHHHHHHHHHh
Q 037567          155 LRTFLL-GVPFVALTATATEKVRIDIINSLKLKNPYVTIASFDRKNLFYGV------KVINRG---QSFVDELVQEILKS  224 (374)
Q Consensus       155 ~~~~~~-~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~---~~~~~~~~~~~~~~  224 (374)
                      +...++ +.++++||||+++.  ..+..+++..   ..........+....      ......   .......+.+.   
T Consensus       162 ll~~l~~~~~ii~lSATl~n~--~~~~~~l~~~---~~~~~~rp~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---  233 (720)
T 2zj8_A          162 ILAHMLGKAQIIGLSATIGNP--EELAEWLNAE---LIVSDWRPVKLRRGVFYQGFVTWEDGSIDRFSSWEELVYDA---  233 (720)
T ss_dssp             HHHHHBTTBEEEEEECCCSCH--HHHHHHTTEE---EEECCCCSSEEEEEEEETTEEEETTSCEEECSSTTHHHHHH---
T ss_pred             HHHHhhcCCeEEEEcCCcCCH--HHHHHHhCCc---ccCCCCCCCcceEEEEeCCeeeccccchhhhhHHHHHHHHH---
Confidence            333222 68899999999864  3566766532   111111111111000      010100   11222333333   


Q ss_pred             hcCCCcEEEEecchhHHHHHHHHHHHcC---------------------------------CceeeeecCCChHHHHHHH
Q 037567          225 VAGAGSIIVYCMTIKDVEEISKALKQLG---------------------------------VKAGTYHGQMGSKAREEAH  271 (374)
Q Consensus       225 ~~~~~~~lVf~~~~~~~~~l~~~l~~~~---------------------------------~~~~~~~~~~~~~~r~~~~  271 (374)
                      ..+++++||||++++.++.+++.|.+..                                 ..+..+||+++.++|..++
T Consensus       234 ~~~~~~~LVF~~sr~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~l~~~~~~~v~~~h~~l~~~~R~~v~  313 (720)
T 2zj8_A          234 IRKKKGALIFVNMRRKAERVALELSKKVKSLLTKPEIRALNELADSLEENPTNEKLAKAIRGGVAFHHAGLGRDERVLVE  313 (720)
T ss_dssp             HHTTCCEEEECSCHHHHHHHHHHHHHHHGGGSCHHHHHHHHHHHHTSCSCHHHHHHHHHHTTTEEEECTTSCHHHHHHHH
T ss_pred             HhCCCCEEEEecCHHHHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHhcccchHHHHHHHhcCeeeecCCCCHHHHHHHH
Confidence            3467999999999999999999987531                                 2488999999999999999


Q ss_pred             HhhhcCCeeEEEEeccccccccccCccEEEE----EC----CCCChhHHHHhhccCCCCC--CceEEEEEeeccCC
Q 037567          272 RLFIRDEIRVMVATMAFGMGIDKPDVRHVIH----YG----CPKTLESYYQESGRCGRDG--IASVCWLYYARSNF  337 (374)
Q Consensus       272 ~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~----~~----~p~s~~~~~Q~~GR~~R~~--~~g~~~~~~~~~~~  337 (374)
                      +.|.+|.++|||||+++++|+|+|++++||+    |+    .|.|..+|.||+|||||.|  ..|.|+++++..+.
T Consensus       314 ~~f~~g~~~vlvaT~~l~~Gvdip~~~~VI~~~~~yd~~g~~~~s~~~~~Qr~GRaGR~g~~~~G~~~~l~~~~~~  389 (720)
T 2zj8_A          314 ENFRKGIIKAVVATPTLSAGINTPAFRVIIRDIWRYSDFGMERIPIIEVHQMLGRAGRPKYDEVGEGIIVSTSDDP  389 (720)
T ss_dssp             HHHHTTSSCEEEECSTTGGGCCCCBSEEEECCSEECCSSSCEECCHHHHHHHHTTBCCTTTCSEEEEEEECSSSCH
T ss_pred             HHHHCCCCeEEEECcHhhccCCCCceEEEEcCCeeecCCCCccCCHHHHHHHHhhcCCCCCCCCceEEEEecCccH
Confidence            9999999999999999999999999999998    54    5889999999999999988  47899999988763

>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=100.00  E-value=3.9e-43  Score=349.56  Aligned_cols=310  Identities=19%  Similarity=0.227  Sum_probs=224.1

Q ss_pred             HhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc---cCCcEEEEcchHHHHHHHHHHHHHcCCceEE
Q 037567            6 KKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV---TGKTALVVSPLISLMQDQVMSLKQRGINAEF   82 (374)
Q Consensus         6 ~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~---~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~   82 (374)
                      ...++| +|+|+|.++++.+.++++++++||||||||++|.++++.   .+.+++|++|+++|+.|+++.+......+.+
T Consensus       178 ~~~~~f-~ltp~Q~~AI~~i~~g~dvLV~ApTGSGKTlva~l~i~~~l~~g~rvlvl~PtraLa~Q~~~~l~~~~~~Vgl  256 (1108)
T 3l9o_A          178 ARTYPF-TLDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLKNKQRVIYTSPIKALSNQKYRELLAEFGDVGL  256 (1108)
T ss_dssp             SSCCSS-CCCHHHHHHHHHHTTTCCEEEECCSSSHHHHHHHHHHHHHHHTTCEEEEEESSHHHHHHHHHHHHHHTSSEEE
T ss_pred             HHhCCC-CCCHHHHHHHHHHHcCCCEEEECCCCCChHHHHHHHHHHHHhcCCeEEEEcCcHHHHHHHHHHHHHHhCCccE
Confidence            344455 599999999999999999999999999999999888765   4889999999999999999999987667777


Q ss_pred             cCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHHhc-CC
Q 037567           83 LGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFL-LG  161 (374)
Q Consensus        83 ~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~-~~  161 (374)
                      ..++...        ...++|+|+||+.|..++..  ....+.++++|||||+|++.++++.     ..+..+...+ ++
T Consensus       257 ltGd~~~--------~~~~~IlV~Tpe~L~~~L~~--~~~~l~~l~lVVIDEaH~l~d~~rg-----~~~e~ii~~l~~~  321 (1108)
T 3l9o_A          257 MTGDITI--------NPDAGCLVMTTEILRSMLYR--GSEVMREVAWVIFDEVHYMRDKERG-----VVWEETIILLPDK  321 (1108)
T ss_dssp             ECSSCBC--------CCSCSEEEEEHHHHHHHHHH--CSSHHHHEEEEEEETGGGTTSHHHH-----HHHHHHHHHSCTT
T ss_pred             EeCcccc--------CCCCCEEEeChHHHHHHHHc--CccccccCCEEEEhhhhhccccchH-----HHHHHHHHhcCCC
Confidence            6665432        23479999999988776544  2334567899999999999875533     2233333333 46


Q ss_pred             CCeeEEEeecCcccHHHHHHhcC---CCCCeEEEeccCCCceeEEEEe---------ecCC-------------------
Q 037567          162 VPFVALTATATEKVRIDIINSLK---LKNPYVTIASFDRKNLFYGVKV---------INRG-------------------  210 (374)
Q Consensus       162 ~~~i~~SaT~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~---------~~~~-------------------  210 (374)
                      .++++||||+++...  +..+++   ..+..+.........+...+..         ....                   
T Consensus       322 ~qvl~lSATipn~~e--~a~~l~~~~~~~~~vi~~~~rp~pl~~~~~~~~~~~~~~~vd~~~~~~~~~~~~~~~~l~~~~  399 (1108)
T 3l9o_A          322 VRYVFLSATIPNAME--FAEWICKIHSQPCHIVYTNFRPTPLQHYLFPAHGDGIYLVVDEKSTFREENFQKAMASISNQI  399 (1108)
T ss_dssp             SEEEEEECSCSSCHH--HHHHHHHHTCSCEEEEEECCCSSCEEEEEEETTSSCCEEEEETTTEECHHHHHHHHTTC----
T ss_pred             ceEEEEcCCCCCHHH--HHHHHHhhcCCCeEEEecCCCcccceEEEeecCCcceeeeeccccchhhhhHHHHHHHHHhhh
Confidence            889999999877532  233322   2222222222221111111100         0000                   


Q ss_pred             --------------------------cchHHHHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHHcCCc----------
Q 037567          211 --------------------------QSFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVK----------  254 (374)
Q Consensus       211 --------------------------~~~~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~----------  254 (374)
                                                ......++..+..  ...+++||||+++..++.++..|...++.          
T Consensus       400 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~li~~l~~--~~~~~vIVF~~sr~~~e~la~~L~~~~~~~~~e~~~i~~  477 (1108)
T 3l9o_A          400 GDDPNSTDSRGKKGQTYKGGSAKGDAKGDIYKIVKMIWK--KKYNPVIVFSFSKRDCEELALKMSKLDFNSDDEKEALTK  477 (1108)
T ss_dssp             -------------------------CHHHHHHHHHHHHH--TTCCCEEEEESCHHHHHHHHHHTCSHHHHCC----CHHH
T ss_pred             cccccccccccccccccccccccccchhHHHHHHHHHHh--cCCCCEEEEeCcHHHHHHHHHHHHhccCCCHHHHHHHHH
Confidence                                      1111222222222  24679999999999999999887643222          


Q ss_pred             -----------------------------eeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEEEEECC
Q 037567          255 -----------------------------AGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGC  305 (374)
Q Consensus       255 -----------------------------~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~~~~  305 (374)
                                                   +..+||++++.+|..+++.|.+|.++|||||+++++|+|+|++++||+++.
T Consensus       478 ~~~~~~~~l~~~d~~l~~~~~l~~~l~~gV~~~Hg~l~~~~R~~v~~~F~~G~ikVLVAT~vla~GIDiP~v~~VI~~~~  557 (1108)
T 3l9o_A          478 IFNNAIALLPETDRELPQIKHILPLLRRGIGIHHSGLLPILKEVIEILFQEGFLKVLFATETFSIGLNMPAKTVVFTSVR  557 (1108)
T ss_dssp             HGGGSCTHHHHHTTCCHHHHHHTHHHHHTEEEECSCSCHHHHHHHHHHHHHTCCCEEEEESCCCSCCCC--CEEEESCSE
T ss_pred             HHHHHHhhcchhhhhhhhHHHHHHhhhcCeeeecCCCCHHHHHHHHHHHhCCCCeEEEECcHHhcCCCCCCceEEEecCc
Confidence                                         688999999999999999999999999999999999999999999996554


Q ss_pred             --------CCChhHHHHhhccCCCCC--CceEEEEEeecc
Q 037567          306 --------PKTLESYYQESGRCGRDG--IASVCWLYYARS  335 (374)
Q Consensus       306 --------p~s~~~~~Q~~GR~~R~~--~~g~~~~~~~~~  335 (374)
                              |.|+.+|+||+||+||.|  ..|.|++++.+.
T Consensus       558 ~~d~~~~r~iS~~eyiQr~GRAGR~G~d~~G~~ill~~~~  597 (1108)
T 3l9o_A          558 KWDGQQFRWVSGGEYIQMSGRAGRRGLDDRGIVIMMIDEK  597 (1108)
T ss_dssp             EESSSCEEECCHHHHHHHHHHSCCSSSCSSEEEEEEECCC
T ss_pred             ccCccccccCCHHHHHHhhcccCCCCCCCceEEEEEecCC
Confidence                    337788999999999999  689999988775

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus}

Probab=100.00  E-value=2.9e-43  Score=333.58  Aligned_cols=317  Identities=16%  Similarity=0.140  Sum_probs=203.2

Q ss_pred             CCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhcccccc--------CCcEEEEcchHHHHHHHHHHHHHc----CCce
Q 037567           13 VFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVT--------GKTALVVSPLISLMQDQVMSLKQR----GINA   80 (374)
Q Consensus        13 ~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~~--------~~~~lil~P~~~l~~q~~~~~~~~----~~~~   80 (374)
                      +|+|+|.++++.+++++++++.+|||+|||++|+++++..        +.++||++|+++|+.||.+.+.++    +..+
T Consensus         4 ~~~~~Q~~~i~~~~~~~~~l~~~~tGsGKT~~~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~   83 (555)
T 3tbk_A            4 KPRNYQLELALPAKKGKNTIICAPTGCGKTFVSLLICEHHLKKFPCGQKGKVVFFANQIPVYEQQATVFSRYFERLGYNI   83 (555)
T ss_dssp             CCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHTCCSSCCCCEEEECSSHHHHHHHHHHHHHHHHTTTCCE
T ss_pred             CCcHHHHHHHHHHhCCCCEEEEeCCCChHHHHHHHHHHHHHHhcccCCCCEEEEEeCCHHHHHHHHHHHHHHhccCCcEE
Confidence            5999999999999999999999999999999998887652        788999999999999999999876    7777


Q ss_pred             EEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHH-HhcCccEEEEeccchhhcccCcchHHHHHHHHHHHhc
Q 037567           81 EFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKL-LKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFL  159 (374)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~-~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~  159 (374)
                      ..+.++........ .....++|+|+||+++...+..  ... .+.++++||+||||++.+.+. +.   ..+.......
T Consensus        84 ~~~~g~~~~~~~~~-~~~~~~~i~v~T~~~l~~~~~~--~~~~~~~~~~~vViDEah~~~~~~~-~~---~~~~~~~~~~  156 (555)
T 3tbk_A           84 ASISGATSDSVSVQ-HIIEDNDIIILTPQILVNNLNN--GAIPSLSVFTLMIFDECHNTSKNHP-YN---QIMFRYLDHK  156 (555)
T ss_dssp             EEECTTTGGGSCHH-HHHHHCSEEEECHHHHHHHHHT--SSSCCGGGCSEEEETTGGGCSTTCH-HH---HHHHHHHHHH
T ss_pred             EEEcCCCcchhhHH-HHhcCCCEEEECHHHHHHHHhc--CcccccccCCEEEEECccccCCcch-HH---HHHHHHHHhh
Confidence            77776654433222 2223479999999998665433  112 456789999999999976542 11   1112222221


Q ss_pred             ------CCCCeeEEEeecCcccH-------H---HHHHhcCCCCCeEEEecc---------CCCceeEEEEee-c-----
Q 037567          160 ------LGVPFVALTATATEKVR-------I---DIINSLKLKNPYVTIASF---------DRKNLFYGVKVI-N-----  208 (374)
Q Consensus       160 ------~~~~~i~~SaT~~~~~~-------~---~~~~~~~~~~~~~~~~~~---------~~~~~~~~~~~~-~-----  208 (374)
                            +..++++||||+.....       .   .+...+..  ..+.....         ..+......... .     
T Consensus       157 ~~~~~~~~~~~l~lSAT~~~~~~~~~~~~~~~~~~l~~~l~~--~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~  234 (555)
T 3tbk_A          157 LGESRDPLPQVVGLTASVGVGDAKTAEEAMQHICKLCAALDA--SVIATVRDNVAELEQVVYKPQKISRKVASRTSNTFK  234 (555)
T ss_dssp             TSSCCSCCCEEEEEESCCCCTTCCSHHHHHHHHHHHHHHTTC--SEEECCCSCHHHHHTTCCCCCEEEEECCCCSCCHHH
T ss_pred             hccccCCCCeEEEEecCcccCccccHHHHHHHHHHHHHhcCC--eeeeccccCHHHHHhhcCCCceEEEEecCcccChHH
Confidence                  34679999999976421       1   11222221  11111000         000000000000 0     


Q ss_pred             --------------------------------------------------------------------------------
Q 037567          209 --------------------------------------------------------------------------------  208 (374)
Q Consensus       209 --------------------------------------------------------------------------------  208 (374)
                                                                                                      
T Consensus       235 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  314 (555)
T 3tbk_A          235 CIISQLMKETEKLAKDVSEELGKLFQIQNREFGTQKYEQWIVGVHKACSVFQMADKEEESRVCKALFLYTSHLRKYNDAL  314 (555)
T ss_dssp             HHHHHHHHHHHHHHHTSCHHHHGGGGCCSCCSSSHHHHHHHHHHHHHHHTCCCSSHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHhhhhhhhcccccccchhhhHHHHHHHHHhhhhhccchhhHHHHHHHHHHHHHHHHHHHHHH
Confidence                                                                                            


Q ss_pred             ----------------------------------------------------CCcchHHHHHHHHHHhh---cCCCcEEE
Q 037567          209 ----------------------------------------------------RGQSFVDELVQEILKSV---AGAGSIIV  233 (374)
Q Consensus       209 ----------------------------------------------------~~~~~~~~~~~~~~~~~---~~~~~~lV  233 (374)
                                                                          .........+.+++...   ..+.++||
T Consensus       315 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~l~~~~~~~~~~k~lV  394 (555)
T 3tbk_A          315 IISEDAQMTDALNYLKAFFHDVREAAFDETERELTRRFEEKLEELEKVSRDPSNENPKLRDLYLVLQEEYHLKPETKTIL  394 (555)
T ss_dssp             HHHHHSCHHHHHHHHHHHHHHHCC-----HHHHHHHHHHTTHHHHHHHHHCGGGCCHHHHHHHHHHHHHHHHCTTCCEEE
T ss_pred             hhhhhhhHHHHHHHHHHHHHHHhhcccchHHHHHHHHHhhhhhhhhhhccCCCcCCHHHHHHHHHHHHHhccCCCceEEE
Confidence                                                                00011111222222221   35689999


Q ss_pred             EecchhHHHHHHHHHHHcC------------CceeeeecCCChHHHHHHHHhhhc-CCeeEEEEeccccccccccCccEE
Q 037567          234 YCMTIKDVEEISKALKQLG------------VKAGTYHGQMGSKAREEAHRLFIR-DEIRVMVATMAFGMGIDKPDVRHV  300 (374)
Q Consensus       234 f~~~~~~~~~l~~~l~~~~------------~~~~~~~~~~~~~~r~~~~~~f~~-g~~~ilv~t~~~~~G~d~~~~~~v  300 (374)
                      ||+++..++.+++.|.+.+            .....+||+++.++|..+++.|++ |+.+|||||+++++|+|+|++++|
T Consensus       395 F~~~~~~~~~l~~~L~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~R~~~~~~F~~~g~~~vLvaT~~~~~GlDlp~v~~V  474 (555)
T 3tbk_A          395 FVKTRALVDALKKWIEENPALSFLKPGILTGRGRTNRATGMTLPAQKCVLEAFRASGDNNILIATSVADEGIDIAECNLV  474 (555)
T ss_dssp             ECSSHHHHHHHHHHHHHCGGGTTCCEEECCC--------------------------CCSEEEECCCTTCCEETTSCSEE
T ss_pred             EeCcHHHHHHHHHHHhhCcCcCceeeeEEEecCCcccccccCHHHHHHHHHHHhcCCCeeEEEEcchhhcCCccccCCEE
Confidence            9999999999999999864            234455679999999999999999 999999999999999999999999


Q ss_pred             EEECCCCChhHHHHhhccCCCCCCceEEEEEeeccCCCcc
Q 037567          301 IHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKG  340 (374)
Q Consensus       301 i~~~~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~~~~~  340 (374)
                      |++++|+|+..|+||+|| ||. .+|.+++++.+.+....
T Consensus       475 I~~d~p~s~~~~~Qr~GR-gR~-~~g~~~~l~~~~~~~~~  512 (555)
T 3tbk_A          475 ILYEYVGNVIKMIQTRGR-GRA-RDSKCFLLTSSADVIEK  512 (555)
T ss_dssp             EEESCCSSCCCEECSSCC-CTT-TSCEEEEEESCHHHHHH
T ss_pred             EEeCCCCCHHHHHHhcCc-CcC-CCceEEEEEcCCCHHHH
Confidence            999999999999999999 998 88999999988765433

>2xgj_A ATP-dependent RNA helicase DOB1; hydrolase-RNA complex, hydrolase, tramp, exosome, DEAD, nucleotide-binding; HET: ADP; 2.90A {Saccharomyces cerevisiae}

Probab=100.00  E-value=1.5e-42  Score=342.43  Aligned_cols=310  Identities=19%  Similarity=0.249  Sum_probs=228.0

Q ss_pred             HhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc---cCCcEEEEcchHHHHHHHHHHHHHcCCceEE
Q 037567            6 KKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV---TGKTALVVSPLISLMQDQVMSLKQRGINAEF   82 (374)
Q Consensus         6 ~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~---~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~   82 (374)
                      ...++|. |+|+|.++++.+.+++++++.+|||||||++|.++++.   .+.+++|++|+++|++|+++++......+..
T Consensus        80 ~~~~~f~-L~~~Q~eai~~l~~g~~vLV~apTGSGKTlva~lai~~~l~~g~rvL~l~PtkaLa~Q~~~~l~~~~~~vgl  158 (1010)
T 2xgj_A           80 ARTYPFT-LDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLKNKQRVIYTSPIKALSNQKYRELLAEFGDVGL  158 (1010)
T ss_dssp             SCCCSSC-CCHHHHHHHHHHHHTCEEEEECCTTSCHHHHHHHHHHHHHHTTCEEEEEESSHHHHHHHHHHHHHHHSCEEE
T ss_pred             HHhCCCC-CCHHHHHHHHHHHcCCCEEEECCCCCChHHHHHHHHHHHhccCCeEEEECChHHHHHHHHHHHHHHhCCEEE
Confidence            3457886 99999999999999999999999999999998776654   5789999999999999999999876556666


Q ss_pred             cCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHHhc-CC
Q 037567           83 LGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFL-LG  161 (374)
Q Consensus        83 ~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~-~~  161 (374)
                      ++++....        ...+|+|+||+.+..++..  ....+.++++||+||+|.+.+++..     ..+..+...+ ++
T Consensus       159 ltGd~~~~--------~~~~IvV~Tpe~L~~~L~~--~~~~l~~l~lVViDEaH~l~d~~rg-----~~~e~il~~l~~~  223 (1010)
T 2xgj_A          159 MTGDITIN--------PDAGCLVMTTEILRSMLYR--GSEVMREVAWVIFDEVHYMRDKERG-----VVWEETIILLPDK  223 (1010)
T ss_dssp             ECSSCEEC--------TTCSEEEEEHHHHHHHHHH--TCTTGGGEEEEEEETGGGGGCTTTH-----HHHHHHHHHSCTT
T ss_pred             EeCCCccC--------CCCCEEEEcHHHHHHHHHc--CcchhhcCCEEEEechhhhcccchh-----HHHHHHHHhcCCC
Confidence            66544322        2468999999988655433  2345678899999999999876543     2233333333 46


Q ss_pred             CCeeEEEeecCcccHHHHHHhcC---CCCCeEEEeccCCCceeEEEEe---------ecCC-------------------
Q 037567          162 VPFVALTATATEKVRIDIINSLK---LKNPYVTIASFDRKNLFYGVKV---------INRG-------------------  210 (374)
Q Consensus       162 ~~~i~~SaT~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~---------~~~~-------------------  210 (374)
                      .++++||||+++..  .+..+++   ..+..+.........+...+..         ....                   
T Consensus       224 ~~il~LSATi~n~~--e~a~~l~~~~~~~~~vi~~~~rp~pl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~  301 (1010)
T 2xgj_A          224 VRYVFLSATIPNAM--EFAEWICKIHSQPCHIVYTNFRPTPLQHYLFPAHGDGIYLVVDEKSTFREENFQKAMASISNQI  301 (1010)
T ss_dssp             CEEEEEECCCTTHH--HHHHHHHHHHTSCEEEEEECCCSSCEEEEEEETTSSCCEEEECTTCCBCHHHHHHHHHTCC---
T ss_pred             CeEEEEcCCCCCHH--HHHHHHHhhcCCCeEEEecCCCcccceEEEEecCCcceeeeeccccccchHHHHHHHHHHhhhh
Confidence            88999999988753  2344332   1122222222111111111100         0000                   


Q ss_pred             --------------------------cchHHHHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHHcCCc----------
Q 037567          211 --------------------------QSFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVK----------  254 (374)
Q Consensus       211 --------------------------~~~~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~----------  254 (374)
                                                ......++..+..  ....++||||+++..++.+++.|...++.          
T Consensus       302 ~~~~~~~~~~g~~~~~~k~~~~~~~~~~~l~~l~~~l~~--~~~~~~IVF~~sr~~~e~la~~L~~~~~~~~~e~~~i~~  379 (1010)
T 2xgj_A          302 GDDPNSTDSRGKKGQTYKGGSAKGDAKGDIYKIVKMIWK--KKYNPVIVFSFSKRDCEELALKMSKLDFNSDDEKEALTK  379 (1010)
T ss_dssp             ---------------------------CHHHHHHHHHHH--HTCCSEEEEESSHHHHHHHHHTTTTSCCCCHHHHHHHHH
T ss_pred             cccccccccccccccccccccccccchHHHHHHHHHHHh--cCCCCEEEEECCHHHHHHHHHHHHhCCCCChHHHHHHHH
Confidence                                      1111223333222  24568999999999999999988764332          


Q ss_pred             -----------------------------eeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEEEE---
Q 037567          255 -----------------------------AGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIH---  302 (374)
Q Consensus       255 -----------------------------~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~---  302 (374)
                                                   +..+||++++.+|..+++.|++|.++|||||+++++|+|+|++++||+   
T Consensus       380 ~~~~~~~~l~~~d~~l~~~~~l~~~l~~gI~~~Hggl~~~eR~~ve~~F~~G~ikVLVAT~~la~GIDiP~~~vVI~~~~  459 (1010)
T 2xgj_A          380 IFNNAIALLPETDRELPQIKHILPLLRRGIGIHHSGLLPILKEVIEILFQEGFLKVLFATETFSIGLNMPAKTVVFTSVR  459 (1010)
T ss_dssp             HHHHHHTTSCGGGTTCHHHHHHHHHHHHTEEEESTTSCHHHHHHHHHHHHTTCCSEEEEEGGGGGSTTCCBSEEEESCSE
T ss_pred             HHHHHHHhcchhhhcchhHHHHHHHHhCCeeEECCCCCHHHHHHHHHHHhcCCCcEEEEehHhhccCCCCCceEEEeCCc
Confidence                                         678999999999999999999999999999999999999999999998   


Q ss_pred             -ECC----CCChhHHHHhhccCCCCCC--ceEEEEEeecc
Q 037567          303 -YGC----PKTLESYYQESGRCGRDGI--ASVCWLYYARS  335 (374)
Q Consensus       303 -~~~----p~s~~~~~Q~~GR~~R~~~--~g~~~~~~~~~  335 (374)
                       |+.    |.|+.+|.||+||+||.|.  .|.|++++.+.
T Consensus       460 kfd~~~~rp~s~~~y~Qr~GRAGR~G~d~~G~vi~l~~~~  499 (1010)
T 2xgj_A          460 KWDGQQFRWVSGGEYIQMSGRAGRRGLDDRGIVIMMIDEK  499 (1010)
T ss_dssp             EECSSCEEECCHHHHHHHHTTBCCTTTCSSEEEEEEECSC
T ss_pred             ccCCcCCccCCHHHHhHhhhhcccCCCCCceEEEEEECCC
Confidence             888    8899999999999999997  59999998765

>4ddu_A Reverse gyrase; topoisomerase, DNA supercoiling, archaea, helicase, hydrolas; 3.00A {Thermotoga maritima} PDB: 4ddt_A 4ddv_A 4ddw_A 4ddx_A

Probab=100.00  E-value=4.9e-42  Score=341.55  Aligned_cols=280  Identities=21%  Similarity=0.268  Sum_probs=206.0

Q ss_pred             hHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc---cCCcEEEEcchHHHHHHHHHHHHHc---
Q 037567            3 STLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV---TGKTALVVSPLISLMQDQVMSLKQR---   76 (374)
Q Consensus         3 ~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~---~~~~~lil~P~~~l~~q~~~~~~~~---   76 (374)
                      +.++..+|| +|+|+|.++++.++++++++++||||||||++++++++.   .+.++||++|+++|+.|+.+.++.+   
T Consensus        69 ~~~~~~~gf-~pt~iQ~~ai~~il~g~dvlv~ApTGSGKTl~~l~~il~~~~~~~~~Lil~PtreLa~Q~~~~l~~l~~~  147 (1104)
T 4ddu_A           69 SFFKKKFGK-DLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLARKGKKSALVFPTVTLVKQTLERLQKLADE  147 (1104)
T ss_dssp             HHHHHHSSS-CCCHHHHHHHHHHTTTCCEEECCSTTCCHHHHHHHHHHHHHTTTCCEEEEESSHHHHHHHHHHHHTTSCT
T ss_pred             HHHHHhcCC-CCCHHHHHHHHHHHcCCCEEEEeCCCCcHHHHHHHHHHHHHhcCCeEEEEechHHHHHHHHHHHHHhhCC
Confidence            346667899 599999999999999999999999999999987777554   6889999999999999999999984   


Q ss_pred             CCceEEcCCCCCc---hhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhc-----------cc
Q 037567           77 GINAEFLGSAQTD---SSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISE-----------WG  142 (374)
Q Consensus        77 ~~~~~~~~~~~~~---~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~-----------~~  142 (374)
                      ++.+..+.++...   .........+.++|+|+||+++.+++.    .....++++||+||+|++..           +|
T Consensus       148 ~i~v~~l~Gg~~~~er~~~~~~l~~g~~~IlV~Tp~rL~~~l~----~l~~~~l~~lViDEaH~l~~~~r~~Dr~L~~~g  223 (1104)
T 4ddu_A          148 KVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNRE----KLSQKRFDFVFVDDVDAVLKASRNIDTLLMMVG  223 (1104)
T ss_dssp             TSCEEEECTTCCTTHHHHHHHHHHTSCCSEEEEEHHHHHHSHH----HHHTSCCSEEEESCHHHHTTSSHHHHHHHHTSS
T ss_pred             CCeEEEEeCCCCHHHHHHHHHHHhCCCCCEEEECHHHHHHHHH----hhcccCcCEEEEeCCCccccccccchhhhHhcC
Confidence            4567777776655   333344445568999999999976644    35667899999999998765           33


Q ss_pred             CcchHHHHHHHHHHHhc------------CCCCeeEEEeecCcc-cHHHHHHh-cCCCCCeEEEeccCCCceeEEEEeec
Q 037567          143 HDFRLEYKQLDKLRTFL------------LGVPFVALTATATEK-VRIDIINS-LKLKNPYVTIASFDRKNLFYGVKVIN  208 (374)
Q Consensus       143 ~~~~~~~~~~~~~~~~~------------~~~~~i~~SaT~~~~-~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~  208 (374)
                      +.  ..  .+..+...+            .+.++++||||+.+. ....+... +.+..   ........++....... 
T Consensus       224 f~--~~--~i~~il~~l~~~~~~~~~~~~~~~q~ll~SAT~~p~~~~~~~~~~~l~i~v---~~~~~~~~~i~~~~~~~-  295 (1104)
T 4ddu_A          224 IP--EE--IIRKAFSTIKQGKIYERPKNLKPGILVVSSATAKPRGIRPLLFRDLLNFTV---GRLVSVARNITHVRISS-  295 (1104)
T ss_dssp             CC--HH--HHHHHHHHHHHTSCCCCCSSCCCCEEEEECBSSCCCSSTTHHHHHHTCCCC---CBCCCCCCCEEEEEESC-
T ss_pred             CC--HH--HHHHHHHhcccchhhhhhccCCCceEEEEcCCCCcHHHHHHHhhcceeEEe---ccCCCCcCCceeEEEec-
Confidence            32  11  123333322            467899999995443 32222222 22111   11112222332222221 


Q ss_pred             CCcchHHHHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHHcCCcee-eeecCCChHHHHHHHHhhhcCCeeEEEE---
Q 037567          209 RGQSFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAG-TYHGQMGSKAREEAHRLFIRDEIRVMVA---  284 (374)
Q Consensus       209 ~~~~~~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~-~~~~~~~~~~r~~~~~~f~~g~~~ilv~---  284 (374)
                      .    ....+.+++..  .++++||||++++.++.+++.|+..|+.+. .+||.     |.+ ++.|++|+.+||||   
T Consensus       296 ~----k~~~L~~ll~~--~~~~~LVF~~s~~~a~~l~~~L~~~g~~~~~~lhg~-----rr~-l~~F~~G~~~VLVatas  363 (1104)
T 4ddu_A          296 R----SKEKLVELLEI--FRDGILIFAQTEEEGKELYEYLKRFKFNVGETWSEF-----EKN-FEDFKVGKINILIGVQA  363 (1104)
T ss_dssp             C----CHHHHHHHHHH--HCSSEEEEESSSHHHHHHHHHHHHTTCCEEESSSSH-----HHH-HHHHHHTSCSEEEEETT
T ss_pred             C----HHHHHHHHHHh--cCCCEEEEECcHHHHHHHHHHHHhCCCCeeeEecCc-----HHH-HHHHHCCCCCEEEEecC
Confidence            1    22333444444  358999999999999999999999999998 99982     555 99999999999999   


Q ss_pred             -eccccccccccC-ccEEEEECCCC
Q 037567          285 -TMAFGMGIDKPD-VRHVIHYGCPK  307 (374)
Q Consensus       285 -t~~~~~G~d~~~-~~~vi~~~~p~  307 (374)
                       |+++++|+|+|+ +++||++++|.
T Consensus       364 ~TdvlarGIDip~~V~~VI~~d~P~  388 (1104)
T 4ddu_A          364 YYGKLTRGVDLPERIKYVIFWGTPS  388 (1104)
T ss_dssp             THHHHCCSCCCTTTCCEEEEESCCE
T ss_pred             CCCeeEecCcCCCCCCEEEEECCCC
Confidence             999999999999 99999999998

>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=100.00  E-value=7.6e-43  Score=341.69  Aligned_cols=324  Identities=17%  Similarity=0.173  Sum_probs=185.2

Q ss_pred             HcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhcccccc--------CCcEEEEcchHHHHHHHHHHHHHc---
Q 037567            8 YFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVT--------GKTALVVSPLISLMQDQVMSLKQR---   76 (374)
Q Consensus         8 ~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~~--------~~~~lil~P~~~l~~q~~~~~~~~---   76 (374)
                      .+|+..|+|+|.++++.+++++++++.+|||+|||++|+++++..        +.++||++|+++|+.||.+.++++   
T Consensus       243 ~~g~~~l~~~Q~~~i~~~l~~~~~ll~~~TGsGKTl~~~~~i~~~l~~~~~~~~~~~Lvl~Pt~~L~~Q~~~~~~~~~~~  322 (797)
T 4a2q_A          243 VYETKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYEQQKNVFKHHFER  322 (797)
T ss_dssp             -----CCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHTCCSSCCCCEEEECSSHHHHHHHHHHHHHHHGG
T ss_pred             hcCCCCCCHHHHHHHHHHHhCCCEEEEeCCCChHHHHHHHHHHHHHHhccccCCCeEEEEeCCHHHHHHHHHHHHHhccc
Confidence            567889999999999999999999999999999999998887652        788999999999999999999876   


Q ss_pred             -CCceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHH-HhcCccEEEEeccchhhcccCcchHHHHHHHH
Q 037567           77 -GINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKL-LKAGVCLFAVDEAHCISEWGHDFRLEYKQLDK  154 (374)
Q Consensus        77 -~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~-~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~  154 (374)
                       ++.+..+.++........ .....++|+|+||+++...+..  ... .+.++++||+||||++...+. +.........
T Consensus       323 ~~~~v~~~~g~~~~~~~~~-~~~~~~~Ivv~Tp~~l~~~l~~--~~~~~~~~~~~iViDEaH~~~~~~~-~~~i~~~~~~  398 (797)
T 4a2q_A          323 QGYSVQGISGENFSNVSVE-KVIEDSDIIVVTPQILVNSFED--GTLTSLSIFTLMIFDECHNTTGNHP-YNVLMTRYLE  398 (797)
T ss_dssp             GTCCEEEECCC-----CHH-HHHHTCSEEEECHHHHHHHHHS--SSCCCGGGCSEEEETTGGGCSTTSH-HHHHHHHHHH
T ss_pred             CCceEEEEeCCcchhhhHH-HhhCCCCEEEEchHHHHHHHHh--ccccccccCCEEEEECccccCCCcc-HHHHHHHHHH
Confidence             777777777654433222 2234579999999998654432  122 356689999999999876442 2211111111


Q ss_pred             H-HH-hcCCCCeeEEEeecCccc----------HHHHHHhcCC-------------------CCCeEEEeccCCCce---
Q 037567          155 L-RT-FLLGVPFVALTATATEKV----------RIDIINSLKL-------------------KNPYVTIASFDRKNL---  200 (374)
Q Consensus       155 ~-~~-~~~~~~~i~~SaT~~~~~----------~~~~~~~~~~-------------------~~~~~~~~~~~~~~~---  200 (374)
                      . .. ..+..++++||||+....          ...+...++.                   ...............   
T Consensus       399 ~~~~~~~~~~~~l~lSATp~~~~~~~~~~~~~~i~~l~~~L~~~~i~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~  478 (797)
T 4a2q_A          399 QKFNSASQLPQILGLTASVGVGNAKNIEETIEHICSLCSYLDIQAISTVRENIQELQRFMNKPEIDVRLVKRRIHNPFAA  478 (797)
T ss_dssp             HHHTTCCCCCEEEEEESCCCCTTCCSHHHHHHHHHHHHHHHTCSEEECCCTTHHHHHHHSCCCCCEEEECCCCSCCHHHH
T ss_pred             HhhccCCCCCeEEEEcCCccccccccHHHHHHHHHHHHHhcCCcEEecccccHHHHHHhcCCCceEEEecCCCCCcHHHH
Confidence            1 11 134577999999996421          1111222211                   111110000000000   


Q ss_pred             ---------------eE------EEEe--e---------------------c----------------------------
Q 037567          201 ---------------FY------GVKV--I---------------------N----------------------------  208 (374)
Q Consensus       201 ---------------~~------~~~~--~---------------------~----------------------------  208 (374)
                                     ..      ....  .                     .                            
T Consensus       479 ~~~~l~~~i~~~~~~~~~l~~l~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~~~~  558 (797)
T 4a2q_A          479 IISNLMSETEALMRTIYSVDTLSQNSKKDFGTQNYEHWIVVTQRKCRLLQLEDKEEESRICRALFICTEHLRKYNDALII  558 (797)
T ss_dssp             HHHHHHHHHHHHHHHC------------CCSSHHHHHHHHHHHHHHHHCCCSSHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHhhHHhhhhccccccchhHHHHHHHHHHHHHHhcccccchhhHHHHHHHHHHHHHHHHHHHHhh
Confidence                           00      0000  0                     0                            


Q ss_pred             ---------------------------------------------------CCcchHHHHHHHHHHh---hcCCCcEEEE
Q 037567          209 ---------------------------------------------------RGQSFVDELVQEILKS---VAGAGSIIVY  234 (374)
Q Consensus       209 ---------------------------------------------------~~~~~~~~~~~~~~~~---~~~~~~~lVf  234 (374)
                                                                         ...... ..+..++..   ...+.++|||
T Consensus       559 ~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~~~~~~~~~~~K~-~~L~~lL~~~~~~~~~~kvLIF  637 (797)
T 4a2q_A          559 SEDARIIDALSYLTEFFTNVKNGPYTELEQHLTAKFQEKEPELIALSKDETNENPKL-EELVCILDDAYRYNPQTRTLLF  637 (797)
T ss_dssp             HHHSCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHTTHHHHHHHHHCTTCCCHHH-HHHHHHHHHHHHHCSSCCEEEE
T ss_pred             hccccHHHHHHHHHHHHHHHhccCccHHHHHHHHHHHHHHHHHHHhhcCCCCCChHH-HHHHHHHHHHhccCCCCeEEEE
Confidence                                                               000011 112222221   1456899999


Q ss_pred             ecchhHHHHHHHHHHHc------------CCceeeeecCCChHHHHHHHHhhhc-CCeeEEEEeccccccccccCccEEE
Q 037567          235 CMTIKDVEEISKALKQL------------GVKAGTYHGQMGSKAREEAHRLFIR-DEIRVMVATMAFGMGIDKPDVRHVI  301 (374)
Q Consensus       235 ~~~~~~~~~l~~~l~~~------------~~~~~~~~~~~~~~~r~~~~~~f~~-g~~~ilv~t~~~~~G~d~~~~~~vi  301 (374)
                      |+++..++.+++.|++.            |.....+||+++..+|..+++.|++ |+.+|||||+++++|+|+|++++||
T Consensus       638 ~~~~~~~~~L~~~L~~~~~~~~~~~~~l~G~~~~~~hg~~~~~eR~~~l~~F~~~g~~~vLVaT~~~~~GIDlp~v~~VI  717 (797)
T 4a2q_A          638 AKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTSKDNRLLIATSVADEGIDIVQCNLVV  717 (797)
T ss_dssp             ESSHHHHHHHHHHHHTCSTTCSCCCEEC----------------------------CCSEEEEECC-------CCCSEEE
T ss_pred             ECcHHHHHHHHHHHHhCcccccccceEEEecCCcccCCCCCHHHHHHHHHHhhccCCceEEEEcCchhcCCCchhCCEEE
Confidence            99999999999999874            4455677889999999999999999 9999999999999999999999999


Q ss_pred             EECCCCChhHHHHhhccCCCCCCceEEEEEeeccCCC
Q 037567          302 HYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFA  338 (374)
Q Consensus       302 ~~~~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~~~  338 (374)
                      ++++|+|+..|+||+|| ||. ..|.++.++.+.+..
T Consensus       718 ~yd~p~s~~~~iQr~GR-GR~-~~g~~i~l~~~~~~e  752 (797)
T 4a2q_A          718 LYEYSGNVTKMIQVRGR-GRA-AGSKCILVTSKTEVV  752 (797)
T ss_dssp             EESCCSCHHHHHTC---------CCCEEEEECCHHHH
T ss_pred             EeCCCCCHHHHHHhcCC-CCC-CCceEEEEEeCCcHH
Confidence            99999999999999999 998 789999998886643

>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=100.00  E-value=6.4e-43  Score=334.98  Aligned_cols=310  Identities=20%  Similarity=0.214  Sum_probs=230.8

Q ss_pred             hhHHHhHcCCCCCchhHHHHHHHHHcC------CCEEEEccCCCCchhhhhccccc---cCCcEEEEcchHHHHHHHHHH
Q 037567            2 VSTLKKYFGYSVFRPYQKDVIQRIIEK------RDCLVVMATGSGKSLCYQLPPLV---TGKTALVVSPLISLMQDQVMS   72 (374)
Q Consensus         2 ~~~l~~~~~~~~~~~~Q~~~~~~~~~~------~~~l~~a~tGsGKT~~~~l~~~~---~~~~~lil~P~~~l~~q~~~~   72 (374)
                      .+.+.+.+|| +|+++|.++++.+.++      .++++.||||||||++|+++++.   .+.+++|++|+++|+.|+.+.
T Consensus       358 ~~~~~~~lpf-~lt~~Q~~ai~~I~~~l~~~~~~~~Ll~a~TGSGKTlvall~il~~l~~g~qvlvlaPtr~La~Q~~~~  436 (780)
T 1gm5_A          358 AEEFIKSLPF-KLTNAQKRAHQEIRNDMISEKPMNRLLQGDVGSGKTVVAQLAILDNYEAGFQTAFMVPTSILAIQHYRR  436 (780)
T ss_dssp             HHHHHHHSSS-CCCHHHHHHHHHHHHHHHSSSCCCCEEECCSSSSHHHHHHHHHHHHHHHTSCEEEECSCHHHHHHHHHH
T ss_pred             HHHHHHhCCC-CCCHHHHHHHHHHHhhccccCCCcEEEEcCCCCCHHHHHHHHHHHHHHcCCeEEEEeCcHHHHHHHHHH
Confidence            3556667999 8999999999998874      58999999999999999888765   488999999999999999999


Q ss_pred             HHHc----CCceEEcCCCCCchhh---hhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcc
Q 037567           73 LKQR----GINAEFLGSAQTDSSV---QTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDF  145 (374)
Q Consensus        73 ~~~~----~~~~~~~~~~~~~~~~---~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~  145 (374)
                      +.++    ++++..++++......   ......+.++|+|+||+.+.       ....+.+++++|+||+|++.....  
T Consensus       437 l~~~~~~~gi~v~~l~G~~~~~~r~~~~~~l~~g~~~IvVgT~~ll~-------~~~~~~~l~lVVIDEaHr~g~~qr--  507 (780)
T 1gm5_A          437 TVESFSKFNIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTHALIQ-------EDVHFKNLGLVIIDEQHRFGVKQR--  507 (780)
T ss_dssp             HHHHHTCSSCCEEECCSSSCHHHHHHHHHHHHSSCCCEEEECTTHHH-------HCCCCSCCCEEEEESCCCC-------
T ss_pred             HHHHhhhcCceEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHh-------hhhhccCCceEEecccchhhHHHH--
Confidence            8865    6777777776654432   23344567899999998663       233467889999999998642111  


Q ss_pred             hHHHHHHHHHHHhcCCCCeeEEEeecCcccHHHHHHhcCCCCCeEEEe-ccCCCceeEEEEeecCCcchHHHHHHHHHHh
Q 037567          146 RLEYKQLDKLRTFLLGVPFVALTATATEKVRIDIINSLKLKNPYVTIA-SFDRKNLFYGVKVINRGQSFVDELVQEILKS  224 (374)
Q Consensus       146 ~~~~~~~~~~~~~~~~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  224 (374)
                             ..+.....+.++++|||||.+....  ...++..+..+... ......+.    ...........++..+.+.
T Consensus       508 -------~~l~~~~~~~~vL~mSATp~p~tl~--~~~~g~~~~s~i~~~p~~r~~i~----~~~~~~~~~~~l~~~i~~~  574 (780)
T 1gm5_A          508 -------EALMNKGKMVDTLVMSATPIPRSMA--LAFYGDLDVTVIDEMPPGRKEVQ----TMLVPMDRVNEVYEFVRQE  574 (780)
T ss_dssp             -------CCCCSSSSCCCEEEEESSCCCHHHH--HHHTCCSSCEEECCCCSSCCCCE----ECCCCSSTHHHHHHHHHHH
T ss_pred             -------HHHHHhCCCCCEEEEeCCCCHHHHH--HHHhCCcceeeeeccCCCCcceE----EEEeccchHHHHHHHHHHH
Confidence                   1112222467899999999876543  22233222222211 11111111    1111223345555666666


Q ss_pred             hcCCCcEEEEecchh--------HHHHHHHHHHH---cCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEecccccccc
Q 037567          225 VAGAGSIIVYCMTIK--------DVEEISKALKQ---LGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGID  293 (374)
Q Consensus       225 ~~~~~~~lVf~~~~~--------~~~~l~~~l~~---~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d  293 (374)
                      ...+++++|||+..+        .++.+++.|++   .+..+..+||+++.++|..+++.|.+|+.+|||||+++++|+|
T Consensus       575 l~~g~qvlVf~~~ie~se~l~~~~a~~l~~~L~~~~~~~~~v~~lHG~m~~~eR~~v~~~F~~G~~~ILVaT~vie~GID  654 (780)
T 1gm5_A          575 VMRGGQAFIVYPLIEESDKLNVKSAVEMYEYLSKEVFPEFKLGLMHGRLSQEEKDRVMLEFAEGRYDILVSTTVIEVGID  654 (780)
T ss_dssp             TTTSCCBCCBCCCC--------CHHHHHHHSGGGSCC---CBCCCCSSSCCSCSHHHHHHHTTTSSSBCCCSSCCCSCSC
T ss_pred             HhcCCcEEEEecchhhhhhhhHHHHHHHHHHHHhhhcCCCcEEEEeCCCCHHHHHHHHHHHHCCCCeEEEECCCCCcccc
Confidence            677899999999653        57788888887   4678999999999999999999999999999999999999999


Q ss_pred             ccCccEEEEECCCC-ChhHHHHhhccCCCCCCceEEEEEeec
Q 037567          294 KPDVRHVIHYGCPK-TLESYYQESGRCGRDGIASVCWLYYAR  334 (374)
Q Consensus       294 ~~~~~~vi~~~~p~-s~~~~~Q~~GR~~R~~~~g~~~~~~~~  334 (374)
                      +|++++||++++|. +...+.||+||+||.|+.|.|++++.+
T Consensus       655 iP~v~~VIi~d~~r~~l~~l~Qr~GRaGR~g~~g~~ill~~~  696 (780)
T 1gm5_A          655 VPRANVMVIENPERFGLAQLHQLRGRVGRGGQEAYCFLVVGD  696 (780)
T ss_dssp             CTTCCEEEBCSCSSSCTTHHHHHHHTSCCSSTTCEEECCCCS
T ss_pred             CCCCCEEEEeCCCCCCHHHHHHHhcccCcCCCCCEEEEEECC
Confidence            99999999999985 788999999999999999999999873

>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=100.00  E-value=1.2e-41  Score=349.92  Aligned_cols=334  Identities=18%  Similarity=0.209  Sum_probs=247.3

Q ss_pred             CCCCCchhHHHHHHHHHc-CCCEEEEccCCCCchhhhhccccc-----cCCcEEEEcchHHHHHHHHHHHHH-c----CC
Q 037567           10 GYSVFRPYQKDVIQRIIE-KRDCLVVMATGSGKSLCYQLPPLV-----TGKTALVVSPLISLMQDQVMSLKQ-R----GI   78 (374)
Q Consensus        10 ~~~~~~~~Q~~~~~~~~~-~~~~l~~a~tGsGKT~~~~l~~~~-----~~~~~lil~P~~~l~~q~~~~~~~-~----~~   78 (374)
                      +|+.|+|+|.++++.++. +++++++||||||||+++.++++.     .+.+++|++|+++|++|.++++.+ +    |.
T Consensus       923 ~f~~fnpiQ~q~~~~l~~~~~nvlv~APTGSGKTliaelail~~l~~~~~~kavyi~P~raLa~q~~~~~~~~f~~~~g~ 1002 (1724)
T 4f92_B          923 KFPFFNPIQTQVFNTVYNSDDNVFVGAPTGSGKTICAEFAILRMLLQSSEGRCVYITPMEALAEQVYMDWYEKFQDRLNK 1002 (1724)
T ss_dssp             TCSBCCHHHHHHHHHHHSCCSCEEEECCTTSCCHHHHHHHHHHHHHHCTTCCEEEECSCHHHHHHHHHHHHHHHTTTSCC
T ss_pred             cCCCCCHHHHHHHHHHhcCCCcEEEEeCCCCCchHHHHHHHHHHHHhCCCCEEEEEcChHHHHHHHHHHHHHHhchhcCC
Confidence            699999999999999986 567999999999999999888764     367899999999999999988864 3    55


Q ss_pred             ceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcc-cCcchHHHHHHHHHHH
Q 037567           79 NAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEW-GHDFRLEYKQLDKLRT  157 (374)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~-~~~~~~~~~~~~~~~~  157 (374)
                      ++...+++.....    .....++|+|+|||++..+.+++.....+.++++||+||+|.+.+. |......+.++..+..
T Consensus      1003 ~V~~ltGd~~~~~----~~~~~~~IiV~TPEkld~llr~~~~~~~l~~v~lvViDE~H~l~d~rg~~le~il~rl~~i~~ 1078 (1724)
T 4f92_B         1003 KVVLLTGETSTDL----KLLGKGNIIISTPEKWDILSRRWKQRKNVQNINLFVVDEVHLIGGENGPVLEVICSRMRYISS 1078 (1724)
T ss_dssp             CEEECCSCHHHHH----HHHHHCSEEEECHHHHHHHHTTTTTCHHHHSCSEEEECCGGGGGSTTHHHHHHHHHHHHHHHH
T ss_pred             EEEEEECCCCcch----hhcCCCCEEEECHHHHHHHHhCcccccccceeeEEEeechhhcCCCCCccHHHHHHHHHHHHh
Confidence            6666655432211    1223469999999998777666555556789999999999988652 2222223334443333


Q ss_pred             hc-CCCCeeEEEeecCcccHHHHHHhcCCCCCeEEEeccCC--CceeEEEEeecCCcc-----hHHHHHHHHHHhhcCCC
Q 037567          158 FL-LGVPFVALTATATEKVRIDIINSLKLKNPYVTIASFDR--KNLFYGVKVINRGQS-----FVDELVQEILKSVAGAG  229 (374)
Q Consensus       158 ~~-~~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~  229 (374)
                      .. ++.++|+||||.++..  ++..|++...........+.  ..+...+........     .....+...+.....++
T Consensus      1079 ~~~~~~riI~lSATl~N~~--dla~WL~~~~~~~~~~~~~~RPvpL~~~i~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~ 1156 (1724)
T 4f92_B         1079 QIERPIRIVALSSSLSNAK--DVAHWLGCSATSTFNFHPNVRPVPLELHIQGFNISHTQTRLLSMAKPVYHAITKHSPKK 1156 (1724)
T ss_dssp             TTSSCCEEEEEESCBTTHH--HHHHHHTCCSTTEEECCGGGCSSCEEEEEEEECCCSHHHHHHTTHHHHHHHHHHHCSSS
T ss_pred             hcCCCceEEEEeCCCCCHH--HHHHHhCCCCCCeEEeCCCCCCCCeEEEEEeccCCCchhhhhhhcchHHHHHHHhcCCC
Confidence            32 4688999999998754  67899987765544333222  222333332222211     11233344455556789


Q ss_pred             cEEEEecchhHHHHHHHHHHHc----------------------------------CCceeeeecCCChHHHHHHHHhhh
Q 037567          230 SIIVYCMTIKDVEEISKALKQL----------------------------------GVKAGTYHGQMGSKAREEAHRLFI  275 (374)
Q Consensus       230 ~~lVf~~~~~~~~~l~~~l~~~----------------------------------~~~~~~~~~~~~~~~r~~~~~~f~  275 (374)
                      ++||||+++..++.++..|...                                  ...++.+|++++..+|..+.+.|.
T Consensus      1157 ~~lVF~~sR~~~~~~A~~L~~~~~~~~~~~~~~~~~~~~l~~~l~~~~d~~L~~~l~~GIa~hHagL~~~~R~~VE~lF~ 1236 (1724)
T 4f92_B         1157 PVIVFVPSRKQTRLTAIDILTTCAADIQRQRFLHCTEKDLIPYLEKLSDSTLKETLLNGVGYLHEGLSPMERRLVEQLFS 1236 (1724)
T ss_dssp             CEEEEESSHHHHHHHHHHHHHHHHHTTCTTTTBCSCHHHHHHHHTTCCCHHHHHHHHTTEEEECTTSCHHHHHHHHHHHH
T ss_pred             CeeeeCCCHHHHHHHHHHHHHHHhhccchhhhhcccHHHHHHHHhhcccHHHHHHHhCCEEEECCCCCHHHHHHHHHHHH
Confidence            9999999999999888766431                                  234788999999999999999999


Q ss_pred             cCCeeEEEEeccccccccccCccEEEE----E------CCCCChhHHHHhhccCCCCCC--ceEEEEEeeccCCCcccce
Q 037567          276 RDEIRVMVATMAFGMGIDKPDVRHVIH----Y------GCPKTLESYYQESGRCGRDGI--ASVCWLYYARSNFAKGDFY  343 (374)
Q Consensus       276 ~g~~~ilv~t~~~~~G~d~~~~~~vi~----~------~~p~s~~~~~Q~~GR~~R~~~--~g~~~~~~~~~~~~~~~~~  343 (374)
                      +|.++|||||+.++.|+|+|...+||.    +      ..|.+..+|.||+|||||.|.  .|.+++++...+...++++
T Consensus      1237 ~G~i~VLvaT~tlA~GVnlPa~~VVI~~~~~~dg~~~~~~~~s~~~~~Qm~GRAGR~g~d~~G~avll~~~~~~~~~~~l 1316 (1724)
T 4f92_B         1237 SGAIQVVVASRSLCWGMNVAAHLVIIMDTQYYNGKIHAYVDYPIYDVLQMVGHANRPLQDDEGRCVIMCQGSKKDFFKKF 1316 (1724)
T ss_dssp             HTSBCEEEEEGGGSSSCCCCBSEEEEECSEEEETTTTEEEECCHHHHHHHHTTBCCTTTCSCEEEEEEEEGGGHHHHHHH
T ss_pred             CCCCeEEEEChHHHcCCCCCccEEEEecCccccCcccccCCCCHHHHHHhhccccCCCCCCceEEEEEecchHHHHHHHH
Confidence            999999999999999999999888873    2      235689999999999999986  7999999999888777777


Q ss_pred             eccccc
Q 037567          344 CGESQT  349 (374)
Q Consensus       344 ~~~~~~  349 (374)
                      +.+..+
T Consensus      1317 l~~~~p 1322 (1724)
T 4f92_B         1317 LYEPLP 1322 (1724)
T ss_dssp             TTSCBC
T ss_pred             hCCCCc
Confidence            665543

>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=100.00  E-value=1.4e-41  Score=349.37  Aligned_cols=336  Identities=21%  Similarity=0.233  Sum_probs=243.2

Q ss_pred             HhHc-CCCCCchhHHHHHHHHHc-CCCEEEEccCCCCchhhhhccccc--------------cCCcEEEEcchHHHHHHH
Q 037567            6 KKYF-GYSVFRPYQKDVIQRIIE-KRDCLVVMATGSGKSLCYQLPPLV--------------TGKTALVVSPLISLMQDQ   69 (374)
Q Consensus         6 ~~~~-~~~~~~~~Q~~~~~~~~~-~~~~l~~a~tGsGKT~~~~l~~~~--------------~~~~~lil~P~~~l~~q~   69 (374)
                      +..| ||.+|+++|+++++.+++ ++|++++||||||||+++.++++.              .+.++++++|+++|++|.
T Consensus        71 ~~~f~g~~~ln~iQs~~~~~al~~~~N~lv~APTGsGKTlva~l~il~~l~~~~~~~~~~~~~~~k~lyiaP~kALa~e~  150 (1724)
T 4f92_B           71 QAGFEGFKTLNRIQSKLYRAALETDENLLLCAPTGAGKTNVALMCMLREIGKHINMDGTINVDDFKIIYIAPMRSLVQEM  150 (1724)
T ss_dssp             STTCTTCSBCCHHHHHTHHHHHTCCCCEEEECCTTSCCHHHHHHHHHHHHGGGCCTTSSCCTTSCEEEEECSSHHHHHHH
T ss_pred             HHhcCCCCCCCHHHHHHHHHHHcCCCcEEEEeCCcchHHHHHHHHHHHHHHhhccccccccCCCCEEEEECCHHHHHHHH
Confidence            3444 799999999999998875 789999999999999999888763              256899999999999999


Q ss_pred             HHHHHH----cCCceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhc-ccCc
Q 037567           70 VMSLKQ----RGINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISE-WGHD  144 (374)
Q Consensus        70 ~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~-~~~~  144 (374)
                      .+++.+    .|+.+...+++......    ....++|+|+|||++..++++......+..+++||+||+|.+.+ .|..
T Consensus       151 ~~~l~~~~~~~gi~V~~~tGd~~~~~~----~~~~~~IlVtTpEkld~llr~~~~~~~l~~v~~vIiDEvH~l~d~RG~~  226 (1724)
T 4f92_B          151 VGSFGKRLATYGITVAELTGDHQLCKE----EISATQIIVCTPEKWDIITRKGGERTYTQLVRLIILDEIHLLHDDRGPV  226 (1724)
T ss_dssp             HHHHHHHHTTTTCCEEECCSSCSSCCT----TGGGCSEEEECHHHHHHHTTSSTTHHHHTTEEEEEETTGGGGGSTTHHH
T ss_pred             HHHHHHHHhhCCCEEEEEECCCCCCcc----ccCCCCEEEECHHHHHHHHcCCccchhhcCcCEEEEecchhcCCccHHH
Confidence            988864    47778777776543322    22457999999999877766544455678899999999998854 2222


Q ss_pred             chHHHHHHHHHH-HhcCCCCeeEEEeecCcccHHHHHHhcCCCCCe-E-EEeccCCC-ceeEEEEeecCCc-----chHH
Q 037567          145 FRLEYKQLDKLR-TFLLGVPFVALTATATEKVRIDIINSLKLKNPY-V-TIASFDRK-NLFYGVKVINRGQ-----SFVD  215 (374)
Q Consensus       145 ~~~~~~~~~~~~-~~~~~~~~i~~SaT~~~~~~~~~~~~~~~~~~~-~-~~~~~~~~-~~~~~~~~~~~~~-----~~~~  215 (374)
                      .+..+.++.+.. ...++.++|+||||.++..  ++..|++..... . ...+..++ .+...+.......     ....
T Consensus       227 lE~~l~rl~~~~~~~~~~~riI~LSATl~N~~--dvA~wL~~~~~~~~~~~~~~~RPvpL~~~~~~~~~~~~~~~~~~~~  304 (1724)
T 4f92_B          227 LEALVARAIRNIEMTQEDVRLIGLSATLPNYE--DVATFLRVDPAKGLFYFDNSFRPVPLEQTYVGITEKKAIKRFQIMN  304 (1724)
T ss_dssp             HHHHHHHHHHHHHHHTCCCEEEEEECSCTTHH--HHHHHTTCCHHHHEEECCGGGCSSCEEEECCEECCCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCCCCcEEEEecccCCHH--HHHHHhCCCCCCCeEEECCCCccCccEEEEeccCCcchhhhhHHHH
Confidence            222223332222 2335789999999998643  678888754321 1 11111111 1111111111111     1122


Q ss_pred             HHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHHc-------------------------------------CCceeee
Q 037567          216 ELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQL-------------------------------------GVKAGTY  258 (374)
Q Consensus       216 ~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~-------------------------------------~~~~~~~  258 (374)
                      +.+.+.+.....++++||||++++.++.+++.|.+.                                     ...++.+
T Consensus       305 ~~~~~~v~~~~~~~~~LVF~~sR~~~~~~A~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Gva~H  384 (1724)
T 4f92_B          305 EIVYEKIMEHAGKNQVLVFVHSRKETGKTARAIRDMCLEKDTLGLFLREGSASTEVLRTEAEQCKNLELKDLLPYGFAIH  384 (1724)
T ss_dssp             HHHHHHHTTCCSSCCEEEECSSTTTTHHHHHHHHHHHHHTTSTTCCSSCCTTCSSHHHHTTSCCSTHHHHHHTTTTEEEE
T ss_pred             HHHHHHHHHHhcCCcEEEECCCHHHHHHHHHHHHHHHhhccchhhhcccchhHHHHHHhhhcccccHHHHHHhhcCEEEE
Confidence            334444444456789999999999999888877542                                     2236789


Q ss_pred             ecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEEEE----EC------CCCChhHHHHhhccCCCCCC--ce
Q 037567          259 HGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIH----YG------CPKTLESYYQESGRCGRDGI--AS  326 (374)
Q Consensus       259 ~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~----~~------~p~s~~~~~Q~~GR~~R~~~--~g  326 (374)
                      ||+++.++|..+.+.|++|.++|||||++++.|+|+|..++||.    ++      .|.++.+|.||+|||||.|.  .|
T Consensus       385 HagL~~~~R~~vE~~F~~G~i~vlvaTsTLa~GVNlPa~~vVI~~~~~~~~~~~~~~~ls~~~~~Qm~GRAGR~g~d~~G  464 (1724)
T 4f92_B          385 HAGMTRVDRTLVEDLFADKHIQVLVSTATLAWGVNLPAHTVIIKGTQVYSPEKGRWTELGALDILQMLGRAGRPQYDTKG  464 (1724)
T ss_dssp             CSSSCTHHHHHHHHHHHTTCCCEEEECHHHHHHSCCCBSEEEEECCEEEETTTTEEEECCHHHHHHHHTTBSCTTTCSCE
T ss_pred             cCCCCHHHHHHHHHHHHCCCCeEEEEcchhHhhCCCCCceEEEeCCEEecCcCCCcccCCHHHHHHhhhhccCCCCCCcc
Confidence            99999999999999999999999999999999999999998884    33      24589999999999999864  79


Q ss_pred             EEEEEeeccCCCcccceeccc
Q 037567          327 VCWLYYARSNFAKGDFYCGES  347 (374)
Q Consensus       327 ~~~~~~~~~~~~~~~~~~~~~  347 (374)
                      .++++..+++......++...
T Consensus       465 ~~ii~~~~~~~~~~~~ll~~~  485 (1724)
T 4f92_B          465 EGILITSHGELQYYLSLLNQQ  485 (1724)
T ss_dssp             EEEEEEESTTCCHHHHHTTTC
T ss_pred             EEEEEecchhHHHHHHHHcCC
Confidence            999999999887776665543

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4}

Probab=100.00  E-value=3.8e-42  Score=321.95  Aligned_cols=310  Identities=13%  Similarity=0.089  Sum_probs=217.3

Q ss_pred             CCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc----cCCcEEEEcchHHHHHHHHHHHHHcCC----ceEEcC
Q 037567           13 VFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV----TGKTALVVSPLISLMQDQVMSLKQRGI----NAEFLG   84 (374)
Q Consensus        13 ~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~----~~~~~lil~P~~~l~~q~~~~~~~~~~----~~~~~~   84 (374)
                      +|+|+|.++++.+++++++++++|||+|||+++++++..    ...++||++|+++|+.||.+++.+++.    .+..+.
T Consensus       113 ~l~~~Q~~ai~~~~~~~~~ll~~~tGsGKT~~~~~~~~~~~~~~~~~vlvl~P~~~L~~Q~~~~~~~~~~~~~~~v~~~~  192 (510)
T 2oca_A          113 EPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALLARYYLENYEGKILIIVPTTALTTQMADDFVDYRLFSHAMIKKIG  192 (510)
T ss_dssp             CCCHHHHHHHHHHHHHSEEEEECCSTTTHHHHHHHHHHHHHHHCSSEEEEEESSHHHHHHHHHHHHHTTSSCGGGEEECG
T ss_pred             CCCHHHHHHHHHHHhcCCcEEEeCCCCCHHHHHHHHHHHHHhCCCCeEEEEECcHHHHHHHHHHHHHhhcCCccceEEEe
Confidence            799999999999999999999999999999998777664    345999999999999999999998733    344444


Q ss_pred             CCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHHhc-CCCC
Q 037567           85 SAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFL-LGVP  163 (374)
Q Consensus        85 ~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~-~~~~  163 (374)
                      ++......    ..+..+|+|+||+.+....     ...+.++++||+||+|++..         ..+..+...+ ...+
T Consensus       193 ~~~~~~~~----~~~~~~I~i~T~~~l~~~~-----~~~~~~~~liIiDE~H~~~~---------~~~~~il~~~~~~~~  254 (510)
T 2oca_A          193 GGASKDDK----YKNDAPVVVGTWQTVVKQP-----KEWFSQFGMMMNDECHLATG---------KSISSIISGLNNCMF  254 (510)
T ss_dssp             GGCCTTGG----GCTTCSEEEEEHHHHTTSC-----GGGGGGEEEEEEETGGGCCH---------HHHHHHGGGCTTCCE
T ss_pred             cCCccccc----cccCCcEEEEeHHHHhhch-----hhhhhcCCEEEEECCcCCCc---------ccHHHHHHhcccCcE
Confidence            43333222    3456899999999876542     23456789999999999865         2344444444 4678


Q ss_pred             eeEEEeecCcccHH--HHHHhcCCCCCeEEEecc--------CCCceeEEEEeec----------CCcc----------h
Q 037567          164 FVALTATATEKVRI--DIINSLKLKNPYVTIASF--------DRKNLFYGVKVIN----------RGQS----------F  213 (374)
Q Consensus       164 ~i~~SaT~~~~~~~--~~~~~~~~~~~~~~~~~~--------~~~~~~~~~~~~~----------~~~~----------~  213 (374)
                      +++|||||+.....  .....++   +.......        ..+..........          ....          .
T Consensus       255 ~l~lSATp~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  331 (510)
T 2oca_A          255 KFGLSGSLRDGKANIMQYVGMFG---EIFKPVTTSKLMEDGQVTELKINSIFLRYPDEFTTKLKGKTYQEEIKIITGLSK  331 (510)
T ss_dssp             EEEEESCGGGCSSCHHHHHHHHC---SEECCCCCC---------CCEEEEEEEECCHHHHHHHTTCCHHHHHHHHHTCHH
T ss_pred             EEEEEeCCCCCcccHHHhHHhhC---CeEEeeCHHHHhhCCcCCCceEEEEeecCChHHhccccccchHHHHHHHhccHH
Confidence            99999999765421  1111221   11100000        0000000000000          0000          1


Q ss_pred             HHHHHHHHHHh-hcCCCc-EEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEe-ccccc
Q 037567          214 VDELVQEILKS-VAGAGS-IIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVAT-MAFGM  290 (374)
Q Consensus       214 ~~~~~~~~~~~-~~~~~~-~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t-~~~~~  290 (374)
                      ....+.+++.. ...+++ ++||++ .+.++.+++.|.+.+..+..+||+++..+|+++++.|.+|+.+||||| +++++
T Consensus       332 ~~~~l~~~l~~~~~~~~~~~ivf~~-~~~~~~l~~~L~~~~~~v~~~~g~~~~~~r~~i~~~f~~g~~~vLv~T~~~~~~  410 (510)
T 2oca_A          332 RNKWIAKLAIKLAQKDENAFVMFKH-VSHGKAIFDLIKNEYDKVYYVSGEVDTETRNIMKTLAENGKGIIIVASYGVFST  410 (510)
T ss_dssp             HHHHHHHHHHHHHTTTCEEEEEESS-HHHHHHHHHHHHTTCSSEEEESSSTTHHHHHHHHHHHHHCCSCEEEEEHHHHHH
T ss_pred             HHHHHHHHHHHHHhcCCCeEEEEec-HHHHHHHHHHHHHcCCCeEEEECCCCHHHHHHHHHHHhCCCCCEEEEEcChhhc
Confidence            11222333222 223444 555555 899999999999988899999999999999999999999999999999 99999


Q ss_pred             cccccCccEEEEECCCCChhHHHHhhccCCCCCCceEEEEEee-ccCCCccccee
Q 037567          291 GIDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYA-RSNFAKGDFYC  344 (374)
Q Consensus       291 G~d~~~~~~vi~~~~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~-~~~~~~~~~~~  344 (374)
                      |+|+|++++||++++|+++..|.|++||+||.|+++.++++++ .++....+.+.
T Consensus       411 GiDip~v~~vi~~~~~~s~~~~~Q~~GR~gR~g~~~~~v~i~~~~~~~~~~~~~~  465 (510)
T 2oca_A          411 GISVKNLHHVVLAHGVKSKIIVLQTIGRVLRKHGSKTIATVWDLIDDAGVKPKSA  465 (510)
T ss_dssp             SCCCCSEEEEEESSCCCSCCHHHHHHHHHHTTTCCCCCCEEEEEEEECCBCCSSS
T ss_pred             ccccccCcEEEEeCCCCCHHHHHHHHhcccccCCCCceEEEEEeecchhhhhhhh
Confidence            9999999999999999999999999999999998874444444 34444444443

>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=100.00  E-value=2.3e-40  Score=331.59  Aligned_cols=310  Identities=19%  Similarity=0.246  Sum_probs=232.8

Q ss_pred             hHHHhHcCCCCCchhHHHHHHHHHc----CC--CEEEEccCCCCchhhhhcccc---ccCCcEEEEcchHHHHHHHHHHH
Q 037567            3 STLKKYFGYSVFRPYQKDVIQRIIE----KR--DCLVVMATGSGKSLCYQLPPL---VTGKTALVVSPLISLMQDQVMSL   73 (374)
Q Consensus         3 ~~l~~~~~~~~~~~~Q~~~~~~~~~----~~--~~l~~a~tGsGKT~~~~l~~~---~~~~~~lil~P~~~l~~q~~~~~   73 (374)
                      +.|...|+|. ++|+|.++++.+++    ++  ++++++|||+|||.+++++++   ..+++++|++||++|+.|+.+.+
T Consensus       594 ~~~~~~f~~~-~t~~Q~~ai~~il~~~~~g~p~d~ll~~~TGsGKT~val~aa~~~~~~g~~vlvlvPt~~La~Q~~~~~  672 (1151)
T 2eyq_A          594 QLFCDSFPFE-TTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVDNHKQVAVLVPTTLLAQQHYDNF  672 (1151)
T ss_dssp             HHHHHTCCSC-CCHHHHHHHHHHHHHHHSSSCCEEEEECCCCTTTHHHHHHHHHHHHTTTCEEEEECSSHHHHHHHHHHH
T ss_pred             HHHHHhCCCC-CCHHHHHHHHHHHHHHhcCCcCcEEEECCCCCCHHHHHHHHHHHHHHhCCeEEEEechHHHHHHHHHHH
Confidence            4566778996 79999999999886    55  899999999999988776553   46789999999999999999999


Q ss_pred             HHc----CCceEEcCCCCCchhh---hhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcch
Q 037567           74 KQR----GINAEFLGSAQTDSSV---QTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFR  146 (374)
Q Consensus        74 ~~~----~~~~~~~~~~~~~~~~---~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~  146 (374)
                      .+.    +..+..+.+.......   ......+.++|+|+||+.+...       ..+.++++||+||+|++..      
T Consensus       673 ~~~~~~~~i~v~~l~~~~~~~~~~~~~~~l~~g~~dIvV~T~~ll~~~-------~~~~~l~lvIiDEaH~~g~------  739 (1151)
T 2eyq_A          673 RDRFANWPVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTHKLLQSD-------VKFKDLGLLIVDEEHRFGV------  739 (1151)
T ss_dssp             HHHSTTTTCCEEEESTTSCHHHHHHHHHHHHTTCCSEEEECTHHHHSC-------CCCSSEEEEEEESGGGSCH------
T ss_pred             HHHhhcCCCeEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHhCC-------ccccccceEEEechHhcCh------
Confidence            853    4556665554333322   2334456789999999866432       2357889999999999632      


Q ss_pred             HHHHHHHHHHHhcCCCCeeEEEeecCcccHHHHHHhcCCCCCeEEEe-ccCCCceeEEEEeecCCcchHHHHHHHHHHhh
Q 037567          147 LEYKQLDKLRTFLLGVPFVALTATATEKVRIDIINSLKLKNPYVTIA-SFDRKNLFYGVKVINRGQSFVDELVQEILKSV  225 (374)
Q Consensus       147 ~~~~~~~~~~~~~~~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  225 (374)
                         .....+.....+.++++|||||.+......  ..+..+...... ......+...  .....   ...+...+++..
T Consensus       740 ---~~~~~l~~l~~~~~vl~lSATp~p~~l~~~--~~~~~~~~~i~~~~~~r~~i~~~--~~~~~---~~~i~~~il~~l  809 (1151)
T 2eyq_A          740 ---RHKERIKAMRANVDILTLTATPIPRTLNMA--MSGMRDLSIIATPPARRLAVKTF--VREYD---SMVVREAILREI  809 (1151)
T ss_dssp             ---HHHHHHHHHHTTSEEEEEESSCCCHHHHHH--HTTTSEEEECCCCCCBCBCEEEE--EEECC---HHHHHHHHHHHH
T ss_pred             ---HHHHHHHHhcCCCCEEEEcCCCChhhHHHH--HhcCCCceEEecCCCCccccEEE--EecCC---HHHHHHHHHHHH
Confidence               112223333456789999999987654322  223222222111 1111122111  11111   234445556666


Q ss_pred             cCCCcEEEEecchhHHHHHHHHHHHc--CCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEEEEE
Q 037567          226 AGAGSIIVYCMTIKDVEEISKALKQL--GVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHY  303 (374)
Q Consensus       226 ~~~~~~lVf~~~~~~~~~l~~~l~~~--~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~~  303 (374)
                      ..+++++|||++++.++.+++.|++.  +..+..+||+++..+|.++++.|.+|+.+|||||+++++|+|+|++++||.+
T Consensus       810 ~~g~qvlvf~~~v~~~~~l~~~L~~~~p~~~v~~lhg~~~~~eR~~il~~F~~g~~~VLVaT~v~e~GiDip~v~~VIi~  889 (1151)
T 2eyq_A          810 LRGGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIE  889 (1151)
T ss_dssp             TTTCEEEEECCCSSCHHHHHHHHHHHCTTSCEEECCSSCCHHHHHHHHHHHHTTSCCEEEESSTTGGGSCCTTEEEEEET
T ss_pred             hcCCeEEEEECCHHHHHHHHHHHHHhCCCCeEEEEeCCCCHHHHHHHHHHHHcCCCcEEEECCcceeeecccCCcEEEEe
Confidence            67899999999999999999999987  7889999999999999999999999999999999999999999999999998


Q ss_pred             CC-CCChhHHHHhhccCCCCCCceEEEEEeeccC
Q 037567          304 GC-PKTLESYYQESGRCGRDGIASVCWLYYARSN  336 (374)
Q Consensus       304 ~~-p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~  336 (374)
                      +. ++++.++.||+||+||.|+.|.|++++++.+
T Consensus       890 ~~~~~~l~~l~Qr~GRvgR~g~~g~~~ll~~~~~  923 (1151)
T 2eyq_A          890 RADHFGLAQLHQLRGRVGRSHHQAYAWLLTPHPK  923 (1151)
T ss_dssp             TTTSSCHHHHHHHHTTCCBTTBCEEEEEEECCGG
T ss_pred             CCCCCCHHHHHHHHhccCcCCCceEEEEEECCcc
Confidence            87 5689999999999999999999999987653

>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=100.00  E-value=1.8e-41  Score=314.37  Aligned_cols=293  Identities=19%  Similarity=0.191  Sum_probs=216.6

Q ss_pred             CCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccccCCcEEEEcchHHHHHHHHHHHHHcCCc-eEEcCCCCCchh
Q 037567           13 VFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVTGKTALVVSPLISLMQDQVMSLKQRGIN-AEFLGSAQTDSS   91 (374)
Q Consensus        13 ~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~-~~~~~~~~~~~~   91 (374)
                      +|+|+|.++++.+.+++++++.+|||+|||++++.++...+.++||++|+++|+.||.+++.+++.. +..+.+....  
T Consensus        93 ~l~~~Q~~ai~~i~~~~~~ll~~~TGsGKT~~~l~~i~~~~~~~Lvl~P~~~L~~Q~~~~~~~~~~~~v~~~~g~~~~--  170 (472)
T 2fwr_A           93 SLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAAINELSTPTLIVVPTLALAEQWKERLGIFGEEYVGEFSGRIKE--  170 (472)
T ss_dssp             CBCHHHHHHHHHHTTTTEEEEECCTTSCHHHHHHHHHHHHCSCEEEEESSHHHHHHHHHHGGGGCGGGEEEBSSSCBC--
T ss_pred             CcCHHHHHHHHHHHhcCCEEEEeCCCCCHHHHHHHHHHHcCCCEEEEECCHHHHHHHHHHHHhCCCcceEEECCCcCC--
Confidence            6999999999999999999999999999999998888877899999999999999999999999888 7777765432  


Q ss_pred             hhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHHhcCCCCeeEEEeec
Q 037567           92 VQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATA  171 (374)
Q Consensus        92 ~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~SaT~  171 (374)
                              ..+|+|+||+.+.....     .....+++||+||+|++.+.+.         ..+...++..+++++||||
T Consensus       171 --------~~~Ivv~T~~~l~~~~~-----~~~~~~~liIvDEaH~~~~~~~---------~~~~~~~~~~~~l~lSATp  228 (472)
T 2fwr_A          171 --------LKPLTVSTYDSAYVNAE-----KLGNRFMLLIFDEVHHLPAESY---------VQIAQMSIAPFRLGLTATF  228 (472)
T ss_dssp             --------CCSEEEEEHHHHHHTHH-----HHTTTCSEEEEETGGGTTSTTT---------HHHHHTCCCSEEEEEESCC
T ss_pred             --------cCCEEEEEcHHHHHHHH-----HhcCCCCEEEEECCcCCCChHH---------HHHHHhcCCCeEEEEecCc
Confidence                    35899999998754422     2235689999999999976442         2244455678899999999


Q ss_pred             CcccHHH--HHHhcC---------------CCCCeEEEeccCCC---------------------ce----eEEEE-ee-
Q 037567          172 TEKVRID--IINSLK---------------LKNPYVTIASFDRK---------------------NL----FYGVK-VI-  207 (374)
Q Consensus       172 ~~~~~~~--~~~~~~---------------~~~~~~~~~~~~~~---------------------~~----~~~~~-~~-  207 (374)
                      .......  +...++               +.++..........                     ..    ...+. .. 
T Consensus       229 ~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~  308 (472)
T 2fwr_A          229 EREDGRHEILKEVVGGKVFELFPDSLAGKHLAKYTIKRIFVPLAEDERVEYEKREKVYKQFLRARGITLRRAEDFNKIVM  308 (472)
T ss_dssp             CCTTSGGGSHHHHTCCEEEECCHHHHTSCCCCSEEECCEEECCCHHHHHHTTTTTHHHHSCSSSCCCTTTCCSSSTTTTT
T ss_pred             cCCCCHHHHHHHHhCCeEeecCHHHHhcCcCCCeEEEEEEcCCCHHHHHHHHHHHHHHHHHHHhcCccccchhhHHHHHH
Confidence            8532110  111110               11111100000000                     00    00000 00 


Q ss_pred             ----c-----------------CCcchHHHHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHH
Q 037567          208 ----N-----------------RGQSFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKA  266 (374)
Q Consensus       208 ----~-----------------~~~~~~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~  266 (374)
                          .                 .......+.+.+++.. ..++++||||++.+.++.+++.|.     +..+||+++..+
T Consensus       309 ~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~l~~-~~~~k~lvF~~~~~~~~~l~~~l~-----~~~~~g~~~~~~  382 (472)
T 2fwr_A          309 ASGYDERAYEALRAWEEARRIAFNSKNKIRKLREILER-HRKDKIIIFTRHNELVYRISKVFL-----IPAITHRTSREE  382 (472)
T ss_dssp             TTCCSSSSSTTTHHHHHHHHHHHSCSHHHHHHHHHHHH-TSSSCBCCBCSCHHHHHHHHHHTT-----CCBCCSSSCSHH
T ss_pred             HhccCHHHHHHHHHHHHHHHHhhcChHHHHHHHHHHHh-CCCCcEEEEECCHHHHHHHHHHhC-----cceeeCCCCHHH
Confidence                0                 0011223445555555 468899999999999999999873     568999999999


Q ss_pred             HHHHHHhhhcCCeeEEEEeccccccccccCccEEEEECCCCChhHHHHhhccCCCCCCc-eEE--EEEeecc
Q 037567          267 REEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIA-SVC--WLYYARS  335 (374)
Q Consensus       267 r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~~~~p~s~~~~~Q~~GR~~R~~~~-g~~--~~~~~~~  335 (374)
                      |+++++.|++|+.+|||+|+++++|+|+|++++||++++|+|+..|.|++||+||.|++ +.+  +.++...
T Consensus       383 R~~~~~~F~~g~~~vLv~T~~~~~Gldlp~~~~Vi~~~~~~s~~~~~Q~~GR~~R~g~~k~~~~i~~lv~~~  454 (472)
T 2fwr_A          383 REEILEGFRTGRFRAIVSSQVLDEGIDVPDANVGVIMSGSGSAREYIQRLGRILRPSKGKKEAVLYELISRG  454 (472)
T ss_dssp             HHTHHHHHHHSSCSBCBCSSCCCSSSCSCCBSEEEEECCSSCCHHHHHHHHHSBCCCTTTCCEEEEEEEECS
T ss_pred             HHHHHHHHhCCCCCEEEEcCchhcCcccccCcEEEEECCCCCHHHHHHHHhhccCCCCCCceEEEEEEEeCC
Confidence            99999999999999999999999999999999999999999999999999999999865 443  4444443

>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=100.00  E-value=2.5e-41  Score=334.15  Aligned_cols=325  Identities=17%  Similarity=0.172  Sum_probs=185.3

Q ss_pred             HcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhcccccc--------CCcEEEEcchHHHHHHHHHHHHHc---
Q 037567            8 YFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVT--------GKTALVVSPLISLMQDQVMSLKQR---   76 (374)
Q Consensus         8 ~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~~--------~~~~lil~P~~~l~~q~~~~~~~~---   76 (374)
                      ..|+.+|+|+|.++++.+++++++++.+|||+|||++|+++++..        +.++||++|+++|+.||.+.++++   
T Consensus       243 l~~~~~~r~~Q~~ai~~il~g~~~ll~a~TGsGKTl~~~~~i~~~l~~~~~~~~~~vLvl~Pt~~L~~Q~~~~~~~~~~~  322 (936)
T 4a2w_A          243 VYETKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYEQQKNVFKHHFER  322 (936)
T ss_dssp             -----CCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHTTTTTCCSSCCCCEEEECSSHHHHHHHHHHHHHHHHT
T ss_pred             ccCCCCCCHHHHHHHHHHHcCCCEEEEeCCCchHHHHHHHHHHHHHHhccccCCCeEEEEeCCHHHHHHHHHHHHHHhcc
Confidence            345778999999999999999999999999999999998887653        778999999999999999999876   


Q ss_pred             -CCceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHH-HhcCccEEEEeccchhhcccCcchHHHHHHHH
Q 037567           77 -GINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKL-LKAGVCLFAVDEAHCISEWGHDFRLEYKQLDK  154 (374)
Q Consensus        77 -~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~-~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~  154 (374)
                       ++.+..+.++........ .....++|+|+||+++...+..  ... .+.++++||+||||++...+. +......+..
T Consensus       323 ~~~~v~~~~G~~~~~~~~~-~~~~~~~IvI~Tp~~L~~~l~~--~~~~~l~~~~liViDEaH~~~~~~~-~~~i~~~~~~  398 (936)
T 4a2w_A          323 QGYSVQGISGENFSNVSVE-KVIEDSDIIVVTPQILVNSFED--GTLTSLSIFTLMIFDECHNTTGNHP-YNVLMTRYLE  398 (936)
T ss_dssp             TTCCEEEECCC-----CCH-HHHHHCSEEEECHHHHHHHHHS--SSCCCGGGCSEEEEETGGGCSTTCH-HHHHHHHHHH
T ss_pred             cCceEEEEECCcchhhHHH-HhccCCCEEEecHHHHHHHHHc--CccccccCCCEEEEECccccCCCcc-HHHHHHHHHH
Confidence             777777776654333221 2223479999999998665432  112 345689999999999876442 2211111111


Q ss_pred             H-HH-hcCCCCeeEEEeecCccc----------HHHHHHhcCC-----------------CCCeEEEeccC--CCce---
Q 037567          155 L-RT-FLLGVPFVALTATATEKV----------RIDIINSLKL-----------------KNPYVTIASFD--RKNL---  200 (374)
Q Consensus       155 ~-~~-~~~~~~~i~~SaT~~~~~----------~~~~~~~~~~-----------------~~~~~~~~~~~--~~~~---  200 (374)
                      . .. ..+..++++||||+....          ...+...+..                 ..+........  ....   
T Consensus       399 ~~~~~~~~~~~~l~LSATp~~~~~~~l~~~~~~i~~L~~~L~~~~i~~~~~~~~~l~~~~~~p~~~~~~~~~~~~~~~~~  478 (936)
T 4a2w_A          399 QKFNSASQLPQILGLTASVGVGNAKNIEETIEHICSLCSYLDIQAISTVRENIQELQRFMNKPEIDVRLVKRRIHNPFAA  478 (936)
T ss_dssp             HHHTTCSCCCEEEEEESCCCCTTCCSHHHHHHHHHHHHHHHTCSEEECCCSSHHHHHHHSCCCCEEEEECCCCSCCHHHH
T ss_pred             HhhccCCCcCeEEEecCCcccccchhHHHHHHHHHHHHHhcCCceeecccccHHHHHHhccCCcceEEecccccCcHHHH
Confidence            1 11 133577999999996421          1111111211                 01111100000  0000   


Q ss_pred             ----------------e-------EEEEeecC------------------------------------------------
Q 037567          201 ----------------F-------YGVKVINR------------------------------------------------  209 (374)
Q Consensus       201 ----------------~-------~~~~~~~~------------------------------------------------  209 (374)
                                      .       ........                                                
T Consensus       479 ~l~~l~~~i~~~~~~~l~~~~l~~~~~~~~g~~~y~~~l~~l~k~~~~~~l~~~~~~~~~~~~l~~~~~~l~~~~~al~i  558 (936)
T 4a2w_A          479 IISNLMSETEALMRTIAYVDTLSQNSKKDFGTQNYEHWIVVTQRKCRLLQLEDKEEESRICRALFICTEHLRKYNDALII  558 (936)
T ss_dssp             HHHHHHHHHHHHHHHC------------CCSSHHHHHHHHHHHHHHHHCCCSCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHhhhhhhhccccccchHHHHHHHHHHHHHHHHhcccccchhhHHHHHHHHHHHHHHHHHHHHhh
Confidence                            0       00000000                                                


Q ss_pred             ---------------------------------------------------CcchHHHHHHHHHHhh---cCCCcEEEEe
Q 037567          210 ---------------------------------------------------GQSFVDELVQEILKSV---AGAGSIIVYC  235 (374)
Q Consensus       210 ---------------------------------------------------~~~~~~~~~~~~~~~~---~~~~~~lVf~  235 (374)
                                                                         ........+.+++...   ..+.++||||
T Consensus       559 ~~~~~~~~~~~~l~~~~~~~~~~~~~~~e~~l~~~~~~~~~~l~~~~~~~~~~~~K~~~L~~lL~~~~~~~~~~rvLIF~  638 (936)
T 4a2w_A          559 SEDARIIDALSYLTEFFTNVKNGPYTELEQHLTAKFQEKEPELIALSKDETNENPKLEELVCILDDAYRYNPQTRTLLFA  638 (936)
T ss_dssp             HHHSCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHTSTTCCCHHHHHHHHHHHHTTTSCTTCCEEEEE
T ss_pred             hcchhHHHHHHHHHHHHHHHhhccCCHHHHHHHHHHHHHHHHHHHhhhccCCCCHHHHHHHHHHHHHhccCCCCeEEEEe
Confidence                                                               0000111122222221   3568999999


Q ss_pred             cchhHHHHHHHHHHHc------------CCceeeeecCCChHHHHHHHHhhhc-CCeeEEEEeccccccccccCccEEEE
Q 037567          236 MTIKDVEEISKALKQL------------GVKAGTYHGQMGSKAREEAHRLFIR-DEIRVMVATMAFGMGIDKPDVRHVIH  302 (374)
Q Consensus       236 ~~~~~~~~l~~~l~~~------------~~~~~~~~~~~~~~~r~~~~~~f~~-g~~~ilv~t~~~~~G~d~~~~~~vi~  302 (374)
                      +++..++.+++.|.+.            |.....+||+++..+|..+++.|++ |+.+|||||+++++|+|+|++++||+
T Consensus       639 ~t~~~ae~L~~~L~~~~~l~~ik~~~l~G~~~~~~hg~m~~~eR~~il~~Fr~~g~~~VLVaT~~~~eGIDlp~v~~VI~  718 (936)
T 4a2w_A          639 KTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTSKDNRLLIATSVADEGIDIVQCNLVVL  718 (936)
T ss_dssp             SSHHHHHHHHHHHHHCSTTSSCCCEEC----------------------------CCSEEEEECC------CCCCSEEEE
T ss_pred             CCHHHHHHHHHHHhhCccccccceeEEecCCCcccCCCCCHHHHHHHHHHhhccCCeeEEEEeCchhcCCcchhCCEEEE
Confidence            9999999999999986            4455567889999999999999999 99999999999999999999999999


Q ss_pred             ECCCCChhHHHHhhccCCCCCCceEEEEEeeccCCC
Q 037567          303 YGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFA  338 (374)
Q Consensus       303 ~~~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~~~  338 (374)
                      +++|+|+..|+||+|| ||. ..|.++.++...+..
T Consensus       719 yD~p~s~~~~iQr~GR-GR~-~~g~vi~Li~~~t~e  752 (936)
T 4a2w_A          719 YEYSGNVTKMIQVRGR-GRA-AGSKCILVTSKTEVV  752 (936)
T ss_dssp             ESCCSCSHHHHCC---------CCCEEEEESCHHHH
T ss_pred             eCCCCCHHHHHHhcCC-CCC-CCCEEEEEEeCCCHH
Confidence            9999999999999999 998 678888888776543

>4a4z_A Antiviral helicase SKI2; hydrolase, ATPase, mRNA degradation, exosome; HET: ANP; 2.40A {Saccharomyces cerevisiae} PDB: 4a4k_A

Probab=100.00  E-value=2.3e-41  Score=334.06  Aligned_cols=308  Identities=22%  Similarity=0.282  Sum_probs=222.9

Q ss_pred             HHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhcccc---ccCCcEEEEcchHHHHHHHHHHHHHc--CCc
Q 037567            5 LKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPL---VTGKTALVVSPLISLMQDQVMSLKQR--GIN   79 (374)
Q Consensus         5 l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~---~~~~~~lil~P~~~l~~q~~~~~~~~--~~~   79 (374)
                      +...++|+ |+|+|.++++.+.+++++++.+|||||||++|++++.   ..+.+++|++|+++|+.|+++.+...  +..
T Consensus        32 ~~~~~~f~-l~~~Q~~aI~~il~g~~vlv~apTGsGKTlv~~~~i~~~~~~g~~vlvl~PtraLa~Q~~~~l~~~~~~~~  110 (997)
T 4a4z_A           32 PARSWPFE-LDTFQKEAVYHLEQGDSVFVAAHTSAGKTVVAEYAIAMAHRNMTKTIYTSPIKALSNQKFRDFKETFDDVN  110 (997)
T ss_dssp             CSCCCSSC-CCHHHHHHHHHHHTTCEEEEECCTTSCSHHHHHHHHHHHHHTTCEEEEEESCGGGHHHHHHHHHTTC--CC
T ss_pred             HHHhCCCC-CCHHHHHHHHHHHcCCCEEEEECCCCcHHHHHHHHHHHHHhcCCeEEEEeCCHHHHHHHHHHHHHHcCCCe
Confidence            45567886 8999999999999999999999999999998776655   35788999999999999999999986  456


Q ss_pred             eEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHHhc
Q 037567           80 AEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFL  159 (374)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~  159 (374)
                      +..+.++...        ....+|+|+||+.|...+..  ....+.++++|||||+|.+.+++....     +.++...+
T Consensus       111 v~~l~G~~~~--------~~~~~IlV~Tpe~L~~~l~~--~~~~l~~l~lvViDEaH~l~d~~~g~~-----~e~ii~~l  175 (997)
T 4a4z_A          111 IGLITGDVQI--------NPDANCLIMTTEILRSMLYR--GADLIRDVEFVIFDEVHYVNDQDRGVV-----WEEVIIML  175 (997)
T ss_dssp             EEEECSSCEE--------CTTSSEEEEEHHHHHHHHHH--TCSGGGGEEEEEECCTTCCCTTCTTCC-----HHHHHHHS
T ss_pred             EEEEeCCCcc--------CCCCCEEEECHHHHHHHHHh--CchhhcCCCEEEEECcccccccchHHH-----HHHHHHhc
Confidence            6666664422        23468999999988655432  223457889999999999988765532     22333333


Q ss_pred             -CCCCeeEEEeecCcccHHHHHHhcCC---CCCeEEEeccCCCceeEEEE-------eec--------------------
Q 037567          160 -LGVPFVALTATATEKVRIDIINSLKL---KNPYVTIASFDRKNLFYGVK-------VIN--------------------  208 (374)
Q Consensus       160 -~~~~~i~~SaT~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~-------~~~--------------------  208 (374)
                       ++.++++||||+++..  .+..+++.   .+..+.........+...+.       ...                    
T Consensus       176 ~~~v~iIlLSAT~~n~~--ef~~~l~~~~~~~~~vi~~~~r~~pl~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~  253 (997)
T 4a4z_A          176 PQHVKFILLSATVPNTY--EFANWIGRTKQKNIYVISTPKRPVPLEINIWAKKELIPVINQNSEFLEANFRKHKEILNGE  253 (997)
T ss_dssp             CTTCEEEEEECCCTTHH--HHHHHHHHHHTCCEEEEECSSCSSCEEEEEEETTEEEEEECTTCCBCHHHHHHHHHHHC--
T ss_pred             ccCCCEEEEcCCCCChH--HHHHHHhcccCCceEEEecCCCCccceEEEecCCcchhcccchhhhhHHHHHHHHHHhhcc
Confidence             4689999999987654  44555542   11111111111111111100       000                    


Q ss_pred             -----------------------------------------------------------------CCcchHHHHHHHHHH
Q 037567          209 -----------------------------------------------------------------RGQSFVDELVQEILK  223 (374)
Q Consensus       209 -----------------------------------------------------------------~~~~~~~~~~~~~~~  223 (374)
                                                                                       ........++..+..
T Consensus       254 ~~~~~~~~~~~~~~~~~~~~~~~~~~~rg~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~li~~l~~  333 (997)
T 4a4z_A          254 SAKGAPSKTDNGRGGSTARGGRGGSNTRDGRGGRGNSTRGGANRGGSRGAGAIGSNKRKFFTQDGPSKKTWPEIVNYLRK  333 (997)
T ss_dssp             ---------------------------------------------------------------CCCCTTHHHHHHHHHHH
T ss_pred             ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccchhHHHHHHHHHHh
Confidence                                                                             001112233333322


Q ss_pred             hhcCCCcEEEEecchhHHHHHHHHHHHcCC---------------------------------------ceeeeecCCCh
Q 037567          224 SVAGAGSIIVYCMTIKDVEEISKALKQLGV---------------------------------------KAGTYHGQMGS  264 (374)
Q Consensus       224 ~~~~~~~~lVf~~~~~~~~~l~~~l~~~~~---------------------------------------~~~~~~~~~~~  264 (374)
                        ....++||||+++..++.++..|.+.++                                       .+..+||++++
T Consensus       334 --~~~~~~IVF~~sr~~~e~la~~L~~~~~~~~~e~~~i~~~~~~~~~~l~~~d~~l~~~~~l~~~l~~gi~~~H~gl~~  411 (997)
T 4a4z_A          334 --RELLPMVVFVFSKKRCEEYADWLEGINFCNNKEKSQIHMFIEKSITRLKKEDRDLPQILKTRSLLERGIAVHHGGLLP  411 (997)
T ss_dssp             --TTCCSEEEECSCHHHHHHHHHTTTTCCCCCHHHHHHHHHHHHHHHTTSCHHHHTCHHHHHHHHHHTTTEEEECTTSCH
T ss_pred             --CCCCCEEEEECCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHhcchhhhcchhHHHHHHHhhcCeeeecCCCCH
Confidence              2457999999999999999999876554                                       46899999999


Q ss_pred             HHHHHHHHhhhcCCeeEEEEeccccccccccCccEEEEECCCC---------ChhHHHHhhccCCCCC--CceEEEEEee
Q 037567          265 KAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPK---------TLESYYQESGRCGRDG--IASVCWLYYA  333 (374)
Q Consensus       265 ~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~~~~p~---------s~~~~~Q~~GR~~R~~--~~g~~~~~~~  333 (374)
                      .+|..+++.|..|.++|||||+++++|+|+|+ ..||+.+.+.         |+.+|.||+|||||.|  ..|.+++++.
T Consensus       412 ~~R~~v~~~F~~G~~kVLvAT~~~a~GIDiP~-~~VVi~~~~k~dg~~~~~~s~~~y~Qr~GRAGR~G~~~~G~vi~l~~  490 (997)
T 4a4z_A          412 IVKELIEILFSKGFIKVLFATETFAMGLNLPT-RTVIFSSIRKHDGNGLRELTPGEFTQMAGRAGRRGLDSTGTVIVMAY  490 (997)
T ss_dssp             HHHHHHHHHHHTTCCSEEEECTHHHHSCCCCC-SEEEESCSEEEETTEEEECCHHHHHHHHGGGCCTTTCSSEEEEEECC
T ss_pred             HHHHHHHHHHHCCCCcEEEEchHhhCCCCCCC-ceEEEeccccccCccCCCCCHHHHhHHhcccccCCCCcceEEEEecC
Confidence            99999999999999999999999999999999 5556555554         9999999999999988  5788888873

>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=100.00  E-value=4.5e-40  Score=309.66  Aligned_cols=323  Identities=15%  Similarity=0.133  Sum_probs=227.1

Q ss_pred             hHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc---cCCcEEEEcchHHHHHHHHHHHHH----
Q 037567            3 STLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV---TGKTALVVSPLISLMQDQVMSLKQ----   75 (374)
Q Consensus         3 ~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~---~~~~~lil~P~~~l~~q~~~~~~~----   75 (374)
                      ++.++.+|| .|+|+|..+++.+++|+  +..++||+|||++|.+|++.   .+..++|++||++||.|..+++..    
T Consensus        74 ea~~r~lG~-~pt~VQ~~~ip~ll~G~--Iaea~TGeGKTlaf~LP~~l~aL~g~~vlVltptreLA~qd~e~~~~l~~~  150 (844)
T 1tf5_A           74 EASRRVTGM-FPFKVQLMGGVALHDGN--IAEMKTGEGKTLTSTLPVYLNALTGKGVHVVTVNEYLASRDAEQMGKIFEF  150 (844)
T ss_dssp             HHHHHHHSC-CCCHHHHHHHHHHHTTS--EEECCTTSCHHHHHHHHHHHHHTTSSCEEEEESSHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHcCC-CCcHHHHHhhHHHhCCC--EEEccCCcHHHHHHHHHHHHHHHcCCCEEEEeCCHHHHHHHHHHHHHHHhh
Confidence            345567999 89999999999999998  99999999999999999873   477899999999999998888765    


Q ss_pred             cCCceEEcCCCCCchhhhhhhhcCCeeEEEEcCccc-ccCchhh----HHHHHhcCccEEEEeccchhh-cccCcc----
Q 037567           76 RGINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKA-CIIPISF----WSKLLKAGVCLFAVDEAHCIS-EWGHDF----  145 (374)
Q Consensus        76 ~~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l-~~~~~~~----~~~~~~~~~~~vviDE~h~~~-~~~~~~----  145 (374)
                      .|+++.++.++......   .....++|+|+||+.| .+++...    .......++.++|+||||.+. +.+...    
T Consensus       151 lgl~v~~i~gg~~~~~r---~~~~~~dIv~gTpgrlgfD~L~D~m~~~~~~l~lr~~~~lVlDEaD~mLiDea~tplIis  227 (844)
T 1tf5_A          151 LGLTVGLNLNSMSKDEK---REAYAADITYSTNNELGFDYLRDNMVLYKEQMVQRPLHFAVIDEVDSILIDEARTPLIIS  227 (844)
T ss_dssp             TTCCEEECCTTSCHHHH---HHHHHSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCCCCEEEEETHHHHHTTTTTCEEEEE
T ss_pred             cCCeEEEEeCCCCHHHH---HHhcCCCEEEECchhhhHHHHHHhhhcchhhhcccCCCEEEECchhhhhhhccccchhhc
Confidence            47888877776543322   2224589999999998 3332221    123445778999999999986 443210    


Q ss_pred             ------hHHHHHHHHHHHhcC----------CCCee-----------------EEEeecCcc---c--------------
Q 037567          146 ------RLEYKQLDKLRTFLL----------GVPFV-----------------ALTATATEK---V--------------  175 (374)
Q Consensus       146 ------~~~~~~~~~~~~~~~----------~~~~i-----------------~~SaT~~~~---~--------------  175 (374)
                            ...+..+..+...++          ..++.                 ++|||.+.-   .              
T Consensus       228 g~~~~~~~~~~~i~~iv~~l~~~~~y~vd~k~rq~~lt~~g~~~~e~~~~i~~Lfsat~~~~~~~i~~al~A~~l~~~d~  307 (844)
T 1tf5_A          228 GQAAKSTKLYVQANAFVRTLKAEKDYTYDIKTKAVQLTEEGMTKAEKAFGIDNLFDVKHVALNHHINQALKAHVAMQKDV  307 (844)
T ss_dssp             EEEECCCHHHHHHHHHHTTCCSSSSBCCCSSSCCCCBCHHHHHHHHHHTTCSCTTSGGGHHHHHHHHHHHHHHHTCCBTT
T ss_pred             CCcccchhHHHHHHHHHHhCcccccceeccccceEEecHHHHHHHHHHhCccccCCCccchhHHHHHHHHHHHHHhhcCC
Confidence                  112334444444443          23333                 566664321   0              


Q ss_pred             -------------------------------------------------------------------------HHHHHHh
Q 037567          176 -------------------------------------------------------------------------RIDIINS  182 (374)
Q Consensus       176 -------------------------------------------------------------------------~~~~~~~  182 (374)
                                                                                               ...+...
T Consensus       308 dYiv~dg~v~ivDe~tgr~m~grr~sdGLhqaieake~v~I~~e~~t~a~It~q~~fr~y~kl~GmTGTa~te~~e~~~i  387 (844)
T 1tf5_A          308 DYVVEDGQVVIVDSFTGRLMKGRRYSEGLHQAIEAKEGLEIQNESMTLATITFQNYFRMYEKLAGMTGTAKTEEEEFRNI  387 (844)
T ss_dssp             TEEEETTEEEEBCTTTCCBCTTCCCSTTHHHHHHHHTTCCCCCCEEEEEEEEHHHHHTTSSEEEEEESCCGGGHHHHHHH
T ss_pred             ceEEecCeeEEeecccccccCCCccchhhHHHHhhcccceecccccccceeeHHHHHHHHhhhccCCcccchhHHHHHHH
Confidence                                                                                     0111111


Q ss_pred             cCCCCCeEEEeccCCCceeEE--EEeecCCcchHHHHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHHcCCceeeeec
Q 037567          183 LKLKNPYVTIASFDRKNLFYG--VKVINRGQSFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHG  260 (374)
Q Consensus       183 ~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~  260 (374)
                      +++.   +.....+.+.....  ...+.........++..+.+....+.++||||+++..++.+++.|.+.|+++..+||
T Consensus       388 Y~l~---vv~IPtn~p~~r~d~~d~v~~~~~~K~~al~~~i~~~~~~~~pvLVft~s~~~se~Ls~~L~~~gi~~~vLhg  464 (844)
T 1tf5_A          388 YNMQ---VVTIPTNRPVVRDDRPDLIYRTMEGKFKAVAEDVAQRYMTGQPVLVGTVAVETSELISKLLKNKGIPHQVLNA  464 (844)
T ss_dssp             HCCC---EEECCCSSCCCCEECCCEEESSHHHHHHHHHHHHHHHHHHTCCEEEEESCHHHHHHHHHHHHTTTCCCEEECS
T ss_pred             hCCc---eEEecCCCCcccccCCcEEEeCHHHHHHHHHHHHHHHHhcCCcEEEEECCHHHHHHHHHHHHHCCCCEEEeeC
Confidence            1111   00011111111111  011222223334444444443346789999999999999999999999999999999


Q ss_pred             CCChHHHHHHHHhhhcCCeeEEEEecccccccccc--------CccEEEEECCCCChhHHHHhhccCCCCCCceEEEEEe
Q 037567          261 QMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKP--------DVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYY  332 (374)
Q Consensus       261 ~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~--------~~~~vi~~~~p~s~~~~~Q~~GR~~R~~~~g~~~~~~  332 (374)
                      ++...++..+...++.|  .|+|||+++++|+|++        +..+||+++.|.|...|+||+||+||.|.+|.+++|+
T Consensus       465 ~~~~rEr~ii~~ag~~g--~VlIATdmAgRG~DI~l~~~V~~~ggl~VIn~d~p~s~r~y~hr~GRTGRqG~~G~s~~~v  542 (844)
T 1tf5_A          465 KNHEREAQIIEEAGQKG--AVTIATNMAGRGTDIKLGEGVKELGGLAVVGTERHESRRIDNQLRGRSGRQGDPGITQFYL  542 (844)
T ss_dssp             SCHHHHHHHHTTTTSTT--CEEEEETTSSTTCCCCCCTTSGGGTSEEEEESSCCSSHHHHHHHHTTSSGGGCCEEEEEEE
T ss_pred             CccHHHHHHHHHcCCCC--eEEEeCCccccCcCccccchhhhcCCcEEEEecCCCCHHHHHhhcCccccCCCCCeEEEEe
Confidence            98877777666666655  6999999999999999        7889999999999999999999999999999999999


Q ss_pred             eccC
Q 037567          333 ARSN  336 (374)
Q Consensus       333 ~~~~  336 (374)
                      +.+|
T Consensus       543 s~eD  546 (844)
T 1tf5_A          543 SMED  546 (844)
T ss_dssp             ETTS
T ss_pred             cHHH
Confidence            9887

>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=100.00  E-value=1.4e-40  Score=331.47  Aligned_cols=310  Identities=19%  Similarity=0.235  Sum_probs=217.9

Q ss_pred             hHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc----cCCcEEEEcchHHHHHHHHHHHHHc--
Q 037567            3 STLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV----TGKTALVVSPLISLMQDQVMSLKQR--   76 (374)
Q Consensus         3 ~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~----~~~~~lil~P~~~l~~q~~~~~~~~--   76 (374)
                      +.|.+.+||. | |+|.++++.+++++++++.||||||||+ |.++++.    .+.+++|++|+++|+.|+.+.++.+  
T Consensus        48 ~~~~~~~g~~-p-~iQ~~ai~~il~g~dvlv~apTGSGKTl-~~lp~l~~~~~~~~~~lil~PtreLa~Q~~~~l~~l~~  124 (1054)
T 1gku_B           48 EFFRKCVGEP-R-AIQKMWAKRILRKESFAATAPTGVGKTS-FGLAMSLFLALKGKRCYVIFPTSLLVIQAAETIRKYAE  124 (1054)
T ss_dssp             HHHHTTTCSC-C-HHHHHHHHHHHTTCCEECCCCBTSCSHH-HHHHHHHHHHTTSCCEEEEESCHHHHHHHHHHHHHHHT
T ss_pred             HHHHHhcCCC-H-HHHHHHHHHHHhCCCEEEEcCCCCCHHH-HHHHHHHHHhhcCCeEEEEeccHHHHHHHHHHHHHHHh
Confidence            4566779999 9 9999999999999999999999999997 6666554    4789999999999999999999865  


Q ss_pred             --CC----ceEEcCCCCCchhh--hhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHH
Q 037567           77 --GI----NAEFLGSAQTDSSV--QTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLE  148 (374)
Q Consensus        77 --~~----~~~~~~~~~~~~~~--~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~  148 (374)
                        +.    .+..+.++......  ....... ++|+|+||++|..++..      +.+++++|+||||++.+++..++..
T Consensus       125 ~~~i~~~~~v~~~~Gg~~~~~~~~~~~~l~~-~~IlV~TP~~L~~~l~~------L~~l~~lViDEah~~l~~~~~~~~i  197 (1054)
T 1gku_B          125 KAGVGTENLIGYYHGRIPKREKENFMQNLRN-FKIVITTTQFLSKHYRE------LGHFDFIFVDDVDAILKASKNVDKL  197 (1054)
T ss_dssp             TTCCSGGGSEEECCSSCCSHHHHHHHHSGGG-CSEEEEEHHHHHHCSTT------SCCCSEEEESCHHHHHTSTHHHHHH
T ss_pred             hcCCCccceEEEEeCCCChhhHHHHHhhccC-CCEEEEcHHHHHHHHHH------hccCCEEEEeChhhhhhccccHHHH
Confidence              34    55666665544432  1122223 89999999999877665      4588999999999998865433222


Q ss_pred             HHHHHHH-----HHhcCCCCeeEEEeecCccc--HHHHHH-hcCCCCCeEEEeccCCCceeEEEEeecCCcchHHHHHHH
Q 037567          149 YKQLDKL-----RTFLLGVPFVALTATATEKV--RIDIIN-SLKLKNPYVTIASFDRKNLFYGVKVINRGQSFVDELVQE  220 (374)
Q Consensus       149 ~~~~~~~-----~~~~~~~~~i~~SaT~~~~~--~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  220 (374)
                      +..+...     .......+.+++|||++...  ...+.. ........   ......++..... ...    ....+.+
T Consensus       198 ~~~lgf~~~~~~~~~~~~~q~~l~SAT~t~~~~~~~~~~~~~~~i~v~~---~~~~~~~i~~~~~-~~~----k~~~L~~  269 (1054)
T 1gku_B          198 LHLLGFHYDLKTKSWVGEARGCLMVSTATAKKGKKAELFRQLLNFDIGS---SRITVRNVEDVAV-NDE----SISTLSS  269 (1054)
T ss_dssp             HHHTTEEEETTTTEEEECCSSEEEECCCCSCCCTTHHHHHHHHCCCCSC---CEECCCCEEEEEE-SCC----CTTTTHH
T ss_pred             HHHhCcchhhhhhhcccCCceEEEEecCCCchhHHHHHhhcceEEEccC---cccCcCCceEEEe-chh----HHHHHHH
Confidence            2211100     00023578999999988862  011111 11111110   1111122222211 111    1223334


Q ss_pred             HHHhhcCCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEE----eccccccccccC
Q 037567          221 ILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVA----TMAFGMGIDKPD  296 (374)
Q Consensus       221 ~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~----t~~~~~G~d~~~  296 (374)
                      +++..  ++++||||+++..++.+++.|++. +.+..+||++     ..+++.|++|+.+||||    |+++++|+|+|+
T Consensus       270 ll~~~--~~~~LVF~~t~~~a~~l~~~L~~~-~~v~~lhg~~-----~~~l~~F~~G~~~VLVaTas~Tdv~~rGIDip~  341 (1054)
T 1gku_B          270 ILEKL--GTGGIIYARTGEEAEEIYESLKNK-FRIGIVTATK-----KGDYEKFVEGEIDHLIGTAHYYGTLVRGLDLPE  341 (1054)
T ss_dssp             HHTTS--CSCEEEEESSHHHHHHHHHTTTTS-SCEEECTTSS-----SHHHHHHHHTSCSEEEEECC------CCSCCTT
T ss_pred             HHhhc--CCCEEEEEcCHHHHHHHHHHHhhc-cCeeEEeccH-----HHHHHHHHcCCCcEEEEecCCCCeeEeccccCC
Confidence            44432  688999999999999999999988 8999999997     37788999999999999    899999999999


Q ss_pred             c-cEEEEECCC---------------------------------------------------------------------
Q 037567          297 V-RHVIHYGCP---------------------------------------------------------------------  306 (374)
Q Consensus       297 ~-~~vi~~~~p---------------------------------------------------------------------  306 (374)
                      + ++||+++.|                                                                     
T Consensus       342 VI~~VI~~~~P~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~  421 (1054)
T 1gku_B          342 RIRFAVFVGCPSFRVTIEDIDSLSPQMVKLLAYLYRNVDEIERLLPAVERHIDEVREILKKVMGKERPQAKDVVVREGEV  421 (1054)
T ss_dssp             TCCEEEEESCCEEEEECSCGGGSCHHHHHHHHTTTSCHHHHHTTCTTTSSCHHHHHHHHHHHHTTSCCSCSSSEEETTEE
T ss_pred             cccEEEEeCCCcccccccccccChHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHhccccccccceeEeecce
Confidence            5 999999999                                                                     


Q ss_pred             --CChhHHHHhhccCCCCCCceE--EEEEeeccCCC
Q 037567          307 --KTLESYYQESGRCGRDGIASV--CWLYYARSNFA  338 (374)
Q Consensus       307 --~s~~~~~Q~~GR~~R~~~~g~--~~~~~~~~~~~  338 (374)
                        .+..+|+||+||+||.|.+|.  ++.++..++..
T Consensus       422 ~~~~~~~yiQr~GRagR~g~~g~~~g~~~~~~~d~~  457 (1054)
T 1gku_B          422 IFPDLRTYIQGSGRTSRLFAGGLTKGASFLLEDDSE  457 (1054)
T ss_dssp             EEECHHHHHHHHHTTCCEETTEECCEEEEEECSCHH
T ss_pred             ecCcHHHHhhhhchhhhccCCCCceEEEEEEecCHH
Confidence              789999999999999877753  66666665543

>3h1t_A Type I site-specific restriction-modification system, R (restriction) subunit; hydrolase, restriction enzyme HSDR, ATP-binding; 2.30A {Vibrio vulnificus}

Probab=100.00  E-value=4.7e-40  Score=312.57  Aligned_cols=305  Identities=15%  Similarity=0.170  Sum_probs=194.2

Q ss_pred             CCchhHHHHHHHHHc----C-CCEEEEccCCCCchhhhhccccc------------cCCcEEEEcchHHHHHHHH-HHHH
Q 037567           13 VFRPYQKDVIQRIIE----K-RDCLVVMATGSGKSLCYQLPPLV------------TGKTALVVSPLISLMQDQV-MSLK   74 (374)
Q Consensus        13 ~~~~~Q~~~~~~~~~----~-~~~l~~a~tGsGKT~~~~l~~~~------------~~~~~lil~P~~~l~~q~~-~~~~   74 (374)
                      .|+|+|.++++.+++    + +++++++|||+|||++++..+..            ..+++||++|+++|+.|+. +.++
T Consensus       178 ~lr~~Q~~ai~~~~~~~~~~~~~~ll~~~TGsGKT~~~~~~~~~l~~~~~~~~~~~~~~~vlil~P~~~L~~Q~~~~~~~  257 (590)
T 3h1t_A          178 SPRYYQQIAINRAVQSVLQGKKRSLITMATGTGKTVVAFQISWKLWSARWNRTGDYRKPRILFLADRNVLVDDPKDKTFT  257 (590)
T ss_dssp             -CCHHHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHHHHHHHHHHTTCCSSCSSSCCCEEEEEC-----------CCT
T ss_pred             CchHHHHHHHHHHHHHHhcCCCceEEEecCCCChHHHHHHHHHHHHhcccccccccCCCeEEEEeCCHHHHHHHHHHHHH
Confidence            699999999999876    4 56899999999999886544321            4588999999999999999 8888


Q ss_pred             HcCCceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCch--hhHHHHHhcCccEEEEeccchhhcccCcchHHHHHH
Q 037567           75 QRGINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPI--SFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQL  152 (374)
Q Consensus        75 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~--~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~  152 (374)
                      .++.....+.+.         ......+|+|+||+++.....  .....+....+++||+||||++...+.      ..+
T Consensus       258 ~~~~~~~~~~~~---------~~~~~~~I~v~T~~~l~~~~~~~~~~~~~~~~~~~lvIiDEaH~~~~~~~------~~~  322 (590)
T 3h1t_A          258 PFGDARHKIEGG---------KVVKSREIYFAIYQSIASDERRPGLYKEFPQDFFDLIIIDECHRGSARDN------SNW  322 (590)
T ss_dssp             TTCSSEEECCC-----------CCSSCSEEEEEGGGC------CCGGGGSCTTSCSEEEESCCC---------------C
T ss_pred             hcchhhhhhhcc---------CCCCCCcEEEEEhhhhccccccccccccCCCCccCEEEEECCccccccch------HHH
Confidence            887766554422         123456999999999876532  112233345689999999999865321      234


Q ss_pred             HHHHHhcCCCCeeEEEeecCcccHHHHHHhcCCC----------------CCeEEEeccCCC--ceeEEE----------
Q 037567          153 DKLRTFLLGVPFVALTATATEKVRIDIINSLKLK----------------NPYVTIASFDRK--NLFYGV----------  204 (374)
Q Consensus       153 ~~~~~~~~~~~~i~~SaT~~~~~~~~~~~~~~~~----------------~~~~~~~~~~~~--~~~~~~----------  204 (374)
                      ..+...+++.++++|||||...........++..                ++..........  ......          
T Consensus       323 ~~il~~~~~~~~l~lTATP~~~~~~~~~~~f~~~~~~~~~~~~i~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  402 (590)
T 3h1t_A          323 REILEYFEPAFQIGMTATPLREDNRDTYRYFGNPIYTYSLRQGIDDGFLAPYRVHRVISEVDAAGWRPSKGDVDRFGREI  402 (590)
T ss_dssp             HHHHHHSTTSEEEEEESSCSCTTTHHHHHHSCSCSEEECHHHHHHHTSSCCEEEEEEEETTCC-----------------
T ss_pred             HHHHHhCCcceEEEeccccccccchhHHHHcCCceEecCHHHHhhCCccCCcEEEEeeeeeecccccccccccccccccc
Confidence            5556666778899999999976655555444321                111111000000  000000          


Q ss_pred             --EeecCC-----------cchHHHHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHHcCCc--------eeeeecCCC
Q 037567          205 --KVINRG-----------QSFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVK--------AGTYHGQMG  263 (374)
Q Consensus       205 --~~~~~~-----------~~~~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~--------~~~~~~~~~  263 (374)
                        ......           ...+.+.+.+.++....++++||||+++..++.+++.|.+.+..        +..+||+++
T Consensus       403 ~~~~~~~~~~~~~~~~~~r~~~i~~~l~~~l~~~~~~~k~lVF~~~~~~a~~l~~~L~~~~~~~~~~~~~~~~~i~g~~~  482 (590)
T 3h1t_A          403 PDGEYQTKDFERVIALKARTDAFAKHLTDFMKRTDRFAKTIVFCVDQEHADEMRRALNNLNSDLSRKHPDYVARVTSEEG  482 (590)
T ss_dssp             ------CCSHHHHHHHHHTHHHHHHHHHHHHHHHCTTSEEEEEESSHHHHHHHHHHHHHHTHHHHTTCTTSEEECSSTTH
T ss_pred             ccccCCHHHhhhHhcChHHHHHHHHHHHHHHHhcCCCccEEEEECCHHHHHHHHHHHHHhhhhhhccCCCeEEEEeCCCh
Confidence              000000           00111223333444456789999999999999999999876432        667888865


Q ss_pred             hHHHHHHHHhhhcCCee---EEEEeccccccccccCccEEEEECCCCChhHHHHhhccCCCCCC--ceEEEEEee
Q 037567          264 SKAREEAHRLFIRDEIR---VMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRDGI--ASVCWLYYA  333 (374)
Q Consensus       264 ~~~r~~~~~~f~~g~~~---ilv~t~~~~~G~d~~~~~~vi~~~~p~s~~~~~Q~~GR~~R~~~--~g~~~~~~~  333 (374)
                       ++|..+++.|++|+.+   |+++|+++++|+|+|++++||++++|+|+..|+||+||++|.+.  ++..+++++
T Consensus       483 -~~r~~~l~~F~~~~~~~~~ilvtt~~l~~GiDip~v~~Vi~~~~~~s~~~~~Q~iGR~~R~~~~~~k~~~~I~D  556 (590)
T 3h1t_A          483 -KIGKGHLSRFQELETSTPVILTTSQLLTTGVDAPTCKNVVLARVVNSMSEFKQIVGRGTRLREDYGKLWFNIID  556 (590)
T ss_dssp             -HHHHHHHHHHHCTTCCCCCEEEESSTTTTTCCCTTEEEEEEESCCCCHHHHHHHHTTSCCCBGGGTBSCEEEEE
T ss_pred             -HHHHHHHHHHhCCCCCCCEEEEECChhhcCccchheeEEEEEecCCChHHHHHHHhhhcccCccCCCCEEEEEe
Confidence             4799999999998765   88899999999999999999999999999999999999999875  444444444

>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=100.00  E-value=1.6e-39  Score=297.72  Aligned_cols=284  Identities=17%  Similarity=0.137  Sum_probs=202.7

Q ss_pred             CCCCCchhHHHHHHHHHcCCCE-EEEccCCCCchhhhhccccc----cCCcEEEEcchHHHHHHHHHHHHHcCCceEEcC
Q 037567           10 GYSVFRPYQKDVIQRIIEKRDC-LVVMATGSGKSLCYQLPPLV----TGKTALVVSPLISLMQDQVMSLKQRGINAEFLG   84 (374)
Q Consensus        10 ~~~~~~~~Q~~~~~~~~~~~~~-l~~a~tGsGKT~~~~l~~~~----~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~   84 (374)
                      |+.+++|.|+ +++.+++++++ ++.+|||||||++|+++++.    .+.+++|++|+++|+.|+.+.+...  .+....
T Consensus         1 G~~q~~~iq~-~i~~~l~~~~~~lv~a~TGsGKT~~~~~~~l~~~~~~~~~~lvl~Ptr~La~Q~~~~l~g~--~v~~~~   77 (451)
T 2jlq_A            1 GSAMGEPDYE-VDEDIFRKKRLTIMDLHPGAGKTKRILPSIVREALLRRLRTLILAPTRVVAAEMEEALRGL--PIRYQT   77 (451)
T ss_dssp             CCCCCSCCCC-CCGGGGSTTCEEEECCCTTSSCCTTHHHHHHHHHHHTTCCEEEEESSHHHHHHHHHHTTTS--CEEECC
T ss_pred             CCCCCCCcHH-HHHHHHhcCCeEEEECCCCCCHhhHHHHHHHHHHHhcCCcEEEECCCHHHHHHHHHHhcCc--eeeeee
Confidence            6789999986 79999998887 88999999999998888754    4779999999999999999998643  322221


Q ss_pred             CCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHHhcCCCCe
Q 037567           85 SAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPF  164 (374)
Q Consensus        85 ~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~~~~~~  164 (374)
                      .....      .......+.++|++.+...+   .....+.++++||+||+|++ +.+.  ......+ ......++.++
T Consensus        78 ~~~~~------~~~~~~~i~~~t~~~l~~~l---~~~~~l~~~~~iViDEah~~-~~~~--~~~~~~~-~~~~~~~~~~~  144 (451)
T 2jlq_A           78 PAVKS------DHTGREIVDLMCHATFTTRL---LSSTRVPNYNLIVMDEAHFT-DPCS--VAARGYI-STRVEMGEAAA  144 (451)
T ss_dssp             TTCSC------CCCSSCCEEEEEHHHHHHHH---HHCSCCCCCSEEEEETTTCC-SHHH--HHHHHHH-HHHHHTTSCEE
T ss_pred             ccccc------cCCCCceEEEEChHHHHHHh---hCcccccCCCEEEEeCCccC-Ccch--HHHHHHH-HHhhcCCCceE
Confidence            11111      12234568889988764322   12233568899999999987 2111  1111112 12223457899


Q ss_pred             eEEEeecCcccHHHHHHhcCCCCCeEEEeccCCCceeEEEEeecCCcchHHHHHHHHHHhhcCCCcEEEEecchhHHHHH
Q 037567          165 VALTATATEKVRIDIINSLKLKNPYVTIASFDRKNLFYGVKVINRGQSFVDELVQEILKSVAGAGSIIVYCMTIKDVEEI  244 (374)
Q Consensus       165 i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l  244 (374)
                      ++||||++.....    ........+.... ..+.         ........    .+..  ..+++||||++++.++.+
T Consensus       145 i~~SAT~~~~~~~----~~~~~~~~~~~~~-~~p~---------~~~~~~~~----~l~~--~~~~~lVF~~s~~~a~~l  204 (451)
T 2jlq_A          145 IFMTATPPGSTDP----FPQSNSPIEDIER-EIPE---------RSWNTGFD----WITD--YQGKTVWFVPSIKAGNDI  204 (451)
T ss_dssp             EEECSSCTTCCCS----SCCCSSCEEEEEC-CCCS---------SCCSSSCH----HHHH--CCSCEEEECSSHHHHHHH
T ss_pred             EEEccCCCccchh----hhcCCCceEecCc-cCCc---------hhhHHHHH----HHHh--CCCCEEEEcCCHHHHHHH
Confidence            9999999875432    1111222222211 1000         00011111    1222  467999999999999999


Q ss_pred             HHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEEEEEC--------------------
Q 037567          245 SKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYG--------------------  304 (374)
Q Consensus       245 ~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~~~--------------------  304 (374)
                      ++.|++.++.+..+|+++    ++++++.|.+|+.+|||||+++++|+|+|+ ++||+++                    
T Consensus       205 ~~~L~~~g~~~~~lh~~~----~~~~~~~f~~g~~~vLVaT~v~~~GiDip~-~~VI~~~~~~~~~~d~~~~~~l~~~~~  279 (451)
T 2jlq_A          205 ANCLRKSGKRVIQLSRKT----FDTEYPKTKLTDWDFVVTTDISEMGANFRA-GRVIDPRRCLKPVILTDGPERVILAGP  279 (451)
T ss_dssp             HHHHHTTTCCEEEECTTT----HHHHGGGGGSSCCSEEEECGGGGSSCCCCC-SEEEECCEEEEEEEECSSSCEEEEEEE
T ss_pred             HHHHHHcCCeEEECCHHH----HHHHHHhhccCCceEEEECCHHHhCcCCCC-CEEEECCCcccccccccccceeeeccc
Confidence            999999999999999864    357899999999999999999999999999 9999988                    


Q ss_pred             CCCChhHHHHhhccCCCCCC-ceEEEEEeec
Q 037567          305 CPKTLESYYQESGRCGRDGI-ASVCWLYYAR  334 (374)
Q Consensus       305 ~p~s~~~~~Q~~GR~~R~~~-~g~~~~~~~~  334 (374)
                      .|.+..+|+||+||+||.|. +|.+++++..
T Consensus       280 ~p~s~~~y~Qr~GRaGR~g~~~g~~~~~~~~  310 (451)
T 2jlq_A          280 IPVTPASAAQRRGRIGRNPAQEDDQYVFSGD  310 (451)
T ss_dssp             EECCHHHHHHHHTTSSCCTTCCCEEEEECSC
T ss_pred             ccCCHHHHHHhccccCCCCCCCccEEEEeCC
Confidence            99999999999999999998 7888877644

>2wv9_A Flavivirin protease NS2B regulatory subunit, FLAV protease NS3 catalytic subunit; nucleotide-binding, capsid protein; 2.75A {Murray valley encephalitis virus}

Probab=100.00  E-value=8.5e-40  Score=309.86  Aligned_cols=273  Identities=15%  Similarity=0.121  Sum_probs=197.5

Q ss_pred             CCchhHH-----HHHHHHH------cCCCEEEEccCCCCchhhhhccccc----cCCcEEEEcchHHHHHHHHHHHHHcC
Q 037567           13 VFRPYQK-----DVIQRII------EKRDCLVVMATGSGKSLCYQLPPLV----TGKTALVVSPLISLMQDQVMSLKQRG   77 (374)
Q Consensus        13 ~~~~~Q~-----~~~~~~~------~~~~~l~~a~tGsGKT~~~~l~~~~----~~~~~lil~P~~~l~~q~~~~~~~~~   77 (374)
                      .|+++|.     ++++.++      +++++++.||||||||++|+++++.    .+.+++|++||++|+.|+.+.+..++
T Consensus       215 ~pt~IQ~~~r~~~aIp~~l~~~~l~~g~dvlv~apTGSGKTl~~ll~il~~l~~~~~~~lilaPTr~La~Q~~~~l~~~~  294 (673)
T 2wv9_A          215 YVSAIVQGERVEEPVPEAYNPEMLKKRQLTVLDLHPGAGKTRRILPQIIKDAIQKRLRTAVLAPTRVVAAEMAEALRGLP  294 (673)
T ss_dssp             EEEEEECC-------CCCCCGGGGSTTCEEEECCCTTTTTTTTHHHHHHHHHHHTTCCEEEEESSHHHHHHHHHHTTTSC
T ss_pred             ccCceeeccccccchHHHhhHHHHhcCCeEEEEeCCCCCHHHHHHHHHHHHHHhCCCcEEEEccHHHHHHHHHHHHhcCC
Confidence            8999999     9999887      8999999999999999998887764    46789999999999999999988664


Q ss_pred             CceEEcCCCCCchhhhhhhhcCCeeE-EEEcCcccccCchhhHHH------HHhcCccEEEEeccchhhcccCcchHHHH
Q 037567           78 INAEFLGSAQTDSSVQTKAETGYFQL-LFMTPEKACIIPISFWSK------LLKAGVCLFAVDEAHCISEWGHDFRLEYK  150 (374)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~~~~i-~i~T~~~l~~~~~~~~~~------~~~~~~~~vviDE~h~~~~~~~~~~~~~~  150 (374)
                      +..  ...                .+ .++||+.+..++......      ..+.++++||+||+|++..   .......
T Consensus       295 i~~--~~~----------------~l~~v~tp~~ll~~l~~~~l~~~l~~~~~l~~l~lvViDEaH~~~~---~~~~~~~  353 (673)
T 2wv9_A          295 VRY--LTP----------------AVQREHSGNEIVDVMCHATLTHRLMSPLRVPNYNLFVMDEAHFTDP---ASIAARG  353 (673)
T ss_dssp             CEE--CCC-------------------CCCCSCCCEEEEEHHHHHHHHHSSSCCCCCSEEEEESTTCCCH---HHHHHHH
T ss_pred             eee--ecc----------------cccccCCHHHHHHHHHhhhhHHHHhcccccccceEEEEeCCcccCc---cHHHHHH
Confidence            321  100                01 167888776665432110      1357899999999999821   1111222


Q ss_pred             HHHHHHHhcCCCCeeEEEeecCcccHHHHHHhcCCCCCeEEEeccCCCceeEEEEeecCCcchHHHHHHHHHHhhcCCCc
Q 037567          151 QLDKLRTFLLGVPFVALTATATEKVRIDIINSLKLKNPYVTIASFDRKNLFYGVKVINRGQSFVDELVQEILKSVAGAGS  230 (374)
Q Consensus       151 ~~~~~~~~~~~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  230 (374)
                      .+..... ..+.++++||||+++....    ......+......          ......   ....+..+.+   .+++
T Consensus       354 ~l~~~~~-~~~~~vl~~SAT~~~~i~~----~~~~~~~i~~v~~----------~~~~~~---~~~~l~~l~~---~~~~  412 (673)
T 2wv9_A          354 YIATRVE-AGEAAAIFMTATPPGTSDP----FPDTNSPVHDVSS----------EIPDRA---WSSGFEWITD---YAGK  412 (673)
T ss_dssp             HHHHHHH-TTSCEEEEECSSCTTCCCS----SCCCSSCEEEEEC----------CCCSSC---CSSCCHHHHS---CCSC
T ss_pred             HHHHhcc-ccCCcEEEEcCCCChhhhh----hcccCCceEEEee----------ecCHHH---HHHHHHHHHh---CCCC
Confidence            3333222 2468999999999876421    1111111111110          000011   1112222222   5789


Q ss_pred             EEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEEEE--------
Q 037567          231 IIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIH--------  302 (374)
Q Consensus       231 ~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~--------  302 (374)
                      +||||++++.++.+++.|++.++.+..+||+    +|.++++.|.+|+.+|||||+++++|+|+| +++||+        
T Consensus       413 ~lVF~~s~~~~e~la~~L~~~g~~v~~lHg~----eR~~v~~~F~~g~~~VLVaTdv~e~GIDip-v~~VI~~g~~~~p~  487 (673)
T 2wv9_A          413 TVWFVASVKMSNEIAQCLQRAGKRVIQLNRK----SYDTEYPKCKNGDWDFVITTDISEMGANFG-ASRVIDCRKSVKPT  487 (673)
T ss_dssp             EEEECSSHHHHHHHHHHHHTTTCCEEEECSS----SHHHHGGGGGTCCCSEEEECGGGGTTCCCC-CSEEEECCEECCEE
T ss_pred             EEEEECCHHHHHHHHHHHHhCCCeEEEeChH----HHHHHHHHHHCCCceEEEECchhhcceeeC-CcEEEECCCcccce
Confidence            9999999999999999999999999999994    889999999999999999999999999999 999997        


Q ss_pred             ------------ECCCCChhHHHHhhccCCCC-CCceEEEEEe
Q 037567          303 ------------YGCPKTLESYYQESGRCGRD-GIASVCWLYY  332 (374)
Q Consensus       303 ------------~~~p~s~~~~~Q~~GR~~R~-~~~g~~~~~~  332 (374)
                                  ++.|.+..+|.||+||+||. ++.|.+++++
T Consensus       488 vi~da~~r~~ll~d~P~s~~~y~Qr~GRaGR~~g~~G~ai~l~  530 (673)
T 2wv9_A          488 ILDEGEGRVILSVPSAITSASAAQRRGRVGRNPSQIGDEYHYG  530 (673)
T ss_dssp             EECSTTCEEEECCSEECCHHHHHHHHTTSSCCSSCCCEEEEEC
T ss_pred             eeecccccceecccCCCCHHHHHHHhhccCCCCCCCCEEEEEE
Confidence                        56889999999999999999 7899999996

>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=100.00  E-value=4.3e-39  Score=293.53  Aligned_cols=269  Identities=14%  Similarity=0.103  Sum_probs=187.2

Q ss_pred             HHcCCCEEEEccCCCCchhhhhccccc----cCCcEEEEcchHHHHHHHHHHHHHcCCceEEcCCCCCchhhhhhhhcCC
Q 037567           25 IIEKRDCLVVMATGSGKSLCYQLPPLV----TGKTALVVSPLISLMQDQVMSLKQRGINAEFLGSAQTDSSVQTKAETGY  100 (374)
Q Consensus        25 ~~~~~~~l~~a~tGsGKT~~~~l~~~~----~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  100 (374)
                      +.+++++++.||||||||++|+++++.    .+.+++|++||++|+.|+.+.+..++..  ....               
T Consensus         5 l~~g~~vlv~a~TGSGKT~~~l~~~l~~~~~~~~~~lil~Ptr~La~Q~~~~l~~~~v~--~~~~---------------   67 (440)
T 1yks_A            5 LKKGMTTVLDFHPGAGKTRRFLPQILAECARRRLRTLVLAPTRVVLSEMKEAFHGLDVK--FHTQ---------------   67 (440)
T ss_dssp             TSTTCEEEECCCTTSSTTTTHHHHHHHHHHHTTCCEEEEESSHHHHHHHHHHTTTSCEE--EESS---------------
T ss_pred             hhCCCCEEEEcCCCCCHHHHHHHHHHHHHHhcCCeEEEEcchHHHHHHHHHHHhcCCeE--Eecc---------------
Confidence            457899999999999999999877764    4679999999999999999999865432  1111               


Q ss_pred             eeE-EEEcCcccccCchhhHHHHH--------hcCccEEEEeccchhhcccCcchHHHHHHHHHHHhcCCCCeeEEEeec
Q 037567          101 FQL-LFMTPEKACIIPISFWSKLL--------KAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATA  171 (374)
Q Consensus       101 ~~i-~i~T~~~l~~~~~~~~~~~~--------~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~SaT~  171 (374)
                       .+ .++||+.+..++..  ..+.        +.+++++|+||+|.+ +.+  +......+..... ..+.++++||||+
T Consensus        68 -~~~~v~Tp~~l~~~l~~--~~l~~~~~~~~~~~~l~~vViDEah~~-~~~--~~~~~~~~~~~~~-~~~~~~l~~SAT~  140 (440)
T 1yks_A           68 -AFSAHGSGREVIDAMCH--ATLTYRMLEPTRVVNWEVIIMDEAHFL-DPA--SIAARGWAAHRAR-ANESATILMTATP  140 (440)
T ss_dssp             -CCCCCCCSSCCEEEEEH--HHHHHHHTSSSCCCCCSEEEETTTTCC-SHH--HHHHHHHHHHHHH-TTSCEEEEECSSC
T ss_pred             -cceeccCCccceeeecc--cchhHhhhCcccccCccEEEEECcccc-Ccc--hHHHHHHHHHHhc-cCCceEEEEeCCC
Confidence             11 38899988776654  2222        578999999999998 211  1122222333222 2468899999999


Q ss_pred             CcccHHHHHHhcCCCCCeEEEeccCCCceeEEEEeecCCcchHHHHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHHc
Q 037567          172 TEKVRIDIINSLKLKNPYVTIASFDRKNLFYGVKVINRGQSFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQL  251 (374)
Q Consensus       172 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~  251 (374)
                      ++....    ......+......          .......   ...+..+.+   .++++||||++++.++.+++.|++.
T Consensus       141 ~~~~~~----~~~~~~~~~~~~~----------~~~~~~~---~~~~~~l~~---~~~~~lVF~~s~~~a~~l~~~L~~~  200 (440)
T 1yks_A          141 PGTSDE----FPHSNGEIEDVQT----------DIPSEPW---NTGHDWILA---DKRPTAWFLPSIRAANVMAASLRKA  200 (440)
T ss_dssp             TTCCCS----SCCCSSCEEEEEC----------CCCSSCC---SSSCHHHHH---CCSCEEEECSCHHHHHHHHHHHHHT
T ss_pred             Cchhhh----hhhcCCCeeEeee----------ccChHHH---HHHHHHHHh---cCCCEEEEeCCHHHHHHHHHHHHHc
Confidence            876431    1111111111100          0001111   111222222   4789999999999999999999999


Q ss_pred             CCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEEEE-------------------ECCCCChhHH
Q 037567          252 GVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIH-------------------YGCPKTLESY  312 (374)
Q Consensus       252 ~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~-------------------~~~p~s~~~~  312 (374)
                      ++++..+||    ++|..+++.|.+|+.+|||||+++++|+|+| +++||+                   ++.|.+..+|
T Consensus       201 ~~~v~~lhg----~~R~~~~~~F~~g~~~vLVaT~v~e~GiDip-v~~VI~~g~~~~pv~~~~~~~~vi~~~~p~~~~~~  275 (440)
T 1yks_A          201 GKSVVVLNR----KTFEREYPTIKQKKPDFILATDIAEMGANLC-VERVLDCRTAFKPVLVDEGRKVAIKGPLRISASSA  275 (440)
T ss_dssp             TCCEEECCS----SSCC--------CCCSEEEESSSTTCCTTCC-CSEEEECCEEEEEEEETTTTEEEEEEEEECCHHHH
T ss_pred             CCCEEEecc----hhHHHHHhhhcCCCceEEEECChhheeeccC-ceEEEeCCccceeeecccccceeeccccccCHHHH
Confidence            999999999    4688899999999999999999999999999 999886                   8889999999


Q ss_pred             HHhhccCCCC-CCceEEEEEe---eccCCCcccc
Q 037567          313 YQESGRCGRD-GIASVCWLYY---ARSNFAKGDF  342 (374)
Q Consensus       313 ~Q~~GR~~R~-~~~g~~~~~~---~~~~~~~~~~  342 (374)
                      .||+||+||. +..|.|++++   ++.+...++.
T Consensus       276 ~Qr~GR~GR~g~~~g~~~~l~~~~~~~~~~~l~~  309 (440)
T 1yks_A          276 AQRRGRIGRNPNRDGDSYYYSEPTSENNAHHVCW  309 (440)
T ss_dssp             HHHHTTSSCCTTCCCEEEEECSCCCCCCTTBHHH
T ss_pred             HHhccccCCCCCCCceEEEEeccCChhhhhhhhh
Confidence            9999999997 6899999997   4555544433

>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=100.00  E-value=7.6e-38  Score=293.77  Aligned_cols=323  Identities=19%  Similarity=0.180  Sum_probs=215.2

Q ss_pred             hHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc---cCCcEEEEcchHHHHHHHHHHHHHc---
Q 037567            3 STLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV---TGKTALVVSPLISLMQDQVMSLKQR---   76 (374)
Q Consensus         3 ~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~---~~~~~lil~P~~~l~~q~~~~~~~~---   76 (374)
                      ++-++.+|. .|+|.|..+++.+++|+  +..++||+|||++|.+|++.   .+..++|++||++||.|..+++..+   
T Consensus        65 ea~~R~lg~-~p~~VQ~~~i~~ll~G~--Iaem~TGsGKTlaf~LP~l~~~l~g~~vlVltPTreLA~Q~~e~~~~l~~~  141 (853)
T 2fsf_A           65 EASKRVFGM-RHFDVQLLGGMVLNERC--IAEMRTGEGKTLTATLPAYLNALTGKGVHVVTVNDYLAQRDAENNRPLFEF  141 (853)
T ss_dssp             HHHHHHHSC-CCCHHHHHHHHHHHSSE--EEECCTTSCHHHHHHHHHHHHHTTSSCCEEEESSHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHcCC-CCChHHHhhcccccCCe--eeeecCCchHHHHHHHHHHHHHHcCCcEEEEcCCHHHHHHHHHHHHHHHHh
Confidence            455677887 69999999999999998  99999999999999998763   4778999999999999988887653   


Q ss_pred             -CCceEEcCCCCCchhhhhhhhcCCeeEEEEcCccc-ccCchhhH----HHHHhcCccEEEEeccchhh-cccCcc----
Q 037567           77 -GINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKA-CIIPISFW----SKLLKAGVCLFAVDEAHCIS-EWGHDF----  145 (374)
Q Consensus        77 -~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l-~~~~~~~~----~~~~~~~~~~vviDE~h~~~-~~~~~~----  145 (374)
                       |+++..+.++.....   ......++|+|+||+.+ .+++....    ......++.++|+||+|.+. +.+...    
T Consensus       142 lgl~v~~i~GG~~~~~---r~~~~~~dIvvgTpgrl~fDyLrd~~~~~~~~~~~~~l~~lVlDEaD~mLiD~a~tpLIiS  218 (853)
T 2fsf_A          142 LGLTVGINLPGMPAPA---KREAYAADITYGTNNEYGFDYLRDNMAFSPEERVQRKLHYALVDEVDSILIDEARTPLIIS  218 (853)
T ss_dssp             TTCCEEECCTTCCHHH---HHHHHHSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCSCCEEEESCHHHHTTTTTTCEEEEE
T ss_pred             cCCeEEEEeCCCCHHH---HHHhcCCCEEEECCchhhHHHHHhhhhccHhHhcccCCcEEEECchHHHHHhcCccccccc
Confidence             788887777654322   12223589999999997 44433221    22345778999999999987 433210    


Q ss_pred             ------hHHHHHHHHHHHhcC---------------------CCCee------------------------EEEeecCcc
Q 037567          146 ------RLEYKQLDKLRTFLL---------------------GVPFV------------------------ALTATATEK  174 (374)
Q Consensus       146 ------~~~~~~~~~~~~~~~---------------------~~~~i------------------------~~SaT~~~~  174 (374)
                            ...+..+..+...++                     ..++.                        ++|||.+.-
T Consensus       219 g~~~~~~~~y~~i~~iv~~L~~~~~~~~~~~~~~~dy~vdek~rqv~lte~g~~~~e~~l~~~~l~~~~~~Lfsat~~~~  298 (853)
T 2fsf_A          219 GPAEDSSEMYKRVNKIIPHLIRQEKEDSETFQGEGHFSVDEKSRQVNLTERGLVLIEELLVKEGIMDEGESLYSPANIML  298 (853)
T ss_dssp             EC------------------------------------------------------------------------------
T ss_pred             CCCccchhHHHHHHHHHHhchhhhccccccccccccceeccccceEEEcHHHHHHHHHHHHhCCcccccccccCcccchH
Confidence                  001111222222221                     11221                        677775421


Q ss_pred             ---cHH--------------------------------------------------------------------------
Q 037567          175 ---VRI--------------------------------------------------------------------------  177 (374)
Q Consensus       175 ---~~~--------------------------------------------------------------------------  177 (374)
                         ...                                                                          
T Consensus       299 ~~~i~~al~A~~l~~~d~dYiV~d~~vviVde~tgR~m~grr~sdGLhQaieake~v~I~~e~~tla~It~qnyfr~Y~k  378 (853)
T 2fsf_A          299 MHHVTAALRAHALFTRDVDYIVKDGEVIIVDEHTGRTMQGRRWSDGLHQAVEAKEGVQIQNENQTLASITFQNYFRLYEK  378 (853)
T ss_dssp             ----------------------------------------------------------CCCCCEEEEEEEHHHHHTTSSE
T ss_pred             HHHHHHHHHHHHHhhcCccceeecCcEEEEecccCcccCCCccchhhhHHHHhcccceecccccccceeehHHHHhhhhh
Confidence               000                                                                          


Q ss_pred             -------------HHHHhcCCCCCeEEEeccCCCceeEEE--EeecCCcchHHHHHHHHHHhhcCCCcEEEEecchhHHH
Q 037567          178 -------------DIINSLKLKNPYVTIASFDRKNLFYGV--KVINRGQSFVDELVQEILKSVAGAGSIIVYCMTIKDVE  242 (374)
Q Consensus       178 -------------~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~lVf~~~~~~~~  242 (374)
                                   .+...+++.   +...+.+.+......  .++.........++..+......+.++||||+|+..++
T Consensus       379 l~GmTGTa~te~~ef~~iY~l~---vv~IPtn~p~~R~d~~d~v~~~~~~K~~al~~~i~~~~~~gqpvLVft~sie~se  455 (853)
T 2fsf_A          379 LAGMTGTADTEAFEFSSIYKLD---TVVVPTNRPMIRKDLPDLVYMTEAEKIQAIIEDIKERTAKGQPVLVGTISIEKSE  455 (853)
T ss_dssp             EEEEECTTCCCHHHHHHHHCCE---EEECCCSSCCCCEECCCEEESSHHHHHHHHHHHHHHHHTTTCCEEEEESSHHHHH
T ss_pred             hhcCCCCchhHHHHHHHHhCCc---EEEcCCCCCceeecCCcEEEeCHHHHHHHHHHHHHHHhcCCCCEEEEECcHHHHH
Confidence                         000000000   000001111111110  11222223333444444444346789999999999999


Q ss_pred             HHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCc-------------------------
Q 037567          243 EISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDV-------------------------  297 (374)
Q Consensus       243 ~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~-------------------------  297 (374)
                      .+++.|++.|+++..+||+....++..+.+.|+.|  .|+|||+++++|+|++..                         
T Consensus       456 ~Ls~~L~~~gi~~~vLnak~~~rEa~iia~agr~G--~VtIATnmAgRGtDI~l~gn~~~~~~~~~~~~~~~~~~~~~~~  533 (853)
T 2fsf_A          456 LVSNELTKAGIKHNVLNAKFHANEAAIVAQAGYPA--AVTIATNMAGRGTDIVLGGSWQAEVAALENPTAEQIEKIKADW  533 (853)
T ss_dssp             HHHHHHHHTTCCCEECCTTCHHHHHHHHHTTTSTT--CEEEEESCCSSCSCCCTTCCHHHHHHHCSSCCSSHHHHHHHHH
T ss_pred             HHHHHHHHCCCCEEEecCChhHHHHHHHHhcCCCC--eEEEecccccCCcCccCCCchHhhhhhcccchhHHHHHHHHHh
Confidence            99999999999999999998888888888889888  699999999999999873                         


Q ss_pred             ------------cEEEEECCCCChhHHHHhhccCCCCCCceEEEEEeeccC
Q 037567          298 ------------RHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSN  336 (374)
Q Consensus       298 ------------~~vi~~~~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~  336 (374)
                                  .+||+++.|.|...|.||+||+||.|.+|.+..|++.+|
T Consensus       534 ~~~~~~V~~~GGl~VI~te~pes~riy~qr~GRTGRqGd~G~s~~fls~eD  584 (853)
T 2fsf_A          534 QVRHDAVLEAGGLHIIGTERHESRRIDNQLRGRSGRQGDAGSSRFYLSMED  584 (853)
T ss_dssp             HHHHHHHHHTTSEEEEESSCCSSHHHHHHHHTTSSGGGCCEEEEEEEETTS
T ss_pred             hhhhhHHHhcCCcEEEEccCCCCHHHHHhhccccccCCCCeeEEEEecccH
Confidence                        599999999999999999999999999999999999877

>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=100.00  E-value=8.9e-39  Score=301.16  Aligned_cols=285  Identities=15%  Similarity=0.099  Sum_probs=200.6

Q ss_pred             CCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc----cCCcEEEEcchHHHHHHHHHHHHHcCCceEEcCCC
Q 037567           11 YSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV----TGKTALVVSPLISLMQDQVMSLKQRGINAEFLGSA   86 (374)
Q Consensus        11 ~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~----~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~   86 (374)
                      ...+.|+|..+++.+.+++++++.||||||||++|+++++.    .+.++||++|+++|+.|+.+.+...  .+......
T Consensus       169 ~~~~lpiq~~~i~~l~~g~dvlv~a~TGSGKT~~~~lpil~~l~~~~~~vLvl~PtreLa~Qi~~~l~~~--~v~~~~~~  246 (618)
T 2whx_A          169 ERIGEPDYEVDEDIFRKKRLTIMDLHPGAGKTKRILPSIVREALKRRLRTLILAPTRVVAAEMEEALRGL--PIRYQTPA  246 (618)
T ss_dssp             CCCCCCCCCCCGGGGSTTCEEEECCCTTSSTTTTHHHHHHHHHHHTTCCEEEEESSHHHHHHHHHHTTTS--CEEECCTT
T ss_pred             cccCCCccccCHHHHhcCCeEEEEcCCCCCHHHHHHHHHHHHHHhCCCeEEEEcChHHHHHHHHHHhcCC--ceeEeccc
Confidence            35678888888888889999999999999999999887764    4679999999999999999988743  22221110


Q ss_pred             CCchhhhhhhhcCCeeEEEEcCcccccCchh------hHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHHhcC
Q 037567           87 QTDSSVQTKAETGYFQLLFMTPEKACIIPIS------FWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLL  160 (374)
Q Consensus        87 ~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~------~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~~  160 (374)
                      .      .         .++||+.+..+...      ......+.++++||+||||++ +.+  +......+..... .+
T Consensus       247 l------~---------~~~tp~~~i~~~t~~~l~~~l~~~~~l~~~~~iViDEah~~-~~~--~~~~~~~i~~~l~-~~  307 (618)
T 2whx_A          247 V------K---------SDHTGREIVDLMCHATFTTRLLSSTRVPNYNLIVMDEAHFT-DPC--SVAARGYISTRVE-MG  307 (618)
T ss_dssp             S------S---------CCCCSSSCEEEEEHHHHHHHHHHCSSCCCCSEEEEESTTCC-SHH--HHHHHHHHHHHHH-HT
T ss_pred             c------e---------eccCCCceEEEEChHHHHHHHhccccccCCeEEEEECCCCC-Ccc--HHHHHHHHHHHhc-cc
Confidence            0      0         13445444433222      111112578999999999997 222  2222233332221 15


Q ss_pred             CCCeeEEEeecCcccHHHHHHhcCCCCCeEEEeccCCCceeEEEEeecCCcchHHHHHHHHHHhhcCCCcEEEEecchhH
Q 037567          161 GVPFVALTATATEKVRIDIINSLKLKNPYVTIASFDRKNLFYGVKVINRGQSFVDELVQEILKSVAGAGSIIVYCMTIKD  240 (374)
Q Consensus       161 ~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lVf~~~~~~  240 (374)
                      +.++++||||++.....    ........+.... ..+         ....   ..++..+.+   ..+++||||++++.
T Consensus       308 ~~q~il~SAT~~~~~~~----~~~~~~~~~~v~~-~~~---------~~~~---~~ll~~l~~---~~~~~LVF~~s~~~  367 (618)
T 2whx_A          308 EAAAIFMTATPPGSTDP----FPQSNSPIEDIER-EIP---------ERSW---NTGFDWITD---YQGKTVWFVPSIKA  367 (618)
T ss_dssp             SCEEEEECSSCTTCCCS----SCCCSSCEEEEEC-CCC---------SSCC---SSSCHHHHH---CCSCEEEECSSHHH
T ss_pred             CccEEEEECCCchhhhh----hhccCCceeeecc-cCC---------HHHH---HHHHHHHHh---CCCCEEEEECChhH
Confidence            78999999999876431    1111111111111 100         0111   112222222   47899999999999


Q ss_pred             HHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEE--------------------
Q 037567          241 VEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHV--------------------  300 (374)
Q Consensus       241 ~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~v--------------------  300 (374)
                      ++.+++.|++.+..+..+||+    +|.++++.|++|+.+|||||+++++|+|+| +++|                    
T Consensus       368 a~~l~~~L~~~g~~v~~lhg~----~R~~~l~~F~~g~~~VLVaTdv~~rGiDi~-v~~VId~g~~~~P~~~~~~~~~~~  442 (618)
T 2whx_A          368 GNDIANCLRKSGKRVIQLSRK----TFDTEYPKTKLTDWDFVVTTDISEMGANFR-AGRVIDPRRCLKPVILTDGPERVI  442 (618)
T ss_dssp             HHHHHHHHHHTTCCEEEECTT----THHHHTTHHHHSCCSEEEECGGGGTTCCCC-CSEEEECCEEEEEEEECSSSCEEE
T ss_pred             HHHHHHHHHHcCCcEEEEChH----HHHHHHHhhcCCCcEEEEECcHHHcCcccC-ceEEEECcceecceecccCCCceE
Confidence            999999999999999999984    788899999999999999999999999997 8887                    


Q ss_pred             EEECCCCChhHHHHhhccCCCCCC-ceEEEEEee---ccCCCccc
Q 037567          301 IHYGCPKTLESYYQESGRCGRDGI-ASVCWLYYA---RSNFAKGD  341 (374)
Q Consensus       301 i~~~~p~s~~~~~Q~~GR~~R~~~-~g~~~~~~~---~~~~~~~~  341 (374)
                      ++++.|.+..+|+||+||+||.|. .|.+++++.   +.|...+.
T Consensus       443 i~~d~P~s~~~yiQR~GRaGR~g~~~G~ai~l~~~~~~~d~~~l~  487 (618)
T 2whx_A          443 LAGPIPVTPASAAQRRGRIGRNPAQEDDQYVFSGDPLKNDEDHAH  487 (618)
T ss_dssp             EEEEEECCHHHHHHHHTTSSCCTTCCCEEEEECSCCCCCCTTCHH
T ss_pred             EcccccCCHHHHHHhccccCCCCCCCCeEEEEccCCchhhHHHHH
Confidence            677779999999999999999965 889999997   55554433

>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=100.00  E-value=4.2e-37  Score=289.12  Aligned_cols=327  Identities=14%  Similarity=0.084  Sum_probs=230.9

Q ss_pred             hhHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc---cCCcEEEEcchHHHHHHHHHHHHH---
Q 037567            2 VSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV---TGKTALVVSPLISLMQDQVMSLKQ---   75 (374)
Q Consensus         2 ~~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~---~~~~~lil~P~~~l~~q~~~~~~~---   75 (374)
                      .++.++.+|+ .|++.|..+++.+++|+  +..++||+|||++|.+|++.   .+..++|++|++.|+.|..+++..   
T Consensus       101 rEa~~R~lG~-rP~~VQ~~~ip~Ll~G~--Iaem~TGeGKTLa~~LP~~l~aL~g~~v~VvTpTreLA~Qdae~m~~l~~  177 (922)
T 1nkt_A          101 REAAWRVLDQ-RPFDVQVMGAAALHLGN--VAEMKTGEGKTLTCVLPAYLNALAGNGVHIVTVNDYLAKRDSEWMGRVHR  177 (922)
T ss_dssp             HHHHHHHHSC-CCCHHHHHHHHHHHTTE--EEECCTTSCHHHHTHHHHHHHHTTTSCEEEEESSHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCC-CCCHHHHHHHHhHhcCC--EEEecCCCccHHHHHHHHHHHHHhCCCeEEEeCCHHHHHHHHHHHHHHHh
Confidence            3466778999 89999999999999988  99999999999999988853   477899999999999988877764   


Q ss_pred             -cCCceEEcCCCCCchhhhhhhhcCCeeEEEEcCccc-ccCchhhH----HHHHhcCccEEEEeccchhh-cccCc----
Q 037567           76 -RGINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKA-CIIPISFW----SKLLKAGVCLFAVDEAHCIS-EWGHD----  144 (374)
Q Consensus        76 -~~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l-~~~~~~~~----~~~~~~~~~~vviDE~h~~~-~~~~~----  144 (374)
                       +|+.+.++.++......   .....++|+++||+.| .+++....    ......++.++|+||||.+. +.+..    
T Consensus       178 ~lGLsv~~i~gg~~~~~r---~~~y~~DIvygTpgrlgfDyLrD~m~~~~~~l~lr~l~~lIVDEaDsmLiDeartPLii  254 (922)
T 1nkt_A          178 FLGLQVGVILATMTPDER---RVAYNADITYGTNNEFGFDYLRDNMAHSLDDLVQRGHHYAIVDEVDSILIDEARTPLII  254 (922)
T ss_dssp             HTTCCEEECCTTCCHHHH---HHHHHSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCCCCEEEETTHHHHHTTGGGSCEEE
T ss_pred             hcCCeEEEEeCCCCHHHH---HHhcCCCEEEECchHhhHHHHHhhhhccHhhhccCCCCEEEEeChHHHHHhcCccceee
Confidence             47888887776543221   2223589999999987 34333221    23445678999999999986 33211    


Q ss_pred             ------chHHHHHHHHHHHhcC----------CCCee-----------------EEEeecCcccH--HHHH--H-hcCCC
Q 037567          145 ------FRLEYKQLDKLRTFLL----------GVPFV-----------------ALTATATEKVR--IDII--N-SLKLK  186 (374)
Q Consensus       145 ------~~~~~~~~~~~~~~~~----------~~~~i-----------------~~SaT~~~~~~--~~~~--~-~~~~~  186 (374)
                            ....+..+..+...++          ..++.                 ++|||.+.-..  ...+  . .+...
T Consensus       255 Sg~~~~~~~~y~~i~~iv~~L~~~~dy~vDek~rqv~Lte~G~~~~e~~l~i~~Lfsat~~~l~~~i~~aL~A~~l~~~d  334 (922)
T 1nkt_A          255 SGPADGASNWYTEFARLAPLMEKDVHYEVDLRKRTVGVHEKGVEFVEDQLGIDNLYEAANSPLVSYLNNALKAKELFSRD  334 (922)
T ss_dssp             EEECCCCHHHHHHHHHHHHHSCBTTTEEEETTTTEEEECHHHHHHHHHHHTCSSTTCSTTCCHHHHHHHHHHHHHHCCBT
T ss_pred             cCCCCcchhHHHHHHHHHHhCcccccceeccCcceEEecHhHHHHHHHHhCCccccCCcchhHHHHHHHHHHHHHHhhcc
Confidence                  1223345555555554          23444                 67777653111  0000  0 01100


Q ss_pred             -------------------------------------------CCeEEE-------------------------------
Q 037567          187 -------------------------------------------NPYVTI-------------------------------  192 (374)
Q Consensus       187 -------------------------------------------~~~~~~-------------------------------  192 (374)
                                                                 ......                               
T Consensus       335 ~dYiV~dg~vviVDe~TGR~m~grr~sdGLHQaieaKe~V~I~~e~~TlatIt~Qnyfr~Y~kL~GMTGTa~te~~Ef~~  414 (922)
T 1nkt_A          335 KDYIVRDGEVLIVDEFTGRVLIGRRYNEGMHQAIEAKEHVEIKAENQTLATITLQNYFRLYDKLAGMTGTAQTEAAELHE  414 (922)
T ss_dssp             TTEEECSSCEEEBCSSSCCBCTTCCCSTTHHHHHHHHTTCCCCCCEEEEEEECHHHHHTTSSEEEEEESCCGGGHHHHHH
T ss_pred             cceeeecCceEEEecccCcccCCccccchhhHHHhccccccccccccccceeehHHHHHhhhhhhccccCchhHHHHHHH
Confidence                                                       000000                               


Q ss_pred             --------eccCCCceeEE--EEeecCCcchHHHHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCC
Q 037567          193 --------ASFDRKNLFYG--VKVINRGQSFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQM  262 (374)
Q Consensus       193 --------~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~  262 (374)
                              .+.+.+.....  ..++.........++..+.+....+.++||||+++..++.+++.|++.|+++..+||+.
T Consensus       415 iY~l~vv~IPtn~p~~R~d~~d~v~~t~~~K~~al~~~i~~~~~~gqpvLVft~Sie~sE~Ls~~L~~~Gi~~~vLnak~  494 (922)
T 1nkt_A          415 IYKLGVVSIPTNMPMIREDQSDLIYKTEEAKYIAVVDDVAERYAKGQPVLIGTTSVERSEYLSRQFTKRRIPHNVLNAKY  494 (922)
T ss_dssp             HHCCEEEECCCSSCCCCEECCCEEESCHHHHHHHHHHHHHHHHHTTCCEEEEESCHHHHHHHHHHHHHTTCCCEEECSSC
T ss_pred             HhCCCeEEeCCCCCcccccCCcEEEeCHHHHHHHHHHHHHHHHhcCCcEEEEECCHHHHHHHHHHHHHCCCCEEEecCCh
Confidence                    00011111100  01122222334445555544445678999999999999999999999999999999998


Q ss_pred             ChHHHHHHHHhhhcCCeeEEEEeccccccccccCc---------------------------------------------
Q 037567          263 GSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDV---------------------------------------------  297 (374)
Q Consensus       263 ~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~---------------------------------------------  297 (374)
                      ...++..+.+.|+.|  .|+|||+++++|+|++..                                             
T Consensus       495 ~~rEa~iia~agr~G--~VtIATnmAgRGtDI~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  572 (922)
T 1nkt_A          495 HEQEATIIAVAGRRG--GVTVATNMAGRGTDIVLGGNVDFLTDQRLRERGLDPVETPEEYEAAWHSELPIVKEEASKEAK  572 (922)
T ss_dssp             HHHHHHHHHTTTSTT--CEEEEETTCSTTCCCCTTCCHHHHHHHHHHHTTCCTTTSHHHHHHHHHHHHHHHHHHTTHHHH
T ss_pred             hHHHHHHHHhcCCCC--eEEEecchhhcCccccCCCCHHHHHHHHHhhccccccccchhhHHHHHHHHHHHHHHHHHhhh
Confidence            777777778888887  699999999999999974                                             


Q ss_pred             -------cEEEEECCCCChhHHHHhhccCCCCCCceEEEEEeeccC
Q 037567          298 -------RHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSN  336 (374)
Q Consensus       298 -------~~vi~~~~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~  336 (374)
                             .+||+++.|.|...|.|++||+||.|.+|.+..|++.+|
T Consensus       573 ~V~~~GGlhVI~te~pes~riy~qr~GRTGRqGdpG~s~fflSleD  618 (922)
T 1nkt_A          573 EVIEAGGLYVLGTERHESRRIDNQLRGRSGRQGDPGESRFYLSLGD  618 (922)
T ss_dssp             HHHHTTSEEEEECSCCSSHHHHHHHHHTSSGGGCCEEEEEEEETTS
T ss_pred             HHHhcCCcEEEeccCCCCHHHHHHHhcccccCCCCeeEEEEechhH
Confidence                   589999999999999999999999999999999998876

>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=100.00  E-value=1.8e-37  Score=307.00  Aligned_cols=317  Identities=16%  Similarity=0.169  Sum_probs=221.6

Q ss_pred             CCchhHHHHHHHHHcC--CCEEEEccCCCCchhhhhccccc---c--CCcEEEEcchHHHHHHHHHHH-HHcCCceEEcC
Q 037567           13 VFRPYQKDVIQRIIEK--RDCLVVMATGSGKSLCYQLPPLV---T--GKTALVVSPLISLMQDQVMSL-KQRGINAEFLG   84 (374)
Q Consensus        13 ~~~~~Q~~~~~~~~~~--~~~l~~a~tGsGKT~~~~l~~~~---~--~~~~lil~P~~~l~~q~~~~~-~~~~~~~~~~~   84 (374)
                      +|+|||.+++..++..  .++++.++||+|||+.++..+..   .  ..++||+||+ .|+.||..++ +.++..+.++.
T Consensus       153 ~LrpyQ~eav~~~l~~~~~~~LLad~tGlGKTi~Ai~~i~~l~~~g~~~rvLIVvP~-sLl~Qw~~E~~~~f~l~v~v~~  231 (968)
T 3dmq_A          153 SLIPHQLNIAHDVGRRHAPRVLLADEVGLGKTIEAGMILHQQLLSGAAERVLIIVPE-TLQHQWLVEMLRRFNLRFALFD  231 (968)
T ss_dssp             CCCHHHHHHHHHHHHSSSCEEEECCCTTSCHHHHHHHHHHHHHHTSSCCCEEEECCT-TTHHHHHHHHHHHSCCCCEECC
T ss_pred             CCcHHHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHHHhCCCCeEEEEeCH-HHHHHHHHHHHHHhCCCEEEEc
Confidence            6999999999988874  47899999999999887655432   2  4589999999 9999999999 56777776665


Q ss_pred             CCCCchhhhh-hhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHHhcCCCC
Q 037567           85 SAQTDSSVQT-KAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVP  163 (374)
Q Consensus        85 ~~~~~~~~~~-~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~~~~~  163 (374)
                      +......... .......+|+|+|++.+...... ...+...++++||+||+|++.+.+......+..+..+..  ...+
T Consensus       232 ~~~~~~~~~~~~~~~~~~dIvI~T~~~L~~~~~~-~~~l~~~~~dlVIvDEAH~~kn~~~~~s~~~~~l~~L~~--~~~~  308 (968)
T 3dmq_A          232 DERYAEAQHDAYNPFDTEQLVICSLDFARRSKQR-LEHLCEAEWDLLVVDEAHHLVWSEDAPSREYQAIEQLAE--HVPG  308 (968)
T ss_dssp             HHHHHHHHHTTCSSSTTCSEEEECHHHHHTSTTT-THHHHTSCCCEEEECCSSCCCCBTTBCCHHHHHHHHHHT--TCSS
T ss_pred             cchhhhhhhhcccccccCCEEEEcHHHHhhCHHH-HHHhhhcCCCEEEehhhHhhcCCCCcchHHHHHHHHHhh--cCCc
Confidence            4322111111 12234579999999988654322 244556789999999999997655544333344444432  3457


Q ss_pred             eeEEEeecCcccHHHH---HHhcCCC---------------------------C--------------------------
Q 037567          164 FVALTATATEKVRIDI---INSLKLK---------------------------N--------------------------  187 (374)
Q Consensus       164 ~i~~SaT~~~~~~~~~---~~~~~~~---------------------------~--------------------------  187 (374)
                      +++|||||..+...++   ...+...                           .                          
T Consensus       309 ~L~LTATPi~n~~~el~sll~~L~p~~~~~~~~f~~~~~~~~~i~~~~~~l~~~~~~~~~~~~~L~~~l~~~~~~~l~~~  388 (968)
T 3dmq_A          309 VLLLTATPEQLGMESHFARLRLLDPNRFHDFAQFVEEQKNYCPVADAVAMLLAGNKLSNDELNMLGEMIGEQDIEPLLQA  388 (968)
T ss_dssp             EEESCSSCSSSCSSCTHHHHHHHCTTTCSSTHHHHHHHHHHHHHHHHHHTTTTSCCCCGGGTTSSTTTTCTTCSSTTGGG
T ss_pred             EEEEEcCCccCCHHHHHHHHHhcCccccCCHHHHHHHHHhHHHHHHHHHHHhccCCCCHHHHHHHHHHhcchhhHHHHhc
Confidence            9999999965321111   1100000                           0                          


Q ss_pred             --------------------------CeEEEe-ccCCCce------eEEEEe----------------------------
Q 037567          188 --------------------------PYVTIA-SFDRKNL------FYGVKV----------------------------  206 (374)
Q Consensus       188 --------------------------~~~~~~-~~~~~~~------~~~~~~----------------------------  206 (374)
                                                ...... .......      ......                            
T Consensus       389 ~~~~~~~~~~~~~~~i~~lld~~g~~~~l~r~~r~~i~~~p~r~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l  468 (968)
T 3dmq_A          389 ANSDSEDAQSARQELVSMLMDRHGTSRVLFRNTRNGVKGFPKRELHTIKLPLPTQYQTAIKVSGIMGARKSAEDRARDML  468 (968)
T ss_dssp             TCCCSSCSTTTHHHHHHHHGGGCTTTTTEECCCTTTCCCCCCCCCCEEEECCCHHHHHHHHHHHHTTCCSSGGGGTHHHH
T ss_pred             ccchhhhhHHHHHHHHHHHHHhhCcchhhhhhhhhhhcccChhheEeeecCCCHHHHHHHHHHhhhhhhhhhHHHHhhhc
Confidence                                      000000 0000000      000000                            


Q ss_pred             --------------ecCCcchHHHHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHH-cCCceeeeecCCChHHHHHHH
Q 037567          207 --------------INRGQSFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQ-LGVKAGTYHGQMGSKAREEAH  271 (374)
Q Consensus       207 --------------~~~~~~~~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~-~~~~~~~~~~~~~~~~r~~~~  271 (374)
                                    ...........+.+++.. ..++++||||+++..++.+++.|.+ .|+++..+||+++..+|..++
T Consensus       469 ~pe~~~~~l~~~~~~~~~~~~K~~~L~~ll~~-~~~~k~iVF~~~~~~~~~l~~~L~~~~g~~~~~lhG~~~~~~R~~~l  547 (968)
T 3dmq_A          469 YPERIYQEFEGDNATWWNFDPRVEWLMGYLTS-HRSQKVLVICAKAATALQLEQVLREREGIRAAVFHEGMSIIERDRAA  547 (968)
T ss_dssp             CSGGGTTTTTSSSCCTTTTSHHHHHHHHHHHH-TSSSCCCEECSSTHHHHHHHHHHHTTTCCCEEEECTTSCTTHHHHHH
T ss_pred             ChHHHHHHhhhhhhcccCccHHHHHHHHHHHh-CCCCCEEEEeCcHHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHH
Confidence                          001112234455555555 4788999999999999999999995 599999999999999999999


Q ss_pred             HhhhcCC--eeEEEEeccccccccccCccEEEEECCCCChhHHHHhhccCCCCCCceEEEEEeec
Q 037567          272 RLFIRDE--IRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYAR  334 (374)
Q Consensus       272 ~~f~~g~--~~ilv~t~~~~~G~d~~~~~~vi~~~~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~  334 (374)
                      +.|++|+  .+|||+|+++++|+|+|++++||++++|+++..|.|++||++|.|+.+.+++++..
T Consensus       548 ~~F~~g~~~~~vLvaT~v~~~GlDl~~~~~VI~~d~p~~~~~~~Q~~GR~~R~Gq~~~v~v~~~~  612 (968)
T 3dmq_A          548 AWFAEEDTGAQVLLCSEIGSEGRNFQFASHMVMFDLPFNPDLLEQRIGRLDRIGQAHDIQIHVPY  612 (968)
T ss_dssp             HHHHSTTSSCEEEECSCCTTCSSCCTTCCEEECSSCCSSHHHHHHHHHTTSCSSSCSCCEEEEEE
T ss_pred             HHHhCCCCcccEEEecchhhcCCCcccCcEEEEecCCCCHHHHHHHhhccccCCCCceEEEEEec
Confidence            9999998  99999999999999999999999999999999999999999999998866555433

>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=100.00  E-value=2.8e-38  Score=295.02  Aligned_cols=277  Identities=18%  Similarity=0.191  Sum_probs=200.4

Q ss_pred             CCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccccCCcEEEEcchHHHHHHHHHHHHH-cCCceEEcCCCCCchh
Q 037567           13 VFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVTGKTALVVSPLISLMQDQVMSLKQ-RGINAEFLGSAQTDSS   91 (374)
Q Consensus        13 ~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~-~~~~~~~~~~~~~~~~   91 (374)
                      .++++|.++++.+.+++++++.||||||||.++.++++.++.+++|++|+++|+.|+.+.+.+ ++.......+...   
T Consensus       217 P~~~~q~~i~~~L~~~~~vlv~ApTGSGKT~a~~l~ll~~g~~vLVl~PTReLA~Qia~~l~~~~g~~vg~~vG~~~---  293 (666)
T 3o8b_A          217 PVFTDNSSPPAVPQSFQVAHLHAPTGSGKSTKVPAAYAAQGYKVLVLNPSVAATLGFGAYMSKAHGIDPNIRTGVRT---  293 (666)
T ss_dssp             CSCCCCCSCCCCCSSCEEEEEECCTTSCTTTHHHHHHHHTTCCEEEEESCHHHHHHHHHHHHHHHSCCCEEECSSCE---
T ss_pred             CcHHHHHHHHHHHHcCCeEEEEeCCchhHHHHHHHHHHHCCCeEEEEcchHHHHHHHHHHHHHHhCCCeeEEECcEe---
Confidence            466777777777777889999999999999999999888888999999999999999988764 4555554444321   


Q ss_pred             hhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHHhcC-CCC--eeEEE
Q 037567           92 VQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLL-GVP--FVALT  168 (374)
Q Consensus        92 ~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~~-~~~--~i~~S  168 (374)
                           .....+|+|+||++|..   .  ..+.+.++++||+||+|.+.. +  +..   .+..+....+ ..+  +++||
T Consensus       294 -----~~~~~~IlV~TPGrLl~---~--~~l~l~~l~~lVlDEAH~l~~-~--~~~---~l~~Il~~l~~~~~~llil~S  357 (666)
T 3o8b_A          294 -----ITTGAPVTYSTYGKFLA---D--GGCSGGAYDIIICDECHSTDS-T--TIL---GIGTVLDQAETAGARLVVLAT  357 (666)
T ss_dssp             -----ECCCCSEEEEEHHHHHH---T--TSCCTTSCSEEEETTTTCCSH-H--HHH---HHHHHHHHTTTTTCSEEEEEE
T ss_pred             -----ccCCCCEEEECcHHHHh---C--CCcccCcccEEEEccchhcCc-c--HHH---HHHHHHHhhhhcCCceEEEEC
Confidence                 34557999999998731   1  233456789999999987642 2  222   2333333333 223  68889


Q ss_pred             eecCcccHHHHHHhcCCCCCeEEEeccCCCceeEEEEeecCCcchHHHHHHHHHHhhcCCCcEEEEecchhHHHHHHHHH
Q 037567          169 ATATEKVRIDIINSLKLKNPYVTIASFDRKNLFYGVKVINRGQSFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKAL  248 (374)
Q Consensus       169 aT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l  248 (374)
                      ||++....        ...+.+..........   ...... ...        + ....++++||||++++.++.+++.|
T Consensus       358 AT~~~~i~--------~~~p~i~~v~~~~~~~---i~~~~~-~~~--------l-~~~~~~~vLVFv~Tr~~ae~la~~L  416 (666)
T 3o8b_A          358 ATPPGSVT--------VPHPNIEEVALSNTGE---IPFYGK-AIP--------I-EAIRGGRHLIFCHSKKKCDELAAKL  416 (666)
T ss_dssp             SSCTTCCC--------CCCTTEEEEECBSCSS---EEETTE-EEC--------G-GGSSSSEEEEECSCHHHHHHHHHHH
T ss_pred             CCCCcccc--------cCCcceEEEeecccch---hHHHHh-hhh--------h-hhccCCcEEEEeCCHHHHHHHHHHH
Confidence            99987421        1221111111110000   000000 000        1 1126789999999999999999999


Q ss_pred             HHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEEE----------EEC-----------CCC
Q 037567          249 KQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVI----------HYG-----------CPK  307 (374)
Q Consensus       249 ~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi----------~~~-----------~p~  307 (374)
                      ++.++.+..+||+++.++       |.++..+|||||+++++|+|+| +++||          +++           .|.
T Consensus       417 ~~~g~~v~~lHG~l~q~e-------r~~~~~~VLVATdVaerGIDId-V~~VI~~Gl~~~~ViNyDydP~~gl~~~~~P~  488 (666)
T 3o8b_A          417 SGLGINAVAYYRGLDVSV-------IPTIGDVVVVATDALMTGYTGD-FDSVIDCNTCVTQTVDFSLDPTFTIETTTVPQ  488 (666)
T ss_dssp             HTTTCCEEEECTTSCGGG-------SCSSSCEEEEECTTHHHHCCCC-BSEEEECCEEEEEEEECCCSSSCEEEEEEEEC
T ss_pred             HhCCCcEEEecCCCCHHH-------HHhCCCcEEEECChHHccCCCC-CcEEEecCcccccccccccccccccccccCcC
Confidence            999999999999998875       4556669999999999999997 99988          455           799


Q ss_pred             ChhHHHHhhccCCCCCCceEEEEEeeccCCCc
Q 037567          308 TLESYYQESGRCGRDGIASVCWLYYARSNFAK  339 (374)
Q Consensus       308 s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~~~~  339 (374)
                      +..+|+||+||+|| +..|. +.++.+.+...
T Consensus       489 s~~syiQRiGRtGR-g~~G~-i~lvt~~e~~~  518 (666)
T 3o8b_A          489 DAVSRSQRRGRTGR-GRRGI-YRFVTPGERPS  518 (666)
T ss_dssp             BHHHHHHHHTTBCS-SSCEE-EEESCCCCBCS
T ss_pred             CHHHHHHHhccCCC-CCCCE-EEEEecchhhc
Confidence            99999999999999 88999 99998887665

>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=100.00  E-value=2.4e-36  Score=281.96  Aligned_cols=304  Identities=16%  Similarity=0.124  Sum_probs=207.8

Q ss_pred             CCchhHHHHHHHHH----cCCCEEEEccCCCCchhhhhccccc-----cCCcEEEEcchHHHHHHHHHHHHHcC--CceE
Q 037567           13 VFRPYQKDVIQRII----EKRDCLVVMATGSGKSLCYQLPPLV-----TGKTALVVSPLISLMQDQVMSLKQRG--INAE   81 (374)
Q Consensus        13 ~~~~~Q~~~~~~~~----~~~~~l~~a~tGsGKT~~~~l~~~~-----~~~~~lil~P~~~l~~q~~~~~~~~~--~~~~   81 (374)
                      .|+|||.++++.+.    .+.++++.++||+|||+.++..+..     ...++||+||+ +|+.||.+++.++.  ..+.
T Consensus        37 ~L~~~Q~~~v~~l~~~~~~~~~~ilad~~GlGKT~~ai~~i~~~~~~~~~~~~LIv~P~-~l~~qw~~e~~~~~~~~~v~  115 (500)
T 1z63_A           37 NLRPYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQTIAVFSDAKKENELTPSLVICPL-SVLKNWEEELSKFAPHLRFA  115 (500)
T ss_dssp             CCCHHHHHHHHHHHHHHHTTCCEEECCCTTSCHHHHHHHHHHHHHHTTCCSSEEEEECS-TTHHHHHHHHHHHCTTSCEE
T ss_pred             cchHHHHHHHHHHHHHhhCCCCEEEEeCCCCcHHHHHHHHHHHHHhcCCCCCEEEEccH-HHHHHHHHHHHHHCCCceEE
Confidence            59999999998763    4788999999999999876544332     24789999995 69999999999884  3444


Q ss_pred             EcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHHhcCC
Q 037567           82 FLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLG  161 (374)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~~~  161 (374)
                      +..+....      .....++|+|+||+.+....     .+....+++||+||||++.+.+..       .......++.
T Consensus       116 ~~~g~~~~------~~~~~~~ivi~t~~~l~~~~-----~l~~~~~~~vIvDEaH~~kn~~~~-------~~~~l~~l~~  177 (500)
T 1z63_A          116 VFHEDRSK------IKLEDYDIILTTYAVLLRDT-----RLKEVEWKYIVIDEAQNIKNPQTK-------IFKAVKELKS  177 (500)
T ss_dssp             ECSSSTTS------CCGGGSSEEEEEHHHHTTCH-----HHHTCCEEEEEEETGGGGSCTTSH-------HHHHHHTSCE
T ss_pred             EEecCchh------ccccCCcEEEeeHHHHhccc-----hhcCCCcCEEEEeCccccCCHhHH-------HHHHHHhhcc
Confidence            44433211      12245789999999986542     244567899999999999764421       2223333456


Q ss_pred             CCeeEEEeecCcccHHHHHHhcCC-----------------------------------CCCeEEEec------cCCCce
Q 037567          162 VPFVALTATATEKVRIDIINSLKL-----------------------------------KNPYVTIAS------FDRKNL  200 (374)
Q Consensus       162 ~~~i~~SaT~~~~~~~~~~~~~~~-----------------------------------~~~~~~~~~------~~~~~~  200 (374)
                      .+++++||||..+...++...+..                                   .+.......      ...+..
T Consensus       178 ~~~l~LTaTP~~n~~~el~~ll~~l~p~~~~~~~~f~~~~~~~~~~~~~~~~~~l~~~l~~~~lrr~k~~~~~~~~lp~~  257 (500)
T 1z63_A          178 KYRIALTGTPIENKVDDLWSIMTFLNPGLLGSYSEFKSKFATPIKKGDNMAKEELKAIISPFILRRTKYDKAIINDLPDK  257 (500)
T ss_dssp             EEEEEECSSCSTTCHHHHHHHHHHHSTTTTCCHHHHHTTTHHHHHTTCHHHHHHHHHHHTTTEECCCTTCHHHHTTSCSE
T ss_pred             CcEEEEecCCCCCCHHHHHHHHHHhCCCcCCCHHHHHHHhccccccccHHHHHHHHHHHhhHeeeecccccchhhcCCCC
Confidence            678999999977654433221110                                   000000000      011111


Q ss_pred             eEEEEeecCC--------------------------------------------------------cchHHHHHHHHHHh
Q 037567          201 FYGVKVINRG--------------------------------------------------------QSFVDELVQEILKS  224 (374)
Q Consensus       201 ~~~~~~~~~~--------------------------------------------------------~~~~~~~~~~~~~~  224 (374)
                      ..........                                                        ......+...+.+.
T Consensus       258 ~~~~v~~~l~~~~~~~y~~~~~~~~~~~~~~~~~~~~~~~~~~l~~lr~~~~~p~l~~~~~~~~~~s~K~~~l~~~l~~~  337 (500)
T 1z63_A          258 IETNVYCNLTPEQAAMYKAEVENLFNNIDSVTGIKRKGMILSTLLKLKQIVDHPALLKGGEQSVRRSGKMIRTMEIIEEA  337 (500)
T ss_dssp             EEEEEEECCCHHHHHHHHHHHHHHTTTTTTCCTHHHHHHHHHHHHHHHHHTTCTHHHHCSCCCSTTCHHHHHHHHHHHHH
T ss_pred             eEEEEEcCCCHHHHHHHHHHHHHHHHHHHhhhcccchHHHHHHHHHHHHHhCCHHHhcCccchhhcchhHHHHHHHHHHH
Confidence            1111110000                                                        01111122222233


Q ss_pred             hcCCCcEEEEecchhHHHHHHHHHHHc-CCceeeeecCCChHHHHHHHHhhhcC-Cee-EEEEeccccccccccCccEEE
Q 037567          225 VAGAGSIIVYCMTIKDVEEISKALKQL-GVKAGTYHGQMGSKAREEAHRLFIRD-EIR-VMVATMAFGMGIDKPDVRHVI  301 (374)
Q Consensus       225 ~~~~~~~lVf~~~~~~~~~l~~~l~~~-~~~~~~~~~~~~~~~r~~~~~~f~~g-~~~-ilv~t~~~~~G~d~~~~~~vi  301 (374)
                      ...+.++|||+++...++.+++.|.+. +..+..+||+++..+|..+++.|++| +.. +|++|.++++|+|+|.+++||
T Consensus       338 ~~~~~k~lvF~~~~~~~~~l~~~l~~~~~~~~~~~~g~~~~~~R~~~~~~F~~~~~~~vil~st~~~~~Glnl~~~~~vi  417 (500)
T 1z63_A          338 LDEGDKIAIFTQFVDMGKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKFIVLSVKAGGFGINLTSANRVI  417 (500)
T ss_dssp             HTTTCCEEEECSCHHHHHHHHHHHHHHHTCCCCEEETTSCHHHHHHHHHHHHHCTTCCCCEEECCCC-CCCCCTTCSEEE
T ss_pred             HccCCcEEEEEehHHHHHHHHHHHHHhhCCCeEEEECCCCHHHHHHHHHHhcCCCCCCEEEEecccccCCCchhhCCEEE
Confidence            346889999999999999999999885 99999999999999999999999998 454 788999999999999999999


Q ss_pred             EECCCCChhHHHHhhccCCCCCCceEE--EEEeecc
Q 037567          302 HYGCPKTLESYYQESGRCGRDGIASVC--WLYYARS  335 (374)
Q Consensus       302 ~~~~p~s~~~~~Q~~GR~~R~~~~g~~--~~~~~~~  335 (374)
                      ++++|+|+..+.|++||++|.|+.+.+  +.++..+
T Consensus       418 ~~d~~~~~~~~~Q~~gR~~R~Gq~~~v~v~~lv~~~  453 (500)
T 1z63_A          418 HFDRWWNPAVEDQATDRVYRIGQTRNVIVHKLISVG  453 (500)
T ss_dssp             ESSCCSCC---CHHHHTTTTTTTTSCEEEEEEEETT
T ss_pred             EeCCCCCcchHHHHHHHHHHcCCCCeeEEEEEEeCC
Confidence            999999999999999999999987655  4444443

>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=100.00  E-value=2.1e-37  Score=284.19  Aligned_cols=272  Identities=18%  Similarity=0.134  Sum_probs=181.8

Q ss_pred             HHHcCCCEEEEccCCCCchhhhhccccc----cCCcEEEEcchHHHHHHHHHHHHHcCCceEEcCCCCCchhhhhhhhcC
Q 037567           24 RIIEKRDCLVVMATGSGKSLCYQLPPLV----TGKTALVVSPLISLMQDQVMSLKQRGINAEFLGSAQTDSSVQTKAETG   99 (374)
Q Consensus        24 ~~~~~~~~l~~a~tGsGKT~~~~l~~~~----~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   99 (374)
                      .+.+++++++.+|||||||++|+++++.    .+.+++|++|+++|+.|+.+.+...  .+..........      ...
T Consensus        17 ~l~~~~~vlv~a~TGsGKT~~~~l~il~~~~~~~~~~lvl~Ptr~La~Q~~~~l~g~--~v~~~~~~~~~~------~t~   88 (459)
T 2z83_A           17 MLRKRQMTVLDLHPGSGKTRKILPQIIKDAIQQRLRTAVLAPTRVVAAEMAEALRGL--PVRYQTSAVQRE------HQG   88 (459)
T ss_dssp             GGSTTCEEEECCCTTSCTTTTHHHHHHHHHHHTTCCEEEEECSHHHHHHHHHHTTTS--CEEECC--------------C
T ss_pred             HHhcCCcEEEECCCCCCHHHHHHHHHHHHHHhCCCcEEEECchHHHHHHHHHHhcCc--eEeEEecccccC------CCC
Confidence            3455788999999999999999888775    5789999999999999999998733  222221111100      011


Q ss_pred             CeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHHhcCCCCeeEEEeecCcccHHHH
Q 037567          100 YFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEKVRIDI  179 (374)
Q Consensus       100 ~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~SaT~~~~~~~~~  179 (374)
                      ...+.++|.+.+..   .......+.++++||+||+|.+...   .......+.. ....++.++++||||++.....  
T Consensus        89 ~~~i~~~~~~~l~~---~l~~~~~l~~~~~iViDEaH~~~~~---~~~~~~~~~~-~~~~~~~~~il~SAT~~~~~~~--  159 (459)
T 2z83_A           89 NEIVDVMCHATLTH---RLMSPNRVPNYNLFVMDEAHFTDPA---SIAARGYIAT-KVELGEAAAIFMTATPPGTTDP--  159 (459)
T ss_dssp             CCSEEEEEHHHHHH---HHHSCC-CCCCSEEEESSTTCCSHH---HHHHHHHHHH-HHHTTSCEEEEECSSCTTCCCS--
T ss_pred             CcEEEEEchHHHHH---HhhccccccCCcEEEEECCccCCch---hhHHHHHHHH-HhccCCccEEEEEcCCCcchhh--
Confidence            12234444443221   1111123568899999999984210   0111111222 2223578999999999875421  


Q ss_pred             HHhcCCCCCeEEEeccCCCceeEEEEeecCCcchHHHHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHHcCCceeeee
Q 037567          180 INSLKLKNPYVTIASFDRKNLFYGVKVINRGQSFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYH  259 (374)
Q Consensus       180 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~  259 (374)
                        ......+.......          ............+    ..  .++++||||+++..++.+++.|++.++.+..+|
T Consensus       160 --~~~~~~pi~~~~~~----------~~~~~~~~~~~~l----~~--~~~~~LVF~~s~~~~~~l~~~L~~~g~~v~~lh  221 (459)
T 2z83_A          160 --FPDSNAPIHDLQDE----------IPDRAWSSGYEWI----TE--YAGKTVWFVASVKMGNEIAMCLQRAGKKVIQLN  221 (459)
T ss_dssp             --SCCCSSCEEEEECC----------CCSSCCSSCCHHH----HH--CCSCEEEECSCHHHHHHHHHHHHHTTCCEEEES
T ss_pred             --hccCCCCeEEeccc----------CCcchhHHHHHHH----Hh--cCCCEEEEeCChHHHHHHHHHHHhcCCcEEecC
Confidence              11112222211110          0001111111222    22  378999999999999999999999999999999


Q ss_pred             cCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEEEE--------------------ECCCCChhHHHHhhccC
Q 037567          260 GQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIH--------------------YGCPKTLESYYQESGRC  319 (374)
Q Consensus       260 ~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~--------------------~~~p~s~~~~~Q~~GR~  319 (374)
                      ++    +|..+++.|.+|+.+|||||+++++|+|+|+ ++||+                    ++.|.|..+|+||+||+
T Consensus       222 ~~----~R~~~~~~f~~g~~~iLVaT~v~~~GiDip~-~~VI~~G~~~~~~~~~~~~~~~~~~~d~p~s~~~~~QR~GRa  296 (459)
T 2z83_A          222 RK----SYDTEYPKCKNGDWDFVITTDISEMGANFGA-SRVIDCRKSVKPTILEEGEGRVILGNPSPITSASAAQRRGRV  296 (459)
T ss_dssp             TT----CCCCCGGGSSSCCCSEEEESSCC---CCCSC-SEEEECCEECCEEEECSSSCEEEECSCEECCHHHHHHHHTTS
T ss_pred             HH----HHHHHHhhccCCCceEEEECChHHhCeecCC-CEEEECCcccccccccccccccccccCCCCCHHHHHHhcccc
Confidence            85    6778899999999999999999999999999 99998                    56999999999999999


Q ss_pred             CCCCC-ceEEEEEeecc
Q 037567          320 GRDGI-ASVCWLYYARS  335 (374)
Q Consensus       320 ~R~~~-~g~~~~~~~~~  335 (374)
                      ||.|. +|.+++++.+.
T Consensus       297 GR~g~~~G~~~~~~~~~  313 (459)
T 2z83_A          297 GRNPNQVGDEYHYGGAT  313 (459)
T ss_dssp             SCCTTCCCEEEEECSCC
T ss_pred             CCCCCCCCeEEEEEccc
Confidence            99997 89999998876

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A

Probab=100.00  E-value=3.7e-36  Score=273.70  Aligned_cols=266  Identities=15%  Similarity=0.150  Sum_probs=176.7

Q ss_pred             cCCCEEEEccCCCCchhhhhcccc----ccCCcEEEEcchHHHHHHHHHHHHHcCCceEEcCCCCCchhhhhhhhcCCee
Q 037567           27 EKRDCLVVMATGSGKSLCYQLPPL----VTGKTALVVSPLISLMQDQVMSLKQRGINAEFLGSAQTDSSVQTKAETGYFQ  102 (374)
Q Consensus        27 ~~~~~l~~a~tGsGKT~~~~l~~~----~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  102 (374)
                      +++++++.+|||||||++|+++++    ..+.+++|++||++|+.|+.+.+.  +..+....+....      .......
T Consensus         1 kg~~~lv~a~TGsGKT~~~l~~~l~~~~~~g~~~lvl~Pt~~La~Q~~~~~~--~~~v~~~~~~~~~------~~~~~~~   72 (431)
T 2v6i_A            1 KRELTVLDLHPGAGKTRRVLPQLVREAVKKRLRTVILAPTRVVASEMYEALR--GEPIRYMTPAVQS------ERTGNEI   72 (431)
T ss_dssp             -CCEEEEECCTTSCTTTTHHHHHHHHHHHTTCCEEEEESSHHHHHHHHHHTT--TSCEEEC---------------CCCS
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHHHHHhCCCCEEEECcHHHHHHHHHHHhC--CCeEEEEecCccc------cCCCCce
Confidence            367899999999999999877766    357899999999999999998887  4444443332111      0111122


Q ss_pred             EEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHHhcCCCCeeEEEeecCcccHHHHHHh
Q 037567          103 LLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEKVRIDIINS  182 (374)
Q Consensus       103 i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~SaT~~~~~~~~~~~~  182 (374)
                      +.+.|.+.+..   .......+.++++||+||+|++...   .......+.... ..++.++++||||+++....    .
T Consensus        73 ~~~~~~~~l~~---~l~~~~~~~~l~~vViDEaH~~~~~---~~~~~~~l~~~~-~~~~~~~l~~SAT~~~~~~~----~  141 (431)
T 2v6i_A           73 VDFMCHSTFTM---KLLQGVRVPNYNLYIMDEAHFLDPA---SVAARGYIETRV-SMGDAGAIFMTATPPGTTEA----F  141 (431)
T ss_dssp             EEEEEHHHHHH---HHHHTCCCCCCSEEEEESTTCCSHH---HHHHHHHHHHHH-HTTSCEEEEEESSCTTCCCS----S
T ss_pred             EEEEchHHHHH---HHhcCccccCCCEEEEeCCccCCcc---HHHHHHHHHHHh-hCCCCcEEEEeCCCCcchhh----h
Confidence            33444443311   1112222578899999999997321   111122232222 23478999999999975321    1


Q ss_pred             cCCCCCeEEEeccCCCceeEEEEeecCCcchHHHHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCC
Q 037567          183 LKLKNPYVTIASFDRKNLFYGVKVINRGQSFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQM  262 (374)
Q Consensus       183 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~  262 (374)
                      .....+......          ..........   +. .+..  .++++||||++++.++.+++.|++.+..+..+||+ 
T Consensus       142 ~~~~~~i~~~~~----------~~~~~~~~~~---~~-~l~~--~~~~~lVF~~~~~~~~~l~~~L~~~~~~v~~lhg~-  204 (431)
T 2v6i_A          142 PPSNSPIIDEET----------RIPDKAWNSG---YE-WITE--FDGRTVWFVHSIKQGAEIGTCLQKAGKKVLYLNRK-  204 (431)
T ss_dssp             CCCSSCCEEEEC----------CCCSSCCSSC---CH-HHHS--CSSCEEEECSSHHHHHHHHHHHHHTTCCEEEESTT-
T ss_pred             cCCCCceeeccc----------cCCHHHHHHH---HH-HHHc--CCCCEEEEeCCHHHHHHHHHHHHHcCCeEEEeCCc-
Confidence            111111111110          0001111111   11 1222  36799999999999999999999999999999987 


Q ss_pred             ChHHHHHHHHhhhcCCeeEEEEeccccccccccCccE-----------------EEEECCCCChhHHHHhhccCCCCCCc
Q 037567          263 GSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRH-----------------VIHYGCPKTLESYYQESGRCGRDGIA  325 (374)
Q Consensus       263 ~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~-----------------vi~~~~p~s~~~~~Q~~GR~~R~~~~  325 (374)
                         +|.++++.|.+|+.+|||||+++++|+|+| +.+                 +|+++.|.+..+|.||+||+||.|..
T Consensus       205 ---~r~~~~~~f~~g~~~vLVaT~v~e~GiDip-~~~VI~~g~~~~~v~d~~~~vi~~~~p~~~~~~~Qr~GR~GR~g~~  280 (431)
T 2v6i_A          205 ---TFESEYPKCKSEKWDFVITTDISEMGANFK-ADRVIDPRKTIKPILLDGRVSMQGPIAITPASAAQRRGRIGRNPEK  280 (431)
T ss_dssp             ---THHHHTTHHHHSCCSEEEECGGGGTSCCCC-CSEEEECCEEEEEEEETTEEEEEEEEECCHHHHHHHHTTSSCCTTC
T ss_pred             ---cHHHHHHhhcCCCCeEEEECchHHcCcccC-CcEEEecCccccceecccceeecccccCCHHHHHHhhhccCCCCCC
Confidence               678899999999999999999999999999 544                 57788999999999999999999854


Q ss_pred             -eEEEEEe
Q 037567          326 -SVCWLYY  332 (374)
Q Consensus       326 -g~~~~~~  332 (374)
                       |.++++.
T Consensus       281 ~~~~~~~~  288 (431)
T 2v6i_A          281 LGDIYAYS  288 (431)
T ss_dssp             CCCEEEEC
T ss_pred             CCeEEEEc
Confidence             4444444

>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=100.00  E-value=8.3e-37  Score=294.74  Aligned_cols=314  Identities=14%  Similarity=0.152  Sum_probs=220.0

Q ss_pred             HHHhHcCCCCCchhHHHHHHHHHc-CCCEEEEccCCCCchhhhhccccc----c--CCcEEEEcchHHHHHHHHHHHHH-
Q 037567            4 TLKKYFGYSVFRPYQKDVIQRIIE-KRDCLVVMATGSGKSLCYQLPPLV----T--GKTALVVSPLISLMQDQVMSLKQ-   75 (374)
Q Consensus         4 ~l~~~~~~~~~~~~Q~~~~~~~~~-~~~~l~~a~tGsGKT~~~~l~~~~----~--~~~~lil~P~~~l~~q~~~~~~~-   75 (374)
                      .++. .+ ..|.+.|.++++.++. ++++++.||||||||+..-..++.    .  +.++++++|+++|+.|+.+.+.. 
T Consensus        86 ~l~~-r~-~lP~~~q~~~i~~~l~~~~~vii~gpTGSGKTtllp~ll~~~~~~~~~g~~ilvl~P~r~La~q~~~~l~~~  163 (773)
T 2xau_A           86 ILKI-RR-ELPVHAQRDEFLKLYQNNQIMVFVGETGSGKTTQIPQFVLFDEMPHLENTQVACTQPRRVAAMSVAQRVAEE  163 (773)
T ss_dssp             HHHH-HT-TSGGGGGHHHHHHHHHHCSEEEEECCTTSSHHHHHHHHHHHHHCGGGGTCEEEEEESCHHHHHHHHHHHHHH
T ss_pred             HHHH-hh-cCChHHHHHHHHHHHhCCCeEEEECCCCCCHHHHHHHHHHHhccccCCCceEEecCchHHHHHHHHHHHHHH
Confidence            4444 34 5688889999887776 567899999999999832111211    2  55699999999999999887754 


Q ss_pred             cCCceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccch-hhcccCcchHHHHHHHH
Q 037567           76 RGINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHC-ISEWGHDFRLEYKQLDK  154 (374)
Q Consensus        76 ~~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~-~~~~~~~~~~~~~~~~~  154 (374)
                      ++..+....+....   .........+|+++||+.+.....   ....+.++++||+||+|. ..+    .......+..
T Consensus       164 ~~~~v~~~vG~~i~---~~~~~~~~~~I~v~T~G~l~r~l~---~~~~l~~~~~lIlDEah~R~ld----~d~~~~~l~~  233 (773)
T 2xau_A          164 MDVKLGEEVGYSIR---FENKTSNKTILKYMTDGMLLREAM---EDHDLSRYSCIILDEAHERTLA----TDILMGLLKQ  233 (773)
T ss_dssp             TTCCBTTTEEEEET---TEEECCTTCSEEEEEHHHHHHHHH---HSTTCTTEEEEEECSGGGCCHH----HHHHHHHHHH
T ss_pred             hCCchhheecceec---cccccCCCCCEEEECHHHHHHHHh---hCccccCCCEEEecCccccccc----hHHHHHHHHH
Confidence            33332211111100   011122457899999998765432   234567899999999995 322    1222344555


Q ss_pred             HHHhcCCCCeeEEEeecCcccHHHHHHhcCCCCCeEEEeccCCCceeEEEEeecC-CcchHHHHHHHHHHhh--cCCCcE
Q 037567          155 LRTFLLGVPFVALTATATEKVRIDIINSLKLKNPYVTIASFDRKNLFYGVKVINR-GQSFVDELVQEILKSV--AGAGSI  231 (374)
Q Consensus       155 ~~~~~~~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~--~~~~~~  231 (374)
                      +....++.++++||||++..   .+..+++ ..+.+...... ..  ........ ........+..+....  ..++++
T Consensus       234 l~~~~~~~~iIl~SAT~~~~---~l~~~~~-~~~vi~v~gr~-~p--v~~~~~~~~~~~~~~~~l~~l~~~~~~~~~g~i  306 (773)
T 2xau_A          234 VVKRRPDLKIIIMSATLDAE---KFQRYFN-DAPLLAVPGRT-YP--VELYYTPEFQRDYLDSAIRTVLQIHATEEAGDI  306 (773)
T ss_dssp             HHHHCTTCEEEEEESCSCCH---HHHHHTT-SCCEEECCCCC-CC--EEEECCSSCCSCHHHHHHHHHHHHHHHSCSCEE
T ss_pred             HHHhCCCceEEEEeccccHH---HHHHHhc-CCCcccccCcc-cc--eEEEEecCCchhHHHHHHHHHHHHHHhcCCCCE
Confidence            55666688999999999653   3444443 22332222211 11  12222221 2223333444433321  257899


Q ss_pred             EEEecchhHHHHHHHHHHH-----------cCCceeeeecCCChHHHHHHHHhhh-----cCCeeEEEEecccccccccc
Q 037567          232 IVYCMTIKDVEEISKALKQ-----------LGVKAGTYHGQMGSKAREEAHRLFI-----RDEIRVMVATMAFGMGIDKP  295 (374)
Q Consensus       232 lVf~~~~~~~~~l~~~l~~-----------~~~~~~~~~~~~~~~~r~~~~~~f~-----~g~~~ilv~t~~~~~G~d~~  295 (374)
                      ||||+++.+++.+++.|.+           .++.+..+||+++.++|..+++.|.     +|..+|||||+++++|+|+|
T Consensus       307 LVF~~~~~~i~~l~~~L~~~~~~l~~~~~~~~~~v~~lhg~l~~~eR~~v~~~f~~~~~~~g~~kVlVAT~iae~GidIp  386 (773)
T 2xau_A          307 LLFLTGEDEIEDAVRKISLEGDQLVREEGCGPLSVYPLYGSLPPHQQQRIFEPAPESHNGRPGRKVVISTNIAETSLTID  386 (773)
T ss_dssp             EEECSCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECTTCCHHHHGGGGSCCCCCSSSSCCEEEEEECTHHHHTCCCT
T ss_pred             EEECCCHHHHHHHHHHHHHHHHhhcccccCCCeEEEEeCCCCCHHHHHHHHhhcccccCCCCceEEEEeCcHHHhCcCcC
Confidence            9999999999999999985           4678999999999999999999999     99999999999999999999


Q ss_pred             CccEEEEECC------------------CCChhHHHHhhccCCCCCCceEEEEEeeccCC
Q 037567          296 DVRHVIHYGC------------------PKTLESYYQESGRCGRDGIASVCWLYYARSNF  337 (374)
Q Consensus       296 ~~~~vi~~~~------------------p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~~  337 (374)
                      ++++||+++.                  |.|..+|.||+||+||. .+|.|+.++++.++
T Consensus       387 ~v~~VId~g~~k~~~yd~~~g~~~L~~~p~S~~s~~QR~GRaGR~-~~G~~~~l~~~~~~  445 (773)
T 2xau_A          387 GIVYVVDPGFSKQKVYNPRIRVESLLVSPISKASAQQRAGRAGRT-RPGKCFRLYTEEAF  445 (773)
T ss_dssp             TEEEEEECSEEEEEEEETTTTEEEEEEEECCHHHHHHHHHGGGSS-SSEEEEESSCHHHH
T ss_pred             CeEEEEeCCCccceeeccccCccccccccCCHHHHHhhccccCCC-CCCEEEEEecHHHh
Confidence            9999999887                  88999999999999999 79999999998766

>3rc3_A ATP-dependent RNA helicase SUPV3L1, mitochondrial; SUV3, nucleus, hydrolase; HET: ANP; 2.08A {Homo sapiens} PDB: 3rc8_A

Probab=100.00  E-value=2.1e-34  Score=272.20  Aligned_cols=280  Identities=16%  Similarity=0.200  Sum_probs=196.0

Q ss_pred             hHHHHHHHHHcCCCEEEEccCCCCchhhhhccccccCCcEEEEcchHHHHHHHHHHHHHcCCceEEcCCCCCchhhhhhh
Q 037567           17 YQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVTGKTALVVSPLISLMQDQVMSLKQRGINAEFLGSAQTDSSVQTKA   96 (374)
Q Consensus        17 ~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~   96 (374)
                      .|.......+++++++++||||||||..++.. +...+..+|++|+++|+.|+++.+...|..+....++.....   ..
T Consensus       144 ~~~~p~ar~l~rk~vlv~apTGSGKT~~al~~-l~~~~~gl~l~PtR~LA~Qi~~~l~~~g~~v~lltG~~~~iv---~T  219 (677)
T 3rc3_A          144 PNWYPDARAMQRKIIFHSGPTNSGKTYHAIQK-YFSAKSGVYCGPLKLLAHEIFEKSNAAGVPCDLVTGEERVTV---QP  219 (677)
T ss_dssp             GGGCHHHHTSCCEEEEEECCTTSSHHHHHHHH-HHHSSSEEEEESSHHHHHHHHHHHHHTTCCEEEECSSCEECC---ST
T ss_pred             hhhCHHHHhcCCCEEEEEcCCCCCHHHHHHHH-HHhcCCeEEEeCHHHHHHHHHHHHHhcCCcEEEEECCeeEEe---cC
Confidence            33333445567889999999999999844433 333466799999999999999999999988887766533311   00


Q ss_pred             hcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHHhc--CCCCeeEEEeecCcc
Q 037567           97 ETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFL--LGVPFVALTATATEK  174 (374)
Q Consensus        97 ~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~--~~~~~i~~SaT~~~~  174 (374)
                      .....+++++|++.+..          ...++++|+||+|.+.+.+..     ..+.......  ...+++++|||.+  
T Consensus       220 pGr~~~il~~T~e~~~l----------~~~v~lvVIDEaH~l~d~~~g-----~~~~~~l~~l~~~~i~il~~SAT~~--  282 (677)
T 3rc3_A          220 NGKQASHVSCTVEMCSV----------TTPYEVAVIDEIQMIRDPARG-----WAWTRALLGLCAEEVHLCGEPAAID--  282 (677)
T ss_dssp             TCCCCSEEEEEGGGCCS----------SSCEEEEEECSGGGGGCTTTH-----HHHHHHHHHCCEEEEEEEECGGGHH--
T ss_pred             CCcccceeEecHhHhhh----------cccCCEEEEecceecCCccch-----HHHHHHHHccCccceEEEeccchHH--
Confidence            11225788888876542          356799999999999765443     2233333322  3567889999842  


Q ss_pred             cHHHHHHhcCCCCCeEEEeccCCCceeEEEEeecCCcchHHHHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHHcCCc
Q 037567          175 VRIDIINSLKLKNPYVTIASFDRKNLFYGVKVINRGQSFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVK  254 (374)
Q Consensus       175 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~  254 (374)
                      ....+....+.  .... ....+.... .  .......        .+..  .....+|||++++.++.+++.|.+.+..
T Consensus       283 ~i~~l~~~~~~--~~~v-~~~~r~~~l-~--~~~~~l~--------~l~~--~~~g~iIf~~s~~~ie~la~~L~~~g~~  346 (677)
T 3rc3_A          283 LVMELMYTTGE--EVEV-RDYKRLTPI-S--VLDHALE--------SLDN--LRPGDCIVCFSKNDIYSVSRQIEIRGLE  346 (677)
T ss_dssp             HHHHHHHHHTC--CEEE-EECCCSSCE-E--ECSSCCC--------SGGG--CCTTEEEECSSHHHHHHHHHHHHHTTCC
T ss_pred             HHHHHHHhcCC--ceEE-EEeeecchH-H--HHHHHHH--------HHHh--cCCCCEEEEcCHHHHHHHHHHHHhcCCC
Confidence            22233333321  1111 111111100 0  0001000        0111  1334588899999999999999999999


Q ss_pred             eeeeecCCChHHHHHHHHhhhc--CCeeEEEEeccccccccccCccEEEEECC--------------CCChhHHHHhhcc
Q 037567          255 AGTYHGQMGSKAREEAHRLFIR--DEIRVMVATMAFGMGIDKPDVRHVIHYGC--------------PKTLESYYQESGR  318 (374)
Q Consensus       255 ~~~~~~~~~~~~r~~~~~~f~~--g~~~ilv~t~~~~~G~d~~~~~~vi~~~~--------------p~s~~~~~Q~~GR  318 (374)
                      +..+||+++.++|.++++.|++  |..+|||||+++++|+|+ ++++||+++.              |.+..+|.||+||
T Consensus       347 v~~lHG~L~~~~R~~~~~~F~~~~g~~~VLVATdi~e~GlDi-~v~~VI~~~~~k~~~~~~G~~~~~p~s~~~~~QR~GR  425 (677)
T 3rc3_A          347 SAVIYGSLPPGTKLAQAKKFNDPNDPCKILVATDAIGMGLNL-SIRRIIFYSLIKPSINEKGERELEPITTSQALQIAGR  425 (677)
T ss_dssp             CEEECTTSCHHHHHHHHHHHHCTTSSCCEEEECGGGGSSCCC-CBSEEEESCSBC-----------CBCCHHHHHHHHTT
T ss_pred             eeeeeccCCHHHHHHHHHHHHccCCCeEEEEeCcHHHCCcCc-CccEEEECCccccccccCCccccccCCHHHHHHHhcC
Confidence            9999999999999999999999  889999999999999999 8999999998              7799999999999


Q ss_pred             CCCCCCc---eEEEEEeec
Q 037567          319 CGRDGIA---SVCWLYYAR  334 (374)
Q Consensus       319 ~~R~~~~---g~~~~~~~~  334 (374)
                      +||.|..   |.|+.++..
T Consensus       426 AGR~g~~g~~G~v~~l~~~  444 (677)
T 3rc3_A          426 AGRFSSRFKEGEVTTMNHE  444 (677)
T ss_dssp             BTCTTSSCSSEEEEESSTT
T ss_pred             CCCCCCCCCCEEEEEEecc
Confidence            9999864   777766544

>3mwy_W Chromo domain-containing protein 1; SWI2/SNF2 ATPase, double chromodomains, hydrolase; HET: ATG; 3.70A {Saccharomyces cerevisiae}

Probab=100.00  E-value=3.9e-34  Score=279.35  Aligned_cols=311  Identities=15%  Similarity=0.148  Sum_probs=214.7

Q ss_pred             CCchhHHHHHHHHH----cCCCEEEEccCCCCchhhhhcccc------ccCCcEEEEcchHHHHHHHHHHHHHcC--Cce
Q 037567           13 VFRPYQKDVIQRII----EKRDCLVVMATGSGKSLCYQLPPL------VTGKTALVVSPLISLMQDQVMSLKQRG--INA   80 (374)
Q Consensus        13 ~~~~~Q~~~~~~~~----~~~~~l~~a~tGsGKT~~~~l~~~------~~~~~~lil~P~~~l~~q~~~~~~~~~--~~~   80 (374)
                      +|+|||.+++..+.    .+.++++..+||+|||+.++..+.      ....++||||| .+++.||.+++.++.  ..+
T Consensus       236 ~Lr~yQ~egv~~l~~~~~~~~~~ILademGlGKT~~ai~~i~~l~~~~~~~~~~LIV~P-~sll~qW~~E~~~~~p~~~v  314 (800)
T 3mwy_W          236 ELRDFQLTGINWMAFLWSKGDNGILADEMGLGKTVQTVAFISWLIFARRQNGPHIIVVP-LSTMPAWLDTFEKWAPDLNC  314 (800)
T ss_dssp             CCCTHHHHHHHHHHHHHTTTCCEEECCCTTSSTTHHHHHHHHHHHHHHSCCSCEEEECC-TTTHHHHHHHHHHHSTTCCE
T ss_pred             CcCHHHHHHHHHHHHHhhcCCCEEEEeCCCcchHHHHHHHHHHHHHhcCCCCCEEEEEC-chHHHHHHHHHHHHCCCceE
Confidence            69999999998776    688999999999999977654432      23678999999 578999999999885  344


Q ss_pred             EEcCCCCCchhhhhh-----------hhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHH
Q 037567           81 EFLGSAQTDSSVQTK-----------AETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEY  149 (374)
Q Consensus        81 ~~~~~~~~~~~~~~~-----------~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~  149 (374)
                      .+..+..........           .....++|+|+|++.+...    ...+....+++||+||||++.+.+.      
T Consensus       315 ~~~~g~~~~r~~~~~~~~~~~~~~~~~~~~~~dvvitTy~~l~~~----~~~l~~~~w~~vIvDEaH~lkn~~s------  384 (800)
T 3mwy_W          315 ICYMGNQKSRDTIREYEFYTNPRAKGKKTMKFNVLLTTYEYILKD----RAELGSIKWQFMAVDEAHRLKNAES------  384 (800)
T ss_dssp             EECCCSSHHHHHHHHHHSCSCC-----CCCCCSEEEECTTHHHHT----HHHHHTSEEEEEEETTGGGGCCSSS------
T ss_pred             EEEeCCHHHHHHHHHHHhhccccccccccccCCEEEecHHHHHhh----HHHHhcCCcceeehhhhhhhcCchh------
Confidence            444443322221111           2234678999999988543    2334445789999999999976443      


Q ss_pred             HHHHHHHHhcCCCCeeEEEeecCcccHHHHHHhcCCCCC-------------------------------eEEEe-cc--
Q 037567          150 KQLDKLRTFLLGVPFVALTATATEKVRIDIINSLKLKNP-------------------------------YVTIA-SF--  195 (374)
Q Consensus       150 ~~~~~~~~~~~~~~~i~~SaT~~~~~~~~~~~~~~~~~~-------------------------------~~~~~-~~--  195 (374)
                       ........+....++++||||..+...++...+..-.+                               .+... ..  
T Consensus       385 -~~~~~l~~l~~~~rl~LTgTPiqN~l~el~~ll~fL~p~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~p~~lRR~k~dv  463 (800)
T 3mwy_W          385 -SLYESLNSFKVANRMLITGTPLQNNIKELAALVNFLMPGRFTIDQEIDFENQDEEQEEYIHDLHRRIQPFILRRLKKDV  463 (800)
T ss_dssp             -HHHHHHTTSEEEEEEEECSCCCSSCSHHHHHHHHHHCSCCC---------CCTTHHHHHHHHHHHTTGGGEEECCGGGG
T ss_pred             -HHHHHHHHhhhccEEEeeCCcCCCCHHHHHHHHHHhCccccCchhhhcccccchhHHHHHHHHHHHHhHHHhhhhHHhh
Confidence             22333344456678999999966544433332111000                               00000 00  


Q ss_pred             --CCCceeEEEEeecCC---------------------------------------------------------------
Q 037567          196 --DRKNLFYGVKVINRG---------------------------------------------------------------  210 (374)
Q Consensus       196 --~~~~~~~~~~~~~~~---------------------------------------------------------------  210 (374)
                        ..+............                                                               
T Consensus       464 ~~~LP~k~~~~v~v~ls~~q~~~Y~~i~~~~~~~l~~~~~~~~~~~l~~l~~Lrk~~~hp~l~~~~~~~~~~~~~~~~~~  543 (800)
T 3mwy_W          464 EKSLPSKTERILRVELSDVQTEYYKNILTKNYSALTAGAKGGHFSLLNIMNELKKASNHPYLFDNAEERVLQKFGDGKMT  543 (800)
T ss_dssp             TTTSCCEEEEEEEECCCHHHHHHHHHHHHHCCC----------CTHHHHHHHHHHHHHCGGGSSSHHHHHCCCC----CC
T ss_pred             hhccCCcEEEEEEeCCCHHHHHHHHHHHHHHHHHHhhccccchhhHHHHHHHHHHHhcChhhhcchHHHHHHhccccccc
Confidence              000000000000000                                                               


Q ss_pred             ----------cchHHHHHHHHHHhh-cCCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCe
Q 037567          211 ----------QSFVDELVQEILKSV-AGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEI  279 (374)
Q Consensus       211 ----------~~~~~~~~~~~~~~~-~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~  279 (374)
                                .......+..++... ..+.++|||+.....++.+...|...|+++..+||+++..+|+.+++.|+.+..
T Consensus       544 ~~~~~~~l~~~s~K~~~L~~lL~~~~~~g~kvLIFsq~~~~ld~L~~~L~~~g~~~~~i~G~~~~~eR~~~i~~F~~~~~  623 (800)
T 3mwy_W          544 RENVLRGLIMSSGKMVLLDQLLTRLKKDGHRVLIFSQMVRMLDILGDYLSIKGINFQRLDGTVPSAQRRISIDHFNSPDS  623 (800)
T ss_dssp             SHHHHHHHHHTCHHHHHHHHHHHHHTTTTCCEEEEESCHHHHHHHHHHHHHHTCCCEEESTTSCHHHHHHHHHTTSSTTC
T ss_pred             HHHHHHHhhhcChHHHHHHHHHHHHhhCCCeEEEEechHHHHHHHHHHHHhCCCCEEEEeCCCCHHHHHHHHHHhhCCCC
Confidence                      011223334444433 457799999999999999999999999999999999999999999999998654


Q ss_pred             ---eEEEEeccccccccccCccEEEEECCCCChhHHHHhhccCCCCCCceEE--EEEeecc
Q 037567          280 ---RVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVC--WLYYARS  335 (374)
Q Consensus       280 ---~ilv~t~~~~~G~d~~~~~~vi~~~~p~s~~~~~Q~~GR~~R~~~~g~~--~~~~~~~  335 (374)
                         .+|++|.++++|+|++.+++||++++|+|+..+.|++||+.|.|+...|  +.++...
T Consensus       624 ~~~v~LlSt~agg~GlNL~~a~~VI~~D~~wnp~~~~Qa~gR~~RiGQ~k~V~Vyrlv~~~  684 (800)
T 3mwy_W          624 NDFVFLLSTRAGGLGINLMTADTVVIFDSDWNPQADLQAMARAHRIGQKNHVMVYRLVSKD  684 (800)
T ss_dssp             SCCCEEEEHHHHTTTCCCTTCCEEEESSCCSCSHHHHHHHTTTSCSSCCSCEEEEEEEETT
T ss_pred             CceEEEEecccccCCCCccccceEEEecCCCChhhHHHHHHHHHhcCCCceEEEEEEecCC
Confidence               4899999999999999999999999999999999999999999987655  4444443

>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=100.00  E-value=5.8e-33  Score=264.68  Aligned_cols=311  Identities=16%  Similarity=0.155  Sum_probs=206.9

Q ss_pred             CCchhHHHHHHHHH---------cCCCEEEEccCCCCchhhhhccccc---c-------CCcEEEEcchHHHHHHHHHHH
Q 037567           13 VFRPYQKDVIQRII---------EKRDCLVVMATGSGKSLCYQLPPLV---T-------GKTALVVSPLISLMQDQVMSL   73 (374)
Q Consensus        13 ~~~~~Q~~~~~~~~---------~~~~~l~~a~tGsGKT~~~~l~~~~---~-------~~~~lil~P~~~l~~q~~~~~   73 (374)
                      .|+|||.+++..++         .+.++++..+||+|||+.++..+..   .       ..++|||+|+ +|+.||.+++
T Consensus        55 ~LrpyQ~~gv~~l~~~~~~~~~~~~~g~ILad~mGlGKT~~~i~~i~~l~~~~~~~~p~~~~~LiV~P~-sll~qW~~E~  133 (644)
T 1z3i_X           55 VLRPHQREGVKFLWDCVTGRRIENSYGCIMADEMGLGKTLQCITLIWTLLKQSPDCKPEIDKVIVVSPS-SLVRNWYNEV  133 (644)
T ss_dssp             TCCHHHHHHHHHHHHHHTTSSSTTCCEEEECCCTTSCHHHHHHHHHHHHHHCCTTSSCSCSCEEEEECH-HHHHHHHHHH
T ss_pred             cccHHHHHHHHHHHHhhhcccccCCCCeEeeeCCCchHHHHHHHHHHHHHHhCccccCCCCcEEEEecH-HHHHHHHHHH
Confidence            69999999999875         3456899999999999776544321   1       3469999998 8999999999


Q ss_pred             HHcC---CceEEcCCCCCchhh--hhhhh-----cCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccC
Q 037567           74 KQRG---INAEFLGSAQTDSSV--QTKAE-----TGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGH  143 (374)
Q Consensus        74 ~~~~---~~~~~~~~~~~~~~~--~~~~~-----~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~  143 (374)
                      .++.   .....+.++......  .....     ...++|+|+|++.+....    ..+....+++||+||+|++.+...
T Consensus       134 ~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~vvi~ty~~l~~~~----~~l~~~~~~~vI~DEaH~ikn~~~  209 (644)
T 1z3i_X          134 GKWLGGRVQPVAIDGGSKDEIDSKLVNFISQQGMRIPTPILIISYETFRLHA----EVLHKGKVGLVICDEGHRLKNSDN  209 (644)
T ss_dssp             HHHHGGGCCEEEECSSCHHHHHHHHHHHHCCCSSCCSCCEEEEEHHHHHHHT----TTTTTSCCCEEEETTGGGCCTTCH
T ss_pred             HHHcCCCeeEEEEeCCCHHHHHHHHHHHHHhcCCCCCCcEEEeeHHHHHhhH----HHhhcCCccEEEEECceecCChhh
Confidence            9873   223333332211110  01100     124789999999874321    122335789999999999976432


Q ss_pred             cchHHHHHHHHHHHhcCCCCeeEEEeecCcccHHHHHHh------------------c----------------------
Q 037567          144 DFRLEYKQLDKLRTFLLGVPFVALTATATEKVRIDIINS------------------L----------------------  183 (374)
Q Consensus       144 ~~~~~~~~~~~~~~~~~~~~~i~~SaT~~~~~~~~~~~~------------------~----------------------  183 (374)
                             ........+...+++++||||..+...++...                  +                      
T Consensus       210 -------~~~~al~~l~~~~rl~LTgTPiqN~l~El~sll~fl~p~~l~~~~~F~~~f~~pi~~~~~~~~~~~~~~~~~~  282 (644)
T 1z3i_X          210 -------QTYLALNSMNAQRRVLISGTPIQNDLLEYFSLVHFVNSGILGTAQEFKKRFEIPILKGRDADASDKDRAAGEQ  282 (644)
T ss_dssp             -------HHHHHHHHHCCSEEEEECSSCSGGGGGGCHHHHHHHHHHHHCCHHHHHHHTHHHHHHHHSTTCCSHHHHHHHH
T ss_pred             -------HHHHHHHhcccCcEEEEecCcccCCHHHHHHHHHhhCCCcCCCHHHHHHhhcchhhhcCCcCCCHHHHHHHHH
Confidence                   22233333456789999999976642211110                  0                      


Q ss_pred             -----------------------CCCCCeEEEeccCCCc----eeE-----------------EE---------------
Q 037567          184 -----------------------KLKNPYVTIASFDRKN----LFY-----------------GV---------------  204 (374)
Q Consensus       184 -----------------------~~~~~~~~~~~~~~~~----~~~-----------------~~---------------  204 (374)
                                             .+++............    .+.                 ..               
T Consensus       283 ~~~~L~~~l~~~~lRR~k~~v~~~LP~k~~~~v~~~ls~~q~~lY~~~~~~~~~~~~~~~g~~~~~~l~~l~~Lrk~c~h  362 (644)
T 1z3i_X          283 KLQELISIVNRCLIRRTSDILSKYLPVKIEQVVCCNLTPLQKELYKLFLKQAKPVESLQTGKISVSSLSSITSLKKLCNH  362 (644)
T ss_dssp             HHHHHHHHHHHHEECCCGGGGGGTSCCEEEEEEEECCCHHHHHHHHHHHHHHCGGGSSCTTCCCHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHhhHHhHhhhCCCceEEEEEeCCCHHHHHHHHHHHHHHHHHHHHhcCccchhHHHHHHHHHHHhCC
Confidence                                   0000000000000000    000                 00               


Q ss_pred             ----------------------------EeecCCcchHHHHHHHHHHhh--cCCCcEEEEecchhHHHHHHHHHHHcCCc
Q 037567          205 ----------------------------KVINRGQSFVDELVQEILKSV--AGAGSIIVYCMTIKDVEEISKALKQLGVK  254 (374)
Q Consensus       205 ----------------------------~~~~~~~~~~~~~~~~~~~~~--~~~~~~lVf~~~~~~~~~l~~~l~~~~~~  254 (374)
                                                  .............+..++...  ..+.++|||++....++.+.+.|...|+.
T Consensus       363 p~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~K~~~l~~ll~~~~~~~~~k~lIFs~~~~~~~~l~~~l~~~g~~  442 (644)
T 1z3i_X          363 PALIYEKCLTGEEGFDGALDLFPQNYSTKAVEPQLSGKMLVLDYILAMTRTTTSDKVVLVSNYTQTLDLFEKLCRNRRYL  442 (644)
T ss_dssp             THHHHHHHHHTCTTCTTGGGTSCSSCCSSSCCGGGSHHHHHHHHHHHHHHHHCCCEEEEEESCHHHHHHHHHHHHHHTCC
T ss_pred             HHHHHHHHhcccchhhhHHhhccccccccccCcccChHHHHHHHHHHHHhhcCCCEEEEEEccHHHHHHHHHHHHHCCCC
Confidence                                        000000011223344444433  25789999999999999999999999999


Q ss_pred             eeeeecCCChHHHHHHHHhhhcCCe---eEEEEeccccccccccCccEEEEECCCCChhHHHHhhccCCCCCCceEEE--
Q 037567          255 AGTYHGQMGSKAREEAHRLFIRDEI---RVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCW--  329 (374)
Q Consensus       255 ~~~~~~~~~~~~r~~~~~~f~~g~~---~ilv~t~~~~~G~d~~~~~~vi~~~~p~s~~~~~Q~~GR~~R~~~~g~~~--  329 (374)
                      +..+||+++.++|+.+++.|++|+.   .+|++|.++++|+|++.+++||++++|+|+..+.|++||++|.|+...+.  
T Consensus       443 ~~~l~G~~~~~~R~~~i~~F~~~~~~~~v~L~st~a~g~Glnl~~a~~Vi~~d~~wnp~~~~Qa~gR~~R~Gq~~~v~v~  522 (644)
T 1z3i_X          443 YVRLDGTMSIKKRAKIVERFNNPSSPEFIFMLSSKAGGCGLNLIGANRLVMFDPDWNPANDEQAMARVWRDGQKKTCYIY  522 (644)
T ss_dssp             EEEECSSCCHHHHHHHHHHHHSTTCCCCEEEEEGGGSCTTCCCTTEEEEEECSCCSSHHHHHHHHTTSSSTTCCSCEEEE
T ss_pred             EEEEeCCCCHHHHHHHHHHhcCCCCCcEEEEEecccccCCcccccCCEEEEECCCCCccHHHHHHHhhhhcCCCCceEEE
Confidence            9999999999999999999999865   48899999999999999999999999999999999999999999876544  


Q ss_pred             EEeecc
Q 037567          330 LYYARS  335 (374)
Q Consensus       330 ~~~~~~  335 (374)
                      .++...
T Consensus       523 ~lv~~~  528 (644)
T 1z3i_X          523 RLLSTG  528 (644)
T ss_dssp             EEEETT
T ss_pred             EEEECC
Confidence            444443

>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=100.00  E-value=1.3e-33  Score=277.39  Aligned_cols=309  Identities=14%  Similarity=0.107  Sum_probs=201.5

Q ss_pred             CCchhHHHHHHHHHc--------------CCCEEEEccCCCCchhhhhcccc--c---cCCcEEEEcchHHHHHHHHHHH
Q 037567           13 VFRPYQKDVIQRIIE--------------KRDCLVVMATGSGKSLCYQLPPL--V---TGKTALVVSPLISLMQDQVMSL   73 (374)
Q Consensus        13 ~~~~~Q~~~~~~~~~--------------~~~~l~~a~tGsGKT~~~~l~~~--~---~~~~~lil~P~~~l~~q~~~~~   73 (374)
                      .|||+|.+|++.+++              +++++++++||||||++++..+.  .   ...++||++|+++|+.||.+.+
T Consensus       271 ~~R~~Q~~AI~~il~~i~~~~~~~~~~~~~~~gli~~~TGSGKT~t~~~l~~ll~~~~~~~rvLvlvpr~eL~~Q~~~~f  350 (1038)
T 2w00_A          271 VMRPYQIAATERILWKIKSSFTAKNWSKPESGGYIWHTTGSGKTLTSFKAARLATELDFIDKVFFVVDRKDLDYQTMKEY  350 (1038)
T ss_dssp             ECCHHHHHHHHHHHHHHHHHHHHTCCSSGGGSEEEEECTTSSHHHHHHHHHHHHTTCTTCCEEEEEECGGGCCHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHHHHhcccccccccCCCCEEEEecCCCCHHHHHHHHHHHHHhcCCCceEEEEeCcHHHHHHHHHHH
Confidence            599999999999875              36899999999999988633221  1   1368999999999999999999


Q ss_pred             HHcCCceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHH
Q 037567           74 KQRGINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLD  153 (374)
Q Consensus        74 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~  153 (374)
                      ..++...  +.+...............++|+|+||+++............+..+.+||+||||+... +       ....
T Consensus       351 ~~f~~~~--v~~~~s~~~l~~~L~~~~~~IiVtTiqkl~~~l~~~~~~~~~~~~~lvIiDEAHrs~~-~-------~~~~  420 (1038)
T 2w00_A          351 QRFSPDS--VNGSENTAGLKRNLDKDDNKIIVTTIQKLNNLMKAESDLPVYNQQVVFIFDECHRSQF-G-------EAQK  420 (1038)
T ss_dssp             HTTSTTC--SSSSCCCHHHHHHHHCSSCCEEEEEHHHHHHHHHHCCCCGGGGSCEEEEEESCCTTHH-H-------HHHH
T ss_pred             HHhcccc--cccccCHHHHHHHhcCCCCCEEEEEHHHHHHHHhcccchhccccccEEEEEccchhcc-h-------HHHH
Confidence            9886431  2222222222222334568999999999865432210001234678999999999753 1       2234


Q ss_pred             HHHHhcCCCCeeEEEeecCcccH----HHHHHhcCC----------------CCCeEEEeccCCCcee-----EE-----
Q 037567          154 KLRTFLLGVPFVALTATATEKVR----IDIINSLKL----------------KNPYVTIASFDRKNLF-----YG-----  203 (374)
Q Consensus       154 ~~~~~~~~~~~i~~SaT~~~~~~----~~~~~~~~~----------------~~~~~~~~~~~~~~~~-----~~-----  203 (374)
                      .+...+++.++++|||||.....    ......++-                .+..+...... +.+.     ..     
T Consensus       421 ~I~~~~p~a~~lgfTATP~~~~~~~~~~~t~~~FG~~i~~Y~l~~AI~dg~l~p~~v~y~~v~-~~~~~~~~e~d~~~~~  499 (1038)
T 2w00_A          421 NLKKKFKRYYQFGFTGTPIFPENALGSETTASVFGRELHSYVITDAIRDEKVLKFKVDYNDVR-PQFKSLETETDEKKLS  499 (1038)
T ss_dssp             HHHHHCSSEEEEEEESSCCCSTTCTTSCCHHHHHCSEEEEECHHHHHHHTSSCCEEEEECCCC-GGGHHHHTCCCHHHHH
T ss_pred             HHHHhCCcccEEEEeCCccccccchhhhHHHHHhCCeeEeecHHHHHhCCCcCCeEEEEEecc-chhhhccccccHHHHH
Confidence            55666778899999999986431    112222221                11111111000 0000     00     


Q ss_pred             -EEe--ecCCcchHHHHHHHHHHhhc----------CCCcEEEEecchhHHHHHHHHHHHcC------------Ccee-e
Q 037567          204 -VKV--INRGQSFVDELVQEILKSVA----------GAGSIIVYCMTIKDVEEISKALKQLG------------VKAG-T  257 (374)
Q Consensus       204 -~~~--~~~~~~~~~~~~~~~~~~~~----------~~~~~lVf~~~~~~~~~l~~~l~~~~------------~~~~-~  257 (374)
                       ...  .-........++..++++..          .+.++||||+++..|..+++.|.+.+            .++. .
T Consensus       500 ~i~~~~~l~~~~ri~~I~~~Il~~~~~~~~~~~~~~~g~kamVf~~S~~~A~~~~~~l~~~~~~~~~~~~~~~~~k~avv  579 (1038)
T 2w00_A          500 AAENQQAFLHPMRIQEITQYILNNFRQKTHRTFPGSKGFNAMLAVSSVDAAKAYYATFKRLQEEAANKSATYKPLRIATI  579 (1038)
T ss_dssp             HTCSTTTTTCHHHHHHHHHHHHHHHHHHTTCSSSSCCCCEEEEEESSHHHHHHHHHHHHHHHHHHTTTSSSCCCCCEEEE
T ss_pred             HHHHHHHhcCHHHHHHHHHHHHHHHHHhhhhhcccCCCCcEEEEECCHHHHHHHHHHHHhhhhhhcccccccccCcEEEE
Confidence             000  00011122333444444321          34689999999999999999998754            4443 4


Q ss_pred             eecC----------C----------Ch-----------------------------HHHHHHHHhhhcCCeeEEEEeccc
Q 037567          258 YHGQ----------M----------GS-----------------------------KAREEAHRLFIRDEIRVMVATMAF  288 (374)
Q Consensus       258 ~~~~----------~----------~~-----------------------------~~r~~~~~~f~~g~~~ilv~t~~~  288 (374)
                      +|++          +          +.                             ..|..++++|++|+++|||+|+++
T Consensus       580 ~s~~~~~~~~~~G~~~~e~~~~~~~~~~~r~~l~~~I~dyn~~f~~~~~~~~~~~~~~R~~i~~~Fk~g~i~ILIvvd~l  659 (1038)
T 2w00_A          580 FSFAANEEQNAIGEISDETFDTSAMDSSAKEFLDAAIREYNSHFKTNFSTDSNGFQNYYRDLAQRVKNQDIDLLIVVGMF  659 (1038)
T ss_dssp             CCCCC------CCCCCCCCSCGGGSCHHHHHHHHHHHHHHHHHHTCCCCSSHHHHHHHHHHHHHHHHTTSSSEEEESSTT
T ss_pred             EeCCCccccccccccccccccccccchhHHHHHHHHHHHHHHHhcccccccchhhhHHHHHHHHHHHcCCCeEEEEcchH
Confidence            4442          1          11                             137788899999999999999999


Q ss_pred             cccccccCccEEEEECCCCChhHHHHhhccCCCCCCc----eEEEEEee
Q 037567          289 GMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIA----SVCWLYYA  333 (374)
Q Consensus       289 ~~G~d~~~~~~vi~~~~p~s~~~~~Q~~GR~~R~~~~----g~~~~~~~  333 (374)
                      .+|+|+|.+ .++.++.|.+...++|++||++|.+.+    |.++.|..
T Consensus       660 ltGfDiP~l-~tlylDkpl~~~~liQaIGRtnR~~~~~K~~G~IVdf~~  707 (1038)
T 2w00_A          660 LTGFDAPTL-NTLFVDKNLRYHGLMQAFSRTNRIYDATKTFGNIVTFRD  707 (1038)
T ss_dssp             SSSCCCTTE-EEEEEESCCCHHHHHHHHHTTCCCCCTTCCSEEEEESSC
T ss_pred             HhCcCcccc-cEEEEccCCCccceeehhhccCcCCCCCCCcEEEEEccc
Confidence            999999999 567789999999999999999998754    66666654

>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=99.97  E-value=2.1e-30  Score=238.88  Aligned_cols=326  Identities=18%  Similarity=0.183  Sum_probs=226.0

Q ss_pred             hhHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc---cCCcEEEEcchHHHHHHHHHHHHH---
Q 037567            2 VSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV---TGKTALVVSPLISLMQDQVMSLKQ---   75 (374)
Q Consensus         2 ~~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~---~~~~~lil~P~~~l~~q~~~~~~~---   75 (374)
                      .++-++.+|+. |++.|.-+.-.+.+|+  +..+.||+|||+++.+|+..   .+..+.|++|+..||.|-.+++..   
T Consensus        65 REAa~R~lg~r-~~dvQligg~~L~~G~--iaEM~TGEGKTLva~lp~~lnAL~G~~vhVvT~ndyLA~rdae~m~~l~~  141 (822)
T 3jux_A           65 REAARRTLGMR-PFDVQVMGGIALHEGK--VAEMKTGEGKTLAATMPIYLNALIGKGVHLVTVNDYLARRDALWMGPVYL  141 (822)
T ss_dssp             HHHHHHHTSCC-CCHHHHHHHHHHHTTC--EEECCTTSCHHHHTHHHHHHHHTTSSCEEEEESSHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhCCC-CcHHHHHHHHHHhCCC--hhhccCCCCccHHHHHHHHHHHhcCCceEEEeccHHHHHhHHHHHHHHHH
Confidence            45677888885 8899998888888777  99999999999999888763   588899999999999987777654   


Q ss_pred             -cCCceEEcCCCCC-----------------------------------------------chhhhhhhhcCCeeEEEEc
Q 037567           76 -RGINAEFLGSAQT-----------------------------------------------DSSVQTKAETGYFQLLFMT  107 (374)
Q Consensus        76 -~~~~~~~~~~~~~-----------------------------------------------~~~~~~~~~~~~~~i~i~T  107 (374)
                       +|+.+.+......                                               ............+||+++|
T Consensus       142 ~Lglsvg~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~err~aY~~DItYgT  221 (822)
T 3jux_A          142 FLGLRVGVINSLGKSYEVVWKNPDLARKAIEENWSVWPDGFNGEVLKEESMNKEAVEAFQVELKEITRKEAYLCDVTYGT  221 (822)
T ss_dssp             HTTCCEEEEETTTEEEEEEESSHHHHHHHHHTTCCSSCTTCCSSSCCGGGSCHHHHTTTCEECCBCCHHHHHHSSEEEEE
T ss_pred             HhCCEEEEEcCCCcccccccccchhhhhhhcccccccccccccccccccccccccchhccccCCHHHHHHHhcCCCEEcc
Confidence             4888877665210                                               0001111222457999999


Q ss_pred             Cccccc-Cchhh----HHHHHhcCccEEEEeccchhh-cc--------c--Ccch-------------------------
Q 037567          108 PEKACI-IPISF----WSKLLKAGVCLFAVDEAHCIS-EW--------G--HDFR-------------------------  146 (374)
Q Consensus       108 ~~~l~~-~~~~~----~~~~~~~~~~~vviDE~h~~~-~~--------~--~~~~-------------------------  146 (374)
                      ..-+.. +++..    ........+.+.||||++.+. +.        |  ....                         
T Consensus       222 n~EfgFDYLRDnm~~~~~~~vqR~~~~aIVDEvDSiLIDeArtPLiISg~~~~~~~~y~~~~~~v~~l~~~~dy~vdek~  301 (822)
T 3jux_A          222 NNEFGFDYLRDNLVLDYNDKVQRGHFYAIVDEADSVLIDEARTPLIISGPSKESPSVYRRFAQIAKKFVKDKDFTVDEKA  301 (822)
T ss_dssp             HHHHHHHHHHHTSCSSTTSCCCCCCCEEEEETHHHHHTTGGGSCEEEECCCCSCHHHHHHHHHHTTSSCBTTTEEECCSS
T ss_pred             CcchhhHhHHhhccCCHHHhccCCCCeEEEecccceeecCCCCCceeeCCCCCccHHHHHHHHHHHhcCcCCcEEEEccc
Confidence            865421 11100    011123557899999999974 10        0  0000                         


Q ss_pred             ----------------------------HHHHHHH-HHH--Hhc------------------------------------
Q 037567          147 ----------------------------LEYKQLD-KLR--TFL------------------------------------  159 (374)
Q Consensus       147 ----------------------------~~~~~~~-~~~--~~~------------------------------------  159 (374)
                                                  .....+. .+.  ..+                                    
T Consensus       302 ~~v~lTe~G~~~~E~~l~i~nly~~~n~~l~~~i~~AL~A~~l~~~d~dYiV~dg~V~iVDe~TGR~m~grr~s~GLHQa  381 (822)
T 3jux_A          302 RTIILTEEGVAKAEKIIGVENLYDPGNVSLLYHLINALKALHLFKKDVDYVVMNGEVIIVDEFTGRLLPGRRYSGGLHQA  381 (822)
T ss_dssp             SCEEECHHHHHHHHHHHTCSCTTSGGGHHHHHHHHHHHHHHHHSTTTSSEEEETTEEEECSSSSCSCCCSCCCGGGHHHH
T ss_pred             CeEEECHHHHHHHHHHhCCccccchhhhHHHHHHHHHHHHHHHHcCCCcEEEECCEEEEEECCCCcCCCCCcCchHHHHH
Confidence                                        0000000 000  000                                    


Q ss_pred             --------------------------CCCCeeEEEeecCcccHHHHHHhcCCCCCeEEEeccCCCceeEEE--EeecCCc
Q 037567          160 --------------------------LGVPFVALTATATEKVRIDIINSLKLKNPYVTIASFDRKNLFYGV--KVINRGQ  211 (374)
Q Consensus       160 --------------------------~~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~  211 (374)
                                                .-.++.+||||..... ..+...+++.   +...+.+.+......  ..+....
T Consensus       382 iEaKEgv~i~~e~~tla~IT~Qn~Fr~Y~kL~GMTGTa~te~-~Ef~~iY~l~---vv~IPtnkp~~R~d~~d~vy~t~~  457 (822)
T 3jux_A          382 IEAKEGVPIKEESITYATITFQNYFRMYEKLAGMTGTAKTEE-SEFVQVYGME---VVVIPTHKPMIRKDHDDLVFRTQK  457 (822)
T ss_dssp             HHHHHSSCCCCCCCEEEEECHHHHHTTSSEEEEEESSCGGGH-HHHHHHSCCC---EEECCCSSCCCCEECCCEEESSHH
T ss_pred             HHHHcCCCCCCCcchhHHHHHHHHHHHhhHHeEECCCCchHH-HHHHHHhCCe---EEEECCCCCcceeecCcEEEecHH
Confidence                                      0013899999998754 3566666644   222233333222222  2344444


Q ss_pred             chHHHHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEecccccc
Q 037567          212 SFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMG  291 (374)
Q Consensus       212 ~~~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G  291 (374)
                      .....++..+......+.++||||+++..++.+++.|.+.|+++..+||+....++..+...++.|  .|+|||+++++|
T Consensus       458 eK~~al~~~I~~~~~~gqpVLVFt~S~e~sE~Ls~~L~~~Gi~~~vLhgkq~~rE~~ii~~ag~~g--~VtVATdmAgRG  535 (822)
T 3jux_A          458 EKYEKIVEEIEKRYKKGQPVLVGTTSIEKSELLSSMLKKKGIPHQVLNAKYHEKEAEIVAKAGQKG--MVTIATNMAGRG  535 (822)
T ss_dssp             HHHHHHHHHHHHHHHHTCCEEEEESSHHHHHHHHHHHHTTTCCCEEECSCHHHHHHHHHHHHHSTT--CEEEEETTTTTT
T ss_pred             HHHHHHHHHHHHHhhCCCCEEEEECCHHHHHHHHHHHHHCCCCEEEeeCCchHHHHHHHHhCCCCC--eEEEEcchhhCC
Confidence            555666666655545688999999999999999999999999999999996655665556666666  699999999999


Q ss_pred             cccc--------CccEEEEECCCCChhHHHHhhccCCCCCCceEEEEEeeccC
Q 037567          292 IDKP--------DVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSN  336 (374)
Q Consensus       292 ~d~~--------~~~~vi~~~~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~  336 (374)
                      +|++        +..+||+++.|.|...|.||+||+||.|.+|.++++++.+|
T Consensus       536 tDI~lg~~V~~~GglhVInte~Pes~r~y~qriGRTGRqG~~G~a~~fvsleD  588 (822)
T 3jux_A          536 TDIKLGPGVAELGGLCIIGTERHESRRIDNQLRGRAGRQGDPGESIFFLSLED  588 (822)
T ss_dssp             CCCCCCTTTTTTTSCEEEESSCCSSHHHHHHHHTTSSCSSCCCEEEEEEETTS
T ss_pred             cCccCCcchhhcCCCEEEecCCCCCHHHHHHhhCccccCCCCeeEEEEechhH
Confidence            9998        56799999999999999999999999999999999999887

>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=99.96  E-value=3.6e-28  Score=231.37  Aligned_cols=124  Identities=23%  Similarity=0.342  Sum_probs=112.7

Q ss_pred             chHHHHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEecccccc
Q 037567          212 SFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMG  291 (374)
Q Consensus       212 ~~~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G  291 (374)
                      .....++..+......+.++||||+++..++.+++.|.+.|+.+..+||+++..+|..+++.|..|+.+|||+|+.+++|
T Consensus       423 ~~~~~Ll~~l~~~~~~~~~vlVf~~t~~~ae~L~~~L~~~gi~~~~lh~~~~~~~R~~~~~~f~~g~~~VLvaT~~l~~G  502 (664)
T 1c4o_A          423 NQILDLMEGIRERAARGERTLVTVLTVRMAEELTSFLVEHGIRARYLHHELDAFKRQALIRDLRLGHYDCLVGINLLREG  502 (664)
T ss_dssp             THHHHHHHHHHHHHHTTCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTCCHHHHHHHHHHHHTTSCSEEEESCCCCTT
T ss_pred             chHHHHHHHHHHHHhcCCEEEEEECCHHHHHHHHHHHHhcCCCceeecCCCCHHHHHHHHHHhhcCCceEEEccChhhcC
Confidence            34556666666666678899999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccCccEEEEECC-----CCChhHHHHhhccCCCCCCceEEEEEeeccC
Q 037567          292 IDKPDVRHVIHYGC-----PKTLESYYQESGRCGRDGIASVCWLYYARSN  336 (374)
Q Consensus       292 ~d~~~~~~vi~~~~-----p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~  336 (374)
                      +|+|++++||+++.     |.|...|+||+||+||.+ .|.+++++++.+
T Consensus       503 lDip~v~lVI~~d~d~~G~p~s~~~~iQr~GRagR~~-~G~~i~~~~~~~  551 (664)
T 1c4o_A          503 LDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNA-RGEVWLYADRVS  551 (664)
T ss_dssp             CCCTTEEEEEETTTTSCSGGGSHHHHHHHHGGGTTST-TCEEEEECSSCC
T ss_pred             ccCCCCCEEEEeCCcccCCCCCHHHHHHHHCccCcCC-CCEEEEEEcCCC
Confidence            99999999999997     889999999999999985 788999887654

>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=99.96  E-value=6.1e-29  Score=207.71  Aligned_cols=167  Identities=19%  Similarity=0.276  Sum_probs=125.5

Q ss_pred             hhHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc------------cCCcEEEEcchHHHHHHH
Q 037567            2 VSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV------------TGKTALVVSPLISLMQDQ   69 (374)
Q Consensus         2 ~~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~------------~~~~~lil~P~~~l~~q~   69 (374)
                      .++|.+ +||.+|+|+|.++++.+++++++++.+|||+|||++|+++++.            .+.+++|++|+++|+.|+
T Consensus        32 ~~~l~~-~g~~~~~~~Q~~~i~~~~~~~~~l~~apTGsGKT~~~~l~~~~~l~~~~~~~~~~~~~~~lil~Pt~~L~~q~  110 (228)
T 3iuy_A           32 LKSIIR-VGILKPTPIQSQAWPIILQGIDLIVVAQTGTGKTLSYLMPGFIHLDSQPISREQRNGPGMLVLTPTRELALHV  110 (228)
T ss_dssp             HHHHHH-HTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHC---------CCCSEEEECSSHHHHHHH
T ss_pred             HHHHHH-CCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhccchhhccCCCcEEEEeCCHHHHHHH
Confidence            456777 7999999999999999999999999999999999999887664            467899999999999999


Q ss_pred             HHHHHHc---CCceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcch
Q 037567           70 VMSLKQR---GINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFR  146 (374)
Q Consensus        70 ~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~  146 (374)
                      .+.+..+   +.......++........ ....+++|+|+||+++......  ....+.+++++|+||||++.++++.  
T Consensus       111 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~iiv~Tp~~l~~~~~~--~~~~~~~~~~lViDEah~~~~~~~~--  185 (228)
T 3iuy_A          111 EAECSKYSYKGLKSICIYGGRNRNGQIE-DISKGVDIIIATPGRLNDLQMN--NSVNLRSITYLVIDEADKMLDMEFE--  185 (228)
T ss_dssp             HHHHHHHCCTTCCEEEECC------CHH-HHHSCCSEEEECHHHHHHHHHT--TCCCCTTCCEEEECCHHHHHHTTCH--
T ss_pred             HHHHHHhcccCceEEEEECCCChHHHHH-HhcCCCCEEEECHHHHHHHHHc--CCcCcccceEEEEECHHHHhccchH--
Confidence            9999986   455555555443333222 2334589999999998665333  2334567899999999999886643  


Q ss_pred             HHHHHHHHHHHhc-CCCCeeEEEeecCcccHH
Q 037567          147 LEYKQLDKLRTFL-LGVPFVALTATATEKVRI  177 (374)
Q Consensus       147 ~~~~~~~~~~~~~-~~~~~i~~SaT~~~~~~~  177 (374)
                         ..+..+.... ++.++++||||+++....
T Consensus       186 ---~~~~~i~~~~~~~~~~l~~SAT~~~~~~~  214 (228)
T 3iuy_A          186 ---PQIRKILLDVRPDRQTVMTSATWPDTVRQ  214 (228)
T ss_dssp             ---HHHHHHHHHSCSSCEEEEEESCCCHHHHH
T ss_pred             ---HHHHHHHHhCCcCCeEEEEEeeCCHHHHH
Confidence               3333333433 468899999999987664

>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=99.95  E-value=9.6e-29  Score=208.21  Aligned_cols=172  Identities=19%  Similarity=0.195  Sum_probs=131.6

Q ss_pred             hhHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc-----------cCCcEEEEcchHHHHHHHH
Q 037567            2 VSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV-----------TGKTALVVSPLISLMQDQV   70 (374)
Q Consensus         2 ~~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~-----------~~~~~lil~P~~~l~~q~~   70 (374)
                      .+++.+ +||..|+|+|.++++.+++++++++.+|||||||++|+++++.           .+.+++|++|+++|+.|+.
T Consensus        41 ~~~l~~-~g~~~~~~~Q~~~i~~~~~g~~~l~~apTGsGKT~~~~l~~l~~l~~~~~~~~~~~~~~lil~Pt~~L~~Q~~  119 (242)
T 3fe2_A           41 MDVIAR-QNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLLPAIVHINHQPFLERGDGPICLVLAPTRELAQQVQ  119 (242)
T ss_dssp             HHHHHT-TTCCSCCHHHHHHHHHHHHTCCEEEEECTTSCHHHHHHHHHHHHHHTSCCCCTTCCCSEEEECSSHHHHHHHH
T ss_pred             HHHHHH-CCCCCCCHHHHHHHHHHhCCCCEEEECCCcCHHHHHHHHHHHHHHHhccccccCCCCEEEEEeCcHHHHHHHH
Confidence            356666 7999999999999999999999999999999999999888764           3677999999999999999


Q ss_pred             HHHHHc----CCceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcch
Q 037567           71 MSLKQR----GINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFR  146 (374)
Q Consensus        71 ~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~  146 (374)
                      +.++.+    +.......++......... ...+++|+|+||+++..++..  ....+.+++++|+||||++.++++.  
T Consensus       120 ~~~~~~~~~~~~~~~~~~g~~~~~~~~~~-~~~~~~I~v~Tp~~l~~~l~~--~~~~~~~~~~lViDEah~l~~~~~~--  194 (242)
T 3fe2_A          120 QVAAEYCRACRLKSTCIYGGAPKGPQIRD-LERGVEICIATPGRLIDFLEC--GKTNLRRTTYLVLDEADRMLDMGFE--  194 (242)
T ss_dssp             HHHHHHHHHTTCCEEEECTTSCHHHHHHH-HHHCCSEEEECHHHHHHHHHH--TSCCCTTCCEEEETTHHHHHHTTCH--
T ss_pred             HHHHHHHhhcCceEEEEECCCChHHHHHH-hcCCCCEEEECHHHHHHHHHc--CCCCcccccEEEEeCHHHHhhhCcH--
Confidence            888765    6666666665444333222 234579999999998766543  2334577899999999999887643  


Q ss_pred             HHHHHHHHHHHhc-CCCCeeEEEeecCcccHHHHHHh
Q 037567          147 LEYKQLDKLRTFL-LGVPFVALTATATEKVRIDIINS  182 (374)
Q Consensus       147 ~~~~~~~~~~~~~-~~~~~i~~SaT~~~~~~~~~~~~  182 (374)
                         ..+..+...+ ++.++++||||+++.........
T Consensus       195 ---~~~~~i~~~~~~~~q~~~~SAT~~~~~~~~~~~~  228 (242)
T 3fe2_A          195 ---PQIRKIVDQIRPDRQTLMWSATWPKEVRQLAEDF  228 (242)
T ss_dssp             ---HHHHHHHTTSCSSCEEEEEESCCCHHHHHHHHHH
T ss_pred             ---HHHHHHHHhCCccceEEEEEeecCHHHHHHHHHH
Confidence               3444444544 46789999999988766433333

>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=99.95  E-value=1.5e-26  Score=220.17  Aligned_cols=124  Identities=23%  Similarity=0.345  Sum_probs=113.3

Q ss_pred             chHHHHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEecccccc
Q 037567          212 SFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMG  291 (374)
Q Consensus       212 ~~~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G  291 (374)
                      .....++..+......+.++||||+++..++.+++.|.+.|+++..+||+++..+|..+++.|+.|+.+|||+|+.+++|
T Consensus       429 ~~~~~Ll~~l~~~~~~~~~vlVf~~t~~~ae~L~~~L~~~gi~~~~lh~~~~~~~R~~~l~~f~~g~~~VLVaT~~l~~G  508 (661)
T 2d7d_A          429 GQIDDLIGEIQARIERNERVLVTTLTKKMSEDLTDYLKEIGIKVNYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREG  508 (661)
T ss_dssp             THHHHHHHHHHHHHTTTCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTCCHHHHHHHHHHHHHTSCSEEEESCCCSTT
T ss_pred             chHHHHHHHHHHHHhcCCeEEEEECCHHHHHHHHHHHHhcCCCeEEEeCCCCHHHHHHHHHHHhcCCeEEEEecchhhCC
Confidence            34566667776666678899999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccCccEEEEECC-----CCChhHHHHhhccCCCCCCceEEEEEeeccC
Q 037567          292 IDKPDVRHVIHYGC-----PKTLESYYQESGRCGRDGIASVCWLYYARSN  336 (374)
Q Consensus       292 ~d~~~~~~vi~~~~-----p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~  336 (374)
                      +|+|++++||+++.     |.+...|+||+||+||. ..|.+++++++.+
T Consensus       509 lDip~v~lVi~~d~d~~G~p~s~~~~iQr~GRagR~-~~G~~i~~~~~~~  557 (661)
T 2d7d_A          509 LDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARN-AEGRVIMYADKIT  557 (661)
T ss_dssp             CCCTTEEEEEETTTTCCTTTTSHHHHHHHHHTTTTS-TTCEEEEECSSCC
T ss_pred             cccCCCCEEEEeCcccccCCCCHHHHHHHhCcccCC-CCCEEEEEEeCCC
Confidence            99999999999997     89999999999999998 6899999987653

>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=99.95  E-value=1.6e-28  Score=204.08  Aligned_cols=168  Identities=15%  Similarity=0.179  Sum_probs=129.5

Q ss_pred             hhHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhcccccc------CCcEEEEcchHHHHHHHHHHHHH
Q 037567            2 VSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVT------GKTALVVSPLISLMQDQVMSLKQ   75 (374)
Q Consensus         2 ~~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~~------~~~~lil~P~~~l~~q~~~~~~~   75 (374)
                      .++|.+ +||..|+|+|.++++.+++++++++.+|||+|||++|+++++..      ..+++|++|+++|+.|+.+.+++
T Consensus        26 ~~~l~~-~g~~~~~~~Q~~~i~~~~~~~~~li~~~TGsGKT~~~~~~~~~~~~~~~~~~~~lil~Pt~~L~~q~~~~~~~  104 (220)
T 1t6n_A           26 LRAIVD-CGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRELAFQISKEYER  104 (220)
T ss_dssp             HHHHHH-TTCCCCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCCCTTCCCEEEECSCHHHHHHHHHHHHH
T ss_pred             HHHHHH-CCCCCCCHHHHHHHHHHhCCCCEEEECCCCCchhhhhhHHHHHhhhccCCCEEEEEEeCCHHHHHHHHHHHHH
Confidence            456766 89999999999999999999999999999999999998877642      45899999999999999999987


Q ss_pred             c-----CCceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcc-cCcchHHH
Q 037567           76 R-----GINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEW-GHDFRLEY  149 (374)
Q Consensus        76 ~-----~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~-~~~~~~~~  149 (374)
                      +     +..+....++............+.++|+|+||+++......  ....+.+++++|+||||++.++ +.  .   
T Consensus       105 ~~~~~~~~~v~~~~g~~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~--~~~~~~~~~~lViDEah~~~~~~~~--~---  177 (220)
T 1t6n_A          105 FSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARN--KSLNLKHIKHFILDECDKMLEQLDM--R---  177 (220)
T ss_dssp             HTTTSTTCCEEEESCCSCHHHHHHHHHHSCCSEEEECHHHHHHHHHT--TSSCCTTCCEEEEESHHHHHSSHHH--H---
T ss_pred             HHhhCCCceEEEEeCCCChHHHHHHHhcCCCCEEEeCHHHHHHHHHh--CCCCcccCCEEEEcCHHHHhcccCc--H---
Confidence            6     56666666655544444444445679999999998765443  2234567899999999998752 32  1   


Q ss_pred             HHHHHHHHhcC-CCCeeEEEeecCcccHH
Q 037567          150 KQLDKLRTFLL-GVPFVALTATATEKVRI  177 (374)
Q Consensus       150 ~~~~~~~~~~~-~~~~i~~SaT~~~~~~~  177 (374)
                      ..+..+....+ +.+++++|||++.....
T Consensus       178 ~~~~~i~~~~~~~~~~i~~SAT~~~~~~~  206 (220)
T 1t6n_A          178 RDVQEIFRMTPHEKQVMMFSATLSKEIRP  206 (220)
T ss_dssp             HHHHHHHHTSCSSSEEEEEESCCCTTTHH
T ss_pred             HHHHHHHHhCCCcCeEEEEEeecCHHHHH
Confidence            33444444443 67899999999988764

>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=99.95  E-value=9.6e-29  Score=208.83  Aligned_cols=177  Identities=24%  Similarity=0.280  Sum_probs=127.6

Q ss_pred             hhHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc-------cCCcEEEEcchHHHHHHHHHHHH
Q 037567            2 VSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV-------TGKTALVVSPLISLMQDQVMSLK   74 (374)
Q Consensus         2 ~~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~-------~~~~~lil~P~~~l~~q~~~~~~   74 (374)
                      .+++.+ +||..|+|+|.++++.+++++++++.+|||+|||++|+++++.       .+.+++|++|+++|+.|+.+.+.
T Consensus        41 ~~~l~~-~g~~~~~~~Q~~~i~~~~~~~~~l~~a~TGsGKT~~~~l~~l~~l~~~~~~~~~~lil~Pt~~L~~q~~~~~~  119 (245)
T 3dkp_A           41 LQNILD-AGFQMPTPIQMQAIPVMLHGRELLASAPTGSGKTLAFSIPILMQLKQPANKGFRALIISPTRELASQIHRELI  119 (245)
T ss_dssp             HHHHHH-TTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHCSCCSSSCCEEEECSSHHHHHHHHHHHH
T ss_pred             HHHHHH-CCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHHhhcccCCceEEEEeCCHHHHHHHHHHHH
Confidence            345666 7999999999999999999999999999999999999888764       35689999999999999999998


Q ss_pred             Hc----CCceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccC-cchHHH
Q 037567           75 QR----GINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGH-DFRLEY  149 (374)
Q Consensus        75 ~~----~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~-~~~~~~  149 (374)
                      .+    +.......++..............++|+|+||+++..++........+.+++++|+||||++.+++. .+.   
T Consensus       120 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~v~Tp~~l~~~l~~~~~~~~~~~~~~lViDEah~~~~~~~~~~~---  196 (245)
T 3dkp_A          120 KISEGTGFRIHMIHKAAVAAKKFGPKSSKKFDILVTTPNRLIYLLKQDPPGIDLASVEWLVVDESDKLFEDGKTGFR---  196 (245)
T ss_dssp             HHTTTSCCCEECCCHHHHHHTTTSTTSCCCCCEEEECHHHHHHHHHSSSCSCCCTTCCEEEESSHHHHHHHC--CHH---
T ss_pred             HHhcccCceEEEEecCccHHHHhhhhhcCCCCEEEECHHHHHHHHHhCCCCcccccCcEEEEeChHHhcccccccHH---
Confidence            86    3444433332222222223345678999999999876554322223456789999999999987542 222   


Q ss_pred             HHHHHHHHhc--CCCCeeEEEeecCcccHHHHHHhc
Q 037567          150 KQLDKLRTFL--LGVPFVALTATATEKVRIDIINSL  183 (374)
Q Consensus       150 ~~~~~~~~~~--~~~~~i~~SaT~~~~~~~~~~~~~  183 (374)
                      ..+..+....  ++.++++||||+++.... +...+
T Consensus       197 ~~~~~i~~~~~~~~~~~~~~SAT~~~~v~~-~~~~~  231 (245)
T 3dkp_A          197 DQLASIFLACTSHKVRRAMFSATFAYDVEQ-WCKLN  231 (245)
T ss_dssp             HHHHHHHHHCCCTTCEEEEEESSCCHHHHH-HHHHH
T ss_pred             HHHHHHHHhcCCCCcEEEEEeccCCHHHHH-HHHHh
Confidence            2333333322  367899999999887654 44433

>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=99.95  E-value=4.2e-28  Score=199.46  Aligned_cols=173  Identities=18%  Similarity=0.154  Sum_probs=128.8

Q ss_pred             hhHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc------cCCcEEEEcchHHHHHHHHHHHHH
Q 037567            2 VSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV------TGKTALVVSPLISLMQDQVMSLKQ   75 (374)
Q Consensus         2 ~~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~------~~~~~lil~P~~~l~~q~~~~~~~   75 (374)
                      .+++.+ +||.+|+|+|.++++.+.+++++++.+|||+|||++|+++++.      .+.+++|++|+++|+.|+.+.+..
T Consensus        15 ~~~l~~-~g~~~~~~~Q~~~i~~~~~~~~~lv~apTGsGKT~~~~~~~~~~~~~~~~~~~~lil~Pt~~L~~q~~~~~~~   93 (206)
T 1vec_A           15 LMGIFE-MGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLERLDLKKDNIQAMVIVPTRELALQVSQICIQ   93 (206)
T ss_dssp             HHHHHT-TTCCSCCHHHHHHHHHHHTTCCEEEECCSSSTTHHHHHHHHHHHCCTTSCSCCEEEECSCHHHHHHHHHHHHH
T ss_pred             HHHHHH-CCCCCCCHHHHHHHHHHccCCCEEEECCCCCchHHHHHHHHHHHhcccCCCeeEEEEeCcHHHHHHHHHHHHH
Confidence            456777 8999999999999999999999999999999999998877664      246799999999999999999887


Q ss_pred             c-----CCceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHH
Q 037567           76 R-----GINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYK  150 (374)
Q Consensus        76 ~-----~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~  150 (374)
                      +     +..+....++...... .......++|+|+||+++......  ....+.+++++|+||||++.+.++.     .
T Consensus        94 ~~~~~~~~~~~~~~g~~~~~~~-~~~~~~~~~i~v~T~~~l~~~~~~--~~~~~~~~~~lViDEah~~~~~~~~-----~  165 (206)
T 1vec_A           94 VSKHMGGAKVMATTGGTNLRDD-IMRLDDTVHVVIATPGRILDLIKK--GVAKVDHVQMIVLDEADKLLSQDFV-----Q  165 (206)
T ss_dssp             HTTTSSSCCEEEECSSSCHHHH-HHHTTSCCSEEEECHHHHHHHHHT--TCSCCTTCCEEEEETHHHHTSTTTH-----H
T ss_pred             HHhhcCCceEEEEeCCccHHHH-HHhcCCCCCEEEeCHHHHHHHHHc--CCcCcccCCEEEEEChHHhHhhCcH-----H
Confidence            5     3445555544433222 222345689999999988654433  2233567899999999998775432     3


Q ss_pred             HHHHHHHhcC-CCCeeEEEeecCcccHHHHHHhc
Q 037567          151 QLDKLRTFLL-GVPFVALTATATEKVRIDIINSL  183 (374)
Q Consensus       151 ~~~~~~~~~~-~~~~i~~SaT~~~~~~~~~~~~~  183 (374)
                      .+..+....+ +.++++||||+++.....+...+
T Consensus       166 ~l~~i~~~~~~~~~~l~~SAT~~~~~~~~~~~~l  199 (206)
T 1vec_A          166 IMEDIILTLPKNRQILLYSATFPLSVQKFMNSHL  199 (206)
T ss_dssp             HHHHHHHHSCTTCEEEEEESCCCHHHHHHHHHHC
T ss_pred             HHHHHHHhCCccceEEEEEeeCCHHHHHHHHHHc
Confidence            4445555444 68899999999887654344333

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19

Probab=99.95  E-value=1.8e-28  Score=203.48  Aligned_cols=172  Identities=17%  Similarity=0.204  Sum_probs=128.8

Q ss_pred             hhHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhcccccc------CCcEEEEcchHHHHHHHHHHHHH
Q 037567            2 VSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVT------GKTALVVSPLISLMQDQVMSLKQ   75 (374)
Q Consensus         2 ~~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~~------~~~~lil~P~~~l~~q~~~~~~~   75 (374)
                      .+++++ +||.+|+|+|.++++.+.+++++++.+|||+|||++|+++++..      +.+++|++|+++|+.|+.+.+++
T Consensus        16 ~~~l~~-~g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~   94 (219)
T 1q0u_A           16 IEAIKT-LRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIMEKIKPERAEVQAVITAPTRELATQIYHETLK   94 (219)
T ss_dssp             HHHHHH-TTCCSCCHHHHHHHHHHHHTCCEEEECCSSHHHHHHHHHHHHHHCCTTSCSCCEEEECSSHHHHHHHHHHHHH
T ss_pred             HHHHHH-CCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhCcCCceEEEEcCcHHHHHHHHHHHHH
Confidence            467776 89999999999999999999999999999999999998887642      56899999999999999999876


Q ss_pred             c--------CCceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchH
Q 037567           76 R--------GINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRL  147 (374)
Q Consensus        76 ~--------~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~  147 (374)
                      +        +.......++...... ......+++|+|+||+++...+..  ....+.+++++|+||||.+.++++.   
T Consensus        95 ~~~~~~~~~~~~~~~~~g~~~~~~~-~~~~~~~~~Iiv~Tp~~l~~~l~~--~~~~~~~~~~lViDEah~~~~~~~~---  168 (219)
T 1q0u_A           95 ITKFCPKDRMIVARCLIGGTDKQKA-LEKLNVQPHIVIGTPGRINDFIRE--QALDVHTAHILVVDEADLMLDMGFI---  168 (219)
T ss_dssp             HHTTSCGGGCCCEEEECCCSHHHHT-TCCCSSCCSEEEECHHHHHHHHHT--TCCCGGGCCEEEECSHHHHHHTTCH---
T ss_pred             HhhhcccccceEEEEEeCCCCHHHH-HHHcCCCCCEEEeCHHHHHHHHHc--CCCCcCcceEEEEcCchHHhhhChH---
Confidence            5        3444444444332222 222234689999999998765433  2234567899999999999876643   


Q ss_pred             HHHHHHHHHHhcC-CCCeeEEEeecCcccHHHHHHhc
Q 037567          148 EYKQLDKLRTFLL-GVPFVALTATATEKVRIDIINSL  183 (374)
Q Consensus       148 ~~~~~~~~~~~~~-~~~~i~~SaT~~~~~~~~~~~~~  183 (374)
                        ..+..+...++ +.++++||||++..... +...+
T Consensus       169 --~~l~~i~~~~~~~~~~l~~SAT~~~~~~~-~~~~~  202 (219)
T 1q0u_A          169 --TDVDQIAARMPKDLQMLVFSATIPEKLKP-FLKKY  202 (219)
T ss_dssp             --HHHHHHHHTSCTTCEEEEEESCCCGGGHH-HHHHH
T ss_pred             --HHHHHHHHhCCcccEEEEEecCCCHHHHH-HHHHH
Confidence              44555555554 67899999999887654 34433

>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=99.95  E-value=1.8e-28  Score=208.59  Aligned_cols=170  Identities=22%  Similarity=0.307  Sum_probs=128.9

Q ss_pred             hhHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc----------cCCcEEEEcchHHHHHHHHH
Q 037567            2 VSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV----------TGKTALVVSPLISLMQDQVM   71 (374)
Q Consensus         2 ~~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~----------~~~~~lil~P~~~l~~q~~~   71 (374)
                      .+++++ +||.+|+|+|.++++.+++++++++.||||||||++|+++++.          .+.+++|++|+++|+.|+.+
T Consensus        66 ~~~l~~-~g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~l~~l~~l~~~~~~~~~~~~~lil~Pt~~La~q~~~  144 (262)
T 3ly5_A           66 LKAIKE-MGFTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPAVELIVKLRFMPRNGTGVLILSPTRELAMQTFG  144 (262)
T ss_dssp             HHHHHH-TTCCBCCHHHHHHHHHHHHTCCCEECCCTTSCHHHHHHHHHHHHHHHTTCCGGGCCCEEEECSSHHHHHHHHH
T ss_pred             HHHHHH-CCCCCCCHHHHHHHHHHhCCCcEEEEccCCCCchHHHHHHHHHHHHhccccccCCceEEEEeCCHHHHHHHHH
Confidence            456777 8999999999999999999999999999999999999988774          47789999999999999999


Q ss_pred             HHHHc----CCceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchH
Q 037567           72 SLKQR----GINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRL  147 (374)
Q Consensus        72 ~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~  147 (374)
                      .++++    +.......++......... ...+++|+|+||+++....... ....+.+++++|+||||++.++++.   
T Consensus       145 ~~~~~~~~~~~~~~~~~g~~~~~~~~~~-~~~~~~Iiv~Tp~~l~~~~~~~-~~~~~~~l~~lViDEah~l~~~~~~---  219 (262)
T 3ly5_A          145 VLKELMTHHVHTYGLIMGGSNRSAEAQK-LGNGINIIVATPGRLLDHMQNT-PGFMYKNLQCLVIDEADRILDVGFE---  219 (262)
T ss_dssp             HHHHHTTTCCSCEEEECSSSCHHHHHHH-HHHCCSEEEECHHHHHHHHHHC-TTCCCTTCCEEEECSHHHHHHTTCH---
T ss_pred             HHHHHHhhcCceEEEEECCCCHHHHHHH-hcCCCCEEEEcHHHHHHHHHcc-CCcccccCCEEEEcChHHHhhhhHH---
Confidence            99875    3444555554443333322 2234899999999986543321 1134567899999999999887643   


Q ss_pred             HHHHHHHHHHhcC-CCCeeEEEeecCcccHHHH
Q 037567          148 EYKQLDKLRTFLL-GVPFVALTATATEKVRIDI  179 (374)
Q Consensus       148 ~~~~~~~~~~~~~-~~~~i~~SaT~~~~~~~~~  179 (374)
                        ..+..+....+ ..++++||||+++......
T Consensus       220 --~~l~~i~~~~~~~~q~l~~SAT~~~~v~~~~  250 (262)
T 3ly5_A          220 --EELKQIIKLLPTRRQTMLFSATQTRKVEDLA  250 (262)
T ss_dssp             --HHHHHHHHHSCSSSEEEEECSSCCHHHHHHH
T ss_pred             --HHHHHHHHhCCCCCeEEEEEecCCHHHHHHH
Confidence              33444445443 5789999999998876433

>2ipc_A Preprotein translocase SECA subunit; nucleotide binding fold, ATPase, parallel dimer; 2.80A {Thermus thermophilus}

Probab=99.95  E-value=3.2e-26  Score=215.05  Aligned_cols=325  Identities=18%  Similarity=0.139  Sum_probs=225.8

Q ss_pred             hhHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhcccc---ccCCcEEEEcchHHHHHHHHHHHHH---
Q 037567            2 VSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPL---VTGKTALVVSPLISLMQDQVMSLKQ---   75 (374)
Q Consensus         2 ~~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~---~~~~~~lil~P~~~l~~q~~~~~~~---   75 (374)
                      .++-++++|+ .|++.|..+++.+++|+  +..+.||+|||++|.+|++   ..+..++|++||+.|+.|...++..   
T Consensus        69 REAs~R~lG~-~Pt~VQ~~~ip~LlqG~--IaeakTGeGKTLvf~Lp~~L~aL~G~qv~VvTPTreLA~Qdae~m~~l~~  145 (997)
T 2ipc_A           69 RESAKRYLGM-RHFDVQLIGGAVLHEGK--IAEMKTGEGKTLVATLAVALNALTGKGVHVVTVNDYLARRDAEWMGPVYR  145 (997)
T ss_dssp             HHHHHHHTCC-CCCHHHHHHHHHHHTTS--EEECCSTHHHHHHHHHHHHHHHTTCSCCEEEESSHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhCC-CCcHHHHhhcccccCCc--eeeccCCCchHHHHHHHHHHHHHhCCCEEEEeCCHHHHHHHHHHHHHHHH
Confidence            4567888999 89999999999999998  9999999999999998884   2477899999999999998888765   


Q ss_pred             -cCCceEEcCCCCCchhhhhhhhcCCeeEEEEcCccc-ccCchhhH----HHHHhc---CccEEEEeccchhh-cccCc-
Q 037567           76 -RGINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKA-CIIPISFW----SKLLKA---GVCLFAVDEAHCIS-EWGHD-  144 (374)
Q Consensus        76 -~~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l-~~~~~~~~----~~~~~~---~~~~vviDE~h~~~-~~~~~-  144 (374)
                       +|+.+.++.++......   .....++|+|+||+.+ .+++....    ....+.   ++.++|+||+|.+. +.+.. 
T Consensus       146 ~lGLsv~~i~Gg~~~~~r---~~ay~~DIvyGTpgrlgfDyLrd~m~~~~~~l~~r~d~~l~~lIIDEaDsmLiDeartP  222 (997)
T 2ipc_A          146 GLGLSVGVIQHASTPAER---RKAYLADVTYVTNSELGFDYLRDNMAISPDQLVLRHDHPLHYAIIDEVDSILIDEARTP  222 (997)
T ss_dssp             TTTCCEEECCTTCCHHHH---HHHHTSSEEEEEHHHHHHHHHHHTSCSSTTTCCSCSSSSSCEEEETTHHHHTTSSTTSC
T ss_pred             hcCCeEEEEeCCCCHHHH---HHHcCCCEEEECchhhhhHHHHHhhhcchhhcccccCCCcceEEEechHHHHHhCCCCC
Confidence             37888877776543221   2223589999999988 44433321    123345   78999999999985 21110 


Q ss_pred             ---------chHHHHHHHHHHH----------------------------------------------------------
Q 037567          145 ---------FRLEYKQLDKLRT----------------------------------------------------------  157 (374)
Q Consensus       145 ---------~~~~~~~~~~~~~----------------------------------------------------------  157 (374)
                               ....+..+..+..                                                          
T Consensus       223 LIISgp~~~~~~lY~~~~~~i~~L~~~~~~~~~~~~~~~~dy~vdek~r~v~LTe~G~~~~E~~l~i~~Ly~~~n~~l~~  302 (997)
T 2ipc_A          223 LIISGPAEKATDLYYKMAEIAKKLERGLPAEPGVRKEPTGDYTVEEKNRSVHLTLQGIAKAEKLLGIEGLFSPENMELAH  302 (997)
T ss_dssp             EEEEESCSSCHHHHHHHHHHHHHSCCCCCCCSSSCCCSSCCCCCTTSCCCCCCCHHHHHHHHHHHSCHHHHTTTCHHHHH
T ss_pred             eeeeCCCccchHHHHHHHHHHHHhhhccccccccccCCCCCeEEecCcceEEEchHHHHHHHHHcCCccccCchhHHHHH
Confidence                     0000000000000                                                          


Q ss_pred             ----------hc------------------------C--------------------------------------CCCee
Q 037567          158 ----------FL------------------------L--------------------------------------GVPFV  165 (374)
Q Consensus       158 ----------~~------------------------~--------------------------------------~~~~i  165 (374)
                                .+                        +                                      -.++.
T Consensus       303 ~i~~ALrA~~lf~rd~dYiV~dgeV~IVDe~TGR~m~grrwsdGLHQAiEAKEgv~I~~e~~TlAsIT~QnyFr~Y~kLs  382 (997)
T 2ipc_A          303 MLIQAIRAKELYHRDRDYIVQDGQVIIVDEFTGRLMPGRRYGEGLHQAIEAKEGVRIERENQTLATITYQNFFRLYEKRA  382 (997)
T ss_dssp             HHHHHHHHHHSSCHHHHEEECSSCEEEEETTTTEECTTCCCGGGHHHHHHHHTTCCCCCSCEEEEEECHHHHHTTSSEEE
T ss_pred             HHHHHHHHHHHHhcCCCeEEECCEEEEEECCCCeeCCCCcccHHHHHHHHHHhCCCCCCCceeeeeeeHHHHHHhChHhe
Confidence                      00                        0                                      01378


Q ss_pred             EEEeecCcccHHHHHHhcCCCCCeEEEeccCCCceeEEEEeecCCcchHHHHHHHHHHhhcCCCcEEEEecchhHHHHHH
Q 037567          166 ALTATATEKVRIDIINSLKLKNPYVTIASFDRKNLFYGVKVINRGQSFVDELVQEILKSVAGAGSIIVYCMTIKDVEEIS  245 (374)
Q Consensus       166 ~~SaT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~  245 (374)
                      +||+|..... ..+...+++.- ..+.+............++.....+...++.++.+....+.++||+|.|.+..+.++
T Consensus       383 GMTGTA~tE~-~Ef~~iY~l~V-v~IPTn~p~~R~D~~d~vy~t~~~K~~AIv~eI~~~~~~GqPVLVgT~SIe~SE~LS  460 (997)
T 2ipc_A          383 GMTGTAKTEE-KEFQEIYGMDV-VVVPTNRPVIRKDFPDVVYRTEKGKFYAVVEEIAEKYERGQPVLVGTISIEKSERLS  460 (997)
T ss_dssp             EEESSCGGGH-HHHHHHHCCCE-EECCCSSCCCCEEEEEEEESSHHHHHHHHHHHHHHHHHHTCCEEEECSSHHHHHHHH
T ss_pred             ecCCCchHHH-HHHHHHhCCCE-EEcCCCCCcccccCCCeEEcCHHHHHHHHHHHHHHHHHCCCCEEEEeCCHHHHHHHH
Confidence            8888887653 35666666652 222222222233334445566666777888888888788999999999999999999


Q ss_pred             HHHH----------------------------------------------------------------------------
Q 037567          246 KALK----------------------------------------------------------------------------  249 (374)
Q Consensus       246 ~~l~----------------------------------------------------------------------------  249 (374)
                      +.|+                                                                            
T Consensus       461 ~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~  540 (997)
T 2ipc_A          461 QMLKEPRLYLPRLEMRLELFKKASQKQQGPEWERLRKLLERPAQLKDEDLAPFEGLIPPKGNLRTAWEGLKRAVHTLAVL  540 (997)
T ss_dssp             HHHHCGGGGHHHHHHHHHHHHHHHTTCCSHHHHHHHHHTSSSTTCSHHHHSGGGGGCCSSHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHhhccccchhhhhhhhhhhhhhhhccccchhhhhhhhhccccccccccccccccccccccccccccccchhhhhhHHH
Confidence            9998                                                                            


Q ss_pred             HcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCc-------------------c------------
Q 037567          250 QLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDV-------------------R------------  298 (374)
Q Consensus       250 ~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~-------------------~------------  298 (374)
                      +.|++...++......+-+.+.+.=+  .-.|.|+|+|+++|.|+.--                   .            
T Consensus       541 ~~gI~H~VLNAK~he~EAeIIAqAG~--~GaVTIATNMAGRGTDIkLggn~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~  618 (997)
T 2ipc_A          541 RQGIPHQVLNAKHHAREAEIVAQAGR--SKTVTIATNMAGRGTDIKLGGNPEYLAAALLEKEGFDRYEWKVELFIKKMVA  618 (997)
T ss_dssp             HHCCCCCEECSSSHHHHHHHHHTTTS--TTCEEEECSSTTTTSCCCSSCCHHHHHHHTTSSSCSSTTHHHHHHHHHHHHH
T ss_pred             HcCCCeeeccccchHHHHHHHHhcCC--CCeEEEEecccCCCcCeecCCCHHHHHHHHHHhhcccccccccccccccccc
Confidence            45566566665543333333333222  23699999999999998532                   1            


Q ss_pred             -------------------------------------------EEEEECCCCChhHHHHhhccCCCCCCceEEEEEeecc
Q 037567          299 -------------------------------------------HVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARS  335 (374)
Q Consensus       299 -------------------------------------------~vi~~~~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~  335 (374)
                                                                 +||....+.|..--.|..||+||.|.+|....|++-+
T Consensus       619 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~V~e~GGLhVIGTeRhESrRIDnQLRGRaGRQGDPGsSrF~LSLe  698 (997)
T 2ipc_A          619 GKEEEARALAQELGIREELLERIREIREECKQDEERVRALGGLFIIGTERHESRRIDNQLRGRAGRQGDPGGSRFYVSFD  698 (997)
T ss_dssp             TCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHTTTCCCCEEESSCCSSHHHHHHHHHTSSCSSCCCEEEEEEESS
T ss_pred             cchhhccccchhhhhhhhHHHHHHHhhhhhhhhhhHHHhcCCeEEEeccCCchHHHHHHHhcccccCCCCCCeEEEEECC
Confidence                                                       6888888899999999999999999999998888776


Q ss_pred             C
Q 037567          336 N  336 (374)
Q Consensus       336 ~  336 (374)
                      |
T Consensus       699 D  699 (997)
T 2ipc_A          699 D  699 (997)
T ss_dssp             S
T ss_pred             h
Confidence            6

>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=99.95  E-value=5.1e-28  Score=202.16  Aligned_cols=166  Identities=19%  Similarity=0.213  Sum_probs=125.5

Q ss_pred             hhHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc------cCCcEEEEcchHHHHHHHHHHHHH
Q 037567            2 VSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV------TGKTALVVSPLISLMQDQVMSLKQ   75 (374)
Q Consensus         2 ~~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~------~~~~~lil~P~~~l~~q~~~~~~~   75 (374)
                      .++|.+ +||.+|+++|.++++.+.+++++++.+|||+|||++|+++++.      .+.+++|++|+++|+.|+.+.++.
T Consensus        36 ~~~l~~-~g~~~~~~~Q~~~i~~~~~~~~~l~~a~TGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~  114 (230)
T 2oxc_A           36 LEGLRA-AGFERPSPVQLKAIPLGRCGLDLIVQAKSGTGKTCVFSTIALDSLVLENLSTQILILAPTREIAVQIHSVITA  114 (230)
T ss_dssp             HHHHHH-TTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCTTSCSCCEEEECSSHHHHHHHHHHHHH
T ss_pred             HHHHHH-CCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHHHhcCCCceEEEEeCCHHHHHHHHHHHHH
Confidence            456766 8999999999999999999999999999999999998877653      256899999999999999999987


Q ss_pred             c-----CCceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHH
Q 037567           76 R-----GINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYK  150 (374)
Q Consensus        76 ~-----~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~  150 (374)
                      +     +..+..+.++.........  ...++|+|+||+++..+...  ....+.+++++|+||||++.++|. +.   .
T Consensus       115 ~~~~~~~~~~~~~~g~~~~~~~~~~--~~~~~Iiv~Tp~~l~~~~~~--~~~~~~~~~~lViDEah~~~~~~~-~~---~  186 (230)
T 2oxc_A          115 IGIKMEGLECHVFIGGTPLSQDKTR--LKKCHIAVGSPGRIKQLIEL--DYLNPGSIRLFILDEADKLLEEGS-FQ---E  186 (230)
T ss_dssp             HTTTSTTCCEEEECTTSCHHHHHHH--TTSCSEEEECHHHHHHHHHT--TSSCGGGCCEEEESSHHHHHSTTS-SH---H
T ss_pred             HhcccCCceEEEEeCCCCHHHHHHh--ccCCCEEEECHHHHHHHHhc--CCcccccCCEEEeCCchHhhcCcc-hH---H
Confidence            6     3455555554433322221  24589999999998765433  223456788999999999987652 22   3


Q ss_pred             HHHHHHHhcC-CCCeeEEEeecCcccH
Q 037567          151 QLDKLRTFLL-GVPFVALTATATEKVR  176 (374)
Q Consensus       151 ~~~~~~~~~~-~~~~i~~SaT~~~~~~  176 (374)
                      .+..+...++ +.++++||||+++...
T Consensus       187 ~~~~i~~~~~~~~~~l~lSAT~~~~~~  213 (230)
T 2oxc_A          187 QINWIYSSLPASKQMLAVSATYPEFLA  213 (230)
T ss_dssp             HHHHHHHHSCSSCEEEEEESCCCHHHH
T ss_pred             HHHHHHHhCCCCCeEEEEEeccCHHHH
Confidence            3444445454 6789999999987654

>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=99.95  E-value=3.1e-28  Score=204.39  Aligned_cols=174  Identities=18%  Similarity=0.192  Sum_probs=124.4

Q ss_pred             hhHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc------cCCcEEEEcchHHHHHHHHHHHHH
Q 037567            2 VSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV------TGKTALVVSPLISLMQDQVMSLKQ   75 (374)
Q Consensus         2 ~~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~------~~~~~lil~P~~~l~~q~~~~~~~   75 (374)
                      .+++.+ +||..|+++|.++++.+++++++++.+|||+|||++|+++++.      .+.+++|++|+++|+.|+.+.++.
T Consensus        42 ~~~l~~-~g~~~~~~~Q~~ai~~i~~~~~~li~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~  120 (237)
T 3bor_A           42 LRGIYA-YGFEKPSAIQQRAIIPCIKGYDVIAQAQSGTGKTATFAISILQQLEIEFKETQALVLAPTRELAQQIQKVILA  120 (237)
T ss_dssp             HHHHHH-HTCCSCCHHHHHHHHHHHTTCCEEECCCSSHHHHHHHHHHHHHHCCTTSCSCCEEEECSSHHHHHHHHHHHHH
T ss_pred             HHHHHH-CCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHHHhcCCCceEEEEECcHHHHHHHHHHHHH
Confidence            456665 8999999999999999999999999999999999999887764      356899999999999999999987


Q ss_pred             cC----CceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHH
Q 037567           76 RG----INAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQ  151 (374)
Q Consensus        76 ~~----~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~  151 (374)
                      ++    .......++............+.++|+|+||+++...+..  .......++++|+||||++.++++.     ..
T Consensus       121 ~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~Ilv~Tp~~l~~~l~~--~~~~~~~~~~lViDEah~~~~~~~~-----~~  193 (237)
T 3bor_A          121 LGDYMGATCHACIGGTNVRNEMQKLQAEAPHIVVGTPGRVFDMLNR--RYLSPKWIKMFVLDEADEMLSRGFK-----DQ  193 (237)
T ss_dssp             HTTTTTCCEEEECC-------------CCCSEEEECHHHHHHHHHT--TSSCSTTCCEEEEESHHHHHHTTCH-----HH
T ss_pred             HhhhcCceEEEEECCCchHHHHHHHhcCCCCEEEECHHHHHHHHHh--CCcCcccCcEEEECCchHhhccCcH-----HH
Confidence            64    4444444444333333333445589999999988665443  2233567899999999999876643     33


Q ss_pred             HHHHHHhc-CCCCeeEEEeecCcccHHHHHHhc
Q 037567          152 LDKLRTFL-LGVPFVALTATATEKVRIDIINSL  183 (374)
Q Consensus       152 ~~~~~~~~-~~~~~i~~SaT~~~~~~~~~~~~~  183 (374)
                      +..+.... ++.++++||||+++.........+
T Consensus       194 l~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~l  226 (237)
T 3bor_A          194 IYEIFQKLNTSIQVVLLSATMPTDVLEVTKKFM  226 (237)
T ss_dssp             HHHHHHHSCTTCEEEEECSSCCHHHHHHHHHHC
T ss_pred             HHHHHHhCCCCCeEEEEEEecCHHHHHHHHHHC
Confidence            33444433 367899999999987664333333

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens}

Probab=99.95  E-value=1.5e-27  Score=200.37  Aligned_cols=177  Identities=23%  Similarity=0.304  Sum_probs=130.2

Q ss_pred             hhHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc----------cCCcEEEEcchHHHHHHHHH
Q 037567            2 VSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV----------TGKTALVVSPLISLMQDQVM   71 (374)
Q Consensus         2 ~~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~----------~~~~~lil~P~~~l~~q~~~   71 (374)
                      .++|++ +||..|+|+|.++++.+.+++++++.+|||+|||++|+++++.          .+.+++|++|+++|+.|+.+
T Consensus        37 ~~~l~~-~~~~~~~~~Q~~~i~~~~~~~~~li~a~TGsGKT~~~~~~~l~~l~~~~~~~~~~~~~lil~Pt~~L~~q~~~  115 (236)
T 2pl3_A           37 LKGLQE-AQYRLVTEIQKQTIGLALQGKDVLGAAKTGSGKTLAFLVPVLEALYRLQWTSTDGLGVLIISPTRELAYQTFE  115 (236)
T ss_dssp             HHHHHH-TTCCBCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHHTTCCGGGCCCEEEECSSHHHHHHHHH
T ss_pred             HHHHHH-CCCCCCCHHHHHHHHHHhCCCCEEEEeCCCCcHHHHHHHHHHHHHHhhcccccCCceEEEEeCCHHHHHHHHH
Confidence            456766 8999999999999999999999999999999999998887663          36789999999999999999


Q ss_pred             HHHHcC----CceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchH
Q 037567           72 SLKQRG----INAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRL  147 (374)
Q Consensus        72 ~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~  147 (374)
                      .++.++    ..+....++..........  ..++|+|+||+++...+... ......+++++|+||||++.++++.   
T Consensus       116 ~~~~~~~~~~~~~~~~~g~~~~~~~~~~~--~~~~iiv~Tp~~l~~~l~~~-~~~~~~~~~~lViDEah~~~~~~~~---  189 (236)
T 2pl3_A          116 VLRKVGKNHDFSAGLIIGGKDLKHEAERI--NNINILVCTPGRLLQHMDET-VSFHATDLQMLVLDEADRILDMGFA---  189 (236)
T ss_dssp             HHHHHTTTSSCCEEEECCC--CHHHHHHH--TTCSEEEECHHHHHHHHHHC-SSCCCTTCCEEEETTHHHHHHTTTH---
T ss_pred             HHHHHhCCCCeeEEEEECCCCHHHHHHhC--CCCCEEEECHHHHHHHHHhc-CCcccccccEEEEeChHHHhcCCcH---
Confidence            998864    4555555544433322222  46899999999986543321 1123467889999999999876653   


Q ss_pred             HHHHHHHHHHhcC-CCCeeEEEeecCcccHHHHHHhcCCCCCe
Q 037567          148 EYKQLDKLRTFLL-GVPFVALTATATEKVRIDIINSLKLKNPY  189 (374)
Q Consensus       148 ~~~~~~~~~~~~~-~~~~i~~SaT~~~~~~~~~~~~~~~~~~~  189 (374)
                        ..+..+...++ +.++++||||+++.... +... .+.++.
T Consensus       190 --~~~~~i~~~~~~~~~~l~~SAT~~~~~~~-~~~~-~~~~p~  228 (236)
T 2pl3_A          190 --DTMNAVIENLPKKRQTLLFSATQTKSVKD-LARL-SLKNPE  228 (236)
T ss_dssp             --HHHHHHHHTSCTTSEEEEEESSCCHHHHH-HHHH-SCSSCE
T ss_pred             --HHHHHHHHhCCCCCeEEEEEeeCCHHHHH-HHHH-hCCCCE
Confidence              34455555554 67799999999887653 3333 334443

>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=99.95  E-value=1.1e-27  Score=202.06  Aligned_cols=168  Identities=20%  Similarity=0.225  Sum_probs=128.2

Q ss_pred             hhHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc------cCCcEEEEcchHHHHHHHHHHHHH
Q 037567            2 VSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV------TGKTALVVSPLISLMQDQVMSLKQ   75 (374)
Q Consensus         2 ~~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~------~~~~~lil~P~~~l~~q~~~~~~~   75 (374)
                      .++|++ +||..|+++|.++++.+++++++++.+|||+|||++|+++++.      .+.+++|++|+++|+.|+.+.++.
T Consensus        55 ~~~l~~-~g~~~~~~~Q~~~i~~i~~~~~~lv~a~TGsGKT~~~~~~il~~l~~~~~~~~~lil~Ptr~L~~q~~~~~~~  133 (249)
T 3ber_A           55 CEACDQ-LGWTKPTKIQIEAIPLALQGRDIIGLAETGSGKTGAFALPILNALLETPQRLFALVLTPTRELAFQISEQFEA  133 (249)
T ss_dssp             HHHHHH-TTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHHSCCSSCEEEECSSHHHHHHHHHHHHH
T ss_pred             HHHHHH-cCCCCCCHHHHHHHHHHhCCCCEEEEcCCCCCchhHhHHHHHHHHhcCCCCceEEEEeCCHHHHHHHHHHHHH
Confidence            456666 8999999999999999999999999999999999999888764      256799999999999999999887


Q ss_pred             c----CCceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHH
Q 037567           76 R----GINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQ  151 (374)
Q Consensus        76 ~----~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~  151 (374)
                      +    +.......++...... .......++|+|+||+++...+... ....+.+++++|+||||++.++++.     ..
T Consensus       134 ~~~~~~~~~~~~~g~~~~~~~-~~~~~~~~~I~v~Tp~~l~~~l~~~-~~~~l~~~~~lViDEah~l~~~~~~-----~~  206 (249)
T 3ber_A          134 LGSSIGVQSAVIVGGIDSMSQ-SLALAKKPHIIIATPGRLIDHLENT-KGFNLRALKYLVMDEADRILNMDFE-----TE  206 (249)
T ss_dssp             HHGGGTCCEEEECTTSCHHHH-HHHHHTCCSEEEECHHHHHHHHHHS-TTCCCTTCCEEEECSHHHHHHTTCH-----HH
T ss_pred             HhccCCeeEEEEECCCChHHH-HHHhcCCCCEEEECHHHHHHHHHcC-CCcCccccCEEEEcChhhhhccChH-----HH
Confidence            6    5666666555433322 2233456899999999986554321 1223567899999999999876543     33


Q ss_pred             HHHHHHhcC-CCCeeEEEeecCcccHH
Q 037567          152 LDKLRTFLL-GVPFVALTATATEKVRI  177 (374)
Q Consensus       152 ~~~~~~~~~-~~~~i~~SaT~~~~~~~  177 (374)
                      +..+...++ +.++++||||++.....
T Consensus       207 l~~i~~~~~~~~~~l~~SAT~~~~v~~  233 (249)
T 3ber_A          207 VDKILKVIPRDRKTFLFSATMTKKVQK  233 (249)
T ss_dssp             HHHHHHSSCSSSEEEEEESSCCHHHHH
T ss_pred             HHHHHHhCCCCCeEEEEeccCCHHHHH
Confidence            444444443 67899999999987654

>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=99.95  E-value=1.4e-27  Score=198.90  Aligned_cols=170  Identities=19%  Similarity=0.196  Sum_probs=123.2

Q ss_pred             hhHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc------cCCcEEEEcchHHHHHHHHHHHHH
Q 037567            2 VSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV------TGKTALVVSPLISLMQDQVMSLKQ   75 (374)
Q Consensus         2 ~~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~------~~~~~lil~P~~~l~~q~~~~~~~   75 (374)
                      .+.+.+ +||.+|+|+|.++++.+.+++++++.+|||+|||++|+++++.      .+.+++|++|+++|+.|+.+.+..
T Consensus        26 ~~~l~~-~g~~~~~~~Q~~~i~~~~~~~~~lv~~pTGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~  104 (224)
T 1qde_A           26 LRGVFG-YGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALMLAPTRELALQIQKVVMA  104 (224)
T ss_dssp             HHHHHH-HTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCTTCCSCCEEEECSSHHHHHHHHHHHHH
T ss_pred             HHHHHH-CCCCCCcHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHHhccCCCceEEEEECCHHHHHHHHHHHHH
Confidence            456766 7999999999999999999999999999999999998877663      356899999999999999999987


Q ss_pred             c----CCceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHH
Q 037567           76 R----GINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQ  151 (374)
Q Consensus        76 ~----~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~  151 (374)
                      +    +..+....++..........  ..++|+|+||+++...+..  ......+++++|+||||++.+++..     ..
T Consensus       105 ~~~~~~~~~~~~~g~~~~~~~~~~~--~~~~iiv~Tp~~l~~~~~~--~~~~~~~~~~iViDEah~~~~~~~~-----~~  175 (224)
T 1qde_A          105 LAFHMDIKVHACIGGTSFVEDAEGL--RDAQIVVGTPGRVFDNIQR--RRFRTDKIKMFILDEADEMLSSGFK-----EQ  175 (224)
T ss_dssp             HTTTSCCCEEEECC----------C--TTCSEEEECHHHHHHHHHT--TSSCCTTCCEEEEETHHHHHHTTCH-----HH
T ss_pred             HhcccCceEEEEeCCcchHHHHhcC--CCCCEEEECHHHHHHHHHh--CCcchhhCcEEEEcChhHHhhhhhH-----HH
Confidence            6    44555555443332222211  2379999999988655433  2233567899999999999876643     33


Q ss_pred             HHHHHHhc-CCCCeeEEEeecCcccHHHHHH
Q 037567          152 LDKLRTFL-LGVPFVALTATATEKVRIDIIN  181 (374)
Q Consensus       152 ~~~~~~~~-~~~~~i~~SaT~~~~~~~~~~~  181 (374)
                      +..+.... ++.++++||||+++........
T Consensus       176 l~~i~~~~~~~~~~i~lSAT~~~~~~~~~~~  206 (224)
T 1qde_A          176 IYQIFTLLPPTTQVVLLSATMPNDVLEVTTK  206 (224)
T ss_dssp             HHHHHHHSCTTCEEEEEESSCCHHHHHHHHH
T ss_pred             HHHHHHhCCccCeEEEEEeecCHHHHHHHHH
Confidence            44444443 3678999999999876543333

>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=99.94  E-value=2.4e-27  Score=195.06  Aligned_cols=172  Identities=19%  Similarity=0.181  Sum_probs=127.9

Q ss_pred             hhHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc---------cCCcEEEEcchHHHHHHHHHH
Q 037567            2 VSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV---------TGKTALVVSPLISLMQDQVMS   72 (374)
Q Consensus         2 ~~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~---------~~~~~lil~P~~~l~~q~~~~   72 (374)
                      .+++++ +||.+|+|+|.++++.+.+++++++.+|||+|||++|+++++.         .+.+++|++|+++|+.|+.+.
T Consensus        13 ~~~l~~-~~~~~~~~~Q~~~i~~~~~~~~~li~~~TGsGKT~~~~~~~~~~l~~~~~~~~~~~~lil~P~~~L~~q~~~~   91 (207)
T 2gxq_A           13 LEALHG-RGLTTPTPIQAAALPLALEGKDLIGQARTGTGKTLAFALPIAERLAPSQERGRKPRALVLTPTRELALQVASE   91 (207)
T ss_dssp             HHHHHH-TTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCCCCCTTCCCSEEEECSSHHHHHHHHHH
T ss_pred             HHHHHH-cCCCCCCHHHHHHHHHHcCCCCEEEECCCCChHHHHHHHHHHHHHhhccccCCCCcEEEEECCHHHHHHHHHH
Confidence            456776 8999999999999999999999999999999999998777653         356899999999999999999


Q ss_pred             HHHcC--CceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHH
Q 037567           73 LKQRG--INAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYK  150 (374)
Q Consensus        73 ~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~  150 (374)
                      +..+.  .......++........ .....++|+|+||+++......  ....+.+++++|+||||++.+.+..     .
T Consensus        92 ~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~i~v~T~~~l~~~~~~--~~~~~~~~~~iViDEah~~~~~~~~-----~  163 (207)
T 2gxq_A           92 LTAVAPHLKVVAVYGGTGYGKQKE-ALLRGADAVVATPGRALDYLRQ--GVLDLSRVEVAVLDEADEMLSMGFE-----E  163 (207)
T ss_dssp             HHHHCTTSCEEEECSSSCSHHHHH-HHHHCCSEEEECHHHHHHHHHH--TSSCCTTCSEEEEESHHHHHHTTCH-----H
T ss_pred             HHHHhhcceEEEEECCCChHHHHH-HhhCCCCEEEECHHHHHHHHHc--CCcchhhceEEEEEChhHhhccchH-----H
Confidence            99874  44555555443332222 2234579999999988665433  2234567899999999999775543     3


Q ss_pred             HHHHHHHhcC-CCCeeEEEeecCcccHHHHHHhc
Q 037567          151 QLDKLRTFLL-GVPFVALTATATEKVRIDIINSL  183 (374)
Q Consensus       151 ~~~~~~~~~~-~~~~i~~SaT~~~~~~~~~~~~~  183 (374)
                      .+..+....+ +.++++||||+++.... +...+
T Consensus       164 ~~~~i~~~~~~~~~~i~~SAT~~~~~~~-~~~~~  196 (207)
T 2gxq_A          164 EVEALLSATPPSRQTLLFSATLPSWAKR-LAERY  196 (207)
T ss_dssp             HHHHHHHTSCTTSEEEEECSSCCHHHHH-HHHHH
T ss_pred             HHHHHHHhCCccCeEEEEEEecCHHHHH-HHHHH
Confidence            3444444443 67899999999887653 44433

>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=99.94  E-value=3.3e-27  Score=200.29  Aligned_cols=167  Identities=19%  Similarity=0.228  Sum_probs=125.0

Q ss_pred             hhHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhcccccc---------------CCcEEEEcchHHHH
Q 037567            2 VSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVT---------------GKTALVVSPLISLM   66 (374)
Q Consensus         2 ~~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~~---------------~~~~lil~P~~~l~   66 (374)
                      .++|.+ +||.+|+|+|.++++.+++++++++.+|||+|||++|+++++..               +.++||++|+++|+
T Consensus        35 ~~~l~~-~g~~~~~~~Q~~~i~~i~~~~~~l~~a~TGsGKT~~~~~~~l~~l~~~~~~~~~~~~~~~~~~lil~Pt~~L~  113 (253)
T 1wrb_A           35 RNNILL-ASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIINHLVCQDLNQQRYSKTAYPKCLILAPTRELA  113 (253)
T ss_dssp             TTTTTT-TTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHTTCC------CCBCCSEEEECSSHHHH
T ss_pred             HHHHHH-CCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhhccccccccccCCceEEEEECCHHHH
Confidence            345665 79999999999999999999999999999999999998887631               35899999999999


Q ss_pred             HHHHHHHHHcC----CceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhccc
Q 037567           67 QDQVMSLKQRG----INAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWG  142 (374)
Q Consensus        67 ~q~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~  142 (374)
                      .|+.+.++.++    .......++....... ......++|+|+||+++...+..  ....+.+++++|+||||++.+++
T Consensus       114 ~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~-~~~~~~~~Ivv~Tp~~l~~~l~~--~~~~~~~~~~lViDEah~~~~~~  190 (253)
T 1wrb_A          114 IQILSESQKFSLNTPLRSCVVYGGADTHSQI-REVQMGCHLLVATPGRLVDFIEK--NKISLEFCKYIVLDEADRMLDMG  190 (253)
T ss_dssp             HHHHHHHHHHHTTSSCCEEEECSSSCSHHHH-HHHSSCCSEEEECHHHHHHHHHT--TSBCCTTCCEEEEETHHHHHHTT
T ss_pred             HHHHHHHHHHhccCCceEEEEECCCCHHHHH-HHhCCCCCEEEECHHHHHHHHHc--CCCChhhCCEEEEeCHHHHHhCc
Confidence            99999988763    4445555544333322 22345689999999998765443  22345678899999999998766


Q ss_pred             CcchHHHHHHHHHHHh--cC---CCCeeEEEeecCcccHH
Q 037567          143 HDFRLEYKQLDKLRTF--LL---GVPFVALTATATEKVRI  177 (374)
Q Consensus       143 ~~~~~~~~~~~~~~~~--~~---~~~~i~~SaT~~~~~~~  177 (374)
                      +.     ..+..+...  .+   +.++++||||+++....
T Consensus       191 ~~-----~~~~~i~~~~~~~~~~~~q~l~~SAT~~~~~~~  225 (253)
T 1wrb_A          191 FE-----PQIRKIIEESNMPSGINRQTLMFSATFPKEIQK  225 (253)
T ss_dssp             CH-----HHHHHHHHSSCCCCGGGCEEEEEESSCCHHHHH
T ss_pred             hH-----HHHHHHHhhccCCCCCCcEEEEEEEeCCHHHHH
Confidence            43     334444442  22   46799999999887654

>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=99.94  E-value=6e-27  Score=202.71  Aligned_cols=165  Identities=16%  Similarity=0.226  Sum_probs=123.2

Q ss_pred             hhHHHhHcCCCCCchhHHHHHHHHHcC--CCEEEEccCCCCchhhhhccccc------cCCcEEEEcchHHHHHHHHHHH
Q 037567            2 VSTLKKYFGYSVFRPYQKDVIQRIIEK--RDCLVVMATGSGKSLCYQLPPLV------TGKTALVVSPLISLMQDQVMSL   73 (374)
Q Consensus         2 ~~~l~~~~~~~~~~~~Q~~~~~~~~~~--~~~l~~a~tGsGKT~~~~l~~~~------~~~~~lil~P~~~l~~q~~~~~   73 (374)
                      .++|.. +||..|+++|.++++.++++  +++++.||||||||++|+++++.      ...++||++|+++|+.|+.+.+
T Consensus       104 ~~~l~~-~g~~~pt~iQ~~ai~~il~~~~~~~l~~a~TGsGKT~a~~lp~l~~l~~~~~~~~~lil~PtreLa~Q~~~~~  182 (300)
T 3fmo_B          104 LQGVYA-MGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSPTYELALQTGKVI  182 (300)
T ss_dssp             HHHHHH-TTCCSCCHHHHHHHHHHTSSSCCCEEEECCTTSSHHHHHHHHHHHHCCTTSCSCCEEEECSSHHHHHHHHHHH
T ss_pred             HHHHHH-cCCCCCCHHHHHHHHHHHcCCCCeEEEECCCCCCccHHHHHHHHHhhhccCCCceEEEEcCcHHHHHHHHHHH
Confidence            456776 89999999999999999987  89999999999999999988774      2457999999999999999888


Q ss_pred             HHcC-----CceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhc-ccCcchH
Q 037567           74 KQRG-----INAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISE-WGHDFRL  147 (374)
Q Consensus        74 ~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~-~~~~~~~  147 (374)
                      ..++     .......++.....    .....++|+|+||+++..++... ....+.+++++|+||+|++.+ .++.   
T Consensus       183 ~~l~~~~~~~~~~~~~~~~~~~~----~~~~~~~IlV~TP~~l~~~l~~~-~~~~l~~l~~lVlDEad~l~~~~~~~---  254 (300)
T 3fmo_B          183 EQMGKFYPELKLAYAVRGNKLER----GQKISEQIVIGTPGTVLDWCSKL-KFIDPKKIKVFVLDEADVMIATQGHQ---  254 (300)
T ss_dssp             HHHTTTSTTCCEEEESTTCCCCT----TCCCCCSEEEECHHHHHHHHTTT-CCCCGGGCSEEEETTHHHHHHSTTHH---
T ss_pred             HHHHhhCCCcEEEEEeCCccHhh----hhcCCCCEEEECHHHHHHHHHhc-CCCChhhceEEEEeCHHHHhhccCcH---
Confidence            8753     34444443332211    11345799999999986654321 223457889999999999986 3422   


Q ss_pred             HHHHHHHHHHhc-CCCCeeEEEeecCcccHH
Q 037567          148 EYKQLDKLRTFL-LGVPFVALTATATEKVRI  177 (374)
Q Consensus       148 ~~~~~~~~~~~~-~~~~~i~~SaT~~~~~~~  177 (374)
                        ..+..+...+ ++.++++||||++.....
T Consensus       255 --~~~~~i~~~~~~~~q~i~~SAT~~~~v~~  283 (300)
T 3fmo_B          255 --DQSIRIQRMLPRNCQMLLFSATFEDSVWK  283 (300)
T ss_dssp             --HHHHHHHTTSCTTCEEEEEESCCCHHHHH
T ss_pred             --HHHHHHHHhCCCCCEEEEEeccCCHHHHH
Confidence              3333444443 368899999999997764

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}

Probab=99.93  E-value=6.8e-26  Score=211.66  Aligned_cols=307  Identities=17%  Similarity=0.224  Sum_probs=170.8

Q ss_pred             HcCCCCCchhHHHHHHHH----HcCCCEEEEccCCCCchhhhhccccccCCcEEEEcchHHHHHHHHHHHHHcCCceEEc
Q 037567            8 YFGYSVFRPYQKDVIQRI----IEKRDCLVVMATGSGKSLCYQLPPLVTGKTALVVSPLISLMQDQVMSLKQRGINAEFL   83 (374)
Q Consensus         8 ~~~~~~~~~~Q~~~~~~~----~~~~~~l~~a~tGsGKT~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~   83 (374)
                      ..|| ++||+|.+++..+    .+++++++.||||+|||++|+++++....+++|++||++|++|+.+++..++.+...+
T Consensus         3 ~~~~-~~r~~Q~~~~~~v~~~~~~~~~~~~~a~TGtGKT~~~l~~~~~~~~~~~~~~~t~~l~~q~~~~~~~l~~~~~~l   81 (540)
T 2vl7_A            3 VLKL-QLRQWQAEKLGEAINALKHGKTLLLNAKPGLGKTVFVEVLGMQLKKKVLIFTRTHSQLDSIYKNAKLLGLKTGFL   81 (540)
T ss_dssp             -------CCHHHHHHHHHHHHHHTTCEEEEECCTTSCHHHHHHHHHHHHTCEEEEEESCHHHHHHHHHHHGGGTCCEEEC
T ss_pred             CCCC-CCCHHHHHHHHHHHHHHHcCCCEEEEcCCCCcHHHHHHHHHHhCCCcEEEEcCCHHHHHHHHHHHHhcCCcEEEe
Confidence            4678 7999999987654    5688999999999999999999999889999999999999999999999887666555


Q ss_pred             CCCCCch-------h-------------------------hh--------------hhhhcCCeeEEEEcCcccccCchh
Q 037567           84 GSAQTDS-------S-------------------------VQ--------------TKAETGYFQLLFMTPEKACIIPIS  117 (374)
Q Consensus        84 ~~~~~~~-------~-------------------------~~--------------~~~~~~~~~i~i~T~~~l~~~~~~  117 (374)
                      .+.....       .                         .+              ........+|+|+|+..+......
T Consensus        82 ~gr~~lC~~~~~~~~~~~~~c~~c~~~~~~~~~gd~~~~~~~~~~~~~~~~Cpy~~~r~~~~~adiVV~n~~~l~~~~~~  161 (540)
T 2vl7_A           82 IGKSASCIYAQGDEEPDEINCSKCRLKDKIKTIEDKEPSKLIEEFKDAVDYCPYYSLRANLKDKDVIAMTYPYLFQKPIR  161 (540)
T ss_dssp             ---------------------------------------------------------CTTGGGCSEEEEETHHHHSHHHH
T ss_pred             cCCccccCCchhcccccccCCCCCCchhcccccccCCcHHHHHHHhhhcCCChHHHHHHHhhcCCEEEEChHHhcCHHHH
Confidence            4322100       0                         00              001123459999999988664322


Q ss_pred             hHHHHH-------hcCccEEEEeccchhhcccCcc----------hHHH-------------------------------
Q 037567          118 FWSKLL-------KAGVCLFAVDEAHCISEWGHDF----------RLEY-------------------------------  149 (374)
Q Consensus       118 ~~~~~~-------~~~~~~vviDE~h~~~~~~~~~----------~~~~-------------------------------  149 (374)
                        ....       .....++||||||++.. ..+.          ....                               
T Consensus       162 --~~~~~~~~~~~~~~~~~vIiDEAHnl~~-a~~~~s~~ls~~~l~~~~~~l~~~~~~~~~~~~~l~~~~~~l~~~l~~~  238 (540)
T 2vl7_A          162 --NSVFCNKDDCLKLEDYLIVIDEAHNLLE-ADKWFTRKISRKMLERALKEIEIVERLNRIDAKKVKDYINLLIDYMSKL  238 (540)
T ss_dssp             --HHHSCSSTTSCCGGGEEEEETTGGGGGG-GGGGGCEEECHHHHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHHTS
T ss_pred             --HhhCcccccccCcCCCEEEEEccccHHH-HHHHhccccCHHHHHHHHHHHHHHHhcchhhHHHHHHHHHHHHHHHHHh
Confidence              2221       24567999999999943 1000          0000                               


Q ss_pred             --------------------HHHHHHH--------------------Hh---------------cCC----------CC-
Q 037567          150 --------------------KQLDKLR--------------------TF---------------LLG----------VP-  163 (374)
Q Consensus       150 --------------------~~~~~~~--------------------~~---------------~~~----------~~-  163 (374)
                                          ..+..+.                    ..               ..+          .. 
T Consensus       239 ~~~~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~l~~~P~~~~~~l~~~~~~  318 (540)
T 2vl7_A          239 IKDGRCHELSLMPLPDRETNGELIVVTRAYLNIDEGPVKKSSLKSLLKFVEMKGDLYNCNGSLVKVPSDVNQLIEDALNV  318 (540)
T ss_dssp             CCSSSEEEESCCCCCCHHHHHHHHHHHHHHHTTCCSSSCCCHHHHHHHHHHSCCEEEEETTEEEEECSCHHHHHHHHTCC
T ss_pred             hccccccchhhcccccHHHHHHHHHHHHHHHHhhccCccHHHHHHHHHHHHhCCCEEEECCeEEEehHHHHHHHHHhcCc
Confidence                                0000000                    00               000          12 


Q ss_pred             ---eeEEEeecCcccHHHHHHhcCCCCCeEEEec-cCCCceeEEEEeecCCc-------chHHHHHHHHHHhhcCCCcEE
Q 037567          164 ---FVALTATATEKVRIDIINSLKLKNPYVTIAS-FDRKNLFYGVKVINRGQ-------SFVDELVQEILKSVAGAGSII  232 (374)
Q Consensus       164 ---~i~~SaT~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~l  232 (374)
                         +|++|||+.+...  +...+.     ..... ......... .......       ..+.+.+..+...  ..++++
T Consensus       319 ~~~~IltSATL~p~~~--~~~~f~-----~~~~~~~g~~~~~~~-~~l~s~f~~r~~~~~~~~~~l~~~~~~--~~g~~l  388 (540)
T 2vl7_A          319 KTFKVLMSGTLPESLT--LTNSYK-----IVVNESYGRGEYYYC-PNVTSELRKRNSNIPIYSILLKRIYEN--SSKSVL  388 (540)
T ss_dssp             SSCEEEEESSCCTTCC--CTTEEE-----EECCCC-CCCEEEEC-TTCCCCGGGHHHHHHHHHHHHHHHHHT--CSSEEE
T ss_pred             cCCeEEEcccCCCCcc--cchhcC-----CchhheecCCcceec-cccCCCcccccCHHHHHHHHHHHHHHh--CCCCEE
Confidence               3777888776200  000000     00000 000000000 0011111       1122233333332  467899


Q ss_pred             EEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEE--EeccccccccccC----ccEEEEECCC
Q 037567          233 VYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMV--ATMAFGMGIDKPD----VRHVIHYGCP  306 (374)
Q Consensus       233 Vf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv--~t~~~~~G~d~~~----~~~vi~~~~p  306 (374)
                      ||++|...++.+++.++.  . ....++..  .++..+++.|+++. .|++  +|..+++|+|+|+    +++||+.+.|
T Consensus       389 vff~S~~~~~~v~~~l~~--~-~~~~q~~~--~~~~~~l~~f~~~~-~il~~V~~~~~~EGiD~~~~~~~~~~Vii~~lP  462 (540)
T 2vl7_A          389 VFFPSYEMLESVRIHLSG--I-PVIEENKK--TRHEEVLELMKTGK-YLVMLVMRAKESEGVEFREKENLFESLVLAGLP  462 (540)
T ss_dssp             EEESCHHHHHHHHTTCTT--S-CEEESTTT--CCHHHHHHHHHTSC-CEEEEEC---------------CEEEEEEESCC
T ss_pred             EEeCCHHHHHHHHHHhcc--C-ceEecCCC--CcHHHHHHHHhcCC-eEEEEEecCceecceecCCCcccccEEEEECCC
Confidence            999999999999988864  2 23455543  57889999998865 5666  7799999999998    7889999988


Q ss_pred             CCh------------------------------hHHHHhhccCCCCCCceEEEEEeec
Q 037567          307 KTL------------------------------ESYYQESGRCGRDGIASVCWLYYAR  334 (374)
Q Consensus       307 ~s~------------------------------~~~~Q~~GR~~R~~~~g~~~~~~~~  334 (374)
                      ...                              ..+.|.+||+.|...+..+++++++
T Consensus       463 f~~~~d~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~Q~~GR~iR~~~D~g~v~llD~  520 (540)
T 2vl7_A          463 YPNVSDDMVRKRIERLSKLTGKDEDSIIHDLTAIVIKQTIGRAFRDPNDYVKIYLCDS  520 (540)
T ss_dssp             CCCTTSHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHCCSTTCCCEEEEESG
T ss_pred             CCCCCCHHHHHHHHHHHHhhCCChhHHHHHHHHHHHHHHhCCcccCCCccEEEEEEcc
Confidence            521                              3457999999998554434444444

>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase; 1.95A {Bacillus subtilis}

Probab=99.93  E-value=3.4e-25  Score=174.42  Aligned_cols=131  Identities=27%  Similarity=0.372  Sum_probs=118.1

Q ss_pred             chHHHHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEecccccc
Q 037567          212 SFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMG  291 (374)
Q Consensus       212 ~~~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G  291 (374)
                      ....+.+.+++... .++++||||+++..++.+++.|.+.++.+..+||+++..+|..+++.|++|+.+|||+|+++++|
T Consensus        20 ~~K~~~L~~ll~~~-~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~hg~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~G   98 (163)
T 2hjv_A           20 ENKFSLLKDVLMTE-NPDSCIIFCRTKEHVNQLTDELDDLGYPCDKIHGGMIQEDRFDVMNEFKRGEYRYLVATDVAARG   98 (163)
T ss_dssp             GGHHHHHHHHHHHH-CCSSEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECGGGTTT
T ss_pred             HHHHHHHHHHHHhc-CCCcEEEEECCHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHHcCCCeEEEECChhhcC
Confidence            34455666666654 67899999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccCccEEEEECCCCChhHHHHhhccCCCCCCceEEEEEeeccCCCcccce
Q 037567          292 IDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFY  343 (374)
Q Consensus       292 ~d~~~~~~vi~~~~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~~~~~~~~  343 (374)
                      +|+|++++||++++|+++.+|+||+||+||.|+.|.+++++.+.+...++.+
T Consensus        99 ld~~~~~~Vi~~~~p~~~~~~~qr~GR~~R~g~~g~~~~~~~~~~~~~~~~i  150 (163)
T 2hjv_A           99 IDIENISLVINYDLPLEKESYVHRTGRTGRAGNKGKAISFVTAFEKRFLADI  150 (163)
T ss_dssp             CCCSCCSEEEESSCCSSHHHHHHHTTTSSCTTCCEEEEEEECGGGHHHHHHH
T ss_pred             CchhcCCEEEEeCCCCCHHHHHHhccccCcCCCCceEEEEecHHHHHHHHHH
Confidence            9999999999999999999999999999999999999999988765444433

>2jgn_A DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosphorylation, nucleotide-binding, hydrolase, RNA-binding, ATP-binding, DNA-binding, nuclear protein; 1.91A {Homo sapiens}

Probab=99.93  E-value=4.2e-25  Score=177.16  Aligned_cols=133  Identities=23%  Similarity=0.379  Sum_probs=107.7

Q ss_pred             hHHHHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccc
Q 037567          213 FVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGI  292 (374)
Q Consensus       213 ~~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~  292 (374)
                      .....+.++++....++++||||+++..++.+++.|+..|+.+..+||+++..+|..+++.|++|+.+|||+|+++++|+
T Consensus        31 ~K~~~L~~ll~~~~~~~k~lVF~~~~~~~~~l~~~L~~~g~~~~~lhg~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gl  110 (185)
T 2jgn_A           31 DKRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILVATAVAARGL  110 (185)
T ss_dssp             GHHHHHHHHHHHC-CCSCEEEEESCHHHHHHHHHHHHHTTCCEEEEC--------CHHHHHHHHTSSSEEEEEC------
T ss_pred             HHHHHHHHHHHhcCCCCeEEEEECCHHHHHHHHHHHHHcCCceEEEeCCCCHHHHHHHHHHHHcCCCeEEEEcChhhcCC
Confidence            34556666766655688999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccCccEEEEECCCCChhHHHHhhccCCCCCCceEEEEEeeccCCCcccceec
Q 037567          293 DKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFYCG  345 (374)
Q Consensus       293 d~~~~~~vi~~~~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~~~~~~~~~~  345 (374)
                      |+|++++||++++|+++.+|+||+||+||.|+.|.+++++++.+...++.+.+
T Consensus       111 di~~~~~VI~~d~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~l~~  163 (185)
T 2jgn_A          111 DISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNERNINITKDLLD  163 (185)
T ss_dssp             CCCSBSEEEESSCCSSHHHHHHHHTTBCCTTSCEEEEEEECGGGGGGHHHHHH
T ss_pred             CcccCCEEEEeCCCCCHHHHHHHccccCCCCCCcEEEEEEchhhHHHHHHHHH
Confidence            99999999999999999999999999999999999999999988777666654

>3eaq_A Heat resistant RNA dependent ATPase; DEAD box RNA helicase, dimer, ATP-binding, helicase, hydrolase, nucleotide-binding; 2.30A {Thermus thermophilus} PDB: 3ear_A 3eas_A

Probab=99.92  E-value=1.6e-24  Score=177.91  Aligned_cols=128  Identities=31%  Similarity=0.460  Sum_probs=115.5

Q ss_pred             chHHHHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEecccccc
Q 037567          212 SFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMG  291 (374)
Q Consensus       212 ~~~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G  291 (374)
                      ....+.+.++++.. .++++||||+++..++.+++.|.+.++.+..+||+++..+|..+++.|++|+.+|||+|+++++|
T Consensus        16 ~~k~~~l~~ll~~~-~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~r~~~~~~f~~g~~~vlvaT~~~~~G   94 (212)
T 3eaq_A           16 RGRLEVLSDLLYVA-SPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDLSQGERERVLGAFRQGEVRVLVATDVAARG   94 (212)
T ss_dssp             TSHHHHHHHHHHHH-CCSCEEEECSSHHHHHHHHHHHHHHTCCEEEECSSSCHHHHHHHHHHHHSSSCCEEEECTTTTCS
T ss_pred             HHHHHHHHHHHHhC-CCCeEEEEeCCHHHHHHHHHHHHHcCCCEEEEECCCCHHHHHHHHHHHHCCCCeEEEecChhhcC
Confidence            34556666666653 67899999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccCccEEEEECCCCChhHHHHhhccCCCCCCceEEEEEeeccCCCcc
Q 037567          292 IDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKG  340 (374)
Q Consensus       292 ~d~~~~~~vi~~~~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~~~~~  340 (374)
                      +|+|++++||++++|++...|+||+||+||.|+.|.+++++++.+...+
T Consensus        95 idi~~v~~Vi~~~~p~~~~~~~qr~GR~gR~g~~g~~~~l~~~~~~~~~  143 (212)
T 3eaq_A           95 LDIPQVDLVVHYRLPDRAEAYQHRSGRTGRAGRGGRVVLLYGPRERRDV  143 (212)
T ss_dssp             SSCCCBSEEEESSCCSSHHHHHHHHTTBCCCC--BEEEEEECGGGHHHH
T ss_pred             CCCccCcEEEECCCCcCHHHHHHHhcccCCCCCCCeEEEEEchhHHHHH
Confidence            9999999999999999999999999999999999999999999874443

>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein, translation; 1.75A {Saccharomyces cerevisiae} SCOP: c.37.1.19

Probab=99.92  E-value=1e-24  Score=172.06  Aligned_cols=129  Identities=22%  Similarity=0.367  Sum_probs=112.8

Q ss_pred             HHHHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEecccccccc
Q 037567          214 VDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGID  293 (374)
Q Consensus       214 ~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d  293 (374)
                      ..+.+.++++.. .++++||||+++..++.+++.|.+.++.+..+||+++..+|..+++.|++|+.+|||+|+++++|+|
T Consensus        17 K~~~l~~ll~~~-~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~G~d   95 (165)
T 1fuk_A           17 KYECLTDLYDSI-SVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLARGID   95 (165)
T ss_dssp             HHHHHHHHHHHT-TCSCEEEEESSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEEEGGGTTTCC
T ss_pred             HHHHHHHHHHhC-CCCCEEEEECCHHHHHHHHHHHHHcCCCEEEEECCCCHHHHHHHHHHHHcCCCEEEEEcChhhcCCC
Confidence            455666666654 6789999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCccEEEEECCCCChhHHHHhhccCCCCCCceEEEEEeeccCCCcccce
Q 037567          294 KPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFY  343 (374)
Q Consensus       294 ~~~~~~vi~~~~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~~~~~~~~  343 (374)
                      +|++++||++++|+++.+|.||+||+||.|+.|.+++++.+.+...+..+
T Consensus        96 ~~~~~~Vi~~~~p~~~~~~~qr~GR~gR~g~~g~~~~~~~~~~~~~~~~~  145 (165)
T 1fuk_A           96 VQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVTNEDVGAMREL  145 (165)
T ss_dssp             CCSCSEEEESSCCSSGGGGGGSSCSCC-----CEEEEEEETTTHHHHHHH
T ss_pred             cccCCEEEEeCCCCCHHHHHHHhcccccCCCCceEEEEEcchHHHHHHHH
Confidence            99999999999999999999999999999999999999998875444433

>2rb4_A ATP-dependent RNA helicase DDX25; rossmann fold, structural genomics, structural consortium, SGC, alternative initiation, ATP-binding, devel protein; 2.80A {Homo sapiens}

Probab=99.92  E-value=1.9e-24  Score=172.25  Aligned_cols=126  Identities=21%  Similarity=0.353  Sum_probs=111.7

Q ss_pred             HHHHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEecccccccc
Q 037567          214 VDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGID  293 (374)
Q Consensus       214 ~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d  293 (374)
                      ..+.+.++++.. ..+++||||+++..++.+++.|.+.++.+..+||+++..+|..+++.|++|+.+|||+|+++++|+|
T Consensus        21 K~~~L~~ll~~~-~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~~g~~~~~~R~~~~~~f~~g~~~vLvaT~~~~~Gid   99 (175)
T 2rb4_A           21 KYQALCNIYGSI-TIGQAIIFCQTRRNAKWLTVEMIQDGHQVSLLSGELTVEQRASIIQRFRDGKEKVLITTNVCARGID   99 (175)
T ss_dssp             HHHHHHHHHTTS-CCSEEEEECSCHHHHHHHHHHHHTTTCCEEEECSSCCHHHHHHHHHHHHTTSCSEEEECCSCCTTTC
T ss_pred             HHHHHHHHHHhC-CCCCEEEEECCHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHHcCCCeEEEEecchhcCCC
Confidence            455666666654 5789999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCccEEEEECCC------CChhHHHHhhccCCCCCCceEEEEEeeccCCCcc
Q 037567          294 KPDVRHVIHYGCP------KTLESYYQESGRCGRDGIASVCWLYYARSNFAKG  340 (374)
Q Consensus       294 ~~~~~~vi~~~~p------~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~~~~~  340 (374)
                      +|++++||++++|      .+..+|+||+||+||.|+.|.+++++.+.+...+
T Consensus       100 ~~~~~~Vi~~d~p~~~~~~~~~~~~~qr~GR~gR~g~~g~~~~~~~~~~~~~~  152 (175)
T 2rb4_A          100 VKQVTIVVNFDLPVKQGEEPDYETYLHRIGRTGRFGKKGLAFNMIEVDELPSL  152 (175)
T ss_dssp             CTTEEEEEESSCCC--CCSCCHHHHHHHHCBC----CCEEEEEEECGGGHHHH
T ss_pred             cccCCEEEEeCCCCCccccCCHHHHHHHhcccccCCCCceEEEEEccchHHHH
Confidence            9999999999999      8999999999999999999999999998764433

>1t5i_A C_terminal domain of A probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA processing protein; 1.90A {Homo sapiens} SCOP: c.37.1.19

Probab=99.91  E-value=2.9e-24  Score=170.34  Aligned_cols=123  Identities=19%  Similarity=0.331  Sum_probs=114.0

Q ss_pred             chHHHHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEecccccc
Q 037567          212 SFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMG  291 (374)
Q Consensus       212 ~~~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G  291 (374)
                      ....+.+.++++.. .++++||||+++..++.+++.|...++.+..+||+++..+|..+++.|++|+.+|||+|+++++|
T Consensus        16 ~~K~~~L~~ll~~~-~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~hg~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~G   94 (172)
T 1t5i_A           16 NEKNRKLFDLLDVL-EFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRG   94 (172)
T ss_dssp             GGHHHHHHHHHHHS-CCSSEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEESSCCSTT
T ss_pred             HHHHHHHHHHHHhC-CCCcEEEEECCHHHHHHHHHHHHhcCCCEEEEECCCCHHHHHHHHHHHHCCCCcEEEECCchhcC
Confidence            34555666666654 67899999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccCccEEEEECCCCChhHHHHhhccCCCCCCceEEEEEeecc
Q 037567          292 IDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARS  335 (374)
Q Consensus       292 ~d~~~~~~vi~~~~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~  335 (374)
                      +|+|++++||++++|+++..|+||+||+||.|+.|.+++++.+.
T Consensus        95 ldi~~~~~Vi~~d~p~~~~~~~qr~GR~~R~g~~g~~~~~~~~~  138 (172)
T 1t5i_A           95 MDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDE  138 (172)
T ss_dssp             CCGGGCSEEEESSCCSSHHHHHHHHHHHTGGGCCCEEEEEECSH
T ss_pred             cchhhCCEEEEECCCCCHHHHHHHhcccccCCCCcEEEEEEcCh
Confidence            99999999999999999999999999999999999999999864

>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; 2.60A {Homo sapiens}

Probab=99.91  E-value=6.6e-24  Score=170.87  Aligned_cols=121  Identities=26%  Similarity=0.422  Sum_probs=108.9

Q ss_pred             hHHHHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccc
Q 037567          213 FVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGI  292 (374)
Q Consensus       213 ~~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~  292 (374)
                      .....+.+++..  .++++||||+++..++.+++.|+..++.+..+||+++..+|..+++.|++|+.+|||+|+++++|+
T Consensus        41 ~K~~~L~~~l~~--~~~~~lVF~~~~~~~~~l~~~L~~~g~~~~~lhg~~~~~~R~~~l~~F~~g~~~vLvaT~~~~~Gl  118 (191)
T 2p6n_A           41 AKMVYLLECLQK--TPPPVLIFAEKKADVDAIHEYLLLKGVEAVAIHGGKDQEERTKAIEAFREGKKDVLVATDVASKGL  118 (191)
T ss_dssp             GHHHHHHHHHTT--SCSCEEEECSCHHHHHHHHHHHHHHTCCEEEECTTSCHHHHHHHHHHHHHTSCSEEEECHHHHTTC
T ss_pred             HHHHHHHHHHHh--CCCCEEEEECCHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHhcCCCEEEEEcCchhcCC
Confidence            344555566554  357899999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccCccEEEEECCCCChhHHHHhhccCCCCCCceEEEEEeecc
Q 037567          293 DKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARS  335 (374)
Q Consensus       293 d~~~~~~vi~~~~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~  335 (374)
                      |+|++++||++++|+++.+|+||+||+||.|+.|.+++++.+.
T Consensus       119 di~~v~~VI~~d~p~~~~~~~qr~GR~gR~g~~g~~i~l~~~~  161 (191)
T 2p6n_A          119 DFPAIQHVINYDMPEEIENYVHRIGRTGCSGNTGIATTFINKA  161 (191)
T ss_dssp             CCCCCSEEEESSCCSSHHHHHHHHTTSCC---CCEEEEEECTT
T ss_pred             CcccCCEEEEeCCCCCHHHHHHHhCccccCCCCcEEEEEEcCc
Confidence            9999999999999999999999999999999999999999875

>3i32_A Heat resistant RNA dependent ATPase; RNA helicase, dimer, RNA recognition motif, ATP-BIND helicase, nucleotide-binding; 2.80A {Thermus thermophilus}

Probab=99.90  E-value=2.5e-23  Score=178.46  Aligned_cols=128  Identities=32%  Similarity=0.467  Sum_probs=113.0

Q ss_pred             chHHHHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEecccccc
Q 037567          212 SFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMG  291 (374)
Q Consensus       212 ~~~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G  291 (374)
                      ....+.+.++++.. .++++||||+++..++.+++.|.+.++.+..+||+++..+|..+++.|++|+.+|||||+++++|
T Consensus        13 ~~K~~~L~~ll~~~-~~~~~LVF~~t~~~~~~l~~~L~~~g~~~~~lhg~l~~~~r~~~~~~f~~g~~~vLVaT~va~~G   91 (300)
T 3i32_A           13 RGRLEVLSDLLYVA-SPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDMSQGERERVMGAFRQGEVRVLVATDVAARG   91 (300)
T ss_dssp             SSHHHHHHHHHHHH-CCSSEEEECSSHHHHHHHHHHHHTTTCCEEEECSCCCTHHHHHHHHHHHHTSCCEEEECSTTTCS
T ss_pred             HHHHHHHHHHHHhc-CCCCEEEEECCHHHHHHHHHHHHhCCCCEEEEeCCCCHHHHHHHHHHhhcCCceEEEEechhhcC
Confidence            34556666666664 48999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccCccEEEEECCCCChhHHHHhhccCCCCCCceEEEEEeeccCCCcc
Q 037567          292 IDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKG  340 (374)
Q Consensus       292 ~d~~~~~~vi~~~~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~~~~~  340 (374)
                      +|+|++++||++++|++...|+||+||+||.|+.|.|++++++.+...+
T Consensus        92 idi~~v~~VI~~d~p~s~~~y~Qr~GRagR~g~~G~~i~l~~~~e~~~~  140 (300)
T 3i32_A           92 LDIPQVDLVVHYRMPDRAEAYQHRSGRTGRAGRGGRVVLLYGPRERRDV  140 (300)
T ss_dssp             TTCCCCSEEEESSCCSSTTHHHHHHTCCC-----CEEEEEECSSTHHHH
T ss_pred             ccccceeEEEEcCCCCCHHHHHHHccCcCcCCCCceEEEEeChHHHHHH
Confidence            9999999999999999999999999999999999999999999884433

>2yjt_D ATP-dependent RNA helicase SRMB, regulator of ribonuclease activity A; hydrolase inhibitor-hydrolase complex, DEAD box RNA helicase; 2.90A {Escherichia coli}

Probab=99.82  E-value=6.2e-25  Score=174.19  Aligned_cols=134  Identities=25%  Similarity=0.349  Sum_probs=120.2

Q ss_pred             HHHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccc
Q 037567          215 DELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDK  294 (374)
Q Consensus       215 ~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~  294 (374)
                      .+.+.++++. ..++++||||+++..++.+++.|++.++.+..+||+++..+|..+++.|++|+.+|||+|+++++|+|+
T Consensus        18 ~~~l~~ll~~-~~~~~~iVF~~~~~~~~~l~~~L~~~~~~~~~~~g~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gid~   96 (170)
T 2yjt_D           18 TALLVHLLKQ-PEATRSIVFVRKRERVHELANWLREAGINNCYLEGEMVQGKRNEAIKRLTEGRVNVLVATDVAARGIDI   96 (170)
Confidence            3344445444 356899999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCccEEEEECCCCChhHHHHhhccCCCCCCceEEEEEeeccCCCcccceeccccc
Q 037567          295 PDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFYCGESQT  349 (374)
Q Consensus       295 ~~~~~vi~~~~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~~~~~~~~~~~~~~  349 (374)
                      |++++||++++|+++..|+||+||+||.|+.|.+++++.+.+...+..+......
T Consensus        97 ~~~~~Vi~~~~p~~~~~~~qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~~~  151 (170)
T 2yjt_D           97 PDVSHVFNFDMPRSGDTYLHRIGRTARAGRKGTAISLVEAHDHLLLGKVGRYIEE  151 (170)
Confidence            9999999999999999999999999999999999999999888777777654433

>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer aging, hydrolase; HET: FLC; 2.00A {Sulfolobus acidocaldarius} PDB: 3crw_1*

Probab=99.88  E-value=2e-21  Score=182.30  Aligned_cols=313  Identities=14%  Similarity=0.117  Sum_probs=193.0

Q ss_pred             CCCCCchhHHHHHHHH----HcCCCEEEEccCCCCchhhhhccccccCCcEEEEcchHHHHHHHHHHHHHc----CCceE
Q 037567           10 GYSVFRPYQKDVIQRI----IEKRDCLVVMATGSGKSLCYQLPPLVTGKTALVVSPLISLMQDQVMSLKQR----GINAE   81 (374)
Q Consensus        10 ~~~~~~~~Q~~~~~~~----~~~~~~l~~a~tGsGKT~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~----~~~~~   81 (374)
                      || ++||+|.+++..+    .+++++++.||||+|||++|+++++....+++|++||++|+.|+.+++..+    +++..
T Consensus         1 ~~-~~r~~Q~~~~~~v~~~l~~~~~~~~~a~TGtGKT~~~l~p~l~~~~~v~i~~pt~~l~~q~~~~~~~l~~~~~~~~~   79 (551)
T 3crv_A            1 MV-KLRDWQEKLKDKVIEGLRNNFLVALNAPTGSGKTLFSLLVSLEVKPKVLFVVRTHNEFYPIYRDLTKIREKRNITFS   79 (551)
T ss_dssp             CC-SCCHHHHHHHHHHHHHHHTTCEEEEECCTTSSHHHHHHHHHHHHCSEEEEEESSGGGHHHHHHHHTTCCCSSCCCEE
T ss_pred             CC-CCCHHHHHHHHHHHHHHHcCCcEEEECCCCccHHHHHHHHHHhCCCeEEEEcCCHHHHHHHHHHHHHHhhhcCccEE
Confidence            45 5999999988754    468899999999999999999999998999999999999999999999876    45555


Q ss_pred             EcCCCCCc---------------------------------hhhh-----------------hhhhcCCeeEEEEcCccc
Q 037567           82 FLGSAQTD---------------------------------SSVQ-----------------TKAETGYFQLLFMTPEKA  111 (374)
Q Consensus        82 ~~~~~~~~---------------------------------~~~~-----------------~~~~~~~~~i~i~T~~~l  111 (374)
                      .+.+....                                 ....                 ........+|+|+||..+
T Consensus        80 ~l~gr~~~c~~~~~~~~~~~~~c~~c~~~~~~~~~g~~~~~~~~~~~~~~~G~~~~~Cpy~~ar~~~~~adIVV~~~~~l  159 (551)
T 3crv_A           80 FLVGKPSSCLYAEKGAESEDIPCKYCELKGSIVEVKTDDSPLSLVKKLKKDGLQDKFCPYYSLLNSLYKADVIALTYPYF  159 (551)
T ss_dssp             ECCCHHHHCTTBCTTCCGGGCCGGGCTTTTCCCCCCCCSCHHHHHHHHHHHHHHHTCCHHHHHHHHGGGCSEEEEETHHH
T ss_pred             EEccccccCcCchhcCCCcccccCCCCCccccccccccCCHHHHHHHHHHcCCcCCcCccHHHHhhhhcCCEEEeCchHh
Confidence            54432100                                 0000                 011123569999999988


Q ss_pred             ccCchhhHHHHH-hcCccEEEEeccchhhcccCcc---------------------------------------------
Q 037567          112 CIIPISFWSKLL-KAGVCLFAVDEAHCISEWGHDF---------------------------------------------  145 (374)
Q Consensus       112 ~~~~~~~~~~~~-~~~~~~vviDE~h~~~~~~~~~---------------------------------------------  145 (374)
                      .+...+  .... .....++||||||++.+ ..+.                                             
T Consensus       160 ~~~~~~--~~~~~~~~~~~vIiDEAHnl~d-~~~~~s~~ls~~~l~~~~~~l~~~~~~~~l~~l~~~l~~~~~~~~~~~~  236 (551)
T 3crv_A          160 FIDRYR--EFIDIDLREYMIVIDEAHNLDK-VNELEERSLSEITIQMAIKQSKSEESRRILSKLLNQLREVVLPDEKYIK  236 (551)
T ss_dssp             HCHHHH--TTSCCCSTTEEEEETTGGGGGG-GGGGGCEEEEHHHHHHHHHHCSCHHHHHHHHHHHHHHTTSCCSCSSCEE
T ss_pred             cCHHHH--HhcCCCcCCeEEEEecccchHH-HHHhhceecCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccc
Confidence            764221  1111 13556899999999875 2110                                             


Q ss_pred             --------hHHH-------------------------HHHH----HH------------------------HHhcCC--C
Q 037567          146 --------RLEY-------------------------KQLD----KL------------------------RTFLLG--V  162 (374)
Q Consensus       146 --------~~~~-------------------------~~~~----~~------------------------~~~~~~--~  162 (374)
                              ...+                         ..+.    .+                        ...+..  .
T Consensus       237 ~~~~~~~~~~~l~~l~~~l~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~~~~~~l~~~pl~~~~~l~~~~~~~~  316 (551)
T 3crv_A          237 VENVPKLSKEELEILADDYEDIRKDSLKQGKVNKIHIGSILRFFSLLSIGSFIPFSYSKRLVIKNPEISYYLNLLNDNEL  316 (551)
T ss_dssp             CSCCCCCCHHHHHHHHHHHHHHHHHHHHTTCBCCCHHHHHHHHHHHHHHSSCEEEEETTEEEEECCCTHHHHGGGGCTTC
T ss_pred             cccChHHHHHHHHHHHHHHHHHHHhhhhcCCcccchHHHHHHHHHHHhccCCeEeccCCEEEEEECCHHHHHHHHhccCc
Confidence                    0000                         0000    00                        001122  5


Q ss_pred             CeeEEEeecCcccHHHHHHhcCCCCCeEE---E---eccCCCceeEEEEe-ecC-----CcchHHHHHHHHHHhh-cCCC
Q 037567          163 PFVALTATATEKVRIDIINSLKLKNPYVT---I---ASFDRKNLFYGVKV-INR-----GQSFVDELVQEILKSV-AGAG  229 (374)
Q Consensus       163 ~~i~~SaT~~~~~~~~~~~~~~~~~~~~~---~---~~~~~~~~~~~~~~-~~~-----~~~~~~~~~~~~~~~~-~~~~  229 (374)
                      .+|++|||+.+  ...+...+++......   .   .++-..+....+.. .+.     ......++...+.+-. ...+
T Consensus       317 svIltSaTL~~--~~~~~~~lGl~~~~~~~~~~~~~~spf~~~~~l~v~~~~~~~~~~r~~~~~~~l~~~i~~l~~~~~g  394 (551)
T 3crv_A          317 SIILMSGTLPP--REYMEKVWGIKRNMLYLDVEREIQKRVSGSYECYIGVDVTSKYDMRSDNMWKRYADYLLKIYFQAKA  394 (551)
T ss_dssp             EEEEEESSCCC--HHHHHHTSCCCSCEEEEEHHHHTTSCCSCEEEEEEECSCCCCTTTCCHHHHHHHHHHHHHHHHHCSS
T ss_pred             eEEEEeeCCCc--HHHHHHHhCCCCccccccceeecCCcCCCceEEEEeCCCCCccccCCHHHHHHHHHHHHHHHHhCCC
Confidence            78999999987  3356777887633321   1   11111222111110 111     1112233333332221 2467


Q ss_pred             cEEEEecchhHHHHHHHHHHHcCCceeeeec-CCChHHHHHHHHhhhcCCeeEEEEe--cccccccccc---C--ccEEE
Q 037567          230 SIIVYCMTIKDVEEISKALKQLGVKAGTYHG-QMGSKAREEAHRLFIRDEIRVMVAT--MAFGMGIDKP---D--VRHVI  301 (374)
Q Consensus       230 ~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~-~~~~~~r~~~~~~f~~g~~~ilv~t--~~~~~G~d~~---~--~~~vi  301 (374)
                      .++||++|...++.+++.   .+..+ +..+ +++   +...++.|+.+.-.||+++  ...++|+|+|   +  ++.||
T Consensus       395 ~~lvlF~Sy~~l~~v~~~---~~~~v-~~q~~~~~---~~~~~~~~~~~~~~vl~~v~gg~~~EGiD~~d~~g~~l~~vi  467 (551)
T 3crv_A          395 NVLVVFPSYEIMDRVMSR---ISLPK-YVESEDSS---VEDLYSAISANNKVLIGSVGKGKLAEGIELRNNDRSLISDVV  467 (551)
T ss_dssp             EEEEEESCHHHHHHHHTT---CCSSE-EECCSSCC---HHHHHHHTTSSSSCEEEEESSCCSCCSSCCEETTEESEEEEE
T ss_pred             CEEEEecCHHHHHHHHHh---cCCcE-EEcCCCCC---HHHHHHHHHhcCCeEEEEEecceecccccccccCCcceeEEE
Confidence            899999999999999873   23332 3333 233   4557777854334799998  5999999999   4  78899


Q ss_pred             EECCCCC------------------------------hhHHHHhhccCCCCCCceEEEEEeecc
Q 037567          302 HYGCPKT------------------------------LESYYQESGRCGRDGIASVCWLYYARS  335 (374)
Q Consensus       302 ~~~~p~s------------------------------~~~~~Q~~GR~~R~~~~g~~~~~~~~~  335 (374)
                      ..+.|..                              ...+.|.+||+-|..++.-++++++..
T Consensus       468 I~~lPfp~~dp~~~ar~~~~~~~~g~~~~~~~y~~pa~~~l~Qa~GRlIR~~~D~G~v~llD~R  531 (551)
T 3crv_A          468 IVGIPYPPPDDYLKILAQRVSLKMNRENEEFLFKIPALVTIKQAIGRAIRDVNDKCNVWLLDKR  531 (551)
T ss_dssp             EESCCCCCCSHHHHHHHHHTTCCSSTTTHHHHTHHHHHHHHHHHHHTTCCSTTCEEEEEEESGG
T ss_pred             EEcCCCCCCCHHHHHHHHHHHHhhCCchhHHHHHHHHHHHHHHHhccCccCCCccEEEEEeehh
Confidence            8887741                              112369999999986665566666553

>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=99.88  E-value=3.3e-23  Score=171.49  Aligned_cols=159  Identities=15%  Similarity=0.095  Sum_probs=102.7

Q ss_pred             CCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc---------cCCcEEEEcchHHHHHH-HHHHHHHc---C
Q 037567           11 YSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV---------TGKTALVVSPLISLMQD-QVMSLKQR---G   77 (374)
Q Consensus        11 ~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~---------~~~~~lil~P~~~l~~q-~~~~~~~~---~   77 (374)
                      ..+|+|+|.++++.+.+++++++.+|||+|||+++++++..         ...+++|++|+++|+.| +.+.+..+   +
T Consensus        31 ~~~l~~~Q~~~i~~~~~~~~~li~~~tGsGKT~~~~~~~~~~~~~~~~~~~~~~~lil~p~~~L~~q~~~~~~~~~~~~~  110 (216)
T 3b6e_A           31 ELQLRPYQMEVAQPALEGKNIIICLPTGSGKTRVAVYIAKDHLDKKKKASEPGKVIVLVNKVLLVEQLFRKEFQPFLKKW  110 (216)
T ss_dssp             CCCCCHHHHHHHHHHHTTCCEEEECSCHHHHHHHHHHHHHHHHHHHHHTTCCCCEEEEESSHHHHHHHHHHTHHHHHTTT
T ss_pred             CCCchHHHHHHHHHHhcCCCEEEEcCCCCCHHHHHHHHHHHHHhhcccccCCCcEEEEECHHHHHHHHHHHHHHHHhccC
Confidence            34799999999999999999999999999999998877664         16789999999999999 77777765   4


Q ss_pred             CceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHH----HHHhcCccEEEEeccchhhcccCcchHHHHHHH
Q 037567           78 INAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWS----KLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLD  153 (374)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~----~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~  153 (374)
                      ..+....++......... ....++|+|+||+++...+.....    ...+.++++||+||||++...+.........+.
T Consensus       111 ~~v~~~~g~~~~~~~~~~-~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~~~~~~~iIiDEah~~~~~~~~~~~~~~~~~  189 (216)
T 3b6e_A          111 YRVIGLSGDTQLKISFPE-VVKSCDIIISTAQILENSLLNLENGEDAGVQLSDFSLIIIDECHHTNKEAVYNNIMRHYLM  189 (216)
T ss_dssp             SCEEECCC---CCCCHHH-HHHHCSEEEEEHHHHHHHHHC-------CCCGGGCSEEEETTC-------CHHHHHHHHHH
T ss_pred             ceEEEEeCCcccchhHHh-hccCCCEEEECHHHHHHHHhccCcccccccchhcccEEEEECchhhccCCcHHHHHHHHHH
Confidence            556555554333222211 123479999999998665443211    033567899999999999754332211111111


Q ss_pred             HHHHh----------cCCCCeeEEEee
Q 037567          154 KLRTF----------LLGVPFVALTAT  170 (374)
Q Consensus       154 ~~~~~----------~~~~~~i~~SaT  170 (374)
                      .....          .+..++++||||
T Consensus       190 ~~~~~~~~~~~~~~~~~~~~~l~lSAT  216 (216)
T 3b6e_A          190 QKLKNNRLKKENKPVIPLPQILGLTAS  216 (216)
T ss_dssp             HHHHHHHHHHTTCCCCCCCEEEEEECC
T ss_pred             HhcccccccccccCCCCcceEEEeecC
Confidence            11110          146789999998

>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=99.87  E-value=3.1e-22  Score=167.04  Aligned_cols=140  Identities=20%  Similarity=0.201  Sum_probs=110.2

Q ss_pred             CCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccccCCcEEEEcchHHHHHHHHHHHHHcCCc-eEEcCCCCCchh
Q 037567           13 VFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVTGKTALVVSPLISLMQDQVMSLKQRGIN-AEFLGSAQTDSS   91 (374)
Q Consensus        13 ~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~-~~~~~~~~~~~~   91 (374)
                      +|+++|.+++..+.+++++++++|||+|||.+++.++...+.+++|++|+++|+.||.+++.+++.. +..+.+....  
T Consensus        93 ~l~~~Q~~ai~~~~~~~~~ll~~~tG~GKT~~a~~~~~~~~~~~liv~P~~~L~~q~~~~~~~~~~~~v~~~~g~~~~--  170 (237)
T 2fz4_A           93 SLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAAINELSTPTLIVVPTLALAEQWKERLGIFGEEYVGEFSGRIKE--  170 (237)
T ss_dssp             CCCHHHHHHHHHHTTTSEEEEEESSSTTHHHHHHHHHHHSCSCEEEEESSHHHHHHHHHHHGGGCGGGEEEESSSCBC--
T ss_pred             CcCHHHHHHHHHHHhCCCEEEEeCCCCCHHHHHHHHHHHcCCCEEEEeCCHHHHHHHHHHHHhCCCCeEEEEeCCCCC--
Confidence            6999999999999999899999999999999988777777889999999999999999999998887 6666554321  


Q ss_pred             hhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHHhcCCCCeeEEEeec
Q 037567           92 VQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATA  171 (374)
Q Consensus        92 ~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~SaT~  171 (374)
                              ..+|+|+|++.+.....     .....+++||+||+|++.+..         ...+...++..++++|||||
T Consensus       171 --------~~~i~v~T~~~l~~~~~-----~~~~~~~llIiDEaH~l~~~~---------~~~i~~~~~~~~~l~LSATp  228 (237)
T 2fz4_A          171 --------LKPLTVSTYDSAYVNAE-----KLGNRFMLLIFDEVHHLPAES---------YVQIAQMSIAPFRLGLTATF  228 (237)
T ss_dssp             --------CCSEEEEEHHHHHHTHH-----HHTTTCSEEEEECSSCCCTTT---------HHHHHHTCCCSEEEEEEESC
T ss_pred             --------cCCEEEEeHHHHHhhHH-----HhcccCCEEEEECCccCCChH---------HHHHHHhccCCEEEEEecCC
Confidence                    35899999998754322     223568999999999987533         23344555677899999999


Q ss_pred             CcccH
Q 037567          172 TEKVR  176 (374)
Q Consensus       172 ~~~~~  176 (374)
                      ...+.
T Consensus       229 ~r~D~  233 (237)
T 2fz4_A          229 EREDG  233 (237)
T ss_dssp             C----
T ss_pred             CCCCC
Confidence            87654

>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=99.86  E-value=2.3e-22  Score=173.13  Aligned_cols=145  Identities=15%  Similarity=0.124  Sum_probs=109.1

Q ss_pred             CCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc----cCCcEEEEcchHHHHHHHHHHHHHcCCc----eEEcC
Q 037567           13 VFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV----TGKTALVVSPLISLMQDQVMSLKQRGIN----AEFLG   84 (374)
Q Consensus        13 ~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~----~~~~~lil~P~~~l~~q~~~~~~~~~~~----~~~~~   84 (374)
                      +|+|+|.++++.++++++.++.+|||+|||+++++++..    ...++||++|+++|++||.+++.+++..    ...+.
T Consensus       113 ~l~~~Q~~ai~~~l~~~~~ll~~~tGsGKT~~~~~~~~~~~~~~~~~~lil~Pt~~L~~q~~~~l~~~~~~~~~~~~~~~  192 (282)
T 1rif_A          113 EPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALLARYYLENYEGKILIIVPTTALTTQMADDFVDYRLFSHAMIKKIG  192 (282)
T ss_dssp             CCCHHHHHHHHHHHHHSEEEECCCTTSCHHHHHHHHHHHHHHHCSSEEEEECSSHHHHHHHHHHHHHHTSCCGGGEEECS
T ss_pred             CccHHHHHHHHHHHhcCCeEEEcCCCCCcHHHHHHHHHHHHHcCCCeEEEEECCHHHHHHHHHHHHHhcccccceEEEEe
Confidence            699999999999998888999999999999988766553    2458999999999999999999988542    23333


Q ss_pred             CCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHHhc-CCCC
Q 037567           85 SAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFL-LGVP  163 (374)
Q Consensus        85 ~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~-~~~~  163 (374)
                      ++.....    ......+|+|+||+.+.....     .....++++|+||||++..         ..+..+...+ ...+
T Consensus       193 ~~~~~~~----~~~~~~~I~v~T~~~l~~~~~-----~~~~~~~~vIiDEaH~~~~---------~~~~~il~~~~~~~~  254 (282)
T 1rif_A          193 GGASKDD----KYKNDAPVVVGTWQTVVKQPK-----EWFSQFGMMMNDECHLATG---------KSISSIISGLNNCMF  254 (282)
T ss_dssp             TTCSSTT----CCCTTCSEEEECHHHHTTSCG-----GGGGGEEEEEEETGGGCCH---------HHHHHHTTTCTTCCE
T ss_pred             CCCcchh----hhccCCcEEEEchHHHHhhHH-----HHHhhCCEEEEECCccCCc---------ccHHHHHHHhhcCCe
Confidence            3322211    222457899999998865532     2356789999999999874         2344444444 4788


Q ss_pred             eeEEEeecCccc
Q 037567          164 FVALTATATEKV  175 (374)
Q Consensus       164 ~i~~SaT~~~~~  175 (374)
                      +++|||||++..
T Consensus       255 ~l~lSATp~~~~  266 (282)
T 1rif_A          255 KFGLSGSLRDGK  266 (282)
T ss_dssp             EEEECSSCCTTS
T ss_pred             EEEEeCCCCCcc
Confidence            999999998764

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A*

Probab=99.83  E-value=3e-19  Score=168.67  Aligned_cols=164  Identities=13%  Similarity=0.125  Sum_probs=96.9

Q ss_pred             eeEEEeecCcccHHHHHHhcCCCCCeEE-Eecc-CCCceeEEEE-eec-----CCcchHHHH---HHHHHHhhcCCCcEE
Q 037567          164 FVALTATATEKVRIDIINSLKLKNPYVT-IASF-DRKNLFYGVK-VIN-----RGQSFVDEL---VQEILKSVAGAGSII  232 (374)
Q Consensus       164 ~i~~SaT~~~~~~~~~~~~~~~~~~~~~-~~~~-~~~~~~~~~~-~~~-----~~~~~~~~~---~~~~~~~~~~~~~~l  232 (374)
                      +|++|||+.+  ...+...+|+. .... ..+. +..+....+. ..+     .......++   +..+.+.  ..++++
T Consensus       378 ~il~SaTL~p--~~~~~~~lGl~-~~~~~~~spf~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~i~~l~~~--~~g~~l  452 (620)
T 4a15_A          378 TIHMSGTLDP--FDFYSDITGFE-IPFKKIGEIFPPENRYIAYYDGVSSKYDTLDEKELDRMATVIEDIILK--VKKNTI  452 (620)
T ss_dssp             EEEEESSCCS--HHHHHHHHCCC-CCEEECCCCSCGGGEEEEEECCC-------CHHHHHHHHHHHHHHHHH--HCSCEE
T ss_pred             EEEEccCCCc--HHHHHHHhCCC-ceeeecCCCCCHHHeEEEEeCCCCCcCCCCCHHHHHHHHHHHHHHHHh--CCCCEE
Confidence            5899999987  33567778876 2222 2211 2222211111 011     111122222   3333333  467799


Q ss_pred             EEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEec--cccccccccC--ccEEEEECCCCC
Q 037567          233 VYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATM--AFGMGIDKPD--VRHVIHYGCPKT  308 (374)
Q Consensus       233 Vf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~--~~~~G~d~~~--~~~vi~~~~p~s  308 (374)
                      ||++|....+.+++.++.  ...- ...+++..++..+++.|. ++-.||+++.  .+++|+|+|+  ++.||..+.|..
T Consensus       453 vlF~Sy~~l~~v~~~l~~--~~~~-~~q~~~~~~~~~ll~~f~-~~~~vL~~v~~gsf~EGiD~~g~~l~~viI~~lPfp  528 (620)
T 4a15_A          453 VYFPSYSLMDRVENRVSF--EHMK-EYRGIDQKELYSMLKKFR-RDHGTIFAVSGGRLSEGINFPGNELEMIILAGLPFP  528 (620)
T ss_dssp             EEESCHHHHHHHTSSCCS--CCEE-CCTTCCSHHHHHHHHHHT-TSCCEEEEETTSCC--------CCCCEEEESSCCCC
T ss_pred             EEeCCHHHHHHHHHHHHh--cchh-ccCCCChhHHHHHHHHhc-cCCcEEEEEecCceeccccCCCCceEEEEEEcCCCC
Confidence            999999999999988862  2211 333445668999999999 7778999985  9999999998  678998888742


Q ss_pred             -----------------------------hhHHHHhhccCCCCCCceEEEEEeeccC
Q 037567          309 -----------------------------LESYYQESGRCGRDGIASVCWLYYARSN  336 (374)
Q Consensus       309 -----------------------------~~~~~Q~~GR~~R~~~~g~~~~~~~~~~  336 (374)
                                                   ...+.|.+||+-|...+.-+++++++.-
T Consensus       529 ~~~p~~~ar~~~~~~~~g~~~~~~y~~pa~~~l~Qa~GRlIR~~~D~G~v~llD~R~  585 (620)
T 4a15_A          529 RPDAINRSLFDYYERKYGKGWEYSVVYPTAIKIRQEIGRLIRSAEDTGACVILDKRA  585 (620)
T ss_dssp             CCCHHHHHHHHHHHHHHSCHHHHHTHHHHHHHHHHHHHTTCCSTTCCEEEEEECGGG
T ss_pred             CCCHHHHHHHHHHHHhhCCCchHHhHHHHHHHHHHHhCccccCCCceEEEEEEccch
Confidence                                         1224799999999866655666665543

>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=99.80  E-value=6.8e-20  Score=153.14  Aligned_cols=159  Identities=14%  Similarity=0.056  Sum_probs=109.8

Q ss_pred             CCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc----c----CCcEEEEcchHHHHHHHHHHHHHc-CCceEE
Q 037567           12 SVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV----T----GKTALVVSPLISLMQDQVMSLKQR-GINAEF   82 (374)
Q Consensus        12 ~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~----~----~~~~lil~P~~~l~~q~~~~~~~~-~~~~~~   82 (374)
                      -.++++|.++++.+.+++++++.||||||||..+.++++.    .    ..++++++|+++++.|+.+.+... +.....
T Consensus        60 ~p~~~~q~~~i~~i~~g~~~~i~g~TGsGKTt~~~~~~~~~~~~~~~~~~~~~l~~~p~~~la~q~~~~~~~~~~~~~~~  139 (235)
T 3llm_A           60 LPVKKFESEILEAISQNSVVIIRGATGCGKTTQVPQFILDDFIQNDRAAECNIVVTQPRRISAVSVAERVAFERGEEPGK  139 (235)
T ss_dssp             SGGGGGHHHHHHHHHHCSEEEEECCTTSSHHHHHHHHHHHHHHHTTCGGGCEEEEEESSHHHHHHHHHHHHHTTTCCTTS
T ss_pred             CChHHHHHHHHHHHhcCCEEEEEeCCCCCcHHhHHHHHhcchhhcCCCCceEEEEeccchHHHHHHHHHHHHHhccccCc
Confidence            3589999999999999999999999999999876655443    1    337999999999999998888653 221110


Q ss_pred             cCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchh-hcccCcchHHHHHHHHHHHhcCC
Q 037567           83 LGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCI-SEWGHDFRLEYKQLDKLRTFLLG  161 (374)
Q Consensus        83 ~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~-~~~~~~~~~~~~~~~~~~~~~~~  161 (374)
                      ..+...  ..........++|+|+||+++.+.+..     .+.+++++|+||+|.. .+.+    .....+..+....++
T Consensus       140 ~~g~~~--~~~~~~~~~~~~Ivv~Tpg~l~~~l~~-----~l~~~~~lVlDEah~~~~~~~----~~~~~l~~i~~~~~~  208 (235)
T 3llm_A          140 SCGYSV--RFESILPRPHASIMFCTVGVLLRKLEA-----GIRGISHVIVDEIHERDINTD----FLLVVLRDVVQAYPE  208 (235)
T ss_dssp             SEEEEE--TTEEECCCSSSEEEEEEHHHHHHHHHH-----CCTTCCEEEECCTTSCCHHHH----HHHHHHHHHHHHCTT
T ss_pred             eEEEee--chhhccCCCCCeEEEECHHHHHHHHHh-----hhcCCcEEEEECCccCCcchH----HHHHHHHHHHhhCCC
Confidence            000000  001111124578999999988765433     3688999999999974 3222    222345566666678


Q ss_pred             CCeeEEEeecCcccHHHHHHhcC
Q 037567          162 VPFVALTATATEKVRIDIINSLK  184 (374)
Q Consensus       162 ~~~i~~SaT~~~~~~~~~~~~~~  184 (374)
                      .++++||||++...   +..+++
T Consensus       209 ~~~il~SAT~~~~~---~~~~~~  228 (235)
T 3llm_A          209 VRIVLMSATIDTSM---FCEYFF  228 (235)
T ss_dssp             SEEEEEECSSCCHH---HHHHTT
T ss_pred             CeEEEEecCCCHHH---HHHHcC
Confidence            89999999998765   344443

>1z5z_A Helicase of the SNF2/RAD54 family; hydrolase, recombination, hydrolase-recombination complex; 2.00A {Sulfolobus solfataricus} SCOP: c.37.1.19

Probab=99.77  E-value=1.4e-18  Score=147.22  Aligned_cols=119  Identities=16%  Similarity=0.209  Sum_probs=89.9

Q ss_pred             HHHHHHHHh-hcCCCcEEEEecchhHHHHHHHHHHHc-CCceeeeecCCChHHHHHHHHhhhcC-Cee-EEEEecccccc
Q 037567          216 ELVQEILKS-VAGAGSIIVYCMTIKDVEEISKALKQL-GVKAGTYHGQMGSKAREEAHRLFIRD-EIR-VMVATMAFGMG  291 (374)
Q Consensus       216 ~~~~~~~~~-~~~~~~~lVf~~~~~~~~~l~~~l~~~-~~~~~~~~~~~~~~~r~~~~~~f~~g-~~~-ilv~t~~~~~G  291 (374)
                      ..+.+++.. ...+.++||||++...++.+.+.|.+. |+.+..+||+++..+|+.+++.|+++ +.+ +|++|.++++|
T Consensus        99 ~~L~~ll~~~~~~~~kvlIFs~~~~~~~~l~~~L~~~~g~~~~~l~G~~~~~~R~~~i~~F~~~~~~~v~L~st~~~g~G  178 (271)
T 1z5z_A           99 IRTMEIIEEALDEGDKIAIFTQFVDMGKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKFIVLSVKAGGFG  178 (271)
T ss_dssp             HHHHHHHHHHHHTTCCEEEEESCHHHHHHHHHHHHHHHCSCCCEECTTSCHHHHHHHHHHHHHCTTCCEEEEECCTTCCC
T ss_pred             HHHHHHHHHHHhCCCeEEEEeccHHHHHHHHHHHHHhcCCcEEEEECCCCHHHHHHHHHHhcCCCCCCEEEEehhhhcCC
Confidence            334444333 346889999999999999999999885 99999999999999999999999998 666 68899999999


Q ss_pred             ccccCccEEEEECCCCChhHHHHhhccCCCCCCceEE--EEEeec
Q 037567          292 IDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVC--WLYYAR  334 (374)
Q Consensus       292 ~d~~~~~~vi~~~~p~s~~~~~Q~~GR~~R~~~~g~~--~~~~~~  334 (374)
                      +|++.+++||++++|+++..+.|++||++|.|+.+.+  +.++..
T Consensus       179 lnl~~a~~VI~~d~~wnp~~~~Q~~gR~~R~Gq~~~v~v~~li~~  223 (271)
T 1z5z_A          179 INLTSANRVIHFDRWWNPAVEDQATDRVYRIGQTRNVIVHKLISV  223 (271)
T ss_dssp             CCCTTCSEEEECSCCSCTTTC--------------CCEEEEEEET
T ss_pred             cCcccCCEEEEECCCCChhHHHHHHHhccccCCCCceEEEEEeeC
Confidence            9999999999999999999999999999999997765  444444

>4b3f_X DNA-binding protein smubp-2; hydrolase, helicase; 2.50A {Homo sapiens} PDB: 4b3g_A

Probab=98.72  E-value=3e-08  Score=94.81  Aligned_cols=72  Identities=17%  Similarity=0.176  Sum_probs=57.7

Q ss_pred             CCchhHHHHHHHHHcCC-CEEEEccCCCCchhhhhc---cccccCCcEEEEcchHHHHHHHHHHHHHcCCceEEcC
Q 037567           13 VFRPYQKDVIQRIIEKR-DCLVVMATGSGKSLCYQL---PPLVTGKTALVVSPLISLMQDQVMSLKQRGINAEFLG   84 (374)
Q Consensus        13 ~~~~~Q~~~~~~~~~~~-~~l~~a~tGsGKT~~~~l---~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~   84 (374)
                      .+.+-|.+|+..++..+ -.+|+||+|||||.+..-   .++.++.++|+++||...++++.+.+...+.++..++
T Consensus       189 ~LN~~Q~~AV~~al~~~~~~lI~GPPGTGKT~ti~~~I~~l~~~~~~ILv~a~TN~AvD~i~erL~~~~~~ilRlG  264 (646)
T 4b3f_X          189 CLDTSQKEAVLFALSQKELAIIHGPPGTGKTTTVVEIILQAVKQGLKVLCCAPSNIAVDNLVERLALCKQRILRLG  264 (646)
T ss_dssp             TCCHHHHHHHHHHHHCSSEEEEECCTTSCHHHHHHHHHHHHHHTTCCEEEEESSHHHHHHHHHHHHHTTCCEEECS
T ss_pred             CCCHHHHHHHHHHhcCCCceEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEcCchHHHHHHHHHHHhcCCceEEec
Confidence            57889999999988765 468999999999966432   2334688999999999999999999988776655443

>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=98.68  E-value=4.9e-08  Score=92.25  Aligned_cols=61  Identities=18%  Similarity=0.196  Sum_probs=50.4

Q ss_pred             chhHHHHHHHHHcCCCEEEEccCCCCch--hhhhccccc-----cCCcEEEEcchHHHHHHHHHHHHH
Q 037567           15 RPYQKDVIQRIIEKRDCLVVMATGSGKS--LCYQLPPLV-----TGKTALVVSPLISLMQDQVMSLKQ   75 (374)
Q Consensus        15 ~~~Q~~~~~~~~~~~~~l~~a~tGsGKT--~~~~l~~~~-----~~~~~lil~P~~~l~~q~~~~~~~   75 (374)
                      .+.|.++++.++.++.+++.|++|||||  +.+++..+.     .+.++++++||..++.++.+.+..
T Consensus       151 ~~~Q~~Ai~~~l~~~~~vi~G~pGTGKTt~l~~ll~~l~~~~~~~~~~vll~APTg~AA~~L~e~~~~  218 (608)
T 1w36_D          151 INWQKVAAAVALTRRISVISGGPGTGKTTTVAKLLAALIQMADGERCRIRLAAPTGKAAARLTESLGK  218 (608)
T ss_dssp             CCHHHHHHHHHHTBSEEEEECCTTSTHHHHHHHHHHHHHHTCSSCCCCEEEEBSSHHHHHHHHHHHTH
T ss_pred             CHHHHHHHHHHhcCCCEEEEeCCCCCHHHHHHHHHHHHHHhhhcCCCeEEEEeCChhHHHHHHHHHHH
Confidence            6889999999999999999999999999  444444443     356899999999999998877654

>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=98.53  E-value=2.5e-07  Score=87.87  Aligned_cols=71  Identities=14%  Similarity=0.178  Sum_probs=57.1

Q ss_pred             CCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhcc---ccc-cCCcEEEEcchHHHHHHHHHHHHHcCCceE
Q 037567           11 YSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLP---PLV-TGKTALVVSPLISLMQDQVMSLKQRGINAE   81 (374)
Q Consensus        11 ~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~---~~~-~~~~~lil~P~~~l~~q~~~~~~~~~~~~~   81 (374)
                      +..+.+.|.+|+..++.+...++.||+|+|||.+....   +.. .+.++++++||...+++..+.+...+..+.
T Consensus       178 ~~~ln~~Q~~av~~~l~~~~~li~GppGTGKT~~~~~~i~~l~~~~~~~ilv~a~tn~A~~~l~~~l~~~~~~~~  252 (624)
T 2gk6_A          178 LPDLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAPSNIAVDQLTEKIHQTGLKVV  252 (624)
T ss_dssp             SCCCCHHHHHHHHHHHTCSEEEEECCTTSCHHHHHHHHHHHHHTSSSCCEEEEESSHHHHHHHHHHHHTTTCCEE
T ss_pred             cCCCCHHHHHHHHHHhcCCCeEEECCCCCCHHHHHHHHHHHHHHcCCCeEEEEeCcHHHHHHHHHHHHhcCCeEE
Confidence            34688999999999888778899999999999654322   122 577999999999999999999987766543

>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=98.42  E-value=1.7e-06  Score=79.10  Aligned_cols=65  Identities=12%  Similarity=0.176  Sum_probs=48.7

Q ss_pred             cCCCCCchhHHHHHHHHHcC-----CCEEEEccCCCCchhhhhcc--cc-ccCC-cEEEEcchHHHHHHHHHHH
Q 037567            9 FGYSVFRPYQKDVIQRIIEK-----RDCLVVMATGSGKSLCYQLP--PL-VTGK-TALVVSPLISLMQDQVMSL   73 (374)
Q Consensus         9 ~~~~~~~~~Q~~~~~~~~~~-----~~~l~~a~tGsGKT~~~~l~--~~-~~~~-~~lil~P~~~l~~q~~~~~   73 (374)
                      +.|..+++-|.+++..+...     ..+++.|++|||||.+....  .+ ..+. .+++++||...+..+.+.+
T Consensus        21 ~~~~~Ln~~Q~~av~~~~~~i~~~~~~~li~G~aGTGKT~ll~~~~~~l~~~~~~~il~~a~T~~Aa~~l~~~~   94 (459)
T 3upu_A           21 MTFDDLTEGQKNAFNIVMKAIKEKKHHVTINGPAGTGATTLTKFIIEALISTGETGIILAAPTHAAKKILSKLS   94 (459)
T ss_dssp             CCSSCCCHHHHHHHHHHHHHHHSSSCEEEEECCTTSCHHHHHHHHHHHHHHTTCCCEEEEESSHHHHHHHHHHH
T ss_pred             CccccCCHHHHHHHHHHHHHHhcCCCEEEEEeCCCCCHHHHHHHHHHHHHhcCCceEEEecCcHHHHHHHHhhh
Confidence            57889999999999977542     37899999999999653211  11 2343 7999999998888766654

>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA degradation, allosteric REGU; HET: ADP 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=98.42  E-value=6.7e-07  Score=86.91  Aligned_cols=71  Identities=14%  Similarity=0.252  Sum_probs=57.3

Q ss_pred             CCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccc---cc-cCCcEEEEcchHHHHHHHHHHHHHcCCceE
Q 037567           11 YSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPP---LV-TGKTALVVSPLISLMQDQVMSLKQRGINAE   81 (374)
Q Consensus        11 ~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~---~~-~~~~~lil~P~~~l~~q~~~~~~~~~~~~~   81 (374)
                      +..+.+.|.+|+..++.+...+|.||+|||||.+....+   .. .+.++++++||...++++.+.+...+..+.
T Consensus       358 ~~~Ln~~Q~~Av~~~l~~~~~lI~GppGTGKT~~i~~~i~~l~~~~~~~ILv~a~tn~A~d~l~~rL~~~g~~il  432 (802)
T 2xzl_A          358 FAQLNSSQSNAVSHVLQRPLSLIQGPPGTGKTVTSATIVYHLSKIHKDRILVCAPSNVAVDHLAAKLRDLGLKVV  432 (802)
T ss_dssp             SCCCCHHHHHHHHHHTTCSEEEEECSTTSSHHHHHHHHHHHHHHHHCCCEEEEESSHHHHHHHHHHHHHTTCCEE
T ss_pred             cccCCHHHHHHHHHHhcCCCEEEECCCCCCHHHHHHHHHHHHHhCCCCeEEEEcCcHHHHHHHHHHHHhhCccEE
Confidence            456789999999999887778999999999996543221   12 578999999999999999999988765543

>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=98.38  E-value=7.6e-07  Score=86.43  Aligned_cols=71  Identities=14%  Similarity=0.178  Sum_probs=56.9

Q ss_pred             CCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhcc---ccc-cCCcEEEEcchHHHHHHHHHHHHHcCCceE
Q 037567           11 YSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLP---PLV-TGKTALVVSPLISLMQDQVMSLKQRGINAE   81 (374)
Q Consensus        11 ~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~---~~~-~~~~~lil~P~~~l~~q~~~~~~~~~~~~~   81 (374)
                      ...+.+.|.+|+..++.+...++.||+|+|||.+....   +.. .+.++++++||...++++.+.+...+..+.
T Consensus       354 ~~~Ln~~Q~~Av~~~l~~~~~lI~GppGTGKT~ti~~~i~~l~~~~~~~ilv~a~tn~A~~~l~~~l~~~g~~vv  428 (800)
T 2wjy_A          354 LPDLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAPSNIAVDQLTEKIHQTGLKVV  428 (800)
T ss_dssp             SCCCCHHHHHHHHHHHTSSEEEEECCTTSCHHHHHHHHHHHHHTTCSSCEEEEESSHHHHHHHHHHHHTTTCCEE
T ss_pred             ccCCCHHHHHHHHHhccCCeEEEEcCCCCCHHHHHHHHHHHHHHcCCCcEEEEcCcHHHHHHHHHHHHHhCcceE
Confidence            34578999999999988878899999999999653321   122 478999999999999999999987776543

>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=98.27  E-value=7.7e-07  Score=83.31  Aligned_cols=61  Identities=15%  Similarity=0.090  Sum_probs=49.0

Q ss_pred             CCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhc--c-ccccCCcEEEEcchHHHHHHHHHHH
Q 037567           13 VFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQL--P-PLVTGKTALVVSPLISLMQDQVMSL   73 (374)
Q Consensus        13 ~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l--~-~~~~~~~~lil~P~~~l~~q~~~~~   73 (374)
                      .+.+.|.+++..+..++.+++.|++|+|||.+...  . +...+.++++++||...+....+..
T Consensus       189 ~L~~~Q~~Av~~~~~~~~~~I~G~pGTGKTt~i~~l~~~l~~~g~~Vl~~ApT~~Aa~~L~e~~  252 (574)
T 3e1s_A          189 GLSEEQASVLDQLAGHRLVVLTGGPGTGKSTTTKAVADLAESLGLEVGLCAPTGKAARRLGEVT  252 (574)
T ss_dssp             TCCHHHHHHHHHHTTCSEEEEECCTTSCHHHHHHHHHHHHHHTTCCEEEEESSHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHhCCEEEEEcCCCCCHHHHHHHHHHHHHhcCCeEEEecCcHHHHHHhHhhh
Confidence            47899999999999999999999999999965321  1 1235788999999998888776543

>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=98.11  E-value=5.8e-05  Score=72.31  Aligned_cols=63  Identities=14%  Similarity=0.167  Sum_probs=49.3

Q ss_pred             CCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccc---cc----cCCcEEEEcchHHHHHHHHHHHHHc
Q 037567           12 SVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPP---LV----TGKTALVVSPLISLMQDQVMSLKQR   76 (374)
Q Consensus        12 ~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~---~~----~~~~~lil~P~~~l~~q~~~~~~~~   76 (374)
                      ..+++-|.+++.  .....++|.|++|||||.+..--+   +.    ...++|++++|+..+.++.+.+...
T Consensus         8 ~~Ln~~Q~~av~--~~~~~~lV~a~aGsGKT~~l~~ri~~l~~~~~~~~~~iL~ltft~~aa~e~~~rl~~~   77 (647)
T 3lfu_A            8 DSLNDKQREAVA--APRSNLLVLAGAGSGKTRVLVHRIAWLMSVENCSPYSIMAVTFTNKAAAEMRHRIGQL   77 (647)
T ss_dssp             TTCCHHHHHHHT--CCSSCEEEEECTTSCHHHHHHHHHHHHHHTSCCCGGGEEEEESSHHHHHHHHHHHHHH
T ss_pred             hcCCHHHHHHHh--CCCCCEEEEECCCCCHHHHHHHHHHHHHHhCCCChhhEEEEeccHHHHHHHHHHHHHH
Confidence            468999999997  346789999999999996643221   11    2368999999999999999888754

>3hgt_A HDA1 complex subunit 3; RECA-like domain, SWI2/SNF2 helical domain, chromatin regulator, coiled coil, nucleus, repressor, transcription; 2.20A {Saccharomyces cerevisiae} PDB: 3hgq_A

Probab=97.72  E-value=0.00022  Score=60.63  Aligned_cols=127  Identities=11%  Similarity=0.024  Sum_probs=87.8

Q ss_pred             HHHHHHHHHhh-cCCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEecccccccc
Q 037567          215 DELVQEILKSV-AGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGID  293 (374)
Q Consensus       215 ~~~~~~~~~~~-~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d  293 (374)
                      -.++..++... ..+.+++||++.....+-+...+...+++...+.|.... .+++.    .+....+.+.|...+-|+|
T Consensus       111 f~~L~~LL~~l~~~~~kVLIfsq~t~~LDilE~~l~~~~~~y~RlDG~~~~-~~~k~----~~~~~~i~Lltsag~~gin  185 (328)
T 3hgt_A          111 FSVLRDLINLVQEYETETAIVCRPGRTMDLLEALLLGNKVHIKRYDGHSIK-SAAAA----NDFSCTVHLFSSEGINFTK  185 (328)
T ss_dssp             HHHHHHHHHHHTTSCEEEEEEECSTHHHHHHHHHHTTSSCEEEESSSCCC------------CCSEEEEEEESSCCCTTT
T ss_pred             HHHHHHHHHHHHhCCCEEEEEECChhHHHHHHHHHhcCCCceEeCCCCchh-hhhhc----ccCCceEEEEECCCCCCcC
Confidence            34455554443 356799999999999999999999999999999988443 32221    2345556666776666776


Q ss_pred             -----ccCccEEEEECCCCChhHH-HHhhccCCCCC----CceEEEEEeeccCCCcccceecc
Q 037567          294 -----KPDVRHVIHYGCPKTLESY-YQESGRCGRDG----IASVCWLYYARSNFAKGDFYCGE  346 (374)
Q Consensus       294 -----~~~~~~vi~~~~p~s~~~~-~Q~~GR~~R~~----~~g~~~~~~~~~~~~~~~~~~~~  346 (374)
                           +...+.||.+|+.+++..- +|.+-|+.|.+    +.-.++-+++....++....+.+
T Consensus       186 ~~~~nl~~aD~VI~~DsdwNp~~d~iQa~~r~~R~~~gq~k~v~V~RLvt~~TiEh~~l~~~~  248 (328)
T 3hgt_A          186 YPIKSKARFDMLICLDTTVDTSQKDIQYLLQYKRERKGLERYAPIVRLVAINSIDHCRLFFGK  248 (328)
T ss_dssp             SCCCCCSCCSEEEECSTTCCTTSHHHHHHHCCC---------CCEEEEEETTSHHHHHHHHHH
T ss_pred             cccccCCCCCEEEEECCCCCCCChHHHHHHHHhhhccCCCCcceEEEEeCCCCHHHHHHHccC
Confidence                 5678999999999999875 89888988873    34467778887777776666543

>3vkw_A Replicase large subunit; alpha/beta domain, helicase, transferase; 1.90A {Tomato mosaic virus}

Probab=97.69  E-value=4e-05  Score=68.36  Aligned_cols=44  Identities=16%  Similarity=-0.001  Sum_probs=34.5

Q ss_pred             EEEEccCCCCchhhhhccccccCCcEEEEcchHHHHHHHHHHHHHc
Q 037567           31 CLVVMATGSGKSLCYQLPPLVTGKTALVVSPLISLMQDQVMSLKQR   76 (374)
Q Consensus        31 ~l~~a~tGsGKT~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~   76 (374)
                      .++.|++|+|||....-.+ . ..+.++++|+++++++|.+.+...
T Consensus       164 ~~I~G~aGsGKTt~I~~~~-~-~~~~lVlTpT~~aa~~l~~kl~~~  207 (446)
T 3vkw_A          164 VLVDGVPGCGKTKEILSRV-N-FEEDLILVPGRQAAEMIRRRANAS  207 (446)
T ss_dssp             EEEEECTTSCHHHHHHHHC-C-TTTCEEEESCHHHHHHHHHHHTTT
T ss_pred             EEEEcCCCCCHHHHHHHHh-c-cCCeEEEeCCHHHHHHHHHHhhhc
Confidence            4789999999997653322 2 267899999999999999888543

>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=97.63  E-value=0.00028  Score=62.20  Aligned_cols=64  Identities=19%  Similarity=0.219  Sum_probs=49.6

Q ss_pred             CCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccc-----cccCCcEEEEcchHHHHHHHHHHHHHc
Q 037567           13 VFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPP-----LVTGKTALVVSPLISLMQDQVMSLKQR   76 (374)
Q Consensus        13 ~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~-----~~~~~~~lil~P~~~l~~q~~~~~~~~   76 (374)
                      .+.|+|...+..+...+.+++..+-+.|||.+....+     ...+..+++++|+...+..+++.+..+
T Consensus       163 ~L~p~Qk~il~~l~~~R~~vi~~sRq~GKT~l~a~~~l~~a~~~~g~~v~~vA~t~~qA~~vf~~i~~m  231 (385)
T 2o0j_A          163 QLRDYQRDMLKIMSSKRMTVCNLSRQLGKTTVVAIFLAHFVCFNKDKAVGILAHKGSMSAEVLDRTKQA  231 (385)
T ss_dssp             CCCHHHHHHHHHHHHSSEEEEEECSSSCHHHHHHHHHHHHHHSSSSCEEEEEESSHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHhhccCcEEEEEEcCcCChhHHHHHHHHHHHHhCCCCeEEEEeCCHHHHHHHHHHHHHH
Confidence            5899999999887655668999999999996543222     234668999999999998888776643

>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=97.49  E-value=0.0007  Score=63.88  Aligned_cols=64  Identities=19%  Similarity=0.215  Sum_probs=50.0

Q ss_pred             CCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhcc-----ccccCCcEEEEcchHHHHHHHHHHHHHc
Q 037567           13 VFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLP-----PLVTGKTALVVSPLISLMQDQVMSLKQR   76 (374)
Q Consensus        13 ~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~-----~~~~~~~~lil~P~~~l~~q~~~~~~~~   76 (374)
                      .++|+|...+..+...+..++..+-|+|||.+....     +...+.+++++.|+...+..++..++..
T Consensus       163 ~l~p~Q~~i~~~l~~~r~~~i~~~Rq~GKS~~~a~~~l~~~~~~~~~~i~~va~t~~qA~~~~~~i~~~  231 (592)
T 3cpe_A          163 QLRDYQRDMLKIMSSKRMTVCNLSRQLGKTTVVAIFLAHFVCFNKDKAVGILAHKGSMSAEVLDRTKQA  231 (592)
T ss_dssp             CCCHHHHHHHHHHHHCSEEEEEECSSSCHHHHHHHHHHHHHHTSSSCEEEEEESSHHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHhhccccEEEEEEcCccChHHHHHHHHHHHHHhCCCCeEEEEECCHHHHHHHHHHHHHH
Confidence            489999999988865677899999999999654322     1224568999999999999888777654

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*

Probab=97.45  E-value=0.00025  Score=55.97  Aligned_cols=36  Identities=19%  Similarity=0.060  Sum_probs=25.4

Q ss_pred             CCCEEEEccCCCCchhhhhcccc---ccCCcEEEEcchH
Q 037567           28 KRDCLVVMATGSGKSLCYQLPPL---VTGKTALVVSPLI   63 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~l~~~---~~~~~~lil~P~~   63 (374)
                      ++-.++.||+|+|||...+-.+.   ..+.+++++.|..
T Consensus         3 g~i~vi~G~~gsGKTT~ll~~~~~~~~~g~~v~~~~~~~   41 (184)
T 2orw_A            3 GKLTVITGPMYSGKTTELLSFVEIYKLGKKKVAVFKPKI   41 (184)
T ss_dssp             CCEEEEEESTTSSHHHHHHHHHHHHHHTTCEEEEEEEC-
T ss_pred             cEEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEeecc
Confidence            44568899999999976532222   2567899998884

>2j9r_A Thymidine kinase; TK1, DNK, lasso, transferase, ATP-binding, deoxyribonucleoside kinase, DNA synthesis, phosphate accept nucleotide-binding; HET: THM; 2.7A {Bacillus anthracis} PDB: 2ja1_A*

Probab=97.37  E-value=0.00023  Score=56.84  Aligned_cols=34  Identities=24%  Similarity=0.132  Sum_probs=24.1

Q ss_pred             EEEEccCCCCchhhhhcccc---ccCCcEEEEcchHH
Q 037567           31 CLVVMATGSGKSLCYQLPPL---VTGKTALVVSPLIS   64 (374)
Q Consensus        31 ~l~~a~tGsGKT~~~~l~~~---~~~~~~lil~P~~~   64 (374)
                      .++.+++|+|||...+-.+.   ..+.+++++.|...
T Consensus        31 ~vitG~MgsGKTT~lL~~a~r~~~~g~kVli~k~~~d   67 (214)
T 2j9r_A           31 EVICGSMFSGKSEELIRRVRRTQFAKQHAIVFKPCID   67 (214)
T ss_dssp             EEEECSTTSCHHHHHHHHHHHHHHTTCCEEEEECC--
T ss_pred             EEEECCCCCcHHHHHHHHHHHHHHCCCEEEEEEeccC
Confidence            46899999999976543332   35889999999864

>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=97.32  E-value=0.00082  Score=52.74  Aligned_cols=57  Identities=16%  Similarity=0.071  Sum_probs=34.3

Q ss_pred             chhHHHHHHHHH---------cCCCEEEEccCCCCchhhhhcc--cc--ccCCcEEEEcchHHHHHHHHHH
Q 037567           15 RPYQKDVIQRII---------EKRDCLVVMATGSGKSLCYQLP--PL--VTGKTALVVSPLISLMQDQVMS   72 (374)
Q Consensus        15 ~~~Q~~~~~~~~---------~~~~~l~~a~tGsGKT~~~~l~--~~--~~~~~~lil~P~~~l~~q~~~~   72 (374)
                      .+.|.+++..+.         .++.+++.||+|+|||..+...  .+  ..+..+++ .+..++..+....
T Consensus        16 ~~~~~~~~~~~~~~~~~~~~~~g~~~~l~G~~G~GKTtL~~~i~~~~~~~~g~~~~~-~~~~~~~~~~~~~   85 (180)
T 3ec2_A           16 NVSQNRALLTIRVFVHNFNPEEGKGLTFVGSPGVGKTHLAVATLKAIYEKKGIRGYF-FDTKDLIFRLKHL   85 (180)
T ss_dssp             SHHHHHHHHHHHHHHHSCCGGGCCEEEECCSSSSSHHHHHHHHHHHHHHHSCCCCCE-EEHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHhccccCCCEEEEECCCCCCHHHHHHHHHHHHHHHcCCeEEE-EEHHHHHHHHHHH
Confidence            346888887664         2577899999999999654222  11  22434444 3444555554443

>1xx6_A Thymidine kinase; NESG, northeast structural genomics consortium, protein STRU initiative, PSI, structural genomics, DNA synthesis; HET: ADP; 2.00A {Clostridium acetobutylicum} SCOP: c.37.1.24 g.39.1.14

Probab=97.21  E-value=0.00018  Score=56.88  Aligned_cols=36  Identities=22%  Similarity=0.046  Sum_probs=25.7

Q ss_pred             CCCEEEEccCCCCchhhhhcccc---ccCCcEEEEcchH
Q 037567           28 KRDCLVVMATGSGKSLCYQLPPL---VTGKTALVVSPLI   63 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~l~~~---~~~~~~lil~P~~   63 (374)
                      ++-.++.||+|+|||...+-.+.   ..+.+++++.|..
T Consensus         8 g~i~v~~G~mgsGKTT~ll~~a~r~~~~g~kV~v~k~~~   46 (191)
T 1xx6_A            8 GWVEVIVGPMYSGKSEELIRRIRRAKIAKQKIQVFKPEI   46 (191)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEEEC-
T ss_pred             CEEEEEECCCCCcHHHHHHHHHHHHHHCCCEEEEEEecc
Confidence            34457899999999976543332   2588999999984

>3e2i_A Thymidine kinase; Zn-binding, ATP-binding, DNA synthesis, nucleotide-B transferase; HET: MSE; 2.01A {Staphylococcus aureus}

Probab=97.14  E-value=0.001  Score=53.08  Aligned_cols=37  Identities=19%  Similarity=-0.005  Sum_probs=24.9

Q ss_pred             CCCEEEEccCCCCchhhhhcccc---ccCCcEEEEcchHH
Q 037567           28 KRDCLVVMATGSGKSLCYQLPPL---VTGKTALVVSPLIS   64 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~l~~~---~~~~~~lil~P~~~   64 (374)
                      |.-.++.+|+|+|||...+-.+.   ..+.+++++.|...
T Consensus        28 G~I~vitG~M~sGKTT~Llr~~~r~~~~g~kvli~kp~~D   67 (219)
T 3e2i_A           28 GWIECITGSMFSGKSEELIRRLRRGIYAKQKVVVFKPAID   67 (219)
T ss_dssp             CEEEEEEECTTSCHHHHHHHHHHHHHHTTCCEEEEEEC--
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHHHHHcCCceEEEEeccC
Confidence            34458899999999965432322   24788999999764

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=97.09  E-value=0.0011  Score=58.39  Aligned_cols=34  Identities=21%  Similarity=0.194  Sum_probs=22.9

Q ss_pred             CCCEEEEccCCCCchhhhhccccccCCcEEEEcc
Q 037567           28 KRDCLVVMATGSGKSLCYQLPPLVTGKTALVVSP   61 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~l~~~~~~~~~lil~P   61 (374)
                      .+.+++.||+|+|||+.+-..+-..+...+.+..
T Consensus       182 prGvLL~GPPGTGKTllAkAiA~e~~~~f~~v~~  215 (405)
T 4b4t_J          182 PKGVILYGPPGTGKTLLARAVAHHTDCKFIRVSG  215 (405)
T ss_dssp             CCCEEEESCSSSSHHHHHHHHHHHHTCEEEEEEG
T ss_pred             CCceEEeCCCCCCHHHHHHHHHHhhCCCceEEEh
Confidence            4789999999999998654443334444444443

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=97.05  E-value=0.0027  Score=47.65  Aligned_cols=19  Identities=11%  Similarity=0.022  Sum_probs=16.3

Q ss_pred             cCCCEEEEccCCCCchhhh
Q 037567           27 EKRDCLVVMATGSGKSLCY   45 (374)
Q Consensus        27 ~~~~~l~~a~tGsGKT~~~   45 (374)
                      ...++++.||+|+|||..+
T Consensus        26 ~~~~vll~G~~GtGKt~lA   44 (143)
T 3co5_A           26 RTSPVFLTGEAGSPFETVA   44 (143)
T ss_dssp             CSSCEEEEEETTCCHHHHH
T ss_pred             CCCcEEEECCCCccHHHHH
Confidence            4678999999999999754

>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=96.93  E-value=0.0054  Score=53.10  Aligned_cols=43  Identities=19%  Similarity=0.152  Sum_probs=25.3

Q ss_pred             CCEEEEccCCCCchhhhhcccc---ccCCcEEEEcchHHHHHHHHHH
Q 037567           29 RDCLVVMATGSGKSLCYQLPPL---VTGKTALVVSPLISLMQDQVMS   72 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~~l~~~---~~~~~~lil~P~~~l~~q~~~~   72 (374)
                      ..+++.||+|+|||..+-..+-   ..+.+++++... .+..+....
T Consensus        38 ~~lll~G~~GtGKT~la~~i~~~~~~~~~~~~~i~~~-~~~~~~~~~   83 (324)
T 1l8q_A           38 NPIFIYGSVGTGKTHLLQAAGNEAKKRGYRVIYSSAD-DFAQAMVEH   83 (324)
T ss_dssp             SSEEEECSSSSSHHHHHHHHHHHHHHTTCCEEEEEHH-HHHHHHHHH
T ss_pred             CeEEEECCCCCcHHHHHHHHHHHHHHCCCEEEEEEHH-HHHHHHHHH
Confidence            5789999999999965432221   124556665443 444443333

>2zpa_A Uncharacterized protein YPFI; RNA modification enzyme, RNA helicase, acetyltransferase, GCN5 acetyltransferase; HET: ACO ADP; 2.35A {Escherichia coli K12}

Probab=96.92  E-value=0.0023  Score=60.21  Aligned_cols=115  Identities=21%  Similarity=0.213  Sum_probs=72.2

Q ss_pred             CCchhHHHHHHHHHc--CCCEEEEccCCCCchhhhhccccccCCcEEEEcchHHHHHHHHHHHHHcCCceEEcCCCCCch
Q 037567           13 VFRPYQKDVIQRIIE--KRDCLVVMATGSGKSLCYQLPPLVTGKTALVVSPLISLMQDQVMSLKQRGINAEFLGSAQTDS   90 (374)
Q Consensus        13 ~~~~~Q~~~~~~~~~--~~~~l~~a~tGsGKT~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~   90 (374)
                      .++.-|.+++..+.+  ....++.|+-|.|||.+.-+.+..-...++|.+|+.+-+....+...+               
T Consensus       175 ~~T~dQ~~al~~~~~~~~~~~vlta~RGRGKSa~lG~~~a~~~~~~~vtAP~~~a~~~l~~~~~~---------------  239 (671)
T 2zpa_A          175 APQPEQQQLLKQLMTMPPGVAAVTAARGRGKSALAGQLISRIAGRAIVTAPAKASTDVLAQFAGE---------------  239 (671)
T ss_dssp             SCCHHHHHHHHHHTTCCSEEEEEEECTTSSHHHHHHHHHHHSSSCEEEECSSCCSCHHHHHHHGG---------------
T ss_pred             CCCHHHHHHHHHHHHhhhCeEEEecCCCCCHHHHHHHHHHHHHhCcEEECCCHHHHHHHHHHhhC---------------
Confidence            578899999999887  345689999999999554333332234579999998766644333221               


Q ss_pred             hhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHHhcCCCCeeEEEee
Q 037567           91 SVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTAT  170 (374)
Q Consensus        91 ~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~SaT  170 (374)
                                 .+-+..|+.+.         ......+++|||||-.+.-         ..+..+..   ..+.++||.|
T Consensus       240 -----------~i~~~~Pd~~~---------~~~~~~dlliVDEAAaIp~---------pll~~ll~---~~~~v~~~tT  287 (671)
T 2zpa_A          240 -----------KFRFIAPDALL---------ASDEQADWLVVDEAAAIPA---------PLLHQLVS---RFPRTLLTTT  287 (671)
T ss_dssp             -----------GCCBCCHHHHH---------HSCCCCSEEEEETGGGSCH---------HHHHHHHT---TSSEEEEEEE
T ss_pred             -----------CeEEeCchhhh---------hCcccCCEEEEEchhcCCH---------HHHHHHHh---hCCeEEEEec
Confidence                       01112222110         1223578999999987753         33333333   5568999999


Q ss_pred             cCcc
Q 037567          171 ATEK  174 (374)
Q Consensus       171 ~~~~  174 (374)
                      ....
T Consensus       288 v~GY  291 (671)
T 2zpa_A          288 VQGY  291 (671)
T ss_dssp             BSST
T ss_pred             CCcC
Confidence            7653

>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=96.86  E-value=0.0029  Score=54.78  Aligned_cols=31  Identities=23%  Similarity=0.196  Sum_probs=20.1

Q ss_pred             CCEEEEccCCCCchhhhhccccccCCcEEEE
Q 037567           29 RDCLVVMATGSGKSLCYQLPPLVTGKTALVV   59 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~~l~~~~~~~~~lil   59 (374)
                      +.+++.||+|+|||..+-..+-..+..++.+
T Consensus        52 ~~vLl~GppGtGKT~la~aia~~~~~~~~~v   82 (322)
T 3eie_A           52 SGILLYGPPGTGKSYLAKAVATEANSTFFSV   82 (322)
T ss_dssp             CEEEEECSSSSCHHHHHHHHHHHHTCEEEEE
T ss_pred             CeEEEECCCCCcHHHHHHHHHHHHCCCEEEE
Confidence            4689999999999976543332334444443

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=96.73  E-value=0.0034  Score=54.30  Aligned_cols=18  Identities=33%  Similarity=0.453  Sum_probs=15.2

Q ss_pred             CCEEEEccCCCCchhhhh
Q 037567           29 RDCLVVMATGSGKSLCYQ   46 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~~   46 (374)
                      +.+++.||+|+|||..+-
T Consensus        46 ~~iLL~GppGtGKT~la~   63 (322)
T 1xwi_A           46 RGILLFGPPGTGKSYLAK   63 (322)
T ss_dssp             SEEEEESSSSSCHHHHHH
T ss_pred             ceEEEECCCCccHHHHHH
Confidence            568999999999997643

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=96.70  E-value=0.0016  Score=59.01  Aligned_cols=17  Identities=18%  Similarity=0.288  Sum_probs=14.5

Q ss_pred             CEEEEccCCCCchhhhh
Q 037567           30 DCLVVMATGSGKSLCYQ   46 (374)
Q Consensus        30 ~~l~~a~tGsGKT~~~~   46 (374)
                      +++++||+|+|||..+-
T Consensus        52 ~vLL~GppGtGKTtlAr   68 (447)
T 3pvs_A           52 SMILWGPPGTGKTTLAE   68 (447)
T ss_dssp             EEEEECSTTSSHHHHHH
T ss_pred             EEEEECCCCCcHHHHHH
Confidence            58999999999997643

>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=96.69  E-value=0.0051  Score=53.48  Aligned_cols=32  Identities=16%  Similarity=0.390  Sum_probs=24.9

Q ss_pred             CchhHHHHHHHHHc----CC---CEEEEccCCCCchhhh
Q 037567           14 FRPYQKDVIQRIIE----KR---DCLVVMATGSGKSLCY   45 (374)
Q Consensus        14 ~~~~Q~~~~~~~~~----~~---~~l~~a~tGsGKT~~~   45 (374)
                      ++|+|.+++..+.+    ++   .+++.||+|+|||..+
T Consensus         3 ~~pw~~~~~~~l~~~i~~~~~~~a~L~~G~~G~GKt~~a   41 (334)
T 1a5t_A            3 WYPWLRPDFEKLVASYQAGRGHHALLIQALPGMGDDALI   41 (334)
T ss_dssp             CCGGGHHHHHHHHHHHHTTCCCSEEEEECCTTSCHHHHH
T ss_pred             CCCchHHHHHHHHHHHHcCCcceeEEEECCCCchHHHHH
Confidence            57999999877653    32   3799999999999654

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=96.63  E-value=0.0026  Score=53.98  Aligned_cols=19  Identities=26%  Similarity=0.420  Sum_probs=15.7

Q ss_pred             CCCEEEEccCCCCchhhhh
Q 037567           28 KRDCLVVMATGSGKSLCYQ   46 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~   46 (374)
                      .+.+++.||+|+|||..+-
T Consensus        51 ~~~~ll~G~~GtGKT~la~   69 (285)
T 3h4m_A           51 PKGILLYGPPGTGKTLLAK   69 (285)
T ss_dssp             CSEEEEESSSSSSHHHHHH
T ss_pred             CCeEEEECCCCCcHHHHHH
Confidence            4678999999999997543

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.54  E-value=0.0023  Score=57.25  Aligned_cols=33  Identities=24%  Similarity=0.269  Sum_probs=21.8

Q ss_pred             CCCEEEEccCCCCchhhhhccccccCCcEEEEc
Q 037567           28 KRDCLVVMATGSGKSLCYQLPPLVTGKTALVVS   60 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~l~~~~~~~~~lil~   60 (374)
                      .+.+++.||+|+|||+.+-..+-..+...+.+.
T Consensus       215 prGvLLyGPPGTGKTllAkAiA~e~~~~f~~v~  247 (434)
T 4b4t_M          215 PKGALMYGPPGTGKTLLARACAAQTNATFLKLA  247 (434)
T ss_dssp             CCEEEEESCTTSSHHHHHHHHHHHHTCEEEEEE
T ss_pred             CCeeEEECcCCCCHHHHHHHHHHHhCCCEEEEe
Confidence            367899999999999865433333344444443

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=96.53  E-value=0.0024  Score=48.30  Aligned_cols=18  Identities=28%  Similarity=0.163  Sum_probs=15.5

Q ss_pred             cCCCEEEEccCCCCchhh
Q 037567           27 EKRDCLVVMATGSGKSLC   44 (374)
Q Consensus        27 ~~~~~l~~a~tGsGKT~~   44 (374)
                      .+..+++.||+|+|||..
T Consensus        35 ~g~~~~l~G~~G~GKTtL   52 (149)
T 2kjq_A           35 HGQFIYVWGEEGAGKSHL   52 (149)
T ss_dssp             CCSEEEEESSSTTTTCHH
T ss_pred             CCCEEEEECCCCCCHHHH
Confidence            467789999999999964

>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=96.50  E-value=0.0053  Score=53.89  Aligned_cols=31  Identities=23%  Similarity=0.196  Sum_probs=20.1

Q ss_pred             CCEEEEccCCCCchhhhhccccccCCcEEEE
Q 037567           29 RDCLVVMATGSGKSLCYQLPPLVTGKTALVV   59 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~~l~~~~~~~~~lil   59 (374)
                      +.+++.||+|+|||..+-..+-..+..++.+
T Consensus        85 ~~iLL~GppGtGKT~la~ala~~~~~~~~~v  115 (355)
T 2qp9_X           85 SGILLYGPPGTGKSYLAKAVATEANSTFFSV  115 (355)
T ss_dssp             CCEEEECSTTSCHHHHHHHHHHHHTCEEEEE
T ss_pred             ceEEEECCCCCcHHHHHHHHHHHhCCCEEEe
Confidence            5689999999999976543332334444443

>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=96.46  E-value=0.013  Score=53.06  Aligned_cols=43  Identities=16%  Similarity=0.131  Sum_probs=25.0

Q ss_pred             CCEEEEccCCCCchhhhhcccc---c--cCCcEEEEcchHHHHHHHHHH
Q 037567           29 RDCLVVMATGSGKSLCYQLPPL---V--TGKTALVVSPLISLMQDQVMS   72 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~~l~~~---~--~~~~~lil~P~~~l~~q~~~~   72 (374)
                      +.+++.||+|+|||..+...+-   .  .+.+++++... .+..+....
T Consensus       131 ~~lll~Gp~G~GKTtLa~aia~~l~~~~~~~~v~~v~~~-~~~~~~~~~  178 (440)
T 2z4s_A          131 NPLFIYGGVGLGKTHLLQSIGNYVVQNEPDLRVMYITSE-KFLNDLVDS  178 (440)
T ss_dssp             CCEEEECSSSSSHHHHHHHHHHHHHHHCCSSCEEEEEHH-HHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEeeHH-HHHHHHHHH
Confidence            5789999999999965432211   1  14555555443 344444333

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=96.45  E-value=0.0048  Score=54.91  Aligned_cols=32  Identities=19%  Similarity=0.251  Sum_probs=20.5

Q ss_pred             CCCEEEEccCCCCchhhhhccccccCCcEEEE
Q 037567           28 KRDCLVVMATGSGKSLCYQLPPLVTGKTALVV   59 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~l~~~~~~~~~lil   59 (374)
                      .+.+++.||+|+|||..+-..+...+..++.+
T Consensus       148 ~~~vLL~GppGtGKT~la~aia~~~~~~~~~v  179 (389)
T 3vfd_A          148 ARGLLLFGPPGNGKTMLAKAVAAESNATFFNI  179 (389)
T ss_dssp             CSEEEEESSTTSCHHHHHHHHHHHTTCEEEEE
T ss_pred             CceEEEECCCCCCHHHHHHHHHHhhcCcEEEe
Confidence            36789999999999976543333333333333

>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=96.44  E-value=0.0075  Score=49.43  Aligned_cols=18  Identities=11%  Similarity=0.043  Sum_probs=15.3

Q ss_pred             CCCEEEEccCCCCchhhh
Q 037567           28 KRDCLVVMATGSGKSLCY   45 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~   45 (374)
                      +..+++.||+|+|||..+
T Consensus        52 ~~~~ll~G~~G~GKT~la   69 (242)
T 3bos_A           52 VQAIYLWGPVKSGRTHLI   69 (242)
T ss_dssp             CSEEEEECSTTSSHHHHH
T ss_pred             CCeEEEECCCCCCHHHHH
Confidence            567899999999999654

>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=96.43  E-value=0.0094  Score=50.95  Aligned_cols=32  Identities=16%  Similarity=0.162  Sum_probs=20.4

Q ss_pred             CCCEEEEccCCCCchhhhhccccccCCcEEEE
Q 037567           28 KRDCLVVMATGSGKSLCYQLPPLVTGKTALVV   59 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~l~~~~~~~~~lil   59 (374)
                      ++.+++.||+|+|||..+-..+-..+...+.+
T Consensus        49 ~~~vLL~Gp~GtGKT~la~ala~~~~~~~i~v   80 (301)
T 3cf0_A           49 SKGVLFYGPPGCGKTLLAKAIANECQANFISI   80 (301)
T ss_dssp             CSEEEEECSSSSSHHHHHHHHHHHTTCEEEEE
T ss_pred             CceEEEECCCCcCHHHHHHHHHHHhCCCEEEE
Confidence            46789999999999976533332233334433

>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=96.43  E-value=0.011  Score=53.59  Aligned_cols=18  Identities=33%  Similarity=0.453  Sum_probs=15.3

Q ss_pred             CCEEEEccCCCCchhhhh
Q 037567           29 RDCLVVMATGSGKSLCYQ   46 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~~   46 (374)
                      +.+++.||+|+|||..+-
T Consensus       168 ~~vLL~GppGtGKT~lA~  185 (444)
T 2zan_A          168 RGILLFGPPGTGKSYLAK  185 (444)
T ss_dssp             SEEEEECSTTSSHHHHHH
T ss_pred             ceEEEECCCCCCHHHHHH
Confidence            578999999999997653

>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=96.39  E-value=0.017  Score=48.06  Aligned_cols=18  Identities=28%  Similarity=0.512  Sum_probs=14.9

Q ss_pred             CCEEEEccCCCCchhhhh
Q 037567           29 RDCLVVMATGSGKSLCYQ   46 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~~   46 (374)
                      +.+++.||+|+|||..+-
T Consensus        40 ~~vll~G~~GtGKT~la~   57 (262)
T 2qz4_A           40 KGALLLGPPGCGKTLLAK   57 (262)
T ss_dssp             CEEEEESCTTSSHHHHHH
T ss_pred             ceEEEECCCCCCHHHHHH
Confidence            468999999999997643

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=96.36  E-value=0.0088  Score=46.74  Aligned_cols=18  Identities=22%  Similarity=0.349  Sum_probs=14.9

Q ss_pred             CCCEEEEccCCCCchhhh
Q 037567           28 KRDCLVVMATGSGKSLCY   45 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~   45 (374)
                      ...+++.||+|+|||..+
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            357899999999999654

>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=96.34  E-value=0.016  Score=56.13  Aligned_cols=91  Identities=11%  Similarity=0.016  Sum_probs=72.2

Q ss_pred             chHHHHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHHc----CCceeeeecCCChHHHHHHHHhhhcCCeeEEEEec-
Q 037567          212 SFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQL----GVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATM-  286 (374)
Q Consensus       212 ~~~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~-  286 (374)
                      .+....+..++.....+.+++|.+|+..-+.+.++.+++.    ++++..+||+.+..++...++.+.+|+.+|+|+|+ 
T Consensus       401 GKTlvall~il~~l~~g~qvlvlaPtr~La~Q~~~~l~~~~~~~gi~v~~l~G~~~~~~r~~~~~~l~~g~~~IvVgT~~  480 (780)
T 1gm5_A          401 GKTVVAQLAILDNYEAGFQTAFMVPTSILAIQHYRRTVESFSKFNIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTHA  480 (780)
T ss_dssp             SHHHHHHHHHHHHHHHTSCEEEECSCHHHHHHHHHHHHHHHTCSSCCEEECCSSSCHHHHHHHHHHHHSSCCCEEEECTT
T ss_pred             CHHHHHHHHHHHHHHcCCeEEEEeCcHHHHHHHHHHHHHHhhhcCceEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHH
Confidence            3334444445555556789999999999998888887763    78899999999999999999999999999999998 


Q ss_pred             cccccccccCccEEEE
Q 037567          287 AFGMGIDKPDVRHVIH  302 (374)
Q Consensus       287 ~~~~G~d~~~~~~vi~  302 (374)
                      .+...+++.++..||.
T Consensus       481 ll~~~~~~~~l~lVVI  496 (780)
T 1gm5_A          481 LIQEDVHFKNLGLVII  496 (780)
T ss_dssp             HHHHCCCCSCCCEEEE
T ss_pred             HHhhhhhccCCceEEe
Confidence            4445667777887774

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=96.30  E-value=0.0057  Score=52.42  Aligned_cols=18  Identities=17%  Similarity=-0.009  Sum_probs=15.3

Q ss_pred             CCCEEEEccCCCCchhhh
Q 037567           28 KRDCLVVMATGSGKSLCY   45 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~   45 (374)
                      +.++++.||||+|||.+.
T Consensus        45 ~~~lli~GpPGTGKT~~v   62 (318)
T 3te6_A           45 NKLFYITNADDSTKFQLV   62 (318)
T ss_dssp             CCEEEEECCCSHHHHHHH
T ss_pred             CCeEEEECCCCCCHHHHH
Confidence            467899999999999764

>4b4t_I 26S protease regulatory subunit 4 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.30  E-value=0.0032  Score=55.83  Aligned_cols=32  Identities=25%  Similarity=0.278  Sum_probs=21.1

Q ss_pred             CCCEEEEccCCCCchhhhhccccccCCcEEEE
Q 037567           28 KRDCLVVMATGSGKSLCYQLPPLVTGKTALVV   59 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~l~~~~~~~~~lil   59 (374)
                      .+.+++.||+|+|||+.+-..+-..+...+.+
T Consensus       216 prGvLLyGPPGTGKTlLAkAiA~e~~~~fi~v  247 (437)
T 4b4t_I          216 PKGVILYGAPGTGKTLLAKAVANQTSATFLRI  247 (437)
T ss_dssp             CSEEEEESSTTTTHHHHHHHHHHHHTCEEEEE
T ss_pred             CCCCceECCCCchHHHHHHHHHHHhCCCEEEE
Confidence            36789999999999986543333334444443

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.29  E-value=0.0027  Score=56.90  Aligned_cols=33  Identities=18%  Similarity=0.276  Sum_probs=22.0

Q ss_pred             CCCEEEEccCCCCchhhhhccccccCCcEEEEc
Q 037567           28 KRDCLVVMATGSGKSLCYQLPPLVTGKTALVVS   60 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~l~~~~~~~~~lil~   60 (374)
                      .+.+++.||+|+|||+.+-..+-..+...+.+.
T Consensus       215 prGvLL~GPPGtGKTllAkAiA~e~~~~~~~v~  247 (437)
T 4b4t_L          215 PKGVLLYGPPGTGKTLLAKAVAATIGANFIFSP  247 (437)
T ss_dssp             CCEEEEESCTTSSHHHHHHHHHHHHTCEEEEEE
T ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhCCCEEEEe
Confidence            367899999999999865443333344444443

>4b4t_H 26S protease regulatory subunit 7 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.27  E-value=0.0027  Score=56.85  Aligned_cols=33  Identities=27%  Similarity=0.345  Sum_probs=21.5

Q ss_pred             CCCEEEEccCCCCchhhhhccccccCCcEEEEc
Q 037567           28 KRDCLVVMATGSGKSLCYQLPPLVTGKTALVVS   60 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~l~~~~~~~~~lil~   60 (374)
                      .+.+++.||+|+|||+.+-..+-..+...+.+.
T Consensus       243 prGILLyGPPGTGKTlLAkAiA~e~~~~fi~vs  275 (467)
T 4b4t_H          243 PKGILLYGPPGTGKTLCARAVANRTDATFIRVI  275 (467)
T ss_dssp             CSEEEECSCTTSSHHHHHHHHHHHHTCEEEEEE
T ss_pred             CCceEeeCCCCCcHHHHHHHHHhccCCCeEEEE
Confidence            467899999999999865433333344444433

>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=96.24  E-value=0.021  Score=46.15  Aligned_cols=36  Identities=17%  Similarity=-0.011  Sum_probs=25.4

Q ss_pred             CCCEEEEccCCCCchhhhhcccc---ccCCcEEEEcchH
Q 037567           28 KRDCLVVMATGSGKSLCYQLPPL---VTGKTALVVSPLI   63 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~l~~~---~~~~~~lil~P~~   63 (374)
                      +.-.++.|++|+|||...+-.+.   ..+.+++++.|..
T Consensus        12 G~i~litG~mGsGKTT~ll~~~~r~~~~g~kVli~~~~~   50 (223)
T 2b8t_A           12 GWIEFITGPMFAGKTAELIRRLHRLEYADVKYLVFKPKI   50 (223)
T ss_dssp             CEEEEEECSTTSCHHHHHHHHHHHHHHTTCCEEEEEECC
T ss_pred             cEEEEEECCCCCcHHHHHHHHHHHHHhcCCEEEEEEecc
Confidence            44567899999999976443322   2577899988764

>2qby_B CDC6 homolog 3, cell division control protein 6 homolog 3; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus}

Probab=96.21  E-value=0.013  Score=51.94  Aligned_cols=17  Identities=29%  Similarity=0.368  Sum_probs=14.5

Q ss_pred             CCEEEEccCCCCchhhh
Q 037567           29 RDCLVVMATGSGKSLCY   45 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~   45 (374)
                      ..+++.||+|+|||...
T Consensus        46 ~~vll~G~~G~GKT~la   62 (384)
T 2qby_B           46 FSNLFLGLTGTGKTFVS   62 (384)
T ss_dssp             CEEEEEECTTSSHHHHH
T ss_pred             CcEEEECCCCCCHHHHH
Confidence            46899999999999654

>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=96.20  E-value=0.0025  Score=61.26  Aligned_cols=62  Identities=18%  Similarity=0.210  Sum_probs=48.1

Q ss_pred             CCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccc---cc----cCCcEEEEcchHHHHHHHHHHHHHc
Q 037567           13 VFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPP---LV----TGKTALVVSPLISLMQDQVMSLKQR   76 (374)
Q Consensus        13 ~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~---~~----~~~~~lil~P~~~l~~q~~~~~~~~   76 (374)
                      .+++-|.+++..  .+..++|.|++|||||.+..--+   +.    ...++|+++.|+..+.++.+.+...
T Consensus         2 ~L~~~Q~~av~~--~~~~~lV~AgaGSGKT~~l~~ri~~ll~~~~~~~~~IL~lTfT~~Aa~em~~Rl~~~   70 (673)
T 1uaa_A            2 RLNPGQQQAVEF--VTGPCLVLAGAGSGKTRVITNKIAHLIRGCGYQARHIAAVTFTNKAAREMKERVGQT   70 (673)
T ss_dssp             CCCHHHHHHHHC--CSSEEEECCCTTSCHHHHHHHHHHHHHHHHCCCGGGEEEEESSHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHhC--CCCCEEEEeCCCCChHHHHHHHHHHHHHhcCCCHHHeEEEeccHHHHHHHHHHHHHH
Confidence            478999999975  46788999999999996543211   11    3468999999999999999888753

>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=96.20  E-value=0.0043  Score=60.02  Aligned_cols=62  Identities=11%  Similarity=0.157  Sum_probs=48.0

Q ss_pred             CCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhcc---ccc----cCCcEEEEcchHHHHHHHHHHHHH
Q 037567           12 SVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLP---PLV----TGKTALVVSPLISLMQDQVMSLKQ   75 (374)
Q Consensus        12 ~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~---~~~----~~~~~lil~P~~~l~~q~~~~~~~   75 (374)
                      ..+++-|.+++..  ....++|.|++|||||.+..--   ++.    ...++|+++.|+..+.++.+.+..
T Consensus        10 ~~Ln~~Q~~av~~--~~g~~lV~AgAGSGKT~vL~~ri~~ll~~~~~~p~~IL~vTFTnkAA~Em~~Rl~~   78 (724)
T 1pjr_A           10 AHLNKEQQEAVRT--TEGPLLIMAGAGSGKTRVLTHRIAYLMAEKHVAPWNILAITFTNKAAREMRERVQS   78 (724)
T ss_dssp             TTSCHHHHHHHHC--CSSCEEEEECTTSCHHHHHHHHHHHHHHTTCCCGGGEEEEESSHHHHHHHHHHHHH
T ss_pred             hhCCHHHHHHHhC--CCCCEEEEEcCCCCHHHHHHHHHHHHHHhcCCCHHHeEEEeccHHHHHHHHHHHHH
Confidence            4689999999875  4678999999999999653211   111    246799999999999998888765

>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=96.15  E-value=0.0042  Score=52.24  Aligned_cols=18  Identities=22%  Similarity=0.119  Sum_probs=15.0

Q ss_pred             CCEEEEccCCCCchhhhh
Q 037567           29 RDCLVVMATGSGKSLCYQ   46 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~~   46 (374)
                      ..+++.||+|+|||..+.
T Consensus        65 ~~vLl~G~~GtGKT~la~   82 (272)
T 1d2n_A           65 VSVLLEGPPHSGKTALAA   82 (272)
T ss_dssp             EEEEEECSTTSSHHHHHH
T ss_pred             eEEEEECCCCCcHHHHHH
Confidence            468999999999997643

>2orv_A Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'- (2'deoxythymidil))tetraphosphate, transferase; HET: 4TA; 2.30A {Homo sapiens} SCOP: c.37.1.24 g.39.1.14

Probab=96.14  E-value=0.0014  Score=52.86  Aligned_cols=37  Identities=16%  Similarity=-0.001  Sum_probs=26.7

Q ss_pred             CCCEEEEccCCCCchhhhhcccc---ccCCcEEEEcchHH
Q 037567           28 KRDCLVVMATGSGKSLCYQLPPL---VTGKTALVVSPLIS   64 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~l~~~---~~~~~~lil~P~~~   64 (374)
                      ++-.++.|++|+|||...+-.+.   ..+.+++++-|...
T Consensus        19 g~l~v~~G~MgsGKTT~lL~~~~r~~~~g~kvli~kp~~D   58 (234)
T 2orv_A           19 GQIQVILGPMFSGKSTELMRRVRRFQIAQYKCLVIKYAKD   58 (234)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHHHHHTTTCCEEEEEETTC
T ss_pred             eEEEEEECCCCCcHHHHHHHHHHHHHHCCCeEEEEeecCC
Confidence            44457899999999966443322   35888999998764

>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=96.10  E-value=0.01  Score=54.39  Aligned_cols=30  Identities=27%  Similarity=0.305  Sum_probs=19.6

Q ss_pred             CCEEEEccCCCCchhhhhccccccCCcEEE
Q 037567           29 RDCLVVMATGSGKSLCYQLPPLVTGKTALV   58 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~~l~~~~~~~~~li   58 (374)
                      ..+++.||+|+|||..+-..+-..+..++.
T Consensus       239 ~~vLL~GppGtGKT~lAraia~~~~~~fv~  268 (489)
T 3hu3_A          239 RGILLYGPPGTGKTLIARAVANETGAFFFL  268 (489)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHCSSEEEE
T ss_pred             CcEEEECcCCCCHHHHHHHHHHHhCCCEEE
Confidence            568999999999997653332223333333

>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=96.09  E-value=0.0076  Score=52.94  Aligned_cols=20  Identities=25%  Similarity=0.371  Sum_probs=16.1

Q ss_pred             CCCEEEEccCCCCchhhhhc
Q 037567           28 KRDCLVVMATGSGKSLCYQL   47 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~l   47 (374)
                      .+.+++.||+|+|||..+-.
T Consensus       117 ~~~vLl~GppGtGKT~la~a  136 (357)
T 3d8b_A          117 PKGILLFGPPGTGKTLIGKC  136 (357)
T ss_dssp             CSEEEEESSTTSSHHHHHHH
T ss_pred             CceEEEECCCCCCHHHHHHH
Confidence            35789999999999976543

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=96.05  E-value=0.012  Score=50.22  Aligned_cols=18  Identities=28%  Similarity=0.423  Sum_probs=15.4

Q ss_pred             CCCEEEEccCCCCchhhh
Q 037567           28 KRDCLVVMATGSGKSLCY   45 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~   45 (374)
                      .+.+++.||+|+|||..+
T Consensus        54 ~~~vll~Gp~GtGKT~la   71 (297)
T 3b9p_A           54 AKGLLLFGPPGNGKTLLA   71 (297)
T ss_dssp             CSEEEEESSSSSCHHHHH
T ss_pred             CCeEEEECcCCCCHHHHH
Confidence            467899999999999764

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=96.04  E-value=0.098  Score=44.62  Aligned_cols=17  Identities=18%  Similarity=0.149  Sum_probs=14.5

Q ss_pred             CCEEEEccCCCCchhhh
Q 037567           29 RDCLVVMATGSGKSLCY   45 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~   45 (374)
                      .++++.||+|+|||..+
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            36899999999999754

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=95.97  E-value=0.008  Score=53.71  Aligned_cols=32  Identities=22%  Similarity=0.249  Sum_probs=21.0

Q ss_pred             CCCEEEEccCCCCchhhhhccccccCCcEEEE
Q 037567           28 KRDCLVVMATGSGKSLCYQLPPLVTGKTALVV   59 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~l~~~~~~~~~lil   59 (374)
                      .+.+++.||+|+|||+.+-..+-..+..++.+
T Consensus       206 prGiLL~GPPGtGKT~lakAiA~~~~~~~~~v  237 (428)
T 4b4t_K          206 PRGVLLYGPPGTGKTMLVKAVANSTKAAFIRV  237 (428)
T ss_dssp             CCEEEEESCTTTTHHHHHHHHHHHHTCEEEEE
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHhCCCeEEE
Confidence            35689999999999976543333334444444

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=95.85  E-value=0.018  Score=50.07  Aligned_cols=18  Identities=22%  Similarity=0.206  Sum_probs=15.3

Q ss_pred             CCEEEEccCCCCchhhhh
Q 037567           29 RDCLVVMATGSGKSLCYQ   46 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~~   46 (374)
                      .++++.||+|+|||..+.
T Consensus        56 ~~vll~G~~GtGKT~la~   73 (338)
T 3pfi_A           56 DHILFSGPAGLGKTTLAN   73 (338)
T ss_dssp             CCEEEECSTTSSHHHHHH
T ss_pred             CeEEEECcCCCCHHHHHH
Confidence            479999999999997643

>1w4r_A Thymidine kinase; type II, human, cytosolic, phosphorylation, transferase; HET: TTP; 1.83A {Homo sapiens} PDB: 1xbt_A* 2wvj_A* 2j87_A*

Probab=95.84  E-value=0.0094  Score=46.81  Aligned_cols=35  Identities=17%  Similarity=0.014  Sum_probs=24.4

Q ss_pred             CCCEEEEccCCCCchhhhhcccc---ccCCcEEEEcch
Q 037567           28 KRDCLVVMATGSGKSLCYQLPPL---VTGKTALVVSPL   62 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~l~~~---~~~~~~lil~P~   62 (374)
                      ++=.++.||+|+|||.-.+-.+-   ..+.+++++.|.
T Consensus        20 g~l~fiyG~MgsGKTt~Ll~~i~n~~~~~~kvl~~kp~   57 (195)
T 1w4r_A           20 GQIQVILGPMFSGKSTELMRRVRRFQIAQYKCLVIKYA   57 (195)
T ss_dssp             CEEEEEEECTTSCHHHHHHHHHHHHHHTTCCEEEEEET
T ss_pred             eEEEEEECCCCCcHHHHHHHHHHHHHHcCCeEEEEccc
Confidence            45568899999999944222221   247889999887

>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=95.80  E-value=0.037  Score=48.81  Aligned_cols=18  Identities=22%  Similarity=0.366  Sum_probs=15.1

Q ss_pred             CCCEEEEccCCCCchhhh
Q 037567           28 KRDCLVVMATGSGKSLCY   45 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~   45 (374)
                      +..+++.||+|+|||...
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            457899999999999654

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=95.75  E-value=0.12  Score=41.03  Aligned_cols=17  Identities=18%  Similarity=0.235  Sum_probs=14.7

Q ss_pred             CCEEEEccCCCCchhhh
Q 037567           29 RDCLVVMATGSGKSLCY   45 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~   45 (374)
                      ..+++.||+|+|||..+
T Consensus        55 ~~~~l~G~~GtGKT~la   71 (202)
T 2w58_A           55 KGLYLHGSFGVGKTYLL   71 (202)
T ss_dssp             CEEEEECSTTSSHHHHH
T ss_pred             CeEEEECCCCCCHHHHH
Confidence            67899999999999654

>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=95.72  E-value=0.01  Score=61.01  Aligned_cols=61  Identities=21%  Similarity=0.189  Sum_probs=47.8

Q ss_pred             CCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhcc---ccc------cCCcEEEEcchHHHHHHHHHHHHH
Q 037567           13 VFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLP---PLV------TGKTALVVSPLISLMQDQVMSLKQ   75 (374)
Q Consensus        13 ~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~---~~~------~~~~~lil~P~~~l~~q~~~~~~~   75 (374)
                      ++++-|.+++..  .+++++|.|+.|||||.+..--   ++.      ...+++++++|++.+.++.+.+..
T Consensus        10 ~~t~eQ~~~i~~--~~~~~~v~a~AGSGKT~vl~~ri~~ll~~~~~~~~~~~il~~Tft~~aa~e~~~ri~~   79 (1232)
T 3u4q_A           10 TWTDDQWNAIVS--TGQDILVAAAAGSGKTAVLVERMIRKITAEENPIDVDRLLVVTFTNASAAEMKHRIAE   79 (1232)
T ss_dssp             CCCHHHHHHHHC--CSSCEEEEECTTCCHHHHHHHHHHHHHSCSSSCCCGGGEEEECSSHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHhC--CCCCEEEEecCCCcHHHHHHHHHHHHHhcCCCCCCccceEEEeccHHHHHHHHHHHHH
Confidence            589999999975  4789999999999999663211   111      235899999999999998888765

>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=95.66  E-value=0.0062  Score=52.68  Aligned_cols=14  Identities=14%  Similarity=0.086  Sum_probs=12.1

Q ss_pred             CccEEEEeccchhh
Q 037567          126 GVCLFAVDEAHCIS  139 (374)
Q Consensus       126 ~~~~vviDE~h~~~  139 (374)
                      ...++++||+|.+.
T Consensus       105 ~~~vliiDEi~~l~  118 (324)
T 3u61_B          105 RQKVIVIDEFDRSG  118 (324)
T ss_dssp             CEEEEEEESCCCGG
T ss_pred             CCeEEEEECCcccC
Confidence            56799999999986

>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=95.59  E-value=0.022  Score=45.79  Aligned_cols=17  Identities=24%  Similarity=0.266  Sum_probs=14.3

Q ss_pred             CCEEEEccCCCCchhhh
Q 037567           29 RDCLVVMATGSGKSLCY   45 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~   45 (374)
                      ..+++.||+|+|||...
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            35899999999999653

>2gno_A DNA polymerase III, gamma subunit-related protein; structural genomics, joint center for structural genomics, J protein structure initiative; HET: DNA; 2.00A {Thermotoga maritima} SCOP: a.80.1.1 c.37.1.20

Probab=95.55  E-value=0.0059  Score=52.23  Aligned_cols=16  Identities=13%  Similarity=-0.224  Sum_probs=13.7

Q ss_pred             CEEEEccCCCCchhhh
Q 037567           30 DCLVVMATGSGKSLCY   45 (374)
Q Consensus        30 ~~l~~a~tGsGKT~~~   45 (374)
                      ..++.||+|+|||..+
T Consensus        20 ~~Lf~Gp~G~GKtt~a   35 (305)
T 2gno_A           20 SILINGEDLSYPREVS   35 (305)
T ss_dssp             EEEEECSSSSHHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            5789999999999654

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A*

Probab=95.44  E-value=0.079  Score=47.37  Aligned_cols=85  Identities=14%  Similarity=0.138  Sum_probs=66.4

Q ss_pred             HHHHHHhhcCCCcEEEEecchhHHHHHHHHHHH---cCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEec-ccc---c
Q 037567          218 VQEILKSVAGAGSIIVYCMTIKDVEEISKALKQ---LGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATM-AFG---M  290 (374)
Q Consensus       218 ~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~---~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~-~~~---~  290 (374)
                      +..++.....+.+++|.+|++.-+.++++.+++   .++.+..++|+.+..++......+..|+.+|+|+|+ .+.   .
T Consensus        54 l~~~~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~~~~l~~~~~~Iiv~Tp~~l~~~l~  133 (414)
T 3oiy_A           54 MMTALWLARKGKKSALVFPTVTLVKQTLERLQKLADEKVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNRE  133 (414)
T ss_dssp             HHHHHHHHTTTCCEEEEESSHHHHHHHHHHHHHHCCSSCCEEECCTTSCHHHHHHHHHHHHHTCCSEEEEEHHHHHHCHH
T ss_pred             HHHHHHHhcCCCEEEEEECCHHHHHHHHHHHHHHccCCceEEEEECCCChhhHHHHHHHhhcCCCCEEEECHHHHHHHHH
Confidence            333344445788999999999999999999998   577999999999998888888889899899999998 221   1


Q ss_pred             cccccCccEEEE
Q 037567          291 GIDKPDVRHVIH  302 (374)
Q Consensus       291 G~d~~~~~~vi~  302 (374)
                      -++..++++||.
T Consensus       134 ~~~~~~~~~iVi  145 (414)
T 3oiy_A          134 KLSQKRFDFVFV  145 (414)
T ss_dssp             HHTTCCCSEEEE
T ss_pred             HhccccccEEEE
Confidence            244456777663

>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=95.39  E-value=0.015  Score=56.30  Aligned_cols=31  Identities=16%  Similarity=0.166  Sum_probs=21.2

Q ss_pred             CCEEEEccCCCCchhhhhccccccCCcEEEE
Q 037567           29 RDCLVVMATGSGKSLCYQLPPLVTGKTALVV   59 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~~l~~~~~~~~~lil   59 (374)
                      +.+++.||+|+|||+.+-..+-..+...+.+
T Consensus       512 ~gvLl~GPPGtGKT~lAkaiA~e~~~~f~~v  542 (806)
T 3cf2_A          512 KGVLFYGPPGCGKTLLAKAIANECQANFISI  542 (806)
T ss_dssp             SCCEEESSTTSSHHHHHHHHHHTTTCEEEEC
T ss_pred             ceEEEecCCCCCchHHHHHHHHHhCCceEEe
Confidence            5689999999999976544444444444433

>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=95.38  E-value=0.015  Score=56.18  Aligned_cols=31  Identities=26%  Similarity=0.328  Sum_probs=20.6

Q ss_pred             CCEEEEccCCCCchhhhhccccccCCcEEEE
Q 037567           29 RDCLVVMATGSGKSLCYQLPPLVTGKTALVV   59 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~~l~~~~~~~~~lil   59 (374)
                      +.+++.||+|+|||+.+-..+-..+..++.+
T Consensus       239 ~GILL~GPPGTGKT~LAraiA~elg~~~~~v  269 (806)
T 3cf2_A          239 RGILLYGPPGTGKTLIARAVANETGAFFFLI  269 (806)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHTTTTCEEEEE
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHhCCeEEEE
Confidence            5689999999999986543333334444433

>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=95.34  E-value=0.047  Score=44.49  Aligned_cols=16  Identities=25%  Similarity=0.225  Sum_probs=13.6

Q ss_pred             CEEEEccCCCCchhhh
Q 037567           30 DCLVVMATGSGKSLCY   45 (374)
Q Consensus        30 ~~l~~a~tGsGKT~~~   45 (374)
                      .+++.||+|+|||...
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            5799999999999653

>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=95.34  E-value=0.047  Score=42.89  Aligned_cols=135  Identities=14%  Similarity=0.062  Sum_probs=63.6

Q ss_pred             CCCEEEEccCCCCchhhhhcccc---ccCCcEEEEcchHH-HHHHHHHHHHHcCCceEEcCCCCCchhhhhhhhcCCeeE
Q 037567           28 KRDCLVVMATGSGKSLCYQLPPL---VTGKTALVVSPLIS-LMQDQVMSLKQRGINAEFLGSAQTDSSVQTKAETGYFQL  103 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~l~~~---~~~~~~lil~P~~~-l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i  103 (374)
                      ...+++..++|.|||.+++-.++   ..+.+|+++-=.+. .-..-..-+..+++.....+.+..-.........     
T Consensus        28 ~g~i~v~tG~GkGKTTaA~GlalRA~g~G~rV~~vQF~Kg~~~~gE~~~l~~L~v~~~~~g~gf~~~~~~~~~~~-----  102 (196)
T 1g5t_A           28 RGIIIVFTGNGKGKTTAAFGTAARAVGHGKNVGVVQFIKGTWPNGERNLLEPHGVEFQVMATGFTWETQNREADT-----  102 (196)
T ss_dssp             CCCEEEEESSSSCHHHHHHHHHHHHHHTTCCEEEEESSCCSSCCHHHHHHGGGTCEEEECCTTCCCCGGGHHHHH-----
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEEeeCCCCCccHHHHHHhCCcEEEEcccccccCCCCcHHHH-----
Confidence            45789999999999977654433   36888988832221 0000011122333332222211110000000000     


Q ss_pred             EEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHHhcCCCCeeEEEeecCccc
Q 037567          104 LFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEKV  175 (374)
Q Consensus       104 ~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~SaT~~~~~  175 (374)
                           ......+......+....+++||+||+-.....+.-..   ..+-.+....+...-+.+|+-..+..
T Consensus       103 -----~~a~~~l~~a~~~l~~~~yDlvILDEi~~al~~g~l~~---~ev~~~l~~Rp~~~~vIlTGr~ap~~  166 (196)
T 1g5t_A          103 -----AACMAVWQHGKRMLADPLLDMVVLDELTYMVAYDYLPL---EEVISALNARPGHQTVIITGRGCHRD  166 (196)
T ss_dssp             -----HHHHHHHHHHHHHTTCTTCSEEEEETHHHHHHTTSSCH---HHHHHHHHTSCTTCEEEEECSSCCHH
T ss_pred             -----HHHHHHHHHHHHHHhcCCCCEEEEeCCCccccCCCCCH---HHHHHHHHhCcCCCEEEEECCCCcHH
Confidence                 00001111111122225689999999976555443322   22334444455666777777766543

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=95.33  E-value=0.014  Score=48.07  Aligned_cols=51  Identities=22%  Similarity=0.201  Sum_probs=31.5

Q ss_pred             cCCCEEEEccCCCCchhhhhc---cccccCCcEEEEcchHHHHHHHHHHHHHcCC
Q 037567           27 EKRDCLVVMATGSGKSLCYQL---PPLVTGKTALVVSPLISLMQDQVMSLKQRGI   78 (374)
Q Consensus        27 ~~~~~l~~a~tGsGKT~~~~l---~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~   78 (374)
                      .|.-+++.||+|+|||..++.   .+...+.+++++.-.. ...+..+.+...+.
T Consensus        22 ~G~~~~i~G~~GsGKTtl~~~~~~~~~~~~~~v~~~~~e~-~~~~~~~~~~~~g~   75 (247)
T 2dr3_A           22 ERNVVLLSGGPGTGKTIFSQQFLWNGLKMGEPGIYVALEE-HPVQVRQNMAQFGW   75 (247)
T ss_dssp             TTCEEEEEECTTSSHHHHHHHHHHHHHHTTCCEEEEESSS-CHHHHHHHHHTTTC
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEEccC-CHHHHHHHHHHcCC
Confidence            356678999999999965332   2223566777776442 34555555555443

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=95.32  E-value=0.02  Score=46.60  Aligned_cols=34  Identities=18%  Similarity=0.132  Sum_probs=22.1

Q ss_pred             CCCEEEEccCCCCchhhhhccc---cccCCcEEEEcc
Q 037567           28 KRDCLVVMATGSGKSLCYQLPP---LVTGKTALVVSP   61 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~l~~---~~~~~~~lil~P   61 (374)
                      |.-+++.||+|+|||......+   ...+.+++++..
T Consensus        23 G~~~~i~G~~GsGKTtl~~~l~~~~~~~~~~v~~~~~   59 (235)
T 2w0m_A           23 GFFIALTGEPGTGKTIFSLHFIAKGLRDGDPCIYVTT   59 (235)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHHHHHHHHTCCEEEEES
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHHHHCCCeEEEEEc
Confidence            5667899999999995433221   224566777653

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=95.30  E-value=0.039  Score=48.75  Aligned_cols=18  Identities=28%  Similarity=0.379  Sum_probs=15.1

Q ss_pred             CCCEEEEccCCCCchhhh
Q 037567           28 KRDCLVVMATGSGKSLCY   45 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~   45 (374)
                      +..+++.||+|+|||...
T Consensus        44 ~~~vll~G~~G~GKT~l~   61 (387)
T 2v1u_A           44 PSNALLYGLTGTGKTAVA   61 (387)
T ss_dssp             CCCEEECBCTTSSHHHHH
T ss_pred             CCcEEEECCCCCCHHHHH
Confidence            457899999999999654

>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=95.19  E-value=0.029  Score=49.01  Aligned_cols=17  Identities=24%  Similarity=0.288  Sum_probs=14.5

Q ss_pred             CCEEEEccCCCCchhhh
Q 037567           29 RDCLVVMATGSGKSLCY   45 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~   45 (374)
                      .++++.||+|+|||...
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            46899999999999654

>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=95.16  E-value=0.032  Score=51.57  Aligned_cols=32  Identities=22%  Similarity=0.236  Sum_probs=21.0

Q ss_pred             CCEEEEccCCCCchhhhhccccccCCcEEEEc
Q 037567           29 RDCLVVMATGSGKSLCYQLPPLVTGKTALVVS   60 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~~l~~~~~~~~~lil~   60 (374)
                      +.+++.||+|+|||..+...+-..+..++.+.
T Consensus        78 ~~lLL~GppGtGKTtla~~la~~l~~~~i~in  109 (516)
T 1sxj_A           78 RAAMLYGPPGIGKTTAAHLVAQELGYDILEQN  109 (516)
T ss_dssp             SEEEEECSTTSSHHHHHHHHHHHTTCEEEEEC
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHcCCCEEEEe
Confidence            57899999999999765433333344454443

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20

Probab=95.16  E-value=0.024  Score=47.07  Aligned_cols=18  Identities=33%  Similarity=0.516  Sum_probs=15.0

Q ss_pred             CCCEEEEccCCCCchhhh
Q 037567           28 KRDCLVVMATGSGKSLCY   45 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~   45 (374)
                      .+.+++.||+|+|||..+
T Consensus        45 ~~~vll~G~~GtGKT~la   62 (257)
T 1lv7_A           45 PKGVLMVGPPGTGKTLLA   62 (257)
T ss_dssp             CCEEEEECCTTSCHHHHH
T ss_pred             CCeEEEECcCCCCHHHHH
Confidence            346899999999999754

>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=95.15  E-value=0.049  Score=48.17  Aligned_cols=16  Identities=19%  Similarity=0.401  Sum_probs=14.0

Q ss_pred             CEEEEccCCCCchhhh
Q 037567           30 DCLVVMATGSGKSLCY   45 (374)
Q Consensus        30 ~~l~~a~tGsGKT~~~   45 (374)
                      .+++.||+|+|||...
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            6899999999999654

>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=94.94  E-value=0.11  Score=45.71  Aligned_cols=15  Identities=27%  Similarity=0.246  Sum_probs=13.1

Q ss_pred             EEEEccCCCCchhhh
Q 037567           31 CLVVMATGSGKSLCY   45 (374)
Q Consensus        31 ~l~~a~tGsGKT~~~   45 (374)
                      +++.||+|+|||...
T Consensus        41 ~ll~G~~G~GKT~la   55 (373)
T 1jr3_A           41 YLFSGTRGVGKTSIA   55 (373)
T ss_dssp             EEEESCTTSSHHHHH
T ss_pred             EEEECCCCCCHHHHH
Confidence            689999999999654

>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=94.71  E-value=0.038  Score=47.55  Aligned_cols=16  Identities=25%  Similarity=0.291  Sum_probs=14.0

Q ss_pred             CEEEEccCCCCchhhh
Q 037567           30 DCLVVMATGSGKSLCY   45 (374)
Q Consensus        30 ~~l~~a~tGsGKT~~~   45 (374)
                      ++++.||+|+|||..+
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            6899999999999654

>2cvh_A DNA repair and recombination protein RADB; filament formation, homologous recombination, ATPase domain, hyperthermophIle; HET: DNA; 2.20A {Thermococcus kodakarensis} PDB: 2cvf_A*

Probab=94.57  E-value=0.049  Score=43.80  Aligned_cols=34  Identities=24%  Similarity=0.113  Sum_probs=23.1

Q ss_pred             CCCEEEEccCCCCchhhhhccccccCCcEEEEcc
Q 037567           28 KRDCLVVMATGSGKSLCYQLPPLVTGKTALVVSP   61 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~l~~~~~~~~~lil~P   61 (374)
                      |.-+++.||+|+|||..+...+...+.+++++.-
T Consensus        20 G~~~~i~G~~GsGKTtl~~~l~~~~~~~v~~i~~   53 (220)
T 2cvh_A           20 GVLTQVYGPYASGKTTLALQTGLLSGKKVAYVDT   53 (220)
T ss_dssp             TSEEEEECSTTSSHHHHHHHHHHHHCSEEEEEES
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHcCCcEEEEEC
Confidence            4567899999999996543322245667777653

>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A 2r6e_A 2vyf_A 2vye_A

Probab=94.51  E-value=0.092  Score=47.66  Aligned_cols=35  Identities=14%  Similarity=0.022  Sum_probs=22.9

Q ss_pred             CCCEEEEccCCCCchhhhhccc---cc-cCCcEEEEcch
Q 037567           28 KRDCLVVMATGSGKSLCYQLPP---LV-TGKTALVVSPL   62 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~l~~---~~-~~~~~lil~P~   62 (374)
                      |.-+++.|++|+|||...+..+   .. .+.+++++..-
T Consensus       203 G~liiI~G~pG~GKTtl~l~ia~~~~~~~g~~Vl~~s~E  241 (454)
T 2r6a_A          203 SDLIIVAARPSVGKTAFALNIAQNVATKTNENVAIFSLE  241 (454)
T ss_dssp             TCEEEEECCTTSCHHHHHHHHHHHHHHHSSCCEEEEESS
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHHHhCCCcEEEEECC
Confidence            4456889999999995543222   12 35578887643

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=94.39  E-value=0.034  Score=58.88  Aligned_cols=96  Identities=16%  Similarity=0.116  Sum_probs=54.6

Q ss_pred             HHHHHHc------CCCEEEEccCCCCchhhhhc---cccccCCcEEEEcchHHHHHHHHHHHHHcCCceEEcCCCCCchh
Q 037567           21 VIQRIIE------KRDCLVVMATGSGKSLCYQL---PPLVTGKTALVVSPLISLMQDQVMSLKQRGINAEFLGSAQTDSS   91 (374)
Q Consensus        21 ~~~~~~~------~~~~l~~a~tGsGKT~~~~l---~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~   91 (374)
                      .+..++.      ++.+++.+|+|+|||..+..   .+...+.+++++.....+....   .+.+|....          
T Consensus      1414 ~LD~lLG~GGi~~g~~vll~GppGtGKT~LA~ala~ea~~~G~~v~Fi~~e~~~~~l~---a~~~G~dl~---------- 1480 (2050)
T 3cmu_A         1414 SLDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEHALDPIY---ARKLGVDID---------- 1480 (2050)
T ss_dssp             HHHHHHSSSSEETTSEEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEECTTSCCCHHH---HHHTTCCTT----------
T ss_pred             HHHHhcCCCCccCCeEEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEEEcccccCHHH---HHHcCCCch----------
Confidence            3566655      67889999999999965432   2334577888887664332222   344443211          


Q ss_pred             hhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhh
Q 037567           92 VQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCIS  139 (374)
Q Consensus        92 ~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~  139 (374)
                                .+.|..|+.................+++|||||..-+.
T Consensus      1481 ----------~l~v~~~~~~E~~l~~~~~lvr~~~~~lVVIDsi~al~ 1518 (2050)
T 3cmu_A         1481 ----------NLLCSQPDTGEQALEICDALARSGAVDVIVVDSVAALT 1518 (2050)
T ss_dssp             ----------TCEEECCSSHHHHHHHHHHHHHHTCCSEEEESCGGGCC
T ss_pred             ----------hceeecCChHHHHHHHHHHHHhcCCCCEEEEcChhHhc
Confidence                      12333444322222222222334678999999997554

>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=94.32  E-value=0.048  Score=49.65  Aligned_cols=50  Identities=10%  Similarity=-0.031  Sum_probs=41.4

Q ss_pred             CCCEEEEccCCCCchhhhhccccccCCcEEEEcchHHHHHHHHHHHHHcC
Q 037567           28 KRDCLVVMATGSGKSLCYQLPPLVTGKTALVVSPLISLMQDQVMSLKQRG   77 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~   77 (374)
                      +....+.+-+|||||+++...+...+.++||++|+...+.+++.+++.+.
T Consensus        14 ~~~~~l~g~~gs~ka~~~a~l~~~~~~p~lvv~~~~~~A~~l~~~l~~~~   63 (483)
T 3hjh_A           14 GEQRLLGELTGAACATLVAEIAERHAGPVVLIAPDMQNALRLHDEISQFT   63 (483)
T ss_dssp             TCEEEEECCCTTHHHHHHHHHHHHSSSCEEEEESSHHHHHHHHHHHHHTC
T ss_pred             CCeEEEeCCCchHHHHHHHHHHHHhCCCEEEEeCCHHHHHHHHHHHHhhC
Confidence            45678899999999987554444456789999999999999999999873

>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus}

Probab=94.28  E-value=0.14  Score=46.39  Aligned_cols=35  Identities=11%  Similarity=-0.018  Sum_probs=22.6

Q ss_pred             CCCEEEEccCCCCchhhhhcc---ccc-cCCcEEEEcch
Q 037567           28 KRDCLVVMATGSGKSLCYQLP---PLV-TGKTALVVSPL   62 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~l~---~~~-~~~~~lil~P~   62 (374)
                      |.-+++.|++|+|||...+-.   +.. .+.+++++..-
T Consensus       200 G~l~ii~G~pg~GKT~lal~ia~~~a~~~g~~vl~~slE  238 (444)
T 2q6t_A          200 GSLNIIAARPAMGKTAFALTIAQNAALKEGVGVGIYSLE  238 (444)
T ss_dssp             TCEEEEEECTTSCHHHHHHHHHHHHHHTTCCCEEEEESS
T ss_pred             CcEEEEEeCCCCCHHHHHHHHHHHHHHhCCCeEEEEECC
Confidence            345688999999999543322   222 35678887653

>1v5w_A DMC1, meiotic recombination protein DMC1/LIM15 homolog; DNA-binding protein, ring protein, octamer, AAA ATPase; 3.20A {Homo sapiens} SCOP: c.37.1.11 PDB: 2zjb_A

Probab=94.24  E-value=0.11  Score=45.22  Aligned_cols=104  Identities=8%  Similarity=0.034  Sum_probs=53.1

Q ss_pred             HHHHHHc-----CCCEEEEccCCCCchhhhhcccc---c------cCCcEEEEcchHHH-HHHHHHHHHHcCCceEEcCC
Q 037567           21 VIQRIIE-----KRDCLVVMATGSGKSLCYQLPPL---V------TGKTALVVSPLISL-MQDQVMSLKQRGINAEFLGS   85 (374)
Q Consensus        21 ~~~~~~~-----~~~~l~~a~tGsGKT~~~~l~~~---~------~~~~~lil~P~~~l-~~q~~~~~~~~~~~~~~~~~   85 (374)
                      .+..++.     |.-+++.||+|+|||..++..+.   .      .+.+++++.-...+ ..+....+..++...     
T Consensus       110 ~LD~~LgGGl~~G~i~~I~G~~GsGKTtla~~la~~~~~~~~~gg~~~~vlyi~~E~~~~~~~l~~~~~~~g~~~-----  184 (343)
T 1v5w_A          110 EFDKLLGGGIESMAITEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDTENTFRPDRLRDIADRFNVDH-----  184 (343)
T ss_dssp             HHHHHTTSSBCSSEEEEEECCTTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEEESSSCCCHHHHHHHHHHTTCCH-----
T ss_pred             hHHHHhcCCCCCCeEEEEECCCCCCHHHHHHHHHHHHhcccccCCCCCeEEEEECCCCCCHHHHHHHHHHcCCCH-----
Confidence            4555553     34568999999999955432221   1      25677777654321 334444444544321     


Q ss_pred             CCCchhhhhhhhcCCeeEEEEcCccc---ccCchhhHHHHHh--cCccEEEEeccchhhc
Q 037567           86 AQTDSSVQTKAETGYFQLLFMTPEKA---CIIPISFWSKLLK--AGVCLFAVDEAHCISE  140 (374)
Q Consensus        86 ~~~~~~~~~~~~~~~~~i~i~T~~~l---~~~~~~~~~~~~~--~~~~~vviDE~h~~~~  140 (374)
                          ...    ..   ++.+..+...   ..++.........  ..+++||||....+..
T Consensus       185 ----~~~----l~---~l~~~~~~~~e~~~~ll~~l~~~i~~~~~~~~lvVIDsl~~l~~  233 (343)
T 1v5w_A          185 ----DAV----LD---NVLYARAYTSEHQMELLDYVAAKFHEEAGIFKLLIIDSIMALFR  233 (343)
T ss_dssp             ----HHH----HH---TEEEEECCSTTHHHHHHHHHHHHHHHSCSSEEEEEEETSGGGHH
T ss_pred             ----HHH----Hh---ceeEeecCCHHHHHHHHHHHHHHHHhcCCCccEEEEechHHHHH
Confidence                000    01   2344333222   1222111122223  5789999999998864

>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=94.22  E-value=0.24  Score=50.49  Aligned_cols=88  Identities=10%  Similarity=0.107  Sum_probs=68.7

Q ss_pred             HHHHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHHc----CCceeeeecCCChHHHHHHHHhhhcCCeeEEEEec-cc
Q 037567          214 VDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQL----GVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATM-AF  288 (374)
Q Consensus       214 ~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~-~~  288 (374)
                      ....+.........+.+++|.+|+..-+.+.++.+++.    +..+..+++..+..++...++.+..|+.+|+|+|+ .+
T Consensus       638 T~val~aa~~~~~~g~~vlvlvPt~~La~Q~~~~~~~~~~~~~i~v~~l~~~~~~~~~~~~~~~l~~g~~dIvV~T~~ll  717 (1151)
T 2eyq_A          638 TEVAMRAAFLAVDNHKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTHKLL  717 (1151)
T ss_dssp             HHHHHHHHHHHHTTTCEEEEECSSHHHHHHHHHHHHHHSTTTTCCEEEESTTSCHHHHHHHHHHHHTTCCSEEEECTHHH
T ss_pred             HHHHHHHHHHHHHhCCeEEEEechHHHHHHHHHHHHHHhhcCCCeEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHH
Confidence            33333334444456789999999999999988888753    56788899999999999999999999999999997 55


Q ss_pred             cccccccCccEEE
Q 037567          289 GMGIDKPDVRHVI  301 (374)
Q Consensus       289 ~~G~d~~~~~~vi  301 (374)
                      ...+++.++..||
T Consensus       718 ~~~~~~~~l~lvI  730 (1151)
T 2eyq_A          718 QSDVKFKDLGLLI  730 (1151)
T ss_dssp             HSCCCCSSEEEEE
T ss_pred             hCCccccccceEE
Confidence            5567777777766

>1sxj_B Activator 1 37 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=94.21  E-value=0.059  Score=46.27  Aligned_cols=16  Identities=19%  Similarity=0.295  Sum_probs=13.8

Q ss_pred             CEEEEccCCCCchhhh
Q 037567           30 DCLVVMATGSGKSLCY   45 (374)
Q Consensus        30 ~~l~~a~tGsGKT~~~   45 (374)
                      ++++.||+|+|||...
T Consensus        44 ~~ll~G~~G~GKt~la   59 (323)
T 1sxj_B           44 HMIISGMPGIGKTTSV   59 (323)
T ss_dssp             CEEEECSTTSSHHHHH
T ss_pred             eEEEECcCCCCHHHHH
Confidence            4899999999999654

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori}

Probab=94.19  E-value=0.097  Score=45.21  Aligned_cols=43  Identities=12%  Similarity=-0.013  Sum_probs=27.1

Q ss_pred             HHHHHHHc----CCCEEEEccCCCCchhhhhcc---ccccCCcEEEEcch
Q 037567           20 DVIQRIIE----KRDCLVVMATGSGKSLCYQLP---PLVTGKTALVVSPL   62 (374)
Q Consensus        20 ~~~~~~~~----~~~~l~~a~tGsGKT~~~~l~---~~~~~~~~lil~P~   62 (374)
                      ..+..++.    |.-+++.|++|+|||..++-.   +...+.+++++..-
T Consensus        34 ~~LD~~~gGl~~G~LiiIaG~pG~GKTt~al~ia~~~a~~g~~Vl~fSlE   83 (338)
T 4a1f_A           34 VQLDNYTSGFNKGSLVIIGARPSMGKTSLMMNMVLSALNDDRGVAVFSLE   83 (338)
T ss_dssp             HHHHHHHCSBCTTCEEEEEECTTSCHHHHHHHHHHHHHHTTCEEEEEESS
T ss_pred             hHHHHHhcCCCCCcEEEEEeCCCCCHHHHHHHHHHHHHHcCCeEEEEeCC
Confidence            34455543    345688999999999543322   22257788887653

>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=94.04  E-value=0.071  Score=48.46  Aligned_cols=18  Identities=33%  Similarity=0.538  Sum_probs=15.1

Q ss_pred             CCEEEEccCCCCchhhhh
Q 037567           29 RDCLVVMATGSGKSLCYQ   46 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~~   46 (374)
                      +.+++.||+|+|||..+-
T Consensus        50 ~gvLL~GppGtGKT~Lar   67 (476)
T 2ce7_A           50 KGILLVGPPGTGKTLLAR   67 (476)
T ss_dssp             SEEEEECCTTSSHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHH
Confidence            568999999999997643

>2vhj_A Ntpase P4, P4; non- hydrolysable ATP analogue, hydrolase, virus dsRNA, molecular motor, packaging ATPase, hexameric helicase; HET: ADP; 1.80A {Pseudomonas phage PHI12} PDB: 2vhq_A* 1w44_A* 1w46_A* 1w47_A* 1w48_A* 1w49_A* 1w4a_A* 1w4b_A* 1w4c_A 2vht_A* 2vhu_A* 2vhc_A*

Probab=93.94  E-value=0.051  Score=46.31  Aligned_cols=19  Identities=21%  Similarity=0.134  Sum_probs=15.0

Q ss_pred             CCCEEEEccCCCCchhhhh
Q 037567           28 KRDCLVVMATGSGKSLCYQ   46 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~   46 (374)
                      +..+++.||+|+|||..+.
T Consensus       123 gsviLI~GpPGsGKTtLAl  141 (331)
T 2vhj_A          123 SGMVIVTGKGNSGKTPLVH  141 (331)
T ss_dssp             SEEEEEECSCSSSHHHHHH
T ss_pred             CcEEEEEcCCCCCHHHHHH
Confidence            4556899999999996544

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=93.92  E-value=0.12  Score=44.41  Aligned_cols=45  Identities=11%  Similarity=-0.015  Sum_probs=26.9

Q ss_pred             CCCEEEEccCCCCchhhhhcc---ccccCCcEEEEcchHHHHHHHHHHH
Q 037567           28 KRDCLVVMATGSGKSLCYQLP---PLVTGKTALVVSPLISLMQDQVMSL   73 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~l~---~~~~~~~~lil~P~~~l~~q~~~~~   73 (374)
                      |.-+++.|++|+|||..++-.   +..++.+++++..- .-..|+...+
T Consensus        68 G~l~li~G~pG~GKTtl~l~ia~~~a~~g~~vl~~slE-~s~~~l~~R~  115 (315)
T 3bh0_A           68 RNFVLIAARPSMGKTAFALKQAKNMSDNDDVVNLHSLE-MGKKENIKRL  115 (315)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHHHHHTTTCEEEEEESS-SCHHHHHHHH
T ss_pred             CcEEEEEeCCCCCHHHHHHHHHHHHHHcCCeEEEEECC-CCHHHHHHHH
Confidence            445789999999999543322   22345678887643 2333344443

>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=93.90  E-value=0.47  Score=42.50  Aligned_cols=51  Identities=22%  Similarity=0.102  Sum_probs=28.6

Q ss_pred             CEEEEccCCCCchhhhhccc---cccCCcEEEEc--chHH-HHHHHHHHHHHcCCce
Q 037567           30 DCLVVMATGSGKSLCYQLPP---LVTGKTALVVS--PLIS-LMQDQVMSLKQRGINA   80 (374)
Q Consensus        30 ~~l~~a~tGsGKT~~~~l~~---~~~~~~~lil~--P~~~-l~~q~~~~~~~~~~~~   80 (374)
                      -+++.+++|+|||.+....+   ...+.+++++.  |.+. ..+|........+...
T Consensus       102 vIlivG~~G~GKTTt~~kLA~~l~~~G~kVllv~~D~~R~aa~eqL~~~~~~~gvpv  158 (443)
T 3dm5_A          102 ILLMVGIQGSGKTTTVAKLARYFQKRGYKVGVVCSDTWRPGAYHQLRQLLDRYHIEV  158 (443)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEEECCCSSTHHHHHHHHHHGGGTCEE
T ss_pred             EEEEECcCCCCHHHHHHHHHHHHHHCCCeEEEEeCCCcchhHHHHHHHHHHhcCCcE
Confidence            45789999999996643221   23466776655  3333 3344444444444443

>4ddu_A Reverse gyrase; topoisomerase, DNA supercoiling, archaea, helicase, hydrolas; 3.00A {Thermotoga maritima} PDB: 4ddt_A 4ddv_A 4ddw_A 4ddx_A

Probab=93.84  E-value=0.25  Score=50.02  Aligned_cols=86  Identities=14%  Similarity=0.121  Sum_probs=68.1

Q ss_pred             HHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHH---cCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEec-cccc--
Q 037567          217 LVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQ---LGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATM-AFGM--  290 (374)
Q Consensus       217 ~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~---~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~-~~~~--  290 (374)
                      .+..++.....+.++||.+|++.-+.++++.+++   .++.+..+||+.+..++....+.+..|+.+|+|+|+ .+..  
T Consensus       110 ~l~~il~~~~~~~~~Lil~PtreLa~Q~~~~l~~l~~~~i~v~~l~Gg~~~~er~~~~~~l~~g~~~IlV~Tp~rL~~~l  189 (1104)
T 4ddu_A          110 GMMTALWLARKGKKSALVFPTVTLVKQTLERLQKLADEKVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNR  189 (1104)
T ss_dssp             HHHHHHHHHTTTCCEEEEESSHHHHHHHHHHHHTTSCTTSCEEEECTTCCTTHHHHHHHHHHTSCCSEEEEEHHHHHHSH
T ss_pred             HHHHHHHHHhcCCeEEEEechHHHHHHHHHHHHHhhCCCCeEEEEeCCCCHHHHHHHHHHHhCCCCCEEEECHHHHHHHH
Confidence            3344444445788999999999999999999998   467899999999998888888999999999999998 2211  


Q ss_pred             -cccccCccEEEE
Q 037567          291 -GIDKPDVRHVIH  302 (374)
Q Consensus       291 -G~d~~~~~~vi~  302 (374)
                       -++..+++++|.
T Consensus       190 ~~l~~~~l~~lVi  202 (1104)
T 4ddu_A          190 EKLSQKRFDFVFV  202 (1104)
T ss_dssp             HHHHTSCCSEEEE
T ss_pred             HhhcccCcCEEEE
Confidence             245567777774

>2zts_A Putative uncharacterized protein PH0186; KAIC like protein, ATP-binding, nucleotide-binding, ATP- binding protein; HET: ADP; 2.07A {Pyrococcus horikoshii}

Probab=93.74  E-value=0.031  Score=46.01  Aligned_cols=49  Identities=18%  Similarity=0.158  Sum_probs=30.1

Q ss_pred             CCCEEEEccCCCCchhhhhc-c---ccccCCcEEEEcchHHHHHHHHHHHHHcC
Q 037567           28 KRDCLVVMATGSGKSLCYQL-P---PLVTGKTALVVSPLISLMQDQVMSLKQRG   77 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~l-~---~~~~~~~~lil~P~~~l~~q~~~~~~~~~   77 (374)
                      |.-+++.|++|+|||..++- +   +...+.+++++.-. .-..+..+.+...+
T Consensus        30 G~l~~i~G~pG~GKT~l~l~~~~~~~~~~~~~v~~~s~E-~~~~~~~~~~~~~~   82 (251)
T 2zts_A           30 GTTVLLTGGTGTGKTTFAAQFIYKGAEEYGEPGVFVTLE-ERARDLRREMASFG   82 (251)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHHHHHHHHCCCEEEEESS-SCHHHHHHHHHTTT
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHHHHhcCCCceeeccc-CCHHHHHHHHHHcC
Confidence            45678999999999954332 1   12336677777643 33455555665543

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=93.73  E-value=0.14  Score=43.73  Aligned_cols=18  Identities=28%  Similarity=0.420  Sum_probs=15.6

Q ss_pred             CCCEEEEccCCCCchhhh
Q 037567           28 KRDCLVVMATGSGKSLCY   45 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~   45 (374)
                      ..++++.|++|+|||..+
T Consensus        25 ~~~vLi~Ge~GtGKt~lA   42 (304)
T 1ojl_A           25 DATVLIHGDSGTGKELVA   42 (304)
T ss_dssp             TSCEEEESCTTSCHHHHH
T ss_pred             CCcEEEECCCCchHHHHH
Confidence            568999999999999764

>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=93.57  E-value=0.044  Score=47.82  Aligned_cols=43  Identities=16%  Similarity=0.033  Sum_probs=28.0

Q ss_pred             HHHHHHHc------CCCEEEEccCCCCchhhhhccc---cccCCcEEEEcch
Q 037567           20 DVIQRIIE------KRDCLVVMATGSGKSLCYQLPP---LVTGKTALVVSPL   62 (374)
Q Consensus        20 ~~~~~~~~------~~~~l~~a~tGsGKT~~~~l~~---~~~~~~~lil~P~   62 (374)
                      ..++.++.      +.-+++.+++|+|||..++-.+   ...+.+++++...
T Consensus        49 ~~LD~~Lg~GGl~~G~ii~I~G~pGsGKTtLal~la~~~~~~g~~vlyid~E  100 (356)
T 1u94_A           49 LSLDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAE  100 (356)
T ss_dssp             HHHHHHTSSSSEETTSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEESS
T ss_pred             HHHHHHhccCCccCCeEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEeCC
Confidence            34666664      3457899999999996543222   2346678877653

>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=93.52  E-value=0.034  Score=48.01  Aligned_cols=97  Identities=13%  Similarity=0.113  Sum_probs=49.8

Q ss_pred             CCCEEEEccCCCCchhhhhccc---ccc------CCcEEEEcchHHH-HHHHHHHHHHcCCceEEcCCCCCchhhhhhhh
Q 037567           28 KRDCLVVMATGSGKSLCYQLPP---LVT------GKTALVVSPLISL-MQDQVMSLKQRGINAEFLGSAQTDSSVQTKAE   97 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~l~~---~~~------~~~~lil~P~~~l-~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   97 (374)
                      +.-+++.||+|+|||..++..+   ...      +.+++++.-...+ ..+..+.+..++....         ...    
T Consensus       107 G~i~~i~G~~GsGKT~la~~la~~~~~~~~~gg~~~~vlyi~~e~~~~~~~l~~~~~~~g~~~~---------~~~----  173 (324)
T 2z43_A          107 RTMTEFFGEFGSGKTQLCHQLSVNVQLPPEKGGLSGKAVYIDTEGTFRWERIENMAKALGLDID---------NVM----  173 (324)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSCEEEEEESSSCCCHHHHHHHHHHTTCCHH---------HHH----
T ss_pred             CcEEEEECCCCCCHhHHHHHHHHHHhcccccCCCCCeEEEEECCCCCCHHHHHHHHHHhCCCHH---------HHh----
Confidence            3557899999999995543222   112      5577777654322 3444444455543210         000    


Q ss_pred             cCCeeEEEEcCcccc---cCchhhHHHHHh-cCccEEEEeccchhhc
Q 037567           98 TGYFQLLFMTPEKAC---IIPISFWSKLLK-AGVCLFAVDEAHCISE  140 (374)
Q Consensus        98 ~~~~~i~i~T~~~l~---~~~~~~~~~~~~-~~~~~vviDE~h~~~~  140 (374)
                      .   ++.+..+....   .++......... .++++||||++..+..
T Consensus       174 ~---~l~~~~~~~~~~~~~~l~~l~~~~~~~~~~~lvVIDsl~~l~~  217 (324)
T 2z43_A          174 N---NIYYIRAINTDHQIAIVDDLQELVSKDPSIKLIVVDSVTSHFR  217 (324)
T ss_dssp             H---TEEEEECCSHHHHHHHHHHHHHHHHHCTTEEEEEETTTTHHHH
T ss_pred             c---cEEEEeCCCHHHHHHHHHHHHHHHHhccCCCEEEEeCcHHHhh
Confidence            0   24444332211   111222122222 5789999999998753

>1w5s_A Origin recognition complex subunit 2 ORC2; replication, CDC6, DNA replication initiation, DNA BIND protein, AAA+ ATPase; HET: ADP; 2.4A {Aeropyrum pernix} SCOP: a.4.5.11 c.37.1.20 PDB: 1w5t_A*

Probab=93.43  E-value=0.15  Score=45.41  Aligned_cols=17  Identities=18%  Similarity=0.219  Sum_probs=13.4

Q ss_pred             CCEEE--EccCCCCchhhh
Q 037567           29 RDCLV--VMATGSGKSLCY   45 (374)
Q Consensus        29 ~~~l~--~a~tGsGKT~~~   45 (374)
                      ..+++  .||+|+|||...
T Consensus        51 ~~~li~i~G~~G~GKT~L~   69 (412)
T 1w5s_A           51 VNMIYGSIGRVGIGKTTLA   69 (412)
T ss_dssp             EEEEEECTTCCSSSHHHHH
T ss_pred             CEEEEeCcCcCCCCHHHHH
Confidence            35677  899999999653

>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=93.36  E-value=0.19  Score=41.40  Aligned_cols=17  Identities=29%  Similarity=0.397  Sum_probs=14.2

Q ss_pred             CCEEEEccCCCCchhhh
Q 037567           29 RDCLVVMATGSGKSLCY   45 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~   45 (374)
                      +.+++.||+|+|||...
T Consensus        50 ~g~ll~G~~G~GKTtl~   66 (254)
T 1ixz_A           50 KGVLLVGPPGVGKTHLA   66 (254)
T ss_dssp             SEEEEECCTTSSHHHHH
T ss_pred             CeEEEECCCCCCHHHHH
Confidence            35899999999999654

>3hr8_A Protein RECA; alpha and beta proteins (A/B, A+B), ATP-binding, cytoplasm, damage, DNA recombination, DNA repair, DNA-binding; 1.95A {Thermotoga maritima}

Probab=93.30  E-value=0.035  Score=48.31  Aligned_cols=97  Identities=18%  Similarity=0.054  Sum_probs=51.1

Q ss_pred             HHHHHHHc------CCCEEEEccCCCCchhhhhcccc---ccCCcEEEEcchHHHHHHHHHHHHHcCCceEEcCCCCCch
Q 037567           20 DVIQRIIE------KRDCLVVMATGSGKSLCYQLPPL---VTGKTALVVSPLISLMQDQVMSLKQRGINAEFLGSAQTDS   90 (374)
Q Consensus        20 ~~~~~~~~------~~~~l~~a~tGsGKT~~~~l~~~---~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~   90 (374)
                      ..++.++.      +.-+++.+|+|+|||...+..+.   ..+.+++++.....+-..   ..++++...          
T Consensus        47 ~~LD~~Lg~GGi~~G~i~~I~GppGsGKSTLal~la~~~~~~gg~VlyId~E~s~~~~---ra~rlgv~~----------  113 (356)
T 3hr8_A           47 LAIDIATGVGGYPRGRIVEIFGQESSGKTTLALHAIAEAQKMGGVAAFIDAEHALDPV---YAKNLGVDL----------  113 (356)
T ss_dssp             HHHHHHTSSSSEETTEEEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEESSCCCCHH---HHHHHTCCG----------
T ss_pred             HHHHHHhccCCccCCcEEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEecccccchH---HHHHcCCch----------
Confidence            45666665      34568899999999965432222   246678777654333222   223333221          


Q ss_pred             hhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhh
Q 037567           91 SVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCIS  139 (374)
Q Consensus        91 ~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~  139 (374)
                                -++.+..+..+...+............+++|||.+..+.
T Consensus       114 ----------~~l~i~~~~~~e~~l~~~~~l~~~~~~dlvVIDSi~~l~  152 (356)
T 3hr8_A          114 ----------KSLLISQPDHGEQALEIVDELVRSGVVDLIVVDSVAALV  152 (356)
T ss_dssp             ----------GGCEEECCSSHHHHHHHHHHHHHTSCCSEEEEECTTTCC
T ss_pred             ----------hhhhhhhccCHHHHHHHHHHHhhhcCCCeEEehHhhhhc
Confidence                      023344443332222211111223568899999988765

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20

Probab=93.10  E-value=0.36  Score=40.43  Aligned_cols=17  Identities=29%  Similarity=0.397  Sum_probs=14.2

Q ss_pred             CCEEEEccCCCCchhhh
Q 037567           29 RDCLVVMATGSGKSLCY   45 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~   45 (374)
                      +.+++.||+|+|||..+
T Consensus        74 ~gvll~Gp~GtGKTtl~   90 (278)
T 1iy2_A           74 KGVLLVGPPGVGKTHLA   90 (278)
T ss_dssp             CEEEEECCTTSSHHHHH
T ss_pred             CeEEEECCCcChHHHHH
Confidence            35899999999999654

>1vma_A Cell division protein FTSY; TM0570, structural genomics, JCS protein structure initiative, PSI, joint center for structu genomics; HET: CIT; 1.60A {Thermotoga maritima} SCOP: a.24.13.1 c.37.1.10

Probab=93.10  E-value=0.28  Score=41.73  Aligned_cols=50  Identities=16%  Similarity=0.216  Sum_probs=26.8

Q ss_pred             CEEEEccCCCCchhhhhc-ccc--ccCCcEEEEc-ch-H-HHHHHHHHHHHHcCCc
Q 037567           30 DCLVVMATGSGKSLCYQL-PPL--VTGKTALVVS-PL-I-SLMQDQVMSLKQRGIN   79 (374)
Q Consensus        30 ~~l~~a~tGsGKT~~~~l-~~~--~~~~~~lil~-P~-~-~l~~q~~~~~~~~~~~   79 (374)
                      -+++.+++|+|||.+... +..  ..+.+++++. ++ + ...+|...+....++.
T Consensus       106 vi~ivG~~GsGKTTl~~~LA~~l~~~g~kV~lv~~D~~r~~a~eqL~~~~~~~gl~  161 (306)
T 1vma_A          106 VIMVVGVNGTGKTTSCGKLAKMFVDEGKSVVLAAADTFRAAAIEQLKIWGERVGAT  161 (306)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEEECTTCHHHHHHHHHHHHHHTCE
T ss_pred             EEEEEcCCCChHHHHHHHHHHHHHhcCCEEEEEccccccHHHHHHHHHHHHHcCCc
Confidence            467899999999965432 211  2355666544 22 2 3334444444444443

>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=93.05  E-value=0.84  Score=40.81  Aligned_cols=31  Identities=23%  Similarity=0.145  Sum_probs=20.1

Q ss_pred             CEEEEccCCCCchhhhhccc---cccCCcEEEEc
Q 037567           30 DCLVVMATGSGKSLCYQLPP---LVTGKTALVVS   60 (374)
Q Consensus        30 ~~l~~a~tGsGKT~~~~l~~---~~~~~~~lil~   60 (374)
                      -+++.|++|+|||.+....+   ...+.+++++.
T Consensus        99 vI~lvG~~GsGKTTt~~kLA~~l~~~G~kVllv~  132 (433)
T 3kl4_A           99 IIMLVGVQGSGKTTTAGKLAYFYKKRGYKVGLVA  132 (433)
T ss_dssp             EEEECCCTTSCHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEe
Confidence            35778999999996543221   22466776654

>2zr9_A Protein RECA, recombinase A; recombination, RECA mutants, DNA-repair, ATP-binding, DNA DA recombination, DNA repair, DNA-binding; HET: DTP; 2.50A {Mycobacterium smegmatis str} PDB: 2zr0_A* 2zra_A* 2zrb_A 2zrm_A* 1ubc_A* 1ubf_A* 1ubg_A* 1ube_A* 2g88_A* 2odw_A* 2oe2_A 2oep_A* 2oes_A 2ofo_A 2zr7_A 2odn_A* 2zrn_A 2zro_A* 2zrp_A* 2zre_A* ...

Probab=93.01  E-value=0.052  Score=47.31  Aligned_cols=43  Identities=14%  Similarity=0.044  Sum_probs=27.7

Q ss_pred             HHHHHHHc------CCCEEEEccCCCCchhhhhccc---cccCCcEEEEcch
Q 037567           20 DVIQRIIE------KRDCLVVMATGSGKSLCYQLPP---LVTGKTALVVSPL   62 (374)
Q Consensus        20 ~~~~~~~~------~~~~l~~a~tGsGKT~~~~l~~---~~~~~~~lil~P~   62 (374)
                      ..++.++.      +.-+++.+|+|+|||...+..+   ...+.+++++.-.
T Consensus        47 ~~LD~~Lg~GGl~~G~iv~I~G~pGsGKTtLal~la~~~~~~g~~vlyi~~E   98 (349)
T 2zr9_A           47 ISLDVALGIGGLPRGRVIEIYGPESSGKTTVALHAVANAQAAGGIAAFIDAE   98 (349)
T ss_dssp             HHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEESS
T ss_pred             HHHHHHhccCCccCCeEEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEECC
Confidence            45566665      3457899999999996543222   2346677777643

>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=92.93  E-value=0.05  Score=47.68  Aligned_cols=97  Identities=13%  Similarity=0.083  Sum_probs=50.6

Q ss_pred             HHHHHHHc------CCCEEEEccCCCCchhhhhccc---cccCCcEEEEcchHHHHHHHHHHHHHcCCceEEcCCCCCch
Q 037567           20 DVIQRIIE------KRDCLVVMATGSGKSLCYQLPP---LVTGKTALVVSPLISLMQDQVMSLKQRGINAEFLGSAQTDS   90 (374)
Q Consensus        20 ~~~~~~~~------~~~~l~~a~tGsGKT~~~~l~~---~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~   90 (374)
                      ..++.++.      +.-+++.+++|+|||..++-.+   ...+.+++++..-..+ .++.  ....+...          
T Consensus        60 ~~LD~~Lg~GGl~~G~li~I~G~pGsGKTtlal~la~~~~~~g~~vlyi~~E~s~-~~~~--a~~~g~d~----------  126 (366)
T 1xp8_A           60 LSLDLALGVGGIPRGRITEIYGPESGGKTTLALAIVAQAQKAGGTCAFIDAEHAL-DPVY--ARALGVNT----------  126 (366)
T ss_dssp             HHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEESSCCC-CHHH--HHHTTCCG----------
T ss_pred             HHHHHHhCCCCccCCcEEEEEcCCCCChHHHHHHHHHHHHHCCCeEEEEECCCCh-hHHH--HHHcCCCH----------
Confidence            45566664      3456889999999996543222   2245677777654322 2221  22333221          


Q ss_pred             hhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhh
Q 037567           91 SVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCIS  139 (374)
Q Consensus        91 ~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~  139 (374)
                                -++.+..|..................+++||||.+..+.
T Consensus       127 ----------~~l~i~~~~~~e~~l~~l~~l~~~~~~~lVVIDsl~~l~  165 (366)
T 1xp8_A          127 ----------DELLVSQPDNGEQALEIMELLVRSGAIDVVVVDSVAALT  165 (366)
T ss_dssp             ----------GGCEEECCSSHHHHHHHHHHHHTTTCCSEEEEECTTTCC
T ss_pred             ----------HHceeecCCcHHHHHHHHHHHHhcCCCCEEEEeChHHhc
Confidence                      023333443322221111111122468999999999886

>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=92.73  E-value=0.11  Score=42.36  Aligned_cols=18  Identities=11%  Similarity=-0.068  Sum_probs=14.8

Q ss_pred             CCCEEEEccCCCCchhhh
Q 037567           28 KRDCLVVMATGSGKSLCY   45 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~   45 (374)
                      |.-+.+.||+|+|||..+
T Consensus        24 G~~~~i~G~~GsGKTtl~   41 (243)
T 1n0w_A           24 GSITEMFGEFRTGKTQIC   41 (243)
T ss_dssp             TSEEEEECCTTSSHHHHH
T ss_pred             CeEEEEECCCCCcHHHHH
Confidence            456789999999999654

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=92.66  E-value=0.072  Score=39.76  Aligned_cols=19  Identities=16%  Similarity=0.129  Sum_probs=16.3

Q ss_pred             cCCCEEEEccCCCCchhhh
Q 037567           27 EKRDCLVVMATGSGKSLCY   45 (374)
Q Consensus        27 ~~~~~l~~a~tGsGKT~~~   45 (374)
                      .+.++++.||+|+|||..+
T Consensus        23 ~~~~vll~G~~GtGKt~lA   41 (145)
T 3n70_A           23 TDIAVWLYGAPGTGRMTGA   41 (145)
T ss_dssp             CCSCEEEESSTTSSHHHHH
T ss_pred             CCCCEEEECCCCCCHHHHH
Confidence            4678999999999999764

>3bgw_A DNAB-like replicative helicase; ATPase, replication; 3.91A {Bacillus phage SPP1}

Probab=91.93  E-value=0.22  Score=44.89  Aligned_cols=35  Identities=11%  Similarity=-0.051  Sum_probs=23.4

Q ss_pred             CCCEEEEccCCCCchhhhhcc---ccccCCcEEEEcch
Q 037567           28 KRDCLVVMATGSGKSLCYQLP---PLVTGKTALVVSPL   62 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~l~---~~~~~~~~lil~P~   62 (374)
                      |.-+++.|+||+|||..++-.   +..++.++++++.-
T Consensus       197 G~liiIaG~pG~GKTtlal~ia~~~a~~g~~vl~fSlE  234 (444)
T 3bgw_A          197 RNFVLIAARPSMGKTAFALKQAKNMSDNDDVVNLHSLE  234 (444)
T ss_dssp             SCEEEEEECSSSSHHHHHHHHHHHHHHTTCEEEEECSS
T ss_pred             CcEEEEEeCCCCChHHHHHHHHHHHHHcCCEEEEEECC
Confidence            345688999999999553322   22346778888654

>1r6b_X CLPA protein; AAA+, N-terminal domain, CLPS, crystal, binding mechanism, hydrolase; HET: ADP; 2.25A {Escherichia coli} SCOP: a.174.1.1 c.37.1.20 c.37.1.20 PDB: 1ksf_X*

Probab=91.89  E-value=0.18  Score=49.02  Aligned_cols=18  Identities=33%  Similarity=0.412  Sum_probs=15.3

Q ss_pred             CCCEEEEccCCCCchhhh
Q 037567           28 KRDCLVVMATGSGKSLCY   45 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~   45 (374)
                      +.++++.||+|+|||...
T Consensus       207 ~~~vlL~G~~GtGKT~la  224 (758)
T 1r6b_X          207 KNNPLLVGESGVGKTAIA  224 (758)
T ss_dssp             SCEEEEECCTTSSHHHHH
T ss_pred             CCCeEEEcCCCCCHHHHH
Confidence            467899999999999654

>3io5_A Recombination and repair protein; storage dimer, inactive conformation, RECA like core domain, binding, DNA damage, DNA recombination; 2.40A {Enterobacteria phage T4}

Probab=91.59  E-value=0.07  Score=45.38  Aligned_cols=86  Identities=8%  Similarity=0.013  Sum_probs=49.7

Q ss_pred             CEEEEccCCCCchhhhhccc---ccc--CCcEEEEcchHHHHHHHHHHHHHcCCceEEcCCCCCchhhhhhhhcCCeeEE
Q 037567           30 DCLVVMATGSGKSLCYQLPP---LVT--GKTALVVSPLISLMQDQVMSLKQRGINAEFLGSAQTDSSVQTKAETGYFQLL  104 (374)
Q Consensus        30 ~~l~~a~tGsGKT~~~~l~~---~~~--~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~  104 (374)
                      -+++.+|+|+|||...+-.+   ...  +.+++++..-.++...   .++++|...                    -+++
T Consensus        30 iteI~G~pGsGKTtL~Lq~~~~~~~~g~g~~vlyId~E~s~~~~---ra~~lGvd~--------------------d~ll   86 (333)
T 3io5_A           30 LLILAGPSKSFKSNFGLTMVSSYMRQYPDAVCLFYDSEFGITPA---YLRSMGVDP--------------------ERVI   86 (333)
T ss_dssp             EEEEEESSSSSHHHHHHHHHHHHHHHCTTCEEEEEESSCCCCHH---HHHHTTCCG--------------------GGEE
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHHhcCCCceEEEEeccchhhHH---HHHHhCCCH--------------------HHeE
Confidence            46889999999996543222   222  5678887765544332   345555431                    1355


Q ss_pred             EEcCcccccC-chhhHHH---HHhcCccEEEEeccchhh
Q 037567          105 FMTPEKACII-PISFWSK---LLKAGVCLFAVDEAHCIS  139 (374)
Q Consensus       105 i~T~~~l~~~-~~~~~~~---~~~~~~~~vviDE~h~~~  139 (374)
                      +..|...... +.. ...   +....+++||||=+..+.
T Consensus        87 v~~~~~~E~~~l~i-~~~l~~i~~~~~~lvVIDSI~aL~  124 (333)
T 3io5_A           87 HTPVQSLEQLRIDM-VNQLDAIERGEKVVVFIDSLGNLA  124 (333)
T ss_dssp             EEECSBHHHHHHHH-HHHHHTCCTTCCEEEEEECSTTCB
T ss_pred             EEcCCCHHHHHHHH-HHHHHHhhccCceEEEEecccccc
Confidence            6666544332 111 111   123468899999999885

>3cmw_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 2.80A {Escherichia coli} PDB: 3cmt_A* 3cmx_A* 3cmv_A*

Probab=91.49  E-value=0.13  Score=53.95  Aligned_cols=89  Identities=17%  Similarity=0.103  Sum_probs=60.0

Q ss_pred             CCEEEEccCCCCchhhhhccc---cccCCcEEEEcchHHHHHHHHHHHHHcCCceEEcCCCCCchhhhhhhhcCCeeEEE
Q 037567           29 RDCLVVMATGSGKSLCYQLPP---LVTGKTALVVSPLISLMQDQVMSLKQRGINAEFLGSAQTDSSVQTKAETGYFQLLF  105 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~~l~~---~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~i  105 (374)
                      +-+.+.+|.|||||..++-.+   ...+..++++.+-.++-..+   ++++|.+..                    ++++
T Consensus      1432 ~~iei~g~~~sGkttl~~~~~a~~~~~g~~~~~i~~e~~~~~~~---~~~~Gv~~~--------------------~l~~ 1488 (1706)
T 3cmw_A         1432 RIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEHALDPIY---ARKLGVDID--------------------NLLC 1488 (1706)
T ss_dssp             SEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEECTTSCCCHHH---HHHTTCCGG--------------------GCEE
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHHHHhcCCeEEEEecCCCCCHHH---HHHcCCCHH--------------------HeEE
Confidence            457899999999997654333   33588899988887776654   566655422                    3667


Q ss_pred             EcCcccccCchhhHHHHHhcCccEEEEeccchhhc
Q 037567          106 MTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISE  140 (374)
Q Consensus       106 ~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~  140 (374)
                      .-|+.-...+......+....+++||||.+-.+..
T Consensus      1489 ~~p~~~e~~l~~~~~~~~s~~~~~vvvDsv~al~~ 1523 (1706)
T 3cmw_A         1489 SQPDTGEQALEICDALARSGAVDVIVVDSVAALTP 1523 (1706)
T ss_dssp             ECCSSHHHHHHHHHHHHHHTCCSEEEESCSTTCCC
T ss_pred             eCCCcHHHHHHHHHHHHHcCCCCEEEEccHHhCCc
Confidence            77765433333333344557799999999988764

>1qvr_A CLPB protein; coiled coil, AAA ATPase, chaperone; HET: ANP; 3.00A {Thermus thermophilus} SCOP: a.174.1.1 c.37.1.20 c.37.1.20

Probab=91.46  E-value=0.22  Score=49.11  Aligned_cols=18  Identities=22%  Similarity=0.361  Sum_probs=15.1

Q ss_pred             CCCEEEEccCCCCchhhh
Q 037567           28 KRDCLVVMATGSGKSLCY   45 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~   45 (374)
                      .+++++.||+|+|||...
T Consensus       191 ~~~vlL~G~pG~GKT~la  208 (854)
T 1qvr_A          191 KNNPVLIGEPGVGKTAIV  208 (854)
T ss_dssp             CCCCEEEECTTSCHHHHH
T ss_pred             CCceEEEcCCCCCHHHHH
Confidence            357899999999999654

>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=91.43  E-value=0.61  Score=43.06  Aligned_cols=60  Identities=17%  Similarity=0.130  Sum_probs=55.0

Q ss_pred             CCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEec
Q 037567          227 GAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATM  286 (374)
Q Consensus       227 ~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~  286 (374)
                      ..+.+||.+|++.-+....+.+++.++.+..++++.+..++......+..|..+++++|+
T Consensus        64 ~~g~~lvi~P~~aL~~q~~~~l~~~gi~~~~l~~~~~~~~~~~~~~~~~~~~~~ilv~Tp  123 (523)
T 1oyw_A           64 LNGLTVVVSPLISLMKDQVDQLQANGVAAACLNSTQTREQQLEVMTGCRTGQIRLLYIAP  123 (523)
T ss_dssp             SSSEEEEECSCHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHHTCCSEEEECH
T ss_pred             hCCCEEEECChHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECH
Confidence            457899999999999999999999999999999999998888888888899999999997

>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=91.30  E-value=0.64  Score=43.65  Aligned_cols=60  Identities=23%  Similarity=0.310  Sum_probs=54.0

Q ss_pred             CCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhh--hcCCeeEEEEec
Q 037567          227 GAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLF--IRDEIRVMVATM  286 (374)
Q Consensus       227 ~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f--~~g~~~ilv~t~  286 (374)
                      ..+.+||.+|++.-+....+.|.+.|+.+..++|+.+..++......+  ..+..+|+++|+
T Consensus        83 ~~g~~lVisP~~~L~~q~~~~l~~~gi~~~~l~~~~~~~~~~~~~~~l~~~~~~~~Ilv~Tp  144 (591)
T 2v1x_A           83 SDGFTLVICPLISLMEDQLMVLKQLGISATMLNASSSKEHVKWVHAEMVNKNSELKLIYVTP  144 (591)
T ss_dssp             SSSEEEEECSCHHHHHHHHHHHHHHTCCEEECCSSCCHHHHHHHHHHHHCTTCCCCEEEECH
T ss_pred             cCCcEEEEeCHHHHHHHHHHHHHhcCCcEEEEeCCCCHHHHHHHHHHhhcccCCCCEEEECh
Confidence            467999999999999999999999999999999999999888888877  467889999998

>2rb4_A ATP-dependent RNA helicase DDX25; rossmann fold, structural genomics, structural consortium, SGC, alternative initiation, ATP-binding, devel protein; 2.80A {Homo sapiens}

Probab=91.24  E-value=1  Score=34.59  Aligned_cols=73  Identities=14%  Similarity=0.064  Sum_probs=52.5

Q ss_pred             cCCcEEEEcchHHHHHHHHHHHHHcCCceEEcCCCCCchhhh---hhhhcCCeeEEEEcCcccccCchhhHHHHHhcCcc
Q 037567           52 TGKTALVVSPLISLMQDQVMSLKQRGINAEFLGSAQTDSSVQ---TKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVC  128 (374)
Q Consensus        52 ~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~  128 (374)
                      ...++||+++++..+..+...+...|..+..+++........   .....+...|+|+|.- +.       ..+....++
T Consensus        33 ~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~~g~~~~~~R~~~~~~f~~g~~~vLvaT~~-~~-------~Gid~~~~~  104 (175)
T 2rb4_A           33 TIGQAIIFCQTRRNAKWLTVEMIQDGHQVSLLSGELTVEQRASIIQRFRDGKEKVLITTNV-CA-------RGIDVKQVT  104 (175)
T ss_dssp             CCSEEEEECSCHHHHHHHHHHHHTTTCCEEEECSSCCHHHHHHHHHHHHTTSCSEEEECCS-CC-------TTTCCTTEE
T ss_pred             CCCCEEEEECCHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHHcCCCeEEEEecc-hh-------cCCCcccCC
Confidence            367899999999999999999999999988888876554332   2334567899999932 22       223345667


Q ss_pred             EEEE
Q 037567          129 LFAV  132 (374)
Q Consensus       129 ~vvi  132 (374)
                      +||.
T Consensus       105 ~Vi~  108 (175)
T 2rb4_A          105 IVVN  108 (175)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            7774

>3b85_A Phosphate starvation-inducible protein; PHOH2, ATPase, PFAM: PF02562, ST genomics, PSI-2, protein structure initiative; 2.35A {Corynebacterium glutamicum atcc 13032}

Probab=91.12  E-value=0.19  Score=40.10  Aligned_cols=35  Identities=20%  Similarity=0.072  Sum_probs=28.0

Q ss_pred             CCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhh
Q 037567           11 YSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCY   45 (374)
Q Consensus        11 ~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~   45 (374)
                      +...+..|..++..+..|.-+.+.||.|+|||...
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            44445567788888888888999999999999643

>2l82_A Designed protein OR32; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, de novo protein; NMR {Artificial gene}

Probab=90.84  E-value=1.3  Score=30.08  Aligned_cols=52  Identities=21%  Similarity=0.315  Sum_probs=44.4

Q ss_pred             EEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEE
Q 037567          231 IIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVM  282 (374)
Q Consensus       231 ~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~il  282 (374)
                      .+||.........+...+++.|..++.++++...+.|..-++.|.....++-
T Consensus         5 fvvfssdpeilkeivreikrqgvrvvllysdqdekrrrerleefekqgvdvr   56 (162)
T 2l82_A            5 FVVFSSDPEILKEIVREIKRQGVRVVLLYSDQDEKRRRERLEEFEKQGVDVR   56 (162)
T ss_dssp             EEEEESCHHHHHHHHHHHHHTTCEEEEEECCSCHHHHHHHHHHHHTTTCEEE
T ss_pred             EEEecCCHHHHHHHHHHHHhCCeEEEEEecCchHHHHHHHHHHHHHcCCcee
Confidence            4678888888899999999999999999999999999999999987655544

>2i1q_A DNA repair and recombination protein RADA; ATPase, recombinase, ATP complex, calcium stimulation, RECA, DMC1; HET: DNA ANP; 1.90A {Methanococcus voltae} SCOP: a.60.4.1 c.37.1.11 PDB: 1xu4_A* 2b21_A* 2fpk_A* 2fpl_A* 2fpm_A* 1t4g_A* 3fyh_A* 2f1j_A* 2f1i_A* 2f1h_A* 3ntu_A* 3ewa_A* 3ew9_A* 3etl_A* 4dc9_A* 2gdj_A*

Probab=90.71  E-value=0.078  Score=45.65  Aligned_cols=17  Identities=24%  Similarity=0.108  Sum_probs=13.7

Q ss_pred             CCEEEEccCCCCchhhh
Q 037567           29 RDCLVVMATGSGKSLCY   45 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~   45 (374)
                      .-+++.|++|+|||...
T Consensus        99 ~i~~i~G~~gsGKT~la  115 (322)
T 2i1q_A           99 SVTEFAGVFGSGKTQIM  115 (322)
T ss_dssp             EEEEEEESTTSSHHHHH
T ss_pred             eEEEEECCCCCCHHHHH
Confidence            45689999999999543

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=90.27  E-value=1.1  Score=43.41  Aligned_cols=16  Identities=25%  Similarity=0.295  Sum_probs=13.9

Q ss_pred             CEEEEccCCCCchhhh
Q 037567           30 DCLVVMATGSGKSLCY   45 (374)
Q Consensus        30 ~~l~~a~tGsGKT~~~   45 (374)
                      ++++.||||+|||..+
T Consensus       523 ~~Ll~Gp~GtGKT~lA  538 (758)
T 3pxi_A          523 SFIFLGPTGVGKTELA  538 (758)
T ss_dssp             EEEEESCTTSSHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            4899999999999754

>1qvr_A CLPB protein; coiled coil, AAA ATPase, chaperone; HET: ANP; 3.00A {Thermus thermophilus} SCOP: a.174.1.1 c.37.1.20 c.37.1.20

Probab=89.77  E-value=1.2  Score=43.92  Aligned_cols=16  Identities=31%  Similarity=0.320  Sum_probs=14.0

Q ss_pred             CEEEEccCCCCchhhh
Q 037567           30 DCLVVMATGSGKSLCY   45 (374)
Q Consensus        30 ~~l~~a~tGsGKT~~~   45 (374)
                      .+++.||||+|||..+
T Consensus       590 ~vLl~Gp~GtGKT~lA  605 (854)
T 1qvr_A          590 SFLFLGPTGVGKTELA  605 (854)
T ss_dssp             EEEEBSCSSSSHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            5799999999999754

>1tue_A Replication protein E1; helicase, replication, E1E2 complex, AAA+ protein; 2.10A {Human papillomavirus type 18} SCOP: c.37.1.20

Probab=89.73  E-value=0.12  Score=40.83  Aligned_cols=27  Identities=11%  Similarity=0.127  Sum_probs=18.5

Q ss_pred             HHHHHHHHcC----CCEEEEccCCCCchhhh
Q 037567           19 KDVIQRIIEK----RDCLVVMATGSGKSLCY   45 (374)
Q Consensus        19 ~~~~~~~~~~----~~~l~~a~tGsGKT~~~   45 (374)
                      ...+..+.++    +.+++.||+|+|||..+
T Consensus        45 ~~~l~~~~~~iPkkn~ili~GPPGtGKTt~a   75 (212)
T 1tue_A           45 LGALKSFLKGTPKKNCLVFCGPANTGKSYFG   75 (212)
T ss_dssp             HHHHHHHHHTCTTCSEEEEESCGGGCHHHHH
T ss_pred             HHHHHHHHhcCCcccEEEEECCCCCCHHHHH
Confidence            3444444443    34788999999999654

>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=89.10  E-value=4.2  Score=32.24  Aligned_cols=73  Identities=23%  Similarity=0.367  Sum_probs=52.7

Q ss_pred             CCcEEEEecchhHHHHHHHHHHHc-----CCceeeeecCCChHHHHHHHHhhhcCCeeEEEEecc-c-----cccccccC
Q 037567          228 AGSIIVYCMTIKDVEEISKALKQL-----GVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMA-F-----GMGIDKPD  296 (374)
Q Consensus       228 ~~~~lVf~~~~~~~~~l~~~l~~~-----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~-~-----~~G~d~~~  296 (374)
                      +.+++|.+|++.-+.++++.+++.     +..+..++|+.+..+....   +..+..+|+|+|+- +     ...+++.+
T Consensus        82 ~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~---~~~~~~~i~v~T~~~l~~~~~~~~~~~~~  158 (220)
T 1t6n_A           82 QVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEV---LKKNCPHIVVGTPGRILALARNKSLNLKH  158 (220)
T ss_dssp             CCCEEEECSCHHHHHHHHHHHHHHTTTSTTCCEEEESCCSCHHHHHHH---HHHSCCSEEEECHHHHHHHHHTTSSCCTT
T ss_pred             CEEEEEEeCCHHHHHHHHHHHHHHHhhCCCceEEEEeCCCChHHHHHH---HhcCCCCEEEeCHHHHHHHHHhCCCCccc
Confidence            348999999999999999888774     6778889998876554433   34566789999972 2     12356667


Q ss_pred             ccEEEEE
Q 037567          297 VRHVIHY  303 (374)
Q Consensus       297 ~~~vi~~  303 (374)
                      ++++|.-
T Consensus       159 ~~~lViD  165 (220)
T 1t6n_A          159 IKHFILD  165 (220)
T ss_dssp             CCEEEEE
T ss_pred             CCEEEEc
Confidence            7777743

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=89.04  E-value=0.39  Score=51.18  Aligned_cols=43  Identities=16%  Similarity=0.068  Sum_probs=29.5

Q ss_pred             cCCCEEEEccCCCCchhhhh---ccccccCCcEEEEcchHHHHHHHH
Q 037567           27 EKRDCLVVMATGSGKSLCYQ---LPPLVTGKTALVVSPLISLMQDQV   70 (374)
Q Consensus        27 ~~~~~l~~a~tGsGKT~~~~---l~~~~~~~~~lil~P~~~l~~q~~   70 (374)
                      .+..+++.+|+|+|||..+.   ..+...+.+++++.-. ++.++..
T Consensus      1080 ~g~~vll~G~~GtGKT~la~~~~~ea~k~Ge~~~Fit~e-e~~~~L~ 1125 (2050)
T 3cmu_A         1080 MGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAE-HALDPIY 1125 (2050)
T ss_dssp             TTSEEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEECTT-SCCCHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEEcc-ccHHHHH
Confidence            46788999999999996543   2344567788887654 4444444

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli}

Probab=88.96  E-value=0.28  Score=44.90  Aligned_cols=26  Identities=15%  Similarity=0.162  Sum_probs=20.3

Q ss_pred             HHHHHHHcCCCEEEEccCCCCchhhh
Q 037567           20 DVIQRIIEKRDCLVVMATGSGKSLCY   45 (374)
Q Consensus        20 ~~~~~~~~~~~~l~~a~tGsGKT~~~   45 (374)
                      .+...+..+.++++.||||+|||..+
T Consensus        33 ~l~~al~~~~~VLL~GpPGtGKT~LA   58 (500)
T 3nbx_X           33 LCLLAALSGESVFLLGPPGIAKSLIA   58 (500)
T ss_dssp             HHHHHHHHTCEEEEECCSSSSHHHHH
T ss_pred             HHHHHHhcCCeeEeecCchHHHHHHH
Confidence            34444556889999999999999654

>2oap_1 GSPE-2, type II secretion system protein; hexameric ATPase, hydrolase; HET: ANP; 2.95A {Archaeoglobus fulgidus} PDB: 2oaq_1

Probab=88.53  E-value=0.53  Score=43.24  Aligned_cols=20  Identities=40%  Similarity=0.393  Sum_probs=16.9

Q ss_pred             HHcCCCEEEEccCCCCchhh
Q 037567           25 IIEKRDCLVVMATGSGKSLC   44 (374)
Q Consensus        25 ~~~~~~~l~~a~tGsGKT~~   44 (374)
                      +..+..+++.||||||||..
T Consensus       257 v~~g~~i~I~GptGSGKTTl  276 (511)
T 2oap_1          257 IEHKFSAIVVGETASGKTTT  276 (511)
T ss_dssp             HHTTCCEEEEESTTSSHHHH
T ss_pred             HhCCCEEEEECCCCCCHHHH
Confidence            44678899999999999965

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=88.33  E-value=0.28  Score=38.05  Aligned_cols=17  Identities=18%  Similarity=0.319  Sum_probs=14.6

Q ss_pred             CCEEEEccCCCCchhhh
Q 037567           29 RDCLVVMATGSGKSLCY   45 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~   45 (374)
                      ..+++.||+|+|||...
T Consensus        44 ~~~ll~G~~G~GKT~l~   60 (195)
T 1jbk_A           44 NNPVLIGEPGVGKTAIV   60 (195)
T ss_dssp             CEEEEECCTTSCHHHHH
T ss_pred             CceEEECCCCCCHHHHH
Confidence            56899999999999654

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A

Probab=88.23  E-value=0.14  Score=43.39  Aligned_cols=33  Identities=21%  Similarity=0.133  Sum_probs=20.9

Q ss_pred             CCEEEEccCCCCchhhhhccccccCCcEEEEcc
Q 037567           29 RDCLVVMATGSGKSLCYQLPPLVTGKTALVVSP   61 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~~l~~~~~~~~~lil~P   61 (374)
                      ..++++||+|+|||..+-..+-.-+..++.+..
T Consensus        37 ~~lLl~GppGtGKT~la~aiA~~l~~~~i~v~~   69 (293)
T 3t15_A           37 LILGIWGGKGQGKSFQCELVFRKMGINPIMMSA   69 (293)
T ss_dssp             SEEEEEECTTSCHHHHHHHHHHHHTCCCEEEEH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCCCEEEEeH
Confidence            357889999999997654333333444554443

>2r44_A Uncharacterized protein; putative ATPase, structural genomics, joint center for struc genomics, JCSG; HET: MSE PG4; 2.00A {Cytophaga hutchinsonii atcc 33406}

Probab=88.05  E-value=0.2  Score=43.19  Aligned_cols=22  Identities=23%  Similarity=0.188  Sum_probs=18.1

Q ss_pred             HHHcCCCEEEEccCCCCchhhh
Q 037567           24 RIIEKRDCLVVMATGSGKSLCY   45 (374)
Q Consensus        24 ~~~~~~~~l~~a~tGsGKT~~~   45 (374)
                      .+..+.++++.||+|+|||..+
T Consensus        42 ~l~~~~~vll~G~pGtGKT~la   63 (331)
T 2r44_A           42 GICTGGHILLEGVPGLAKTLSV   63 (331)
T ss_dssp             HHHHTCCEEEESCCCHHHHHHH
T ss_pred             HHHcCCeEEEECCCCCcHHHHH
Confidence            3445889999999999999654

>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=87.74  E-value=2.3  Score=34.46  Aligned_cols=72  Identities=10%  Similarity=0.074  Sum_probs=51.2

Q ss_pred             CCCcEEEEecchhHHHHHHHHHHH----cCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEec-cc----c-ccccccC
Q 037567          227 GAGSIIVYCMTIKDVEEISKALKQ----LGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATM-AF----G-MGIDKPD  296 (374)
Q Consensus       227 ~~~~~lVf~~~~~~~~~l~~~l~~----~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~-~~----~-~G~d~~~  296 (374)
                      .+.+++|.+|++.-+.++++.+++    .+..+..++|+.+.......+.   . ..+|+|+|+ .+    . ..+++.+
T Consensus       101 ~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~---~-~~~I~v~Tp~~l~~~l~~~~~~~~~  176 (242)
T 3fe2_A          101 DGPICLVLAPTRELAQQVQQVAAEYCRACRLKSTCIYGGAPKGPQIRDLE---R-GVEICIATPGRLIDFLECGKTNLRR  176 (242)
T ss_dssp             CCCSEEEECSSHHHHHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHH---H-CCSEEEECHHHHHHHHHHTSCCCTT
T ss_pred             CCCEEEEEeCcHHHHHHHHHHHHHHHhhcCceEEEEECCCChHHHHHHhc---C-CCCEEEECHHHHHHHHHcCCCCccc
Confidence            456799999999999888877765    3788889999987765554433   2 368999997 22    1 2346667


Q ss_pred             ccEEEE
Q 037567          297 VRHVIH  302 (374)
Q Consensus       297 ~~~vi~  302 (374)
                      ++++|.
T Consensus       177 ~~~lVi  182 (242)
T 3fe2_A          177 TTYLVL  182 (242)
T ss_dssp             CCEEEE
T ss_pred             ccEEEE
Confidence            777663

>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=87.58  E-value=3.8  Score=33.43  Aligned_cols=72  Identities=18%  Similarity=0.210  Sum_probs=51.3

Q ss_pred             CCCcEEEEecchhHHHHHHHHHHHc----CCceeeeecCCChHHHHHHHHhhhcCCeeEEEEec-cc----c--cccccc
Q 037567          227 GAGSIIVYCMTIKDVEEISKALKQL----GVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATM-AF----G--MGIDKP  295 (374)
Q Consensus       227 ~~~~~lVf~~~~~~~~~l~~~l~~~----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~-~~----~--~G~d~~  295 (374)
                      .+.+++|.+|++.-+..+++.+++.    +..+..++|+.+..+....+    .+..+|+|+|+ .+    .  .++++.
T Consensus       110 ~~~~~lil~Ptr~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~----~~~~~I~v~Tp~~l~~~l~~~~~~~l~  185 (249)
T 3ber_A          110 QRLFALVLTPTRELAFQISEQFEALGSSIGVQSAVIVGGIDSMSQSLAL----AKKPHIIIATPGRLIDHLENTKGFNLR  185 (249)
T ss_dssp             CSSCEEEECSSHHHHHHHHHHHHHHHGGGTCCEEEECTTSCHHHHHHHH----HTCCSEEEECHHHHHHHHHHSTTCCCT
T ss_pred             CCceEEEEeCCHHHHHHHHHHHHHHhccCCeeEEEEECCCChHHHHHHh----cCCCCEEEECHHHHHHHHHcCCCcCcc
Confidence            3457999999999999988887764    77888899987765444332    24578999996 22    1  345666


Q ss_pred             CccEEEE
Q 037567          296 DVRHVIH  302 (374)
Q Consensus       296 ~~~~vi~  302 (374)
                      .++++|.
T Consensus       186 ~~~~lVi  192 (249)
T 3ber_A          186 ALKYLVM  192 (249)
T ss_dssp             TCCEEEE
T ss_pred             ccCEEEE
Confidence            7777764

>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase; 1.95A {Bacillus subtilis}

Probab=87.55  E-value=1.3  Score=33.44  Aligned_cols=75  Identities=9%  Similarity=0.106  Sum_probs=52.9

Q ss_pred             cCCcEEEEcchHHHHHHHHHHHHHcCCceEEcCCCCCchhhh---hhhhcCCeeEEEEcCcccccCchhhHHHHHhcCcc
Q 037567           52 TGKTALVVSPLISLMQDQVMSLKQRGINAEFLGSAQTDSSVQ---TKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVC  128 (374)
Q Consensus        52 ~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~  128 (374)
                      ...++||+++++..+..+.+.+...|..+..+++........   .....+...|+|+|. .+.       ..+....++
T Consensus        34 ~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~hg~~~~~~r~~~~~~f~~g~~~vlv~T~-~~~-------~Gld~~~~~  105 (163)
T 2hjv_A           34 NPDSCIIFCRTKEHVNQLTDELDDLGYPCDKIHGGMIQEDRFDVMNEFKRGEYRYLVATD-VAA-------RGIDIENIS  105 (163)
T ss_dssp             CCSSEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECG-GGT-------TTCCCSCCS
T ss_pred             CCCcEEEEECCHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHHcCCCeEEEECC-hhh-------cCCchhcCC
Confidence            467899999999999999999999999988888766544322   233356788999993 222       223345566


Q ss_pred             EEEEec
Q 037567          129 LFAVDE  134 (374)
Q Consensus       129 ~vviDE  134 (374)
                      +||.-+
T Consensus       106 ~Vi~~~  111 (163)
T 2hjv_A          106 LVINYD  111 (163)
T ss_dssp             EEEESS
T ss_pred             EEEEeC
Confidence            666533

>1ls1_A Signal recognition particle protein; FFH, SRP54, SRP, GTPase, ultrahigh resolution, protein transport; 1.10A {Thermus aquaticus} SCOP: a.24.13.1 c.37.1.10 PDB: 1jpn_B* 1jpj_A* 1ry1_U* 2j45_A* 1o87_A* 2c04_A* 2j46_A* 1rj9_B* 2c03_A* 2j7p_A* 1okk_A* 2cnw_A* 1ng1_A* 2xkv_A 3ng1_A 1ffh_A 2ng1_A*

Probab=87.41  E-value=1.8  Score=36.51  Aligned_cols=31  Identities=29%  Similarity=0.344  Sum_probs=19.2

Q ss_pred             CEEEEccCCCCchhhhh-cccc--ccCCcEEEEc
Q 037567           30 DCLVVMATGSGKSLCYQ-LPPL--VTGKTALVVS   60 (374)
Q Consensus        30 ~~l~~a~tGsGKT~~~~-l~~~--~~~~~~lil~   60 (374)
                      -+.+.++.|+|||.... ++..  ..+.+++++-
T Consensus       100 ~i~i~g~~G~GKTT~~~~la~~~~~~~~~v~l~~  133 (295)
T 1ls1_A          100 LWFLVGLQGSGKTTTAAKLALYYKGKGRRPLLVA  133 (295)
T ss_dssp             EEEEECCTTTTHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEec
Confidence            45678999999995533 2222  2456666653

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=87.27  E-value=0.49  Score=40.35  Aligned_cols=33  Identities=15%  Similarity=0.140  Sum_probs=21.6

Q ss_pred             CCCEEEEccCCCCchhhhhcc---cc-ccCCcEEEEc
Q 037567           28 KRDCLVVMATGSGKSLCYQLP---PL-VTGKTALVVS   60 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~l~---~~-~~~~~~lil~   60 (374)
                      +.++++.||+|+|||..+...   +. ..+.+++++.
T Consensus       152 ~~~lll~G~~GtGKT~La~aia~~~~~~~g~~v~~~~  188 (308)
T 2qgz_A          152 QKGLYLYGDMGIGKSYLLAAMAHELSEKKGVSTTLLH  188 (308)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHHHHHHSCCCEEEEE
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHHHHhcCCcEEEEE
Confidence            468899999999999653221   22 3455565543

>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=87.14  E-value=0.52  Score=41.23  Aligned_cols=32  Identities=25%  Similarity=0.272  Sum_probs=21.2

Q ss_pred             CCCEEEEccCCCCchhhhhccccccCCcEEEE
Q 037567           28 KRDCLVVMATGSGKSLCYQLPPLVTGKTALVV   59 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~l~~~~~~~~~lil   59 (374)
                      ..++++.||||+|||..+-..+...+...+.+
T Consensus        51 ~~~vll~GppGtGKT~la~~ia~~~~~~~~~~   82 (363)
T 3hws_A           51 KSNILLIGPTGSGKTLLAETLARLLDVPFTMA   82 (363)
T ss_dssp             CCCEEEECCTTSSHHHHHHHHHHHTTCCEEEE
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHcCCCEEEe
Confidence            46799999999999976543333334444444

>3nwn_A Kinesin-like protein KIF9; motor domain, ADP, structural genomics, structural consortium, SGC, contractIle protein; HET: ADP; 2.00A {Homo sapiens}

Probab=87.09  E-value=0.44  Score=41.43  Aligned_cols=32  Identities=19%  Similarity=0.181  Sum_probs=22.4

Q ss_pred             hHHHHHHH--------HHcCCCE--EEEccCCCCchhhhhcc
Q 037567           17 YQKDVIQR--------IIEKRDC--LVVMATGSGKSLCYQLP   48 (374)
Q Consensus        17 ~Q~~~~~~--------~~~~~~~--l~~a~tGsGKT~~~~l~   48 (374)
                      -|.+.+..        +++|.++  +..|.||||||.++.-+
T Consensus        84 sQ~~Vy~~~~~plv~~~l~G~N~tifAYGQTGSGKTyTM~G~  125 (359)
T 3nwn_A           84 SQDLVYETVAKDVVSQALDGYNGTIMCYGQTGAGKTYTMMGA  125 (359)
T ss_dssp             CHHHHHHHHTHHHHHHHHTTCCEEEEEEESTTSSHHHHHTBC
T ss_pred             CHHHHHHHHHHHHHHHHhCCCCEEEEEeCCCCCCccEEeCCc
Confidence            46666544        4556654  66899999999987644

>3cmw_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 2.80A {Escherichia coli} PDB: 3cmt_A* 3cmx_A* 3cmv_A*

Probab=86.98  E-value=0.33  Score=50.94  Aligned_cols=89  Identities=16%  Similarity=0.091  Sum_probs=49.2

Q ss_pred             CCCEEEEccCCCCchhhhhccc---cccCCcEEEEcchHHHHHHHHHHHHHcCCceEEcCCCCCchhhhhhhhcCCeeEE
Q 037567           28 KRDCLVVMATGSGKSLCYQLPP---LVTGKTALVVSPLISLMQDQVMSLKQRGINAEFLGSAQTDSSVQTKAETGYFQLL  104 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~l~~---~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~  104 (374)
                      +..+++.||+|+|||..++..+   ...+.+++++.--.. ..|..  ....|...                    -++.
T Consensus       732 G~lVlI~G~PG~GKTtLal~lA~~aa~~g~~VlyiS~Ees-~~ql~--A~~lGvd~--------------------~~L~  788 (1706)
T 3cmw_A          732 GRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEHA-LDPIY--ARKLGVDI--------------------DNLL  788 (1706)
T ss_dssp             TSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEECTTSC-CCHHH--HHHTTCCG--------------------GGCE
T ss_pred             CceEEEECCCCCCcHHHHHHHHHHHHHcCCCeEEEeccch-HHHHH--HHHcCCCh--------------------hheE
Confidence            4567899999999996543222   234557777654432 23332  23333221                    0234


Q ss_pred             EEcCcccccCchhhHHHHHhcCccEEEEeccchhh
Q 037567          105 FMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCIS  139 (374)
Q Consensus       105 i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~  139 (374)
                      +..+..+..+............+++||||+...+.
T Consensus       789 i~~~~~leei~~~l~~lv~~~~~~lVVIDsLq~l~  823 (1706)
T 3cmw_A          789 CSQPDTGEQALEICDALARSGAVDVIVVDSVAALT  823 (1706)
T ss_dssp             EECCSSHHHHHHHHHHHHHHTCCSEEEESCSTTCC
T ss_pred             EecCCcHHHHHHHHHHHHHccCCCEEEEechhhhc
Confidence            55554443332222222223578999999999886

>3lda_A DNA repair protein RAD51; DNA binding protein, ATP-binding, DNA damage, DNA recombinat repair, nucleotide-binding; HET: DNA; 2.50A {Saccharomyces cerevisiae} PDB: 1szp_A*

Probab=86.80  E-value=1.2  Score=39.42  Aligned_cols=19  Identities=16%  Similarity=-0.034  Sum_probs=14.9

Q ss_pred             CCCEEEEccCCCCchhhhh
Q 037567           28 KRDCLVVMATGSGKSLCYQ   46 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~   46 (374)
                      +.-+.+.+|+|+|||....
T Consensus       178 Gei~~I~G~sGsGKTTLl~  196 (400)
T 3lda_A          178 GSITELFGEFRTGKSQLCH  196 (400)
T ss_dssp             TSEEEEEESTTSSHHHHHH
T ss_pred             CcEEEEEcCCCCChHHHHH
Confidence            4567899999999995543

>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=86.75  E-value=0.35  Score=40.00  Aligned_cols=25  Identities=12%  Similarity=0.085  Sum_probs=18.2

Q ss_pred             HHHHHcCC-----CEEEEccCCCCchhhhh
Q 037567           22 IQRIIEKR-----DCLVVMATGSGKSLCYQ   46 (374)
Q Consensus        22 ~~~~~~~~-----~~l~~a~tGsGKT~~~~   46 (374)
                      +..+++++     .+++.||+|+|||+.+.
T Consensus        93 l~~~l~~~~~~~n~~~l~GppgtGKt~~a~  122 (267)
T 1u0j_A           93 FLGWATKKFGKRNTIWLFGPATTGKTNIAE  122 (267)
T ss_dssp             HHHHHTTCSTTCCEEEEECSTTSSHHHHHH
T ss_pred             HHHHHhCCCCCCcEEEEECCCCCCHHHHHH
Confidence            44555543     47899999999997654

>1ofh_A ATP-dependent HSL protease ATP-binding subunit HSLU; chaperone, hydrolase, ATP-binding; HET: ADP; 2.5A {Haemophilus influenzae} SCOP: c.37.1.20 PDB: 1ofi_A*

Probab=86.56  E-value=0.32  Score=41.30  Aligned_cols=18  Identities=28%  Similarity=0.409  Sum_probs=15.6

Q ss_pred             CCCEEEEccCCCCchhhh
Q 037567           28 KRDCLVVMATGSGKSLCY   45 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~   45 (374)
                      ..++++.||+|+|||..+
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            568999999999999754

>1q57_A DNA primase/helicase; dntpase, DNA replication, transferase; HET: DNA; 3.45A {Enterobacteria phage T7} SCOP: c.37.1.11 e.13.1.2

Probab=86.55  E-value=1  Score=41.42  Aligned_cols=45  Identities=13%  Similarity=-0.017  Sum_probs=27.3

Q ss_pred             CCCEEEEccCCCCchhhhhc---ccccc-CCcEEEEcchHHHHHHHHHHH
Q 037567           28 KRDCLVVMATGSGKSLCYQL---PPLVT-GKTALVVSPLISLMQDQVMSL   73 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~l---~~~~~-~~~~lil~P~~~l~~q~~~~~   73 (374)
                      |.-+++.|++|+|||...+-   .+... +.+++++.--. -..|+...+
T Consensus       242 G~l~li~G~pG~GKT~lal~~a~~~a~~~g~~vl~~s~E~-s~~~l~~r~  290 (503)
T 1q57_A          242 GEVIMVTSGSGMVMSTFVRQQALQWGTAMGKKVGLAMLEE-SVEETAEDL  290 (503)
T ss_dssp             TCEEEEEESSCHHHHHHHHHHHHHHTTTSCCCEEEEESSS-CHHHHHHHH
T ss_pred             CeEEEEeecCCCCchHHHHHHHHHHHHhcCCcEEEEeccC-CHHHHHHHH
Confidence            45578999999999955332   22233 66788876532 234444443

>1lvg_A Guanylate kinase, GMP kinase; transferase; HET: ADP 5GP; 2.10A {Mus musculus} SCOP: c.37.1.1

Probab=86.43  E-value=0.29  Score=38.64  Aligned_cols=19  Identities=26%  Similarity=0.359  Sum_probs=14.7

Q ss_pred             cCCCEEEEccCCCCchhhh
Q 037567           27 EKRDCLVVMATGSGKSLCY   45 (374)
Q Consensus        27 ~~~~~l~~a~tGsGKT~~~   45 (374)
                      .++-+.+.||+|+|||...
T Consensus         3 ~g~~i~lvGpsGaGKSTLl   21 (198)
T 1lvg_A            3 GPRPVVLSGPSGAGKSTLL   21 (198)
T ss_dssp             --CCEEEECCTTSSHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            4677899999999999653

>3vaa_A Shikimate kinase, SK; structural genomics, center for structural genomics of infec diseases, csgid, metal binding, transferase; 1.70A {Bacteroides thetaiotaomicron}

Probab=86.33  E-value=0.28  Score=38.73  Aligned_cols=21  Identities=14%  Similarity=0.059  Sum_probs=16.5

Q ss_pred             HcCCCEEEEccCCCCchhhhh
Q 037567           26 IEKRDCLVVMATGSGKSLCYQ   46 (374)
Q Consensus        26 ~~~~~~l~~a~tGsGKT~~~~   46 (374)
                      ..++.+++.|++|||||...-
T Consensus        23 ~~~~~i~l~G~~GsGKsTl~~   43 (199)
T 3vaa_A           23 NAMVRIFLTGYMGAGKTTLGK   43 (199)
T ss_dssp             -CCCEEEEECCTTSCHHHHHH
T ss_pred             CCCCEEEEEcCCCCCHHHHHH
Confidence            346778999999999997643

>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; 2.60A {Homo sapiens}

Probab=86.27  E-value=1.8  Score=33.83  Aligned_cols=69  Identities=16%  Similarity=0.108  Sum_probs=49.0

Q ss_pred             CCCchhhhhcccc-ccCCcEEEEcchHHHHHHHHHHHHHcCCceEEcCCCCCchhhh---hhhhcCCeeEEEEc
Q 037567           38 GSGKSLCYQLPPL-VTGKTALVVSPLISLMQDQVMSLKQRGINAEFLGSAQTDSSVQ---TKAETGYFQLLFMT  107 (374)
Q Consensus        38 GsGKT~~~~l~~~-~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~i~i~T  107 (374)
                      ...|... +..++ ....++||+++++..++.+.+.+...|..+..+++........   .....+...|+|+|
T Consensus        39 ~~~K~~~-L~~~l~~~~~~~lVF~~~~~~~~~l~~~L~~~g~~~~~lhg~~~~~~R~~~l~~F~~g~~~vLvaT  111 (191)
T 2p6n_A           39 EEAKMVY-LLECLQKTPPPVLIFAEKKADVDAIHEYLLLKGVEAVAIHGGKDQEERTKAIEAFREGKKDVLVAT  111 (191)
T ss_dssp             GGGHHHH-HHHHHTTSCSCEEEECSCHHHHHHHHHHHHHHTCCEEEECTTSCHHHHHHHHHHHHHTSCSEEEEC
T ss_pred             hHHHHHH-HHHHHHhCCCCEEEEECCHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHhcCCCEEEEEc
Confidence            3455533 22233 3467899999999999999999999999988888766544322   23335678899999

>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=86.20  E-value=4.5  Score=32.27  Aligned_cols=72  Identities=11%  Similarity=0.149  Sum_probs=46.9

Q ss_pred             CCCcEEEEecchhHHHHHHHHHHHc---CCceeeeecCCChHHHHHHHHhhhcCCeeEEEEec-cc-----cccccccCc
Q 037567          227 GAGSIIVYCMTIKDVEEISKALKQL---GVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATM-AF-----GMGIDKPDV  297 (374)
Q Consensus       227 ~~~~~lVf~~~~~~~~~l~~~l~~~---~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~-~~-----~~G~d~~~~  297 (374)
                      .+.+++|.+|++.-+.++++.+++.   +..+..++|+.+..+....+   . ...+|+|+|+ .+     ...+++.++
T Consensus        93 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~-~~~~iiv~Tp~~l~~~~~~~~~~~~~~  168 (228)
T 3iuy_A           93 NGPGMLVLTPTRELALHVEAECSKYSYKGLKSICIYGGRNRNGQIEDI---S-KGVDIIIATPGRLNDLQMNNSVNLRSI  168 (228)
T ss_dssp             CCCSEEEECSSHHHHHHHHHHHHHHCCTTCCEEEECC------CHHHH---H-SCCSEEEECHHHHHHHHHTTCCCCTTC
T ss_pred             CCCcEEEEeCCHHHHHHHHHHHHHhcccCceEEEEECCCChHHHHHHh---c-CCCCEEEECHHHHHHHHHcCCcCcccc
Confidence            5678999999999999999998874   66777888876654433222   2 3468999997 22     124556667


Q ss_pred             cEEEE
Q 037567          298 RHVIH  302 (374)
Q Consensus       298 ~~vi~  302 (374)
                      +++|.
T Consensus       169 ~~lVi  173 (228)
T 3iuy_A          169 TYLVI  173 (228)
T ss_dssp             CEEEE
T ss_pred             eEEEE
Confidence            77663

>1kgd_A CASK, peripheral plasma membrane CASK; maguk, guanylate kinase like domain, protein binding; 1.31A {Homo sapiens} SCOP: c.37.1.1

Probab=86.12  E-value=0.27  Score=38.13  Aligned_cols=19  Identities=16%  Similarity=0.274  Sum_probs=15.4

Q ss_pred             cCCCEEEEccCCCCchhhh
Q 037567           27 EKRDCLVVMATGSGKSLCY   45 (374)
Q Consensus        27 ~~~~~l~~a~tGsGKT~~~   45 (374)
                      .++-+++.||+|+|||...
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            4566789999999999653

>2bjv_A PSP operon transcriptional activator; AAA, transcription activation, gene regulation, sigma54 activator, enhancer binding protein, PSPF; 1.7A {Escherichia coli} PDB: 2bjw_A 2c96_A* 2c98_A* 2c99_A* 2c9c_A* 2vii_A*

Probab=86.08  E-value=0.4  Score=39.75  Aligned_cols=18  Identities=28%  Similarity=0.516  Sum_probs=15.7

Q ss_pred             CCCEEEEccCCCCchhhh
Q 037567           28 KRDCLVVMATGSGKSLCY   45 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~   45 (374)
                      +.++++.||+|+|||..+
T Consensus        29 ~~~vll~G~~GtGKt~la   46 (265)
T 2bjv_A           29 DKPVLIIGERGTGKELIA   46 (265)
T ss_dssp             CSCEEEECCTTSCHHHHH
T ss_pred             CCCEEEECCCCCcHHHHH
Confidence            578999999999999654

>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein, translation; 1.75A {Saccharomyces cerevisiae} SCOP: c.37.1.19

Probab=86.00  E-value=1.6  Score=32.99  Aligned_cols=57  Identities=11%  Similarity=0.120  Sum_probs=44.6

Q ss_pred             cCCcEEEEcchHHHHHHHHHHHHHcCCceEEcCCCCCchhhh---hhhhcCCeeEEEEcC
Q 037567           52 TGKTALVVSPLISLMQDQVMSLKQRGINAEFLGSAQTDSSVQ---TKAETGYFQLLFMTP  108 (374)
Q Consensus        52 ~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~i~i~T~  108 (374)
                      ...++||+++++..+..+...+...+..+..+++........   .....+...|+|+|.
T Consensus        29 ~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~   88 (165)
T 1fuk_A           29 SVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTD   88 (165)
T ss_dssp             TCSCEEEEESSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEEEG
T ss_pred             CCCCEEEEECCHHHHHHHHHHHHHcCCCEEEEECCCCHHHHHHHHHHHHcCCCEEEEEcC
Confidence            467899999999999999999999999888888766544332   233456788999993

>1t5i_A C_terminal domain of A probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA processing protein; 1.90A {Homo sapiens} SCOP: c.37.1.19

Probab=85.97  E-value=1.8  Score=33.08  Aligned_cols=57  Identities=7%  Similarity=-0.046  Sum_probs=44.8

Q ss_pred             cCCcEEEEcchHHHHHHHHHHHHHcCCceEEcCCCCCchhh---hhhhhcCCeeEEEEcC
Q 037567           52 TGKTALVVSPLISLMQDQVMSLKQRGINAEFLGSAQTDSSV---QTKAETGYFQLLFMTP  108 (374)
Q Consensus        52 ~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~i~i~T~  108 (374)
                      ...++||+++++..+..+.+.+...|..+..+++.......   ......+...|+|+|.
T Consensus        30 ~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~hg~~~~~~r~~~~~~f~~g~~~vLvaT~   89 (172)
T 1t5i_A           30 EFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATN   89 (172)
T ss_dssp             CCSSEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEESS
T ss_pred             CCCcEEEEECCHHHHHHHHHHHHhcCCCEEEEECCCCHHHHHHHHHHHHCCCCcEEEECC
Confidence            45789999999999999999999999998888876654432   2233457789999993

>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=85.95  E-value=0.56  Score=40.18  Aligned_cols=57  Identities=18%  Similarity=0.148  Sum_probs=32.7

Q ss_pred             chhHHHHHHH--------HHcCCCE--EEEccCCCCchhhhhccccccCCcEEEEcchHHHHHHHHHHHHH
Q 037567           15 RPYQKDVIQR--------IIEKRDC--LVVMATGSGKSLCYQLPPLVTGKTALVVSPLISLMQDQVMSLKQ   75 (374)
Q Consensus        15 ~~~Q~~~~~~--------~~~~~~~--l~~a~tGsGKT~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~   75 (374)
                      ..-|.+.+..        +++|.++  +..|.||||||.++.-..-.....-  +.|+  .+.++++.+..
T Consensus        55 ~~sQ~~Vy~~~~~plv~~~l~G~n~tifAYGqTGSGKTyTm~G~~~~~~~~G--iipr--~~~~lF~~i~~  121 (325)
T 1bg2_A           55 STSQEQVYNDCAKKIVKDVLEGYNGTIFAYGQTSSGKTHTMEGKLHDPEGMG--IIPR--IVQDIFNYIYS  121 (325)
T ss_dssp             TCCHHHHHHHHTHHHHHHHHTTCCEEEEEECSTTSSHHHHHTBSTTCTTTBC--HHHH--HHHHHHHHHHH
T ss_pred             CCCHHHHHHHHhhhhHHHHhCCCeEEEEEECCCCCCCceEecccCCCcccCc--cHHH--HHHHHHHHHHh
Confidence            3456665544        4567664  6689999999998764432222222  3354  34556665544

>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=85.69  E-value=3.7  Score=31.24  Aligned_cols=15  Identities=33%  Similarity=0.113  Sum_probs=12.3

Q ss_pred             CEEEEccCCCCchhh
Q 037567           30 DCLVVMATGSGKSLC   44 (374)
Q Consensus        30 ~~l~~a~tGsGKT~~   44 (374)
                      -+.+.|+.|||||..
T Consensus         6 ~i~i~G~sGsGKTTl   20 (169)
T 1xjc_A            6 VWQVVGYKHSGKTTL   20 (169)
T ss_dssp             EEEEECCTTSSHHHH
T ss_pred             EEEEECCCCCCHHHH
Confidence            357899999999964

>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=85.66  E-value=3.1  Score=42.04  Aligned_cols=74  Identities=15%  Similarity=0.231  Sum_probs=56.0

Q ss_pred             cCCCcEEEEecchhHHHHHHHHHHHc----CC----ceeeeecCCChHHHHHHHHhhhcCCeeEEEEec-ccccccc-cc
Q 037567          226 AGAGSIIVYCMTIKDVEEISKALKQL----GV----KAGTYHGQMGSKAREEAHRLFIRDEIRVMVATM-AFGMGID-KP  295 (374)
Q Consensus       226 ~~~~~~lVf~~~~~~~~~l~~~l~~~----~~----~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~-~~~~G~d-~~  295 (374)
                      ..+.+++|.+|++.-+.++++.+++.    +.    .+..++|+.+..++....+.+..  .+|+|+|+ .+..-+. +.
T Consensus        97 ~~~~~~lil~PtreLa~Q~~~~l~~l~~~~~i~~~~~v~~~~Gg~~~~~~~~~~~~l~~--~~IlV~TP~~L~~~l~~L~  174 (1054)
T 1gku_B           97 LKGKRCYVIFPTSLLVIQAAETIRKYAEKAGVGTENLIGYYHGRIPKREKENFMQNLRN--FKIVITTTQFLSKHYRELG  174 (1054)
T ss_dssp             TTSCCEEEEESCHHHHHHHHHHHHHHHTTTCCSGGGSEEECCSSCCSHHHHHHHHSGGG--CSEEEEEHHHHHHCSTTSC
T ss_pred             hcCCeEEEEeccHHHHHHHHHHHHHHHhhcCCCccceEEEEeCCCChhhHHHHHhhccC--CCEEEEcHHHHHHHHHHhc
Confidence            35678999999999999999888763    45    78899999998887777777766  89999998 3322222 44


Q ss_pred             CccEEE
Q 037567          296 DVRHVI  301 (374)
Q Consensus       296 ~~~~vi  301 (374)
                      .++++|
T Consensus       175 ~l~~lV  180 (1054)
T 1gku_B          175 HFDFIF  180 (1054)
T ss_dssp             CCSEEE
T ss_pred             cCCEEE
Confidence            566666

>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=85.42  E-value=0.29  Score=40.69  Aligned_cols=18  Identities=33%  Similarity=0.519  Sum_probs=15.1

Q ss_pred             CCCEEEEccCCCCchhhh
Q 037567           28 KRDCLVVMATGSGKSLCY   45 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~   45 (374)
                      .+.+++.||+|+|||..+
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            356899999999999764

>3dr5_A Putative O-methyltransferase; Q8NRD3, CGL1119, PF01596, CGR117, NESG, structural genomics, PSI-2, protein structure initiative; 2.25A {Corynebacterium glutamicum}

Probab=85.36  E-value=5.1  Score=31.99  Aligned_cols=127  Identities=15%  Similarity=0.184  Sum_probs=74.8

Q ss_pred             hHcCCCCCchhHHHHHHHHHc--CCC---EEEEccCCCCchhhhhccccccCCcEEEEcchHHHHHHHHHHHHHcCCc--
Q 037567            7 KYFGYSVFRPYQKDVIQRIIE--KRD---CLVVMATGSGKSLCYQLPPLVTGKTALVVSPLISLMQDQVMSLKQRGIN--   79 (374)
Q Consensus         7 ~~~~~~~~~~~Q~~~~~~~~~--~~~---~l~~a~tGsGKT~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~--   79 (374)
                      ...|+..+.|.+.+.+..+..  +..   -++...||+|-+..++...+..+.++.-+=.....+....+.+...|..  
T Consensus        30 ~~~~~p~i~~~~~~~l~~l~~~~~~~~~~~vLdiG~G~G~~~~~la~~~~~~~~v~~vD~~~~~~~~a~~~~~~~g~~~~  109 (221)
T 3dr5_A           30 AEFGLPAPDEMTGQLLTTLAATTNGNGSTGAIAITPAAGLVGLYILNGLADNTTLTCIDPESEHQRQAKALFREAGYSPS  109 (221)
T ss_dssp             HHTTCCCCCHHHHHHHHHHHHHSCCTTCCEEEEESTTHHHHHHHHHHHSCTTSEEEEECSCHHHHHHHHHHHHHTTCCGG
T ss_pred             HHcCCCCCCHHHHHHHHHHHHhhCCCCCCCEEEEcCCchHHHHHHHHhCCCCCEEEEEECCHHHHHHHHHHHHHcCCCcC
Confidence            346777788888888877754  222   6778999999876665555545677777777777777777777776653  


Q ss_pred             -eEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHH--HhcCccEEEEeccch
Q 037567           80 -AEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKL--LKAGVCLFAVDEAHC  137 (374)
Q Consensus        80 -~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~--~~~~~~~vviDE~h~  137 (374)
                       +.+..+....  .......+.+|+++.....-. . .......  .+..=.++++|++..
T Consensus       110 ~i~~~~gda~~--~l~~~~~~~fD~V~~d~~~~~-~-~~~l~~~~~~LkpGG~lv~dn~~~  166 (221)
T 3dr5_A          110 RVRFLLSRPLD--VMSRLANDSYQLVFGQVSPMD-L-KALVDAAWPLLRRGGALVLADALL  166 (221)
T ss_dssp             GEEEECSCHHH--HGGGSCTTCEEEEEECCCTTT-H-HHHHHHHHHHEEEEEEEEETTTTG
T ss_pred             cEEEEEcCHHH--HHHHhcCCCcCeEEEcCcHHH-H-HHHHHHHHHHcCCCcEEEEeCCCC
Confidence             5554433211  111111356888887654211 1 1111111  122335788888764

>2yhs_A FTSY, cell division protein FTSY; cell cycle, protein targeting, simibi class GTPase, GTP-BIND membrane, nucleotide-binding; 1.60A {Escherichia coli} PDB: 2qy9_A 2xxa_B* 1fts_A

Probab=85.32  E-value=3.4  Score=37.55  Aligned_cols=30  Identities=23%  Similarity=0.259  Sum_probs=19.5

Q ss_pred             CEEEEccCCCCchhhhhcc-cc--ccCCcEEEE
Q 037567           30 DCLVVMATGSGKSLCYQLP-PL--VTGKTALVV   59 (374)
Q Consensus        30 ~~l~~a~tGsGKT~~~~l~-~~--~~~~~~lil   59 (374)
                      -+.+.|++|+|||...... .+  ..++++++.
T Consensus       295 VI~LVGpNGSGKTTLl~~LAgll~~~~G~V~l~  327 (503)
T 2yhs_A          295 VILMVGVNGVGKTTTIGKLARQFEQQGKSVMLA  327 (503)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             EEEEECCCcccHHHHHHHHHHHhhhcCCeEEEe
Confidence            4578999999999654322 11  235667775

>2gza_A Type IV secretion system protein VIRB11; ATPase, hydrolase; 2.60A {Brucella suis}

Probab=85.20  E-value=0.43  Score=41.71  Aligned_cols=22  Identities=32%  Similarity=0.321  Sum_probs=17.8

Q ss_pred             HHHcCCCEEEEccCCCCchhhh
Q 037567           24 RIIEKRDCLVVMATGSGKSLCY   45 (374)
Q Consensus        24 ~~~~~~~~l~~a~tGsGKT~~~   45 (374)
                      .+..|..+++.||||||||...
T Consensus       171 ~i~~G~~i~ivG~sGsGKSTll  192 (361)
T 2gza_A          171 AVQLERVIVVAGETGSGKTTLM  192 (361)
T ss_dssp             HHHTTCCEEEEESSSSCHHHHH
T ss_pred             HHhcCCEEEEECCCCCCHHHHH
Confidence            3446889999999999999653

>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=85.16  E-value=0.54  Score=41.94  Aligned_cols=30  Identities=37%  Similarity=0.416  Sum_probs=21.0

Q ss_pred             chhHHHHHHHHHc--CCCEEEEccCCCCchhh
Q 037567           15 RPYQKDVIQRIIE--KRDCLVVMATGSGKSLC   44 (374)
Q Consensus        15 ~~~Q~~~~~~~~~--~~~~l~~a~tGsGKT~~   44 (374)
                      .+-+..++..++.  +.-+++.||||||||..
T Consensus       152 ~~~~~~~L~~l~~~~ggii~I~GpnGSGKTTl  183 (418)
T 1p9r_A          152 TAHNHDNFRRLIKRPHGIILVTGPTGSGKSTT  183 (418)
T ss_dssp             CHHHHHHHHHHHTSSSEEEEEECSTTSCHHHH
T ss_pred             CHHHHHHHHHHHHhcCCeEEEECCCCCCHHHH
Confidence            3445566666654  33468999999999965

>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=85.11  E-value=0.64  Score=40.26  Aligned_cols=39  Identities=21%  Similarity=0.200  Sum_probs=25.3

Q ss_pred             cCCCC---CchhHHHHHH--------HHHcCCCE--EEEccCCCCchhhhhc
Q 037567            9 FGYSV---FRPYQKDVIQ--------RIIEKRDC--LVVMATGSGKSLCYQL   47 (374)
Q Consensus         9 ~~~~~---~~~~Q~~~~~--------~~~~~~~~--l~~a~tGsGKT~~~~l   47 (374)
                      |.|+.   +..-|.+.+.        .+++|.++  +..|.||||||.++.-
T Consensus        46 F~FD~Vf~~~~tQ~~Vy~~~~~plv~~~l~G~n~tifAYGqTGSGKTyTM~G   97 (349)
T 1t5c_A           46 FNFDRVFHGNETTKNVYEEIAAPIIDSAIQGYNGTIFAYGQTASGKTYTMMG   97 (349)
T ss_dssp             EECSCEECTTSCHHHHHHHTTHHHHHHHHTTCCEEEEEEESTTSSHHHHHTB
T ss_pred             EECCEEECCCCCHHHHHHHHHHHHHHHHHcCCccceeeecCCCCCCCeEEec
Confidence            44553   3335666554        34567654  6689999999998754

>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=85.10  E-value=0.63  Score=40.38  Aligned_cols=33  Identities=24%  Similarity=0.196  Sum_probs=22.8

Q ss_pred             hhHHHHHH--------HHHcCCCE--EEEccCCCCchhhhhcc
Q 037567           16 PYQKDVIQ--------RIIEKRDC--LVVMATGSGKSLCYQLP   48 (374)
Q Consensus        16 ~~Q~~~~~--------~~~~~~~~--l~~a~tGsGKT~~~~l~   48 (374)
                      .-|.+.+.        .+++|.++  +..|.||||||.++.-.
T Consensus        71 a~Q~~vy~~~~~~lv~~~l~G~n~tifAYGqTGSGKTyTm~G~  113 (354)
T 3gbj_A           71 AGQDIVFKCLGENILQNAFDGYNACIFAYGQTGSGKSYTMMGT  113 (354)
T ss_dssp             CCHHHHHHHHHHHHHHHHHTTCCEEEEEEECTTSSHHHHHTBC
T ss_pred             ccHHHHHHHhhHHHHHHHhCCceeEEEeeCCCCCCCceEEecC
Confidence            34766553        44567665  66889999999987543

>1c9k_A COBU, adenosylcobinamide kinase; alpha/beta structure rossmann fold P-loop, transferase; HET: 5GP; 2.20A {Salmonella typhimurium} SCOP: c.37.1.11 PDB: 1cbu_A

Probab=85.09  E-value=0.34  Score=37.51  Aligned_cols=41  Identities=20%  Similarity=0.034  Sum_probs=23.9

Q ss_pred             EEEEccCCCCchhhhhccccccCCcEEEEcchHHHHHHHHHH
Q 037567           31 CLVVMATGSGKSLCYQLPPLVTGKTALVVSPLISLMQDQVMS   72 (374)
Q Consensus        31 ~l~~a~tGsGKT~~~~l~~~~~~~~~lil~P~~~l~~q~~~~   72 (374)
                      +++.|++|||||..+.-.+.. +.+++++......-.++.+.
T Consensus         2 ilV~Gg~~SGKS~~A~~la~~-~~~~~yiaT~~~~d~e~~~r   42 (180)
T 1c9k_A            2 ILVTGGARSGKSRHAEALIGD-APQVLYIATSQILDDEMAAR   42 (180)
T ss_dssp             EEEEECTTSSHHHHHHHHHCS-CSSEEEEECCCC------CH
T ss_pred             EEEECCCCCcHHHHHHHHHhc-CCCeEEEecCCCCCHHHHHH
Confidence            578999999999654433333 56778877755443333333

>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=85.08  E-value=0.64  Score=40.60  Aligned_cols=58  Identities=14%  Similarity=0.155  Sum_probs=32.6

Q ss_pred             CchhHHHHHHH--------HHcCCCE--EEEccCCCCchhhhhccccccCCcEEEEcchHHHHHHHHHHHHH
Q 037567           14 FRPYQKDVIQR--------IIEKRDC--LVVMATGSGKSLCYQLPPLVTGKTALVVSPLISLMQDQVMSLKQ   75 (374)
Q Consensus        14 ~~~~Q~~~~~~--------~~~~~~~--l~~a~tGsGKT~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~   75 (374)
                      +..-|.+.+..        +++|.++  +..|.||||||.++.-..-.....-  ++|+  .+.+++..+..
T Consensus        78 ~~~~Q~~Vy~~~~~plv~~~l~G~n~tifAYGqTGSGKTyTM~G~~~~~~~~G--iipr--~~~~lF~~i~~  145 (372)
T 3b6u_A           78 WNAKQFELYDETFRPLVDSVLQGFNGTIFAYGQTGTGKTYTMEGIRGDPEKRG--VIPN--SFDHIFTHISR  145 (372)
T ss_dssp             TTCCHHHHHHHTHHHHHHHHHTTCCEEEEEEESTTSSHHHHHTBCTTSGGGBC--HHHH--HHHHHHHHHHT
T ss_pred             CcCchHHHHHHHHHHHHHHHhCCCeeeEEeecCCCCCCCEeEecCCCCcccCC--cHHH--HHHHHHHHhhh
Confidence            34456666654        4567654  5688999999998754321111111  2344  34556666553

>2h58_A Kinesin-like protein KIFC3 variant; motor domain, ADP, structural genomics, structur Al genomics consortium, SGC; HET: ADP; 1.85A {Homo sapiens}

Probab=85.07  E-value=0.65  Score=39.87  Aligned_cols=48  Identities=13%  Similarity=0.188  Sum_probs=29.0

Q ss_pred             HHHHHHcCCCE--EEEccCCCCchhhhhccccccCCcEEEEcchHHHHHHHHHHHHH
Q 037567           21 VIQRIIEKRDC--LVVMATGSGKSLCYQLPPLVTGKTALVVSPLISLMQDQVMSLKQ   75 (374)
Q Consensus        21 ~~~~~~~~~~~--l~~a~tGsGKT~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~   75 (374)
                      .+..+++|.++  +..|.||||||.++.-.--   ..-  +.|+  .+.+++..+..
T Consensus        72 lv~~~l~G~n~tifAYGqTGSGKTyTm~G~~~---~~G--iipr--~~~~lF~~i~~  121 (330)
T 2h58_A           72 LVTSCIDGFNVCIFAYGQTGAGKTYTMEGTAE---NPG--INQR--ALQLLFSEVQE  121 (330)
T ss_dssp             HHHHHHTTCCEEEEEESSTTSSHHHHHTBCSS---SBC--HHHH--HHHHHHHHHHT
T ss_pred             HHHHHhCCCEEEEEeECCCCCCCcEEEecCCC---CCc--HHHH--HHHHHHHhhhc
Confidence            34456677765  5689999999998754321   111  2344  34556666654

>2vvg_A Kinesin-2; motor protein, nucleotide-binding, microtubule, ATP-binding; HET: ADP; 1.60A {Giardia intestinalis}

Probab=85.00  E-value=0.66  Score=40.18  Aligned_cols=40  Identities=18%  Similarity=0.270  Sum_probs=26.4

Q ss_pred             cCCCC---CchhHHHHHHH--------HHcCCCE--EEEccCCCCchhhhhcc
Q 037567            9 FGYSV---FRPYQKDVIQR--------IIEKRDC--LVVMATGSGKSLCYQLP   48 (374)
Q Consensus         9 ~~~~~---~~~~Q~~~~~~--------~~~~~~~--l~~a~tGsGKT~~~~l~   48 (374)
                      |.|+.   +..-|.+.+..        +++|.++  +..|.||||||.++.-.
T Consensus        58 f~FD~Vf~~~~~Q~~Vy~~~~~plv~~~l~G~n~tifAYGqTGSGKTyTm~G~  110 (350)
T 2vvg_A           58 FTFDAVYDQTSCNYGIFQASFKPLIDAVLEGFNSTIFAYGQTGAGKTWTMGGN  110 (350)
T ss_dssp             EECSEEECTTCCHHHHHHHTTHHHHHHHHTTCCEEEEEECSTTSSHHHHHTBC
T ss_pred             eeCCEEECCCcchhHHHHHHHHHHHHHHhCCCceeEEeecCCCCCCCEEeecC
Confidence            55553   34457666643        4567654  66899999999987543

>3trf_A Shikimate kinase, SK; amino acid biosynthesis, transferase; 2.60A {Coxiella burnetii}

Probab=84.93  E-value=0.35  Score=37.50  Aligned_cols=19  Identities=16%  Similarity=0.204  Sum_probs=15.5

Q ss_pred             CCCEEEEccCCCCchhhhh
Q 037567           28 KRDCLVVMATGSGKSLCYQ   46 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~   46 (374)
                      .+.+++.|++|||||...-
T Consensus         5 ~~~i~l~G~~GsGKst~a~   23 (185)
T 3trf_A            5 LTNIYLIGLMGAGKTSVGS   23 (185)
T ss_dssp             CCEEEEECSTTSSHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHH
Confidence            4568899999999997643

>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=84.93  E-value=7.5  Score=33.83  Aligned_cols=72  Identities=25%  Similarity=0.419  Sum_probs=52.1

Q ss_pred             CCCcEEEEecchhHHHHHHHHHHHc-----CCceeeeecCCChHHHHHHHHhhhcCCeeEEEEec-cc-----ccccccc
Q 037567          227 GAGSIIVYCMTIKDVEEISKALKQL-----GVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATM-AF-----GMGIDKP  295 (374)
Q Consensus       227 ~~~~~lVf~~~~~~~~~l~~~l~~~-----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~-~~-----~~G~d~~  295 (374)
                      .+.++||.+|++.-+..+++.+++.     +..+..++|+.+..+....   +..+..+|+|+|+ .+     ...+++.
T Consensus        75 ~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~---~~~~~~~iiv~T~~~l~~~~~~~~~~~~  151 (391)
T 1xti_A           75 GQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEV---LKKNCPHIVVGTPGRILALARNKSLNLK  151 (391)
T ss_dssp             TCCCEEEECSCHHHHHHHHHHHHHHTTTCTTCCEEEECTTSCHHHHHHH---HHHSCCSEEEECHHHHHHHHHTTSSCCT
T ss_pred             CCeeEEEECCCHHHHHHHHHHHHHHHhhCCCeEEEEEeCCCCHHHHHHH---HhcCCCCEEEECHHHHHHHHHcCCcccc
Confidence            3568999999999999998888774     6788899998876555443   3446678999997 22     1234556


Q ss_pred             CccEEE
Q 037567          296 DVRHVI  301 (374)
Q Consensus       296 ~~~~vi  301 (374)
                      +++.||
T Consensus       152 ~~~~vV  157 (391)
T 1xti_A          152 HIKHFI  157 (391)
T ss_dssp             TCSEEE
T ss_pred             ccCEEE
Confidence            666666

>2qor_A Guanylate kinase; phosphotransferase, purine metabolism, structural genomics, structural genomics of pathogenic protozoa consortium; HET: 5GP POP; 1.80A {Plasmodium vivax}

Probab=84.91  E-value=0.3  Score=38.74  Aligned_cols=21  Identities=19%  Similarity=0.203  Sum_probs=16.9

Q ss_pred             HHcCCCEEEEccCCCCchhhh
Q 037567           25 IIEKRDCLVVMATGSGKSLCY   45 (374)
Q Consensus        25 ~~~~~~~l~~a~tGsGKT~~~   45 (374)
                      +..+.-+++.||+|||||...
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            345778899999999999653

>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=84.78  E-value=0.35  Score=36.93  Aligned_cols=18  Identities=39%  Similarity=0.362  Sum_probs=14.2

Q ss_pred             CEEEEccCCCCchhhhhc
Q 037567           30 DCLVVMATGSGKSLCYQL   47 (374)
Q Consensus        30 ~~l~~a~tGsGKT~~~~l   47 (374)
                      -+++.|++|||||...-.
T Consensus         3 ~I~l~G~~GsGKsT~a~~   20 (179)
T 3lw7_A            3 VILITGMPGSGKSEFAKL   20 (179)
T ss_dssp             EEEEECCTTSCHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHH
Confidence            367899999999976543

>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=84.69  E-value=0.37  Score=37.09  Aligned_cols=18  Identities=22%  Similarity=0.185  Sum_probs=14.6

Q ss_pred             CCEEEEccCCCCchhhhh
Q 037567           29 RDCLVVMATGSGKSLCYQ   46 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~~   46 (374)
                      .-+++.|++|||||...-
T Consensus         4 ~~i~l~G~~GsGKST~a~   21 (178)
T 1qhx_A            4 RMIILNGGSSAGKSGIVR   21 (178)
T ss_dssp             CEEEEECCTTSSHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHH
Confidence            457899999999997643

>2y65_A Kinesin, kinesin heavy chain; motor protein; HET: ADP; 2.20A {Drosophila melanogaster} PDB: 2y5w_A*

Probab=84.65  E-value=0.69  Score=40.30  Aligned_cols=59  Identities=15%  Similarity=0.093  Sum_probs=33.9

Q ss_pred             CchhHHHHHHH--------HHcCCCE--EEEccCCCCchhhhhccccccCCcEEEEcchHHHHHHHHHHHHHc
Q 037567           14 FRPYQKDVIQR--------IIEKRDC--LVVMATGSGKSLCYQLPPLVTGKTALVVSPLISLMQDQVMSLKQR   76 (374)
Q Consensus        14 ~~~~Q~~~~~~--------~~~~~~~--l~~a~tGsGKT~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~   76 (374)
                      +..-|.+.+..        +++|.++  +..|.||||||.++.-..-.....-  +.|+  .+.+++..+...
T Consensus        61 ~~~~Q~~Vy~~~~~plv~~~l~G~n~tifAYGqTGSGKTyTm~G~~~~~~~~G--iipr--~~~~lF~~i~~~  129 (365)
T 2y65_A           61 PNASQEKVYNEAAKSIVTDVLAGYNGTIFAYGQTSSGKTHTMEGVIGDSVKQG--IIPR--IVNDIFNHIYAM  129 (365)
T ss_dssp             TTCCHHHHHHHHTHHHHHHHHTTCCEEEEEECSTTSSHHHHHTBSTTCTTTBC--HHHH--HHHHHHHHHHHC
T ss_pred             CCCCHHHHHHHhhhhHHHHHhCCCceEEEeecCCCCCCceEEecCCCCcccCC--hHHH--HHHHHHHHHHhc
Confidence            34456666544        4567654  6689999999998754322222222  2354  345566666543

>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=84.64  E-value=0.6  Score=40.29  Aligned_cols=33  Identities=30%  Similarity=0.405  Sum_probs=22.6

Q ss_pred             CchhHHHHHHH--------HHcCCCE--EEEccCCCCchhhhh
Q 037567           14 FRPYQKDVIQR--------IIEKRDC--LVVMATGSGKSLCYQ   46 (374)
Q Consensus        14 ~~~~Q~~~~~~--------~~~~~~~--l~~a~tGsGKT~~~~   46 (374)
                      +..-|.+.+..        +++|.++  +..|.||||||.++.
T Consensus        71 ~~~sQ~~Vy~~~~~plv~~~l~G~N~tifAYGQTGSGKTyTM~  113 (344)
T 3dc4_A           71 ATISQDEMYQALILPLVDKLLEGFQCTALAYGQTGTGKSYSMG  113 (344)
T ss_dssp             TTCCHHHHHHHHTHHHHHHHHHTCCEEEEEESSTTSSHHHHHT
T ss_pred             CCCCHHHHHHhhccchhhHhhCCCceEEEEecCCCCCCCeEEc
Confidence            33456666654        3456654  668999999999864

>4etp_A Kinesin-like protein KAR3; kinesin motor protein, kinesin motor homology domain, karyog mitosis, microtubules; HET: ADP EBC; 2.30A {Saccharomyces cerevisiae}

Probab=84.52  E-value=0.68  Score=41.00  Aligned_cols=25  Identities=24%  Similarity=0.377  Sum_probs=18.6

Q ss_pred             HHHHHcCCCE--EEEccCCCCchhhhh
Q 037567           22 IQRIIEKRDC--LVVMATGSGKSLCYQ   46 (374)
Q Consensus        22 ~~~~~~~~~~--l~~a~tGsGKT~~~~   46 (374)
                      ++.+++|.++  +..|.||||||.++.
T Consensus       133 v~~~l~G~N~tifAYGqTGSGKTyTM~  159 (403)
T 4etp_A          133 VQSSLDGYNVAIFAYGQTGSGKTFTML  159 (403)
T ss_dssp             HHHHHTTCCEEEEEESCTTSSHHHHHH
T ss_pred             HHHHhCCcceEEEEECCCCCCCceEeC
Confidence            3445567665  568899999999875

>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=84.50  E-value=0.65  Score=40.32  Aligned_cols=34  Identities=26%  Similarity=0.397  Sum_probs=23.1

Q ss_pred             chhHHHHHH--------HHHcCCCE--EEEccCCCCchhhhhcc
Q 037567           15 RPYQKDVIQ--------RIIEKRDC--LVVMATGSGKSLCYQLP   48 (374)
Q Consensus        15 ~~~Q~~~~~--------~~~~~~~~--l~~a~tGsGKT~~~~l~   48 (374)
                      ..-|.+.+.        .+++|.++  +..|.||||||.++.-.
T Consensus        83 ~~~Q~~Vy~~~~~plv~~~l~G~n~tifAYGqTGSGKTyTm~G~  126 (355)
T 3lre_A           83 TSTQSEVFEHTTKPILRSFLNGYNCTVLAYGATGAGKTHTMLGS  126 (355)
T ss_dssp             TCCHHHHHHTTHHHHHHHHTTTCCEEEEEECCTTSSHHHHHTBC
T ss_pred             CCChHHHHHHHHHHHHHHHhCCCceEEEEeCCCCCCceeeeccC
Confidence            335666654        34567654  66889999999987543

>1goj_A Kinesin, kinesin heavy chain; motor protein, ATPase; HET: ADP; 2.3A {Neurospora crassa} SCOP: c.37.1.9

Probab=84.47  E-value=0.66  Score=40.28  Aligned_cols=57  Identities=19%  Similarity=0.217  Sum_probs=32.6

Q ss_pred             chhHHHHHHH--------HHcCCCE--EEEccCCCCchhhhhccccc-cCCcEEEEcchHHHHHHHHHHHHH
Q 037567           15 RPYQKDVIQR--------IIEKRDC--LVVMATGSGKSLCYQLPPLV-TGKTALVVSPLISLMQDQVMSLKQ   75 (374)
Q Consensus        15 ~~~Q~~~~~~--------~~~~~~~--l~~a~tGsGKT~~~~l~~~~-~~~~~lil~P~~~l~~q~~~~~~~   75 (374)
                      ..-|.+.+..        +++|.++  +..|.||||||.++.-.-.. ....-  +.|+  .+.+++..+..
T Consensus        58 ~~~Q~~Vy~~~~~plv~~~l~G~n~tifAYGqTGSGKTyTm~G~~~~~~~~~G--iipr--~~~~lF~~i~~  125 (355)
T 1goj_A           58 SCKQSDIFDFSIKPTVDDILNGYNGTVFAYGQTGAGKSYTMMGTSIDDPDGRG--VIPR--IVEQIFTSILS  125 (355)
T ss_dssp             TCCHHHHHHHHTHHHHHHHTTTCCEEEEEECSTTSSHHHHHTBSCTTSTTTBC--HHHH--HHHHHHHHHHT
T ss_pred             CCccHHHHHHHHHHHHHHHhCCCcceEEEECCCCCCcceEeecCCCCCcccCC--chHH--HHHHHHHHHHh
Confidence            3457666653        4456654  66899999999987543211 11122  2344  44556666554

>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=84.41  E-value=0.71  Score=40.26  Aligned_cols=55  Identities=22%  Similarity=0.248  Sum_probs=32.1

Q ss_pred             hhHHHHHHH--------HHcCCCE--EEEccCCCCchhhhhccccccCCcEEEEcchHHHHHHHHHHHHH
Q 037567           16 PYQKDVIQR--------IIEKRDC--LVVMATGSGKSLCYQLPPLVTGKTALVVSPLISLMQDQVMSLKQ   75 (374)
Q Consensus        16 ~~Q~~~~~~--------~~~~~~~--l~~a~tGsGKT~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~   75 (374)
                      .-|.+.+..        +++|.++  +..|.||||||.++.-.--. ...-  ++|+  .+.+++..+..
T Consensus        68 asQ~~Vy~~~~~plv~~~l~G~N~tifAYGqTGSGKTyTm~G~~~~-~~~G--iipr--~~~~lF~~i~~  132 (366)
T 2zfi_A           68 ASQKQVYRDIGEEMLQHAFEGYNVCIFAYGQTGAGKSYTMMGKQEK-DQQG--IIPQ--LCEDLFSRIND  132 (366)
T ss_dssp             CCHHHHHHHTHHHHHHHHHTTCCEEEEEECSTTSSHHHHHTBCSGG-GCBC--HHHH--HHHHHHHHHHT
T ss_pred             CcHHHHHHHHHHHHHHHHhcCCeeEEEEeCCCCCCCceEeeCCCcc-CCCc--cHHH--HHHHHHHHHhh
Confidence            347666543        4567654  56889999999986543211 1111  2354  45566666654

>1j8m_F SRP54, signal recognition 54 kDa protein; signaling protein; 2.00A {Acidianus ambivalens} SCOP: a.24.13.1 c.37.1.10 PDB: 1j8y_F

Probab=84.40  E-value=3  Score=35.22  Aligned_cols=30  Identities=20%  Similarity=0.166  Sum_probs=18.6

Q ss_pred             EEEEccCCCCchhhhhccc---cccCCcEEEEc
Q 037567           31 CLVVMATGSGKSLCYQLPP---LVTGKTALVVS   60 (374)
Q Consensus        31 ~l~~a~tGsGKT~~~~l~~---~~~~~~~lil~   60 (374)
                      +.+.+++|+|||.+....+   ...+.+++++.
T Consensus       101 i~i~G~~G~GKTT~~~~la~~~~~~g~~v~l~~  133 (297)
T 1j8m_F          101 IMLVGVQGTGKTTTAGKLAYFYKKKGFKVGLVG  133 (297)
T ss_dssp             EEEECSSCSSTTHHHHHHHHHHHHTTCCEEEEE
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEe
Confidence            5678999999996543221   12456666543

>1kag_A SKI, shikimate kinase I; transferase, structural genomics, PSI, protein structure initiative; 2.05A {Escherichia coli} SCOP: c.37.1.2

Probab=84.34  E-value=0.46  Score=36.28  Aligned_cols=18  Identities=39%  Similarity=0.477  Sum_probs=15.1

Q ss_pred             CCCEEEEccCCCCchhhh
Q 037567           28 KRDCLVVMATGSGKSLCY   45 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~   45 (374)
                      +..+.+.|++|||||...
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            456899999999999654

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens}

Probab=84.27  E-value=4.9  Score=32.24  Aligned_cols=70  Identities=16%  Similarity=0.208  Sum_probs=48.1

Q ss_pred             CCCcEEEEecchhHHHHHHHHHHHc----CCceeeeecCCChHHHHHHHHhhhcCCeeEEEEec-ccc----c--ccccc
Q 037567          227 GAGSIIVYCMTIKDVEEISKALKQL----GVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATM-AFG----M--GIDKP  295 (374)
Q Consensus       227 ~~~~~lVf~~~~~~~~~l~~~l~~~----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~-~~~----~--G~d~~  295 (374)
                      .+.+++|.+|++.-+..+++.+++.    +..+..++|+.+.......+     +..+|+|+|+ .+.    .  .+++.
T Consensus        96 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~-----~~~~iiv~Tp~~l~~~l~~~~~~~~~  170 (236)
T 2pl3_A           96 DGLGVLIISPTRELAYQTFEVLRKVGKNHDFSAGLIIGGKDLKHEAERI-----NNINILVCTPGRLLQHMDETVSFHAT  170 (236)
T ss_dssp             GCCCEEEECSSHHHHHHHHHHHHHHTTTSSCCEEEECCC--CHHHHHHH-----TTCSEEEECHHHHHHHHHHCSSCCCT
T ss_pred             CCceEEEEeCCHHHHHHHHHHHHHHhCCCCeeEEEEECCCCHHHHHHhC-----CCCCEEEECHHHHHHHHHhcCCcccc
Confidence            4678999999999999999988875    36778888887655443332     3578999997 221    1  24556


Q ss_pred             CccEEE
Q 037567          296 DVRHVI  301 (374)
Q Consensus       296 ~~~~vi  301 (374)
                      +++++|
T Consensus       171 ~~~~lV  176 (236)
T 2pl3_A          171 DLQMLV  176 (236)
T ss_dssp             TCCEEE
T ss_pred             cccEEE
Confidence            666666

>2eyu_A Twitching motility protein PILT; pilus retraction motor, C-terminal domain PILT, protein transport; 1.87A {Aquifex aeolicus}

Probab=84.27  E-value=0.33  Score=40.30  Aligned_cols=20  Identities=40%  Similarity=0.273  Sum_probs=15.9

Q ss_pred             HcCCCEEEEccCCCCchhhh
Q 037567           26 IEKRDCLVVMATGSGKSLCY   45 (374)
Q Consensus        26 ~~~~~~l~~a~tGsGKT~~~   45 (374)
                      ..+.-+++.||+|||||...
T Consensus        23 ~~g~~v~i~Gp~GsGKSTll   42 (261)
T 2eyu_A           23 RKMGLILVTGPTGSGKSTTI   42 (261)
T ss_dssp             CSSEEEEEECSTTCSHHHHH
T ss_pred             CCCCEEEEECCCCccHHHHH
Confidence            34666789999999999653

>1um8_A ATP-dependent CLP protease ATP-binding subunit CL; CLPP binding loop, chaperone; HET: ADP; 2.60A {Helicobacter pylori} SCOP: c.37.1.20

Probab=84.21  E-value=0.49  Score=41.57  Aligned_cols=19  Identities=47%  Similarity=0.632  Sum_probs=15.8

Q ss_pred             CCCEEEEccCCCCchhhhh
Q 037567           28 KRDCLVVMATGSGKSLCYQ   46 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~   46 (374)
                      ..++++.||+|+|||..+-
T Consensus        72 ~~~ill~Gp~GtGKT~la~   90 (376)
T 1um8_A           72 KSNILLIGPTGSGKTLMAQ   90 (376)
T ss_dssp             CCCEEEECCTTSSHHHHHH
T ss_pred             CCCEEEECCCCCCHHHHHH
Confidence            4579999999999997653

>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=84.20  E-value=0.64  Score=40.44  Aligned_cols=34  Identities=26%  Similarity=0.396  Sum_probs=23.2

Q ss_pred             chhHHHHHHH--------HHcCCCE--EEEccCCCCchhhhhcc
Q 037567           15 RPYQKDVIQR--------IIEKRDC--LVVMATGSGKSLCYQLP   48 (374)
Q Consensus        15 ~~~Q~~~~~~--------~~~~~~~--l~~a~tGsGKT~~~~l~   48 (374)
                      ..-|.+.+..        +++|.++  +..|.||||||.++.-.
T Consensus        66 ~~~Q~~Vy~~~~~plv~~~l~G~n~tifAYGqTGSGKTyTM~G~  109 (359)
T 1x88_A           66 STKQIDVYRSVVCPILDEVIMGYNCTIFAYGQTGTGKTFTMEGE  109 (359)
T ss_dssp             TCCHHHHHHHHHHHHHHHHHTTCEEEEEEEECTTSSHHHHHTBC
T ss_pred             cCchhHHHHHHHHHhHHHHhCCCceEEEEeCCCCCCCceEEecc
Confidence            3456666654        3456654  66899999999987543

>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=84.19  E-value=4.2  Score=31.76  Aligned_cols=72  Identities=18%  Similarity=0.092  Sum_probs=50.0

Q ss_pred             CCCcEEEEecchhHHHHHHHHHHHc--CCceeeeecCCChHHHHHHHHhhhcCCeeEEEEec-cc----c-ccccccCcc
Q 037567          227 GAGSIIVYCMTIKDVEEISKALKQL--GVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATM-AF----G-MGIDKPDVR  298 (374)
Q Consensus       227 ~~~~~lVf~~~~~~~~~l~~~l~~~--~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~-~~----~-~G~d~~~~~  298 (374)
                      .+.+++|.+|++..+..+++.+++.  +..+..++|+.+.......+.    ...+|+|+|+ .+    . ..+++.+++
T Consensus        71 ~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~i~v~T~~~l~~~~~~~~~~~~~~~  146 (207)
T 2gxq_A           71 RKPRALVLTPTRELALQVASELTAVAPHLKVVAVYGGTGYGKQKEALL----RGADAVVATPGRALDYLRQGVLDLSRVE  146 (207)
T ss_dssp             CCCSEEEECSSHHHHHHHHHHHHHHCTTSCEEEECSSSCSHHHHHHHH----HCCSEEEECHHHHHHHHHHTSSCCTTCS
T ss_pred             CCCcEEEEECCHHHHHHHHHHHHHHhhcceEEEEECCCChHHHHHHhh----CCCCEEEECHHHHHHHHHcCCcchhhce
Confidence            4568999999999999999999875  456778888876544333322    2468999997 21    1 234566677


Q ss_pred             EEEE
Q 037567          299 HVIH  302 (374)
Q Consensus       299 ~vi~  302 (374)
                      .+|.
T Consensus       147 ~iVi  150 (207)
T 2gxq_A          147 VAVL  150 (207)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            7664

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=84.01  E-value=0.37  Score=42.12  Aligned_cols=17  Identities=29%  Similarity=0.450  Sum_probs=14.6

Q ss_pred             CCEEEEccCCCCchhhh
Q 037567           29 RDCLVVMATGSGKSLCY   45 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~   45 (374)
                      +.+++.||+|+|||..+
T Consensus        71 ~~vLl~GppGtGKT~la   87 (368)
T 3uk6_A           71 RAVLIAGQPGTGKTAIA   87 (368)
T ss_dssp             CEEEEEESTTSSHHHHH
T ss_pred             CEEEEECCCCCCHHHHH
Confidence            46899999999999654

>3a8t_A Adenylate isopentenyltransferase; rossmann fold protein; HET: ATP; 2.37A {Humulus lupulus}

Probab=84.00  E-value=0.41  Score=41.15  Aligned_cols=18  Identities=33%  Similarity=0.305  Sum_probs=14.4

Q ss_pred             CCEEEEccCCCCchhhhh
Q 037567           29 RDCLVVMATGSGKSLCYQ   46 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~~   46 (374)
                      +-++|.||||+|||....
T Consensus        41 ~lIvI~GPTgsGKTtLa~   58 (339)
T 3a8t_A           41 KLLVLMGATGTGKSRLSI   58 (339)
T ss_dssp             EEEEEECSTTSSHHHHHH
T ss_pred             ceEEEECCCCCCHHHHHH
Confidence            357899999999996543

>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=83.97  E-value=0.42  Score=38.04  Aligned_cols=19  Identities=16%  Similarity=0.100  Sum_probs=15.1

Q ss_pred             cCCCEEEEccCCCCchhhh
Q 037567           27 EKRDCLVVMATGSGKSLCY   45 (374)
Q Consensus        27 ~~~~~l~~a~tGsGKT~~~   45 (374)
                      .+.-+++.||+|+|||...
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            3556788999999999654

>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=83.91  E-value=0.34  Score=37.80  Aligned_cols=19  Identities=32%  Similarity=0.176  Sum_probs=15.5

Q ss_pred             cCCCEEEEccCCCCchhhh
Q 037567           27 EKRDCLVVMATGSGKSLCY   45 (374)
Q Consensus        27 ~~~~~l~~a~tGsGKT~~~   45 (374)
                      .|..+++.||+|||||...
T Consensus         8 ~g~~i~l~G~~GsGKSTl~   26 (191)
T 1zp6_A            8 GGNILLLSGHPGSGKSTIA   26 (191)
T ss_dssp             TTEEEEEEECTTSCHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHH
Confidence            4566789999999999654

>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=83.87  E-value=0.76  Score=39.73  Aligned_cols=33  Identities=27%  Similarity=0.231  Sum_probs=22.8

Q ss_pred             CchhHHHHHHH--------HHcCCCE--EEEccCCCCchhhhh
Q 037567           14 FRPYQKDVIQR--------IIEKRDC--LVVMATGSGKSLCYQ   46 (374)
Q Consensus        14 ~~~~Q~~~~~~--------~~~~~~~--l~~a~tGsGKT~~~~   46 (374)
                      +..-|.+.+..        +++|.++  +..|.||||||.++.
T Consensus        60 ~~~~Q~~vy~~~~~plv~~~l~G~n~tifAYGqTGSGKTyTm~  102 (344)
T 4a14_A           60 EDAGQEAVYQACVQPLLEAFFEGFNATVFAYGQTGSGKTYTMG  102 (344)
T ss_dssp             TTCCHHHHHHHHTHHHHHHHHTTCCEEEEEESSTTSSHHHHHC
T ss_pred             cCcchhHHHHHHHHHHHHHHHhhcCeeEEEecccCCCceEeec
Confidence            34456666654        3457654  668899999999864

>3eaq_A Heat resistant RNA dependent ATPase; DEAD box RNA helicase, dimer, ATP-binding, helicase, hydrolase, nucleotide-binding; 2.30A {Thermus thermophilus} PDB: 3ear_A 3eas_A

Probab=83.85  E-value=2.3  Score=33.83  Aligned_cols=57  Identities=16%  Similarity=0.149  Sum_probs=45.5

Q ss_pred             cCCcEEEEcchHHHHHHHHHHHHHcCCceEEcCCCCCchhhh---hhhhcCCeeEEEEcC
Q 037567           52 TGKTALVVSPLISLMQDQVMSLKQRGINAEFLGSAQTDSSVQ---TKAETGYFQLLFMTP  108 (374)
Q Consensus        52 ~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~i~i~T~  108 (374)
                      ...++||+++++.-++.+.+.+...|..+..+++........   .....+..+|+|+|.
T Consensus        30 ~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~r~~~~~~f~~g~~~vlvaT~   89 (212)
T 3eaq_A           30 SPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDLSQGERERVLGAFRQGEVRVLVATD   89 (212)
T ss_dssp             CCSCEEEECSSHHHHHHHHHHHHHHTCCEEEECSSSCHHHHHHHHHHHHSSSCCEEEECT
T ss_pred             CCCeEEEEeCCHHHHHHHHHHHHHcCCCEEEEECCCCHHHHHHHHHHHHCCCCeEEEecC
Confidence            477999999999999999999999999988888876554432   233457789999993

>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=83.72  E-value=0.61  Score=40.69  Aligned_cols=48  Identities=19%  Similarity=0.299  Sum_probs=28.6

Q ss_pred             HHHHHcCCCE--EEEccCCCCchhhhhccccccCCcEEEEcchHHHHHHHHHHHHHc
Q 037567           22 IQRIIEKRDC--LVVMATGSGKSLCYQLPPLVTGKTALVVSPLISLMQDQVMSLKQR   76 (374)
Q Consensus        22 ~~~~~~~~~~--l~~a~tGsGKT~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~   76 (374)
                      ++.+++|.++  +..|.||||||.++.-.-   ...-  +.|+  .+.++++.+...
T Consensus        72 v~~~l~G~n~tifAYGqTGSGKTyTM~G~~---~~~G--iipr--~~~~lF~~i~~~  121 (369)
T 3cob_A           72 VQSAVDGYNVCIFAYGQTGSGKTFTIYGAD---SNPG--LTPR--AMSELFRIMKKD  121 (369)
T ss_dssp             HHHHHTTCEEEEEEEECTTSSHHHHHTBCS---SSBC--HHHH--HHHHHHHHHHHT
T ss_pred             hHhhhcCCceEEEEECCCCCCCeEeecCCC---CCCc--hhHH--HHHHHHHHHHhh
Confidence            3445667664  568899999999875432   1122  2354  345566666543

>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=83.71  E-value=0.51  Score=36.37  Aligned_cols=20  Identities=20%  Similarity=0.167  Sum_probs=16.4

Q ss_pred             cCCCEEEEccCCCCchhhhh
Q 037567           27 EKRDCLVVMATGSGKSLCYQ   46 (374)
Q Consensus        27 ~~~~~l~~a~tGsGKT~~~~   46 (374)
                      .+..+++.|++|||||...-
T Consensus        10 ~~~~i~i~G~~GsGKst~~~   29 (180)
T 3iij_A           10 LLPNILLTGTPGVGKTTLGK   29 (180)
T ss_dssp             CCCCEEEECSTTSSHHHHHH
T ss_pred             cCCeEEEEeCCCCCHHHHHH
Confidence            45678999999999997543

>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=83.70  E-value=0.68  Score=40.95  Aligned_cols=34  Identities=24%  Similarity=0.136  Sum_probs=23.3

Q ss_pred             CchhHHHHHHH--------HHcCCCE--EEEccCCCCchhhhhc
Q 037567           14 FRPYQKDVIQR--------IIEKRDC--LVVMATGSGKSLCYQL   47 (374)
Q Consensus        14 ~~~~Q~~~~~~--------~~~~~~~--l~~a~tGsGKT~~~~l   47 (374)
                      +..-|.+.+..        +++|.++  +..|.||||||.++.-
T Consensus       131 ~~~tQ~~Vy~~~~~plV~~~l~G~N~tifAYGQTGSGKTyTM~G  174 (410)
T 1v8k_A          131 ETASNEVVYRFTARPLVQTIFEGGKATCFAYGQTGSGKTHTMGG  174 (410)
T ss_dssp             TTCCHHHHHHHTTHHHHHHHHTTCEEEEEEEESTTSSHHHHHHC
T ss_pred             cCCChhhhhHHHHHHHHHHHhcCCceeEEeecCCCCCCCeEeec
Confidence            34456666643        4566654  6688999999998754

>2jgn_A DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosphorylation, nucleotide-binding, hydrolase, RNA-binding, ATP-binding, DNA-binding, nuclear protein; 1.91A {Homo sapiens}

Probab=83.65  E-value=1.8  Score=33.51  Aligned_cols=73  Identities=14%  Similarity=0.023  Sum_probs=46.5

Q ss_pred             cCCcEEEEcchHHHHHHHHHHHHHcCCceEEcCCCCCchhh---hhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCcc
Q 037567           52 TGKTALVVSPLISLMQDQVMSLKQRGINAEFLGSAQTDSSV---QTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVC  128 (374)
Q Consensus        52 ~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~  128 (374)
                      ...++||+++++..+..+.+.+...|..+..+++.......   ......+...|+|+|. .+.       ..+....++
T Consensus        45 ~~~k~lVF~~~~~~~~~l~~~L~~~g~~~~~lhg~~~~~~r~~~~~~f~~g~~~vLvaT~-~~~-------~Gldi~~~~  116 (185)
T 2jgn_A           45 KDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILVATA-VAA-------RGLDISNVK  116 (185)
T ss_dssp             CCSCEEEEESCHHHHHHHHHHHHHTTCCEEEEC--------CHHHHHHHHTSSSEEEEEC--------------CCCSBS
T ss_pred             CCCeEEEEECCHHHHHHHHHHHHHcCCceEEEeCCCCHHHHHHHHHHHHcCCCeEEEEcC-hhh-------cCCCcccCC
Confidence            46789999999999999999999999988888776544332   2233456788999993 221       334455667


Q ss_pred             EEEE
Q 037567          129 LFAV  132 (374)
Q Consensus       129 ~vvi  132 (374)
                      +||.
T Consensus       117 ~VI~  120 (185)
T 2jgn_A          117 HVIN  120 (185)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            6665

>2j37_W Signal recognition particle 54 kDa protein (SRP54); ribosome, SRP, translation/RNA; 8.00A {Canis SP} PDB: 1wgw_A

Probab=83.64  E-value=4  Score=37.26  Aligned_cols=32  Identities=19%  Similarity=0.181  Sum_probs=21.1

Q ss_pred             CEEEEccCCCCchhhhhccc--c-ccCCcEEEEcc
Q 037567           30 DCLVVMATGSGKSLCYQLPP--L-VTGKTALVVSP   61 (374)
Q Consensus        30 ~~l~~a~tGsGKT~~~~l~~--~-~~~~~~lil~P   61 (374)
                      .+++.+++|+|||.+....+  + ..+.+++++..
T Consensus       103 vI~ivG~~GvGKTTl~~kLA~~l~~~G~kVllVd~  137 (504)
T 2j37_W          103 VIMFVGLQGSGKTTTCSKLAYYYQRKGWKTCLICA  137 (504)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEec
Confidence            36788999999996543222  1 23667777765

>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=83.60  E-value=0.7  Score=40.97  Aligned_cols=27  Identities=26%  Similarity=0.333  Sum_probs=20.1

Q ss_pred             HHHHHHcCCCE--EEEccCCCCchhhhhc
Q 037567           21 VIQRIIEKRDC--LVVMATGSGKSLCYQL   47 (374)
Q Consensus        21 ~~~~~~~~~~~--l~~a~tGsGKT~~~~l   47 (374)
                      .++.+++|.++  +..|.||||||.++.-
T Consensus       130 lv~~~l~G~n~tifAYGqTGSGKTyTM~G  158 (412)
T 3u06_A          130 LIQSALDGYNICIFAYGQTGSGKTYTMDG  158 (412)
T ss_dssp             HHHHHHTTCCEEEEEESSTTSSHHHHHTE
T ss_pred             HHHHHHCCCceEEEEecCCCCCCeeEecC
Confidence            44556677765  5688999999998753

>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=83.58  E-value=0.51  Score=40.64  Aligned_cols=20  Identities=35%  Similarity=0.473  Sum_probs=16.9

Q ss_pred             HHcCCCEEEEccCCCCchhh
Q 037567           25 IIEKRDCLVVMATGSGKSLC   44 (374)
Q Consensus        25 ~~~~~~~l~~a~tGsGKT~~   44 (374)
                      +..+..+.+.||+|||||..
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            34588999999999999964

>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=83.57  E-value=2  Score=38.67  Aligned_cols=55  Identities=15%  Similarity=0.088  Sum_probs=40.2

Q ss_pred             CCcEEEEcchHHHHHHHHHHHHHcCCceEEcCCCCCchhhhhhhhcCCeeEEEEcC
Q 037567           53 GKTALVVSPLISLMQDQVMSLKQRGINAEFLGSAQTDSSVQTKAETGYFQLLFMTP  108 (374)
Q Consensus        53 ~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~  108 (374)
                      +.+++|+||++.-++.+.+.++..+..+..+++. ...........+..+|+|+|.
T Consensus       177 ~~~~lVF~~s~~~a~~l~~~L~~~~~~v~~lhg~-~R~~~~~~F~~g~~~vLVaT~  231 (440)
T 1yks_A          177 KRPTAWFLPSIRAANVMAASLRKAGKSVVVLNRK-TFEREYPTIKQKKPDFILATD  231 (440)
T ss_dssp             CSCEEEECSCHHHHHHHHHHHHHTTCCEEECCSS-SCC--------CCCSEEEESS
T ss_pred             CCCEEEEeCCHHHHHHHHHHHHHcCCCEEEecch-hHHHHHhhhcCCCceEEEECC
Confidence            6789999999999999999999999888888873 333333444567789999994

>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=83.52  E-value=0.73  Score=40.30  Aligned_cols=34  Identities=24%  Similarity=0.311  Sum_probs=23.4

Q ss_pred             chhHHHHHHH--------HHcCCCE--EEEccCCCCchhhhhcc
Q 037567           15 RPYQKDVIQR--------IIEKRDC--LVVMATGSGKSLCYQLP   48 (374)
Q Consensus        15 ~~~Q~~~~~~--------~~~~~~~--l~~a~tGsGKT~~~~l~   48 (374)
                      ..-|.+.+..        +++|.++  +..|.||||||.++.-.
T Consensus        78 ~~~Q~~Vy~~~~~plv~~~l~G~n~tifAYGqTGSGKTyTm~G~  121 (373)
T 2wbe_C           78 ESKQCDVYSVVVSPLIEEVLNGYNCTVFAYGQTGTGKTHTMVGN  121 (373)
T ss_dssp             TCCHHHHHHHHHHHHHHHHHHTCCEEEEEECSTTSSHHHHHTBS
T ss_pred             ccchhHHHHHHHHHHHHHHhCCceEEEEeecCCCCCcceecccC
Confidence            3457666654        3456654  66889999999987543

>3tr0_A Guanylate kinase, GMP kinase; purines, pyrimidines, nucleosides, nucleotides, transferase; HET: 5GP; 1.85A {Coxiella burnetii}

Probab=83.47  E-value=0.4  Score=37.81  Aligned_cols=19  Identities=16%  Similarity=0.293  Sum_probs=15.4

Q ss_pred             cCCCEEEEccCCCCchhhh
Q 037567           27 EKRDCLVVMATGSGKSLCY   45 (374)
Q Consensus        27 ~~~~~l~~a~tGsGKT~~~   45 (374)
                      .|.-+.+.||+|||||...
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            4666789999999999653

>1ex7_A Guanylate kinase; substrate-induced FIT, domain movement, GMP, ATP, substrate specificity, X-RAY diffraction, transferase; HET: 5GP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1ex6_A* 1gky_A* 3sqk_A 4f4j_A

Probab=83.38  E-value=0.53  Score=36.70  Aligned_cols=16  Identities=31%  Similarity=0.468  Sum_probs=13.8

Q ss_pred             CCEEEEccCCCCchhh
Q 037567           29 RDCLVVMATGSGKSLC   44 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~   44 (374)
                      +.+++.||+|+|||..
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            4689999999999964

>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=83.21  E-value=0.61  Score=41.96  Aligned_cols=40  Identities=33%  Similarity=0.414  Sum_probs=29.5

Q ss_pred             CCCEEEEccCCCCchhhh--hcc-ccccCCcEEEEcchHHHHH
Q 037567           28 KRDCLVVMATGSGKSLCY--QLP-PLVTGKTALVVSPLISLMQ   67 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~--~l~-~~~~~~~~lil~P~~~l~~   67 (374)
                      ..++++.|+||||||...  ++. ++..+..++|+=|..+...
T Consensus        53 ~~h~~i~G~tGsGKs~~~~~li~~~~~~g~~viv~Dpkge~~~   95 (437)
T 1e9r_A           53 PRHLLVNGATGTGKSVLLRELAYTGLLRGDRMVIVDPNGDMLS   95 (437)
T ss_dssp             GGCEEEEECTTSSHHHHHHHHHHHHHHTTCEEEEEEETTHHHH
T ss_pred             cceEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEeCCCchhH
Confidence            467899999999999764  222 2335778888888877764

>1ly1_A Polynucleotide kinase; PNK, phosphatase, transferase; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.1

Probab=83.07  E-value=0.46  Score=36.51  Aligned_cols=16  Identities=38%  Similarity=0.326  Sum_probs=13.3

Q ss_pred             CEEEEccCCCCchhhh
Q 037567           30 DCLVVMATGSGKSLCY   45 (374)
Q Consensus        30 ~~l~~a~tGsGKT~~~   45 (374)
                      -+++.|++|||||..+
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            3678999999999754

>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=83.05  E-value=0.41  Score=37.66  Aligned_cols=18  Identities=28%  Similarity=0.255  Sum_probs=14.3

Q ss_pred             CCCEEEEccCCCCchhhh
Q 037567           28 KRDCLVVMATGSGKSLCY   45 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~   45 (374)
                      ++.+++.||||+|||..+
T Consensus        34 g~~ilI~GpsGsGKStLA   51 (205)
T 2qmh_A           34 GLGVLITGDSGVGKSETA   51 (205)
T ss_dssp             TEEEEEECCCTTTTHHHH
T ss_pred             CEEEEEECCCCCCHHHHH
Confidence            455789999999999543

>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=82.97  E-value=0.49  Score=36.76  Aligned_cols=18  Identities=22%  Similarity=0.300  Sum_probs=15.2

Q ss_pred             CCCEEEEccCCCCchhhh
Q 037567           28 KRDCLVVMATGSGKSLCY   45 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~   45 (374)
                      +..+++.|++|||||...
T Consensus        10 ~~~I~l~G~~GsGKSTv~   27 (184)
T 1y63_A           10 GINILITGTPGTGKTSMA   27 (184)
T ss_dssp             SCEEEEECSTTSSHHHHH
T ss_pred             CCEEEEECCCCCCHHHHH
Confidence            556899999999999754

>2c9o_A RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-binding, chromatin regulator, growth regulation, hydrolase, nuclear protein, DNA recombination; HET: ADP; 2.2A {Homo sapiens} PDB: 2xsz_A*

Probab=82.88  E-value=0.44  Score=43.17  Aligned_cols=18  Identities=28%  Similarity=0.373  Sum_probs=15.3

Q ss_pred             CCEEEEccCCCCchhhhh
Q 037567           29 RDCLVVMATGSGKSLCYQ   46 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~~   46 (374)
                      +++++.||+|+|||..+.
T Consensus        64 ~~iLl~GppGtGKT~la~   81 (456)
T 2c9o_A           64 RAVLLAGPPGTGKTALAL   81 (456)
T ss_dssp             CEEEEECCTTSSHHHHHH
T ss_pred             CeEEEECCCcCCHHHHHH
Confidence            579999999999997643

>2owm_A Nckin3-434, related to kinesin-like protein KIF1C; motor domain, ADP, NECK linker, motor PR; HET: ADP; 3.25A {Neurospora crassa}

Probab=82.84  E-value=0.88  Score=40.78  Aligned_cols=53  Identities=23%  Similarity=0.246  Sum_probs=32.1

Q ss_pred             hhHHHHHHH--------HHcCCCE--EEEccCCCCchhhhhccccccCCcEEEEcchHHHHHHHHHHHHH
Q 037567           16 PYQKDVIQR--------IIEKRDC--LVVMATGSGKSLCYQLPPLVTGKTALVVSPLISLMQDQVMSLKQ   75 (374)
Q Consensus        16 ~~Q~~~~~~--------~~~~~~~--l~~a~tGsGKT~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~   75 (374)
                      .-|.+.+..        +++|.++  +..|.||||||.++.-.-   ...-  +.|+  .+.+++..+..
T Consensus       115 asQ~~Vy~~~~~plv~~~l~GyN~tIfAYGQTGSGKTyTM~G~~---~~~G--Iipr--~~~~lF~~i~~  177 (443)
T 2owm_A          115 ATQEHVYDSLGEEFLDHNFEGYHTCIFAYGQTGSGKSYTMMGTP---DQPG--LIPR--TCEDLFQRIAS  177 (443)
T ss_dssp             CCHHHHHHHHHHHHHHHHHTTCCEEEEEESSTTSSHHHHHTCCT---TSCC--HHHH--HHHHHHHHHHH
T ss_pred             CCHHHHHHhhhhhHHHHhhcCCceEEEEeCCCCCCCCEEeecCC---CCCc--hHHH--HHHHHHHHHHh
Confidence            457776654        3567654  668899999999875431   1122  2354  35556666654

>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=82.69  E-value=0.64  Score=40.77  Aligned_cols=40  Identities=23%  Similarity=0.373  Sum_probs=27.2

Q ss_pred             cCCCC---CchhHHHHHHH--------HHcCCCE--EEEccCCCCchhhhhcc
Q 037567            9 FGYSV---FRPYQKDVIQR--------IIEKRDC--LVVMATGSGKSLCYQLP   48 (374)
Q Consensus         9 ~~~~~---~~~~Q~~~~~~--------~~~~~~~--l~~a~tGsGKT~~~~l~   48 (374)
                      |.|+.   +..-|.+.+..        +++|.++  +..|.||||||.++.-.
T Consensus        67 f~FD~Vf~~~~tQ~~Vy~~~~~plv~~~l~G~N~tifAYGqTGSGKTyTM~G~  119 (388)
T 3bfn_A           67 YQFDAFYGERSTQQDIYAGSVQPILRHLLEGQNASVLAYGPTGAGKTHTMLGS  119 (388)
T ss_dssp             EECSEEECTTCCHHHHHHHHTGGGHHHHTTTCCEEEEEESCTTSSHHHHHTBC
T ss_pred             EEcceEecCCCCHhHHHHHHHHHHHHHhhcCceeeEeeecCCCCCCCeEeecC
Confidence            44553   44568887764        3456654  56899999999987543

>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=82.66  E-value=0.49  Score=36.03  Aligned_cols=16  Identities=13%  Similarity=-0.222  Sum_probs=13.3

Q ss_pred             CEEEEccCCCCchhhh
Q 037567           30 DCLVVMATGSGKSLCY   45 (374)
Q Consensus        30 ~~l~~a~tGsGKT~~~   45 (374)
                      .+++.|++|||||...
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            3688999999999754

>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=82.60  E-value=0.79  Score=40.20  Aligned_cols=34  Identities=24%  Similarity=0.136  Sum_probs=22.8

Q ss_pred             CchhHHHHHHH--------HHcCCCE--EEEccCCCCchhhhhc
Q 037567           14 FRPYQKDVIQR--------IIEKRDC--LVVMATGSGKSLCYQL   47 (374)
Q Consensus        14 ~~~~Q~~~~~~--------~~~~~~~--l~~a~tGsGKT~~~~l   47 (374)
                      +..-|.+.+..        +++|.++  +..|.||||||.++.-
T Consensus       111 ~~~sQ~~Vy~~~~~plv~~~l~G~N~tifAYGQTGSGKTyTM~G  154 (387)
T 2heh_A          111 ETASNEVVYRFTARPLVQTIFEGGKATCFAYGQTGSGKTHTMGG  154 (387)
T ss_dssp             TTCCHHHHHHHTTHHHHHHHHTTCEEEEEEESCTTSSHHHHHC-
T ss_pred             cCCCceeehhhhHHHHHHHHhcCCceEEEEecCCCCCCCeEecc
Confidence            34456666653        4566654  6688999999998654

>2j41_A Guanylate kinase; GMP, GMK, transferase, ATP-binding, nucleotide- binding; HET: 5GP; 1.9A {Staphylococcus aureus}

Probab=82.53  E-value=0.46  Score=37.50  Aligned_cols=19  Identities=16%  Similarity=0.114  Sum_probs=15.5

Q ss_pred             cCCCEEEEccCCCCchhhh
Q 037567           27 EKRDCLVVMATGSGKSLCY   45 (374)
Q Consensus        27 ~~~~~l~~a~tGsGKT~~~   45 (374)
                      .+.-+.+.||+|||||...
T Consensus         5 ~g~~i~l~G~~GsGKSTl~   23 (207)
T 2j41_A            5 KGLLIVLSGPSGVGKGTVR   23 (207)
T ss_dssp             CCCEEEEECSTTSCHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            4666789999999999654

>2ze6_A Isopentenyl transferase; crown GALL tumor, cytokinin biosynthesis; HET: DST AMP; 2.10A {Agrobacterium tumefaciens} PDB: 2ze5_A* 2ze7_A* 2ze8_A

Probab=82.51  E-value=0.48  Score=39.03  Aligned_cols=15  Identities=33%  Similarity=0.189  Sum_probs=12.8

Q ss_pred             EEEEccCCCCchhhh
Q 037567           31 CLVVMATGSGKSLCY   45 (374)
Q Consensus        31 ~l~~a~tGsGKT~~~   45 (374)
                      +++.||||||||..+
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            578999999999654

>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=82.49  E-value=5.1  Score=31.28  Aligned_cols=72  Identities=17%  Similarity=0.125  Sum_probs=49.0

Q ss_pred             CCCcEEEEecchhHHHHHHHHHHHc-----CCceeeeecCCChHHHHHHHHhhhcCCeeEEEEec-cc----cc-ccccc
Q 037567          227 GAGSIIVYCMTIKDVEEISKALKQL-----GVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATM-AF----GM-GIDKP  295 (374)
Q Consensus       227 ~~~~~lVf~~~~~~~~~l~~~l~~~-----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~-~~----~~-G~d~~  295 (374)
                      .+.+++|.+|++.-+..+++.+++.     +..+..++|+.+..+....   + .+..+|+|+|+ .+    .. .+++.
T Consensus        70 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~---~-~~~~~i~v~T~~~l~~~~~~~~~~~~  145 (206)
T 1vec_A           70 DNIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMR---L-DDTVHVVIATPGRILDLIKKGVAKVD  145 (206)
T ss_dssp             CSCCEEEECSCHHHHHHHHHHHHHHTTTSSSCCEEEECSSSCHHHHHHH---T-TSCCSEEEECHHHHHHHHHTTCSCCT
T ss_pred             CCeeEEEEeCcHHHHHHHHHHHHHHHhhcCCceEEEEeCCccHHHHHHh---c-CCCCCEEEeCHHHHHHHHHcCCcCcc
Confidence            3457999999999999998888764     5667788888765543322   2 24568999997 22    22 23455


Q ss_pred             CccEEEE
Q 037567          296 DVRHVIH  302 (374)
Q Consensus       296 ~~~~vi~  302 (374)
                      +++++|.
T Consensus       146 ~~~~lVi  152 (206)
T 1vec_A          146 HVQMIVL  152 (206)
T ss_dssp             TCCEEEE
T ss_pred             cCCEEEE
Confidence            6777664

>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=82.42  E-value=2.9  Score=33.54  Aligned_cols=70  Identities=11%  Similarity=0.169  Sum_probs=50.4

Q ss_pred             CCCcEEEEecchhHHHHHHHHHHHc-----CCceeeeecCCChHHHHHHHHhhhcCCeeEEEEecc-cc-----cccccc
Q 037567          227 GAGSIIVYCMTIKDVEEISKALKQL-----GVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMA-FG-----MGIDKP  295 (374)
Q Consensus       227 ~~~~~lVf~~~~~~~~~l~~~l~~~-----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~-~~-----~G~d~~  295 (374)
                      .+.+++|.+|++.-+.++++.+++.     +..+..++|+.+..+....+     ...+|+|+|+- +.     ..+++.
T Consensus        91 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~-----~~~~Iiv~Tp~~l~~~~~~~~~~~~  165 (230)
T 2oxc_A           91 LSTQILILAPTREIAVQIHSVITAIGIKMEGLECHVFIGGTPLSQDKTRL-----KKCHIAVGSPGRIKQLIELDYLNPG  165 (230)
T ss_dssp             CSCCEEEECSSHHHHHHHHHHHHHHTTTSTTCCEEEECTTSCHHHHHHHT-----TSCSEEEECHHHHHHHHHTTSSCGG
T ss_pred             CCceEEEEeCCHHHHHHHHHHHHHHhcccCCceEEEEeCCCCHHHHHHhc-----cCCCEEEECHHHHHHHHhcCCcccc
Confidence            4568999999999999999988874     56788889988766554432     24689999982 21     234555


Q ss_pred             CccEEE
Q 037567          296 DVRHVI  301 (374)
Q Consensus       296 ~~~~vi  301 (374)
                      +++++|
T Consensus       166 ~~~~lV  171 (230)
T 2oxc_A          166 SIRLFI  171 (230)
T ss_dssp             GCCEEE
T ss_pred             cCCEEE
Confidence            666666

>1z6g_A Guanylate kinase; structural genomics, SGC, structural genom consortium, transferase; HET: EPE; 2.18A {Plasmodium falciparum}

Probab=82.31  E-value=0.62  Score=37.38  Aligned_cols=21  Identities=14%  Similarity=0.161  Sum_probs=16.1

Q ss_pred             HHcCCCEEEEccCCCCchhhh
Q 037567           25 IIEKRDCLVVMATGSGKSLCY   45 (374)
Q Consensus        25 ~~~~~~~l~~a~tGsGKT~~~   45 (374)
                      +..|+-+.+.||+|+|||...
T Consensus        20 i~~G~~~~lvGpsGsGKSTLl   40 (218)
T 1z6g_A           20 MNNIYPLVICGPSGVGKGTLI   40 (218)
T ss_dssp             --CCCCEEEECSTTSSHHHHH
T ss_pred             cCCCCEEEEECCCCCCHHHHH
Confidence            345778899999999999653

>3t0q_A AGR253WP; kinesin, alpha and beta proteins, P-loop containing nucleosi triphosphate hydrolases, microtubule motor protein; HET: ADP; 2.35A {Ashbya gossypii}

Probab=81.83  E-value=0.65  Score=40.25  Aligned_cols=32  Identities=19%  Similarity=0.316  Sum_probs=21.7

Q ss_pred             chhHHHHHHH-------HHcCCCE--EEEccCCCCchhhhh
Q 037567           15 RPYQKDVIQR-------IIEKRDC--LVVMATGSGKSLCYQ   46 (374)
Q Consensus        15 ~~~Q~~~~~~-------~~~~~~~--l~~a~tGsGKT~~~~   46 (374)
                      ..-|.+.+..       +++|.++  +..|.||||||.++.
T Consensus        64 ~~~Q~~vf~~v~~lv~~~l~G~n~tifAYGqTGSGKTyTm~  104 (349)
T 3t0q_A           64 SHTNKEIFEEIRQLVQSSLDGYNVCIFAYGQTGSGKTYTML  104 (349)
T ss_dssp             TCCHHHHHHHHHHHHHGGGTTCEEEEEEECSTTSSHHHHHH
T ss_pred             CccHHHHHHHHHHHHHHHHCCcceeEEEeCCCCCCCceEeC
Confidence            3456655544       3456654  668999999999875

>4gp7_A Metallophosphoesterase; polynucleotide kinase phosphatase, RNA repair, transferase; HET: ATP CIT; 2.00A {Clostridium thermocellum} PDB: 4gp6_A*

Probab=81.69  E-value=0.47  Score=36.36  Aligned_cols=19  Identities=26%  Similarity=0.308  Sum_probs=15.0

Q ss_pred             CCCEEEEccCCCCchhhhh
Q 037567           28 KRDCLVVMATGSGKSLCYQ   46 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~   46 (374)
                      |.-+.+.||+|||||..+-
T Consensus         9 gei~~l~G~nGsGKSTl~~   27 (171)
T 4gp7_A            9 LSLVVLIGSSGSGKSTFAK   27 (171)
T ss_dssp             SEEEEEECCTTSCHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHH
Confidence            4557899999999997543

>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=81.64  E-value=0.57  Score=40.07  Aligned_cols=17  Identities=24%  Similarity=0.255  Sum_probs=14.9

Q ss_pred             CCEEEEccCCCCchhhh
Q 037567           29 RDCLVVMATGSGKSLCY   45 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~   45 (374)
                      ..+++.||+|+|||..+
T Consensus        39 ~~vll~G~~GtGKT~la   55 (324)
T 1hqc_A           39 EHLLLFGPPGLGKTTLA   55 (324)
T ss_dssp             CCCEEECCTTCCCHHHH
T ss_pred             CcEEEECCCCCCHHHHH
Confidence            67899999999999754

>3cm0_A Adenylate kinase; ATP-binding, cytoplasm, nucleotide biosynthesis, nucleotide-binding, transferase, structural genomics; 1.80A {Thermus thermophilus}

Probab=81.48  E-value=0.4  Score=37.17  Aligned_cols=19  Identities=16%  Similarity=0.246  Sum_probs=15.1

Q ss_pred             CCCEEEEccCCCCchhhhh
Q 037567           28 KRDCLVVMATGSGKSLCYQ   46 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~   46 (374)
                      +..+++.|++|||||...-
T Consensus         4 g~~I~l~G~~GsGKST~~~   22 (186)
T 3cm0_A            4 GQAVIFLGPPGAGKGTQAS   22 (186)
T ss_dssp             EEEEEEECCTTSCHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHH
Confidence            4457899999999997543

>4fcw_A Chaperone protein CLPB; AAA domain; HET: ADP; 2.35A {Thermus thermophilus} PDB: 4fcv_A* 4fd2_A* 4fct_A*

Probab=81.47  E-value=0.68  Score=39.30  Aligned_cols=17  Identities=29%  Similarity=0.282  Sum_probs=14.4

Q ss_pred             CCEEEEccCCCCchhhh
Q 037567           29 RDCLVVMATGSGKSLCY   45 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~   45 (374)
                      ..+++.||+|+|||..+
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            36899999999999764

>3ney_A 55 kDa erythrocyte membrane protein; structural genomics consortium, SGC, 55 kDa erythrocyte MEMB protein; 2.26A {Homo sapiens} SCOP: c.37.1.0

Probab=81.43  E-value=0.62  Score=36.67  Aligned_cols=19  Identities=21%  Similarity=0.391  Sum_probs=15.6

Q ss_pred             cCCCEEEEccCCCCchhhh
Q 037567           27 EKRDCLVVMATGSGKSLCY   45 (374)
Q Consensus        27 ~~~~~l~~a~tGsGKT~~~   45 (374)
                      .++-+++.||+|+|||...
T Consensus        18 ~g~~ivl~GPSGaGKsTL~   36 (197)
T 3ney_A           18 GRKTLVLIGASGVGRSHIK   36 (197)
T ss_dssp             SCCEEEEECCTTSSHHHHH
T ss_pred             CCCEEEEECcCCCCHHHHH
Confidence            4667889999999999653

>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=81.40  E-value=0.67  Score=40.12  Aligned_cols=32  Identities=22%  Similarity=0.380  Sum_probs=22.2

Q ss_pred             chhHHHHHHHH-------HcCCCE--EEEccCCCCchhhhh
Q 037567           15 RPYQKDVIQRI-------IEKRDC--LVVMATGSGKSLCYQ   46 (374)
Q Consensus        15 ~~~Q~~~~~~~-------~~~~~~--l~~a~tGsGKT~~~~   46 (374)
                      ..-|.+.+..+       ++|.++  +..|.||||||.++.
T Consensus        63 ~~~Q~~Vy~~v~~lv~~~l~G~n~tifAYGqTGSGKTyTM~  103 (347)
T 1f9v_A           63 QDTNVDVFKEVGQLVQSSLDGYNVCIFAYGQTGSGKTFTML  103 (347)
T ss_dssp             TCCHHHHHHHHHHHHGGGGGTCCEEEEEECCTTSSHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHhcCCceeEEEEECCCCCCCcEecc
Confidence            34566666543       456654  668999999999875

>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=81.39  E-value=13  Score=30.03  Aligned_cols=71  Identities=10%  Similarity=0.046  Sum_probs=48.9

Q ss_pred             CCcEEEEecchhHHHHHHHHHHHc----CCceeeeecCCChHHHHHHHHhhhcCCeeEEEEec-ccc-----ccccccCc
Q 037567          228 AGSIIVYCMTIKDVEEISKALKQL----GVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATM-AFG-----MGIDKPDV  297 (374)
Q Consensus       228 ~~~~lVf~~~~~~~~~l~~~l~~~----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~-~~~-----~G~d~~~~  297 (374)
                      +.++||.+|++.-+..+++.+++.    +..+..++|+.+.......+    ....+|+|+|+ .+.     ..+++..+
T Consensus       100 ~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~----~~~~~Ivv~Tp~~l~~~l~~~~~~~~~~  175 (253)
T 1wrb_A          100 YPKCLILAPTRELAIQILSESQKFSLNTPLRSCVVYGGADTHSQIREV----QMGCHLLVATPGRLVDFIEKNKISLEFC  175 (253)
T ss_dssp             CCSEEEECSSHHHHHHHHHHHHHHHTTSSCCEEEECSSSCSHHHHHHH----SSCCSEEEECHHHHHHHHHTTSBCCTTC
T ss_pred             CceEEEEECCHHHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHHh----CCCCCEEEECHHHHHHHHHcCCCChhhC
Confidence            468999999999999998888764    45677788887655433322    24568999997 222     23456667


Q ss_pred             cEEEE
Q 037567          298 RHVIH  302 (374)
Q Consensus       298 ~~vi~  302 (374)
                      +++|.
T Consensus       176 ~~lVi  180 (253)
T 1wrb_A          176 KYIVL  180 (253)
T ss_dssp             CEEEE
T ss_pred             CEEEE
Confidence            77664

>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=81.36  E-value=0.57  Score=39.79  Aligned_cols=16  Identities=25%  Similarity=0.146  Sum_probs=13.2

Q ss_pred             CEEEEccCCCCchhhh
Q 037567           30 DCLVVMATGSGKSLCY   45 (374)
Q Consensus        30 ~~l~~a~tGsGKT~~~   45 (374)
                      -++|.||||+|||..+
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

>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=81.29  E-value=0.61  Score=36.98  Aligned_cols=22  Identities=18%  Similarity=0.098  Sum_probs=16.3

Q ss_pred             HHHcCCCEEEEccCCCCchhhh
Q 037567           24 RIIEKRDCLVVMATGSGKSLCY   45 (374)
Q Consensus        24 ~~~~~~~~l~~a~tGsGKT~~~   45 (374)
                      .+..|.-+.+.||.|+|||...
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            5566788889999999999653

>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=81.06  E-value=0.63  Score=37.39  Aligned_cols=22  Identities=23%  Similarity=0.303  Sum_probs=16.1

Q ss_pred             HHHcCCCEEEEccCCCCchhhh
Q 037567           24 RIIEKRDCLVVMATGSGKSLCY   45 (374)
Q Consensus        24 ~~~~~~~~l~~a~tGsGKT~~~   45 (374)
                      .+-.|.-+.+.||.|+|||...
T Consensus        12 ~~~~G~ii~l~GpsGsGKSTLl   33 (219)
T 1s96_A           12 HMAQGTLYIVSAPSGAGKSSLI   33 (219)
T ss_dssp             ---CCCEEEEECCTTSCHHHHH
T ss_pred             cCCCCcEEEEECCCCCCHHHHH
Confidence            3456777899999999999653

>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=80.96  E-value=0.6  Score=39.56  Aligned_cols=16  Identities=25%  Similarity=0.260  Sum_probs=13.2

Q ss_pred             CEEEEccCCCCchhhh
Q 037567           30 DCLVVMATGSGKSLCY   45 (374)
Q Consensus        30 ~~l~~a~tGsGKT~~~   45 (374)
                      -+++.||||||||..+
T Consensus        12 ~i~i~GptgsGKt~la   27 (316)
T 3foz_A           12 AIFLMGPTASGKTALA   27 (316)
T ss_dssp             EEEEECCTTSCHHHHH
T ss_pred             EEEEECCCccCHHHHH
Confidence            3678999999999654

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens}

Probab=80.92  E-value=0.69  Score=38.62  Aligned_cols=17  Identities=29%  Similarity=0.405  Sum_probs=14.4

Q ss_pred             CCEEEEccCCCCchhhh
Q 037567           29 RDCLVVMATGSGKSLCY   45 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~   45 (374)
                      +.+++.||+|+|||..+
T Consensus        45 ~GvlL~Gp~GtGKTtLa   61 (274)
T 2x8a_A           45 AGVLLAGPPGCGKTLLA   61 (274)
T ss_dssp             SEEEEESSTTSCHHHHH
T ss_pred             CeEEEECCCCCcHHHHH
Confidence            45899999999999754

>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=80.78  E-value=0.75  Score=40.23  Aligned_cols=40  Identities=23%  Similarity=0.316  Sum_probs=26.3

Q ss_pred             cCCCC---CchhHHHHHHHH-------HcCCCE--EEEccCCCCchhhhhcc
Q 037567            9 FGYSV---FRPYQKDVIQRI-------IEKRDC--LVVMATGSGKSLCYQLP   48 (374)
Q Consensus         9 ~~~~~---~~~~Q~~~~~~~-------~~~~~~--l~~a~tGsGKT~~~~l~   48 (374)
                      |.|+.   +..-|.+.+..+       ++|.++  +..|.||||||.++.-.
T Consensus        85 F~FD~Vf~~~~~Q~~Vy~~v~~lv~~~l~G~N~tifAYGqTGSGKTyTM~G~  136 (376)
T 2rep_A           85 FSFDRVFPPGSGQDEVFEEIAMLVQSALDGYPVCIFAYGQTGSGKTFTMEGG  136 (376)
T ss_dssp             EECSEEECTTCCHHHHHHHHHHHHHGGGGTCCEEEEEECSTTSSHHHHHTBC
T ss_pred             eeecEEcCCcccchhhhhhHHHHHHHhcCCCceEEEEeCCCCCCCceEeecC
Confidence            55553   344677666543       356654  66889999999987543

>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=80.64  E-value=7.4  Score=31.28  Aligned_cols=73  Identities=12%  Similarity=0.142  Sum_probs=43.7

Q ss_pred             CCCcEEEEecchhHHHHHHHHHHHc----CCceeeeecCCChHHHHHHHHhhhcCCeeEEEEec-----cccc-cccccC
Q 037567          227 GAGSIIVYCMTIKDVEEISKALKQL----GVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATM-----AFGM-GIDKPD  296 (374)
Q Consensus       227 ~~~~~lVf~~~~~~~~~l~~~l~~~----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~-----~~~~-G~d~~~  296 (374)
                      .+.+++|.+|++..+..+++.+++.    +..+..++|+.+...   ....+..+..+|+|+|+     .+.. .+++..
T Consensus        97 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~---~~~~l~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~  173 (237)
T 3bor_A           97 KETQALVLAPTRELAQQIQKVILALGDYMGATCHACIGGTNVRN---EMQKLQAEAPHIVVGTPGRVFDMLNRRYLSPKW  173 (237)
T ss_dssp             CSCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECC----------------CCCSEEEECHHHHHHHHHTTSSCSTT
T ss_pred             CCceEEEEECcHHHHHHHHHHHHHHhhhcCceEEEEECCCchHH---HHHHHhcCCCCEEEECHHHHHHHHHhCCcCccc
Confidence            4568999999999999999988875    455666666654322   23344556688999995     2222 345566


Q ss_pred             ccEEEE
Q 037567          297 VRHVIH  302 (374)
Q Consensus       297 ~~~vi~  302 (374)
                      ++.+|.
T Consensus       174 ~~~lVi  179 (237)
T 3bor_A          174 IKMFVL  179 (237)
T ss_dssp             CCEEEE
T ss_pred             CcEEEE
Confidence            777664

>2xxa_A Signal recognition particle protein; protein transport, RNA/RNA binding protein, hydrolase, gtpas; HET: GCP; 3.94A {Escherichia coli} PDB: 2j28_9

Probab=80.54  E-value=3.2  Score=37.12  Aligned_cols=31  Identities=29%  Similarity=0.207  Sum_probs=19.7

Q ss_pred             CEEEEccCCCCchhhhhccc---ccc-CCcEEEEc
Q 037567           30 DCLVVMATGSGKSLCYQLPP---LVT-GKTALVVS   60 (374)
Q Consensus        30 ~~l~~a~tGsGKT~~~~l~~---~~~-~~~~lil~   60 (374)
                      .+++.+++|+|||.+..-.+   ... +.+++++.
T Consensus       102 vI~ivG~~GvGKTT~a~~LA~~l~~~~G~kVllvd  136 (433)
T 2xxa_A          102 VVLMAGLQGAGKTTSVGKLGKFLREKHKKKVLVVS  136 (433)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHHTSCCCEEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHhcCCeEEEEe
Confidence            35678999999996543222   123 66776654

>4eun_A Thermoresistant glucokinase; putative sugar kinase, enzyme function initiative, EFI, STRU genomics, transferase; 1.60A {Janibacter SP}

Probab=80.51  E-value=0.67  Score=36.49  Aligned_cols=19  Identities=32%  Similarity=0.441  Sum_probs=15.4

Q ss_pred             cCCCEEEEccCCCCchhhh
Q 037567           27 EKRDCLVVMATGSGKSLCY   45 (374)
Q Consensus        27 ~~~~~l~~a~tGsGKT~~~   45 (374)
                      .+..+++.||+|||||..+
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            3566789999999999654

>2ffh_A Protein (FFH); SRP54, signal recognition particle, GTPase, M domain, RNA-binding, signal sequence-binding, helix-turn-helix, protein targeting; 3.20A {Thermus aquaticus} SCOP: a.24.13.1 a.36.1.1 c.37.1.10 PDB: 2iy3_A

Probab=80.38  E-value=6.1  Score=35.17  Aligned_cols=31  Identities=26%  Similarity=0.279  Sum_probs=19.2

Q ss_pred             CEEEEccCCCCchhhhhccc--c-ccCCcEEEEc
Q 037567           30 DCLVVMATGSGKSLCYQLPP--L-VTGKTALVVS   60 (374)
Q Consensus        30 ~~l~~a~tGsGKT~~~~l~~--~-~~~~~~lil~   60 (374)
                      .+.+.++.|+|||.+....+  + ..+.+++++.
T Consensus       100 vi~i~G~~GsGKTT~~~~LA~~l~~~g~~Vllvd  133 (425)
T 2ffh_A          100 LWFLVGLQGSGKTTTAAKLALYYKGKGRRPLLVA  133 (425)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEee
Confidence            35678999999996543221  1 2456666654

>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=80.20  E-value=0.67  Score=35.95  Aligned_cols=19  Identities=21%  Similarity=0.281  Sum_probs=15.1

Q ss_pred             CCCEEEEccCCCCchhhhh
Q 037567           28 KRDCLVVMATGSGKSLCYQ   46 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~   46 (374)
                      +..+++.|++|||||...-
T Consensus         3 ~~~I~i~G~~GsGKsT~~~   21 (192)
T 1kht_A            3 NKVVVVTGVPGVGSTTSSQ   21 (192)
T ss_dssp             CCEEEEECCTTSCHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHH
Confidence            4557899999999997543

---

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	374
d1oywa2	206	c.37.1.19 (A:1-206) RecQ helicase domain {Escheric	3e-39
d2bmfa2	305	c.37.1.14 (A:178-482) Dengue virus helicase {Dengu	7e-33
d1a1va2	299	c.37.1.14 (A:326-624) HCV helicase domain {Human h	1e-24
d1oywa3	200	c.37.1.19 (A:207-406) RecQ helicase domain {Escher	2e-23
d1wp9a2	286	c.37.1.19 (A:201-486) putative ATP-dependent RNA h	4e-20
d1t5la2	181	c.37.1.19 (A:415-595) Nucleotide excision repair e	8e-19
d1c4oa2	174	c.37.1.19 (A:410-583) Nucleotide excision repair e	5e-18
d1gkub2	248	c.37.1.16 (B:251-498) Helicase-like "domain" of re	6e-18
d1fuka_	162	c.37.1.19 (A:) Initiation factor 4a {Baker's yeast	7e-16
d1jr6a_	138	c.37.1.14 (A:) HCV helicase domain {Human hepatiti	2e-15
d2p6ra3	202	c.37.1.19 (A:1-202) Hel308 helicase {Archaeoglobus	9e-14
d2fwra1	200	c.37.1.19 (A:257-456) DNA repair protein RAD25 {Ar	1e-13
d2p6ra4	201	c.37.1.19 (A:203-403) Hel308 helicase {Archaeoglob	9e-13
d1wp9a1	200	c.37.1.19 (A:1-200) putative ATP-dependent RNA hel	7e-12
d1gkub1	237	c.37.1.16 (B:1-250) Helicase-like "domain" of reve	1e-11
d1yksa2	299	c.37.1.14 (A:325-623) YFV helicase domain {Yellow	5e-11
d1hv8a2	155	c.37.1.19 (A:211-365) Putative DEAD box RNA helica	8e-11
d2j0sa2	168	c.37.1.19 (A:244-411) Probable ATP-dependent RNA h	1e-10
d2rb4a1	168	c.37.1.19 (A:307-474) ATP-dependent RNA helicase D	9e-09
d2eyqa5	211	c.37.1.19 (A:779-989) Transcription-repair couplin	1e-08
d2fz4a1	206	c.37.1.19 (A:24-229) DNA repair protein RAD25 {Arc	1e-08
d1gm5a4	206	c.37.1.19 (A:550-755) RecG helicase domain {Thermo	7e-08
d1tf5a4	175	c.37.1.19 (A:396-570) Translocation ATPase SecA, n	2e-06
d1veca_	206	c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Huma	5e-04
d1t5ia_	168	c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP5	6e-04
d1s2ma2	171	c.37.1.19 (A:252-422) Putative ATP-dependent RNA h	0.001
d2g9na1	218	c.37.1.19 (A:21-238) Initiation factor 4a {Human (	0.002
d1qdea_	212	c.37.1.19 (A:) Initiation factor 4a {Baker's yeast	0.003

>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 =  136 bits (343), Expect = 3e-39
 Identities = 87/193 (45%), Positives = 114/193 (59%), Gaps = 5/193 (2%)

Query: 4   TLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVTGKTALVVSPLI 63
            L++ FGY  FRP Q+++I  ++  RDCLVVM TG GKSLCYQ+P L+     +VVSPLI
Sbjct: 16  VLQETFGYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPALLLNGLTVVVSPLI 75

Query: 64  SLMQDQVMSLKQRGINAEFLGSAQTDSSVQTKAET---GYFQLLFMTPEKACIIPISFWS 120
           SLM+DQV  L+  G+ A  L S QT             G  +LL++ PE+  +       
Sbjct: 76  SLMKDQVDQLQANGVAAACLNSTQTREQQLEVMTGCRTGQIRLLYIAPERLMLDNFLEHL 135

Query: 121 KLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEKVRIDII 180
                   L AVDEAHCIS+WGHDFR EY  L +LR     +PF+ALTATA +  R DI+
Sbjct: 136 AHWN--PVLLAVDEAHCISQWGHDFRPEYAALGQLRQRFPTLPFMALTATADDTTRQDIV 193

Query: 181 NSLKLKNPYVTIA 193
             L L +P + I+
Sbjct: 194 RLLGLNDPLIQIS 206

>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 =  122 bits (307), Expect = 7e-33
 Identities = 48/335 (14%), Positives = 98/335 (29%), Gaps = 59/335 (17%)

Query: 18  QKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV-----TGKTALVVSPLISLMQDQVMS 72
           + D+ +   +KR  ++ +  G+GK+  Y LP +V      G   L+++P   +  +   +
Sbjct: 2   EDDIFR---KKRLTIMDLHPGAGKTKRY-LPAIVREAIKRGLRTLILAPTRVVAAEMEEA 57

Query: 73  LKQRGINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAV 132
           L+   I        +  +       TG   +  M         +   S +      L  +
Sbjct: 58  LRGLPI--------RYQTPAIRAEHTGREIVDLMCHA---TFTMRLLSPIRVPNYNLIIM 106

Query: 133 DEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEKVRIDIINSLKLKNPYVTI 192
           DEAH         R       ++         + +TAT          ++  + +    I
Sbjct: 107 DEAHFTDPASIAARGYISTRVEMGEAAG----IFMTATPPGSRDPFPQSNAPIMDEEREI 162

Query: 193 ASFDRKNLFYGVKVINRGQSFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLG 252
                 +    V                        G  + +  +IK   +I+  L++ G
Sbjct: 163 PERSWNSGHEWVTDFK--------------------GKTVWFVPSIKAGNDIAACLRKNG 202

Query: 253 VKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDK---------------PDV 297
            K      +       +         +   ++ M      ++                + 
Sbjct: 203 KKVIQLSRKTFDSEYIKTRTNDWDFVVTTDISEMGANFKAERVIDPRRCMKPVILTDGEE 262

Query: 298 RHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYY 332
           R ++    P T  S  Q  GR GR+         Y
Sbjct: 263 RVILAGPMPVTHSSAAQRRGRVGRNPKNENDQYIY 297

>d1a1va2 c.37.1.14 (A:326-624) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]} Length = 299

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]

 Score =   99 bits (249), Expect = 1e-24
 Identities = 22/131 (16%), Positives = 39/131 (29%), Gaps = 15/131 (11%)

Query: 211 QSFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHG---------- 260
              +    + I   V   G  +++C + K  +E++  L  LG+ A  Y+           
Sbjct: 19  TGEIPFYGKAIPLEVIKGGRHLIFCHSKKKCDELAAKLVALGINAVAYYRGLDVSVIPTS 78

Query: 261 QMGSKAREEAHRLFIRDEIRVMVAT--MAFGMGIDKPD-VRHVIHYGCPKTLESYYQESG 317
                   +A       +   ++              D    +     P+   S  Q  G
Sbjct: 79  GDVVVVATDALMTGFTGDFDSVIDCNTCVTQTVDFSLDPTFTIETTTLPQDAVSRTQRRG 138

Query: 318 RCGR--DGIAS 326
           R GR   GI  
Sbjct: 139 RTGRGKPGIYR 149

>d1oywa3 c.37.1.19 (A:207-406) RecQ helicase domain {Escherichia coli [TaxId: 562]} 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: RecQ helicase domain
species: Escherichia coli [TaxId: 562]

 Score = 94.3 bits (233), Expect = 2e-23
 Identities = 60/181 (33%), Positives = 98/181 (54%), Gaps = 5/181 (2%)

Query: 194 SFDRKNLFYGVKVINRGQSFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGV 253
           SFDR N+ Y   ++ + +    + +   ++   G  S I+YC +   VE+ +  L+  G+
Sbjct: 1   SFDRPNIRY--MLMEKFKPL--DQLMRYVQEQRG-KSGIIYCNSRAKVEDTAARLQSKGI 55

Query: 254 KAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYY 313
            A  YH  + +  R +    F RD+++++VAT+AFGMGI+KP+VR V+H+  P+ +ESYY
Sbjct: 56  SAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGMGINKPNVRFVVHFDIPRNIESYY 115

Query: 314 QESGRCGRDGIASVCWLYYARSNFAKGDFYCGESQTENQRTAIMESLLAAQRYCLLTTCR 373
           QE+GR GRDG+ +   L+Y  ++ A       E      +      L A   +    TCR
Sbjct: 116 QETGRAGRDGLPAEAMLFYDPADMAWLRRCLEEKPQGQLQDIERHKLNAMGAFAEAQTCR 175

Query: 374 R 374
           R
Sbjct: 176 R 176

>d1wp9a2 c.37.1.19 (A:201-486) putative ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]} Length = 286

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 = 87.3 bits (215), Expect = 4e-20
 Identities = 33/127 (25%), Positives = 54/127 (42%), Gaps = 9/127 (7%)

Query: 214 VDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQ--------MGSK 265
           + E+++E L+       IIV+    +  ++I   L + G+KA  + GQ        +  +
Sbjct: 148 LKEIIREQLQRKQN-SKIIVFTNYRETAKKIVNELVKDGIKAKRFVGQASKENDRGLSQR 206

Query: 266 AREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIA 325
            ++     F R E  V+VAT     G+D P+V  V+ Y    +     Q  GR GR    
Sbjct: 207 EQKLILDEFARGEFNVLVATSVGEEGLDVPEVDLVVFYEPVPSAIRSIQRRGRTGRHMPG 266

Query: 326 SVCWLYY 332
            V  L  
Sbjct: 267 RVIILMA 273

>d1t5la2 c.37.1.19 (A:415-595) Nucleotide excision repair enzyme UvrB {Bacillus caldotenax [TaxId: 1395]} Length = 181

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]

 Score = 81.0 bits (199), Expect = 8e-19
 Identities = 31/124 (25%), Positives = 51/124 (41%), Gaps = 5/124 (4%)

Query: 214 VDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRL 273
           +D+L+ EI + V      +V  +T K  E+++  LK+ G+K    H ++ +  R E  R 
Sbjct: 17  IDDLIGEIRERVERNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRD 76

Query: 274 FIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPK-----TLESYYQESGRCGRDGIASVC 328
               +  V+V       G+D P+V  V      K     +  S  Q  GR  R+    V 
Sbjct: 77  LRLGKYDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNANGHVI 136

Query: 329 WLYY 332
               
Sbjct: 137 MYAD 140

>d1c4oa2 c.37.1.19 (A:410-583) Nucleotide excision repair enzyme UvrB {Thermus thermophilus [TaxId: 274]} Length = 174

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]

 Score = 78.6 bits (193), Expect = 5e-18
 Identities = 27/133 (20%), Positives = 51/133 (38%), Gaps = 7/133 (5%)

Query: 209 RGQSFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKARE 268
             Q  + +L++ I +  A     +V  +T++  EE++  L + G++A   H ++ +  R+
Sbjct: 14  ENQ--ILDLMEGIRERAARGERTLVTVLTVRMAEELTSFLVEHGIRARYLHHELDAFKRQ 71

Query: 269 EAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYG-----CPKTLESYYQESGRCGRDG 323
              R         +V       G+D P+V  V           ++  S  Q  GR  R+ 
Sbjct: 72  ALIRDLRLGHYDCLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNA 131

Query: 324 IASVCWLYYARSN 336
              V       S 
Sbjct: 132 RGEVWLYADRVSE 144

>d1gkub2 c.37.1.16 (B:251-498) Helicase-like "domain" of reverse gyrase {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} Length = 248

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 = 80.2 bits (197), Expect = 6e-18
 Identities = 26/132 (19%), Positives = 51/132 (38%), Gaps = 17/132 (12%)

Query: 216 ELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFI 275
             +  IL+ +   G  I+Y  T ++ EEI ++LK        +   + +  ++  +  F+
Sbjct: 15  STLSSILEKLGTGG--IIYARTGEEAEEIYESLKNK------FRIGIVTATKKGDYEKFV 66

Query: 276 RDEIRVMVATMAF----GMGIDKPD-VRHVIHYGCPKTLESYYQESGRCGRDGIASVCWL 330
             EI  ++ T  +      G+D P+ +R  +  GCP     +              V  L
Sbjct: 67  EGEIDHLIGTAHYYGTLVRGLDLPERIRFAVFVGCPS----FRVTIEDIDSLSPQMVKLL 122

Query: 331 YYARSNFAKGDF 342
            Y   N  + + 
Sbjct: 123 AYLYRNVDEIER 134

>d1fuka_ c.37.1.19 (A:) Initiation factor 4a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 162

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 = 72.3 bits (176), Expect = 7e-16
 Identities = 28/121 (23%), Positives = 53/121 (43%), Gaps = 1/121 (0%)

Query: 216 ELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFI 275
           E + ++  S++     +++C T + VEE++  L+         +  +  + R+   + F 
Sbjct: 16  ECLTDLYDSISV-TQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFR 74

Query: 276 RDEIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARS 335
               R++++T     GID   V  VI+Y  P   E+Y    GR GR G   V   +    
Sbjct: 75  SGSSRILISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVTNE 134

Query: 336 N 336
           +
Sbjct: 135 D 135

>d1jr6a_ c.37.1.14 (A:) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]} Length = 138

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]

 Score = 70.5 bits (172), Expect = 2e-15
 Identities = 25/111 (22%), Positives = 42/111 (37%), Gaps = 10/111 (9%)

Query: 214 VDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRL 273
           +    + I   V   G  +++C + K  +E++  L  LG+ A  Y+  +          +
Sbjct: 21  IPFYGKAIPLEVIKGGRHLIFCHSKKKCDELAAKLVALGINAVAYYRGLD-------VSV 73

Query: 274 FIRDEIRVMVATMAFGMGIDKPD---VRHVIHYGCPKTLESYYQESGRCGR 321
              +   V+VAT A   G        +      G P+   S  Q  GR GR
Sbjct: 74  IPTNGDVVVVATDALMTGFTGDFDSVIDCNTSDGKPQDAVSRTQRRGRTGR 124

>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 = 67.3 bits (163), Expect = 9e-14
 Identities = 38/173 (21%), Positives = 71/173 (41%), Gaps = 8/173 (4%)

Query: 1   MVSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQL---PPLVTGKTAL 57
            V  LK+  G     P Q + ++++   ++ L+ M T +GK+L  ++      + G  +L
Sbjct: 14  AVGILKE-EGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIKGGKSL 72

Query: 58  VVSPLISLMQDQVMSLKQRGINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPIS 117
            V PL +L  ++  S K+       +G +  D         G   ++  T EKA  +  +
Sbjct: 73  YVVPLRALAGEKYESFKKWEKIGLRIGISTGD-YESRDEHLGDCDIIVTTSEKADSLIRN 131

Query: 118 FWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTAT 170
             S +      +   DE H +        LE   + K+R     +  + L+AT
Sbjct: 132 RASWIKAVSCLVV--DEIHLLDSEKRGATLEI-LVTKMRRMNKALRVIGLSAT 181

>d2fwra1 c.37.1.19 (A:257-456) DNA repair protein RAD25 {Archaeoglobus fulgidus [TaxId: 2234]} 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: DNA repair protein RAD25
species: Archaeoglobus fulgidus [TaxId: 2234]

 Score = 66.8 bits (162), Expect = 1e-13
 Identities = 26/117 (22%), Positives = 40/117 (34%), Gaps = 6/117 (5%)

Query: 216 ELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFI 275
             ++EIL+       II++    + V  ISK              +   + REE    F 
Sbjct: 82  RKLREILERHRK-DKIIIFTRHNELVYRISK-----VFLIPAITHRTSREEREEILEGFR 135

Query: 276 RDEIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYY 332
               R +V++     GID PD    +      +   Y Q  GR  R        + Y
Sbjct: 136 TGRFRAIVSSQVLDEGIDVPDANVGVIMSGSGSAREYIQRLGRILRPSKGKKEAVLY 192

>d2p6ra4 c.37.1.19 (A:203-403) Hel308 helicase {Archaeoglobus fulgidus [TaxId: 2234]} Length = 201

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 = 64.6 bits (156), Expect = 9e-13
 Identities = 30/183 (16%), Positives = 59/183 (32%), Gaps = 43/183 (23%)

Query: 197 RKNLFYGVKVI----NRGQSFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLG 252
            + +     +         S   +  + + + VA  G ++V+  T +  E+ +  L  + 
Sbjct: 5   VEGVLCEGTLELFDGAFSTSRRVKFEELVEECVAENGGVLVFESTRRGAEKTAVKLSAIT 64

Query: 253 VK------------------------------AGTYHGQMGSKAREEAHRLFIRDEIRVM 282
            K                              A  +H  + +  R      F R  I+V+
Sbjct: 65  AKYVENEGLEKAILEENEGEMSRKLAECVRKGAAFHHAGLLNGQRRVVEDAFRRGNIKVV 124

Query: 283 VATMAFGMGIDKPDVRHVIH-------YGCPKTLESYYQESGRCGRDGI--ASVCWLYYA 333
           VAT     G++ P  R ++        Y     +  Y Q +GR GR G+       +   
Sbjct: 125 VATPTLAAGVNLPARRVIVRSLYRFDGYSKRIKVSEYKQMAGRAGRPGMDERGEAIIIVG 184

Query: 334 RSN 336
           + +
Sbjct: 185 KRD 187

>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 = 61.7 bits (148), Expect = 7e-12
 Identities = 33/192 (17%), Positives = 69/192 (35%), Gaps = 13/192 (6%)

Query: 15  RPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV----TGKTALVVSPLISLMQDQV 70
           R YQ+ +  +  E  +CL+V+ TG GK+L   +         G   L+++P   L+    
Sbjct: 11  RIYQEVIYAKCKE-TNCLIVLPTGLGKTLIAMMIAEYRLTKYGGKVLMLAPTKPLVLQHA 69

Query: 71  MSLKQRGINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLF 130
            S ++          A T      +    + +   +      I       ++    V L 
Sbjct: 70  ESFRRLFNLPPEKIVALTGEKSPEERSKAWARAKVIVATPQTIENDLLAGRISLEDVSLI 129

Query: 131 AVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEKVRI--DIINSLKLKNP 188
             DEAH          +  +   + +        + LTA+         ++IN+L +++ 
Sbjct: 130 VFDEAHRAVGNYAYVFIAREYKRQAKN----PLVIGLTASPGSTPEKIMEVINNLGIEH- 184

Query: 189 YVTIASFDRKNL 200
            +   S +  ++
Sbjct: 185 -IEYRSENSPDV 195

>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 = 61.8 bits (149), Expect = 1e-11
 Identities = 32/200 (16%), Positives = 59/200 (29%), Gaps = 19/200 (9%)

Query: 1   MVSTLKKYF--GYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV---TGKT 55
           ++    ++F       R  QK   +RI+ K        TG GK+       L     GK 
Sbjct: 29  LLKEFVEFFRKCVGEPRAIQKMWAKRILRKESFAATAPTGVGKTSFGLAMSLFLALKGKR 88

Query: 56  ALVVSPLISLMQDQVMSLKQR----GINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKA 111
             V+ P   L+     ++++     G+  E L         + + E           +  
Sbjct: 89  CYVIFPTSLLVIQAAETIRKYAEKAGVGTENLIGYYHGRIPKREKENFMQN--LRNFKIV 146

Query: 112 CIIPISFWSKLLK-AGVCLFAVDEAHCISEWGHDFRLEYKQL---DKLRTFLLGVP---- 163
                       +        VD+   I +   +       L     L+T          
Sbjct: 147 ITTTQFLSKHYRELGHFDFIFVDDVDAILKASKNVDKLLHLLGFHYDLKTKSWVGEARGC 206

Query: 164 FVALTATATEKVRIDIINSL 183
            +  TATA +  + ++   L
Sbjct: 207 LMVSTATAKKGKKAELFRQL 226

>d1yksa2 c.37.1.14 (A:325-623) YFV helicase domain {Yellow fever virus [TaxId: 11089]} Length = 299

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 = 60.8 bits (147), Expect = 5e-11
 Identities = 19/147 (12%), Positives = 41/147 (27%), Gaps = 25/147 (17%)

Query: 206 VINRGQSFVDELVQEILKSVA-GAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGS 264
           + +       E        +         +  +I+    ++ +L++ G      + +   
Sbjct: 13  IEDVQTDIPSEPWNTGHDWILADKRPTAWFLPSIRAANVMAASLRKAGKSVVVLNRKT-- 70

Query: 265 KAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYG-------------------C 305
              E  +    + +   ++AT    MG +   V  V+                       
Sbjct: 71  --FEREYPTIKQKKPDFILATDIAEMGANL-CVERVLDCRTAFKPVLVDEGRKVAIKGPL 127

Query: 306 PKTLESYYQESGRCGRDGIASVCWLYY 332
             +  S  Q  GR GR+        YY
Sbjct: 128 RISASSAAQRRGRIGRNPNRDGDSYYY 154

>d1hv8a2 c.37.1.19 (A:211-365) Putative DEAD box RNA helicase {Archaeon Methanococcus jannaschii [TaxId: 2190]} Length = 155

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 = 57.7 bits (138), Expect = 8e-11
 Identities = 42/124 (33%), Positives = 64/124 (51%), Gaps = 2/124 (1%)

Query: 216 ELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFI 275
           E +  +LK+       +V+C T +D +E++  L+ +G KAG  HG +    RE+  RLF 
Sbjct: 18  EALCRLLKN--KEFYGLVFCKTKRDTKELASMLRDIGFKAGAIHGDLSQSQREKVIRLFK 75

Query: 276 RDEIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARS 335
           + +IR+++AT     GID  D+  VI+Y  P+  ESY    GR GR G          R 
Sbjct: 76  QKKIRILIATDVMSRGIDVNDLNCVINYHLPQNPESYMHRIGRTGRAGKKGKAISIINRR 135

Query: 336 NFAK 339
            + K
Sbjct: 136 EYKK 139

>d2j0sa2 c.37.1.19 (A:244-411) Probable ATP-dependent RNA helicase DDX48 {Human (Homo sapiens) [TaxId: 9606]} Length = 168

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 = 57.3 bits (137), Expect = 1e-10
 Identities = 28/124 (22%), Positives = 56/124 (45%), Gaps = 1/124 (0%)

Query: 216 ELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFI 275
           + + ++  ++      +++C T + V+ +++ +++      + HG M  K RE   + F 
Sbjct: 23  DTLCDLYDTLTI-TQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFR 81

Query: 276 RDEIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARS 335
               RV+++T  +  G+D P V  +I+Y  P   E Y    GR GR G   V   +    
Sbjct: 82  SGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKND 141

Query: 336 NFAK 339
           +   
Sbjct: 142 DIRI 145

>d2eyqa5 c.37.1.19 (A:779-989) Transcription-repair coupling factor, TRCF {Escherichia coli [TaxId: 562]} Length = 211

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Transcription-repair coupling factor, TRCF
species: Escherichia coli [TaxId: 562]

 Score = 52.7 bits (126), Expect = 1e-08
 Identities = 30/149 (20%), Positives = 53/149 (35%), Gaps = 11/149 (7%)

Query: 215 DELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQL--GVKAGTYHGQMGSKAREEAHR 272
             + + IL+ +   G +      ++++++ ++ L +L    +    HGQM  +  E    
Sbjct: 18  MVVREAILREILRGGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMN 77

Query: 273 LFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPK-TLESYYQESGRCGRDGIASVCWLY 331
            F      V+V T     GID P    +I        L   +Q  GR GR    +  WL 
Sbjct: 78  DFHHQRFNVLVCTTIIETGIDIPTANTIIIERADHFGLAQLHQLRGRVGRSHHQAYAWLL 137

Query: 332 YARSNFAKGDFYCGESQTENQRTAIMESL 360
                          +    +R   + SL
Sbjct: 138 T--------PHPKAMTTDAQKRLEAIASL 158

>d2fz4a1 c.37.1.19 (A:24-229) DNA repair protein RAD25 {Archaeoglobus fulgidus [TaxId: 2234]} 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: DNA repair protein RAD25
species: Archaeoglobus fulgidus [TaxId: 2234]

 Score = 52.6 bits (125), Expect = 1e-08
 Identities = 26/156 (16%), Positives = 47/156 (30%), Gaps = 23/156 (14%)

Query: 15  RPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVTGKTALVVSPLISLMQDQVMSLK 74
           R YQ+  ++R +  +   +V+ TGSGK+              L+V P ++L +     L 
Sbjct: 72  RDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAAINELSTPTLIVVPTLALAEQWKERLG 131

Query: 75  QRGINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDE 134
             G                   E             +        ++ L     L   DE
Sbjct: 132 IFGEEYVG--------------EFSGRIKELKPLTVSTYDSAYVNAEKLGNRFMLLIFDE 177

Query: 135 AHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTAT 170
            H +           +   ++    +    + LTAT
Sbjct: 178 VHHLP---------AESYVQIAQMSIAPFRLGLTAT 204

>d1gm5a4 c.37.1.19 (A:550-755) RecG helicase domain {Thermotoga maritima [TaxId: 2336]} 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: RecG helicase domain
species: Thermotoga maritima [TaxId: 2336]

 Score = 50.2 bits (119), Expect = 7e-08
 Identities = 24/143 (16%), Positives = 52/143 (36%), Gaps = 12/143 (8%)

Query: 214 VDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQL-----------GVKAGTYHGQM 262
           V+E+ + + + V   G   +    I++ ++++                   K G  HG++
Sbjct: 15  VNEVYEFVRQEVMRGGQAFIVYPLIEESDKLNVKSAVEMYEYLSKEVFPEFKLGLMHGRL 74

Query: 263 GSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYY-QESGRCGR 321
             + ++     F      ++V+T    +GID P    ++     +   +   Q  GR GR
Sbjct: 75  SQEEKDRVMLEFAEGRYDILVSTTVIEVGIDVPRANVMVIENPERFGLAQLHQLRGRVGR 134

Query: 322 DGIASVCWLYYARSNFAKGDFYC 344
            G  + C+L          +   
Sbjct: 135 GGQEAYCFLVVGDVGEEAMERLR 157

>d1tf5a4 c.37.1.19 (A:396-570) Translocation ATPase SecA, nucleotide-binding domains {Bacillus subtilis [TaxId: 1423]} Length = 175

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]

 Score = 45.3 bits (107), Expect = 2e-06
 Identities = 24/125 (19%), Positives = 45/125 (36%), Gaps = 10/125 (8%)

Query: 217 LVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIR 276
           + +++ +       ++V  + ++  E ISK LK  G+     + +     RE        
Sbjct: 23  VAEDVAQRYMTGQPVLVGTVAVETSELISKLLKNKGIPHQVLNAKN--HEREAQIIEEAG 80

Query: 277 DEIRVMVATMAFGMGID--------KPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVC 328
            +  V +AT   G G D        +     V+     ++     Q  GR GR G   + 
Sbjct: 81  QKGAVTIATNMAGRGTDIKLGEGVKELGGLAVVGTERHESRRIDNQLRGRSGRQGDPGIT 140

Query: 329 WLYYA 333
             Y +
Sbjct: 141 QFYLS 145

>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 = 38.4 bits (88), Expect = 5e-04
 Identities = 42/201 (20%), Positives = 69/201 (34%), Gaps = 23/201 (11%)

Query: 1   MVSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV------TGK 54
           ++  + +  G+    P Q++ I   +  RD L     G+GKS  Y +P L          
Sbjct: 14  LLMGIFEM-GWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLERLDLKKDNI 72

Query: 55  TALVVSPLISLMQDQV----MSLKQRGINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEK 110
            A+V+ P   L            K  G       +  T+             ++  TP +
Sbjct: 73  QAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDDTVHVVIATPGR 132

Query: 111 ACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLE--YKQLDKLRTFLLGVPFVALT 168
             I+ +          V +  +DEA  +        +E     L K R  LL       +
Sbjct: 133 --ILDLIKKGVAKVDHVQMIVLDEADKLLSQDFVQIMEDIILTLPKNRQILL------YS 184

Query: 169 ATATEKVRIDIINSLKLKNPY 189
           AT    V+   +NS  L+ PY
Sbjct: 185 ATFPLSVQ-KFMNSH-LEKPY 203

>d1t5ia_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]} Length = 168

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 = 38.1 bits (87), Expect = 6e-04
 Identities = 26/125 (20%), Positives = 56/125 (44%), Gaps = 1/125 (0%)

Query: 215 DELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLF 274
           +  + ++L  +     ++++  +++    +++ L +    A   H  M  + R   ++ F
Sbjct: 15  NRKLFDLLDVLEF-NQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQF 73

Query: 275 IRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYAR 334
              + R++VAT  FG G+D   V    +Y  P+  ++Y     R GR G   +   + + 
Sbjct: 74  KDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSD 133

Query: 335 SNFAK 339
            N AK
Sbjct: 134 ENDAK 138

>d1s2ma2 c.37.1.19 (A:252-422) Putative ATP-dependent RNA helicase DHH1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 171

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 = 37.3 bits (85), Expect = 0.001
 Identities = 29/124 (23%), Positives = 52/124 (41%), Gaps = 1/124 (0%)

Query: 216 ELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFI 275
             +  +   +      I++C +   VE ++K +  LG      H +M  + R +    F 
Sbjct: 21  HCLNTLFSKLQI-NQAIIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVFHEFR 79

Query: 276 RDEIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARS 335
           + ++R +V +     GID   V  VI++  PKT E+Y    GR GR G   +       +
Sbjct: 80  QGKVRTLVCSDLLTRGIDIQAVNVVINFDFPKTAETYLHRIGRSGRFGHLGLAINLINWN 139

Query: 336 NFAK 339
           +   
Sbjct: 140 DRFN 143

>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 = 37.1 bits (85), Expect = 0.002
 Identities = 28/202 (13%), Positives = 68/202 (33%), Gaps = 20/202 (9%)

Query: 1   MVSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCY------QLPPLVTGK 54
           ++  +  Y G+      Q+  I   I+  D +    +G+GK+  +      Q+   +   
Sbjct: 23  LLRGIYAY-GFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIELDLKAT 81

Query: 55  TALVVSPLISLMQD----QVMSLKQRGINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEK 110
            ALV++P   L Q      +      G +           +   K +     ++  TP +
Sbjct: 82  QALVLAPTRELAQQIQKVVMALGDYMGASCHACIGGTNVRAEVQKLQMEAPHIIVGTPGR 141

Query: 111 ACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTAT 170
              +    +       + +    +      +       +++L+     +L      L+AT
Sbjct: 142 VFDMLNRRYLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKLNSNTQVVL------LSAT 195

Query: 171 ATEKVRIDIINSLKLKNPYVTI 192
               V  ++     +++P + I
Sbjct: 196 MPSDVL-EVTKKF-MRDP-IRI 214

>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 = 36.7 bits (84), Expect = 0.003
 Identities = 36/202 (17%), Positives = 66/202 (32%), Gaps = 22/202 (10%)

Query: 1   MVSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPP---LVTGKTAL 57
           ++  +  Y G+      Q+  I  IIE  D L    +G+GK+  + +     + T   A 
Sbjct: 21  LLRGVFGY-GFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAP 79

Query: 58  VVSPLISLMQDQVMSLKQRGINAEFLGSAQTDSSVQTKAETGYFQL-----LFMTPEKAC 112
               L    +  +   K     A  +          T        L     +  TP +  
Sbjct: 80  QALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGLRDAQIVVGTPGRVF 139

Query: 113 IIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLE--YKQLDKLRTFLLGVPFVALTAT 170
                   +     + +F +DEA  +   G   ++   +  L      +L      L+AT
Sbjct: 140 DNIQRRRFRT--DKIKMFILDEADEMLSSGFKEQIYQIFTLLPPTTQVVL------LSAT 191

Query: 171 ATEKVRIDIINSLKLKNPYVTI 192
               V  ++     ++NP V I
Sbjct: 192 MPNDVL-EVTTKF-MRNP-VRI 210

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	374
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	100.0
d1oywa3	200	RecQ helicase domain {Escherichia coli [TaxId: 562	100.0
d1oywa2	206	RecQ helicase domain {Escherichia coli [TaxId: 562	99.97
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	99.96
d1t6na_	207	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	99.96
d1veca_	206	DEAD box RNA helicase rck/p54 {Human (Homo sapiens	99.96
d2g9na1	218	Initiation factor 4a {Human (Homo sapiens) [TaxId:	99.96
d1qdea_	212	Initiation factor 4a {Baker's yeast (Saccharomyces	99.95
d1hv8a1	208	Putative DEAD box RNA helicase {Archaeon Methanoco	99.95
d1wrba1	238	putative ATP-dependent RNA helicase VlgB {Flatworm	99.95
d1fuka_	162	Initiation factor 4a {Baker's yeast (Saccharomyces	99.95
d2j0sa2	168	Probable ATP-dependent RNA helicase DDX48 {Human (	99.94
d1s2ma2	171	Putative ATP-dependent RNA helicase DHH1 {Baker's	99.94
d1hv8a2	155	Putative DEAD box RNA helicase {Archaeon Methanoco	99.94
d1c4oa2	174	Nucleotide excision repair enzyme UvrB {Thermus th	99.94
d1s2ma1	206	Putative ATP-dependent RNA helicase DHH1 {Baker's	99.94
d1q0ua_	209	Probable DEAD box RNA helicase YqfR {Bacillus stea	99.93
d1t5ia_	168	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	99.93
d2rb4a1	168	ATP-dependent RNA helicase DDX25 {Human (Homo sapi	99.93
d2p6ra3	202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	99.93
d1t5la2	181	Nucleotide excision repair enzyme UvrB {Bacillus c	99.92
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	99.91
d1wp9a1	200	putative ATP-dependent RNA helicase PF2015 {Pyroco	99.88
d2fz4a1	206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	99.87
d1jr6a_	138	HCV helicase domain {Human hepatitis C virus (HCV)	99.87
d1rifa_	282	DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]	99.85
d1wp9a2	286	putative ATP-dependent RNA helicase PF2015 {Pyroco	99.82
d2p6ra4	201	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	99.82
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	99.79
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	99.79
d2eyqa5	211	Transcription-repair coupling factor, TRCF {Escher	99.79
d2fwra1	200	DNA repair protein RAD25 {Archaeoglobus fulgidus [	99.77
d1gm5a4	206	RecG helicase domain {Thermotoga maritima [TaxId:	99.76
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	99.76
d1yksa1	140	YFV helicase domain {Yellow fever virus [TaxId: 11	99.75
d1a1va2	299	HCV helicase domain {Human hepatitis C virus (HCV)	99.75
d1gkub2	248	Helicase-like "domain" of reverse gyrase {Archaeon	99.67
d1z63a1	230	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	99.62
d1z3ix1	346	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	99.6
d1z3ix2	298	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	99.55
d1z5za1	244	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	99.54
d1yksa2	299	YFV helicase domain {Yellow fever virus [TaxId: 11	99.49
d1tf5a4	175	Translocation ATPase SecA, nucleotide-binding doma	99.49
d1nkta4	219	Translocation ATPase SecA, nucleotide-binding doma	99.08
d1tf5a3	273	Translocation ATPase SecA, nucleotide-binding doma	98.56
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	98.5
d1nkta3	288	Translocation ATPase SecA, nucleotide-binding doma	98.46
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	97.74
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	97.57
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	97.44
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	97.38
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	97.36
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	97.33
d2qy9a2	211	GTPase domain of the signal recognition particle r	97.33
d1t5la1	413	Nucleotide excision repair enzyme UvrB {Bacillus c	97.23
d1okkd2	207	GTPase domain of the signal recognition particle r	97.15
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	97.0
d1vmaa2	213	GTPase domain of the signal recognition particle r	96.87
d1ls1a2	207	GTPase domain of the signal sequence recognition p	96.82
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	96.78
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	96.75
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	96.71
d1j8yf2	211	GTPase domain of the signal sequence recognition p	96.63
g1qhh.1	623	DEXX box DNA helicase {Bacillus stearothermophilus	96.6
d1xx6a1	141	Thymidine kinase, TK1, N-terminal domain {Clostrid	96.41
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	96.31
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	96.17
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	95.99
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	95.98
d1c4oa1	408	Nucleotide excision repair enzyme UvrB {Thermus th	95.97
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	95.81
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	95.72
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	95.59
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	95.49
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	95.4
d2b8ta1	139	Thymidine kinase, TK1, N-terminal domain {Ureaplas	95.17
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	94.59
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	94.54
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	94.2
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	94.07
d1c4oa2	174	Nucleotide excision repair enzyme UvrB {Thermus th	93.95
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	93.94
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	93.86
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	93.59
d2eyqa5	211	Transcription-repair coupling factor, TRCF {Escher	93.26
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	93.19
d1p9ra_	401	Extracellular secretion NTPase EpsE {Vibrio choler	93.11
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	93.05
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	92.16
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	92.08
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	92.06
d1jr6a_	138	HCV helicase domain {Human hepatitis C virus (HCV)	91.94
d1u94a1	263	RecA protein, ATPase-domain {Escherichia coli [Tax	91.82
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	91.77
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	91.53
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	91.47
d1mo6a1	269	RecA protein, ATPase-domain {Mycobacterium tubercu	91.46
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	91.21
d1hv8a2	155	Putative DEAD box RNA helicase {Archaeon Methanoco	91.18
d1t5la2	181	Nucleotide excision repair enzyme UvrB {Bacillus c	91.07
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	90.81
d2eyqa2	117	Transcription-repair coupling factor, TRCF {Escher	90.5
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	90.42
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	90.41
d1svma_	362	Papillomavirus large T antigen helicase domain {Si	90.06
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	89.93
d1t5ia_	168	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	89.64
d1viaa_	161	Shikimate kinase (AroK) {Campylobacter jejuni [Tax	89.37
d1tf7a1	242	Circadian clock protein KaiC {Synechococcus sp. st	89.35
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	89.25
d1xp8a1	268	RecA protein, ATPase-domain {Deinococcus radiodura	89.1
d1qvra3	315	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	88.56
d1qhxa_	178	Chloramphenicol phosphotransferase {Streptomyces v	88.11
d2avda1	219	COMT domain-containing protein 1, COMTD1 {Human (H	87.94
d1g8pa_	333	ATPase subunit of magnesium chelatase, BchI {Rhodo	87.91
d1e6ca_	170	Shikimate kinase (AroK) {Erwinia chrysanthemi [Tax	87.76
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	87.74
d1fuka_	162	Initiation factor 4a {Baker's yeast (Saccharomyces	87.69
d3adka_	194	Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}	87.48
d1e9ra_	433	Bacterial conjugative coupling protein TrwB {Esche	87.25
d1yj5a2	172	5' polynucleotide kinase-3' phosphatase, C-termina	87.22
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	87.0
d1zaka1	189	Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}	86.8
d1bg2a_	323	Kinesin {Human (Homo sapiens) [TaxId: 9606]}	86.8
d1ak2a1	190	Adenylate kinase {Cow (Bos taurus), mitochondrial	86.77
d2cdna1	181	Adenylate kinase {Mycobacterium tuberculosis [TaxI	86.51
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	86.46
d1zina1	182	Adenylate kinase {Bacillus stearothermophilus [Tax	86.44
d1hv8a1	208	Putative DEAD box RNA helicase {Archaeon Methanoco	86.22
d1g5ta_	157	ATP:corrinoid adenosyltransferase CobA {Salmonella	86.11
d1qf9a_	194	UMP/CMP kinase {Dictyostelium discoideum [TaxId: 4	85.94
d1oywa3	200	RecQ helicase domain {Escherichia coli [TaxId: 562	85.87
d1s2ma2	171	Putative ATP-dependent RNA helicase DHH1 {Baker's	85.71
d1e4va1	179	Adenylate kinase {Escherichia coli [TaxId: 562]}	85.67
d1khta_	190	Adenylate kinase {Archaeon Methanococcus voltae [T	85.47
d1s3ga1	182	Adenylate kinase {Bacillus globisporus [TaxId: 145	85.42
d1w36b1	485	Exodeoxyribonuclease V beta chain (RecB), N-termin	85.39
d1yksa2	299	YFV helicase domain {Yellow fever virus [TaxId: 11	85.16
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	85.08
d1ny5a2	247	Transcriptional activator sigm54 (NtrC1), C-termin	84.92
d1ukza_	196	Uridylate kinase {Baker's yeast (Saccharomyces cer	84.7
d1r6bx3	315	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	84.67
d2iyva1	165	Shikimate kinase (AroK) {Mycobacterium tuberculosi	84.66
d1gkya_	186	Guanylate kinase {Baker's yeast (Saccharomyces cer	84.56
d1goja_	354	Kinesin {Neurospora crassa [TaxId: 5141]}	84.16
d2ak3a1	189	Adenylate kinase {Cow (Bos taurus), mitochondrial	84.13
d1akya1	180	Adenylate kinase {Baker's yeast (Saccharomyces cer	84.04
d1sdma_	364	Kinesin heavy chain-like protein {Potato (Solanum	83.69
d1v8ka_	362	Kinesin {Mouse (Mus musculus), kif2c [TaxId: 10090	83.58
d1teva_	194	UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]	83.34
d1x6va3	195	Adenosine-5'phosphosulfate kinase (APS kinase) {Hu	83.18
d1x88a1	345	Kinesin {Human (Homo sapiens), mitotic kinesin eg5	83.01
d1lvga_	190	Guanylate kinase {Mouse (Mus musculus) [TaxId: 100	82.99
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	82.82
d2zfia1	349	Kinesin {Mouse (Mus musculus), kif1a [TaxId: 10090	82.71
d2j0sa2	168	Probable ATP-dependent RNA helicase DDX48 {Human (	82.56
d2rb4a1	168	ATP-dependent RNA helicase DDX25 {Human (Homo sapi	82.25
d1znwa1	182	Guanylate kinase {Mycobacterium tuberculosis [TaxI	82.2
d1s96a_	205	Guanylate kinase {Escherichia coli [TaxId: 562]}	82.03
d2ncda_	368	Kinesin motor Ncd (non-claret disjunctional) {Frui	81.95
d1pzna2	254	DNA repair protein Rad51, catalytic domain {Archae	81.91
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	81.76
d1xbta1	133	Thymidine kinase, TK1, N-terminal domain {Human (H	81.49
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	81.47
d1n0wa_	242	DNA repair protein Rad51, catalytic domain {Human	81.32
d1krwa_	123	NTRC receiver domain {Salmonella typhimurium [TaxI	81.3
d1w44a_	321	NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}	81.22
d1a1va2	299	HCV helicase domain {Human hepatitis C virus (HCV)	80.37
d1bifa1	213	6-phosphofructo-2-kinase/fructose-2,6-bisphosphata	80.01

>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=100.00  E-value=4.4e-36  Score=260.54  Aligned_cols=273  Identities=18%  Similarity=0.113  Sum_probs=185.6

Q ss_pred             HcCCCEEEEccCCCCchhhhhccccc----cCCcEEEEcchHHHHHHHHHHHHHcCCceEEcCCCCCchhhhhhhhcCCe
Q 037567           26 IEKRDCLVVMATGSGKSLCYQLPPLV----TGKTALVVSPLISLMQDQVMSLKQRGINAEFLGSAQTDSSVQTKAETGYF  101 (374)
Q Consensus        26 ~~~~~~l~~a~tGsGKT~~~~l~~~~----~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  101 (374)
                      .+++++++.||||||||++|+.+++.    ++.+++|++|+++|++|+.+.++.++........        ........
T Consensus         7 ~~~~~~lv~~~TGsGKT~~~l~~~~~~~~~~~~~~lvi~Ptr~La~q~~~~l~~~~~~~~~~~~--------~~~~~~~~   78 (305)
T d2bmfa2           7 RKKRLTIMDLHPGAGKTKRYLPAIVREAIKRGLRTLILAPTRVVAAEMEEALRGLPIRYQTPAI--------RAEHTGRE   78 (305)
T ss_dssp             STTCEEEECCCTTSSTTTTHHHHHHHHHHHHTCCEEEEESSHHHHHHHHHHTTTSCCBCCC----------------CCC
T ss_pred             hcCCcEEEEECCCCCHHHHHHHHHHHHHHhcCCEEEEEccHHHHHHHHHHHHhcCCcceeeeEE--------eecccCcc
Confidence            36788999999999999888656543    5789999999999999999999877554322111        11122345


Q ss_pred             eEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHHhcCCCCeeEEEeecCcccHHHHHH
Q 037567          102 QLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEKVRIDIIN  181 (374)
Q Consensus       102 ~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~SaT~~~~~~~~~~~  181 (374)
                      .++++|++.+.....   ......+++++|+||+|++..++.....   .+... ...++.+++++|||++.....    
T Consensus        79 ~i~~~t~~~l~~~~~---~~~~~~~~~~vViDE~H~~~~~~~~~~~---~l~~~-~~~~~~~~v~~SAT~~~~~~~----  147 (305)
T d2bmfa2          79 IVDLMCHATFTMRLL---SPIRVPNYNLIIMDEAHFTDPASIAARG---YISTR-VEMGEAAGIFMTATPPGSRDP----  147 (305)
T ss_dssp             SEEEEEHHHHHHHHT---SSSCCCCCSEEEEESTTCCSHHHHHHHH---HHHHH-HHHTSCEEEEECSSCTTCCCS----
T ss_pred             ccccCCcHHHHHHHh---cCccccceeEEEeeeeeecchhhHHHHH---HHHHh-hccccceEEEeecCCCcceee----
Confidence            789999986643221   2233467899999999998765543322   22222 223467899999998765421    


Q ss_pred             hcCCCCCeEEEeccCCCceeEEEEeecCCcchHHHHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHHcCCceeeeecC
Q 037567          182 SLKLKNPYVTIASFDRKNLFYGVKVINRGQSFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQ  261 (374)
Q Consensus       182 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~  261 (374)
                       .......+........         .......   ...   ....+++++|||+++++++.+++.|++.++.+..+||+
T Consensus       148 -~~~~~~~~~~~~~~~~---------~~~~~~~---~~~---~~~~~~~~lvf~~~~~~~~~l~~~L~~~~~~~~~l~~~  211 (305)
T d2bmfa2         148 -FPQSNAPIMDEEREIP---------ERSWNSG---HEW---VTDFKGKTVWFVPSIKAGNDIAACLRKNGKKVIQLSRK  211 (305)
T ss_dssp             -SCCCSSCEEEEECCCC---------CSCCSSC---CHH---HHSSCSCEEEECSCHHHHHHHHHHHHHHTCCCEECCTT
T ss_pred             -ecccCCcceEEEEecc---------HHHHHHH---HHH---HHhhCCCEEEEeccHHHHHHHHHHHHhCCCCEEEeCCc
Confidence             1111111111110000         0000000   111   12367899999999999999999999999999999998


Q ss_pred             CChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEEEE----------EC----------CCCChhHHHHhhccCCC
Q 037567          262 MGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIH----------YG----------CPKTLESYYQESGRCGR  321 (374)
Q Consensus       262 ~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~----------~~----------~p~s~~~~~Q~~GR~~R  321 (374)
                      +....    ...|.+|..+++++|+++++|+|++ ++.|+.          ++          .|.|..+|.||+||+||
T Consensus       212 ~~~~~----~~~~~~~~~~~lvaT~~~~~G~~~~-~~~Vi~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~Qr~GR~GR  286 (305)
T d2bmfa2         212 TFDSE----YIKTRTNDWDFVVTTDISEMGANFK-AERVIDPRRCMKPVILTDGEERVILAGPMPVTHSSAAQRRGRVGR  286 (305)
T ss_dssp             CHHHH----GGGGGTSCCSEEEECGGGGTTCCCC-CSEEEECCEEEEEEEECSSSCEEEEEEEEECCHHHHHHHHTTSSC
T ss_pred             ChHHH----HhhhhccchhhhhhhHHHHhcCCCC-ccEEEEcCCceeeeEecCCCCceEEeccccCCHHHHhhhhcCcCc
Confidence            75543    4468889999999999999999995 455442          22          34588999999999999


Q ss_pred             CCCceEEEEEeeccCCC
Q 037567          322 DGIASVCWLYYARSNFA  338 (374)
Q Consensus       322 ~~~~g~~~~~~~~~~~~  338 (374)
                      .|+++..+++|.....+
T Consensus       287 ~~~~~~~~~~~~~~~~~  303 (305)
T d2bmfa2         287 NPKNENDQYIYMGEPLE  303 (305)
T ss_dssp             SSSCCCEEEEECSCCCC
T ss_pred             CCCCceEEEEECCCCCC
Confidence            99999888888776543

>d1oywa3 c.37.1.19 (A:207-406) 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=100.00  E-value=1.5e-32  Score=219.36  Aligned_cols=176  Identities=34%  Similarity=0.596  Sum_probs=156.8

Q ss_pred             ccCCCceeEEEEeecCCcchHHHHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHh
Q 037567          194 SFDRKNLFYGVKVINRGQSFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRL  273 (374)
Q Consensus       194 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~  273 (374)
                      +++++|+.+.+.....   ... .+..+++.. .+.++||||++++.++.+++.|...++.+..+||+++..+|.++++.
T Consensus         1 s~~RpNi~y~v~~~~~---k~~-~L~~~l~~~-~~~~~IIF~~t~~~~~~l~~~l~~~~~~~~~~h~~~~~~~r~~~~~~   75 (200)
T d1oywa3           1 SFDRPNIRYMLMEKFK---PLD-QLMRYVQEQ-RGKSGIIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEK   75 (200)
T ss_dssp             CCCCTTEEEEEEECSS---HHH-HHHHHHHHT-TTCCEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHH
T ss_pred             CCCCCCcEEEEEcCCc---HHH-HHHHHHHhc-CCCCEEEEEeeehhhHHhhhhhccCCceeEEecCCCcHHHHHHHHHH
Confidence            3577888766543322   233 344444443 57799999999999999999999999999999999999999999999


Q ss_pred             hhcCCeeEEEEeccccccccccCccEEEEECCCCChhHHHHhhccCCCCCCceEEEEEeeccCCCcccceeccccchHHH
Q 037567          274 FIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFYCGESQTENQR  353 (374)
Q Consensus       274 f~~g~~~ilv~t~~~~~G~d~~~~~~vi~~~~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~  353 (374)
                      |.+|+.+|||+|+++++|+|+|++++||++++|.++.+|+||+||+||.|+.|.+++++.+.|...+++++.........
T Consensus        76 f~~g~~~ilvaTd~~~~GiD~p~v~~VI~~~~P~~~~~y~qr~GR~gR~g~~g~ai~~~~~~d~~~l~~~i~~~~~~~~~  155 (200)
T d1oywa3          76 FQRDDLQIVVATVAFGMGINKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAMLFYDPADMAWLRRCLEEKPQGQLQ  155 (200)
T ss_dssp             HHTTSCSEEEECTTSCTTTCCTTCCEEEESSCCSSHHHHHHHHTTSCTTSSCEEEEEEECHHHHHHHHHHHHTSCCSHHH
T ss_pred             HhcccceEEEecchhhhccCCCCCCEEEECCCccchHHHHHHhhhhhcCCCCceEEEecCHHHHHHHHhhhhccccccch
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999888888888


Q ss_pred             HHHHHHHHHHHHHhhhcccCC
Q 037567          354 TAIMESLLAAQRYCLLTTCRR  374 (374)
Q Consensus       354 ~~~~~~l~~~~~~~~~~~~~~  374 (374)
                      ....+.+..|..|++.+.|||
T Consensus       156 ~~~~~~~~~m~~~~~~~~Crr  176 (200)
T d1oywa3         156 DIERHKLNAMGAFAEAQTCRR  176 (200)
T ss_dssp             HHHHHHHHHHHHHHTCSSCHH
T ss_pred             hhhHHHHHHHHHHHhchhhHH
Confidence            888899999999999999996

>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=99.97  E-value=4.3e-31  Score=214.94  Aligned_cols=188  Identities=48%  Similarity=0.797  Sum_probs=157.8

Q ss_pred             hhHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccccCCcEEEEcchHHHHHHHHHHHHHcCCceE
Q 037567            2 VSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVTGKTALVVSPLISLMQDQVMSLKQRGINAE   81 (374)
Q Consensus         2 ~~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~   81 (374)
                      .+.|++.|||++|+|+|.++++++++|+|+++.+|||||||++|.++++....++++++|+++|++|+.+.++..+....
T Consensus        14 ~~~l~~~fg~~~~rp~Q~~ai~~~l~g~~vlv~apTGsGKT~~~~~~~~~~~~~~~~v~P~~~L~~q~~~~l~~~~~~~~   93 (206)
T d1oywa2          14 KQVLQETFGYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPALLLNGLTVVVSPLISLMKDQVDQLQANGVAAA   93 (206)
T ss_dssp             HHHHHHTTCCSSCCTTHHHHHHHHHTTCCEEEECSCHHHHHHHHHHHHHHSSSEEEEECSCHHHHHHHHHHHHHTTCCEE
T ss_pred             HHHHHHhcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCCCcchhhhhhhhccCceEEeccchhhhhhHHHHHHhhccccc
Confidence            46789999999999999999999999999999999999999999999999999999999999999999999999887766


Q ss_pred             EcCCCCCchh---hhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHHh
Q 037567           82 FLGSAQTDSS---VQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTF  158 (374)
Q Consensus        82 ~~~~~~~~~~---~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~  158 (374)
                      ..........   .......+...++++||+.+......  .......++++|+||+|.+.+++..++..+..+..+...
T Consensus        94 ~~~~~~~~~~~~~~~~~~~~~~~~i~~~t~~~~~~~~~~--~~~~~~~v~~lviDEaH~~~~~~~~~~~~~~~~~~l~~~  171 (206)
T d1oywa2          94 CLNSTQTREQQLEVMTGCRTGQIRLLYIAPERLMLDNFL--EHLAHWNPVLLAVDEAHCISQWGHDFRPEYAALGQLRQR  171 (206)
T ss_dssp             EECTTSCHHHHHHHHHHHHHTCCSEEEECHHHHTSTTHH--HHHTTSCEEEEEESSGGGGCTTSSCCCHHHHGGGGHHHH
T ss_pred             ccccccccccchhHHHHHhcCCceEEEEechhhhchhhc--ccchhheeeeeeeeeeeeeeccccchHHHHHHHHHHHHh
Confidence            5544333322   22333456789999999987665333  555667899999999999999888877777777777788


Q ss_pred             cCCCCeeEEEeecCcccHHHHHHhcCCCCCeEE
Q 037567          159 LLGVPFVALTATATEKVRIDIINSLKLKNPYVT  191 (374)
Q Consensus       159 ~~~~~~i~~SaT~~~~~~~~~~~~~~~~~~~~~  191 (374)
                      +++.++++||||+++....++..++++.+|.+.
T Consensus       172 ~~~~~ii~lSATl~~~v~~di~~~L~l~~p~v~  204 (206)
T d1oywa2         172 FPTLPFMALTATADDTTRQDIVRLLGLNDPLIQ  204 (206)
T ss_dssp             CTTSCEEEEESCCCHHHHHHHHHHHTCCSCEEE
T ss_pred             CCCCceEEEEeCCCHHHHHHHHHHcCCCCCcEE
Confidence            889999999999998877789999999988654

>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=99.96  E-value=1.5e-30  Score=211.67  Aligned_cols=167  Identities=17%  Similarity=0.242  Sum_probs=132.4

Q ss_pred             ChhHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc------cCCcEEEEcchHHHHHHHHHHHH
Q 037567            1 MVSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV------TGKTALVVSPLISLMQDQVMSLK   74 (374)
Q Consensus         1 l~~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~------~~~~~lil~P~~~l~~q~~~~~~   74 (374)
                      |.++|++ +||..|+|+|.+++|.+++|+|+++.||||||||++|++|++.      ...+++|++|+++|+.|..+.+.
T Consensus        28 l~~~L~~-~g~~~pt~IQ~~aIp~il~g~dvi~~a~TGSGKTlayllPil~~l~~~~~~~~~lil~PtreLa~Qi~~~~~  106 (222)
T d2j0sa1          28 LLRGIYA-YGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGLL  106 (222)
T ss_dssp             HHHHHHH-HTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHTCCTTSCSCCEEEECSSHHHHHHHHHHHH
T ss_pred             HHHHHHH-CCCCCCCHHHHHHHHHHHCCCCeEEEcCcchhhhhhhcccccccccccccCceeEEecchHHHHHHHHHHHH
Confidence            3577887 7999999999999999999999999999999999999999875      36679999999999999999988


Q ss_pred             HcC----CceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHH
Q 037567           75 QRG----INAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYK  150 (374)
Q Consensus        75 ~~~----~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~  150 (374)
                      +++    +....+.++....... .....+++|+|+||+++.++...  ......+++++|+||||.+.+.|+.     .
T Consensus       107 ~l~~~~~i~~~~~~g~~~~~~~~-~~l~~~~~Ilv~TPgrl~~~~~~--~~~~~~~l~~lVlDEaD~ll~~~f~-----~  178 (222)
T d2j0sa1         107 ALGDYMNVQCHACIGGTNVGEDI-RKLDYGQHVVAGTPGRVFDMIRR--RSLRTRAIKMLVLDEADEMLNKGFK-----E  178 (222)
T ss_dssp             HHTTTTTCCEEEECTTSCHHHHH-HHHHHCCSEEEECHHHHHHHHHT--TSSCCTTCCEEEEETHHHHTSTTTH-----H
T ss_pred             HHhCccceeEEEEeecccchhhH-HHhccCCeEEeCCCCcHHhcccc--cccccccceeeeecchhHhhhcCcH-----H
Confidence            763    4455555544433333 33344579999999998776544  3445678899999999999987764     4


Q ss_pred             HHHHHHHhcC-CCCeeEEEeecCcccH
Q 037567          151 QLDKLRTFLL-GVPFVALTATATEKVR  176 (374)
Q Consensus       151 ~~~~~~~~~~-~~~~i~~SaT~~~~~~  176 (374)
                      .+..+...++ +.|++++|||.+.+..
T Consensus       179 ~i~~I~~~l~~~~Q~ilfSAT~~~~v~  205 (222)
T d2j0sa1         179 QIYDVYRYLPPATQVVLISATLPHEIL  205 (222)
T ss_dssp             HHHHHHTTSCTTCEEEEEESCCCHHHH
T ss_pred             HHHHHHHhCCCCCEEEEEEEeCCHHHH
Confidence            5566666554 6789999999987654

>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=99.96  E-value=3.2e-30  Score=208.48  Aligned_cols=179  Identities=14%  Similarity=0.186  Sum_probs=137.9

Q ss_pred             ChhHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc------cCCcEEEEcchHHHHHHHHHHHH
Q 037567            1 MVSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV------TGKTALVVSPLISLMQDQVMSLK   74 (374)
Q Consensus         1 l~~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~------~~~~~lil~P~~~l~~q~~~~~~   74 (374)
                      |.++|.+ +||.+|+|+|.+++|.+++|+|+++.||||||||++|++|++.      ...++++++|+++|+.|+.+.++
T Consensus        12 l~~~l~~-~g~~~pt~iQ~~aip~il~g~dvl~~A~TGsGKTla~~lp~l~~~~~~~~~~~~lil~PtreL~~qi~~~~~   90 (207)
T d1t6na_          12 LLRAIVD-CGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRELAFQISKEYE   90 (207)
T ss_dssp             HHHHHHH-TTCCCCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCCCTTCCCEEEECSCHHHHHHHHHHHH
T ss_pred             HHHHHHH-CCCCCCCHHHHHHHHHHHcCCCeEEEeccccccccccccceeeeecccCCCceEEEEeccchhhHHHHHHHH
Confidence            3567887 7999999999999999999999999999999999999999875      25679999999999999999988


Q ss_pred             HcCC-----ceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcc-cCcchHH
Q 037567           75 QRGI-----NAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEW-GHDFRLE  148 (374)
Q Consensus        75 ~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~-~~~~~~~  148 (374)
                      .++.     ......++..............++|+|+||+++..+...  ....+.++.++|+||||.+.+. ++.    
T Consensus        91 ~~~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~ilI~TP~rl~~~~~~--~~~~l~~l~~lVlDEaD~ll~~~~~~----  164 (207)
T d1t6na_          91 RFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARN--KSLNLKHIKHFILDECDKMLEQLDMR----  164 (207)
T ss_dssp             HHTTTSTTCCEEEESCCSCHHHHHHHHHHSCCSEEEECHHHHHHHHHT--TSSCCTTCCEEEEESHHHHHSSHHHH----
T ss_pred             HHHhhCCCceeEEEeccccHHHHHHHHHhcCCCEEEeCcchhhhhccC--CceeccccceeehhhhhhhhhcCCcH----
Confidence            7642     334455555545555555567789999999999877654  3456788999999999998762 332    


Q ss_pred             HHHHHHHHHhcC-CCCeeEEEeecCcccHHHHHHhcCCCCCe
Q 037567          149 YKQLDKLRTFLL-GVPFVALTATATEKVRIDIINSLKLKNPY  189 (374)
Q Consensus       149 ~~~~~~~~~~~~-~~~~i~~SaT~~~~~~~~~~~~~~~~~~~  189 (374)
                       ..+..+....+ +.|++++|||.++.... +.+.+ +.+|.
T Consensus       165 -~~i~~I~~~~~~~~Q~il~SAT~~~~v~~-l~~~~-l~~P~  203 (207)
T d1t6na_         165 -RDVQEIFRMTPHEKQVMMFSATLSKEIRP-VCRKF-MQDPM  203 (207)
T ss_dssp             -HHHHHHHHTSCSSSEEEEEESCCCTTTHH-HHHTT-CSSCE
T ss_pred             -HHHHHHHHhCCCCCEEEEEeeeCCHHHHH-HHHHH-CCCCE
Confidence             34555555554 68899999999887664 44443 44443

>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=99.96  E-value=4.2e-30  Score=207.57  Aligned_cols=172  Identities=19%  Similarity=0.171  Sum_probs=133.3

Q ss_pred             hhHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc------cCCcEEEEcchHHHHHHHHHHHHH
Q 037567            2 VSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV------TGKTALVVSPLISLMQDQVMSLKQ   75 (374)
Q Consensus         2 ~~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~------~~~~~lil~P~~~l~~q~~~~~~~   75 (374)
                      .++|.+ +||..|+|+|.++++.+++|+|+++.||||||||++|++|++.      .+..++|++|+++|+.|..+.+..
T Consensus        15 ~~~l~~-~g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKTlayllP~l~~~~~~~~~~~~lil~pt~el~~q~~~~~~~   93 (206)
T d1veca_          15 LMGIFE-MGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLERLDLKKDNIQAMVIVPTRELALQVSQICIQ   93 (206)
T ss_dssp             HHHHHT-TTCCSCCHHHHHHHHHHHTTCCEEEECCSSSTTHHHHHHHHHHHCCTTSCSCCEEEECSCHHHHHHHHHHHHH
T ss_pred             HHHHHH-CCCCCCCHHHHHHHHHHHcCCCEEeeccCccccccccccchhhcccccccCcceEEEeecchhhHHHHHHHHH
Confidence            567877 7999999999999999999999999999999999999999875      367899999999999999998876


Q ss_pred             cC-----CceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHH
Q 037567           76 RG-----INAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYK  150 (374)
Q Consensus        76 ~~-----~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~  150 (374)
                      +.     .......++ .............++|+|+||+++..+...  ....+.+++++|+||||.+.+.++.     .
T Consensus        94 ~~~~~~~~~~~~~~g~-~~~~~~~~~l~~~~~ivv~TPgrl~~~~~~--~~~~~~~l~~lVlDEaD~ll~~~f~-----~  165 (206)
T d1veca_          94 VSKHMGGAKVMATTGG-TNLRDDIMRLDDTVHVVIATPGRILDLIKK--GVAKVDHVQMIVLDEADKLLSQDFV-----Q  165 (206)
T ss_dssp             HTTTSSSCCEEEECSS-SCHHHHHHHTTSCCSEEEECHHHHHHHHHT--TCSCCTTCCEEEEETHHHHTSTTTH-----H
T ss_pred             HhhcccCcccccccCC-ccHHHHHHHHHhccCeEEeCCccccccccc--hhccccccceEEEeccccccccchH-----H
Confidence            52     233333332 333333344456789999999998776544  3455678999999999999987654     4


Q ss_pred             HHHHHHHhc-CCCCeeEEEeecCcccHHHHHHhc
Q 037567          151 QLDKLRTFL-LGVPFVALTATATEKVRIDIINSL  183 (374)
Q Consensus       151 ~~~~~~~~~-~~~~~i~~SaT~~~~~~~~~~~~~  183 (374)
                      .+..+.... ++.|++++|||.+..... +.+.+
T Consensus       166 ~i~~I~~~~~~~~Q~~l~SAT~~~~v~~-l~~~~  198 (206)
T d1veca_         166 IMEDIILTLPKNRQILLYSATFPLSVQK-FMNSH  198 (206)
T ss_dssp             HHHHHHHHSCTTCEEEEEESCCCHHHHH-HHHHH
T ss_pred             HHHHHHHhCCCCCEEEEEEecCCHHHHH-HHHHH
Confidence            455555555 468899999999877653 44443

>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=99.96  E-value=4.4e-30  Score=208.83  Aligned_cols=173  Identities=18%  Similarity=0.205  Sum_probs=136.0

Q ss_pred             hhHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc------cCCcEEEEcchHHHHHHHHHHHHH
Q 037567            2 VSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV------TGKTALVVSPLISLMQDQVMSLKQ   75 (374)
Q Consensus         2 ~~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~------~~~~~lil~P~~~l~~q~~~~~~~   75 (374)
                      .++|.+ +||..|+|+|.++++.++.|+|+++.||||||||++|++++++      ...+++|++|+++|+.|..+.+..
T Consensus        24 ~~~L~~-~g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKTlayllp~l~~i~~~~~~~~alil~Pt~eL~~Q~~~~~~~  102 (218)
T d2g9na1          24 LRGIYA-YGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIELDLKATQALVLAPTRELAQQIQKVVMA  102 (218)
T ss_dssp             HHHHHH-HTCCSCCHHHHHHHHHHHHTCCEEEECCTTSSHHHHHHHHHHHHCCTTCCSCCEEEECSSHHHHHHHHHHHHH
T ss_pred             HHHHHH-CCCCCCCHHHHHHHHHHHcCCCEEEEcccchhhhhhhhhhhhheecccccCccEEEEcccchhhhhHHHHHhh
Confidence            467776 7999999999999999999999999999999999999999875      367899999999999999998876


Q ss_pred             c----CCceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHH
Q 037567           76 R----GINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQ  151 (374)
Q Consensus        76 ~----~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~  151 (374)
                      +    +.......++............+.++|+|+||+++..++..  ......+++++|+||||.+.+.++.     ..
T Consensus       103 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IvV~TP~rl~~~l~~--~~~~~~~l~~lVlDEaD~ll~~~f~-----~~  175 (218)
T d2g9na1         103 LGDYMGASCHACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNR--RYLSPKYIKMFVLDEADEMLSRGFK-----DQ  175 (218)
T ss_dssp             HHTTTTCCEEEECC--CCCSTTTSSSSCCCSEEEECHHHHHHHHHT--TSSCSTTCCEEEEESHHHHHHTTCH-----HH
T ss_pred             hccccceeEEeeecccchhHHHHHHhcCCCEEEEeCChhHHHHHhc--CCcccccceEEEeeecchhhcCchH-----HH
Confidence            5    44455555554444444455556789999999999877655  3455678999999999999887654     44


Q ss_pred             HHHHHHhcC-CCCeeEEEeecCcccHHHHHHhc
Q 037567          152 LDKLRTFLL-GVPFVALTATATEKVRIDIINSL  183 (374)
Q Consensus       152 ~~~~~~~~~-~~~~i~~SaT~~~~~~~~~~~~~  183 (374)
                      +..+....+ +.|++++|||.+.+... +...+
T Consensus       176 ~~~Il~~~~~~~Q~il~SAT~~~~v~~-~~~~~  207 (218)
T d2g9na1         176 IYDIFQKLNSNTQVVLLSATMPSDVLE-VTKKF  207 (218)
T ss_dssp             HHHHHHHSCTTCEEEEEESCCCHHHHH-HHHHH
T ss_pred             HHHHHHhCCCCCeEEEEEecCCHHHHH-HHHHH
Confidence            555555544 68899999999887653 44433

>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=99.95  E-value=3.9e-29  Score=202.51  Aligned_cols=172  Identities=19%  Similarity=0.227  Sum_probs=129.4

Q ss_pred             ChhHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc------cCCcEEEEcchHHHHHHHHHHHH
Q 037567            1 MVSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV------TGKTALVVSPLISLMQDQVMSLK   74 (374)
Q Consensus         1 l~~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~------~~~~~lil~P~~~l~~q~~~~~~   74 (374)
                      |.++|++ +||.+|+|+|.++++.+++|+|+++.+|||||||++|+++++.      .++.+++++|+++++.|....+.
T Consensus        21 l~~~L~~-~g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKT~a~~lp~i~~l~~~~~~~~~lil~pt~el~~q~~~~~~   99 (212)
T d1qdea_          21 LLRGVFG-YGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALMLAPTRELALQIQKVVM   99 (212)
T ss_dssp             HHHHHHH-HTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCTTCCSCCEEEECSSHHHHHHHHHHHH
T ss_pred             HHHHHHH-CCCCCCCHHHHHHHHHHHcCCCEEeecccccchhhhhHhhhHhhhhccCCCcceEEEcccHHHhhhhhhhhc
Confidence            3578887 8999999999999999999999999999999999999999875      36789999999999999999987


Q ss_pred             HcC----CceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHH
Q 037567           75 QRG----INAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYK  150 (374)
Q Consensus        75 ~~~----~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~  150 (374)
                      .+.    .......++........  ...+++|+|+||+++..+...  ....+.+++++|+||||.+.+.++.     .
T Consensus       100 ~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~IvI~TP~~l~~~~~~--~~~~l~~l~~lVlDEad~lld~~f~-----~  170 (212)
T d1qdea_         100 ALAFHMDIKVHACIGGTSFVEDAE--GLRDAQIVVGTPGRVFDNIQR--RRFRTDKIKMFILDEADEMLSSGFK-----E  170 (212)
T ss_dssp             HHTTTSCCCEEEECC------------CTTCSEEEECHHHHHHHHHT--TSSCCTTCCEEEEETHHHHHHTTCH-----H
T ss_pred             ccccccccceeeEeeccchhHHHH--HhcCCcEEEECCCcccccccc--CceecCcceEEeehhhhhhcccchH-----H
Confidence            653    22333333222222222  224579999999998876554  4456778999999999999987654     4


Q ss_pred             HHHHHHHhc-CCCCeeEEEeecCcccHHHHHHhc
Q 037567          151 QLDKLRTFL-LGVPFVALTATATEKVRIDIINSL  183 (374)
Q Consensus       151 ~~~~~~~~~-~~~~~i~~SaT~~~~~~~~~~~~~  183 (374)
                      .+..+.... ++.|++++|||.++... ++.+.+
T Consensus       171 ~v~~I~~~~~~~~Q~vl~SAT~~~~v~-~l~~~~  203 (212)
T d1qdea_         171 QIYQIFTLLPPTTQVVLLSATMPNDVL-EVTTKF  203 (212)
T ss_dssp             HHHHHHHHSCTTCEEEEEESSCCHHHH-HHHHHH
T ss_pred             HHHHHHHhCCCCCeEEEEEeeCCHHHH-HHHHHH
Confidence            445555544 46889999999987755 455544

>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=99.95  E-value=1.1e-28  Score=199.95  Aligned_cols=171  Identities=16%  Similarity=0.209  Sum_probs=130.5

Q ss_pred             hhHHHhHcCCCCCchhHHHHHHHHHcCC-CEEEEccCCCCchhhhhccccc-----cCCcEEEEcchHHHHHHHHHHHHH
Q 037567            2 VSTLKKYFGYSVFRPYQKDVIQRIIEKR-DCLVVMATGSGKSLCYQLPPLV-----TGKTALVVSPLISLMQDQVMSLKQ   75 (374)
Q Consensus         2 ~~~l~~~~~~~~~~~~Q~~~~~~~~~~~-~~l~~a~tGsGKT~~~~l~~~~-----~~~~~lil~P~~~l~~q~~~~~~~   75 (374)
                      +++|.+ +||.+|+|+|.++++.+++++ ++++.+|||+|||++|.++++.     .+.+++|++|+++|+.|+.+.+..
T Consensus        16 ~~~l~~-~g~~~pt~iQ~~~ip~~l~g~~d~iv~a~TGsGKT~~~~l~~~~~~~~~~~~~~lil~pt~~l~~q~~~~~~~   94 (208)
T d1hv8a1          16 LNAIRN-KGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIELVNENNGIEAIILTPTRELAIQVADEIES   94 (208)
T ss_dssp             HHHHHH-HTCCSCCHHHHHHHHHHHHTCSEEEEECCSSSSHHHHHHHHHHHHSCSSSSCCEEEECSCHHHHHHHHHHHHH
T ss_pred             HHHHHH-CCCCCCCHHHHHHHHHHHcCCCCeeeechhcccccceeecccccccccccCcceEEEeeccccchhhhhhhhh
Confidence            567777 899999999999999999875 8999999999999999888764     467899999999999999988887


Q ss_pred             c----CCceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHH
Q 037567           76 R----GINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQ  151 (374)
Q Consensus        76 ~----~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~  151 (374)
                      +    +..+....+...........  .+++|+|+||+++..++.+  ....+++++++|+||||.+.+.+..     ..
T Consensus        95 ~~~~~~~~v~~~~g~~~~~~~~~~l--~~~~IlV~TP~~l~~~l~~--~~~~~~~l~~lViDEad~l~~~~~~-----~~  165 (208)
T d1hv8a1          95 LKGNKNLKIAKIYGGKAIYPQIKAL--KNANIVVGTPGRILDHINR--GTLNLKNVKYFILDEADEMLNMGFI-----KD  165 (208)
T ss_dssp             HHCSSCCCEEEECTTSCHHHHHHHH--HTCSEEEECHHHHHHHHHT--TCSCTTSCCEEEEETHHHHHTTTTH-----HH
T ss_pred             hcccCCeEEEEeeCCCChHHHHHhc--CCCCEEEEChHHHHHHHHc--CCCCcccCcEEEEEChHHhhcCCCh-----HH
Confidence            5    34445555544333332222  3589999999998776554  3445688999999999998775543     44


Q ss_pred             HHHHHHhcC-CCCeeEEEeecCcccHHHHHHhc
Q 037567          152 LDKLRTFLL-GVPFVALTATATEKVRIDIINSL  183 (374)
Q Consensus       152 ~~~~~~~~~-~~~~i~~SaT~~~~~~~~~~~~~  183 (374)
                      +..+....+ +.|++++|||.+++.. ++...+
T Consensus       166 i~~I~~~~~~~~Q~i~~SAT~~~~v~-~~~~~~  197 (208)
T d1hv8a1         166 VEKILNACNKDKRILLFSATMPREIL-NLAKKY  197 (208)
T ss_dssp             HHHHHHTSCSSCEEEEECSSCCHHHH-HHHHHH
T ss_pred             HHHHHHhCCCCCeEEEEEccCCHHHH-HHHHHH
Confidence            555555553 6889999999987655 344444

>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=3.8e-28  Score=200.26  Aligned_cols=172  Identities=19%  Similarity=0.227  Sum_probs=131.8

Q ss_pred             ChhHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhcccccc---------------CCcEEEEcchHHH
Q 037567            1 MVSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVT---------------GKTALVVSPLISL   65 (374)
Q Consensus         1 l~~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~~---------------~~~~lil~P~~~l   65 (374)
                      |.++|.+ +||..|+|+|.++++.+++|+|+++.||||||||++|+++++..               ..+++|++|+++|
T Consensus        32 l~~~L~~-~g~~~pt~iQ~~~ip~il~g~dvvi~a~TGsGKTlayllp~l~~l~~~~~~~~~~~~~~~~~alil~pt~el  110 (238)
T d1wrba1          32 IRNNILL-ASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIINHLVCQDLNQQRYSKTAYPKCLILAPTREL  110 (238)
T ss_dssp             TTTTTTT-TTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHTTCC------CCBCCSEEEECSSHHH
T ss_pred             HHHHHHH-CCCCCCCHHHHHHhhhhhCCCCEEEECCCCCCcceeeHHHHHHHHHhcccccccccCCCCceEEEeccchhh
Confidence            3456776 89999999999999999999999999999999999999998742               4679999999999


Q ss_pred             HHHHHHHHHHc----CCceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcc
Q 037567           66 MQDQVMSLKQR----GINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEW  141 (374)
Q Consensus        66 ~~q~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~  141 (374)
                      +.|+.+.+..+    +++.....++....... ......++|+|+||+++..+...  ....+.++.++|+||+|.+.+.
T Consensus       111 ~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~-~~~~~~~~ivV~TP~~l~~~~~~--~~~~l~~v~~lViDEaD~ll~~  187 (238)
T d1wrba1         111 AIQILSESQKFSLNTPLRSCVVYGGADTHSQI-REVQMGCHLLVATPGRLVDFIEK--NKISLEFCKYIVLDEADRMLDM  187 (238)
T ss_dssp             HHHHHHHHHHHHTTSSCCEEEECSSSCSHHHH-HHHSSCCSEEEECHHHHHHHHHT--TSBCCTTCCEEEEETHHHHHHT
T ss_pred             hcchheeeeecccCCCcEEEEEeccchhhHHH-hhcccCCceeecCHHHHHhHHcc--Cceeccccceeeeehhhhhhhh
Confidence            99999888764    45555555554444332 33456789999999999876544  3445678999999999999886


Q ss_pred             cCcchHHHHHHHHHHHhc-----CCCCeeEEEeecCcccHHHHHHh
Q 037567          142 GHDFRLEYKQLDKLRTFL-----LGVPFVALTATATEKVRIDIINS  182 (374)
Q Consensus       142 ~~~~~~~~~~~~~~~~~~-----~~~~~i~~SaT~~~~~~~~~~~~  182 (374)
                      ++.     ..+..+....     .+.|++++|||++.+... +.+.
T Consensus       188 ~f~-----~~i~~Il~~~~~~~~~~~Q~il~SAT~~~~v~~-l~~~  227 (238)
T d1wrba1         188 GFE-----PQIRKIIEESNMPSGINRQTLMFSATFPKEIQK-LAAD  227 (238)
T ss_dssp             TCH-----HHHHHHHHSSCCCCGGGCEEEEEESSCCHHHHH-HHHH
T ss_pred             ccH-----HHHHHHHHHhcCCCCCCCEEEEEeeeCCHHHHH-HHHH
Confidence            654     3344444322     146899999999877653 4443

>d1fuka_ 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=99.95  E-value=1.6e-27  Score=184.05  Aligned_cols=132  Identities=21%  Similarity=0.376  Sum_probs=115.5

Q ss_pred             cchHHHHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccc
Q 037567          211 QSFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGM  290 (374)
Q Consensus       211 ~~~~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~  290 (374)
                      .+...+.+.++++.. +..++||||+++..++.+++.|...++.+..+||+++.++|..+++.|+.|+.++||||+++++
T Consensus        11 ~e~K~~~L~~ll~~~-~~~k~iIF~~s~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~l~~f~~~~~~iLv~Tdv~~r   89 (162)
T d1fuka_          11 EEYKYECLTDLYDSI-SVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLAR   89 (162)
T ss_dssp             GGGHHHHHHHHHHHT-TCSCEEEEESSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEEEGGGTT
T ss_pred             cHHHHHHHHHHHHhC-CCCcEEEEEEEEchHHHHHHHHhhcCceEEEeccCCchhhHHHHHHHHhhcccceeeccccccc
Confidence            344566677777664 6789999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccccCccEEEEECCCCChhHHHHhhccCCCCCCceEEEEEeeccCCCcccce
Q 037567          291 GIDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFY  343 (374)
Q Consensus       291 G~d~~~~~~vi~~~~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~~~~~~~~  343 (374)
                      |+|+|++++||++++|+++..|+||+||+||.|+.|.+++++++.|...+..+
T Consensus        90 GiDi~~v~~VI~~d~P~~~~~yihR~GR~gR~g~~g~~i~~~~~~d~~~~~~i  142 (162)
T d1fuka_          90 GIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVTNEDVGAMREL  142 (162)
T ss_dssp             TCCCCSCSEEEESSCCSSGGGGGGSSCSCC-----CEEEEEEETTTHHHHHHH
T ss_pred             cccCCCceEEEEeccchhHHHHHhhccccccCCCccEEEEEcCHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999998876554443

>d2j0sa2 c.37.1.19 (A:244-411) 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=99.94  E-value=5.8e-27  Score=181.88  Aligned_cols=128  Identities=22%  Similarity=0.408  Sum_probs=117.2

Q ss_pred             HHHHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEecccccccc
Q 037567          214 VDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGID  293 (374)
Q Consensus       214 ~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d  293 (374)
                      ..+.+.++++.. ...++||||+++..++.+++.|+..++++..+||+++..+|...++.|++|+.++||||+++++|+|
T Consensus        21 K~~~L~~ll~~~-~~~k~iiF~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~fk~g~~~iLv~Td~~~rGiD   99 (168)
T d2j0sa2          21 KFDTLCDLYDTL-TITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLD   99 (168)
T ss_dssp             HHHHHHHHHHHH-TSSEEEEECSSHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHHTSSCEEEECGGGSSSCC
T ss_pred             HHHHHHHHHHhC-CCCceEEEeeeHHHHHHHHHHhhhcccchhhhhhhhhHHHHHHHHHHHhcCCccEEeccchhccccc
Confidence            445555666554 6789999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCccEEEEECCCCChhHHHHhhccCCCCCCceEEEEEeeccCCCcccc
Q 037567          294 KPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDF  342 (374)
Q Consensus       294 ~~~~~~vi~~~~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~~~~~~~  342 (374)
                      +|++++||++++|+++..|+||+||+||.|+.|.+++++.+.|...++.
T Consensus       100 i~~v~~VIn~d~P~~~~~yihR~GR~gR~g~~G~~i~~~~~~d~~~~~~  148 (168)
T d2j0sa2         100 VPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRD  148 (168)
T ss_dssp             CTTEEEEEESSCCSSHHHHHHHHTTSSGGGCCEEEEEEEEGGGHHHHHH
T ss_pred             ccCcceEEEecCCcCHHHHHhhhccccccCCCcEEEEEECHHHHHHHHH
Confidence            9999999999999999999999999999999999999999987654443

>d1s2ma2 c.37.1.19 (A:252-422) 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=99.94  E-value=4.7e-27  Score=183.78  Aligned_cols=131  Identities=22%  Similarity=0.331  Sum_probs=119.4

Q ss_pred             chHHHHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEecccccc
Q 037567          212 SFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMG  291 (374)
Q Consensus       212 ~~~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G  291 (374)
                      ....+.+.++++.. +.+++||||++++.++.++..|...|+.+..+||+++..+|.+++..|.+|..++||||+++++|
T Consensus        17 ~~K~~~L~~ll~~~-~~~k~iVF~~~~~~~~~l~~~L~~~g~~~~~~h~~~~~~~r~~~~~~f~~~~~~ilv~Td~~~~G   95 (171)
T d1s2ma2          17 RQKLHCLNTLFSKL-QINQAIIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSDLLTRG   95 (171)
T ss_dssp             GGHHHHHHHHHHHS-CCSEEEEECSSHHHHHHHHHHHHHHTCCEEEECTTSCHHHHHHHHHHHHTTSSSEEEESSCSSSS
T ss_pred             HHHHHHHHHHHHhC-CCCceEEEEeeeehhhHhHHhhhcccccccccccccchhhhhhhhhhcccCccccccchhHhhhc
Confidence            34566667777664 67899999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccCccEEEEECCCCChhHHHHhhccCCCCCCceEEEEEeeccCCCcccce
Q 037567          292 IDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFY  343 (374)
Q Consensus       292 ~d~~~~~~vi~~~~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~~~~~~~~  343 (374)
                      +|+|++++||++++|+++..|+||+||+||.|+.|.+++++.+.|...++.+
T Consensus        96 id~~~v~~VI~~d~p~~~~~y~qr~GR~gR~g~~g~~i~~v~~~e~~~~~~i  147 (171)
T d1s2ma2          96 IDIQAVNVVINFDFPKTAETYLHRIGRSGRFGHLGLAINLINWNDRFNLYKI  147 (171)
T ss_dssp             CCCTTEEEEEESSCCSSHHHHHHHHCBSSCTTCCEEEEEEECGGGHHHHHHH
T ss_pred             cccceeEEEEecCCcchHHHHHHHhhhcccCCCccEEEEEeCHHHHHHHHHH
Confidence            9999999999999999999999999999999999999999998765444433

>d1hv8a2 c.37.1.19 (A:211-365) 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=99.94  E-value=5.4e-27  Score=180.43  Aligned_cols=126  Identities=33%  Similarity=0.525  Sum_probs=115.4

Q ss_pred             hHHHHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccc
Q 037567          213 FVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGI  292 (374)
Q Consensus       213 ~~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~  292 (374)
                      ...+.+..+++.  .+.++||||++++.++.+++.|++.|+.+..+||+++..+|..++++|++|+.++||||+++++|+
T Consensus        15 ~K~~~L~~ll~~--~~~k~IIF~~s~~~~~~l~~~L~~~g~~~~~~~~~~~~~~r~~~~~~f~~~~~~ilv~T~~~~~Gi   92 (155)
T d1hv8a2          15 ERFEALCRLLKN--KEFYGLVFCKTKRDTKELASMLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATDVMSRGI   92 (155)
T ss_dssp             GHHHHHHHHHCS--TTCCEEEECSSHHHHHHHHHHHHHTTCCEEEECSSSCHHHHHHHHHHHHTTSSSEEEECTTHHHHC
T ss_pred             HHHHHHHHHHcc--CCCCEEEEECchHHHHHHHhhhcccccccccccccchhhhhhhhhhhhhcccceeeeehhHHhhhh
Confidence            345556666664  467899999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccCccEEEEECCCCChhHHHHhhccCCCCCCceEEEEEeeccCCCcc
Q 037567          293 DKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKG  340 (374)
Q Consensus       293 d~~~~~~vi~~~~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~~~~~  340 (374)
                      |+|++++||++++|+|+..|+||+||+||.|+.|.+++++.+.|...+
T Consensus        93 d~~~v~~Vi~~d~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~d~~~~  140 (155)
T d1hv8a2          93 DVNDLNCVINYHLPQNPESYMHRIGRTGRAGKKGKAISIINRREYKKL  140 (155)
T ss_dssp             CCSCCSEEEESSCCSCHHHHHHHSTTTCCSSSCCEEEEEECTTSHHHH
T ss_pred             hhccCcEEEEecCCCCHHHHHHHHHhcCcCCCCceEEEEEchHHHHHH
Confidence            999999999999999999999999999999999999999988765433

>d1c4oa2 c.37.1.19 (A:410-583) 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=99.94  E-value=2.2e-26  Score=176.26  Aligned_cols=120  Identities=23%  Similarity=0.342  Sum_probs=109.2

Q ss_pred             chHHHHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEecccccc
Q 037567          212 SFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMG  291 (374)
Q Consensus       212 ~~~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G  291 (374)
                      ..+.+++.++.+....++++||||++++.++.+++.|.+.|+.+..+||+++..+|.+++++|++|+++|||+|+++++|
T Consensus        15 ~qv~dll~~i~~~~~~g~r~lvfc~t~~~~~~l~~~L~~~Gi~a~~~Hg~~~~~eR~~~l~~F~~G~~~vLVaT~v~~~G   94 (174)
T d1c4oa2          15 NQILDLMEGIRERAARGERTLVTVLTVRMAEELTSFLVEHGIRARYLHHELDAFKRQALIRDLRLGHYDCLVGINLLREG   94 (174)
T ss_dssp             THHHHHHHHHHHHHHTTCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTCCHHHHHHHHHHHHTTSCSEEEESCCCCTT
T ss_pred             CCHHHHHHHHHHHHhcCCcEEEEEcchhHHHHHHHHHHhcCCceEEEecccchHHHHHHHHHHHCCCeEEEEeeeeeeee
Confidence            35677888888887789999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccCccEEEEECCCC-----ChhHHHHhhccCCCCCCceEEEEEe
Q 037567          292 IDKPDVRHVIHYGCPK-----TLESYYQESGRCGRDGIASVCWLYY  332 (374)
Q Consensus       292 ~d~~~~~~vi~~~~p~-----s~~~~~Q~~GR~~R~~~~g~~~~~~  332 (374)
                      +|+|++++||++++|.     +...|+|++||+||.++ |.+++++
T Consensus        95 iDip~V~~Vi~~~~~~~~~~~~~~~~iq~~GR~gR~~~-g~~~~~~  139 (174)
T d1c4oa2          95 LDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNAR-GEVWLYA  139 (174)
T ss_dssp             CCCTTEEEEEETTTTSCSGGGSHHHHHHHHGGGTTSTT-CEEEEEC
T ss_pred             ccCCCCcEEEEeccccccccchhHHHHHHhhhhhhcCC-CeeEEee
Confidence            9999999999999775     55789999999999876 5555444

>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=99.94  E-value=5.6e-27  Score=189.68  Aligned_cols=173  Identities=18%  Similarity=0.226  Sum_probs=135.3

Q ss_pred             ChhHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc------cCCcEEEEcchHHHHHHHHHHHH
Q 037567            1 MVSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV------TGKTALVVSPLISLMQDQVMSLK   74 (374)
Q Consensus         1 l~~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~------~~~~~lil~P~~~l~~q~~~~~~   74 (374)
                      |.++|.+ .||..|+|+|.+++|.+++|+|+++.||||||||++|+++++.      .+..+++++|+.+++.|....+.
T Consensus        12 l~~~L~~-~g~~~pt~iQ~~aip~il~g~dvi~~a~tGsGKTlay~lp~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   90 (206)
T d1s2ma1          12 LLMGIFE-AGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEKVKPKLNKIQALIMVPTRELALQTSQVVR   90 (206)
T ss_dssp             HHHHHHH-TTCCSCCHHHHHHHHHHHHTCCEEEECCTTSCHHHHHHHHHHHHCCTTSCSCCEEEECSSHHHHHHHHHHHH
T ss_pred             HHHHHHH-CCCCCCCHHHHHHHHHHHcCCCEEEecCCcchhhhhhccccccccccccccccceeeccchhhhhhhhhhhh
Confidence            3577887 7999999999999999999999999999999999999998774      36779999999999998887776


Q ss_pred             Hc----CCceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHH
Q 037567           75 QR----GINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYK  150 (374)
Q Consensus        75 ~~----~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~  150 (374)
                      .+    ++.+....+........ ......++|+|+||+++..++..  ....+.+++++|+||||.+.+.++.     .
T Consensus        91 ~~~~~~~~~~~~~~g~~~~~~~~-~~l~~~~~Ili~TP~~l~~~l~~--~~~~l~~l~~lV~DEaD~l~~~~f~-----~  162 (206)
T d1s2ma1          91 TLGKHCGISCMVTTGGTNLRDDI-LRLNETVHILVGTPGRVLDLASR--KVADLSDCSLFIMDEADKMLSRDFK-----T  162 (206)
T ss_dssp             HHTTTTTCCEEEECSSSCHHHHH-HHTTSCCSEEEECHHHHHHHHHT--TCSCCTTCCEEEEESHHHHSSHHHH-----H
T ss_pred             hcccccCeeEEeecCccchhhHH-HHhcccceEEEECCccccccccc--ceeecccceEEEeechhhhhhhhhH-----H
Confidence            54    45555555544443333 33456689999999999877654  4455678899999999999876543     4


Q ss_pred             HHHHHHHhcC-CCCeeEEEeecCcccHHHHHHhc
Q 037567          151 QLDKLRTFLL-GVPFVALTATATEKVRIDIINSL  183 (374)
Q Consensus       151 ~~~~~~~~~~-~~~~i~~SaT~~~~~~~~~~~~~  183 (374)
                      .+..+...++ ..|++++|||.+++... +...+
T Consensus       163 ~v~~I~~~l~~~~Q~il~SATl~~~v~~-~~~~~  195 (206)
T d1s2ma1         163 IIEQILSFLPPTHQSLLFSATFPLTVKE-FMVKH  195 (206)
T ss_dssp             HHHHHHTTSCSSCEEEEEESCCCHHHHH-HHHHH
T ss_pred             HHHHHHHhCCCCCEEEEEEEeCCHHHHH-HHHHH
Confidence            5666666665 57899999999877654 44443

>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=99.93  E-value=6.2e-27  Score=190.48  Aligned_cols=173  Identities=18%  Similarity=0.215  Sum_probs=129.2

Q ss_pred             ChhHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc------cCCcEEEEcchHHHHHHHHHHHH
Q 037567            1 MVSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV------TGKTALVVSPLISLMQDQVMSLK   74 (374)
Q Consensus         1 l~~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~------~~~~~lil~P~~~l~~q~~~~~~   74 (374)
                      |+++|++ +||.+|+|+|.++++.+++|+|+++.||||||||++|++++++      .....++++|+..++.+....+.
T Consensus        12 l~~~l~~-~g~~~pt~iQ~~aip~~l~G~dvii~a~TGSGKTlayllp~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   90 (209)
T d1q0ua_          12 IIEAIKT-LRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIMEKIKPERAEVQAVITAPTRELATQIYHETL   90 (209)
T ss_dssp             HHHHHHH-TTCCSCCHHHHHHHHHHHHTCCEEEECCSSHHHHHHHHHHHHHHCCTTSCSCCEEEECSSHHHHHHHHHHHH
T ss_pred             HHHHHHH-CCCCCCCHHHHHHHHHHHCCCCeEeecccccccceeeeeeeccccccccccccccccccccchhHHHHHHHH
Confidence            3577887 8999999999999999999999999999999999999999875      25678999999999988877765


Q ss_pred             Hc--------CCceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcch
Q 037567           75 QR--------GINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFR  146 (374)
Q Consensus        75 ~~--------~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~  146 (374)
                      ..        ........+ .............+++|+|+||+++..+..+  ......+++++|+||||.+.++++.  
T Consensus        91 ~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~Ilv~TP~~l~~~~~~--~~~~~~~l~~lViDEad~ll~~~f~--  165 (209)
T d1q0ua_          91 KITKFCPKDRMIVARCLIG-GTDKQKALEKLNVQPHIVIGTPGRINDFIRE--QALDVHTAHILVVDEADLMLDMGFI--  165 (209)
T ss_dssp             HHHTTSCGGGCCCEEEECC-CSHHHHTTCCCSSCCSEEEECHHHHHHHHHT--TCCCGGGCCEEEECSHHHHHHTTCH--
T ss_pred             hhhcccccccccccccccc-chhhHHHHHHhccCceEEEecCchhhhhhhh--hccccccceEEEEeecccccccccH--
Confidence            42        122222222 2222223333456789999999998776544  3345578899999999999987754  


Q ss_pred             HHHHHHHHHHHhc-CCCCeeEEEeecCcccHHHHHHhc
Q 037567          147 LEYKQLDKLRTFL-LGVPFVALTATATEKVRIDIINSL  183 (374)
Q Consensus       147 ~~~~~~~~~~~~~-~~~~~i~~SaT~~~~~~~~~~~~~  183 (374)
                         ..+..+.... ++.|++++|||.++.... +.+.+
T Consensus       166 ---~~v~~I~~~~~~~~Q~il~SATl~~~v~~-l~~~~  199 (209)
T d1q0ua_         166 ---TDVDQIAARMPKDLQMLVFSATIPEKLKP-FLKKY  199 (209)
T ss_dssp             ---HHHHHHHHTSCTTCEEEEEESCCCGGGHH-HHHHH
T ss_pred             ---HHHHHHHHHCCCCCEEEEEEccCCHHHHH-HHHHH
Confidence               3445555544 478999999999887654 55544

>d1t5ia_ 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=99.93  E-value=5.8e-26  Score=176.49  Aligned_cols=124  Identities=19%  Similarity=0.330  Sum_probs=115.2

Q ss_pred             cchHHHHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccc
Q 037567          211 QSFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGM  290 (374)
Q Consensus       211 ~~~~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~  290 (374)
                      .....+.+.++++.. ..+++||||+++..++.+++.|.+.++.+..+||+++..+|..+++.|++|+.++||+|+++++
T Consensus        11 ~~~K~~~L~~ll~~~-~~~k~iIF~~~~~~~~~l~~~L~~~~~~~~~ihg~~~~~~r~~~l~~F~~g~~~iLv~T~~~~~   89 (168)
T d1t5ia_          11 DNEKNRKLFDLLDVL-EFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGR   89 (168)
T ss_dssp             GGGHHHHHHHHHHHS-CCSSEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEESSCCST
T ss_pred             hHHHHHHHHHHHHhC-CCCeEEEEEeeeecchhhhhhhccccccccccccccchhhhhhhhhhhccccceeeeccccccc
Confidence            345566777777765 6789999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccccCccEEEEECCCCChhHHHHhhccCCCCCCceEEEEEeecc
Q 037567          291 GIDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARS  335 (374)
Q Consensus       291 G~d~~~~~~vi~~~~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~  335 (374)
                      |+|+|.+++||++++|.++..|+||+||+||.|+.|.+++++.+.
T Consensus        90 Gid~~~~~~vi~~~~p~~~~~yiqr~GR~gR~g~~g~~i~l~~~~  134 (168)
T d1t5ia_          90 GMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDE  134 (168)
T ss_dssp             TCCGGGCSEEEESSCCSSHHHHHHHHHHHTGGGCCCEEEEEECSH
T ss_pred             hhhcccchhhhhhhcccchhhHhhhhhhcccCCCccEEEEEECch
Confidence            999999999999999999999999999999999999999988763

>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=99.93  E-value=1.5e-26  Score=187.11  Aligned_cols=172  Identities=23%  Similarity=0.296  Sum_probs=123.2

Q ss_pred             hHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc---cCCcEEEEcchHHHHHHHHHHHHHcC--
Q 037567            3 STLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV---TGKTALVVSPLISLMQDQVMSLKQRG--   77 (374)
Q Consensus         3 ~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~---~~~~~lil~P~~~l~~q~~~~~~~~~--   77 (374)
                      ..|++ .||.+|+|+|.++++.+.+++++++.+|||+|||.++.++++.   +.+++++++|+++|+.|+.+.++++.  
T Consensus        16 ~~l~~-~g~~~l~~~Q~~ai~~l~~~~~~il~apTGsGKT~~a~l~i~~~~~~~~~vl~l~P~~~L~~q~~~~~~~~~~~   94 (202)
T d2p6ra3          16 GILKE-EGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIKGGKSLYVVPLRALAGEKYESFKKWEKI   94 (202)
T ss_dssp             HHHHC-C---CCCCCCHHHHHHHTTCSCEEEECSSHHHHHHHHHHHHHHHHHTTCCEEEEESSHHHHHHHHHHHTTTTTT
T ss_pred             HHHHH-cCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCchhHHHHHHHHHHhhccCcceeecccHHHHHHHHHHHHHHhhc
Confidence            45666 7999999999999999999999999999999999988776654   57899999999999999999998763  


Q ss_pred             -CceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHH
Q 037567           78 -INAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLR  156 (374)
Q Consensus        78 -~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~  156 (374)
                       ..+....+.....    ......++++++||..+..+...  ....+.++++||+||+|.+.+.+...... ..+..+.
T Consensus        95 ~~~v~~~~~~~~~~----~~~~~~~~ii~~~~~~~~~~~~~--~~~~~~~~~~ii~DE~h~~~~~~r~~~~~-~~l~~i~  167 (202)
T d2p6ra3          95 GLRIGISTGDYESR----DEHLGDCDIIVTTSEKADSLIRN--RASWIKAVSCLVVDEIHLLDSEKRGATLE-ILVTKMR  167 (202)
T ss_dssp             TCCEEEECSSCBCC----SSCSTTCSEEEEEHHHHHHHHHT--TCSGGGGCCEEEETTGGGGGCTTTHHHHH-HHHHHHH
T ss_pred             cccceeeccCcccc----cccccccceeeeccHHHHHHHhc--cchhhhhhhhccccHHHHhcccccchHHH-HHHHHHH
Confidence             2333333322221    12224578999999988665443  22345678999999999987644322211 2345555


Q ss_pred             HhcCCCCeeEEEeecCcccHHHHHHhcC
Q 037567          157 TFLLGVPFVALTATATEKVRIDIINSLK  184 (374)
Q Consensus       157 ~~~~~~~~i~~SaT~~~~~~~~~~~~~~  184 (374)
                      ...++.++++||||.++.  .++..+++
T Consensus       168 ~~~~~~~~l~lSATl~n~--~~~~~~l~  193 (202)
T d2p6ra3         168 RMNKALRVIGLSATAPNV--TEIAEWLD  193 (202)
T ss_dssp             HHCTTCEEEEEECCCTTH--HHHHHHTT
T ss_pred             hcCCCCcEEEEcCCCCcH--HHHHHHcC
Confidence            555688999999998653  35677774

>d1t5la2 c.37.1.19 (A:415-595) 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=99.92  E-value=4.4e-25  Score=172.14  Aligned_cols=117  Identities=26%  Similarity=0.350  Sum_probs=108.2

Q ss_pred             cchHHHHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccc
Q 037567          211 QSFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGM  290 (374)
Q Consensus       211 ~~~~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~  290 (374)
                      .....+++.++.+....+.++||||++++.++.++..|++.|+++..+||+++..+|.+++++|++|+++|||||+++++
T Consensus        14 ~~qvd~ll~~i~~~~~~~~~~iif~~~~~~~~~~~~~l~~~g~~~~~~hg~~~~~eR~~~l~~Fr~g~~~vLVaTdv~~r   93 (181)
T d1t5la2          14 KGQIDDLIGEIRERVERNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLRE   93 (181)
T ss_dssp             TTHHHHHHHHHHHHHHTTCEEEEECSSHHHHHHHHHHHHTTTCCEEEECSSCCHHHHHHHHHHHHHTSCSEEEESCCCSS
T ss_pred             CCcHHHHHHHHHHHHhcCCeEEEEeehhhhhHHHHHHHHhCCcceeEecCCccHHHHHHHHHHHHCCCCCEEEehhHHHc
Confidence            34567788888877778889999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccccCccEEEEECCCC-----ChhHHHHhhccCCCCCCceE
Q 037567          291 GIDKPDVRHVIHYGCPK-----TLESYYQESGRCGRDGIASV  327 (374)
Q Consensus       291 G~d~~~~~~vi~~~~p~-----s~~~~~Q~~GR~~R~~~~g~  327 (374)
                      |+|+|++++||++++|.     |...|+||+||+||.|..+.
T Consensus        94 GiDip~v~~VI~~d~p~~~~~~s~~~yi~R~GRagR~g~~~~  135 (181)
T d1t5la2          94 GLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNANGHV  135 (181)
T ss_dssp             SCCCTTEEEEEETTTTSCSGGGSHHHHHHHHGGGTTSTTCEE
T ss_pred             cCCCCCCCEEEEecCCcccccccHHHHHHHHHhhccccCcee
Confidence            99999999999999995     68999999999999986543

>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=99.91  E-value=1.5e-24  Score=179.64  Aligned_cols=160  Identities=18%  Similarity=0.149  Sum_probs=111.2

Q ss_pred             CCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc---cCCcEEEEcchHHHHHHHHHHHHHc----CCceE-
Q 037567           10 GYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV---TGKTALVVSPLISLMQDQVMSLKQR----GINAE-   81 (374)
Q Consensus        10 ~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~---~~~~~lil~P~~~l~~q~~~~~~~~----~~~~~-   81 (374)
                      ++.+|+++|.++++.+++|+++++.||||+|||++++++++.   ++.+++|++|+++|++|+.++++++    +.... 
T Consensus        40 ~~~~p~~~Q~~~i~~~l~g~~~~i~apTGsGKT~~~~~~~~~~~~~~~rvliv~Pt~~La~Q~~~~l~~~~~~~~~~~~~  119 (237)
T d1gkub1          40 CVGEPRAIQKMWAKRILRKESFAATAPTGVGKTSFGLAMSLFLALKGKRCYVIFPTSLLVIQAAETIRKYAEKAGVGTEN  119 (237)
T ss_dssp             TTCSCCHHHHHHHHHHHTTCCEECCCCBTSCSHHHHHHHHHHHHTTSCCEEEEESCHHHHHHHHHHHHHHHTTTCCSGGG
T ss_pred             ccCCCCHHHHHHHHHHHCCCCEEEEecCCChHHHHHHHHHHHHHHhcCeEEEEeccHHHHHHHHHHHHHHHHHcCCceEE
Confidence            677999999999999999999999999999999888776653   5789999999999999999999875    22221 


Q ss_pred             ---EcCCCCCchhh-hhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHH
Q 037567           82 ---FLGSAQTDSSV-QTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRT  157 (374)
Q Consensus        82 ---~~~~~~~~~~~-~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~  157 (374)
                         ...+....... ........++|+|+||+.+.....      ...+++++|+||+|.+.+.+...    ........
T Consensus       120 ~~~~~~~~~~~~~~~~~l~~~~~~~Ilv~Tp~~l~~~~~------~~~~~~~vVvDE~d~~l~~~~~~----~~~~~~~g  189 (237)
T d1gkub1         120 LIGYYHGRIPKREKENFMQNLRNFKIVITTTQFLSKHYR------ELGHFDFIFVDDVDAILKASKNV----DKLLHLLG  189 (237)
T ss_dssp             SEEECCSSCCSHHHHHHHHSGGGCSEEEEEHHHHHHCST------TSCCCSEEEESCHHHHHTSTHHH----HHHHHHTT
T ss_pred             EEeeeecccchhhhhhhhccccccceeccChHHHHHhhh------hcCCCCEEEEEChhhhhhcccch----hHHHHhcC
Confidence               12222222221 122233557899999997654322      34678999999999987644221    11111110


Q ss_pred             -----------hcCCCCeeEEEeecCcccHHHH
Q 037567          158 -----------FLLGVPFVALTATATEKVRIDI  179 (374)
Q Consensus       158 -----------~~~~~~~i~~SaT~~~~~~~~~  179 (374)
                                 .....+++++|||+++.....+
T Consensus       190 ~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~l  222 (237)
T d1gkub1         190 FHYDLKTKSWVGEARGCLMVSTATAKKGKKAEL  222 (237)
T ss_dssp             EEEETTTTEEEECCSSEEEECCCCSCCCTTHHH
T ss_pred             ChHHHHHHHhhCCCCCeEEEEeCCCCcccHHHH
Confidence                       1123458999999987655443

>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=99.88  E-value=3.6e-23  Score=167.02  Aligned_cols=155  Identities=18%  Similarity=0.177  Sum_probs=107.0

Q ss_pred             CCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhcccc----ccCCcEEEEcchHHHHHHHHHHHHHc----CCceEEc
Q 037567           12 SVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPL----VTGKTALVVSPLISLMQDQVMSLKQR----GINAEFL   83 (374)
Q Consensus        12 ~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~----~~~~~~lil~P~~~l~~q~~~~~~~~----~~~~~~~   83 (374)
                      -+|++||.++++.+. ++++++++|||+|||+++++++.    ..+.++++++|+++|++|+.+++.++    +..+...
T Consensus         8 ~~pr~~Q~~~~~~~~-~~n~lv~~pTGsGKT~i~~~~~~~~~~~~~~~il~i~P~~~L~~q~~~~~~~~~~~~~~~v~~~   86 (200)
T d1wp9a1           8 IQPRIYQEVIYAKCK-ETNCLIVLPTGLGKTLIAMMIAEYRLTKYGGKVLMLAPTKPLVLQHAESFRRLFNLPPEKIVAL   86 (200)
T ss_dssp             HCCCHHHHHHHHHGG-GSCEEEECCTTSCHHHHHHHHHHHHHHHSCSCEEEECSSHHHHHHHHHHHHHHBCSCGGGEEEE
T ss_pred             CCCCHHHHHHHHHHh-cCCeEEEeCCCCcHHHHHHHHHHHHHHhcCCcEEEEcCchHHHHHHHHHHHHhhcccccceeee
Confidence            369999999998875 56799999999999988776554    24778999999999999999999976    2333333


Q ss_pred             CCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHHhcCCCC
Q 037567           84 GSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVP  163 (374)
Q Consensus        84 ~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~~~~~  163 (374)
                      .++.......  .....+.++++||+.+......  ......+++++|+||+|++......    ............+.+
T Consensus        87 ~~~~~~~~~~--~~~~~~~i~i~t~~~~~~~~~~--~~~~~~~~~~vIiDE~H~~~~~~~~----~~~~~~~~~~~~~~~  158 (200)
T d1wp9a1          87 TGEKSPEERS--KAWARAKVIVATPQTIENDLLA--GRISLEDVSLIVFDEAHRAVGNYAY----VFIAREYKRQAKNPL  158 (200)
T ss_dssp             CSCSCHHHHH--HHHHHCSEEEECHHHHHHHHHT--TSCCTTSCSEEEEETGGGCSTTCHH----HHHHHHHHHHCSSCC
T ss_pred             ecccchhHHH--HhhhcccccccccchhHHHHhh--hhhhccccceEEEEehhhhhcchhH----HHHHHHHHhcCCCCc
Confidence            3332222221  1123358999999988654333  3344567899999999998653211    122223333445678


Q ss_pred             eeEEEeecCccc
Q 037567          164 FVALTATATEKV  175 (374)
Q Consensus       164 ~i~~SaT~~~~~  175 (374)
                      +++|||||....
T Consensus       159 ~l~~SATp~~~~  170 (200)
T d1wp9a1         159 VIGLTASPGSTP  170 (200)
T ss_dssp             EEEEESCSCSSH
T ss_pred             EEEEEecCCCcH
Confidence            999999986543

>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=99.87  E-value=1.1e-22  Score=164.16  Aligned_cols=137  Identities=21%  Similarity=0.191  Sum_probs=104.0

Q ss_pred             CCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccccCCcEEEEcchHHHHHHHHHHHHHcCCceEEcCCCCCchhh
Q 037567           13 VFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLVTGKTALVVSPLISLMQDQVMSLKQRGINAEFLGSAQTDSSV   92 (374)
Q Consensus        13 ~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~   92 (374)
                      +|++||.+++..+.++++.++.+|||+|||++++..+.....++||+||+++|++||.++++.++........+..    
T Consensus        70 ~Lr~yQ~eav~~~~~~~~~ll~~~tG~GKT~~a~~~~~~~~~~~Liv~p~~~L~~q~~~~~~~~~~~~~~~~~~~~----  145 (206)
T d2fz4a1          70 SLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAAINELSTPTLIVVPTLALAEQWKERLGIFGEEYVGEFSGRI----  145 (206)
T ss_dssp             CCCHHHHHHHHHHTTTSEEEEEESSSTTHHHHHHHHHHHSCSCEEEEESSHHHHHHHHHHHGGGCGGGEEEESSSC----
T ss_pred             CcCHHHHHHHHHHHhCCCcEEEeCCCCCceehHHhHHHHhcCceeEEEcccchHHHHHHHHHhhcccchhhccccc----
Confidence            6999999999999999999999999999999877766667889999999999999999999998765332222111    


Q ss_pred             hhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHHhcCCCCeeEEEeecC
Q 037567           93 QTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATAT  172 (374)
Q Consensus        93 ~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~SaT~~  172 (374)
                           .....++++|++++...     .......+++||+||+|++...         .+..+........+++||||+.
T Consensus       146 -----~~~~~i~i~t~~~~~~~-----~~~~~~~~~lvIiDEaH~~~a~---------~~~~i~~~~~~~~~lgLTATl~  206 (206)
T d2fz4a1         146 -----KELKPLTVSTYDSAYVN-----AEKLGNRFMLLIFDEVHHLPAE---------SYVQIAQMSIAPFRLGLTATFE  206 (206)
T ss_dssp             -----BCCCSEEEEEHHHHHHT-----HHHHTTTCSEEEEECSSCCCTT---------THHHHHHTCCCSEEEEEEESCC
T ss_pred             -----ccccccccceehhhhhh-----hHhhCCcCCEEEEECCeeCCcH---------HHHHHHhccCCCcEEEEecCCC
Confidence                 12246899998876543     2233467899999999998531         1234445555667899999973

>d1jr6a_ c.37.1.14 (A:) 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=99.87  E-value=1.7e-22  Score=149.95  Aligned_cols=100  Identities=27%  Similarity=0.425  Sum_probs=90.6

Q ss_pred             CCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEEEEEC--
Q 037567          227 GAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYG--  304 (374)
Q Consensus       227 ~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~~~--  304 (374)
                      .++++||||++++.++.+++.|+..|+.+..+|++++.+       .|++|+.++||||+++++|+| |+++.||+++  
T Consensus        34 ~~~k~IVFc~t~~~ae~la~~L~~~G~~~~~~H~~~~~~-------~~~~~~~~vlvaTd~~~~GiD-~~v~~Vi~~~~~  105 (138)
T d1jr6a_          34 KGGRHLIFCHSKKKCDELAAKLVALGINAVAYYRGLDVS-------VIPTNGDVVVVATDALMTGFT-GDFDSVIDCNTS  105 (138)
T ss_dssp             TTSCEEEECSCHHHHHHHHHHHHHHTCEEEEECTTCCSC-------CCTTSSCEEEEESSSSCSSSC-CCBSEEEECSEE
T ss_pred             CCCCEEEEeCcHHHHHHHHHHHhccccchhhhhccchhh-------hhhhhhcceeehhHHHHhccc-cccceEEEEEec
Confidence            678999999999999999999999999999999999854       477899999999999999999 9999999854  


Q ss_pred             --CCCChhHHHHhhccCCCCCCceEEEEEeeccC
Q 037567          305 --CPKTLESYYQESGRCGRDGIASVCWLYYARSN  336 (374)
Q Consensus       305 --~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~  336 (374)
                        +|.+..+|+||+||+|| |++|. +.|+.+.|
T Consensus       106 ~~~P~~~~~y~qr~GR~gR-g~~G~-~~~i~~~e  137 (138)
T d1jr6a_         106 DGKPQDAVSRTQRRGRTGR-GKPGI-YRFVAPGE  137 (138)
T ss_dssp             TTEECCHHHHHHHHTTBCS-SSCEE-EEECCSSC
T ss_pred             CCCCCCHHHHHhHhccccC-CCCcE-EEEEcCCC
Confidence              69999999999999999 99995 66777654

>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=99.85  E-value=2.5e-22  Score=169.22  Aligned_cols=145  Identities=15%  Similarity=0.133  Sum_probs=105.6

Q ss_pred             CCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhcccc----ccCCcEEEEcchHHHHHHHHHHHHHcCCceE----EcC
Q 037567           13 VFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPL----VTGKTALVVSPLISLMQDQVMSLKQRGINAE----FLG   84 (374)
Q Consensus        13 ~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~----~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~----~~~   84 (374)
                      +||+||.+++..++++++.++.+|||+|||+++...+.    ....++||++|+++|+.||.+++..++....    ...
T Consensus       113 ~~rdyQ~~av~~~l~~~~~il~~pTGsGKT~i~~~i~~~~~~~~~~k~Liivp~~~Lv~Q~~~~f~~~~~~~~~~~~~~~  192 (282)
T d1rifa_         113 EPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALLARYYLENYEGKILIIVPTTALTTQMADDFVDYRLFSHAMIKKIG  192 (282)
T ss_dssp             CCCHHHHHHHHHHHHHSEEEECCCTTSCHHHHHHHHHHHHHHHCSSEEEEECSSHHHHHHHHHHHHHHTSCCGGGEEECS
T ss_pred             ccchHHHHHHHHHHhcCCceeEEEcccCccHHHHHHHHHhhhcccceEEEEEcCchhHHHHHHHHHHhhccccccceeec
Confidence            59999999999999999999999999999987654432    2467899999999999999999998764332    222


Q ss_pred             CCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHHhcCCC-C
Q 037567           85 SAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGV-P  163 (374)
Q Consensus        85 ~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~~~~-~  163 (374)
                      ++....    ........++++|++++......     .+..+++||+||||+...         ..+..+.....+. .
T Consensus       193 ~g~~~~----~~~~~~~~i~i~t~qs~~~~~~~-----~~~~f~~VIvDEaH~~~a---------~~~~~il~~~~~~~~  254 (282)
T d1rifa_         193 GGASKD----DKYKNDAPVVVGTWQTVVKQPKE-----WFSQFGMMMNDECHLATG---------KSISSIISGLNNCMF  254 (282)
T ss_dssp             TTCSST----TCCCTTCSEEEECHHHHTTSCGG-----GGGGEEEEEEETGGGCCH---------HHHHHHTTTCTTCCE
T ss_pred             ceeccc----ccccccceEEEEeeehhhhhccc-----ccCCCCEEEEECCCCCCc---------hhHHHHHHhccCCCe
Confidence            221111    11123358999999988766544     346789999999998753         3344555555444 4


Q ss_pred             eeEEEeecCccc
Q 037567          164 FVALTATATEKV  175 (374)
Q Consensus       164 ~i~~SaT~~~~~  175 (374)
                      +++||||+....
T Consensus       255 rlGlTaT~~~~~  266 (282)
T d1rifa_         255 KFGLSGSLRDGK  266 (282)
T ss_dssp             EEEECSSCCTTS
T ss_pred             EEEEEeecCCCC
Confidence            699999987654

>d1wp9a2 c.37.1.19 (A:201-486) 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=99.82  E-value=2.3e-20  Score=158.64  Aligned_cols=121  Identities=26%  Similarity=0.356  Sum_probs=102.9

Q ss_pred             HHHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHHcCCceeeeec--------CCChHHHHHHHHhhhcCCeeEEEEec
Q 037567          215 DELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHG--------QMGSKAREEAHRLFIRDEIRVMVATM  286 (374)
Q Consensus       215 ~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~--------~~~~~~r~~~~~~f~~g~~~ilv~t~  286 (374)
                      .+++.+++.. .++.++||||++...++.+++.|.+.++++..++|        +++..++..+++.|++|+.+|||+|+
T Consensus       149 ~~~l~~~~~~-~~~~k~iiF~~~~~~~~~~~~~L~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~F~~g~~~vLv~T~  227 (286)
T d1wp9a2         149 KEIIREQLQR-KQNSKIIVFTNYRETAKKIVNELVKDGIKAKRFVGQASKENDRGLSQREQKLILDEFARGEFNVLVATS  227 (286)
T ss_dssp             HHHHHHHHHH-CTTCCEEEECSCHHHHHHHHHHHHHTTCCEEEECCSSCC-------CCHHHHHHHHHHHTSCSEEEECG
T ss_pred             HHHHHHHHHh-CCCCcEEEEeCcHHhHHHHHHHHHHcCCceEEeeccccccccchhchHHHHHHHHHHHcCCCcEEEEcc
Confidence            3444444433 46789999999999999999999999999888866        45566899999999999999999999


Q ss_pred             cccccccccCccEEEEECCCCChhHHHHhhccCCCCCCceEEEEEeeccCC
Q 037567          287 AFGMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNF  337 (374)
Q Consensus       287 ~~~~G~d~~~~~~vi~~~~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~~  337 (374)
                      ++++|+|+|++++||++++|+|+..|+||+||+||.+ .|.++.++.+...
T Consensus       228 ~~~~Gld~~~~~~Vi~~d~~~~~~~~~Qr~GR~gR~~-~~~~~~l~~~~~~  277 (286)
T d1wp9a2         228 VGEEGLDVPEVDLVVFYEPVPSAIRSIQRRGRTGRHM-PGRVIILMAKGTR  277 (286)
T ss_dssp             GGGGGGGSTTCCEEEESSCCHHHHHHHHHHTTSCSCC-CSEEEEEEETTSH
T ss_pred             ceeccccCCCCCEEEEeCCCCCHHHHHHHHHhCCCCC-CCEEEEEEeCCCH
Confidence            9999999999999999999999999999999999965 6778888877643

>d2p6ra4 c.37.1.19 (A:203-403) 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=99.82  E-value=9.5e-21  Score=151.03  Aligned_cols=122  Identities=25%  Similarity=0.402  Sum_probs=102.2

Q ss_pred             HHHHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHHc------------------------------CCceeeeecCCC
Q 037567          214 VDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQL------------------------------GVKAGTYHGQMG  263 (374)
Q Consensus       214 ~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~------------------------------~~~~~~~~~~~~  263 (374)
                      ..+++.+.++   .++++||||++++.++.++..|.+.                              ...++++|++++
T Consensus        29 ~~~l~~~~i~---~~~~~LVF~~sRk~~~~~A~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~GIa~hh~~l~  105 (201)
T d2p6ra4          29 FEELVEECVA---ENGGVLVFESTRRGAEKTAVKLSAITAKYVENEGLEKAILEENEGEMSRKLAECVRKGAAFHHAGLL  105 (201)
T ss_dssp             HHHHHHHHHH---TTCCEEEECSSHHHHHHHHHHHHHHHHTTCCCSSHHHHHHTTCCSHHHHHHHHHHHTTCCEECTTSC
T ss_pred             HHHHHHHHHH---cCCcEEEEeCCHHHHHHHHHHHHHHHHhhhchhHHHHHHHHhhhhhhhHHHHHHHhccHHHHHHHhh
Confidence            4455555444   5789999999999999888887652                              122678999999


Q ss_pred             hHHHHHHHHhhhcCCeeEEEEeccccccccccCccEEEE-------ECCCCChhHHHHhhccCCCCCC--ceEEEEEeec
Q 037567          264 SKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIH-------YGCPKTLESYYQESGRCGRDGI--ASVCWLYYAR  334 (374)
Q Consensus       264 ~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~-------~~~p~s~~~~~Q~~GR~~R~~~--~g~~~~~~~~  334 (374)
                      .++|..+.+.|++|.++|||||+.+++|+|+|..++||.       .+.|.+..+|.||+|||||.|.  .|.+++++.+
T Consensus       106 ~~~r~~ie~~f~~g~i~vlvaT~~l~~Gin~p~~~vvi~~~~~~d~~~~~~~~~~~~q~~GRAGR~g~~~~G~~~l~~~~  185 (201)
T d2p6ra4         106 NGQRRVVEDAFRRGNIKVVVATPTLAAGVNLPARRVIVRSLYRFDGYSKRIKVSEYKQMAGRAGRPGMDERGEAIIIVGK  185 (201)
T ss_dssp             HHHHHHHHHHHHTTSCCEEEECSTTTSSSCCCBSEEEECCSEEESSSEEECCHHHHHHHHTTBSCTTTCSCEEEEEECCG
T ss_pred             hhhHHHHHHHHhCCCceEEEechHHHhhcCCCCceEEEecceeccCCcCCCCHHHHHHHhcccCCCCCCCeeEEEEEeCC
Confidence            999999999999999999999999999999998888885       4567789999999999999884  7888888877


Q ss_pred             cCCC
Q 037567          335 SNFA  338 (374)
Q Consensus       335 ~~~~  338 (374)
                      .+..
T Consensus       186 ~~~~  189 (201)
T d2p6ra4         186 RDRE  189 (201)
T ss_dssp             GGHH
T ss_pred             CChH
Confidence            6543

>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=99.79  E-value=1.9e-19  Score=147.59  Aligned_cols=158  Identities=20%  Similarity=0.177  Sum_probs=117.6

Q ss_pred             hhHHHhHcCCCCCchhHHHHHHHHHc----C--CCEEEEccCCCCchhhhhcccc---ccCCcEEEEcchHHHHHHHHHH
Q 037567            2 VSTLKKYFGYSVFRPYQKDVIQRIIE----K--RDCLVVMATGSGKSLCYQLPPL---VTGKTALVVSPLISLMQDQVMS   72 (374)
Q Consensus         2 ~~~l~~~~~~~~~~~~Q~~~~~~~~~----~--~~~l~~a~tGsGKT~~~~l~~~---~~~~~~lil~P~~~l~~q~~~~   72 (374)
                      .+.+.+.++|. +++-|.+++..+.+    +  .+.++.|.+|||||..|+.++.   .++.++++++|+..|+.|+++.
T Consensus        73 ~~~f~~~LPFe-LT~~Q~~ai~ei~~d~~~~~~m~rLL~GdvGSGKT~Va~~a~~~~~~~g~q~~~m~Pt~~La~Qh~~~  151 (264)
T d1gm5a3          73 AEEFIKSLPFK-LTNAQKRAHQEIRNDMISEKPMNRLLQGDVGSGKTVVAQLAILDNYEAGFQTAFMVPTSILAIQHYRR  151 (264)
T ss_dssp             HHHHHHHSSSC-CCHHHHHHHHHHHHHHHSSSCCCCEEECCSSSSHHHHHHHHHHHHHHHTSCEEEECSCHHHHHHHHHH
T ss_pred             HHHHHhhcccc-CCchHHHHHHHHHHHhhccCcceeeeeccccccccHHHHHHHHHHHhcccceeEEeehHhhhHHHHHH
Confidence            45667778885 99999999998864    2  3669999999999988876654   4799999999999999999988


Q ss_pred             HHHc----CCceEEcCCCCCchh---hhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcc
Q 037567           73 LKQR----GINAEFLGSAQTDSS---VQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDF  145 (374)
Q Consensus        73 ~~~~----~~~~~~~~~~~~~~~---~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~  145 (374)
                      ++++    |..+.++++.....+   .+.....+..+|+|+|...+.       ....+.++++|||||-|...-.+.. 
T Consensus       152 ~~~~f~~~~~~v~~l~~~~~~~~r~~~~~~~~~g~~~iiIGThsl~~-------~~~~f~~LglviiDEqH~fgv~Qr~-  223 (264)
T d1gm5a3         152 TVESFSKFNIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTHALIQ-------EDVHFKNLGLVIIDEQHRFGVKQRE-  223 (264)
T ss_dssp             HHHHHTCSSCCEEECCSSSCHHHHHHHHHHHHSSCCCEEEECTTHHH-------HCCCCSCCCEEEEESCCCC-----C-
T ss_pred             HHHhhhhccccceeeccccchHHHHHHHHHHHCCCCCEEEeehHHhc-------CCCCccccceeeeccccccchhhHH-
Confidence            8753    677888877665543   344556788999999975432       3345678999999999987542221 


Q ss_pred             hHHHHHHHHHHHhcCCCCeeEEEeecCcccH
Q 037567          146 RLEYKQLDKLRTFLLGVPFVALTATATEKVR  176 (374)
Q Consensus       146 ~~~~~~~~~~~~~~~~~~~i~~SaT~~~~~~  176 (374)
                              .+.....+..++.|||||.+...
T Consensus       224 --------~l~~~~~~~~~l~~SATPiprtl  246 (264)
T d1gm5a3         224 --------ALMNKGKMVDTLVMSATPIPRSM  246 (264)
T ss_dssp             --------CCCSSSSCCCEEEEESSCCCHHH
T ss_pred             --------HHHHhCcCCCEEEEECCCCHHHH
Confidence                    11222235789999999999764

>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=99.79  E-value=7e-19  Score=141.48  Aligned_cols=158  Identities=19%  Similarity=0.250  Sum_probs=119.6

Q ss_pred             hHHHhHcCCCCCchhHHHHHHHHHc----C--CCEEEEccCCCCchhhhhcccc---ccCCcEEEEcchHHHHHHHHHHH
Q 037567            3 STLKKYFGYSVFRPYQKDVIQRIIE----K--RDCLVVMATGSGKSLCYQLPPL---VTGKTALVVSPLISLMQDQVMSL   73 (374)
Q Consensus         3 ~~l~~~~~~~~~~~~Q~~~~~~~~~----~--~~~l~~a~tGsGKT~~~~l~~~---~~~~~~lil~P~~~l~~q~~~~~   73 (374)
                      +.+.+.++|. +++-|.+++..+.+    +  .+.+++|+||||||..|+.++.   .+++++++++|+..|+.|+++.+
T Consensus        46 ~~~~~~lP~~-lt~~Q~~~~~~i~~~~~~~~~~~~LL~GdvGsGKT~V~~~a~~~~~~~g~qv~~l~Pt~~La~Q~~~~~  124 (233)
T d2eyqa3          46 QLFCDSFPFE-TTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVDNHKQVAVLVPTTLLAQQHYDNF  124 (233)
T ss_dssp             HHHHHTCCSC-CCHHHHHHHHHHHHHHHSSSCCEEEEECCCCTTTHHHHHHHHHHHHTTTCEEEEECSSHHHHHHHHHHH
T ss_pred             Hhhhhccccc-cchhHHHHHHHHHHHHhccCccCeEEEcCCCCCcHHHHHHHHHHHHHcCCceEEEccHHHhHHHHHHHH
Confidence            4556667885 99999999988764    2  3679999999999988876654   47999999999999999999999


Q ss_pred             HH----cCCceEEcCCCCCchh---hhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcch
Q 037567           74 KQ----RGINAEFLGSAQTDSS---VQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFR  146 (374)
Q Consensus        74 ~~----~~~~~~~~~~~~~~~~---~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~  146 (374)
                      ++    ++.++..+++......   .......+..+|+|+|...+.       ....+.++.+||+||-|...-      
T Consensus       125 ~~~~~~~~~~v~~l~~~~~~~~~~~~~~~~~~g~~~iviGths~l~-------~~~~f~~LgLiIiDEeH~fg~------  191 (233)
T d2eyqa3         125 RDRFANWPVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTHKLLQ-------SDVKFKDLGLLIVDEEHRFGV------  191 (233)
T ss_dssp             HHHSTTTTCCEEEESTTSCHHHHHHHHHHHHTTCCSEEEECTHHHH-------SCCCCSSEEEEEEESGGGSCH------
T ss_pred             HHHHhhCCCEEEeccCcccchhHHHHHHHHhCCCCCEEEeehhhhc-------cCCccccccceeeechhhhhh------
Confidence            86    4677777777665443   345566788999999964332       123457889999999997543      


Q ss_pred             HHHHHHHHHHHhcCCCCeeEEEeecCcccHH
Q 037567          147 LEYKQLDKLRTFLLGVPFVALTATATEKVRI  177 (374)
Q Consensus       147 ~~~~~~~~~~~~~~~~~~i~~SaT~~~~~~~  177 (374)
                         ..-..+.....+..++.+||||.+....
T Consensus       192 ---kQ~~~l~~~~~~~~~l~~SATPiprtl~  219 (233)
T d2eyqa3         192 ---RHKERIKAMRANVDILTLTATPIPRTLN  219 (233)
T ss_dssp             ---HHHHHHHHHHTTSEEEEEESSCCCHHHH
T ss_pred             ---HHHHHHHhhCCCCCEEEEecchhHHHHH
Confidence               2223344445678899999999997643

>d2eyqa5 c.37.1.19 (A:779-989) 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=99.79  E-value=1.4e-18  Score=135.57  Aligned_cols=120  Identities=23%  Similarity=0.376  Sum_probs=109.3

Q ss_pred             HHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHHc--CCceeeeecCCChHHHHHHHHhhhcCCeeEEEEecccccccc
Q 037567          216 ELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQL--GVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGID  293 (374)
Q Consensus       216 ~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~--~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d  293 (374)
                      .+...+.+.+..++++.+.||..+..+.+++.+++.  +.++..+||.|+.++++.++.+|.+|+++|||||.+++.|+|
T Consensus        19 ~i~~~I~~El~rGgQvy~V~p~I~~~e~~~~~l~~~~p~~~i~~lHGkm~~~eke~im~~F~~g~~~ILv~TtvIEvGiD   98 (211)
T d2eyqa5          19 VVREAILREILRGGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGID   98 (211)
T ss_dssp             HHHHHHHHHHTTTCEEEEECCCSSCHHHHHHHHHHHCTTSCEEECCSSCCHHHHHHHHHHHHTTSCCEEEESSTTGGGSC
T ss_pred             HHHHHHHHHHHcCCeEEEEEcCccchhhHHHHHHHhCCceEEEEEEeccCHHHHHHHHHHHHcCCcceEEEehhhhhccC
Confidence            455566677788999999999999999999999884  678999999999999999999999999999999999999999


Q ss_pred             ccCccEEEEECCCC-ChhHHHHhhccCCCCCCceEEEEEeecc
Q 037567          294 KPDVRHVIHYGCPK-TLESYYQESGRCGRDGIASVCWLYYARS  335 (374)
Q Consensus       294 ~~~~~~vi~~~~p~-s~~~~~Q~~GR~~R~~~~g~~~~~~~~~  335 (374)
                      +|+++++|..+... ...++-|..||+||.+..+.|+++++..
T Consensus        99 vpnA~~iiI~~a~rfGLaQLhQLRGRVGR~~~~s~c~l~~~~~  141 (211)
T d2eyqa5          99 IPTANTIIIERADHFGLAQLHQLRGRVGRSHHQAYAWLLTPHP  141 (211)
T ss_dssp             CTTEEEEEETTTTSSCHHHHHHHHTTCCBTTBCEEEEEEECCG
T ss_pred             CCCCcEEEEecchhccccccccccceeeecCccceEEEEecCC
Confidence            99999999888764 8899999999999999999999998754

>d2fwra1 c.37.1.19 (A:257-456) 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=99.77  E-value=1.3e-19  Score=145.41  Aligned_cols=106  Identities=24%  Similarity=0.268  Sum_probs=94.4

Q ss_pred             HHHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccc
Q 037567          215 DELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDK  294 (374)
Q Consensus       215 ~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~  294 (374)
                      .+.+.++++.. .+.++||||++...++.+++.|     .+..+||+++.++|+.+++.|++|+.+|||+|+++++|+|+
T Consensus        81 ~~~l~~ll~~~-~~~k~lvf~~~~~~~~~l~~~l-----~~~~i~g~~~~~~R~~~l~~F~~~~~~vLv~~~~~~~Gidl  154 (200)
T d2fwra1          81 IRKLREILERH-RKDKIIIFTRHNELVYRISKVF-----LIPAITHRTSREEREEILEGFRTGRFRAIVSSQVLDEGIDV  154 (200)
T ss_dssp             HHHHHHHHHHT-SSSCBCCBCSCHHHHHHHHHHT-----TCCBCCSSSCSHHHHTHHHHHHHSSCSBCBCSSCCCSSSCS
T ss_pred             HHHHHHHHHhC-CCCcEEEEeCcHHHHHHHHhhc-----CcceeeCCCCHHHHHHHHHHhhcCCeeeeeecchhhcccCC
Confidence            34556666653 6789999999999999998876     34568999999999999999999999999999999999999


Q ss_pred             cCccEEEEECCCCChhHHHHhhccCCCCCCce
Q 037567          295 PDVRHVIHYGCPKTLESYYQESGRCGRDGIAS  326 (374)
Q Consensus       295 ~~~~~vi~~~~p~s~~~~~Q~~GR~~R~~~~g  326 (374)
                      |.+++||++++|+|+..++||+||++|.|+++
T Consensus       155 ~~~~~vi~~~~~~s~~~~~Q~iGR~~R~~~~k  186 (200)
T d2fwra1         155 PDANVGVIMSGSGSAREYIQRLGRILRPSKGK  186 (200)
T ss_dssp             CCBSEEEEECCSSCCHHHHHHHHHSBCCCTTT
T ss_pred             CCCCEEEEeCCCCCHHHHHHHHHhcCCCCCCC
Confidence            99999999999999999999999999998753

>d1gm5a4 c.37.1.19 (A:550-755) 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=99.76  E-value=8.4e-20  Score=144.20  Aligned_cols=122  Identities=21%  Similarity=0.374  Sum_probs=99.6

Q ss_pred             hHHHHHHHHHHhhcCCCcEEEEecchhHHHHH--------HHHHHHc---CCceeeeecCCChHHHHHHHHhhhcCCeeE
Q 037567          213 FVDELVQEILKSVAGAGSIIVYCMTIKDVEEI--------SKALKQL---GVKAGTYHGQMGSKAREEAHRLFIRDEIRV  281 (374)
Q Consensus       213 ~~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l--------~~~l~~~---~~~~~~~~~~~~~~~r~~~~~~f~~g~~~i  281 (374)
                      ....+...+.+.+..++++.|.||..+..+.+        .+.|.+.   +.++..+||.|+++++++++++|.+|+++|
T Consensus        14 ~~~~v~~~I~~el~~g~QvyvVcP~Ieese~~~~~~~~e~~~~l~~~~~p~~~v~~lHG~m~~~eke~~m~~F~~g~~~i   93 (206)
T d1gm5a4          14 RVNEVYEFVRQEVMRGGQAFIVYPLIEESDKLNVKSAVEMYEYLSKEVFPEFKLGLMHGRLSQEEKDRVMLEFAEGRYDI   93 (206)
T ss_dssp             THHHHHHHHHHHTTTSCCBCCBCCCC--------CHHHHHHHSGGGSCC---CBCCCCSSSCCSCSHHHHHHHTTTSSSB
T ss_pred             cHHHHHHHHHHHHHcCCCEEEEEeeecccccccchhhHHHHHHHHHhcCCCCeEEEEeecccHHHHHHHHHHHHCCCEEE
Confidence            34566777777788899999999977655433        3333332   567889999999999999999999999999


Q ss_pred             EEEeccccccccccCccEEEEECCCC-ChhHHHHhhccCCCCCCceEEEEEeec
Q 037567          282 MVATMAFGMGIDKPDVRHVIHYGCPK-TLESYYQESGRCGRDGIASVCWLYYAR  334 (374)
Q Consensus       282 lv~t~~~~~G~d~~~~~~vi~~~~p~-s~~~~~Q~~GR~~R~~~~g~~~~~~~~  334 (374)
                      ||||.++++|+|+|++++||++++|. ...++.|..||+||.+..|.|++++++
T Consensus        94 LVaTtViE~GIDip~a~~iii~~a~~fglsqlhQlrGRvGR~~~~~~~~l~~~~  147 (206)
T d1gm5a4          94 LVSTTVIEVGIDVPRANVMVIENPERFGLAQLHQLRGRVGRGGQEAYCFLVVGD  147 (206)
T ss_dssp             CCCSSCCCSCSCCTTCCEEEBCSCSSSCTTHHHHHHHTSCCSSTTCEEECCCCS
T ss_pred             EEEehhhhccccccCCcEEEEEccCCccHHHHHhhhhheeeccccceeEeeecc
Confidence            99999999999999999999999886 788889999999999999999999865

>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=99.76  E-value=2.1e-19  Score=134.93  Aligned_cols=128  Identities=18%  Similarity=0.066  Sum_probs=85.7

Q ss_pred             CCCEEEEccCCCCchhhhhccccccCCcEEEEcchHHHHHHHHHHHHHc-CCceEEcCCCCCchhhhhhhhcCCeeEEEE
Q 037567           28 KRDCLVVMATGSGKSLCYQLPPLVTGKTALVVSPLISLMQDQVMSLKQR-GINAEFLGSAQTDSSVQTKAETGYFQLLFM  106 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~  106 (374)
                      .+..++.+|||||||+.+...+...+.+++|++|++.|++||.+.+... +........+..        ......+.++
T Consensus         8 ~~~~ll~apTGsGKT~~~~~~~~~~~~~vli~~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~--------~~~~~~~~~~   79 (136)
T d1a1va1           8 FQVAHLHAPTGSGKSTKVPAAYAAQGYKVLVLNPSVAATLGFGAYMSKAHGVDPNIRTGVRT--------ITTGSPITYS   79 (136)
T ss_dssp             CEEEEEECCTTSCTTTHHHHHHHTTTCCEEEEESCHHHHHHHHHHHHHHHSCCCEEECSSCE--------ECCCCSEEEE
T ss_pred             CCEEEEEeCCCCCHHHHHHHHHHHcCCcEEEEcChHHHHHHHHHHHHHHhhccccccccccc--------cccccceEEE
Confidence            3567999999999998776667778899999999999999999998864 332222222111        1112357778


Q ss_pred             cCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHHhcCCCCeeEEEeec
Q 037567          107 TPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATA  171 (374)
Q Consensus       107 T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~SaT~  171 (374)
                      |++......     ...+.++++||+||+|++....   ...+..+.+.....++..+++|||||
T Consensus        80 ~~~~~~~~~-----~~~~~~~~~vIiDE~H~~~~~~---~~~~~~~l~~~~~~~~~~~l~~TATP  136 (136)
T d1a1va1          80 TYGKFLADG-----GCSGGAYDIIICDECHSTDATS---ILGIGTVLDQAETAGARLVVLATATP  136 (136)
T ss_dssp             EHHHHHHTT-----GGGGCCCSEEEEETTTCCSHHH---HHHHHHHHHHTTTTTCSEEEEEESSC
T ss_pred             eeeeecccc-----chhhhcCCEEEEecccccCHHH---HHHHHHHHHHHHHCCCCcEEEEeCCC
Confidence            877654332     2345789999999999874321   11123333333334466789999997

>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=99.75  E-value=1.1e-19  Score=137.62  Aligned_cols=131  Identities=13%  Similarity=0.084  Sum_probs=85.2

Q ss_pred             cCCCEEEEccCCCCchhhhhcccc----ccCCcEEEEcchHHHHHHHHHHHHHcCCceEEcCCCCCchhhhhhhhcCCee
Q 037567           27 EKRDCLVVMATGSGKSLCYQLPPL----VTGKTALVVSPLISLMQDQVMSLKQRGINAEFLGSAQTDSSVQTKAETGYFQ  102 (374)
Q Consensus        27 ~~~~~l~~a~tGsGKT~~~~l~~~----~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  102 (374)
                      +++++++.+|||+|||..++..++    ..+.++++++|++.+++|+.+.+...+............        .....
T Consensus         6 ~~~~~il~~~tGsGKT~~~~~~~~~~~~~~~~~vli~~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~--------~~~~~   77 (140)
T d1yksa1           6 KGMTTVLDFHPGAGKTRRFLPQILAECARRRLRTLVLAPTRVVLSEMKEAFHGLDVKFHTQAFSAHG--------SGREV   77 (140)
T ss_dssp             TTCEEEECCCTTSSTTTTHHHHHHHHHHHTTCCEEEEESSHHHHHHHHHHTTTSCEEEESSCCCCCC--------CSSCC
T ss_pred             cCCcEEEEcCCCCChhHHHHHHHHHHhhhcCceeeeeecchhHHHHHHHHhhhhhhhhccccccccc--------ccccc
Confidence            578899999999999977654443    357889999999999999998887665443332221111        11124


Q ss_pred             EEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHHhcCCCCeeEEEeecC
Q 037567          103 LLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATAT  172 (374)
Q Consensus       103 i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~SaT~~  172 (374)
                      +.+.|...+..   .........++++||+||||++...+...    ..+........+.++++|||||+
T Consensus        78 ~~~~~~~~l~~---~~~~~~~~~~~~lvIiDEaH~~~~~~~~~----~~~~~~~~~~~~~~~l~lTATPp  140 (140)
T d1yksa1          78 IDAMCHATLTY---RMLEPTRVVNWEVIIMDEAHFLDPASIAA----RGWAAHRARANESATILMTATPP  140 (140)
T ss_dssp             EEEEEHHHHHH---HHTSSSCCCCCSEEEETTTTCCSHHHHHH----HHHHHHHHHTTSCEEEEECSSCT
T ss_pred             hhhhhHHHHHH---HHhccccccceeEEEEccccccChhhHHH----HHHHHHHhhCCCCCEEEEEcCCC
Confidence            55556554322   11223345679999999999885433221    22223333346889999999996

>d1a1va2 c.37.1.14 (A:326-624) 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=99.75  E-value=6e-19  Score=143.96  Aligned_cols=107  Identities=17%  Similarity=0.240  Sum_probs=92.0

Q ss_pred             CCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHH----------HHHHHhhhcCCeeEEEEeccccc---ccc
Q 037567          227 GAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAR----------EEAHRLFIRDEIRVMVATMAFGM---GID  293 (374)
Q Consensus       227 ~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r----------~~~~~~f~~g~~~ilv~t~~~~~---G~d  293 (374)
                      .++++||||+++..++.+++.|++.|+++..+|++++.+.|          ...++.|..|+.+++|+|+.+.+   |+|
T Consensus        35 kggk~LVFcnSR~~aE~La~~L~~~Gi~a~~~Hgglsq~~R~~~gd~~i~~~~aLe~f~~G~~dvVVaT~~~a~g~~giD  114 (299)
T d1a1va2          35 KGGRHLIFCHSKKKCDELAAKLVALGINAVAYYRGLDVSVIPTSGDVVVVATDALMTGFTGDFDSVIDCNTCVTQTVDFS  114 (299)
T ss_dssp             HSSEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCGGGSCSSSSEEEEECTTC---CCCCBSEEEECCEEEEEEEECC
T ss_pred             cCCCEEEECCcHHHHHHHHHHHHHCCCCEEEEeCCchHHHHHhccchHHHHHHHHHHHhcCCCcEEEEEeehhccCCCCC
Confidence            47899999999999999999999999999999999998776          45678889999999999999888   566


Q ss_pred             ccCccEEEEECCCCChhHHHHhhccCCCCCCceEEEEEeec
Q 037567          294 KPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYAR  334 (374)
Q Consensus       294 ~~~~~~vi~~~~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~  334 (374)
                      ++.+.+|++++.|.|..+|+||+||+|| |++|....++..
T Consensus       115 id~V~~VI~~d~P~SvesyIQRiGRTGR-Gr~G~~~~l~~~  154 (299)
T d1a1va2         115 LDPTFTIETTTLPQDAVSRTQRRGRTGR-GKPGIYRFVAPG  154 (299)
T ss_dssp             CSSSCEEEEEEEECBHHHHHHHHTTBCS-SSCEEEEESCSC
T ss_pred             CCcceEEEeCCCCCCHHHHHhhccccCC-CCCceEEEEecC
Confidence            6667789999999999999999999999 888877655444

>d1gkub2 c.37.1.16 (B:251-498) 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=99.67  E-value=7.2e-19  Score=145.78  Aligned_cols=121  Identities=21%  Similarity=0.316  Sum_probs=100.4

Q ss_pred             HHHHHHhhcCCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEe----cccccccc
Q 037567          218 VQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVAT----MAFGMGID  293 (374)
Q Consensus       218 ~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t----~~~~~G~d  293 (374)
                      +.++++.+  +.++||||++++.++.+++.|++      .+||+++..+|.+++++|.+|+++|||||    +.+++|+|
T Consensus        17 l~~~l~~~--~~~~iif~~~~~~~~~l~~~l~~------~~hg~~~~~~R~~~~~~f~~g~~~vLVaT~a~~~v~~rGlD   88 (248)
T d1gkub2          17 LSSILEKL--GTGGIIYARTGEEAEEIYESLKN------KFRIGIVTATKKGDYEKFVEGEIDHLIGTAHYYGTLVRGLD   88 (248)
T ss_dssp             THHHHTTS--CSCEEEEESSHHHHHHHHHTTTT------SSCEEECTTSSSHHHHHHHHTSCSEEEEECC------CCSC
T ss_pred             HHHHHHHh--CCCEEEEECCHHHHHHHHHHHHH------hccCCCCHHHHHHHHHHHHhCCCeEEEEeccccchhhhccC
Confidence            44455543  56899999999999999999975      37999999999999999999999999999    67899999


Q ss_pred             ccC-ccEEEEECCCCChhHHHHhhccCCCCCCceEEEEEeeccCCCcccceeccccch
Q 037567          294 KPD-VRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSNFAKGDFYCGESQTE  350 (374)
Q Consensus       294 ~~~-~~~vi~~~~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~~~~~~~~~~~~~~~  350 (374)
                      +|+ +++||++++|+    |.|++||+||.|..|.+++++...+......+.......
T Consensus        89 ip~~v~~VI~~d~P~----~~~r~gR~~R~g~~~~~~~~~~~~~~~~~~~l~~~~~~~  142 (248)
T d1gkub2          89 LPERIRFAVFVGCPS----FRVTIEDIDSLSPQMVKLLAYLYRNVDEIERLLPAVERH  142 (248)
T ss_dssp             CTTTCCEEEEESCCE----EEEECSCGGGSCHHHHHHHHTTTSCHHHHHTTCTTTSSC
T ss_pred             ccccccEEEEeCCCc----chhhhhhhhccCcceEeeeeccHhhHHHHHHHHHHHHHh
Confidence            996 99999999995    779999999999999999888888777666665544443

>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=99.62  E-value=6.4e-16  Score=126.51  Aligned_cols=156  Identities=20%  Similarity=0.126  Sum_probs=105.8

Q ss_pred             CCchhHHHHHHHHHc----CCCEEEEccCCCCchhhhhccccc-----cCCcEEEEcchHHHHHHHHHHHHHcCCceEEc
Q 037567           13 VFRPYQKDVIQRIIE----KRDCLVVMATGSGKSLCYQLPPLV-----TGKTALVVSPLISLMQDQVMSLKQRGINAEFL   83 (374)
Q Consensus        13 ~~~~~Q~~~~~~~~~----~~~~l~~a~tGsGKT~~~~l~~~~-----~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~   83 (374)
                      .++|||.+++..+..    +..+++..++|+|||+.++..+..     ...++||++|. .+..||.+++.++.......
T Consensus        12 ~L~~yQ~~~v~~~~~~~~~~~g~iLaDe~GlGKT~~~i~~~~~~~~~~~~~~~LIv~p~-~l~~~W~~e~~~~~~~~~~~   90 (230)
T d1z63a1          12 NLRPYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQTIAVFSDAKKENELTPSLVICPL-SVLKNWEEELSKFAPHLRFA   90 (230)
T ss_dssp             CCCHHHHHHHHHHHHHHHTTCCEEECCCTTSCHHHHHHHHHHHHHHTTCCSSEEEEECS-TTHHHHHHHHHHHCTTSCEE
T ss_pred             chhHHHHHHHHHHHHhhhcCCCEEEEeCCCCChHHHHHHhhhhhhhcccccccceecch-hhhhHHHHHHHhhcccccce
Confidence            589999999976643    566888999999999876543321     35689999996 78899999998875433222


Q ss_pred             CCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHHhcCCCC
Q 037567           84 GSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVP  163 (374)
Q Consensus        84 ~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~~~~~  163 (374)
                      .......    .......+++++|++.+...     .......++++|+||+|.+.+....       .......+....
T Consensus        91 ~~~~~~~----~~~~~~~~vvi~~~~~~~~~-----~~l~~~~~~~vI~DEah~~k~~~s~-------~~~~~~~l~a~~  154 (230)
T d1z63a1          91 VFHEDRS----KIKLEDYDIILTTYAVLLRD-----TRLKEVEWKYIVIDEAQNIKNPQTK-------IFKAVKELKSKY  154 (230)
T ss_dssp             ECSSSTT----SCCGGGSSEEEEEHHHHTTC-----HHHHTCCEEEEEEETGGGGSCTTSH-------HHHHHHTSCEEE
T ss_pred             eeccccc----hhhccCcCEEEeeHHHHHhH-----HHHhcccceEEEEEhhhcccccchh-------hhhhhhhhccce
Confidence            2111111    11123458999999987654     3344467899999999999765432       122223334566


Q ss_pred             eeEEEeecCcccHHHHHHhcCC
Q 037567          164 FVALTATATEKVRIDIINSLKL  185 (374)
Q Consensus       164 ~i~~SaT~~~~~~~~~~~~~~~  185 (374)
                      ++++||||..+...++...+.+
T Consensus       155 r~~LTgTPi~n~~~dl~~ll~~  176 (230)
T d1z63a1         155 RIALTGTPIENKVDDLWSIMTF  176 (230)
T ss_dssp             EEEECSSCSTTCHHHHHHHHHH
T ss_pred             EEEEecchHHhHHHHHHHHHHh
Confidence            8999999999887776665543

>d1z3ix1 c.37.1.19 (X:390-735) 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=99.60  E-value=6e-15  Score=126.77  Aligned_cols=118  Identities=16%  Similarity=0.198  Sum_probs=102.0

Q ss_pred             HHHHHHHHHHhh--cCCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCe---eEEEEeccc
Q 037567          214 VDELVQEILKSV--AGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEI---RVMVATMAF  288 (374)
Q Consensus       214 ~~~~~~~~~~~~--~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~---~ilv~t~~~  288 (374)
                      +...+..++...  ..+.|+|||+......+.+.+.|...|+....++|+++..+|..+++.|+++..   -+|++|.+.
T Consensus       102 Kl~~L~~ll~~~~~~~g~KvlIFs~~~~~ld~l~~~l~~~g~~~~~l~G~~~~~~R~~~i~~F~~~~~~~~vlLls~~ag  181 (346)
T d1z3ix1         102 KMLVLDYILAMTRTTTSDKVVLVSNYTQTLDLFEKLCRNRRYLYVRLDGTMSIKKRAKIVERFNNPSSPEFIFMLSSKAG  181 (346)
T ss_dssp             HHHHHHHHHHHHHHHCCCEEEEEESCHHHHHHHHHHHHHHTCCEEEECSSCCHHHHHHHHHHHHSTTCCCCEEEEEGGGS
T ss_pred             HHHHHHHHHHHHHHhcCCceeEEeehhhhhHHHHHHHhhhhccccccccchhHHHHHHHHHhhhcccccceeeeecchhh
Confidence            344555555432  467899999999999999999999999999999999999999999999998753   256688899


Q ss_pred             cccccccCccEEEEECCCCChhHHHHhhccCCCCCCceEEEEE
Q 037567          289 GMGIDKPDVRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLY  331 (374)
Q Consensus       289 ~~G~d~~~~~~vi~~~~p~s~~~~~Q~~GR~~R~~~~g~~~~~  331 (374)
                      +.|+|++.++.||+++++|++....|++||+.|.|+...|.++
T Consensus       182 g~GlnL~~a~~vi~~d~~wnp~~~~Qa~~R~~R~GQ~~~V~v~  224 (346)
T d1z3ix1         182 GCGLNLIGANRLVMFDPDWNPANDEQAMARVWRDGQKKTCYIY  224 (346)
T ss_dssp             CTTCCCTTEEEEEECSCCSSHHHHHHHHTTSSSTTCCSCEEEE
T ss_pred             hhccccccceEEEEecCCCccchHhHhhhcccccCCCCceEEE
Confidence            9999999999999999999999999999999999997765544

>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=99.55  E-value=3.9e-15  Score=126.63  Aligned_cols=158  Identities=18%  Similarity=0.185  Sum_probs=99.0

Q ss_pred             CCchhHHHHHHHHHc---------CCCEEEEccCCCCchhhhhc---cccc-------cCCcEEEEcchHHHHHHHHHHH
Q 037567           13 VFRPYQKDVIQRIIE---------KRDCLVVMATGSGKSLCYQL---PPLV-------TGKTALVVSPLISLMQDQVMSL   73 (374)
Q Consensus        13 ~~~~~Q~~~~~~~~~---------~~~~l~~a~tGsGKT~~~~l---~~~~-------~~~~~lil~P~~~l~~q~~~~~   73 (374)
                      .++|||.+++..+++         +..+|+...+|+|||+..+.   ..+.       ...++||+||. .+..||.+++
T Consensus        55 ~Lr~hQ~~gv~~l~~~~~~~~~~~~~g~iLaDemGlGKT~qaia~l~~l~~~~~~~~~~~~~~LIV~P~-sl~~qW~~Ei  133 (298)
T d1z3ix2          55 VLRPHQREGVKFLWDCVTGRRIENSYGCIMADEMGLGKTLQCITLIWTLLKQSPDCKPEIDKVIVVSPS-SLVRNWYNEV  133 (298)
T ss_dssp             TCCHHHHHHHHHHHHHHTTSSSTTCCEEEECCCTTSCHHHHHHHHHHHHHHCCTTSSCSCSCEEEEECH-HHHHHHHHHH
T ss_pred             cccHHHHHHHHHHHHHHHhhhhccCCceEEEeCCCCCHHHHHHHHHHHHHHhcccccCCCCcEEEEccc-hhhHHHHHHH
Confidence            589999999987642         34678888999999975332   2222       13469999998 5889999999


Q ss_pred             HHcC---CceEEcCCCCCchhhhh--h-----hhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccC
Q 037567           74 KQRG---INAEFLGSAQTDSSVQT--K-----AETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGH  143 (374)
Q Consensus        74 ~~~~---~~~~~~~~~~~~~~~~~--~-----~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~  143 (374)
                      .++.   .......++........  .     ......+++++|++.+....    ......++++||+||+|++.+.+.
T Consensus       134 ~k~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~i~sy~~~~~~~----~~l~~~~~~~vI~DEaH~ikn~~s  209 (298)
T d1z3ix2         134 GKWLGGRVQPVAIDGGSKDEIDSKLVNFISQQGMRIPTPILIISYETFRLHA----EVLHKGKVGLVICDEGHRLKNSDN  209 (298)
T ss_dssp             HHHHGGGCCEEEECSSCHHHHHHHHHHHHCCCSSCCSCCEEEEEHHHHHHHT----TTTTTSCCCEEEETTGGGCCTTCH
T ss_pred             HhhcCCceeEEEEeCchHHHHHHHHHHhhhccCccccceEEEEeecccccch----hcccccceeeeecccccccccccc
Confidence            8762   22223332221111110  0     01234578899987664321    122234688999999999976442


Q ss_pred             cchHHHHHHHHHHHhcCCCCeeEEEeecCcccHHHHHHh
Q 037567          144 DFRLEYKQLDKLRTFLLGVPFVALTATATEKVRIDIINS  182 (374)
Q Consensus       144 ~~~~~~~~~~~~~~~~~~~~~i~~SaT~~~~~~~~~~~~  182 (374)
                             ........+....++++||||..+...++...
T Consensus       210 -------~~~~a~~~l~~~~rllLTGTPi~N~~~dl~~l  241 (298)
T d1z3ix2         210 -------QTYLALNSMNAQRRVLISGTPIQNDLLEYFSL  241 (298)
T ss_dssp             -------HHHHHHHHHCCSEEEEECSSCSGGGGGGCHHH
T ss_pred             -------hhhhhhhccccceeeeecchHHhhhhHHHHHH
Confidence                   22223333456678999999988765544443

>d1z5za1 c.37.1.19 (A:663-906) 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=99.54  E-value=1.5e-14  Score=119.19  Aligned_cols=108  Identities=17%  Similarity=0.222  Sum_probs=81.0

Q ss_pred             HhhcCCCcEEEEecchhHHHHHHHHHHHc-CCceeeeecCCChHHHHHHHHhhhcCC-eeEEEE-eccccccccccCccE
Q 037567          223 KSVAGAGSIIVYCMTIKDVEEISKALKQL-GVKAGTYHGQMGSKAREEAHRLFIRDE-IRVMVA-TMAFGMGIDKPDVRH  299 (374)
Q Consensus       223 ~~~~~~~~~lVf~~~~~~~~~l~~~l~~~-~~~~~~~~~~~~~~~r~~~~~~f~~g~-~~ilv~-t~~~~~G~d~~~~~~  299 (374)
                      +...++.++||||......+.+...+... +..+..+||+++..+|+.+++.|+++. ..++++ +.+.+.|+|++.+++
T Consensus        80 ~~~~~g~kviIFs~~~~~~~~l~~~l~~~~~~~~~~i~G~~~~~~R~~~i~~F~~~~~~~vll~~~~~~g~Glnl~~a~~  159 (244)
T d1z5za1          80 EALDEGDKIAIFTQFVDMGKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKFIVLSVKAGGFGINLTSANR  159 (244)
T ss_dssp             HHHHTTCCEEEEESCHHHHHHHHHHHHHHHCSCCCEECTTSCHHHHHHHHHHHHHCTTCCEEEEECCTTCCCCCCTTCSE
T ss_pred             hhcccccceEEEeeceehHHHHHHHHHhhccceEEEEecccchhccchhhhhhhccccchhccccccccccccccchhhh
Confidence            33457889999999999999999888754 888899999999999999999998764 566654 568999999999999


Q ss_pred             EEEECCCCChhHHHHhhccCCCCCCceEEEE
Q 037567          300 VIHYGCPKTLESYYQESGRCGRDGIASVCWL  330 (374)
Q Consensus       300 vi~~~~p~s~~~~~Q~~GR~~R~~~~g~~~~  330 (374)
                      +|++++|||+..+.|++||+.|.|+...+.+
T Consensus       160 vi~~~~~wn~~~~~Qa~~R~~R~Gq~~~v~i  190 (244)
T d1z5za1         160 VIHFDRWWNPAVEDQATDRVYRIGQTRNVIV  190 (244)
T ss_dssp             EEECSCCSCTTTC--------------CCEE
T ss_pred             hhhcCchhhhHHHhhhcceeeecCCCCceEE
Confidence            9999999999999999999999998654443

>d1yksa2 c.37.1.14 (A:325-623) 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=99.49  E-value=5.5e-14  Score=117.16  Aligned_cols=103  Identities=17%  Similarity=0.184  Sum_probs=82.6

Q ss_pred             CCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEEEEECCC
Q 037567          227 GAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYGCP  306 (374)
Q Consensus       227 ~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~~~~p  306 (374)
                      ..++++|||++..+++.+++.|++.|..+..+||.+...+.++    |.+|+.+++|+|+++++|+|+ ++.+||+.+.+
T Consensus        35 ~~g~~~~F~~s~~~~~~~a~~L~~~g~~V~~l~~~~~~~e~~~----~~~~~~~~~~~t~~~~~~~~~-~~~~vid~g~~  109 (299)
T d1yksa2          35 DKRPTAWFLPSIRAANVMAASLRKAGKSVVVLNRKTFEREYPT----IKQKKPDFILATDIAEMGANL-CVERVLDCRTA  109 (299)
T ss_dssp             CCSCEEEECSCHHHHHHHHHHHHHTTCCEEECCSSSCC------------CCCSEEEESSSTTCCTTC-CCSEEEECCEE
T ss_pred             cCCCEEEEeCCHHHHHHHHHHHHhcCCeEEEEcCcCcHhHHhh----hhcCCcCEEEEechhhhceec-CceEEEecCce
Confidence            4789999999999999999999999999999999998877654    678999999999999999999 59988866532


Q ss_pred             -------------------CChhHHHHhhccCCCCCCceEEEEEeec
Q 037567          307 -------------------KTLESYYQESGRCGRDGIASVCWLYYAR  334 (374)
Q Consensus       307 -------------------~s~~~~~Q~~GR~~R~~~~g~~~~~~~~  334 (374)
                                         .|..+..||.||+||.+....++++|..
T Consensus       110 ~~~~~~~~~~~~~~~~~~~~~~~~~~qr~gr~gr~~~~~~~~~~y~~  156 (299)
T d1yksa2         110 FKPVLVDEGRKVAIKGPLRISASSAAQRRGRIGRNPNRDGDSYYYSE  156 (299)
T ss_dssp             EEEEEETTTTEEEEEEEEECCHHHHHHHHTTSSCCTTCCCEEEEECS
T ss_pred             eceeeecCCCCeeEEeeeecCHHHHHHhcccccccCCCceEEEEeCC
Confidence                               3778889999999998655556666553

>d1tf5a4 c.37.1.19 (A:396-570) 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=99.49  E-value=2.6e-13  Score=101.97  Aligned_cols=129  Identities=17%  Similarity=0.193  Sum_probs=105.0

Q ss_pred             eecCCcchHHHHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEe
Q 037567          206 VINRGQSFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVAT  285 (374)
Q Consensus       206 ~~~~~~~~~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t  285 (374)
                      ++.....+...++.++.+....+.++||++.|++.++.+++.|++.+++...++......+-..+.+  ....-.|.|+|
T Consensus        12 vf~T~~eK~~AIi~eV~~~~~~grPVLIgT~SIe~SE~ls~~L~~~gi~h~vLnAk~~~~Ea~II~~--Ag~~g~VtIAT   89 (175)
T d1tf5a4          12 IYRTMEGKFKAVAEDVAQRYMTGQPVLVGTVAVETSELISKLLKNKGIPHQVLNAKNHEREAQIIEE--AGQKGAVTIAT   89 (175)
T ss_dssp             EESSHHHHHHHHHHHHHHHHHHTCCEEEEESCHHHHHHHHHHHHTTTCCCEEECSSCHHHHHHHHTT--TTSTTCEEEEE
T ss_pred             EEcCHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHcCCCceeehhhhHHHHHHHHHh--ccCCCceeehh
Confidence            3444556677888888887788999999999999999999999999999989988754444333332  22334799999


Q ss_pred             ccccccccccC--------ccEEEEECCCCChhHHHHhhccCCCCCCceEEEEEeeccC
Q 037567          286 MAFGMGIDKPD--------VRHVIHYGCPKTLESYYQESGRCGRDGIASVCWLYYARSN  336 (374)
Q Consensus       286 ~~~~~G~d~~~--------~~~vi~~~~p~s~~~~~Q~~GR~~R~~~~g~~~~~~~~~~  336 (374)
                      +++++|.|+.-        --+||....|.|..-..|..||+||.|.+|....+++-+|
T Consensus        90 NmAGRGtDikl~~~v~~~GGLhVI~t~~~~s~Rid~Ql~GR~gRQGdpGs~~~~~sleD  148 (175)
T d1tf5a4          90 NMAGRGTDIKLGEGVKELGGLAVVGTERHESRRIDNQLRGRSGRQGDPGITQFYLSMED  148 (175)
T ss_dssp             TTSSTTCCCCCCTTSGGGTSEEEEESSCCSSHHHHHHHHTTSSGGGCCEEEEEEEETTS
T ss_pred             hHHHcCCCccchHHHHhCCCcEEEEeccCcchhHHHHHhcchhhhCCCcccEEEEEcCH
Confidence            99999999843        1268889999999999999999999999999999987766

>d1nkta4 c.37.1.19 (A:397-615) Translocation ATPase SecA, nucleotide-binding domains {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: Tandem AAA-ATPase domain
domain: Translocation ATPase SecA, nucleotide-binding domains
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=99.08  E-value=1.9e-09  Score=82.07  Aligned_cols=130  Identities=15%  Similarity=0.111  Sum_probs=104.4

Q ss_pred             EeecCCcchHHHHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEE
Q 037567          205 KVINRGQSFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVA  284 (374)
Q Consensus       205 ~~~~~~~~~~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~  284 (374)
                      .++.........++.++......+.++||-+.|++..+.+++.|.+.+++...++......+-..+.+.=+  .-.|.|+
T Consensus        11 ~Vy~T~~~K~~Avv~ei~~~h~~GqPVLVGT~SVe~SE~lS~lL~~~gi~h~vLNAK~herEAeIIAqAG~--~GaVTIA   88 (219)
T d1nkta4          11 LIYKTEEAKYIAVVDDVAERYAKGQPVLIGTTSVERSEYLSRQFTKRRIPHNVLNAKYHEQEATIIAVAGR--RGGVTVA   88 (219)
T ss_dssp             EEESCHHHHHHHHHHHHHHHHHTTCCEEEEESCHHHHHHHHHHHHHTTCCCEEECSSCHHHHHHHHHTTTS--TTCEEEE
T ss_pred             eEEcCHHHHHHHHHHHHHHHHhcCCCEEEeeCcHHHHHHHHHHHHHhccchhccchhhHHHHHHHHHhccc--CCcEEee
Confidence            34455566778888888888889999999999999999999999999999999998754444333333222  3469999


Q ss_pred             eccccccccccC----------------------------------------------------ccEEEEECCCCChhHH
Q 037567          285 TMAFGMGIDKPD----------------------------------------------------VRHVIHYGCPKTLESY  312 (374)
Q Consensus       285 t~~~~~G~d~~~----------------------------------------------------~~~vi~~~~p~s~~~~  312 (374)
                      |+|+++|.|+.=                                                    =-+||......|..--
T Consensus        89 TNMAGRGTDI~LGgn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~~GGL~VIGTErHeSrRID  168 (219)
T d1nkta4          89 TNMAGRGTDIVLGGNVDFLTDQRLRERGLDPVETPEEYEAAWHSELPIVKEEASKEAKEVIEAGGLYVLGTERHESRRID  168 (219)
T ss_dssp             ETTCSTTCCCCTTCCHHHHHHHHHHHTTCCTTTSHHHHHHHHHHHHHHHHHHTTHHHHHHHHTTSEEEEECSCCSSHHHH
T ss_pred             ccccCCCCceeecCchhhhhHHHhhhcccCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcEEEecccccccccc
Confidence            999999999931                                                    1257777777788888


Q ss_pred             HHhhccCCCCCCceEEEEEeeccC
Q 037567          313 YQESGRCGRDGIASVCWLYYARSN  336 (374)
Q Consensus       313 ~Q~~GR~~R~~~~g~~~~~~~~~~  336 (374)
                      .|..||+||.|.+|....|++-+|
T Consensus       169 nQLRGRsGRQGDPGsSrFflSLeD  192 (219)
T d1nkta4         169 NQLRGRSGRQGDPGESRFYLSLGD  192 (219)
T ss_dssp             HHHHHTSSGGGCCEEEEEEEETTS
T ss_pred             ccccccccccCCCccceeEEeccH
Confidence            999999999999999999988765

>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=98.56  E-value=8.4e-08  Score=76.46  Aligned_cols=174  Identities=15%  Similarity=0.121  Sum_probs=108.2

Q ss_pred             hhHHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccccc---cCCcEEEEcchHHHHHHHHHHHH----
Q 037567            2 VSTLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPPLV---TGKTALVVSPLISLMQDQVMSLK----   74 (374)
Q Consensus         2 ~~~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~~~---~~~~~lil~P~~~l~~q~~~~~~----   74 (374)
                      .++-++.+|.. +++.|.-+--.+.+|+  +..+.||-|||++..+++..   .++.|-|++...-|+.--.+++.    
T Consensus        70 REAakRtlG~R-hyDVQLiGgi~L~~G~--iaem~TGEGKTL~a~l~a~l~al~g~~vhvvTvNdyLA~RDae~m~~iy~  146 (273)
T d1tf5a3          70 REASRRVTGMF-PFKVQLMGGVALHDGN--IAEMKTGEGKTLTSTLPVYLNALTGKGVHVVTVNEYLASRDAEQMGKIFE  146 (273)
T ss_dssp             HHHHHHHHSCC-CCHHHHHHHHHHHTTS--EEECCTTSCHHHHHHHHHHHHHTTSSCEEEEESSHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHhhceE-EehhHHHHHHHHHhhh--heeecCCCcchhHHHHHHHHHHhcCCCceEEecCccccchhhhHHhHHHH
Confidence            35566777873 7777777777777765  99999999999988777654   57889999999999975555543    


Q ss_pred             HcCCceEEcCCCCCchhhhhhhhcCCeeEEEEcCccccc-Cchh----hHHHHHhcCccEEEEeccchhh-cccCcc---
Q 037567           75 QRGINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACI-IPIS----FWSKLLKAGVCLFAVDEAHCIS-EWGHDF---  145 (374)
Q Consensus        75 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~-~~~~----~~~~~~~~~~~~vviDE~h~~~-~~~~~~---  145 (374)
                      .+|+.+............   .....++|+++|...+.. +++.    .........+.+.||||++.+. +.....   
T Consensus       147 ~lGlsvg~~~~~~~~~~r---~~~Y~~di~Ygt~~e~~fDyLrd~~~~~~~~~~~r~~~~aIvDEvDsiliDeartplii  223 (273)
T d1tf5a3         147 FLGLTVGLNLNSMSKDEK---REAYAADITYSTNNELGFDYLRDNMVLYKEQMVQRPLHFAVIDEVDSILIDEARTPLII  223 (273)
T ss_dssp             HTTCCEEECCTTSCHHHH---HHHHHSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCCCCEEEEETHHHHHTTTTTCEEEE
T ss_pred             HcCCCccccccccCHHHH---HHHhhCCceecchhhhhhhhcchhhhcChhhhccCCCCEEEEEcchhhhhhccCCceEe
Confidence            469998877655433322   223457999999875522 1111    0111223567899999999984 211100   


Q ss_pred             ------hHHHHHHHHHHHhcCCCCeeEEEeecCcccHHHHHHhcCC
Q 037567          146 ------RLEYKQLDKLRTFLLGVPFVALTATATEKVRIDIINSLKL  185 (374)
Q Consensus       146 ------~~~~~~~~~~~~~~~~~~~i~~SaT~~~~~~~~~~~~~~~  185 (374)
                            ...+. .......  -.++.+||+|...... ++...+++
T Consensus       224 sg~~~~~a~it-~q~~f~~--y~~l~gmtgta~~~~~-e~~~iy~l  265 (273)
T d1tf5a3         224 SGQSMTLATIT-FQNYFRM--YEKLAGMTGTAKTEEE-EFRNIYNM  265 (273)
T ss_dssp             EEEEEEEEEEE-HHHHHTT--SSEEEEEESCCGGGHH-HHHHHHCC
T ss_pred             ccCccchhhhh-HHHHHHH--HHHHhCCccccHHHHH-HHHhccCC
Confidence                  00000 1112222  2367889999865433 45555553

>d1w36d1 c.37.1.19 (D:2-360) Exodeoxyribonuclease V alpha chain (RecD) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Exodeoxyribonuclease V alpha chain (RecD)
species: Escherichia coli [TaxId: 562]

Probab=98.50  E-value=1.8e-07  Score=80.08  Aligned_cols=71  Identities=23%  Similarity=0.171  Sum_probs=53.9

Q ss_pred             HHHhHcCCCCCchhHHHHHHHHHcCCCEEEEccCCCCchhhhh--cccc-----ccCCcEEEEcchHHHHHHHHHHHH
Q 037567            4 TLKKYFGYSVFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQ--LPPL-----VTGKTALVVSPLISLMQDQVMSLK   74 (374)
Q Consensus         4 ~l~~~~~~~~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~--l~~~-----~~~~~~lil~P~~~l~~q~~~~~~   74 (374)
                      .+...+.-....+.|.+|+..++.++-++|.||+|||||.+..  +..+     ..+.++++++||..-+....+...
T Consensus       139 ~~~~~~~~~~~~~~Q~~A~~~al~~~~~vI~G~pGTGKTt~i~~~l~~l~~~~~~~~~~I~l~ApTgkAA~~L~e~~~  216 (359)
T d1w36d1         139 TLDKLFPVSDEINWQKVAAAVALTRRISVISGGPGTGKTTTVAKLLAALIQMADGERCRIRLAAPTGKAAARLTESLG  216 (359)
T ss_dssp             HHHTTCCCTTSCCHHHHHHHHHHTBSEEEEECCTTSTHHHHHHHHHHHHHHTCSSCCCCEEEEBSSHHHHHHHHHHHT
T ss_pred             HHHHhccCcccccHHHHHHHHHHcCCeEEEEcCCCCCceehHHHHHHHHHHHHhccCCeEEEecCcHHHHHHHHHHHH
Confidence            3444455556778999999999998889999999999996532  1111     246789999999988888776654

>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=97.74  E-value=8.7e-06  Score=68.14  Aligned_cols=62  Identities=18%  Similarity=0.210  Sum_probs=47.6

Q ss_pred             CCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccc---cc----cCCcEEEEcchHHHHHHHHHHHHHc
Q 037567           13 VFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPP---LV----TGKTALVVSPLISLMQDQVMSLKQR   76 (374)
Q Consensus        13 ~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~---~~----~~~~~lil~P~~~l~~q~~~~~~~~   76 (374)
                      +|+|-|.+++..  ...+++|.|++|||||.+.+..+   +.    +..+++++++++++++.....+.+.
T Consensus         1 ~L~~eQ~~av~~--~~~~~lI~g~aGTGKTt~l~~rv~~ll~~~~~~~~~ILvlt~tn~a~~~i~~~~~~~   69 (306)
T d1uaaa1           1 RLNPGQQQAVEF--VTGPCLVLAGAGSGKTRVITNKIAHLIRGCGYQARHIAAVTFTNKAAREMKERVGQT   69 (306)
T ss_dssp             CCCHHHHHHHHC--CSSEEEECCCTTSCHHHHHHHHHHHHHHHHCCCGGGEEEEESSHHHHHHHHHHHHHH
T ss_pred             CcCHHHHHHHhC--CCCCEEEEeeCCccHHHHHHHHHHHHHHhcCCChhHEEEEeCcHHHHHHHHHHHHHh
Confidence            478999999964  45668999999999997643221   11    3458999999999999888877653

>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=97.57  E-value=0.00024  Score=55.34  Aligned_cols=34  Identities=12%  Similarity=0.291  Sum_probs=26.1

Q ss_pred             CCchhHHHHHHHHHc----C---CCEEEEccCCCCchhhhh
Q 037567           13 VFRPYQKDVIQRIIE----K---RDCLVVMATGSGKSLCYQ   46 (374)
Q Consensus        13 ~~~~~Q~~~~~~~~~----~---~~~l~~a~tGsGKT~~~~   46 (374)
                      .++|||..+++.+.+    +   +..++.||+|+|||..+.
T Consensus         2 ~~yPw~~~~~~~l~~~~~~~~l~h~lLl~Gp~G~GKtt~a~   42 (207)
T d1a5ta2           2 RWYPWLRPDFEKLVASYQAGRGHHALLIQALPGMGDDALIY   42 (207)
T ss_dssp             CCCGGGHHHHHHHHHHHHTTCCCSEEEEECCTTSCHHHHHH
T ss_pred             CCCcccHHHHHHHHHHHHcCCcCeEEEEECCCCCcHHHHHH
Confidence            367999998887754    2   237899999999996643

>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=97.44  E-value=0.00037  Score=55.87  Aligned_cols=103  Identities=12%  Similarity=-0.007  Sum_probs=75.2

Q ss_pred             chHHHHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHH----cCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEecc
Q 037567          212 SFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQ----LGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMA  287 (374)
Q Consensus       212 ~~~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~----~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~  287 (374)
                      ....-.+..+......+.++++.+|+..-+.+.++.+++    .+..+..+||+++..+|..+.....+|+.+|+|+|.+
T Consensus       116 GKT~Va~~a~~~~~~~g~q~~~m~Pt~~La~Qh~~~~~~~f~~~~~~v~~l~~~~~~~~r~~~~~~~~~g~~~iiIGThs  195 (264)
T d1gm5a3         116 GKTVVAQLAILDNYEAGFQTAFMVPTSILAIQHYRRTVESFSKFNIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTHA  195 (264)
T ss_dssp             SHHHHHHHHHHHHHHHTSCEEEECSCHHHHHHHHHHHHHHHTCSSCCEEECCSSSCHHHHHHHHHHHHSSCCCEEEECTT
T ss_pred             cccHHHHHHHHHHHhcccceeEEeehHhhhHHHHHHHHHhhhhccccceeeccccchHHHHHHHHHHHCCCCCEEEeehH
Confidence            334445555566667889999999999988887777765    3788999999999999999999999999999999985


Q ss_pred             cc-ccccccCccEEEEECCCCChhHHHHhh
Q 037567          288 FG-MGIDKPDVRHVIHYGCPKTLESYYQES  316 (374)
Q Consensus       288 ~~-~G~d~~~~~~vi~~~~p~s~~~~~Q~~  316 (374)
                      +- ..+.+.++..||.-.-  .--.+.||.
T Consensus       196 l~~~~~~f~~LglviiDEq--H~fgv~Qr~  223 (264)
T d1gm5a3         196 LIQEDVHFKNLGLVIIDEQ--HRFGVKQRE  223 (264)
T ss_dssp             HHHHCCCCSCCCEEEEESC--CCC-----C
T ss_pred             HhcCCCCccccceeeeccc--cccchhhHH
Confidence            54 4576667777664321  123455654

>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=97.38  E-value=0.00051  Score=53.54  Aligned_cols=102  Identities=16%  Similarity=0.107  Sum_probs=53.9

Q ss_pred             CEEEEccCCCCchhhhhcc---ccccCCcEEEEcchHHHHHHHHHHHHHcCCceEEcCCCCCchhhhhhhhcCCeeEEEE
Q 037567           30 DCLVVMATGSGKSLCYQLP---PLVTGKTALVVSPLISLMQDQVMSLKQRGINAEFLGSAQTDSSVQTKAETGYFQLLFM  106 (374)
Q Consensus        30 ~~l~~a~tGsGKT~~~~l~---~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~  106 (374)
                      .++++||+|+|||-.....   +..++..++ ..+...+..+....+....                             
T Consensus        38 ~l~l~G~~G~GKTHLl~A~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~-----------------------------   87 (213)
T d1l8qa2          38 PIFIYGSVGTGKTHLLQAAGNEAKKRGYRVI-YSSADDFAQAMVEHLKKGT-----------------------------   87 (213)
T ss_dssp             SEEEECSSSSSHHHHHHHHHHHHHHTTCCEE-EEEHHHHHHHHHHHHHHTC-----------------------------
T ss_pred             cEEEECCCCCcHHHHHHHHHHHhccCccceE-EechHHHHHHHHHHHHccc-----------------------------
Confidence            4899999999999532211   122344444 4455566665555543210                             


Q ss_pred             cCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHHhcCCCCeeEEEeecCcc
Q 037567          107 TPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEK  174 (374)
Q Consensus       107 T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~SaT~~~~  174 (374)
                              ...  ......+.+++++|++|.+......-...+..++....   ....+.+|+..++.
T Consensus        88 --------~~~--~~~~~~~~dll~iDDi~~i~~~~~~~~~lf~lin~~~~---~~~~iiits~~~p~  142 (213)
T d1l8qa2          88 --------INE--FRNMYKSVDLLLLDDVQFLSGKERTQIEFFHIFNTLYL---LEKQIILASDRHPQ  142 (213)
T ss_dssp             --------HHH--HHHHHHTCSEEEEECGGGGTTCHHHHHHHHHHHHHHHH---TTCEEEEEESSCGG
T ss_pred             --------hhh--HHHHHhhccchhhhhhhhhcCchHHHHHHHHHHHHHhh---ccceEEEecCCcch
Confidence                    001  11123567899999999985422111122234444333   44456666665543

>d2eyqa3 c.37.1.19 (A:546-778) Transcription-repair coupling factor, TRCF {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Transcription-repair coupling factor, TRCF
species: Escherichia coli [TaxId: 562]

Probab=97.36  E-value=0.00077  Score=52.90  Aligned_cols=91  Identities=10%  Similarity=0.081  Sum_probs=75.8

Q ss_pred             chHHHHHHHHHHhhcCCCcEEEEecchhHHHHHHHHHHH----cCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEecc
Q 037567          212 SFVDELVQEILKSVAGAGSIIVYCMTIKDVEEISKALKQ----LGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMA  287 (374)
Q Consensus       212 ~~~~~~~~~~~~~~~~~~~~lVf~~~~~~~~~l~~~l~~----~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~  287 (374)
                      ....-.+..+......+.++++.+|+..-+...++.+++    .+..+..+||..+..++..+...+.+|+.+|+|.|.+
T Consensus        88 GKT~V~~~a~~~~~~~g~qv~~l~Pt~~La~Q~~~~~~~~~~~~~~~v~~l~~~~~~~~~~~~~~~~~~g~~~iviGths  167 (233)
T d2eyqa3          88 GKTEVAMRAAFLAVDNHKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTHK  167 (233)
T ss_dssp             TTHHHHHHHHHHHHTTTCEEEEECSSHHHHHHHHHHHHHHSTTTTCCEEEESTTSCHHHHHHHHHHHHTTCCSEEEECTH
T ss_pred             CcHHHHHHHHHHHHHcCCceEEEccHHHhHHHHHHHHHHHHhhCCCEEEeccCcccchhHHHHHHHHhCCCCCEEEeehh
Confidence            344555666667777899999999999999999999986    3677889999999999999999999999999999985


Q ss_pred             cc-ccccccCccEEEE
Q 037567          288 FG-MGIDKPDVRHVIH  302 (374)
Q Consensus       288 ~~-~G~d~~~~~~vi~  302 (374)
                      +- ..+.++++..||.
T Consensus       168 ~l~~~~~f~~LgLiIi  183 (233)
T d2eyqa3         168 LLQSDVKFKDLGLLIV  183 (233)
T ss_dssp             HHHSCCCCSSEEEEEE
T ss_pred             hhccCCccccccceee
Confidence            54 4677777777664

>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=97.33  E-value=9.9e-05  Score=61.85  Aligned_cols=62  Identities=11%  Similarity=0.138  Sum_probs=47.7

Q ss_pred             CCchhHHHHHHHHHcCCCEEEEccCCCCchhhhhccc---cc----cCCcEEEEcchHHHHHHHHHHHHHc
Q 037567           13 VFRPYQKDVIQRIIEKRDCLVVMATGSGKSLCYQLPP---LV----TGKTALVVSPLISLMQDQVMSLKQR   76 (374)
Q Consensus        13 ~~~~~Q~~~~~~~~~~~~~l~~a~tGsGKT~~~~l~~---~~----~~~~~lil~P~~~l~~q~~~~~~~~   76 (374)
                      .|++-|.+++..  ....++|.|++|||||.+.+--+   +.    ...+++++++++..+++....+...
T Consensus        11 ~L~~eQ~~~v~~--~~g~~lV~g~aGSGKTt~l~~ri~~ll~~~~~~p~~il~lt~t~~aa~~~~~~~~~~   79 (318)
T d1pjra1          11 HLNKEQQEAVRT--TEGPLLIMAGAGSGKTRVLTHRIAYLMAEKHVAPWNILAITFTNKAAREMRERVQSL   79 (318)
T ss_dssp             TSCHHHHHHHHC--CSSCEEEEECTTSCHHHHHHHHHHHHHHTTCCCGGGEEEEESSHHHHHHHHHHHHHH
T ss_pred             hCCHHHHHHHhC--CCCCEEEEecCCccHHHHHHHHHHHHHHcCCCCHHHeEeEeccHHHHHHHHHHHHhh
Confidence            488999999974  45679999999999997653221   11    2357999999999999988887653

>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=97.33  E-value=0.00071  Score=52.19  Aligned_cols=127  Identities=10%  Similarity=0.060  Sum_probs=64.9

Q ss_pred             EEEEccCCCCchhhhhcccc---ccCCcEEEE-cch--HHHHHHHHHHHHHcCCceEEcCCCCCchhhhhhhhcCCeeEE
Q 037567           31 CLVVMATGSGKSLCYQLPPL---VTGKTALVV-SPL--ISLMQDQVMSLKQRGINAEFLGSAQTDSSVQTKAETGYFQLL  104 (374)
Q Consensus        31 ~l~~a~tGsGKT~~~~l~~~---~~~~~~lil-~P~--~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~  104 (374)
                      ++++||||+|||.+..-.+.   .++.++.++ +.+  ..-.+|.....+..++..........                
T Consensus        12 i~lvGptGvGKTTTiAKLA~~~~~~g~kV~lit~Dt~R~gA~eQL~~~a~~l~v~~~~~~~~~d----------------   75 (211)
T d2qy9a2          12 ILMVGVNGVGKTTTIGKLARQFEQQGKSVMLAAGDTFRAAAVEQLQVWGQRNNIPVIAQHTGAD----------------   75 (211)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHHHTTTCCEEEECCCTTCHHHHHHHHHHHHHTTCCEECCSTTCC----------------
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEecccccccchhhhhhhhhhcCCcccccccCCC----------------
Confidence            46799999999976543221   234555444 443  23456666666666666543332221                


Q ss_pred             EEcCcccccCchhhHHHHHhcCccEEEEeccchhhcccCcchHHHHHHHHHHHhc-------CCCCeeEEEeecCcccHH
Q 037567          105 FMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFL-------LGVPFVALTATATEKVRI  177 (374)
Q Consensus       105 i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~i~~SaT~~~~~~~  177 (374)
                            +...+..........++++|+||=+-+.....    .....+..+....       +....+.++||.......
T Consensus        76 ------~~~~l~~~~~~a~~~~~d~ilIDTaGr~~~d~----~~~~el~~l~~~~~~~~~~~p~~~~LVl~a~~~~~~~~  145 (211)
T d2qy9a2          76 ------SASVIFDAIQAAKARNIDVLIADTAGRLQNKS----HLMEELKKIVRVMKKLDVEAPHEVMLTIDASTGQNAVS  145 (211)
T ss_dssp             ------HHHHHHHHHHHHHHTTCSEEEECCCCCGGGHH----HHHHHHHHHHHHHTTTCTTCCSEEEEEEEGGGTHHHHH
T ss_pred             ------HHHHHHHHHHHHHHcCCCEEEeccCCCccccH----HHHHHHHHHHHHHhhhcccCcceeeeehhcccCcchHH
Confidence                  11111222223334567888888775432211    1112222222221       234568888888776655


Q ss_pred             HHHHhc
Q 037567          178 DIINSL  183 (374)
Q Consensus       178 ~~~~~~  183 (374)
                      .....+
T Consensus       146 ~~~~~~  151 (211)
T d2qy9a2         146 QAKLFH  151 (211)
T ss_dssp             HHHHHH
T ss_pred             HHhhhh
Confidence            444443

>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=97.23  E-value=0.00012  Score=63.00  Aligned_cols=65  Identities=20%  Similarity=0.177  Sum_probs=53.3

Q ss_pred             CCchhHHHHHHHHHc----C-CCEEEEccCCCCchhhhhccccccCCcEEEEcchHHHHHHHHHHHHHcC
Q 037567           13 VFRPYQKDVIQRIIE----K-RDCLVVMATGSGKSLCYQLPPLVTGKTALVVSPLISLMQDQVMSLKQRG   77 (374)
Q Consensus        13 ~~~~~Q~~~~~~~~~----~-~~~l~~a~tGsGKT~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~   77 (374)
                      .|..-|-+|+..+.+    | +..++.|-||||||+++...+...+.++||++|+..+|.|++++++.+.
T Consensus        11 ~p~gDQP~aI~~l~~~l~~g~~~q~l~GltGS~ka~~iA~l~~~~~rp~LVVt~n~~~A~qL~~dL~~~l   80 (413)
T d1t5la1          11 EPQGDQPQAIAKLVDGLRRGVKHQTLLGATGTGKTFTISNVIAQVNKPTLVIAHNKTLAGQLYSELKEFF   80 (413)
T ss_dssp             CCCTTHHHHHHHHHHHHHHTCSEEEEEECTTSCHHHHHHHHHHHHTCCEEEECSSHHHHHHHHHHHHHHC
T ss_pred             CCCCCCHHHHHHHHHHHhcCCCcEEEeCCCCcHHHHHHHHHHHHhCCCEEEEeCCHHHHHHHHHHHHHHc
Confidence            367788888887765    3 4578899999999987655555568889999999999999999999863

>d1okkd2 c.37.1.10 (D:97-303) GTPase domain of the signal recognition particle receptor FtsY {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Thermus aquaticus [TaxId: 271]

Probab=97.15  E-value=0.002  Score=49.56  Aligned_cols=54  Identities=20%  Similarity=0.035  Sum_probs=32.3

Q ss_pred             CCEEEEccCCCCchhhhhcccc---ccCCcEEEE-cch--HHHHHHHHHHHHHcCCceEE
Q 037567           29 RDCLVVMATGSGKSLCYQLPPL---VTGKTALVV-SPL--ISLMQDQVMSLKQRGINAEF   82 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~~l~~~---~~~~~~lil-~P~--~~l~~q~~~~~~~~~~~~~~   82 (374)
                      +-++++||||+|||.+..-.+.   ..+.++.++ +.+  ..-.+|+....+..++....
T Consensus         7 ~vi~lvGptGvGKTTTiaKLA~~~~~~g~kV~lit~Dt~R~gA~eQL~~~a~~l~i~~~~   66 (207)
T d1okkd2           7 RVVLVVGVNGVGKTTTIAKLGRYYQNLGKKVMFCAGDTFRAAGGTQLSEWGKRLSIPVIQ   66 (207)
T ss_dssp             SEEEEECSTTSSHHHHHHHHHHHHHTTTCCEEEECCCCSSTTHHHHHHHHHHHHTCCEEC
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEEeccccccchhhHhhcccccCceEEe
Confidence            4467899999999976432221   234555444 443  34556666666666666443

>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=97.00  E-value=0.00089  Score=53.42  Aligned_cols=34  Identities=18%  Similarity=0.098  Sum_probs=24.3

Q ss_pred             CCEEEEccCCCCchhhhhccccccCCcEEEEcch
Q 037567           29 RDCLVVMATGSGKSLCYQLPPLVTGKTALVVSPL   62 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~~l~~~~~~~~~lil~P~   62 (374)
                      +.+++.||+|+|||..+-..+-..+.+++.+.++
T Consensus        43 ~giLl~GppGtGKT~la~aia~~~~~~~~~i~~~   76 (247)
T d1ixza_          43 KGVLLVGPPGVGKTHLARAVAGEARVPFITASGS   76 (247)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHHHTTCCEEEEEHH
T ss_pred             ceEEEecCCCCChhHHHHHHHHHcCCCEEEEEhH
Confidence            4689999999999977544444446666666554

>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=96.87  E-value=0.0021  Score=49.63  Aligned_cols=51  Identities=18%  Similarity=0.221  Sum_probs=29.2

Q ss_pred             EEEEccCCCCchhhhhccc---cccCCc-EEEEcchH--HHHHHHHHHHHHcCCceE
Q 037567           31 CLVVMATGSGKSLCYQLPP---LVTGKT-ALVVSPLI--SLMQDQVMSLKQRGINAE   81 (374)
Q Consensus        31 ~l~~a~tGsGKT~~~~l~~---~~~~~~-~lil~P~~--~l~~q~~~~~~~~~~~~~   81 (374)
                      ++++||||+|||.+..-.+   ..++.+ .++-+.+.  .-.+|.....+..+....
T Consensus        14 i~lvGptGvGKTTTiAKLAa~~~~~~~kV~lit~Dt~R~gA~eQL~~~a~~l~i~~~   70 (213)
T d1vmaa2          14 IMVVGVNGTGKTTSCGKLAKMFVDEGKSVVLAAADTFRAAAIEQLKIWGERVGATVI   70 (213)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEEECTTCHHHHHHHHHHHHHHTCEEE
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCceEEEeecccccchhHHHHHHhhhcCcccc
Confidence            5679999999997643222   223444 45555533  334455555556665544

>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=96.82  E-value=0.0055  Score=47.00  Aligned_cols=54  Identities=19%  Similarity=0.150  Sum_probs=31.8

Q ss_pred             EEEEccCCCCchhhhhcccc---ccCCcEEEEcc---hHHHHHHHHHHHHHcCCceEEcC
Q 037567           31 CLVVMATGSGKSLCYQLPPL---VTGKTALVVSP---LISLMQDQVMSLKQRGINAEFLG   84 (374)
Q Consensus        31 ~l~~a~tGsGKT~~~~l~~~---~~~~~~lil~P---~~~l~~q~~~~~~~~~~~~~~~~   84 (374)
                      +++.||||+|||.+..-.+.   .++.++.+++.   +..-.+|.....+..+.......
T Consensus        13 i~lvGp~GvGKTTTiaKLA~~~~~~g~kV~lit~Dt~R~gA~eQL~~~a~~l~v~~~~~~   72 (207)
T d1ls1a2          13 WFLVGLQGSGKTTTAAKLALYYKGKGRRPLLVAADTQRPAAREQLRLLGEKVGVPVLEVM   72 (207)
T ss_dssp             EEEECCTTTTHHHHHHHHHHHHHHTTCCEEEEECCSSCHHHHHHHHHHHHHHTCCEEECC
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEecccccchHHHHHHHHHHhcCCcccccc
Confidence            46799999999966442222   24556655544   23344565555566666655443

>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=96.78  E-value=0.0029  Score=49.96  Aligned_cols=27  Identities=19%  Similarity=0.332  Sum_probs=19.2

Q ss_pred             HHHHHHHHcC---CCEEEEccCCCCchhhh
Q 037567           19 KDVIQRIIEK---RDCLVVMATGSGKSLCY   45 (374)
Q Consensus        19 ~~~~~~~~~~---~~~l~~a~tGsGKT~~~   45 (374)
                      .+.+..++.+   .+.++.||+|+|||...
T Consensus        21 ~~~l~~~i~~~~~~~lll~Gp~G~GKTtl~   50 (237)
T d1sxjd2          21 VTVLKKTLKSANLPHMLFYGPPGTGKTSTI   50 (237)
T ss_dssp             HHHHHHHTTCTTCCCEEEECSTTSSHHHHH
T ss_pred             HHHHHHHHHcCCCCeEEEECCCCCChHHHH
Confidence            4455555543   35799999999999653

>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=96.75  E-value=0.0013  Score=52.98  Aligned_cols=34  Identities=24%  Similarity=0.270  Sum_probs=23.8

Q ss_pred             CCEEEEccCCCCchhhhhccccccCCcEEEEcch
Q 037567           29 RDCLVVMATGSGKSLCYQLPPLVTGKTALVVSPL   62 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~~l~~~~~~~~~lil~P~   62 (374)
                      +.+++.||+|+|||...-..+...+..++.+.++
T Consensus        39 ~giLL~GppGtGKT~l~~ala~~~~~~~~~i~~~   72 (258)
T d1e32a2          39 RGILLYGPPGTGKTLIARAVANETGAFFFLINGP   72 (258)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHTTCEEEEECHH
T ss_pred             ceeEEecCCCCCchHHHHHHHHHhCCeEEEEEch
Confidence            5789999999999986544444445566666554

>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=96.71  E-value=0.0047  Score=47.22  Aligned_cols=29  Identities=28%  Similarity=0.142  Sum_probs=22.1

Q ss_pred             HHHHHHHHHcC---CCEEEEccCCCCchhhhh
Q 037567           18 QKDVIQRIIEK---RDCLVVMATGSGKSLCYQ   46 (374)
Q Consensus        18 Q~~~~~~~~~~---~~~l~~a~tGsGKT~~~~   46 (374)
                      |.+.+..+.+.   ..+++.||+|+|||..+.
T Consensus         2 ~~~~l~~~i~~~~~~~~l~~G~~g~gk~~~a~   33 (198)
T d2gnoa2           2 QLETLKRIIEKSEGISILINGEDLSYPREVSL   33 (198)
T ss_dssp             HHHHHHHHHHTCSSEEEEEECSSSSHHHHHHH
T ss_pred             HHHHHHHHHhcCCCceEEEECCCCCCHHHHHH
Confidence            66777777663   467999999999996543

>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=96.63  E-value=0.011  Score=45.26  Aligned_cols=52  Identities=17%  Similarity=0.082  Sum_probs=26.7

Q ss_pred             EEEEccCCCCchhhhhcccc---ccCCcE-EEEcc--hHHHHHHHHHHHHHcCCceEE
Q 037567           31 CLVVMATGSGKSLCYQLPPL---VTGKTA-LVVSP--LISLMQDQVMSLKQRGINAEF   82 (374)
Q Consensus        31 ~l~~a~tGsGKT~~~~l~~~---~~~~~~-lil~P--~~~l~~q~~~~~~~~~~~~~~   82 (374)
                      ++++||||+|||.+..-.+.   .++.++ +|-+.  +..-.+|.....+..+.....
T Consensus        15 i~lvGptGvGKTTTiAKLA~~~~~~g~kV~lit~Dt~R~ga~eQL~~~a~~l~v~~~~   72 (211)
T d1j8yf2          15 IMLVGVQGTGKATTAGKLAYFYKKKGFKVGLVGADVYRPAALEQLQQLGQQIGVPVYG   72 (211)
T ss_dssp             EEEECSCCC----HHHHHHHHHHHTTCCEEEEECCCSSHHHHHHHHHHHHHHTCCEEC
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCceEEEEeeccccchhHHHHHhccccCcceee
Confidence            46699999999976432221   234454 44444  344456666666666665543

>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=96.41  E-value=0.0028  Score=45.38  Aligned_cols=34  Identities=24%  Similarity=0.108  Sum_probs=23.4

Q ss_pred             EEEEccCCCCchhhhhcccc---ccCCcEEEEcchHH
Q 037567           31 CLVVMATGSGKSLCYQLPPL---VTGKTALVVSPLIS   64 (374)
Q Consensus        31 ~l~~a~tGsGKT~~~~l~~~---~~~~~~lil~P~~~   64 (374)
                      -++.||+.||||.-.+-.+.   ..+.+++++.|..+
T Consensus        10 ~lI~GpMfSGKTteLi~~~~~~~~~g~~vl~i~~~~D   46 (141)
T d1xx6a1          10 EVIVGPMYSGKSEELIRRIRRAKIAKQKIQVFKPEID   46 (141)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEEEC--
T ss_pred             EEEEeccccHHHHHHHHHHHHhhhcCCcEEEEEeccc
Confidence            37899999999965332221   24788999999864

>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=96.31  E-value=0.0019  Score=51.49  Aligned_cols=16  Identities=25%  Similarity=0.179  Sum_probs=14.1

Q ss_pred             CEEEEccCCCCchhhh
Q 037567           30 DCLVVMATGSGKSLCY   45 (374)
Q Consensus        30 ~~l~~a~tGsGKT~~~   45 (374)
                      .+++.||+|+|||..+
T Consensus        42 ~vLL~GppGtGKT~la   57 (246)
T d1d2na_          42 SVLLEGPPHSGKTALA   57 (246)
T ss_dssp             EEEEECSTTSSHHHHH
T ss_pred             EEEEECcCCCCHHHHH
Confidence            5899999999999764

>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=96.17  E-value=0.012  Score=46.92  Aligned_cols=17  Identities=35%  Similarity=0.479  Sum_probs=14.6

Q ss_pred             CCCEEEEccCCCCchhh
Q 037567           28 KRDCLVVMATGSGKSLC   44 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~   44 (374)
                      .++++++||+|.|||..
T Consensus        39 k~n~lLVG~~GvGKTal   55 (268)
T d1r6bx2          39 KNNPLLVGESGVGKTAI   55 (268)
T ss_dssp             SCEEEEECCTTSSHHHH
T ss_pred             cCCcEEECCCCCcHHHH
Confidence            46899999999999953

>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=95.99  E-value=0.00081  Score=53.53  Aligned_cols=16  Identities=25%  Similarity=0.262  Sum_probs=13.7

Q ss_pred             EEEEccCCCCchhhhh
Q 037567           31 CLVVMATGSGKSLCYQ   46 (374)
Q Consensus        31 ~l~~a~tGsGKT~~~~   46 (374)
                      +++.||+|+|||..+.
T Consensus        37 ~Ll~Gp~G~GKtt~a~   52 (239)
T d1njfa_          37 YLFSGTRGVGKTSIAR   52 (239)
T ss_dssp             EEEECSTTSSHHHHHH
T ss_pred             EEEECCCCCcHHHHHH
Confidence            7899999999997654

>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=95.98  E-value=0.0048  Score=49.26  Aligned_cols=32  Identities=22%  Similarity=0.241  Sum_probs=20.5

Q ss_pred             CCEEEEccCCCCchhhhhccccccCCcEEEEc
Q 037567           29 RDCLVVMATGSGKSLCYQLPPLVTGKTALVVS   60 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~~l~~~~~~~~~lil~   60 (374)
                      +.+++.||+|+|||+.+-..+-.-+..++.+.
T Consensus        46 ~~iLL~GppGtGKT~la~~iA~~~~~~~~~i~   77 (256)
T d1lv7a_          46 KGVLMVGPPGTGKTLLAKAIAGEAKVPFFTIS   77 (256)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHHTCCEEEEC
T ss_pred             CeEEeeCCCCCCccHHHHHHHHHcCCCEEEEE
Confidence            56899999999999765333322344444443

>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=95.97  E-value=0.0054  Score=52.44  Aligned_cols=65  Identities=22%  Similarity=0.232  Sum_probs=50.5

Q ss_pred             CCchhHHHHHHHHHc----CCC-EEEEccCCCCchhhhhccccccCCcEEEEcchHHHHHHHHHHHHHcC
Q 037567           13 VFRPYQKDVIQRIIE----KRD-CLVVMATGSGKSLCYQLPPLVTGKTALVVSPLISLMQDQVMSLKQRG   77 (374)
Q Consensus        13 ~~~~~Q~~~~~~~~~----~~~-~l~~a~tGsGKT~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~   77 (374)
                      .|+.-|-++++.+.+    +.. ..+.|.+|||||++........+.++|||+|+...|.++++++..+.
T Consensus         8 ~p~~dqp~aI~~l~~~L~~g~~~~~L~GlsgS~ka~~~A~l~~~~~rp~LvVt~~~~~A~~l~~dL~~~l   77 (408)
T d1c4oa1           8 SPKGDQPKAIAGLVEALRDGERFVTLLGATGTGKTVTMAKVIEALGRPALVLAPNKILAAQLAAEFRELF   77 (408)
T ss_dssp             CCCTTHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHHHHHHHHTCCEEEEESSHHHHHHHHHHHHHHC
T ss_pred             CCCCCCHHHHHHHHHHHhcCCCcEEEecCCCCHHHHHHHHHHHHhCCCEEEEeCCHHHHHHHHHHHHHhc
Confidence            466678777777654    444 58899999999976544444457789999999999999999999873

>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=95.81  E-value=0.01  Score=47.65  Aligned_cols=34  Identities=15%  Similarity=0.115  Sum_probs=23.5

Q ss_pred             CCEEEEccCCCCchhhhhccccccCCcEEEEcch
Q 037567           29 RDCLVVMATGSGKSLCYQLPPLVTGKTALVVSPL   62 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~~l~~~~~~~~~lil~P~   62 (374)
                      +.+++.||+|+|||...-..+-.-+..++.+.+.
T Consensus        42 ~giLL~Gp~GtGKT~l~~ala~~~~~~~~~~~~~   75 (265)
T d1r7ra3          42 KGVLFYGPPGCGKTLLAKAIANECQANFISIKGP   75 (265)
T ss_dssp             CEEEEBCCTTSSHHHHHHHHHHHTTCEEEEECHH
T ss_pred             CeEEEECCCCCcchhHHHHHHHHhCCcEEEEEHH
Confidence            5789999999999976544444445566666543

>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=95.72  E-value=0.0033  Score=50.16  Aligned_cols=17  Identities=24%  Similarity=0.276  Sum_probs=14.4

Q ss_pred             CCEEEEccCCCCchhhh
Q 037567           29 RDCLVVMATGSGKSLCY   45 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~   45 (374)
                      .++++.||+|+|||..+
T Consensus        34 ~~lll~Gp~G~GKTt~~   50 (252)
T d1sxje2          34 PHLLLYGPNGTGKKTRC   50 (252)
T ss_dssp             CCEEEECSTTSSHHHHH
T ss_pred             CeEEEECCCCCCHHHHH
Confidence            35899999999999764

>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=95.59  E-value=0.022  Score=44.25  Aligned_cols=16  Identities=25%  Similarity=0.312  Sum_probs=13.8

Q ss_pred             CEEEEccCCCCchhhh
Q 037567           30 DCLVVMATGSGKSLCY   45 (374)
Q Consensus        30 ~~l~~a~tGsGKT~~~   45 (374)
                      ++++.||+|+|||.+.
T Consensus        37 ~lLl~Gp~G~GKttl~   52 (227)
T d1sxjc2          37 HLLFYGPPGTGKTSTI   52 (227)
T ss_dssp             CEEEECSSSSSHHHHH
T ss_pred             eEEEECCCCCChhHHH
Confidence            5899999999999654

>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=95.49  E-value=0.011  Score=46.90  Aligned_cols=32  Identities=22%  Similarity=0.236  Sum_probs=21.0

Q ss_pred             CCEEEEccCCCCchhhhhccccccCCcEEEEc
Q 037567           29 RDCLVVMATGSGKSLCYQLPPLVTGKTALVVS   60 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~~l~~~~~~~~~lil~   60 (374)
                      +.+++.||+|+|||.++-..+-.-+..++.+-
T Consensus        53 ~~lll~GPpG~GKTt~a~~la~~~~~~~~~~~   84 (253)
T d1sxja2          53 RAAMLYGPPGIGKTTAAHLVAQELGYDILEQN   84 (253)
T ss_dssp             SEEEEECSTTSSHHHHHHHHHHHTTCEEEEEC
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHHHhhhhccc
Confidence            35899999999999765444433344444443

>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=95.40  E-value=0.069  Score=40.03  Aligned_cols=17  Identities=24%  Similarity=0.403  Sum_probs=14.7

Q ss_pred             CCCEEEEccCCCCchhh
Q 037567           28 KRDCLVVMATGSGKSLC   44 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~   44 (374)
                      .++.++.|++|.|||..
T Consensus        43 k~n~lLvG~pGVGKTal   59 (195)
T d1jbka_          43 KNNPVLIGEPGVGKTAI   59 (195)
T ss_dssp             SCEEEEECCTTSCHHHH
T ss_pred             CCCeEEEecCCcccHHH
Confidence            46889999999999954

>d2b8ta1 c.37.1.24 (A:11-149) Thymidine kinase, TK1, N-terminal domain {Ureaplasma urealyticum [TaxId: 2130]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Type II thymidine kinase
domain: Thymidine kinase, TK1, N-terminal domain
species: Ureaplasma urealyticum [TaxId: 2130]

Probab=95.17  E-value=0.014  Score=41.52  Aligned_cols=33  Identities=18%  Similarity=0.088  Sum_probs=23.6

Q ss_pred             EEEccCCCCchhhhhcccc---ccCCcEEEEcchHH
Q 037567           32 LVVMATGSGKSLCYQLPPL---VTGKTALVVSPLIS   64 (374)
Q Consensus        32 l~~a~tGsGKT~~~~l~~~---~~~~~~lil~P~~~   64 (374)
                      ++.||+.||||.-.+-.+.   ..+.+++++-|..+
T Consensus         6 ~i~GpMfsGKTteLi~~~~~~~~~~~kv~~ikp~~D   41 (139)
T d2b8ta1           6 FITGPMFAGKTAELIRRLHRLEYADVKYLVFKPKID   41 (139)
T ss_dssp             EEECSTTSCHHHHHHHHHHHHHHTTCCEEEEEECCC
T ss_pred             EEEccccCHHHHHHHHHHHHHHHCCCcEEEEEEccc
Confidence            7889999999964332221   24778999999754

>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=94.59  E-value=0.01  Score=48.96  Aligned_cols=41  Identities=17%  Similarity=0.221  Sum_probs=29.0

Q ss_pred             HHcCCCEEEEccCCCCchhh--hhccccccCCcEEEEcchHHH
Q 037567           25 IIEKRDCLVVMATGSGKSLC--YQLPPLVTGKTALVVSPLISL   65 (374)
Q Consensus        25 ~~~~~~~l~~a~tGsGKT~~--~~l~~~~~~~~~lil~P~~~l   65 (374)
                      +..++++++.|+||||||..  +++..+....+++.+-.+.++
T Consensus       163 v~~~~nili~G~tgSGKTT~l~al~~~i~~~~rivtiEd~~El  205 (323)
T d1g6oa_         163 IAIGKNVIVCGGTGSGKTTYIKSIMEFIPKEERIISIEDTEEI  205 (323)
T ss_dssp             HHHTCCEEEEESTTSSHHHHHHHHGGGSCTTCCEEEEESSCCC
T ss_pred             HHhCCCEEEEeeccccchHHHHHHhhhcccccceeeccchhhh
Confidence            34578999999999999954  233334456777777666665

>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=94.54  E-value=0.011  Score=48.69  Aligned_cols=18  Identities=28%  Similarity=0.409  Sum_probs=15.8

Q ss_pred             CCCEEEEccCCCCchhhh
Q 037567           28 KRDCLVVMATGSGKSLCY   45 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~   45 (374)
                      .+++++.||||+|||..+
T Consensus        49 ~~~iLl~GPpG~GKT~lA   66 (309)
T d1ofha_          49 PKNILMIGPTGVGKTEIA   66 (309)
T ss_dssp             CCCEEEECCTTSSHHHHH
T ss_pred             CceEEEECCCCCCHHHHH
Confidence            478999999999999765

>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=94.20  E-value=0.056  Score=42.26  Aligned_cols=106  Identities=12%  Similarity=0.034  Sum_probs=55.2

Q ss_pred             HHHHHHc-----CCCEEEEccCCCCchhhhh---ccccccCCcEEEEcchHHHHHHHHHHHHHcCCceEEcCCCCCchhh
Q 037567           21 VIQRIIE-----KRDCLVVMATGSGKSLCYQ---LPPLVTGKTALVVSPLISLMQDQVMSLKQRGINAEFLGSAQTDSSV   92 (374)
Q Consensus        21 ~~~~~~~-----~~~~l~~a~tGsGKT~~~~---l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~   92 (374)
                      .++.++.     +.-.++.|++|+|||...+   ..+...+.++++++-. .-..++.+.+..++.....          
T Consensus        14 ~LD~~l~GGi~~gsl~li~G~pGsGKT~l~~qia~~~~~~~~~~~~is~e-~~~~~~~~~~~~~~~~~~~----------   82 (242)
T d1tf7a2          14 RLDEMCGGGFFKDSIILATGATGTGKTLLVSRFVENACANKERAILFAYE-ESRAQLLRNAYSWGMDFEE----------   82 (242)
T ss_dssp             HHHHHTTSSEESSCEEEEEECTTSSHHHHHHHHHHHHHTTTCCEEEEESS-SCHHHHHHHHHTTSCCHHH----------
T ss_pred             HHHHhhcCCCcCCeEEEEEeCCCCCHHHHHHHHHHHHHHhccccceeecc-CCHHHHHHHHHHcCCChHH----------
Confidence            4555565     3567899999999996543   2233456677777643 2334455566655433110          


Q ss_pred             hhhhhcCCeeEEEEcC---cccccCchhhHHHHHhcCccEEEEeccchhhc
Q 037567           93 QTKAETGYFQLLFMTP---EKACIIPISFWSKLLKAGVCLFAVDEAHCISE  140 (374)
Q Consensus        93 ~~~~~~~~~~i~i~T~---~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~~  140 (374)
                        ....+. ..++..+   ..+...+............+++|+|-++.+..
T Consensus        83 --~~~~~~-~~~~~~~~~~~~~~~~~~~i~~~i~~~~~~~vviDs~~~~~~  130 (242)
T d1tf7a2          83 --MERQNL-LKIVCAYPESAGLEDHLQIIKSEINDFKPARIAIDSLSALAR  130 (242)
T ss_dssp             --HHHTTS-EEECCCCGGGSCHHHHHHHHHHHHHTTCCSEEEEECHHHHTS
T ss_pred             --HhhcCc-eEEEEeecchhhHHHHHHHHHHHHHhcCCceeeeecchhhhc
Confidence              000111 1111111   11111122222333446788999999998764

>d1w5sa2 c.37.1.20 (A:7-293) CDC6-like protein APE0152, N-terminal domain {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6-like protein APE0152, N-terminal domain
species: Aeropyrum pernix [TaxId: 56636]

Probab=94.07  E-value=0.03  Score=45.02  Aligned_cols=17  Identities=18%  Similarity=0.108  Sum_probs=12.8

Q ss_pred             cCccEEEEeccchhhcc
Q 037567          125 AGVCLFAVDEAHCISEW  141 (374)
Q Consensus       125 ~~~~~vviDE~h~~~~~  141 (374)
                      .....+++||+|.+...
T Consensus       131 ~~~~~~iide~d~l~~~  147 (287)
T d1w5sa2         131 NHYLLVILDEFQSMLSS  147 (287)
T ss_dssp             TCEEEEEEESTHHHHSC
T ss_pred             cCccccceeEEEEeccc
Confidence            34567889999998653

>d1c4oa2 c.37.1.19 (A:410-583) 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=93.95  E-value=0.061  Score=39.53  Aligned_cols=77  Identities=19%  Similarity=0.182  Sum_probs=59.4

Q ss_pred             cCCcEEEEcchHHHHHHHHHHHHHcCCceEEcCCCCCchhh---hhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCcc
Q 037567           52 TGKTALVVSPLISLMQDQVMSLKQRGINAEFLGSAQTDSSV---QTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVC  128 (374)
Q Consensus        52 ~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~  128 (374)
                      ++.++||+|+++.-++++...|...|+.+..+++.....+.   ......+..+|+|+|.--     .   ..+...+++
T Consensus        30 ~g~r~lvfc~t~~~~~~l~~~L~~~Gi~a~~~Hg~~~~~eR~~~l~~F~~G~~~vLVaT~v~-----~---~GiDip~V~  101 (174)
T d1c4oa2          30 RGERTLVTVLTVRMAEELTSFLVEHGIRARYLHHELDAFKRQALIRDLRLGHYDCLVGINLL-----R---EGLDIPEVS  101 (174)
T ss_dssp             TTCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTCCHHHHHHHHHHHHTTSCSEEEESCCC-----C---TTCCCTTEE
T ss_pred             cCCcEEEEEcchhHHHHHHHHHHhcCCceEEEecccchHHHHHHHHHHHCCCeEEEEeeeee-----e---eeccCCCCc
Confidence            57899999999999999999999999999999988766543   334456889999999521     1   334556777


Q ss_pred             EEEEeccc
Q 037567          129 LFAVDEAH  136 (374)
Q Consensus       129 ~vviDE~h  136 (374)
                      +||+=.++
T Consensus       102 ~Vi~~~~~  109 (174)
T d1c4oa2         102 LVAILDAD  109 (174)
T ss_dssp             EEEETTTT
T ss_pred             EEEEeccc
Confidence            88874444

>d1ixsb2 c.37.1.20 (B:4-242) Holliday junction helicase RuvB {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Holliday junction helicase RuvB
species: Thermus thermophilus [TaxId: 274]

Probab=93.94  E-value=0.0077  Score=47.52  Aligned_cols=18  Identities=22%  Similarity=0.263  Sum_probs=15.4

Q ss_pred             CCEEEEccCCCCchhhhh
Q 037567           29 RDCLVVMATGSGKSLCYQ   46 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~~   46 (374)
                      .++++.||+|+|||.++-
T Consensus        36 ~~~Ll~GPpG~GKTtla~   53 (239)
T d1ixsb2          36 EHLLLFGPPGLGKTTLAH   53 (239)
T ss_dssp             CCEEEECCTTSCHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHH
Confidence            478999999999997653

>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=93.86  E-value=0.011  Score=51.23  Aligned_cols=19  Identities=26%  Similarity=0.413  Sum_probs=16.4

Q ss_pred             CCCEEEEccCCCCchhhhh
Q 037567           28 KRDCLVVMATGSGKSLCYQ   46 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~   46 (374)
                      .+|+|+.||||+|||+.+-
T Consensus        49 ksNILliGPTGvGKTlLAr   67 (443)
T d1g41a_          49 PKNILMIGPTGVGKTEIAR   67 (443)
T ss_dssp             CCCEEEECCTTSSHHHHHH
T ss_pred             cccEEEECCCCCCHHHHHH
Confidence            5689999999999997653

>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=93.59  E-value=0.12  Score=43.55  Aligned_cols=25  Identities=28%  Similarity=0.453  Sum_probs=18.0

Q ss_pred             HHHHHHHc--CCCEEEEccCCCCchhh
Q 037567           20 DVIQRIIE--KRDCLVVMATGSGKSLC   44 (374)
Q Consensus        20 ~~~~~~~~--~~~~l~~a~tGsGKT~~   44 (374)
                      +++..+..  .++.+++|++|.|||..
T Consensus        33 ~~~~~L~r~~k~n~llvG~~GvGKtai   59 (387)
T d1qvra2          33 RVIQILLRRTKNNPVLIGEPGVGKTAI   59 (387)
T ss_dssp             HHHHHHHCSSCCCCEEEECTTSCHHHH
T ss_pred             HHHHHHhcCCCCCCeEECCCCCCHHHH
Confidence            34444443  46789999999999964

>d2eyqa5 c.37.1.19 (A:779-989) 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=93.26  E-value=0.039  Score=41.84  Aligned_cols=82  Identities=9%  Similarity=0.063  Sum_probs=59.2

Q ss_pred             cccCCcEEEEcchHHHHHHHHHHHHHc--CCceEEcCCCCCchhhh---hhhhcCCeeEEEEcCcccccCchhhHHHHHh
Q 037567           50 LVTGKTALVVSPLISLMQDQVMSLKQR--GINAEFLGSAQTDSSVQ---TKAETGYFQLLFMTPEKACIIPISFWSKLLK  124 (374)
Q Consensus        50 ~~~~~~~lil~P~~~l~~q~~~~~~~~--~~~~~~~~~~~~~~~~~---~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~  124 (374)
                      +.++.+++||||..+-.+.....+++.  +.++.++++.....+..   .....+..+|+|+|.-     ..   ..+..
T Consensus        28 l~rGgQvy~V~p~I~~~e~~~~~l~~~~p~~~i~~lHGkm~~~eke~im~~F~~g~~~ILv~Ttv-----IE---vGiDv   99 (211)
T d2eyqa5          28 ILRGGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTI-----IE---TGIDI   99 (211)
T ss_dssp             HTTTCEEEEECCCSSCHHHHHHHHHHHCTTSCEEECCSSCCHHHHHHHHHHHHTTSCCEEEESST-----TG---GGSCC
T ss_pred             HHcCCeEEEEEcCccchhhHHHHHHHhCCceEEEEEEeccCHHHHHHHHHHHHcCCcceEEEehh-----hh---hccCC
Confidence            346899999999988888888888764  45677777766555433   3344688999999952     22   33455


Q ss_pred             cCccEEEEeccchhh
Q 037567          125 AGVCLFAVDEAHCIS  139 (374)
Q Consensus       125 ~~~~~vviDE~h~~~  139 (374)
                      .+..++||.+|+++.
T Consensus       100 pnA~~iiI~~a~rfG  114 (211)
T d2eyqa5         100 PTANTIIIERADHFG  114 (211)
T ss_dssp             TTEEEEEETTTTSSC
T ss_pred             CCCcEEEEecchhcc
Confidence            677899999999763

>d1in4a2 c.37.1.20 (A:17-254) Holliday junction helicase RuvB {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Holliday junction helicase RuvB
species: Thermotoga maritima [TaxId: 2336]

Probab=93.19  E-value=0.017  Score=45.42  Aligned_cols=18  Identities=22%  Similarity=0.277  Sum_probs=15.4

Q ss_pred             CCEEEEccCCCCchhhhh
Q 037567           29 RDCLVVMATGSGKSLCYQ   46 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~~   46 (374)
                      .++++.||+|+|||.++-
T Consensus        36 ~~~L~~GPpGtGKT~lA~   53 (238)
T d1in4a2          36 DHVLLAGPPGLGKTTLAH   53 (238)
T ss_dssp             CCEEEESSTTSSHHHHHH
T ss_pred             CeEEEECCCCCcHHHHHH
Confidence            478999999999997653

>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=93.11  E-value=0.032  Score=47.54  Aligned_cols=32  Identities=34%  Similarity=0.473  Sum_probs=25.2

Q ss_pred             CchhHHHHHHHHHcCCC--EEEEccCCCCchhhh
Q 037567           14 FRPYQKDVIQRIIEKRD--CLVVMATGSGKSLCY   45 (374)
Q Consensus        14 ~~~~Q~~~~~~~~~~~~--~l~~a~tGsGKT~~~   45 (374)
                      +.+.|.+.+..+.....  +++.||||||||.+.
T Consensus       142 ~~~~~~~~l~~l~~~~~GliLvtGpTGSGKSTTl  175 (401)
T d1p9ra_         142 MTAHNHDNFRRLIKRPHGIILVTGPTGSGKSTTL  175 (401)
T ss_dssp             CCHHHHHHHHHHHTSSSEEEEEECSTTSCHHHHH
T ss_pred             ccHHHHHHHHHHHhhhhceEEEEcCCCCCccHHH
Confidence            56788888888876544  578999999999764

>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=93.05  E-value=0.019  Score=41.84  Aligned_cols=22  Identities=32%  Similarity=0.359  Sum_probs=17.5

Q ss_pred             CCCEEEEccCCCCchhhhhccc
Q 037567           28 KRDCLVVMATGSGKSLCYQLPP   49 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~l~~   49 (374)
                      .+++++.||+|+|||..+-..+
T Consensus         2 ~k~I~l~G~~GsGKSTvak~La   23 (169)
T d1kaga_           2 KRNIFLVGPMGAGKSTIGRQLA   23 (169)
T ss_dssp             CCCEEEECCTTSCHHHHHHHHH
T ss_pred             CCeEEEECCCCCCHHHHHHHHH
Confidence            5789999999999997654433

>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=92.16  E-value=0.027  Score=41.56  Aligned_cols=33  Identities=21%  Similarity=0.121  Sum_probs=20.8

Q ss_pred             cCCCEEEEccCCCCchhhhhccccccCCcEEEE
Q 037567           27 EKRDCLVVMATGSGKSLCYQLPPLVTGKTALVV   59 (374)
Q Consensus        27 ~~~~~l~~a~tGsGKT~~~~l~~~~~~~~~lil   59 (374)
                      .|+-+++.||+|||||..+-..+-..+.+.+.+
T Consensus         3 ~g~iI~l~G~~GsGKSTia~~La~~lg~~~~~~   35 (176)
T d1zp6a1           3 GGNILLLSGHPGSGKSTIAEALANLPGVPKVHF   35 (176)
T ss_dssp             TTEEEEEEECTTSCHHHHHHHHHTCSSSCEEEE
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHhCCCEEEe
Confidence            355578999999999986543333334444443

>d1gvnb_ c.37.1.21 (B:) Plasmid maintenance system epsilon/zeta, toxin zeta subunit {Streptococcus pyogenes [TaxId: 1314]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
domain: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
species: Streptococcus pyogenes [TaxId: 1314]

Probab=92.08  E-value=0.028  Score=44.90  Aligned_cols=32  Identities=22%  Similarity=0.109  Sum_probs=20.8

Q ss_pred             CEEEEccCCCCchhhhhccccccCCcEEEEcc
Q 037567           30 DCLVVMATGSGKSLCYQLPPLVTGKTALVVSP   61 (374)
Q Consensus        30 ~~l~~a~tGsGKT~~~~l~~~~~~~~~lil~P   61 (374)
                      .+++.||||+|||..+-..+-..+...+.+..
T Consensus        34 ~ilL~GpPGtGKT~la~~la~~~~~~~~~i~~   65 (273)
T d1gvnb_          34 AFLLGGQPGSGKTSLRSAIFEETQGNVIVIDN   65 (273)
T ss_dssp             EEEEECCTTSCTHHHHHHHHHHTTTCCEEECT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhhcceEEEec
Confidence            47899999999997654333333444555543

>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=92.06  E-value=0.033  Score=44.44  Aligned_cols=17  Identities=18%  Similarity=0.360  Sum_probs=14.6

Q ss_pred             CCEEEEccCCCCchhhh
Q 037567           29 RDCLVVMATGSGKSLCY   45 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~   45 (374)
                      .++++.||+|+|||.+.
T Consensus        44 ~~lll~GppGtGKT~l~   60 (276)
T d1fnna2          44 PRATLLGRPGTGKTVTL   60 (276)
T ss_dssp             CEEEEECCTTSSHHHHH
T ss_pred             CceEEECCCCCCHHHHH
Confidence            47899999999999654

>d1jr6a_ c.37.1.14 (A:) 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=91.94  E-value=0.18  Score=35.39  Aligned_cols=53  Identities=19%  Similarity=0.047  Sum_probs=43.6

Q ss_pred             cCCcEEEEcchHHHHHHHHHHHHHcCCceEEcCCCCCchhhhhhhhcCCeeEEEEcC
Q 037567           52 TGKTALVVSPLISLMQDQVMSLKQRGINAEFLGSAQTDSSVQTKAETGYFQLLFMTP  108 (374)
Q Consensus        52 ~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~  108 (374)
                      +..++||.|+++.-++++.+.|++.|..+..++++.....    ...+..+++|+|.
T Consensus        34 ~~~k~IVFc~t~~~ae~la~~L~~~G~~~~~~H~~~~~~~----~~~~~~~vlvaTd   86 (138)
T d1jr6a_          34 KGGRHLIFCHSKKKCDELAAKLVALGINAVAYYRGLDVSV----IPTNGDVVVVATD   86 (138)
T ss_dssp             TTSCEEEECSCHHHHHHHHHHHHHHTCEEEEECTTCCSCC----CTTSSCEEEEESS
T ss_pred             CCCCEEEEeCcHHHHHHHHHHHhccccchhhhhccchhhh----hhhhhcceeehhH
Confidence            5788999999999999999999999999988887654332    3346679999995

>d1u94a1 c.37.1.11 (A:6-268) RecA protein, ATPase-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Escherichia coli [TaxId: 562]

Probab=91.82  E-value=0.044  Score=43.52  Aligned_cols=43  Identities=16%  Similarity=0.058  Sum_probs=26.9

Q ss_pred             HHHHHHHHc-C-----CCEEEEccCCCCchhhhhcccc---ccCCcEEEEcc
Q 037567           19 KDVIQRIIE-K-----RDCLVVMATGSGKSLCYQLPPL---VTGKTALVVSP   61 (374)
Q Consensus        19 ~~~~~~~~~-~-----~~~l~~a~tGsGKT~~~~l~~~---~~~~~~lil~P   61 (374)
                      ..+++.++. |     +-..+.+|+|+|||...+..+.   .++..++|+--
T Consensus        39 ~~~lD~~Lg~GGi~~g~itei~G~~gsGKTtl~l~~~~~~q~~g~~~vyidt   90 (263)
T d1u94a1          39 SLSLDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDA   90 (263)
T ss_dssp             CHHHHHHTSSSSEETTSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEES
T ss_pred             CHHHHHHhcCCCccCceEEEEecCCCcHHHHHHHHHHHHHHcCCCEEEEEcc
Confidence            356777774 3     3457899999999966443322   24555655443

>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=91.77  E-value=0.047  Score=45.73  Aligned_cols=18  Identities=44%  Similarity=0.617  Sum_probs=15.3

Q ss_pred             CCCEEEEccCCCCchhhh
Q 037567           28 KRDCLVVMATGSGKSLCY   45 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~   45 (374)
                      ..++++.||||+|||..+
T Consensus        68 ~~niLfiGPTGvGKTElA   85 (364)
T d1um8a_          68 KSNILLIGPTGSGKTLMA   85 (364)
T ss_dssp             CCCEEEECCTTSSHHHHH
T ss_pred             CcceeeeCCCCccHHHHH
Confidence            367999999999999654

>d1iqpa2 c.37.1.20 (A:2-232) Replication factor C {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=91.53  E-value=0.04  Score=42.85  Aligned_cols=17  Identities=24%  Similarity=0.257  Sum_probs=14.6

Q ss_pred             CCEEEEccCCCCchhhh
Q 037567           29 RDCLVVMATGSGKSLCY   45 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~   45 (374)
                      .++++.||+|+|||.++
T Consensus        46 ~~lll~Gp~G~GKTtla   62 (231)
T d1iqpa2          46 PHLLFAGPPGVGKTTAA   62 (231)
T ss_dssp             CEEEEESCTTSSHHHHH
T ss_pred             CeEEEECCCCCcHHHHH
Confidence            46899999999999764

>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=91.47  E-value=0.033  Score=39.99  Aligned_cols=15  Identities=40%  Similarity=0.432  Sum_probs=12.8

Q ss_pred             EEEEccCCCCchhhh
Q 037567           31 CLVVMATGSGKSLCY   45 (374)
Q Consensus        31 ~l~~a~tGsGKT~~~   45 (374)
                      +++.|++|||||..+
T Consensus         5 Iii~G~pGsGKTTla   19 (152)
T d1ly1a_           5 ILTIGCPGSGKSTWA   19 (152)
T ss_dssp             EEEECCTTSSHHHHH
T ss_pred             EEEECCCCCCHHHHH
Confidence            578999999999754

>d1mo6a1 c.37.1.11 (A:1-269) RecA protein, ATPase-domain {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=91.46  E-value=0.051  Score=43.26  Aligned_cols=98  Identities=14%  Similarity=0.093  Sum_probs=52.9

Q ss_pred             HHHHHHHHc------CCCEEEEccCCCCchhhhhcccc---ccCCcEEEEcchHHHHHHHHHHHHHcCCceEEcCCCCCc
Q 037567           19 KDVIQRIIE------KRDCLVVMATGSGKSLCYQLPPL---VTGKTALVVSPLISLMQDQVMSLKQRGINAEFLGSAQTD   89 (374)
Q Consensus        19 ~~~~~~~~~------~~~~l~~a~tGsGKT~~~~l~~~---~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~   89 (374)
                      ...++.++.      ++-..+.+|+|+|||..++..+.   ..+..++++---..+-.++   ++++|...         
T Consensus        45 ~~~lD~~lg~gG~~~g~i~e~~G~~~~GKT~l~l~~~~~~q~~g~~~vyIDtE~~~~~e~---a~~~GvD~---------  112 (269)
T d1mo6a1          45 SIALDVALGIGGLPRGRVIEIYGPESSGKTTVALHAVANAQAAGGVAAFIDAEHALDPDY---AKKLGVDT---------  112 (269)
T ss_dssp             CHHHHHHTSSSSBCSSSEEEEECSSSSSHHHHHHHHHHHHHHTTCEEEEEESSCCCCHHH---HHHHTCCG---------
T ss_pred             CHHHHHhhccCCcccceeEEEecCCCcHHHHHHHHHHHHHhcCCCEEEEEECCccCCHHH---HHHhCCCH---------
Confidence            346676664      24457899999999966543322   2456666654433343333   33334321         


Q ss_pred             hhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhh
Q 037567           90 SSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCIS  139 (374)
Q Consensus        90 ~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~  139 (374)
                                 -++++..|+.....+.....-.....+++||+|=+-.+.
T Consensus       113 -----------d~il~~~~~~~E~~~~~~~~l~~~~~~~liIiDSi~al~  151 (269)
T d1mo6a1         113 -----------DSLLVSQPDTGEQALEIADMLIRSGALDIVVIDSVAALV  151 (269)
T ss_dssp             -----------GGCEEECCSSHHHHHHHHHHHHHTTCEEEEEEECSTTCC
T ss_pred             -----------HHeEEecCCCHHHHHHHHHHHHhcCCCCEEEEecccccc
Confidence                       135566665543332221111223457889998886554

>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=91.21  E-value=0.041  Score=40.84  Aligned_cols=17  Identities=24%  Similarity=0.384  Sum_probs=14.7

Q ss_pred             CCCEEEEccCCCCchhh
Q 037567           28 KRDCLVVMATGSGKSLC   44 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~   44 (374)
                      .+++++.||+|+|||..
T Consensus         1 ~k~v~ItG~~GtGKTtl   17 (189)
T d2i3ba1           1 ARHVFLTGPPGVGKTTL   17 (189)
T ss_dssp             CCCEEEESCCSSCHHHH
T ss_pred             CcEEEEECCCCCcHHHH
Confidence            36799999999999964

>d1hv8a2 c.37.1.19 (A:211-365) 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=91.18  E-value=0.35  Score=34.61  Aligned_cols=73  Identities=11%  Similarity=-0.000  Sum_probs=54.1

Q ss_pred             cCCcEEEEcchHHHHHHHHHHHHHcCCceEEcCCCCCchhh---hhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCcc
Q 037567           52 TGKTALVVSPLISLMQDQVMSLKQRGINAEFLGSAQTDSSV---QTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVC  128 (374)
Q Consensus        52 ~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~  128 (374)
                      .+.++||.|+++.-++++.+.+...|.....+++.......   ......+...++|+|.-        ....+....++
T Consensus        27 ~~~k~IIF~~s~~~~~~l~~~L~~~g~~~~~~~~~~~~~~r~~~~~~f~~~~~~ilv~T~~--------~~~Gid~~~v~   98 (155)
T d1hv8a2          27 KEFYGLVFCKTKRDTKELASMLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATDV--------MSRGIDVNDLN   98 (155)
T ss_dssp             TTCCEEEECSSHHHHHHHHHHHHHTTCCEEEECSSSCHHHHHHHHHHHHTTSSSEEEECTT--------HHHHCCCSCCS
T ss_pred             CCCCEEEEECchHHHHHHHhhhcccccccccccccchhhhhhhhhhhhhcccceeeeehhH--------HhhhhhhccCc
Confidence            45689999999999999999999999999888877655433   23334577899999942        12455667777


Q ss_pred             EEEE
Q 037567          129 LFAV  132 (374)
Q Consensus       129 ~vvi  132 (374)
                      +||.
T Consensus        99 ~Vi~  102 (155)
T d1hv8a2          99 CVIN  102 (155)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            7774

>d1t5la2 c.37.1.19 (A:415-595) 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=91.07  E-value=0.22  Score=36.77  Aligned_cols=78  Identities=21%  Similarity=0.173  Sum_probs=60.6

Q ss_pred             cCCcEEEEcchHHHHHHHHHHHHHcCCceEEcCCCCCchhh---hhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCcc
Q 037567           52 TGKTALVVSPLISLMQDQVMSLKQRGINAEFLGSAQTDSSV---QTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVC  128 (374)
Q Consensus        52 ~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~  128 (374)
                      ++.+++|+++++.-++.....++..|..+..+++.....+.   ......+..+|+|+|.-. .       ..+...+++
T Consensus        30 ~~~~~iif~~~~~~~~~~~~~l~~~g~~~~~~hg~~~~~eR~~~l~~Fr~g~~~vLVaTdv~-~-------rGiDip~v~  101 (181)
T d1t5la2          30 RNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLL-R-------EGLDIPEVS  101 (181)
T ss_dssp             TTCEEEEECSSHHHHHHHHHHHHTTTCCEEEECSSCCHHHHHHHHHHHHHTSCSEEEESCCC-S-------SSCCCTTEE
T ss_pred             cCCeEEEEeehhhhhHHHHHHHHhCCcceeEecCCccHHHHHHHHHHHHCCCCCEEEehhHH-H-------ccCCCCCCC
Confidence            57789999999999999999999999999999988766543   334456889999999421 1       234457788


Q ss_pred             EEEEeccch
Q 037567          129 LFAVDEAHC  137 (374)
Q Consensus       129 ~vviDE~h~  137 (374)
                      +||.-++..
T Consensus       102 ~VI~~d~p~  110 (181)
T d1t5la2         102 LVAILDADK  110 (181)
T ss_dssp             EEEETTTTS
T ss_pred             EEEEecCCc
Confidence            888877664

>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=90.81  E-value=0.043  Score=40.21  Aligned_cols=19  Identities=21%  Similarity=0.212  Sum_probs=15.1

Q ss_pred             CCEEEEccCCCCchhhhhc
Q 037567           29 RDCLVVMATGSGKSLCYQL   47 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~~l   47 (374)
                      ..+++.||+|||||..+..
T Consensus         5 ~~I~i~G~pGsGKTTia~~   23 (173)
T d1rkba_           5 PNILLTGTPGVGKTTLGKE   23 (173)
T ss_dssp             CCEEEECSTTSSHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHH
Confidence            3578999999999975443

>d2eyqa2 c.37.1.19 (A:349-465) 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=90.50  E-value=0.4  Score=32.43  Aligned_cols=66  Identities=8%  Similarity=-0.011  Sum_probs=50.3

Q ss_pred             CCCcEEEEecchhHHHHHHHHHHHcCCceeeeecCCChHHHHHHHHhhhcCCeeEEEEeccccccccccCccEEEEEC
Q 037567          227 GAGSIIVYCMTIKDVEEISKALKQLGVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMAFGMGIDKPDVRHVIHYG  304 (374)
Q Consensus       227 ~~~~~lVf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~~~~G~d~~~~~~vi~~~  304 (374)
                      .+.++|+.+.+....+.+.+.|++.++.+..+.+ .+         ++.++.  +.++...+..|+-+|+...++...
T Consensus        33 ~~~~Vli~a~s~g~~erl~e~L~~~~i~~~~~~~-~~---------~~~~~~--~~i~~~~l~~GF~~~~~~l~vItE   98 (117)
T d2eyqa2          33 FDGPVVFSVESEGRREALGELLARIKIAPQRIMR-LD---------EASDRG--RYLMIGAAEHGFVDTVRNLALICE   98 (117)
T ss_dssp             CCSCCCEEESSHHHHHHHHHHHGGGTCCCEECSS-GG---------GCCTTC--CEEEECCCCSCEEETTTTEEEEEH
T ss_pred             CCCeEEEEECCccHHHHHHHHHHHcCCCceEecC-hh---------hhcCce--EEEEEecCccccccCCCCEEEEEc
Confidence            3568999999999999999999999988755533 11         233343  556678899999999988888664

>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=90.42  E-value=0.047  Score=40.01  Aligned_cols=16  Identities=25%  Similarity=0.409  Sum_probs=13.5

Q ss_pred             EEEEccCCCCchhhhh
Q 037567           31 CLVVMATGSGKSLCYQ   46 (374)
Q Consensus        31 ~l~~a~tGsGKT~~~~   46 (374)
                      +++.||+|||||..+-
T Consensus         5 I~i~G~~GsGKTTva~   20 (176)
T d2bdta1           5 YIITGPAGVGKSTTCK   20 (176)
T ss_dssp             EEEECSTTSSHHHHHH
T ss_pred             EEEECCCCCCHHHHHH
Confidence            6889999999997643

>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=90.41  E-value=0.049  Score=40.01  Aligned_cols=19  Identities=21%  Similarity=0.314  Sum_probs=15.3

Q ss_pred             CCCEEEEccCCCCchhhhh
Q 037567           28 KRDCLVVMATGSGKSLCYQ   46 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~   46 (374)
                      +.++++.||+|||||..+-
T Consensus         5 ~~~I~i~G~~GsGKTT~~~   23 (174)
T d1y63a_           5 GINILITGTPGTGKTSMAE   23 (174)
T ss_dssp             SCEEEEECSTTSSHHHHHH
T ss_pred             CCEEEEEeCCCCCHHHHHH
Confidence            3468999999999997643

>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=90.06  E-value=0.064  Score=44.79  Aligned_cols=31  Identities=29%  Similarity=0.150  Sum_probs=21.1

Q ss_pred             CCEEEEccCCCCchhhhhccccccCCcEEEE
Q 037567           29 RDCLVVMATGSGKSLCYQLPPLVTGKTALVV   59 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~~l~~~~~~~~~lil   59 (374)
                      +.+++.||+|+|||..+...+-.-+.+++-+
T Consensus       155 ~~~~~~g~~~~gk~~~~~~~~~~~~~~~i~i  185 (362)
T d1svma_         155 RYWLFKGPIDSGKTTLAAALLELCGGKALNV  185 (362)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHHCCEEECC
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHcCCCEEEE
Confidence            4678999999999976544443345555544

>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=89.93  E-value=0.055  Score=41.85  Aligned_cols=18  Identities=17%  Similarity=0.268  Sum_probs=15.0

Q ss_pred             CCEEEEccCCCCchhhhh
Q 037567           29 RDCLVVMATGSGKSLCYQ   46 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~~   46 (374)
                      .++++.||+|+|||.++.
T Consensus        37 ~~~ll~Gp~G~GKTt~a~   54 (224)
T d1sxjb2          37 PHMIISGMPGIGKTTSVH   54 (224)
T ss_dssp             CCEEEECSTTSSHHHHHH
T ss_pred             CeEEEECCCCCCchhhHH
Confidence            368999999999997653

>d1t5ia_ 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=89.64  E-value=0.37  Score=35.00  Aligned_cols=58  Identities=7%  Similarity=-0.061  Sum_probs=46.2

Q ss_pred             cCCcEEEEcchHHHHHHHHHHHHHcCCceEEcCCCCCchhhh---hhhhcCCeeEEEEcCc
Q 037567           52 TGKTALVVSPLISLMQDQVMSLKQRGINAEFLGSAQTDSSVQ---TKAETGYFQLLFMTPE  109 (374)
Q Consensus        52 ~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~i~i~T~~  109 (374)
                      ...+++|.|+++.-++.+.+.+.+.|..+..++++....+..   .....+...++|+|.-
T Consensus        26 ~~~k~iIF~~~~~~~~~l~~~L~~~~~~~~~ihg~~~~~~r~~~l~~F~~g~~~iLv~T~~   86 (168)
T d1t5ia_          26 EFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNL   86 (168)
T ss_dssp             CCSSEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEESSC
T ss_pred             CCCeEEEEEeeeecchhhhhhhccccccccccccccchhhhhhhhhhhccccceeeecccc
Confidence            456899999999999999999999999998888876555432   3344677899999943

>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=89.37  E-value=0.071  Score=38.76  Aligned_cols=19  Identities=26%  Similarity=0.326  Sum_probs=15.3

Q ss_pred             CCEEEEccCCCCchhhhhc
Q 037567           29 RDCLVVMATGSGKSLCYQL   47 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~~l   47 (374)
                      +++++.|++|+|||...-.
T Consensus         1 k~I~liG~~GsGKsTi~k~   19 (161)
T d1viaa_           1 KNIVFIGFMGSGKSTLARA   19 (161)
T ss_dssp             CCEEEECCTTSCHHHHHHH
T ss_pred             CcEEEECCCCCCHHHHHHH
Confidence            4688999999999976433

>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=89.35  E-value=0.03  Score=43.69  Aligned_cols=35  Identities=23%  Similarity=0.243  Sum_probs=23.0

Q ss_pred             CCCEEEEccCCCCchhhhh-cc---ccccCCcEEEEcch
Q 037567           28 KRDCLVVMATGSGKSLCYQ-LP---PLVTGKTALVVSPL   62 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~-l~---~~~~~~~~lil~P~   62 (374)
                      |.-.++.|++|+|||..++ ++   +.....+++++..-
T Consensus        26 G~~~~I~G~~G~GKT~la~~~~~~~~~~~~~~~~~~s~e   64 (242)
T d1tf7a1          26 GRSTLVSGTSGTGKTLFSIQFLYNGIIEFDEPGVFVTFE   64 (242)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHHHHHHCCCEEEEESS
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHHHHhcCCCccccccc
Confidence            4567899999999995543 22   22345677776653

>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=89.25  E-value=0.049  Score=40.43  Aligned_cols=19  Identities=21%  Similarity=0.307  Sum_probs=15.5

Q ss_pred             CCCEEEEccCCCCchhhhh
Q 037567           28 KRDCLVVMATGSGKSLCYQ   46 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~   46 (374)
                      .+.+++.||+|+|||..+-
T Consensus         7 ~K~I~i~G~~GsGKTTla~   25 (192)
T d1lw7a2           7 AKTVAILGGESSGKSVLVN   25 (192)
T ss_dssp             CEEEEEECCTTSHHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHH
Confidence            4678999999999997543

>d1xp8a1 c.37.1.11 (A:15-282) RecA protein, ATPase-domain {Deinococcus radiodurans [TaxId: 1299]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Deinococcus radiodurans [TaxId: 1299]

Probab=89.10  E-value=0.09  Score=41.76  Aligned_cols=98  Identities=13%  Similarity=0.065  Sum_probs=52.1

Q ss_pred             HHHHHHHHc-C-----CCEEEEccCCCCchhhhhcccc---ccCCcEEEEcchHHHHHHHHHHHHHcCCceEEcCCCCCc
Q 037567           19 KDVIQRIIE-K-----RDCLVVMATGSGKSLCYQLPPL---VTGKTALVVSPLISLMQDQVMSLKQRGINAEFLGSAQTD   89 (374)
Q Consensus        19 ~~~~~~~~~-~-----~~~l~~a~tGsGKT~~~~l~~~---~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~   89 (374)
                      ..+++.++. |     +-..+.+|+|+|||..++..+.   ..+.+++|+---..+-.+   .++.+|...         
T Consensus        42 s~~lD~~Lg~GGip~g~itei~G~~~sGKT~l~l~~~~~aqk~g~~v~yiDtE~~~~~~---~a~~~Gvd~---------  109 (268)
T d1xp8a1          42 SLSLDLALGVGGIPRGRITEIYGPESGGKTTLALAIVAQAQKAGGTCAFIDAEHALDPV---YARALGVNT---------  109 (268)
T ss_dssp             CHHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEESSCCCCHH---HHHHTTCCG---------
T ss_pred             CHHHHHHhcCCCccCceEEEEecCCccchHHHHHHHHHHHHhCCCEEEEEECCccCCHH---HHHHhCCCc---------
Confidence            356677774 3     3357899999999965443222   245666665443333333   334444431         


Q ss_pred             hhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEEeccchhh
Q 037567           90 SSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAVDEAHCIS  139 (374)
Q Consensus        90 ~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vviDE~h~~~  139 (374)
                                 -++++..|......+...........+++||+|=+-.+.
T Consensus       110 -----------d~i~~~~~~~~E~~~~~~~~l~~~~~~~liIiDSi~al~  148 (268)
T d1xp8a1         110 -----------DELLVSQPDNGEQALEIMELLVRSGAIDVVVVDSVAALT  148 (268)
T ss_dssp             -----------GGCEEECCSSHHHHHHHHHHHHTTTCCSEEEEECTTTCC
T ss_pred             -----------hhEEEEcCCCHHHHHHHHHHHHhcCCCcEEEEecccccc
Confidence                       034555555443322221111222457899999887654

>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=88.56  E-value=0.48  Score=38.45  Aligned_cols=16  Identities=31%  Similarity=0.320  Sum_probs=12.9

Q ss_pred             CEEEEccCCCCchhhh
Q 037567           30 DCLVVMATGSGKSLCY   45 (374)
Q Consensus        30 ~~l~~a~tGsGKT~~~   45 (374)
                      .++++||||+|||..+
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            3578899999999754

>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=88.11  E-value=0.11  Score=37.98  Aligned_cols=20  Identities=20%  Similarity=0.144  Sum_probs=15.3

Q ss_pred             CCCEEEEccCCCCchhhhhc
Q 037567           28 KRDCLVVMATGSGKSLCYQL   47 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~l   47 (374)
                      .+-+++.|++|||||..+-.
T Consensus         3 ~kiI~l~G~~GsGKsTva~~   22 (178)
T d1qhxa_           3 TRMIILNGGSSAGKSGIVRC   22 (178)
T ss_dssp             CCEEEEECCTTSSHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHH
Confidence            44567889999999976533

>d2avda1 c.66.1.1 (A:44-262) COMT domain-containing protein 1, COMTD1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: COMT-like
domain: COMT domain-containing protein 1, COMTD1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=87.94  E-value=4.1  Score=30.61  Aligned_cols=124  Identities=11%  Similarity=0.068  Sum_probs=76.5

Q ss_pred             CCchhHHHHHHHHHc--CCCEEEEccCCCCchhhhhccccccCCcEEEEcchHHHHHHHHHHHHHcCCc--eEEcCCCCC
Q 037567           13 VFRPYQKDVIQRIIE--KRDCLVVMATGSGKSLCYQLPPLVTGKTALVVSPLISLMQDQVMSLKQRGIN--AEFLGSAQT   88 (374)
Q Consensus        13 ~~~~~Q~~~~~~~~~--~~~~l~~a~tGsGKT~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~--~~~~~~~~~   88 (374)
                      ...|.|.+.+..+.+  +-..++.-.||+|-|..++..++..+.+++-+-+..+.+....+.+...|..  +....+...
T Consensus        42 ~i~~~~g~lL~~L~~~~~~k~vLEiGt~~GyStl~~a~al~~~g~i~tie~~~~~~~~A~~~~~~ag~~~~i~~~~Gda~  121 (219)
T d2avda1          42 MMTCEQAQLLANLARLIQAKKALDLGTFTGYSALALALALPADGRVVTCEVDAQPPELGRPLWRQAEAEHKIDLRLKPAL  121 (219)
T ss_dssp             SCCHHHHHHHHHHHHHTTCCEEEEECCTTSHHHHHHHTTSCTTCEEEEEESCSHHHHHHHHHHHHTTCTTTEEEEESCHH
T ss_pred             ccCHHHHHHHHHHHHccCCCeEEEEechhhHHHHHHHHhCCCCceEEEEeechhHHHHHHHHHHhcCccceEEEEEeehh
Confidence            356778887777664  4456899999999998888877776777777777666776666666665543  333333222


Q ss_pred             ch--hhhhhhhcCCeeEEEEcCcccccCchhhHHH-H-HhcCccEEEEeccchh
Q 037567           89 DS--SVQTKAETGYFQLLFMTPEKACIIPISFWSK-L-LKAGVCLFAVDEAHCI  138 (374)
Q Consensus        89 ~~--~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~-~-~~~~~~~vviDE~h~~  138 (374)
                      ..  ........+.+|+++...++-...  .++.. . .+..=.++|+|.++.-
T Consensus       122 e~l~~~~~~~~~~~fD~ifiD~dk~~y~--~~~~~~~~lL~~GGvii~Dn~l~~  173 (219)
T d2avda1         122 ETLDELLAAGEAGTFDVAVVDADKENCS--AYYERCLQLLRPGGILAVLRVLWR  173 (219)
T ss_dssp             HHHHHHHHTTCTTCEEEEEECSCSTTHH--HHHHHHHHHEEEEEEEEEECCSGG
T ss_pred             hcchhhhhhcccCCccEEEEeCCHHHHH--HHHHHHHHHhcCCcEEEEeCCccc
Confidence            21  111222346789999887763221  11111 1 2233358999999753

>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=87.91  E-value=0.1  Score=43.11  Aligned_cols=19  Identities=32%  Similarity=0.316  Sum_probs=16.0

Q ss_pred             cCCCEEEEccCCCCchhhh
Q 037567           27 EKRDCLVVMATGSGKSLCY   45 (374)
Q Consensus        27 ~~~~~l~~a~tGsGKT~~~   45 (374)
                      .++++++.||+|+|||..+
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            4578999999999999653

>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=87.76  E-value=0.095  Score=38.41  Aligned_cols=27  Identities=19%  Similarity=0.127  Sum_probs=18.7

Q ss_pred             CCEEEEccCCCCchhhhhccccccCCc
Q 037567           29 RDCLVVMATGSGKSLCYQLPPLVTGKT   55 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~~l~~~~~~~~   55 (374)
                      +.+++.|++|||||..+-..+-.-+..
T Consensus         3 ~~Iil~G~~GsGKSTia~~LA~~Lg~~   29 (170)
T d1e6ca_           3 EPIFMVGARGCGMTTVGRELARALGYE   29 (170)
T ss_dssp             CCEEEESCTTSSHHHHHHHHHHHHTCE
T ss_pred             CCEEEECCCCCCHHHHHHHHHHHhCCC
Confidence            567889999999997655444333443

>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=87.74  E-value=0.094  Score=38.23  Aligned_cols=17  Identities=29%  Similarity=0.327  Sum_probs=13.7

Q ss_pred             CEEEEccCCCCchhhhh
Q 037567           30 DCLVVMATGSGKSLCYQ   46 (374)
Q Consensus        30 ~~l~~a~tGsGKT~~~~   46 (374)
                      -+++.||+|||||..+-
T Consensus         8 iivl~G~~GsGKsT~a~   24 (171)
T d1knqa_           8 IYVLMGVSGSGKSAVAS   24 (171)
T ss_dssp             EEEEECSTTSCHHHHHH
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            36789999999997643

>d1fuka_ 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=87.69  E-value=0.58  Score=33.68  Aligned_cols=75  Identities=12%  Similarity=0.077  Sum_probs=54.4

Q ss_pred             cCCcEEEEcchHHHHHHHHHHHHHcCCceEEcCCCCCchhhh---hhhhcCCeeEEEEcCcccccCchhhHHHHHhcCcc
Q 037567           52 TGKTALVVSPLISLMQDQVMSLKQRGINAEFLGSAQTDSSVQ---TKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVC  128 (374)
Q Consensus        52 ~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~  128 (374)
                      ...++||.|.++..++++.+.+...+..+...++........   .....+...++|+|.-.-        ..+...+++
T Consensus        26 ~~~k~iIF~~s~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~l~~f~~~~~~iLv~Tdv~~--------rGiDi~~v~   97 (162)
T d1fuka_          26 SVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLA--------RGIDVQQVS   97 (162)
T ss_dssp             TCSCEEEEESSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEEEGGGT--------TTCCCCSCS
T ss_pred             CCCcEEEEEEEEchHHHHHHHHhhcCceEEEeccCCchhhHHHHHHHHhhcccceeecccccc--------ccccCCCce
Confidence            467899999999999999999999999999888876555432   333457789999995321        233456666


Q ss_pred             EEEEec
Q 037567          129 LFAVDE  134 (374)
Q Consensus       129 ~vviDE  134 (374)
                      +||.=+
T Consensus        98 ~VI~~d  103 (162)
T d1fuka_          98 LVINYD  103 (162)
T ss_dssp             EEEESS
T ss_pred             EEEEec
Confidence            666533

>d3adka_ c.37.1.1 (A:) Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Pig (Sus scrofa) [TaxId: 9823]

Probab=87.48  E-value=0.13  Score=38.54  Aligned_cols=23  Identities=26%  Similarity=0.362  Sum_probs=17.6

Q ss_pred             HHHcCCCEEEEccCCCCchhhhh
Q 037567           24 RIIEKRDCLVVMATGSGKSLCYQ   46 (374)
Q Consensus        24 ~~~~~~~~l~~a~tGsGKT~~~~   46 (374)
                      .+.+++-+++.||+|||||..+-
T Consensus         4 ~~~~~~iI~l~G~pGSGKsT~a~   26 (194)
T d3adka_           4 KLKKSKIIFVVGGPGSGKGTQCE   26 (194)
T ss_dssp             HHHTSCEEEEEECTTSSHHHHHH
T ss_pred             cccCCcEEEEECCCCCCHHHHHH
Confidence            34456778899999999997543

>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=87.25  E-value=0.15  Score=43.70  Aligned_cols=40  Identities=33%  Similarity=0.476  Sum_probs=28.8

Q ss_pred             CCCEEEEccCCCCchhhhh---ccccccCCcEEEEcchHHHHH
Q 037567           28 KRDCLVVMATGSGKSLCYQ---LPPLVTGKTALVVSPLISLMQ   67 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~---l~~~~~~~~~lil~P~~~l~~   67 (374)
                      .+++++.|+||||||.++.   ..++..+..++|+=|..++..
T Consensus        50 ~~H~~I~G~tGsGKT~~l~~li~~~~~~g~~~iiiD~kge~~~   92 (433)
T d1e9ra_          50 PRHLLVNGATGTGKSVLLRELAYTGLLRGDRMVIVDPNGDMLS   92 (433)
T ss_dssp             GGCEEEEECTTSSHHHHHHHHHHHHHHTTCEEEEEEETTHHHH
T ss_pred             cceEEEEeCCCCcHHHHHHHHHHHHHhCCCCEEEEeCChhHHH
Confidence            4678999999999997642   123345777888888876543

>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=87.22  E-value=0.11  Score=38.27  Aligned_cols=16  Identities=31%  Similarity=0.285  Sum_probs=13.0

Q ss_pred             CEEEEccCCCCchhhh
Q 037567           30 DCLVVMATGSGKSLCY   45 (374)
Q Consensus        30 ~~l~~a~tGsGKT~~~   45 (374)
                      -++++|++|||||..+
T Consensus        16 liil~G~pGsGKST~a   31 (172)
T d1yj5a2          16 VVVAVGFPGAGKSTFI   31 (172)
T ss_dssp             EEEEECCTTSSHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            3578999999999643

>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=87.00  E-value=0.056  Score=39.86  Aligned_cols=19  Identities=16%  Similarity=0.041  Sum_probs=14.9

Q ss_pred             cCCCEEEEccCCCCchhhh
Q 037567           27 EKRDCLVVMATGSGKSLCY   45 (374)
Q Consensus        27 ~~~~~l~~a~tGsGKT~~~   45 (374)
                      +|..+++.|++|||||..+
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            3445678999999999764

>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=86.80  E-value=0.12  Score=38.58  Aligned_cols=17  Identities=24%  Similarity=0.292  Sum_probs=14.1

Q ss_pred             CEEEEccCCCCchhhhh
Q 037567           30 DCLVVMATGSGKSLCYQ   46 (374)
Q Consensus        30 ~~l~~a~tGsGKT~~~~   46 (374)
                      .+++.||+|||||..+.
T Consensus         5 ~I~i~GppGsGKsT~a~   21 (189)
T d1zaka1           5 KVMISGAPASGKGTQCE   21 (189)
T ss_dssp             CEEEEESTTSSHHHHHH
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            47899999999997553

>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=86.80  E-value=0.22  Score=40.78  Aligned_cols=49  Identities=16%  Similarity=0.137  Sum_probs=27.8

Q ss_pred             HHHHcCCCE--EEEccCCCCchhhhhccccccCCcEEEEcchHHHHHHHHHHHHH
Q 037567           23 QRIIEKRDC--LVVMATGSGKSLCYQLPPLVTGKTALVVSPLISLMQDQVMSLKQ   75 (374)
Q Consensus        23 ~~~~~~~~~--l~~a~tGsGKT~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~   75 (374)
                      +.+++|.++  +..|+||||||.+..-..-....  .-+.|+  .+.+.+..+..
T Consensus        69 ~~~l~G~n~~i~aYGqtgSGKTyT~~G~~~~~~~--~gii~r--~l~~l~~~~~~  119 (323)
T d1bg2a_          69 KDVLEGYNGTIFAYGQTSSGKTHTMEGKLHDPEG--MGIIPR--IVQDIFNYIYS  119 (323)
T ss_dssp             HHHHTTCCEEEEEECSTTSSHHHHHTBSTTCTTT--BCHHHH--HHHHHHHHHHH
T ss_pred             HHHHcCCCcceeeecccCCCCceeccCCcccccc--cchhhh--HHHHHHhhhhc
Confidence            344567654  67999999999886543322222  223454  34445555443

>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=86.77  E-value=0.12  Score=38.55  Aligned_cols=20  Identities=15%  Similarity=0.154  Sum_probs=15.7

Q ss_pred             CCCEEEEccCCCCchhhhhc
Q 037567           28 KRDCLVVMATGSGKSLCYQL   47 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~l   47 (374)
                      |-.+++.||+|||||..+-.
T Consensus         3 ~~riil~G~pGSGKsT~a~~   22 (190)
T d1ak2a1           3 GVRAVLLGPPGAGKGTQAPK   22 (190)
T ss_dssp             CCEEEEECCTTSSHHHHHHH
T ss_pred             ccEEEEECCCCCCHHHHHHH
Confidence            44678899999999976543

>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=86.51  E-value=0.11  Score=38.44  Aligned_cols=18  Identities=22%  Similarity=0.235  Sum_probs=14.5

Q ss_pred             CEEEEccCCCCchhhhhc
Q 037567           30 DCLVVMATGSGKSLCYQL   47 (374)
Q Consensus        30 ~~l~~a~tGsGKT~~~~l   47 (374)
                      ++++.||+|||||..+-.
T Consensus         2 ~I~i~G~pGsGKsT~a~~   19 (181)
T d2cdna1           2 RVLLLGPPGAGKGTQAVK   19 (181)
T ss_dssp             EEEEECCTTSSHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHH
Confidence            468899999999976543

>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=86.46  E-value=2.6  Score=32.12  Aligned_cols=79  Identities=15%  Similarity=0.228  Sum_probs=50.9

Q ss_pred             HHhhcCCCcEEEEecchhHHHHHHHHHHHc----CCce----eeeecCCChHHHHHHHHhhhcCCeeEEEEec-cccccc
Q 037567          222 LKSVAGAGSIIVYCMTIKDVEEISKALKQL----GVKA----GTYHGQMGSKAREEAHRLFIRDEIRVMVATM-AFGMGI  292 (374)
Q Consensus       222 ~~~~~~~~~~lVf~~~~~~~~~l~~~l~~~----~~~~----~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~-~~~~G~  292 (374)
                      +....++.+++|.+|++.-+++.++.+++.    +..+    ..++++.....+...+....  ..+|+|+|+ .+....
T Consensus        80 ~~~~~~~~rvliv~Pt~~La~Q~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~--~~~Ilv~Tp~~l~~~~  157 (237)
T d1gkub1          80 LFLALKGKRCYVIFPTSLLVIQAAETIRKYAEKAGVGTENLIGYYHGRIPKREKENFMQNLR--NFKIVITTTQFLSKHY  157 (237)
T ss_dssp             HHHHTTSCCEEEEESCHHHHHHHHHHHHHHHTTTCCSGGGSEEECCSSCCSHHHHHHHHSGG--GCSEEEEEHHHHHHCS
T ss_pred             HHHHHhcCeEEEEeccHHHHHHHHHHHHHHHHHcCCceEEEEeeeecccchhhhhhhhcccc--ccceeccChHHHHHhh
Confidence            333446789999999999999999888763    3333    34455556666666554433  357899996 333332


Q ss_pred             -cccCccEEEE
Q 037567          293 -DKPDVRHVIH  302 (374)
Q Consensus       293 -d~~~~~~vi~  302 (374)
                       ++..+++||.
T Consensus       158 ~~~~~~~~vVv  168 (237)
T d1gkub1         158 RELGHFDFIFV  168 (237)
T ss_dssp             TTSCCCSEEEE
T ss_pred             hhcCCCCEEEE
Confidence             4556777663

>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=86.44  E-value=0.092  Score=38.84  Aligned_cols=17  Identities=18%  Similarity=0.296  Sum_probs=14.1

Q ss_pred             CEEEEccCCCCchhhhh
Q 037567           30 DCLVVMATGSGKSLCYQ   46 (374)
Q Consensus        30 ~~l~~a~tGsGKT~~~~   46 (374)
                      ++++.||+|||||..+.
T Consensus         2 ~I~i~G~pGSGKsT~a~   18 (182)
T d1zina1           2 NLVLMGLPGAGKGTQAE   18 (182)
T ss_dssp             EEEEECSTTSSHHHHHH
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            36899999999997654

>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=86.22  E-value=1.6  Score=32.61  Aligned_cols=72  Identities=14%  Similarity=0.135  Sum_probs=51.9

Q ss_pred             CCCcEEEEecchhHHHHHHHHHHHc----CCceeeeecCCChHHHHHHHHhhhcCCeeEEEEecc-----c-cccccccC
Q 037567          227 GAGSIIVYCMTIKDVEEISKALKQL----GVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATMA-----F-GMGIDKPD  296 (374)
Q Consensus       227 ~~~~~lVf~~~~~~~~~l~~~l~~~----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~~-----~-~~G~d~~~  296 (374)
                      .+.+++|.++++..+..+.+.+.+.    +..+...+|+.+..+....++     ..+|+|+|+-     + ...+++.+
T Consensus        71 ~~~~~lil~pt~~l~~q~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~-----~~~IlV~TP~~l~~~l~~~~~~~~~  145 (208)
T d1hv8a1          71 NGIEAIILTPTRELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKALK-----NANIVVGTPGRILDHINRGTLNLKN  145 (208)
T ss_dssp             SSCCEEEECSCHHHHHHHHHHHHHHHCSSCCCEEEECTTSCHHHHHHHHH-----TCSEEEECHHHHHHHHHTTCSCTTS
T ss_pred             cCcceEEEeeccccchhhhhhhhhhcccCCeEEEEeeCCCChHHHHHhcC-----CCCEEEEChHHHHHHHHcCCCCccc
Confidence            4557999999999999998887763    556778888877665444332     3579999962     2 33567888


Q ss_pred             ccEEEEE
Q 037567          297 VRHVIHY  303 (374)
Q Consensus       297 ~~~vi~~  303 (374)
                      +.++|.-
T Consensus       146 l~~lViD  152 (208)
T d1hv8a1         146 VKYFILD  152 (208)
T ss_dssp             CCEEEEE
T ss_pred             CcEEEEE
Confidence            8887743

>d1g5ta_ c.37.1.11 (A:) ATP:corrinoid adenosyltransferase CobA {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: ATP:corrinoid adenosyltransferase CobA
species: Salmonella typhimurium [TaxId: 90371]

Probab=86.11  E-value=1  Score=31.98  Aligned_cols=49  Identities=10%  Similarity=0.013  Sum_probs=33.1

Q ss_pred             hcCccEEEEeccchhhcccCcchHHHHHHHHHHHhcCCCCeeEEEeecCccc
Q 037567          124 KAGVCLFAVDEAHCISEWGHDFRLEYKQLDKLRTFLLGVPFVALTATATEKV  175 (374)
Q Consensus       124 ~~~~~~vviDE~h~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~SaT~~~~~  175 (374)
                      ...+++||+||+-.....|.-..   ..+..+....|...=+.+|+...+..
T Consensus        92 ~~~~dllILDEi~~Ai~~gli~~---~~v~~ll~~rp~~~evVlTGr~~p~~  140 (157)
T d1g5ta_          92 DPLLDMVVLDELTYMVAYDYLPL---EEVISALNARPGHQTVIITGRGCHRD  140 (157)
T ss_dssp             CTTCSEEEEETHHHHHHTTSSCH---HHHHHHHHTSCTTCEEEEECSSCCHH
T ss_pred             cCccCEEeHHHHHHHHHcCCCCH---HHHHHHHHhCCCCCEEEEECCCCCHH
Confidence            45689999999998877665433   33444445556666788888765543

>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=85.94  E-value=0.13  Score=38.44  Aligned_cols=19  Identities=26%  Similarity=0.184  Sum_probs=14.6

Q ss_pred             CEEEEccCCCCchhhhhcc
Q 037567           30 DCLVVMATGSGKSLCYQLP   48 (374)
Q Consensus        30 ~~l~~a~tGsGKT~~~~l~   48 (374)
                      -+++.||+|||||..+...
T Consensus         8 iI~i~G~pGSGKsT~a~~L   26 (194)
T d1qf9a_           8 VVFVLGGPGSGKGTQCANI   26 (194)
T ss_dssp             EEEEEESTTSSHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHH
Confidence            3678999999999765433

>d1oywa3 c.37.1.19 (A:207-406) 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=85.87  E-value=0.81  Score=34.20  Aligned_cols=73  Identities=18%  Similarity=0.218  Sum_probs=53.1

Q ss_pred             cCCcEEEEcchHHHHHHHHHHHHHcCCceEEcCCCCCchhh---hhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCcc
Q 037567           52 TGKTALVVSPLISLMQDQVMSLKQRGINAEFLGSAQTDSSV---QTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVC  128 (374)
Q Consensus        52 ~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~  128 (374)
                      ...++||.++|+..++.+...+...++.+...+++......   ......+..+|+|+|.-.-        ..+...+++
T Consensus        29 ~~~~~IIF~~t~~~~~~l~~~l~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~ilvaTd~~~--------~GiD~p~v~  100 (200)
T d1oywa3          29 RGKSGIIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFG--------MGINKPNVR  100 (200)
T ss_dssp             TTCCEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECTTSC--------TTTCCTTCC
T ss_pred             CCCCEEEEEeeehhhHHhhhhhccCCceeEEecCCCcHHHHHHHHHHHhcccceEEEecchhh--------hccCCCCCC
Confidence            46689999999999999999999999999888887655432   2333457789999995321        233445666


Q ss_pred             EEEE
Q 037567          129 LFAV  132 (374)
Q Consensus       129 ~vvi  132 (374)
                      +||.
T Consensus       101 ~VI~  104 (200)
T d1oywa3         101 FVVH  104 (200)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            6664

>d1s2ma2 c.37.1.19 (A:252-422) 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=85.71  E-value=0.87  Score=33.01  Aligned_cols=76  Identities=7%  Similarity=-0.019  Sum_probs=54.6

Q ss_pred             cCCcEEEEcchHHHHHHHHHHHHHcCCceEEcCCCCCchhh---hhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCcc
Q 037567           52 TGKTALVVSPLISLMQDQVMSLKQRGINAEFLGSAQTDSSV---QTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVC  128 (374)
Q Consensus        52 ~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~  128 (374)
                      ...++||.|+++.-++.+...+...|..+..+++.....+.   ......+..+++|+|.-. .       ..+.+.+++
T Consensus        31 ~~~k~iVF~~~~~~~~~l~~~L~~~g~~~~~~h~~~~~~~r~~~~~~f~~~~~~ilv~Td~~-~-------~Gid~~~v~  102 (171)
T d1s2ma2          31 QINQAIIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSDLL-T-------RGIDIQAVN  102 (171)
T ss_dssp             CCSEEEEECSSHHHHHHHHHHHHHHTCCEEEECTTSCHHHHHHHHHHHHTTSSSEEEESSCS-S-------SSCCCTTEE
T ss_pred             CCCceEEEEeeeehhhHhHHhhhcccccccccccccchhhhhhhhhhcccCccccccchhHh-h-------hccccceeE
Confidence            46789999999999999999999999999888876655432   233446788999999632 1       233345666


Q ss_pred             EEEEecc
Q 037567          129 LFAVDEA  135 (374)
Q Consensus       129 ~vviDE~  135 (374)
                      +||.=+.
T Consensus       103 ~VI~~d~  109 (171)
T d1s2ma2         103 VVINFDF  109 (171)
T ss_dssp             EEEESSC
T ss_pred             EEEecCC
Confidence            6665433

>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=85.67  E-value=0.13  Score=37.98  Aligned_cols=17  Identities=24%  Similarity=0.175  Sum_probs=13.9

Q ss_pred             CEEEEccCCCCchhhhh
Q 037567           30 DCLVVMATGSGKSLCYQ   46 (374)
Q Consensus        30 ~~l~~a~tGsGKT~~~~   46 (374)
                      .+++.||+|||||..+-
T Consensus         2 ~I~i~G~pGSGKsT~~~   18 (179)
T d1e4va1           2 RIILLGAPVAGKGTQAQ   18 (179)
T ss_dssp             EEEEEESTTSSHHHHHH
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            36889999999997653

>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=85.47  E-value=0.15  Score=37.64  Aligned_cols=17  Identities=18%  Similarity=0.245  Sum_probs=13.9

Q ss_pred             CCEEEEccCCCCchhhh
Q 037567           29 RDCLVVMATGSGKSLCY   45 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~   45 (374)
                      +-+++.|++|||||...
T Consensus         2 kiI~i~G~~GsGKsT~~   18 (190)
T d1khta_           2 KVVVVTGVPGVGSTTSS   18 (190)
T ss_dssp             CEEEEECCTTSCHHHHH
T ss_pred             CEEEEECCCCCCHHHHH
Confidence            45688999999999654

>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=85.42  E-value=0.12  Score=38.23  Aligned_cols=17  Identities=18%  Similarity=0.202  Sum_probs=14.0

Q ss_pred             EEEEccCCCCchhhhhc
Q 037567           31 CLVVMATGSGKSLCYQL   47 (374)
Q Consensus        31 ~l~~a~tGsGKT~~~~l   47 (374)
                      +++.||+|||||..+..
T Consensus         3 I~i~G~pGSGKsT~a~~   19 (182)
T d1s3ga1           3 IVLMGLPGAGKGTQADR   19 (182)
T ss_dssp             EEEECSTTSSHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHH
Confidence            68899999999976543

>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=85.39  E-value=0.31  Score=42.09  Aligned_cols=48  Identities=19%  Similarity=0.182  Sum_probs=33.7

Q ss_pred             CCCEEEEccCCCCchhhhhcc---cc-c-----------cCCcEEEEcchHHHHHHHHHHHHH
Q 037567           28 KRDCLVVMATGSGKSLCYQLP---PL-V-----------TGKTALVVSPLISLMQDQVMSLKQ   75 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~~l~---~~-~-----------~~~~~lil~P~~~l~~q~~~~~~~   75 (374)
                      ....+|.|..|||||.+..--   ++ .           ....+|+++=|+.-+.++.+.+..
T Consensus        16 ~g~~lv~A~AGsGKT~~l~~r~~~ll~~~~~~~~~~~~~~~~~IL~lTFT~kAA~Emk~RI~~   78 (485)
T d1w36b1          16 QGERLIEASAGTGKTFTIAALYLRLLLGLGGSAAFPRPLTVEELLVVTFTEAATAELRGRIRS   78 (485)
T ss_dssp             SSCEEEECCTTSCHHHHHHHHHHHHHTTCSSSSSCSSCCCGGGEEEEESCHHHHHHHHHHHHH
T ss_pred             CCCeEEEEcCchHHHHHHHHHHHHHHhhCcccccccCCCCcccEeEeccHHHHHHHHHHHHHH
Confidence            456899999999999653211   11 1           124599999999999888877643

>d1yksa2 c.37.1.14 (A:325-623) 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=85.16  E-value=0.89  Score=36.36  Aligned_cols=56  Identities=13%  Similarity=0.116  Sum_probs=41.5

Q ss_pred             cCCcEEEEcchHHHHHHHHHHHHHcCCceEEcCCCCCchhhhhhhhcCCeeEEEEcC
Q 037567           52 TGKTALVVSPLISLMQDQVMSLKQRGINAEFLGSAQTDSSVQTKAETGYFQLLFMTP  108 (374)
Q Consensus        52 ~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~  108 (374)
                      ..++++|++|+..-+++....+++.|..+..+++.....+. .....+..+++|+|.
T Consensus        35 ~~g~~~~F~~s~~~~~~~a~~L~~~g~~V~~l~~~~~~~e~-~~~~~~~~~~~~~t~   90 (299)
T d1yksa2          35 DKRPTAWFLPSIRAANVMAASLRKAGKSVVVLNRKTFEREY-PTIKQKKPDFILATD   90 (299)
T ss_dssp             CCSCEEEECSCHHHHHHHHHHHHHTTCCEEECCSSSCC---------CCCSEEEESS
T ss_pred             cCCCEEEEeCCHHHHHHHHHHHHhcCCeEEEEcCcCcHhHH-hhhhcCCcCEEEEec
Confidence            47889999999999999999999999988887776554433 334556789999995

>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=85.08  E-value=0.16  Score=37.25  Aligned_cols=16  Identities=19%  Similarity=0.312  Sum_probs=13.3

Q ss_pred             CEEEEccCCCCchhhh
Q 037567           30 DCLVVMATGSGKSLCY   45 (374)
Q Consensus        30 ~~l~~a~tGsGKT~~~   45 (374)
                      .+++.||+|+|||...
T Consensus         2 ki~I~G~~G~GKSTLl   17 (178)
T d1ye8a1           2 KIIITGEPGVGKTTLV   17 (178)
T ss_dssp             EEEEECCTTSSHHHHH
T ss_pred             EEEEECCCCcHHHHHH
Confidence            3789999999999653

>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=84.92  E-value=0.19  Score=39.41  Aligned_cols=19  Identities=21%  Similarity=0.328  Sum_probs=16.1

Q ss_pred             cCCCEEEEccCCCCchhhh
Q 037567           27 EKRDCLVVMATGSGKSLCY   45 (374)
Q Consensus        27 ~~~~~l~~a~tGsGKT~~~   45 (374)
                      .+..+++.|++|+|||..+
T Consensus        22 ~~~pvlI~Ge~GtGK~~~A   40 (247)
T d1ny5a2          22 AECPVLITGESGVGKEVVA   40 (247)
T ss_dssp             CCSCEEEECSTTSSHHHHH
T ss_pred             CCCCEEEECCCCcCHHHHH
Confidence            3678999999999999654

>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=84.70  E-value=0.17  Score=37.95  Aligned_cols=17  Identities=24%  Similarity=0.309  Sum_probs=13.6

Q ss_pred             CEEEEccCCCCchhhhh
Q 037567           30 DCLVVMATGSGKSLCYQ   46 (374)
Q Consensus        30 ~~l~~a~tGsGKT~~~~   46 (374)
                      -+++.||+|||||..+-
T Consensus        10 iI~i~GppGSGKsT~a~   26 (196)
T d1ukza_          10 VIFVLGGPGAGKGTQCE   26 (196)
T ss_dssp             EEEEECSTTSSHHHHHH
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            46789999999997543

>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=84.67  E-value=0.18  Score=41.20  Aligned_cols=31  Identities=26%  Similarity=0.216  Sum_probs=21.4

Q ss_pred             chhHHHHHHHHHc------------C---CCEEEEccCCCCchhhh
Q 037567           15 RPYQKDVIQRIIE------------K---RDCLVVMATGSGKSLCY   45 (374)
Q Consensus        15 ~~~Q~~~~~~~~~------------~---~~~l~~a~tGsGKT~~~   45 (374)
                      --.|.+|+..+..            +   ..+++.||||+|||..+
T Consensus        24 viGQ~~a~~~v~~~v~~~~~~l~~~~~p~~~~lf~Gp~GvGKT~la   69 (315)
T d1r6bx3          24 VFGQDKAIEALTEAIKMARAGLGHEHKPVGSFLFAGPTGVGKTEVT   69 (315)
T ss_dssp             SCSCHHHHHHHHHHHHHHHTTCSCTTSCSEEEEEECSTTSSHHHHH
T ss_pred             ecChHHHHHHHHHHHHHHHccCCCCCCCceEEEEECCCcchhHHHH
Confidence            3467777776532            1   14688999999999654

>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=84.66  E-value=0.2  Score=36.25  Aligned_cols=21  Identities=29%  Similarity=0.227  Sum_probs=15.8

Q ss_pred             CCEEEEccCCCCchhhhhccc
Q 037567           29 RDCLVVMATGSGKSLCYQLPP   49 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~~l~~   49 (374)
                      .++++.|++|+|||...-+.+
T Consensus         2 p~IvliG~~G~GKSTig~~La   22 (165)
T d2iyva1           2 PKAVLVGLPGSGKSTIGRRLA   22 (165)
T ss_dssp             CSEEEECSTTSSHHHHHHHHH
T ss_pred             CcEEEECCCCCCHHHHHHHHH
Confidence            357888999999997654443

>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=84.56  E-value=0.19  Score=37.33  Aligned_cols=16  Identities=31%  Similarity=0.468  Sum_probs=14.0

Q ss_pred             CCEEEEccCCCCchhh
Q 037567           29 RDCLVVMATGSGKSLC   44 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~   44 (374)
                      +.+++.||+|+|||..
T Consensus         2 rpIvl~GpsG~GK~tl   17 (186)
T d1gkya_           2 RPIVISGPSGTGKSTL   17 (186)
T ss_dssp             CCEEEECCTTSSHHHH
T ss_pred             CeEEEECCCCCCHHHH
Confidence            4689999999999964

>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=84.16  E-value=0.32  Score=40.34  Aligned_cols=32  Identities=25%  Similarity=0.269  Sum_probs=22.1

Q ss_pred             hHHHHHHH--------HHcCCCE--EEEccCCCCchhhhhcc
Q 037567           17 YQKDVIQR--------IIEKRDC--LVVMATGSGKSLCYQLP   48 (374)
Q Consensus        17 ~Q~~~~~~--------~~~~~~~--l~~a~tGsGKT~~~~l~   48 (374)
                      -|.+++..        +++|.++  +..|+||||||.+..-.
T Consensus        59 ~q~~vy~~~~~plv~~~l~G~n~ti~aYG~tgSGKT~Tm~G~  100 (354)
T d1goja_          59 KQSDIFDFSIKPTVDDILNGYNGTVFAYGQTGAGKSYTMMGT  100 (354)
T ss_dssp             CHHHHHHHHTHHHHHHHTTTCCEEEEEECSTTSSHHHHHTBS
T ss_pred             CHHHHHHHHHHHHHHHhhccCceeEEecccCCCCcceeeecc
Confidence            46665543        3567664  66899999999886543

>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=84.13  E-value=0.17  Score=37.81  Aligned_cols=18  Identities=28%  Similarity=0.307  Sum_probs=14.6

Q ss_pred             CEEEEccCCCCchhhhhc
Q 037567           30 DCLVVMATGSGKSLCYQL   47 (374)
Q Consensus        30 ~~l~~a~tGsGKT~~~~l   47 (374)
                      .+++.||+|||||..+..
T Consensus         8 rIiliG~PGSGKtT~a~~   25 (189)
T d2ak3a1           8 RAAIMGAPGSGKGTVSSR   25 (189)
T ss_dssp             EEEEECCTTSSHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHH
Confidence            578899999999976543

>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=84.04  E-value=0.19  Score=37.10  Aligned_cols=17  Identities=18%  Similarity=0.280  Sum_probs=13.9

Q ss_pred             CEEEEccCCCCchhhhh
Q 037567           30 DCLVVMATGSGKSLCYQ   46 (374)
Q Consensus        30 ~~l~~a~tGsGKT~~~~   46 (374)
                      .+++.||+|||||..+-
T Consensus         4 rIvl~G~pGSGKtT~a~   20 (180)
T d1akya1           4 RMVLIGPPGAGKGTQAP   20 (180)
T ss_dssp             EEEEECCTTSSHHHHHH
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            46889999999997643

>d1sdma_ c.37.1.9 (A:) Kinesin heavy chain-like protein {Potato (Solanum tuberosum) [TaxId: 4113]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin heavy chain-like protein
species: Potato (Solanum tuberosum) [TaxId: 4113]

Probab=83.69  E-value=0.28  Score=40.80  Aligned_cols=47  Identities=21%  Similarity=0.311  Sum_probs=27.9

Q ss_pred             HHHHHcCCCE--EEEccCCCCchhhhhccccccCCcEEEEcchHHHHHHHHHHHHH
Q 037567           22 IQRIIEKRDC--LVVMATGSGKSLCYQLPPLVTGKTALVVSPLISLMQDQVMSLKQ   75 (374)
Q Consensus        22 ~~~~~~~~~~--l~~a~tGsGKT~~~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~   75 (374)
                      ++.+++|.++  +..|+||||||.+..-.--..+     ++|+  .+.+.+..+..
T Consensus        67 v~~~l~G~n~~i~aYGqTGSGKTyTm~G~~~~~G-----iipr--~~~~lf~~i~~  115 (364)
T d1sdma_          67 VQSAVDGYNVCIFAYGQTGSGKTFTIYGADSNPG-----LTPR--AMSELFRIMKK  115 (364)
T ss_dssp             HHHHHTTCEEEEEEECSTTSSHHHHHTBCSSSBC-----HHHH--HHHHHHHHHHH
T ss_pred             HHHHhcCCceeeeccccCCCCcccccccCccccc-----hhHH--HHHHHHhhhhh
Confidence            4555677654  6689999999998654432222     4454  23445555543

>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=83.58  E-value=0.32  Score=40.43  Aligned_cols=33  Identities=24%  Similarity=0.175  Sum_probs=22.2

Q ss_pred             hhHHHHHHH--------HHcCCCE--EEEccCCCCchhhhhcc
Q 037567           16 PYQKDVIQR--------IIEKRDC--LVVMATGSGKSLCYQLP   48 (374)
Q Consensus        16 ~~Q~~~~~~--------~~~~~~~--l~~a~tGsGKT~~~~l~   48 (374)
                      .-|.+.+..        +++|.++  +..|.||||||.++.-.
T Consensus        92 ~~Q~~Vy~~~~~plv~~~l~G~n~tifaYGqTGSGKTyTm~G~  134 (362)
T d1v8ka_          92 ASNEVVYRFTARPLVQTIFEGGKATCFAYGQTGSGKTHTMGGD  134 (362)
T ss_dssp             CCHHHHHHHTTHHHHHHHHTTCEEEEEEEESTTSSHHHHHHCB
T ss_pred             CCHHHHHHHHHHHHHHHHHhccCceEEeeccCCCCCceeeeec
Confidence            356665543        4566654  56799999999986543

>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=83.34  E-value=0.21  Score=37.29  Aligned_cols=16  Identities=25%  Similarity=0.372  Sum_probs=13.4

Q ss_pred             EEEEccCCCCchhhhh
Q 037567           31 CLVVMATGSGKSLCYQ   46 (374)
Q Consensus        31 ~l~~a~tGsGKT~~~~   46 (374)
                      +++.||+|||||..+.
T Consensus         4 I~i~GppGSGKsT~a~   19 (194)
T d1teva_           4 VFVLGGPGAGKGTQCA   19 (194)
T ss_dssp             EEEECCTTSSHHHHHH
T ss_pred             EEEECCCCCCHHHHHH
Confidence            5789999999997653

>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=83.18  E-value=0.088  Score=39.36  Aligned_cols=17  Identities=18%  Similarity=0.251  Sum_probs=13.3

Q ss_pred             CEEEEccCCCCchhhhh
Q 037567           30 DCLVVMATGSGKSLCYQ   46 (374)
Q Consensus        30 ~~l~~a~tGsGKT~~~~   46 (374)
                      .+++.|++|||||..+-
T Consensus        21 vI~L~G~pGSGKTTiAk   37 (195)
T d1x6va3          21 TVWLTGLSGAGKTTVSM   37 (195)
T ss_dssp             EEEEESSCHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            44678999999997543

>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=83.01  E-value=0.35  Score=39.87  Aligned_cols=23  Identities=26%  Similarity=0.559  Sum_probs=17.3

Q ss_pred             HHHcCCCE--EEEccCCCCchhhhh
Q 037567           24 RIIEKRDC--LVVMATGSGKSLCYQ   46 (374)
Q Consensus        24 ~~~~~~~~--l~~a~tGsGKT~~~~   46 (374)
                      .+++|.++  +..|+||||||.+..
T Consensus        75 ~~l~G~n~~i~aYGqtgSGKTyTm~   99 (345)
T d1x88a1          75 EVIMGYNCTIFAYGQTGTGKTFTME   99 (345)
T ss_dssp             HHHTTCEEEEEEEECTTSSHHHHHT
T ss_pred             HHhccCCceEEeeeeccccceEEee
Confidence            34567654  679999999998864

>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=82.99  E-value=0.24  Score=36.89  Aligned_cols=17  Identities=29%  Similarity=0.429  Sum_probs=14.0

Q ss_pred             CCEEEEccCCCCchhhh
Q 037567           29 RDCLVVMATGSGKSLCY   45 (374)
Q Consensus        29 ~~~l~~a~tGsGKT~~~   45 (374)
                      +.+++.||+|+|||..+
T Consensus         1 rpIvl~GPsGsGK~tl~   17 (190)
T d1lvga_           1 RPVVLSGPSGAGKSTLL   17 (190)
T ss_dssp             CCEEEECCTTSSHHHHH
T ss_pred             CeEEEECCCCCCHHHHH
Confidence            35789999999999753

>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=82.82  E-value=0.22  Score=38.60  Aligned_cols=26  Identities=12%  Similarity=0.045  Sum_probs=19.3

Q ss_pred             HHHHHHHc-----CCCEEEEccCCCCchhhh
Q 037567           20 DVIQRIIE-----KRDCLVVMATGSGKSLCY   45 (374)
Q Consensus        20 ~~~~~~~~-----~~~~l~~a~tGsGKT~~~   45 (374)
                      ..++.++.     |+-+++.||+|+|||...
T Consensus        21 ~~LD~ll~GGi~~G~~~li~G~pGsGKT~l~   51 (251)
T d1szpa2          21 KNLDTLLGGGVETGSITELFGEFRTGKSQLC   51 (251)
T ss_dssp             HHHHHHHTSSEESSSEEEEEESTTSSHHHHH
T ss_pred             HHHHhhhCCCCcCCeEEEEEcCCCCCHHHHH
Confidence            45666665     356789999999999654

>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=82.71  E-value=0.43  Score=39.43  Aligned_cols=24  Identities=25%  Similarity=0.239  Sum_probs=18.0

Q ss_pred             HHHcCCCE--EEEccCCCCchhhhhc
Q 037567           24 RIIEKRDC--LVVMATGSGKSLCYQL   47 (374)
Q Consensus        24 ~~~~~~~~--l~~a~tGsGKT~~~~l   47 (374)
                      .+++|.++  +..|.||||||.+..-
T Consensus        81 ~~l~G~n~ti~aYGqTgSGKT~Tm~G  106 (349)
T d2zfia1          81 HAFEGYNVCIFAYGQTGAGKSYTMMG  106 (349)
T ss_dssp             HHHTTCCEEEEEECSTTSSHHHHHTB
T ss_pred             HHHhccCceeeeeccCCCCCceeecc
Confidence            34667654  6689999999988644

>d2j0sa2 c.37.1.19 (A:244-411) 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=82.56  E-value=1.3  Score=31.96  Aligned_cols=73  Identities=12%  Similarity=0.049  Sum_probs=53.2

Q ss_pred             cCCcEEEEcchHHHHHHHHHHHHHcCCceEEcCCCCCchhhh---hhhhcCCeeEEEEcCcccccCchhhHHHHHhcCcc
Q 037567           52 TGKTALVVSPLISLMQDQVMSLKQRGINAEFLGSAQTDSSVQ---TKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVC  128 (374)
Q Consensus        52 ~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~  128 (374)
                      ...+++|.|+++.-++.....+...+..+...++.....+..   .....+..+++|+|.-.-        ..+...+++
T Consensus        33 ~~~k~iiF~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~fk~g~~~iLv~Td~~~--------rGiDi~~v~  104 (168)
T d2j0sa2          33 TITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWA--------RGLDVPQVS  104 (168)
T ss_dssp             TSSEEEEECSSHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHHTSSCEEEECGGGS--------SSCCCTTEE
T ss_pred             CCCceEEEeeeHHHHHHHHHHhhhcccchhhhhhhhhHHHHHHHHHHHhcCCccEEeccchhc--------ccccccCcc
Confidence            467899999999999999999999999988888776665432   233457789999995321        233445566


Q ss_pred             EEEE
Q 037567          129 LFAV  132 (374)
Q Consensus       129 ~vvi  132 (374)
                      +||.
T Consensus       105 ~VIn  108 (168)
T d2j0sa2         105 LIIN  108 (168)
T ss_dssp             EEEE
T ss_pred             eEEE
Confidence            6654

>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=82.20  E-value=0.25  Score=36.45  Aligned_cols=18  Identities=22%  Similarity=0.200  Sum_probs=14.5

Q ss_pred             CCCEEEEccCCCCchhhh
Q 037567           28 KRDCLVVMATGSGKSLCY   45 (374)
Q Consensus        28 ~~~~l~~a~tGsGKT~~~   45 (374)
                      |+=+++.||+|+|||...
T Consensus         2 G~iivl~GpsG~GK~tl~   19 (182)
T d1znwa1           2 GRVVVLSGPSAVGKSTVV   19 (182)
T ss_dssp             CCEEEEECSTTSSHHHHH
T ss_pred             CeEEEEECCCCCCHHHHH
Confidence            455789999999999753

>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=82.03  E-value=0.26  Score=37.25  Aligned_cols=19  Identities=26%  Similarity=0.310  Sum_probs=15.5

Q ss_pred             cCCCEEEEccCCCCchhhh
Q 037567           27 EKRDCLVVMATGSGKSLCY   45 (374)
Q Consensus        27 ~~~~~l~~a~tGsGKT~~~   45 (374)
                      +|+=++++||+|+|||...
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            4566789999999999754

>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=81.95  E-value=0.36  Score=40.19  Aligned_cols=26  Identities=27%  Similarity=0.402  Sum_probs=19.2

Q ss_pred             HHHHHHcCCCE--EEEccCCCCchhhhh
Q 037567           21 VIQRIIEKRDC--LVVMATGSGKSLCYQ   46 (374)
Q Consensus        21 ~~~~~~~~~~~--l~~a~tGsGKT~~~~   46 (374)
                      .++.+++|.++  +..|+||||||.+..
T Consensus       116 lv~~vl~G~n~ti~aYGqtGSGKT~Tm~  143 (368)
T d2ncda_         116 LIQSALDGYNICIFAYGQTGSGKTYTMD  143 (368)
T ss_dssp             HHHHHHTTCEEEEEEECSTTSSHHHHHT
T ss_pred             HHHHHhcccceeEEeeccCCCccceEec
Confidence            34456677654  678999999998864

>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=81.91  E-value=0.21  Score=38.96  Aligned_cols=26  Identities=19%  Similarity=0.188  Sum_probs=19.3

Q ss_pred             HHHHHHHcC-----CCEEEEccCCCCchhhh
Q 037567           20 DVIQRIIEK-----RDCLVVMATGSGKSLCY   45 (374)
Q Consensus        20 ~~~~~~~~~-----~~~l~~a~tGsGKT~~~   45 (374)
                      ..++.++.|     +-+++.||+|+|||...
T Consensus        23 ~~LD~ll~GGlp~G~~~li~G~pGsGKT~~~   53 (254)
T d1pzna2          23 KSLDKLLGGGIETQAITEVFGEFGSGKTQLA   53 (254)
T ss_dssp             HHHHHHHTSSEESSEEEEEEESTTSSHHHHH
T ss_pred             HHHHHhhcCCccCCEEEEEEcCCCCCHHHHH
Confidence            455666654     46789999999999654

>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=81.76  E-value=2.6  Score=31.90  Aligned_cols=72  Identities=13%  Similarity=0.076  Sum_probs=51.2

Q ss_pred             CCcEEEEecchhHHHHHHHHHHHc----CCceeeeecCCChHHHHHHHHhhhcCCeeEEEEec------cccccccccCc
Q 037567          228 AGSIIVYCMTIKDVEEISKALKQL----GVKAGTYHGQMGSKAREEAHRLFIRDEIRVMVATM------AFGMGIDKPDV  297 (374)
Q Consensus       228 ~~~~lVf~~~~~~~~~l~~~l~~~----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~ilv~t~------~~~~G~d~~~~  297 (374)
                      .-+++|++++++-+..+++.++..    ++.+..+.|+.+..+....++   .+ .+|+|+|+      .....+++.++
T Consensus        85 ~~~~lil~PtreLa~Qi~~~~~~l~~~~~i~~~~~~g~~~~~~~~~~l~---~~-~~Ilv~TPgrl~~~~~~~~~~~~~l  160 (222)
T d2j0sa1          85 ETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLD---YG-QHVVAGTPGRVFDMIRRRSLRTRAI  160 (222)
T ss_dssp             SCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECTTSCHHHHHHHHH---HC-CSEEEECHHHHHHHHHTTSSCCTTC
T ss_pred             CceeEEecchHHHHHHHHHHHHHHhCccceeEEEEeecccchhhHHHhc---cC-CeEEeCCCCcHHhcccccccccccc
Confidence            446899999999999999888764    456777888877655444332   23 57999997      12456677778


Q ss_pred             cEEEEE
Q 037567          298 RHVIHY  303 (374)
Q Consensus       298 ~~vi~~  303 (374)
                      +++|.-
T Consensus       161 ~~lVlD  166 (222)
T d2j0sa1         161 KMLVLD  166 (222)
T ss_dssp             CEEEEE
T ss_pred             eeeeec
Confidence            887743

>d1xbta1 c.37.1.24 (A:18-150) Thymidine kinase, TK1, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Type II thymidine kinase
domain: Thymidine kinase, TK1, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=81.49  E-value=0.32  Score=33.82  Aligned_cols=34  Identities=18%  Similarity=0.032  Sum_probs=23.8

Q ss_pred             EEEEccCCCCchhhhhcccc---ccCCcEEEEcchHH
Q 037567           31 CLVVMATGSGKSLCYQLPPL---VTGKTALVVSPLIS   64 (374)
Q Consensus        31 ~l~~a~tGsGKT~~~~l~~~---~~~~~~lil~P~~~   64 (374)
                      -++.||+.||||.-.+-.+.   ..+.+++++-|..+
T Consensus         5 ~li~GpMfsGKTt~Li~~~~~~~~~g~~v~~ikp~~D   41 (133)
T d1xbta1           5 QVILGPMFSGKSTELMRRVRRFQIAQYKCLVIKYAKD   41 (133)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHHHTTTCCEEEEEETTC
T ss_pred             EEEEecccCHHHHHHHHHHHHHHHcCCcEEEEecccc
Confidence            37899999999964332221   24778999998754

>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=81.47  E-value=0.33  Score=38.52  Aligned_cols=36  Identities=19%  Similarity=0.124  Sum_probs=24.5

Q ss_pred             cCCCEEEEccCCCCchhhhh-cc---ccccCCcEEEEcch
Q 037567           27 EKRDCLVVMATGSGKSLCYQ-LP---PLVTGKTALVVSPL   62 (374)
Q Consensus        27 ~~~~~l~~a~tGsGKT~~~~-l~---~~~~~~~~lil~P~   62 (374)
                      .|.-+++.|+||+|||...+ ++   +...+.+++++..-
T Consensus        34 ~G~l~vi~G~~G~GKT~~~~~la~~~a~~~g~~v~~~s~E   73 (277)
T d1cr2a_          34 GGEVIMVTSGSGMGKSTFVRQQALQWGTAMGKKVGLAMLE   73 (277)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHHHHHHHTSCCCEEEEESS
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHhhhhhcccceeEeeec
Confidence            45567889999999995432 21   22357789888754

>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=81.32  E-value=0.27  Score=37.32  Aligned_cols=26  Identities=8%  Similarity=0.111  Sum_probs=19.0

Q ss_pred             HHHHHHHc-----CCCEEEEccCCCCchhhh
Q 037567           20 DVIQRIIE-----KRDCLVVMATGSGKSLCY   45 (374)
Q Consensus        20 ~~~~~~~~-----~~~~l~~a~tGsGKT~~~   45 (374)
                      ..++.++.     |.-+++.||+|+|||..+
T Consensus        10 ~~LD~ll~GGi~~G~v~~i~G~~GsGKT~l~   40 (242)
T d1n0wa_          10 KELDKLLQGGIETGSITEMFGEFRTGKTQIC   40 (242)
T ss_dssp             HHHHHHTTTSEETTSEEEEECCTTSSHHHHH
T ss_pred             HHHHHhhcCCCcCCEEEEEEeCCCCCHHHHH
Confidence            44566665     456789999999999543

>d1krwa_ c.23.1.1 (A:) NTRC receiver domain {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: NTRC receiver domain
species: Salmonella typhimurium [TaxId: 90371]

Probab=81.30  E-value=5.7  Score=26.47  Aligned_cols=88  Identities=14%  Similarity=0.098  Sum_probs=54.6

Q ss_pred             CCcEEEEcchHHHHHHHHHHHHHcCCceEEcCCCCCchhhhhhhhcCCeeEEEEcCcccccCchhhHHHHHhcCccEEEE
Q 037567           53 GKTALVVSPLISLMQDQVMSLKQRGINAEFLGSAQTDSSVQTKAETGYFQLLFMTPEKACIIPISFWSKLLKAGVCLFAV  132 (374)
Q Consensus        53 ~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~T~~~l~~~~~~~~~~~~~~~~~~vvi  132 (374)
                      ++++||+=............++..|..+.....+.                             .....+....++++++
T Consensus         3 k~~ILIVDDd~~~~~~l~~~L~~~g~~v~~a~~~~-----------------------------~a~~~l~~~~~dlii~   53 (123)
T d1krwa_           3 RGIVWVVDDDSSIRWVLERALAGAGLTCTTFENGN-----------------------------EVLAALASKTPDVLLS   53 (123)
T ss_dssp             CCEEEEESSSHHHHHHHHHHHHHTTCEEEEESSSH-----------------------------HHHHHHTTCCCSEEEE
T ss_pred             CCEEEEEECCHHHHHHHHHHHHHCCCEEEEeCCHH-----------------------------HHHHHHHhCCCCEEEe
Confidence            45688888887777777788887776554433211                             1112223356789999


Q ss_pred             eccchhhc-ccCcchHHHHHHHHHHHhcCCCCeeEEEeecCcccHH
Q 037567          133 DEAHCISE-WGHDFRLEYKQLDKLRTFLLGVPFVALTATATEKVRI  177 (374)
Q Consensus       133 DE~h~~~~-~~~~~~~~~~~~~~~~~~~~~~~~i~~SaT~~~~~~~  177 (374)
                      | . .+.+ .|.      ..+.+++...++.++|++||........
T Consensus        54 D-~-~mp~~~G~------el~~~l~~~~~~~piI~~t~~~~~~~~~   91 (123)
T d1krwa_          54 D-I-RMPGMDGL------ALLKQIKQRHPMLPVIIMTAHSDLDAAV   91 (123)
T ss_dssp             C-C-SSSSSTTH------HHHHHHHHHSSSCCEEESCCCSCHHHHH
T ss_pred             h-h-hcCCchHH------HHHHHHHHhCCCCeEEEEecCCCHHHHH
Confidence            8 2 2433 232      3445555666789999999987766543

>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=81.22  E-value=0.22  Score=40.47  Aligned_cols=15  Identities=27%  Similarity=0.228  Sum_probs=12.2

Q ss_pred             EEEEccCCCCchhhh
Q 037567           31 CLVVMATGSGKSLCY   45 (374)
Q Consensus        31 ~l~~a~tGsGKT~~~   45 (374)
                      .++.||+|+|||+.+
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            455899999999764

>d1a1va2 c.37.1.14 (A:326-624) 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=80.37  E-value=1.8  Score=34.16  Aligned_cols=38  Identities=18%  Similarity=0.086  Sum_probs=33.2

Q ss_pred             cCCcEEEEcchHHHHHHHHHHHHHcCCceEEcCCCCCc
Q 037567           52 TGKTALVVSPLISLMQDQVMSLKQRGINAEFLGSAQTD   89 (374)
Q Consensus        52 ~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~   89 (374)
                      ++.++||+|+++..++++...+++.|++....+++...
T Consensus        35 kggk~LVFcnSR~~aE~La~~L~~~Gi~a~~~Hgglsq   72 (299)
T d1a1va2          35 KGGRHLIFCHSKKKCDELAAKLVALGINAVAYYRGLDV   72 (299)
T ss_dssp             HSSEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCG
T ss_pred             cCCCEEEECCcHHHHHHHHHHHHHCCCCEEEEeCCchH
Confidence            57899999999999999999999999998887765443

>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=80.01  E-value=0.32  Score=36.63  Aligned_cols=16  Identities=19%  Similarity=0.235  Sum_probs=13.1

Q ss_pred             EEEEccCCCCchhhhh
Q 037567           31 CLVVMATGSGKSLCYQ   46 (374)
Q Consensus        31 ~l~~a~tGsGKT~~~~   46 (374)
                      ++++|.+|||||..+-
T Consensus         5 i~l~GlpgsGKSTla~   20 (213)
T d1bifa1           5 IVMVGLPARGKTYISK   20 (213)
T ss_dssp             EEEECCTTSSHHHHHH
T ss_pred             EEEECCCCCCHHHHHH
Confidence            5789999999997653