Citrus Sinensis ID: 030396

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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-------18
Protein Sequence
MKKELVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQVF
Secondary Structure (PSIPRED)
ccHHHHHHHHHHcccccEEEccccHHHHHHHccccccccccEEEEEcccccccccccHHHHHHHHHHcccccccEEEEEccccHHHHHHHHHHccccEEEEEcccccccccEEEEEEEccccccHHHHHHHHHHccccccEEEEEccHHHHHHHHHHHHHccccEEEccccccccccc
Secondary Structure Prediction (SSPRO)
ccccHHHHHHHHHccccEEEEcccHHHHHHHcccccHccEEEEEEcHHHHHHcccccHHHHHHHHHccccccccEEEEEccccHHHHHHHHHHHcccEEEEEEccccccccEEEEEEEEccHHHHHHHHHHHHHcccccEEEEEEEccHcHHHHHHHHHHccccEEEEcccccHHHcc
Coil and Loop (DISEMBL)
mkkelvrstdlskfscdilisTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDpvvkacsnpsivRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFaeslnppvliFVQSKDRAKELYGelafddiragvihsdlsqtqvf
Flexible Loop (DISEMBL)
mkkelvrstdlskfscdilistplrlrlairrkkidlsrveyLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGrkntasesiKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQVF
Low Complexity Region (SEG)
MKKELVRSTDLSKFSCDILISTPlrlrlairrkkidlSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQVF
Disordered region (IsUnstruct)
**********LSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIH*********
Disordered Region (DISOPRED)
**********LSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLS*****
Disordered Region (DISEMBL)
**********LSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQVF
Disordered Region (DISPRO)
**KELVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSD*******
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MKKELVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQVF
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	178	2.2.26 [Sep-21-2011]
Q84TG1	541	DEAD-box ATP-dependent RN	yes	no	0.960	0.316	0.813	1e-74
Q5K5B6	540	DEAD-box ATP-dependent RN	yes	no	0.983	0.324	0.738	2e-69
A3GHW9	558	ATP-dependent RNA helicas	yes	no	0.893	0.284	0.521	7e-41
Q75AE1	569	ATP-dependent RNA helicas	yes	no	0.893	0.279	0.527	1e-40
Q6BP45	550	ATP-dependent RNA helicas	yes	no	0.893	0.289	0.503	1e-39
Q86IZ9	668	Probable ATP-dependent RN	yes	no	0.893	0.238	0.518	2e-39
A7TT88	570	ATP-dependent RNA helicas	N/A	no	0.955	0.298	0.470	2e-39
A5E1N2	553	ATP-dependent RNA helicas	N/A	no	0.943	0.303	0.502	3e-39
A5DIX5	537	ATP-dependent RNA helicas	N/A	no	0.893	0.296	0.503	4e-39
Q6FN65	565	ATP-dependent RNA helicas	yes	no	0.955	0.300	0.459	8e-39

>sp|Q84TG1|RH57_ARATH DEAD-box ATP-dependent RNA helicase 57 OS=Arabidopsis thaliana GN=RH57 PE=2 SV=1

 Score =  278 bits (711), Expect = 1e-74,   Method: Compositional matrix adjust.
 Identities = 140/172 (81%), Positives = 156/172 (90%), Gaps = 1/172 (0%)

Query: 1   MKKELVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKH 60
           M K LV++ D SK  CD+LISTP+RL+ AI+ KKIDLS+VEYLVLDE+DKLFE  +LLK 
Sbjct: 244 MTKPLVKTADFSKLWCDVLISTPMRLKRAIKAKKIDLSKVEYLVLDESDKLFE-QSLLKQ 302

Query: 61  IDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAG 120
           ID VVKACSNPSI+RSLFSATLPD VEELARSIMHDAVRVI+GRKNTASE++KQKLVFAG
Sbjct: 303 IDCVVKACSNPSIIRSLFSATLPDSVEELARSIMHDAVRVIIGRKNTASETVKQKLVFAG 362

Query: 121 SEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDL 172
           SEEGKLLALRQSFAESLNPPVLIFVQSK+RAKELY EL  ++IRAGVIHSDL
Sbjct: 363 SEEGKLLALRQSFAESLNPPVLIFVQSKERAKELYDELKCENIRAGVIHSDL 414

Arabidopsis thaliana (taxid: 3702)
EC: 3EC: .EC: 6EC: .EC: 4EC: .EC: 1EC: 3

>sp|Q5K5B6|RH57_ORYSJ DEAD-box ATP-dependent RNA helicase 57 OS=Oryza sativa subsp. japonica GN=Os07g0647900 PE=2 SV=2

 Score =  261 bits (666), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 130/176 (73%), Positives = 153/176 (86%), Gaps = 1/176 (0%)

Query: 1   MKKELVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKH 60
           M K+L +S +     CDILISTPLRL  A++++ +DLSRVEYLVLDE+DKLFE+G  ++ 
Sbjct: 249 MTKDLSKSGNFKDMHCDILISTPLRLDHAVQKRDLDLSRVEYLVLDESDKLFELG-FVEV 307

Query: 61  IDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAG 120
           ID VVKACSNPSI+RSLFSATLPD +E LAR+IMHDAVRVIVGRKN+AS  IKQKL+FAG
Sbjct: 308 IDSVVKACSNPSIIRSLFSATLPDSIETLARTIMHDAVRVIVGRKNSASSLIKQKLIFAG 367

Query: 121 SEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQ 176
           +E+GKLLALRQSFAESLNPPVLIFVQSK+RAKELY ELAFDD+RA VIH+DL + Q
Sbjct: 368 TEKGKLLALRQSFAESLNPPVLIFVQSKERAKELYKELAFDDVRADVIHADLDEEQ 423

Oryza sativa subsp. japonica (taxid: 39947)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|A3GHW9|ROK1_PICST ATP-dependent RNA helicase ROK1 OS=Scheffersomyces stipitis (strain ATCC 58785 / CBS 6054 / NBRC 10063 / NRRL Y-11545) GN=ROK1 PE=3 SV=1

 Score =  166 bits (420), Expect = 7e-41,   Method: Compositional matrix adjust.
 Identities = 84/161 (52%), Positives = 115/161 (71%), Gaps = 2/161 (1%)

Query: 17  DILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRS 76
           DI++STPLRL   ++ +K+DLS+VE LV+DEADKLF+ G  ++  D ++  C+   I +S
Sbjct: 247 DIIVSTPLRLIDIVKNEKVDLSKVEQLVIDEADKLFDQG-FVEQTDDILSHCTYTKIRKS 305

Query: 77  LFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAES 136
           +FSAT+P  VEE+A SIM D +RVI+GRK  AS +I QKLVF GSEEGKLLA+RQ   E 
Sbjct: 306 MFSATIPSGVEEMAHSIMRDPIRVIIGRKEAASNTIDQKLVFTGSEEGKLLAIRQMIQEG 365

Query: 137 -LNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQ 176
              PP++IF+QS  RAK L+ EL +D +   VIH++ +  Q
Sbjct: 366 EFKPPIIIFLQSIHRAKALFHELLYDKLNVDVIHAERTPKQ 406

ATP-dependent RNA helicase involved in 40S ribosomal subunit biogenesis. Required for the processing and cleavage of 35S pre-rRNA at sites A0, A1, and A2, leading to mature 18S rRNA.

Scheffersomyces stipitis (strain ATCC 58785 / CBS 6054 / NBRC 10063 / NRRL Y-11545) (taxid: 322104)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q75AE1|ROK1_ASHGO ATP-dependent RNA helicase ROK1 OS=Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056) GN=ROK1 PE=3 SV=1

 Score =  165 bits (418), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 85/161 (52%), Positives = 118/161 (73%), Gaps = 2/161 (1%)

Query: 17  DILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRS 76
           DI+ISTPLRL   ++ + +DLS V+YL+ DEADKLF+    ++  D ++ ACS+P+I + 
Sbjct: 253 DIIISTPLRLIDIVKSESLDLSAVKYLIFDEADKLFD-KTFVEQTDDILSACSHPNISKV 311

Query: 77  LFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAES 136
           LFSATLP  VEELA+SIM D VRVI+G K  A+ +I+QKLVF G+EEGKL+A+RQ   E 
Sbjct: 312 LFSATLPSSVEELAQSIMTDPVRVIIGHKEAANTNIEQKLVFCGNEEGKLVAIRQLIQEG 371

Query: 137 L-NPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQ 176
           +  PPV+IF++S  RAK L+ EL +D +   VIH++ +Q Q
Sbjct: 372 MFRPPVIIFLESITRAKALFHELLYDKLNVDVIHAERTQVQ 412

ATP-dependent RNA helicase involved in 40S ribosomal subunit biogenesis. Required for the processing and cleavage of 35S pre-rRNA at sites A0, A1, and A2, leading to mature 18S rRNA.

Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056) (taxid: 284811)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q6BP45|ROK1_DEBHA ATP-dependent RNA helicase ROK1 OS=Debaryomyces hansenii (strain ATCC 36239 / CBS 767 / JCM 1990 / NBRC 0083 / IGC 2968) GN=ROK1 PE=3 SV=2

 Score =  162 bits (409), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 81/161 (50%), Positives = 115/161 (71%), Gaps = 2/161 (1%)

Query: 17  DILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRS 76
           DIL+STPLRL  +I+ + I LS+VE LV+DE DKLF+ G  ++  D ++  C+N  + +S
Sbjct: 240 DILVSTPLRLIDSIKNETISLSKVEQLVIDETDKLFDQG-FVEQTDEILSNCTNTKLRKS 298

Query: 77  LFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAES 136
           +FSAT+P  VEE+A+SIM D +RVI+G K  AS +I+QKLVF G+EEGKLLA+RQ   + 
Sbjct: 299 MFSATIPSGVEEMAQSIMKDPIRVIIGHKEAASNTIEQKLVFTGNEEGKLLAIRQMIQQG 358

Query: 137 -LNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQ 176
              PP++IF+QS  RAK L+ EL +D +   VIH++ +  Q
Sbjct: 359 EFKPPIIIFLQSITRAKALFHELLYDRLNVDVIHAERTPKQ 399

ATP-dependent RNA helicase involved in 40S ribosomal subunit biogenesis. Required for the processing and cleavage of 35S pre-rRNA at sites A0, A1, and A2, leading to mature 18S rRNA.

Debaryomyces hansenii (strain ATCC 36239 / CBS 767 / JCM 1990 / NBRC 0083 / IGC 2968) (taxid: 284592)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q86IZ9|DDX52_DICDI Probable ATP-dependent RNA helicase ddx52 OS=Dictyostelium discoideum GN=ddx52 PE=3 SV=1

 Score =  162 bits (409), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 83/160 (51%), Positives = 112/160 (70%), Gaps = 1/160 (0%)

Query: 17  DILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRS 76
           DILI+TPLRL   I+   + L++VEYLV DEADKLF+  N  + +D VV AC NP +   
Sbjct: 320 DILITTPLRLVYLIKENLLSLNKVEYLVFDEADKLFD-KNFQEQVDIVVTACQNPKLKIC 378

Query: 77  LFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAES 136
           LFSAT+   VEEL  SIM + +++I+G +N A+ ++ QKL++ G EEGKLLA+RQ   + 
Sbjct: 379 LFSATMNQQVEELGHSIMKNPIKIIIGEQNAAAITVDQKLIYVGKEEGKLLAVRQLIQKG 438

Query: 137 LNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQ 176
           L PP+LIF QSK+RA +L+ EL FD I   VIHS+ +Q Q
Sbjct: 439 LEPPILIFTQSKERAHDLFQELIFDGINVDVIHSERTQFQ 478

ATP-binding RNA helicase which may be involved in the ribosome biogenesis.

Dictyostelium discoideum (taxid: 44689)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|A7TT88|ROK1_VANPO ATP-dependent RNA helicase ROK1 OS=Vanderwaltozyma polyspora (strain ATCC 22028 / DSM 70294) GN=ROK1 PE=3 SV=1

 Score =  161 bits (408), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 81/172 (47%), Positives = 123/172 (71%), Gaps = 2/172 (1%)

Query: 6   VRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVV 65
           +R+  +S    DI++STPLRL   ++ + +DLS+V++L+ DEADKLF+    ++  D ++
Sbjct: 249 LRNKVISDKKYDIIVSTPLRLIDVVKNEALDLSQVKHLIFDEADKLFD-KTFVEQSDDIL 307

Query: 66  KACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGK 125
            +CS+ S+ +S+FSAT+P  VEE+A+SIM D VRVI+G K  A+ SI+QKLVF G+EEGK
Sbjct: 308 SSCSHSSLRKSMFSATIPSNVEEIAKSIMMDPVRVIIGHKEAANTSIEQKLVFCGNEEGK 367

Query: 126 LLALRQSFAES-LNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQ 176
           L+A++Q   E    PPV+IF++S  RAK LY E+ +D +   VIH++ +Q Q
Sbjct: 368 LIAIKQLVQEGEFKPPVIIFLESITRAKALYHEMMYDSLNVDVIHAERTQVQ 419

ATP-dependent RNA helicase involved in 40S ribosomal subunit biogenesis. Required for the processing and cleavage of 35S pre-rRNA at sites A0, A1, and A2, leading to mature 18S rRNA.

Vanderwaltozyma polyspora (strain ATCC 22028 / DSM 70294) (taxid: 436907)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|A5E1N2|ROK1_LODEL ATP-dependent RNA helicase ROK1 OS=Lodderomyces elongisporus (strain ATCC 11503 / CBS 2605 / JCM 1781 / NBRC 1676 / NRRL YB-4239) GN=ROK1 PE=3 SV=1

 Score =  161 bits (407), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 86/171 (50%), Positives = 117/171 (68%), Gaps = 3/171 (1%)

Query: 8   STDLSKFS-CDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVK 66
           S D+ K S  DIL+STPLRL   ++  K+DLS+V  LV+DEADKLF+ G   +  D ++ 
Sbjct: 235 SNDVVKASKYDILVSTPLRLIDVVKLGKVDLSKVTQLVIDEADKLFDHG-FAEQTDELLS 293

Query: 67  ACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKL 126
            C+N  I +S+FSAT+P  VEE+A SIM D +RVI+G K  AS +I+QKLVF G+EEGKL
Sbjct: 294 HCTNVKIRKSMFSATIPSGVEEMAHSIMKDPIRVIIGHKEAASNTIEQKLVFTGNEEGKL 353

Query: 127 LALRQSFAES-LNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQ 176
           LA+RQ        PP++IF+QS  RAK L+ EL +D +   VIH++ +  Q
Sbjct: 354 LAIRQMIQNGEFKPPIIIFLQSITRAKALFHELVYDKLNVDVIHAERTPKQ 404

ATP-dependent RNA helicase involved in 40S ribosomal subunit biogenesis. Required for the processing and cleavage of 35S pre-rRNA at sites A0, A1, and A2, leading to mature 18S rRNA.

Lodderomyces elongisporus (strain ATCC 11503 / CBS 2605 / JCM 1781 / NBRC 1676 / NRRL YB-4239) (taxid: 379508)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|A5DIX5|ROK1_PICGU ATP-dependent RNA helicase ROK1 OS=Meyerozyma guilliermondii (strain ATCC 6260 / CBS 566 / DSM 6381 / JCM 1539 / NBRC 10279 / NRRL Y-324) GN=ROK1 PE=3 SV=2

 Score =  160 bits (405), Expect = 4e-39,   Method: Compositional matrix adjust.
 Identities = 81/161 (50%), Positives = 115/161 (71%), Gaps = 2/161 (1%)

Query: 17  DILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRS 76
           D+LI TPLRL   ++++++DLS+VE+LV+DEADKLF+ G  ++  D ++  C+ P+   S
Sbjct: 231 DVLICTPLRLIDLVKKEQVDLSKVEHLVIDEADKLFDHG-FVEQTDEILSHCTLPTRRTS 289

Query: 77  LFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAES 136
           +FSAT+P  VEE+A SIM D +R+IVG K  AS SI QKLVF G+EEGKLLA+RQ   + 
Sbjct: 290 MFSATIPSGVEEMANSIMKDQIRIIVGHKEGASTSIDQKLVFTGNEEGKLLAIRQMVQQG 349

Query: 137 -LNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQ 176
              PP++IF+QS  RAK L+ EL +D +   VIH++ +  Q
Sbjct: 350 EFKPPIIIFLQSIPRAKALFHELIYDKLNVEVIHAERTPKQ 390

ATP-dependent RNA helicase involved in 40S ribosomal subunit biogenesis. Required for the processing and cleavage of 35S pre-rRNA at sites A0, A1, and A2, leading to mature 18S rRNA.

Meyerozyma guilliermondii (strain ATCC 6260 / CBS 566 / DSM 6381 / JCM 1539 / NBRC 10279 / NRRL Y-324) (taxid: 294746)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q6FN65|ROK1_CANGA ATP-dependent RNA helicase ROK1 OS=Candida glabrata (strain ATCC 2001 / CBS 138 / JCM 3761 / NBRC 0622 / NRRL Y-65) GN=ROK1 PE=3 SV=1

 Score =  159 bits (402), Expect = 8e-39,   Method: Compositional matrix adjust.
 Identities = 79/172 (45%), Positives = 121/172 (70%), Gaps = 2/172 (1%)

Query: 6   VRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVV 65
           +R+  +S    D++ISTPLRL   ++ + +DLS V++L+ DEADKLF+    ++  D ++
Sbjct: 242 LRNKVISDKKYDLIISTPLRLIDVVKNEALDLSNVKHLIFDEADKLFD-KTFIEQTDDIL 300

Query: 66  KACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGK 125
            +C++PS+ +S+FSAT+P  VEE A SIM+D VRVI+G K  A+ +I+QKL+F G+EEGK
Sbjct: 301 NSCTDPSMRKSMFSATIPSSVEETANSIMNDPVRVIIGHKEAANTNIEQKLIFCGNEEGK 360

Query: 126 LLALRQSFAES-LNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQ 176
           L+A+RQ   +    PP++IF++S  RAK LY EL +D I   VIH++ +  Q
Sbjct: 361 LIAIRQLVQQGEFKPPIIIFLESIARAKALYHELMYDRINVDVIHAERTAIQ 412

ATP-dependent RNA helicase involved in 40S ribosomal subunit biogenesis. Required for the processing and cleavage of 35S pre-rRNA at sites A0, A1, and A2, leading to mature 18S rRNA.

Candida glabrata (strain ATCC 2001 / CBS 138 / JCM 3761 / NBRC 0622 / NRRL Y-65) (taxid: 284593)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

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	178
449440077	616	PREDICTED: DEAD-box ATP-dependent RNA he	0.960	0.277	0.866	1e-79
449516225	441	PREDICTED: DEAD-box ATP-dependent RNA he	0.971	0.392	0.856	1e-79
225439904	524	PREDICTED: DEAD-box ATP-dependent RNA he	0.983	0.333	0.835	3e-78
297741568	523	unnamed protein product [Vitis vinifera]	0.983	0.334	0.835	4e-78
147784525	554	hypothetical protein VITISV_032421 [Viti	0.983	0.315	0.829	5e-78
255559765	535	dead box ATP-dependent RNA helicase, put	0.983	0.327	0.812	6e-76
356572415	536	PREDICTED: DEAD-box ATP-dependent RNA he	0.983	0.326	0.801	3e-75
357510607	619	DEAD-box ATP-dependent RNA helicase [Med	0.983	0.282	0.784	3e-74
356505198	537	PREDICTED: DEAD-box ATP-dependent RNA he	0.983	0.325	0.795	7e-74
22330935	541	DEAD-box ATP-dependent RNA helicase 57 [	0.960	0.316	0.813	6e-73

>gi|449440077|ref|XP_004137811.1| PREDICTED: DEAD-box ATP-dependent RNA helicase 57-like [Cucumis sativus]

 Score =  300 bits (769), Expect = 1e-79,   Method: Compositional matrix adjust.
 Identities = 149/172 (86%), Positives = 164/172 (95%), Gaps = 1/172 (0%)

Query: 3   KELVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHID 62
           KE++R  D SKFSCD+LISTPLRLRLAIR+KKIDLSRVEYLVLDE+DKLFE+G L+K ID
Sbjct: 243 KEVLRHADFSKFSCDVLISTPLRLRLAIRKKKIDLSRVEYLVLDESDKLFELG-LIKQID 301

Query: 63  PVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSE 122
            VVKACSNPSIVRSLFSATLPDFVE+LARS+MHDAVRVIVGRKNTASE++KQKLVFAGSE
Sbjct: 302 AVVKACSNPSIVRSLFSATLPDFVEDLARSVMHDAVRVIVGRKNTASETVKQKLVFAGSE 361

Query: 123 EGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQ 174
           EGKLLALRQSF+ESLNPPVLIFVQSK+RAKELYGELAF++IR  VIHSDLSQ
Sbjct: 362 EGKLLALRQSFSESLNPPVLIFVQSKERAKELYGELAFENIRVSVIHSDLSQ 413

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449516225|ref|XP_004165148.1| PREDICTED: DEAD-box ATP-dependent RNA helicase 57-like, partial [Cucumis sativus]

 Score =  300 bits (769), Expect = 1e-79,   Method: Compositional matrix adjust.
 Identities = 149/174 (85%), Positives = 165/174 (94%), Gaps = 1/174 (0%)

Query: 3   KELVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHID 62
           KE++R  D SKFSCD+LISTPLRLRLAIR+KKIDLSRVEYLVLDE+DKLFE+G L+K ID
Sbjct: 269 KEVLRHADFSKFSCDVLISTPLRLRLAIRKKKIDLSRVEYLVLDESDKLFELG-LIKQID 327

Query: 63  PVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSE 122
            VVKACSNPSIVRSLFSATLPDFVE+LARS+MHDAVRVIVGRKNTASE++KQKLVFAGSE
Sbjct: 328 AVVKACSNPSIVRSLFSATLPDFVEDLARSVMHDAVRVIVGRKNTASETVKQKLVFAGSE 387

Query: 123 EGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQ 176
           EGKLLALRQSF+ESLNPPVLIFVQSK+RAKELYGELAF++IR  VIHSDLSQ +
Sbjct: 388 EGKLLALRQSFSESLNPPVLIFVQSKERAKELYGELAFENIRVSVIHSDLSQLE 441

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225439904|ref|XP_002279705.1| PREDICTED: DEAD-box ATP-dependent RNA helicase 57 [Vitis vinifera]

 Score =  296 bits (757), Expect = 3e-78,   Method: Compositional matrix adjust.
 Identities = 147/176 (83%), Positives = 164/176 (93%), Gaps = 1/176 (0%)

Query: 1   MKKELVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKH 60
           + KEL+RS D+SK  CDILISTPLRLR AIR+KK+DLSRVEYLVLDE+DKLFE+G L+K 
Sbjct: 231 LTKELLRSGDISKLPCDILISTPLRLRSAIRKKKLDLSRVEYLVLDESDKLFELG-LVKQ 289

Query: 61  IDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAG 120
           ID VVKACSNPSI+RSLFSATLPDFVEELAR+IMHDAVRVI+GRKN+ASE IKQKLVFAG
Sbjct: 290 IDAVVKACSNPSIIRSLFSATLPDFVEELARTIMHDAVRVIIGRKNSASELIKQKLVFAG 349

Query: 121 SEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQ 176
           SEEGKLLALRQSFAESLNPP+L+FVQSK+RAKELY ELAFDDIR  VIH+DLSQ+Q
Sbjct: 350 SEEGKLLALRQSFAESLNPPILLFVQSKERAKELYTELAFDDIRVDVIHADLSQSQ 405

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297741568|emb|CBI32700.3| unnamed protein product [Vitis vinifera]

 Score =  295 bits (756), Expect = 4e-78,   Method: Compositional matrix adjust.
 Identities = 147/176 (83%), Positives = 164/176 (93%), Gaps = 1/176 (0%)

Query: 1   MKKELVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKH 60
           + KEL+RS D+SK  CDILISTPLRLR AIR+KK+DLSRVEYLVLDE+DKLFE+G L+K 
Sbjct: 230 LTKELLRSGDISKLPCDILISTPLRLRSAIRKKKLDLSRVEYLVLDESDKLFELG-LVKQ 288

Query: 61  IDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAG 120
           ID VVKACSNPSI+RSLFSATLPDFVEELAR+IMHDAVRVI+GRKN+ASE IKQKLVFAG
Sbjct: 289 IDAVVKACSNPSIIRSLFSATLPDFVEELARTIMHDAVRVIIGRKNSASELIKQKLVFAG 348

Query: 121 SEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQ 176
           SEEGKLLALRQSFAESLNPP+L+FVQSK+RAKELY ELAFDDIR  VIH+DLSQ+Q
Sbjct: 349 SEEGKLLALRQSFAESLNPPILLFVQSKERAKELYTELAFDDIRVDVIHADLSQSQ 404

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147784525|emb|CAN61726.1| hypothetical protein VITISV_032421 [Vitis vinifera]

 Score =  295 bits (755), Expect = 5e-78,   Method: Compositional matrix adjust.
 Identities = 146/176 (82%), Positives = 164/176 (93%), Gaps = 1/176 (0%)

Query: 1   MKKELVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKH 60
           + KEL+RS D+SK  CDILISTPLRLR AIR+KK+DLSRVEYLVLDE+DKLFE+G L+K 
Sbjct: 227 LTKELLRSGDISKLPCDILISTPLRLRSAIRKKKLDLSRVEYLVLDESDKLFELG-LVKQ 285

Query: 61  IDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAG 120
           ID VVKACSNPSI+RSLFSATLPDFVEELAR+IMHDAVRVI+GRKN+ASE IKQKLVFAG
Sbjct: 286 IDAVVKACSNPSIIRSLFSATLPDFVEELARTIMHDAVRVIIGRKNSASELIKQKLVFAG 345

Query: 121 SEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQ 176
           +EEGKLLALRQSFAESLNPP+L+FVQSK+RAKELY ELAFDDIR  VIH+DLSQ+Q
Sbjct: 346 NEEGKLLALRQSFAESLNPPILLFVQSKERAKELYTELAFDDIRVDVIHADLSQSQ 401

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255559765|ref|XP_002520902.1| dead box ATP-dependent RNA helicase, putative [Ricinus communis] gi|223540033|gb|EEF41611.1| dead box ATP-dependent RNA helicase, putative [Ricinus communis]

 Score =  288 bits (737), Expect = 6e-76,   Method: Compositional matrix adjust.
 Identities = 143/176 (81%), Positives = 159/176 (90%), Gaps = 1/176 (0%)

Query: 1   MKKELVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKH 60
           M KELVR+ DLS+  CDIL+STPLRL+LAIR+KK+DLSRVEYLVLDE+DKLFE+G LLK 
Sbjct: 242 MTKELVRTKDLSRLPCDILVSTPLRLQLAIRKKKVDLSRVEYLVLDESDKLFELG-LLKQ 300

Query: 61  IDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAG 120
           ID V KACSNPS++RSLFSATLP+ VEELAR+IMHDAVRVIVGRKN ASE+IKQKLVF G
Sbjct: 301 IDSVFKACSNPSVIRSLFSATLPESVEELARTIMHDAVRVIVGRKNAASETIKQKLVFTG 360

Query: 121 SEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQ 176
           SEEGKL+ALRQSFAESLNPPVLIFVQ+K+RA ELY EL FD IR GVIHSDL QTQ
Sbjct: 361 SEEGKLIALRQSFAESLNPPVLIFVQNKERANELYEELKFDSIRVGVIHSDLLQTQ 416

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356572415|ref|XP_003554364.1| PREDICTED: DEAD-box ATP-dependent RNA helicase 57-like [Glycine max]

 Score =  286 bits (731), Expect = 3e-75,   Method: Compositional matrix adjust.
 Identities = 141/176 (80%), Positives = 157/176 (89%), Gaps = 1/176 (0%)

Query: 1   MKKELVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKH 60
           M K L+R+ D SKF CD+LISTPLRLRLAI+RKKIDLSRVEYLVLDE+DKLFE   L K 
Sbjct: 246 MTKNLLRNADFSKFPCDVLISTPLRLRLAIKRKKIDLSRVEYLVLDESDKLFE-PELFKQ 304

Query: 61  IDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAG 120
           ID V+KACSNPSI+RSLFSATLPDFVE+ AR +MHDAVRVIVGRKN ASE+IKQKLVF G
Sbjct: 305 IDSVIKACSNPSIIRSLFSATLPDFVEDQARELMHDAVRVIVGRKNMASETIKQKLVFTG 364

Query: 121 SEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQ 176
           SEEGKLLA+RQSFAESLNPPVL+F+QSK+RAKELY ELAFD+IR  VIHSDLSQ +
Sbjct: 365 SEEGKLLAIRQSFAESLNPPVLVFLQSKERAKELYSELAFDNIRVDVIHSDLSQAE 420

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357510607|ref|XP_003625592.1| DEAD-box ATP-dependent RNA helicase [Medicago truncatula] gi|355500607|gb|AES81810.1| DEAD-box ATP-dependent RNA helicase [Medicago truncatula]

 Score =  282 bits (722), Expect = 3e-74,   Method: Compositional matrix adjust.
 Identities = 138/176 (78%), Positives = 158/176 (89%), Gaps = 1/176 (0%)

Query: 1   MKKELVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKH 60
           M K L+R+ D SKFSCDILISTPLRL LAI++KK+DLSRVEYLVLDE+DKLFE   L K 
Sbjct: 236 MTKNLLRNADFSKFSCDILISTPLRLCLAIKKKKVDLSRVEYLVLDESDKLFE-PQLFKQ 294

Query: 61  IDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAG 120
           ID ++KAC+NPSI+RSLFSATLPDFVE+ AR +MHDAVRVIVGRKN AS++IKQKLVF G
Sbjct: 295 IDSIIKACTNPSIIRSLFSATLPDFVEDRARELMHDAVRVIVGRKNMASDTIKQKLVFTG 354

Query: 121 SEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQ 176
           SEEGKLLA+RQSFAESLNPPVL+F+QSK+RAKELYGELAFD+IR  VIHSDLSQ +
Sbjct: 355 SEEGKLLAIRQSFAESLNPPVLVFLQSKERAKELYGELAFDNIRVDVIHSDLSQEE 410

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356505198|ref|XP_003521379.1| PREDICTED: DEAD-box ATP-dependent RNA helicase 57-like [Glycine max]

 Score =  281 bits (719), Expect = 7e-74,   Method: Compositional matrix adjust.
 Identities = 140/176 (79%), Positives = 155/176 (88%), Gaps = 1/176 (0%)

Query: 1   MKKELVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKH 60
           M K L+R+ D SKF CD+LISTPLRLRLAI+RKKIDLSRVEYLVLDE+DKLFE   L K 
Sbjct: 247 MTKNLLRNADFSKFPCDVLISTPLRLRLAIKRKKIDLSRVEYLVLDESDKLFE-PELFKQ 305

Query: 61  IDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAG 120
           ID V+KACSNPSI+RSLFSATLPDFVE+ AR +MHDAVRVIVGRKN ASE+IKQKLVF G
Sbjct: 306 IDSVIKACSNPSIIRSLFSATLPDFVEDRARELMHDAVRVIVGRKNMASETIKQKLVFTG 365

Query: 121 SEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQ 176
           SEEGKLLA+RQSFAESLNPPVL+F+QSK+RAKEL  ELAFD IR  VIHSDLSQ +
Sbjct: 366 SEEGKLLAIRQSFAESLNPPVLVFLQSKERAKELCSELAFDSIRVDVIHSDLSQAE 421

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|22330935|ref|NP_187583.2| DEAD-box ATP-dependent RNA helicase 57 [Arabidopsis thaliana] gi|75328099|sp|Q84TG1.1|RH57_ARATH RecName: Full=DEAD-box ATP-dependent RNA helicase 57 gi|29028778|gb|AAO64768.1| At3g09720 [Arabidopsis thaliana] gi|110742885|dbj|BAE99340.1| RNA helicase like protein [Arabidopsis thaliana] gi|332641282|gb|AEE74803.1| DEAD-box ATP-dependent RNA helicase 57 [Arabidopsis thaliana]

 Score =  278 bits (711), Expect = 6e-73,   Method: Compositional matrix adjust.
 Identities = 140/172 (81%), Positives = 156/172 (90%), Gaps = 1/172 (0%)

Query: 1   MKKELVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKH 60
           M K LV++ D SK  CD+LISTP+RL+ AI+ KKIDLS+VEYLVLDE+DKLFE  +LLK 
Sbjct: 244 MTKPLVKTADFSKLWCDVLISTPMRLKRAIKAKKIDLSKVEYLVLDESDKLFE-QSLLKQ 302

Query: 61  IDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAG 120
           ID VVKACSNPSI+RSLFSATLPD VEELARSIMHDAVRVI+GRKNTASE++KQKLVFAG
Sbjct: 303 IDCVVKACSNPSIIRSLFSATLPDSVEELARSIMHDAVRVIIGRKNTASETVKQKLVFAG 362

Query: 121 SEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDL 172
           SEEGKLLALRQSFAESLNPPVLIFVQSK+RAKELY EL  ++IRAGVIHSDL
Sbjct: 363 SEEGKLLALRQSFAESLNPPVLIFVQSKERAKELYDELKCENIRAGVIHSDL 414

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	178
TAIR|locus:2075034	541	AT3G09720 [Arabidopsis thalian	0.960	0.316	0.761	2.1e-61
DICTYBASE|DDB_G0274325	668	ddx52 "DEAD/DEAH box helicase"	0.893	0.238	0.487	1.8e-34
SGD|S000003139	564	ROK1 "RNA-dependent ATPase" [S	0.893	0.281	0.459	5.4e-33
POMBASE|SPAC22F3.08c	481	rok1 "ATP-dependent RNA helica	0.887	0.328	0.447	4.2e-31
FB|FBgn0036754	594	CG5589 [Drosophila melanogaste	0.898	0.269	0.439	1.6e-28
ZFIN|ZDB-GENE-060623-1	606	ddx52 "DEAD (Asp-Glu-Ala-Asp)	0.898	0.264	0.426	3.6e-28
RGD|621743	598	Ddx52 "DEAD (Asp-Glu-Ala-Asp)	0.898	0.267	0.408	7.1e-27
UNIPROTKB|A5D7C1	596	DDX52 "Probable ATP-dependent	0.898	0.268	0.414	9.1e-27
UNIPROTKB|I3LJA0	507	DDX52 "Uncharacterized protein	0.898	0.315	0.402	9.8e-27
MGI|MGI:1925644	598	Ddx52 "DEAD (Asp-Glu-Ala-Asp)	0.898	0.267	0.402	1.2e-26

TAIR|locus:2075034 AT3G09720 [Arabidopsis thaliana (taxid:3702)]

 Score = 628 (226.1 bits), Expect = 2.1e-61, P = 2.1e-61
 Identities = 131/172 (76%), Positives = 144/172 (83%)

Query:     1 MKKELVRSTDLSKFSCDILISTPXXXXXXXXXXXXXXSRVEYLVLDEADKLFEVGNLLKH 60
             M K LV++ D SK  CD+LISTP              S+VEYLVLDE+DKLFE  +LLK 
Sbjct:   244 MTKPLVKTADFSKLWCDVLISTPMRLKRAIKAKKIDLSKVEYLVLDESDKLFEQ-SLLKQ 302

Query:    61 IDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAG 120
             ID VVKACSNPSI+RSLFSATLPD VEELARSIMHDAVRVI+GRKNTASE++KQKLVFAG
Sbjct:   303 IDCVVKACSNPSIIRSLFSATLPDSVEELARSIMHDAVRVIIGRKNTASETVKQKLVFAG 362

Query:   121 SEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDL 172
             SEEGKLLALRQSFAESLNPPVLIFVQSK+RAKELY EL  ++IRAGVIHSDL
Sbjct:   363 SEEGKLLALRQSFAESLNPPVLIFVQSKERAKELYDELKCENIRAGVIHSDL 414

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

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

GO:0009220 "pyrimidine ribonucleotide biosynthetic process" evidence=RCA

DICTYBASE|DDB_G0274325 ddx52 "DEAD/DEAH box helicase" [Dictyostelium discoideum (taxid:44689)]

 Score = 380 (138.8 bits), Expect = 1.8e-34, P = 1.8e-34
 Identities = 78/160 (48%), Positives = 105/160 (65%)

Query:    17 DILISTPXXXXXXXXXXXXXXSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRS 76
             DILI+TP              ++VEYLV DEADKLF+  N  + +D VV AC NP +   
Sbjct:   320 DILITTPLRLVYLIKENLLSLNKVEYLVFDEADKLFDK-NFQEQVDIVVTACQNPKLKIC 378

Query:    77 LFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAES 136
             LFSAT+   VEEL  SIM + +++I+G +N A+ ++ QKL++ G EEGKLLA+RQ   + 
Sbjct:   379 LFSATMNQQVEELGHSIMKNPIKIIIGEQNAAAITVDQKLIYVGKEEGKLLAVRQLIQKG 438

Query:   137 LNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQ 176
             L PP+LIF QSK+RA +L+ EL FD I   VIHS+ +Q Q
Sbjct:   439 LEPPILIFTQSKERAHDLFQELIFDGINVDVIHSERTQFQ 478

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

GO:0005524 "ATP binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0008150 "biological_process" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0016887 "ATPase activity" evidence=ISS

GO:0006200 "ATP catabolic process" evidence=ISS

GO:0042254 "ribosome biogenesis" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

GO:0006364 "rRNA processing" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

SGD|S000003139 ROK1 "RNA-dependent ATPase" [Saccharomyces cerevisiae (taxid:4932)]

 Score = 363 (132.8 bits), Expect = 5.4e-33, P = 5.4e-33
 Identities = 74/161 (45%), Positives = 107/161 (66%)

Query:    17 DILISTPXXXXXXXXXXXXXXSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRS 76
             DI+ISTP              S+V++L+ DEADKLF+    ++  D ++ AC  PS+ ++
Sbjct:   251 DIIISTPLRLIDVVKNEALDLSKVKHLIFDEADKLFDK-TFVEQSDDILSACREPSLRKA 309

Query:    77 LFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAES 136
             +FSAT+P  VEE+A+SIM D VRVI+G K  A+ +I+QKL+F G+EEGKL+A+RQ   E 
Sbjct:   310 MFSATIPSNVEEIAQSIMMDPVRVIIGHKEAANTNIEQKLIFCGNEEGKLIAIRQLVQEG 369

Query:   137 -LNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQ 176
                PP++IF++S  RAK LY EL +D I   VIH++ +  Q
Sbjct:   370 EFKPPIIIFLESITRAKALYHELMYDRINVDVIHAERTALQ 410

GO:0000447 "endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)" evidence=IMP

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

GO:0000480 "endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)" evidence=IMP

GO:0005730 "nucleolus" evidence=IEA;IDA

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

GO:0030686 "90S preribosome" evidence=IDA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0006364 "rRNA processing" evidence=IEA

GO:0042254 "ribosome biogenesis" evidence=IEA

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

GO:0048254 "snoRNA localization" evidence=IMP

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000472 "endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)" evidence=IMP

POMBASE|SPAC22F3.08c rok1 "ATP-dependent RNA helicase Rok1 (predicted)" [Schizosaccharomyces pombe (taxid:4896)]

 Score = 342 (125.4 bits), Expect = 4.2e-31, P = 4.2e-31
 Identities = 72/161 (44%), Positives = 104/161 (64%)

Query:    17 DILISTPXXXXXXXXXXXXXXSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRS 76
             D+ I TP               +VE+ V+DEAD+LFE G  ++  D ++ AC++ +I +S
Sbjct:   168 DMCIGTPMRLVQAIQTGLSF-EKVEFFVMDEADRLFEPG-FIEQTDHILSACTSSNICKS 225

Query:    77 LFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAES 136
             LFSAT+P  VEELA+ +  D +R+IVG K+ A++SI Q+L+F GS+  K++ LRQ  +  
Sbjct:   226 LFSATIPSRVEELAKVVTVDPIRIIVGLKDAATDSIDQRLLFVGSDTSKIVILRQMISNG 285

Query:   137 -LNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQ 176
              L P V+IFVQ  +RAK LY EL FD+I  GVIH +L Q +
Sbjct:   286 ELKPRVVIFVQDIERAKALYTELLFDEIHVGVIHGELPQAK 326

GO:0003723 "RNA binding" evidence=IEA

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

GO:0005524 "ATP binding" evidence=IC

GO:0005730 "nucleolus" evidence=ISO

GO:0005829 "cytosol" evidence=IDA

GO:0006364 "rRNA processing" evidence=ISO

FB|FBgn0036754 CG5589 [Drosophila melanogaster (taxid:7227)]

 Score = 324 (119.1 bits), Expect = 1.6e-28, P = 1.6e-28
 Identities = 72/164 (43%), Positives = 103/164 (62%)

Query:    17 DILISTPXXXXXXXXXX--XXXXSRVEYLVLDEADKLFEVG--NLLKHIDPVVKACSNPS 72
             DIL+STP                S VE+ VLDEAD+L E G  N  + +D +  ACSNP+
Sbjct:   241 DILVSTPNRVRFLLQQEPPLLDLSHVEWFVLDEADRLMEEGQNNFKEQLDDIYAACSNPT 300

Query:    73 IVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQS 132
                + FSAT    V + A   + + VR+ +G +N+A+E+++Q+L+F GSE GKL+A+R  
Sbjct:   301 KCVAFFSATYTVPVAKWALRHLKNLVRITIGVQNSATETVQQELLFVGSEGGKLVAIRDL 360

Query:   133 FAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQ 176
               + L PPVL+FVQSK+RAK+L+ EL +D I   VIH++ SQ Q
Sbjct:   361 VRQGLQPPVLVFVQSKERAKQLFEELLYDGINVDVIHAERSQHQ 404

GO:0003729 "mRNA binding" evidence=ISS

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

GO:0005524 "ATP binding" evidence=IEA

ZFIN|ZDB-GENE-060623-1 ddx52 "DEAD (Asp-Glu-Ala-Asp) box polypeptide 52" [Danio rerio (taxid:7955)]

 Score = 321 (118.1 bits), Expect = 3.6e-28, P = 3.6e-28
 Identities = 70/164 (42%), Positives = 102/164 (62%)

Query:    17 DILISTPXXXXXXXXXX--XXXXSRVEYLVLDEADKLFEVGN--LLKHIDPVVKACSNPS 72
             DIL++TP                S VE+LV+DE+DKLFE G     + +  +  ACS+P+
Sbjct:   289 DILVTTPNRLIYLLNQDPPAINLSSVEWLVVDESDKLFEDGKTGFREQLATIFLACSSPN 348

Query:    73 IVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQS 132
             + R LFSAT    VE   +  + + V V +G +N+A+E+++Q+L+F GSE GK+LA+R  
Sbjct:   349 VRRVLFSATFATDVERWCKLNLDNLVSVSIGARNSAAETVEQQLLFVGSENGKILAMRNL 408

Query:   133 FAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQ 176
               +   PPVL+FVQS DRA+ELY EL ++ I   VIH+D +Q Q
Sbjct:   409 IKQGFLPPVLVFVQSIDRARELYHELVYEGINVDVIHADRTQQQ 452

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

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

GO:0016787 "hydrolase activity" evidence=IEA

RGD|621743 Ddx52 "DEAD (Asp-Glu-Ala-Asp) box polypeptide 52" [Rattus norvegicus (taxid:10116)]

 Score = 309 (113.8 bits), Expect = 7.1e-27, P = 7.1e-27
 Identities = 67/164 (40%), Positives = 103/164 (62%)

Query:    17 DILISTPXXXXXXXXXX--XXXXSRVEYLVLDEADKLFEVGN--LLKHIDPVVKACSNPS 72
             DIL++TP                + VE+LV+DE+DKLFE G       +  +  AC++P 
Sbjct:   288 DILVTTPNRLIYLLKQEPPGIDLTSVEWLVVDESDKLFEDGKTGFRDQLASIFLACTSPK 347

Query:    73 IVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQS 132
             + R++FSAT    VE+  +  + + V V +G +N+A E+++Q+L+F GSE GKLLA+R+ 
Sbjct:   348 VRRAMFSATFAYDVEQWCKLNLDNIVSVSIGARNSAVETVEQELLFVGSETGKLLAMREL 407

Query:   133 FAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQ 176
               +  NPPVL+FVQS +RAKEL+ EL ++ I   VIH++ +Q Q
Sbjct:   408 VKKGFNPPVLVFVQSIERAKELFHELIYEGINVDVIHAERTQQQ 451

GO:0003723 "RNA binding" evidence=IEA

GO:0003724 "RNA helicase activity" evidence=NAS

GO:0005524 "ATP binding" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

GO:0005730 "nucleolus" evidence=IEA

GO:0006364 "rRNA processing" evidence=TAS

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

UNIPROTKB|A5D7C1 DDX52 "Probable ATP-dependent RNA helicase DDX52" [Bos taurus (taxid:9913)]

 Score = 308 (113.5 bits), Expect = 9.1e-27, P = 9.1e-27
 Identities = 68/164 (41%), Positives = 101/164 (61%)

Query:    17 DILISTPXXXXXXXXXX--XXXXSRVEYLVLDEADKLFEVGN--LLKHIDPVVKACSNPS 72
             DIL++TP                + VE+LV+DE+DKLFE G       +  +  AC++  
Sbjct:   285 DILVTTPNRLIYLLKQDPPGIDLTSVEWLVVDESDKLFEDGKTGFRDQLASIFLACTSHK 344

Query:    73 IVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQS 132
             + R++FSAT    VE+  R  +   + V VG +N+A E+++Q+L+F GSE GKLLA+R+ 
Sbjct:   345 VKRAMFSATFAYDVEQWCRLNLDSVITVSVGARNSAVETVEQELLFVGSETGKLLAMREL 404

Query:   133 FAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQ 176
               +  NPPVL+FVQS +RAKEL+ EL ++ I   VIH+D +Q Q
Sbjct:   405 VKKGFNPPVLVFVQSIERAKELFHELIYEGINVDVIHADRTQQQ 448

GO:0005730 "nucleolus" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

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

UNIPROTKB|I3LJA0 DDX52 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 305 (112.4 bits), Expect = 9.8e-27, P = 9.8e-27
 Identities = 66/164 (40%), Positives = 102/164 (62%)

Query:    17 DILISTPXXXXXXXXXX--XXXXSRVEYLVLDEADKLFEVGN--LLKHIDPVVKACSNPS 72
             DIL++TP                + VE+LV+DE+DKLFE G       +  +  AC++  
Sbjct:   195 DILVTTPNRLIYLLKQDPPGIDLTSVEWLVVDESDKLFEDGKTGFRDQLASIFLACTSHK 254

Query:    73 IVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQS 132
             + R++FSAT    VE+  +  + + + V +G +N+A E+++Q+L+F GSE GKLLA+R+ 
Sbjct:   255 VKRAMFSATFAYDVEQWCKLNLDNVITVSIGARNSAVETVEQELLFVGSETGKLLAMREL 314

Query:   133 FAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQ 176
               +  NPPVL+FVQS +RAKEL+ EL ++ I   VIH+D +Q Q
Sbjct:   315 VKKGFNPPVLVFVQSIERAKELFHELIYEGINVDVIHADRTQQQ 358

GO:0005524 "ATP binding" evidence=IEA

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

GO:0003676 "nucleic acid binding" evidence=IEA

MGI|MGI:1925644 Ddx52 "DEAD (Asp-Glu-Ala-Asp) box polypeptide 52" [Mus musculus (taxid:10090)]

 Score = 307 (113.1 bits), Expect = 1.2e-26, P = 1.2e-26
 Identities = 66/164 (40%), Positives = 103/164 (62%)

Query:    17 DILISTPXXXXXXXXXX--XXXXSRVEYLVLDEADKLFEVGN--LLKHIDPVVKACSNPS 72
             DIL++TP                + VE+LV+DE+DKLFE G     + +  +  AC++P 
Sbjct:   288 DILVTTPNRLIYLLKQDPPGIDLTNVEWLVVDESDKLFEDGKTGFREQLASIFLACTSPK 347

Query:    73 IVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQS 132
             + R++FSAT    VE+  +  + + V V +G +N+A E+++Q+L+F GSE GKLLA+R+ 
Sbjct:   348 VRRAMFSATFAYDVEQWCKLNLDNVVSVSIGARNSAVETVEQELLFVGSETGKLLAMREL 407

Query:   133 FAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQ 176
               +   PPVL+FVQS +RAKEL+ EL ++ I   VIH++ +Q Q
Sbjct:   408 VKKGFKPPVLVFVQSIERAKELFHELIYEGINVDVIHAERTQQQ 451

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

GO:0005634 "nucleus" evidence=IEA

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

GO:0008150 "biological_process" evidence=ND

GO:0016787 "hydrolase activity" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q5K5B6	RH57_ORYSJ	3, ., 6, ., 4, ., 1, 3	0.7386	0.9831	0.3240	yes	no
Q84TG1	RH57_ARATH	3, ., 6, ., 4, ., 1, 3	0.8139	0.9606	0.3160	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
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	178
COG0513	513	COG0513, SrmB, Superfamily II DNA and RNA helicase	5e-37
PRK10590	456	PRK10590, PRK10590, ATP-dependent RNA helicase Rhl	1e-20
cd00268	203	cd00268, DEADc, DEAD-box helicases	5e-20
PRK01297	475	PRK01297, PRK01297, ATP-dependent RNA helicase Rhl	2e-17
PRK11776	460	PRK11776, PRK11776, ATP-dependent RNA helicase Dbp	4e-17
PRK04837	423	PRK04837, PRK04837, ATP-dependent RNA helicase Rhl	3e-16
PTZ00110	545	PTZ00110, PTZ00110, helicase; Provisional	5e-15
smart00487	201	smart00487, DEXDc, DEAD-like helicases superfamily	7e-14
PLN00206	518	PLN00206, PLN00206, DEAD-box ATP-dependent RNA hel	2e-11
pfam00270	169	pfam00270, DEAD, DEAD/DEAH box helicase	2e-11
PTZ00424	401	PTZ00424, PTZ00424, helicase 45; Provisional	3e-10
PRK04537	572	PRK04537, PRK04537, ATP-dependent RNA helicase Rhl	4e-10
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	8e-10
cd00046	144	cd00046, DEXDc, DEAD-like helicases superfamily	2e-07
PRK11634	629	PRK11634, PRK11634, ATP-dependent RNA helicase Dea	3e-06
cd00079	131	cd00079, HELICc, Helicase superfamily c-terminal d	6e-05
pfam06862	436	pfam06862, DUF1253, Protein of unknown function (D	0.002
COG0514	590	COG0514, RecQ, Superfamily II DNA helicase [DNA re	0.003

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

 Score =  132 bits (335), Expect = 5e-37
 Identities = 60/163 (36%), Positives = 91/163 (55%), Gaps = 4/163 (2%)

Query: 16  CDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVR 75
            DI+++TP RL   I+R K+DLS VE LVLDEAD++ ++G  +  I+ ++KA   P    
Sbjct: 151 VDIVVATPGRLLDLIKRGKLDLSGVETLVLDEADRMLDMG-FIDDIEKILKAL-PPDRQT 208

Query: 76  SLFSATLPDFVEELARSIMHDAVRVIVGRKNT--ASESIKQKLVFAGSEEGKLLALRQSF 133
            LFSAT+PD + ELAR  ++D V + V  +      + IKQ  +   SEE KL  L +  
Sbjct: 209 LLFSATMPDDIRELARRYLNDPVEIEVSVEKLERTLKKIKQFYLEVESEEEKLELLLKLL 268

Query: 134 AESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQ 176
            +     V++FV++K   +EL   L     +   +H DL Q +
Sbjct: 269 KDEDEGRVIVFVRTKRLVEELAESLRKRGFKVAALHGDLPQEE 311

Length = 513

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

 Score = 87.6 bits (217), Expect = 1e-20
 Identities = 55/158 (34%), Positives = 85/158 (53%), Gaps = 3/158 (1%)

Query: 17  DILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRS 76
           D+L++TP RL     +  + L +VE LVLDEAD++ ++G +  H    V A         
Sbjct: 127 DVLVATPGRLLDLEHQNAVKLDQVEILVLDEADRMLDMGFI--HDIRRVLAKLPAKRQNL 184

Query: 77  LFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAES 136
           LFSAT  D ++ LA  ++H+ + + V R+NTASE + Q + F   +  + L L Q   + 
Sbjct: 185 LFSATFSDDIKALAEKLLHNPLEIEVARRNTASEQVTQHVHFVDKKRKREL-LSQMIGKG 243

Query: 137 LNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQ 174
               VL+F ++K  A  L  +L  D IR+  IH + SQ
Sbjct: 244 NWQQVLVFTRTKHGANHLAEQLNKDGIRSAAIHGNKSQ 281

Length = 456

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

 Score = 82.5 bits (205), Expect = 5e-20
 Identities = 34/85 (40%), Positives = 52/85 (61%), Gaps = 2/85 (2%)

Query: 16  CDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVR 75
             I+++TP RL   + R K+DLS+V+YLVLDEAD++ ++G     I  ++K         
Sbjct: 120 PHIVVATPGRLLDLLERGKLDLSKVKYLVLDEADRMLDMG-FEDQIREILKLL-PKDRQT 177

Query: 76  SLFSATLPDFVEELARSIMHDAVRV 100
            LFSAT+P  V +LAR  + + VR+
Sbjct: 178 LLFSATMPKEVRDLARKFLRNPVRI 202

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

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

 Score = 78.0 bits (192), Expect = 2e-17
 Identities = 56/172 (32%), Positives = 87/172 (50%), Gaps = 27/172 (15%)

Query: 16  CDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVR 75
           CDIL++TP RL    +R ++ L  VE +VLDEAD++ ++G +     P V+      I+R
Sbjct: 214 CDILVATPGRLLDFNQRGEVHLDMVEVMVLDEADRMLDMGFI-----PQVR-----QIIR 263

Query: 76  S----------LFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKL-VFAGSEEG 124
                      LFSAT  D V  LA+    D   V +  +N AS++++Q +   AGS++ 
Sbjct: 264 QTPRKEERQTLLFSATFTDDVMNLAKQWTTDPAIVEIEPENVASDTVEQHVYAVAGSDKY 323

Query: 125 KLL--ALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQ 174
           KLL   + Q+  E     V++F   KD  + +   L  D I A  +  D+ Q
Sbjct: 324 KLLYNLVTQNPWER----VMVFANRKDEVRRIEERLVKDGINAAQLSGDVPQ 371

Length = 475

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

 Score = 77.5 bits (192), Expect = 4e-17
 Identities = 44/160 (27%), Positives = 81/160 (50%), Gaps = 10/160 (6%)

Query: 18  ILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRS- 76
           I++ TP R+   +R+  +DL  +  LVLDEAD++ ++G     ID +++    P+  ++ 
Sbjct: 126 IIVGTPGRILDHLRKGTLDLDALNTLVLDEADRMLDMG-FQDAIDAIIRQA--PARRQTL 182

Query: 77  LFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAES 136
           LFSAT P+ +  +++    D V V V   +    +I+Q   +  S + +L AL++     
Sbjct: 183 LFSATYPEGIAAISQRFQRDPVEVKVESTHDLP-AIEQ-RFYEVSPDERLPALQRLLLH- 239

Query: 137 LNPPV--LIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQ 174
            + P   ++F  +K   +E+   L      A  +H DL Q
Sbjct: 240 -HQPESCVVFCNTKKECQEVADALNAQGFSALALHGDLEQ 278

Length = 460

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

 Score = 75.0 bits (185), Expect = 3e-16
 Identities = 56/160 (35%), Positives = 86/160 (53%), Gaps = 5/160 (3%)

Query: 17  DILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNP-SIVR 75
           DILI T  RL    ++  I+L  ++ +VLDEAD++F++G  +K I  + +        + 
Sbjct: 135 DILIGTTGRLIDYAKQNHINLGAIQVVVLDEADRMFDLG-FIKDIRWLFRRMPPANQRLN 193

Query: 76  SLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAE 135
            LFSATL   V ELA   M++   V V  +      IK++L F  S E K + L Q+  E
Sbjct: 194 MLFSATLSYRVRELAFEHMNNPEYVEVEPEQKTGHRIKEEL-FYPSNEEK-MRLLQTLIE 251

Query: 136 SLNPP-VLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQ 174
              P   +IF  +K R +E++G LA D  R G++  D++Q
Sbjct: 252 EEWPDRAIIFANTKHRCEEIWGHLAADGHRVGLLTGDVAQ 291

Length = 423

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

 Score = 71.3 bits (175), Expect = 5e-15
 Identities = 58/162 (35%), Positives = 80/162 (49%), Gaps = 7/162 (4%)

Query: 17  DILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRS 76
           +ILI+ P RL   +     +L RV YLVLDEAD++ ++G     I  +V     P     
Sbjct: 255 EILIACPGRLIDFLESNVTNLRRVTYLVLDEADRMLDMG-FEPQIRKIVSQI-RPDRQTL 312

Query: 77  LFSATLPDFVEELARSIM-HDAVRVIVGRKN-TASESIKQKLVFAGSEEGKLLALRQSFA 134
           ++SAT P  V+ LAR +   + V V VG  + TA  +IKQ+ VF   E  K   L+    
Sbjct: 313 MWSATWPKEVQSLARDLCKEEPVHVNVGSLDLTACHNIKQE-VFVVEEHEKRGKLKMLLQ 371

Query: 135 ESL--NPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQ 174
             +     +LIFV++K  A  L  EL  D   A  IH D  Q
Sbjct: 372 RIMRDGDKILIFVETKKGADFLTKELRLDGWPALCIHGDKKQ 413

Length = 545

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

 Score = 66.0 bits (161), Expect = 7e-14
 Identities = 34/106 (32%), Positives = 55/106 (51%), Gaps = 4/106 (3%)

Query: 10  DLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACS 69
            L     DIL++TP RL   +   K+ LS V+ ++LDEA +L + G     ++ ++K   
Sbjct: 100 KLESGKTDILVTTPGRLLDLLENDKLSLSNVDLVILDEAHRLLDGGF-GDQLEKLLKLL- 157

Query: 70  NPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQK 115
             ++   L SAT P+ +E L    ++D V + VG   T  E I+Q 
Sbjct: 158 PKNVQLLLLSATPPEEIENLLELFLNDPVFIDVGF--TPLEPIEQF 201

Length = 201

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

 Score = 61.3 bits (149), Expect = 2e-11
 Identities = 41/137 (29%), Positives = 74/137 (54%), Gaps = 12/137 (8%)

Query: 17  DILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRS 76
           ++++ TP RL   + +  I+L  V  LVLDE D + E G     +  + +A S P ++  
Sbjct: 248 ELIVGTPGRLIDLLSKHDIELDNVSVLVLDEVDCMLERG-FRDQVMQIFQALSQPQVL-- 304

Query: 77  LFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGK-----LLALRQ 131
           LFSAT+   VE+ A S+  D + + +G  N  ++++KQ  ++  +++ K     +L  +Q
Sbjct: 305 LFSATVSPEVEKFASSLAKDIILISIGNPNRPNKAVKQLAIWVETKQKKQKLFDILKSKQ 364

Query: 132 SFAESLNPPVLIFVQSK 148
            F     PP ++FV S+
Sbjct: 365 HF----KPPAVVFVSSR 377

Length = 518

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

 Score = 58.8 bits (143), Expect = 2e-11
 Identities = 30/84 (35%), Positives = 47/84 (55%), Gaps = 3/84 (3%)

Query: 7   RSTDLSKFSCDILISTPLRLRLAIRRKKIDLSR-VEYLVLDEADKLFEVGNLLKHIDPVV 65
           ++  L K   DIL+ TP RL   +RR K+ L + ++ LVLDEA +L ++G     ++ ++
Sbjct: 88  QARKLKKGKADILVGTPGRLLDLLRRGKLKLLKNLKLLVLDEAHRLLDMG-FGDDLEEIL 146

Query: 66  KACSNPSIVRSLFSATLPDFVEEL 89
                P     L SATLP  +E+L
Sbjct: 147 SRL-PPDRQILLLSATLPRNLEDL 169

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|185609 PTZ00424, PTZ00424, helicase 45; Provisional

 Score = 57.5 bits (139), Expect = 3e-10
 Identities = 40/157 (25%), Positives = 72/157 (45%), Gaps = 2/157 (1%)

Query: 18  ILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSL 77
           +++ TP R+   I ++ + +  ++  +LDEAD++   G     I  V K    P +  +L
Sbjct: 149 MVVGTPGRVYDMIDKRHLRVDDLKLFILDEADEMLSRG-FKGQIYDVFKKLP-PDVQVAL 206

Query: 78  FSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESL 137
           FSAT+P+ + EL    M D  R++V +     E I+Q  V    EE K   L   +    
Sbjct: 207 FSATMPNEILELTTKFMRDPKRILVKKDELTLEGIRQFYVAVEKEEWKFDTLCDLYETLT 266

Query: 138 NPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQ 174
               +I+  ++ +   L  ++   D     +H D+ Q
Sbjct: 267 ITQAIIYCNTRRKVDYLTKKMHERDFTVSCMHGDMDQ 303

Length = 401

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

 Score = 57.3 bits (138), Expect = 4e-10
 Identities = 47/163 (28%), Positives = 84/163 (51%), Gaps = 10/163 (6%)

Query: 17  DILISTPLRLRLAIRRKKI-DLSRVEYLVLDEADKLFEVGNLLKHIDPVVKA----CSNP 71
           D++I+TP RL   +++ K+  L   E  VLDEAD++F++G  +K I  +++      +  
Sbjct: 136 DVIIATPGRLIDYVKQHKVVSLHACEICVLDEADRMFDLG-FIKDIRFLLRRMPERGTRQ 194

Query: 72  SIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQ 131
           ++   LFSATL   V ELA   M++  +++V  +   +  ++Q++ F   EE K   L  
Sbjct: 195 TL---LFSATLSHRVLELAYEHMNEPEKLVVETETITAARVRQRIYFPADEE-KQTLLLG 250

Query: 132 SFAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQ 174
             + S     ++FV +K   + +   L     R GV+  D+ Q
Sbjct: 251 LLSRSEGARTMVFVNTKAFVERVARTLERHGYRVGVLSGDVPQ 293

Length = 572

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

 Score = 56.1 bits (136), Expect = 8e-10
 Identities = 48/168 (28%), Positives = 79/168 (47%), Gaps = 17/168 (10%)

Query: 17  DILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRS 76
           DI+++TP RL   I+ +  D   VE L+LDEAD++ ++G         ++  +  +  R 
Sbjct: 125 DIVVATPGRLLQYIKEENFDCRAVETLILDEADRMLDMG-----FAQDIETIAAETRWRK 179

Query: 77  ---LFSATLP-DFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGK--LLA-- 128
              LFSATL  D V++ A  +++D V V         + I Q    A   E K  LL   
Sbjct: 180 QTLLFSATLEGDAVQDFAERLLNDPVEVEAEPSRRERKKIHQWYYRADDLEHKTALLCHL 239

Query: 129 LRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQ 176
           L+Q          ++FV++++R  EL G L    I    +  ++ Q +
Sbjct: 240 LKQPEVTR----SIVFVRTRERVHELAGWLRKAGINCCYLEGEMVQAK 283

Length = 434

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

 Score = 47.3 bits (113), Expect = 2e-07
 Identities = 20/67 (29%), Positives = 31/67 (46%), Gaps = 2/67 (2%)

Query: 16  CDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVR 75
            DI++ TP RL   + R K+ L +++ L+LDEA +L   G     +   +          
Sbjct: 80  TDIVVGTPGRLLDELERLKLSLKKLDLLILDEAHRLLNQG--FGLLGLKILLKLPKDRQV 137

Query: 76  SLFSATL 82
            L SAT 
Sbjct: 138 LLLSATP 144

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

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

 Score = 46.0 bits (109), Expect = 3e-06
 Identities = 41/164 (25%), Positives = 74/164 (45%), Gaps = 15/164 (9%)

Query: 18  ILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVG------NLLKHIDPVVKACSNP 71
           I++ TP RL   ++R  +DLS++  LVLDEAD++  +G       ++  I    +     
Sbjct: 128 IVVGTPGRLLDHLKRGTLDLSKLSGLVLDEADEMLRMGFIEDVETIMAQIPEGHQT---- 183

Query: 72  SIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQ 131
               +LFSAT+P+ +  + R  M +   V +    T    I Q              +R 
Sbjct: 184 ----ALFSATMPEAIRRITRRFMKEPQEVRIQSSVTTRPDISQSYWTVWGMRKNEALVRF 239

Query: 132 SFAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQT 175
             AE  +  + IFV++K+   E+   L  +   +  ++ D++Q 
Sbjct: 240 LEAEDFDAAI-IFVRTKNATLEVAEALERNGYNSAALNGDMNQA 282

Length = 629

>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 = 40.7 bits (96), Expect = 6e-05
 Identities = 24/67 (35%), Positives = 31/67 (46%), Gaps = 4/67 (5%)

Query: 112 IKQKLVFAGSEEGKLLALRQSFAESLNPP--VLIFVQSKDRAKELYGELAFDDIRAGVIH 169
           IKQ ++    E+ KL AL +   E L     VLIF  SK    EL   L    I+   +H
Sbjct: 2   IKQYVLP--VEDEKLEALLELLKEHLKKGGKVLIFCPSKKMLDELAELLRKPGIKVAALH 59

Query: 170 SDLSQTQ 176
            D SQ +
Sbjct: 60  GDGSQEE 66

Length = 131

>gnl|CDD|219205 pfam06862, DUF1253, Protein of unknown function (DUF1253)

 Score = 37.6 bits (88), Expect = 0.002
 Identities = 22/59 (37%), Positives = 34/59 (57%), Gaps = 11/59 (18%)

Query: 14  FSCDILISTPLRLRLAIRR---KKID---LSRVEYLVLDEADKLF-----EVGNLLKHI 61
           +S DI+I++PL LR+ I     KK D   LS +E L++D+AD +       V  + KH+
Sbjct: 125 YSSDIIIASPLGLRMIIENEDKKKRDYDFLSSIEVLIVDQADVILMQNWEHVLTVFKHL 183

This family represents the C-terminal portion (approximately 500 residues) of several hypothetical eukaryotic proteins of unknown function. Length = 436

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

 Score = 37.3 bits (87), Expect = 0.003
 Identities = 30/160 (18%), Positives = 60/160 (37%), Gaps = 4/160 (2%)

Query: 16  CDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLK--HIDPVVKACSNPSI 73
             +L  +P RL      + +    +  + +DEA  + + G+  +  +          P+ 
Sbjct: 108 LKLLYISPERLMSPRFLELLKRLPISLVAIDEAHCISQWGHDFRPDYRRLGRLRAGLPNP 167

Query: 74  VRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSF 133
                +AT    V +  R  +      I  R +    ++  K+V  G    +L  L    
Sbjct: 168 PVLALTATATPRVRDDIREQLGLQDANIF-RGSFDRPNLALKVVEKGEPSDQLAFLATVL 226

Query: 134 AESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLS 173
            +      +I+  ++ + +EL   L  + I AG  H+ LS
Sbjct: 227 PQLSKS-GIIYCLTRKKVEELAEWLRKNGISAGAYHAGLS 265

Length = 590

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	178
KOG0328	400	consensus Predicted ATP-dependent RNA helicase FAL	100.0
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	100.0
KOG0331	519	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0330	476	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0338	691	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0326	459	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG4284	980	consensus DEAD box protein [Transcription]	99.98
KOG0333	673	consensus U5 snRNP-like RNA helicase subunit [RNA	99.98
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	99.98
KOG0339	731	consensus ATP-dependent RNA helicase [RNA processi	99.97
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	99.97
KOG0327	397	consensus Translation initiation factor 4F, helica	99.97
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	99.97
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	99.97
KOG0342	543	consensus ATP-dependent RNA helicase pitchoune [RN	99.97
KOG0343	758	consensus RNA Helicase [RNA processing and modific	99.97
KOG0335	482	consensus ATP-dependent RNA helicase [RNA processi	99.97
PTZ00110	545	helicase; Provisional	99.97
KOG0332	477	consensus ATP-dependent RNA helicase [RNA processi	99.97
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	99.97
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	99.97
KOG0341	610	consensus DEAD-box protein abstrakt [RNA processin	99.97
KOG0336	629	consensus ATP-dependent RNA helicase [RNA processi	99.96
KOG0346	569	consensus RNA helicase [RNA processing and modific	99.96
PLN00206	518	DEAD-box ATP-dependent RNA helicase; Provisional	99.96
KOG0345	567	consensus ATP-dependent RNA helicase [RNA processi	99.96
KOG0347	731	consensus RNA helicase [RNA processing and modific	99.96
PTZ00424	401	helicase 45; Provisional	99.96
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	99.96
KOG0340	442	consensus ATP-dependent RNA helicase [RNA processi	99.94
KOG0334	997	consensus RNA helicase [RNA processing and modific	99.94
KOG0337	529	consensus ATP-dependent RNA helicase [RNA processi	99.94
KOG0348	708	consensus ATP-dependent RNA helicase [RNA processi	99.93
KOG0329	387	consensus ATP-dependent RNA helicase [RNA processi	99.93
TIGR02621	844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	99.91
PRK09401	1176	reverse gyrase; Reviewed	99.89
KOG0349	725	consensus Putative DEAD-box RNA helicase DDX1 [RNA	99.89
TIGR03817	742	DECH_helic helicase/secretion neighborhood putativ	99.87
KOG0344	593	consensus ATP-dependent RNA helicase [RNA processi	99.86
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	99.86
PLN03137	1195	ATP-dependent DNA helicase; Q4-like; Provisional	99.86
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	99.85
PRK09751	1490	putative ATP-dependent helicase Lhr; Provisional	99.85
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	99.84
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	99.83
PRK13767	876	ATP-dependent helicase; Provisional	99.81
TIGR01587	358	cas3_core CRISPR-associated helicase Cas3. This mo	99.81
PRK00254	720	ski2-like helicase; Provisional	99.81
TIGR01970	819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	99.81
PRK14701	1638	reverse gyrase; Provisional	99.81
COG1202	830	Superfamily II helicase, archaea-specific [General	99.8
PRK02362	737	ski2-like helicase; Provisional	99.8
COG0514	590	RecQ Superfamily II DNA helicase [DNA replication,	99.8
PRK11664	812	ATP-dependent RNA helicase HrpB; Provisional	99.79
PHA02653	675	RNA helicase NPH-II; Provisional	99.79
PRK11131	1294	ATP-dependent RNA helicase HrpA; Provisional	99.78
PRK10689	1147	transcription-repair coupling factor; Provisional	99.78
TIGR03158	357	cas3_cyano CRISPR-associated helicase, Cyano-type.	99.77
COG1201	814	Lhr Lhr-like helicases [General function predictio	99.77
KOG0350	620	consensus DEAD-box ATP-dependent RNA helicase [RNA	99.77
PRK01172	674	ski2-like helicase; Provisional	99.75
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	99.74
TIGR01967	1283	DEAH_box_HrpA ATP-dependent helicase HrpA. This mo	99.65
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	99.63
cd00268	203	DEADc DEAD-box helicases. A diverse family of prot	99.61
PHA02558	501	uvsW UvsW helicase; Provisional	99.61
KOG0351	941	consensus ATP-dependent DNA helicase [Replication,	99.6
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	99.55
COG1205	851	Distinct helicase family with a unique C-terminal	99.54
COG1204	766	Superfamily II helicase [General function predicti	99.49
PF00270	169	DEAD: DEAD/DEAH box helicase; InterPro: IPR011545	99.47
PRK13766	773	Hef nuclease; Provisional	99.45
KOG0952	1230	consensus DNA/RNA helicase MER3/SLH1, DEAD-box sup	99.44
PRK09694	878	helicase Cas3; Provisional	99.43
KOG0352	641	consensus ATP-dependent DNA helicase [Replication,	99.43
TIGR03714	762	secA2 accessory Sec system translocase SecA2. Memb	99.42
KOG0353	695	consensus ATP-dependent DNA helicase [General func	99.38
KOG0948	1041	consensus Nuclear exosomal RNA helicase MTR4, DEAD	99.34
PRK09200	790	preprotein translocase subunit SecA; Reviewed	99.26
KOG0951	1674	consensus RNA helicase BRR2, DEAD-box superfamily	99.26
COG4581	1041	Superfamily II RNA helicase [DNA replication, reco	99.2
PRK12904	830	preprotein translocase subunit SecA; Reviewed	99.17
TIGR00963	745	secA preprotein translocase, SecA subunit. The pro	99.16
KOG0947	1248	consensus Cytoplasmic exosomal RNA helicase SKI2,	99.16
PRK13104	896	secA preprotein translocase subunit SecA; Reviewed	99.15
COG1111	542	MPH1 ERCC4-like helicases [DNA replication, recomb	99.11
TIGR00595	505	priA primosomal protein N'. All proteins in this f	99.07
smart00487	201	DEXDc DEAD-like helicases superfamily.	99.06
PRK04914	956	ATP-dependent helicase HepA; Validated	99.06
COG1203	733	CRISPR-associated helicase Cas3 [Defense mechanism	99.06
PRK05580	679	primosome assembly protein PriA; Validated	98.95
COG1643	845	HrpA HrpA-like helicases [DNA replication, recombi	98.95
PF06862	442	DUF1253: Protein of unknown function (DUF1253); In	98.83
TIGR00603	732	rad25 DNA repair helicase rad25. All proteins in t	98.82
PRK12898	656	secA preprotein translocase subunit SecA; Reviewed	98.81
PRK13107	908	preprotein translocase subunit SecA; Reviewed	98.78
KOG0950	1008	consensus DNA polymerase theta/eta, DEAD-box super	98.74
COG1061	442	SSL2 DNA or RNA helicases of superfamily II [Trans	98.66
KOG0922	674	consensus DEAH-box RNA helicase [RNA processing an	98.65
COG4098	441	comFA Superfamily II DNA/RNA helicase required for	98.61
cd00046	144	DEXDc DEAD-like helicases superfamily. A diverse f	98.48
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	98.43
KOG0920	924	consensus ATP-dependent RNA helicase A [RNA proces	98.41
PRK11448	1123	hsdR type I restriction enzyme EcoKI subunit R; Pr	98.38
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	98.36
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	98.33
TIGR00631	655	uvrb excinuclease ABC, B subunit. This family is b	98.27
PRK12899	970	secA preprotein translocase subunit SecA; Reviewed	98.25
KOG0354	746	consensus DEAD-box like helicase [General function	98.21
PF14617	252	CMS1: U3-containing 90S pre-ribosomal complex subu	98.2
PLN03142	1033	Probable chromatin-remodeling complex ATPase chain	98.19
COG0556	663	UvrB Helicase subunit of the DNA excision repair c	98.13
cd00079	131	HELICc Helicase superfamily c-terminal domain; ass	98.13
PRK05298	652	excinuclease ABC subunit B; Provisional	98.1
COG4096	875	HsdR Type I site-specific restriction-modification	97.94
PRK12906	796	secA preprotein translocase subunit SecA; Reviewed	97.87
KOG0923	902	consensus mRNA splicing factor ATP-dependent RNA h	97.72
TIGR00348	667	hsdR type I site-specific deoxyribonuclease, HsdR	97.56
KOG0949	1330	consensus Predicted helicase, DEAD-box superfamily	97.54
PRK12900	1025	secA preprotein translocase subunit SecA; Reviewed	97.52
TIGR02562	1110	cas3_yersinia CRISPR-associated helicase Cas3. The	97.46
KOG0925	699	consensus mRNA splicing factor ATP-dependent RNA h	97.4
KOG0385	971	consensus Chromatin remodeling complex WSTF-ISWI,	97.35
PF02399	824	Herpes_ori_bp: Origin of replication binding prote	97.34
KOG0926	1172	consensus DEAH-box RNA helicase [RNA processing an	97.24
PF04851	184	ResIII: Type III restriction enzyme, res subunit;	97.22
KOG0951	1674	consensus RNA helicase BRR2, DEAD-box superfamily	97.11
KOG2340	698	consensus Uncharacterized conserved protein [Funct	96.93
KOG0924	1042	consensus mRNA splicing factor ATP-dependent RNA h	96.9
KOG3089	271	consensus Predicted DEAD-box-containing helicase [	96.59
PF07652	148	Flavi_DEAD: Flavivirus DEAD domain ; InterPro: IPR	96.3
TIGR00596	814	rad1 DNA repair protein (rad1). This family is bas	96.24
KOG4150	1034	consensus Predicted ATP-dependent RNA helicase [RN	96.2
COG1198	730	PriA Primosomal protein N' (replication factor Y)	95.85
KOG0952	1230	consensus DNA/RNA helicase MER3/SLH1, DEAD-box sup	95.48
PF00176	299	SNF2_N: SNF2 family N-terminal domain; InterPro: I	95.35
cd01524	90	RHOD_Pyr_redox Member of the Rhodanese Homology Do	95.03
smart00450	100	RHOD Rhodanese Homology Domain. An alpha beta fold	95.01
cd01523	100	RHOD_Lact_B Member of the Rhodanese Homology Domai	94.79
KOG0384	1373	consensus Chromodomain-helicase DNA-binding protei	94.75
KOG1000	689	consensus Chromatin remodeling protein HARP/SMARCA	94.74
TIGR03117	636	cas_csf4 CRISPR-associated DEAD/DEAH-box helicase	94.73
KOG1123	776	consensus RNA polymerase II transcription initiati	94.28
PRK12898	656	secA preprotein translocase subunit SecA; Reviewed	94.26
KOG0387	923	consensus Transcription-coupled repair protein CSB	93.94
cd01529	96	4RHOD_Repeats Member of the Rhodanese Homology Dom	93.87
cd01518	101	RHOD_YceA Member of the Rhodanese Homology Domain	93.83
PF06733	174	DEAD_2: DEAD_2; InterPro: IPR010614 This represent	93.36
PF13872	303	AAA_34: P-loop containing NTP hydrolase pore-1	93.29
cd01521	110	RHOD_PspE2 Member of the Rhodanese Homology Domain	93.26
cd01534	95	4RHOD_Repeat_3 Member of the Rhodanese Homology Do	93.23
cd01526	122	RHOD_ThiF Member of the Rhodanese Homology Domain	93.22
cd01533	109	4RHOD_Repeat_2 Member of the Rhodanese Homology Do	93.1
PRK12326	764	preprotein translocase subunit SecA; Reviewed	93.03
cd00158	89	RHOD Rhodanese Homology Domain (RHOD); an alpha be	92.92
PRK06893	229	DNA replication initiation factor; Validated	92.91
cd01527	99	RHOD_YgaP Member of the Rhodanese Homology Domain	92.88
cd01449	118	TST_Repeat_2 Thiosulfate sulfurtransferase (TST),	92.79
cd01519	106	RHOD_HSP67B2 Member of the Rhodanese Homology Doma	92.75
cd01448	122	TST_Repeat_1 Thiosulfate sulfurtransferase (TST),	92.73
cd01520	128	RHOD_YbbB Member of the Rhodanese Homology Domain	92.6
cd01532	92	4RHOD_Repeat_1 Member of the Rhodanese Homology Do	92.58
cd01528	101	RHOD_2 Member of the Rhodanese Homology Domain sup	92.41
cd01525	105	RHOD_Kc Member of the Rhodanese Homology Domain su	92.38
cd01444	96	GlpE_ST GlpE sulfurtransferase (ST) and homologs a	92.16
TIGR01407	850	dinG_rel DnaQ family exonuclease/DinG family helic	92.11
TIGR01407	850	dinG_rel DnaQ family exonuclease/DinG family helic	91.98
PF05872	502	DUF853: Bacterial protein of unknown function (DUF	91.93
cd01447	103	Polysulfide_ST Polysulfide-sulfurtransferase - Rho	91.62
PRK14087	450	dnaA chromosomal replication initiation protein; P	91.47
smart00489	289	DEXDc3 DEAD-like helicases superfamily.	91.44
smart00488	289	DEXDc2 DEAD-like helicases superfamily.	91.44
PRK12903	925	secA preprotein translocase subunit SecA; Reviewed	91.36
PRK12422	445	chromosomal replication initiation protein; Provis	91.25
PF11019	252	DUF2608: Protein of unknown function (DUF2608); In	91.11
PRK05642	234	DNA replication initiation factor; Validated	90.93
PF07517	266	SecA_DEAD: SecA DEAD-like domain; InterPro: IPR011	90.85
PRK08727	233	hypothetical protein; Validated	90.59
cd01535	145	4RHOD_Repeat_4 Member of the Rhodanese Homology Do	90.31
PRK05320	257	rhodanese superfamily protein; Provisional	90.29
KOG0921	1282	consensus Dosage compensation complex, subunit MLE	90.14
PRK07246	820	bifunctional ATP-dependent DNA helicase/DNA polyme	90.04
PRK08074	928	bifunctional ATP-dependent DNA helicase/DNA polyme	89.57
PRK14088	440	dnaA chromosomal replication initiation protein; P	89.15
PF02463	220	SMC_N: RecF/RecN/SMC N terminal domain; InterPro:	89.0
PRK11747	697	dinG ATP-dependent DNA helicase DinG; Provisional	88.95
PRK14873	665	primosome assembly protein PriA; Provisional	88.86
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	88.7
PRK00162	108	glpE thiosulfate sulfurtransferase; Validated	88.59
KOG0964	1200	consensus Structural maintenance of chromosome pro	88.44
cd01522	117	RHOD_1 Member of the Rhodanese Homology Domain sup	88.09
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	87.99
PLN02160	136	thiosulfate sulfurtransferase	87.99
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	87.97
PRK14086	617	dnaA chromosomal replication initiation protein; P	87.96
PRK06526	254	transposase; Provisional	87.91
CHL00122	870	secA preprotein translocase subunit SecA; Validate	87.86
PRK10287	104	thiosulfate:cyanide sulfurtransferase; Provisional	87.78
PRK01415	247	hypothetical protein; Validated	87.61
PRK00149	450	dnaA chromosomal replication initiation protein; R	87.54
PF13177	162	DNA_pol3_delta2: DNA polymerase III, delta subunit	87.32
PF09848	352	DUF2075: Uncharacterized conserved protein (DUF207	87.18
cd01445	138	TST_Repeats Thiosulfate sulfurtransferases (TST) c	86.58
KOG0989	346	consensus Replication factor C, subunit RFC4 [Repl	86.44
TIGR03865	162	PQQ_CXXCW PQQ-dependent catabolism-associated CXXC	86.08
PF15586	116	Imm47: Immunity protein 47	85.89
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	85.86
PRK12902	939	secA preprotein translocase subunit SecA; Reviewed	85.85
KOG0389	941	consensus SNF2 family DNA-dependent ATPase [Chroma	85.85
PF00581	113	Rhodanese: Rhodanese-like domain This Prosite entr	85.78
COG1199	654	DinG Rad3-related DNA helicases [Transcription / D	85.71
PRK13103	913	secA preprotein translocase subunit SecA; Reviewed	85.64
TIGR02981	101	phageshock_pspE phage shock operon rhodanese PspE.	85.55
PRK08084	235	DNA replication initiation factor; Provisional	85.25
cd01530	121	Cdc25 Cdc25 phosphatases are members of the Rhodan	85.16
PRK00142	314	putative rhodanese-related sulfurtransferase; Prov	84.96
PRK06835	329	DNA replication protein DnaC; Validated	84.64
KOG2170	344	consensus ATPase of the AAA+ superfamily [General	84.63
PF10100	429	DUF2338: Uncharacterized protein conserved in bact	84.63
KOG2228	408	consensus Origin recognition complex, subunit 4 [R	84.57
PF05621	302	TniB: Bacterial TniB protein; InterPro: IPR008868	84.3
TIGR00604	705	rad3 DNA repair helicase (rad3). All proteins in t	84.15
KOG0354	746	consensus DEAD-box like helicase [General function	83.93
PRK12899	970	secA preprotein translocase subunit SecA; Reviewed	83.46
PRK08181	269	transposase; Validated	83.16
COG0607	110	PspE Rhodanese-related sulfurtransferase [Inorgani	83.11
COG1054	308	Predicted sulfurtransferase [General function pred	82.59
KOG1132	945	consensus Helicase of the DEAD superfamily [Replic	82.58
PRK07764	824	DNA polymerase III subunits gamma and tau; Validat	82.39
COG1199	654	DinG Rad3-related DNA helicases [Transcription / D	82.3
PRK08116	268	hypothetical protein; Validated	81.99
PRK12902	939	secA preprotein translocase subunit SecA; Reviewed	81.78
cd01446	132	DSP_MapKP N-terminal regulatory rhodanese domain o	81.71
PRK13103	913	secA preprotein translocase subunit SecA; Reviewed	81.49
KOG0991	333	consensus Replication factor C, subunit RFC2 [Repl	81.45
PF13173	128	AAA_14: AAA domain	81.12
PRK11493	281	sseA 3-mercaptopyruvate sulfurtransferase; Provisi	81.08
PRK11747	697	dinG ATP-dependent DNA helicase DinG; Provisional	80.8
KOG0390	776	consensus DNA repair protein, SNF2 family [Replica	80.78
PRK05580	679	primosome assembly protein PriA; Validated	80.56
PLN03025	319	replication factor C subunit; Provisional	80.43
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	80.43
COG4408	431	Uncharacterized protein conserved in bacteria [Fun	80.02

>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=6.5e-39  Score=235.94  Aligned_cols=172  Identities=27%  Similarity=0.363  Sum_probs=164.7

Q ss_pred             HhHHhHHhccCCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCc
Q 030396            4 ELVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLP   83 (178)
Q Consensus         4 ~~~~q~~~l~~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~   83 (178)
                      ++-+-.+.+.-|++++.|||||++++++++++..+.++++|+||||.|++.| |.+++.+|.++ +|+..|++++|||+|
T Consensus       134 n~gedikkld~G~hvVsGtPGrv~dmikr~~L~tr~vkmlVLDEaDemL~kg-fk~Qiydiyr~-lp~~~Qvv~~SATlp  211 (400)
T KOG0328|consen  134 NLGEDIKKLDYGQHVVSGTPGRVLDMIKRRSLRTRAVKMLVLDEADEMLNKG-FKEQIYDIYRY-LPPGAQVVLVSATLP  211 (400)
T ss_pred             ccchhhhhhcccceEeeCCCchHHHHHHhccccccceeEEEeccHHHHHHhh-HHHHHHHHHHh-CCCCceEEEEeccCc
Confidence            3444556677899999999999999999999999999999999999999999 99999999999 899999999999999


Q ss_pred             HHHHHHHHHhccCcEEEEEcCCccccCCceEEEEEcCChhhHHHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhhhCCC
Q 030396           84 DFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDI  163 (178)
Q Consensus        84 ~~~~~~~~~~~~~~~~v~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~~~g~  163 (178)
                      .++.+..++|+.||..+.+.+++.+..+++|+|+.+..++.|++.|+++.+.....+++|||||++.+++|.+.|.+..+
T Consensus       212 ~eilemt~kfmtdpvrilvkrdeltlEgIKqf~v~ve~EewKfdtLcdLYd~LtItQavIFcnTk~kVdwLtekm~~~nf  291 (400)
T KOG0328|consen  212 HEILEMTEKFMTDPVRILVKRDELTLEGIKQFFVAVEKEEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREANF  291 (400)
T ss_pred             HHHHHHHHHhcCCceeEEEecCCCchhhhhhheeeechhhhhHhHHHHHhhhhehheEEEEecccchhhHHHHHHHhhCc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ceEeeecCCCcccc
Q 030396          164 RAGVIHSDLSQTQV  177 (178)
Q Consensus       164 ~~~~lh~~~~~~~R  177 (178)
                      .+.++||+|+|+||
T Consensus       292 tVssmHGDm~qkER  305 (400)
T KOG0328|consen  292 TVSSMHGDMEQKER  305 (400)
T ss_pred             eeeeccCCcchhHH
Confidence            99999999999998

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

Probab=100.00  E-value=5.6e-37  Score=250.61  Aligned_cols=171  Identities=36%  Similarity=0.496  Sum_probs=161.2

Q ss_pred             hHHhHHhccCCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcH
Q 030396            5 LVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPD   84 (178)
Q Consensus         5 ~~~q~~~l~~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~   84 (178)
                      ...|.+.++.++||||||||||++++.++.++++.++++|+||||.|++.| |.+++..|+.. .+.++|+++||||+|.
T Consensus       140 ~~~q~~~l~~~~~ivVaTPGRllD~i~~~~l~l~~v~~lVlDEADrmLd~G-f~~~i~~I~~~-~p~~~qtllfSAT~~~  217 (513)
T COG0513         140 IRKQIEALKRGVDIVVATPGRLLDLIKRGKLDLSGVETLVLDEADRMLDMG-FIDDIEKILKA-LPPDRQTLLFSATMPD  217 (513)
T ss_pred             HHHHHHHHhcCCCEEEECccHHHHHHHcCCcchhhcCEEEeccHhhhhcCC-CHHHHHHHHHh-CCcccEEEEEecCCCH
Confidence            467888888899999999999999999999999999999999999999999 99999999999 7889999999999999


Q ss_pred             HHHHHHHHhccCcEEEEEcCCcc--ccCCceEEEEEcCChhhHHHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhhhCC
Q 030396           85 FVEELARSIMHDAVRVIVGRKNT--ASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDD  162 (178)
Q Consensus        85 ~~~~~~~~~~~~~~~v~~~~~~~--~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~~~g  162 (178)
                      .+..+...++.+|..+.+.....  ....+.|+++.+.+..+|...|..+++.....++||||+|+..|+.++..|...|
T Consensus       218 ~i~~l~~~~l~~p~~i~v~~~~~~~~~~~i~q~~~~v~~~~~k~~~L~~ll~~~~~~~~IVF~~tk~~~~~l~~~l~~~g  297 (513)
T COG0513         218 DIRELARRYLNDPVEIEVSVEKLERTLKKIKQFYLEVESEEEKLELLLKLLKDEDEGRVIVFVRTKRLVEELAESLRKRG  297 (513)
T ss_pred             HHHHHHHHHccCCcEEEEccccccccccCceEEEEEeCCHHHHHHHHHHHHhcCCCCeEEEEeCcHHHHHHHHHHHHHCC
Confidence            99999999999999888886655  8899999999987766799999999998888899999999999999999999999


Q ss_pred             CceEeeecCCCcccc
Q 030396          163 IRAGVIHSDLSQTQV  177 (178)
Q Consensus       163 ~~~~~lh~~~~~~~R  177 (178)
                      +++..+||+|+|++|
T Consensus       298 ~~~~~lhG~l~q~~R  312 (513)
T COG0513         298 FKVAALHGDLPQEER  312 (513)
T ss_pred             CeEEEecCCCCHHHH
Confidence            999999999999988

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

Probab=100.00  E-value=1.3e-36  Score=242.58  Aligned_cols=170  Identities=31%  Similarity=0.435  Sum_probs=154.7

Q ss_pred             HHhHHhccCCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcHH
Q 030396            6 VRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDF   85 (178)
Q Consensus         6 ~~q~~~l~~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~   85 (178)
                      ..|++.++++++|+|||||||.++++.+.++++++.|+|+||||.|+++| |.++++.|++.+.+..+|++++|||||.+
T Consensus       206 ~~Q~~~l~~gvdiviaTPGRl~d~le~g~~~l~~v~ylVLDEADrMldmG-Fe~qI~~Il~~i~~~~rQtlm~saTwp~~  284 (519)
T KOG0331|consen  206 GPQLRDLERGVDVVIATPGRLIDLLEEGSLNLSRVTYLVLDEADRMLDMG-FEPQIRKILSQIPRPDRQTLMFSATWPKE  284 (519)
T ss_pred             cHHHHHHhcCCcEEEeCChHHHHHHHcCCccccceeEEEeccHHhhhccc-cHHHHHHHHHhcCCCcccEEEEeeeccHH
Confidence            56999999999999999999999999999999999999999999999999 99999999999437778999999999999


Q ss_pred             HHHHHHHhccCcEEEEEcCCc--cccCCceEEEEEcCChhhHHHHHHHHHHhc---CCCCEEEEeCCchHHHHHHHHhhh
Q 030396           86 VEELARSIMHDAVRVIVGRKN--TASESIKQKLVFAGSEEGKLLALRQSFAES---LNPPVLIFVQSKDRAKELYGELAF  160 (178)
Q Consensus        86 ~~~~~~~~~~~~~~v~~~~~~--~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~---~~~~~lIF~~t~~~~~~l~~~L~~  160 (178)
                      ++.++..|+.+|..+.+....  ....++.|....+ +...|...|..+|...   ...|+||||+|++.|+.|+..|+.
T Consensus       285 v~~lA~~fl~~~~~i~ig~~~~~~a~~~i~qive~~-~~~~K~~~l~~lL~~~~~~~~~KvIIFc~tkr~~~~l~~~l~~  363 (519)
T KOG0331|consen  285 VRQLAEDFLNNPIQINVGNKKELKANHNIRQIVEVC-DETAKLRKLGKLLEDISSDSEGKVIIFCETKRTCDELARNLRR  363 (519)
T ss_pred             HHHHHHHHhcCceEEEecchhhhhhhcchhhhhhhc-CHHHHHHHHHHHHHHHhccCCCcEEEEecchhhHHHHHHHHHh
Confidence            999999999999999887553  5556777766555 5778999999999866   466899999999999999999999


Q ss_pred             CCCceEeeecCCCcccc
Q 030396          161 DDIRAGVIHSDLSQTQV  177 (178)
Q Consensus       161 ~g~~~~~lh~~~~~~~R  177 (178)
                      .|+++.++||+.+|.||
T Consensus       364 ~~~~a~~iHGd~sQ~eR  380 (519)
T KOG0331|consen  364 KGWPAVAIHGDKSQSER  380 (519)
T ss_pred             cCcceeeecccccHHHH
Confidence            99999999999999998

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

Probab=100.00  E-value=2.8e-36  Score=229.96  Aligned_cols=172  Identities=26%  Similarity=0.340  Sum_probs=163.2

Q ss_pred             HhHHhHHhccCCCcEEEeCcHHHHHHHH-cCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecC
Q 030396            4 ELVRSTDLSKFSCDILISTPLRLRLAIR-RKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATL   82 (178)
Q Consensus         4 ~~~~q~~~l~~~~~Iii~TP~~l~~~l~-~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~   82 (178)
                      +.+.|..++.+.|||+|+|||||++++. .+.++++.++++|+||||.++++. |.+.+..|++. +|..+|+++||||+
T Consensus       168 ~m~~q~~~L~kkPhilVaTPGrL~dhl~~Tkgf~le~lk~LVlDEADrlLd~d-F~~~ld~ILk~-ip~erqt~LfsATM  245 (476)
T KOG0330|consen  168 DMMLQANQLSKKPHILVATPGRLWDHLENTKGFSLEQLKFLVLDEADRLLDMD-FEEELDYILKV-IPRERQTFLFSATM  245 (476)
T ss_pred             hHHHHHHHhhcCCCEEEeCcHHHHHHHHhccCccHHHhHHHhhchHHhhhhhh-hHHHHHHHHHh-cCccceEEEEEeec
Confidence            4678899999999999999999999998 478899999999999999999999 99999999999 89999999999999


Q ss_pred             cHHHHHHHHHhccCcEEEEEcCCccccCCceEEEEEcCChhhHHHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhhhCC
Q 030396           83 PDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDD  162 (178)
Q Consensus        83 ~~~~~~~~~~~~~~~~~v~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~~~g  162 (178)
                      |..+.++....+.+|..+.+.....+.+.+.|.|.+++ ...|..+|..+++......+||||||...+++++-.|...|
T Consensus       246 t~kv~kL~rasl~~p~~v~~s~ky~tv~~lkQ~ylfv~-~k~K~~yLV~ll~e~~g~s~iVF~~t~~tt~~la~~L~~lg  324 (476)
T KOG0330|consen  246 TKKVRKLQRASLDNPVKVAVSSKYQTVDHLKQTYLFVP-GKDKDTYLVYLLNELAGNSVIVFCNTCNTTRFLALLLRNLG  324 (476)
T ss_pred             chhhHHHHhhccCCCeEEeccchhcchHHhhhheEecc-ccccchhHHHHHHhhcCCcEEEEEeccchHHHHHHHHHhcC
Confidence            99999999999999999999999999999999998884 45799999999999989999999999999999999999999


Q ss_pred             CceEeeecCCCccccC
Q 030396          163 IRAGVIHSDLSQTQVF  178 (178)
Q Consensus       163 ~~~~~lh~~~~~~~R~  178 (178)
                      +.+..+||+|+|..|+
T Consensus       325 ~~a~~LhGqmsq~~Rl  340 (476)
T KOG0330|consen  325 FQAIPLHGQMSQSKRL  340 (476)
T ss_pred             cceecccchhhHHHHH
Confidence            9999999999999884

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

Probab=100.00  E-value=2.5e-33  Score=220.11  Aligned_cols=173  Identities=27%  Similarity=0.422  Sum_probs=160.6

Q ss_pred             HhHHhHHhccCCCcEEEeCcHHHHHHHHc-CCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecC
Q 030396            4 ELVRSTDLSKFSCDILISTPLRLRLAIRR-KKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATL   82 (178)
Q Consensus         4 ~~~~q~~~l~~~~~Iii~TP~~l~~~l~~-~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~   82 (178)
                      +++.|...|+.+|||||+||||+.+++++ .+++++++..+|+||||+|++.| |.+++..|++. .+.++|+++||||+
T Consensus       291 ~lk~QE~~LRs~PDIVIATPGRlIDHlrNs~sf~ldsiEVLvlDEADRMLeeg-FademnEii~l-cpk~RQTmLFSATM  368 (691)
T KOG0338|consen  291 DLKAQEAVLRSRPDIVIATPGRLIDHLRNSPSFNLDSIEVLVLDEADRMLEEG-FADEMNEIIRL-CPKNRQTMLFSATM  368 (691)
T ss_pred             cHHHHHHHHhhCCCEEEecchhHHHHhccCCCccccceeEEEechHHHHHHHH-HHHHHHHHHHh-ccccccceeehhhh
Confidence            46789999999999999999999999987 57899999999999999999999 99999999999 89999999999999


Q ss_pred             cHHHHHHHHHhccCcEEEEEcCCccccCCceEEEEEcCC--hhhHHHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhhh
Q 030396           83 PDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGS--EEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAF  160 (178)
Q Consensus        83 ~~~~~~~~~~~~~~~~~v~~~~~~~~~~~i~~~~~~~~~--~~~k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~~  160 (178)
                      +..+..++...++.|+.+.+.+.......+.|.|+.+-.  +.++-..+..++.+.-...+|||+.|++.|+.+.-.|.-
T Consensus       369 teeVkdL~slSL~kPvrifvd~~~~~a~~LtQEFiRIR~~re~dRea~l~~l~~rtf~~~~ivFv~tKk~AHRl~IllGL  448 (691)
T KOG0338|consen  369 TEEVKDLASLSLNKPVRIFVDPNKDTAPKLTQEFIRIRPKREGDREAMLASLITRTFQDRTIVFVRTKKQAHRLRILLGL  448 (691)
T ss_pred             HHHHHHHHHhhcCCCeEEEeCCccccchhhhHHHheeccccccccHHHHHHHHHHhcccceEEEEehHHHHHHHHHHHHH
Confidence            999999999999999999999999999999999986643  345777788888877678899999999999999999999


Q ss_pred             CCCceEeeecCCCccccC
Q 030396          161 DDIRAGVIHSDLSQTQVF  178 (178)
Q Consensus       161 ~g~~~~~lh~~~~~~~R~  178 (178)
                      .|+++..+||+|+|+||+
T Consensus       449 lgl~agElHGsLtQ~QRl  466 (691)
T KOG0338|consen  449 LGLKAGELHGSLTQEQRL  466 (691)
T ss_pred             hhchhhhhcccccHHHHH
Confidence            999999999999999995

>KOG0326 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=100.00  E-value=5.2e-33  Score=207.91  Aligned_cols=163  Identities=21%  Similarity=0.264  Sum_probs=154.4

Q ss_pred             hccCCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcHHHHHHH
Q 030396           11 LSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELA   90 (178)
Q Consensus        11 ~l~~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~~~~~~   90 (178)
                      .+.++++++||||||++++.+++.-++++..++|+||||+|++.. |.+.++.++.. +|.++|++++|||||-.+..+.
T Consensus       199 Rl~~~VH~~vgTPGRIlDL~~KgVa~ls~c~~lV~DEADKlLs~~-F~~~~e~li~~-lP~~rQillySATFP~tVk~Fm  276 (459)
T KOG0326|consen  199 RLNQTVHLVVGTPGRILDLAKKGVADLSDCVILVMDEADKLLSVD-FQPIVEKLISF-LPKERQILLYSATFPLTVKGFM  276 (459)
T ss_pred             eecCceEEEEcCChhHHHHHhcccccchhceEEEechhhhhhchh-hhhHHHHHHHh-CCccceeeEEecccchhHHHHH
Confidence            356789999999999999999999999999999999999999999 99999999999 9999999999999999999999


Q ss_pred             HHhccCcEEEEEcCCccccCCceEEEEEcCChhhHHHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhhhCCCceEeeec
Q 030396           91 RSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHS  170 (178)
Q Consensus        91 ~~~~~~~~~v~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~  170 (178)
                      .++++.|..+.+- ++.++.++.|+|.++ .+..|+..|.-++.+....+.||||||..++|.+|....+.||+|+++|+
T Consensus       277 ~~~l~kPy~INLM-~eLtl~GvtQyYafV-~e~qKvhCLntLfskLqINQsIIFCNS~~rVELLAkKITelGyscyyiHa  354 (459)
T KOG0326|consen  277 DRHLKKPYEINLM-EELTLKGVTQYYAFV-EERQKVHCLNTLFSKLQINQSIIFCNSTNRVELLAKKITELGYSCYYIHA  354 (459)
T ss_pred             HHhccCcceeehh-hhhhhcchhhheeee-chhhhhhhHHHHHHHhcccceEEEeccchHhHHHHHHHHhccchhhHHHH
Confidence            9999999999885 677889999999888 55679999999999998999999999999999999999999999999999


Q ss_pred             CCCcccc
Q 030396          171 DLSQTQV  177 (178)
Q Consensus       171 ~~~~~~R  177 (178)
                      .|-|+.|
T Consensus       355 kM~Q~hR  361 (459)
T KOG0326|consen  355 KMAQEHR  361 (459)
T ss_pred             HHHHhhh
Confidence            9999988

>KOG4284 consensus DEAD box protein [Transcription]

Probab=99.98  E-value=2.6e-32  Score=219.37  Aligned_cols=164  Identities=26%  Similarity=0.313  Sum_probs=155.7

Q ss_pred             CCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcHHHHHHHHHh
Q 030396           14 FSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSI   93 (178)
Q Consensus        14 ~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~~~~~~~~~   93 (178)
                      +.++|+||||||+..+++.+.+|++++++||+||||.|++.++|..+|..|+.. +|..+|+++||||.|..+..++.++
T Consensus       142 k~~rIvIGtPGRi~qL~el~~~n~s~vrlfVLDEADkL~~t~sfq~~In~ii~s-lP~~rQv~a~SATYp~nLdn~Lsk~  220 (980)
T KOG4284|consen  142 KQTRIVIGTPGRIAQLVELGAMNMSHVRLFVLDEADKLMDTESFQDDINIIINS-LPQIRQVAAFSATYPRNLDNLLSKF  220 (980)
T ss_pred             hhceEEecCchHHHHHHHhcCCCccceeEEEeccHHhhhchhhHHHHHHHHHHh-cchhheeeEEeccCchhHHHHHHHH
Confidence            568999999999999999999999999999999999999988899999999999 9999999999999999999999999


Q ss_pred             ccCcEEEEEcCCccccCCceEEEEEcCChh-------hHHHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhhhCCCceE
Q 030396           94 MHDAVRVIVGRKNTASESIKQKLVFAGSEE-------GKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDIRAG  166 (178)
Q Consensus        94 ~~~~~~v~~~~~~~~~~~i~~~~~~~~~~~-------~k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~  166 (178)
                      +++|..|........+.+|+|+++..+..+       .|...|..+++..+..++||||+...+|+-++.+|...|++|.
T Consensus       221 mrdp~lVr~n~~d~~L~GikQyv~~~~s~nnsveemrlklq~L~~vf~~ipy~QAlVF~~~~sra~~~a~~L~ssG~d~~  300 (980)
T KOG4284|consen  221 MRDPALVRFNADDVQLFGIKQYVVAKCSPNNSVEEMRLKLQKLTHVFKSIPYVQALVFCDQISRAEPIATHLKSSGLDVT  300 (980)
T ss_pred             hcccceeecccCCceeechhheeeeccCCcchHHHHHHHHHHHHHHHhhCchHHHHhhhhhhhhhhHHHHHhhccCCCeE
Confidence            999999999999999999999998776653       4788888888999999999999999999999999999999999


Q ss_pred             eeecCCCccccC
Q 030396          167 VIHSDLSQTQVF  178 (178)
Q Consensus       167 ~lh~~~~~~~R~  178 (178)
                      ++.|.|+|.+|+
T Consensus       301 ~ISgaM~Q~~Rl  312 (980)
T KOG4284|consen  301 FISGAMSQKDRL  312 (980)
T ss_pred             EeccccchhHHH
Confidence            999999999995

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

Probab=99.98  E-value=1.7e-31  Score=210.35  Aligned_cols=164  Identities=29%  Similarity=0.479  Sum_probs=154.4

Q ss_pred             hccCCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCC------------------
Q 030396           11 LSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPS------------------   72 (178)
Q Consensus        11 ~l~~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~------------------   72 (178)
                      +++.+|+|+|+|||||.+.+.+.-+-++.+-+||+||||.|+++| |.+++..|+.+ +|..                  
T Consensus       368 qls~gceiviatPgrLid~Lenr~lvl~qctyvvldeadrmiDmg-fE~dv~~iL~~-mPssn~k~~tde~~~~~~~~~~  445 (673)
T KOG0333|consen  368 QLSMGCEIVIATPGRLIDSLENRYLVLNQCTYVVLDEADRMIDMG-FEPDVQKILEQ-MPSSNAKPDTDEKEGEERVRKN  445 (673)
T ss_pred             hhhccceeeecCchHHHHHHHHHHHHhccCceEeccchhhhhccc-ccHHHHHHHHh-CCccccCCCccchhhHHHHHhh
Confidence            677899999999999999999998999999999999999999999 99999999999 6631                  


Q ss_pred             -------ceEEEEeecCcHHHHHHHHHhccCcEEEEEcCCccccCCceEEEEEcCChhhHHHHHHHHHHhcCCCCEEEEe
Q 030396           73 -------IVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFV  145 (178)
Q Consensus        73 -------~q~i~~SAT~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~  145 (178)
                             +|+++||||+|+.+..++..|+.+|.++.++..+...+.+.|.++.++.+ .|...|.++++....+++|||+
T Consensus       446 ~~~~k~yrqT~mftatm~p~verlar~ylr~pv~vtig~~gk~~~rveQ~v~m~~ed-~k~kkL~eil~~~~~ppiIIFv  524 (673)
T KOG0333|consen  446 FSSSKKYRQTVMFTATMPPAVERLARSYLRRPVVVTIGSAGKPTPRVEQKVEMVSED-EKRKKLIEILESNFDPPIIIFV  524 (673)
T ss_pred             cccccceeEEEEEecCCChHHHHHHHHHhhCCeEEEeccCCCCccchheEEEEecch-HHHHHHHHHHHhCCCCCEEEEE
Confidence                   79999999999999999999999999999999999999999999888655 5699999999998889999999


Q ss_pred             CCchHHHHHHHHhhhCCCceEeeecCCCcccc
Q 030396          146 QSKDRAKELYGELAFDDIRAGVIHSDLSQTQV  177 (178)
Q Consensus       146 ~t~~~~~~l~~~L~~~g~~~~~lh~~~~~~~R  177 (178)
                      |+++.|+.+|+.|.+.||+++.+||+-+|+||
T Consensus       525 N~kk~~d~lAk~LeK~g~~~~tlHg~k~qeQR  556 (673)
T KOG0333|consen  525 NTKKGADALAKILEKAGYKVTTLHGGKSQEQR  556 (673)
T ss_pred             echhhHHHHHHHHhhccceEEEeeCCccHHHH
Confidence            99999999999999999999999999999998

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=99.98  E-value=7.3e-31  Score=213.10  Aligned_cols=169  Identities=25%  Similarity=0.405  Sum_probs=153.0

Q ss_pred             hHHhHHhccCCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcH
Q 030396            5 LVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPD   84 (178)
Q Consensus         5 ~~~q~~~l~~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~   84 (178)
                      ...|.+.++.+++|+|||||++.+++.++.+++++++++|+||||.+++++ |...+..+++. ++..+|+++||||+|+
T Consensus       113 ~~~~~~~l~~~~~IvV~Tp~rl~~~l~~~~~~l~~l~~lViDEad~~l~~g-~~~~l~~i~~~-~~~~~q~ll~SAT~~~  190 (460)
T PRK11776        113 MGPQIDSLEHGAHIIVGTPGRILDHLRKGTLDLDALNTLVLDEADRMLDMG-FQDAIDAIIRQ-APARRQTLLFSATYPE  190 (460)
T ss_pred             hHHHHHHhcCCCCEEEEChHHHHHHHHcCCccHHHCCEEEEECHHHHhCcC-cHHHHHHHHHh-CCcccEEEEEEecCcH
Confidence            345677778899999999999999999999999999999999999999999 99999999999 8899999999999999


Q ss_pred             HHHHHHHHhccCcEEEEEcCCccccCCceEEEEEcCChhhHHHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhhhCCCc
Q 030396           85 FVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDIR  164 (178)
Q Consensus        85 ~~~~~~~~~~~~~~~v~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~~~g~~  164 (178)
                      .+..+...++.+|..+.+.... ....+.+.++.+.. .+|...+..++......++||||||++.|+.+++.|.+.|++
T Consensus       191 ~~~~l~~~~~~~~~~i~~~~~~-~~~~i~~~~~~~~~-~~k~~~l~~ll~~~~~~~~lVF~~t~~~~~~l~~~L~~~~~~  268 (460)
T PRK11776        191 GIAAISQRFQRDPVEVKVESTH-DLPAIEQRFYEVSP-DERLPALQRLLLHHQPESCVVFCNTKKECQEVADALNAQGFS  268 (460)
T ss_pred             HHHHHHHHhcCCCEEEEECcCC-CCCCeeEEEEEeCc-HHHHHHHHHHHHhcCCCceEEEECCHHHHHHHHHHHHhCCCc
Confidence            9999999999999988886554 44568888876654 459999999998887889999999999999999999999999


Q ss_pred             eEeeecCCCcccc
Q 030396          165 AGVIHSDLSQTQV  177 (178)
Q Consensus       165 ~~~lh~~~~~~~R  177 (178)
                      +..+||+|++.+|
T Consensus       269 v~~~hg~~~~~eR  281 (460)
T PRK11776        269 ALALHGDLEQRDR  281 (460)
T ss_pred             EEEEeCCCCHHHH
Confidence            9999999999887

>KOG0339 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.97  E-value=3.5e-31  Score=208.07  Aligned_cols=169  Identities=36%  Similarity=0.504  Sum_probs=159.8

Q ss_pred             HhHHhccCCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcHHH
Q 030396            7 RSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFV   86 (178)
Q Consensus         7 ~q~~~l~~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~~   86 (178)
                      +|.+.|+.+|.|||+|||||.+++.-+..++.++.++||||||.|++.| |.++++.|.+. ..+.+|+++|||||+..+
T Consensus       338 eQ~k~Lk~g~EivVaTPgRlid~VkmKatn~~rvS~LV~DEadrmfdmG-fe~qVrSI~~h-irpdrQtllFsaTf~~kI  415 (731)
T KOG0339|consen  338 EQSKELKEGAEIVVATPGRLIDMVKMKATNLSRVSYLVLDEADRMFDMG-FEPQVRSIKQH-IRPDRQTLLFSATFKKKI  415 (731)
T ss_pred             HHHHhhhcCCeEEEechHHHHHHHHhhcccceeeeEEEEechhhhhccc-cHHHHHHHHhh-cCCcceEEEeeccchHHH
Confidence            6788889999999999999999999999999999999999999999999 99999999999 899999999999999999


Q ss_pred             HHHHHHhccCcEEEEEcCCccccCCceEEEEEcCChhhHHHHHHHHHHhc-CCCCEEEEeCCchHHHHHHHHhhhCCCce
Q 030396           87 EELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAES-LNPPVLIFVQSKDRAKELYGELAFDDIRA  165 (178)
Q Consensus        87 ~~~~~~~~~~~~~v~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~-~~~~~lIF~~t~~~~~~l~~~L~~~g~~~  165 (178)
                      +.+++.++.+|+.+...........|.|.+..+.+...|...|..-|... ..+++|||+..+..++.++..|.-.|+++
T Consensus       416 e~lard~L~dpVrvVqg~vgean~dITQ~V~V~~s~~~Kl~wl~~~L~~f~S~gkvlifVTKk~~~e~i~a~Lklk~~~v  495 (731)
T KOG0339|consen  416 EKLARDILSDPVRVVQGEVGEANEDITQTVSVCPSEEKKLNWLLRHLVEFSSEGKVLIFVTKKADAEEIAANLKLKGFNV  495 (731)
T ss_pred             HHHHHHHhcCCeeEEEeehhccccchhheeeeccCcHHHHHHHHHHhhhhccCCcEEEEEeccCCHHHHHHHhcccccee
Confidence            99999999999999998888888899999999999999999988877654 46799999999999999999999999999


Q ss_pred             EeeecCCCcccc
Q 030396          166 GVIHSDLSQTQV  177 (178)
Q Consensus       166 ~~lh~~~~~~~R  177 (178)
                      ..+||+|.|.+|
T Consensus       496 ~llhgdkdqa~r  507 (731)
T KOG0339|consen  496 SLLHGDKDQAER  507 (731)
T ss_pred             eeecCchhhHHH
Confidence            999999999888

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=99.97  E-value=1.2e-30  Score=217.34  Aligned_cols=171  Identities=23%  Similarity=0.327  Sum_probs=156.4

Q ss_pred             HhHHhHHhccCCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCc
Q 030396            4 ELVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLP   83 (178)
Q Consensus         4 ~~~~q~~~l~~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~   83 (178)
                      ++..|.+.++.+++|||||||++.+++.++.+++++++++|+||||.|++++ |.+.+..|++. ++...|+++||||+|
T Consensus       114 ~~~~q~~~l~~~~~IVVgTPgrl~d~l~r~~l~l~~l~~lVlDEAd~ml~~g-f~~di~~Il~~-lp~~~q~llfSAT~p  191 (629)
T PRK11634        114 RYDVQLRALRQGPQIVVGTPGRLLDHLKRGTLDLSKLSGLVLDEADEMLRMG-FIEDVETIMAQ-IPEGHQTALFSATMP  191 (629)
T ss_pred             CHHHHHHHhcCCCCEEEECHHHHHHHHHcCCcchhhceEEEeccHHHHhhcc-cHHHHHHHHHh-CCCCCeEEEEEccCC
Confidence            3456777888899999999999999999999999999999999999999999 99999999999 888999999999999


Q ss_pred             HHHHHHHHHhccCcEEEEEcCCccccCCceEEEEEcCChhhHHHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhhhCCC
Q 030396           84 DFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDI  163 (178)
Q Consensus        84 ~~~~~~~~~~~~~~~~v~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~~~g~  163 (178)
                      +.+..+...++.+|..+.+.........+.+.++.+ ....|...+..++......++||||+|+..|+.++..|...|+
T Consensus       192 ~~i~~i~~~~l~~~~~i~i~~~~~~~~~i~q~~~~v-~~~~k~~~L~~~L~~~~~~~~IVF~~tk~~a~~l~~~L~~~g~  270 (629)
T PRK11634        192 EAIRRITRRFMKEPQEVRIQSSVTTRPDISQSYWTV-WGMRKNEALVRFLEAEDFDAAIIFVRTKNATLEVAEALERNGY  270 (629)
T ss_pred             hhHHHHHHHHcCCCeEEEccCccccCCceEEEEEEe-chhhHHHHHHHHHHhcCCCCEEEEeccHHHHHHHHHHHHhCCC
Confidence            999999999999999988877777777888888666 4556888999999888788999999999999999999999999


Q ss_pred             ceEeeecCCCcccc
Q 030396          164 RAGVIHSDLSQTQV  177 (178)
Q Consensus       164 ~~~~lh~~~~~~~R  177 (178)
                      .+..+||+|++.+|
T Consensus       271 ~~~~lhgd~~q~~R  284 (629)
T PRK11634        271 NSAALNGDMNQALR  284 (629)
T ss_pred             CEEEeeCCCCHHHH
Confidence            99999999999887

>KOG0327 consensus Translation initiation factor 4F, helicase subunit (eIF-4A) and related helicases [Translation, ribosomal structure and biogenesis]

Probab=99.97  E-value=3.9e-31  Score=201.49  Aligned_cols=160  Identities=26%  Similarity=0.391  Sum_probs=153.0

Q ss_pred             cCCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcHHHHHHHHH
Q 030396           13 KFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARS   92 (178)
Q Consensus        13 ~~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~~~~~~~~   92 (178)
                      ...++|++|||||+.+++..+.+....++++|+||||.+++.| |.++|..|+++ ++++.|++++|||.|.++....++
T Consensus       143 ~~~~hivvGTpgrV~dml~~~~l~~~~iKmfvlDEaDEmLs~g-fkdqI~~if~~-lp~~vQv~l~SAT~p~~vl~vt~~  220 (397)
T KOG0327|consen  143 KDKPHIVVGTPGRVFDMLNRGSLSTDGIKMFVLDEADEMLSRG-FKDQIYDIFQE-LPSDVQVVLLSATMPSDVLEVTKK  220 (397)
T ss_pred             ccCceeecCCchhHHHhhccccccccceeEEeecchHhhhccc-hHHHHHHHHHH-cCcchhheeecccCcHHHHHHHHH
Confidence            3569999999999999999999999999999999999999999 99999999999 999999999999999999999999


Q ss_pred             hccCcEEEEEcCCccccCCceEEEEEcCChhhHHHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhhhCCCceEeeecCC
Q 030396           93 IMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDL  172 (178)
Q Consensus        93 ~~~~~~~v~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~~  172 (178)
                      |+.+|..+.+..+..+..+++|+++.+..+. |+..|+++.+  ...+.+|||||++.+.++...|...|+.+.++||+|
T Consensus       221 f~~~pv~i~vkk~~ltl~gikq~~i~v~k~~-k~~~l~dl~~--~~~q~~if~nt~r~v~~l~~~L~~~~~~~s~~~~d~  297 (397)
T KOG0327|consen  221 FMREPVRILVKKDELTLEGIKQFYINVEKEE-KLDTLCDLYR--RVTQAVIFCNTRRKVDNLTDKLRAHGFTVSAIHGDM  297 (397)
T ss_pred             hccCceEEEecchhhhhhheeeeeeeccccc-cccHHHHHHH--hhhcceEEecchhhHHHHHHHHhhCCceEEEeeccc
Confidence            9999999999999999999999999886665 9999999999  569999999999999999999999999999999999


Q ss_pred             Ccccc
Q 030396          173 SQTQV  177 (178)
Q Consensus       173 ~~~~R  177 (178)
                      .|.+|
T Consensus       298 ~q~~R  302 (397)
T KOG0327|consen  298 EQNER  302 (397)
T ss_pred             chhhh
Confidence            99988

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.97  E-value=4.5e-30  Score=206.54  Aligned_cols=170  Identities=31%  Similarity=0.453  Sum_probs=152.6

Q ss_pred             hHHhHHhccCCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCC--CCceEEEEeecC
Q 030396            5 LVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSN--PSIVRSLFSATL   82 (178)
Q Consensus         5 ~~~q~~~l~~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~--~~~q~i~~SAT~   82 (178)
                      ...|.+.++++++|+|||||++.+++..+.+++++++++|+||||.+++++ |..++..+++. ++  ..+|.+++|||+
T Consensus       123 ~~~~~~~l~~~~~IlV~TP~~l~~~l~~~~~~l~~v~~lViDEad~l~~~~-f~~~i~~i~~~-~~~~~~~~~~l~SAT~  200 (423)
T PRK04837        123 YDKQLKVLESGVDILIGTTGRLIDYAKQNHINLGAIQVVVLDEADRMFDLG-FIKDIRWLFRR-MPPANQRLNMLFSATL  200 (423)
T ss_pred             HHHHHHHhcCCCCEEEECHHHHHHHHHcCCcccccccEEEEecHHHHhhcc-cHHHHHHHHHh-CCCccceeEEEEeccC
Confidence            456677778899999999999999999999999999999999999999999 99999999998 55  357889999999


Q ss_pred             cHHHHHHHHHhccCcEEEEEcCCccccCCceEEEEEcCChhhHHHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhhhCC
Q 030396           83 PDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDD  162 (178)
Q Consensus        83 ~~~~~~~~~~~~~~~~~v~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~~~g  162 (178)
                      +..+..+...++.+|..+.+.........+.+.++.. +...|...+..+++.....++||||+|+..|+.++..|...|
T Consensus       201 ~~~~~~~~~~~~~~p~~i~v~~~~~~~~~i~~~~~~~-~~~~k~~~l~~ll~~~~~~~~lVF~~t~~~~~~l~~~L~~~g  279 (423)
T PRK04837        201 SYRVRELAFEHMNNPEYVEVEPEQKTGHRIKEELFYP-SNEEKMRLLQTLIEEEWPDRAIIFANTKHRCEEIWGHLAADG  279 (423)
T ss_pred             CHHHHHHHHHHCCCCEEEEEcCCCcCCCceeEEEEeC-CHHHHHHHHHHHHHhcCCCeEEEEECCHHHHHHHHHHHHhCC
Confidence            9999999999999999998887777777777776544 566789999999988778899999999999999999999999


Q ss_pred             CceEeeecCCCcccc
Q 030396          163 IRAGVIHSDLSQTQV  177 (178)
Q Consensus       163 ~~~~~lh~~~~~~~R  177 (178)
                      +++..+||+|++++|
T Consensus       280 ~~v~~lhg~~~~~~R  294 (423)
T PRK04837        280 HRVGLLTGDVAQKKR  294 (423)
T ss_pred             CcEEEecCCCChhHH
Confidence            999999999999987

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=99.97  E-value=4.1e-30  Score=208.39  Aligned_cols=170  Identities=32%  Similarity=0.440  Sum_probs=153.1

Q ss_pred             hHHhHHhccCCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcH
Q 030396            5 LVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPD   84 (178)
Q Consensus         5 ~~~q~~~l~~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~   84 (178)
                      +.+|...+.++++|+|+|||+|++++..+.+++++++++|+||||.+++++ |...+..++.. ++...|++++|||+++
T Consensus       115 ~~~~~~~l~~~~~IiV~TP~rL~~~~~~~~~~l~~v~~lViDEah~ll~~~-~~~~i~~il~~-l~~~~q~l~~SAT~~~  192 (456)
T PRK10590        115 INPQMMKLRGGVDVLVATPGRLLDLEHQNAVKLDQVEILVLDEADRMLDMG-FIHDIRRVLAK-LPAKRQNLLFSATFSD  192 (456)
T ss_pred             HHHHHHHHcCCCcEEEEChHHHHHHHHcCCcccccceEEEeecHHHHhccc-cHHHHHHHHHh-CCccCeEEEEeCCCcH
Confidence            345666677889999999999999999998999999999999999999999 99999999999 8889999999999999


Q ss_pred             HHHHHHHHhccCcEEEEEcCCccccCCceEEEEEcCChhhHHHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhhhCCCc
Q 030396           85 FVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDIR  164 (178)
Q Consensus        85 ~~~~~~~~~~~~~~~v~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~~~g~~  164 (178)
                      .+..+...++.+|..+.+.........+.+++..+ +...|...+..++......++||||||+..|+.++..|.+.|++
T Consensus       193 ~~~~l~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~-~~~~k~~~l~~l~~~~~~~~~lVF~~t~~~~~~l~~~L~~~g~~  271 (456)
T PRK10590        193 DIKALAEKLLHNPLEIEVARRNTASEQVTQHVHFV-DKKRKRELLSQMIGKGNWQQVLVFTRTKHGANHLAEQLNKDGIR  271 (456)
T ss_pred             HHHHHHHHHcCCCeEEEEecccccccceeEEEEEc-CHHHHHHHHHHHHHcCCCCcEEEEcCcHHHHHHHHHHHHHCCCC
Confidence            99999999999999888877766777788877655 55677888888888877889999999999999999999999999


Q ss_pred             eEeeecCCCcccc
Q 030396          165 AGVIHSDLSQTQV  177 (178)
Q Consensus       165 ~~~lh~~~~~~~R  177 (178)
                      +..+||+|++++|
T Consensus       272 ~~~lhg~~~~~~R  284 (456)
T PRK10590        272 SAAIHGNKSQGAR  284 (456)
T ss_pred             EEEEECCCCHHHH
Confidence            9999999999887

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

Probab=99.97  E-value=1.5e-30  Score=203.53  Aligned_cols=168  Identities=27%  Similarity=0.367  Sum_probs=147.5

Q ss_pred             HhHHhccCCCcEEEeCcHHHHHHHHcC-CCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcHH
Q 030396            7 RSTDLSKFSCDILISTPLRLRLAIRRK-KIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDF   85 (178)
Q Consensus         7 ~q~~~l~~~~~Iii~TP~~l~~~l~~~-~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~   85 (178)
                      ...+.+.++|+|+|+|||||++++++. .+-+..++++|+||||++++.| |.++++.|++. ++.++|+++||||.|+.
T Consensus       197 ~e~~kl~k~~niliATPGRLlDHlqNt~~f~~r~~k~lvlDEADrlLd~G-F~~di~~Ii~~-lpk~rqt~LFSAT~~~k  274 (543)
T KOG0342|consen  197 VEADKLVKGCNILIATPGRLLDHLQNTSGFLFRNLKCLVLDEADRLLDIG-FEEDVEQIIKI-LPKQRQTLLFSATQPSK  274 (543)
T ss_pred             HHHHHhhccccEEEeCCchHHhHhhcCCcchhhccceeEeecchhhhhcc-cHHHHHHHHHh-ccccceeeEeeCCCcHH
Confidence            344455569999999999999999884 4557888999999999999999 99999999999 89999999999999999


Q ss_pred             HHHHHHHhcc-CcEEEEEc--CCccccCCceEEEEEcCChhhHHHHHHHHHHhcCC-CCEEEEeCCchHHHHHHHHhhhC
Q 030396           86 VEELARSIMH-DAVRVIVG--RKNTASESIKQKLVFAGSEEGKLLALRQSFAESLN-PPVLIFVQSKDRAKELYGELAFD  161 (178)
Q Consensus        86 ~~~~~~~~~~-~~~~v~~~--~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~-~~~lIF~~t~~~~~~l~~~L~~~  161 (178)
                      |++++...+. +|..+...  ....+..++.|-|+.++.. .++..+..+++++.. .++||||.|...+..+++.|...
T Consensus       275 V~~l~~~~L~~d~~~v~~~d~~~~~The~l~Qgyvv~~~~-~~f~ll~~~LKk~~~~~KiiVF~sT~~~vk~~~~lL~~~  353 (543)
T KOG0342|consen  275 VKDLARGALKRDPVFVNVDDGGERETHERLEQGYVVAPSD-SRFSLLYTFLKKNIKRYKIIVFFSTCMSVKFHAELLNYI  353 (543)
T ss_pred             HHHHHHHhhcCCceEeecCCCCCcchhhcccceEEecccc-chHHHHHHHHHHhcCCceEEEEechhhHHHHHHHHHhhc
Confidence            9999999877 57777664  3456778899988766554 469999999998876 89999999999999999999999


Q ss_pred             CCceEeeecCCCcccc
Q 030396          162 DIRAGVIHSDLSQTQV  177 (178)
Q Consensus       162 g~~~~~lh~~~~~~~R  177 (178)
                      .++|..+||+++|..|
T Consensus       354 dlpv~eiHgk~~Q~kR  369 (543)
T KOG0342|consen  354 DLPVLEIHGKQKQNKR  369 (543)
T ss_pred             CCchhhhhcCCccccc
Confidence            9999999999999987

>KOG0343 consensus RNA Helicase [RNA processing and modification]

Probab=99.97  E-value=1.4e-30  Score=206.36  Aligned_cols=170  Identities=26%  Similarity=0.339  Sum_probs=152.8

Q ss_pred             hHHhHHhccCCCcEEEeCcHHHHHHHHcC-CCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCc
Q 030396            5 LVRSTDLSKFSCDILISTPLRLRLAIRRK-KIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLP   83 (178)
Q Consensus         5 ~~~q~~~l~~~~~Iii~TP~~l~~~l~~~-~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~   83 (178)
                      .+-....+ ++.+|+|||||||++++..+ .++..+++++|+||||+++++| |...++.|+.. +|..+|+++||||-+
T Consensus       181 ~k~E~eRi-~~mNILVCTPGRLLQHmde~~~f~t~~lQmLvLDEADR~LDMG-Fk~tL~~Ii~~-lP~~RQTLLFSATqt  257 (758)
T KOG0343|consen  181 VKFELERI-SQMNILVCTPGRLLQHMDENPNFSTSNLQMLVLDEADRMLDMG-FKKTLNAIIEN-LPKKRQTLLFSATQT  257 (758)
T ss_pred             hHHHHHhh-hcCCeEEechHHHHHHhhhcCCCCCCcceEEEeccHHHHHHHh-HHHHHHHHHHh-CChhheeeeeecccc
Confidence            34444555 47999999999999999774 6789999999999999999999 99999999999 999999999999999


Q ss_pred             HHHHHHHHHhccCcEEEEEc--CCccccCCceEEEEEcCChhhHHHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhhhC
Q 030396           84 DFVEELARSIMHDAVRVIVG--RKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFD  161 (178)
Q Consensus        84 ~~~~~~~~~~~~~~~~v~~~--~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~~~  161 (178)
                      ..+..+++..+.||..|.+.  ....+|.++.|+|+.+ +..+|++.|-.+++.+...++|||+.|.+++.++++.|...
T Consensus       258 ~svkdLaRLsL~dP~~vsvhe~a~~atP~~L~Q~y~~v-~l~~Ki~~L~sFI~shlk~K~iVF~SscKqvkf~~e~F~rl  336 (758)
T KOG0343|consen  258 KSVKDLARLSLKDPVYVSVHENAVAATPSNLQQSYVIV-PLEDKIDMLWSFIKSHLKKKSIVFLSSCKQVKFLYEAFCRL  336 (758)
T ss_pred             hhHHHHHHhhcCCCcEEEEeccccccChhhhhheEEEE-ehhhHHHHHHHHHHhccccceEEEEehhhHHHHHHHHHHhc
Confidence            99999999999999777665  3367888898888766 66789999999999999999999999999999999999765


Q ss_pred             --CCceEeeecCCCccccC
Q 030396          162 --DIRAGVIHSDLSQTQVF  178 (178)
Q Consensus       162 --g~~~~~lh~~~~~~~R~  178 (178)
                        |++...+||.|+|..|.
T Consensus       337 rpg~~l~~L~G~~~Q~~R~  355 (758)
T KOG0343|consen  337 RPGIPLLALHGTMSQKKRI  355 (758)
T ss_pred             CCCCceeeeccchhHHHHH
Confidence              99999999999999883

>KOG0335 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.97  E-value=1.1e-30  Score=205.90  Aligned_cols=171  Identities=35%  Similarity=0.492  Sum_probs=154.8

Q ss_pred             HhHHhHHhccCCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccc-cCCChhhHHHHHhhCCC----CCceEEEE
Q 030396            4 ELVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFE-VGNLLKHIDPVVKACSN----PSIVRSLF   78 (178)
Q Consensus         4 ~~~~q~~~l~~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~-~~~~~~~i~~i~~~~~~----~~~q~i~~   78 (178)
                      ++..|.+.+.++|||+|+|||||.++++.+.+.+..+++||+||||.|++ .+ |.++|++|+... .    .++|+++|
T Consensus       191 ~~~~q~~~~~~gcdIlvaTpGrL~d~~e~g~i~l~~~k~~vLDEADrMlD~mg-F~p~Ir~iv~~~-~~~~~~~~qt~mF  268 (482)
T KOG0335|consen  191 DLGAQLRFIKRGCDILVATPGRLKDLIERGKISLDNCKFLVLDEADRMLDEMG-FEPQIRKIVEQL-GMPPKNNRQTLLF  268 (482)
T ss_pred             chhhhhhhhccCccEEEecCchhhhhhhcceeehhhCcEEEecchHHhhhhcc-ccccHHHHhccc-CCCCccceeEEEE
Confidence            46688999999999999999999999999999999999999999999999 77 999999999984 3    47999999


Q ss_pred             eecCcHHHHHHHHHhccC-cEEEEEcCCccccCCceEEEEEcCChhhHHHHHHHHHHhcC----CC-----CEEEEeCCc
Q 030396           79 SATLPDFVEELARSIMHD-AVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESL----NP-----PVLIFVQSK  148 (178)
Q Consensus        79 SAT~~~~~~~~~~~~~~~-~~~v~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~----~~-----~~lIF~~t~  148 (178)
                      |||+|..+..++..|+.+ ...+.+...+....++.|.+.++ ++.+|...|++++....    ..     +++|||.|+
T Consensus       269 SAtfp~~iq~l~~~fl~~~yi~laV~rvg~~~~ni~q~i~~V-~~~~kr~~Lldll~~~~~~~~~~~~~~e~tlvFvEt~  347 (482)
T KOG0335|consen  269 SATFPKEIQRLAADFLKDNYIFLAVGRVGSTSENITQKILFV-NEMEKRSKLLDLLNKDDGPPSDGEPKWEKTLVFVETK  347 (482)
T ss_pred             eccCChhhhhhHHHHhhccceEEEEeeeccccccceeEeeee-cchhhHHHHHHHhhcccCCcccCCcccceEEEEeecc
Confidence            999999999988888886 88888999999999999999888 55567788888887432    22     799999999


Q ss_pred             hHHHHHHHHhhhCCCceEeeecCCCcccc
Q 030396          149 DRAKELYGELAFDDIRAGVIHSDLSQTQV  177 (178)
Q Consensus       149 ~~~~~l~~~L~~~g~~~~~lh~~~~~~~R  177 (178)
                      +.|..++.+|...|+++..+||+.+|.||
T Consensus       348 ~~~d~l~~~l~~~~~~~~sIhg~~tq~er  376 (482)
T KOG0335|consen  348 RGADELAAFLSSNGYPAKSIHGDRTQIER  376 (482)
T ss_pred             chhhHHHHHHhcCCCCceeecchhhhhHH
Confidence            99999999999999999999999999987

>PTZ00110 helicase; Provisional

Probab=99.97  E-value=6.4e-30  Score=210.72  Aligned_cols=169  Identities=33%  Similarity=0.417  Sum_probs=147.8

Q ss_pred             HHhHHhccCCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcHH
Q 030396            6 VRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDF   85 (178)
Q Consensus         6 ~~q~~~l~~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~   85 (178)
                      ..|...+.++++|+|+|||+|.+++..+..++++++++|+||||.+++++ |.+++..|+.. +++.+|++++|||+|..
T Consensus       244 ~~q~~~l~~~~~IlVaTPgrL~d~l~~~~~~l~~v~~lViDEAd~mld~g-f~~~i~~il~~-~~~~~q~l~~SAT~p~~  321 (545)
T PTZ00110        244 RGQIYALRRGVEILIACPGRLIDFLESNVTNLRRVTYLVLDEADRMLDMG-FEPQIRKIVSQ-IRPDRQTLMWSATWPKE  321 (545)
T ss_pred             HHHHHHHHcCCCEEEECHHHHHHHHHcCCCChhhCcEEEeehHHhhhhcc-hHHHHHHHHHh-CCCCCeEEEEEeCCCHH
Confidence            45667778899999999999999999998999999999999999999999 99999999999 78899999999999999


Q ss_pred             HHHHHHHhcc-CcEEEEEcCCc-cccCCceEEEEEcCChhhHHHHHHHHHHhc--CCCCEEEEeCCchHHHHHHHHhhhC
Q 030396           86 VEELARSIMH-DAVRVIVGRKN-TASESIKQKLVFAGSEEGKLLALRQSFAES--LNPPVLIFVQSKDRAKELYGELAFD  161 (178)
Q Consensus        86 ~~~~~~~~~~-~~~~v~~~~~~-~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~--~~~~~lIF~~t~~~~~~l~~~L~~~  161 (178)
                      +..+...++. +|..+.+.... ....++.+.+..+ ....|...|.+++...  ...++||||+|++.|+.++..|...
T Consensus       322 v~~l~~~l~~~~~v~i~vg~~~l~~~~~i~q~~~~~-~~~~k~~~L~~ll~~~~~~~~k~LIF~~t~~~a~~l~~~L~~~  400 (545)
T PTZ00110        322 VQSLARDLCKEEPVHVNVGSLDLTACHNIKQEVFVV-EEHEKRGKLKMLLQRIMRDGDKILIFVETKKGADFLTKELRLD  400 (545)
T ss_pred             HHHHHHHHhccCCEEEEECCCccccCCCeeEEEEEE-echhHHHHHHHHHHHhcccCCeEEEEecChHHHHHHHHHHHHc
Confidence            9999998886 57777776544 3345677777555 5566888888888764  4679999999999999999999999


Q ss_pred             CCceEeeecCCCcccc
Q 030396          162 DIRAGVIHSDLSQTQV  177 (178)
Q Consensus       162 g~~~~~lh~~~~~~~R  177 (178)
                      |+++..+||+|++++|
T Consensus       401 g~~~~~ihg~~~~~eR  416 (545)
T PTZ00110        401 GWPALCIHGDKKQEER  416 (545)
T ss_pred             CCcEEEEECCCcHHHH
Confidence            9999999999999987

>KOG0332 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.97  E-value=9.4e-31  Score=198.97  Aligned_cols=162  Identities=27%  Similarity=0.349  Sum_probs=155.7

Q ss_pred             CCcEEEeCcHHHHHHHHc-CCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcHHHHHHHHHh
Q 030396           15 SCDILISTPLRLRLAIRR-KKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSI   93 (178)
Q Consensus        15 ~~~Iii~TP~~l~~~l~~-~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~~~~~~~~~   93 (178)
                      ..+|+|||||.+.+++.. +-+++..++.+|+||||.|++.+.|.++-.+|.+. ++.+.|.++||||+.+.++.++.+.
T Consensus       207 ~eqIviGTPGtv~Dlm~klk~id~~kikvfVlDEAD~Mi~tqG~~D~S~rI~~~-lP~~~QllLFSATf~e~V~~Fa~ki  285 (477)
T KOG0332|consen  207 TEQIVIGTPGTVLDLMLKLKCIDLEKIKVFVLDEADVMIDTQGFQDQSIRIMRS-LPRNQQLLLFSATFVEKVAAFALKI  285 (477)
T ss_pred             hhheeeCCCccHHHHHHHHHhhChhhceEEEecchhhhhhcccccccchhhhhh-cCCcceEEeeechhHHHHHHHHHHh
Confidence            368999999999999988 88999999999999999999876699999999999 8899999999999999999999999


Q ss_pred             ccCcEEEEEcCCccccCCceEEEEEcCChhhHHHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhhhCCCceEeeecCCC
Q 030396           94 MHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLS  173 (178)
Q Consensus        94 ~~~~~~v~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~~~  173 (178)
                      .++|..+.+..+.....+|+|+++.|..+.+|+..|.++......+++||||.|++.|++++..|...|+.+.++||+|.
T Consensus       286 vpn~n~i~Lk~eel~L~~IkQlyv~C~~~~~K~~~l~~lyg~~tigqsiIFc~tk~ta~~l~~~m~~~Gh~V~~l~G~l~  365 (477)
T KOG0332|consen  286 VPNANVIILKREELALDNIKQLYVLCACRDDKYQALVNLYGLLTIGQSIIFCHTKATAMWLYEEMRAEGHQVSLLHGDLT  365 (477)
T ss_pred             cCCCceeeeehhhccccchhhheeeccchhhHHHHHHHHHhhhhhhheEEEEeehhhHHHHHHHHHhcCceeEEeeccch
Confidence            99999999999999999999999999999999999999999888999999999999999999999999999999999999


Q ss_pred             cccc
Q 030396          174 QTQV  177 (178)
Q Consensus       174 ~~~R  177 (178)
                      ..+|
T Consensus       366 ~~~R  369 (477)
T KOG0332|consen  366 VEQR  369 (477)
T ss_pred             hHHH
Confidence            9988

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=99.97  E-value=2.8e-29  Score=202.52  Aligned_cols=170  Identities=26%  Similarity=0.363  Sum_probs=154.6

Q ss_pred             HHhHHhccCCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcH-
Q 030396            6 VRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPD-   84 (178)
Q Consensus         6 ~~q~~~l~~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~-   84 (178)
                      .+|...+.++++|+|||||+|.+++..+.+++.+++++|+||||.+++++ |...+..+... .+...|+++||||++. 
T Consensus       114 ~~~~~~l~~~~~IlV~Tp~rl~~~~~~~~~~~~~v~~lViDEah~~l~~~-~~~~~~~i~~~-~~~~~q~~~~SAT~~~~  191 (434)
T PRK11192        114 MNHAEVFSENQDIVVATPGRLLQYIKEENFDCRAVETLILDEADRMLDMG-FAQDIETIAAE-TRWRKQTLLFSATLEGD  191 (434)
T ss_pred             HHHHHHhcCCCCEEEEChHHHHHHHHcCCcCcccCCEEEEECHHHHhCCC-cHHHHHHHHHh-CccccEEEEEEeecCHH
Confidence            45666777899999999999999999999999999999999999999999 99999999998 7888999999999985 


Q ss_pred             HHHHHHHHhccCcEEEEEcCCccccCCceEEEEEcCChhhHHHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhhhCCCc
Q 030396           85 FVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDIR  164 (178)
Q Consensus        85 ~~~~~~~~~~~~~~~v~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~~~g~~  164 (178)
                      .+..+...++.+|..+..........++.+.++.+.....|...+..+++.....++||||+|+++|+.++..|.+.|++
T Consensus       192 ~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~l~~~~~~~~~lVF~~s~~~~~~l~~~L~~~~~~  271 (434)
T PRK11192        192 AVQDFAERLLNDPVEVEAEPSRRERKKIHQWYYRADDLEHKTALLCHLLKQPEVTRSIVFVRTRERVHELAGWLRKAGIN  271 (434)
T ss_pred             HHHHHHHHHccCCEEEEecCCcccccCceEEEEEeCCHHHHHHHHHHHHhcCCCCeEEEEeCChHHHHHHHHHHHhCCCC
Confidence            47888888899999998887777778888888777777789999999998777889999999999999999999999999


Q ss_pred             eEeeecCCCcccc
Q 030396          165 AGVIHSDLSQTQV  177 (178)
Q Consensus       165 ~~~lh~~~~~~~R  177 (178)
                      +..+||+|++.+|
T Consensus       272 ~~~l~g~~~~~~R  284 (434)
T PRK11192        272 CCYLEGEMVQAKR  284 (434)
T ss_pred             EEEecCCCCHHHH
Confidence            9999999999887

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.97  E-value=2.2e-29  Score=208.38  Aligned_cols=170  Identities=27%  Similarity=0.416  Sum_probs=150.8

Q ss_pred             hHHhHHhccCCCcEEEeCcHHHHHHHHcC-CCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCC--CceEEEEeec
Q 030396            5 LVRSTDLSKFSCDILISTPLRLRLAIRRK-KIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNP--SIVRSLFSAT   81 (178)
Q Consensus         5 ~~~q~~~l~~~~~Iii~TP~~l~~~l~~~-~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~--~~q~i~~SAT   81 (178)
                      ...|.+.++++++|||+|||+|++++.++ .+++..+++||+||||.+++++ |...+..|++. ++.  ..|+++||||
T Consensus       124 ~~~q~~~l~~~~dIiV~TP~rL~~~l~~~~~~~l~~v~~lViDEAh~lld~g-f~~~i~~il~~-lp~~~~~q~ll~SAT  201 (572)
T PRK04537        124 YDKQRELLQQGVDVIIATPGRLIDYVKQHKVVSLHACEICVLDEADRMFDLG-FIKDIRFLLRR-MPERGTRQTLLFSAT  201 (572)
T ss_pred             HHHHHHHHhCCCCEEEECHHHHHHHHHhccccchhheeeeEecCHHHHhhcc-hHHHHHHHHHh-cccccCceEEEEeCC
Confidence            34667778888999999999999999775 5789999999999999999999 99999999998 554  7899999999


Q ss_pred             CcHHHHHHHHHhccCcEEEEEcCCccccCCceEEEEEcCChhhHHHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhhhC
Q 030396           82 LPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFD  161 (178)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~~~  161 (178)
                      ++..+..+...++.+|..+...........+.+.++.+ ....|...+..++......++||||||++.|+.+++.|.+.
T Consensus       202 l~~~v~~l~~~~l~~p~~i~v~~~~~~~~~i~q~~~~~-~~~~k~~~L~~ll~~~~~~k~LVF~nt~~~ae~l~~~L~~~  280 (572)
T PRK04537        202 LSHRVLELAYEHMNEPEKLVVETETITAARVRQRIYFP-ADEEKQTLLLGLLSRSEGARTMVFVNTKAFVERVARTLERH  280 (572)
T ss_pred             ccHHHHHHHHHHhcCCcEEEeccccccccceeEEEEec-CHHHHHHHHHHHHhcccCCcEEEEeCCHHHHHHHHHHHHHc
Confidence            99999999999999998887776666677788877655 56678899999998877889999999999999999999999


Q ss_pred             CCceEeeecCCCcccc
Q 030396          162 DIRAGVIHSDLSQTQV  177 (178)
Q Consensus       162 g~~~~~lh~~~~~~~R  177 (178)
                      |+++..+||+|++.+|
T Consensus       281 g~~v~~lhg~l~~~eR  296 (572)
T PRK04537        281 GYRVGVLSGDVPQKKR  296 (572)
T ss_pred             CCCEEEEeCCCCHHHH
Confidence            9999999999999887

>KOG0341 consensus DEAD-box protein abstrakt [RNA processing and modification]

Probab=99.97  E-value=5.4e-31  Score=201.62  Aligned_cols=170  Identities=28%  Similarity=0.452  Sum_probs=159.4

Q ss_pred             HhHHhHHhccCCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCc
Q 030396            4 ELVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLP   83 (178)
Q Consensus         4 ~~~~q~~~l~~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~   83 (178)
                      .+.+|++.++.+.+|+|+|||||.+++.++.+++.-++++++||||+|++.| |.++++.|+.+ ....+|+++||||+|
T Consensus       291 ~v~eql~~v~~GvHivVATPGRL~DmL~KK~~sLd~CRyL~lDEADRmiDmG-FEddir~iF~~-FK~QRQTLLFSATMP  368 (610)
T KOG0341|consen  291 PVREQLDVVRRGVHIVVATPGRLMDMLAKKIMSLDACRYLTLDEADRMIDMG-FEDDIRTIFSF-FKGQRQTLLFSATMP  368 (610)
T ss_pred             cHHHHHHHHhcCeeEEEcCcchHHHHHHHhhccHHHHHHhhhhhHHHHhhcc-chhhHHHHHHH-Hhhhhheeeeecccc
Confidence            3578999999999999999999999999999999999999999999999999 99999999999 899999999999999


Q ss_pred             HHHHHHHHHhccCcEEEEEcCCccccCCceEEEEEcCChhhHHHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhhhCCC
Q 030396           84 DFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDI  163 (178)
Q Consensus        84 ~~~~~~~~~~~~~~~~v~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~~~g~  163 (178)
                      ..+..+++..+-.|+.+.+++.+...-++.|.+-++ ..+.|+-++++.|.+. .+|++|||..+.+++.+.++|.-.|.
T Consensus       369 ~KIQ~FAkSALVKPvtvNVGRAGAAsldViQevEyV-kqEaKiVylLeCLQKT-~PpVLIFaEkK~DVD~IhEYLLlKGV  446 (610)
T KOG0341|consen  369 KKIQNFAKSALVKPVTVNVGRAGAASLDVIQEVEYV-KQEAKIVYLLECLQKT-SPPVLIFAEKKADVDDIHEYLLLKGV  446 (610)
T ss_pred             HHHHHHHHhhcccceEEecccccccchhHHHHHHHH-HhhhhhhhHHHHhccC-CCceEEEeccccChHHHHHHHHHccc
Confidence            999999999999999999999999888888888666 5567888888888877 78999999999999999999999999


Q ss_pred             ceEeeecCCCcccc
Q 030396          164 RAGVIHSDLSQTQV  177 (178)
Q Consensus       164 ~~~~lh~~~~~~~R  177 (178)
                      .++++|||-.|++|
T Consensus       447 EavaIHGGKDQedR  460 (610)
T KOG0341|consen  447 EAVAIHGGKDQEDR  460 (610)
T ss_pred             eeEEeecCcchhHH
Confidence            99999999999998

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

Probab=99.96  E-value=1.6e-29  Score=194.62  Aligned_cols=169  Identities=28%  Similarity=0.403  Sum_probs=155.0

Q ss_pred             HHhHHhccCCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcHH
Q 030396            6 VRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDF   85 (178)
Q Consensus         6 ~~q~~~l~~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~   85 (178)
                      .+|.+.++++.+|+|+|||||.++.-.+.+++.++-|+|+||||+|+++| |.++|+.|+-- ..+++|+++.|||||+.
T Consensus       334 ~eqie~lkrgveiiiatPgrlndL~~~n~i~l~siTYlVlDEADrMLDMg-FEpqIrkilld-iRPDRqtvmTSATWP~~  411 (629)
T KOG0336|consen  334 NEQIEDLKRGVEIIIATPGRLNDLQMDNVINLASITYLVLDEADRMLDMG-FEPQIRKILLD-IRPDRQTVMTSATWPEG  411 (629)
T ss_pred             hhHHHHHhcCceEEeeCCchHhhhhhcCeeeeeeeEEEEecchhhhhccc-ccHHHHHHhhh-cCCcceeeeecccCchH
Confidence            46889999999999999999999999999999999999999999999999 99999999988 88999999999999999


Q ss_pred             HHHHHHHhccCcEEEEEcCCcccc-CCceEEEEEcCChhhHHHHHHHHHHhc-CCCCEEEEeCCchHHHHHHHHhhhCCC
Q 030396           86 VEELARSIMHDAVRVIVGRKNTAS-ESIKQKLVFAGSEEGKLLALRQSFAES-LNPPVLIFVQSKDRAKELYGELAFDDI  163 (178)
Q Consensus        86 ~~~~~~~~~~~~~~v~~~~~~~~~-~~i~~~~~~~~~~~~k~~~l~~ll~~~-~~~~~lIF~~t~~~~~~l~~~L~~~g~  163 (178)
                      ++.+...|+++|..+.++.-+... ..++|.+ .+..+.+|.+.+..+++.+ .+.++||||..+..|+.|.+-|.-.|+
T Consensus       412 VrrLa~sY~Kep~~v~vGsLdL~a~~sVkQ~i-~v~~d~~k~~~~~~f~~~ms~ndKvIiFv~~K~~AD~LSSd~~l~gi  490 (629)
T KOG0336|consen  412 VRRLAQSYLKEPMIVYVGSLDLVAVKSVKQNI-IVTTDSEKLEIVQFFVANMSSNDKVIIFVSRKVMADHLSSDFCLKGI  490 (629)
T ss_pred             HHHHHHHhhhCceEEEecccceeeeeeeeeeE-EecccHHHHHHHHHHHHhcCCCceEEEEEechhhhhhccchhhhccc
Confidence            999999999999999888766554 4566666 7778888999999998865 467999999999999999999999999


Q ss_pred             ceEeeecCCCcccc
Q 030396          164 RAGVIHSDLSQTQV  177 (178)
Q Consensus       164 ~~~~lh~~~~~~~R  177 (178)
                      .+-.+||+.+|.+|
T Consensus       491 ~~q~lHG~r~Q~Dr  504 (629)
T KOG0336|consen  491 SSQSLHGNREQSDR  504 (629)
T ss_pred             chhhccCChhhhhH
Confidence            99999999999876

>KOG0346 consensus RNA helicase [RNA processing and modification]

Probab=99.96  E-value=4.4e-29  Score=193.32  Aligned_cols=166  Identities=25%  Similarity=0.270  Sum_probs=151.2

Q ss_pred             HhccCCCcEEEeCcHHHHHHHHcCC-CCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcHHHHH
Q 030396           10 DLSKFSCDILISTPLRLRLAIRRKK-IDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEE   88 (178)
Q Consensus        10 ~~l~~~~~Iii~TP~~l~~~l~~~~-~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~~~~   88 (178)
                      .+|...|+||||||++++.++..+. ..+..++++|+||||.+++-| |.+++..+.++ +|...|.+++|||++.++..
T Consensus       140 ~~L~d~pdIvV~TP~~ll~~~~~~~~~~~~~l~~LVvDEADLllsfG-Yeedlk~l~~~-LPr~~Q~~LmSATl~dDv~~  217 (569)
T KOG0346|consen  140 VALMDLPDIVVATPAKLLRHLAAGVLEYLDSLSFLVVDEADLLLSFG-YEEDLKKLRSH-LPRIYQCFLMSATLSDDVQA  217 (569)
T ss_pred             HHHccCCCeEEeChHHHHHHHhhccchhhhheeeEEechhhhhhhcc-cHHHHHHHHHh-CCchhhheeehhhhhhHHHH
Confidence            5777899999999999999999987 678999999999999999999 99999999999 89999999999999999999


Q ss_pred             HHHHhccCcEEEEEcCCccc-cCCceEEEEEcCChhhHHHHHHHHHH-hcCCCCEEEEeCCchHHHHHHHHhhhCCCceE
Q 030396           89 LARSIMHDAVRVIVGRKNTA-SESIKQKLVFAGSEEGKLLALRQSFA-ESLNPPVLIFVQSKDRAKELYGELAFDDIRAG  166 (178)
Q Consensus        89 ~~~~~~~~~~~v~~~~~~~~-~~~i~~~~~~~~~~~~k~~~l~~ll~-~~~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~  166 (178)
                      +-..++++|..+.+...+.. ++.+.|+++.|. +.+|+..+..+++ +...+++|||+||..+|.+|.-.|.+.|++.+
T Consensus       218 LKkL~l~nPviLkl~e~el~~~dqL~Qy~v~cs-e~DKflllyallKL~LI~gKsliFVNtIdr~YrLkLfLeqFGiksc  296 (569)
T KOG0346|consen  218 LKKLFLHNPVILKLTEGELPNPDQLTQYQVKCS-EEDKFLLLYALLKLRLIRGKSLIFVNTIDRCYRLKLFLEQFGIKSC  296 (569)
T ss_pred             HHHHhccCCeEEEeccccCCCcccceEEEEEec-cchhHHHHHHHHHHHHhcCceEEEEechhhhHHHHHHHHHhCcHhh
Confidence            99999999999888655544 466777777665 7889999999998 55689999999999999999999999999999


Q ss_pred             eeecCCCccccC
Q 030396          167 VIHSDLSQTQVF  178 (178)
Q Consensus       167 ~lh~~~~~~~R~  178 (178)
                      ++.|+||.+.|+
T Consensus       297 iLNseLP~NSR~  308 (569)
T KOG0346|consen  297 ILNSELPANSRC  308 (569)
T ss_pred             hhcccccccchh
Confidence            999999999885

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

Probab=99.96  E-value=2.1e-28  Score=200.99  Aligned_cols=169  Identities=25%  Similarity=0.368  Sum_probs=147.3

Q ss_pred             hHHhHHhccCCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcH
Q 030396            5 LVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPD   84 (178)
Q Consensus         5 ~~~q~~~l~~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~   84 (178)
                      ...|...+..+++|+|||||+|.+++.++.+++++++++|+||||.|+++| |.+.+..|++. + ++.|++++|||+++
T Consensus       236 ~~~q~~~l~~~~~IiV~TPgrL~~~l~~~~~~l~~v~~lViDEad~ml~~g-f~~~i~~i~~~-l-~~~q~l~~SATl~~  312 (518)
T PLN00206        236 MPQQLYRIQQGVELIVGTPGRLIDLLSKHDIELDNVSVLVLDEVDCMLERG-FRDQVMQIFQA-L-SQPQVLLFSATVSP  312 (518)
T ss_pred             hHHHHHHhcCCCCEEEECHHHHHHHHHcCCccchheeEEEeecHHHHhhcc-hHHHHHHHHHh-C-CCCcEEEEEeeCCH
Confidence            345667778899999999999999999999999999999999999999999 99999999998 4 47899999999999


Q ss_pred             HHHHHHHHhccCcEEEEEcCCccccCCceEEEEEcCChhhHHHHHHHHHHhcC--CCCEEEEeCCchHHHHHHHHhhh-C
Q 030396           85 FVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESL--NPPVLIFVQSKDRAKELYGELAF-D  161 (178)
Q Consensus        85 ~~~~~~~~~~~~~~~v~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~--~~~~lIF~~t~~~~~~l~~~L~~-~  161 (178)
                      .+..+...++.++..+...........+.+.++.+ ....|...+.+++....  ..++||||||+..|+.++..|.. .
T Consensus       313 ~v~~l~~~~~~~~~~i~~~~~~~~~~~v~q~~~~~-~~~~k~~~l~~~l~~~~~~~~~~iVFv~s~~~a~~l~~~L~~~~  391 (518)
T PLN00206        313 EVEKFASSLAKDIILISIGNPNRPNKAVKQLAIWV-ETKQKKQKLFDILKSKQHFKPPAVVFVSSRLGADLLANAITVVT  391 (518)
T ss_pred             HHHHHHHHhCCCCEEEEeCCCCCCCcceeEEEEec-cchhHHHHHHHHHHhhcccCCCEEEEcCCchhHHHHHHHHhhcc
Confidence            99999999999999888877666666777777655 44557778888887532  46899999999999999999975 6


Q ss_pred             CCceEeeecCCCcccc
Q 030396          162 DIRAGVIHSDLSQTQV  177 (178)
Q Consensus       162 g~~~~~lh~~~~~~~R  177 (178)
                      |+++..+||+|++++|
T Consensus       392 g~~~~~~Hg~~~~~eR  407 (518)
T PLN00206        392 GLKALSIHGEKSMKER  407 (518)
T ss_pred             CcceEEeeCCCCHHHH
Confidence            9999999999999887

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

Probab=99.96  E-value=5e-29  Score=194.21  Aligned_cols=163  Identities=26%  Similarity=0.336  Sum_probs=147.6

Q ss_pred             ccCCCcEEEeCcHHHHHHHHcC--CCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcHHHHHH
Q 030396           12 SKFSCDILISTPLRLRLAIRRK--KIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEEL   89 (178)
Q Consensus        12 l~~~~~Iii~TP~~l~~~l~~~--~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~~~~~   89 (178)
                      ..++|+|+|||||||.+++.+.  .++++++.++|+||||+|++.| |...++.|++. +|.++++.+||||....+.++
T Consensus       128 kee~~nIlVgTPGRL~di~~~~~~~l~~rsLe~LVLDEADrLldmg-Fe~~~n~ILs~-LPKQRRTGLFSATq~~~v~dL  205 (567)
T KOG0345|consen  128 KEEGPNILVGTPGRLLDILQREAEKLSFRSLEILVLDEADRLLDMG-FEASVNTILSF-LPKQRRTGLFSATQTQEVEDL  205 (567)
T ss_pred             HHhCCcEEEeCchhHHHHHhchhhhccccccceEEecchHhHhccc-HHHHHHHHHHh-cccccccccccchhhHHHHHH
Confidence            3478999999999999999874  4567799999999999999999 99999999999 999999999999999999999


Q ss_pred             HHHhccCcEEEEEcCCcc--ccCCceEEEEEcCChhhHHHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhhhC--CCce
Q 030396           90 ARSIMHDAVRVIVGRKNT--ASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFD--DIRA  165 (178)
Q Consensus        90 ~~~~~~~~~~v~~~~~~~--~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~~~--g~~~  165 (178)
                      ....++||..|.+...+.  +|..+.-+|..| +...|...+.+++......++|||+.|.+.++.-...|...  +.++
T Consensus       206 ~raGLRNpv~V~V~~k~~~~tPS~L~~~Y~v~-~a~eK~~~lv~~L~~~~~kK~iVFF~TCasVeYf~~~~~~~l~~~~i  284 (567)
T KOG0345|consen  206 ARAGLRNPVRVSVKEKSKSATPSSLALEYLVC-EADEKLSQLVHLLNNNKDKKCIVFFPTCASVEYFGKLFSRLLKKREI  284 (567)
T ss_pred             HHhhccCceeeeecccccccCchhhcceeeEe-cHHHHHHHHHHHHhccccccEEEEecCcchHHHHHHHHHHHhCCCcE
Confidence            999999999998876665  787888878666 66679999999999999999999999999999999998654  6799


Q ss_pred             EeeecCCCcccc
Q 030396          166 GVIHSDLSQTQV  177 (178)
Q Consensus       166 ~~lh~~~~~~~R  177 (178)
                      ..+||.|.+.+|
T Consensus       285 ~~iHGK~~q~~R  296 (567)
T KOG0345|consen  285 FSIHGKMSQKAR  296 (567)
T ss_pred             EEecchhcchhH
Confidence            999999999887

>KOG0347 consensus RNA helicase [RNA processing and modification]

Probab=99.96  E-value=3.9e-30  Score=203.65  Aligned_cols=171  Identities=25%  Similarity=0.284  Sum_probs=147.0

Q ss_pred             hHHhHHhccCCCcEEEeCcHHHHHHHHcCCC---CCCCeeEEEEeccccccccCCChhhHHHHHhhCC----CCCceEEE
Q 030396            5 LVRSTDLSKFSCDILISTPLRLRLAIRRKKI---DLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACS----NPSIVRSL   77 (178)
Q Consensus         5 ~~~q~~~l~~~~~Iii~TP~~l~~~l~~~~~---~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~----~~~~q~i~   77 (178)
                      .++|.++|+..|+|||+||||||+++..++.   +++.++++|+||+|+|++.| +.+.+..|+..+.    +..+|+++
T Consensus       303 vqKQqRlL~~~p~IVVATPGRlweli~e~n~~l~~~k~vkcLVlDEaDRmvekg-hF~Els~lL~~L~e~~~~~qrQTlV  381 (731)
T KOG0347|consen  303 VQKQQRLLNQRPDIVVATPGRLWELIEEDNTHLGNFKKVKCLVLDEADRMVEKG-HFEELSKLLKHLNEEQKNRQRQTLV  381 (731)
T ss_pred             HHHHHHHHhcCCCEEEecchHHHHHHHhhhhhhhhhhhceEEEEccHHHHhhhc-cHHHHHHHHHHhhhhhcccccceEE
Confidence            5789999999999999999999999988765   68999999999999999999 8888999988842    35689999


Q ss_pred             EeecCcH---------------------HHHHHHHH--hccCcEEEEEcCCccccCCceEEEEEcCChhhHHHHHHHHHH
Q 030396           78 FSATLPD---------------------FVEELARS--IMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFA  134 (178)
Q Consensus        78 ~SAT~~~---------------------~~~~~~~~--~~~~~~~v~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~  134 (178)
                      ||||++-                     .+..++..  +...|.++++.+...+...+.+..+.| +..+|..+|..+|.
T Consensus       382 FSATlt~~~~~~~~~~~k~~~k~~~~~~kiq~Lmk~ig~~~kpkiiD~t~q~~ta~~l~Es~I~C-~~~eKD~ylyYfl~  460 (731)
T KOG0347|consen  382 FSATLTLVLQQPLSSSRKKKDKEDELNAKIQHLMKKIGFRGKPKIIDLTPQSATASTLTESLIEC-PPLEKDLYLYYFLT  460 (731)
T ss_pred             EEEEeehhhcChhHHhhhccchhhhhhHHHHHHHHHhCccCCCeeEecCcchhHHHHHHHHhhcC-CccccceeEEEEEe
Confidence            9999873                     12333433  344678899988888888888888888 44567788888888


Q ss_pred             hcCCCCEEEEeCCchHHHHHHHHhhhCCCceEeeecCCCccccC
Q 030396          135 ESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQVF  178 (178)
Q Consensus       135 ~~~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~~~~~~R~  178 (178)
                      ++ ++++|||||++..+..|+.+|...+++...+|+.|.|.+|+
T Consensus       461 ry-PGrTlVF~NsId~vKRLt~~L~~L~i~p~~LHA~M~QKqRL  503 (731)
T KOG0347|consen  461 RY-PGRTLVFCNSIDCVKRLTVLLNNLDIPPLPLHASMIQKQRL  503 (731)
T ss_pred             ec-CCceEEEechHHHHHHHHHHHhhcCCCCchhhHHHHHHHHH
Confidence            88 89999999999999999999999999999999999999985

>PTZ00424 helicase 45; Provisional

Probab=99.96  E-value=2.9e-27  Score=189.00  Aligned_cols=169  Identities=24%  Similarity=0.382  Sum_probs=151.9

Q ss_pred             HhHHhccCCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcHHH
Q 030396            7 RSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFV   86 (178)
Q Consensus         7 ~q~~~l~~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~~   86 (178)
                      ++.+.+.++++|+||||+++.+++..+...+++++++|+||+|.+++.+ +...+..+++. .+.+.|++++|||+|+++
T Consensus       138 ~~~~~~~~~~~Ivv~Tp~~l~~~l~~~~~~l~~i~lvViDEah~~~~~~-~~~~~~~i~~~-~~~~~~~i~~SAT~~~~~  215 (401)
T PTZ00424        138 DDINKLKAGVHMVVGTPGRVYDMIDKRHLRVDDLKLFILDEADEMLSRG-FKGQIYDVFKK-LPPDVQVALFSATMPNEI  215 (401)
T ss_pred             HHHHHHcCCCCEEEECcHHHHHHHHhCCcccccccEEEEecHHHHHhcc-hHHHHHHHHhh-CCCCcEEEEEEecCCHHH
Confidence            4555667789999999999999999888889999999999999999988 89999999999 788999999999999999


Q ss_pred             HHHHHHhccCcEEEEEcCCccccCCceEEEEEcCChhhHHHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhhhCCCceE
Q 030396           87 EELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDIRAG  166 (178)
Q Consensus        87 ~~~~~~~~~~~~~v~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~  166 (178)
                      ..+...++.+|..+..........++.++++.+.....+...+.+++......++||||+|++.|+.++..|.+.|+.+.
T Consensus       216 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~ivF~~t~~~~~~l~~~l~~~~~~~~  295 (401)
T PTZ00424        216 LELTTKFMRDPKRILVKKDELTLEGIRQFYVAVEKEEWKFDTLCDLYETLTITQAIIYCNTRRKVDYLTKKMHERDFTVS  295 (401)
T ss_pred             HHHHHHHcCCCEEEEeCCCCcccCCceEEEEecChHHHHHHHHHHHHHhcCCCeEEEEecCcHHHHHHHHHHHHCCCcEE
Confidence            99999999999888877767777788888877766666888888888877788999999999999999999999999999


Q ss_pred             eeecCCCcccc
Q 030396          167 VIHSDLSQTQV  177 (178)
Q Consensus       167 ~lh~~~~~~~R  177 (178)
                      .+||+|++++|
T Consensus       296 ~~h~~~~~~~R  306 (401)
T PTZ00424        296 CMHGDMDQKDR  306 (401)
T ss_pred             EEeCCCCHHHH
Confidence            99999999887

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.96  E-value=2.3e-27  Score=193.30  Aligned_cols=170  Identities=27%  Similarity=0.386  Sum_probs=148.6

Q ss_pred             HHhHHhc-cCCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCC-CCceEEEEeecCc
Q 030396            6 VRSTDLS-KFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSN-PSIVRSLFSATLP   83 (178)
Q Consensus         6 ~~q~~~l-~~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~-~~~q~i~~SAT~~   83 (178)
                      ..|.+.+ ++.++|+|+||++|++++..+...+++++++|+||+|.+++.+ |.+.+..|++.+.. .+.|++++|||++
T Consensus       203 ~~~~~~~~~~~~~Iiv~TP~~Ll~~~~~~~~~l~~l~~lViDEah~l~~~~-~~~~l~~i~~~~~~~~~~q~i~~SAT~~  281 (475)
T PRK01297        203 DKQLKQLEARFCDILVATPGRLLDFNQRGEVHLDMVEVMVLDEADRMLDMG-FIPQVRQIIRQTPRKEERQTLLFSATFT  281 (475)
T ss_pred             HHHHHHHhCCCCCEEEECHHHHHHHHHcCCcccccCceEEechHHHHHhcc-cHHHHHHHHHhCCCCCCceEEEEEeecC
Confidence            3455544 3579999999999999999888899999999999999999999 99999999998422 3689999999999


Q ss_pred             HHHHHHHHHhccCcEEEEEcCCccccCCceEEEEEcCChhhHHHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhhhCCC
Q 030396           84 DFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDI  163 (178)
Q Consensus        84 ~~~~~~~~~~~~~~~~v~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~~~g~  163 (178)
                      .++..+...++.+|..+.+.........+.+.++.+ ...+|...+..++......++||||+++++|+.++..|...|+
T Consensus       282 ~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~-~~~~k~~~l~~ll~~~~~~~~IVF~~s~~~~~~l~~~L~~~~~  360 (475)
T PRK01297        282 DDVMNLAKQWTTDPAIVEIEPENVASDTVEQHVYAV-AGSDKYKLLYNLVTQNPWERVMVFANRKDEVRRIEERLVKDGI  360 (475)
T ss_pred             HHHHHHHHHhccCCEEEEeccCcCCCCcccEEEEEe-cchhHHHHHHHHHHhcCCCeEEEEeCCHHHHHHHHHHHHHcCC
Confidence            999999999999999888877776667777777655 4456888899999887778999999999999999999999999


Q ss_pred             ceEeeecCCCcccc
Q 030396          164 RAGVIHSDLSQTQV  177 (178)
Q Consensus       164 ~~~~lh~~~~~~~R  177 (178)
                      ++..+||+|++++|
T Consensus       361 ~~~~~~g~~~~~~R  374 (475)
T PRK01297        361 NAAQLSGDVPQHKR  374 (475)
T ss_pred             CEEEEECCCCHHHH
Confidence            99999999999887

>KOG0340 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.94  E-value=3.6e-27  Score=178.52  Aligned_cols=171  Identities=21%  Similarity=0.262  Sum_probs=148.3

Q ss_pred             hHHhHHhccCCCcEEEeCcHHHHHHHHcC----CCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEee
Q 030396            5 LVRSTDLSKFSCDILISTPLRLRLAIRRK----KIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSA   80 (178)
Q Consensus         5 ~~~q~~~l~~~~~Iii~TP~~l~~~l~~~----~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SA   80 (178)
                      ...|...|..+||+||+||||+.+++..+    ..-+++++++|+||||.+++.+ |...++.|.+. +|..+|+.+|||
T Consensus       115 ~i~qa~~L~~rPHvVvatPGRlad~l~sn~~~~~~~~~rlkflVlDEADrvL~~~-f~d~L~~i~e~-lP~~RQtLlfSA  192 (442)
T KOG0340|consen  115 MIMQAAILSDRPHVVVATPGRLADHLSSNLGVCSWIFQRLKFLVLDEADRVLAGC-FPDILEGIEEC-LPKPRQTLLFSA  192 (442)
T ss_pred             HhhhhhhcccCCCeEecCccccccccccCCccchhhhhceeeEEecchhhhhccc-hhhHHhhhhcc-CCCccceEEEEe
Confidence            45677788899999999999999999875    2348999999999999999998 99999999999 888899999999


Q ss_pred             cCcHHHHHHHHHhccC--cEEEEEcCCccccCCceEEEEEcCChhhHHHHHHHHHHhcC---CCCEEEEeCCchHHHHHH
Q 030396           81 TLPDFVEELARSIMHD--AVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESL---NPPVLIFVQSKDRAKELY  155 (178)
Q Consensus        81 T~~~~~~~~~~~~~~~--~~~v~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~---~~~~lIF~~t~~~~~~l~  155 (178)
                      |+++.+.++...-...  +..+...+....++.+.+.|+.+ +...|..++..++....   ...++||+||...|+.|+
T Consensus       193 Titd~i~ql~~~~i~k~~a~~~e~~~~vstvetL~q~yI~~-~~~vkdaYLv~~Lr~~~~~~~~simIFvnttr~cQ~l~  271 (442)
T KOG0340|consen  193 TITDTIKQLFGCPITKSIAFELEVIDGVSTVETLYQGYILV-SIDVKDAYLVHLLRDFENKENGSIMIFVNTTRECQLLS  271 (442)
T ss_pred             ehhhHHHHhhcCCcccccceEEeccCCCCchhhhhhheeec-chhhhHHHHHHHHhhhhhccCceEEEEeehhHHHHHHH
Confidence            9999888876665554  56666667778888899999887 55568899999997543   567999999999999999


Q ss_pred             HHhhhCCCceEeeecCCCccccC
Q 030396          156 GELAFDDIRAGVIHSDLSQTQVF  178 (178)
Q Consensus       156 ~~L~~~g~~~~~lh~~~~~~~R~  178 (178)
                      ..|...++.+.++||.|+|.+|+
T Consensus       272 ~~l~~le~r~~~lHs~m~Q~eR~  294 (442)
T KOG0340|consen  272 MTLKNLEVRVVSLHSQMPQKERL  294 (442)
T ss_pred             HHHhhhceeeeehhhcchHHHHH
Confidence            99999999999999999999984

>KOG0334 consensus RNA helicase [RNA processing and modification]

Probab=99.94  E-value=1.7e-26  Score=194.00  Aligned_cols=172  Identities=28%  Similarity=0.455  Sum_probs=157.9

Q ss_pred             HhHHhHHhccCCCcEEEeCcHHHHHHHHcC---CCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEee
Q 030396            4 ELVRSTDLSKFSCDILISTPLRLRLAIRRK---KIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSA   80 (178)
Q Consensus         4 ~~~~q~~~l~~~~~Iii~TP~~l~~~l~~~---~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SA   80 (178)
                      ...+|+..+++++.|+|+||||..+++..+   ..++.++.++|+||||+|++.+ |.|++..|++. +++.+|+++|||
T Consensus       477 ~~~~qiaelkRg~eIvV~tpGRmiD~l~~n~grvtnlrR~t~lv~deaDrmfdmg-fePq~~~Ii~n-lrpdrQtvlfSa  554 (997)
T KOG0334|consen  477 GISQQIAELKRGAEIVVCTPGRMIDILCANSGRVTNLRRVTYLVLDEADRMFDMG-FEPQITRILQN-LRPDRQTVLFSA  554 (997)
T ss_pred             cHHHHHHHHhcCCceEEeccchhhhhHhhcCCccccccccceeeechhhhhheec-cCcccchHHhh-cchhhhhhhhhh
Confidence            357899999999999999999999998643   4567777899999999999999 99999999999 899999999999


Q ss_pred             cCcHHHHHHHHHhccCcEEEEEcCCccccCCceEEEEEcCChhhHHHHHHHHHHh-cCCCCEEEEeCCchHHHHHHHHhh
Q 030396           81 TLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAE-SLNPPVLIFVQSKDRAKELYGELA  159 (178)
Q Consensus        81 T~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~-~~~~~~lIF~~t~~~~~~l~~~L~  159 (178)
                      |||..++.+.+..++-|..+.+.........+.+.+..+..++.|+..|.++|.. ....++||||.+...|..+...|.
T Consensus       555 tfpr~m~~la~~vl~~Pveiiv~~~svV~k~V~q~v~V~~~e~eKf~kL~eLl~e~~e~~~tiiFv~~qe~~d~l~~~L~  634 (997)
T KOG0334|consen  555 TFPRSMEALARKVLKKPVEIIVGGRSVVCKEVTQVVRVCAIENEKFLKLLELLGERYEDGKTIIFVDKQEKADALLRDLQ  634 (997)
T ss_pred             hhhHHHHHHHHHhhcCCeeEEEccceeEeccceEEEEEecCchHHHHHHHHHHHHHhhcCCEEEEEcCchHHHHHHHHHH
Confidence            9999999999999999999999888888889999998887689999999999984 457899999999999999999999


Q ss_pred             hCCCceEeeecCCCcccc
Q 030396          160 FDDIRAGVIHSDLSQTQV  177 (178)
Q Consensus       160 ~~g~~~~~lh~~~~~~~R  177 (178)
                      +.||+|..+||+.+|.+|
T Consensus       635 ~ag~~~~slHGgv~q~dR  652 (997)
T KOG0334|consen  635 KAGYNCDSLHGGVDQHDR  652 (997)
T ss_pred             hcCcchhhhcCCCchHHH
Confidence            999999999999999987

>KOG0337 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.94  E-value=2.9e-26  Score=176.85  Aligned_cols=171  Identities=28%  Similarity=0.311  Sum_probs=155.6

Q ss_pred             HhHHhHHhccCCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCc
Q 030396            4 ELVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLP   83 (178)
Q Consensus         4 ~~~~q~~~l~~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~   83 (178)
                      .+.+|-..|..+||||++|||++..+.-.-.+.++++.|+||||+|.+++.| |.+++.+++.. ++.++|+++||||+|
T Consensus       129 ~~eeqf~~l~~npDii~ATpgr~~h~~vem~l~l~sveyVVfdEadrlfemg-fqeql~e~l~r-l~~~~QTllfSatlp  206 (529)
T KOG0337|consen  129 SIEEQFILLNENPDIIIATPGRLLHLGVEMTLTLSSVEYVVFDEADRLFEMG-FQEQLHEILSR-LPESRQTLLFSATLP  206 (529)
T ss_pred             hHHHHHHHhccCCCEEEecCceeeeeehheeccccceeeeeehhhhHHHhhh-hHHHHHHHHHh-CCCcceEEEEeccCc
Confidence            4678888999999999999999998887777999999999999999999999 99999999999 899999999999999


Q ss_pred             HHHHHHHHHhccCcEEEEEcCCccccCCceEEEEEcCChhhHHHHHHHHHHhcC-CCCEEEEeCCchHHHHHHHHhhhCC
Q 030396           84 DFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESL-NPPVLIFVQSKDRAKELYGELAFDD  162 (178)
Q Consensus        84 ~~~~~~~~~~~~~~~~v~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~-~~~~lIF~~t~~~~~~l~~~L~~~g  162 (178)
                      ..+....+.-+.+|..|.++-+....+.+...+..+ ...+|..+|+.++.... .++++|||.|...++.+.+.|...|
T Consensus       207 ~~lv~fakaGl~~p~lVRldvetkise~lk~~f~~~-~~a~K~aaLl~il~~~~~~~~t~vf~~tk~hve~~~~ll~~~g  285 (529)
T KOG0337|consen  207 RDLVDFAKAGLVPPVLVRLDVETKISELLKVRFFRV-RKAEKEAALLSILGGRIKDKQTIVFVATKHHVEYVRGLLRDFG  285 (529)
T ss_pred             hhhHHHHHccCCCCceEEeehhhhcchhhhhheeee-ccHHHHHHHHHHHhccccccceeEEecccchHHHHHHHHHhcC
Confidence            999999999999999999888888888888888666 45568899999988653 5689999999999999999999999


Q ss_pred             CceEeeecCCCcccc
Q 030396          163 IRAGVIHSDLSQTQV  177 (178)
Q Consensus       163 ~~~~~lh~~~~~~~R  177 (178)
                      +.+..+-|.|.++-|
T Consensus       286 ~~~s~iysslD~~aR  300 (529)
T KOG0337|consen  286 GEGSDIYSSLDQEAR  300 (529)
T ss_pred             CCccccccccChHhh
Confidence            999999999998876

>KOG0348 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.93  E-value=2.1e-26  Score=182.19  Aligned_cols=170  Identities=28%  Similarity=0.374  Sum_probs=138.3

Q ss_pred             HHhHHhccCCCcEEEeCcHHHHHHHHc-CCCCCCCeeEEEEeccccccccCCChhhHHHHHhhC------------CCCC
Q 030396            6 VRSTDLSKFSCDILISTPLRLRLAIRR-KKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKAC------------SNPS   72 (178)
Q Consensus         6 ~~q~~~l~~~~~Iii~TP~~l~~~l~~-~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~------------~~~~   72 (178)
                      +++...|++|++|+|||||||.+++.+ .++.+++++|+||||+|++++.| |...|..|++.+            ++..
T Consensus       253 KSEKARLRKGiNILIgTPGRLvDHLknT~~i~~s~LRwlVlDEaDrlleLG-fekdit~Il~~v~~~~~~e~~~~~lp~q  331 (708)
T KOG0348|consen  253 KSEKARLRKGINILIGTPGRLVDHLKNTKSIKFSRLRWLVLDEADRLLELG-FEKDITQILKAVHSIQNAECKDPKLPHQ  331 (708)
T ss_pred             ccHHHHHhcCceEEEcCchHHHHHHhccchheeeeeeEEEecchhHHHhcc-chhhHHHHHHHHhhccchhcccccccHH
Confidence            445667789999999999999999987 78899999999999999999999 999999999884            1124


Q ss_pred             ceEEEEeecCcHHHHHHHHHhccCcEEEEEcCC-------------------------ccccCCceEEEEEcCChhhHHH
Q 030396           73 IVRSLFSATLPDFVEELARSIMHDAVRVIVGRK-------------------------NTASESIKQKLVFAGSEEGKLL  127 (178)
Q Consensus        73 ~q~i~~SAT~~~~~~~~~~~~~~~~~~v~~~~~-------------------------~~~~~~i~~~~~~~~~~~~k~~  127 (178)
                      .|.+++|||+.+.|..+....++||..+..+..                         ...|.++.|.|..+++. -+.-
T Consensus       332 ~q~mLlSATLtd~V~rLa~~sLkDpv~I~ld~s~~~~~p~~~a~~ev~~~~~~~~l~~~~iPeqL~qry~vVPpK-LRLV  410 (708)
T KOG0348|consen  332 LQNMLLSATLTDGVNRLADLSLKDPVYISLDKSHSQLNPKDKAVQEVDDGPAGDKLDSFAIPEQLLQRYTVVPPK-LRLV  410 (708)
T ss_pred             HHhHhhhhhhHHHHHHHhhccccCceeeeccchhhhcCcchhhhhhcCCcccccccccccCcHHhhhceEecCCc-hhHH
Confidence            789999999999999999999999998873111                         23456677888777654 3544


Q ss_pred             HHHHHH----HhcCCCCEEEEeCCchHHHHHHHHhhhC----------------------CCceEeeecCCCcccc
Q 030396          128 ALRQSF----AESLNPPVLIFVQSKDRAKELYGELAFD----------------------DIRAGVIHSDLSQTQV  177 (178)
Q Consensus       128 ~l~~ll----~~~~~~~~lIF~~t~~~~~~l~~~L~~~----------------------g~~~~~lh~~~~~~~R  177 (178)
                      .|..+|    +....+++|||+.+...+++=++.|.+.                      +.+++-+||+|+|++|
T Consensus       411 ~Laa~L~~~~k~~~~qk~iVF~S~~d~VeFHy~lf~~~l~~~~e~~s~~~~s~g~~~l~~~~k~~rLHGsm~QeeR  486 (708)
T KOG0348|consen  411 ALAALLLNKVKFEEKQKMIVFFSCSDSVEFHYSLFSEALLSHLEGSSGAPDSEGLPPLFMDLKFYRLHGSMEQEER  486 (708)
T ss_pred             HHHHHHHHHhhhhhhceeEEEEechhHHHHHHHHHHhhhhcccccccCCcccCCChhhhhcceEEEecCchhHHHH
Confidence            555544    3455779999999999999988887531                      3578999999999998

>KOG0329 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.93  E-value=2.9e-26  Score=167.35  Aligned_cols=146  Identities=24%  Similarity=0.350  Sum_probs=131.4

Q ss_pred             hHHhHHhccCCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcH
Q 030396            5 LVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPD   84 (178)
Q Consensus         5 ~~~q~~~l~~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~   84 (178)
                      +++-.+.+++.|+|+||||||++.+.+.+.+++++++.+|+||+|+|+++-..+.++++|.+. .|...|+++||||++.
T Consensus       151 Ikkdee~lk~~PhivVgTPGrilALvr~k~l~lk~vkhFvlDEcdkmle~lDMrRDvQEifr~-tp~~KQvmmfsatlsk  229 (387)
T KOG0329|consen  151 IKKDEELLKNCPHIVVGTPGRILALVRNRSLNLKNVKHFVLDECDKMLEQLDMRRDVQEIFRM-TPHEKQVMMFSATLSK  229 (387)
T ss_pred             ccccHHHHhCCCeEEEcCcHHHHHHHHhccCchhhcceeehhhHHHHHHHHHHHHHHHHHhhc-Ccccceeeeeeeecch
Confidence            566778889999999999999999999999999999999999999999886699999999999 9999999999999999


Q ss_pred             HHHHHHHHhccCcEEEEEcCC-ccccCCceEEEEEcCChhhHHHHHHHHHHhcCCCCEEEEeCCchHHH
Q 030396           85 FVEELARSIMHDAVRVIVGRK-NTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKDRAK  152 (178)
Q Consensus        85 ~~~~~~~~~~~~~~~v~~~~~-~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~~t~~~~~  152 (178)
                      +++..+.+|+.||..+.++.+ ..+..++-|+|+.. .+..|...+.++++.....+++||+.+..+..
T Consensus       230 eiRpvC~kFmQdPmEi~vDdE~KLtLHGLqQ~YvkL-ke~eKNrkl~dLLd~LeFNQVvIFvKsv~Rl~  297 (387)
T KOG0329|consen  230 EIRPVCHKFMQDPMEIFVDDEAKLTLHGLQQYYVKL-KENEKNRKLNDLLDVLEFNQVVIFVKSVQRLS  297 (387)
T ss_pred             hhHHHHHhhhcCchhhhccchhhhhhhhHHHHHHhh-hhhhhhhhhhhhhhhhhhcceeEeeehhhhhh
Confidence            999999999999988877665 45667787777666 56679999999999988999999999988854

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

Probab=99.91  E-value=5.6e-23  Score=173.42  Aligned_cols=163  Identities=13%  Similarity=0.168  Sum_probs=126.9

Q ss_pred             HhHHhHHhccCCCcEEEeCcHHHHHHHHcCCCC----------------CCCeeEEEEeccccccccCCChhhHHHHHhh
Q 030396            4 ELVRSTDLSKFSCDILISTPLRLRLAIRRKKID----------------LSRVEYLVLDEADKLFEVGNLLKHIDPVVKA   67 (178)
Q Consensus         4 ~~~~q~~~l~~~~~Iii~TP~~l~~~l~~~~~~----------------~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~   67 (178)
                      +...|.+.+..+|+|||||+    +++.++.++                +++++++|+||||  ++.+ |.+.+..|++.
T Consensus       124 ~~~~q~~~l~~~p~IIVgT~----D~i~sr~L~~gYg~~~~~~pi~ag~L~~v~~LVLDEAD--Ld~g-F~~~l~~Il~~  196 (844)
T TIGR02621       124 ADNDEWMLDPHRPAVIVGTV----DMIGSRLLFSGYGCGFKSRPLHAGFLGQDALIVHDEAH--LEPA-FQELLKQIMNE  196 (844)
T ss_pred             ChHHHHHhcCCCCcEEEECH----HHHcCCccccccccccccccchhhhhccceEEEEehhh--hccc-cHHHHHHHHHh
Confidence            35678888999999999995    666666652                7899999999999  6788 99999999997


Q ss_pred             C-CCC---CceEEEEeecCcHHHHHHHHHhccCcEEEEEcCCccccCCceEEEEEcCChhhHHHHHHHHH---HhcCCCC
Q 030396           68 C-SNP---SIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSF---AESLNPP  140 (178)
Q Consensus        68 ~-~~~---~~q~i~~SAT~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll---~~~~~~~  140 (178)
                      + .+.   .+|+++||||++.++......++.+|..+.+........++.+++ .+. ...|...+...+   .....++
T Consensus       197 l~rp~~~rprQtLLFSAT~p~ei~~l~~~~~~~p~~i~V~~~~l~a~ki~q~v-~v~-~e~Kl~~lv~~L~~ll~e~g~~  274 (844)
T TIGR02621       197 QQRPPDFLPLRVVELTATSRTDGPDRTTLLSAEDYKHPVLKKRLAAKKIVKLV-PPS-DEKFLSTMVKELNLLMKDSGGA  274 (844)
T ss_pred             cccCcccccceEEEEecCCCccHHHHHHHHccCCceeecccccccccceEEEE-ecC-hHHHHHHHHHHHHHHHhhCCCc
Confidence            3 133   269999999999988888888888887776665556666666643 443 333443333322   1234678


Q ss_pred             EEEEeCCchHHHHHHHHhhhCCCceEeeecCCCcccc
Q 030396          141 VLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQV  177 (178)
Q Consensus       141 ~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~~~~~~R  177 (178)
                      +||||||+++|+.+++.|.+.|+  ..+||+|++.+|
T Consensus       275 vLVF~NTv~~Aq~L~~~L~~~g~--~lLHG~m~q~dR  309 (844)
T TIGR02621       275 ILVFCRTVKHVRKVFAKLPKEKF--ELLTGTLRGAER  309 (844)
T ss_pred             EEEEECCHHHHHHHHHHHHhcCC--eEeeCCCCHHHH
Confidence            99999999999999999999987  999999999987

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.

>PRK09401 reverse gyrase; Reviewed

Probab=99.89  E-value=4.6e-22  Score=174.63  Aligned_cols=156  Identities=19%  Similarity=0.171  Sum_probs=124.4

Q ss_pred             HHhHHhcc-CCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccc-----------cCCCh-hhHHHHHhhCCCC-
Q 030396            6 VRSTDLSK-FSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFE-----------VGNLL-KHIDPVVKACSNP-   71 (178)
Q Consensus         6 ~~q~~~l~-~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~-----------~~~~~-~~i~~i~~~~~~~-   71 (178)
                      .++.+.++ +.++|+|||||+|.+++.  .+...+++++|+||||.+++           .| |. +++..+++. ++. 
T Consensus       169 ~~~~~~l~~~~~~IlV~Tp~rL~~~~~--~l~~~~~~~lVvDEaD~~L~~~k~id~~l~~lG-F~~~~i~~i~~~-i~~~  244 (1176)
T PRK09401        169 EEFLERLKEGDFDILVTTSQFLSKNFD--ELPKKKFDFVFVDDVDAVLKSSKNIDKLLYLLG-FSEEDIEKAMEL-IRLK  244 (1176)
T ss_pred             HHHHHHHhcCCCCEEEECHHHHHHHHH--hccccccCEEEEEChHHhhhcccchhhHHHhCC-CCHHHHHHHHHh-cccc
Confidence            33444455 469999999999999887  45667799999999999996           45 74 678888877 443 


Q ss_pred             -----------------------CceEEEEeecCcHH-HHHHHHHhccCcEEEEEcCCccccCCceEEEEEcCChhhHHH
Q 030396           72 -----------------------SIVRSLFSATLPDF-VEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLL  127 (178)
Q Consensus        72 -----------------------~~q~i~~SAT~~~~-~~~~~~~~~~~~~~v~~~~~~~~~~~i~~~~~~~~~~~~k~~  127 (178)
                                             ..|+++||||+++. +..   .++.++..+.++.......++.|.++.+.   +|..
T Consensus       245 ~~~~~~~~~i~~l~~~i~~~~~~~~q~ilfSAT~~~~~~~~---~l~~~ll~~~v~~~~~~~rnI~~~yi~~~---~k~~  318 (1176)
T PRK09401        245 RKYEEIYEKIRELEEKIAELKDKKGVLVVSSATGRPRGNRV---KLFRELLGFEVGSPVFYLRNIVDSYIVDE---DSVE  318 (1176)
T ss_pred             cccchhhhHHHHHHHhhhhcccCCceEEEEeCCCCccchHH---HHhhccceEEecCcccccCCceEEEEEcc---cHHH
Confidence                                   68999999999875 332   34456666677766667788999887654   5777


Q ss_pred             HHHHHHHhcCCCCEEEEeCCchH---HHHHHHHhhhCCCceEeeecCC
Q 030396          128 ALRQSFAESLNPPVLIFVQSKDR---AKELYGELAFDDIRAGVIHSDL  172 (178)
Q Consensus       128 ~l~~ll~~~~~~~~lIF~~t~~~---~~~l~~~L~~~g~~~~~lh~~~  172 (178)
                      .+.++++.. ..++||||+|+..   |+++++.|...|+++..+||+|
T Consensus       319 ~L~~ll~~l-~~~~LIFv~t~~~~~~ae~l~~~L~~~gi~v~~~hg~l  365 (1176)
T PRK09401        319 KLVELVKRL-GDGGLIFVPSDKGKEYAEELAEYLEDLGINAELAISGF  365 (1176)
T ss_pred             HHHHHHHhc-CCCEEEEEecccChHHHHHHHHHHHHCCCcEEEEeCcH
Confidence            888888876 4689999999888   9999999999999999999998

>KOG0349 consensus Putative DEAD-box RNA helicase DDX1 [RNA processing and modification]

Probab=99.89  E-value=4.6e-23  Score=160.30  Aligned_cols=171  Identities=20%  Similarity=0.185  Sum_probs=144.6

Q ss_pred             hHHhHHhccCCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCC------CCceEEEE
Q 030396            5 LVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSN------PSIVRSLF   78 (178)
Q Consensus         5 ~~~q~~~l~~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~------~~~q~i~~   78 (178)
                      .+.|.++++++.+|+||||||+.+++..+.+.+..++++|+||+|.++..+ +-+.|.+...+ ++      ...|.+++
T Consensus       329 ~r~Q~~ql~~g~~ivvGtpgRl~~~is~g~~~lt~crFlvlDead~lL~qg-y~d~I~r~h~q-ip~~tsdg~rlq~~vC  406 (725)
T KOG0349|consen  329 KRTQCKQLKDGTHIVVGTPGRLLQPISKGLVTLTHCRFLVLDEADLLLGQG-YDDKIYRFHGQ-IPHMTSDGFRLQSPVC  406 (725)
T ss_pred             hHHHHHHhhcCceeeecCchhhhhhhhccceeeeeeEEEEecchhhhhhcc-cHHHHHHHhcc-chhhhcCCccccccee
Confidence            567899999999999999999999999999999999999999999999999 88999998888 44      35799999


Q ss_pred             eecCcH-HHHHHHHHhccCcEEEEEcCCccccCCceEEEEEcCChhh---------------------------------
Q 030396           79 SATLPD-FVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEG---------------------------------  124 (178)
Q Consensus        79 SAT~~~-~~~~~~~~~~~~~~~v~~~~~~~~~~~i~~~~~~~~~~~~---------------------------------  124 (178)
                      |||+.. ++..+.++.++-|.||++..++..+..++|.+..+++.-+                                 
T Consensus       407 satlh~feVkk~~ervmhfptwVdLkgeD~vpetvHhvv~lv~p~~d~sw~~lr~~i~td~vh~kdn~~pg~~Spe~~s~  486 (725)
T KOG0349|consen  407 SATLHIFEVKKVGERVMHFPTWVDLKGEDLVPETVHHVVKLVCPSVDGSWCDLRQFIETDKVHTKDNLLPGQVSPENPSS  486 (725)
T ss_pred             eeEEeEEEeeehhhhhccCceeEecccccccchhhccceeecCCccCccHHHHhhhhccCCcccccccccccCCCCChhh
Confidence            999985 5888999999999999999999888888887765544310                                 


Q ss_pred             -----HHHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhhhCC---CceEeeecCCCcccc
Q 030396          125 -----KLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDD---IRAGVIHSDLSQTQV  177 (178)
Q Consensus       125 -----k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~~~g---~~~~~lh~~~~~~~R  177 (178)
                           |-++-...++++...++||||.|+.+|+.|...|.+.|   |.|.++||+..+.||
T Consensus       487 a~kilkgEy~v~ai~~h~mdkaiifcrtk~dcDnLer~~~qkgg~~~scvclhgDrkP~Er  547 (725)
T KOG0349|consen  487 ATKILKGEYGVVAIRRHAMDKAIIFCRTKQDCDNLERMMNQKGGKHYSCVCLHGDRKPDER  547 (725)
T ss_pred             hhHHhcCchhhhhhhhhccCceEEEEeccccchHHHHHHHHcCCccceeEEEecCCChhHH
Confidence                 22222334556667899999999999999999998764   799999999976665

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

Probab=99.87  E-value=3.5e-21  Score=163.60  Aligned_cols=164  Identities=18%  Similarity=0.150  Sum_probs=116.1

Q ss_pred             HhHHhccCCCcEEEeCcHHHHHHHHcC----CCCCCCeeEEEEeccccccccCCChhhHHHHHhhC------CCCCceEE
Q 030396            7 RSTDLSKFSCDILISTPLRLRLAIRRK----KIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKAC------SNPSIVRS   76 (178)
Q Consensus         7 ~q~~~l~~~~~Iii~TP~~l~~~l~~~----~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~------~~~~~q~i   76 (178)
                      +|.+.++++++|||+||+++...+...    ...+++++++|+||||.+.+ . |...+..+++.+      .+.+.|++
T Consensus       121 ~~r~~i~~~~~IivtTPd~L~~~~L~~~~~~~~~l~~l~~vViDEah~~~g-~-fg~~~~~il~rL~ri~~~~g~~~q~i  198 (742)
T TIGR03817       121 EERRWAREHARYVLTNPDMLHRGILPSHARWARFLRRLRYVVIDECHSYRG-V-FGSHVALVLRRLRRLCARYGASPVFV  198 (742)
T ss_pred             HHHHHHhcCCCEEEEChHHHHHhhccchhHHHHHHhcCCEEEEeChhhccC-c-cHHHHHHHHHHHHHHHHhcCCCCEEE
Confidence            455667778999999999987543211    12378999999999999965 3 666655554442      35678999


Q ss_pred             EEeecCcHHHHHHHHHhccCcEEEEEcCCccccCCceEEEEEcCC----------------hhhHHHHHHHHHHhcCCCC
Q 030396           77 LFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGS----------------EEGKLLALRQSFAESLNPP  140 (178)
Q Consensus        77 ~~SAT~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~i~~~~~~~~~----------------~~~k~~~l~~ll~~~~~~~  140 (178)
                      ++|||+++... .+..+++.|..+ +..+. .+....+..+..+.                ...+...+.++++.  ..+
T Consensus       199 ~~SATi~n~~~-~~~~l~g~~~~~-i~~~~-~~~~~~~~~~~~p~~~~~~~~~~~~~r~~~~~~~~~~l~~l~~~--~~~  273 (742)
T TIGR03817       199 LASATTADPAA-AASRLIGAPVVA-VTEDG-SPRGARTVALWEPPLTELTGENGAPVRRSASAEAADLLADLVAE--GAR  273 (742)
T ss_pred             EEecCCCCHHH-HHHHHcCCCeEE-ECCCC-CCcCceEEEEecCCccccccccccccccchHHHHHHHHHHHHHC--CCC
Confidence            99999998754 677788877554 33222 22222333322221                12466677777765  479


Q ss_pred             EEEEeCCchHHHHHHHHhhhC--------CCceEeeecCCCcccc
Q 030396          141 VLIFVQSKDRAKELYGELAFD--------DIRAGVIHSDLSQTQV  177 (178)
Q Consensus       141 ~lIF~~t~~~~~~l~~~L~~~--------g~~~~~lh~~~~~~~R  177 (178)
                      +||||||++.|+.++..|.+.        +.++..+||++++++|
T Consensus       274 ~IVF~~sr~~ae~l~~~l~~~l~~~~~~l~~~v~~~hgg~~~~eR  318 (742)
T TIGR03817       274 TLTFVRSRRGAELVAAIARRLLGEVDPDLAERVAAYRAGYLPEDR  318 (742)
T ss_pred             EEEEcCCHHHHHHHHHHHHHHHHhhccccccchhheecCCCHHHH
Confidence            999999999999999998753        6789999999999988

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.

>KOG0344 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.86  E-value=4e-22  Score=159.31  Aligned_cols=170  Identities=52%  Similarity=0.756  Sum_probs=157.9

Q ss_pred             HhHHhccCCCcEEEeCcHHHHHHHHcCC--CCCCCeeEEEEecccccccc-CCChhhHHHHHhhCCCCCceEEEEeecCc
Q 030396            7 RSTDLSKFSCDILISTPLRLRLAIRRKK--IDLSRVEYLVLDEADKLFEV-GNLLKHIDPVVKACSNPSIVRSLFSATLP   83 (178)
Q Consensus         7 ~q~~~l~~~~~Iii~TP~~l~~~l~~~~--~~~~~l~~lViDE~d~ll~~-~~~~~~i~~i~~~~~~~~~q~i~~SAT~~   83 (178)
                      ++.......++|+|+||-|+..++..+.  ++++.+.++|+||+|.+++. + |..++..|++.+..+...+-+||||++
T Consensus       254 k~a~~~~~k~dili~TP~ri~~~~~~~~~~idl~~V~~lV~dEaD~lfe~~~-f~~Qla~I~sac~s~~i~~a~FSat~~  332 (593)
T KOG0344|consen  254 KPAFLSDEKYDILISTPMRIVGLLGLGKLNIDLSKVEWLVVDEADLLFEPEF-FVEQLADIYSACQSPDIRVALFSATIS  332 (593)
T ss_pred             ccchhHHHHHHHHhcCHHHHHHHhcCCCccchhheeeeEeechHHhhhChhh-HHHHHHHHHHHhcCcchhhhhhhcccc
Confidence            4444555678999999999999998876  78999999999999999999 7 999999999998888888899999999


Q ss_pred             HHHHHHHHHhccCcEEEEEcCCccccCCceEEEEEcCChhhHHHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHh-hhCC
Q 030396           84 DFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGEL-AFDD  162 (178)
Q Consensus        84 ~~~~~~~~~~~~~~~~v~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L-~~~g  162 (178)
                      ..++++++....++..+.++..+.....+.|..++|.+...|+-.+.+++...-.+|++||+.+.++|..|...| ...+
T Consensus       333 ~~VEE~~~~i~~~~~~vivg~~~sa~~~V~QelvF~gse~~K~lA~rq~v~~g~~PP~lIfVQs~eRak~L~~~L~~~~~  412 (593)
T KOG0344|consen  333 VYVEEWAELIKSDLKRVIVGLRNSANETVDQELVFCGSEKGKLLALRQLVASGFKPPVLIFVQSKERAKQLFEELEIYDN  412 (593)
T ss_pred             HHHHHHHHHhhccceeEEEecchhHhhhhhhhheeeecchhHHHHHHHHHhccCCCCeEEEEecHHHHHHHHHHhhhccC
Confidence            999999999999999999998888888999999999999999999999999998999999999999999999999 8889


Q ss_pred             CceEeeecCCCcccc
Q 030396          163 IRAGVIHSDLSQTQV  177 (178)
Q Consensus       163 ~~~~~lh~~~~~~~R  177 (178)
                      +.+..+||+.++.+|
T Consensus       413 i~v~vIh~e~~~~qr  427 (593)
T KOG0344|consen  413 INVDVIHGERSQKQR  427 (593)
T ss_pred             cceeeEecccchhHH
Confidence            999999999999887

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=99.86  E-value=8.1e-21  Score=154.70  Aligned_cols=159  Identities=15%  Similarity=0.141  Sum_probs=114.9

Q ss_pred             cCCCcEEEeCcHHHHHHH-HcCCC-CCCCeeEEEEeccccccccC-CChhhHHHHH--hhCCCCCceEEEEeecCcHHHH
Q 030396           13 KFSCDILISTPLRLRLAI-RRKKI-DLSRVEYLVLDEADKLFEVG-NLLKHIDPVV--KACSNPSIVRSLFSATLPDFVE   87 (178)
Q Consensus        13 ~~~~~Iii~TP~~l~~~l-~~~~~-~~~~l~~lViDE~d~ll~~~-~~~~~i~~i~--~~~~~~~~q~i~~SAT~~~~~~   87 (178)
                      .+.++|+++||+++.... ....+ ...+++++|+||||.+.+|| .|++.+..+.  .. ..++.+++++|||.++.+.
T Consensus        99 ~~~~~il~~TPe~l~~~~~~~~~l~~~~~i~~iViDEaH~i~~~g~~fr~~~~~l~~l~~-~~~~~~~l~lTAT~~~~~~  177 (470)
T TIGR00614        99 DGKIKLLYVTPEKCSASNRLLQTLEERKGITLIAVDEAHCISQWGHDFRPDYKALGSLKQ-KFPNVPIMALTATASPSVR  177 (470)
T ss_pred             cCCCCEEEECHHHHcCchhHHHHHHhcCCcCEEEEeCCcccCccccccHHHHHHHHHHHH-HcCCCceEEEecCCCHHHH
Confidence            356899999999976422 11112 56889999999999999987 5778776652  22 2357889999999999887


Q ss_pred             HHHHHhcc--CcEEEEEcCCccccCCceEEEEEcCChhhHHHHHHHHHH-hcCCCCEEEEeCCchHHHHHHHHhhhCCCc
Q 030396           88 ELARSIMH--DAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFA-ESLNPPVLIFVQSKDRAKELYGELAFDDIR  164 (178)
Q Consensus        88 ~~~~~~~~--~~~~v~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~-~~~~~~~lIF~~t~~~~~~l~~~L~~~g~~  164 (178)
                      ..+...+.  +|..+...   ...+++...+..  ...+....+..++. ....+++||||+|+++|+.++..|...|++
T Consensus       178 ~di~~~l~l~~~~~~~~s---~~r~nl~~~v~~--~~~~~~~~l~~~l~~~~~~~~~IIF~~s~~~~e~la~~L~~~g~~  252 (470)
T TIGR00614       178 EDILRQLNLKNPQIFCTS---FDRPNLYYEVRR--KTPKILEDLLRFIRKEFKGKSGIIYCPSRKKSEQVTASLQNLGIA  252 (470)
T ss_pred             HHHHHHcCCCCCcEEeCC---CCCCCcEEEEEe--CCccHHHHHHHHHHHhcCCCceEEEECcHHHHHHHHHHHHhcCCC
Confidence            76666543  55444332   233444333322  22245566777776 444556799999999999999999999999


Q ss_pred             eEeeecCCCcccc
Q 030396          165 AGVIHSDLSQTQV  177 (178)
Q Consensus       165 ~~~lh~~~~~~~R  177 (178)
                      +..+||+|++++|
T Consensus       253 ~~~~H~~l~~~eR  265 (470)
T TIGR00614       253 AGAYHAGLEISAR  265 (470)
T ss_pred             eeEeeCCCCHHHH
Confidence            9999999999887

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

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

Probab=99.86  E-value=1.2e-20  Score=162.25  Aligned_cols=158  Identities=16%  Similarity=0.177  Sum_probs=115.2

Q ss_pred             CCCcEEEeCcHHHHH---HHHc-CCC-CCCCeeEEEEeccccccccC-CChhhHHHH--HhhCCCCCceEEEEeecCcHH
Q 030396           14 FSCDILISTPLRLRL---AIRR-KKI-DLSRVEYLVLDEADKLFEVG-NLLKHIDPV--VKACSNPSIVRSLFSATLPDF   85 (178)
Q Consensus        14 ~~~~Iii~TP~~l~~---~l~~-~~~-~~~~l~~lViDE~d~ll~~~-~~~~~i~~i--~~~~~~~~~q~i~~SAT~~~~   85 (178)
                      +.++||++|||+|..   ++.. ..+ ....+.+|||||||++.+|| .|++.+..+  +.. ..+..|++++|||.++.
T Consensus       551 g~~~ILyvTPERL~~~d~ll~~L~~L~~~~~LslIVIDEAHcVSqWGhDFRpdYr~L~~Lr~-~fp~vPilALTATAT~~  629 (1195)
T PLN03137        551 SKYKLLYVTPEKVAKSDSLLRHLENLNSRGLLARFVIDEAHCVSQWGHDFRPDYQGLGILKQ-KFPNIPVLALTATATAS  629 (1195)
T ss_pred             CCCCEEEEChHHhhcchHHHHHHHhhhhccccceeccCcchhhhhcccchHHHHHHHHHHHH-hCCCCCeEEEEecCCHH
Confidence            578999999999862   2221 111 24568999999999999998 788988874  444 33578899999999999


Q ss_pred             HHHHHHHhcc--CcEEEEEcCCccccCCceEEEEEcCChhhHHHHHHHHHHhc-CCCCEEEEeCCchHHHHHHHHhhhCC
Q 030396           86 VEELARSIMH--DAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAES-LNPPVLIFVQSKDRAKELYGELAFDD  162 (178)
Q Consensus        86 ~~~~~~~~~~--~~~~v~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~-~~~~~lIF~~t~~~~~~l~~~L~~~g  162 (178)
                      +.+.+...+.  ++..+.   .....+++...+  +.........+..++... ...+.||||+|+++|+.++..|...|
T Consensus       630 V~eDI~~~L~l~~~~vfr---~Sf~RpNL~y~V--v~k~kk~le~L~~~I~~~~~~esgIIYC~SRke~E~LAe~L~~~G  704 (1195)
T PLN03137        630 VKEDVVQALGLVNCVVFR---QSFNRPNLWYSV--VPKTKKCLEDIDKFIKENHFDECGIIYCLSRMDCEKVAERLQEFG  704 (1195)
T ss_pred             HHHHHHHHcCCCCcEEee---cccCccceEEEE--eccchhHHHHHHHHHHhcccCCCceeEeCchhHHHHHHHHHHHCC
Confidence            8876666554  333322   223344553333  223223345667777644 35689999999999999999999999


Q ss_pred             CceEeeecCCCcccc
Q 030396          163 IRAGVIHSDLSQTQV  177 (178)
Q Consensus       163 ~~~~~lh~~~~~~~R  177 (178)
                      +++..+||+|++++|
T Consensus       705 ika~~YHAGLs~eeR  719 (1195)
T PLN03137        705 HKAAFYHGSMDPAQR  719 (1195)
T ss_pred             CCeeeeeCCCCHHHH
Confidence            999999999999988

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=99.85  E-value=2.7e-20  Score=155.51  Aligned_cols=160  Identities=18%  Similarity=0.202  Sum_probs=121.6

Q ss_pred             ccCCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccC-CChhhHHHHHhhC-CCCCceEEEEeecCcHHHHHH
Q 030396           12 SKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVG-NLLKHIDPVVKAC-SNPSIVRSLFSATLPDFVEEL   89 (178)
Q Consensus        12 l~~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~-~~~~~i~~i~~~~-~~~~~q~i~~SAT~~~~~~~~   89 (178)
                      ..+.++|+++||+++......+.+...+++++|+||||.+.+|| .|++.+..+.... .-++.+++++|||.++.+...
T Consensus       100 ~~~~~~il~~tpe~l~~~~~~~~l~~~~l~~iViDEaH~i~~~g~~frp~y~~l~~l~~~~~~~~vi~lTAT~~~~~~~~  179 (591)
T TIGR01389       100 VNGELKLLYVAPERLEQDYFLNMLQRIPIALVAVDEAHCVSQWGHDFRPEYQRLGSLAERFPQVPRIALTATADAETRQD  179 (591)
T ss_pred             hCCCCCEEEEChhHhcChHHHHHHhcCCCCEEEEeCCcccccccCccHHHHHHHHHHHHhCCCCCEEEEEeCCCHHHHHH
Confidence            34678999999999976544444566789999999999999987 6888877764431 113455999999999998877


Q ss_pred             HHHhcc--CcEEEEEcCCccccCCceEEEEEcCChhhHHHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhhhCCCceEe
Q 030396           90 ARSIMH--DAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGV  167 (178)
Q Consensus        90 ~~~~~~--~~~~v~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~  167 (178)
                      +..++.  ++..+.   .....+++...+.   ....+...+.+++......++||||+|++.|+.+++.|...|+++..
T Consensus       180 i~~~l~~~~~~~~~---~~~~r~nl~~~v~---~~~~~~~~l~~~l~~~~~~~~IIf~~sr~~~e~la~~L~~~g~~~~~  253 (591)
T TIGR01389       180 IRELLRLADANEFI---TSFDRPNLRFSVV---KKNNKQKFLLDYLKKHRGQSGIIYASSRKKVEELAERLESQGISALA  253 (591)
T ss_pred             HHHHcCCCCCCeEe---cCCCCCCcEEEEE---eCCCHHHHHHHHHHhcCCCCEEEEECcHHHHHHHHHHHHhCCCCEEE
Confidence            777665  333332   2233344433332   33456778888888777789999999999999999999999999999


Q ss_pred             eecCCCcccc
Q 030396          168 IHSDLSQTQV  177 (178)
Q Consensus       168 lh~~~~~~~R  177 (178)
                      +||+|+.++|
T Consensus       254 ~H~~l~~~~R  263 (591)
T TIGR01389       254 YHAGLSNKVR  263 (591)
T ss_pred             EECCCCHHHH
Confidence            9999999887

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.

>PRK09751 putative ATP-dependent helicase Lhr; Provisional

Probab=99.85  E-value=3e-20  Score=164.67  Aligned_cols=166  Identities=21%  Similarity=0.231  Sum_probs=109.5

Q ss_pred             HhHHhccCCCcEEEeCcHHHHHHHHcC-CCCCCCeeEEEEeccccccccC---CChhhHHHHHhhCCCCCceEEEEeecC
Q 030396            7 RSTDLSKFSCDILISTPLRLRLAIRRK-KIDLSRVEYLVLDEADKLFEVG---NLLKHIDPVVKACSNPSIVRSLFSATL   82 (178)
Q Consensus         7 ~q~~~l~~~~~Iii~TP~~l~~~l~~~-~~~~~~l~~lViDE~d~ll~~~---~~~~~i~~i~~~~~~~~~q~i~~SAT~   82 (178)
                      ++.++++++|+|||+|||+|..++.++ ...+++++++|+||+|.+++..   .+...++++... .+.+.|+|++|||+
T Consensus        91 eR~rll~~ppdILVTTPEsL~~LLtsk~r~~L~~Vr~VIVDE~H~L~g~kRG~~Lel~LeRL~~l-~~~~~QrIgLSATI  169 (1490)
T PRK09751         91 ERSKLTRNPPDILITTPESLYLMLTSRARETLRGVETVIIDEVHAVAGSKRGAHLALSLERLDAL-LHTSAQRIGLSATV  169 (1490)
T ss_pred             HHHHHhcCCCCEEEecHHHHHHHHhhhhhhhhccCCEEEEecHHHhcccccccHHHHHHHHHHHh-CCCCCeEEEEEeeC
Confidence            444567788999999999999988654 3468999999999999998753   233455555555 66789999999999


Q ss_pred             cHHHHHHHHHhcc--CcEEEEEcCCccccCCceEEEEEcCChhh----------------H----HHHHHHHHHh-cCCC
Q 030396           83 PDFVEELARSIMH--DAVRVIVGRKNTASESIKQKLVFAGSEEG----------------K----LLALRQSFAE-SLNP  139 (178)
Q Consensus        83 ~~~~~~~~~~~~~--~~~~v~~~~~~~~~~~i~~~~~~~~~~~~----------------k----~~~l~~ll~~-~~~~  139 (178)
                      ++. +++. .|+.  +|..+.. ........+. .++...+..+                .    -.....++.. ....
T Consensus       170 ~n~-eevA-~~L~g~~pv~Iv~-~~~~r~~~l~-v~vp~~d~~~~~~~~~~~~~~~~~~r~~~i~~~v~~~il~~i~~~~  245 (1490)
T PRK09751        170 RSA-SDVA-AFLGGDRPVTVVN-PPAMRHPQIR-IVVPVANMDDVSSVASGTGEDSHAGREGSIWPYIETGILDEVLRHR  245 (1490)
T ss_pred             CCH-HHHH-HHhcCCCCEEEEC-CCCCcccceE-EEEecCchhhccccccccccccchhhhhhhhHHHHHHHHHHHhcCC
Confidence            974 4544 4543  3554433 2222222332 2222211100                0    0111122322 2357


Q ss_pred             CEEEEeCCchHHHHHHHHhhhCC---------------------------------CceEeeecCCCcccc
Q 030396          140 PVLIFVQSKDRAKELYGELAFDD---------------------------------IRAGVIHSDLSQTQV  177 (178)
Q Consensus       140 ~~lIF~~t~~~~~~l~~~L~~~g---------------------------------~~~~~lh~~~~~~~R  177 (178)
                      ++||||||++.|+.++..|.+.+                                 +.+..+||+|++++|
T Consensus       246 stLVFvNSR~~AE~La~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ia~~HHGsLSkeeR  316 (1490)
T PRK09751        246 STIVFTNSRGLAEKLTARLNELYAARLQRSPSIAVDAAHFESTSGATSNRVQSSDVFIARSHHGSVSKEQR  316 (1490)
T ss_pred             CEEEECCCHHHHHHHHHHHHHhhhhhccccccccchhhhhhhccccchhccccccceeeeeccccCCHHHH
Confidence            89999999999999999997531                                 236789999999988

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=99.84  E-value=6.4e-20  Score=153.36  Aligned_cols=159  Identities=17%  Similarity=0.168  Sum_probs=115.2

Q ss_pred             cCCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccC-CChhhHHHHHhhC-CCCCceEEEEeecCcHHHHHHH
Q 030396           13 KFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVG-NLLKHIDPVVKAC-SNPSIVRSLFSATLPDFVEELA   90 (178)
Q Consensus        13 ~~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~-~~~~~i~~i~~~~-~~~~~q~i~~SAT~~~~~~~~~   90 (178)
                      .+.++++++||+++........+...+++++|+||||.+.+|| +|++.+..+.... ..++.+++++|||.++.+...+
T Consensus       113 ~g~~~il~~tPe~l~~~~~~~~l~~~~l~~iVIDEaH~i~~~G~~fr~~y~~L~~l~~~~p~~~~v~lTAT~~~~~~~di  192 (607)
T PRK11057        113 TGQIKLLYIAPERLMMDNFLEHLAHWNPALLAVDEAHCISQWGHDFRPEYAALGQLRQRFPTLPFMALTATADDTTRQDI  192 (607)
T ss_pred             CCCCcEEEEChHHhcChHHHHHHhhCCCCEEEEeCccccccccCcccHHHHHHHHHHHhCCCCcEEEEecCCChhHHHHH
Confidence            3568999999999874322222344578999999999999987 5777776552210 2257899999999998876654


Q ss_pred             HHhc--cCcEEEEEcCCccccCCceEEEEEcCChhhHHHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhhhCCCceEee
Q 030396           91 RSIM--HDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVI  168 (178)
Q Consensus        91 ~~~~--~~~~~v~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~l  168 (178)
                      ...+  .+|.....   ....+++...+  + ....+...+..++......++||||+|+++|+.++..|...|+++..+
T Consensus       193 ~~~l~l~~~~~~~~---~~~r~nl~~~v--~-~~~~~~~~l~~~l~~~~~~~~IIFc~tr~~~e~la~~L~~~g~~v~~~  266 (607)
T PRK11057        193 VRLLGLNDPLIQIS---SFDRPNIRYTL--V-EKFKPLDQLMRYVQEQRGKSGIIYCNSRAKVEDTAARLQSRGISAAAY  266 (607)
T ss_pred             HHHhCCCCeEEEEC---CCCCCcceeee--e-eccchHHHHHHHHHhcCCCCEEEEECcHHHHHHHHHHHHhCCCCEEEe
Confidence            4443  35543322   22233443222  2 233456677777777778899999999999999999999999999999


Q ss_pred             ecCCCcccc
Q 030396          169 HSDLSQTQV  177 (178)
Q Consensus       169 h~~~~~~~R  177 (178)
                      ||+|++++|
T Consensus       267 Ha~l~~~~R  275 (607)
T PRK11057        267 HAGLDNDVR  275 (607)
T ss_pred             cCCCCHHHH
Confidence            999999887

>TIGR01054 rgy reverse gyrase

Probab=99.83  E-value=2.4e-19  Score=157.72  Aligned_cols=154  Identities=17%  Similarity=0.195  Sum_probs=115.6

Q ss_pred             Hhcc-CCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccc-----------cCCChhh-HHHHHhhC--------
Q 030396           10 DLSK-FSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFE-----------VGNLLKH-IDPVVKAC--------   68 (178)
Q Consensus        10 ~~l~-~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~-----------~~~~~~~-i~~i~~~~--------   68 (178)
                      +.++ ++++|+|||||+|.+.+..-  .. +++++|+||||.|++           .| |.++ ++.|+..+        
T Consensus       172 ~~l~~~~~dIlV~Tp~rL~~~~~~l--~~-~~~~iVvDEaD~~L~~~k~vd~il~llG-F~~e~i~~il~~~~~~~~~~~  247 (1171)
T TIGR01054       172 ERIENGDFDILITTTMFLSKNYDEL--GP-KFDFIFVDDVDALLKASKNVDKLLKLLG-FSEELIEKAWKLIRLRLKLYR  247 (1171)
T ss_pred             HHHhcCCCCEEEECHHHHHHHHHHh--cC-CCCEEEEeChHhhhhccccHHHHHHHcC-CCHHHHHHHHHHhhhccccch
Confidence            3344 45999999999999887652  12 899999999999998           56 7664 56654320        


Q ss_pred             -------------CCCCce--EEEEeec-CcHHHHHHHHHhccCcEEEEEcCCccccCCceEEEEEcCChhhHHHHHHHH
Q 030396           69 -------------SNPSIV--RSLFSAT-LPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQS  132 (178)
Q Consensus        69 -------------~~~~~q--~i~~SAT-~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~l  132 (178)
                                   .+..+|  ++++||| .|..+..   .++.++..+.+........++.+.++....   +...+.++
T Consensus       248 ~~~~~~~~~~~~~~~~~~q~~li~~SAT~~p~~~~~---~l~r~ll~~~v~~~~~~~r~I~~~~~~~~~---~~~~L~~l  321 (1171)
T TIGR01054       248 ALHAKKRLELLEAIPGKKRGCLIVSSATGRPRGKRA---KLFRELLGFEVGGGSDTLRNVVDVYVEDED---LKETLLEI  321 (1171)
T ss_pred             HHHHHHHHHHHHhhhhccCcEEEEEeCCCCccccHH---HHcccccceEecCccccccceEEEEEeccc---HHHHHHHH
Confidence                         334445  5678999 5654432   456666677777777778889888865533   24567788


Q ss_pred             HHhcCCCCEEEEeCCc---hHHHHHHHHhhhCCCceEeeecCCCc
Q 030396          133 FAESLNPPVLIFVQSK---DRAKELYGELAFDDIRAGVIHSDLSQ  174 (178)
Q Consensus       133 l~~~~~~~~lIF~~t~---~~~~~l~~~L~~~g~~~~~lh~~~~~  174 (178)
                      ++.. ..++||||+|+   +.|+.++..|.+.|+++..+||+|++
T Consensus       322 l~~l-~~~~IVFv~t~~~~~~a~~l~~~L~~~g~~a~~lhg~~~~  365 (1171)
T TIGR01054       322 VKKL-GTGGIVYVSIDYGKEKAEEIAEFLENHGVKAVAYHATKPK  365 (1171)
T ss_pred             HHHc-CCCEEEEEeccccHHHHHHHHHHHHhCCceEEEEeCCCCH
Confidence            8776 47899999999   99999999999999999999999964

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.

>PRK13767 ATP-dependent helicase; Provisional

Probab=99.81  E-value=3.3e-19  Score=154.09  Aligned_cols=165  Identities=24%  Similarity=0.291  Sum_probs=105.0

Q ss_pred             hHHhccCCCcEEEeCcHHHHHHHHcCCC--CCCCeeEEEEeccccccccCCChhhHH----HHHhhCCCCCceEEEEeec
Q 030396            8 STDLSKFSCDILISTPLRLRLAIRRKKI--DLSRVEYLVLDEADKLFEVGNLLKHID----PVVKACSNPSIVRSLFSAT   81 (178)
Q Consensus         8 q~~~l~~~~~Iii~TP~~l~~~l~~~~~--~~~~l~~lViDE~d~ll~~~~~~~~i~----~i~~~~~~~~~q~i~~SAT   81 (178)
                      +.++++++|+|+|+|||++..++.....  .+++++++|+||+|.+.+.. ....+.    ++... .+...|++++|||
T Consensus       139 r~~~l~~~p~IlVtTPE~L~~ll~~~~~~~~l~~l~~VVIDE~H~l~~~~-RG~~l~~~L~rL~~l-~~~~~q~IglSAT  216 (876)
T PRK13767        139 KQKMLKKPPHILITTPESLAILLNSPKFREKLRTVKWVIVDEIHSLAENK-RGVHLSLSLERLEEL-AGGEFVRIGLSAT  216 (876)
T ss_pred             HHHHHhCCCCEEEecHHHHHHHhcChhHHHHHhcCCEEEEechhhhccCc-cHHHHHHHHHHHHHh-cCCCCeEEEEecc
Confidence            4456677899999999999888865543  47899999999999998765 444443    33343 4467899999999


Q ss_pred             CcHH--HHHHHHHhc----cCcEEEEEcCCccccCCceEE-----EEEcCCh---hhHHHHHHHHHHhcCCCCEEEEeCC
Q 030396           82 LPDF--VEELARSIM----HDAVRVIVGRKNTASESIKQK-----LVFAGSE---EGKLLALRQSFAESLNPPVLIFVQS  147 (178)
Q Consensus        82 ~~~~--~~~~~~~~~----~~~~~v~~~~~~~~~~~i~~~-----~~~~~~~---~~k~~~l~~ll~~~~~~~~lIF~~t  147 (178)
                      +++.  +..++....    ..+..+. .........+...     .......   ......+.++++.  .+++||||||
T Consensus       217 l~~~~~va~~L~~~~~~~~~r~~~iv-~~~~~k~~~i~v~~p~~~l~~~~~~~~~~~l~~~L~~~i~~--~~~~LVF~nT  293 (876)
T PRK13767        217 IEPLEEVAKFLVGYEDDGEPRDCEIV-DARFVKPFDIKVISPVDDLIHTPAEEISEALYETLHELIKE--HRTTLIFTNT  293 (876)
T ss_pred             cCCHHHHHHHhcCccccCCCCceEEE-ccCCCccceEEEeccCccccccccchhHHHHHHHHHHHHhc--CCCEEEEeCC
Confidence            9863  222222211    1122221 1111111111000     0011111   1223444444443  4789999999


Q ss_pred             chHHHHHHHHhhh------CCCceEeeecCCCcccc
Q 030396          148 KDRAKELYGELAF------DDIRAGVIHSDLSQTQV  177 (178)
Q Consensus       148 ~~~~~~l~~~L~~------~g~~~~~lh~~~~~~~R  177 (178)
                      ++.|+.++..|.+      .+..+..+||+|++++|
T Consensus       294 r~~ae~la~~L~~~~~~~~~~~~i~~hHg~ls~~~R  329 (876)
T PRK13767        294 RSGAERVLYNLRKRFPEEYDEDNIGAHHSSLSREVR  329 (876)
T ss_pred             HHHHHHHHHHHHHhchhhccccceeeeeCCCCHHHH
Confidence            9999999999976      25789999999999987

>TIGR01587 cas3_core CRISPR-associated helicase Cas3

Probab=99.81  E-value=7.3e-20  Score=144.45  Aligned_cols=160  Identities=21%  Similarity=0.219  Sum_probs=107.2

Q ss_pred             CCcEEEeCcHHHHHHHHcCC----CCC--CCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcHHHHH
Q 030396           15 SCDILISTPLRLRLAIRRKK----IDL--SRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEE   88 (178)
Q Consensus        15 ~~~Iii~TP~~l~~~l~~~~----~~~--~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~~~~   88 (178)
                      .++|+|+||+++...+..+.    ..+  -..+++|+||+|.+.+.+ +. .+..+++.+...+.|++++|||+|+.+.+
T Consensus        94 ~~~I~v~T~~~l~~~~~~~~~~~~~~~~~~~~~~iViDE~h~~~~~~-~~-~l~~~l~~l~~~~~~~i~~SATlp~~l~~  171 (358)
T TIGR01587        94 LDPITVCTIDQVLKSVFGEFGHYEFTLASIANSLLIFDEVHFYDEYT-LA-LILAVLEVLKDNDVPILLMSATLPKFLKE  171 (358)
T ss_pred             hCCeeeCCHHHHHHHHhcccchHHHHHHHhcCCEEEEeCCCCCCHHH-HH-HHHHHHHHHHHcCCCEEEEecCchHHHHH
Confidence            36799999999998776521    111  123799999999998865 33 36666666334578999999999987777


Q ss_pred             HHHHhccCcEEEEEcCCccccCCceEEEEEc-CChhhHHHHHHHHHHhc-CCCCEEEEeCCchHHHHHHHHhhhCCC--c
Q 030396           89 LARSIMHDAVRVIVGRKNTASESIKQKLVFA-GSEEGKLLALRQSFAES-LNPPVLIFVQSKDRAKELYGELAFDDI--R  164 (178)
Q Consensus        89 ~~~~~~~~~~~v~~~~~~~~~~~i~~~~~~~-~~~~~k~~~l~~ll~~~-~~~~~lIF~~t~~~~~~l~~~L~~~g~--~  164 (178)
                      +...+...+.......... .....+.+..+ .....+...+..+++.. ..+++||||||+++|+.++..|.+.+.  .
T Consensus       172 ~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~lVf~~t~~~~~~~~~~L~~~~~~~~  250 (358)
T TIGR01587       172 YAEKIGYVEFNEPLDLKEE-RRFERHRFIKIESDKVGEISSLERLLEFIKKGGKIAIIVNTVDRAQEFYQQLKENAPEEE  250 (358)
T ss_pred             HHhcCCCcccccCCCCccc-cccccccceeeccccccCHHHHHHHHHHhhCCCeEEEEECCHHHHHHHHHHHHhhcCCCe
Confidence            7666544321111111100 00112333222 22234556666666543 467999999999999999999988876  5


Q ss_pred             eEeeecCCCcccc
Q 030396          165 AGVIHSDLSQTQV  177 (178)
Q Consensus       165 ~~~lh~~~~~~~R  177 (178)
                      +..+||+|++.+|
T Consensus       251 ~~~~h~~~~~~~r  263 (358)
T TIGR01587       251 IMLLHSRFTEKDR  263 (358)
T ss_pred             EEEEECCCCHHHH
Confidence            9999999999877

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.

>PRK00254 ski2-like helicase; Provisional

Probab=99.81  E-value=3e-19  Score=152.08  Aligned_cols=154  Identities=19%  Similarity=0.144  Sum_probs=108.8

Q ss_pred             CCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcHHHHHHHHHh
Q 030396           14 FSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSI   93 (178)
Q Consensus        14 ~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~~~~~~~~~   93 (178)
                      +.++|+|+||+++..+++++...+++++++|+||+|.+.+.+ +.+.++.++.. +..+.|++++|||+++. .++. .|
T Consensus       113 ~~~~IiV~Tpe~~~~ll~~~~~~l~~l~lvViDE~H~l~~~~-rg~~le~il~~-l~~~~qiI~lSATl~n~-~~la-~w  188 (720)
T PRK00254        113 GKYDIIIATAEKFDSLLRHGSSWIKDVKLVVADEIHLIGSYD-RGATLEMILTH-MLGRAQILGLSATVGNA-EELA-EW  188 (720)
T ss_pred             ccCCEEEEcHHHHHHHHhCCchhhhcCCEEEEcCcCccCCcc-chHHHHHHHHh-cCcCCcEEEEEccCCCH-HHHH-HH
Confidence            468999999999999998877778999999999999998887 89999999999 77889999999999863 4443 35


Q ss_pred             ccCcEEEEEcCCccccCCc-----eEEEEEcCCh------hhHHHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhhhC-
Q 030396           94 MHDAVRVIVGRKNTASESI-----KQKLVFAGSE------EGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFD-  161 (178)
Q Consensus        94 ~~~~~~v~~~~~~~~~~~i-----~~~~~~~~~~------~~k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~~~-  161 (178)
                      ++.+....    ...+..+     .+.+....+.      ......+.+.++.  .+++||||||++.|+.++..|... 
T Consensus       189 l~~~~~~~----~~rpv~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~--~~~vLVF~~sr~~~~~~a~~l~~~~  262 (720)
T PRK00254        189 LNAELVVS----DWRPVKLRKGVFYQGFLFWEDGKIERFPNSWESLVYDAVKK--GKGALVFVNTRRSAEKEALELAKKI  262 (720)
T ss_pred             hCCccccC----CCCCCcceeeEecCCeeeccCcchhcchHHHHHHHHHHHHh--CCCEEEEEcChHHHHHHHHHHHHHH
Confidence            55332111    1111111     1112222221      1112334444443  579999999999999988777421 


Q ss_pred             --------------------------------CCceEeeecCCCcccc
Q 030396          162 --------------------------------DIRAGVIHSDLSQTQV  177 (178)
Q Consensus       162 --------------------------------g~~~~~lh~~~~~~~R  177 (178)
                                                      +..+..+||+|++++|
T Consensus       263 ~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~gv~~hHagl~~~eR  310 (720)
T PRK00254        263 KRFLTKPELRALKELADSLEENPTNEKLKKALRGGVAFHHAGLGRTER  310 (720)
T ss_pred             HHhcCchhHHHHHHHHHHHhcCCCcHHHHHHHhhCEEEeCCCCCHHHH
Confidence                                            2358999999999988

>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB

Probab=99.81  E-value=1.4e-18  Score=148.45  Aligned_cols=156  Identities=17%  Similarity=0.138  Sum_probs=114.8

Q ss_pred             ccCCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEecccc-ccccCCChh-hHHHHHhhCCCCCceEEEEeecCcHHHHHH
Q 030396           12 SKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADK-LFEVGNLLK-HIDPVVKACSNPSIVRSLFSATLPDFVEEL   89 (178)
Q Consensus        12 l~~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~-ll~~~~~~~-~i~~i~~~~~~~~~q~i~~SAT~~~~~~~~   89 (178)
                      .+.+.+|+|+|||+|++++... .++++++++||||+|. .++.+ +.- .+..+.+. ++.+.|+++||||++...   
T Consensus        87 ~s~~t~I~v~T~G~Llr~l~~d-~~L~~v~~VIiDEaHER~L~~D-l~L~ll~~i~~~-lr~dlqlIlmSATl~~~~---  160 (819)
T TIGR01970        87 VSRRTRLEVVTEGILTRMIQDD-PELDGVGALIFDEFHERSLDAD-LGLALALDVQSS-LREDLKILAMSATLDGER---  160 (819)
T ss_pred             cCCCCcEEEECCcHHHHHHhhC-cccccCCEEEEeccchhhhccc-hHHHHHHHHHHh-cCCCceEEEEeCCCCHHH---
Confidence            3456899999999999998764 5799999999999995 67655 433 34556666 678899999999999653   


Q ss_pred             HHHhccCcEEEEEcCCccccCCceEEEEEcCChhhH----HHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhhh---CC
Q 030396           90 ARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGK----LLALRQSFAESLNPPVLIFVQSKDRAKELYGELAF---DD  162 (178)
Q Consensus        90 ~~~~~~~~~~v~~~~~~~~~~~i~~~~~~~~~~~~k----~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~~---~g  162 (178)
                      +..++.++..+.+....   ..+.++|.........    ...+..+++. ..+++||||++..+++.+++.|.+   .+
T Consensus       161 l~~~l~~~~vI~~~gr~---~pVe~~y~~~~~~~~~~~~v~~~l~~~l~~-~~g~iLVFlpg~~eI~~l~~~L~~~~~~~  236 (819)
T TIGR01970       161 LSSLLPDAPVVESEGRS---FPVEIRYLPLRGDQRLEDAVSRAVEHALAS-ETGSILVFLPGQAEIRRVQEQLAERLDSD  236 (819)
T ss_pred             HHHHcCCCcEEEecCcc---eeeeeEEeecchhhhHHHHHHHHHHHHHHh-cCCcEEEEECCHHHHHHHHHHHHhhcCCC
Confidence            46677776666554322   2355666544332211    2334444444 367899999999999999999987   48


Q ss_pred             CceEeeecCCCcccc
Q 030396          163 IRAGVIHSDLSQTQV  177 (178)
Q Consensus       163 ~~~~~lh~~~~~~~R  177 (178)
                      +.+..+||+|++++|
T Consensus       237 ~~v~pLHg~L~~~eq  251 (819)
T TIGR01970       237 VLICPLYGELSLAAQ  251 (819)
T ss_pred             cEEEEecCCCCHHHH
Confidence            999999999999876

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.

>PRK14701 reverse gyrase; Provisional

Probab=99.81  E-value=1.4e-18  Score=156.17  Aligned_cols=153  Identities=18%  Similarity=0.171  Sum_probs=116.5

Q ss_pred             hccC-CCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEecccccccc-----------CCChhhHHH----HHh--------
Q 030396           11 LSKF-SCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEV-----------GNLLKHIDP----VVK--------   66 (178)
Q Consensus        11 ~l~~-~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~-----------~~~~~~i~~----i~~--------   66 (178)
                      .+.+ .++|+|+|||+|.+.+... .. .+++++|+||||.++++           | |.+++..    |++        
T Consensus       173 ~l~~g~~dILV~TPgrL~~~~~~l-~~-~~i~~iVVDEAD~ml~~~knid~~L~llG-F~~e~~~~~~~il~~~~~~~~~  249 (1638)
T PRK14701        173 RIENGDFDILVTTAQFLARNFPEM-KH-LKFDFIFVDDVDAFLKASKNIDRSLQLLG-FYEEIIEKAWKIIYLKKQGNIE  249 (1638)
T ss_pred             HHhcCCCCEEEECCchhHHhHHHH-hh-CCCCEEEEECceeccccccccchhhhcCC-ChHHHHHHHHHhhhcccccccc
Confidence            3444 5999999999999877642 22 77999999999999873           5 8888875    432        


Q ss_pred             --------------hCCCCCce-EEEEeecCcHHHHHHHHHhccCcEEEEEcCCccccCCceEEEEEcCChhhHHHHHHH
Q 030396           67 --------------ACSNPSIV-RSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQ  131 (178)
Q Consensus        67 --------------~~~~~~~q-~i~~SAT~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~  131 (178)
                                    . .+...| .+++|||.++.  .....+++++..+.++.......++.|.++.+. ...+ ..+.+
T Consensus       250 ~~~~~~~~l~~~~~~-~~~~~~~ll~~SAT~~~r--~~~~~l~~~~l~f~v~~~~~~lr~i~~~yi~~~-~~~k-~~L~~  324 (1638)
T PRK14701        250 DAMEKREILNKEIEK-IGNKIGCLIVASATGKAK--GDRVKLYRELLGFEVGSGRSALRNIVDVYLNPE-KIIK-EHVRE  324 (1638)
T ss_pred             hhhhhhhhhhhhhhh-cCCCccEEEEEecCCCch--hHHHHHhhcCeEEEecCCCCCCCCcEEEEEECC-HHHH-HHHHH
Confidence                          1 234455 67799999964  112244577888888887778888999887653 3334 57888


Q ss_pred             HHHhcCCCCEEEEeCCchH---HHHHHHHhhhCCCceEeeecCC
Q 030396          132 SFAESLNPPVLIFVQSKDR---AKELYGELAFDDIRAGVIHSDL  172 (178)
Q Consensus       132 ll~~~~~~~~lIF~~t~~~---~~~l~~~L~~~g~~~~~lh~~~  172 (178)
                      +++.. ..++||||+|++.   |+.+++.|.+.|+++..+||+.
T Consensus       325 ll~~~-g~~gIVF~~t~~~~e~ae~la~~L~~~Gi~a~~~h~~R  367 (1638)
T PRK14701        325 LLKKL-GKGGLIFVPIDEGAEKAEEIEKYLLEDGFKIELVSAKN  367 (1638)
T ss_pred             HHHhC-CCCeEEEEeccccchHHHHHHHHHHHCCCeEEEecchH
Confidence            88876 5789999999886   4899999999999999999974

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

Probab=99.80  E-value=6.4e-19  Score=141.29  Aligned_cols=156  Identities=22%  Similarity=0.243  Sum_probs=123.2

Q ss_pred             CCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccC--CChhhHHHHHhhCCCCCceEEEEeecCcHHHHHHHH
Q 030396           14 FSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVG--NLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELAR   91 (178)
Q Consensus        14 ~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~--~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~~~~~~~   91 (178)
                      ..+||||||=+-+-.+++.+ -++.++..+|+||+|.|-+..  ...+=+-.-+++ +-+..|++.+|||..++ .+++.
T Consensus       314 ~dADIIVGTYEGiD~lLRtg-~~lgdiGtVVIDEiHtL~deERG~RLdGLI~RLr~-l~~~AQ~i~LSATVgNp-~elA~  390 (830)
T COG1202         314 PDADIIVGTYEGIDYLLRTG-KDLGDIGTVVIDEIHTLEDEERGPRLDGLIGRLRY-LFPGAQFIYLSATVGNP-EELAK  390 (830)
T ss_pred             CCCcEEEeechhHHHHHHcC-CcccccceEEeeeeeeccchhcccchhhHHHHHHH-hCCCCeEEEEEeecCCh-HHHHH
Confidence            46899999999998889887 689999999999999997643  333334444555 55799999999999876 56666


Q ss_pred             HhccCcEEEEEcCCccccCCceEEEEEcCChhhHHHHHHHHHHhc--------CCCCEEEEeCCchHHHHHHHHhhhCCC
Q 030396           92 SIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAES--------LNPPVLIFVQSKDRAKELYGELAFDDI  163 (178)
Q Consensus        92 ~~~~~~~~v~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~--------~~~~~lIF~~t~~~~~~l~~~L~~~g~  163 (178)
                      .+...++...-     .|-.+..+.+++.++.+|-+.+..+.+..        -.+|+|||+||++.|..+++.|...|+
T Consensus       391 ~l~a~lV~y~~-----RPVplErHlvf~~~e~eK~~ii~~L~k~E~~~~sskg~rGQtIVFT~SRrr~h~lA~~L~~kG~  465 (830)
T COG1202         391 KLGAKLVLYDE-----RPVPLERHLVFARNESEKWDIIARLVKREFSTESSKGYRGQTIVFTYSRRRCHELADALTGKGL  465 (830)
T ss_pred             HhCCeeEeecC-----CCCChhHeeeeecCchHHHHHHHHHHHHHHhhhhccCcCCceEEEecchhhHHHHHHHhhcCCc
Confidence            66555443322     22334556778888889989888888632        266999999999999999999999999


Q ss_pred             ceEeeecCCCcccc
Q 030396          164 RAGVIHSDLSQTQV  177 (178)
Q Consensus       164 ~~~~lh~~~~~~~R  177 (178)
                      ++..+|+||++.+|
T Consensus       466 ~a~pYHaGL~y~eR  479 (830)
T COG1202         466 KAAPYHAGLPYKER  479 (830)
T ss_pred             ccccccCCCcHHHH
Confidence            99999999999887

>PRK02362 ski2-like helicase; Provisional

Probab=99.80  E-value=5.2e-19  Score=150.98  Aligned_cols=159  Identities=18%  Similarity=0.158  Sum_probs=106.0

Q ss_pred             CCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhC--CCCCceEEEEeecCcHHHHHHHH
Q 030396           14 FSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKAC--SNPSIVRSLFSATLPDFVEELAR   91 (178)
Q Consensus        14 ~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~--~~~~~q~i~~SAT~~~~~~~~~~   91 (178)
                      +.++|+|+|||++..+++++...+++++++|+||+|.+.+.+ +.+.++.++..+  .+++.|++++|||+++. .++ .
T Consensus       112 ~~~~IiV~Tpek~~~llr~~~~~l~~v~lvViDE~H~l~d~~-rg~~le~il~rl~~~~~~~qii~lSATl~n~-~~l-a  188 (737)
T PRK02362        112 GDNDIIVATSEKVDSLLRNGAPWLDDITCVVVDEVHLIDSAN-RGPTLEVTLAKLRRLNPDLQVVALSATIGNA-DEL-A  188 (737)
T ss_pred             CCCCEEEECHHHHHHHHhcChhhhhhcCEEEEECccccCCCc-chHHHHHHHHHHHhcCCCCcEEEEcccCCCH-HHH-H
Confidence            458999999999999998876678999999999999998877 888888776652  35689999999999853 222 2


Q ss_pred             HhccC--------cEEEEE--cCCccccCCceEEEEEcCChhhHHHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhhhC
Q 030396           92 SIMHD--------AVRVIV--GRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFD  161 (178)
Q Consensus        92 ~~~~~--------~~~v~~--~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~~~  161 (178)
                      .|++.        |..+..  .........-.+..+...........+.+.+.  ..+++||||+|++.|+.++..|...
T Consensus       189 ~wl~~~~~~~~~rpv~l~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~LVF~~sr~~~~~~a~~L~~~  266 (737)
T PRK02362        189 DWLDAELVDSEWRPIDLREGVFYGGAIHFDDSQREVEVPSKDDTLNLVLDTLE--EGGQCLVFVSSRRNAEGFAKRAASA  266 (737)
T ss_pred             HHhCCCcccCCCCCCCCeeeEecCCeeccccccccCCCccchHHHHHHHHHHH--cCCCeEEEEeCHHHHHHHHHHHHHH
Confidence            33331        111110  00000000001111111122234444555444  3589999999999999999888643


Q ss_pred             C------------------------------------CceEeeecCCCcccc
Q 030396          162 D------------------------------------IRAGVIHSDLSQTQV  177 (178)
Q Consensus       162 g------------------------------------~~~~~lh~~~~~~~R  177 (178)
                      .                                    ..++.+||||++++|
T Consensus       267 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~L~~~l~~gva~hHagl~~~eR  318 (737)
T PRK02362        267 LKKTLTAAERAELAELAEEIREVSDTETSKDLADCVAKGAAFHHAGLSREHR  318 (737)
T ss_pred             hhhcCCHHHHHHHHHHHHHHHhccCccccHHHHHHHHhCEEeecCCCCHHHH
Confidence            1                                    368899999999987

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

Probab=99.80  E-value=3.8e-19  Score=145.17  Aligned_cols=160  Identities=19%  Similarity=0.184  Sum_probs=121.5

Q ss_pred             cCCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccC-CChhhHHHHHhhC--CCCCceEEEEeecCcHHHHHH
Q 030396           13 KFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVG-NLLKHIDPVVKAC--SNPSIVRSLFSATLPDFVEEL   89 (178)
Q Consensus        13 ~~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~-~~~~~i~~i~~~~--~~~~~q~i~~SAT~~~~~~~~   89 (178)
                      ....+++.-+|+++..---...+.-.++..+||||||++.+|| +|++++.++-...  + ++..++++|||.++.+.+.
T Consensus       105 ~g~~klLyisPErl~~~~f~~~L~~~~i~l~vIDEAHCiSqWGhdFRP~Y~~lg~l~~~~-~~~p~~AlTATA~~~v~~D  183 (590)
T COG0514         105 SGQLKLLYISPERLMSPRFLELLKRLPISLVAIDEAHCISQWGHDFRPDYRRLGRLRAGL-PNPPVLALTATATPRVRDD  183 (590)
T ss_pred             cCceeEEEECchhhcChHHHHHHHhCCCceEEechHHHHhhcCCccCHhHHHHHHHHhhC-CCCCEEEEeCCCChHHHHH
Confidence            3458999999999885433333346778899999999999998 8999999986653  2 3789999999999998887


Q ss_pred             HHHhcc--CcEEEEEcCCccccCCceEEEEEcCChhhHHHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhhhCCCceEe
Q 030396           90 ARSIMH--DAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGV  167 (178)
Q Consensus        90 ~~~~~~--~~~~v~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~  167 (178)
                      +...+.  ++..+.   .+...+++...++...+...+...+.+ ......+..||||.|++.|+.++++|...|+++..
T Consensus       184 I~~~L~l~~~~~~~---~sfdRpNi~~~v~~~~~~~~q~~fi~~-~~~~~~~~GIIYc~sRk~~E~ia~~L~~~g~~a~~  259 (590)
T COG0514         184 IREQLGLQDANIFR---GSFDRPNLALKVVEKGEPSDQLAFLAT-VLPQLSKSGIIYCLTRKKVEELAEWLRKNGISAGA  259 (590)
T ss_pred             HHHHhcCCCcceEE---ecCCCchhhhhhhhcccHHHHHHHHHh-hccccCCCeEEEEeeHHhHHHHHHHHHHCCCceEE
Confidence            777655  332332   334556665555444334445554443 22455677999999999999999999999999999


Q ss_pred             eecCCCcccc
Q 030396          168 IHSDLSQTQV  177 (178)
Q Consensus       168 lh~~~~~~~R  177 (178)
                      |||||+.++|
T Consensus       260 YHaGl~~~eR  269 (590)
T COG0514         260 YHAGLSNEER  269 (590)
T ss_pred             ecCCCCHHHH
Confidence            9999999887

>PRK11664 ATP-dependent RNA helicase HrpB; Provisional

Probab=99.79  E-value=3e-18  Score=146.49  Aligned_cols=155  Identities=17%  Similarity=0.172  Sum_probs=113.7

Q ss_pred             cCCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEecccc-ccccCCChhhHHHHHhhCCCCCceEEEEeecCcHHHHHHHH
Q 030396           13 KFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADK-LFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELAR   91 (178)
Q Consensus        13 ~~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~-ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~~~~~~~   91 (178)
                      .+..+|+|+|||+|++++... ..+++++++||||+|. .++.+-....+..+.+. ++.+.|++++|||++..   ...
T Consensus        91 ~~~t~I~v~T~G~Llr~l~~d-~~L~~v~~IIlDEaHER~l~~Dl~L~ll~~i~~~-lr~~lqlilmSATl~~~---~l~  165 (812)
T PRK11664         91 GPNTRLEVVTEGILTRMIQRD-PELSGVGLVILDEFHERSLQADLALALLLDVQQG-LRDDLKLLIMSATLDND---RLQ  165 (812)
T ss_pred             CCCCcEEEEChhHHHHHHhhC-CCcCcCcEEEEcCCCccccccchHHHHHHHHHHh-CCccceEEEEecCCCHH---HHH
Confidence            345689999999999998764 5799999999999997 34443123445566676 67889999999999965   235


Q ss_pred             HhccCcEEEEEcCCccccCCceEEEEEcCChhhHHH-----HHHHHHHhcCCCCEEEEeCCchHHHHHHHHhhh---CCC
Q 030396           92 SIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLL-----ALRQSFAESLNPPVLIFVQSKDRAKELYGELAF---DDI  163 (178)
Q Consensus        92 ~~~~~~~~v~~~~~~~~~~~i~~~~~~~~~~~~k~~-----~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~~---~g~  163 (178)
                      .++.++..+.....   ...+.++|..... .++..     .+..+++. ..+.+||||++.++++.+++.|.+   .++
T Consensus       166 ~~~~~~~~I~~~gr---~~pV~~~y~~~~~-~~~~~~~v~~~l~~~l~~-~~g~iLVFlpg~~ei~~l~~~L~~~~~~~~  240 (812)
T PRK11664        166 QLLPDAPVIVSEGR---SFPVERRYQPLPA-HQRFDEAVARATAELLRQ-ESGSLLLFLPGVGEIQRVQEQLASRVASDV  240 (812)
T ss_pred             HhcCCCCEEEecCc---cccceEEeccCch-hhhHHHHHHHHHHHHHHh-CCCCEEEEcCCHHHHHHHHHHHHHhccCCc
Confidence            67776666655432   2236666654433 33332     34444443 368899999999999999999987   588


Q ss_pred             ceEeeecCCCcccc
Q 030396          164 RAGVIHSDLSQTQV  177 (178)
Q Consensus       164 ~~~~lh~~~~~~~R  177 (178)
                      .+..+||+|++++|
T Consensus       241 ~v~~Lhg~l~~~eq  254 (812)
T PRK11664        241 LLCPLYGALSLAEQ  254 (812)
T ss_pred             eEEEeeCCCCHHHH
Confidence            99999999998765

>PHA02653 RNA helicase NPH-II; Provisional

Probab=99.79  E-value=3.6e-18  Score=143.04  Aligned_cols=150  Identities=17%  Similarity=0.107  Sum_probs=109.2

Q ss_pred             CCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcHHHHHHHHHh
Q 030396           14 FSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSI   93 (178)
Q Consensus        14 ~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~~~~~~~~~   93 (178)
                      ++.+|+|+||+.       ...++++++++|+||||.+...+   +.+..+++...+..+|+++||||++.++..+ ..+
T Consensus       273 k~~~Ilv~T~~L-------~l~~L~~v~~VVIDEaHEr~~~~---DllL~llk~~~~~~rq~ILmSATl~~dv~~l-~~~  341 (675)
T PHA02653        273 KPYGLVFSTHKL-------TLNKLFDYGTVIIDEVHEHDQIG---DIIIAVARKHIDKIRSLFLMTATLEDDRDRI-KEF  341 (675)
T ss_pred             CCCCEEEEeCcc-------cccccccCCEEEccccccCccch---hHHHHHHHHhhhhcCEEEEEccCCcHhHHHH-HHH
Confidence            467999999862       12357899999999999997765   4556666653444569999999999888776 678


Q ss_pred             ccCcEEEEEcCCccccCCceEEEEEcCC---------hhhHHHHHHHHHHh--cCCCCEEEEeCCchHHHHHHHHhhhC-
Q 030396           94 MHDAVRVIVGRKNTASESIKQKLVFAGS---------EEGKLLALRQSFAE--SLNPPVLIFVQSKDRAKELYGELAFD-  161 (178)
Q Consensus        94 ~~~~~~v~~~~~~~~~~~i~~~~~~~~~---------~~~k~~~l~~ll~~--~~~~~~lIF~~t~~~~~~l~~~L~~~-  161 (178)
                      +++|..+.++.  .....+.+.++....         ...+...+..+.+.  ...+++||||+++++|+.+++.|.+. 
T Consensus       342 ~~~p~~I~I~g--rt~~pV~~~yi~~~~~~~~~~~y~~~~k~~~l~~L~~~~~~~~g~iLVFlpg~~ei~~l~~~L~~~~  419 (675)
T PHA02653        342 FPNPAFVHIPG--GTLFPISEVYVKNKYNPKNKRAYIEEEKKNIVTALKKYTPPKGSSGIVFVASVSQCEEYKKYLEKRL  419 (675)
T ss_pred             hcCCcEEEeCC--CcCCCeEEEEeecCcccccchhhhHHHHHHHHHHHHHhhcccCCcEEEEECcHHHHHHHHHHHHhhc
Confidence            89998888753  334567776654321         12232333333222  23468999999999999999999887 


Q ss_pred             -CCceEeeecCCCccc
Q 030396          162 -DIRAGVIHSDLSQTQ  176 (178)
Q Consensus       162 -g~~~~~lh~~~~~~~  176 (178)
                       |+++..+||+|++.+
T Consensus       420 ~~~~v~~LHG~Lsq~e  435 (675)
T PHA02653        420 PIYDFYIIHGKVPNID  435 (675)
T ss_pred             CCceEEeccCCcCHHH
Confidence             799999999999853

>PRK11131 ATP-dependent RNA helicase HrpA; Provisional

Probab=99.78  E-value=7.8e-18  Score=147.52  Aligned_cols=155  Identities=15%  Similarity=0.204  Sum_probs=109.5

Q ss_pred             cCCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccc-cccccCCChh-hHHHHHhhCCCCCceEEEEeecCcHHHHHHH
Q 030396           13 KFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEAD-KLFEVGNLLK-HIDPVVKACSNPSIVRSLFSATLPDFVEELA   90 (178)
Q Consensus        13 ~~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d-~ll~~~~~~~-~i~~i~~~~~~~~~q~i~~SAT~~~~~~~~~   90 (178)
                      .++++|+++|||+|++.+.... .+++++++|+|||| .+++.+ |.. .+..++..  .++.|++++|||++.  ..+.
T Consensus       161 s~~t~I~v~TpG~LL~~l~~d~-~Ls~~~~IIIDEAHERsLn~D-fLLg~Lk~lL~~--rpdlKvILmSATid~--e~fs  234 (1294)
T PRK11131        161 SDNTMVKLMTDGILLAEIQQDR-LLMQYDTIIIDEAHERSLNID-FILGYLKELLPR--RPDLKVIITSATIDP--ERFS  234 (1294)
T ss_pred             CCCCCEEEEChHHHHHHHhcCC-ccccCcEEEecCccccccccc-hHHHHHHHhhhc--CCCceEEEeeCCCCH--HHHH
Confidence            4678999999999999987654 48999999999999 577777 654 34444432  257899999999985  3555


Q ss_pred             HHhccCcEEEEEcCCccccCCceEEEEEcCCh-----hhHHHHHHHHHH---hcCCCCEEEEeCCchHHHHHHHHhhhCC
Q 030396           91 RSIMHDAVRVIVGRKNTASESIKQKLVFAGSE-----EGKLLALRQSFA---ESLNPPVLIFVQSKDRAKELYGELAFDD  162 (178)
Q Consensus        91 ~~~~~~~~~v~~~~~~~~~~~i~~~~~~~~~~-----~~k~~~l~~ll~---~~~~~~~lIF~~t~~~~~~l~~~L~~~g  162 (178)
                      +.|.+.| .+.+....   ..+.++|......     .+....+.+.+.   ....+++||||++..+++.+++.|.+.|
T Consensus       235 ~~F~~ap-vI~V~Gr~---~pVei~y~p~~~~~~~~~~d~l~~ll~~V~~l~~~~~GdILVFLpg~~EIe~lae~L~~~~  310 (1294)
T PRK11131        235 RHFNNAP-IIEVSGRT---YPVEVRYRPIVEEADDTERDQLQAIFDAVDELGREGPGDILIFMSGEREIRDTADALNKLN  310 (1294)
T ss_pred             HHcCCCC-EEEEcCcc---ccceEEEeecccccchhhHHHHHHHHHHHHHHhcCCCCCEEEEcCCHHHHHHHHHHHHhcC
Confidence            5555555 45554322   2245555444221     123333333322   2346789999999999999999999887


Q ss_pred             Cc---eEeeecCCCcccc
Q 030396          163 IR---AGVIHSDLSQTQV  177 (178)
Q Consensus       163 ~~---~~~lh~~~~~~~R  177 (178)
                      ++   +..+||+|++++|
T Consensus       311 ~~~~~VlpLhg~Ls~~eQ  328 (1294)
T PRK11131        311 LRHTEILPLYARLSNSEQ  328 (1294)
T ss_pred             CCcceEeecccCCCHHHH
Confidence            75   6789999999876

>PRK10689 transcription-repair coupling factor; Provisional

Probab=99.78  E-value=1.1e-17  Score=147.05  Aligned_cols=147  Identities=18%  Similarity=0.149  Sum_probs=109.9

Q ss_pred             CCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcHHHHHHHHHh
Q 030396           14 FSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSI   93 (178)
Q Consensus        14 ~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~~~~~~~~~   93 (178)
                      ++++||||||+.+     .+.+.+++++++|+||+|.+   | +.  ....++. ++.+.|++++|||.++....+....
T Consensus       702 g~~dIVVgTp~lL-----~~~v~~~~L~lLVIDEahrf---G-~~--~~e~lk~-l~~~~qvLl~SATpiprtl~l~~~g  769 (1147)
T PRK10689        702 GKIDILIGTHKLL-----QSDVKWKDLGLLIVDEEHRF---G-VR--HKERIKA-MRADVDILTLTATPIPRTLNMAMSG  769 (1147)
T ss_pred             CCCCEEEECHHHH-----hCCCCHhhCCEEEEechhhc---c-hh--HHHHHHh-cCCCCcEEEEcCCCCHHHHHHHHhh
Confidence            4699999999633     24567889999999999997   4 22  2344566 6789999999999888877777778


Q ss_pred             ccCcEEEEEcCCccccCCceEEEEEcCChhhHHHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhhhC--CCceEeeecC
Q 030396           94 MHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFD--DIRAGVIHSD  171 (178)
Q Consensus        94 ~~~~~~v~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~~~--g~~~~~lh~~  171 (178)
                      +.++..+...+..  ...+.+.+........+...+.++.   ..++++||||+++.++.+++.|.+.  ++++..+||+
T Consensus       770 l~d~~~I~~~p~~--r~~v~~~~~~~~~~~~k~~il~el~---r~gqv~vf~n~i~~ie~la~~L~~~~p~~~v~~lHG~  844 (1147)
T PRK10689        770 MRDLSIIATPPAR--RLAVKTFVREYDSLVVREAILREIL---RGGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQ  844 (1147)
T ss_pred             CCCcEEEecCCCC--CCCceEEEEecCcHHHHHHHHHHHh---cCCeEEEEECCHHHHHHHHHHHHHhCCCCcEEEEeCC
Confidence            8888877665433  2345555544433333434444443   2478999999999999999999887  7899999999


Q ss_pred             CCcccc
Q 030396          172 LSQTQV  177 (178)
Q Consensus       172 ~~~~~R  177 (178)
                      |++++|
T Consensus       845 m~q~eR  850 (1147)
T PRK10689        845 MREREL  850 (1147)
T ss_pred             CCHHHH
Confidence            999887

>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type

Probab=99.77  E-value=2.3e-17  Score=130.11  Aligned_cols=161  Identities=14%  Similarity=-0.006  Sum_probs=108.0

Q ss_pred             CCCcEEEeCcHHHHHHHHcCC----C----CCCCeeEEEEeccccccccC-CChh---hHHHHHhhCCCCCceEEEEeec
Q 030396           14 FSCDILISTPLRLRLAIRRKK----I----DLSRVEYLVLDEADKLFEVG-NLLK---HIDPVVKACSNPSIVRSLFSAT   81 (178)
Q Consensus        14 ~~~~Iii~TP~~l~~~l~~~~----~----~~~~l~~lViDE~d~ll~~~-~~~~---~i~~i~~~~~~~~~q~i~~SAT   81 (178)
                      +.|+|+++||+.+..+++...    .    .+.+++++|+||+|.+-.++ ....   ....+++. .....+++++|||
T Consensus       112 ~~p~illT~p~~l~~llr~~~~~~~~~~~~~~~~~~~iV~DE~H~~~~~~~~~~~~~l~~~~~~~~-~~~~~~~i~lSAT  190 (357)
T TIGR03158       112 STPIILLTNPDIFVYLTRFAYIDRGDIAAGFYTKFSTVIFDEFHLYDAKQLVGMLFLLAYMQLIRF-FECRRKFVFLSAT  190 (357)
T ss_pred             CCCCEEEecHHHHHHHHhhhccCcccchhhhhcCCCEEEEecccccCcccchhhhhhhHHHHHHHh-hhcCCcEEEEecC
Confidence            579999999999887765321    1    15799999999999986443 1111   23334444 3345799999999


Q ss_pred             CcHHHHHHHHHh--ccCcEEEEEcCCc------------------cccCCceEEEEEcCChhhHHHHHHHHHH-------
Q 030396           82 LPDFVEELARSI--MHDAVRVIVGRKN------------------TASESIKQKLVFAGSEEGKLLALRQSFA-------  134 (178)
Q Consensus        82 ~~~~~~~~~~~~--~~~~~~v~~~~~~------------------~~~~~i~~~~~~~~~~~~k~~~l~~ll~-------  134 (178)
                      +++.+.+.+...  ++.|..+..+..-                  ...+.+.+.+..  ....|...+..+++       
T Consensus       191 ~~~~~~~~l~~~~~~~~~~~~v~g~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~--~~~~~~~~l~~l~~~i~~~~~  268 (357)
T TIGR03158       191 PDPALILRLQNAKQAGVKIAPIDGEKYQFPDNPELEADNKTQSFRPVLPPVELELIP--APDFKEEELSELAEEVIERFR  268 (357)
T ss_pred             CCHHHHHHHHhccccCceeeeecCcccccCCChhhhccccccccceeccceEEEEEe--CCchhHHHHHHHHHHHHHHHh
Confidence            999988887765  5555433332200                  011256665544  22233333333222       


Q ss_pred             hcCCCCEEEEeCCchHHHHHHHHhhhCC--CceEeeecCCCcccc
Q 030396          135 ESLNPPVLIFVQSKDRAKELYGELAFDD--IRAGVIHSDLSQTQV  177 (178)
Q Consensus       135 ~~~~~~~lIF~~t~~~~~~l~~~L~~~g--~~~~~lh~~~~~~~R  177 (178)
                      ....+++||||||++.|+.++..|++.|  +++..+||.+++.+|
T Consensus       269 ~~~~~k~LIf~nt~~~~~~l~~~L~~~~~~~~~~~l~g~~~~~~R  313 (357)
T TIGR03158       269 QLPGERGAIILDSLDEVNRLSDLLQQQGLGDDIGRITGFAPKKDR  313 (357)
T ss_pred             ccCCCeEEEEECCHHHHHHHHHHHhhhCCCceEEeeecCCCHHHH
Confidence            2346799999999999999999998865  688999999999877

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.

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

Probab=99.77  E-value=1.1e-17  Score=141.04  Aligned_cols=165  Identities=21%  Similarity=0.193  Sum_probs=115.3

Q ss_pred             HhHHhccCCCcEEEeCcHHHHHHHHcCCC--CCCCeeEEEEeccccccccC--CChhhHHHHHhhCCCCCceEEEEeecC
Q 030396            7 RSTDLSKFSCDILISTPLRLRLAIRRKKI--DLSRVEYLVLDEADKLFEVG--NLLKHIDPVVKACSNPSIVRSLFSATL   82 (178)
Q Consensus         7 ~q~~~l~~~~~Iii~TP~~l~~~l~~~~~--~~~~l~~lViDE~d~ll~~~--~~~~~i~~i~~~~~~~~~q~i~~SAT~   82 (178)
                      +..++.+++|||+|+|||.|.-++..+.+  .+++++++|+||+|.+.++.  .....-..-++.+.+ +.|.+.+|||.
T Consensus       115 er~r~~~~PPdILiTTPEsL~lll~~~~~r~~l~~vr~VIVDEiHel~~sKRG~~Lsl~LeRL~~l~~-~~qRIGLSATV  193 (814)
T COG1201         115 EKQKMLKNPPHILITTPESLAILLNSPKFRELLRDVRYVIVDEIHALAESKRGVQLALSLERLRELAG-DFQRIGLSATV  193 (814)
T ss_pred             HhhhccCCCCcEEEeChhHHHHHhcCHHHHHHhcCCcEEEeehhhhhhccccchhhhhhHHHHHhhCc-ccEEEeehhcc
Confidence            34456778999999999999888876443  48999999999999998664  333333333444244 99999999999


Q ss_pred             cHHHHHHHHHhccC--cEEEEEcCCccccCCceEEEEEcCCh--------hhHHHHHHHHHHhcCCCCEEEEeCCchHHH
Q 030396           83 PDFVEELARSIMHD--AVRVIVGRKNTASESIKQKLVFAGSE--------EGKLLALRQSFAESLNPPVLIFVQSKDRAK  152 (178)
Q Consensus        83 ~~~~~~~~~~~~~~--~~~v~~~~~~~~~~~i~~~~~~~~~~--------~~k~~~l~~ll~~~~~~~~lIF~~t~~~~~  152 (178)
                      .+. .+..+...+.  +..+.......   .....++.....        ......+.++++++  ..++||+||+..|+
T Consensus       194 ~~~-~~varfL~g~~~~~~Iv~~~~~k---~~~i~v~~p~~~~~~~~~~~~~~~~~i~~~v~~~--~ttLIF~NTR~~aE  267 (814)
T COG1201         194 GPP-EEVAKFLVGFGDPCEIVDVSAAK---KLEIKVISPVEDLIYDEELWAALYERIAELVKKH--RTTLIFTNTRSGAE  267 (814)
T ss_pred             CCH-HHHHHHhcCCCCceEEEEcccCC---cceEEEEecCCccccccchhHHHHHHHHHHHhhc--CcEEEEEeChHHHH
Confidence            854 3333333333  44444332222   122223222222        23456666666666  59999999999999


Q ss_pred             HHHHHhhhCC-CceEeeecCCCccccC
Q 030396          153 ELYGELAFDD-IRAGVIHSDLSQTQVF  178 (178)
Q Consensus       153 ~l~~~L~~~g-~~~~~lh~~~~~~~R~  178 (178)
                      .++..|.+.+ .++...||.++.++|.
T Consensus       268 ~l~~~L~~~~~~~i~~HHgSlSre~R~  294 (814)
T COG1201         268 RLAFRLKKLGPDIIEVHHGSLSRELRL  294 (814)
T ss_pred             HHHHHHHHhcCCceeeecccccHHHHH
Confidence            9999999887 8999999999999873

>KOG0350 consensus DEAD-box ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.77  E-value=6.7e-19  Score=138.88  Aligned_cols=173  Identities=25%  Similarity=0.326  Sum_probs=131.3

Q ss_pred             hHhHHhHHhccC-CC----cEEEeCcHHHHHHHHc-CCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCC-----
Q 030396            3 KELVRSTDLSKF-SC----DILISTPLRLRLAIRR-KKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNP-----   71 (178)
Q Consensus         3 ~~~~~q~~~l~~-~~----~Iii~TP~~l~~~l~~-~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~-----   71 (178)
                      +.++.+.++|.+ .+    ||+|+|||||.+++.. +.+++++++|+|+||||+|++.. |.+-+..++..+...     
T Consensus       253 ~sl~~E~~qL~~~~~~~~~DIlVaTPGRLVDHl~~~k~f~Lk~LrfLVIDEADRll~qs-fQ~Wl~~v~~~~~~~k~~~~  331 (620)
T KOG0350|consen  253 NSLEDEARQLASDPPECRIDILVATPGRLVDHLNNTKSFDLKHLRFLVIDEADRLLDQS-FQEWLDTVMSLCKTMKRVAC  331 (620)
T ss_pred             cchHHHHHHHhcCCCccccceEEcCchHHHHhccCCCCcchhhceEEEechHHHHHHHH-HHHHHHHHHHHhCCchhhcC
Confidence            445555665554 34    8999999999999985 88999999999999999999876 555444444442111     


Q ss_pred             ----------------------------CceEEEEeecCcHHHHHHHHHhccCcEEEEEc----CCccccCCceEEEEEc
Q 030396           72 ----------------------------SIVRSLFSATLPDFVEELARSIMHDAVRVIVG----RKNTASESIKQKLVFA  119 (178)
Q Consensus        72 ----------------------------~~q~i~~SAT~~~~~~~~~~~~~~~~~~v~~~----~~~~~~~~i~~~~~~~  119 (178)
                                                  ..+.+++|||++.+-..+...-++.|....+.    .....+..+.|+.+.+
T Consensus       332 ~~nii~~~~~~~pt~~~e~~t~~~~~~~~l~kL~~satLsqdP~Kl~~l~l~~Prl~~v~~~~~~ryslp~~l~~~~vv~  411 (620)
T KOG0350|consen  332 LDNIIRQRQAPQPTVLSELLTKLGKLYPPLWKLVFSATLSQDPSKLKDLTLHIPRLFHVSKPLIGRYSLPSSLSHRLVVT  411 (620)
T ss_pred             hhhhhhhcccCCchhhHHHHhhcCCcCchhHhhhcchhhhcChHHHhhhhcCCCceEEeecccceeeecChhhhhceeec
Confidence                                        13477899999987778888888888555554    3345666777777666


Q ss_pred             CChhhHHHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhh----hCCCceEeeecCCCcccc
Q 030396          120 GSEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELA----FDDIRAGVIHSDLSQTQV  177 (178)
Q Consensus       120 ~~~~~k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~----~~g~~~~~lh~~~~~~~R  177 (178)
                      .. .-|--.+..++......++|+|+|+.+.+.+++..|.    ...+++..+.|++++..|
T Consensus       412 ~~-~~kpl~~~~lI~~~k~~r~lcf~~S~~sa~Rl~~~L~v~~~~~~~~~s~~t~~l~~k~r  472 (620)
T KOG0350|consen  412 EP-KFKPLAVYALITSNKLNRTLCFVNSVSSANRLAHVLKVEFCSDNFKVSEFTGQLNGKRR  472 (620)
T ss_pred             cc-ccchHhHHHHHHHhhcceEEEEecchHHHHHHHHHHHHHhccccchhhhhhhhhhHHHH
Confidence            44 3466777788888889999999999999999999886    446788889999988776

>PRK01172 ski2-like helicase; Provisional

Probab=99.75  E-value=6.3e-18  Score=143.24  Aligned_cols=157  Identities=20%  Similarity=0.202  Sum_probs=103.5

Q ss_pred             CCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhC--CCCCceEEEEeecCcHHHHHHHH
Q 030396           14 FSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKAC--SNPSIVRSLFSATLPDFVEELAR   91 (178)
Q Consensus        14 ~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~--~~~~~q~i~~SAT~~~~~~~~~~   91 (178)
                      +.++|+|+|||++..+++++...+.+++++|+||+|.+.+.+ +.+.++.++..+  .++..|++++|||+++. .++. 
T Consensus       110 ~~~dIiv~Tpek~~~l~~~~~~~l~~v~lvViDEaH~l~d~~-rg~~le~ll~~~~~~~~~~riI~lSATl~n~-~~la-  186 (674)
T PRK01172        110 KRYDVVILTSEKADSLIHHDPYIINDVGLIVADEIHIIGDED-RGPTLETVLSSARYVNPDARILALSATVSNA-NELA-  186 (674)
T ss_pred             ccCCEEEECHHHHHHHHhCChhHHhhcCEEEEecchhccCCC-ccHHHHHHHHHHHhcCcCCcEEEEeCccCCH-HHHH-
Confidence            468999999999999988876678999999999999998776 777777765542  45689999999999853 3433 


Q ss_pred             HhccCcEEEEEcCCccccCCceEEEE-----EcCChhhHHHHHHHHHHh--cCCCCEEEEeCCchHHHHHHHHhhhCC--
Q 030396           92 SIMHDAVRVIVGRKNTASESIKQKLV-----FAGSEEGKLLALRQSFAE--SLNPPVLIFVQSKDRAKELYGELAFDD--  162 (178)
Q Consensus        92 ~~~~~~~~v~~~~~~~~~~~i~~~~~-----~~~~~~~k~~~l~~ll~~--~~~~~~lIF~~t~~~~~~l~~~L~~~g--  162 (178)
                      .|++.+... .   ...+..+...+.     ...........+..++..  ...+++||||+|+++|+.++..|.+..  
T Consensus       187 ~wl~~~~~~-~---~~r~vpl~~~i~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~vLVF~~sr~~~~~~a~~L~~~~~~  262 (674)
T PRK01172        187 QWLNASLIK-S---NFRPVPLKLGILYRKRLILDGYERSQVDINSLIKETVNDGGQVLVFVSSRKNAEDYAEMLIQHFPE  262 (674)
T ss_pred             HHhCCCccC-C---CCCCCCeEEEEEecCeeeecccccccccHHHHHHHHHhCCCcEEEEeccHHHHHHHHHHHHHhhhh
Confidence            354432111 0   001111111110     111111111112233332  236799999999999999999886531  


Q ss_pred             -----------------------CceEeeecCCCcccc
Q 030396          163 -----------------------IRAGVIHSDLSQTQV  177 (178)
Q Consensus       163 -----------------------~~~~~lh~~~~~~~R  177 (178)
                                             ..+..+||+|++++|
T Consensus       263 ~~~~~~~~~~~~~~~~~L~~~l~~gv~~~hagl~~~eR  300 (674)
T PRK01172        263 FNDFKVSSENNNVYDDSLNEMLPHGVAFHHAGLSNEQR  300 (674)
T ss_pred             cccccccccccccccHHHHHHHhcCEEEecCCCCHHHH
Confidence                                   247889999999987

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=99.74  E-value=1e-16  Score=138.44  Aligned_cols=155  Identities=17%  Similarity=0.171  Sum_probs=107.2

Q ss_pred             HHhHHhccC-CCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcH
Q 030396            6 VRSTDLSKF-SCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPD   84 (178)
Q Consensus         6 ~~q~~~l~~-~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~   84 (178)
                      .++.+.++. .++||||||. +   + .+.+.+++++++|+||+|.+   |   ......++. ++.+.|++++|||..+
T Consensus       544 ~~~~~~l~~g~~dIVIGTp~-l---l-~~~v~f~~L~llVIDEahrf---g---v~~~~~L~~-~~~~~~vL~~SATpip  611 (926)
T TIGR00580       544 NEILKELASGKIDILIGTHK-L---L-QKDVKFKDLGLLIIDEEQRF---G---VKQKEKLKE-LRTSVDVLTLSATPIP  611 (926)
T ss_pred             HHHHHHHHcCCceEEEchHH-H---h-hCCCCcccCCEEEeeccccc---c---hhHHHHHHh-cCCCCCEEEEecCCCH
Confidence            344444544 5999999994 2   2 35578899999999999996   2   223445566 6678999999999877


Q ss_pred             HHHHHHHHhccCcEEEEEcCCccccCCceEEEEEcCChhhHHHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhhhC--C
Q 030396           85 FVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFD--D  162 (178)
Q Consensus        85 ~~~~~~~~~~~~~~~v~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~~~--g  162 (178)
                      ...........++..+...+..  ...+..++.... ...-...+..-+.  ..++++||||++++++.+++.|.+.  +
T Consensus       612 rtl~~~l~g~~d~s~I~~~p~~--R~~V~t~v~~~~-~~~i~~~i~~el~--~g~qv~if~n~i~~~e~l~~~L~~~~p~  686 (926)
T TIGR00580       612 RTLHMSMSGIRDLSIIATPPED--RLPVRTFVMEYD-PELVREAIRRELL--RGGQVFYVHNRIESIEKLATQLRELVPE  686 (926)
T ss_pred             HHHHHHHhcCCCcEEEecCCCC--ccceEEEEEecC-HHHHHHHHHHHHH--cCCeEEEEECCcHHHHHHHHHHHHhCCC
Confidence            6555555556677766654433  223555554332 2111222222222  3579999999999999999999885  7


Q ss_pred             CceEeeecCCCcccc
Q 030396          163 IRAGVIHSDLSQTQV  177 (178)
Q Consensus       163 ~~~~~lh~~~~~~~R  177 (178)
                      +++..+||+|++++|
T Consensus       687 ~~v~~lHG~m~~~eR  701 (926)
T TIGR00580       687 ARIAIAHGQMTENEL  701 (926)
T ss_pred             CeEEEecCCCCHHHH
Confidence            899999999999887

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.

>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA

Probab=99.65  E-value=4.8e-15  Score=130.50  Aligned_cols=155  Identities=16%  Similarity=0.197  Sum_probs=108.7

Q ss_pred             cCCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccc-cccccCCChh-hHHHHHhhCCCCCceEEEEeecCcHHHHHHH
Q 030396           13 KFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEAD-KLFEVGNLLK-HIDPVVKACSNPSIVRSLFSATLPDFVEELA   90 (178)
Q Consensus        13 ~~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d-~ll~~~~~~~-~i~~i~~~~~~~~~q~i~~SAT~~~~~~~~~   90 (178)
                      +.+.+|+++|||+|+..+.... .+++++++|||||| ..++.+ +.- .+..++..  .++.|++++|||++.  ..+.
T Consensus       154 s~~T~I~~~TdGiLLr~l~~d~-~L~~~~~IIIDEaHERsL~~D-~LL~lLk~il~~--rpdLKlIlmSATld~--~~fa  227 (1283)
T TIGR01967       154 SSNTLVKLMTDGILLAETQQDR-FLSRYDTIIIDEAHERSLNID-FLLGYLKQLLPR--RPDLKIIITSATIDP--ERFS  227 (1283)
T ss_pred             CCCceeeeccccHHHHHhhhCc-ccccCcEEEEcCcchhhccch-hHHHHHHHHHhh--CCCCeEEEEeCCcCH--HHHH
Confidence            4567899999999999887654 48899999999999 488877 554 36666654  357899999999984  4555


Q ss_pred             HHhccCcEEEEEcCCccccCCceEEEEEcCC-----hhhHHHHHHHHHHh---cCCCCEEEEeCCchHHHHHHHHhhhCC
Q 030396           91 RSIMHDAVRVIVGRKNTASESIKQKLVFAGS-----EEGKLLALRQSFAE---SLNPPVLIFVQSKDRAKELYGELAFDD  162 (178)
Q Consensus        91 ~~~~~~~~~v~~~~~~~~~~~i~~~~~~~~~-----~~~k~~~l~~ll~~---~~~~~~lIF~~t~~~~~~l~~~L~~~g  162 (178)
                      +.|.+.| .+.+.....   .+..+|.....     ..++...+.+.+..   ...+.+|||+++..+++.+++.|.+.+
T Consensus       228 ~~F~~ap-vI~V~Gr~~---PVev~Y~~~~~~~~~~~~~~~~~i~~~I~~l~~~~~GdILVFLpg~~EI~~l~~~L~~~~  303 (1283)
T TIGR01967       228 RHFNNAP-IIEVSGRTY---PVEVRYRPLVEEQEDDDLDQLEAILDAVDELFAEGPGDILIFLPGEREIRDAAEILRKRN  303 (1283)
T ss_pred             HHhcCCC-EEEECCCcc---cceeEEecccccccchhhhHHHHHHHHHHHHHhhCCCCEEEeCCCHHHHHHHHHHHHhcC
Confidence            5554455 354543222   23334433221     11233444444432   246889999999999999999998775


Q ss_pred             C---ceEeeecCCCcccc
Q 030396          163 I---RAGVIHSDLSQTQV  177 (178)
Q Consensus       163 ~---~~~~lh~~~~~~~R  177 (178)
                      +   .+..+||+|++++|
T Consensus       304 ~~~~~VlpLhg~Ls~~eQ  321 (1283)
T TIGR01967       304 LRHTEILPLYARLSNKEQ  321 (1283)
T ss_pred             CCCcEEEeccCCCCHHHH
Confidence            4   58899999998875

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.

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=99.63  E-value=1.9e-14  Score=122.03  Aligned_cols=154  Identities=12%  Similarity=0.137  Sum_probs=94.9

Q ss_pred             hHHhccC-CCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcHHH
Q 030396            8 STDLSKF-SCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFV   86 (178)
Q Consensus         8 q~~~l~~-~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~~   86 (178)
                      +.+.+.+ .++|+||||+++.+     ...+++++++|+||+|.+...      ....+.. .....+++++|||..+..
T Consensus       356 ~~~~l~~g~~~IvVgT~~ll~~-----~v~~~~l~lvVIDE~Hrfg~~------qr~~l~~-~~~~~~iL~~SATp~prt  423 (681)
T PRK10917        356 ILEAIASGEADIVIGTHALIQD-----DVEFHNLGLVIIDEQHRFGVE------QRLALRE-KGENPHVLVMTATPIPRT  423 (681)
T ss_pred             HHHHHhCCCCCEEEchHHHhcc-----cchhcccceEEEechhhhhHH------HHHHHHh-cCCCCCEEEEeCCCCHHH
Confidence            3344444 59999999988743     346789999999999997322      2233334 445789999999976653


Q ss_pred             HHHHHHhccCcEEEEEcCCccccCCceEEEEEcCChhhHHHHHHHHHHhcCCCCEEEEeCCc--------hHHHHHHHHh
Q 030396           87 EELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSK--------DRAKELYGEL  158 (178)
Q Consensus        87 ~~~~~~~~~~~~~v~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~~t~--------~~~~~l~~~L  158 (178)
                      ..+......++..+...+  .....+...++.......-...+.+.+  ....+++|||++.        ..++.+++.|
T Consensus       424 l~~~~~g~~~~s~i~~~p--~~r~~i~~~~~~~~~~~~~~~~i~~~~--~~g~q~~v~~~~ie~s~~l~~~~~~~~~~~L  499 (681)
T PRK10917        424 LAMTAYGDLDVSVIDELP--PGRKPITTVVIPDSRRDEVYERIREEI--AKGRQAYVVCPLIEESEKLDLQSAEETYEEL  499 (681)
T ss_pred             HHHHHcCCCceEEEecCC--CCCCCcEEEEeCcccHHHHHHHHHHHH--HcCCcEEEEEcccccccchhHHHHHHHHHHH
Confidence            333221111333332222  222335554433322222223333333  2357999999954        4567778888


Q ss_pred             hhC--CCceEeeecCCCcccc
Q 030396          159 AFD--DIRAGVIHSDLSQTQV  177 (178)
Q Consensus       159 ~~~--g~~~~~lh~~~~~~~R  177 (178)
                      .+.  ++++..+||+|++++|
T Consensus       500 ~~~~~~~~v~~lHG~m~~~eR  520 (681)
T PRK10917        500 QEAFPELRVGLLHGRMKPAEK  520 (681)
T ss_pred             HHHCCCCcEEEEeCCCCHHHH
Confidence            765  5799999999999887

>cd00268 DEADc DEAD-box helicases

Probab=99.61  E-value=5.7e-15  Score=107.71  Aligned_cols=90  Identities=39%  Similarity=0.579  Sum_probs=81.6

Q ss_pred             HHhccCCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcHHHHH
Q 030396            9 TDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEE   88 (178)
Q Consensus         9 ~~~l~~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~~~~   88 (178)
                      ...+.++++|+|+||+++.+++.++..++.+++++|+||+|.+.+.+ +...+..+.+. ++...|++++|||+++++..
T Consensus       113 ~~~~~~~~~iiv~T~~~l~~~l~~~~~~~~~l~~lIvDE~h~~~~~~-~~~~~~~~~~~-l~~~~~~~~~SAT~~~~~~~  190 (203)
T cd00268         113 IRKLKRGPHIVVATPGRLLDLLERGKLDLSKVKYLVLDEADRMLDMG-FEDQIREILKL-LPKDRQTLLFSATMPKEVRD  190 (203)
T ss_pred             HHHhcCCCCEEEEChHHHHHHHHcCCCChhhCCEEEEeChHHhhccC-hHHHHHHHHHh-CCcccEEEEEeccCCHHHHH
Confidence            34445689999999999999999888889999999999999998877 99999999999 77899999999999999999


Q ss_pred             HHHHhccCcEEE
Q 030396           89 LARSIMHDAVRV  100 (178)
Q Consensus        89 ~~~~~~~~~~~v  100 (178)
                      ++..++.+|..+
T Consensus       191 ~~~~~~~~~~~~  202 (203)
T cd00268         191 LARKFLRNPVRI  202 (203)
T ss_pred             HHHHHCCCCEEe
Confidence            999999998776

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.

>PHA02558 uvsW UvsW helicase; Provisional

Probab=99.61  E-value=2.9e-15  Score=123.06  Aligned_cols=153  Identities=9%  Similarity=0.068  Sum_probs=97.4

Q ss_pred             CCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcHHHHHH--HHH
Q 030396           15 SCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEEL--ARS   92 (178)
Q Consensus        15 ~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~~~~~--~~~   92 (178)
                      +++|+|+||+++.+...   ..+++++++|+||||.+....     +..++.. .+..+|++++|||.+......  ...
T Consensus       201 ~~~I~VaT~qsl~~~~~---~~~~~~~~iIvDEaH~~~~~~-----~~~il~~-~~~~~~~lGLTATp~~~~~~~~~~~~  271 (501)
T PHA02558        201 DAPIVVSTWQSAVKQPK---EWFDQFGMVIVDECHLFTGKS-----LTSIITK-LDNCKFKFGLTGSLRDGKANILQYVG  271 (501)
T ss_pred             CCCEEEeeHHHHhhchh---hhccccCEEEEEchhcccchh-----HHHHHHh-hhccceEEEEeccCCCccccHHHHHH
Confidence            47899999999875432   246789999999999996544     6677777 666789999999997532111  111


Q ss_pred             hccCcEEEEEcCCccc------cCCceEEEE--------------------EcCChhhHHHHHHHHHHh--cCCCCEEEE
Q 030396           93 IMHDAVRVIVGRKNTA------SESIKQKLV--------------------FAGSEEGKLLALRQSFAE--SLNPPVLIF  144 (178)
Q Consensus        93 ~~~~~~~v~~~~~~~~------~~~i~~~~~--------------------~~~~~~~k~~~l~~ll~~--~~~~~~lIF  144 (178)
                      +++ |....+......      ...+.....                    ...+...+...+.++...  ....+++||
T Consensus       272 ~fG-~i~~~v~~~~li~~g~l~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~l~~~~~Rn~~I~~~~~~~~~~~~~~lV~  350 (501)
T PHA02558        272 LFG-DIFKPVTTSQLMEEGQVTDLKINSIFLRYPDEDRVKLKGEDYQEEIKYITSHTKRNKWIANLALKLAKKGENTFVM  350 (501)
T ss_pred             hhC-CceEEecHHHHHhCCCcCCceEEEEeccCCHHHhhhhcccchHHHHHHHhccHHHHHHHHHHHHHHHhcCCCEEEE
Confidence            222 111111100000      000000000                    011122344445544432  235789999


Q ss_pred             eCCchHHHHHHHHhhhCCCceEeeecCCCcccc
Q 030396          145 VQSKDRAKELYGELAFDDIRAGVIHSDLSQTQV  177 (178)
Q Consensus       145 ~~t~~~~~~l~~~L~~~g~~~~~lh~~~~~~~R  177 (178)
                      |++.++|+.+++.|.+.|+++..+||+|++++|
T Consensus       351 ~~~~~h~~~L~~~L~~~g~~v~~i~G~~~~~eR  383 (501)
T PHA02558        351 FKYVEHGKPLYEMLKKVYDKVYYVSGEVDTEDR  383 (501)
T ss_pred             EEEHHHHHHHHHHHHHcCCCEEEEeCCCCHHHH
Confidence            999999999999999999999999999999987

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

Probab=99.60  E-value=8.2e-15  Score=125.92  Aligned_cols=159  Identities=16%  Similarity=0.167  Sum_probs=118.7

Q ss_pred             CCcEEEeCcHHHHHH--HHcCCCCCCC---eeEEEEeccccccccC-CChhhHHHHHhhCC-CCCceEEEEeecCcHHHH
Q 030396           15 SCDILISTPLRLRLA--IRRKKIDLSR---VEYLVLDEADKLFEVG-NLLKHIDPVVKACS-NPSIVRSLFSATLPDFVE   87 (178)
Q Consensus        15 ~~~Iii~TP~~l~~~--l~~~~~~~~~---l~~lViDE~d~ll~~~-~~~~~i~~i~~~~~-~~~~q~i~~SAT~~~~~~   87 (178)
                      ..+|+..||+.+...  +.....++..   +..+|+||||+..+|| +|++++.++..... .....+++++||.+..++
T Consensus       356 ~ikilYvtPE~v~~~~~l~~~~~~L~~~~~lal~vIDEAHCVSqWgHdFRp~Yk~l~~l~~~~~~vP~iALTATAT~~v~  435 (941)
T KOG0351|consen  356 IIKILYVTPEKVVASEGLLESLADLYARGLLALFVIDEAHCVSQWGHDFRPSYKRLGLLRIRFPGVPFIALTATATERVR  435 (941)
T ss_pred             eEEEEEeCHHHhhcccchhhHHHhccCCCeeEEEEecHHHHhhhhcccccHHHHHHHHHHhhCCCCCeEEeehhccHHHH
Confidence            589999999998743  2222223333   8999999999999998 99999999755421 134789999999999988


Q ss_pred             HHHHHhcc--CcEEEEEcCCccccCCceEEEEEcCChhhHHHHHHHHHH-hcCCCCEEEEeCCchHHHHHHHHhhhCCCc
Q 030396           88 ELARSIMH--DAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFA-ESLNPPVLIFVQSKDRAKELYGELAFDDIR  164 (178)
Q Consensus        88 ~~~~~~~~--~~~~v~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~-~~~~~~~lIF~~t~~~~~~l~~~L~~~g~~  164 (178)
                      +-+-..++  +|.   +......++|+...+. .....+....+.+..+ ....+.+||||.++.+|+.++..|...|++
T Consensus       436 ~DIi~~L~l~~~~---~~~~sfnR~NL~yeV~-~k~~~~~~~~~~~~~~~~~~~~s~IIYC~sr~~ce~vs~~L~~~~~~  511 (941)
T KOG0351|consen  436 EDVIRSLGLRNPE---LFKSSFNRPNLKYEVS-PKTDKDALLDILEESKLRHPDQSGIIYCLSRKECEQVSAVLRSLGKS  511 (941)
T ss_pred             HHHHHHhCCCCcc---eecccCCCCCceEEEE-eccCccchHHHHHHhhhcCCCCCeEEEeCCcchHHHHHHHHHHhchh
Confidence            87766655  554   3345567777766663 3232233333333333 456778999999999999999999999999


Q ss_pred             eEeeecCCCcccc
Q 030396          165 AGVIHSDLSQTQV  177 (178)
Q Consensus       165 ~~~lh~~~~~~~R  177 (178)
                      +..||+||+..+|
T Consensus       512 a~~YHAGl~~~~R  524 (941)
T KOG0351|consen  512 AAFYHAGLPPKER  524 (941)
T ss_pred             hHhhhcCCCHHHH
Confidence            9999999999988

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=99.55  E-value=2.1e-13  Score=114.85  Aligned_cols=153  Identities=14%  Similarity=0.154  Sum_probs=90.8

Q ss_pred             hHHhcc-CCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCC--CCceEEEEeecCcH
Q 030396            8 STDLSK-FSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSN--PSIVRSLFSATLPD   84 (178)
Q Consensus         8 q~~~l~-~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~--~~~q~i~~SAT~~~   84 (178)
                      +.+.+. +.++|+||||+.+.+     ...+++++++|+||+|.+....  ..   .+... ..  ...+++++|||..+
T Consensus       330 ~~~~i~~g~~~IiVgT~~ll~~-----~~~~~~l~lvVIDEaH~fg~~q--r~---~l~~~-~~~~~~~~~l~~SATp~p  398 (630)
T TIGR00643       330 LLETIASGQIHLVVGTHALIQE-----KVEFKRLALVIIDEQHRFGVEQ--RK---KLREK-GQGGFTPHVLVMSATPIP  398 (630)
T ss_pred             HHHHHhCCCCCEEEecHHHHhc-----cccccccceEEEechhhccHHH--HH---HHHHh-cccCCCCCEEEEeCCCCc
Confidence            333444 468999999997753     3567899999999999973322  22   23333 22  26899999999765


Q ss_pred             HHHHHHHHhccCcEEEEEcCCccccCCceEEEEEcCChhhHHHHHHHHHH-h-cCCCCEEEEeCCc--------hHHHHH
Q 030396           85 FVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFA-E-SLNPPVLIFVQSK--------DRAKEL  154 (178)
Q Consensus        85 ~~~~~~~~~~~~~~~v~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~-~-~~~~~~lIF~~t~--------~~~~~l  154 (178)
                      ....+  ....+.....+...+.....+...++..   ..+ ..+.+.+. . ....+++|||++.        +.++.+
T Consensus       399 rtl~l--~~~~~l~~~~i~~~p~~r~~i~~~~~~~---~~~-~~~~~~i~~~l~~g~q~~v~~~~i~~s~~~~~~~a~~~  472 (630)
T TIGR00643       399 RTLAL--TVYGDLDTSIIDELPPGRKPITTVLIKH---DEK-DIVYEFIEEEIAKGRQAYVVYPLIEESEKLDLKAAEAL  472 (630)
T ss_pred             HHHHH--HhcCCcceeeeccCCCCCCceEEEEeCc---chH-HHHHHHHHHHHHhCCcEEEEEccccccccchHHHHHHH
Confidence            43222  1122211111111111122343433222   222 33333333 2 2357899999876        456677


Q ss_pred             HHHhhh--CCCceEeeecCCCcccc
Q 030396          155 YGELAF--DDIRAGVIHSDLSQTQV  177 (178)
Q Consensus       155 ~~~L~~--~g~~~~~lh~~~~~~~R  177 (178)
                      ++.|.+  .++++..+||+|++++|
T Consensus       473 ~~~L~~~~~~~~v~~lHG~m~~~eR  497 (630)
T TIGR00643       473 YERLKKAFPKYNVGLLHGRMKSDEK  497 (630)
T ss_pred             HHHHHhhCCCCcEEEEeCCCCHHHH
Confidence            888865  37899999999999887

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

Probab=99.54  E-value=2.7e-13  Score=116.74  Aligned_cols=164  Identities=19%  Similarity=0.208  Sum_probs=111.7

Q ss_pred             HhccCCCcEEEeCcHHHHHHHHcC----CCCCCCeeEEEEeccccccccCCChhhHHHHHhhC------CCCCceEEEEe
Q 030396           10 DLSKFSCDILISTPLRLRLAIRRK----KIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKAC------SNPSIVRSLFS   79 (178)
Q Consensus        10 ~~l~~~~~Iii~TP~~l~~~l~~~----~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~------~~~~~q~i~~S   79 (178)
                      +.+.++|+||+++|..|..++-..    ...+++++++|+||+|.+-  |.|..++.-+++.+      .+...|+++.|
T Consensus       162 ~~~~~pp~IllTNpdMLh~~llr~~~~~~~~~~~Lk~lVvDElHtYr--Gv~GS~vA~llRRL~~~~~~~~~~~q~i~~S  239 (851)
T COG1205         162 AIIRNPPDILLTNPDMLHYLLLRNHDAWLWLLRNLKYLVVDELHTYR--GVQGSEVALLLRRLLRRLRRYGSPLQIICTS  239 (851)
T ss_pred             HHHhCCCCEEEeCHHHHHHHhccCcchHHHHHhcCcEEEEecceecc--ccchhHHHHHHHHHHHHHhccCCCceEEEEe
Confidence            567789999999999999855332    2347889999999999993  33455554444443      44689999999


Q ss_pred             ecCcHHHHHHHHHhccCcEEEEEcCCccccCCceEEEEEcCC--------hhhHHHHHHHHHHhc--CCCCEEEEeCCch
Q 030396           80 ATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGS--------EEGKLLALRQSFAES--LNPPVLIFVQSKD  149 (178)
Q Consensus        80 AT~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~i~~~~~~~~~--------~~~k~~~l~~ll~~~--~~~~~lIF~~t~~  149 (178)
                      ||+... .+....+++.+....+. ++..+...++++..-+.        ...+...+..+....  ..-++|+|+.+++
T Consensus       240 AT~~np-~e~~~~l~~~~f~~~v~-~~g~~~~~~~~~~~~p~~~~~~~~~r~s~~~~~~~~~~~~~~~~~~tL~F~~sr~  317 (851)
T COG1205         240 ATLANP-GEFAEELFGRDFEVPVD-EDGSPRGLRYFVRREPPIRELAESIRRSALAELATLAALLVRNGIQTLVFFRSRK  317 (851)
T ss_pred             ccccCh-HHHHHHhcCCcceeecc-CCCCCCCceEEEEeCCcchhhhhhcccchHHHHHHHHHHHHHcCceEEEEEehhh
Confidence            999977 45555565654444333 33444455554543330        123334444444322  3679999999999


Q ss_pred             HHHHHH----HHhhhCC----CceEeeecCCCcccc
Q 030396          150 RAKELY----GELAFDD----IRAGVIHSDLSQTQV  177 (178)
Q Consensus       150 ~~~~l~----~~L~~~g----~~~~~lh~~~~~~~R  177 (178)
                      .++.+.    ..+...|    ..+..++|+|..++|
T Consensus       318 ~~e~~~~~~~~~~~~~~~~l~~~v~~~~~~~~~~er  353 (851)
T COG1205         318 QVELLYLSPRRRLVREGGKLLDAVSTYRAGLHREER  353 (851)
T ss_pred             hhhhhhhchhHHHhhcchhhhhheeeccccCCHHHH
Confidence            999997    5555555    689999999999887

>COG1204 Superfamily II helicase [General function prediction only]

Probab=99.49  E-value=2.3e-13  Score=115.81  Aligned_cols=144  Identities=23%  Similarity=0.212  Sum_probs=92.7

Q ss_pred             CCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhC--CCCCceEEEEeecCcHHHHHHHH
Q 030396           14 FSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKAC--SNPSIVRSLFSATLPDFVEELAR   91 (178)
Q Consensus        14 ~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~--~~~~~q~i~~SAT~~~~~~~~~~   91 (178)
                      .+++|+|+||+++..++++.......++++|+||+|.+.+.. ..+.++.|+...  .....|++.+|||+|+. .+++.
T Consensus       121 ~~~~ViVtT~EK~Dsl~R~~~~~~~~V~lvViDEiH~l~d~~-RG~~lE~iv~r~~~~~~~~rivgLSATlpN~-~evA~  198 (766)
T COG1204         121 ARYDVIVTTPEKLDSLTRKRPSWIEEVDLVVIDEIHLLGDRT-RGPVLESIVARMRRLNELIRIVGLSATLPNA-EEVAD  198 (766)
T ss_pred             ccCCEEEEchHHhhHhhhcCcchhhcccEEEEeeeeecCCcc-cCceehhHHHHHHhhCcceEEEEEeeecCCH-HHHHH
Confidence            468999999999999999887788999999999999998874 466666666552  33458999999999974 33333


Q ss_pred             HhccCcEEEEEcCCccccC-CceEEEEEcCChh------hHHHHHHHHHHh-cCCCCEEEEeCCchHHHHHHHHhh
Q 030396           92 SIMHDAVRVIVGRKNTASE-SIKQKLVFAGSEE------GKLLALRQSFAE-SLNPPVLIFVQSKDRAKELYGELA  159 (178)
Q Consensus        92 ~~~~~~~~v~~~~~~~~~~-~i~~~~~~~~~~~------~k~~~l~~ll~~-~~~~~~lIF~~t~~~~~~l~~~L~  159 (178)
                      ..-.++..-...+.+.... ...+.+.......      .....+...+.. ...++++|||+|++.+...|..|.
T Consensus       199 wL~a~~~~~~~rp~~l~~~v~~~~~~~~~~~~~k~~~~~~~~~~~~~v~~~~~~~~qvLvFv~sR~~a~~~A~~l~  274 (766)
T COG1204         199 WLNAKLVESDWRPVPLRRGVPYVGAFLGADGKKKTWPLLIDNLALELVLESLAEGGQVLVFVHSRKEAEKTAKKLR  274 (766)
T ss_pred             HhCCcccccCCCCcccccCCccceEEEEecCccccccccchHHHHHHHHHHHhcCCeEEEEEecCchHHHHHHHHH
Confidence            3322333111112211111 1222332222111      112222223332 235899999999999999999987

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

Probab=99.47  E-value=1.6e-13  Score=97.00  Aligned_cols=81  Identities=31%  Similarity=0.432  Sum_probs=67.7

Q ss_pred             HhHHhccCCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCC-CCceEEEEeecCcHH
Q 030396            7 RSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSN-PSIVRSLFSATLPDF   85 (178)
Q Consensus         7 ~q~~~l~~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~-~~~q~i~~SAT~~~~   85 (178)
                      .+...+.++++|+|+||+++.+++..+..++.+++++|+||+|.+..++ +...+..|++.+.. .+.|++++|||+++.
T Consensus        87 ~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~iViDE~h~l~~~~-~~~~~~~i~~~~~~~~~~~~i~~SAT~~~~  165 (169)
T PF00270_consen   87 DQREVLSNQADILVTTPEQLLDLISNGKINISRLSLIVIDEAHHLSDET-FRAMLKSILRRLKRFKNIQIILLSATLPSN  165 (169)
T ss_dssp             HHHHHHHTTSSEEEEEHHHHHHHHHTTSSTGTTESEEEEETHHHHHHTT-HHHHHHHHHHHSHTTTTSEEEEEESSSTHH
T ss_pred             cccccccccccccccCcchhhccccccccccccceeeccCccccccccc-HHHHHHHHHHHhcCCCCCcEEEEeeCCChh
Confidence            3444556789999999999999999866688889999999999999987 88889999888422 368999999999976


Q ss_pred             HHH
Q 030396           86 VEE   88 (178)
Q Consensus        86 ~~~   88 (178)
                      ++.
T Consensus       166 ~~~  168 (169)
T PF00270_consen  166 VEK  168 (169)
T ss_dssp             HHH
T ss_pred             Hhh
Confidence            654

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 ....

>PRK13766 Hef nuclease; Provisional

Probab=99.45  E-value=4.4e-12  Score=109.39  Aligned_cols=68  Identities=16%  Similarity=0.151  Sum_probs=53.1

Q ss_pred             cCCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecC
Q 030396           13 KFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATL   82 (178)
Q Consensus        13 ~~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~   82 (178)
                      -.+++|+|+||+.+...+..+.+++.+++++|+||||.+.... ....+...... .....+++++|||-
T Consensus       105 ~~~~~iiv~T~~~l~~~l~~~~~~~~~~~liVvDEaH~~~~~~-~~~~i~~~~~~-~~~~~~il~lTaTP  172 (773)
T PRK13766        105 WEKAKVIVATPQVIENDLIAGRISLEDVSLLIFDEAHRAVGNY-AYVYIAERYHE-DAKNPLVLGLTASP  172 (773)
T ss_pred             HhCCCEEEECHHHHHHHHHcCCCChhhCcEEEEECCccccccc-cHHHHHHHHHh-cCCCCEEEEEEcCC
Confidence            3467999999999998888888889999999999999997654 33334444443 44567899999996

>KOG0952 consensus DNA/RNA helicase MER3/SLH1, DEAD-box superfamily [RNA processing and modification]

Probab=99.44  E-value=3.8e-13  Score=114.35  Aligned_cols=141  Identities=18%  Similarity=0.212  Sum_probs=100.8

Q ss_pred             CCCcEEEeCcHHHHHHHHcC-CC---CCCCeeEEEEeccccccccCCChhhHHHHHhhCC------CCCceEEEEeecCc
Q 030396           14 FSCDILISTPLRLRLAIRRK-KI---DLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACS------NPSIVRSLFSATLP   83 (178)
Q Consensus        14 ~~~~Iii~TP~~l~~~l~~~-~~---~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~------~~~~q~i~~SAT~~   83 (178)
                      ..++|||+||++ ++.+.++ .-   -++.++++|+||+|.|-++.  ++.++.|+.+.+      ....+++++|||+|
T Consensus       210 ~~tqiiVTTPEK-wDvvTRk~~~d~~l~~~V~LviIDEVHlLhd~R--GpvlEtiVaRtlr~vessqs~IRivgLSATlP  286 (1230)
T KOG0952|consen  210 ADTQIIVTTPEK-WDVVTRKSVGDSALFSLVRLVIIDEVHLLHDDR--GPVLETIVARTLRLVESSQSMIRIVGLSATLP  286 (1230)
T ss_pred             HhcCEEEecccc-eeeeeeeeccchhhhhheeeEEeeeehhhcCcc--cchHHHHHHHHHHHHHhhhhheEEEEeeccCC
Confidence            368999999998 6666443 32   27899999999999997765  788888877632      14578999999999


Q ss_pred             HHHHHHHHHhcc-C-cEEEEEcCCccccCCceEEEEEcCChh----------hHHHHHHHHHHhcCCCCEEEEeCCchHH
Q 030396           84 DFVEELARSIMH-D-AVRVIVGRKNTASESIKQKLVFAGSEE----------GKLLALRQSFAESLNPPVLIFVQSKDRA  151 (178)
Q Consensus        84 ~~~~~~~~~~~~-~-~~~v~~~~~~~~~~~i~~~~~~~~~~~----------~k~~~l~~ll~~~~~~~~lIF~~t~~~~  151 (178)
                      +- .++ -.|++ + +.-+........|--+.+.++.++..+          -......+++.+.  .+++|||.+++.+
T Consensus       287 N~-eDv-A~fL~vn~~~glfsFd~~yRPvpL~~~~iG~k~~~~~~~~~~~d~~~~~kv~e~~~~g--~qVlvFvhsR~~T  362 (1230)
T KOG0952|consen  287 NY-EDV-ARFLRVNPYAGLFSFDQRYRPVPLTQGFIGIKGKKNRQQKKNIDEVCYDKVVEFLQEG--HQVLVFVHSRNET  362 (1230)
T ss_pred             CH-HHH-HHHhcCCCccceeeecccccccceeeeEEeeecccchhhhhhHHHHHHHHHHHHHHcC--CeEEEEEecChHH
Confidence            74 333 33444 3 355555566677777888887665541          1234444454444  8999999999999


Q ss_pred             HHHHHHhhhC
Q 030396          152 KELYGELAFD  161 (178)
Q Consensus       152 ~~l~~~L~~~  161 (178)
                      ...|..|.+.
T Consensus       363 i~tA~~l~~~  372 (1230)
T KOG0952|consen  363 IRTAKKLRER  372 (1230)
T ss_pred             HHHHHHHHHH
Confidence            9999998653

>PRK09694 helicase Cas3; Provisional

Probab=99.43  E-value=1.7e-12  Score=111.80  Aligned_cols=158  Identities=17%  Similarity=0.178  Sum_probs=96.2

Q ss_pred             CcEEEeCcHHHHHHHHc-CC-----CCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcHHHHHH
Q 030396           16 CDILISTPLRLRLAIRR-KK-----IDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEEL   89 (178)
Q Consensus        16 ~~Iii~TP~~l~~~l~~-~~-----~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~~~~~   89 (178)
                      ..|+|||+..++...-. +.     +.+. -+.+||||+|.+-.  ++...+..+++.+......++++|||+|...++.
T Consensus       411 api~V~TiDQlL~a~l~~kh~~lR~~~La-~svvIiDEVHAyD~--ym~~lL~~~L~~l~~~g~~vIllSATLP~~~r~~  487 (878)
T PRK09694        411 GQIGVCTIDQVLISVLPVKHRFIRGFGLG-RSVLIVDEVHAYDA--YMYGLLEAVLKAQAQAGGSVILLSATLPATLKQK  487 (878)
T ss_pred             CCEEEcCHHHHHHHHHccchHHHHHHhhc-cCeEEEechhhCCH--HHHHHHHHHHHHHHhcCCcEEEEeCCCCHHHHHH
Confidence            68999999998854322 21     1222 25899999999932  2566677777764344677999999999887654


Q ss_pred             -HHHhccC-c--------EEEEEcC--------Ccc-ccCCceEEEEEc-----CChhhHHHHHHHHHHh-cCCCCEEEE
Q 030396           90 -ARSIMHD-A--------VRVIVGR--------KNT-ASESIKQKLVFA-----GSEEGKLLALRQSFAE-SLNPPVLIF  144 (178)
Q Consensus        90 -~~~~~~~-~--------~~v~~~~--------~~~-~~~~i~~~~~~~-----~~~~~k~~~l~~ll~~-~~~~~~lIF  144 (178)
                       .+.+... +        .......        ... ......+.+ .+     .........+..+++. ...++++||
T Consensus       488 L~~a~~~~~~~~~~~~YPlvt~~~~~~~~~~~~~~~~~~~~~~~~v-~v~~~~~~~~~~~~~~l~~i~~~~~~g~~vLVf  566 (878)
T PRK09694        488 LLDTYGGHDPVELSSAYPLITWRGVNGAQRFDLSAHPEQLPARFTI-QLEPICLADMLPDLTLLQRMIAAANAGAQVCLI  566 (878)
T ss_pred             HHHHhccccccccccccccccccccccceeeeccccccccCcceEE-EEEeeccccccCHHHHHHHHHHHHhcCCEEEEE
Confidence             3333211 1        0000000        000 000011111 11     1111223334444443 335789999


Q ss_pred             eCCchHHHHHHHHhhhCC---CceEeeecCCCcccc
Q 030396          145 VQSKDRAKELYGELAFDD---IRAGVIHSDLSQTQV  177 (178)
Q Consensus       145 ~~t~~~~~~l~~~L~~~g---~~~~~lh~~~~~~~R  177 (178)
                      |||+++|+.+++.|++.+   .++..+||.+++.+|
T Consensus       567 ~NTV~~Aq~ly~~L~~~~~~~~~v~llHsrf~~~dR  602 (878)
T PRK09694        567 CNLVDDAQKLYQRLKELNNTQVDIDLFHARFTLNDR  602 (878)
T ss_pred             ECCHHHHHHHHHHHHhhCCCCceEEEEeCCCCHHHH
Confidence            999999999999998765   689999999998877

>KOG0352 consensus ATP-dependent DNA helicase [Replication, recombination and repair]

Probab=99.43  E-value=1.8e-13  Score=107.12  Aligned_cols=164  Identities=15%  Similarity=0.122  Sum_probs=113.9

Q ss_pred             hccCCCcEEEeCcHHHHHHHH----cCCCCCCCeeEEEEeccccccccC-CChhhHHHHH--hhCCCCCceEEEEeecCc
Q 030396           11 LSKFSCDILISTPLRLRLAIR----RKKIDLSRVEYLVLDEADKLFEVG-NLLKHIDPVV--KACSNPSIVRSLFSATLP   83 (178)
Q Consensus        11 ~l~~~~~Iii~TP~~l~~~l~----~~~~~~~~l~~lViDE~d~ll~~~-~~~~~i~~i~--~~~~~~~~q~i~~SAT~~   83 (178)
                      .-+.+..++..||+.-..-..    ++..+-.-+.++|+||||+.-+|| +|++++..+-  ++ .-+....++++||.+
T Consensus       109 ~ekp~~K~LYITPE~AAt~~FQ~lLn~L~~r~~L~Y~vVDEAHCVSQWGHDFRPDYL~LG~LRS-~~~~vpwvALTATA~  187 (641)
T KOG0352|consen  109 KEKPTIKMLYITPEGAATDGFQKLLNGLANRDVLRYIVVDEAHCVSQWGHDFRPDYLTLGSLRS-VCPGVPWVALTATAN  187 (641)
T ss_pred             hcCCceeEEEEchhhhhhhhHHHHHHHHhhhceeeeEEechhhhHhhhccccCcchhhhhhHHh-hCCCCceEEeecccC
Confidence            334566799999998654332    233346778999999999999998 8999999873  33 336788999999999


Q ss_pred             HHHHHHHHHh--ccCcEEEEEcCCccccCCceEEEEEcCChhhHHHHHHHHHHhc-------------CCCCEEEEeCCc
Q 030396           84 DFVEELARSI--MHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAES-------------LNPPVLIFVQSK  148 (178)
Q Consensus        84 ~~~~~~~~~~--~~~~~~v~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~-------------~~~~~lIF~~t~  148 (178)
                      +.+.+.+-..  ++.|+.+.-.  +.-..++-.-+.+-..-.+-+..|.++-...             ..+-.||||.|+
T Consensus       188 ~~VqEDi~~qL~L~~PVAiFkT--P~FR~NLFYD~~~K~~I~D~~~~LaDF~~~~LG~~~~~~~~~K~~~GCGIVYCRTR  265 (641)
T KOG0352|consen  188 AKVQEDIAFQLKLRNPVAIFKT--PTFRDNLFYDNHMKSFITDCLTVLADFSSSNLGKHEKASQNKKTFTGCGIVYCRTR  265 (641)
T ss_pred             hhHHHHHHHHHhhcCcHHhccC--cchhhhhhHHHHHHHHhhhHhHhHHHHHHHhcCChhhhhcCCCCcCcceEEEeccH
Confidence            9988765554  4577555432  2333333211111111123344444443211             133589999999


Q ss_pred             hHHHHHHHHhhhCCCceEeeecCCCcccc
Q 030396          149 DRAKELYGELAFDDIRAGVIHSDLSQTQV  177 (178)
Q Consensus       149 ~~~~~l~~~L~~~g~~~~~lh~~~~~~~R  177 (178)
                      ..|+.++-.|...|+++.++|+|+...||
T Consensus       266 ~~cEq~AI~l~~~Gi~A~AYHAGLK~~ER  294 (641)
T KOG0352|consen  266 NECEQVAIMLEIAGIPAMAYHAGLKKKER  294 (641)
T ss_pred             HHHHHHHHHhhhcCcchHHHhcccccchh
Confidence            99999999999999999999999998887

>TIGR03714 secA2 accessory Sec system translocase SecA2

Probab=99.42  E-value=3.9e-12  Score=107.36  Aligned_cols=57  Identities=18%  Similarity=0.218  Sum_probs=50.2

Q ss_pred             ChhhHHHHHHHHHHh--cCCCCEEEEeCCchHHHHHHHHhhhCCCceEeeecCCCcccc
Q 030396          121 SEEGKLLALRQSFAE--SLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQV  177 (178)
Q Consensus       121 ~~~~k~~~l~~ll~~--~~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~~~~~~R  177 (178)
                      ....|...+.+.+..  ...+|+||||+|++.++.++..|.+.|+++..+||++.+++|
T Consensus       405 ~~~~K~~ai~~~i~~~~~~~~pvLIft~s~~~se~ls~~L~~~gi~~~~L~a~~~~~E~  463 (762)
T TIGR03714       405 TLPEKLMATLEDVKEYHETGQPVLLITGSVEMSEIYSELLLREGIPHNLLNAQNAAKEA  463 (762)
T ss_pred             CHHHHHHHHHHHHHHHhhCCCCEEEEECcHHHHHHHHHHHHHCCCCEEEecCCChHHHH
Confidence            445688888888865  457899999999999999999999999999999999998775

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.

>KOG0353 consensus ATP-dependent DNA helicase [General function prediction only]

Probab=99.38  E-value=5.9e-12  Score=97.57  Aligned_cols=162  Identities=14%  Similarity=0.177  Sum_probs=122.8

Q ss_pred             CCCcEEEeCcHHHHHH---HH--cCCCCCCCeeEEEEeccccccccC-CChhhHHH--HHhhCCCCCceEEEEeecCcHH
Q 030396           14 FSCDILISTPLRLRLA---IR--RKKIDLSRVEYLVLDEADKLFEVG-NLLKHIDP--VVKACSNPSIVRSLFSATLPDF   85 (178)
Q Consensus        14 ~~~~Iii~TP~~l~~~---l~--~~~~~~~~l~~lViDE~d~ll~~~-~~~~~i~~--i~~~~~~~~~q~i~~SAT~~~~   85 (178)
                      .....+..||+.+...   +.  .+.+....++.+-+||+|+-.+|| +|++++..  |++. .-++..++.++||.+..
T Consensus       185 se~kliyvtpekiaksk~~mnkleka~~~~~~~~iaidevhccsqwghdfr~dy~~l~ilkr-qf~~~~iigltatatn~  263 (695)
T KOG0353|consen  185 SEFKLIYVTPEKIAKSKKFMNKLEKALEAGFFKLIAIDEVHCCSQWGHDFRPDYKALGILKR-QFKGAPIIGLTATATNH  263 (695)
T ss_pred             ceeEEEEecHHHHHHHHHHHHHHHHHhhcceeEEEeecceeehhhhCcccCcchHHHHHHHH-hCCCCceeeeehhhhcc
Confidence            3577999999998842   32  256778899999999999999998 89998876  5666 55788899999999988


Q ss_pred             HHHHHHHhccCcEEEEEcCCccccCCceEEEEEcCC-hhhHHHHHHHHHH-hcCCCCEEEEeCCchHHHHHHHHhhhCCC
Q 030396           86 VEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGS-EEGKLLALRQSFA-ESLNPPVLIFVQSKDRAKELYGELAFDDI  163 (178)
Q Consensus        86 ~~~~~~~~~~~~~~v~~~~~~~~~~~i~~~~~~~~~-~~~k~~~l~~ll~-~~~~~~~lIF~~t~~~~~~l~~~L~~~g~  163 (178)
                      +.......+.-...+. ...+...+++...+..-+. .++=.+-+..+++ .+..+..||||-++++|+.++..|+.+|+
T Consensus       264 vl~d~k~il~ie~~~t-f~a~fnr~nl~yev~qkp~n~dd~~edi~k~i~~~f~gqsgiiyc~sq~d~ekva~alkn~gi  342 (695)
T KOG0353|consen  264 VLDDAKDILCIEAAFT-FRAGFNRPNLKYEVRQKPGNEDDCIEDIAKLIKGDFAGQSGIIYCFSQKDCEKVAKALKNHGI  342 (695)
T ss_pred             hhhHHHHHHhHHhhhe-eecccCCCCceeEeeeCCCChHHHHHHHHHHhccccCCCcceEEEeccccHHHHHHHHHhcCc
Confidence            7776666554222221 2345566677666654333 3334555555665 45577899999999999999999999999


Q ss_pred             ceEeeecCCCcccc
Q 030396          164 RAGVIHSDLSQTQV  177 (178)
Q Consensus       164 ~~~~lh~~~~~~~R  177 (178)
                      .+..+|++|.+++|
T Consensus       343 ~a~~yha~lep~dk  356 (695)
T KOG0353|consen  343 HAGAYHANLEPEDK  356 (695)
T ss_pred             cccccccccCcccc
Confidence            99999999999887

>KOG0948 consensus Nuclear exosomal RNA helicase MTR4, DEAD-box superfamily [RNA processing and modification]

Probab=99.34  E-value=1e-11  Score=102.92  Aligned_cols=148  Identities=17%  Similarity=0.204  Sum_probs=110.9

Q ss_pred             hccCCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcHH--HHH
Q 030396           11 LSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDF--VEE   88 (178)
Q Consensus        11 ~l~~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~--~~~   88 (178)
                      .++..+.++|.|.+-|.+++.+|+--++.+.|+||||+|.|-+.. .+-.|++-+-. +|.+.+.+++|||+|+.  ..+
T Consensus       207 TInP~ASCLVMTTEILRsMLYRGSEvmrEVaWVIFDEIHYMRDkE-RGVVWEETIIl-lP~~vr~VFLSATiPNA~qFAe  284 (1041)
T KOG0948|consen  207 TINPDASCLVMTTEILRSMLYRGSEVMREVAWVIFDEIHYMRDKE-RGVVWEETIIL-LPDNVRFVFLSATIPNARQFAE  284 (1041)
T ss_pred             eeCCCCceeeeHHHHHHHHHhccchHhheeeeEEeeeehhccccc-cceeeeeeEEe-ccccceEEEEeccCCCHHHHHH
Confidence            356788999999999999999999889999999999999998776 67778777777 88999999999999975  345


Q ss_pred             HHHHhccCcEEEEEcCCccccCCceEEEEEcCC---------h-----hhH-----------------------------
Q 030396           89 LARSIMHDAVRVIVGRKNTASESIKQKLVFAGS---------E-----EGK-----------------------------  125 (178)
Q Consensus        89 ~~~~~~~~~~~v~~~~~~~~~~~i~~~~~~~~~---------~-----~~k-----------------------------  125 (178)
                      |+......|..|....-..+|  +-| |++...         .     ++.                             
T Consensus       285 WI~~ihkQPcHVVYTdyRPTP--LQH-yifP~ggdGlylvVDek~~FrednF~~am~~l~~~~~~~~~~~~~~k~~kG~~  361 (1041)
T KOG0948|consen  285 WICHIHKQPCHVVYTDYRPTP--LQH-YIFPAGGDGLYLVVDEKGKFREDNFQKAMSVLRKAGESDGKKKANKKGRKGGT  361 (1041)
T ss_pred             HHHHHhcCCceEEeecCCCCc--cee-eeecCCCCeeEEEEecccccchHHHHHHHHHhhccCCCccccccccccccCCc
Confidence            777777788777765433333  223 322211         1     111                             


Q ss_pred             ---------HHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhhhCCC
Q 030396          126 ---------LLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDI  163 (178)
Q Consensus       126 ---------~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~~~g~  163 (178)
                               +..+..++-.....|+|||+-++++|+.+|-.|.+..+
T Consensus       362 ~~~~~~~s~i~kiVkmi~~~~~~PVIvFSFSkkeCE~~Alqm~kldf  408 (1041)
T KOG0948|consen  362 GGKGPGDSDIYKIVKMIMERNYLPVIVFSFSKKECEAYALQMSKLDF  408 (1041)
T ss_pred             CCCCCCcccHHHHHHHHHhhcCCceEEEEecHhHHHHHHHhhccCcC
Confidence                     23444444444567999999999999999999987654

>PRK09200 preprotein translocase subunit SecA; Reviewed

Probab=99.26  E-value=1.5e-10  Score=98.54  Aligned_cols=57  Identities=18%  Similarity=0.190  Sum_probs=50.0

Q ss_pred             ChhhHHHHHHHHHHh--cCCCCEEEEeCCchHHHHHHHHhhhCCCceEeeecCCCcccc
Q 030396          121 SEEGKLLALRQSFAE--SLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQV  177 (178)
Q Consensus       121 ~~~~k~~~l~~ll~~--~~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~~~~~~R  177 (178)
                      +..+|...+.+.+..  ...+|+||||+|++.++.++..|.+.|+++..+||++.+++|
T Consensus       409 ~~~~K~~al~~~i~~~~~~~~pvLIf~~t~~~se~l~~~L~~~gi~~~~L~~~~~~~e~  467 (790)
T PRK09200        409 TLDEKYKAVIEEVKERHETGRPVLIGTGSIEQSETFSKLLDEAGIPHNLLNAKNAAKEA  467 (790)
T ss_pred             CHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHCCCCEEEecCCccHHHH
Confidence            445788989888875  357899999999999999999999999999999999887765

>KOG0951 consensus RNA helicase BRR2, DEAD-box superfamily [RNA processing and modification]

Probab=99.26  E-value=2.2e-11  Score=105.40  Aligned_cols=158  Identities=18%  Similarity=0.242  Sum_probs=111.2

Q ss_pred             CCcEEEeCcHHHHHHHHcCCCC---CCCeeEEEEeccccccccCCChhhHHHHHhhC------CCCCceEEEEeecCcHH
Q 030396           15 SCDILISTPLRLRLAIRRKKID---LSRVEYLVLDEADKLFEVGNLLKHIDPVVKAC------SNPSIVRSLFSATLPDF   85 (178)
Q Consensus        15 ~~~Iii~TP~~l~~~l~~~~~~---~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~------~~~~~q~i~~SAT~~~~   85 (178)
                      +-+|+||||+. ++.+.++..|   .+-++.+|+||+|.+.++.  ++.++.|....      -....+.+.+|||+|+-
T Consensus       411 eTqVIV~TPEK-~DiITRk~gdraY~qlvrLlIIDEIHLLhDdR--GpvLESIVaRt~r~ses~~e~~RlVGLSATLPNy  487 (1674)
T KOG0951|consen  411 ETQVIVTTPEK-WDIITRKSGDRAYEQLVRLLIIDEIHLLHDDR--GPVLESIVARTFRRSESTEEGSRLVGLSATLPNY  487 (1674)
T ss_pred             cceeEEeccch-hhhhhcccCchhHHHHHHHHhhhhhhhccccc--chHHHHHHHHHHHHhhhcccCceeeeecccCCch
Confidence            56899999998 6677665444   4566888999999997754  67777765552      12357899999999974


Q ss_pred             HHHHHHHhcc-CcEEEEEcCCccccCCceEEEEEcCChh--hHHH-----HHHHHHHhcCCCCEEEEeCCchHHHHHHHH
Q 030396           86 VEELARSIMH-DAVRVIVGRKNTASESIKQKLVFAGSEE--GKLL-----ALRQSFAESLNPPVLIFVQSKDRAKELYGE  157 (178)
Q Consensus        86 ~~~~~~~~~~-~~~~v~~~~~~~~~~~i~~~~~~~~~~~--~k~~-----~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~  157 (178)
                       .+ ...|++ +|.-+.....+..|--+.|+|+.+...+  .++.     .....++-....|+|||+.+++++-++|..
T Consensus       488 -~D-V~~Fl~v~~~glf~fd~syRpvPL~qq~Igi~ek~~~~~~qamNe~~yeKVm~~agk~qVLVFVHsRkET~ktA~a  565 (1674)
T KOG0951|consen  488 -ED-VASFLRVDPEGLFYFDSSYRPVPLKQQYIGITEKKPLKRFQAMNEACYEKVLEHAGKNQVLVFVHSRKETAKTARA  565 (1674)
T ss_pred             -hh-hHHHhccCcccccccCcccCcCCccceEeccccCCchHHHHHHHHHHHHHHHHhCCCCcEEEEEEechHHHHHHHH
Confidence             22 233333 4444445555667777899998776543  2222     233344555579999999999999998887


Q ss_pred             hhh-------------------------------------CCCceEeeecCCCcccc
Q 030396          158 LAF-------------------------------------DDIRAGVIHSDLSQTQV  177 (178)
Q Consensus       158 L~~-------------------------------------~g~~~~~lh~~~~~~~R  177 (178)
                      ++.                                     ..+-.+..|+||+..+|
T Consensus       566 IRd~~le~dtls~fmre~s~s~eilrtea~~~kn~dLkdLLpygfaIHhAGl~R~dR  622 (1674)
T KOG0951|consen  566 IRDKALEEDTLSRFMREDSASREILRTEAGQAKNPDLKDLLPYGFAIHHAGLNRKDR  622 (1674)
T ss_pred             HHHHHhhhhHHHHHHhcccchhhhhhhhhhcccChhHHHHhhccceeeccCCCcchH
Confidence            762                                     13678899999999887

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

Probab=99.20  E-value=6e-10  Score=96.46  Aligned_cols=146  Identities=18%  Similarity=0.197  Sum_probs=106.5

Q ss_pred             hccCCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcHHHH--H
Q 030396           11 LSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVE--E   88 (178)
Q Consensus        11 ~l~~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~~~--~   88 (178)
                      .+++++.|+|.|-+-|.+++.++...+..+.++||||+|.+-+.. -+..++.++-+ ++...|++++|||+|+..+  .
T Consensus       201 ~IN~~A~clvMTTEILRnMlyrg~~~~~~i~~ViFDEvHyi~D~e-RG~VWEE~Ii~-lP~~v~~v~LSATv~N~~EF~~  278 (1041)
T COG4581         201 SINPDAPCLVMTTEILRNMLYRGSESLRDIEWVVFDEVHYIGDRE-RGVVWEEVIIL-LPDHVRFVFLSATVPNAEEFAE  278 (1041)
T ss_pred             eeCCCCceEEeeHHHHHHHhccCcccccccceEEEEeeeeccccc-cchhHHHHHHh-cCCCCcEEEEeCCCCCHHHHHH
Confidence            566789999999999999999999999999999999999998877 88999999999 8889999999999997633  3


Q ss_pred             HHHHhccCcEEEEEcCCccccCCceEEEEEcCC-------hhhH------------------------------------
Q 030396           89 LARSIMHDAVRVIVGRKNTASESIKQKLVFAGS-------EEGK------------------------------------  125 (178)
Q Consensus        89 ~~~~~~~~~~~v~~~~~~~~~~~i~~~~~~~~~-------~~~k------------------------------------  125 (178)
                      ++...-..|..+........|  +.|++ .+..       .+.+                                    
T Consensus       279 Wi~~~~~~~~~vv~t~~RpvP--L~~~~-~~~~~l~~lvde~~~~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~a~~~~  355 (1041)
T COG4581         279 WIQRVHSQPIHVVSTEHRPVP--LEHFV-YVGKGLFDLVDEKKKFNAENFPSANRSLSCFSEKVRETDDGDVGRYARRTK  355 (1041)
T ss_pred             HHHhccCCCeEEEeecCCCCC--eEEEE-ecCCceeeeecccccchhhcchhhhhhhhccchhccccCcccccccccccc
Confidence            444444456666554433332  33333 2221       0000                                    


Q ss_pred             -----------HHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhhhC
Q 030396          126 -----------LLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFD  161 (178)
Q Consensus       126 -----------~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~~~  161 (178)
                                 ...+...+.....-|+|+|+-+++.|+..+..+...
T Consensus       356 ~~~~~~~~~~~~~~iv~~l~~~~~lP~I~F~FSr~~Ce~~a~~~~~l  402 (1041)
T COG4581         356 ALRGSAKGPAGRPEIVNKLDKDNLLPAIVFSFSRRGCEEAAQILSTL  402 (1041)
T ss_pred             ccCCcccccccchHHHhhhhhhcCCceEEEEEchhhHHHHHHHhccc
Confidence                       011233333444669999999999999999998643

>PRK12904 preprotein translocase subunit SecA; Reviewed

Probab=99.17  E-value=5.8e-10  Score=95.10  Aligned_cols=51  Identities=24%  Similarity=0.262  Sum_probs=45.7

Q ss_pred             ChhhHHHHHHHHHHh--cCCCCEEEEeCCchHHHHHHHHhhhCCCceEeeecC
Q 030396          121 SEEGKLLALRQSFAE--SLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSD  171 (178)
Q Consensus       121 ~~~~k~~~l~~ll~~--~~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~  171 (178)
                      ...+|...+.+.+..  ...+|+||||+|+..++.++..|.+.|++...+||.
T Consensus       411 t~~~K~~aI~~~I~~~~~~grpVLIft~Si~~se~Ls~~L~~~gi~~~vLnak  463 (830)
T PRK12904        411 TEKEKFDAVVEDIKERHKKGQPVLVGTVSIEKSELLSKLLKKAGIPHNVLNAK  463 (830)
T ss_pred             CHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHCCCceEeccCc
Confidence            455788999998865  557899999999999999999999999999999996

>TIGR00963 secA preprotein translocase, SecA subunit

Probab=99.16  E-value=4.8e-10  Score=94.54  Aligned_cols=51  Identities=25%  Similarity=0.290  Sum_probs=43.1

Q ss_pred             ChhhHHHHHHHHHHh--cCCCCEEEEeCCchHHHHHHHHhhhCCCceEeeecC
Q 030396          121 SEEGKLLALRQSFAE--SLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSD  171 (178)
Q Consensus       121 ~~~~k~~~l~~ll~~--~~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~  171 (178)
                      +..+|...+.+.+..  ...+|+||||+|+..++.++..|.+.|++...+||.
T Consensus       386 t~~~k~~ai~~~i~~~~~~grpvLV~t~si~~se~ls~~L~~~gi~~~~Lna~  438 (745)
T TIGR00963       386 TEEEKWKAVVDEIKERHAKGQPVLVGTTSVEKSELLSNLLKERGIPHNVLNAK  438 (745)
T ss_pred             CHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHcCCCeEEeeCC
Confidence            345677777776632  357899999999999999999999999999999998

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.

>KOG0947 consensus Cytoplasmic exosomal RNA helicase SKI2, DEAD-box superfamily [RNA processing and modification]

Probab=99.16  E-value=4.5e-10  Score=95.41  Aligned_cols=74  Identities=23%  Similarity=0.195  Sum_probs=67.6

Q ss_pred             hccCCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcHHH
Q 030396           11 LSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFV   86 (178)
Q Consensus        11 ~l~~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~~   86 (178)
                      ++...+.++|.|-+-|.+++.++.--.+++.++||||+|.+-+.. .+-.+++++-+ +|...++|++|||.|+..
T Consensus       375 qinPeAsCLIMTTEILRsMLYrgadliRDvE~VIFDEVHYiND~e-RGvVWEEViIM-lP~HV~~IlLSATVPN~~  448 (1248)
T KOG0947|consen  375 QINPEASCLIMTTEILRSMLYRGADLIRDVEFVIFDEVHYINDVE-RGVVWEEVIIM-LPRHVNFILLSATVPNTL  448 (1248)
T ss_pred             eeCCCcceEeehHHHHHHHHhcccchhhccceEEEeeeeeccccc-ccccceeeeee-ccccceEEEEeccCCChH
Confidence            566788999999999999999998888999999999999997776 88899999999 899999999999999763

>PRK13104 secA preprotein translocase subunit SecA; Reviewed

Probab=99.15  E-value=3e-10  Score=97.15  Aligned_cols=55  Identities=20%  Similarity=0.268  Sum_probs=47.0

Q ss_pred             hhHHHHHHHHHHh--cCCCCEEEEeCCchHHHHHHHHhhhCCCceEeeecCCCcccc
Q 030396          123 EGKLLALRQSFAE--SLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQV  177 (178)
Q Consensus       123 ~~k~~~l~~ll~~--~~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~~~~~~R  177 (178)
                      ..|...+.+-+..  ...+|+||||+|++.++.++..|.+.|++...+||.+.+.+|
T Consensus       427 ~~k~~av~~~i~~~~~~g~PVLVgt~Sie~sE~ls~~L~~~gi~h~vLnak~~q~Ea  483 (896)
T PRK13104        427 ADKFQAIIEDVRECGVRKQPVLVGTVSIEASEFLSQLLKKENIKHQVLNAKFHEKEA  483 (896)
T ss_pred             HHHHHHHHHHHHHHHhCCCCEEEEeCcHHHHHHHHHHHHHcCCCeEeecCCCChHHH
Confidence            4577777666643  347899999999999999999999999999999999998876

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

Probab=99.11  E-value=2.4e-09  Score=85.67  Aligned_cols=69  Identities=16%  Similarity=0.206  Sum_probs=57.0

Q ss_pred             CCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcH
Q 030396           14 FSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPD   84 (178)
Q Consensus        14 ~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~   84 (178)
                      ...+|+|+||+.+.+-+..|.+|+.++.++||||||+-..+-.+.......+++  ..+..++.+|||-..
T Consensus       106 ~~~kVfvaTPQvveNDl~~Grid~~dv~~lifDEAHRAvGnyAYv~Va~~y~~~--~k~~~ilgLTASPGs  174 (542)
T COG1111         106 AKKKVFVATPQVVENDLKAGRIDLDDVSLLIFDEAHRAVGNYAYVFVAKEYLRS--AKNPLILGLTASPGS  174 (542)
T ss_pred             hhCCEEEeccHHHHhHHhcCccChHHceEEEechhhhccCcchHHHHHHHHHHh--ccCceEEEEecCCCC
Confidence            456899999999999999999999999999999999987665355555555554  467789999999764

>TIGR00595 priA primosomal protein N'

Probab=99.07  E-value=1.5e-08  Score=83.55  Aligned_cols=64  Identities=14%  Similarity=-0.010  Sum_probs=43.7

Q ss_pred             cCCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccC--CC---hhhHHHHHhhCCCCCceEEEEeecCcHH
Q 030396           13 KFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVG--NL---LKHIDPVVKACSNPSIVRSLFSATLPDF   85 (178)
Q Consensus        13 ~~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~--~~---~~~i~~i~~~~~~~~~q~i~~SAT~~~~   85 (178)
                      .+.++|||||+..+.       ..+++++++|+||.|...-.+  ..   ..++.....  ...+.+++++|||-+.+
T Consensus        74 ~g~~~IVVGTrsalf-------~p~~~l~lIIVDEeh~~sykq~~~p~y~ar~~a~~ra--~~~~~~vil~SATPsle  142 (505)
T TIGR00595        74 NGEILVVIGTRSALF-------LPFKNLGLIIVDEEHDSSYKQEEGPRYHARDVAVYRA--KKFNCPVVLGSATPSLE  142 (505)
T ss_pred             cCCCCEEECChHHHc-------CcccCCCEEEEECCCccccccccCCCCcHHHHHHHHH--HhcCCCEEEEeCCCCHH
Confidence            456899999998763       357789999999999875433  11   122222333  33678999999996544

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).

>smart00487 DEXDc DEAD-like helicases superfamily

Probab=99.06  E-value=2.1e-09  Score=77.00  Aligned_cols=92  Identities=30%  Similarity=0.435  Sum_probs=78.0

Q ss_pred             hccCCC-cEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcHHHHHH
Q 030396           11 LSKFSC-DILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEEL   89 (178)
Q Consensus        11 ~l~~~~-~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~~~~~   89 (178)
                      .+..+. +++++||+++.+.+........+++++|+||+|.+.... +...+..+++. .+...+++++|||.++.....
T Consensus       100 ~~~~~~~~v~~~t~~~l~~~~~~~~~~~~~~~~iIiDE~h~~~~~~-~~~~~~~~~~~-~~~~~~~v~~saT~~~~~~~~  177 (201)
T smart00487      100 KLESGKTDILVTTPGRLLDLLENDLLELSNVDLVILDEAHRLLDGG-FGDQLEKLLKL-LPKNVQLLLLSATPPEEIENL  177 (201)
T ss_pred             HHhcCCCCEEEeChHHHHHHHHcCCcCHhHCCEEEEECHHHHhcCC-cHHHHHHHHHh-CCccceEEEEecCCchhHHHH
Confidence            344455 999999999999998877788899999999999998755 78999999998 677899999999999999999


Q ss_pred             HHHhccCcEEEEEcC
Q 030396           90 ARSIMHDAVRVIVGR  104 (178)
Q Consensus        90 ~~~~~~~~~~v~~~~  104 (178)
                      ...++.+...+....
T Consensus       178 ~~~~~~~~~~~~~~~  192 (201)
T smart00487      178 LELFLNDPVFIDVGP  192 (201)
T ss_pred             HHHhcCCCEEEeCCc
Confidence            999888766665543

>PRK04914 ATP-dependent helicase HepA; Validated

Probab=99.06  E-value=2.9e-09  Score=92.79  Aligned_cols=54  Identities=22%  Similarity=0.226  Sum_probs=49.6

Q ss_pred             hHHHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHh-hhCCCceEeeecCCCcccc
Q 030396          124 GKLLALRQSFAESLNPPVLIFVQSKDRAKELYGEL-AFDDIRAGVIHSDLSQTQV  177 (178)
Q Consensus       124 ~k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L-~~~g~~~~~lh~~~~~~~R  177 (178)
                      .|...|.++++.....|+||||+++..+..+++.| ...|+++..+||+|++.+|
T Consensus       479 ~Ki~~L~~~L~~~~~~KvLVF~~~~~t~~~L~~~L~~~~Gi~~~~ihG~~s~~eR  533 (956)
T PRK04914        479 PRVEWLIDFLKSHRSEKVLVICAKAATALQLEQALREREGIRAAVFHEGMSIIER  533 (956)
T ss_pred             HHHHHHHHHHHhcCCCeEEEEeCcHHHHHHHHHHHhhccCeeEEEEECCCCHHHH
Confidence            57788999998887889999999999999999999 5679999999999999887

>COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms]

Probab=99.06  E-value=5.9e-10  Score=95.52  Aligned_cols=159  Identities=21%  Similarity=0.265  Sum_probs=100.6

Q ss_pred             CcEEEeCcHHHHHHHH-cCCCC---CCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcHHHHHHHH
Q 030396           16 CDILISTPLRLRLAIR-RKKID---LSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELAR   91 (178)
Q Consensus        16 ~~Iii~TP~~l~~~l~-~~~~~---~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~~~~~~~   91 (178)
                      ..+.++||-.+..... .....   .=..+.+||||+|.+-... ....+..++..+......++++|||+|+..++.+.
T Consensus       311 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~S~vIlDE~h~~~~~~-~~~~l~~~i~~l~~~g~~ill~SATlP~~~~~~l~  389 (733)
T COG1203         311 LALIVVTPIQILIFSVKGFKFEFLALLLTSLVILDEVHLYADET-MLAALLALLEALAEAGVPVLLMSATLPPFLKEKLK  389 (733)
T ss_pred             ccccccCHhHhhhhhccccchHHHHHHHhhchhhccHHhhcccc-hHHHHHHHHHHHHhCCCCEEEEecCCCHHHHHHHH
Confidence            4566677766555221 11112   1233688999999998874 46666666665344678899999999999998888


Q ss_pred             HhccCcEEEEEcCCc---cccCCceEEEEEcCChhhH--HHHHHHHHH-hcCCCCEEEEeCCchHHHHHHHHhhhCCCce
Q 030396           92 SIMHDAVRVIVGRKN---TASESIKQKLVFAGSEEGK--LLALRQSFA-ESLNPPVLIFVQSKDRAKELYGELAFDDIRA  165 (178)
Q Consensus        92 ~~~~~~~~v~~~~~~---~~~~~i~~~~~~~~~~~~k--~~~l~~ll~-~~~~~~~lIF~~t~~~~~~l~~~L~~~g~~~  165 (178)
                      ..+.....+......   ..-..+.+.. .. +..+.  ......... .....+++|-|||+..|..++..|+..+.++
T Consensus       390 ~~~~~~~~~~~~~~~~~~~~e~~~~~~~-~~-~~~~~~~~~~~~~~~~~~~~~~kvlvI~NTV~~Aie~Y~~Lk~~~~~v  467 (733)
T COG1203         390 KALGKGREVVENAKFCPKEDEPGLKRKE-RV-DVEDGPQEELIELISEEVKEGKKVLVIVNTVDRAIELYEKLKEKGPKV  467 (733)
T ss_pred             HHHhcccceecccccccccccccccccc-ch-hhhhhhhHhhhhcchhhhccCCcEEEEEecHHHHHHHHHHHHhcCCCE
Confidence            877765444332110   0011111111 00 11111  011111122 2336799999999999999999999999899


Q ss_pred             EeeecCCCcccc
Q 030396          166 GVIHSDLSQTQV  177 (178)
Q Consensus       166 ~~lh~~~~~~~R  177 (178)
                      ..+||.+...+|
T Consensus       468 ~LlHSRf~~~dR  479 (733)
T COG1203         468 LLLHSRFTLKDR  479 (733)
T ss_pred             EEEecccchhhH
Confidence            999999999887

>PRK05580 primosome assembly protein PriA; Validated

Probab=98.95  E-value=6.8e-08  Score=82.33  Aligned_cols=70  Identities=17%  Similarity=0.061  Sum_probs=47.3

Q ss_pred             ccCCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccC--CChhhHHHH--HhhCCCCCceEEEEeecCcHHHH
Q 030396           12 SKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVG--NLLKHIDPV--VKACSNPSIVRSLFSATLPDFVE   87 (178)
Q Consensus        12 l~~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~--~~~~~i~~i--~~~~~~~~~q~i~~SAT~~~~~~   87 (178)
                      ..+.++||||||+.+.       ..++++.++|+||+|...-.+  ...-+.+.+  .+. ...+.|++++|||.+.+..
T Consensus       238 ~~g~~~IVVgTrsal~-------~p~~~l~liVvDEeh~~s~~~~~~p~y~~r~va~~ra-~~~~~~~il~SATps~~s~  309 (679)
T PRK05580        238 KRGEAKVVIGARSALF-------LPFKNLGLIIVDEEHDSSYKQQEGPRYHARDLAVVRA-KLENIPVVLGSATPSLESL  309 (679)
T ss_pred             HcCCCCEEEeccHHhc-------ccccCCCEEEEECCCccccccCcCCCCcHHHHHHHHh-hccCCCEEEEcCCCCHHHH
Confidence            3456899999998764       457889999999999864332  111122332  223 4468999999999775544


Q ss_pred             HH
Q 030396           88 EL   89 (178)
Q Consensus        88 ~~   89 (178)
                      ..
T Consensus       310 ~~  311 (679)
T PRK05580        310 AN  311 (679)
T ss_pred             HH
Confidence            43

>COG1643 HrpA HrpA-like helicases [DNA replication, recombination, and repair]

Probab=98.95  E-value=1.2e-08  Score=87.56  Aligned_cols=155  Identities=16%  Similarity=0.150  Sum_probs=105.8

Q ss_pred             CCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccc-cccCCChhhHHHHHhhCCCCCceEEEEeecCcHHHHHHHHH
Q 030396           14 FSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKL-FEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARS   92 (178)
Q Consensus        14 ~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~l-l~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~~~~~~~~   92 (178)
                      ..-.|-+.|.|.|+..+.... .++..+++|+||+|.= ++..-..-.+..++.. .+....++++|||+..   +.+..
T Consensus       138 ~~Trik~mTdGiLlrei~~D~-~Ls~ys~vIiDEaHERSl~tDilLgllk~~~~~-rr~DLKiIimSATld~---~rfs~  212 (845)
T COG1643         138 PRTRIKVMTDGILLREIQNDP-LLSGYSVVIIDEAHERSLNTDILLGLLKDLLAR-RRDDLKLIIMSATLDA---ERFSA  212 (845)
T ss_pred             CCceeEEeccHHHHHHHhhCc-ccccCCEEEEcchhhhhHHHHHHHHHHHHHHhh-cCCCceEEEEecccCH---HHHHH
Confidence            455799999999999988654 3789999999999984 3332123445555665 6667899999999994   44556


Q ss_pred             hccCcEEEEEcCCccccCCceEEEEEcCChh----hHHHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhhh----CCCc
Q 030396           93 IMHDAVRVIVGRKNTASESIKQKLVFAGSEE----GKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAF----DDIR  164 (178)
Q Consensus        93 ~~~~~~~v~~~~~~~~~~~i~~~~~~~~~~~----~k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~~----~g~~  164 (178)
                      +++++..+.++......   .-+|.......    ..+....+.......+.++||.+-.++.+.+++.|.+    ....
T Consensus       213 ~f~~apvi~i~GR~fPV---ei~Y~~~~~~d~~l~~ai~~~v~~~~~~~~GdILvFLpG~~EI~~~~~~L~~~~l~~~~~  289 (845)
T COG1643         213 YFGNAPVIEIEGRTYPV---EIRYLPEAEADYILLDAIVAAVDIHLREGSGSILVFLPGQREIERTAEWLEKAELGDDLE  289 (845)
T ss_pred             HcCCCCEEEecCCccce---EEEecCCCCcchhHHHHHHHHHHHhccCCCCCEEEECCcHHHHHHHHHHHHhccccCCcE
Confidence            66766566655433222   22231221111    2233333333344588999999999999999999987    4589


Q ss_pred             eEeeecCCCccc
Q 030396          165 AGVIHSDLSQTQ  176 (178)
Q Consensus       165 ~~~lh~~~~~~~  176 (178)
                      +..+||.|+.++
T Consensus       290 i~PLy~~L~~~e  301 (845)
T COG1643         290 ILPLYGALSAEE  301 (845)
T ss_pred             EeeccccCCHHH
Confidence            999999998764

>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=98.83  E-value=3.5e-07  Score=73.53  Aligned_cols=160  Identities=22%  Similarity=0.255  Sum_probs=113.6

Q ss_pred             CCcEEEeCcHHHHHHHHc-----CCCC-CCCeeEEEEeccccccccCCChhhHHHHHhhC--CCC---------------
Q 030396           15 SCDILISTPLRLRLAIRR-----KKID-LSRVEYLVLDEADKLFEVGNLLKHIDPVVKAC--SNP---------------   71 (178)
Q Consensus        15 ~~~Iii~TP~~l~~~l~~-----~~~~-~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~--~~~---------------   71 (178)
                      ++||||++|=-|...+..     +..| ++++..+|+|.||.++-..  -+.+..+++.+  .|.               
T Consensus       131 ~SDIIiASPLGLr~~i~~~~~~~~d~DFLSSIEv~iiD~ad~l~MQN--W~Hv~~v~~~lN~~P~~~~~~DfsRVR~w~L  208 (442)
T PF06862_consen  131 SSDIIIASPLGLRMIIGEEGEKKRDYDFLSSIEVLIIDQADVLLMQN--WEHVLHVFEHLNLQPKKSHDTDFSRVRPWYL  208 (442)
T ss_pred             cCCEEEEChHHHHHHhccccccccccchhheeeeEeechhhHHHHhh--HHHHHHHHHHhccCCCCCCCCCHHHHHHHHH
Confidence            689999999888888874     2223 8999999999999987544  45555555553  222               


Q ss_pred             ------CceEEEEeecCcHHHHHHHHHhccCc-EEEEEcC--C-----ccccCCceEEEEEcCCh------hhHHHHHHH
Q 030396           72 ------SIVRSLFSATLPDFVEELARSIMHDA-VRVIVGR--K-----NTASESIKQKLVFAGSE------EGKLLALRQ  131 (178)
Q Consensus        72 ------~~q~i~~SAT~~~~~~~~~~~~~~~~-~~v~~~~--~-----~~~~~~i~~~~~~~~~~------~~k~~~l~~  131 (178)
                            -+|++++|+...+++..+....+.|. ..+.+..  .     ......+.|.|...+..      ..++.....
T Consensus       209 dg~a~~~RQtii~S~~~~pe~~slf~~~~~N~~G~v~~~~~~~~~g~i~~v~~~v~Q~F~r~~~~s~~~~~d~Rf~yF~~  288 (442)
T PF06862_consen  209 DGQAKYYRQTIIFSSFQTPEINSLFNRHCQNYAGKVRLKPPYEASGVISQVVVQVRQVFQRFDCSSPADDPDARFKYFTK  288 (442)
T ss_pred             cCcchheeEeEEecCCCCHHHHHHHHhhCcCccceEEEeeccccceeeeccccCCceEEEEecCCCcchhhhHHHHHHHH
Confidence                  17999999999999999999966653 3333322  2     23445677877654332      234444433


Q ss_pred             ----HHH-hcCCCCEEEEeCCchHHHHHHHHhhhCCCceEeeecCCCccc
Q 030396          132 ----SFA-ESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQ  176 (178)
Q Consensus       132 ----ll~-~~~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~~~~~~  176 (178)
                          -+. ....+.+|||++|=-+=-.+-.+|.+.++..+.+|...++.+
T Consensus       289 ~iLP~l~~~~~~~~~LIfIPSYfDfVRlRN~lk~~~~sF~~i~EYts~~~  338 (442)
T PF06862_consen  289 KILPQLKRDSKMSGTLIFIPSYFDFVRLRNYLKKENISFVQISEYTSNSD  338 (442)
T ss_pred             HHHHHhhhccCCCcEEEEecchhhhHHHHHHHHhcCCeEEEecccCCHHH
Confidence                222 445678999999999999999999999999999888766543

; GO: 0005634 nucleus

>TIGR00603 rad25 DNA repair helicase rad25

Probab=98.82  E-value=1.7e-08  Score=85.54  Aligned_cols=149  Identities=13%  Similarity=0.004  Sum_probs=87.6

Q ss_pred             CcEEEeCcHHHHHHHHcC--------CCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcHH--
Q 030396           16 CDILISTPLRLRLAIRRK--------KIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDF--   85 (178)
Q Consensus        16 ~~Iii~TP~~l~~~l~~~--------~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~--   85 (178)
                      ..|+|+|...+.....+.        .+.-....++|+||+|.+-.     +.+..++.. +. ....+.+|||....  
T Consensus       344 ~~VvVtTYq~l~~~~~r~~~~~~~l~~l~~~~~gLII~DEvH~lpA-----~~fr~il~~-l~-a~~RLGLTATP~ReD~  416 (732)
T TIGR00603       344 AGVVVSTYSMVAHTGKRSYESEKVMEWLTNREWGLILLDEVHVVPA-----AMFRRVLTI-VQ-AHCKLGLTATLVREDD  416 (732)
T ss_pred             CcEEEEEHHHhhcccccchhhhHHHHHhccccCCEEEEEccccccH-----HHHHHHHHh-cC-cCcEEEEeecCcccCC
Confidence            679999998765332211        12224567999999999943     446667766 33 44569999998632  


Q ss_pred             HHHHHHHhccCcEEEEEcCC-----c-cccCCceEEEEEc--------------------CChhhHHHHHHHHHHhc--C
Q 030396           86 VEELARSIMHDAVRVIVGRK-----N-TASESIKQKLVFA--------------------GSEEGKLLALRQSFAES--L  137 (178)
Q Consensus        86 ~~~~~~~~~~~~~~v~~~~~-----~-~~~~~i~~~~~~~--------------------~~~~~k~~~l~~ll~~~--~  137 (178)
                      -...+..+ -.|......-.     + ..+.......+..                    .....|+..+..+++.+  .
T Consensus       417 ~~~~L~~L-iGP~vye~~~~eLi~~G~LA~~~~~ev~v~~t~~~~~~yl~~~~~~k~~l~~~np~K~~~~~~Li~~he~~  495 (732)
T TIGR00603       417 KITDLNFL-IGPKLYEANWMELQKKGFIANVQCAEVWCPMTPEFYREYLRENSRKRMLLYVMNPNKFRACQFLIRFHEQR  495 (732)
T ss_pred             chhhhhhh-cCCeeeecCHHHHHhCCccccceEEEEEecCCHHHHHHHHHhcchhhhHHhhhChHHHHHHHHHHHHHhhc
Confidence            11112111 22332222111     1 0110000001010                    11234667777777654  5


Q ss_pred             CCCEEEEeCCchHHHHHHHHhhhCCCceEeeecCCCcccc
Q 030396          138 NPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQV  177 (178)
Q Consensus       138 ~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~~~~~~R  177 (178)
                      ..++||||++...++.++..|.     +..+||++++.+|
T Consensus       496 g~kiLVF~~~~~~l~~~a~~L~-----~~~I~G~ts~~ER  530 (732)
T TIGR00603       496 GDKIIVFSDNVFALKEYAIKLG-----KPFIYGPTSQQER  530 (732)
T ss_pred             CCeEEEEeCCHHHHHHHHHHcC-----CceEECCCCHHHH
Confidence            7899999999999999999883     4569999999988

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).

>PRK12898 secA preprotein translocase subunit SecA; Reviewed

Probab=98.81  E-value=2.4e-08  Score=83.75  Aligned_cols=100  Identities=18%  Similarity=0.151  Sum_probs=77.2

Q ss_pred             EEEEeecCcHHHHHHHHHhccCcEEEEEcCCccccCCceEEEEEcCChhhHHHHHHHHHHhcC--CCCEEEEeCCchHHH
Q 030396           75 RSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESL--NPPVLIFVQSKDRAK  152 (178)
Q Consensus        75 ~i~~SAT~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~--~~~~lIF~~t~~~~~  152 (178)
                      ...||||.+....++.+.|.-++..+-...  .......+.++++ +..+|...+.+.++...  .+++||||+|++.++
T Consensus       411 l~GmTGTa~~~~~El~~~y~l~vv~IPt~k--p~~r~~~~~~v~~-t~~~K~~aL~~~i~~~~~~~~pvLIft~t~~~se  487 (656)
T PRK12898        411 LAGMTGTAREVAGELWSVYGLPVVRIPTNR--PSQRRHLPDEVFL-TAAAKWAAVAARVRELHAQGRPVLVGTRSVAASE  487 (656)
T ss_pred             HhcccCcChHHHHHHHHHHCCCeEEeCCCC--CccceecCCEEEe-CHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHH
Confidence            558999999887788887877865554332  2333344445455 56679999999997643  578999999999999


Q ss_pred             HHHHHhhhCCCceEeeecCCCcccc
Q 030396          153 ELYGELAFDDIRAGVIHSDLSQTQV  177 (178)
Q Consensus       153 ~l~~~L~~~g~~~~~lh~~~~~~~R  177 (178)
                      .++..|.+.|+++..+||++.+++|
T Consensus       488 ~L~~~L~~~gi~~~~Lhg~~~~rE~  512 (656)
T PRK12898        488 RLSALLREAGLPHQVLNAKQDAEEA  512 (656)
T ss_pred             HHHHHHHHCCCCEEEeeCCcHHHHH
Confidence            9999999999999999999876654

>PRK13107 preprotein translocase subunit SecA; Reviewed

Probab=98.78  E-value=6.4e-08  Score=83.10  Aligned_cols=55  Identities=16%  Similarity=0.253  Sum_probs=46.2

Q ss_pred             hhHHHHHHHHHHh--cCCCCEEEEeCCchHHHHHHHHhhhCCCceEeeecCCCcccc
Q 030396          123 EGKLLALRQSFAE--SLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQV  177 (178)
Q Consensus       123 ~~k~~~l~~ll~~--~~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~~~~~~R  177 (178)
                      ..|...+.+-+..  ...+|+||||+|++.++.++..|...|++...+|+.+.+.+|
T Consensus       432 ~~K~~Aii~ei~~~~~~GrpVLV~t~sv~~se~ls~~L~~~gi~~~vLnak~~~~Ea  488 (908)
T PRK13107        432 DEKYQAIIKDIKDCRERGQPVLVGTVSIEQSELLARLMVKEKIPHEVLNAKFHEREA  488 (908)
T ss_pred             HHHHHHHHHHHHHHHHcCCCEEEEeCcHHHHHHHHHHHHHCCCCeEeccCcccHHHH
Confidence            3566666665553  247899999999999999999999999999999999988775

>KOG0950 consensus DNA polymerase theta/eta, DEAD-box superfamily [General function prediction only]

Probab=98.74  E-value=9e-08  Score=81.75  Aligned_cols=77  Identities=18%  Similarity=0.157  Sum_probs=55.7

Q ss_pred             CCCcEEEeCcHHHHHHH----HcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhC----CCCCceEEEEeecCcHH
Q 030396           14 FSCDILISTPLRLRLAI----RRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKAC----SNPSIVRSLFSATLPDF   85 (178)
Q Consensus        14 ~~~~Iii~TP~~l~~~l----~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~----~~~~~q~i~~SAT~~~~   85 (178)
                      +.-++-|+|-++-+.++    +.+  .+..+.++|+||.|.+.+.+ ....++.++..+    .....|+|.+|||+|+-
T Consensus       314 k~~sv~i~tiEkanslin~lie~g--~~~~~g~vvVdElhmi~d~~-rg~~lE~~l~k~~y~~~~~~~~iIGMSATi~N~  390 (1008)
T KOG0950|consen  314 KRESVAIATIEKANSLINSLIEQG--RLDFLGMVVVDELHMIGDKG-RGAILELLLAKILYENLETSVQIIGMSATIPNN  390 (1008)
T ss_pred             cceeeeeeehHhhHhHHHHHHhcC--CccccCcEEEeeeeeeeccc-cchHHHHHHHHHHHhccccceeEeeeecccCCh
Confidence            45679999999855444    445  45678899999999999988 666676666554    33457899999999963


Q ss_pred             HHHHHHHhcc
Q 030396           86 VEELARSIMH   95 (178)
Q Consensus        86 ~~~~~~~~~~   95 (178)
                        .++..|++
T Consensus       391 --~lL~~~L~  398 (1008)
T KOG0950|consen  391 --SLLQDWLD  398 (1008)
T ss_pred             --HHHHHHhh
Confidence              44444544

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

Probab=98.66  E-value=2.3e-07  Score=75.50  Aligned_cols=154  Identities=14%  Similarity=0.081  Sum_probs=89.4

Q ss_pred             CcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcHHH---HHHHHH
Q 030396           16 CDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFV---EELARS   92 (178)
Q Consensus        16 ~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~~---~~~~~~   92 (178)
                      ..|.|+|=..+...-...........++|+||+|++....     ...+.+.+ ....-.+.+|||.+..-   ...+..
T Consensus       123 ~~i~vat~qtl~~~~~l~~~~~~~~~liI~DE~Hh~~a~~-----~~~~~~~~-~~~~~~LGLTATp~R~D~~~~~~l~~  196 (442)
T COG1061         123 AKVTVATVQTLARRQLLDEFLGNEFGLIIFDEVHHLPAPS-----YRRILELL-SAAYPRLGLTATPEREDGGRIGDLFD  196 (442)
T ss_pred             CcEEEEEhHHHhhhhhhhhhcccccCEEEEEccccCCcHH-----HHHHHHhh-hcccceeeeccCceeecCCchhHHHH
Confidence            3699999988776421122223367899999999997766     44444442 21111899999976211   011111


Q ss_pred             hccCcEEEEEcCCcccc----CCceEEEEEc-------------------------------------CChhhHHHHHHH
Q 030396           93 IMHDAVRVIVGRKNTAS----ESIKQKLVFA-------------------------------------GSEEGKLLALRQ  131 (178)
Q Consensus        93 ~~~~~~~v~~~~~~~~~----~~i~~~~~~~-------------------------------------~~~~~k~~~l~~  131 (178)
                      .+ .|............    .......+.+                                     .....+...+..
T Consensus       197 ~~-g~~vy~~~~~~li~~g~Lap~~~~~i~~~~t~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  275 (442)
T COG1061         197 LI-GPIVYEVSLKELIDEGYLAPYKYVEIKVTLTEDEEREYAKESARFRELLRARGTLRAENEARRIAIASERKIAAVRG  275 (442)
T ss_pred             hc-CCeEeecCHHHHHhCCCccceEEEEEEeccchHHHHHhhhhhhhhhhhhhhhhhhhHHHHHHHHhhccHHHHHHHHH
Confidence            11 12222221110000    0000000011                                     011234455555


Q ss_pred             HHHhc-CCCCEEEEeCCchHHHHHHHHhhhCCCceEeeecCCCcccc
Q 030396          132 SFAES-LNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQV  177 (178)
Q Consensus       132 ll~~~-~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~~~~~~R  177 (178)
                      ++..+ ...+++|||.+..+++.++..|...|+ +..+.|+.++.+|
T Consensus       276 ~~~~~~~~~~~lif~~~~~~a~~i~~~~~~~~~-~~~it~~t~~~eR  321 (442)
T COG1061         276 LLLKHARGDKTLIFASDVEHAYEIAKLFLAPGI-VEAITGETPKEER  321 (442)
T ss_pred             HHHHhcCCCcEEEEeccHHHHHHHHHHhcCCCc-eEEEECCCCHHHH
Confidence            55544 367999999999999999999999988 9999999999887

>KOG0922 consensus DEAH-box RNA helicase [RNA processing and modification]

Probab=98.65  E-value=5.5e-07  Score=74.52  Aligned_cols=152  Identities=17%  Similarity=0.163  Sum_probs=96.2

Q ss_pred             CCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccc-cccCCChhhHHHHHhhCCCCCceEEEEeecCcHHHHHHHHHh
Q 030396           15 SCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKL-FEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSI   93 (178)
Q Consensus        15 ~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~l-l~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~~~~~~~~~   93 (178)
                      .-.|.+.|-|.|+.-+.... .++.-+.+|+||||.= +..+-..-.+..|++.  +....++++|||+..   +....|
T Consensus       140 ~TrikymTDG~LLRE~l~Dp-~LskYsvIIlDEAHERsl~TDiLlGlLKki~~~--R~~LklIimSATlda---~kfS~y  213 (674)
T KOG0922|consen  140 DTRIKYMTDGMLLREILKDP-LLSKYSVIILDEAHERSLHTDILLGLLKKILKK--RPDLKLIIMSATLDA---EKFSEY  213 (674)
T ss_pred             ceeEEEecchHHHHHHhcCC-ccccccEEEEechhhhhhHHHHHHHHHHHHHhc--CCCceEEEEeeeecH---HHHHHH
Confidence            44699999999997665443 4677799999999984 1111133344445543  356789999999993   445566


Q ss_pred             ccCcEEEEEcCCccccCCceEEEEEcCChhhH----HHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhhhC----C--C
Q 030396           94 MHDAVRVIVGRKNTASESIKQKLVFAGSEEGK----LLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFD----D--I  163 (178)
Q Consensus        94 ~~~~~~v~~~~~~~~~~~i~~~~~~~~~~~~k----~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~~~----g--~  163 (178)
                      +.+...+.++.....   +..+|.. .+..+-    .....++-...+.+-++||....++.+.+++.|.+.    +  .
T Consensus       214 F~~a~i~~i~GR~fP---Vei~y~~-~p~~dYv~a~~~tv~~Ih~~E~~GDILvFLtGqeEIe~~~~~l~e~~~~~~~~~  289 (674)
T KOG0922|consen  214 FNNAPILTIPGRTFP---VEILYLK-EPTADYVDAALITVIQIHLTEPPGDILVFLTGQEEIEAACELLRERAKSLPEDC  289 (674)
T ss_pred             hcCCceEeecCCCCc---eeEEecc-CCchhhHHHHHHHHHHHHccCCCCCEEEEeCCHHHHHHHHHHHHHHhhhccccC
Confidence            666445555432222   2223322 122221    222233333456778999999999999999999764    1  1


Q ss_pred             --ceEeeecCCCccc
Q 030396          164 --RAGVIHSDLSQTQ  176 (178)
Q Consensus       164 --~~~~lh~~~~~~~  176 (178)
                        -+..+||.|+.++
T Consensus       290 ~~~~lply~aL~~e~  304 (674)
T KOG0922|consen  290 PELILPLYGALPSEE  304 (674)
T ss_pred             cceeeeecccCCHHH
Confidence              2578999998765

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

Probab=98.61  E-value=3.1e-06  Score=65.39  Aligned_cols=146  Identities=17%  Similarity=0.168  Sum_probs=91.2

Q ss_pred             CcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcHHHHHHHHHhcc
Q 030396           16 CDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMH   95 (178)
Q Consensus        16 ~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~~~~~~~~~~~   95 (178)
                      ..++|+|--.|+..-.       -.+++|+||+|.+--..  -+.+..-.+.-...+.-++.+|||-+...+.-+..  .
T Consensus       186 ~plvVaTtHQLlrFk~-------aFD~liIDEVDAFP~~~--d~~L~~Av~~ark~~g~~IylTATp~k~l~r~~~~--g  254 (441)
T COG4098         186 APLVVATTHQLLRFKQ-------AFDLLIIDEVDAFPFSD--DQSLQYAVKKARKKEGATIYLTATPTKKLERKILK--G  254 (441)
T ss_pred             ccEEEEehHHHHHHHh-------hccEEEEeccccccccC--CHHHHHHHHHhhcccCceEEEecCChHHHHHHhhh--C
Confidence            5678888866554432       34589999999984322  23333333332456777899999999765553332  2


Q ss_pred             CcEEEEEcCCccccCCceEEEEEcCChhhHHH------HHHHHHHhc--CCCCEEEEeCCchHHHHHHHHh-hhCCC-ce
Q 030396           96 DAVRVIVGRKNTASESIKQKLVFAGSEEGKLL------ALRQSFAES--LNPPVLIFVQSKDRAKELYGEL-AFDDI-RA  165 (178)
Q Consensus        96 ~~~~v~~~~~~~~~~~i~~~~~~~~~~~~k~~------~l~~ll~~~--~~~~~lIF~~t~~~~~~l~~~L-~~~g~-~~  165 (178)
                      +-..+.++..-...+-..-.++...+-.+++.      .|...+++.  ...|++||+++++..+.+++.| ...+. .+
T Consensus       255 ~~~~~klp~RfH~~pLpvPkf~w~~~~~k~l~r~kl~~kl~~~lekq~~~~~P~liF~p~I~~~eq~a~~lk~~~~~~~i  334 (441)
T COG4098         255 NLRILKLPARFHGKPLPVPKFVWIGNWNKKLQRNKLPLKLKRWLEKQRKTGRPVLIFFPEIETMEQVAAALKKKLPKETI  334 (441)
T ss_pred             CeeEeecchhhcCCCCCCCceEEeccHHHHhhhccCCHHHHHHHHHHHhcCCcEEEEecchHHHHHHHHHHHhhCCccce
Confidence            33344444433333333334556656555542      455666543  3579999999999999999999 44454 55


Q ss_pred             EeeecCC
Q 030396          166 GVIHSDL  172 (178)
Q Consensus       166 ~~lh~~~  172 (178)
                      +..|+.-
T Consensus       335 ~~Vhs~d  341 (441)
T COG4098         335 ASVHSED  341 (441)
T ss_pred             eeeeccC
Confidence            7888763

>cd00046 DEXDc DEAD-like helicases superfamily

Probab=98.48  E-value=8.1e-07  Score=59.87  Aligned_cols=68  Identities=29%  Similarity=0.314  Sum_probs=51.4

Q ss_pred             cCCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecC
Q 030396           13 KFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATL   82 (178)
Q Consensus        13 ~~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~   82 (178)
                      ..+++|+++|++.+..............+++|+||+|.+.... ........... .....+++++|||.
T Consensus        77 ~~~~~i~i~t~~~~~~~~~~~~~~~~~~~~iiiDE~h~~~~~~-~~~~~~~~~~~-~~~~~~~i~~saTp  144 (144)
T cd00046          77 SGKTDIVVGTPGRLLDELERLKLSLKKLDLLILDEAHRLLNQG-FGLLGLKILLK-LPKDRQVLLLSATP  144 (144)
T ss_pred             cCCCCEEEECcHHHHHHHHcCCcchhcCCEEEEeCHHHHhhcc-hHHHHHHHHhh-CCccceEEEEeccC
Confidence            4679999999999998887765556778899999999997765 33332222333 45778899999994

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

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

Probab=98.43  E-value=2.3e-06  Score=74.02  Aligned_cols=145  Identities=22%  Similarity=0.237  Sum_probs=99.1

Q ss_pred             cCCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhC-------------------CC---
Q 030396           13 KFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKAC-------------------SN---   70 (178)
Q Consensus        13 ~~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~-------------------~~---   70 (178)
                      +++.||+|+|.+-|..-...=  .--+.+++.+|.+|.++..+   ..+.+++..+                   +.   
T Consensus       179 ~gdfdIlitTs~FL~k~~e~L--~~~kFdfifVDDVDA~Lkas---kNvDriL~LlGf~eE~i~~a~~~~~lr~~~~~~~  253 (1187)
T COG1110         179 SGDFDILITTSQFLSKRFEEL--SKLKFDFIFVDDVDAILKAS---KNVDRLLRLLGFSEEVIESAYELIKLRRKLYGEK  253 (1187)
T ss_pred             cCCccEEEEeHHHHHhhHHHh--cccCCCEEEEccHHHHHhcc---ccHHHHHHHcCCCHHHHHHHHHHHHHHHHhhhhh
Confidence            357999999997766555421  11356799999999998765   2222222221                   00   


Q ss_pred             ---------------------CCceEEEEeecCcHHH--HHHHHHhccCcEEEEEcCCccccCCceEEEEEcCChhhHHH
Q 030396           71 ---------------------PSIVRSLFSATLPDFV--EELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLL  127 (178)
Q Consensus        71 ---------------------~~~q~i~~SAT~~~~~--~~~~~~~~~~~~~v~~~~~~~~~~~i~~~~~~~~~~~~k~~  127 (178)
                                           ...+.++.|||..+.-  ..+.+..++    ..++.......||..-++..    .-..
T Consensus       254 ~~~~~~e~~~~~e~~~~~~r~k~g~LvvsSATg~~rg~R~~LfReLlg----FevG~~~~~LRNIvD~y~~~----~~~e  325 (1187)
T COG1110         254 RAERVREELREVEREREKKRRKLGILVVSSATGKPRGSRLKLFRELLG----FEVGSGGEGLRNIVDIYVES----ESLE  325 (1187)
T ss_pred             hHHHHHHHHHHHHHHHHHhccCCceEEEeeccCCCCCchHHHHHHHhC----CccCccchhhhheeeeeccC----ccHH
Confidence                                 1257889999998652  234444444    24455566677777777544    3445


Q ss_pred             HHHHHHHhcCCCCEEEEeCC---chHHHHHHHHhhhCCCceEeeecC
Q 030396          128 ALRQSFAESLNPPVLIFVQS---KDRAKELYGELAFDDIRAGVIHSD  171 (178)
Q Consensus       128 ~l~~ll~~~~~~~~lIF~~t---~~~~~~l~~~L~~~g~~~~~lh~~  171 (178)
                      ...+++++. ..=.|||+++   ++-|+.++++|..+|+++..+|++
T Consensus       326 ~~~elvk~l-G~GgLIfV~~d~G~e~aeel~e~Lr~~Gi~a~~~~a~  371 (1187)
T COG1110         326 KVVELVKKL-GDGGLIFVPIDYGREKAEELAEYLRSHGINAELIHAE  371 (1187)
T ss_pred             HHHHHHHHh-CCCeEEEEEcHHhHHHHHHHHHHHHhcCceEEEeecc
Confidence            566677776 3469999999   999999999999999999999986

>KOG0920 consensus ATP-dependent RNA helicase A [RNA processing and modification]

Probab=98.41  E-value=6.1e-06  Score=71.50  Aligned_cols=155  Identities=17%  Similarity=0.159  Sum_probs=102.0

Q ss_pred             CCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcHHHHHHHHHhc
Q 030396           15 SCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIM   94 (178)
Q Consensus        15 ~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~~~~~~~~~~   94 (178)
                      .-.++++|-|-|++.+.. .-.+..+..+|+||+|.=--+.+|.-.+.+-+-. .++..++|++|||+.   .+....|+
T Consensus       264 ~t~L~fcTtGvLLr~L~~-~~~l~~vthiivDEVHER~i~~DflLi~lk~lL~-~~p~LkvILMSAT~d---ae~fs~YF  338 (924)
T KOG0920|consen  264 ETRLLFCTTGVLLRRLQS-DPTLSGVTHIIVDEVHERSINTDFLLILLKDLLP-RNPDLKVILMSATLD---AELFSDYF  338 (924)
T ss_pred             ceeEEEecHHHHHHHhcc-CcccccCceeeeeeEEEccCCcccHHHHHHHHhh-hCCCceEEEeeeecc---hHHHHHHh
Confidence            467999999999999887 4568899999999999964444355555444444 568999999999999   45556666


Q ss_pred             cCcEEEEEcCCccc----------------cCCceEEEEEcC-----------ChhhHHHHHHHHHH----hcCCCCEEE
Q 030396           95 HDAVRVIVGRKNTA----------------SESIKQKLVFAG-----------SEEGKLLALRQSFA----ESLNPPVLI  143 (178)
Q Consensus        95 ~~~~~v~~~~~~~~----------------~~~i~~~~~~~~-----------~~~~k~~~l~~ll~----~~~~~~~lI  143 (178)
                      ++...+.+......                ...-.+......           ..+-..+.+.+++.    ....+.+||
T Consensus       339 ~~~pvi~i~grtfpV~~~fLEDil~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~id~~Li~~li~~I~~~~~~GaILV  418 (924)
T KOG0920|consen  339 GGCPVITIPGRTFPVKEYFLEDILSKTGYVSEDDSARSGPERSQLRLARLKLWEPEIDYDLIEDLIEYIDEREFEGAILV  418 (924)
T ss_pred             CCCceEeecCCCcchHHHHHHHHHHHhcccccccccccccccCccccccchhccccccHHHHHHHHHhcccCCCCceEEE
Confidence            66555555322110                000011100000           11123344444443    333778999


Q ss_pred             EeCCchHHHHHHHHhhhC-------CCceEeeecCCCc
Q 030396          144 FVQSKDRAKELYGELAFD-------DIRAGVIHSDLSQ  174 (178)
Q Consensus       144 F~~t~~~~~~l~~~L~~~-------g~~~~~lh~~~~~  174 (178)
                      |.+...+...+...|...       .+-+..+||.|+.
T Consensus       419 FLPG~~eI~~~~~~L~~~~~f~~~~~~~ilplHs~~~s  456 (924)
T KOG0920|consen  419 FLPGWEEILQLKELLEVNLPFADSLKFAILPLHSSIPS  456 (924)
T ss_pred             EcCCHHHHHHHHHHhhhccccccccceEEEeccccCCh
Confidence            999999999999999642       3578899999987

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

Probab=98.38  E-value=9.7e-06  Score=72.52  Aligned_cols=67  Identities=16%  Similarity=0.203  Sum_probs=47.9

Q ss_pred             CCCcEEEeCcHHHHHHHHcC-----CCCCCCeeEEEEeccccccc------cC--------CChhhHHHHHhhCCCCCce
Q 030396           14 FSCDILISTPLRLRLAIRRK-----KIDLSRVEYLVLDEADKLFE------VG--------NLLKHIDPVVKACSNPSIV   74 (178)
Q Consensus        14 ~~~~Iii~TP~~l~~~l~~~-----~~~~~~l~~lViDE~d~ll~------~~--------~~~~~i~~i~~~~~~~~~q   74 (178)
                      ....|+|+|..++...+...     ...+...+++|+||||+-..      .+        .+...++.++.++   +.-
T Consensus       510 ~~~~I~iaTiQtl~~~~~~~~~~~~~~~~~~fdlIIiDEaHRs~~~d~~~~~~~~~~~~~~~~~~~yr~iL~yF---dA~  586 (1123)
T PRK11448        510 DETKVHVATVQGMVKRILYSDDPMDKPPVDQYDCIIVDEAHRGYTLDKEMSEGELQFRDQLDYVSKYRRVLDYF---DAV  586 (1123)
T ss_pred             CCCCEEEEEHHHHHHhhhccccccccCCCCcccEEEEECCCCCCccccccccchhccchhhhHHHHHHHHHhhc---Ccc
Confidence            35789999999987765321     23567888999999999631      11        1246788888873   356


Q ss_pred             EEEEeecCc
Q 030396           75 RSLFSATLP   83 (178)
Q Consensus        75 ~i~~SAT~~   83 (178)
                      .+.||||-.
T Consensus       587 ~IGLTATP~  595 (1123)
T PRK11448        587 KIGLTATPA  595 (1123)
T ss_pred             EEEEecCCc
Confidence            799999975

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

Probab=98.36  E-value=2.1e-05  Score=65.85  Aligned_cols=150  Identities=15%  Similarity=0.206  Sum_probs=91.5

Q ss_pred             hccC-CCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCC-CceEEEEeecCcHHHHH
Q 030396           11 LSKF-SCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNP-SIVRSLFSATLPDFVEE   88 (178)
Q Consensus        11 ~l~~-~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~-~~q~i~~SAT~~~~~~~   88 (178)
                      .+.+ ..+|||||..     +-+...+++++.++|+||=|++--.+      +..++. ... ..-.+++|||-=|.  .
T Consensus       360 ~l~~G~~~ivVGTHA-----LiQd~V~F~~LgLVIiDEQHRFGV~Q------R~~L~~-KG~~~Ph~LvMTATPIPR--T  425 (677)
T COG1200         360 QLASGEIDIVVGTHA-----LIQDKVEFHNLGLVIIDEQHRFGVHQ------RLALRE-KGEQNPHVLVMTATPIPR--T  425 (677)
T ss_pred             HHhCCCCCEEEEcch-----hhhcceeecceeEEEEeccccccHHH------HHHHHH-hCCCCCcEEEEeCCCchH--H
Confidence            4444 4999999984     44556779999999999999984333      333443 444 57789999996543  3


Q ss_pred             HHHHhccCcEEEEEcCCccccCCceEEEEEcCChhhHHHHHHHHHHhcCCCCEEEEeCCch--------HHHHHHHHhhh
Q 030396           89 LARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKD--------RAKELYGELAF  160 (178)
Q Consensus        89 ~~~~~~~~~~~v~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~~t~~--------~~~~l~~~L~~  160 (178)
                      ++-..+.|-..-.++.-+.-+..|.-..+......+-.+.+..-+.  ...|+-+-|+-++        .|+.+++.|+.
T Consensus       426 LAlt~fgDldvS~IdElP~GRkpI~T~~i~~~~~~~v~e~i~~ei~--~GrQaY~VcPLIeESE~l~l~~a~~~~~~L~~  503 (677)
T COG1200         426 LALTAFGDLDVSIIDELPPGRKPITTVVIPHERRPEVYERIREEIA--KGRQAYVVCPLIEESEKLELQAAEELYEELKS  503 (677)
T ss_pred             HHHHHhccccchhhccCCCCCCceEEEEeccccHHHHHHHHHHHHH--cCCEEEEEeccccccccchhhhHHHHHHHHHH
Confidence            3334444422222222222223344445444333333444433333  4588999996554        45567777764


Q ss_pred             C--CCceEeeecCCCccc
Q 030396          161 D--DIRAGVIHSDLSQTQ  176 (178)
Q Consensus       161 ~--g~~~~~lh~~~~~~~  176 (178)
                      .  ++++..+||.|+..|
T Consensus       504 ~~~~~~vgL~HGrm~~~e  521 (677)
T COG1200         504 FLPELKVGLVHGRMKPAE  521 (677)
T ss_pred             HcccceeEEEecCCChHH
Confidence            3  568999999999765

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

Probab=98.33  E-value=1.3e-05  Score=70.59  Aligned_cols=145  Identities=15%  Similarity=0.104  Sum_probs=98.2

Q ss_pred             CCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcHHHHHHHHHh
Q 030396           14 FSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSI   93 (178)
Q Consensus        14 ~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~~~~~~~~~   93 (178)
                      +..||||||.-     +-++.+.++++..+|+||=|++--..  .    +-++. +..+.-++-+|||-=|.-....-.-
T Consensus       696 G~vDIvIGTHr-----LL~kdv~FkdLGLlIIDEEqRFGVk~--K----EkLK~-Lr~~VDvLTLSATPIPRTL~Msm~G  763 (1139)
T COG1197         696 GKVDIVIGTHR-----LLSKDVKFKDLGLLIIDEEQRFGVKH--K----EKLKE-LRANVDVLTLSATPIPRTLNMSLSG  763 (1139)
T ss_pred             CCccEEEechH-----hhCCCcEEecCCeEEEechhhcCccH--H----HHHHH-HhccCcEEEeeCCCCcchHHHHHhc
Confidence            56999999983     23466789999999999999984333  3    33444 6678889999999655544444445


Q ss_pred             ccCcEEEEEcCCccccCCceEEEEEcCChh-hHHHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhhhC--CCceEeeec
Q 030396           94 MHDAVRVIVGRKNTASESIKQKLVFAGSEE-GKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFD--DIRAGVIHS  170 (178)
Q Consensus        94 ~~~~~~v~~~~~~~~~~~i~~~~~~~~~~~-~k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~~~--g~~~~~lh~  170 (178)
                      .++-..+..++.+..+  +.=++ ...+.. -+-+.+.++   ...+|+-.-+|.+++.+.++..|++.  ..+++.-||
T Consensus       764 iRdlSvI~TPP~~R~p--V~T~V-~~~d~~~ireAI~REl---~RgGQvfYv~NrV~~Ie~~~~~L~~LVPEarI~vaHG  837 (1139)
T COG1197         764 IRDLSVIATPPEDRLP--VKTFV-SEYDDLLIREAILREL---LRGGQVFYVHNRVESIEKKAERLRELVPEARIAVAHG  837 (1139)
T ss_pred             chhhhhccCCCCCCcc--eEEEE-ecCChHHHHHHHHHHH---hcCCEEEEEecchhhHHHHHHHHHHhCCceEEEEeec
Confidence            5565566555544433  33333 322222 222222222   23588888899999999999999887  568999999


Q ss_pred             CCCccc
Q 030396          171 DLSQTQ  176 (178)
Q Consensus       171 ~~~~~~  176 (178)
                      .|+.++
T Consensus       838 QM~e~e  843 (1139)
T COG1197         838 QMRERE  843 (1139)
T ss_pred             CCCHHH
Confidence            998754

>TIGR00631 uvrb excinuclease ABC, B subunit

Probab=98.27  E-value=3.3e-06  Score=71.72  Aligned_cols=56  Identities=21%  Similarity=0.274  Sum_probs=46.5

Q ss_pred             hhhHHHHHHHHHHh--cCCCCEEEEeCCchHHHHHHHHhhhCCCceEeeecCCCcccc
Q 030396          122 EEGKLLALRQSFAE--SLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQV  177 (178)
Q Consensus       122 ~~~k~~~l~~ll~~--~~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~~~~~~R  177 (178)
                      ...++..+.+-++.  ....+++|||+|++.|+.+++.|.+.|+++..+||++++.+|
T Consensus       424 ~~~qi~~Ll~eI~~~~~~g~~vLIf~~tk~~ae~L~~~L~~~gi~~~~lh~~~~~~eR  481 (655)
T TIGR00631       424 TDGQVDDLLSEIRQRVARNERVLVTTLTKKMAEDLTDYLKELGIKVRYLHSEIDTLER  481 (655)
T ss_pred             ccchHHHHHHHHHHHHcCCCEEEEEECCHHHHHHHHHHHhhhccceeeeeCCCCHHHH
Confidence            34456666666653  346789999999999999999999999999999999998776

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

>PRK12899 secA preprotein translocase subunit SecA; Reviewed

Probab=98.25  E-value=7.9e-07  Score=76.83  Aligned_cols=48  Identities=23%  Similarity=0.248  Sum_probs=38.2

Q ss_pred             hHHHHHHHHHHhc--CCCCEEEEeCCchHHHHHHHHhhhCCCceEeeecC
Q 030396          124 GKLLALRQSFAES--LNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSD  171 (178)
Q Consensus       124 ~k~~~l~~ll~~~--~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~  171 (178)
                      .|...+.+-+...  ..+|+||-|.|....+.++..|.+.|++...+++.
T Consensus       552 ~k~~ai~~ei~~~~~~grPvLigt~si~~se~ls~~L~~~gi~h~vLNak  601 (970)
T PRK12899        552 EKYHAIVAEIASIHRKGNPILIGTESVEVSEKLSRILRQNRIEHTVLNAK  601 (970)
T ss_pred             HHHHHHHHHHHHHHhCCCCEEEEeCcHHHHHHHHHHHHHcCCcceecccc
Confidence            4666665555432  46789999999999999999999999988877764

>KOG0354 consensus DEAD-box like helicase [General function prediction only]

Probab=98.21  E-value=4e-06  Score=70.85  Aligned_cols=75  Identities=17%  Similarity=0.110  Sum_probs=59.2

Q ss_pred             ccCCCcEEEeCcHHHHHHHHcCCCC-CCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcHHHH
Q 030396           12 SKFSCDILISTPLRLRLAIRRKKID-LSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVE   87 (178)
Q Consensus        12 l~~~~~Iii~TP~~l~~~l~~~~~~-~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~~~   87 (178)
                      +-...+|+|.||+-|.+.|..+..+ ++++.++||||||+-..+..+...++..+.. .....|++++|||......
T Consensus       151 i~~s~~vff~TpQil~ndL~~~~~~~ls~fs~iv~DE~Hra~kn~~Y~~Vmr~~l~~-k~~~~qILgLTASpG~~~~  226 (746)
T KOG0354|consen  151 IVASKRVFFRTPQILENDLKSGLHDELSDFSLIVFDECHRTSKNHPYNNIMREYLDL-KNQGNQILGLTASPGSKLE  226 (746)
T ss_pred             hhcccceEEeChHhhhhhcccccccccceEEEEEEcccccccccccHHHHHHHHHHh-hhccccEEEEecCCCccHH
Confidence            3457899999999999999887665 5999999999999998776455555566665 4555699999999986433

>PF14617 CMS1: U3-containing 90S pre-ribosomal complex subunit

Probab=98.20  E-value=2.1e-06  Score=64.38  Aligned_cols=47  Identities=28%  Similarity=0.309  Sum_probs=42.8

Q ss_pred             hHhHHhHHhccC-CCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccc
Q 030396            3 KELVRSTDLSKF-SCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEAD   49 (178)
Q Consensus         3 ~~~~~q~~~l~~-~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d   49 (178)
                      -++.+|...+++ ..+|.|||||||..+++.+.+.+++++++|+|--|
T Consensus       164 ~Kl~eqv~~L~~~~~~i~vGTP~Rl~kLle~~~L~l~~l~~ivlD~s~  211 (252)
T PF14617_consen  164 IKLEEQVKLLKKTRVHIAVGTPGRLSKLLENGALSLSNLKRIVLDWSY  211 (252)
T ss_pred             ccHHHHHHHHHhCCceEEEeChHHHHHHHHcCCCCcccCeEEEEcCCc
Confidence            468899999985 79999999999999999999999999999999753

>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional

Probab=98.19  E-value=1.9e-05  Score=69.89  Aligned_cols=54  Identities=20%  Similarity=0.221  Sum_probs=46.5

Q ss_pred             hHHHHHHHHHHhc--CCCCEEEEeCCchHHHHHHHHhhhCCCceEeeecCCCcccc
Q 030396          124 GKLLALRQSFAES--LNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQV  177 (178)
Q Consensus       124 ~k~~~l~~ll~~~--~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~~~~~~R  177 (178)
                      .|+..|..++...  ...++|||+......+.+.++|...|++...++|+++..+|
T Consensus       471 gKl~lLdkLL~~Lk~~g~KVLIFSQft~~LdiLed~L~~~g~~y~rIdGsts~~eR  526 (1033)
T PLN03142        471 GKMVLLDKLLPKLKERDSRVLIFSQMTRLLDILEDYLMYRGYQYCRIDGNTGGEDR  526 (1033)
T ss_pred             hHHHHHHHHHHHHHhcCCeEEeehhHHHHHHHHHHHHHHcCCcEEEECCCCCHHHH
Confidence            5677777777643  36799999999999999999999999999999999998877

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

Probab=98.13  E-value=2.6e-05  Score=63.57  Aligned_cols=98  Identities=21%  Similarity=0.156  Sum_probs=64.7

Q ss_pred             CceEEEEeecCcHHHHHHHHHhccCcEEEEEcCCccccCCceEEEEEcCChhhHHHHHHHHHH--hcCCCCEEEEeCCch
Q 030396           72 SIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFA--ESLNPPVLIFVQSKD  149 (178)
Q Consensus        72 ~~q~i~~SAT~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~--~~~~~~~lIF~~t~~  149 (178)
                      ..|++++|||-.+.-.+.   ..++-..-.+.+.+...+-+     .+.+....++-|++-++  ...+.+++|=+=|++
T Consensus       386 ~~q~i~VSATPg~~E~e~---s~~~vveQiIRPTGLlDP~i-----evRp~~~QvdDL~~EI~~r~~~~eRvLVTtLTKk  457 (663)
T COG0556         386 IPQTIYVSATPGDYELEQ---SGGNVVEQIIRPTGLLDPEI-----EVRPTKGQVDDLLSEIRKRVAKNERVLVTTLTKK  457 (663)
T ss_pred             cCCEEEEECCCChHHHHh---ccCceeEEeecCCCCCCCce-----eeecCCCcHHHHHHHHHHHHhcCCeEEEEeehHH
Confidence            369999999988653332   22232333444444443332     22232333343443333  234689999999999


Q ss_pred             HHHHHHHHhhhCCCceEeeecCCCcccc
Q 030396          150 RAKELYGELAFDDIRAGVIHSDLSQTQV  177 (178)
Q Consensus       150 ~~~~l~~~L~~~g~~~~~lh~~~~~~~R  177 (178)
                      .|+.|.++|.+.|+++..+||+...-+|
T Consensus       458 mAEdLT~Yl~e~gikv~YlHSdidTlER  485 (663)
T COG0556         458 MAEDLTEYLKELGIKVRYLHSDIDTLER  485 (663)
T ss_pred             HHHHHHHHHHhcCceEEeeeccchHHHH
Confidence            9999999999999999999999877665

>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=98.13  E-value=1.6e-05  Score=53.26  Aligned_cols=54  Identities=37%  Similarity=0.366  Sum_probs=48.2

Q ss_pred             hHHHHHHHHHHhcC--CCCEEEEeCCchHHHHHHHHhhhCCCceEeeecCCCcccc
Q 030396          124 GKLLALRQSFAESL--NPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQV  177 (178)
Q Consensus       124 ~k~~~l~~ll~~~~--~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~~~~~~R  177 (178)
                      .|...+.+++....  .+++||||++...++.+++.|.+.+.++..+||+++..+|
T Consensus        12 ~k~~~i~~~i~~~~~~~~~~lvf~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~   67 (131)
T cd00079          12 EKLEALLELLKEHLKKGGKVLIFCPSKKMLDELAELLRKPGIKVAALHGDGSQEER   67 (131)
T ss_pred             HHHHHHHHHHHhcccCCCcEEEEeCcHHHHHHHHHHHHhcCCcEEEEECCCCHHHH
Confidence            68888888888664  7899999999999999999999999999999999987765

>PRK05298 excinuclease ABC subunit B; Provisional

Probab=98.10  E-value=8.7e-06  Score=69.34  Aligned_cols=54  Identities=22%  Similarity=0.252  Sum_probs=45.0

Q ss_pred             hHHHHHHHHHHh--cCCCCEEEEeCCchHHHHHHHHhhhCCCceEeeecCCCcccc
Q 030396          124 GKLLALRQSFAE--SLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQV  177 (178)
Q Consensus       124 ~k~~~l~~ll~~--~~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~~~~~~R  177 (178)
                      .++..+.+.+..  ....+++|||+|++.|+.+++.|.+.|+++..+||++++.+|
T Consensus       430 ~q~~~L~~~L~~~~~~g~~viIf~~t~~~ae~L~~~L~~~gi~~~~~h~~~~~~~R  485 (652)
T PRK05298        430 GQVDDLLSEIRKRVAKGERVLVTTLTKRMAEDLTDYLKELGIKVRYLHSDIDTLER  485 (652)
T ss_pred             ccHHHHHHHHHHHHhCCCEEEEEeCCHHHHHHHHHHHhhcceeEEEEECCCCHHHH
Confidence            445566666653  236789999999999999999999999999999999998765

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

Probab=97.94  E-value=3.2e-05  Score=65.91  Aligned_cols=152  Identities=15%  Similarity=0.150  Sum_probs=86.7

Q ss_pred             CCcEEEeCcHHHHHHHHcC-----CCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcHHHHHH
Q 030396           15 SCDILISTPLRLRLAIRRK-----KIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEEL   89 (178)
Q Consensus        15 ~~~Iii~TP~~l~~~l~~~-----~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~~~~~   89 (178)
                      .++|.++|=.++...+.+.     .+.....+++|+||||+=+     ......|+.++ ..-.|  .++||....+..-
T Consensus       256 s~~i~lsTyqt~~~~~~~~~~~~~~f~~g~FDlIvIDEaHRgi-----~~~~~~I~dYF-dA~~~--gLTATP~~~~d~~  327 (875)
T COG4096         256 SSEIYLSTYQTMTGRIEQKEDEYRRFGPGFFDLIVIDEAHRGI-----YSEWSSILDYF-DAATQ--GLTATPKETIDRS  327 (875)
T ss_pred             ceeEEEeehHHHHhhhhccccccccCCCCceeEEEechhhhhH-----HhhhHHHHHHH-HHHHH--hhccCcccccccc
Confidence            5799999999999888765     3446779999999999853     34455777773 32333  3377766533332


Q ss_pred             HHHhc-cCc------------------EEEEE----cCCccccCCc-------------eEEEEEc----------CChh
Q 030396           90 ARSIM-HDA------------------VRVIV----GRKNTASESI-------------KQKLVFA----------GSEE  123 (178)
Q Consensus        90 ~~~~~-~~~------------------~~v~~----~~~~~~~~~i-------------~~~~~~~----------~~~~  123 (178)
                      --.++ +.|                  ..+.+    ..++..+...             ..+....          ....
T Consensus       328 T~~~F~g~Pt~~YsleeAV~DGfLvpy~vi~i~~~~~~~G~~~~~~serek~~g~~i~~dd~~~~~~d~dr~~v~~~~~~  407 (875)
T COG4096         328 TYGFFNGEPTYAYSLEEAVEDGFLVPYKVIRIDTDFDLDGWKPDAGSEREKLQGEAIDEDDQNFEARDFDRTLVIPFRTE  407 (875)
T ss_pred             cccccCCCcceeecHHHHhhccccCCCCceEEeeeccccCcCcCccchhhhhhccccCcccccccccccchhccccchHH
Confidence            22333 222                  11111    1112222111             0011000          0111


Q ss_pred             hHHHHHHHHHHh--cC--CCCEEEEeCCchHHHHHHHHhhhC-----CCceEeeecCCCc
Q 030396          124 GKLLALRQSFAE--SL--NPPVLIFVQSKDRAKELYGELAFD-----DIRAGVIHSDLSQ  174 (178)
Q Consensus       124 ~k~~~l~~ll~~--~~--~~~~lIF~~t~~~~~~l~~~L~~~-----g~~~~~lh~~~~~  174 (178)
                      .-...+.+.++.  ..  .+||||||.+..+|+.+...|.+.     |--+..+.|+-.+
T Consensus       408 ~V~r~~~~~l~~~~~g~~~~KTIvFa~n~dHAe~i~~~~~~~ype~~~~~a~~IT~d~~~  467 (875)
T COG4096         408 TVARELTEYLKRGATGDEIGKTIVFAKNHDHAERIREALVNEYPEYNGRYAMKITGDAEQ  467 (875)
T ss_pred             HHHHHHHHHhccccCCCccCceEEEeeCcHHHHHHHHHHHHhCccccCceEEEEeccchh
Confidence            234555566665  33  679999999999999999999653     3345555555443

>PRK12906 secA preprotein translocase subunit SecA; Reviewed

Probab=97.87  E-value=6.1e-05  Score=64.81  Aligned_cols=57  Identities=18%  Similarity=0.197  Sum_probs=49.8

Q ss_pred             ChhhHHHHHHHHHHhc--CCCCEEEEeCCchHHHHHHHHhhhCCCceEeeecCCCcccc
Q 030396          121 SEEGKLLALRQSFAES--LNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQV  177 (178)
Q Consensus       121 ~~~~k~~~l~~ll~~~--~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~~~~~~R  177 (178)
                      +...|...+.+.+...  ..+|+||||+|+..++.++..|.+.|++...+||++.++++
T Consensus       421 t~~~K~~al~~~i~~~~~~g~pvLI~t~si~~se~ls~~L~~~gi~~~~Lna~~~~~Ea  479 (796)
T PRK12906        421 TLDSKFNAVVKEIKERHAKGQPVLVGTVAIESSERLSHLLDEAGIPHAVLNAKNHAKEA  479 (796)
T ss_pred             CHHHHHHHHHHHHHHHHhCCCCEEEEeCcHHHHHHHHHHHHHCCCCeeEecCCcHHHHH
Confidence            4567888888888643  57899999999999999999999999999999999887664

>KOG0923 consensus mRNA splicing factor ATP-dependent RNA helicase [RNA processing and modification]

Probab=97.72  E-value=0.00074  Score=56.70  Aligned_cols=150  Identities=16%  Similarity=0.150  Sum_probs=93.6

Q ss_pred             cEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccc-cccCCChhhHHHHHhhCCCCCceEEEEeecCcHHHHHHHHHhcc
Q 030396           17 DILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKL-FEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMH   95 (178)
Q Consensus        17 ~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~l-l~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~~~~~~~~~~~   95 (178)
                      -+-+.|-|.|+.-+... .++.+-+.+|+||||.= +...=....+..|.+  ..+....++.|||+..   +-...|+.
T Consensus       357 vlKYMTDGmLlREfL~e-pdLasYSViiiDEAHERTL~TDILfgLvKDIar--~RpdLKllIsSAT~DA---ekFS~fFD  430 (902)
T KOG0923|consen  357 VLKYMTDGMLLREFLSE-PDLASYSVIIVDEAHERTLHTDILFGLVKDIAR--FRPDLKLLISSATMDA---EKFSAFFD  430 (902)
T ss_pred             eeeeecchhHHHHHhcc-ccccceeEEEeehhhhhhhhhhHHHHHHHHHHh--hCCcceEEeeccccCH---HHHHHhcc
Confidence            46678999888655433 46888899999999984 222213455666666  4578899999999984   34455666


Q ss_pred             CcEEEEEcCCccccCCceEEEEEcCChhhHHH-HHHHHHH---hcCCCCEEEEeCCchHHHHHHHHhhhC---------C
Q 030396           96 DAVRVIVGRKNTASESIKQKLVFAGSEEGKLL-ALRQSFA---ESLNPPVLIFVQSKDRAKELYGELAFD---------D  162 (178)
Q Consensus        96 ~~~~v~~~~~~~~~~~i~~~~~~~~~~~~k~~-~l~~ll~---~~~~~~~lIF~~t~~~~~~l~~~L~~~---------g  162 (178)
                      +.....++.....   +.-+|-.. ++.+-+. .+.-+++   ..+.+-+|||..-....+...+.|.+.         .
T Consensus       431 dapIF~iPGRRyP---Vdi~Yt~~-PEAdYldAai~tVlqIH~tqp~GDILVFltGQeEIEt~~e~l~~~~~~LGski~e  506 (902)
T KOG0923|consen  431 DAPIFRIPGRRYP---VDIFYTKA-PEADYLDAAIVTVLQIHLTQPLGDILVFLTGQEEIETVKENLKERCRRLGSKIRE  506 (902)
T ss_pred             CCcEEeccCcccc---eeeecccC-CchhHHHHHHhhheeeEeccCCccEEEEeccHHHHHHHHHHHHHHHHHhccccce
Confidence            6544444432222   22334233 3323332 3333333   223567999998888888777776542         3


Q ss_pred             CceEeeecCCCccc
Q 030396          163 IRAGVIHSDLSQTQ  176 (178)
Q Consensus       163 ~~~~~lh~~~~~~~  176 (178)
                      +-+..+|+++|.+.
T Consensus       507 liv~PiYaNLPsel  520 (902)
T KOG0923|consen  507 LIVLPIYANLPSEL  520 (902)
T ss_pred             EEEeeccccCChHH
Confidence            57788899998753

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

Probab=97.56  E-value=0.0027  Score=54.55  Aligned_cols=62  Identities=16%  Similarity=0.127  Sum_probs=40.2

Q ss_pred             CCcEEEeCcHHHHHHHHcC--CCC--CCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCc
Q 030396           15 SCDILISTPLRLRLAIRRK--KID--LSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLP   83 (178)
Q Consensus        15 ~~~Iii~TP~~l~~~l~~~--~~~--~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~   83 (178)
                      ...|+|+|.+++...+...  ...  ..+ -++|+||||+.....     +...++. .-++...+.||||--
T Consensus       338 ~~~iivtTiQk~~~~~~~~~~~~~~~~~~-~lvIvDEaHrs~~~~-----~~~~l~~-~~p~a~~lGfTaTP~  403 (667)
T TIGR00348       338 DGGIIITTIQKFDKKLKEEEEKFPVDRKE-VVVIFDEAHRSQYGE-----LAKNLKK-ALKNASFFGFTGTPI  403 (667)
T ss_pred             CCCEEEEEhHHhhhhHhhhhhccCCCCCC-EEEEEEcCccccchH-----HHHHHHh-hCCCCcEEEEeCCCc
Confidence            4689999999998654321  111  122 279999999874333     4444433 224678899999974

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

>KOG0949 consensus Predicted helicase, DEAD-box superfamily [General function prediction only]

Probab=97.54  E-value=0.00017  Score=62.69  Aligned_cols=67  Identities=18%  Similarity=0.197  Sum_probs=53.2

Q ss_pred             CCcEEEeCcHHHHHHHHc---CCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcHH
Q 030396           15 SCDILISTPLRLRLAIRR---KKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDF   85 (178)
Q Consensus        15 ~~~Iii~TP~~l~~~l~~---~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~   85 (178)
                      +|+|+|+-|+++-+++-.   -.-...+++++|+||+|.+.+.. -.-.++.++-.   ....++++|||+.+.
T Consensus       605 nCQVLITvPecleslLlspp~~q~~cerIRyiIfDEVH~iG~~e-d~l~~Eqll~l---i~CP~L~LSATigN~  674 (1330)
T KOG0949|consen  605 NCQVLITVPECLESLLLSPPHHQKFCERIRYIIFDEVHLIGNEE-DGLLWEQLLLL---IPCPFLVLSATIGNP  674 (1330)
T ss_pred             hceEEEEchHHHHHHhcCchhhhhhhhcceEEEechhhhccccc-cchHHHHHHHh---cCCCeeEEecccCCH
Confidence            799999999999998866   33457899999999999997655 34455555555   467899999999864

>PRK12900 secA preprotein translocase subunit SecA; Reviewed

Probab=97.52  E-value=0.00054  Score=60.14  Aligned_cols=51  Identities=22%  Similarity=0.208  Sum_probs=45.3

Q ss_pred             ChhhHHHHHHHHHHhc--CCCCEEEEeCCchHHHHHHHHhhhCCCceEeeecC
Q 030396          121 SEEGKLLALRQSFAES--LNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSD  171 (178)
Q Consensus       121 ~~~~k~~~l~~ll~~~--~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~  171 (178)
                      ....|...+.+.+...  ..+|+||||+|++.++.++..|...|++...+|+.
T Consensus       579 t~~eK~~Ali~~I~~~~~~grpVLIft~Sve~sE~Ls~~L~~~gI~h~vLnak  631 (1025)
T PRK12900        579 TRREKYNAIVLKVEELQKKGQPVLVGTASVEVSETLSRMLRAKRIAHNVLNAK  631 (1025)
T ss_pred             CHHHHHHHHHHHHHHHhhCCCCEEEEeCcHHHHHHHHHHHHHcCCCceeecCC
Confidence            5567889999988654  57899999999999999999999999999999974

>TIGR02562 cas3_yersinia CRISPR-associated helicase Cas3

Probab=97.46  E-value=0.00018  Score=63.39  Aligned_cols=72  Identities=26%  Similarity=0.165  Sum_probs=50.5

Q ss_pred             CCcEEEeCcHHHHHHHH--c-CCC-----CCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcHHH
Q 030396           15 SCDILISTPLRLRLAIR--R-KKI-----DLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFV   86 (178)
Q Consensus        15 ~~~Iii~TP~~l~~~l~--~-~~~-----~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~~   86 (178)
                      ...++|||+..++....  + +-.     .+. =+.|||||+|.+-..  ....+.++++.+-.-...++++|||+|+.+
T Consensus       562 ~apv~V~TIDQlL~a~~~~r~~~~~l~ll~La-~svlVlDEVHaYD~~--~~~~L~rlL~w~~~lG~~VlLmSATLP~~l  638 (1110)
T TIGR02562       562 AAPVLVCTIDHLIPATESHRGGHHIAPMLRLM-SSDLILDEPDDYEPE--DLPALLRLVQLAGLLGSRVLLSSATLPPAL  638 (1110)
T ss_pred             cCCeEEecHHHHHHHhhhcccchhHHHHHHhc-CCCEEEECCccCCHH--HHHHHHHHHHHHHHcCCCEEEEeCCCCHHH
Confidence            46899999999997762  2 211     122 268899999999443  356677777653335678899999999986


Q ss_pred             HHH
Q 030396           87 EEL   89 (178)
Q Consensus        87 ~~~   89 (178)
                      ...
T Consensus       639 ~~~  641 (1110)
T TIGR02562       639 VKT  641 (1110)
T ss_pred             HHH
Confidence            653

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.

>KOG0925 consensus mRNA splicing factor ATP-dependent RNA helicase [RNA processing and modification]

Probab=97.40  E-value=0.00087  Score=54.49  Aligned_cols=140  Identities=18%  Similarity=0.211  Sum_probs=88.4

Q ss_pred             eCcHHHHHHHHcCCC--------CCCCeeEEEEeccccc-cccCCChhhHHHHHhhCCCCCceEEEEeecCcHHHHHHHH
Q 030396           21 STPLRLRLAIRRKKI--------DLSRVEYLVLDEADKL-FEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELAR   91 (178)
Q Consensus        21 ~TP~~l~~~l~~~~~--------~~~~l~~lViDE~d~l-l~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~~~~~~~   91 (178)
                      +||..++..+..+.+        .+++-+.+|+||||.= +......-.+.++...  .++..++++|||+..   .-.+
T Consensus       133 ~~~~T~Lky~tDgmLlrEams~p~l~~y~viiLDeahERtlATDiLmGllk~v~~~--rpdLk~vvmSatl~a---~Kfq  207 (699)
T KOG0925|consen  133 TSPNTLLKYCTDGMLLREAMSDPLLGRYGVIILDEAHERTLATDILMGLLKEVVRN--RPDLKLVVMSATLDA---EKFQ  207 (699)
T ss_pred             CChhHHHHHhcchHHHHHHhhCcccccccEEEechhhhhhHHHHHHHHHHHHHHhh--CCCceEEEeecccch---HHHH
Confidence            578787766544322        3788899999999973 2211234455555554  358999999999983   4456


Q ss_pred             HhccCcEEEEEcCCccccCCceEEEEEcCChhhHHHHHHH----HHHhcCCCCEEEEeCCchHHHHHHHHhhhC------
Q 030396           92 SIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQ----SFAESLNPPVLIFVQSKDRAKELYGELAFD------  161 (178)
Q Consensus        92 ~~~~~~~~v~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~----ll~~~~~~~~lIF~~t~~~~~~l~~~L~~~------  161 (178)
                      .|+.++..+.++.  .-|  +.- ++......+.++..+.    +-.....+-+++|....++.+..++.+...      
T Consensus       208 ~yf~n~Pll~vpg--~~P--vEi-~Yt~e~erDylEaairtV~qih~~ee~GDilvFLtgeeeIe~aC~~i~re~~~L~~  282 (699)
T KOG0925|consen  208 RYFGNAPLLAVPG--THP--VEI-FYTPEPERDYLEAAIRTVLQIHMCEEPGDILVFLTGEEEIEDACRKISREVDNLGP  282 (699)
T ss_pred             HHhCCCCeeecCC--CCc--eEE-EecCCCChhHHHHHHHHHHHHHhccCCCCEEEEecCHHHHHHHHHHHHHHHHhhcc
Confidence            6778877777764  222  222 3233333333333333    333445788999999999999988887532      


Q ss_pred             ---CCceEeeec
Q 030396          162 ---DIRAGVIHS  170 (178)
Q Consensus       162 ---g~~~~~lh~  170 (178)
                         ..++..+|-
T Consensus       283 ~~g~l~v~PLyP  294 (699)
T KOG0925|consen  283 QVGPLKVVPLYP  294 (699)
T ss_pred             ccCCceEEecCc
Confidence               246676763

>KOG0385 consensus Chromatin remodeling complex WSTF-ISWI, small subunit [Transcription]

Probab=97.35  E-value=0.0035  Score=53.58  Aligned_cols=54  Identities=20%  Similarity=0.195  Sum_probs=46.0

Q ss_pred             hHHHHHHHHHHh--cCCCCEEEEeCCchHHHHHHHHhhhCCCceEeeecCCCcccc
Q 030396          124 GKLLALRQSFAE--SLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQV  177 (178)
Q Consensus       124 ~k~~~l~~ll~~--~~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~~~~~~R  177 (178)
                      .|+.+|-.+|.+  ....+++||..=....+-|.++.--+||...-+.|.++.++|
T Consensus       471 GKm~vLDkLL~~Lk~~GhRVLIFSQmt~mLDILeDyc~~R~y~ycRiDGSt~~eeR  526 (971)
T KOG0385|consen  471 GKMLVLDKLLPKLKEQGHRVLIFSQMTRMLDILEDYCMLRGYEYCRLDGSTSHEER  526 (971)
T ss_pred             cceehHHHHHHHHHhCCCeEEEeHHHHHHHHHHHHHHHhcCceeEeecCCCCcHHH
Confidence            477777777763  337899999988888899999999999999999999999988

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

Probab=97.34  E-value=0.006  Score=52.70  Aligned_cols=157  Identities=17%  Similarity=0.109  Sum_probs=97.4

Q ss_pred             CCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccC-----CChhhHHHHHhhCCCCCceEEEEeecCcHHHHHH
Q 030396           15 SCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVG-----NLLKHIDPVVKACSNPSIVRSLFSATLPDFVEEL   89 (178)
Q Consensus        15 ~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~-----~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~~~~~   89 (178)
                      ..+-++...++|..+-.   -.+.+-+++|+||+...+..-     ...+.+..++..++.....+|++-|+++...-++
T Consensus       121 ~~~rLivqIdSL~R~~~---~~l~~yDvVIIDEv~svL~qL~S~Tm~~~~~v~~~L~~lI~~ak~VI~~DA~ln~~tvdF  197 (824)
T PF02399_consen  121 PYDRLIVQIDSLHRLDG---SLLDRYDVVIIDEVMSVLNQLFSPTMRQREEVDNLLKELIRNAKTVIVMDADLNDQTVDF  197 (824)
T ss_pred             ccCeEEEEehhhhhccc---ccccccCEEEEehHHHHHHHHhHHHHhhHHHHHHHHHHHHHhCCeEEEecCCCCHHHHHH
Confidence            35677777777665542   235567899999999887542     1233444455555677888999999999998888


Q ss_pred             HHHhccCc-EEEEEcCCccccCCceEEEEEcCC-----------------------------------hhhHHHHHHHHH
Q 030396           90 ARSIMHDA-VRVIVGRKNTASESIKQKLVFAGS-----------------------------------EEGKLLALRQSF  133 (178)
Q Consensus        90 ~~~~~~~~-~~v~~~~~~~~~~~i~~~~~~~~~-----------------------------------~~~k~~~l~~ll  133 (178)
                      ++.+-++. +.+.. ++...+.......+.+..                                   ..+.....-.++
T Consensus       198 l~~~Rp~~~i~vI~-n~y~~~~fs~R~~~~~~~l~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~tF~~~L~  276 (824)
T PF02399_consen  198 LASCRPDENIHVIV-NTYASPGFSNRRCTFLRSLGTDTLAAALNPEDENADTSPTPKHSPDPTATAAISNDETTFFSELL  276 (824)
T ss_pred             HHHhCCCCcEEEEE-eeeecCCcccceEEEecccCcHHHHHHhCCcccccccCCCcCCCCccccccccccchhhHHHHHH
Confidence            88876543 33333 121111111111111000                                   012233333344


Q ss_pred             Hhc-CCCCEEEEeCCchHHHHHHHHhhhCCCceEeeecCCCcc
Q 030396          134 AES-LNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQT  175 (178)
Q Consensus       134 ~~~-~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~~~~~  175 (178)
                      ... ..+++.||++|.+-++.+++..+..+.++..++|.-+..
T Consensus       277 ~~L~~gknIcvfsSt~~~~~~v~~~~~~~~~~Vl~l~s~~~~~  319 (824)
T PF02399_consen  277 ARLNAGKNICVFSSTVSFAEIVARFCARFTKKVLVLNSTDKLE  319 (824)
T ss_pred             HHHhCCCcEEEEeChHHHHHHHHHHHHhcCCeEEEEcCCCCcc
Confidence            432 246788999999999999999999999999998865543

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

>KOG0926 consensus DEAH-box RNA helicase [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=97.24  E-value=0.0013  Score=56.52  Aligned_cols=142  Identities=18%  Similarity=0.163  Sum_probs=85.3

Q ss_pred             cCCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccC----CChhhHHHHHhhCCCC------CceEEEEeecC
Q 030396           13 KFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVG----NLLKHIDPVVKACSNP------SIVRSLFSATL   82 (178)
Q Consensus        13 ~~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~----~~~~~i~~i~~~~~~~------~~q~i~~SAT~   82 (178)
                      ...-.|.+.|-|-|+.-+.+.- .+..-+.+|+||||.=--+.    .++.-+-.+-+. ...      ....|++|||+
T Consensus       347 ~e~T~IkFMTDGVLLrEi~~Df-lL~kYSvIIlDEAHERSvnTDILiGmLSRiV~LR~k-~~ke~~~~kpLKLIIMSATL  424 (1172)
T KOG0926|consen  347 GEDTSIKFMTDGVLLREIENDF-LLTKYSVIILDEAHERSVNTDILIGMLSRIVPLRQK-YYKEQCQIKPLKLIIMSATL  424 (1172)
T ss_pred             CCCceeEEecchHHHHHHHHhH-hhhhceeEEechhhhccchHHHHHHHHHHHHHHHHH-HhhhhcccCceeEEEEeeeE
Confidence            3556799999999998776543 35566899999999852111    133333333333 222      35689999999


Q ss_pred             cHHHHHHH--HHhcc-CcEEEEEcCCccccCCceEEEEEcCCh---hhHHHHHHHHHHhcCCCCEEEEeCCchHHHHHHH
Q 030396           83 PDFVEELA--RSIMH-DAVRVIVGRKNTASESIKQKLVFAGSE---EGKLLALRQSFAESLNPPVLIFVQSKDRAKELYG  156 (178)
Q Consensus        83 ~~~~~~~~--~~~~~-~~~~v~~~~~~~~~~~i~~~~~~~~~~---~~k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~  156 (178)
                      .  +.++.  .+.+. -|..+.++... -|-.|  +|-.-...   .+-+...+.+=++.+.+-+|||+....+++.|+.
T Consensus       425 R--VsDFtenk~LFpi~pPlikVdARQ-fPVsI--HF~krT~~DYi~eAfrKtc~IH~kLP~G~ILVFvTGQqEV~qL~~  499 (1172)
T KOG0926|consen  425 R--VSDFTENKRLFPIPPPLIKVDARQ-FPVSI--HFNKRTPDDYIAEAFRKTCKIHKKLPPGGILVFVTGQQEVDQLCE  499 (1172)
T ss_pred             E--ecccccCceecCCCCceeeeeccc-CceEE--EeccCCCchHHHHHHHHHHHHhhcCCCCcEEEEEeChHHHHHHHH
Confidence            7  33433  22344 23344444322 22122  22111111   1234445555567778899999999999999999


Q ss_pred             HhhhC
Q 030396          157 ELAFD  161 (178)
Q Consensus       157 ~L~~~  161 (178)
                      .|++.
T Consensus       500 kLRK~  504 (1172)
T KOG0926|consen  500 KLRKR  504 (1172)
T ss_pred             HHHhh
Confidence            99765

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

Probab=97.22  E-value=0.0011  Score=46.87  Aligned_cols=66  Identities=17%  Similarity=0.174  Sum_probs=46.0

Q ss_pred             hccCCCcEEEeCcHHHHHHHHcCC-----------CCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEe
Q 030396           11 LSKFSCDILISTPLRLRLAIRRKK-----------IDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFS   79 (178)
Q Consensus        11 ~l~~~~~Iii~TP~~l~~~l~~~~-----------~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~S   79 (178)
                      .-....+++++|..++........           .......++|+||||.+....    .+..++.   .....++.+|
T Consensus       107 ~~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~vI~DEaH~~~~~~----~~~~i~~---~~~~~~l~lT  179 (184)
T PF04851_consen  107 SDNNDKDIILTTYQSLQSDIKEEKKIDESARRSYKLLKNKFDLVIIDEAHHYPSDS----SYREIIE---FKAAFILGLT  179 (184)
T ss_dssp             HCBSS-SEEEEEHHHHHHHHHH---------GCHHGGGGSESEEEEETGGCTHHHH----HHHHHHH---SSCCEEEEEE
T ss_pred             cccccccchhhHHHHHHhhcccccccccchhhhhhhccccCCEEEEehhhhcCCHH----HHHHHHc---CCCCeEEEEE
Confidence            334678999999999998875421           123466799999999995543    1666666   2577789999


Q ss_pred             ecCc
Q 030396           80 ATLP   83 (178)
Q Consensus        80 AT~~   83 (178)
                      ||.+
T Consensus       180 ATp~  183 (184)
T PF04851_consen  180 ATPF  183 (184)
T ss_dssp             SS-S
T ss_pred             eCcc
Confidence            9975

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 ....

>KOG0951 consensus RNA helicase BRR2, DEAD-box superfamily [RNA processing and modification]

Probab=97.11  E-value=0.0025  Score=57.08  Aligned_cols=136  Identities=15%  Similarity=0.175  Sum_probs=80.6

Q ss_pred             cCCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhh------HHHHHhhCCCCCceEEEEeecCcHHH
Q 030396           13 KFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKH------IDPVVKACSNPSIVRSLFSATLPDFV   86 (178)
Q Consensus        13 ~~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~------i~~i~~~~~~~~~q~i~~SAT~~~~~   86 (178)
                      ...-+|+|+||++ +++++    ....++++|.||.|.+....  .+.      ++.|.+. +.++.+++++|..+.+. 
T Consensus      1232 ~~~~~vii~tpe~-~d~lq----~iQ~v~l~i~d~lh~igg~~--g~v~evi~S~r~ia~q-~~k~ir~v~ls~~lana- 1302 (1674)
T KOG0951|consen 1232 LQKGQVIISTPEQ-WDLLQ----SIQQVDLFIVDELHLIGGVY--GAVYEVICSMRYIASQ-LEKKIRVVALSSSLANA- 1302 (1674)
T ss_pred             hhhcceEEechhH-HHHHh----hhhhcceEeeehhhhhcccC--CceEEEEeeHHHHHHH-HHhheeEEEeehhhccc-
Confidence            3456999999998 45553    67889999999999986322  222      4555555 56678899998888753 


Q ss_pred             HHHHHHhccCcEEEEEcCC-ccccCCceEEEEEcCChhhHHHHHHH-----HHH-hcCCCCEEEEeCCchHHHHHHHHhh
Q 030396           87 EELARSIMHDAVRVIVGRK-NTASESIKQKLVFAGSEEGKLLALRQ-----SFA-ESLNPPVLIFVQSKDRAKELYGELA  159 (178)
Q Consensus        87 ~~~~~~~~~~~~~v~~~~~-~~~~~~i~~~~~~~~~~~~k~~~l~~-----ll~-~~~~~~~lIF~~t~~~~~~l~~~L~  159 (178)
                      +.+  ..+.....+...+. ...|..+.-+.+...........+.+     +.+ ....++++||+++++.|..++.-|.
T Consensus      1303 ~d~--ig~s~~~v~Nf~p~~R~~Pl~i~i~~~~~~~~~~~~~am~~~~~~ai~~~a~~~k~~~vf~p~rk~~~~~a~~~~ 1380 (1674)
T KOG0951|consen 1303 RDL--IGASSSGVFNFSPSVRPVPLEIHIQSVDISHFESRMLAMTKPTYTAIVRHAGNRKPAIVFLPTRKHARLVAVDLV 1380 (1674)
T ss_pred             hhh--ccccccceeecCcccCCCceeEEEEEeccchhHHHHHHhhhhHHHHHHHHhcCCCCeEEEeccchhhhhhhhccc
Confidence            333  11222222222222 23333333333333333322222221     111 3347789999999999999887663

>KOG2340 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.93  E-value=0.00081  Score=55.09  Aligned_cols=154  Identities=19%  Similarity=0.282  Sum_probs=97.6

Q ss_pred             CCCcEEEeCcHHHHHHHHc---CC--CC-CCCeeEEEEeccccccccCCChhhHHHHHhhC--CCCC-------------
Q 030396           14 FSCDILISTPLRLRLAIRR---KK--ID-LSRVEYLVLDEADKLFEVGNLLKHIDPVVKAC--SNPS-------------   72 (178)
Q Consensus        14 ~~~~Iii~TP~~l~~~l~~---~~--~~-~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~--~~~~-------------   72 (178)
                      ...||+||+|--|.-++.+   +.  .+ ++++.++|+|.||.++...  -+.+..|+.++  +|..             
T Consensus       384 y~SDIlVaSPLGLRmil~n~gdkkrd~dfLSSIEl~iIDQa~~~l~QN--wEhl~~ifdHLn~~P~k~h~~DfSRVR~wy  461 (698)
T KOG2340|consen  384 YKSDILVASPLGLRMILGNTGDKKRDFDFLSSIELLIIDQADIMLMQN--WEHLLHIFDHLNLQPSKQHDVDFSRVRMWY  461 (698)
T ss_pred             cccCeEEecchhhhhhhcCCCcccccchhhhhhhhhhhhhHHHHHHhh--HHHHHHHHHHhhcCcccccCCChhheehhe
Confidence            3689999999887777752   11  22 7999999999999998766  66777777773  2211             


Q ss_pred             --------ceEEEEeecCcHHHHHHHHHhccCc-EEEEEcCC--c----cccCCceEEE--EEcCC----hhhHHHHHHH
Q 030396           73 --------IVRSLFSATLPDFVEELARSIMHDA-VRVIVGRK--N----TASESIKQKL--VFAGS----EEGKLLALRQ  131 (178)
Q Consensus        73 --------~q~i~~SAT~~~~~~~~~~~~~~~~-~~v~~~~~--~----~~~~~i~~~~--~~~~~----~~~k~~~l~~  131 (178)
                              +|+++||+-..+....+...++.+- ..|...+.  +    ...-.+.|.+  +.+.+    ...++.+..+
T Consensus       462 L~~qsr~~rQtl~Fs~y~~~~~nS~fn~~c~N~~Gkv~~~~~~~~gsi~~v~~~l~Qvf~ri~~~si~~~~D~RFkyFv~  541 (698)
T KOG2340|consen  462 LDGQSRYFRQTLLFSRYSHPLFNSLFNQYCQNMAGKVKARNLQSGGSISNVGIPLCQVFQRIEVKSIIETPDARFKYFVD  541 (698)
T ss_pred             eccHHHHHHHHHHHHhhccHHHHHHHHHhhhhhcceeeeccccCCCchhhccchhhhhhhheeccCcccCchHHHHHHHH
Confidence                    6899999999998888888877652 22222111  1    1111122222  12222    1245555554


Q ss_pred             HHH----hcCCCCEEEEeCCchHHHHHHHHhhhCCCceEeee
Q 030396          132 SFA----ESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIH  169 (178)
Q Consensus       132 ll~----~~~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh  169 (178)
                      -+-    +....-++||.++=-+--.+-.+|++.++....+|
T Consensus       542 ~ImPq~~k~t~s~~LiyIPSYfDFVRvRNy~K~e~i~F~~i~  583 (698)
T KOG2340|consen  542 KIMPQLIKRTESGILIYIPSYFDFVRVRNYMKKEEISFVMIN  583 (698)
T ss_pred             hhchhhcccccCceEEEecchhhHHHHHHHhhhhhcchHHHh
Confidence            432    22244579999998888888888887765544443

>KOG0924 consensus mRNA splicing factor ATP-dependent RNA helicase [RNA processing and modification]

Probab=96.90  E-value=0.013  Score=49.82  Aligned_cols=148  Identities=17%  Similarity=0.140  Sum_probs=84.6

Q ss_pred             CcEEEeCcHHHHH-HHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhC--CCCCceEEEEeecCcHHHHHHHHH
Q 030396           16 CDILISTPLRLRL-AIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKAC--SNPSIVRSLFSATLPDFVEELARS   92 (178)
Q Consensus        16 ~~Iii~TP~~l~~-~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~--~~~~~q~i~~SAT~~~~~~~~~~~   92 (178)
                      -.|-..|-|-|+. .+..+.  +.+-+.+|+||||.=--+   .+.+.-+++..  -..+..+|+.|||+..  ..+...
T Consensus       446 T~IkymTDGiLLrEsL~d~~--L~kYSviImDEAHERslN---tDilfGllk~~larRrdlKliVtSATm~a--~kf~nf  518 (1042)
T KOG0924|consen  446 TKIKYMTDGILLRESLKDRD--LDKYSVIIMDEAHERSLN---TDILFGLLKKVLARRRDLKLIVTSATMDA--QKFSNF  518 (1042)
T ss_pred             eeEEEeccchHHHHHhhhhh--hhheeEEEechhhhcccc---hHHHHHHHHHHHHhhccceEEEeeccccH--HHHHHH
Confidence            3467788888774 344443  556789999999985222   12223333332  2357889999999984  355555


Q ss_pred             hccCcEEEEEcCCccccCCceEEEEEcCChhhHHH-HHHHHHH---hcCCCCEEEEeCCchHHHHHHHHhhhC-------
Q 030396           93 IMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLL-ALRQSFA---ESLNPPVLIFVQSKDRAKELYGELAFD-------  161 (178)
Q Consensus        93 ~~~~~~~v~~~~~~~~~~~i~~~~~~~~~~~~k~~-~l~~ll~---~~~~~~~lIF~~t~~~~~~l~~~L~~~-------  161 (178)
                      |.+.|.+-.-+. . -|-.+  .+... +-++-+. .+...+.   ....+-++||....+..+-.+..+.+.       
T Consensus       519 Fgn~p~f~IpGR-T-yPV~~--~~~k~-p~eDYVeaavkq~v~Ihl~~~~GdilIfmtGqediE~t~~~i~~~l~ql~~~  593 (1042)
T KOG0924|consen  519 FGNCPQFTIPGR-T-YPVEI--MYTKT-PVEDYVEAAVKQAVQIHLSGPPGDILIFMTGQEDIECTCDIIKEKLEQLDSA  593 (1042)
T ss_pred             hCCCceeeecCC-c-cceEE--EeccC-chHHHHHHHHhhheEeeccCCCCCEEEecCCCcchhHHHHHHHHHHHhhhcC
Confidence            554554443322 2 22122  22112 1122222 2222222   223567999998888877777766432       


Q ss_pred             ---CCceEeeecCCCcc
Q 030396          162 ---DIRAGVIHSDLSQT  175 (178)
Q Consensus       162 ---g~~~~~lh~~~~~~  175 (178)
                         +..+..+-+.||+.
T Consensus       594 ~~~~L~vlpiYSQLp~d  610 (1042)
T KOG0924|consen  594 PTTDLAVLPIYSQLPAD  610 (1042)
T ss_pred             CCCceEEEeehhhCchh
Confidence               56788888888764

>KOG3089 consensus Predicted DEAD-box-containing helicase [General function prediction only]

Probab=96.59  E-value=0.0043  Score=45.33  Aligned_cols=42  Identities=24%  Similarity=0.370  Sum_probs=35.4

Q ss_pred             HHhHHhccC-CCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEec
Q 030396            6 VRSTDLSKF-SCDILISTPLRLRLAIRRKKIDLSRVEYLVLDE   47 (178)
Q Consensus         6 ~~q~~~l~~-~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE   47 (178)
                      ..|.+.+++ ..++-||||||+.+++.++.++.+.++++|+|=
T Consensus       186 ~~~~k~~k~~~v~~gIgTp~Ri~~lv~~~~f~~~~lk~iIlD~  228 (271)
T KOG3089|consen  186 QAQVKLLKKRVVHLGIGTPGRIKELVKQGGFNLSPLKFIILDW  228 (271)
T ss_pred             HHHHHHHhhcceeEeecCcHHHHHHHHhcCCCCCcceeEEeec
Confidence            455555554 578899999999999999989999999999984

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

Probab=96.30  E-value=0.0099  Score=40.94  Aligned_cols=68  Identities=12%  Similarity=0.035  Sum_probs=38.1

Q ss_pred             CCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccC-CChhhHHHHHhhCCCCCceEEEEeecCcHHH
Q 030396           15 SCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVG-NLLKHIDPVVKACSNPSIVRSLFSATLPDFV   86 (178)
Q Consensus        15 ~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~-~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~~   86 (178)
                      +--|-+.|-+.+...+.+ .....+-+++|+||+|..-... .+.-.+.+....   ....+|++|||-|...
T Consensus        72 ~~~i~vMc~at~~~~~~~-p~~~~~yd~II~DEcH~~Dp~sIA~rg~l~~~~~~---g~~~~i~mTATPPG~~  140 (148)
T PF07652_consen   72 SSIIDVMCHATYGHFLLN-PCRLKNYDVIIMDECHFTDPTSIAARGYLRELAES---GEAKVIFMTATPPGSE  140 (148)
T ss_dssp             SSSEEEEEHHHHHHHHHT-SSCTTS-SEEEECTTT--SHHHHHHHHHHHHHHHT---TS-EEEEEESS-TT--
T ss_pred             CCcccccccHHHHHHhcC-cccccCccEEEEeccccCCHHHHhhheeHHHhhhc---cCeeEEEEeCCCCCCC
Confidence            344666777777766654 3446788999999999974332 122223333222   3467899999988654

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 ....

>TIGR00596 rad1 DNA repair protein (rad1)

Probab=96.24  E-value=0.025  Score=49.64  Aligned_cols=67  Identities=16%  Similarity=0.092  Sum_probs=55.8

Q ss_pred             CCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCc
Q 030396           15 SCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLP   83 (178)
Q Consensus        15 ~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~   83 (178)
                      ...|+++||.-|..=+-.+.+++..+..+|+||||++.... ...-|-++.+. .+...-+.+|||.-.
T Consensus         7 ~ggi~~~T~rIl~~DlL~~ri~~~~itgiiv~~Ahr~~~~~-~eaFI~rlyr~-~n~~gfIkafSdsP~   73 (814)
T TIGR00596         7 EGGIFSITSRILVVDLLTGIIPPELITGILVLRADRIIESS-QEAFILRLYRQ-KNKTGFIKAFSDNPE   73 (814)
T ss_pred             cCCEEEEechhhHhHHhcCCCCHHHccEEEEeecccccccc-cHHHHHHHHHH-hCCCcceEEecCCCc
Confidence            35799999998887777788999999999999999998766 67777777777 666677888988865

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

>KOG4150 consensus Predicted ATP-dependent RNA helicase [RNA processing and modification]

Probab=96.20  E-value=0.084  Score=44.33  Aligned_cols=147  Identities=10%  Similarity=0.013  Sum_probs=90.9

Q ss_pred             HhccCCCcEEEeCcHHHHHHHHcCCCC----CCCeeEEEEeccccccccC--CChhhHHHHHhhC----CCCCceEEEEe
Q 030396           10 DLSKFSCDILISTPLRLRLAIRRKKID----LSRVEYLVLDEADKLFEVG--NLLKHIDPVVKAC----SNPSIVRSLFS   79 (178)
Q Consensus        10 ~~l~~~~~Iii~TP~~l~~~l~~~~~~----~~~l~~lViDE~d~ll~~~--~~~~~i~~i~~~~----~~~~~q~i~~S   79 (178)
                      ..++.+++++.+-|..+....--+..+    +-...+.+.||+|..+...  ....+++.+++.+    -+.+.|++-+|
T Consensus       379 A~~R~~~~~~~s~~~~~~s~~L~~~~~~~~~~~~~~~~~~~~~~~Y~~~~~~~~~~~~R~L~~L~~~F~~~~~~~~~~~~  458 (1034)
T KOG4150|consen  379 ALKRIGLNTLYSHQAEAISAALAKSLCYNVPVFEELCKDTNSCALYLFPTKALAQDQLRALSDLIKGFEASINMGVYDGD  458 (1034)
T ss_pred             HHHhcCcceeecCHHHHHHHHhhhccccccHHHHHHHhcccceeeeecchhhHHHHHHHHHHHHHHHHHhhcCcceEeCC
Confidence            345578999999999988766443333    4456788999999986542  1223333444332    33578999999


Q ss_pred             ecCcHHHHHHHHHhccCcEEEEEcCCccccCCceEEEEEcCC-----hhhH---HHHHHHHHHh--cCCCCEEEEeCCch
Q 030396           80 ATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGS-----EEGK---LLALRQSFAE--SLNPPVLIFVQSKD  149 (178)
Q Consensus        80 AT~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~i~~~~~~~~~-----~~~k---~~~l~~ll~~--~~~~~~lIF~~t~~  149 (178)
                      ||+...++-..+.+.-+......  .+..|.+-++++++-++     +.+|   +...-.++.+  .++-++|-||.+++
T Consensus       459 ~~~K~~~~~~~~~~~~~E~~Li~--~DGSPs~~K~~V~WNP~~~P~~~~~~~~~i~E~s~~~~~~i~~~~R~IAFC~~R~  536 (1034)
T KOG4150|consen  459 TPYKDRTRLRSELANLSELELVT--IDGSPSSEKLFVLWNPSAPPTSKSEKSSKVVEVSHLFAEMVQHGLRCIAFCPSRK  536 (1034)
T ss_pred             CCcCCHHHHHHHhcCCcceEEEE--ecCCCCccceEEEeCCCCCCcchhhhhhHHHHHHHHHHHHHHcCCcEEEeccHHH
Confidence            99998877666665545433333  23345556666654332     1223   2222223322  23579999999999


Q ss_pred             HHHHHHHHh
Q 030396          150 RAKELYGEL  158 (178)
Q Consensus       150 ~~~~l~~~L  158 (178)
                      -|+-+-..-
T Consensus       537 ~CEL~~~~~  545 (1034)
T KOG4150|consen  537 LCELVLCLT  545 (1034)
T ss_pred             HHHHHHHHH
Confidence            999865543

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

Probab=95.85  E-value=0.18  Score=43.78  Aligned_cols=131  Identities=15%  Similarity=0.100  Sum_probs=73.0

Q ss_pred             hccCCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEecccccc---ccC--CChhhHHHHHhhCCCCCceEEEEeecCcHH
Q 030396           11 LSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLF---EVG--NLLKHIDPVVKACSNPSIVRSLFSATLPDF   85 (178)
Q Consensus        11 ~l~~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll---~~~--~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~   85 (178)
                      ...+.+.|||||=--+.       ..++++..+|+||=|.--   +++  +...++--...+  ..+.++++-|||-+-+
T Consensus       292 ~~~G~~~vVIGtRSAlF-------~Pf~~LGLIIvDEEHD~sYKq~~~prYhARdvA~~Ra~--~~~~pvvLgSATPSLE  362 (730)
T COG1198         292 ARRGEARVVIGTRSALF-------LPFKNLGLIIVDEEHDSSYKQEDGPRYHARDVAVLRAK--KENAPVVLGSATPSLE  362 (730)
T ss_pred             HhcCCceEEEEechhhc-------CchhhccEEEEeccccccccCCcCCCcCHHHHHHHHHH--HhCCCEEEecCCCCHH
Confidence            44577999999963322       247788999999999853   112  344444443443  3688999999997743


Q ss_pred             HHHHHHHhccCcEEEEEcCCccccCCceEEEEEcCChhhHH-----HHHHHHHHh--cCCCCEEEEeCCchHHH
Q 030396           86 VEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKL-----LALRQSFAE--SLNPPVLIFVQSKDRAK  152 (178)
Q Consensus        86 ~~~~~~~~~~~~~~v~~~~~~~~~~~i~~~~~~~~~~~~k~-----~~l~~ll~~--~~~~~~lIF~~t~~~~~  152 (178)
                        .+....-+....+.+........-....++.+..+..+.     ..|++.+++  ....|+|+|.|.+.-+-
T Consensus       363 --S~~~~~~g~y~~~~L~~R~~~a~~p~v~iiDmr~e~~~~~~~lS~~Ll~~i~~~l~~geQ~llflnRRGys~  434 (730)
T COG1198         363 --SYANAESGKYKLLRLTNRAGRARLPRVEIIDMRKEPLETGRSLSPALLEAIRKTLERGEQVLLFLNRRGYAP  434 (730)
T ss_pred             --HHHhhhcCceEEEEccccccccCCCcceEEeccccccccCccCCHHHHHHHHHHHhcCCeEEEEEccCCccc
Confidence              333332222233333322221111222344444443333     345555532  34689999999876543

>KOG0952 consensus DNA/RNA helicase MER3/SLH1, DEAD-box superfamily [RNA processing and modification]

Probab=95.48  E-value=0.003  Score=55.63  Aligned_cols=50  Identities=28%  Similarity=0.289  Sum_probs=37.1

Q ss_pred             CCcEEEeCcHHHHHHHHc--CCCCCCCeeEEEEeccccccccCCChhhHHHHHh
Q 030396           15 SCDILISTPLRLRLAIRR--KKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVK   66 (178)
Q Consensus        15 ~~~Iii~TP~~l~~~l~~--~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~   66 (178)
                      .++|+|+||++.....+.  +.--+.+++.+|+||.|.+-+.  ..+.++.|..
T Consensus      1020 ~~~~~ittpek~dgi~Rsw~~r~~v~~v~~iv~de~hllg~~--rgPVle~ivs 1071 (1230)
T KOG0952|consen 1020 EADIVITTPEKWDGISRSWQTRKYVQSVSLIVLDEIHLLGED--RGPVLEVIVS 1071 (1230)
T ss_pred             cCceEEcccccccCccccccchhhhccccceeecccccccCC--CcceEEEEee
Confidence            578999999998777763  3334889999999999999765  2444444433

>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=95.35  E-value=0.058  Score=41.22  Aligned_cols=59  Identities=22%  Similarity=0.229  Sum_probs=39.3

Q ss_pred             CCCcEEEeCcHHHH--------HHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecC
Q 030396           14 FSCDILISTPLRLR--------LAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATL   82 (178)
Q Consensus        14 ~~~~Iii~TP~~l~--------~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~   82 (178)
                      ...+++|+|.+.+.        +.+..     -+.+.+|+||+|.+=+   ........+.. +. ....+++|||-
T Consensus       106 ~~~~vvi~ty~~~~~~~~~~~~~~l~~-----~~~~~vIvDEaH~~k~---~~s~~~~~l~~-l~-~~~~~lLSgTP  172 (299)
T PF00176_consen  106 PKYDVVITTYETLRKARKKKDKEDLKQ-----IKWDRVIVDEAHRLKN---KDSKRYKALRK-LR-ARYRWLLSGTP  172 (299)
T ss_dssp             CCSSEEEEEHHHHH--TSTHTTHHHHT-----SEEEEEEETTGGGGTT---TTSHHHHHHHC-CC-ECEEEEE-SS-
T ss_pred             ccceeeecccccccccccccccccccc-----ccceeEEEeccccccc---ccccccccccc-cc-cceEEeecccc
Confidence            56889999999888        22322     3378999999999932   23444445554 33 66678899994

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.

>cd01524 RHOD_Pyr_redox Member of the Rhodanese Homology Domain superfamily

Probab=95.03  E-value=0.045  Score=34.26  Aligned_cols=37  Identities=5%  Similarity=0.100  Sum_probs=33.0

Q ss_pred             CCCEEEEeCCchHHHHHHHHhhhCCCceEeeecCCCc
Q 030396          138 NPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQ  174 (178)
Q Consensus       138 ~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~~~~  174 (178)
                      .+++++||++-..+...+..|+..|+++..+.||++.
T Consensus        51 ~~~vvl~c~~g~~a~~~a~~L~~~G~~v~~l~GG~~~   87 (90)
T cd01524          51 DKEIIVYCAVGLRGYIAARILTQNGFKVKNLDGGYKT   87 (90)
T ss_pred             CCcEEEEcCCChhHHHHHHHHHHCCCCEEEecCCHHH
Confidence            5689999999888999999999999999999999853

Included in this CD are the Lactococcus lactis NADH oxidase, Bacillus cereus NADH dehydrogenase, and Bacteroides thetaiotaomicron pyridine nucleotide-disulphide oxidoreductase, and similar rhodanese-like domains found C-terminal of the pyridine nucleotide-disulphide oxidoreductase (Pyr-redox) domain and the Pyr-redox dimerization domain.

>smart00450 RHOD Rhodanese Homology Domain

Probab=95.01  E-value=0.055  Score=33.85  Aligned_cols=40  Identities=13%  Similarity=0.186  Sum_probs=34.6

Q ss_pred             hcCCCCEEEEeCCchHHHHHHHHhhhCCCc-eEeeecCCCc
Q 030396          135 ESLNPPVLIFVQSKDRAKELYGELAFDDIR-AGVIHSDLSQ  174 (178)
Q Consensus       135 ~~~~~~~lIF~~t~~~~~~l~~~L~~~g~~-~~~lh~~~~~  174 (178)
                      .....+++|||++-..+..++..|...|++ +..+.||+..
T Consensus        53 ~~~~~~iv~~c~~g~~a~~~~~~l~~~G~~~v~~l~GG~~~   93 (100)
T smart00450       53 LDKDKPVVVYCRSGNRSAKAAWLLRELGFKNVYLLDGGYKE   93 (100)
T ss_pred             CCCCCeEEEEeCCCcHHHHHHHHHHHcCCCceEEecCCHHH
Confidence            344678999999999999999999999997 8999998753

An alpha beta fold found duplicated in the Rhodanese protein. The the Cysteine containing enzymatically active version of the domain is also found in the CDC25 class of protein phosphatases and a variety of proteins such as sulfide dehydrogenases and stress proteins such as Senesence specific protein 1 in plants, PspE and GlpE in bacteria and cyanide and arsenate resistance proteins. Inactive versions with a loss of the cysteine are also seen in Dual specificity phosphatases, ubiquitin hydrolases from yeast and in sulfuryltransferases. These are likely to play a role in protein interactions.

>cd01523 RHOD_Lact_B Member of the Rhodanese Homology Domain superfamily

Probab=94.79  E-value=0.044  Score=34.96  Aligned_cols=38  Identities=8%  Similarity=0.046  Sum_probs=33.8

Q ss_pred             CCCCEEEEeCCchHHHHHHHHhhhCCCceEeeecCCCc
Q 030396          137 LNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQ  174 (178)
Q Consensus       137 ~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~~~~  174 (178)
                      ..++++++|.+-.++...+..|...|+.+..+.||+..
T Consensus        60 ~~~~ivv~C~~G~rs~~aa~~L~~~G~~~~~l~GG~~~   97 (100)
T cd01523          60 DDQEVTVICAKEGSSQFVAELLAERGYDVDYLAGGMKA   97 (100)
T ss_pred             CCCeEEEEcCCCCcHHHHHHHHHHcCceeEEeCCcHHh
Confidence            35789999999889999999999999999999999854

This CD includes predicted proteins with rhodanese-like domains found N-terminal of the metallo-beta-lactamase domain.

>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]

Probab=94.75  E-value=0.15  Score=46.13  Aligned_cols=40  Identities=18%  Similarity=0.080  Sum_probs=36.7

Q ss_pred             CCCEEEEeCCchHHHHHHHHhhhCCCceEeeecCCCcccc
Q 030396          138 NPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQV  177 (178)
Q Consensus       138 ~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~~~~~~R  177 (178)
                      ..++|||..=....+-|+++|..+||+.--+.|+++.+.|
T Consensus       699 GHrVLIFSQMVRmLDIL~eYL~~r~ypfQRLDGsvrgelR  738 (1373)
T KOG0384|consen  699 GHRVLIFSQMVRMLDILAEYLSLRGYPFQRLDGSVRGELR  738 (1373)
T ss_pred             CceEEEhHHHHHHHHHHHHHHHHcCCcceeccCCcchHHH
Confidence            6799999999999999999999999999999999887655

>KOG1000 consensus Chromatin remodeling protein HARP/SMARCAL1, DEAD-box superfamily [Chromatin structure and dynamics]

Probab=94.74  E-value=0.69  Score=38.39  Aligned_cols=40  Identities=10%  Similarity=0.070  Sum_probs=37.3

Q ss_pred             CCCEEEEeCCchHHHHHHHHhhhCCCceEeeecCCCcccc
Q 030396          138 NPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQV  177 (178)
Q Consensus       138 ~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~~~~~~R  177 (178)
                      ..+.+|||.-..--+.+...+.++++...-+.|..+.++|
T Consensus       492 ~~KflVFaHH~~vLd~Iq~~~~~r~vg~IRIDGst~s~~R  531 (689)
T KOG1000|consen  492 PRKFLVFAHHQIVLDTIQVEVNKRKVGSIRIDGSTPSHRR  531 (689)
T ss_pred             CceEEEEehhHHHHHHHHHHHHHcCCCeEEecCCCCchhH
Confidence            6689999999999999999999999999999999998877

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

Probab=94.73  E-value=0.058  Score=46.08  Aligned_cols=41  Identities=34%  Similarity=0.366  Sum_probs=31.4

Q ss_pred             cCCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccc
Q 030396           13 KFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFE   53 (178)
Q Consensus        13 ~~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~   53 (178)
                      ...+||||+++.-|...++.+.--+-..+++||||||.+.+
T Consensus       180 a~~AdivItNHalL~~~~~~~~~iLP~~~~lIiDEAH~L~d  220 (636)
T TIGR03117       180 ARRCRILFCTHAMLGLAFRDKWGLLPQPDILIVDEAHLFEQ  220 (636)
T ss_pred             cccCCEEEECHHHHHHHhhhhcCCCCCCCEEEEeCCcchHH
Confidence            36789999999888876655432345578999999999953

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.

>KOG1123 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, 3'-5' helicase subunit SSL2 [Transcription; Replication, recombination and repair]

Probab=94.28  E-value=0.24  Score=41.03  Aligned_cols=59  Identities=19%  Similarity=0.176  Sum_probs=38.0

Q ss_pred             cCCCcEEEeCcHHHH-------------HHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEe
Q 030396           13 KFSCDILISTPLRLR-------------LAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFS   79 (178)
Q Consensus        13 ~~~~~Iii~TP~~l~-------------~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~S   79 (178)
                      ..++.|+|+|=..+.             +.++.     ..-.++++||+|.+-..- |+..+.-+-.++      .+.++
T Consensus       388 ~~~~gvvvsTYsMva~t~kRS~eaek~m~~l~~-----~EWGllllDEVHvvPA~M-FRRVlsiv~aHc------KLGLT  455 (776)
T KOG1123|consen  388 PSGAGVVVTTYSMVAYTGKRSHEAEKIMDFLRG-----REWGLLLLDEVHVVPAKM-FRRVLSIVQAHC------KLGLT  455 (776)
T ss_pred             CCCCcEEEEeeehhhhcccccHHHHHHHHHHhc-----CeeeeEEeehhccchHHH-HHHHHHHHHHHh------hccce
Confidence            457889999864433             23332     233589999999997766 666555554442      35677


Q ss_pred             ecCc
Q 030396           80 ATLP   83 (178)
Q Consensus        80 AT~~   83 (178)
                      ||+-
T Consensus       456 ATLv  459 (776)
T KOG1123|consen  456 ATLV  459 (776)
T ss_pred             eEEe
Confidence            8864

>PRK12898 secA preprotein translocase subunit SecA; Reviewed

Probab=94.26  E-value=0.044  Score=46.86  Aligned_cols=45  Identities=22%  Similarity=0.313  Sum_probs=32.8

Q ss_pred             hHHhccCCCcEEEeCcHHH-HHHHHcCCC-------------------------CCCCeeEEEEecccccc
Q 030396            8 STDLSKFSCDILISTPLRL-RLAIRRKKI-------------------------DLSRVEYLVLDEADKLF   52 (178)
Q Consensus         8 q~~~l~~~~~Iii~TP~~l-~~~l~~~~~-------------------------~~~~l~~lViDE~d~ll   52 (178)
                      +.+....+|||++||...+ .++++.+..                         -...+.+.|+||+|.++
T Consensus       185 ~~r~~~y~~dIvygT~~e~~FDyLrd~~~~~~~~~~~~~~~~~l~~~~~~~~~~v~r~~~~aIvDEvDSiL  255 (656)
T PRK12898        185 DERRAAYGADITYCTNKELVFDYLRDRLALGQRASDARLALESLHGRSSRSTQLLLRGLHFAIVDEADSVL  255 (656)
T ss_pred             HHHHHHcCCCEEEECCCchhhhhccccccccccccchhhhhhhhccccCchhhhcccccceeEeeccccee
Confidence            4444556899999999998 466654321                         13667899999999975

>KOG0387 consensus Transcription-coupled repair protein CSB/RAD26 (contains SNF2 family DNA-dependent ATPase domain) [Transcription; Replication, recombination and repair]

Probab=93.94  E-value=1.1  Score=39.28  Aligned_cols=55  Identities=18%  Similarity=0.148  Sum_probs=46.0

Q ss_pred             hhHHHHHHHHHHh--cCCCCEEEEeCCchHHHHHHHHhh-hCCCceEeeecCCCcccc
Q 030396          123 EGKLLALRQSFAE--SLNPPVLIFVQSKDRAKELYGELA-FDDIRAGVIHSDLSQTQV  177 (178)
Q Consensus       123 ~~k~~~l~~ll~~--~~~~~~lIF~~t~~~~~~l~~~L~-~~g~~~~~lh~~~~~~~R  177 (178)
                      ..|+..+..+++.  ....+++.|..|+.....+...|. ..||...-+.|..+-..|
T Consensus       529 sGKm~vl~~ll~~W~kqg~rvllFsqs~~mLdilE~fL~~~~~ysylRmDGtT~~~~R  586 (923)
T KOG0387|consen  529 SGKMKVLAKLLKDWKKQGDRVLLFSQSRQMLDILESFLRRAKGYSYLRMDGTTPAALR  586 (923)
T ss_pred             cchHHHHHHHHHHHhhCCCEEEEehhHHHHHHHHHHHHHhcCCceEEEecCCCccchh
Confidence            3577788777763  335699999999999999999998 689999999999887766

>cd01529 4RHOD_Repeats Member of the Rhodanese Homology Domain superfamily

Probab=93.87  E-value=0.14  Score=32.38  Aligned_cols=38  Identities=11%  Similarity=-0.066  Sum_probs=32.9

Q ss_pred             cCCCCEEEEeCCchHHHHHHHHhhhCCC-ceEeeecCCC
Q 030396          136 SLNPPVLIFVQSKDRAKELYGELAFDDI-RAGVIHSDLS  173 (178)
Q Consensus       136 ~~~~~~lIF~~t~~~~~~l~~~L~~~g~-~~~~lh~~~~  173 (178)
                      ....+++++|++-..+...+..|...|+ ++..+.||+.
T Consensus        54 ~~~~~ivv~c~~g~~s~~~~~~l~~~G~~~v~~l~GG~~   92 (96)
T cd01529          54 GRATRYVLTCDGSLLARFAAQELLALGGKPVALLDGGTS   92 (96)
T ss_pred             CCCCCEEEEeCChHHHHHHHHHHHHcCCCCEEEeCCCHH
Confidence            3467899999998999999999999999 6888999874

This CD includes putative rhodanese-related sulfurtransferases which contain 4 copies of the Rhodanese Homology Domain. Only the second and most of the fourth repeats contain the putative catalytic Cys residue. This CD aligns the 1st , 2nd, 3rd, and 4th repeats.

>cd01518 RHOD_YceA Member of the Rhodanese Homology Domain superfamily

Probab=93.83  E-value=0.12  Score=33.07  Aligned_cols=38  Identities=11%  Similarity=0.092  Sum_probs=32.4

Q ss_pred             cCCCCEEEEeCCchHHHHHHHHhhhCCCc-eEeeecCCC
Q 030396          136 SLNPPVLIFVQSKDRAKELYGELAFDDIR-AGVIHSDLS  173 (178)
Q Consensus       136 ~~~~~~lIF~~t~~~~~~l~~~L~~~g~~-~~~lh~~~~  173 (178)
                      .+.++++|||.+-.++...+..|...|++ +..+.||+.
T Consensus        59 ~~~~~ivvyC~~G~rs~~a~~~L~~~G~~~v~~l~GG~~   97 (101)
T cd01518          59 LKGKKVLMYCTGGIRCEKASAYLKERGFKNVYQLKGGIL   97 (101)
T ss_pred             cCCCEEEEECCCchhHHHHHHHHHHhCCcceeeechhHH
Confidence            45678999999988888899999999994 888999875

This CD includes Escherichia coli YceA, Bacillus subtilis YbfQ, and similar uncharacterized proteins.

>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=93.36  E-value=0.059  Score=38.24  Aligned_cols=43  Identities=28%  Similarity=0.242  Sum_probs=27.9

Q ss_pred             hccCCCcEEEeCcHHHHHHHHc-C--CCCCCCeeEEEEecccccccc
Q 030396           11 LSKFSCDILISTPLRLRLAIRR-K--KIDLSRVEYLVLDEADKLFEV   54 (178)
Q Consensus        11 ~l~~~~~Iii~TP~~l~~~l~~-~--~~~~~~l~~lViDE~d~ll~~   54 (178)
                      .....++|||++=.-|++-... .  .+++++ ..+||||||.+.+.
T Consensus       115 ~~~~~adivi~~y~yl~~~~~~~~~~~~~~~~-~ivI~DEAHNL~~~  160 (174)
T PF06733_consen  115 ELAKNADIVICNYNYLFDPSIRKSLFGIDLKD-NIVIFDEAHNLEDA  160 (174)
T ss_dssp             HCGGG-SEEEEETHHHHSHHHHHHHCT--CCC-EEEEETTGGGCGGG
T ss_pred             HhcccCCEEEeCHHHHhhHHHHhhhccccccC-cEEEEecccchHHH
Confidence            4446789999998777654322 2  234444 68999999999664

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.

>PF13872 AAA_34: P-loop containing NTP hydrolase pore-1

Probab=93.29  E-value=0.17  Score=39.23  Aligned_cols=45  Identities=18%  Similarity=0.053  Sum_probs=30.0

Q ss_pred             EEEEeccccccccCC-------ChhhHHHHHhhCCCCCceEEEEeecCcHHHHH
Q 030396           42 YLVLDEADKLFEVGN-------LLKHIDPVVKACSNPSIVRSLFSATLPDFVEE   88 (178)
Q Consensus        42 ~lViDE~d~ll~~~~-------~~~~i~~i~~~~~~~~~q~i~~SAT~~~~~~~   88 (178)
                      .+||||+|..-+...       ....+..+-+. + ++.+++.+|||--.+.+.
T Consensus       175 vivfDEcH~akn~~~~~~~~sk~g~avl~LQ~~-L-P~ARvvY~SATgasep~N  226 (303)
T PF13872_consen  175 VIVFDECHKAKNLSSGSKKPSKTGIAVLELQNR-L-PNARVVYASATGASEPRN  226 (303)
T ss_pred             eEEeccchhcCCCCccCccccHHHHHHHHHHHh-C-CCCcEEEecccccCCCce
Confidence            899999999855431       12344445555 3 566799999998755443

>cd01521 RHOD_PspE2 Member of the Rhodanese Homology Domain superfamily

Probab=93.26  E-value=0.16  Score=33.03  Aligned_cols=37  Identities=11%  Similarity=0.057  Sum_probs=31.5

Q ss_pred             CCCCEEEEeCCc--hHHHHHHHHhhhCCCceEeeecCCC
Q 030396          137 LNPPVLIFVQSK--DRAKELYGELAFDDIRAGVIHSDLS  173 (178)
Q Consensus       137 ~~~~~lIF~~t~--~~~~~l~~~L~~~g~~~~~lh~~~~  173 (178)
                      ...++++||++-  ..+...+..|...|+++..+.||+.
T Consensus        63 ~~~~vvvyc~~g~~~~s~~~a~~l~~~G~~v~~l~GG~~  101 (110)
T cd01521          63 KEKLFVVYCDGPGCNGATKAALKLAELGFPVKEMIGGLD  101 (110)
T ss_pred             CCCeEEEEECCCCCchHHHHHHHHHHcCCeEEEecCCHH
Confidence            357899999875  3788899999999999999999874

This CD includes the putative rhodanese-like protein, Psp2, of Yersinia pestis biovar Medievalis and other similar uncharacterized proteins.

>cd01534 4RHOD_Repeat_3 Member of the Rhodanese Homology Domain superfamily, repeat 3

Probab=93.23  E-value=0.13  Score=32.51  Aligned_cols=36  Identities=17%  Similarity=0.055  Sum_probs=31.8

Q ss_pred             CCCEEEEeCCchHHHHHHHHhhhCCCceEeeecCCC
Q 030396          138 NPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLS  173 (178)
Q Consensus       138 ~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~~~  173 (178)
                      ..++++||.+-.++...+..|...|+++..+.||+.
T Consensus        56 ~~~iv~~c~~G~rs~~aa~~L~~~G~~v~~l~GG~~   91 (95)
T cd01534          56 GARIVLADDDGVRADMTASWLAQMGWEVYVLEGGLA   91 (95)
T ss_pred             CCeEEEECCCCChHHHHHHHHHHcCCEEEEecCcHH
Confidence            568999999988888899999999999888999875

This CD includes putative rhodanese-related sulfurtransferases which contain 4 copies of the Rhodanese Homology Domain. This CD aligns the 3rd repeat which does not contain the putative catalytic Cys residue.

>cd01526 RHOD_ThiF Member of the Rhodanese Homology Domain superfamily

Probab=93.22  E-value=0.11  Score=34.50  Aligned_cols=37  Identities=11%  Similarity=0.136  Sum_probs=33.0

Q ss_pred             CCCCEEEEeCCchHHHHHHHHhhhCCC--ceEeeecCCC
Q 030396          137 LNPPVLIFVQSKDRAKELYGELAFDDI--RAGVIHSDLS  173 (178)
Q Consensus       137 ~~~~~lIF~~t~~~~~~l~~~L~~~g~--~~~~lh~~~~  173 (178)
                      ..+++++||++-.++...+..|...|+  ++..+.||+.
T Consensus        71 ~~~~ivv~C~~G~rs~~aa~~L~~~G~~~~v~~l~GG~~  109 (122)
T cd01526          71 KDSPIYVVCRRGNDSQTAVRKLKELGLERFVRDIIGGLK  109 (122)
T ss_pred             CCCcEEEECCCCCcHHHHHHHHHHcCCccceeeecchHH
Confidence            467899999998899999999999999  6999999874

This CD includes several putative molybdopterin synthase sulfurylases including the molybdenum cofactor biosynthetic protein (CnxF) of Aspergillus nidulans and the molybdenum cofactor synthesis protein 3 (MOCS3) of Homo sapiens. These rhodanese-like domains are found C-terminal of the ThiF and MoeZ_MoeB domains.

>cd01533 4RHOD_Repeat_2 Member of the Rhodanese Homology Domain superfamily, repeat 2

Probab=93.10  E-value=0.25  Score=32.02  Aligned_cols=38  Identities=8%  Similarity=0.107  Sum_probs=32.3

Q ss_pred             CCCCEEEEeCCchHHHHHHHHhhhCCCc--eEeeecCCCc
Q 030396          137 LNPPVLIFVQSKDRAKELYGELAFDDIR--AGVIHSDLSQ  174 (178)
Q Consensus       137 ~~~~~lIF~~t~~~~~~l~~~L~~~g~~--~~~lh~~~~~  174 (178)
                      ...+++|||.+-.++...+..|...|++  +..+.||++.
T Consensus        65 ~~~~ivv~C~~G~rs~~a~~~L~~~G~~~~v~~l~gG~~~  104 (109)
T cd01533          65 PRTPIVVNCAGRTRSIIGAQSLINAGLPNPVAALRNGTQG  104 (109)
T ss_pred             CCCeEEEECCCCchHHHHHHHHHHCCCCcceeEecCCHHH
Confidence            3568999999988888889999999994  8899999853

This CD includes putative rhodanese-related sulfurtransferases which contain 4 copies of the Rhodanese Homology Domain. This CD aligns the 2nd repeat which does contain the putative catalytic Cys residue.

>PRK12326 preprotein translocase subunit SecA; Reviewed

Probab=93.03  E-value=1  Score=39.25  Aligned_cols=93  Identities=18%  Similarity=0.173  Sum_probs=58.9

Q ss_pred             EEEEeecCcHHHHHHHHHhccCcEEEEEcCC-ccccCCceEEEEEcCChhhHHHHHHHHHHh--cCCCCEEEEeCCchHH
Q 030396           75 RSLFSATLPDFVEELARSIMHDAVRVIVGRK-NTASESIKQKLVFAGSEEGKLLALRQSFAE--SLNPPVLIFVQSKDRA  151 (178)
Q Consensus        75 ~i~~SAT~~~~~~~~~~~~~~~~~~v~~~~~-~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~--~~~~~~lIF~~t~~~~  151 (178)
                      .-.+|.|......++.+-| +=+ .+.+++. +....+....+ +. ....|...+.+-+.+  ...+|+||.|.|.+.+
T Consensus       365 LsGMTGTa~t~~~Ef~~iY-~l~-Vv~IPtnkp~~R~d~~d~i-y~-t~~~k~~Aii~ei~~~~~~GrPVLVgt~sI~~S  440 (764)
T PRK12326        365 VCGMTGTAVAAGEQLRQFY-DLG-VSVIPPNKPNIREDEADRV-YA-TAAEKNDAIVEHIAEVHETGQPVLVGTHDVAES  440 (764)
T ss_pred             heeecCCChhHHHHHHHHh-CCc-EEECCCCCCceeecCCCce-Ee-CHHHHHHHHHHHHHHHHHcCCCEEEEeCCHHHH
Confidence            4466777765544444444 332 3333322 22222222223 33 445677777776653  2478999999999999


Q ss_pred             HHHHHHhhhCCCceEeeecC
Q 030396          152 KELYGELAFDDIRAGVIHSD  171 (178)
Q Consensus       152 ~~l~~~L~~~g~~~~~lh~~  171 (178)
                      +.++..|.+.|++...+++.
T Consensus       441 E~ls~~L~~~gI~h~vLNAk  460 (764)
T PRK12326        441 EELAERLRAAGVPAVVLNAK  460 (764)
T ss_pred             HHHHHHHHhCCCcceeeccC
Confidence            99999999999999888774

>cd00158 RHOD Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein

Probab=92.92  E-value=0.23  Score=30.39  Aligned_cols=39  Identities=10%  Similarity=0.132  Sum_probs=33.2

Q ss_pred             hcCCCCEEEEeCCchHHHHHHHHhhhCCC-ceEeeecCCC
Q 030396          135 ESLNPPVLIFVQSKDRAKELYGELAFDDI-RAGVIHSDLS  173 (178)
Q Consensus       135 ~~~~~~~lIF~~t~~~~~~l~~~L~~~g~-~~~~lh~~~~  173 (178)
                      .....+++++|++...+...+..|...|+ ++..+-||+.
T Consensus        47 ~~~~~~vv~~c~~~~~a~~~~~~l~~~G~~~v~~l~gG~~   86 (89)
T cd00158          47 LDKDKPIVVYCRSGNRSARAAKLLRKAGGTNVYNLEGGML   86 (89)
T ss_pred             cCCCCeEEEEeCCCchHHHHHHHHHHhCcccEEEecCChh
Confidence            34567899999999999999999999987 6778888874

The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins such as sulfide dehydrogenases and certain stress proteins such as senesence specific protein 1 in plants, PspE and GlpE in bacteria and cyanide and arsenate resistance proteins. Inactive versions (no active site cysteine) are also seen in dual specificity phosphatases, ubiquitin hydrolases from yeast and in sulfuryltransferases, where they are believed to play a regulatory role in multidomain proteins.

>PRK06893 DNA replication initiation factor; Validated

Probab=92.91  E-value=0.13  Score=38.35  Aligned_cols=49  Identities=14%  Similarity=0.106  Sum_probs=32.5

Q ss_pred             CCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcHH
Q 030396           37 LSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDF   85 (178)
Q Consensus        37 ~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~   85 (178)
                      +.+.+.+++||+|.+.........+..++........+++++|++.++.
T Consensus        89 ~~~~dlLilDDi~~~~~~~~~~~~l~~l~n~~~~~~~~illits~~~p~  137 (229)
T PRK06893         89 LEQQDLVCLDDLQAVIGNEEWELAIFDLFNRIKEQGKTLLLISADCSPH  137 (229)
T ss_pred             cccCCEEEEeChhhhcCChHHHHHHHHHHHHHHHcCCcEEEEeCCCChH
Confidence            4567899999999986443234456666665333345677888887665

>cd01527 RHOD_YgaP Member of the Rhodanese Homology Domain superfamily

Probab=92.88  E-value=0.22  Score=31.55  Aligned_cols=37  Identities=19%  Similarity=0.132  Sum_probs=31.8

Q ss_pred             CCCCEEEEeCCchHHHHHHHHhhhCCC-ceEeeecCCC
Q 030396          137 LNPPVLIFVQSKDRAKELYGELAFDDI-RAGVIHSDLS  173 (178)
Q Consensus       137 ~~~~~lIF~~t~~~~~~l~~~L~~~g~-~~~~lh~~~~  173 (178)
                      ..++++++|++-.++...+..|.+.|+ ++..+.||+.
T Consensus        53 ~~~~iv~~c~~g~~s~~~~~~L~~~g~~~v~~l~gG~~   90 (99)
T cd01527          53 GANAIIFHCRSGMRTQQNAERLAAISAGEAYVLEGGLD   90 (99)
T ss_pred             CCCcEEEEeCCCchHHHHHHHHHHcCCccEEEeeCCHH
Confidence            357899999999889999999999888 6888999864

This CD includes Escherichia coli YgaP, and similar uncharacterized putative rhodanese-related sulfurtransferases.

>cd01449 TST_Repeat_2 Thiosulfate sulfurtransferase (TST), C-terminal, catalytic domain

Probab=92.79  E-value=0.25  Score=32.37  Aligned_cols=37  Identities=19%  Similarity=0.185  Sum_probs=32.2

Q ss_pred             CCCCEEEEeCCchHHHHHHHHhhhCCC-ceEeeecCCC
Q 030396          137 LNPPVLIFVQSKDRAKELYGELAFDDI-RAGVIHSDLS  173 (178)
Q Consensus       137 ~~~~~lIF~~t~~~~~~l~~~L~~~g~-~~~~lh~~~~  173 (178)
                      +..++++||++-..+...+..|...|+ ++..+.||++
T Consensus        77 ~~~~iv~yc~~g~~s~~~~~~l~~~G~~~v~~l~GG~~  114 (118)
T cd01449          77 PDKPVIVYCGSGVTACVLLLALELLGYKNVRLYDGSWS  114 (118)
T ss_pred             CCCCEEEECCcHHHHHHHHHHHHHcCCCCeeeeCChHH
Confidence            467899999998899999999999999 5888888874

TST contains 2 copies of the Rhodanese Homology Domain; this is the second repeat. Only the second repeat contains the catalytically active Cys residue.

>cd01519 RHOD_HSP67B2 Member of the Rhodanese Homology Domain superfamily

Probab=92.75  E-value=0.16  Score=32.58  Aligned_cols=37  Identities=8%  Similarity=0.022  Sum_probs=32.1

Q ss_pred             CCCCEEEEeCCchHHHHHHHHhhhCCC-ceEeeecCCC
Q 030396          137 LNPPVLIFVQSKDRAKELYGELAFDDI-RAGVIHSDLS  173 (178)
Q Consensus       137 ~~~~~lIF~~t~~~~~~l~~~L~~~g~-~~~~lh~~~~  173 (178)
                      +..++++||++-..+...+..|...|+ .+..+.||+.
T Consensus        65 ~~~~ivv~c~~g~~s~~~~~~l~~~G~~~v~~~~Gg~~  102 (106)
T cd01519          65 KDKELIFYCKAGVRSKAAAELARSLGYENVGNYPGSWL  102 (106)
T ss_pred             CCCeEEEECCCcHHHHHHHHHHHHcCCccceecCCcHH
Confidence            356899999998899999999999999 4888888875

This CD includes the heat shock protein 67B2 of Drosophila melanogaster and other similar proteins, many of which are uncharacterized.

>cd01448 TST_Repeat_1 Thiosulfate sulfurtransferase (TST), N-terminal, inactive domain

Probab=92.73  E-value=0.23  Score=32.86  Aligned_cols=39  Identities=15%  Similarity=0.152  Sum_probs=32.5

Q ss_pred             cCCCCEEEEeCC-chHHHHHHHHhhhCCCc-eEeeecCCCc
Q 030396          136 SLNPPVLIFVQS-KDRAKELYGELAFDDIR-AGVIHSDLSQ  174 (178)
Q Consensus       136 ~~~~~~lIF~~t-~~~~~~l~~~L~~~g~~-~~~lh~~~~~  174 (178)
                      ...+++++||++ -..+...+..|...|++ +..+.||+..
T Consensus        77 ~~~~~vv~~c~~g~~~a~~~~~~l~~~G~~~v~~l~GG~~~  117 (122)
T cd01448          77 SNDDTVVVYDDGGGFFAARAWWTLRYFGHENVRVLDGGLQA  117 (122)
T ss_pred             CCCCEEEEECCCCCccHHHHHHHHHHcCCCCEEEecCCHHH
Confidence            346789999999 58898999999999985 8899998753

TST contains 2 copies of the Rhodanese Homology Domain; this is the 1st repeat, which does not contain the catalytically active Cys residue. The role of the 1st repeat is uncertain, but it is believed to be involved in protein interaction.

>cd01520 RHOD_YbbB Member of the Rhodanese Homology Domain superfamily

Probab=92.60  E-value=0.17  Score=34.00  Aligned_cols=38  Identities=18%  Similarity=0.225  Sum_probs=31.8

Q ss_pred             CCCCEEEEeC-CchHHHHHHHHhhhCCCceEeeecCCCc
Q 030396          137 LNPPVLIFVQ-SKDRAKELYGELAFDDIRAGVIHSDLSQ  174 (178)
Q Consensus       137 ~~~~~lIF~~-t~~~~~~l~~~L~~~g~~~~~lh~~~~~  174 (178)
                      +..+++|||+ +-.++...+..|...|+++..+.||+..
T Consensus        85 ~~~~vvvyC~~~G~rs~~a~~~L~~~G~~v~~L~GG~~a  123 (128)
T cd01520          85 RDPKLLIYCARGGMRSQSLAWLLESLGIDVPLLEGGYKA  123 (128)
T ss_pred             CCCeEEEEeCCCCccHHHHHHHHHHcCCceeEeCCcHHH
Confidence            4568999997 5677888888999999999999999754

This CD includes several putative ATP /GTP binding proteins including E. coli YbbB.

>cd01532 4RHOD_Repeat_1 Member of the Rhodanese Homology Domain superfamily, repeat 1

Probab=92.58  E-value=0.22  Score=31.31  Aligned_cols=36  Identities=14%  Similarity=0.282  Sum_probs=30.2

Q ss_pred             CCCEEEEeCC--chHHHHHHHHhhhCCC-ceEeeecCCC
Q 030396          138 NPPVLIFVQS--KDRAKELYGELAFDDI-RAGVIHSDLS  173 (178)
Q Consensus       138 ~~~~lIF~~t--~~~~~~l~~~L~~~g~-~~~~lh~~~~  173 (178)
                      ..++++||.+  +..+...+..|...|+ ++..+.||+.
T Consensus        50 ~~~ivl~c~~G~~~~s~~aa~~L~~~G~~~v~~l~GG~~   88 (92)
T cd01532          50 DTPIVVYGEGGGEDLAPRAARRLSELGYTDVALLEGGLQ   88 (92)
T ss_pred             CCeEEEEeCCCCchHHHHHHHHHHHcCccCEEEccCCHH
Confidence            5689999998  4557888999999998 6888999875

This CD includes putative rhodanese-related sulfurtransferases which contain 4 copies of the Rhodanese Homology Domain. This CD aligns the 1st repeat which does not contain the putative catalytic Cys residue.

>cd01528 RHOD_2 Member of the Rhodanese Homology Domain superfamily, subgroup 2

Probab=92.41  E-value=0.25  Score=31.52  Aligned_cols=38  Identities=5%  Similarity=0.111  Sum_probs=32.8

Q ss_pred             CCCCEEEEeCCchHHHHHHHHhhhCCC-ceEeeecCCCc
Q 030396          137 LNPPVLIFVQSKDRAKELYGELAFDDI-RAGVIHSDLSQ  174 (178)
Q Consensus       137 ~~~~~lIF~~t~~~~~~l~~~L~~~g~-~~~~lh~~~~~  174 (178)
                      ...++++||++-.++...+..|.+.|+ ++..+.||+..
T Consensus        57 ~~~~vv~~c~~g~rs~~~~~~l~~~G~~~v~~l~GG~~~   95 (101)
T cd01528          57 PDKDIVVLCHHGGRSMQVAQWLLRQGFENVYNLQGGIDA   95 (101)
T ss_pred             CCCeEEEEeCCCchHHHHHHHHHHcCCccEEEecCCHHH
Confidence            367899999998899999999999999 58889998753

Subgroup 2 includes uncharacterized putative rhodanese-related domains.

>cd01525 RHOD_Kc Member of the Rhodanese Homology Domain superfamily

Probab=92.38  E-value=0.32  Score=31.12  Aligned_cols=36  Identities=11%  Similarity=0.135  Sum_probs=31.5

Q ss_pred             CCCEEEEeCCchHHHHHHHHhhhCCCc-eEeeecCCC
Q 030396          138 NPPVLIFVQSKDRAKELYGELAFDDIR-AGVIHSDLS  173 (178)
Q Consensus       138 ~~~~lIF~~t~~~~~~l~~~L~~~g~~-~~~lh~~~~  173 (178)
                      ..+++++|.+-..+...+..|...|++ +..+.||++
T Consensus        65 ~~~vv~~c~~g~~s~~~a~~L~~~G~~~v~~l~GG~~  101 (105)
T cd01525          65 GKIIVIVSHSHKHAALFAAFLVKCGVPRVCILDGGIN  101 (105)
T ss_pred             CCeEEEEeCCCccHHHHHHHHHHcCCCCEEEEeCcHH
Confidence            568999999888888999999999995 888999875

Included in this CD are the rhodanese-like domains found C-terminal of the serine/threonine protein kinases catalytic (S_TKc) domain and the Tre-2, BUB2p, Cdc16p (TBC) domain. The putative active site Cys residue is not present in this CD.

>cd01444 GlpE_ST GlpE sulfurtransferase (ST) and homologs are members of the Rhodanese Homology Domain superfamily

Probab=92.16  E-value=0.26  Score=30.86  Aligned_cols=37  Identities=11%  Similarity=0.228  Sum_probs=32.4

Q ss_pred             CCCCEEEEeCCchHHHHHHHHhhhCCC-ceEeeecCCC
Q 030396          137 LNPPVLIFVQSKDRAKELYGELAFDDI-RAGVIHSDLS  173 (178)
Q Consensus       137 ~~~~~lIF~~t~~~~~~l~~~L~~~g~-~~~~lh~~~~  173 (178)
                      ...+++|+|++-..+...+..|...|+ ++..+.||+.
T Consensus        55 ~~~~ivv~c~~g~~s~~a~~~l~~~G~~~v~~l~gG~~   92 (96)
T cd01444          55 RDRPVVVYCYHGNSSAQLAQALREAGFTDVRSLAGGFE   92 (96)
T ss_pred             CCCCEEEEeCCCChHHHHHHHHHHcCCceEEEcCCCHH
Confidence            467899999999999999999999999 5788888864

Unlike other rhodanese sulfurtransferases, GlpE is a single domain protein but indications are that it functions as a dimer. The active site contains a catalytically active cysteine.

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

Probab=92.11  E-value=1.4  Score=39.31  Aligned_cols=40  Identities=23%  Similarity=0.190  Sum_probs=28.4

Q ss_pred             cCCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEecccccc
Q 030396           13 KFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLF   52 (178)
Q Consensus        13 ~~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll   52 (178)
                      ...++|||+.-.-|++.+....-.+..-+++|+||||.|.
T Consensus       414 a~~AdivItNHa~L~~~~~~~~~ilp~~~~lIiDEAH~L~  453 (850)
T TIGR01407       414 AEQAQILITNHAYLITRLVDNPELFPSFRDLIIDEAHHLP  453 (850)
T ss_pred             HhcCCEEEecHHHHHHHhhcccccCCCCCEEEEECcchHH
Confidence            4678999999887776664332222333699999999985

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.

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

Probab=91.98  E-value=0.22  Score=44.26  Aligned_cols=24  Identities=21%  Similarity=0.347  Sum_probs=21.7

Q ss_pred             CCCCEEEEeCCchHHHHHHHHhhh
Q 030396          137 LNPPVLIFVQSKDRAKELYGELAF  160 (178)
Q Consensus       137 ~~~~~lIF~~t~~~~~~l~~~L~~  160 (178)
                      ..++++||++|.+..+.+++.|..
T Consensus       673 ~~g~~LVlftS~~~l~~v~~~L~~  696 (850)
T TIGR01407       673 TSPKILVLFTSYEMLHMVYDMLNE  696 (850)
T ss_pred             cCCCEEEEeCCHHHHHHHHHHHhh
Confidence            367999999999999999999975

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.

>PF05872 DUF853: Bacterial protein of unknown function (DUF853); InterPro: IPR008571 Members of this family have a P-loop containing nucleotide triphosphate hydrolases fold

Probab=91.93  E-value=0.33  Score=39.79  Aligned_cols=47  Identities=26%  Similarity=0.370  Sum_probs=34.2

Q ss_pred             CCCCCeeEE-EEeccccccccC--CChhhHHHHHhhCCCCCceEEEEeec
Q 030396           35 IDLSRVEYL-VLDEADKLFEVG--NLLKHIDPVVKACSNPSIVRSLFSAT   81 (178)
Q Consensus        35 ~~~~~l~~l-ViDE~d~ll~~~--~~~~~i~~i~~~~~~~~~q~i~~SAT   81 (178)
                      -|+.+.+++ .|||||.++++.  .+.+.|+.+.+.+-+...-+.++|-+
T Consensus       250 GD~dkPklVfFfDEAHLLF~da~kall~~ieqvvrLIRSKGVGv~fvTQ~  299 (502)
T PF05872_consen  250 GDLDKPKLVFFFDEAHLLFNDAPKALLDKIEQVVRLIRSKGVGVYFVTQN  299 (502)
T ss_pred             CCCCCceEEEEEechhhhhcCCCHHHHHHHHHHHHHhhccCceEEEEeCC
Confidence            367777874 599999999876  67888888888844445556666544

This family is restricted to bacterial proteins, none of which have currently been characterised.

>cd01447 Polysulfide_ST Polysulfide-sulfurtransferase - Rhodanese Homology Domain

Probab=91.62  E-value=0.21  Score=31.79  Aligned_cols=37  Identities=14%  Similarity=0.084  Sum_probs=31.6

Q ss_pred             CCCCEEEEeCCchHHHHHHHHhhhCCCc-eEeeecCCC
Q 030396          137 LNPPVLIFVQSKDRAKELYGELAFDDIR-AGVIHSDLS  173 (178)
Q Consensus       137 ~~~~~lIF~~t~~~~~~l~~~L~~~g~~-~~~lh~~~~  173 (178)
                      ...+++|||++-..+...+..|...|+. +..+.||+.
T Consensus        60 ~~~~ivv~c~~g~~s~~~~~~l~~~G~~~v~~l~Gg~~   97 (103)
T cd01447          60 EDKPFVFYCASGWRSALAGKTLQDMGLKPVYNIEGGFK   97 (103)
T ss_pred             CCCeEEEEcCCCCcHHHHHHHHHHcChHHhEeecCcHH
Confidence            4578999998888888899999999996 888888874

This domain is believed to serve as a polysulfide binding and transferase domain in anaerobic gram-negative bacteria, functioning in oxidative phosphorylation with polysulfide-sulfur as a terminal electron acceptor. The active site contains the same conserved cysteine that is the catalytic residue in other Rhodanese Homology Domain proteins.

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=91.47  E-value=0.31  Score=40.09  Aligned_cols=79  Identities=9%  Similarity=0.040  Sum_probs=48.0

Q ss_pred             HhHHhccCCCcEEEeCcHHHHHHHH----c--CCC-----CCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceE
Q 030396            7 RSTDLSKFSCDILISTPLRLRLAIR----R--KKI-----DLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVR   75 (178)
Q Consensus         7 ~q~~~l~~~~~Iii~TP~~l~~~l~----~--~~~-----~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~   75 (178)
                      ........+..++..|++.+...+.    .  +.+     .+.+.+++|+||+|.+-......+.+..++..+.....|+
T Consensus       163 ~~l~~~~~~~~v~yv~~~~f~~~~~~~l~~~~~~~~~~~~~~~~~dvLiIDDiq~l~~k~~~~e~lf~l~N~~~~~~k~i  242 (450)
T PRK14087        163 NYIESNFSDLKVSYMSGDEFARKAVDILQKTHKEIEQFKNEICQNDVLIIDDVQFLSYKEKTNEIFFTIFNNFIENDKQL  242 (450)
T ss_pred             HHHHHhCCCCeEEEEEHHHHHHHHHHHHHHhhhHHHHHHHHhccCCEEEEeccccccCCHHHHHHHHHHHHHHHHcCCcE
Confidence            3333334567888888887765442    1  111     1567889999999988533224566777777744455676


Q ss_pred             EEEeecCcHH
Q 030396           76 SLFSATLPDF   85 (178)
Q Consensus        76 i~~SAT~~~~   85 (178)
                      ++.|-.-|..
T Consensus       243 Iltsd~~P~~  252 (450)
T PRK14087        243 FFSSDKSPEL  252 (450)
T ss_pred             EEECCCCHHH
Confidence            5554444433

>smart00489 DEXDc3 DEAD-like helicases superfamily

Probab=91.44  E-value=0.21  Score=38.56  Aligned_cols=40  Identities=20%  Similarity=0.189  Sum_probs=28.9

Q ss_pred             cCCCcEEEeCcHHHHHHHHcC--CCCCCCeeEEEEeccccccc
Q 030396           13 KFSCDILISTPLRLRLAIRRK--KIDLSRVEYLVLDEADKLFE   53 (178)
Q Consensus        13 ~~~~~Iii~TP~~l~~~l~~~--~~~~~~l~~lViDE~d~ll~   53 (178)
                      ...+||||++-.-|++-..++  ..++ .-.++||||||.+.+
T Consensus       209 ~~~Adivi~ny~yll~~~~r~~~~~~l-~~~~lIiDEAHnL~d  250 (289)
T smart00489      209 IEFANVVVLPYQYLLDPKIRQALSIEL-KDSIVIFDEAHNLDN  250 (289)
T ss_pred             hhcCCEEEECHHHHhcHHHHHHhcccc-cccEEEEeCccChHH
Confidence            367999999988877654222  2344 358999999999954

>smart00488 DEXDc2 DEAD-like helicases superfamily

Probab=91.44  E-value=0.21  Score=38.56  Aligned_cols=40  Identities=20%  Similarity=0.189  Sum_probs=28.9

Q ss_pred             cCCCcEEEeCcHHHHHHHHcC--CCCCCCeeEEEEeccccccc
Q 030396           13 KFSCDILISTPLRLRLAIRRK--KIDLSRVEYLVLDEADKLFE   53 (178)
Q Consensus        13 ~~~~~Iii~TP~~l~~~l~~~--~~~~~~l~~lViDE~d~ll~   53 (178)
                      ...+||||++-.-|++-..++  ..++ .-.++||||||.+.+
T Consensus       209 ~~~Adivi~ny~yll~~~~r~~~~~~l-~~~~lIiDEAHnL~d  250 (289)
T smart00488      209 IEFANVVVLPYQYLLDPKIRQALSIEL-KDSIVIFDEAHNLDN  250 (289)
T ss_pred             hhcCCEEEECHHHHhcHHHHHHhcccc-cccEEEEeCccChHH
Confidence            367999999988877654222  2344 358999999999954

>PRK12903 secA preprotein translocase subunit SecA; Reviewed

Probab=91.36  E-value=0.96  Score=40.11  Aligned_cols=51  Identities=18%  Similarity=0.210  Sum_probs=40.6

Q ss_pred             ChhhHHHHHHHHHHh--cCCCCEEEEeCCchHHHHHHHHhhhCCCceEeeecC
Q 030396          121 SEEGKLLALRQSFAE--SLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSD  171 (178)
Q Consensus       121 ~~~~k~~~l~~ll~~--~~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~  171 (178)
                      ....|...+.+-+..  ...+|+||.|.|.+.++.++..|.+.|++...+++.
T Consensus       407 t~~~K~~Aii~ei~~~~~~gqPVLVgT~SIe~SE~ls~~L~~~gi~h~vLNAk  459 (925)
T PRK12903        407 TKHAKWKAVVKEVKRVHKKGQPILIGTAQVEDSETLHELLLEANIPHTVLNAK  459 (925)
T ss_pred             cHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHCCCCceeeccc
Confidence            344566666665553  247799999999999999999999999998888764

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=91.25  E-value=0.55  Score=38.64  Aligned_cols=74  Identities=11%  Similarity=0.092  Sum_probs=44.1

Q ss_pred             CCCcEEEeCcHHHHHHH----HcCCC-----CCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcH
Q 030396           14 FSCDILISTPLRLRLAI----RRKKI-----DLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPD   84 (178)
Q Consensus        14 ~~~~Iii~TP~~l~~~l----~~~~~-----~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~   84 (178)
                      .+..++..|...+...+    ..+..     .+.+.+.+++||+|.+.......+.+..++..+.....|+++.|.+-|.
T Consensus       168 ~~~~v~yi~~~~f~~~~~~~l~~~~~~~f~~~~~~~dvLiIDDiq~l~~k~~~qeelf~l~N~l~~~~k~IIlts~~~p~  247 (445)
T PRK12422        168 SGGKILYVRSELFTEHLVSAIRSGEMQRFRQFYRNVDALFIEDIEVFSGKGATQEEFFHTFNSLHTEGKLIVISSTCAPQ  247 (445)
T ss_pred             cCCCEEEeeHHHHHHHHHHHHhcchHHHHHHHcccCCEEEEcchhhhcCChhhHHHHHHHHHHHHHCCCcEEEecCCCHH
Confidence            35677777776554332    22221     1567889999999998654324566666766533345676665555555


Q ss_pred             HHH
Q 030396           85 FVE   87 (178)
Q Consensus        85 ~~~   87 (178)
                      ++.
T Consensus       248 ~l~  250 (445)
T PRK12422        248 DLK  250 (445)
T ss_pred             HHh
Confidence            443

>PF11019 DUF2608: Protein of unknown function (DUF2608); InterPro: IPR022565 This family is conserved in Bacteria

Probab=91.11  E-value=3.7  Score=31.14  Aligned_cols=110  Identities=13%  Similarity=0.093  Sum_probs=63.4

Q ss_pred             hHHHHHhhCCCCCceEEEEeecCcHHHHHHHHHhcc------Cc-----EEEEE--cCCccccCCceEEEEEcCChhhHH
Q 030396           60 HIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMH------DA-----VRVIV--GRKNTASESIKQKLVFAGSEEGKL  126 (178)
Q Consensus        60 ~i~~i~~~~~~~~~q~i~~SAT~~~~~~~~~~~~~~------~~-----~~v~~--~~~~~~~~~i~~~~~~~~~~~~k~  126 (178)
                      .+-.+++.+...+.-++++|+-.++......+..-.      +.     .++..  ........-+-+.-+......+|-
T Consensus        85 ~~~~~i~~lq~~~~~v~alT~~~~~~~~~t~~~Lk~~gi~fs~~~~~~~~~~~~~~~~~~~~~~~~~~~GIlft~~~~KG  164 (252)
T PF11019_consen   85 DVPNIINSLQNKGIPVIALTARGPNMEDWTLRELKSLGIDFSSSSFPEDGIISFPVFDSALSRAPSFYDGILFTGGQDKG  164 (252)
T ss_pred             hHHHHHHHHHHCCCcEEEEcCCChhhHHHHHHHHHHCCCCccccccccCcceecccccCCCCCCceeecCeEEeCCCccH
Confidence            344444443334677899998886543332222211      11     11100  001111112223333444667899


Q ss_pred             HHHHHHHHhcC-CCCEEEEe-CCchHHHHHHHHhhhCCCceEeee
Q 030396          127 LALRQSFAESL-NPPVLIFV-QSKDRAKELYGELAFDDIRAGVIH  169 (178)
Q Consensus       127 ~~l~~ll~~~~-~~~~lIF~-~t~~~~~~l~~~L~~~g~~~~~lh  169 (178)
                      ..|..++...+ ..+.|||. ++.+..+.+.+++...|+...-+|
T Consensus       165 ~~L~~fL~~~~~~pk~IIfIDD~~~nl~sv~~a~k~~~I~f~G~~  209 (252)
T PF11019_consen  165 EVLKYFLDKINQSPKKIIFIDDNKENLKSVEKACKKSGIDFIGFH  209 (252)
T ss_pred             HHHHHHHHHcCCCCCeEEEEeCCHHHHHHHHHHHhhCCCcEEEEE
Confidence            99999998765 34466666 788889999999999998777766

The function is not known.

>PRK05642 DNA replication initiation factor; Validated

Probab=90.93  E-value=0.3  Score=36.51  Aligned_cols=48  Identities=15%  Similarity=0.143  Sum_probs=30.8

Q ss_pred             CCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcHH
Q 030396           37 LSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDF   85 (178)
Q Consensus        37 ~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~   85 (178)
                      +.+.+++|+|++|.+-........+..+++.+.....+ ++++++.++.
T Consensus        95 ~~~~d~LiiDDi~~~~~~~~~~~~Lf~l~n~~~~~g~~-ilits~~~p~  142 (234)
T PRK05642         95 LEQYELVCLDDLDVIAGKADWEEALFHLFNRLRDSGRR-LLLAASKSPR  142 (234)
T ss_pred             hhhCCEEEEechhhhcCChHHHHHHHHHHHHHHhcCCE-EEEeCCCCHH
Confidence            45567999999998854332456677777763333455 5666666543

>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=90.85  E-value=0.26  Score=37.61  Aligned_cols=40  Identities=18%  Similarity=0.281  Sum_probs=29.8

Q ss_pred             CCcEEEeCcHHHH-HHHHcCC----CC--CCCeeEEEEecccccccc
Q 030396           15 SCDILISTPLRLR-LAIRRKK----ID--LSRVEYLVLDEADKLFEV   54 (178)
Q Consensus        15 ~~~Iii~TP~~l~-~~l~~~~----~~--~~~l~~lViDE~d~ll~~   54 (178)
                      .++|+.||.+.+. +.++...    ..  .....+.|+||+|.++-+
T Consensus       166 ~~dI~Y~t~~~~~fD~Lrd~~~~~~~~~~~r~~~~~ivDEvDs~LiD  212 (266)
T PF07517_consen  166 AADIVYGTNSEFGFDYLRDNLALSKNEQVQRGFDFAIVDEVDSILID  212 (266)
T ss_dssp             HSSEEEEEHHHHHHHHHHHTT-SSGGG--SSSSSEEEECTHHHHTTT
T ss_pred             hCcccccccchhhHHHHHHHHhhccchhccCCCCEEEEeccceEEEe
Confidence            4789999999977 5565421    11  578899999999997644

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 ....

>PRK08727 hypothetical protein; Validated

Probab=90.59  E-value=0.38  Score=35.90  Aligned_cols=71  Identities=10%  Similarity=-0.069  Sum_probs=36.6

Q ss_pred             CCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcHH
Q 030396           14 FSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDF   85 (178)
Q Consensus        14 ~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~   85 (178)
                      .+..+++.+.+.+...+..-.-.+.+...+|+||+|.+.........+..++........+ +++++..++.
T Consensus        68 ~~~~~~y~~~~~~~~~~~~~~~~l~~~dlLiIDDi~~l~~~~~~~~~lf~l~n~~~~~~~~-vI~ts~~~p~  138 (233)
T PRK08727         68 AGRSSAYLPLQAAAGRLRDALEALEGRSLVALDGLESIAGQREDEVALFDFHNRARAAGIT-LLYTARQMPD  138 (233)
T ss_pred             cCCcEEEEeHHHhhhhHHHHHHHHhcCCEEEEeCcccccCChHHHHHHHHHHHHHHHcCCe-EEEECCCChh
Confidence            3455555555444432221111245667999999999865432333444555552222344 4455554443

>cd01535 4RHOD_Repeat_4 Member of the Rhodanese Homology Domain superfamily, repeat 4

Probab=90.31  E-value=1.1  Score=30.90  Aligned_cols=37  Identities=14%  Similarity=-0.010  Sum_probs=32.4

Q ss_pred             CCCCEEEEeCCchHHHHHHHHhhhCCC-ceEeeecCCC
Q 030396          137 LNPPVLIFVQSKDRAKELYGELAFDDI-RAGVIHSDLS  173 (178)
Q Consensus       137 ~~~~~lIF~~t~~~~~~l~~~L~~~g~-~~~~lh~~~~  173 (178)
                      ...+++|+|.+-..+...+..|...|+ ++..+.||+.
T Consensus        48 ~~~~vVv~c~~g~~a~~aa~~L~~~G~~~v~~L~GG~~   85 (145)
T cd01535          48 AAERYVLTCGSSLLARFAAADLAALTVKPVFVLEGGTA   85 (145)
T ss_pred             CCCCEEEEeCCChHHHHHHHHHHHcCCcCeEEecCcHH
Confidence            357899999999999999999999998 8999999864

This CD includes putative rhodanese-related sulfurtransferases which contain 4 copies of the Rhodanese Homology Domain. This CD aligns the 4th repeat which, in general, contains the putative catalytic Cys residue.

>PRK05320 rhodanese superfamily protein; Provisional

Probab=90.29  E-value=0.64  Score=35.35  Aligned_cols=37  Identities=11%  Similarity=0.032  Sum_probs=33.4

Q ss_pred             CCCCEEEEeCCchHHHHHHHHhhhCCCc-eEeeecCCC
Q 030396          137 LNPPVLIFVQSKDRAKELYGELAFDDIR-AGVIHSDLS  173 (178)
Q Consensus       137 ~~~~~lIF~~t~~~~~~l~~~L~~~g~~-~~~lh~~~~  173 (178)
                      ..+++++||.+=.+|+..+..|++.|++ +..+.||+.
T Consensus       174 kdk~IvvyC~~G~Rs~~Aa~~L~~~Gf~~V~~L~GGi~  211 (257)
T PRK05320        174 AGKTVVSFCTGGIRCEKAAIHMQEVGIDNVYQLEGGIL  211 (257)
T ss_pred             CCCeEEEECCCCHHHHHHHHHHHHcCCcceEEeccCHH
Confidence            5678999999999999999999999994 889999874

>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]

Probab=90.14  E-value=0.64  Score=41.26  Aligned_cols=44  Identities=14%  Similarity=0.091  Sum_probs=32.1

Q ss_pred             cEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHH
Q 030396           17 DILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDP   63 (178)
Q Consensus        17 ~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~   63 (178)
                      .|..+|-|-+++.+..+   +.-+.++++||+|...-.+.|...+.+
T Consensus       474 ~i~fctvgvllr~~e~g---lrg~sh~i~deiherdv~~dfll~~lr  517 (1282)
T KOG0921|consen  474 SIMFCTVGVLLRMMENG---LRGISHVIIDEIHERDVDTDFVLIVLR  517 (1282)
T ss_pred             ceeeeccchhhhhhhhc---ccccccccchhhhhhccchHHHHHHHH
Confidence            37888888888888876   345678999999998665545444443

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

Probab=90.04  E-value=0.52  Score=41.80  Aligned_cols=41  Identities=27%  Similarity=0.340  Sum_probs=31.0

Q ss_pred             hccCCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEecccccc
Q 030396           11 LSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLF   52 (178)
Q Consensus        11 ~l~~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll   52 (178)
                      .-...+||||+-.--|...+..+.. +..-+++||||||.+-
T Consensus       409 ~~a~~AdivItNHall~~~~~~~~~-~p~~~~lIiDEAH~l~  449 (820)
T PRK07246        409 EKAKTARLLITNHAYFLTRVQDDKD-FARNKVLVFDEAQKLM  449 (820)
T ss_pred             HHHHhCCEEEEchHHHHHHHhhccC-CCCCCEEEEECcchhH
Confidence            3346799999999877776644432 4567899999999995

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

Probab=89.57  E-value=0.53  Score=42.37  Aligned_cols=40  Identities=20%  Similarity=0.220  Sum_probs=29.6

Q ss_pred             cCCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEecccccc
Q 030396           13 KFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLF   52 (178)
Q Consensus        13 ~~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll   52 (178)
                      ...+||||+-.--|+..+..+.-.+..-+++||||||.+-
T Consensus       429 a~~AdivItNHalLl~dl~~~~~ilp~~~~lViDEAH~l~  468 (928)
T PRK08074        429 AKFADLVITNHALLLTDLTSEEPLLPSYEHIIIDEAHHFE  468 (928)
T ss_pred             HhcCCEEEECHHHHHHHHhhhcccCCCCCeEEEECCchHH
Confidence            4679999999987776653322233446899999999995

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=89.15  E-value=1.3  Score=36.49  Aligned_cols=75  Identities=12%  Similarity=0.174  Sum_probs=42.3

Q ss_pred             CCCcEEEeCcHHHHHHH----HcCCCC-----C-CCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCc
Q 030396           14 FSCDILISTPLRLRLAI----RRKKID-----L-SRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLP   83 (178)
Q Consensus        14 ~~~~Iii~TP~~l~~~l----~~~~~~-----~-~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~   83 (178)
                      .+..++..|...+..-+    ..+..+     + ...+.+++||+|.+.........+..++..+.....|+++.|..-|
T Consensus       159 ~~~~v~yi~~~~f~~~~~~~~~~~~~~~f~~~~~~~~dvLlIDDi~~l~~~~~~q~elf~~~n~l~~~~k~iIitsd~~p  238 (440)
T PRK14088        159 PDLRVMYITSEKFLNDLVDSMKEGKLNEFREKYRKKVDVLLIDDVQFLIGKTGVQTELFHTFNELHDSGKQIVICSDREP  238 (440)
T ss_pred             CCCeEEEEEHHHHHHHHHHHHhcccHHHHHHHHHhcCCEEEEechhhhcCcHHHHHHHHHHHHHHHHcCCeEEEECCCCH
Confidence            35678888887755433    222211     1 2578999999999865431334555566553334556555544444


Q ss_pred             HHHHH
Q 030396           84 DFVEE   88 (178)
Q Consensus        84 ~~~~~   88 (178)
                      ..+..
T Consensus       239 ~~l~~  243 (440)
T PRK14088        239 QKLSE  243 (440)
T ss_pred             HHHHH
Confidence            44443

>PF02463 SMC_N: RecF/RecN/SMC N terminal domain; InterPro: IPR003395 This domain is found at the N terminus of structural maintenance of chromosomes (SMC) proteins, which function together with other proteins in a range of chromosomal transactions, including chromosome condensation, sister-chromatid cohesion, recombination, DNA repair and epigenetic silencing of gene expression []

Probab=89.00  E-value=0.34  Score=35.55  Aligned_cols=40  Identities=18%  Similarity=0.223  Sum_probs=29.7

Q ss_pred             CCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEe
Q 030396           38 SRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFS   79 (178)
Q Consensus        38 ~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~S   79 (178)
                      ...-++|+||+|.-++.. ....+-.+++. ...+.|+++.|
T Consensus       157 ~~~p~~ilDEvd~~LD~~-~~~~l~~~l~~-~~~~~Q~ii~T  196 (220)
T PF02463_consen  157 KPSPFLILDEVDAALDEQ-NRKRLADLLKE-LSKQSQFIITT  196 (220)
T ss_dssp             S--SEEEEESTTTTS-HH-HHHHHHHHHHH-HTTTSEEEEE-
T ss_pred             cccccccccccccccccc-ccccccccccc-ccccccccccc
Confidence            345689999999999988 67777777777 66789988764

The domain is also found in RecF and RecN proteins, which are involved in DNA metabolism and recombination.; PDB: 3HTK_A 1W1W_C 2WD5_A 3L51_A 1XEW_Y 3KTA_B 3NWC_B 1XEX_A 1GXL_C 1GXK_A ....

>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional

Probab=88.95  E-value=0.66  Score=40.40  Aligned_cols=40  Identities=15%  Similarity=0.075  Sum_probs=28.2

Q ss_pred             cCCCcEEEeCcHHHHHHHH--cCCCCCC-CeeEEEEecccccc
Q 030396           13 KFSCDILISTPLRLRLAIR--RKKIDLS-RVEYLVLDEADKLF   52 (178)
Q Consensus        13 ~~~~~Iii~TP~~l~~~l~--~~~~~~~-~l~~lViDE~d~ll   52 (178)
                      ...+||||+-.--|+.-+.  .+.+-.. .-..+||||||.|-
T Consensus       217 a~~AdivVtNH~LLladl~~~~~~iLp~~~~~~lViDEAH~L~  259 (697)
T PRK11747        217 IDEADVVVANHDLVLADLELGGGVVLPDPENLLYVLDEGHHLP  259 (697)
T ss_pred             HhhCCEEEECcHHHHhhhhccCCcccCCCCCCEEEEECccchH
Confidence            3678999999987775553  2322221 35789999999995

>PRK14873 primosome assembly protein PriA; Provisional

Probab=88.86  E-value=9.1  Score=33.35  Aligned_cols=71  Identities=4%  Similarity=-0.050  Sum_probs=42.6

Q ss_pred             hccCCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccc-cccC-CChhhHHHHHhhC-CCCCceEEEEeecCcHHHH
Q 030396           11 LSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKL-FEVG-NLLKHIDPVVKAC-SNPSIVRSLFSATLPDFVE   87 (178)
Q Consensus        11 ~l~~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~l-l~~~-~~~~~i~~i~~~~-~~~~~q~i~~SAT~~~~~~   87 (178)
                      ...+.++|||||-.-+.       ..+.++..+|+||=|.- ...+ ...-+.+++.-.. ...+..+++-|||-+-+..
T Consensus       236 ~~~G~~~IViGtRSAvF-------aP~~~LgLIIvdEEhd~sykq~~~p~yhaRdvA~~Ra~~~~~~lvLgSaTPSles~  308 (665)
T PRK14873        236 VLRGQARVVVGTRSAVF-------APVEDLGLVAIWDDGDDLLAEPRAPYPHAREVALLRAHQHGCALLIGGHARTAEAQ  308 (665)
T ss_pred             HhCCCCcEEEEcceeEE-------eccCCCCEEEEEcCCchhhcCCCCCCccHHHHHHHHHHHcCCcEEEECCCCCHHHH
Confidence            33456889999864332       24678889999998764 2222 1222333332210 2367889999999885544


Q ss_pred             H
Q 030396           88 E   88 (178)
Q Consensus        88 ~   88 (178)
                      .
T Consensus       309 ~  309 (665)
T PRK14873        309 A  309 (665)
T ss_pred             H
Confidence            3

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

Probab=88.70  E-value=0.4  Score=34.95  Aligned_cols=39  Identities=15%  Similarity=0.277  Sum_probs=23.6

Q ss_pred             hccCCCcEEEeCcHHHHHHHHcCCCC-C-CCeeEEEEeccccccc
Q 030396           11 LSKFSCDILISTPLRLRLAIRRKKID-L-SRVEYLVLDEADKLFE   53 (178)
Q Consensus        11 ~l~~~~~Iii~TP~~l~~~l~~~~~~-~-~~l~~lViDE~d~ll~   53 (178)
                      .+-+.++||++|+.....    ..+. . ...+++|+|||-.+..
T Consensus       166 ~~l~~~~vi~~T~~~~~~----~~~~~~~~~~d~vIvDEAsq~~e  206 (236)
T PF13086_consen  166 FILKEADVIFTTLSSAAS----PFLSNFKEKFDVVIVDEASQITE  206 (236)
T ss_dssp             HHHHT-SEEEEETCGGG-----CCGTT-----SEEEETTGGGS-H
T ss_pred             hhcccccccccccccchh----hHhhhhcccCCEEEEeCCCCcch
Confidence            444679999999976522    2222 2 2788999999998844

>PRK00162 glpE thiosulfate sulfurtransferase; Validated

Probab=88.59  E-value=0.73  Score=29.73  Aligned_cols=37  Identities=11%  Similarity=0.188  Sum_probs=31.7

Q ss_pred             CCCCEEEEeCCchHHHHHHHHhhhCCCc-eEeeecCCC
Q 030396          137 LNPPVLIFVQSKDRAKELYGELAFDDIR-AGVIHSDLS  173 (178)
Q Consensus       137 ~~~~~lIF~~t~~~~~~l~~~L~~~g~~-~~~lh~~~~  173 (178)
                      ..++++|+|.+-..+...+..|...|+. +..+.||++
T Consensus        57 ~~~~ivv~c~~g~~s~~a~~~L~~~G~~~v~~l~GG~~   94 (108)
T PRK00162         57 FDTPVMVMCYHGNSSQGAAQYLLQQGFDVVYSIDGGFE   94 (108)
T ss_pred             CCCCEEEEeCCCCCHHHHHHHHHHCCchheEEecCCHH
Confidence            3567999999988999999999999995 788888874

>KOG0964 consensus Structural maintenance of chromosome protein 3 (sister chromatid cohesion complex Cohesin, subunit SMC3) [Cell cycle control, cell division, chromosome partitioning]

Probab=88.44  E-value=0.25  Score=43.71  Aligned_cols=50  Identities=14%  Similarity=0.237  Sum_probs=44.8

Q ss_pred             EEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcHHHHHHHHHhcc
Q 030396           42 YLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMH   95 (178)
Q Consensus        42 ~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~~~~~~~~~~~   95 (178)
                      +-+|||+|.-++.+ ++..+..+++. +..+.|  |.+.||.|++...+.+|++
T Consensus      1122 FYlfDEIDAaLDaQ-yR~aVa~lIke-lS~~aQ--FI~TTFRpEll~vAdKfyg 1171 (1200)
T KOG0964|consen 1122 FYLFDEIDAALDAQ-YRTAVADLIKE-LSDSAQ--FITTTFRPELLSVADKFYG 1171 (1200)
T ss_pred             hhhHhHHhhhccHH-HHHHHHHHHHH-Hhhccc--eEeecccHHHHHHHHhhhc
Confidence            67999999999999 99999999999 888899  5568999999999999866

>cd01522 RHOD_1 Member of the Rhodanese Homology Domain superfamily, subgroup 1

Probab=88.09  E-value=0.82  Score=30.12  Aligned_cols=38  Identities=16%  Similarity=0.170  Sum_probs=32.4

Q ss_pred             CCCCEEEEeCCchHHHHHHHHhhhCCCc-eEeeecCCCc
Q 030396          137 LNPPVLIFVQSKDRAKELYGELAFDDIR-AGVIHSDLSQ  174 (178)
Q Consensus       137 ~~~~~lIF~~t~~~~~~l~~~L~~~g~~-~~~lh~~~~~  174 (178)
                      ...++++||++-..+...+..|...|++ +..+.||++.
T Consensus        63 ~~~~ivv~C~~G~rs~~aa~~L~~~G~~~v~~l~gG~~~  101 (117)
T cd01522          63 KDRPVLLLCRSGNRSIAAAEAAAQAGFTNVYNVLEGFEG  101 (117)
T ss_pred             CCCeEEEEcCCCccHHHHHHHHHHCCCCeEEECcCceec
Confidence            4677999999989999999999999995 7778888764

This CD includes the putative rhodanese-related sulfurtransferases of several uncharacterized proteins.

>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=87.99  E-value=0.28  Score=36.32  Aligned_cols=114  Identities=12%  Similarity=0.103  Sum_probs=64.7

Q ss_pred             HhHHhccCCCcEEEeCcHHHHHHH----HcCCC-----CCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEE
Q 030396            7 RSTDLSKFSCDILISTPLRLRLAI----RRKKI-----DLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSL   77 (178)
Q Consensus         7 ~q~~~l~~~~~Iii~TP~~l~~~l----~~~~~-----~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~   77 (178)
                      .+.....++..|+..|...+.+.+    ..+.+     .+...+++++|.+|.+-......+.+..++..+.....|+++
T Consensus        56 ~~~~~~~~~~~v~y~~~~~f~~~~~~~~~~~~~~~~~~~~~~~DlL~iDDi~~l~~~~~~q~~lf~l~n~~~~~~k~li~  135 (219)
T PF00308_consen   56 NEAQKQHPGKRVVYLSAEEFIREFADALRDGEIEEFKDRLRSADLLIIDDIQFLAGKQRTQEELFHLFNRLIESGKQLIL  135 (219)
T ss_dssp             HHHHHHCTTS-EEEEEHHHHHHHHHHHHHTTSHHHHHHHHCTSSEEEEETGGGGTTHHHHHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHhccccccceeecHHHHHHHHHHHHHcccchhhhhhhhcCCEEEEecchhhcCchHHHHHHHHHHHHHHhhCCeEEE
Confidence            333333456788888887766433    33332     267889999999999855432455666666664445678777


Q ss_pred             EeecCcHHHH----HHHHHhccCcEEEEEcCCccccCCceEEEEEcCChhhHHHHHHHHHHhc
Q 030396           78 FSATLPDFVE----ELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAES  136 (178)
Q Consensus        78 ~SAT~~~~~~----~~~~~~~~~~~~v~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~  136 (178)
                      .|...|..+.    ++..++... ..+.+               ..++.+.+...+.......
T Consensus       136 ts~~~P~~l~~~~~~L~SRl~~G-l~~~l---------------~~pd~~~r~~il~~~a~~~  182 (219)
T PF00308_consen  136 TSDRPPSELSGLLPDLRSRLSWG-LVVEL---------------QPPDDEDRRRILQKKAKER  182 (219)
T ss_dssp             EESS-TTTTTTS-HHHHHHHHCS-EEEEE-------------------HHHHHHHHHHHHHHT
T ss_pred             EeCCCCccccccChhhhhhHhhc-chhhc---------------CCCCHHHHHHHHHHHHHHh
Confidence            7767665432    333343222 22222               3345566777777766654

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.

>PLN02160 thiosulfate sulfurtransferase

Probab=87.99  E-value=0.87  Score=31.01  Aligned_cols=37  Identities=16%  Similarity=0.040  Sum_probs=32.5

Q ss_pred             CCCCEEEEeCCchHHHHHHHHhhhCCC-ceEeeecCCC
Q 030396          137 LNPPVLIFVQSKDRAKELYGELAFDDI-RAGVIHSDLS  173 (178)
Q Consensus       137 ~~~~~lIF~~t~~~~~~l~~~L~~~g~-~~~~lh~~~~  173 (178)
                      ...++++||.+=.++...+..|...|+ .+..+.||+.
T Consensus        80 ~~~~IivyC~sG~RS~~Aa~~L~~~G~~~v~~l~GG~~  117 (136)
T PLN02160         80 PADDILVGCQSGARSLKATTELVAAGYKKVRNKGGGYL  117 (136)
T ss_pred             CCCcEEEECCCcHHHHHHHHHHHHcCCCCeeecCCcHH
Confidence            457899999999999999999999999 5888888875

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

Probab=87.97  E-value=2.2  Score=28.09  Aligned_cols=35  Identities=29%  Similarity=0.369  Sum_probs=20.8

Q ss_pred             eEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEe
Q 030396           41 EYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFS   79 (178)
Q Consensus        41 ~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~S   79 (178)
                      .++|+||+|.+.  .  .+.++.+.+..-....++++++
T Consensus        89 ~~lviDe~~~l~--~--~~~l~~l~~l~~~~~~~vvl~G  123 (131)
T PF13401_consen   89 VLLVIDEADHLF--S--DEFLEFLRSLLNESNIKVVLVG  123 (131)
T ss_dssp             EEEEEETTHHHH--T--HHHHHHHHHHTCSCBEEEEEEE
T ss_pred             eEEEEeChHhcC--C--HHHHHHHHHHHhCCCCeEEEEE
Confidence            799999999974  2  4444444444113445555543

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=87.96  E-value=0.92  Score=38.78  Aligned_cols=80  Identities=11%  Similarity=0.003  Sum_probs=48.6

Q ss_pred             HHhHHhccCCCcEEEeCcHHHHHHH----HcCCC-----CCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEE
Q 030396            6 VRSTDLSKFSCDILISTPLRLRLAI----RRKKI-----DLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRS   76 (178)
Q Consensus         6 ~~q~~~l~~~~~Iii~TP~~l~~~l----~~~~~-----~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i   76 (178)
                      ..+......+..++..|.+.+.+.+    ..+..     .+.++++|+||++|.+.........+..+++.+...+.+++
T Consensus       335 a~~a~~~~~g~~V~Yitaeef~~el~~al~~~~~~~f~~~y~~~DLLlIDDIq~l~gke~tqeeLF~l~N~l~e~gk~II  414 (617)
T PRK14086        335 GHYARRLYPGTRVRYVSSEEFTNEFINSIRDGKGDSFRRRYREMDILLVDDIQFLEDKESTQEEFFHTFNTLHNANKQIV  414 (617)
T ss_pred             HHHHHHhCCCCeEEEeeHHHHHHHHHHHHHhccHHHHHHHhhcCCEEEEehhccccCCHHHHHHHHHHHHHHHhcCCCEE
Confidence            3333333456788888887766333    22221     14678899999999986543245666677777444567777


Q ss_pred             EEeecCcHH
Q 030396           77 LFSATLPDF   85 (178)
Q Consensus        77 ~~SAT~~~~   85 (178)
                      +.|-.-|.+
T Consensus       415 ITSd~~P~e  423 (617)
T PRK14086        415 LSSDRPPKQ  423 (617)
T ss_pred             EecCCChHh
Confidence            655444443

>PRK06526 transposase; Provisional

Probab=87.91  E-value=1.9  Score=32.76  Aligned_cols=70  Identities=13%  Similarity=0.070  Sum_probs=38.9

Q ss_pred             cCCCcEEEeCcHHHHHHHHc----CCC-----CCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCc
Q 030396           13 KFSCDILISTPLRLRLAIRR----KKI-----DLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLP   83 (178)
Q Consensus        13 ~~~~~Iii~TP~~l~~~l~~----~~~-----~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~   83 (178)
                      ..+..+++.|...+.+.+..    +.+     .+.+.+++|+||++..-....-...+..++.. ...+..+++.|..-+
T Consensus       124 ~~g~~v~f~t~~~l~~~l~~~~~~~~~~~~l~~l~~~dlLIIDD~g~~~~~~~~~~~L~~li~~-r~~~~s~IitSn~~~  202 (254)
T PRK06526        124 QAGHRVLFATAAQWVARLAAAHHAGRLQAELVKLGRYPLLIVDEVGYIPFEPEAANLFFQLVSS-RYERASLIVTSNKPF  202 (254)
T ss_pred             HCCCchhhhhHHHHHHHHHHHHhcCcHHHHHHHhccCCEEEEcccccCCCCHHHHHHHHHHHHH-HHhcCCEEEEcCCCH
Confidence            34667777777666655431    111     25677899999999874322123455666654 222344555444433

>CHL00122 secA preprotein translocase subunit SecA; Validated

Probab=87.86  E-value=2.9  Score=37.20  Aligned_cols=51  Identities=16%  Similarity=0.148  Sum_probs=40.5

Q ss_pred             ChhhHHHHHHHHHH-h-cCCCCEEEEeCCchHHHHHHHHhhhCCCceEeeecC
Q 030396          121 SEEGKLLALRQSFA-E-SLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSD  171 (178)
Q Consensus       121 ~~~~k~~~l~~ll~-~-~~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~  171 (178)
                      ....|...+.+-+. . ...+|+||-|.|.+..+.++..|.+.|++...+++.
T Consensus       405 t~~~K~~AI~~ei~~~~~~grPVLIgT~SIe~SE~ls~~L~~~gi~h~vLNAk  457 (870)
T CHL00122        405 DELSKWRAIADECLQMHQTGRPILIGTTTIEKSELLSQLLKEYRLPHQLLNAK  457 (870)
T ss_pred             CHHHHHHHHHHHHHHHHhcCCCEEEeeCCHHHHHHHHHHHHHcCCccceeeCC
Confidence            44456666655544 2 347899999999999999999999999999888874

>PRK10287 thiosulfate:cyanide sulfurtransferase; Provisional

Probab=87.78  E-value=2.1  Score=27.71  Aligned_cols=36  Identities=11%  Similarity=0.052  Sum_probs=29.9

Q ss_pred             CCCEEEEeCCchHHHHHHHHhhhCCCceEeeecCCC
Q 030396          138 NPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLS  173 (178)
Q Consensus       138 ~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~~~  173 (178)
                      ..++++||++-.++...+..|.+.|++....-||+.
T Consensus        60 ~~~IVlyC~~G~rS~~aa~~L~~~G~~~v~~~GG~~   95 (104)
T PRK10287         60 NDTVKLYCNAGRQSGQAKEILSEMGYTHAENAGGLK   95 (104)
T ss_pred             CCeEEEEeCCChHHHHHHHHHHHcCCCeEEecCCHH
Confidence            457999999999999999999999997665567753

>PRK01415 hypothetical protein; Validated

Probab=87.61  E-value=1.1  Score=33.85  Aligned_cols=38  Identities=5%  Similarity=-0.076  Sum_probs=33.3

Q ss_pred             cCCCCEEEEeCCchHHHHHHHHhhhCCCc-eEeeecCCC
Q 030396          136 SLNPPVLIFVQSKDRAKELYGELAFDDIR-AGVIHSDLS  173 (178)
Q Consensus       136 ~~~~~~lIF~~t~~~~~~l~~~L~~~g~~-~~~lh~~~~  173 (178)
                      ...+++++||.+=.+|+..+..|.+.|++ +..+.||+.
T Consensus       169 ~k~k~Iv~yCtgGiRs~kAa~~L~~~Gf~~Vy~L~GGi~  207 (247)
T PRK01415        169 LKGKKIAMVCTGGIRCEKSTSLLKSIGYDEVYHLKGGIL  207 (247)
T ss_pred             cCCCeEEEECCCChHHHHHHHHHHHcCCCcEEEechHHH
Confidence            45678999999999999999999999995 888999853

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=87.54  E-value=1.9  Score=35.50  Aligned_cols=69  Identities=13%  Similarity=0.166  Sum_probs=39.0

Q ss_pred             CCcEEEeCcHHHHHHH----HcCCC-----CCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcH
Q 030396           15 SCDILISTPLRLRLAI----RRKKI-----DLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPD   84 (178)
Q Consensus        15 ~~~Iii~TP~~l~~~l----~~~~~-----~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~   84 (178)
                      +..++..|...+...+    ..+..     .+.+.+.+++||+|.+.......+.+..++..+.....++++ +++.++
T Consensus       178 ~~~v~yi~~~~~~~~~~~~~~~~~~~~~~~~~~~~dlLiiDDi~~l~~~~~~~~~l~~~~n~l~~~~~~iii-ts~~~p  255 (450)
T PRK00149        178 NAKVVYVTSEKFTNDFVNALRNNTMEEFKEKYRSVDVLLIDDIQFLAGKERTQEEFFHTFNALHEAGKQIVL-TSDRPP  255 (450)
T ss_pred             CCeEEEEEHHHHHHHHHHHHHcCcHHHHHHHHhcCCEEEEehhhhhcCCHHHHHHHHHHHHHHHHCCCcEEE-ECCCCH
Confidence            5667777766554322    21111     245678999999999854321234555666553334556544 555554

>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=87.32  E-value=1.4  Score=30.97  Aligned_cols=65  Identities=20%  Similarity=0.214  Sum_probs=41.0

Q ss_pred             CCCcEEEeCcHH---------HHHHHHc---CCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeec
Q 030396           14 FSCDILISTPLR---------LRLAIRR---KKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSAT   81 (178)
Q Consensus        14 ~~~~Iii~TP~~---------l~~~l~~---~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT   81 (178)
                      .-||+.+..|+.         +.++...   ... -..-+.+||||||.|-...  ...+.+++.. .+.+..+++.+..
T Consensus        66 ~~~d~~~~~~~~~~~~i~i~~ir~i~~~~~~~~~-~~~~KviiI~~ad~l~~~a--~NaLLK~LEe-pp~~~~fiL~t~~  141 (162)
T PF13177_consen   66 NHPDFIIIKPDKKKKSIKIDQIREIIEFLSLSPS-EGKYKVIIIDEADKLTEEA--QNALLKTLEE-PPENTYFILITNN  141 (162)
T ss_dssp             -CTTEEEEETTTSSSSBSHHHHHHHHHHCTSS-T-TSSSEEEEEETGGGS-HHH--HHHHHHHHHS-TTTTEEEEEEES-
T ss_pred             cCcceEEEecccccchhhHHHHHHHHHHHHHHHh-cCCceEEEeehHhhhhHHH--HHHHHHHhcC-CCCCEEEEEEECC
Confidence            468888877763         2222222   222 3578999999999997665  7777777887 6666666665543


Q ss_pred             C
Q 030396           82 L   82 (178)
Q Consensus        82 ~   82 (178)
                      .
T Consensus       142 ~  142 (162)
T PF13177_consen  142 P  142 (162)
T ss_dssp             G
T ss_pred             h
Confidence            3

...

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

Probab=87.18  E-value=1.6  Score=34.66  Aligned_cols=120  Identities=13%  Similarity=0.088  Sum_probs=63.8

Q ss_pred             CCCeeEEEEeccccccccC------CChhhHHHHHhhCCC------CCceEEEEeecCcHH-HHHHHHHhccCcEEEEEc
Q 030396           37 LSRVEYLVLDEADKLFEVG------NLLKHIDPVVKACSN------PSIVRSLFSATLPDF-VEELARSIMHDAVRVIVG  103 (178)
Q Consensus        37 ~~~l~~lViDE~d~ll~~~------~~~~~i~~i~~~~~~------~~~q~i~~SAT~~~~-~~~~~~~~~~~~~~v~~~  103 (178)
                      ....+++|+||||.|...+      ...+++..+++. ..      -..|++--+...... +.+....+-...      
T Consensus        81 ~~~~DviivDEAqrl~~~~~~~~~~~~~~~L~~i~~~-~kv~v~f~D~~Q~i~~~e~~~~~~l~~~~~~~~~~~------  153 (352)
T PF09848_consen   81 KNKYDVIIVDEAQRLRTKGDQYNNFSEPNQLDEIIKR-AKVVVFFYDENQSIRPSEIGTLENLEEIAENLGIEV------  153 (352)
T ss_pred             CCcCCEEEEehhHhhhhccccccccccHHHHHHHHhc-CCEEEEEEccccEeecccCCCHHHHHHHHHhcCCcc------
Confidence            4678899999999998832      235777787776 22      123444433333322 333333321111      


Q ss_pred             CCccccC-CceEEEEEcCChhhHHHHHHHHHHhcCC---------CCEEEEeCCchHHHHHHHHhhhCCCceEee
Q 030396          104 RKNTASE-SIKQKLVFAGSEEGKLLALRQSFAESLN---------PPVLIFVQSKDRAKELYGELAFDDIRAGVI  168 (178)
Q Consensus       104 ~~~~~~~-~i~~~~~~~~~~~~k~~~l~~ll~~~~~---------~~~lIF~~t~~~~~~l~~~L~~~g~~~~~l  168 (178)
                          ... .+..++ .+.....-...+..++.....         .--+-++.+.+.++.......+.+..+..+
T Consensus       154 ----~~~~~L~~q~-R~~~~~~~~~wI~~ll~~~~~~~~~~~~~~~yd~~~f~~~~~~~~~i~~k~~~~~~~rlv  223 (352)
T PF09848_consen  154 ----RHFFELKTQF-RCHGSKEYIDWIDNLLDNKNISPKPFNPDENYDFRVFDSPEEMKEAIKEKNKEGGLSRLV  223 (352)
T ss_pred             ----ccCcCcCcce-ecCCCHHHHHHHHHHHhccccCccccccCCceeEEEECCHHHHHHHHHHHhcccCCceEE
Confidence                111 344444 554455566777777753221         123556667777776666665554444443

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

>cd01445 TST_Repeats Thiosulfate sulfurtransferases (TST) contain 2 copies of the Rhodanese Homology Domain

Probab=86.58  E-value=1.9  Score=29.41  Aligned_cols=49  Identities=6%  Similarity=-0.024  Sum_probs=32.8

Q ss_pred             HHHHHHHHHHhcCCCCEEEEeCC---chHHHHHHHHhhhCCC-ceEeeecCCC
Q 030396          125 KLLALRQSFAESLNPPVLIFVQS---KDRAKELYGELAFDDI-RAGVIHSDLS  173 (178)
Q Consensus       125 k~~~l~~ll~~~~~~~~lIF~~t---~~~~~~l~~~L~~~g~-~~~~lh~~~~  173 (178)
                      .+..++.-+.-....++||||++   -..|-.+.-.|...|+ ++..+.|+++
T Consensus        82 ~~~~~~~~~GI~~~~~vVvY~~~~~~g~~A~r~~~~l~~~G~~~v~ildGG~~  134 (138)
T cd01445          82 EFAAMFEAKGIDLDKHLIATDGDDLGGFTACHIALAARLCGHPDVAILDGGFF  134 (138)
T ss_pred             HHHHHHHHcCCCCCCeEEEECCCCCcchHHHHHHHHHHHcCCCCeEEeCCCHH
Confidence            33333333333346689999986   4556677777888898 4889999875

Only the second repeat contains the catalytically active Cys residue. The role of the 1st repeat is uncertain, but believed to be involved in protein interaction. This CD aligns the 1st and 2nd repeats.

>KOG0989 consensus Replication factor C, subunit RFC4 [Replication, recombination and repair]

Probab=86.44  E-value=1.4  Score=34.43  Aligned_cols=54  Identities=11%  Similarity=0.089  Sum_probs=37.2

Q ss_pred             CCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecC---cHHHHHHHHHh
Q 030396           37 LSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATL---PDFVEELARSI   93 (178)
Q Consensus        37 ~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~---~~~~~~~~~~~   93 (178)
                      ....+.+|+||||.|-.+.  ...+++.+.. .+....+++...-+   ++.+...+.+|
T Consensus       127 ~~~fKiiIlDEcdsmtsda--q~aLrr~mE~-~s~~trFiLIcnylsrii~pi~SRC~Kf  183 (346)
T KOG0989|consen  127 CPPFKIIILDECDSMTSDA--QAALRRTMED-FSRTTRFILICNYLSRIIRPLVSRCQKF  183 (346)
T ss_pred             CCcceEEEEechhhhhHHH--HHHHHHHHhc-cccceEEEEEcCChhhCChHHHhhHHHh
Confidence            3455999999999997766  6667777777 66677777665543   34555555554

>TIGR03865 PQQ_CXXCW PQQ-dependent catabolism-associated CXXCW motif protein

Probab=86.08  E-value=1.2  Score=31.41  Aligned_cols=38  Identities=3%  Similarity=-0.083  Sum_probs=30.6

Q ss_pred             cCCCCEEEEeCCch-HHHHHHHHhhhCCC-ceEeeecCCC
Q 030396          136 SLNPPVLIFVQSKD-RAKELYGELAFDDI-RAGVIHSDLS  173 (178)
Q Consensus       136 ~~~~~~lIF~~t~~-~~~~l~~~L~~~g~-~~~~lh~~~~  173 (178)
                      ...+++|+||++-. .+...+..|...|+ ++..+.||+.
T Consensus       114 ~~d~~IVvYC~~G~~~S~~aa~~L~~~G~~~V~~l~GG~~  153 (162)
T TIGR03865       114 DKDRPLVFYCLADCWMSWNAAKRALAYGYSNVYWYPDGTD  153 (162)
T ss_pred             CCCCEEEEEECCCCHHHHHHHHHHHhcCCcceEEecCCHH
Confidence            35678999999854 67778888899999 4888999875

Members of this protein family have a CXXXCW motif, consistent with a possible role in redox cofactor binding. This protein family shows strong relationships by phylogenetic profiling and conserved gene neighborhoods with a transport system for alcohols metabolized by PQQ-dependent enzymes.

>PF15586 Imm47: Immunity protein 47

Probab=85.89  E-value=1  Score=29.90  Aligned_cols=49  Identities=20%  Similarity=0.295  Sum_probs=32.9

Q ss_pred             CCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhh
Q 030396           14 FSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKA   67 (178)
Q Consensus        14 ~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~   67 (178)
                      ...++.|+||+.|.....+..+-..+ .++|++|.|.=    .-...+++++..
T Consensus        43 d~F~v~VcTP~wL~~~~~~~~~~~gr-~~LIv~~yd~~----~I~~~i~~~i~~   91 (116)
T PF15586_consen   43 DYFQVFVCTPKWLSKNCWKPGILWGR-HMLIVEEYDYD----EIKKTIERIIES   91 (116)
T ss_pred             ceEEEEEEcHHHHHHhhcCCcceecc-ceEEEecCCHH----HHHHHHHHHHHH
Confidence            34789999999999988775533333 68899887632    134446666665

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=85.86  E-value=1.2  Score=36.00  Aligned_cols=70  Identities=11%  Similarity=0.148  Sum_probs=38.8

Q ss_pred             CCcEEEeCcHHHHHHH----HcCCC-----CCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcHH
Q 030396           15 SCDILISTPLRLRLAI----RRKKI-----DLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDF   85 (178)
Q Consensus        15 ~~~Iii~TP~~l~~~l----~~~~~-----~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~   85 (178)
                      +..++..|...+...+    ..+..     .+...+++++||+|.+.........+..++..+...+.+++ ++++.++.
T Consensus       166 ~~~v~yi~~~~~~~~~~~~~~~~~~~~~~~~~~~~dlLiiDDi~~l~~~~~~~~~l~~~~n~~~~~~~~ii-its~~~p~  244 (405)
T TIGR00362       166 NAKVVYVSSEKFTNDFVNALRNNKMEEFKEKYRSVDLLLIDDIQFLAGKERTQEEFFHTFNALHENGKQIV-LTSDRPPK  244 (405)
T ss_pred             CCcEEEEEHHHHHHHHHHHHHcCCHHHHHHHHHhCCEEEEehhhhhcCCHHHHHHHHHHHHHHHHCCCCEE-EecCCCHH
Confidence            5667777766544322    11111     14567899999999985542123445555555333456655 45555543

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).

>PRK12902 secA preprotein translocase subunit SecA; Reviewed

Probab=85.85  E-value=4.2  Score=36.40  Aligned_cols=51  Identities=24%  Similarity=0.254  Sum_probs=41.5

Q ss_pred             ChhhHHHHHHHHHHh--cCCCCEEEEeCCchHHHHHHHHhhhCCCceEeeecC
Q 030396          121 SEEGKLLALRQSFAE--SLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSD  171 (178)
Q Consensus       121 ~~~~k~~~l~~ll~~--~~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~  171 (178)
                      ....|...+.+-+.+  ...+|+||-|.|.+.++.++..|...|++...+++.
T Consensus       420 t~~~K~~Ai~~ei~~~~~~GrPVLIgT~SVe~SE~ls~~L~~~gi~h~vLNAk  472 (939)
T PRK12902        420 TEIAKWRAVANETAEMHKQGRPVLVGTTSVEKSELLSALLQEQGIPHNLLNAK  472 (939)
T ss_pred             CHHHHHHHHHHHHHHHHhCCCCEEEeeCCHHHHHHHHHHHHHcCCchheeeCC
Confidence            445677777665553  247899999999999999999999999998888874

>KOG0389 consensus SNF2 family DNA-dependent ATPase [Chromatin structure and dynamics]

Probab=85.85  E-value=3.3  Score=36.36  Aligned_cols=74  Identities=20%  Similarity=0.243  Sum_probs=42.4

Q ss_pred             cCCCcEEEeCcHHHHHHH-HcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeec-CcHHHHHHH
Q 030396           13 KFSCDILISTPLRLRLAI-RRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSAT-LPDFVEELA   90 (178)
Q Consensus        13 ~~~~~Iii~TP~~l~~~l-~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT-~~~~~~~~~   90 (178)
                      +...+|+++|=.....-- .++.+.-.++.++|+||.|.|=+.+  .+-+..++.  .+.+.+ ++++.| +-+.+.+++
T Consensus       497 ~~~ydVllTTY~la~~~kdDRsflk~~~~n~viyDEgHmLKN~~--SeRy~~LM~--I~An~R-lLLTGTPLQNNL~ELi  571 (941)
T KOG0389|consen  497 KDDYDVLLTTYNLAASSKDDRSFLKNQKFNYVIYDEGHMLKNRT--SERYKHLMS--INANFR-LLLTGTPLQNNLKELI  571 (941)
T ss_pred             CCCccEEEEEeecccCChHHHHHHHhccccEEEecchhhhhccc--hHHHHHhcc--ccccce-EEeeCCcccccHHHHH
Confidence            347899999864333110 1111223456699999999996555  555666666  344444 555555 444444443


Q ss_pred             H
Q 030396           91 R   91 (178)
Q Consensus        91 ~   91 (178)
                      .
T Consensus       572 S  572 (941)
T KOG0389|consen  572 S  572 (941)
T ss_pred             H
Confidence            3

>PF00581 Rhodanese: Rhodanese-like domain This Prosite entry represents a subset of this family

Probab=85.78  E-value=2.3  Score=27.10  Aligned_cols=36  Identities=8%  Similarity=0.121  Sum_probs=28.7

Q ss_pred             CCCEEEEeCCchHHHHHHHH-----hhhCCC-ceEeeecCCC
Q 030396          138 NPPVLIFVQSKDRAKELYGE-----LAFDDI-RAGVIHSDLS  173 (178)
Q Consensus       138 ~~~~lIF~~t~~~~~~l~~~-----L~~~g~-~~~~lh~~~~  173 (178)
                      ...+|+||++-.++...+..     |...|+ ++..+.||+.
T Consensus        67 ~~~iv~yc~~~~~~~~~~~~~~~~~l~~~g~~~v~~l~GG~~  108 (113)
T PF00581_consen   67 DKDIVFYCSSGWRSGSAAAARVAWILKKLGFKNVYILDGGFE  108 (113)
T ss_dssp             TSEEEEEESSSCHHHHHHHHHHHHHHHHTTTSSEEEETTHHH
T ss_pred             cccceeeeecccccchhHHHHHHHHHHHcCCCCEEEecChHH
Confidence            44688899777777777776     888899 9999999864

; InterPro: IPR001763 Rhodanese, a sulphurtransferase involved in cyanide detoxification (see IPR001307 from INTERPRO) shares evolutionary relationship with a large family of proteins [], including Cdc25 phosphatase catalytic domain. non-catalytic domains of eukaryotic dual-specificity MAPK-phosphatases. non-catalytic domains of yeast PTP-type MAPK-phosphatases. non-catalytic domains of yeast Ubp4, Ubp5, Ubp7. non-catalytic domains of mammalian Ubp-Y. Drosophila heat shock protein HSP-67BB. several bacterial cold-shock and phage shock proteins. plant senescence associated proteins. catalytic and non-catalytic domains of rhodanese (see IPR001307 from INTERPRO). Rhodanese has an internal duplication. This domain is found as a single copy in other proteins, including phosphatases and ubiquitin C-terminal hydrolases [].; PDB: 2J6P_D 2FSX_A 1UAR_A 1OKG_A 1GMX_A 1GN0_A 3NTD_B 3NTA_B 3NT6_A 1C25_A ....

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

Probab=85.71  E-value=7.5  Score=33.59  Aligned_cols=47  Identities=17%  Similarity=0.092  Sum_probs=33.5

Q ss_pred             HHHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhhhCCC-ceEeeecCC
Q 030396          125 KLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDI-RAGVIHSDL  172 (178)
Q Consensus       125 k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~~~g~-~~~~lh~~~  172 (178)
                      -...+..+++.. ++.++||+.|-+..+.+++.+..... .....+|.-
T Consensus       467 ~~~~i~~~~~~~-~~~~lvlF~Sy~~l~~~~~~~~~~~~~~~v~~q~~~  514 (654)
T COG1199         467 LAAYLREILKAS-PGGVLVLFPSYEYLKRVAERLKDERSTLPVLTQGED  514 (654)
T ss_pred             HHHHHHHHHhhc-CCCEEEEeccHHHHHHHHHHHhhcCccceeeecCCC
Confidence            344555555555 55999999999999999999987665 344445443

>PRK13103 secA preprotein translocase subunit SecA; Reviewed

Probab=85.64  E-value=0.75  Score=40.91  Aligned_cols=49  Identities=22%  Similarity=0.323  Sum_probs=38.5

Q ss_pred             hhHHHHHHHHHHh--cCCCCEEEEeCCchHHHHHHHHhhhCCCceEeeecC
Q 030396          123 EGKLLALRQSFAE--SLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSD  171 (178)
Q Consensus       123 ~~k~~~l~~ll~~--~~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~  171 (178)
                      ..|...+.+-+..  ...+|+||-|.|.+.++.++..|...|++.-.+++.
T Consensus       432 ~eK~~Ai~~ei~~~~~~GrPVLVGT~SVe~SE~ls~~L~~~gi~h~VLNAk  482 (913)
T PRK13103        432 EEKYAAIITDIKECMALGRPVLVGTATIETSEHMSNLLKKEGIEHKVLNAK  482 (913)
T ss_pred             HHHHHHHHHHHHHHHhCCCCEEEEeCCHHHHHHHHHHHHHcCCcHHHhccc
Confidence            3566666666653  247899999999999999999999999877666553

>TIGR02981 phageshock_pspE phage shock operon rhodanese PspE

Probab=85.55  E-value=3.5  Score=26.47  Aligned_cols=36  Identities=8%  Similarity=-0.011  Sum_probs=29.0

Q ss_pred             CCCEEEEeCCchHHHHHHHHhhhCCCceEeeecCCC
Q 030396          138 NPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLS  173 (178)
Q Consensus       138 ~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~~~  173 (178)
                      ..+++++|++-.++...+..|.+.|+.....-||+.
T Consensus        58 ~~~vvlyC~~G~rS~~aa~~L~~~G~~~v~~~GG~~   93 (101)
T TIGR02981        58 NDTVKLYCNAGRQSGMAKDILLDMGYTHAENAGGIK   93 (101)
T ss_pred             CCeEEEEeCCCHHHHHHHHHHHHcCCCeEEecCCHH
Confidence            457889999999999999999999996554447653

Members of this very narrowly defined protein family are proteins active as rhodanese (EC 2.8.1.1) and found in the extended variants of the phage shock protein (psp operon) in Escherichia coli and a few closely related species. Note that the designation phage shock protein PspE has been applied, incorrectly, in many instances where the genome lacks the phage shock regulon entirely.

>PRK08084 DNA replication initiation factor; Provisional

Probab=85.25  E-value=0.87  Score=33.99  Aligned_cols=47  Identities=9%  Similarity=0.019  Sum_probs=27.9

Q ss_pred             CCeeEEEEeccccccccCCChhhHHHHHhhCCCCC-ceEEEEeecCcHH
Q 030396           38 SRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPS-IVRSLFSATLPDF   85 (178)
Q Consensus        38 ~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~-~q~i~~SAT~~~~   85 (178)
                      .+.+++++||+|.+-........+..++..+.... .+ +++|++.|+.
T Consensus        96 ~~~dlliiDdi~~~~~~~~~~~~lf~l~n~~~e~g~~~-li~ts~~~p~  143 (235)
T PRK08084         96 EQLSLVCIDNIECIAGDELWEMAIFDLYNRILESGRTR-LLITGDRPPR  143 (235)
T ss_pred             hhCCEEEEeChhhhcCCHHHHHHHHHHHHHHHHcCCCe-EEEeCCCChH
Confidence            34578999999998543324555666666533223 35 4556666553

>cd01530 Cdc25 Cdc25 phosphatases are members of the Rhodanese Homology Domain superfamily

Probab=85.16  E-value=1.1  Score=29.74  Aligned_cols=38  Identities=8%  Similarity=0.059  Sum_probs=30.7

Q ss_pred             CCCCEEEEeC-CchHHHHHHHHhhhC------------CC-ceEeeecCCCc
Q 030396          137 LNPPVLIFVQ-SKDRAKELYGELAFD------------DI-RAGVIHSDLSQ  174 (178)
Q Consensus       137 ~~~~~lIF~~-t~~~~~~l~~~L~~~------------g~-~~~~lh~~~~~  174 (178)
                      ...+++++|+ +-.++...+..|+..            |+ ++..+.||+..
T Consensus        67 ~~~~vv~yC~~sg~rs~~aa~~L~~~~~~~~~~~~~~~g~~~v~~L~GG~~~  118 (121)
T cd01530          67 KRRVLIFHCEFSSKRGPRMARHLRNLDRELNSNRYPLLYYPEIYILEGGYKN  118 (121)
T ss_pred             CCCEEEEECCCccccHHHHHHHHHHHhhhhccccCCCCCCCeEEEEcChhHh
Confidence            4567999996 888888888888874            77 79999999753

They activate the cell division kinases throughout the cell cycle progression. Cdc25 phosphatases dephosphorylate phosphotyrosine and phosphothreonine residues, in order to activate their Cdk/cyclin substrates. Cdc25A phosphatase functions to regulate S phase entry and Cdc25B is required for G2/M phase transition of the cell cycle. The Cdc25 domain binds oxyanions at the catalytic site and has the signature motif (H/YCxxxxxR).

>PRK00142 putative rhodanese-related sulfurtransferase; Provisional

Probab=84.96  E-value=1.6  Score=34.20  Aligned_cols=38  Identities=5%  Similarity=0.104  Sum_probs=33.4

Q ss_pred             cCCCCEEEEeCCchHHHHHHHHhhhCCC-ceEeeecCCC
Q 030396          136 SLNPPVLIFVQSKDRAKELYGELAFDDI-RAGVIHSDLS  173 (178)
Q Consensus       136 ~~~~~~lIF~~t~~~~~~l~~~L~~~g~-~~~~lh~~~~  173 (178)
                      .+.+++++||.+=.+++..+.+|.+.|+ ++..+.||+.
T Consensus       169 ~kdk~IvvyC~~G~Rs~~aa~~L~~~Gf~~V~~L~GGi~  207 (314)
T PRK00142        169 LKDKKVVMYCTGGIRCEKASAWMKHEGFKEVYQLEGGII  207 (314)
T ss_pred             CCcCeEEEECCCCcHHHHHHHHHHHcCCCcEEEecchHH
Confidence            3567899999999999999999999999 5889999864

>PRK06835 DNA replication protein DnaC; Validated

Probab=84.64  E-value=4.5  Score=31.96  Aligned_cols=73  Identities=12%  Similarity=0.002  Sum_probs=46.3

Q ss_pred             hccCCCcEEEeCcHHHHHHHHcC----C-------CCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEe
Q 030396           11 LSKFSCDILISTPLRLRLAIRRK----K-------IDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFS   79 (178)
Q Consensus        11 ~l~~~~~Iii~TP~~l~~~l~~~----~-------~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~S   79 (178)
                      ++..+..|+..|...+.+.+...    .       -.+.+++++|||+.............+..|+.........+ ++|
T Consensus       207 l~~~g~~V~y~t~~~l~~~l~~~~~~~~~~~~~~~~~l~~~DLLIIDDlG~e~~t~~~~~~Lf~iin~R~~~~k~t-IiT  285 (329)
T PRK06835        207 LLDRGKSVIYRTADELIEILREIRFNNDKELEEVYDLLINCDLLIIDDLGTEKITEFSKSELFNLINKRLLRQKKM-IIS  285 (329)
T ss_pred             HHHCCCeEEEEEHHHHHHHHHHHHhccchhHHHHHHHhccCCEEEEeccCCCCCCHHHHHHHHHHHHHHHHCCCCE-EEE
Confidence            34567889888888887766331    1       12568899999999887443323556667777633334554 555


Q ss_pred             ecCcH
Q 030396           80 ATLPD   84 (178)
Q Consensus        80 AT~~~   84 (178)
                      +.+++
T Consensus       286 SNl~~  290 (329)
T PRK06835        286 TNLSL  290 (329)
T ss_pred             CCCCH
Confidence            55554

>KOG2170 consensus ATPase of the AAA+ superfamily [General function prediction only]

Probab=84.63  E-value=1.5  Score=34.10  Aligned_cols=56  Identities=20%  Similarity=0.243  Sum_probs=37.7

Q ss_pred             CCCeeEEEEeccccccccCCChhhHHHHHhhCCC-------CCceEEEEeecCcHHHHHHHHHhcc
Q 030396           37 LSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSN-------PSIVRSLFSATLPDFVEELARSIMH   95 (178)
Q Consensus        37 ~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~-------~~~q~i~~SAT~~~~~~~~~~~~~~   95 (178)
                      -..-+.|||||+|+|-. | ..+.+.-.+++ .+       .+.-+|++|-+-...+...+-.+..
T Consensus       176 ~C~rslFIFDE~DKmp~-g-Lld~lkpfLdy-yp~v~gv~frkaIFIfLSN~gg~eI~~~aL~~~~  238 (344)
T KOG2170|consen  176 ACQRSLFIFDEVDKLPP-G-LLDVLKPFLDY-YPQVSGVDFRKAIFIFLSNAGGSEIARIALENAR  238 (344)
T ss_pred             hcCCceEEechhhhcCH-h-HHHHHhhhhcc-ccccccccccceEEEEEcCCcchHHHHHHHHHHH
Confidence            34457999999999933 4 56666666665 33       2456788898888777665555433

>PF10100 DUF2338: Uncharacterized protein conserved in bacteria (DUF2338); InterPro: IPR016935 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function

Probab=84.63  E-value=4.7  Score=32.72  Aligned_cols=58  Identities=17%  Similarity=0.056  Sum_probs=39.4

Q ss_pred             EEeccccccccCCChhhHHHHHhhC----CCCCceEEEEeecCcHH--HHHHHHHhccCcEEEEE
Q 030396           44 VLDEADKLFEVGNLLKHIDPVVKAC----SNPSIVRSLFSATLPDF--VEELARSIMHDAVRVIV  102 (178)
Q Consensus        44 ViDE~d~ll~~~~~~~~i~~i~~~~----~~~~~q~i~~SAT~~~~--~~~~~~~~~~~~~~v~~  102 (178)
                      |.+|.|.++-.- ..+.+..+++.+    +..-.+++++|.|+...  ++.++.....++..+..
T Consensus        80 i~g~WdtlILav-taDAY~~VL~ql~~~~L~~vk~iVLvSPtfGS~~lv~~~l~~~~~~~EVISF  143 (429)
T PF10100_consen   80 IEGEWDTLILAV-TADAYLDVLQQLPWEVLKRVKSIVLVSPTFGSHLLVKGFLNDLGPDAEVISF  143 (429)
T ss_pred             hcccccEEEEEe-chHHHHHHHHhcCHHHHhhCCEEEEECcccchHHHHHHHHHhcCCCceEEEe
Confidence            678888877655 567777777773    33457899999999865  44555555555555544

>KOG2228 consensus Origin recognition complex, subunit 4 [Replication, recombination and repair]

Probab=84.57  E-value=7.3  Score=31.08  Aligned_cols=90  Identities=14%  Similarity=0.034  Sum_probs=49.3

Q ss_pred             hHhHHhHHhccCCCcEEEeCc----HHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEE
Q 030396            3 KELVRSTDLSKFSCDILISTP----LRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLF   78 (178)
Q Consensus         3 ~~~~~q~~~l~~~~~Iii~TP----~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~   78 (178)
                      +.+.+|++.-.+.-.+.+|.-    ..++..++.+.-..+.-=+||+||+|...... -.-.+...++.-......+.++
T Consensus        97 ~~I~rql~~e~~~~~k~~gsfte~l~~lL~~L~~~~~~t~~~ViFIldEfDlf~~h~-rQtllYnlfDisqs~r~Picii  175 (408)
T KOG2228|consen   97 KGITRQLALELNRIVKSFGSFTENLSKLLEALKKGDETTSGKVIFILDEFDLFAPHS-RQTLLYNLFDISQSARAPICII  175 (408)
T ss_pred             HHHHHHHHHHHhhhheeecccchhHHHHHHHHhcCCCCCCceEEEEeehhhccccch-hhHHHHHHHHHHhhcCCCeEEE
Confidence            456677776554445555532    23445556666566666789999999987665 4444444444322233444444


Q ss_pred             eecCcHHHHHHHHHh
Q 030396           79 SATLPDFVEELARSI   93 (178)
Q Consensus        79 SAT~~~~~~~~~~~~   93 (178)
                      .-|-.-++.+.+++-
T Consensus       176 g~Ttrld~lE~LEKR  190 (408)
T KOG2228|consen  176 GVTTRLDILELLEKR  190 (408)
T ss_pred             EeeccccHHHHHHHH
Confidence            444443344444443

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

Probab=84.30  E-value=1  Score=34.97  Aligned_cols=41  Identities=15%  Similarity=0.139  Sum_probs=27.0

Q ss_pred             CCCeeEEEEeccccccccC-CChhhHHHHHhhCCCCCceEEEE
Q 030396           37 LSRVEYLVLDEADKLFEVG-NLLKHIDPVVKACSNPSIVRSLF   78 (178)
Q Consensus        37 ~~~l~~lViDE~d~ll~~~-~~~~~i~~i~~~~~~~~~q~i~~   78 (178)
                      --.++++||||+|.++... .-...+...+++ +.+..++-++
T Consensus       143 ~~~vrmLIIDE~H~lLaGs~~~qr~~Ln~LK~-L~NeL~ipiV  184 (302)
T PF05621_consen  143 RLGVRMLIIDEFHNLLAGSYRKQREFLNALKF-LGNELQIPIV  184 (302)
T ss_pred             HcCCcEEEeechHHHhcccHHHHHHHHHHHHH-HhhccCCCeE
Confidence            4678999999999988754 234445556666 5555554333

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

>TIGR00604 rad3 DNA repair helicase (rad3)

Probab=84.15  E-value=10  Score=33.17  Aligned_cols=26  Identities=8%  Similarity=0.109  Sum_probs=22.1

Q ss_pred             CCCCEEEEeCCchHHHHHHHHhhhCC
Q 030396          137 LNPPVLIFVQSKDRAKELYGELAFDD  162 (178)
Q Consensus       137 ~~~~~lIF~~t~~~~~~l~~~L~~~g  162 (178)
                      .++.++||++|-+.-+.+++.+.+.|
T Consensus       521 ~pgg~lvfFpSy~~l~~v~~~~~~~~  546 (705)
T TIGR00604       521 IPDGIVVFFPSYSYLENIVSTWKEMG  546 (705)
T ss_pred             CCCcEEEEccCHHHHHHHHHHHHhcC
Confidence            36889999999999999998887654

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).

>KOG0354 consensus DEAD-box like helicase [General function prediction only]

Probab=83.93  E-value=2.3  Score=37.05  Aligned_cols=50  Identities=24%  Similarity=0.280  Sum_probs=38.1

Q ss_pred             hhhHHHHHHHHHH----hcCCCCEEEEeCCchHHHHHHHHhh---hCCCceEeeecC
Q 030396          122 EEGKLLALRQSFA----ESLNPPVLIFVQSKDRAKELYGELA---FDDIRAGVIHSD  171 (178)
Q Consensus       122 ~~~k~~~l~~ll~----~~~~~~~lIF~~t~~~~~~l~~~L~---~~g~~~~~lh~~  171 (178)
                      .+.|...+.+.+.    ..+..++||||.++++|..+..+|.   ..|+++..+.|.
T Consensus       393 ~npkle~l~~~l~e~f~~~~dsR~IIFve~R~sa~~l~~~l~~~~~~~ir~~~fiGq  449 (746)
T KOG0354|consen  393 ENPKLEKLVEILVEQFEQNPDSRTIIFVETRESALALKKWLLQLHELGIKAEIFIGQ  449 (746)
T ss_pred             cChhHHHHHHHHHHHhhcCCCccEEEEEehHHHHHHHHHHHHhhhhcccccceeeec
Confidence            3467777777664    3456789999999999999999987   346677777763

>PRK12899 secA preprotein translocase subunit SecA; Reviewed

Probab=83.46  E-value=7.1  Score=35.26  Aligned_cols=47  Identities=19%  Similarity=0.390  Sum_probs=38.1

Q ss_pred             hHHhHHhccCCCcEEEeCcHHH-HHHHHcCCCCCC-------CeeEEEEeccccccc
Q 030396            5 LVRSTDLSKFSCDILISTPLRL-RLAIRRKKIDLS-------RVEYLVLDEADKLFE   53 (178)
Q Consensus         5 ~~~q~~~l~~~~~Iii~TP~~l-~~~l~~~~~~~~-------~l~~lViDE~d~ll~   53 (178)
                      ..+|.+..  +|+|+|||||+| .++++.+.+.++       .++++|+||||.|+-
T Consensus       175 ~~eq~~~y--~~DIVygTPgRLgfDyLrd~~~~~~~~~~vqr~~~~~IIDEADsmLi  229 (970)
T PRK12899        175 LEKRKEIY--QCDVVYGTASEFGFDYLRDNSIATRKEEQVGRGFYFAIIDEVDSILI  229 (970)
T ss_pred             HHHHHHHc--CCCEEEECCChhHHHHhhCCCCCcCHHHhhcccccEEEEechhhhhh
Confidence            34455554  599999999999 999999877766       458999999999863

>PRK08181 transposase; Validated

Probab=83.16  E-value=5.2  Score=30.68  Aligned_cols=71  Identities=14%  Similarity=0.130  Sum_probs=41.5

Q ss_pred             cCCCcEEEeCcHHHHHHHHc----CCC-----CCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCc
Q 030396           13 KFSCDILISTPLRLRLAIRR----KKI-----DLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLP   83 (178)
Q Consensus        13 ~~~~~Iii~TP~~l~~~l~~----~~~-----~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~   83 (178)
                      ..+..+++.|...|.+.+..    +..     .+.+.+.+|+||++..-....-...+..++.... .+. -+++++.++
T Consensus       132 ~~g~~v~f~~~~~L~~~l~~a~~~~~~~~~l~~l~~~dLLIIDDlg~~~~~~~~~~~Lf~lin~R~-~~~-s~IiTSN~~  209 (269)
T PRK08181        132 ENGWRVLFTRTTDLVQKLQVARRELQLESAIAKLDKFDLLILDDLAYVTKDQAETSVLFELISARY-ERR-SILITANQP  209 (269)
T ss_pred             HcCCceeeeeHHHHHHHHHHHHhCCcHHHHHHHHhcCCEEEEeccccccCCHHHHHHHHHHHHHHH-hCC-CEEEEcCCC
Confidence            35667777666666655432    111     1567899999999987443313445666666522 333 456666666


Q ss_pred             HH
Q 030396           84 DF   85 (178)
Q Consensus        84 ~~   85 (178)
                      +.
T Consensus       210 ~~  211 (269)
T PRK08181        210 FG  211 (269)
T ss_pred             HH
Confidence            43

>COG0607 PspE Rhodanese-related sulfurtransferase [Inorganic ion transport and metabolism]

Probab=83.11  E-value=1.4  Score=28.10  Aligned_cols=38  Identities=11%  Similarity=0.234  Sum_probs=32.5

Q ss_pred             cCCCCEEEEeCCchHHHHHHHHhhhCCCceE-eeecCCC
Q 030396          136 SLNPPVLIFVQSKDRAKELYGELAFDDIRAG-VIHSDLS  173 (178)
Q Consensus       136 ~~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~-~lh~~~~  173 (178)
                      ...++++|+|.+=.+....+..|.+.|+... .+.||+.
T Consensus        59 ~~~~~ivv~C~~G~rS~~aa~~L~~~G~~~~~~l~gG~~   97 (110)
T COG0607          59 PDDDPIVVYCASGVRSAAAAAALKLAGFTNVYNLDGGID   97 (110)
T ss_pred             CCCCeEEEEeCCCCChHHHHHHHHHcCCccccccCCcHH
Confidence            3467899999999999999999999999887 7777764

>COG1054 Predicted sulfurtransferase [General function prediction only]

Probab=82.59  E-value=3.7  Score=31.80  Aligned_cols=82  Identities=7%  Similarity=0.082  Sum_probs=52.1

Q ss_pred             HHhccCcEEEEEcCCccccCCceEEEEEcCChhhHHHHHHH----HHHhcCCCCEEEEeCCchHHHHHHHHhhhCCC-ce
Q 030396           91 RSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQ----SFAESLNPPVLIFVQSKDRAKELYGELAFDDI-RA  165 (178)
Q Consensus        91 ~~~~~~~~~v~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~----ll~~~~~~~~lIF~~t~~~~~~l~~~L~~~g~-~~  165 (178)
                      ...+.+|-.+.++..+.---.+=++--.+......+..+..    ..+....++++-||.-=-+||+.+.+|.+.|+ .|
T Consensus       121 n~~l~D~~~vviDtRN~YE~~iG~F~gAv~p~~~tFrefP~~v~~~~~~~~~KkVvmyCTGGIRCEKas~~m~~~GF~eV  200 (308)
T COG1054         121 NELLSDPDVVVIDTRNDYEVAIGHFEGAVEPDIETFREFPAWVEENLDLLKDKKVVMYCTGGIRCEKASAWMKENGFKEV  200 (308)
T ss_pred             HHHhcCCCeEEEEcCcceeEeeeeecCccCCChhhhhhhHHHHHHHHHhccCCcEEEEcCCceeehhhHHHHHHhcchhh
Confidence            44556665555543332222222322223333344444444    34455577999999999999999999999999 88


Q ss_pred             EeeecCC
Q 030396          166 GVIHSDL  172 (178)
Q Consensus       166 ~~lh~~~  172 (178)
                      +-++||.
T Consensus       201 yhL~GGI  207 (308)
T COG1054         201 YHLEGGI  207 (308)
T ss_pred             hcccchH
Confidence            8899884

>KOG1132 consensus Helicase of the DEAD superfamily [Replication, recombination and repair]

Probab=82.58  E-value=1.3  Score=39.05  Aligned_cols=43  Identities=26%  Similarity=0.281  Sum_probs=30.4

Q ss_pred             HhccCCCcEEEeCcHHHHHHHHcC--CCCCCCeeEEEEeccccccc
Q 030396           10 DLSKFSCDILISTPLRLRLAIRRK--KIDLSRVEYLVLDEADKLFE   53 (178)
Q Consensus        10 ~~l~~~~~Iii~TP~~l~~~l~~~--~~~~~~l~~lViDE~d~ll~   53 (178)
                      +.+.+.++||++-=.-|.+-.-++  .+++++ ..+||||||.+-+
T Consensus       217 R~l~edAdIIF~PYnYLiDp~iR~~~~v~Lkn-sIVIfDEAHNiEd  261 (945)
T KOG1132|consen  217 RELKEDADIIFCPYNYLIDPKIRRSHKVDLKN-SIVIFDEAHNIED  261 (945)
T ss_pred             hhhcccCcEEEechhhhcCHhhhccccccccc-cEEEEeccccHHH
Confidence            345678999998555555554443  467776 7899999999853

>PRK07764 DNA polymerase III subunits gamma and tau; Validated

Probab=82.39  E-value=2.4  Score=37.73  Aligned_cols=43  Identities=23%  Similarity=0.343  Sum_probs=27.9

Q ss_pred             CCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcH
Q 030396           38 SRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPD   84 (178)
Q Consensus        38 ~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~   84 (178)
                      .+-+++||||+|.|-..+  .+.+.+++.. .+....+|+.+ |-+.
T Consensus       119 ~~~KV~IIDEad~lt~~a--~NaLLK~LEE-pP~~~~fIl~t-t~~~  161 (824)
T PRK07764        119 SRYKIFIIDEAHMVTPQG--FNALLKIVEE-PPEHLKFIFAT-TEPD  161 (824)
T ss_pred             CCceEEEEechhhcCHHH--HHHHHHHHhC-CCCCeEEEEEe-CChh
Confidence            566899999999996655  4455555655 45555555543 5443

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

Probab=82.30  E-value=1.6  Score=37.63  Aligned_cols=41  Identities=20%  Similarity=0.307  Sum_probs=30.1

Q ss_pred             CCCcEEEeCcHHHHHHHHcCCCC--CCCeeEEEEecccccccc
Q 030396           14 FSCDILISTPLRLRLAIRRKKID--LSRVEYLVLDEADKLFEV   54 (178)
Q Consensus        14 ~~~~Iii~TP~~l~~~l~~~~~~--~~~l~~lViDE~d~ll~~   54 (178)
                      ..++++|+++..+..-.......  +-.-+.+|+||||.+-+.
T Consensus       193 ~~ad~vv~nh~~~~~~~~~~~~~~~~p~~~v~v~DEAH~l~d~  235 (654)
T COG1199         193 ENADLVVTNHALLLADVALEESRILLPENDVVVFDEAHNLPDI  235 (654)
T ss_pred             hhCCEEEEccHHHHhHHHhhhhhccCCcccEEEEeccccchHH
Confidence            57999999999888654433222  335579999999999663

>PRK08116 hypothetical protein; Validated

Probab=81.99  E-value=7.4  Score=29.74  Aligned_cols=72  Identities=10%  Similarity=0.101  Sum_probs=40.1

Q ss_pred             CCcEEEeCcHHHHHHHHcC----C-------C-CCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecC
Q 030396           15 SCDILISTPLRLRLAIRRK----K-------I-DLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATL   82 (178)
Q Consensus        15 ~~~Iii~TP~~l~~~l~~~----~-------~-~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~   82 (178)
                      +..+++.|...+.+.+...    .       + .+.+.++||||+++.--........+..|+.........+|+.|-.-
T Consensus       142 ~~~v~~~~~~~ll~~i~~~~~~~~~~~~~~~~~~l~~~dlLviDDlg~e~~t~~~~~~l~~iin~r~~~~~~~IiTsN~~  221 (268)
T PRK08116        142 GVPVIFVNFPQLLNRIKSTYKSSGKEDENEIIRSLVNADLLILDDLGAERDTEWAREKVYNIIDSRYRKGLPTIVTTNLS  221 (268)
T ss_pred             CCeEEEEEHHHHHHHHHHHHhccccccHHHHHHHhcCCCEEEEecccCCCCCHHHHHHHHHHHHHHHHCCCCEEEECCCC
Confidence            5566666665555554321    0       1 16788999999996532221135556667766334455665555544


Q ss_pred             cHHH
Q 030396           83 PDFV   86 (178)
Q Consensus        83 ~~~~   86 (178)
                      |.++
T Consensus       222 ~~eL  225 (268)
T PRK08116        222 LEEL  225 (268)
T ss_pred             HHHH
Confidence            4443

>PRK12902 secA preprotein translocase subunit SecA; Reviewed

Probab=81.78  E-value=1.3  Score=39.40  Aligned_cols=39  Identities=28%  Similarity=0.529  Sum_probs=29.0

Q ss_pred             CCCcEEEeCcHHH-----HHHHHc--CCCCCCCeeEEEEecccccc
Q 030396           14 FSCDILISTPLRL-----RLAIRR--KKIDLSRVEYLVLDEADKLF   52 (178)
Q Consensus        14 ~~~~Iii~TP~~l-----~~~l~~--~~~~~~~l~~lViDE~d~ll   52 (178)
                      =.|||+.||+..+     .+.+..  +..-...+.+.|+||+|.++
T Consensus       173 Y~~DItYgTn~e~gFDYLRDnm~~~~~~~vqR~~~faIVDEvDSIL  218 (939)
T PRK12902        173 YACDITYATNSELGFDYLRDNMATDISEVVQRPFNYCVIDEVDSIL  218 (939)
T ss_pred             cCCCeEEecCCcccccchhhhhcccccccccCccceEEEeccccee
Confidence            4799999999997     333332  22335788899999999976

>cd01446 DSP_MapKP N-terminal regulatory rhodanese domain of dual specificity phosphatases (DSP), such as Mapk Phosphatase

Probab=81.71  E-value=4.3  Score=27.14  Aligned_cols=38  Identities=16%  Similarity=0.282  Sum_probs=31.0

Q ss_pred             CCCCEEEEeCCchH---------HHHHHHHhhh---CCCceEeeecCCCc
Q 030396          137 LNPPVLIFVQSKDR---------AKELYGELAF---DDIRAGVIHSDLSQ  174 (178)
Q Consensus       137 ~~~~~lIF~~t~~~---------~~~l~~~L~~---~g~~~~~lh~~~~~  174 (178)
                      ...++||||.+-..         +..++..|.+   .+.++..+.||+..
T Consensus        74 ~~~~VVvYd~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~v~~L~GG~~~  123 (132)
T cd01446          74 ESLAVVVYDESSSDRERLREDSTAESVLGKLLRKLQEGCSVYLLKGGFEQ  123 (132)
T ss_pred             CCCeEEEEeCCCcchhhccccchHHHHHHHHHHhcCCCceEEEEcchHHH
Confidence            56789999987765         8888899987   56689999999753

This domain is believed to determine substrate specificity by binding the substrate, such as ERK2, and activating the C-terminal catalytic domain by inducing a conformational change. This domain has homology to the Rhodanese Homology Domain.

>PRK13103 secA preprotein translocase subunit SecA; Reviewed

Probab=81.49  E-value=4.9  Score=36.00  Aligned_cols=37  Identities=22%  Similarity=0.259  Sum_probs=25.3

Q ss_pred             CcEEEeCcHHH-HHHHHcCC------CCCCCeeEEEEecccccc
Q 030396           16 CDILISTPLRL-RLAIRRKK------IDLSRVEYLVLDEADKLF   52 (178)
Q Consensus        16 ~~Iii~TP~~l-~~~l~~~~------~~~~~l~~lViDE~d~ll   52 (178)
                      ++|++||..-+ .++|+.+.      .-...+.+.|+||+|.++
T Consensus       172 ~dI~YGT~~e~gFDYLrD~~~~~~~~~vqr~l~~aIVDEvDsiL  215 (913)
T PRK13103        172 ADITYGTNNEFGFDYLRDNMAFSLDDKFQRELNFAVIDEVDSIL  215 (913)
T ss_pred             CCEEEEcccccccchhhccceechhhhcccccceeEechhhhee
Confidence            88999998775 24454331      124778888888888865

>KOG0991 consensus Replication factor C, subunit RFC2 [Replication, recombination and repair]

Probab=81.45  E-value=2  Score=32.46  Aligned_cols=39  Identities=18%  Similarity=0.205  Sum_probs=27.9

Q ss_pred             CCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEE
Q 030396           37 LSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLF   78 (178)
Q Consensus        37 ~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~   78 (178)
                      ..+-+.+|+||||.|-+..  ...+++.+.. ..+..++.+.
T Consensus       111 ~grhKIiILDEADSMT~gA--QQAlRRtMEi-yS~ttRFala  149 (333)
T KOG0991|consen  111 PGRHKIIILDEADSMTAGA--QQALRRTMEI-YSNTTRFALA  149 (333)
T ss_pred             CCceeEEEeeccchhhhHH--HHHHHHHHHH-Hcccchhhhh
Confidence            4888999999999996543  6677777776 5555554443

>PF13173 AAA_14: AAA domain

Probab=81.12  E-value=3.4  Score=27.51  Aligned_cols=40  Identities=20%  Similarity=0.250  Sum_probs=26.9

Q ss_pred             CeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCc
Q 030396           39 RVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLP   83 (178)
Q Consensus        39 ~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~   83 (178)
                      .-.+++|||++.+-  + +...+..+.+. . .+.++++.+....
T Consensus        61 ~~~~i~iDEiq~~~--~-~~~~lk~l~d~-~-~~~~ii~tgS~~~  100 (128)
T PF13173_consen   61 GKKYIFIDEIQYLP--D-WEDALKFLVDN-G-PNIKIILTGSSSS  100 (128)
T ss_pred             CCcEEEEehhhhhc--c-HHHHHHHHHHh-c-cCceEEEEccchH
Confidence            45789999999993  3 56777777776 3 4567665544433

>PRK11493 sseA 3-mercaptopyruvate sulfurtransferase; Provisional

Probab=81.08  E-value=3.1  Score=31.94  Aligned_cols=37  Identities=19%  Similarity=0.155  Sum_probs=32.2

Q ss_pred             CCCCEEEEeCCchHHHHHHHHhhhCCC-ceEeeecCCC
Q 030396          137 LNPPVLIFVQSKDRAKELYGELAFDDI-RAGVIHSDLS  173 (178)
Q Consensus       137 ~~~~~lIF~~t~~~~~~l~~~L~~~g~-~~~~lh~~~~  173 (178)
                      ..+++++||++=.+|-.++..|...|+ ++..+.|++.
T Consensus       230 ~~~~ii~yC~~G~~A~~~~~~l~~~G~~~v~~y~Gs~~  267 (281)
T PRK11493        230 FDRPIIASCGSGVTAAVVVLALATLDVPNVKLYDGAWS  267 (281)
T ss_pred             CCCCEEEECCcHHHHHHHHHHHHHcCCCCceeeCCCHH
Confidence            356899999999999999999999999 5889999864

>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional

Probab=80.80  E-value=18  Score=31.77  Aligned_cols=34  Identities=12%  Similarity=0.145  Sum_probs=24.6

Q ss_pred             CCCCEEEEeCCchHHHHHHHHhhh-CCCceEeeecC
Q 030396          137 LNPPVLIFVQSKDRAKELYGELAF-DDIRAGVIHSD  171 (178)
Q Consensus       137 ~~~~~lIF~~t~~~~~~l~~~L~~-~g~~~~~lh~~  171 (178)
                      ..+.++||++|.+..+.+++.|.. .+++ ...+|.
T Consensus       533 ~~gg~LVlFtSy~~l~~v~~~l~~~~~~~-ll~Q~~  567 (697)
T PRK11747        533 KHKGSLVLFASRRQMQKVADLLPRDLRLM-LLVQGD  567 (697)
T ss_pred             cCCCEEEEeCcHHHHHHHHHHHHHhcCCc-EEEeCC
Confidence            355699999999999999999864 3433 333453

>KOG0390 consensus DNA repair protein, SNF2 family [Replication, recombination and repair]

Probab=80.78  E-value=33  Score=30.49  Aligned_cols=76  Identities=18%  Similarity=0.041  Sum_probs=43.7

Q ss_pred             EEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCc-HHHHHHHHH-hcc
Q 030396           18 ILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLP-DFVEELARS-IMH   95 (178)
Q Consensus        18 Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~-~~~~~~~~~-~~~   95 (178)
                      |++-+=+.+.+.++.  +....+.++|+||.|.+=+.   ...+...+.. +...++ |++|.|.= +++.+.... -+-
T Consensus       357 vli~sye~~~~~~~~--il~~~~glLVcDEGHrlkN~---~s~~~kaL~~-l~t~rR-VLLSGTp~QNdl~EyFnlL~fv  429 (776)
T KOG0390|consen  357 VLIISYETASDYCRK--ILLIRPGLLVCDEGHRLKNS---DSLTLKALSS-LKTPRR-VLLTGTPIQNDLKEYFNLLDFV  429 (776)
T ss_pred             EEeccHHHHHHHHHH--HhcCCCCeEEECCCCCccch---hhHHHHHHHh-cCCCce-EEeeCCcccccHHHHHHHHhhc
Confidence            344444444444432  34567889999999999442   4666666776 554555 66777754 444443333 233


Q ss_pred             CcEEE
Q 030396           96 DAVRV  100 (178)
Q Consensus        96 ~~~~v  100 (178)
                      +|..+
T Consensus       430 rP~~L  434 (776)
T KOG0390|consen  430 RPGFL  434 (776)
T ss_pred             Chhhc
Confidence            55444

>PRK05580 primosome assembly protein PriA; Validated

Probab=80.56  E-value=6.8  Score=34.19  Aligned_cols=62  Identities=21%  Similarity=0.217  Sum_probs=45.2

Q ss_pred             EEEcCChhhHHHHHHHHHHh--cCCCCEEEEeCCchHHHHHHHHhhh-CCCceEeeecCCCcccc
Q 030396          116 LVFAGSEEGKLLALRQSFAE--SLNPPVLIFVQSKDRAKELYGELAF-DDIRAGVIHSDLSQTQV  177 (178)
Q Consensus       116 ~~~~~~~~~k~~~l~~ll~~--~~~~~~lIF~~t~~~~~~l~~~L~~-~g~~~~~lh~~~~~~~R  177 (178)
                      .+.......|.......+..  ....+++|.++|++-+..+.+.|++ .|.++..+||+++..+|
T Consensus       166 Ll~~~TGSGKT~v~l~~i~~~l~~g~~vLvLvPt~~L~~Q~~~~l~~~fg~~v~~~~s~~s~~~r  230 (679)
T PRK05580        166 LLDGVTGSGKTEVYLQAIAEVLAQGKQALVLVPEIALTPQMLARFRARFGAPVAVLHSGLSDGER  230 (679)
T ss_pred             EEECCCCChHHHHHHHHHHHHHHcCCeEEEEeCcHHHHHHHHHHHHHHhCCCEEEEECCCCHHHH
Confidence            33333445566555544432  1256899999999999999999976 48899999999987665

>PLN03025 replication factor C subunit; Provisional

Probab=80.43  E-value=3  Score=32.63  Aligned_cols=41  Identities=17%  Similarity=0.233  Sum_probs=26.7

Q ss_pred             CCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecC
Q 030396           38 SRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATL   82 (178)
Q Consensus        38 ~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~   82 (178)
                      ...+.+|+||+|.|-...  ...+.+++.. .+....+++ +++.
T Consensus        98 ~~~kviiiDE~d~lt~~a--q~aL~~~lE~-~~~~t~~il-~~n~  138 (319)
T PLN03025         98 GRHKIVILDEADSMTSGA--QQALRRTMEI-YSNTTRFAL-ACNT  138 (319)
T ss_pred             CCeEEEEEechhhcCHHH--HHHHHHHHhc-ccCCceEEE-EeCC
Confidence            346899999999996554  5556666665 455555444 4443

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=80.43  E-value=2.7  Score=36.37  Aligned_cols=40  Identities=13%  Similarity=0.155  Sum_probs=25.6

Q ss_pred             CCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEe
Q 030396           37 LSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFS   79 (178)
Q Consensus        37 ~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~S   79 (178)
                      ..+-+.+||||+|.|-...  .+.+.+++.. .+.+..+|+.|
T Consensus       122 ~gr~KViIIDEah~Ls~~A--aNALLKTLEE-PP~~v~FILaT  161 (700)
T PRK12323        122 AGRFKVYMIDEVHMLTNHA--FNAMLKTLEE-PPEHVKFILAT  161 (700)
T ss_pred             cCCceEEEEEChHhcCHHH--HHHHHHhhcc-CCCCceEEEEe
Confidence            3567899999999996544  3444445554 44556555554

>COG4408 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=80.02  E-value=18  Score=28.80  Aligned_cols=150  Identities=15%  Similarity=0.103  Sum_probs=82.7

Q ss_pred             hccCCCcEEEeCcHHHHHHHHcCC-CC--CCCeeEEEEeccccccccCCChhhHHHHHhhC----CCCCceEEEEeecCc
Q 030396           11 LSKFSCDILISTPLRLRLAIRRKK-ID--LSRVEYLVLDEADKLFEVGNLLKHIDPVVKAC----SNPSIVRSLFSATLP   83 (178)
Q Consensus        11 ~l~~~~~Iii~TP~~l~~~l~~~~-~~--~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~----~~~~~q~i~~SAT~~   83 (178)
                      .++.++.+=+---|..+..++.+. +|  .+++.- +.||.+.++-.- ..+.+..+++.+    ++.-.-++++|+|+.
T Consensus        47 ala~~~ql~l~~q~eahr~leg~~~id~~~kd~a~-~~~dwqtlilav-~aDaY~dvlqqi~~e~L~~vk~viLiSptfG  124 (431)
T COG4408          47 ALALTPQLYLQGQGEAHRQLEGSVTIDCYIKDLAQ-AVGDWQTLILAV-PADAYYDVLQQIPWEALPQVKSVILISPTFG  124 (431)
T ss_pred             HHhcCCeEEEEeccHHHHhhcCceehhHHHhhHHH-hhchhheEEEEe-ecHHHHHHHhcCCHhHhccccEEEEeccccc
Confidence            334445555554555555555432 22  222222 567777765443 456666666663    344567899999998


Q ss_pred             HH--HHHHHHHhccCcEEEEEcCCccccCCceEEEEEcCChhhHHHHHHHHHHhcCCCCEEEEe----CCchHHHHHHHH
Q 030396           84 DF--VEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFV----QSKDRAKELYGE  157 (178)
Q Consensus        84 ~~--~~~~~~~~~~~~~~v~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~----~t~~~~~~l~~~  157 (178)
                      ..  +......+..+..++....--...     .++.   .+.....+-.-+++.      ||.    .+...|+.+...
T Consensus       125 sn~lv~~~mnk~~~daeViS~SsY~~dT-----k~id---~~~p~~alTkavKkr------iYlgs~~~ns~~~e~l~~v  190 (431)
T COG4408         125 SNLLVQNLMNKAGRDAEVISLSSYYADT-----KYID---AEQPNRALTKAVKKR------IYLGSQHGNSGSAEMLTAV  190 (431)
T ss_pred             ccHHHHHHHhhhCCCceEEEeehhcccc-----eeec---ccCcchHHHHHHhHh------eeeccCCCCChHHHHHHHH
Confidence            65  556667777676666554322221     1221   122233333333322      222    345678888888


Q ss_pred             hhhCCCceEeeecCCCccc
Q 030396          158 LAFDDIRAGVIHSDLSQTQ  176 (178)
Q Consensus       158 L~~~g~~~~~lh~~~~~~~  176 (178)
                      |...|+.+....+-+..+.
T Consensus       191 ~aq~~I~v~~~esp~~AEt  209 (431)
T COG4408         191 LAQHGIDVEPCESPLAAET  209 (431)
T ss_pred             HHhcCCceEEcCChhhhhh
Confidence            9888888777665444433

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	178
2i4i_A	417	Crystal Structure Of Human Dead-Box Rna Helicase Dd		1e-11
2zu6_A	388	Crystal Structure Of The Eif4a-Pdcd4 Complex Length		3e-09
3eiq_A	414	Crystal Structure Of Pdcd4-eif4a Length = 414		4e-09
1hv8_A	367	Crystal Structure Of A Dead Box Protein From The Hy		9e-09
1wrb_A	253	Crystal Structure Of The N-Terminal Reca-Like Domai		2e-08
2vso_A	395	Crystal Structure Of A Translation Initiation Compl		7e-08
2j0u_B	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		6e-07
2xb2_A	411	Crystal Structure Of The Core Mago-Y14-Eif4aiii-Bar		6e-07
2hxy_A	391	Crystal Structure Of Human Apo-Eif4aiii Length = 39		7e-07
2j0q_A	410	The Crystal Structure Of The Exon Junction Complex		7e-07
2hyi_C	413	Structure Of The Human Exon Junction Complex With A		7e-07
2j0u_A	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		7e-07
3pew_A	395	S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3		2e-06
3pey_A	395	S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3 Length		2e-06
2z0m_A	337	Crystal Structure Of Hypothetical Atp-Dependent Rna		3e-06
1fuu_A	394	Yeast Initiation Factor 4a Length = 394		3e-06
2db3_A	434	Structural Basis For Rna Unwinding By The Dead-Box		5e-06
3dkp_A	245	Human Dead-Box Rna-Helicase Ddx52, Conserved Domain		5e-06
3fho_B	508	Structure Of S. Pombe Dbp5 Length = 508		1e-05
2gxq_A	207	Hera N-Terminal Domain In Complex With Amp, Crystal		9e-05
3mwj_A	207	Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Ap		1e-04
3sqw_A	579	Structure Of Mss116p (Nte Deletion) Bound To Ssrna		2e-04
3i5x_A	563	Structure Of Mss116p Bound To Ssrna And Amp-Pnp Len		2e-04
3sqx_A	512	Structure Of Mss116p (Nte And C-Tail Double Deletio		2e-04
4a4d_A	253	Crystal Structure Of The N-Terminal Domain Of The H		3e-04
3fe2_A	242	Human Dead-Box Rna Helicase Ddx5 (P68), Conserved D		3e-04
3iuy_A	228	Crystal Structure Of Ddx53 Dead-Box Domain Length =		7e-04

>pdb|2I4I|A Chain A, Crystal Structure Of Human Dead-Box Rna Helicase Ddx3x Length = 417

Iteration: 1
 Score = 65.5 bits (158), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 50/167 (29%), Positives = 79/167 (47%), Gaps = 3/167 (1%)
Query: 10  DLSKFSCDILISTPXXXXXXXXXXXXXXSRVEYLVLDEADKLFEVGNLLKHIDPVVKACS 69
           DL +  C +L++TP                 +YLVLDEAD++ ++G   +    V +   
Sbjct: 147 DLER-GCHLLVATPGRLVDMMERGKIGLDFCKYLVLDEADRMLDMGFEPQIRRIVEQDTM 205
Query: 70  NPSIVRS--LFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLL 127
            P  VR   +FSAT P  ++ LAR  + + + + VGR  + SE+I QK+V+    + +  
Sbjct: 206 PPKGVRHTMMFSATFPKEIQMLARDFLDEYIFLAVGRVGSTSENITQKVVWVEESDKRSF 265
Query: 128 ALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQ 174
            L    A   +   L+FV++K  A  L   L  +      IH D SQ
Sbjct: 266 LLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQ 312

>pdb|2ZU6|A Chain A, Crystal Structure Of The Eif4a-Pdcd4 Complex Length = 388

Iteration: 1
 Score = 57.8 bits (138), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 41/159 (25%), Positives = 70/159 (44%), Gaps = 2/159 (1%)
Query: 18  ILISTPXXXXXXXXXXXXXXSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSL 77
           I++ TP                ++  VLDEAD++   G   +  D   K  SN  +V  L
Sbjct: 136 IIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKLNSNTQVV--L 193
Query: 78  FSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESL 137
            SAT+P  V E+ +  M D +R++V ++    E I+Q  +    EE KL  L   +    
Sbjct: 194 LSATMPSDVLEVTKKFMRDPIRILVKKEELTLEGIRQFYINVEREEWKLDTLCDLYETLT 253
Query: 138 NPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQ 176
               +IF+ ++ +   L  ++   D     +H D+ Q +
Sbjct: 254 ITQAVIFINTRRKVDWLTEKMHARDFTVSAMHGDMDQKE 292

>pdb|3EIQ|A Chain A, Crystal Structure Of Pdcd4-eif4a Length = 414

Iteration: 1
 Score = 57.4 bits (137), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 41/159 (25%), Positives = 70/159 (44%), Gaps = 2/159 (1%)
Query: 18  ILISTPXXXXXXXXXXXXXXSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSL 77
           I++ TP                ++  VLDEAD++   G   +  D   K  SN  +V  L
Sbjct: 162 IIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKLNSNTQVV--L 219
Query: 78  FSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESL 137
            SAT+P  V E+ +  M D +R++V ++    E I+Q  +    EE KL  L   +    
Sbjct: 220 LSATMPSDVLEVTKKFMRDPIRILVKKEELTLEGIRQFYINVEREEWKLDTLCDLYETLT 279
Query: 138 NPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQ 176
               +IF+ ++ +   L  ++   D     +H D+ Q +
Sbjct: 280 ITQAVIFINTRRKVDWLTEKMHARDFTVSAMHGDMDQKE 318

>pdb|1HV8|A Chain A, Crystal Structure Of A Dead Box Protein From The Hyperthermophile Methanococcus Jannaschii Length = 367

Iteration: 1
 Score = 56.2 bits (134), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 46/167 (27%), Positives = 75/167 (44%), Gaps = 18/167 (10%)
Query: 15  SCDILISTPXXXXXXXXXXXXXXSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIV 74
           + +I++ TP                V+Y +LDEAD+    G  +K ++ ++ AC+    +
Sbjct: 123 NANIVVGTPGRILDHINRGTLNLKNVKYFILDEADEXLNXG-FIKDVEKILNACNKDKRI 181
Query: 75  RSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEE-----GKLLAL 129
             LFSAT P  +  LA+    D   +    K   + +I+Q  V     E      +LL  
Sbjct: 182 -LLFSATXPREILNLAKKYXGDYSFI----KAKINANIEQSYVEVNENERFEALCRLLKN 236
Query: 130 RQSFAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQ 176
           ++ +        L+F ++K   KEL   L     +AG IH DLSQ+Q
Sbjct: 237 KEFYG-------LVFCKTKRDTKELASXLRDIGFKAGAIHGDLSQSQ 276

>pdb|1WRB|A Chain A, Crystal Structure Of The N-Terminal Reca-Like Domain Of Djvlgb, A Pranarian Vasa-Like Rna Helicase Length = 253

Iteration: 1
 Score = 55.1 bits (131), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 30/107 (28%), Positives = 58/107 (54%), Gaps = 4/107 (3%)
Query: 13  KFSCDILISTPXXXXXXXXXXXXXXSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPS 72
           +  C +L++TP                 +Y+VLDEAD++ ++G     I  +++  + PS
Sbjct: 148 QMGCHLLVATPGRLVDFIEKNKISLEFCKYIVLDEADRMLDMG-FEPQIRKIIEESNMPS 206
Query: 73  IVRS---LFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKL 116
            +     +FSAT P  +++LA   +++ + + VGR  + S+SIKQ++
Sbjct: 207 GINRQTLMFSATFPKEIQKLAADFLYNYIFMTVGRVGSTSDSIKQEI 253

>pdb|2VSO|A Chain A, Crystal Structure Of A Translation Initiation Complex Length = 395

Iteration: 1
 Score = 53.1 bits (126), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 42/159 (26%), Positives = 68/159 (42%), Gaps = 2/159 (1%)
Query: 18  ILISTPXXXXXXXXXXXXXXSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSL 77
           I++ TP               +++  +LDEAD++   G   K     +     P+    L
Sbjct: 142 IVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSG--FKEQIYQIFTLLPPTTQVVL 199
Query: 78  FSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESL 137
            SAT+P+ V E+    M + VR++V +     E IKQ  V    EE K   L   +    
Sbjct: 200 LSATMPNDVLEVTTKFMRNPVRILVKKDELTLEGIKQFYVNVEEEEYKYECLTDLYDSIS 259
Query: 138 NPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQ 176
               +IF  ++ + +EL  +L  D      I+SDL Q +
Sbjct: 260 VTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQE 298

>pdb|2J0U|B Chain B, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0 A Resolution Length = 374

Iteration: 1
 Score = 50.4 bits (119), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 38/143 (26%), Positives = 62/143 (43%), Gaps = 14/143 (9%)
Query: 40  VEYLVLDEADKLFEVG------NLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSI 93
           ++ LVLDEAD++   G      ++ +++ P  +          L SATLP  V E+    
Sbjct: 144 IKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVV--------LISATLPHEVLEMTNKF 195
Query: 94  MHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKDRAKE 153
           M D +R++V R     E IKQ  V    EE K   L   +        +IF  +K +   
Sbjct: 196 MTDPIRILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDW 255
Query: 154 LYGELAFDDIRAGVIHSDLSQTQ 176
           L  ++   +     +H D+ Q +
Sbjct: 256 LTEKMREANFTVSSMHGDMPQKE 278

>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 = 50.1 bits (118), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 37/143 (25%), Positives = 62/143 (43%), Gaps = 14/143 (9%)
Query: 40  VEYLVLDEADKLFEVG------NLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSI 93
           ++ LVLDEAD++   G      ++ +++ P  +          L SATLP  + E+    
Sbjct: 181 IKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVV--------LISATLPHEILEMTNKF 232
Query: 94  MHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKDRAKE 153
           M D +R++V R     E IKQ  V    EE K   L   +        +IF  +K +   
Sbjct: 233 MTDPIRILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDW 292
Query: 154 LYGELAFDDIRAGVIHSDLSQTQ 176
           L  ++   +     +H D+ Q +
Sbjct: 293 LTEKMREANFTVSSMHGDMPQKE 315

>pdb|2HXY|A Chain A, Crystal Structure Of Human Apo-Eif4aiii Length = 391

Iteration: 1
 Score = 50.1 bits (118), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 37/143 (25%), Positives = 62/143 (43%), Gaps = 14/143 (9%)
Query: 40  VEYLVLDEADKLFEVG------NLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSI 93
           ++ LVLDEAD++   G      ++ +++ P  +          L SATLP  + E+    
Sbjct: 159 IKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVV--------LISATLPHEILEMTNKF 210
Query: 94  MHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKDRAKE 153
           M D +R++V R     E IKQ  V    EE K   L   +        +IF  +K +   
Sbjct: 211 MTDPIRILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDW 270
Query: 154 LYGELAFDDIRAGVIHSDLSQTQ 176
           L  ++   +     +H D+ Q +
Sbjct: 271 LTEKMREANFTVSSMHGDMPQKE 293

>pdb|2J0Q|A Chain A, The Crystal Structure Of The Exon Junction Complex At 3.2 A Resolution Length = 410

Iteration: 1
 Score = 50.1 bits (118), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 37/143 (25%), Positives = 62/143 (43%), Gaps = 14/143 (9%)
Query: 40  VEYLVLDEADKLFEVG------NLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSI 93
           ++ LVLDEAD++   G      ++ +++ P  +          L SATLP  + E+    
Sbjct: 180 IKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVV--------LISATLPHEILEMTNKF 231
Query: 94  MHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKDRAKE 153
           M D +R++V R     E IKQ  V    EE K   L   +        +IF  +K +   
Sbjct: 232 MTDPIRILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDW 291
Query: 154 LYGELAFDDIRAGVIHSDLSQTQ 176
           L  ++   +     +H D+ Q +
Sbjct: 292 LTEKMREANFTVSSMHGDMPQKE 314

>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 = 50.1 bits (118), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 37/143 (25%), Positives = 62/143 (43%), Gaps = 14/143 (9%)
Query: 40  VEYLVLDEADKLFEVG------NLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSI 93
           ++ LVLDEAD++   G      ++ +++ P  +          L SATLP  + E+    
Sbjct: 181 IKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVV--------LISATLPHEILEMTNKF 232
Query: 94  MHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKDRAKE 153
           M D +R++V R     E IKQ  V    EE K   L   +        +IF  +K +   
Sbjct: 233 MTDPIRILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDW 292
Query: 154 LYGELAFDDIRAGVIHSDLSQTQ 176
           L  ++   +     +H D+ Q +
Sbjct: 293 LTEKMREANFTVSSMHGDMPQKE 315

>pdb|2J0U|A Chain A, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0 A Resolution Length = 374

Iteration: 1
 Score = 50.1 bits (118), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 37/143 (25%), Positives = 62/143 (43%), Gaps = 14/143 (9%)
Query: 40  VEYLVLDEADKLFEVG------NLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSI 93
           ++ LVLDEAD++   G      ++ +++ P  +          L SATLP  + E+    
Sbjct: 144 IKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVV--------LISATLPHEILEMTNKF 195
Query: 94  MHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKDRAKE 153
           M D +R++V R     E IKQ  V    EE K   L   +        +IF  +K +   
Sbjct: 196 MTDPIRILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDW 255
Query: 154 LYGELAFDDIRAGVIHSDLSQTQ 176
           L  ++   +     +H D+ Q +
Sbjct: 256 LTEKMREANFTVSSMHGDMPQKE 278

>pdb|3PEW|A Chain A, S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3 Length = 395

Iteration: 1
 Score = 48.9 bits (115), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 41/164 (25%), Positives = 72/164 (43%), Gaps = 2/164 (1%)
Query: 13  KFSCDILISTPXXXXXXXXXXXXXXSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPS 72
           + +  +++ TP               +++  VLDEAD + +   L      V +     +
Sbjct: 119 QINAQVIVGTPGTVLDLMRRKLMQLQKIKIFVLDEADNMLDQQGLGDQCIRVKRFLPKDT 178
Query: 73  IVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQS 132
            +  LFSAT  D V + A+ I+ +A  + +       ++IKQ  +   +E  K   L + 
Sbjct: 179 QL-VLFSATFADAVRQYAKKIVPNANTLELQTNEVNVDAIKQLYMDCKNEADKFDVLTEL 237
Query: 133 FAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQ 176
           +        +IFV +K  A  LYG+L  +     ++H DL QTQ
Sbjct: 238 YGVMTIGSSIIFVATKKTANVLYGKLKSEGHEVSILHGDL-QTQ 280

>pdb|3PEY|A Chain A, S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3 Length = 395

Iteration: 1
 Score = 48.5 bits (114), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 41/164 (25%), Positives = 72/164 (43%), Gaps = 2/164 (1%)
Query: 13  KFSCDILISTPXXXXXXXXXXXXXXSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPS 72
           + +  +++ TP               +++  VLDEAD + +   L      V +     +
Sbjct: 119 QINAQVIVGTPGTVLDLMRRKLMQLQKIKIFVLDEADNMLDQQGLGDQCIRVKRFLPKDT 178
Query: 73  IVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQS 132
            +  LFSAT  D V + A+ I+ +A  + +       ++IKQ  +   +E  K   L + 
Sbjct: 179 QL-VLFSATFADAVRQYAKKIVPNANTLELQTNEVNVDAIKQLYMDCKNEADKFDVLTEL 237
Query: 133 FAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQ 176
           +        +IFV +K  A  LYG+L  +     ++H DL QTQ
Sbjct: 238 YGLMTIGSSIIFVATKKTANVLYGKLKSEGHEVSILHGDL-QTQ 280

>pdb|2Z0M|A Chain A, Crystal Structure Of Hypothetical Atp-Dependent Rna Helicase From Sulfolobus Tokodaii Length = 337

Iteration: 1
 Score = 47.8 bits (112), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 37/143 (25%), Positives = 73/143 (51%), Gaps = 14/143 (9%)
Query: 15  SCDILISTPXXXXXXXXXXXXXXSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIV 74
           + DI+++TP              S  E +++DEAD +FE+G  +  I  ++   SN  I 
Sbjct: 105 NADIVVATPGRLLDLWSKGVIDLSSFEIVIIDEADLMFEMG-FIDDIKIILAQTSNRKIT 163
Query: 75  RSLFSATLPDFVEELARSIM--HDAVRVIVGRKNTASESIKQKLVFAGSE-EGKLLALRQ 131
             LFSAT+P+ + ++ +  +  ++ +   +G  N     ++ K V    +   K+ ALR 
Sbjct: 164 -GLFSATIPEEIRKVVKDFITNYEEIEACIGLAN-----VEHKFVHVKDDWRSKVQALR- 216
Query: 132 SFAESLNPPVLIFVQSKDRAKEL 154
              E+ +  V++FV++++R  +L
Sbjct: 217 ---ENKDKGVIVFVRTRNRVAKL 236

>pdb|1FUU|A Chain A, Yeast Initiation Factor 4a Length = 394

Iteration: 1
 Score = 47.8 bits (112), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 41/159 (25%), Positives = 65/159 (40%), Gaps = 2/159 (1%)
Query: 18  ILISTPXXXXXXXXXXXXXXSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSL 77
           I++ TP               +++  +LDEAD+    G   K     +     P+    L
Sbjct: 141 IVVGTPGRVFDNIQRRRFRTDKIKXFILDEADEXLSSG--FKEQIYQIFTLLPPTTQVVL 198
Query: 78  FSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESL 137
            SAT P+ V E+      + VR++V +     E IKQ  V    EE K   L   +    
Sbjct: 199 LSATXPNDVLEVTTKFXRNPVRILVKKDELTLEGIKQFYVNVEEEEYKYECLTDLYDSIS 258
Query: 138 NPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQ 176
               +IF  ++ + +EL  +L  D      I+SDL Q +
Sbjct: 259 VTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQE 297

>pdb|2DB3|A Chain A, Structural Basis For Rna Unwinding By The Dead-Box Protein Drosophila Vasa Length = 434

Iteration: 1
 Score = 47.4 bits (111), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 40/170 (23%), Positives = 74/170 (43%), Gaps = 18/170 (10%)
Query: 15  SCDILISTPXXXXXXXXXXXXXXSRVEYLVLDEADKLFEVG------NLLKHIDPVVKAC 68
            C ++I+TP                  ++VLDEAD++ ++G       ++ H+       
Sbjct: 179 GCHVVIATPGRLLDFVDRTFITFEDTRFVVLDEADRMLDMGFSEDMRRIMTHV------T 232
Query: 69  SNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKL--VFAGSEEGKL 126
             P     +FSAT P+ ++ +A   + + V V +G    A   +KQ +  V   ++  KL
Sbjct: 233 MRPEHQTLMFSATFPEEIQRMAGEFLKNYVFVAIGIVGGACSDVKQTIYEVNKYAKRSKL 292
Query: 127 LALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQ 176
           + +    A+      ++FV++K  A  L   L+  +     IH D  Q+Q
Sbjct: 293 IEILSEQADG----TIVFVETKRGADFLASFLSEKEFPTTSIHGDRLQSQ 338

>pdb|3DKP|A Chain A, Human Dead-Box Rna-Helicase Ddx52, Conserved Domain I In Complex With Adp Length = 245

Iteration: 1
 Score = 47.4 bits (111), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 29/95 (30%), Positives = 50/95 (52%), Gaps = 4/95 (4%)
Query: 17  DILISTPXXXXXXXXX--XXXXXSRVEYLVLDEADKLFEVG--NLLKHIDPVVKACSNPS 72
           DIL++TP                + VE+LV+DE+DKLFE G       +  +  AC++  
Sbjct: 151 DILVTTPNRLIYLLKQDPPGIDLASVEWLVVDESDKLFEDGKTGFRDQLASIFLACTSHK 210
Query: 73  IVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNT 107
           + R++FSAT    VE+  +  + + + V +G +N+
Sbjct: 211 VRRAMFSATFAYDVEQWCKLNLDNVISVSIGARNS 245

>pdb|2GXQ|A Chain A, Hera N-Terminal Domain In Complex With Amp, Crystal Form 1 Length = 207

Iteration: 1
 Score = 43.1 bits (100), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 29/88 (32%), Positives = 45/88 (51%), Gaps = 2/88 (2%)
Query: 15  SCDILISTPXXXXXXXXXXXXXXSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIV 74
             D +++TP              SRVE  VLDEAD++  +G   + ++ ++ A + PS  
Sbjct: 120 GADAVVATPGRALDYLRQGVLDLSRVEVAVLDEADEMLSMG-FEEEVEALLSA-TPPSRQ 177
Query: 75  RSLFSATLPDFVEELARSIMHDAVRVIV 102
             LFSATLP + + LA   M + V + V
Sbjct: 178 TLLFSATLPSWAKRLAERYMKNPVLINV 205

>pdb|3MWJ|A Chain A, Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Apo Form Length = 207

Iteration: 1
 Score = 42.7 bits (99), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 29/88 (32%), Positives = 45/88 (51%), Gaps = 2/88 (2%)
Query: 15  SCDILISTPXXXXXXXXXXXXXXSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIV 74
             D +++TP              SRVE  VLDEAD++  +G   + ++ ++ A + PS  
Sbjct: 120 GADAVVATPGRALDYLRQGVLDLSRVEVAVLDEADEMLSMG-FEEEVEALLSA-TPPSRQ 177
Query: 75  RSLFSATLPDFVEELARSIMHDAVRVIV 102
             LFSATLP + + LA   M + V + V
Sbjct: 178 TLLFSATLPSWAKRLAERYMKNPVLINV 205

>pdb|3SQW|A Chain A, Structure Of Mss116p (Nte Deletion) Bound To Ssrna And Amp-Pnp Length = 579

Iteration: 1
 Score = 42.0 bits (97), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 33/91 (36%), Positives = 51/91 (56%), Gaps = 6/91 (6%)
Query: 11  LSKFSCDILISTPXXXXXXXXXXXXXXSR-VEYLVLDEADKLFEVG--NLLKHIDPVVKA 67
           ++K   +I+I+TP               R V+Y VLDEAD+L E+G  + L+ I  ++  
Sbjct: 146 MNKLRPNIVIATPGRLIDVLEKYSNKFFRFVDYKVLDEADRLLEIGFRDDLETISGILNE 205
Query: 68  CSNPS---IVRSLFSATLPDFVEELARSIMH 95
            ++ S   I   LFSATL D V++LA +IM+
Sbjct: 206 KNSKSADNIKTLLFSATLDDKVQKLANNIMN 236

>pdb|3I5X|A Chain A, Structure Of Mss116p Bound To Ssrna And Amp-Pnp Length = 563

Iteration: 1
 Score = 42.0 bits (97), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 33/91 (36%), Positives = 51/91 (56%), Gaps = 6/91 (6%)
Query: 11  LSKFSCDILISTPXXXXXXXXXXXXXXSR-VEYLVLDEADKLFEVG--NLLKHIDPVVKA 67
           ++K   +I+I+TP               R V+Y VLDEAD+L E+G  + L+ I  ++  
Sbjct: 197 MNKLRPNIVIATPGRLIDVLEKYSNKFFRFVDYKVLDEADRLLEIGFRDDLETISGILNE 256
Query: 68  CSNPS---IVRSLFSATLPDFVEELARSIMH 95
            ++ S   I   LFSATL D V++LA +IM+
Sbjct: 257 KNSKSADNIKTLLFSATLDDKVQKLANNIMN 287

>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 = 41.6 bits (96), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 33/91 (36%), Positives = 51/91 (56%), Gaps = 6/91 (6%)
Query: 11  LSKFSCDILISTPXXXXXXXXXXXXXXSR-VEYLVLDEADKLFEVG--NLLKHIDPVVKA 67
           ++K   +I+I+TP               R V+Y VLDEAD+L E+G  + L+ I  ++  
Sbjct: 146 MNKLRPNIVIATPGRLIDVLEKYSNKFFRFVDYKVLDEADRLLEIGFRDDLETISGILNE 205
Query: 68  CSNPS---IVRSLFSATLPDFVEELARSIMH 95
            ++ S   I   LFSATL D V++LA +IM+
Sbjct: 206 KNSKSADNIKTLLFSATLDDKVQKLANNIMN 236

>pdb|4A4D|A Chain A, Crystal Structure Of The N-Terminal Domain Of The Human Dead-Box Rna Helicase Ddx5 (P68) Length = 253

Iteration: 1
 Score = 41.2 bits (95), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 26/90 (28%), Positives = 42/90 (46%), Gaps = 8/90 (8%)
Query: 17  DILISTPXXXXXXXXXXXXXXSRVEYLVLDEADKLFEVG---NLLKHIDPVVKACSNPSI 73
           +I I+TP               R  YLVLDEAD++ ++G    + K +D +      P  
Sbjct: 168 EICIATPGRLIDFLECGKTNLRRTTYLVLDEADRMLDMGFEPQIRKIVDQI-----RPDR 222
Query: 74  VRSLFSATLPDFVEELARSIMHDAVRVIVG 103
              ++SAT P  V +LA   + D + + +G
Sbjct: 223 QTLMWSATWPKEVRQLAEDFLKDYIHINIG 252

>pdb|3FE2|A Chain A, Human Dead-Box Rna Helicase Ddx5 (P68), Conserved Domain I In Complex With Adp Length = 242

Iteration: 1
 Score = 41.2 bits (95), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 26/90 (28%), Positives = 42/90 (46%), Gaps = 8/90 (8%)
Query: 17  DILISTPXXXXXXXXXXXXXXSRVEYLVLDEADKLFEVG---NLLKHIDPVVKACSNPSI 73
           +I I+TP               R  YLVLDEAD++ ++G    + K +D +      P  
Sbjct: 154 EICIATPGRLIDFLECGKTNLRRTTYLVLDEADRMLDMGFEPQIRKIVDQI-----RPDR 208
Query: 74  VRSLFSATLPDFVEELARSIMHDAVRVIVG 103
              ++SAT P  V +LA   + D + + +G
Sbjct: 209 QTLMWSATWPKEVRQLAEDFLKDYIHINIG 238

>pdb|3IUY|A Chain A, Crystal Structure Of Ddx53 Dead-Box Domain Length = 228

Iteration: 1
 Score = 40.0 bits (92), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 30/96 (31%), Positives = 45/96 (46%), Gaps = 9/96 (9%)
Query: 10  DLSKFSCDILISTPXXXXXXXXXXXXXXSRVEYLVLDEADKLFEVGNLLKHIDPVVKAC- 68
           D+SK   DI+I+TP                + YLV+DEADK+ ++       +P ++   
Sbjct: 139 DISK-GVDIIIATPGRLNDLQMNNSVNLRSITYLVIDEADKMLDM-----EFEPQIRKIL 192
Query: 69  --SNPSIVRSLFSATLPDFVEELARSIMHDAVRVIV 102
               P     + SAT PD V +LA S + D + V V
Sbjct: 193 LDVRPDRQTVMTSATWPDTVRQLALSYLKDPMIVYV 228

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	178
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	1e-37
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	6e-34
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	9e-33
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	1e-32
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	2e-31
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	6e-28
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	6e-27
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	1e-26
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	2e-26
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	2e-26
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	6e-26
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	9e-26
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	1e-25
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	1e-25
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	9e-25
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	3e-23
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	1e-22
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	7e-21
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	3e-18
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	5e-18
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	2e-16
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	2e-15
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	5e-15
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	7e-15
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	2e-14
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	7e-14
3bor_A	237	Human initiation factor 4A-II; translation initiat	1e-13
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	3e-13
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	5e-13
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	3e-12
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	1e-11
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	4e-09
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	5e-09
2yjt_D	170	ATP-dependent RNA helicase SRMB, regulator of ribo	4e-07
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	2e-06
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	2e-06
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-06
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	4e-06
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	2e-04

>3dkp_A Probable ATP-dependent RNA helicase DDX52; DEAD, ADP, structural genomics, structural GEN consortium, SGC, rRNA, ATP-binding, hydrolase; HET: ADP; 2.10A {Homo sapiens} Length = 245

 Score =  128 bits (325), Expect = 1e-37
 Identities = 34/96 (35%), Positives = 58/96 (60%), Gaps = 4/96 (4%)

Query: 16  CDILISTPLRLRLAIRRKK--IDLSRVEYLVLDEADKLFEVGNL--LKHIDPVVKACSNP 71
            DIL++TP RL   +++    IDL+ VE+LV+DE+DKLFE G       +  +  AC++ 
Sbjct: 150 FDILVTTPNRLIYLLKQDPPGIDLASVEWLVVDESDKLFEDGKTGFRDQLASIFLACTSH 209

Query: 72  SIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNT 107
            + R++FSAT    VE+  +  + + + V +G +N+
Sbjct: 210 KVRRAMFSATFAYDVEQWCKLNLDNVISVSIGARNS 245

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A* Length = 414

 Score =  122 bits (309), Expect = 6e-34
 Identities = 37/189 (19%), Positives = 76/189 (40%), Gaps = 32/189 (16%)

Query: 10  DLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACS 69
              +    IL+ +   +  +  R+K+   R +++ +D+ D + +     ++ID ++    
Sbjct: 112 SFEEDDYHILVFSTQFV--SKNREKLSQKRFDFVFVDDVDAVLKAS---RNIDTLLMMVG 166

Query: 70  NP-SIVRSLFSATLPDFVEELARSI---------------------MHDAVRVIVGRKNT 107
            P  I+R  FS      + E  +++                       D +   VGR  +
Sbjct: 167 IPEEIIRKAFSTIKQGKIYERPKNLKPGILVVSSATAKPRGIRPLLFRDLLNFTVGRLVS 226

Query: 108 ASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGV 167
            + +I    + + S+E KL+ L + F +     +LIF Q+++  KELY  L       G 
Sbjct: 227 VARNITHVRISSRSKE-KLVELLEIFRDG----ILIFAQTEEEGKELYEYLKRFKFNVGE 281

Query: 168 IHSDLSQTQ 176
             S+  +  
Sbjct: 282 TWSEFEKNF 290

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens} Length = 417

 Score =  119 bits (301), Expect = 1e-32
 Identities = 54/171 (31%), Positives = 85/171 (49%), Gaps = 18/171 (10%)

Query: 16  CDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVG------NLLKHIDPVVKACS 69
           C +L++TP RL   + R KI L   +YLVLDEAD++ ++G       +++          
Sbjct: 152 CHLLVATPGRLVDMMERGKIGLDFCKYLVLDEADRMLDMGFEPQIRRIVEQDT------M 205

Query: 70  NPSIVRS--LFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEE--GK 125
            P  VR   +FSAT P  ++ LAR  + + + + VGR  + SE+I QK+V+    +    
Sbjct: 206 PPKGVRHTMMFSATFPKEIQMLARDFLDEYIFLAVGRVGSTSENITQKVVWVEESDKRSF 265

Query: 126 LLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQ 176
           LL L  +  +  +   L+FV++K  A  L   L  +      IH D SQ  
Sbjct: 266 LLDLLNATGK--DSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRD 314

>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 =  116 bits (293), Expect = 2e-31
 Identities = 41/166 (24%), Positives = 74/166 (44%), Gaps = 12/166 (7%)

Query: 16  CDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVR 75
           C ++I+TP RL   + R  I      ++VLDEAD++ ++G         ++       +R
Sbjct: 180 CHVVIATPGRLLDFVDRTFITFEDTRFVVLDEADRMLDMG-----FSEDMRRIMTHVTMR 234

Query: 76  S-----LFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALR 130
                 +FSAT P+ ++ +A   + + V V +G    A   +KQ +    ++  K   L 
Sbjct: 235 PEHQTLMFSATFPEEIQRMAGEFLKNYVFVAIGIVGGACSDVKQTIYEV-NKYAKRSKLI 293

Query: 131 QSFAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQ 176
           +          ++FV++K  A  L   L+  +     IH D  Q+Q
Sbjct: 294 E-ILSEQADGTIVFVETKRGADFLASFLSEKEFPTTSIHGDRLQSQ 338

>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 =  106 bits (267), Expect = 6e-28
 Identities = 42/165 (25%), Positives = 74/165 (44%), Gaps = 3/165 (1%)

Query: 13  KFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPS 72
           + +  +++ TP  +   +RRK + L +++  VLDEAD + +   L      V +      
Sbjct: 119 QINAQVIVGTPGTVLDLMRRKLMQLQKIKIFVLDEADNMLDQQGLGDQCIRVKRFL-PKD 177

Query: 73  IVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQS 132
               LFSAT  D V + A+ I+ +A  + +       ++IKQ  +   +E  K   L   
Sbjct: 178 TQLVLFSATFADAVRQYAKKIVPNANTLELQTNEVNVDAIKQLYMDCKNEADKFDVL-TE 236

Query: 133 FAESLNPP-VLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQ 176
               +     +IFV +K  A  LYG+L  +     ++H DL   +
Sbjct: 237 LYGLMTIGSSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQE 281

>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 =  103 bits (260), Expect = 6e-27
 Identities = 41/166 (24%), Positives = 73/166 (43%), Gaps = 4/166 (2%)

Query: 13  KFSCDILISTPLR-LRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNP 71
           K S  I+I TP   L    + K ID  +++  VLDEAD +            + +     
Sbjct: 141 KISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRML-PR 199

Query: 72  SIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQ 131
           +    LFSAT  D V + A+ ++ D   + + R+    ++IKQ  V   S + K  AL  
Sbjct: 200 NCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEETLDTIKQYYVLCSSRDEKFQALCN 259

Query: 132 SFAESLNPP-VLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQ 176
            +  ++     +IF  ++  A  L  EL+ +  +  ++  ++   Q
Sbjct: 260 LY-GAITIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQ 304

>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 =  102 bits (257), Expect = 1e-26
 Identities = 45/168 (26%), Positives = 79/168 (47%), Gaps = 16/168 (9%)

Query: 16  CDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVG------NLLKHIDPVVKACS 69
             I++ TP R+   I+R++    +++  +LDEAD++   G       +   +        
Sbjct: 139 AQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSGFKEQIYQIFTLL-------- 190

Query: 70  NPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLAL 129
            P+    L SAT+P+ V E+    M + VR++V +     E IKQ  V    EE K   L
Sbjct: 191 PPTTQVVLLSATMPNDVLEVTTKFMRNPVRILVKKDELTLEGIKQFYVNVEEEEYKYECL 250

Query: 130 RQSFAESLNPP-VLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQ 176
              + +S++    +IF  ++ + +EL  +L  D      I+SDL Q +
Sbjct: 251 TDLY-DSISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQE 297

>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 =  103 bits (258), Expect = 2e-26
 Identities = 41/166 (24%), Positives = 73/166 (43%), Gaps = 4/166 (2%)

Query: 13  KFSCDILISTPLR-LRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNP 71
           K S  I+I TP   L    + K ID  +++  VLDEAD +            + +     
Sbjct: 208 KISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRML-PR 266

Query: 72  SIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQ 131
           +    LFSAT  D V + A+ ++ D   + + R+    ++IKQ  V   S + K  AL  
Sbjct: 267 NCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEETLDTIKQYYVLCSSRDEKFQALCN 326

Query: 132 SFAESLNPP-VLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQ 176
            +  ++     +IF  ++  A  L  EL+ +  +  ++  ++   Q
Sbjct: 327 LY-GAITIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQ 371

>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 =  102 bits (256), Expect = 2e-26
 Identities = 42/173 (24%), Positives = 80/173 (46%), Gaps = 16/173 (9%)

Query: 11  LSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVG------NLLKHIDPV 64
           L   +  I++ TP R+   + R+ +    ++  VLDEAD++   G      ++ + +   
Sbjct: 155 LQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKL--- 211

Query: 65  VKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEG 124
                N +    L SAT+P  V E+ +  M D +R++V ++    E I+Q  +    EE 
Sbjct: 212 -----NSNTQVVLLSATMPSDVLEVTKKFMRDPIRILVKKEELTLEGIRQFYINVEREEW 266

Query: 125 KLLALRQSFAESLNPP-VLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQ 176
           KL  L   + E+L     +IF+ ++ +   L  ++   D     +H D+ Q +
Sbjct: 267 KLDTLCDLY-ETLTITQAVIFINTRRKVDWLTEKMHARDFTVSAMHGDMDQKE 318

>1wrb_A DJVLGB; RNA helicase, DEAD BOX, VASA, structural genomics, NPPSFA, N project on protein structural and functional analyses; 2.40A {Dugesia japonica} SCOP: c.37.1.19 Length = 253

 Score = 98.4 bits (246), Expect = 6e-26
 Identities = 35/109 (32%), Positives = 62/109 (56%), Gaps = 14/109 (12%)

Query: 16  CDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVG------NLLKHIDPVVKACS 69
           C +L++TP RL   I + KI L   +Y+VLDEAD++ ++G       +++  +       
Sbjct: 151 CHLLVATPGRLVDFIEKNKISLEFCKYIVLDEADRMLDMGFEPQIRKIIEESNM------ 204

Query: 70  NPSIVR--SLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKL 116
              I R   +FSAT P  +++LA   +++ + + VGR  + S+SIKQ++
Sbjct: 205 PSGINRQTLMFSATFPKEIQKLAADFLYNYIFMTVGRVGSTSDSIKQEI 253

>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 =  100 bits (252), Expect = 9e-26
 Identities = 44/168 (26%), Positives = 76/168 (45%), Gaps = 16/168 (9%)

Query: 16  CDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVG------NLLKHIDPVVKACS 69
             ++  TP R+   IRR+ +    ++ LVLDEAD++   G      ++ +++        
Sbjct: 156 QHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYL-------- 207

Query: 70  NPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLAL 129
            P+    L SATLP  + E+    M D +R++V R     E IKQ  V    EE K   L
Sbjct: 208 PPATQVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWKFDTL 267

Query: 130 RQSFAESLNPP-VLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQ 176
              + ++L     +IF  +K +   L  ++   +     +H D+ Q +
Sbjct: 268 CDLY-DTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKE 314

>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 =  101 bits (253), Expect = 1e-25
 Identities = 45/186 (24%), Positives = 77/186 (41%), Gaps = 22/186 (11%)

Query: 11  LSKFSCDILISTPLRLRLAIRRKKIDLSR-VEYLVLDEADKLFEVG------NLLKHIDP 63
           ++K   +I+I+TP RL   + +      R V+Y VLDEAD+L E+G       +   +  
Sbjct: 197 MNKLRPNIVIATPGRLIDVLEKYSNKFFRFVDYKVLDEADRLLEIGFRDDLETISGIL-N 255

Query: 64  VVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVG----RKNTASESIKQKLVFA 119
              + S  +I   LFSATL D V++LA +IM+    + +      +  A E I Q +V +
Sbjct: 256 EKNSKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFLDTVDKNEPEAHERIDQSVVIS 315

Query: 120 GSEEGKLLALRQSFAES----LNPP--VLIFVQSKDRAKELYGEL---AFDDIRAGVIHS 170
                  +       +      +     +IF  +      L   L      D+     H 
Sbjct: 316 EKFA-NSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHG 374

Query: 171 DLSQTQ 176
            ++Q +
Sbjct: 375 KITQNK 380

>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 =  101 bits (253), Expect = 1e-25
 Identities = 45/186 (24%), Positives = 77/186 (41%), Gaps = 22/186 (11%)

Query: 11  LSKFSCDILISTPLRLRLAIRRKKIDLSR-VEYLVLDEADKLFEVG------NLLKHIDP 63
           ++K   +I+I+TP RL   + +      R V+Y VLDEAD+L E+G       +   +  
Sbjct: 146 MNKLRPNIVIATPGRLIDVLEKYSNKFFRFVDYKVLDEADRLLEIGFRDDLETISGIL-N 204

Query: 64  VVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVG----RKNTASESIKQKLVFA 119
              + S  +I   LFSATL D V++LA +IM+    + +      +  A E I Q +V +
Sbjct: 205 EKNSKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFLDTVDKNEPEAHERIDQSVVIS 264

Query: 120 GSEEGKLLALRQSFAES----LNPP--VLIFVQSKDRAKELYGEL---AFDDIRAGVIHS 170
                  +       +      +     +IF  +      L   L      D+     H 
Sbjct: 265 EKFA-NSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHG 323

Query: 171 DLSQTQ 176
            ++Q +
Sbjct: 324 KITQNK 329

>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 = 98.0 bits (245), Expect = 9e-25
 Identities = 43/168 (25%), Positives = 66/168 (39%), Gaps = 18/168 (10%)

Query: 16  CDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVG------NLLKHIDPVVKACS 69
             IL+ TP R+     RK  DLS     ++DEADK+           +L  + P  ++  
Sbjct: 140 VHILVGTPGRVLDLASRKVADLSDCSLFIMDEADKMLSRDFKTIIEQILSFLPPTHQSL- 198

Query: 70  NPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLAL 129
                  LFSAT P  V+E     +H    + +  + T  + I Q   F   E  KL  L
Sbjct: 199 -------LFSATFPLTVKEFMVKHLHKPYEINLMEELTL-KGITQYYAFV-EERQKLHCL 249

Query: 130 RQSFAESLNPP-VLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQ 176
              F   L     +IF  S +R + L  ++          H+ + Q +
Sbjct: 250 NTLF-SKLQINQAIIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQE 296

>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 = 93.4 bits (233), Expect = 3e-23
 Identities = 51/160 (31%), Positives = 86/160 (53%), Gaps = 8/160 (5%)

Query: 17  DILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRS 76
           +I++ TP R+   I R  ++L  V+Y +LDEAD++  +G  +K ++ ++ AC+    +  
Sbjct: 125 NIVVGTPGRILDHINRGTLNLKNVKYFILDEADEMLNMG-FIKDVEKILNACNKDKRI-L 182

Query: 77  LFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAES 136
           LFSAT+P  +  LA+  M D   +    K   + +I+Q  V   +E  +  AL +   ++
Sbjct: 183 LFSATMPREILNLAKKYMGDYSFI----KAKINANIEQSYVEV-NENERFEALCR-LLKN 236

Query: 137 LNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQ 176
                L+F ++K   KEL   L     +AG IH DLSQ+Q
Sbjct: 237 KEFYGLVFCKTKRDTKELASMLRDIGFKAGAIHGDLSQSQ 276

>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 = 91.9 bits (229), Expect = 1e-22
 Identities = 39/161 (24%), Positives = 71/161 (44%), Gaps = 5/161 (3%)

Query: 18  ILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSL 77
           I++ TP R+    R K ++L  +++ +LDE DK+ E  ++ + +  + +          +
Sbjct: 131 IVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMT-PHEKQVMM 189

Query: 78  FSATLPDFVEELARSIMHDAVRVIVGRKNTAS-ESIKQKLVFAGSEEGKLLALRQSFAES 136
           FSATL   +  + R  M D + + V  +   +   ++Q  V    +  K   L     + 
Sbjct: 190 FSATLSKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQYYVKL-KDNEKNRKLFDLL-DV 247

Query: 137 LNPP-VLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQ 176
           L    V+IFV+S  R   L   L   +  A  IH  + Q +
Sbjct: 248 LEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEE 288

>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 = 86.4 bits (215), Expect = 7e-21
 Identities = 38/162 (23%), Positives = 75/162 (46%), Gaps = 16/162 (9%)

Query: 17  DILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVR- 75
           DI+++TP RL     +  IDLS  E +++DEAD +FE+G     ID +    +  S  + 
Sbjct: 107 DIVVATPGRLLDLWSKGVIDLSSFEIVIIDEADLMFEMG----FIDDIKIILAQTSNRKI 162

Query: 76  -SLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFA 134
             LFSAT+P+ + ++ +  + +   +          +++ K V    +    +   +   
Sbjct: 163 TGLFSATIPEEIRKVVKDFITNYEEIEA---CIGLANVEHKFVHVKDDWRSKVQALRENK 219

Query: 135 ESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQ 176
           +     V++FV++++R  +L          A  +  DL Q+ 
Sbjct: 220 DKG---VIVFVRTRNRVAKLVRLF----DNAIELRGDLPQSV 254

>3iuy_A Probable ATP-dependent RNA helicase DDX53; REC-A-like, DEAD-BOX, structural genomics, structural genomi consortium, SGC, ATP-binding, hydrolase; HET: AMP; 2.40A {Homo sapiens} Length = 228

 Score = 77.6 bits (192), Expect = 3e-18
 Identities = 30/95 (31%), Positives = 47/95 (49%), Gaps = 18/95 (18%)

Query: 16  CDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVR 75
            DI+I+TP RL        ++L  + YLV+DEADK+ ++       +P ++      I+ 
Sbjct: 144 VDIIIATPGRLNDLQMNNSVNLRSITYLVIDEADKMLDME-----FEPQIR-----KILL 193

Query: 76  S--------LFSATLPDFVEELARSIMHDAVRVIV 102
                    + SAT PD V +LA S + D + V V
Sbjct: 194 DVRPDRQTVMTSATWPDTVRQLALSYLKDPMIVYV 228

>3fe2_A Probable ATP-dependent RNA helicase DDX5; DEAD, ADP, ATP-binding, hydrolase, nucleotide- RNA-binding, methylation, mRNA processing, mRNA S nucleus; HET: ADP; 2.60A {Homo sapiens} Length = 242

 Score = 77.2 bits (191), Expect = 5e-18
 Identities = 30/96 (31%), Positives = 48/96 (50%), Gaps = 18/96 (18%)

Query: 16  CDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVR 75
            +I I+TP RL   +   K +L R  YLVLDEAD++ ++G      +P ++      IV 
Sbjct: 153 VEICIATPGRLIDFLECGKTNLRRTTYLVLDEADRMLDMG-----FEPQIR-----KIVD 202

Query: 76  S--------LFSATLPDFVEELARSIMHDAVRVIVG 103
                    ++SAT P  V +LA   + D + + +G
Sbjct: 203 QIRPDRQTLMWSATWPKEVRQLAEDFLKDYIHINIG 238

>3ber_A Probable ATP-dependent RNA helicase DDX47; DEAD, AMP, structural genomics, structural GEN consortium, SGC, ATP-binding, hydrolase; HET: AMP PGE; 1.40A {Homo sapiens} Length = 249

 Score = 73.1 bits (180), Expect = 2e-16
 Identities = 28/88 (31%), Positives = 50/88 (56%), Gaps = 5/88 (5%)

Query: 17  DILISTPLRLRLAIRRKK-IDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVR 75
            I+I+TP RL   +   K  +L  ++YLV+DEAD++  +      +D ++K    P   +
Sbjct: 163 HIIIATPGRLIDHLENTKGFNLRALKYLVMDEADRILNMD-FETEVDKILKVI--PRDRK 219

Query: 76  S-LFSATLPDFVEELARSIMHDAVRVIV 102
           + LFSAT+   V++L R+ + + V+  V
Sbjct: 220 TFLFSATMTKKVQKLQRAALKNPVKCAV 247

>2gxq_A Heat resistant RNA dependent ATPase; RNA helicase, atomic resolution, AMP complex, ribosome biogenesis, thermophilic, hydrolase; HET: AMP; 1.20A {Thermus thermophilus HB27} PDB: 2gxs_A* 2gxu_A 3mwj_A 3mwk_A* 3mwl_A* 3nbf_A* 3nej_A Length = 207

 Score = 69.9 bits (172), Expect = 2e-15
 Identities = 33/90 (36%), Positives = 48/90 (53%), Gaps = 6/90 (6%)

Query: 17  DILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVR- 75
           D +++TP R    +R+  +DLSRVE  VLDEAD++  +G      + V    S     R 
Sbjct: 122 DAVVATPGRALDYLRQGVLDLSRVEVAVLDEADEMLSMG----FEEEVEALLSATPPSRQ 177

Query: 76  -SLFSATLPDFVEELARSIMHDAVRVIVGR 104
             LFSATLP + + LA   M + V + V +
Sbjct: 178 TLLFSATLPSWAKRLAERYMKNPVLINVIK 207

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens} Length = 236

 Score = 69.2 bits (170), Expect = 5e-15
 Identities = 28/92 (30%), Positives = 48/92 (52%), Gaps = 5/92 (5%)

Query: 16  CDILISTPLRLRLAIRRKK-IDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIV 74
            +IL+ TP RL   +        + ++ LVLDEAD++ ++G     ++ V++    P   
Sbjct: 147 INILVCTPGRLLQHMDETVSFHATDLQMLVLDEADRILDMG-FADTMNAVIENL--PKKR 203

Query: 75  RS-LFSATLPDFVEELARSIMHDAVRVIVGRK 105
           ++ LFSAT    V++LAR  + +   V V  K
Sbjct: 204 QTLLFSATQTKSVKDLARLSLKNPEYVWVHEK 235

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19 Length = 219

 Score = 68.7 bits (169), Expect = 7e-15
 Identities = 24/90 (26%), Positives = 45/90 (50%), Gaps = 2/90 (2%)

Query: 17  DILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRS 76
            I+I TP R+   IR + +D+     LV+DEAD + ++G  +  +D +        +   
Sbjct: 128 HIVIGTPGRINDFIREQALDVHTAHILVVDEADLMLDMG-FITDVDQIAARM-PKDLQML 185

Query: 77  LFSATLPDFVEELARSIMHDAVRVIVGRKN 106
           +FSAT+P+ ++   +  M +   V V   +
Sbjct: 186 VFSATIPEKLKPFLKKYMENPTFVHVLEHH 215

>2oxc_A Probable ATP-dependent RNA helicase DDX20; DEAD, structural genomics, structural genomics consortium, SGC, hydrolase; HET: ADP; 1.30A {Homo sapiens} PDB: 3b7g_A* Length = 230

 Score = 67.6 bits (166), Expect = 2e-14
 Identities = 24/87 (27%), Positives = 40/87 (45%), Gaps = 1/87 (1%)

Query: 16  CDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVR 75
           C I + +P R++  I    ++   +   +LDEADKL E G+  + I+ +  +    S   
Sbjct: 143 CHIAVGSPGRIKQLIELDYLNPGSIRLFILDEADKLLEEGSFQEQINWIYSSL-PASKQM 201

Query: 76  SLFSATLPDFVEELARSIMHDAVRVIV 102
              SAT P+F+       M D   V +
Sbjct: 202 LAVSATYPEFLANALTKYMRDPTFVRL 228

>1t6n_A Probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA processing protein; HET: FLC; 1.94A {Homo sapiens} SCOP: c.37.1.19 Length = 220

 Score = 65.7 bits (161), Expect = 7e-14
 Identities = 25/92 (27%), Positives = 47/92 (51%), Gaps = 1/92 (1%)

Query: 11  LSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSN 70
           L K    I++ TP R+    R K ++L  +++ +LDE DK+ E  ++ + +  + +   +
Sbjct: 130 LKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPH 189

Query: 71  PSIVRSLFSATLPDFVEELARSIMHDAVRVIV 102
              V  +FSATL   +  + R  M D + + V
Sbjct: 190 EKQV-MMFSATLSKEIRPVCRKFMQDPMEIFV 220

>3bor_A Human initiation factor 4A-II; translation initiation, DEAD BOX, structural genomics, helic binding, HOST-virus interaction, hydrolase; 1.85A {Homo sapiens} PDB: 2g9n_A* Length = 237

 Score = 65.7 bits (161), Expect = 1e-13
 Identities = 27/101 (26%), Positives = 49/101 (48%), Gaps = 14/101 (13%)

Query: 11  LSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVG------NLLKHIDPV 64
           L   +  I++ TP R+   + R+ +    ++  VLDEAD++   G       + + +   
Sbjct: 145 LQAEAPHIVVGTPGRVFDMLNRRYLSPKWIKMFVLDEADEMLSRGFKDQIYEIFQKL--- 201

Query: 65  VKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRK 105
                N SI   L SAT+P  V E+ +  M D +R++V ++
Sbjct: 202 -----NTSIQVVLLSATMPTDVLEVTKKFMRDPIRILVKKE 237

>1qde_A EIF4A, translation initiation factor 4A; DEAD box protein family, gene regulation; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 1qva_A Length = 224

 Score = 64.5 bits (158), Expect = 3e-13
 Identities = 24/96 (25%), Positives = 46/96 (47%), Gaps = 14/96 (14%)

Query: 16  CDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVG------NLLKHIDPVVKACS 69
             I++ TP R+   I+R++    +++  +LDEAD++   G       +   +        
Sbjct: 132 AQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSGFKEQIYQIFTLL-------- 183

Query: 70  NPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRK 105
            P+    L SAT+P+ V E+    M + VR++V + 
Sbjct: 184 PPTTQVVLLSATMPNDVLEVTTKFMRNPVRILVKKD 219

>3fmo_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 2.51A {Homo sapiens} Length = 300

 Score = 64.7 bits (158), Expect = 5e-13
 Identities = 24/89 (26%), Positives = 40/89 (44%), Gaps = 2/89 (2%)

Query: 18  ILISTPLR-LRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRS 76
           I+I TP   L    + K ID  +++  VLDEAD +             ++     +    
Sbjct: 213 IVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSI-RIQRMLPRNCQML 271

Query: 77  LFSATLPDFVEELARSIMHDAVRVIVGRK 105
           LFSAT  D V + A+ ++ D   + + R+
Sbjct: 272 LFSATFEDSVWKFAQKVVPDPNVIKLKRE 300

>1vec_A ATP-dependent RNA helicase P54; DEAD-box protein, RNA binding protein; HET: TLA; 2.01A {Homo sapiens} SCOP: c.37.1.19 Length = 206

 Score = 61.0 bits (149), Expect = 3e-12
 Identities = 21/84 (25%), Positives = 42/84 (50%), Gaps = 2/84 (2%)

Query: 17  DILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRS 76
            ++I+TP R+   I++    +  V+ +VLDEADKL      ++ ++ ++      +    
Sbjct: 124 HVVIATPGRILDLIKKGVAKVDHVQMIVLDEADKLLSQD-FVQIMEDIILTL-PKNRQIL 181

Query: 77  LFSATLPDFVEELARSIMHDAVRV 100
           L+SAT P  V++   S +     +
Sbjct: 182 LYSATFPLSVQKFMNSHLEKPYEI 205

>3ly5_A ATP-dependent RNA helicase DDX18; alpha-beta, structural genomics, structural genomics consort ATP-binding, hydrolase, nucleotide-binding, RNA-B; 2.80A {Homo sapiens} Length = 262

 Score = 60.4 bits (147), Expect = 1e-11
 Identities = 27/88 (30%), Positives = 50/88 (56%), Gaps = 6/88 (6%)

Query: 16  CDILISTPLRLRLAIRRKK-IDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIV 74
            +I+++TP RL   ++         ++ LV+DEAD++ +VG   + +  ++K    P+  
Sbjct: 177 INIIVATPGRLLDHMQNTPGFMYKNLQCLVIDEADRILDVG-FEEELKQIIKLL--PTRR 233

Query: 75  RS-LFSATLPDFVEELAR-SIMHDAVRV 100
           ++ LFSAT    VE+LAR S+  + + V
Sbjct: 234 QTMLFSATQTRKVEDLARISLKKEPLYV 261

>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 = 52.2 bits (126), Expect = 4e-09
 Identities = 22/84 (26%), Positives = 33/84 (39%), Gaps = 4/84 (4%)

Query: 95  HDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPP--VLIFVQSKDRAK 152
           H      +  + + SE+I QK+V+   E  K   L      +       L+FV++K  A 
Sbjct: 3   HHHHHENLYFQGSTSENITQKVVWV-EESDKRSFLLD-LLNATGKDSLTLVFVETKKGAD 60

Query: 153 ELYGELAFDDIRAGVIHSDLSQTQ 176
            L   L  +      IH D SQ  
Sbjct: 61  SLEDFLYHEGYACTSIHGDRSQRD 84

>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; 2.60A {Homo sapiens} Length = 191

 Score = 52.2 bits (126), Expect = 5e-09
 Identities = 19/79 (24%), Positives = 33/79 (41%), Gaps = 2/79 (2%)

Query: 98  VRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGE 157
             +       AS  + Q++ +   EE K++ L +   +   PPVLIF + K     ++  
Sbjct: 16  ENLYFQSMGAASLDVIQEVEYV-KEEAKMVYLLE-CLQKTPPPVLIFAEKKADVDAIHEY 73

Query: 158 LAFDDIRAGVIHSDLSQTQ 176
           L    + A  IH    Q +
Sbjct: 74  LLLKGVEAVAIHGGKDQEE 92

>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 = 46.8 bits (112), Expect = 4e-07
 Identities = 14/67 (20%), Positives = 25/67 (37%)

Query: 110 ESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIH 169
           + I Q    A   E K   L     +      ++FV+ ++R  EL   L    I    + 
Sbjct: 2   KKIHQWYYRADDLEHKTALLVHLLKQPEATRSIVFVRKRERVHELANWLREAGINNCYLE 61

Query: 170 SDLSQTQ 176
            ++ Q +
Sbjct: 62  GEMVQGK 68

>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein, translation; 1.75A {Saccharomyces cerevisiae} SCOP: c.37.1.19 Length = 165

 Score = 44.9 bits (107), Expect = 2e-06
 Identities = 21/68 (30%), Positives = 33/68 (48%), Gaps = 2/68 (2%)

Query: 110 ESIKQKLVFAGSEEGKLLALRQSFAESLNPP-VLIFVQSKDRAKELYGELAFDDIRAGVI 168
           E IKQ  V    EE K   L   + +S++    +IF  ++ + +EL  +L  D      I
Sbjct: 2   EGIKQFYVNVEEEEYKYECLTDLY-DSISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAI 60

Query: 169 HSDLSQTQ 176
           +SDL Q +
Sbjct: 61  YSDLPQQE 68

>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 = 44.5 bits (106), Expect = 2e-06
 Identities = 17/68 (25%), Positives = 31/68 (45%), Gaps = 2/68 (2%)

Query: 110 ESIKQKLVFAGSEEGKLLALRQSFAESLNPP-VLIFVQSKDRAKELYGELAFDDIRAGVI 168
            +I+Q  V     + K  AL   +  S+     +IF Q++  AK L  E+  D  +  ++
Sbjct: 6   NNIRQYYVLCEHRKDKYQALCNIY-GSITIGQAIIFCQTRRNAKWLTVEMIQDGHQVSLL 64

Query: 169 HSDLSQTQ 176
             +L+  Q
Sbjct: 65  SGELTVEQ 72

>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 = 46.0 bits (108), Expect = 2e-06
 Identities = 32/184 (17%), Positives = 57/184 (30%), Gaps = 65/184 (35%)

Query: 3   KELVRSTDLSKFSCDILISTPLRLR------LAIRRKKIDLSRVEY-LVLDEADKLFEVG 55
            +   + +    SC IL++T  R +       A     I L      L  DE   L    
Sbjct: 256 AKAWNAFN---LSCKILLTT--RFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLL--- 307

Query: 56  NLLKHID------PVVKACS-NPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTA 108
             LK++D      P  +  + NP  + S+ + ++ D    LA               N  
Sbjct: 308 --LKYLDCRPQDLP-REVLTTNPRRL-SIIAESIRDG---LATW------------DNWK 348

Query: 109 SESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELA-FDD---IR 164
             +             KL  + +S    L P            ++++  L+ F     I 
Sbjct: 349 HVNCD-----------KLTTIIESSLNVLEPAEY---------RKMFDRLSVFPPSAHIP 388

Query: 165 AGVI 168
             ++
Sbjct: 389 TILL 392

>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase; 1.95A {Bacillus subtilis} Length = 163

 Score = 43.7 bits (104), Expect = 4e-06
 Identities = 16/73 (21%), Positives = 29/73 (39%), Gaps = 3/73 (4%)

Query: 105 KNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPP-VLIFVQSKDRAKELYGELAFDDI 163
               + +I+  ++    EE K   L+     + NP   +IF ++K+   +L  EL     
Sbjct: 3   AGLTTRNIEHAVIQV-REENKFSLLKD-VLMTENPDSCIIFCRTKEHVNQLTDELDDLGY 60

Query: 164 RAGVIHSDLSQTQ 176
               IH  + Q  
Sbjct: 61  PCDKIHGGMIQED 73

>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 = 39.5 bits (93), Expect = 2e-04
 Identities = 17/68 (25%), Positives = 26/68 (38%), Gaps = 3/68 (4%)

Query: 110 ESIKQKLVFAGSEEGKLLALRQSFAESLNPP-VLIFVQSKDRAKELYGELAFDDIRAGVI 168
             ++Q  V    +  K   L     + L    V+IFV+S  R   L   L   +  A  I
Sbjct: 4   HGLQQYYVKL-KDNEKNRKLFDLL-DVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAI 61

Query: 169 HSDLSQTQ 176
           H  + Q +
Sbjct: 62  HRGMPQEE 69

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	178
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	99.97
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	99.96
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	99.95
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	99.95
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	99.94
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	99.94
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	99.93
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	99.93
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	99.93
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	99.93
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	99.92
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	99.92
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	99.92
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	99.91
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	99.88
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	99.88
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	99.86
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	99.86
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	99.84
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	99.84
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	99.83
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	99.82
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	99.82
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	99.82
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	99.8
1tf5_A	844	Preprotein translocase SECA subunit; ATPase, helic	99.8
2fsf_A	853	Preprotein translocase SECA subunit; ATPase, DNA-R	99.79
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	99.79
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	99.78
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	99.78
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	99.78
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	99.78
3bor_A	237	Human initiation factor 4A-II; translation initiat	99.78
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	99.77
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	99.77
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	99.77
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	99.77
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	99.76
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	99.76
1nkt_A	922	Preprotein translocase SECA 1 subunit; preprotein	99.75
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	99.75
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	99.75
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	99.74
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	99.74
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	99.74
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	99.74
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	99.73
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	99.72
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	99.7
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	99.7
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	99.69
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	99.67
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	99.66
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.66
4gl2_A	699	Interferon-induced helicase C domain-containing P;	99.65
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.64
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	99.58
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	99.55
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	99.54
1yks_A	440	Genome polyprotein [contains: flavivirin protease	99.52
3h1t_A	590	Type I site-specific restriction-modification syst	99.52
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	99.5
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	99.47
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	99.47
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	99.44
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	99.43
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	99.42
3rc3_A	677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	99.42
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	99.41
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	99.35
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	99.31
1z63_A	500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	99.3
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	99.27
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	99.26
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	99.2
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	99.18
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	99.18
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	99.14
2w00_A	1038	HSDR, R.ECOR124I; ATP-binding, DNA-binding, restri	99.09
3b6e_A	216	Interferon-induced helicase C domain-containing P;	99.05
2yjt_D	170	ATP-dependent RNA helicase SRMB, regulator of ribo	98.47
3mwy_W	800	Chromo domain-containing protein 1; SWI2/SNF2 ATPa	98.92
1z3i_X	644	Similar to RAD54-like; recombination ATPase helica	98.91
3i32_A	300	Heat resistant RNA dependent ATPase; RNA helicase,	98.88
3eaq_A	212	Heat resistant RNA dependent ATPase; DEAD box RNA	98.83
1rif_A	282	DAR protein, DNA helicase UVSW; bacteriophage, REC	98.74
2ipc_A	997	Preprotein translocase SECA subunit; nucleotide bi	98.63
3jux_A	822	Protein translocase subunit SECA; protein transloc	98.55
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	98.34
1z5z_A	271	Helicase of the SNF2/RAD54 family; hydrolase, reco	97.98
3crv_A	551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	97.21
2vl7_A	540	XPD; helicase, unknown function; 2.25A {Sulfolobus	96.13
3gk5_A	108	Uncharacterized rhodanese-related protein TVG08686	95.02
1wv9_A	94	Rhodanese homolog TT1651; CDC25, phosphatase, sulf	94.87
3foj_A	100	Uncharacterized protein; protein SSP1007, structur	94.68
3eme_A	103	Rhodanese-like domain protein; alpha-beta-alpha sa	94.55
3iwh_A	103	Rhodanese-like domain protein; alpha-beta-alpha sa	94.51
2k0z_A	110	Uncharacterized protein HP1203; A/B domain, struct	93.89
3hix_A	106	ALR3790 protein; rhodanese, rhodanese_3, Q8YQN0, Q	93.72
2fsx_A	148	RV0390, COG0607: rhodanese-related sulfurtransfera	93.33
1tq1_A	129	AT5G66040, senescence-associated family protein; C	93.07
3g5j_A	134	Putative ATP/GTP binding protein; N-terminal domai	92.98
1gmx_A	108	GLPE protein; transferase, rhodanese, sulfurtransf	92.91
1qxn_A	137	SUD, sulfide dehydrogenase; polysulfide-sulfur tra	92.8
3nhv_A	144	BH2092 protein; alpha-beta protein, structural gen	92.79
3flh_A	124	Uncharacterized protein LP_1913; alpha-beta protei	92.66
2jtq_A	85	Phage shock protein E; solution structure rhodanes	92.55
3d1p_A	139	Putative thiosulfate sulfurtransferase YOR285W; at	91.89
2hhg_A	139	Hypothetical protein RPA3614; MCSG, structural gen	91.73
3ilm_A	141	ALR3790 protein; rhodanese-like, NSR437H, NESG, st	91.3
1vee_A	134	Proline-rich protein family; hypothetical protein,	90.27
4f67_A	265	UPF0176 protein LPG2838; structural genomics, PSI-	90.13
3tg1_B	158	Dual specificity protein phosphatase 10; kinase/rh	89.93
1urh_A	280	3-mercaptopyruvate sulfurtransferase; rhodanese; 2	88.82
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	87.43
2ouc_A	142	Dual specificity protein phosphatase 10; rhodanese	86.51
1w36_D	608	RECD, exodeoxyribonuclease V alpha chain; recombin	85.83
1uar_A	285	Rhodanese; sulfurtransferase, riken structural gen	85.73
3hgt_A	328	HDA1 complex subunit 3; RECA-like domain, SWI2/SNF	85.25
1urh_A	280	3-mercaptopyruvate sulfurtransferase; rhodanese; 2	84.61
1e0c_A	271	Rhodanese, sulfurtransferase; sulfur metabolism, t	84.15
1rhs_A	296	Sulfur-substituted rhodanese; transferase, sulfurt	83.87
2eg4_A	230	Probable thiosulfate sulfurtransferase; structural	83.48
1e0c_A	271	Rhodanese, sulfurtransferase; sulfur metabolism, t	82.89
3aay_A	277	Putative thiosulfate sulfurtransferase; sulfurtran	82.66
3crv_A	551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	82.33
3aay_A	277	Putative thiosulfate sulfurtransferase; sulfurtran	81.45
2chg_A	226	Replication factor C small subunit; DNA-binding pr	81.41
2j6p_A	152	SB(V)-AS(V) reductase; arsenate reductase, antimon	80.84
3hzu_A	318	Thiosulfate sulfurtransferase SSEA; niaid, ssgcid,	80.62
3i2v_A	127	Adenylyltransferase and sulfurtransferase MOCS3; r	80.33

>2db3_A ATP-dependent RNA helicase VASA; DEAD-BOX, protein-RNA complex, ATPase, riken structural genomics/proteomics initiative, RSGI; HET: ANP; 2.20A {Drosophila melanogaster}

Probab=99.97  E-value=6.6e-30  Score=205.02  Aligned_cols=169  Identities=25%  Similarity=0.372  Sum_probs=152.6

Q ss_pred             HHhHHhccCCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhC-CCCCceEEEEeecCcH
Q 030396            6 VRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKAC-SNPSIVRSLFSATLPD   84 (178)
Q Consensus         6 ~~q~~~l~~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~-~~~~~q~i~~SAT~~~   84 (178)
                      ..|.+.+.++++|+|+|||+|.+++.++..++++++++|+||||.+++++ |.+.+..|+..+ .+..+|+++||||+|+
T Consensus       170 ~~~~~~l~~~~~Ivv~Tp~~l~~~l~~~~~~l~~~~~lVlDEah~~~~~g-f~~~~~~i~~~~~~~~~~q~l~~SAT~~~  248 (434)
T 2db3_A          170 RHQNECITRGCHVVIATPGRLLDFVDRTFITFEDTRFVVLDEADRMLDMG-FSEDMRRIMTHVTMRPEHQTLMFSATFPE  248 (434)
T ss_dssp             HHHHHHHTTCCSEEEECHHHHHHHHHTTSCCCTTCCEEEEETHHHHTSTT-THHHHHHHHHCTTSCSSCEEEEEESCCCH
T ss_pred             HHHHHHhhcCCCEEEEChHHHHHHHHhCCcccccCCeEEEccHhhhhccC-cHHHHHHHHHhcCCCCCceEEEEeccCCH
Confidence            45666777899999999999999999998899999999999999999999 999999999984 3578999999999999


Q ss_pred             HHHHHHHHhccCcEEEEEcCCccccCCceEEEEEcCChhhHHHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhhhCCCc
Q 030396           85 FVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDIR  164 (178)
Q Consensus        85 ~~~~~~~~~~~~~~~v~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~~~g~~  164 (178)
                      .+..++..++.++..+.+........++.+.++.+ ....|...+.+++.... .++||||+|++.|+.+++.|.+.|++
T Consensus       249 ~~~~~~~~~l~~~~~i~~~~~~~~~~~i~~~~~~~-~~~~k~~~l~~~l~~~~-~~~lVF~~t~~~a~~l~~~L~~~~~~  326 (434)
T 2db3_A          249 EIQRMAGEFLKNYVFVAIGIVGGACSDVKQTIYEV-NKYAKRSKLIEILSEQA-DGTIVFVETKRGADFLASFLSEKEFP  326 (434)
T ss_dssp             HHHHHHHTTCSSCEEEEESSTTCCCTTEEEEEEEC-CGGGHHHHHHHHHHHCC-TTEEEECSSHHHHHHHHHHHHHTTCC
T ss_pred             HHHHHHHHhccCCEEEEeccccccccccceEEEEe-CcHHHHHHHHHHHHhCC-CCEEEEEeCcHHHHHHHHHHHhCCCC
Confidence            99999999999999999988777788888888766 55668899999998874 45999999999999999999999999


Q ss_pred             eEeeecCCCcccc
Q 030396          165 AGVIHSDLSQTQV  177 (178)
Q Consensus       165 ~~~lh~~~~~~~R  177 (178)
                      +..+||+|++.+|
T Consensus       327 ~~~lhg~~~~~~R  339 (434)
T 2db3_A          327 TTSIHGDRLQSQR  339 (434)
T ss_dssp             EEEESTTSCHHHH
T ss_pred             EEEEeCCCCHHHH
Confidence            9999999999887

>2j0s_A ATP-dependent RNA helicase DDX48; mRNA processing, phosphorylation, rRNA processing, mRNA splicing, mRNA transport; HET: ANP; 2.21A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 2j0q_A* 2hyi_C* 3ex7_C* 2xb2_A* 2hxy_A 2j0u_A 2j0u_B 2zu6_A

Probab=99.96  E-value=1.4e-28  Score=195.21  Aligned_cols=170  Identities=26%  Similarity=0.362  Sum_probs=155.3

Q ss_pred             HHhHHhccCCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcHH
Q 030396            6 VRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDF   85 (178)
Q Consensus         6 ~~q~~~l~~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~   85 (178)
                      ..+.+.+..+++|+|+|||++.+++..+.+.+.+++++|+||||.+.+++ +...+..+++. ++...|++++|||+++.
T Consensus       146 ~~~~~~~~~~~~ivv~Tp~~l~~~l~~~~~~~~~~~~vViDEah~~~~~~-~~~~~~~i~~~-~~~~~~~i~~SAT~~~~  223 (410)
T 2j0s_A          146 GEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKG-FKEQIYDVYRY-LPPATQVVLISATLPHE  223 (410)
T ss_dssp             HHHHHHHHHCCSEEEECHHHHHHHHHTTSSCCTTCCEEEEETHHHHTSTT-THHHHHHHHTT-SCTTCEEEEEESCCCHH
T ss_pred             HHHHHHhhcCCCEEEcCHHHHHHHHHhCCccHhheeEEEEccHHHHHhhh-hHHHHHHHHHh-CccCceEEEEEcCCCHH
Confidence            34555666789999999999999999988889999999999999999998 99999999998 88899999999999999


Q ss_pred             HHHHHHHhccCcEEEEEcCCccccCCceEEEEEcCChhhHHHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhhhCCCce
Q 030396           86 VEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDIRA  165 (178)
Q Consensus        86 ~~~~~~~~~~~~~~v~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~~~g~~~  165 (178)
                      +.++...++.+|..+..........++.+.+..+.....|...+.++++.....++||||+|++.++.+++.|.+.|+++
T Consensus       224 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~~~~~~~~~~lVf~~~~~~~~~l~~~L~~~~~~~  303 (410)
T 2j0s_A          224 ILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREANFTV  303 (410)
T ss_dssp             HHTTGGGTCSSCEEECCCGGGCSCTTEEEEEEEESSTTHHHHHHHHHHHHHTSSEEEEECSSHHHHHHHHHHHHHTTCCC
T ss_pred             HHHHHHHHcCCCEEEEecCccccCCCceEEEEEeCcHHhHHHHHHHHHHhcCCCcEEEEEcCHHHHHHHHHHHHhCCCce
Confidence            99988999999998888777778888999998887777799999999998878899999999999999999999999999


Q ss_pred             EeeecCCCcccc
Q 030396          166 GVIHSDLSQTQV  177 (178)
Q Consensus       166 ~~lh~~~~~~~R  177 (178)
                      ..+||+|++++|
T Consensus       304 ~~~h~~~~~~~r  315 (410)
T 2j0s_A          304 SSMHGDMPQKER  315 (410)
T ss_dssp             EEECTTSCHHHH
T ss_pred             EEeeCCCCHHHH
Confidence            999999999876

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens}

Probab=99.95  E-value=3.3e-27  Score=187.48  Aligned_cols=170  Identities=31%  Similarity=0.422  Sum_probs=147.0

Q ss_pred             HHhHHhccCCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhC-CC--CCceEEEEeecC
Q 030396            6 VRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKAC-SN--PSIVRSLFSATL   82 (178)
Q Consensus         6 ~~q~~~l~~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~-~~--~~~q~i~~SAT~   82 (178)
                      .++.+.+.++++|+|+|||++.+++..+.+.+.+++++|+||||.+++++ |.+.+..++... .+  ...|++++|||+
T Consensus       142 ~~~~~~~~~~~~I~v~Tp~~l~~~l~~~~~~~~~~~~iViDEah~~~~~~-~~~~~~~i~~~~~~~~~~~~~~i~~SAT~  220 (417)
T 2i4i_A          142 GQQIRDLERGCHLLVATPGRLVDMMERGKIGLDFCKYLVLDEADRMLDMG-FEPQIRRIVEQDTMPPKGVRHTMMFSATF  220 (417)
T ss_dssp             HHHHHHHTTCCSEEEECHHHHHHHHHTTSBCCTTCCEEEESSHHHHHHTT-CHHHHHHHHTSSSCCCBTTBEEEEEESCC
T ss_pred             HHHHHHhhCCCCEEEEChHHHHHHHHcCCcChhhCcEEEEEChhHhhccC-cHHHHHHHHHhccCCCcCCcEEEEEEEeC
Confidence            34556667789999999999999999988889999999999999999999 999999999852 22  368999999999


Q ss_pred             cHHHHHHHHHhccCcEEEEEcCCccccCCceEEEEEcCChhhHHHHHHHHHHhc-CCCCEEEEeCCchHHHHHHHHhhhC
Q 030396           83 PDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAES-LNPPVLIFVQSKDRAKELYGELAFD  161 (178)
Q Consensus        83 ~~~~~~~~~~~~~~~~~v~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~-~~~~~lIF~~t~~~~~~l~~~L~~~  161 (178)
                      ++.+..+...++.+|..+..........++.+.++.+ ....|...+.++++.. ...++||||+|++.|+.+++.|.+.
T Consensus       221 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~-~~~~~~~~l~~~l~~~~~~~~~lVf~~~~~~~~~l~~~L~~~  299 (417)
T 2i4i_A          221 PKEIQMLARDFLDEYIFLAVGRVGSTSENITQKVVWV-EESDKRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHE  299 (417)
T ss_dssp             CHHHHHHHHHHCSSCEEEEEC----CCSSEEEEEEEC-CGGGHHHHHHHHHHTCCTTCEEEEECSSHHHHHHHHHHHHHT
T ss_pred             CHHHHHHHHHHcCCCEEEEeCCCCCCccCceEEEEEe-ccHhHHHHHHHHHHhcCCCCeEEEEECCHHHHHHHHHHHHHC
Confidence            9999999999999999888887777788888888766 5567889999999876 4678999999999999999999999


Q ss_pred             CCceEeeecCCCcccc
Q 030396          162 DIRAGVIHSDLSQTQV  177 (178)
Q Consensus       162 g~~~~~lh~~~~~~~R  177 (178)
                      |+.+..+||+|++++|
T Consensus       300 ~~~~~~~h~~~~~~~r  315 (417)
T 2i4i_A          300 GYACTSIHGDRSQRDR  315 (417)
T ss_dssp             TCCEEEECTTSCHHHH
T ss_pred             CCCeeEecCCCCHHHH
Confidence            9999999999999877

>3eiq_A Eukaryotic initiation factor 4A-I; PDCD4, anti-oncogene, apoptosis, cell cycle, nucleus, phosph RNA-binding, ATP-binding, helicase, hydrolase; 3.50A {Homo sapiens}

Probab=99.95  E-value=2.3e-27  Score=188.07  Aligned_cols=162  Identities=25%  Similarity=0.374  Sum_probs=149.2

Q ss_pred             CCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcHHHHHHHHHh
Q 030396           14 FSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSI   93 (178)
Q Consensus        14 ~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~~~~~~~~~   93 (178)
                      ++++|+|+|||++.+++..+.+.+.+++++|+||||.+.+++ +...+..++.. ++.+.|++++|||+++.+......+
T Consensus       158 ~~~~iiv~T~~~l~~~l~~~~~~~~~~~~vViDEah~~~~~~-~~~~~~~~~~~-~~~~~~~i~~SAT~~~~~~~~~~~~  235 (414)
T 3eiq_A          158 EAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRG-FKDQIYDIFQK-LNSNTQVVLLSATMPSDVLEVTKKF  235 (414)
T ss_dssp             TCCSEEEECHHHHHHHHHHTSSCSTTCCEEEECSHHHHHHTT-THHHHHHHHTT-SCTTCEEEEECSCCCHHHHHHHTTT
T ss_pred             CCCCEEEECHHHHHHHHHcCCcccccCcEEEEECHHHhhccC-cHHHHHHHHHh-CCCCCeEEEEEEecCHHHHHHHHHH
Confidence            679999999999999999988889999999999999999988 99999999999 7889999999999999999999999


Q ss_pred             ccCcEEEEEcCCccccCCceEEEEEcCChhhHHHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhhhCCCceEeeecCCC
Q 030396           94 MHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLS  173 (178)
Q Consensus        94 ~~~~~~v~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~~~  173 (178)
                      +.+|..+...........+.+.+..+.....|...+.++++....+++||||++++.++.+++.|.+.|+.+..+||+|+
T Consensus       236 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~lvf~~~~~~~~~l~~~l~~~~~~~~~~h~~~~  315 (414)
T 3eiq_A          236 MRDPIRILVKKEELTLEGIRQFYINVEREEWKLDTLCDLYETLTITQAVIFINTRRKVDWLTEKMHARDFTVSAMHGDMD  315 (414)
T ss_dssp             CSSCEEECCCCCCCCTTSCCEEEEECSSSTTHHHHHHHHHHSSCCSSCEEECSCHHHHHHHHHHHHTTTCCCEEC---CH
T ss_pred             cCCCEEEEecCCccCCCCceEEEEEeChHHhHHHHHHHHHHhCCCCcEEEEeCCHHHHHHHHHHHHhcCCeEEEecCCCC
Confidence            99999988888888888899999888888889999999999988899999999999999999999999999999999999


Q ss_pred             cccc
Q 030396          174 QTQV  177 (178)
Q Consensus       174 ~~~R  177 (178)
                      +++|
T Consensus       316 ~~~r  319 (414)
T 3eiq_A          316 QKER  319 (414)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            8876

>3fht_A ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box helicase, RNA dependent ATPase, mRNA export, nucleocytoplasmic transport, NUP214, CAN; HET: ANP; 2.20A {Homo sapiens} PDB: 3ews_A* 3g0h_A* 3fhc_B

Probab=99.94  E-value=2.8e-26  Score=181.63  Aligned_cols=163  Identities=24%  Similarity=0.286  Sum_probs=149.3

Q ss_pred             CCCcEEEeCcHHHHHHHHc-CCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcHHHHHHHHH
Q 030396           14 FSCDILISTPLRLRLAIRR-KKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARS   92 (178)
Q Consensus        14 ~~~~Iii~TP~~l~~~l~~-~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~~~~~~~~   92 (178)
                      .+++|+|+||+++.+++.+ +.+++.+++++|+||||.+++...+...+..+.+. .+.+.|++++|||+++.+......
T Consensus       142 ~~~~ivv~T~~~l~~~~~~~~~~~~~~~~~iViDEah~~~~~~~~~~~~~~~~~~-~~~~~~~i~~SAT~~~~~~~~~~~  220 (412)
T 3fht_A          142 ISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRM-LPRNCQMLLFSATFEDSVWKFAQK  220 (412)
T ss_dssp             CCCSEEEECHHHHHHHHTTSCSSCGGGCCEEEEETHHHHHSTTTTHHHHHHHHHT-SCTTCEEEEEESCCCHHHHHHHHH
T ss_pred             CCCCEEEECchHHHHHHHhcCCcChhhCcEEEEeCHHHHhhcCCcHHHHHHHHhh-CCCCceEEEEEeecCHHHHHHHHH
Confidence            4579999999999999965 67788999999999999998843388899999988 888999999999999999999999


Q ss_pred             hccCcEEEEEcCCccccCCceEEEEEcCChhhHHHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhhhCCCceEeeecCC
Q 030396           93 IMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDL  172 (178)
Q Consensus        93 ~~~~~~~v~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~~  172 (178)
                      ++.+|..+...........+.+.++.+.....+...+.+++.....+++||||+|++.|+.++..|.+.|+.+..+||+|
T Consensus       221 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~lvf~~~~~~~~~l~~~L~~~~~~~~~~~~~~  300 (412)
T 3fht_A          221 VVPDPNVIKLKREEETLDTIKQYYVLCSSRDEKFQALCNLYGAITIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEM  300 (412)
T ss_dssp             HSSSCEEECCCGGGSSCTTEEEEEEECSSHHHHHHHHHHHHHHHSSSEEEEECSSHHHHHHHHHHHHHTTCCCEEECTTS
T ss_pred             hcCCCeEEeeccccccccCceEEEEEcCChHHHHHHHHHHHhhcCCCCEEEEeCCHHHHHHHHHHHHhCCCeEEEecCCC
Confidence            99999999888888888889999988888889999999999988889999999999999999999999999999999999


Q ss_pred             Ccccc
Q 030396          173 SQTQV  177 (178)
Q Consensus       173 ~~~~R  177 (178)
                      ++++|
T Consensus       301 ~~~~r  305 (412)
T 3fht_A          301 MVEQR  305 (412)
T ss_dssp             CHHHH
T ss_pred             CHHHH
Confidence            99887

>3pey_A ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, ATPase, helicase, mRNA-export, nuclear pore, hydrolase-RNA complex; HET: ADP; 1.40A {Saccharomyces cerevisiae} PDB: 3pew_A* 3pex_A* 3pez_A* 3rrm_A* 3rrn_A* 2kbe_A 3gfp_A 2kbf_A 3pev_A* 3peu_A*

Probab=99.94  E-value=1.1e-25  Score=177.08  Aligned_cols=163  Identities=26%  Similarity=0.367  Sum_probs=149.4

Q ss_pred             CCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcHHHHHHHHHh
Q 030396           14 FSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSI   93 (178)
Q Consensus        14 ~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~~~~~~~~~   93 (178)
                      .+++|+|+||+++.+.+..+...+.+++++|+||||.+.+...+...+..+.+. .+...|++++|||+++.+......+
T Consensus       120 ~~~~iiv~T~~~l~~~~~~~~~~~~~~~~iIiDEah~~~~~~~~~~~~~~~~~~-~~~~~~~i~~SAT~~~~~~~~~~~~  198 (395)
T 3pey_A          120 INAQVIVGTPGTVLDLMRRKLMQLQKIKIFVLDEADNMLDQQGLGDQCIRVKRF-LPKDTQLVLFSATFADAVRQYAKKI  198 (395)
T ss_dssp             BCCSEEEECHHHHHHHHHTTCBCCTTCCEEEEETHHHHHHSTTHHHHHHHHHHT-SCTTCEEEEEESCCCHHHHHHHHHH
T ss_pred             CCCCEEEEcHHHHHHHHHcCCcccccCCEEEEEChhhhcCccccHHHHHHHHHh-CCCCcEEEEEEecCCHHHHHHHHHh
Confidence            368999999999999999988889999999999999998843388889999988 7889999999999999999999999


Q ss_pred             ccCcEEEEEcCCccccCCceEEEEEcCChhhHHHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhhhCCCceEeeecCCC
Q 030396           94 MHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLS  173 (178)
Q Consensus        94 ~~~~~~v~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~~~  173 (178)
                      +.++..+...........+.+.+..+.....+...+..++.....+++||||++++.|+.+++.|.+.|+++..+||+|+
T Consensus       199 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~lvf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~  278 (395)
T 3pey_A          199 VPNANTLELQTNEVNVDAIKQLYMDCKNEADKFDVLTELYGLMTIGSSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQ  278 (395)
T ss_dssp             SCSCEEECCCGGGCSCTTEEEEEEECSSHHHHHHHHHHHHTTTTSSEEEEECSCHHHHHHHHHHHHHTTCCCEEECTTSC
T ss_pred             CCCCeEEEccccccccccccEEEEEcCchHHHHHHHHHHHHhccCCCEEEEeCCHHHHHHHHHHHHhcCCcEEEeCCCCC
Confidence            99998888877777888888888888888889999999999888899999999999999999999999999999999999


Q ss_pred             cccc
Q 030396          174 QTQV  177 (178)
Q Consensus       174 ~~~R  177 (178)
                      +++|
T Consensus       279 ~~~r  282 (395)
T 3pey_A          279 TQER  282 (395)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            8876

>1xti_A Probable ATP-dependent RNA helicase P47; alpha-beta fold, gene regulation; 1.95A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 1xtj_A* 1xtk_A

Probab=99.93  E-value=2e-25  Score=175.79  Aligned_cols=162  Identities=23%  Similarity=0.311  Sum_probs=142.1

Q ss_pred             CCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcHHHHHHHHHh
Q 030396           14 FSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSI   93 (178)
Q Consensus        14 ~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~~~~~~~~~   93 (178)
                      .+++|+|+||+++.+++..+...+.+++++|+||||.+.++..+...+..+++. .+...|++++|||+++.+...+..+
T Consensus       127 ~~~~iiv~T~~~l~~~~~~~~~~~~~~~~vViDEaH~~~~~~~~~~~~~~~~~~-~~~~~~~i~~SAT~~~~~~~~~~~~  205 (391)
T 1xti_A          127 NCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRM-TPHEKQVMMFSATLSKEIRPVCRKF  205 (391)
T ss_dssp             SCCSEEEECHHHHHHHHHTTSSCCTTCSEEEECSHHHHTSSHHHHHHHHHHHHT-SCSSSEEEEEESSCCSTHHHHHHHH
T ss_pred             CCCCEEEECHHHHHHHHHcCCccccccCEEEEeCHHHHhhccchHHHHHHHHhh-CCCCceEEEEEeeCCHHHHHHHHHH
Confidence            458999999999999999988889999999999999998852288889999988 7889999999999999999999999


Q ss_pred             ccCcEEEEEcCCc-cccCCceEEEEEcCChhhHHHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhhhCCCceEeeecCC
Q 030396           94 MHDAVRVIVGRKN-TASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDL  172 (178)
Q Consensus        94 ~~~~~~v~~~~~~-~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~~  172 (178)
                      +.+|..+...... .....+.+.+..+ ....|...+.++++....+++||||++++.|+.+++.|.+.|+++..+||+|
T Consensus       206 ~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~l~~~l~~~~~~~~lvf~~~~~~~~~l~~~L~~~~~~~~~~~~~~  284 (391)
T 1xti_A          206 MQDPMEIFVDDETKLTLHGLQQYYVKL-KDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGM  284 (391)
T ss_dssp             CSSCEEEECCCCCCCCCTTCEEEEEEC-CGGGHHHHHHHHHHHSCCSEEEEECSCHHHHHHHHHHHHHTTCCEEEECTTS
T ss_pred             cCCCeEEEecCccccCcccceEEEEEc-CchhHHHHHHHHHHhcCCCcEEEEeCcHHHHHHHHHHHHhCCCcEEEEeCCC
Confidence            9999888776543 3445666766555 5667889999999988889999999999999999999999999999999999


Q ss_pred             Ccccc
Q 030396          173 SQTQV  177 (178)
Q Consensus       173 ~~~~R  177 (178)
                      ++++|
T Consensus       285 ~~~~r  289 (391)
T 1xti_A          285 PQEER  289 (391)
T ss_dssp             CHHHH
T ss_pred             CHHHH
Confidence            98876

>3fmp_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 3.19A {Homo sapiens}

Probab=99.93  E-value=1.3e-26  Score=187.71  Aligned_cols=163  Identities=24%  Similarity=0.286  Sum_probs=80.0

Q ss_pred             CCCcEEEeCcHHHHHHHHc-CCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcHHHHHHHHH
Q 030396           14 FSCDILISTPLRLRLAIRR-KKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARS   92 (178)
Q Consensus        14 ~~~~Iii~TP~~l~~~l~~-~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~~~~~~~~   92 (178)
                      .+++|+|||||++.+++.+ +.+++.+++++|+||+|.+++...+...+..+.+. .+...|++++|||++..+..+...
T Consensus       209 ~~~~Ivv~Tp~~l~~~l~~~~~~~~~~~~~iViDEah~~~~~~~~~~~~~~i~~~-~~~~~~~i~~SAT~~~~~~~~~~~  287 (479)
T 3fmp_B          209 ISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRM-LPRNCQMLLFSATFEDSVWKFAQK  287 (479)
T ss_dssp             CCCSEEEECHHHHHHHHTTSCCCCGGGCCEEEECCHHHHHTSTTHHHHHHHHHTT-SCTTSEEEEEESCCCHHHHHHHHH
T ss_pred             CCCCEEEECchHHHHHHHhcCCcCcccCCEEEEECHHHHhhcCCcHHHHHHHHhh-CCccceEEEEeCCCCHHHHHHHHH
Confidence            3578999999999999965 66788999999999999998743388888889888 788999999999999999999999


Q ss_pred             hccCcEEEEEcCCccccCCceEEEEEcCChhhHHHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhhhCCCceEeeecCC
Q 030396           93 IMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDL  172 (178)
Q Consensus        93 ~~~~~~~v~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~~  172 (178)
                      ++.+|..+...........+.+.++.+.....+...+..++......++||||+|++.|+.++..|...|+.+..+||+|
T Consensus       288 ~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~lvF~~s~~~~~~l~~~L~~~~~~v~~lh~~~  367 (479)
T 3fmp_B          288 VVPDPNVIKLKREEETLDTIKQYYVLCSSRDEKFQALCNLYGAITIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEM  367 (479)
T ss_dssp             HSSSEEEEEEC---------------------------------------------------------------------
T ss_pred             HcCCCeEEeccccccCcCCceEEEEEeCCHHHHHHHHHHHHhhccCCceEEEeCcHHHHHHHHHHHHhCCccEEEecCCC
Confidence            99999999998888888889998888877778999999999888788999999999999999999999999999999999


Q ss_pred             Ccccc
Q 030396          173 SQTQV  177 (178)
Q Consensus       173 ~~~~R  177 (178)
                      ++.+|
T Consensus       368 ~~~~R  372 (479)
T 3fmp_B          368 MVEQR  372 (479)
T ss_dssp             -----
T ss_pred             CHHHH
Confidence            99887

>1s2m_A Putative ATP-dependent RNA helicase DHH1; ATP-binding, RNA-binding, RNA binding protein; 2.10A {Saccharomyces cerevisiae} SCOP: c.37.1.19 c.37.1.19 PDB: 2wax_A* 2way_A

Probab=99.93  E-value=2.7e-25  Score=175.71  Aligned_cols=167  Identities=25%  Similarity=0.284  Sum_probs=145.3

Q ss_pred             HhHHhccCCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcHHH
Q 030396            7 RSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFV   86 (178)
Q Consensus         7 ~q~~~l~~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~~   86 (178)
                      ++...+..+++|+|+||+++.+++..+...+.+++++|+||||.+.+.+ +...+..++.. .+...|++++|||++..+
T Consensus       131 ~~~~~~~~~~~Ivv~T~~~l~~~~~~~~~~~~~~~~vIiDEaH~~~~~~-~~~~~~~i~~~-~~~~~~~i~lSAT~~~~~  208 (400)
T 1s2m_A          131 DDILRLNETVHILVGTPGRVLDLASRKVADLSDCSLFIMDEADKMLSRD-FKTIIEQILSF-LPPTHQSLLFSATFPLTV  208 (400)
T ss_dssp             HHHHHTTSCCSEEEECHHHHHHHHHTTCSCCTTCCEEEEESHHHHSSHH-HHHHHHHHHTT-SCSSCEEEEEESCCCHHH
T ss_pred             HHHHHhcCCCCEEEEchHHHHHHHHhCCcccccCCEEEEeCchHhhhhc-hHHHHHHHHHh-CCcCceEEEEEecCCHHH
Confidence            3444556789999999999999999888889999999999999998888 88999999988 788899999999999999


Q ss_pred             HHHHHHhccCcEEEEEcCCccccCCceEEEEEcCChhhHHHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhhhCCCceE
Q 030396           87 EELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDIRAG  166 (178)
Q Consensus        87 ~~~~~~~~~~~~~v~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~  166 (178)
                      ...+..++.+|..+.... .....++.+++..+ ....|...+..+++....+++||||++++.++.+++.|.+.|+.+.
T Consensus       209 ~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~-~~~~k~~~l~~~~~~~~~~~~lVf~~~~~~~~~l~~~L~~~~~~~~  286 (400)
T 1s2m_A          209 KEFMVKHLHKPYEINLME-ELTLKGITQYYAFV-EERQKLHCLNTLFSKLQINQAIIFCNSTNRVELLAKKITDLGYSCY  286 (400)
T ss_dssp             HHHHHHHCSSCEEESCCS-SCBCTTEEEEEEEC-CGGGHHHHHHHHHHHSCCSEEEEECSSHHHHHHHHHHHHHHTCCEE
T ss_pred             HHHHHHHcCCCeEEEecc-ccccCCceeEEEEe-chhhHHHHHHHHHhhcCCCcEEEEEecHHHHHHHHHHHHhcCCCeE
Confidence            999999999987775543 34556677776555 5667889999999988888999999999999999999999999999


Q ss_pred             eeecCCCcccc
Q 030396          167 VIHSDLSQTQV  177 (178)
Q Consensus       167 ~lh~~~~~~~R  177 (178)
                      .+||+|++++|
T Consensus       287 ~~~~~~~~~~r  297 (400)
T 1s2m_A          287 YSHARMKQQER  297 (400)
T ss_dssp             EECTTSCHHHH
T ss_pred             EecCCCCHHHH
Confidence            99999998876

>1fuu_A Yeast initiation factor 4A; IF4A, helicase, DEAD-box protein, translation; 2.50A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 2vso_A* 2vsx_A*

Probab=99.93  E-value=3.2e-26  Score=180.36  Aligned_cols=161  Identities=28%  Similarity=0.416  Sum_probs=82.7

Q ss_pred             CCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcHHHHHHHHHhc
Q 030396           15 SCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIM   94 (178)
Q Consensus        15 ~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~~~~~~~~~~   94 (178)
                      +++|+|+||+++.+.+..+...+.+++++|+||||.+.+++ +...+..++.. .+...|++++|||+++.+......++
T Consensus       138 ~~~i~v~T~~~l~~~~~~~~~~~~~~~~vIiDEah~~~~~~-~~~~~~~~~~~-~~~~~~~i~~SAT~~~~~~~~~~~~~  215 (394)
T 1fuu_A          138 DAQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSG-FKEQIYQIFTL-LPPTTQVVLLSATMPNDVLEVTTKFM  215 (394)
T ss_dssp             HCSEEEECHHHHHHHHHTTSSCCTTCCEEEEETHHHHHHTT-CHHHHHHHHHH-SCTTCEEEEECSSCCHHHHHHHHHHC
T ss_pred             CCCEEEECHHHHHHHHHhCCcchhhCcEEEEEChHHhhCCC-cHHHHHHHHHh-CCCCceEEEEEEecCHHHHHHHHHhc
Confidence            68999999999999999888889999999999999999988 99999999999 78899999999999999999999999


Q ss_pred             cCcEEEEEcCCccccCCceEEEEEcCChhhHHHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhhhCCCceEeeecCCCc
Q 030396           95 HDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQ  174 (178)
Q Consensus        95 ~~~~~v~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~~~~  174 (178)
                      .+|..+..........++.+.+..+.....+...+.++++....+++||||+|++.++.+++.|.+.|+.+..+||+|++
T Consensus       216 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~lVf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~  295 (394)
T 1fuu_A          216 RNPVRILVKKDELTLEGIKQFYVNVEEEEYKYECLTDLYDSISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQ  295 (394)
T ss_dssp             CSCEEEEECC----------------------------------------------------------------------
T ss_pred             CCCeEEEecCccccCCCceEEEEEcCchhhHHHHHHHHHhcCCCCcEEEEECCHHHHHHHHHHHHHcCCeEEEeeCCCCH
Confidence            99999988877777778888887776666688888888888778899999999999999999999999999999999999


Q ss_pred             ccc
Q 030396          175 TQV  177 (178)
Q Consensus       175 ~~R  177 (178)
                      ++|
T Consensus       296 ~~r  298 (394)
T 1fuu_A          296 QER  298 (394)
T ss_dssp             ---
T ss_pred             HHH
Confidence            887

>1hv8_A Putative ATP-dependent RNA helicase MJ0669; RNA-binding protein, ATPase, RNA binding protein; 3.00A {Methanocaldococcus jannaschii} SCOP: c.37.1.19 c.37.1.19

Probab=99.92  E-value=1.1e-23  Score=164.08  Aligned_cols=155  Identities=32%  Similarity=0.453  Sum_probs=136.5

Q ss_pred             CCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcHHHHHHHHHhc
Q 030396           15 SCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIM   94 (178)
Q Consensus        15 ~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~~~~~~~~~~   94 (178)
                      +++|+|+||+++.+.+..+...+.+++++|+||||.+.+++ +...+..++.. .+...|++++|||.++........++
T Consensus       123 ~~~iiv~T~~~l~~~~~~~~~~~~~~~~iIiDEah~~~~~~-~~~~~~~~~~~-~~~~~~~i~~SAT~~~~~~~~~~~~~  200 (367)
T 1hv8_A          123 NANIVVGTPGRILDHINRGTLNLKNVKYFILDEADEMLNMG-FIKDVEKILNA-CNKDKRILLFSATMPREILNLAKKYM  200 (367)
T ss_dssp             TCSEEEECHHHHHHHHHTTCSCTTSCCEEEEETHHHHHTTT-THHHHHHHHHT-SCSSCEEEEECSSCCHHHHHHHHHHC
T ss_pred             CCCEEEecHHHHHHHHHcCCcccccCCEEEEeCchHhhhhc-hHHHHHHHHHh-CCCCceEEEEeeccCHHHHHHHHHHc
Confidence            68999999999999999988889999999999999999988 99999999998 78899999999999999999999999


Q ss_pred             cCcEEEEEcCCccccCCceEEEEEcCChhhHHHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhhhCCCceEeeecCCCc
Q 030396           95 HDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQ  174 (178)
Q Consensus        95 ~~~~~v~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~~~~  174 (178)
                      .++..+....    ...+.+.++.+ ....+...+.++++. ...++||||+|++.++.+++.|.+.|+++..+||++++
T Consensus       201 ~~~~~~~~~~----~~~~~~~~~~~-~~~~~~~~l~~~l~~-~~~~~lvf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~  274 (367)
T 1hv8_A          201 GDYSFIKAKI----NANIEQSYVEV-NENERFEALCRLLKN-KEFYGLVFCKTKRDTKELASMLRDIGFKAGAIHGDLSQ  274 (367)
T ss_dssp             CSEEEEECCS----SSSSEEEEEEC-CGGGHHHHHHHHHCS-TTCCEEEECSSHHHHHHHHHHHHHTTCCEEEECSSSCH
T ss_pred             CCCeEEEecC----CCCceEEEEEe-ChHHHHHHHHHHHhc-CCCcEEEEECCHHHHHHHHHHHHhcCCCeEEeeCCCCH
Confidence            9877665433    23566666555 566788888888874 47899999999999999999999999999999999998


Q ss_pred             ccc
Q 030396          175 TQV  177 (178)
Q Consensus       175 ~~R  177 (178)
                      ++|
T Consensus       275 ~~r  277 (367)
T 1hv8_A          275 SQR  277 (367)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            876

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C}

Probab=99.92  E-value=9.1e-25  Score=180.79  Aligned_cols=170  Identities=27%  Similarity=0.350  Sum_probs=133.0

Q ss_pred             HhHHhc-cCCCcEEEeCcHHHHHHHHcC-CCCCCCeeEEEEeccccccccCCChhhHHHHHhhC------CCCCceEEEE
Q 030396            7 RSTDLS-KFSCDILISTPLRLRLAIRRK-KIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKAC------SNPSIVRSLF   78 (178)
Q Consensus         7 ~q~~~l-~~~~~Iii~TP~~l~~~l~~~-~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~------~~~~~q~i~~   78 (178)
                      .+.+.+ ..+++|+|+|||+|.+++.+. ...++.++++|+||||.+++++ |.+.+..|+..+      .+...|++++
T Consensus       141 ~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~~~~~lViDEah~l~~~g-f~~~~~~i~~~l~~~~~~~~~~~~~l~~  219 (579)
T 3sqw_A          141 AAMNKMNKLRPNIVIATPGRLIDVLEKYSNKFFRFVDYKVLDEADRLLEIG-FRDDLETISGILNEKNSKSADNIKTLLF  219 (579)
T ss_dssp             HHHHHHHHHCCSEEEECHHHHHHHHHHHHHHHCTTCCEEEEETHHHHTSTT-THHHHHHHHHHHHHHCSSCTTCCEEEEE
T ss_pred             HHHHHHhcCCCCEEEECHHHHHHHHHhccccccccCCEEEEEChHHhhcCC-CHHHHHHHHHHhhhhhcccccCceEEEE
Confidence            344444 347999999999999998764 4568889999999999999999 999999998773      1236799999


Q ss_pred             eecCcHHHHHHHHHhccCcEEEEEcCC----ccccCCceEEEEEcCChhhHH----HHHHHHHHh-cCCCCEEEEeCCch
Q 030396           79 SATLPDFVEELARSIMHDAVRVIVGRK----NTASESIKQKLVFAGSEEGKL----LALRQSFAE-SLNPPVLIFVQSKD  149 (178)
Q Consensus        79 SAT~~~~~~~~~~~~~~~~~~v~~~~~----~~~~~~i~~~~~~~~~~~~k~----~~l~~ll~~-~~~~~~lIF~~t~~  149 (178)
                      |||+++.+..++..++.+|..+.+...    ......+.+.++.......+.    ..+...+.. ....++||||+|++
T Consensus       220 SAT~~~~v~~~~~~~l~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~iVF~~t~~  299 (579)
T 3sqw_A          220 SATLDDKVQKLANNIMNKKECLFLDTVDKNEPEAHERIDQSVVISEKFANSIFAAVEHIKKQIKERDSNYKAIIFAPTVK  299 (579)
T ss_dssp             ESSCCTHHHHHTTTTCCSSEEEEEESSCSSSCSSCTTEEEEEEEESSTTHHHHHHHHHHHHHHHHTTTCCEEEEECSSHH
T ss_pred             eccCChHHHHHHHHHcCCCceEEEeecCccccccccccceEEEEecchhhhHHHHHHHHHHHHhhcCCCCcEEEECCcHH
Confidence            999999999999999998877766432    334455677776665544333    223333333 45678999999999


Q ss_pred             HHHHHHHHhhhC---CCceEeeecCCCcccc
Q 030396          150 RAKELYGELAFD---DIRAGVIHSDLSQTQV  177 (178)
Q Consensus       150 ~~~~l~~~L~~~---g~~~~~lh~~~~~~~R  177 (178)
                      .|+.+++.|.+.   |+++..+||+|++++|
T Consensus       300 ~~~~l~~~L~~~~~~~~~v~~~hg~~~~~~R  330 (579)
T 3sqw_A          300 FTSFLCSILKNEFKKDLPILEFHGKITQNKR  330 (579)
T ss_dssp             HHHHHHHHHHHHHTTTSCEEEESTTSCHHHH
T ss_pred             HHHHHHHHHHHhhcCCCcEEEecCCCCHHHH
Confidence            999999999876   9999999999999887

>3i5x_A ATP-dependent RNA helicase MSS116; protein-RNA complex, RNA helicase, DEAD-BOX, ATP-binding, HE hydrolase, mitochondrion; HET: ANP; 1.90A {Saccharomyces cerevisiae} PDB: 3i5y_A* 3i61_A* 3i62_A* 3sqx_A* 4db2_A 4db4_A

Probab=99.91  E-value=1.9e-24  Score=178.06  Aligned_cols=164  Identities=29%  Similarity=0.364  Sum_probs=130.2

Q ss_pred             cCCCcEEEeCcHHHHHHHHcC-CCCCCCeeEEEEeccccccccCCChhhHHHHHhhC------CCCCceEEEEeecCcHH
Q 030396           13 KFSCDILISTPLRLRLAIRRK-KIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKAC------SNPSIVRSLFSATLPDF   85 (178)
Q Consensus        13 ~~~~~Iii~TP~~l~~~l~~~-~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~------~~~~~q~i~~SAT~~~~   85 (178)
                      ..+++|+|+|||++.+++.+. ...++.++++|+||||.+++++ |.+.+..|+..+      .....|++++|||+++.
T Consensus       199 ~~~~~Iiv~Tp~~l~~~l~~~~~~~~~~~~~lViDEah~l~~~~-f~~~~~~i~~~l~~~~~~~~~~~~~l~~SAT~~~~  277 (563)
T 3i5x_A          199 KLRPNIVIATPGRLIDVLEKYSNKFFRFVDYKVLDEADRLLEIG-FRDDLETISGILNEKNSKSADNIKTLLFSATLDDK  277 (563)
T ss_dssp             HHCCSEEEECHHHHHHHHHHHHHHHCTTCCEEEEETHHHHTSTT-THHHHHHHHHHHHHHCSSCTTCCEEEEEESSCCTH
T ss_pred             cCCCCEEEECcHHHHHHHHhccccccccceEEEEeCHHHHhccc-hHHHHHHHHHhhhhccccCccCceEEEEEccCCHH
Confidence            458999999999999998764 3457889999999999999999 999999998763      12378999999999999


Q ss_pred             HHHHHHHhccCcEEEEEcCC----ccccCCceEEEEEcCChhhHHHHHH----HHHHh-cCCCCEEEEeCCchHHHHHHH
Q 030396           86 VEELARSIMHDAVRVIVGRK----NTASESIKQKLVFAGSEEGKLLALR----QSFAE-SLNPPVLIFVQSKDRAKELYG  156 (178)
Q Consensus        86 ~~~~~~~~~~~~~~v~~~~~----~~~~~~i~~~~~~~~~~~~k~~~l~----~ll~~-~~~~~~lIF~~t~~~~~~l~~  156 (178)
                      +..+...++.+|..+.....    ......+.+.+........+...+.    ..+.. ....++||||+|++.|+.++.
T Consensus       278 v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~iVF~~s~~~~~~l~~  357 (563)
T 3i5x_A          278 VQKLANNIMNKKECLFLDTVDKNEPEAHERIDQSVVISEKFANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCS  357 (563)
T ss_dssp             HHHHTTTTCCSSEEEEEESSCSSSCSSCTTEEEEEEEESSTTHHHHHHHHHHHHHHHHTTTCCEEEEECSCHHHHHHHHH
T ss_pred             HHHHHHHhcCCCceEEEeccCCCCccccccCceEEEECchhHhhHHHHHHHHHHHHhhcCCCCcEEEEcCcHHHHHHHHH
Confidence            99999999998877765432    3344556777766655444433332    33332 456799999999999999999


Q ss_pred             HhhhC---CCceEeeecCCCcccc
Q 030396          157 ELAFD---DIRAGVIHSDLSQTQV  177 (178)
Q Consensus       157 ~L~~~---g~~~~~lh~~~~~~~R  177 (178)
                      .|.+.   |+++..+||+|++.+|
T Consensus       358 ~L~~~~~~~~~v~~~h~~~~~~~R  381 (563)
T 3i5x_A          358 ILKNEFKKDLPILEFHGKITQNKR  381 (563)
T ss_dssp             HHHHHHTTTSCEEEESTTSCHHHH
T ss_pred             HHHHhccCCceEEEecCCCCHHHH
Confidence            99876   9999999999999887

>2z0m_A 337AA long hypothetical ATP-dependent RNA helicase DEAD; ATP-binding, hydrolase, nucleotide-binding, RNA binding protein, structural genomics; 1.90A {Sulfolobus tokodaii}

Probab=99.88  E-value=9.2e-22  Score=151.73  Aligned_cols=151  Identities=25%  Similarity=0.423  Sum_probs=128.2

Q ss_pred             CCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcHHHHHHHHHhc
Q 030396           15 SCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIM   94 (178)
Q Consensus        15 ~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~~~~~~~~~~   94 (178)
                      +++|+|+||+++.+.+..+.+++.+++++|+||||.+.+++ +...+..++.. .+...+++++|||+++.+......++
T Consensus       105 ~~~i~v~T~~~l~~~~~~~~~~~~~~~~iViDEah~~~~~~-~~~~~~~~~~~-~~~~~~~~~~SAT~~~~~~~~~~~~~  182 (337)
T 2z0m_A          105 NADIVVATPGRLLDLWSKGVIDLSSFEIVIIDEADLMFEMG-FIDDIKIILAQ-TSNRKITGLFSATIPEEIRKVVKDFI  182 (337)
T ss_dssp             TCSEEEECHHHHHHHHHTTSCCGGGCSEEEEESHHHHHHTT-CHHHHHHHHHH-CTTCSEEEEEESCCCHHHHHHHHHHS
T ss_pred             CCCEEEECHHHHHHHHHcCCcchhhCcEEEEEChHHhhccc-cHHHHHHHHhh-CCcccEEEEEeCcCCHHHHHHHHHhc
Confidence            58999999999999999888889999999999999999999 99999999999 78889999999999999999999999


Q ss_pred             cCcEEEEEcCCccccCCceEEEEEcCChhhHHHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhhhCCCceEeeecCCCc
Q 030396           95 HDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQ  174 (178)
Q Consensus        95 ~~~~~v~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~~~~  174 (178)
                      .++..+...   ....++.+.++.+.+...   ...+.+.....+++||||++++.++.+++.|.    .+..+||+|++
T Consensus       183 ~~~~~~~~~---~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~lvf~~~~~~~~~l~~~l~----~~~~~~~~~~~  252 (337)
T 2z0m_A          183 TNYEEIEAC---IGLANVEHKFVHVKDDWR---SKVQALRENKDKGVIVFVRTRNRVAKLVRLFD----NAIELRGDLPQ  252 (337)
T ss_dssp             CSCEEEECS---GGGGGEEEEEEECSSSSH---HHHHHHHTCCCSSEEEECSCHHHHHHHHTTCT----TEEEECTTSCH
T ss_pred             CCceeeecc---cccCCceEEEEEeChHHH---HHHHHHHhCCCCcEEEEEcCHHHHHHHHHHhh----hhhhhcCCCCH
Confidence            988766432   345566777766654432   22356666778899999999999999999987    68899999998


Q ss_pred             ccc
Q 030396          175 TQV  177 (178)
Q Consensus       175 ~~R  177 (178)
                      .+|
T Consensus       253 ~~r  255 (337)
T 2z0m_A          253 SVR  255 (337)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            876

>2v1x_A ATP-dependent DNA helicase Q1; DNA strand annealing, mismatch repair, nucleotide-binding, DNA-binding, polymorphism, nuclear protein, ATPase; HET: ADP; 2.00A {Homo sapiens} PDB: 2wwy_A*

Probab=99.88  E-value=7.4e-22  Score=163.55  Aligned_cols=163  Identities=15%  Similarity=0.138  Sum_probs=122.6

Q ss_pred             cCCCcEEEeCcHHHHH---HHH--cCCCCCCCeeEEEEeccccccccC-CChhhHHH--HHhhCCCCCceEEEEeecCcH
Q 030396           13 KFSCDILISTPLRLRL---AIR--RKKIDLSRVEYLVLDEADKLFEVG-NLLKHIDP--VVKACSNPSIVRSLFSATLPD   84 (178)
Q Consensus        13 ~~~~~Iii~TP~~l~~---~l~--~~~~~~~~l~~lViDE~d~ll~~~-~~~~~i~~--i~~~~~~~~~q~i~~SAT~~~   84 (178)
                      ..+++|+|+||++|..   ++.  .+...+.+++++|+||||.+.++| .|.+.+..  ++.. ..++.|++++|||.++
T Consensus       134 ~~~~~Ilv~Tpe~L~~~~~~~~~l~~~~~~~~i~~iViDEAH~is~~g~dfr~~~~~l~~l~~-~~~~~~ii~lSAT~~~  212 (591)
T 2v1x_A          134 NSELKLIYVTPEKIAKSKMFMSRLEKAYEARRFTRIAVDEVHCCSQWGHDFRPDYKALGILKR-QFPNASLIGLTATATN  212 (591)
T ss_dssp             TCCCCEEEECHHHHHSCHHHHHHHHHHHHTTCEEEEEEETGGGGSTTCTTCCGGGGGGGHHHH-HCTTSEEEEEESSCCH
T ss_pred             cCCCCEEEEChhHhhccHHHHHHHHhhhhccCCcEEEEECcccccccccccHHHHHHHHHHHH-hCCCCcEEEEecCCCH
Confidence            4679999999998752   221  123457889999999999999987 57787765  3444 3457999999999999


Q ss_pred             HHHHHHHHhccCcEEEEEcCCccccCCceEEEEEcCC-hhhHHHHHHHHHHh-cCCCCEEEEeCCchHHHHHHHHhhhCC
Q 030396           85 FVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGS-EEGKLLALRQSFAE-SLNPPVLIFVQSKDRAKELYGELAFDD  162 (178)
Q Consensus        85 ~~~~~~~~~~~~~~~v~~~~~~~~~~~i~~~~~~~~~-~~~k~~~l~~ll~~-~~~~~~lIF~~t~~~~~~l~~~L~~~g  162 (178)
                      .+...+..++..+..+... .....+++...+..... ...+...+.+++.. ....++||||+|++.|+.++..|...|
T Consensus       213 ~v~~~i~~~l~~~~~~~~~-~~~~r~nl~~~v~~~~~~~~~~~~~l~~~l~~~~~~~~~IVf~~sr~~~e~la~~L~~~g  291 (591)
T 2v1x_A          213 HVLTDAQKILCIEKCFTFT-ASFNRPNLYYEVRQKPSNTEDFIEDIVKLINGRYKGQSGIIYCFSQKDSEQVTVSLQNLG  291 (591)
T ss_dssp             HHHHHHHHHTTCCSCEEEE-CCCCCTTEEEEEEECCSSHHHHHHHHHHHHTTTTTTCEEEEECSSHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHhCCCCcEEEe-cCCCCcccEEEEEeCCCcHHHHHHHHHHHHHHhccCCCeEEEeCcHHHHHHHHHHHHHCC
Confidence            9888888887754333222 23344555554443322 34567778888764 356789999999999999999999999


Q ss_pred             CceEeeecCCCcccc
Q 030396          163 IRAGVIHSDLSQTQV  177 (178)
Q Consensus       163 ~~~~~lh~~~~~~~R  177 (178)
                      +.+..+||+|++++|
T Consensus       292 ~~~~~~h~~l~~~~R  306 (591)
T 2v1x_A          292 IHAGAYHANLEPEDK  306 (591)
T ss_dssp             CCEEEECTTSCHHHH
T ss_pred             CCEEEecCCCCHHHH
Confidence            999999999999887

>3l9o_A ATP-dependent RNA helicase DOB1; REC-A fold, winged-helix-turn-helix, antiparallel-coiled-COI domain, ATP-binding, helicase, hydrolase; 3.39A {Saccharomyces cerevisiae}

Probab=99.86  E-value=1.7e-21  Score=170.71  Aligned_cols=161  Identities=18%  Similarity=0.209  Sum_probs=125.7

Q ss_pred             cCCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcHH--HHHHH
Q 030396           13 KFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDF--VEELA   90 (178)
Q Consensus        13 ~~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~--~~~~~   90 (178)
                      ..+++|+|+|||+|.+++.++...+.+++++|+||||.+.+++ +...+..++.. ++...|++++|||+|+.  +..++
T Consensus       264 ~~~~~IlV~Tpe~L~~~L~~~~~~l~~l~lVVIDEaH~l~d~~-rg~~~e~ii~~-l~~~~qvl~lSATipn~~e~a~~l  341 (1108)
T 3l9o_A          264 NPDAGCLVMTTEILRSMLYRGSEVMREVAWVIFDEVHYMRDKE-RGVVWEETIIL-LPDKVRYVFLSATIPNAMEFAEWI  341 (1108)
T ss_dssp             CCSCSEEEEEHHHHHHHHHHCSSHHHHEEEEEEETGGGTTSHH-HHHHHHHHHHH-SCTTSEEEEEECSCSSCHHHHHHH
T ss_pred             CCCCCEEEeChHHHHHHHHcCccccccCCEEEEhhhhhccccc-hHHHHHHHHHh-cCCCceEEEEcCCCCCHHHHHHHH
Confidence            4568999999999999999988888999999999999999988 99999999999 88899999999999864  55777


Q ss_pred             HHhccCcEEEEEcCCccccCCceEEEEEcCCh------------------------------------------------
Q 030396           91 RSIMHDAVRVIVGRKNTASESIKQKLVFAGSE------------------------------------------------  122 (178)
Q Consensus        91 ~~~~~~~~~v~~~~~~~~~~~i~~~~~~~~~~------------------------------------------------  122 (178)
                      ......|..+........  .+.++++.....                                                
T Consensus       342 ~~~~~~~~~vi~~~~rp~--pl~~~~~~~~~~~~~~~vd~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~  419 (1108)
T 3l9o_A          342 CKIHSQPCHIVYTNFRPT--PLQHYLFPAHGDGIYLVVDEKSTFREENFQKAMASISNQIGDDPNSTDSRGKKGQTYKGG  419 (1108)
T ss_dssp             HHHTCSCEEEEEECCCSS--CEEEEEEETTSSCCEEEEETTTEECHHHHHHHHTTC------------------------
T ss_pred             HhhcCCCeEEEecCCCcc--cceEEEeecCCcceeeeeccccchhhhhHHHHHHHHHhhhcccccccccccccccccccc
Confidence            777777766665443322  233333221100                                                


Q ss_pred             ------hhHHHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhhhCCCc--------------------------------
Q 030396          123 ------EGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDIR--------------------------------  164 (178)
Q Consensus       123 ------~~k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~~~g~~--------------------------------  164 (178)
                            ..+...+...+......++||||+|++.|+.++..|...|+.                                
T Consensus       420 ~~~~~~~~~l~~li~~l~~~~~~~vIVF~~sr~~~e~la~~L~~~~~~~~~e~~~i~~~~~~~~~~l~~~d~~l~~~~~l  499 (1108)
T 3l9o_A          420 SAKGDAKGDIYKIVKMIWKKKYNPVIVFSFSKRDCEELALKMSKLDFNSDDEKEALTKIFNNAIALLPETDRELPQIKHI  499 (1108)
T ss_dssp             -----CHHHHHHHHHHHHHTTCCCEEEEESCHHHHHHHHHHTCSHHHHCC----CHHHHGGGSCTHHHHHTTCCHHHHHH
T ss_pred             cccccchhHHHHHHHHHHhcCCCCEEEEeCcHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHhhcchhhhhhhhHHHH
Confidence                  234445555666666789999999999999999999765543                                


Q ss_pred             -------eEeeecCCCcccc
Q 030396          165 -------AGVIHSDLSQTQV  177 (178)
Q Consensus       165 -------~~~lh~~~~~~~R  177 (178)
                             +..+||+|++.+|
T Consensus       500 ~~~l~~gV~~~Hg~l~~~~R  519 (1108)
T 3l9o_A          500 LPLLRRGIGIHHSGLLPILK  519 (1108)
T ss_dssp             THHHHHTEEEECSCSCHHHH
T ss_pred             HHhhhcCeeeecCCCCHHHH
Confidence                   7899999999876

>1oyw_A RECQ helicase, ATP-dependent DNA helicase; winged helix, helix-turn-helix, ATP binding, Zn(2+) binding, hydrolase; 1.80A {Escherichia coli} SCOP: a.4.5.43 c.37.1.19 c.37.1.19 PDB: 1oyy_A*

Probab=99.86  E-value=5.8e-21  Score=156.32  Aligned_cols=157  Identities=18%  Similarity=0.182  Sum_probs=118.2

Q ss_pred             cCCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccC-CChhhHHHH---HhhCCCCCceEEEEeecCcHHHHH
Q 030396           13 KFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVG-NLLKHIDPV---VKACSNPSIVRSLFSATLPDFVEE   88 (178)
Q Consensus        13 ~~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~-~~~~~i~~i---~~~~~~~~~q~i~~SAT~~~~~~~   88 (178)
                      .+.++|+++||+++........+...+++++|+||||.+.++| .|.+.+..+   .+. . ++.+++++|||.++.+..
T Consensus       113 ~~~~~ilv~Tpe~l~~~~~~~~l~~~~~~~vViDEaH~i~~~g~~fr~~~~~l~~l~~~-~-~~~~~i~lSAT~~~~~~~  190 (523)
T 1oyw_A          113 TGQIRLLYIAPERLMLDNFLEHLAHWNPVLLAVDEAHCISQWGHDFRPEYAALGQLRQR-F-PTLPFMALTATADDTTRQ  190 (523)
T ss_dssp             HTCCSEEEECHHHHTSTTHHHHHTTSCEEEEEESSGGGGCTTSSCCCHHHHGGGGHHHH-C-TTSCEEEEESCCCHHHHH
T ss_pred             cCCCCEEEECHHHHhChHHHHHHhhCCCCEEEEeCccccCcCCCccHHHHHHHHHHHHh-C-CCCCEEEEeCCCCHHHHH
Confidence            4679999999999863322222345789999999999999887 577776654   333 2 468999999999998766


Q ss_pred             HHHHhc--cCcEEEEEcCCccccCCceEEEEEcCChhhHHHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhhhCCCceE
Q 030396           89 LARSIM--HDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDIRAG  166 (178)
Q Consensus        89 ~~~~~~--~~~~~v~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~  166 (178)
                      .+..++  .+|..+. .  ....+++...+.   ...++...+.+++......++||||+|++.|+.+++.|...|+++.
T Consensus       191 ~i~~~l~~~~~~~~~-~--~~~r~~l~~~v~---~~~~~~~~l~~~l~~~~~~~~IVf~~sr~~~e~l~~~L~~~g~~~~  264 (523)
T 1oyw_A          191 DIVRLLGLNDPLIQI-S--SFDRPNIRYMLM---EKFKPLDQLMRYVQEQRGKSGIIYCNSRAKVEDTAARLQSKGISAA  264 (523)
T ss_dssp             HHHHHHTCCSCEEEE-C--CCCCTTEEEEEE---ECSSHHHHHHHHHHHTTTCCEEEECSSHHHHHHHHHHHHHTTCCEE
T ss_pred             HHHHHhCCCCCeEEe-C--CCCCCceEEEEE---eCCCHHHHHHHHHHhcCCCcEEEEeCCHHHHHHHHHHHHHCCCCEE
Confidence            555444  3554332 2  223445544333   2345778888888887788999999999999999999999999999


Q ss_pred             eeecCCCcccc
Q 030396          167 VIHSDLSQTQV  177 (178)
Q Consensus       167 ~lh~~~~~~~R  177 (178)
                      .+||+|++++|
T Consensus       265 ~~h~~l~~~~R  275 (523)
T 1oyw_A          265 AYHAGLENNVR  275 (523)
T ss_dssp             EECTTSCHHHH
T ss_pred             EecCCCCHHHH
Confidence            99999999887

>2xgj_A ATP-dependent RNA helicase DOB1; hydrolase-RNA complex, hydrolase, tramp, exosome, DEAD, nucleotide-binding; HET: ADP; 2.90A {Saccharomyces cerevisiae}

Probab=99.84  E-value=1.3e-19  Score=157.55  Aligned_cols=160  Identities=18%  Similarity=0.208  Sum_probs=121.8

Q ss_pred             CCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcHHH--HHHHH
Q 030396           14 FSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFV--EELAR   91 (178)
Q Consensus        14 ~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~~--~~~~~   91 (178)
                      .+++|+|+|||+|.+++.++...+++++++|+||+|.+.+++ +...++.++.. ++...|++++|||+|+..  ..++.
T Consensus       167 ~~~~IvV~Tpe~L~~~L~~~~~~l~~l~lVViDEaH~l~d~~-rg~~~e~il~~-l~~~~~il~LSATi~n~~e~a~~l~  244 (1010)
T 2xgj_A          167 PDAGCLVMTTEILRSMLYRGSEVMREVAWVIFDEVHYMRDKE-RGVVWEETIIL-LPDKVRYVFLSATIPNAMEFAEWIC  244 (1010)
T ss_dssp             TTCSEEEEEHHHHHHHHHHTCTTGGGEEEEEEETGGGGGCTT-THHHHHHHHHH-SCTTCEEEEEECCCTTHHHHHHHHH
T ss_pred             CCCCEEEEcHHHHHHHHHcCcchhhcCCEEEEechhhhcccc-hhHHHHHHHHh-cCCCCeEEEEcCCCCCHHHHHHHHH
Confidence            468999999999999999888889999999999999999988 88999999999 788999999999998753  34555


Q ss_pred             HhccCcEEEEEcCCccccCCceEEEEEcC--------C-h----------------------------------------
Q 030396           92 SIMHDAVRVIVGRKNTASESIKQKLVFAG--------S-E----------------------------------------  122 (178)
Q Consensus        92 ~~~~~~~~v~~~~~~~~~~~i~~~~~~~~--------~-~----------------------------------------  122 (178)
                      ...+.+..+......  +..+.++++...        + .                                        
T Consensus       245 ~~~~~~~~vi~~~~r--p~pl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~g~~~~~~k~~~  322 (1010)
T 2xgj_A          245 KIHSQPCHIVYTNFR--PTPLQHYLFPAHGDGIYLVVDEKSTFREENFQKAMASISNQIGDDPNSTDSRGKKGQTYKGGS  322 (1010)
T ss_dssp             HHHTSCEEEEEECCC--SSCEEEEEEETTSSCCEEEECTTCCBCHHHHHHHHHTCC------------------------
T ss_pred             hhcCCCeEEEecCCC--cccceEEEEecCCcceeeeeccccccchHHHHHHHHHHhhhhccccccccccccccccccccc
Confidence            455666666554332  233444443211        0 0                                        


Q ss_pred             -----hhHHHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhhhCCCc---------------------------------
Q 030396          123 -----EGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDIR---------------------------------  164 (178)
Q Consensus       123 -----~~k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~~~g~~---------------------------------  164 (178)
                           ......+...+......++||||+|++.|+.++..|...|+.                                 
T Consensus       323 ~~~~~~~~l~~l~~~l~~~~~~~~IVF~~sr~~~e~la~~L~~~~~~~~~e~~~i~~~~~~~~~~l~~~d~~l~~~~~l~  402 (1010)
T 2xgj_A          323 AKGDAKGDIYKIVKMIWKKKYNPVIVFSFSKRDCEELALKMSKLDFNSDDEKEALTKIFNNAIALLPETDRELPQIKHIL  402 (1010)
T ss_dssp             ------CHHHHHHHHHHHHTCCSEEEEESSHHHHHHHHHTTTTSCCCCHHHHHHHHHHHHHHHTTSCGGGTTCHHHHHHH
T ss_pred             ccccchHHHHHHHHHHHhcCCCCEEEEECCHHHHHHHHHHHHhCCCCChHHHHHHHHHHHHHHHhcchhhhcchhHHHHH
Confidence                 112334555555555679999999999999999999886653                                 


Q ss_pred             ------eEeeecCCCcccc
Q 030396          165 ------AGVIHSDLSQTQV  177 (178)
Q Consensus       165 ------~~~lh~~~~~~~R  177 (178)
                            +..+||+|++.+|
T Consensus       403 ~~l~~gI~~~Hggl~~~eR  421 (1010)
T 2xgj_A          403 PLLRRGIGIHHSGLLPILK  421 (1010)
T ss_dssp             HHHHHTEEEESTTSCHHHH
T ss_pred             HHHhCCeeEECCCCCHHHH
Confidence                  7889999999876

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A*

Probab=99.84  E-value=3.1e-21  Score=153.40  Aligned_cols=153  Identities=19%  Similarity=0.232  Sum_probs=116.6

Q ss_pred             HHhHHhccCC-CcEEEeCcHHHHHHHHcCCCCCCCeeEEEEecccccc----------c-cCCChhh-HHHHHhhCCC--
Q 030396            6 VRSTDLSKFS-CDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLF----------E-VGNLLKH-IDPVVKACSN--   70 (178)
Q Consensus         6 ~~q~~~l~~~-~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll----------~-~~~~~~~-i~~i~~~~~~--   70 (178)
                      .++.+.+..+ ++|+|+|||++.+++..  +.+.+++++|+||||.+.          + .+ |.+. +..+++. ++  
T Consensus       107 ~~~~~~l~~~~~~Iiv~Tp~~l~~~l~~--~~~~~~~~iViDEaH~~~~~~~~~d~~l~~~~-~~~~~~~~i~~~-~~~~  182 (414)
T 3oiy_A          107 EKFEKSFEEDDYHILVFSTQFVSKNREK--LSQKRFDFVFVDDVDAVLKASRNIDTLLMMVG-IPEEIIRKAFST-IKQG  182 (414)
T ss_dssp             HHHHHHHHHTCCSEEEEEHHHHHHCHHH--HTTCCCSEEEESCHHHHHHCHHHHHHHHHHTT-CCHHHHHHHHHH-HHHT
T ss_pred             HHHHHHhhcCCCCEEEECHHHHHHHHHH--hccccccEEEEeChHhhhhccchhhhHHhhcC-CcHHHHHHHHHh-cccc
Confidence            4556666655 99999999999988875  667799999999997654          4 66 8888 8888887 54  


Q ss_pred             ---------CCceEEEEeec-CcHHHH-HHHHHhccCcEEEEEcCCccccCCceEEEEEcCChhhHHHHHHHHHHhcCCC
Q 030396           71 ---------PSIVRSLFSAT-LPDFVE-ELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNP  139 (178)
Q Consensus        71 ---------~~~q~i~~SAT-~~~~~~-~~~~~~~~~~~~v~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~  139 (178)
                               ...|++++||| .|..+. .+...++.    +..........++.+.++.+    ++...+.++++.. ..
T Consensus       183 ~~~~~l~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~----~~~~~~~~~~~~i~~~~~~~----~~~~~l~~~l~~~-~~  253 (414)
T 3oiy_A          183 KIYERPKNLKPGILVVSSATAKPRGIRPLLFRDLLN----FTVGRLVSVARNITHVRISS----RSKEKLVELLEIF-RD  253 (414)
T ss_dssp             CCCCCCTTCCCCEEEESSCCSSCCSSTTHHHHHHHS----CCSSCCCCCCCSEEEEEESS----CCHHHHHHHHHHH-CS
T ss_pred             hhhhhcccCCCceEEEEecCCCcchhHHHHHHHhhc----cCcCccccccccchheeecc----CHHHHHHHHHHHc-CC
Confidence                     78999999999 565544 33333333    22334445566777777544    3556677777774 58


Q ss_pred             CEEEEeCCchHHHHHHHHhhhCCCceE-eeecC
Q 030396          140 PVLIFVQSKDRAKELYGELAFDDIRAG-VIHSD  171 (178)
Q Consensus       140 ~~lIF~~t~~~~~~l~~~L~~~g~~~~-~lh~~  171 (178)
                      ++||||+|++.|+.++..|...|+++. .+||+
T Consensus       254 ~~lVF~~~~~~~~~l~~~L~~~~~~~~~~~h~~  286 (414)
T 3oiy_A          254 GILIFAQTEEEGKELYEYLKRFKFNVGETWSEF  286 (414)
T ss_dssp             SEEEEESSHHHHHHHHHHHHHTTCCEEESSSCH
T ss_pred             CEEEEECCHHHHHHHHHHHHHcCCceehhhcCc
Confidence            999999999999999999999999998 99985

>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=99.83  E-value=3.2e-20  Score=137.88  Aligned_cols=98  Identities=31%  Similarity=0.434  Sum_probs=89.6

Q ss_pred             HHhHHhccCCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcHH
Q 030396            6 VRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDF   85 (178)
Q Consensus         6 ~~q~~~l~~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~   85 (178)
                      ..+.+.+.++++|+|+|||++.+++..+..++++++++|+||||.+++++ |.+.+..+++. ++.+.|++++|||+|+.
T Consensus       143 ~~~~~~~~~~~~I~v~Tp~~l~~~l~~~~~~~~~~~~lViDEah~l~~~~-~~~~~~~i~~~-~~~~~q~~~~SAT~~~~  220 (242)
T 3fe2_A          143 GPQIRDLERGVEICIATPGRLIDFLECGKTNLRRTTYLVLDEADRMLDMG-FEPQIRKIVDQ-IRPDRQTLMWSATWPKE  220 (242)
T ss_dssp             HHHHHHHHHCCSEEEECHHHHHHHHHHTSCCCTTCCEEEETTHHHHHHTT-CHHHHHHHHTT-SCSSCEEEEEESCCCHH
T ss_pred             HHHHHHhcCCCCEEEECHHHHHHHHHcCCCCcccccEEEEeCHHHHhhhC-cHHHHHHHHHh-CCccceEEEEEeecCHH
Confidence            34555666789999999999999999988899999999999999999999 99999999999 78899999999999999


Q ss_pred             HHHHHHHhccCcEEEEEcCC
Q 030396           86 VEELARSIMHDAVRVIVGRK  105 (178)
Q Consensus        86 ~~~~~~~~~~~~~~v~~~~~  105 (178)
                      +..+++.++++|..+.++..
T Consensus       221 ~~~~~~~~l~~~~~i~~~~~  240 (242)
T 3fe2_A          221 VRQLAEDFLKDYIHINIGAL  240 (242)
T ss_dssp             HHHHHHHHCSSCEEEEECC-
T ss_pred             HHHHHHHHCCCCEEEEecCC
Confidence            99999999999999988754

>4a4z_A Antiviral helicase SKI2; hydrolase, ATPase, mRNA degradation, exosome; HET: ANP; 2.40A {Saccharomyces cerevisiae} PDB: 4a4k_A

Probab=99.82  E-value=3.3e-19  Score=154.98  Aligned_cols=160  Identities=19%  Similarity=0.166  Sum_probs=120.0

Q ss_pred             CCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcHHH--HHHHH
Q 030396           14 FSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFV--EELAR   91 (178)
Q Consensus        14 ~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~~--~~~~~   91 (178)
                      ..++|+|+|||+|.+++..+...+.+++++|+||||.+.+++ +...++.++.. ++...|++++|||+++..  ..++.
T Consensus       122 ~~~~IlV~Tpe~L~~~l~~~~~~l~~l~lvViDEaH~l~d~~-~g~~~e~ii~~-l~~~v~iIlLSAT~~n~~ef~~~l~  199 (997)
T 4a4z_A          122 PDANCLIMTTEILRSMLYRGADLIRDVEFVIFDEVHYVNDQD-RGVVWEEVIIM-LPQHVKFILLSATVPNTYEFANWIG  199 (997)
T ss_dssp             TTSSEEEEEHHHHHHHHHHTCSGGGGEEEEEECCTTCCCTTC-TTCCHHHHHHH-SCTTCEEEEEECCCTTHHHHHHHHH
T ss_pred             CCCCEEEECHHHHHHHHHhCchhhcCCCEEEEECcccccccc-hHHHHHHHHHh-cccCCCEEEEcCCCCChHHHHHHHh
Confidence            458999999999999999888888999999999999999998 99999999999 888999999999998643  22332


Q ss_pred             HhccCcEEEEEcCCccccCCceEEEE------------------------------------------------------
Q 030396           92 SIMHDAVRVIVGRKNTASESIKQKLV------------------------------------------------------  117 (178)
Q Consensus        92 ~~~~~~~~v~~~~~~~~~~~i~~~~~------------------------------------------------------  117 (178)
                      .....+..+......  +..+.+++.                                                      
T Consensus       200 ~~~~~~~~vi~~~~r--~~pl~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~  277 (997)
T 4a4z_A          200 RTKQKNIYVISTPKR--PVPLEINIWAKKELIPVINQNSEFLEANFRKHKEILNGESAKGAPSKTDNGRGGSTARGGRGG  277 (997)
T ss_dssp             HHHTCCEEEEECSSC--SSCEEEEEEETTEEEEEECTTCCBCHHHHHHHHHHHC--------------------------
T ss_pred             cccCCceEEEecCCC--CccceEEEecCCcchhcccchhhhhHHHHHHHHHHhhcccccccccccccccccccccccccc
Confidence            222233333222111  111111111                                                      


Q ss_pred             --------------------------------------EcCChhhHHHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhh
Q 030396          118 --------------------------------------FAGSEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELA  159 (178)
Q Consensus       118 --------------------------------------~~~~~~~k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~  159 (178)
                                                            .......+...+...+......++||||+|++.|+.++..|.
T Consensus       278 ~~~rg~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~li~~l~~~~~~~~IVF~~sr~~~e~la~~L~  357 (997)
T 4a4z_A          278 SNTRDGRGGRGNSTRGGANRGGSRGAGAIGSNKRKFFTQDGPSKKTWPEIVNYLRKRELLPMVVFVFSKKRCEEYADWLE  357 (997)
T ss_dssp             ---------------------------------------CCCCTTHHHHHHHHHHHTTCCSEEEECSCHHHHHHHHHTTT
T ss_pred             ccccccccccccccccccccccccccccccccccccccccccchhHHHHHHHHHHhCCCCCEEEEECCHHHHHHHHHHHh
Confidence                                                  111223456678888888878899999999999999999998


Q ss_pred             hCCC---------------------------------------ceEeeecCCCcccc
Q 030396          160 FDDI---------------------------------------RAGVIHSDLSQTQV  177 (178)
Q Consensus       160 ~~g~---------------------------------------~~~~lh~~~~~~~R  177 (178)
                      ..|+                                       .+..+||+|++.+|
T Consensus       358 ~~~~~~~~e~~~i~~~~~~~~~~l~~~d~~l~~~~~l~~~l~~gi~~~H~gl~~~~R  414 (997)
T 4a4z_A          358 GINFCNNKEKSQIHMFIEKSITRLKKEDRDLPQILKTRSLLERGIAVHHGGLLPIVK  414 (997)
T ss_dssp             TCCCCCHHHHHHHHHHHHHHHTTSCHHHHTCHHHHHHHHHHTTTEEEECTTSCHHHH
T ss_pred             cCCCCCHHHHHHHHHHHHHHHHhcchhhhcchhHHHHHHHhhcCeeeecCCCCHHHH
Confidence            8777                                       47899999999776

>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=99.82  E-value=8.9e-20  Score=136.22  Aligned_cols=109  Identities=31%  Similarity=0.521  Sum_probs=87.4

Q ss_pred             HHhHHhccCCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhC-CCC--CceEEEEeecC
Q 030396            6 VRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKAC-SNP--SIVRSLFSATL   82 (178)
Q Consensus         6 ~~q~~~l~~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~-~~~--~~q~i~~SAT~   82 (178)
                      .++.+.+..+++|+|+|||++.+++..+..++++++++|+||||.+++++ |.+.+..+++.+ .+.  ..|++++|||+
T Consensus       141 ~~~~~~~~~~~~Ivv~Tp~~l~~~l~~~~~~~~~~~~lViDEah~~~~~~-~~~~~~~i~~~~~~~~~~~~q~l~~SAT~  219 (253)
T 1wrb_A          141 HSQIREVQMGCHLLVATPGRLVDFIEKNKISLEFCKYIVLDEADRMLDMG-FEPQIRKIIEESNMPSGINRQTLMFSATF  219 (253)
T ss_dssp             HHHHHHHSSCCSEEEECHHHHHHHHHTTSBCCTTCCEEEEETHHHHHHTT-CHHHHHHHHHSSCCCCGGGCEEEEEESSC
T ss_pred             HHHHHHhCCCCCEEEECHHHHHHHHHcCCCChhhCCEEEEeCHHHHHhCc-hHHHHHHHHhhccCCCCCCcEEEEEEEeC
Confidence            34556667889999999999999999988899999999999999999999 999999999963 333  78999999999


Q ss_pred             cHHHHHHHHHhccCcEEEEEcCCccccCCceEE
Q 030396           83 PDFVEELARSIMHDAVRVIVGRKNTASESIKQK  115 (178)
Q Consensus        83 ~~~~~~~~~~~~~~~~~v~~~~~~~~~~~i~~~  115 (178)
                      ++.+.+++..++.+|..+.++.......++.|+
T Consensus       220 ~~~~~~~~~~~l~~~~~i~~~~~~~~~~~i~q~  252 (253)
T 1wrb_A          220 PKEIQKLAADFLYNYIFMTVGRVGSTSDSIKQE  252 (253)
T ss_dssp             CHHHHHHHHHHCSSCEEEEEC------------
T ss_pred             CHHHHHHHHHHcCCCEEEEECCCCCCcCCceec
Confidence            999999999999999999998877777777765

>4ddu_A Reverse gyrase; topoisomerase, DNA supercoiling, archaea, helicase, hydrolas; 3.00A {Thermotoga maritima} PDB: 4ddt_A 4ddv_A 4ddw_A 4ddx_A

Probab=99.82  E-value=1.9e-20  Score=164.12  Aligned_cols=153  Identities=20%  Similarity=0.242  Sum_probs=119.5

Q ss_pred             HHhHHhccCC-CcEEEeCcHHHHHHHHcCCCCCCCeeEEEEecccc----------ccc-cCCChhh-HHHHHhhCCC--
Q 030396            6 VRSTDLSKFS-CDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADK----------LFE-VGNLLKH-IDPVVKACSN--   70 (178)
Q Consensus         6 ~~q~~~l~~~-~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~----------ll~-~~~~~~~-i~~i~~~~~~--   70 (178)
                      .++.+.+.++ ++|+|||||+|.+++..  +++++++++|+||||.          +++ +| |.+. +..+++. ++  
T Consensus       164 ~~~~~~l~~g~~~IlV~Tp~rL~~~l~~--l~~~~l~~lViDEaH~l~~~~r~~Dr~L~~~g-f~~~~i~~il~~-l~~~  239 (1104)
T 4ddu_A          164 EKFEKSFEEDDYHILVFSTQFVSKNREK--LSQKRFDFVFVDDVDAVLKASRNIDTLLMMVG-IPEEIIRKAFST-IKQG  239 (1104)
T ss_dssp             HHHHHHHHTSCCSEEEEEHHHHHHSHHH--HHTSCCSEEEESCHHHHTTSSHHHHHHHHTSS-CCHHHHHHHHHH-HHHT
T ss_pred             HHHHHHHhCCCCCEEEECHHHHHHHHHh--hcccCcCEEEEeCCCccccccccchhhhHhcC-CCHHHHHHHHHh-cccc
Confidence            5566667665 99999999999988875  6678999999999965          555 78 8888 8899987 55  


Q ss_pred             ---------CCceEEEEeec-CcHHHHH-HHHHhccCcEEEEEcCCccccCCceEEEEEcCChhhHHHHHHHHHHhcCCC
Q 030396           71 ---------PSIVRSLFSAT-LPDFVEE-LARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNP  139 (178)
Q Consensus        71 ---------~~~q~i~~SAT-~~~~~~~-~~~~~~~~~~~v~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~  139 (178)
                               ...|++++||| .|..+.. +....+.    +.+......+.++.+.++.+    +|...+.++++.. .+
T Consensus       240 ~~~~~~~~~~~~q~ll~SAT~~p~~~~~~~~~~~l~----i~v~~~~~~~~~i~~~~~~~----~k~~~L~~ll~~~-~~  310 (1104)
T 4ddu_A          240 KIYERPKNLKPGILVVSSATAKPRGIRPLLFRDLLN----FTVGRLVSVARNITHVRISS----RSKEKLVELLEIF-RD  310 (1104)
T ss_dssp             SCCCCCSSCCCCEEEEECBSSCCCSSTTHHHHHHTC----CCCCBCCCCCCCEEEEEESC----CCHHHHHHHHHHH-CS
T ss_pred             hhhhhhccCCCceEEEEcCCCCcHHHHHHHhhccee----EEeccCCCCcCCceeEEEec----CHHHHHHHHHHhc-CC
Confidence                     78999999999 5655442 3333333    44445556677888887655    3556677777775 58


Q ss_pred             CEEEEeCCchHHHHHHHHhhhCCCceE-eeecC
Q 030396          140 PVLIFVQSKDRAKELYGELAFDDIRAG-VIHSD  171 (178)
Q Consensus       140 ~~lIF~~t~~~~~~l~~~L~~~g~~~~-~lh~~  171 (178)
                      ++||||||++.|+.++..|...|+++. .+||+
T Consensus       311 ~~LVF~~s~~~a~~l~~~L~~~g~~~~~~lhg~  343 (1104)
T 4ddu_A          311 GILIFAQTEEEGKELYEYLKRFKFNVGETWSEF  343 (1104)
T ss_dssp             SEEEEESSSHHHHHHHHHHHHTTCCEEESSSSH
T ss_pred             CEEEEECcHHHHHHHHHHHHhCCCCeeeEecCc
Confidence            999999999999999999999999998 99993

>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=99.80  E-value=2.1e-19  Score=132.11  Aligned_cols=93  Identities=31%  Similarity=0.429  Sum_probs=85.4

Q ss_pred             HhHHhccCCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcHHH
Q 030396            7 RSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFV   86 (178)
Q Consensus         7 ~q~~~l~~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~~   86 (178)
                      .+.+.+.++++|+|+|||++.+++..+..++++++++|+||||.+++++ |.+.+..+++. .+.+.|++++|||+|+.+
T Consensus       135 ~~~~~~~~~~~iiv~Tp~~l~~~~~~~~~~~~~~~~lViDEah~~~~~~-~~~~~~~i~~~-~~~~~~~l~~SAT~~~~~  212 (228)
T 3iuy_A          135 GQIEDISKGVDIIIATPGRLNDLQMNNSVNLRSITYLVIDEADKMLDME-FEPQIRKILLD-VRPDRQTVMTSATWPDTV  212 (228)
T ss_dssp             -CHHHHHSCCSEEEECHHHHHHHHHTTCCCCTTCCEEEECCHHHHHHTT-CHHHHHHHHHH-SCSSCEEEEEESCCCHHH
T ss_pred             HHHHHhcCCCCEEEECHHHHHHHHHcCCcCcccceEEEEECHHHHhccc-hHHHHHHHHHh-CCcCCeEEEEEeeCCHHH
Confidence            4455666789999999999999999988899999999999999999999 99999999999 788999999999999999


Q ss_pred             HHHHHHhccCcEEEE
Q 030396           87 EELARSIMHDAVRVI  101 (178)
Q Consensus        87 ~~~~~~~~~~~~~v~  101 (178)
                      ++++..++++|..+.
T Consensus       213 ~~~~~~~l~~p~~i~  227 (228)
T 3iuy_A          213 RQLALSYLKDPMIVY  227 (228)
T ss_dssp             HHHHHTTCSSCEEEE
T ss_pred             HHHHHHHCCCCEEEe
Confidence            999999999998775

>1tf5_A Preprotein translocase SECA subunit; ATPase, helicase, translocation, secretion, protein transport; 2.18A {Bacillus subtilis} SCOP: a.162.1.1 a.172.1.1 c.37.1.19 c.37.1.19 PDB: 1tf2_A 3iqy_A 1m6n_A 1m74_A* 3iqm_A 3jv2_A* 2ibm_A* 3dl8_A 1sx0_A 1sx1_A 1tm6_A

Probab=99.80  E-value=1.2e-20  Score=158.92  Aligned_cols=164  Identities=20%  Similarity=0.294  Sum_probs=115.1

Q ss_pred             ccCCCcEEEeCcHHH-HHHHHcC------CCCCCCeeEEEEecccccc-ccC--------------CChhhHHHHHhhCC
Q 030396           12 SKFSCDILISTPLRL-RLAIRRK------KIDLSRVEYLVLDEADKLF-EVG--------------NLLKHIDPVVKACS   69 (178)
Q Consensus        12 l~~~~~Iii~TP~~l-~~~l~~~------~~~~~~l~~lViDE~d~ll-~~~--------------~~~~~i~~i~~~~~   69 (178)
                      ...+|||+|||||+| .++++.+      .+.++.++++|+||||.|+ +.+              .|.+.+..|++. +
T Consensus       169 ~~~~~dIv~gTpgrlgfD~L~D~m~~~~~~l~lr~~~~lVlDEaD~mLiDea~tplIisg~~~~~~~~~~~i~~iv~~-l  247 (844)
T 1tf5_A          169 EAYAADITYSTNNELGFDYLRDNMVLYKEQMVQRPLHFAVIDEVDSILIDEARTPLIISGQAAKSTKLYVQANAFVRT-L  247 (844)
T ss_dssp             HHHHSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCCCCEEEEETHHHHHTTTTTCEEEEEEEEECCCHHHHHHHHHHTT-C
T ss_pred             HhcCCCEEEECchhhhHHHHHHhhhcchhhhcccCCCEEEECchhhhhhhccccchhhcCCcccchhHHHHHHHHHHh-C
Confidence            345799999999999 6777643      3668999999999999998 553              156889999999 5


Q ss_pred             C---------CCceEE-----------------EEeecCcH---HHHHHHH--Hhcc-CcEEE-------EE--------
Q 030396           70 N---------PSIVRS-----------------LFSATLPD---FVEELAR--SIMH-DAVRV-------IV--------  102 (178)
Q Consensus        70 ~---------~~~q~i-----------------~~SAT~~~---~~~~~~~--~~~~-~~~~v-------~~--------  102 (178)
                      +         ..+|+.                 +||||.+.   .+...+.  .++. ++..+       .+        
T Consensus       248 ~~~~~y~vd~k~rq~~lt~~g~~~~e~~~~i~~Lfsat~~~~~~~i~~al~A~~l~~~d~dYiv~dg~v~ivDe~tgr~m  327 (844)
T 1tf5_A          248 KAEKDYTYDIKTKAVQLTEEGMTKAEKAFGIDNLFDVKHVALNHHINQALKAHVAMQKDVDYVVEDGQVVIVDSFTGRLM  327 (844)
T ss_dssp             CSSSSBCCCSSSCCCCBCHHHHHHHHHHTTCSCTTSGGGHHHHHHHHHHHHHHHTCCBTTTEEEETTEEEEBCTTTCCBC
T ss_pred             cccccceeccccceEEecHHHHHHHHHHhCccccCCCccchhHHHHHHHHHHHHHhhcCCceEEecCeeEEeeccccccc
Confidence            5         478887                 89999874   3433322  2222 22111       00        


Q ss_pred             ---------------------cCCccccCCce----------------------------------------------E-
Q 030396          103 ---------------------GRKNTASESIK----------------------------------------------Q-  114 (178)
Q Consensus       103 ---------------------~~~~~~~~~i~----------------------------------------------~-  114 (178)
                                           .....+...+.                                              + 
T Consensus       328 ~grr~sdGLhqaieake~v~I~~e~~t~a~It~q~~fr~y~kl~GmTGTa~te~~e~~~iY~l~vv~IPtn~p~~r~d~~  407 (844)
T 1tf5_A          328 KGRRYSEGLHQAIEAKEGLEIQNESMTLATITFQNYFRMYEKLAGMTGTAKTEEEEFRNIYNMQVVTIPTNRPVVRDDRP  407 (844)
T ss_dssp             TTCCCSTTHHHHHHHHTTCCCCCCEEEEEEEEHHHHHTTSSEEEEEESCCGGGHHHHHHHHCCCEEECCCSSCCCCEECC
T ss_pred             CCCccchhhHHHHhhcccceecccccccceeeHHHHHHHHhhhccCCcccchhHHHHHHHhCCceEEecCCCCcccccCC
Confidence                                 00000000111                                              1 


Q ss_pred             EEEEcCChhhHHHHHHHHHHh--cCCCCEEEEeCCchHHHHHHHHhhhCCCceEeeecCCCcccc
Q 030396          115 KLVFAGSEEGKLLALRQSFAE--SLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQV  177 (178)
Q Consensus       115 ~~~~~~~~~~k~~~l~~ll~~--~~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~~~~~~R  177 (178)
                      .++++ ...+|...+.+.+..  ...+++||||+|++.++.++..|...|+++..+||++.+++|
T Consensus       408 d~v~~-~~~~K~~al~~~i~~~~~~~~pvLVft~s~~~se~Ls~~L~~~gi~~~vLhg~~~~rEr  471 (844)
T 1tf5_A          408 DLIYR-TMEGKFKAVAEDVAQRYMTGQPVLVGTVAVETSELISKLLKNKGIPHQVLNAKNHEREA  471 (844)
T ss_dssp             CEEES-SHHHHHHHHHHHHHHHHHHTCCEEEEESCHHHHHHHHHHHHTTTCCCEEECSSCHHHHH
T ss_pred             cEEEe-CHHHHHHHHHHHHHHHHhcCCcEEEEECCHHHHHHHHHHHHHCCCCEEEeeCCccHHHH
Confidence            13333 566788999888864  246789999999999999999999999999999999887765

>2fsf_A Preprotein translocase SECA subunit; ATPase, DNA-RNA helicase, protein translocation, protein transport; 2.00A {Escherichia coli} PDB: 2fsg_A* 2fsh_A* 2fsi_A* 2vda_A 3bxz_A*

Probab=99.79  E-value=7.7e-20  Score=153.92  Aligned_cols=166  Identities=19%  Similarity=0.275  Sum_probs=92.7

Q ss_pred             HhccCCCcEEEeCcHHH-HHHHHcCC------CCCCCeeEEEEecccccc-ccC--------------CChhhHHHHHhh
Q 030396           10 DLSKFSCDILISTPLRL-RLAIRRKK------IDLSRVEYLVLDEADKLF-EVG--------------NLLKHIDPVVKA   67 (178)
Q Consensus        10 ~~l~~~~~Iii~TP~~l-~~~l~~~~------~~~~~l~~lViDE~d~ll-~~~--------------~~~~~i~~i~~~   67 (178)
                      +.+..+|+|+|||||+| .++++.+.      +.++.++++|+||||.|+ +.+              .|...+..|+..
T Consensus       158 r~~~~~~dIvvgTpgrl~fDyLrd~~~~~~~~~~~~~l~~lVlDEaD~mLiD~a~tpLIiSg~~~~~~~~y~~i~~iv~~  237 (853)
T 2fsf_A          158 KREAYAADITYGTNNEYGFDYLRDNMAFSPEERVQRKLHYALVDEVDSILIDEARTPLIISGPAEDSSEMYKRVNKIIPH  237 (853)
T ss_dssp             HHHHHHSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCSCCEEEESCHHHHTTTTTTCEEEEEEC-----------------
T ss_pred             HHHhcCCCEEEECCchhhHHHHHhhhhccHhHhcccCCcEEEECchHHHHHhcCcccccccCCCccchhHHHHHHHHHHh
Confidence            33445799999999999 79887653      668999999999999998 432              256788888888


Q ss_pred             CCCC--------------------CceEE------------------------EEeecCcH---HHHHHH--HHhcc-C-
Q 030396           68 CSNP--------------------SIVRS------------------------LFSATLPD---FVEELA--RSIMH-D-   96 (178)
Q Consensus        68 ~~~~--------------------~~q~i------------------------~~SAT~~~---~~~~~~--~~~~~-~-   96 (178)
                       ++.                    .+|+.                        +||||.++   .+...+  ..++. + 
T Consensus       238 -L~~~~~~~~~~~~~~~dy~vdek~rqv~lte~g~~~~e~~l~~~~l~~~~~~Lfsat~~~~~~~i~~al~A~~l~~~d~  316 (853)
T 2fsf_A          238 -LIRQEKEDSETFQGEGHFSVDEKSRQVNLTERGLVLIEELLVKEGIMDEGESLYSPANIMLMHHVTAALRAHALFTRDV  316 (853)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             -chhhhccccccccccccceeccccceEEEcHHHHHHHHHHHHhCCcccccccccCcccchHHHHHHHHHHHHHHhhcCc
Confidence             443                    56654                        89999864   222211  11110 0 


Q ss_pred             -----------------------------------cEEEEEcCCccccCCceE---------------------------
Q 030396           97 -----------------------------------AVRVIVGRKNTASESIKQ---------------------------  114 (178)
Q Consensus        97 -----------------------------------~~~v~~~~~~~~~~~i~~---------------------------  114 (178)
                                                         +..+.+.+...+...|.+                           
T Consensus       317 dYiV~d~~vviVde~tgR~m~grr~sdGLhQaieake~v~I~~e~~tla~It~qnyfr~Y~kl~GmTGTa~te~~ef~~i  396 (853)
T 2fsf_A          317 DYIVKDGEVIIVDEHTGRTMQGRRWSDGLHQAVEAKEGVQIQNENQTLASITFQNYFRLYEKLAGMTGTADTEAFEFSSI  396 (853)
T ss_dssp             ----------------------------------------CCCCCEEEEEEEHHHHHTTSSEEEEEECTTCCCHHHHHHH
T ss_pred             cceeecCcEEEEecccCcccCCCccchhhhHHHHhcccceecccccccceeehHHHHhhhhhhhcCCCCchhHHHHHHHH
Confidence                                               112233333333333332                           


Q ss_pred             --------------------EEEEcCChhhHHHHHHHHHHh--cCCCCEEEEeCCchHHHHHHHHhhhCCCceEeeecCC
Q 030396          115 --------------------KLVFAGSEEGKLLALRQSFAE--SLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDL  172 (178)
Q Consensus       115 --------------------~~~~~~~~~~k~~~l~~ll~~--~~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~~  172 (178)
                                          .++++ ....|...+.+.+..  ...+|+||||+|+..++.++..|...|+++..+||++
T Consensus       397 Y~l~vv~IPtn~p~~R~d~~d~v~~-~~~~K~~al~~~i~~~~~~gqpvLVft~sie~se~Ls~~L~~~gi~~~vLnak~  475 (853)
T 2fsf_A          397 YKLDTVVVPTNRPMIRKDLPDLVYM-TEAEKIQAIIEDIKERTAKGQPVLVGTISIEKSELVSNELTKAGIKHNVLNAKF  475 (853)
T ss_dssp             HCCEEEECCCSSCCCCEECCCEEES-SHHHHHHHHHHHHHHHHTTTCCEEEEESSHHHHHHHHHHHHHTTCCCEECCTTC
T ss_pred             hCCcEEEcCCCCCceeecCCcEEEe-CHHHHHHHHHHHHHHHhcCCCCEEEEECcHHHHHHHHHHHHHCCCCEEEecCCh
Confidence                                12333 567899999988864  3467899999999999999999999999999999998


Q ss_pred             Ccccc
Q 030396          173 SQTQV  177 (178)
Q Consensus       173 ~~~~R  177 (178)
                      .+++|
T Consensus       476 ~~rEa  480 (853)
T 2fsf_A          476 HANEA  480 (853)
T ss_dssp             HHHHH
T ss_pred             hHHHH
Confidence            76654

>1gku_B Reverse gyrase, TOP-RG; topoisomerase, DNA supercoiling, archaea, helicase; 2.7A {Archaeoglobus fulgidus} SCOP: c.37.1.16 c.37.1.16 e.10.1.1 PDB: 1gl9_B*

Probab=99.79  E-value=1.9e-20  Score=163.77  Aligned_cols=152  Identities=14%  Similarity=0.264  Sum_probs=119.8

Q ss_pred             hHHhccCCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCC----------CCCceEEE
Q 030396            8 STDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACS----------NPSIVRSL   77 (178)
Q Consensus         8 q~~~l~~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~----------~~~~q~i~   77 (178)
                      +.+.+++ ++|+|||||+|.+++.+    +++++++|+||||.++++   ...++.++..+.          +...|+++
T Consensus       149 ~~~~l~~-~~IlV~TP~~L~~~l~~----L~~l~~lViDEah~~l~~---~~~~~~i~~~lgf~~~~~~~~~~~~~q~~l  220 (1054)
T 1gku_B          149 FMQNLRN-FKIVITTTQFLSKHYRE----LGHFDFIFVDDVDAILKA---SKNVDKLLHLLGFHYDLKTKSWVGEARGCL  220 (1054)
T ss_dssp             HHHSGGG-CSEEEEEHHHHHHCSTT----SCCCSEEEESCHHHHHTS---THHHHHHHHHTTEEEETTTTEEEECCSSEE
T ss_pred             HHhhccC-CCEEEEcHHHHHHHHHH----hccCCEEEEeChhhhhhc---cccHHHHHHHhCcchhhhhhhcccCCceEE
Confidence            4556666 99999999999998775    669999999999999884   467777777621          35689999


Q ss_pred             EeecCcHHHHHHHHHhccCcEEEEEcCCccccCCceEEEEEcCChhhHHHHHHHHHHhcCCCCEEEEeCCchHHHHHHHH
Q 030396           78 FSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGE  157 (178)
Q Consensus        78 ~SAT~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~  157 (178)
                      +|||+++. ..+...++.++..+.+........++.+.++    ..+|...+.++++.. ..++||||+|++.|+.++..
T Consensus       221 ~SAT~t~~-~~~~~~~~~~~~~i~v~~~~~~~~~i~~~~~----~~~k~~~L~~ll~~~-~~~~LVF~~t~~~a~~l~~~  294 (1054)
T 1gku_B          221 MVSTATAK-KGKKAELFRQLLNFDIGSSRITVRNVEDVAV----NDESISTLSSILEKL-GTGGIIYARTGEEAEEIYES  294 (1054)
T ss_dssp             EECCCCSC-CCTTHHHHHHHHCCCCSCCEECCCCEEEEEE----SCCCTTTTHHHHTTS-CSCEEEEESSHHHHHHHHHT
T ss_pred             EEecCCCc-hhHHHHHhhcceEEEccCcccCcCCceEEEe----chhHHHHHHHHHhhc-CCCEEEEEcCHHHHHHHHHH
Confidence            99999987 6555555555555555555666677877775    235667788888776 57899999999999999999


Q ss_pred             hhhCCCceEeeecCCCc
Q 030396          158 LAFDDIRAGVIHSDLSQ  174 (178)
Q Consensus       158 L~~~g~~~~~lh~~~~~  174 (178)
                      |... +++..+||+|..
T Consensus       295 L~~~-~~v~~lhg~~~~  310 (1054)
T 1gku_B          295 LKNK-FRIGIVTATKKG  310 (1054)
T ss_dssp             TTTS-SCEEECTTSSSH
T ss_pred             Hhhc-cCeeEEeccHHH
Confidence            9988 999999999853

>2zj8_A DNA helicase, putative SKI2-type helicase; RECA fold, ATP-binding, hydrolase, nucleotide- binding; 2.00A {Pyrococcus furiosus} PDB: 2zj5_A* 2zj2_A 2zja_A*

Probab=99.78  E-value=3.3e-19  Score=150.89  Aligned_cols=154  Identities=16%  Similarity=0.115  Sum_probs=111.2

Q ss_pred             CCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcHHHHHHHHHh
Q 030396           14 FSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSI   93 (178)
Q Consensus        14 ~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~~~~~~~~~   93 (178)
                      ++++|+|+|||++..++.++...+++++++|+||+|.+.+++ +...++.++.. ++...|++++|||+++. .. +..|
T Consensus       113 ~~~~Iiv~Tpe~l~~~~~~~~~~l~~~~~vIiDE~H~l~~~~-r~~~~~~ll~~-l~~~~~ii~lSATl~n~-~~-~~~~  188 (720)
T 2zj8_A          113 GKYDIIIATAEKFDSLLRHGSSWIKDVKILVADEIHLIGSRD-RGATLEVILAH-MLGKAQIIGLSATIGNP-EE-LAEW  188 (720)
T ss_dssp             GGCSEEEECHHHHHHHHHHTCTTGGGEEEEEEETGGGGGCTT-THHHHHHHHHH-HBTTBEEEEEECCCSCH-HH-HHHH
T ss_pred             CCCCEEEECHHHHHHHHHcChhhhhcCCEEEEECCcccCCCc-ccHHHHHHHHH-hhcCCeEEEEcCCcCCH-HH-HHHH
Confidence            368999999999999998877778999999999999998877 89999999998 55589999999999863 33 3445


Q ss_pred             ccCcEEEEEcCCccccCCceEEEE-----EcCC-----hhhHHHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhhhC--
Q 030396           94 MHDAVRVIVGRKNTASESIKQKLV-----FAGS-----EEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFD--  161 (178)
Q Consensus        94 ~~~~~~v~~~~~~~~~~~i~~~~~-----~~~~-----~~~k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~~~--  161 (178)
                      +..+. +...   ..+..+...+.     ...+     ...+...+.+.+..  .+++||||+|++.|+.++..|.+.  
T Consensus       189 l~~~~-~~~~---~rp~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~LVF~~sr~~~~~~a~~L~~~~~  262 (720)
T 2zj8_A          189 LNAEL-IVSD---WRPVKLRRGVFYQGFVTWEDGSIDRFSSWEELVYDAIRK--KKGALIFVNMRRKAERVALELSKKVK  262 (720)
T ss_dssp             TTEEE-EECC---CCSSEEEEEEEETTEEEETTSCEEECSSTTHHHHHHHHT--TCCEEEECSCHHHHHHHHHHHHHHHG
T ss_pred             hCCcc-cCCC---CCCCcceEEEEeCCeeeccccchhhhhHHHHHHHHHHhC--CCCEEEEecCHHHHHHHHHHHHHHHH
Confidence            54321 1111   11111111111     1111     23445666666553  489999999999999999999753  


Q ss_pred             ----------------C---------------CceEeeecCCCcccc
Q 030396          162 ----------------D---------------IRAGVIHSDLSQTQV  177 (178)
Q Consensus       162 ----------------g---------------~~~~~lh~~~~~~~R  177 (178)
                                      +               ..+..+||+|++++|
T Consensus       263 ~~~~~~~~~~~~~~~~~i~~~~~~~~l~~~~~~~v~~~h~~l~~~~R  309 (720)
T 2zj8_A          263 SLLTKPEIRALNELADSLEENPTNEKLAKAIRGGVAFHHAGLGRDER  309 (720)
T ss_dssp             GGSCHHHHHHHHHHHHTSCSCHHHHHHHHHHTTTEEEECTTSCHHHH
T ss_pred             HhcChhhHHHHHHHHHHHhcccchHHHHHHHhcCeeeecCCCCHHHH
Confidence                            1               248999999999887

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19

Probab=99.78  E-value=5e-19  Score=129.43  Aligned_cols=96  Identities=25%  Similarity=0.417  Sum_probs=86.3

Q ss_pred             HhHHhccCCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcHHH
Q 030396            7 RSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFV   86 (178)
Q Consensus         7 ~q~~~l~~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~~   86 (178)
                      ++.+.+.++++|+|+|||++.+++..+..++.+++++|+||||.+.+++ +...+..+++. ++.+.|++++|||+|+++
T Consensus       118 ~~~~~~~~~~~Iiv~Tp~~l~~~l~~~~~~~~~~~~lViDEah~~~~~~-~~~~l~~i~~~-~~~~~~~l~~SAT~~~~~  195 (219)
T 1q0u_A          118 KALEKLNVQPHIVIGTPGRINDFIREQALDVHTAHILVVDEADLMLDMG-FITDVDQIAAR-MPKDLQMLVFSATIPEKL  195 (219)
T ss_dssp             HTTCCCSSCCSEEEECHHHHHHHHHTTCCCGGGCCEEEECSHHHHHHTT-CHHHHHHHHHT-SCTTCEEEEEESCCCGGG
T ss_pred             HHHHHcCCCCCEEEeCHHHHHHHHHcCCCCcCcceEEEEcCchHHhhhC-hHHHHHHHHHh-CCcccEEEEEecCCCHHH
Confidence            3444555689999999999999999988889999999999999999998 99999999999 788899999999999999


Q ss_pred             HHHHHHhccCcEEEEEcC
Q 030396           87 EELARSIMHDAVRVIVGR  104 (178)
Q Consensus        87 ~~~~~~~~~~~~~v~~~~  104 (178)
                      .++++.++++|..+.+..
T Consensus       196 ~~~~~~~~~~p~~~~~~~  213 (219)
T 1q0u_A          196 KPFLKKYMENPTFVHVLE  213 (219)
T ss_dssp             HHHHHHHCSSCEEEECC-
T ss_pred             HHHHHHHcCCCeEEEeec
Confidence            999999999998887654

>2p6r_A Afuhel308 helicase; protein-DNA complex, SF2 helicase, archaeal helicase, DNA repair,, DNA binding protein/DNA complex; 3.00A {Archaeoglobus fulgidus} SCOP: a.4.5.43 a.289.1.2 c.37.1.19 c.37.1.19 PDB: 2p6u_A

Probab=99.78  E-value=4.8e-19  Score=149.49  Aligned_cols=155  Identities=20%  Similarity=0.175  Sum_probs=110.3

Q ss_pred             CCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhC--CCCCceEEEEeecCcHHHHHHHH
Q 030396           14 FSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKAC--SNPSIVRSLFSATLPDFVEELAR   91 (178)
Q Consensus        14 ~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~--~~~~~q~i~~SAT~~~~~~~~~~   91 (178)
                      ++++|+|+|||++..++.++...+++++++|+||+|.+.+++ +...++.++..+  ..+..|++++|||+++ ...+ .
T Consensus       113 ~~~~Iiv~Tpe~l~~~l~~~~~~l~~~~~vIiDE~H~l~~~~-r~~~~~~ll~~l~~~~~~~~ii~lSATl~n-~~~~-~  189 (702)
T 2p6r_A          113 GDCDIIVTTSEKADSLIRNRASWIKAVSCLVVDEIHLLDSEK-RGATLEILVTKMRRMNKALRVIGLSATAPN-VTEI-A  189 (702)
T ss_dssp             TTCSEEEEEHHHHHHHHHTTCSGGGGCCEEEETTGGGGGCTT-THHHHHHHHHHHHHHCTTCEEEEEECCCTT-HHHH-H
T ss_pred             cCCCEEEECHHHHHHHHHcChhHHhhcCEEEEeeeeecCCCC-cccHHHHHHHHHHhcCcCceEEEECCCcCC-HHHH-H
Confidence            378999999999999998877678999999999999998877 788888877662  2568999999999996 3343 3


Q ss_pred             HhccCcEEEEEcCCccccCCceEEEE------EcCCh------hhHHHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhh
Q 030396           92 SIMHDAVRVIVGRKNTASESIKQKLV------FAGSE------EGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELA  159 (178)
Q Consensus        92 ~~~~~~~~v~~~~~~~~~~~i~~~~~------~~~~~------~~k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~  159 (178)
                      .|+..+. +...   ..+..+...+.      .....      ..+...+.+.+.  ..+++||||+|++.|+.++..|.
T Consensus       190 ~~l~~~~-~~~~---~r~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~LVF~~s~~~~~~~a~~L~  263 (702)
T 2p6r_A          190 EWLDADY-YVSD---WRPVPLVEGVLCEGTLELFDGAFSTSRRVKFEELVEECVA--ENGGVLVFESTRRGAEKTAVKLS  263 (702)
T ss_dssp             HHTTCEE-EECC---CCSSCEEEEEECSSEEEEEETTEEEEEECCHHHHHHHHHH--TTCCEEEECSSHHHHHHHHHHHH
T ss_pred             HHhCCCc-ccCC---CCCccceEEEeeCCeeeccCcchhhhhhhhHHHHHHHHHh--cCCCEEEEcCCHHHHHHHHHHHH
Confidence            4555432 2111   11111222111      11110      015666666665  35899999999999999999986


Q ss_pred             hC------------------------------CCceEeeecCCCcccc
Q 030396          160 FD------------------------------DIRAGVIHSDLSQTQV  177 (178)
Q Consensus       160 ~~------------------------------g~~~~~lh~~~~~~~R  177 (178)
                      +.                              ++.+..+||+|++++|
T Consensus       264 ~~~~~~~~~~~~~~~i~~~~~~~~~~~l~~~~~~~v~~~h~~l~~~~R  311 (702)
T 2p6r_A          264 AITAKYVENEGLEKAILEENEGEMSRKLAECVRKGAAFHHAGLLNGQR  311 (702)
T ss_dssp             HHHHTTCCCSSHHHHHHTTCCSHHHHHHHHHHHTTCCEECTTSCHHHH
T ss_pred             HHHHhhcChHHHHHHHHhhccccccHHHHHHHhcCeEEecCCCCHHHH
Confidence            53                              2458899999999887

>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=99.78  E-value=5.2e-19  Score=135.43  Aligned_cols=90  Identities=29%  Similarity=0.306  Sum_probs=82.3

Q ss_pred             cCCCcEEEeCcHHHHHHHHc-CCCCCCCeeEEEEeccccccc-cCCChhhHHHHHhhCCCCCceEEEEeecCcHHHHHHH
Q 030396           13 KFSCDILISTPLRLRLAIRR-KKIDLSRVEYLVLDEADKLFE-VGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELA   90 (178)
Q Consensus        13 ~~~~~Iii~TP~~l~~~l~~-~~~~~~~l~~lViDE~d~ll~-~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~~~~~~   90 (178)
                      +.+++|+|||||+|++++.+ +.+++++++++|+||||.+++ .+ |...+..|++. ++.+.|+++||||+++.+..++
T Consensus       208 ~~~~~IlV~TP~~l~~~l~~~~~~~l~~l~~lVlDEad~l~~~~~-~~~~~~~i~~~-~~~~~q~i~~SAT~~~~v~~~a  285 (300)
T 3fmo_B          208 KISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQG-HQDQSIRIQRM-LPRNCQMLLFSATFEDSVWKFA  285 (300)
T ss_dssp             CCCCSEEEECHHHHHHHHTTTCCCCGGGCSEEEETTHHHHHHSTT-HHHHHHHHHTT-SCTTCEEEEEESCCCHHHHHHH
T ss_pred             cCCCCEEEECHHHHHHHHHhcCCCChhhceEEEEeCHHHHhhccC-cHHHHHHHHHh-CCCCCEEEEEeccCCHHHHHHH
Confidence            45789999999999999966 678899999999999999998 56 99999999998 7889999999999999999999


Q ss_pred             HHhccCcEEEEEcC
Q 030396           91 RSIMHDAVRVIVGR  104 (178)
Q Consensus        91 ~~~~~~~~~v~~~~  104 (178)
                      ..++.+|..+.+..
T Consensus       286 ~~~l~~p~~i~~~~  299 (300)
T 3fmo_B          286 QKVVPDPNVIKLKR  299 (300)
T ss_dssp             HHHSSSCEEEEECC
T ss_pred             HHHCCCCeEEEecC
Confidence            99999999988754

>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=99.78  E-value=9.2e-19  Score=129.63  Aligned_cols=94  Identities=29%  Similarity=0.425  Sum_probs=80.5

Q ss_pred             hHHhccCC-CcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcHHH
Q 030396            8 STDLSKFS-CDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFV   86 (178)
Q Consensus         8 q~~~l~~~-~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~~   86 (178)
                      +.+.+..+ ++|+|+|||++.+++..+...+.+++++|+||||.+++++ |...+..+++. .+...|++++|||+|+.+
T Consensus       141 ~~~~l~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~~~~lViDEah~~~~~~-~~~~l~~i~~~-~~~~~~~i~~SAT~~~~~  218 (237)
T 3bor_A          141 EMQKLQAEAPHIVVGTPGRVFDMLNRRYLSPKWIKMFVLDEADEMLSRG-FKDQIYEIFQK-LNTSIQVVLLSATMPTDV  218 (237)
T ss_dssp             -------CCCSEEEECHHHHHHHHHTTSSCSTTCCEEEEESHHHHHHTT-CHHHHHHHHHH-SCTTCEEEEECSSCCHHH
T ss_pred             HHHHHhcCCCCEEEECHHHHHHHHHhCCcCcccCcEEEECCchHhhccC-cHHHHHHHHHh-CCCCCeEEEEEEecCHHH
Confidence            33344444 9999999999999999888889999999999999999998 99999999999 788999999999999999


Q ss_pred             HHHHHHhccCcEEEEEc
Q 030396           87 EELARSIMHDAVRVIVG  103 (178)
Q Consensus        87 ~~~~~~~~~~~~~v~~~  103 (178)
                      .+++..++++|..+.++
T Consensus       219 ~~~~~~~l~~p~~i~v~  235 (237)
T 3bor_A          219 LEVTKKFMRDPIRILVK  235 (237)
T ss_dssp             HHHHHHHCSSCEEEC--
T ss_pred             HHHHHHHCCCCEEEEec
Confidence            99999999999888664

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus}

Probab=99.77  E-value=3.2e-18  Score=144.73  Aligned_cols=152  Identities=21%  Similarity=0.200  Sum_probs=109.7

Q ss_pred             CCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcHHHHHHHHHhc
Q 030396           15 SCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIM   94 (178)
Q Consensus        15 ~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~~~~~~~~~~   94 (178)
                      +++|+|+|||++..++.++...+++++++|+||+|.+.+++ +...++.++.. ++ ..|++++|||+++. ..+. .|+
T Consensus       121 ~~~Iiv~Tpe~l~~~~~~~~~~l~~~~~vIiDE~H~l~~~~-~~~~l~~i~~~-~~-~~~ii~lSATl~n~-~~~~-~~l  195 (715)
T 2va8_A          121 NYDIIITTYEKLDSLWRHRPEWLNEVNYFVLDELHYLNDPE-RGPVVESVTIR-AK-RRNLLALSATISNY-KQIA-KWL  195 (715)
T ss_dssp             GCSEEEECHHHHHHHHHHCCGGGGGEEEEEECSGGGGGCTT-THHHHHHHHHH-HH-TSEEEEEESCCTTH-HHHH-HHH
T ss_pred             CCCEEEEcHHHHHHHHhCChhHhhccCEEEEechhhcCCcc-cchHHHHHHHh-cc-cCcEEEEcCCCCCH-HHHH-HHh
Confidence            68999999999999998877678999999999999988767 88999999887 44 89999999999853 3333 344


Q ss_pred             cCcEEEEEcCCccccCCceEEE-----------EEcCC--------hhhHHHHHHHHHHhcCCCCEEEEeCCchHHHHHH
Q 030396           95 HDAVRVIVGRKNTASESIKQKL-----------VFAGS--------EEGKLLALRQSFAESLNPPVLIFVQSKDRAKELY  155 (178)
Q Consensus        95 ~~~~~v~~~~~~~~~~~i~~~~-----------~~~~~--------~~~k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~  155 (178)
                      ..+. +...   ..+..+...+           +...+        ...+...+.+.+.  ..+++||||+|+++|+.++
T Consensus       196 ~~~~-~~~~---~r~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~LVF~~s~~~~~~~a  269 (715)
T 2va8_A          196 GAEP-VATN---WRPVPLIEGVIYPERKKKEYNVIFKDNTTKKVHGDDAIIAYTLDSLS--KNGQVLVFRNSRKMAESTA  269 (715)
T ss_dssp             TCEE-EECC---CCSSCEEEEEEEECSSTTEEEEEETTSCEEEEESSSHHHHHHHHHHT--TTCCEEEECSSHHHHHHHH
T ss_pred             CCCc-cCCC---CCCCCceEEEEecCCcccceeeecCcchhhhcccchHHHHHHHHHHh--cCCCEEEEECCHHHHHHHH
Confidence            4322 1111   0111111111           11111        2345666666654  3589999999999999999


Q ss_pred             HHhhhCC------------------------------------CceEeeecCCCcccc
Q 030396          156 GELAFDD------------------------------------IRAGVIHSDLSQTQV  177 (178)
Q Consensus       156 ~~L~~~g------------------------------------~~~~~lh~~~~~~~R  177 (178)
                      ..|.+..                                    ..+..+||+|++++|
T Consensus       270 ~~L~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~l~~~~~~~v~~~h~~l~~~~r  327 (715)
T 2va8_A          270 LKIANYMNFVSLDENALSEILKQLDDIEEGGSDEKELLKSLISKGVAYHHAGLSKALR  327 (715)
T ss_dssp             HHHHHTTTSSCCCHHHHHHHHHHHHTCCSSCHHHHHHHHHHHTTTEEEECTTSCHHHH
T ss_pred             HHHHHHHhhccCChHHHHHHHHHHHHhhhccccccHHHHHHHhcCEEEECCCCCHHHH
Confidence            9997642                                    248999999999887

>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=99.77  E-value=2.8e-18  Score=124.07  Aligned_cols=93  Identities=23%  Similarity=0.310  Sum_probs=84.6

Q ss_pred             HHhHHhccCCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcHH
Q 030396            6 VRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDF   85 (178)
Q Consensus         6 ~~q~~~l~~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~   85 (178)
                      .++...+.++++|+|+|||++.+.+.++...+++++++|+||||.+.+.+ +...+..+++. .+.+.|++++|||+|+.
T Consensus       113 ~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~lViDEah~~~~~~-~~~~l~~i~~~-~~~~~~~l~~SAT~~~~  190 (206)
T 1vec_A          113 RDDIMRLDDTVHVVIATPGRILDLIKKGVAKVDHVQMIVLDEADKLLSQD-FVQIMEDIILT-LPKNRQILLYSATFPLS  190 (206)
T ss_dssp             HHHHHHTTSCCSEEEECHHHHHHHHHTTCSCCTTCCEEEEETHHHHTSTT-THHHHHHHHHH-SCTTCEEEEEESCCCHH
T ss_pred             HHHHHhcCCCCCEEEeCHHHHHHHHHcCCcCcccCCEEEEEChHHhHhhC-cHHHHHHHHHh-CCccceEEEEEeeCCHH
Confidence            34555667789999999999999999988889999999999999999888 99999999999 78899999999999999


Q ss_pred             HHHHHHHhccCcEEE
Q 030396           86 VEELARSIMHDAVRV  100 (178)
Q Consensus        86 ~~~~~~~~~~~~~~v  100 (178)
                      +.++++.++++|..+
T Consensus       191 ~~~~~~~~l~~p~~i  205 (206)
T 1vec_A          191 VQKFMNSHLEKPYEI  205 (206)
T ss_dssp             HHHHHHHHCSSCEEE
T ss_pred             HHHHHHHHcCCCeEe
Confidence            999999999999765

>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=99.77  E-value=2.8e-18  Score=128.00  Aligned_cols=95  Identities=28%  Similarity=0.418  Sum_probs=85.3

Q ss_pred             HhHHhccCCCcEEEeCcHHHHHHHHc-CCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcHH
Q 030396            7 RSTDLSKFSCDILISTPLRLRLAIRR-KKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDF   85 (178)
Q Consensus         7 ~q~~~l~~~~~Iii~TP~~l~~~l~~-~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~   85 (178)
                      ++...+.++++|+|+|||++.+.+.. +.+++.+++++|+||||.+++++ |...+..+++. ++...|++++|||+++.
T Consensus       153 ~~~~~~~~~~~I~v~Tp~~l~~~l~~~~~~~l~~~~~lViDEah~l~~~~-~~~~l~~i~~~-~~~~~~~l~~SAT~~~~  230 (249)
T 3ber_A          153 SQSLALAKKPHIIIATPGRLIDHLENTKGFNLRALKYLVMDEADRILNMD-FETEVDKILKV-IPRDRKTFLFSATMTKK  230 (249)
T ss_dssp             HHHHHHHTCCSEEEECHHHHHHHHHHSTTCCCTTCCEEEECSHHHHHHTT-CHHHHHHHHHS-SCSSSEEEEEESSCCHH
T ss_pred             HHHHHhcCCCCEEEECHHHHHHHHHcCCCcCccccCEEEEcChhhhhccC-hHHHHHHHHHh-CCCCCeEEEEeccCCHH
Confidence            44555667899999999999999876 56789999999999999999998 99999999999 78899999999999999


Q ss_pred             HHHHHHHhccCcEEEEEc
Q 030396           86 VEELARSIMHDAVRVIVG  103 (178)
Q Consensus        86 ~~~~~~~~~~~~~~v~~~  103 (178)
                      +.++++.++++|..+.++
T Consensus       231 v~~~~~~~l~~p~~i~v~  248 (249)
T 3ber_A          231 VQKLQRAALKNPVKCAVS  248 (249)
T ss_dssp             HHHHHHHHCSSCEEEECC
T ss_pred             HHHHHHHHCCCCEEEEec
Confidence            999999999999888653

>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=99.77  E-value=2.3e-18  Score=124.50  Aligned_cols=95  Identities=35%  Similarity=0.498  Sum_probs=85.5

Q ss_pred             HhHHhccCCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcHHH
Q 030396            7 RSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFV   86 (178)
Q Consensus         7 ~q~~~l~~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~~   86 (178)
                      ++.+.+.++++|+|+||+++.+++..+..++.+++++|+||||.+.+++ +...+..+++. .+...|++++|||+++.+
T Consensus       112 ~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~iViDEah~~~~~~-~~~~~~~i~~~-~~~~~~~i~~SAT~~~~~  189 (207)
T 2gxq_A          112 KQKEALLRGADAVVATPGRALDYLRQGVLDLSRVEVAVLDEADEMLSMG-FEEEVEALLSA-TPPSRQTLLFSATLPSWA  189 (207)
T ss_dssp             HHHHHHHHCCSEEEECHHHHHHHHHHTSSCCTTCSEEEEESHHHHHHTT-CHHHHHHHHHT-SCTTSEEEEECSSCCHHH
T ss_pred             HHHHHhhCCCCEEEECHHHHHHHHHcCCcchhhceEEEEEChhHhhccc-hHHHHHHHHHh-CCccCeEEEEEEecCHHH
Confidence            3444555689999999999999999988889999999999999999988 99999999998 788999999999999999


Q ss_pred             HHHHHHhccCcEEEEEc
Q 030396           87 EELARSIMHDAVRVIVG  103 (178)
Q Consensus        87 ~~~~~~~~~~~~~v~~~  103 (178)
                      .++.+.++.+|..+.+.
T Consensus       190 ~~~~~~~~~~p~~i~~~  206 (207)
T 2gxq_A          190 KRLAERYMKNPVLINVI  206 (207)
T ss_dssp             HHHHHHHCSSCEEEECC
T ss_pred             HHHHHHHcCCCeEEEcC
Confidence            99999999999887653

>1wp9_A ATP-dependent RNA helicase, putative; ATPase, DNA replication, DNA repair, DNA recombina hydrolase; 2.90A {Pyrococcus furiosus} SCOP: c.37.1.19 c.37.1.19

Probab=99.76  E-value=1.4e-17  Score=133.39  Aligned_cols=78  Identities=17%  Similarity=0.195  Sum_probs=60.9

Q ss_pred             CCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcH---HHHHHH
Q 030396           14 FSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPD---FVEELA   90 (178)
Q Consensus        14 ~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~---~~~~~~   90 (178)
                      .+++|+|+||+++...+..+.+.+.+++++|+||||.+.+.. ....+...+.. .....+++++|||.+.   .+..+.
T Consensus       100 ~~~~ivv~T~~~l~~~~~~~~~~~~~~~~vIiDEaH~~~~~~-~~~~~~~~~~~-~~~~~~~l~lTaTp~~~~~~~~~l~  177 (494)
T 1wp9_A          100 ARAKVIVATPQTIENDLLAGRISLEDVSLIVFDEAHRAVGNY-AYVFIAREYKR-QAKNPLVIGLTASPGSTPEKIMEVI  177 (494)
T ss_dssp             HHCSEEEECHHHHHHHHHTTSCCTTSCSEEEEETGGGCSTTC-HHHHHHHHHHH-HCSSCCEEEEESCSCSSHHHHHHHH
T ss_pred             cCCCEEEecHHHHHHHHhcCCcchhhceEEEEECCcccCCCC-cHHHHHHHHHh-cCCCCeEEEEecCCCCCcHHHHHHH
Confidence            468999999999999999888889999999999999998765 44445555555 4568899999999973   344444


Q ss_pred             HHh
Q 030396           91 RSI   93 (178)
Q Consensus        91 ~~~   93 (178)
                      ..+
T Consensus       178 ~~l  180 (494)
T 1wp9_A          178 NNL  180 (494)
T ss_dssp             HHT
T ss_pred             Hhc
Confidence            443

>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=99.76  E-value=2.1e-18  Score=143.47  Aligned_cols=140  Identities=19%  Similarity=0.116  Sum_probs=100.0

Q ss_pred             ccCCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCce--EEEEeecCcHHHHHH
Q 030396           12 SKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIV--RSLFSATLPDFVEEL   89 (178)
Q Consensus        12 l~~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q--~i~~SAT~~~~~~~~   89 (178)
                      +.++++|+|+|||+|   +..+.+++++++++|+||||.+ +.+ |...+..|++. .+...|  ++++|||++..+.  
T Consensus       294 ~~~~~~IlV~TPGrL---l~~~~l~l~~l~~lVlDEAH~l-~~~-~~~~l~~Il~~-l~~~~~~llil~SAT~~~~i~--  365 (666)
T 3o8b_A          294 ITTGAPVTYSTYGKF---LADGGCSGGAYDIIICDECHST-DST-TILGIGTVLDQ-AETAGARLVVLATATPPGSVT--  365 (666)
T ss_dssp             ECCCCSEEEEEHHHH---HHTTSCCTTSCSEEEETTTTCC-SHH-HHHHHHHHHHH-TTTTTCSEEEEEESSCTTCCC--
T ss_pred             ccCCCCEEEECcHHH---HhCCCcccCcccEEEEccchhc-Ccc-HHHHHHHHHHh-hhhcCCceEEEECCCCCcccc--
Confidence            356799999999997   5677788999999999999654 666 78889999998 666666  6777999997421  


Q ss_pred             HHHhccCcEEEEEcCCccccCCceEEEEEcCChhhHHHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhhhCCCceEeee
Q 030396           90 ARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIH  169 (178)
Q Consensus        90 ~~~~~~~~~~v~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh  169 (178)
                          ...|....+.....  ..+ ..   . .....       ++....+++||||||+++|+.+++.|.+.|+++..+|
T Consensus       366 ----~~~p~i~~v~~~~~--~~i-~~---~-~~~~~-------l~~~~~~~vLVFv~Tr~~ae~la~~L~~~g~~v~~lH  427 (666)
T 3o8b_A          366 ----VPHPNIEEVALSNT--GEI-PF---Y-GKAIP-------IEAIRGGRHLIFCHSKKKCDELAAKLSGLGINAVAYY  427 (666)
T ss_dssp             ----CCCTTEEEEECBSC--SSE-EE---T-TEEEC-------GGGSSSSEEEEECSCHHHHHHHHHHHHTTTCCEEEEC
T ss_pred             ----cCCcceEEEeeccc--chh-HH---H-Hhhhh-------hhhccCCcEEEEeCCHHHHHHHHHHHHhCCCcEEEec
Confidence                12221111110000  000 10   0 10000       2233578999999999999999999999999999999


Q ss_pred             cCCCcccc
Q 030396          170 SDLSQTQV  177 (178)
Q Consensus       170 ~~~~~~~R  177 (178)
                      |+|++++|
T Consensus       428 G~l~q~er  435 (666)
T 3o8b_A          428 RGLDVSVI  435 (666)
T ss_dssp             TTSCGGGS
T ss_pred             CCCCHHHH
Confidence            99999876

>1nkt_A Preprotein translocase SECA 1 subunit; preprotein translocation, ATPase, transmembrane transport, helicase-like motor domain; HET: ADP; 2.60A {Mycobacterium tuberculosis} SCOP: a.162.1.1 a.172.1.1 c.37.1.19 c.37.1.19 PDB: 1nl3_A

Probab=99.75  E-value=1.7e-19  Score=152.37  Aligned_cols=164  Identities=20%  Similarity=0.295  Sum_probs=116.1

Q ss_pred             ccCCCcEEEeCcHHH-HHHHHcC------CCCCCCeeEEEEeccccccc-cC--------------CChhhHHHHHhhCC
Q 030396           12 SKFSCDILISTPLRL-RLAIRRK------KIDLSRVEYLVLDEADKLFE-VG--------------NLLKHIDPVVKACS   69 (178)
Q Consensus        12 l~~~~~Iii~TP~~l-~~~l~~~------~~~~~~l~~lViDE~d~ll~-~~--------------~~~~~i~~i~~~~~   69 (178)
                      ...+|+|++||||+| .++++.+      .+.++.+.++|+||||.|+. .+              .|...+..|+.. +
T Consensus       197 ~~y~~DIvygTpgrlgfDyLrD~m~~~~~~l~lr~l~~lIVDEaDsmLiDeartPLiiSg~~~~~~~~y~~i~~iv~~-L  275 (922)
T 1nkt_A          197 VAYNADITYGTNNEFGFDYLRDNMAHSLDDLVQRGHHYAIVDEVDSILIDEARTPLIISGPADGASNWYTEFARLAPL-M  275 (922)
T ss_dssp             HHHHSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCCCCEEEETTHHHHHTTGGGSCEEEEEECCCCHHHHHHHHHHHHH-S
T ss_pred             HhcCCCEEEECchHhhHHHHHhhhhccHhhhccCCCCEEEEeChHHHHHhcCccceeecCCCCcchhHHHHHHHHHHh-C
Confidence            334699999999999 7888765      36688999999999999984 21              277899999999 5


Q ss_pred             C---------CCceEE-----------------EEeecCcH---HHHHHHHH--hcc-Cc-------EEEEEc-------
Q 030396           70 N---------PSIVRS-----------------LFSATLPD---FVEELARS--IMH-DA-------VRVIVG-------  103 (178)
Q Consensus        70 ~---------~~~q~i-----------------~~SAT~~~---~~~~~~~~--~~~-~~-------~~v~~~-------  103 (178)
                      +         ..+|+.                 +||||.++   .+...+..  ++. +.       ..+.++       
T Consensus       276 ~~~~dy~vDek~rqv~Lte~G~~~~e~~l~i~~Lfsat~~~l~~~i~~aL~A~~l~~~d~dYiV~dg~vviVDe~TGR~m  355 (922)
T 1nkt_A          276 EKDVHYEVDLRKRTVGVHEKGVEFVEDQLGIDNLYEAANSPLVSYLNNALKAKELFSRDKDYIVRDGEVLIVDEFTGRVL  355 (922)
T ss_dssp             CBTTTEEEETTTTEEEECHHHHHHHHHHHTCSSTTCSTTCCHHHHHHHHHHHHHHCCBTTTEEECSSCEEEBCSSSCCBC
T ss_pred             cccccceeccCcceEEecHhHHHHHHHHhCCccccCCcchhHHHHHHHHHHHHHHhhcccceeeecCceEEEecccCccc
Confidence            5         678988                 99999875   34333222  222 21       111111       


Q ss_pred             ----------------------CCccccCCceE-----------------------------------------------
Q 030396          104 ----------------------RKNTASESIKQ-----------------------------------------------  114 (178)
Q Consensus       104 ----------------------~~~~~~~~i~~-----------------------------------------------  114 (178)
                                            ++..+...|.+                                               
T Consensus       356 ~grr~sdGLHQaieaKe~V~I~~e~~TlatIt~Qnyfr~Y~kL~GMTGTa~te~~Ef~~iY~l~vv~IPtn~p~~R~d~~  435 (922)
T 1nkt_A          356 IGRRYNEGMHQAIEAKEHVEIKAENQTLATITLQNYFRLYDKLAGMTGTAQTEAAELHEIYKLGVVSIPTNMPMIREDQS  435 (922)
T ss_dssp             TTCCCSTTHHHHHHHHTTCCCCCCEEEEEEECHHHHHTTSSEEEEEESCCGGGHHHHHHHHCCEEEECCCSSCCCCEECC
T ss_pred             CCccccchhhHHHhccccccccccccccceeehHHHHHhhhhhhccccCchhHHHHHHHHhCCCeEEeCCCCCcccccCC
Confidence                                  11111111111                                               


Q ss_pred             EEEEcCChhhHHHHHHHHHHhc--CCCCEEEEeCCchHHHHHHHHhhhCCCceEeeecCCCcccc
Q 030396          115 KLVFAGSEEGKLLALRQSFAES--LNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQV  177 (178)
Q Consensus       115 ~~~~~~~~~~k~~~l~~ll~~~--~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~~~~~~R  177 (178)
                      .+++. ....|...+.+.+...  ..+|+||||+|++.++.|+..|...|+++..+||++.+++|
T Consensus       436 d~v~~-t~~~K~~al~~~i~~~~~~gqpvLVft~Sie~sE~Ls~~L~~~Gi~~~vLnak~~~rEa  499 (922)
T 1nkt_A          436 DLIYK-TEEAKYIAVVDDVAERYAKGQPVLIGTTSVERSEYLSRQFTKRRIPHNVLNAKYHEQEA  499 (922)
T ss_dssp             CEEES-CHHHHHHHHHHHHHHHHHTTCCEEEEESCHHHHHHHHHHHHHTTCCCEEECSSCHHHHH
T ss_pred             cEEEe-CHHHHHHHHHHHHHHHHhcCCcEEEEECCHHHHHHHHHHHHHCCCCEEEecCChhHHHH
Confidence            12333 5667998888888642  46799999999999999999999999999999999876654

>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=99.75  E-value=5.6e-18  Score=125.78  Aligned_cols=94  Identities=36%  Similarity=0.610  Sum_probs=82.8

Q ss_pred             ccCCCcEEEeCcHHHHHHHHcC--CCCCCCeeEEEEeccccccccC--CChhhHHHHHhhCCCCCceEEEEeecCcHHHH
Q 030396           12 SKFSCDILISTPLRLRLAIRRK--KIDLSRVEYLVLDEADKLFEVG--NLLKHIDPVVKACSNPSIVRSLFSATLPDFVE   87 (178)
Q Consensus        12 l~~~~~Iii~TP~~l~~~l~~~--~~~~~~l~~lViDE~d~ll~~~--~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~~~   87 (178)
                      ..++++|+|+|||++.+++..+  .+++++++++|+||||.+++++  .|.+.+..++..+.+...|++++|||+|+++.
T Consensus       146 ~~~~~~I~v~Tp~~l~~~l~~~~~~~~~~~~~~lViDEah~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~SAT~~~~v~  225 (245)
T 3dkp_A          146 SSKKFDILVTTPNRLIYLLKQDPPGIDLASVEWLVVDESDKLFEDGKTGFRDQLASIFLACTSHKVRRAMFSATFAYDVE  225 (245)
T ss_dssp             SCCCCCEEEECHHHHHHHHHSSSCSCCCTTCCEEEESSHHHHHHHC--CHHHHHHHHHHHCCCTTCEEEEEESSCCHHHH
T ss_pred             hcCCCCEEEECHHHHHHHHHhCCCCcccccCcEEEEeChHHhcccccccHHHHHHHHHHhcCCCCcEEEEEeccCCHHHH
Confidence            4567999999999999999876  5789999999999999999852  38999999988855678999999999999999


Q ss_pred             HHHHHhccCcEEEEEcCC
Q 030396           88 ELARSIMHDAVRVIVGRK  105 (178)
Q Consensus        88 ~~~~~~~~~~~~v~~~~~  105 (178)
                      ++++.++++|..+.++..
T Consensus       226 ~~~~~~l~~p~~i~~~~~  243 (245)
T 3dkp_A          226 QWCKLNLDNVISVSIGAR  243 (245)
T ss_dssp             HHHHHHSSSCEEEEECC-
T ss_pred             HHHHHhCCCCEEEEeCCC
Confidence            999999999999988654

>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=99.75  E-value=6.2e-18  Score=123.83  Aligned_cols=90  Identities=28%  Similarity=0.510  Sum_probs=80.6

Q ss_pred             CCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcHHHHHHHHHhc
Q 030396           15 SCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIM   94 (178)
Q Consensus        15 ~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~~~~~~~~~~   94 (178)
                      +++|+|+||+++.+.+..+...+++++++|+||||.+.+++ +...+..+++. .+...|++++|||+++.+.++++.++
T Consensus       131 ~~~iiv~Tp~~l~~~~~~~~~~~~~~~~iViDEah~~~~~~-~~~~l~~i~~~-~~~~~~~i~lSAT~~~~~~~~~~~~~  208 (224)
T 1qde_A          131 DAQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSG-FKEQIYQIFTL-LPPTTQVVLLSATMPNDVLEVTTKFM  208 (224)
T ss_dssp             TCSEEEECHHHHHHHHHTTSSCCTTCCEEEEETHHHHHHTT-CHHHHHHHHHH-SCTTCEEEEEESSCCHHHHHHHHHHC
T ss_pred             CCCEEEECHHHHHHHHHhCCcchhhCcEEEEcChhHHhhhh-hHHHHHHHHHh-CCccCeEEEEEeecCHHHHHHHHHHC
Confidence            48999999999999999988889999999999999999988 99999999999 78899999999999999999999999


Q ss_pred             cCcEEEEEcCCc
Q 030396           95 HDAVRVIVGRKN  106 (178)
Q Consensus        95 ~~~~~v~~~~~~  106 (178)
                      ++|..+.+....
T Consensus       209 ~~p~~i~~~~~~  220 (224)
T 1qde_A          209 RNPVRILVKKDE  220 (224)
T ss_dssp             SSCEEEC-----
T ss_pred             CCCEEEEecCCc
Confidence            999988776543

>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=99.74  E-value=4.9e-18  Score=125.14  Aligned_cols=88  Identities=27%  Similarity=0.412  Sum_probs=81.3

Q ss_pred             CCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcHHHHHHHHHh
Q 030396           14 FSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSI   93 (178)
Q Consensus        14 ~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~~~~~~~~~   93 (178)
                      ++++|+|+|||++.+++..+.+++++++++|+||||.+++++.|.+.+..+++. ++...|++++|||+++.+.+++..+
T Consensus       141 ~~~~Iiv~Tp~~l~~~~~~~~~~~~~~~~lViDEah~~~~~~~~~~~~~~i~~~-~~~~~~~l~lSAT~~~~~~~~~~~~  219 (230)
T 2oxc_A          141 KKCHIAVGSPGRIKQLIELDYLNPGSIRLFILDEADKLLEEGSFQEQINWIYSS-LPASKQMLAVSATYPEFLANALTKY  219 (230)
T ss_dssp             TSCSEEEECHHHHHHHHHTTSSCGGGCCEEEESSHHHHHSTTSSHHHHHHHHHH-SCSSCEEEEEESCCCHHHHHHHTTT
T ss_pred             cCCCEEEECHHHHHHHHhcCCcccccCCEEEeCCchHhhcCcchHHHHHHHHHh-CCCCCeEEEEEeccCHHHHHHHHHH
Confidence            478999999999999999888889999999999999999886699999999999 7889999999999999999999999


Q ss_pred             ccCcEEEEE
Q 030396           94 MHDAVRVIV  102 (178)
Q Consensus        94 ~~~~~~v~~  102 (178)
                      +++|..+.+
T Consensus       220 ~~~p~~i~~  228 (230)
T 2oxc_A          220 MRDPTFVRL  228 (230)
T ss_dssp             CSSCEEECC
T ss_pred             cCCCeEEEc
Confidence            999988754

>4a2p_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.00A {Anas platyrhynchos} PDB: 4a36_A*

Probab=99.74  E-value=2.1e-17  Score=135.33  Aligned_cols=74  Identities=14%  Similarity=0.105  Sum_probs=55.3

Q ss_pred             HHhccCCCcEEEeCcHHHHHHHHcCCC-CCCCeeEEEEeccccccccCCChhhH-HHHHhhC---CCCCceEEEEeecCc
Q 030396            9 TDLSKFSCDILISTPLRLRLAIRRKKI-DLSRVEYLVLDEADKLFEVGNLLKHI-DPVVKAC---SNPSIVRSLFSATLP   83 (178)
Q Consensus         9 ~~~l~~~~~Iii~TP~~l~~~l~~~~~-~~~~l~~lViDE~d~ll~~~~~~~~i-~~i~~~~---~~~~~q~i~~SAT~~   83 (178)
                      .+.+..+++|+|+|||++.+++..+.+ .+.+++++|+||||.+.+++ ....+ ...+...   ..+..|++++|||.+
T Consensus        99 ~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~~vViDEah~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~l~lSAT~~  177 (556)
T 4a2p_A           99 VEKVIEDSDIIVVTPQILVNSFEDGTLTSLSIFTLMIFDECHNTTGNH-PYNVLMTRYLEQKFNSASQLPQILGLTASVG  177 (556)
T ss_dssp             HHHHHHHCSEEEECHHHHHHHHHSSSCCCSTTCSEEEEETGGGCSTTS-HHHHHHHHHHHHHHCC---CCEEEEEESCCC
T ss_pred             HHHhhCCCCEEEECHHHHHHHHHhCcccccccCCEEEEECCcccCCcc-hHHHHHHHHHHhhhcccCCCCeEEEEeCCcc
Confidence            334456799999999999999998887 79999999999999998877 33332 2222210   135689999999995

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*

Probab=99.74  E-value=1.5e-18  Score=146.02  Aligned_cols=74  Identities=19%  Similarity=0.149  Sum_probs=56.0

Q ss_pred             HhccCCCcEEEeCcHHHHHHHHcCCC-CCCCeeEEEEeccccccccCCChhhHHHHHhh----CCCCCceEEEEeecCc
Q 030396           10 DLSKFSCDILISTPLRLRLAIRRKKI-DLSRVEYLVLDEADKLFEVGNLLKHIDPVVKA----CSNPSIVRSLFSATLP   83 (178)
Q Consensus        10 ~~l~~~~~Iii~TP~~l~~~l~~~~~-~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~----~~~~~~q~i~~SAT~~   83 (178)
                      +.+..+++|+|+|||+|.+.+..+.+ .+.+++++|+||||.+.....+...+...+..    ..+...|++++|||..
T Consensus       106 ~~~~~~~~Iiv~Tp~~L~~~l~~~~~~~l~~~~~vViDEaH~~~~~~~~~~i~~~~l~~~~~~~~~~~~~il~LTATp~  184 (696)
T 2ykg_A          106 EQIVENNDIIILTPQILVNNLKKGTIPSLSIFTLMIFDECHNTSKQHPYNMIMFNYLDQKLGGSSGPLPQVIGLTASVG  184 (696)
T ss_dssp             HHHHHTCSEEEECHHHHHHHHHTTSSCCGGGCSEEEEETGGGCSTTCHHHHHHHHHHHHHHTTCCSCCCEEEEEESCCC
T ss_pred             HHhccCCCEEEECHHHHHHHHhcCcccccccccEEEEeCCCcccCcccHHHHHHHHHHHhhcccCCCCCeEEEEeCccc
Confidence            33445799999999999999998877 78999999999999997655233333222222    1346789999999986

>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=99.74  E-value=7.2e-18  Score=126.69  Aligned_cols=89  Identities=27%  Similarity=0.378  Sum_probs=79.7

Q ss_pred             HhHHhccCCCcEEEeCcHHHHHHHHcC-CCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcHH
Q 030396            7 RSTDLSKFSCDILISTPLRLRLAIRRK-KIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDF   85 (178)
Q Consensus         7 ~q~~~l~~~~~Iii~TP~~l~~~l~~~-~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~   85 (178)
                      .+.+.+.++++|+|||||++.+++... ...+++++++|+||||.+++++ |.+.+..|++. ++...|++++|||++++
T Consensus       168 ~~~~~~~~~~~Iiv~Tp~~l~~~~~~~~~~~~~~l~~lViDEah~l~~~~-~~~~l~~i~~~-~~~~~q~l~~SAT~~~~  245 (262)
T 3ly5_A          168 AEAQKLGNGINIIVATPGRLLDHMQNTPGFMYKNLQCLVIDEADRILDVG-FEEELKQIIKL-LPTRRQTMLFSATQTRK  245 (262)
T ss_dssp             HHHHHHHHCCSEEEECHHHHHHHHHHCTTCCCTTCCEEEECSHHHHHHTT-CHHHHHHHHHH-SCSSSEEEEECSSCCHH
T ss_pred             HHHHHhcCCCCEEEEcHHHHHHHHHccCCcccccCCEEEEcChHHHhhhh-HHHHHHHHHHh-CCCCCeEEEEEecCCHH
Confidence            445556678999999999999988764 4788999999999999999999 99999999999 88899999999999999


Q ss_pred             HHHHHHHhccCc
Q 030396           86 VEELARSIMHDA   97 (178)
Q Consensus        86 ~~~~~~~~~~~~   97 (178)
                      +.++++.+++++
T Consensus       246 v~~~~~~~l~~~  257 (262)
T 3ly5_A          246 VEDLARISLKKE  257 (262)
T ss_dssp             HHHHHHHHCSSC
T ss_pred             HHHHHHHHcCCC
Confidence            999999998854

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus}

Probab=99.73  E-value=6.1e-17  Score=132.33  Aligned_cols=75  Identities=17%  Similarity=0.087  Sum_probs=57.1

Q ss_pred             HhccCCCcEEEeCcHHHHHHHHcCCC-CCCCeeEEEEeccccccccCCChhhHHHHHhhCC----CCCceEEEEeecCcH
Q 030396           10 DLSKFSCDILISTPLRLRLAIRRKKI-DLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACS----NPSIVRSLFSATLPD   84 (178)
Q Consensus        10 ~~l~~~~~Iii~TP~~l~~~l~~~~~-~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~----~~~~q~i~~SAT~~~   84 (178)
                      +.+.++++|+|+|||++.+++..+.+ .+.+++++|+||||.+.+.+.+...+...+....    ....|++++|||.+.
T Consensus        97 ~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~~vViDEah~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~lSAT~~~  176 (555)
T 3tbk_A           97 QHIIEDNDIIILTPQILVNNLNNGAIPSLSVFTLMIFDECHNTSKNHPYNQIMFRYLDHKLGESRDPLPQVVGLTASVGV  176 (555)
T ss_dssp             HHHHHHCSEEEECHHHHHHHHHTSSSCCGGGCSEEEETTGGGCSTTCHHHHHHHHHHHHHTSSCCSCCCEEEEEESCCCC
T ss_pred             HHHhcCCCEEEECHHHHHHHHhcCcccccccCCEEEEECccccCCcchHHHHHHHHHHhhhccccCCCCeEEEEecCccc
Confidence            34445799999999999999998877 7899999999999999887633333334333311    255799999999953

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens}

Probab=99.72  E-value=2.7e-17  Score=121.45  Aligned_cols=88  Identities=30%  Similarity=0.421  Sum_probs=80.8

Q ss_pred             CCCcEEEeCcHHHHHHHHcC-CCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcHHHHHHHHH
Q 030396           14 FSCDILISTPLRLRLAIRRK-KIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARS   92 (178)
Q Consensus        14 ~~~~Iii~TP~~l~~~l~~~-~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~~~~~~~~   92 (178)
                      ++++|+|+|||++.+.+..+ ...+.+++++|+||||.+.+++ |.+.+..+++. ++...|++++|||+++.+.++.+.
T Consensus       145 ~~~~iiv~Tp~~l~~~l~~~~~~~~~~~~~lViDEah~~~~~~-~~~~~~~i~~~-~~~~~~~l~~SAT~~~~~~~~~~~  222 (236)
T 2pl3_A          145 NNINILVCTPGRLLQHMDETVSFHATDLQMLVLDEADRILDMG-FADTMNAVIEN-LPKKRQTLLFSATQTKSVKDLARL  222 (236)
T ss_dssp             TTCSEEEECHHHHHHHHHHCSSCCCTTCCEEEETTHHHHHHTT-THHHHHHHHHT-SCTTSEEEEEESSCCHHHHHHHHH
T ss_pred             CCCCEEEECHHHHHHHHHhcCCcccccccEEEEeChHHHhcCC-cHHHHHHHHHh-CCCCCeEEEEEeeCCHHHHHHHHH
Confidence            47899999999999988764 5778999999999999999999 99999999999 788999999999999999999999


Q ss_pred             hccCcEEEEEc
Q 030396           93 IMHDAVRVIVG  103 (178)
Q Consensus        93 ~~~~~~~v~~~  103 (178)
                      ++.+|..+.++
T Consensus       223 ~~~~p~~i~~~  233 (236)
T 2pl3_A          223 SLKNPEYVWVH  233 (236)
T ss_dssp             SCSSCEEEECC
T ss_pred             hCCCCEEEEeC
Confidence            99999888764

>4a2q_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.40A {Anas platyrhynchos}

Probab=99.70  E-value=7.9e-17  Score=137.70  Aligned_cols=75  Identities=13%  Similarity=0.084  Sum_probs=56.6

Q ss_pred             HHhccCCCcEEEeCcHHHHHHHHcCCC-CCCCeeEEEEeccccccccCCChhhHHHHHhhC---CCCCceEEEEeecCc
Q 030396            9 TDLSKFSCDILISTPLRLRLAIRRKKI-DLSRVEYLVLDEADKLFEVGNLLKHIDPVVKAC---SNPSIVRSLFSATLP   83 (178)
Q Consensus         9 ~~~l~~~~~Iii~TP~~l~~~l~~~~~-~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~---~~~~~q~i~~SAT~~   83 (178)
                      .+.+..+++|+|+|||+|.+.+..+.+ .+.+++++|+||||.+...+.+...+.......   .....|++++|||.+
T Consensus       340 ~~~~~~~~~Ivv~Tp~~l~~~l~~~~~~~~~~~~~iViDEaH~~~~~~~~~~i~~~~~~~~~~~~~~~~~~l~lSATp~  418 (797)
T 4a2q_A          340 VEKVIEDSDIIVVTPQILVNSFEDGTLTSLSIFTLMIFDECHNTTGNHPYNVLMTRYLEQKFNSASQLPQILGLTASVG  418 (797)
T ss_dssp             HHHHHHTCSEEEECHHHHHHHHHSSSCCCGGGCSEEEETTGGGCSTTSHHHHHHHHHHHHHHTTCCCCCEEEEEESCCC
T ss_pred             HHHhhCCCCEEEEchHHHHHHHHhccccccccCCEEEEECccccCCCccHHHHHHHHHHHhhccCCCCCeEEEEcCCcc
Confidence            344556899999999999999998877 789999999999999987662233232333220   145689999999995

>2xau_A PRE-mRNA-splicing factor ATP-dependent RNA helica; hydrolase, ribosome biogenesis, ATPase, ATP-binding, OB-fold; HET: ADP; 1.90A {Saccharomyces cerevisiae} PDB: 3kx2_B*

Probab=99.70  E-value=1.2e-16  Score=135.93  Aligned_cols=155  Identities=19%  Similarity=0.188  Sum_probs=109.3

Q ss_pred             CCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEecccc-ccccCCChhhHHHHHhhCCCCCceEEEEeecCcHHHHHHHHH
Q 030396           14 FSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADK-LFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARS   92 (178)
Q Consensus        14 ~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~-ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~~~~~~~~   92 (178)
                      .+.+|+++|||++.+.+... ..+.+++++|+||+|. .++.......+..+...  .++.|++++|||++..  . +..
T Consensus       184 ~~~~I~v~T~G~l~r~l~~~-~~l~~~~~lIlDEah~R~ld~d~~~~~l~~l~~~--~~~~~iIl~SAT~~~~--~-l~~  257 (773)
T 2xau_A          184 NKTILKYMTDGMLLREAMED-HDLSRYSCIILDEAHERTLATDILMGLLKQVVKR--RPDLKIIIMSATLDAE--K-FQR  257 (773)
T ss_dssp             TTCSEEEEEHHHHHHHHHHS-TTCTTEEEEEECSGGGCCHHHHHHHHHHHHHHHH--CTTCEEEEEESCSCCH--H-HHH
T ss_pred             CCCCEEEECHHHHHHHHhhC-ccccCCCEEEecCccccccchHHHHHHHHHHHHh--CCCceEEEEeccccHH--H-HHH
Confidence            56899999999999877654 4588999999999996 55543234555566654  2578999999999743  3 345


Q ss_pred             hccCcEEEEEcCCccccCCceEEEEEcCChh---hHHHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhhh---------
Q 030396           93 IMHDAVRVIVGRKNTASESIKQKLVFAGSEE---GKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAF---------  160 (178)
Q Consensus        93 ~~~~~~~v~~~~~~~~~~~i~~~~~~~~~~~---~k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~~---------  160 (178)
                      ++.++..+.+....   ..+.+++.......   .....+.++......+++||||+++++++.++..|.+         
T Consensus       258 ~~~~~~vi~v~gr~---~pv~~~~~~~~~~~~~~~~l~~l~~~~~~~~~g~iLVF~~~~~~i~~l~~~L~~~~~~l~~~~  334 (773)
T 2xau_A          258 YFNDAPLLAVPGRT---YPVELYYTPEFQRDYLDSAIRTVLQIHATEEAGDILLFLTGEDEIEDAVRKISLEGDQLVREE  334 (773)
T ss_dssp             HTTSCCEEECCCCC---CCEEEECCSSCCSCHHHHHHHHHHHHHHHSCSCEEEEECSCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HhcCCCcccccCcc---cceEEEEecCCchhHHHHHHHHHHHHHHhcCCCCEEEECCCHHHHHHHHHHHHHHHHhhcccc
Confidence            66655455543322   23555553332222   1233444444455678999999999999999999975         


Q ss_pred             --CCCceEeeecCCCcccc
Q 030396          161 --DDIRAGVIHSDLSQTQV  177 (178)
Q Consensus       161 --~g~~~~~lh~~~~~~~R  177 (178)
                        .|+.+..+||+|++++|
T Consensus       335 ~~~~~~v~~lhg~l~~~eR  353 (773)
T 2xau_A          335 GCGPLSVYPLYGSLPPHQQ  353 (773)
T ss_dssp             CCCCEEEEEECTTCCHHHH
T ss_pred             cCCCeEEEEeCCCCCHHHH
Confidence              68899999999998876

>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=99.69  E-value=5.7e-17  Score=118.42  Aligned_cols=86  Identities=24%  Similarity=0.447  Sum_probs=78.8

Q ss_pred             CCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEecccccccc-CCChhhHHHHHhhCCCCCceEEEEeecCcHHHHHHHHH
Q 030396           14 FSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEV-GNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARS   92 (178)
Q Consensus        14 ~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~-~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~~~~~~~~   92 (178)
                      .+++|+|+||+++.+++..+...+.+++++|+||||.++++ + +...+..+++. .+.+.|++++|||+++.+.++++.
T Consensus       133 ~~~~i~v~T~~~l~~~~~~~~~~~~~~~~lViDEah~~~~~~~-~~~~~~~i~~~-~~~~~~~i~~SAT~~~~~~~~~~~  210 (220)
T 1t6n_A          133 NCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLD-MRRDVQEIFRM-TPHEKQVMMFSATLSKEIRPVCRK  210 (220)
T ss_dssp             SCCSEEEECHHHHHHHHHTTSSCCTTCCEEEEESHHHHHSSHH-HHHHHHHHHHT-SCSSSEEEEEESCCCTTTHHHHHT
T ss_pred             CCCCEEEeCHHHHHHHHHhCCCCcccCCEEEEcCHHHHhcccC-cHHHHHHHHHh-CCCcCeEEEEEeecCHHHHHHHHH
Confidence            46899999999999999998888999999999999999874 6 88999999998 778999999999999999999999


Q ss_pred             hccCcEEEE
Q 030396           93 IMHDAVRVI  101 (178)
Q Consensus        93 ~~~~~~~v~  101 (178)
                      ++.+|..+.
T Consensus       211 ~~~~p~~i~  219 (220)
T 1t6n_A          211 FMQDPMEIF  219 (220)
T ss_dssp             TCSSCEEEE
T ss_pred             HcCCCeEEe
Confidence            999998764

>4a2w_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.70A {Anas platyrhynchos}

Probab=99.67  E-value=2.7e-16  Score=136.38  Aligned_cols=74  Identities=14%  Similarity=0.086  Sum_probs=55.7

Q ss_pred             HhccCCCcEEEeCcHHHHHHHHcCCC-CCCCeeEEEEeccccccccCCChhhHHHHHhhC---CCCCceEEEEeecCc
Q 030396           10 DLSKFSCDILISTPLRLRLAIRRKKI-DLSRVEYLVLDEADKLFEVGNLLKHIDPVVKAC---SNPSIVRSLFSATLP   83 (178)
Q Consensus        10 ~~l~~~~~Iii~TP~~l~~~l~~~~~-~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~---~~~~~q~i~~SAT~~   83 (178)
                      +.+..+++|+|+|||+|.+.+..+.+ .+.+++++|+||||.+...+.+...+..+....   .....|++++|||.+
T Consensus       341 ~~~~~~~~IvI~Tp~~L~~~l~~~~~~~l~~~~liViDEaH~~~~~~~~~~i~~~~~~~~~~~~~~~~~~l~LSATp~  418 (936)
T 4a2w_A          341 EKVIEDSDIIVVTPQILVNSFEDGTLTSLSIFTLMIFDECHNTTGNHPYNVLMTRYLEQKFNSASQLPQILGLTASVG  418 (936)
T ss_dssp             HHHHHHCSEEEECHHHHHHHHHSSSCCCGGGCSEEEEETGGGCSTTCHHHHHHHHHHHHHHTTCSCCCEEEEEESCCC
T ss_pred             HHhccCCCEEEecHHHHHHHHHcCccccccCCCEEEEECccccCCCccHHHHHHHHHHHhhccCCCcCeEEEecCCcc
Confidence            34445789999999999999998877 789999999999999987662333333333220   145689999999995

>2eyq_A TRCF, transcription-repair coupling factor; MFD, SF2 ATPase, hydrolase; HET: EPE; 3.20A {Escherichia coli} SCOP: b.34.18.1 c.37.1.19 c.37.1.19 c.37.1.19 c.37.1.19 d.315.1.1

Probab=99.66  E-value=6.7e-16  Score=136.09  Aligned_cols=153  Identities=16%  Similarity=0.113  Sum_probs=105.4

Q ss_pred             hHHhccC-CCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcHHH
Q 030396            8 STDLSKF-SCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFV   86 (178)
Q Consensus         8 q~~~l~~-~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~~   86 (178)
                      +.+.+.. .++|+||||+.+     .+.+.+++++++|+||+|.+   +   .....+++. ++.+.+++++|||.++..
T Consensus       698 ~~~~l~~g~~dIvV~T~~ll-----~~~~~~~~l~lvIiDEaH~~---g---~~~~~~l~~-l~~~~~vl~lSATp~p~~  765 (1151)
T 2eyq_A          698 ILAEVAEGKIDILIGTHKLL-----QSDVKFKDLGLLIVDEEHRF---G---VRHKERIKA-MRANVDILTLTATPIPRT  765 (1151)
T ss_dssp             HHHHHHTTCCSEEEECTHHH-----HSCCCCSSEEEEEEESGGGS---C---HHHHHHHHH-HHTTSEEEEEESSCCCHH
T ss_pred             HHHHHhcCCCCEEEECHHHH-----hCCccccccceEEEechHhc---C---hHHHHHHHH-hcCCCCEEEEcCCCChhh
Confidence            3344444 599999999765     24567899999999999995   2   234455565 566889999999988776


Q ss_pred             HHHHHHhccCcEEEEEcCCccccCCceEEEEEcCChhhHHHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhhhC--CCc
Q 030396           87 EELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFD--DIR  164 (178)
Q Consensus        87 ~~~~~~~~~~~~~v~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~~~--g~~  164 (178)
                      .......+.++..+...  ......+..++... +.......+...+  ...++++||||++++++.+++.|.+.  |+.
T Consensus       766 l~~~~~~~~~~~~i~~~--~~~r~~i~~~~~~~-~~~~i~~~il~~l--~~g~qvlvf~~~v~~~~~l~~~L~~~~p~~~  840 (1151)
T 2eyq_A          766 LNMAMSGMRDLSIIATP--PARRLAVKTFVREY-DSMVVREAILREI--LRGGQVYYLYNDVENIQKAAERLAELVPEAR  840 (1151)
T ss_dssp             HHHHHTTTSEEEECCCC--CCBCBCEEEEEEEC-CHHHHHHHHHHHH--TTTCEEEEECCCSSCHHHHHHHHHHHCTTSC
T ss_pred             HHHHHhcCCCceEEecC--CCCccccEEEEecC-CHHHHHHHHHHHH--hcCCeEEEEECCHHHHHHHHHHHHHhCCCCe
Confidence            66655555555444322  22223444444332 3222222222222  23578999999999999999999887  889


Q ss_pred             eEeeecCCCcccc
Q 030396          165 AGVIHSDLSQTQV  177 (178)
Q Consensus       165 ~~~lh~~~~~~~R  177 (178)
                      +..+||+|++++|
T Consensus       841 v~~lhg~~~~~eR  853 (1151)
T 2eyq_A          841 IAIGHGQMREREL  853 (1151)
T ss_dssp             EEECCSSCCHHHH
T ss_pred             EEEEeCCCCHHHH
Confidence            9999999999876

>4f92_B U5 small nuclear ribonucleoprotein 200 kDa helica; RNP remodeling, PRE-mRNA splicing, spliceosome catalytic ACT DEXD/H-box RNA helicase; HET: SAN; 2.66A {Homo sapiens} PDB: 4f93_B* 4f91_B

Probab=99.66  E-value=1e-15  Score=138.82  Aligned_cols=161  Identities=17%  Similarity=0.189  Sum_probs=103.3

Q ss_pred             CCCcEEEeCcHHHHHHHHcCC--CCCCCeeEEEEeccccccccCCChhhHHHHHhhC------CCCCceEEEEeecCcHH
Q 030396           14 FSCDILISTPLRLRLAIRRKK--IDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKAC------SNPSIVRSLFSATLPDF   85 (178)
Q Consensus        14 ~~~~Iii~TP~~l~~~l~~~~--~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~------~~~~~q~i~~SAT~~~~   85 (178)
                      ++++|+|+|||++..++++..  -.+++++++|+||+|.+.+.  .++.++.++..+      .+...|++++|||+++.
T Consensus      1019 ~~~~IiV~TPEkld~llr~~~~~~~l~~v~lvViDE~H~l~d~--rg~~le~il~rl~~i~~~~~~~~riI~lSATl~N~ 1096 (1724)
T 4f92_B         1019 GKGNIIISTPEKWDILSRRWKQRKNVQNINLFVVDEVHLIGGE--NGPVLEVICSRMRYISSQIERPIRIVALSSSLSNA 1096 (1724)
T ss_dssp             HHCSEEEECHHHHHHHHTTTTTCHHHHSCSEEEECCGGGGGST--THHHHHHHHHHHHHHHHTTSSCCEEEEEESCBTTH
T ss_pred             CCCCEEEECHHHHHHHHhCcccccccceeeEEEeechhhcCCC--CCccHHHHHHHHHHHHhhcCCCceEEEEeCCCCCH
Confidence            468999999999988887533  24789999999999988653  466665554431      45789999999999863


Q ss_pred             HHHHHHHhccCcEEEEEcCCccccCCceEEEEEcCChh--hHH----HHHHHHHH-hcCCCCEEEEeCCchHHHHHHHHh
Q 030396           86 VEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEE--GKL----LALRQSFA-ESLNPPVLIFVQSKDRAKELYGEL  158 (178)
Q Consensus        86 ~~~~~~~~~~~~~~v~~~~~~~~~~~i~~~~~~~~~~~--~k~----~~l~~ll~-~~~~~~~lIF~~t~~~~~~l~~~L  158 (178)
                       .++.+....++..+........+..+..++.......  .+.    ..+...+. ....+++||||+|++.|+.++..|
T Consensus      1097 -~dla~WL~~~~~~~~~~~~~~RPvpL~~~i~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~lVF~~sR~~~~~~A~~L 1175 (1724)
T 4f92_B         1097 -KDVAHWLGCSATSTFNFHPNVRPVPLELHIQGFNISHTQTRLLSMAKPVYHAITKHSPKKPVIVFVPSRKQTRLTAIDI 1175 (1724)
T ss_dssp             -HHHHHHHTCCSTTEEECCGGGCSSCEEEEEEEECCCSHHHHHHTTHHHHHHHHHHHCSSSCEEEEESSHHHHHHHHHHH
T ss_pred             -HHHHHHhCCCCCCeEEeCCCCCCCCeEEEEEeccCCCchhhhhhhcchHHHHHHHhcCCCCeeeeCCCHHHHHHHHHHH
Confidence             4444433333322222223333434444443332221  111    11222233 345679999999999999998776


Q ss_pred             hhC----------------------------------CCceEeeecCCCcccc
Q 030396          159 AFD----------------------------------DIRAGVIHSDLSQTQV  177 (178)
Q Consensus       159 ~~~----------------------------------g~~~~~lh~~~~~~~R  177 (178)
                      ...                                  ...++.+||||++++|
T Consensus      1176 ~~~~~~~~~~~~~~~~~~~~l~~~l~~~~d~~L~~~l~~GIa~hHagL~~~~R 1228 (1724)
T 4f92_B         1176 LTTCAADIQRQRFLHCTEKDLIPYLEKLSDSTLKETLLNGVGYLHEGLSPMER 1228 (1724)
T ss_dssp             HHHHHHTTCTTTTBCSCHHHHHHHHTTCCCHHHHHHHHTTEEEECTTSCHHHH
T ss_pred             HHHHhhccchhhhhcccHHHHHHHHhhcccHHHHHHHhCCEEEECCCCCHHHH
Confidence            321                                  2358899999999887

>4gl2_A Interferon-induced helicase C domain-containing P; MDA5, dsRNA, anti-viral signaling, RIG-I, MAVS, oligomerizat helicase, ATPase; HET: ANP; 3.56A {Homo sapiens}

Probab=99.65  E-value=8.1e-17  Score=135.58  Aligned_cols=74  Identities=19%  Similarity=0.135  Sum_probs=53.3

Q ss_pred             hccCCCcEEEeCcHHHHHHH------HcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhC------------CCCC
Q 030396           11 LSKFSCDILISTPLRLRLAI------RRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKAC------------SNPS   72 (178)
Q Consensus        11 ~l~~~~~Iii~TP~~l~~~l------~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~------------~~~~   72 (178)
                      .+.++++|+|+||++|.+.+      ..+.+.+.+++++|+||||.+...+.+...+...+...            ..+.
T Consensus       102 ~~~~~~~Ilv~Tp~~L~~~l~~~~~~~~~~~~~~~~~lvViDEaH~~~~~~~~~~i~~~~l~~~~~~~~~~~~~~~~~~~  181 (699)
T 4gl2_A          102 EVVKSCDIIISTAQILENSLLNLENGEDAGVQLSDFSLIIIDECHHTNKEAVYNNIMRHYLMQKLKNNRLKKENKPVIPL  181 (699)
T ss_dssp             HHHHSCSEEEEEHHHHHHHTC--------CCCGGGCSEEEEESGGGCBTTBSSCSHHHHHHHHHHHHHHHHC----CCCC
T ss_pred             hhhcCCCEEEECHHHHHHHHhccccccccceecccCcEEEEECccccCccchHHHHHHHHHHhhhcccccccccccCCCC
Confidence            34467999999999999988      45567889999999999999966553444444333320            1156


Q ss_pred             ceEEEEeecCcH
Q 030396           73 IVRSLFSATLPD   84 (178)
Q Consensus        73 ~q~i~~SAT~~~   84 (178)
                      .|++++|||.+.
T Consensus       182 ~~il~lTATp~~  193 (699)
T 4gl2_A          182 PQILGLTASPGV  193 (699)
T ss_dssp             CEEEEECSCCCC
T ss_pred             CEEEEecccccc
Confidence            799999999986

>4f92_B U5 small nuclear ribonucleoprotein 200 kDa helica; RNP remodeling, PRE-mRNA splicing, spliceosome catalytic ACT DEXD/H-box RNA helicase; HET: SAN; 2.66A {Homo sapiens} PDB: 4f93_B* 4f91_B

Probab=99.64  E-value=7.8e-16  Score=139.56  Aligned_cols=160  Identities=16%  Similarity=0.237  Sum_probs=104.1

Q ss_pred             CCCcEEEeCcHHHHHHHHcCCC--CCCCeeEEEEeccccccccCCChhhHHHHHhhC------CCCCceEEEEeecCcHH
Q 030396           14 FSCDILISTPLRLRLAIRRKKI--DLSRVEYLVLDEADKLFEVGNLLKHIDPVVKAC------SNPSIVRSLFSATLPDF   85 (178)
Q Consensus        14 ~~~~Iii~TP~~l~~~l~~~~~--~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~------~~~~~q~i~~SAT~~~~   85 (178)
                      .+++|+|+|||++..+++++..  .+++++++|+||+|.+-+ . .+..++.++..+      .+...|++++|||+|+.
T Consensus       180 ~~~~IlVtTpEkld~llr~~~~~~~l~~v~~vIiDEvH~l~d-~-RG~~lE~~l~rl~~~~~~~~~~~riI~LSATl~N~  257 (1724)
T 4f92_B          180 SATQIIVCTPEKWDIITRKGGERTYTQLVRLIILDEIHLLHD-D-RGPVLEALVARAIRNIEMTQEDVRLIGLSATLPNY  257 (1724)
T ss_dssp             GGCSEEEECHHHHHHHTTSSTTHHHHTTEEEEEETTGGGGGS-T-THHHHHHHHHHHHHHHHHHTCCCEEEEEECSCTTH
T ss_pred             CCCCEEEECHHHHHHHHcCCccchhhcCcCEEEEecchhcCC-c-cHHHHHHHHHHHHHHHHhCCCCCcEEEEecccCCH
Confidence            4689999999998666655432  378999999999997754 4 566666655431      45688999999999863


Q ss_pred             HHHHHHHhcc-Cc-EEEEEcCCccccCCceEEEEEcCChh--hHHHHH----HHHHH-hcCCCCEEEEeCCchHHHHHHH
Q 030396           86 VEELARSIMH-DA-VRVIVGRKNTASESIKQKLVFAGSEE--GKLLAL----RQSFA-ESLNPPVLIFVQSKDRAKELYG  156 (178)
Q Consensus        86 ~~~~~~~~~~-~~-~~v~~~~~~~~~~~i~~~~~~~~~~~--~k~~~l----~~ll~-~~~~~~~lIF~~t~~~~~~l~~  156 (178)
                       .+++ .|++ ++ ..+........|-.+.+.++......  .+...+    .+.+. ....+++||||+|++.|+.+|.
T Consensus       258 -~dvA-~wL~~~~~~~~~~~~~~~RPvpL~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~LVF~~sR~~~~~~A~  335 (1724)
T 4f92_B          258 -EDVA-TFLRVDPAKGLFYFDNSFRPVPLEQTYVGITEKKAIKRFQIMNEIVYEKIMEHAGKNQVLVFVHSRKETGKTAR  335 (1724)
T ss_dssp             -HHHH-HHTTCCHHHHEEECCGGGCSSCEEEECCEECCCCHHHHHHHHHHHHHHHHTTCCSSCCEEEECSSTTTTHHHHH
T ss_pred             -HHHH-HHhCCCCCCCeEEECCCCccCccEEEEeccCCcchhhhhHHHHHHHHHHHHHHhcCCcEEEECCCHHHHHHHHH
Confidence             3443 4544 22 11222223334445666665544322  222222    22222 2346789999999999999998


Q ss_pred             HhhhC-------------------------------------CCceEeeecCCCcccc
Q 030396          157 ELAFD-------------------------------------DIRAGVIHSDLSQTQV  177 (178)
Q Consensus       157 ~L~~~-------------------------------------g~~~~~lh~~~~~~~R  177 (178)
                      .|.+.                                     ..-++..||||++++|
T Consensus       336 ~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Gva~HHagL~~~~R  393 (1724)
T 4f92_B          336 AIRDMCLEKDTLGLFLREGSASTEVLRTEAEQCKNLELKDLLPYGFAIHHAGMTRVDR  393 (1724)
T ss_dssp             HHHHHHHHTTSTTCCSSCCTTCSSHHHHTTSCCSTHHHHHHTTTTEEEECSSSCTHHH
T ss_pred             HHHHHHhhccchhhhcccchhHHHHHHhhhcccccHHHHHHhhcCEEEEcCCCCHHHH
Confidence            88531                                     1347899999999987

>2jlq_A Serine protease subunit NS3; ribonucleoprotein, nucleotide-binding, viral nucleoprotein, endoplasmic reticulum, helicase, hydrolase; 1.67A {Dengue virus 4} PDB: 2jly_A* 2jls_A* 2jlu_A 2jlv_A* 2jlw_A 2jlx_A* 2jlz_A* 2jlr_A* 2bmf_A 2bhr_A

Probab=99.58  E-value=1.5e-15  Score=122.15  Aligned_cols=138  Identities=10%  Similarity=0.014  Sum_probs=94.1

Q ss_pred             CCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcHHHHHHHHHhc
Q 030396           15 SCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIM   94 (178)
Q Consensus        15 ~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~~~~~~~~~~   94 (178)
                      +..|.++|||.+...+... ..+++++++|+||||.+ +.+ +......+......++.|++++|||+++.+..   .+.
T Consensus        87 ~~~i~~~t~~~l~~~l~~~-~~l~~~~~iViDEah~~-~~~-~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~---~~~  160 (451)
T 2jlq_A           87 REIVDLMCHATFTTRLLSS-TRVPNYNLIVMDEAHFT-DPC-SVAARGYISTRVEMGEAAAIFMTATPPGSTDP---FPQ  160 (451)
T ss_dssp             SCCEEEEEHHHHHHHHHHC-SCCCCCSEEEEETTTCC-SHH-HHHHHHHHHHHHHTTSCEEEEECSSCTTCCCS---SCC
T ss_pred             CceEEEEChHHHHHHhhCc-ccccCCCEEEEeCCccC-Ccc-hHHHHHHHHHhhcCCCceEEEEccCCCccchh---hhc
Confidence            4579999999998877644 46789999999999987 433 33334334333244689999999999875433   233


Q ss_pred             cCcEEEEEcCCccccCCceEEEEEcCChhhHHHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhhhCCCceEeeecCCCc
Q 030396           95 HDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQ  174 (178)
Q Consensus        95 ~~~~~v~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~~~~  174 (178)
                      .++..+.....  .+..   .+          ..+.+.+... .+++||||+|+++|+.+++.|.+.|+++..+||++.+
T Consensus       161 ~~~~~~~~~~~--~p~~---~~----------~~~~~~l~~~-~~~~lVF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~  224 (451)
T 2jlq_A          161 SNSPIEDIERE--IPER---SW----------NTGFDWITDY-QGKTVWFVPSIKAGNDIANCLRKSGKRVIQLSRKTFD  224 (451)
T ss_dssp             CSSCEEEEECC--CCSS---CC----------SSSCHHHHHC-CSCEEEECSSHHHHHHHHHHHHTTTCCEEEECTTTHH
T ss_pred             CCCceEecCcc--CCch---hh----------HHHHHHHHhC-CCCEEEEcCCHHHHHHHHHHHHHcCCeEEECCHHHHH
Confidence            44444443311  1110   01          0112233333 5799999999999999999999999999999998764

>1gm5_A RECG; helicase, replication restart; HET: DNA ADP; 3.24A {Thermotoga maritima} SCOP: a.24.21.1 b.40.4.9 c.37.1.19 c.37.1.19

Probab=99.55  E-value=1.5e-14  Score=122.86  Aligned_cols=152  Identities=14%  Similarity=0.172  Sum_probs=91.4

Q ss_pred             hHHhccC-CCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcHHH
Q 030396            8 STDLSKF-SCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFV   86 (178)
Q Consensus         8 q~~~l~~-~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~~   86 (178)
                      +.+.+.. .++|+||||+.+.+     ...+.+++++|+||+|.+....  .    ..+.. .....|++++|||.++..
T Consensus       463 ~~~~l~~g~~~IvVgT~~ll~~-----~~~~~~l~lVVIDEaHr~g~~q--r----~~l~~-~~~~~~vL~mSATp~p~t  530 (780)
T 1gm5_A          463 IKSGLRNGQIDVVIGTHALIQE-----DVHFKNLGLVIIDEQHRFGVKQ--R----EALMN-KGKMVDTLVMSATPIPRS  530 (780)
T ss_dssp             HHHHHHSSCCCEEEECTTHHHH-----CCCCSCCCEEEEESCCCC-----------CCCCS-SSSCCCEEEEESSCCCHH
T ss_pred             HHHHHhcCCCCEEEECHHHHhh-----hhhccCCceEEecccchhhHHH--H----HHHHH-hCCCCCEEEEeCCCCHHH
Confidence            3444444 59999999997744     4568899999999999973322  1    12222 335789999999987653


Q ss_pred             HHHHHHhccCcEEEEEcCCccccCCceEEEEEcCChhhHHHHHHHHHHh--cCCCCEEEEeCCc--------hHHHHHHH
Q 030396           87 EELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAE--SLNPPVLIFVQSK--------DRAKELYG  156 (178)
Q Consensus        87 ~~~~~~~~~~~~~v~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~--~~~~~~lIF~~t~--------~~~~~l~~  156 (178)
                      ...  .++.+.....+.........+...++   ... +...+.+.+..  ....+++|||++.        +.++.+++
T Consensus       531 l~~--~~~g~~~~s~i~~~p~~r~~i~~~~~---~~~-~~~~l~~~i~~~l~~g~qvlVf~~~ie~se~l~~~~a~~l~~  604 (780)
T 1gm5_A          531 MAL--AFYGDLDVTVIDEMPPGRKEVQTMLV---PMD-RVNEVYEFVRQEVMRGGQAFIVYPLIEESDKLNVKSAVEMYE  604 (780)
T ss_dssp             HHH--HHTCCSSCEEECCCCSSCCCCEECCC---CSS-THHHHHHHHHHHTTTSCCBCCBCCCC--------CHHHHHHH
T ss_pred             HHH--HHhCCcceeeeeccCCCCcceEEEEe---ccc-hHHHHHHHHHHHHhcCCcEEEEecchhhhhhhhHHHHHHHHH
Confidence            332  23333221222211112222333221   222 22333344432  2367899999966        45888999


Q ss_pred             Hhhh---CCCceEeeecCCCcccc
Q 030396          157 ELAF---DDIRAGVIHSDLSQTQV  177 (178)
Q Consensus       157 ~L~~---~g~~~~~lh~~~~~~~R  177 (178)
                      .|.+   .|+.+..+||+|++++|
T Consensus       605 ~L~~~~~~~~~v~~lHG~m~~~eR  628 (780)
T 1gm5_A          605 YLSKEVFPEFKLGLMHGRLSQEEK  628 (780)
T ss_dssp             SGGGSCC---CBCCCCSSSCCSCS
T ss_pred             HHHhhhcCCCcEEEEeCCCCHHHH
Confidence            9988   58899999999999887

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4}

Probab=99.54  E-value=1.7e-15  Score=123.29  Aligned_cols=155  Identities=11%  Similarity=0.082  Sum_probs=100.6

Q ss_pred             cCCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcHHHHHHHH-
Q 030396           13 KFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELAR-   91 (178)
Q Consensus        13 ~~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~~~~~~~-   91 (178)
                      ..+++|+||||+++.   ..+...+.+++++|+||+|.+..     +.+..+++. +....+++++|||.+........ 
T Consensus       202 ~~~~~I~i~T~~~l~---~~~~~~~~~~~liIiDE~H~~~~-----~~~~~il~~-~~~~~~~l~lSATp~~~~~~~~~~  272 (510)
T 2oca_A          202 KNDAPVVVGTWQTVV---KQPKEWFSQFGMMMNDECHLATG-----KSISSIISG-LNNCMFKFGLSGSLRDGKANIMQY  272 (510)
T ss_dssp             CTTCSEEEEEHHHHT---TSCGGGGGGEEEEEEETGGGCCH-----HHHHHHGGG-CTTCCEEEEEESCGGGCSSCHHHH
T ss_pred             ccCCcEEEEeHHHHh---hchhhhhhcCCEEEEECCcCCCc-----ccHHHHHHh-cccCcEEEEEEeCCCCCcccHHHh
Confidence            467899999999654   33445678899999999999854     457888888 67788999999999765322111 


Q ss_pred             HhccCcEEEEEcCCc------cccCCceEEEEEcC----------C----------hhhHHHHHHHHHHhc---CCCCEE
Q 030396           92 SIMHDAVRVIVGRKN------TASESIKQKLVFAG----------S----------EEGKLLALRQSFAES---LNPPVL  142 (178)
Q Consensus        92 ~~~~~~~~v~~~~~~------~~~~~i~~~~~~~~----------~----------~~~k~~~l~~ll~~~---~~~~~l  142 (178)
                      ..+.++.........      ..+..+....+...          .          ...+...+.+++...   ..++++
T Consensus       273 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~i  352 (510)
T 2oca_A          273 VGMFGEIFKPVTTSKLMEDGQVTELKINSIFLRYPDEFTTKLKGKTYQEEIKIITGLSKRNKWIAKLAIKLAQKDENAFV  352 (510)
T ss_dssp             HHHHCSEECCCCCC---------CCEEEEEEEECCHHHHHHHTTCCHHHHHHHHHTCHHHHHHHHHHHHHHHTTTCEEEE
T ss_pred             HHhhCCeEEeeCHHHHhhCCcCCCceEEEEeecCChHHhccccccchHHHHHHHhccHHHHHHHHHHHHHHHhcCCCeEE
Confidence            112233332222211      11111111111111          1          113445566666543   355667


Q ss_pred             EEeCCchHHHHHHHHhhhCCCceEeeecCCCcccc
Q 030396          143 IFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQV  177 (178)
Q Consensus       143 IF~~t~~~~~~l~~~L~~~g~~~~~lh~~~~~~~R  177 (178)
                      |||+ .+.++.+++.|.+.|.++..+||+|++++|
T Consensus       353 vf~~-~~~~~~l~~~L~~~~~~v~~~~g~~~~~~r  386 (510)
T 2oca_A          353 MFKH-VSHGKAIFDLIKNEYDKVYYVSGEVDTETR  386 (510)
T ss_dssp             EESS-HHHHHHHHHHHHTTCSSEEEESSSTTHHHH
T ss_pred             EEec-HHHHHHHHHHHHHcCCCeEEEECCCCHHHH
Confidence            7776 899999999999999999999999998876

>1yks_A Genome polyprotein [contains: flavivirin protease NS3 catalytic subunit]; helicase, flavivirus, DEAD-BOX, ATPase, rtpase, hydrolase; 1.80A {Yellow fever virus} SCOP: c.37.1.14 c.37.1.14 PDB: 1ymf_A*

Probab=99.52  E-value=2.9e-16  Score=126.05  Aligned_cols=132  Identities=15%  Similarity=0.086  Sum_probs=84.4

Q ss_pred             EEeCcHHHHHHHHcCC--------CCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcHHHHHHH
Q 030396           19 LISTPLRLRLAIRRKK--------IDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELA   90 (178)
Q Consensus        19 ii~TP~~l~~~l~~~~--------~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~~~~~~   90 (178)
                      .++||+++.+++..+.        ..+++++++|+||+|.+ +.+ +...+..+.+...+.+.|++++|||+++.+..+.
T Consensus        71 ~v~Tp~~l~~~l~~~~l~~~~~~~~~~~~l~~vViDEah~~-~~~-~~~~~~~~~~~~~~~~~~~l~~SAT~~~~~~~~~  148 (440)
T 1yks_A           71 AHGSGREVIDAMCHATLTYRMLEPTRVVNWEVIIMDEAHFL-DPA-SIAARGWAAHRARANESATILMTATPPGTSDEFP  148 (440)
T ss_dssp             CCCCSSCCEEEEEHHHHHHHHTSSSCCCCCSEEEETTTTCC-SHH-HHHHHHHHHHHHHTTSCEEEEECSSCTTCCCSSC
T ss_pred             eccCCccceeeecccchhHhhhCcccccCccEEEEECcccc-Ccc-hHHHHHHHHHHhccCCceEEEEeCCCCchhhhhh
Confidence            4889988765443322        34789999999999999 333 4444444444422368999999999987644322


Q ss_pred             HHhccCcEEEEEcCCccccCCceEEEEEcCChhhHHHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhhhCCCceEeeec
Q 030396           91 RSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHS  170 (178)
Q Consensus        91 ~~~~~~~~~v~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~  170 (178)
                      ..  ..|....              ...+... .+.. +...+.+. .++++|||+|++.|+.+++.|.+.|+++..+||
T Consensus       149 ~~--~~~~~~~--------------~~~~~~~-~~~~-~~~~l~~~-~~~~lVF~~s~~~a~~l~~~L~~~~~~v~~lhg  209 (440)
T 1yks_A          149 HS--NGEIEDV--------------QTDIPSE-PWNT-GHDWILAD-KRPTAWFLPSIRAANVMAASLRKAGKSVVVLNR  209 (440)
T ss_dssp             CC--SSCEEEE--------------ECCCCSS-CCSS-SCHHHHHC-CSCEEEECSCHHHHHHHHHHHHHTTCCEEECCS
T ss_pred             hc--CCCeeEe--------------eeccChH-HHHH-HHHHHHhc-CCCEEEEeCCHHHHHHHHHHHHHcCCCEEEecc
Confidence            11  1111110              0011111 1111 12223333 579999999999999999999999999999999


Q ss_pred             C
Q 030396          171 D  171 (178)
Q Consensus       171 ~  171 (178)
                      +
T Consensus       210 ~  210 (440)
T 1yks_A          210 K  210 (440)
T ss_dssp             S
T ss_pred             h
Confidence            4

>3h1t_A Type I site-specific restriction-modification system, R (restriction) subunit; hydrolase, restriction enzyme HSDR, ATP-binding; 2.30A {Vibrio vulnificus}

Probab=99.52  E-value=1.1e-14  Score=120.55  Aligned_cols=159  Identities=11%  Similarity=0.030  Sum_probs=85.7

Q ss_pred             ccCCCcEEEeCcHHHHHHHHc----CCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcHHHH
Q 030396           12 SKFSCDILISTPLRLRLAIRR----KKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVE   87 (178)
Q Consensus        12 l~~~~~Iii~TP~~l~~~l~~----~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~~~   87 (178)
                      ...+++|+|+||+++......    +.+....++++|+||||.+...+  ...+..+++. ++ ..+++++|||......
T Consensus       271 ~~~~~~I~v~T~~~l~~~~~~~~~~~~~~~~~~~lvIiDEaH~~~~~~--~~~~~~il~~-~~-~~~~l~lTATP~~~~~  346 (590)
T 3h1t_A          271 VVKSREIYFAIYQSIASDERRPGLYKEFPQDFFDLIIIDECHRGSARD--NSNWREILEY-FE-PAFQIGMTATPLREDN  346 (590)
T ss_dssp             CCSSCSEEEEEGGGC------CCGGGGSCTTSCSEEEESCCC-----------CHHHHHH-ST-TSEEEEEESSCSCTTT
T ss_pred             CCCCCcEEEEEhhhhccccccccccccCCCCccCEEEEECCccccccc--hHHHHHHHHh-CC-cceEEEeccccccccc
Confidence            346789999999999887652    33456789999999999997653  4567778887 43 5789999999764322


Q ss_pred             HHHHHhccCc------------------EEEEEcCCccc-------------cCCceEEEEEcCCh------hhHH----
Q 030396           88 ELARSIMHDA------------------VRVIVGRKNTA-------------SESIKQKLVFAGSE------EGKL----  126 (178)
Q Consensus        88 ~~~~~~~~~~------------------~~v~~~~~~~~-------------~~~i~~~~~~~~~~------~~k~----  126 (178)
                      .....+++.+                  ..+.+......             ...+....+.....      ..+.    
T Consensus       347 ~~~~~~f~~~~~~~~~~~~i~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~i~  426 (590)
T 3h1t_A          347 RDTYRYFGNPIYTYSLRQGIDDGFLAPYRVHRVISEVDAAGWRPSKGDVDRFGREIPDGEYQTKDFERVIALKARTDAFA  426 (590)
T ss_dssp             HHHHHHSCSCSEEECHHHHHHHTSSCCEEEEEEEETTCC-----------------------CCSHHHHHHHHHTHHHHH
T ss_pred             hhHHHHcCCceEecCHHHHhhCCccCCcEEEEeeeeeeccccccccccccccccccccccCCHHHhhhHhcChHHHHHHH
Confidence            2222333322                  11111110000             00000000001000      0111    


Q ss_pred             HHHHHHHHh-cCCCCEEEEeCCchHHHHHHHHhhhCCC--------ceEeeecCCCc
Q 030396          127 LALRQSFAE-SLNPPVLIFVQSKDRAKELYGELAFDDI--------RAGVIHSDLSQ  174 (178)
Q Consensus       127 ~~l~~ll~~-~~~~~~lIF~~t~~~~~~l~~~L~~~g~--------~~~~lh~~~~~  174 (178)
                      ..+.+.++. ...+++||||+++++|+.++..|.+.+.        .+..+||++++
T Consensus       427 ~~l~~~l~~~~~~~k~lVF~~~~~~a~~l~~~L~~~~~~~~~~~~~~~~~i~g~~~~  483 (590)
T 3h1t_A          427 KHLTDFMKRTDRFAKTIVFCVDQEHADEMRRALNNLNSDLSRKHPDYVARVTSEEGK  483 (590)
T ss_dssp             HHHHHHHHHHCTTSEEEEEESSHHHHHHHHHHHHHHTHHHHTTCTTSEEECSSTTHH
T ss_pred             HHHHHHHHhcCCCccEEEEECCHHHHHHHHHHHHHhhhhhhccCCCeEEEEeCCChH
Confidence            223333443 3357899999999999999999977654        37889999875

>2whx_A Serine protease/ntpase/helicase NS3; transcription, hydrolase, ATP-binding, reticulum, nucleotidyltransferase, multifunctional enzyme; HET: ADP; 2.20A {Dengue virus 4} PDB: 2vbc_A 2wzq_A

Probab=99.50  E-value=7.1e-15  Score=122.34  Aligned_cols=132  Identities=10%  Similarity=0.049  Sum_probs=89.9

Q ss_pred             EEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcHHHHHHHHHhccCc
Q 030396           18 ILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDA   97 (178)
Q Consensus        18 Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~   97 (178)
                      +.+.|.+.+...+... ..+++++++|+||||.+ +.+ +...+..+.+.+...+.|++++|||++..+..+..   .++
T Consensus       257 i~~~t~~~l~~~l~~~-~~l~~~~~iViDEah~~-~~~-~~~~~~~i~~~l~~~~~q~il~SAT~~~~~~~~~~---~~~  330 (618)
T 2whx_A          257 VDLMCHATFTTRLLSS-TRVPNYNLIVMDEAHFT-DPC-SVAARGYISTRVEMGEAAAIFMTATPPGSTDPFPQ---SNS  330 (618)
T ss_dssp             EEEEEHHHHHHHHHHC-SSCCCCSEEEEESTTCC-SHH-HHHHHHHHHHHHHHTSCEEEEECSSCTTCCCSSCC---CSS
T ss_pred             EEEEChHHHHHHHhcc-ccccCCeEEEEECCCCC-Ccc-HHHHHHHHHHHhcccCccEEEEECCCchhhhhhhc---cCC
Confidence            4445555555444333 35789999999999998 556 78888888887323689999999999976443221   234


Q ss_pred             EEEEEcCCccccCCceEEEEEcCChhhHHHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhhhCCCceEeeecC
Q 030396           98 VRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSD  171 (178)
Q Consensus        98 ~~v~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~  171 (178)
                      ..+.+....             +..  +...+...+.+. .+++||||+|++.|+.+++.|.+.|+++..+||+
T Consensus       331 ~~~~v~~~~-------------~~~--~~~~ll~~l~~~-~~~~LVF~~s~~~a~~l~~~L~~~g~~v~~lhg~  388 (618)
T 2whx_A          331 PIEDIEREI-------------PER--SWNTGFDWITDY-QGKTVWFVPSIKAGNDIANCLRKSGKRVIQLSRK  388 (618)
T ss_dssp             CEEEEECCC-------------CSS--CCSSSCHHHHHC-CSCEEEECSSHHHHHHHHHHHHHTTCCEEEECTT
T ss_pred             ceeeecccC-------------CHH--HHHHHHHHHHhC-CCCEEEEECChhHHHHHHHHHHHcCCcEEEEChH
Confidence            333332211             000  011122233333 6799999999999999999999999999999995

>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=99.47  E-value=1.2e-13  Score=115.88  Aligned_cols=141  Identities=18%  Similarity=0.147  Sum_probs=87.1

Q ss_pred             eCcHHHHHHHHcCCCCCCCeeEEEEeccccccccC-CChhhHHH----HHhh-----------------CCCCCceEEEE
Q 030396           21 STPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVG-NLLKHIDP----VVKA-----------------CSNPSIVRSLF   78 (178)
Q Consensus        21 ~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~-~~~~~i~~----i~~~-----------------~~~~~~q~i~~   78 (178)
                      +|||+|++++..+.       ++|+||+|.+++.. .+...+..    ....                 +.+...|++++
T Consensus       320 ~tpg~LlDyl~~~~-------llVlDEa~~~l~~~~~~~~~~~~~~~~l~~~G~~lp~~l~~~~l~~~e~~~~~~q~i~~  392 (661)
T 2d7d_A          320 STPYTLLDYFPDDF-------MIVVDESHVTIPQVRGMFNGDQARKQVLVDHGFRLPSALDNRPLRFEEFEKHMHNIVYV  392 (661)
T ss_dssp             CCCBCGGGGSCSSC-------EEEEETHHHHHHHHHHHHHHHHHHHHHHHHTTSSCGGGGGSCCCCHHHHHHTCSEEEEE
T ss_pred             CCccHHHHHcccCc-------EEEEecHHHHHHHHHHHHHHHHHHHHHHHHccccchhhhhcccccHHHHhccCCCEEEE
Confidence            89999999986543       89999999986321 01111110    0000                 01236899999


Q ss_pred             eecCcHHHHHHHHHhccCcEEEEEcCCccccCCceEEEEEcCChhhHHHHHHHHHHh--cCCCCEEEEeCCchHHHHHHH
Q 030396           79 SATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAE--SLNPPVLIFVQSKDRAKELYG  156 (178)
Q Consensus        79 SAT~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~--~~~~~~lIF~~t~~~~~~l~~  156 (178)
                      |||.++.....    ..........+.....+.     +.+.....+...+...+..  ....++||||+|++.|+.+++
T Consensus       393 SAT~~~~~~~~----~~~~~~~~~r~~~l~~p~-----i~v~~~~~~~~~Ll~~l~~~~~~~~~vlVf~~t~~~ae~L~~  463 (661)
T 2d7d_A          393 SATPGPYEIEH----TDEMVEQIIRPTGLLDPL-----IDVRPIEGQIDDLIGEIQARIERNERVLVTTLTKKMSEDLTD  463 (661)
T ss_dssp             CSSCCHHHHHH----CSSCEEECCCTTCCCCCE-----EEEECSTTHHHHHHHHHHHHHTTTCEEEEECSSHHHHHHHHH
T ss_pred             ecCCChhHHHh----hhCeeeeeecccCCCCCe-----EEEecccchHHHHHHHHHHHHhcCCeEEEEECCHHHHHHHHH
Confidence            99998654222    112122211111111111     1222333444555444443  245799999999999999999


Q ss_pred             HhhhCCCceEeeecCCCcccc
Q 030396          157 ELAFDDIRAGVIHSDLSQTQV  177 (178)
Q Consensus       157 ~L~~~g~~~~~lh~~~~~~~R  177 (178)
                      .|.+.|+++..+||++++.+|
T Consensus       464 ~L~~~gi~~~~lh~~~~~~~R  484 (661)
T 2d7d_A          464 YLKEIGIKVNYLHSEIKTLER  484 (661)
T ss_dssp             HHHHTTCCEEEECTTCCHHHH
T ss_pred             HHHhcCCCeEEEeCCCCHHHH
Confidence            999999999999999998877

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A

Probab=99.47  E-value=1.5e-13  Score=110.02  Aligned_cols=135  Identities=12%  Similarity=0.055  Sum_probs=86.6

Q ss_pred             CcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcHHHHHHHHHhcc
Q 030396           16 CDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMH   95 (178)
Q Consensus        16 ~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~~~~~~~~~~~   95 (178)
                      .-+.+.|.|.+...+.. ...+++++++|+||+|.+ ..+ +......+.....+.+.|++++|||.++.+..+...  .
T Consensus        71 ~~~~~~~~~~l~~~l~~-~~~~~~l~~vViDEaH~~-~~~-~~~~~~~l~~~~~~~~~~~l~~SAT~~~~~~~~~~~--~  145 (431)
T 2v6i_A           71 EIVDFMCHSTFTMKLLQ-GVRVPNYNLYIMDEAHFL-DPA-SVAARGYIETRVSMGDAGAIFMTATPPGTTEAFPPS--N  145 (431)
T ss_dssp             CSEEEEEHHHHHHHHHH-TCCCCCCSEEEEESTTCC-SHH-HHHHHHHHHHHHHTTSCEEEEEESSCTTCCCSSCCC--S
T ss_pred             ceEEEEchHHHHHHHhc-CccccCCCEEEEeCCccC-Ccc-HHHHHHHHHHHhhCCCCcEEEEeCCCCcchhhhcCC--C
Confidence            44566677777655554 456889999999999998 433 334444444432246899999999999743221100  0


Q ss_pred             CcEEEEEcCCccccCCceEEEEEcCChhhHHHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhhhCCCceEeeecCC
Q 030396           96 DAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDL  172 (178)
Q Consensus        96 ~~~~v~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~~  172 (178)
                      .|. .....             ..+.  .+...+.+.+... .++++|||+|+++|+.+++.|.+.|+++..+||++
T Consensus       146 ~~i-~~~~~-------------~~~~--~~~~~~~~~l~~~-~~~~lVF~~~~~~~~~l~~~L~~~~~~v~~lhg~~  205 (431)
T 2v6i_A          146 SPI-IDEET-------------RIPD--KAWNSGYEWITEF-DGRTVWFVHSIKQGAEIGTCLQKAGKKVLYLNRKT  205 (431)
T ss_dssp             SCC-EEEEC-------------CCCS--SCCSSCCHHHHSC-SSCEEEECSSHHHHHHHHHHHHHTTCCEEEESTTT
T ss_pred             Cce-eeccc-------------cCCH--HHHHHHHHHHHcC-CCCEEEEeCCHHHHHHHHHHHHHcCCeEEEeCCcc
Confidence            111 11100             0111  1112223444444 57899999999999999999999999999999984

>2fwr_A DNA repair protein RAD25; DNA unwinding, XPB, DNA binding protein; HET: DNA; 2.60A {Archaeoglobus fulgidus} SCOP: c.37.1.19 c.37.1.19 PDB: 2fzl_A*

Probab=99.44  E-value=4.1e-14  Score=114.16  Aligned_cols=149  Identities=15%  Similarity=0.148  Sum_probs=97.9

Q ss_pred             CCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcH---------
Q 030396           14 FSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPD---------   84 (178)
Q Consensus        14 ~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~---------   84 (178)
                      ..++|+|+||+++...+..-   ..+++++|+||+|.+.+.+ +.    .+.+. . ...+++++|||.+.         
T Consensus       170 ~~~~Ivv~T~~~l~~~~~~~---~~~~~liIvDEaH~~~~~~-~~----~~~~~-~-~~~~~l~lSATp~~~~~~~~~l~  239 (472)
T 2fwr_A          170 ELKPLTVSTYDSAYVNAEKL---GNRFMLLIFDEVHHLPAES-YV----QIAQM-S-IAPFRLGLTATFEREDGRHEILK  239 (472)
T ss_dssp             CCCSEEEEEHHHHHHTHHHH---TTTCSEEEEETGGGTTSTT-TH----HHHHT-C-CCSEEEEEESCCCCTTSGGGSHH
T ss_pred             CcCCEEEEEcHHHHHHHHHh---cCCCCEEEEECCcCCCChH-HH----HHHHh-c-CCCeEEEEecCccCCCCHHHHHH
Confidence            35789999999988776521   1457899999999998777 54    35565 3 46788999999972         


Q ss_pred             ----------HHHHHHHHhccCcEEEEE--cCCcc------------------------ccCCceEEEE-----------
Q 030396           85 ----------FVEELARSIMHDAVRVIV--GRKNT------------------------ASESIKQKLV-----------  117 (178)
Q Consensus        85 ----------~~~~~~~~~~~~~~~v~~--~~~~~------------------------~~~~i~~~~~-----------  117 (178)
                                ...++...++.++....+  .....                        ...++.+.+.           
T Consensus       240 ~~~~~~~~~~~~~~l~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  319 (472)
T 2fwr_A          240 EVVGGKVFELFPDSLAGKHLAKYTIKRIFVPLAEDERVEYEKREKVYKQFLRARGITLRRAEDFNKIVMASGYDERAYEA  319 (472)
T ss_dssp             HHTCCEEEECCHHHHTSCCCCSEEECCEEECCCHHHHHHTTTTTHHHHSCSSSCCCTTTCCSSSTTTTTTTCCSSSSSTT
T ss_pred             HHhCCeEeecCHHHHhcCcCCCeEEEEEEcCCCHHHHHHHHHHHHHHHHHHHhcCccccchhhHHHHHHHhccCHHHHHH
Confidence                      233333333443322211  10000                        0000000000           


Q ss_pred             ---------EcCChhhHHHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhhhCCCceEeeecCCCcccc
Q 030396          118 ---------FAGSEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQV  177 (178)
Q Consensus       118 ---------~~~~~~~k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~~~~~~R  177 (178)
                               .......|...+.++++.....++||||++.+.++.+++.|.     +..+||+++..+|
T Consensus       320 ~~~~~~~~~~~~~~~~k~~~l~~~l~~~~~~k~lvF~~~~~~~~~l~~~l~-----~~~~~g~~~~~~R  383 (472)
T 2fwr_A          320 LRAWEEARRIAFNSKNKIRKLREILERHRKDKIIIFTRHNELVYRISKVFL-----IPAITHRTSREER  383 (472)
T ss_dssp             THHHHHHHHHHHSCSHHHHHHHHHHHHTSSSCBCCBCSCHHHHHHHHHHTT-----CCBCCSSSCSHHH
T ss_pred             HHHHHHHHHHhhcChHHHHHHHHHHHhCCCCcEEEEECCHHHHHHHHHHhC-----cceeeCCCCHHHH
Confidence                     001234578889999998878999999999999999999984     6689999998776

>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=99.43  E-value=1.2e-13  Score=101.88  Aligned_cols=76  Identities=18%  Similarity=0.235  Sum_probs=60.1

Q ss_pred             CCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccc-cccCCCh-hhHHHHHhhCCCCCceEEEEeecCcHHHHHHHH
Q 030396           14 FSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKL-FEVGNLL-KHIDPVVKACSNPSIVRSLFSATLPDFVEELAR   91 (178)
Q Consensus        14 ~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~l-l~~~~~~-~~i~~i~~~~~~~~~q~i~~SAT~~~~~~~~~~   91 (178)
                      .+++|+|||||++.+++..   .+++++++|+||||.+ ++.+ +. ..++.+... . ++.|++++|||++.+.  +.+
T Consensus       154 ~~~~Ivv~Tpg~l~~~l~~---~l~~~~~lVlDEah~~~~~~~-~~~~~l~~i~~~-~-~~~~~il~SAT~~~~~--~~~  225 (235)
T 3llm_A          154 PHASIMFCTVGVLLRKLEA---GIRGISHVIVDEIHERDINTD-FLLVVLRDVVQA-Y-PEVRIVLMSATIDTSM--FCE  225 (235)
T ss_dssp             SSSEEEEEEHHHHHHHHHH---CCTTCCEEEECCTTSCCHHHH-HHHHHHHHHHHH-C-TTSEEEEEECSSCCHH--HHH
T ss_pred             CCCeEEEECHHHHHHHHHh---hhcCCcEEEEECCccCCcchH-HHHHHHHHHHhh-C-CCCeEEEEecCCCHHH--HHH
Confidence            5688999999999999976   4889999999999996 6666 55 567777776 3 5799999999999775  444


Q ss_pred             HhccCc
Q 030396           92 SIMHDA   97 (178)
Q Consensus        92 ~~~~~~   97 (178)
                      .+.+.|
T Consensus       226 ~~~~~p  231 (235)
T 3llm_A          226 YFFNCP  231 (235)
T ss_dssp             HTTSCC
T ss_pred             HcCCCC
Confidence            444444

>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=99.42  E-value=4.5e-13  Score=112.40  Aligned_cols=141  Identities=21%  Similarity=0.118  Sum_probs=86.5

Q ss_pred             eCcHHHHHHHHcCCCCCCCeeEEEEeccccccccC-CChhhHH----HHHhh-----------------CCCCCceEEEE
Q 030396           21 STPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVG-NLLKHID----PVVKA-----------------CSNPSIVRSLF   78 (178)
Q Consensus        21 ~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~-~~~~~i~----~i~~~-----------------~~~~~~q~i~~   78 (178)
                      +||++|++++..+       .++|+||+|.+++.. .+.....    .....                 +.+...|++++
T Consensus       314 ~tp~~LlDyl~~~-------~llVlDEah~~~~~~~~~~~~~~~~~~~l~~~G~~lp~~l~~~~l~~~e~~~~~~q~i~~  386 (664)
T 1c4o_A          314 EPPYTLLDYFPED-------FLVFLDESHVTVPQLQGMYRGDYARKKTLVDYGFRLPSALDNRPLRFEEFLERVSQVVFV  386 (664)
T ss_dssp             SCCCCGGGGSCTT-------CEEEEETHHHHHHHHHHHHHHHHHHHHHHHHTTSSCGGGGGSSCCCHHHHHHTCSEEEEE
T ss_pred             CCchHHHHHHhhc-------cEEEEecccccHHHHHHHHHHHHHHHHHHHHccccchhhhhcCcccHHHHHhhcCCEEEE
Confidence            8999999988543       289999999986321 0111111    00000                 01135799999


Q ss_pred             eecCcHHHHHHHHHhccCcEEEEEcCCccccCCceEEEEEcCChhhHHHHHHHHHHh--cCCCCEEEEeCCchHHHHHHH
Q 030396           79 SATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAE--SLNPPVLIFVQSKDRAKELYG  156 (178)
Q Consensus        79 SAT~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~--~~~~~~lIF~~t~~~~~~l~~  156 (178)
                      |||.++.....    ..  ..+.......   ++....+.+.+...+...+...+..  ....++||||+|++.|+.+++
T Consensus       387 SAT~~~~~~~~----~~--~~~~~~~r~~---~l~~p~i~v~~~~~~~~~Ll~~l~~~~~~~~~vlVf~~t~~~ae~L~~  457 (664)
T 1c4o_A          387 SATPGPFELAH----SG--RVVEQIIRPT---GLLDPLVRVKPTENQILDLMEGIRERAARGERTLVTVLTVRMAEELTS  457 (664)
T ss_dssp             ESSCCHHHHHH----CS--EEEEECSCTT---CCCCCEEEEECSTTHHHHHHHHHHHHHHTTCEEEEECSSHHHHHHHHH
T ss_pred             ecCCCHHHHHh----hh--CeeeeeeccC---CCCCCeEEEecccchHHHHHHHHHHHHhcCCEEEEEECCHHHHHHHHH
Confidence            99998653221    11  1122211111   1111112222333455555554543  246799999999999999999


Q ss_pred             HhhhCCCceEeeecCCCcccc
Q 030396          157 ELAFDDIRAGVIHSDLSQTQV  177 (178)
Q Consensus       157 ~L~~~g~~~~~lh~~~~~~~R  177 (178)
                      .|.+.|+++..+||+|++.+|
T Consensus       458 ~L~~~gi~~~~lh~~~~~~~R  478 (664)
T 1c4o_A          458 FLVEHGIRARYLHHELDAFKR  478 (664)
T ss_dssp             HHHHTTCCEEEECTTCCHHHH
T ss_pred             HHHhcCCCceeecCCCCHHHH
Confidence            999999999999999998877

>3rc3_A ATP-dependent RNA helicase SUPV3L1, mitochondrial; SUV3, nucleus, hydrolase; HET: ANP; 2.08A {Homo sapiens} PDB: 3rc8_A

Probab=99.42  E-value=7.4e-14  Score=117.04  Aligned_cols=146  Identities=14%  Similarity=0.066  Sum_probs=98.0

Q ss_pred             CCCcEEEeCcHHHHHHHHcC--CC-CCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcHHHHHHH
Q 030396           14 FSCDILISTPLRLRLAIRRK--KI-DLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELA   90 (178)
Q Consensus        14 ~~~~Iii~TP~~l~~~l~~~--~~-~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~~~~~~   90 (178)
                      ++.+++++|||++.+++...  .+ ....++++|+||+|.+++.+ +...+..++..+.....|++++|||.+ .+..+.
T Consensus       211 G~~~~iv~TpGr~~~il~~T~e~~~l~~~v~lvVIDEaH~l~d~~-~g~~~~~~l~~l~~~~i~il~~SAT~~-~i~~l~  288 (677)
T 3rc3_A          211 GEERVTVQPNGKQASHVSCTVEMCSVTTPYEVAVIDEIQMIRDPA-RGWAWTRALLGLCAEEVHLCGEPAAID-LVMELM  288 (677)
T ss_dssp             SSCEECCSTTCCCCSEEEEEGGGCCSSSCEEEEEECSGGGGGCTT-THHHHHHHHHHCCEEEEEEEECGGGHH-HHHHHH
T ss_pred             CCeeEEecCCCcccceeEecHhHhhhcccCCEEEEecceecCCcc-chHHHHHHHHccCccceEEEeccchHH-HHHHHH
Confidence            34456667777666655332  12 24678999999999998888 999999999983337889999999953 344444


Q ss_pred             HHhccCcEEEEEcCCccccCCceEEEEEcCChhhHHHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhhhCCCceEeeec
Q 030396           91 RSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHS  170 (178)
Q Consensus        91 ~~~~~~~~~v~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~  170 (178)
                      ... ..+..+.... ...+  .  .+  ....   .    ..+... ....+|||+|+++++.++..|.+.|+.+..+||
T Consensus       289 ~~~-~~~~~v~~~~-r~~~--l--~~--~~~~---l----~~l~~~-~~g~iIf~~s~~~ie~la~~L~~~g~~v~~lHG  352 (677)
T 3rc3_A          289 YTT-GEEVEVRDYK-RLTP--I--SV--LDHA---L----ESLDNL-RPGDCIVCFSKNDIYSVSRQIEIRGLESAVIYG  352 (677)
T ss_dssp             HHH-TCCEEEEECC-CSSC--E--EE--CSSC---C----CSGGGC-CTTEEEECSSHHHHHHHHHHHHHTTCCCEEECT
T ss_pred             Hhc-CCceEEEEee-ecch--H--HH--HHHH---H----HHHHhc-CCCCEEEEcCHHHHHHHHHHHHhcCCCeeeeec
Confidence            443 3444442221 1111  0  01  0000   0    111222 355699999999999999999999999999999


Q ss_pred             CCCcccc
Q 030396          171 DLSQTQV  177 (178)
Q Consensus       171 ~~~~~~R  177 (178)
                      +|++++|
T Consensus       353 ~L~~~~R  359 (677)
T 3rc3_A          353 SLPPGTK  359 (677)
T ss_dssp             TSCHHHH
T ss_pred             cCCHHHH
Confidence            9999876

>2wv9_A Flavivirin protease NS2B regulatory subunit, FLAV protease NS3 catalytic subunit; nucleotide-binding, capsid protein; 2.75A {Murray valley encephalitis virus}

Probab=99.41  E-value=1.4e-14  Score=121.50  Aligned_cols=131  Identities=11%  Similarity=0.056  Sum_probs=81.1

Q ss_pred             EeCcHHHHHHHHcC--------CCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcHHHHHHHH
Q 030396           20 ISTPLRLRLAIRRK--------KIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELAR   91 (178)
Q Consensus        20 i~TP~~l~~~l~~~--------~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~~~~~~~   91 (178)
                      ++||+++.+++..+        ...+++++++|+||+|.+ +.+ +......+.+.+.+...|++++|||+++.+..+..
T Consensus       305 v~tp~~ll~~l~~~~l~~~l~~~~~l~~l~lvViDEaH~~-~~~-~~~~~~~l~~~~~~~~~~vl~~SAT~~~~i~~~~~  382 (673)
T 2wv9_A          305 EHSGNEIVDVMCHATLTHRLMSPLRVPNYNLFVMDEAHFT-DPA-SIAARGYIATRVEAGEAAAIFMTATPPGTSDPFPD  382 (673)
T ss_dssp             CCCSCCCEEEEEHHHHHHHHHSSSCCCCCSEEEEESTTCC-CHH-HHHHHHHHHHHHHTTSCEEEEECSSCTTCCCSSCC
T ss_pred             cCCHHHHHHHHHhhhhHHHHhcccccccceEEEEeCCccc-Ccc-HHHHHHHHHHhccccCCcEEEEcCCCChhhhhhcc
Confidence            67777665433222        236889999999999999 222 23333344443123679999999999976433211


Q ss_pred             HhccCcEEEEEcCCccccCCceEEEEEcCChhhHHHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhhhCCCceEeeecC
Q 030396           92 SIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSD  171 (178)
Q Consensus        92 ~~~~~~~~v~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~  171 (178)
                      .  ..|.. .+..             .... ..... +...+.+ ..+++||||+|+++|+.+++.|.+.|+++..+||+
T Consensus       383 ~--~~~i~-~v~~-------------~~~~-~~~~~-~l~~l~~-~~~~~lVF~~s~~~~e~la~~L~~~g~~v~~lHg~  443 (673)
T 2wv9_A          383 T--NSPVH-DVSS-------------EIPD-RAWSS-GFEWITD-YAGKTVWFVASVKMSNEIAQCLQRAGKRVIQLNRK  443 (673)
T ss_dssp             C--SSCEE-EEEC-------------CCCS-SCCSS-CCHHHHS-CCSCEEEECSSHHHHHHHHHHHHTTTCCEEEECSS
T ss_pred             c--CCceE-EEee-------------ecCH-HHHHH-HHHHHHh-CCCCEEEEECCHHHHHHHHHHHHhCCCeEEEeChH
Confidence            0  11111 1110             0111 11111 1222333 36899999999999999999999999999999994

>2z83_A Helicase/nucleoside triphosphatase; hydrolase, membrane, nucleotide-binding, RNA replication, transmembrane, viral protein; 1.80A {Japanese encephalitis virus} PDB: 2v8o_A 2qeq_A

Probab=99.35  E-value=6.9e-13  Score=106.93  Aligned_cols=129  Identities=13%  Similarity=0.071  Sum_probs=82.2

Q ss_pred             CcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccc-----cccCCChhhHHHHHhhCCCCCceEEEEeecCcHHHHHHH
Q 030396           16 CDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKL-----FEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELA   90 (178)
Q Consensus        16 ~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~l-----l~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~~~~~~   90 (178)
                      -.+.+.|.+.+...+... ..+++++++|+||||.+     +..+ +...   +.   .....|++++|||++..+..+.
T Consensus        90 ~~i~~~~~~~l~~~l~~~-~~l~~~~~iViDEaH~~~~~~~~~~~-~~~~---~~---~~~~~~~il~SAT~~~~~~~~~  161 (459)
T 2z83_A           90 EIVDVMCHATLTHRLMSP-NRVPNYNLFVMDEAHFTDPASIAARG-YIAT---KV---ELGEAAAIFMTATPPGTTDPFP  161 (459)
T ss_dssp             CSEEEEEHHHHHHHHHSC-C-CCCCSEEEESSTTCCSHHHHHHHH-HHHH---HH---HTTSCEEEEECSSCTTCCCSSC
T ss_pred             cEEEEEchHHHHHHhhcc-ccccCCcEEEEECCccCCchhhHHHH-HHHH---Hh---ccCCccEEEEEcCCCcchhhhc
Confidence            346667777766555443 45789999999999984     3333 2222   11   2368999999999997643321


Q ss_pred             HHhccCcEEEEEcCCccccCCceEEEEEcCChhhHHHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhhhCCCceEeeec
Q 030396           91 RSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHS  170 (178)
Q Consensus        91 ~~~~~~~~~v~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~  170 (178)
                      ..  ..|.......   .+           .  .+...+.+++... .+++||||+|++.|+.+++.|...|+++..+||
T Consensus       162 ~~--~~pi~~~~~~---~~-----------~--~~~~~~~~~l~~~-~~~~LVF~~s~~~~~~l~~~L~~~g~~v~~lh~  222 (459)
T 2z83_A          162 DS--NAPIHDLQDE---IP-----------D--RAWSSGYEWITEY-AGKTVWFVASVKMGNEIAMCLQRAGKKVIQLNR  222 (459)
T ss_dssp             CC--SSCEEEEECC---CC-----------S--SCCSSCCHHHHHC-CSCEEEECSCHHHHHHHHHHHHHTTCCEEEEST
T ss_pred             cC--CCCeEEeccc---CC-----------c--chhHHHHHHHHhc-CCCEEEEeCChHHHHHHHHHHHhcCCcEEecCH
Confidence            11  2333221110   00           0  0001112233333 689999999999999999999999999999999


Q ss_pred             C
Q 030396          171 D  171 (178)
Q Consensus       171 ~  171 (178)
                      +
T Consensus       223 ~  223 (459)
T 2z83_A          223 K  223 (459)
T ss_dssp             T
T ss_pred             H
Confidence            6

>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; 2.60A {Homo sapiens}

Probab=99.31  E-value=4.4e-12  Score=90.86  Aligned_cols=85  Identities=22%  Similarity=0.335  Sum_probs=60.1

Q ss_pred             HHhccCcEEEEEcCCccccCCceEEEEEcCChhhHHHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhhhCCCceEeeec
Q 030396           91 RSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHS  170 (178)
Q Consensus        91 ~~~~~~~~~v~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~  170 (178)
                      ..++.+|..+.+........++.|.++.+ +...|...|.+++... .+++||||++++.++.+++.|...|+++..+||
T Consensus         9 ~~~~~~p~~i~v~~~~~~~~~i~q~~~~~-~~~~K~~~L~~~l~~~-~~~~lVF~~~~~~~~~l~~~L~~~g~~~~~lhg   86 (191)
T 2p6n_A            9 SGVDLGTENLYFQSMGAASLDVIQEVEYV-KEEAKMVYLLECLQKT-PPPVLIFAEKKADVDAIHEYLLLKGVEAVAIHG   86 (191)
T ss_dssp             -------------------CCSEEEEEEC-CGGGHHHHHHHHHTTS-CSCEEEECSCHHHHHHHHHHHHHHTCCEEEECT
T ss_pred             ccccCCCEEEEECCCCCCCcCceEEEEEc-ChHHHHHHHHHHHHhC-CCCEEEEECCHHHHHHHHHHHHHcCCcEEEEeC
Confidence            46788999999888888888999999777 5567999999999876 568999999999999999999999999999999


Q ss_pred             CCCcccc
Q 030396          171 DLSQTQV  177 (178)
Q Consensus       171 ~~~~~~R  177 (178)
                      +|++.+|
T Consensus        87 ~~~~~~R   93 (191)
T 2p6n_A           87 GKDQEER   93 (191)
T ss_dssp             TSCHHHH
T ss_pred             CCCHHHH
Confidence            9999887

>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=99.30  E-value=2.3e-11  Score=98.68  Aligned_cols=54  Identities=19%  Similarity=0.258  Sum_probs=45.5

Q ss_pred             hHHHHHHHHHHhc--CCCCEEEEeCCchHHHHHHHHhhhC-CCceEeeecCCCcccc
Q 030396          124 GKLLALRQSFAES--LNPPVLIFVQSKDRAKELYGELAFD-DIRAGVIHSDLSQTQV  177 (178)
Q Consensus       124 ~k~~~l~~ll~~~--~~~~~lIF~~t~~~~~~l~~~L~~~-g~~~~~lh~~~~~~~R  177 (178)
                      .|...+.+++...  ...++||||++...++.++..|... |+++..+||++++.+|
T Consensus       325 ~K~~~l~~~l~~~~~~~~k~lvF~~~~~~~~~l~~~l~~~~~~~~~~~~g~~~~~~R  381 (500)
T 1z63_A          325 GKMIRTMEIIEEALDEGDKIAIFTQFVDMGKIIRNIIEKELNTEVPFLYGELSKKER  381 (500)
T ss_dssp             HHHHHHHHHHHHHHTTTCCEEEECSCHHHHHHHHHHHHHHHTCCCCEEETTSCHHHH
T ss_pred             hhHHHHHHHHHHHHccCCcEEEEEehHHHHHHHHHHHHHhhCCCeEEEECCCCHHHH
Confidence            4556666666643  5679999999999999999999885 9999999999998876

>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=99.27  E-value=5e-12  Score=110.08  Aligned_cols=56  Identities=21%  Similarity=0.198  Sum_probs=51.3

Q ss_pred             hhhHHHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhhh-CCCceEeeecCCCcccc
Q 030396          122 EEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAF-DDIRAGVIHSDLSQTQV  177 (178)
Q Consensus       122 ~~~k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~~-~g~~~~~lh~~~~~~~R  177 (178)
                      ...|...+.++++.....++||||++++.++.++..|.+ .|+++..+||+|++.+|
T Consensus       487 ~~~K~~~L~~ll~~~~~~k~iVF~~~~~~~~~l~~~L~~~~g~~~~~lhG~~~~~~R  543 (968)
T 3dmq_A          487 FDPRVEWLMGYLTSHRSQKVLVICAKAATALQLEQVLREREGIRAAVFHEGMSIIER  543 (968)
T ss_dssp             TSHHHHHHHHHHHHTSSSCCCEECSSTHHHHHHHHHHHTTTCCCEEEECTTSCTTHH
T ss_pred             ccHHHHHHHHHHHhCCCCCEEEEeCcHHHHHHHHHHHHHHcCCcEEEEeCCCCHHHH
Confidence            446899999999988889999999999999999999985 69999999999999887

>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=99.26  E-value=1.6e-11  Score=86.59  Aligned_cols=71  Identities=23%  Similarity=0.266  Sum_probs=65.6

Q ss_pred             cccCCceEEEEEcCChhhHHHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhhhCCCceEeeecCCCcccc
Q 030396          107 TASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQV  177 (178)
Q Consensus       107 ~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~~~~~~R  177 (178)
                      ..+.++.|+++.+.....|...|.++++....+++||||++++.|+.++..|...|+.+..+||+|++.+|
T Consensus         3 ~~~~~i~q~~~~~~~~~~K~~~L~~ll~~~~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~~g~~~~~~R   73 (175)
T 2rb4_A            3 LTLNNIRQYYVLCEHRKDKYQALCNIYGSITIGQAIIFCQTRRNAKWLTVEMIQDGHQVSLLSGELTVEQR   73 (175)
T ss_dssp             CCBCCEEEEEEECSSHHHHHHHHHHHHTTSCCSEEEEECSCHHHHHHHHHHHHTTTCCEEEECSSCCHHHH
T ss_pred             CccCCceEEEEEcCChHhHHHHHHHHHHhCCCCCEEEEECCHHHHHHHHHHHHHcCCcEEEEeCCCCHHHH
Confidence            45678999999888777799999999998888899999999999999999999999999999999999887

>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase; 1.95A {Bacillus subtilis}

Probab=99.20  E-value=5.4e-11  Score=82.90  Aligned_cols=71  Identities=20%  Similarity=0.289  Sum_probs=63.0

Q ss_pred             ccccCCceEEEEEcCChhhHHHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhhhCCCceEeeecCCCcccc
Q 030396          106 NTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQV  177 (178)
Q Consensus       106 ~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~~~~~~R  177 (178)
                      +..+.++.|+++.+ +...|...|.++++....+++||||+|++.++.++..|...|+++..+||+|++.+|
T Consensus         4 ~~~~~~i~~~~~~~-~~~~K~~~L~~ll~~~~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~hg~~~~~~r   74 (163)
T 2hjv_A            4 GLTTRNIEHAVIQV-REENKFSLLKDVLMTENPDSCIIFCRTKEHVNQLTDELDDLGYPCDKIHGGMIQEDR   74 (163)
T ss_dssp             --CCCCEEEEEEEC-CGGGHHHHHHHHHHHHCCSSEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHH
T ss_pred             ccCcccceEEEEEC-ChHHHHHHHHHHHHhcCCCcEEEEECCHHHHHHHHHHHHHcCCcEEEEeCCCCHHHH
Confidence            44567799988776 567799999999998888899999999999999999999999999999999999887

>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=99.18  E-value=7.1e-11  Score=83.07  Aligned_cols=68  Identities=24%  Similarity=0.167  Sum_probs=61.0

Q ss_pred             cCCceEEEEEcCChhhHHHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhhhCCCceEeeecCCCcccc
Q 030396          109 SESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQV  177 (178)
Q Consensus       109 ~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~~~~~~R  177 (178)
                      +.++.|+++.+ +...|...|.++++....+++||||++++.|+.++..|...|+++..+||+|++.+|
T Consensus         3 ~~~i~q~~~~~-~~~~K~~~L~~ll~~~~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~hg~~~~~~r   70 (172)
T 1t5i_A            3 LHGLQQYYVKL-KDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEER   70 (172)
T ss_dssp             --CCEEEEEEC-CGGGHHHHHHHHHHHSCCSSEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHH
T ss_pred             cCCeEEEEEEC-ChHHHHHHHHHHHHhCCCCcEEEEECCHHHHHHHHHHHHhcCCCEEEEECCCCHHHH
Confidence            56788988777 556799999999998888999999999999999999999999999999999999887

>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein, translation; 1.75A {Saccharomyces cerevisiae} SCOP: c.37.1.19

Probab=99.18  E-value=7.1e-11  Score=82.41  Aligned_cols=68  Identities=29%  Similarity=0.323  Sum_probs=61.3

Q ss_pred             CCceEEEEEcCChhhHHHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhhhCCCceEeeecCCCcccc
Q 030396          110 ESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQV  177 (178)
Q Consensus       110 ~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~~~~~~R  177 (178)
                      .++.|+++.+.....|...|.++++....+++||||+|++.|+.++..|...|+.+..+||+|++.+|
T Consensus         2 ~~i~~~~~~~~~~~~K~~~l~~ll~~~~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r   69 (165)
T 1fuk_A            2 EGIKQFYVNVEEEEYKYECLTDLYDSISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQER   69 (165)
T ss_dssp             --CEEEEEEEESGGGHHHHHHHHHHHTTCSCEEEEESSHHHHHHHHHHHHHTTCCEEEECTTSCHHHH
T ss_pred             CCcEEEEEECCcchhHHHHHHHHHHhCCCCCEEEEECCHHHHHHHHHHHHHcCCCEEEEECCCCHHHH
Confidence            46889998887666699999999998888999999999999999999999999999999999999877

>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=99.14  E-value=2.2e-10  Score=81.52  Aligned_cols=72  Identities=29%  Similarity=0.346  Sum_probs=55.2

Q ss_pred             CccccCCceEEEEEcCChhhHHHHHHHHHHhc-CCCCEEEEeCCchHHHHHHHHhhhCCCceEeeecCCCcccc
Q 030396          105 KNTASESIKQKLVFAGSEEGKLLALRQSFAES-LNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQV  177 (178)
Q Consensus       105 ~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~-~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~~~~~~R  177 (178)
                      ....+.++.|.++.+ +...|...|.++++.. ...++||||+|++.|+.++..|...|+++..+||+|++.+|
T Consensus        13 ~~~~~~~i~q~~~~v-~~~~K~~~L~~ll~~~~~~~k~lVF~~~~~~~~~l~~~L~~~g~~~~~lhg~~~~~~r   85 (185)
T 2jgn_A           13 QGSTSENITQKVVWV-EESDKRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDR   85 (185)
T ss_dssp             ---CCTTEEEEEEEC-CGGGHHHHHHHHHHHC-CCSCEEEEESCHHHHHHHHHHHHHTTCCEEEEC--------
T ss_pred             cCCCCCCceEEEEEe-CcHHHHHHHHHHHHhcCCCCeEEEEECCHHHHHHHHHHHHHcCCceEEEeCCCCHHHH
Confidence            445677899999877 4567999999999876 57899999999999999999999999999999999999887

>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=99.09  E-value=3.8e-10  Score=98.51  Aligned_cols=65  Identities=12%  Similarity=0.054  Sum_probs=50.6

Q ss_pred             CCCcEEEeCcHHHHHHHHcCC-C-CCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcH
Q 030396           14 FSCDILISTPLRLRLAIRRKK-I-DLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPD   84 (178)
Q Consensus        14 ~~~~Iii~TP~~l~~~l~~~~-~-~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~   84 (178)
                      .+++|+|+||+++..++.... . .++...++|+||||++...    .....|.+. + ++.++++||||...
T Consensus       374 ~~~~IiVtTiqkl~~~l~~~~~~~~~~~~~lvIiDEAHrs~~~----~~~~~I~~~-~-p~a~~lgfTATP~~  440 (1038)
T 2w00_A          374 DDNKIIVTTIQKLNNLMKAESDLPVYNQQVVFIFDECHRSQFG----EAQKNLKKK-F-KRYYQFGFTGTPIF  440 (1038)
T ss_dssp             SSCCEEEEEHHHHHHHHHHCCCCGGGGSCEEEEEESCCTTHHH----HHHHHHHHH-C-SSEEEEEEESSCCC
T ss_pred             CCCCEEEEEHHHHHHHHhcccchhccccccEEEEEccchhcch----HHHHHHHHh-C-CcccEEEEeCCccc
Confidence            579999999999999887542 2 4567889999999998542    335667777 4 46899999999874

>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=99.05  E-value=1.1e-10  Score=84.21  Aligned_cols=67  Identities=22%  Similarity=0.256  Sum_probs=44.0

Q ss_pred             CCCcEEEeCcHHHHHHHHcCC------CCCCCeeEEEEeccccccccCCChhhH-HHHHhhCC------------CCCce
Q 030396           14 FSCDILISTPLRLRLAIRRKK------IDLSRVEYLVLDEADKLFEVGNLLKHI-DPVVKACS------------NPSIV   74 (178)
Q Consensus        14 ~~~~Iii~TP~~l~~~l~~~~------~~~~~l~~lViDE~d~ll~~~~~~~~i-~~i~~~~~------------~~~~q   74 (178)
                      .+++|+|+||+++...+....      ..+.+++++|+||||.+...+ +...+ ..++....            .+..+
T Consensus       131 ~~~~i~v~T~~~l~~~~~~~~~~~~~~~~~~~~~~iIiDEah~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  209 (216)
T 3b6e_A          131 KSCDIIISTAQILENSLLNLENGEDAGVQLSDFSLIIIDECHHTNKEA-VYNNIMRHYLMQKLKNNRLKKENKPVIPLPQ  209 (216)
T ss_dssp             HHCSEEEEEHHHHHHHHHC-------CCCGGGCSEEEETTC--------CHHHHHHHHHHHHHHHHHHHHTTCCCCCCCE
T ss_pred             cCCCEEEECHHHHHHHHhccCcccccccchhcccEEEEECchhhccCC-cHHHHHHHHHHHhcccccccccccCCCCcce
Confidence            458999999999999987643      567899999999999998776 44444 33332211            15789


Q ss_pred             EEEEeec
Q 030396           75 RSLFSAT   81 (178)
Q Consensus        75 ~i~~SAT   81 (178)
                      ++++|||
T Consensus       210 ~l~lSAT  216 (216)
T 3b6e_A          210 ILGLTAS  216 (216)
T ss_dssp             EEEEECC
T ss_pred             EEEeecC
Confidence            9999998

>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=98.47  E-value=9.8e-11  Score=82.11  Aligned_cols=68  Identities=21%  Similarity=0.209  Sum_probs=61.2

Q ss_pred             CCceEEEEEcCChhhHHHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhhhCCCceEeeecCCCcccc
Q 030396          110 ESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQV  177 (178)
Q Consensus       110 ~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~~~~~~R  177 (178)
                      .++.|.++.+.....|...|.++++.....++||||++++.|+.++..|...|+.+..+||+|++.+|
T Consensus         2 ~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~~~iVF~~~~~~~~~l~~~L~~~~~~~~~~~g~~~~~~r   69 (170)
T 2yjt_D            2 KKIHQWYYRADDLEHKTALLVHLLKQPEATRSIVFVRKRERVHELANWLREAGINNCYLEGEMVQGKR   69 (170)
Confidence            45778887776647899999999998778899999999999999999999999999999999999887

>3mwy_W Chromo domain-containing protein 1; SWI2/SNF2 ATPase, double chromodomains, hydrolase; HET: ATG; 3.70A {Saccharomyces cerevisiae}

Probab=98.92  E-value=1.6e-08  Score=86.64  Aligned_cols=54  Identities=24%  Similarity=0.217  Sum_probs=47.4

Q ss_pred             hHHHHHHHHHHhc--CCCCEEEEeCCchHHHHHHHHhhhCCCceEeeecCCCcccc
Q 030396          124 GKLLALRQSFAES--LNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQV  177 (178)
Q Consensus       124 ~k~~~l~~ll~~~--~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~~~~~~R  177 (178)
                      .|...+.+++...  ...++||||+....++.++..|...|+++..+||+++..+|
T Consensus       556 ~K~~~L~~lL~~~~~~g~kvLIFsq~~~~ld~L~~~L~~~g~~~~~i~G~~~~~eR  611 (800)
T 3mwy_W          556 GKMVLLDQLLTRLKKDGHRVLIFSQMVRMLDILGDYLSIKGINFQRLDGTVPSAQR  611 (800)
T ss_dssp             HHHHHHHHHHHHHTTTTCCEEEEESCHHHHHHHHHHHHHHTCCCEEESTTSCHHHH
T ss_pred             hHHHHHHHHHHHHhhCCCeEEEEechHHHHHHHHHHHHhCCCCEEEEeCCCCHHHH
Confidence            4677777777754  35799999999999999999999999999999999999887

>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=98.91  E-value=3.5e-08  Score=82.62  Aligned_cols=54  Identities=13%  Similarity=0.051  Sum_probs=45.3

Q ss_pred             hHHHHHHHHHHh---cCCCCEEEEeCCchHHHHHHHHhhhCCCceEeeecCCCcccc
Q 030396          124 GKLLALRQSFAE---SLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQV  177 (178)
Q Consensus       124 ~k~~~l~~ll~~---~~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~~~~~~R  177 (178)
                      .|...+..++..   ....++||||++...++.++..|...|+++..+||++++++|
T Consensus       399 ~K~~~l~~ll~~~~~~~~~k~lIFs~~~~~~~~l~~~l~~~g~~~~~l~G~~~~~~R  455 (644)
T 1z3i_X          399 GKMLVLDYILAMTRTTTSDKVVLVSNYTQTLDLFEKLCRNRRYLYVRLDGTMSIKKR  455 (644)
T ss_dssp             HHHHHHHHHHHHHHHHCCCEEEEEESCHHHHHHHHHHHHHHTCCEEEECSSCCHHHH
T ss_pred             hHHHHHHHHHHHHhhcCCCEEEEEEccHHHHHHHHHHHHHCCCCEEEEeCCCCHHHH
Confidence            355555555543   347899999999999999999999999999999999998877

>3i32_A Heat resistant RNA dependent ATPase; RNA helicase, dimer, RNA recognition motif, ATP-BIND helicase, nucleotide-binding; 2.80A {Thermus thermophilus}

Probab=98.88  E-value=4.5e-09  Score=80.17  Aligned_cols=66  Identities=21%  Similarity=0.244  Sum_probs=59.4

Q ss_pred             CceEEEEEcCChhhHHHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhhhCCCceEeeecCCCcccc
Q 030396          111 SIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQV  177 (178)
Q Consensus       111 ~i~~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~~~~~~R  177 (178)
                      .+.|+++.+. ..+|...+.++++....+++||||+|++.++.++..|...|+.+..+||+|++++|
T Consensus         2 ~v~~~~i~~~-~~~K~~~L~~ll~~~~~~~~LVF~~t~~~~~~l~~~L~~~g~~~~~lhg~l~~~~r   67 (300)
T 3i32_A            2 TYEEEAVPAP-VRGRLEVLSDLLYVASPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDMSQGER   67 (300)
T ss_dssp             CSEEEEEECC-SSSHHHHHHHHHHHHCCSSEEEECSSHHHHHHHHHHHHTTTCCEEEECSCCCTHHH
T ss_pred             ceEEEEEECC-HHHHHHHHHHHHHhcCCCCEEEEECCHHHHHHHHHHHHhCCCCEEEEeCCCCHHHH
Confidence            3567777764 46799999999998889999999999999999999999999999999999999876

>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=98.83  E-value=5.4e-09  Score=75.80  Aligned_cols=65  Identities=23%  Similarity=0.257  Sum_probs=57.7

Q ss_pred             ceEEEEEcCChhhHHHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhhhCCCceEeeecCCCcccc
Q 030396          112 IKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQV  177 (178)
Q Consensus       112 i~~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~~~~~~R  177 (178)
                      +.+..+.+ +...|...+.++++....+++||||+|++.++.++..|...|+++..+||+|++++|
T Consensus         6 ~~~~~~~~-~~~~k~~~l~~ll~~~~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~r   70 (212)
T 3eaq_A            6 YEEEAVPA-PVRGRLEVLSDLLYVASPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDLSQGER   70 (212)
T ss_dssp             BCCEEEEC-CTTSHHHHHHHHHHHHCCSCEEEECSSHHHHHHHHHHHHHHTCCEEEECSSSCHHHH
T ss_pred             eeeeEEeC-CHHHHHHHHHHHHHhCCCCeEEEEeCCHHHHHHHHHHHHHcCCCEEEEECCCCHHHH
Confidence            44555555 556799999999998888999999999999999999999999999999999999876

>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=98.74  E-value=5.2e-09  Score=78.91  Aligned_cols=63  Identities=17%  Similarity=0.135  Sum_probs=50.9

Q ss_pred             CCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcHH
Q 030396           14 FSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDF   85 (178)
Q Consensus        14 ~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~   85 (178)
                      .+++|+|+||+++...   ....+.+++++|+||||.+..     +.+..+++. +....+++++|||.+..
T Consensus       203 ~~~~I~v~T~~~l~~~---~~~~~~~~~~vIiDEaH~~~~-----~~~~~il~~-~~~~~~~l~lSATp~~~  265 (282)
T 1rif_A          203 NDAPVVVGTWQTVVKQ---PKEWFSQFGMMMNDECHLATG-----KSISSIISG-LNNCMFKFGLSGSLRDG  265 (282)
T ss_dssp             TTCSEEEECHHHHTTS---CGGGGGGEEEEEEETGGGCCH-----HHHHHHTTT-CTTCCEEEEECSSCCTT
T ss_pred             cCCcEEEEchHHHHhh---HHHHHhhCCEEEEECCccCCc-----ccHHHHHHH-hhcCCeEEEEeCCCCCc
Confidence            5689999999976433   334567899999999999964     468888888 66689999999999865

>2ipc_A Preprotein translocase SECA subunit; nucleotide binding fold, ATPase, parallel dimer; 2.80A {Thermus thermophilus}

Probab=98.63  E-value=2.1e-06  Score=73.52  Aligned_cols=44  Identities=20%  Similarity=0.300  Sum_probs=36.3

Q ss_pred             HhccCCCcEEEeCcHHH-HHHHHcCC------CCCC---CeeEEEEeccccccc
Q 030396           10 DLSKFSCDILISTPLRL-RLAIRRKK------IDLS---RVEYLVLDEADKLFE   53 (178)
Q Consensus        10 ~~l~~~~~Iii~TP~~l-~~~l~~~~------~~~~---~l~~lViDE~d~ll~   53 (178)
                      +....+|+|+|||||++ .++++.+.      +.++   .+.++|+||+|.++.
T Consensus       163 r~~ay~~DIvyGTpgrlgfDyLrd~m~~~~~~l~~r~d~~l~~lIIDEaDsmLi  216 (997)
T 2ipc_A          163 RRKAYLADVTYVTNSELGFDYLRDNMAISPDQLVLRHDHPLHYAIIDEVDSILI  216 (997)
T ss_dssp             HHHHHTSSEEEEEHHHHHHHHHHHTSCSSTTTCCSCSSSSSCEEEETTHHHHTT
T ss_pred             HHHHcCCCEEEECchhhhhHHHHHhhhcchhhcccccCCCcceEEEechHHHHH
Confidence            33345799999999999 89998763      5677   899999999999873

>3jux_A Protein translocase subunit SECA; protein translocation, ATPase, conformational change, peptide binding, ATP-binding, cell inner membrane; HET: ADP; 3.10A {Thermotoga maritima} PDB: 3din_A*

Probab=98.55  E-value=2.8e-07  Score=77.35  Aligned_cols=100  Identities=15%  Similarity=0.173  Sum_probs=73.2

Q ss_pred             eEEEEeecCcHHHHHHHHHhccCcEEEEEcCCccccCCceEE-EEEcCChhhHHHHHHHHHHhc--CCCCEEEEeCCchH
Q 030396           74 VRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQK-LVFAGSEEGKLLALRQSFAES--LNPPVLIFVQSKDR  150 (178)
Q Consensus        74 q~i~~SAT~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~i~~~-~~~~~~~~~k~~~l~~ll~~~--~~~~~lIF~~t~~~  150 (178)
                      .+..+|+|......++.+.|.-+  .+.++. ......+.+. .++. +...|...+.+.+...  ..+|+||||+|++.
T Consensus       411 kL~GMTGTa~te~~Ef~~iY~l~--vv~IPt-nkp~~R~d~~d~vy~-t~~eK~~al~~~I~~~~~~gqpVLVFt~S~e~  486 (822)
T 3jux_A          411 KLAGMTGTAKTEESEFVQVYGME--VVVIPT-HKPMIRKDHDDLVFR-TQKEKYEKIVEEIEKRYKKGQPVLVGTTSIEK  486 (822)
T ss_dssp             EEEEEESSCGGGHHHHHHHSCCC--EEECCC-SSCCCCEECCCEEES-SHHHHHHHHHHHHHHHHHHTCCEEEEESSHHH
T ss_pred             HHeEECCCCchHHHHHHHHhCCe--EEEECC-CCCcceeecCcEEEe-cHHHHHHHHHHHHHHHhhCCCCEEEEECCHHH
Confidence            47799999998777766655333  444433 2232333332 3344 6677888888888753  47899999999999


Q ss_pred             HHHHHHHhhhCCCceEeeecCCCcccc
Q 030396          151 AKELYGELAFDDIRAGVIHSDLSQTQV  177 (178)
Q Consensus       151 ~~~l~~~L~~~g~~~~~lh~~~~~~~R  177 (178)
                      ++.++..|...|+++..+||+..+++|
T Consensus       487 sE~Ls~~L~~~Gi~~~vLhgkq~~rE~  513 (822)
T 3jux_A          487 SELLSSMLKKKGIPHQVLNAKYHEKEA  513 (822)
T ss_dssp             HHHHHHHHHTTTCCCEEECSCHHHHHH
T ss_pred             HHHHHHHHHHCCCCEEEeeCCchHHHH
Confidence            999999999999999999999665554

>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=98.34  E-value=9.5e-07  Score=65.00  Aligned_cols=60  Identities=18%  Similarity=0.101  Sum_probs=45.2

Q ss_pred             CCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcH
Q 030396           15 SCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPD   84 (178)
Q Consensus        15 ~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~   84 (178)
                      ..+|+|+||+++......-   ..+++++|+||+|.+.+..     +..++.. . ...+++++|||.+.
T Consensus       171 ~~~i~v~T~~~l~~~~~~~---~~~~~llIiDEaH~l~~~~-----~~~i~~~-~-~~~~~l~LSATp~r  230 (237)
T 2fz4_A          171 LKPLTVSTYDSAYVNAEKL---GNRFMLLIFDEVHHLPAES-----YVQIAQM-S-IAPFRLGLTATFER  230 (237)
T ss_dssp             CCSEEEEEHHHHHHTHHHH---TTTCSEEEEECSSCCCTTT-----HHHHHHT-C-CCSEEEEEEESCC-
T ss_pred             cCCEEEEeHHHHHhhHHHh---cccCCEEEEECCccCCChH-----HHHHHHh-c-cCCEEEEEecCCCC
Confidence            5689999999987666521   2457899999999997665     4556666 3 36788999999874

>1z5z_A Helicase of the SNF2/RAD54 family; hydrolase, recombination, hydrolase-recombination complex; 2.00A {Sulfolobus solfataricus} SCOP: c.37.1.19

Probab=97.98  E-value=7.7e-06  Score=61.38  Aligned_cols=57  Identities=18%  Similarity=0.247  Sum_probs=51.1

Q ss_pred             ChhhHHHHHHHHHHhc--CCCCEEEEeCCchHHHHHHHHhhhC-CCceEeeecCCCcccc
Q 030396          121 SEEGKLLALRQSFAES--LNPPVLIFVQSKDRAKELYGELAFD-DIRAGVIHSDLSQTQV  177 (178)
Q Consensus       121 ~~~~k~~~l~~ll~~~--~~~~~lIF~~t~~~~~~l~~~L~~~-g~~~~~lh~~~~~~~R  177 (178)
                      ....|...+.+++...  ...++||||++...++.++..|... |+++..+||++++++|
T Consensus        93 ~~s~K~~~L~~ll~~~~~~~~kvlIFs~~~~~~~~l~~~L~~~~g~~~~~l~G~~~~~~R  152 (271)
T 1z5z_A           93 RRSGKMIRTMEIIEEALDEGDKIAIFTQFVDMGKIIRNIIEKELNTEVPFLYGELSKKER  152 (271)
T ss_dssp             TTCHHHHHHHHHHHHHHHTTCCEEEEESCHHHHHHHHHHHHHHHCSCCCEECTTSCHHHH
T ss_pred             ccCHHHHHHHHHHHHHHhCCCeEEEEeccHHHHHHHHHHHHHhcCCcEEEEECCCCHHHH
Confidence            4567999999999865  6789999999999999999999885 9999999999998877

>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer aging, hydrolase; HET: FLC; 2.00A {Sulfolobus acidocaldarius} PDB: 3crw_1*

Probab=97.21  E-value=0.00026  Score=58.17  Aligned_cols=43  Identities=28%  Similarity=0.284  Sum_probs=33.3

Q ss_pred             hccCCCcEEEeCcHHHHHHHHcCCCCC-CCeeEEEEeccccccc
Q 030396           11 LSKFSCDILISTPLRLRLAIRRKKIDL-SRVEYLVLDEADKLFE   53 (178)
Q Consensus        11 ~l~~~~~Iii~TP~~l~~~l~~~~~~~-~~l~~lViDE~d~ll~   53 (178)
                      .....++|||+||+.|.+...++.+.+ .....+||||||.|.+
T Consensus       144 ~~~~~adIVV~~~~~l~~~~~~~~~~~~~~~~~vIiDEAHnl~d  187 (551)
T 3crv_A          144 NSLYKADVIALTYPYFFIDRYREFIDIDLREYMIVIDEAHNLDK  187 (551)
T ss_dssp             HHGGGCSEEEEETHHHHCHHHHTTSCCCSTTEEEEETTGGGGGG
T ss_pred             hhhhcCCEEEeCchHhcCHHHHHhcCCCcCCeEEEEecccchHH
Confidence            334679999999999998764443332 4668999999999987

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}

Probab=96.13  E-value=0.0013  Score=53.91  Aligned_cols=40  Identities=23%  Similarity=0.102  Sum_probs=29.8

Q ss_pred             cCCCcEEEeCcHHHHHHHHcCCC-------CCCCeeEEEEecccccc
Q 030396           13 KFSCDILISTPLRLRLAIRRKKI-------DLSRVEYLVLDEADKLF   52 (178)
Q Consensus        13 ~~~~~Iii~TP~~l~~~l~~~~~-------~~~~l~~lViDE~d~ll   52 (178)
                      ...++|||+|++.+.+....+.+       .+.....+||||||.+.
T Consensus       142 ~~~adiVV~n~~~l~~~~~~~~~~~~~~~~~~~~~~~vIiDEAHnl~  188 (540)
T 2vl7_A          142 LKDKDVIAMTYPYLFQKPIRNSVFCNKDDCLKLEDYLIVIDEAHNLL  188 (540)
T ss_dssp             GGGCSEEEEETHHHHSHHHHHHHSCSSTTSCCGGGEEEEETTGGGGG
T ss_pred             hhcCCEEEEChHHhcCHHHHHhhCcccccccCcCCCEEEEEccccHH
Confidence            45789999999999975432221       23567899999999994

>3gk5_A Uncharacterized rhodanese-related protein TVG0868615; alpha-beta protein, structural genomics, PSI-2, protein structure initiative; 2.40A {Thermoplasma volcanium GSS1}

Probab=95.02  E-value=0.021  Score=36.18  Aligned_cols=44  Identities=7%  Similarity=0.050  Sum_probs=36.1

Q ss_pred             HHHHHhc-CCCCEEEEeCCchHHHHHHHHhhhCCCceEeeecCCC
Q 030396          130 RQSFAES-LNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLS  173 (178)
Q Consensus       130 ~~ll~~~-~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~~~  173 (178)
                      .+.+... ..+++++||.+-.++...+..|.+.|+++..+.||+.
T Consensus        46 ~~~~~~l~~~~~ivvyC~~G~rs~~aa~~L~~~G~~v~~l~GG~~   90 (108)
T 3gk5_A           46 REKWKILERDKKYAVICAHGNRSAAAVEFLSQLGLNIVDVEGGIQ   90 (108)
T ss_dssp             HHHGGGSCTTSCEEEECSSSHHHHHHHHHHHTTTCCEEEETTHHH
T ss_pred             HHHHHhCCCCCeEEEEcCCCcHHHHHHHHHHHcCCCEEEEcCcHH
Confidence            3344433 3568999999999999999999999999999999864

>1wv9_A Rhodanese homolog TT1651; CDC25, phosphatase, sulfurtransferase, structural genomics, NPPSFA; 2.00A {Thermus thermophilus}

Probab=94.87  E-value=0.023  Score=34.98  Aligned_cols=36  Identities=14%  Similarity=0.094  Sum_probs=32.9

Q ss_pred             CCEEEEeCCchHHHHHHHHhhhCCCceEeeecCCCc
Q 030396          139 PPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQ  174 (178)
Q Consensus       139 ~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~~~~  174 (178)
                      +++++||.+-.++...+..|...|+++..+.||+..
T Consensus        54 ~~ivvyC~~g~rs~~a~~~L~~~G~~v~~l~GG~~~   89 (94)
T 1wv9_A           54 RPLLLVCEKGLLSQVAALYLEAEGYEAMSLEGGLQA   89 (94)
T ss_dssp             SCEEEECSSSHHHHHHHHHHHHHTCCEEEETTGGGC
T ss_pred             CCEEEEcCCCChHHHHHHHHHHcCCcEEEEcccHHH
Confidence            789999999999999999999999998899998763

>3foj_A Uncharacterized protein; protein SSP1007, structural genomics, PSI-2, protein structure initiative; 1.60A {Staphylococcus saprophyticus subsp}

Probab=94.68  E-value=0.023  Score=35.44  Aligned_cols=36  Identities=14%  Similarity=0.227  Sum_probs=32.8

Q ss_pred             CCCEEEEeCCchHHHHHHHHhhhCCCceEeeecCCC
Q 030396          138 NPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLS  173 (178)
Q Consensus       138 ~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~~~  173 (178)
                      .+++++||.+-.++...+..|...|+++..+.||+.
T Consensus        56 ~~~ivvyC~~g~rs~~a~~~L~~~G~~v~~l~GG~~   91 (100)
T 3foj_A           56 NETYYIICKAGGRSAQVVQYLEQNGVNAVNVEGGMD   91 (100)
T ss_dssp             TSEEEEECSSSHHHHHHHHHHHTTTCEEEEETTHHH
T ss_pred             CCcEEEEcCCCchHHHHHHHHHHCCCCEEEecccHH
Confidence            567999999999999999999999999999999864

>3iwh_A Rhodanese-like domain protein; alpha-beta-alpha sandwich, structural genomics, C structural genomics of infectious diseases, csgid; 2.00A {Staphylococcus aureus subsp} PDB: 3mzz_A

Probab=94.51  E-value=0.023  Score=35.82  Aligned_cols=36  Identities=17%  Similarity=0.140  Sum_probs=32.2

Q ss_pred             CCCEEEEeCCchHHHHHHHHhhhCCCceEeeecCCC
Q 030396          138 NPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLS  173 (178)
Q Consensus       138 ~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~~~  173 (178)
                      .++++++|.+-.++...+..|.+.||++..+.||+.
T Consensus        56 ~~~ivv~C~~G~rS~~aa~~L~~~G~~~~~l~GG~~   91 (103)
T 3iwh_A           56 NEIYYIVCAGGVRSAKVVEYLEANGIDAVNVEGGMH   91 (103)
T ss_dssp             TSEEEEECSSSSHHHHHHHHHHTTTCEEEEETTHHH
T ss_pred             CCeEEEECCCCHHHHHHHHHHHHcCCCEEEecChHH
Confidence            567999999999999999999999999998888764

>2k0z_A Uncharacterized protein HP1203; A/B domain, structural genomics, unknown function, PSI-2, PR structure initiative; NMR {Helicobacter pylori}

Probab=93.89  E-value=0.09  Score=33.29  Aligned_cols=39  Identities=10%  Similarity=0.075  Sum_probs=33.8

Q ss_pred             cCCCCEEEEeCCchHHHHHHHHhhhCCCceEeeecCCCc
Q 030396          136 SLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQ  174 (178)
Q Consensus       136 ~~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~~~~  174 (178)
                      .+.+++++||++-.++...+..|...|++...+.||+..
T Consensus        54 ~~~~~ivvyC~~G~rs~~aa~~L~~~G~~~~~l~GG~~~   92 (110)
T 2k0z_A           54 HKDKKVLLHCRAGRRALDAAKSMHELGYTPYYLEGNVYD   92 (110)
T ss_dssp             CSSSCEEEECSSSHHHHHHHHHHHHTTCCCEEEESCGGG
T ss_pred             CCCCEEEEEeCCCchHHHHHHHHHHCCCCEEEecCCHHH
Confidence            346789999999999999999999999966889898753

>3hix_A ALR3790 protein; rhodanese, rhodanese_3, Q8YQN0, Q8YQN0_anAsp, NSR437I, NESG, structural genomics, PSI-2, protein structure initiative; 1.92A {Anabaena SP} PDB: 3k9r_A

Probab=93.72  E-value=0.052  Score=34.19  Aligned_cols=37  Identities=5%  Similarity=0.157  Sum_probs=32.4

Q ss_pred             CCCCEEEEeCCchHHHHHHHHhhhCCCc-eEeeecCCC
Q 030396          137 LNPPVLIFVQSKDRAKELYGELAFDDIR-AGVIHSDLS  173 (178)
Q Consensus       137 ~~~~~lIF~~t~~~~~~l~~~L~~~g~~-~~~lh~~~~  173 (178)
                      ...++++||++-.++...+..|...|++ +..+.||+.
T Consensus        51 ~~~~ivvyc~~g~rs~~a~~~L~~~G~~~v~~l~GG~~   88 (106)
T 3hix_A           51 KSRDIYVYGAGDEQTSQAVNLLRSAGFEHVSELKGGLA   88 (106)
T ss_dssp             TTSCEEEECSSHHHHHHHHHHHHHTTCSCEEECTTHHH
T ss_pred             CCCeEEEEECCCChHHHHHHHHHHcCCcCEEEecCCHH
Confidence            3568999999999999999999999994 888988864

>2fsx_A RV0390, COG0607: rhodanese-related sulfurtransferase; RV0390 BR SAD DATA with FBAR, structural genomics, PSI; 1.80A {Mycobacterium tuberculosis}

Probab=93.33  E-value=0.1  Score=34.93  Aligned_cols=37  Identities=16%  Similarity=0.138  Sum_probs=32.1

Q ss_pred             CCCCEEEEeCCchHHHHHHHHhhhCCC-ceEeeecCCC
Q 030396          137 LNPPVLIFVQSKDRAKELYGELAFDDI-RAGVIHSDLS  173 (178)
Q Consensus       137 ~~~~~lIF~~t~~~~~~l~~~L~~~g~-~~~~lh~~~~  173 (178)
                      ...+++|||++-.++...+..|...|+ ++..+.||+.
T Consensus        79 ~~~~ivvyC~~G~rS~~aa~~L~~~G~~~v~~l~GG~~  116 (148)
T 2fsx_A           79 HERPVIFLCRSGNRSIGAAEVATEAGITPAYNVLDGFE  116 (148)
T ss_dssp             --CCEEEECSSSSTHHHHHHHHHHTTCCSEEEETTTTT
T ss_pred             CCCEEEEEcCCChhHHHHHHHHHHcCCcceEEEcCChh
Confidence            457899999998899999999999999 5999999984

>1tq1_A AT5G66040, senescence-associated family protein; CESG, structural genomics, protein structure initiative; NMR {Arabidopsis thaliana} SCOP: c.46.1.3

Probab=93.07  E-value=0.07  Score=34.86  Aligned_cols=37  Identities=16%  Similarity=0.118  Sum_probs=32.7

Q ss_pred             CCCCEEEEeCCchHHHHHHHHhhhCCCc-eEeeecCCC
Q 030396          137 LNPPVLIFVQSKDRAKELYGELAFDDIR-AGVIHSDLS  173 (178)
Q Consensus       137 ~~~~~lIF~~t~~~~~~l~~~L~~~g~~-~~~lh~~~~  173 (178)
                      ..+++++||++-.++...+..|...|++ +..+.||+.
T Consensus        81 ~~~~ivvyC~~G~rs~~aa~~L~~~G~~~v~~l~GG~~  118 (129)
T 1tq1_A           81 QSDNIIVGCQSGGRSIKATTDLLHAGFTGVKDIVGGYS  118 (129)
T ss_dssp             TTSSEEEEESSCSHHHHHHHHHHHHHCCSEEEEECCHH
T ss_pred             CCCeEEEECCCCcHHHHHHHHHHHcCCCCeEEeCCcHH
Confidence            3578999999999999999999999995 889999874

>3g5j_A Putative ATP/GTP binding protein; N-terminal domain of ATP/GTP binding protein, PSI, MCSG, STR genomics, protein structure initiative; HET: PGE; 1.76A {Clostridium difficile}

Probab=92.98  E-value=0.11  Score=33.77  Aligned_cols=35  Identities=9%  Similarity=0.141  Sum_probs=31.6

Q ss_pred             CCEEEEe-CCchHHHHHHHHhhhCCCceEeeecCCC
Q 030396          139 PPVLIFV-QSKDRAKELYGELAFDDIRAGVIHSDLS  173 (178)
Q Consensus       139 ~~~lIF~-~t~~~~~~l~~~L~~~g~~~~~lh~~~~  173 (178)
                      +++++|| ++-.++...+..|...|+++..+.||+.
T Consensus        90 ~~ivvyC~~~G~rs~~a~~~L~~~G~~v~~l~GG~~  125 (134)
T 3g5j_A           90 DNIVIYCARGGMRSGSIVNLLSSLGVNVYQLEGGYK  125 (134)
T ss_dssp             SEEEEECSSSSHHHHHHHHHHHHTTCCCEEETTHHH
T ss_pred             CeEEEEECCCChHHHHHHHHHHHcCCceEEEeCcHH
Confidence            6899999 5888899999999999999999999875

>1gmx_A GLPE protein; transferase, rhodanese, sulfurtransferase, glycerol metabolism; 1.1A {Escherichia coli} SCOP: c.46.1.3 PDB: 1gn0_A

Probab=92.91  E-value=0.062  Score=33.85  Aligned_cols=37  Identities=14%  Similarity=0.172  Sum_probs=32.2

Q ss_pred             CCCCEEEEeCCchHHHHHHHHhhhCCC-ceEeeecCCC
Q 030396          137 LNPPVLIFVQSKDRAKELYGELAFDDI-RAGVIHSDLS  173 (178)
Q Consensus       137 ~~~~~lIF~~t~~~~~~l~~~L~~~g~-~~~~lh~~~~  173 (178)
                      +.+++++||.+-.++...+..|...|+ ++..+.||+.
T Consensus        57 ~~~~ivvyc~~g~rs~~a~~~L~~~G~~~v~~l~GG~~   94 (108)
T 1gmx_A           57 FDTPVMVMCYHGNSSKGAAQYLLQQGYDVVYSIDGGFE   94 (108)
T ss_dssp             TTSCEEEECSSSSHHHHHHHHHHHHTCSSEEEETTHHH
T ss_pred             CCCCEEEEcCCCchHHHHHHHHHHcCCceEEEecCCHH
Confidence            357899999999999999999999999 4888888864

>1qxn_A SUD, sulfide dehydrogenase; polysulfide-sulfur transferase, homodimer; NMR {Wolinella succinogenes} SCOP: c.46.1.3

Probab=92.80  E-value=0.076  Score=35.14  Aligned_cols=37  Identities=16%  Similarity=0.126  Sum_probs=33.0

Q ss_pred             CCCCEEEEeCCchHHHHHHHHhhhCCC-ceEeeecCCC
Q 030396          137 LNPPVLIFVQSKDRAKELYGELAFDDI-RAGVIHSDLS  173 (178)
Q Consensus       137 ~~~~~lIF~~t~~~~~~l~~~L~~~g~-~~~~lh~~~~  173 (178)
                      +.++++|||.+-.++...+..|...|+ ++..+.||+.
T Consensus        81 ~~~~ivvyC~~G~rS~~aa~~L~~~G~~~v~~l~GG~~  118 (137)
T 1qxn_A           81 PEKPVVVFCKTAARAALAGKTLREYGFKTIYNSEGGMD  118 (137)
T ss_dssp             TTSCEEEECCSSSCHHHHHHHHHHHTCSCEEEESSCHH
T ss_pred             CCCeEEEEcCCCcHHHHHHHHHHHcCCcceEEEcCcHH
Confidence            467899999999999999999999999 5899999864

>3nhv_A BH2092 protein; alpha-beta protein, structural genomics, PSI-2, protein STRU initiative, northeast structural genomics consortium, NESG; 2.50A {Bacillus halodurans} PDB: 3o3w_A

Probab=92.79  E-value=0.072  Score=35.61  Aligned_cols=36  Identities=8%  Similarity=0.132  Sum_probs=31.8

Q ss_pred             CCCEEEEeCCc--hHHHHHHHHhhhCCCceEeeecCCC
Q 030396          138 NPPVLIFVQSK--DRAKELYGELAFDDIRAGVIHSDLS  173 (178)
Q Consensus       138 ~~~~lIF~~t~--~~~~~l~~~L~~~g~~~~~lh~~~~  173 (178)
                      .++++|||.+-  .++...+..|...|+++..+.||+.
T Consensus        72 ~~~ivvyC~~g~~~rs~~aa~~L~~~G~~v~~l~GG~~  109 (144)
T 3nhv_A           72 EKVIITYCWGPACNGATKAAAKFAQLGFRVKELIGGIE  109 (144)
T ss_dssp             TSEEEEECSCTTCCHHHHHHHHHHHTTCEEEEEESHHH
T ss_pred             CCeEEEEECCCCccHHHHHHHHHHHCCCeEEEeCCcHH
Confidence            56799999987  6899999999999999999999864

>3flh_A Uncharacterized protein LP_1913; alpha-beta protein, structural genomics, PSI-2, protein structure initiative; 2.00A {Lactobacillus plantarum} PDB: 3fnj_A 3i3u_A

Probab=92.66  E-value=0.043  Score=35.65  Aligned_cols=45  Identities=13%  Similarity=0.053  Sum_probs=35.0

Q ss_pred             HHHHHHhc-CCCCEEEEeCCchH--HHHHHHHhhhCCCceEeeecCCC
Q 030396          129 LRQSFAES-LNPPVLIFVQSKDR--AKELYGELAFDDIRAGVIHSDLS  173 (178)
Q Consensus       129 l~~ll~~~-~~~~~lIF~~t~~~--~~~l~~~L~~~g~~~~~lh~~~~  173 (178)
                      +.+.+... +.+++++||.+-.+  +...+..|...|+++..+.||+.
T Consensus        61 l~~~~~~l~~~~~ivvyC~~g~r~~s~~a~~~L~~~G~~v~~l~GG~~  108 (124)
T 3flh_A           61 LATRIGELDPAKTYVVYDWTGGTTLGKTALLVLLSAGFEAYELAGALE  108 (124)
T ss_dssp             HHHHGGGSCTTSEEEEECSSSSCSHHHHHHHHHHHHTCEEEEETTHHH
T ss_pred             HHHHHhcCCCCCeEEEEeCCCCchHHHHHHHHHHHcCCeEEEeCCcHH
Confidence            33444443 34679999998877  89999999999999999988864

>2jtq_A Phage shock protein E; solution structure rhodanese, stress response, transferase; NMR {Escherichia coli} PDB: 2jtr_A 2jts_A

Probab=92.55  E-value=0.32  Score=28.94  Aligned_cols=37  Identities=11%  Similarity=0.062  Sum_probs=31.0

Q ss_pred             CCCCEEEEeCCchHHHHHHHHhhhCCCc-eEeeecCCCc
Q 030396          137 LNPPVLIFVQSKDRAKELYGELAFDDIR-AGVIHSDLSQ  174 (178)
Q Consensus       137 ~~~~~lIF~~t~~~~~~l~~~L~~~g~~-~~~lh~~~~~  174 (178)
                      +..++++||++-.++...+..|.+.|++ +..+ ||+..
T Consensus        40 ~~~~ivv~C~~g~rs~~aa~~L~~~G~~~v~~l-GG~~~   77 (85)
T 2jtq_A           40 KNDTVKVYCNAGRQSGQAKEILSEMGYTHVENA-GGLKD   77 (85)
T ss_dssp             TTSEEEEEESSSHHHHHHHHHHHHTTCSSEEEE-EETTT
T ss_pred             CCCcEEEEcCCCchHHHHHHHHHHcCCCCEEec-cCHHH
Confidence            4577999999999999999999999995 6666 87653

>3d1p_A Putative thiosulfate sulfurtransferase YOR285W; atomic structure, atomic resolution structure, PSI, MCSG; HET: MSE; 0.98A {Saccharomyces cerevisiae}

Probab=91.89  E-value=0.1  Score=34.37  Aligned_cols=37  Identities=8%  Similarity=0.117  Sum_probs=32.2

Q ss_pred             CCCCEEEEeCCchHHHHHHHHhhhCCCc-eEeeecCCC
Q 030396          137 LNPPVLIFVQSKDRAKELYGELAFDDIR-AGVIHSDLS  173 (178)
Q Consensus       137 ~~~~~lIF~~t~~~~~~l~~~L~~~g~~-~~~lh~~~~  173 (178)
                      ..+++++||.+-.++...+..|.+.|++ +..+.||+.
T Consensus        90 ~~~~ivvyC~~G~rs~~aa~~L~~~G~~~v~~l~GG~~  127 (139)
T 3d1p_A           90 SAKELIFYCASGKRGGEAQKVASSHGYSNTSLYPGSMN  127 (139)
T ss_dssp             TTSEEEEECSSSHHHHHHHHHHHTTTCCSEEECTTHHH
T ss_pred             CCCeEEEECCCCchHHHHHHHHHHcCCCCeEEeCCcHH
Confidence            3567999999999999999999999994 888988864

>2hhg_A Hypothetical protein RPA3614; MCSG, structural genomics, rohopseudom palustris, PSI-2, protein structure initiative; 1.20A {Rhodopseudomonas palustris}

Probab=91.73  E-value=0.086  Score=34.71  Aligned_cols=37  Identities=5%  Similarity=0.020  Sum_probs=32.4

Q ss_pred             CCCCEEEEeCCchHHHHHHHHhhhCCCc-eEeeecCCC
Q 030396          137 LNPPVLIFVQSKDRAKELYGELAFDDIR-AGVIHSDLS  173 (178)
Q Consensus       137 ~~~~~lIF~~t~~~~~~l~~~L~~~g~~-~~~lh~~~~  173 (178)
                      ...+++|||.+-.++...+..|...|++ +..+.||+.
T Consensus        85 ~~~~ivvyC~~G~rs~~a~~~L~~~G~~~v~~l~GG~~  122 (139)
T 2hhg_A           85 EDKKFVFYCAGGLRSALAAKTAQDMGLKPVAHIEGGFG  122 (139)
T ss_dssp             SSSEEEEECSSSHHHHHHHHHHHHHTCCSEEEETTHHH
T ss_pred             CCCeEEEECCCChHHHHHHHHHHHcCCCCeEEecCCHH
Confidence            3578999999999999999999999995 999998864

>3ilm_A ALR3790 protein; rhodanese-like, NSR437H, NESG, structural genomics, protein structure initiative, northeast structural genomics consortium; 2.26A {Nostoc SP} PDB: 2kl3_A

Probab=91.30  E-value=0.12  Score=34.32  Aligned_cols=36  Identities=6%  Similarity=0.181  Sum_probs=31.3

Q ss_pred             CCCEEEEeCCchHHHHHHHHhhhCCCc-eEeeecCCC
Q 030396          138 NPPVLIFVQSKDRAKELYGELAFDDIR-AGVIHSDLS  173 (178)
Q Consensus       138 ~~~~lIF~~t~~~~~~l~~~L~~~g~~-~~~lh~~~~  173 (178)
                      ..++++||++-.++...+..|...|+. +..+.||+.
T Consensus        56 ~~~ivvyC~~g~rs~~aa~~L~~~G~~~v~~l~GG~~   92 (141)
T 3ilm_A           56 SRDIYVYGAGDEQTSQAVNLLRSAGFEHVSELKGGLA   92 (141)
T ss_dssp             TSEEEEECSSHHHHHHHHHHHHHTTCCSEEECTTHHH
T ss_pred             CCeEEEEECCChHHHHHHHHHHHcCCCCEEEecCHHH
Confidence            467999999999999999999999994 888888764

>1vee_A Proline-rich protein family; hypothetical protein, structural genomics, rhodanese domain, riken structural genomics/proteomics initiative; NMR {Arabidopsis thaliana} PDB: 2dcq_A

Probab=90.27  E-value=0.19  Score=32.96  Aligned_cols=37  Identities=14%  Similarity=0.121  Sum_probs=32.6

Q ss_pred             CCCCEEEEeCCchHHHHHHHHhhhCCC-ceEeeecCCC
Q 030396          137 LNPPVLIFVQSKDRAKELYGELAFDDI-RAGVIHSDLS  173 (178)
Q Consensus       137 ~~~~~lIF~~t~~~~~~l~~~L~~~g~-~~~~lh~~~~  173 (178)
                      +.+++++||.+=.++...+..|.+.|| ++..+.||+.
T Consensus        73 ~~~~ivv~C~sG~RS~~aa~~L~~~G~~~v~~l~GG~~  110 (134)
T 1vee_A           73 ENTTLYILDKFDGNSELVAELVALNGFKSAYAIKDGAE  110 (134)
T ss_dssp             GGCEEEEECSSSTTHHHHHHHHHHHTCSEEEECTTTTT
T ss_pred             CCCEEEEEeCCCCcHHHHHHHHHHcCCcceEEecCCcc
Confidence            357899999999999999999999999 5889999983

>4f67_A UPF0176 protein LPG2838; structural genomics, PSI-biology, protein structure initiati northeast structural genomics consortium; 1.79A {Legionella pneumophila subsp}

Probab=90.13  E-value=0.29  Score=36.29  Aligned_cols=47  Identities=6%  Similarity=0.090  Sum_probs=38.2

Q ss_pred             HHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhhhCCC-ceEeeecCCC
Q 030396          127 LALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDI-RAGVIHSDLS  173 (178)
Q Consensus       127 ~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~~~g~-~~~~lh~~~~  173 (178)
                      ..+...+...+.+++++||.+-.+|...+..|...|+ ++..+.||+.
T Consensus       170 ~~l~~~l~~~kdk~IVvyC~~G~RS~~Aa~~L~~~Gf~nV~~L~GGi~  217 (265)
T 4f67_A          170 DYVQRNLIDKKDKKIAMFCTGGIRCEKTTAYMKELGFEHVYQLHDGIL  217 (265)
T ss_dssp             HHHHHHTGGGTTSCEEEECSSSHHHHHHHHHHHHHTCSSEEEETTHHH
T ss_pred             HHHHHhhhhCCCCeEEEEeCCChHHHHHHHHHHHcCCCCEEEecCHHH
Confidence            3444445555678999999999999999999999999 6889998864

>3tg1_B Dual specificity protein phosphatase 10; kinase/rhodanese-like domain, docking interaction, transfera hydrolase complex; 2.71A {Homo sapiens}

Probab=89.93  E-value=0.24  Score=33.44  Aligned_cols=36  Identities=11%  Similarity=0.210  Sum_probs=31.3

Q ss_pred             CCCEEEEeCCc---------hHHHHHHHHhhhCCCceEeeecCCC
Q 030396          138 NPPVLIFVQSK---------DRAKELYGELAFDDIRAGVIHSDLS  173 (178)
Q Consensus       138 ~~~~lIF~~t~---------~~~~~l~~~L~~~g~~~~~lh~~~~  173 (178)
                      .++++|||.+-         ..+..++..|...|+++..+.||+.
T Consensus        93 ~~~IVvyc~~g~~~~~~~~~~~s~~a~~~L~~~G~~v~~L~GG~~  137 (158)
T 3tg1_B           93 SKEIIVYDENTNEPSRVMPSQPLHIVLESLKREGKEPLVLKGGLS  137 (158)
T ss_dssp             TSCEEEECSCCSCTTSCCSSSHHHHHHHHHHTTTCCEEEETTHHH
T ss_pred             CCeEEEEECCCCcccccCcchHHHHHHHHHHhCCCcEEEeCCcHH
Confidence            57899999887         4588899999999999999999864

>1urh_A 3-mercaptopyruvate sulfurtransferase; rhodanese; 2.8A {Escherichia coli} SCOP: c.46.1.2 c.46.1.2

Probab=88.82  E-value=0.66  Score=34.24  Aligned_cols=38  Identities=18%  Similarity=0.195  Sum_probs=33.7

Q ss_pred             CCCCEEEEeCCchHHHHHHHHhhhCCC-ceEeeecCCCc
Q 030396          137 LNPPVLIFVQSKDRAKELYGELAFDDI-RAGVIHSDLSQ  174 (178)
Q Consensus       137 ~~~~~lIF~~t~~~~~~l~~~L~~~g~-~~~~lh~~~~~  174 (178)
                      ..+++++||.+-.++...+..|...|+ ++..+.||+..
T Consensus       229 ~~~~ivv~C~~G~rs~~a~~~L~~~G~~~v~~~~GG~~~  267 (280)
T 1urh_A          229 YDKPIIVSCGSGVTAAVVLLALATLDVPNVKLYDGAWSE  267 (280)
T ss_dssp             SSSCEEEECCSSSTHHHHHHHHHHTTCSSCEEECCSCCC
T ss_pred             CCCCEEEECChHHHHHHHHHHHHHcCCCCceeeCChHHH
Confidence            467899999999999999999999999 59999999863

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A*

Probab=87.43  E-value=2  Score=35.71  Aligned_cols=84  Identities=8%  Similarity=0.065  Sum_probs=46.8

Q ss_pred             CCceEEEEeecCcHHHHHHHHHhccCcEEEEEcCCccccCCceEEEEEcCC--------hhh----HHHHHHHHHHhcCC
Q 030396           71 PSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGS--------EEG----KLLALRQSFAESLN  138 (178)
Q Consensus        71 ~~~q~i~~SAT~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~i~~~~~~~~~--------~~~----k~~~l~~ll~~~~~  138 (178)
                      ....+|++|||+++ ...+.....-++..+..+. .....+.  ..+.+.+        ...    -...+..+++.. +
T Consensus       374 ~~~~~il~SaTL~p-~~~~~~~lGl~~~~~~~~s-pf~~~~~--~~~~~~~~~~~~~~r~~~~~~~~~~~i~~l~~~~-~  448 (620)
T 4a15_A          374 KESKTIHMSGTLDP-FDFYSDITGFEIPFKKIGE-IFPPENR--YIAYYDGVSSKYDTLDEKELDRMATVIEDIILKV-K  448 (620)
T ss_dssp             GGSEEEEEESSCCS-HHHHHHHHCCCCCEEECCC-CSCGGGE--EEEEECCC-------CHHHHHHHHHHHHHHHHHH-C
T ss_pred             hCCeEEEEccCCCc-HHHHHHHhCCCceeeecCC-CCCHHHe--EEEEeCCCCCcCCCCCHHHHHHHHHHHHHHHHhC-C
Confidence            56778999999987 4444444433333333221 1122222  1211111        111    122334444444 6


Q ss_pred             CCEEEEeCCchHHHHHHHHhh
Q 030396          139 PPVLIFVQSKDRAKELYGELA  159 (178)
Q Consensus       139 ~~~lIF~~t~~~~~~l~~~L~  159 (178)
                      +.++||++|-...+.+++.|.
T Consensus       449 g~~lvlF~Sy~~l~~v~~~l~  469 (620)
T 4a15_A          449 KNTIVYFPSYSLMDRVENRVS  469 (620)
T ss_dssp             SCEEEEESCHHHHHHHTSSCC
T ss_pred             CCEEEEeCCHHHHHHHHHHHH
Confidence            789999999999999999887

>2ouc_A Dual specificity protein phosphatase 10; rhodanese fold, hydrolase; 2.20A {Homo sapiens}

Probab=86.51  E-value=0.38  Score=31.34  Aligned_cols=36  Identities=11%  Similarity=0.234  Sum_probs=29.8

Q ss_pred             CCCEEEEeCCchH---------HHHHHHHhhhCCCceEeeecCCC
Q 030396          138 NPPVLIFVQSKDR---------AKELYGELAFDDIRAGVIHSDLS  173 (178)
Q Consensus       138 ~~~~lIF~~t~~~---------~~~l~~~L~~~g~~~~~lh~~~~  173 (178)
                      ..+++|||++-.+         +.+++..|...|+++..+.||+.
T Consensus        83 ~~~ivvyc~~g~~~~~~~~~~~~~~~~~~L~~~G~~v~~l~GG~~  127 (142)
T 2ouc_A           83 SKEIIVYDENTNEPSRVMPSQPLHIVLESLKREGKEPLVLKGGLS  127 (142)
T ss_dssp             HSCEEEECSSCCCGGGCCTTSHHHHHHHHHHHTTCCCEEETTHHH
T ss_pred             CCcEEEEECCCCchhhcCcccHHHHHHHHHHHcCCcEEEEccCHH
Confidence            4789999987665         46788899999999999999864

>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=85.83  E-value=1.3  Score=36.71  Aligned_cols=36  Identities=19%  Similarity=0.339  Sum_probs=28.8

Q ss_pred             CeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEee
Q 030396           39 RVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSA   80 (178)
Q Consensus        39 ~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SA   80 (178)
                      ..+++|+|||+ |++    .+.+..+++. ++...|++++.-
T Consensus       262 ~~d~lIIDEAs-ml~----~~~~~~Ll~~-l~~~~~liLvGD  297 (608)
T 1w36_D          262 HLDVLVVDEAS-MID----LPMMSRLIDA-LPDHARVIFLGD  297 (608)
T ss_dssp             SCSEEEECSGG-GCB----HHHHHHHHHT-CCTTCEEEEEEC
T ss_pred             CCCEEEEechh-hCC----HHHHHHHHHh-CCCCCEEEEEcc
Confidence            67899999999 444    5667888888 788899998853

>1uar_A Rhodanese; sulfurtransferase, riken structural genomics/PROT initiative, RSGI, structural genomics, transferase; 1.70A {Thermus thermophilus} SCOP: c.46.1.2 c.46.1.2

Probab=85.73  E-value=0.99  Score=33.33  Aligned_cols=47  Identities=9%  Similarity=0.176  Sum_probs=36.4

Q ss_pred             HHHHHHHHh---cCCCCEEEEeCCchHHHHHHHHhh-hCCC-ceEeeecCCC
Q 030396          127 LALRQSFAE---SLNPPVLIFVQSKDRAKELYGELA-FDDI-RAGVIHSDLS  173 (178)
Q Consensus       127 ~~l~~ll~~---~~~~~~lIF~~t~~~~~~l~~~L~-~~g~-~~~~lh~~~~  173 (178)
                      ..+.+.+..   ...++++|||.+-.++...+..|. ..|+ ++..+.||+.
T Consensus       219 ~~l~~~~~~~g~~~~~~ivvyC~~G~rs~~a~~~L~~~~G~~~v~~l~GG~~  270 (285)
T 1uar_A          219 EELRALYEPLGITKDKDIVVYCRIAERSSHSWFVLKYLLGYPHVKNYDGSWT  270 (285)
T ss_dssp             HHHHHHHGGGTCCTTSEEEEECSSHHHHHHHHHHHHTTSCCSCEEEESSHHH
T ss_pred             HHHHHHHHHcCCCCCCCEEEECCchHHHHHHHHHHHHHcCCCCcceeCchHH
Confidence            344455554   235679999999999999999998 8999 6889998864

>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=85.25  E-value=1.8  Score=33.03  Aligned_cols=53  Identities=13%  Similarity=0.085  Sum_probs=44.6

Q ss_pred             hhhHHHHHHHHHHhc--CCCCEEEEeCCchHHHHHHHHhhhCCCceEeeecCCCc
Q 030396          122 EEGKLLALRQSFAES--LNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQ  174 (178)
Q Consensus       122 ~~~k~~~l~~ll~~~--~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~~~~  174 (178)
                      .+.|+..|..++...  ...+++||++..+.-+-+.+++...|++..-+.|....
T Consensus       107 ~SGKf~~L~~LL~~l~~~~~kVLIfsq~t~~LDilE~~l~~~~~~y~RlDG~~~~  161 (328)
T 3hgt_A          107 NSGKFSVLRDLINLVQEYETETAIVCRPGRTMDLLEALLLGNKVHIKRYDGHSIK  161 (328)
T ss_dssp             TCHHHHHHHHHHHHHTTSCEEEEEEECSTHHHHHHHHHHTTSSCEEEESSSCCC-
T ss_pred             cCccHHHHHHHHHHHHhCCCEEEEEECChhHHHHHHHHHhcCCCceEeCCCCchh
Confidence            457888888888743  36689999999999999999999999999999988543

>1urh_A 3-mercaptopyruvate sulfurtransferase; rhodanese; 2.8A {Escherichia coli} SCOP: c.46.1.2 c.46.1.2

Probab=84.61  E-value=0.87  Score=33.59  Aligned_cols=37  Identities=8%  Similarity=0.153  Sum_probs=31.1

Q ss_pred             CCCCEEEEeCCchH-HHHHHHHhhhCCC-ceEeeecCCC
Q 030396          137 LNPPVLIFVQSKDR-AKELYGELAFDDI-RAGVIHSDLS  173 (178)
Q Consensus       137 ~~~~~lIF~~t~~~-~~~l~~~L~~~g~-~~~~lh~~~~  173 (178)
                      ...+++|||.+-.. +..++..|...|+ ++..+.||+.
T Consensus        85 ~~~~ivvyc~~g~~~a~~a~~~L~~~G~~~v~~l~GG~~  123 (280)
T 1urh_A           85 QDKHLIVYDEGNLFSAPRAWWMLRTFGVEKVSILGGGLA  123 (280)
T ss_dssp             TTSEEEEECSSSCSSHHHHHHHHHHTTCSCEEEETTHHH
T ss_pred             CCCeEEEECCCCCccHHHHHHHHHHcCCCCEEEecCCHH
Confidence            46779999988666 8899999999999 6889998754

>1e0c_A Rhodanese, sulfurtransferase; sulfur metabolism, thiosulfate:cyanide sulfurtransferase; 1.8A {Azotobacter vinelandii} SCOP: c.46.1.2 c.46.1.2 PDB: 1h4k_X 1h4m_X

Probab=84.15  E-value=0.77  Score=33.66  Aligned_cols=37  Identities=11%  Similarity=0.007  Sum_probs=32.2

Q ss_pred             CCCCEEEEeCCchHHHHHHHHhhhCCC-ceEeeecCCC
Q 030396          137 LNPPVLIFVQSKDRAKELYGELAFDDI-RAGVIHSDLS  173 (178)
Q Consensus       137 ~~~~~lIF~~t~~~~~~l~~~L~~~g~-~~~~lh~~~~  173 (178)
                      +.+++++||++-.++...+..|...|+ ++..+.||+.
T Consensus       222 ~~~~ivvyC~~G~rs~~a~~~L~~~G~~~v~~l~GG~~  259 (271)
T 1e0c_A          222 PDKEIVTHCQTHHRSGLTYLIAKALGYPRVKGYAGSWG  259 (271)
T ss_dssp             TTSEEEEECSSSSHHHHHHHHHHHTTCSCEEECSSHHH
T ss_pred             CCCCEEEECCchHHHHHHHHHHHHcCCCCceeeCCcHH
Confidence            456799999999999999999999999 5889988764

>1rhs_A Sulfur-substituted rhodanese; transferase, sulfurtransferase; 1.36A {Bos taurus} SCOP: c.46.1.2 c.46.1.2 PDB: 1boh_A 1boi_A 1orb_A 2ora_A 1dp2_A* 1rhd_A

Probab=83.87  E-value=1.3  Score=33.05  Aligned_cols=37  Identities=8%  Similarity=0.002  Sum_probs=32.2

Q ss_pred             CCCCEEEEeCCchHHHHHHHHhhhCCCc-eEeeecCCC
Q 030396          137 LNPPVLIFVQSKDRAKELYGELAFDDIR-AGVIHSDLS  173 (178)
Q Consensus       137 ~~~~~lIF~~t~~~~~~l~~~L~~~g~~-~~~lh~~~~  173 (178)
                      ..+++++||.+=.++...+..|...|++ +..+.|++.
T Consensus       239 ~~~~ivv~C~sG~rs~~a~~~L~~~G~~~v~~~~GG~~  276 (296)
T 1rhs_A          239 LTKPLIATCRKGVTACHIALAAYLCGKPDVAIYDGSWF  276 (296)
T ss_dssp             TTSCEEEECSSSSTHHHHHHHHHHTTCCCCEEESSHHH
T ss_pred             CCCCEEEECCcHHHHHHHHHHHHHcCCCCceeeCCcHH
Confidence            4678999999999999999999999995 888988764

>2eg4_A Probable thiosulfate sulfurtransferase; structural genomics, NPPSFA, national Pro protein structural and functional analyses; 1.70A {Thermus thermophilus} PDB: 2eg3_A

Probab=83.48  E-value=0.72  Score=33.02  Aligned_cols=37  Identities=16%  Similarity=0.106  Sum_probs=32.5

Q ss_pred             CCCCEEEEeCCchHHHHHHHHhhhCCCceEeeecCCC
Q 030396          137 LNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLS  173 (178)
Q Consensus       137 ~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~~~  173 (178)
                      ..+++++||++-.++...+..|...|.++..+.||+.
T Consensus       183 ~~~~iv~~C~~G~rs~~a~~~L~~~G~~v~~~~Gg~~  219 (230)
T 2eg4_A          183 PGQEVGVYCHSGARSAVAFFVLRSLGVRARNYLGSMH  219 (230)
T ss_dssp             TTCEEEEECSSSHHHHHHHHHHHHTTCEEEECSSHHH
T ss_pred             CCCCEEEEcCChHHHHHHHHHHHHcCCCcEEecCcHH
Confidence            4567999999999999999999999977888888764

>1e0c_A Rhodanese, sulfurtransferase; sulfur metabolism, thiosulfate:cyanide sulfurtransferase; 1.8A {Azotobacter vinelandii} SCOP: c.46.1.2 c.46.1.2 PDB: 1h4k_X 1h4m_X

Probab=82.89  E-value=1.6  Score=31.95  Aligned_cols=37  Identities=11%  Similarity=0.056  Sum_probs=30.7

Q ss_pred             CCCCEEEEeCCch-HHHHHHHHhhhCCC-ceEeeecCCC
Q 030396          137 LNPPVLIFVQSKD-RAKELYGELAFDDI-RAGVIHSDLS  173 (178)
Q Consensus       137 ~~~~~lIF~~t~~-~~~~l~~~L~~~g~-~~~~lh~~~~  173 (178)
                      ...+++|||++-. .+...+..|...|+ ++..+.||+.
T Consensus        80 ~~~~vvvyc~~g~~~s~~a~~~L~~~G~~~v~~L~GG~~  118 (271)
T 1e0c_A           80 PEAVYVVYDDEGGGWAGRFIWLLDVIGQQRYHYLNGGLT  118 (271)
T ss_dssp             TTCEEEEECSSSSHHHHHHHHHHHHTTCCCEEEETTHHH
T ss_pred             CCCeEEEEcCCCCccHHHHHHHHHHcCCCCeEEecCCHH
Confidence            4567999998776 88899999999999 5888988754

>3aay_A Putative thiosulfate sulfurtransferase; sulfurtranserase, structural genomics, PSI, structure initiative; 1.90A {Mycobacterium tuberculosis} PDB: 3aax_A 3hwi_A

Probab=82.66  E-value=2.2  Score=31.23  Aligned_cols=37  Identities=5%  Similarity=-0.006  Sum_probs=31.5

Q ss_pred             CCCCEEEEeCCchHHHHHHHHhhh-CCC-ceEeeecCCC
Q 030396          137 LNPPVLIFVQSKDRAKELYGELAF-DDI-RAGVIHSDLS  173 (178)
Q Consensus       137 ~~~~~lIF~~t~~~~~~l~~~L~~-~g~-~~~~lh~~~~  173 (178)
                      ..+++++||.+-.++...+..|.+ .|+ ++..+.||+.
T Consensus       225 ~~~~iv~yC~~G~rs~~a~~~L~~~~G~~~v~~l~GG~~  263 (277)
T 3aay_A          225 NSKETIAYCRIGERSSHTWFVLRELLGHQNVKNYDGSWT  263 (277)
T ss_dssp             TTSCEEEECSSHHHHHHHHHHHHTTSCCSCEEEESSHHH
T ss_pred             CCCCEEEEcCcHHHHHHHHHHHHHHcCCCcceeeCchHH
Confidence            467899999999999999999986 899 4889988764

>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer aging, hydrolase; HET: FLC; 2.00A {Sulfolobus acidocaldarius} PDB: 3crw_1*

Probab=82.33  E-value=6  Score=32.22  Aligned_cols=20  Identities=15%  Similarity=0.204  Sum_probs=17.9

Q ss_pred             CCCCEEEEeCCchHHHHHHH
Q 030396          137 LNPPVLIFVQSKDRAKELYG  156 (178)
Q Consensus       137 ~~~~~lIF~~t~~~~~~l~~  156 (178)
                      .++.++||++|-+..+.+++
T Consensus       392 ~~g~~lvlF~Sy~~l~~v~~  411 (551)
T 3crv_A          392 AKANVLVVFPSYEIMDRVMS  411 (551)
T ss_dssp             CSSEEEEEESCHHHHHHHHT
T ss_pred             CCCCEEEEecCHHHHHHHHH
Confidence            36789999999999999987

>3aay_A Putative thiosulfate sulfurtransferase; sulfurtranserase, structural genomics, PSI, structure initiative; 1.90A {Mycobacterium tuberculosis} PDB: 3aax_A 3hwi_A

Probab=81.45  E-value=1.9  Score=31.58  Aligned_cols=37  Identities=8%  Similarity=0.033  Sum_probs=29.7

Q ss_pred             CCCCEEEEeCCc-hHHHHHHHHhhhCCC-ceEeeecCCC
Q 030396          137 LNPPVLIFVQSK-DRAKELYGELAFDDI-RAGVIHSDLS  173 (178)
Q Consensus       137 ~~~~~lIF~~t~-~~~~~l~~~L~~~g~-~~~~lh~~~~  173 (178)
                      ...+++|||++- ..+...+..|...|+ ++..+.||+.
T Consensus        76 ~~~~vvvyc~~g~~~s~~a~~~L~~~G~~~v~~l~GG~~  114 (277)
T 3aay_A           76 NEDTVILYGGNNNWFAAYAYWYFKLYGHEKVKLLDGGRK  114 (277)
T ss_dssp             TTSEEEEECSGGGHHHHHHHHHHHHTTCCSEEEETTHHH
T ss_pred             CCCeEEEECCCCCchHHHHHHHHHHcCCCcEEEecCCHH
Confidence            356799999884 467888889999999 6889998753

>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=81.41  E-value=3.9  Score=28.01  Aligned_cols=39  Identities=21%  Similarity=0.146  Sum_probs=25.8

Q ss_pred             CCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEe
Q 030396           38 SRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFS   79 (178)
Q Consensus        38 ~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~S   79 (178)
                      ..-..+++||+|.+....  ...+..++.. .+.+..+++.|
T Consensus       101 ~~~~vliiDe~~~l~~~~--~~~l~~~l~~-~~~~~~~i~~~  139 (226)
T 2chg_A          101 APFKIIFLDEADALTADA--QAALRRTMEM-YSKSCRFILSC  139 (226)
T ss_dssp             CSCEEEEEETGGGSCHHH--HHHHHHHHHH-TTTTEEEEEEE
T ss_pred             cCceEEEEeChhhcCHHH--HHHHHHHHHh-cCCCCeEEEEe
Confidence            456789999999985533  5566666666 45555555443

>2j6p_A SB(V)-AS(V) reductase; arsenate reductase, antimonate reductase, CDC25 phosphatase, rhodanese, C-MYC epitope, oxidoreductase; HET: EPE; 2.15A {Leishmania major}

Probab=80.84  E-value=1.8  Score=28.89  Aligned_cols=47  Identities=17%  Similarity=0.046  Sum_probs=28.1

Q ss_pred             HHHHHHHHHhcCCCCEEEE-e-CCchHHHHHH----HHhhhCCC---ceEeeecCCC
Q 030396          126 LLALRQSFAESLNPPVLIF-V-QSKDRAKELY----GELAFDDI---RAGVIHSDLS  173 (178)
Q Consensus       126 ~~~l~~ll~~~~~~~~lIF-~-~t~~~~~~l~----~~L~~~g~---~~~~lh~~~~  173 (178)
                      ...+...+... ..+++|| | .+-.++...+    ..|...|+   ++..+.||+.
T Consensus        56 ~~~l~~~l~~~-~~~~vV~yC~~sg~rs~~aa~~~~~~L~~~G~~~~~v~~L~GG~~  111 (152)
T 2j6p_A           56 YEKLAKTLFEE-KKELAVFHCAQSLVRAPKGANRFALAQKKLGYVLPAVYVLRGGWE  111 (152)
T ss_dssp             HHHHHHHHHHT-TCCEEEEECSSSSSHHHHHHHHHHHHHHHHTCCCSEEEEETTHHH
T ss_pred             HHHHHHHhccc-CCCEEEEEcCCCCCccHHHHHHHHHHHHHcCCCCCCEEEEcCcHH
Confidence            33344444332 3455555 9 4554544444    78888897   6888998864

>3hzu_A Thiosulfate sulfurtransferase SSEA; niaid, ssgcid, infectious disease, transferase structural genomics; 2.10A {Mycobacterium tuberculosis} PDB: 3p3a_A

Probab=80.62  E-value=2  Score=32.48  Aligned_cols=46  Identities=7%  Similarity=0.070  Sum_probs=34.7

Q ss_pred             HHHHHHHh---cCCCCEEEEeCCch-HHHHHHHHhhhCCC-ceEeeecCCC
Q 030396          128 ALRQSFAE---SLNPPVLIFVQSKD-RAKELYGELAFDDI-RAGVIHSDLS  173 (178)
Q Consensus       128 ~l~~ll~~---~~~~~~lIF~~t~~-~~~~l~~~L~~~g~-~~~~lh~~~~  173 (178)
                      .+...+..   ....+++|||++-. .+...+..|+..|+ ++..+.||+.
T Consensus        98 ~~~~~l~~lgi~~~~~vVvyc~~g~~~a~~a~~~L~~~G~~~V~~L~GG~~  148 (318)
T 3hzu_A           98 QFAELMDRKGIARDDTVVIYGDKSNWWAAYALWVFTLFGHADVRLLNGGRD  148 (318)
T ss_dssp             HHHHHHHHTTCCTTCEEEEECSGGGHHHHHHHHHHHHTTCSCEEEETTHHH
T ss_pred             HHHHHHHHcCCCCCCeEEEECCCCCccHHHHHHHHHHcCCCceEEccCCHH
Confidence            34444443   24578999998776 78999999999999 5899988753

>3i2v_A Adenylyltransferase and sulfurtransferase MOCS3; rhodanese, UBA4, structural genomics, ubiquitin biology, structural genomics consortium, SGC; 1.25A {Homo sapiens}

Probab=80.33  E-value=0.89  Score=28.98  Aligned_cols=34  Identities=12%  Similarity=0.120  Sum_probs=29.2

Q ss_pred             CEEEEeCCchHHHHHHHHhhhC------CC-ceEeeecCCC
Q 030396          140 PVLIFVQSKDRAKELYGELAFD------DI-RAGVIHSDLS  173 (178)
Q Consensus       140 ~~lIF~~t~~~~~~l~~~L~~~------g~-~~~~lh~~~~  173 (178)
                      ++++||.+-.++...+..|...      |+ ++..+.||+.
T Consensus        74 ~ivv~C~~G~rs~~a~~~L~~~gg~~~~G~~~v~~l~GG~~  114 (127)
T 3i2v_A           74 PIYVICKLGNDSQKAVKILQSLSAAQELDPLTVRDVVGGLM  114 (127)
T ss_dssp             EEEEECSSSSHHHHHHHHHHHHHHTTSSSCEEEEEETTHHH
T ss_pred             eEEEEcCCCCcHHHHHHHHHHhhccccCCCceEEEecCCHH
Confidence            8999999999999999999887      45 7888988864

---

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	178
d1hv8a1	208	c.37.1.19 (A:3-210) Putative DEAD box RNA helicase	7e-22
d1t6na_	207	c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP5	7e-17
d1qdea_	212	c.37.1.19 (A:) Initiation factor 4a {Baker's yeast	3e-16
d2g9na1	218	c.37.1.19 (A:21-238) Initiation factor 4a {Human (	5e-16
d1wrba1	238	c.37.1.19 (A:164-401) putative ATP-dependent RNA h	8e-15
d2j0sa1	222	c.37.1.19 (A:22-243) Probable ATP-dependent RNA he	5e-12
d1s2ma1	206	c.37.1.19 (A:46-251) Putative ATP-dependent RNA he	1e-10
d1veca_	206	c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Huma	3e-10
d1q0ua_	209	c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR	3e-08
d2bmfa2	305	c.37.1.14 (A:178-482) Dengue virus helicase {Dengu	1e-05
d1a1va2	299	c.37.1.14 (A:326-624) HCV helicase domain {Human h	1e-05
d1fuka_	162	c.37.1.19 (A:) Initiation factor 4a {Baker's yeast	7e-05
d2rb4a1	168	c.37.1.19 (A:307-474) ATP-dependent RNA helicase D	3e-04
d1gkub1	237	c.37.1.16 (B:1-250) Helicase-like "domain" of reve	0.001
d1oywa2	206	c.37.1.19 (A:1-206) RecQ helicase domain {Escheric	0.002

>d1hv8a1 c.37.1.19 (A:3-210) Putative DEAD box RNA helicase {Archaeon Methanococcus jannaschii [TaxId: 2190]} Length = 208

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative DEAD box RNA helicase
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

 Score = 85.9 bits (212), Expect = 7e-22
 Identities = 29/87 (33%), Positives = 49/87 (56%), Gaps = 2/87 (2%)

Query: 16  CDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVR 75
            +I++ TP R+   I R  ++L  V+Y +LDEAD++  +G  +K ++ ++ AC N     
Sbjct: 122 ANIVVGTPGRILDHINRGTLNLKNVKYFILDEADEMLNMGF-IKDVEKILNAC-NKDKRI 179

Query: 76  SLFSATLPDFVEELARSIMHDAVRVIV 102
            LFSAT+P  +  LA+  M D   +  
Sbjct: 180 LLFSATMPREILNLAKKYMGDYSFIKA 206

>d1t6na_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]} Length = 207

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Spliceosome RNA helicase BAT1 (UAP56)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 72.6 bits (177), Expect = 7e-17
 Identities = 24/92 (26%), Positives = 45/92 (48%), Gaps = 1/92 (1%)

Query: 11  LSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSN 70
           L K    I++ TP R+    R K ++L  +++ +LDE DK+ E  ++ + +  + +    
Sbjct: 117 LKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMT-P 175

Query: 71  PSIVRSLFSATLPDFVEELARSIMHDAVRVIV 102
                 +FSATL   +  + R  M D + + V
Sbjct: 176 HEKQVMMFSATLSKEIRPVCRKFMQDPMEIFV 207

>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 = 71.0 bits (173), Expect = 3e-16
 Identities = 25/87 (28%), Positives = 46/87 (52%), Gaps = 2/87 (2%)

Query: 16  CDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVR 75
             I++ TP R+   I+R++    +++  +LDEAD++   G   + I  +      P+   
Sbjct: 128 AQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSGFK-EQIYQIFTLLP-PTTQV 185

Query: 76  SLFSATLPDFVEELARSIMHDAVRVIV 102
            L SAT+P+ V E+    M + VR++V
Sbjct: 186 VLLSATMPNDVLEVTTKFMRNPVRILV 212

>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 = 70.7 bits (172), Expect = 5e-16
 Identities = 25/89 (28%), Positives = 45/89 (50%), Gaps = 2/89 (2%)

Query: 16  CDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVR 75
             I++ TP R+   + R+ +    ++  VLDEAD++   G     I  + +   N +   
Sbjct: 132 PHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRG-FKDQIYDIFQKL-NSNTQV 189

Query: 76  SLFSATLPDFVEELARSIMHDAVRVIVGR 104
            L SAT+P  V E+ +  M D +R++V +
Sbjct: 190 VLLSATMPSDVLEVTKKFMRDPIRILVKK 218

>d1wrba1 c.37.1.19 (A:164-401) putative ATP-dependent RNA helicase VlgB {Flatworm (Dugesia japonica) [TaxId: 6161]} Length = 238

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase VlgB
species: Flatworm (Dugesia japonica) [TaxId: 6161]

 Score = 67.6 bits (164), Expect = 8e-15
 Identities = 29/91 (31%), Positives = 50/91 (54%), Gaps = 4/91 (4%)

Query: 16  CDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVR 75
           C +L++TP RL   I + KI L   +Y+VLDEAD+          I  +++  + PS + 
Sbjct: 149 CHLLVATPGRLVDFIEKNKISLEFCKYIVLDEADR-MLDMGFEPQIRKIIEESNMPSGIN 207

Query: 76  S---LFSATLPDFVEELARSIMHDAVRVIVG 103
               +FSAT P  +++LA   +++ + + VG
Sbjct: 208 RQTLMFSATFPKEIQKLAADFLYNYIFMTVG 238

>d2j0sa1 c.37.1.19 (A:22-243) Probable ATP-dependent RNA helicase DDX48 {Human (Homo sapiens) [TaxId: 9606]} Length = 222

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable ATP-dependent RNA helicase DDX48
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.9 bits (144), Expect = 5e-12
 Identities = 29/92 (31%), Positives = 47/92 (51%), Gaps = 2/92 (2%)

Query: 13  KFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPS 72
            +   ++  TP R+   IRR+ +    ++ LVLDEAD++   G   + I  V +    P+
Sbjct: 133 DYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKG-FKEQIYDVYRYL-PPA 190

Query: 73  IVRSLFSATLPDFVEELARSIMHDAVRVIVGR 104
               L SATLP  + E+    M D +R++V R
Sbjct: 191 TQVVLISATLPHEILEMTNKFMTDPIRILVKR 222

>d1s2ma1 c.37.1.19 (A:46-251) Putative ATP-dependent RNA helicase DHH1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 206

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative ATP-dependent RNA helicase DHH1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 55.8 bits (133), Expect = 1e-10
 Identities = 25/91 (27%), Positives = 38/91 (41%), Gaps = 2/91 (2%)

Query: 13  KFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPS 72
             +  IL+ TP R+     RK  DLS     ++DEADK+             + +   P+
Sbjct: 117 NETVHILVGTPGRVLDLASRKVADLSDCSLFIMDEADKMLSRDFKTIIEQ--ILSFLPPT 174

Query: 73  IVRSLFSATLPDFVEELARSIMHDAVRVIVG 103
               LFSAT P  V+E     +H    + + 
Sbjct: 175 HQSLLFSATFPLTVKEFMVKHLHKPYEINLM 205

>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 = 54.6 bits (130), Expect = 3e-10
 Identities = 21/88 (23%), Positives = 43/88 (48%), Gaps = 2/88 (2%)

Query: 13  KFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPS 72
             +  ++I+TP R+   I++    +  V+ +VLDEADKL     + + ++ ++      +
Sbjct: 120 DDTVHVVIATPGRILDLIKKGVAKVDHVQMIVLDEADKLLSQDFV-QIMEDIILTL-PKN 177

Query: 73  IVRSLFSATLPDFVEELARSIMHDAVRV 100
               L+SAT P  V++   S +     +
Sbjct: 178 RQILLYSATFPLSVQKFMNSHLEKPYEI 205

>d1q0ua_ c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR {Bacillus stearothermophilus [TaxId: 1422]} Length = 209

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable DEAD box RNA helicase YqfR
species: Bacillus stearothermophilus [TaxId: 1422]

 Score = 49.3 bits (116), Expect = 3e-08
 Identities = 24/90 (26%), Positives = 44/90 (48%), Gaps = 2/90 (2%)

Query: 13  KFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPS 72
                I+I TP R+   IR + +D+     LV+DEAD + ++G +   +D +        
Sbjct: 121 NVQPHIVIGTPGRINDFIREQALDVHTAHILVVDEADLMLDMGFI-TDVDQIAARM-PKD 178

Query: 73  IVRSLFSATLPDFVEELARSIMHDAVRVIV 102
           +   +FSAT+P+ ++   +  M +   V V
Sbjct: 179 LQMLVFSATIPEKLKPFLKKYMENPTFVHV 208

>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 = 41.8 bits (97), Expect = 1e-05
 Identities = 17/167 (10%), Positives = 40/167 (23%), Gaps = 27/167 (16%)

Query: 13  KFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPS 72
               +I+               I +     +++DEA          +    +        
Sbjct: 74  HTGREIVDLMCHATFTMRLLSPIRVPNYNLIIMDEAHFTDPASIAARGY--ISTRVEMGE 131

Query: 73  IVRSLFSATLPDFVEELARS---IMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLAL 129
                 +AT P   +   +S   IM +   +     N+  E +                 
Sbjct: 132 AAGIFMTATPPGSRDPFPQSNAPIMDEEREIPERSWNSGHEWVTDF-------------- 177

Query: 130 RQSFAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQ 176
                       + FV S     ++   L  +  +   +      ++
Sbjct: 178 --------KGKTVWFVPSIKAGNDIAACLRKNGKKVIQLSRKTFDSE 216

>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 = 41.8 bits (98), Expect = 1e-05
 Identities = 17/77 (22%), Positives = 26/77 (33%), Gaps = 7/77 (9%)

Query: 103 GRKNTASESIKQKLVFAGSEE---GKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELA 159
           G       +I++  +    E    GK + L            LIF  SK +  EL  +L 
Sbjct: 2   GSVTVPHPNIEEVALSTTGEIPFYGKAIPLEVIKGGR----HLIFCHSKKKCDELAAKLV 57

Query: 160 FDDIRAGVIHSDLSQTQ 176
              I A   +  L  + 
Sbjct: 58  ALGINAVAYYRGLDVSV 74

>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 = 39.1 bits (90), Expect = 7e-05
 Identities = 19/65 (29%), Positives = 28/65 (43%)

Query: 112 IKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSD 171
           IKQ  V    EE K   L   +        +IF  ++ + +EL  +L  D      I+SD
Sbjct: 1   IKQFYVNVEEEEYKYECLTDLYDSISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSD 60

Query: 172 LSQTQ 176
           L Q +
Sbjct: 61  LPQQE 65

>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 = 36.0 bits (82), Expect = 0.001
 Identities = 7/74 (9%), Positives = 23/74 (31%), Gaps = 9/74 (12%)

Query: 30  IRRKKIDLSRVEYLVLDEADKLFEVG-------NLLKHIDPVVK--ACSNPSIVRSLFSA 80
           + +   +L   +++ +D+ D + +         +LL     +              + +A
Sbjct: 153 LSKHYRELGHFDFIFVDDVDAILKASKNVDKLLHLLGFHYDLKTKSWVGEARGCLMVSTA 212

Query: 81  TLPDFVEELARSIM 94
           T     +      +
Sbjct: 213 TAKKGKKAELFRQL 226

>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 = 35.4 bits (80), Expect = 0.002
 Identities = 15/87 (17%), Positives = 32/87 (36%), Gaps = 4/87 (4%)

Query: 16  CDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKA--CSNPSI 73
             +L   P RL L    + +       L +DEA  + + G+  +     +       P++
Sbjct: 116 IRLLYIAPERLMLDNFLEHLAHWNPVLLAVDEAHCISQWGHDFRPEYAALGQLRQRFPTL 175

Query: 74  VRSLFSATLPDFVEE--LARSIMHDAV 98
                +AT  D   +  +    ++D +
Sbjct: 176 PFMALTATADDTTRQDIVRLLGLNDPL 202

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	178
d1veca_	206	DEAD box RNA helicase rck/p54 {Human (Homo sapiens	99.91
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	99.9
d1s2ma1	206	Putative ATP-dependent RNA helicase DHH1 {Baker's	99.89
d1hv8a1	208	Putative DEAD box RNA helicase {Archaeon Methanoco	99.88
d2g9na1	218	Initiation factor 4a {Human (Homo sapiens) [TaxId:	99.88
d1qdea_	212	Initiation factor 4a {Baker's yeast (Saccharomyces	99.87
d1t6na_	207	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	99.87
d1q0ua_	209	Probable DEAD box RNA helicase YqfR {Bacillus stea	99.87
d1wrba1	238	putative ATP-dependent RNA helicase VlgB {Flatworm	99.85
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	99.51
d2rb4a1	168	ATP-dependent RNA helicase DDX25 {Human (Homo sapi	99.41
d2j0sa2	168	Probable ATP-dependent RNA helicase DDX48 {Human (	99.39
d1fuka_	162	Initiation factor 4a {Baker's yeast (Saccharomyces	99.37
d1t5ia_	168	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	99.37
d1s2ma2	171	Putative ATP-dependent RNA helicase DHH1 {Baker's	99.37
d1hv8a2	155	Putative DEAD box RNA helicase {Archaeon Methanoco	99.23
d1oywa2	206	RecQ helicase domain {Escherichia coli [TaxId: 562	99.17
d2p6ra3	202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	99.16
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	99.05
d1oywa3	200	RecQ helicase domain {Escherichia coli [TaxId: 562	99.0
d1wp9a1	200	putative ATP-dependent RNA helicase PF2015 {Pyroco	98.96
d1c4oa2	174	Nucleotide excision repair enzyme UvrB {Thermus th	98.86
d1jr6a_	138	HCV helicase domain {Human hepatitis C virus (HCV)	98.81
d1t5la2	181	Nucleotide excision repair enzyme UvrB {Bacillus c	98.69
d1a1va2	299	HCV helicase domain {Human hepatitis C virus (HCV)	98.42
d1yksa1	140	YFV helicase domain {Yellow fever virus [TaxId: 11	98.27
d2p6ra4	201	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	97.83
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	97.8
d1rifa_	282	DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]	97.69
d2fz4a1	206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	97.52
d2fwra1	200	DNA repair protein RAD25 {Archaeoglobus fulgidus [	97.47
d1wp9a2	286	putative ATP-dependent RNA helicase PF2015 {Pyroco	97.33
d1z5za1	244	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	97.16
d1yksa2	299	YFV helicase domain {Yellow fever virus [TaxId: 11	97.15
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	96.97
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	96.89
d1z3ix1	346	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	96.78
d1tf5a4	175	Translocation ATPase SecA, nucleotide-binding doma	96.48
d1gkub2	248	Helicase-like "domain" of reverse gyrase {Archaeon	95.58
d1yt8a4	130	Thiosulfate sulfurtransferase PA2603 {Pseudomonas	95.32
d1z3ix2	298	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	94.74
d1tq1a_	119	Thiosulfate sulfurtransferase/Senescence-associate	94.64
d1z63a1	230	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	94.44
d1qxna_	137	Polysulfide-sulfur transferase (sulfide dehydrogen	93.83
d2eyqa5	211	Transcription-repair coupling factor, TRCF {Escher	93.56
d1gmxa_	108	Sulfurtransferase GlpE {Escherichia coli [TaxId: 5	93.4
d1urha2	120	3-mercaptopyruvate sulfurtransferase {Escherichia	93.37
d1nkta4	219	Translocation ATPase SecA, nucleotide-binding doma	92.91
d1yt8a1	136	Thiosulfate sulfurtransferase PA2603 {Pseudomonas	92.74
d1yt8a2	101	Thiosulfate sulfurtransferase PA2603 {Pseudomonas	92.37
d2eyqa2	117	Transcription-repair coupling factor, TRCF {Escher	91.02
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	90.46
d1gm5a4	206	RecG helicase domain {Thermotoga maritima [TaxId:	89.87
d1tf5a3	273	Translocation ATPase SecA, nucleotide-binding doma	89.04
d1nkta3	288	Translocation ATPase SecA, nucleotide-binding doma	88.32
d1e0ca2	136	Sulfurtransferase {Azotobacter vinelandii [TaxId:	87.62
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	86.26
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	86.22
d1yt8a3	157	Thiosulfate sulfurtransferase PA2603 {Pseudomonas	84.92
d1rhsa2	144	Rhodanese {Cow (Bos taurus) [TaxId: 9913]}	82.44
d1uara2	141	Sulfurtransferase {Thermus thermophilus [TaxId: 27	82.26

>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=99.91  E-value=4.4e-24  Score=153.67  Aligned_cols=94  Identities=23%  Similarity=0.321  Sum_probs=88.5

Q ss_pred             hHHhHHhccCCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcH
Q 030396            5 LVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPD   84 (178)
Q Consensus         5 ~~~q~~~l~~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~   84 (178)
                      ..++...++++++||||||||+.+++..+.+++++++++|+||||.|++.+ |.+++..|++. ++.++|+++||||+|+
T Consensus       112 ~~~~~~~l~~~~~ivv~TPgrl~~~~~~~~~~~~~l~~lVlDEaD~ll~~~-f~~~i~~I~~~-~~~~~Q~~l~SAT~~~  189 (206)
T d1veca_         112 LRDDIMRLDDTVHVVIATPGRILDLIKKGVAKVDHVQMIVLDEADKLLSQD-FVQIMEDIILT-LPKNRQILLYSATFPL  189 (206)
T ss_dssp             HHHHHHHTTSCCSEEEECHHHHHHHHHTTCSCCTTCCEEEEETHHHHTSTT-THHHHHHHHHH-SCTTCEEEEEESCCCH
T ss_pred             HHHHHHHHHhccCeEEeCCccccccccchhccccccceEEEeccccccccc-hHHHHHHHHHh-CCCCCEEEEEEecCCH
Confidence            346667788999999999999999999999999999999999999999999 99999999999 8999999999999999


Q ss_pred             HHHHHHHHhccCcEEE
Q 030396           85 FVEELARSIMHDAVRV  100 (178)
Q Consensus        85 ~~~~~~~~~~~~~~~v  100 (178)
                      ++.++++.++++|..|
T Consensus       190 ~v~~l~~~~l~~P~~I  205 (206)
T d1veca_         190 SVQKFMNSHLEKPYEI  205 (206)
T ss_dssp             HHHHHHHHHCSSCEEE
T ss_pred             HHHHHHHHHCCCCEEE
Confidence            9999999999999876

>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=99.90  E-value=1.6e-24  Score=157.52  Aligned_cols=97  Identities=29%  Similarity=0.436  Sum_probs=90.4

Q ss_pred             hHHhHHhccCCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcH
Q 030396            5 LVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPD   84 (178)
Q Consensus         5 ~~~q~~~l~~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~   84 (178)
                      ..++.+.++.+++|+||||||+.+++..+.+++++++++|+||||.|++.| |.+.+..|++. ++.++|+++||||+|+
T Consensus       125 ~~~~~~~l~~~~~Ilv~TPgrl~~~~~~~~~~~~~l~~lVlDEaD~ll~~~-f~~~i~~I~~~-l~~~~Q~ilfSAT~~~  202 (222)
T d2j0sa1         125 VGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKG-FKEQIYDVYRY-LPPATQVVLISATLPH  202 (222)
T ss_dssp             HHHHHHHHHHCCSEEEECHHHHHHHHHTTSSCCTTCCEEEEETHHHHTSTT-THHHHHHHHTT-SCTTCEEEEEESCCCH
T ss_pred             chhhHHHhccCCeEEeCCCCcHHhcccccccccccceeeeecchhHhhhcC-cHHHHHHHHHh-CCCCCEEEEEEEeCCH
Confidence            356677778899999999999999999999999999999999999999999 99999999999 8999999999999999


Q ss_pred             HHHHHHHHhccCcEEEEEc
Q 030396           85 FVEELARSIMHDAVRVIVG  103 (178)
Q Consensus        85 ~~~~~~~~~~~~~~~v~~~  103 (178)
                      ++.++++.++++|..|.++
T Consensus       203 ~v~~l~~~~l~~Pv~I~V~  221 (222)
T d2j0sa1         203 EILEMTNKFMTDPIRILVK  221 (222)
T ss_dssp             HHHTTGGGTCSSCEEECCC
T ss_pred             HHHHHHHHHCCCCEEEEEe
Confidence            9999999999999888664

>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=99.89  E-value=1.1e-23  Score=151.53  Aligned_cols=96  Identities=28%  Similarity=0.342  Sum_probs=89.9

Q ss_pred             hHHhHHhccCCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcH
Q 030396            5 LVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPD   84 (178)
Q Consensus         5 ~~~q~~~l~~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~   84 (178)
                      ..++.+.+.++|+|+|||||+|.++++.+.+++.+++++|+||||.|++.+ |.+.+..|++. ++.++|+++||||+|+
T Consensus       109 ~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~lV~DEaD~l~~~~-f~~~v~~I~~~-l~~~~Q~il~SATl~~  186 (206)
T d1s2ma1         109 LRDDILRLNETVHILVGTPGRVLDLASRKVADLSDCSLFIMDEADKMLSRD-FKTIIEQILSF-LPPTHQSLLFSATFPL  186 (206)
T ss_dssp             HHHHHHHTTSCCSEEEECHHHHHHHHHTTCSCCTTCCEEEEESHHHHSSHH-HHHHHHHHHTT-SCSSCEEEEEESCCCH
T ss_pred             hhhHHHHhcccceEEEECCcccccccccceeecccceEEEeechhhhhhhh-hHHHHHHHHHh-CCCCCEEEEEEEeCCH
Confidence            456677788999999999999999999999999999999999999999999 99999999999 8899999999999999


Q ss_pred             HHHHHHHHhccCcEEEEE
Q 030396           85 FVEELARSIMHDAVRVIV  102 (178)
Q Consensus        85 ~~~~~~~~~~~~~~~v~~  102 (178)
                      ++.+++..++++|..|.+
T Consensus       187 ~v~~~~~~~l~~P~~I~~  204 (206)
T d1s2ma1         187 TVKEFMVKHLHKPYEINL  204 (206)
T ss_dssp             HHHHHHHHHCSSCEEESC
T ss_pred             HHHHHHHHHCCCCEEEEe
Confidence            999999999999988765

>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=99.88  E-value=7.4e-23  Score=147.40  Aligned_cols=94  Identities=30%  Similarity=0.473  Sum_probs=86.5

Q ss_pred             HHhHHhccCCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcHH
Q 030396            6 VRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDF   85 (178)
Q Consensus         6 ~~q~~~l~~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~   85 (178)
                      .+|.+.+ ++|+|+|||||++.++++++.+++++++++|+||||.+++.+ +.+++..|++. +++++|++++|||+|++
T Consensus       113 ~~~~~~l-~~~~IlV~TP~~l~~~l~~~~~~~~~l~~lViDEad~l~~~~-~~~~i~~I~~~-~~~~~Q~i~~SAT~~~~  189 (208)
T d1hv8a1         113 YPQIKAL-KNANIVVGTPGRILDHINRGTLNLKNVKYFILDEADEMLNMG-FIKDVEKILNA-CNKDKRILLFSATMPRE  189 (208)
T ss_dssp             HHHHHHH-HTCSEEEECHHHHHHHHHTTCSCTTSCCEEEEETHHHHHTTT-THHHHHHHHHT-SCSSCEEEEECSSCCHH
T ss_pred             HHHHHhc-CCCCEEEEChHHHHHHHHcCCCCcccCcEEEEEChHHhhcCC-ChHHHHHHHHh-CCCCCeEEEEEccCCHH
Confidence            4455555 479999999999999999999999999999999999999999 99999999999 88899999999999999


Q ss_pred             HHHHHHHhccCcEEEEE
Q 030396           86 VEELARSIMHDAVRVIV  102 (178)
Q Consensus        86 ~~~~~~~~~~~~~~v~~  102 (178)
                      +.++++++++||..|.+
T Consensus       190 v~~~~~~~l~~~~~I~~  206 (208)
T d1hv8a1         190 ILNLAKKYMGDYSFIKA  206 (208)
T ss_dssp             HHHHHHHHCCSEEEEEC
T ss_pred             HHHHHHHHCCCCeEEEE
Confidence            99999999999988865

>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=99.88  E-value=8.8e-23  Score=147.92  Aligned_cols=91  Identities=29%  Similarity=0.438  Sum_probs=85.5

Q ss_pred             hccCCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcHHHHHHH
Q 030396           11 LSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELA   90 (178)
Q Consensus        11 ~l~~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~~~~~~   90 (178)
                      ...++++|+|||||++.+++.++..++++++++|+||||.|++.+ |.+.+..|++. ++.++|+++||||+|+++.+++
T Consensus       127 ~~~~~~~IvV~TP~rl~~~l~~~~~~~~~l~~lVlDEaD~ll~~~-f~~~~~~Il~~-~~~~~Q~il~SAT~~~~v~~~~  204 (218)
T d2g9na1         127 LQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRG-FKDQIYDIFQK-LNSNTQVVLLSATMPSDVLEVT  204 (218)
T ss_dssp             SSSCCCSEEEECHHHHHHHHHTTSSCSTTCCEEEEESHHHHHHTT-CHHHHHHHHHH-SCTTCEEEEEESCCCHHHHHHH
T ss_pred             HhcCCCEEEEeCChhHHHHHhcCCcccccceEEEeeecchhhcCc-hHHHHHHHHHh-CCCCCeEEEEEecCCHHHHHHH
Confidence            334689999999999999999999999999999999999999999 99999999999 8999999999999999999999


Q ss_pred             HHhccCcEEEEEc
Q 030396           91 RSIMHDAVRVIVG  103 (178)
Q Consensus        91 ~~~~~~~~~v~~~  103 (178)
                      +.++++|..|.++
T Consensus       205 ~~~l~~pv~i~v~  217 (218)
T d2g9na1         205 KKFMRDPIRILVK  217 (218)
T ss_dssp             HHHCSSCEEEECC
T ss_pred             HHHCCCCEEEEEe
Confidence            9999999988764

>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=99.87  E-value=1.2e-22  Score=146.55  Aligned_cols=93  Identities=27%  Similarity=0.463  Sum_probs=82.8

Q ss_pred             HHhHHhccCCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcHH
Q 030396            6 VRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDF   85 (178)
Q Consensus         6 ~~q~~~l~~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~   85 (178)
                      .+|...+ ++|+|+|||||++.+++..+.+++++++++|+||||.+++.+ |.+++..|++. +++++|+++||||++++
T Consensus       119 ~~~~~~~-~~~~IvI~TP~~l~~~~~~~~~~l~~l~~lVlDEad~lld~~-f~~~v~~I~~~-~~~~~Q~vl~SAT~~~~  195 (212)
T d1qdea_         119 VEDAEGL-RDAQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSG-FKEQIYQIFTL-LPPTTQVVLLSATMPND  195 (212)
T ss_dssp             ------C-TTCSEEEECHHHHHHHHHTTSSCCTTCCEEEEETHHHHHHTT-CHHHHHHHHHH-SCTTCEEEEEESSCCHH
T ss_pred             hHHHHHh-cCCcEEEECCCccccccccCceecCcceEEeehhhhhhcccc-hHHHHHHHHHh-CCCCCeEEEEEeeCCHH
Confidence            3444444 478999999999999999999999999999999999999999 99999999999 88999999999999999


Q ss_pred             HHHHHHHhccCcEEEE
Q 030396           86 VEELARSIMHDAVRVI  101 (178)
Q Consensus        86 ~~~~~~~~~~~~~~v~  101 (178)
                      ++++++.++++|..|.
T Consensus       196 v~~l~~~~l~~Pv~i~  211 (212)
T d1qdea_         196 VLEVTTKFMRNPVRIL  211 (212)
T ss_dssp             HHHHHHHHCSSCEEEC
T ss_pred             HHHHHHHHCCCCEEEe
Confidence            9999999999998774

>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=99.87  E-value=1.4e-22  Score=145.73  Aligned_cols=92  Identities=24%  Similarity=0.439  Sum_probs=84.0

Q ss_pred             hHHhc-cCCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEecccccccc-CCChhhHHHHHhhCCCCCceEEEEeecCcHH
Q 030396            8 STDLS-KFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEV-GNLLKHIDPVVKACSNPSIVRSLFSATLPDF   85 (178)
Q Consensus         8 q~~~l-~~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~-~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~   85 (178)
                      +.+.+ +.+|+|+|||||++.++++.+.+++++++++|+||||.|++. + |.+.+..|++. .+.++|+++||||++++
T Consensus       113 ~~~~l~~~~~~ilI~TP~rl~~~~~~~~~~l~~l~~lVlDEaD~ll~~~~-~~~~i~~I~~~-~~~~~Q~il~SAT~~~~  190 (207)
T d1t6na_         113 DEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLD-MRRDVQEIFRM-TPHEKQVMMFSATLSKE  190 (207)
T ss_dssp             HHHHHHHSCCSEEEECHHHHHHHHHTTSSCCTTCCEEEEESHHHHHSSHH-HHHHHHHHHHT-SCSSSEEEEEESCCCTT
T ss_pred             HHHHHHhcCCCEEEeCcchhhhhccCCceeccccceeehhhhhhhhhcCC-cHHHHHHHHHh-CCCCCEEEEEeeeCCHH
Confidence            33433 568999999999999999999999999999999999999985 6 99999999999 89999999999999999


Q ss_pred             HHHHHHHhccCcEEEE
Q 030396           86 VEELARSIMHDAVRVI  101 (178)
Q Consensus        86 ~~~~~~~~~~~~~~v~  101 (178)
                      ++++++.++++|..|.
T Consensus       191 v~~l~~~~l~~P~~I~  206 (207)
T d1t6na_         191 IRPVCRKFMQDPMEIF  206 (207)
T ss_dssp             THHHHHTTCSSCEEEE
T ss_pred             HHHHHHHHCCCCEEEe
Confidence            9999999999998775

>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=99.87  E-value=2e-22  Score=145.07  Aligned_cols=96  Identities=25%  Similarity=0.418  Sum_probs=88.8

Q ss_pred             hHHhHHhccCCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcH
Q 030396            5 LVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPD   84 (178)
Q Consensus         5 ~~~q~~~l~~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~   84 (178)
                      ...+.+.++.+|+|+||||+++.+++.++...+++++++|+||||.+++++ |.+++..|++. +++++|++++|||+|+
T Consensus       113 ~~~~~~~~~~~~~Ilv~TP~~l~~~~~~~~~~~~~l~~lViDEad~ll~~~-f~~~v~~I~~~-~~~~~Q~il~SATl~~  190 (209)
T d1q0ua_         113 KQKALEKLNVQPHIVIGTPGRINDFIREQALDVHTAHILVVDEADLMLDMG-FITDVDQIAAR-MPKDLQMLVFSATIPE  190 (209)
T ss_dssp             HHHTTCCCSSCCSEEEECHHHHHHHHHTTCCCGGGCCEEEECSHHHHHHTT-CHHHHHHHHHT-SCTTCEEEEEESCCCG
T ss_pred             hHHHHHHhccCceEEEecCchhhhhhhhhccccccceEEEEeecccccccc-cHHHHHHHHHH-CCCCCEEEEEEccCCH
Confidence            445556677899999999999999999998999999999999999999999 99999999999 8899999999999999


Q ss_pred             HHHHHHHHhccCcEEEEE
Q 030396           85 FVEELARSIMHDAVRVIV  102 (178)
Q Consensus        85 ~~~~~~~~~~~~~~~v~~  102 (178)
                      ++.++++.++++|..|.+
T Consensus       191 ~v~~l~~~~l~~p~~i~V  208 (209)
T d1q0ua_         191 KLKPFLKKYMENPTFVHV  208 (209)
T ss_dssp             GGHHHHHHHCSSCEEEEC
T ss_pred             HHHHHHHHHCCCCEEEEe
Confidence            999999999999988764

>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=99.85  E-value=2.1e-21  Score=142.32  Aligned_cols=97  Identities=29%  Similarity=0.506  Sum_probs=87.2

Q ss_pred             HHhHHhccCCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCC---CCCceEEEEeecC
Q 030396            6 VRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACS---NPSIVRSLFSATL   82 (178)
Q Consensus         6 ~~q~~~l~~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~---~~~~q~i~~SAT~   82 (178)
                      ..|.+.+..++||||||||+|.+++..+...+.+++++|+||||.+++.+ |.+++..|++.+.   +.++|+++||||+
T Consensus       139 ~~~~~~~~~~~~ivV~TP~~l~~~~~~~~~~l~~v~~lViDEaD~ll~~~-f~~~i~~Il~~~~~~~~~~~Q~il~SAT~  217 (238)
T d1wrba1         139 HSQIREVQMGCHLLVATPGRLVDFIEKNKISLEFCKYIVLDEADRMLDMG-FEPQIRKIIEESNMPSGINRQTLMFSATF  217 (238)
T ss_dssp             HHHHHHHSSCCSEEEECHHHHHHHHHTTSBCCTTCCEEEEETHHHHHHTT-CHHHHHHHHHSSCCCCGGGCEEEEEESSC
T ss_pred             hHHHhhcccCCceeecCHHHHHhHHccCceeccccceeeeehhhhhhhhc-cHHHHHHHHHHhcCCCCCCCEEEEEeeeC
Confidence            45666778899999999999999999999999999999999999999999 9999999998742   2367999999999


Q ss_pred             cHHHHHHHHHhccCcEEEEEc
Q 030396           83 PDFVEELARSIMHDAVRVIVG  103 (178)
Q Consensus        83 ~~~~~~~~~~~~~~~~~v~~~  103 (178)
                      +.+++.+++.++++|..+.++
T Consensus       218 ~~~v~~l~~~~~~~p~~i~vg  238 (238)
T d1wrba1         218 PKEIQKLAADFLYNYIFMTVG  238 (238)
T ss_dssp             CHHHHHHHHHHCSSCEEEEEC
T ss_pred             CHHHHHHHHHHCCCCEEEEeC
Confidence            999999999999999888653

>d2bmfa2 c.37.1.14 (A:178-482) Dengue virus helicase {Dengue virus type 2 [TaxId: 11060]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: Dengue virus helicase
species: Dengue virus type 2 [TaxId: 11060]

Probab=99.51  E-value=9.3e-15  Score=109.51  Aligned_cols=142  Identities=10%  Similarity=-0.004  Sum_probs=90.4

Q ss_pred             cCCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccC-CChhhHHHHHhhCCCCCceEEEEeecCcHHHHHHHH
Q 030396           13 KFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVG-NLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELAR   91 (178)
Q Consensus        13 ~~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~-~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~~~~~~~   91 (178)
                      .....++++||+.+..... ....+.+++++|+||+|.+..++ .+...+..+..   ....|++++|||.+......  
T Consensus        75 ~~~~~i~~~t~~~l~~~~~-~~~~~~~~~~vViDE~H~~~~~~~~~~~~l~~~~~---~~~~~~v~~SAT~~~~~~~~--  148 (305)
T d2bmfa2          75 TGREIVDLMCHATFTMRLL-SPIRVPNYNLIIMDEAHFTDPASIAARGYISTRVE---MGEAAGIFMTATPPGSRDPF--  148 (305)
T ss_dssp             -CCCSEEEEEHHHHHHHHT-SSSCCCCCSEEEEESTTCCSHHHHHHHHHHHHHHH---HTSCEEEEECSSCTTCCCSS--
T ss_pred             cCccccccCCcHHHHHHHh-cCccccceeEEEeeeeeecchhhHHHHHHHHHhhc---cccceEEEeecCCCcceeee--
Confidence            3557899999998776654 34457889999999999997665 12222222222   35789999999998532110  


Q ss_pred             HhccCcEEEEEcCCccccCCceEEEEEcCChhhHHHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhhhCCCceEeeecC
Q 030396           92 SIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSD  171 (178)
Q Consensus        92 ~~~~~~~~v~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~  171 (178)
                       ....+.....             ....... .+...+ ..+ .....+++|||+++++++.++..|.+.|+++..+||+
T Consensus       149 -~~~~~~~~~~-------------~~~~~~~-~~~~~~-~~~-~~~~~~~lvf~~~~~~~~~l~~~L~~~~~~~~~l~~~  211 (305)
T d2bmfa2         149 -PQSNAPIMDE-------------EREIPER-SWNSGH-EWV-TDFKGKTVWFVPSIKAGNDIAACLRKNGKKVIQLSRK  211 (305)
T ss_dssp             -CCCSSCEEEE-------------ECCCCCS-CCSSCC-HHH-HSSCSCEEEECSCHHHHHHHHHHHHHHTCCCEECCTT
T ss_pred             -cccCCcceEE-------------EEeccHH-HHHHHH-HHH-HhhCCCEEEEeccHHHHHHHHHHHHhCCCCEEEeCCc
Confidence             0001111110             0001011 011111 112 2236899999999999999999999999999999999


Q ss_pred             CCcccc
Q 030396          172 LSQTQV  177 (178)
Q Consensus       172 ~~~~~R  177 (178)
                      +++++|
T Consensus       212 ~~~~~~  217 (305)
T d2bmfa2         212 TFDSEY  217 (305)
T ss_dssp             CHHHHG
T ss_pred             ChHHHH
Confidence            987665

>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=99.39  E-value=3.1e-13  Score=93.25  Aligned_cols=72  Identities=22%  Similarity=0.253  Sum_probs=67.8

Q ss_pred             ccccCCceEEEEEcCChhhHHHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhhhCCCceEeeecCCCcccc
Q 030396          106 NTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQV  177 (178)
Q Consensus       106 ~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~~~~~~R  177 (178)
                      ..++.+++|+|+.+.+...|...|.++++.....++||||++++.|+.++..|...|+++..+||+|++++|
T Consensus         2 ~~tl~~i~q~~v~v~~~~~K~~~L~~ll~~~~~~k~iiF~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r   73 (168)
T d2j0sa2           2 ELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKER   73 (168)
T ss_dssp             GCSCTTEEEEEEEESSTTHHHHHHHHHHHHHTSSEEEEECSSHHHHHHHHHHHHHTTCCCEEECTTSCHHHH
T ss_pred             CCCCCCcEEEEEEecChHHHHHHHHHHHHhCCCCceEEEeeeHHHHHHHHHHhhhcccchhhhhhhhhHHHH
Confidence            457789999999998888899999999999888999999999999999999999999999999999999987

>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=99.37  E-value=7.7e-13  Score=90.72  Aligned_cols=66  Identities=29%  Similarity=0.313  Sum_probs=62.6

Q ss_pred             ceEEEEEcCChhhHHHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhhhCCCceEeeecCCCcccc
Q 030396          112 IKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQV  177 (178)
Q Consensus       112 i~~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~~~~~~R  177 (178)
                      |+|+|+.+.+.+.|...|.++++.....++||||+|+..|+.++..|...|+++..+||+|++++|
T Consensus         1 I~q~~~~v~~~e~K~~~L~~ll~~~~~~k~iIF~~s~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r   66 (162)
T d1fuka_           1 IKQFYVNVEEEEYKYECLTDLYDSISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQER   66 (162)
T ss_dssp             CEEEEEEEESGGGHHHHHHHHHHHTTCSCEEEEESSHHHHHHHHHHHHHTTCCEEEECTTSCHHHH
T ss_pred             CEEEEEEeCCcHHHHHHHHHHHHhCCCCcEEEEEEEEchHHHHHHHHhhcCceEEEeccCCchhhH
Confidence            578999998888899999999999989999999999999999999999999999999999999887

>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=99.37  E-value=8.9e-13  Score=90.92  Aligned_cols=66  Identities=24%  Similarity=0.181  Sum_probs=61.3

Q ss_pred             CceEEEEEcCChhhHHHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhhhCCCceEeeecCCCcccc
Q 030396          111 SIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQV  177 (178)
Q Consensus       111 ~i~~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~~~~~~R  177 (178)
                      +++|+|+.+ ..++|.+.|.++++.....++|||||+++.++.++..|...|+++..+||+|++++|
T Consensus         1 ~l~q~~v~~-~~~~K~~~L~~ll~~~~~~k~iIF~~~~~~~~~l~~~L~~~~~~~~~ihg~~~~~~r   66 (168)
T d1t5ia_           1 GLQQYYVKL-KDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEER   66 (168)
T ss_dssp             CCEEEEEEC-CGGGHHHHHHHHHHHSCCSSEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHH
T ss_pred             CcEEEEEEe-ChHHHHHHHHHHHHhCCCCeEEEEEeeeecchhhhhhhccccccccccccccchhhh
Confidence            478889877 467899999999999988999999999999999999999999999999999999887

>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=99.37  E-value=6.5e-13  Score=91.88  Aligned_cols=70  Identities=21%  Similarity=0.224  Sum_probs=64.7

Q ss_pred             cccCCceEEEEEcCChhhHHHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhhhCCCceEeeecCCCcccc
Q 030396          107 TASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQV  177 (178)
Q Consensus       107 ~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~~~~~~R  177 (178)
                      .++.++.|+|+.+. ..+|...|.++++.....++||||+|++.|+.++..|...|+++..+||+|++++|
T Consensus         2 ~tl~~i~q~yi~v~-~~~K~~~L~~ll~~~~~~k~iVF~~~~~~~~~l~~~L~~~g~~~~~~h~~~~~~~r   71 (171)
T d1s2ma2           2 LTLKGITQYYAFVE-ERQKLHCLNTLFSKLQINQAIIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQER   71 (171)
T ss_dssp             CBCTTEEEEEEECC-GGGHHHHHHHHHHHSCCSEEEEECSSHHHHHHHHHHHHHHTCCEEEECTTSCHHHH
T ss_pred             CCccceEEEEEEcC-HHHHHHHHHHHHHhCCCCceEEEEeeeehhhHhHHhhhcccccccccccccchhhh
Confidence            46788999998874 56899999999999988999999999999999999999999999999999999887

>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=99.23  E-value=1.4e-11  Score=83.63  Aligned_cols=66  Identities=33%  Similarity=0.372  Sum_probs=60.0

Q ss_pred             CCceEEEEEcCChhhHHHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhhhCCCceEeeecCCCcccc
Q 030396          110 ESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQV  177 (178)
Q Consensus       110 ~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~~~~~~R  177 (178)
                      .+|.|+|+.+ +..+|...|.++++.. ..++||||+|+++|+.+++.|...|+++..+||++++++|
T Consensus         2 ~nI~~~~i~v-~~~~K~~~L~~ll~~~-~~k~IIF~~s~~~~~~l~~~L~~~g~~~~~~~~~~~~~~r   67 (155)
T d1hv8a2           2 ANIEQSYVEV-NENERFEALCRLLKNK-EFYGLVFCKTKRDTKELASMLRDIGFKAGAIHGDLSQSQR   67 (155)
T ss_dssp             SSSEEEEEEC-CGGGHHHHHHHHHCST-TCCEEEECSSHHHHHHHHHHHHHTTCCEEEECSSSCHHHH
T ss_pred             CCeEEEEEEe-ChHHHHHHHHHHHccC-CCCEEEEECchHHHHHHHhhhcccccccccccccchhhhh
Confidence            5789999888 5568999999999865 5689999999999999999999999999999999999887

>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=99.17  E-value=1.9e-11  Score=86.56  Aligned_cols=86  Identities=17%  Similarity=0.173  Sum_probs=63.0

Q ss_pred             hccCCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccC-CChhh---HHHHHhhCCCCCceEEEEeecCcHHH
Q 030396           11 LSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVG-NLLKH---IDPVVKACSNPSIVRSLFSATLPDFV   86 (178)
Q Consensus        11 ~l~~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~-~~~~~---i~~i~~~~~~~~~q~i~~SAT~~~~~   86 (178)
                      .....++|+++||+++............+++++|+||+|.+.+++ .+...   +..+.+. . ++.|++++|||+++.+
T Consensus       111 ~~~~~~~i~~~t~~~~~~~~~~~~~~~~~v~~lviDEaH~~~~~~~~~~~~~~~~~~l~~~-~-~~~~ii~lSATl~~~v  188 (206)
T d1oywa2         111 CRTGQIRLLYIAPERLMLDNFLEHLAHWNPVLLAVDEAHCISQWGHDFRPEYAALGQLRQR-F-PTLPFMALTATADDTT  188 (206)
T ss_dssp             HHHTCCSEEEECHHHHTSTTHHHHHTTSCEEEEEESSGGGGCTTSSCCCHHHHGGGGHHHH-C-TTSCEEEEESCCCHHH
T ss_pred             HhcCCceEEEEechhhhchhhcccchhheeeeeeeeeeeeeeccccchHHHHHHHHHHHHh-C-CCCceEEEEeCCCHHH
Confidence            344678999999999876655555667889999999999998886 23322   2334444 3 4789999999999988


Q ss_pred             HHHHHHh--ccCcE
Q 030396           87 EELARSI--MHDAV   98 (178)
Q Consensus        87 ~~~~~~~--~~~~~   98 (178)
                      .+.+.++  +.+|.
T Consensus       189 ~~di~~~L~l~~p~  202 (206)
T d1oywa2         189 RQDIVRLLGLNDPL  202 (206)
T ss_dssp             HHHHHHHHTCCSCE
T ss_pred             HHHHHHHcCCCCCc
Confidence            7645444  67884

>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=99.16  E-value=6.2e-11  Score=83.65  Aligned_cols=84  Identities=24%  Similarity=0.249  Sum_probs=64.2

Q ss_pred             CCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhC--CCCCceEEEEeecCcHHHHHHHH
Q 030396           14 FSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKAC--SNPSIVRSLFSATLPDFVEELAR   91 (178)
Q Consensus        14 ~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~--~~~~~q~i~~SAT~~~~~~~~~~   91 (178)
                      ..++|+++||+.+..++.++...+.+++++|+||+|.+.+++ ....++.+++.+  .+++.|++++|||+|+. +++ .
T Consensus       113 ~~~~ii~~~~~~~~~~~~~~~~~~~~~~~ii~DE~h~~~~~~-r~~~~~~~l~~i~~~~~~~~~l~lSATl~n~-~~~-~  189 (202)
T d2p6ra3         113 GDCDIIVTTSEKADSLIRNRASWIKAVSCLVVDEIHLLDSEK-RGATLEILVTKMRRMNKALRVIGLSATAPNV-TEI-A  189 (202)
T ss_dssp             TTCSEEEEEHHHHHHHHHTTCSGGGGCCEEEETTGGGGGCTT-THHHHHHHHHHHHHHCTTCEEEEEECCCTTH-HHH-H
T ss_pred             cccceeeeccHHHHHHHhccchhhhhhhhccccHHHHhcccc-cchHHHHHHHHHHhcCCCCcEEEEcCCCCcH-HHH-H
Confidence            568999999999999998888888999999999999998776 555444443331  45688999999999763 444 4


Q ss_pred             HhccCcEEE
Q 030396           92 SIMHDAVRV  100 (178)
Q Consensus        92 ~~~~~~~~v  100 (178)
                      .|+..+..+
T Consensus       190 ~~l~~~~~~  198 (202)
T d2p6ra3         190 EWLDADYYV  198 (202)
T ss_dssp             HHTTCEEEE
T ss_pred             HHcCCCeee
Confidence            676655443

>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=99.05  E-value=1.3e-11  Score=89.29  Aligned_cols=75  Identities=17%  Similarity=0.252  Sum_probs=51.1

Q ss_pred             cCCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhC------------CCCCceEEEEee
Q 030396           13 KFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKAC------------SNPSIVRSLFSA   80 (178)
Q Consensus        13 ~~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~------------~~~~~q~i~~SA   80 (178)
                      ..+++|+|+||++|.+.    ..++++++++|+||+|.+++.+   ..+..+...+            .+...|++++||
T Consensus       140 ~~~~~Ilv~Tp~~l~~~----~~~~~~~~~vVvDE~d~~l~~~---~~~~~~~~~~g~~~~~~~~~~~~~~~~~~i~~SA  212 (237)
T d1gkub1         140 LRNFKIVITTTQFLSKH----YRELGHFDFIFVDDVDAILKAS---KNVDKLLHLLGFHYDLKTKSWVGEARGCLMVSTA  212 (237)
T ss_dssp             GGGCSEEEEEHHHHHHC----STTSCCCSEEEESCHHHHHTST---HHHHHHHHHTTEEEETTTTEEEECCSSEEEECCC
T ss_pred             ccccceeccChHHHHHh----hhhcCCCCEEEEEChhhhhhcc---cchhHHHHhcCChHHHHHHHhhCCCCCeEEEEeC
Confidence            35689999999987653    3356789999999999998765   2222222220            345679999999


Q ss_pred             cCcHHHHH-HHHHhc
Q 030396           81 TLPDFVEE-LARSIM   94 (178)
Q Consensus        81 T~~~~~~~-~~~~~~   94 (178)
                      |+++..+. +.+.++
T Consensus       213 T~~~~~~~~l~r~ll  227 (237)
T d1gkub1         213 TAKKGKKAELFRQLL  227 (237)
T ss_dssp             CSCCCTTHHHHHHHH
T ss_pred             CCCcccHHHHHHHHh
Confidence            99865443 334443

>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=99.00  E-value=4.1e-10  Score=79.35  Aligned_cols=67  Identities=18%  Similarity=0.216  Sum_probs=57.9

Q ss_pred             ccCCceEEEEEcCChhhHHHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhhhCCCceEeeecCCCcccc
Q 030396          108 ASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQV  177 (178)
Q Consensus       108 ~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~~~~~~R  177 (178)
                      ..+||.+.++   +..+|...|..+++.....++||||+|++.|+.++..|...|+++..+||+|++++|
T Consensus         3 ~RpNi~y~v~---~~~~k~~~L~~~l~~~~~~~~IIF~~t~~~~~~l~~~l~~~~~~~~~~h~~~~~~~r   69 (200)
T d1oywa3           3 DRPNIRYMLM---EKFKPLDQLMRYVQEQRGKSGIIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVR   69 (200)
T ss_dssp             CCTTEEEEEE---ECSSHHHHHHHHHHHTTTCCEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHH
T ss_pred             CCCCcEEEEE---cCCcHHHHHHHHHHhcCCCCEEEEEeeehhhHHhhhhhccCCceeEEecCCCcHHHH
Confidence            4566754443   334689999999998888899999999999999999999999999999999999887

>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=98.96  E-value=1.4e-09  Score=76.18  Aligned_cols=73  Identities=18%  Similarity=0.183  Sum_probs=56.0

Q ss_pred             CCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcHHHHH
Q 030396           14 FSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEE   88 (178)
Q Consensus        14 ~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~~~~   88 (178)
                      ..++++++||+++...+......+++++++|+||||.+.... ....+...+.. .....+++++|||.+.....
T Consensus       100 ~~~~i~i~t~~~~~~~~~~~~~~~~~~~~vIiDE~H~~~~~~-~~~~~~~~~~~-~~~~~~~l~~SATp~~~~~~  172 (200)
T d1wp9a1         100 ARAKVIVATPQTIENDLLAGRISLEDVSLIVFDEAHRAVGNY-AYVFIAREYKR-QAKNPLVIGLTASPGSTPEK  172 (200)
T ss_dssp             HHCSEEEECHHHHHHHHHTTSCCTTSCSEEEEETGGGCSTTC-HHHHHHHHHHH-HCSSCCEEEEESCSCSSHHH
T ss_pred             hcccccccccchhHHHHhhhhhhccccceEEEEehhhhhcch-hHHHHHHHHHh-cCCCCcEEEEEecCCCcHHH
Confidence            457899999999999999888889999999999999987665 33333333333 34678899999997644333

>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=98.86  E-value=1.7e-09  Score=74.24  Aligned_cols=41  Identities=27%  Similarity=0.243  Sum_probs=39.3

Q ss_pred             CCCCEEEEeCCchHHHHHHHHhhhCCCceEeeecCCCcccc
Q 030396          137 LNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQV  177 (178)
Q Consensus       137 ~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~~~~~~R  177 (178)
                      ...++||||+|++.|+.++..|.+.|+++..+||+|++.+|
T Consensus        30 ~g~r~lvfc~t~~~~~~l~~~L~~~Gi~a~~~Hg~~~~~eR   70 (174)
T d1c4oa2          30 RGERTLVTVLTVRMAEELTSFLVEHGIRARYLHHELDAFKR   70 (174)
T ss_dssp             TTCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTCCHHHH
T ss_pred             cCCcEEEEEcchhHHHHHHHHHHhcCCceEEEecccchHHH
Confidence            46799999999999999999999999999999999999987

>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=98.81  E-value=1.8e-09  Score=71.59  Aligned_cols=45  Identities=24%  Similarity=0.220  Sum_probs=41.3

Q ss_pred             HHhcCCCCEEEEeCCchHHHHHHHHhhhCCCceEeeecCCCcccc
Q 030396          133 FAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQV  177 (178)
Q Consensus       133 l~~~~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~~~~~~R  177 (178)
                      ++....+++||||||++.|+.+++.|.+.|+++..+||+|++++|
T Consensus        30 l~~~~~~k~IVFc~t~~~ae~la~~L~~~G~~~~~~H~~~~~~~~   74 (138)
T d1jr6a_          30 LEVIKGGRHLIFCHSKKKCDELAAKLVALGINAVAYYRGLDVSVI   74 (138)
T ss_dssp             HHHHTTSCEEEECSCHHHHHHHHHHHHHHTCEEEEECTTCCSCCC
T ss_pred             HhhcCCCCEEEEeCcHHHHHHHHHHHhccccchhhhhccchhhhh
Confidence            345567899999999999999999999999999999999999886

>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=98.69  E-value=1.1e-08  Score=70.70  Aligned_cols=41  Identities=22%  Similarity=0.274  Sum_probs=39.1

Q ss_pred             CCCCEEEEeCCchHHHHHHHHhhhCCCceEeeecCCCcccc
Q 030396          137 LNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQV  177 (178)
Q Consensus       137 ~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~~~~~~R  177 (178)
                      ...++||||+|+++++.++..|.+.|+++..+||+|++++|
T Consensus        30 ~~~~~iif~~~~~~~~~~~~~l~~~g~~~~~~hg~~~~~eR   70 (181)
T d1t5la2          30 RNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLER   70 (181)
T ss_dssp             TTCEEEEECSSHHHHHHHHHHHHTTTCCEEEECSSCCHHHH
T ss_pred             cCCeEEEEeehhhhhHHHHHHHHhCCcceeEecCCccHHHH
Confidence            46789999999999999999999999999999999999988

>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=98.42  E-value=7e-08  Score=70.81  Aligned_cols=40  Identities=28%  Similarity=0.279  Sum_probs=38.2

Q ss_pred             CCCEEEEeCCchHHHHHHHHhhhCCCceEeeecCCCcccc
Q 030396          138 NPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQV  177 (178)
Q Consensus       138 ~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~~~~~~R  177 (178)
                      .+++||||||++.|+.++..|.+.|+++..+||+|+++.|
T Consensus        36 ggk~LVFcnSR~~aE~La~~L~~~Gi~a~~~Hgglsq~~R   75 (299)
T d1a1va2          36 GGRHLIFCHSKKKCDELAAKLVALGINAVAYYRGLDVSVI   75 (299)
T ss_dssp             SSEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCGGGS
T ss_pred             CCCEEEECCcHHHHHHHHHHHHHCCCCEEEEeCCchHHHH
Confidence            6789999999999999999999999999999999999876

>d1yksa1 c.37.1.14 (A:185-324) YFV helicase domain {Yellow fever virus [TaxId: 11089]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: YFV helicase domain
species: Yellow fever virus [TaxId: 11089]

Probab=98.27  E-value=5.1e-07  Score=58.60  Aligned_cols=65  Identities=17%  Similarity=0.060  Sum_probs=42.5

Q ss_pred             CCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccC-CChhhHHHHHhhCCCCCceEEEEeecCc
Q 030396           15 SCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVG-NLLKHIDPVVKACSNPSIVRSLFSATLP   83 (178)
Q Consensus        15 ~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~-~~~~~i~~i~~~~~~~~~q~i~~SAT~~   83 (178)
                      ...+.+.|.+.+.... .....+.+++++|+||||.+...+ ..+..+..+. .  .++.+++++|||.|
T Consensus        75 ~~~~~~~~~~~l~~~~-~~~~~~~~~~lvIiDEaH~~~~~~~~~~~~~~~~~-~--~~~~~~l~lTATPp  140 (140)
T d1yksa1          75 REVIDAMCHATLTYRM-LEPTRVVNWEVIIMDEAHFLDPASIAARGWAAHRA-R--ANESATILMTATPP  140 (140)
T ss_dssp             SCCEEEEEHHHHHHHH-TSSSCCCCCSEEEETTTTCCSHHHHHHHHHHHHHH-H--TTSCEEEEECSSCT
T ss_pred             ccchhhhhHHHHHHHH-hccccccceeEEEEccccccChhhHHHHHHHHHHh-h--CCCCCEEEEEcCCC
Confidence            3457777777765543 344567889999999999874443 1112222222 2  35799999999987

>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=97.83  E-value=4e-06  Score=58.46  Aligned_cols=51  Identities=22%  Similarity=0.144  Sum_probs=39.8

Q ss_pred             HHHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhhhCC------------------------------CceEeeecCCCc
Q 030396          125 KLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDD------------------------------IRAGVIHSDLSQ  174 (178)
Q Consensus       125 k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~~~g------------------------------~~~~~lh~~~~~  174 (178)
                      ....+.+.+++.  .++||||+|++.|+.+|..|....                              .-++++||+|++
T Consensus        29 ~~~l~~~~i~~~--~~~LVF~~sRk~~~~~A~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~GIa~hh~~l~~  106 (201)
T d2p6ra4          29 FEELVEECVAEN--GGVLVFESTRRGAEKTAVKLSAITAKYVENEGLEKAILEENEGEMSRKLAECVRKGAAFHHAGLLN  106 (201)
T ss_dssp             HHHHHHHHHHTT--CCEEEECSSHHHHHHHHHHHHHHHHTTCCCSSHHHHHHTTCCSHHHHHHHHHHHTTCCEECTTSCH
T ss_pred             HHHHHHHHHHcC--CcEEEEeCCHHHHHHHHHHHHHHHHhhhchhHHHHHHHHhhhhhhhHHHHHHHhccHHHHHHHhhh
Confidence            445666666654  799999999999999998886421                              127899999999


Q ss_pred             ccc
Q 030396          175 TQV  177 (178)
Q Consensus       175 ~~R  177 (178)
                      ++|
T Consensus       107 ~~r  109 (201)
T d2p6ra4         107 GQR  109 (201)
T ss_dssp             HHH
T ss_pred             hhH
Confidence            887

>d1a1va1 c.37.1.14 (A:190-325) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: HCV helicase domain
species: Human hepatitis C virus (HCV), different isolates [TaxId: 11103]

Probab=97.80  E-value=1.6e-05  Score=51.44  Aligned_cols=62  Identities=16%  Similarity=0.091  Sum_probs=41.4

Q ss_pred             CCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhC-CCCCceEEEEeec
Q 030396           15 SCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKAC-SNPSIVRSLFSAT   81 (178)
Q Consensus        15 ~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~-~~~~~q~i~~SAT   81 (178)
                      ...++++|++.....   ....+.+++++|+||+|.+-...  ...+..+++.+ ...+..++++|||
T Consensus        73 ~~~~~~~~~~~~~~~---~~~~~~~~~~vIiDE~H~~~~~~--~~~~~~~l~~~~~~~~~~~l~~TAT  135 (136)
T d1a1va1          73 GSPITYSTYGKFLAD---GGCSGGAYDIIICDECHSTDATS--ILGIGTVLDQAETAGARLVVLATAT  135 (136)
T ss_dssp             CCSEEEEEHHHHHHT---TGGGGCCCSEEEEETTTCCSHHH--HHHHHHHHHHTTTTTCSEEEEEESS
T ss_pred             ccceEEEeeeeeccc---cchhhhcCCEEEEecccccCHHH--HHHHHHHHHHHHHCCCCcEEEEeCC
Confidence            456888888765433   33356788999999999874332  34455555552 2356678899998

>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=97.69  E-value=1.6e-05  Score=58.14  Aligned_cols=63  Identities=17%  Similarity=0.105  Sum_probs=45.2

Q ss_pred             CCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcHH
Q 030396           14 FSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDF   85 (178)
Q Consensus        14 ~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~   85 (178)
                      ....|+|+|++.+....   ...+++.+++|+||||.+-     .+.+..|+.. .......+.+|||++..
T Consensus       203 ~~~~i~i~t~qs~~~~~---~~~~~~f~~VIvDEaH~~~-----a~~~~~il~~-~~~~~~rlGlTaT~~~~  265 (282)
T d1rifa_         203 NDAPVVVGTWQTVVKQP---KEWFSQFGMMMNDECHLAT-----GKSISSIISG-LNNCMFKFGLSGSLRDG  265 (282)
T ss_dssp             TTCSEEEECHHHHTTSC---GGGGGGEEEEEEETGGGCC-----HHHHHHHTTT-CTTCCEEEEECSSCCTT
T ss_pred             ccceEEEEeeehhhhhc---ccccCCCCEEEEECCCCCC-----chhHHHHHHh-ccCCCeEEEEEeecCCC
Confidence            34679999998754332   2345688999999999873     4557888887 44344458999998653

>d2fz4a1 c.37.1.19 (A:24-229) DNA repair protein RAD25 {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DNA repair protein RAD25
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=97.52  E-value=0.00011  Score=51.03  Aligned_cols=60  Identities=18%  Similarity=0.077  Sum_probs=41.6

Q ss_pred             CCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCc
Q 030396           14 FSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLP   83 (178)
Q Consensus        14 ~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~   83 (178)
                      ....|+|+|...+......-   ..+.+++|+||||.+-..     .+..++.. .+ ....+++|||+.
T Consensus       147 ~~~~i~i~t~~~~~~~~~~~---~~~~~lvIiDEaH~~~a~-----~~~~i~~~-~~-~~~~lgLTATl~  206 (206)
T d2fz4a1         147 ELKPLTVSTYDSAYVNAEKL---GNRFMLLIFDEVHHLPAE-----SYVQIAQM-SI-APFRLGLTATFE  206 (206)
T ss_dssp             CCCSEEEEEHHHHHHTHHHH---TTTCSEEEEECSSCCCTT-----THHHHHHT-CC-CSEEEEEEESCC
T ss_pred             cccccccceehhhhhhhHhh---CCcCCEEEEECCeeCCcH-----HHHHHHhc-cC-CCcEEEEecCCC
Confidence            34579999998877654431   245679999999998433     36677776 33 445688999973

>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=97.47  E-value=2.4e-05  Score=54.09  Aligned_cols=50  Identities=14%  Similarity=0.219  Sum_probs=43.9

Q ss_pred             hhHHHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhhhCCCceEeeecCCCcccc
Q 030396          123 EGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQV  177 (178)
Q Consensus       123 ~~k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~~~~~~R  177 (178)
                      ..|+..+.++++.....++||||++...++.+++.|.     +..+||++++++|
T Consensus        78 ~~K~~~l~~ll~~~~~~k~lvf~~~~~~~~~l~~~l~-----~~~i~g~~~~~~R  127 (200)
T d2fwra1          78 KNKIRKLREILERHRKDKIIIFTRHNELVYRISKVFL-----IPAITHRTSREER  127 (200)
T ss_dssp             SHHHHHHHHHHHHTSSSCBCCBCSCHHHHHHHHHHTT-----CCBCCSSSCSHHH
T ss_pred             HHHHHHHHHHHHhCCCCcEEEEeCcHHHHHHHHhhcC-----cceeeCCCCHHHH
Confidence            3689999999999888899999999999999998873     4568999999887

>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=97.33  E-value=0.00023  Score=51.64  Aligned_cols=50  Identities=24%  Similarity=0.367  Sum_probs=41.2

Q ss_pred             hHHHHHHHHHH----hcCCCCEEEEeCCchHHHHHHHHhhhCCCceEeeecCCC
Q 030396          124 GKLLALRQSFA----ESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLS  173 (178)
Q Consensus       124 ~k~~~l~~ll~----~~~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~~~  173 (178)
                      .|...+.+++.    .....++||||+++..|+.+++.|.+.|+++..+||..+
T Consensus       143 pK~~~l~~~l~~~~~~~~~~k~iiF~~~~~~~~~~~~~L~~~~~~~~~~~g~~~  196 (286)
T d1wp9a2         143 PKMDKLKEIIREQLQRKQNSKIIVFTNYRETAKKIVNELVKDGIKAKRFVGQAS  196 (286)
T ss_dssp             HHHHHHHHHHHHHHHHCTTCCEEEECSCHHHHHHHHHHHHHTTCCEEEECCSSC
T ss_pred             cHHHHHHHHHHHHHHhCCCCcEEEEeCcHHhHHHHHHHHHHcCCceEEeecccc
Confidence            46666665554    456789999999999999999999999999999988544

>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=97.16  E-value=0.00023  Score=50.58  Aligned_cols=56  Identities=18%  Similarity=0.249  Sum_probs=47.8

Q ss_pred             hhhHHHHHHHHHHh--cCCCCEEEEeCCchHHHHHHHHhhhC-CCceEeeecCCCcccc
Q 030396          122 EEGKLLALRQSFAE--SLNPPVLIFVQSKDRAKELYGELAFD-DIRAGVIHSDLSQTQV  177 (178)
Q Consensus       122 ~~~k~~~l~~ll~~--~~~~~~lIF~~t~~~~~~l~~~L~~~-g~~~~~lh~~~~~~~R  177 (178)
                      .+.|+..+.+++..  ....++||||+.....+.+...|... |+++..+||+++..+|
T Consensus        67 ~S~K~~~l~~~l~~~~~~g~kviIFs~~~~~~~~l~~~l~~~~~~~~~~i~G~~~~~~R  125 (244)
T d1z5za1          67 RSGKMIRTMEIIEEALDEGDKIAIFTQFVDMGKIIRNIIEKELNTEVPFLYGELSKKER  125 (244)
T ss_dssp             TCHHHHHHHHHHHHHHHTTCCEEEEESCHHHHHHHHHHHHHHHCSCCCEECTTSCHHHH
T ss_pred             hhhHHHHHHHHHHhhcccccceEEEeeceehHHHHHHHHHhhccceEEEEecccchhcc
Confidence            34689999999874  35779999999999999999999654 8999999999999876

>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=97.15  E-value=0.0002  Score=52.55  Aligned_cols=40  Identities=15%  Similarity=0.127  Sum_probs=35.6

Q ss_pred             CCCEEEEeCCchHHHHHHHHhhhCCCceEeeecCCCcccc
Q 030396          138 NPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQV  177 (178)
Q Consensus       138 ~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~~~~~~R  177 (178)
                      .++++|||++..+++.++..|...|+++..+||.+..+++
T Consensus        36 ~g~~~~F~~s~~~~~~~a~~L~~~g~~V~~l~~~~~~~e~   75 (299)
T d1yksa2          36 KRPTAWFLPSIRAANVMAASLRKAGKSVVVLNRKTFEREY   75 (299)
T ss_dssp             CSCEEEECSCHHHHHHHHHHHHHTTCCEEECCSSSCC---
T ss_pred             CCCEEEEeCCHHHHHHHHHHHHhcCCeEEEEcCcCcHhHH
Confidence            6899999999999999999999999999999999887653

>d1gm5a3 c.37.1.19 (A:286-549) RecG helicase domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecG helicase domain
species: Thermotoga maritima [TaxId: 2336]

Probab=96.97  E-value=0.00032  Score=50.49  Aligned_cols=61  Identities=15%  Similarity=0.167  Sum_probs=40.2

Q ss_pred             cCCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcHH
Q 030396           13 KFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDF   85 (178)
Q Consensus        13 ~~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~   85 (178)
                      ++.++|||||--    ++. ..+.++++.++|+||-|...-.+  +.    .+.+ ...+..++++|||-.+.
T Consensus       184 ~g~~~iiIGThs----l~~-~~~~f~~LglviiDEqH~fgv~Q--r~----~l~~-~~~~~~~l~~SATPipr  244 (264)
T d1gm5a3         184 NGQIDVVIGTHA----LIQ-EDVHFKNLGLVIIDEQHRFGVKQ--RE----ALMN-KGKMVDTLVMSATPIPR  244 (264)
T ss_dssp             SSCCCEEEECTT----HHH-HCCCCSCCCEEEEESCCCC-------C----CCCS-SSSCCCEEEEESSCCCH
T ss_pred             CCCCCEEEeehH----Hhc-CCCCccccceeeeccccccchhh--HH----HHHH-hCcCCCEEEEECCCCHH
Confidence            357999999983    333 33457789999999999984433  11    1222 33567899999996554

>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=96.89  E-value=0.0018  Score=45.60  Aligned_cols=64  Identities=22%  Similarity=0.267  Sum_probs=44.6

Q ss_pred             hccCCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcHHH
Q 030396           11 LSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFV   86 (178)
Q Consensus        11 ~l~~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~~~   86 (178)
                      ..++.++|||||---+    . ..+.++++.++|+||-|..--     .+-+. ++. ...+..++++|||-.+.-
T Consensus       154 ~~~g~~~iviGths~l----~-~~~~f~~LgLiIiDEeH~fg~-----kQ~~~-l~~-~~~~~~~l~~SATPiprt  217 (233)
T d2eyqa3         154 VAEGKIDILIGTHKLL----Q-SDVKFKDLGLLIVDEEHRFGV-----RHKER-IKA-MRANVDILTLTATPIPRT  217 (233)
T ss_dssp             HHTTCCSEEEECTHHH----H-SCCCCSSEEEEEEESGGGSCH-----HHHHH-HHH-HHTTSEEEEEESSCCCHH
T ss_pred             HhCCCCCEEEeehhhh----c-cCCccccccceeeechhhhhh-----HHHHH-HHh-hCCCCCEEEEecchhHHH
Confidence            3446799999998432    2 446688999999999998622     22222 333 346788999999987653

>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=96.78  E-value=0.00071  Score=50.59  Aligned_cols=55  Identities=13%  Similarity=0.051  Sum_probs=48.2

Q ss_pred             hhHHHHHHHHHHh---cCCCCEEEEeCCchHHHHHHHHhhhCCCceEeeecCCCcccc
Q 030396          123 EGKLLALRQSFAE---SLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLSQTQV  177 (178)
Q Consensus       123 ~~k~~~l~~ll~~---~~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~~~~~~R  177 (178)
                      ..|+..|.+++..   ....|+|||++.....+.+...|...|+++..++|+++..+|
T Consensus       100 S~Kl~~L~~ll~~~~~~~g~KvlIFs~~~~~ld~l~~~l~~~g~~~~~l~G~~~~~~R  157 (346)
T d1z3ix1         100 SGKMLVLDYILAMTRTTTSDKVVLVSNYTQTLDLFEKLCRNRRYLYVRLDGTMSIKKR  157 (346)
T ss_dssp             SHHHHHHHHHHHHHHHHCCCEEEEEESCHHHHHHHHHHHHHHTCCEEEECSSCCHHHH
T ss_pred             CHHHHHHHHHHHHHHHhcCCceeEEeehhhhhHHHHHHHhhhhccccccccchhHHHH
Confidence            4688888887763   446799999999999999999999999999999999998876

>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=96.48  E-value=0.0028  Score=42.43  Aligned_cols=52  Identities=21%  Similarity=0.249  Sum_probs=43.8

Q ss_pred             ChhhHHHHHHHHHHh--cCCCCEEEEeCCchHHHHHHHHhhhCCCceEeeecCC
Q 030396          121 SEEGKLLALRQSFAE--SLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDL  172 (178)
Q Consensus       121 ~~~~k~~~l~~ll~~--~~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~~  172 (178)
                      ....|.+.+.+.+..  ...+|+||+|.|.+.++.++..|.+.|++...+++..
T Consensus        15 T~~eK~~AIi~eV~~~~~~grPVLIgT~SIe~SE~ls~~L~~~gi~h~vLnAk~   68 (175)
T d1tf5a4          15 TMEGKFKAVAEDVAQRYMTGQPVLVGTVAVETSELISKLLKNKGIPHQVLNAKN   68 (175)
T ss_dssp             SHHHHHHHHHHHHHHHHHHTCCEEEEESCHHHHHHHHHHHHTTTCCCEEECSSC
T ss_pred             CHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHcCCCceeehhhh
Confidence            566788888777753  2378999999999999999999999999998888754

>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=95.58  E-value=0.0019  Score=45.66  Aligned_cols=39  Identities=15%  Similarity=0.329  Sum_probs=33.5

Q ss_pred             hhhHHHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhhhC
Q 030396          122 EEGKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFD  161 (178)
Q Consensus       122 ~~~k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~~~  161 (178)
                      .++|...|..+++.. ..++||||+|++.|+.++++|...
T Consensus        10 ~~~~~~~l~~~l~~~-~~~~iif~~~~~~~~~l~~~l~~~   48 (248)
T d1gkub2          10 NDESISTLSSILEKL-GTGGIIYARTGEEAEEIYESLKNK   48 (248)
T ss_dssp             SCCCTTTTHHHHTTS-CSCEEEEESSHHHHHHHHHTTTTS
T ss_pred             CchHHHHHHHHHHHh-CCCEEEEECCHHHHHHHHHHHHHh
Confidence            356888999999876 468999999999999999999754

>d1yt8a4 c.46.1.2 (A:243-372) Thiosulfate sulfurtransferase PA2603 {Pseudomonas aeruginosa [TaxId: 287]}

class: Alpha and beta proteins (a/b)
fold: Rhodanese/Cell cycle control phosphatase
superfamily: Rhodanese/Cell cycle control phosphatase
family: Multidomain sulfurtransferase (rhodanese)
domain: Thiosulfate sulfurtransferase PA2603
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=95.32  E-value=0.01  Score=37.57  Aligned_cols=41  Identities=15%  Similarity=0.005  Sum_probs=35.9

Q ss_pred             HHhcCCCCEEEEeCCchHHHHHHHHhhhCCCceEeeecCCC
Q 030396          133 FAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSDLS  173 (178)
Q Consensus       133 l~~~~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~~~  173 (178)
                      +.....+++++||++-.++...+..|.+.||++..+.||+.
T Consensus        75 ~~~~~~~~ivl~C~~G~rS~~aa~~L~~~G~~v~~l~GG~~  115 (130)
T d1yt8a4          75 VASVRGARLVLVDDDGVRANMSASWLAQMGWQVAVLDGLSE  115 (130)
T ss_dssp             HCCSBTCEEEEECSSSSHHHHHHHHHHHTTCEEEEECSCCG
T ss_pred             ccCCccceEEeecCCCccHHHHHHHHHHcCCCeEEEcCchH
Confidence            44445678999999999999999999999999999999975

>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=94.74  E-value=0.046  Score=39.24  Aligned_cols=62  Identities=21%  Similarity=0.214  Sum_probs=38.2

Q ss_pred             CCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCc
Q 030396           15 SCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLP   83 (178)
Q Consensus        15 ~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~   83 (178)
                      ..+++|+|.+.+.....  .+.-.+.+++|+||+|.+-+.+   ......+.. + .....+++|||--
T Consensus       170 ~~~v~i~sy~~~~~~~~--~l~~~~~~~vI~DEaH~ikn~~---s~~~~a~~~-l-~~~~rllLTGTPi  231 (298)
T d1z3ix2         170 PTPILIISYETFRLHAE--VLHKGKVGLVICDEGHRLKNSD---NQTYLALNS-M-NAQRRVLISGTPI  231 (298)
T ss_dssp             SCCEEEEEHHHHHHHTT--TTTTSCCCEEEETTGGGCCTTC---HHHHHHHHH-H-CCSEEEEECSSCS
T ss_pred             cceEEEEeecccccchh--cccccceeeeeccccccccccc---chhhhhhhc-c-ccceeeeecchHH
Confidence            35688888876654332  2222345689999999996544   233333444 2 2345688999974

>d1tq1a_ c.46.1.3 (A:) Thiosulfate sulfurtransferase/Senescence-associated protein {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Alpha and beta proteins (a/b)
fold: Rhodanese/Cell cycle control phosphatase
superfamily: Rhodanese/Cell cycle control phosphatase
family: Single-domain sulfurtransferase
domain: Thiosulfate sulfurtransferase/Senescence-associated protein
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=94.64  E-value=0.011  Score=36.65  Aligned_cols=37  Identities=16%  Similarity=0.111  Sum_probs=33.1

Q ss_pred             CCCCEEEEeCCchHHHHHHHHhhhCCC-ceEeeecCCC
Q 030396          137 LNPPVLIFVQSKDRAKELYGELAFDDI-RAGVIHSDLS  173 (178)
Q Consensus       137 ~~~~~lIF~~t~~~~~~l~~~L~~~g~-~~~~lh~~~~  173 (178)
                      +..++++||++-.++...+..|.+.|| ++..+.||+.
T Consensus        71 ~~~~iv~~C~~G~rs~~a~~~L~~~G~~nv~~l~GG~~  108 (119)
T d1tq1a_          71 QSDNIIVGCQSGGRSIKATTDLLHAGFTGVKDIVGGYS  108 (119)
T ss_dssp             TTSSEEEEESSCSHHHHHHHHHHHHHCCSEEEEECCHH
T ss_pred             CCcEEEEEcCCcCcHHHHHHHHHhcccCCeEEecChHH
Confidence            457899999999999999999999999 6999999874

>d1z63a1 c.37.1.19 (A:432-661) Helicase of the SNF2/Rad54 hamily {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Helicase of the SNF2/Rad54 hamily
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=94.44  E-value=0.013  Score=40.54  Aligned_cols=62  Identities=27%  Similarity=0.248  Sum_probs=39.0

Q ss_pred             CCCcEEEeCcHHHHHHHHcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCc
Q 030396           14 FSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLP   83 (178)
Q Consensus        14 ~~~~Iii~TP~~l~~~l~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~   83 (178)
                      ...+|+++|.+.+...-.-..   -.-.++|+||+|.+-+..   ......+.. +. ....+++|||--
T Consensus       102 ~~~~vvi~~~~~~~~~~~l~~---~~~~~vI~DEah~~k~~~---s~~~~~~~~-l~-a~~r~~LTgTPi  163 (230)
T d1z63a1         102 EDYDIILTTYAVLLRDTRLKE---VEWKYIVIDEAQNIKNPQ---TKIFKAVKE-LK-SKYRIALTGTPI  163 (230)
T ss_dssp             GGSSEEEEEHHHHTTCHHHHT---CCEEEEEEETGGGGSCTT---SHHHHHHHT-SC-EEEEEEECSSCS
T ss_pred             cCcCEEEeeHHHHHhHHHHhc---ccceEEEEEhhhcccccc---hhhhhhhhh-hc-cceEEEEecchH
Confidence            346899999987654322111   234689999999997655   222333444 33 345688899964

>d1qxna_ c.46.1.3 (A:) Polysulfide-sulfur transferase (sulfide dehydrogenase, Sud) {Wolinella succinogenes [TaxId: 844]}

class: Alpha and beta proteins (a/b)
fold: Rhodanese/Cell cycle control phosphatase
superfamily: Rhodanese/Cell cycle control phosphatase
family: Single-domain sulfurtransferase
domain: Polysulfide-sulfur transferase (sulfide dehydrogenase, Sud)
species: Wolinella succinogenes [TaxId: 844]

Probab=93.83  E-value=0.031  Score=35.56  Aligned_cols=39  Identities=15%  Similarity=0.100  Sum_probs=33.9

Q ss_pred             hcCCCCEEEEeCCchHHHHHHHHhhhCCC-ceEeeecCCC
Q 030396          135 ESLNPPVLIFVQSKDRAKELYGELAFDDI-RAGVIHSDLS  173 (178)
Q Consensus       135 ~~~~~~~lIF~~t~~~~~~l~~~L~~~g~-~~~~lh~~~~  173 (178)
                      ..+..++++||++-.++...+..|.+.|| ++..+.||+.
T Consensus        79 ~~~~~~ivvyC~~G~rs~~aa~~L~~~G~~nV~~l~GG~~  118 (137)
T d1qxna_          79 LDPEKPVVVFCKTAARAALAGKTLREYGFKTIYNSEGGMD  118 (137)
T ss_dssp             CCTTSCEEEECCSSSCHHHHHHHHHHHTCSCEEEESSCHH
T ss_pred             cCcccceeeeecccchHHHHHHHHHHcCCCcEEEecCHHH
Confidence            34567899999999999999999999999 6888999863

>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=93.56  E-value=0.081  Score=36.17  Aligned_cols=41  Identities=12%  Similarity=0.156  Sum_probs=36.1

Q ss_pred             CCCCEEEEeCCchHHHHHHHHhhhC--CCceEeeecCCCcccc
Q 030396          137 LNPPVLIFVQSKDRAKELYGELAFD--DIRAGVIHSDLSQTQV  177 (178)
Q Consensus       137 ~~~~~lIF~~t~~~~~~l~~~L~~~--g~~~~~lh~~~~~~~R  177 (178)
                      ..+|+-+.||..+..+.+++.+.+.  ++++..+||.|+.+++
T Consensus        30 rGgQvy~V~p~I~~~e~~~~~l~~~~p~~~i~~lHGkm~~~ek   72 (211)
T d2eyqa5          30 RGGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMREREL   72 (211)
T ss_dssp             TTCEEEEECCCSSCHHHHHHHHHHHCTTSCEEECCSSCCHHHH
T ss_pred             cCCeEEEEEcCccchhhHHHHHHHhCCceEEEEEEeccCHHHH
Confidence            4689999999999999999999764  7899999999998764

>d1gmxa_ c.46.1.3 (A:) Sulfurtransferase GlpE {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Rhodanese/Cell cycle control phosphatase
superfamily: Rhodanese/Cell cycle control phosphatase
family: Single-domain sulfurtransferase
domain: Sulfurtransferase GlpE
species: Escherichia coli [TaxId: 562]

Probab=93.40  E-value=0.022  Score=34.60  Aligned_cols=44  Identities=11%  Similarity=0.147  Sum_probs=35.5

Q ss_pred             HHHHHh-cCCCCEEEEeCCchHHHHHHHHhhhCCC-ceEeeecCCC
Q 030396          130 RQSFAE-SLNPPVLIFVQSKDRAKELYGELAFDDI-RAGVIHSDLS  173 (178)
Q Consensus       130 ~~ll~~-~~~~~~lIF~~t~~~~~~l~~~L~~~g~-~~~~lh~~~~  173 (178)
                      ...+.. .+..++++||++-.++...+..|.+.|+ ++..+.||+.
T Consensus        49 ~~~~~~~~~~~~ivv~c~~g~rs~~~a~~L~~~G~~~v~~l~GG~~   94 (108)
T d1gmxa_          49 GAFMRDNDFDTPVMVMCYHGNSSKGAAQYLLQQGYDVVYSIDGGFE   94 (108)
T ss_dssp             HHHHHHSCTTSCEEEECSSSSHHHHHHHHHHHHTCSSEEEETTHHH
T ss_pred             HHHhhhccccCcccccCCCChHHHHHHHHHHHcCCCCEEEEcChHH
Confidence            333433 3467899999999999999999999999 5888998864

>d1urha2 c.46.1.2 (A:149-268) 3-mercaptopyruvate sulfurtransferase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Rhodanese/Cell cycle control phosphatase
superfamily: Rhodanese/Cell cycle control phosphatase
family: Multidomain sulfurtransferase (rhodanese)
domain: 3-mercaptopyruvate sulfurtransferase
species: Escherichia coli [TaxId: 562]

Probab=93.37  E-value=0.078  Score=32.43  Aligned_cols=39  Identities=21%  Similarity=0.209  Sum_probs=33.8

Q ss_pred             cCCCCEEEEeCCchHHHHHHHHhhhCCC-ceEeeecCCCc
Q 030396          136 SLNPPVLIFVQSKDRAKELYGELAFDDI-RAGVIHSDLSQ  174 (178)
Q Consensus       136 ~~~~~~lIF~~t~~~~~~l~~~L~~~g~-~~~~lh~~~~~  174 (178)
                      ....++|+||+|=.+|-..+..|...|+ ++..+.|++..
T Consensus        80 ~~~~~ii~yC~sG~~A~~~~~~L~~lG~~~v~~y~Gs~~e  119 (120)
T d1urha2          80 SYDKPIIVSCGSGVTAAVVLLALATLDVPNVKLYDGAWSE  119 (120)
T ss_dssp             CSSSCEEEECCSSSTHHHHHHHHHHTTCSSCEEECCSCCC
T ss_pred             CccCceEEEccchhHHHHHHHHHHHcCCCCceEcCCChhh
Confidence            3467899999999999999999999999 59999999863

>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=92.91  E-value=0.16  Score=34.58  Aligned_cols=51  Identities=29%  Similarity=0.384  Sum_probs=43.3

Q ss_pred             ChhhHHHHHHHHHHh--cCCCCEEEEeCCchHHHHHHHHhhhCCCceEeeecC
Q 030396          121 SEEGKLLALRQSFAE--SLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHSD  171 (178)
Q Consensus       121 ~~~~k~~~l~~ll~~--~~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~~  171 (178)
                      ....|...+.+-+..  ...+|+||.+.|++..+.++..|.+.|++...+++.
T Consensus        15 T~~~K~~Avv~ei~~~h~~GqPVLVGT~SVe~SE~lS~lL~~~gi~h~vLNAK   67 (219)
T d1nkta4          15 TEEAKYIAVVDDVAERYAKGQPVLIGTTSVERSEYLSRQFTKRRIPHNVLNAK   67 (219)
T ss_dssp             CHHHHHHHHHHHHHHHHHTTCCEEEEESCHHHHHHHHHHHHHTTCCCEEECSS
T ss_pred             CHHHHHHHHHHHHHHHHhcCCCEEEeeCcHHHHHHHHHHHHHhccchhccchh
Confidence            556788888777763  347899999999999999999999999999988874

>d1yt8a1 c.46.1.2 (A:107-242) Thiosulfate sulfurtransferase PA2603 {Pseudomonas aeruginosa [TaxId: 287]}

class: Alpha and beta proteins (a/b)
fold: Rhodanese/Cell cycle control phosphatase
superfamily: Rhodanese/Cell cycle control phosphatase
family: Multidomain sulfurtransferase (rhodanese)
domain: Thiosulfate sulfurtransferase PA2603
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=92.74  E-value=0.059  Score=34.11  Aligned_cols=38  Identities=11%  Similarity=0.049  Sum_probs=32.4

Q ss_pred             cCCCCEEEEeCCchHHHHHHHHhhhCCC--ceEeeecCCC
Q 030396          136 SLNPPVLIFVQSKDRAKELYGELAFDDI--RAGVIHSDLS  173 (178)
Q Consensus       136 ~~~~~~lIF~~t~~~~~~l~~~L~~~g~--~~~~lh~~~~  173 (178)
                      .+..++++||.+-.++...+..|...|+  .+..+.||+.
T Consensus        78 ~~~~~iV~~C~~g~rs~~aa~~L~~~G~~~~V~~L~GG~~  117 (136)
T d1yt8a1          78 DPRTRVIVNCAGRTRSIIGTQSLLNAGIPNPVAALRNGTI  117 (136)
T ss_dssp             STTSEEEEECSSSHHHHHHHHHHHHTTCSSCEEEETTHHH
T ss_pred             cccceEEEEcCCCCchHHHHHHHHHcCCCceEEEeCCcHH
Confidence            3456799999999999999999999999  3788998863

>d1yt8a2 c.46.1.2 (A:6-106) Thiosulfate sulfurtransferase PA2603 {Pseudomonas aeruginosa [TaxId: 287]}

class: Alpha and beta proteins (a/b)
fold: Rhodanese/Cell cycle control phosphatase
superfamily: Rhodanese/Cell cycle control phosphatase
family: Multidomain sulfurtransferase (rhodanese)
domain: Thiosulfate sulfurtransferase PA2603
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=92.37  E-value=0.089  Score=31.12  Aligned_cols=39  Identities=13%  Similarity=0.143  Sum_probs=33.4

Q ss_pred             hcCCCCEEEEeCCchHHHHHHHHhhhCCC-ceEeeecCCC
Q 030396          135 ESLNPPVLIFVQSKDRAKELYGELAFDDI-RAGVIHSDLS  173 (178)
Q Consensus       135 ~~~~~~~lIF~~t~~~~~~l~~~L~~~g~-~~~~lh~~~~  173 (178)
                      .....+++++|++-.++...+..|.+.|+ ++..+.||+.
T Consensus        55 ~~~~~~vv~~~~~g~~s~~~~~~l~~~G~~nV~~l~GG~~   94 (101)
T d1yt8a2          55 PRRDTPITVYDDGEGLAPVAAQRLHDLGYSDVALLDGGLS   94 (101)
T ss_dssp             CCTTSCEEEECSSSSHHHHHHHHHHHTTCSSEEEETTHHH
T ss_pred             cccCceeeeccchhhhHHHHHHHHHHcCCCcEEEeCChHH
Confidence            34467899999999999999999999999 5888888864

>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=91.02  E-value=0.13  Score=31.55  Aligned_cols=46  Identities=30%  Similarity=0.247  Sum_probs=36.8

Q ss_pred             hHHHHHHHHHHhcCCCCEEEEeCCchHHHHHHHHhhhCCCceEeeec
Q 030396          124 GKLLALRQSFAESLNPPVLIFVQSKDRAKELYGELAFDDIRAGVIHS  170 (178)
Q Consensus       124 ~k~~~l~~ll~~~~~~~~lIF~~t~~~~~~l~~~L~~~g~~~~~lh~  170 (178)
                      +-+..|..+++.. ..++||.|.|..+++.+.+.|.+.|+++..+.+
T Consensus        21 ~p~~~L~~~i~~~-~~~Vli~a~s~g~~erl~e~L~~~~i~~~~~~~   66 (117)
T d2eyqa2          21 APLDALRKFLETF-DGPVVFSVESEGRREALGELLARIKIAPQRIMR   66 (117)
T ss_dssp             STTHHHHHHHTTC-CSCCCEEESSHHHHHHHHHHHGGGTCCCEECSS
T ss_pred             cHHHHHHHHHHhC-CCeEEEEECCccHHHHHHHHHHHcCCCceEecC
Confidence            3456677777765 568999999999999999999999987766544

>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=90.46  E-value=0.39  Score=32.15  Aligned_cols=65  Identities=12%  Similarity=0.178  Sum_probs=43.2

Q ss_pred             CCCcEEEeCcHH-------HHHHH---HcCCCCCCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecC
Q 030396           14 FSCDILISTPLR-------LRLAI---RRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATL   82 (178)
Q Consensus        14 ~~~~Iii~TP~~-------l~~~l---~~~~~~~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~   82 (178)
                      +-||++.-.|+.       +.++.   .... ..+.-+.+|+||||.|-..+  ...+..++.. .+.+..++++|...
T Consensus        45 ~h~D~~~i~~~~~~I~Id~IR~i~~~~~~~~-~~~~~KviIId~ad~l~~~a--qNaLLK~LEE-Pp~~t~fiLit~~~  119 (198)
T d2gnoa2          45 KASDVLEIDPEGENIGIDDIRTIKDFLNYSP-ELYTRKYVIVHDCERMTQQA--ANAFLKALEE-PPEYAVIVLNTRRW  119 (198)
T ss_dssp             CTTTEEEECCSSSCBCHHHHHHHHHHHTSCC-SSSSSEEEEETTGGGBCHHH--HHHTHHHHHS-CCTTEEEEEEESCG
T ss_pred             CCCCEEEEeCCcCCCCHHHHHHHHHHHhhCc-ccCCCEEEEEeCccccchhh--hhHHHHHHhC-CCCCceeeeccCCh
Confidence            347888888842       33332   2232 23666899999999996655  6667777776 67777777765543

>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=89.87  E-value=0.081  Score=36.07  Aligned_cols=53  Identities=17%  Similarity=0.305  Sum_probs=32.3

Q ss_pred             HHHHHHHHHHh--cCCCCEEEEeCCchHHH--------HHHHHhhhC---CCceEeeecCCCcccc
Q 030396          125 KLLALRQSFAE--SLNPPVLIFVQSKDRAK--------ELYGELAFD---DIRAGVIHSDLSQTQV  177 (178)
Q Consensus       125 k~~~l~~ll~~--~~~~~~lIF~~t~~~~~--------~l~~~L~~~---g~~~~~lh~~~~~~~R  177 (178)
                      +.+.+.+.+++  ...+|+-+.|+.++..+        ...+.|.+.   ++++..+||.|++++|
T Consensus        14 ~~~~v~~~I~~el~~g~QvyvVcP~Ieese~~~~~~~~e~~~~l~~~~~p~~~v~~lHG~m~~~ek   79 (206)
T d1gm5a4          14 RVNEVYEFVRQEVMRGGQAFIVYPLIEESDKLNVKSAVEMYEYLSKEVFPEFKLGLMHGRLSQEEK   79 (206)
T ss_dssp             THHHHHHHHHHHTTTSCCBCCBCCCC--------CHHHHHHHSGGGSCC---CBCCCCSSSCCSCS
T ss_pred             cHHHHHHHHHHHHHcCCCEEEEEeeecccccccchhhHHHHHHHHHhcCCCCeEEEEeecccHHHH
Confidence            44555555553  23578888898765444        444555443   6789999999999987

>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=89.04  E-value=0.15  Score=36.13  Aligned_cols=40  Identities=25%  Similarity=0.294  Sum_probs=31.1

Q ss_pred             CCcEEEeCcHHHH-HHHHcCCC------CCCCeeEEEEecccccccc
Q 030396           15 SCDILISTPLRLR-LAIRRKKI------DLSRVEYLVLDEADKLFEV   54 (178)
Q Consensus        15 ~~~Iii~TP~~l~-~~l~~~~~------~~~~l~~lViDE~d~ll~~   54 (178)
                      .|||+.||...+. +.++.+..      -.+.+.+.|+||+|.++=+
T Consensus       169 ~~di~Ygt~~e~~fDyLrd~~~~~~~~~~~r~~~~aIvDEvDsiliD  215 (273)
T d1tf5a3         169 AADITYSTNNELGFDYLRDNMVLYKEQMVQRPLHFAVIDEVDSILID  215 (273)
T ss_dssp             HSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCCCCEEEEETHHHHHTT
T ss_pred             hCCceecchhhhhhhhcchhhhcChhhhccCCCCEEEEEcchhhhhh
Confidence            5899999999876 77765422      2577899999999997643

>d1e0ca2 c.46.1.2 (A:136-271) Sulfurtransferase {Azotobacter vinelandii [TaxId: 354]}

class: Alpha and beta proteins (a/b)
fold: Rhodanese/Cell cycle control phosphatase
superfamily: Rhodanese/Cell cycle control phosphatase
family: Multidomain sulfurtransferase (rhodanese)
domain: Sulfurtransferase
species: Azotobacter vinelandii [TaxId: 354]

Probab=87.62  E-value=0.22  Score=31.30  Aligned_cols=38  Identities=11%  Similarity=0.020  Sum_probs=32.0

Q ss_pred             cCCCCEEEEeCCchHHHHHHHHhhhCCC-ceEeeecCCC
Q 030396          136 SLNPPVLIFVQSKDRAKELYGELAFDDI-RAGVIHSDLS  173 (178)
Q Consensus       136 ~~~~~~lIF~~t~~~~~~l~~~L~~~g~-~~~~lh~~~~  173 (178)
                      ...+++++||++=.+|-..+..|...|+ ++..+.|++.
T Consensus        86 ~~~~~vV~yC~~G~~a~~~~~~l~~~G~~~v~~ydGg~~  124 (136)
T d1e0ca2          86 TPDKEIVTHCQTHHRSGLTYLIAKALGYPRVKGYAGSWG  124 (136)
T ss_dssp             CTTSEEEEECSSSSHHHHHHHHHHHTTCSCEEECSSHHH
T ss_pred             CCCCceEEeCCChHHHHHHHHHHHHcCCCCcEEecCCHH
Confidence            3467899999998889899999999999 6888888764

>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=86.26  E-value=0.36  Score=33.05  Aligned_cols=43  Identities=16%  Similarity=0.193  Sum_probs=26.8

Q ss_pred             CCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEeecCcH
Q 030396           38 SRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPD   84 (178)
Q Consensus        38 ~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~SAT~~~   84 (178)
                      +.-+++|+||+|.|-...  ...+..++.. .+.+..+++. ++-++
T Consensus       114 ~~~kviiIde~d~l~~~~--q~~Llk~lE~-~~~~~~~il~-tn~~~  156 (239)
T d1njfa_         114 GRFKVYLIDEVHMLSRHS--FNALLKTLEE-PPEHVKFLLA-TTDPQ  156 (239)
T ss_dssp             SSSEEEEEETGGGSCHHH--HHHHHHHHHS-CCTTEEEEEE-ESCGG
T ss_pred             CCCEEEEEECcccCCHHH--HHHHHHHHhc-CCCCeEEEEE-cCCcc
Confidence            345789999999985444  4556666665 4455554444 44443

>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=86.22  E-value=0.34  Score=32.54  Aligned_cols=40  Identities=10%  Similarity=0.056  Sum_probs=28.1

Q ss_pred             CCCeeEEEEeccccccccCCChhhHHHHHhhCCCCCceEEEEe
Q 030396           37 LSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFS   79 (178)
Q Consensus        37 ~~~l~~lViDE~d~ll~~~~~~~~i~~i~~~~~~~~~q~i~~S   79 (178)
                      .+.-+++|+||+|.|-...  ...+..++.. .+.+..+++.+
T Consensus       106 ~~~~kviIide~d~l~~~a--~n~Llk~lEe-p~~~~~fIl~t  145 (207)
T d1a5ta2         106 LGGAKVVWVTDAALLTDAA--ANALLKTLEE-PPAETWFFLAT  145 (207)
T ss_dssp             TSSCEEEEESCGGGBCHHH--HHHHHHHHTS-CCTTEEEEEEE
T ss_pred             cCccceEEechhhhhhhhh--hHHHHHHHHh-hcccceeeeee
Confidence            4567899999999996655  6667777776 55555555543

>d1yt8a3 c.46.1.2 (A:373-529) Thiosulfate sulfurtransferase PA2603 {Pseudomonas aeruginosa [TaxId: 287]}

class: Alpha and beta proteins (a/b)
fold: Rhodanese/Cell cycle control phosphatase
superfamily: Rhodanese/Cell cycle control phosphatase
family: Multidomain sulfurtransferase (rhodanese)
domain: Thiosulfate sulfurtransferase PA2603
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=84.92  E-value=0.17  Score=32.62  Aligned_cols=38  Identities=11%  Similarity=-0.098  Sum_probs=32.2

Q ss_pred             cCCCCEEEEeCCchHHHHHHHHhhhCCC-ceEeeecCCC
Q 030396          136 SLNPPVLIFVQSKDRAKELYGELAFDDI-RAGVIHSDLS  173 (178)
Q Consensus       136 ~~~~~~lIF~~t~~~~~~l~~~L~~~g~-~~~~lh~~~~  173 (178)
                      ...+++++||++-..+...+..|...|+ ++..+.||+.
T Consensus        56 ~~~~~vv~~c~~g~rs~~~a~~l~~~G~~~v~~L~GG~~   94 (157)
T d1yt8a3          56 GTAERYVLTCGSSLLARFAVAEVQALSGKPVFLLDGGTS   94 (157)
T ss_dssp             CCCSEEEEECSSSHHHHHHHHHHHHHHCSCEEEETTHHH
T ss_pred             ccCcceeeccCCcchHHHHHHHHhcccCceEEEecCCHH
Confidence            3457899999999999999999999988 7888888753

>d1rhsa2 c.46.1.2 (A:150-293) Rhodanese {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: Rhodanese/Cell cycle control phosphatase
superfamily: Rhodanese/Cell cycle control phosphatase
family: Multidomain sulfurtransferase (rhodanese)
domain: Rhodanese
species: Cow (Bos taurus) [TaxId: 9913]

Probab=82.44  E-value=0.88  Score=28.66  Aligned_cols=46  Identities=13%  Similarity=0.112  Sum_probs=34.7

Q ss_pred             HHHHHHHh---cCCCCEEEEeCCchHHHHHHHHhhhCCC-ceEeeecCCC
Q 030396          128 ALRQSFAE---SLNPPVLIFVQSKDRAKELYGELAFDDI-RAGVIHSDLS  173 (178)
Q Consensus       128 ~l~~ll~~---~~~~~~lIF~~t~~~~~~l~~~L~~~g~-~~~~lh~~~~  173 (178)
                      .+..++..   ....++|+||++=-+|-..+..|...|+ ++..+.|++.
T Consensus        78 ~l~~~~~~~gi~~~~~iI~yC~sG~~A~~~~~~l~~lG~~~v~~YdGsw~  127 (144)
T d1rhsa2          78 ELRAMFEAKKVDLTKPLIATCRKGVTACHIALAAYLCGKPDVAIYDGSWF  127 (144)
T ss_dssp             HHHHHHHHTTCCTTSCEEEECSSSSTHHHHHHHHHHTTCCCCEEESSHHH
T ss_pred             HHHHHHHHcCCCCCCCEEEEecccchHHHHHHHHHHcCCCCCEEeCCCHH
Confidence            34444443   3467899999988888888888999999 6888888754

>d1uara2 c.46.1.2 (A:145-285) Sulfurtransferase {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: Rhodanese/Cell cycle control phosphatase
superfamily: Rhodanese/Cell cycle control phosphatase
family: Multidomain sulfurtransferase (rhodanese)
domain: Sulfurtransferase
species: Thermus thermophilus [TaxId: 274]

Probab=82.26  E-value=0.7  Score=29.05  Aligned_cols=47  Identities=9%  Similarity=0.198  Sum_probs=34.3

Q ss_pred             HHHHHHHHh---cCCCCEEEEeCCchHHHHHHHHhhh-CCC-ceEeeecCCC
Q 030396          127 LALRQSFAE---SLNPPVLIFVQSKDRAKELYGELAF-DDI-RAGVIHSDLS  173 (178)
Q Consensus       127 ~~l~~ll~~---~~~~~~lIF~~t~~~~~~l~~~L~~-~g~-~~~~lh~~~~  173 (178)
                      ..+..++..   .+.+++|+||++=..|-..+-.|.. .|+ ++..+.|++.
T Consensus        75 ~~~~~~~~~~gi~~d~~vV~yC~~G~~As~~~~~l~~~~G~~~v~~ydGs~~  126 (141)
T d1uara2          75 EELRALYEPLGITKDKDIVVYCRIAERSSHSWFVLKYLLGYPHVKNYDGSWT  126 (141)
T ss_dssp             HHHHHHHGGGTCCTTSEEEEECSSHHHHHHHHHHHHTTSCCSCEEEESSHHH
T ss_pred             HHHHHHHHHhCCCCCCeEEEEecCcchHHHHHHHHHHHcCCCCeeEeCCcHH
Confidence            344444443   3466799999998888888888875 799 5888888754